Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	X1000gp3_AA	X1000gp3_AC	X1000gp3_AF	X1000gp3_AFR_AF	X1000gp3_AMR_AF	X1000gp3_AN	X1000gp3_CIEND	X1000gp3_CIPOS	X1000gp3_CS	X1000gp3_DP	X1000gp3_EAS_AF	X1000gp3_END	X1000gp3_EUR_AF	X1000gp3_IMPRECISE	X1000gp3_MC	X1000gp3_MEINFO	X1000gp3_MEND	X1000gp3_MLEN	X1000gp3_MSTART	X1000gp3_NS	X1000gp3_SAS_AF	X1000gp3_SVLEN	X1000gp3_SVTYPE	X1000gp3_TSD	ACHILLES_Lineage_Results_Top_Genes	CGC_Cancer.Germline.Mut	CGC_Cancer.Molecular.Genetics	CGC_Cancer.Somatic.Mut	CGC_Cancer.Syndrome	CGC_Chr	CGC_Chr.Band	CGC_GeneID	CGC_Name	CGC_Other.Germline.Mut	CGC_Tissue.Type	COSMIC_n_overlapping_mutations	COSMIC_overlapping_mutation_descriptions	COSMIC_overlapping_primary_sites	ClinVar_ASSEMBLY	ClinVar_HGMD_ID	ClinVar_SYM	ClinVar_TYPE	ClinVar_rs	ESP_AA	ESP_AAC	ESP_AA_AC	ESP_AA_AGE	ESP_AA_GTC	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_CA	ESP_CDP	ESP_CG	ESP_CP	ESP_Chromosome	ESP_DBSNP	ESP_DP	ESP_EA_AC	ESP_EA_AGE	ESP_EA_GTC	ESP_EXOME_CHIP	ESP_FG	ESP_GL	ESP_GM	ESP_GS	ESP_GTC	ESP_GTS	ESP_GWAS_PUBMED	ESP_MAF	ESP_PH	ESP_PP	ESP_Position	ESP_TAC	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	Familial_Cancer_Genes_Reference	Familial_Cancer_Genes_Synonym	HGNC_Accession.Numbers	HGNC_CCDS.IDs	HGNC_Chromosome	HGNC_Date.Modified	HGNC_Date.Name.Changed	HGNC_Date.Symbol.Changed	HGNC_Ensembl.Gene.ID	HGNC_Ensembl.ID.supplied.by.Ensembl.	HGNC_Entrez.Gene.ID.supplied.by.NCBI.	HGNC_Enzyme.IDs	HGNC_Gene.family.description	HGNC_HGNC.ID	HGNC_Locus.Group	HGNC_Locus.Type	HGNC_Name.Synonyms	HGNC_OMIM.ID.supplied.by.NCBI.	HGNC_Previous.Names	HGNC_Previous.Symbols	HGNC_Primary.IDs	HGNC_Pubmed.IDs	HGNC_Record.Type	HGNC_RefSeq.IDs	HGNC_RefSeq.supplied.by.NCBI.	HGNC_Secondary.IDs	HGNC_Status	HGNC_Synonyms	HGNC_UCSC.ID.supplied.by.UCSC.	HGNC_UniProt.ID.supplied.by.UniProt.	HGNC_VEGA.IDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	ORegAnno_bin	UniProt_alt_uniprot_accessions	build	ccds_id	contaminant_fraction	contaminant_lod	context	covered	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP.._NR	dbNSFP_GERP.._RS	dbNSFP_GERP.._RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_fold.degenerate	dbNSFP_genename	dbNSFP_hg18_pos.1.coor.	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	dbsnp_site	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_id	gene_type	havana_transcript	improper_pairs	init_n_lod	judgement	map_Q0_reads	n_alt_count	n_alt_sum	n_ref_count	n_ref_sum	normal_best_gt	normal_power	power	score	secondary_variant_classification	strand	t_alt_count	t_alt_max_mapq	t_alt_sum	t_del_count	t_ins_count	t_lod_fstar	t_ref_count	t_ref_max_mapq	t_ref_sum	total_pairs	transcript_id	tumor_f	tumor_power
NOC2L	26155	__UNKNOWN__	__UNKNOWN__	1	887591	887591	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:887591G>T	ENST00000327044.6	-	11	1241					NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	NA		NA			apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		CTCCTGGGCCGGCACAGGAAT	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976	26155			24517	protein-coding gene	gene with protein product	novel INHAT repressor, protein phosphatase 1, regulatory subunit 12	610770			NA		Standard	NM_015658	NM_015658	NA	Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.1192-72C>A	chr1.hg19:g.887591G>T		NA	Q5SVA3|Q9BTN6	hg19	CCDS3.1	0.02	7.008244	GCCxGCA	COVERED																																																																																			NOVEL	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097869.1	1	13.843155	KEEP	0	0	0	46	1532	GG	1	1	0		-	28	60	1005	0	0	81.188148	138	60	4803	259	ENST00000327044.6	0.168675	1
C1orf170	0	__UNKNOWN__	__UNKNOWN__	1	915157	915157	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:915157C>T	ENST00000341290.2	-	3	946	c.911G>A	c.(910-912)gGc>gAc	p.G304D	C1orf170_ENST00000433179.2_Missense_Mutation_p.G324D			Q5SV97	PERM1_HUMAN		418		NA			regulation of transcription, DNA-templated (GO:0006355)|response to muscle activity (GO:0014850)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)					NA						AGCCACTGGGCCTGCTGTAGG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000341290.2:c.911G>A	chr1.hg19:g.915157C>T	ENSP00000343864:p.Gly304Asp	NA	Q6ZVZ7|Q9BRF2|S5G239	hg19		0.02	9.085975	GGGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	13.53	2.265748	0.40095	.	.	ENSG00000187642	ENST00000433179;ENST00000341290	T;T	0.59502	0.26;0.26	4.0	0.65	0.17812	.	1.015390	0.07898	N	0.972151	T	0.48169	0.1485	.	.	.	0.09310	N	1	P	0.49635	0.926	P	0.46718	0.525	T	0.38373	-0.9664	9	0.41790	T	0.15	-2.9007	1.9553	0.03375	0.4058:0.3281:0.1582:0.1079	.	324	Q5SV97	CA170_HUMAN	D	324;304	ENSP00000414022:G324D;ENSP00000343864:G304D	ENSP00000343864:G304D	G	-	2	0	C1orf170	905020	0.010000	0.17322	0.000000	0.03702	0.019000	0.09904	-0.083000	0.11286	0.376000	0.24707	0.472000	0.43445	GGC	NOVEL	C1orf170-001	PUTATIVE	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000097943.2	4	10.518277	KEEP	0	0	0	35	1193	CC	0.999999	0.999999	0		-	49	60	1702	0	0	143.975706	162	60	5755	292	ENST00000341290.2	0.232227	1
C1orf159	54991	__UNKNOWN__	__UNKNOWN__	1	1017548	1017548	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1017548G>A	ENST00000421241.2	-	0	1495				C1orf159_ENST00000379339.1_3'UTR|C1orf159_ENST00000294576.5_3'UTR|C1orf159_ENST00000448924.1_3'UTR	NM_017891.4	NP_060361.4	Q96HA4	CA159_HUMAN	chromosome 1 open reading frame 159	NA		NA				integral component of membrane (GO:0016021)					NA	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.96e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.77e-22)|Colorectal(212;6.51e-05)|COAD - Colon adenocarcinoma(227;0.000214)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CCTGCCCCACGTGGGCAGGGA	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK128434	CCDS7.2	1p36.33	2008-02-05			ENSG00000131591	ENSG00000131591	54991			26062	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_017891	NM_017891	NA	Approved	FLJ20584	uc001acu.2	Q96HA4	OTTHUMG00000000745	ENST00000421241.2:c.*725C>T	chr1.hg19:g.1017548G>A		NA	B3KQ46|Q5T2W6|Q6UX67|Q6ZR77|Q9NWV0	hg19	CCDS7.2	0.02	9.015949	CACxTGG	COVERED																																																																																			NOVEL	C1orf159-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001852.2	1	14.746158	KEEP	0	0	0	49	1671	GG	1	1	0		-	53	60	1930	0	0	164.268098	178	60	6128	348	ENST00000421241.2	0.229437	1
ATAD3B	83858	__UNKNOWN__	__UNKNOWN__	1	1423354	1423354	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1423354A>C	ENST00000308647.7	+	12	1382					NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	NA		NA				mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CGCGGCTGTCATCCTGGGCCA	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	34	35	NA		NA	NA	1		NA											NA				1423354		692	1591	2283	SO:0001627	intron_variant			AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072	83858		ATPases / AAA-type	24007	protein-coding gene	gene with protein product		612317			NA	10574462	Standard	NM_031921	XM_005244806	NA	Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1266+60A>C	chr1.hg19:g.1423354A>C		NA	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	hg19	CCDS30.1	0.02	9.67291	GTCxTCC	COVERED																																																																																			NOVEL	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001369.2	3	17.145443	KEEP	0	0	0	57	1760	AA	1	1	0		+	28	60	1059	0	0	83.208903	186	60	6652	371	ENST00000308647.7	0.130841	1
ATAD3A	55210	__UNKNOWN__	__UNKNOWN__	1	1452615	1452615	__UNKNOWN__	Intron	SNP	C	C	T	rs2478791	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1452615C>T	ENST00000378756.3	+	3	400				ATAD3A_ENST00000378755.5_Silent_p.A117A|ATAD3A_ENST00000536055.1_Intron	NM_001170535.1	NP_001164006.1	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	NA		NA			cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		GTGCCGGAGCCGTGCAGACAC	0.647	NA	NA											c|||	617	0.123203	0.1649	0.0793	5008	,	,	NA	14505	0.2153	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.1278	NA	NA	NA						NA		NA				0								C	,,	62,3962		4,54,1954	22	25	24	NA	,,351	-1.8	0	1	dbSNP_100	24	0,8290		0,0,4145	no	intron,intron,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	4,54,6099	TT,TC,CC	NA	0.0,1.5408,0.5035	,,	,,117/635	1452615	62,12252	2012	4145	6157	SO:0001627	intron_variant			AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785	55210		ATPases / AAA-type	25567	protein-coding gene	gene with protein product		612316			NA	12477932	Standard	NM_018188	NM_018188	NA	Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378756.3:c.283-76C>T	chr1.hg19:g.1452615C>T		NA	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	hg19	CCDS53259.1	0.02	2.334793	AGCxGTG	COVERED																																																																																			NOVEL	ATAD3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001363.3	0	3.911886	KEEP	0	0	0	13	433	CC	0.994391	0.986529	0		+	4	40	156	0	0	11.068477	58	60	1992	93	ENST00000378756.3	0.064516	0.992094
MIB2	142678	__UNKNOWN__	__UNKNOWN__	1	1563751	1563751	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1563751G>A	ENST00000505820.2	+	15	2302	c.2285G>A	c.(2284-2286)cGc>cAc	p.R762H	MIB2_ENST00000378708.1_Missense_Mutation_p.R611H|MIB2_ENST00000360522.4_Missense_Mutation_p.R670H|MIB2_ENST00000378710.3_Missense_Mutation_p.R669H|MIB2_ENST00000355826.5_Missense_Mutation_p.R748H|MIB2_ENST00000357210.4_Missense_Mutation_p.R705H|MIB2_ENST00000504599.1_Missense_Mutation_p.R661H|MIB2_ENST00000378712.1_Missense_Mutation_p.R582H|MIB2_ENST00000520777.1_Missense_Mutation_p.R758H|MIB2_ENST00000518681.1_Missense_Mutation_p.R697H			Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	705		NA			Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AACAACCACCGCGAGGTGGCC	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													19	24	22	NA		NA	NA	1		NA											NA				1563751		2046	4188	6234	SO:0001583	missense			AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530	142678		Zinc fingers, ZZ-type, Ankyrin repeat domain containing	30577	protein-coding gene	gene with protein product		611141	zinc finger, ZZ type with ankyrin repeat domain 1, mindbomb homolog 2 (Drosophila)	ZZANK1	NA	12761501	Standard	NM_080875	NM_080875	NA	Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000505820.2:c.2285G>A	chr1.hg19:g.1563751G>A	ENSP00000426103:p.Arg762His	NA	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	hg19	CCDS41224.2	0.02	11.220755	ACCxCGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.47	1.946169	0.34377	.	.	ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000378712;ENST00000504599;ENST00000378708	T;T;T;T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	4.15	3.24	0.37175	Ankyrin repeat-containing domain (3);	0.220397	0.40302	N	0.001137	T	0.48429	0.1499	N	0.20401	0.57	0.24954	N	0.99178	P;P;P;D;D;P;P	0.55385	0.932;0.645;0.952;0.971;0.971;0.84;0.901	P;P;P;P;P;P;P	0.53954	0.537;0.475;0.564;0.738;0.714;0.467;0.667	T	0.35919	-0.9769	10	0.13470	T	0.59	-17.0243	3.0494	0.06164	0.2912:0.0:0.5141:0.1947	.	670;611;582;697;758;691;705	Q96AX9-5;F2Z2L2;B3KXY1;E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9	.;.;.;.;.;.;MIB2_HUMAN	H	758;705;670;669;748;697;762;582;661;611	ENSP00000428660:R758H;ENSP00000349741:R705H;ENSP00000353713:R670H;ENSP00000367982:R669H;ENSP00000348081:R748H;ENSP00000428264:R697H;ENSP00000426103:R762H;ENSP00000367984:R582H;ENSP00000426128:R661H;ENSP00000367980:R611H	ENSP00000348081:R748H	R	+	2	0	MIB2	1553614	0.000000	0.05858	0.382000	0.26119	0.279000	0.26890	0.383000	0.20651	0.945000	0.37605	0.491000	0.48974	CGC	NOVEL	MIB2-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365928.2	2	26.11342	KEEP	0	0	0	87	2953	GG	1	1	0		+	51	60	1774	0	0	143.43282	236	60	8538	488	ENST00000505820.2	0.1777	1
CDK11A	728642	__UNKNOWN__	__UNKNOWN__	1	1646231	1646231	__UNKNOWN__	Intron	SNP	T	T	C	rs3820002		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1646231T>C	ENST00000358779.5	-	5	538				CDK11A_ENST00000404249.3_Intron|CDK11A_ENST00000378635.3_Intron|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000356200.3_Intron|CDK11A_ENST00000378633.1_Intron|CDK11A_ENST00000378638.2_Intron|CDK11A_ENST00000357760.2_Intron	NM_033488.1|NM_033493.1|NM_033529.2	NP_277023.1|NP_277028.1|NP_277071.2	Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	NA		NA			apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						TATTTTCTGCTAGGTCCTTTC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(186;965 2119 30274 40311 50569)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128	728642		Cyclin-dependent kinases	1730	protein-coding gene	gene with protein product		116951	cell division cycle 2-like 2, cell division cycle 2-like 2 (PITSLRE proteins)	CDC2L3, CDC2L2	NA	7920654, 9750192, 19884882	Standard	NM_024011	NM_033529	NA	Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000358779.5:c.458+1553A>G	chr1.hg19:g.1646231T>C		NA	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	hg19	CCDS44043.1	0.02	1.755567	TGCxAGG	COVERED																																																																																			NOVEL	CDK11A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001734.1	2	8.417673	KEEP	3	0	0	28	852	TT	0.999997	0.999916	0		-	17	40	555	0	0	44.262644	78	60	2709	166	ENST00000358779.5	0.178947	0.999919
CDK11A	728642	__UNKNOWN__	__UNKNOWN__	1	1646236	1646236	__UNKNOWN__	Intron	SNP	C	C	T	rs61776849		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1646236C>T	ENST00000358779.5	-	5	538				CDK11A_ENST00000404249.3_Intron|CDK11A_ENST00000378635.3_Intron|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000356200.3_Intron|CDK11A_ENST00000378633.1_Intron|CDK11A_ENST00000378638.2_Intron|CDK11A_ENST00000357760.2_Intron	NM_033488.1|NM_033493.1|NM_033529.2	NP_277023.1|NP_277028.1|NP_277071.2	Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	NA		NA			apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						TCTGCTAGGTCCTTTCACGCA	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(186;965 2119 30274 40311 50569)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128	728642		Cyclin-dependent kinases	1730	protein-coding gene	gene with protein product		116951	cell division cycle 2-like 2, cell division cycle 2-like 2 (PITSLRE proteins)	CDC2L3, CDC2L2	NA	7920654, 9750192, 19884882	Standard	NM_024011	NM_033529	NA	Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000358779.5:c.458+1548G>A	chr1.hg19:g.1646236C>T		NA	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	hg19	CCDS44043.1	0.02	1.772701	GGTxCTT	COVERED																																																																																			NOVEL	CDK11A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001734.1	2	7.824043	KEEP	3	0	0	26	856	CC	0.999988	0.999882	0		-	17	40	566	0	0	45.512216	76	60	2634	155	ENST00000358779.5	0.182796	0.999895
CDK11A	728642	__UNKNOWN__	__UNKNOWN__	1	1646657	1646657	__UNKNOWN__	Intron	SNP	T	T	C	rs760926	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1646657T>C	ENST00000358779.5	-	5	538				CDK11A_ENST00000404249.3_Intron|CDK11A_ENST00000378635.3_Intron|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000356200.3_Intron|CDK11A_ENST00000378633.1_Intron|CDK11A_ENST00000378638.2_Intron|CDK11A_ENST00000357760.2_Intron	NM_033488.1|NM_033493.1|NM_033529.2	NP_277023.1|NP_277028.1|NP_277071.2	Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	NA		NA			apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						acaaggtctctctacgttgcc	0.502	NA	NA											-|||	3752	0.749201	0.5053	0.879	5008	,	,	NA	12776	0.7798	NA	0.9215	False	NA	,,,	NA	NA	NA	2504	0.7781	NA	NA	NA	Pancreas(186;965 2119 30274 40311 50569)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128	728642		Cyclin-dependent kinases	1730	protein-coding gene	gene with protein product		116951	cell division cycle 2-like 2, cell division cycle 2-like 2 (PITSLRE proteins)	CDC2L3, CDC2L2	NA	7920654, 9750192, 19884882	Standard	NM_024011	NM_033529	NA	Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000358779.5:c.458+1127A>G	chr1.hg19:g.1646657T>C		NA	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	hg19	CCDS44043.1	0.02	1.718786	CTCxCTA	COVERED																																																																																			NOVEL	CDK11A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001734.1	1	5.717649	KEEP	2	0	0	19	618	TT	0.99986	0.993563	0		-	5	40	162	0	0	10.934808	60	60	2229	113	ENST00000358779.5	0.076923	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	1858215	1858215	__UNKNOWN__	IGR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1858215G>T			NA	NA				TMEM52 (7503 upstream) : C1orf222 (61347 downstream)						NA		NA									NA						GATAGGAAGGGCATGCTGAGG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.1858215G>T		NA		hg19		0.02	20.595694	AGGxCAT	COVERED																																																																																			NOVEL					0			4	24.979095	KEEP	0	0	0	83	2836	GG	1	1	0			28	60	920	0	0	58.502451	483	60	17153	729		0.054795	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	1878459	1878459	__UNKNOWN__	IGR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:1878459G>A			NA	NA				TMEM52 (27747 upstream) : C1orf222 (41103 downstream)						NA		NA									NA						TCTGCTCTTCGCTGGGAGGTA	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.1878459G>A		NA		hg19		0.02	11.965231	TTCxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	1.534	-0.543515	0.04053	.	.	ENSG00000142609	ENST00000493316	.	.	.	2.84	-5.67	0.02444	.	.	.	.	.	T	0.18635	0.0447	.	.	.	0.18873	N	0.999983	.	.	.	.	.	.	T	0.14420	-1.0473	4	.	.	.	.	3.2302	0.06746	0.5507:0.1212:0.206:0.1222	.	.	.	.	V	143	.	.	A	-	2	0	C1orf222	1868319	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.753000	0.01818	-2.558000	0.00475	-1.520000	0.00934	GCG	NOVEL					0			3	17.152822	KEEP	0	0	0	57	1955	GG	1	1	0			59	60	2066	0	0	171.969419	223	60	7827	436		0.20922	1
C1orf86	199990	__UNKNOWN__	__UNKNOWN__	1	2121112	2121112	__UNKNOWN__	3'UTR	SNP	G	G	C	rs376647953		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:2121112G>C	ENST00000378546.4	-	0	603				C1orf86_ENST00000378545.3_3'UTR|C1orf86_ENST00000400919.3_Intron|C1orf86_ENST00000487186.1_5'UTR	NM_182533.2	NP_872339	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GAGCGTGTCCGGGCGCCGCAC	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	,	0,4402		0,0,2201	30	26	27	NA	,	-0.3	0	1		27	1,8595		0,1,4297	no	intron,utr-3	C1orf86	NM_001146310.1,NM_182533.2	,	0,1,6498	CC,CG,GG	NA	0.0116,0.0,0.0077	,	,	2121112	1,12997	2201	4298	6499	SO:0001624	3_prime_UTR_variant			AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585	199990			26428	protein-coding gene	gene with protein product		615183			NA	14702039	Standard	NM_182533	NM_182533	NA	Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378546.4:c.*36C>G	chr1.hg19:g.2121112G>C		NA	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	hg19	CCDS38.2	0.02	3.965527	TCCxGGC	COVERED																																																																																			NOVEL	C1orf86-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316541.1	1	29.744229	KEEP	0	0	0	99	3108	GG	1	1	0		-	42	60	1400	0	1	123.53066	94	60	3152	306	ENST00000378546.4	0.308824	1
ARHGEF16	27237	__UNKNOWN__	__UNKNOWN__	1	3383761	3383761	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:3383761C>T	ENST00000378378.4	+	4	1069	c.664C>T	c.(664-666)Cgg>Tgg	p.R222W	ARHGEF16_ENST00000378373.1_5'UTR|ARHGEF16_ENST00000378371.2_5'UTR	NM_014448.3	NP_055263.2	Q5VV41	ARHGG_HUMAN	Rho guanine nucleotide exchange factor (GEF) 16	222		NA			activation of Cdc42 GTPase activity (GO:0032864)|activation of Rac GTPase activity (GO:0032863)|apoptotic signaling pathway (GO:0097190)|cell chemotaxis (GO:0060326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	PDZ domain binding (GO:0030165)|receptor tyrosine kinase binding (GO:0030971)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			lung(6)|ovary(1)	7	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GATCCAGGAGCGGGGCCTGAA	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	75	72	NA		NA	NA	1		NA											NA				3383761		692	1591	2283	SO:0001583	missense			D89016	CCDS46.2	1p36.3	2013-01-10	2010-04-13		ENSG00000130762	ENSG00000130762	27237		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	15515	protein-coding gene	gene with protein product	putative neuroblastoma protein	NA			NA		Standard	NM_014448	NM_014448	NA	Approved	NBR, GEF16	uc001akg.4	Q5VV41	OTTHUMG00000000625	ENST00000378378.4:c.664C>T	chr1.hg19:g.3383761C>T	ENSP00000367629:p.Arg222Trp	NA	Q86TF0|Q99434	hg19	CCDS46.2	0.02	15.552486	GAGxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.32	3.359165	0.61403	.	.	ENSG00000130762	ENST00000378378	T	0.66638	-0.22	4.37	3.36	0.38483	.	0.090958	0.43579	D	0.000544	T	0.77811	0.4186	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.80051	-0.1544	10	0.87932	D	0	-27.4267	11.8782	0.52560	0.2539:0.746:0.0:0.0	.	222	Q5VV41	ARHGG_HUMAN	W	222	ENSP00000367629:R222W	ENSP00000367629:R222W	R	+	1	2	ARHGEF16	3373621	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.382000	0.44345	2.353000	0.79882	0.591000	0.81541	CGG	NOVEL	ARHGEF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001515.1	4	13.207702	KEEP	0	0	0	44	1521	CC	1	1	0		+	12	60	414	0	0	23.522856	405	60	14555	605	ENST00000378378.4	0.028777	1
CEP104	9731	__UNKNOWN__	__UNKNOWN__	1	3768889	3768889	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs150169294		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:3768889G>A	ENST00000378230.3	-	2	407	c.83C>T	c.(82-84)gCg>gTg	p.A28V	CEP104_ENST00000378223.3_Missense_Mutation_p.A28V	NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	28		NA				centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						GACAGTTGGCGCGTGGATCAT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	VAL/ALA	0,4406		0,0,2203	63	56	58	NA	83	5.2	0.5	1	dbSNP_134	58	1,8599	1.2+/-3.3	0,1,4299	no	missense	CEP104	NM_014704.3	64	0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077	probably-damaging	28/926	3768889	1,13005	2203	4300	6503	SO:0001583	missense			AB011134	CCDS30571.1	1p36.32	2014-02-20	2011-05-06	2011-05-06	ENSG00000116198	ENSG00000116198	9731			24866	protein-coding gene	gene with protein product	glycine, glutamate, thienylcyclohexylpiperidine binding protein	NA	KIAA0562	KIAA0562	NA	7488117, 21399614	Standard	NM_014704	NM_014704	NA	Approved	GlyBP, RP1-286D6.4	uc001aky.2	O60308	OTTHUMG00000003507	ENST00000378230.3:c.83C>T	chr1.hg19:g.3768889G>A	ENSP00000367476:p.Ala28Val	NA	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	hg19	CCDS30571.1	0.02	18.928629	GGCxCGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.87	3.242160	0.58995	0.0	1.16E-4	ENSG00000116198	ENST00000378230;ENST00000428079;ENST00000378223	T;T	0.80214	-1.35;-1.35	5.2	5.2	0.72013	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.88081	0.6341	L	0.58669	1.825	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.85130	0.983;0.997	D	0.88416	0.3025	10	0.54805	T	0.06	.	17.7109	0.88321	0.0:0.0:1.0:0.0	.	28;28	O60308-3;O60308	.;CE104_HUMAN	V	28	ENSP00000367476:A28V;ENSP00000367468:A28V	ENSP00000367468:A28V	A	-	2	0	CEP104	3758749	1.000000	0.71417	0.481000	0.27354	0.226000	0.24999	7.716000	0.84723	2.406000	0.81754	0.467000	0.42956	GCG	NOVEL	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009747.3	1	32.632394	KEEP	0	1	30	119	3890	GG	1	1	0		-	71	60	2569	0	0	207.201483	358	60	11879	666	ENST00000378230.3	0.165501	1
NPHP4	261734	__UNKNOWN__	__UNKNOWN__	1	5926395	5926395	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:5926395C>T	ENST00000378156.4	-	26	3910				NPHP4_ENST00000478423.2_Intron	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	NA		NA			actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTCTCCTCCGCCACCGCCT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													20	23	22	NA		NA	NA	1		NA											NA				5926395		1963	4142	6105	SO:0001627	intron_variant			AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697	261734			19104	protein-coding gene	gene with protein product	nephroretinin, nephrocystin-4, POC10 centriolar protein homolog (Chlamydomonas)	607215			NA	11920287, 12205563	Standard		XR_244787	NA	Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.3644+37G>A	chr1.hg19:g.5926395C>T		NA	Q8IWC0	hg19	CCDS44052.1	0.02	7.321693	CTCxGCC	COVERED																																																																																			NOVEL	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001715.2	2	15.040312	KEEP	0	0	0	50	1689	CC	1	1	0		-	33	60	1251	0	0	103.091323	153	60	5498	309	ENST00000378156.4	0.177419	1
NOL9	79707	__UNKNOWN__	__UNKNOWN__	1	6583333	6583333	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:6583333A>C	ENST00000377705.5	-	0	4722					NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	NA		NA			maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		TCCTTCTTCTAAATGCCCTTA	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408	79707			26265	protein-coding gene	gene with protein product	polynucleotide 5'-kinase	NA			NA	21063389	Standard	NM_024654	NM_024654	NA	Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.*2581T>G	chr1.hg19:g.6583333A>C		NA	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	hg19	CCDS80.1	0.02	7.479489	TCTxAAT	COVERED																																																																																			NOVEL	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000002625.1	7	12.335865	KEEP	0	0	0	41	1273	AA	1	1	0		-	35	60	1318	0	0	111.064814	134	60	4848	277	ENST00000377705.5	0.207101	1
NOL9	79707	__UNKNOWN__	__UNKNOWN__	1	6584489	6584489	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:6584489A>G	ENST00000377705.5	-	0	3566					NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	NA		NA			maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		TCACCCGTTTACACAAACCAC	0.537	NA	NA									OREG0013044	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408	79707			26265	protein-coding gene	gene with protein product	polynucleotide 5'-kinase	NA			NA	21063389	Standard	NM_024654	NM_024654	NA	Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.*1425T>C	chr1.hg19:g.6584489A>G		635	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	hg19	CCDS80.1	0.02	12.110653	TTTxCAC	COVERED																																																																																			NOVEL	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000002625.1	4	15.944767	KEEP	0	0	0	53	1618	AA	1	1	0		-	27	60	1004	0	0	74.37782	261	60	9154	417	ENST00000377705.5	0.09375	1
ZBTB48	3104	__UNKNOWN__	__UNKNOWN__	1	6642233	6642233	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:6642233C>T	ENST00000377674.4	+	3	964	c.806C>T	c.(805-807)cCa>cTa	p.P269L		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	269		NA			transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		GCAGCTGAGCCAGCCCTGAGC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(125;1449 1657 4031 29866 49542)					NA		NA				0													71	69	70	NA		NA	NA	1		NA											NA				6642233		2203	4300	6503	SO:0001583	missense			BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859	3104		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	4930	protein-coding gene	gene with protein product		165270	GLI-Kruppel family member HKR3	HKR3	NA	2850480, 8661141	Standard	NM_005341	NM_001278647	NA	Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.806C>T	chr1.hg19:g.6642233C>T	ENSP00000366902:p.Pro269Leu	NA	Q5SY19	hg19	CCDS84.1	0.02	15.215028	AGCxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	24.0	4.484129	0.84854	.	.	ENSG00000204859	ENST00000319084;ENST00000435905;ENST00000377674	T;T;T	0.28666	1.88;1.6;2.79	5.67	5.67	0.87782	.	0.256046	0.41938	D	0.000787	T	0.33818	0.0876	N	0.17312	0.475	0.58432	D	0.999997	D	0.76494	0.999	P	0.61874	0.895	T	0.04320	-1.0960	10	0.29301	T	0.29	-11.1753	12.301	0.54874	0.1689:0.8311:0.0:0.0	.	269	P10074	ZBT48_HUMAN	L	269	ENSP00000313416:P269L;ENSP00000416054:P269L;ENSP00000366902:P269L	ENSP00000313416:P269L	P	+	2	0	ZBTB48	6564820	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	3.910000	0.56371	2.677000	0.91161	0.561000	0.74099	CCA	NOVEL	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000004193.1	3	21.603795	KEEP	0	0	0	72	2475	CC	1	1	0		+	143	60	5188	0	0	494.62239	165	60	5999	453	ENST00000377674.4	0.464286	1
CAMTA1	23261	__UNKNOWN__	__UNKNOWN__	1	7289748	7289748	__UNKNOWN__	Intron	SNP	C	C	G	rs117245551	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:7289748C>G	ENST00000303635.7	+	5	509				CAMTA1_ENST00000439411.2_Intron	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CTGGAGGGAGCGAGCCTGTGA	0.602	NA	NA	T	WWTR1	epitheliod hemangioendothelioma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735	23261			18806	protein-coding gene	gene with protein product		611501			NA	11925432	Standard	NM_015215	NM_001195563	NA	Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.303-19803C>G	chr1.hg19:g.7289748C>G		NA	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	hg19	CCDS30576.1	0.02	2.253253	GAGxGAG	COVERED																																																																																			NOVEL	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003588.3	5	7.487894	KEEP	0	0	0	25	791	CC	0.999931	0.989474	0		+	10	60	372	0	0	30.161078	51	60	1751	123	ENST00000303635.7	0.163934	0.989542
PER3	8863	__UNKNOWN__	__UNKNOWN__	1	7848137	7848137	__UNKNOWN__	Silent	SNP	T	T	C	rs531385815		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:7848137T>C	ENST00000377532.3	+	4	647	c.423T>C	c.(421-423)tcT>tcC	p.S141S	PER3_ENST00000361923.2_Silent_p.S141S|PER3_ENST00000377541.1_Silent_p.S141S			P56645	PER3_HUMAN	period circadian clock 3	141	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.	NA			circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		CATTTCTGTCTGGAAGGTTAG	0.383	NA	NA											T|||	1	0.000199681	8e-04	0	5008	,	,	NA	21258	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													115	122	120	NA		NA	NA	1		NA											NA				7848137		2203	4300	6503	SO:0001819	synonymous_variant			BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246	8863			8847	protein-coding gene	gene with protein product		603427	period (Drosophila) homolog 3, period homolog 3 (Drosophila)		NA	9427249	Standard	NM_016831	XM_005263520	NA	Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000377532.3:c.423T>C	chr1.hg19:g.7848137T>C		NA	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	hg19		0.02	8.892324	GTCxGGA	COVERED																																																																																			NOVEL	PER3-001	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000003606.1	3	18.956468	KEEP	0	0	0	63	2028	TT	1	1	0		+	54	60	1905	0	0	160.040846	192	60	7266	387	ENST00000377532.3	0.219512	1
TNFRSF9	3604	__UNKNOWN__	__UNKNOWN__	1	7998903	7998903	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:7998903C>T	ENST00000377507.3	-	3	267					NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	NA		NA			apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		GAAAGGCAGACAATAGTGGTA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													105	94	98	NA		NA	NA	1		NA											NA				7998903		2203	4300	6503	SO:0001627	intron_variant			L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249	3604		Tumor necrosis factor receptor superfamily, CD molecules	11924	protein-coding gene	gene with protein product		602250		ILA	NA	8262389, 8639902	Standard		NM_001561	NA	Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.101-15G>A	chr1.hg19:g.7998903C>T		NA		hg19	CCDS92.1	0.02	9.023985	AGAxAAT	COVERED																																																																																			NOVEL	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003622.1	1	14.44672	KEEP	0	0	0	48	1699	CC	1	1	0		-	41	60	1479	0	0	120.564569	190	60	7279	346	ENST00000377507.3	0.177489	1
RERE	473	__UNKNOWN__	__UNKNOWN__	1	8413909	8413909	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:8413909C>T	ENST00000337907.3	-	0	6573				RERE_ENST00000377464.1_3'UTR	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	NA		NA			chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTCTTAACTCCAGGATCTCCC	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599	473		GATA zinc finger domain containing	9965	protein-coding gene	gene with protein product		605226		ATN1L	NA	10814707, 10729226	Standard		NM_012102	NA	Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.*1238G>A	chr1.hg19:g.8413909C>T		NA	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	hg19	CCDS95.1	0.02	6.610392	CTCxAGG	COVERED																																																																																			NOVEL	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000004916.1	0	13.832893	KEEP	0	0	0	46	1621	CC	1	1	0		-	6	60	220	0	0	13.506664	170	60	6321	277	ENST00000337907.3	0.034091	1
PGD	5226	__UNKNOWN__	__UNKNOWN__	1	10478947	10478947	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:10478947G>T	ENST00000270776.8	+	11	1212	c.1174G>T	c.(1174-1176)Gac>Tac	p.D392Y	PGD_ENST00000498356.1_3'UTR|PGD_ENST00000538557.1_Missense_Mutation_p.D379Y|PGD_ENST00000541529.1_Missense_Mutation_p.D370Y	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	392		NA			carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	CCTCCTACTGGACGACTTCTT	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	114	115	NA		NA	NA	1		NA											NA				10478947		2203	4300	6503	SO:0001583	missense			BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	5226	1.1.1.43		8891	protein-coding gene	gene with protein product		172200			NA		Standard	NM_002631	NM_002631	NA	Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.1174G>T	chr1.hg19:g.10478947G>T	ENSP00000270776:p.Asp392Tyr	NA	A8K2Y9|B4DQJ8|Q9BWD8	hg19	CCDS113.1	0.02	12.933875	CTGxACG	COVERED	.	.	.	.	.	.	.	.	.	.	g	24.0	4.486997	0.84854	.	.	ENSG00000142657	ENST00000541529;ENST00000543846;ENST00000270776;ENST00000538557	T;T;T	0.47177	0.85;0.85;0.85	5.08	5.08	0.68730	6-phosphogluconate dehydrogenase, C-terminal (1);Dehydrogenase, multihelical (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	T	0.76421	0.3985	M	0.91354	3.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.82293	-0.0529	10	0.72032	D	0.01	-33.7824	18.8956	0.92421	0.0:0.0:1.0:0.0	.	370;392;392	F5H7U0;A8K2Y9;P52209	.;.;6PGD_HUMAN	Y	370;338;392;379	ENSP00000442285:D370Y;ENSP00000270776:D392Y;ENSP00000437822:D379Y	ENSP00000270776:D392Y	D	+	1	0	PGD	10401534	1.000000	0.71417	0.935000	0.37517	0.938000	0.57974	8.949000	0.93012	2.531000	0.85337	0.645000	0.84053	GAC	NOVEL	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005398.1	5	16.854158	KEEP	0	0	0	56	1926	GG	1	1	0		+	52	60	1800	0	0	142.489938	277	60	10180	523	ENST00000270776.8	0.158055	1
FHAD1	114827	__UNKNOWN__	__UNKNOWN__	1	15578415	15578415	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:15578415C>A	ENST00000375998.4	+	1	93				FHAD1_ENST00000358897.4_Intron|FHAD1_ENST00000417793.1_Intron|FHAD1_ENST00000375999.3_Intron			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	NA		NA								skin(1)|stomach(1)	2						TCCCTGACCCCTTCCTTCTCC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													73	65	67	NA		NA	NA	1		NA											NA				15578415		692	1591	2283	SO:0001627	intron_variant			AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621	114827			29408	protein-coding gene	gene with protein product		NA			NA	11572484	Standard	NM_052929	NM_052929	NA	Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.93+42C>A	chr1.hg19:g.15578415C>A		NA	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	hg19		0.02	6.601609	CCCxTTC	COVERED																																																																																			NOVEL	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000393400.2	3	16.253172	KEEP	0	0	0	54	1931	CC	1	1	0		+	6	60	231	0	0	14.571367	172	60	6399	283	ENST00000375998.4	0.033708	1
SPATA21	374955	__UNKNOWN__	__UNKNOWN__	1	16754504	16754504	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:16754504A>C	ENST00000335496.1	-	3	517				SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Intron|SPATA21_ENST00000375577.1_Missense_Mutation_p.F46V	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	NA		NA					calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		GCATCCGGAAACATGACCTGG	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144	374955		EF-hand domain containing	28026	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198546	NM_198546	NA	Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.34+3328T>G	chr1.hg19:g.16754504A>C		NA	B9EK40|F5GXP5	hg19	CCDS172.1	0.02	19.504405	GAAxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	A	12.06	1.825710	0.32237	.	.	ENSG00000187144	ENST00000375577	.	.	.	4.29	-0.0331	0.13902	.	.	.	.	.	T	0.19525	0.0469	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25047	-1.0143	5	0.21540	T	0.41	.	2.6491	0.04993	0.5032:0.0:0.2967:0.2001	.	.	.	.	V	46	.	ENSP00000364727:F46V	F	-	1	0	SPATA21	16627091	0.000000	0.05858	0.002000	0.10522	0.181000	0.23173	0.366000	0.20365	-0.013000	0.14199	0.459000	0.35465	TTT	NOVEL	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006677.2	7	22.562201	KEEP	0	0	0	75	2381	AA	1	1	0		-	62	60	2311	0	0	182.79679	381	60	13640	653	ENST00000335496.1	0.139955	1
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16946438	16946438	__UNKNOWN__	lincRNA	SNP	G	G	C	rs28392876	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:16946438G>C	ENST00000412962.1	-	0	1081							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						GCCTTCCGCCGGGCCAGCAGC	0.672	NA	NA											.|||	426	0.0850639	0.0673	0.0591	5008	,	,	NA	60824	0.0952	NA	0.0815	False	NA	,,,	NA	NA	NA	2504	0.1207	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16946438G>C		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.245486	GCCxGGC	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	0	2.407747	KEEP	0	0	0	8	274	GG	0.99257	0.636582	0		-	5	60	184	0	0	15.081971	23	60	779	44	ENST00000412962.1	0.178571	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16973423	16973423	__UNKNOWN__	IGR	SNP	C	C	T	rs61499416		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:16973423C>T			NA	NA				CROCCP2 (12369 upstream) : RNU1-3 (19856 downstream)						NA		NA									NA						CCCTCCGTCCCGGCCTGGGAC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16973423C>T		NA		hg19		0.02	25.333573	TCCxGGC	COVERED																																																																																			NOVEL					0			6	17.764639	KEEP	327	18	552	253	8373	CC	1	1	0			17	40	632	0	0	38.554265	522	60	17862	1330		0.03154	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16974666	16974666	__UNKNOWN__	IGR	SNP	C	C	T	rs28503658		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:16974666C>T			NA	NA				CROCCP2 (13612 upstream) : RNU1-3 (18613 downstream)						NA		NA									NA						CCAGATCCGGCGTTGTACAGA	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16974666C>T		NA		hg19		0.02	9.392037	CGGxGTT	COVERED																																																																																			NOVEL					0			5	14.105731	KEEP	16	5	136	95	3068	CC	1	1	0			23	60	816	0	0	60.98534	189	60	6354	399		0.108491	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16975365	16975365	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:16975365C>T			NA	NA				CROCCP2 (14311 upstream) : RNU1-3 (17914 downstream)						NA		NA									NA						CCAGCCCACCCCATCCTACAG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16975365C>T		NA		hg19		0.02	24.811551	ACCxCAT	COVERED																																																																																			NOVEL					0			12	12.433932	KEEP	136	13	412	186	6141	CC	1	1	0			18	49	649	0	0	38.135387	603	50	21054	1045		0.028986	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16975868	16975868	__UNKNOWN__	IGR	SNP	T	T	A	rs200822664	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:16975868T>A			NA	NA				CROCCP2 (14814 upstream) : RNU1-3 (17411 downstream)						NA		NA									NA						AGAGCTTCTCTCCCAGCCATA	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16975868T>A		NA		hg19		0.02	18.660518	CTCxCCC	COVERED																																																																																			NOVEL					0			8	4.073002	KEEP	143	8	219	91	2817	TT	1	1	0			40	50	1206	0	0	81.282184	409	50	14048	814		0.089087	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17084175	17084175	__UNKNOWN__	RNA	SNP	A	A	G	rs200317021		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:17084175A>G	ENST00000455405.2	-	0	560							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						GAATGGGGAGAAGGAGACGGT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17084175A>G		NA	B7WPB1|Q13209	hg19		0.02	33.460502	GAGxAGG	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	7	9.491353	KEEP	96	16	562	228	6865	AA	1	1	0		-	66	49	2416	1	0	178.128791	635	51	22504	1230	ENST00000455405.2	0.094151	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17084234	17084234	__UNKNOWN__	RNA	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:17084234G>A	ENST00000455405.2	-	0	560							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						GCAGTCCTGTGCACTATGCTC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17084234G>A		NA	B7WPB1|Q13209	hg19		0.02	33.574662	TGTxCAC	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	4	25.466362	KEEP	73	10	287	186	6575	GG	1	1	0		-	63	49	2194	0	0	153.677805	738	60	27677	1253	ENST00000455405.2	0.078652	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17084670	17084670	__UNKNOWN__	RNA	SNP	A	A	G	rs199536872		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:17084670A>G	ENST00000455405.2	-	0	306							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						GAAAGGGGAAAGTGGGATGAG	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17084670A>G		NA	B7WPB1|Q13209	hg19		0.02	7.127506	GAAxGTG	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	2	2.911336	KEEP	16	3	95	43	1372	AA	1	1	0		-	30	40	1065	0	0	86.002926	145	60	5423	295	ENST00000455405.2	0.171429	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17085028	17085028	__UNKNOWN__	RNA	SNP	G	G	A	rs2761534		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:17085028G>A	ENST00000455405.2	-	0	160							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.R483C(1)|p.R452C(1)			NA						AGCTTGGAACGACGCTGATCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)											NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17085028G>A		NA	B7WPB1|Q13209	hg19		0.02	19.371396	AACxACG	COVERED	.	.	.	.	.	.	.	.	.	.	.	9.858	1.195618	0.22037	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);	.	.	.	.	T	0.40956	0.1138	.	.	.	.	.	.	D;D	0.67145	0.996;0.981	P;P	0.53549	0.729;0.613	T	0.44221	-0.9342	5	0.39692	T	0.17	.	2.6507	0.04998	0.5:0.0:0.5:0.0	rs2761534;rs3882324;rs3981970;rs3982159	483;483	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	C	452;483;483	.	ENSP00000439273:R483C	R	-	1	0	MST1P9	16957615	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.159000	0.16442	-0.000000	0.14550	0.000000	0.15137	CGT	NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	8	9.242844	KEEP	38	16	436	185	5904	GG	1	1	0		-	25	31	842	0	0	52.992391	479	60	15465	990	ENST00000455405.2	0.049603	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17087432	17087432	__UNKNOWN__	IGR	SNP	G	G	T	rs2446554	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:17087432G>T			NA	NA				MST1L (2065 upstream) : RP11-108M9.1 (90383 downstream)						NA		NA									NA						GTCTTATCTAGGCCCAGTGGC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17087432G>T		NA		hg19		0.02	22.240974	CTAxGCC	COVERED																																																																																			NOVEL					0			4	3.168465	KEEP	1	14	398	151	5073	GG	1	1	0			36	49	1311	0	0	90.860224	504	60	18139	811		0.066667	1
PADI2	11240	__UNKNOWN__	__UNKNOWN__	1	17393298	17393298	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:17393298G>A	ENST00000375486.4	-	0	4302					NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	NA		NA			chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	CTTTAGTCGAGCTCTTCCCTA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	11240	3.5.3.15	Peptidyl arginine deiminases	18341	protein-coding gene	gene with protein product		607935			NA	2768262	Standard		NM_007365	NA	Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.*2241C>T	chr1.hg19:g.17393298G>A		NA	Q96DA7|Q9UPN2	hg19	CCDS177.1	0.02	6.118714	CGAxCTC	COVERED																																																																																			NOVEL	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006624.1	4	7.222886	KEEP	0	0	0	24	854	GG	0.999909	0.999909	0		-	6	60	209	0	0	12.581312	159	60	5914	234	ENST00000375486.4	0.036364	1
IGSF21	84966	__UNKNOWN__	__UNKNOWN__	1	18703430	18703430	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:18703430G>A	ENST00000251296.1	+	8	1621	c.1238G>A	c.(1237-1239)tGc>tAc	p.C413Y		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	413	Ig-like 2.	NA				extracellular region (GO:0005576)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		ATGTATCGCTGCACCGCCCAG	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	45	46	NA		NA	NA	1		NA											NA				18703430		2203	4300	6503	SO:0001583	missense			AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154	84966		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	28246	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032880	NM_032880	NA	Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.1238G>A	chr1.hg19:g.18703430G>A	ENSP00000251296:p.Cys413Tyr	NA	Q8NBR8	hg19	CCDS184.1	0.02	8.22986	GCTxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348626	0.82132	.	.	ENSG00000117154	ENST00000251296	T	0.58940	0.3	5.17	5.17	0.71159	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.82268	0.5000	M	0.93241	3.395	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.87315	0.2314	10	0.87932	D	0	-11.9823	17.2254	0.86969	0.0:0.0:1.0:0.0	.	413	Q96ID5	IGS21_HUMAN	Y	413	ENSP00000251296:C413Y	ENSP00000251296:C413Y	C	+	2	0	IGSF21	18576017	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	9.300000	0.96151	2.391000	0.81399	0.491000	0.48974	TGC	NOVEL	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006924.1	3	24.968995	KEEP	0	0	0	83	2895	GG	1	1	0		+	43	60	1383	0	0	109.692981	199	60	7283	422	ENST00000251296.1	0.177686	1
PAX7	5081	__UNKNOWN__	__UNKNOWN__	1	19029744	19029744	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs199662942		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:19029744C>T	ENST00000420770.2	+	7	1192	c.1109C>T	c.(1108-1110)gCg>gTg	p.A370V	PAX7_ENST00000375375.3_Missense_Mutation_p.A370V|PAX7_ENST00000400661.3_Missense_Mutation_p.A368V	NM_001135254.1	NP_001128726.1	P23759	PAX7_HUMAN	paired box 7	370		NA			anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		AATCCGGCGGCGCCCTCCAAC	0.652	NA	NA	T	FOXO1A	alveolar rhabdomyosarcoma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	0													51	54	53	NA		NA	NA	1		NA											NA				19029744		2203	4300	6503	SO:0001583	missense			X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709	5081		Paired boxes, Homeoboxes / PRD class	8621	protein-coding gene	gene with protein product		167410	paired box gene 7		NA	7981748, 8431641	Standard	NM_002584	NM_001135254	NA	Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000420770.2:c.1109C>T	chr1.hg19:g.19029744C>T	ENSP00000403389:p.Ala370Val	NA	E9PFV9|Q0VA99|Q2PJS5	hg19	CCDS44074.1	0.02	13.659602	CGGxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.93	2.384468	0.42308	.	.	ENSG00000009709	ENST00000375375;ENST00000420770;ENST00000400661	T;T;T	0.80214	-1.35;-1.35;-1.35	5.41	4.49	0.54785	.	0.071035	0.56097	D	0.000032	T	0.77246	0.4102	L	0.54323	1.7	0.44579	D	0.997544	P;D;P	0.54601	0.789;0.967;0.907	B;B;B	0.43658	0.183;0.407;0.426	T	0.76293	-0.3012	10	0.33141	T	0.24	.	13.7256	0.62756	0.0:0.7053:0.2947:0.0	.	370;368;370	E9PFV9;P23759-2;P23759	.;.;PAX7_HUMAN	V	370;370;368	ENSP00000364524:A370V;ENSP00000403389:A370V;ENSP00000383502:A368V	ENSP00000364524:A370V	A	+	2	0	PAX7	18902331	0.965000	0.33210	0.322000	0.25334	0.630000	0.37929	2.249000	0.43169	1.396000	0.46663	0.561000	0.74099	GCG	NOVEL	PAX7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372482.1	4	27.308455	KEEP	0	0	0	91	2926	CC	1	1	0		+	78	60	2604	1	0	220.230527	244	60	8477	529	ENST00000420770.2	0.242236	1
TAS1R2	80834	__UNKNOWN__	__UNKNOWN__	1	19166168	19166168	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:19166168G>A	ENST00000375371.3	-	6	2466	c.2445C>T	c.(2443-2445)atC>atT	p.I815I		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	815		NA			detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GGTAGAAGAGGATCATGTAGC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													104	83	90	NA		NA	NA	1		NA											NA				19166168		2203	4300	6503	SO:0001819	synonymous_variant				CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002	80834		Taste receptors / Type 1, GPCR / Unclassified : Taste receptors	14905	protein-coding gene	gene with protein product		606226	G protein-coupled receptor 71	GPR71	NA		Standard		NM_152232	NA	Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.2445C>T	chr1.hg19:g.19166168G>A		NA	Q5TZ19	hg19	CCDS187.1	0.02	9.158974	GAGxATC	COVERED																																																																																			NOVEL	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006953.1	4	15.949105	KEEP	0	0	0	53	1810	GG	1	1	0		-	69	60	2449	0	0	217.271304	158	60	5767	367	ENST00000375371.3	0.303965	1
UBR4	23352	__UNKNOWN__	__UNKNOWN__	1	19411101	19411101	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:19411101C>T	ENST00000375254.3	-	102	14932	c.14905G>A	c.(14905-14907)Gcc>Acc	p.A4969T	UBR4_ENST00000429347.2_Missense_Mutation_p.A492T|UBR4_ENST00000375224.1_Missense_Mutation_p.A676T|UBR4_ENST00000375226.2_Missense_Mutation_p.A4945T|UBR4_ENST00000543981.1_Missense_Mutation_p.A633T|UBR4_ENST00000375267.2_Missense_Mutation_p.A4969T|UBR4_ENST00000375217.2_Missense_Mutation_p.A4962T	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4969		NA			protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A4969T(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TGCTCCATGGCGAAGCGCAGG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	endometrium(1)											117	102	107	NA		NA	NA	1		NA											NA				19411101		2203	4300	6503	SO:0001583	missense			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481	23352		Ubiquitin protein ligase E3 component n-recognins	30313	protein-coding gene	gene with protein product		609890	zinc finger, UBR1 type 1	ZUBR1	NA	14702039, 10718198, 16055722	Standard	NM_020765	XM_005245802	NA	Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.14905G>A	chr1.hg19:g.19411101C>T	ENSP00000364403:p.Ala4969Thr	NA	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	hg19	CCDS189.1	0.02	9.318581	TGGxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.6	4.169060	0.78339	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375224;ENST00000429347;ENST00000543981	T;T;T;T;T;T;T	0.39406	1.08;1.08;1.08;1.08;1.08;1.08;1.08	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.69115	0.3075	M	0.82823	2.61	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.79784	0.989;0.989;0.993;0.982	T	0.72297	-0.4335	10	0.72032	D	0.01	.	18.5952	0.91227	0.0:1.0:0.0:0.0	.	633;492;4969;4945	B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3	.;.;UBR4_HUMAN;.	T	4969;4969;4962;4945;676;492;633	ENSP00000364403:A4969T;ENSP00000364416:A4969T;ENSP00000364365:A4962T;ENSP00000364374:A4945T;ENSP00000364372:A676T;ENSP00000394173:A492T;ENSP00000444070:A633T	ENSP00000364365:A4962T	A	-	1	0	UBR4	19283688	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.440000	0.80464	2.746000	0.94184	0.655000	0.94253	GCC	NOVEL	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007085.1	1	27.984002	KEEP	0	0	0	93	3179	CC	1	1	0		-	28	60	979	0	0	75.544089	181	60	6259	374	ENST00000375254.3	0.133971	1
PQLC2	54896	__UNKNOWN__	__UNKNOWN__	1	19655051	19655051	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:19655051C>T	ENST00000375153.3	+	8	1444				PQLC2_ENST00000375155.3_Intron|PQLC2_ENST00000400548.2_Intron	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	NA		NA			amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TTGGCCTTAACGGCGGCACCC	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													56	40	46	NA		NA	NA	1		NA											NA				19655051		2203	4299	6502	SO:0001627	intron_variant			BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487	54896			26001	protein-coding gene	gene with protein product		614760			NA	23169667	Standard	NM_017765	XM_005245915	NA	Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.805-15C>T	chr1.hg19:g.19655051C>T		NA	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	hg19	CCDS195.2	0.02	8.861758	TAAxGGC	COVERED																																																																																			NOVEL	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007255.1	6	39.121652	KEEP	0	0	0	130	4459	CC	1	1	0		+	10	60	376	0	0	25.089117	192	60	6942	483	ENST00000375153.3	0.049505	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	21758450	21758450	__UNKNOWN__	IGR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:21758450G>T			NA	NA				RP11-293F5.1 (14465 upstream) : NBPF3 (8170 downstream)						NA		NA									NA						GTCCCCTCCTGGAAGGGGAAG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.21758450G>T		NA		hg19		0.02	8.945651	CCTxGAA	COVERED																																																																																			NOVEL					0			2	11.738537	KEEP	64	0	0	39	1405	GG	0.999892	0.999892	0			18	49	664	0	0	47.231932	222	60	8179	408		0.075	1
CELA3B	23436	__UNKNOWN__	__UNKNOWN__	1	22315762	22315762	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs202129706	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:22315762C>A	ENST00000337107.6	+	8	822	c.803C>A	c.(802-804)gCa>gAa	p.A268E	CELA3B_ENST00000473526.1_3'UTR	NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	268	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CAGACCATAGCAAGCCACTAG	0.463	NA	NA											C|||	262	0.0523163	0.0492	0.036	5008	,	,	NA	18475	0.0942	NA	0.0368	False	NA	,,,	NA	NA	NA	2504	0.0409	NA	NA	NA						NA		NA				0													14	14	14	NA		NA	NA	1		NA											NA				22315762		2164	4205	6369	SO:0001583	missense			M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	23436	3.4.21.70		15945	protein-coding gene	gene with protein product	proteinase E, elastase 1, cholesterol-binding pancreatic protease, pancreatic endopeptidase E	NA	elastase 3B, pancreatic	ELA3B	NA	2826474, 2460440	Standard	NM_007352	NM_007352	NA	Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.803C>A	chr1.hg19:g.22315762C>A	ENSP00000338369:p.Ala268Glu	NA	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	hg19	CCDS219.1	0.02	3.645654	TAGxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.664	1.144792	0.21288	.	.	ENSG00000219073	ENST00000337107	D	0.88124	-2.34	2.98	2.98	0.34508	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	.	.	.	.	T	0.77824	0.4188	N	0.21583	0.68	0.09310	N	0.999998	B	0.09022	0.002	B	0.08055	0.003	T	0.65903	-0.6055	9	0.38643	T	0.18	-0.5697	9.7286	0.40348	0.0:1.0:0.0:0.0	.	268	P08861	CEL3B_HUMAN	E	268	ENSP00000338369:A268E	ENSP00000338369:A268E	A	+	2	0	CELA3B	22188349	0.067000	0.21026	0.205000	0.23548	0.013000	0.08279	0.910000	0.28571	1.991000	0.58162	0.597000	0.82753	GCA	NOVEL	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007797.1	11	22.854069	KEEP	504	7	96	112	3624	CC	0.999863	0.999863	0		+	14	40	267	0	0	13.162654	150	40	4110	1070	ENST00000337107.6	0.085366	1
CELA3A	10136	__UNKNOWN__	__UNKNOWN__	1	22332610	22332610	__UNKNOWN__	Intron	SNP	T	T	G	rs76694312		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:22332610T>G	ENST00000290122.3	+	4	381					NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	NA		NA			cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTCCCCCATATCCGAGGGTTT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789	10136			15944	protein-coding gene	gene with protein product	protease E	NA	elastase 3A, pancreatic (protease E), elastase 3A, pancreatic	ELA3A	NA	2826474, 2460440	Standard	NM_005747	NM_005747	NA	Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.362+321T>G	chr1.hg19:g.22332610T>G		NA	B1AQ53|Q9BRW4	hg19	CCDS220.1	0.02	6.012367	ATAxCCG	COVERED																																																																																			NOVEL	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007791.1	3	9.630479	KEEP	1	0	0	32	1057	TT	0.999997	0.999997	0		+	6	33	223	0	0	13.818543	169	60	5953	268	ENST00000290122.3	0.034286	1
CELA3A	10136	__UNKNOWN__	__UNKNOWN__	1	22338950	22338950	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs80099629	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:22338950C>A	ENST00000290122.3	+	8	822	c.803C>A	c.(802-804)gCa>gAa	p.A268E		NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	268	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CAGACCATAGCAAGCCACTAG	0.463	NA	NA											C|||	361	0.0720847	0.0809	0.0447	5008	,	,	NA	15490	0.0754	NA	0.0626	False	NA	,,,	NA	NA	NA	2504	0.0859	NA	NA	NA						NA		NA				0													8	10	9	NA		NA	NA	1		NA											NA				22338950		1720	3884	5604	SO:0001583	missense			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789	10136			15944	protein-coding gene	gene with protein product	protease E	NA	elastase 3A, pancreatic (protease E), elastase 3A, pancreatic	ELA3A	NA	2826474, 2460440	Standard	NM_005747	NM_005747	NA	Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.803C>A	chr1.hg19:g.22338950C>A	ENSP00000290122:p.Ala268Glu	NA	B1AQ53|Q9BRW4	hg19	CCDS220.1	0.02	3.241267	TAGxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	7.651	0.682822	0.14907	.	.	ENSG00000142789	ENST00000290122	D	0.88354	-2.37	3.2	-0.00181	0.14032	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	1.318870	0.05648	U	0.584670	T	0.79741	0.4498	N	0.16903	0.455	0.09310	N	1	B	0.15719	0.014	B	0.12837	0.008	T	0.65274	-0.6208	10	0.46703	T	0.11	-0.5697	6.3593	0.21419	0.1985:0.4142:0.3873:0.0	.	268	P09093	CEL3A_HUMAN	E	268	ENSP00000290122:A268E	ENSP00000290122:A268E	A	+	2	0	CELA3A	22211537	0.298000	0.24417	0.000000	0.03702	0.087000	0.18053	1.121000	0.31283	0.015000	0.14971	-0.475000	0.04921	GCA	NOVEL	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007791.1	15	21.271321	KEEP	494	7	106	110	3514	CC	0.997832	0.997832	0		+	18	40	269	0	0	11.20318	159	40	4191	1023	ENST00000290122.3	0.101695	1
HTR1D	3352	__UNKNOWN__	__UNKNOWN__	1	23518900	23518900	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:23518900C>G	ENST00000374619.1	-	0	2322				HTR1D_ENST00000314113.3_Intron	NM_000864.4	NP_000855.1	P28221	5HT1D_HUMAN	5-hydroxytryptamine (serotonin) receptor 1D, G protein-coupled	NA		NA			adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intestine smooth muscle contraction (GO:0014827)|regulation of behavior (GO:0050795)|regulation of locomotion (GO:0040012)|response to toxic substance (GO:0009636)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Naratriptan(DB00952)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CTCCTTTAAGCTCCATATAGA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M89955	CCDS231.1	1p36.3-p34.3	2012-08-08	2012-02-03		ENSG00000179546	ENSG00000179546	3352		5-HT (serotonin) receptors, GPCR / Class A : 5-HT (serotonin) receptors, GPCR only	5289	protein-coding gene	gene with protein product		182133	5-hydroxytryptamine (serotonin) receptor 1D	HTRL	NA	2541503, 1662665	Standard	NM_000864	NM_000864	NA	Approved	RDC4, HT1DA, 5-HT1D	uc001bgn.3	P28221	OTTHUMG00000003235	ENST00000374619.1:c.*679G>C	chr1.hg19:g.23518900C>G		NA		hg19	CCDS231.1	0.02	4.83586	AAGxTCC	COVERED																																																																																			NOVEL	HTR1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000008924.1	0	8.427771	KEEP	0	0	0	28	1017	CC	0.999997	0.999997	0		-	29	60	1045	0	0	88.397298	101	60	3824	199	ENST00000374619.1	0.223077	1
LYPLA2	11313	__UNKNOWN__	__UNKNOWN__	1	24120793	24120793	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:24120793C>G	ENST00000374514.3	+	8	756	c.449C>G	c.(448-450)cCt>cGt	p.P150R	LYPLA2_ENST00000400061.1_Silent_p.A125A|LYPLA2_ENST00000374501.1_Missense_Mutation_p.P83R|LYPLA2_ENST00000374505.2_Silent_p.A125A|LYPLA2_ENST00000495365.1_3'UTR|LYPLA2_ENST00000374502.3_Missense_Mutation_p.P150R|LYPLA2_ENST00000374503.3_Missense_Mutation_p.P150R	NM_007260.2	NP_009191.1	O95372	LYPA2_HUMAN	lysophospholipase II	150		NA			fatty acid metabolic process (GO:0006631)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;1.79e-24)|Colorectal(126;4.8e-08)|COAD - Colon adenocarcinoma(152;2.83e-06)|GBM - Glioblastoma multiforme(114;4.22e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000946)|KIRC - Kidney renal clear cell carcinoma(1967;0.00314)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0827)|LUSC - Lung squamous cell carcinoma(448;0.184)		TGCTGGCTGCCTCTGCACCGG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													38	41	40	NA		NA	NA	1		NA											NA				24120793		2203	4298	6501	SO:0001583	missense			AF098668	CCDS241.1	1p36.11	2008-08-08			ENSG00000011009	ENSG00000011009	11313	3.1.1.5		6738	protein-coding gene	gene with protein product		NA			NA		Standard		NM_007260	NA	Approved	APT-2	uc001bht.3	O95372	OTTHUMG00000002961	ENST00000374514.3:c.449C>G	chr1.hg19:g.24120793C>G	ENSP00000363638:p.Pro150Arg	NA	Q7Z4Z2	hg19	CCDS241.1	0.02	4.737827	TGCxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	20.3	3.960195	0.74016	.	.	ENSG00000011009	ENST00000374514;ENST00000374506;ENST00000420982;ENST00000374503;ENST00000374502;ENST00000374501	T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78	5.16	5.16	0.70880	Phospholipase/carboxylesterase/thioesterase (1);	0.000000	0.85682	D	0.000000	T	0.61837	0.2379	M	0.91663	3.23	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.72154	-0.4376	10	0.87932	D	0	.	18.6358	0.91378	0.0:1.0:0.0:0.0	.	127;150;150	E9PH41;O95372;Q5QPQ2	.;LYPA2_HUMAN;.	R	150;127;127;150;150;83	ENSP00000363638:P150R;ENSP00000409004:P127R;ENSP00000363627:P150R;ENSP00000363626:P150R;ENSP00000363625:P83R	ENSP00000363625:P83R	P	+	2	0	LYPLA2	23993380	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	6.061000	0.71148	2.404000	0.81709	0.462000	0.41574	CCT	NOVEL	LYPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000008245.1	4	28.591412	KEEP	0	0	0	95	3255	CC	1	1	0		+	71	60	2356	0	0	227.629754	68	60	2447	308	ENST00000374514.3	0.510791	1
CNR2	1269	__UNKNOWN__	__UNKNOWN__	1	24255629	24255629	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:24255629A>C	ENST00000536471.1	-	2	214				MIR378F_ENST00000578143.1_RNA			P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	NA		NA			G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	tggagccagaagtcttgggct	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822	1269		GPCR / Class A : Cannabinoid receptors	2160	protein-coding gene	gene with protein product		605051			NA		Standard	NM_001841	NM_001841	NA	Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000536471.1:c.44+20286T>G	chr1.hg19:g.24255629A>C		NA	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	hg19	CCDS245.1	0.02	7.26033	AGAxGTC	COVERED																																																																																			NOVEL	CNR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		0	12.337942	KEEP	0	0	0	41	1330	AA	1	1	0		-	52	60	1859	0	0	161.737544	142	60	5243	293	ENST00000536471.1	0.268041	1
PNRC2	55629	__UNKNOWN__	__UNKNOWN__	1	24288193	24288193	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:24288193G>C	ENST00000334351.7	+	3	657	c.246G>C	c.(244-246)agG>agC	p.R82S	PNRC2_ENST00000374468.1_Missense_Mutation_p.R82S	NM_017761.3	NP_060231.1	Q9NPJ4	PNRC2_HUMAN	proline-rich nuclear receptor coactivator 2	82		NA			deadenylation-independent decapping of nuclear-transcribed mRNA (GO:0031087)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)					NA		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.0034)|all_lung(284;0.00519)|Myeloproliferative disorder(586;0.0393)|Breast(348;0.0448)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;8.59e-24)|Colorectal(126;2.18e-08)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;2.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|KIRC - Kidney renal clear cell carcinoma(1967;0.00325)|STAD - Stomach adenocarcinoma(196;0.00841)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.141)		CAGGTCCCAGGTTACTTTTTA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AF151042	CCDS246.1	1p36.11	2008-02-05			ENSG00000189266	ENSG00000189266	55629			23158	protein-coding gene	gene with protein product		611882			NA	11574675	Standard	NM_017761	NM_017761	NA	Approved		uc001big.3	Q9NPJ4	OTTHUMG00000013891	ENST00000334351.7:c.246G>C	chr1.hg19:g.24288193G>C	ENSP00000334840:p.Arg82Ser	NA	B4DU72	hg19	CCDS246.1	0.02	4.230624	CAGxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	g	0.437	-0.900520	0.02472	.	.	ENSG00000189266	ENST00000334351;ENST00000374468	T;T	0.40756	1.02;1.02	3.59	1.69	0.24217	.	0.423369	0.21276	N	0.077225	T	0.12689	0.0308	N	0.01352	-0.895	0.21841	N	0.999512	B	0.02656	0.0	B	0.01281	0.0	T	0.28299	-1.0048	9	.	.	.	-30.5121	6.1468	0.20291	0.0:0.5361:0.291:0.1729	.	82	Q9NPJ4	PNRC2_HUMAN	S	82	ENSP00000334840:R82S;ENSP00000363592:R82S	.	R	+	3	2	PNRC2	24160780	0.826000	0.29277	0.915000	0.36163	0.981000	0.71138	0.364000	0.20325	0.342000	0.23796	-0.224000	0.12420	AGG	NOVEL	PNRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000038946.1	4	8.533179	KEEP	9	3	114	68	2356	GG	1	1	0		+	12	27	427	0	0	30.588645	130	60	4734	258	ENST00000334351.7	0.084507	1
GRHL3	57822	__UNKNOWN__	__UNKNOWN__	1	24646079	24646079	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:24646079A>C	ENST00000361548.4	+	1	247				GRHL3_ENST00000350501.5_Intron|GRHL3_ENST00000342072.4_Intron|GRHL3_ENST00000530984.1_Intron|RP11-10N16.3_ENST00000437965.1_RNA|GRHL3_ENST00000356046.2_5'UTR	NM_198173.2	NP_937816.1	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	NA		NA			central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		ATCGGTGGATACCTGCCGCTC	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055	57822			25839	protein-coding gene	gene with protein product		608317	transcription factor CP2-like 4	TFCP2L4	NA	12549979	Standard	NM_021180	NM_021180	NA	Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000361548.4:c.17+21A>C	chr1.hg19:g.24646079A>C		NA	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	hg19	CCDS44088.1	0.02	2.964536	GATxCCT	COVERED																																																																																			NOVEL	GRHL3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000392498.1	0	12.313276	KEEP	0	7	50	60	1516	AA	1	1	0		+	19	60	281	0	0	11.932608	167	60	4825	350	ENST00000361548.4	0.102151	1
RHD	6007	__UNKNOWN__	__UNKNOWN__	1	25656474	25656474	__UNKNOWN__	3'UTR	SNP	T	T	C	rs368881741		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:25656474T>C	ENST00000328664.4	+	0	2468					NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	NA		NA				integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TACCATTTGGTGTTTTGAAGA	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010	6007		CD molecules, Blood group antigens	10009	protein-coding gene	gene with protein product		111680	Rhesus blood group, D antigen, Rh blood group, D antigen	RH	NA	8220426	Standard	NM_016124	NM_016124	NA	Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.*1059T>C	chr1.hg19:g.25656474T>C		NA	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	hg19	CCDS262.1	0.02	9.653458	TGGxGTT	COVERED																																																																																			NOVEL	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009660.5	5	17.079519	KEEP	17	1	38	70	2077	TT	1	1	0		+	12	40	467	0	0	31.762651	227	60	7806	367	ENST00000328664.4	0.050209	1
RHD	6007	__UNKNOWN__	__UNKNOWN__	1	25656807	25656807	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:25656807C>T	ENST00000328664.4	+	0	2801					NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	NA		NA				integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGTCACTGAACATAGCTATAT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010	6007		CD molecules, Blood group antigens	10009	protein-coding gene	gene with protein product		111680	Rhesus blood group, D antigen, Rh blood group, D antigen	RH	NA	8220426	Standard	NM_016124	NM_016124	NA	Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.*1392C>T	chr1.hg19:g.25656807C>T		NA	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	hg19	CCDS262.1	0.02	11.313524	GAAxATA	COVERED																																																																																			NOVEL	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009660.5	12	23.710162	KEEP	6	1	26	88	3103	CC	1	1	0		+	10	40	336	0	0	19.221308	299	60	11314	467	ENST00000328664.4	0.032362	1
MTFR1L	56181	__UNKNOWN__	__UNKNOWN__	1	26146812	26146812	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:26146812C>T	ENST00000526894.1	+	1	51				AL020996.1_ENST00000536896.1_Missense_Mutation_p.A147T|MTFR1L_ENST00000374307.5_Intron|MTFR1L_ENST00000474295.1_Intron|RP1-317E23.6_ENST00000527604.1_Intron|MTFR1L_ENST00000524618.1_Intron|MTFR1L_ENST00000469815.1_Intron|MTFR1L_ENST00000374303.2_Intron|MTFR1L_ENST00000374301.3_5'UTR			Q9H019	MFR1L_HUMAN	mitochondrial fission regulator 1-like	NA		NA									NA						TGAGACCTGGCCGCGGCTCGG	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41284.1, CCDS44089.1	1p36.11	2012-11-30	2012-11-29	2012-11-29	ENSG00000117640	ENSG00000117640	56181			28836	protein-coding gene	gene with protein product		NA	family with sequence similarity 54, member B	FAM54B	NA	8619474, 9110174	Standard	NM_019557	NM_019557	NA	Approved		uc001bkq.4	Q9H019	OTTHUMG00000007377	ENST00000526894.1:c.-87+292C>T	chr1.hg19:g.26146812C>T		NA	A6NCB4|B7WNV5|D3DPJ4|Q63HP1|Q7Z2S7|Q9NUI7	hg19		0.02	8.65352	TGGxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.82	2.351401	0.41700	.	.	ENSG00000223474	ENST00000536896	.	.	.	2.13	1.2	0.21068	.	.	.	.	.	T	0.38188	0.1031	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.37079	-0.9721	5	0.87932	D	0	.	4.4916	0.11817	0.0:0.8059:0.0:0.1941	.	.	.	.	T	147	.	ENSP00000442451:A147T	A	-	1	0	AL020996.1	26019399	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-1.480000	0.02325	0.434000	0.26340	0.462000	0.41574	GCC	NOVEL	MTFR1L-017	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000393349.1	2	47.725316	KEEP	0	1	35	171	5828	CC	1	1	0		+	25	60	863	0	0	65.28207	179	60	6326	489	ENST00000526894.1	0.122549	1
SFN	2810	__UNKNOWN__	__UNKNOWN__	1	27190857	27190857	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:27190857C>T	ENST00000339276.4	+	0	1225					NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	NA		NA			nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		tgtgtgtgtgCGCGCGCGCCA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793	2810			10773	protein-coding gene	gene with protein product	14-3-3 sigma	601290			NA	8515476	Standard	NM_006142	NM_006142	NA	Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.*407C>T	chr1.hg19:g.27190857C>T		NA	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	hg19	CCDS288.1	0.02	5.898915	GTGxGCG	COVERED																																																																																			NOVEL	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011709.1	18	13.853176	KEEP	0	9	266	140	4618	CC	1	1	0		+	9	60	287	0	1	18.20897	142	60	4782	419	ENST00000339276.4	0.059603	1
C1orf172	0	__UNKNOWN__	__UNKNOWN__	1	27277974	27277974	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:27277974C>A	ENST00000320567.5	-	2	986	c.898G>T	c.(898-900)Ggc>Tgc	p.G300C		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		300		NA			developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CGAATGATGCCGCGTACCAGG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	53	55	NA		NA	NA	1		NA											NA				27277974		2203	4300	6503	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000320567.5:c.898G>T	chr1.hg19:g.27277974C>A	ENSP00000319179:p.Gly300Cys	NA	Q5QP32|Q8N0S7	hg19	CCDS293.1	0.02	12.140431	TGCxGCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.18	3.777434	0.70107	.	.	ENSG00000175707	ENST00000320567	T	0.43688	0.94	5.5	5.5	0.81552	.	0.060335	0.64402	D	0.000004	T	0.56978	0.2022	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.59695	-0.7406	10	0.87932	D	0	.	19.397	0.94611	0.0:1.0:0.0:0.0	.	300	Q8NAX2	CA172_HUMAN	C	300	ENSP00000319179:G300C	ENSP00000319179:G300C	G	-	1	0	C1orf172	27150561	1.000000	0.71417	0.922000	0.36590	0.413000	0.31143	7.433000	0.80362	2.594000	0.87642	0.555000	0.69702	GGC	NOVEL	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012340.1	5	33.970262	KEEP	0	0	0	113	3751	CC	1	1	0		-	108	60	3977	0	0	364.87988	188	60	6511	529	ENST00000320567.5	0.364865	1
PTPRU	10076	__UNKNOWN__	__UNKNOWN__	1	29652327	29652327	__UNKNOWN__	3'UTR	SNP	T	T	C	rs68078224	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:29652327T>C	ENST00000373779.3	+	0	4594				PTPRU_ENST00000428026.2_3'UTR|PTPRU_ENST00000356870.3_3'UTR|PTPRU_ENST00000460170.2_3'UTR|PTPRU_ENST00000323874.8_3'UTR	NM_001195001.1|NM_133178.3	NP_001181930.1|NP_573439.2	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	NA		NA			canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CCCCTTCCACTGTGGGCAGGG	0.632	NA	NA											T|||	407	0.08127	0.0257	0.036	5008	,	,	NA	17694	0.0129	NA	0.1243	False	NA	,,,	NA	NA	NA	2504	0.2147	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656	10076		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Fibronectin type III domain containing	9683	protein-coding gene	gene with protein product	pi R-PTP-Psi	602454			NA	8700514, 9434160	Standard		NM_133178	NA	Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000373779.3:c.*154T>C	chr1.hg19:g.29652327T>C		NA	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	hg19	CCDS335.1	0.02	2.152668	CACxGTG	COVERED																																																																																			NOVEL	PTPRU-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010445.2	1	2.707811	KEEP	0	0	0	9	276	TT	0.99254	0.982161	0		+	36	60	1206	0	0	119.836594	25	60	927	87	ENST00000373779.3	0.590164	0.989542
SPOCD1	90853	__UNKNOWN__	__UNKNOWN__	1	32280981	32280981	__UNKNOWN__	Intron	SNP	G	G	A	rs185828167		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:32280981G>A	ENST00000360482.2	-	2	91				SPOCD1_ENST00000373648.2_Intron|SPOCD1_ENST00000257100.3_Intron	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	NA		NA			negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		GCCCTGTGTGGAGACAGAAAG	0.607	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	18857	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													16	17	16	NA		NA	NA	1		NA											NA				32280981		2183	4264	6447	SO:0001627	intron_variant			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668	90853			26338	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 146	NA			NA	12477932	Standard	NM_144569	NM_144569	NA	Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.39-8C>T	chr1.hg19:g.32280981G>A		NA	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	hg19	CCDS347.1	0.02	3.99507	GTGxAGA	COVERED																																																																																			NOVEL	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381912.1	0	12.012583	KEEP	0	0	0	40	1366	GG	1	1	0		-	5	60	184	0	0	11.329605	141	60	5167	227	ENST00000360482.2	0.034247	1
S100PBP	64766	__UNKNOWN__	__UNKNOWN__	1	33293593	33293593	__UNKNOWN__	Splice_Site	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:33293593G>A	ENST00000373475.5	+	4	1085		c.e4-1		S100PBP_ENST00000356689.3_Splice_Site|S100PBP_ENST00000373476.1_Splice_Site|S100PBP_ENST00000398243.3_Intron	NM_022753.3	NP_073590.2			S100P binding protein	NA		NA								endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				CCTCAAAAAAGCAGGATGTTC	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													106	109	108	NA		NA	NA	1		NA											NA				33293593		2203	4300	6503	SO:0001630	splice_region_variant			BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497	64766			25768	protein-coding gene	gene with protein product	S100P binding protein 1	611889			NA	12477932	Standard	NM_022753	NM_022753	NA	Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.832-1G>A	chr1.hg19:g.33293593G>A		NA		hg19	CCDS30666.1	0.02	4.104865	AAAxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.015	-0.203037	0.06180	.	.	ENSG00000116497	ENST00000373476;ENST00000373475;ENST00000356689	.	.	.	4.98	0.00412	0.14057	.	.	.	.	.	.	.	.	.	.	.	0.40882	D	0.984006	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.1791	0.10367	0.3736:0.1667:0.4597:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	S100PBP	33066180	0.871000	0.30034	0.012000	0.15200	0.222000	0.24845	0.250000	0.18235	-0.202000	0.10268	-0.140000	0.14226	.	NOVEL	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011266.1	1	15.333877	KEEP	0	0	0	51	1806	GG	1	1	0	Intron	+	8	60	302	0	0	20.606062	136	60	5181	262	ENST00000373475.5	0.055556	1
CSMD2	114784	__UNKNOWN__	__UNKNOWN__	1	34006147	34006147	__UNKNOWN__	Silent	SNP	G	G	T	rs200819682		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:34006147G>T	ENST00000373381.4	-	60	9785	c.9609C>A	c.(9607-9609)acC>acA	p.T3203T		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	3179	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.	NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GCAGCTCTCCGGTCCAGGACC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													110	92	98	NA		NA	NA	1		NA											NA				34006147		2203	4300	6503	SO:0001819	synonymous_variant			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904	114784			19290	protein-coding gene	gene with protein product		608398			NA	11472063, 11572484	Standard	NM_052896	NM_001281956	NA	Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.9609C>A	chr1.hg19:g.34006147G>T		NA	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	hg19		0.02	9.890155	TCCxGTC	COVERED																																																																																			NOVEL	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		2	6.922072	KEEP	0	0	0	23	773	GG	0.999892	0.999892	0		-	52	60	1897	0	0	163.350259	159	60	5293	283	ENST00000373381.4	0.246445	1
DLGAP3	58512	__UNKNOWN__	__UNKNOWN__	1	35370989	35370989	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:35370989T>C	ENST00000373347.1	-	0	264				DLGAP3_ENST00000495979.1_5'UTR			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	NA		NA			cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				CCTCATGGCCTCAGCAAAGGC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	3	3	NA		NA	NA	1		NA											NA				35370989		1873	3788	5661	SO:0001623	5_prime_UTR_variant			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544	58512			30368	protein-coding gene	gene with protein product		611413			NA	8619474, 9110174	Standard	NM_021234	NM_001080418	NA	Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.-5A>G	chr1.hg19:g.35370989T>C		NA	Q5TDD5|Q9H3X7	hg19	CCDS30670.1	0.02	9.115558	GCCxCAG	COVERED																																																																																			NOVEL	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011554.1	1	9.630308	KEEP	0	0	0	32	1055	TT	0.999997	0.999997	0		-	60	60	2126	0	0	183.643255	172	60	6418	323	ENST00000373347.1	0.258621	1
ZMYM6NB	100506144	__UNKNOWN__	__UNKNOWN__	1	35447344	35447344	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:35447344C>T	ENST00000373337.3	-	0	713				ZMYM6_ENST00000487874.1_3'UTR|RP11-244H3.1_ENST00000417456.1_RNA	NM_001195156.1	NP_001182085.1	Q8NCS4	ZMYNB_HUMAN	ZMYM6 neighbor	NA		NA				integral component of membrane (GO:0016021)					NA						tttcATATGACATGAGGAATG	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS53296.1	1p34.3	2011-05-23			ENSG00000243749	ENSG00000243749	100506144			40021	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001195156	NA	Approved		uc001bye.3	Q8NCS4	OTTHUMG00000004158	ENST00000373337.3:c.*201G>A	chr1.hg19:g.35447344C>T		NA		hg19	CCDS53296.1	0.02	4.182516	TGAxATG	COVERED																																																																																			NOVEL	ZMYM6NB-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011985.1	0	11.131612	KEEP	0	0	0	37	1291	CC	1	1	0		-	12	60	438	0	0	31.902541	124	60	4694	191	ENST00000373337.3	0.088235	1
KIAA0319L	79932	__UNKNOWN__	__UNKNOWN__	1	35899406	35899406	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:35899406C>T	ENST00000325722.3	-	0	4473					NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	NA		NA				cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GGGACCACAGCGGGGCCATCG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687	79932			30071	protein-coding gene	gene with protein product		613535			NA	11347906	Standard	NM_024874	NM_024874	NA	Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.*1089G>A	chr1.hg19:g.35899406C>T		NA	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	hg19	CCDS390.1	0.02	6.094076	CAGxGGG	COVERED																																																																																			NOVEL	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012684.2	1	7.222994	KEEP	0	0	0	24	820	CC	0.999909	0.999909	0		-	6	60	212	0	0	12.661528	173	60	5904	246	ENST00000325722.3	0.03352	1
GRIK3	2899	__UNKNOWN__	__UNKNOWN__	1	37264714	37264714	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:37264714A>G	ENST00000373091.3	-	0	5514					NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	NA		NA			adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				TACCTTCATTAGAATCCTGTT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873	2899		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4581	protein-coding gene	gene with protein product		138243			NA	8128318	Standard	NM_000831	NM_000831	NA	Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.*2738T>C	chr1.hg19:g.37264714A>G		NA	A9Z1Z8|B1AMS6|Q13004|Q16136	hg19	CCDS416.1	0.02	4.717018	ATTxGAA	COVERED																																																																																			NOVEL	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012053.1	4	2.407365	KEEP	0	0	0	8	253	AA	0.99257	0.99257	0		-	11	60	400	0	0	28.862044	121	60	4365	151	ENST00000373091.3	0.083333	1
MEAF6	64769	__UNKNOWN__	__UNKNOWN__	1	37958187	37958187	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:37958187C>A	ENST00000373075.2	-	0	2135					NM_022756.5	NP_073593.2	Q9HAF1	EAF6_HUMAN	MYST/Esa1-associated factor 6	NA		NA			chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)	7						aaaaaaCCCACAAAAGTTTAT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC016328	CCDS418.1, CCDS59195.1, CCDS59196.1	1p35.3-p33	2011-08-12	2009-07-13	2009-07-13	ENSG00000163875	ENSG00000163875	64769			25674	protein-coding gene	gene with protein product	Esa1p-associated factor 6 homolog (S. cerevisiae), centromere protein 28	611001	chromosome 1 open reading frame 149	C1orf149	NA	8619474, 9110174, 12963728, 14966270, 16387653	Standard	NM_022756	NM_022756	NA	Approved	NY-SAR-91, FLJ11730, Eaf6, CENP-28	uc001cbe.2	Q9HAF1	OTTHUMG00000004223	ENST00000373075.2:c.*1513G>T	chr1.hg19:g.37958187C>A		NA	B1AK64|Q4F967|Q7Z311|Q86WE3	hg19	CCDS418.1	0.02	-0.411869	CCAxAAA	COVERED																																																																																			NOVEL	MEAF6-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012162.1	4	6.484415	KEEP	0	0	0	22	672	CC	0.999879	0.948287	0		-	8	60	146	0	1	9.407896	37	60	1037	98	ENST00000373075.2	0.177778	0.948402
EPHA10	284656	__UNKNOWN__	__UNKNOWN__	1	38185072	38185072	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:38185072A>C	ENST00000373048.4	-	15	2756				EPHA10_ENST00000540011.1_Intron|EPHA10_ENST00000446149.2_Intron|EPHA10_ENST00000330210.7_Intron|EPHA10_ENST00000427468.2_Intron	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	NA		NA			ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TGGCTGTCCCATGTGGGAACG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													15	20	19	NA		NA	NA	1		NA											NA				38185072		2050	4175	6225	SO:0001627	intron_variant			AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317	284656		EPH receptors, Sterile alpha motif (SAM) domain containing, Fibronectin type III domain containing	19987	protein-coding gene	gene with protein product		611123			NA	12477932	Standard	NM_173641	NM_001099439	NA	Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.2756+13T>G	chr1.hg19:g.38185072A>C		NA	A4FU89|J3KPB5|Q6NW42	hg19	CCDS41305.1	0.02	1.043469	CCCxTGT	COVERED																																																																																			NOVEL	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012497.2	0	3.607668	KEEP	0	0	0	12	338	AA	0.993634	0.993313	0		-	9	60	163	0	0	8.575141	77	60	2355	145	ENST00000373048.4	0.104651	0.999678
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39823104	39823104	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:39823104G>T	ENST00000372915.3	+	44	11584	c.11497G>T	c.(11497-11499)Gct>Tct	p.A3833S	MACF1_ENST00000564288.1_Missense_Mutation_p.A3828S|MACF1_ENST00000361689.2_Missense_Mutation_p.A1766S|MACF1_ENST00000289893.4_Missense_Mutation_p.A2268S|MACF1_ENST00000545844.1_Missense_Mutation_p.A1766S|MACF1_ENST00000539005.1_Missense_Mutation_p.A1766S|MACF1_ENST00000317713.7_Missense_Mutation_p.A1766S|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000567887.1_Missense_Mutation_p.A3865S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3833		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CACCCAGTCAGCTCAGGCCTT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													74	73	73	NA		NA	NA	1		NA											NA				39823104		2203	4300	6503	SO:0001583	missense			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.11497G>T	chr1.hg19:g.39823104G>T	ENSP00000362006:p.Ala3833Ser	NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	6.627132	TCAxCTC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.15|15.15	2.748497|2.748497	0.49257|0.49257	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893|ENST00000372925	T;T;T;T;T;T;T|T	0.38077|0.34859	1.16;1.16;1.16;1.16;1.16;1.16;1.16|1.34	6.07|6.07	6.07|6.07	0.98685|0.98685	.|.	0.100805|.	0.43579|.	D|.	0.000542|.	T|T	0.62744|0.62744	0.2453|0.2453	M|M	0.77313|0.77313	2.365|2.365	0.80722|0.80722	D|D	1|1	P;P;P;P|.	0.50156|.	0.881;0.915;0.624;0.932|.	P;P;B;P|.	0.56916|.	0.781;0.809;0.341;0.782|.	T|T	0.63839|0.63839	-0.6546|-0.6546	10|7	0.52906|0.87932	T|D	0.07|0	.|.	20.6439|20.6439	0.99570|0.99570	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3833;1766;1766;1731|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	S|I	1766;3833;1766;1766;1766;1915;2268|899	ENSP00000439537:A1766S;ENSP00000362006:A3833S;ENSP00000354573:A1766S;ENSP00000313438:A1766S;ENSP00000444364:A1766S;ENSP00000437059:A1915S;ENSP00000289893:A2268S|ENSP00000362016:S899I	ENSP00000289893:A2268S|ENSP00000362016:S899I	A|S	+|+	1|2	0|0	MACF1|MACF1	39595691|39595691	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.218000|0.218000	0.24690|0.24690	6.314000|6.314000	0.72848|0.72848	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GCT|AGC	NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	3	19.556793	KEEP	0	0	0	65	2255	GG	1	1	0		+	52	60	1852	0	0	160.513143	146	60	5533	326	ENST00000372915.3	0.262626	1
COL9A2	1298	__UNKNOWN__	__UNKNOWN__	1	40776469	40776469	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:40776469G>A	ENST00000372748.3	-	13	727					NM_001852.3	NP_001843.1	Q14055	CO9A2_HUMAN	collagen, type IX, alpha 2	NA		NA			axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(4)|stomach(2)|urinary_tract(2)	22	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.08e-17)			TGTcagacaggcaggcagatg	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													40	38	39	NA		NA	NA	1		NA											NA				40776469		2188	4268	6456	SO:0001627	intron_variant			M95610	CCDS450.1	1p33-p32	2013-01-16			ENSG00000049089	ENSG00000049089	1298		Proteoglycans / Extracellular Matrix : Collagen proteoglycans, Collagens	2218	protein-coding gene	gene with protein product		120260		EDM2	NA	8454052, 8528240, 1429648	Standard	NM_001852	NM_001852	NA	Approved	MED	uc001cfh.1	Q14055	OTTHUMG00000005761	ENST00000372748.3:c.631-30C>T	chr1.hg19:g.40776469G>A		NA	B2RMP9	hg19	CCDS450.1	0.02	9.098909	CAGxCAG	COVERED																																																																																			NOVEL	COL9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000015764.3	4	13.844567	KEEP	0	0	0	46	1633	GG	1	1	0		-	55	60	1974	0	0	168.249893	179	60	6451	359	ENST00000372748.3	0.235043	1
CTPS1	1503	__UNKNOWN__	__UNKNOWN__	1	41467865	41467865	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:41467865A>G	ENST00000372621.4	+	11	1636	c.1128A>G	c.(1126-1128)cgA>cgG	p.R376R	CTPS1_ENST00000372616.1_Silent_p.R376R|CTPS1_ENST00000541520.1_Silent_p.R145R	NM_001905.2	NP_001896.2			CTP synthase 1	NA		NA								endometrium(3)|lung(10)	13						TTGGTGTTCGAGGAACAGAAG	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													211	201	204	NA		NA	NA	1		NA											NA				41467865		2203	4300	6503	SO:0001819	synonymous_variant			BC009408	CCDS459.1	1p34.1	2012-05-02	2012-05-02	2012-05-02	ENSG00000171793	ENSG00000171793	1503	6.3.4.2		2519	protein-coding gene	gene with protein product		123860	CTP synthase	CTPS	NA	1783378	Standard	NM_001905	XM_005270536	NA	Approved		uc001cgk.4	P17812	OTTHUMG00000005712	ENST00000372621.4:c.1128A>G	chr1.hg19:g.41467865A>G		NA		hg19	CCDS459.1	0.02	1.963322	TCGxGGA	COVERED																																																																																			NOVEL	CTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000015629.1	0	11.428409	KEEP	0	0	0	38	1184	AA	1	0.999907	0		+	18	60	641	0	0	52.757309	76	60	2784	172	ENST00000372621.4	0.191489	0.999907
HIVEP3	59269	__UNKNOWN__	__UNKNOWN__	1	41978668	41978668	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:41978668C>T	ENST00000372583.1	-	8	7109	c.6224G>A	c.(6223-6225)gGt>gAt	p.G2075D	HIVEP3_ENST00000247584.5_Missense_Mutation_p.G2075D|HIVEP3_ENST00000429157.2_Missense_Mutation_p.G2075D|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000372584.1_Missense_Mutation_p.G2075D	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	2075	6 X 4 AA tandem repeats of S-P-X-[RK].	NA			positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				CTCGGCCTGACCTGGAGACCA	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	32	33	NA		NA	NA	1		NA											NA				41978668		2203	4300	6503	SO:0001583	missense			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124	59269		Zinc fingers, C2H2-type	13561	protein-coding gene	gene with protein product	kappabinding protein-1	606649	human immunodeficiency virus type I enhancer-binding protein 3		NA	11161801	Standard	NM_024503	NR_038260	NA	Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.6224G>A	chr1.hg19:g.41978668C>T	ENSP00000361664:p.Gly2075Asp	NA	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	hg19	CCDS463.1	0.02	1.836991	TGAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.64	2.892170	0.52014	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.06218	3.34;3.33;3.33;3.34	4.12	4.12	0.48240	.	0.137450	0.33591	N	0.004749	T	0.11793	0.0287	L	0.27053	0.805	0.41782	D	0.989822	D;D	0.63046	0.992;0.987	P;P	0.62740	0.906;0.808	T	0.38023	-0.9680	10	0.14252	T	0.57	-3.2188	16.497	0.84247	0.0:1.0:0.0:0.0	.	2075;2075	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	D	2075	ENSP00000361665:G2075D;ENSP00000361664:G2075D;ENSP00000247584:G2075D;ENSP00000410828:G2075D	ENSP00000247584:G2075D	G	-	2	0	HIVEP3	41751255	0.704000	0.27836	0.872000	0.34217	0.845000	0.48019	1.589000	0.36644	2.267000	0.75376	0.655000	0.94253	GGT	NOVEL	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000016978.1	0	9.329101	KEEP	0	0	0	31	1053	CC	0.999997	0.999937	0		-	28	60	997	0	0	87.747315	69	60	2463	144	ENST00000372583.1	0.28866	0.99994
ERMAP	114625	__UNKNOWN__	__UNKNOWN__	1	43296253	43296253	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:43296253G>A	ENST00000372517.2	+	3	329				ERMAP_ENST00000487556.1_Intron|ERMAP_ENST00000328249.3_5'UTR|ERMAP_ENST00000372514.3_Intron	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	NA		NA				cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGATATTGGCGTCCCCAGAAT	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													60	50	54	NA		NA	NA	1		NA											NA				43296253		2203	4300	6503	SO:0001627	intron_variant			AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010	114625		Blood group antigens, Immunoglobulin superfamily / V-set domain containing, Butyrophilins	15743	protein-coding gene	gene with protein product		609017	Radin blood group, Scianna blood group, erythroblast membrane-associated protein, erythroblast membrane-associated protein (RD and SC blood groups)	RD, SC	NA	11549310	Standard	NM_018538	XM_005270415	NA	Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.85+49G>A	chr1.hg19:g.43296253G>A		NA	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	hg19	CCDS475.1	0.02	26.858606	GGCxTCC	COVERED																																																																																			NOVEL	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020180.1	14	42.063197	KEEP	0	0	0	140	4675	GG	1	1	0		+	139	60	5082	0	0	438.376548	420	60	14606	862	ENST00000372517.2	0.248658	1
TMEM125	128218	__UNKNOWN__	__UNKNOWN__	1	43738285	43738285	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:43738285G>T	ENST00000432792.2	+	0	462				TMEM125_ENST00000439858.1_5'UTR			Q96AQ2	TM125_HUMAN	transmembrane protein 125	NA		NA				integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGAGGAATGGGACTCTGGGC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178	128218			28275	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144626	NM_144626	NA	Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.-109G>T	chr1.hg19:g.43738285G>T		NA	D3DPX1	hg19	CCDS480.1	0.02	6.630427	ATGxGAC	COVERED																																																																																			NOVEL	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019032.2	1	5.417385	KEEP	0	0	0	18	615	GG	0.999859	0.999859	0		+	22	60	742	0	0	57.411248	130	60	4526	194	ENST00000432792.2	0.144737	1
CDC20	991	__UNKNOWN__	__UNKNOWN__	1	43828871	43828871	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:43828871T>A	ENST00000372462.1	+	0	1774				CDC20_ENST00000310955.6_3'UTR			Q12834	CDC20_HUMAN	cell division cycle 20	NA		NA			activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GTTTTTTTTTTAAATCTGTTT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(137;1154 1759 10362 10401 46925)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399	991		WD repeat domain containing	1723	protein-coding gene	gene with protein product		603618	CDC20 (cell division cycle 20, S. cerevisiae, homolog), CDC20 cell division cycle 20 homolog (S. cerevisiae), cell division cycle 20 homolog (S. cerevisiae)		NA	7513050, 9353311	Standard	NM_001255	NM_001255	NA	Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.*71T>A	chr1.hg19:g.43828871T>A		NA	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	hg19	CCDS484.1	0.02	18.071292	TTTxAAA	COVERED																																																																																			NOVEL	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019488.1	5	29.786425	KEEP	0	0	0	99	3047	TT	1	1	0		+	45	60	1585	1	0	116.876695	396	60	14140	667	ENST00000372462.1	0.102041	1
SZT2	23334	__UNKNOWN__	__UNKNOWN__	1	43908488	43908488	__UNKNOWN__	Splice_Site	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:43908488A>G	ENST00000562955.1	+	58	7980		c.e58-1		SZT2_ENST00000372442.1_Splice_Site	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	NA		NA			central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						TCCATCTCTCAGGAGCCAAAC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	116	116	NA		NA	NA	1		NA											NA				43908488		2203	4300	6503	SO:0001630	splice_region_variant			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198	23334			29040	protein-coding gene	gene with protein product	seizure threshold 2 homolog A (mouse), seizure threshold 2 homolog B (mouse)	615463	chromosome 1 open reading frame 84, KIAA0467	C1orf84, KIAA0467	NA	9455484	Standard	NM_015284	NM_015284	NA	Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.7981-1A>G	chr1.hg19:g.43908488A>G		NA	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	hg19	CCDS30694.2	0.02	8.933185	CTCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	18.80	3.700683	0.68501	.	.	ENSG00000198198	ENST00000372442	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9043	0.79412	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SZT2	43681075	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	7.408000	0.80041	2.169000	0.68431	0.459000	0.35465	.	NOVEL	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019517.3	3	22.865272	KEEP	0	0	0	76	2390	AA	1	1	0	Intron	+	73	60	2420	0	0	214.407818	157	60	5837	371	ENST00000562955.1	0.317391	1
ATP6V0B	533	__UNKNOWN__	__UNKNOWN__	1	44443364	44443364	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:44443364T>C	ENST00000472174.2	+	8	984				ATP6V0B_ENST00000498664.1_Intron|ATP6V0B_ENST00000532642.1_3'UTR|ATP6V0B_ENST00000236067.4_Intron|ATP6V0B_ENST00000471859.2_Intron	NM_004047.3	NP_004038.1	Q99437	VATO_HUMAN	ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuole (GO:0005773)	hydrogen ion transmembrane transporter activity (GO:0015078)|transporter activity (GO:0005215)			breast(2)|kidney(1)|large_intestine(3)|lung(3)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)				TGTGAGTTTGTGACTAAGGAT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC000423	CCDS505.1, CCDS41315.1, CCDS72772.1	1p32.3	2010-04-21	2006-01-20	2002-05-10	ENSG00000117410	ENSG00000117410	533		ATPases / V-type	861	protein-coding gene	gene with protein product		603717	ATPase, H+ transporting, lysosomal (vacuolar proton pump) 21kD, ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c''	ATP6F	NA	9653649	Standard	NM_004047	XM_005270944	NA	Approved	VMA16, HATPL	uc001cld.3	Q99437	OTTHUMG00000008298	ENST00000472174.2:c.592-289T>C	chr1.hg19:g.44443364T>C		NA	D3DPY5|Q6IB32	hg19	CCDS505.1	0.02	7.03621	TTGxGAC	COVERED																																																																																			NOVEL	ATP6V0B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022854.2	6	14.13725	KEEP	0	0	0	47	1436	TT	1	1	0		+	22	60	747	0	0	56.593704	151	60	5445	258	ENST00000472174.2	0.127168	1
SLC6A9	6536	__UNKNOWN__	__UNKNOWN__	1	44482839	44482839	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:44482839G>A	ENST00000372310.3	-	3	196				SLC6A9_ENST00000357730.2_5'UTR|SLC6A9_ENST00000475075.2_Intron|SLC6A9_ENST00000537678.1_Intron|SLC6A9_ENST00000372306.3_Intron|SLC6A9_ENST00000360584.2_5'UTR|SLC6A9_ENST00000492434.2_Intron	NM_001024845.2	NP_001020016.1	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	NA		NA			transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	CGACACTGACGCATCCCCTGC	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	17	16	NA		NA	NA	1		NA											NA				44482839		2192	4286	6478	SO:0001627	intron_variant			S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517	6536		Solute carriers	11056	protein-coding gene	gene with protein product		601019			NA	8183239, 7587377	Standard	NM_201649	NM_006934	NA	Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000372310.3:c.31-6285C>T	chr1.hg19:g.44482839G>A		NA	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	hg19	CCDS30695.1	0.02	16.273253	GACxCAT	COVERED																																																																																			NOVEL	SLC6A9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022827.1	9	71.616157	KEEP	0	0	0	238	8078	GG	1	1	0		-	43	60	1553	0	0	117.585685	337	60	11456	859	ENST00000372310.3	0.113158	1
TESK2	10420	__UNKNOWN__	__UNKNOWN__	1	45810768	45810768	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:45810768C>T	ENST00000372086.3	-	11	1860	c.1460G>A	c.(1459-1461)aGt>aAt	p.S487N	TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000372084.1_Missense_Mutation_p.S458N|TESK2_ENST00000538496.1_Missense_Mutation_p.S404N|TESK2_ENST00000341771.6_Missense_Mutation_p.S458N	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	487		NA			actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					CTTGAGACTACTTAGGCGTGG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													132	137	136	NA		NA	NA	1		NA											NA				45810768		1907	4124	6031	SO:0001583	missense			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	10420	2.7.12.1		11732	protein-coding gene	gene with protein product		604746			NA	10512679	Standard	NM_007170	NM_007170	NA	Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.1460G>A	chr1.hg19:g.45810768C>T	ENSP00000361158:p.Ser487Asn	NA	Q5T422|Q5T423|Q8N520|Q9Y3Q6	hg19	CCDS41323.1	0.02	11.340105	CTAxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.64	1.698188	0.30142	.	.	ENSG00000070759	ENST00000372084;ENST00000372086;ENST00000372083;ENST00000341771;ENST00000538496	T;T;T;T	0.78481	-1.15;-0.93;-1.15;-1.18	5.89	4.02	0.46733	.	0.131467	0.53938	N	0.000050	T	0.63082	0.2481	N	0.20986	0.625	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.003	T	0.57159	-0.7859	10	0.51188	T	0.08	-7.3619	8.1287	0.31014	0.0:0.7326:0.1299:0.1375	.	458;487	Q96S53-3;Q96S53	.;TESK2_HUMAN	N	458;487;471;458;404	ENSP00000361156:S458N;ENSP00000361158:S487N;ENSP00000343940:S458N;ENSP00000441746:S404N	ENSP00000343940:S458N	S	-	2	0	TESK2	45583355	1.000000	0.71417	0.999000	0.59377	0.931000	0.56810	2.082000	0.41605	0.824000	0.34613	0.555000	0.69702	AGT	NOVEL	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020523.1	3	22.571769	KEEP	0	0	0	75	2587	CC	1	1	0		-	32	60	1195	0	0	92.541631	230	60	8605	408	ENST00000372086.3	0.122137	1
AGBL4	84871	__UNKNOWN__	__UNKNOWN__	1	48999826	48999826	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:48999826C>A	ENST00000371839.1	-	0	1647					NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	NA		NA			C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		CCCATAAGACCTCCCAGGACT	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													128	119	122	NA		NA	NA	1		NA											NA				48999826		692	1591	2283	SO:0001624	3_prime_UTR_variant			AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094	84871			25892	protein-coding gene	gene with protein product	cytosolic carboxypeptidase 6	NA			NA	21074048	Standard	NM_032785	NM_032785	NA	Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.*19G>T	chr1.hg19:g.48999826C>A		NA	B3KT26|B4DG37	hg19	CCDS44137.1	0.02	26.526401	GACxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.185	-1.058875	0.01950	.	.	ENSG00000186094	ENST00000411952	.	.	.	4.83	2.67	0.31697	.	.	.	.	.	T	0.40015	0.1100	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34775	-0.9815	5	0.72032	D	0.01	.	5.6263	0.17485	0.0:0.7167:0.0:0.2833	.	.	.	.	M	504	.	ENSP00000411423:R504M	R	-	2	0	AGBL4	48772413	0.008000	0.16893	0.040000	0.18447	0.016000	0.09150	0.564000	0.23563	1.136000	0.42199	0.655000	0.94253	AGG	NOVEL	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021346.4	7	23.17545	KEEP	0	0	0	77	2788	CC	1	1	0		-	163	60	5989	0	0	524.708127	434	60	16329	833	ENST00000371839.1	0.273032	1
OSBPL9	114883	__UNKNOWN__	__UNKNOWN__	1	52253853	52253853	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:52253853C>T	ENST00000428468.1	+	0	2605				OSBPL9_ENST00000361556.5_3'UTR|OSBPL9_ENST00000453295.1_3'UTR|OSBPL9_ENST00000435686.2_3'UTR|OSBPL9_ENST00000447887.1_3'UTR|OSBPL9_ENST00000371714.1_3'UTR|OSBPL9_ENST00000462759.1_3'UTR|OSBPL9_ENST00000486942.1_3'UTR|OSBPL9_ENST00000371710.3_3'UTR|OSBPL9_ENST00000337809.4_3'UTR			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	NA		NA			lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						catatatatacacacacatac	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859	114883		Oxysterol binding proteins, Pleckstrin homology (PH) domain containing	16386	protein-coding gene	gene with protein product		606737			NA		Standard		NM_148904	NA	Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.*392C>T	chr1.hg19:g.52253853C>T		NA	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	hg19	CCDS41332.3	0.02	6.862811	ATAxACA	COVERED																																																																																			NOVEL	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022584.4	8	16.281581	KEEP	0	1	34	66	2281	CC	1	1	0		+	25	60	906	0	0	71.711429	145	60	5406	274	ENST00000428468.1	0.147059	1
RAB3B	5865	__UNKNOWN__	__UNKNOWN__	1	52385225	52385225	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:52385225C>T	ENST00000371655.3	-	0	1246					NM_002867.3	NP_002858.2	P20337	RAB3B_HUMAN	RAB3B, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle size (GO:0097494)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9						CCTCACTTTACGCAATTGGCA	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC005035	CCDS560.1	1p32-p31	2008-02-05			ENSG00000169213	ENSG00000169213	5865		RAB, member RAS oncogene	9778	protein-coding gene	gene with protein product		179510			NA		Standard	NM_002867	NM_002867	NA	Approved		uc001cth.3	P20337	OTTHUMG00000008627	ENST00000371655.3:c.*374G>A	chr1.hg19:g.52385225C>T		NA	Q5VUL2|Q9BSI1	hg19	CCDS560.1	0.02	4.610229	TTAxGCA	COVERED																																																																																			NOVEL	RAB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023816.1	1	3.009393	KEEP	0	0	0	10	335	CC	0.992708	0.992701	0		-	23	60	863	0	0	72.883562	86	60	3076	137	ENST00000371655.3	0.211009	0.999993
ZYG11B	79699	__UNKNOWN__	__UNKNOWN__	1	53279355	53279355	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:53279355C>T	ENST00000294353.6	+	11	1988	c.1843C>T	c.(1843-1845)Caa>Taa	p.Q615*	ZYG11B_ENST00000443756.2_Nonsense_Mutation_p.Q545*|ZYG11B_ENST00000545132.1_3'UTR	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	615		NA								breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						CAGAGGTGAACAAGCTTGGAC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													126	114	118	NA		NA	NA	1		NA											NA				53279355		2203	4300	6503	SO:0001587	stop_gained			AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378	79699		ZYG11 cell cycle regulator family	25820	protein-coding gene	gene with protein product		NA	zyg-11 homolog (C. elegans), zyg-11 homolog B (C. elegans)	ZYG11	NA	11214970	Standard	NM_024646	NM_024646	NA	Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1843C>T	chr1.hg19:g.53279355C>T	ENSP00000294353:p.Gln615*	NA	Q8N2X3|Q9H8L8	hg19	CCDS30717.1	0.02	9.027669	GAAxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	38	6.732443	0.97796	.	.	ENSG00000162378	ENST00000443756;ENST00000294353	.	.	.	5.37	5.37	0.77165	.	0.173002	0.52532	D	0.000064	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	14.6835	0.69035	0.0:0.855:0.145:0.0	.	.	.	.	X	545;615	.	ENSP00000294353:Q615X	Q	+	1	0	ZYG11B	53051943	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.460000	0.45031	2.504000	0.84457	0.655000	0.94253	CAA	NOVEL	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024749.1	1	18.055053	KEEP	0	0	0	60	2125	CC	1	1	0		+	48	60	1759	0	0	146.460734	194	60	7380	381	ENST00000294353.6	0.198347	1
PODN	127435	__UNKNOWN__	__UNKNOWN__	1	53535607	53535607	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:53535607C>T	ENST00000312553.5	+	2	231	c.224C>T	c.(223-225)gCc>gTc	p.A75V	PODN_ENST00000371500.3_Missense_Mutation_p.A56V|PODN_ENST00000395871.2_Missense_Mutation_p.A75V	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	27	LRRNT.	NA			negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GCCGTGAGGGCCCCAGGATTT	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													9	12	11	NA		NA	NA	1		NA											NA				53535607		2189	4287	6476	SO:0001583	missense			AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348	127435		Proteoglycans / Extracellular Matrix : Small leucine-rich repeats	23174	protein-coding gene	gene with protein product	podocan proteoglycan	608661			NA		Standard	NM_153703	NM_153703	NA	Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.224C>T	chr1.hg19:g.53535607C>T	ENSP00000308315:p.Ala75Val	NA	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	hg19	CCDS573.1	0.02	4.69151	GGGxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.37	1.917234	0.33815	.	.	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.60299	0.86;0.2;0.95	4.19	4.19	0.49359	.	0.590677	0.15180	N	0.276161	T	0.47451	0.1446	N	0.22421	0.69	0.09310	N	1	B;B;B	0.31790	0.34;0.069;0.069	B;B;B	0.37731	0.257;0.025;0.025	T	0.46400	-0.9194	10	0.48119	T	0.1	.	11.8647	0.52486	0.0:1.0:0.0:0.0	.	75;56;75	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	V	56;75;75	ENSP00000360555:A56V;ENSP00000379212:A75V;ENSP00000308315:A75V	ENSP00000308315:A75V	A	+	2	0	PODN	53308195	0.910000	0.30920	0.111000	0.21465	0.018000	0.09664	2.119000	0.41958	2.165000	0.68154	0.491000	0.48974	GCC	NOVEL	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024735.1	0	8.757988	KEEP	0	1	25	38	1309	CC	1	0.999968	0		+	9	60	318	0	0	22.929949	92	60	3265	175	ENST00000312553.5	0.089109	0.999968
DMRTB1	63948	__UNKNOWN__	__UNKNOWN__	1	53925599	53925599	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:53925599C>T	ENST00000371445.3	+	1	528	c.473C>T	c.(472-474)gCg>gTg	p.A158V		NM_033067.1	NP_149056.1	Q96MA1	DMRTB_HUMAN	DMRT-like family B with proline-rich C-terminal, 1	158	Pro-rich.	NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(5)|ovary(1)|skin(1)	10						CCCAGCCTTGCGGGACCCCCT	0.756	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	5	5	NA		NA	NA	1		NA											NA				53925599		1728	3497	5225	SO:0001583	missense			AJ291671	CCDS581.1	1p32	2008-08-29			ENSG00000143006	ENSG00000143006	63948			13913	protein-coding gene	gene with protein product		614805			NA		Standard		NM_033067	NA	Approved		uc001cvq.1	Q96MA1	OTTHUMG00000008080	ENST00000371445.3:c.473C>T	chr1.hg19:g.53925599C>T	ENSP00000360500:p.Ala158Val	NA	Q96SD2	hg19	CCDS581.1	0.02	1.935679	TTGxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	5.946	0.358608	0.11239	.	.	ENSG00000143006	ENST00000371445;ENST00000431335	.	.	.	3.54	-1.78	0.07957	.	5.035710	0.00166	N	0.000007	T	0.22820	0.0551	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.15694	-1.0428	9	0.14656	T	0.56	0.0246	8.7201	0.34436	0.0:0.7046:0.0:0.2954	.	158	Q96MA1	DMRTB_HUMAN	V	158;5	.	ENSP00000360500:A158V	A	+	2	0	DMRTB1	53698187	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.331000	0.07914	-0.178000	0.10672	-0.350000	0.07774	GCG	NOVEL	DMRTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022110.1	1	6.91933	KEEP	0	0	0	23	772	CC	0.999892	0.991987	0		+	4	60	133	0	0	8.743216	59	60	2091	108	ENST00000371445.3	0.063492	0.992094
GLIS1	148979	__UNKNOWN__	__UNKNOWN__	1	54060220	54060220	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs138426090		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:54060220C>T	ENST00000312233.2	-	3	922	c.356G>A	c.(355-357)cGg>cAg	p.R119Q		NM_147193.2	NP_671726.2			GLIS family zinc finger 1	NA		NA								endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						AGGCCGGGCCCGCTTGGAAGG	0.647	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	16227	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0								C	GLN/ARG	0,4384		0,0,2192	22	27	25	NA	356	4.8	1	1	dbSNP_134	25	2,8560		0,2,4279	no	missense	GLIS1	NM_147193.2	43	0,2,6471	TT,TC,CC	NA	0.0234,0.0,0.0154	possibly-damaging	119/621	54060220	2,12944	2192	4281	6473	SO:0001583	missense			AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332	148979		Zinc fingers, C2H2-type	29525	protein-coding gene	gene with protein product		610378			NA	12042312, 14500813	Standard	NM_147193	NM_147193	NA	Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.356G>A	chr1.hg19:g.54060220C>T	ENSP00000309653:p.Arg119Gln	NA		hg19	CCDS582.1	0.02	4.671817	GCCxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.357	1.066903	0.20067	0.0	2.34E-4	ENSG00000174332	ENST00000312233	T	0.10192	2.9	4.8	4.8	0.61643	.	0.286767	0.24917	N	0.034575	T	0.05547	0.0146	L	0.27053	0.805	0.09310	N	1	P	0.40107	0.703	B	0.27380	0.079	T	0.37572	-0.9700	10	0.27082	T	0.32	.	7.8214	0.29290	0.0:0.7307:0.1787:0.0906	.	119	Q8NBF1	GLIS1_HUMAN	Q	119	ENSP00000309653:R119Q	ENSP00000309653:R119Q	R	-	2	0	GLIS1	53832808	0.940000	0.31905	0.971000	0.41717	0.131000	0.20780	1.405000	0.34635	2.606000	0.88127	0.563000	0.77884	CGG	NOVEL	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022109.1	4	16.846378	KEEP	0	0	0	56	1778	CC	1	0.999978	0		-	11	60	396	0	0	29.655705	92	60	3013	192	ENST00000312233.2	0.106796	0.999978
NDC1	55706	__UNKNOWN__	__UNKNOWN__	1	54303867	54303867	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:54303867G>T	ENST00000371429.3	-	1	656				NDC1_ENST00000480952.1_Intron|NDC1_ENST00000540001.1_Intron|NDC1_ENST00000537333.1_Intron|NDC1_ENST00000234725.8_Intron	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	NA		NA			mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)				NA						CACAGTGCACGCCGCACTCAC	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	4	3	NA		NA	NA	1		NA											NA				54303867		1769	3380	5149	SO:0001627	intron_variant			AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804	55706			25525	protein-coding gene	gene with protein product	nuclear division cycle 1 homolog (S. cerevisiae)	610115	transmembrane protein 48	TMEM48	NA	16779818, 12958361	Standard	NM_018087	NR_033142	NA	Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.57+10C>A	chr1.hg19:g.54303867G>T		NA	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	hg19	CCDS583.1	0.02	-0.350793	CACxCCG	COVERED																																																																																			NOVEL	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022101.1	0	11.729518	KEEP	0	0	0	39	1213	GG	1	0.877708	0		-	24	60	896	0	0	89.36793	16	60	513	92	ENST00000371429.3	0.6	0.877708
USP24	23358	__UNKNOWN__	__UNKNOWN__	1	55537466	55537466	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:55537466A>G	ENST00000294383.6	-	67	7800				USP24_ENST00000484447.1_Intron|USP24_ENST00000407756.1_Intron	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	NA		NA			ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TTTGCACACAAGGACATGCTG	0.463	NA	NA									OREG0013507	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													110	106	107	NA		NA	NA	1		NA											NA				55537466		2070	4209	6279	SO:0001627	intron_variant			AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402	23358		Ubiquitin-specific peptidases	12623	protein-coding gene	gene with protein product		610569	ubiquitin specific protease 24		NA	12838346	Standard		NM_015306	NA	Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.7800+20T>C	chr1.hg19:g.55537466A>G		1008	Q6ZSY2|Q8N2Y4|Q9NXD1	hg19	CCDS44154.2	0.02	2.224322	ACAxGGA	COVERED																																																																																			NOVEL	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022275.2	2	4.815021	KEEP	0	0	0	16	520	AA	0.997832	0.997558	0		-	19	60	696	0	0	58.838532	68	60	2435	120	ENST00000294383.6	0.218391	0.999726
INADL	10207	__UNKNOWN__	__UNKNOWN__	1	62256958	62256958	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:62256958T>C	ENST00000371158.2	+	9	1182				INADL_ENST00000316485.6_Intron	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	NA		NA			cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						TTGCACAGATTGACTATGTAC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849	10207			28881	protein-coding gene	gene with protein product		603199			NA	9280290, 11374908	Standard	NM_170605	NM_176877	NA	Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1069-62T>C	chr1.hg19:g.62256958T>C		NA	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	hg19	CCDS617.2	0.02	5.062676	GATxGAC	COVERED																																																																																			NOVEL	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023639.2	1	6.017659	KEEP	0	0	0	20	623	TT	0.999863	0.999844	0		+	23	60	803	0	0	67.416442	81	60	2944	160	ENST00000371158.2	0.221154	0.999981
AK4	205	__UNKNOWN__	__UNKNOWN__	1	65614249	65614249	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:65614249G>T	ENST00000327299.7	+	1	350				AK4_ENST00000470888.2_Intron|AK4_ENST00000545314.1_Intron|AK4_ENST00000395334.2_Intron|AK4_ENST00000546702.1_Intron	NM_013410.3	NP_037542.1			adenylate kinase 4	NA		NA								breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						AGGGGCTGCGGGGACGAGGGC	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	6	6	NA		NA	NA	1		NA											NA				65614249		2128	4190	6318	SO:0001627	intron_variant			AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	205	2.7.4.3	Adenylate kinases	363	protein-coding gene	gene with protein product		103030	adenylate kinase 3, adenylate kinase 3-like 1	AK3, AK3L1	NA	11485571	Standard	NM_013410	NM_203464	NA	Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.145+14G>T	chr1.hg19:g.65614249G>T		NA		hg19	CCDS629.1	0.02	1.90703	GCGxGGA	COVERED																																																																																			NOVEL	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025040.2	1	15.950403	KEEP	0	0	0	53	1820	GG	1	0.999804	0		+	18	60	592	0	0	48.429337	70	60	2475	192	ENST00000327299.7	0.204545	0.999804
IL12RB2	3595	__UNKNOWN__	__UNKNOWN__	1	67861657	67861657	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:67861657A>G	ENST00000262345.1	+	16	3114	c.2474A>G	c.(2473-2475)cAg>cGg	p.Q825R	IL12RB2_ENST00000544434.1_Missense_Mutation_p.Q739R|IL12RB2_ENST00000371000.1_3'UTR	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	825		NA			cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						CTGGAGCCTCAGCACATCTCC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													294	278	283	NA		NA	NA	1		NA											NA				67861657		2203	4300	6503	SO:0001583	missense			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985	3595		Interleukins and interleukin receptors, Fibronectin type III domain containing	5972	protein-coding gene	gene with protein product		601642			NA	9284929, 8943050	Standard	NM_001559	NM_001559	NA	Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.2474A>G	chr1.hg19:g.67861657A>G	ENSP00000262345:p.Gln825Arg	NA	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	hg19	CCDS638.1	0.02	8.766321	CTCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	6.793	0.515279	0.12944	.	.	ENSG00000081985	ENST00000262345;ENST00000544434	T;T	0.42131	0.98;1.84	5.29	2.91	0.33838	.	0.672940	0.14910	N	0.291281	T	0.19846	0.0477	L	0.29908	0.895	0.18873	N	0.999985	D;P	0.57899	0.981;0.791	P;B	0.53593	0.73;0.273	T	0.04065	-1.0980	10	0.30854	T	0.27	-6.5407	4.9295	0.13910	0.7492:0.0:0.089:0.1618	.	739;825	F5H7L6;Q99665	.;I12R2_HUMAN	R	825;739	ENSP00000262345:Q825R;ENSP00000442443:Q739R	ENSP00000262345:Q825R	Q	+	2	0	IL12RB2	67634245	0.080000	0.21391	0.808000	0.32385	0.317000	0.28152	1.740000	0.38228	0.387000	0.25024	-0.353000	0.07706	CAG	NOVEL	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025202.2	3	18.054446	KEEP	0	0	0	60	1894	AA	1	1	0		+	25	60	883	0	0	64.990346	224	60	8376	385	ENST00000262345.1	0.100402	1
LRRC53	100144878	__UNKNOWN__	__UNKNOWN__	1	74946350	74946350	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:74946350T>A	ENST00000294635.4	-	3	505	c.391A>T	c.(391-393)Agc>Tgc	p.S131C	LRRC53_ENST00000416014.2_Missense_Mutation_p.S131C|FPGT-TNNI3K_ENST00000557284.2_Intron|TNNI3K_ENST00000370891.2_Intron|TNNI3K_ENST00000326637.3_Intron			A6NM62	LRC53_HUMAN	leucine rich repeat containing 53	131		NA				integral component of membrane (GO:0016021)				NS(1)|breast(1)|lung(2)	4						GTCAGGCCGCTTGTGTTTCGG	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					1p31.3	2010-08-31			ENSG00000162621	ENSG00000162621	100144878			25255	protein-coding gene	gene with protein product		NA			NA		Standard			NA	Approved			A6NM62	OTTHUMG00000009621	ENST00000294635.4:c.391A>T	chr1.hg19:g.74946350T>A	ENSP00000294635:p.Ser131Cys	NA		hg19		0.02	4.704633	CGCxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.992	1.231005	0.22626	.	.	ENSG00000162621	ENST00000416014;ENST00000294635	T;T	0.54866	0.55;0.55	5.19	-3.56	0.04626	.	1.155260	0.06667	N	0.765523	T	0.22589	0.0545	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.42327	-0.9458	7	0.45353	T	0.12	-8.0E-4	5.5048	0.16848	0.097:0.0712:0.422:0.4098	.	.	.	.	C	131	ENSP00000391861:S131C;ENSP00000294635:S131C	ENSP00000294635:S131C	S	-	1	0	LRRC53	74718938	0.000000	0.05858	0.008000	0.14137	0.611000	0.37282	-0.178000	0.09782	-0.285000	0.09089	-0.689000	0.03729	AGC	NOVEL	LRRC53-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000026515.2	0	5.108693	KEEP	0	0	0	17	542	TT	0.999366	0.999366	0		-	37	60	1404	0	0	125.543461	85	60	3128	172	ENST00000294635.4	0.303279	0.999999
C1orf173	0	__UNKNOWN__	__UNKNOWN__	1	75055368	75055368	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:75055368C>T	ENST00000326665.5	-	12	2341	c.2123G>A	c.(2122-2124)aGc>aAc	p.S708N	C1orf173_ENST00000420661.2_Missense_Mutation_p.S511N	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		708	Glu-rich.	NA								NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						CTGAGCAGTGCTTTCTTCCCA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													274	263	267	NA		NA	NA	1		NA											NA				75055368		2203	4300	6503	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000326665.5:c.2123G>A	chr1.hg19:g.75055368C>T	ENSP00000322609:p.Ser708Asn	NA	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	hg19	CCDS30755.1	0.02	9.260811	GTGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.132	1.011584	0.19277	.	.	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.19250	2.65;2.16	5.34	0.964	0.19655	.	.	.	.	.	T	0.02929	0.0087	N	0.14661	0.345	0.09310	N	0.999994	B;B	0.20052	0.008;0.041	B;B	0.23419	0.011;0.046	T	0.47407	-0.9120	9	0.14656	T	0.56	-4.2281	5.0749	0.14626	0.0:0.4453:0.3597:0.1951	.	511;708	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	N	708;511	ENSP00000322609:S708N;ENSP00000398581:S511N	ENSP00000322609:S708N	S	-	2	0	C1orf173	74827956	0.708000	0.27876	0.914000	0.36105	0.444000	0.32077	0.334000	0.19787	0.591000	0.29711	0.643000	0.83706	AGC	NOVEL	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026516.1	1	11.736786	KEEP	0	0	0	39	1407	CC	1	1	0		-	51	60	1804	0	0	154.914179	153	60	5751	291	ENST00000326665.5	0.25	1
SLC44A5	204962	__UNKNOWN__	__UNKNOWN__	1	75684163	75684163	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:75684163C>G	ENST00000370855.5	-	17	1643				SLC44A5_ENST00000535611.1_Intron|SLC44A5_ENST00000370859.3_Intron	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TAGGCTTCAACTTGAAACTTA	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													153	143	146	NA		NA	NA	1		NA											NA				75684163		2203	4300	6503	SO:0001627	intron_variant			BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968	204962		Solute carriers	28524	protein-coding gene	gene with protein product		NA			NA	15715662	Standard	NM_152697	NM_152697	NA	Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.1529+11G>C	chr1.hg19:g.75684163C>G		NA	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	hg19	CCDS667.1	0.02	10.072047	CAAxTTG	COVERED																																																																																			NOVEL	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026921.1	0	9.329478	KEEP	0	0	0	31	1072	CC	0.999997	0.999997	0		-	55	60	2134	0	0	187.068453	156	60	5848	291	ENST00000370855.5	0.260664	1
ZZZ3	26009	__UNKNOWN__	__UNKNOWN__	1	78030471	78030471	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:78030471A>C	ENST00000370801.3	-	0	4041				ZZZ3_ENST00000476275.1_5'UTR	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	NA		NA			chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						TGATTTTTATATTAGGCAGTT	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549	26009		Zinc fingers, ZZ-type	24523	protein-coding gene	gene with protein product	ATAC component 1 homolog (Drosophila)	NA			NA	16428443, 21304275	Standard	NM_015534	NM_015534	NA	Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.*854T>G	chr1.hg19:g.78030471A>C		NA	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	hg19	CCDS677.1	0.02	4.974558	TATxTTA	COVERED																																																																																			NOVEL	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026615.1	2	9.927273	KEEP	0	0	0	33	1005	AA	0.999998	0.999994	0		-	33	60	1278	0	0	113.757339	81	60	2935	184	ENST00000370801.3	0.289474	0.999996
PRKACB	5567	__UNKNOWN__	__UNKNOWN__	1	84702131	84702131	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:84702131G>T	ENST00000370685.3	+	0	2431				PRKACB_ENST00000394838.2_3'UTR|PRKACB_ENST00000370689.2_3'UTR|PRKACB_ENST00000370682.3_3'UTR|PRKACB_ENST00000394839.2_3'UTR	NM_001242862.1|NM_182948.2	NP_001229791.1|NP_891993.1	P22694	KAPCB_HUMAN	protein kinase, cAMP-dependent, catalytic, beta	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of protein processing (GO:0070613)|response to clozapine (GO:0097338)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|magnesium ion binding (GO:0000287)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(2)|kidney(1)|lung(11)|ovary(1)	16				all cancers(265;0.00536)|Epithelial(280;0.0161)|OV - Ovarian serous cystadenocarcinoma(397;0.141)		TAGGGGCACTGCTGCAACTTC	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC035058	CCDS691.1, CCDS692.1, CCDS693.1, CCDS55610.1, CCDS55611.1, CCDS72812.1, CCDS72813.1, CCDS72814.1, CCDS72815.1, CCDS72816.1	1p36.1	2012-10-02			ENSG00000142875	ENSG00000142875	5567	2.7.11.1		9381	protein-coding gene	gene with protein product		176892			NA		Standard	NM_182948	XM_005271016	NA	Approved	PKACb	uc001djl.3	P22694	OTTHUMG00000009975	ENST00000370685.3:c.*1143G>T	chr1.hg19:g.84702131G>T		NA	B1APG4|B4DKB0|B4E2Q1|Q14VH1|Q59GC0|Q5BNE9|Q5BNF0|Q5BNF1|Q5BNF2|Q5BNF3|Q5CZ92|Q5T1K3|Q7Z3M1|Q8IYR5|Q8IZQ0|Q96B09	hg19	CCDS693.1	0.02	1.989422	ACTxCTG	COVERED																																																																																			NOVEL	PRKACB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027644.1	2	3.912558	KEEP	0	0	0	13	463	GG	0.994391	0.994253	0		+	12	60	431	0	0	33.419591	79	60	2986	122	ENST00000370685.3	0.131868	0.999862
DDAH1	23576	__UNKNOWN__	__UNKNOWN__	1	85816155	85816155	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:85816155C>T	ENST00000284031.8	-	4	634	c.540G>A	c.(538-540)atG>atA	p.M180I	RP11-131L23.1_ENST00000427819.1_RNA|RP11-131L23.1_ENST00000426125.1_RNA|DDAH1_ENST00000539042.1_Missense_Mutation_p.M180I|DDAH1_ENST00000542148.1_Missense_Mutation_p.M80I|DDAH1_ENST00000426972.3_Missense_Mutation_p.M87I|DDAH1_ENST00000535924.2_Missense_Mutation_p.M77I|DDAH1_ENST00000483110.1_5'UTR	NM_012137.3	NP_036269.1	O94760	DDAH1_HUMAN	dimethylarginine dimethylaminohydrolase 1	180		NA			arginine catabolic process (GO:0006527)|citrulline metabolic process (GO:0000052)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of angiogenesis (GO:0045766)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|regulation of systemic arterial blood pressure (GO:0003073)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|catalytic activity (GO:0003824)|dimethylargininase activity (GO:0016403)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|skin(1)	5				all cancers(265;0.0318)|Epithelial(280;0.0657)	L-Citrulline(DB00155)	TAGGCCCAGCCATGCTGCAGA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													158	147	151	NA		NA	NA	1		NA											NA				85816155		2203	4300	6503	SO:0001583	missense			AB001915	CCDS705.1, CCDS44170.1	1p22	2008-02-05			ENSG00000153904	ENSG00000153904	23576	3.5.3.18		2715	protein-coding gene	gene with protein product		604743			NA	9874257	Standard		NM_012137	NA	Approved	DDAH	uc001dlb.3	O94760	OTTHUMG00000010578	ENST00000284031.8:c.540G>A	chr1.hg19:g.85816155C>T	ENSP00000284031:p.Met180Ile	NA	Q5HYC8|Q86XK5	hg19	CCDS705.1	0.02	4.826335	AGCxATG	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.5	4.926895	0.92319	.	.	ENSG00000153904	ENST00000284031;ENST00000539042;ENST00000535924;ENST00000426972;ENST00000542148	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.70718	0.3256	M	0.80508	2.5	0.80722	D	1	P;P	0.52316	0.952;0.691	P;B	0.58928	0.848;0.308	T	0.65804	-0.6079	9	0.15952	T	0.53	-30.068	18.8761	0.92337	0.0:1.0:0.0:0.0	.	80;180	B4DYP1;O94760	.;DDAH1_HUMAN	I	180;180;77;87;80	.	ENSP00000284031:M180I	M	-	3	0	DDAH1	85588743	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.063000	0.76714	2.827000	0.97445	0.650000	0.86243	ATG	NOVEL	DDAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029189.1	3	17.15537	KEEP	0	0	0	57	2020	CC	1	1	0		-	32	60	1161	0	0	99.747296	99	60	3703	244	ENST00000284031.8	0.244275	1
LRRC8D	55144	__UNKNOWN__	__UNKNOWN__	1	90399435	90399435	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:90399435G>A	ENST00000337338.5	+	3	1215	c.808G>A	c.(808-810)Gtt>Att	p.V270I	LRRC8D_ENST00000394593.3_Missense_Mutation_p.V270I	NM_001134479.1	NP_001127951.1	Q7L1W4	LRC8D_HUMAN	leucine rich repeat containing 8 family, member D	270		NA			ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(2)|skin(1)	29		all_lung(203;0.0894)|Lung NSC(277;0.227)		all cancers(265;0.0109)|Epithelial(280;0.0427)		TGTGATTGAAGTTCCCAGCAT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													40	40	40	NA		NA	NA	1		NA											NA				90399435		2203	4300	6503	SO:0001583	missense			AK001332	CCDS726.1	1p22.2	2008-02-05	2005-06-29	2005-06-29	ENSG00000171492	ENSG00000171492	55144			16992	protein-coding gene	gene with protein product		612890	leucine rich repeat containing 5	LRRC5	NA		Standard	NM_018103	NM_018103	NA	Approved	FLJ10470	uc001dnn.3	Q7L1W4	OTTHUMG00000010583	ENST00000337338.5:c.808G>A	chr1.hg19:g.90399435G>A	ENSP00000338887:p.Val270Ile	NA	D3DT29|Q6UWB2|Q9NVW3	hg19	CCDS726.1	0.02	10.865412	GAAxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.297	0.612168	0.14066	.	.	ENSG00000171492	ENST00000337338;ENST00000394593;ENST00000441269	T;T;T	0.49720	1.5;1.5;0.77	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.23965	0.0580	L	0.36672	1.1	0.47374	D	0.999401	B	0.02656	0.0	B	0.04013	0.001	T	0.04320	-1.0960	9	.	.	.	.	15.3324	0.74223	0.0682:0.0:0.9318:0.0	.	270	Q7L1W4	LRC8D_HUMAN	I	270	ENSP00000338887:V270I;ENSP00000378093:V270I;ENSP00000405784:V270I	.	V	+	1	0	LRRC8D	90172023	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	5.824000	0.69279	2.782000	0.95742	0.655000	0.94253	GTT	NOVEL	LRRC8D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029203.2	4	12.340243	KEEP	0	0	0	41	1461	GG	1	1	0		+	25	60	892	0	0	64.542754	257	60	9692	371	ENST00000337338.5	0.088652	1
ALG14	199857	__UNKNOWN__	__UNKNOWN__	1	95492633	95492633	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:95492633G>A	ENST00000370205.5	-	3	467					NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		TGTTACTAACGAAAGATCTAC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													24	23	23	NA		NA	NA	1		NA											NA				95492633		876	1991	2867	SO:0001627	intron_variant				CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339	199857			28287	protein-coding gene	gene with protein product		612866	asparagine-linked glycosylation 14 homolog (yeast), asparagine-linked glycosylation 14 homolog (S. cerevisiae)		NA	15615718	Standard	NM_144988	NM_144988	NA	Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.420+51C>T	chr1.hg19:g.95492633G>A		NA	A8K030	hg19	CCDS752.1	0.02	2.200169	AACxAAA	COVERED																																																																																			NOVEL	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029699.2	0	2.407236	KEEP	0	0	0	8	257	GG	0.99257	0.98769	0		-	7	60	228	0	0	16.519933	59	60	2017	87	ENST00000370205.5	0.106061	0.995084
RP11-57H12.6	0	__UNKNOWN__	__UNKNOWN__	1	95710298	95710298	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:95710298G>C	ENST00000604534.1	+	0	1278				RP11-57H12.5_ENST00000444665.1_RNA|RWDD3_ENST00000263893.6_Intron|RWDD3_ENST00000495272.1_Intron|RWDD3_ENST00000370202.4_Intron|RWDD3_ENST00000429514.2_3'UTR	NM_001199691.1	NP_001186620.1				NA		NA									NA						GCTATTTTCTGCTTTAAATGG	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													50	47	48	NA		NA	NA	1		NA											NA				95710298		1840	4075	5915	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000604534.1:c.*492G>C	chr1.hg19:g.95710298G>C		NA		hg19		0.02	29.261543	TCTxCTT	COVERED																																																																																			NOVEL	RP11-57H12.6-001	NOVEL	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000469000.1	7	32.507285	KEEP	0	0	0	108	3955	GG	1	1	0		+	108	60	3905	0	0	318.968437	495	60	18866	867	ENST00000604534.1	0.179104	1
GPR88	54112	__UNKNOWN__	__UNKNOWN__	1	101005211	101005211	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:101005211A>T	ENST00000315033.4	+	2	1128	c.689A>T	c.(688-690)aAc>aTc	p.N230I		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	230		NA			G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuronal action potential (GO:0019228)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|skin(1)	3		all_epithelial(167;1.19e-05)|all_lung(203;0.00159)|Lung NSC(277;0.00171)		Epithelial(280;0.0372)|all cancers(265;0.0558)|COAD - Colon adenocarcinoma(174;0.141)|Colorectal(144;0.156)|Lung(183;0.189)		AGCGTGCTCAACTTCCACCTG	0.771	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	5	5	NA		NA	NA	1		NA											NA				101005211		1945	3952	5897	SO:0001583	missense			AB042411	CCDS772.1	1p21.3	2012-08-21	2006-02-15		ENSG00000181656	ENSG00000181656	54112		GPCR / Class A : Orphans	4539	protein-coding gene	gene with protein product		607468	G-protein coupled receptor 88, G protein coupled receptor 88		NA		Standard	NM_022049	NM_022049	NA	Approved		uc001dth.3	Q9GZN0	OTTHUMG00000010981	ENST00000315033.4:c.689A>T	chr1.hg19:g.101005211A>T	ENSP00000314223:p.Asn230Ile	NA	Q29S24|Q6VN48	hg19	CCDS772.1	0.02	4.074267	TCAxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291925	0.40594	.	.	ENSG00000181656	ENST00000315033	T	0.72051	-0.62	3.42	3.42	0.39159	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	U	0.000117	T	0.64216	0.2578	L	0.38175	1.15	0.29270	N	0.870754	D	0.67145	0.996	D	0.81914	0.995	T	0.57917	-0.7728	10	0.27082	T	0.32	-8.53	12.1504	0.54046	1.0:0.0:0.0:0.0	.	230	Q9GZN0	GPR88_HUMAN	I	230	ENSP00000314223:N230I	ENSP00000314223:N230I	N	+	2	0	GPR88	100777799	1.000000	0.71417	1.000000	0.80357	0.293000	0.27360	3.598000	0.54038	1.449000	0.47699	0.240000	0.17902	AAC	NOVEL	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030212.1	1	15.942422	KEEP	0	0	0	53	1637	AA	1	1	0		+	8	60	282	0	0	18.787603	129	60	4382	293	ENST00000315033.4	0.058394	1
VCAM1	7412	__UNKNOWN__	__UNKNOWN__	1	101204454	101204454	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:101204454G>A	ENST00000294728.2	+	0	2936				VCAM1_ENST00000370115.1_3'UTR|VCAM1_ENST00000347652.2_3'UTR	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	NA		NA			acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	TATAGTACTGGCATGGTACGG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692	7412		CD molecules, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Endogenous ligands	12663	protein-coding gene	gene with protein product		192225			NA		Standard	NM_001078	NM_080682	NA	Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.*615G>A	chr1.hg19:g.101204454G>A		NA	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	hg19	CCDS773.1	0.02	4.361212	CTGxCAT	COVERED																																																																																			NOVEL	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030213.1	4	11.690214	KEEP	0	0	0	39	1344	GG	1	1	0		+	21	60	777	0	0	62.988153	106	60	3936	217	ENST00000294728.2	0.165354	1
CLCC1	23155	__UNKNOWN__	__UNKNOWN__	1	109492425	109492425	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:109492425T>C	ENST00000369971.2	-	3	361				CLCC1_ENST00000369970.3_Intron|CLCC1_ENST00000415331.1_Intron|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000348264.2_Intron|CLCC1_ENST00000356970.2_Intron|CLCC1_ENST00000369969.2_Intron|CLCC1_ENST00000302500.4_Intron|CLCC1_ENST00000369968.2_Intron|CLCC1_ENST00000369976.1_Intron	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	NA		NA				chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		ataaaatttatcaataaaaaa	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													14	16	15	NA		NA	NA	1		NA											NA				109492425		2167	4251	6418	SO:0001627	intron_variant			AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940	23155			29675	protein-coding gene	gene with protein product	Mid1-related chloride channel (yeast)	NA			NA	9872452, 11279057	Standard	NM_015127	NM_001048210	NA	Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.231+16A>G	chr1.hg19:g.109492425T>C		NA	O94861|Q8WYP8|Q8WYP9|Q9BU25	hg19	CCDS41362.1	0.02	-0.412329	TTAxCAA	COVERED																																																																																			NOVEL	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032405.1	1	5.113975	KEEP	0	0	0	17	504	TT	0.999366	0.941145	0		-	17	60	633	0	0	58.054007	30	60	1080	70	ENST00000369971.2	0.361702	0.941741
KCNC4	3749	__UNKNOWN__	__UNKNOWN__	1	110775434	110775434	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:110775434C>T	ENST00000413138.3	+	4	1827				KCNC4_ENST00000369787.3_3'UTR|KCNC4_ENST00000412512.2_Intron|KCNC4_ENST00000438661.2_Intron			Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	NA		NA			potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of neurotransmitter secretion (GO:0046928)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(2)	32		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		TTGTTTCTCCCTTTCTTTTGC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC101769	CCDS821.1, CCDS44193.1	1p21	2012-07-05			ENSG00000116396	ENSG00000116396	3749		Potassium channels, Voltage-gated ion channels / Potassium channels	6236	protein-coding gene	gene with protein product		176265	chromosome 1 open reading frame 30	C1orf30	NA	1920536, 1740329, 16382104	Standard	NM_001039574	NM_004978	NA	Approved	Kv3.4, HKSHIIIC	uc001dzh.3	Q03721	OTTHUMG00000011037	ENST00000413138.3:c.1820-37C>T	chr1.hg19:g.110775434C>T		NA	Q3MIM4|Q5TBI6	hg19		0.02	31.358329	TCCxTTT	COVERED																																																																																			NOVEL	KCNC4-006	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000390341.1	9	41.296568	KEEP	0	1	12	142	4920	CC	1	1	0		+	62	60	2313	0	0	171.692988	596	60	21568	1034	ENST00000413138.3	0.094225	1
RBM15	64783	__UNKNOWN__	__UNKNOWN__	1	110883052	110883052	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:110883052C>A	ENST00000602849.1	+	1	1108	c.1025C>A	c.(1024-1026)gCa>gAa	p.A342E	RBM15_ENST00000369784.3_Missense_Mutation_p.A342E|RBM15_ENST00000487146.2_Missense_Mutation_p.A342E			Q96T37	RBM15_HUMAN	RNA binding motif protein 15	342		NA			negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GTGCGCCCTGCATACAGTCTT	0.587	NA	NA	T	MKL1	acute megakaryocytic leukemia									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	0													64	66	65	NA		NA	NA	1		NA											NA				110883052		2203	4300	6503	SO:0001583	missense			AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775	64783		RNA binding motif (RRM) containing	14959	protein-coding gene	gene with protein product	one twenty-two	606077			NA	11431691, 11344311	Standard	NM_022768	NM_001201545	NA	Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000602849.1:c.1025C>A	chr1.hg19:g.110883052C>A	ENSP00000473638:p.Ala342Glu	NA	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	hg19		0.02	16.084547	CTGxATA	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.22	1.575741	0.28092	.	.	ENSG00000162775	ENST00000369784	T	0.18502	2.21	4.55	4.55	0.56014	.	0.157757	0.29646	N	0.011579	T	0.03915	0.0110	N	0.24115	0.695	0.26714	N	0.970913	B;P	0.34522	0.186;0.455	B;B	0.30855	0.121;0.104	T	0.30765	-0.9967	10	0.07813	T	0.8	-0.0368	17.0658	0.86558	0.0:1.0:0.0:0.0	.	342;342	Q96T37-3;Q96T37	.;RBM15_HUMAN	E	342	ENSP00000358799:A342E	ENSP00000358799:A342E	A	+	2	0	RBM15	110684575	0.982000	0.34865	0.085000	0.20634	0.959000	0.62525	4.327000	0.59247	2.365000	0.80145	0.655000	0.94253	GCA	NOVEL	RBM15-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000467905.1	7	54.463436	KEEP	0	0	0	181	6513	CC	1	1	0		+	77	60	2811	0	0	233.619434	314	60	11742	714	ENST00000602849.1	0.196931	1
RSBN1	54665	__UNKNOWN__	__UNKNOWN__	1	114305633	114305633	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:114305633C>A	ENST00000261441.5	-	0	5441					NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	NA		NA				nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAATTAAACCTAGGAACCAA	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019	54665			25642	protein-coding gene	gene with protein product		615858			NA	12477932	Standard	NM_018364	NM_018364	NA	Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.*2969G>T	chr1.hg19:g.114305633C>A		NA	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	hg19	CCDS862.1	0.02	7.223573	AACxTAG	COVERED																																																																																			NOVEL	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033022.2	6	16.854709	KEEP	0	0	0	56	1972	CC	1	1	0		-	40	60	1486	0	0	128.118972	124	60	4556	262	ENST00000261441.5	0.243902	1
IGSF3	3321	__UNKNOWN__	__UNKNOWN__	1	117158745	117158745	__UNKNOWN__	Missense_Mutation	SNP	A	A	C	rs373093989		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:117158745A>C	ENST00000318837.6	-	2	482	c.378T>G	c.(376-378)gaT>gaG	p.D126E	IGSF3_ENST00000369483.1_Missense_Mutation_p.D126E|IGSF3_ENST00000369486.3_Missense_Mutation_p.D126E			O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	126	Ig-like C2-type 1.	NA			lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D126E(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		AGTATTGCTTATCAGTGCTGG	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	skin(1)											61	55	57	NA		NA	NA	1		NA											NA				117158745		2203	4300	6503	SO:0001583	missense			AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061	3321		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	5950	protein-coding gene	gene with protein product		603491			NA	9790749	Standard	NM_001542	NM_001007237	NA	Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000318837.6:c.378T>G	chr1.hg19:g.117158745A>C	ENSP00000321184:p.Asp126Glu	NA	A6NJZ6|A6NMC7	hg19	CCDS30814.1	0.02	8.71869	CTTxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	8.319	0.823848	0.16678	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.65364	-0.15;-0.15;-0.15	4.63	-8.69	0.00855	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.109427	0.64402	N	0.000011	T	0.34250	0.0891	M	0.69523	2.12	0.30895	N	0.729963	B;B	0.10296	0.003;0.002	B;B	0.20384	0.015;0.029	T	0.06481	-1.0824	10	0.66056	D	0.02	-9.8434	10.4193	0.44341	0.1981:0.2275:0.5744:0.0	.	126;126	O75054;A6NJZ6	IGSF3_HUMAN;.	E	126	ENSP00000358498:D126E;ENSP00000358495:D126E;ENSP00000321184:D126E	ENSP00000321184:D126E	D	-	3	2	IGSF3	116960268	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.110000	0.01334	-1.801000	0.01245	0.454000	0.30748	GAT	NOVEL	IGSF3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059041.1	3	9.158838	KEEP	27	1	24	39	1193	AA	0.999997	0.999997	0		-	7	24	251	0	0	15.180973	199	60	7122	313	ENST00000318837.6	0.033981	1
TTF2	8458	__UNKNOWN__	__UNKNOWN__	1	117624553	117624553	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:117624553G>A	ENST00000369466.4	+	10	1931	c.1887G>A	c.(1885-1887)acG>acA	p.T629T		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	629	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.	NA			ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)	p.T629T(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		CAGCTTTGACGTGGCTCTCCA	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	endometrium(1)											117	114	115	NA		NA	NA	1		NA											NA				117624553		2203	4300	6503	SO:0001819	synonymous_variant			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830	8458			12398	protein-coding gene	gene with protein product	zinc finger, GRF-type containing 6	604718			NA	9748214	Standard		NM_003594	NA	Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.1887G>A	chr1.hg19:g.117624553G>A		NA	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	hg19	CCDS892.1	0.02	19.085985	GACxTGG	COVERED																																																																																			NOVEL	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033277.3	1	16.385695	KEEP	0	1	30	65	2206	GG	1	1	0		+	83	60	3032	0	0	250.770524	352	60	12593	607	ENST00000369466.4	0.190805	1
SPAG17	200162	__UNKNOWN__	__UNKNOWN__	1	118628697	118628697	__UNKNOWN__	Splice_Site	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:118628697T>C	ENST00000336338.5	-	13	1677		c.e13-2			NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	NA		NA				cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CTTTTGGTCCTGATGAAAAAG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	86	87	NA		NA	NA	1		NA											NA				118628697		2203	4300	6503	SO:0001630	splice_region_variant				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761	200162			26620	protein-coding gene	gene with protein product		NA			NA		Standard	NM_206996	NM_206996	NA	Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1612-2A>G	chr1.hg19:g.118628697T>C		NA	Q8NAZ1|Q9NT21	hg19	CCDS899.1	0.02	4.443789	TCCxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	7.100	0.573972	0.13623	.	.	ENSG00000155761	ENST00000336338	.	.	.	5.57	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3757	0.38281	0.0:0.083:0.0:0.917	.	.	.	.	.	-1	.	.	.	-	.	.	SPAG17	118430220	1.000000	0.71417	0.991000	0.47740	0.056000	0.15407	5.032000	0.64140	0.939000	0.37446	-0.297000	0.09499	.	NOVEL	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033723.1	0	4.513263	KEEP	0	0	0	15	463	TT	0.99649	0.99649	0	Intron	-	14	60	483	0	0	35.759762	115	60	4223	162	ENST00000336338.5	0.108527	1
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120456746	120456746	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:120456746G>T	ENST00000256646.2	-	0	8818					NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	NA		NA			apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAATGGCAAGGGTACAACATT	0.438	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.*1183C>A	chr1.hg19:g.120456746G>T		NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	4.245665	AAGxGTA	COVERED																																																																																			NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	2	5.416874	KEEP	0	0	0	18	602	GG	0.999859	0.999859	0		-	24	60	809	0	0	65.46406	105	60	3676	167	ENST00000256646.2	0.186047	1
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120611808	120611808	__UNKNOWN__	Intron	SNP	T	T	C	rs2794168		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:120611808T>C	ENST00000256646.2	-	1	293					NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	NA		NA			apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCAAACTCTTGGGAACCCAG	0.751	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.73+139A>G	chr1.hg19:g.120611808T>C		NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	3.827708	TCTxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	t	7.275	0.607864	0.14002	.	.	ENSG00000134250	ENST00000538680	.	.	.	2.08	-1.96	0.07525	.	.	.	.	.	T	0.16300	0.0392	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.35674	-0.9779	5	0.87932	D	0	.	2.8148	0.05453	0.0:0.4053:0.247:0.3478	.	.	.	.	R	88	.	ENSP00000439516:Q88R	Q	-	2	0	NOTCH2	120413331	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.137000	0.01304	-0.654000	0.05394	-0.788000	0.03338	CAA	NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	1	14.187407	KEEP	1	2	50	65	1894	TT	1	1	0		-	6	21	187	0	0	11.003182	125	60	4342	222	ENST00000256646.2	0.045802	1
RP11-343N15.1	0	__UNKNOWN__	__UNKNOWN__	1	121116846	121116846	__UNKNOWN__	lincRNA	SNP	C	C	A	rs368445474		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:121116846C>A	ENST00000437515.1	-	0	329					NR_104189.1					NA		NA									NA						GCCTGAGGGCCCCTCTTTTCT	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437515.1:	chr1.hg19:g.121116846C>A		NA		hg19		0.02	4.761194	GGCxCCT	COVERED																																																																																			NOVEL	RP11-343N15.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000098477.2	0	2.576852	KEEP	4	2	61	30	1017	CC	0.999997	0.999997	0		-	8	40	247	0	0	14.103515	187	60	6559	278	ENST00000437515.1	0.041026	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144902234	144902234	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:144902234A>G	ENST00000530740.1	-	24	3265				PDE4DIP_ENST00000313431.9_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000529945.1_3'UTR|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000524974.1_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369354.3_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTGACTCTGGAAGACCATTCT	0.318	NA	NA	T	PDGFRB	MPD									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.3226+842T>C	chr1.hg19:g.144902234A>G		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	7.293888	TGGxAGA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	2	11.135276	KEEP	0	0	0	37	1241	AA	1	1	0		-	19	60	714	0	0	55.368415	137	60	4972	265	ENST00000530740.1	0.121795	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145014096	145014096	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:145014096G>A	ENST00000493130.2	-	4	607	c.446C>T	c.(445-447)gCc>gTc	p.A149V	PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2029		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GAACATGCAGGCTGGCTGGCC	0.468	NA	NA	T	PDGFRB	MPD									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000493130.2:c.446C>T	chr1.hg19:g.145014096G>A	ENSP00000432251:p.Ala149Val	NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	8.587969	CAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312046	0.23821	.	.	ENSG00000178104	ENST00000493130	.	.	.	4.65	-0.526	0.11913	.	.	.	.	.	T	0.22085	0.0532	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30060	-0.9991	5	0.87932	D	0	.	7.2407	0.26094	0.5282:0.0:0.4718:0.0	.	.	.	.	V	149	.	ENSP00000432251:A149V	A	-	2	0	PDE4DIP	143725453	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.153000	0.16323	-0.173000	0.10761	0.558000	0.71614	GCC	NOVEL	PDE4DIP-027	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000099618.2	5	5.512408	KEEP	0	3	96	52	1754	GG	1	1	0		-	22	60	727	0	0	52.24982	201	60	7112	316	ENST00000493130.2	0.098655	1
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145273302	145273302	__UNKNOWN__	Silent	SNP	A	A	G	rs201646101	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:145273302A>G	ENST00000468030.1	+	3	492	c.156A>G	c.(154-156)cgA>cgG	p.R52R	NOTCH2NL_ENST00000362074.6_Silent_p.R52R|NOTCH2NL_ENST00000369340.3_Silent_p.R52R|NOTCH2NL_ENST00000344859.3_Silent_p.R52R						NA		NA									NA						CCACGTGCCGATGTGCCTCAG	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													302	276	284	NA		NA	NA	1		NA											NA				145273302		2203	4300	6503	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.156A>G	chr1.hg19:g.145273302A>G		NA		hg19		0.02	34.889673	CCGxTGT	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	7	6.965338	KEEP	156	22	767	291	9158	AA	1	1	0		+	97	60	3465	0	0	266.386002	670	70	23689	1428	ENST00000468030.1	0.126467	1
TXNIP	10628	__UNKNOWN__	__UNKNOWN__	1	145442105	145442105	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:145442105A>G	ENST00000369317.4	+	0	2397				TXNIP_ENST00000475171.1_3'UTR	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	NA		NA			cell cycle (GO:0007049)|cellular response to tumor cell (GO:0071228)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|negative regulation of cell division (GO:0051782)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|protein import into nucleus (GO:0006606)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGGTTAAGCCAAAAGACAAAA	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			S73591	CCDS72876.1	1q11	2008-07-18			ENSG00000117289	ENSG00000265972	10628			16952	protein-coding gene	gene with protein product	upregulated by 1,25-dihydroxyvitamin D-3, thioredoxin binding protein 2	606599			NA	8086474	Standard	NM_006472	NM_006472	NA	Approved	VDUP1, EST01027, HHCPA78, THIF	uc001enn.4	Q9H3M7	OTTHUMG00000013755	ENST00000369317.4:c.*887A>G	chr1.hg19:g.145442105A>G		NA	B4E3D3|Q16226|Q6PML0|Q9BXG9	hg19	CCDS913.1	0.02	15.266191	GCCxAAA	COVERED																																																																																			NOVEL	TXNIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000038547.1	3	42.701114	KEEP	0	0	0	142	4325	AA	1	1	0		+	135	60	4830	0	0	456.975023	168	60	6198	541	ENST00000369317.4	0.445545	1
SV2A	9900	__UNKNOWN__	__UNKNOWN__	1	149883389	149883389	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:149883389C>T	ENST00000369146.3	-	3	1256	c.766G>A	c.(766-768)Ggc>Agc	p.G256S	SV2A_ENST00000369145.1_Missense_Mutation_p.G256S	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	256		NA			cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	AGGAAAGTGCCGTAACCCTGG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	84	95	NA		NA	NA	1		NA											NA				149883389		2203	4300	6503	SO:0001583	missense			AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164	9900			20566	protein-coding gene	gene with protein product		185860			NA	7681585, 10611374	Standard		NM_014849	NA	Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.766G>A	chr1.hg19:g.149883389C>T	ENSP00000358142:p.Gly256Ser	NA	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	hg19	CCDS940.1	0.02	9.776328	TGCxGTA	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153548	0.78114	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.74315	-0.83;-0.83	5.2	5.2	0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.151595	0.64402	D	0.000013	T	0.46870	0.1415	L	0.31065	0.9	0.44092	D	0.996856	P	0.44478	0.836	B	0.35073	0.195	T	0.51068	-0.8752	10	0.18710	T	0.47	-20.4731	16.2778	0.82654	0.0:1.0:0.0:0.0	.	256	Q7L0J3	SV2A_HUMAN	S	256	ENSP00000358142:G256S;ENSP00000358141:G256S	ENSP00000358141:G256S	G	-	1	0	SV2A	148150013	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.433000	0.59929	2.711000	0.92665	0.655000	0.94253	GGC	NOVEL	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033754.1	1	16.853609	KEEP	0	0	0	56	1900	CC	1	1	0		-	39	60	1455	0	0	119.07545	186	60	6305	359	ENST00000369146.3	0.173333	1
ENSA	2029	__UNKNOWN__	__UNKNOWN__	1	150596419	150596419	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:150596419C>A	ENST00000369016.4	-	4	494				ENSA_ENST00000339643.5_Intron|ENSA_ENST00000361631.5_Intron|ENSA_ENST00000361532.5_Intron|ENSA_ENST00000271690.8_3'UTR|ENSA_ENST00000356527.5_3'UTR|ENSA_ENST00000369014.5_Intron|ENSA_ENST00000369009.3_Intron			O43768	ENSA_HUMAN	endosulfine alpha	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|regulation of catalytic activity (GO:0050790)|regulation of insulin secretion (GO:0050796)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|transport (GO:0006810)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ion channel inhibitor activity (GO:0008200)|phosphatase inhibitor activity (GO:0019212)|potassium channel inhibitor activity (GO:0019870)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)	4	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			CACCTCATCCCCCCACATGCA	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(188;763 2078 3002 3411 26027)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X99906	CCDS958.1, CCDS959.1, CCDS960.1, CCDS961.1, CCDS962.1, CCDS963.1, CCDS964.1, CCDS965.1	1q21.3	2010-03-11			ENSG00000143420	ENSG00000143420	2029			3360	protein-coding gene	gene with protein product		603061			NA	9653196	Standard	NM_207042	NM_004436	NA	Approved	MGC4319, MGC8394, MGC78563, ARPP-19e	uc001eve.3	O43768	OTTHUMG00000035004	ENST00000369016.4:c.398+1698G>T	chr1.hg19:g.150596419C>A		NA	A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	hg19		0.02	9.476161	TCCxCCC	COVERED																																																																																			NOVEL	ENSA-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000087245.1	5	24.98072	KEEP	0	0	0	83	2888	CC	1	1	0		-	37	60	1287	0	0	102.686942	188	60	6663	394	ENST00000369016.4	0.164444	1
ENSA	2029	__UNKNOWN__	__UNKNOWN__	1	150601778	150601778	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:150601778G>C	ENST00000369016.4	-	1	153				ENSA_ENST00000362052.7_Intron|ENSA_ENST00000369009.3_Intron|ENSA_ENST00000339643.5_Intron|ENSA_ENST00000503345.1_Intron|ENSA_ENST00000271690.8_Intron|ENSA_ENST00000369014.5_Intron|ENSA_ENST00000356527.5_Intron|ENSA_ENST00000503241.1_Intron			O43768	ENSA_HUMAN	endosulfine alpha	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|regulation of catalytic activity (GO:0050790)|regulation of insulin secretion (GO:0050796)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|transport (GO:0006810)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ion channel inhibitor activity (GO:0008200)|phosphatase inhibitor activity (GO:0019212)|potassium channel inhibitor activity (GO:0019870)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)	4	all_cancers(9;3.09e-52)|all_epithelial(9;4.47e-43)|all_lung(15;1.09e-34)|Lung NSC(24;4.04e-31)|Breast(34;0.000615)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;9.85e-23)|all cancers(9;5.06e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.67e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000701)|LUSC - Lung squamous cell carcinoma(543;0.171)			GCAAAAAGTGGCCAACCCCTG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(188;763 2078 3002 3411 26027)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X99906	CCDS958.1, CCDS959.1, CCDS960.1, CCDS961.1, CCDS962.1, CCDS963.1, CCDS964.1, CCDS965.1	1q21.3	2010-03-11			ENSG00000143420	ENSG00000143420	2029			3360	protein-coding gene	gene with protein product		603061			NA	9653196	Standard	NM_207042	NM_004436	NA	Approved	MGC4319, MGC8394, MGC78563, ARPP-19e	uc001eve.3	O43768	OTTHUMG00000035004	ENST00000369016.4:c.57+111C>G	chr1.hg19:g.150601778G>C		NA	A8K1Z9|E9PB69|Q5T5H2|Q68D48|Q6FHW0|Q6IAM4|Q6NUL2|Q6VUC6|Q6VUC7|Q6VUC8|Q6VUC9|Q6VUD0|Q6VUD1|Q9NRZ0	hg19		0.02	28.173477	GTGxCCA	COVERED																																																																																			NOVEL	ENSA-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000087245.1	5	138.161126	KEEP	0	1	6	462	15660	GG	1	1	0		-	141	60	5075	0	0	427.573421	506	60	17462	1460	ENST00000369016.4	0.217929	1
ARNT	405	__UNKNOWN__	__UNKNOWN__	1	150783768	150783768	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:150783768G>A	ENST00000354396.2	-	0	3104				ARNT_ENST00000358595.5_3'UTR			P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	NA		NA			cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CAGCAAAGACGTTTATTTAAA	0.368	NA	NA	T	ETV6	AML									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437	405		Basic helix-loop-helix proteins	700	protein-coding gene	gene with protein product		126110			NA		Standard		NM_001668	NA	Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000354396.2:c.*729C>T	chr1.hg19:g.150783768G>A		NA	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	hg19		0.02	6.309143	GACxTTT	COVERED																																																																																			NOVEL	ARNT-010	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000360630.1	6	14.143153	KEEP	0	0	0	47	1564	GG	1	1	0		-	9	60	323	0	1	20.672224	191	60	6467	297	ENST00000354396.2	0.045	1
SETDB1	9869	__UNKNOWN__	__UNKNOWN__	1	150921896	150921896	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:150921896C>T	ENST00000271640.5	+	12	1665	c.1475C>T	c.(1474-1476)aCg>aTg	p.T492M	SETDB1_ENST00000368969.4_Missense_Mutation_p.T492M|SETDB1_ENST00000459773.1_Intron	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	492		NA			bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			AAAAAGAGCACGTCCTTTCGA	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													135	137	136	NA		NA	NA	1		NA											NA				150921896		2203	4300	6503	SO:0001583	missense			D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379	9869		Chromatin-modifying enzymes / K-methyltransferases, Tudor domain containing	10761	protein-coding gene	gene with protein product	tudor domain containing 21	604396			NA	10343109	Standard		NM_001145415	NA	Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.1475C>T	chr1.hg19:g.150921896C>T	ENSP00000271640:p.Thr492Met	NA	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	hg19	CCDS44217.1	0.02	6.978929	GCAxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	25.5	4.643856	0.87859	.	.	ENSG00000143379	ENST00000271640;ENST00000534805;ENST00000368969;ENST00000498193	D;T;D;T	0.92545	-3.05;0.98;-3.06;0.44	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	D	0.92655	0.7666	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.996;0.991	D	0.93980	0.7257	10	0.87932	D	0	.	18.1851	0.89790	0.0:1.0:0.0:0.0	.	492;493;492;492	E9PRF4;E9PQM8;Q15047-3;Q15047	.;.;.;SETB1_HUMAN	M	492;493;492;492	ENSP00000271640:T492M;ENSP00000436148:T493M;ENSP00000357965:T492M;ENSP00000432348:T492M	ENSP00000271640:T492M	T	+	2	0	SETDB1	149188520	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.912000	0.69948	2.528000	0.85240	0.561000	0.74099	ACG	NOVEL	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084717.2	1	9.328555	KEEP	0	0	0	31	1033	CC	0.999997	0.999997	0		+	15	60	561	0	0	41.738526	143	60	4797	221	ENST00000271640.5	0.094937	1
ANXA9	8416	__UNKNOWN__	__UNKNOWN__	1	150967808	150967808	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:150967808G>A	ENST00000368947.4	+	0	1524					NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	NA		NA			single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			AGACTTCCCTGCCCCACCCCA	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	108	111	NA		NA	NA	1		NA											NA				150967808		2203	4300	6503	SO:0001624	3_prime_UTR_variant			AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412	8416		Annexins	547	protein-coding gene	gene with protein product		603319		ANX31	NA	9742942, 9931420	Standard	NM_003568	NM_003568	NA	Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.*10G>A	chr1.hg19:g.150967808G>A		NA	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	hg19	CCDS975.2	0.02	-0.420906	CCTxCCC	COVERED																																																																																			NOVEL	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084895.2	0	6.017664	KEEP	0	0	0	20	669	GG	0.999863	0.948272	0		+	21	60	659	0	0	61.623545	27	60	974	75	ENST00000368947.4	0.4375	0.948402
PIP5K1A	8394	__UNKNOWN__	__UNKNOWN__	1	151171401	151171401	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:151171401G>T	ENST00000409426.1	+	0	374				PIP5K1A_ENST00000368890.4_5'UTR|PIP5K1A_ENST00000368888.4_5'UTR|PIP5K1A_ENST00000441902.2_5'UTR			Q99755	PI51A_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, alpha	NA		NA			actin cytoskeleton reorganization (GO:0031532)|activation of Rac GTPase activity (GO:0032863)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|fibroblast migration (GO:0010761)|focal adhesion assembly (GO:0048041)|glycerophospholipid metabolic process (GO:0006650)|keratinocyte differentiation (GO:0030216)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|protein targeting to plasma membrane (GO:0072661)|ruffle assembly (GO:0097178)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|kinase binding (GO:0019900)			breast(1)|central_nervous_system(1)|ovary(1)|skin(1)|stomach(1)	5	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.181)			ACGTTGGGAAGATTCGATTCC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(80;36 1443 2325 16095 21302)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U78575	CCDS990.1, CCDS44219.1, CCDS44220.1, CCDS44221.1	1q21.3	2010-04-08			ENSG00000143398	ENSG00000143398	8394			8994	protein-coding gene	gene with protein product		603275			NA	8955136, 10828584	Standard	NM_003557	NM_003557	NA	Approved		uc001exj.3	Q99755	OTTHUMG00000012351	ENST00000409426.1:c.-72G>T	chr1.hg19:g.151171401G>T		NA	A8K4Q0|B4DIN0|Q99754|Q99756	hg19		0.02	13.187955	GAAxATT	COVERED																																																																																			NOVEL	PIP5K1A-015	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000316366.4	4	53.851887	KEEP	0	0	0	179	6150	GG	1	1	0		+	55	60	1930	0	0	158.363476	232	70	8492	595	ENST00000409426.1	0.191638	1
POGZ	23126	__UNKNOWN__	__UNKNOWN__	1	151380630	151380630	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:151380630G>A	ENST00000409503.1	-	15	2322	c.2294C>T	c.(2293-2295)tCt>tTt	p.S765F	POGZ_ENST00000368863.2_Missense_Mutation_p.S679F|POGZ_ENST00000361398.3_Missense_Mutation_p.S721F|POGZ_ENST00000271715.2_Missense_Mutation_p.S774F|POGZ_ENST00000491586.1_Missense_Mutation_p.S730F|POGZ_ENST00000392723.1_Missense_Mutation_p.S721F|POGZ_ENST00000531094.1_Missense_Mutation_p.S712F|POGZ_ENST00000540984.1_Missense_Mutation_p.S136F			Q7Z3K3	POGZ_HUMAN	pogo transposable element with ZNF domain	774		NA			kinetochore assembly (GO:0051382)|mitotic sister chromatid cohesion (GO:0007064)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(10)|kidney(3)|large_intestine(10)|liver(2)|lung(11)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	47	Lung SC(34;0.00471)|Ovarian(49;0.00672)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GCGACACAGAGAGCAGTGTAC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													152	134	140	NA		NA	NA	1		NA											NA				151380630		2203	4300	6503	SO:0001583	missense			AB007930	CCDS997.1, CCDS998.1, CCDS44222.1, CCDS44222.2, CCDS53365.1, CCDS53366.1	1q21.1	2013-07-22			ENSG00000143442	ENSG00000143442	23126			18801	protein-coding gene	gene with protein product	zinc finger protein 280E, putative protein product of Nbla00003	614787			NA	10976766	Standard	NM_207171	NM_015100	NA	Approved	KIAA0461, ZNF635m, ZNF280E	uc001eyd.2	Q7Z3K3	OTTHUMG00000012499	ENST00000409503.1:c.2294C>T	chr1.hg19:g.151380630G>A	ENSP00000386836:p.Ser765Phe	NA	B4DTP8|B4DYL9|B7ZBY5|E9PM80|O75049|Q3LIC4|Q5SZS1|Q5SZS2|Q5SZS3|Q5SZS4|Q8TDZ7|Q9Y4X7	hg19	CCDS53366.1	0.02	6.87133	AGAxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191828	0.78902	.	.	ENSG00000143442	ENST00000392723;ENST00000271715;ENST00000361398;ENST00000368863;ENST00000409503;ENST00000531094;ENST00000540984;ENST00000491586;ENST00000529669	T;T;T;T;T;T;T;T;T	0.36157	5.61;5.64;5.61;5.57;5.62;5.61;1.68;5.09;1.27	5.51	5.51	0.81932	Zinc finger, C2H2-like (1);	0.000000	0.64402	D	0.000004	T	0.49167	0.1541	L	0.52011	1.625	0.54753	D	0.999989	D;D;D;D;D;D	0.76494	0.998;0.995;0.999;0.998;0.994;0.998	D;P;D;D;D;D	0.83275	0.991;0.852;0.996;0.992;0.989;0.991	T	0.50285	-0.8846	10	0.87932	D	0	-17.1403	17.971	0.89112	0.0:0.0:1.0:0.0	.	712;765;679;730;721;774	E9PM80;B7ZBY5;Q7Z3K3-5;Q7Z3K3-3;Q7Z3K3-2;Q7Z3K3	.;.;.;.;.;POGZ_HUMAN	F	721;774;721;679;765;712;136;730;174	ENSP00000376484:S721F;ENSP00000271715:S774F;ENSP00000354467:S721F;ENSP00000357856:S679F;ENSP00000386836:S765F;ENSP00000431259:S712F;ENSP00000443547:S136F;ENSP00000418408:S730F;ENSP00000432295:S174F	ENSP00000271715:S774F	S	-	2	0	POGZ	149647254	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.127000	0.77210	2.592000	0.87571	0.655000	0.94253	TCT	NOVEL	POGZ-016	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330643.1	3	15.049546	KEEP	0	0	0	50	1814	GG	1	1	0		-	34	60	1225	0	0	101.780943	136	60	5251	297	ENST00000409503.1	0.2	1
FLG2	388698	__UNKNOWN__	__UNKNOWN__	1	152324452	152324452	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:152324452T>C	ENST00000388718.5	-	3	5882	c.5810A>G	c.(5809-5811)cAt>cGt	p.H1937R	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1937		NA			establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGTTTGTCCATGACTAGGGTG	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													328	302	311	NA		NA	NA	1		NA											NA				152324452		2203	4300	6503	SO:0001583	missense			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520	388698		EF-hand domain containing	33276	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_001014342	NM_001014342	NA	Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.5810A>G	chr1.hg19:g.152324452T>C	ENSP00000373370:p.His1937Arg	NA	Q9H4U1	hg19	CCDS30861.1	0.02	24.401003	CCAxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	T	13.05	2.119959	0.37436	.	.	ENSG00000143520	ENST00000388718	T	0.08458	3.09	3.66	1.26	0.21427	.	.	.	.	.	T	0.03695	0.0105	L	0.59436	1.845	0.09310	N	1	D	0.53885	0.963	P	0.49361	0.608	T	0.30208	-0.9986	9	0.12430	T	0.62	-3.5748	5.54	0.17033	0.0:0.2338:0.0:0.7662	.	1937	Q5D862	FILA2_HUMAN	R	1937	ENSP00000373370:H1937R	ENSP00000373370:H1937R	H	-	2	0	FLG2	150591076	0.001000	0.12720	0.003000	0.11579	0.014000	0.08584	0.172000	0.16704	0.275000	0.22094	0.449000	0.29647	CAT	NOVEL	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034018.5	13	20.459756	KEEP	0	0	0	68	2102	TT	1	1	0		-	64	60	2254	0	0	172.306904	446	60	16259	666	ENST00000388718.5	0.12549	1
TPM3	7170	__UNKNOWN__	__UNKNOWN__	1	154141786	154141786	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:154141786G>T	ENST00000368530.2	-	9	1041	c.849C>A	c.(847-849)acC>acA	p.T283T	TPM3_ENST00000368533.3_Intron|TPM3_ENST00000341485.5_Intron|TPM3_ENST00000330188.9_Intron|TPM3_ENST00000469717.1_Intron|TPM3_ENST00000323144.7_Intron|TPM3_ENST00000271850.7_Intron|TPM3_ENST00000302206.5_Intron|TPM3_ENST00000341372.3_Intron|TPM3_ENST00000328159.4_Silent_p.T246T|TPM3_ENST00000368531.2_Intron	NM_152263.2	NP_689476.2	P06753	TPM3_HUMAN	tropomyosin 3	283		NA			cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle thin filament tropomyosin (GO:0005862)|stress fiber (GO:0001725)			TPM3/NTRK1_ENST00000392302(70)|TPM3/ALK(33)	breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					GTTACATAGAGGTCATGTCAT	0.512	NA	NA	T	NTRK1, ALK, ROS1	papillary thyroid, ALCL, NSCLC									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q22-q23	7170	tropomyosin 3		E, L	0													174	168	170	NA		NA	NA	1		NA											NA				154141786		2203	4300	6503	SO:0001819	synonymous_variant			BC008425	CCDS1060.1, CCDS41400.1, CCDS41401.1, CCDS41402.1, CCDS41403.1, CCDS60274.1, CCDS60275.1, CCDS72922.1	1q21.2	2014-09-17			ENSG00000143549	ENSG00000143549	7170		Tropomyosins	12012	protein-coding gene	gene with protein product		191030		NEM1	NA	1829807	Standard	NM_152263	NM_153649	NA	Approved	TRK	uc001fec.2	P06753	OTTHUMG00000035853	ENST00000368530.2:c.849C>A	chr1.hg19:g.154141786G>T		NA	D3DV71|P12324|Q2QD06|Q5VU58|Q5VU63|Q5VU66|Q5VU71|Q5VU72|Q8TCG3|Q969Q2|Q9NQH8	hg19	CCDS41403.1	0.02	16.748999	AGAxGTC	COVERED																																																																																			NOVEL	TPM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087271.2	6	28.885438	KEEP	0	0	0	96	3326	GG	1	1	0		-	66	60	2448	0	0	198.911255	329	60	11982	632	ENST00000368530.2	0.167089	1
ATP8B2	57198	__UNKNOWN__	__UNKNOWN__	1	154322833	154322833	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:154322833C>A	ENST00000368489.3	+	0	4911					NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	NA		NA			ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			gcgtgagccaccacacccagc	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515	57198		ATPases / P-type	13534	protein-coding gene	gene with protein product		605867	ATPase, class I, type 8B, member 2		NA	10574461, 11015572	Standard	NM_020452	NM_020452	NA	Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.*1239C>A	chr1.hg19:g.154322833C>A		NA	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	hg19	CCDS1066.1	0.02	2.270197	CCAxCAC	COVERED																																																																																			NOVEL	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087658.2	3	4.815784	KEEP	0	0	0	16	567	CC	0.997832	0.984015	0		+	15	60	551	0	0	47.734106	44	60	1564	93	ENST00000368489.3	0.254237	0.986153
IL6R	3570	__UNKNOWN__	__UNKNOWN__	1	154403037	154403037	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:154403037G>A	ENST00000368485.3	+	3	850	c.413G>A	c.(412-414)aGc>aAc	p.S138N	IL6R_ENST00000344086.4_Missense_Mutation_p.S138N	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	138	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	GGTCCTCGGAGCACCCCATCC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													60	57	58	NA		NA	NA	1		NA											NA				154403037		2203	4300	6503	SO:0001583	missense			X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712	3570		Interleukins and interleukin receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6019	protein-coding gene	gene with protein product		147880			NA		Standard	NM_000565	NM_000565	NA	Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.413G>A	chr1.hg19:g.154403037G>A	ENSP00000357470:p.Ser138Asn	NA	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	hg19	CCDS1067.1	0.02	4.36487	GGAxCAC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.570|7.570	0.666583|0.666583	0.14710|0.14710	.|.	.|.	ENSG00000160712|ENSG00000160712	ENST00000476006|ENST00000368485;ENST00000344086;ENST00000512471	.|T;T;T	.|0.25085	.|1.82;1.82;1.82	4.8|4.8	1.89|1.89	0.25635|0.25635	.|Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	.|1.380240	.|0.04785	.|N	.|0.430445	T|T	0.05502|0.05502	0.0145|0.0145	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	.|B;B	.|0.06786	.|0.001;0.001	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.34153|0.34153	-0.9840|-0.9840	5|10	.|0.33141	.|T	.|0.24	-4.3095|-4.3095	4.3378|4.3378	0.11095|0.11095	0.1926:0.0:0.6286:0.1788|0.1926:0.0:0.6286:0.1788	.|.	.|138;138	.|P08887-2;P08887	.|.;IL6RA_HUMAN	T|N	61|138	.|ENSP00000357470:S138N;ENSP00000340589:S138N;ENSP00000423184:S138N	.|ENSP00000340589:S138N	A|S	+|+	1|2	0|0	IL6R|IL6R	152669661|152669661	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.027000|0.027000	0.11550|0.11550	-0.870000|-0.870000	0.04228|0.04228	0.098000|0.098000	0.17522|0.17522	0.557000|0.557000	0.71058|0.71058	GCA|AGC	NOVEL	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087911.1	2	18.059482	KEEP	0	0	0	60	2183	GG	1	1	0		+	36	60	1291	0	0	111.883972	102	60	3819	263	ENST00000368485.3	0.26087	1
CHRNB2	1141	__UNKNOWN__	__UNKNOWN__	1	154540625	154540625	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:154540625G>A	ENST00000368476.3	+	1	328					NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	NA		NA			action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	TCCTACCCCAGCCAACGGCCC	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													9	9	9	NA		NA	NA	1		NA											NA				154540625		2182	4282	6464	SO:0001627	intron_variant			U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716	1141		Cholinergic receptors, Ligand-gated ion channels / Acetylcholine receptors, nicotinic	1962	protein-coding gene	gene with protein product	acetylcholine receptor, nicotinic, beta 2 (neuronal)	118507	cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)		NA	1505988	Standard	NM_000748	NM_000748	NA	Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.64+41G>A	chr1.hg19:g.154540625G>A		NA	Q9UEH9	hg19	CCDS1070.1	0.02	11.36973	CCAxCCA	COVERED																																																																																			NOVEL	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090697.1	1	35.816082	KEEP	0	0	0	119	4263	GG	1	1	0		+	68	60	2361	0	0	202.371953	202	60	7587	515	ENST00000368476.3	0.251852	1
UBQLN4	56893	__UNKNOWN__	__UNKNOWN__	1	156011378	156011378	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156011378T>G	ENST00000368309.3	-	10	1643	c.1551A>C	c.(1549-1551)tcA>tcC	p.S517S		NM_020131.3	NP_064516.2	Q9NRR5	UBQL4_HUMAN	ubiquilin 4	517		NA			regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|polyubiquitin binding (GO:0031593)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)	16	Hepatocellular(266;0.133)|all_neural(408;0.195)					GCGTGGCTGGTGAGGAAGTGG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	36	35	NA		NA	NA	1		NA											NA				156011378		2203	4298	6501	SO:0001819	synonymous_variant			BC018403	CCDS1127.1	1q21	2013-02-12	2004-11-05	2004-11-06	ENSG00000160803	ENSG00000160803	56893		Ubiquilin family	1237	protein-coding gene	gene with protein product	ataxin-1 ubiquitin-like interacting protein	605440	chromosome 1 open reading frame 6	C1orf6	NA	10575211, 11001934	Standard	NM_020131	NM_020131	NA	Approved	A1U, UBIN	uc001fna.3	Q9NRR5	OTTHUMG00000017461	ENST00000368309.3:c.1551A>C	chr1.hg19:g.156011378T>G		NA	A6ND44|B2RAY7|Q5VYA0|Q5VYA1|Q9BR98|Q9UHX4	hg19	CCDS1127.1	0.02	1.011212	TGGxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	10.68	1.418982	0.25552	.	.	ENSG00000160803	ENST00000368307	T	0.51817	0.69	4.62	-9.24	0.00669	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23904	-1.0175	6	0.42905	T	0.14	-26.811	5.803	0.18424	0.0808:0.1138:0.2626:0.5428	.	.	.	.	P	170	ENSP00000357290:T170P	ENSP00000357290:T170P	T	-	1	0	UBQLN4	154278002	.	.	0.017000	0.16124	0.798000	0.45092	.	.	-2.537000	0.00488	-0.755000	0.03482	ACC	NOVEL	UBQLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046193.1	0	3.166922	KEEP	1	2	20	18	478	TT	0.99986	0.979389	0		-	7	49	132	1	0	7.581238	49	60	1350	109	ENST00000368309.3	0.125	0.979526
PAQR6	79957	__UNKNOWN__	__UNKNOWN__	1	156217819	156217819	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156217819G>A	ENST00000292291.5	-	0	62				PAQR6_ENST00000335852.1_5'UTR|PAQR6_ENST00000368270.1_5'UTR|PAQR6_ENST00000356983.2_5'UTR|PAQR6_ENST00000540423.1_5'UTR|PAQR6_ENST00000492619.1_5'UTR	NM_001272104.1|NM_001272105.1|NM_198406.2	NP_001259033.1|NP_001259034.1|NP_940798.1	Q6TCH4	PAQR6_HUMAN	progestin and adipoQ receptor family member VI	NA		NA				integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			lung(4)|ovary(1)	5	Hepatocellular(266;0.158)					GTCCAAGGCTGCTGCCAGCCA	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(16;219 398 12385 32425 38531)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF455045	CCDS1135.1, CCDS1136.1, CCDS60301.1, CCDS72945.1, CCDS72946.1	1q23	2008-02-05			ENSG00000160781	ENSG00000160781	79957			30132	protein-coding gene	gene with protein product		614579			NA	12477932	Standard	NM_024897	NM_024897	NA	Approved	FLJ22672	uc010phh.2	Q6TCH4	OTTHUMG00000017490	ENST00000292291.5:c.-97C>T	chr1.hg19:g.156217819G>A		NA	B7Z9R9|D3DVB4|D3DVB6|Q5TCK9|Q6PDU0|Q7Z4Q7|Q7Z4Q9|Q8N121|Q8N3M2|Q9H621	hg19	CCDS1136.1	0.02	1.628757	GCTxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186718	0.78789	.	.	ENSG00000160781	ENST00000340183	T	0.55760	0.5	4.1	3.18	0.36537	.	0.260060	0.36338	N	0.002658	T	0.50240	0.1604	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56691	-0.7937	7	0.87932	D	0	-20.1064	9.7849	0.40670	0.0:0.7752:0.2248:0.0	.	.	.	.	V	10	ENSP00000341926:A10V	ENSP00000341926:A10V	A	-	2	0	PAQR6	154484443	0.051000	0.20477	0.986000	0.45419	0.881000	0.50899	0.655000	0.24933	1.071000	0.40834	-0.344000	0.07964	GCA	NOVEL	PAQR6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046297.2	2	8.728483	KEEP	0	0	0	29	1030	GG	0.999997	0.999945	0		-	19	60	630	0	0	51.426974	76	60	2827	164	ENST00000292291.5	0.2	0.999948
SMG5	23381	__UNKNOWN__	__UNKNOWN__	1	156233269	156233269	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs373014142		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156233269T>C	ENST00000361813.5	-	13	2092	c.1948A>G	c.(1948-1950)Atg>Gtg	p.M650V	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	650		NA			gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					CCTTCGGCCATCAGGACCTGA	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								T	VAL/MET	0,4406		0,0,2203	127	106	113	NA	1948	-0.6	0.5	1		113	2,8598	2.2+/-6.3	0,2,4298	no	missense	SMG5	NM_015327.2	21	0,2,6501	CC,CT,TT	NA	0.0233,0.0,0.0154	benign	650/1017	156233269	2,13004	2203	4300	6503	SO:0001583	missense			AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952	23381			24644	protein-coding gene	gene with protein product	EST1 telomerase component homolog B (S. cerevisiae)	610962	smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)		NA	12676087, 12699629	Standard	NM_015327	NM_015327	NA	Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.1948A>G	chr1.hg19:g.156233269T>C	ENSP00000355261:p.Met650Val	NA	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	hg19	CCDS1137.1	0.02	14.632262	CCAxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	11.51	1.659424	0.29515	0.0	2.33E-4	ENSG00000198952	ENST00000361813	T	0.26957	1.7	5.8	-0.559	0.11792	.	0.531735	0.22331	N	0.061480	T	0.04452	0.0122	N	0.08118	0	0.49213	D	0.999767	B	0.02656	0.0	B	0.04013	0.001	T	0.31420	-0.9944	10	0.46703	T	0.11	-0.7687	9.8162	0.40853	0.0:0.3718:0.0:0.6282	.	650	Q9UPR3	SMG5_HUMAN	V	650	ENSP00000355261:M650V	ENSP00000355261:M650V	M	-	1	0	SMG5	154499893	1.000000	0.71417	0.527000	0.27925	0.824000	0.46624	1.549000	0.36212	-0.331000	0.08501	-0.379000	0.06801	ATG	NOVEL	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046308.1	1	14.728425	KEEP	0	0	0	49	1527	TT	1	1	0		-	66	60	2407	0	0	203.021228	239	60	8550	437	ENST00000361813.5	0.216393	1
CCT3	7203	__UNKNOWN__	__UNKNOWN__	1	156304734	156304734	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156304734C>T	ENST00000295688.3	-	3	374				CCT3_ENST00000368256.3_Intron|CCT3_ENST00000368259.2_Intron|CCT3_ENST00000368261.3_Intron|CCT3_ENST00000472765.2_Intron	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					ACATAAAATACGCAAGCACAA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	84	85	NA		NA	NA	1		NA											NA				156304734		2203	4300	6503	SO:0001627	intron_variant			BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468	7203		Heat Shock Proteins / Chaperonins	1616	protein-coding gene	gene with protein product		600114		TRIC5	NA	8110840	Standard	NM_005998	NM_005998	NA	Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.94-25G>A	chr1.hg19:g.156304734C>T		NA	A6NE14|Q5SZY1|Q9BR64	hg19	CCDS1140.2	0.02	24.418267	ATAxGCA	COVERED																																																																																			NOVEL	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060602.3	6	38.221406	KEEP	0	0	0	127	4300	CC	1	1	0		-	111	60	4157	0	0	352.845529	397	60	13634	774	ENST00000295688.3	0.218504	1
BCAN	63827	__UNKNOWN__	__UNKNOWN__	1	156617837	156617837	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156617837G>A	ENST00000329117.5	+	5	1040	c.704G>A	c.(703-705)cGg>cAg	p.R235Q	RP11-284F21.7_ENST00000448869.1_RNA|BCAN_ENST00000361588.5_Missense_Mutation_p.R235Q	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	235	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.	NA			carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCGGGGTCCGGAACTATGGT	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													143	135	137	NA		NA	NA	1		NA											NA				156617837		2203	4300	6503	SO:0001583	missense			BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692	63827		Immunoglobulin superfamily / V-set domain containing, Proteoglycans / Extracellular Matrix : Hyalectans	23059	protein-coding gene	gene with protein product	chondroitin sulfate proteoglycan 7, brevican proteoglycan	600347			NA	11054543, 11873941	Standard	NM_021948	NM_021948	NA	Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.704G>A	chr1.hg19:g.156617837G>A	ENSP00000331210:p.Arg235Gln	NA	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	hg19	CCDS1149.1	0.02	7.321696	TCCxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	33	5.221964	0.95139	.	.	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000424639;ENST00000361588	T;T;T	0.10668	2.85;2.85;2.85	3.9	3.9	0.45041	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.52532	D	0.000075	T	0.26882	0.0658	M	0.82923	2.615	0.50813	D	0.999894	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.10132	-1.0643	10	0.66056	D	0.02	-17.5131	14.6115	0.68519	0.0:0.0:1.0:0.0	.	235;235	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	Q	176;235;133;235	ENSP00000331210:R235Q;ENSP00000401709:R133Q;ENSP00000354925:R235Q	ENSP00000255029:R176Q	R	+	2	0	BCAN	154884461	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.536000	0.98067	2.005000	0.58758	0.555000	0.69702	CGG	NOVEL	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000081844.2	1	4.514364	KEEP	0	0	0	15	502	GG	0.99649	0.99649	0		+	41	60	1538	0	0	130.654751	146	60	5175	249	ENST00000329117.5	0.219251	1
INSRR	3645	__UNKNOWN__	__UNKNOWN__	1	156816284	156816284	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156816284T>C	ENST00000368195.3	-	8	2207				NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	NA		NA			actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGCGTCTGACTGACTCTTGCA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	47	51	NA		NA	NA	1		NA											NA				156816284		2203	4300	6503	SO:0001627	intron_variant			J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644	3645		Fibronectin type III domain containing	6093	protein-coding gene	gene with protein product		147671			NA	2768234, 2249481	Standard	NM_014215	NM_014215	NA	Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.1810+26A>G	chr1.hg19:g.156816284T>C		NA	O60724|Q5VZS3	hg19	CCDS1160.1	0.02	8.229546	GACxGAC	COVERED																																																																																			NOVEL	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098929.1	4	11.435531	KEEP	0	0	0	38	1219	TT	1	1	0		-	40	60	1324	0	0	104.493564	201	60	7478	347	ENST00000368195.3	0.165975	1
NTRK1	4914	__UNKNOWN__	__UNKNOWN__	1	156841438	156841438	__UNKNOWN__	Silent	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:156841438G>C	ENST00000524377.1	+	7	782	c.741G>C	c.(739-741)ctG>ctC	p.L247L	NTRK1_ENST00000358660.3_Silent_p.L247L|NTRK1_ENST00000368196.3_Silent_p.L247L|NTRK1_ENST00000392302.2_Silent_p.L217L	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	247	Ig-like C2-type 1.	NA			activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	TGCCATCCCTGGGGCTGACCC	0.577	NA	NA	T	TPM3, TPR, TFG	papillary thyroid					TSP Lung(10;0.080)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q21-q22	4914	neurotrophic tyrosine kinase, receptor, type 1		E	0													67	64	65	NA		NA	NA	1		NA											NA				156841438		2203	4300	6503	SO:0001819	synonymous_variant			Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	4914	2.7.10.1	Immunoglobulin superfamily / Immunoglobulin-like domain containing	8031	protein-coding gene	gene with protein product	high affinity nerve growth factor receptor	191315			NA	2869410	Standard	NM_002529	NM_001007792	NA	Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.741G>C	chr1.hg19:g.156841438G>C		NA	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	hg19	CCDS1161.1	0.02	15.167515	CCTxGGG	COVERED																																																																																			NOVEL	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000392279.1	0	16.55445	KEEP	0	0	0	55	1992	GG	1	1	0		+	62	60	2276	0	1	190.539217	241	60	8900	470	ENST00000524377.1	0.20462	1
ARHGEF11	9826	__UNKNOWN__	__UNKNOWN__	1	157015056	157015056	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:157015056C>T	ENST00000368194.3	-	0	106					NM_198236.2	NP_937879.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	NA		NA			actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TACGTTCGGCCTTTTTCTGAA	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694	9826		Rho guanine nucleotide exchange factors	14580	protein-coding gene	gene with protein product		605708			NA	10526156, 9205841	Standard	NM_198236	NM_014784	NA	Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000368194.3:c.-934G>A	chr1.hg19:g.157015056C>T		NA	D3DVD0|Q5VY40|Q6PFW2	hg19	CCDS1163.1	0.02	6.788524	GGCxTTT	COVERED																																																																																			NOVEL	ARHGEF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098930.1	3	24.886309	KEEP	0	0	0	83	2797	CC	1	1	0		-	9	60	327	0	0	21.2493	182	60	6584	337	ENST00000368194.3	0.04712	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	157680469	157680469	__UNKNOWN__	IGR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:157680469T>A			NA	NA				FCRL3 (9822 upstream) : FCRL2 (35053 downstream)						NA		NA									NA						TAGAAACATCTCCAGGCTTTG	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.157680469T>A		NA		hg19		0.02	20.052844	ATCxCCA	COVERED																																																																																			NOVEL					0			3	12.337806	KEEP	0	0	0	41	1342	TT	1	1	0			98	60	3479	0	0	288.981064	384	60	14339	649		0.20332	1
OR10R2	343406	__UNKNOWN__	__UNKNOWN__	1	158450554	158450554	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:158450554T>C	ENST00000368152.1	+	1	887	c.887T>C	c.(886-888)gTg>gCg	p.V296A	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	296		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					CTGGTGACGGTGACATACACG	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													162	138	146	NA		NA	NA	1		NA											NA				158450554		2203	4300	6503	SO:0001583	missense			AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965	343406		GPCR / Class A : Olfactory receptors	14820	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004472	NM_001004472	NA	Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.887T>C	chr1.hg19:g.158450554T>C	ENSP00000357134:p.Val296Ala	NA	Q5VWM8|Q6IFS1|Q96R61	hg19	CCDS30898.1	0.02	9.464698	CGGxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	t	12.83	2.056106	0.36277	.	.	ENSG00000198965	ENST00000368152	T	0.00272	8.36	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00328	0.0010	M	0.77313	2.365	0.18873	N	0.999981	D	0.69078	0.997	D	0.72075	0.976	T	0.39099	-0.9630	9	0.87932	D	0	.	12.409	0.55455	0.0:0.0:0.0:1.0	.	296	Q8NGX6	O10R2_HUMAN	A	296	ENSP00000357134:V296A	ENSP00000357134:V296A	V	+	2	0	OR10R2	156717178	0.045000	0.20229	0.132000	0.22025	0.058000	0.15608	2.525000	0.45598	1.735000	0.51646	0.533000	0.62120	GTG	NOVEL	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051847.2	4	7.517694	KEEP	0	0	0	25	744	TT	0.999931	0.999931	0		+	22	60	742	0	0	53.901487	193	60	6647	297	ENST00000368152.1	0.102326	1
NHLH1	4807	__UNKNOWN__	__UNKNOWN__	1	160342552	160342552	__UNKNOWN__	3'UTR	SNP	G	G	A	rs533808138	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:160342552G>A	ENST00000302101.5	+	0	2477					NM_005598.3	NP_005589.1	Q02575	HEN1_HUMAN	nescient helix loop helix 1	NA		NA			cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7	all_cancers(52;7.11e-19)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGGGTCTGTGTCACATATCT	0.502	NA	NA											G|||	2	0.000399361	0	0	5008	,	,	NA	19607	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC013789	CCDS1204.1	1q22	2013-05-21			ENSG00000171786	ENSG00000171786	4807		Basic helix-loop-helix proteins	7817	protein-coding gene	gene with protein product		162360		HEN1	NA		Standard	NM_005598	NM_005598	NA	Approved	NSCL, NSCL1, bHLHa35	uc001fwa.2	Q02575	OTTHUMG00000033121	ENST00000302101.5:c.*1629G>A	chr1.hg19:g.160342552G>A		NA		hg19	CCDS1204.1	0.02	10.671645	TGTxTCA	COVERED																																																																																			NOVEL	NHLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080676.1	4	9.350849	KEEP	0	1	31	42	1427	GG	1	1	0		+	13	60	475	0	0	31.099555	256	60	9742	381	ENST00000302101.5	0.048327	1
FCGR2B	2213	__UNKNOWN__	__UNKNOWN__	1	161561424	161561424	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:161561424C>T	ENST00000403078.3	+	2	260				FCGR2C_ENST00000473530.2_RNA|FCGR2B_ENST00000367960.5_Intron|FCGR3A_ENST00000540048.1_Intron|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2B_ENST00000367962.4_Intron|FCGR2C_ENST00000466542.2_RNA|FCGR2B_ENST00000428605.2_Intron			P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)					NA	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GAAATGCAGGCCCCAGACTAA	0.542	NA	NA	T	?	ALL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q23	2213	Fc fragment of IgG, low affinity IIb, receptor for (CD32)		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694	2213		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	3618	protein-coding gene	gene with protein product		604590	Fc fragment of IgG, low affinity IIb, receptor for (CD32)	FCG2, FCGR2	NA	2139735	Standard	NM_004001	NM_004001	NA	Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000403078.3:c.133+3192C>T	chr1.hg19:g.161561424C>T		NA	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	hg19		0.02	1.955516	AGGxCCC	COVERED																																																																																			NOVEL	FCGR2B-203	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		1	8.080552	KEEP	31	0	0	27	935	CC	0.997832	0.997751	0		+	16	49	577	0	0	46.644042	79	50	2880	177	ENST00000403078.3	0.168421	0.999919
C1orf111	284680	__UNKNOWN__	__UNKNOWN__	1	162343986	162343986	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:162343986T>A	ENST00000367935.5	-	3	717	c.638A>T	c.(637-639)aAg>aTg	p.K213M	RP11-565P22.6_ENST00000431696.1_Intron	NM_182581.3	NP_872387.2	Q5T0L3	CA111_HUMAN	chromosome 1 open reading frame 111	213		NA								central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			GTAGTACACCTTGCAGCTGAA	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													98	97	97	NA		NA	NA	1		NA											NA				162343986		2203	4300	6503	SO:0001583	missense			BC032957	CCDS1238.1	1q23.3	2008-02-05			ENSG00000171722	ENSG00000171722	284680			27648	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182581	NM_182581	NA	Approved		uc001gbx.2	Q5T0L3	OTTHUMG00000031375	ENST00000367935.5:c.638A>T	chr1.hg19:g.162343986T>A	ENSP00000356912:p.Lys213Met	NA	Q6X961|Q8NEC3	hg19	CCDS1238.1	0.02	14.105935	ACCxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	T	17.94	3.512044	0.64522	.	.	ENSG00000171722	ENST00000367935	T	0.29917	1.55	5.14	0.147	0.14838	.	0.455791	0.21113	N	0.079957	T	0.19565	0.0470	L	0.32530	0.975	0.33834	D	0.630582	D	0.65815	0.995	P	0.58873	0.847	T	0.07986	-1.0744	9	0.72032	D	0.01	-7.1586	7.7498	0.28890	0.0:0.3844:0.0:0.6156	.	213	Q5T0L3	CA111_HUMAN	M	213	ENSP00000356912:K213M	ENSP00000356912:K213M	K	-	2	0	C1orf111	160610610	0.670000	0.27512	0.969000	0.41365	0.972000	0.66771	0.069000	0.14552	-0.230000	0.09840	0.533000	0.62120	AAG	NOVEL	C1orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076791.2	1	10.522061	KEEP	0	0	0	35	1111	TT	0.999999	0.999999	0		-	68	60	2516	0	0	213.330546	241	60	8779	379	ENST00000367935.5	0.220065	1
SH2D1B	117157	__UNKNOWN__	__UNKNOWN__	1	162366542	162366542	__UNKNOWN__	3'UTR	SNP	G	G	A	rs182723758	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:162366542G>A	ENST00000367929.2	-	0	1036				SH2D1B_ENST00000359567.3_3'UTR	NM_053282.4	NP_444512.2	O14796	SH21B_HUMAN	SH2 domain containing 1B	NA		NA			leukocyte activation involved in immune response (GO:0002366)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of innate immune response (GO:0045089)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of natural killer cell activation (GO:0032814)	intracellular (GO:0005622)	protein binding, bridging (GO:0030674)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CATCACTCCCGATCCCTCACC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF484964	CCDS30928.1	1q23.3	2013-02-14			ENSG00000198574	ENSG00000198574	117157		SH2 domain containing	30416	protein-coding gene	gene with protein product		608510			NA	9000139, 11689425	Standard	NM_053282	NM_053282	NA	Approved	EAT2	uc001gbz.1	O14796	OTTHUMG00000031377	ENST00000367929.2:c.*528C>T	chr1.hg19:g.162366542G>A		NA	B2RBN6|Q5T0L1|Q8NI18|Q969K9	hg19	CCDS30928.1	0.02	11.570261	CCCxATC	COVERED																																																																																			NOVEL	SH2D1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076794.1	3	10.231747	KEEP	0	0	0	34	1126	GG	0.999998	0.999998	0		-	31	60	1131	0	0	86.722732	228	60	7691	358	ENST00000367929.2	0.119691	1
UHMK1	127933	__UNKNOWN__	__UNKNOWN__	1	162469961	162469961	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs375343785		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:162469961G>A	ENST00000489294.1	+	2	643	c.485G>A	c.(484-486)cGt>cAt	p.R162H	UHMK1_ENST00000538489.1_Missense_Mutation_p.R162H|UHMK1_ENST00000282169.8_3'UTR|UHMK1_ENST00000545294.1_Missense_Mutation_p.R88H	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	162	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.	NA			cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CTCAAACCACGTAACATATTG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													118	104	109	NA		NA	NA	1		NA											NA				162469961		2203	4300	6503	SO:0001583	missense			BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332	127933		RNA binding motif (RRM) containing	19683	protein-coding gene	gene with protein product		608849			NA	12093740, 12782393	Standard	NM_175866	NM_175866	NA	Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.485G>A	chr1.hg19:g.162469961G>A	ENSP00000420270:p.Arg162His	NA	A8K8K4|G3V1M1|Q96C22	hg19	CCDS1239.1	0.02	4.513651	CACxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	22.3	4.267562	0.80469	.	.	ENSG00000152332	ENST00000545294;ENST00000538489;ENST00000489294	T;T;T	0.20463	2.07;2.07;2.07	5.73	5.73	0.89815	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.21427	0.0516	N	0.12746	0.255	.	.	.	D;D;D	0.76494	0.999;0.979;0.999	D;P;D	0.80764	0.991;0.515;0.994	T	0.16247	-1.0409	9	0.87932	D	0	-5.7634	16.9872	0.86342	0.0:0.0:1.0:0.0	.	162;162;88	Q8TAS1-2;Q8TAS1;G3V1M1	.;UHMK1_HUMAN;.	H	88;162;162	ENSP00000441226:R88H;ENSP00000446416:R162H;ENSP00000420270:R162H	ENSP00000420270:R162H	R	+	2	0	UHMK1	160736585	1.000000	0.71417	0.786000	0.31890	0.959000	0.62525	8.887000	0.92456	2.854000	0.98071	0.655000	0.94253	CGT	NOVEL	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076788.1	2	8.125385	KEEP	0	0	0	27	914	GG	0.999988	0.999987	0		+	13	60	496	0	0	37.878792	108	60	3939	177	ENST00000489294.1	0.107438	0.999999
PBX1	5087	__UNKNOWN__	__UNKNOWN__	1	164819513	164819513	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:164819513G>A	ENST00000420696.2	+	0	5081				PBX1_ENST00000540246.1_Intron	NM_001204961.1|NM_001204963.1|NM_002585.3	NP_001191890.1|NP_001191892.1|NP_002576.1	P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	NA		NA			adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						GAAAAGTGTCGAGTTGTGCAC	0.289	NA	NA	T	TCF3, EWSR1	pre B-ALL, myoepithelioma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		L, M	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630	5087		Homeoboxes / TALE class	8632	protein-coding gene	gene with protein product		176310	pre-B-cell leukemia transcription factor 1		NA		Standard	NM_002585	NM_002585	NA	Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000420696.2:c.*3600G>A	chr1.hg19:g.164819513G>A		NA	B4DSC1|F5H4U9|Q5T488	hg19	CCDS1246.1	0.02	3.770163	GTCxAGT	COVERED																																																																																			NOVEL	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000082864.4	3	20.162989	KEEP	6	0	0	67	2225	GG	1	1	0		+	6	60	209	0	0	12.85118	143	60	4860	267	ENST00000420696.2	0.040268	1
PRRX1	5396	__UNKNOWN__	__UNKNOWN__	1	170696399	170696399	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:170696399G>A	ENST00000239461.6	+	3	912				PRRX1_ENST00000367760.3_Intron|PRRX1_ENST00000497230.2_3'UTR|PRRX1_ENST00000476867.2_Intron	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	NA		NA			artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCATTATTATGCTGTTCAGAA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132	5396		Homeoboxes / PRD class	9142	protein-coding gene	gene with protein product		167420	paired mesoderm homeo box 1	PMX1	NA	1509260	Standard	NM_006902	NM_006902	NA	Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.599+857G>A	chr1.hg19:g.170696399G>A		NA	B5BUM7|O60807	hg19	CCDS1290.1	0.02	4.375385	TATxCTG	COVERED																																																																																			NOVEL	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085236.3	2	7.223923	KEEP	0	0	0	24	882	GG	0.999909	0.999906	0		+	20	60	709	0	0	57.452547	94	60	3621	173	ENST00000239461.6	0.175439	0.999997
TNFSF4	7292	__UNKNOWN__	__UNKNOWN__	1	173174617	173174617	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:173174617G>A	ENST00000281834.3	-	1	290				TNFSF4_ENST00000488053.1_5'UTR|TNFSF4_ENST00000367718.1_5'UTR	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	NA		NA			acute inflammatory response (GO:0002526)|CD4-positive, alpha-beta T cell costimulation (GO:0035783)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nitrogen dioxide (GO:0035714)|cellular response to prostaglandin E stimulus (GO:0071380)|chemokine (C-C motif) ligand 11 production (GO:0071954)|cholesterol metabolic process (GO:0008203)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|memory T cell activation (GO:0035709)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell activation (GO:0050871)|positive regulation of CD4-positive, alpha-beta T cell costimulation (GO:1900281)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-4-dependent isotype switching to IgE isotypes (GO:2000572)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of memory T cell activation (GO:2000568)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T-helper 2 cell activation (GO:2000570)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of type 2 immune response (GO:0002830)|regulation of adaptive immune response (GO:0002819)|regulation of inflammatory response (GO:0050727)|response to nitrogen dioxide (GO:0035713)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)|T-helper 2 cell activation (GO:0035712)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor binding (GO:0005102)|tumor necrosis factor receptor superfamily binding (GO:0032813)			breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	12						CTGTACAACTGTGGTTCACCT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D90224	CCDS1306.1, CCDS72985.1	1q25	2008-07-31	2008-07-31		ENSG00000117586	ENSG00000117586	7292		Tumor necrosis factor (ligand) superfamily, CD molecules	11934	protein-coding gene	gene with protein product		603594	tax-transcriptionally activated glycoprotein 1, 34kD	TXGP1	NA	1996093, 8076595	Standard		XM_005245475	NA	Approved	OX-40L, gp34, CD252	uc001giw.3	P23510	OTTHUMG00000034838	ENST00000281834.3:c.153+1545C>T	chr1.hg19:g.173174617G>A		NA	Q5JZA5|Q8IV74|Q9HCN9	hg19	CCDS1306.1	0.02	35.199245	ACTxTGG	COVERED																																																																																			NOVEL	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084271.1	2	42.739537	KEEP	0	0	0	142	5080	GG	1	1	0		-	164	60	5902	0	0	496.962425	590	60	22608	1122	ENST00000281834.3	0.217507	1
RALGPS2	55103	__UNKNOWN__	__UNKNOWN__	1	178885440	178885440	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:178885440A>G	ENST00000367635.3	+	20	2060				RALGPS2_ENST00000367634.2_Intron	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	NA		NA			small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TTTTAAACTCAGTTTTTAATG	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	37	37	NA		NA	NA	1		NA											NA				178885440		2201	4300	6501	SO:0001627	intron_variant			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191	55103		Pleckstrin homology (PH) domain containing	30279	protein-coding gene	gene with protein product		NA			NA	10747847, 12102558	Standard	NM_152663	NM_152663	NA	Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.1723-25A>G	chr1.hg19:g.178885440A>G		NA	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	hg19	CCDS1325.1	0.02	6.916652	CTCxGTT	COVERED																																																																																			NOVEL	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084926.2	6	15.947218	KEEP	0	0	0	53	1651	AA	1	1	0		+	9	60	296	0	0	17.774363	201	60	7386	295	ENST00000367635.3	0.042857	1
SOAT1	6646	__UNKNOWN__	__UNKNOWN__	1	179271942	179271942	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:179271942G>C	ENST00000367619.3	+	2	261				SOAT1_ENST00000539888.1_Intron|SOAT1_ENST00000535686.1_Intron|SOAT1_ENST00000540564.1_Intron	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	NA		NA			cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	GTAATGGTGAGGCTTAATTTT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													74	85	81	NA		NA	NA	1		NA											NA				179271942		2203	4300	6503	SO:0001627	intron_variant			L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	6646	2.3.1.26		11177	protein-coding gene	gene with protein product	acyl-Coenzyme A: cholesterol acyltransferase	102642	sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1	SOAT, STAT	NA	8407899	Standard	NM_003101	NM_003101	NA	Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.118+5G>C	chr1.hg19:g.179271942G>C		NA	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	hg19	CCDS1330.1	0.02	16.850187	TGAxGCT	COVERED																																																																																			NOVEL	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085286.2	3	27.974308	KEEP	0	0	0	93	3204	GG	1	1	0		+	54	60	1751	0	0	134.844376	306	60	10807	555	ENST00000367619.3	0.15	1
IER5	51278	__UNKNOWN__	__UNKNOWN__	1	181058489	181058489	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:181058489G>A	ENST00000367577.4	+	1	852	c.451G>A	c.(451-453)Gcg>Acg	p.A151T		NM_016545.4	NP_057629.2	Q5VY09	IER5_HUMAN	immediate early response 5	151		NA								lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	4						GCGCCAGGCGGCGGCCAGAGA	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	7	6	NA		NA	NA	1		NA											NA				181058489		1985	3934	5919	SO:0001583	missense			BC000128	CCDS1343.1	1q25.3	2008-02-05			ENSG00000162783	ENSG00000162783	51278			5393	protein-coding gene	gene with protein product		607177			NA	10049588, 11102586	Standard	NM_016545	NM_016545	NA	Approved		uc001got.4	Q5VY09	OTTHUMG00000035178	ENST00000367577.4:c.451G>A	chr1.hg19:g.181058489G>A	ENSP00000356549:p.Ala151Thr	NA	B2RBV3|Q8WY68|Q9NY49|Q9NZP9	hg19	CCDS1343.1	0.02	1.897496	GCGxCGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	1.887	-0.456405	0.04540	.	.	ENSG00000162783	ENST00000367577	T	0.10573	2.86	3.02	0.974	0.19715	.	.	.	.	.	T	0.04770	0.0129	N	0.08118	0	0.09310	N	1	B	0.21606	0.058	B	0.22880	0.042	T	0.40175	-0.9577	9	0.44086	T	0.13	.	2.3884	0.04372	0.1136:0.1918:0.4975:0.1971	.	151	Q5VY09	IER5_HUMAN	T	151	ENSP00000356549:A151T	ENSP00000356549:A151T	A	+	1	0	IER5	179325112	0.324000	0.24652	0.001000	0.08648	0.061000	0.15899	1.331000	0.33793	0.102000	0.17638	0.448000	0.29417	GCG	NOVEL	IER5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085142.1	0	19.863829	KEEP	0	0	0	66	2331	GG	1	0.979526	0		+	5	60	168	0	0	11.87215	51	60	1782	173	ENST00000367577.4	0.089286	0.979526
GLUL	2752	__UNKNOWN__	__UNKNOWN__	1	182353209	182353209	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:182353209C>T	ENST00000331872.6	-	0	1993				GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000417584.2_3'UTR|GLUL_ENST00000311223.5_3'UTR|GLUL_ENST00000339526.4_3'UTR	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	NA		NA			cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	CCCCCTTCTGCAAACGTGCTC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	2752	6.3.1.2		4341	protein-coding gene	gene with protein product	glutamine synthetase	138290	glutamate-ammonia ligase (glutamine synthase)	GLNS	NA	1681907, 2888076	Standard	NM_002065	NM_002065	NA	Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.*331G>A	chr1.hg19:g.182353209C>T		NA	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	hg19	CCDS1344.1	0.02	4.000401	CTGxAAA	COVERED																																																																																			NOVEL	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091043.1	3	6.320643	KEEP	0	0	0	21	749	CC	0.999869	0.999869	0		-	19	60	656	0	0	51.047829	113	60	4301	182	ENST00000331872.6	0.143939	1
APOBEC4	403314	__UNKNOWN__	__UNKNOWN__	1	183616274	183616274	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:183616274G>A	ENST00000308641.4	-	0	1914				RGL1_ENST00000536277.1_Intron|RGL1_ENST00000304685.4_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	NA		NA			mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						TATGTAATCAGCAGAAGAGCT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627	403314		Apolipoprotein B mRNA editing enzymes	32152	protein-coding gene	gene with protein product		609908	chromosome 1 open reading frame 169	C1orf169	NA	16082223	Standard	NM_203454	NM_203454	NA	Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.*539C>T	chr1.hg19:g.183616274G>A		NA	Q8N7F6	hg19	CCDS1358.1	0.02	4.484299	TCAxCAG	COVERED																																																																																			NOVEL	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086126.1	1	7.524335	KEEP	0	0	0	25	890	GG	0.999931	0.999926	0		-	23	60	794	0	0	65.59211	90	60	3433	169	ENST00000308641.4	0.20354	0.999995
TRMT1L	81627	__UNKNOWN__	__UNKNOWN__	1	185087538	185087538	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:185087538T>C	ENST00000367506.5	-	0	4083				TRMT1L_ENST00000367504.3_3'UTR	NM_001202423.1|NM_030934.4	NP_001189352.1|NP_112196.3	Q7Z2T5	TRM1L_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)-like	NA		NA			adult locomotory behavior (GO:0008344)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	21						TAAGCCCAACTCATCACTGAT	0.259	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF288399	CCDS1366.1	1q25.2	2012-06-29	2012-06-29	2011-01-24	ENSG00000121486	ENSG00000121486	81627			16782	protein-coding gene	gene with protein product	TRM1-like	611673	chromosome 1 open reading frame 25, TRM1 tRNA methyltransferase 1-like	C1orf25	NA	11318611, 17198746	Standard	NM_030934	NM_030934	NA	Approved		uc001grf.4	Q7Z2T5	OTTHUMG00000035389	ENST00000367506.5:c.*1613A>G	chr1.hg19:g.185087538T>C		NA	Q5TEN0|Q6ZMX0|Q8IWH5|Q8NC68|Q9BZQ1	hg19	CCDS1366.1	0.02	6.099643	AACxCAT	COVERED																																																																																			NOVEL	TRMT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085787.1	3	9.328392	KEEP	0	0	0	31	1005	TT	0.999997	0.999997	0		-	12	60	428	0	0	29.789284	155	60	5777	234	ENST00000367506.5	0.071856	1
HMCN1	83872	__UNKNOWN__	__UNKNOWN__	1	185985140	185985140	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:185985140G>C	ENST00000271588.4	+	32	5189	c.4960G>C	c.(4960-4962)Gtt>Ctt	p.V1654L	HMCN1_ENST00000367492.2_Missense_Mutation_p.V1654L	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1654	Ig-like C2-type 14.	NA			response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TAAGCAAGTAGTTATTGCTCA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													93	87	89	NA		NA	NA	1		NA											NA				185985140		2203	4300	6503	SO:0001583	missense			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341	83872		Fibulins, Immunoglobulin superfamily / I-set domain containing	19194	protein-coding gene	gene with protein product	fibulin 6	608548	age-related macular degeneration 1 (senile macular degeneration)	ARMD1	NA	11222143	Standard	NM_031935	NM_031935	NA	Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4960G>C	chr1.hg19:g.185985140G>C	ENSP00000271588:p.Val1654Leu	NA	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	hg19	CCDS30956.1	0.02	14.843342	GTAxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630757	0.46944	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66280	-0.2;-0.2	5.87	-4.27	0.03744	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.707340	0.14376	N	0.323475	T	0.41949	0.1181	L	0.33753	1.03	0.09310	N	0.999999	B	0.19935	0.04	B	0.25291	0.059	T	0.31613	-0.9937	10	0.18710	T	0.47	.	7.2482	0.26133	0.4219:0.1947:0.3834:0.0	.	1654	Q96RW7	HMCN1_HUMAN	L	1654	ENSP00000271588:V1654L;ENSP00000356462:V1654L	ENSP00000271588:V1654L	V	+	1	0	HMCN1	184251763	0.997000	0.39634	0.000000	0.03702	0.993000	0.82548	0.553000	0.23391	-0.676000	0.05238	0.655000	0.94253	GTT	NOVEL	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131848.1	5	17.456961	KEEP	0	0	0	58	2082	GG	1	1	0		+	10	60	390	0	0	24.509235	306	60	11668	456	ENST00000271588.4	0.031646	1
HMCN1	83872	__UNKNOWN__	__UNKNOWN__	1	186047189	186047189	__UNKNOWN__	Intron	SNP	G	G	T	rs202127721		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:186047189G>T	ENST00000271588.4	+	55	8714				HMCN1_ENST00000367492.2_Intron	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	NA		NA			response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TTTATGGCTTGTGTTCACTCT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	41	41	NA		NA	NA	1		NA											NA				186047189		2201	4299	6500	SO:0001627	intron_variant			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341	83872		Fibulins, Immunoglobulin superfamily / I-set domain containing	19194	protein-coding gene	gene with protein product	fibulin 6	608548	age-related macular degeneration 1 (senile macular degeneration)	ARMD1	NA	11222143	Standard	NM_031935	NM_031935	NA	Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8486-50G>T	chr1.hg19:g.186047189G>T		NA	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	hg19	CCDS30956.1	0.02	0.75789	CTTxTGT	COVERED																																																																																			NOVEL	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131848.1	1	4.195987	KEEP	0	0	0	14	399	GG	0.995343	0.995273	0		+	9	60	183	0	0	9.755675	87	60	2475	150	ENST00000271588.4	0.09375	0.99993
HMCN1	83872	__UNKNOWN__	__UNKNOWN__	1	186135379	186135379	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:186135379A>G	ENST00000271588.4	+	99	15612	c.15383A>G	c.(15382-15384)tAc>tGc	p.Y5128C	HMCN1_ENST00000367492.2_Missense_Mutation_p.Y5128C	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5128	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.	NA			response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATGGGGACTTACTACTGCTCC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													96	81	86	NA		NA	NA	1		NA											NA				186135379		2203	4300	6503	SO:0001583	missense			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341	83872		Fibulins, Immunoglobulin superfamily / I-set domain containing	19194	protein-coding gene	gene with protein product	fibulin 6	608548	age-related macular degeneration 1 (senile macular degeneration)	ARMD1	NA	11222143	Standard	NM_031935	NM_031935	NA	Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15383A>G	chr1.hg19:g.186135379A>G	ENSP00000271588:p.Tyr5128Cys	NA	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	hg19	CCDS30956.1	0.02	7.300658	CTTxCTA	COVERED	.	.	.	.	.	.	.	.	.	.	A	14.37	2.516072	0.44763	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.94966	-3.57;-3.57	5.44	5.44	0.79542	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.058130	0.64402	D	0.000001	D	0.95996	0.8696	M	0.85630	2.765	0.51482	D	0.999927	D	0.59767	0.986	P	0.53722	0.733	D	0.96153	0.9109	10	0.87932	D	0	.	10.6996	0.45920	0.8576:0.0:0.0:0.1423	.	5128	Q96RW7	HMCN1_HUMAN	C	5128	ENSP00000271588:Y5128C;ENSP00000356462:Y5128C	ENSP00000271588:Y5128C	Y	+	2	0	HMCN1	184402002	1.000000	0.71417	0.138000	0.22173	0.131000	0.20780	9.210000	0.95106	2.067000	0.61834	0.528000	0.53228	TAC	NOVEL	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131848.1	2	9.281928	KEEP	0	0	0	31	936	AA	0.999997	0.999997	0		+	13	60	495	0	0	35.499351	165	60	5887	258	ENST00000271588.4	0.073034	1
TPR	7175	__UNKNOWN__	__UNKNOWN__	1	186282795	186282795	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:186282795G>A	ENST00000367478.4	-	0	7696				PRG4_ENST00000367485.4_Intron|PRG4_ENST00000367486.3_Intron|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000445192.2_Intron|PRG4_ENST00000367483.4_Intron	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTAAAAAAATGTTTTCTCTTC	0.308	NA	NA	T	NTRK1	papillary thyroid									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q25	7175	translocated promoter region		E	0													56	57	57	NA		NA	NA	1		NA											NA				186282795		2203	4297	6500	SO:0001624	3_prime_UTR_variant			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410	7175			12017	protein-coding gene	gene with protein product		189940	translocated promoter region (to activated MET oncogene)		NA	1611909, 15229283	Standard	NM_003292	NM_003292	NA	Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.*308C>T	chr1.hg19:g.186282795G>A		NA	Q15655|Q5SWY0|Q99968	hg19	CCDS41446.1	0.02	6.155611	AATxTTT	COVERED																																																																																			NOVEL	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086353.2	0	8.727627	KEEP	0	0	0	29	1007	GG	0.999997	0.999997	0		-	11	60	400	0	0	27.497932	161	60	6030	225	ENST00000367478.4	0.063953	1
CFH	3075	__UNKNOWN__	__UNKNOWN__	1	196712586	196712586	__UNKNOWN__	Silent	SNP	C	C	T	rs61822181	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:196712586C>T	ENST00000367429.4	+	20	3378	c.3138C>T	c.(3136-3138)acC>acT	p.T1046T		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1046	Sushi 18. {ECO:0000255|PROSITE- ProRule:PRU00302}.	NA			complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATTCAGACACCTCCTGTGTGA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													112	109	110	NA		NA	NA	1		NA											NA				196712586		2203	4300	6503	SO:0001819	synonymous_variant			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971	3075		Complement system	4883	protein-coding gene	gene with protein product	beta-1H, H factor 2 (complement), age-related maculopathy susceptibility 1	134370	H factor 1 (complement)	HF, HF1, HF2	NA	2889480, 2963625	Standard	NM_000186	NM_000186	NA	Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.3138C>T	chr1.hg19:g.196712586C>T		NA	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	hg19	CCDS1385.1	0.02	16.407499	CACxTCC	COVERED																																																																																			NOVEL	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086412.2	1	2.683027	KEEP	5	5	160	65	2315	CC	1	1	0		+	50	60	1855	0	0	146.891112	302	60	11091	544	ENST00000367429.4	0.142045	1
CFHR3	10878	__UNKNOWN__	__UNKNOWN__	1	196759037	196759037	__UNKNOWN__	Intron	SNP	G	G	A	rs199930467|rs374905	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:196759037G>A	ENST00000367425.4	+	5	705				CFHR3_ENST00000391985.3_Intron|CFHR3_ENST00000471440.2_3'UTR	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	NA		NA				blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GACTTAAAAAGAAAAAACAAC	0.279	NA	NA											-|||	1881	0.375599	0.5076	0.2839	5008	,	,	NA	10365	0.5357	NA	0.2326	False	NA	,,,	NA	NA	NA	2504	0.2444	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785	10878		Complement system	16980	protein-coding gene	gene with protein product	complement factor H related 3	605336		CFHL3	NA	8428964, 10380701	Standard	NM_021023	NM_021023	NA	Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.614-138G>A	chr1.hg19:g.196759037G>A		NA	B4DPR0|Q9UJ16	hg19	CCDS30958.1	0.02	11.413715	AAAxAAA	COVERED																																																																																			NOVEL	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087505.2	3	5.285622	KEEP	0	2	64	40	1419	GG	1	1	0		+	15	33	564	1	0	38.529973	250	60	9466	377	ENST00000367425.4	0.056604	1
ASPM	259266	__UNKNOWN__	__UNKNOWN__	1	197098396	197098396	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:197098396A>G	ENST00000367409.4	-	9	2937	c.2681T>C	c.(2680-2682)gTc>gCc	p.V894A	ASPM_ENST00000294732.7_Missense_Mutation_p.V894A|ASPM_ENST00000367408.1_Missense_Mutation_p.V144A	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	894		NA			developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						AAGAAAACAGACCAACAACAA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													101	102	101	NA		NA	NA	1		NA											NA				197098396		2203	4297	6500	SO:0001583	missense			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279	259266			19048	protein-coding gene	gene with protein product		605481	microcephaly, primary autosomal recessive 5, asp (abnormal spindle)-like, microcephaly associated (Drosophila)	MCPH5	NA	11078481	Standard	NM_018136	NM_018136	NA	Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.2681T>C	chr1.hg19:g.197098396A>G	ENSP00000356379:p.Val894Ala	NA	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	hg19	CCDS1389.1	0.02	4.966212	CAGxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	17.82	3.483001	0.63962	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.58210	0.35;0.35;0.35	4.99	4.99	0.66335	Calponin homology domain (1);	0.513073	0.18706	N	0.133449	T	0.70228	0.3200	M	0.79805	2.47	0.35513	D	0.800793	P;D	0.69078	0.914;0.997	B;P	0.58331	0.351;0.837	T	0.81145	-0.1066	10	0.87932	D	0	.	14.9944	0.71418	1.0:0.0:0.0:0.0	.	894;894	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	A	894;894;144	ENSP00000356379:V894A;ENSP00000294732:V894A;ENSP00000356378:V144A	ENSP00000294732:V894A	V	-	2	0	ASPM	195365019	1.000000	0.71417	0.994000	0.49952	0.854000	0.48673	8.880000	0.92407	2.008000	0.58898	0.459000	0.35465	GTC	NOVEL	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000088256.1	1	6.319236	KEEP	0	0	0	21	673	AA	0.999869	0.999866	0		-	19	60	701	0	0	56.786515	96	60	3487	177	ENST00000367409.4	0.165217	0.999997
PTPRC	5788	__UNKNOWN__	__UNKNOWN__	1	198662259	198662259	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:198662259T>G	ENST00000442510.2	+	3	241				PTPRC_ENST00000594404.1_Intron|PTPRC_ENST00000352140.3_Intron|PTPRC_ENST00000367364.1_3'UTR|PTPRC_ENST00000598951.1_3'UTR|PTPRC_ENST00000413409.2_Intron|PTPRC_ENST00000391970.3_Intron|PTPRC_ENST00000348564.6_Intron|PTPRC_ENST00000367376.2_Intron			P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	NA		NA			axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						CAATTCCAACTAACGTACATT	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237	5788		CD molecules, Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Fibronectin type III domain containing	9666	protein-coding gene	gene with protein product		151460		CD45	NA	2169617	Standard		NM_001267798	NA	Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000442510.2:c.100+757T>G	chr1.hg19:g.198662259T>G		NA	A8K7W6|Q16614|Q9H0Y6	hg19	CCDS1397.2	0.02	7.409337	AACxAAC	COVERED																																																																																			NOVEL	PTPRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086814.4	0	6.620585	KEEP	0	0	0	22	717	TT	0.999879	0.999879	0		+	20	60	744	0	0	56.833208	157	60	5782	243	ENST00000442510.2	0.112994	1
PTPRC	5788	__UNKNOWN__	__UNKNOWN__	1	198698297	198698297	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:198698297A>G	ENST00000442510.2	+	17	2002	c.1861A>G	c.(1861-1863)Agg>Ggg	p.R621G	PTPRC_ENST00000594404.1_Missense_Mutation_p.R458G|PTPRC_ENST00000352140.3_Missense_Mutation_p.R571G|PTPRC_ENST00000348564.6_Missense_Mutation_p.R460G|PTPRC_ENST00000367376.2_Missense_Mutation_p.R619G			P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	619		NA			axon guidance (GO:0007411)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|bone marrow development (GO:0048539)|cell cycle phase transition (GO:0044770)|cell surface receptor signaling pathway (GO:0007166)|defense response to virus (GO:0051607)|dephosphorylation (GO:0016311)|hematopoietic progenitor cell differentiation (GO:0002244)|immunoglobulin biosynthetic process (GO:0002378)|negative regulation of cell adhesion involved in substrate-bound cell migration (GO:0006933)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of antigen receptor-mediated signaling pathway (GO:0050857)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of T cell proliferation (GO:0042102)|protein dephosphorylation (GO:0006470)|regulation of cell cycle (GO:0051726)|release of sequestered calcium ion into cytosol (GO:0051209)|stem cell development (GO:0048864)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(22)|lung(41)|ovary(4)|pancreas(2)|prostate(1)|skin(13)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	111						GCTTGTTGAAAGGGGTAAGTA	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													94	98	97	NA		NA	NA	1		NA											NA				198698297		2203	4300	6503	SO:0001583	missense			Y00062	CCDS1397.1, CCDS1398.1, CCDS44291.1, CCDS1397.2, CCDS1398.2, CCDS44291.2	1q31-q32	2014-09-17			ENSG00000081237	ENSG00000081237	5788		CD molecules, Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Fibronectin type III domain containing	9666	protein-coding gene	gene with protein product		151460		CD45	NA	2169617	Standard		NM_001267798	NA	Approved	LCA, T200, GP180	uc001gur.2	P08575	OTTHUMG00000035702	ENST00000442510.2:c.1861A>G	chr1.hg19:g.198698297A>G	ENSP00000411355:p.Arg621Gly	NA	A8K7W6|Q16614|Q9H0Y6	hg19	CCDS1397.2	0.02	-0.307052	GAAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.14	2.744950	0.49151	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.02763	4.17	5.37	4.23	0.50019	.	0.275703	0.25925	N	0.027419	T	0.07863	0.0197	M	0.70595	2.14	0.44036	D	0.996763	P;D;B;P;P	0.55800	0.877;0.973;0.415;0.615;0.745	P;P;B;B;B	0.51229	0.572;0.663;0.276;0.276;0.276	T	0.11060	-1.0603	10	0.44086	T	0.13	.	10.5357	0.45002	0.8373:0.1627:0.0:0.0	.	555;555;460;571;619	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	G	621;555;571;571;505;619;553;458	ENSP00000193532:R571G	ENSP00000306782:R458G	R	+	1	2	PTPRC	196964920	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.888000	0.63164	0.968000	0.38212	0.528000	0.53228	AGG	NOVEL	PTPRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086814.4	1	3.611384	KEEP	0	0	0	12	393	AA	0.993634	0.795151	0		+	4	60	150	0	0	11.507267	31	60	1177	68	ENST00000442510.2	0.114286	0.800245
KIF14	9928	__UNKNOWN__	__UNKNOWN__	1	200522847	200522847	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:200522847C>T	ENST00000367350.4	-	30	5054	c.4616G>A	c.(4615-4617)cGc>cAc	p.R1539H		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1539	Required for CIT-binding.	NA			ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GGCCAAGTTGCGAATACTTTC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													97	94	95	NA		NA	NA	1		NA											NA				200522847		2203	4300	6503	SO:0001583	missense			D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193	9928		Kinesins	19181	protein-coding gene	gene with protein product		611279			NA	7584044	Standard	NM_014875	NM_014875	NA	Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.4616G>A	chr1.hg19:g.200522847C>T	ENSP00000356319:p.Arg1539His	NA	Q14CI8|Q4G0A5|Q5T1W3	hg19	CCDS30963.1	0.02	9.300736	TTGxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.34	2.504907	0.44558	.	.	ENSG00000118193	ENST00000367350	T	0.73047	-0.71	5.74	5.74	0.90152	.	0.422586	0.26875	N	0.022058	T	0.50769	0.1635	N	0.22421	0.69	0.09310	N	1	P	0.41978	0.767	B	0.27715	0.082	T	0.54443	-0.8293	10	0.41790	T	0.15	.	13.1013	0.59222	0.0:0.8392:0.1608:0.0	.	1539	Q15058	KIF14_HUMAN	H	1539	ENSP00000356319:R1539H	ENSP00000356319:R1539H	R	-	2	0	KIF14	198789470	0.383000	0.25156	0.125000	0.21846	0.030000	0.12068	2.554000	0.45845	2.709000	0.92574	0.655000	0.94253	CGC	NOVEL	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086878.1	1	7.825047	KEEP	0	0	0	26	904	CC	0.999957	0.999957	0		-	43	60	1594	0	0	130.581058	201	60	6887	316	ENST00000367350.4	0.17623	1
DDX59	83479	__UNKNOWN__	__UNKNOWN__	1	200593815	200593815	__UNKNOWN__	3'UTR	SNP	G	G	C	rs554162143	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:200593815G>C	ENST00000447706.2	-	0	2108							Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	NA		NA				cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						gattacaggcgtgagccacca	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197	83479		Zinc fingers, HIT-type, DEAD-boxes	25360	protein-coding gene	gene with protein product		615464			NA		Standard	NM_001031725.4	NM_001031725	NA	Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000447706.2:c.*214C>G	chr1.hg19:g.200593815G>C		NA	Q6PJL2|Q8IVW3|Q9H0W3	hg19		0.02	-0.21055	GGCxTGA	COVERED																																																																																			NOVEL	DDX59-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000086882.3	2	5.416289	KEEP	0	0	0	18	601	GG	0.999859	0.522088	0		-	3	60	114	0	0	8.904699	21	60	742	54	ENST00000447706.2	0.125	0.522161
KIF21B	23046	__UNKNOWN__	__UNKNOWN__	1	200968476	200968476	__UNKNOWN__	Splice_Site	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:200968476C>A	ENST00000422435.2	-	13	2202		c.e13+1		KIF21B_ENST00000461742.2_Splice_Site|KIF21B_ENST00000360529.5_Splice_Site|KIF21B_ENST00000332129.2_Splice_Site	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	NA		NA			ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						GGCCCACGCACCCTTCTCCTC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													141	112	122	NA		NA	NA	1		NA											NA				200968476		2203	4300	6503	SO:0001630	splice_region_variant			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852	23046		Kinesins, WD repeat domain containing	29442	protein-coding gene	gene with protein product		608322			NA	9455484	Standard	XM_371332	NM_001252100	NA	Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.1885+1G>T	chr1.hg19:g.200968476C>A		NA	B2RP62|B7ZMI0|Q5T4J3	hg19	CCDS58056.1	0.02	22.782915	GCAxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	c	21.2	4.120661	0.77323	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	.	.	.	4.45	4.45	0.53987	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4567	0.87609	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIF21B	199235099	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	6.846000	0.75399	2.189000	0.69895	0.479000	0.44913	.	NOVEL	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382635.1	8	35.420366	KEEP	0	1	11	122	4203	CC	1	1	0	Intron	-	98	60	3396	0	0	278.862137	403	60	14637	773	ENST00000422435.2	0.195609	1
ELF3	1999	__UNKNOWN__	__UNKNOWN__	1	201986215	201986215	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:201986215T>A	ENST00000367284.5	+	0	3078					NM_001114309.1|NM_004433.4	NP_001107781.1|NP_004424.3			E74-like factor 3 (ets domain transcription factor, epithelial-specific )	NA		NA								breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CACATTAAAATCCCATTCATG	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435	1999			3318	protein-coding gene	gene with protein product		602191		ESX	NA	9395241, 9129154	Standard	NM_004433	NM_001114309	NA	Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000367284.5:c.*1764T>A	chr1.hg19:g.201986215T>A		NA		hg19	CCDS1419.1	0.02	8.671465	AAAxCCC	COVERED																																																																																			NOVEL	ELF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087358.1	2	9.02713	KEEP	0	0	0	30	949	TT	0.999997	0.999997	0		+	8	60	290	0	0	18.185193	195	60	7063	271	ENST00000367284.5	0.039409	1
PIK3C2B	5287	__UNKNOWN__	__UNKNOWN__	1	204403017	204403017	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:204403017C>A	ENST00000367187.3	-	26	4303	c.3747G>T	c.(3745-3747)aaG>aaT	p.K1249N	RP11-739N20.2_ENST00000443515.1_RNA|PIK3C2B_ENST00000424712.2_Missense_Mutation_p.K1221N	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1249	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.	NA			phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GGCTGGAAGGCTTGTCACCCC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													119	104	109	NA		NA	NA	1		NA											NA				204403017		2203	4300	6503	SO:0001583	missense			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	5287	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	phosphoinositide-3-kinase, class 2, beta polypeptide		NA	9144573, 9830063	Standard	NM_002646	NM_002646	NA	Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3747G>T	chr1.hg19:g.204403017C>A	ENSP00000356155:p.Lys1249Asn	NA	O95666|Q5SW99	hg19	CCDS1446.1	0.02	6.473791	AGGxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.0	4.236630	0.79800	.	.	ENSG00000133056	ENST00000367187;ENST00000391949;ENST00000424712	T;T	0.80738	-1.41;-1.41	5.93	3.74	0.42951	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.103087	0.64402	D	0.000005	D	0.84247	0.5430	L	0.55017	1.72	0.41585	D	0.988767	P;D	0.71674	0.863;0.998	P;D	0.69824	0.614;0.966	D	0.84438	0.0581	10	0.72032	D	0.01	.	7.1735	0.25732	0.0:0.6721:0.0:0.3279	.	1221;1249	F5GWN5;O00750	.;P3C2B_HUMAN	N	1249;27;1221	ENSP00000356155:K1249N;ENSP00000400561:K1221N	ENSP00000356155:K1249N	K	-	3	2	PIK3C2B	202669640	0.927000	0.31430	1.000000	0.80357	0.999000	0.98932	0.070000	0.14573	1.510000	0.48803	0.655000	0.94253	AAG	NOVEL	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087965.1	2	10.232175	KEEP	0	0	0	34	1154	CC	0.999999	0.999999	0		-	11	60	397	0	0	27.603357	148	60	5212	256	ENST00000367187.3	0.069182	1
PIK3C2B	5287	__UNKNOWN__	__UNKNOWN__	1	204426281	204426281	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:204426281C>T	ENST00000367187.3	-	11	2270				PIK3C2B_ENST00000424712.2_Intron	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TTCACAGCTGCGCTCATCTGG	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	39	39	NA		NA	NA	1		NA											NA				204426281		692	1591	2283	SO:0001627	intron_variant			Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	5287	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	phosphoinositide-3-kinase, class 2, beta polypeptide		NA	9144573, 9830063	Standard	NM_002646	NM_002646	NA	Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.1714-83G>A	chr1.hg19:g.204426281C>T		NA	O95666|Q5SW99	hg19	CCDS1446.1	0.02	2.098131	CTGxGCT	COVERED																																																																																			NOVEL	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087965.1	1	5.113668	KEEP	0	0	0	17	548	CC	0.999366	0.999202	0		-	27	60	978	0	0	86.956782	62	60	2175	137	ENST00000367187.3	0.303371	0.999835
DSTYK	25778	__UNKNOWN__	__UNKNOWN__	1	205129211	205129211	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:205129211T>C	ENST00000367162.3	-	8	2136				DSTYK_ENST00000367160.4_Intron|DSTYK_ENST00000367161.3_Intron	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	NA		NA			cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						TCTGGATCTTTCTCATAGAGA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													101	108	106	NA		NA	NA	1		NA											NA				205129211		2203	4300	6503	SO:0001627	intron_variant			AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059	25778			29043	protein-coding gene	gene with protein product		612666	receptor interacting protein kinase 5	RIPK5	NA	15178406	Standard	NM_015375	NM_015375	NA	Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.2105+30A>G	chr1.hg19:g.205129211T>C		NA	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	hg19	CCDS1451.1	0.02	6.785848	CTTxCTC	COVERED																																																																																			NOVEL	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090345.1	0	7.522113	KEEP	0	0	0	25	781	TT	0.999931	0.999931	0		-	6	60	228	0	0	14.604516	151	60	5414	227	ENST00000367162.3	0.038217	1
IL20	50604	__UNKNOWN__	__UNKNOWN__	1	207042016	207042016	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:207042016C>A	ENST00000367098.1	+	0	1001				IL20_ENST00000367096.3_3'UTR			Q9UHF5	IL17B_HUMAN	interleukin 20	NA		NA			cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			endometrium(2)|large_intestine(3)|lung(2)|pancreas(1)|urinary_tract(1)	9	Breast(84;0.201)			OV - Ovarian serous cystadenocarcinoma(81;0.00459)		CTGTACTAGTCTTGTGCTGGT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF224266	CCDS1470.1	1q32	2008-02-05			ENSG00000162891	ENSG00000162891	50604		Interleukins and interleukin receptors	6002	protein-coding gene	gene with protein product		605619			NA	11163236	Standard	NM_018724	NM_018724	NA	Approved	ZCYTO10, IL10D, IL-20	uc001her.3	Q9NYY1	OTTHUMG00000036456	ENST00000367098.1:c.*107C>A	chr1.hg19:g.207042016C>A		NA	Q14CE5	hg19	CCDS1470.1	0.02	20.759989	AGTxTTG	COVERED																																																																																			NOVEL	IL20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000088676.1	3	22.874962	KEEP	0	0	0	76	2747	CC	1	1	0		+	71	60	2592	0	0	205.605556	411	60	15744	686	ENST00000367098.1	0.147303	1
PIGR	5284	__UNKNOWN__	__UNKNOWN__	1	207107865	207107865	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:207107865G>A	ENST00000356495.4	-	6	1788	c.1605C>T	c.(1603-1605)acC>acT	p.T535T		NM_002644.3	NP_002635.2	P01833	PIGR_HUMAN	polymeric immunoglobulin receptor	535	Ig-like V-type 5.	NA			detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc receptor signaling pathway (GO:0038093)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|receptor clustering (GO:0043113)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	polymeric immunoglobulin receptor activity (GO:0001792)	p.T535T(1)		central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						CATCAGCCCTGGTCACCAGGT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	lung(1)											94	86	89	NA		NA	NA	1		NA											NA				207107865		2203	4300	6503	SO:0001819	synonymous_variant				CCDS1474.1	1q31-q41	2013-01-11			ENSG00000162896	ENSG00000162896	5284		Immunoglobulin superfamily / V-set domain containing	8968	protein-coding gene	gene with protein product		173880			NA		Standard	NM_002644	NM_002644	NA	Approved		uc001hez.3	P01833	OTTHUMG00000036581	ENST00000356495.4:c.1605C>T	chr1.hg19:g.207107865G>A		NA	Q68D81|Q8IZY7	hg19	CCDS1474.1	0.02	11.998446	CCTxGTC	COVERED																																																																																			NOVEL	PIGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000088975.1	4	16.249528	KEEP	0	0	0	54	1894	GG	1	1	0		-	26	60	949	0	0	69.815167	252	60	9319	414	ENST00000356495.4	0.093525	1
C1orf116	79098	__UNKNOWN__	__UNKNOWN__	1	207192618	207192618	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:207192618C>A	ENST00000359470.5	-	0	4740					NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	NA		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					GCACAGACCCCCCTATCATGC	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795	79098			28667	protein-coding gene	gene with protein product	specifically androgen-regulated gene	611680			NA	15525603, 9389513	Standard	NM_024115	NM_023938	NA	Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.*2685G>T	chr1.hg19:g.207192618C>A		NA	C9JV41|Q658X3	hg19	CCDS1475.1	0.02	11.316662	CCCxCCT	COVERED																																																																																			NOVEL	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000088973.1	6	14.445738	KEEP	0	0	0	48	1651	CC	1	1	0		-	20	60	707	0	0	49.472926	245	60	8674	384	ENST00000359470.5	0.075472	1
CD55	1604	__UNKNOWN__	__UNKNOWN__	1	207504471	207504471	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:207504471C>A	ENST00000391921.4	+	5	614	c.491C>A	c.(490-492)cCa>cAa	p.P164Q	CD55_ENST00000367062.4_Missense_Mutation_p.P228Q|CD55_ENST00000314754.8_Missense_Mutation_p.P228Q|CD55_ENST00000367063.2_Missense_Mutation_p.P228Q|CD55_ENST00000367067.4_3'UTR|CD55_ENST00000465534.1_3'UTR|CD55_ENST00000367065.5_Missense_Mutation_p.P228Q|CD55_ENST00000367064.3_Missense_Mutation_p.P228Q|CD55_ENST00000391920.4_Missense_Mutation_p.P228Q			P08174	DAF_HUMAN	CD55 molecule, decay accelerating factor for complement (Cromer blood group)	228	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.	NA			CD4-positive, alpha-beta T cell cytokine production (GO:0035743)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|maternal process involved in parturition (GO:0060137)|negative regulation of complement activation (GO:0045916)|positive regulation of CD4-positive, alpha-beta T cell activation (GO:2000516)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of complement activation (GO:0030449)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|respiratory burst (GO:0045730)|response to peptide hormone (GO:0043434)|response to virus (GO:0009615)|spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	enzyme inhibitor activity (GO:0004857)|lipid binding (GO:0008289)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16					Chloramphenicol(DB00446)	TGTCCAGCACCACCACAAATT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	92	95	NA		NA	NA	1		NA											NA				207504471		2203	4300	6503	SO:0001583	missense			BC001288	CCDS31006.1, CCDS44307.1, CCDS73022.1	1q32	2014-09-17	2006-03-28	2006-02-23	ENSG00000196352	ENSG00000196352	1604		CD molecules, Blood group antigens	2665	protein-coding gene	gene with protein product		125240	decay accelerating factor for complement (CD55, Cromer blood group system)	DAF	NA		Standard	NM_000574	XM_005273077	NA	Approved	CR, TC, CROM	uc001hfr.4	P08174	OTTHUMG00000036255	ENST00000391921.4:c.491C>A	chr1.hg19:g.207504471C>A	ENSP00000375788:p.Pro164Gln	NA	B1AP14|D3DT83|D3DT84|E7ER69|P09679|P78361|Q14UF2|Q14UF3|Q14UF4|Q14UF5|Q14UF6	hg19		0.02	13.277123	CACxACC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.55|17.55	3.418583|3.418583	0.62622|0.62622	.|.	.|.	ENSG00000196352|ENSG00000196352	ENST00000343420|ENST00000367064;ENST00000367063;ENST00000391921;ENST00000536840;ENST00000314754;ENST00000367065;ENST00000391920;ENST00000367062	.|D;D;D;D;D;D;D	.|0.84873	.|-1.91;-1.91;-1.91;-1.91;-1.91;-1.91;-1.91	5.13|5.13	5.13|5.13	0.70059|0.70059	.|Complement control module (2);Sushi/SCR/CCP (3);	.|0.072956	.|0.53938	.|D	.|0.000050	D|D	0.93585|0.93585	0.7952|0.7952	M|M	0.91717|0.91717	3.235|3.235	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.998;1.0;0.999;1.0;0.999	D|D	0.94636|0.94636	0.7826|0.7826	5|10	.|0.87932	.|D	.|0	.|.	14.4235|14.4235	0.67200|0.67200	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|164;228;228;228;228	.|B1AP15;Q14UF4;P08174-2;P08174;B1AP13	.|.;.;.;DAF_HUMAN;.	N|Q	238|228;228;164;164;228;228;228;228	.|ENSP00000356031:P228Q;ENSP00000356030:P228Q;ENSP00000375788:P164Q;ENSP00000316333:P228Q;ENSP00000356032:P228Q;ENSP00000375787:P228Q;ENSP00000356029:P228Q	.|ENSP00000316333:P228Q	H|P	+|+	1|2	0|0	CD55|CD55	205571094|205571094	0.989000|0.989000	0.36119|0.36119	0.604000|0.604000	0.28916|0.28916	0.017000|0.017000	0.09413|0.09413	3.395000|3.395000	0.52558|0.52558	2.551000|2.551000	0.86045|0.86045	0.650000|0.650000	0.86243|0.86243	CAC|CCA	NOVEL	CD55-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000088209.2	2	29.795076	KEEP	0	0	0	99	3438	CC	1	1	0		+	9	60	336	0	0	19.773778	339	60	12313	553	ENST00000391921.4	0.025862	1
IRF6	3664	__UNKNOWN__	__UNKNOWN__	1	209963882	209963882	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:209963882G>A	ENST00000367021.3	-	7	1190	c.1018C>T	c.(1018-1020)Caa>Taa	p.Q340*	IRF6_ENST00000542854.1_Nonsense_Mutation_p.Q245*	NM_006147.3	NP_006138.1	O14896	IRF6_HUMAN	interferon regulatory factor 6	340		NA			cell cycle arrest (GO:0007050)|cell development (GO:0048468)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	28				OV - Ovarian serous cystadenocarcinoma(81;0.0351)		ACCTTCTTTTGTCTCTCAATC	0.478	NA	NA								HNSCC(57;0.16)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	67	70	NA		NA	NA	1		NA											NA				209963882		2203	4300	6503	SO:0001587	stop_gained			AL022398	CCDS1492.1, CCDS55681.1	1q32.2-q32.3	2011-02-10			ENSG00000117595	ENSG00000117595	3664			6121	protein-coding gene	gene with protein product		607199	Van der Woude syndrome	VWS, LPS	NA	12219090	Standard	NM_006147	NM_006147	NA	Approved	OFC6, VWS1	uc001hhq.2	O14896	OTTHUMG00000036521	ENST00000367021.3:c.1018C>T	chr1.hg19:g.209963882G>A	ENSP00000355988:p.Gln340*	NA	B4DLE2|D3DT90|F5GWX8|G0ZTL0	hg19	CCDS1492.1	0.02	2.05064	TTTxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	39	7.412777	0.98269	.	.	ENSG00000117595	ENST00000367021;ENST00000542854	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	.	.	.	X	340;245	.	.	Q	-	1	0	IRF6	208030505	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.291000	0.78721	2.941000	0.99782	0.655000	0.94253	CAA	NOVEL	IRF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000088827.1	1	3.911143	KEEP	0	0	0	13	423	GG	0.994391	0.993952	0		-	8	60	290	0	0	21.346461	76	60	2895	110	ENST00000367021.3	0.095238	0.999559
DIEXF	27042	__UNKNOWN__	__UNKNOWN__	1	210025247	210025247	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:210025247G>T	ENST00000491415.2	+	0	2783					NM_014388.6	NP_055203.4	Q68CQ4	DIEXF_HUMAN	digestive organ expansion factor homolog (zebrafish)	NA		NA			multicellular organismal development (GO:0007275)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(15)|large_intestine(7)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(2)	53						AATTTTGGATGGCATGGGTTT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC022964	CCDS1493.1	1q32.2	2011-08-12	2011-02-16	2011-02-16	ENSG00000117597	ENSG00000117597	27042			28440	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 107	C1orf107	NA	16322560	Standard	NM_014388	NM_014388	NA	Approved	MGC29875, DEF, UTP25	uc001hhr.2	Q68CQ4	OTTHUMG00000036654	ENST00000491415.2:c.*455G>T	chr1.hg19:g.210025247G>T		NA	O75992|Q4VY00|Q63HL9	hg19	CCDS1493.1	0.02	4.469783	GATxGCA	COVERED																																																																																			NOVEL	DIEXF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089127.2	3	8.417274	KEEP	0	0	0	28	951	GG	0.999997	0.999997	0		+	5	60	186	0	0	11.855169	121	60	4499	190	ENST00000491415.2	0.039683	1
ANGEL2	90806	__UNKNOWN__	__UNKNOWN__	1	213165580	213165580	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:213165580G>A	ENST00000366962.3	-	0	4592				ANGEL2_ENST00000360506.2_3'UTR	NM_144567.3	NP_653168.2	Q5VTE6	ANGE2_HUMAN	angel homolog 2 (Drosophila)	NA		NA								central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(1)	24				OV - Ovarian serous cystadenocarcinoma(81;0.00446)|all cancers(67;0.0169)|Epithelial(68;0.0921)|GBM - Glioblastoma multiforme(131;0.185)		ATGACTTGACGCCTCTCTTTC	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL079275	CCDS1512.1, CCDS73027.1	1q32.3	2014-06-17			ENSG00000174606	ENSG00000174606	90806			30534	protein-coding gene	gene with protein product		NA			NA	11943475	Standard	NM_144567	XM_005273344	NA	Approved	KIAA0759L, FLJ12793, Ccr4d	uc001hjz.3	Q5VTE6	OTTHUMG00000036927	ENST00000366962.3:c.*2803C>T	chr1.hg19:g.213165580G>A		NA	B7Z2U4|D3DTA3|Q86X13|Q8NHH3	hg19	CCDS1512.1	0.02	4.438184	GACxCCT	COVERED																																																																																			NOVEL	ANGEL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089693.1	3	13.536572	KEEP	0	0	0	45	1566	GG	1	1	0		-	8	60	307	0	0	21.177235	133	60	4596	230	ENST00000366962.3	0.056738	1
SPATA17	128153	__UNKNOWN__	__UNKNOWN__	1	217804685	217804685	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:217804685T>C	ENST00000366933.4	+	0	20					NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	NA		NA				cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		TGGAGACCGGTAGTAACACCA	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	54	57	NA		NA	NA	1		NA											NA				217804685		2203	4300	6503	SO:0001623	5_prime_UTR_variant			AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814	128153			25184	protein-coding gene	gene with protein product	IQ motif containing H	611032			NA	16395525	Standard	NM_138796	NM_138796	NA	Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.-36T>C	chr1.hg19:g.217804685T>C		NA	A5D6N2	hg19	CCDS1519.1	0.02	18.814643	CGGxAGT	COVERED																																																																																			NOVEL	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092433.2	3	97.710237	KEEP	0	0	0	325	9929	TT	1	1	0		+	23	60	824	0	0	54.209727	419	60	14431	1018	ENST00000366933.4	0.052036	1
IARS2	55699	__UNKNOWN__	__UNKNOWN__	1	220276125	220276125	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:220276125T>C	ENST00000366922.1	+	7	1065				IARS2_ENST00000302637.5_Intron			Q9NSE4	SYIM_HUMAN	isoleucyl-tRNA synthetase 2, mitochondrial	NA		NA			gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)			NS(1)|breast(1)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(7)|lung(17)|ovary(2)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51				GBM - Glioblastoma multiforme(131;0.0554)	L-Isoleucine(DB00167)	TCAAAGTGGGTATATTATTGC	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	95	96	NA		NA	NA	1		NA											NA				220276125		2203	4300	6503	SO:0001627	intron_variant			AK022665	CCDS1523.1	1q41	2011-07-01	2007-02-26		ENSG00000067704	ENSG00000067704	55699	6.1.1.5	Aminoacyl tRNA synthetases / Class I	29685	protein-coding gene	gene with protein product	isoleucine tRNA ligase 2, mitochondrial	612801			NA		Standard	NM_018060	NM_018060	NA	Approved	FLJ10326	uc001hmc.3	Q9NSE4	OTTHUMG00000037287	ENST00000366922.1:c.734+6T>C	chr1.hg19:g.220276125T>C		NA	B2RPG8|Q1M2P9|Q6PI85|Q7L439|Q86WU9|Q96D91|Q9H9Q8|Q9NW42	hg19		0.02	7.488835	GGGxATA	COVERED																																																																																			NOVEL	IARS2-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000090761.1	3	9.925621	KEEP	0	0	0	33	1030	TT	0.999998	0.999998	0		+	19	60	757	0	0	59.02094	149	60	5253	239	ENST00000366922.1	0.113095	1
FBXO28	23219	__UNKNOWN__	__UNKNOWN__	1	224346204	224346204	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:224346204C>T	ENST00000366862.5	+	0	1906					NM_015176.3	NP_055991.1	Q9NVF7	FBX28_HUMAN	F-box protein 28	NA		NA								endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(2)|skin(1)	10	Breast(184;0.206)			GBM - Glioblastoma multiforme(131;0.0363)		TTTAGAGCGGCGTCTTAGTTT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001628	CCDS1539.1, CCDS44320.1	1q42.12	2011-08-12			ENSG00000143756	ENSG00000143756	23219		F-boxes /  other	29046	protein-coding gene	gene with protein product	centromere protein 30	609100			NA	9455484	Standard	NM_015176	NM_015176	NA	Approved	FLJ10766, KIAA0483, Fbx28, CENP-30	uc001hoh.3	Q9NVF7	OTTHUMG00000037495	ENST00000366862.5:c.*756C>T	chr1.hg19:g.224346204C>T		NA	E9PEM8|O75070	hg19	CCDS1539.1	0.02	4.277323	CGGxGTC	COVERED																																																																																			NOVEL	FBXO28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091283.2	1	6.61352	KEEP	0	0	0	22	732	CC	0.999879	0.999875	0		+	12	60	421	0	0	31.179729	102	60	3518	158	ENST00000366862.5	0.105263	0.999996
CNIH3	149111	__UNKNOWN__	__UNKNOWN__	1	224868737	224868737	__UNKNOWN__	Intron	SNP	C	C	T	rs369762199		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:224868737C>T	ENST00000272133.3	+	2	1032					NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3	NA		NA			intracellular signal transduction (GO:0035556)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|postsynaptic membrane (GO:0045211)	channel regulator activity (GO:0016247)			large_intestine(5)|lung(4)	9	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		CGGTAAGTGGCGGGTACTGGT	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													103	100	101	NA		NA	NA	1		NA											NA				224868737		2203	4300	6503	SO:0001627	intron_variant			AF070524	CCDS1544.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143786	ENSG00000143786	149111			26802	protein-coding gene	gene with protein product		NA	cornichon homolog 3 (Drosophila)		NA	8619474, 9110174	Standard	NM_152495	NM_152495	NA	Approved	FLJ38993, CNIH-3	uc001hos.1	Q8TBE1	OTTHUMG00000037634	ENST00000272133.3:c.150+9C>T	chr1.hg19:g.224868737C>T		NA		hg19	CCDS1544.1	0.02	13.536713	TGGxGGG	COVERED																																																																																			NOVEL	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091752.2	3	11.4339	KEEP	0	0	0	38	1278	CC	1	1	0		+	38	60	1389	0	0	105.293848	303	70	10387	471	ENST00000272133.3	0.111437	1
CNIH3	149111	__UNKNOWN__	__UNKNOWN__	1	224927286	224927286	__UNKNOWN__	3'UTR	SNP	C	C	T	rs569682914	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:224927286C>T	ENST00000272133.3	+	0	1593					NM_152495.1	NP_689708.1	Q8TBE1	CNIH3_HUMAN	cornichon family AMPA receptor auxiliary protein 3	NA		NA			intracellular signal transduction (GO:0035556)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of membrane potential (GO:0042391)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|postsynaptic membrane (GO:0045211)	channel regulator activity (GO:0016247)			large_intestine(5)|lung(4)	9	Breast(184;0.218)			GBM - Glioblastoma multiforme(131;0.073)		GAATTCCACACACGGGGTCCT	0.532	NA	NA											C|||	2	0.000399361	0.0015	0	5008	,	,	NA	19373	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF070524	CCDS1544.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143786	ENSG00000143786	149111			26802	protein-coding gene	gene with protein product		NA	cornichon homolog 3 (Drosophila)		NA	8619474, 9110174	Standard	NM_152495	NM_152495	NA	Approved	FLJ38993, CNIH-3	uc001hos.1	Q8TBE1	OTTHUMG00000037634	ENST00000272133.3:c.*228C>T	chr1.hg19:g.224927286C>T		NA		hg19	CCDS1544.1	0.02	8.404591	ACAxACG	COVERED																																																																																			NOVEL	CNIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091752.2	1	11.136105	KEEP	0	0	0	37	1304	CC	1	1	0		+	10	60	352	0	0	22.283458	212	60	7862	318	ENST00000272133.3	0.045045	1
C1orf95	375057	__UNKNOWN__	__UNKNOWN__	1	226795272	226795272	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:226795272C>T	ENST00000366788.3	+	0	6062				C1orf95_ENST00000366789.4_3'UTR	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95	NA		NA				integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		GCCTCACCTCCTCGCTGCAGC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685	375057			30491	protein-coding gene	gene with protein product		NA			NA	8619474, 9110174	Standard	NM_001003665	NM_001003665	NA	Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.*5531C>T	chr1.hg19:g.226795272C>T		NA	A6NGL2	hg19	CCDS31044.1	0.02	19.673326	CTCxTCG	COVERED																																																																																			NOVEL	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091634.1	6	22.571056	KEEP	0	0	0	75	2640	CC	1	1	0		+	59	60	2200	0	0	175.432934	342	60	12585	582	ENST00000366788.3	0.147132	1
ADCK3	56997	__UNKNOWN__	__UNKNOWN__	1	227170605	227170605	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:227170605A>G	ENST00000366779.1	+	13	3721	c.950A>G	c.(949-951)aAc>aGc	p.N317S	ADCK3_ENST00000366777.3_Missense_Mutation_p.N317S|ADCK3_ENST00000433743.2_Intron|ADCK3_ENST00000478406.1_3'UTR|ADCK3_ENST00000458507.2_Missense_Mutation_p.N38S|ADCK3_ENST00000366778.1_Missense_Mutation_p.N265S			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	317		NA			cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						AAAACTCTCAACAACGACCTG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													23	24	23	NA		NA	NA	1		NA											NA				227170605		2201	4299	6500	SO:0001583	missense			AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050	56997			16812	protein-coding gene	gene with protein product	coenzyme Q8 homolog (yeast)	606980	chaperone-ABC1 (activity of bc1 complex, S.pombe)-like, chaperone, ABC1 activity of bc1 complex like (S. pombe), chaperone, ABC1 activity of bc1 complex homolog (S. pombe)	CABC1	NA		Standard	NM_020247	NM_020247	NA	Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.950A>G	chr1.hg19:g.227170605A>G	ENSP00000355741:p.Asn317Ser	NA	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	hg19	CCDS1557.1	0.02	7.232504	TCAxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	A	6.052	0.377898	0.11466	.	.	ENSG00000163050	ENST00000366779;ENST00000366778;ENST00000366777;ENST00000366776;ENST00000458507;ENST00000366775;ENST00000405743	T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8	5.66	5.66	0.87406	.	0.039642	0.85682	D	0.000000	T	0.38719	0.1051	L	0.39020	1.185	0.80722	D	1	B	0.11235	0.004	B	0.12837	0.008	T	0.20338	-1.0278	10	0.15066	T	0.55	-48.1575	15.8882	0.79269	1.0:0.0:0.0:0.0	.	317	Q8NI60	ADCK3_HUMAN	S	317;265;317;242;38;162;268	ENSP00000355741:N317S;ENSP00000355740:N265S;ENSP00000355739:N317S;ENSP00000355738:N242S;ENSP00000403704:N38S;ENSP00000355737:N162S	ENSP00000355737:N162S	N	+	2	0	ADCK3	225237228	0.999000	0.42202	0.994000	0.49952	0.286000	0.27126	2.353000	0.44089	2.166000	0.68216	0.454000	0.30748	AAC	NOVEL	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091712.1	2	15.646052	KEEP	0	0	0	52	1638	AA	1	1	0		+	21	60	804	0	0	63.288228	141	60	5012	278	ENST00000366779.1	0.12963	1
JMJD4	65094	__UNKNOWN__	__UNKNOWN__	1	227921638	227921638	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:227921638C>T	ENST00000366758.3	-	3	661	c.662G>A	c.(661-663)cGc>cAc	p.R221H	JMJD4_ENST00000438896.2_Missense_Mutation_p.R221H|JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000480897.1_3'UTR|SNAP47_ENST00000366760.1_Intron	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	221	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.	NA								endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	9		Prostate(94;0.0885)				GTAGACAAAGCGGTAGTCATC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													125	104	111	NA		NA	NA	1		NA											NA				227921638		2203	4300	6503	SO:0001583	missense			AK022579	CCDS1561.1, CCDS59203.1	1q42.13	2008-02-05			ENSG00000081692	ENSG00000081692	65094			25724	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_023007	NM_023007	NA	Approved	FLJ12517	uc001hrb.3	Q9H9V9	OTTHUMG00000037698	ENST00000366758.3:c.662G>A	chr1.hg19:g.227921638C>T	ENSP00000355720:p.Arg221His	NA	Q5TBZ1|Q5TBZ6|Q9H970	hg19	CCDS1561.1	0.02	9.236089	AAGxGGT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	24.6|24.6	4.546876|4.546876	0.86022|0.86022	.|.	.|.	ENSG00000081692|ENSG00000081692	ENST00000438896|ENST00000366758	T|T	0.13778|0.18810	2.56|2.19	4.34|4.34	4.34|4.34	0.51931|0.51931	.|Transcription factor jumonji/aspartyl beta-hydroxylase (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.57388|0.57388	0.2050|0.2050	H|H	0.95004|0.95004	3.61|3.61	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.996;0.998	T|T	0.70868|0.70868	-0.4755|-0.4755	6|10	.|0.87932	.|D	.|0	-35.5273|-35.5273	14.7253|14.7253	0.69341|0.69341	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|221;221	.|Q9H9V9-2;Q9H9V9	.|.;JMJD4_HUMAN	T|H	214|221	ENSP00000387830:A214T|ENSP00000355720:R221H	.|ENSP00000355720:R221H	A|R	-|-	1|2	0|0	JMJD4|JMJD4	225988261|225988261	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.559000|0.559000	0.35586|0.35586	6.960000|6.960000	0.76036|0.76036	2.394000|2.394000	0.81467|0.81467	0.650000|0.650000	0.86243|0.86243	GCT|CGC	NOVEL	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091970.1	1	25.281016	KEEP	0	0	0	84	2935	CC	1	1	0		-	28	60	983	0	0	74.073913	213	60	7629	446	ENST00000366758.3	0.116183	1
COG2	22796	__UNKNOWN__	__UNKNOWN__	1	230829601	230829601	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:230829601C>T	ENST00000366669.4	+	0	2794				COG2_ENST00000534989.1_3'UTR|COG2_ENST00000366668.3_3'UTR	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	NA		NA			Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AAAGAGGCTGCGGGAAGCCAT	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775	22796		Components of oligomeric golgi complex	6546	protein-coding gene	gene with protein product		606974	low density lipoprotein receptor defect C complementing	LDLC	NA	7962052	Standard	NM_007357	NM_007357	NA	Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.*462C>T	chr1.hg19:g.230829601C>T		NA	Q86U99	hg19	CCDS1584.1	0.02	6.510578	CTGxGGG	COVERED																																																																																			NOVEL	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092087.1	1	6.019194	KEEP	0	0	0	20	690	CC	0.999863	0.999863	0		+	24	60	873	0	0	68.247419	153	60	5436	236	ENST00000366669.4	0.135593	1
CAPN9	10753	__UNKNOWN__	__UNKNOWN__	1	230898368	230898368	__UNKNOWN__	Intron	SNP	G	G	A	rs28359629	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:230898368G>A	ENST00000271971.2	+	4	515				RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Intron|CAPN9_ENST00000354537.1_Intron	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	NA		NA			digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				TAGCTGACTCGCATCATTTCT	0.522	NA	NA											G|||	70	0.0139776	0.0499	0.0058	5008	,	,	NA	18332	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	,	199,4207	123.7+/-161.0	7,185,2011	84	81	82	NA	,	-9	0	1	dbSNP_125	82	1,8599		0,1,4299	no	intron,intron	CAPN9	NM_006615.2,NM_016452.1	,	7,186,6310	AA,AG,GG	NA	0.0116,4.5166,1.5378	,	,	230898368	200,12806	2203	4300	6503	SO:0001627	intron_variant			AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773	10753		EF-hand domain containing	1486	protein-coding gene	gene with protein product	novel calpain large subunit-4	606401	calpain 9 (nCL-4)		NA	9524069, 10835488	Standard	NM_006615	XM_005273010	NA	Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.403-31G>A	chr1.hg19:g.230898368G>A		NA	B1APS1|B1AQI0|Q9NS74	hg19	CCDS1586.1	0.02	14.045191	CTCxCAT	COVERED																																																																																			NOVEL	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092179.1	2	7.821432	KEEP	0	0	0	26	855	GG	0.999957	0.999957	0		+	34	60	1243	0	0	93.625961	283	60	9701	412	ENST00000271971.2	0.107256	1
C1orf198	84886	__UNKNOWN__	__UNKNOWN__	1	230979290	230979290	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:230979290C>T	ENST00000427697.2	-	3	686	c.86G>A	c.(85-87)aGc>aAc	p.S29N	C1orf198_ENST00000470540.1_Missense_Mutation_p.S208N|C1orf198_ENST00000366663.5_Missense_Mutation_p.S246N|C1orf198_ENST00000523410.1_Missense_Mutation_p.S116N			Q9H425	CA198_HUMAN	chromosome 1 open reading frame 198	246		NA				cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	17	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				ACGGAGGGTGCTGGGCCTTTC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													56	55	56	NA		NA	NA	1		NA											NA				230979290		2203	4300	6503	SO:0001583	missense			BC066649	CCDS1587.1, CCDS44330.1, CCDS44331.1	1q42.2	2008-02-05			ENSG00000119280	ENSG00000119280	84886			25900	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032800	NM_032800	NA	Approved	FLJ14525, MGC10710, FLJ16283, DKFZp667D152, FLJ38847	uc001hub.3	Q9H425	OTTHUMG00000037790	ENST00000427697.2:c.86G>A	chr1.hg19:g.230979290C>T	ENSP00000411384:p.Ser29Asn	NA	A8K8R8|B3KTW1|G5EA08	hg19		0.02	31.845307	GTGxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333687	0.81801	.	.	ENSG00000119280	ENST00000366663;ENST00000470540;ENST00000427697;ENST00000523410	T;T;T;T	0.36520	1.46;1.46;1.25;1.45	3.81	3.81	0.43845	.	1.158490	0.06223	N	0.687194	T	0.38081	0.1027	L	0.34521	1.04	0.09310	N	1	P	0.44139	0.827	P	0.46026	0.501	T	0.34104	-0.9842	10	0.28530	T	0.3	-2.4769	13.8763	0.63655	0.0:1.0:0.0:0.0	.	246	Q9H425	CA198_HUMAN	N	246;208;29;116	ENSP00000355623:S246N;ENSP00000428172:S208N;ENSP00000411384:S29N;ENSP00000430967:S116N	ENSP00000355623:S246N	S	-	2	0	C1orf198	229045913	0.001000	0.12720	0.012000	0.15200	0.670000	0.39368	1.140000	0.31516	1.664000	0.50801	0.462000	0.41574	AGC	NOVEL	C1orf198-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000381500.1	3	38.250596	KEEP	0	1	34	139	4692	CC	1	1	0		-	21	60	726	0	0	39.661453	853	60	30005	1179	ENST00000427697.2	0.024027	1
C1orf131	128061	__UNKNOWN__	__UNKNOWN__	1	231360142	231360142	__UNKNOWN__	Silent	SNP	G	G	A	rs143666971	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:231360142G>A	ENST00000366649.2	-	7	790	c.765C>T	c.(763-765)tcC>tcT	p.S255S	C1orf131_ENST00000366651.3_Silent_p.S254S|C1orf131_ENST00000318906.2_3'UTR			Q8NDD1	CA131_HUMAN	chromosome 1 open reading frame 131	256	Lys-rich.	NA					poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	8	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TACTGGGAGCGGACTTCTTTT	0.383	NA	NA											G|||	2	0.000399361	0.0015	0	5008	,	,	NA	18953	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G		0,4406		0,0,2203	66	65	66	NA	765	-5.8	0	1	dbSNP_134	66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C1orf131	NM_152379.2		0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077		255/294	231360142	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			BC062353	CCDS1591.2, CCDS73049.1	1q42.2	2012-06-27			ENSG00000143633	ENSG00000143633	128061			25332	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_152379	XM_005273051	NA	Approved	DKFZp547B1713	uc001hul.3	Q8NDD1	OTTHUMG00000038023	ENST00000366649.2:c.765C>T	chr1.hg19:g.231360142G>A		NA	Q5TBI0|Q5TBI1|Q6P6B4|Q7Z6H5|Q8N432|Q96NM6	hg19	CCDS1591.2	0.02	28.881618	AGCxGAC	COVERED																																																																																			NOVEL	C1orf131-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092864.1	1	23.299498	KEEP	0	1	33	89	3033	GG	1	1	0		-	47	60	1763	0	0	126.356932	577	60	19962	828	ENST00000366649.2	0.075321	1
GNPAT	8443	__UNKNOWN__	__UNKNOWN__	1	231401088	231401088	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:231401088C>T	ENST00000366647.4	+	5	787	c.618C>T	c.(616-618)gcC>gcT	p.A206A	GNPAT_ENST00000366646.3_Silent_p.A145A	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	206		NA			cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				TGTCGGGTGCCTTTTTCATGC	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	121	120	NA		NA	NA	1		NA											NA				231401088		2203	4300	6503	SO:0001819	synonymous_variant			AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	8443	2.3.1.42		4416	protein-coding gene	gene with protein product		602744			NA	9459311, 9536089	Standard		NM_014236	NA	Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.618C>T	chr1.hg19:g.231401088C>T		NA	B4DNM9|Q5TBH7|Q9BWC2	hg19	CCDS1592.1	0.02	23.890946	TGCxTTT	COVERED																																																																																			NOVEL	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092871.1	6	27.652504	KEEP	0	0	0	92	3207	CC	1	1	0		+	70	60	2562	0	0	200.26909	453	60	16547	808	ENST00000366647.4	0.133843	1
GNPAT	8443	__UNKNOWN__	__UNKNOWN__	1	231401107	231401107	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:231401107T>A	ENST00000366647.4	+	5	806	c.637T>A	c.(637-639)Ttt>Att	p.F213I	GNPAT_ENST00000366646.3_Missense_Mutation_p.F152I	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase	213		NA			cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				GCGGCGTACCTTTGGTGGCAA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													130	131	131	NA		NA	NA	1		NA											NA				231401107		2203	4300	6503	SO:0001583	missense			AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	8443	2.3.1.42		4416	protein-coding gene	gene with protein product		602744			NA	9459311, 9536089	Standard		NM_014236	NA	Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024	ENST00000366647.4:c.637T>A	chr1.hg19:g.231401107T>A	ENSP00000355607:p.Phe213Ile	NA	B4DNM9|Q5TBH7|Q9BWC2	hg19	CCDS1592.1	0.02	21.46834	ACCxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	22.3	4.269359	0.80469	.	.	ENSG00000116906	ENST00000436239;ENST00000366647;ENST00000366646;ENST00000416000	D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.17	5.25	5.25	0.73442	Phospholipid/glycerol acyltransferase (2);	0.000000	0.85682	D	0.000000	D	0.94026	0.8086	L	0.37466	1.105	0.80722	D	1	D;D	0.64830	0.994;0.967	P;P	0.62298	0.9;0.838	D	0.94500	0.7709	10	0.56958	D	0.05	.	15.4621	0.75366	0.0:0.0:0.0:1.0	.	152;213	B4DNM9;O15228	.;GNPAT_HUMAN	I	152;213;152;203	ENSP00000402811:F152I;ENSP00000355607:F213I;ENSP00000355606:F152I;ENSP00000411640:F203I	ENSP00000355606:F152I	F	+	1	0	GNPAT	229467730	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	4.754000	0.62191	2.120000	0.65058	0.383000	0.25322	TTT	NOVEL	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092871.1	6	23.762775	KEEP	0	0	0	79	2605	TT	1	1	0		+	65	60	2385	0	0	186.805113	416	60	15362	711	ENST00000366647.4	0.135135	1
PCNXL2	80003	__UNKNOWN__	__UNKNOWN__	1	233296068	233296068	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:233296068T>C	ENST00000258229.9	-	19	3712	c.3478A>G	c.(3478-3480)Att>Gtt	p.I1160V	PCNXL2_ENST00000520463.1_5'UTR|PCNXL2_ENST00000488780.2_Missense_Mutation_p.I293V	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1160		NA				integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				TTTTTGAGAATGGGGTGTGAA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													84	81	82	NA		NA	NA	1		NA											NA				233296068		1896	4121	6017	SO:0001583	missense			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749	80003			8736	protein-coding gene	gene with protein product		NA	pecanex (Drosophila)-like 2		NA	12477932	Standard	NM_014801	NM_014801	NA	Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.3478A>G	chr1.hg19:g.233296068T>C	ENSP00000258229:p.Ile1160Val	NA	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	hg19	CCDS44335.1	0.02	11.506493	GAAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.092	-1.164902	0.01673	.	.	ENSG00000135749	ENST00000258229;ENST00000488780	T	0.06849	3.25	4.54	-1.02	0.10135	.	.	.	.	.	T	0.03520	0.0101	N	0.12422	0.21	0.37320	D	0.909511	B	0.02656	0.0	B	0.06405	0.002	T	0.48801	-0.9003	9	0.02654	T	1	.	9.9656	0.41723	0.0:0.426:0.0:0.574	.	1160	A6NKB5	PCX2_HUMAN	V	1160;293	ENSP00000258229:I1160V	ENSP00000258229:I1160V	I	-	1	0	PCNXL2	231362691	0.032000	0.19561	0.011000	0.14972	0.787000	0.44495	0.296000	0.19083	-0.357000	0.08175	-0.297000	0.09499	ATT	NOVEL	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092480.3	2	9.327365	KEEP	0	0	0	31	969	TT	0.999997	0.999997	0		-	26	60	914	0	0	67.021888	240	70	8622	376	ENST00000258229.9	0.097744	1
GREM2	64388	__UNKNOWN__	__UNKNOWN__	1	240655448	240655448	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:240655448C>T	ENST00000318160.4	-	0	1594					NM_022469.3	NP_071914.3	Q9H772	GREM2_HUMAN	gremlin 2, DAN family BMP antagonist	NA		NA			BMP signaling pathway (GO:0030509)|cytokine-mediated signaling pathway (GO:0019221)|determination of dorsal identity (GO:0048263)|embryonic body morphogenesis (GO:0010172)|regulation of cytokine activity (GO:0060300)|sequestering of BMP from receptor via BMP binding (GO:0038098)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	10		all_cancers(173;0.0196)	OV - Ovarian serous cystadenocarcinoma(106;0.0123)			TTACAATATACGGTCACTTAT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK024848	CCDS31070.1	1q43	2013-02-26	2013-02-26		ENSG00000180875	ENSG00000180875	64388			17655	protein-coding gene	gene with protein product	protein related to DAN and cerberus	608832	gremlin 2, cysteine knot superfamily, homolog (Xenopus laevis), gremlin 2		NA	15039429	Standard	NM_022469	XM_005273226	NA	Approved	Prdc, FLJ21195, CKTSF1B2, DAND3	uc001hys.3	Q9H772	OTTHUMG00000039909	ENST00000318160.4:c.*821G>A	chr1.hg19:g.240655448C>T		NA	Q86UD9	hg19	CCDS31070.1	0.02	23.406879	ATAxGGT	COVERED																																																																																			NOVEL	GREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096286.1	8	10.533822	KEEP	0	0	0	35	1207	CC	0.999999	0.999999	0		-	30	60	1061	0	0	70.808814	490	60	17669	656	ENST00000318160.4	0.057692	1
ZNF124	7678	__UNKNOWN__	__UNKNOWN__	1	247287248	247287248	__UNKNOWN__	Intron	SNP	T	T	C	rs548502246	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:247287248T>C	ENST00000472531.1	-	4	346					NM_001243740.1	NP_001230669.1	Q15973	ZN124_HUMAN	zinc finger protein 124	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			atgccctttgtgatgtgcttt	0.448	NA	NA											t|||	18	0.00359425	0.0136	0	5008	,	,	NA	20623	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418	7678		Zinc fingers, C2H2-type, -	12907	protein-coding gene	gene with protein product		194631	zinc finger protein 124 (HZF-16)		NA	7916577	Standard	NM_003431	XM_005273256	NA	Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000472531.1:c.219-75A>G	chr1.hg19:g.247287248T>C		NA	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	hg19	CCDS58067.1	0.02	27.708646	TTGxGAT	COVERED																																																																																			NOVEL	ZNF124-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098570.2	92	21.664054	KEEP	45	0	0	72	2278	TT	1	1	0		-	27	60	933	0	0	60.115524	493	60	17712	902	ENST00000472531.1	0.051923	1
ZNF124	7678	__UNKNOWN__	__UNKNOWN__	1	247320642	247320642	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:247320642A>G	ENST00000543802.2	-	4	371	c.282T>C	c.(280-282)tgT>tgC	p.C94C	ZNF124_ENST00000491848.1_Intron|ZNF124_ENST00000491356.1_Intron|ZNF124_ENST00000340684.6_Intron|ZNF124_ENST00000472531.1_Intron			Q15973	ZN124_HUMAN	zinc finger protein 124	94	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			GTTTACATGTACATGGCTTCT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418	7678		Zinc fingers, C2H2-type, -	12907	protein-coding gene	gene with protein product		194631	zinc finger protein 124 (HZF-16)		NA	7916577	Standard	NM_003431	XM_005273256	NA	Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000543802.2:c.282T>C	chr1.hg19:g.247320642A>G		NA	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	hg19		0.02	31.765797	TGTxCAT	COVERED																																																																																			NOVEL	ZNF124-009	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000447393.1	5	21.363806	KEEP	0	0	0	71	2208	AA	1	1	0		-	31	60	1179	0	0	78.458503	627	60	22174	880	ENST00000543802.2	0.047112	1
OR2W5	441932	__UNKNOWN__	__UNKNOWN__	1	247654526	247654526	__UNKNOWN__	RNA	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:247654526A>T	ENST00000522351.1	+	0	157							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TGTTATCTTGATCTTCTGCAT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													159	143	148	NA		NA	NA	1		NA											NA				247654526		2203	4300	6503							1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664	441932		GPCR / Class A : Olfactory receptors	15424	other	unknown		NA		OR2W5P	NA	12213199	Standard	NM_001004698	NM_001004698	NA	Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573	ENST00000522351.1:	chr1.hg19:g.247654526A>T		NA	B9EH85	hg19		0.02	20.428115	TTGxTCT	COVERED																																																																																			NOVEL	OR2W5-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000375789.1	8	5.417114	KEEP	0	0	0	18	605	AA	0.999859	0.999859	0		+	50	60	1802	0	0	135.244727	413	60	14901	577	ENST00000522351.1	0.107991	1
OR14K1	343170	__UNKNOWN__	__UNKNOWN__	1	247902140	247902140	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:247902140C>T	ENST00000283225.2	+	1	224	c.224C>T	c.(223-225)aCa>aTa	p.T75I	RP11-634B7.4_ENST00000449298.1_RNA			Q8NGZ2	O14K1_HUMAN	olfactory receptor, family 14, subfamily K, member 1	75		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|lung(18)|ovary(1)|urinary_tract(1)	27						ATTTCTGCCACAGTCCCCAAA	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													132	131	131	NA		NA	NA	1		NA											NA				247902140		2170	4280	6450	SO:0001583	missense			BK004377		1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000153230	ENSG00000153230	343170		GPCR / Class A : Olfactory receptors	15025	protein-coding gene	gene with protein product		NA	olfactory receptor, family 5, subfamily AY, member 1	OR5AY1	NA		Standard	NM_001004732	NG_007559	NA	Approved			Q8NGZ2	OTTHUMG00000040211	ENST00000283225.2:c.224C>T	chr1.hg19:g.247902140C>T	ENSP00000283225:p.Thr75Ile	NA	A8MPV5|Q6IF85|Q96R53	hg19		0.02	32.779621	CCAxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.94	3.259624	0.59321	.	.	ENSG00000153230	ENST00000283225	T	0.00675	5.88	3.74	1.69	0.24217	.	0.000000	0.33457	U	0.004882	T	0.00967	0.0032	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.48115	-0.9063	7	0.49607	T	0.09	.	4.6688	0.12678	0.0:0.6077:0.1819:0.2104	.	.	.	.	I	75	ENSP00000283225:T75I	ENSP00000283225:T75I	T	+	2	0	OR14K1	245968763	0.000000	0.05858	0.004000	0.12327	0.998000	0.95712	0.070000	0.14573	0.743000	0.32719	0.609000	0.83330	ACA	NOVEL	OR14K1-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000096868.1	7	19.56257	KEEP	0	0	0	65	2303	CC	1	1	0		+	44	60	1527	0	0	101.054464	710	60	26725	1008	ENST00000283225.2	0.058355	1
OR2T7	81458	__UNKNOWN__	__UNKNOWN__	1	248604839	248604839	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs61834488	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr1:248604839G>A	ENST00000460972.3	+	1	332	c.332G>A	c.(331-333)tGt>tAt	p.C111Y				P0C7T2	OR2T7_HUMAN	olfactory receptor, family 2, subfamily T, member 7	111		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)				NA						CTCATGTCCTGTGATCGCTAC	0.552	NA	NA											.|||	495	0.0988419	0.2632	0.0346	5008	,	,	NA	23933	0.0367	NA	0.0477	False	NA	,,,	NA	NA	NA	2504	0.0389	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					1q44	2013-09-05		2004-03-10	ENSG00000227152	ENSG00000227152	81458		GPCR / Class A : Olfactory receptors	15019	protein-coding gene	gene with protein product		NA		OR2T7P	NA		Standard		NG_004272	NA	Approved	OST723		P0C7T2	OTTHUMG00000040449	ENST00000460972.3:c.332G>A	chr1.hg19:g.248604839G>A	ENSP00000475521:p.Cys111Tyr	NA		hg19		0.02	19.998423	CCTxTGA	COVERED																																																																																			NOVEL	OR2T7-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000097345.3	9	6.656207	KEEP	77	1	31	33	1175	GG	0.999998	0.999998	0		+	30	27	1008	0	0	65.273838	493	60	18379	751	ENST00000460972.3	0.057361	1
SH3YL1	26751	__UNKNOWN__	__UNKNOWN__	2	262562	262562	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:262562A>T	ENST00000405430.1	-	3	378				SH3YL1_ENST00000403658.1_Intron|SH3YL1_ENST00000356150.5_Intron|SH3YL1_ENST00000402632.1_Intron|SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000403712.2_Intron			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		CTCAGAGAAAATTTTTTTAAA	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115	26751			29546	protein-coding gene	gene with protein product		NA	SH3 domain containing, Ysc84-like 1 (S. cerevisiae)		NA	21624956	Standard	NM_015677	NM_001282687	NA	Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.1+68T>A	chr2.hg19:g.262562A>T		NA	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	hg19		0.02	6.669647	AAAxTTT	COVERED																																																																																			NOVEL	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000322352.1	2	12.939573	KEEP	0	0	0	43	1408	AA	1	1	0		-	39	60	1428	0	0	119.228924	154	60	5571	273	ENST00000405430.1	0.202073	1
TRAPPC12	51112	__UNKNOWN__	__UNKNOWN__	2	3447501	3447501	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:3447501C>T	ENST00000324266.5	+	6	1612				TRAPPC12_ENST00000382110.2_Intron|TRAPPC12_ENST00000469147.1_Intron	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	NA		NA			vesicle-mediated transport (GO:0016192)						NA						AGTATGAATGCGTGCTCAGTT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	52	54	NA		NA	NA	2		NA											NA				3447501		2202	4298	6500	SO:0001627	intron_variant			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853	51112		Trafficking protein particle complex, Tetratricopeptide (TTC) repeat domain containing	24284	protein-coding gene	gene with protein product		614139	tetratricopeptide repeat domain 15	TTC15	NA	10810093, 21525244, 20562859	Standard	NM_016030	NM_016030	NA	Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1418-49C>T	chr2.hg19:g.3447501C>T		NA	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	hg19	CCDS1652.1	0.02	16.763527	ATGxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	5.127	0.209041	0.09757	.	.	ENSG00000171853	ENST00000433382	.	.	.	3.29	-6.57	0.01842	.	.	.	.	.	T	0.26955	0.0660	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.30268	-0.9984	4	.	.	.	.	7.8133	0.29243	0.0:0.1966:0.1334:0.67	.	.	.	.	V	2	.	.	A	+	2	0	TTC15	3426508	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.166000	0.00575	-1.730000	0.01362	-0.678000	0.03780	GCG	NOVEL	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206693.2	5	26.183087	KEEP	0	0	0	87	3002	CC	1	1	0		+	45	60	1659	0	0	128.534147	314	60	11399	579	ENST00000324266.5	0.125348	1
RSAD2	91543	__UNKNOWN__	__UNKNOWN__	2	7037598	7037598	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:7037598G>A	ENST00000382040.3	+	0	2747					NM_080657.4	NP_542388.2			radical S-adenosyl methionine domain containing 2	NA		NA								endometrium(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)	20	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		TGTTTCTCAGGAAAAAAAATA	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF442151	CCDS1656.1	2p25.2	2008-02-05			ENSG00000134321	ENSG00000134321	91543			30908	protein-coding gene	gene with protein product		607810			NA	11752458	Standard	NM_080657	NM_080657	NA	Approved	cig5, viperin, vig1	uc002qyp.1	Q8WXG1	OTTHUMG00000090352	ENST00000382040.3:c.*1525G>A	chr2.hg19:g.7037598G>A		NA		hg19	CCDS1656.1	0.02	4.311889	CAGxAAA	COVERED																																																																																			NOVEL	RSAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206724.2	1	11.726002	KEEP	0	0	0	39	1358	GG	1	1	0		+	27	60	964	1	0	79.107094	117	60	4274	221	ENST00000382040.3	0.1875	1
ODC1	4953	__UNKNOWN__	__UNKNOWN__	2	10580951	10580951	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:10580951C>A	ENST00000234111.4	-	12	1795	c.1285G>T	c.(1285-1287)Gta>Tta	p.V429L	ODC1_ENST00000405333.1_Missense_Mutation_p.V429L	NM_002539.1	NP_002530.1	P11926	DCOR_HUMAN	ornithine decarboxylase 1	429		NA			cellular nitrogen compound metabolic process (GO:0034641)|kidney development (GO:0001822)|polyamine metabolic process (GO:0006595)|positive regulation of cell proliferation (GO:0008284)|putrescine biosynthetic process from ornithine (GO:0033387)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ornithine decarboxylase activity (GO:0004586)|protein homodimerization activity (GO:0042803)			NS(1)|central_nervous_system(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(3)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.161)	Spermine(DB00127)	TGTTCCTCTACTTCGGGTGGG	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													103	100	101	NA		NA	NA	2		NA											NA				10580951		2203	4300	6503	SO:0001583	missense				CCDS1672.1	2p25	2012-10-02			ENSG00000115758	ENSG00000115758	4953	4.1.1.17		8109	protein-coding gene	gene with protein product		165640			NA		Standard		NM_002539	NA	Approved	ODC	uc002rao.1	P11926	OTTHUMG00000090450	ENST00000234111.4:c.1285G>T	chr2.hg19:g.10580951C>A	ENSP00000234111:p.Val429Leu	NA	Q53TU3|Q6LDS9	hg19	CCDS1672.1	0.02	3.921512	CTAxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.24	1.579372	0.28180	.	.	ENSG00000115758	ENST00000234111;ENST00000405333	T;T	0.44083	0.93;0.93	5.82	5.82	0.92795	.	0.399847	0.25361	N	0.031239	T	0.37571	0.1008	L	0.38175	1.15	0.25872	N	0.983691	B	0.02656	0.0	B	0.04013	0.001	T	0.11446	-1.0587	10	0.23891	T	0.37	.	20.0863	0.97801	0.0:1.0:0.0:0.0	.	429	P11926	DCOR_HUMAN	L	429	ENSP00000234111:V429L;ENSP00000385333:V429L	ENSP00000234111:V429L	V	-	1	0	ODC1	10498402	0.080000	0.21391	0.015000	0.15790	0.299000	0.27559	3.503000	0.53340	2.754000	0.94517	0.591000	0.81541	GTA	NOVEL	ODC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206896.2	0	9.329431	KEEP	0	0	0	31	1077	CC	0.999997	0.999997	0		-	6	60	209	0	0	12.956246	137	60	5127	196	ENST00000234111.4	0.041958	1
KCNF1	3754	__UNKNOWN__	__UNKNOWN__	2	11053255	11053255	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:11053255C>G	ENST00000295082.1	+	1	1193	c.703C>G	c.(703-705)Ctg>Gtg	p.L235V		NM_002236.4	NP_002227.2	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F, member 1	235		NA			potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(2)|skin(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)		CTGGTTCACCCTGGAGTACCT	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													77	70	72	NA		NA	NA	2		NA											NA				11053255		2203	4300	6503	SO:0001583	missense			AF033382	CCDS1676.1	2p25	2011-07-05			ENSG00000162975	ENSG00000162975	3754		Potassium channels, Voltage-gated ion channels / Potassium channels	6246	protein-coding gene	gene with protein product		603787		KCNF	NA	9434767, 16382104	Standard	NM_002236	NM_002236	NA	Approved	Kv5.1, kH1, IK8	uc002rax.3	Q9H3M0	OTTHUMG00000119054	ENST00000295082.1:c.703C>G	chr2.hg19:g.11053255C>G	ENSP00000295082:p.Leu235Val	NA	O43527|Q585L3	hg19	CCDS1676.1	0.02	15.266427	ACCxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.043	0.764302	0.15914	.	.	ENSG00000162975	ENST00000295082	D	0.98455	-4.94	5.21	5.21	0.72293	Ion transport (1);	0.311228	0.32785	N	0.005644	D	0.91666	0.7366	N	0.04655	-0.195	0.38306	D	0.943119	B	0.02656	0.0	B	0.04013	0.001	D	0.87102	0.2179	10	0.19147	T	0.46	.	5.8099	0.18460	0.1426:0.6447:0.1377:0.075	.	235	Q9H3M0	KCNF1_HUMAN	V	235	ENSP00000295082:L235V	ENSP00000295082:L235V	L	+	1	2	KCNF1	10970706	0.583000	0.26757	1.000000	0.80357	0.997000	0.91878	0.262000	0.18460	2.581000	0.87130	0.655000	0.94253	CTG	NOVEL	KCNF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239265.1	1	26.176295	KEEP	0	0	0	87	3049	CC	1	1	0		+	154	60	5147	0	0	496.919267	149	60	5457	478	ENST00000295082.1	0.508251	1
GREB1	9687	__UNKNOWN__	__UNKNOWN__	2	11733065	11733065	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:11733065G>A	ENST00000381486.2	+	11	1809	c.1509G>A	c.(1507-1509)tgG>tgA	p.W503*	GREB1_ENST00000234142.5_Nonsense_Mutation_p.W503*	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	503		NA				integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		AGCTGCCCTGGCTGGCCAGCC	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(39;850 945 2785 23371 33093)					NA		NA				0													10	11	11	NA		NA	NA	2		NA											NA				11733065		1967	4116	6083	SO:0001587	stop_gained				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208	9687			24885	protein-coding gene	gene with protein product	gene regulated by estrogen in breast cancer	611736			NA	11103799	Standard	NM_014668	NM_014668	NA	Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1509G>A	chr2.hg19:g.11733065G>A	ENSP00000370896:p.Trp503*	NA	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	hg19	CCDS42655.1	0.02	8.870366	CTGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	42	9.268259	0.99120	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	.	.	.	4.83	4.83	0.62350	.	0.083603	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-46.0394	17.9242	0.88977	0.0:0.0:1.0:0.0	.	.	.	.	X	503;503;137	.	ENSP00000234142:W503X	W	+	3	0	GREB1	11650516	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.558000	0.98132	2.211000	0.71520	0.591000	0.81541	TGG	NOVEL	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280490.1	3	36.044957	KEEP	0	0	0	120	3890	GG	1	1	0		+	61	60	2082	0	0	180.238783	164	60	5588	453	ENST00000381486.2	0.271111	1
SMC6	79677	__UNKNOWN__	__UNKNOWN__	2	17922927	17922927	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:17922927G>A	ENST00000448223.2	-	4	459	c.190C>T	c.(190-192)Cct>Tct	p.P64S	SMC6_ENST00000381272.4_Missense_Mutation_p.P64S|SMC6_ENST00000351948.4_Missense_Mutation_p.P64S|SMC6_ENST00000402989.1_Missense_Mutation_p.P64S	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	64		NA			cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AACTTAAAAGGTCCAAGCATT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													137	137	137	NA		NA	NA	2		NA											NA				17922927		2203	4299	6502	SO:0001583	missense			AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029	79677		Structural maintenance of chromosomes proteins	20466	protein-coding gene	gene with protein product		609387	SMC6 structural maintenance of chromosomes 6-like 1 (yeast)	SMC6L1	NA	11230166	Standard	NM_024624	NM_024624	NA	Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.190C>T	chr2.hg19:g.17922927G>A	ENSP00000404092:p.Pro64Ser	NA	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	hg19	CCDS1690.1	0.02	4.593303	AAGxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	35	5.518136	0.96416	.	.	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.38077	3.63;3.63;1.91;3.63;1.16	5.89	5.89	0.94794	RecF/RecN/SMC (1);	0.000000	0.85682	D	0.000000	T	0.53254	0.1785	L	0.43152	1.355	0.80722	D	1	P;B;D	0.58970	0.926;0.178;0.984	P;B;D	0.66497	0.835;0.171;0.944	T	0.44267	-0.9339	10	0.48119	T	0.1	.	19.0291	0.92948	0.0:0.0:1.0:0.0	.	64;64;64	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	S	64	ENSP00000404092:P64S;ENSP00000323439:P64S;ENSP00000370672:P64S;ENSP00000384539:P64S;ENSP00000408644:P64S	ENSP00000323439:P64S	P	-	1	0	SMC6	17786408	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.783000	0.95769	0.655000	0.94253	CCT	NOVEL	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207359.1	0	12.038702	KEEP	0	0	0	40	1386	GG	1	0.999995	0		-	30	60	1123	0	0	98.361212	82	60	3050	190	ENST00000448223.2	0.267857	0.999995
GDF7	151449	__UNKNOWN__	__UNKNOWN__	2	20866457	20866457	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:20866457C>T	ENST00000272224.3	+	0	34					NM_182828.2	NP_878248.2	Q7Z4P5	GDF7_HUMAN	growth differentiation factor 7	NA		NA			activin receptor signaling pathway (GO:0032924)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching morphogenesis of an epithelial tube (GO:0048754)|cell fate commitment (GO:0045165)|epithelial cell differentiation (GO:0030855)|forebrain morphogenesis (GO:0048853)|gland morphogenesis (GO:0022612)|growth (GO:0040007)|midbrain development (GO:0030901)|morphogenesis of an epithelial fold (GO:0060571)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of tendon cell differentiation (GO:2001051)|positive regulation of transcription, DNA-templated (GO:0045893)|reproductive structure development (GO:0048608)|roof plate formation (GO:0021509)|spinal cord association neuron differentiation (GO:0021527)	extracellular space (GO:0005615)				breast(1)|cervix(1)|endometrium(2)|lung(1)|prostate(1)|skin(1)	7	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTGGCCTCTCTCTGCGCGGC	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF522369	CCDS1701.1	2p24.1	2008-05-22			ENSG00000143869	ENSG00000143869	151449			4222	protein-coding gene	gene with protein product		604651			NA	10022976, 9808626	Standard	NM_182828	NM_182828	NA	Approved	BMP12	uc002rdz.1	Q7Z4P5	OTTHUMG00000090781	ENST00000272224.3:c.-543C>T	chr2.hg19:g.20866457C>T		NA		hg19	CCDS1701.1	0.02	4.212971	TCTxTCT	COVERED																																																																																			NOVEL	GDF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207563.2	0	37.619943	KEEP	0	0	0	125	4322	CC	1	1	0		+	22	60	795	0	0	63.418424	120	60	4372	359	ENST00000272224.3	0.15493	1
TDRD15	100129278	__UNKNOWN__	__UNKNOWN__	2	21361918	21361918	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:21361918A>T	ENST00000405799.1	+	4	1909	c.1579A>T	c.(1579-1581)Atg>Ttg	p.M527L				B5MCY1	TDR15_HUMAN	tudor domain containing 15	527		NA					hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)				NA						AAACGATGAAATGATTCTAAG	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					2p24.1	2013-01-23	2013-01-23	2013-01-23	ENSG00000218819	ENSG00000218819	100129278		Tudor domain containing	45037	protein-coding gene	gene with protein product		NA			NA		Standard		XR_425376	NA	Approved			B5MCY1	OTTHUMG00000151795	ENST00000405799.1:c.1579A>T	chr2.hg19:g.21361918A>T	ENSP00000384376:p.Met527Leu	NA		hg19		0.02	4.601382	GAAxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	8.773	0.926335	0.18056	.	.	ENSG00000218819	ENST00000405799	T	0.08193	3.12	5.28	-0.469	0.12142	.	.	.	.	.	T	0.02727	0.0082	.	.	.	.	.	.	.	.	.	.	.	.	T	0.45527	-0.9255	5	0.07813	T	0.8	-12.6232	2.9002	0.05703	0.4104:0.3488:0.0873:0.1535	.	.	.	.	L	527	ENSP00000384376:M527L	ENSP00000384376:M527L	M	+	1	0	AC010872.2	21215423	0.592000	0.26832	0.879000	0.34478	0.992000	0.81027	0.801000	0.27055	-0.013000	0.14199	0.402000	0.26972	ATG	NOVEL	TDRD15-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323948.1	2	5.718159	KEEP	0	0	0	19	635	AA	0.99986	0.999853	0		+	20	60	714	0	0	58.208272	91	60	3371	166	ENST00000405799.1	0.18018	0.999994
GAREML	150946	__UNKNOWN__	__UNKNOWN__	2	26410358	26410358	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:26410358T>C	ENST00000407684.1	+	5	3208				GAREML_ENST00000401533.2_Silent_p.H619H	NM_001191033.1	NP_001177962.1	Q75VX8	GAREL_HUMAN	GRB2 associated, regulator of MAPK1-like	NA		NA				extracellular vesicular exosome (GO:0070062)					NA						AGCCCTCACATCCCCAGAAGC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													98	89	92	NA		NA	NA	2		NA											NA				26410358		692	1591	2283	SO:0001627	intron_variant			AK090454, AB015349, AB124552	CCDS54336.1, CCDS54337.1	2p23.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000157833	ENSG00000157833	150946			27172	protein-coding gene	gene with protein product		NA	family with sequence similarity 59, member B	FAM59B	NA		Standard	NM_001168241	NM_001168241	NA	Approved	KIAA2038, FLJ00375	uc002rgw.2	Q75VX8	OTTHUMG00000151935	ENST00000407684.1:c.1452+174T>C	chr2.hg19:g.26410358T>C		NA	B5MC97|B7WNK9|Q8NF27|Q9UIK8	hg19	CCDS54337.1	0.02	24.570847	ACAxCCC	COVERED																																																																																			NOVEL	GAREML-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324499.1	8	49.295368	KEEP	0	0	0	164	5073	TT	1	1	0		+	60	60	2230	0	0	170.6268	465	60	16253	906	ENST00000407684.1	0.114286	1
GPR113	165082	__UNKNOWN__	__UNKNOWN__	2	26538452	26538452	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:26538452G>C	ENST00000421160.2	-	5	705	c.653C>G	c.(652-654)tCt>tGt	p.S218C	GPR113_ENST00000541401.1_Intron|GPR113_ENST00000311519.1_Missense_Mutation_p.S287C|GPR113_ENST00000333478.6_Intron|GPR113_ENST00000459892.1_5'UTR	NM_001145169.1	NP_001138641.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	287		NA			G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAAGTCACAGACACCTGTGT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													49	58	55	NA		NA	NA	2		NA											NA				26538452		692	1591	2283	SO:0001583	missense			AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567	165082		-, GPCR / Class B : Orphans	18989	protein-coding gene	gene with protein product		NA			NA	12435584	Standard	NM_153835	NM_153835	NA	Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000421160.2:c.653C>G	chr2.hg19:g.26538452G>C	ENSP00000388537:p.Ser218Cys	NA	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	hg19	CCDS46238.1	0.02	2.259186	ACAxACA	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511131	0.64522	.	.	ENSG00000173567	ENST00000421160;ENST00000311519	T;T	0.12361	2.69;2.69	5.35	2.38	0.29361	.	.	.	.	.	T	0.20577	0.0495	L	0.55481	1.735	0.80722	D	1	D;D	0.67145	0.989;0.996	P;P	0.56700	0.72;0.804	T	0.02326	-1.1176	9	0.56958	D	0.05	-10.4425	4.8571	0.13564	0.1963:0.0:0.6304:0.1733	.	218;287	E9PEV1;Q8IZF5	.;GP113_HUMAN	C	218;287	ENSP00000388537:S218C;ENSP00000307831:S287C	ENSP00000307831:S287C	S	-	2	0	GPR113	26391956	0.996000	0.38824	0.988000	0.46212	0.894000	0.52154	1.230000	0.32612	1.226000	0.43582	0.655000	0.94253	TCT	NOVEL	GPR113-006	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317215.2	0	6.922561	KEEP	0	0	0	23	821	GG	0.999892	0.99938	0		-	9	60	350	0	0	26.923304	74	60	2758	126	ENST00000421160.2	0.108434	0.999487
KCNK3	3777	__UNKNOWN__	__UNKNOWN__	2	26955730	26955730	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:26955730C>T	ENST00000302909.3	+	0	5604					NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	NA		NA			brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	CTTTCTTTATCGCCTGGGACA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(80;1457 1631 27100 45946)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303	3777		Potassium channels, Voltage-gated ion channels / Potassium channels, Two-P	6278	protein-coding gene	gene with protein product		603220			NA	9312005, 9721223, 16382106	Standard	NM_002246	NM_002246	NA	Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.*4294C>T	chr2.hg19:g.26955730C>T		NA	Q53SU2	hg19	CCDS1727.1	0.02	2.168087	TATxGCC	COVERED																																																																																			NOVEL	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246861.2	2	2.407763	KEEP	0	0	0	8	276	CC	0.99257	0.992062	0		+	45	60	1661	0	0	163.055926	37	60	1259	103	ENST00000302909.3	0.54878	0.999487
SLC5A6	8884	__UNKNOWN__	__UNKNOWN__	2	27424682	27424682	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs537327169		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:27424682T>C	ENST00000310574.3	-	14	1869	c.1396A>G	c.(1396-1398)Atg>Gtg	p.M466V	SLC5A6_ENST00000461319.1_5'UTR|SLC5A6_ENST00000408041.1_Missense_Mutation_p.M466V	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	466		NA			biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	CAGAAGGCCATGACGAGCCCA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													89	74	79	NA		NA	NA	2		NA											NA				27424682		2203	4300	6503	SO:0001583	missense			AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074	8884		Solute carriers	11041	protein-coding gene	gene with protein product		604024	solute carrier family 5 (sodium-dependent vitamin transporter), member 6		NA	9516450, 10329687	Standard	NM_021095	NM_021095	NA	Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.1396A>G	chr2.hg19:g.27424682T>C	ENSP00000310208:p.Met466Val	NA	B2RB85|D6W549|Q969Y5	hg19	CCDS1740.1	0.02	12.121164	CCAxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	T	8.472	0.857761	0.17178	.	.	ENSG00000138074	ENST00000310574;ENST00000408041	D;D	0.82984	-1.67;-1.67	5.66	4.51	0.55191	.	0.034941	0.85682	D	0.000000	T	0.75496	0.3857	L	0.48986	1.54	0.58432	D	0.999997	B	0.11235	0.004	B	0.09377	0.004	T	0.66176	-0.5989	10	0.15952	T	0.53	.	9.7684	0.40574	0.0:0.0817:0.0:0.9183	.	466	Q9Y289	SC5A6_HUMAN	V	466	ENSP00000310208:M466V;ENSP00000384853:M466V	ENSP00000310208:M466V	M	-	1	0	SLC5A6	27278186	1.000000	0.71417	0.971000	0.41717	0.326000	0.28443	4.781000	0.62389	0.979000	0.38497	0.460000	0.39030	ATG	NOVEL	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214194.1	3	20.755443	KEEP	0	0	0	69	2061	TT	1	1	0		-	17	60	603	0	0	40.477088	270	60	9480	463	ENST00000310574.3	0.059233	1
ZNF513	130557	__UNKNOWN__	__UNKNOWN__	2	27600731	27600731	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:27600731C>T	ENST00000323703.6	-	4	1505	c.1307G>A	c.(1306-1308)cGc>cAc	p.R436H	ZNF513_ENST00000407879.1_Missense_Mutation_p.R374H|ZNF513_ENST00000491924.1_5'UTR	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	436		NA			regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGTGGATGCGACCATGACG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													164	158	160	NA		NA	NA	2		NA											NA				27600731		2203	4300	6503	SO:0001583	missense			AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795	130557		Zinc fingers, C2H2-type	26498	protein-coding gene	gene with protein product		613598			NA	12477932	Standard	NM_144631	NM_001201459	NA	Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.1307G>A	chr2.hg19:g.27600731C>T	ENSP00000318373:p.Arg436His	NA	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	hg19	CCDS1751.1	0.02	8.660513	ATGxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098026	0.56183	.	.	ENSG00000163795	ENST00000323703;ENST00000407879	T;T	0.25749	1.78;1.78	5.19	5.19	0.71726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000141	T	0.52289	0.1725	M	0.80028	2.48	0.47511	D	0.999443	D	0.69078	0.997	D	0.63283	0.913	T	0.57394	-0.7819	10	0.87932	D	0	-18.5435	17.441	0.87565	0.0:1.0:0.0:0.0	.	436	Q8N8E2	ZN513_HUMAN	H	436;374	ENSP00000318373:R436H;ENSP00000384874:R374H	ENSP00000318373:R436H	R	-	2	0	ZNF513	27454235	1.000000	0.71417	0.996000	0.52242	0.530000	0.34684	7.264000	0.78432	2.702000	0.92279	0.655000	0.94253	CGC	NOVEL	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215026.2	5	19.85568	KEEP	0	0	0	66	2213	CC	1	1	0		-	15	60	531	0	0	36.277048	212	60	7364	341	ENST00000323703.6	0.066079	1
ZNF513	130557	__UNKNOWN__	__UNKNOWN__	2	27601657	27601657	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:27601657G>A	ENST00000323703.6	-	3	674	c.476C>T	c.(475-477)tCc>tTc	p.S159F	ZNF513_ENST00000407879.1_Missense_Mutation_p.S97F|ZNF513_ENST00000491924.1_Intron	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	159		NA			regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CGAGTAGTGGGACACGAAGGT	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	48	47	NA		NA	NA	2		NA											NA				27601657		2203	4300	6503	SO:0001583	missense			AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795	130557		Zinc fingers, C2H2-type	26498	protein-coding gene	gene with protein product		613598			NA	12477932	Standard	NM_144631	NM_001201459	NA	Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.476C>T	chr2.hg19:g.27601657G>A	ENSP00000318373:p.Ser159Phe	NA	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	hg19	CCDS1751.1	0.02	6.56397	TGGxACA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101003	0.37048	.	.	ENSG00000163795	ENST00000323703;ENST00000407879;ENST00000436006	T;T;T	0.54479	2.25;2.25;0.57	4.62	4.62	0.57501	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.51477	D	0.000095	T	0.27629	0.0679	N	0.08118	0	0.44275	D	0.997131	B	0.29909	0.261	B	0.20767	0.031	T	0.25152	-1.0140	10	0.02654	T	1	-7.5506	16.211	0.82158	0.0:0.0:1.0:0.0	.	159	Q8N8E2	ZN513_HUMAN	F	159;97;97	ENSP00000318373:S159F;ENSP00000384874:S97F;ENSP00000394226:S97F	ENSP00000318373:S159F	S	-	2	0	ZNF513	27455161	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.478000	0.60230	2.402000	0.81655	0.561000	0.74099	TCC	NOVEL	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215026.2	3	25.6375	KEEP	0	1	33	97	3192	GG	1	1	0		-	51	70	1779	0	0	156.995246	120	60	4271	335	ENST00000323703.6	0.298246	1
FOSL2	2355	__UNKNOWN__	__UNKNOWN__	2	28627036	28627036	__UNKNOWN__	Silent	SNP	G	G	A	rs144955498		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:28627036G>A	ENST00000379619.1	+	2	98	c.90G>A	c.(88-90)acG>acA	p.T30T	FOSL2_ENST00000545753.1_Silent_p.T16T|FOSL2_ENST00000460736.1_3'UTR|FOSL2_ENST00000264716.4_Silent_p.T55T			P15408	FOSL2_HUMAN	FOS-like antigen 2	55		NA			cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					ACGCCATCACGACCAGCCAGG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G		0,4406		0,0,2203	144	126	132	NA	165	-8.8	0.8	2	dbSNP_134	132	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FOSL2	NM_005253.3		0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077		55/327	28627036	1,13005	2203	4300	6503	SO:0001819	synonymous_variant				CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426	2355		basic leucine zipper proteins	3798	protein-coding gene	gene with protein product		601575			NA		Standard	NM_005253	NM_005253	NA	Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000379619.1:c.90G>A	chr2.hg19:g.28627036G>A		NA	B2RD58|B3KP27|B4DYV4|Q6FG46	hg19		0.02	34.825958	CACxACC	COVERED																																																																																			NOVEL	FOSL2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000215117.1	20	149.967329	KEEP	0	1	30	509	17008	GG	1	1	0		+	74	60	2696	0	0	198.086365	722	60	24971	1696	ENST00000379619.1	0.092965	1
PLB1	151056	__UNKNOWN__	__UNKNOWN__	2	28761137	28761137	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:28761137C>A	ENST00000327757.5	+	10	599				PLB1_ENST00000422425.2_Intron	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					GGCCTCACCTCGTGGTCCTCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													36	33	34	NA		NA	NA	2		NA											NA				28761137		2203	4300	6503	SO:0001627	intron_variant				CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	151056	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179			NA	12150957	Standard		NM_153021	NA	Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.556-49C>A	chr2.hg19:g.28761137C>A		NA	A8KAX2|Q53S03|Q8IUP7|Q96DP9	hg19	CCDS33168.1	0.02	7.229156	CCTxGTG	COVERED																																																																																			NOVEL	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353348.2	4	13.543347	KEEP	0	0	0	45	1543	CC	1	1	0		+	15	60	556	0	0	41.538982	136	60	4757	246	ENST00000327757.5	0.099338	1
EHD3	30845	__UNKNOWN__	__UNKNOWN__	2	31491403	31491403	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:31491403G>T	ENST00000322054.5	+	0	3726					NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	NA		NA			blood coagulation (GO:0007596)|endocytic recycling (GO:0032456)|protein homooligomerization (GO:0051260)|protein targeting to plasma membrane (GO:0072661)|regulation of cardiac muscle cell membrane potential (GO:0086036)	cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					CTTCCCAGTGGGCTGGAGTTT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016	30845		EF-hand domain containing	3244	protein-coding gene	gene with protein product		605891		PAST3	NA	10673336	Standard	NM_014600	NM_014600	NA	Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.*1833G>T	chr2.hg19:g.31491403G>T		NA	B4DFR5|D6W574|Q8N514|Q9NZB3	hg19	CCDS1774.1	0.02	1.977175	GTGxGCT	COVERED																																																																																			NOVEL	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216810.1	0	4.815169	KEEP	0	0	0	16	537	GG	0.997832	0.997151	0		+	6	60	220	0	0	15.576168	75	60	2651	113	ENST00000322054.5	0.074074	0.999317
TTC27	55622	__UNKNOWN__	__UNKNOWN__	2	33037621	33037621	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:33037621T>C	ENST00000317907.4	+	18	2478	c.2247T>C	c.(2245-2247)tgT>tgC	p.C749C		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	749		NA								breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						AGTCCAATTGTTGGGAGAAAG	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													145	137	140	NA		NA	NA	2		NA											NA				33037621		2203	4300	6503	SO:0001819	synonymous_variant			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699	55622		Tetratricopeptide (TTC) repeat domain containing	25986	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017735	NM_001193509	NA	Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.2247T>C	chr2.hg19:g.33037621T>C		NA	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	hg19	CCDS33176.1	0.02	7.312695	TTGxTGG	COVERED																																																																																			NOVEL	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325395.1	6	18.05152	KEEP	0	0	0	60	1928	TT	1	1	0		+	52	60	1975	0	0	174.16369	136	60	4948	317	ENST00000317907.4	0.276596	1
AC007401.2	0	__UNKNOWN__	__UNKNOWN__	2	36777209	36777209	__UNKNOWN__	Intron	SNP	T	T	C	rs1045234|rs34148376|rs374839318	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:36777209T>C	ENST00000406220.1	-	1	213				CRIM1_ENST00000280527.2_3'UTR						NA		NA									NA						tgtgtgtgtgtgCGCGCGCAC	0.413	NA	NA											-|||	1065	0.21266	0.1241	0.2118	5008	,	,	NA	13575	0.127	NA	0.2575	False	NA	,,,	NA	NA	NA	2504	0.3753	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000406220.1:c.64+1989A>G	chr2.hg19:g.36777209T>C		NA		hg19		0.02	2.080514	GTGxGCG	COVERED																																																																																			NOVEL	AC007401.2-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325456.1	5	8.091625	KEEP	0	2	66	50	1532	TT	1	0.999881	0		-	19	60	644	2	0	53.222719	72	60	2561	183	ENST00000406220.1	0.208791	0.999881
VIT	5212	__UNKNOWN__	__UNKNOWN__	2	37032582	37032582	__UNKNOWN__	Splice_Site	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:37032582T>G	ENST00000404084.1	+	11	1141	c.975T>G	c.(973-975)ggT>ggG	p.G325G	VIT_ENST00000401530.1_Splice_Site_p.G352G|VIT_ENST00000389975.3_Splice_Site_p.G373G|VIT_ENST00000379242.3_Splice_Site_p.G388G|VIT_ENST00000497382.1_Splice_Site_p.G42G|VIT_ENST00000379241.3_Splice_Site_p.G351G			Q6UXI7	VITRN_HUMAN	vitrin	373	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.	NA			extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TTCTTCCAGGTCGGGCCATCT	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													53	54	53	NA		NA	NA	2		NA											NA				37032582		2203	4300	6503	SO:0001630	splice_region_variant			AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221	5212			12697	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001177969	NA	Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000404084.1:c.974-1T>G	chr2.hg19:g.37032582T>G		NA	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	hg19		0.02	2.145143	AGGxCGG	COVERED																																																																																			NOVEL	VIT-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325453.1	1	5.717983	KEEP	0	0	0	19	635	TT	0.99986	0.99979	0	Silent	+	19	60	696	0	0	57.925229	77	60	2756	143	ENST00000404084.1	0.197917	0.99993
COX7A2L	9167	__UNKNOWN__	__UNKNOWN__	2	42578286	42578286	__UNKNOWN__	3'UTR	SNP	T	T	A	rs189853616	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:42578286T>A	ENST00000378669.1	-	0	1247				COX7A2L_ENST00000234301.2_3'UTR|COX7A2L_ENST00000482463.1_5'UTR			O14548	COX7R_HUMAN	cytochrome c oxidase subunit VIIa polypeptide 2 like	NA		NA			cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			lung(4)	4						aaaaaaaaaattttaatttaa	0.333	NA	NA											T|||	34	0.00678914	0.0234	0.0014	5008	,	,	NA	19417	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB007618	CCDS1808.1	2p21	2010-06-14			ENSG00000115944	ENSG00000115944	9167			2289	protein-coding gene	gene with protein product		605771			NA	9418891	Standard	NM_004718	NM_004718	NA	Approved	EB1, COX7RP, COX7AR, SIG81	uc002rsk.3	O14548	OTTHUMG00000128605	ENST00000378669.1:c.*73A>T	chr2.hg19:g.42578286T>A		NA	Q9P118	hg19	CCDS1808.1	0.02	4.219989	AAAxTTT	COVERED																																																																																			NOVEL	COX7A2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250466.3	2	10.532554	KEEP	0	0	0	35	1134	TT	0.999999	0.99999	0		-	16	60	541	2	0	42.023685	93	60	3303	170	ENST00000378669.1	0.146789	0.999992
PLEKHH2	130271	__UNKNOWN__	__UNKNOWN__	2	43994118	43994118	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:43994118G>T	ENST00000282406.4	+	0	5973					NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	NA		NA			negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GTACTTAAATGCATTACTTTA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527	130271		Pleckstrin homology (PH) domain containing	30506	protein-coding gene	gene with protein product		612723			NA		Standard	NM_172069	NM_172069	NA	Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.*1381G>T	chr2.hg19:g.43994118G>T		NA	Q5JPJ6|Q6P4Q1|Q8N3Q3	hg19	CCDS1812.1	0.02	4.66292	AATxCAT	COVERED																																																																																			NOVEL	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250537.1	1	15.951772	KEEP	0	0	0	53	1903	GG	1	0.999981	0		+	24	60	873	0	0	74.355083	80	60	3016	200	ENST00000282406.4	0.230769	0.999981
LRPPRC	10128	__UNKNOWN__	__UNKNOWN__	2	44116923	44116923	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs147302249	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:44116923C>T	ENST00000260665.7	-	37	4135	c.4078G>A	c.(4078-4080)Gca>Aca	p.A1360T		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1360	RNA-binding.	NA			mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGCAAAGATGCGTAACGCTTT	0.393	NA	NA											C|||	11	0.00219649	0	0	5008	,	,	NA	20488	0.0109	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													112	107	109	NA		NA	NA	2		NA											NA				44116923		2203	4300	6503	SO:0001583	missense			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095	10128			15714	protein-coding gene	gene with protein product		607544	Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)	LSFC	NA	8012652, 8619474, 22045337	Standard	NM_133259	NM_133259	NA	Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.4078G>A	chr2.hg19:g.44116923C>T	ENSP00000260665:p.Ala1360Thr	NA	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	hg19	CCDS33189.1	0.02	9.541943	ATGxGTA	COVERED	7	0.003205128205128205	0	0.0	0	0.0	7	0.012237762237762238	0	0.0	C	28.1	4.889861	0.91889	.	.	ENSG00000138095	ENST00000260665	T	0.75154	-0.91	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.81791	0.4897	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.80096	-0.1525	10	0.26408	T	0.33	-8.295	19.9064	0.97008	0.0:1.0:0.0:0.0	.	1360	P42704	LPPRC_HUMAN	T	1360	ENSP00000260665:A1360T	ENSP00000260665:A1360T	A	-	1	0	LRPPRC	43970427	0.996000	0.38824	0.172000	0.22920	0.008000	0.06430	3.578000	0.53892	2.693000	0.91896	0.655000	0.94253	GCA	NOVEL	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327823.1	0	22.272091	KEEP	0	0	0	74	2607	CC	1	1	0		-	52	60	1958	0	0	167.463125	176	60	6253	399	ENST00000260665.7	0.22807	1
PRKCE	5581	__UNKNOWN__	__UNKNOWN__	2	45879060	45879060	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:45879060A>G	ENST00000306156.3	+	0	148					NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	NA		NA			activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	GCGAGGAAATACATGCACTGG	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	5581	2.7.11.1		9401	protein-coding gene	gene with protein product		176975			NA	1382605, 7877991	Standard		NM_005400	NA	Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.-180A>G	chr2.hg19:g.45879060A>G		NA	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	hg19	CCDS1824.1	0.02	2.229913	AATxCAT	COVERED																																																																																			NOVEL	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250751.2	0	25.543347	KEEP	0	0	0	85	2421	AA	1	0.998465	0		+	22	60	833	0	0	74.248649	52	60	1747	217	ENST00000306156.3	0.297297	0.998465
TTC7A	57217	__UNKNOWN__	__UNKNOWN__	2	47301611	47301611	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:47301611C>T	ENST00000319190.5	+	0	3494				RP11-761B3.1_ENST00000422269.1_Intron|C2orf61_ENST00000464527.2_Intron|TTC7A_ENST00000394850.2_3'UTR	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	NA		NA			cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			TTTCCCCCTGCTACCAAGTGC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724	57217		Tetratricopeptide (TTC) repeat domain containing	19750	protein-coding gene	gene with protein product		609332	tetratricopeptide repeat domain 7	TTC7	NA	10574461	Standard	XM_372927	XM_005264439	NA	Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.*549C>T	chr2.hg19:g.47301611C>T		NA	Q6PIX4|Q8ND67|Q9BUS3	hg19	CCDS33193.1	0.02	13.455853	CTGxTAC	COVERED																																																																																			NOVEL	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329667.2	1	33.992363	KEEP	0	0	0	113	3940	CC	1	1	0		+	70	70	2451	0	0	206.062359	245	70	9153	521	ENST00000319190.5	0.222222	1
RP11-761B3.1	0	__UNKNOWN__	__UNKNOWN__	2	47378398	47378398	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:47378398T>C	ENST00000422269.1	-	0	418				C2orf61_ENST00000445927.2_Splice_Site_p.Q133R|C2orf61_ENST00000294947.2_Splice_Site_p.Q133R						NA		NA						p.0?(2)			NA						GCGCTTTACCTGATCTTTGTC	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)											104	100	101	NA		NA	NA	2		NA											NA				47378398		2203	4300	6503	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000422269.1:c.*288A>G	chr2.hg19:g.47378398T>C		NA		hg19		0.02	6.760113	ACCxGAT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.69|14.69	2.609259|2.609259	0.46527|0.46527	.|.	.|.	ENSG00000239605|ENSG00000239605	ENST00000445927;ENST00000294947|ENST00000449846	T;T|.	0.29655|.	1.56;1.57|.	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	0.957042|.	0.08603|.	N|.	0.921102|.	T|T	0.49966|0.49966	0.1588|0.1588	L|L	0.47716|0.47716	1.5|1.5	0.30759|0.30759	N|N	0.744284|0.744284	B|.	0.32829|.	0.386|.	B|.	0.25291|.	0.059|.	T|T	0.53823|0.53823	-0.8384|-0.8384	10|5	0.36615|.	T|.	0.2|.	-17.8789|-17.8789	12.871|12.871	0.57965|0.57965	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	133|.	Q8N801|.	CB061_HUMAN|.	R|G	133|13	ENSP00000408527:Q133R;ENSP00000294947:Q133R|.	ENSP00000294947:Q133R|.	Q|S	-|-	2|1	0|0	C2orf61|C2orf61	47231902|47231902	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.832000|0.832000	0.47134|0.47134	5.211000|5.211000	0.65219|0.65219	1.874000|1.874000	0.54306|0.54306	0.383000|0.383000	0.25322|0.25322	CAG|AGT	NOVEL	RP11-761B3.1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000471753.1	2	10.531797	KEEP	0	0	0	35	1106	TT	0.999999	0.999999	0		-	45	60	1510	0	0	128.268894	137	60	5146	258	ENST00000422269.1	0.247253	1
NRXN1	9378	__UNKNOWN__	__UNKNOWN__	2	50149079	50149079	__UNKNOWN__	3'UTR	SNP	G	G	A	rs200583259		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:50149079G>A	ENST00000404971.1	-	0	5986				NRXN1_ENST00000401710.1_3'UTR|NRXN1_ENST00000406316.2_3'UTR|NRXN1_ENST00000401669.2_3'UTR|NRXN1_ENST00000405472.3_3'UTR|NRXN1_ENST00000342183.5_3'UTR	NM_001135659.1	NP_001129131.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	NA		NA			adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TAAGATCTTGGGATCAGACAT	0.333	NA	NA											G|||	1	0.000199681	8e-04	0	5008	,	,	NA	18474	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													114	108	110	NA		NA	NA	2		NA											NA				50149079		2203	4300	6503	SO:0001624	3_prime_UTR_variant			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915	9378			8008	protein-coding gene	gene with protein product		600565			NA		Standard		NM_001135659	NA	Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000404971.1:c.*3C>T	chr2.hg19:g.50149079G>A		NA	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	hg19	CCDS46282.1	0.02	4.913243	TTGxGAT	COVERED																																																																																			NOVEL	NRXN1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323894.3	3	4.815439	KEEP	0	0	0	16	556	GG	0.997832	0.99783	0		-	35	60	1263	0	0	111.390704	86	60	3033	154	ENST00000404971.1	0.289256	0.999999
NRXN1	9378	__UNKNOWN__	__UNKNOWN__	2	50170968	50170968	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:50170968T>C	ENST00000404971.1	-	23	5588				NRXN1_ENST00000406859.3_Intron|NRXN1_ENST00000401710.1_Intron|NRXN1_ENST00000406316.2_Intron|NRXN1_ENST00000402717.3_Intron|NRXN1_ENST00000401669.2_Intron|NRXN1_ENST00000405472.3_Intron|NRXN1_ENST00000342183.5_Intron	NM_001135659.1	NP_001129131.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	NA		NA			adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ATTTAAAGGGTCCTAACAGAT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	31	31	NA		NA	NA	2		NA											NA				50170968		2202	4300	6502	SO:0001627	intron_variant			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915	9378			8008	protein-coding gene	gene with protein product		600565			NA		Standard		NM_001135659	NA	Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000404971.1:c.4249-39A>G	chr2.hg19:g.50170968T>C		NA	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	hg19	CCDS46282.1	0.02	2.126296	GGGxCCT	COVERED																																																																																			NOVEL	NRXN1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323894.3	0	3.611376	KEEP	0	0	0	12	396	TT	0.993634	0.987376	0		-	15	60	521	0	0	44.123215	49	60	1760	85	ENST00000404971.1	0.234375	0.993703
EML6	400954	__UNKNOWN__	__UNKNOWN__	2	55191724	55191724	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:55191724G>A	ENST00000356458.6	+	37	5868	c.5348G>A	c.(5347-5349)cGa>cAa	p.R1783Q	EML6_ENST00000490828.1_3'UTR	NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	1783		NA				cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						CCAGACAACCGATTCTTAGCC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													152	119	129	NA		NA	NA	2		NA											NA				55191724		692	1591	2283	SO:0001583	missense				CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595	400954		WD repeat domain containing	35412	protein-coding gene	gene with protein product		NA			NA		Standard	XM_001725002	NM_001039753	NA	Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.5348G>A	chr2.hg19:g.55191724G>A	ENSP00000348842:p.Arg1783Gln	NA	A8MUB5|B6ZDG7	hg19	CCDS46286.1	0.02	4.426294	ACCxATT	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591996	0.66219	.	.	ENSG00000214595	ENST00000356458	T	0.17854	2.25	5.58	3.76	0.43208	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.055112	0.64402	D	0.000001	T	0.16938	0.0407	L	0.49126	1.545	0.30456	N	0.774737	B	0.18610	0.029	B	0.14023	0.01	T	0.06041	-1.0849	10	0.33940	T	0.23	.	13.2214	0.59890	0.1358:0.0:0.8642:0.0	.	1783	Q6ZMW3	EMAL6_HUMAN	Q	1783	ENSP00000348842:R1783Q	ENSP00000348842:R1783Q	R	+	2	0	EML6	55045228	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.328000	0.65887	1.484000	0.48361	0.655000	0.94253	CGA	NOVEL	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324997.3	2	11.43552	KEEP	0	0	0	38	1248	GG	1	1	0		+	34	60	1227	0	0	106.48426	96	60	3182	203	ENST00000356458.6	0.261538	1
CCDC88A	55704	__UNKNOWN__	__UNKNOWN__	2	55522407	55522407	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:55522407G>A	ENST00000263630.8	-	30	6244				CCDC88A_ENST00000422883.2_Intron|CCDC88A_ENST00000436346.1_Intron|CCDC88A_ENST00000413716.2_Intron|CCDC88A_ENST00000336838.6_Intron	NM_018084.4	NP_060554.3	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	NA		NA			activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CAGAAGCCTGGTCAGTTATTC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355	55704			25523	protein-coding gene	gene with protein product	Galpha-interacting vesicle-associated protein, Akt-phosphorylation enhancer, girdin, girders of actin filaments	609736	KIAA1212	KIAA1212	NA	15749703, 15753085	Standard	NM_017571	NM_001135597	NA	Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000263630.8:c.5467+325C>T	chr2.hg19:g.55522407G>A		NA	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	hg19	CCDS33203.1	0.02	6.924129	CTGxTCA	COVERED																																																																																			NOVEL	CCDC88A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324406.3	3	8.365122	KEEP	0	0	0	28	947	GG	0.999997	0.999997	0		-	35	60	1291	0	0	108.877521	129	60	4640	212	ENST00000263630.8	0.213415	1
ARHGAP25	9938	__UNKNOWN__	__UNKNOWN__	2	69034407	69034407	__UNKNOWN__	Splice_Site	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:69034407G>C	ENST00000467265.1	+	4	667		c.e4-1		ARHGAP25_ENST00000497079.1_Missense_Mutation_p.V150L|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.V150L|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.V157L|ARHGAP25_ENST00000544262.1_Missense_Mutation_p.V131L|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000295381.3_Splice_Site|ARHGAP25_ENST00000409030.3_Splice_Site	NM_001166277.1	NP_001159749.1	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTCCTCAGCAGTGTTTGGCCA	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	83	84	NA		NA	NA	2		NA											NA				69034407		2203	4300	6503	SO:0001630	splice_region_variant			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219	9938		Rho GTPase activating proteins, Pleckstrin homology (PH) domain containing	28951	protein-coding gene	gene with protein product		610587			NA	7584044	Standard	NM_014882	NM_001007231	NA	Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000467265.1:c.350-1G>C	chr2.hg19:g.69034407G>C		NA	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	hg19	CCDS54363.1	0.02	9.250292	GCAxTGT	COVERED	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	11.87|11.87|11.87	1.768457|1.768457|1.768457	0.31320|0.31320|0.31320	.|.|.	.|.|.	ENSG00000163219|ENSG00000163219|ENSG00000163219	ENST00000295381;ENST00000467265;ENST00000409030|ENST00000497259|ENST00000544262;ENST00000409202;ENST00000409220;ENST00000482106;ENST00000497079;ENST00000543533	.|.|T;T;T;T	.|.|0.43688	.|.|0.94;2.76;2.76;2.76	4.88|4.88|4.88	4.88|4.88|4.88	0.63580|0.63580|0.63580	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.53802|0.53802	.|0.1819|0.1819	L|L|L	0.58428|0.58428|0.58428	1.81|1.81|1.81	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|B;D;D;P	.|.|0.55385	.|.|0.137;0.971;0.971;0.935	.|.|B;P;P;P	.|.|0.53224	.|.|0.157;0.721;0.637;0.513	.|T|T	.|0.57997|0.57997	.|-0.7714|-0.7714	.|6|9	.|0.87932|0.66056	.|D|D	.|0|0.02	.|.|.	17.1999|17.1999|17.1999	0.86903|0.86903|0.86903	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	.|.|131;157;150;150	.|.|B7Z8K7;P42331-4;G5E9G2;P42331-2	.|.|.;.;.;.	.|H|L	-1|15|131;157;150;150;150;141	.|.|ENSP00000439917:V131L;ENSP00000386911:V157L;ENSP00000386241:V150L;ENSP00000417139:V150L	.|ENSP00000420427:Q88H|ENSP00000386911:V157L	.|Q|V	+|+|+	.|3|1	.|2|0	ARHGAP25|ARHGAP25|ARHGAP25	68887911|68887911|68887911	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.952000|0.952000|0.952000	0.39060|0.39060|0.39060	0.392000|0.392000|0.392000	0.30506|0.30506|0.30506	5.659000|5.659000|5.659000	0.68010|0.68010|0.68010	2.545000|2.545000|2.545000	0.85829|0.85829|0.85829	0.555000|0.555000|0.555000	0.69702|0.69702|0.69702	.|CAG|GTG	NOVEL	ARHGAP25-008	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353949.1	2	23.475019	KEEP	0	0	0	78	2779	GG	1	1	0	Intron	+	11	60	409	0	0	27.0228	217	60	8208	369	ENST00000467265.1	0.048246	1
EXOC6B	23233	__UNKNOWN__	__UNKNOWN__	2	72691305	72691305	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:72691305C>T	ENST00000272427.6	-	18	2111				EXOC6B_ENST00000410104.1_3'UTR	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	NA		NA			protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						GGTAAAGTAACACTGACAATC	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036	23233			17085	protein-coding gene	gene with protein product		607880	SEC15-like 2 (S. cerevisiae), SEC15 homolog B (S. cerevisiae)	SEC15L2, SEC15B	NA	10231032, 11406615	Standard	XM_039570	NM_015189	NA	Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.1980+983G>A	chr2.hg19:g.72691305C>T		NA	B8ZZY3	hg19	CCDS46333.1	0.02	2.340213	TAAxACT	COVERED																																																																																			NOVEL	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327558.1	1	2.708537	KEEP	0	0	0	9	309	CC	0.99254	0.956584	0		-	10	60	366	0	0	30.410825	41	60	1471	69	ENST00000272427.6	0.196078	0.963774
MOB1A	55233	__UNKNOWN__	__UNKNOWN__	2	74405722	74405722	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:74405722G>T	ENST00000396049.4	-	1	208				MOB1A_ENST00000497054.1_Intron	NM_018221.3	NP_060691.2	Q9H8S9	MOB1A_HUMAN	MOB kinase activator 1A	NA		NA			hippo signaling (GO:0035329)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)				NA						CTCGCCTCAGGTCCGGGGAGG	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													2	3	3	NA		NA	NA	2		NA											NA				74405722		477	1218	1695	SO:0001627	intron_variant				CCDS46340.1	2p13.1	2011-09-28	2011-09-28	2011-09-27	ENSG00000114978	ENSG00000114978	55233		MOB kinase activators	16015	protein-coding gene	gene with protein product		609281	chromosome 2 open reading frame 6, MOB1, Mps One Binder kinase activator-like 1B (yeast), MOB1 Mps One Binder homolog A (yeast)	C2orf6, MOBK1B, MOBKL1B	NA	11319234, 20624913	Standard	NM_018221	NM_018221	NA	Approved	FLJ10788, MOB1, FLJ11595, Mob4B, Mats1	uc002skh.4	Q9H8S9	OTTHUMG00000152833	ENST00000396049.4:c.14+65C>A	chr2.hg19:g.74405722G>T		NA	Q53S34|Q9H3T5|Q9HAI0|Q9NVE2	hg19	CCDS46340.1	0.02	-0.419554	CAGxTCC	COVERED																																																																																			NOVEL	MOB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328200.2	1	17.983902	KEEP	0	0	0	60	1886	GG	1	0.948402	0		-	9	60	310	0	0	25.733992	34	60	1063	129	ENST00000396049.4	0.209302	0.948402
DNAH6	1768	__UNKNOWN__	__UNKNOWN__	2	84844085	84844085	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:84844085C>T	ENST00000237449.6	+	22	3559	c.3551C>T	c.(3550-3552)tCa>tTa	p.S1184L	DNAH6_ENST00000398278.2_Missense_Mutation_p.S1184L|DNAH6_ENST00000389394.3_Missense_Mutation_p.S1184L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1184	Stem. {ECO:0000250}.	NA			cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TACTTAGAATCAAAAAGAGTT	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													57	52	53	NA		NA	NA	2		NA											NA				84844085		692	1578	2270	SO:0001583	missense			U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423	1768		Axonemal dyneins	2951	protein-coding gene	gene with protein product		603336	dynein, axonemal, heavy polypeptide 6, dynein heavy chain-like 1	DNHL1	NA	8812413	Standard	NM_001370	NM_001370	NA	Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.3551C>T	chr2.hg19:g.84844085C>T	ENSP00000237449:p.Ser1184Leu	NA	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	hg19	CCDS46348.1	0.02	-0.403557	AATxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.60	3.857509	0.71834	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.62639	0.01;0.01;0.01	5.0	5.0	0.66597	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.64034	0.2562	L	0.55103	1.725	0.30845	N	0.735249	B	0.32968	0.392	B	0.37943	0.261	T	0.68812	-0.5310	9	0.56958	D	0.05	.	17.0658	0.86558	0.0:1.0:0.0:0.0	.	1184	Q9C0G6	DYH6_HUMAN	L	1184	ENSP00000374045:S1184L;ENSP00000381326:S1184L;ENSP00000237449:S1184L	ENSP00000237449:S1184L	S	+	2	0	DNAH6	84697596	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	3.267000	0.51577	2.295000	0.77249	0.557000	0.71058	TCA	NOVEL	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328537.2	0	3.009997	KEEP	0	0	0	10	370	CC	0.992708	0.927678	0		+	10	60	354	0	0	29.712295	36	60	1413	73	ENST00000237449.6	0.217391	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87408281	87408281	__UNKNOWN__	IGR	SNP	T	T	G	rs373956158	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:87408281T>G			NA	NA				PLGLB1 (159306 upstream) : MIR4771-2 (13627 downstream)						NA		NA									NA						GCTGGGTGTGTTCGGGAGTTG	0.423	NA	NA											G|||	2339	0.467053	0.8275	0.2464	5008	,	,	NA	8277	0.4683	NA	0.2823	False	NA	,,,	NA	NA	NA	2504	0.3252	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87408281T>G		NA		hg19		0.02	2.206925	GTGxTCG	COVERED																																																																																			NOVEL					0			1	6.319154	KEEP	17	0	0	21	677	TT	0.999869	0.999673	0			4	27	138	0	0	8.630049	85	60	3023	151		0.044944	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	89495886	89495886	__UNKNOWN__	IGR	SNP	A	A	G	rs443522	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:89495886A>G			NA	NA				IGKV2-24 (19242 upstream) : IGKV1-27 (17021 downstream)						NA		NA									NA						TCCTAAAATAAATAGAAAGAA	0.368	NA	NA											a|||	921	0.183906	0.118	0.1974	5008	,	,	NA	12516	0.4038	NA	0.0447	False	NA	,,,	NA	NA	NA	2504	0.18	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.89495886A>G		NA		hg19		0.02	5.05352	ATAxATA	COVERED																																																																																			NOVEL					0			1	3.610189	KEEP	5	0	0	12	371	AA	0.993634	0.993618	0			44	40	1643	0	0	154.285333	61	50	2236	145		0.419048	0.999984
IGKV1-27	28935	__UNKNOWN__	__UNKNOWN__	2	89512959	89512959	__UNKNOWN__	RNA	SNP	C	C	T	rs61735918	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:89512959C>T	ENST00000498435.1	-	0	330									immunoglobulin kappa variable 1-27	NA		NA									NA						CTTCAGGCTGCAGGCTGCTGA	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													79	75	76	NA		NA	NA	2		NA											NA				89512959		1878	4101	5979					X63398		2p11.2	2012-02-10			ENSG00000244575	ENSG00000244575	28935		Immunoglobulins / IGK locus	5735	other	immunoglobulin gene		NA			NA		Standard	NG_000834	NG_000834	NA	Approved	IGKV127, A20			OTTHUMG00000151640	ENST00000498435.1:	chr2.hg19:g.89512959C>T		NA		hg19		0.02	8.28529	CTGxAGG	COVERED																																																																																			NOVEL	IGKV1-27-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000323389.1	4	3.380955	KEEP	27	2	62	33	1198	CC	0.999998	0.999998	0		-	25	50	854	0	0	62.224062	222	60	8329	370	ENST00000498435.1	0.101215	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91766609	91766609	__UNKNOWN__	IGR	SNP	G	G	A	rs2433883		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:91766609G>A			NA	NA				None (None upstream) : RP11-575H3.1 (1783 downstream)						NA		NA									NA						TATGGGGGTTGTAATGTTTAT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91766609G>A		NA		hg19		0.02	39.265959	GTTxTAA	COVERED																																																																																			NOVEL					0			15	14.192755	KEEP	0	13	410	191	6749	GG	1	1	0			64	60	2350	0	0	166.024878	814	60	30358	1293		0.072893	1
AC027612.6	0	__UNKNOWN__	__UNKNOWN__	2	91809402	91809402	__UNKNOWN__	RNA	SNP	T	T	G	rs4244681	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:91809402T>G	ENST00000609777.1	-	0	199										NA		NA									NA						CTATTTTCTATGGAATGCACG	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000609777.1:	chr2.hg19:g.91809402T>G		NA		hg19		0.02	40.759772	CTAxGGA	COVERED																																																																																			NOVEL	AC027612.6-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000471986.1	5	11.471862	KEEP	39	10	358	163	5097	TT	1	1	0		-	75	60	2835	0	0	214.34932	655	60	24026	1244	ENST00000609777.1	0.10274	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91872052	91872052	__UNKNOWN__	IGR	SNP	C	C	G	rs151001	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:91872052C>G			NA	NA				RNA5SP100 (9060 upstream) : AC027612.3 (2075 downstream)						NA		NA									NA						AAGCTGTGCTCCCACCACATC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91872052C>G		NA		hg19		0.02	39.405535	GCTxCCA	COVERED																																																																																			NOVEL					0			58	36.112168	KEEP	35	14	521	302	10311	CC	1	1	0			70	49	2652	0	1	193.974962	771	50	28039	1416		0.083234	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91872069	91872069	__UNKNOWN__	IGR	SNP	C	C	T	rs2537164	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:91872069C>T			NA	NA				RNA5SP100 (9077 upstream) : AC027612.3 (2058 downstream)						NA		NA									NA						CATCACTGCACACACACAAAA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91872069C>T		NA		hg19		0.02	35.677698	GCAxACA	COVERED																																																																																			NOVEL					0			58	43.891066	KEEP	101	14	424	295	10442	CC	1	1	0			62	49	2216	0	1	156.492618	739	50	28111	1376		0.077403	1
SNRNP200	23020	__UNKNOWN__	__UNKNOWN__	2	96944694	96944694	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:96944694A>G	ENST00000323853.5	-	37	5253	c.5176T>C	c.(5176-5178)Tct>Cct	p.S1726P	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1726	Helicase C-terminal 2. {ECO:0000255|PROSITE-ProRule:PRU00542}.	NA			ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCCAGGTGAGATTCTACTGGC	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													107	97	101	NA		NA	NA	2		NA											NA				96944694		2203	4300	6503	SO:0001583	missense			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028	23020			30859	protein-coding gene	gene with protein product	U5 snRNP specific protein, 200 KD	601664	activating signal cointegrator 1 complex subunit 3-like 1, retinitis pigmentosa 33 (autosomal dominant)	ASCC3L1, RP33	NA	9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014	NM_014014	NA	Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5176T>C	chr2.hg19:g.96944694A>G	ENSP00000317123:p.Ser1726Pro	NA	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	hg19	CCDS2020.1	0.02	17.797047	GAGxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	22.0	4.229880	0.79688	.	.	ENSG00000144028	ENST00000323853;ENST00000536601;ENST00000543553	T	0.63096	-0.02	5.58	4.35	0.52113	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86990	0.6066	H	0.99475	4.585	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90679	0.4604	10	0.87932	D	0	-12.3007	10.9503	0.47325	0.8598:0.0:0.0:0.1402	.	1726	O75643	U520_HUMAN	P	1726;185;309	ENSP00000317123:S1726P	ENSP00000317123:S1726P	S	-	1	0	SNRNP200	96308421	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.588000	0.74076	2.246000	0.74042	0.533000	0.62120	TCT	NOVEL	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252846.2	4	20.459885	KEEP	0	0	0	68	2169	AA	1	1	0		-	68	60	2475	0	0	204.647688	287	60	10667	525	ENST00000323853.5	0.191549	1
SNRNP200	23020	__UNKNOWN__	__UNKNOWN__	2	96965148	96965148	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:96965148T>G	ENST00000323853.5	-	6	725	c.648A>C	c.(646-648)gtA>gtC	p.V216V	SNRNP200_ENST00000349783.5_Silent_p.V216V	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	216		NA			ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						CCTCCCCGTATACGTCTTCAT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													215	191	199	NA		NA	NA	2		NA											NA				96965148		2203	4300	6503	SO:0001819	synonymous_variant			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028	23020			30859	protein-coding gene	gene with protein product	U5 snRNP specific protein, 200 KD	601664	activating signal cointegrator 1 complex subunit 3-like 1, retinitis pigmentosa 33 (autosomal dominant)	ASCC3L1, RP33	NA	9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014	NM_014014	NA	Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.648A>C	chr2.hg19:g.96965148T>G		NA	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	hg19	CCDS2020.1	0.02	7.595033	GTAxACG	COVERED																																																																																			NOVEL	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252846.2	1	11.427551	KEEP	0	0	0	38	1152	TT	1	1	0		-	56	60	2083	0	0	190.83275	100	60	3340	244	ENST00000323853.5	0.358974	1
FAHD2B	151313	__UNKNOWN__	__UNKNOWN__	2	97749417	97749417	__UNKNOWN__	3'UTR	SNP	C	C	T	rs140620633		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:97749417C>T	ENST00000414820.1	-	0	1290				FAHD2B_ENST00000272610.3_3'UTR|FAHD2B_ENST00000440566.2_3'UTR			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	NA		NA					hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						CCCACACCTGCCACTGGGCCT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199	151313			25318	protein-coding gene	gene with protein product		NA			NA		Standard	NM_199336	NM_199336	NA	Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.*75G>A	chr2.hg19:g.97749417C>T		NA	D3DXH7|Q8NDK1	hg19	CCDS2030.1	0.02	19.477304	CTGxCAC	COVERED																																																																																			NOVEL	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339482.1	6	11.929161	KEEP	1	3	86	70	2342	CC	1	1	0		-	18	60	607	1	0	35.488245	493	60	17461	666	ENST00000414820.1	0.035225	1
ANKRD36	375248	__UNKNOWN__	__UNKNOWN__	2	97808495	97808495	__UNKNOWN__	Intron	SNP	C	C	T	rs62153045		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:97808495C>T	ENST00000461153.2	+	8	1072				ANKRD36_ENST00000420699.2_Intron			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	NA		NA								endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						TCAAATCCCACTCAGGCTACA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													56	53	54	NA		NA	NA	2		NA											NA				97808495		692	1590	2282	SO:0001627	intron_variant			BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976	375248		Ankyrin repeat domain containing	24079	protein-coding gene	gene with protein product		NA			NA	12975309	Standard		NM_001164315	NA	Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.829-5C>T	chr2.hg19:g.97808495C>T		NA	B4E3I8|Q6UX02|Q86X62|Q9HCD1	hg19	CCDS54379.1	0.02	6.42632	CCAxTCA	COVERED																																																																																			NOVEL	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339154.5	0	15.950941	KEEP	0	0	0	53	1911	CC	1	1	0		+	6	27	220	0	0	13.196187	192	60	7283	329	ENST00000461153.2	0.030303	1
ANKRD36	375248	__UNKNOWN__	__UNKNOWN__	2	97833468	97833468	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs199720452		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:97833468G>A	ENST00000461153.2	+	22	1841	c.1597G>A	c.(1597-1599)Gcc>Acc	p.A533T	ANKRD36_ENST00000420699.2_Missense_Mutation_p.A533T			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	533		NA								endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						TTCAAAAGCAGCCATGAGAAG	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													7	5	6	NA		NA	NA	2		NA											NA				97833468		679	1549	2228	SO:0001583	missense			BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976	375248		Ankyrin repeat domain containing	24079	protein-coding gene	gene with protein product		NA			NA	12975309	Standard		NM_001164315	NA	Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.1597G>A	chr2.hg19:g.97833468G>A	ENSP00000419530:p.Ala533Thr	NA	B4E3I8|Q6UX02|Q86X62|Q9HCD1	hg19	CCDS54379.1	0.02	14.558897	GCAxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	.	8.204	0.798820	0.16397	.	.	ENSG00000135976	ENST00000461153;ENST00000420699	T;T	0.76709	-1.04;-1.04	1.22	-0.841	0.10752	.	.	.	.	.	T	0.52025	0.1709	N	0.19112	0.55	0.09310	N	1	P	0.35700	0.516	B	0.20955	0.032	T	0.39333	-0.9619	9	0.41790	T	0.15	.	2.6585	0.05019	0.2227:0.3105:0.4669:0.0	.	533	A6QL64	AN36A_HUMAN	T	533	ENSP00000419530:A533T;ENSP00000391950:A533T	ENSP00000391950:A533T	A	+	1	0	ANKRD36	97197195	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.263000	0.18478	-0.309000	0.08779	-1.547000	0.00903	GCC	NOVEL	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339154.5	4	23.745978	KEEP	199	2	63	101	3692	GG	1	1	0		+	10	40	368	1	0	21.835534	342	50	12998	775	ENST00000461153.2	0.028409	1
INPP4A	3631	__UNKNOWN__	__UNKNOWN__	2	99163174	99163174	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:99163174G>A	ENST00000409016.4	+	13	1560				INPP4A_ENST00000409851.3_Intron|INPP4A_ENST00000409540.3_Intron|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000545415.1_Intron|INPP4A_ENST00000074304.5_Intron|INPP4A_ENST00000523221.1_Intron			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	NA		NA			inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						AGCCAGAGAGGGTTTGTGGTC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													44	43	43	NA		NA	NA	2		NA											NA				99163174		1854	4099	5953	SO:0001627	intron_variant			U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933	3631			6074	protein-coding gene	gene with protein product		600916	inositol polyphosphate-4-phosphatase, type I, 107kD	INPP4	NA	7608176, 9295334	Standard	NM_001566	NM_004027	NA	Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000409016.4:c.1163+17G>A	chr2.hg19:g.99163174G>A		NA	O15326|Q13187|Q53TD8|Q8TC02	hg19	CCDS46370.1	0.02	6.772987	GAGxGTT	COVERED																																																																																			NOVEL	INPP4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329566.2	1	9.868274	KEEP	0	0	0	33	1110	GG	0.999998	0.999998	0		+	8	60	306	0	0	20.413523	162	60	5742	260	ENST00000409016.4	0.047059	1
REV1	51455	__UNKNOWN__	__UNKNOWN__	2	100041322	100041322	__UNKNOWN__	Intron	SNP	C	C	G	rs541777179		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:100041322C>G	ENST00000258428.3	-	10	1776				REV1_ENST00000393445.3_Intron|REV1_ENST00000465835.1_Intron	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGTAGGACATCACTCTGGGCA	0.458	NA	NA						Direct reversal of damage						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945	51455		DNA polymerases	14060	protein-coding gene	gene with protein product		606134	REV1 (yeast homolog)- like, REV1-like (yeast), REV1 homolog (S. cerevisiae)	REV1L	NA	10536157	Standard	NM_016316	XM_005263968	NA	Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.1548-580G>C	chr2.hg19:g.100041322C>G		NA	O95941|Q53SI7|Q9C0J4|Q9NUP2	hg19	CCDS2045.1	0.02	12.182845	CATxACT	COVERED																																																																																			NOVEL	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253123.2	4	24.970698	KEEP	0	0	0	83	2884	CC	1	1	0		-	22	60	803	0	0	58.237048	235	60	8903	439	ENST00000258428.3	0.085603	1
PDCL3	79031	__UNKNOWN__	__UNKNOWN__	2	101188470	101188470	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:101188470G>A	ENST00000264254.6	+	5	955					NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3	NA		NA			angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)			endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						TTCAAGGAAGGCGTGATAGAC	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF267853	CCDS33261.1	2q12	2008-02-05			ENSG00000115539	ENSG00000115539	79031			28860	protein-coding gene	gene with protein product		611678			NA		Standard	NM_024065	NM_024065	NA	Approved	VIAF1	uc002tao.2	Q9H2J4	OTTHUMG00000153141	ENST00000264254.6:c.577+210G>A	chr2.hg19:g.101188470G>A		NA	B2RA00|Q53S68	hg19	CCDS33261.1	0.02	4.404958	AAGxCGT	COVERED																																																																																			NOVEL	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329734.1	0	4.514925	KEEP	0	0	0	15	547	GG	0.99649	0.996484	0		+	27	60	951	0	0	81.288526	84	70	2906	143	ENST00000264254.6	0.243243	0.999994
C2orf40	84417	__UNKNOWN__	__UNKNOWN__	2	106682254	106682254	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:106682254G>A	ENST00000409944.1	+	2	202				C2orf40_ENST00000489174.1_Intron|C2orf40_ENST00000238044.3_Missense_Mutation_p.A12T			Q9H1Z8	AUGN_HUMAN	chromosome 2 open reading frame 40	NA		NA			cellular senescence (GO:0090398)|cyclin catabolic process (GO:0008054)|G1 to G0 transition (GO:0070314)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)				lung(7)|urinary_tract(1)	8						TGCTGTCCTGGCCCTGACCGG	0.741	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	4	3	NA		NA	NA	2		NA											NA				106682254		1859	3718	5577	SO:0001627	intron_variant			BC021742	CCDS2072.1	2q12.2	2014-01-28			ENSG00000119147	ENSG00000119147	84417			24642	protein-coding gene	gene with protein product	esophageal cancer related gene 4 protein	611752			NA	12800218	Standard	NM_032411	NM_032411	NA	Approved	ECRG4, augurin	uc010fjf.3	Q9H1Z8	OTTHUMG00000130921	ENST00000409944.1:c.-30+1436G>A	chr2.hg19:g.106682254G>A		NA	D3DVK2	hg19		0.02	1.837879	CTGxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.55	1.383041	0.25031	.	.	ENSG00000119147	ENST00000238044	T	0.44482	0.92	4.28	4.28	0.50868	.	0.412070	0.19887	N	0.103821	T	0.27967	0.0689	N	0.22421	0.69	0.24938	N	0.991872	B	0.32245	0.361	B	0.31614	0.133	T	0.12553	-1.0543	10	0.25106	T	0.35	-12.1293	12.0666	0.53592	0.0:0.0:1.0:0.0	.	12	Q9H1Z8	AUGN_HUMAN	T	12	ENSP00000238044:A12T	ENSP00000238044:A12T	A	+	1	0	C2orf40	106048686	0.956000	0.32656	0.933000	0.37362	0.057000	0.15508	2.217000	0.42880	2.216000	0.71823	0.561000	0.74099	GCC	NOVEL	C2orf40-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000329791.1	0	9.63071	KEEP	0	0	0	32	1079	GG	0.999997	0.999937	0		+	12	60	401	0	0	30.432564	79	60	2711	160	ENST00000409944.1	0.131868	0.99994
SLC5A7	60482	__UNKNOWN__	__UNKNOWN__	2	108629307	108629307	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:108629307A>G	ENST00000264047.2	+	0	4009					NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	NA		NA			acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	GACACATAAAAGTAATTAATT	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665	60482		Solute carriers	14025	protein-coding gene	gene with protein product		608761	solute carrier family 5 (choline transporter), member 7		NA	11027560	Standard		NM_021815	NA	Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.*1990A>G	chr2.hg19:g.108629307A>G		NA	Q53TF2	hg19	CCDS2074.1	0.02	13.71002	AAAxGTA	COVERED																																																																																			NOVEL	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253562.1	2	9.92938	KEEP	0	0	0	33	1073	AA	0.999998	0.999998	0		+	20	60	742	0	0	51.262069	300	60	11201	419	ENST00000264047.2	0.0625	1
TMEM87B	84910	__UNKNOWN__	__UNKNOWN__	2	112849355	112849355	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:112849355T>C	ENST00000283206.4	+	11	1468	c.1099T>C	c.(1099-1101)Tgg>Cgg	p.W367R	TMEM87B_ENST00000463427.1_3'UTR	NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	367		NA				integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						CATTTTTGTGTGGTTCATATC	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													250	214	226	NA		NA	NA	2		NA											NA				112849355		2203	4298	6501	SO:0001583	missense			AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214	84910			25913	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032824	NM_032824	NA	Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.1099T>C	chr2.hg19:g.112849355T>C	ENSP00000283206:p.Trp367Arg	NA	A8K2M9|Q1RLN2|Q53R54	hg19	CCDS33275.1	0.02	2.118851	GTGxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	T	21.6	4.169133	0.78339	.	.	ENSG00000153214	ENST00000283206	.	.	.	5.74	5.74	0.90152	.	0.065749	0.64402	D	0.000003	T	0.78419	0.4280	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.81132	-0.1072	9	0.87932	D	0	-8.599	12.7238	0.57159	0.0:0.0:0.0:1.0	.	367	Q96K49	TM87B_HUMAN	R	367	.	ENSP00000283206:W367R	W	+	1	0	TMEM87B	112565826	1.000000	0.71417	0.955000	0.39395	0.967000	0.64934	6.856000	0.75450	2.317000	0.78254	0.460000	0.39030	TGG	NOVEL	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330500.1	1	7.822753	KEEP	0	0	0	26	805	TT	0.999957	0.999913	0		+	12	60	419	0	0	31.751265	87	60	3210	154	ENST00000283206.4	0.121212	0.999956
DPP10	57628	__UNKNOWN__	__UNKNOWN__	2	116600901	116600901	__UNKNOWN__	3'UTR	SNP	C	C	T	rs76588665	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:116600901C>T	ENST00000410059.1	+	0	3851				DPP10_ENST00000409163.1_3'UTR	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	NA		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						ATTTTGTTAACAATGCAATGC	0.299	NA	NA											C|||	66	0.0131789	8e-04	0.0029	5008	,	,	NA	15457	0.0238	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0399	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497	57628			20823	protein-coding gene	gene with protein product		608209	dipeptidylpeptidase 10, dipeptidyl-peptidase 10		NA	10819331, 12662155	Standard	NM_020868	NM_020868	NA	Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.*980C>T	chr2.hg19:g.116600901C>T		NA	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	hg19	CCDS46400.1	0.02	2.042017	TAAxAAT	COVERED																																																																																			NOVEL	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330580.4	1	3.009888	KEEP	0	0	0	10	363	CC	0.992708	0.992333	0		+	32	60	1125	0	0	103.320556	53	60	1944	105	ENST00000410059.1	0.376471	0.999622
LIMS2	55679	__UNKNOWN__	__UNKNOWN__	2	128401637	128401637	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:128401637C>A	ENST00000410038.1	-	2	217				LIMS2_ENST00000409254.1_Intron|LIMS2_ENST00000324938.5_Intron|LIMS2_ENST00000409808.2_Intron|LIMS2_ENST00000545738.2_Intron|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000409754.1_Intron|LIMS2_ENST00000355119.4_Intron|LIMS2_ENST00000410011.1_Intron	NM_001256542.1	NP_001243471.1	Q7Z4I7	LIMS2_HUMAN	LIM and senescent cell antigen-like domains 2	NA		NA			cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0681)		TCCCTGGACCCCAGGACCTGC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF520987	CCDS2147.1, CCDS54394.1, CCDS54395.1, CCDS54396.1, CCDS58725.1	2q21.1	2008-02-05			ENSG00000072163	ENSG00000072163	55679			16084	protein-coding gene	gene with protein product		607908			NA		Standard	NM_017980	NM_017980	NA	Approved		uc002tox.3	Q7Z4I7	OTTHUMG00000131529	ENST00000410038.1:c.97-990G>T	chr2.hg19:g.128401637C>A		NA	A6NLH0|B4DMV1|F5H6E6|Q7Z4I2|Q7Z4I6|Q7Z4I8|Q8NFE7|Q9HA13	hg19	CCDS58725.1	0.02	9.409745	ACCxCAG	COVERED																																																																																			NOVEL	LIMS2-006	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331115.1	0	16.490712	KEEP	0	0	0	55	1874	CC	1	1	0		-	48	60	1703	0	0	140.677598	196	60	6915	363	ENST00000410038.1	0.196721	1
SAP130	79595	__UNKNOWN__	__UNKNOWN__	2	128735513	128735513	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:128735513G>A	ENST00000259234.6	-	15	2247				SAP130_ENST00000357702.5_Intron|SAP130_ENST00000259235.3_Intron			Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	NA		NA			chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		CAACTGCAACGATGTGTGGGT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													78	76	76	NA		NA	NA	2		NA											NA				128735513		692	1591	2283	SO:0001627	intron_variant			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715	79595			29813	protein-coding gene	gene with protein product		609697	sin3A-associated protein, 130kDa		NA	11230166, 12724404	Standard	NM_024545	NM_001145928	NA	Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259234.6:c.2060+45C>T	chr2.hg19:g.128735513G>A		NA	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	hg19		0.02	4.347069	AACxATG	COVERED																																																																																			NOVEL	SAP130-002	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000254437.3	0	6.320199	KEEP	0	0	0	21	724	GG	0.999869	0.999869	0		-	9	60	338	0	0	23.590468	131	60	4645	202	ENST00000259234.6	0.064286	1
SAP130	79595	__UNKNOWN__	__UNKNOWN__	2	128784830	128784830	__UNKNOWN__	Intron	SNP	A	A	C	rs536678266	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:128784830A>C	ENST00000259234.6	-	1	181				SAP130_ENST00000357702.5_5'UTR|SAP130_ENST00000259235.3_5'UTR			Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	NA		NA			chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		GGCCCCACTCACCCCCGCCAC	0.801	NA	NA											A|||	18	0.00359425	0.0023	0.0029	5008	,	,	NA	4276	0.001	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0061	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715	79595			29813	protein-coding gene	gene with protein product		609697	sin3A-associated protein, 130kDa		NA	11230166, 12724404	Standard	NM_024545	NM_001145928	NA	Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259234.6:c.5+683T>G	chr2.hg19:g.128784830A>C		NA	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	hg19		0.02	-0.235829	CTCxCCC	COVERED																																																																																			NOVEL	SAP130-002	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000254437.3	0	2.716771	KEEP	0	1	16	15	355	AA	0.997832	0.639957	0		-	5	60	97	0	0	6.492149	22	60	529	59	ENST00000259234.6	0.185185	0.641347
HS6ST1	9394	__UNKNOWN__	__UNKNOWN__	2	129075877	129075877	__UNKNOWN__	5'UTR	SNP	G	G	T	rs200979099		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:129075877G>T	ENST00000494089.1	-	0	169				HS6ST1_ENST00000259241.6_Missense_Mutation_p.D87E			O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	NA		NA			angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		AGACGATCACGTCGTCGCCCT	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	16	14	NA		NA	NA	2		NA											NA				129075877		1658	4004	5662	SO:0001623	5_prime_UTR_variant			AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720	9394		Sulfotransferases, membrane-bound	5201	protein-coding gene	gene with protein product		604846		HS6ST	NA	9535912	Standard	NM_004807	NM_004807	NA	Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000494089.1:c.-416C>A	chr2.hg19:g.129075877G>T		NA	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	hg19		0.02	4.63937	CACxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	g	21.7	4.181914	0.78677	.	.	ENSG00000136720	ENST00000259241	T	0.74947	-0.89	3.69	2.78	0.32641	.	0.000000	0.85682	U	0.000000	D	0.84924	0.5580	M	0.88031	2.925	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	D	0.84908	0.0846	9	.	.	.	.	6.5213	0.22277	0.2434:0.0:0.7566:0.0	.	87	O60243	H6ST1_HUMAN	E	87	ENSP00000259241:D87E	.	D	-	3	2	HS6ST1	128792347	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	1.938000	0.40203	1.600000	0.50102	0.313000	0.20887	GAC	NOVEL	HS6ST1-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000331573.1	0	3.680713	KEEP	80	5	165	70	2287	GG	1	1	0		-	7	27	259	0	0	17.284137	129	60	4333	366	ENST00000494089.1	0.051471	1
CCDC74B	91409	__UNKNOWN__	__UNKNOWN__	2	130897559	130897559	__UNKNOWN__	Intron	SNP	C	C	A	rs2258632		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:130897559C>A	ENST00000310463.6	-	6	1088				CCDC74B_ENST00000392984.3_Intron|CCDC74B_ENST00000409943.3_Intron	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	NA		NA								endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					TGTGGATAGGCCCCCAGGGAT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													55	54	54	NA		NA	NA	2		NA											NA				130897559		2197	4289	6486	SO:0001627	intron_variant				CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076	91409			25267	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207310	NM_001258307	NA	Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.950+36G>T	chr2.hg19:g.130897559C>A		NA	Q6NW18	hg19	CCDS2155.1	0.02	3.781923	AGGxCCC	COVERED																																																																																			NOVEL	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254522.3	1	2.707506	KEEP	3	0	0	9	290	CC	0.99254	0.99254	0		-	18	40	597	0	0	45.932706	107	60	3758	159	ENST00000310463.6	0.144	0.999999
CCDC74B	91409	__UNKNOWN__	__UNKNOWN__	2	130900468	130900468	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:130900468T>C	ENST00000310463.6	-	2	433				CCDC74B_ENST00000392984.3_Missense_Mutation_p.M30V|CCDC74B_ENST00000409943.3_Intron|CCDC74B_ENST00000409128.1_Intron|CCDC74B_ENST00000409234.3_Silent_p.L223L	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	NA		NA								endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					CTCAGAGCCATAGGGCTGGAG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2155.1, CCDS58726.1	2q21.1	2006-11-29		2006-02-16	ENSG00000152076	ENSG00000152076	91409			25267	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207310	NM_001258307	NA	Approved	DKFZp434E2321	uc002tqn.2	Q96LY2	OTTHUMG00000131629	ENST00000310463.6:c.295+373A>G	chr2.hg19:g.130900468T>C		NA	Q6NW18	hg19	CCDS2155.1	0.02	12.626735	CCAxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	.	0	-2.590052	0.00126	.	.	ENSG00000152076	ENST00000392984	T	0.24723	1.84	1.81	-0.45	0.12223	.	1.145110	0.07403	N	0.891069	T	0.16727	0.0402	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	9	0.87932	D	0	.	3.0622	0.06203	0.0:0.5167:0.2851:0.1982	.	30	E7ESC5	.	V	30	ENSP00000376710:M30V	ENSP00000376710:M30V	M	-	1	0	CCDC74B	130616938	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.448000	0.02394	-0.328000	0.08539	-0.742000	0.03525	ATG	NOVEL	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254522.3	4	12.636056	KEEP	0	0	0	42	1272	TT	1	1	0		-	39	60	1501	0	0	121.562311	213	60	7516	347	ENST00000310463.6	0.154762	1
ARHGEF4	50649	__UNKNOWN__	__UNKNOWN__	2	131672563	131672563	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:131672563C>T	ENST00000409359.1	+	2	1252	c.54C>T	c.(52-54)ccC>ccT	p.P18P				Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	0		NA			apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CAGAGTGCCCCGAGGATCCCG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002	50649		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	684	protein-coding gene	gene with protein product	APC-stimulated guanine nucleotide exchange factor	605216			NA	10873612	Standard		NM_015320	NA	Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000409359.1:c.54C>T	chr2.hg19:g.131672563C>T		NA	Q9HDC6|Q9UPP0	hg19		0.02	15.394153	CCCxGAG	COVERED																																																																																			NOVEL	ARHGEF4-003	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000331307.2	3	9.629843	KEEP	0	0	0	32	1065	CC	0.999997	0.999997	0		+	10	60	378	0	0	22.78687	346	60	11597	449	ENST00000409359.1	0.02809	1
TUBA3D	113457	__UNKNOWN__	__UNKNOWN__	2	132240363	132240363	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:132240363A>G	ENST00000321253.6	+	5	1402	c.1295A>G	c.(1294-1296)tAt>tGt	p.Y432C		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	432		NA			'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GAGAAGGATTATGAAGAGGTG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(137;2059 2432 35543 39401)					NA		NA				0													142	144	143	NA		NA	NA	2		NA											NA				132240363		2203	4300	6503	SO:0001583	missense			K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886	113457		Tubulins	24071	protein-coding gene	gene with protein product	alpha-tubulin isotype H2-alpha	NA			NA	3785200	Standard	NM_080386	NM_080386	NA	Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.1295A>G	chr2.hg19:g.132240363A>G	ENSP00000326042:p.Tyr432Cys	NA	A6NJQ0|Q5W099|Q6PEY3|Q96F18	hg19	CCDS33290.1	0.02	18.682602	ATTxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	g	8.730	0.916383	0.17907	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	D	0.94497	-3.44	2.41	2.41	0.29592	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.43416	U	0.000561	D	0.98185	0.9400	H	0.99435	4.565	0.47621	D	0.999475	D	0.71674	0.998	D	0.79784	0.993	D	0.96794	0.9584	10	0.72032	D	0.01	.	8.339	0.32232	1.0:0.0:0.0:0.0	.	432	Q13748	TBA3C_HUMAN	C	432;400	ENSP00000326042:Y432C	ENSP00000326042:Y432C	Y	+	2	0	TUBA3D	131956833	1.000000	0.71417	0.986000	0.45419	0.199000	0.23934	5.545000	0.67237	1.095000	0.41419	0.163000	0.16589	TAT	NOVEL	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331800.2	6	5.041023	KEEP	10	7	229	97	2937	AA	1	1	0		+	14	27	535	0	0	33.47697	410	60	14491	649	ENST00000321253.6	0.033019	1
NCKAP5	344148	__UNKNOWN__	__UNKNOWN__	2	134275142	134275142	__UNKNOWN__	De_novo_Start_OutOfFrame	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:134275142G>A	ENST00000409261.1	-	0	329				NCKAP5_ENST00000409213.1_De_novo_Start_OutOfFrame	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	NA		NA								NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						AGAATCCCCCGTCTGTTTCCA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													30	29	30	NA		NA	NA	2		NA											NA				134275142		1786	3983	5769					AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771	344148			29847	protein-coding gene	gene with protein product	Nck associated protein 5, peripheral clock protein	608789			NA	9344857	Standard	NM_207481	NM_207363	NA	Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.-45C>T	chr2.hg19:g.134275142G>A		NA	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	hg19	CCDS46418.1	0.02	21.125912	CCCxTCT	COVERED																																																																																			NOVEL	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331663.1	3	24.078034	KEEP	0	0	0	80	2803	GG	1	1	0		-	56	60	2057	0	0	157.028342	430	70	15364	695	ENST00000409261.1	0.115226	1
UBXN4	23190	__UNKNOWN__	__UNKNOWN__	2	136541329	136541329	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:136541329C>A	ENST00000272638.9	+	0	2710				UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	NA		NA			response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						TACACAAGGACCTAGAGTACC	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224	23190		UBX domain containing	14860	protein-coding gene	gene with protein product	erasin	611216	UBX domain-containing 2, UBX domain containing 2	UBXDC1, UBXD2	NA	16968747	Standard	NM_014607	NM_014607	NA	Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.*872C>A	chr2.hg19:g.136541329C>A		NA	A8K9W4|Q4ZG56|Q8IYM5	hg19	CCDS42761.1	0.02	4.618923	GGAxCTA	COVERED																																																																																			NOVEL	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331696.1	3	5.717831	KEEP	0	0	0	19	641	CC	0.99986	0.999851	0		+	47	60	1682	0	0	158.260592	62	60	2251	153	ENST00000272638.9	0.431193	0.999992
LCT	3938	__UNKNOWN__	__UNKNOWN__	2	136579705	136579705	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:136579705G>A	ENST00000264162.2	-	5	918				AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	NA		NA			carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CTATGTAAATGCCAACTAAGA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	83	82	NA		NA	NA	2		NA											NA				136579705		2203	4300	6503	SO:0001627	intron_variant			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3938	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202			NA		Standard	NM_002299	NM_002299	NA	Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.908-37C>T	chr2.hg19:g.136579705G>A		NA	Q4ZG58	hg19	CCDS2178.1	0.02	13.179753	AATxCCA	COVERED																																																																																			NOVEL	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254657.1	0	12.374563	KEEP	0	1	28	51	1836	GG	1	1	0		-	125	60	4365	0	0	399.770084	211	60	8022	468	ENST00000264162.2	0.372024	1
LRP1B	53353	__UNKNOWN__	__UNKNOWN__	2	141032028	141032028	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:141032028G>A	ENST00000389484.3	-	85	14078	c.13107C>T	c.(13105-13107)tgC>tgT	p.C4369C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4369	EGF-like 21. {ECO:0000255|PROSITE- ProRule:PRU00076}.	NA			protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TATTTATAATGCAGTGCCCCC	0.418	NA	NA								TSP Lung(27;0.18)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(99;50 2074 2507 20106)					NA		NA				0													136	121	126	NA		NA	NA	2		NA											NA				141032028		2203	4300	6503	SO:0001819	synonymous_variant			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702	53353		Low density lipoprotein receptors	6693	protein-coding gene	gene with protein product	LRP-deleted in tumors	608766			NA	10766186	Standard	NM_018557	NM_018557	NA	Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.13107C>T	chr2.hg19:g.141032028G>A		NA	Q8WY29|Q8WY30|Q8WY31	hg19	CCDS2182.1	0.02	11.219326	AATxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.912	1.209822	0.22289	.	.	ENSG00000168702	ENST00000437977;ENST00000442974	.	.	.	5.32	2.75	0.32379	.	.	.	.	.	T	0.57227	0.2039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48340	-0.9044	4	.	.	.	.	8.005	0.30319	0.4532:0.0:0.5468:0.0	.	.	.	.	V	601;101	.	.	A	-	2	0	LRP1B	140748498	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.298000	0.33412	0.227000	0.20999	0.655000	0.94253	GCA	NOVEL	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254736.2	3	12.039529	KEEP	0	0	0	40	1454	GG	1	1	0		-	26	60	928	0	0	68.927034	225	60	8611	358	ENST00000389484.3	0.103586	1
LRP1B	53353	__UNKNOWN__	__UNKNOWN__	2	141108328	141108328	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:141108328A>G	ENST00000389484.3	-	77	12864					NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	NA		NA			protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GGTGGGGAAAAGGTATGGACT	0.299	NA	NA								TSP Lung(27;0.18)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(99;50 2074 2507 20106)					NA		NA				0													42	42	42	NA		NA	NA	2		NA											NA				141108328		2199	4298	6497	SO:0001627	intron_variant			AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702	53353		Low density lipoprotein receptors	6693	protein-coding gene	gene with protein product	LRP-deleted in tumors	608766			NA	10766186	Standard	NM_018557	NM_018557	NA	Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.11892+37T>C	chr2.hg19:g.141108328A>G		NA	Q8WY29|Q8WY30|Q8WY31	hg19	CCDS2182.1	0.02	4.628069	AAAxGGT	COVERED																																																																																			NOVEL	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254736.2	0	4.212522	KEEP	0	0	0	14	452	AA	0.995343	0.995334	0		-	24	60	867	0	0	73.31362	84	60	2997	140	ENST00000389484.3	0.222222	0.999991
KIF5C	3800	__UNKNOWN__	__UNKNOWN__	2	149850977	149850977	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:149850977A>G	ENST00000435030.1	+	17	2316	c.1948A>G	c.(1948-1950)Atg>Gtg	p.M650V	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000414838.2_Missense_Mutation_p.M555V|KIF5C_ENST00000397413.1_Missense_Mutation_p.M418V			O60282	KIF5C_HUMAN	kinesin family member 5C	650		NA			ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CATGCAGAACATGGAACAGAA	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	42	41	NA		NA	NA	2		NA											NA				149850977		1986	4168	6154	SO:0001583	missense			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280	3800		Kinesins	6325	protein-coding gene	gene with protein product		604593			NA	7514426	Standard	NM_004522	NM_004522	NA	Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.1948A>G	chr2.hg19:g.149850977A>G	ENSP00000393379:p.Met650Val	NA	O95079|Q2YDC5	hg19		0.02	7.330292	AACxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	2.353	-0.348372	0.05208	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	T;T;T	0.74106	-0.81;-0.81;-0.81	5.31	5.31	0.75309	.	0.141330	0.64402	D	0.000008	T	0.63379	0.2506	.	.	.	0.37317	D	0.909402	B;B	0.15141	0.0;0.012	B;B	0.11329	0.001;0.006	T	0.61860	-0.6976	8	.	.	.	.	15.4391	0.75168	1.0:0.0:0.0:0.0	.	650;216	O60282;Q3LIE3	KIF5C_HUMAN;.	V	650;555;553;418	ENSP00000393379:M650V;ENSP00000410115:M555V;ENSP00000380560:M418V	.	M	+	1	0	KIF5C	149559223	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.920000	0.40025	2.219000	0.72066	0.528000	0.53228	ATG	NOVEL	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000332562.3	0	12.939073	KEEP	0	0	0	43	1361	AA	1	1	0		+	35	60	1253	0	0	102.945855	151	60	5691	307	ENST00000435030.1	0.188172	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	151324699	151324699	__UNKNOWN__	IGR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:151324699A>G			NA	NA				AC016682.1 (167105 upstream) : RND3 (9 downstream)						NA		NA									NA						ATAATAAAAGACAGATCACAT	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.151324699A>G		NA		hg19		0.02	2.127595	AAGxCAG	COVERED																																																																																			NOVEL					0			3	9.630479	KEEP	0	0	0	32	1064	AA	0.999997	0.999946	0			20	60	725	0	0	60.50794	78	60	2782	149		0.204082	0.999948
CYTIP	9595	__UNKNOWN__	__UNKNOWN__	2	158272613	158272613	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:158272613T>C	ENST00000264192.3	-	8	777	c.656A>G	c.(655-657)gAt>gGt	p.D219G	CYTIP_ENST00000540637.1_Missense_Mutation_p.D113G	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	219		NA			regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						AGACAATTCATCCAAGTCCAT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													55	49	51	NA		NA	NA	2		NA											NA				158272613		2203	4300	6503	SO:0001583	missense			L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165	9595			9506	protein-coding gene	gene with protein product	cytohesin binding protein HE, cytohesin binder and regulator	604448	pleckstrin homology, Sec7 and coiled-coil domains, binding protein	PSCDBP	NA	18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288	NM_004288	NA	Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.656A>G	chr2.hg19:g.158272613T>C	ENSP00000264192:p.Asp219Gly	NA	B4DWH9|Q15630|Q8NE32	hg19	CCDS2204.1	0.02	4.729358	TCAxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	T	6.781	0.513027	0.12944	.	.	ENSG00000115165	ENST00000264192;ENST00000540637;ENST00000418920	T;T;T	0.42513	2.27;0.97;1.44	5.71	4.55	0.56014	.	0.780131	0.12451	N	0.467781	T	0.34600	0.0903	L	0.44542	1.39	0.44843	D	0.997858	B	0.06786	0.001	B	0.06405	0.002	T	0.08371	-1.0725	10	0.22706	T	0.39	-12.1431	10.8914	0.46998	0.0:0.0757:0.0:0.9243	.	219	O60759	CYTIP_HUMAN	G	219;113;113	ENSP00000264192:D219G;ENSP00000440801:D113G;ENSP00000394308:D113G	ENSP00000264192:D219G	D	-	2	0	CYTIP	157980859	0.999000	0.42202	0.989000	0.46669	0.046000	0.14306	3.622000	0.54217	2.180000	0.69256	0.533000	0.62120	GAT	NOVEL	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254926.1	5	10.532752	KEEP	0	0	0	35	1147	TT	0.999999	0.999998	0		-	27	60	961	0	0	78.99267	115	60	4193	214	ENST00000264192.3	0.190141	1
LY75-CD302	100526664	__UNKNOWN__	__UNKNOWN__	2	160750452	160750452	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A	rs371307279		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:160750452G>A	ENST00000504764.1	-	3	637	c.610C>T	c.(610-612)Cga>Tga	p.R204*	LY75_ENST00000263636.4_Nonsense_Mutation_p.R204*|LY75_ENST00000553424.1_Nonsense_Mutation_p.R204*|LY75-CD302_ENST00000505052.1_Nonsense_Mutation_p.R204*|LY75_ENST00000554112.1_Nonsense_Mutation_p.R204*	NM_001198759.1	NP_001185688.1			LY75-CD302 readthrough	NA		NA									NA						CCCCACTTTCGGTCATATTCA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	93	95	NA		NA	NA	2		NA											NA				160750452		2203	4300	6503	SO:0001587	stop_gained				CCDS56140.1, CCDS56141.1	2q24.2	2011-04-19			ENSG00000248672	ENSG00000248672	100526664			38828	other	readthrough		NA			NA		Standard		NM_001198759	NA	Approved		uc002ubb.4		OTTHUMG00000161661	ENST00000504764.1:c.610C>T	chr2.hg19:g.160750452G>A	ENSP00000423463:p.Arg204*	NA		hg19	CCDS56141.1	0.02	17.524743	TTCxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165218	0.78339	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	.	.	.	5.54	2.5	0.30297	.	0.806422	0.10081	N	0.718454	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	-4.4453	8.3792	0.32461	0.0:0.322:0.4509:0.2271	.	.	.	.	X	204	.	ENSP00000423463:R204X	R	-	1	2	LY75;LY75-CD302	160458698	0.434000	0.25570	0.995000	0.50966	0.555000	0.35460	0.440000	0.21592	0.772000	0.33382	0.557000	0.71058	CGA	NOVEL	LY75-CD302-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365654.1	0	16.217448	KEEP	0	0	0	54	1833	GG	1	1	0		-	89	60	3383	0	0	294.347111	263	60	9111	534	ENST00000504764.1	0.252841	1
DPP4	1803	__UNKNOWN__	__UNKNOWN__	2	162875825	162875825	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:162875825T>G	ENST00000360534.3	-	15	1805					NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	NA		NA			cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	ttaattatgttttttaaGAAG	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													9	10	10	NA		NA	NA	2		NA											NA				162875825		2083	4216	6299	SO:0001627	intron_variant			M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	1803	3.4.14.5	CD molecules	3009	protein-coding gene	gene with protein product		102720	dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2), adenosine deaminase complexing protein 2	CD26, ADCP2	NA	8101391	Standard		NM_001935	NA	Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.1245-39A>C	chr2.hg19:g.162875825T>G		NA	Q53TN1	hg19	CCDS2216.1	0.02	-0.429872	TGTxTTT	COVERED																																																																																			NOVEL	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255079.2	1	12.937685	KEEP	0	0	0	43	1330	TT	1	0.954491	0		-	25	60	936	0	0	90.780191	24	60	862	115	ENST00000360534.3	0.510204	0.954491
XIRP2	129446	__UNKNOWN__	__UNKNOWN__	2	168100955	168100955	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:168100955G>T	ENST00000409728.1	+	9	1364				XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409195.1_Missense_Mutation_p.R1018M|XIRP2_ENST00000295237.9_Missense_Mutation_p.R1018M|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R796M|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	NA		NA			actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGAAGCTGTAGGTGGCTTTTT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	63	64	NA		NA	NA	2		NA											NA				168100955		1857	4099	5956	SO:0001627	intron_variant			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092	129446			14303	protein-coding gene	gene with protein product	myomaxin	609778	cardiomyopathy associated 3	CMYA3	NA	17046827, 12203715, 15454575	Standard	NM_152381	NM_001079810	NA	Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.1275+2535G>T	chr2.hg19:g.168100955G>T		NA	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	hg19	CCDS56143.1	0.02	12.044839	GTAxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437280	0.43224	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.39056	1.1;1.1;1.1	6.08	6.08	0.98989	.	0.046390	0.85682	D	0.000000	T	0.62708	0.2450	M	0.70595	2.14	0.39880	D	0.973629	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.98;0.98	T	0.66056	-0.6018	10	0.87932	D	0	-14.8076	12.7223	0.57149	0.0757:0.0:0.9243:0.0	.	843;843;796	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	M	1018;1018;796	ENSP00000386840:R1018M;ENSP00000295237:R1018M;ENSP00000387255:R796M	ENSP00000295237:R1018M	R	+	2	0	XIRP2	167809201	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.160000	0.50739	2.894000	0.99253	0.655000	0.94253	AGG	NOVEL	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333552.1	4	12.626333	KEEP	0	0	0	42	1477	GG	1	1	0		+	54	60	2053	0	0	172.133785	219	60	8084	385	ENST00000409728.1	0.197802	1
CERS6	253782	__UNKNOWN__	__UNKNOWN__	2	169628381	169628381	__UNKNOWN__	3'UTR	SNP	C	C	T	rs190339315	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:169628381C>T	ENST00000305747.6	+	0	3951				CERS6_ENST00000392687.4_3'UTR	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)				NA						AATCATTTTTCCCCCCAGAAG	0.388	NA	NA											C|||	3	0.000599042	0	0.0014	5008	,	,	NA	17635	0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292	253782		Homeoboxes / CERS class	23826	protein-coding gene	gene with protein product		615336	LAG1 longevity assurance homolog 6 (S. cerevisiae), LAG1 homolog, ceramide synthase 6	LASS6	NA		Standard	NM_203463	NM_203463	NA	Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.*2209C>T	chr2.hg19:g.169628381C>T		NA	Q32M63|Q8N617	hg19	CCDS2228.1	0.02	11.250397	TTTxCCC	COVERED																																																																																			NOVEL	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255235.2	2	18.058309	KEEP	0	0	0	60	2099	CC	1	1	0		+	18	60	659	0	0	45.098845	276	60	10207	460	ENST00000305747.6	0.061224	1
LRP2	4036	__UNKNOWN__	__UNKNOWN__	2	170009286	170009286	__UNKNOWN__	Intron	SNP	G	G	A	rs375334036		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:170009286G>A	ENST00000263816.3	-	67	12747					NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	NA		NA			cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)	AACAGGTAAGGGGGGAATGTA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													127	117	120	NA		NA	NA	2		NA											NA				170009286		2203	4300	6503	SO:0001627	intron_variant				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479	4036		Low density lipoprotein receptors	6694	protein-coding gene	gene with protein product	megalin	600073			NA	7959795	Standard	NM_004525	NM_004525	NA	Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12461+22C>T	chr2.hg19:g.170009286G>A		NA	O00711|Q16215	hg19	CCDS2232.1	0.02	7.083418	AAGxGGG	COVERED																																																																																			NOVEL	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255231.2	1	8.427223	KEEP	0	0	0	28	976	GG	0.999997	0.999997	0		-	32	60	1184	0	0	97.087751	148	60	5285	259	ENST00000263816.3	0.177778	1
RP11-724O16.1	0	__UNKNOWN__	__UNKNOWN__	2	170366209	170366209	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:170366209T>C	ENST00000513963.1	+	12	998				BBS5_ENST00000554017.1_Intron						NA		NA									NA						CACACTGATCTGCCTTTTTAC	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000513963.1:c.925-4875T>C	chr2.hg19:g.170366209T>C		NA		hg19		0.02	11.167753	ATCxGCC	COVERED																																																																																			NOVEL	RP11-724O16.1-001	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000368400.1	5	18.054031	KEEP	0	0	0	60	1924	TT	1	1	0		+	56	60	1982	0	0	162.845679	237	60	8981	454	ENST00000513963.1	0.191126	1
UBR3	130507	__UNKNOWN__	__UNKNOWN__	2	170684030	170684030	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:170684030G>T	ENST00000272793.5	+	1	63	c.13G>T	c.(13-15)Gcc>Tcc	p.A5S	UBR3_ENST00000418381.1_Missense_Mutation_p.A5S			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	5	Ala-rich.	NA			embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						ggcggcggcggccgcggcggc	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													1	1	1	NA		NA	NA	2		NA											NA				170684030		69	158	227	SO:0001583	missense			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357	130507		Ubiquitin protein ligase E3 component n-recognins	30467	protein-coding gene	gene with protein product		613831	zinc finger protein 650	ZNF650	NA	17462990	Standard	NM_172070	NM_172070	NA	Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.13G>T	chr2.hg19:g.170684030G>T	ENSP00000272793:p.Ala5Ser	NA	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	hg19		0.02	-0.147777	GCGxCCG	COVERED	.	.	.	.	.	.	.	.	.	.	g	15.72	2.917845	0.52546	.	.	ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381	T;T	0.55588	0.51;0.51	3.43	3.43	0.39272	.	.	.	.	.	T	0.34135	0.0887	N	0.14661	0.345	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.11792	-1.0573	9	0.24483	T	0.36	.	13.1609	0.59544	0.0:0.0:1.0:0.0	.	5	Q6ZT12	UBR3_HUMAN	S	5	ENSP00000272793:A5S;ENSP00000396068:A5S	ENSP00000272793:A5S	A	+	1	0	UBR3	170392276	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.012000	0.57131	1.852000	0.53769	0.450000	0.29827	GCC	NOVEL	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000255290.2	1	3.912525	KEEP	0	0	0	13	442	GG	0.994391	0.290363	0		+	3	60	102	0	0	8.205462	14	60	481	46	ENST00000272793.5	0.176471	0.292001
AC007405.2	0	__UNKNOWN__	__UNKNOWN__	2	171570634	171570634	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:171570634C>T	ENST00000409786.1	-	1	443	c.320G>A	c.(319-321)gGg>gAg	p.G107E							NA		NA									NA						AAAGCACGCCCCGCGCCTGGT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000409786.1:c.320G>A	chr2.hg19:g.171570634C>T	ENSP00000387118:p.Gly107Glu	NA		hg19		0.02	7.072852	GCCxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	7.302	0.613168	0.14066	.	.	ENSG00000222033	ENST00000409786	.	.	.	2.5	0.625	0.17665	.	.	.	.	.	T	0.28732	0.0712	.	.	.	.	.	.	P	0.50943	0.94	B	0.43809	0.432	T	0.33954	-0.9848	6	0.87932	D	0	.	3.0513	0.06169	0.2649:0.5814:0.0:0.1536	.	107	E9PB92	.	E	107	.	ENSP00000387118:G107E	G	-	2	0	AC007405.2	171278880	0.000000	0.05858	0.001000	0.08648	0.102000	0.19082	0.408000	0.21065	0.154000	0.19237	0.462000	0.41574	GGG	NOVEL	AC007405.2-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000333672.1	2	24.075972	KEEP	0	0	0	80	2700	CC	1	1	0		-	10	60	373	0	0	25.590372	159	60	5515	308	ENST00000409786.1	0.059172	1
AC007405.2	0	__UNKNOWN__	__UNKNOWN__	2	171570643	171570643	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:171570643G>A	ENST00000409786.1	-	1	434	c.311C>T	c.(310-312)aCc>aTc	p.T104I							NA		NA									NA						CCCGCGCCTGGTGAGGAACTT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000409786.1:c.311C>T	chr2.hg19:g.171570643G>A	ENSP00000387118:p.Thr104Ile	NA		hg19		0.02	6.115256	CTGxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.068	0.567696	0.13560	.	.	ENSG00000222033	ENST00000409786	.	.	.	3.14	-1.15	0.09709	.	.	.	.	.	T	0.24236	0.0587	.	.	.	.	.	.	P	0.41848	0.763	B	0.38803	0.282	T	0.22871	-1.0204	6	0.87932	D	0	.	3.596	0.08006	0.1925:0.0:0.2034:0.6041	.	104	E9PB92	.	I	104	.	ENSP00000387118:T104I	T	-	2	0	AC007405.2	171278889	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.395000	0.07287	-0.214000	0.10078	0.462000	0.41574	ACC	NOVEL	AC007405.2-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000333672.1	2	25.57971	KEEP	0	0	0	85	2877	GG	1	1	0		-	12	60	414	0	0	27.814684	174	60	6179	329	ENST00000409786.1	0.064516	1
METAP1D	254042	__UNKNOWN__	__UNKNOWN__	2	172946113	172946113	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:172946113C>A	ENST00000315796.4	+	0	2374					NM_199227.1	NP_954697.1	Q6UB28	MAP12_HUMAN	methionyl aminopeptidase type 1D (mitochondrial)	NA		NA			N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|protein initiator methionine removal (GO:0070084)	mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235)			NS(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)	8						CGAGAGGGTCCCAGAGAGAGG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY374142, BC029123	CCDS2246.1	2q31.1	2010-09-21			ENSG00000172878	ENSG00000172878	254042			32583	protein-coding gene	gene with protein product	methionine aminopeptidase 1D	610267			NA	14532271, 16568094	Standard	NM_199227	NM_199227	NA	Approved	MAP1D, Metap1l	uc002uhk.3	Q6UB28	OTTHUMG00000132283	ENST00000315796.4:c.*979C>A	chr2.hg19:g.172946113C>A		NA	Q1WNX3	hg19	CCDS2246.1	0.02	9.073583	GTCxCAG	COVERED																																																																																			NOVEL	METAP1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255378.2	2	21.004275	KEEP	0	0	0	70	2371	CC	1	1	0		+	27	60	964	0	0	72.932085	208	60	7054	365	ENST00000315796.4	0.114894	1
NFE2L2	4780	__UNKNOWN__	__UNKNOWN__	2	178097478	178097478	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:178097478A>G	ENST00000446151.2	-	4	527				NFE2L2_ENST00000464747.1_Intron|NFE2L2_ENST00000423513.1_3'UTR|NFE2L2_ENST00000397062.3_Intron|NFE2L2_ENST00000397063.4_Intron			Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	NA		NA			cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TTCCTACCCCACTGACTCAAA	0.328	NA	NA	Mis		NSCLC, HNSCC					HNSCC(56;0.16)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044	4780		basic leucine zipper proteins	7782	protein-coding gene	gene with protein product	NF-E2-related factor 2	600492	nuclear factor (erythroid-derived 2)-like 2		NA	7937919	Standard	NM_006164	NM_006164	NA	Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000446151.2:c.355-188T>C	chr2.hg19:g.178097478A>G		NA	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	hg19	CCDS46458.1	0.02	7.159166	CCCxCTG	COVERED																																																																																			NOVEL	NFE2L2-008	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334263.1	8	16.851414	KEEP	0	0	0	56	1776	AA	1	1	0		-	26	60	938	0	0	75.374142	134	60	4712	266	ENST00000446151.2	0.1625	1
TTC30B	150737	__UNKNOWN__	__UNKNOWN__	2	178415851	178415851	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:178415851A>T	ENST00000408939.3	-	1	1891	c.1641T>A	c.(1639-1641)aaT>aaA	p.N547K		NM_152517.2	NP_689730.2	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	547		NA			cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				cervix(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			CTATCACCAAATTCACAATGC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													211	223	219	NA		NA	NA	2		NA											NA				178415851		2203	4300	6503	SO:0001583	missense			AK055552	CCDS42784.1	2q31.2	2014-02-21			ENSG00000196659	ENSG00000196659	150737		Tetratricopeptide (TTC) repeat domain containing, Intraflagellar transport homologs	26425	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152517	NM_152517	NA	Approved	FLJ30990, fleer, IFT70	uc002uln.3	Q8N4P2	OTTHUMG00000154166	ENST00000408939.3:c.1641T>A	chr2.hg19:g.178415851A>T	ENSP00000386181:p.Asn547Lys	NA	Q63HQ1|Q96NE6	hg19	CCDS42784.1	0.02	18.397271	CAAxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	14.40	2.524176	0.44866	.	.	ENSG00000196659	ENST00000500357;ENST00000408939	T	0.23552	1.9	4.87	1.2	0.21068	.	0.000000	0.85682	D	0.000000	T	0.52092	0.1713	M	0.90252	3.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51965	-0.8638	10	0.59425	D	0.04	.	8.4386	0.32801	0.6539:0.0:0.3461:0.0	.	547	Q8N4P2	TT30B_HUMAN	K	500;547	ENSP00000386181:N547K	ENSP00000386181:N547K	N	-	3	2	TTC30B	178124097	0.955000	0.32602	0.996000	0.52242	0.992000	0.81027	0.733000	0.26087	0.107000	0.17824	-0.256000	0.11100	AAT	NOVEL	TTC30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334193.2	11	40.621384	KEEP	1	0	0	135	4362	AA	1	1	0		-	85	60	3127	0	0	259.018904	360	60	12987	713	ENST00000408939.3	0.191011	1
TTC30A	92104	__UNKNOWN__	__UNKNOWN__	2	178481391	178481391	__UNKNOWN__	3'UTR	SNP	C	C	T	rs202031677	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:178481391C>T	ENST00000355689.5	-	0	2303				AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	NA		NA			cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				autonomic_ganglia(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(117;0.000423)|Epithelial(96;0.00373)|all cancers(119;0.0169)			AAGTGTGGTACGTAAGAAAGC	0.313	NA	NA											c|||	8	0.00159744	0	0	5008	,	,	NA	21499	0.001	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA						NA		NA				0								T		0,4404		0,0,2202	77	76	76	NA		-8.2	0	2		76	15,8585	10.5+/-38.8	0,15,4285	no	utr-3	TTC30A	NM_152275.3		0,15,6487	TT,TC,CC	NA	0.1744,0.0,0.1153			178481391	15,12989	2202	4300	6502	SO:0001624	3_prime_UTR_variant			AK024008	CCDS2276.1	2q31.2	2013-01-11			ENSG00000197557	ENSG00000197557	92104		Tetratricopeptide (TTC) repeat domain containing	25853	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152275	NM_152275	NA	Approved	FLJ13946	uc002ulo.3	Q86WT1	OTTHUMG00000132528	ENST00000355689.5:c.*41G>A	chr2.hg19:g.178481391C>T		NA	A8K8N0|Q8IVP2	hg19	CCDS2276.1	0.02	21.417683	GTAxGTA	COVERED																																																																																			NOVEL	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255728.2	9	46.482782	KEEP	0	1	33	166	5725	CC	1	1	0		-	54	60	2014	0	0	153.564859	432	60	15603	847	ENST00000355689.5	0.111111	1
DFNB59	494513	__UNKNOWN__	__UNKNOWN__	2	179325792	179325792	__UNKNOWN__	Missense_Mutation	SNP	A	A	C	rs529801316		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:179325792A>C	ENST00000409117.3	+	7	1206	c.850A>C	c.(850-852)Atg>Ctg	p.M284L	DFNB59_ENST00000375129.4_Missense_Mutation_p.M284L	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	284		NA			sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			ACCTCTCAGCATGACTGATAT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													219	197	203	NA		NA	NA	2		NA											NA				179325792		1860	4107	5967	SO:0001583	missense			BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311	494513			29502	protein-coding gene	gene with protein product		610219			NA	16804542	Standard		NM_001042702	NA	Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.850A>C	chr2.hg19:g.179325792A>C	ENSP00000386647:p.Met284Leu	NA	A0PK14|B9EJE2	hg19	CCDS42787.1	0.02	19.373145	AGCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	17.36	3.370270	0.61624	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.58652	0.32;0.32	5.93	5.93	0.95920	.	0.000000	0.64402	U	0.000001	T	0.43919	0.1269	L	0.29908	0.895	0.51767	D	0.999936	B	0.02656	0.0	B	0.04013	0.001	T	0.33317	-0.9873	10	0.20046	T	0.44	-0.4457	12.0431	0.53464	0.8709:0.0:0.0:0.1291	.	284	Q0ZLH3	PJVK_HUMAN	L	284	ENSP00000386647:M284L;ENSP00000364271:M284L	ENSP00000364271:M284L	M	+	1	0	DFNB59	179034038	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.841000	0.69409	2.270000	0.75569	0.460000	0.39030	ATG	NOVEL	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335160.1	9	16.850422	KEEP	0	0	0	56	1754	AA	1	1	0		+	73	60	2726	0	0	224.717285	329	60	12212	558	ENST00000409117.3	0.181592	1
TTN	7273	__UNKNOWN__	__UNKNOWN__	2	179432133	179432133	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:179432133T>C	ENST00000589042.1	-	326	78950	c.78726A>G	c.(78724-78726)atA>atG	p.I26242M	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I17369M|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.I24601M|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I17302M|TTN_ENST00000460472.2_Missense_Mutation_p.I17177M|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I23674M	NM_001267550.1	NP_001254479.1	Q8WZ42	TITIN_HUMAN	titin	24601	Fibronectin type-III 91. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGTGTTCTTTATTTCACATC	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													138	142	141	NA		NA	NA	2		NA											NA				179432133		1840	4088	5928	SO:0001583	missense			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657	7273		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	12403	protein-coding gene	gene with protein product		188840	cardiomyopathy, dilated 1G (autosomal dominant)	CMD1G	NA	2129545, 10051295	Standard	NM_133378	NM_003319	NA	Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000589042.1:c.78726A>G	chr2.hg19:g.179432133T>C	ENSP00000467141:p.Ile26242Met	NA	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	hg19	CCDS59435.1	0.02	14.850673	CTTxATT	COVERED	.	.	.	.	.	.	.	.	.	.	T	7.549	0.662391	0.14645	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.41	4.22	0.49857	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73210	0.3558	L	0.58925	1.835	0.42711	D	0.993641	D;D;D;D	0.61080	0.989;0.989;0.989;0.979	D;D;D;P	0.63283	0.913;0.913;0.913;0.876	T	0.73694	-0.3902	9	0.87932	D	0	.	6.6938	0.23187	0.1352:0.073:0.0:0.7918	.	17177;17302;17369;24601	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	23674;17177;17369;17302;17175	ENSP00000343764:I23674M;ENSP00000434586:I17177M;ENSP00000340554:I17369M;ENSP00000352154:I17302M	ENSP00000340554:I17369M	I	-	3	3	TTN	179140379	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.466000	0.35310	0.847000	0.35167	0.459000	0.35465	ATA	NOVEL	TTN-018	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450680.2	8	18.955914	KEEP	0	0	0	63	1939	TT	1	1	0		-	37	60	1422	0	0	109.111104	302	60	10780	450	ENST00000589042.1	0.109145	1
TTN	7273	__UNKNOWN__	__UNKNOWN__	2	179455289	179455289	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs397517648		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:179455289G>A	ENST00000589042.1	-	304	61387	c.61163C>T	c.(61162-61164)gCt>gTt	p.A20388V	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A11515V|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.A18747V|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A11448V|TTN_ENST00000460472.2_Missense_Mutation_p.A11323V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A17820V	NM_001267550.1	NP_001254479.1	Q8WZ42	TITIN_HUMAN	titin	18747	Fibronectin type-III 47. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACCAAATCAGCTGTTTCTCT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													104	105	105	NA		NA	NA	2		NA											NA				179455289		1937	4137	6074	SO:0001583	missense			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657	7273		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	12403	protein-coding gene	gene with protein product		188840	cardiomyopathy, dilated 1G (autosomal dominant)	CMD1G	NA	2129545, 10051295	Standard	NM_133378	NM_003319	NA	Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000589042.1:c.61163C>T	chr2.hg19:g.179455289G>A	ENSP00000467141:p.Ala20388Val	NA	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	hg19	CCDS59435.1	0.02	13.564066	TCAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720889	0.30503	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	6.11	6.11	0.99139	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.23133	0.0559	N	0.03238	-0.38	0.58432	D	0.999995	P;P;P;P	0.41978	0.619;0.619;0.619;0.767	B;B;B;B	0.38683	0.172;0.172;0.172;0.279	T	0.24440	-1.0160	9	0.87932	D	0	.	20.7342	0.99715	0.0:0.0:1.0:0.0	.	11323;11448;11515;18747	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	17820;11323;11515;11448;11321	ENSP00000343764:A17820V;ENSP00000434586:A11323V;ENSP00000340554:A11515V;ENSP00000352154:A11448V	ENSP00000340554:A11515V	A	-	2	0	TTN	179163535	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.742000	0.68646	2.906000	0.99361	0.655000	0.94253	GCT	NOVEL	TTN-018	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450680.2	9	10.835158	KEEP	0	0	0	36	1293	GG	0.999999	0.999999	0		-	55	60	1934	0	0	156.309446	260	60	9864	408	ENST00000589042.1	0.174603	1
ITGA4	3676	__UNKNOWN__	__UNKNOWN__	2	182344812	182344812	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:182344812T>G	ENST00000397033.2	+	6	1054					NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	NA		NA			B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TGGAGGAGGTTTGGGGTGGTG	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													25	25	25	NA		NA	NA	2		NA											NA				182344812		870	1991	2861	SO:0001627	intron_variant				CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232	3676		CD molecules, Integrins	6140	protein-coding gene	gene with protein product		192975		CD49D	NA	1537388	Standard		NM_000885	NA	Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.625-52T>G	chr2.hg19:g.182344812T>G		NA	D3DPG4|Q7Z4L6	hg19	CCDS42788.1	0.02	-0.20178	GGTxTGG	COVERED																																																																																			NOVEL	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334427.1	1	4.512984	KEEP	0	0	0	15	458	TT	0.99649	0.488823	0		+	7	60	256	0	0	22.963655	15	70	539	47	ENST00000397033.2	0.318182	0.490544
TFPI	7035	__UNKNOWN__	__UNKNOWN__	2	188343547	188343547	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:188343547T>C	ENST00000233156.3	-	6	923				TFPI_ENST00000339091.4_Intron|TFPI_ENST00000392365.1_Intron|AC007319.1_ENST00000412276.1_RNA|AC007319.1_ENST00000453517.1_RNA|TFPI_ENST00000409676.1_Intron	NM_006287.4	NP_006278.1	P10646	TFPI1_HUMAN	tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor)	NA		NA			blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0554)		Coagulation factor VIIa(DB00036)|Dalteparin(DB06779)	ATCACAAAATTGATAAATAAA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	81	83	NA		NA	NA	2		NA											NA				188343547		2203	4300	6503	SO:0001627	intron_variant				CCDS2294.1, CCDS33349.1	2q32	2008-06-02			ENSG00000003436	ENSG00000003436	7035			11760	protein-coding gene	gene with protein product	extrinsic pathway inhibitor	152310		LACI	NA	1993173	Standard	NM_006287	XM_005246818	NA	Approved	EPI, TFI, TFPI1	uc002upy.3	P10646	OTTHUMG00000132634	ENST00000233156.3:c.628+5303A>G	chr2.hg19:g.188343547T>C		NA	O95103|Q53TS4	hg19	CCDS2294.1	0.02	2.129059	AATxGAT	COVERED																																																																																			NOVEL	TFPI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255881.1	2	3.610784	KEEP	0	0	0	12	373	TT	0.993634	0.993582	0		-	27	60	868	0	0	74.751871	70	60	2560	118	ENST00000233156.3	0.278351	0.999948
C2orf88	84281	__UNKNOWN__	__UNKNOWN__	2	190927514	190927514	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:190927514A>G	ENST00000478197.1	+	2	219							Q9BSF0	SMAKA_HUMAN	chromosome 2 open reading frame 88	NA		NA				plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(1)	3						AAGTGTCGTCAGGATCTATGA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005083	CCDS42792.1	2q32.2	2014-02-12	2009-04-08		ENSG00000187699	ENSG00000187699	84281			28191	protein-coding gene	gene with protein product	small membrane AKAP	615117			NA	23996002	Standard	NM_032321	NM_032321	NA	Approved	MGC13057, smAKAP	uc002urt.3	Q9BSF0	OTTHUMG00000154361	ENST00000478197.1:c.220-16435A>G	chr2.hg19:g.190927514A>G		NA	D3DPI3|P0C876|Q53TC7	hg19		0.02	2.13509	GTCxGGA	COVERED																																																																																			NOVEL	C2orf88-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000334952.1	0	6.01902	KEEP	0	0	0	20	655	AA	0.999863	0.991958	0		+	12	60	433	0	0	35.704695	51	60	1918	107	ENST00000478197.1	0.190476	0.992094
GLS	2744	__UNKNOWN__	__UNKNOWN__	2	191829264	191829264	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:191829264G>C	ENST00000320717.3	+	0	3820					NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	NA		NA			cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate secretion (GO:0014047)|glutamine catabolic process (GO:0006543)|neurotransmitter secretion (GO:0007269)|protein homotetramerization (GO:0051289)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|small molecule metabolic process (GO:0044281)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.00625)|Epithelial(96;0.0744)|all cancers(119;0.181)		L-Glutamine(DB00130)	TCCAGTCTAAGCCAGTGGCTC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB020645	CCDS2308.1, CCDS58744.1	2q32-q34	2013-01-10			ENSG00000115419	ENSG00000115419	2744	3.5.1.2	Ankyrin repeat domain containing	4331	protein-coding gene	gene with protein product		138280			NA	10048485	Standard		NM_014905	NA	Approved	KIAA0838, GLS1	uc002usf.3	O94925	OTTHUMG00000132701	ENST00000320717.3:c.*1552G>C	chr2.hg19:g.191829264G>C		NA	Q9UL05|Q9UL06|Q9UL07|Q9UN40	hg19	CCDS2308.1	0.02	10.04726	TAAxCCA	COVERED																																																																																			NOVEL	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255999.2	2	8.95227	KEEP	0	1	35	42	1323	GG	1	1	0		+	109	60	4027	0	0	389.763211	107	60	3660	345	ENST00000320717.3	0.50463	1
STAT4	6775	__UNKNOWN__	__UNKNOWN__	2	191996656	191996656	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:191996656C>A	ENST00000392320.2	-	3	588				STAT4_ENST00000409995.1_Intron|STAT4_ENST00000358470.4_Intron	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	NA		NA			cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(4)|endometrium(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.0864)|all cancers(119;0.204)			TGTTTATTCTCTACACTTGTG	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2310.1	2q32.2-q32.3	2013-02-14			ENSG00000138378	ENSG00000138378	6775		SH2 domain containing	11365	protein-coding gene	gene with protein product		600558			NA	8007943, 8700208	Standard	NM_003151	NM_003151	NA	Approved		uc002usn.2	Q14765	OTTHUMG00000132700	ENST00000392320.2:c.273+14682G>T	chr2.hg19:g.191996656C>A		NA	Q96NZ6	hg19	CCDS2310.1	0.02	9.159559	TCTxTAC	COVERED																																																																																			NOVEL	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335586.1	4	9.932461	KEEP	0	0	0	33	1177	CC	0.999998	0.999998	0		-	46	60	1656	0	0	137.983586	180	60	6863	300	ENST00000392320.2	0.20354	1
HECW2	57520	__UNKNOWN__	__UNKNOWN__	2	197184367	197184367	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:197184367A>G	ENST00000409111.1	-	7	1193	c.179T>C	c.(178-180)cTc>cCc	p.L60P	HECW2_ENST00000260983.3_Missense_Mutation_p.L416P			Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	416		NA			protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						GTAATCATTGAGTGAATCCTG	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	82	81	NA		NA	NA	2		NA											NA				197184367		2203	4300	6503	SO:0001583	missense			AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411	57520			29853	protein-coding gene	gene with protein product		NA			NA	10718198, 12890487	Standard	NM_020760	NM_020760	NA	Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000409111.1:c.179T>C	chr2.hg19:g.197184367A>G	ENSP00000386775:p.Leu60Pro	NA	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	hg19		0.02	6.317747	TTGxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	22.7	4.324636	0.81580	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	T;T	0.51817	0.69;0.82	5.64	5.64	0.86602	.	0.527792	0.17446	N	0.173953	T	0.57725	0.2073	L	0.29908	0.895	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.56469	-0.7974	10	0.48119	T	0.1	.	14.5846	0.68315	1.0:0.0:0.0:0.0	.	416	Q9P2P5	HECW2_HUMAN	P	60;416	ENSP00000386775:L60P;ENSP00000260983:L416P	ENSP00000260983:L416P	L	-	2	0	HECW2	196892612	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.170000	0.89673	2.367000	0.80283	0.528000	0.53228	CTC	NOVEL	HECW2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000335314.2	5	5.111396	KEEP	0	0	0	17	539	AA	0.999366	0.999366	0		-	15	60	522	0	0	36.268871	184	60	6719	243	ENST00000409111.1	0.075377	1
BOLL	66037	__UNKNOWN__	__UNKNOWN__	2	198622123	198622123	__UNKNOWN__	Splice_Site	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:198622123G>A	ENST00000430004.1	-	9	1016	c.620C>T	c.(619-621)gCc>gTc	p.A207V	AC011997.1_ENST00000409845.1_Intron|BOLL_ENST00000282278.8_Splice_Site_p.A76V|BOLL_ENST00000392296.4_Splice_Site_p.A185V|BOLL_ENST00000321801.7_Splice_Site_p.A197V|BOLL_ENST00000433157.1_Splice_Site_p.A185V	NM_001284361.1	NP_001271290.1	Q8N9W6	BOLL_HUMAN	boule-like RNA-binding protein	185		NA			cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of translational initiation (GO:0045948)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|translation activator activity (GO:0008494)			central_nervous_system(1)|endometrium(2)|lung(6)|ovary(3)|prostate(1)	13						CTGTGTGGTGGCCTAAAATTA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													40	44	43	NA		NA	NA	2		NA											NA				198622123		2203	4296	6499	SO:0001630	splice_region_variant				CCDS2324.1, CCDS2325.1, CCDS63081.1	2q33	2013-10-17	2013-10-17		ENSG00000152430	ENSG00000152430	66037		RNA binding motif (RRM) containing	14273	protein-coding gene	gene with protein product		606165	bol (Drosophila boule homolog)-like, bol, boule-like (Drosophila)		NA	11390979, 16001084	Standard	NM_033030	NM_197970	NA	Approved	BOULE	uc002uut.2	Q8N9W6	OTTHUMG00000132747	ENST00000430004.1:c.619-1C>T	chr2.hg19:g.198622123G>A		NA	B4DZA4|Q0JW32|Q53T62|Q969U3	hg19		0.02	2.114237	GTGxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.39	1.923134	0.33908	.	.	ENSG00000152430	ENST00000430004;ENST00000392296;ENST00000321801;ENST00000282278;ENST00000433157	T;T;T;T	0.32988	1.43;1.66;1.65;1.66	4.92	4.92	0.64577	.	2.304040	0.02866	U	0.130902	T	0.29190	0.0726	N	0.19112	0.55	0.45129	D	0.998142	P;P;B;B;B	0.43788	0.817;0.573;0.004;0.361;0.277	B;B;B;B;B	0.38562	0.276;0.197;0.013;0.154;0.203	T	0.31668	-0.9935	10	0.87932	D	0	.	16.2636	0.82563	0.0:0.0:1.0:0.0	.	76;213;197;185;191	B4DZA4;Q8N9W6-2;Q8N9W6-3;Q8N9W6;Q8N9W6-4	.;.;.;BOLL_HUMAN;.	V	207;185;197;76;185	ENSP00000397711:A207V;ENSP00000376116:A185V;ENSP00000314792:A197V;ENSP00000396099:A185V	ENSP00000282278:A76V	A	-	2	0	BOLL	198330368	1.000000	0.71417	1.000000	0.80357	0.146000	0.21551	4.288000	0.59007	2.455000	0.83008	0.467000	0.42956	GCC	NOVEL	BOLL-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000256108.3	1	4.213805	KEEP	0	0	0	14	501	GG	0.995343	0.96943	0	Missense_Mutation	-	5	60	168	0	0	11.954235	49	60	1823	87	ENST00000430004.1	0.092593	0.973965
AOX1	316	__UNKNOWN__	__UNKNOWN__	2	201467080	201467080	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:201467080G>T	ENST00000374700.2	+	6	739					NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	NA		NA			inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TAAGTGGAAAGGACCACATGT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													175	159	164	NA		NA	NA	2		NA											NA				201467080		2203	4300	6503	SO:0001627	intron_variant			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356	316			553	protein-coding gene	gene with protein product		602841			NA	7570184	Standard	NM_001159	NM_001159	NA	Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.498+12G>T	chr2.hg19:g.201467080G>T		NA	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	hg19	CCDS33360.1	0.02	11.842862	AAAxGAC	COVERED																																																																																			NOVEL	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335844.1	2	11.736562	KEEP	0	0	0	39	1373	GG	1	1	0		+	35	60	1294	0	0	100.734096	238	60	8704	387	ENST00000374700.2	0.128205	1
PPIL3	53938	__UNKNOWN__	__UNKNOWN__	2	201746193	201746193	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:201746193T>C	ENST00000409361.1	-	5	436	c.179A>G	c.(178-180)aAc>aGc	p.N60S	PPIL3_ENST00000286175.8_Missense_Mutation_p.N68S|PPIL3_ENST00000465823.1_5'UTR|PPIL3_ENST00000392283.4_Missense_Mutation_p.N64S|PPIL3_ENST00000409449.1_Missense_Mutation_p.N68S			Q9H2H8	PPIL3_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 3	64	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.	NA			mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			endometrium(1)|lung(2)	3						CCAAATACTGTTGCCTCCTCT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													167	149	155	NA		NA	NA	2		NA											NA				201746193		2203	4300	6503	SO:0001583	missense			AF251049	CCDS2332.1, CCDS2333.1	2q33.1	2008-02-05			ENSG00000240344	ENSG00000240344	53938			9262	protein-coding gene	gene with protein product	Cyclophilin J	615811			NA	11435694	Standard		NM_032472	NA	Approved	CyPJ	uc002uwi.3	Q9H2H8	OTTHUMG00000132782	ENST00000409361.1:c.179A>G	chr2.hg19:g.201746193T>C	ENSP00000386235:p.Asn60Ser	NA	Q86WF9|Q96IA9|Q9BXZ1	hg19		0.02	9.05595	CTGxTGC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.461|3.461	-0.110032|-0.110032	0.06924|0.06924	.|.	.|.	ENSG00000240344|ENSG00000240344	ENST00000286175;ENST00000392283;ENST00000409264;ENST00000409361;ENST00000409449;ENST00000457063|ENST00000443398	T;T;T;T;T;T|.	0.39592|.	1.07;2.01;2.01;2.03;1.07;2.01|.	5.65|5.65	-3.93|-3.93	0.04143|0.04143	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);|.	0.493023|.	0.24980|.	N|.	0.034070|.	T|T	0.10508|0.10508	0.0257|0.0257	N|N	0.00446|0.00446	-1.495|-1.495	0.09310|0.09310	N|N	0.999997|0.999997	B;B|B	0.02656|0.02656	0.0;0.0|0.0	B;B|B	0.04013|0.01281	0.001;0.001|0.0	T|T	0.36744|0.36744	-0.9735|-0.9735	10|8	0.45353|0.87932	T|D	0.12|0	.|.	10.4717|10.4717	0.44640|0.44640	0.0:0.4024:0.0903:0.5073|0.0:0.4024:0.0903:0.5073	.|.	68;64|33	Q9H2H8-2;Q9H2H8|Q86UR0	.;PPIL3_HUMAN|.	S|A	68;64;83;60;68;64|33	ENSP00000286175:N68S;ENSP00000376107:N64S;ENSP00000386893:N83S;ENSP00000386235:N60S;ENSP00000387012:N68S;ENSP00000401196:N64S|.	ENSP00000286175:N68S|ENSP00000391082:T33A	N|T	-|-	2|1	0|0	PPIL3|PPIL3	201454438|201454438	0.952000|0.952000	0.32445|0.32445	0.880000|0.880000	0.34516|0.34516	0.010000|0.010000	0.07245|0.07245	-0.065000|-0.065000	0.11617|0.11617	-1.151000|-1.151000	0.02836|0.02836	-1.489000|-1.489000	0.00976|0.00976	AAC|ACA	NOVEL	PPIL3-007	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336124.1	2	18.657584	KEEP	0	0	0	62	2024	TT	1	1	0		-	7	60	260	0	0	15.932244	209	60	7711	365	ENST00000409361.1	0.032407	1
FAM126B	285172	__UNKNOWN__	__UNKNOWN__	2	201857652	201857652	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:201857652G>T	ENST00000418596.3	-	9	888	c.701C>A	c.(700-702)cCt>cAt	p.P234H	AC005037.3_ENST00000413848.1_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	234		NA				intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						CATAAATTCAGGATCCAATAC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	113	115	NA		NA	NA	2		NA											NA				201857652		2203	4300	6503	SO:0001583	missense			BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744	285172			28593	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173822	NM_173822	NA	Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.701C>A	chr2.hg19:g.201857652G>T	ENSP00000393667:p.Pro234His	NA	B2RCG7|Q4ZG87|Q53TX6	hg19	CCDS2335.1	0.02	23.658259	TCAxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004546	0.93287	.	.	ENSG00000155744	ENST00000418596	T	0.77489	-1.1	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.84866	0.5567	L	0.41236	1.265	0.80722	D	1	D;D	0.89917	0.986;1.0	P;D	0.91635	0.89;0.999	T	0.82816	-0.0270	10	0.42905	T	0.14	-4.2473	20.6282	0.99521	0.0:0.0:1.0:0.0	.	40;234	B3KUG1;Q8IXS8	.;F126B_HUMAN	H	234	ENSP00000393667:P234H	ENSP00000393667:P234H	P	-	2	0	FAM126B	201565897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.883000	0.92426	2.871000	0.98454	0.655000	0.94253	CCT	NOVEL	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256285.3	156	31.58374	KEEP	0	0	0	105	3736	GG	1	1	0		-	54	60	2017	0	0	154.636184	417	60	15627	787	ENST00000418596.3	0.11465	1
FAM126B	285172	__UNKNOWN__	__UNKNOWN__	2	201929018	201929018	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:201929018G>C	ENST00000418596.3	-	1	60					NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	NA		NA				intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						TCCAACAAAGGGTTTTAATGT	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744	285172			28593	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173822	NM_173822	NA	Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.127+7314C>G	chr2.hg19:g.201929018G>C		NA	B2RCG7|Q4ZG87|Q53TX6	hg19	CCDS2335.1	0.02	8.939181	AAGxGTT	COVERED																																																																																			NOVEL	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256285.3	2	14.746774	KEEP	6	0	0	49	1677	GG	1	1	0		-	43	37	1576	0	0	131.232736	174	60	6197	358	ENST00000418596.3	0.198157	1
ALS2	57679	__UNKNOWN__	__UNKNOWN__	2	202608968	202608968	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:202608968G>A	ENST00000264276.6	-	10	2543				ALS2_ENST00000457679.2_Intron	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	NA		NA			behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						GGAGAGAGGGGGTTGCAACTT	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													119	115	116	NA		NA	NA	2		NA											NA				202608968		1871	4117	5988	SO:0001627	intron_variant			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393	57679		Rho guanine nucleotide exchange factors	443	protein-coding gene	gene with protein product	alsin	606352	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6	ALS2CR6	NA	11586298	Standard	NM_020919	NM_020919	NA	Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.2170+12C>T	chr2.hg19:g.202608968G>A		NA	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	hg19	CCDS42800.1	0.02	9.295607	GGGxGTT	COVERED																																																																																			NOVEL	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335562.3	0	15.04817	KEEP	0	0	0	50	1718	GG	1	1	0		-	52	60	1663	0	0	138.53692	171	60	6092	336	ENST00000264276.6	0.233184	1
ALS2	57679	__UNKNOWN__	__UNKNOWN__	2	202619246	202619246	__UNKNOWN__	Silent	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:202619246C>G	ENST00000264276.6	-	6	1992	c.1620G>C	c.(1618-1620)ggG>ggC	p.G540G		NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	540		NA			behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						CATCGCCGTGCCCCAGCTGCC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	119	118	NA		NA	NA	2		NA											NA				202619246		1971	4149	6120	SO:0001819	synonymous_variant			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393	57679		Rho guanine nucleotide exchange factors	443	protein-coding gene	gene with protein product	alsin	606352	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6	ALS2CR6	NA	11586298	Standard	NM_020919	NM_020919	NA	Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.1620G>C	chr2.hg19:g.202619246C>G		NA	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	hg19	CCDS42800.1	0.02	14.499703	GTGxCCC	COVERED																																																																																			NOVEL	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335562.3	2	22.869979	KEEP	0	0	0	76	2660	CC	1	1	0		-	70	60	2526	0	0	210.454595	275	60	10051	513	ENST00000264276.6	0.202899	1
INO80D	54891	__UNKNOWN__	__UNKNOWN__	2	206869150	206869150	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:206869150G>A	ENST00000403263.1	-	11	3430	c.3026C>T	c.(3025-3027)aCa>aTa	p.T1009I		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	0		NA			DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						TGTGGCACCTGTTACTGTGAA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	53	52	NA		NA	NA	2		NA											NA				206869150		2017	4182	6199	SO:0001583	missense				CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933	54891		INO80 complex subunits	25997	protein-coding gene	gene with protein product		NA			NA	16230350	Standard	NM_017759	NM_017759	NA	Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.3026C>T	chr2.hg19:g.206869150G>A	ENSP00000384198:p.Thr1009Ile	NA	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	hg19	CCDS46500.1	0.02	20.588863	CCTxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.14	3.314629	0.60524	.	.	ENSG00000114933	ENST00000403263	T	0.33216	1.42	5.73	5.73	0.89815	.	.	.	.	.	T	0.24314	0.0589	N	0.19112	0.55	0.48236	D	0.999619	B	0.32829	0.386	B	0.28305	0.088	T	0.05666	-1.0871	9	0.66056	D	0.02	.	19.9022	0.96990	0.0:0.0:1.0:0.0	.	1009	Q53TQ3-2	.	I	1009	ENSP00000384198:T1009I	ENSP00000384198:T1009I	T	-	2	0	INO80D	206577395	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.244000	0.78228	2.687000	0.91594	0.655000	0.94253	ACA	NOVEL	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336459.1	8	21.968917	KEEP	0	0	0	73	2519	GG	1	1	0		-	72	60	2609	0	0	208.897802	384	60	14506	653	ENST00000403263.1	0.157895	1
ZDBF2	57683	__UNKNOWN__	__UNKNOWN__	2	207173068	207173068	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:207173068C>T	ENST00000374423.3	+	5	4202	c.3816C>T	c.(3814-3816)gaC>gaT	p.D1272D		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1272		NA					nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AGCATGTTGACTTGGAAAATA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													46	48	47	NA		NA	NA	2		NA											NA				207173068		1828	4088	5916	SO:0001819	synonymous_variant			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186	57683		Zinc fingers, DBF-type	29313	protein-coding gene	gene with protein product		NA			NA	10997877	Standard	NM_020923	XM_005246711	NA	Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.3816C>T	chr2.hg19:g.207173068C>T		NA	Q6ZNP7|Q6ZSN8	hg19	CCDS46501.1	0.02	16.281468	TGAxTTG	COVERED																																																																																			NOVEL	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336458.1	5	24.617791	KEEP	0	0	0	82	2894	CC	1	1	0		+	31	60	1094	0	0	78.452274	326	60	12357	532	ENST00000374423.3	0.086835	1
UNC80	285175	__UNKNOWN__	__UNKNOWN__	2	210769682	210769682	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:210769682A>G	ENST00000272845.6	+	28	4596	c.4562A>G	c.(4561-4563)cAg>cGg	p.Q1521R	UNC80_ENST00000439458.1_Missense_Mutation_p.Q1526R	NM_182587.3	NP_872393.3	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1526		NA			ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						GGCAAGAAACAGAAAGAAGTA	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													70	74	73	NA		NA	NA	2		NA											NA				210769682		692	1591	2283	SO:0001583	missense			AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406	285175			26582	protein-coding gene	gene with protein product		612636	chromosome 2 open reading frame 21	C2orf21	NA	19092807	Standard	NM_182587	NM_032504	NA	Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000272845.6:c.4562A>G	chr2.hg19:g.210769682A>G	ENSP00000272845:p.Gln1521Arg	NA	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	hg19	CCDS2387.2	0.02	9.229384	AACxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	A	9.822	1.185937	0.21870	.	.	ENSG00000144406	ENST00000439458;ENST00000272845	T;T	0.29655	1.56;1.56	5.76	5.76	0.90799	.	0.312349	0.32578	N	0.005912	T	0.17662	0.0424	N	0.14661	0.345	0.80722	D	1	B	0.22146	0.065	B	0.18561	0.022	T	0.12477	-1.0546	10	0.19590	T	0.45	-19.6695	11.188	0.48669	0.8629:0.0:0.0:0.1371	.	1526	Q8N2C7	UNC80_HUMAN	R	1526;1521	ENSP00000391088:Q1526R;ENSP00000272845:Q1521R	ENSP00000272845:Q1521R	Q	+	2	0	UNC80	210477927	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.852000	0.48310	2.197000	0.70478	0.533000	0.62120	CAG	NOVEL	UNC80-007	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336930.2	0	9.027175	KEEP	0	0	0	30	946	AA	0.999997	0.999997	0		+	89	60	3104	0	0	288.821978	129	60	4781	291	ENST00000272845.6	0.408257	1
RPE	6120	__UNKNOWN__	__UNKNOWN__	2	210867331	210867331	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:210867331G>A	ENST00000359429.6	+	0	43				RPE_ENST00000436630.2_5'UTR	NM_199229.1	NP_954699.1	Q96AT9	RPE_HUMAN	ribulose-5-phosphate-3-epimerase	NA		NA			carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|ribulose-phosphate 3-epimerase activity (GO:0004750)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	9				Epithelial(149;0.00241)|Lung(261;0.041)|all cancers(144;0.0429)|LUSC - Lung squamous cell carcinoma(261;0.0431)		CAATCGGGGTGACGCTCTAGC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS2388.1, CCDS42810.1, CCDS63107.1, CCDS63108.1	2q32-q33.3	2012-10-02			ENSG00000197713	ENSG00000197713	6120	5.1.3.1		10293	protein-coding gene	gene with protein product		180480			NA		Standard	NM_006916	NM_199229	NA	Approved		uc002vdn.4	Q96AT9	OTTHUMG00000154690	ENST00000359429.6:c.-55G>A	chr2.hg19:g.210867331G>A		NA	A8K4S0|B4E016|C9JPQ7|O43767|Q53TV9|Q8N215|Q96N34|Q9BSB5	hg19	CCDS2388.1	0.02	7.991215	GGTxACG	COVERED																																																																																			NOVEL	RPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336574.2	2	26.46702	KEEP	0	0	0	88	2870	GG	1	1	0		+	38	60	1114	0	0	85.365378	186	60	6349	410	ENST00000359429.6	0.169643	1
LANCL1	10314	__UNKNOWN__	__UNKNOWN__	2	211296934	211296934	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:211296934C>T	ENST00000443314.1	-	0	3819				LANCL1_ENST00000441020.3_3'UTR|LANCL1_ENST00000450366.2_3'UTR|AC007970.1_ENST00000433296.1_RNA|AC007970.1_ENST00000420418.1_RNA			O43813	LANC1_HUMAN	LanC lantibiotic synthetase component C-like 1 (bacterial)	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|G-protein coupled receptor activity (GO:0004930)|glutathione binding (GO:0043295)|low-density lipoprotein particle receptor binding (GO:0050750)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12				Epithelial(149;0.00562)|Lung(261;0.0468)|LUSC - Lung squamous cell carcinoma(261;0.0495)|all cancers(144;0.0569)		ATTTAAAATCCCATCAAAACT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Y11395	CCDS2392.1	2q33-q35	2008-05-23	2001-12-04		ENSG00000115365	ENSG00000115365	10314			6508	protein-coding gene	gene with protein product		604155	LanC (bacterial lantibiotic synthetase component C)-like 1	GPR69A	NA	9512664	Standard	NM_006055	NM_001136574	NA	Approved	p40	uc010zjh.2	O43813	OTTHUMG00000132991	ENST00000443314.1:c.*2277G>A	chr2.hg19:g.211296934C>T		NA		hg19	CCDS2392.1	0.02	6.983407	ATCxCAT	COVERED																																																																																			NOVEL	LANCL1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336817.1	2	11.737662	KEEP	0	0	0	39	1346	CC	1	1	0		-	26	60	951	0	0	75.229314	154	70	5500	256	ENST00000443314.1	0.144444	1
CPS1	1373	__UNKNOWN__	__UNKNOWN__	2	211464338	211464338	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:211464338A>G	ENST00000233072.5	+	14	1745				CPS1_ENST00000430249.2_Intron|CPS1_ENST00000451903.2_Intron	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	NA		NA			anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CTGCTGTGTAATGTATTTTAT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	1373	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	carbamoyl-phosphate synthetase 1, mitochondrial		NA		Standard		NM_001122633	NA	Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1549+53A>G	chr2.hg19:g.211464338A>G		NA	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	hg19	CCDS2393.1	0.02	2.127579	GTAxTGT	COVERED																																																																																			NOVEL	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256569.5	0	2.707629	KEEP	0	0	0	9	274	AA	0.99254	0.992489	0		+	14	60	524	0	0	41.626751	84	60	3078	122	ENST00000233072.5	0.142857	0.999948
AC079610.2	0	__UNKNOWN__	__UNKNOWN__	2	214142616	214142616	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:214142616G>A	ENST00000360083.3	-	0	386										NA		NA									NA						taggaaaaatgcctccagggc	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000360083.3:	chr2.hg19:g.214142616G>A		NA		hg19		0.02	4.329711	AATxCCT	COVERED																																																																																			NOVEL	AC079610.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000337357.1	1	12.340656	KEEP	0	0	0	41	1491	GG	1	0.999991	0		-	21	60	685	0	0	55.438341	87	60	3296	198	ENST00000360083.3	0.194444	0.999991
XRCC5	7520	__UNKNOWN__	__UNKNOWN__	2	216990661	216990661	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:216990661C>T	ENST00000392133.3	+	9	1166	c.705C>T	c.(703-705)tgC>tgT	p.C235C	XRCC5_ENST00000392132.2_Silent_p.C235C			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	235		NA			brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to fatty acid (GO:0071398)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|hematopoietic stem cell differentiation (GO:0060218)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|positive regulation of type I interferon production (GO:0032481)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear chromosome, telomeric region (GO:0000784)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|kidney(3)|large_intestine(8)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Renal(323;0.0328)		Epithelial(149;9.78e-06)|all cancers(144;0.000632)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.0117)		GAAAACTGTGCGTCTTCAAGA	0.368	NA	NA						Non-homologous end-joining						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													103	105	104	NA		NA	NA	2		NA											NA				216990661		2203	4300	6503	SO:0001819	synonymous_variant			AF039597	CCDS2402.1	2q35	2008-07-31	2008-07-31		ENSG00000079246	ENSG00000079246	7520			12833	protein-coding gene	gene with protein product	Ku autoantigen, 80kDa	194364	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining; Ku autoantigen, 80kD)		NA	9636207, 9214634	Standard	NM_021141	NM_021141	NA	Approved	KU80, KARP-1, Ku86, KUB2	uc002vfy.3	P13010	OTTHUMG00000133059	ENST00000392133.3:c.705C>T	chr2.hg19:g.216990661C>T		NA	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	hg19	CCDS2402.1	0.02	8.956614	GTGxGTC	COVERED																																																																																			NOVEL	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256675.3	3	22.868838	KEEP	0	0	0	76	2622	CC	1	1	0		+	11	60	382	0	0	24.622035	205	60	7416	389	ENST00000392133.3	0.050926	1
AAMP	14	__UNKNOWN__	__UNKNOWN__	2	219130593	219130593	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:219130593C>A	ENST00000444053.1	-	7	934	c.843G>T	c.(841-843)gtG>gtT	p.V281V	AAMP_ENST00000420660.1_Silent_p.V261V|AAMP_ENST00000248450.4_Silent_p.V280V	NM_001087.3	NP_001078.2	Q13685	AAMP_HUMAN	angio-associated, migratory cell protein	280		NA			angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|positive regulation of endothelial cell migration (GO:0010595)|smooth muscle cell migration (GO:0014909)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(4)|ovary(2)|skin(1)	11		Renal(207;0.0474)		Epithelial(149;7.19e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTGGCAGTCCACAGAGCCAG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	36	36	NA		NA	NA	2		NA											NA				219130593		2203	4300	6503	SO:0001819	synonymous_variant			AB209790	CCDS33378.1	2q	2013-01-10			ENSG00000127837	ENSG00000127837	14		WD repeat domain containing	18	protein-coding gene	gene with protein product		603488			NA	7743515	Standard	NM_001087	XM_005246325	NA	Approved		uc002vhk.3	Q13685	OTTHUMG00000155202	ENST00000444053.1:c.843G>T	chr2.hg19:g.219130593C>A		NA	Q8WUJ9|Q96H92	hg19		0.02	6.810673	GTCxACA	COVERED	.	.	.	.	.	.	.	.	.	.	C	10.54	1.379577	0.24944	.	.	ENSG00000127837	ENST00000422731	.	.	.	5.69	4.8	0.61643	.	.	.	.	.	T	0.62282	0.2415	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60561	-0.7239	4	.	.	.	-16.8326	10.7051	0.45950	0.1313:0.7999:0.0:0.0689	.	.	.	.	L	35	.	.	W	-	2	0	AAMP	218838837	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.547000	0.45786	1.367000	0.46095	0.650000	0.86243	TGG	NOVEL	AAMP-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000338757.1	2	7.524009	KEEP	0	0	0	25	872	CC	0.999931	0.999931	0		-	18	60	655	0	0	48.846843	159	60	5655	226	ENST00000444053.1	0.101695	1
NHEJ1	79840	__UNKNOWN__	__UNKNOWN__	2	219940091	219940091	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:219940091T>C	ENST00000356853.5	-	0	2045				NHEJ1_ENST00000409720.1_3'UTR	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	NA		NA			B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		GATCATCTTCTCTCGAGACTT	0.299	NA	NA						Non-homologous end-joining						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736	79840			25737	protein-coding gene	gene with protein product		611290			NA	16439204, 16439205	Standard	NM_024782	NM_024782	NA	Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.*1012A>G	chr2.hg19:g.219940091T>C		NA	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	hg19	CCDS2432.1	0.02	1.810534	TTCxCTC	COVERED																																																																																			NOVEL	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256817.2	3	7.821087	KEEP	0	0	0	26	848	TT	0.999957	0.999919	0		-	8	60	288	0	0	20.513596	92	60	3419	174	ENST00000356853.5	0.08	0.999962
ABCB6	10058	__UNKNOWN__	__UNKNOWN__	2	220078879	220078879	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220078879T>C	ENST00000265316.3	-	8	1732	c.1416A>G	c.(1414-1416)gaA>gaG	p.E472E	ABCB6_ENST00000439002.2_Silent_p.E426E	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	472	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.	NA			brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCGTTCCACTTCGTAACTCT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													147	135	139	NA		NA	NA	2		NA											NA				220078879		2203	4300	6503	SO:0001819	synonymous_variant			AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657	10058		ATP binding cassette transporters / subfamily B	47	protein-coding gene	gene with protein product	ATP-binding cassette half-transporter	605452	ATP-binding cassette, sub-family B (MDR/TAP), member 6		NA	8894702, 9110174	Standard	NM_005689	NM_005689	NA	Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1416A>G	chr2.hg19:g.220078879T>C		NA	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	hg19	CCDS2436.1	0.02	9.514695	CACxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	T	5.458	0.269653	0.10349	.	.	ENSG00000115657	ENST00000295750	.	.	.	5.33	1.56	0.23342	.	.	.	.	.	T	0.54581	0.1867	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44651	-0.9314	4	.	.	.	-11.9847	7.0017	0.24813	0.0:0.4272:0.0:0.5728	.	.	.	.	R	320	.	.	K	-	2	0	ABCB6	219787123	1.000000	0.71417	0.960000	0.40013	0.441000	0.31987	1.112000	0.31172	0.325000	0.23359	0.482000	0.46254	AAG	NOVEL	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256820.2	4	21.966681	KEEP	0	0	0	73	2357	TT	1	1	0		-	37	60	1311	0	0	104.568246	195	60	7380	382	ENST00000265316.3	0.159483	1
TUBA4A	7277	__UNKNOWN__	__UNKNOWN__	2	220115217	220115217	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220115217T>C	ENST00000392088.2	-	4	1714	c.1159A>G	c.(1159-1161)Agg>Ggg	p.R387G	TUBA4A_ENST00000248437.4_Missense_Mutation_p.R402G	NM_001278552.1	NP_001265481.1	P68366	TBA4A_HUMAN	tubulin, alpha 4a	402		NA			'de novo' posttranslational protein folding (GO:0051084)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Cabazitaxel(DB06772)|Podofilox(DB01179)|Vincristine(DB00541)	ACAAACGCCCTCTTGGCATAC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													128	114	119	NA		NA	NA	2		NA											NA				220115217		2203	4300	6503	SO:0001583	missense			AK054731	CCDS2438.1, CCDS63131.1	2q36.1	2012-10-02	2007-02-12	2007-02-12	ENSG00000127824	ENSG00000127824	7277		Tubulins	12407	protein-coding gene	gene with protein product		191110	tubulin, alpha 1 (testis specific), tubulin, alpha 1	TUBA1	NA	3785200	Standard	NM_006000	NM_006000	NA	Approved	FLJ30169, H2-ALPHA	uc002vkt.1	P68366	OTTHUMG00000133126	ENST00000392088.2:c.1159A>G	chr2.hg19:g.220115217T>C	ENSP00000375938:p.Arg387Gly	NA	A8MUB1|B3KNQ6|P05215	hg19		0.02	15.669673	CCCxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	12.79	2.043341	0.36085	.	.	ENSG00000127824	ENST00000248437;ENST00000392088	D;D	0.85861	-2.04;-2.04	5.06	1.02	0.19986	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.64402	D	0.000001	D	0.93015	0.7777	H	0.95294	3.65	0.80722	D	1	P	0.47302	0.893	P	0.56398	0.797	D	0.94174	0.7426	10	0.87932	D	0	.	15.2738	0.73726	0.0:0.0:0.6277:0.3722	.	402	P68366	TBA4A_HUMAN	G	402;387	ENSP00000248437:R402G;ENSP00000375938:R387G	ENSP00000248437:R402G	R	-	1	2	TUBA4A	219823461	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.136000	0.42121	0.019000	0.15079	0.533000	0.62120	AGG	NOVEL	TUBA4A-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000259055.3	6	21.301382	KEEP	0	1	38	84	2705	TT	1	1	0		-	74	60	2633	0	0	218.320158	295	60	10524	521	ENST00000392088.2	0.200542	1
GMPPA	29926	__UNKNOWN__	__UNKNOWN__	2	220364787	220364787	__UNKNOWN__	Intron	SNP	G	G	A	rs377642282		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220364787G>A	ENST00000358215.3	+	2	409				AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000341142.3_Intron|GMPPA_ENST00000373908.1_Intron|GMPPA_ENST00000313597.5_Intron|GMPPA_ENST00000373917.3_Intron	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		AGTGGTAGGCGGGATGGGGGC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	,	0,4406		0,0,2203	70	65	66	NA	,	-0.6	0	2		66	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron	GMPPA	NM_013335.3,NM_205847.2	,	0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077	,	,	220364787	1,13005	2203	4300	6503	SO:0001627	intron_variant			AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591	29926			22923	protein-coding gene	gene with protein product		615495			NA		Standard	NM_013335	NM_205847	NA	Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.40+50G>A	chr2.hg19:g.220364787G>A		NA	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	hg19	CCDS2441.1	0.02	14.759147	GGCxGGA	COVERED																																																																																			NOVEL	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130230.1	8	38.815643	KEEP	0	0	0	129	4279	GG	1	1	0		+	29	60	1075	0	0	79.918019	272	60	9065	545	ENST00000358215.3	0.096346	1
CHPF	79586	__UNKNOWN__	__UNKNOWN__	2	220404865	220404865	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220404865G>T	ENST00000243776.6	-	4	1816	c.1568C>A	c.(1567-1569)cCt>cAt	p.P523H	CHPF_ENST00000535926.1_Missense_Mutation_p.P361H	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	523	Ala-rich.	NA			carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CAAGAAGCCAGGGGCCAGGTC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													16	15	16	NA		NA	NA	2		NA											NA				220404865		2197	4288	6485	SO:0001583	missense			BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	79586	2.4.1.175, 2.4.1.226	Beta 3-glycosyltransferases, Beta 4-glycosyltransferases	24291	protein-coding gene	gene with protein product	chondroitin sulfate synthase 2	610405			NA	11230166, 12716890	Standard	NM_024536	NM_024536	NA	Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1568C>A	chr2.hg19:g.220404865G>T	ENSP00000243776:p.Pro523His	NA	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	hg19	CCDS2443.1	0.02	1.751565	CCAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.46	1.646670	0.29246	.	.	ENSG00000123989	ENST00000243776;ENST00000535926	T;T	0.15017	2.46;2.46	4.72	4.72	0.59763	.	0.751824	0.13094	N	0.414286	T	0.11922	0.0290	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.13407	0.009	T	0.22556	-1.0213	10	0.38643	T	0.18	-0.0867	18.2462	0.89986	0.0:0.0:1.0:0.0	.	523	Q8IZ52	CHSS2_HUMAN	H	523;361	ENSP00000243776:P523H;ENSP00000445571:P361H	ENSP00000243776:P523H	P	-	2	0	CHPF	220113109	0.018000	0.18449	0.096000	0.21009	0.998000	0.95712	2.019000	0.41001	2.619000	0.88677	0.561000	0.74099	CCT	NOVEL	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130268.1	1	10.233107	KEEP	0	0	0	34	1203	GG	0.999998	0.999557	0		-	5	60	172	0	0	11.360807	79	60	2906	150	ENST00000243776.6	0.059524	0.999559
OBSL1	23363	__UNKNOWN__	__UNKNOWN__	2	220432799	220432799	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220432799G>A	ENST00000404537.1	-	2	1316	c.1260C>T	c.(1258-1260)acC>acT	p.T420T	OBSL1_ENST00000265318.4_Silent_p.T420T|OBSL1_ENST00000373873.4_Silent_p.T420T|OBSL1_ENST00000373876.1_Silent_p.T420T|OBSL1_ENST00000289656.3_Silent_p.T7T|OBSL1_ENST00000603926.1_Silent_p.T420T	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	420	Ig-like 4.	NA			cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)				NA		Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CGTTGGCCACGGTGCGCACCC	0.622	NA	NA									OREG0003988	type=REGULATORY REGION|Gene=OBSL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													71	79	77	NA		NA	NA	2		NA											NA				220432799		2147	4247	6394	SO:0001819	synonymous_variant			BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006	23363		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	29092	protein-coding gene	gene with protein product		610991			NA	9734811	Standard		NM_015311	NA	Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1260C>T	chr2.hg19:g.220432799G>A		2266	A4KVA4|A4KVA5|Q96IW3|S4R3M6	hg19	CCDS46520.1	0.02	13.993157	CACxGTG	COVERED																																																																																			NOVEL	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322012.1	6	31.293011	KEEP	0	0	0	104	3430	GG	1	1	0		-	65	60	2337	0	0	192.265631	280	60	9289	533	ENST00000404537.1	0.188406	1
STK11IP	114790	__UNKNOWN__	__UNKNOWN__	2	220470396	220470396	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220470396C>T	ENST00000456909.1	+	8	775	c.685C>T	c.(685-687)Ccc>Tcc	p.P229S	STK11IP_ENST00000295641.10_Missense_Mutation_p.P240S|STK11IP_ENST00000459692.1_3'UTR			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	240		NA			protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)			breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AAGAATGGGACCCTCAGGGGC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	34	35	NA		NA	NA	2		NA											NA				220470396		1900	4105	6005	SO:0001583	missense			AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589	114790			19184	protein-coding gene	gene with protein product	LKB1 interacting protein	607172			NA	11741830	Standard	NM_052902	NM_052902	NA	Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.685C>T	chr2.hg19:g.220470396C>T	ENSP00000389383:p.Pro229Ser	NA	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	hg19		0.02	11.385219	GGAxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.67	3.445804	0.63178	.	.	ENSG00000144589	ENST00000456909;ENST00000426736;ENST00000295641	T;T	0.20200	2.09;2.09	4.21	4.21	0.49690	.	0.399918	0.22492	N	0.059357	T	0.23926	0.0579	N	0.16790	0.44	0.30954	N	0.724409	P;D;D;D	0.89917	0.713;0.974;1.0;0.993	B;P;D;P	0.87578	0.33;0.521;0.998;0.79	T	0.05321	-1.0892	10	0.18276	T	0.48	-16.3068	7.8597	0.29504	0.0:0.8891:0.0:0.1109	.	240;240;240;240	B4DUE4;B4DII2;Q8N1F8-2;Q8N1F8	.;.;.;S11IP_HUMAN	S	229;240;240	ENSP00000389383:P229S;ENSP00000295641:P240S	ENSP00000295641:P240S	P	+	1	0	STK11IP	220178640	0.137000	0.22531	0.994000	0.49952	0.799000	0.45148	1.929000	0.40114	2.188000	0.69820	0.643000	0.83706	CCC	NOVEL	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000131432.1	6	23.980395	KEEP	0	0	0	80	2711	CC	1	1	0		+	43	60	1570	0	0	124.595839	248	60	9037	495	ENST00000456909.1	0.147766	1
SLC4A3	6508	__UNKNOWN__	__UNKNOWN__	2	220498718	220498718	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220498718G>A	ENST00000358055.3	+	11	2073				SLC4A3_ENST00000373762.3_Intron|SLC4A3_ENST00000273063.6_Intron|SLC4A3_ENST00000373760.2_Intron|SLC4A3_ENST00000317151.3_Intron			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	NA		NA			bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGGCCGGGCGCCGGGGGCAG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													19	14	16	NA		NA	NA	2		NA											NA				220498718		2124	4187	6311	SO:0001627	intron_variant				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923	6508		Solute carriers	11029	protein-coding gene	gene with protein product	Anion exchanger 3, neuronal	106195	solute carrier family 4, anion exchanger, member 3		NA	8001971	Standard	NM_005070	NM_005070	NA	Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1561+17G>A	chr2.hg19:g.220498718G>A		NA	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	hg19	CCDS2445.1	0.02	4.613747	GGCxCCG	COVERED																																																																																			NOVEL	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316472.1	2	9.02819	KEEP	0	0	0	30	1004	GG	0.999997	0.999996	0		+	26	60	851	0	0	70.168564	95	60	3470	185	ENST00000358055.3	0.214876	0.999999
SLC4A3	6508	__UNKNOWN__	__UNKNOWN__	2	220499161	220499161	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:220499161G>A	ENST00000358055.3	+	12	2093	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	SLC4A3_ENST00000373762.3_Silent_p.E554E|SLC4A3_ENST00000273063.6_Silent_p.E554E|SLC4A3_ENST00000373760.2_Silent_p.E527E|SLC4A3_ENST00000317151.3_Silent_p.E527E			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	527		NA			bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTTCTTGGAGCAGCCTGCAG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													129	114	119	NA		NA	NA	2		NA											NA				220499161		2203	4300	6503	SO:0001819	synonymous_variant				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923	6508		Solute carriers	11029	protein-coding gene	gene with protein product	Anion exchanger 3, neuronal	106195	solute carrier family 4, anion exchanger, member 3		NA	8001971	Standard	NM_005070	NM_005070	NA	Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.1581G>A	chr2.hg19:g.220499161G>A		NA	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	hg19	CCDS2445.1	0.02	13.256606	GGAxCAG	COVERED																																																																																			NOVEL	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316472.1	5	19.865071	KEEP	0	0	0	66	2382	GG	1	1	0		+	43	60	1547	0	0	119.263091	296	60	10999	507	ENST00000358055.3	0.126844	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	228336800	228336800	__UNKNOWN__	IGR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:228336800G>C			NA	NA				TM4SF20 (92778 upstream) : MIR5703 (47 downstream)						NA		NA									NA						GGCCAGCAGAGGGCGCCAGCG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.228336800G>C		NA		hg19		0.02	4.704348	AGAxGGC	COVERED																																																																																			NOVEL					0			1	23.470657	KEEP	0	0	0	78	2680	GG	1	1	0			20	60	676	0	0	51.964421	124	60	4448	298		0.138889	1
SPHKAP	80309	__UNKNOWN__	__UNKNOWN__	2	228845191	228845191	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:228845191A>T	ENST00000392056.3	-	0	6391				SPHKAP_ENST00000344657.5_3'UTR	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	NA		NA				extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TTTGATCAAGAAAATAAAAGT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820	80309		A-kinase anchor proteins	30619	protein-coding gene	gene with protein product	sphingosine kinase type 1-interacting protein	611646			NA	12080051, 11214970	Standard	NM_030623	NM_030623	NA	Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.*1242T>A	chr2.hg19:g.228845191A>T		NA	Q68DA3|Q68DR8|Q9C0I5	hg19	CCDS46537.1	0.02	4.296443	AAGxAAA	COVERED																																																																																			NOVEL	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331750.1	1	5.114229	KEEP	0	0	0	17	523	AA	0.999366	0.999366	0		-	14	60	516	0	0	39.349441	109	60	3933	167	ENST00000392056.3	0.113821	0.999999
SPHKAP	80309	__UNKNOWN__	__UNKNOWN__	2	228890174	228890174	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:228890174T>C	ENST00000392056.3	-	5	423	c.377A>G	c.(376-378)aAt>aGt	p.N126S	SPHKAP_ENST00000344657.5_Missense_Mutation_p.N126S	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	126		NA				extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		AACAATTTCATTTTCTTTTGG	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													126	121	123	NA		NA	NA	2		NA											NA				228890174		2203	4300	6503	SO:0001583	missense				CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820	80309		A-kinase anchor proteins	30619	protein-coding gene	gene with protein product	sphingosine kinase type 1-interacting protein	611646			NA	12080051, 11214970	Standard	NM_030623	NM_030623	NA	Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.377A>G	chr2.hg19:g.228890174T>C	ENSP00000375909:p.Asn126Ser	NA	Q68DA3|Q68DR8|Q9C0I5	hg19	CCDS46537.1	0.02	12.454259	TCAxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	24.8	4.569979	0.86542	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.16324	2.35;2.36	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.33030	0.0849	L	0.32530	0.975	0.50813	D	0.999898	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	T	0.03443	-1.1036	10	0.87932	D	0	.	16.0034	0.80327	0.0:0.0:0.0:1.0	.	126;126	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	S	126	ENSP00000375909:N126S;ENSP00000339886:N126S	ENSP00000339886:N126S	N	-	2	0	SPHKAP	228598418	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.930000	0.75858	2.371000	0.80710	0.533000	0.62120	AAT	NOVEL	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331750.1	2	9.930603	KEEP	0	0	0	33	1087	TT	0.999998	0.999998	0		-	25	60	975	0	0	72.765832	257	60	9376	381	ENST00000392056.3	0.088652	1
TRIP12	9320	__UNKNOWN__	__UNKNOWN__	2	230654530	230654530	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:230654530C>T	ENST00000389045.3	-	28	3581				TRIP12_ENST00000283943.5_Intron|TRIP12_ENST00000389044.4_Intron			Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		AAAGGCTAAGCCAGTGCAGCC	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													56	57	57	NA		NA	NA	2		NA											NA				230654530		1326	2309	3635	SO:0001627	intron_variant			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827	9320			12306	protein-coding gene	gene with protein product		604506			NA	7776974	Standard	NM_004238	XM_005246961	NA	Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000389045.3:c.3509-52G>A	chr2.hg19:g.230654530C>T		NA	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	hg19		0.02	4.223147	AAGxCAG	COVERED																																																																																			NOVEL	TRIP12-005	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331865.1	0	9.931975	KEEP	0	0	0	33	1136	CC	0.999998	0.999996	0		-	9	60	311	0	0	21.519055	111	60	3917	184	ENST00000389045.3	0.075	0.999999
SLC16A14	151473	__UNKNOWN__	__UNKNOWN__	2	230900319	230900319	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:230900319C>T	ENST00000295190.4	-	0	3768					NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		GATTCTTTAACAGCAGCCAAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053	151473		Solute carriers	26417	protein-coding gene	gene with protein product	monocarboxylic acid transporter 14	NA	solute carrier family 16 (monocarboxylic acid transporters), member 14		NA		Standard	NM_152527	NM_152527	NA	Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.*1777G>A	chr2.hg19:g.230900319C>T		NA	A8KA08|Q53R92|Q96NI7	hg19	CCDS2473.1	0.02	9.073481	TAAxAGC	COVERED																																																																																			NOVEL	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256918.2	4	7.8252	KEEP	0	0	0	26	920	CC	0.999957	0.999957	0		-	34	60	1241	0	0	99.639162	180	60	6813	269	ENST00000295190.4	0.158879	1
B3GNT7	93010	__UNKNOWN__	__UNKNOWN__	2	232263361	232263361	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:232263361C>T	ENST00000287590.5	+	2	1192	c.931C>T	c.(931-933)Cgg>Tgg	p.R311W		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	311		NA			carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		CAGCCTGGCCCGGCGCCTGCA	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													24	30	28	NA		NA	NA	2		NA											NA				232263361		1978	4146	6124	SO:0001583	missense			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966	93010		Beta 3-glycosyltransferases	18811	protein-coding gene	gene with protein product		615313			NA	12061784	Standard	NM_145236	NM_145236	NA	Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.931C>T	chr2.hg19:g.232263361C>T	ENSP00000287590:p.Arg311Trp	NA	B3KWY4|B7WNP0	hg19	CCDS46540.1	0.02	7.122031	GCCxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.92	3.254262	0.59212	.	.	ENSG00000156966	ENST00000287590	T	0.45276	0.9	5.05	4.15	0.48705	.	0.266100	0.36854	N	0.002378	T	0.64068	0.2565	M	0.84082	2.675	0.47094	D	0.999318	D	0.89917	1.0	D	0.68192	0.956	T	0.68477	-0.5398	10	0.72032	D	0.01	.	11.4455	0.50120	0.4611:0.5389:0.0:0.0	.	311	Q8NFL0	B3GN7_HUMAN	W	311	ENSP00000287590:R311W	ENSP00000287590:R311W	R	+	1	2	B3GNT7	231971605	0.723000	0.28027	0.998000	0.56505	0.987000	0.75469	1.317000	0.33631	1.087000	0.41251	0.561000	0.74099	CGG	NOVEL	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000332827.1	5	8.077721	KEEP	0	0	0	27	850	CC	0.999988	0.999988	0		+	82	60	2885	0	0	271.927421	105	60	3516	226	ENST00000287590.5	0.438503	1
AC106876.2	0	__UNKNOWN__	__UNKNOWN__	2	233880422	233880422	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:233880422C>A	ENST00000409905.1	+	3	470	c.232C>A	c.(232-234)Caa>Aaa	p.Q78K							NA		NA									NA						CAAAGCCTTCCAACAGAGCCT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000409905.1:c.232C>A	chr2.hg19:g.233880422C>A	ENSP00000386846:p.Gln78Lys	NA		hg19		0.02	29.84114	TTCxAAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	3.106	-0.183683	0.06340	.	.	ENSG00000222001	ENST00000409905	.	.	.	2.43	0.558	0.17266	.	.	.	.	.	T	0.44746	0.1308	.	.	.	.	.	.	.	.	.	.	.	.	T	0.53358	-0.8450	4	0.87932	D	0	.	4.6843	0.12750	0.0:0.6744:0.0:0.3256	.	.	.	.	K	78	.	ENSP00000386846:Q78K	Q	+	1	0	AC106876.2	233588666	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-0.177000	0.09796	0.135000	0.18707	0.591000	0.81541	CAA	NOVEL	AC106876.2-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000330277.1	8	32.168545	KEEP	0	0	0	107	3696	CC	1	1	0		+	63	60	2270	0	0	165.964825	618	60	22481	941	ENST00000409905.1	0.092511	1
UGT1A6	54578	__UNKNOWN__	__UNKNOWN__	2	234676947	234676947	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:234676947T>G	ENST00000305139.6	+	4	1302	c.1163T>G	c.(1162-1164)gTg>gGg	p.V388G	UGT1A3_ENST00000482026.1_Missense_Mutation_p.V390G|UGT1A4_ENST00000373409.3_Missense_Mutation_p.V390G|UGT1A1_ENST00000608381.1_Missense_Mutation_p.V390G|UGT1A1_ENST00000608383.1_Missense_Mutation_p.V389G|UGT1A6_ENST00000373424.1_Missense_Mutation_p.V121G|UGT1A5_ENST00000373414.3_Missense_Mutation_p.V390G|UGT1A6_ENST00000406651.1_Missense_Mutation_p.V121G|UGT1A1_ENST00000373450.4_Missense_Mutation_p.V386G|UGT1A7_ENST00000373426.3_Missense_Mutation_p.V386G|UGT1A9_ENST00000354728.4_Missense_Mutation_p.V386G|UGT1A1_ENST00000609637.1_Missense_Mutation_p.V386G|UGT1A10_ENST00000344644.5_Missense_Mutation_p.V386G|UGT1A10_ENST00000373445.1_Missense_Mutation_p.V386G|UGT1A1_ENST00000360418.3_Missense_Mutation_p.V389G|UGT1A1_ENST00000609767.1_Missense_Mutation_p.V390G|UGT1A8_ENST00000305208.5_Missense_Mutation_p.V389G	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6	388		NA			cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(86;0.000765)|all_lung(227;0.00267)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0457)|Lung SC(224;0.128)		Epithelial(121;5.86e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000384)|Lung(119;0.00306)|LUSC - Lung squamous cell carcinoma(224;0.00702)	Acetaminophen(DB00316)|Deferiprone(DB08826)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Propofol(DB00818)|Valproic Acid(DB00313)	GTTCCCATGGTGATGATGCCC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													231	202	212	NA		NA	NA	2		NA											NA				234676947		2203	4300	6503	SO:0001583	missense			M84130	CCDS2507.1, CCDS2508.1	2q37	2010-03-05	2005-07-20		ENSG00000167165	ENSG00000167165	54578		UDP glucuronosyltransferases	12538	other	complex locus constituent		606431	UDP glycosyltransferase 1 family, polypeptide A6		NA	9295054, 1339448	Standard	NM_205862	NM_001072	NA	Approved	HLUGP, GNT1, UGT1F		P19224	OTTHUMG00000059122	ENST00000305139.6:c.1163T>G	chr2.hg19:g.234676947T>G	ENSP00000303174:p.Val388Gly	NA	A6NKK6|B8K289|Q96TE7	hg19	CCDS2507.1	0.02	6.657633	TGGxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	22.2	4.256724	0.80246	.	.	ENSG00000242366;ENSG00000242515;ENSG00000242515;ENSG00000241119;ENSG00000244122;ENSG00000167165;ENSG00000167165;ENSG00000167165;ENSG00000240224;ENSG00000244474;ENSG00000243135;ENSG00000241635;ENSG00000241635	ENST00000373450;ENST00000344644;ENST00000373445;ENST00000354728;ENST00000373426;ENST00000373424;ENST00000305139;ENST00000406651;ENST00000373414;ENST00000373409;ENST00000482026;ENST00000305208;ENST00000360418	T;T;T;T;T;T;T;T;T;T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49;2.73;2.73;2.73;-0.27;-0.49;-0.49;-0.49;-0.49;-0.49	5.88	5.88	0.94601	.	0.068071	0.56097	D	0.000023	D	0.89996	0.6877	H	0.97315	3.98	0.58432	D	0.999996	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.993;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.999;1.0;0.79;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.93422	0.6778	10	0.87932	D	0	.	16.3015	0.82820	0.0:0.0:0.0:1.0	.	389;390;390;390;388;386;386;386;389;390;390;390;388;386;386;386;386;386	A6NJC3;Q5DT01;B8K288;Q5DSZ9;B8K289;Q5DSZ7;Q5DSZ5;Q5DSZ6;P22309;P35503;P22310;P35504;P19224;Q9HAW7;O60656;Q9HAW8;Q7Z6H8;Q9HAW9	.;.;.;.;.;.;.;.;UD11_HUMAN;UD13_HUMAN;UD14_HUMAN;UD15_HUMAN;UD16_HUMAN;UD17_HUMAN;UD19_HUMAN;UD110_HUMAN;.;UD18_HUMAN	G	386;386;386;386;386;121;388;121;390;390;390;389;389	ENSP00000362549:V386G;ENSP00000343838:V386G;ENSP00000362544:V386G;ENSP00000346768:V386G;ENSP00000362525:V386G;ENSP00000362523:V121G;ENSP00000303174:V388G;ENSP00000386107:V121G;ENSP00000362513:V390G;ENSP00000362508:V390G;ENSP00000418532:V390G;ENSP00000304845:V389G;ENSP00000353593:V389G	ENSP00000343838:V386G	V	+	2	0	UGT1A7;UGT1A6;UGT1A10;UGT1A9;UGT1A8;UGT1A3;UGT1A5;UGT1A4;UGT1A1	234341686	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.545000	0.82128	2.239000	0.73571	0.533000	0.62120	GTG	NOVEL	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130988.1	2	4.212237	KEEP	0	0	0	14	432	TT	0.995343	0.995343	0		+	36	60	1287	0	0	106.475452	147	60	5210	252	ENST00000305139.6	0.196721	1
ASB18	401036	__UNKNOWN__	__UNKNOWN__	2	237150130	237150130	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:237150130G>T	ENST00000409749.3	-	2	205				AC079135.1_ENST00000415226.1_RNA|ASB18_ENST00000330842.6_Missense_Mutation_p.L12I	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	NA		NA			intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		AATATTTGAAGTTTTCCTCTC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177	401036		Ankyrin repeat domain containing	19770	protein-coding gene	gene with protein product		NA	ankyrin repeat and SOCS box-containing 18		NA	12076535	Standard	NM_212556	NM_212556	NA	Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.206-85C>A	chr2.hg19:g.237150130G>T		NA	B6ZDL7	hg19	CCDS46548.1	0.02	6.540498	GAAxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.16	1.558374	0.27827	.	.	ENSG00000182177	ENST00000330842	T	0.40225	1.04	4.88	4.88	0.63580	.	1.620550	0.04021	N	0.299849	T	0.54775	0.1879	.	.	.	0.09310	N	1	D	0.56035	0.974	P	0.56612	0.802	T	0.34725	-0.9817	8	.	.	.	.	8.1062	0.30887	0.0854:0.1611:0.7534:0.0	.	12	Q6ZVZ8-2	.	I	12	ENSP00000329970:L12I	.	L	-	1	0	ASB18	236814869	0.818000	0.29161	0.030000	0.17652	0.668000	0.39293	1.964000	0.40462	2.260000	0.74910	0.655000	0.94253	CTT	NOVEL	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329436.1	3	7.222777	KEEP	0	0	0	24	840	GG	0.999909	0.999909	0		-	27	60	973	0	0	76.798498	158	60	5879	250	ENST00000409749.3	0.145946	1
IQCA1	79781	__UNKNOWN__	__UNKNOWN__	2	237402405	237402405	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:237402405A>G	ENST00000409907.3	-	3	731				IQCA1_ENST00000309507.5_Intron|IQCA1_ENST00000431676.2_Intron	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	NA		NA					ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						AAAATGATATACAAACCATGT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													83	78	80	NA		NA	NA	2		NA											NA				237402405		1843	4079	5922	SO:0001627	intron_variant			AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321	79781		ATPases / AAA-type	26195	protein-coding gene	gene with protein product	dynein regulatory complex subunit 11	NA	IQ motif containing with AAA domain	IQCA	NA	23427265	Standard	NM_024726	NM_024726	NA	Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.456+5T>C	chr2.hg19:g.237402405A>G		NA	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	hg19	CCDS46549.1	0.02	2.224519	TATxCAA	COVERED																																																																																			NOVEL	IQCA1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329266.1	2	5.114418	KEEP	0	0	0	17	512	AA	0.999366	0.999093	0		-	6	60	230	0	0	16.384268	81	60	2900	125	ENST00000409907.3	0.068966	0.999726
ESPNL	339768	__UNKNOWN__	__UNKNOWN__	2	239039789	239039789	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:239039789A>G	ENST00000343063.3	+	9	2697	c.2434A>G	c.(2434-2436)Aag>Gag	p.K812E	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409169.1_Missense_Mutation_p.K768E|ESPNL_ENST00000409506.1_Missense_Mutation_p.K444E	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	812		NA								endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGGCAACTGGAAGGCCATCAT	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	4	3	NA		NA	NA	2		NA											NA				239039789		1919	3765	5684	SO:0001583	missense			AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488	339768		Ankyrin repeat domain containing	27937	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_194312	NM_194312	NA	Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2434A>G	chr2.hg19:g.239039789A>G	ENSP00000339115:p.Lys812Glu	NA	Q66K27|Q6ZVG1|Q8IVU2	hg19	CCDS2525.1	0.02	7.083707	TGGxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	19.79	3.892789	0.72524	.	.	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.67865	-0.29;0.78;0.39	4.62	4.62	0.57501	.	0.072279	0.53938	D	0.000051	T	0.78432	0.4282	M	0.61703	1.905	0.37729	D	0.925211	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.957	T	0.82993	-0.0181	10	0.87932	D	0	-32.81	13.0296	0.58835	1.0:0.0:0.0:0.0	.	768;812	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	E	812;768;444	ENSP00000339115:K812E;ENSP00000386577:K768E;ENSP00000386579:K444E	ENSP00000339115:K812E	K	+	1	0	ESPNL	238704528	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	3.032000	0.49736	1.722000	0.51474	0.377000	0.23210	AAG	NOVEL	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257164.2	3	15.64692	KEEP	0	0	0	52	1645	AA	1	1	0		+	33	60	1163	0	0	94.912758	146	60	5208	295	ENST00000343063.3	0.184358	1
KLHL30	377007	__UNKNOWN__	__UNKNOWN__	2	239049673	239049673	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:239049673C>T	ENST00000409223.1	+	2	385	c.278C>T	c.(277-279)aCa>aTa	p.T93I	KLHL30_ENST00000305959.4_Missense_Mutation_p.T75I			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	93	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.	NA								lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		TTCGTGTACACAGGCCGGCTG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	94	90	NA		NA	NA	2		NA											NA				239049673		2175	4258	6433	SO:0001583	missense				CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427	377007		Kelch-like, BTB/POZ domain containing	24770	protein-coding gene	gene with protein product		NA	kelch-like 30 (Drosophila)		NA		Standard	NM_198582	NM_198582	NA	Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.278C>T	chr2.hg19:g.239049673C>T	ENSP00000386389:p.Thr93Ile	NA	Q6ZUS1	hg19	CCDS46555.2	0.02	10.903859	ACAxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	25.0	4.596522	0.86953	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.75050	-0.9;-0.9	5.75	4.87	0.63330	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.051918	0.85682	D	0.000000	D	0.89746	0.6804	H	0.94620	3.56	0.53688	D	0.999976	D	0.89917	1.0	D	0.97110	1.0	D	0.92539	0.6040	10	0.87932	D	0	.	15.0085	0.71530	0.1439:0.8561:0.0:0.0	.	93	Q0D2K2	KLH30_HUMAN	I	93;75	ENSP00000386389:T93I;ENSP00000302386:T75I	ENSP00000302386:T75I	T	+	2	0	KLHL30	238714412	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	5.975000	0.70475	1.412000	0.46977	0.655000	0.94253	ACA	NOVEL	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328518.1	1	26.485166	KEEP	0	0	0	88	3080	CC	1	1	0		+	16	60	550	0	0	36.717156	239	60	8995	417	ENST00000409223.1	0.062745	1
KLHL30	377007	__UNKNOWN__	__UNKNOWN__	2	239049946	239049946	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:239049946C>G	ENST00000409223.1	+	2	658	c.551C>G	c.(550-552)gCc>gGc	p.A184G	KLHL30_ENST00000305959.4_Missense_Mutation_p.A166G			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	184	BACK.	NA								lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ACTTGTCTGGCCGGCGACCTG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													12	16	14	NA		NA	NA	2		NA											NA				239049946		2065	4186	6251	SO:0001583	missense				CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427	377007		Kelch-like, BTB/POZ domain containing	24770	protein-coding gene	gene with protein product		NA	kelch-like 30 (Drosophila)		NA		Standard	NM_198582	NM_198582	NA	Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.551C>G	chr2.hg19:g.239049946C>G	ENSP00000386389:p.Ala184Gly	NA	Q6ZUS1	hg19	CCDS46555.2	0.02	16.509287	TGGxCGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108884	0.37242	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.68903	-0.36;-0.36	5.82	4.93	0.64822	BTB/Kelch-associated (2);	0.345497	0.30446	N	0.009614	T	0.54695	0.1874	N	0.25890	0.77	0.27124	N	0.962067	B	0.19073	0.033	B	0.20577	0.03	T	0.49409	-0.8943	10	0.39692	T	0.17	.	14.2238	0.65845	0.0:0.7156:0.2844:0.0	.	184	Q0D2K2	KLH30_HUMAN	G	184;166	ENSP00000386389:A184G;ENSP00000302386:A166G	ENSP00000302386:A166G	A	+	2	0	KLHL30	238714685	0.996000	0.38824	0.994000	0.49952	0.920000	0.55202	2.897000	0.48664	1.420000	0.47138	0.655000	0.94253	GCC	NOVEL	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328518.1	1	38.18199	KEEP	0	1	5	129	4336	CC	1	1	0		+	63	60	2289	0	0	185.202414	313	60	10678	689	ENST00000409223.1	0.167553	1
HES6	55502	__UNKNOWN__	__UNKNOWN__	2	239147105	239147105	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:239147105G>A	ENST00000272937.5	-	0	1256				AC096574.4_ENST00000456601.1_RNA|HES6_ENST00000409002.3_3'UTR|HES6_ENST00000409160.3_3'UTR					hes family bHLH transcription factor 6	NA		NA								lung(1)|skin(1)	2		Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.23e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.29e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.19e-08)|BRCA - Breast invasive adenocarcinoma(100;5.98e-05)|Lung(119;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.0148)		AGGGCTGCCTGGAACACTAGT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB035179	CCDS2527.1, CCDS46556.1, CCDS63180.1	2q37.3	2013-10-17	2013-10-17		ENSG00000144485	ENSG00000144485	55502		Basic helix-loop-helix proteins	18254	protein-coding gene	gene with protein product		610331	hairy and enhancer of split 6 (Drosophila)		NA	10851137	Standard	NM_018645	XM_005246095	NA	Approved	bHLHb41	uc002vxz.3	Q96HZ4	OTTHUMG00000133340	ENST00000272937.5:c.*363C>T	chr2.hg19:g.239147105G>A		NA		hg19	CCDS2527.1	0.02	4.860808	CCTxGAA	COVERED																																																																																			NOVEL	HES6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257170.2	0	14.446663	KEEP	0	0	0	48	1667	GG	1	1	0		-	26	60	960	0	0	80.453751	101	60	3632	216	ENST00000272937.5	0.204724	1
PER2	8864	__UNKNOWN__	__UNKNOWN__	2	239161879	239161879	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:239161879G>A	ENST00000254657.3	-	19	3064	c.2785C>T	c.(2785-2787)Cct>Tct	p.P929S	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	929	Interaction with PPARG. {ECO:0000250|UniProtKB:O54943}.|Pro-rich.	NA			circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		GGAAACTGAGGCTGGCTGGGG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													44	51	48	NA		NA	NA	2		NA											NA				239161879		2203	4300	6503	SO:0001583	missense			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326	8864			8846	protein-coding gene	gene with protein product		603426	period (Drosophila) homolog 2, period homolog 2 (Drosophila)		NA	9427249, 17218255	Standard	NM_022817	NM_022817	NA	Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2785C>T	chr2.hg19:g.239161879G>A	ENSP00000254657:p.Pro929Ser	NA	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	hg19	CCDS2528.1	0.02	6.231061	GAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	1.774	-0.483634	0.04383	.	.	ENSG00000132326	ENST00000254657	T	0.11712	2.75	2.89	0.73	0.18271	.	2.885350	0.03960	N	0.289837	T	0.10637	0.0260	L	0.46947	1.48	0.80722	D	1	P;B	0.37061	0.58;0.267	B;B	0.35114	0.196;0.058	T	0.31110	-0.9955	10	0.19147	T	0.46	-0.4575	6.6501	0.22957	0.0:0.1839:0.6015:0.2147	.	929;929	B4DH14;O15055	.;PER2_HUMAN	S	929	ENSP00000254657:P929S	ENSP00000254657:P929S	P	-	1	0	PER2	238826618	0.128000	0.22383	0.071000	0.20095	0.022000	0.10575	0.255000	0.18333	0.010000	0.14839	0.549000	0.68633	CCT	NOVEL	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257167.1	6	16.493206	KEEP	0	0	0	55	1853	GG	1	1	0		-	26	60	867	0	0	68.909964	126	60	4556	257	ENST00000254657.3	0.171053	1
HDAC4	9759	__UNKNOWN__	__UNKNOWN__	2	240112694	240112694	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:240112694T>C	ENST00000345617.3	-	4	886				HDAC4_ENST00000541256.1_5'UTR	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	NA		NA			B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GCACTGCTCCTGGCACAGCCC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024	9759			14063	protein-coding gene	gene with protein product		605314	brachydactyly-mental retardation syndrome	BDMR	NA	10206986, 10220385, 20691407	Standard	NM_006037	NM_006037	NA	Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.95-921A>G	chr2.hg19:g.240112694T>C		NA	Q9UND6	hg19	CCDS2529.1	0.02	9.912934	TCCxGGC	COVERED																																																																																			NOVEL	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257174.2	1	24.068456	KEEP	0	0	0	80	2492	TT	1	1	0		-	24	60	783	0	0	54.528366	253	60	9274	483	ENST00000345617.3	0.086643	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	241929108	241929108	__UNKNOWN__	IGR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:241929108G>A			NA	NA				AC104809.2 (3619 upstream) : SNED1 (9146 downstream)						NA		NA									NA						CACACCCAGCGGCTCCAGGAC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.241929108G>A		NA		hg19		0.02	7.276331	AGCxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893925	0.33442	.	.	ENSG00000226321	ENST00000443866	.	.	.	2.28	1.34	0.21922	.	.	.	.	.	T	0.40619	0.1124	.	.	.	.	.	.	.	.	.	.	.	.	T	0.44128	-0.9348	4	0.12430	T	0.62	.	11.2559	0.49054	0.1194:0.0:0.8806:0.0	.	.	.	.	Q	163	.	ENSP00000397968:R163Q	R	+	2	0	AC104809.3	241577781	0.874000	0.30092	0.670000	0.29842	0.312000	0.27988	0.880000	0.28159	-0.129000	0.11620	-1.595000	0.00837	CGG	NOVEL					0			4	30.991953	KEEP	0	0	0	103	3434	GG	1	1	0			35	60	1334	0	0	113.815825	123	60	4288	358		0.221519	1
PPP1R7	5510	__UNKNOWN__	__UNKNOWN__	2	242102694	242102694	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:242102694C>T	ENST00000234038.6	+	7	1071				PPP1R7_ENST00000406106.3_Intron|PPP1R7_ENST00000402734.1_Intron|PPP1R7_ENST00000401987.1_Intron|PPP1R7_ENST00000407025.1_Intron|PPP1R7_ENST00000404405.3_Intron|PPP1R7_ENST00000272983.8_Intron|PPP1R7_ENST00000485630.1_Intron	NM_001282412.1|NM_001282413.1|NM_002712.1	NP_001269341.1|NP_001269342.1|NP_002703.1	Q15435	PP1R7_HUMAN	protein phosphatase 1, regulatory subunit 7	NA		NA			positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	enzyme regulator activity (GO:0030234)|protein phosphatase type 1 regulator activity (GO:0008599)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|ovary(3)	23		all_cancers(19;6.1e-33)|all_epithelial(40;1.07e-13)|Breast(86;0.000141)|Renal(207;0.00528)|all_lung(227;0.0446)|Ovarian(221;0.104)|Lung NSC(271;0.115)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.92e-32)|all cancers(36;5.35e-29)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-14)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.24e-08)|BRCA - Breast invasive adenocarcinoma(100;3.56e-06)|Lung(119;0.000588)|LUSC - Lung squamous cell carcinoma(224;0.0048)|Colorectal(34;0.0137)|COAD - Colon adenocarcinoma(134;0.096)		TCTGTCCTTTCCACAGGCAAT	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(62;446 1299 5417 11238 27640)					NA		NA				0													177	187	183	NA		NA	NA	2		NA											NA				242102694		2203	4300	6503	SO:0001627	intron_variant			AF067136	CCDS2546.1, CCDS63190.1, CCDS63192.1, CCDS63193.1, CCDS63194.1	2q37.3	2012-04-17	2011-10-04		ENSG00000115685	ENSG00000115685	5510		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	9295	protein-coding gene	gene with protein product		602877	protein phosphatase 1, regulatory (inhibitor) subunit 7		NA	7498485, 7670491, 10231361	Standard	NM_002712	NM_001282413	NA	Approved	sds22	uc002wat.1	Q15435	OTTHUMG00000133390	ENST00000234038.6:c.598-6C>T	chr2.hg19:g.242102694C>T		NA	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	hg19	CCDS2546.1	0.02	6.757316	TTTxCAC	COVERED																																																																																			NOVEL	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257244.4	3	19.863098	KEEP	0	0	0	66	2271	CC	1	1	0		+	37	60	1339	0	0	111.547239	146	60	5403	337	ENST00000234038.6	0.202186	1
SEPT2	4735	__UNKNOWN__	__UNKNOWN__	2	242285528	242285528	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:242285528A>G	ENST00000391973.2	+	10	1370				SEPT2_ENST00000407971.1_Intron|SEPT2_ENST00000402092.2_Intron|SEPT2_ENST00000391971.2_Intron|SEPT2_ENST00000360051.3_Intron|SEPT2_ENST00000401990.1_Intron	NM_006155.1	NP_006146.1	Q15019	SEPT2_HUMAN	septin 2	NA		NA			cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|neuron projection development (GO:0031175)|regulation of L-glutamate transport (GO:0002036)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|synapse (GO:0045202)	enzyme regulator activity (GO:0030234)|GTP binding (GO:0005525)			central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12		all_cancers(19;7.62e-41)|all_epithelial(40;1.71e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.24e-34)|all cancers(36;7.15e-32)|OV - Ovarian serous cystadenocarcinoma(60;1.21e-15)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;3.16e-06)|Lung(119;7.81e-05)|LUSC - Lung squamous cell carcinoma(224;0.000742)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0889)		TTTTTTTCTCATGAGAATGTC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													42	32	35	NA		NA	NA	2		NA											NA				242285528		692	1591	2283	SO:0001627	intron_variant			D28540	CCDS2548.1, CCDS63195.1, CCDS74682.1	2q37.3	2013-01-21	2005-01-11	2005-01-12	ENSG00000168385	ENSG00000168385	4735		Septins	7729	protein-coding gene	gene with protein product		601506	neural precursor cell expressed, developmentally down-regulated 5	DIFF6, NEDD5	NA	8697812	Standard	NM_006155	XM_005247011	NA	Approved	KIAA0158, hNedd5, Pnutl3	uc002wbd.3	Q15019	OTTHUMG00000133394	ENST00000391973.2:c.843-53A>G	chr2.hg19:g.242285528A>G		NA	B4DGE8|Q14132|Q53QU3|Q8IUK9|Q96CB0	hg19	CCDS2548.1	0.02	4.780199	CTCxTGA	COVERED																																																																																			NOVEL	SEPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323177.3	1	7.523351	KEEP	0	0	0	25	801	AA	0.999931	0.999904	0		+	19	60	639	0	0	51.670625	83	60	3085	151	ENST00000391973.2	0.186275	0.999973
STK25	10494	__UNKNOWN__	__UNKNOWN__	2	242432954	242432954	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:242432954C>T	ENST00000316586.4	-	0	3753				FARP2_ENST00000264042.3_Intron	NM_001271977.1|NM_001271978.1|NM_001282308.1	NP_001258906.1|NP_001258907.1|NP_001269237.1	O00506	STK25_HUMAN	serine/threonine kinase 25	NA		NA			establishment or maintenance of cell polarity (GO:0007163)|Golgi localization (GO:0051645)|positive regulation of axonogenesis (GO:0050772)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;8.24e-34)|all cancers(36;3.46e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.6e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.1e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0839)		GTTTTCTGGGCCCTGGAAAGG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(99;1100 1566 7679 28647 48345)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D63780	CCDS2549.1, CCDS63199.1, CCDS63200.1	2q37.3	2010-06-25	2010-06-25		ENSG00000115694	ENSG00000115694	10494			11404	protein-coding gene	gene with protein product		602255	serine/threonine kinase 25 (Ste20, yeast homolog)		NA	8887545, 9160885, 15037601	Standard	NM_006374	NM_001271977	NA	Approved	SOK1, YSK1	uc002wbp.4	O00506	OTTHUMG00000133408	ENST00000316586.4:c.*2123G>A	chr2.hg19:g.242432954C>T		NA	A8K6Z3|A8K7D2|B7Z9K1|Q15522|Q5BJF1	hg19	CCDS2549.1	0.02	10.587925	GGGxCCT	COVERED																																																																																			NOVEL	STK25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257265.4	5	10.230294	KEEP	0	0	0	34	1162	CC	0.999998	0.999998	0		-	38	60	1347	0	0	104.653005	241	70	8288	379	ENST00000316586.4	0.136201	1
NEU4	129807	__UNKNOWN__	__UNKNOWN__	2	242754597	242754597	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr2:242754597G>A	ENST00000391969.2	+	0	654				NEU4_ENST00000325935.6_Intron|NEU4_ENST00000404257.1_Intron|NEU4_ENST00000405370.1_Intron|NEU4_ENST00000407683.1_Intron	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	NA		NA			ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CGGGCTGTGCGTGCTCACGCT	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099	129807			21328	protein-coding gene	gene with protein product		608527			NA		Standard	NM_080741	NM_001167600	NA	Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.-58G>A	chr2.hg19:g.242754597G>A		NA	A8K056|J3KNJ5|Q96D64	hg19	CCDS54442.1	0.02	12.027665	TGCxTGC	COVERED																																																																																			NOVEL	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257270.2	0	17.756322	KEEP	0	0	0	59	2003	GG	1	1	0		+	57	60	2068	0	0	175.501574	195	60	6816	403	ENST00000391969.2	0.22619	1
RAD18	56852	__UNKNOWN__	__UNKNOWN__	3	8922389	8922389	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:8922389C>T	ENST00000264926.2	-	0	2256					NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	NA		NA			DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		GAAGAATATGCGCAATGTTTC	0.308	NA	NA						Rad6 pathway						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950	56852		RING-type (C3HC4) zinc fingers	18278	protein-coding gene	gene with protein product		605256	RAD18 homolog (S. cerevisiae)		NA	10884424, 10908344	Standard	NM_020165	NM_020165	NA	Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.*652G>A	chr3.hg19:g.8922389C>T		NA	Q58F55|Q9NRT6	hg19	CCDS2571.1	0.02	1.852071	ATGxGCA	COVERED																																																																																			NOVEL	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207071.2	2	9.26085	KEEP	0	1	23	39	1331	CC	1	0.999559	0		-	5	60	186	0	0	12.75873	79	60	2723	155	ENST00000264926.2	0.059524	0.999559
PPARG	5468	__UNKNOWN__	__UNKNOWN__	3	12458621	12458621	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:12458621C>T	ENST00000397000.1	+	5	803				PPARG_ENST00000397015.2_Missense_Mutation_p.A385V|PPARG_ENST00000397026.2_Missense_Mutation_p.A391V|PPARG_ENST00000539812.1_Intron|PPARG_ENST00000309576.6_Missense_Mutation_p.A385V|PPARG_ENST00000397010.2_Missense_Mutation_p.A385V|PPARG_ENST00000287820.6_Missense_Mutation_p.A413V|PPARG_ENST00000397012.2_Missense_Mutation_p.A385V			P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|brown fat cell differentiation (GO:0050873)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|cellular response to lithium ion (GO:0071285)|epithelial cell differentiation (GO:0030855)|fatty acid oxidation (GO:0019395)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|innate immune response (GO:0045087)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|lipoprotein transport (GO:0042953)|long-chain fatty acid transport (GO:0015909)|low-density lipoprotein particle receptor biosynthetic process (GO:0045713)|monocyte differentiation (GO:0030224)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of cell growth (GO:0030308)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ regeneration (GO:0031100)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|placenta development (GO:0001890)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood pressure (GO:0008217)|regulation of cholesterol transporter activity (GO:0060694)|regulation of transcription involved in cell fate commitment (GO:0060850)|response to caffeine (GO:0031000)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to lipid (GO:0033993)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|arachidonic acid binding (GO:0050544)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|prostaglandin receptor activity (GO:0004955)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		PAX8/PPARG(117)	breast(2)|endometrium(4)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20					Balsalazide(DB01014)|Bezafibrate(DB01393)|Glipizide(DB01067)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Mesalazine(DB00244)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Pioglitazone(DB01132)|Repaglinide(DB00912)|Rosiglitazone(DB00412)|Sulfasalazine(DB00795)|Telmisartan(DB00966)	AGCGACTTGGCAATATTTATT	0.413	NA	NA	T	PAX8	follicular thyroid		Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension							NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		3	3p25	5468	peroxisome proliferative activated receptor, gamma	yes	E	0													35	36	36	NA		NA	NA	3		NA											NA				12458621		2203	4300	6503	SO:0001627	intron_variant			X90563	CCDS2609.1, CCDS2610.2	3p25	2013-01-16	2006-10-17		ENSG00000132170	ENSG00000132170	5468		Nuclear hormone receptors	9236	protein-coding gene	gene with protein product		601487	peroxisome proliferative activated receptor, gamma		NA	7862171, 9750197	Standard	NM_005037	NM_005037	NA	Approved	PPARG1, PPARG2, NR1C3, PPARgamma	uc003bwx.3	P37231	OTTHUMG00000129764	ENST00000397000.1:c.735+11041C>T	chr3.hg19:g.12458621C>T		NA	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	hg19		0.02	8.804537	TGGxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	29.7	5.025095	0.93518	.	.	ENSG00000132170	ENST00000397010;ENST00000309576;ENST00000397015;ENST00000397012;ENST00000397026;ENST00000287820	T;T;T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94;-0.94;-0.94	5.99	5.12	0.69794	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	T	0.81908	0.4922	M	0.73372	2.23	0.80722	D	1	D	0.61080	0.989	P	0.55303	0.773	D	0.84529	0.0632	10	0.87932	D	0	.	15.0869	0.72162	0.0:0.9326:0.0:0.0674	.	413	P37231	PPARG_HUMAN	V	385;385;385;385;391;413	ENSP00000380205:A385V;ENSP00000312472:A385V;ENSP00000380210:A385V;ENSP00000380207:A385V;ENSP00000380221:A391V;ENSP00000287820:A413V	ENSP00000287820:A413V	A	+	2	0	PPARG	12433621	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.787000	0.85759	1.540000	0.49301	0.655000	0.94253	GCA	NOVEL	PPARG-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000290127.1	2	18.961783	KEEP	0	0	0	63	2270	CC	1	1	0		+	29	60	1035	0	0	79.983471	193	60	7349	345	ENST00000397000.1	0.130631	1
IQSEC1	9922	__UNKNOWN__	__UNKNOWN__	3	12978010	12978010	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:12978010C>T	ENST00000273221.4	-	3	764	c.548G>A	c.(547-549)gGg>gAg	p.G183E		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	183		NA			actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TTTCTCAGGCCCCTCAAAGGA	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	56	60	NA		NA	NA	3		NA											NA				12978010		2203	4300	6503	SO:0001583	missense			BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711	9922			29112	protein-coding gene	gene with protein product	brefeldin A-resistant ARF-GEF2	610166			NA	9872452, 8619474	Standard	NM_014869	NM_001134382	NA	Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.548G>A	chr3.hg19:g.12978010C>T	ENSP00000273221:p.Gly183Glu	NA	O94863|Q96D85	hg19	CCDS33703.1	0.02	20.30242	GGCxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.462555	0.01062	.	.	ENSG00000144711	ENST00000273221;ENST00000435445;ENST00000429247	T;T	0.49720	0.77;0.77	4.72	3.83	0.44106	.	0.000000	0.85682	D	0.000000	T	0.43433	0.1247	.	.	.	0.58432	D	0.999999	D;B;B	0.71674	0.998;0.298;0.38	P;B;B	0.59546	0.859;0.079;0.063	T	0.49263	-0.8958	9	0.02654	T	1	.	7.9561	0.30045	0.1611:0.7588:0.0:0.0802	.	169;169;183	E9PG60;C9JMG9;Q6DN90	.;.;IQEC1_HUMAN	E	183;169;169	ENSP00000273221:G183E;ENSP00000402299:G169E	ENSP00000273221:G183E	G	-	2	0	IQSEC1	12953010	0.998000	0.40836	0.989000	0.46669	0.092000	0.18411	3.728000	0.54991	1.178000	0.42870	-0.311000	0.09066	GGG	NOVEL	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339865.2	3	68.001335	KEEP	0	1	10	230	7811	CC	1	1	0		-	113	60	4227	0	0	371.794246	297	60	10429	806	ENST00000273221.4	0.27561	1
COLQ	8292	__UNKNOWN__	__UNKNOWN__	3	15512183	15512183	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:15512183C>A	ENST00000383788.5	-	11	762				COLQ_ENST00000383785.2_Intron|COLQ_ENST00000383781.4_Intron|COLQ_ENST00000383786.5_Intron|COLQ_ENST00000383787.2_Intron|COLQ_ENST00000435459.2_Intron|COLQ_ENST00000603808.1_Intron	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	NA		NA			acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						GGCACATCTACACAGGTCTAG	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													52	54	54	NA		NA	NA	3		NA											NA				15512183		692	1591	2283	SO:0001627	intron_variant			AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561	8292			2226	protein-coding gene	gene with protein product	single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase, collagenic tail of endplate acetylcholinesterase, AChE Q subunit, acetylcholinesterase-associated collagen	603033			NA	9689136	Standard	NM_005677	NM_005677	NA	Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.637-60G>T	chr3.hg19:g.15512183C>A		NA	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	hg19	CCDS33709.1	0.02	4.601359	CTAxACA	COVERED																																																																																			NOVEL	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343575.1	0	9.931931	KEEP	0	0	0	33	1168	CC	0.999998	0.999991	0		-	67	60	2439	0	0	243.490558	44	60	1666	182	ENST00000383788.5	0.603604	0.999994
UBP1	7342	__UNKNOWN__	__UNKNOWN__	3	33437769	33437769	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:33437769C>T	ENST00000283629.3	-	13	1804	c.1275G>A	c.(1273-1275)tcG>tcA	p.S425S	UBP1_ENST00000283628.5_Silent_p.S425S|UBP1_ENST00000486388.1_5'UTR|UBP1_ENST00000447368.2_Silent_p.S389S	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	425		NA			angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						GGGGTCTAACCGACCTGCAAT	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													57	50	53	NA		NA	NA	3		NA											NA				33437769		2203	4300	6503	SO:0001819	synonymous_variant			AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560	7342			12507	protein-coding gene	gene with protein product		609784			NA	8114710	Standard	NM_014517	NM_014517	NA	Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.1275G>A	chr3.hg19:g.33437769C>T		NA	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	hg19	CCDS2659.1	0.02	4.948318	AACxGAC	COVERED																																																																																			NOVEL	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253249.2	0	19.862326	KEEP	0	0	0	66	2228	CC	1	0.999998	0		-	46	60	1758	0	0	163.699035	71	60	2463	242	ENST00000283629.3	0.393162	0.999998
TRANK1	9881	__UNKNOWN__	__UNKNOWN__	3	36873903	36873903	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:36873903C>T	ENST00000428977.2	-	11	5664	c.5389G>A	c.(5389-5391)Gca>Aca	p.A1797T	TRANK1_ENST00000429976.2_Missense_Mutation_p.A2347T|TRANK1_ENST00000301807.6_Missense_Mutation_p.A1797T			O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2347		NA					ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						CTGTTGGGTGCCAGCATGCCA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													111	115	114	NA		NA	NA	3		NA											NA				36873903		1962	4140	6102	SO:0001583	missense			AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016	9881		Ankyrin repeat domain containing, Tetratricopeptide (TTC) repeat domain containing	29011	protein-coding gene	gene with protein product	lupus brain antigen 1, KIAA0342	NA			NA	9205841	Standard	NM_014831	NM_014831	NA	Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000428977.2:c.5389G>A	chr3.hg19:g.36873903C>T	ENSP00000416826:p.Ala1797Thr	NA	Q8N8K0	hg19		0.02	3.830727	GTGxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	3.752	-0.051480	0.07407	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.32272	1.46;1.87;1.46	4.92	0.69	0.18039	.	1.523050	0.04249	N	0.338268	T	0.19644	0.0472	L	0.27053	0.805	0.09310	N	1	B	0.23937	0.094	B	0.19666	0.026	T	0.18461	-1.0336	10	0.26408	T	0.33	.	2.6855	0.05106	0.1041:0.3765:0.2914:0.2281	.	2347	O15050	TRNK1_HUMAN	T	1797;2347;1797	ENSP00000416826:A1797T;ENSP00000416168:A2347T;ENSP00000301807:A1797T	ENSP00000301807:A1797T	A	-	1	0	TRANK1	36848907	0.023000	0.18921	0.940000	0.37924	0.350000	0.29205	0.065000	0.14466	0.203000	0.20529	-0.258000	0.10820	GCA	NOVEL	TRANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000369655.1	3	19.117341	KEEP	0	0	0	64	2085	CC	1	1	0		-	7	60	230	0	0	14.286066	135	60	4849	263	ENST00000428977.2	0.049296	1
OXSR1	9943	__UNKNOWN__	__UNKNOWN__	3	38207318	38207318	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:38207318C>T	ENST00000446845.1	+	0	323				OXSR1_ENST00000492714.1_Intron|OXSR1_ENST00000311806.3_5'UTR					oxidative stress responsive 1	NA		NA								skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GGCGAGGAGACGAGCGAGGTC	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	13	13	NA		NA	NA	3		NA											NA				38207318		2179	4282	6461	SO:0001623	5_prime_UTR_variant			AB017642	CCDS2675.1	3p22.2	2013-05-17	2013-05-17	2004-11-26	ENSG00000172939	ENSG00000172939	9943			8508	protein-coding gene	gene with protein product		604046	oxidative-stress responsive 1	OSR1	NA	10083736	Standard	NM_005109	XM_005265638	NA	Approved	KIAA1101	uc003chy.3	O95747	OTTHUMG00000131084	ENST00000446845.1:c.-50C>T	chr3.hg19:g.38207318C>T		NA		hg19		0.02	-0.22798	AGAxGAG	COVERED																																																																																			NOVEL	OXSR1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000342708.1	0	13.326059	KEEP	0	1	21	52	1615	CC	1	0.58293	0		+	13	60	399	0	0	38.58076	12	60	383	144	ENST00000446845.1	0.52	0.58293
CSRNP1	64651	__UNKNOWN__	__UNKNOWN__	3	39185266	39185266	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:39185266G>A	ENST00000273153.5	-	5	1227	c.1050C>T	c.(1048-1050)agC>agT	p.S350S	CSRNP1_ENST00000514182.1_Silent_p.S350S	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	350		NA			apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						CAGTCATGTCGCTGCTGCAGC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	61	63	NA		NA	NA	3		NA											NA				39185266		2203	4300	6503	SO:0001819	synonymous_variant			AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655	64651			14300	protein-coding gene	gene with protein product		606458	AXIN1 up-regulated 1	AXUD1	NA	11526492, 17726538	Standard	NM_033027	NM_033027	NA	Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.1050C>T	chr3.hg19:g.39185266G>A		NA	Q69YY5	hg19	CCDS2682.1	0.02	4.212182	GTCxCTG	COVERED																																																																																			NOVEL	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254061.1	9	25.881492	KEEP	0	0	0	86	2947	GG	1	1	0		-	25	60	896	0	0	72.667137	119	60	4194	286	ENST00000273153.5	0.173611	1
KLHL40	131377	__UNKNOWN__	__UNKNOWN__	3	42728038	42728038	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs554767539		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:42728038C>A	ENST00000287777.4	+	1	1028	c.928C>A	c.(928-930)Ctg>Atg	p.L310M		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	310		NA			multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)					NA						CAATGACACCCTGCGCTTCGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													164	160	161	NA		NA	NA	3		NA											NA				42728038		2203	4300	6503	SO:0001583	missense			AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119	131377		Kelch-like, BTB/POZ domain containing	30372	protein-coding gene	gene with protein product	sarcosynapsin, nemaline myopathy type 8	615340	kelch repeat and BTB (POZ) domain containing 5, kelch-like 40 (Drosophila)	KBTBD5	NA	23746549	Standard	NM_152393	NM_152393	NA	Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.928C>A	chr3.hg19:g.42728038C>A	ENSP00000287777:p.Leu310Met	NA	Q86SI1|Q96MR2	hg19	CCDS2703.1	0.02	4.618913	ACCxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	6.868	0.529437	0.13127	.	.	ENSG00000157119	ENST00000287777;ENST00000452129	T	0.72282	-0.64	5.09	3.08	0.35506	.	0.218798	0.40144	N	0.001161	T	0.50854	0.1640	N	0.20401	0.57	0.33878	D	0.63577	B	0.28552	0.215	B	0.19946	0.027	T	0.58836	-0.7566	10	0.34782	T	0.22	.	9.9789	0.41802	0.1859:0.727:0.0:0.0872	.	310	Q2TBA0	KBTB5_HUMAN	M	310;55	ENSP00000287777:L310M	ENSP00000287777:L310M	L	+	1	2	KBTBD5	42703042	0.979000	0.34478	0.956000	0.39512	0.741000	0.42261	2.646000	0.46630	1.169000	0.42739	-0.136000	0.14681	CTG	NOVEL	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256651.1	1	10.833156	KEEP	0	0	0	36	1232	CC	0.999999	0.999991	0		+	14	60	507	0	0	39.233139	95	60	3524	177	ENST00000287777.4	0.12844	0.999992
CXCR6	10663	__UNKNOWN__	__UNKNOWN__	3	45988802	45988802	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:45988802G>A	ENST00000458629.1	+	1	2292	c.829G>A	c.(829-831)Gca>Aca	p.A277T	CXCR6_ENST00000457814.1_Missense_Mutation_p.A277T|FYCO1_ENST00000296137.2_Intron|FYCO1_ENST00000438446.1_Intron|CXCR6_ENST00000304552.4_Missense_Mutation_p.A277T|FYCO1_ENST00000535325.1_Intron|CXCR6_ENST00000438735.1_Missense_Mutation_p.A277T			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	277		NA			chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|viral genome replication (GO:0019079)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)	p.A277T(1)		central_nervous_system(1)|endometrium(1)|kidney(3)|lung(1)|prostate(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		AGAGGCCATCGCATACCTGAG	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(63;1005 1117 15521 45762 47089)					NA		NA				1	Substitution - Missense(1)	prostate(1)											116	97	103	NA		NA	NA	3		NA											NA				45988802		2203	4300	6503	SO:0001583	missense			AF007545	CCDS2735.1	3p21	2012-08-08			ENSG00000172215	ENSG00000172215	10663		CD molecules, GPCR / Class A : Chemokine receptors : C-X-C motif	16647	protein-coding gene	gene with protein product		605163			NA	9166430, 9230441	Standard		XM_005264809	NA	Approved	TYMSTR, STRL33, BONZO, CD186	uc003cpc.1	O00574	OTTHUMG00000133448	ENST00000458629.1:c.829G>A	chr3.hg19:g.45988802G>A	ENSP00000395704:p.Ala277Thr	NA	O00575|Q9HCA5	hg19	CCDS2735.1	0.02	7.016014	ATCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.65	3.868166	0.72065	.	.	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	5.96	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67439	0.2893	M	0.87827	2.91	0.53005	D	0.999969	D	0.76494	0.999	D	0.65010	0.931	T	0.74372	-0.3687	10	0.62326	D	0.03	.	15.2957	0.73906	0.0:0.0:0.8586:0.1414	.	277	O00574	CXCR6_HUMAN	T	277	ENSP00000396218:A277T;ENSP00000304414:A277T;ENSP00000395704:A277T;ENSP00000396886:A277T	ENSP00000304414:A277T	A	+	1	0	CXCR6	45963806	1.000000	0.71417	0.838000	0.33150	0.265000	0.26407	5.464000	0.66719	1.489000	0.48450	0.655000	0.94253	GCA	NOVEL	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344395.1	3	19.253126	KEEP	0	0	0	64	2099	GG	1	1	0		+	20	60	742	0	0	57.286193	145	60	4973	271	ENST00000458629.1	0.121212	1
NBEAL2	23218	__UNKNOWN__	__UNKNOWN__	3	47046670	47046670	__UNKNOWN__	Splice_Site	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:47046670G>T	ENST00000450053.3	+	40	6598		c.e40-1		NBEAL2_ENST00000292309.5_Splice_Site|NBEAL2_ENST00000383740.2_Splice_Site	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	NA		NA			blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		TGTGGCCCCAGGTATGAAAGC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	83	80	NA		NA	NA	3		NA											NA				47046670		2126	4233	6359	SO:0001630	splice_region_variant			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796	23218		WD repeat domain containing	31928	protein-coding gene	gene with protein product		614169			NA		Standard	XM_291064	NM_015175	NA	Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.6420-1G>T	chr3.hg19:g.47046670G>T		NA	O60288|Q6P994|Q6UX91|Q8NAC9	hg19	CCDS46817.1	0.02	20.284902	CCAxGTA	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.87	3.714853	0.68844	.	.	ENSG00000160796	ENST00000292309;ENST00000383740;ENST00000450053;ENST00000416683;ENST00000443829;ENST00000445550	.	.	.	4.86	4.86	0.63082	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.729	0.85430	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NBEAL2	47021674	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	9.595000	0.98260	2.527000	0.85204	0.561000	0.74099	.	NOVEL	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344363.3	2	26.481951	KEEP	0	0	0	88	2992	GG	1	1	0	Intron	+	16	60	587	0	0	36.098629	450	60	16596	696	ENST00000450053.3	0.034335	1
ELP6	54859	__UNKNOWN__	__UNKNOWN__	3	47546029	47546029	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:47546029C>T	ENST00000446787.1	-	3	174				ELP6_ENST00000296149.4_Intron|ELP6_ENST00000439305.1_Intron			Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	NA		NA			chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)					NA						AGACACCTTCCAAACTTGGCA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832	54859		Elongator acetyltransferase complex subunits	25976	protein-coding gene	gene with protein product		615020	transmembrane protein 103, chromosome 3 open reading frame 75	TMEM103, C3orf75	NA	22854966	Standard	NM_017713	XM_005265241	NA	Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000446787.1:c.15-91G>A	chr3.hg19:g.47546029C>T		NA	Q9BW57|Q9NXJ3	hg19		0.02	12.699968	TTCxAAA	COVERED																																																																																			NOVEL	ELP6-016	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345349.2	0	12.941328	KEEP	0	0	0	43	1522	CC	1	1	0		-	94	60	3400	0	0	311.952542	161	60	6034	356	ENST00000446787.1	0.368627	1
FBXW12	285231	__UNKNOWN__	__UNKNOWN__	3	48419842	48419842	__UNKNOWN__	Intron	SNP	C	C	A	rs369622651		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:48419842C>A	ENST00000436231.1	+	3	165				FBXW12_ENST00000415155.1_Intron|FBXW12_ENST00000296438.5_Missense_Mutation_p.F147L|FBXW12_ENST00000445170.1_Missense_Mutation_p.F128L			Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	NA		NA								breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCCAGGAGTTCCATTTCTCAA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													105	88	94	NA		NA	NA	3		NA											NA				48419842		2203	4300	6503	SO:0001627	intron_variant			AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049	285231		F-boxes / WD-40 domains, WD repeat domain containing	20729	protein-coding gene	gene with protein product		609075	F-box only protein 35, F-box and WD-40 domain protein 12	FBXO35	NA	15040455	Standard	NM_207102	NM_207102	NA	Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000436231.1:c.0-31C>A	chr3.hg19:g.48419842C>A		NA	E9PG36|Q494Y9|Q494Z0	hg19		0.02	2.152682	GTTxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841993	0.32513	.	.	ENSG00000164049	ENST00000296438;ENST00000445170	T;T	0.28666	1.6;1.6	4.63	-5.03	0.02973	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	2.241760	0.01717	N	0.028045	T	0.19046	0.0457	L	0.29908	0.895	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.11329	0.006;0.004	T	0.20706	-1.0267	10	0.59425	D	0.04	-17.4255	1.1181	0.01718	0.2488:0.441:0.1238:0.1865	.	128;147	E9PG36;Q6X9E4	.;FBW12_HUMAN	L	147;128	ENSP00000296438:F147L;ENSP00000406139:F128L	ENSP00000296438:F147L	F	+	3	2	FBXW12	48394846	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.875000	0.01634	-0.619000	0.05648	0.650000	0.86243	TTC	NOVEL	FBXW12-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344439.2	0	3.00966	KEEP	0	0	0	10	343	CC	0.992708	0.982326	0		+	23	60	803	0	0	73.714953	38	60	1421	93	ENST00000436231.1	0.377049	0.989542
PLXNB1	5364	__UNKNOWN__	__UNKNOWN__	3	48465653	48465653	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs543884018		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:48465653C>T	ENST00000358536.4	-	3	637	c.368G>A	c.(367-369)cGc>cAc	p.R123H	PLXNB1_ENST00000358459.4_Missense_Mutation_p.R123H|PLXNB1_ENST00000456774.1_Missense_Mutation_p.R123H|PLXNB1_ENST00000296440.6_Missense_Mutation_p.R123H|PLXNB1_ENST00000448774.2_Intron	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	123	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.	NA			axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTGCCCCAGGCGCCGCTGTTC	0.667	NA	NA											C|||	1	0.000199681	0	0.0014	5008	,	,	NA	17833	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													13	16	15	NA		NA	NA	3		NA											NA				48465653		2199	4296	6495	SO:0001583	missense			X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050	5364		Plexins	9103	protein-coding gene	gene with protein product		601053		PLXN5	NA	8570614, 11035813	Standard	NM_002673	XM_005265234	NA	Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.368G>A	chr3.hg19:g.48465653C>T	ENSP00000351338:p.Arg123His	NA	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	hg19	CCDS2765.1	0.02	2.238697	AGGxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.96	2.095309	0.36952	.	.	ENSG00000164050	ENST00000296440;ENST00000358459;ENST00000358536;ENST00000456774	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	4.14	3.26	0.37387	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.410379	0.23282	N	0.049884	T	0.09158	0.0226	L	0.58101	1.795	0.80722	D	1	B;P	0.42620	0.006;0.785	B;B	0.24974	0.001;0.057	T	0.12630	-1.0540	10	0.54805	T	0.06	.	11.0148	0.47682	0.0:0.9077:0.0:0.0923	.	123;123	O43157;O43157-2	PLXB1_HUMAN;.	H	123	ENSP00000296440:R123H;ENSP00000351242:R123H;ENSP00000351338:R123H;ENSP00000414199:R123H	ENSP00000296440:R123H	R	-	2	0	PLXNB1	48440657	0.998000	0.40836	1.000000	0.80357	0.940000	0.58332	1.517000	0.35867	0.722000	0.32252	0.655000	0.94253	CGC	NOVEL	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344454.1	1	11.435671	KEEP	0	0	0	38	1298	CC	1	0.998465	0		-	22	60	752	0	0	66.147841	52	60	1805	131	ENST00000358536.4	0.297297	0.998465
SLC26A6	65010	__UNKNOWN__	__UNKNOWN__	3	48669743	48669743	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:48669743T>C	ENST00000455886.2	-	5	481				SLC26A6_ENST00000420764.2_Missense_Mutation_p.T174A|SLC26A6_ENST00000383733.3_Missense_Mutation_p.T174A|SLC26A6_ENST00000395550.2_Missense_Mutation_p.T174A|SLC26A6_ENST00000358747.6_Missense_Mutation_p.T153A|SLC26A6_ENST00000482282.1_5'UTR|SLC26A6_ENST00000337000.8_Intron	NM_001281732.1	NP_001268661.1	Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	NA		NA			angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TCTCTGGCTGTCTCATTGATC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(13;369 479 28271 30152 44026)					NA		NA				0													62	69	66	NA		NA	NA	3		NA											NA				48669743		2140	4241	6381	SO:0001627	intron_variant			AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697	65010		Solute carriers	14472	protein-coding gene	gene with protein product	pendrin-like protein 1, pendrin L1, sulfate anion transporter, anion transporter 1	610068	solute carrier family 26, member 6		NA	11087667, 11247665	Standard	NM_022911	NM_022911	NA	Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000455886.2:c.434-218A>G	chr3.hg19:g.48669743T>C		NA	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	hg19		0.02	7.508554	CTGxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	T	5.324	0.245159	0.10077	.	.	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000447978;ENST00000358747;ENST00000421649	D;D;D;D;D	0.93763	-3.06;-3.06;-3.17;-3.05;-3.28	4.52	-6.66	0.01789	.	.	.	.	.	T	0.81950	0.4931	N	0.13327	0.33	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.001;0.0	T	0.70831	-0.4765	9	0.06891	T	0.86	.	11.6478	0.51271	0.0967:0.7372:0.0:0.1662	.	187;174;174;174;3579	Q86YZ4;Q9BXS9-2;Q548A7;Q9BXS9;Q5Y190	.;.;.;S26A6_HUMAN;.	A	174;174;174;187;153;20	ENSP00000404684:T174A;ENSP00000378920:T174A;ENSP00000373239:T174A;ENSP00000351597:T153A;ENSP00000389922:T20A	ENSP00000351597:T153A	T	-	1	0	SLC26A6	48644747	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.693000	0.05121	-0.986000	0.03498	-0.379000	0.06801	ACA	NOVEL	SLC26A6-009	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345045.1	1	13.223508	KEEP	0	0	0	44	1359	TT	1	1	0		-	67	60	2398	0	0	223.019018	99	60	3526	272	ENST00000455886.2	0.403614	1
NCKIPSD	51517	__UNKNOWN__	__UNKNOWN__	3	48720379	48720379	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs199690056		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:48720379G>A	ENST00000294129.2	-	2	357	c.238C>T	c.(238-240)Cgg>Tgg	p.R80W	NCKIPSD_ENST00000416649.2_Missense_Mutation_p.R80W|NCKIPSD_ENST00000341520.4_Missense_Mutation_p.R80W	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	80		NA			cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CCACCATCCCGCATGGCTGTG	0.627	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	17815	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													121	65	84	NA		NA	NA	3		NA											NA				48720379		2179	4250	6429	SO:0001583	missense			AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672	51517			15486	protein-coding gene	gene with protein product	dia interacting protein, diaphanous protein interacting protein, SH3 protein interacting with Nck, 90 kDa	606671			NA	10648423, 10619843	Standard	NM_016453	NM_016453	NA	Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.238C>T	chr3.hg19:g.48720379G>A	ENSP00000294129:p.Arg80Trp	NA	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	hg19	CCDS2776.1	0.02	-0.236861	CCCxCAT	COVERED	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	23.4	4.416241	0.83449	.	.	ENSG00000213672	ENST00000341520;ENST00000416649;ENST00000294129;ENST00000439518;ENST00000453349	T;T;T;T	0.47177	0.85;1.46;1.46;1.45	4.87	3.9	0.45041	.	0.082456	0.47093	U	0.000260	T	0.51483	0.1677	L	0.36672	1.1	0.36769	D	0.883702	D;D;D	0.76494	0.999;0.997;0.998	P;P;P	0.60415	0.874;0.723;0.857	T	0.60757	-0.7200	10	0.72032	D	0.01	.	10.117	0.42596	0.0:0.0:0.5324:0.4676	.	80;80;80	C9JSC3;Q9NZQ3;Q9NZQ3-3	.;SPN90_HUMAN;.	W	80;80;80;80;2	ENSP00000342621:R80W;ENSP00000389059:R80W;ENSP00000294129:R80W;ENSP00000409675:R80W	ENSP00000294129:R80W	R	-	1	2	NCKIPSD	48695383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.811000	0.62606	2.258000	0.74832	0.591000	0.81541	CGG	NOVEL	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257520.1	0	3.610628	KEEP	0	0	0	12	387	GG	0.993634	0.608508	0		-	4	60	157	0	0	12.69013	23	60	787	44	ENST00000294129.2	0.148148	0.612407
MST1	4485	__UNKNOWN__	__UNKNOWN__	3	49722702	49722702	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs71262351	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:49722702G>C	ENST00000449682.2	-	13	1898	c.1537C>G	c.(1537-1539)Cgg>Ggg	p.R513G		NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth factor-like)	499	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			embryo implantation (GO:0007566)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CACCGATTCCGCAAGCTGACT	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(110;181 1524 8005 22865 46297)					NA		NA				0													17	19	18	NA		NA	NA	3		NA											NA				49722702		2199	4288	6487	SO:0001583	missense			M74178	CCDS33757.2	3p21	2008-09-05			ENSG00000173531	ENSG00000173531	4485			7380	protein-coding gene	gene with protein product	hepatocyte growth factor-like protein homolog	142408		D3F15S2, HGFL, DNF15S2	NA	2902784, 8393443	Standard	NM_020998	NM_020998	NA	Approved	MSP, NF15S2	uc003cxg.3	P26927	OTTHUMG00000155918	ENST00000449682.2:c.1537C>G	chr3.hg19:g.49722702G>C	ENSP00000414287:p.Arg513Gly	NA	A6NLA3|A8MSX3|Q13350|Q14870|Q6GTN4	hg19	CCDS33757.2	0.02	4.293263	TCCxCAA	COVERED	126	0.057692307692307696	25	0.0508130081300813	34	0.09392265193370165	32	0.055944055944055944	35	0.04617414248021108	G	20.2	3.949375	0.73787	.	.	ENSG00000173531	ENST00000449682	D	0.88664	-2.41	5.18	4.25	0.50352	.	0.000000	0.38959	N	0.001513	T	0.46814	0.1412	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73678	-0.3907	10	0.72032	D	0.01	.	14.589	0.68351	0.0:0.0:0.854:0.146	.	513	G3XAK1	.	G	513	ENSP00000414287:R513G	ENSP00000414287:R513G	R	-	1	2	MST1	49697706	1.000000	0.71417	0.985000	0.45067	0.831000	0.47069	3.834000	0.55798	2.544000	0.85801	0.655000	0.94253	CGG	NOVEL	MST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342315.3	4	13.539401	KEEP	15	0	0	45	1481	GG	1	0.999995	0		-	5	25	174	0	0	10.927521	107	60	3642	206	ENST00000449682.2	0.044643	0.999995
MST1	4485	__UNKNOWN__	__UNKNOWN__	3	49723009	49723009	__UNKNOWN__	Intron	SNP	G	G	C	rs9713632		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:49723009G>C	ENST00000449682.2	-	11	1749				MST1_ENST00000383728.3_Intron	NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth factor-like)	NA		NA			embryo implantation (GO:0007566)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGTCATGGGGGAAGCGTCACT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(110;181 1524 8005 22865 46297)					NA		NA				0													34	36	35	NA		NA	NA	3		NA											NA				49723009		2203	4300	6503	SO:0001627	intron_variant			M74178	CCDS33757.2	3p21	2008-09-05			ENSG00000173531	ENSG00000173531	4485			7380	protein-coding gene	gene with protein product	hepatocyte growth factor-like protein homolog	142408		D3F15S2, HGFL, DNF15S2	NA	2902784, 8393443	Standard	NM_020998	NM_020998	NA	Approved	MSP, NF15S2	uc003cxg.3	P26927	OTTHUMG00000155918	ENST00000449682.2:c.1387+19C>G	chr3.hg19:g.49723009G>C		NA	A6NLA3|A8MSX3|Q13350|Q14870|Q6GTN4	hg19	CCDS33757.2	0.02	9.176578	GGGxAAG	COVERED																																																																																			NOVEL	MST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342315.3	3	17.440928	KEEP	5	0	0	58	1913	GG	1	1	0		-	11	25	385	0	0	25.34618	203	60	7343	325	ENST00000449682.2	0.051402	1
MST1	4485	__UNKNOWN__	__UNKNOWN__	3	49726174	49726174	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:49726174A>G	ENST00000449682.2	-	0	312					NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth factor-like)	NA		NA			embryo implantation (GO:0007566)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CTCTGGCTCCACACGTCAGCT	0.632	NA	NA									OREG0000235	type=REGULATORY REGION|Gene=MST1		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(110;181 1524 8005 22865 46297)					NA		NA				0													8	9	9	NA		NA	NA	3		NA											NA				49726174		688	1586	2274	SO:0001623	5_prime_UTR_variant			M74178	CCDS33757.2	3p21	2008-09-05			ENSG00000173531	ENSG00000173531	4485			7380	protein-coding gene	gene with protein product	hepatocyte growth factor-like protein homolog	142408		D3F15S2, HGFL, DNF15S2	NA	2902784, 8393443	Standard	NM_020998	NM_020998	NA	Approved	MSP, NF15S2	uc003cxg.3	P26927	OTTHUMG00000155918	ENST00000449682.2:c.-50T>C	chr3.hg19:g.49726174A>G		964	A6NLA3|A8MSX3|Q13350|Q14870|Q6GTN4	hg19	CCDS33757.2	0.02	-0.403304	TCCxCAC	COVERED																																																																																			NOVEL	MST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342315.3	0	6.316769	KEEP	4	0	0	21	619	AA	0.999869	0.93437	0		-	4	33	145	0	0	10.508864	42	60	1467	77	ENST00000449682.2	0.086957	0.934492
FAM212A	389119	__UNKNOWN__	__UNKNOWN__	3	49842341	49842341	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:49842341C>T	ENST00000333323.4	+	2	918	c.785C>T	c.(784-786)gCg>gTg	p.A262V		NM_203370.1	NP_976248.1	Q96EL1	F212A_HUMAN	family with sequence similarity 212, member A	260		NA			neural tube development (GO:0021915)	extracellular vesicular exosome (GO:0070062)					NA						GAACTGCCTGCGGATGTCTCA	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													101	113	109	NA		NA	NA	3		NA											NA				49842341		2203	4300	6503	SO:0001583	missense			BC012170	CCDS2804.1	3p21.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000185614	ENSG00000185614	389119			32480	protein-coding gene	gene with protein product		NA	chromosome 3 open reading frame 54	C3orf54	NA		Standard	NM_203370	NM_203370	NA	Approved		uc003cxq.1	Q96EL1	OTTHUMG00000158268	ENST00000333323.4:c.785C>T	chr3.hg19:g.49842341C>T	ENSP00000329735:p.Ala262Val	NA		hg19	CCDS2804.1	0.02	4.060085	CTGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	10.03	1.238364	0.22711	.	.	ENSG00000185614	ENST00000333323	.	.	.	5.7	3.9	0.45041	.	0.681709	0.12844	N	0.434574	T	0.40398	0.1115	L	0.40543	1.245	0.23848	N	0.996673	B	0.15930	0.015	B	0.09377	0.004	T	0.34775	-0.9815	9	0.66056	D	0.02	.	11.0917	0.48119	0.0:0.8007:0.1295:0.0699	.	260	Q96EL1	CC054_HUMAN	V	262	.	ENSP00000329735:A262V	A	+	2	0	C3orf54	49817345	0.073000	0.21202	0.075000	0.20258	0.003000	0.03518	3.607000	0.54102	0.762000	0.33152	-0.300000	0.09419	GCG	NOVEL	FAM212A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350514.1	3	27.079783	KEEP	0	0	0	90	2912	CC	1	1	0		+	7	60	253	0	0	16.360783	143	60	4934	276	ENST00000333323.4	0.046667	1
CTD-2330K9.3	0	__UNKNOWN__	__UNKNOWN__	3	49946706	49946706	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:49946706T>G	ENST00000419183.1	+	1	104				MON1A_ENST00000455683.2_Missense_Mutation_p.N438H|MON1A_ENST00000417270.1_Missense_Mutation_p.N511H|MON1A_ENST00000296473.3_Missense_Mutation_p.N600H						NA		NA									NA						AGGTTCTCGTTGGGGCCCGTG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													61	56	58	NA		NA	NA	3		NA											NA				49946706		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000419183.1:c.26+5183T>G	chr3.hg19:g.49946706T>G		NA		hg19		0.02	4.531632	CGTxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	T	17.14	3.312540	0.60414	.	.	ENSG00000164077	ENST00000296473;ENST00000417270;ENST00000455683	.	.	.	5.38	5.38	0.77491	.	0.322570	0.35708	N	0.003032	T	0.36991	0.0987	N	0.16903	0.455	0.32158	N	0.583286	P;P	0.46220	0.874;0.865	P;P	0.51229	0.568;0.663	T	0.44034	-0.9354	8	.	.	.	-20.4615	12.23	0.54482	0.0:0.0:0.1519:0.8481	.	438;503	G5E9N1;Q86VX9	.;MON1A_HUMAN	H	600;511;438	.	.	N	-	1	0	MON1A	49921710	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	2.272000	0.43373	2.042000	0.60477	0.529000	0.55759	AAC	NOVEL	CTD-2330K9.3-003	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345527.2	2	9.325801	KEEP	0	0	0	31	963	TT	0.999997	0.999996	0		+	18	60	651	0	0	51.736166	101	60	3646	189	ENST00000419183.1	0.151261	0.999999
ABHD14A-ACY1	100526760	__UNKNOWN__	__UNKNOWN__	3	52018219	52018219	__UNKNOWN__	Intron	SNP	C	C	T	rs185045735	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:52018219C>T	ENST00000463937.1	+	4	473				ACY1_ENST00000476351.1_Intron|ACY1_ENST00000476854.1_Intron|ACY1_ENST00000494103.1_Intron|ACY1_ENST00000404366.2_Intron|ACY1_ENST00000458031.2_Intron					ABHD14A-ACY1 readthrough (NMD candidate)	NA		NA									NA						GCCTAAGGGACGGGGACTGTG	0.617	NA	NA											C|||	19	0.00379393	0.0076	0.0101	5008	,	,	NA	17014	0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								C	,,,,	48,4358	47.5+/-82.1	0,48,2155	43	35	38	NA	,,,,	-0.1	0	3		38	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,intron,intron	ACY1	NM_000666.2,NM_001198895.1,NM_001198896.1,NM_001198897.1,NM_001198898.1	,,,,	0,50,6452	TT,TC,CC	NA	0.0233,1.0894,0.3845	,,,,	,,,,	52018219	50,12954	2203	4299	6502	SO:0001627	intron_variant					3p21.2	2013-05-09	2013-05-09		ENSG00000114786	ENSG00000114786	100526760			38856	other	readthrough		NA			NA		Standard		NR_037192	NA	Approved				OTTHUMG00000166447	ENST00000463937.1:c.398-1004C>T	chr3.hg19:g.52018219C>T		NA		hg19		0.02	6.861016	GGAxGGG	COVERED																																																																																			NOVEL	ABHD14A-ACY1-001	PUTATIVE	not_organism_supported|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000365268.1	0	45.670819	KEEP	0	1	26	161	5333	CC	1	1	0		+	65	60	2363	0	0	213.578193	129	60	4385	475	ENST00000463937.1	0.335052	1
TLR9	54106	__UNKNOWN__	__UNKNOWN__	3	52257079	52257079	__UNKNOWN__	Silent	SNP	C	C	T	rs550092930		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:52257079C>T	ENST00000494383.1	-	5	1712	c.1713G>A	c.(1711-1713)gcG>gcA	p.A571A	TLR9_ENST00000597542.1_Missense_Mutation_p.R442H|TLR9_ENST00000360658.2_Missense_Mutation_p.R418H			Q9NR96	TLR9_HUMAN	toll-like receptor 9	0		NA			defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	GTCCACGTAGCGCAGGCCAGG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	78	77	NA		NA	NA	3		NA											NA				52257079		2203	4300	6503	SO:0001819	synonymous_variant			AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732	54106		CD molecules	15633	protein-coding gene	gene with protein product		605474			NA	11022119	Standard		NM_017442	NA	Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000494383.1:c.1713G>A	chr3.hg19:g.52257079C>T		NA	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	hg19		0.02	6.405397	TAGxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.29	1.593820	0.28445	.	.	ENSG00000239732	ENST00000360658	T	0.44482	0.92	5.13	-3.53	0.04667	.	0.994785	0.08145	N	0.991059	T	0.33469	0.0864	M	0.68728	2.09	0.09310	N	1	B;B	0.17667	0.007;0.023	B;B	0.06405	0.002;0.002	T	0.38308	-0.9667	10	0.44086	T	0.13	.	2.4574	0.04532	0.1223:0.343:0.1131:0.4216	.	515;418	B4E0A1;Q9NR96	.;TLR9_HUMAN	H	418	ENSP00000353874:R418H	ENSP00000353874:R418H	R	-	2	0	TLR9	52232119	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.010000	0.03656	-0.527000	0.06374	-0.768000	0.03414	CGC	NOVEL	TLR9-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367019.1	5	23.174914	KEEP	0	0	0	77	2712	CC	1	1	0		-	60	60	2059	0	0	183.224264	129	60	4669	338	ENST00000494383.1	0.31746	1
TMEM110	375346	__UNKNOWN__	__UNKNOWN__	3	52876995	52876995	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:52876995C>T	ENST00000355083.5	-	7	764				TMEM110-MUSTN1_ENST00000504329.1_Intron|TMEM110_ENST00000464769.1_Intron	NM_198563.2	NP_940965.1	Q86TL2	TM110_HUMAN	transmembrane protein 110	NA		NA				integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)	4				BRCA - Breast invasive adenocarcinoma(193;7.72e-05)|Kidney(197;0.000777)|KIRC - Kidney renal clear cell carcinoma(197;0.000915)|OV - Ovarian serous cystadenocarcinoma(275;0.0541)		AGGAAAAGTGCAGGTTACTTT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													89	82	84	NA		NA	NA	3		NA											NA				52876995		2203	4300	6503	SO:0001627	intron_variant			BC047015	CCDS2866.1	3p21.1	2010-08-13			ENSG00000213533	ENSG00000213533	375346			30526	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_198563	NM_198563	NA	Approved	MGC52022		Q86TL2	OTTHUMG00000150346	ENST00000355083.5:c.619-19G>A	chr3.hg19:g.52876995C>T		NA		hg19	CCDS2866.1	0.02	4.487758	GTGxAGG	COVERED																																																																																			NOVEL	TMEM110-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352949.2	1	22.572881	KEEP	0	0	0	75	2702	CC	1	0.999999	0		-	26	60	916	0	0	76.356399	98	60	3728	257	ENST00000355083.5	0.209677	0.999999
RFT1	91869	__UNKNOWN__	__UNKNOWN__	3	53157820	53157820	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:53157820G>T	ENST00000394738.3	-	3	202				RFT1_ENST00000296292.3_Silent_p.A62A			Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	NA		NA			carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		AGGCCTCTCTGGCCAGGAAGA	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	73	74	NA		NA	NA	3		NA											NA				53157820		2203	4300	6503	SO:0001627	intron_variant			AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933	91869			30220	protein-coding gene	gene with protein product	congenital disorder of glycosylation 1N	611908	RFT1, requiring fifty three 1 homolog (S. cerevisiae)		NA	12477932	Standard	NM_052859	NM_052859	NA	Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000394738.3:c.150-1241C>A	chr3.hg19:g.53157820G>T		NA	Q96J03	hg19		0.02	4.473497	TCTxGCC	COVERED																																																																																			NOVEL	RFT1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000157137.1	3	26.485739	KEEP	0	0	0	88	3181	GG	1	1	0		-	24	60	874	0	0	71.256396	113	60	4106	316	ENST00000394738.3	0.175182	1
FLNB	2317	__UNKNOWN__	__UNKNOWN__	3	58127525	58127525	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:58127525G>T	ENST00000490882.1	+	31	5367				FLNB_ENST00000295956.4_Intron|FLNB_ENST00000419752.2_Intron|FLNB_ENST00000348383.5_Intron|FLNB_ENST00000493452.1_Intron|FLNB_ENST00000429972.2_Intron|FLNB_ENST00000358537.3_Intron|FLNB_ENST00000357272.4_Intron	NM_001164317.1	NP_001157789.1	O75369	FLNB_HUMAN	filamin B, beta	NA		NA			actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		TGTGGTGGTAGTCTACTGAGT	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													124	104	110	NA		NA	NA	3		NA											NA				58127525		692	1591	2283	SO:0001627	intron_variant			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068	2317			3755	protein-coding gene	gene with protein product	actin binding protein 278	603381	filamin B, beta (actin binding protein 278), Larsen syndrome 1 (autosomal dominant)	FLN1L, LRS1	NA	8327473, 10449914, 14991055, 16801345	Standard	NM_001457	NM_001457	NA	Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000490882.1:c.5203-60G>T	chr3.hg19:g.58127525G>T		NA	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	hg19	CCDS54599.1	0.02	2.015915	GTAxTCT	COVERED																																																																																			NOVEL	FLNB-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353570.1	0	6.621657	KEEP	0	0	0	22	783	GG	0.999879	0.999647	0		+	27	60	940	0	0	83.313333	61	60	2249	135	ENST00000490882.1	0.306818	0.999768
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	58703084	58703084	__UNKNOWN__	IGR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:58703084A>T			NA	NA				FAM3D (50509 upstream) : C3orf67 (24648 downstream)						NA		NA									NA						ggaatgctgaatctcagggct	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.58703084A>T		NA		hg19		0.02	2.147176	TGAxTCT	COVERED																																																																																			NOVEL					0			0	5.115473	KEEP	0	0	0	17	540	AA	0.999366	0.997265	0			17	60	595	0	0	50.405864	56	60	2050	110		0.232877	0.997898
ADAMTS9	56999	__UNKNOWN__	__UNKNOWN__	3	64672450	64672450	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:64672450C>A	ENST00000498707.1	-	2	652	c.310G>T	c.(310-312)Gcc>Tcc	p.A104S	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.A104S|ADAMTS9-AS2_ENST00000485174.1_RNA|ADAMTS9-AS2_ENST00000460833.1_RNA|ADAMTS9-AS2_ENST00000474768.1_RNA|ADAMTS9_ENST00000459780.1_Missense_Mutation_p.A104S|ADAMTS9-AS2_ENST00000481312.1_RNA	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	104		NA			glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		TGGCCGAAGGCAGAGAGGCGG	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	45	46	NA		NA	NA	3		NA											NA				64672450		2203	4300	6503	SO:0001583	missense			AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638	56999		ADAM metallopeptidases with thrombospondin type 1 motif	13202	protein-coding gene	gene with protein product		605421	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9		NA	10936055	Standard		NM_182920	NA	Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.310G>T	chr3.hg19:g.64672450C>A	ENSP00000418735:p.Ala104Ser	NA	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	hg19	CCDS2903.1	0.02	9.226051	AGGxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	27.8	4.861901	0.91433	.	.	ENSG00000163638	ENST00000295903;ENST00000498707;ENST00000459780	T;T;T	0.08896	3.04;3.04;3.04	4.89	4.89	0.63831	Peptidase M12B, propeptide (1);	0.000000	0.64402	D	0.000003	T	0.39835	0.1093	M	0.92738	3.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.51725	-0.8669	10	0.51188	T	0.08	.	18.4465	0.90686	0.0:1.0:0.0:0.0	.	104;104;104	B7ZVX9;Q9P2N4-2;Q9P2N4	.;.;ATS9_HUMAN	S	104	ENSP00000295903:A104S;ENSP00000418735:A104S;ENSP00000419217:A104S	ENSP00000295903:A104S	A	-	1	0	ADAMTS9	64647490	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.787000	0.69013	2.452000	0.82932	0.491000	0.48974	GCC	NOVEL	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351891.1	6	26.183458	KEEP	0	0	0	87	3118	CC	1	1	0		-	56	60	1988	0	0	172.90297	152	60	5719	370	ENST00000498707.1	0.269231	1
MITF	4286	__UNKNOWN__	__UNKNOWN__	3	70015048	70015048	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:70015048C>A	ENST00000352241.4	+	0	2375				MITF_ENST00000394355.2_3'UTR|MITF_ENST00000328528.6_3'UTR|MITF_ENST00000448226.2_3'UTR	NM_198159.2	NP_937802.1	O75030	MITF_HUMAN	microphthalmia-associated transcription factor	NA		NA			bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		GGAGTTAGACCAAGGCTCTGA	0.338	NA	NA	A		melanoma		Waardenburg syndrome type 2, Tietz syndrome							NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098	4286		Basic helix-loop-helix proteins	7105	protein-coding gene	gene with protein product	homolog of mouse microphthalmia	156845	Waardenburg syndrome, type 2A	WS2A, WS2	NA	8069297, 7874167, 7951321	Standard	NM_198159	NM_198159	NA	Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000352241.4:c.*649C>A	chr3.hg19:g.70015048C>A		NA	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	hg19	CCDS43106.1	0.02	6.69404	GACxAAG	COVERED																																																																																			NOVEL	MITF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313920.2	4	18.660836	KEEP	0	0	0	62	2231	CC	1	1	0		+	8	60	302	0	0	19.831018	171	60	6370	326	ENST00000352241.4	0.044693	1
FRG2C	100288801	__UNKNOWN__	__UNKNOWN__	3	75716090	75716090	__UNKNOWN__	3'UTR	SNP	T	T	C	rs73840342	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:75716090T>C	ENST00000464571.1	+	0	1794				FRG2C_ENST00000308062.3_3'UTR			A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	NA		NA				nucleus (GO:0005634)				breast(2)|ovary(1)	3						TGAATTTATATTTTATTGTAT	0.239	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969	100288801			33626	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001124759.1	NM_001124759	NA	Approved			A6NGY1	OTTHUMG00000158963	ENST00000464571.1:c.*898T>C	chr3.hg19:g.75716090T>C		NA		hg19		0.02	9.365821	ATAxTTT	COVERED																																																																																			NOVEL	FRG2C-002	NOVEL	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352695.1	16	4.248763	KEEP	0	1	37	27	868	TT	0.999997	0.999997	0		+	14	60	482	0	0	32.495837	201	60	7308	315	ENST00000464571.1	0.065116	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788411	75788411	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs149968740		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:75788411G>C	ENST00000478296.1	-	4	489	c.213C>G	c.(211-213)aaC>aaG	p.N71K	ZNF717_ENST00000422325.1_Missense_Mutation_p.N121K|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.N114K|ZNF717_ENST00000477374.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	114	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GAGTTGATGTGTTGCTGTTGG	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													1	1	1	NA		NA	NA	3		NA											NA				75788411		277	683	960	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.213C>G	chr3.hg19:g.75788411G>C	ENSP00000419377:p.Asn71Lys	NA		hg19		0.02	14.678794	TGTxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.398198	0.00198	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.42131	0.98;0.98;0.98	2.13	-4.26	0.03755	.	.	.	.	.	T	0.17280	0.0415	N	0.14661	0.345	0.09310	N	1	B	0.17852	0.024	B	0.12837	0.008	T	0.32348	-0.9910	9	0.06099	T	0.92	.	5.869	0.18793	0.1271:0.0:0.6195:0.2533	rs4011156	121	C9JSV9	.	K	71;121;114	ENSP00000419377:N71K;ENSP00000409514:N121K;ENSP00000383643:N114K	ENSP00000383643:N114K	N	-	3	2	ZNF717	75871101	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.826000	0.04429	-1.403000	0.02053	-1.851000	0.00568	AAC	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	7	15.350246	KEEP	0	0	0	51	1850	GG	1	1	0		-	14	60	521	0	0	34.583477	269	60	10113	434	ENST00000478296.1	0.04947	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	94225279	94225279	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:94225279C>T			NA	NA				NSUN3 (377890 upstream) : LINC00879 (431827 downstream)						NA		NA									NA						AATACTGATGCTGTCTCAGAT	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.94225279C>T		NA		hg19		0.02	24.064355	ATGxTGT	COVERED																																																																																			NOVEL					0			7	48.740306	KEEP	184	0	0	162	5735	CC	1	1	0			23	50	843	0	0	53.04502	570	50	21650	1021		0.038786	1
GABRR3	200959	__UNKNOWN__	__UNKNOWN__	3	97744480	97744480	__UNKNOWN__	RNA	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:97744480G>A	ENST00000472788.1	-	0	170					NM_001105580.2	NP_001099050.1	A8MPY1	GBRR3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 3 (gene/pseudogene)	NA		NA			gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			large_intestine(2)|lung(1)	3					Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	TTCTGAGGCCGCGCTTTGGTA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													165	156	159	NA		NA	NA	3		NA											NA				97744480		1839	4090	5929					Y18994	CCDS54617.1	3q11.2	2014-03-25	2014-03-25		ENSG00000183185	ENSG00000183185	200959		GABA receptors, Ligand-gated ion channels / GABA(A) receptors	17969	protein-coding gene	gene with protein product	GABA(A) receptor, rho 3	NA	gamma-aminobutyric acid (GABA) receptor, rho 3, gamma-aminobutyric acid (GABA) A receptor, rho 3		NA	10542332	Standard		NM_001105580	NA	Approved		uc021xbp.1	A8MPY1	OTTHUMG00000159135	ENST00000472788.1:	chr3.hg19:g.97744480G>A		NA	Q9UIV9	hg19		0.02	11.535724	GCCxCGC	COVERED																																																																																			NOVEL	GABRR3-002	KNOWN	not_organism_supported|basic	polymorphic_pseudogene	NA	polymorphic_pseudogene	OTTHUMT00000353445.2	3	21.365853	KEEP	0	0	0	71	2407	GG	1	1	0		-	22	60	797	0	0	56.962506	252	60	9039	445	ENST00000472788.1	0.080292	1
NFKBIZ	64332	__UNKNOWN__	__UNKNOWN__	3	101575921	101575921	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs140077856		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:101575921G>A	ENST00000326172.5	+	10	1944	c.1829G>A	c.(1828-1830)cGc>cAc	p.R610H	NFKBIZ_ENST00000394054.2_Missense_Mutation_p.R510H|NFKBIZ_ENST00000326151.5_Missense_Mutation_p.R488H	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	610	Interaction with NFKB1/p50. {ECO:0000250}.	NA			inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R610L(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						GACAAGGATCGCAAAAGTGGC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	endometrium(1)						G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	110	126	120	NA	1529,1829	6	1	3	dbSNP_134	120	0,8600		0,0,4300	no	missense,missense	NFKBIZ	NM_001005474.2,NM_031419.3	29,29	0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077	probably-damaging,probably-damaging	510/619,610/719	101575921	1,13005	2203	4300	6503	SO:0001583	missense			AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802	64332		Ankyrin repeat domain containing	29805	protein-coding gene	gene with protein product	IL-1 inducible nuclear ankyrin-repeat protein	608004			NA	12565889, 16513645	Standard	NM_031419	NM_031419	NA	Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1829G>A	chr3.hg19:g.101575921G>A	ENSP00000325663:p.Arg610His	NA	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	hg19	CCDS2946.1	0.02	8.888984	ATCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.21	3.572565	0.65765	2.27E-4	0.0	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172	T;T;T;T	0.36157	1.27;1.27;1.27;1.27	5.98	5.98	0.97165	Ankyrin repeat-containing domain (4);	0.187199	0.47455	D	0.000233	T	0.50000	0.1590	L	0.37850	1.14	0.40346	D	0.979086	D;D	0.89917	0.999;1.0	D;D	0.71414	0.933;0.973	T	0.41556	-0.9502	10	0.46703	T	0.11	-6.8335	15.8809	0.79205	0.0:0.1347:0.8653:0.0	.	488;610	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	H	510;510;488;610	ENSP00000419800:R510H;ENSP00000377618:R510H;ENSP00000325593:R488H;ENSP00000325663:R610H	ENSP00000325593:R488H	R	+	2	0	NFKBIZ	103058611	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.082000	0.57635	2.838000	0.97847	0.591000	0.81541	CGC	NOVEL	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353793.1	3	19.470942	KEEP	0	0	0	65	2035	GG	1	1	0		+	44	60	1535	0	0	124.381287	202	60	6698	422	ENST00000326172.5	0.178862	1
PHLDB2	90102	__UNKNOWN__	__UNKNOWN__	3	111633466	111633466	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:111633466C>T	ENST00000495180.1	+	2	499				PHLDB2_ENST00000393923.3_Intron|PHLDB2_ENST00000477695.1_3'UTR|PHLDB2_ENST00000481953.1_Intron|PHLDB2_ENST00000431670.2_Intron|PHLDB2_ENST00000412622.1_Intron|PHLDB2_ENST00000393925.3_Intron			Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	NA		NA				cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						tgttcttcacccattttttta	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824	90102		Pleckstrin homology (PH) domain containing	29573	protein-coding gene	gene with protein product		610298			NA	12376540	Standard	NM_145753	NM_145753	NA	Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000495180.1:c.477+917C>T	chr3.hg19:g.111633466C>T		NA	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	hg19		0.02	7.505728	CACxCAT	COVERED																																																																																			NOVEL	PHLDB2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000354340.1	2	11.135855	KEEP	0	0	0	37	1282	CC	1	1	0		+	23	60	869	0	1	68.87206	143	60	5089	235	ENST00000495180.1	0.138554	1
BOC	91653	__UNKNOWN__	__UNKNOWN__	3	113003634	113003634	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:113003634T>C	ENST00000495514.1	+	18	3596	c.2892T>C	c.(2890-2892)agT>agC	p.S964S	BOC_ENST00000355385.3_Silent_p.S964S|BOC_ENST00000273395.4_Silent_p.S965S			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	964		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			AGCAGCAGAGTGACACCAGCA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													121	108	113	NA		NA	NA	3		NA											NA				113003634		2203	4300	6503	SO:0001819	synonymous_variant			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857	91653		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	17173	protein-coding gene	gene with protein product	brother of CDO, brother of CDON, cell adhesion associated, oncogene regulated 2	608708	Boc homolog (mouse)		NA	11782431	Standard	NM_033254	NM_033254	NA	Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.2892T>C	chr3.hg19:g.113003634T>C		NA	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	hg19	CCDS2971.1	0.02	26.538561	GAGxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	t	5.950	0.359228	0.11239	.	.	ENSG00000144857	ENST00000473008	.	.	.	4.95	-0.382	0.12481	.	.	.	.	.	T	0.20861	0.0502	.	.	.	0.20307	N	0.999914	.	.	.	.	.	.	T	0.23797	-1.0178	4	.	.	.	.	2.2855	0.04125	0.1469:0.0836:0.253:0.5165	.	.	.	.	A	5	.	.	V	+	2	0	BOC	114486324	0.023000	0.18921	0.568000	0.28447	0.621000	0.37620	-1.101000	0.03336	-0.192000	0.10432	0.529000	0.55759	GTG	NOVEL	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354485.3	9	42.093258	KEEP	0	2	13	145	4343	TT	1	1	0		+	109	60	3806	0	0	309.765904	486	60	16981	995	ENST00000495514.1	0.183193	1
SIDT1	54847	__UNKNOWN__	__UNKNOWN__	3	113295788	113295788	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:113295788T>A	ENST00000264852.4	+	4	1261	c.535T>A	c.(535-537)Ttt>Att	p.F179I	SIDT1_ENST00000393830.3_Missense_Mutation_p.F179I	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	179		NA			dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGCCTTTCACTTTACTGCCAG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													231	229	230	NA		NA	NA	3		NA											NA				113295788		2203	4300	6503	SO:0001583	missense			AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858	54847			25967	protein-coding gene	gene with protein product		606816			NA		Standard	NM_017699	NM_017699	NA	Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.535T>A	chr3.hg19:g.113295788T>A	ENSP00000264852:p.Phe179Ile	NA	Q17RR4	hg19	CCDS2974.1	0.02	14.508652	CACxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430876	0.83776	.	.	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.15487	2.42;2.42	4.78	4.78	0.61160	.	0.101886	0.43579	D	0.000554	T	0.14570	0.0352	L	0.39147	1.195	0.48975	D	0.999737	B	0.34264	0.446	B	0.32677	0.15	T	0.08146	-1.0736	10	0.19590	T	0.45	-15.1836	14.4293	0.67238	0.0:0.0:0.0:1.0	.	179	Q9NXL6	SIDT1_HUMAN	I	179	ENSP00000264852:F179I;ENSP00000377416:F179I	ENSP00000264852:F179I	F	+	1	0	SIDT1	114778478	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.339000	0.65953	2.130000	0.65690	0.482000	0.46254	TTT	NOVEL	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317564.1	2	12.968439	KEEP	0	1	5	45	1468	TT	1	1	0		+	61	60	2267	0	0	188.020991	260	60	9723	456	ENST00000264852.4	0.190031	1
ADPRH	141	__UNKNOWN__	__UNKNOWN__	3	119301181	119301181	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs149799527	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:119301181C>G	ENST00000478399.1	+	2	1570	c.165C>G	c.(163-165)gaC>gaG	p.D55E	ADPRH_ENST00000478927.1_Missense_Mutation_p.D55E|ADPRH_ENST00000357003.3_Missense_Mutation_p.D55E|ADPRH_ENST00000465513.1_Missense_Mutation_p.D55E|ADPRH_ENST00000471850.1_Intron			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	55		NA			cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		GAGTTAGTGACGACACAGTGA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(133;579 1804 5989 9967 40052)					NA		NA				0													105	93	97	NA		NA	NA	3		NA											NA				119301181		2203	4300	6503	SO:0001583	missense			L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843	141			269	protein-coding gene	gene with protein product		603081			NA	8349667, 12070318	Standard	NM_001125	NM_001125	NA	Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.165C>G	chr3.hg19:g.119301181C>G	ENSP00000420200:p.Asp55Glu	NA	B2R8H1|D3DN83	hg19	CCDS2990.1	0.02	14.021712	TGAxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.21	2.764828	0.49574	.	.	ENSG00000144843	ENST00000478399;ENST00000481816;ENST00000478927;ENST00000357003;ENST00000465513	T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56	5.75	-0.577	0.11727	.	0.048643	0.85682	D	0.000000	T	0.74129	0.3676	M	0.93720	3.45	0.51012	D	0.999907	D	0.89917	1.0	D	0.81914	0.995	T	0.75235	-0.3389	10	0.72032	D	0.01	-22.1791	9.427	0.38586	0.0:0.3839:0.0:0.6161	.	55	P54922	ADPRH_HUMAN	E	55	ENSP00000420200:D55E;ENSP00000419703:D55E;ENSP00000417528:D55E;ENSP00000349496:D55E;ENSP00000417430:D55E	ENSP00000349496:D55E	D	+	3	2	ADPRH	120783871	0.954000	0.32549	0.991000	0.47740	0.291000	0.27294	0.009000	0.13219	-0.095000	0.12351	-2.049000	0.00408	GAC	NOVEL	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355199.1	2	11.736578	KEEP	0	0	0	39	1289	CC	1	1	0		+	61	60	2214	0	0	181.829015	270	60	9287	439	ENST00000478399.1	0.18429	1
GSK3B	2932	__UNKNOWN__	__UNKNOWN__	3	119541160	119541160	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:119541160G>A	ENST00000264235.8	-	0	6720					NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	NA		NA			axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	AAGTGGTCACGCTAATTGGTA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701	2932			4617	protein-coding gene	gene with protein product		605004			NA	10486203	Standard		NM_002093	NA	Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.*4475C>T	chr3.hg19:g.119541160G>A		NA	D3DN89|Q9BWH3|Q9UL47	hg19	CCDS54628.1	0.02	1.872192	CACxCTA	COVERED																																																																																			NOVEL	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258240.2	3	3.611557	KEEP	0	0	0	12	406	GG	0.993634	0.993529	0		-	10	60	372	0	0	28.239187	82	60	2633	119	ENST00000264235.8	0.108696	0.999895
KALRN	8997	__UNKNOWN__	__UNKNOWN__	3	124196268	124196268	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:124196268C>T	ENST00000240874.3	+	27	4342				KALRN_ENST00000360013.3_Intron|KALRN_ENST00000460856.1_Intron	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	NA		NA			apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						ATTTAGCTATCCTTTTTTCCT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145	8997		Rho guanine nucleotide exchange factors, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	4814	protein-coding gene	gene with protein product	serine/threonine kinase with Dbl and pleckstrin homology domains	604605	huntingtin-associated protein interacting protein (duo)	HAPIP	NA	9285789, 10023074	Standard	NM_003947	NM_001024660	NA	Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4185+87C>T	chr3.hg19:g.124196268C>T		NA	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	hg19	CCDS3027.1	0.02	6.889707	TATxCTT	COVERED																																																																																			NOVEL	KALRN-005	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258843.4	0	6.019346	KEEP	0	0	0	20	690	CC	0.999863	0.999863	0		+	21	60	774	0	0	59.941012	147	60	5154	216	ENST00000240874.3	0.125	1
HEG1	57493	__UNKNOWN__	__UNKNOWN__	3	124688014	124688014	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:124688014T>C	ENST00000311127.4	-	0	5695					NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	NA		NA			cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						AGACAATTCTTTTACCTCTGT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706	57493			29227	protein-coding gene	gene with protein product	heart of glass	614182	HEG homolog 1 (zebrafish)		NA	10574462, 19151727, 23007647	Standard	XM_087386	NM_020733	NA	Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.*1482A>G	chr3.hg19:g.124688014T>C		NA	Q6NX66|Q8NC40|Q9BSV0	hg19	CCDS46898.1	0.02	12.289338	TCTxTTA	COVERED																																																																																			NOVEL	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355732.2	1	7.221936	KEEP	0	0	0	24	766	TT	0.999909	0.999909	0		-	45	60	1691	0	0	137.276681	231	60	8299	348	ENST00000311127.4	0.163043	1
ALDH1L1-AS2	100862662	__UNKNOWN__	__UNKNOWN__	3	125900107	125900107	__UNKNOWN__	RNA	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:125900107G>T	ENST00000502278.1	+	0	290				ALDH1L1-AS2_ENST00000500232.2_RNA					ALDH1L1 antisense RNA 2	NA		NA									NA						AGTGATAATTGCGTATTGTTT	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							3q21.3	2012-10-12	2012-08-15		ENSG00000246022	ENSG00000246022	100862662		Long non-coding RNAs	42446	non-coding RNA	RNA, long non-coding		NA	ALDH1L1 antisense RNA 2 (non-protein coding)		NA		Standard		NR_046383	NA	Approved		uc003eiq.4		OTTHUMG00000162642	ENST00000502278.1:	chr3.hg19:g.125900107G>T		NA		hg19		0.02	2.252435	ATTxCGT	COVERED																																																																																			NOVEL	ALDH1L1-AS2-002	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000369891.1	1	5.417256	KEEP	0	0	0	18	613	GG	0.999859	0.989403	0		+	18	60	650	0	0	57.517172	43	60	1593	91	ENST00000502278.1	0.295082	0.989542
PLXNA1	5361	__UNKNOWN__	__UNKNOWN__	3	126722257	126722257	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:126722257C>T	ENST00000393409.2	+	3	1462	c.1462C>T	c.(1462-1464)Cga>Tga	p.R488*	PLXNA1_ENST00000251772.4_Nonsense_Mutation_p.R465*	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	488	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.	NA			axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		CCCCATCCTGCGAGACCTCGT	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	68	70	NA		NA	NA	3		NA											NA				126722257		2202	4300	6502	SO:0001587	stop_gained			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554	5361		Plexins	9099	protein-coding gene	gene with protein product		601055		PLXN1	NA	8570614	Standard	NM_032242	NM_032242	NA	Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.1462C>T	chr3.hg19:g.126722257C>T	ENSP00000377061:p.Arg488*	NA		hg19	CCDS33847.2	0.02	24.33201	CTGxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	38	6.994459	0.97990	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	.	.	.	3.86	2.87	0.33458	.	0.000000	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.7785	0.46363	0.3166:0.6834:0.0:0.0	.	.	.	.	X	488;465	.	ENSP00000251772:R465X	R	+	1	2	PLXNA1	128204947	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.689000	0.37700	2.108000	0.64289	0.467000	0.42956	CGA	NOVEL	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356451.1	1	81.583539	KEEP	0	1	31	282	9700	CC	1	1	0		+	76	60	2777	1	0	220.189026	442	60	15722	1138	ENST00000393409.2	0.146718	1
PLXNA1	5361	__UNKNOWN__	__UNKNOWN__	3	126748912	126748912	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:126748912G>A	ENST00000393409.2	+	27	5061				PLXNA1_ENST00000251772.4_Intron	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	NA		NA			axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			breast(3)|central_nervous_system(5)|endometrium(10)|kidney(5)|large_intestine(4)|lung(32)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	67				GBM - Glioblastoma multiforme(114;0.155)		ACCAAGGTGGGCCTGGCTGGC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													57	60	59	NA		NA	NA	3		NA											NA				126748912		2203	4300	6503	SO:0001627	intron_variant			X87832	CCDS33847.1, CCDS33847.2	3q21.2	2006-12-19				ENSG00000114554	5361		Plexins	9099	protein-coding gene	gene with protein product		601055		PLXN1	NA	8570614	Standard	NM_032242	NM_032242	NA	Approved	NOV	uc003ejg.3	Q9UIW2		ENST00000393409.2:c.5061+5G>A	chr3.hg19:g.126748912G>A		NA		hg19	CCDS33847.2	0.02	10.52504	TGGxCCT	COVERED																																																																																			NOVEL	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356451.1	1	13.539368	KEEP	0	1	16	51	1706	GG	1	1	0		+	17	60	586	0	0	39.034977	259	60	9030	386	ENST00000393409.2	0.061594	1
EFCC1	79825	__UNKNOWN__	__UNKNOWN__	3	128753140	128753140	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs114087327	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:128753140G>A	ENST00000480450.1	+	5	1417	c.1417G>A	c.(1417-1419)Ggt>Agt	p.G473S	EFCC1_ENST00000436022.2_Missense_Mutation_p.G36S			Q9HA90	EFCC1_HUMAN	EF-hand and coiled-coil domain containing 1	473		NA					calcium ion binding (GO:0005509)				NA						TCAGGGCTGCGGTGGGAGGAC	0.602	NA	NA											G|||	41	0.0081869	0.0303	0.0014	5008	,	,	NA	16713	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	SER/GLY	100,4306	80.4+/-118.8	1,98,2104	54	53	53	NA	1417	-3.6	0	3	dbSNP_132	53	1,8599		0,1,4299	yes	missense	CCDC48	NM_024768.2	56	1,99,6403	AA,AG,GG	NA	0.0116,2.2696,0.7766	benign	473/599	128753140	101,12905	2203	4300	6503	SO:0001583	missense			AK022119	CCDS3054.1, CCDS3054.2	3q21.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000114654	ENSG00000114654	79825		EF-hand domain containing	25692	protein-coding gene	gene with protein product		NA	chromosome 3 open reading frame 73, coiled-coil domain containing 48	C3orf73, CCDC48	NA		Standard	NM_024768	NM_024768	NA	Approved	FLJ12057	uc011bkt.2	Q9HA90	OTTHUMG00000158996	ENST00000480450.1:c.1417G>A	chr3.hg19:g.128753140G>A	ENSP00000420075:p.Gly473Ser	NA	A8MYE2	hg19	CCDS3054.2	0.02	4.613479	TGCxGTG	COVERED	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	9.071	0.996886	0.19043	0.022696	1.16E-4	ENSG00000114654	ENST00000480450;ENST00000436022	T;T	0.40476	1.03;1.06	4.16	-3.63	0.04529	.	0.914557	0.09214	N	0.832880	T	0.10121	0.0248	N	0.16368	0.405	0.09310	N	1	B	0.32350	0.366	B	0.21360	0.034	T	0.13388	-1.0511	10	0.15066	T	0.55	.	10.9822	0.47501	0.2705:0.0:0.7295:0.0	.	473	Q9HA90	CCD48_HUMAN	S	473;36	ENSP00000420075:G473S;ENSP00000414597:G36S	ENSP00000414597:G36S	G	+	1	0	CCDC48	130235830	0.000000	0.05858	0.003000	0.11579	0.909000	0.53808	-0.134000	0.10436	-0.996000	0.03455	0.306000	0.20318	GGT	NOVEL	EFCC1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352832.1	1	5.417064	KEEP	0	0	0	18	609	GG	0.999859	0.999859	0		+	22	60	847	0	0	68.481466	122	60	4225	190	ENST00000480450.1	0.152778	1
IFT122	55764	__UNKNOWN__	__UNKNOWN__	3	129207184	129207184	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs528383242		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:129207184T>C	ENST00000348417.2	+	16	2013	c.1936T>C	c.(1936-1938)Tgg>Cgg	p.W646R	IFT122_ENST00000296266.3_Missense_Mutation_p.W697R|IFT122_ENST00000504021.1_Missense_Mutation_p.W540R|IFT122_ENST00000347300.2_Missense_Mutation_p.W587R|IFT122_ENST00000431818.2_Missense_Mutation_p.W496R|IFT122_ENST00000349441.2_Missense_Mutation_p.W535R|IFT122_ENST00000507564.1_Missense_Mutation_p.W638R|IFT122_ENST00000440957.2_Missense_Mutation_p.W437R	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	646		NA			camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						AGACACTGATTGGCGTGAACT	0.498	NA	NA											T|||	1	0.000199681	0	0	5008	,	,	NA	23353	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													92	85	87	NA		NA	NA	3		NA											NA				129207184		2203	4300	6503	SO:0001583	missense			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913	55764		WD repeat domain containing, Intraflagellar transport homologs	13556	protein-coding gene	gene with protein product		606045	WD repeat domain 10, intraflagellar transport 122 homolog (Chlamydomonas)	WDR10	NA	11242542	Standard	NM_018262	NM_052985	NA	Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.1936T>C	chr3.hg19:g.129207184T>C	ENSP00000324005:p.Trp646Arg	NA	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	hg19	CCDS3061.1	0.02	26.726725	GATxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	T	19.86	3.906143	0.72868	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000454840;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957;ENST00000509522;ENST00000507221	D;D;D;D;T;D;D;D;T	0.86297	-2.1;-2.1;-2.1;-2.1;-1.0;-2.1;-2.1;-2.1;-1.0	4.73	4.73	0.59995	.	0.062472	0.64402	D	0.000001	D	0.94716	0.8295	M	0.92077	3.27	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.998;1.0;0.99;0.999;0.998;0.996;0.996;0.999;0.996;0.998	D	0.95846	0.8870	10	0.87932	D	0	-9.5975	14.2449	0.65981	0.0:0.0:0.0:1.0	.	437;26;638;51;540;486;535;587;646;697	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	R	587;697;638;587;496;540;535;646;486;437;161;26	ENSP00000323973:W587R;ENSP00000296266:W697R;ENSP00000425536:W638R;ENSP00000410946:W496R;ENSP00000422179:W540R;ENSP00000324165:W535R;ENSP00000324005:W646R;ENSP00000401569:W437R;ENSP00000424727:W161R	ENSP00000296266:W697R	W	+	1	0	IFT122	130689874	1.000000	0.71417	0.906000	0.35671	0.937000	0.57800	7.762000	0.85270	1.764000	0.52075	0.413000	0.27773	TGG	NOVEL	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355852.1	3	34.648511	KEEP	2	2	74	141	4347	TT	1	1	0		+	28	47	970	0	0	60.451606	613	60	22495	959	ENST00000348417.2	0.043682	1
COL6A6	131873	__UNKNOWN__	__UNKNOWN__	3	130292968	130292968	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:130292968A>G	ENST00000358511.6	+	7	3177	c.3146A>G	c.(3145-3147)cAc>cGc	p.H1049R	COL6A6_ENST00000453409.2_Missense_Mutation_p.H1049R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1049	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.	NA			cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GATACCTATCACCCGGAGTTT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													60	57	58	NA		NA	NA	3		NA											NA				130292968		1860	4102	5962	SO:0001583	missense			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384	131873		Collagens	27023	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001102608	NM_001102608	NA	Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.3146A>G	chr3.hg19:g.130292968A>G	ENSP00000351310:p.His1049Arg	NA	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	hg19	CCDS46911.1	0.02	12.62094	ATCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.021	-1.423461	0.01126	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.82526	-1.62;-1.62	5.15	-8.72	0.00845	von Willebrand factor, type A (3);	1.058100	0.07403	N	0.891118	T	0.49029	0.1533	N	0.00554	-1.385	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54563	-0.8275	10	0.15066	T	0.55	.	12.0783	0.53657	0.628:0.0:0.2875:0.0844	.	1049	A6NMZ7	CO6A6_HUMAN	R	1049	ENSP00000351310:H1049R;ENSP00000399236:H1049R	ENSP00000351310:H1049R	H	+	2	0	COL6A6	131775658	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.517000	0.06275	-2.323000	0.00639	-2.151000	0.00333	CAC	NOVEL	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356705.5	2	9.626349	KEEP	0	0	0	32	996	AA	0.999997	0.999997	0		+	83	60	2931	0	0	261.490533	180	60	6358	374	ENST00000358511.6	0.315589	1
NEK11	79858	__UNKNOWN__	__UNKNOWN__	3	130903536	130903536	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:130903536C>G	ENST00000510769.1	+	10	1337				NEK11_ENST00000356918.4_Intron|NEK11_ENST00000508196.1_Intron|NEK11_ENST00000383366.4_Intron|NEK11_ENST00000507910.1_Intron|NEK11_ENST00000412440.2_Intron|NEK11_ENST00000429253.2_Intron|NEK11_ENST00000510688.1_Intron					NIMA-related kinase 11	NA		NA								breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						TTTTCTCTTTCTTCTTAAAGG	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	3	3	NA		NA	NA	3		NA											NA				130903536		753	1793	2546	SO:0001627	intron_variant			AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670	79858			18593	protein-coding gene	gene with protein product		609779	NIMA (never in mitosis gene a)- related kinase 11		NA		Standard	NM_024800	NM_024800	NA	Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1084+13805C>G	chr3.hg19:g.130903536C>G		NA		hg19		0.02	15.03791	TTTxTTC	COVERED																																																																																			NOVEL	NEK11-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000356757.1	2	14.428736	KEEP	0	0	0	48	1643	CC	1	1	0		+	150	60	5569	0	0	530.233835	178	60	6665	430	ENST00000510769.1	0.457317	1
MRPL3	11222	__UNKNOWN__	__UNKNOWN__	3	131221573	131221573	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:131221573C>T	ENST00000425847.2	-	1	254		c.e1+1		MRPL3_ENST00000264995.3_Splice_Site			P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	NA		NA			translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CACCTTCCTACCTGTTCCCCG	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	48	47	NA		NA	NA	3		NA											NA				131221573		2203	4300	6503	SO:0001630	splice_region_variant			X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686	11222		Mitochondrial ribosomal proteins / large subunits	10379	protein-coding gene	gene with protein product		607118		RPML3	NA	2891103	Standard	NM_007208	NM_007208	NA	Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000425847.2:c.92+1G>A	chr3.hg19:g.131221573C>T		NA	Q6IBT2	hg19		0.02	18.424351	CTAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.47	2.247668	0.39697	.	.	ENSG00000114686	ENST00000264995;ENST00000425847;ENST00000512877	.	.	.	3.68	3.68	0.42216	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.2046	0.48762	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MRPL3	132704263	1.000000	0.71417	0.986000	0.45419	0.041000	0.13682	1.545000	0.36169	2.352000	0.79861	0.455000	0.32223	.	NOVEL	MRPL3-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000356535.1	4	61.394658	KEEP	0	0	0	204	7079	CC	1	1	0	Intron	-	63	60	2170	0	0	170.910888	345	60	12585	820	ENST00000425847.2	0.154412	1
DNAJC13	23317	__UNKNOWN__	__UNKNOWN__	3	132202364	132202364	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:132202364A>T	ENST00000260818.6	+	28	3373	c.3125A>T	c.(3124-3126)gAc>gTc	p.D1042V		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1042		NA			osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						AATGAAACTGACCTTGCTACC	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													186	161	169	NA		NA	NA	3		NA											NA				132202364		2203	4300	6503	SO:0001583	missense			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246	23317		Heat shock proteins / DNAJ (HSP40)	30343	protein-coding gene	gene with protein product		614334			NA	12438707	Standard	NM_015268	NM_015268	NA	Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.3125A>T	chr3.hg19:g.132202364A>T	ENSP00000260818:p.Asp1042Val	NA	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	hg19	CCDS33857.1	0.02	10.77104	CTGxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	A	23.1	4.369599	0.82463	.	.	ENSG00000138246	ENST00000260818	T	0.51574	0.7	5.76	4.61	0.57282	Armadillo-type fold (1);	0.108034	0.64402	D	0.000008	T	0.47358	0.1441	M	0.64997	1.995	0.80722	D	1	P	0.39216	0.664	B	0.39299	0.296	T	0.51276	-0.8726	10	0.87932	D	0	.	11.8075	0.52163	0.9316:0.0:0.0684:0.0	.	1042	O75165	DJC13_HUMAN	V	1042	ENSP00000260818:D1042V	ENSP00000260818:D1042V	D	+	2	0	DNAJC13	133685054	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.287000	0.95975	1.127000	0.42034	0.533000	0.62120	GAC	NOVEL	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356807.2	0	14.442653	KEEP	0	0	0	48	1538	AA	1	1	0		+	15	60	533	0	0	35.310064	255	60	8999	404	ENST00000260818.6	0.055556	1
DNAJC13	23317	__UNKNOWN__	__UNKNOWN__	3	132219741	132219741	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:132219741T>C	ENST00000260818.6	+	39	4768	c.4520T>C	c.(4519-4521)gTa>gCa	p.V1507A		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1507		NA			osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CTCTGTCGGGTACTATATTTT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													189	182	185	NA		NA	NA	3		NA											NA				132219741		2203	4300	6503	SO:0001583	missense			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246	23317		Heat shock proteins / DNAJ (HSP40)	30343	protein-coding gene	gene with protein product		614334			NA	12438707	Standard	NM_015268	NM_015268	NA	Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4520T>C	chr3.hg19:g.132219741T>C	ENSP00000260818:p.Val1507Ala	NA	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	hg19	CCDS33857.1	0.02	15.180086	GGGxACT	COVERED	.	.	.	.	.	.	.	.	.	.	T	18.68	3.675889	0.67928	.	.	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.47528	0.84	5.86	5.86	0.93980	Armadillo-like helical (1);Armadillo-type fold (1);	0.152719	0.46442	D	0.000300	T	0.41604	0.1166	L	0.39898	1.24	0.54753	D	0.999988	B	0.12013	0.005	B	0.08055	0.003	T	0.15867	-1.0422	10	0.30854	T	0.27	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	1507	O75165	DJC13_HUMAN	A	1507;154	ENSP00000260818:V1507A	ENSP00000260818:V1507A	V	+	2	0	DNAJC13	133702431	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	7.774000	0.85478	2.367000	0.80283	0.528000	0.53228	GTA	NOVEL	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356807.2	3	21.912071	KEEP	0	0	0	73	2164	TT	1	1	0		+	36	60	1299	0	0	98.665398	277	60	9457	474	ENST00000260818.6	0.115016	1
SLCO2A1	6578	__UNKNOWN__	__UNKNOWN__	3	133692737	133692737	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:133692737C>T	ENST00000493729.1	-	3	346				SLCO2A1_ENST00000310926.4_Intron|SLCO2A1_ENST00000478651.1_Intron			Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	NA		NA			lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	AGAGAAGACCCGATCACACTT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640	6578		Solute carriers	10955	protein-coding gene	gene with protein product		601460	solute carrier family 21 (prostaglandin transporter), member 2, matrin F/G 1	SLC21A2, MATR1	NA	8787677, 9618293	Standard	NM_005630	NM_005630	NA	Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000493729.1:c.235-68G>A	chr3.hg19:g.133692737C>T		NA	Q86V98|Q8IUN2	hg19		0.02	4.702702	ACCxGAT	COVERED																																																																																			NOVEL	SLCO2A1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357134.1	1	5.717407	KEEP	0	0	0	19	618	CC	0.99986	0.99986	0		-	13	60	491	0	0	36.347595	131	60	4405	196	ENST00000493729.1	0.090278	1
C3orf72	0	__UNKNOWN__	__UNKNOWN__	3	138670246	138670246	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:138670246A>G	ENST00000383165.3	+	0	1491					NM_001040061.2	NP_001035150.1	Q6ZUU3	FOXNB_HUMAN		NA		NA								large_intestine(1)|lung(3)	4						AGTAGACCAGAGCTCTGGGCT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000383165.3:c.*832A>G	chr3.hg19:g.138670246A>G		NA	A6NGX0	hg19	CCDS43155.1	0.02	8.942802	CAGxGCT	COVERED																																																																																			NOVEL	C3orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357986.1	1	17.726752	KEEP	0	0	0	59	1828	AA	1	1	0		+	43	60	1492	0	0	121.704514	186	60	6737	346	ENST00000383165.3	0.187773	1
PRR23A	729627	__UNKNOWN__	__UNKNOWN__	3	138724917	138724917	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:138724917G>A	ENST00000383163.2	-	1	193	c.194C>T	c.(193-195)gCg>gTg	p.A65V	MRPS22_ENST00000495075.1_5'UTR	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	65		NA								endometrium(3)|kidney(1)|lung(7)	11						GGCACAGCCCGCGGCCAGGAC	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													8	12	11	NA		NA	NA	3		NA											NA				138724917		682	1571	2253	SO:0001583	missense				CCDS46923.1	3q22.3	2014-06-03				ENSG00000206260	729627			37172	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001134659	NM_001134659	NA	Approved		uc011bms.2	A6NEV1		ENST00000383163.2:c.194C>T	chr3.hg19:g.138724917G>A	ENSP00000372649:p.Ala65Val	NA		hg19	CCDS46923.1	0.02	4.411564	CCCxCGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.66	2.603205	0.46423	.	.	ENSG00000206260	ENST00000383163	.	.	.	2.65	0.63	0.17693	.	1.656350	0.03654	N	0.241435	T	0.36110	0.0955	L	0.55481	1.735	0.09310	N	1	D	0.58268	0.982	B	0.42522	0.39	T	0.36529	-0.9744	9	0.66056	D	0.02	.	6.8768	0.24151	0.0:0.0:0.5013:0.4987	.	65	A6NEV1	PR23A_HUMAN	V	65	.	ENSP00000372649:A65V	A	-	2	0	PRR23A	140207607	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.073000	0.14640	0.151000	0.19162	0.491000	0.48974	GCG	NOVEL	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361503.1	0	7.823302	KEEP	0	0	0	26	842	GG	0.999957	0.99995	0		-	7	60	243	0	0	16.362178	102	60	3557	158	ENST00000383163.2	0.06422	0.999993
PRR23B	389151	__UNKNOWN__	__UNKNOWN__	3	138737902	138737902	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:138737902T>C	ENST00000329447.5	-	0	1866				MRPS22_ENST00000495075.1_Intron	NM_001013650.2	NP_001013672.1	Q6ZRT6	PR23B_HUMAN	proline rich 23B	NA		NA								NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTATCTCCTATATAAAAATAT	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC137146	CCDS33868.1	3q22.3	2014-06-03			ENSG00000184814	ENSG00000184814	389151			33764	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013650	NM_001013650	NA	Approved	FLJ46116	uc003esy.1	Q6ZRT6	OTTHUMG00000160633	ENST00000329447.5:c.*804A>G	chr3.hg19:g.138737902T>C		NA	B2RNV9	hg19	CCDS33868.1	0.02	9.269626	CTAxATA	COVERED																																																																																			NOVEL	PRR23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361501.1	3	8.424907	KEEP	0	0	0	28	877	TT	0.999997	0.999997	0		-	7	60	260	0	0	16.123629	196	60	7227	292	ENST00000329447.5	0.034483	1
CLSTN2	64084	__UNKNOWN__	__UNKNOWN__	3	140286035	140286035	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:140286035T>C	ENST00000458420.3	+	0	3998					NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	NA		NA			homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						AACGTAGGCTTCATGGTGGGT	0.542	NA	NA								HNSCC(16;0.037)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(45;858 913 3709 36904 37282)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258	64084		Cadherins / Cadherin-related	17448	protein-coding gene	gene with protein product	cadherin-related family member 13	611323			NA	12498782	Standard	NM_022131	NM_022131	NA	Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.*940T>C	chr3.hg19:g.140286035T>C		NA	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	hg19	CCDS3112.1	0.02	16.945465	GCTxCAT	COVERED																																																																																			NOVEL	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359393.3	9	16.216048	KEEP	0	0	0	54	1676	TT	1	1	0		+	46	60	1554	0	0	118.570506	304	60	10912	481	ENST00000458420.3	0.131429	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	141457041	141457041	__UNKNOWN__	IGR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:141457041A>G			NA	NA				RP11-340E6.1 (17126 upstream) : RNF7 (4 downstream)						NA		NA									NA						GCGCCAGCCAATCGTGGGCAG	0.756	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.141457041A>G		NA		hg19		0.02	-0.227517	CCAxTCG	COVERED																																																																																			NOVEL					0			0	2.705175	KEEP	0	0	0	9	270	AA	0.99254	0.578582	0			4	60	102	0	0	7.363646	21	60	718	39		0.16	0.58293
RNF7	9616	__UNKNOWN__	__UNKNOWN__	3	141461681	141461681	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:141461681C>A	ENST00000480908.1	+	2	240				RNF7_ENST00000393000.3_Intron|RNF7_ENST00000273480.3_Intron	NM_001201370.1	NP_001188299.1	Q9UBF6	RBX2_HUMAN	ring finger protein 7	NA		NA			intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of apoptotic process (GO:0043066)|protein neddylation (GO:0045116)|protein ubiquitination (GO:0016567)|response to redox state (GO:0051775)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|NEDD8 ligase activity (GO:0019788)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|upper_aerodigestive_tract(1)	5						TAGAGGAACTCTCAAGTGTCT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF092878	CCDS3118.1, CCDS43158.1, CCDS56283.1	3q22-q24	2008-07-18			ENSG00000114125	ENSG00000114125	9616		RING-type (C3HC4) zinc fingers	10070	protein-coding gene	gene with protein product	sensitive to apoptosis, zinc RING finger protein SAG, regulator of cullins 2	603863			NA	10082581, 10230407	Standard	NM_014245	NM_014245	NA	Approved	SAG, ROC2, CKBBP1	uc003eud.3	Q9UBF6	OTTHUMG00000141305	ENST00000480908.1:c.176-2320C>A	chr3.hg19:g.141461681C>A		NA	A8K1H9|A8MTB5|C9JYL3|D3DNF7|D3DNF8|Q9BXN8|Q9Y5M7	hg19	CCDS56283.1	0.02	4.50159	ACTxTCA	COVERED																																																																																			NOVEL	RNF7-007	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353057.2	2	11.136373	KEEP	0	0	0	37	1314	CC	1	0.999994	0		+	10	60	372	0	0	27.379659	101	60	3787	178	ENST00000480908.1	0.09009	0.999994
XRN1	54464	__UNKNOWN__	__UNKNOWN__	3	142084024	142084024	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:142084024G>A	ENST00000392981.2	-	29	3309				XRN1_ENST00000264951.4_Intron			Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	NA		NA			exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						TCTAAAGGCTGAAGAGAAGAA	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	50	51	NA		NA	NA	3		NA											NA				142084024		2203	4299	6502	SO:0001627	intron_variant			AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127	54464			30654	protein-coding gene	gene with protein product		607994			NA	12515382	Standard	NM_019001	XM_005247544	NA	Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000392981.2:c.3262-3C>T	chr3.hg19:g.142084024G>A		NA	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	hg19		0.02	6.511467	GCTxAAG	COVERED																																																																																			NOVEL	XRN1-004	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000354200.1	1	15.048365	KEEP	0	0	0	50	1757	GG	1	1	0		-	7	60	257	0	0	16.248015	170	60	6362	273	ENST00000392981.2	0.039548	1
TRPC1	7220	__UNKNOWN__	__UNKNOWN__	3	142443117	142443117	__UNKNOWN__	5'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:142443117C>A	ENST00000476941.1	+	0	202				TRPC1_ENST00000273482.6_5'UTR	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	NA		NA			axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						ACTGTCGTCCCCGGAcgggcg	0.801	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935	7220		Voltage-gated ion channels / Transient receptor potential cation channels	12333	protein-coding gene	gene with protein product		602343			NA	7568191, 16382100	Standard	NM_003304	NM_001251845	NA	Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.-285C>A	chr3.hg19:g.142443117C>A		NA	Q14CE4	hg19	CCDS58856.1	0.02	7.784712	TCCxCGG	COVERED																																																																																			NOVEL	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354520.1	0	43.307473	KEEP	0	0	0	144	4563	CC	1	1	0		+	12	60	385	1	0	23.705	222	70	7411	411	ENST00000476941.1	0.051282	1
CHST2	9435	__UNKNOWN__	__UNKNOWN__	3	142840525	142840525	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:142840525G>A	ENST00000309575.3	+	2	2251	c.867G>A	c.(865-867)gcG>gcA	p.A289A		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	289		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|multicellular organismal development (GO:0007275)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)|trans-Golgi network (GO:0005802)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(2)	22						AGCGCCTGGCGCGTTTCGAGG	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													22	23	23	NA		NA	NA	3		NA											NA				142840525		2194	4296	6490	SO:0001819	synonymous_variant			BC042160	CCDS3129.1	3q24	2007-03-14			ENSG00000175040	ENSG00000175040	9435		Sulfotransferases, membrane-bound	1970	protein-coding gene	gene with protein product		603798			NA	10049591	Standard	NM_004267	NM_004267	NA	Approved	C6ST	uc003evm.3	Q9Y4C5	OTTHUMG00000159351	ENST00000309575.3:c.867G>A	chr3.hg19:g.142840525G>A		NA	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	hg19	CCDS3129.1	0.02	6.605186	GGCxCGT	COVERED																																																																																			NOVEL	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354850.1	1	20.461843	KEEP	0	0	0	68	2259	GG	1	1	0		+	36	60	1284	0	0	105.802219	151	60	5182	300	ENST00000309575.3	0.192513	1
ZIC1	7545	__UNKNOWN__	__UNKNOWN__	3	147128446	147128446	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:147128446A>G	ENST00000282928.4	+	1	1276	c.547A>G	c.(547-549)Agc>Ggc	p.S183G		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	183		NA			adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						CCAGGTGACCAGCCCGCGTTC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	41	39	NA		NA	NA	3		NA											NA				147128446		2203	4299	6502	SO:0001583	missense			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977	7545		Zinc fingers, C2H2-type	12872	protein-coding gene	gene with protein product		600470	Zic family member 1 (odd-paired Drosophila homolog), Zic family member 1 (odd-paired homolog, Drosophila)		NA	8542595	Standard	NM_003412	NM_003412	NA	Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.547A>G	chr3.hg19:g.147128446A>G	ENSP00000282928:p.Ser183Gly	NA	Q2M3N1	hg19	CCDS3136.1	0.02	17.376543	ACCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	13.82	2.350795	0.41599	.	.	ENSG00000152977	ENST00000282928	T	0.58797	0.31	3.31	3.31	0.37934	.	0.000000	0.85682	D	0.000000	T	0.58836	0.2150	L	0.37750	1.13	0.58432	D	0.999999	P	0.46220	0.874	P	0.54706	0.759	T	0.58295	-0.7661	10	0.40728	T	0.16	.	12.1208	0.53889	1.0:0.0:0.0:0.0	.	183	Q15915	ZIC1_HUMAN	G	183	ENSP00000282928:S183G	ENSP00000282928:S183G	S	+	1	0	ZIC1	148611136	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.554000	0.67294	1.506000	0.48736	0.448000	0.29417	AGC	NOVEL	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355497.1	4	33.717224	KEEP	0	1	5	114	3433	AA	1	1	0		+	19	60	643	0	0	38.840827	451	60	15920	723	ENST00000282928.4	0.040426	1
CP	1356	__UNKNOWN__	__UNKNOWN__	3	148939468	148939468	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:148939468C>T	ENST00000264613.6	-	1	374	c.112G>A	c.(112-114)Gac>Aac	p.D38N		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	38	F5/8 type A 1.|Plastocyanin-like 1.	NA			cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	TCCCCATGGTCAGAGGCATAA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													69	72	71	NA		NA	NA	3		NA											NA				148939468		2203	4300	6503	SO:0001583	missense			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1356	1.16.3.1		2295	protein-coding gene	gene with protein product		117700			NA		Standard	NM_000096	NM_000096	NA	Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.112G>A	chr3.hg19:g.148939468C>T	ENSP00000264613:p.Asp38Asn	NA	Q14063|Q2PP18|Q9UKS4	hg19	CCDS3141.1	0.02	8.874911	GGTxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.80	1.748186	0.30955	.	.	ENSG00000047457	ENST00000264613;ENST00000455472	D;D	0.99089	-4.86;-5.41	5.2	3.01	0.34805	Cupredoxin (2);	0.493631	0.23165	N	0.051181	D	0.95351	0.8491	N	0.16368	0.405	0.09310	N	1	B;B	0.20550	0.046;0.046	B;B	0.16289	0.015;0.015	D	0.90977	0.4824	10	0.39692	T	0.17	-9.6362	7.8193	0.29278	0.0:0.7544:0.0:0.2456	.	38;38	A8K5A4;P00450	.;CERU_HUMAN	N	38	ENSP00000264613:D38N;ENSP00000426888:D38N	ENSP00000264613:D38N	D	-	1	0	CP	150422158	0.232000	0.23762	0.549000	0.28204	0.762000	0.43233	1.437000	0.34991	1.337000	0.45525	0.591000	0.81541	GAC	NOVEL	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317498.1	3	14.745752	KEEP	0	0	0	49	1717	CC	1	1	0		-	44	60	1578	0	0	128.458098	204	60	7763	378	ENST00000264613.6	0.177419	1
RNF13	11342	__UNKNOWN__	__UNKNOWN__	3	149679482	149679482	__UNKNOWN__	3'UTR	SNP	C	C	T	rs115731746	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:149679482C>T	ENST00000344229.3	+	0	2439				RNF13_ENST00000361785.6_3'UTR|RNF13_ENST00000392894.3_3'UTR	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	NA		NA			protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TTTTTTTTAACGTTTTAATTA	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996	11342		RING-type (C3HC4) zinc fingers	10057	protein-coding gene	gene with protein product		609247			NA		Standard	NM_183384	NM_183381	NA	Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.*591C>T	chr3.hg19:g.149679482C>T		NA	A6NC87|B3KR12|Q05D66|Q6IBJ9	hg19	CCDS3146.1	0.02	22.389124	TAAxGTT	COVERED																																																																																			NOVEL	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356876.1	14	36.41476	KEEP	1	0	0	121	4113	CC	1	1	0		+	15	21	576	0	0	34.930343	531	60	18522	837	ENST00000344229.3	0.027473	1
TSC22D2	9819	__UNKNOWN__	__UNKNOWN__	3	150156080	150156080	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:150156080G>A	ENST00000361875.3	+	2	3046				TSC22D2_ENST00000361136.2_Intron	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	NA		NA			response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			CATGGTTGGAGGGTTATTCTA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428	9819			29095	protein-coding gene	gene with protein product		NA			NA	9734811	Standard	NM_014779	NM_014779	NA	Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.2030+15173G>A	chr3.hg19:g.150156080G>A		NA	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	hg19	CCDS3149.1	0.02	4.807872	GGAxGGT	COVERED																																																																																			NOVEL	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357123.2	1	14.430273	KEEP	0	0	0	48	1656	GG	1	1	0		+	18	60	709	0	0	56.593001	115	60	4235	236	ENST00000361875.3	0.135338	1
RP11-166N6.3	0	__UNKNOWN__	__UNKNOWN__	3	150611197	150611197	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:150611197C>T	ENST00000569170.1	-	6	751				RP11-166N6.2_ENST00000469268.1_RNA|CLRN1-AS1_ENST00000476886.1_RNA|FAM188B2_ENST00000397891.3_Silent_p.G41G						NA		NA									NA						TGCTTCGGGCCCCTCCCTGAA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000569170.1:c.215+775G>A	chr3.hg19:g.150611197C>T		NA		hg19		0.02	17.091556	GGCxCCT	COVERED																																																																																			NOVEL	RP11-166N6.3-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000430534.1	3	9.630201	KEEP	0	0	0	32	1102	CC	0.999997	0.999997	0		-	79	60	2898	0	0	242.164204	311	60	11007	497	ENST00000569170.1	0.202564	1
MED12L	116931	__UNKNOWN__	__UNKNOWN__	3	151130884	151130884	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:151130884C>T	ENST00000474524.1	+	40	6073				MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	NA		NA				mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AAAAGTTTGACATTATGCTTG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													46	45	45	NA		NA	NA	3		NA											NA				151130884		2203	4300	6503	SO:0001627	intron_variant			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893	116931			16050	protein-coding gene	gene with protein product		611318	mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like		NA	11524702	Standard	NM_053002	XM_006713487	NA	Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6036-43C>T	chr3.hg19:g.151130884C>T		NA	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	hg19	CCDS33876.1	0.02	4.399588	TGAxATT	COVERED																																																																																			NOVEL	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357707.2	3	3.611603	KEEP	0	0	0	12	414	CC	0.993634	0.993633	0		+	26	60	955	0	0	79.274438	108	60	4051	161	ENST00000474524.1	0.19403	1
RAP2B	5912	__UNKNOWN__	__UNKNOWN__	3	152884230	152884230	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:152884230G>A	ENST00000323534.2	+	0	4202					NM_002886.2	NP_002877.2	P61225	RAP2B_HUMAN	RAP2B, member of RAS oncogene family	NA		NA			GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of protein tyrosine kinase activity (GO:0061097)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			TTGTTGTAAGGCAATCACCTG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3170.1	3q25.2	2014-05-09			ENSG00000181467	ENSG00000181467	5912			9862	protein-coding gene	gene with protein product	Ras-related protein RAP-2B, small GTP binding protein, Ras family small GTP binding protein RAP2B	179541			NA	2118648	Standard	NM_002886	NM_002886	NA	Approved		uc003ezr.3	P61225	OTTHUMG00000159655	ENST00000323534.2:c.*3196G>A	chr3.hg19:g.152884230G>A		NA	P17964|Q96EG5|Q9CXG0	hg19	CCDS3170.1	0.02	4.226443	AAGxCAA	COVERED																																																																																			NOVEL	RAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356707.1	5	9.323028	KEEP	0	0	0	31	1083	GG	0.999997	0.999997	0		+	16	60	570	1	0	43.579683	114	60	4143	190	ENST00000323534.2	0.123077	1
ARHGEF26	26084	__UNKNOWN__	__UNKNOWN__	3	153840346	153840346	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:153840346T>A	ENST00000356448.4	+	2	849	c.565T>A	c.(565-567)Tcg>Acg	p.S189T	ARHGEF26_ENST00000465093.1_Missense_Mutation_p.S189T|ARHGEF26_ENST00000465817.1_Missense_Mutation_p.S189T	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	189		NA			endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						TGGGTCAGGTTCGCAGTCCGG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)					NA		NA				0													21	23	22	NA		NA	NA	3		NA											NA				153840346		1869	4097	5966	SO:0001583	missense			BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790	26084		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	24490	protein-coding gene	gene with protein product	Src homology 3 domain-containing guanine nucleotide exchange factor	NA			NA	15133129, 12697679	Standard	NM_015595	NM_015595	NA	Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.565T>A	chr3.hg19:g.153840346T>A	ENSP00000348828:p.Ser189Thr	NA	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	hg19	CCDS46938.1	0.02	15.548519	GGTxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	T	12.26	1.884879	0.33255	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	T;T;T	0.57273	0.41;0.41;2.2	4.4	0.615	0.17608	.	0.392934	0.23074	N	0.052222	T	0.32823	0.0842	L	0.27053	0.805	0.09310	N	1	B;B	0.16166	0.016;0.008	B;B	0.16722	0.016;0.016	T	0.14309	-1.0477	10	0.42905	T	0.14	-0.0158	4.9187	0.13858	0.0:0.2462:0.1538:0.5999	.	189;189	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	T	189	ENSP00000348828:S189T;ENSP00000423418:S189T;ENSP00000423295:S189T	ENSP00000348828:S189T	S	+	1	0	ARHGEF26	155323036	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.203000	0.09438	0.099000	0.17552	0.459000	0.35465	TCG	NOVEL	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353287.3	3	43.582998	KEEP	0	0	0	145	4360	TT	1	1	0		+	28	60	997	0	0	70.353337	332	60	11626	626	ENST00000356448.4	0.077778	1
ARHGEF26	26084	__UNKNOWN__	__UNKNOWN__	3	153840347	153840347	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A	rs368674648	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:153840347C>A	ENST00000356448.4	+	2	850	c.566C>A	c.(565-567)tCg>tAg	p.S189*	ARHGEF26_ENST00000465093.1_Nonsense_Mutation_p.S189*|ARHGEF26_ENST00000465817.1_Nonsense_Mutation_p.S189*	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	189		NA			endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						GGGTCAGGTTCGCAGTCCGGC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)					NA		NA				0													21	23	22	NA		NA	NA	3		NA											NA				153840347		1867	4094	5961	SO:0001587	stop_gained			BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790	26084		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	24490	protein-coding gene	gene with protein product	Src homology 3 domain-containing guanine nucleotide exchange factor	NA			NA	15133129, 12697679	Standard	NM_015595	NM_015595	NA	Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.566C>A	chr3.hg19:g.153840347C>A	ENSP00000348828:p.Ser189*	NA	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	hg19	CCDS46938.1	0.02	16.656057	GTTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	31	5.060781	0.93846	.	.	ENSG00000114790	ENST00000356448;ENST00000465093;ENST00000465817	.	.	.	4.4	1.55	0.23275	.	0.392934	0.23074	N	0.052222	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0158	4.4381	0.11561	0.0:0.4712:0.1786:0.3503	.	.	.	.	X	189	.	ENSP00000348828:S189X	S	+	2	0	ARHGEF26	155323037	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.261000	0.18442	0.297000	0.22615	0.561000	0.74099	TCG	NOVEL	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353287.3	3	43.900705	KEEP	0	0	0	146	4822	CC	1	1	0		+	28	60	1037	0	0	74.379469	331	60	11440	623	ENST00000356448.4	0.077994	1
PLCH1	23007	__UNKNOWN__	__UNKNOWN__	3	155197912	155197912	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:155197912G>T	ENST00000340059.7	-	0	5926				PLCH1_ENST00000447496.2_3'UTR|PLCH1_ENST00000334686.6_3'UTR|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000460012.1_3'UTR|PLCH1_ENST00000414191.1_3'UTR	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	NA		NA			inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TGAAAGCTTTGGGGAAGTTTT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	23007	3.1.4.11	EF-hand domain containing	29185	protein-coding gene	gene with protein product		612835	phospholipase C-like 3	PLCL3	NA	15702972	Standard	NM_014996	NM_014996	NA	Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.*845C>A	chr3.hg19:g.155197912G>T		NA	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	hg19	CCDS46939.1	0.02	6.97454	TTTxGGG	COVERED																																																																																			NOVEL	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351125.1	2	8.124814	KEEP	0	0	0	27	924	GG	0.999988	0.999988	0		-	28	60	1016	0	0	81.101374	153	60	5793	261	ENST00000340059.7	0.154696	1
KCNAB1	7881	__UNKNOWN__	__UNKNOWN__	3	156255409	156255409	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:156255409A>G	ENST00000302490.8	+	0	2950				KCNAB1_ENST00000490337.1_3'UTR|KCNAB1_ENST00000471742.1_3'UTR	NM_172159.3	NP_751891.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	NA		NA			learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TTAGGTGTTCATTTTTTACTA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282	7881		Potassium channels, Aldo-keto reductases	6228	protein-coding gene	gene with protein product		601141			NA	8838324, 7499366	Standard	NM_003471	NM_172160	NA	Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000302490.8:c.*873A>G	chr3.hg19:g.156255409A>G		NA	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	hg19	CCDS33882.1	0.02	13.519134	TTCxTTT	COVERED																																																																																			NOVEL	KCNAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351265.1	3	23.468524	KEEP	0	0	0	78	2424	AA	1	1	0		+	22	60	757	0	0	51.420154	298	60	10998	458	ENST00000302490.8	0.06875	1
LEKR1	389170	__UNKNOWN__	__UNKNOWN__	3	156547144	156547144	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:156547144C>T	ENST00000491763.1	+	2	821	c.26C>T	c.(25-27)gCg>gTg	p.A9V	LEKR1_ENST00000489350.1_3'UTR|LEKR1_ENST00000498839.1_Missense_Mutation_p.A9V|LEKR1_ENST00000483177.1_Missense_Mutation_p.A9V|LEKR1_ENST00000477399.1_Missense_Mutation_p.A9V|LEKR1_ENST00000470811.1_5'UTR|LEKR1_ENST00000356539.4_Missense_Mutation_p.A9V	NM_001193283.1	NP_001180212.1	Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	0		NA								breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			CCCATGCATGCGTTGCCTGAA	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													122	102	108	NA		NA	NA	3		NA											NA				156547144		692	1591	2283	SO:0001583	missense			AK131473	CCDS54660.1	3q25.31	2014-02-12	2008-02-21		ENSG00000197980	ENSG00000197980	389170			33765	protein-coding gene	gene with protein product		613536			NA		Standard	NM_001004316	NM_001004316	NA	Approved	FLJ16641	uc021xgh.1	Q6ZMV7	OTTHUMG00000160130	ENST00000491763.1:c.26C>T	chr3.hg19:g.156547144C>T	ENSP00000474182:p.Ala9Val	NA		hg19	CCDS54660.1	0.02	31.422245	ATGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541555	0.65085	.	.	ENSG00000197980;ENSG00000197980;ENSG00000197980;ENSG00000178110	ENST00000498839;ENST00000483177;ENST00000477399;ENST00000356539	T	0.53423	0.62	4.86	4.86	0.63082	.	.	.	.	.	T	0.59224	0.2178	L	0.47716	1.5	0.24577	N	0.993896	D	0.89917	1.0	D	0.83275	0.996	T	0.49123	-0.8972	9	0.17369	T	0.5	1.193	13.3772	0.60745	0.0:1.0:0.0:0.0	.	9	D3DNK7	.	V	9	ENSP00000348936:A9V	ENSP00000348936:A9V	A	+	2	0	RP11-6F2.7;LEKR1	158029838	0.862000	0.29867	0.993000	0.49108	0.604000	0.37047	1.358000	0.34102	2.528000	0.85240	0.591000	0.81541	GCG	NOVEL	LEKR1-004	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351626.3	4	42.698407	KEEP	0	0	0	142	4783	CC	1	1	0		+	97	60	3569	0	0	281.850879	589	60	20541	1029	ENST00000491763.1	0.141399	1
IFT80	57560	__UNKNOWN__	__UNKNOWN__	3	160003639	160003639	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:160003639C>T	ENST00000326448.7	-	13	1765	c.1333G>A	c.(1333-1335)Gca>Aca	p.A445T	IFT80_ENST00000496589.1_Missense_Mutation_p.A308T|IFT80_ENST00000483465.1_Missense_Mutation_p.A308T|RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.A616T	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	445		NA			bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CCGGTTGATGCCTCAAAGAGG	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	43	43	NA		NA	NA	3		NA											NA				160003639		2203	4294	6497	SO:0001583	missense			AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885	57560		Intraflagellar transport homologs, WD repeat domain containing	29262	protein-coding gene	gene with protein product		611177	WD repeat domain 56, intraflagellar transport 80 homolog (Chlamydomonas)	WDR56	NA	10718198	Standard	NM_020800	NM_020800	NA	Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1333G>A	chr3.hg19:g.160003639C>T	ENSP00000312778:p.Ala445Thr	NA	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	hg19	CCDS3188.1	0.02	1.98924	ATGxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.12	1.841176	0.32513	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	T;T;T	0.70045	2.35;-0.45;-0.45	5.15	4.27	0.50696	WD40 repeat-like-containing domain (1);	0.093164	0.41001	U	0.000973	T	0.46151	0.1378	N	0.16743	0.435	0.54753	D	0.999984	B	0.22746	0.074	B	0.21917	0.037	T	0.36359	-0.9751	10	0.18276	T	0.48	.	9.606	0.39634	0.0:0.7785:0.1439:0.0776	.	445	Q9P2H3	IFT80_HUMAN	T	445;308;308	ENSP00000312778:A445T;ENSP00000418196:A308T;ENSP00000420646:A308T	ENSP00000312778:A445T	A	-	1	0	IFT80	161486333	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.573000	0.46007	2.404000	0.81709	0.467000	0.42956	GCA	NOVEL	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352651.2	0	7.524542	KEEP	0	0	0	25	887	CC	0.999931	0.999793	0		-	16	60	593	0	0	48.642744	74	60	2722	152	ENST00000326448.7	0.177778	0.999862
SI	6476	__UNKNOWN__	__UNKNOWN__	3	164766930	164766930	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:164766930G>A	ENST00000264382.3	-	15	1762	c.1700C>T	c.(1699-1701)gCt>gTt	p.A567V		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	567	Isomaltase.	NA			carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TGTGGCTATAGCCATGCTGTA	0.333	NA	NA								HNSCC(35;0.089)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													96	88	90	NA		NA	NA	3		NA											NA				164766930		2203	4300	6503	SO:0001583	missense			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	6476	3.2.1.10		10856	protein-coding gene	gene with protein product	Oligosaccharide alpha-1,6-glucosidase	609845	sucrase-isomaltase		NA	2962903, 1353958	Standard	NM_001041	NM_001041	NA	Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.1700C>T	chr3.hg19:g.164766930G>A	ENSP00000264382:p.Ala567Val	NA	A2RUC3|Q1JQ80|Q1RMC2	hg19	CCDS3196.1	0.02	8.756409	ATAxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.92	1.781642	0.31502	.	.	ENSG00000090402	ENST00000264382	D	0.92858	-3.12	5.24	5.24	0.73138	Glycoside hydrolase, superfamily (1);	0.267967	0.36066	N	0.002813	D	0.89591	0.6759	L	0.45285	1.41	0.39412	D	0.96677	B	0.23540	0.087	B	0.21708	0.036	D	0.87179	0.2226	10	0.54805	T	0.06	.	18.1694	0.89740	0.0:0.0:1.0:0.0	.	567	P14410	SUIS_HUMAN	V	567	ENSP00000264382:A567V	ENSP00000264382:A567V	A	-	2	0	SI	166249624	0.969000	0.33509	0.958000	0.39756	0.289000	0.27227	5.091000	0.64505	2.613000	0.88420	0.460000	0.39030	GCT	NOVEL	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350116.1	0	7.222022	KEEP	0	0	0	24	865	GG	0.999909	0.999909	0		-	14	60	507	0	0	34.871708	202	60	7765	298	ENST00000264382.3	0.064815	1
SLITRK3	22865	__UNKNOWN__	__UNKNOWN__	3	164907103	164907103	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:164907103A>G	ENST00000475390.1	-	2	1959	c.1516T>C	c.(1516-1518)Ttg>Ctg	p.L506L	SLITRK3_ENST00000241274.3_Silent_p.L506L			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	506		NA			axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGCAGCTTCAAGTTGGGCATG	0.507	NA	NA								HNSCC(40;0.11)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													65	69	68	NA		NA	NA	3		NA											NA				164907103		2203	4300	6503	SO:0001819	synonymous_variant			AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871	22865			23501	protein-coding gene	gene with protein product		609679			NA	10048485, 14557068	Standard	NM_014926	NM_014926	NA	Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1516T>C	chr3.hg19:g.164907103A>G		NA	Q1RMY6	hg19	CCDS3197.1	0.02	9.073546	TCAxGTT	COVERED																																																																																			NOVEL	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350126.1	2	6.920509	KEEP	0	0	0	23	724	AA	0.999892	0.999892	0		-	11	60	402	0	0	26.625052	203	60	7431	274	ENST00000475390.1	0.051402	1
BCHE	590	__UNKNOWN__	__UNKNOWN__	3	165547692	165547692	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:165547692T>G	ENST00000264381.3	-	2	1296	c.1130A>C	c.(1129-1131)gAa>gCa	p.E377A	BCHE_ENST00000540653.1_Intron	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	377		NA			cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	TTCCTGAAATTCTTTTCTAGT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													28	31	30	NA		NA	NA	3		NA											NA				165547692		2200	4290	6490	SO:0001583	missense			M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	590	3.1.1.8		983	protein-coding gene	gene with protein product		177400	cholinesterase 1, cholinesterase (serum) 2	CHE1, CHE2	NA	1769657, 2318303	Standard		NM_000055	NA	Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1130A>C	chr3.hg19:g.165547692T>G	ENSP00000264381:p.Glu377Ala	NA	A8K7P8	hg19	CCDS3198.1	0.02	14.477126	AATxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	12.27	1.887175	0.33348	.	.	ENSG00000114200	ENST00000264381	T	0.67698	-0.28	5.55	5.55	0.83447	Carboxylesterase, type B (1);	0.222920	0.45606	D	0.000343	T	0.62085	0.2399	L	0.43923	1.385	0.80722	D	1	B	0.14012	0.009	B	0.24541	0.054	T	0.60737	-0.7204	10	0.66056	D	0.02	.	14.8719	0.70465	0.0:0.0:0.0:1.0	.	377	P06276	CHLE_HUMAN	A	377	ENSP00000264381:E377A	ENSP00000264381:E377A	E	-	2	0	BCHE	167030386	0.879000	0.30193	0.935000	0.37517	0.570000	0.35934	4.678000	0.61641	2.115000	0.64714	0.533000	0.62120	GAA	NOVEL	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350254.1	6	17.44483	KEEP	0	0	0	58	1782	TT	1	1	0		-	61	60	2312	0	0	191.185022	275	60	9869	449	ENST00000264381.3	0.181548	1
ZBBX	79740	__UNKNOWN__	__UNKNOWN__	3	166958494	166958494	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:166958494A>T	ENST00000455345.2	-	0	2890				ZBBX_ENST00000392767.2_3'UTR|ZBBX_ENST00000392766.2_3'UTR|ZBBX_ENST00000392764.1_3'UTR|ZBBX_ENST00000307529.5_3'UTR			A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	NA		NA				intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AATCTCCAGCACTTGGATAGG	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064	79740			26245	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024687	NM_024687	NA	Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000455345.2:c.*87T>A	chr3.hg19:g.166958494A>T		NA	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	hg19	CCDS56296.1	0.02	19.080517	AGCxCTT	COVERED																																																																																			NOVEL	ZBBX-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257658.2	5	14.745608	KEEP	0	0	0	49	1571	AA	1	1	0		-	34	60	1280	0	0	92.820847	390	60	14320	564	ENST00000455345.2	0.080189	1
MECOM	2122	__UNKNOWN__	__UNKNOWN__	3	168810874	168810874	__UNKNOWN__	Silent	SNP	C	C	T	rs17466625	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:168810874C>T	ENST00000464456.1	-	12	3645	c.2445G>A	c.(2443-2445)tcG>tcA	p.S815S	MECOM_ENST00000472280.1_Silent_p.S825S|MECOM_ENST00000264674.3_Silent_p.S889S|MECOM_ENST00000460814.1_Silent_p.S815S|MECOM_ENST00000494292.1_Silent_p.S1003S|MECOM_ENST00000433243.2_Silent_p.S825S|MECOM_ENST00000392736.3_Silent_p.S824S|MECOM_ENST00000468789.1_Silent_p.S824S	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0		NA			regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CAGAATGAGGCGACGATGTTG	0.393	NA	NA											C|||	455	0.0908546	0.0159	0.1037	5008	,	,	NA	18533	0.0694	NA	0.2008	False	NA	,,,	NA	NA	NA	2504	0.092	NA	NA	NA						NA		NA				0								C	,,,,,,	206,4200	127.8+/-164.7	5,196,2002	111	100	104	NA	2667,2472,2448,2445,2472,3036,2472	-1.1	1	3	dbSNP_123	104	1750,6850	317.2+/-313.1	180,1390,2730	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MECOM	NM_001105077.3,NM_001105078.3,NM_001163999.1,NM_001164000.1,NM_001205194.1,NM_004991.3,NM_005241.3	,,,,,,	185,1586,4732	TT,TC,CC	NA	20.3488,4.6754,15.0392	,,,,,,	889/1117,824/1052,816/1044,815/1043,824/1052,1012/1240,824/1052	168810874	1956,11050	2203	4300	6503	SO:0001819	synonymous_variant			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276	2122		Zinc fingers, C2H2-type	3498	protein-coding gene	gene with protein product		165215	myelodysplasia syndrome 1, ecotropic viral integration site 1	MDS1, EVI1	NA	2115646, 8171026, 8643684	Standard	NM_005241, NM_004991	NM_001105077	NA	Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2445G>A	chr3.hg19:g.168810874C>T		NA	Q13466|Q6FH90	hg19	CCDS54669.1	0.02	18.560598	AGGxGAC	COVERED																																																																																			NOVEL	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351519.1	1	22.872713	KEEP	0	0	0	76	2626	CC	1	1	0		-	61	60	2189	0	0	171.299987	377	60	13294	660	ENST00000464456.1	0.139269	1
SAMD7	344658	__UNKNOWN__	__UNKNOWN__	3	169656475	169656475	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:169656475C>T	ENST00000428432.2	+	0	1911				SAMD7_ENST00000335556.3_3'UTR	NM_182610.2	NP_872416.1	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	NA		NA								NS(1)|biliary_tract(1)|breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			ATGACCCCAGCACCAAATGAC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX537903	CCDS3209.1	3q26.31	2013-01-10			ENSG00000187033	ENSG00000187033	344658		Sterile alpha motif (SAM) domain containing	25394	protein-coding gene	gene with protein product		NA			NA		Standard	NM_182610	NM_182610	NA	Approved	DKFZp686E1583	uc003fgd.3	Q7Z3H4	OTTHUMG00000158730	ENST00000428432.2:c.*181C>T	chr3.hg19:g.169656475C>T		NA		hg19	CCDS3209.1	0.02	10.993539	CAGxACC	COVERED																																																																																			NOVEL	SAMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351959.1	3	6.020041	KEEP	0	0	0	20	753	CC	0.999863	0.999863	0		+	19	60	683	0	0	48.011085	236	60	9030	344	ENST00000428432.2	0.07451	1
SEC62	7095	__UNKNOWN__	__UNKNOWN__	3	169713579	169713579	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:169713579C>T	ENST00000337002.4	+	0	3986					NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	NA		NA			cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						acattttcatcaagcagtcaa	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952	7095			11846	protein-coding gene	gene with protein product		602173	translocation protein 1	TLOC1	NA	9020021, 10799540	Standard		NM_003262	NA	Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.*2728C>T	chr3.hg19:g.169713579C>T		NA	D3DNQ0|O00682|O00729	hg19	CCDS3210.1	0.02	9.386908	CATxAAG	COVERED																																																																																			NOVEL	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352043.1	3	13.845854	KEEP	0	0	0	46	1693	CC	1	1	0		+	35	60	1285	0	0	104.840131	166	60	6434	323	ENST00000337002.4	0.174129	1
SLC2A2	6514	__UNKNOWN__	__UNKNOWN__	3	170723080	170723080	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:170723080G>A	ENST00000314251.3	-	7	1036	c.957C>T	c.(955-957)atC>atT	p.I319I	SLC2A2_ENST00000382808.4_Silent_p.I200I	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	319	Monosaccharide binding. {ECO:0000250}.	NA			carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TTACGCCATTGATTCCGGAAA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													164	154	157	NA		NA	NA	3		NA											NA				170723080		2203	4300	6503	SO:0001819	synonymous_variant			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581	6514		Solute carriers	11006	protein-coding gene	gene with protein product		138160		GLUT2	NA	1852621	Standard	NM_000340	NM_000340	NA	Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.957C>T	chr3.hg19:g.170723080G>A		NA	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	hg19	CCDS3215.1	0.02	13.05876	ATTxATT	COVERED																																																																																			NOVEL	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352834.1	2	14.744633	KEEP	0	0	0	49	1752	GG	1	1	0		-	21	60	756	0	0	51.772691	306	60	11635	447	ENST00000314251.3	0.06422	1
ZMAT3	64393	__UNKNOWN__	__UNKNOWN__	3	178785283	178785283	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs377585101		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:178785283C>A	ENST00000311417.2	-	2	999	c.258G>T	c.(256-258)caG>caT	p.Q86H	ZMAT3_ENST00000432729.1_Missense_Mutation_p.Q86H	NM_022470.3	NP_071915.1			zinc finger, matrin-type 3	NA		NA								breast(1)|endometrium(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(1)|skin(1)	14	all_cancers(143;3.31e-18)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;6.74e-27)|GBM - Glioblastoma multiforme(14;0.00448)|BRCA - Breast invasive adenocarcinoma(182;0.0527)			GATAATGAGCCTGGGCTTGCT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													154	153	153	NA		NA	NA	3		NA											NA				178785283		2203	4300	6503	SO:0001583	missense			AK122768	CCDS3224.1, CCDS46962.1	3q26.32	2012-10-05	2010-09-15		ENSG00000172667	ENSG00000172667	64393		Zinc fingers, matrin-type	29983	protein-coding gene	gene with protein product		606452			NA	9400996, 11689294	Standard	NM_152240	NM_022470	NA	Approved	WIG1, MGC10613, FLJ12296, WIG-1, PAG608	uc003fjg.3	Q9HA38	OTTHUMG00000157290	ENST00000311417.2:c.258G>T	chr3.hg19:g.178785283C>A	ENSP00000311221:p.Gln86His	NA		hg19	CCDS3224.1	0.02	11.93907	AGCxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.33	3.091576	0.55968	.	.	ENSG00000172667	ENST00000311417;ENST00000432729;ENST00000414084	T;T;T	0.24350	1.86;1.86;1.86	5.86	1.6	0.23607	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	M	0.84948	2.725	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.87578	0.997;0.998	T	0.50693	-0.8798	10	0.46703	T	0.11	-25.3107	10.5855	0.45280	0.0:0.6489:0.0:0.3511	.	86;86	Q9HA38-2;Q9HA38	.;ZMAT3_HUMAN	H	86	ENSP00000311221:Q86H;ENSP00000396506:Q86H;ENSP00000398920:Q86H	ENSP00000311221:Q86H	Q	-	3	2	ZMAT3	180267977	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.510000	0.35790	0.400000	0.25396	0.563000	0.77884	CAG	NOVEL	ZMAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348336.2	1	16.251847	KEEP	0	0	0	54	1872	CC	1	1	0		-	47	60	1726	0	0	141.499638	215	60	7901	397	ENST00000311417.2	0.179389	1
KCNMB3	27094	__UNKNOWN__	__UNKNOWN__	3	178976431	178976431	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:178976431G>T	ENST00000349697.2	-	2	323				KCNMB3_ENST00000497599.1_Intron|KCNMB3_ENST00000485523.1_Intron	NM_171828.1	NP_741979.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	NA		NA			action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	AATGCTATTTGGTCATTTCAA	0.254	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121	27094		Potassium channels	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL	NA	10585773	Standard		NM_001163677	NA	Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000349697.2:c.63-7709C>A	chr3.hg19:g.178976431G>T		NA	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	hg19	CCDS3225.1	0.02	1.804969	TTTxGTC	COVERED																																																																																			NOVEL	KCNMB3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358530.1	6	3.310571	KEEP	2	0	0	11	381	GG	0.992708	0.991708	0		-	16	60	559	0	0	46.358819	62	60	2253	95	ENST00000349697.2	0.205128	0.998993
KCNMB3	27094	__UNKNOWN__	__UNKNOWN__	3	178976432	178976432	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:178976432G>T	ENST00000349697.2	-	2	323				KCNMB3_ENST00000497599.1_Intron|KCNMB3_ENST00000485523.1_Intron	NM_171828.1	NP_741979.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	NA		NA			action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_cancers(143;5.6e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;2.41e-27)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.03)		Miconazole(DB01110)|Procaine(DB00721)	ATGCTATTTGGTCATTTCAAT	0.254	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF139471	CCDS3225.1, CCDS3226.1, CCDS43172.1, CCDS43173.1, CCDS54683.1	3q26.3-q27	2010-09-30			ENSG00000171121	ENSG00000171121	27094		Potassium channels	6287	protein-coding gene	gene with protein product		605222		KCNMB2, KCNMBL	NA	10585773	Standard		NM_001163677	NA	Approved		uc003fjm.3	Q9NPA1	OTTHUMG00000157337	ENST00000349697.2:c.63-7710C>A	chr3.hg19:g.178976432G>T		NA	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	hg19	CCDS3225.1	0.02	1.822977	TTGxTCA	COVERED																																																																																			NOVEL	KCNMB3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358530.1	6	3.300898	KEEP	2	0	0	11	350	GG	0.992708	0.991413	0		-	15	60	534	0	0	44.180424	61	60	2200	93	ENST00000349697.2	0.197368	0.998696
USP13	8975	__UNKNOWN__	__UNKNOWN__	3	179501792	179501792	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:179501792T>C	ENST00000263966.3	+	21	2969				USP13_ENST00000496897.1_Intron	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	NA		NA			autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TAAAGTTTCCTGGAACTGACT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													78	84	82	NA		NA	NA	3		NA											NA				179501792		2203	4300	6503	SO:0001627	intron_variant			U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056	8975		Ubiquitin-specific peptidases	12611	protein-coding gene	gene with protein product		603591	ubiquitin specific protease 13 (isopeptidase T-3)		NA	12838346	Standard		NM_003940	NA	Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.2499-44T>C	chr3.hg19:g.179501792T>C		NA	A8K2S3|B4DYF3|D3DNS2|Q96B25	hg19	CCDS3235.1	0.02	6.739706	TCCxGGA	COVERED																																																																																			NOVEL	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349617.1	0	9.026436	KEEP	0	0	0	30	923	TT	0.999997	0.999997	0		+	16	60	577	0	0	41.692482	169	60	6405	254	ENST00000263966.3	0.086486	1
CCDC39	339829	__UNKNOWN__	__UNKNOWN__	3	180370038	180370038	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:180370038G>A	ENST00000442201.2	-	8	1066	c.947C>T	c.(946-948)gCc>gTc	p.A316V	CCDC39_ENST00000273654.4_Missense_Mutation_p.A400V	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	316		NA			axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			ATTCACAGTGGCTTTTAAAGA	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													31	27	28	NA		NA	NA	3		NA											NA				180370038		1727	3875	5602	SO:0001583	missense			BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075	339829			25244	protein-coding gene	gene with protein product		613798			NA	21131972	Standard	XM_291028	NM_181426	NA	Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.947C>T	chr3.hg19:g.180370038G>A	ENSP00000405708:p.Ala316Val	NA	B4E2H1	hg19	CCDS46964.1	0.02	-0.429884	GTGxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.32	2.202937	0.38905	.	.	ENSG00000145075	ENST00000273654;ENST00000442201	T;T	0.78595	-1.19;-1.19	4.66	2.75	0.32379	.	0.547563	0.18910	N	0.127782	T	0.68787	0.3039	L	0.53249	1.67	0.20975	N	0.999811	P	0.43826	0.818	B	0.39840	0.311	T	0.56396	-0.7986	10	0.25751	T	0.34	4.0E-4	8.1548	0.31162	0.0:0.3287:0.5022:0.1691	.	316	Q9UFE4	CCD39_HUMAN	V	400;316	ENSP00000273654:A400V;ENSP00000405708:A316V	ENSP00000273654:A400V	A	-	2	0	CCDC39	181852732	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.380000	0.34351	0.422000	0.26005	0.655000	0.94253	GCC	NOVEL	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349783.3	2	5.11687	KEEP	0	0	0	17	621	GG	0.999366	0.953887	0		-	4	60	150	0	0	10.892713	45	60	1671	90	ENST00000442201.2	0.081633	0.954491
FXR1	8087	__UNKNOWN__	__UNKNOWN__	3	180633441	180633441	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:180633441T>C	ENST00000357559.4	+	1	435				FXR1_ENST00000491674.1_Intron|FXR1_ENST00000468861.1_Intron|FXR1_ENST00000491062.1_Intron|FXR1_ENST00000445140.2_Intron|FXR1_ENST00000480918.1_Intron|FXR1_ENST00000305586.7_Intron	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	NA		NA			apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			TTCCCTTTTTTCCCCTCCTCT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416	8087			4023	protein-coding gene	gene with protein product		600819			NA	7781595, 9642279	Standard		NM_005087	NA	Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.51+2917T>C	chr3.hg19:g.180633441T>C		NA	A8K9B8|Q7Z450|Q8N6R8	hg19	CCDS3238.1	0.02	27.250548	TTTxCCC	COVERED																																																																																			NOVEL	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350265.5	11	43.939573	KEEP	0	1	5	148	4579	TT	1	1	0		+	89	60	3262	1	0	262.348267	469	60	16620	871	ENST00000357559.4	0.159498	1
YEATS2	55689	__UNKNOWN__	__UNKNOWN__	3	183476738	183476738	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:183476738A>G	ENST00000305135.5	+	13	1836	c.1641A>G	c.(1639-1641)gtA>gtG	p.V547V		NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	547		NA			chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			GTAGTTTTGTAACATCTACTG	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													109	97	101	NA		NA	NA	3		NA											NA				183476738		1826	4089	5915	SO:0001819	synonymous_variant			AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872	55689			25489	protein-coding gene	gene with protein product		613373			NA	10574462	Standard	NM_018023	NM_018023	NA	Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.1641A>G	chr3.hg19:g.183476738A>G		NA	A7E2B9|D3DNS9|Q641P6|Q9NW96	hg19	CCDS43175.1	0.02	15.037933	TGTxACA	COVERED																																																																																			NOVEL	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346507.2	3	14.741286	KEEP	0	0	0	49	1484	AA	1	1	0		+	55	60	2079	0	0	169.667906	274	60	9873	465	ENST00000305135.5	0.167173	1
AP2M1	1173	__UNKNOWN__	__UNKNOWN__	3	183901109	183901109	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:183901109T>C	ENST00000382456.3	+	11	1481				EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000292807.5_Intron|AP2M1_ENST00000411763.2_Intron|AP2M1_ENST00000439647.1_Intron|AP2M1_ENST00000461733.1_Intron	NM_001025205.1	NP_001020376.1	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTTTCTTCTTTAGTCACCTCT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203	1173			564	protein-coding gene	gene with protein product	clathrin-associated/assembly/adaptor protein, medium 1, plasma membrane adaptor AP-2 50kDA protein, clathrin coat adaptor protein AP50, clathrin adaptor complex AP2, mu subunit, HA2 50 kDA subunit, clathrin assembly protein complex 2 medium chain, AP-2 mu 2 chain	601024		CLAPM1	NA	8595912	Standard	NM_004068	NM_004068	NA	Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000382456.3:c.1168-161T>C	chr3.hg19:g.183901109T>C		NA	A6NE12|D3DNT1|P20172|P53679	hg19	CCDS43178.1	0.02	7.488454	CTTxAGT	COVERED																																																																																			NOVEL	AP2M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346011.1	0	10.53136	KEEP	0	0	0	35	1081	TT	0.999999	0.999999	0		+	40	60	1522	0	0	131.244637	128	60	4422	247	ENST00000382456.3	0.238095	1
TMEM41A	90407	__UNKNOWN__	__UNKNOWN__	3	185209168	185209168	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:185209168G>C	ENST00000296254.3	-	0	676				TMEM41A_ENST00000421852.1_3'UTR|TMEM41A_ENST00000475480.1_Intron			Q96HV5	TM41A_HUMAN	transmembrane protein 41A	NA		NA				integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|skin(1)	4	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			ACACCTTCAAGAGCAGAGTGT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC019884	CCDS3271.1	3q27.2	2006-04-12			ENSG00000163900	ENSG00000163900	90407			30544	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_080652	NM_080652	NA	Approved	MGC15397	uc003fpj.2	Q96HV5	OTTHUMG00000156660	ENST00000296254.3:c.*372C>G	chr3.hg19:g.185209168G>C		NA	A8K4B3|D3DNU2|Q6ZMJ0	hg19		0.02	2.154885	CAAxAGC	COVERED																																																																																			NOVEL	TMEM41A-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345178.1	2	2.407826	KEEP	0	0	0	8	285	GG	0.99257	0.99249	0		-	9	60	290	0	0	20.558741	86	60	3304	135	ENST00000296254.3	0.094737	0.999919
IGF2BP2	10644	__UNKNOWN__	__UNKNOWN__	3	185362689	185362689	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:185362689G>C	ENST00000382199.2	-	0	2525				IGF2BP2_ENST00000457616.2_3'UTR|IGF2BP2_ENST00000346192.3_3'UTR|IGF2BP2_ENST00000421047.2_3'UTR	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	NA		NA			anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GGTGAATTTTGTGCGGGTGGC	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792	10644		RNA binding motif (RRM) containing	28867	protein-coding gene	gene with protein product	IGF II mRNA binding protein 2	608289			NA	10190901, 9891060	Standard	NM_006548	NM_001007225	NA	Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.*630C>G	chr3.hg19:g.185362689G>C		NA	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	hg19	CCDS3273.2	0.02	9.887681	TTTxTGC	COVERED																																																																																			NOVEL	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157087.2	4	14.146356	KEEP	0	0	0	47	1697	GG	1	1	0		-	42	60	1648	0	0	136.930297	193	60	7418	372	ENST00000382199.2	0.178723	1
IGF2BP2	10644	__UNKNOWN__	__UNKNOWN__	3	185485596	185485596	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:185485596C>T	ENST00000382199.2	-	2	335				IGF2BP2_ENST00000457616.2_Intron|IGF2BP2_ENST00000346192.3_Intron|IGF2BP2_ENST00000421047.2_Intron	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	NA		NA			anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			ttagtgcagccattttggaaa	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792	10644		RNA binding motif (RRM) containing	28867	protein-coding gene	gene with protein product	IGF II mRNA binding protein 2	608289			NA	10190901, 9891060	Standard	NM_006548	NM_001007225	NA	Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.239+55344G>A	chr3.hg19:g.185485596C>T		NA	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	hg19	CCDS3273.2	0.02	7.42671	AGCxATT	COVERED																																																																																			NOVEL	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157087.2	0	11.73771	KEEP	0	0	0	39	1376	CC	1	1	0		-	26	60	981	0	0	78.570497	149	60	5688	272	ENST00000382199.2	0.148571	1
MASP1	5648	__UNKNOWN__	__UNKNOWN__	3	186964664	186964664	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:186964664G>C	ENST00000392472.2	-	8	1203				MASP1_ENST00000337774.5_Intron|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000169293.6_3'UTR|MASP1_ENST00000296280.6_Intron			P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	NA		NA			complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		TGGTGGTTAAGAAAGCAGCAA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241	5648		Serine peptidases / Serine peptidases	6901	protein-coding gene	gene with protein product		600521	mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)	CRARF, PRSS5	NA	8018603, 8240317	Standard	NM_001879	NR_033519	NA	Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000392472.2:c.752-3255C>G	chr3.hg19:g.186964664G>C		NA	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	hg19		0.02	12.638221	TAAxAAA	COVERED																																																																																			NOVEL	MASP1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344266.2	1	10.23329	KEEP	0	0	0	34	1210	GG	0.999998	0.999998	0		-	85	60	3258	0	0	294.654872	177	60	6776	351	ENST00000392472.2	0.324427	1
TPRG1	285386	__UNKNOWN__	__UNKNOWN__	3	189039515	189039515	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:189039515T>A	ENST00000345063.3	+	0	1901					NM_198485.3	NP_940887.1	Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	NA		NA				cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|skin(2)|urinary_tract(1)	16	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		AAATATATAttttttaataac	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK125682	CCDS3292.1	3q28	2008-02-04	2008-01-16	2008-01-16	ENSG00000188001	ENSG00000188001	285386			24759	protein-coding gene	gene with protein product		NA	family with sequence similarity 79, member B	FAM79B	NA		Standard	NM_198485	NM_198485	NA	Approved	FLJ41238, FLJ43694	uc003frw.2	Q6ZUI0	OTTHUMG00000156321	ENST00000345063.3:c.*906T>A	chr3.hg19:g.189039515T>A		NA		hg19	CCDS3292.1	0.02	1.937034	TATxTTT	COVERED																																																																																			NOVEL	TPRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343931.1	4	2.707168	KEEP	0	0	0	9	271	TT	0.99254	0.99248	0		+	22	60	742	0	0	62.151435	75	60	2648	117	ENST00000345063.3	0.226804	0.99994
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195395399	195395399	__UNKNOWN__	lincRNA	SNP	G	G	A	rs62287990	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:195395399G>A	ENST00000445430.1	+	0	806									long intergenic non-protein coding RNA 969	NA		NA									NA						GGCTACGGGCGCACCTACTTG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195395399G>A		NA		hg19		0.02	21.797987	GGCxCAC	COVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	4	10.236864	KEEP	21	9	261	126	4222	GG	1	1	0		+	47	40	1650	0	0	121.305628	419	60	13986	842	ENST00000445430.1	0.100858	1
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195395402	195395402	__UNKNOWN__	lincRNA	SNP	C	C	A	rs199554501	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:195395402C>A	ENST00000445430.1	+	0	809									long intergenic non-protein coding RNA 969	NA		NA									NA						TACGGGCGCACCTACTTGAGC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195395402C>A		NA		hg19		0.02	21.800196	GCAxCTA	COVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	4	4.162208	KEEP	22	10	335	131	4465	CC	1	1	0		+	57	40	1994	0	0	151.050701	416	60	15209	852	ENST00000445430.1	0.120507	1
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195400728	195400728	__UNKNOWN__	lincRNA	SNP	A	A	G	rs12107841	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:195400728A>G	ENST00000445430.1	+	0	1324									long intergenic non-protein coding RNA 969	NA		NA									NA						GATTGTGCCCAGCCTGTACGC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195400728A>G		NA		hg19		0.02	3.860377	CCCxGCC	COVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	0	7.522865	KEEP	0	0	0	25	793	AA	0.999931	0.999931	0		+	6	40	184	1	0	10.367279	143	60	5274	197	ENST00000445430.1	0.040268	1
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195480028	195480028	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:195480028G>T	ENST00000346145.4	-	19	2733	c.2694C>A	c.(2692-2694)taC>taA	p.Y898*	MUC4_ENST00000463781.3_Nonsense_Mutation_p.Y5134*|MUC4_ENST00000475231.1_Nonsense_Mutation_p.Y5082*|MUC4_ENST00000349607.4_Nonsense_Mutation_p.Y847*	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1891	Ser-rich.	NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCTGGGAGATGTAGCAGTGGC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													152	144	146	NA		NA	NA	3		NA											NA				195480028		2203	4300	6503	SO:0001587	stop_gained			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.2694C>A	chr3.hg19:g.195480028G>T	ENSP00000304207:p.Tyr898*	NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	6.455405	GATxTAG	COVERED	.	.	.	.	.	.	.	.	.	.	.	57	27.649886	0.99972	.	.	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	.	.	.	5.58	3.47	0.39725	.	0.876484	0.09579	N	0.783110	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.5052	10.6088	0.45410	0.1812:0.0:0.8188:0.0	.	.	.	.	X	847;898;5134;5082;1634	.	ENSP00000304207:Y898X	Y	-	3	2	MUC4	196965699	0.029000	0.19370	0.831000	0.32960	0.163000	0.22366	1.197000	0.32211	1.365000	0.46057	-0.272000	0.10252	TAC	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	1	8.728328	KEEP	0	0	0	29	1030	GG	0.999997	0.999997	0		-	23	60	782	0	0	59.90913	148	60	5391	251	ENST00000346145.4	0.134503	1
SDHAP1	255812	__UNKNOWN__	__UNKNOWN__	3	195690286	195690286	__UNKNOWN__	RNA	SNP	C	C	G	rs200290177	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:195690286C>G	ENST00000427841.1	-	0	2209					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1	NA		NA									NA						CTATATTCCACAGTGACCTTG	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(67;1158 1227 12109 20189 43170)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485	255812			32455	pseudogene	pseudogene		NA	succinate dehydrogenase complex, subunit A, flavoprotein-like 1	SDHAL1, SDHALP1	NA		Standard		NR_003264	NA	Approved		uc003fvy.3		OTTHUMG00000155716	ENST00000427841.1:	chr3.hg19:g.195690286C>G		NA		hg19		0.02	33.001914	CCAxAGT	COVERED																																																																																			NOVEL	SDHAP1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000341367.1	20	8.389527	KEEP	172	13	480	195	7044	CC	1	1	0		-	22	42	842	0	0	53.928685	567	60	21641	1255	ENST00000427841.1	0.037351	1
ZDHHC19	131540	__UNKNOWN__	__UNKNOWN__	3	195936167	195936167	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:195936167C>A	ENST00000296326.3	-	3	488				ZDHHC19_ENST00000488508.1_Intron	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		CACACCCAGCCCTGGCCCCTG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958	131540		Zinc fingers, DHHC-type	20713	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144637	XR_246038	NA	Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.408+79G>T	chr3.hg19:g.195936167C>A		NA	A8MSY6|B3KVI1	hg19	CCDS43190.1	0.02	4.355916	AGCxCTG	COVERED																																																																																			NOVEL	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341533.1	0	6.018748	KEEP	0	0	0	20	668	CC	0.999863	0.999862	0		-	17	60	580	0	0	44.378438	111	60	3917	158	ENST00000296326.3	0.132812	1
PAK2	5062	__UNKNOWN__	__UNKNOWN__	3	196558240	196558240	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:196558240C>T	ENST00000327134.3	+	0	4861					NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	NA		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CTTTTTTCTTCTGCTGCTTTT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	5062	2.7.11.1		8591	protein-coding gene	gene with protein product	S6/H4 kinase	605022	p21 (CDKN1A)-activated kinase 2		NA	7744004, 7618083	Standard	NM_002577	NM_002577	NA	Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.*2964C>T	chr3.hg19:g.196558240C>T		NA	Q13154|Q6ISC3	hg19	CCDS3321.1	0.02	1.962912	CTTxTGC	COVERED																																																																																			NOVEL	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340548.1	2	6.018944	KEEP	0	0	0	20	695	CC	0.999863	0.99977	0		+	14	60	493	0	0	38.801006	80	60	2980	128	ENST00000327134.3	0.148936	0.999907
DLG1	1739	__UNKNOWN__	__UNKNOWN__	3	196771233	196771233	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:196771233G>A	ENST00000346964.2	-	0	3231				DLG1_ENST00000422288.1_3'UTR|DLG1_ENST00000419354.1_3'UTR|DLG1_ENST00000452595.1_3'UTR|DLG1_ENST00000357674.4_3'UTR|DLG1_ENST00000314062.3_3'UTR	NM_004087.2	NP_004078.2	Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	NA		NA			actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CACAATTTCTGCGTCTCCCCA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711	1739			2900	protein-coding gene	gene with protein product	discs large homolog 1, presynaptic protein SAP97, synapse-associated protein 97	601014	discs, large (Drosophila) homolog 1		NA	7937897, 8825652	Standard	NM_004087	NM_004087	NA	Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000346964.2:c.*261C>T	chr3.hg19:g.196771233G>A		NA	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	hg19	CCDS3327.1	0.02	4.091539	TCTxCGT	COVERED																																																																																			NOVEL	DLG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000242864.1	3	5.116273	KEEP	0	0	0	17	605	GG	0.999366	0.999366	0		-	20	60	666	0	0	51.62908	114	60	4275	176	ENST00000346964.2	0.149254	1
LMLN	89782	__UNKNOWN__	__UNKNOWN__	3	197770468	197770468	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr3:197770468G>T	ENST00000330198.4	+	0	6920					NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	NA		NA			cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		GGATGGAGTGGTTGTTTTATG	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	89782	3.4.24.36		15991	protein-coding gene	gene with protein product		609380			NA		Standard	NM_033029	NM_033029	NA	Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.*4930G>T	chr3.hg19:g.197770468G>T		NA	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	hg19	CCDS3332.1	0.02	2.059519	GTGxTTG	COVERED																																																																																			NOVEL	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339701.1	8	3.009932	KEEP	0	0	0	10	361	GG	0.992708	0.992199	0		+	11	60	402	0	0	31.350733	72	60	2613	109	ENST00000330198.4	0.13253	0.999487
ZNF595	152687	__UNKNOWN__	__UNKNOWN__	4	59475	59475	__UNKNOWN__	Intron	SNP	C	C	T	rs6856700	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:59475C>T	ENST00000509152.2	+	2	315				ZNF595_ENST00000339368.6_Intron|ZNF595_ENST00000526473.2_Intron			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		ATACATAATTCCTAATACTTC	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C		274,4132	108.2+/-146.6	0,274,1929	263	290	281	NA		0.3	0	4	dbSNP_116	281	0,8600		0,0,4300	no	intron	ZNF595	NM_182524.2		0,274,6229	TT,TC,CC	NA	0.0,6.2188,2.1067			59475	274,12732	2203	4300	6503	SO:0001627	intron_variant			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602	152687		Zinc fingers, C2H2-type, -	27196	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182524	NM_182524	NA	Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.130+26C>T	chr4.hg19:g.59475C>T		NA		hg19		0.02	36.430736	ATTxCTA	COVERED																																																																																			NOVEL	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357817.2	6	15.587991	KEEP	1	11	366	180	6201	CC	1	1	0		+	42	60	1536	0	0	100.530182	831	60	30186	1285	ENST00000509152.2	0.04811	1
ZNF595	152687	__UNKNOWN__	__UNKNOWN__	4	60367	60367	__UNKNOWN__	Intron	SNP	C	C	T	rs79951480		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:60367C>T	ENST00000509152.2	+	3	411				ZNF595_ENST00000339368.6_Intron			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TTGAGGACCTCTATGTTAAAG	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602	152687		Zinc fingers, C2H2-type, -	27196	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182524	NM_182524	NA	Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.226+321C>T	chr4.hg19:g.60367C>T		NA		hg19		0.02	13.698169	CCTxTAT	COVERED																																																																																			NOVEL	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357817.2	4	14.141118	KEEP	0	0	0	47	1650	CC	1	1	0		+	10	60	372	0	0	22.962951	289	60	10973	435	ENST00000509152.2	0.033445	1
FGFRL1	53834	__UNKNOWN__	__UNKNOWN__	4	1018967	1018967	__UNKNOWN__	Silent	SNP	G	G	A	rs200350207	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:1018967G>A	ENST00000398484.2	+	8	1927	c.1347G>A	c.(1345-1347)gaG>gaA	p.E449E	FGFRL1_ENST00000504138.1_Silent_p.E449E|FGFRL1_ENST00000510644.1_Silent_p.E449E|FGFRL1_ENST00000264748.6_Silent_p.E449E			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	449		NA			diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TGTGTGAGGAGCATGGGTCTC	0.677	NA	NA											G|||	6	0.00119808	0.0045	0	5008	,	,	NA	15735	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	,,	6,4376		0,6,2185	14	15	14	NA	1347,1347,1347	-2.9	0	4		14	0,8586		0,0,4293	yes	coding-synonymous,coding-synonymous,coding-synonymous	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	,,	0,6,6478	AA,AG,GG	NA	0.0,0.1369,0.0463	,,	449/505,449/505,449/505	1018967	6,12962	2191	4293	6484	SO:0001819	synonymous_variant				CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418	53834		Immunoglobulin superfamily / I-set domain containing	3693	protein-coding gene	gene with protein product		605830			NA		Standard	NM_021923	NM_021923	NA	Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.1347G>A	chr4.hg19:g.1018967G>A		NA	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	hg19	CCDS3344.1	0.02	6.690318	GGAxCAT	COVERED																																																																																			NOVEL	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239195.2	8	19.863561	KEEP	0	0	0	66	2319	GG	1	1	0		+	34	60	1208	0	0	100.289196	134	60	4954	289	ENST00000398484.2	0.202381	1
TACC3	10460	__UNKNOWN__	__UNKNOWN__	4	1730252	1730252	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:1730252C>G	ENST00000313288.4	+	4	1229	c.1123C>G	c.(1123-1125)Caa>Gaa	p.Q375E		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	375		NA			astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			AGTGAGGCAGCAAAAGGCCCC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(120;482 2294 11894 35824)					NA		NA				0													57	69	65	NA		NA	NA	4		NA											NA				1730252		2203	4300	6503	SO:0001583	missense			AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810	10460			11524	protein-coding gene	gene with protein product		605303			NA	17675670	Standard		NM_006342	NA	Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.1123C>G	chr4.hg19:g.1730252C>G	ENSP00000326550:p.Gln375Glu	NA	Q2NKK4|Q3KQS5|Q9UMQ1	hg19	CCDS3352.1	0.02	10.016545	CAGxAAA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.025|0.025	-1.377669|-1.377669	0.01204|0.01204	.|.	.|.	ENSG00000013810|ENSG00000013810	ENST00000470136|ENST00000313288	.|T	.|0.08193	.|3.12	4.84|4.84	1.96|1.96	0.26148|0.26148	.|.	.|1.216240	.|0.06238	.|N	.|0.689800	T|T	0.04679|0.04679	0.0127|0.0127	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	N|N	1|1	.|B;B	.|0.11235	.|0.004;0.001	.|B;B	.|0.08055	.|0.003;0.0	T|T	0.38178|0.38178	-0.9673|-0.9673	5|10	.|0.02654	.|T	.|1	0.0148|0.0148	8.9502|8.9502	0.35785|0.35785	0.0886:0.4498:0.4616:0.0|0.0886:0.4498:0.4616:0.0	.|.	.|375;375	.|B4DYJ1;Q9Y6A5	.|.;TACC3_HUMAN	G|E	41|375	.|ENSP00000326550:Q375E	.|ENSP00000326550:Q375E	A|Q	+|+	2|1	0|0	TACC3|TACC3	1700050|1700050	0.087000|0.087000	0.21565|0.21565	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	1.220000|1.220000	0.32491|0.32491	0.068000|0.068000	0.16574|0.16574	-0.340000|-0.340000	0.08031|0.08031	GCA|CAA	NOVEL	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000203730.2	2	22.548464	KEEP	0	0	0	75	2607	CC	1	1	0		+	54	60	1962	0	0	170.117307	155	60	5723	345	ENST00000313288.4	0.258373	1
SH3BP2	6452	__UNKNOWN__	__UNKNOWN__	4	2822433	2822433	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:2822433C>G	ENST00000356331.5	+	2	350	c.89C>G	c.(88-90)gCt>gGt	p.A30G	SH3BP2_ENST00000503393.2_Missense_Mutation_p.A87G|SH3BP2_ENST00000442312.2_Missense_Mutation_p.A58G|SH3BP2_ENST00000435136.2_Missense_Mutation_p.A30G|SH3BP2_ENST00000511747.1_Missense_Mutation_p.A30G|SH3BP2_ENST00000389838.2_Missense_Mutation_p.A30G|SH3BP2_ENST00000452765.2_Missense_Mutation_p.A30G	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	30	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.	NA			positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GTGGCCAAGGCTGGCTACCTG	0.602	NA	NA							Cherubism					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	62	63	NA		NA	NA	4		NA											NA				2822433		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266	6452		Pleckstrin homology (PH) domain containing, SH2 domain containing	10825	protein-coding gene	gene with protein product		602104	Cherubism		NA	9299232, 11381256	Standard	NM_003023	NM_003023	NA	Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.89C>G	chr4.hg19:g.2822433C>G	ENSP00000348685:p.Ala30Gly	NA	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	hg19	CCDS33944.1	0.02	17.490145	AGGxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	25.7	4.662375	0.88251	.	.	ENSG00000087266	ENST00000452765;ENST00000389838;ENST00000503219;ENST00000504294;ENST00000508385;ENST00000512014;ENST00000513095;ENST00000442312;ENST00000502260;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	T;T;T;T;T;T;T;T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63;2.63	4.97	4.97	0.65823	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.186379	0.47455	D	0.000223	T	0.27454	0.0674	L	0.61036	1.89	0.28974	N	0.889049	P;P;P;P	0.52692	0.584;0.955;0.698;0.565	B;P;B;B	0.52424	0.338;0.698;0.253;0.253	T	0.03910	-1.0993	10	0.38643	T	0.18	-10.1919	17.8167	0.88637	0.0:1.0:0.0:0.0	.	58;58;87;30	B4DT04;B7Z9B6;D6R919;P78314	.;.;.;3BP2_HUMAN	G	30;30;30;30;30;30;30;58;30;30;30;87;30	ENSP00000409746:A30G;ENSP00000374488:A30G;ENSP00000422796:A30G;ENSP00000423275:A30G;ENSP00000424917:A30G;ENSP00000424105:A30G;ENSP00000423823:A30G;ENSP00000388152:A58G;ENSP00000425537:A30G;ENSP00000403231:A30G;ENSP00000424846:A30G;ENSP00000422168:A87G;ENSP00000348685:A30G	ENSP00000348685:A30G	A	+	2	0	SH3BP2	2792231	1.000000	0.71417	0.990000	0.47175	0.987000	0.75469	5.244000	0.65400	2.322000	0.78497	0.313000	0.20887	GCT	NOVEL	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362406.2	3	24.369849	KEEP	0	0	0	81	2825	CC	1	1	0		+	88	60	3201	0	0	275.777417	267	60	9737	532	ENST00000356331.5	0.247887	1
SH3BP2	6452	__UNKNOWN__	__UNKNOWN__	4	2828620	2828620	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:2828620C>A	ENST00000356331.5	+	6	689				SH3BP2_ENST00000503393.2_Intron|SH3BP2_ENST00000442312.2_Intron|SH3BP2_ENST00000435136.2_Intron|SH3BP2_ENST00000511747.1_Intron|SH3BP2_ENST00000515183.1_Intron|SH3BP2_ENST00000452765.2_Intron	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	NA		NA			positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GCGCGTGTCCCTGTGTCTTTG	0.463	NA	NA							Cherubism					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266	6452		Pleckstrin homology (PH) domain containing, SH2 domain containing	10825	protein-coding gene	gene with protein product		602104	Cherubism		NA	9299232, 11381256	Standard	NM_003023	NM_003023	NA	Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.429-337C>A	chr4.hg19:g.2828620C>A		NA	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	hg19	CCDS33944.1	0.02	4.168164	TCCxTGT	COVERED																																																																																			NOVEL	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362406.2	10	20.465967	KEEP	0	0	0	68	2424	CC	1	1	0		+	19	60	689	0	0	53.333023	129	60	4835	292	ENST00000356331.5	0.128378	1
LRPAP1	4043	__UNKNOWN__	__UNKNOWN__	4	3514551	3514551	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:3514551G>A	ENST00000500728.2	-	0	1370					NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	NA		NA			extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		GACGGCAGCGGCTGCAGTCAC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956	4043			6701	protein-coding gene	gene with protein product		104225	low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)	A2MRAP	NA	1712782	Standard		NM_002337	NA	Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.*150C>T	chr4.hg19:g.3514551G>A		NA	D3DVR9|Q2M310|Q53HQ3|Q53HS6	hg19	CCDS3371.1	0.02	8.804478	GCGxCTG	COVERED																																																																																			NOVEL	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206659.4	4	25.866214	KEEP	0	0	0	86	2917	GG	1	1	0		-	65	60	2231	0	0	196.118648	155	60	5508	416	ENST00000500728.2	0.295455	1
STK32B	55351	__UNKNOWN__	__UNKNOWN__	4	5448308	5448308	__UNKNOWN__	Intron	SNP	C	C	A	rs76186248		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:5448308C>A	ENST00000282908.5	+	7	984				STK32B_ENST00000512636.1_Intron|STK32B_ENST00000508728.1_Intron|STK32B_ENST00000510398.1_Intron	NM_018401.1	NP_060871.1			serine/threonine kinase 32B	NA		NA								breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						aaaaaaaaaacaaGCTCAATT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953	55351			14217	protein-coding gene	gene with protein product		NA			NA	10700184	Standard	NM_018401	XM_005247982	NA	Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.563-92C>A	chr4.hg19:g.5448308C>A		NA		hg19	CCDS3380.1	0.02	2.388659	AAAxAAG	COVERED																																																																																			NOVEL	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206854.4	7	3.252441	KEEP	0	4	53	31	950	CC	0.999999	0.999999	0		+	12	60	218	2	0	10.009375	138	70	3820	248	ENST00000282908.5	0.08	1
HS3ST1	9957	__UNKNOWN__	__UNKNOWN__	4	11400200	11400200	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:11400200A>T	ENST00000002596.5	-	0	2604					NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|sulfotransferase activity (GO:0008146)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|skin(3)	15						GAGGAGATAAATCTTACAATC	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF019386	CCDS3408.1	4p16	2008-02-05			ENSG00000002587	ENSG00000002587	9957	2.8.2.23	Sulfotransferases, membrane-bound	5194	protein-coding gene	gene with protein product		603244			NA	9988767	Standard	NM_005114	NM_005114	NA	Approved	3OST1	uc003gmq.3	O14792	OTTHUMG00000090547	ENST00000002596.5:c.*506T>A	chr4.hg19:g.11400200A>T		NA	B3KUA6|Q6PEY8	hg19	CCDS3408.1	0.02	2.033683	TAAxTCT	COVERED																																																																																			NOVEL	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207073.3	1	6.618856	KEEP	0	0	0	22	691	AA	0.999879	0.999556	0		-	11	60	402	1	0	31.173077	75	60	2649	132	ENST00000002596.5	0.127907	0.999678
LDB2	9079	__UNKNOWN__	__UNKNOWN__	4	16900203	16900203	__UNKNOWN__	De_novo_Start_OutOfFrame	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:16900203C>T	ENST00000304523.5	-	0	229				LDB2_ENST00000441778.2_De_novo_Start_OutOfFrame|LDB2_ENST00000502640.1_De_novo_Start_OutOfFrame	NM_001290.3	NP_001281.1	O43679	LDB2_HUMAN	LIM domain binding 2	NA		NA			epithelial structure maintenance (GO:0010669)|hair follicle development (GO:0001942)|positive regulation of cellular component biogenesis (GO:0044089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell maintenance (GO:0035019)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	LIM domain binding (GO:0030274)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(23)|urinary_tract(1)	33						AGTAGACGCACGCACACACGC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF068651	CCDS3420.1, CCDS47031.1	4p16	2008-08-01			ENSG00000169744	ENSG00000169744	9079			6533	protein-coding gene	gene with protein product		603450			NA	9853615, 9880598, 10861853	Standard		NM_001290	NA	Approved	CLIM1, LDB1	uc003goz.3	O43679	OTTHUMG00000048212	ENST00000304523.5:c.-95G>A	chr4.hg19:g.16900203C>T		NA	O60619|O75480	hg19	CCDS3420.1	0.02	12.620061	GCAxGCA	COVERED																																																																																			NOVEL	LDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250321.2	13	55.059547	KEEP	0	0	0	183	6144	CC	1	1	0		-	10	60	372	0	0	22.811748	299	60	10007	627	ENST00000304523.5	0.032362	1
MED28	80306	__UNKNOWN__	__UNKNOWN__	4	17634010	17634010	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:17634010G>A	ENST00000237380.7	+	0	9150				MED28_ENST00000499786.4_3'UTR|FAM184B_ENST00000265018.3_3'UTR	NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	NA		NA			negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						ACAGTATGAAGTGTTAACGCC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579	80306			24628	protein-coding gene	gene with protein product		610311	mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)		NA	11779215, 15467741	Standard	NM_025205	NM_025205	NA	Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.*8589G>A	chr4.hg19:g.17634010G>A		NA	Q9BZJ5	hg19	CCDS33963.1	0.02	9.264218	GAAxTGT	COVERED																																																																																			NOVEL	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360055.3	4	23.777375	KEEP	0	0	0	79	2825	GG	1	1	0		+	137	60	5039	0	0	508.086371	78	60	2980	369	ENST00000237380.7	0.637209	1
LCORL	254251	__UNKNOWN__	__UNKNOWN__	4	18023409	18023409	__UNKNOWN__	5'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:18023409G>C	ENST00000326877.4	-	0	90				LCORL_ENST00000382226.5_5'UTR	NM_153686.7	NP_710153.2	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	NA		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						ATTTACATACGAGCAGCGCAG	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	4	4	NA		NA	NA	4		NA											NA				18023409		1780	3856	5636	SO:0001623	5_prime_UTR_variant				CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177	254251			30776	protein-coding gene	gene with protein product		611799			NA	12560079	Standard	NM_153686	NM_153686	NA	Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000326877.4:c.-35C>G	chr4.hg19:g.18023409G>C		NA	Q96NK1	hg19	CCDS3425.1	0.02	6.927683	TACxAGC	COVERED																																																																																			NOVEL	LCORL-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250373.2	3	62.598014	KEEP	0	1	5	210	6871	GG	1	1	0		-	43	60	1547	0	0	133.09181	130	60	4475	526	ENST00000326877.4	0.248555	1
ARAP2	116984	__UNKNOWN__	__UNKNOWN__	4	36231150	36231150	__UNKNOWN__	De_novo_Start_InFrame	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:36231150C>T	ENST00000303965.4	-	0	448					NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	NA		NA			regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						AAAAGTGGCACGATGAGACAC	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													42	45	44	NA		NA	NA	4		NA											NA				36231150		2000	3937	5937					AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365	116984		ADP-ribosylation factor GTPase activating proteins, Sterile alpha motif (SAM) domain containing, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16924	protein-coding gene	gene with protein product		606645	centaurin, delta 1	CENTD1	NA		Standard	NM_015230	NM_015230	NA	Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:	chr4.hg19:g.36231150C>T		NA	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	hg19	CCDS3441.1	0.02	4.85376	GCAxGAT	COVERED																																																																																			NOVEL	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215074.2	1	5.116541	KEEP	0	0	0	17	588	CC	0.999366	0.999351	0		-	32	60	1208	0	0	108.0318	73	60	2644	146	ENST00000303965.4	0.304762	0.999984
WDR19	57728	__UNKNOWN__	__UNKNOWN__	4	39280297	39280297	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:39280297C>T	ENST00000399820.3	+	36	4196				WDR19_ENST00000288634.7_Intron	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	NA		NA			ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						AGTGGCAGAGCGCCCACGCAC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	47	47	NA		NA	NA	4		NA											NA				39280297		2100	4219	6319	SO:0001627	intron_variant			AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796	57728		WD repeat domain containing, Intraflagellar transport homologs	18340	protein-coding gene	gene with protein product	intraflagellar transport 144 homolog (Chlamydomonas)	608151			NA	12906858, 22019273	Standard		XM_005262658	NA	Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.4026+14C>T	chr4.hg19:g.39280297C>T		NA	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	hg19	CCDS47042.1	0.02	16.495744	GAGxGCC	COVERED																																																																																			NOVEL	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360689.1	1	22.684314	KEEP	0	1	30	86	2827	CC	1	1	0		+	103	60	3610	0	0	315.581826	264	60	8722	555	ENST00000399820.3	0.280654	1
APBB2	323	__UNKNOWN__	__UNKNOWN__	4	40814953	40814953	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:40814953A>C	ENST00000295974.8	-	0	6062				APBB2_ENST00000543538.1_3'UTR|RP11-632F7.3_ENST00000513127.1_RNA	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	NA		NA			axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CTTAGATGAAATCACACATGT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(3;20 75 16686 49997)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697	323			582	protein-coding gene	gene with protein product	Fe65-like	602710			NA	8955346, 9585438	Standard	NM_173075	NM_173075	NA	Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.*3156T>G	chr4.hg19:g.40814953A>C		NA	B4DSL4|E9PG87|Q8IUI6	hg19	CCDS54761.1	0.02	2.127696	GAAxTCA	COVERED																																																																																			NOVEL	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360523.3	0	6.319188	KEEP	0	0	0	21	678	AA	0.999869	0.999817	0		-	24	60	925	0	0	80.261933	74	60	2691	145	ENST00000295974.8	0.244898	0.999948
LIMCH1	22998	__UNKNOWN__	__UNKNOWN__	4	41605836	41605836	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:41605836T>C	ENST00000313860.7	+	5	398				LIMCH1_ENST00000512632.1_Intron|LIMCH1_ENST00000509638.1_Intron|LIMCH1_ENST00000503057.1_Intron|LIMCH1_ENST00000512820.1_Intron|LIMCH1_ENST00000508501.1_Intron|LIMCH1_ENST00000512946.1_Intron|LIMCH1_ENST00000511496.1_Intron|LIMCH1_ENST00000513024.1_Intron	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	NA		NA			actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						TAAGGAAAGGTCACAATTTAG	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													191	163	172	NA		NA	NA	4		NA											NA				41605836		692	1590	2282	SO:0001627	intron_variant			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042	22998			29191	protein-coding gene	gene with protein product		NA			NA	10470851	Standard	NM_014988	XM_005248057	NA	Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.345-56T>C	chr4.hg19:g.41605836T>C		NA	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	hg19	CCDS33977.1	0.02	-0.350773	AGGxCAC	COVERED																																																																																			NOVEL	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361249.2	0	2.407709	KEEP	0	0	0	8	271	TT	0.99257	0.871187	0		+	15	60	558	0	0	51.454787	25	60	905	64	ENST00000313860.7	0.375	0.877708
BEND4	389206	__UNKNOWN__	__UNKNOWN__	4	42117922	42117922	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:42117922G>A	ENST00000502486.1	-	0	3797				BEND4_ENST00000504360.1_3'UTR	NM_207406.3	NP_997289.2	Q6ZU67	BEND4_HUMAN	BEN domain containing 4	NA		NA								NS(2)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26						TGAAATATTAGTGCCCACTAC	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK092951	CCDS47048.1	4p13	2012-11-22	2008-10-03	2008-10-03	ENSG00000188848	ENSG00000188848	389206		BEN domain containing	23815	protein-coding gene	gene with protein product		NA	coiled-coil domain containing 4	CCDC4	NA		Standard	NM_207406	NM_207406	NA	Approved	FLJ35632, FLJ43965	uc003gwn.3	Q6ZU67	OTTHUMG00000160531	ENST00000502486.1:c.*1613C>T	chr4.hg19:g.42117922G>A		NA	A1A5D6|A1A5D7|C9JQZ5|Q58A26|Q58A27	hg19	CCDS47048.1	0.02	6.783583	TTAxTGC	COVERED																																																																																			NOVEL	BEND4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360975.2	0	7.223125	KEEP	0	0	0	24	825	GG	0.999909	0.999909	0		-	41	60	1494	0	0	127.018009	139	60	5289	242	ENST00000502486.1	0.227778	1
GNPDA2	132789	__UNKNOWN__	__UNKNOWN__	4	44708459	44708459	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:44708459G>A	ENST00000507917.1	-	5	799				GNPDA2_ENST00000295448.3_Intron|GNPDA2_ENST00000507534.1_Intron|GNPDA2_ENST00000511187.1_5'UTR|GNPDA2_ENST00000509756.1_3'UTR	NM_001270880.1	NP_001257809.1	Q8TDQ7	GNPI2_HUMAN	glucosamine-6-phosphate deaminase 2	NA		NA			carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(1)|lung(7)|ovary(1)	11						tatatacaaagcatgatcagc	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(54;743 1010 7604 16453 19544)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF247786	CCDS3469.1, CCDS59472.1, CCDS59473.1	4p13	2006-04-12			ENSG00000163281	ENSG00000163281	132789	3.5.99.6		21526	protein-coding gene	gene with protein product	glucosamine-6-phosphate isomerase	613222			NA	12965206	Standard	NM_138335	NM_001270880	NA	Approved	SB52	uc003gwy.4	Q8TDQ7	OTTHUMG00000099415	ENST00000507917.1:c.667+1309C>T	chr4.hg19:g.44708459G>A		NA	B4DJF3|Q2VYF1|Q59EA7|Q8NCZ8|Q96BJ4|Q96NC6	hg19	CCDS59473.1	0.02	1.810438	AAAxCAT	COVERED																																																																																			NOVEL	GNPDA2-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360776.2	1	12.641192	KEEP	0	0	0	42	1503	GG	1	0.999962	0		-	24	60	871	0	0	74.618714	76	60	2896	178	ENST00000507917.1	0.24	0.999962
GABRA4	2557	__UNKNOWN__	__UNKNOWN__	4	46928560	46928560	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:46928560T>A	ENST00000264318.3	-	0	4329					NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	NA		NA			central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	ATCTGAAAAATCGATGCCAAT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(6;283 369 8234 12290 33402)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158	2557		GABA receptors, Ligand-gated ion channels / GABA(A) receptors	4078	protein-coding gene	gene with protein product	GABA(A) receptor, alpha 4	137141			NA	7607683	Standard		NM_000809	NA	Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.*1682A>T	chr4.hg19:g.46928560T>A		NA	Q8IYR7	hg19	CCDS3473.1	0.02	6.967908	AAAxCGA	COVERED																																																																																			NOVEL	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216893.1	2	6.618125	KEEP	0	0	0	22	680	TT	0.999879	0.999879	0		-	49	60	1753	0	0	156.027312	110	60	4074	212	ENST00000264318.3	0.308176	1
ATP10D	57205	__UNKNOWN__	__UNKNOWN__	4	47574224	47574224	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:47574224G>A	ENST00000273859.3	+	17	3486	c.3217G>A	c.(3217-3219)Gtc>Atc	p.V1073I		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1073		NA			cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						TGGGATAGGGGTCTCAGGTCA	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													291	245	260	NA		NA	NA	4		NA											NA				47574224		2203	4300	6503	SO:0001583	missense			AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246	57205		ATPases / P-type	13549	protein-coding gene	gene with protein product		NA	ATPase, Class V, type 10D		NA	12532265	Standard	NM_020453	NM_020453	NA	Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.3217G>A	chr4.hg19:g.47574224G>A	ENSP00000273859:p.Val1073Ile	NA	A2RRC8|D6REN2|Q8NC70|Q96SR3	hg19	CCDS3476.1	0.02	6.616101	GGGxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.923	-0.715382	0.03206	.	.	ENSG00000145246	ENST00000273859	T	0.08984	3.03	5.76	3.66	0.41972	HAD-like domain (2);	0.203589	0.49305	N	0.000154	T	0.01092	0.0036	N	0.00028	-2.64	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35525	-0.9785	10	0.02654	T	1	-6.6972	6.6203	0.22800	0.8349:0.0:0.1651:0.0	.	1073	Q9P241	AT10D_HUMAN	I	1073	ENSP00000273859:V1073I	ENSP00000273859:V1073I	V	+	1	0	ATP10D	47268981	1.000000	0.71417	0.518000	0.27811	0.218000	0.24690	3.764000	0.55264	0.618000	0.30179	0.585000	0.79938	GTC	NOVEL	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216900.1	0	13.544079	KEEP	0	0	0	45	1596	GG	1	1	0		+	18	60	643	0	0	48.266193	147	60	5478	260	ENST00000273859.3	0.109091	1
SCFD2	152579	__UNKNOWN__	__UNKNOWN__	4	53786975	53786975	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:53786975T>C	ENST00000401642.3	-	6	1757	c.1624A>G	c.(1624-1626)Act>Gct	p.T542A	SCFD2_ENST00000388940.4_Missense_Mutation_p.T542A	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	542		NA			protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CGAAGTGAAGTAAAGAGTTCA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	83	82	NA		NA	NA	4		NA											NA				53786975		2203	4300	6503	SO:0001583	missense			AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178	152579			30676	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152540	NM_152540	NA	Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1624A>G	chr4.hg19:g.53786975T>C	ENSP00000384182:p.Thr542Ala	NA	Q8N5F3|Q8N8H0|Q96ED3	hg19	CCDS33984.1	0.02	7.251438	AAGxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.276184	0.00254	.	.	ENSG00000184178	ENST00000401642;ENST00000388940	T;T	0.79352	-0.92;-1.26	4.96	-9.92	0.00455	.	1.141120	0.06318	N	0.703925	T	0.59542	0.2201	L	0.36672	1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38693	-0.9649	10	0.12766	T	0.61	.	8.9474	0.35767	0.3192:0.5236:0.0:0.1573	.	542;542	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	A	542	ENSP00000384182:T542A;ENSP00000373592:T542A	ENSP00000373592:T542A	T	-	1	0	SCFD2	53481732	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-0.247000	0.08866	-2.121000	0.00825	-1.288000	0.01363	ACT	NOVEL	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361311.3	0	17.451709	KEEP	0	0	0	58	1816	TT	1	1	0		-	49	60	1851	0	0	160.7419	146	60	5160	339	ENST00000401642.3	0.251282	1
EXOC1	55763	__UNKNOWN__	__UNKNOWN__	4	56759789	56759789	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:56759789C>A	ENST00000381295.2	+	15	2144	c.1796C>A	c.(1795-1797)gCa>gAa	p.A599E	EXOC1_ENST00000346134.7_Missense_Mutation_p.A599E|EXOC1_ENST00000349598.6_Missense_Mutation_p.A584E	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	599		NA			cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					AACCTAATTGCATTAGGAGAC	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	114	115	NA		NA	NA	4		NA											NA				56759789		2203	4300	6503	SO:0001583	missense			AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989	55763			30380	protein-coding gene	gene with protein product		607879	SEC3-like 1 (S. cerevisiae)	SEC3L1	NA	11042152, 11406615	Standard	NM_018261	XM_005265747	NA	Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1796C>A	chr4.hg19:g.56759789C>A	ENSP00000370695:p.Ala599Glu	NA	Q504V4|Q8WUE7|Q96T15|Q9NZE4	hg19	CCDS3502.1	0.02	4.504997	TTGxATT	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.12	2.143396	0.37825	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.49270	0.1547	L	0.33485	1.01	0.80722	D	1	P;B	0.37573	0.6;0.127	B;B	0.36808	0.233;0.173	T	0.37291	-0.9712	9	0.13853	T	0.58	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	584;599	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	E	599;599;584	.	ENSP00000326514:A599E	A	+	2	0	EXOC1	56454546	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	7.487000	0.81328	2.894000	0.99253	0.655000	0.94253	GCA	NOVEL	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361799.1	1	6.621275	KEEP	0	0	0	22	785	CC	0.999879	0.999878	0		+	39	60	1410	0	0	126.409846	83	60	3157	178	ENST00000381295.2	0.319672	0.999999
TECRL	253017	__UNKNOWN__	__UNKNOWN__	4	65175556	65175556	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:65175556T>C	ENST00000381210.3	-	6	755	c.645A>G	c.(643-645)aaA>aaG	p.K215K	TECRL_ENST00000513125.1_5'UTR|TECRL_ENST00000507440.1_Silent_p.K215K	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	215		NA			lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						TTATCAAATTTTTCAAAGGTG	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	107	104	NA		NA	NA	4		NA											NA				65175556		2203	4300	6503	SO:0001819	synonymous_variant			AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678	253017			27365	protein-coding gene	gene with protein product	glycoprotein, synaptic 2-like	NA			NA	12477932	Standard	NM_001010874	NM_001010874	NA	Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.645A>G	chr4.hg19:g.65175556T>C		NA		hg19	CCDS33990.1	0.02	4.546685	ATTxTTC	COVERED																																																																																			NOVEL	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361705.4	2	9.924702	KEEP	0	0	0	33	1005	TT	0.999998	0.999998	0		-	6	60	234	0	0	15.508219	134	60	4924	228	ENST00000381210.3	0.042857	1
UGT2A3	79799	__UNKNOWN__	__UNKNOWN__	4	69796308	69796308	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:69796308G>A	ENST00000251566.4	-	5	1290	c.1260C>T	c.(1258-1260)agC>agT	p.S420S	UGT2A3_ENST00000420231.2_Silent_p.S131S	NM_024743.3	NP_079019.3	Q6UWM9	UD2A3_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A3	420		NA			cellular glucuronidation (GO:0052695)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GTAAATCTTCGCTTGTCATAG	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													164	163	163	NA		NA	NA	4		NA											NA				69796308		2203	4300	6503	SO:0001819	synonymous_variant				CCDS3525.1	4q13.2	2010-12-14			ENSG00000135220	ENSG00000135220	79799		UDP glucuronosyltransferases	28528	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024743	NM_024743	NA	Approved	FLJ21934	uc003hef.2	Q6UWM9	OTTHUMG00000129408	ENST00000251566.4:c.1260C>T	chr4.hg19:g.69796308G>A		NA	Q9H6S4	hg19	CCDS3525.1	0.02	4.818672	TTCxCTT	COVERED																																																																																			NOVEL	UGT2A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251564.1	0	6.019619	KEEP	0	0	0	20	705	GG	0.999863	0.999855	0		-	12	60	448	0	0	34.115648	97	60	3464	165	ENST00000251566.4	0.110092	0.999992
SHROOM3	57619	__UNKNOWN__	__UNKNOWN__	4	77660380	77660380	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs554492056		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:77660380C>G	ENST00000296043.6	+	5	2007	c.1054C>G	c.(1054-1056)Cgg>Ggg	p.R352G		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	352		NA			actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TAATATTCCTCGGGGCAAGGG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													54	58	57	NA		NA	NA	4		NA											NA				77660380		2203	4300	6503	SO:0001583	missense			AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771	57619			30422	protein-coding gene	gene with protein product		604570			NA	10589677, 16615870	Standard	NM_020859	NM_020859	NA	Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1054C>G	chr4.hg19:g.77660380C>G	ENSP00000296043:p.Arg352Gly	NA	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	hg19	CCDS3579.2	0.02	7.251529	CCTxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.16	1.853589	0.32791	.	.	ENSG00000138771	ENST00000296043	T	0.54675	0.56	5.65	3.8	0.43715	.	0.659044	0.14305	N	0.328058	T	0.66684	0.2814	M	0.71581	2.175	0.33489	D	0.588456	D;D;D	0.76494	0.982;0.999;0.999	P;D;D	0.64042	0.694;0.921;0.921	T	0.74743	-0.3562	10	0.72032	D	0.01	-16.7683	9.1606	0.37021	0.1549:0.7652:0.0:0.0799	.	176;352;130	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	G	352	ENSP00000296043:R352G	ENSP00000296043:R352G	R	+	1	2	SHROOM3	77879404	0.217000	0.23597	0.995000	0.50966	0.203000	0.24098	1.738000	0.38207	1.631000	0.50456	0.655000	0.94253	CGG	NOVEL	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252408.2	2	30.380379	KEEP	0	0	0	101	3365	CC	1	1	0		+	91	60	3423	0	0	327.213771	104	60	3774	370	ENST00000296043.6	0.466667	1
CNOT6L	246175	__UNKNOWN__	__UNKNOWN__	4	78641210	78641210	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:78641210C>T	ENST00000504123.1	-	0	2173				CNOT6L_ENST00000264903.4_3'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	NA		NA			gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						TTAAAAATTGCCTTTTATAAA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767	246175			18042	protein-coding gene	gene with protein product		NA			NA		Standard		NM_144571	NA	Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.*375G>A	chr4.hg19:g.78641210C>T		NA	Q9UF92	hg19		0.02	8.205786	TTGxCTT	COVERED																																																																																			NOVEL	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000362515.1	2	20.461243	KEEP	36	0	0	68	2328	CC	1	1	0		-	8	49	293	0	0	18.16801	214	50	7667	369	ENST00000504123.1	0.036036	1
MRPL1	65008	__UNKNOWN__	__UNKNOWN__	4	78873892	78873892	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:78873892G>A	ENST00000315567.8	+	0	1438					NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	NA		NA			translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						TTGAAAAATCGTACAGTCATT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288	65008		Mitochondrial ribosomal proteins / large subunits	14275	protein-coding gene	gene with protein product		611821			NA		Standard	NM_020236	NM_020236	NA	Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.*131G>A	chr4.hg19:g.78873892G>A		NA	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	hg19	CCDS3583.2	0.02	9.324974	ATCxTAC	COVERED																																																																																			NOVEL	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252518.3	4	15.048055	KEEP	0	0	0	50	1719	GG	1	1	0		+	56	60	2090	0	0	180.17985	175	60	6241	334	ENST00000315567.8	0.242424	1
THAP9	79725	__UNKNOWN__	__UNKNOWN__	4	83831856	83831856	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:83831856C>T	ENST00000302236.5	+	4	782				LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	NA		NA			DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				tcaggagcggccagtgaggca	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152	79725		THAP (C2CH-type zinc finger) domain containing	23192	protein-coding gene	gene with protein product		612537			NA	12575992	Standard	NM_024672	NM_024672	NA	Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.731+2768C>T	chr4.hg19:g.83831856C>T		NA	B3KRE2|Q59AC9	hg19	CCDS3598.1	0.02	-0.333355	CGGxCAG	COVERED																																																																																			NOVEL	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252633.1	0	5.415412	KEEP	0	0	0	18	617	CC	0.999859	0.851864	0		+	15	60	518	0	0	47.886172	23	60	816	62	ENST00000302236.5	0.394737	0.851984
FAM13A	10144	__UNKNOWN__	__UNKNOWN__	4	89660204	89660204	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:89660204G>C	ENST00000264344.5	-	20	2746	c.2539C>G	c.(2539-2541)Cga>Gga	p.R847G	FAM13A_ENST00000503556.1_Missense_Mutation_p.R507G|FAM13A_ENST00000508369.1_Missense_Mutation_p.R521G|FAM13A_ENST00000513837.1_Missense_Mutation_p.R493G|FAM13A_ENST00000395002.2_Missense_Mutation_p.R521G|FAM13A_ENST00000511976.1_Missense_Mutation_p.R433G	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	847		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						GTGTTAGCTCGGGAGAGGATC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													218	175	189	NA		NA	NA	4		NA											NA				89660204		2203	4300	6503	SO:0001583	missense			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640	10144		Rho GTPase activating proteins	19367	protein-coding gene	gene with protein product		613299	family with sequence similarity 13, member A1	FAM13A1	NA		Standard		NM_014883	NA	Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.2539C>G	chr4.hg19:g.89660204G>C	ENSP00000264344:p.Arg847Gly	NA	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	hg19	CCDS34029.1	0.02	4.646417	CTCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.96	3.734217	0.69189	.	.	ENSG00000138640	ENST00000395002;ENST00000264344;ENST00000503556;ENST00000511976;ENST00000508369;ENST00000513837	T;T;T;T;T;T	0.53640	0.61;1.87;1.2;1.26;1.2;1.21	5.17	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.69024	0.3065	M	0.80183	2.485	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.995;0.998;0.997;0.998;0.993;0.995	T	0.74244	-0.3728	10	0.87932	D	0	.	13.2598	0.60098	0.0:0.0:0.6559:0.344	.	493;433;847;521;507;521	O94988-6;E9PGM7;O94988;O94988-3;O94988-5;O94988-1	.;.;FA13A_HUMAN;.;.;.	G	521;847;507;433;521;493	ENSP00000378450:R521G;ENSP00000264344:R847G;ENSP00000427189:R507G;ENSP00000421914:R433G;ENSP00000421562:R521G;ENSP00000423252:R493G	ENSP00000264344:R847G	R	-	1	2	FAM13A	89879227	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.933000	0.48948	1.398000	0.46701	0.650000	0.86243	CGA	NOVEL	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363371.1	0	22.269113	KEEP	0	0	0	74	2449	GG	1	0.999987	0		-	35	60	1140	0	0	101.514624	71	60	2434	242	ENST00000264344.5	0.330189	0.999987
RP11-9B6.1	0	__UNKNOWN__	__UNKNOWN__	4	93218535	93218535	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:93218535G>T	ENST00000504213.1	-	0	458										NA		NA									NA						ATACAGATTTGTGATCTGGCT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000504213.1:c.*116C>A	chr4.hg19:g.93218535G>T		NA		hg19		0.02	-0.429894	TTTxTGA	COVERED																																																																																			NOVEL	RP11-9B6.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000362943.1	4	5.41764	KEEP	0	0	0	18	636	GG	0.999859	0.954357	0		-	14	60	508	0	0	44.748276	35	60	1349	75	ENST00000504213.1	0.285714	0.954491
UNC5C	8633	__UNKNOWN__	__UNKNOWN__	4	96169736	96169736	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:96169736G>A	ENST00000504962.1	-	0	1149				UNC5C_ENST00000453304.1_Intron|UNC5C_ENST00000506749.1_Intron			O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	NA		NA			anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		aggactagcagagtgatcttg	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168	8633		Immunoglobulin superfamily / I-set domain containing	12569	protein-coding gene	gene with protein product		603610	unc5 (C.elegans homolog) c		NA	9126742, 9782087	Standard	NM_003728	NM_003728	NA	Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000504962.1:c.*24C>T	chr4.hg19:g.96169736G>A		NA	Q8IUT0	hg19		0.02	16.145553	GCAxAGT	COVERED																																																																																			NOVEL	UNC5C-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363047.1	2	33.710755	KEEP	0	0	0	112	4089	GG	1	1	0		-	91	60	3400	0	0	292.123817	293	60	11210	672	ENST00000504962.1	0.236979	1
METAP1	23173	__UNKNOWN__	__UNKNOWN__	4	99956576	99956576	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:99956576A>G	ENST00000296411.6	+	4	439	c.305A>G	c.(304-306)tAt>tGt	p.Y102C	METAP1_ENST00000544031.1_Missense_Mutation_p.Y52C|METAP1_ENST00000506548.1_3'UTR	NM_015143.2	NP_055958.2	P53582	MAP11_HUMAN	methionyl aminopeptidase 1	102		NA			N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|phototransduction, visible light (GO:0007603)|platelet aggregation (GO:0070527)|protein initiator methionine removal (GO:0070084)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of translation (GO:0006417)|rhodopsin mediated signaling pathway (GO:0016056)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic ribosome (GO:0022626)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metalloaminopeptidase activity (GO:0070006)|metalloexopeptidase activity (GO:0008235)			endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(123;3.12e-07)		GTGCCAAGTTATATTCAAAGA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													309	242	263	NA		NA	NA	4		NA											NA				99956576		692	1591	2283	SO:0001583	missense			D42084	CCDS47110.1	4q23	2010-08-20			ENSG00000164024	ENSG00000164024	23173	3.4.11.18		15789	protein-coding gene	gene with protein product	Peptidase M	610151			NA	7788527, 12144506	Standard	NM_015143	NM_015143	NA	Approved	KIAA0094, MetAP1A, MAP1A	uc003huf.4	P53582	OTTHUMG00000161231	ENST00000296411.6:c.305A>G	chr4.hg19:g.99956576A>G	ENSP00000296411:p.Tyr102Cys	NA	B4E2E6	hg19	CCDS47110.1	0.02	4.376164	GTTxTAT	COVERED	.	.	.	.	.	.	.	.	.	.	A	14.27	2.485568	0.44147	.	.	ENSG00000164024	ENST00000296411;ENST00000544031	.	.	.	4.49	4.49	0.54785	Peptidase M24, structural domain (2);	0.197648	0.44688	D	0.000430	T	0.44350	0.1289	L	0.29908	0.895	0.49915	D	0.999831	B	0.02656	0.0	B	0.01281	0.0	T	0.31503	-0.9941	8	.	.	.	-21.6175	14.2508	0.66019	1.0:0.0:0.0:0.0	.	102	P53582	AMPM1_HUMAN	C	102;52	.	.	Y	+	2	0	METAP1	100175599	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.267000	0.72546	2.014000	0.59158	0.528000	0.53228	TAT	NOVEL	METAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364237.1	3	9.024368	KEEP	0	0	0	30	910	AA	0.999997	0.999993	0		+	5	60	182	0	0	11.678567	109	60	3873	165	ENST00000296411.6	0.04386	0.999996
BDH2	56898	__UNKNOWN__	__UNKNOWN__	4	104007597	104007597	__UNKNOWN__	Intron	SNP	G	G	A	rs376822009		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:104007597G>A	ENST00000296424.4	-	6	539					NM_020139.3	NP_064524.3	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	NA		NA			epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|heme metabolic process (GO:0042168)|iron ion homeostasis (GO:0055072)|siderophore biosynthetic process (GO:0019290)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		AATGATGTGCGTGTATGAGCA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G		1,4405	2.1+/-5.4	0,1,2202	58	50	53	NA		-1.8	0	4		53	0,8600		0,0,4300	no	intron	BDH2	NM_020139.3		0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077			104007597	1,13005	2203	4300	6503	SO:0001627	intron_variant			AF164790	CCDS3663.1	4q24	2011-09-14			ENSG00000164039	ENSG00000164039	56898	1.1.1.30	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1	32389	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 15C, member 1	NA	dehydrogenase/reductase (SDR family) member 6	DHRS6	NA	16380372, 19027726	Standard	NM_020139	XM_005263140	NA	Approved	UCPA-OR, FLJ13261, UNQ6308, PRO20933, SDR15C1	uc003hwz.3	Q9BUT1	OTTHUMG00000074039	ENST00000296424.4:c.418+39C>T	chr4.hg19:g.104007597G>A		NA	A8K295|B4DUF6|Q503A0|Q6IA46|Q6UWD3|Q9H8S8|Q9NRX8	hg19	CCDS3663.1	0.02	4.828162	TGCxTGT	COVERED																																																																																			NOVEL	BDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157159.2	1	12.639271	KEEP	0	0	0	42	1424	GG	1	0.999991	0		-	33	60	1250	0	0	111.892273	75	60	2657	200	ENST00000296424.4	0.305556	0.999991
TACR3	6870	__UNKNOWN__	__UNKNOWN__	4	104510377	104510377	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:104510377A>T	ENST00000304883.2	-	0	2000				RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	NA		NA			aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		GAATCATTTAACTTTTTTTCC	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836	6870		GPCR / Class A : Tachykinin receptors	11528	protein-coding gene	gene with protein product	neurokinin beta receptor	162332			NA	1374246	Standard	NM_001059	NM_001059	NA	Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.*462T>A	chr4.hg19:g.104510377A>T		NA	Q0P510	hg19	CCDS3664.1	0.02	1.998225	TTAxCTT	COVERED																																																																																			NOVEL	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253804.1	0	3.911481	KEEP	0	0	0	13	407	AA	0.994391	0.994227	0		-	27	60	977	0	0	86.709913	63	60	2225	115	ENST00000304883.2	0.3	0.999835
NPNT	255743	__UNKNOWN__	__UNKNOWN__	4	106861791	106861791	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:106861791T>C	ENST00000427316.2	+	8	1063	c.851T>C	c.(850-852)gTg>gCg	p.V284A	NPNT_ENST00000379987.2_Missense_Mutation_p.V254A|NPNT_ENST00000305572.8_Missense_Mutation_p.V254A|NPNT_ENST00000514622.1_Missense_Mutation_p.V254A|NPNT_ENST00000506666.1_Missense_Mutation_p.V284A|NPNT_ENST00000453617.2_Missense_Mutation_p.V271A	NM_001184691.1	NP_001171620.1	Q6UXI9	NPNT_HUMAN	nephronectin	254		NA			branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		CTGACTTGTGTGTGTGAGTAG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													208	184	193	NA		NA	NA	4		NA											NA				106861791		2203	4300	6503	SO:0001583	missense				CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07					255743			27405	protein-coding gene	gene with protein product		610306			NA	15754038	Standard	NM_198278	NM_001033047	NA	Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000427316.2:c.851T>C	chr4.hg19:g.106861791T>C	ENSP00000389252:p.Val284Ala	NA	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	hg19	CCDS54785.1	0.02	12.550822	GTGxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	8.148	0.786695	0.16189	.	.	ENSG00000168743	ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451	D;D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	5.29	4.1	0.47936	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.421595	0.27375	N	0.019655	T	0.77226	0.4099	L	0.31476	0.935	0.21984	N	0.999437	B;B;B;B;B;B;B	0.18310	0.027;0.001;0.001;0.015;0.001;0.023;0.015	B;B;B;B;B;B;B	0.23574	0.013;0.003;0.002;0.01;0.002;0.047;0.013	T	0.56486	-0.7971	10	0.06365	T	0.9	.	11.0554	0.47915	0.0:0.0731:0.0:0.9269	.	254;284;284;271;301;254;254	E9PF04;E9PE64;E9PCQ1;E9PCK8;D6RH31;Q6UXI9-2;Q6UXI9	.;.;.;.;.;.;NPNT_HUMAN	A	254;271;284;254;254;284;301	ENSP00000369323:V254A;ENSP00000402884:V271A;ENSP00000389252:V284A;ENSP00000422044:V254A;ENSP00000302557:V254A;ENSP00000422474:V284A;ENSP00000426146:V301A	ENSP00000302557:V254A	V	+	2	0	NPNT	107081240	0.153000	0.22777	0.629000	0.29254	0.105000	0.19272	0.273000	0.18662	0.844000	0.35094	0.533000	0.62120	GTG	NOVEL	NPNT-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364085.1	2	19.852142	KEEP	0	0	0	66	2013	TT	1	1	0		+	72	60	2613	0	0	227.391962	200	60	7274	440	ENST00000427316.2	0.264706	1
SGMS2	166929	__UNKNOWN__	__UNKNOWN__	4	108832191	108832191	__UNKNOWN__	3'UTR	SNP	C	C	T	rs536359763		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:108832191C>T	ENST00000394684.4	+	0	2137				RP11-286E11.1_ENST00000513071.1_RNA|RP11-286E11.1_ENST00000499098.1_RNA	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	NA		NA			small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		GTGGGTTGTGCGTCAGCTTTG	0.478	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	15656	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	166929	2.7.8.27		28395	protein-coding gene	gene with protein product		611574			NA	14685263	Standard	NM_152621	NM_152621	NA	Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.*482C>T	chr4.hg19:g.108832191C>T		NA	A8K2S9|B2RA61	hg19	CCDS3677.1	0.02	4.610258	GTGxGTC	COVERED																																																																																			NOVEL	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254752.1	4	6.653111	KEEP	0	1	31	33	1106	CC	0.999998	0.999991	0		+	11	60	388	0	0	28.523898	99	60	3425	181	ENST00000394684.4	0.1	0.999993
UGT8	7368	__UNKNOWN__	__UNKNOWN__	4	115598690	115598690	__UNKNOWN__	3'UTR	SNP	C	C	T	rs531546783	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:115598690C>T	ENST00000310836.6	+	0	3394					NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	NA		NA			axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		ACCCCAGCAGCCTTTTCCGGT	0.433	NA	NA											C|||	2	0.000399361	0.0015	0	5008	,	,	NA	20188	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	7368	2.4.1.45	UDP glucuronosyltransferases	12555	protein-coding gene	gene with protein product	2-hydroxyacylsphingosine 1-beta-galactosyltransferase	601291	UDP-galactose ceramide galactosyltransferase	CGT	NA	8661025	Standard	NM_003360	NM_003360	NA	Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.*1246C>T	chr4.hg19:g.115598690C>T		NA	B3KXU7|O00196	hg19	CCDS3705.1	0.02	1.864426	CAGxCTT	COVERED																																																																																			NOVEL	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256426.2	1	5.718947	KEEP	0	0	0	19	698	CC	0.99986	0.999767	0		+	12	60	432	0	0	33.406055	81	60	2901	148	ENST00000310836.6	0.129032	0.999907
TNIP3	79931	__UNKNOWN__	__UNKNOWN__	4	122079890	122079890	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:122079890C>T	ENST00000509841.1	-	6	474	c.396G>A	c.(394-396)caG>caA	p.Q132Q	TNIP3_ENST00000057513.3_Silent_p.Q55Q|TNIP3_ENST00000454328.1_Silent_p.Q55Q|TNIP3_ENST00000507879.1_Silent_p.Q125Q	NM_001244764.1	NP_001231693.1			TNFAIP3 interacting protein 3	NA		NA								NS(1)|endometrium(4)|large_intestine(4)|lung(9)|ovary(1)|prostate(3)|skin(2)	24						GATCCCATTGCTGGTTAACTT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													79	82	81	NA		NA	NA	4		NA											NA				122079890		2202	4300	6502	SO:0001819	synonymous_variant			AJ320534	CCDS3718.1, CCDS58925.1, CCDS58926.1	4q27	2008-02-05			ENSG00000050730	ENSG00000050730	79931			19315	protein-coding gene	gene with protein product		608019			NA	11345586	Standard	NM_024873	NM_024873	NA	Approved	LIND, FLJ21162, ABIN-3	uc021xrj.1	Q96KP6	OTTHUMG00000132969	ENST00000509841.1:c.396G>A	chr4.hg19:g.122079890C>T		NA		hg19	CCDS58926.1	0.02	2.094498	TTGxTGG	COVERED																																																																																			NOVEL	TNIP3-003	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364000.4	1	5.116868	KEEP	0	0	0	17	624	CC	0.999366	0.998477	0		-	23	60	849	0	0	75.179779	56	60	2142	113	ENST00000509841.1	0.291139	0.99911
ANXA5	308	__UNKNOWN__	__UNKNOWN__	4	122589621	122589621	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:122589621C>T	ENST00000296511.5	-	0	1250				ANXA5_ENST00000501272.2_3'UTR|ANXA5_ENST00000515017.1_3'UTR	NM_001154.3	NP_001145.1	P08758	ANXA5_HUMAN	annexin A5	NA		NA			blood coagulation (GO:0007596)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of coagulation (GO:0050819)|response to organic substance (GO:0010033)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipase inhibitor activity (GO:0004859)|phospholipid binding (GO:0005543)			NS(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)	15						CCCCGTGACACGTTAGTCATC	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(191;1279 2147 16046 17806 52646)|GBM(88;628 1285 16585 32846 50188)					NA		NA				0													153	128	136	NA		NA	NA	4		NA											NA				122589621		2203	4300	6503	SO:0001624	3_prime_UTR_variant			U05770	CCDS3720.1	4q27	2008-02-05			ENSG00000164111	ENSG00000164111	308		Annexins	543	protein-coding gene	gene with protein product		131230		ENX2, ANX5	NA	2960376	Standard	NM_001154	NM_001154	NA	Approved		uc003idv.4	P08758	OTTHUMG00000133034	ENST00000296511.5:c.*2G>A	chr4.hg19:g.122589621C>T		NA	D3DNW7|Q6FHB3|Q6FI16|Q8WV69|Q9UDH9	hg19	CCDS3720.1	0.02	9.162528	ACAxGTT	COVERED																																																																																			NOVEL	ANXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256636.2	2	23.474183	KEEP	0	0	0	78	2658	CC	1	1	0		-	54	60	1976	0	0	168.021857	184	60	6408	371	ENST00000296511.5	0.226891	1
EXOSC9	5393	__UNKNOWN__	__UNKNOWN__	4	122737519	122737519	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:122737519C>A	ENST00000243498.5	+	11	1264				EXOSC9_ENST00000512454.1_Intron|EXOSC9_ENST00000379663.3_Intron	NM_005033.2	NP_005024.2	Q06265	EXOS9_HUMAN	exosome component 9	NA		NA			exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|immune response (GO:0006955)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear polyadenylation-dependent rRNA catabolic process (GO:0071035)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|intermediate filament cytoskeleton (GO:0045111)|nuclear exosome (RNase complex) (GO:0000176)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|AU-rich element binding (GO:0017091)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|urinary_tract(1)	16						aataaaaaaaCAAAGATGCTC	0.259	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	36	35	NA		NA	NA	4		NA											NA				122737519		2160	4275	6435	SO:0001627	intron_variant			M58460	CCDS3722.2, CCDS34057.1	4q27	2010-05-07	2004-06-16	2004-06-18	ENSG00000123737	ENSG00000123737	5393	3.1.13.-		9137	protein-coding gene	gene with protein product	polymyositis/scleroderma autoantigen 1 (75kD)	606180	polymyositis/scleroderma autoantigen 1, 75kDa	PMSCL1	NA		Standard	NM_005033	XR_427545	NA	Approved	PM/Scl-75, Rrp45p, RRP45, p5, p6	uc003idz.3	Q06265	OTTHUMG00000128783	ENST00000243498.5:c.1157-5C>A	chr4.hg19:g.122737519C>A		NA	Q12883|Q4W5P5|Q86Y41|Q86Y48	hg19	CCDS3722.2	0.02	1.542811	AAAxAAA	COVERED																																																																																			NOVEL	EXOSC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250708.2	1	5.793383	KEEP	0	2	22	28	865	CC	0.999997	0.998198	0		+	6	60	141	0	0	8.17528	66	60	2194	132	ENST00000243498.5	0.083333	0.9982
BBS7	55212	__UNKNOWN__	__UNKNOWN__	4	122784397	122784397	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:122784397A>G	ENST00000264499.4	-	3	323	c.140T>C	c.(139-141)tTt>tCt	p.F47S	BBS7_ENST00000506636.1_Missense_Mutation_p.F47S	NM_176824.2	NP_789794.1	Q8IWZ6	BBS7_HUMAN	Bardet-Biedl syndrome 7	47		NA			brain development (GO:0007420)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|digestive tract morphogenesis (GO:0048546)|eye development (GO:0001654)|fat cell differentiation (GO:0045444)|heart looping (GO:0001947)|limb development (GO:0060173)|melanosome transport (GO:0032402)|nonmotile primary cilium assembly (GO:0035058)|palate development (GO:0060021)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein transport (GO:0015031)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|visual perception (GO:0007601)	axoneme (GO:0005930)|BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						CTTCATGCCAAAGCACATAAC	0.303	NA	NA							Bardet-Biedl syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													160	170	167	NA		NA	NA	4		NA											NA				122784397		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AF521644	CCDS3724.1, CCDS54799.1	4q27	2013-01-08			ENSG00000138686	ENSG00000138686	55212			18758	protein-coding gene	gene with protein product		607590			NA		Standard		NM_176824	NA	Approved	FLJ10715, BBS2L1	uc003ied.3	Q8IWZ6	OTTHUMG00000133076	ENST00000264499.4:c.140T>C	chr4.hg19:g.122784397A>G	ENSP00000264499:p.Phe47Ser	NA	Q4W5P8|Q8N581|Q9NVI4	hg19	CCDS3724.1	0.02	4.599692	CCAxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	28.8	4.952303	0.92660	.	.	ENSG00000138686	ENST00000264499;ENST00000506636	T;T	0.72282	-0.64;-0.64	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.85678	0.5752	M	0.85710	2.77	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	D	0.88153	0.2852	10	0.87932	D	0	-20.7903	15.7316	0.77810	1.0:0.0:0.0:0.0	.	47;47	Q8IWZ6-2;Q8IWZ6	.;BBS7_HUMAN	S	47	ENSP00000264499:F47S;ENSP00000423626:F47S	ENSP00000264499:F47S	F	-	2	0	BBS7	123003847	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.712000	0.91403	2.103000	0.63969	0.533000	0.62120	TTT	NOVEL	BBS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256716.1	1	19.859767	KEEP	0	0	0	66	2134	AA	1	1	0		-	5	60	199	0	0	13.017168	129	60	4680	282	ENST00000264499.4	0.037313	1
FAT4	79633	__UNKNOWN__	__UNKNOWN__	4	126239267	126239267	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:126239267G>A	ENST00000394329.3	+	1	1714	c.1701G>A	c.(1699-1701)caG>caA	p.Q567Q		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	567	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCTATGCCCAGCTTGTAGTAA	0.522	NA	NA									OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	49	49	NA		NA	NA	4		NA											NA				126239267		1942	4151	6093	SO:0001819	synonymous_variant			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159	79633		Cadherins / Cadherin-related	23109	protein-coding gene	gene with protein product	cadherin-related family member 11	612411	FAT tumor suppressor homolog 4 (Drosophila)		NA	15003449	Standard	NM_024582	NM_024582	NA	Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1701G>A	chr4.hg19:g.126239267G>A		1548	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	hg19	CCDS3732.3	0.02	11.317191	CCAxCTT	COVERED																																																																																			NOVEL	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256765.2	4	31.132628	KEEP	0	1	30	114	4071	GG	1	1	0		+	87	60	3091	0	0	275.898571	189	60	7119	477	ENST00000394329.3	0.315217	1
PLK4	10733	__UNKNOWN__	__UNKNOWN__	4	128814571	128814571	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:128814571G>C	ENST00000507249.1	+	11	2343	c.2137G>C	c.(2137-2139)Gag>Cag	p.E713Q	PLK4_ENST00000513090.1_Missense_Mutation_p.E742Q|PLK4_ENST00000515069.1_Missense_Mutation_p.E696Q|PLK4_ENST00000270861.5_Missense_Mutation_p.E774Q|PLK4_ENST00000514379.1_Missense_Mutation_p.E733Q			O00444	PLK4_HUMAN	polo-like kinase 4	774		NA			centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.E774*(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						CCATGCTAATGAGGTACATAC	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(135;508 1718 19061 31832 42879)					NA		NA				1	Substitution - Nonsense(1)	endometrium(1)											93	94	94	NA		NA	NA	4		NA											NA				128814571		2202	4299	6501	SO:0001583	missense			Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731	10733			11397	protein-coding gene	gene with protein product		605031	serine/threonine kinase 18, polo-like kinase 4 (Drosophila)	STK18	NA		Standard		NM_014264	NA	Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000507249.1:c.2137G>C	chr4.hg19:g.128814571G>C	ENSP00000423412:p.Glu713Gln	NA	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	hg19		0.02	5.079863	AATxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.1	4.090594	0.76756	.	.	ENSG00000142731	ENST00000270861;ENST00000515069;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	M	0.61703	1.905	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.57551	-0.7792	10	0.87932	D	0	-7.5324	18.6726	0.91517	0.0:0.0:1.0:0.0	.	742;774	O00444-2;O00444	.;PLK4_HUMAN	Q	774;696;742;713;733	ENSP00000270861:E774Q;ENSP00000421774:E696Q;ENSP00000427554:E742Q;ENSP00000423412:E713Q;ENSP00000423582:E733Q	ENSP00000270861:E774Q	E	+	1	0	PLK4	129034021	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	8.612000	0.90909	2.631000	0.89168	0.655000	0.94253	GAG	NOVEL	PLK4-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000364138.1	2	6.922575	KEEP	0	0	0	23	816	GG	0.999892	0.999865	0		+	25	60	957	0	0	82.960715	77	60	2879	144	ENST00000507249.1	0.245098	0.999973
LARP1B	55132	__UNKNOWN__	__UNKNOWN__	4	129043929	129043929	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:129043929A>T	ENST00000512292.1	+	0	2010				LARP1B_ENST00000264584.5_Intron|LARP1B_ENST00000326639.6_Intron|LARP1B_ENST00000354456.3_Intron|LARP1B_ENST00000441387.1_Intron			Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	NA		NA				nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TCTTGTTCTAATTTTTTTTAA	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709	55132		La ribonucleoprotein domain containing	24704	protein-coding gene	gene with protein product		NA	La ribonucleoprotein domain family, member 2	LARP2	NA	12045101	Standard	NM_018078	NM_018078	NA	Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000512292.1:c.*260A>T	chr4.hg19:g.129043929A>T		NA	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	hg19		0.02	4.285773	CTAxTTT	COVERED																																																																																			NOVEL	LARP1B-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000364011.1	3	7.824226	KEEP	0	0	0	26	854	AA	0.999957	0.999957	0		+	27	60	995	0	0	81.940832	120	60	4335	209	ENST00000512292.1	0.183673	1
SETD7	80854	__UNKNOWN__	__UNKNOWN__	4	140453745	140453745	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:140453745T>G	ENST00000406354.1	-	0	1117				SETD7_ENST00000404104.3_3'UTR|SETD7_ENST00000274031.3_Intron|SETD7_ENST00000506866.2_Intron			Q8WTS6	SETD7_HUMAN	SET domain containing (lysine methyltransferase) 7	NA		NA			chromatin modification (GO:0016568)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8	all_hematologic(180;0.156)					CTGCCATATCTTTTTACTTTA	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB051504	CCDS3748.1	4q31.1	2011-07-01			ENSG00000145391	ENSG00000145391	80854		Chromatin-modifying enzymes / K-methyltransferases	30412	protein-coding gene	gene with protein product		606594			NA	11850410, 11779497	Standard	NM_030648	NM_030648	NA	Approved	KIAA1717, SET7, SET7/9, Set9, KMT7	uc003ihw.3	Q8WTS6	OTTHUMG00000133385	ENST00000406354.1:c.*684A>C	chr4.hg19:g.140453745T>G		NA	B5WWL3|Q0VAH3|Q4W5A9|Q9C0E6	hg19		0.02	2.373216	ATCxTTT	COVERED																																																																																			NOVEL	SETD7-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000318414.1	1	6.018588	KEEP	0	0	0	20	644	TT	0.999863	0.996587	0		-	19	60	670	0	0	58.290957	51	60	1959	112	ENST00000406354.1	0.271429	0.996724
TBC1D9	23158	__UNKNOWN__	__UNKNOWN__	4	141591982	141591982	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:141591982T>G	ENST00000442267.2	-	7	1232	c.1158A>C	c.(1156-1158)aaA>aaC	p.K386N		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	386		NA					calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				AGTCTCTATCTTTCAAGTTGG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													159	159	159	NA		NA	NA	4		NA											NA				141591982		1911	4123	6034	SO:0001583	missense			AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436	23158		EF-hand domain containing	21710	protein-coding gene	gene with protein product		NA	TBC1 domain family, member 9		NA	12970790	Standard	NM_015130	NM_015130	NA	Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.1158A>C	chr4.hg19:g.141591982T>G	ENSP00000411197:p.Lys386Asn	NA	A6H8U8|D3DNZ1|O94958	hg19	CCDS47136.1	0.02	1.91027	ATCxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	T	14.75	2.629522	0.46944	.	.	ENSG00000109436	ENST00000442267	T	0.09538	2.97	5.45	1.73	0.24493	.	0.043866	0.85682	D	0.000000	T	0.15435	0.0372	M	0.82823	2.61	0.80722	D	1	B	0.10296	0.003	B	0.22386	0.039	T	0.02567	-1.1140	10	0.39692	T	0.17	-7.7273	8.5157	0.33244	0.0:0.2829:0.0:0.7171	.	386	Q6ZT07	TBCD9_HUMAN	N	386	ENSP00000411197:K386N	ENSP00000411197:K386N	K	-	3	2	TBC1D9	141811432	0.987000	0.35691	0.975000	0.42487	0.983000	0.72400	0.222000	0.17699	0.125000	0.18397	-0.280000	0.10049	AAA	NOVEL	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364806.1	3	11.435928	KEEP	0	0	0	38	1258	TT	1	0.999962	0		-	12	60	417	0	0	31.49403	88	60	3302	181	ENST00000442267.2	0.12	0.999962
INPP4B	8821	__UNKNOWN__	__UNKNOWN__	4	142946788	142946788	__UNKNOWN__	3'UTR	SNP	C	C	T	rs528892089		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:142946788C>T	ENST00000513000.1	-	0	6355					NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	NA		NA			cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CCTTTTTTACCTCTTATTTTA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452	8821			6075	protein-coding gene	gene with protein product		607494	inositol polyphosphate-4-phosphatase, type II, 105kD		NA	9295334	Standard	NM_003866	NM_003866	NA	Approved		uc003iiw.4	O15327		ENST00000513000.1:c.*3147G>A	chr4.hg19:g.142946788C>T		NA	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	hg19	CCDS3757.1	0.02	1.808527	TACxTCT	COVERED																																																																																			NOVEL	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364587.1	2	7.523756	KEEP	0	0	0	25	874	CC	0.999931	0.999735	0		-	5	60	179	0	1	11.931191	84	60	3099	131	ENST00000513000.1	0.05618	0.999804
INPP4B	8821	__UNKNOWN__	__UNKNOWN__	4	143043281	143043281	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:143043281C>T	ENST00000513000.1	-	22	2568	c.2135G>A	c.(2134-2136)cGa>cAa	p.R712Q	INPP4B_ENST00000509777.1_Splice_Site_p.R712Q|INPP4B_ENST00000308502.4_Splice_Site_p.R712Q|INPP4B_ENST00000262992.4_Splice_Site_p.R712Q|INPP4B_ENST00000508116.1_Splice_Site_p.R712Q	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	712		NA			cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CACTGCTTACCGTCTTCCTGT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													137	120	126	NA		NA	NA	4		NA											NA				143043281		2203	4300	6503	SO:0001630	splice_region_variant			U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452	8821			6075	protein-coding gene	gene with protein product		607494	inositol polyphosphate-4-phosphatase, type II, 105kD		NA	9295334	Standard	NM_003866	NM_003866	NA	Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2135+1G>A	chr4.hg19:g.143043281C>T		NA	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	hg19	CCDS3757.1	0.02	4.93853	TACxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	31	5.072869	0.93950	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.39787	1.5;1.5;1.5;1.5;1.45;1.49;1.06;1.1	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.73094	0.3543	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.68192	0.956	T	0.77760	-0.2467	9	.	.	.	.	20.2119	0.98289	0.0:1.0:0.0:0.0	.	712	O15327	INP4B_HUMAN	Q	712;712;712;583;712;712;527;527;712;583	ENSP00000425487:R712Q;ENSP00000262992:R712Q;ENSP00000308441:R712Q;ENSP00000423954:R712Q;ENSP00000422793:R712Q;ENSP00000426207:R527Q;ENSP00000427250:R712Q;ENSP00000421065:R583Q	.	R	-	2	0	INPP4B	143262731	1.000000	0.71417	1.000000	0.80357	0.749000	0.42624	6.658000	0.74407	2.784000	0.95788	0.585000	0.79938	CGA	NOVEL	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364587.1	1	10.232275	KEEP	0	0	0	34	1147	CC	0.999998	0.999987	0	Missense_Mutation	-	9	60	342	0	0	25.092138	98	60	3389	185	ENST00000513000.1	0.084112	0.999989
RP11-6L6.2	0	__UNKNOWN__	__UNKNOWN__	4	147145734	147145734	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:147145734T>C	ENST00000504313.1	+	1	26	c.23T>C	c.(22-24)cTg>cCg	p.L8P							NA		NA									NA						CACCAGAGGCTGGGCGATGTT	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000504313.1:c.23T>C	chr4.hg19:g.147145734T>C	ENSP00000421542:p.Leu8Pro	NA		hg19		0.02	2.030754	GGCxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.902	1.207104	0.22205	.	.	ENSG00000250673	ENST00000504313	.	.	.	4.7	-1.62	0.08372	.	.	.	.	.	T	0.55114	0.1900	.	.	.	.	.	.	.	.	.	.	.	.	T	0.62699	-0.6799	4	0.62326	D	0.03	.	10.7049	0.45950	0.0:0.5622:0.0:0.4378	.	.	.	.	P	8	.	ENSP00000421542:L8P	L	+	2	0	RP11-6L6.2	147365184	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.337000	0.07852	-0.902000	0.03886	-0.250000	0.11733	CTG	NOVEL	RP11-6L6.2-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000364920.3	2	5.717825	KEEP	0	0	0	19	615	TT	0.99986	0.998325	0		+	16	60	543	0	0	45.075722	59	60	2262	123	ENST00000504313.1	0.213333	0.998465
RPS3A	6189	__UNKNOWN__	__UNKNOWN__	4	152021132	152021132	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:152021132G>A	ENST00000509736.1	+	1	91				RPS3A_ENST00000322686.6_Intron|RPS3A_ENST00000514682.1_Intron|RPS3A_ENST00000512690.1_Intron|RPS3A_ENST00000506126.1_Intron|RPS3A_ENST00000274065.4_Intron					ribosomal protein S3A	NA		NA								endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					AGTTTTGTGGGCTCACGAGCT	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425	6189		S ribosomal proteins	10421	protein-coding gene	gene with protein product		180478		MFTL	NA	8647443, 1398113	Standard		NM_001006	NA	Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000509736.1:c.-4+266G>A	chr4.hg19:g.152021132G>A		NA		hg19		0.02	7.882321	TGGxCTC	COVERED																																																																																			NOVEL	RPS3A-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000364962.2	0	46.707657	KEEP	0	1	26	165	5541	GG	1	1	0		+	17	60	564	0	0	39.348286	181	60	6308	507	ENST00000509736.1	0.085859	1
TMEM154	201799	__UNKNOWN__	__UNKNOWN__	4	153565495	153565495	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:153565495A>G	ENST00000304385.3	-	4	624					NM_152680.2	NP_689893.1	Q6P9G4	TM154_HUMAN	transmembrane protein 154	NA		NA				integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)	3	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				AAAACACCTGAAAAGGCAGCT	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	68	71	NA		NA	NA	4		NA											NA				153565495		692	1591	2283	SO:0001627	intron_variant			AK056590	CCDS3779.1	4q31.3	2008-02-05			ENSG00000170006	ENSG00000170006	201799			26489	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152680	NM_152680	NA	Approved	FLJ32028	uc003imw.2	Q6P9G4	OTTHUMG00000161463	ENST00000304385.3:c.392+71T>C	chr4.hg19:g.153565495A>G		NA	Q8WUT7|Q96MQ8	hg19	CCDS3779.1	0.02	2.460999	CTGxAAA	COVERED																																																																																			NOVEL	TMEM154-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365024.1	3	6.011102	KEEP	0	0	0	20	626	AA	0.999863	0.987808	0		-	14	60	480	0	0	40.524551	46	60	1683	105	ENST00000304385.3	0.233333	0.987943
LRAT	9227	__UNKNOWN__	__UNKNOWN__	4	155673176	155673176	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:155673176G>A	ENST00000336356.3	+	0	3834					NM_004744.3	NP_004735.2	O95237	LRAT_HUMAN	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)	NA		NA			phototransduction, visible light (GO:0007603)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)	phosphatidylcholine-retinol O-acyltransferase activity (GO:0047173)|retinoic acid binding (GO:0001972)|retinol binding (GO:0019841)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)	16	all_hematologic(180;0.215)	Renal(120;0.0458)			Vitamin A(DB00162)	atactaggcaggtgttaggga	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF071510	CCDS3789.1	4q32.1	2014-01-28			ENSG00000121207	ENSG00000121207	9227	2.3.1.135		6685	protein-coding gene	gene with protein product		604863			NA	9920938	Standard	NM_004744	XM_006714412	NA	Approved	LCA14	uc003ion.1	O95237	OTTHUMG00000161418	ENST00000336356.3:c.*2888G>A	chr4.hg19:g.155673176G>A		NA	A8K983|Q8N716	hg19	CCDS3789.1	0.02	4.693807	GCAxGTG	COVERED																																																																																			NOVEL	LRAT-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365246.1	1	5.11669	KEEP	0	0	0	17	614	GG	0.999366	0.999366	0		+	15	60	543	0	0	40.46986	131	60	4929	204	ENST00000336356.3	0.10274	1
FAM198B	51313	__UNKNOWN__	__UNKNOWN__	4	159047471	159047471	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:159047471G>A	ENST00000296530.8	-	0	3269				FAM198B_ENST00000585682.1_3'UTR|FAM198B_ENST00000393807.5_3'UTR	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	NA		NA				Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(14)|skin(2)|urinary_tract(1)	26						GCTTAATATTGTCCAAATTTA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3798.1, CCDS34087.1	4q32.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000164125	ENSG00000164125	51313			25312	protein-coding gene	gene with protein product		NA	chromosome 4 open reading frame 18	C4orf18	NA	12975309	Standard	NM_001031700, NM_016613	NM_001031700	NA	Approved	FLJ38155, DKFZp434L142	uc003ipr.4	Q6UWH4	OTTHUMG00000161537	ENST00000296530.8:c.*1088C>T	chr4.hg19:g.159047471G>A		NA	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	hg19	CCDS3798.1	0.02	4.471874	ATTxTCC	COVERED																																																																																			NOVEL	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365230.1	0	14.748136	KEEP	0	0	0	49	1774	GG	1	0.999978	0		-	25	60	927	0	0	79.83852	78	60	2991	189	ENST00000296530.8	0.242718	0.999978
NPY1R	4886	__UNKNOWN__	__UNKNOWN__	4	164246426	164246426	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:164246426T>C	ENST00000296533.2	-	0	1715				NPY1R_ENST00000509586.1_3'UTR	NM_000909.5	NP_000900.1	P25929	NPY1R_HUMAN	neuropeptide Y receptor Y1	NA		NA			adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose metabolic process (GO:0006006)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|regulation of blood pressure (GO:0008217)|regulation of multicellular organism growth (GO:0040014)|sensory perception of pain (GO:0019233)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			breast(1)|cervix(1)|large_intestine(4)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)	30	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TAAACAGATGTCATCCGGGAC	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													73	73	73	NA		NA	NA	4		NA											NA				164246426		2203	4300	6503	SO:0001624	3_prime_UTR_variant				CCDS34089.1	4q31.3-q32	2012-08-08				ENSG00000164128	4886		GPCR / Class A : Neuropeptide receptors : Y	7956	protein-coding gene	gene with protein product		162641		NPYR	NA	8095935	Standard		NM_000909	NA	Approved		uc003iqm.2	P25929		ENST00000296533.2:c.*29A>G	chr4.hg19:g.164246426T>C		NA	B2R6H5	hg19	CCDS34089.1	0.02	29.734486	ATGxCAT	COVERED																																																																																			NOVEL	NPY1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364685.1	8	35.205456	KEEP	0	0	0	117	3739	TT	1	1	0		-	77	60	2855	0	0	220.113557	563	60	20142	961	ENST00000296533.2	0.120312	1
MARCH1	55016	__UNKNOWN__	__UNKNOWN__	4	165118579	165118579	__UNKNOWN__	Intron	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:165118579T>A	ENST00000503008.1	-	2	864				MARCH1_ENST00000514618.1_Intron|MARCH1_ENST00000508725.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase	NA		NA			antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GGTCTTTAATTTTGTTGCCAC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													142	148	146	NA		NA	NA	4		NA											NA				165118579		2203	4300	6503	SO:0001627	intron_variant			AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416	55016		MARCH membrane-associated ring fingers, RING-type (C3HC4) zinc fingers	26077	protein-coding gene	gene with protein product		613331	membrane-associated ring finger (C3HC4) 1		NA	14722266	Standard	NM_017923	NM_017923	NA	Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85765A>T	chr4.hg19:g.165118579T>A		NA	D3DP29|Q9NWR0	hg19	CCDS54814.1	0.02	13.743983	AATxTTG	COVERED																																																																																			NOVEL	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364493.2	4	14.140313	KEEP	0	0	0	47	1437	TT	1	1	0		-	81	60	2870	0	0	244.71648	258	60	9227	444	ENST00000503008.1	0.238938	1
TLL1	7092	__UNKNOWN__	__UNKNOWN__	4	166935542	166935542	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:166935542T>C	ENST00000061240.2	+	8	1564				TLL1_ENST00000507499.1_Intron|TLL1_ENST00000513213.1_Intron	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	NA		NA			cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		AATTCATGAGTTTTCATTTGG	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													155	162	160	NA		NA	NA	4		NA											NA				166935542		2203	4300	6503	SO:0001627	intron_variant			AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295	7092			11843	protein-coding gene	gene with protein product		606742			NA	10516436	Standard		NM_012464	NA	Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.918-46T>C	chr4.hg19:g.166935542T>C		NA	B2RMU2|Q96AN3|Q9NQS4	hg19	CCDS3811.1	0.02	12.68226	GAGxTTT	COVERED																																																																																			NOVEL	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363821.1	3	12.938022	KEEP	0	0	0	43	1343	TT	1	1	0		+	67	60	2537	0	0	221.630894	190	60	6656	356	ENST00000061240.2	0.2607	1
CLCN3	1182	__UNKNOWN__	__UNKNOWN__	4	170616847	170616847	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:170616847G>C	ENST00000347613.4	+	8	1571				CLCN3_ENST00000504131.2_Intron|CLCN3_ENST00000513761.1_Intron|CLCN3_ENST00000360642.3_Intron	NM_173872.3	NP_776297.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	NA		NA			chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		GGAAGAGGTAGGTGAAAAGAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	70	69	NA		NA	NA	4		NA											NA				170616847		2203	4300	6503	SO:0001627	intron_variant			X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572	1182		Ion channels / Chloride channels : Voltage-sensitive	2021	protein-coding gene	gene with protein product		600580	chloride channel 3		NA		Standard		NM_001243374	NA	Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000347613.4:c.1017+4G>C	chr4.hg19:g.170616847G>C		NA	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	hg19	CCDS34100.1	0.02	2.143854	GTAxGTG	COVERED																																																																																			NOVEL	CLCN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363287.1	0	8.427463	KEEP	0	0	0	28	989	GG	0.999997	0.990961	0		+	15	60	488	0	0	41.059332	47	60	1716	114	ENST00000347613.4	0.241935	0.990964
ADAM29	11086	__UNKNOWN__	__UNKNOWN__	4	175899288	175899288	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:175899288A>T	ENST00000359240.3	+	0	3282				ADAM29_ENST00000404450.4_3'UTR|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_3'UTR	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	NA		NA			spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCAATTCCAAAAACTGTATCC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(140;1727 1835 21805 25838 41440)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594	11086		ADAM metallopeptidase domain containing	207	protein-coding gene	gene with protein product	cancer/testis antigen 73	604778	a disintegrin and metalloproteinase domain 29		NA	10644455	Standard		NM_014269	NA	Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.*149A>T	chr4.hg19:g.175899288A>T		NA	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	hg19	CCDS3823.1	0.02	4.478741	CAAxAAC	COVERED																																																																																			NOVEL	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding		2	7.20944	KEEP	0	0	0	24	735	AA	0.999909	0.999909	0		+	34	60	1198	0	0	104.249232	91	60	3320	184	ENST00000359240.3	0.272	0.999999
VEGFC	7424	__UNKNOWN__	__UNKNOWN__	4	177713829	177713829	__UNKNOWN__	5'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:177713829A>C	ENST00000280193.2	-	0	52					NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		ACACCAGAACACCCCGCGATG	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630	7424			12682	protein-coding gene	gene with protein product	vascular endothelial growth factor-related protein	601528			NA	8617204	Standard	NM_005429	NM_005429	NA	Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.-364T>G	chr4.hg19:g.177713829A>C		NA	B2R9Q8	hg19	CCDS43285.1	0.02	0.773044	AACxCCC	COVERED																																																																																			NOVEL	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361991.1	0	11.031142	KEEP	0	10	112	78	1806	AA	1	0.99994	0		-	13	60	175	0	0	7.985163	82	60	2161	241	ENST00000280193.2	0.136842	0.99994
TENM3	55714	__UNKNOWN__	__UNKNOWN__	4	183721257	183721257	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:183721257C>T	ENST00000511685.1	+	28	7976	c.7853C>T	c.(7852-7854)gCg>gTg	p.A2618V	TENM3_ENST00000406950.2_Missense_Mutation_p.A2618V			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2618		NA			camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)				NA						GAGGAGAAGGCGCGCATCCTG	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	12	12	NA		NA	NA	4		NA											NA				183721257		2109	4220	6329	SO:0001583	missense			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336	55714			29944	protein-coding gene	gene with protein product		610083	odz, odd Oz/ten-m homolog 3 (Drosophila)	ODZ3	NA	10331952, 10625539	Standard		NM_001080477	NA	Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7853C>T	chr4.hg19:g.183721257C>T	ENSP00000424226:p.Ala2618Val	NA	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	hg19	CCDS47165.1	0.02	4.130278	AGGxGCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.00	1.805680	0.31961	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86562	-2.14;-2.14	4.16	4.16	0.48862	.	.	.	.	.	T	0.76564	0.4005	N	0.11651	0.15	0.58432	D	0.99999	B	0.11235	0.004	B	0.10450	0.005	T	0.70550	-0.4841	9	0.25751	T	0.34	.	16.9951	0.86365	0.0:1.0:0.0:0.0	.	2618	Q9P273	TEN3_HUMAN	V	2618	ENSP00000424226:A2618V;ENSP00000385276:A2618V	ENSP00000385276:A2618V	A	+	2	0	ODZ3	183958251	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.738000	0.62073	2.312000	0.78011	0.455000	0.32223	GCG	NOVEL	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361734.1	1	10.810169	KEEP	0	0	0	36	1089	CC	0.999999	0.99999	0		+	13	60	427	0	0	31.674328	95	60	3139	172	ENST00000511685.1	0.12037	0.999991
FAT1	2195	__UNKNOWN__	__UNKNOWN__	4	187517005	187517005	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:187517005A>T	ENST00000441802.2	-	26	13210					NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	NA		NA			actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GACAAACAGTAAGTATATGGG	0.458	NA	NA								HNSCC(5;0.00058)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(197;1040 2055 4143 4984 49344)					NA		NA				0													52	53	53	NA		NA	NA	4		NA											NA				187517005		1953	4144	6097	SO:0001627	intron_variant			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857	2195		Cadherins / Cadherin-related	3595	protein-coding gene	gene with protein product	cadherin-related family member 8	600976	FAT tumor suppressor (Drosophila) homolog, FAT tumor suppressor homolog 1 (Drosophila)	FAT	NA	8586420	Standard	NM_005245	XM_005262834	NA	Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13001-25T>A	chr4.hg19:g.187517005A>T		NA		hg19	CCDS47177.1	0.02	4.30323	AGTxAGT	COVERED																																																																																			NOVEL	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360209.3	2	17.151043	KEEP	0	0	0	57	1769	AA	1	1	0		-	81	60	2870	0	0	282.773147	63	60	2226	268	ENST00000441802.2	0.5625	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878577	190878577	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs200267221		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:190878577A>G	ENST00000226798.4	+	6	679	c.457A>G	c.(457-459)Aat>Gat	p.N153D	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	153		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GTTGGCCTCAAATAGCTGCTT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													14	18	17	NA		NA	NA	4		NA											NA				190878577		2154	4261	6415	SO:0001583	missense			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.457A>G	chr4.hg19:g.190878577A>G	ENSP00000226798:p.Asn153Asp	NA	A8K775	hg19	CCDS34121.1	0.02	39.537665	TCAxATA	COVERED	.	.	.	.	.	.	.	.	.	.	.	16.34	3.096595	0.56075	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.50548	1.75;0.74	4.19	2.99	0.34606	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.88105	2.93	0.58432	D	0.999994	P	0.35033	0.481	P	0.49085	0.6	T	0.60182	-0.7313	10	0.38643	T	0.18	-7.9248	8.2154	0.31507	0.9006:0.0:0.0994:0.0	.	153	Q14331	FRG1_HUMAN	D	153;25;90	ENSP00000226798:N153D;ENSP00000435943:N90D	ENSP00000226798:N153D	N	+	1	0	FRG1	191115571	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	9.035000	0.93752	0.593000	0.29745	-0.580000	0.04137	AAT	NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	23	17.53173	KEEP	55	8	280	156	5034	AA	1	1	0		+	48	49	1793	0	0	128.156249	595	54	21385	1129	ENST00000226798.4	0.07465	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878626	190878626	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr4:190878626G>A	ENST00000226798.4	+	6	728	c.506G>A	c.(505-507)aGt>aAt	p.S169N	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	169		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.S169N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GAAGCAAAAAGTAAAACAGCA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	skin(1)											49	46	47	NA		NA	NA	4		NA											NA				190878626		2184	4282	6466	SO:0001583	missense			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.506G>A	chr4.hg19:g.190878626G>A	ENSP00000226798:p.Ser169Asn	NA	A8K775	hg19	CCDS34121.1	0.02	36.038979	AAAxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	.	14.80	2.642895	0.47153	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.48522	1.77;0.81	4.19	2.41	0.29592	Actin cross-linking (1);	0.160510	0.64402	N	0.000002	T	0.36552	0.0971	N	0.17723	0.515	0.45777	D	0.998661	P	0.35982	0.531	P	0.45406	0.479	T	0.07578	-1.0765	10	0.30854	T	0.27	0.1847	7.6816	0.28518	0.219:0.0:0.781:0.0	.	169	Q14331	FRG1_HUMAN	N	169;41;106	ENSP00000226798:S169N;ENSP00000435943:S106N	ENSP00000226798:S169N	S	+	2	0	FRG1	191115620	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.784000	0.38674	0.340000	0.23745	0.454000	0.30748	AGT	NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	29	30.443605	KEEP	34	13	440	255	9175	GG	1	1	0		+	28	60	1011	0	0	64.291146	633	60	24013	1414	ENST00000226798.4	0.04236	1
TPPP	11076	__UNKNOWN__	__UNKNOWN__	5	663182	663182	__UNKNOWN__	3'UTR	SNP	T	T	G	rs11738488		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:663182T>G	ENST00000360578.5	-	0	2816				CEP72_ENST00000514507.1_Intron	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	NA		NA			microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		GATCGGGTGATTCCGATGACT	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368	11076			24164	protein-coding gene	gene with protein product	brain specific protein p25 alpha	608773			NA	10083737, 12093283, 15590652, 17105200	Standard	NM_007030	NM_007030	NA	Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.*2035A>C	chr5.hg19:g.663182T>G		NA		hg19	CCDS3856.1	0.02	3.883763	TGAxTCC	COVERED																																																																																			NOVEL	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253645.3	0	11.095513	KEEP	11	2	66	60	1850	TT	1	1	0		-	5	24	180	0	0	11.660932	100	60	3430	256	ENST00000360578.5	0.047619	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840644	840644	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs200038670		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:840644G>C	ENST00000283441.8	-	5	1133	c.750C>G	c.(748-750)caC>caG	p.H250Q	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.H250Q|ZDHHC11_ENST00000511539.1_Missense_Mutation_p.H37Q	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	250		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.H250Q(2)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCTGGCCCAGGTGCACCAAGC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	lung(2)											137	146	143	NA		NA	NA	5		NA											NA				840644		2203	4300	6503	SO:0001583	missense			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.750C>G	chr5.hg19:g.840644G>C	ENSP00000283441:p.His250Gln	NA	Q6UWR9	hg19	CCDS3857.1	0.02	16.73925	CAGxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	g	5.277	0.236438	0.10023	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193;ENST00000511539	T;T;T;T	0.43688	1.86;1.86;0.99;0.94	2.74	-0.394	0.12434	.	642.914000	0.00961	U	0.003101	T	0.25494	0.0620	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.15870	0.014;0.001	T	0.27606	-1.0069	10	0.29301	T	0.29	-6.9343	13.336	0.60518	0.0:0.2548:0.7452:0.0	.	250;37	Q9H8X9;Q6UWR9	ZDH11_HUMAN;.	Q	250;250;25;37	ENSP00000397719:H250Q;ENSP00000283441:H250Q;ENSP00000426873:H25Q;ENSP00000427067:H37Q	ENSP00000283441:H250Q	H	-	3	2	ZDHHC11	893644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.474000	0.06607	-0.110000	0.12022	-2.048000	0.00412	CAC	NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	10	2.585692	KEEP	5	5	167	67	2304	GG	1	1	0		-	22	60	809	0	0	55.403049	340	60	11881	539	ENST00000283441.8	0.060773	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840704	840704	__UNKNOWN__	Silent	SNP	G	G	A	rs139300052	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:840704G>A	ENST00000283441.8	-	5	1073	c.690C>T	c.(688-690)acC>acT	p.T230T	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Silent_p.T230T|ZDHHC11_ENST00000511539.1_Silent_p.T17T	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	230		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CGACTATCAGGGTCTGCACCT	0.567	NA	NA											G|||	34	0.00678914	0.0083	0	5008	,	,	NA	28789	0.0208	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													237	270	258	NA		NA	NA	5		NA											NA				840704		2203	4300	6503	SO:0001819	synonymous_variant			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.690C>T	chr5.hg19:g.840704G>A		NA	Q6UWR9	hg19	CCDS3857.1	0.02	18.718013	CAGxGTC	COVERED																																																																																			NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	5	21.638069	KEEP	8	2	57	92	3170	GG	1	1	0		-	15	40	567	0	1	35.86226	399	60	13978	665	ENST00000283441.8	0.036232	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840712	840712	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs148433225		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:840712C>G	ENST00000283441.8	-	5	1065	c.682G>C	c.(682-684)Gtg>Ctg	p.V228L	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.V228L|ZDHHC11_ENST00000511539.1_Missense_Mutation_p.V15L	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	228		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			AGGGTCTGCACCTGCACCGGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													239	274	263	NA		NA	NA	5		NA											NA				840712		2203	4300	6503	SO:0001583	missense			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.682G>C	chr5.hg19:g.840712C>G	ENSP00000283441:p.Val228Leu	NA	Q6UWR9	hg19	CCDS3857.1	0.02	17.918434	GCAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	c	10.57	1.387420	0.25031	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193;ENST00000511539	T;T;T;T	0.55234	1.63;1.63;0.53;0.67	2.74	-0.481	0.12082	.	.	.	.	.	T	0.45196	0.1330	L	0.35487	1.065	0.09310	N	1	P;P	0.43352	0.804;0.75	P;B	0.52031	0.688;0.373	T	0.35649	-0.9780	9	0.07175	T	0.84	-12.4675	8.1063	0.30887	0.0:0.7384:0.0:0.2616	.	228;15	Q9H8X9;Q6UWR9	ZDH11_HUMAN;.	L	228;228;3;15	ENSP00000397719:V228L;ENSP00000283441:V228L;ENSP00000426873:V3L;ENSP00000427067:V15L	ENSP00000283441:V228L	V	-	1	0	ZDHHC11	893712	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	-0.010000	0.12743	-0.121000	0.11787	0.400000	0.26472	GTG	NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	4	20.336701	KEEP	8	2	73	93	3195	CC	1	1	0		-	16	40	605	0	0	38.728342	398	60	14369	662	ENST00000283441.8	0.038647	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840785	840785	__UNKNOWN__	Intron	SNP	C	C	A	rs200106329		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:840785C>A	ENST00000283441.8	-	5	1012				ZDHHC11_ENST00000503758.2_Intron|ZDHHC11_ENST00000424784.2_Intron|ZDHHC11_ENST00000511539.1_Intron	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			CAAGGGAGAGCCACTGTGTCC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								A		50,4356	812.5+/-416.1	0,50,2153	149	178	168	NA		0.6	0	5	dbSNP_132	168	4,8596	817.5+/-406.9	0,4,4296	no	intron	ZDHHC11	NM_024786.2		0,54,6449	AA,AC,CC	NA	0.0465,1.1348,0.4152			840785	54,12952	2203	4300	6503	SO:0001627	intron_variant			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.629-20G>T	chr5.hg19:g.840785C>A		NA	Q6UWR9	hg19	CCDS3857.1	0.02	8.566882	GAGxCAC	COVERED																																																																																			NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	3	8.494496	KEEP	5	2	65	51	1770	CC	1	1	0		-	18	60	633	0	0	43.90688	229	60	8179	400	ENST00000283441.8	0.072874	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840833	840833	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:840833C>G	ENST00000283441.8	-	5	1012				ZDHHC11_ENST00000503758.2_Intron|ZDHHC11_ENST00000424784.2_Intron|ZDHHC11_ENST00000511539.1_Intron	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GTGGACGTCACAGACCAGAGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.629-68G>C	chr5.hg19:g.840833C>G		NA	Q6UWR9	hg19	CCDS3857.1	0.02	6.803391	TCAxAGA	COVERED																																																																																			NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	2	2.34344	KEEP	2	1	35	20	714	CC	0.999869	0.999869	0		-	14	60	517	0	0	38.177061	136	60	5071	186	ENST00000283441.8	0.093333	1
BRD9	65980	__UNKNOWN__	__UNKNOWN__	5	878460	878460	__UNKNOWN__	Intron	SNP	C	C	T	rs112921031	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:878460C>T	ENST00000467963.1	-	11	1438				BRD9_ENST00000323510.4_Intron|BRD9_ENST00000388890.4_Intron|BRD9_ENST00000483173.1_Intron|BRD9_ENST00000435709.2_Intron	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	NA		NA			chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			TCCCCGGGGCCGACACTTGCC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	85	90	NA		NA	NA	5		NA											NA				878460		2203	4300	6503	SO:0001627	intron_variant			AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310	65980			25818	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_023924	NM_023924	NA	Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1271+9G>A	chr5.hg19:g.878460C>T		NA	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	hg19	CCDS34127.2	0.02	9.195961	GGCxGAC	COVERED																																																																																			NOVEL	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354113.1	1	10.94433	KEEP	5	9	269	131	4478	CC	1	1	0		-	11	60	408	0	0	27.393519	196	60	6782	536	ENST00000467963.1	0.05314	1
BRD9	65980	__UNKNOWN__	__UNKNOWN__	5	878478	878478	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:878478A>G	ENST00000467963.1	-	11	1429	c.1263T>C	c.(1261-1263)tgT>tgC	p.C421C	BRD9_ENST00000323510.4_Silent_p.C325C|BRD9_ENST00000388890.4_Silent_p.C305C|BRD9_ENST00000483173.1_Silent_p.C368C|BRD9_ENST00000494422.1_5'UTR|BRD9_ENST00000435709.2_3'UTR	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	421		NA			chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			GCCTCAGCGCACACTGCACGC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													122	101	108	NA		NA	NA	5		NA											NA				878478		2203	4300	6503	SO:0001819	synonymous_variant			AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310	65980			25818	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_023924	NM_023924	NA	Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1263T>C	chr5.hg19:g.878478A>G		NA	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	hg19	CCDS34127.2	0.02	8.721272	CGCxCAC	COVERED																																																																																			NOVEL	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354113.1	1	41.218033	KEEP	5	0	0	137	4216	AA	1	1	0		-	15	60	533	0	0	37.164256	190	60	6856	537	ENST00000467963.1	0.073171	1
TRIP13	9319	__UNKNOWN__	__UNKNOWN__	5	893897	893897	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:893897G>A	ENST00000166345.3	+	1	448					NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	NA		NA			double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			CAGAATAGCTGTTGACTGGGT	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539	9319		ATPases / AAA-type	12307	protein-coding gene	gene with protein product	thyroid receptor interacting protein 13	604507			NA	7776974	Standard	NM_004237	NM_004237	NA	Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.92+692G>A	chr5.hg19:g.893897G>A		NA	C9K0T3|D3DTC0|O15324	hg19	CCDS3858.1	0.02	-0.245648	GCTxTTG	COVERED																																																																																			NOVEL	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206721.2	1	7.523921	KEEP	0	0	0	25	884	GG	0.999931	0.641303	0		+	12	60	426	0	0	40.02054	16	60	606	66	ENST00000166345.3	0.428571	0.641347
SLC12A7	10723	__UNKNOWN__	__UNKNOWN__	5	1051462	1051462	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:1051462G>A	ENST00000264930.5	-	0	4308					NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	NA		NA			cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GATGGCACGTGTGAGCCAGCT	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504	10723		Solute carriers	10915	protein-coding gene	gene with protein product		604879			NA	10347194	Standard	NM_006598	NM_006598	NA	Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.*1013C>T	chr5.hg19:g.1051462G>A		NA	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	hg19	CCDS34129.1	0.02	1.918163	CGTxTGA	COVERED																																																																																			NOVEL	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366446.2	0	10.818208	KEEP	0	0	0	36	1210	GG	0.999999	0.993702	0		-	4	60	141	0	0	9.485989	61	60	2222	118	ENST00000264930.5	0.061538	0.993703
ADAMTS16	170690	__UNKNOWN__	__UNKNOWN__	5	5303429	5303429	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:5303429T>G	ENST00000274181.7	+	19	2976	c.2838T>G	c.(2836-2838)ggT>ggG	p.G946G		NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	946	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.	NA			branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						GTGGCGGGGGTGCCCAGAGCC	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													14	18	17	NA		NA	NA	5		NA											NA				5303429		2040	4175	6215	SO:0001819	synonymous_variant			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536	170690		ADAM metallopeptidases with thrombospondin type 1 motif	17108	protein-coding gene	gene with protein product		607510	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16		NA	11867212	Standard	NM_139056	NM_139056	NA	Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.2838T>G	chr5.hg19:g.5303429T>G		NA	C6G490|Q8IVE2	hg19	CCDS43299.1	0.02	-0.277116	GGGxGCC	COVERED																																																																																			NOVEL	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365657.1	0	4.250819	KEEP	0	3	15	20	411	TT	0.999892	0.780976	0		+	6	60	101	0	0	6.628881	23	60	579	89	ENST00000274181.7	0.206897	0.78106
SEMA5A	9037	__UNKNOWN__	__UNKNOWN__	5	9038266	9038266	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:9038266A>G	ENST00000382496.5	-	0	8633				CTD-2215L10.1_ENST00000506519.1_RNA	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	NA		NA			axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GGCAAGGCCAAGGCCATCTGT	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902	9037		Semaphorins	10736	protein-coding gene	gene with protein product		609297		SEMAF	NA	8817451, 9464278	Standard		NM_003966	NA	Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.*4743T>C	chr5.hg19:g.9038266A>G		NA	D3DTC6|O60408|Q1RLL9	hg19	CCDS3875.1	0.02	2.285505	CCAxGGC	COVERED																																																																																			NOVEL	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206989.2	3	6.320147	KEEP	0	0	0	21	703	AA	0.999869	0.999088	0		-	7	60	273	0	0	20.332281	73	60	2725	131	ENST00000382496.5	0.0875	0.999218
MARCH11	441061	__UNKNOWN__	__UNKNOWN__	5	16090975	16090975	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:16090975A>G	ENST00000332432.8	-	3	1086					NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	NA		NA			protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(14)|urinary_tract(1)	20						ACAGTGTGTTAACGTTGAAGG	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													79	75	76	NA		NA	NA	5		NA											NA				16090975		1980	4160	6140	SO:0001627	intron_variant			BC150513	CCDS47192.1	5p15.1	2013-01-09			ENSG00000183654	ENSG00000183654	441061		RING-type (C3HC4) zinc fingers, MARCH membrane-associated ring fingers	33609	protein-coding gene	gene with protein product		613338			NA	17604280	Standard	NM_001102562	NM_001102562	NA	Approved	MARCH-XI	uc003jfo.2	A6NNE9	OTTHUMG00000161789	ENST00000332432.8:c.886+22T>C	chr5.hg19:g.16090975A>G		NA	A7E2S6	hg19	CCDS47192.1	0.02	2.28553	GTTxACG	COVERED																																																																																			NOVEL	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366096.2	1	3.911885	KEEP	0	0	0	13	412	AA	0.994391	0.993613	0		-	10	60	391	0	0	30.78232	70	60	2511	105	ENST00000332432.8	0.125	0.999218
CDH6	1004	__UNKNOWN__	__UNKNOWN__	5	31326381	31326381	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:31326381C>T	ENST00000265071.2	+	0	5604					NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	NA		NA			adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TATGTTTTTGCCCTCTATTCA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361	1004		Cadherins / Major cadherins	1765	protein-coding gene	gene with protein product	K-Cadherin	603007			NA	7743525, 10191097	Standard	NM_004932	NM_004932	NA	Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.*2966C>T	chr5.hg19:g.31326381C>T		NA	A8K5H5|Q9BWS0	hg19	CCDS3894.1	0.02	4.389313	TTGxCCT	COVERED																																																																																			NOVEL	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207355.2	1	8.080388	KEEP	0	0	0	27	918	CC	0.999988	0.999987	0		+	8	60	306	0	0	21.543136	116	60	4148	189	ENST00000265071.2	0.064516	0.999999
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	32108581	32108581	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:32108581C>T	ENST00000438447.1	+	0	9248				PDZD2_ENST00000513490.1_3'UTR|PDZD2_ENST00000282493.3_3'UTR|CTD-2152M20.2_ENST00000503441.1_RNA			O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						TTGCTTCCTTCTTGCCAGCTC	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.*340C>T	chr5.hg19:g.32108581C>T		NA	Q9BXD4	hg19	CCDS34137.1	0.02	4.200359	CTTxTTG	COVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	3	7.523428	KEEP	0	0	0	25	843	CC	0.999931	0.999931	0		+	7	60	244	0	0	15.837104	127	60	4809	186	ENST00000438447.1	0.052239	1
ZFR	51663	__UNKNOWN__	__UNKNOWN__	5	32397358	32397358	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:32397358G>A	ENST00000265069.8	-	10	1902	c.1800C>T	c.(1798-1800)caC>caT	p.H600H		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	600		NA			multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		GCCCTTTTAAGTGCATCTCCT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													151	152	152	NA		NA	NA	5		NA											NA				32397358		2202	4300	6502	SO:0001819	synonymous_variant			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097	51663			17277	protein-coding gene	gene with protein product		615635			NA	11574164, 24482476	Standard		NM_016107	NA	Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1800C>T	chr5.hg19:g.32397358G>A		NA	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	hg19	CCDS34139.1	0.02	11.65703	TAAxTGC	COVERED																																																																																			NOVEL	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366586.1	4	24.669215	KEEP	0	0	0	82	2963	GG	1	1	0		-	60	60	2239	0	0	191.533748	200	60	7679	461	ENST00000265069.8	0.230769	1
ZFR	51663	__UNKNOWN__	__UNKNOWN__	5	32400236	32400236	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:32400236G>T	ENST00000265069.8	-	9	1691	c.1589C>A	c.(1588-1590)cCt>cAt	p.P530H		NM_016107.3	NP_057191.2	Q96KR1	ZFR_HUMAN	zinc finger RNA binding protein	530		NA			multicellular organismal development (GO:0007275)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|upper_aerodigestive_tract(2)	32				STAD - Stomach adenocarcinoma(35;0.19)		AGAAGTGACAGGAGTACTTTT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													152	136	142	NA		NA	NA	5		NA											NA				32400236		2203	4300	6503	SO:0001583	missense			AF100742	CCDS34139.1	5p15.2	2014-03-03			ENSG00000056097	ENSG00000056097	51663			17277	protein-coding gene	gene with protein product		615635			NA	11574164, 24482476	Standard		NM_016107	NA	Approved	ZFR1, SPG71	uc003jhr.1	Q96KR1	OTTHUMG00000161979	ENST00000265069.8:c.1589C>A	chr5.hg19:g.32400236G>T	ENSP00000265069:p.Pro530His	NA	B2RNR5|Q05C08|Q3B7X5|Q6P5A3|Q86UA0|Q9H6V4|Q9NTI1|Q9Y687	hg19	CCDS34139.1	0.02	7.220299	ACAxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.19	3.325256	0.60743	.	.	ENSG00000056097	ENST00000265069;ENST00000382126	T	0.05199	3.48	6.16	6.16	0.99307	.	0.141997	0.64402	D	0.000004	T	0.11879	0.0289	L	0.52573	1.65	0.53005	D	0.999969	P	0.40000	0.698	B	0.40329	0.326	T	0.00406	-1.1759	10	0.72032	D	0.01	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	530	Q96KR1	ZFR_HUMAN	H	530;508	ENSP00000265069:P530H	ENSP00000265069:P530H	P	-	2	0	ZFR	32435993	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.122000	0.77169	2.937000	0.99478	0.650000	0.86243	CCT	NOVEL	ZFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366586.1	2	14.444785	KEEP	0	0	0	48	1670	GG	1	1	0		-	12	60	459	0	0	33.361013	141	60	5142	251	ENST00000265069.8	0.078431	1
SUB1	10923	__UNKNOWN__	__UNKNOWN__	5	32602521	32602521	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:32602521G>T	ENST00000265073.4	+	0	1843					NM_006713.3	NP_006704.3	P53999	TCP4_HUMAN	SUB1 homolog (S. cerevisiae)	NA		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|single-stranded DNA binding (GO:0003697)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						AAAAAGGAAAGTTTTAAAGAC	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X79805	CCDS3897.1	5p13.3	2008-02-05			ENSG00000113387	ENSG00000113387	10923			19985	protein-coding gene	gene with protein product		600503			NA	8062392, 8062391	Standard	NM_006713	NM_006713	NA	Approved	PC4, p15, p14	uc003jhs.2	P53999	OTTHUMG00000131071	ENST00000265073.4:c.*1331G>T	chr5.hg19:g.32602521G>T		NA	Q96L29	hg19	CCDS3897.1	0.02	10.424314	AAAxTTT	COVERED																																																																																			NOVEL	SUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253730.1	5	28.292027	KEEP	0	0	0	94	3376	GG	1	1	0		+	11	60	404	0	0	25.797488	253	60	9678	465	ENST00000265073.4	0.041667	1
DNAJC21	134218	__UNKNOWN__	__UNKNOWN__	5	34956223	34956223	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:34956223G>A	ENST00000382021.2	+	0	3362				DNAJC21_ENST00000303525.7_3'UTR	NM_194283.3	NP_919259.3	Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	NA		NA			protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			TGTGCTTTCTGTACAATGAAG	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724	134218		Heat shock proteins / DNAJ (HSP40)	27030	protein-coding gene	gene with protein product	JJJ1 DnaJ domain protein homolog (S. cerevisiae)	NA			NA	15067379	Standard	NM_194283	XM_005248250	NA	Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000382021.2:c.*1404G>A	chr5.hg19:g.34956223G>A		NA	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	hg19	CCDS3907.2	0.02	2.086339	TCTxTAC	COVERED																																																																																			NOVEL	DNAJC21-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157338.1	8	12.639007	KEEP	0	0	0	42	1438	GG	1	0.999218	0		+	6	60	218	0	0	15.446488	73	60	2610	149	ENST00000382021.2	0.075949	0.999218
PRLR	5618	__UNKNOWN__	__UNKNOWN__	5	35089700	35089700	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:35089700G>A	ENST00000382002.5	-	3	449	c.23C>T	c.(22-24)gCa>gTa	p.A8V	PRLR_ENST00000397391.3_5'UTR|PRLR_ENST00000342362.5_Missense_Mutation_p.A8V|PRLR_ENST00000310101.5_Missense_Mutation_p.A8V|PRLR_ENST00000513753.1_Missense_Mutation_p.A8V|PRLR_ENST00000511486.1_Missense_Mutation_p.A8V|PRLR_ENST00000542609.1_Missense_Mutation_p.A8V|PRLR_ENST00000348262.3_Missense_Mutation_p.A8V|PRLR_ENST00000231423.3_Missense_Mutation_p.A8V	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	8		NA			activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	GAAAACGGTTGCAGATGCCAC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													139	126	130	NA		NA	NA	5		NA											NA				35089700		2203	4300	6503	SO:0001583	missense				CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494	5618			9446	protein-coding gene	gene with protein product		176761			NA		Standard		NM_001204315	NA	Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.23C>T	chr5.hg19:g.35089700G>A	ENSP00000371432:p.Ala8Val	NA	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	hg19	CCDS3909.1	0.02	11.176179	GTTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	8.279	0.815074	0.16607	.	.	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000348262;ENST00000542609;ENST00000342362;ENST00000382002;ENST00000511486;ENST00000310101;ENST00000514206;ENST00000509839;ENST00000503330;ENST00000504500;ENST00000515839	T;T;T;T;D;T;D;T;T;T;T;T;T	0.88586	0.01;0.01;0.01;0.01;-2.4;0.01;-2.4;0.01;0.01;0.01;0.01;0.01;0.01	5.96	3.18	0.36537	.	0.888434	0.10011	N	0.727144	D	0.83746	0.5321	L	0.47190	1.495	0.09310	N	1	B;B;P;P;P	0.39424	0.278;0.228;0.673;0.673;0.673	B;B;B;B;B	0.33254	0.057;0.121;0.16;0.115;0.16	T	0.70561	-0.4838	10	0.52906	T	0.07	-0.6544	9.635	0.39802	0.0724:0.2662:0.6614:0.0	.	8;8;8;8;8	P16471;P16471-2;P16471-7;P16471-6;P16471-4	PRLR_HUMAN;.;.;.;.	V	8	ENSP00000231423:A8V;ENSP00000424841:A8V;ENSP00000311613:A8V;ENSP00000441813:A8V;ENSP00000339213:A8V;ENSP00000371432:A8V;ENSP00000422556:A8V;ENSP00000309008:A8V;ENSP00000423493:A8V;ENSP00000427060:A8V;ENSP00000422385:A8V;ENSP00000422867:A8V;ENSP00000421864:A8V	ENSP00000231423:A8V	A	-	2	0	PRLR	35125457	0.011000	0.17503	0.001000	0.08648	0.003000	0.03518	0.960000	0.29253	0.393000	0.25203	0.655000	0.94253	GCA	NOVEL	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207575.2	3	36.392703	KEEP	0	0	0	121	4301	GG	1	1	0		-	10	60	337	0	0	18.958406	326	60	12313	531	ENST00000382002.5	0.029762	1
NIPBL	25836	__UNKNOWN__	__UNKNOWN__	5	37022273	37022273	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:37022273T>C	ENST00000282516.8	+	28	5926				NIPBL_ENST00000448238.2_Intron	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	NA		NA			brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AAATGATTCTTTCTTTTCTAC	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	108	111	NA		NA	NA	5		NA											NA				37022273		2203	4300	6503	SO:0001627	intron_variant			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190	25836			28862	protein-coding gene	gene with protein product	sister chromatid cohesion 2 homolog (yeast)	608667			NA	15146186, 15146185	Standard	NM_015384	NM_133433	NA	Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.5427+22T>C	chr5.hg19:g.37022273T>C		NA	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	hg19	CCDS3920.1	0.02	7.353165	TCTxTCT	COVERED																																																																																			NOVEL	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207582.1	1	13.540817	KEEP	0	0	0	45	1433	TT	1	1	0		+	40	60	1522	0	0	130.774133	132	60	4816	247	ENST00000282516.8	0.232558	1
OSMR	9180	__UNKNOWN__	__UNKNOWN__	5	38925333	38925333	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs63750567		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:38925333T>C	ENST00000274276.3	+	15	2474	c.2072T>C	c.(2071-2073)aTt>aCt	p.I691T		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	691	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA	I -> T (in PLCA1). {ECO:0000269|PubMed:18179886}.		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					AAATACAAAATTGACAACCCG	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0			GRCh37	CM080473	OSMR	M	rs63750567						104	98	100	NA		NA	NA	5		NA											NA				38925333		2203	4300	6503	SO:0001583	missense			U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623	9180		Fibronectin type III domain containing	8507	protein-coding gene	gene with protein product		601743			NA	8999038	Standard	NM_003999	NM_001168355	NA	Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.2072T>C	chr5.hg19:g.38925333T>C	ENSP00000274276:p.Ile691Thr	NA	Q6P4E8|Q96QJ6	hg19	CCDS3928.1	0.02	9.879494	AAAxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	T	12.69	2.013511	0.35511	.	.	ENSG00000145623	ENST00000274276	T	0.53640	0.61	5.76	5.76	0.90799	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.365437	0.32041	N	0.006670	T	0.61438	0.2347	L	0.56769	1.78	0.09310	A	2.37732e-07	D	0.69078	0.997	P	0.61874	0.895	T	0.69300	-0.5181	9	0.49607	T	0.09	.	13.4528	0.61180	0.0:0.0:0.0:1.0	rs63750567	691	Q99650	OSMR_HUMAN	T	691	ENSP00000274276:I691T	ENSP00000274276:I691T	I	+	2	0	OSMR	38961090	0.923000	0.31300	0.019000	0.16419	0.101000	0.19017	4.051000	0.57412	2.206000	0.71126	0.533000	0.62120	ATT	NOVEL	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207609.2	2	26.169044	KEEP	0	0	0	87	2771	TT	1	1	0		+	56	60	2116	0	0	182.168612	180	60	6527	408	ENST00000274276.3	0.237288	1
MROH2B	133558	__UNKNOWN__	__UNKNOWN__	5	41018980	41018980	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:41018980C>T	ENST00000399564.4	-	25	3028				MROH2B_ENST00000506092.2_Intron	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	NA		NA									NA						CTCACTAGTGCATACTTGAAT	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													125	122	123	NA		NA	NA	5		NA											NA				41018980		2047	4195	6242	SO:0001627	intron_variant				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495	133558		maestro heat-like repeat containing	26857	protein-coding gene	gene with protein product		NA	HEAT repeat family member 7B2	HEATR7B2	NA	12477932	Standard	NM_173489	NM_173489	NA	Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.2577+4G>A	chr5.hg19:g.41018980C>T		NA	Q68DM1|Q7Z4U4|Q8N7X3	hg19	CCDS47202.1	0.02	3.730943	GTGxATA	COVERED																																																																																			NOVEL	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367558.2	1	3.84644	KEEP	0	1	29	23	807	CC	0.999909	0.999909	0		-	9	60	310	0	0	20.742691	133	60	4982	194	ENST00000399564.4	0.06338	1
C6	729	__UNKNOWN__	__UNKNOWN__	5	41201800	41201800	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:41201800T>C	ENST00000263413.3	-	3	424	c.160A>G	c.(160-162)Aag>Gag	p.K54E	C6_ENST00000337836.5_Missense_Mutation_p.K54E	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	54	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.	NA			complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TGGTAGTACTTATCTACTACT	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													93	94	94	NA		NA	NA	5		NA											NA				41201800		2203	4300	6503	SO:0001583	missense			J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537	729		Complement system	1339	protein-coding gene	gene with protein product		217050			NA		Standard		NM_001115131	NA	Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.160A>G	chr5.hg19:g.41201800T>C	ENSP00000263413:p.Lys54Glu	NA		hg19	CCDS3936.1	0.02	2.241848	ACTxATC	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.695	1.153023	0.21371	.	.	ENSG00000039537	ENST00000337836;ENST00000263413;ENST00000417809	T;T;T	0.60299	0.2;0.2;0.2	5.92	-11.8	0.00035	.	0.775970	0.12471	N	0.465980	T	0.21387	0.0515	N	0.04320	-0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38156	-0.9674	10	0.05351	T	0.99	0.8553	12.6401	0.56705	0.0:0.3621:0.1073:0.5306	.	54	P13671	CO6_HUMAN	E	54	ENSP00000338861:K54E;ENSP00000263413:K54E;ENSP00000396565:K54E	ENSP00000263413:K54E	K	-	1	0	C6	41237557	0.143000	0.22626	0.000000	0.03702	0.835000	0.47333	-0.255000	0.08769	-1.956000	0.01022	-0.316000	0.08728	AAG	NOVEL	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211592.1	2	9.9295	KEEP	0	0	0	33	1020	TT	0.999998	0.99962	0		-	15	60	544	0	0	44.370826	70	60	2491	142	ENST00000263413.3	0.176471	0.999622
MIER3	166968	__UNKNOWN__	__UNKNOWN__	5	56255225	56255225	__UNKNOWN__	5'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:56255225C>A	ENST00000546593.1	-	0	165							Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		gatgccagtgcctctgttctc	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545	166968			26678	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152622	XM_005248448	NA	Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000546593.1:c.-79G>T	chr5.hg19:g.56255225C>A		NA	B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	hg19		0.02	16.103549	GTGxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	3.453	-0.111530	0.06881	.	.	ENSG00000155545	ENST00000440000	.	.	.	2.7	-0.921	0.10472	.	.	.	.	.	T	0.34424	0.0897	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.37957	-0.9683	5	0.87932	D	0	.	3.0724	0.06235	0.4359:0.2632:0.3009:0.0	.	.	.	.	S	7	.	ENSP00000407169:A7S	A	-	1	0	MIER3	56290982	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.238000	0.08977	-0.210000	0.10140	-0.976000	0.02587	GCA	NOVEL	MIER3-009	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000268445.2	1	30.092594	KEEP	0	0	0	100	3552	CC	1	1	0		-	104	60	3746	0	0	326.184132	285	60	10569	609	ENST00000546593.1	0.267352	1
SLC30A5	64924	__UNKNOWN__	__UNKNOWN__	5	68412384	68412384	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:68412384G>A	ENST00000396591.3	+	10	1846	c.1236G>A	c.(1234-1236)gaG>gaA	p.E412E	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	412		NA			cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		AAATTCTTGAGGAGAGTGACT	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	65	65	NA		NA	NA	5		NA											NA				68412384		2203	4300	6503	SO:0001819	synonymous_variant			AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740	64924		Solute carriers	19089	protein-coding gene	gene with protein product		607819			NA	11937503, 11904301	Standard		NM_022902	NA	Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1236G>A	chr5.hg19:g.68412384G>A		NA	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	hg19	CCDS3996.1	0.02	2.267956	TGAxGAG	COVERED																																																																																			NOVEL	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254017.2	1	13.544099	KEEP	0	0	0	45	1595	GG	1	0.999407	0		+	53	60	2000	0	0	202.149949	29	60	1077	163	ENST00000396591.3	0.646341	0.999407
MRPS36	92259	__UNKNOWN__	__UNKNOWN__	5	68525062	68525062	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:68525062C>T	ENST00000256441.4	+	0	392				MRPS36_ENST00000512880.1_3'UTR|MRPS36_ENST00000602380.1_3'UTR	NM_033281.5	NP_150597.1	P82909	RT36_HUMAN	mitochondrial ribosomal protein S36	NA		NA			translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(1)|urinary_tract(1)	7		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.04e-56)|Epithelial(20;8.79e-53)|all cancers(19;2.01e-48)|Lung(70;0.0176)		ACCATGGTGGCTGCTGTTTGT	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													108	100	103	NA		NA	NA	5		NA											NA				68525062		2203	4300	6503	SO:0001624	3_prime_UTR_variant				CCDS34174.1	5q13.2	2013-09-20			ENSG00000134056	ENSG00000134056	92259		Mitochondrial ribosomal proteins / small subunits	16631	protein-coding gene	gene with protein product		611996			NA	11279123	Standard	NM_033281	NM_033281	NA	Approved	DC47, MRP-S36	uc003jvq.3	P82909	OTTHUMG00000162443	ENST00000256441.4:c.*10C>T	chr5.hg19:g.68525062C>T		NA	Q9H2H4	hg19	CCDS34174.1	0.02	4.211138	TGGxTGC	COVERED																																																																																			NOVEL	MRPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368940.1	2	16.253196	KEEP	0	0	0	54	1966	CC	1	0.999993	0		+	14	60	488	0	0	37.275258	96	60	3711	221	ENST00000256441.4	0.127273	0.999993
MARVELD2	153562	__UNKNOWN__	__UNKNOWN__	5	68715166	68715166	__UNKNOWN__	Intron	SNP	A	A	T	rs576222665		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:68715166A>T	ENST00000325631.5	+	2	59					NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	NA		NA			cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		TAAGTAACTAATCATAAGTGA	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													25	26	26	NA		NA	NA	5		NA											NA				68715166		2202	4300	6502	SO:0001627	intron_variant			AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939	153562			26401	protein-coding gene	gene with protein product	tricellulin	610572	MARVEL (membrane-associating) domain containing 2, deafness, autosomal recessive 49	MRVLDC2, DFNB49	NA	17186462	Standard	NM_144724	NM_001038603	NA	Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.-15-32A>T	chr5.hg19:g.68715166A>T		NA	A1BQX0|A1BQX1|A8KA97|Q96NM9	hg19	CCDS34175.1	0.02	11.604656	CTAxTCA	COVERED																																																																																			NOVEL	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369583.1	2	15.647273	KEEP	0	0	0	52	1683	AA	1	1	0		+	99	60	3621	0	0	333.282472	166	60	5994	379	ENST00000325631.5	0.373585	1
MAP1B	4131	__UNKNOWN__	__UNKNOWN__	5	71492603	71492603	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:71492603G>A	ENST00000296755.7	+	5	3719	c.3421G>A	c.(3421-3423)Gac>Aac	p.D1141N		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1141		NA			axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		TACCCCTCGAGACGTGATGAG	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(17;367 822 11631 31730 47712)					NA		NA				0													60	56	57	NA		NA	NA	5		NA											NA				71492603		2203	4300	6503	SO:0001583	missense			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711	4131			6836	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 102	157129			NA	1881920	Standard	NM_005909	NM_005909	NA	Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.3421G>A	chr5.hg19:g.71492603G>A	ENSP00000296755:p.Asp1141Asn	NA	A2BDK5	hg19	CCDS4012.1	0.02	11.569864	CGAxACG	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.47	3.398408	0.62177	.	.	ENSG00000131711	ENST00000296755	T	0.04551	3.6	5.79	5.79	0.91817	.	0.000000	0.64402	D	0.000002	T	0.12135	0.0295	L	0.29908	0.895	0.80722	D	1	D;D	0.67145	0.996;0.992	P;P	0.58013	0.831;0.831	T	0.01048	-1.1469	10	0.72032	D	0.01	-27.6254	20.032	0.97543	0.0:0.0:1.0:0.0	.	1015;1141	A2BDK6;P46821	.;MAP1B_HUMAN	N	1141	ENSP00000296755:D1141N	ENSP00000296755:D1141N	D	+	1	0	MAP1B	71528359	1.000000	0.71417	0.105000	0.21289	0.955000	0.61496	9.281000	0.95811	2.743000	0.94032	0.655000	0.94253	GAC	NOVEL	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000218561.6	4	32.804994	KEEP	0	0	0	109	3867	GG	1	1	0		+	83	60	2928	0	0	260.194998	186	60	6969	473	ENST00000296755.7	0.30855	1
MEF2C-AS1	101929423	__UNKNOWN__	__UNKNOWN__	5	88215090	88215090	__UNKNOWN__	RNA	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:88215090T>G	ENST00000514011.1	+	0	208				MEF2C-AS1_ENST00000514794.1_RNA|MEF2C-AS1_ENST00000513704.1_RNA|MEF2C-AS1_ENST00000508718.1_RNA|MEF2C-AS1_ENST00000514092.1_RNA|MEF2C-AS1_ENST00000512585.1_RNA|MEF2C-AS1_ENST00000506665.1_RNA|MEF2C-AS1_ENST00000514158.1_RNA|MEF2C-AS1_ENST00000509179.1_RNA|MEF2C-AS1_ENST00000511100.1_RNA	NR_104031.1				MEF2C antisense RNA 1	NA		NA									NA						GTAAGCAAAATTAAGGAATGA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					CD702404		5q14.3	2014-01-06			ENSG00000248309	ENSG00000248309	101929423		Long non-coding RNAs	48908	non-coding RNA	RNA, long non-coding		NA			NA	23801869	Standard		NR_104031	NA	Approved				OTTHUMG00000162630	ENST00000514011.1:	chr5.hg19:g.88215090T>G		NA		hg19		0.02	4.377177	AAAxTAA	COVERED																																																																																			NOVEL	MEF2C-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000369795.1	2	14.745494	KEEP	4	0	0	49	1607	TT	1	1	0		+	5	60	195	0	0	12.398311	143	60	5086	234	ENST00000514011.1	0.033784	1
GPR98	84059	__UNKNOWN__	__UNKNOWN__	5	89949307	89949307	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:89949307G>A	ENST00000405460.2	+	20	4012	c.3916G>A	c.(3916-3918)Gga>Aga	p.G1306R		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1306		NA			detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTTACTGGTTGGAATTTTCCC	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													107	97	100	NA		NA	NA	5		NA											NA				89949307		1917	4122	6039	SO:0001583	missense			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199	84059		-, GPCR / Class B : Orphans	17416	protein-coding gene	gene with protein product		602851	monogenic, audiogenic seizure susceptibility 1 homolog (mouse)	USH2C, MASS1	NA	10976914, 14740321	Standard	NM_032119	NM_032119	NA	Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3916G>A	chr5.hg19:g.89949307G>A	ENSP00000384582:p.Gly1306Arg	NA	O75171|Q8TF58|Q9H0X5|Q9UL61	hg19	CCDS47246.1	0.02	3.988593	GTTxGAA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	31|31	5.078046|5.078046	0.94000|0.94000	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043|ENST00000504142	T|.	0.37411|.	1.2|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Concanavalin A-like lectin/glucanase (1);|.	0.100250|.	0.64402|.	D|.	0.000003|.	T|.	0.73148|.	0.3550|.	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D|.	0.64830|.	0.994|.	P|.	0.58780|.	0.845|.	T|.	0.69910|.	-0.5017|.	10|.	0.87932|.	D|.	0|.	.|.	19.4938|19.4938	0.95064|0.95064	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1306|.	Q8WXG9|.	GPR98_HUMAN|.	R|X	1306|894	ENSP00000384582:G1306R|.	ENSP00000296619:G1306R|.	G|W	+|+	1|2	0|0	GPR98|GPR98	89985063|89985063	1.000000|1.000000	0.71417|0.71417	0.286000|0.286000	0.24833|0.24833	0.989000|0.989000	0.77384|0.77384	9.391000|9.391000	0.97249|0.97249	2.691000|2.691000	0.91804|0.91804	0.650000|0.650000	0.86243|0.86243	GGA|TGG	NOVEL	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369993.2	2	6.019428	KEEP	0	0	0	20	716	GG	0.999863	0.999862	0		+	5	60	176	0	0	10.892797	119	60	4360	170	ENST00000405460.2	0.040323	0.999999
CHD1	1105	__UNKNOWN__	__UNKNOWN__	5	98236920	98236920	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:98236920T>C	ENST00000284049.3	-	5	706	c.557A>G	c.(556-558)aAc>aGc	p.N186S		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	186		NA			chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TTTGACTTTGTTTTTTGGCTC	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													212	200	204	NA		NA	NA	5		NA											NA				98236920		2203	4300	6503	SO:0001583	missense			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922	1105			1915	protein-coding gene	gene with protein product		602118			NA	8460153, 9326634	Standard	NM_001270	XM_005271866	NA	Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.557A>G	chr5.hg19:g.98236920T>C	ENSP00000284049:p.Asn186Ser	NA	Q17RZ3	hg19	CCDS34204.1	0.02	8.698256	TTGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	11.77	1.738842	0.30774	.	.	ENSG00000153922	ENST00000284049;ENST00000540681	D	0.88896	-2.44	5.76	5.76	0.90799	.	0.000000	0.36234	U	0.002719	T	0.77046	0.4073	N	0.16368	0.405	0.40576	D	0.981345	B	0.25609	0.13	B	0.17722	0.019	T	0.72374	-0.4313	10	0.08381	T	0.77	.	10.7992	0.46478	0.1409:0.0:0.0:0.8591	.	186	O14646	CHD1_HUMAN	S	186	ENSP00000284049:N186S	ENSP00000284049:N186S	N	-	2	0	CHD1	98264820	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.549000	0.60726	2.323000	0.78572	0.528000	0.53228	AAC	NOVEL	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370295.1	4	34.690266	KEEP	0	1	7	118	3714	TT	1	1	0		-	29	60	1021	0	0	77.938713	204	60	7342	432	ENST00000284049.3	0.124464	1
SLCO4C1	353189	__UNKNOWN__	__UNKNOWN__	5	101592891	101592891	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs145600550		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:101592891G>A	ENST00000310954.6	-	8	1683	c.1397C>T	c.(1396-1398)aCg>aTg	p.T466M		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1	NA		NA								breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		AAAACTCAGCGTAAGTGCAAC	0.353	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	18172	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	103	101	102	NA	1397	-7.1	0	5	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLCO4C1	NM_180991.4	81	0,2,6501	AA,AG,GG	NA	0.0116,0.0227,0.0154	benign	466/725	101592891	2,13004	2203	4300	6503	SO:0001583	missense			AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930	353189		Solute carriers	23612	protein-coding gene	gene with protein product		609013			NA		Standard	NM_180991	NM_180991	NA	Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1397C>T	chr5.hg19:g.101592891G>A	ENSP00000309741:p.Thr466Met	NA		hg19	CCDS34205.1	0.02	4.373383	AGCxTAA	COVERED	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	5.756	0.323901	0.10900	2.27E-4	1.16E-4	ENSG00000173930	ENST00000310954	T	0.81078	-1.45	5.78	-7.13	0.01532	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	2.033910	0.01821	N	0.034053	T	0.56543	0.1992	N	0.01729	-0.75	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.53947	-0.8366	10	0.45353	T	0.12	.	10.7214	0.46042	0.3748:0.1134:0.5118:0.0	.	466	Q6ZQN7	SO4C1_HUMAN	M	466	ENSP00000309741:T466M	ENSP00000309741:T466M	T	-	2	0	SLCO4C1	101620790	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	0.229000	0.17833	-1.548000	0.01712	-0.438000	0.05819	ACG	NOVEL	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370332.1	2	9.02897	KEEP	0	0	0	30	1032	GG	0.999997	0.999997	0		-	25	60	901	0	0	73.763047	112	60	3933	213	ENST00000310954.6	0.182482	1
APC	324	__UNKNOWN__	__UNKNOWN__	5	112177936	112177936	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:112177936G>A	ENST00000457016.1	+	16	7025	c.6645G>A	c.(6643-6645)caG>caA	p.Q2215Q	APC_ENST00000508376.2_Silent_p.Q2215Q|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.Q2215Q			P25054	APC_HUMAN	adenomatous polyposis coli	2215	Ser-rich.	NA			anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAATGAAACAGCCCCTTCAAG	0.363	NA	12	D, Mis, N, F, S		colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS	colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		E, M, O	1	Unknown(1)	skin(1)											74	81	79	NA		NA	NA	5		NA											NA				112177936		2190	4293	6483	SO:0001819	synonymous_variant	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982	324		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Armadillo repeat containing	583	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 46	611731	adenomatosis polyposis coli		NA	1651563	Standard	NM_000038	NM_001127511	NA	Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.6645G>A	chr5.hg19:g.112177936G>A		NA	D3DT03|Q15162|Q15163|Q93042	hg19	CCDS4107.1	0.02	2.006769	ACAxCCC	COVERED																																																																																			NOVEL	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250738.2	2	20.159605	KEEP	0	0	0	67	2392	GG	1	0.999804	0		+	19	60	676	0	0	56.623967	70	60	2664	182	ENST00000457016.1	0.213483	0.999804
TSSK1B	83942	__UNKNOWN__	__UNKNOWN__	5	112768611	112768611	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:112768611G>A	ENST00000390666.3	-	0	2117				CTD-2201G3.1_ENST00000416046.2_RNA|MCC_ENST00000408903.3_Intron	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	NA		NA			multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		AAATATTATCGCTGCAAGGTT	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122	83942			14968	protein-coding gene	gene with protein product		610709	serine/threonine kinase 22D (spermiogenesis associated), testis-specific serine kinase 1	STK22D, TSSK1	NA	15044604	Standard	NM_032028	NM_032028	NA	Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.*822C>T	chr5.hg19:g.112768611G>A		NA	B2R8D9	hg19	CCDS4112.1	0.02	2.273388	ATCxCTG	COVERED																																																																																			NOVEL	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250774.2	1	7.825016	KEEP	0	0	0	26	890	GG	0.999957	0.996681	0		-	10	60	373	0	0	29.605148	60	60	2092	122	ENST00000390666.3	0.142857	0.996724
YTHDC2	64848	__UNKNOWN__	__UNKNOWN__	5	112876806	112876806	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs367975063		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:112876806G>A	ENST00000515883.1	+	9	1539	c.1352G>A	c.(1351-1353)aGt>aAt	p.S451N	YTHDC2_ENST00000161863.4_Missense_Mutation_p.S451N			Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	451		NA			ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GCTGTCTTCAGTCAGCTGGTA	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	ASN/SER	1,4403	2.1+/-5.4	0,1,2201	207	189	195	NA	1352	5.4	1	5		195	0,8600		0,0,4300	no	missense	YTHDC2	NM_022828.3	46	0,1,6501	AA,AG,GG	NA	0.0,0.0227,0.0077	benign	451/1431	112876806	1,13003	2202	4300	6502	SO:0001583	missense			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188	64848			24721	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_022828	NM_022828	NA	Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000515883.1:c.1352G>A	chr5.hg19:g.112876806G>A	ENSP00000423101:p.Ser451Asn	NA	B2RP66	hg19		0.02	4.434721	TCAxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.40	1.927917	0.34002	2.27E-4	0.0	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.06608	4.28;3.28	5.39	5.39	0.77823	.	0.237616	0.49305	D	0.000144	T	0.03305	0.0096	N	0.04636	-0.2	0.31437	N	0.672439	B	0.09022	0.002	B	0.06405	0.002	T	0.27872	-1.0061	10	0.14656	T	0.56	.	12.9285	0.58275	0.0846:0.0:0.9154:0.0	.	451	Q9H6S0	YTDC2_HUMAN	N	451;451;361	ENSP00000161863:S451N;ENSP00000423101:S451N	ENSP00000161863:S451N	S	+	2	0	YTHDC2	112904705	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	4.751000	0.62169	2.521000	0.84997	0.655000	0.94253	AGT	NOVEL	YTHDC2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370842.1	6	20.165846	KEEP	0	0	0	67	2422	GG	1	1	0		+	60	60	2225	0	0	212.157218	70	60	2678	265	ENST00000515883.1	0.461538	1
AP3S1	1176	__UNKNOWN__	__UNKNOWN__	5	115249635	115249635	__UNKNOWN__	3'UTR	SNP	T	T	C	rs6876614		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:115249635T>C	ENST00000316788.7	+	0	1587					NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	NA		NA			anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		ACATTATGACTTTTTTCTCTT	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879	1176			2013	protein-coding gene	gene with protein product		601507		CLAPS3	NA	8697810, 9118953	Standard		NM_001284	NA	Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.*448T>C	chr5.hg19:g.115249635T>C		NA	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	hg19	CCDS4123.1	0.02	6.904486	GACxTTT	COVERED																																																																																			NOVEL	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250847.2	3	15.31715	KEEP	7	2	72	76	2481	TT	1	1	0		+	7	40	251	0	0	15.783508	163	60	5945	305	ENST00000316788.7	0.041176	1
AQPEP	0	__UNKNOWN__	__UNKNOWN__	5	115298647	115298647	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:115298647G>A	ENST00000357872.4	+	1	457	c.333G>A	c.(331-333)ctG>ctA	p.L111L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		111		NA				integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)				NA						ATCTGGAGCTGTGGCCGCAGC	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	42	40	NA		NA	NA	5		NA											NA				115298647		2201	4296	6497	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000357872.4:c.333G>A	chr5.hg19:g.115298647G>A		NA	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	hg19	CCDS4124.1	0.02	4.103617	GCTxTGG	COVERED																																																																																			NOVEL	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250852.1	1	30.095322	KEEP	0	0	0	100	3419	GG	1	1	0		+	10	60	344	0	0	23.379203	135	60	4916	304	ENST00000357872.4	0.068966	1
SEMA6A	57556	__UNKNOWN__	__UNKNOWN__	5	115803387	115803387	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:115803387C>T	ENST00000343348.6	-	18	2573	c.1786G>A	c.(1786-1788)Ggg>Agg	p.G596R	CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000282394.6_Intron|SEMA6A_ENST00000510263.1_Missense_Mutation_p.G596R|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000257414.8_Missense_Mutation_p.G613R|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000513137.1_Missense_Mutation_p.G23R|CTB-118N6.3_ENST00000510682.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	596		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		GACTCATACCCCTCTTGAGCC	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													108	105	106	NA		NA	NA	5		NA											NA				115803387		1988	4169	6157	SO:0001583	missense			AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421		57556		Semaphorins	10738	protein-coding gene	gene with protein product	sema VIa	605885		SEMAQ	NA	9204478, 10993894	Standard	NM_020796	XM_006714663	NA	Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.1786G>A	chr5.hg19:g.115803387C>T	ENSP00000345512:p.Gly596Arg	NA	Q9P2H9	hg19	CCDS47256.1	0.02	7.432133	ACCxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.65	3.868004	0.72065	.	.	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000510263	T;T;T;T	0.60171	2.26;2.26;0.21;2.26	5.95	5.95	0.96441	.	2.441060	0.01024	N	0.004032	T	0.70919	0.3279	N	0.19112	0.55	0.80722	D	1	P;D;P;D	0.89917	0.535;0.964;0.631;1.0	B;P;B;D	0.91635	0.403;0.621;0.165;0.999	T	0.60131	-0.7323	10	0.23891	T	0.37	.	19.9975	0.97389	0.0:1.0:0.0:0.0	.	596;140;613;23	Q9H2E6;Q96SM8;Q9H2E6-2;B3KU01	SEM6A_HUMAN;.;.;.	R	596;613;23;596	ENSP00000345512:G596R;ENSP00000257414:G613R;ENSP00000422997:G23R;ENSP00000424388:G596R	ENSP00000257414:G613R	G	-	1	0	SEMA6A	115831286	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.078000	0.57606	2.827000	0.97445	0.650000	0.86243	GGG	NOVEL	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371270.1	1	15.628117	KEEP	0	0	0	52	1704	CC	1	1	0		-	25	60	934	0	0	75.069383	137	60	4964	256	ENST00000343348.6	0.154321	1
PRRC1	133619	__UNKNOWN__	__UNKNOWN__	5	126860268	126860268	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:126860268C>A	ENST00000296666.8	+	3	337	c.149C>A	c.(148-150)tCc>tAc	p.S50Y	PRRC1_ENST00000442138.2_Missense_Mutation_p.S50Y|PRRC1_ENST00000512635.2_Missense_Mutation_p.S50Y	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	50	Pro-rich.	NA				Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		TCCATGGAGTCCTTCCCACCA	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													182	173	176	NA		NA	NA	5		NA											NA				126860268		2203	4300	6503	SO:0001583	missense			AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244	133619			28164	protein-coding gene	gene with protein product		NA			NA	15541471	Standard	NM_130809	NM_130809	NA	Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.149C>A	chr5.hg19:g.126860268C>A	ENSP00000296666:p.Ser50Tyr	NA	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	hg19	CCDS4143.1	0.02	4.100429	AGTxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.46	3.130283	0.56721	.	.	ENSG00000164244	ENST00000296666;ENST00000442138;ENST00000330542;ENST00000414018;ENST00000512635;ENST00000512535	.	.	.	4.99	4.11	0.48088	.	0.513397	0.22513	N	0.059065	T	0.22627	0.0546	N	0.17082	0.46	0.27903	N	0.938896	B;P	0.45474	0.306;0.859	B;B	0.37304	0.08;0.246	T	0.08534	-1.0717	9	0.72032	D	0.01	-1.8994	13.0231	0.58800	0.0:0.8366:0.1634:0.0	.	50;50	Q96M27;Q96M27-5	PRRC1_HUMAN;.	Y	50	.	ENSP00000296666:S50Y	S	+	2	0	PRRC1	126888167	0.002000	0.14202	0.609000	0.28983	0.611000	0.37282	0.880000	0.28159	1.304000	0.44892	0.655000	0.94253	TCC	NOVEL	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250971.3	10	22.556818	KEEP	0	0	0	75	2510	CC	1	1	0		+	33	60	1122	0	0	95.46593	101	60	3734	265	ENST00000296666.8	0.246269	1
SEC24A	10802	__UNKNOWN__	__UNKNOWN__	5	134061651	134061651	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:134061651G>T	ENST00000398844.2	+	0	4437					NM_021982.2	NP_068817.1	O95486	SC24A_HUMAN	SEC24 family member A	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of protein secretion (GO:0050714)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045714)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	36			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGGGTTTTTGGTGAAATGAGT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ131244	CCDS43363.1, CCDS58967.1	5q31.1	2013-10-21	2013-10-21		ENSG00000113615	ENSG00000113615	10802			10703	protein-coding gene	gene with protein product		607183	SEC24 (S. cerevisiae) related gene family, member A, SEC24 family, member A (S. cerevisiae)		NA	10075675, 10329445	Standard		NM_021982	NA	Approved		uc003kzs.3	O95486	OTTHUMG00000163064	ENST00000398844.2:c.*867G>T	chr5.hg19:g.134061651G>T		NA	A8MVW3|Q8WUV2|Q96GP7	hg19	CCDS43363.1	0.02	6.680573	TTGxTGA	COVERED																																																																																			NOVEL	SEC24A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371563.1	3	14.443243	KEEP	0	0	0	48	1634	GG	1	1	0		+	20	60	723	0	0	55.160905	149	60	5498	256	ENST00000398844.2	0.118343	1
TRPC7	57113	__UNKNOWN__	__UNKNOWN__	5	135610378	135610378	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:135610378T>G	ENST00000513104.1	-	4	1393	c.1111A>C	c.(1111-1113)Att>Ctt	p.I371L	TRPC7_ENST00000426057.2_Intron|TRPC7_ENST00000355180.3_Missense_Mutation_p.I310L	NM_020389.2	NP_065122.1	Q9HCX4	TRPC7_HUMAN	transient receptor potential cation channel, subfamily C, member 7	371		NA			axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|manganese ion transport (GO:0006828)|platelet activation (GO:0030168)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(3)	46			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CACGGAGCAATCCAATAGGCT	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	72	73	NA		NA	NA	5		NA											NA				135610378		1903	4135	6038	SO:0001583	missense			AJ272034	CCDS47267.1, CCDS47267.2, CCDS54905.1, CCDS54906.1	5q31.2	2011-12-14			ENSG00000069018	ENSG00000069018	57113		Voltage-gated ion channels / Transient receptor potential cation channels	20754	protein-coding gene	gene with protein product		NA			NA	11805119, 16382100	Standard	NM_020389	NM_020389	NA	Approved		uc003lbn.2	Q9HCX4	OTTHUMG00000162035	ENST00000513104.1:c.1111A>C	chr5.hg19:g.135610378T>G	ENSP00000426070:p.Ile371Leu	NA	A1A4Z4|F5H5U9|Q70T26|Q8IWP7	hg19	CCDS47267.2	0.02	7.593474	CAAxCCA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.47|14.47	2.544058|2.544058	0.45280|0.45280	.|.	.|.	ENSG00000069018|ENSG00000069018	ENST00000378459|ENST00000355180;ENST00000513104;ENST00000265193	.|T;T	.|0.53857	.|0.6;0.6	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|0.053292	.|0.64402	.|D	.|0.000001	T|T	0.37972|0.37972	0.1023|0.1023	N|N	0.25825|0.25825	0.765|0.765	0.80722|0.80722	D|D	1|1	.|B;B	.|0.10296	.|0.003;0.001	.|B;B	.|0.17098	.|0.017;0.002	T|T	0.22347|0.22347	-1.0219|-1.0219	5|10	.|0.06757	.|T	.|0.87	-13.0473|-13.0473	15.6116|15.6116	0.76727|0.76727	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|310;371	.|F5H5U9;Q9HCX4	.|.;TRPC7_HUMAN	A|L	309|310;371;371	.|ENSP00000347312:I310L;ENSP00000426070:I371L	.|ENSP00000265193:I371L	D|I	-|-	2|1	0|0	TRPC7|TRPC7	135638277|135638277	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.113000|6.113000	0.71553|0.71553	2.333000|2.333000	0.79357|0.79357	0.533000|0.533000	0.62120|0.62120	GAT|ATT	NOVEL	TRPC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366975.1	1	8.42585	KEEP	0	0	0	28	900	TT	0.999997	0.999997	0		-	46	60	1764	0	0	157.261237	110	60	3999	224	ENST00000513104.1	0.294872	1
SPOCK1	6695	__UNKNOWN__	__UNKNOWN__	5	136313088	136313088	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:136313088A>T	ENST00000394945.1	-	0	2744					NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	NA		NA			cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGTTCTTTGTAGGCCTCCATT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377	6695			11251	protein-coding gene	gene with protein product		602264	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)	TIC1, SPOCK	NA	9545645	Standard	NM_004598	NM_004598	NA	Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.*1255T>A	chr5.hg19:g.136313088A>T		NA	B3KSW3|Q59EW0|Q8N630|Q9UCL8	hg19	CCDS4191.1	0.02	1.989692	TGTxGGC	COVERED																																																																																			NOVEL	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251222.1	3	7.21891	KEEP	0	0	0	24	744	AA	0.999909	0.999771	0		-	5	60	177	0	0	11.680962	86	70	3079	144	ENST00000394945.1	0.054945	0.999862
PCDHA2	56146	__UNKNOWN__	__UNKNOWN__	5	140175836	140175836	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:140175836C>T	ENST00000520672.2	+	1	1393	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000378132.1_Silent_p.D429D|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Silent_p.D429D	NM_031496.1	NP_113684.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	429	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCACGGGACGGGGGCTCGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													92	89	90	NA		NA	NA	5		NA											NA				140175836		2203	4300	6503	SO:0001819	synonymous_variant			AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969	56146		Cadherins / Protocadherins : Clustered	8668	other	complex locus constituent	KIAA0345-like 12	606308			NA	10380929	Standard	NM_018905	NM_018905	NA	Approved			Q9Y5H9		ENST00000520672.2:c.1287C>T	chr5.hg19:g.140175836C>T		NA	O75287|Q9BTV3	hg19		0.02	1.963871	GGAxGGG	COVERED																																																																																			NOVEL	PCDHA2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000374265.2	3	14.445225	KEEP	0	0	0	48	1627	CC	1	0.999907	0		+	32	60	1061	0	0	95.326833	61	60	2101	167	ENST00000520672.2	0.344086	0.999907
PCDHA12	56137	__UNKNOWN__	__UNKNOWN__	5	140256146	140256146	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:140256146T>C	ENST00000398631.2	+	1	1089	c.1089T>C	c.(1087-1089)gcT>gcC	p.A363A	PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA6_ENST00000529310.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	363	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGAGGATGCTCAGGTGGGTA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(113;759 1672 13322 24104 50104)					NA		NA				0													97	98	98	NA		NA	NA	5		NA											NA				140256146		2203	4300	6503	SO:0001819	synonymous_variant			AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664	56137		Cadherins / Protocadherins : Clustered	8666	other	complex locus constituent	KIAA0345-like 2	606318			NA	10380929	Standard	NM_018903	NM_018903	NA	Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1089T>C	chr5.hg19:g.140256146T>C		NA	O75278|Q2M1N8	hg19	CCDS47285.1	0.02	6.61083	TGCxCAG	COVERED																																																																																			NOVEL	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372882.2	2	14.140867	KEEP	0	0	0	47	1468	TT	1	1	0		+	66	60	2265	0	0	202.870415	134	60	4849	291	ENST00000398631.2	0.33	1
GNPDA1	10007	__UNKNOWN__	__UNKNOWN__	5	141381051	141381051	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:141381051G>T	ENST00000513454.1	-	6	808				GNPDA1_ENST00000508177.1_3'UTR|GNPDA1_ENST00000311337.6_3'UTR|GNPDA1_ENST00000503794.1_3'UTR|GNPDA1_ENST00000500692.2_3'UTR|GNPDA1_ENST00000458112.2_3'UTR			P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucosamine catabolic process (GO:0006043)|N-acetylglucosamine metabolic process (GO:0006044)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)			central_nervous_system(1)|lung(1)|skin(3)|stomach(1)	6		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGAAGGAAGGGATCGTTTTC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF048826	CCDS4272.1	5q21	2008-02-05	2003-10-17	2003-10-22	ENSG00000113552	ENSG00000113552	10007	3.5.99.6		4417	protein-coding gene	gene with protein product	glucosamine-6-phosphate deaminase, oscillin	601798	glucosamine-6-phosphate isomerase	GNPI	NA	9714720, 9438414	Standard	NM_005471	NM_005471	NA	Approved	GNPDA, HLN, GPI, KIAA0060	uc010jgh.3	P46926	OTTHUMG00000129657	ENST00000513454.1:c.769+1601C>A	chr5.hg19:g.141381051G>T		NA	B7Z3X4|D3DQE7	hg19		0.02	2.261226	AAGxGAT	COVERED																																																																																			NOVEL	GNPDA1-013	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370641.1	1	6.320252	KEEP	0	0	0	21	729	GG	0.999869	0.987814	0		-	15	60	527	0	0	45.204538	45	60	1580	99	ENST00000513454.1	0.25	0.987943
STK32A	202374	__UNKNOWN__	__UNKNOWN__	5	146766342	146766342	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:146766342T>C	ENST00000397936.3	+	0	4320					NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	NA		NA					ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACCATGGTATCTGACAGTGC	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302	202374			28317	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_145001	NM_001112724	NA	Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.*2796T>C	chr5.hg19:g.146766342T>C		NA	B3KSY0	hg19	CCDS47299.1	0.02	4.352471	GTAxCTG	COVERED																																																																																			NOVEL	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373306.1	3	15.337065	KEEP	0	0	0	51	1583	TT	1	1	0		+	9	60	314	0	0	21.556893	119	60	4330	223	ENST00000397936.3	0.070312	1
JAKMIP2	9832	__UNKNOWN__	__UNKNOWN__	5	147016651	147016651	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:147016651G>T	ENST00000265272.5	-	11	1998				JAKMIP2_ENST00000507386.1_Intron|JAKMIP2_ENST00000333010.6_Intron	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	NA		NA				Golgi apparatus (GO:0005794)				NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGTAAAATGGTTATTCAATA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	70	69	NA		NA	NA	5		NA											NA				147016651		2203	4300	6503	SO:0001627	intron_variant			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049	9832			29067	protein-coding gene	gene with protein product		611197			NA	9628581	Standard	NM_014790	NM_001270941	NA	Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.1531-40C>A	chr5.hg19:g.147016651G>T		NA	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	hg19	CCDS4285.1	0.02	2.243673	ATGxTTA	COVERED																																																																																			NOVEL	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251941.1	1	7.524271	KEEP	0	0	0	25	879	GG	0.999931	0.990896	0		-	23	60	844	0	0	77.615984	39	60	1436	106	ENST00000265272.5	0.370968	0.990964
CSF1R	1436	__UNKNOWN__	__UNKNOWN__	5	149456743	149456743	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:149456743G>A	ENST00000286301.3	-	6	1181				CSF1R_ENST00000543093.1_Intron	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	NA		NA			cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	ATCCTCAGCAGGTCTCCTTCC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578	1436		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	2433	protein-coding gene	gene with protein product		164770	McDonough feline sarcoma viral (v-fms) oncogene homolog	FMS	NA	1611909	Standard	NM_005211	NM_005211	NA	Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.889+95C>T	chr5.hg19:g.149456743G>A		NA	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	hg19	CCDS4302.1	0.02	14.62345	GCAxGTC	COVERED																																																																																			NOVEL	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252329.2	8	21.068668	KEEP	0	0	0	70	2495	GG	1	1	0		-	33	60	1214	0	0	91.612767	275	70	10194	448	ENST00000286301.3	0.107143	1
SLC6A7	6534	__UNKNOWN__	__UNKNOWN__	5	149597136	149597136	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:149597136C>T	ENST00000524041.1	+	15	2102	c.1859C>T	c.(1858-1860)gCa>gTa	p.A620V				Q99884	SC6A7_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 7	0		NA			proline transport (GO:0015824)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(1)|stomach(1)	16		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Proline(DB00172)	CTTCTCTATGCAAGAATGACA	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			S80071	CCDS4305.1	5q32	2013-07-19	2013-07-19		ENSG00000011083	ENSG00000011083	6534		Solute carriers	11054	protein-coding gene	gene with protein product	brain-specific L-proline transporter, sodium-dependent proline transporter	606205	solute carrier family 6 (neurotransmitter transporter, L-proline), member 7		NA	7651355	Standard	NM_014228	NM_014228	NA	Approved	PROT	uc003lrr.3	Q99884	OTTHUMG00000130046	ENST00000524041.1:c.1859C>T	chr5.hg19:g.149597136C>T	ENSP00000428200:p.Ala620Val	NA	Q0VG81|Q52LU6	hg19		0.02	1.880637	ATGxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	4.088	0.014388	0.07959	.	.	ENSG00000011083	ENST00000524041	T	0.73789	-0.78	2.61	0.773	0.18516	.	.	.	.	.	T	0.63355	0.2504	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.53034	-0.8495	6	0.35671	T	0.21	.	4.7008	0.12827	0.0:0.683:0.0:0.317	.	.	.	.	V	620	ENSP00000428200:A620V	ENSP00000428200:A620V	A	+	2	0	SLC6A7	149577329	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.728000	0.04925	0.180000	0.19960	0.561000	0.74099	GCA	NOVEL	SLC6A7-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000377501.1	2	20.158414	KEEP	0	0	0	67	2364	CC	1	0.999881	0		+	15	60	528	0	0	42.192192	77	60	2922	202	ENST00000524041.1	0.163043	0.999881
G3BP1	10146	__UNKNOWN__	__UNKNOWN__	5	151166155	151166155	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:151166155T>C	ENST00000356245.3	+	0	117				G3BP1_ENST00000543466.1_5'UTR|G3BP1_ENST00000394123.3_Intron	NM_005754.2|NM_198395.1	NP_005745.1|NP_938405.1	Q13283	G3BP1_HUMAN	GTPase activating protein (SH3 domain) binding protein 1	NA		NA			ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Ras protein signal transduction (GO:0007265)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|skin(3)|urinary_tract(2)	29		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			TTGACTCTTTTCCCCCCAGGT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													92	97	95	NA		NA	NA	5		NA											NA				151166155		2203	4300	6503	SO:0001623	5_prime_UTR_variant			BC006997	CCDS4319.1	5q33.1	2013-02-12	2006-11-01		ENSG00000145907	ENSG00000145907	10146		RNA binding motif (RRM) containing	30292	protein-coding gene	gene with protein product	Ras-GTPase-activating protein SH3-domain-binding protein	608431			NA	8649363, 9889278	Standard	NM_005754	NM_005754	NA	Approved	HDH-VIII, G3BP	uc003lum.3	Q13283	OTTHUMG00000130123	ENST00000356245.3:c.-27T>C	chr5.hg19:g.151166155T>C		NA	Q5HYE9	hg19	CCDS4319.1	0.02	21.089813	TTTxCCC	COVERED																																																																																			NOVEL	G3BP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373965.1	4	49.006087	KEEP	0	0	0	163	4845	TT	1	1	0		+	13	60	479	0	0	27.571096	521	60	17552	879	ENST00000356245.3	0.024345	1
MED7	9443	__UNKNOWN__	__UNKNOWN__	5	156565056	156565056	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:156565056A>C	ENST00000286317.5	-	0	1768					NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	NA		NA			gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTAGCTTTAAAGAAAATGTA	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868	9443			2378	protein-coding gene	gene with protein product		605045	cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa	CRSP9	NA	9989412	Standard	NM_004270	NM_004270	NA	Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.*685T>G	chr5.hg19:g.156565056A>C		NA		hg19	CCDS4334.1	0.02	5.018447	TTAxAGA	COVERED																																																																																			NOVEL	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252567.2	2	9.026162	KEEP	0	0	0	30	946	AA	0.999997	0.999989	0		-	10	60	385	0	0	28.763159	99	60	3566	171	ENST00000286317.5	0.091743	0.999992
FAM71B	153745	__UNKNOWN__	__UNKNOWN__	5	156592941	156592941	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:156592941A>T	ENST00000302938.4	-	1	334	c.239T>A	c.(238-240)aTc>aAc	p.I80N		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	80		NA				nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CAGTGGGAGGATGGGGCTGGT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													111	105	107	NA		NA	NA	5		NA											NA				156592941		2203	4300	6503	SO:0001583	missense				CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613	153745			28397	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_130899	NM_130899	NA	Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.239T>A	chr5.hg19:g.156592941A>T	ENSP00000305596:p.Ile80Asn	NA	Q1EDD9|Q8TC64|Q96LY8	hg19	CCDS4335.1	0.02	6.847267	AGGxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	13.54	2.266852	0.40095	.	.	ENSG00000170613	ENST00000302938	T	0.04119	3.7	4.67	4.67	0.58626	.	0.719634	0.13005	N	0.421368	T	0.07413	0.0187	M	0.61703	1.905	0.30414	N	0.778769	B	0.33883	0.43	B	0.30943	0.122	T	0.02698	-1.1122	10	0.49607	T	0.09	-12.1086	11.0786	0.48047	1.0:0.0:0.0:0.0	.	80	Q8TC56	FA71B_HUMAN	N	80	ENSP00000305596:I80N	ENSP00000305596:I80N	I	-	2	0	FAM71B	156525519	0.668000	0.27493	0.976000	0.42696	0.722000	0.41435	1.007000	0.29860	2.036000	0.60181	0.460000	0.39030	ATC	NOVEL	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252570.2	3	8.725678	KEEP	0	0	0	29	904	AA	0.999997	0.999997	0		-	25	60	824	0	0	64.987583	125	60	4514	215	ENST00000302938.4	0.166667	1
CYFIP2	26999	__UNKNOWN__	__UNKNOWN__	5	156819961	156819961	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs371399881		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:156819961C>T	ENST00000521420.1	+	30	3728	c.3637C>T	c.(3637-3639)Cgc>Tgc	p.R1213C	CYFIP2_ENST00000541131.1_Missense_Mutation_p.R1164C|CYFIP2_ENST00000435847.2_Missense_Mutation_p.R938C|CYFIP2_ENST00000377576.3_Missense_Mutation_p.R1239C|CYFIP2_ENST00000318218.6_Missense_Mutation_p.R1264C|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000522463.1_Missense_Mutation_p.R1043C|CYFIP2_ENST00000347377.6_Missense_Mutation_p.R1239C					cytoplasmic FMR1 interacting protein 2	NA		NA								breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGAGCATGTGCGCTGCTTCCA	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C	CYS/ARG,CYS/ARG,CYS/ARG	0,4350		0,0,2175	76	82	80	NA	3715,3715,3715	5.4	1	5		80	1,8581		0,1,4290	no	missense,missense,missense	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	180,180,180	0,1,6465	TT,TC,CC	NA	0.0117,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	1239/1254,1239/1254,1239/1254	156819961	1,12931	2175	4291	6466	SO:0001583	missense			AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163	26999			13760	protein-coding gene	gene with protein product	p53 inducible protein	606323			NA	11438699	Standard	NM_001037332	NM_001037333	NA	Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.3637C>T	chr5.hg19:g.156819961C>T	ENSP00000430904:p.Arg1213Cys	NA		hg19		0.02	4.06954	GTGxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	33	5.281215	0.95489	0.0	1.17E-4	ENSG00000055163	ENST00000318218;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T	0.33216	1.74;1.74;1.75;1.73;1.73;1.75;1.42	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.46795	0.1411	L	0.29908	0.895	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.992	D;D;D;D;D;D	0.79784	0.993;0.993;0.98;0.925;0.993;0.919	T	0.46735	-0.9170	10	0.87932	D	0	-25.145	19.5107	0.95140	0.0:1.0:0.0:0.0	.	1103;1043;1213;1239;1239;1264	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	C	1264;1043;1213;1239;1239;1164;938	ENSP00000325817:R1264C;ENSP00000428009:R1043C;ENSP00000430904:R1213C;ENSP00000313567:R1239C;ENSP00000366799:R1239C;ENSP00000444645:R1164C;ENSP00000403793:R938C	ENSP00000325817:R1264C	R	+	1	0	CYFIP2	156752539	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.679000	0.91253	0.655000	0.94253	CGC	NOVEL	CYFIP2-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000373710.1	0	12.337651	KEEP	0	0	0	41	1387	CC	1	1	0		+	5	60	180	0	0	10.888058	144	60	4783	236	ENST00000521420.1	0.033557	1
NIPAL4	348938	__UNKNOWN__	__UNKNOWN__	5	156901351	156901351	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:156901351G>T	ENST00000311946.7	+	0	2900				ADAM19_ENST00000430702.2_Intron	NM_001099287.1	NP_001092757.1	Q0D2K0	NIPA4_HUMAN	NIPA-like domain containing 4	NA		NA				integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(3)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|prostate(1)|skin(1)	22						CAAGAGTGTGGGGGTTGGAGA	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK026158	CCDS47328.1, CCDS54944.1	5q33.3	2009-03-24	2009-03-24		ENSG00000172548	ENSG00000172548	348938			28018	protein-coding gene	gene with protein product	ichthyin	609383	NIPA-like 4		NA	8619474, 9110174, 15317751	Standard	NM_001099287	NM_001099287	NA	Approved	ICHYN	uc003lwx.4	Q0D2K0	OTTHUMG00000163497	ENST00000311946.7:c.*1383G>T	chr5.hg19:g.156901351G>T		NA	A8S6F1|A8S6F5|A8S6F8|B4DLF3|Q0D2J8|Q0D2J9	hg19	CCDS47328.1	0.02	2.028119	GTGxGGG	COVERED																																																																																			NOVEL	NIPAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373789.1	1	5.718172	KEEP	0	0	0	19	640	GG	0.99986	0.999808	0		+	31	60	1092	0	0	97.434576	67	60	2339	137	ENST00000311946.7	0.316327	0.999948
ATP10B	23120	__UNKNOWN__	__UNKNOWN__	5	159991980	159991980	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:159991980C>G	ENST00000327245.5	-	0	5712					NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	NA		NA			phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCAGCCATTACTGCAATACAC	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322	23120		ATPases / P-type	13543	protein-coding gene	gene with protein product		NA	ATPase, Class V, type 10B		NA	9872452, 11015572	Standard	NM_025153	NM_025153	NA	Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.*480G>C	chr5.hg19:g.159991980C>G		NA	Q9H725	hg19	CCDS43394.1	0.02	4.816602	TTAxTGC	COVERED																																																																																			NOVEL	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374127.1	3	3.912983	KEEP	0	0	0	13	480	CC	0.994391	0.99439	0		-	38	60	1444	0	0	128.120986	94	60	3626	175	ENST00000327245.5	0.287879	1
ARL10	285598	__UNKNOWN__	__UNKNOWN__	5	175806587	175806587	__UNKNOWN__	3'UTR	SNP	C	C	T	rs140034114	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:175806587C>T	ENST00000310389.5	+	0	8520					NM_173664.4	NP_775935.1	Q8N8L6	ARL10_HUMAN	ADP-ribosylation factor-like 10	NA		NA			small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(2)|lung(1)|ovary(1)	4	all_cancers(89;0.0064)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		AATTAGACTGCGAAGTTCTGA	0.353	NA	NA											C|||	34	0.00678914	0.0015	0.0058	5008	,	,	NA	19836	0	NA	0.0129	False	NA	,,,	NA	NA	NA	2504	0.0153	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BK001673	CCDS4400.1	5q35.3	2014-05-09	2005-11-03	2005-11-03	ENSG00000175414	ENSG00000175414	285598		ADP-ribosylation factors-like, ADP-ribosylation factors	22042	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 10A	ARL10A	NA		Standard	NM_173664	NM_173664	NA	Approved		uc003mec.1	Q8N8L6	OTTHUMG00000130655	ENST00000310389.5:c.*7689C>T	chr5.hg19:g.175806587C>T		NA		hg19	CCDS4400.1	0.02	4.618968	CTGxGAA	COVERED																																																																																			NOVEL	ARL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253145.2	0	10.834736	KEEP	0	0	0	36	1244	CC	0.999999	0.999991	0		+	17	60	598	0	0	47.420914	92	60	3359	177	ENST00000310389.5	0.155963	0.999992
PHYKPL	85007	__UNKNOWN__	__UNKNOWN__	5	177637895	177637895	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:177637895C>T	ENST00000308158.5	-	12	1619				HNRNPAB_ENST00000515193.1_3'UTR|HNRNPAB_ENST00000504898.1_3'UTR|HNRNPAB_ENST00000506339.1_3'UTR|HNRNPAB_ENST00000358344.3_3'UTR|HNRNPAB_ENST00000506259.1_3'UTR|PHYKPL_ENST00000481811.1_Intron|HNRNPAB_ENST00000355836.5_3'UTR|HNRNPAB_ENST00000514633.1_3'UTR	NM_153373.2	NP_699204.1	Q8IUZ5	AT2L2_HUMAN	5-phosphohydroxy-L-lysine phospho-lyase	NA		NA				mitochondrion (GO:0005739)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)				NA					L-Alanine(DB00160)	GGCTCTGCTTCCTGCTGCCGC	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037567	CCDS4434.1	5q35.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000175309	ENSG00000175309	85007	4.2.3.134		28249	protein-coding gene	gene with protein product	5-phosphonooxy-L-lysine phospho-lyase	614683	alanine-glyoxylate aminotransferase 2-like 2	AGXT2L2	NA	22241472	Standard	NM_032921	NM_153373	NA	Approved	MGC15875	uc003miz.3	Q8IUZ5	OTTHUMG00000130892	ENST00000308158.5:c.1350+995G>A	chr5.hg19:g.177637895C>T		NA	A8K7P6|B3KN36|D3DWP9|Q8WYS6|Q96HW8	hg19	CCDS4434.1	0.02	2.050668	CTTxCTG	COVERED																																																																																			NOVEL	PHYKPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253477.1	1	8.72798	KEEP	0	0	0	29	988	CC	0.999997	0.999556	0		-	26	60	960	0	0	85.834626	58	60	2107	128	ENST00000308158.5	0.309524	0.999559
ADAMTS2	9509	__UNKNOWN__	__UNKNOWN__	5	178541234	178541234	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:178541234G>C	ENST00000251582.7	-	22	3371	c.3270C>G	c.(3268-3270)tgC>tgG	p.C1090W		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	1090	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.	NA			collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TACAGGACTTGCAGCACAGCT	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	90	99	NA		NA	NA	5		NA											NA				178541234		2203	4300	6503	SO:0001583	missense			AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116	9509		ADAM metallopeptidases with thrombospondin type 1 motif	218	protein-coding gene	gene with protein product	procollagen I N-proteinase, procollagen N-endopeptidase	604539	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2		NA	10094461, 15373769	Standard	NM_014244	NM_014244	NA	Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.3270C>G	chr5.hg19:g.178541234G>C	ENSP00000251582:p.Cys1090Trp	NA		hg19	CCDS4444.1	0.02	2.259323	CTTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.71	3.455506	0.63401	.	.	ENSG00000087116	ENST00000251582	T	0.71222	-0.55	5.39	3.58	0.41010	PLAC (1);	0.000000	0.64402	D	0.000007	T	0.81278	0.4789	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82396	-0.0478	10	0.87932	D	0	.	9.4404	0.38666	0.2298:0.0:0.7702:0.0	.	1090	O95450	ATS2_HUMAN	W	1090	ENSP00000251582:C1090W	ENSP00000251582:C1090W	C	-	3	2	ADAMTS2	178473840	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	3.410000	0.52664	1.414000	0.47017	0.561000	0.74099	TGC	NOVEL	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253507.1	2	4.51492	KEEP	0	0	0	15	546	GG	0.99649	0.996051	0		-	25	60	902	0	0	80.067073	58	60	2225	123	ENST00000251582.7	0.301205	0.999559
ZFP62	643836	__UNKNOWN__	__UNKNOWN__	5	180276334	180276334	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:180276334T>G	ENST00000502412.1	-	2	2218	c.2161A>C	c.(2161-2163)Aga>Cga	p.R721R	ZFP62_ENST00000512132.1_Silent_p.R688R|ZFP62_ENST00000359141.6_Silent_p.R661R|ZFP62_ENST00000506377.1_Intron	NM_001172638.1	NP_001166109.1	Q8NB50	ZFP62_HUMAN	ZFP62 zinc finger protein	721		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|endometrium(2)|pancreas(1)	4	all_cancers(89;4.01e-05)|all_epithelial(37;4.69e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00469)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGATGGACTCTTTTATGGCTT	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													91	89	90	NA		NA	NA	5		NA											NA				180276334		692	1591	2283	SO:0001819	synonymous_variant			AK002206	CCDS47357.1, CCDS47357.2, CCDS54955.1	5q35.3	2013-01-08	2012-11-27			ENSG00000196670	643836		Zinc fingers, C2H2-type	23241	protein-coding gene	gene with protein product		610281	zinc finger protein 62 homolog (mouse), zinc finger protein 62		NA	8808410	Standard	NM_152283	NM_152283	NA	Approved	FLJ34231, ZET, ZNF755	uc011dhf.2	Q8NB50		ENST00000502412.1:c.2161A>C	chr5.hg19:g.180276334T>G		NA	B4DIP6|B4E0N3|B5MDX6|B7ZVZ2|B9EIP6|E9PFT8|J3QTA9	hg19	CCDS54955.1	0.02	4.711485	CTCxTTT	COVERED																																																																																			NOVEL	ZFP62-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368386.2	3	15.342122	KEEP	0	0	0	51	1628	TT	1	1	0		-	23	60	828	0	0	66.31104	121	60	4456	228	ENST00000502412.1	0.159722	1
BTNL8	79908	__UNKNOWN__	__UNKNOWN__	5	180338566	180338566	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs143894862	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:180338566C>T	ENST00000231229.4	+	3	859	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	BTNL8_ENST00000400707.3_Missense_Mutation_p.R84W|BTNL8_ENST00000505126.1_Missense_Mutation_p.R2W|BTNL8_ENST00000340184.4_Missense_Mutation_p.R209W|BTNL8_ENST00000511704.1_Missense_Mutation_p.R93W|BTNL8_ENST00000508408.1_Missense_Mutation_p.R209W|BTNL8_ENST00000533815.2_Missense_Mutation_p.R25W	NM_001159708.1|NM_024850.2	NP_001153180.1|NP_079126.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	209	Ig-like V-type 2.	NA			immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGTTCCATGCGGCATGCTCA	0.552	NA	NA											C|||	23	0.00459265	0.0174	0	5008	,	,	NA	18512	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	52,4354	52.3+/-87.9	0,52,2151	69	68	68	NA	625,277,625,250,73,625	2.7	0	5	dbSNP_134	68	0,8592		0,0,4296	yes	missense,missense,missense,missense,missense,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	101,101,101,101,101,101	0,52,6447	TT,TC,CC	NA	0.0,1.1802,0.4001	benign,benign,benign,benign,benign,benign	209/501,93/385,209/341,84/376,25/317,209/348	180338566	52,12946	2203	4296	6499	SO:0001583	missense			AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303	79908		Immunoglobulin superfamily / V-set domain containing, Butyrophilins	26131	protein-coding gene	gene with protein product		615606			NA	12975309	Standard	NM_024850	NM_024850	NA	Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000231229.4:c.625C>T	chr5.hg19:g.180338566C>T	ENSP00000231229:p.Arg209Trp	NA	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	hg19	CCDS4459.1	0.02	14.085376	ATGxGGC	COVERED	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	8.734	0.917376	0.17982	0.011802	0.0	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T;T;T	0.62639	3.27;3.27;3.27;3.27;3.27;0.01;0.18	3.59	2.69	0.31865	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.37100	0.0991	N	0.26042	0.785	0.09310	N	1	D;B;P;D;B	0.56968	0.978;0.24;0.947;0.97;0.002	B;B;B;B;B	0.40534	0.12;0.011;0.332;0.332;0.0	T	0.15867	-1.0422	9	0.45353	T	0.12	.	8.4213	0.32703	0.2343:0.7657:0.0:0.0	.	84;93;209;209;209	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	W	209;209;84;209;93;2;25	ENSP00000231229:R209W;ENSP00000342197:R209W;ENSP00000383543:R84W;ENSP00000424585:R209W;ENSP00000425207:R93W;ENSP00000427441:R2W;ENSP00000435098:R25W	ENSP00000231229:R209W	R	+	1	2	BTNL8	180271172	0.005000	0.15991	0.024000	0.17045	0.033000	0.12548	1.008000	0.29872	0.611000	0.30052	0.205000	0.17691	CGG	NOVEL	BTNL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253528.2	7	21.398947	KEEP	0	1	28	81	2789	CC	1	1	0		+	12	60	409	0	0	23.68489	357	60	12344	575	ENST00000231229.4	0.03252	1
GNB2L1	10399	__UNKNOWN__	__UNKNOWN__	5	180668742	180668742	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr5:180668742C>A	ENST00000511900.1	-	2	365				GNB2L1_ENST00000511566.1_Intron|GNB2L1_ENST00000456394.2_Intron|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000376817.4_Intron|GNB2L1_ENST00000512805.1_Intron|GNB2L1_ENST00000505461.1_Intron			P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		ATCACTCATACAACCCTGGAT	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628	10399		WD repeat domain containing	4399	protein-coding gene	gene with protein product	Receptor for Activated C Kinase 1	176981			NA	8302854, 2499885	Standard	NM_006098	NM_006098	NA	Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000511900.1:c.285+427G>T	chr5.hg19:g.180668742C>A		NA	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	hg19		0.02	8.950546	ATAxAAC	COVERED																																																																																			NOVEL	GNB2L1-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000373430.1	1	27.989521	KEEP	0	0	0	93	3332	CC	1	1	0		-	22	60	785	0	0	57.586084	206	60	7824	414	ENST00000511900.1	0.096491	1
SERPINB1	1992	__UNKNOWN__	__UNKNOWN__	6	2833961	2833961	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:2833961C>T	ENST00000380739.5	-	7	1223	c.1021G>A	c.(1021-1023)Gca>Aca	p.A341T	SERPINB1_ENST00000537185.1_Missense_Mutation_p.A190T	NM_030666.3	NP_109591.1	P30740	ILEU_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 1	341		NA			negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|ovary(2)	13	Ovarian(93;0.0412)			OV - Ovarian serous cystadenocarcinoma(45;0.0717)		CAGAAAGTTGCGATGCCTGCT	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	54	53	NA		NA	NA	6		NA											NA				2833961		2203	4300	6503	SO:0001583	missense			M93056	CCDS4477.1	6p25.2	2014-02-18	2005-08-18		ENSG00000021355	ENSG00000021355	1992		Serine (or cysteine) peptidase inhibitors	3311	protein-coding gene	gene with protein product		130135	serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1	ELANH2	NA	1376927, 24172014	Standard		NM_030666	NA	Approved	EI, PI2, anti-elastase	uc003mub.4	P30740	OTTHUMG00000014124	ENST00000380739.5:c.1021G>A	chr6.hg19:g.2833961C>T	ENSP00000370115:p.Ala341Thr	NA	A8K5L2|B4DNT0|Q53FB9|Q5W0E1|Q9UDF8	hg19	CCDS4477.1	0.02	17.964477	TTGxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010254	0.35511	.	.	ENSG00000021355	ENST00000380739;ENST00000542771;ENST00000537185	T;T	0.17370	2.28;2.78	5.57	3.68	0.42216	Serpin domain (3);	0.485574	0.23700	N	0.045430	T	0.06142	0.0159	L	0.42632	1.34	0.09310	N	0.999999	B	0.15719	0.014	B	0.17722	0.019	T	0.20907	-1.0261	10	0.48119	T	0.1	.	9.711	0.40245	0.1401:0.7865:0.0:0.0733	.	341	P30740	ILEU_HUMAN	T	341;303;190	ENSP00000370115:A341T;ENSP00000444543:A190T	ENSP00000370115:A341T	A	-	1	0	SERPINB1	2778960	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.219000	0.17641	1.512000	0.48834	0.650000	0.86243	GCA	NOVEL	SERPINB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039637.1	4	22.265931	KEEP	0	0	0	74	2484	CC	1	1	0		-	28	60	1002	0	0	69.072708	387	60	13326	582	ENST00000380739.5	0.06747	1
SLC22A23	63027	__UNKNOWN__	__UNKNOWN__	6	3410517	3410517	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:3410517G>A	ENST00000436008.2	-	3	1280	c.818C>T	c.(817-819)aCt>aTt	p.T273I	SLC22A23_ENST00000406686.3_Missense_Mutation_p.T273I|SLC22A23_ENST00000490273.1_5'UTR|SLC22A23_ENST00000380302.4_5'UTR|SLC22A23_ENST00000380298.2_Missense_Mutation_p.T273I			A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	273		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				CAGTGCCACAGTCAGTCCAAA	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													90	78	82	NA		NA	NA	6		NA											NA				3410517		2203	4300	6503	SO:0001583	missense			AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266	63027		Solute carriers	21106	protein-coding gene	gene with protein product		611697	chromosome 6 open reading frame 85	C6orf85	NA	17714910	Standard	NM_021945	NM_015482	NA	Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000436008.2:c.818C>T	chr6.hg19:g.3410517G>A	ENSP00000410245:p.Thr273Ile	NA	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	hg19		0.02	23.522967	ACAxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.50	3.141029	0.56936	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000485307;ENST00000467177;ENST00000380298	T;T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57;-0.57	5.17	5.17	0.71159	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.	.	.	.	T	0.58538	0.2129	N	0.21373	0.66	0.41919	D	0.990502	D;P	0.56287	0.975;0.728	P;P	0.50136	0.632;0.511	T	0.61426	-0.7065	9	0.39692	T	0.17	-10.7714	18.6697	0.91506	0.0:0.0:1.0:0.0	.	273;273	C9J4Z0;A1A5C7	.;S22AN_HUMAN	I	273;273;101;99;273	ENSP00000410245:T273I;ENSP00000385028:T273I;ENSP00000418134:T101I;ENSP00000418985:T99I;ENSP00000369653:T273I	ENSP00000369653:T273I	T	-	2	0	SLC22A23	3355516	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.689000	0.68234	2.421000	0.82119	0.563000	0.77884	ACT	NOVEL	SLC22A23-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039683.2	2	48.75568	KEEP	0	0	0	162	5834	GG	1	1	0		-	23	60	816	0	0	50.423518	575	60	21810	974	ENST00000436008.2	0.038462	1
SSR1	6745	__UNKNOWN__	__UNKNOWN__	6	7285591	7285591	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:7285591G>A	ENST00000244763.4	-	0	5453				SSR1_ENST00000474597.1_Intron|RP11-69L16.4_ENST00000379928.4_RNA	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					AGCAAAATCCGTAATACAACA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783	6745			11323	protein-coding gene	gene with protein product	translocon-associated protein alpha	600868			NA		Standard		NM_001292008	NA	Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000244763.4:c.*4506C>T	chr6.hg19:g.7285591G>A		NA	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	hg19	CCDS4499.1	0.02	4.622544	TCCxTAA	COVERED																																																																																			NOVEL	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039775.2	3	5.116417	KEEP	0	0	0	17	580	GG	0.999366	0.999365	0		-	20	60	731	0	0	59.166296	100	60	3503	166	ENST00000244763.4	0.166667	0.999999
TFAP2A	7020	__UNKNOWN__	__UNKNOWN__	6	10412348	10412348	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:10412348C>A	ENST00000482890.1	-	3	398				TFAP2A-AS1_ENST00000420777.1_RNA|TFAP2A_ENST00000379604.2_Intron|TFAP2A_ENST00000379613.3_Intron|TFAP2A_ENST00000319516.4_Intron|TFAP2A_ENST00000379608.3_5'UTR			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	NA		NA			anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				CAACTCGCGCCGGAGCCGGCT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203	7020			11742	protein-coding gene	gene with protein product		107580	transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)	TFAP2, AP2TF	NA	1916817, 3063603	Standard	NM_003220	NM_001032280	NA	Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.46-1780G>T	chr6.hg19:g.10412348C>A		NA	Q13777|Q5TAV5|Q8N1C6	hg19	CCDS4510.1	0.02	7.239732	CGCxGGA	COVERED																																																																																			NOVEL	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353619.2	0	13.842594	KEEP	0	0	0	46	1530	CC	1	1	0		-	37	60	1373	0	0	114.75934	148	60	5080	290	ENST00000482890.1	0.2	1
EDN1	1906	__UNKNOWN__	__UNKNOWN__	6	12297177	12297177	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:12297177T>A	ENST00000379375.5	+	0	1783					NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	NA		NA			artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				TTTAAAGCAGTAAAATTATTT	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401	1906		Endogenous ligands	3176	protein-coding gene	gene with protein product		131240			NA		Standard	NM_001955	NM_001168319	NA	Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.*877T>A	chr6.hg19:g.12297177T>A		NA	Q96DA1	hg19	CCDS4522.1	0.02	4.182757	CAGxAAA	COVERED																																																																																			NOVEL	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039872.1	1	7.221608	KEEP	0	0	0	24	757	TT	0.999909	0.999909	0		+	29	60	1038	0	0	87.035203	107	60	3796	209	ENST00000379375.5	0.213235	1
GMPR	2766	__UNKNOWN__	__UNKNOWN__	6	16247086	16247086	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:16247086G>A	ENST00000259727.4	+	2	215	c.101G>A	c.(100-102)cGc>cAc	p.R34H		NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	34		NA			nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				GATCTTGAACGCACCTTCACG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													135	124	128	NA		NA	NA	6		NA											NA				16247086		2203	4300	6503	SO:0001583	missense				CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	2766	1.7.1.7		4376	protein-coding gene	gene with protein product		139265			NA	2194676	Standard		NM_006877	NA	Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.101G>A	chr6.hg19:g.16247086G>A	ENSP00000259727:p.Arg34His	NA	Q96HQ6	hg19	CCDS4537.1	0.02	17.021002	AACxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	23.0	4.359465	0.82353	.	.	ENSG00000137198	ENST00000259727	T	0.78816	-1.21	5.37	5.37	0.77165	Aldolase-type TIM barrel (1);IMP dehydrogenase/GMP reductase (1);	0.094612	0.64402	D	0.000003	D	0.84179	0.5415	H	0.96269	3.795	0.80722	D	1	P	0.48350	0.909	B	0.42361	0.385	D	0.89721	0.3919	10	0.87932	D	0	-4.8474	19.4857	0.95027	0.0:0.0:1.0:0.0	.	34	P36959	GMPR1_HUMAN	H	34	ENSP00000259727:R34H	ENSP00000259727:R34H	R	+	2	0	GMPR	16355065	1.000000	0.71417	0.986000	0.45419	0.935000	0.57460	6.291000	0.72719	2.677000	0.91161	0.561000	0.74099	CGC	NOVEL	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039942.2	5	21.367465	KEEP	0	0	0	71	2414	GG	1	1	0		+	61	60	2109	0	0	168.66869	302	60	10416	554	ENST00000259727.4	0.168044	1
ATXN1	6310	__UNKNOWN__	__UNKNOWN__	6	16327660	16327660	__UNKNOWN__	Silent	SNP	G	G	T	rs200105223	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:16327660G>T	ENST00000244769.4	-	8	1818	c.882C>A	c.(880-882)gcC>gcA	p.A294A	ATXN1_ENST00000436367.1_Silent_p.A294A	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	294		NA			adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				TGCCGGAGTCGGCGTATTGCA	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	36	35	NA		NA	NA	6		NA											NA				16327660		2203	4300	6503	SO:0001819	synonymous_variant			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788	6310		Ataxins	10548	protein-coding gene	gene with protein product		601556	spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)	SCA1	NA	1582256	Standard	NM_000332	NM_000332	NA	Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.882C>A	chr6.hg19:g.16327660G>T		NA	Q17S02|Q9UJG2|Q9Y4J1	hg19	CCDS34342.1	0.02	13.501726	GTCxGCG	COVERED																																																																																			NOVEL	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039943.3	6	39.115108	KEEP	0	0	0	130	4211	GG	1	1	0		-	41	60	1429	0	0	108.69158	290	60	9389	579	ENST00000244769.4	0.123867	1
KIF13A	63971	__UNKNOWN__	__UNKNOWN__	6	17822031	17822031	__UNKNOWN__	Intron	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:17822031T>A	ENST00000259711.6	-	16	1892				KIF13A_ENST00000378826.2_Intron|KIF13A_ENST00000378816.5_Intron|KIF13A_ENST00000378814.5_Intron|KIF13A_ENST00000378843.2_Intron	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	NA		NA			ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			ATCCCAGTGTTTGTGGAGGAG	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177	63971		Kinesins	14566	protein-coding gene	gene with protein product		605433			NA	11106728	Standard		NM_022113	NA	Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.1786+3967A>T	chr6.hg19:g.17822031T>A		NA	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	hg19	CCDS47381.1	0.02	6.696936	TGTxTGT	COVERED																																																																																			NOVEL	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039954.4	1	12.337654	KEEP	0	0	0	41	1322	TT	1	1	0		-	35	60	1202	0	0	97.611003	154	60	5592	299	ENST00000259711.6	0.185185	1
HFE	3077	__UNKNOWN__	__UNKNOWN__	6	26098346	26098346	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:26098346T>G	ENST00000357618.5	+	0	5061					NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	NA		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACTACAATATTAAAGTATTTT	0.338	NA	NA							Hemochromatosis					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database			CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704	3077		Immunoglobulin superfamily / C1-set domain containing	4886	protein-coding gene	gene with protein product	high Fe	613609			NA	3460331	Standard		XR_241893	NA	Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.*3892T>G	chr6.hg19:g.26098346T>G		NA	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	hg19	CCDS4578.1	0.02	7.303937	TATxAAA	COVERED																																																																																			NOVEL	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356133.1	0	9.928583	KEEP	0	0	0	33	1012	TT	0.999998	0.999998	0		+	43	60	1628	0	0	139.302232	146	60	5244	244	ENST00000357618.5	0.227513	1
BTN2A2	10385	__UNKNOWN__	__UNKNOWN__	6	26394646	26394646	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:26394646C>A	ENST00000356709.4	+	0	3134				BTN2A2_ENST00000352867.2_3'UTR|BTN2A2_ENST00000469230.1_3'UTR	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	NA		NA			negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						ttctctccttctgttggctgg	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508	10385		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Butyrophilins	1137	protein-coding gene	gene with protein product		613591			NA	10354554, 9149941	Standard		NM_006995	NA	Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.*1451C>A	chr6.hg19:g.26394646C>A		NA	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	hg19	CCDS4606.1	0.02	13.216079	CTTxTGT	COVERED																																																																																			NOVEL	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040117.1	10	25.884447	KEEP	0	0	0	86	3099	CC	1	1	0		+	21	60	764	0	0	53.103765	288	60	11075	527	ENST00000356709.4	0.067961	1
ZSCAN9	7746	__UNKNOWN__	__UNKNOWN__	6	28195761	28195761	__UNKNOWN__	Intron	SNP	C	C	T	rs187306906		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:28195761C>T	ENST00000425468.2	+	3	733				ZSCAN9_ENST00000527436.1_Silent_p.C238C|ZSCAN9_ENST00000531979.1_Intron|ZSCAN9_ENST00000252207.5_Intron	NM_001199479.1	NP_001186408.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	NA		NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)				NA						GCCTAGTGTGCTCATCTTTGA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185	7746		-, Zinc fingers, C2H2-type	12984	protein-coding gene	gene with protein product		602246	zinc finger protein 193	ZNF193	NA		Standard	NM_006299	NM_001199479	NA	Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000425468.2:c.568+146C>T	chr6.hg19:g.28195761C>T		NA	B4E1W6|E7EVQ2|Q2TTR1	hg19	CCDS56407.1	0.02	15.197461	GTGxTCA	COVERED																																																																																			NOVEL	ZSCAN9-003	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383022.1	5	26.785765	KEEP	0	0	0	89	3165	CC	1	1	0		+	12	60	405	1	0	22.319141	434	60	16388	637	ENST00000425468.2	0.026906	1
ZNF311	282890	__UNKNOWN__	__UNKNOWN__	6	28964043	28964043	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:28964043G>A	ENST00000377179.3	-	7	1248	c.736C>T	c.(736-738)Ctc>Ttc	p.L246F	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	246		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						CATTCATGGAGTTTCTGTGCT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	97	91	NA		NA	NA	6		NA											NA				28964043		1510	2707	4217	SO:0001583	missense			AL833166	CCDS34357.1	6p21.33	2013-01-08			ENSG00000197935	ENSG00000197935	282890		Zinc fingers, C2H2-type, -	13847	protein-coding gene	gene with protein product		NA			NA		Standard	XM_212581	XM_006715067	NA	Approved		uc003nlu.2	Q5JNZ3	OTTHUMG00000031292	ENST00000377179.3:c.736C>T	chr6.hg19:g.28964043G>A	ENSP00000366384:p.Leu246Phe	NA	A2BFK5|B0S7Y4|Q92971	hg19	CCDS34357.1	0.02	16.004418	GGAxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.20	2.463589	0.43736	.	.	ENSG00000197935	ENST00000377179;ENST00000535083	T	0.29655	1.56	3.03	1.23	0.21249	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.15435	0.0372	L	0.38733	1.17	0.09310	N	1	P	0.44309	0.832	P	0.52267	0.694	T	0.09862	-1.0655	9	0.40728	T	0.16	0.5131	4.9634	0.14078	0.2869:0.0:0.7131:0.0	.	246	Q5JNZ3	ZN311_HUMAN	F	246;154	ENSP00000366384:L246F	ENSP00000366384:L246F	L	-	1	0	ZNF311	29072022	0.233000	0.23772	0.002000	0.10522	0.216000	0.24613	3.146000	0.50631	0.317000	0.23160	-0.225000	0.12378	CTC	NOVEL	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076631.3	8	18.961904	KEEP	0	0	0	63	2243	GG	1	1	0		-	81	60	2911	0	0	242.240054	319	60	11984	521	ENST00000377179.3	0.2025	1
TRIM10	10107	__UNKNOWN__	__UNKNOWN__	6	30128386	30128386	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:30128386G>A	ENST00000449742.2	-	1	325	c.250C>T	c.(250-252)Cgc>Tgc	p.R84C	TRIM10_ENST00000376704.3_Missense_Mutation_p.R84C	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	84		NA			erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						AGCTGGAGGCGCTCAATGTTC	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													144	142	143	NA		NA	NA	6		NA											NA				30128386		2203	4300	6503	SO:0001583	missense			Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613	10107		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	10072	protein-coding gene	gene with protein product		605701	tripartite motif-containing 10	RNF9	NA	9271628, 10207104	Standard		NM_052828	NA	Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.250C>T	chr6.hg19:g.30128386G>A	ENSP00000397073:p.Arg84Cys	NA	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	hg19	CCDS34375.1	0.02	31.246884	GGCxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.88	2.369316	0.42003	.	.	ENSG00000204613	ENST00000449742;ENST00000376704;ENST00000376706	D;D	0.84516	-1.86;-1.86	5.37	2.02	0.26589	Zinc finger, RING/FYVE/PHD-type (1);	0.152547	0.30723	N	0.009006	D	0.85695	0.5756	M	0.74647	2.275	0.21527	N	0.999656	D;D	0.89917	0.999;1.0	P;P	0.62014	0.791;0.897	T	0.78732	-0.2089	10	0.87932	D	0	.	10.9649	0.47406	0.0:0.0:0.4243:0.5757	.	84;84	Q9UDY6;Q9UDY6-2	TRI10_HUMAN;.	C	84	ENSP00000397073:R84C;ENSP00000365894:R84C	ENSP00000365894:R84C	R	-	1	0	TRIM10	30236365	0.000000	0.05858	0.924000	0.36721	0.274000	0.26718	0.506000	0.22658	0.722000	0.32252	0.549000	0.68633	CGC	NOVEL	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076634.1	6	25.578806	KEEP	0	0	0	85	2918	GG	1	1	0		-	121	60	4353	0	0	355.498902	551	60	19488	983	ENST00000449742.2	0.18006	1
GNL1	2794	__UNKNOWN__	__UNKNOWN__	6	30512336	30512336	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:30512336C>T	ENST00000376621.3	-	0	4307					NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						TTTCTCTCAGCTGGGACCTTT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590	2794			4413	protein-coding gene	gene with protein product		143024			NA	8180467	Standard		NM_005275	NA	Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.*1513G>A	chr6.hg19:g.30512336C>T		NA	B0S838|Q96CT5	hg19	CCDS4680.1	0.02	7.003047	CAGxTGG	COVERED																																																																																			NOVEL	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076241.2	1	12.03798	KEEP	0	0	0	40	1395	CC	1	1	0		-	45	60	1632	0	0	144.119752	110	60	4158	231	ENST00000376621.3	0.290323	1
GNL1	2794	__UNKNOWN__	__UNKNOWN__	6	30512473	30512473	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:30512473A>G	ENST00000376621.3	-	0	4170					NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GATGAACCTAAAGCAATATGT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590	2794			4413	protein-coding gene	gene with protein product		143024			NA	8180467	Standard		NM_005275	NA	Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.*1376T>C	chr6.hg19:g.30512473A>G		NA	B0S838|Q96CT5	hg19	CCDS4680.1	0.02	7.216256	CTAxAGC	COVERED																																																																																			NOVEL	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076241.2	0	12.33757	KEEP	0	0	0	41	1326	AA	1	1	0		-	20	60	778	0	0	59.155546	179	60	6517	292	ENST00000376621.3	0.100503	1
ATAT1	79969	__UNKNOWN__	__UNKNOWN__	6	30611806	30611806	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:30611806T>G	ENST00000376485.4	+	10	998				ATAT1_ENST00000330083.5_Intron|ATAT1_ENST00000318999.7_3'UTR|ATAT1_ENST00000376483.4_3'UTR|ATAT1_ENST00000468713.1_Intron|ATAT1_ENST00000319027.5_3'UTR|ATAT1_ENST00000376478.2_Intron|ATAT1_ENST00000329992.8_3'UTR					alpha tubulin acetyltransferase 1	NA		NA								cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	9						CCTGCCACACTTGCCCTTTGA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023220	CCDS4683.2, CCDS54978.1, CCDS59002.1	6p21.32	2014-06-17	2010-10-11	2010-10-11	ENSG00000137343	ENSG00000137343	79969	2.3.1.108		21186	protein-coding gene	gene with protein product	alpha-tubulin N-acetyltransferase	615556	chromosome 6 open reading frame 134	C6orf134	NA	20829795	Standard	NM_024909	NM_024909	NA	Approved	FLJ13158, Em:AB023049.7, MEC17	uc003nqv.3	Q5SQI0	OTTHUMG00000031219	ENST00000376485.4:c.968+1018T>G	chr6.hg19:g.30611806T>G		NA		hg19		0.02	9.208621	CACxTGC	COVERED																																																																																			NOVEL	ATAT1-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000076449.2	5	8.125122	KEEP	0	0	0	27	879	TT	0.999988	0.999988	0		+	17	60	577	0	0	40.205018	193	60	7119	275	ENST00000376485.4	0.080952	1
MDC1	9656	__UNKNOWN__	__UNKNOWN__	6	30673085	30673085	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs200569280		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:30673085C>T	ENST00000376406.3	-	10	4522	c.3875G>A	c.(3874-3876)cGg>cAg	p.R1292Q	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000376405.2_Missense_Mutation_p.R1028Q	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1292	Interaction with the PRKDC complex.|Pro-rich.	NA		Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GGTGGAAGGCCGGAGCTCAGG	0.547	NA	NA						Other conserved DNA damage response genes						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													134	150	144	NA		NA	NA	6		NA											NA				30673085		2203	4300	6503	SO:0001583	missense			D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337	9656			21163	protein-coding gene	gene with protein product		607593			NA	10975465, 12607005	Standard	NM_014641	NM_014641	NA	Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.3875G>A	chr6.hg19:g.30673085C>T	ENSP00000365588:p.Arg1292Gln	NA	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	hg19	CCDS34384.1	0.02	18.122141	GGCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.461	-0.889245	0.02511	.	.	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000422104	T;T	0.03580	3.88;3.88	3.06	1.87	0.25490	.	.	.	.	.	T	0.00328	0.0010	N	0.00642	-1.3	0.09310	N	1	B;B	0.28178	0.202;0.0	B;B	0.17979	0.02;0.0	T	0.32322	-0.9911	9	0.12766	T	0.61	.	5.0301	0.14405	0.0:0.2672:0.0:0.7328	.	1028;1292	Q14676-2;Q14676	.;MDC1_HUMAN	Q	1292;1028;899	ENSP00000365588:R1292Q;ENSP00000365587:R1028Q	ENSP00000365587:R1028Q	R	-	2	0	MDC1	30781064	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.260000	0.18424	0.132000	0.18615	-0.540000	0.04249	CGG	NOVEL	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076103.1	14	7.06154	KEEP	1	7	212	98	3277	CC	1	1	0		-	27	60	944	0	0	63.59562	403	60	13253	681	ENST00000376406.3	0.062791	1
DDR1	780	__UNKNOWN__	__UNKNOWN__	6	30858991	30858991	__UNKNOWN__	Intron	SNP	C	C	T	rs2524257		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:30858991C>T	ENST00000508312.1	+	5	871				DDR1_ENST00000513240.1_Intron|DDR1_ENST00000508472.1_Intron|DDR1_ENST00000454612.2_Intron|DDR1_ENST00000452441.1_Intron|DDR1_ENST00000324771.8_Intron|DDR1_ENST00000418800.2_Intron|DDR1_ENST00000376575.3_Intron|DDR1_ENST00000376568.3_Intron|DDR1_ENST00000446312.1_Intron|DDR1_ENST00000376570.4_Intron|DDR1_ENST00000376569.3_Intron|DDR1_ENST00000376567.2_Intron	NM_001202523.1	NP_001189452.1	Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	NA		NA			branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CCTTCTCCTGCTGGGAAGCTG	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	780	2.7.10.1	CD molecules	2730	protein-coding gene	gene with protein product		600408	discoidin domain receptor family, member 1	NTRK4, PTK3A, NEP, CAK, EDDR1	NA	7789998	Standard	NM_013994	NM_001954	NA	Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000508312.1:c.619+94C>T	chr6.hg19:g.30858991C>T		NA	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	hg19	CCDS56411.1	0.02	4.452657	CTGxTGG	COVERED																																																																																			NOVEL	DDR1-020	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369045.2	4	8.727951	KEEP	0	0	0	29	1012	CC	0.999997	0.999997	0		+	5	60	195	0	0	12.718987	123	60	4574	191	ENST00000508312.1	0.039062	1
HLA-B	3106	__UNKNOWN__	__UNKNOWN__	6	31324176	31324176	__UNKNOWN__	Silent	SNP	C	C	G	rs12721836	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:31324176C>G	ENST00000412585.2	-	3	415	c.387G>C	c.(385-387)ccG>ccC	p.P129P		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	129	Alpha-2.	NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GGCGCCCGTCCGGCCCCACGT	0.731	NA	NA							Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													20	17	18	NA		NA	NA	6		NA											NA				31324176		1973	4106	6079	SO:0001819	synonymous_variant	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745	3106		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4932	protein-coding gene	gene with protein product		142830	ankylosing spondylitis	AS	NA	3459708	Standard	NM_005514	NM_005514	NA	Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.387G>C	chr6.hg19:g.31324176C>G		NA	Q29764	hg19	CCDS34394.1	0.02	3.446536	GTCxGGC	COVERED																																																																																			NOVEL	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076280.4	4	11.732844	KEEP	1	3	85	69	2277	CC	1	1	0		-	4	39	137	0	0	11.701245	12	60	404	270	ENST00000412585.2	0.25	1
ABHD16A	7920	__UNKNOWN__	__UNKNOWN__	6	31657401	31657401	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:31657401G>T	ENST00000440843.2	-	10	1240	c.939C>A	c.(937-939)ccC>ccA	p.P313P	ABHD16A_ENST00000395952.3_Silent_p.P346P|XXbac-BPG32J3.20_ENST00000461287.1_3'UTR|ABHD16A_ENST00000471644.1_5'UTR|ABHD16A_ENST00000375842.4_Silent_p.P127P	NM_001177515.1	NP_001170986.1	O95870	ABHGA_HUMAN	abhydrolase domain containing 16A	346		NA				integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10						TGATGTCCTGGGGCTGGAAGC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													78	49	59	NA		NA	NA	6		NA											NA				31657401		1510	2708	4218	SO:0001819	synonymous_variant			AF129756	CCDS4713.1, CCDS54988.1	6p21.3	2013-01-17	2010-12-09	2010-12-09	ENSG00000204427	ENSG00000204427	7920		Abhydrolase domain containing	13921	protein-coding gene	gene with protein product		142620	HLA-B associated transcript 5	BAT5	NA	2911734, 2813433	Standard		NM_021160	NA	Approved	NG26, D6S82E	uc003nvy.2	O95870	OTTHUMG00000031177	ENST00000440843.2:c.939C>A	chr6.hg19:g.31657401G>T		NA	A2BEY3|B7Z4R6|Q5SRR1|Q5SRR2|Q8WYH0|Q9NW33	hg19	CCDS54988.1	0.02	6.48244	CTGxGGC	COVERED																																																																																			NOVEL	ABHD16A-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268005.2	3	11.436155	KEEP	0	0	0	38	1307	GG	1	1	0		-	6	60	212	0	0	12.817515	163	60	5794	262	ENST00000440843.2	0.035503	1
HSPA1A	3303	__UNKNOWN__	__UNKNOWN__	6	31785243	31785243	__UNKNOWN__	Silent	SNP	G	G	T	rs541340	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:31785243G>T	ENST00000375651.5	+	1	1953	c.1710G>T	c.(1708-1710)gtG>gtT	p.V570V	HSPA1A_ENST00000458062.2_Silent_p.V479V|HSPA1A_ENST00000608703.1_Silent_p.V405V	NM_005345.5	NP_005336.3	P08107	HSP71_HUMAN	heat shock 70kDa protein 1A	570		NA			ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)	aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618)			endometrium(1)|ovary(1)|stomach(1)	3						AGAAGAAGGTGCTGGACAAGT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													107	66	79	NA		NA	NA	6		NA											NA				31785243		1995	4077	6072	SO:0001819	synonymous_variant			BC002453	CCDS34414.1	6p21.3	2012-10-02	2002-08-29		ENSG00000204389	ENSG00000204389	3303		Heat shock proteins / HSP70	5232	protein-coding gene	gene with protein product		140550	heat shock 70kD protein 1A	HSPA1	NA		Standard		NM_005345	NA	Approved	HSP70-1	uc003nxj.3	P08107	OTTHUMG00000031201	ENST00000375651.5:c.1710G>T	chr6.hg19:g.31785243G>T		NA	B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0	hg19	CCDS34414.1	0.02	-0.349729	GGTxCTG	COVERED																																																																																			NOVEL	HSPA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076401.2	0	6.957623	KEEP	3	1	31	34	1224	GG	0.999998	0.877706	0		+	4	40	140	0	0	10.269023	36	50	1275	96	ENST00000375651.5	0.1	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	31978824	31978824	__UNKNOWN__	IGR	SNP	G	G	A	rs148766553	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:31978824G>A			NA	NA				CYP21A1P (2596 upstream) : C4B (3714 downstream)						NA		NA									NA						CCCTGAAAACGTTGGGGATCG	0.632	NA	NA											A|||	356	0.0710863	0.0794	0.0461	5008	,	,	NA	16533	0.127	NA	0.0249	False	NA	,,,	NA	NA	NA	2504	0.0675	NA	NA	NA						NA		NA				0													48	52	51	NA		NA	NA	6		NA											NA				31978824		682	1542	2224	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.31978824G>A		NA		hg19		0.02	4.005695	AACxTTG	COVERED																																																																																			NOVEL					0			1	3.112661	KEEP	4	3	90	42	1419	GG	1	1	0			5	39	187	0	0	11.647197	140	60	4920	249		0.034483	1
NOTCH4	4855	__UNKNOWN__	__UNKNOWN__	6	32181881	32181881	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:32181881T>C	ENST00000375023.3	-	13	2306				NOTCH4_ENST00000465528.1_Intron	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	NA		NA			cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TTAGGGAGGGTCTCACCTGTG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													97	92	94	NA		NA	NA	6		NA											NA				32181881		2203	4300	6503	SO:0001627	intron_variant				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301	4855		Ankyrin repeat domain containing	7884	protein-coding gene	gene with protein product		164951	Notch (Drosophila) homolog 4, Notch homolog 4 (Drosophila)	INT3	NA	7835890	Standard		NM_004557	NA	Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.2167+5A>G	chr6.hg19:g.32181881T>C		NA	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	hg19	CCDS34420.1	0.02	2.11759	GGGxCTC	COVERED																																																																																			NOVEL	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076045.2	1	3.609911	KEEP	0	0	0	12	363	TT	0.994391	0.988129	0		-	5	60	172	0	0	11.933846	60	60	2070	94	ENST00000375023.3	0.076923	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	32242010	32242010	__UNKNOWN__	IGR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:32242010C>A			NA	NA				XXbac-BPG154L12.4 (8395 upstream) : C6orf10 (14292 downstream)						NA		NA									NA						AAATAACATACAGCTACTAAA	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.32242010C>A		NA		hg19		0.02	3.915028	ATAxAGC	COVERED																																																																																			NOVEL					0			1	6.320654	KEEP	0	0	0	21	749	CC	0.999869	0.999868	0			6	27	214	0	0	13.899017	115	60	4385	171		0.049587	0.999999
HLA-DRB1	3123	__UNKNOWN__	__UNKNOWN__	6	32551911	32551911	__UNKNOWN__	Silent	SNP	C	C	A	rs17882028	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:32551911C>A	ENST00000360004.5	-	2	450	c.345G>T	c.(343-345)gtG>gtT	p.V115V		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	115	Beta-1.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TGAAGCTCTCCACAACCCCGT	0.642	NA	NA								Multiple Myeloma(14;0.17)			A|||	1757	0.350839	0.3306	0.3602	5008	,	,	NA	5381	0.37	NA	0.3579	False	NA	,,,	NA	NA	NA	2504	0.3446	NA	NA	NA						NA		NA				0			GRCh37	CP044520	HLA-DRB1	X	rs17882028						32	31	31	NA		NA	NA	6		NA											NA				32551911		2139	4237	6376	SO:0001819	synonymous_variant			AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126	3123		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B	NA		Standard	NM_002124	NM_001243965	NA	Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.345G>T	chr6.hg19:g.32551911C>A		NA	P01914|Q9MYF5	hg19	CCDS47409.1	0.02	7.127346	CTCxACA	COVERED																																																																																			NOVEL	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076393.3	7	3.115311	KEEP	3	3	66	34	1190	CC	1	1	0		-	13	40	456	0	0	51.80025	0	0	0	250	ENST00000360004.5	1	1
HLA-DOA	3111	__UNKNOWN__	__UNKNOWN__	6	32975870	32975870	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:32975870C>A	ENST00000229829.5	-	2	326	c.251G>T	c.(250-252)gGc>gTc	p.G84V	HLA-DOA_ENST00000495532.1_5'UTR|HLA-DOA_ENST00000450833.2_Missense_Mutation_p.G54V	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	84	Alpha-1.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						GGCCAGCCCGCCCTGCGGGTC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													49	50	50	NA		NA	NA	6		NA											NA				32975870		1511	2709	4220	SO:0001583	missense			M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252	3111		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA	NA	2370084	Standard	NM_002119	XM_005272804	NA	Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.251G>T	chr6.hg19:g.32975870C>A	ENSP00000229829:p.Gly84Val	NA	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	hg19	CCDS4763.1	0.02	13.567553	CCGxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.17	2.156739	0.38119	.	.	ENSG00000204252	ENST00000229829;ENST00000450833	T;T	0.33865	1.39;1.39	4.5	-4.31	0.03698	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	2.302910	0.01371	N	0.012582	T	0.30885	0.0779	M	0.81497	2.545	0.09310	N	1	D;B	0.53312	0.959;0.306	P;B	0.48304	0.573;0.094	T	0.48007	-0.9072	10	0.87932	D	0	.	11.1375	0.48383	0.0:0.3607:0.0:0.6393	.	54;84	B4DW77;P06340	.;DOA_HUMAN	V	84;54	ENSP00000229829:G84V;ENSP00000403896:G54V	ENSP00000229829:G84V	G	-	2	0	HLA-DOA	33083848	0.000000	0.05858	0.000000	0.03702	0.194000	0.23727	-1.488000	0.02308	-1.178000	0.02741	0.561000	0.74099	GGC	NOVEL	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076426.2	2	50.240925	KEEP	0	0	0	167	5770	CC	1	1	0		-	110	60	3781	0	0	340.092046	216	60	7858	655	ENST00000229829.5	0.337423	1
PNPLA1	285848	__UNKNOWN__	__UNKNOWN__	6	36238217	36238217	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:36238217G>T	ENST00000312917.5	+	2	59				PNPLA1_ENST00000388715.3_Intron			Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	NA		NA			lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						GCCTTCCGCAGAAAGTCAGAG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	16	15	NA		NA	NA	6		NA											NA				36238217		692	1590	2282	SO:0001627	intron_variant				CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316	285848		Patatin-like phospholipase domain containing	21246	protein-coding gene	gene with protein product		612121			NA	16799181, 19029121	Standard	NM_173676	NM_001145717	NA	Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000312917.5:c.-80-20880G>T	chr6.hg19:g.36238217G>T		NA	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	hg19	CCDS47416.1	0.02	2.14723	GCAxAAA	COVERED																																																																																			NOVEL	PNPLA1-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280647.1	2	3.586961	KEEP	0	1	8	15	521	GG	0.997832	0.995734	0		+	28	60	1002	0	0	92.453003	45	60	1683	104	ENST00000312917.5	0.383562	0.997898
UNC5CL	222643	__UNKNOWN__	__UNKNOWN__	6	40996274	40996274	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:40996274G>C	ENST00000373164.1	-	8	1455	c.1395C>G	c.(1393-1395)aaC>aaG	p.N465K	UNC5CL_ENST00000244565.3_Missense_Mutation_p.N465K|UNC5CL_ENST00000470102.1_5'UTR			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	465	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.	NA			positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCAGGCTGCCGTTCTGCTCCT	0.642	NA	NA									OREG0017423	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	46	46	NA		NA	NA	6		NA											NA				40996274		2193	4285	6478	SO:0001583	missense			BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602	222643			21203	protein-coding gene	gene with protein product	ZU5 and death domain containing	NA			NA	14769797	Standard	NM_173561	NM_173561	NA	Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1395C>G	chr6.hg19:g.40996274G>C	ENSP00000362258:p.Asn465Lys	897	Q5TGU1	hg19	CCDS4847.1	0.02	4.361356	GCCxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814613	0.70912	.	.	ENSG00000124602	ENST00000244565;ENST00000373164	D;D	0.85484	-1.99;-1.99	4.53	-1.26	0.09376	Death (3);DEATH-like (2);	0.000000	0.45867	D	0.000328	T	0.67692	0.2920	L	0.29908	0.895	0.33601	D	0.602311	P	0.44734	0.842	P	0.48270	0.572	T	0.64373	-0.6423	10	0.42905	T	0.14	-22.2371	8.3846	0.32493	0.5513:0.0:0.4487:0.0	.	465	Q8IV45	UN5CL_HUMAN	K	465	ENSP00000244565:N465K;ENSP00000362258:N465K	ENSP00000244565:N465K	N	-	3	2	UNC5CL	41104252	0.094000	0.21725	0.996000	0.52242	0.998000	0.95712	-1.392000	0.02523	-0.202000	0.10268	0.563000	0.77884	AAC	NOVEL	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040491.1	0	17.754424	KEEP	0	0	0	59	1961	GG	1	1	0		-	6	60	205	0	0	12.878198	121	60	4258	261	ENST00000373164.1	0.047244	1
PRPH2	5961	__UNKNOWN__	__UNKNOWN__	6	42665682	42665682	__UNKNOWN__	3'UTR	SNP	C	C	T	rs551934443		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:42665682C>T	ENST00000230381.5	-	0	1631					NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	NA		NA			cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			CCCTCAGATACGGCCAGTGGC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619	5961		Tetraspanins	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	retinal degeneration, slow (retinitis pigmentosa 7), retinal degeneration, slow	RP7, RDS	NA	1749427	Standard	NM_000322	NM_000322	NA	Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.*351G>A	chr6.hg19:g.42665682C>T		NA	Q5TFH5|Q6DK65	hg19	CCDS4871.1	0.02	4.889125	ATAxGGC	COVERED																																																																																			NOVEL	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040556.1	5	6.887417	KEEP	0	0	0	23	744	CC	0.999892	0.99986	0		-	41	60	1475	0	0	137.647095	59	60	2104	142	ENST00000230381.5	0.41	0.999968
SRF	6722	__UNKNOWN__	__UNKNOWN__	6	43147720	43147720	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:43147720G>A	ENST00000265354.4	+	0	2677					NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	NA		NA			angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			CGTTTTTCTCGTCCCCCTCCC	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658	6722			11291	protein-coding gene	gene with protein product		600589			NA	3203386	Standard	NM_003131	NM_003131	NA	Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.*792G>A	chr6.hg19:g.43147720G>A		NA	Q5T648	hg19	CCDS4889.1	0.02	-0.254384	CTCxTCC	COVERED																																																																																			NOVEL	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040581.1	1	3.91048	KEEP	0	0	0	13	405	GG	0.994391	0.664773	0		+	4	60	141	0	0	11.022603	24	60	769	50	ENST00000265354.4	0.142857	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	43474650	43474650	__UNKNOWN__	IGR	SNP	G	G	A	rs541185783		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:43474650G>A			NA	NA				TJAP1 (356 upstream) : LRRC73 (56 downstream)						NA		NA									NA						CTTACTGGTAGTTCCAATTCC	0.562	NA	NA									OREG0017453	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.43474650G>A		916		hg19		0.02	6.90339	GTAxTTC	COVERED																																																																																			NOVEL					0			2	17.738992	KEEP	0	0	0	59	2062	GG	1	1	0			64	60	2283	0	0	213.193146	91	60	3407	282		0.412903	1
HSP90AB1	3326	__UNKNOWN__	__UNKNOWN__	6	44221293	44221293	__UNKNOWN__	Silent	SNP	C	C	T	rs147025760	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:44221293C>T	ENST00000371554.1	+	12	2347	c.2133C>T	c.(2131-2133)ctC>ctT	p.L711L	HSP90AB1_ENST00000371646.5_Silent_p.L711L|HSP90AB1_ENST00000353801.3_Silent_p.L711L			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	711		NA			axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TCCCCCCTCTCGAGGGCGATG	0.493	NA	NA									OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													78	80	79	NA		NA	NA	6		NA											NA				44221293		2203	4300	6503	SO:0001819	synonymous_variant			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384	3326		Heat shock proteins / HSPC	5258	protein-coding gene	gene with protein product		140572	heat shock 90kD protein 1, beta, heat shock 90kDa protein 1, beta	HSPC2, HSPCB	NA	2768249, 16269234	Standard	NM_007355	NM_001271969	NA	Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2133C>T	chr6.hg19:g.44221293C>T		922	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	hg19	CCDS4909.1	0.02	19.160607	TCTxGAG	COVERED																																																																																			NOVEL	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040730.1	4	10.174395	KEEP	0	10	308	142	4776	CC	1	1	0		+	20	51	720	0	0	45.75634	444	60	16031	766	ENST00000371554.1	0.043103	1
HSP90AB1	3326	__UNKNOWN__	__UNKNOWN__	6	44221299	44221299	__UNKNOWN__	Silent	SNP	C	C	T	rs143048794	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:44221299C>T	ENST00000371554.1	+	12	2353	c.2139C>T	c.(2137-2139)ggC>ggT	p.G713G	HSP90AB1_ENST00000371646.5_Silent_p.G713G|HSP90AB1_ENST00000353801.3_Silent_p.G713G			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	713		NA			axon guidance (GO:0007411)|cellular response to interleukin-4 (GO:0071353)|cellular response to organic cyclic compound (GO:0071407)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|placenta development (GO:0001890)|positive regulation of cell size (GO:0045793)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein folding (GO:0006457)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to salt stress (GO:0009651)|response to unfolded protein (GO:0006986)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP binding (GO:0002135)|dATP binding (GO:0032564)|double-stranded RNA binding (GO:0003725)|GTP binding (GO:0005525)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|poly(A) RNA binding (GO:0044822)|TPR domain binding (GO:0030911)|UTP binding (GO:0002134)	p.G713G(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(12)|prostate(2)|skin(2)|urinary_tract(2)	33	all_cancers(18;1.7e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTCTCGAGGGCGATGAGGATG	0.498	NA	NA									OREG0017471	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	lung(1)											79	82	81	NA		NA	NA	6		NA											NA				44221299		2203	4300	6503	SO:0001819	synonymous_variant			AF275719	CCDS4909.1	6p12	2011-09-02	2006-02-24	2006-02-24	ENSG00000096384	ENSG00000096384	3326		Heat shock proteins / HSPC	5258	protein-coding gene	gene with protein product		140572	heat shock 90kD protein 1, beta, heat shock 90kDa protein 1, beta	HSPC2, HSPCB	NA	2768249, 16269234	Standard	NM_007355	NM_001271969	NA	Approved		uc031sor.1	P08238	OTTHUMG00000014761	ENST00000371554.1:c.2139C>T	chr6.hg19:g.44221299C>T		922	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	hg19	CCDS4909.1	0.02	19.485002	GGGxGAT	COVERED																																																																																			NOVEL	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040730.1	6	3.546645	KEEP	0	13	378	145	4977	CC	1	1	0		+	23	59	747	0	0	45.570631	462	60	16677	811	ENST00000371554.1	0.047423	1
RUNX2	860	__UNKNOWN__	__UNKNOWN__	6	45516580	45516580	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:45516580C>G	ENST00000371438.1	+	0	3462				RUNX2_ENST00000371432.3_3'UTR|RUNX2_ENST00000359524.5_3'UTR|RUNX2_ENST00000576263.1_Intron	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	NA		NA			BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						CTGCCTTACCCAAGGCCCCAC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813	860			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1	NA	7835892	Standard	NM_004348	NM_001024630	NA	Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.*1538C>G	chr6.hg19:g.45516580C>G		NA	O14614|O14615|O95181	hg19	CCDS43467.2	0.02	7.315135	ACCxAAG	COVERED																																																																																			NOVEL	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040755.2	2	19.862017	KEEP	0	0	0	66	2291	CC	1	1	0		+	56	60	1975	0	0	178.30308	109	60	4055	284	ENST00000371438.1	0.339394	1
GPR116	221395	__UNKNOWN__	__UNKNOWN__	6	46821625	46821625	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:46821625G>A	ENST00000283296.7	-	0	4433				GPR116_ENST00000362015.4_3'UTR|GPR116_ENST00000456426.2_3'UTR|GPR116_ENST00000545669.1_3'UTR|GPR116_ENST00000265417.7_3'UTR	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	NA		NA			energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			ATCTGCTCCCGGAAACCTGCC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(59;410 1274 8751 36715 50546)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122	221395		-, GPCR / Class B : Orphans, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	19030	protein-coding gene	gene with protein product		NA			NA	12435584	Standard	NM_015234	NM_001098518	NA	Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.*104C>T	chr6.hg19:g.46821625G>A		NA	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	hg19	CCDS4919.1	0.02	24.632045	CCCxGAA	COVERED																																																																																			NOVEL	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040806.2	7	44.230591	KEEP	0	0	0	147	4970	GG	1	1	0		-	65	60	2506	0	0	196.666797	453	60	15611	886	ENST00000283296.7	0.125483	1
GPR116	221395	__UNKNOWN__	__UNKNOWN__	6	46838416	46838416	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:46838416G>C	ENST00000283296.7	-	11	1700				GPR116_ENST00000362015.4_Intron|GPR116_ENST00000456426.2_Intron|GPR116_ENST00000545669.1_Intron|GPR116_ENST00000265417.7_Intron	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	NA		NA			energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CCATGAATTTGGTCCTCTTGA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(59;410 1274 8751 36715 50546)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122	221395		-, GPCR / Class B : Orphans, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	19030	protein-coding gene	gene with protein product		NA			NA	12435584	Standard	NM_015234	NM_001098518	NA	Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.1411+1163C>G	chr6.hg19:g.46838416G>C		NA	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	hg19	CCDS4919.1	0.02	4.807861	TTTxGTC	COVERED																																																																																			NOVEL	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040806.2	1	9.029653	KEEP	0	0	0	30	1090	GG	0.999997	0.999997	0		-	52	60	1913	0	0	177.455953	81	60	3094	199	ENST00000283296.7	0.390977	1
GPR111	222611	__UNKNOWN__	__UNKNOWN__	6	47650123	47650123	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:47650123C>A	ENST00000507065.1	+	6	1902	c.1624C>A	c.(1624-1626)Cca>Aca	p.P542T	GPR111_ENST00000398742.2_Missense_Mutation_p.P542T|GPR111_ENST00000296862.1_Missense_Mutation_p.P610T			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	610		NA			G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						CTTCGTGATCCCAGCTTTGGC	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	59	59	NA		NA	NA	6		NA											NA				47650123		2057	4205	6262	SO:0001583	missense			AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393	222611		-, GPCR / Class B : Orphans	18991	protein-coding gene	gene with protein product		NA			NA	12435584	Standard	NM_153839	NM_153839	NA	Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000507065.1:c.1624C>A	chr6.hg19:g.47650123C>A	ENSP00000422934:p.Pro542Thr	NA	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	hg19		0.02	4.622328	ATCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	23.9	4.465747	0.84425	.	.	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.60171	0.21;0.21;0.21	5.64	5.64	0.86602	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000006	T	0.80904	0.4713	M	0.93854	3.465	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85457	0.1164	10	0.87932	D	0	.	18.6743	0.91523	0.0:1.0:0.0:0.0	.	542;610	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	T	542;610;542	ENSP00000422934:P542T;ENSP00000296862:P610T;ENSP00000381727:P542T	ENSP00000296862:P610T	P	+	1	0	GPR111	47758082	1.000000	0.71417	0.998000	0.56505	0.918000	0.54935	6.069000	0.71209	2.651000	0.90000	0.655000	0.94253	CCA	NOVEL	GPR111-003	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000358929.1	2	6.620477	KEEP	0	0	0	22	736	CC	0.999879	0.999877	0		+	21	60	760	0	0	61.855477	99	60	3517	160	ENST00000507065.1	0.175	0.999999
ICK	22858	__UNKNOWN__	__UNKNOWN__	6	52878665	52878665	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:52878665T>C	ENST00000350082.5	-	9	1293	c.947A>G	c.(946-948)tAt>tGt	p.Y316C	ICK_ENST00000356971.3_Missense_Mutation_p.Y316C	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	316		NA			intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					TGGCTTAATATAAGGAGGTGG	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													140	117	125	NA		NA	NA	6		NA											NA				52878665		2203	4300	6503	SO:0001583	missense			AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144	22858			21219	protein-coding gene	gene with protein product		612325			NA	12103360	Standard	NM_016513	NM_014920	NA	Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.947A>G	chr6.hg19:g.52878665T>C	ENSP00000263043:p.Tyr316Cys	NA	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	hg19	CCDS4949.1	0.02	4.896891	ATAxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	12.70	2.015416	0.35511	.	.	ENSG00000112144	ENST00000350082;ENST00000356971	T;T	0.71934	-0.61;-0.61	6.06	4.88	0.63580	.	0.523104	0.21644	N	0.071290	T	0.37865	0.1019	N	0.08118	0	0.09310	N	1	B	0.28258	0.205	B	0.38056	0.264	T	0.40701	-0.9549	10	0.36615	T	0.2	-5.7039	12.6634	0.56826	0.1239:0.0:0.0:0.8761	.	316	Q9UPZ9	ICK_HUMAN	C	316	ENSP00000263043:Y316C;ENSP00000349458:Y316C	ENSP00000263043:Y316C	Y	-	2	0	ICK	52986624	1.000000	0.71417	0.068000	0.19968	0.942000	0.58702	2.627000	0.46469	1.087000	0.41251	0.533000	0.62120	TAT	NOVEL	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040952.1	3	14.535563	KEEP	0	1	24	57	1624	TT	1	0.999999	0		-	38	60	1377	0	0	122.825904	85	60	2886	232	ENST00000350082.5	0.308943	0.999999
GCM1	8521	__UNKNOWN__	__UNKNOWN__	6	52998966	52998966	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:52998966C>A	ENST00000259803.7	-	3	443	c.232G>T	c.(232-234)Ggt>Tgt	p.G78C		NM_003643.3	NP_003634.2	Q9NP62	GCM1_HUMAN	glial cells missing homolog 1 (Drosophila)	78		NA			anatomical structure morphogenesis (GO:0009653)|astrocyte fate commitment (GO:0060018)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell differentiation involved in embryonic placenta development (GO:0060706)|positive regulation of syncytium formation by plasma membrane fusion (GO:0060143)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|skin(1)	24	Lung NSC(77;0.0755)					ACCACCACACCCAGGCAGGAC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													113	106	108	NA		NA	NA	6		NA											NA				52998966		2203	4300	6503	SO:0001583	missense			D88613	CCDS4950.1	6p21-p12	2008-08-29	2001-11-28	2002-09-27	ENSG00000137270	ENSG00000137270	8521			4197	protein-coding gene	gene with protein product		603715	glial cells missing (Drosophila) homolog a	GCMA	NA	8962155	Standard		NM_003643	NA	Approved	hGCMa	uc003pbp.3	Q9NP62	OTTHUMG00000014871	ENST00000259803.7:c.232G>T	chr6.hg19:g.52998966C>A	ENSP00000259803:p.Gly78Cys	NA	Q4VAQ7|Q5T0X0|Q99468|Q9P1X3	hg19	CCDS4950.1	0.02	6.019556	CACxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.4	4.916080	0.92178	.	.	ENSG00000137270	ENST00000259803	D	0.85258	-1.96	4.84	4.84	0.62591	.	0.076501	0.53938	D	0.000043	D	0.91212	0.7231	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92116	0.5700	10	0.87932	D	0	0.0187	18.1392	0.89633	0.0:1.0:0.0:0.0	.	78	Q9NP62	GCM1_HUMAN	C	78	ENSP00000259803:G78C	ENSP00000259803:G78C	G	-	1	0	GCM1	53106925	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.530000	0.81962	2.492000	0.84095	0.655000	0.94253	GGT	NOVEL	GCM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040953.1	1	14.982448	KEEP	0	0	0	50	1691	CC	1	1	0		-	6	60	221	0	0	13.280444	193	60	6838	319	ENST00000259803.7	0.030151	1
DST	667	__UNKNOWN__	__UNKNOWN__	6	56418200	56418200	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:56418200C>A	ENST00000361203.3	-	57	14764	c.14757G>T	c.(14755-14757)ggG>ggT	p.G4919G	DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Silent_p.G2833G|DST_ENST00000370788.2_Silent_p.G2833G|DST_ENST00000370769.4_Silent_p.G4921G|DST_ENST00000370754.5_Silent_p.G5099G|DST_ENST00000244364.6_Silent_p.G2507G|DST_ENST00000446842.2_Silent_p.G4595G			Q03001	DYST_HUMAN	dystonin	4919		NA			axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CCTTCTCAGACCCTTGTGTTT	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													114	108	110	NA		NA	NA	6		NA											NA				56418200		1822	4084	5906	SO:0001819	synonymous_variant			M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914	667		EF-hand domain containing	1090	protein-coding gene	gene with protein product		113810	bullous pemphigoid antigen 1, 230/240kDa	BPAG1	NA	2461961, 2276744	Standard	NM_001723	NM_001144770	NA	Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.14757G>T	chr6.hg19:g.56418200C>A		NA	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	hg19		0.02	4.681985	AGAxCCT	COVERED																																																																																			NOVEL	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000041021.3	6	12.641141	KEEP	0	0	0	42	1474	CC	1	0.999973	0		-	30	60	1059	0	0	93.411051	72	60	2515	175	ENST00000361203.3	0.294118	0.999973
ZNF451	26036	__UNKNOWN__	__UNKNOWN__	6	56989164	56989164	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:56989164G>A	ENST00000370706.4	+	4	430				RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|ZNF451_ENST00000491832.2_Intron|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|ZNF451_ENST00000370702.1_Intron|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000586668.1_RNA|ZNF451_ENST00000357489.3_Intron	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			gttcctgctagaaggtttctg	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200	26036		Zinc fingers, C2H2-type	21091	protein-coding gene	gene with protein product		615708			NA	9628581	Standard	NM_015555	NM_001031623	NA	Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.187-368G>A	chr6.hg19:g.56989164G>A		NA	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	hg19	CCDS43477.1	0.02	4.212527	CTAxAAG	COVERED																																																																																			NOVEL	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041035.2	0	15.348578	KEEP	0	0	0	51	1781	GG	1	1	0		+	23	60	837	0	0	67.213761	121	60	4525	225	ENST00000370706.4	0.159722	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58445582	58445582	__UNKNOWN__	IGR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:58445582T>C			NA	NA				XXbac-BPG55C20.7 (147086 upstream) : RP11-143A22.1 (43305 downstream)						NA		NA									NA						CTATATGACTTGAATCTCCCC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58445582T>C		NA		hg19		0.02	10.259977	ACTxGAA	COVERED																																																																																			NOVEL					0			3	18.055852	KEEP	4	0	0	60	1916	TT	1	1	0			9	41	330	0	0	20.314889	251	60	9274	412		0.034615	1
PTP4A1	7803	__UNKNOWN__	__UNKNOWN__	6	64292331	64292331	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:64292331T>C	ENST00000370651.3	+	0	3927				PTP4A1_ENST00000370650.2_3'UTR	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	NA		NA			cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			TTATAAACCTTATCTGTACAT	0.239	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(91;1019 1502 28028 38110 51645)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245	7803		Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs	9634	protein-coding gene	gene with protein product		601585			NA	9642300	Standard		NM_003463	NA	Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.*2252T>C	chr6.hg19:g.64292331T>C		NA	B2R6C8|O00648|Q49A54	hg19	CCDS4965.1	0.02	4.755407	CCTxATC	COVERED																																																																																			NOVEL	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041083.2	2	9.623841	KEEP	0	0	0	32	954	TT	0.999997	0.999997	0		+	24	60	884	0	0	72.081989	115	60	4097	192	ENST00000370651.3	0.172662	1
PHF3	23469	__UNKNOWN__	__UNKNOWN__	6	64416013	64416013	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:64416013T>C	ENST00000262043.3	+	12	3802	c.3462T>C	c.(3460-3462)agT>agC	p.S1154S	PHF3_ENST00000393387.1_Silent_p.S1154S			Q92576	PHF3_HUMAN	PHD finger protein 3	1154		NA			multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			AAGCAGAAAGTATAGCAGATG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(135;136 1820 29512 34071 46235)					NA		NA				0													118	107	111	NA		NA	NA	6		NA											NA				64416013		2203	4300	6503	SO:0001819	synonymous_variant			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482	23469		Zinc fingers, PHD-type	8921	protein-coding gene	gene with protein product		607789			NA	11856869	Standard		XM_005248701	NA	Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.3462T>C	chr6.hg19:g.64416013T>C		NA	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	hg19	CCDS4966.1	0.02	13.845204	AAGxATA	COVERED																																																																																			NOVEL	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041086.2	2	20.151353	KEEP	0	0	0	67	2038	TT	1	1	0		+	16	60	600	0	0	40.12284	301	60	10541	465	ENST00000262043.3	0.050473	1
EYS	346007	__UNKNOWN__	__UNKNOWN__	6	65300193	65300193	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs563441026		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:65300193C>T	ENST00000503581.1	-	26	6104	c.5567G>A	c.(5566-5568)cGg>cAg	p.R1856Q	EYS_ENST00000370616.2_Missense_Mutation_p.R1856Q|EYS_ENST00000370621.3_Missense_Mutation_p.R1856Q	NM_001142800.1	NP_001136272.1	Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1856		NA			detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GGGAAGATGCCGGCTTGCAGT	0.433	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	19879	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													132	130	131	NA		NA	NA	6		NA											NA				65300193		692	1591	2283	SO:0001583	missense				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107	346007			21555	protein-coding gene	gene with protein product		612424	chromosome 6 open reading frame 180, EGF-like-domain, multiple 11, retinitis pigmentosa 25 (autosomal recessive), EGF-like-domain, multiple 10, chromosome 6 open reading frame 178, chromosome 6 open reading frame 179	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179	NA	18836446, 18976725	Standard	XM_294050	NM_001142800	NA	Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000503581.1:c.5567G>A	chr6.hg19:g.65300193C>T	ENSP00000424243:p.Arg1856Gln	NA	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	hg19	CCDS47445.1	0.02	19.532276	TGCxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.544	-0.540933	0.04053	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84516	-1.86;-1.84;-1.84	6.17	0.337	0.15966	.	.	.	.	.	T	0.43233	0.1238	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29427	-1.0012	9	0.24483	T	0.36	.	2.3658	0.04318	0.221:0.086:0.4069:0.286	.	1856;1856	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	Q	1856	ENSP00000424243:R1856Q;ENSP00000359655:R1856Q;ENSP00000359650:R1856Q	ENSP00000359650:R1856Q	R	-	2	0	EYS	65356914	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.585000	0.05794	0.500000	0.27991	-0.302000	0.09304	CGG	NOVEL	EYS-012	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359944.1	3	14.747281	KEEP	0	0	0	49	1683	CC	1	1	0		-	85	70	3198	0	0	266.508586	356	60	12263	626	ENST00000503581.1	0.192744	1
COL9A1	1297	__UNKNOWN__	__UNKNOWN__	6	70993305	70993305	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:70993305C>G	ENST00000357250.6	-	6	939				COL9A1_ENST00000370496.3_Intron	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	NA		NA			axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|organ morphogenesis (GO:0009887)|tissue homeostasis (GO:0001894)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(44)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)	80						CTAGTCAGTACAGCAAAGCAC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4971.1, CCDS47447.1	6q13	2013-05-07			ENSG00000112280	ENSG00000112280	1297		Proteoglycans / Extracellular Matrix : Collagen proteoglycans, Collagens	2217	protein-coding gene	gene with protein product		120210			NA	1429648	Standard		NM_001851	NA	Approved		uc003pfg.4	P20849	OTTHUMG00000014988	ENST00000357250.6:c.780+134G>C	chr6.hg19:g.70993305C>G		NA	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	hg19	CCDS4971.1	0.02	2.012249	GTAxAGC	COVERED																																																																																			NOVEL	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041131.2	2	5.417908	KEEP	0	0	0	18	656	CC	0.999859	0.998727	0		-	5	60	178	0	0	12.15326	72	60	2705	110	ENST00000357250.6	0.064935	0.998867
OGFRL1	79627	__UNKNOWN__	__UNKNOWN__	6	72006075	72006075	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:72006075G>A	ENST00000370435.4	+	4	590	c.456G>A	c.(454-456)gaG>gaA	p.E152E	RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000591156.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	152		NA				membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						AAAAACTGGAGCACAACCACA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	97	98	NA		NA	NA	6		NA											NA				72006075		2203	4298	6501	SO:0001819	synonymous_variant				CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900	79627			21378	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024576	NM_024576	NA	Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.456G>A	chr6.hg19:g.72006075G>A		NA	Q2TAC1|Q8NEQ4|Q9H7B5	hg19	CCDS34482.1	0.02	1.936779	GGAxCAC	COVERED																																																																																			NOVEL	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041153.2	0	9.930946	KEEP	0	0	0	33	1143	GG	0.999998	0.999937	0		+	15	60	567	0	0	45.717292	82	60	3145	170	ENST00000370435.4	0.154639	0.99994
EEF1A1	1915	__UNKNOWN__	__UNKNOWN__	6	74226849	74226849	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:74226849T>A	ENST00000316292.9	-	0	3064					NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	NA		NA			cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						TGGCAAATAGTCAACTTTCAC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508	1915			3189	protein-coding gene	gene with protein product		130590	leukocyte receptor cluster (LRC) member 7	EF1A, EEF1A, LENG7	NA	8812466, 10941842	Standard	NM_001402	NM_001402	NA	Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.*684A>T	chr6.hg19:g.74226849T>A		NA	P04719|P04720|Q6IQ15	hg19	CCDS4980.1	0.02	8.073881	TAGxCAA	COVERED																																																																																			NOVEL	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041210.2	2	22.868587	KEEP	0	0	0	76	2422	TT	1	1	0		-	11	60	396	0	0	25.546932	225	60	7983	401	ENST00000316292.9	0.04661	1
CD109	135228	__UNKNOWN__	__UNKNOWN__	6	74533922	74533922	__UNKNOWN__	3'UTR	SNP	G	G	A	rs538732902		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:74533922G>A	ENST00000287097.5	+	0	5015				CD109_ENST00000422508.2_3'UTR|CD109_ENST00000437994.2_3'UTR			Q6YHK3	CD109_HUMAN	CD109 molecule	NA		NA			negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TAAGTGGCACGGTCTTTTTCT	0.453	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	14181	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535	135228		CD molecules	21685	protein-coding gene	gene with protein product		608859	CD109 antigen (Gov platelet alloantigens)		NA	11861284, 11861285	Standard	NM_133493	XM_005248659	NA	Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.*565G>A	chr6.hg19:g.74533922G>A		NA	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	hg19	CCDS4982.1	0.02	2.035149	CACxGTC	COVERED																																																																																			NOVEL	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041230.3	1	8.125258	KEEP	0	0	0	27	902	GG	0.999988	0.999665	0		+	13	60	479	0	0	38.259087	73	60	2416	152	ENST00000287097.5	0.151163	0.999678
ME1	4199	__UNKNOWN__	__UNKNOWN__	6	84108134	84108134	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:84108134G>A	ENST00000369705.3	-	3	430	c.314C>T	c.(313-315)aCt>aTt	p.T105I	ME1_ENST00000543031.1_Missense_Mutation_p.T30I|ME1_ENST00000541327.1_Intron	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	105		NA			carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)			NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		CAGACCCACAGTGGGAGTATA	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	62	63	NA		NA	NA	6		NA											NA				84108134		2203	4300	6503	SO:0001583	missense			X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	4199	1.1.1.40		6983	protein-coding gene	gene with protein product		154250			NA	8187880	Standard		NM_002395	NA	Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.314C>T	chr6.hg19:g.84108134G>A	ENSP00000358719:p.Thr105Ile	NA	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	hg19	CCDS34492.1	0.02	2.006752	ACAxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	29.0	4.967132	0.92855	.	.	ENSG00000065833	ENST00000369705;ENST00000543031	T;T	0.56275	0.47;0.47	5.86	5.86	0.93980	Malic enzyme, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.75874	0.3909	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79410	-0.1815	10	0.87932	D	0	-23.7321	20.1876	0.98223	0.0:0.0:1.0:0.0	.	105	P48163	MAOX_HUMAN	I	105;30	ENSP00000358719:T105I;ENSP00000446114:T30I	ENSP00000358719:T105I	T	-	2	0	ME1	84164853	1.000000	0.71417	0.996000	0.52242	0.976000	0.68499	9.864000	0.99589	2.765000	0.95021	0.655000	0.94253	ACT	NOVEL	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041350.1	0	11.437942	KEEP	0	0	0	38	1409	GG	1	0.999804	0		-	10	60	376	0	0	28.789936	79	60	3100	193	ENST00000369705.3	0.11236	0.999804
SNX14	57231	__UNKNOWN__	__UNKNOWN__	6	86299084	86299084	__UNKNOWN__	Intron	SNP	G	G	A	rs535392163	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:86299084G>A	ENST00000314673.3	-	1	317				SNX14_ENST00000513865.1_Intron|RP11-321N4.5_ENST00000503906.1_Intron|SNX14_ENST00000369627.2_Intron|SNX14_ENST00000346348.3_Intron|SNX14_ENST00000505648.1_Intron	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	NA		NA			protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		gactacagacgtgtacctcca	0.527	NA	NA											G|||	2	0.000399361	0	0	5008	,	,	NA	16159	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317	57231		Sorting nexins	14977	protein-coding gene	gene with protein product		NA			NA	11485546, 11736640	Standard	NM_153816	XM_005248738	NA	Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.140+4212C>T	chr6.hg19:g.86299084G>A		NA	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	hg19	CCDS5004.1	0.02	2.143856	GACxTGT	COVERED																																																																																			NOVEL	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041393.2	5	11.433989	KEEP	0	0	0	38	1292	GG	1	0.990964	0		-	11	60	409	0	0	33.56273	51	60	1851	119	ENST00000314673.3	0.177419	0.990964
RNGTT	8732	__UNKNOWN__	__UNKNOWN__	6	89322348	89322348	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:89322348T>C	ENST00000369485.4	-	0	2070				RNGTT_ENST00000538899.1_3'UTR|RNGTT_ENST00000265607.6_3'UTR	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		CAAGCCACAGTCGTTTTTCAA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	8732	2.7.7.50	Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases	10073	protein-coding gene	gene with protein product		603512			NA	9828141, 9512541	Standard		NM_001286428	NA	Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.*90A>G	chr6.hg19:g.89322348T>C		NA	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	hg19	CCDS5017.1	0.02	2.024351	CAGxCGT	COVERED																																																																																			NOVEL	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041469.1	2	5.115467	KEEP	0	0	0	17	563	TT	0.999366	0.999093	0		-	6	60	223	0	0	15.682979	81	60	2919	125	ENST00000369485.4	0.068966	0.999726
MDN1	23195	__UNKNOWN__	__UNKNOWN__	6	90405412	90405412	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:90405412C>A	ENST00000369393.3	-	61	9798	c.9683G>T	c.(9682-9684)gGc>gTc	p.G3228V	MDN1_ENST00000428876.1_Missense_Mutation_p.G3228V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3228		NA			ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTGGAGCAAGCCGAGGCTCAC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	52	52	NA		NA	NA	6		NA											NA				90405412		2203	4299	6502	SO:0001583	missense			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159	23195			18302	protein-coding gene	gene with protein product		NA			NA	9205841, 12102729	Standard		XM_005248699	NA	Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.9683G>T	chr6.hg19:g.90405412C>A	ENSP00000358400:p.Gly3228Val	NA	O15019|Q5T794	hg19	CCDS5024.1	0.02	4.557621	AAGxCGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602079	0.66445	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.08546	3.08;3.08	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.24661	0.0598	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.02852	-1.1102	10	0.87932	D	0	.	18.6816	0.91548	0.0:1.0:0.0:0.0	.	3228	Q9NU22	MDN1_HUMAN	V	3228	ENSP00000358400:G3228V;ENSP00000413970:G3228V	ENSP00000358400:G3228V	G	-	2	0	MDN1	90462133	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.451000	0.80668	2.420000	0.82092	0.655000	0.94253	GGC	NOVEL	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041514.2	0	11.133669	KEEP	0	0	0	37	1262	CC	1	0.999997	0		-	43	60	1542	0	0	141.503152	73	60	2607	195	ENST00000369393.3	0.37069	0.999997
MANEA	79694	__UNKNOWN__	__UNKNOWN__	6	96034883	96034883	__UNKNOWN__	Intron	SNP	G	G	A	rs202081145		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:96034883G>A	ENST00000358812.4	+	2	678				MANEA_ENST00000369293.1_Missense_Mutation_p.V190M	NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	NA		NA			cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		atatatatatgtgtgtttgtg	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													18	22	21	NA		NA	NA	6		NA											NA				96034883		1761	3295	5056	SO:0001627	intron_variant			AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469	79694			21072	protein-coding gene	gene with protein product		612327			NA		Standard	NM_024641	NM_024641	NA	Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.544+24G>A	chr6.hg19:g.96034883G>A		NA	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	hg19	CCDS5032.1	0.02	-0.333369	TATxTGT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.675|9.675	1.147818|1.147818	0.21288|0.21288	.|.	.|.	ENSG00000172469|ENSG00000172469	ENST00000542500|ENST00000369293	.|.	.|.	.|.	4.95|4.95	1.15|1.15	0.20763|0.20763	.|.	.|.	.|.	.|.	.|.	T|T	0.17238|0.17238	0.0414|0.0414	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.28427|0.28427	-1.0044|-1.0044	5|5	0.10377|0.52906	T|T	0.69|0.07	.|.	3.4897|3.4897	0.07633|0.07633	0.3796:0.0:0.4482:0.1723|0.3796:0.0:0.4482:0.1723	.|.	.|.	.|.	.|.	Y|M	189|190	.|.	ENSP00000439775:C189Y|ENSP00000358299:V190M	C|V	+|+	2|1	0|0	MANEA|MANEA	96141604|96141604	0.000000|0.000000	0.05858|0.05858	0.003000|0.003000	0.11579|0.11579	0.001000|0.001000	0.01503|0.01503	-0.298000|-0.298000	0.08265|0.08265	0.021000|0.021000	0.15133|0.15133	-0.907000|-0.907000	0.02831|0.02831	TGT|GTG	NOVEL	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043644.1	1	6.019803	KEEP	0	0	0	20	721	GG	0.999863	0.851867	0		+	3	60	111	0	0	7.974244	35	60	1340	70	ENST00000358812.4	0.078947	0.851984
SCML4	256380	__UNKNOWN__	__UNKNOWN__	6	108071042	108071042	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:108071042A>T	ENST00000369020.3	-	3	402				SCML4_ENST00000369021.3_Intron|SCML4_ENST00000369022.2_Intron	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CCATTTGGTCAATGAGAATCT	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	49	48	NA		NA	NA	6		NA											NA				108071042		2203	4300	6503	SO:0001627	intron_variant				CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285	256380		Sterile alpha motif (SAM) domain containing	21397	protein-coding gene	gene with protein product		NA			NA		Standard	XM_171128	NM_001286409	NA	Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.157-25T>A	chr6.hg19:g.108071042A>T		NA	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	hg19	CCDS5060.2	0.02	4.643182	GTCxATG	COVERED																																																																																			NOVEL	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041700.3	1	11.733597	KEEP	0	0	0	39	1189	AA	1	1	0		-	8	60	310	0	0	21.794995	121	60	4507	230	ENST00000369020.3	0.062016	1
FOXO3	2309	__UNKNOWN__	__UNKNOWN__	6	108985092	108985092	__UNKNOWN__	Silent	SNP	C	C	G	rs200866771		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:108985092C>G	ENST00000343882.6	+	3	1360	c.1056C>G	c.(1054-1056)gcC>gcG	p.A352A	FOXO3_ENST00000406360.1_Silent_p.A352A|FOXO3_ENST00000540898.1_Silent_p.A132A	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	352		NA		PMLYSSSASLSPSVSKP -> AHALQHVSQPVTFSKQA (in Ref. 6; CAA04860). {ECO:0000305}.	antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A352A(2)		central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		GCAGCTCAGCCAGCCTGTCAC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|prostate(1)											63	54	57	NA		NA	NA	6		NA											NA				108985092		2203	4300	6503	SO:0001819	synonymous_variant			AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689	2309		Forkhead boxes	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A	NA	9479491	Standard		NM_001455	NA	Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.1056C>G	chr6.hg19:g.108985092C>G		NA	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	hg19	CCDS5068.1	0.02	6.365368	AGCxAGC	COVERED																																																																																			NOVEL	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041722.2	4	21.302763	KEEP	0	1	32	82	2857	CC	1	1	0		+	14	39	431	0	0	28.766963	157	70	5722	309	ENST00000343882.6	0.081871	1
FIG4	9896	__UNKNOWN__	__UNKNOWN__	6	110036293	110036293	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs370608837		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:110036293G>A	ENST00000230124.3	+	2	203	c.79G>A	c.(79-81)Gtt>Att	p.V27I	FIG4_ENST00000441478.2_De_novo_Start_InFrame	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	27		NA			cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		ATACTTTCTAGTTGGGAGCAA	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													68	71	70	NA		NA	NA	6		NA											NA				110036293		2203	4300	6503	SO:0001583	missense			D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367	9896			16873	protein-coding gene	gene with protein product		609390	KIAA0274, FIG4 homolog (S. cerevisiae), FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)	KIAA0274	NA	9039502, 11274189, 17572665	Standard	NM_014845	NM_014845	NA	Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.79G>A	chr6.hg19:g.110036293G>A	ENSP00000230124:p.Val27Ile	NA	Q53H49|Q5TCS6	hg19	CCDS5078.1	0.02	2.131767	CTAxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.25	3.342277	0.61073	.	.	ENSG00000112367	ENST00000230124;ENST00000454215	T;T	0.76968	0.2;-1.06	5.68	5.68	0.88126	.	0.213063	0.40144	N	0.001161	T	0.57095	0.2030	L	0.33293	1	0.80722	D	1	P	0.49559	0.925	B	0.38683	0.279	T	0.59637	-0.7417	10	0.18710	T	0.47	-26.9801	19.3889	0.94570	0.0:0.0:1.0:0.0	.	27	Q92562	FIG4_HUMAN	I	27;6	ENSP00000230124:V27I;ENSP00000412156:V6I	ENSP00000230124:V27I	V	+	1	0	FIG4	110142986	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	8.993000	0.93524	2.668000	0.90789	0.563000	0.77884	GTT	NOVEL	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041768.1	1	5.05429	KEEP	0	0	0	17	570	GG	0.999859	0.967289	0		+	4	60	144	0	0	10.185627	48	60	1818	80	ENST00000230124.3	0.076923	0.967425
SLC16A10	117247	__UNKNOWN__	__UNKNOWN__	6	111543357	111543357	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:111543357G>T	ENST00000368851.5	+	6	1642	c.1467G>T	c.(1465-1467)atG>atT	p.M489I	SLC16A10_ENST00000368850.3_Missense_Mutation_p.M175I	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	489		NA			amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	AAGAAAAGATGGAGAAAATGT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													112	115	114	NA		NA	NA	6		NA											NA				111543357		2203	4300	6503	SO:0001583	missense			AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394	117247		Solute carriers	17027	protein-coding gene	gene with protein product		607550	solute carrier family 16 (monocarboxylic acid transporters), member 10		NA	11278508, 11827462	Standard		NM_018593	NA	Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.1467G>T	chr6.hg19:g.111543357G>T	ENSP00000357844:p.Met489Ile	NA	B3KWY0|Q6ZMG0|Q8WVI5	hg19	CCDS5089.1	0.02	7.1676	GATxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.135	0.580572	0.13686	.	.	ENSG00000112394	ENST00000368851;ENST00000368850	T;T	0.22539	3.32;1.95	5.52	3.76	0.43208	Major facilitator superfamily domain (1);	1.071010	0.07088	N	0.838293	T	0.07143	0.0181	L	0.42245	1.32	0.22762	N	0.998763	B	0.09022	0.002	B	0.22386	0.039	T	0.40289	-0.9571	10	0.36615	T	0.2	.	5.4065	0.16324	0.2246:0.0:0.625:0.1505	.	489	Q8TF71	MOT10_HUMAN	I	489;175	ENSP00000357844:M489I;ENSP00000357843:M175I	ENSP00000357843:M175I	M	+	3	0	SLC16A10	111650050	0.869000	0.29996	0.960000	0.40013	0.081000	0.17604	0.931000	0.28871	0.694000	0.31654	0.655000	0.94253	ATG	NOVEL	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041822.2	4	13.543172	KEEP	0	0	0	45	1589	GG	1	1	0		+	41	60	1492	0	0	129.347393	118	60	4406	252	ENST00000368851.5	0.257862	1
FABP7	2173	__UNKNOWN__	__UNKNOWN__	6	123102727	123102727	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:123102727C>T	ENST00000368444.3	+	3	668				FABP7_ENST00000356535.4_3'UTR	NM_001446.3	NP_001437.1	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain	NA		NA			cell proliferation in forebrain (GO:0021846)|epithelial cell proliferation (GO:0050673)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|prepulse inhibition (GO:0060134)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5				GBM - Glioblastoma multiforme(226;0.226)	Alpha-Linolenic Acid(DB00132)|Dihomo-gamma-linolenic acid(DB00154)|Icosapent(DB00159)	AAGAGAATCTCAGACAGATGA	0.249	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D88648	CCDS5127.1	6q22-q23	2013-03-01			ENSG00000164434	ENSG00000164434	2173		Fatty acid binding protein family	3562	protein-coding gene	gene with protein product	brain lipid binding protein	602965			NA	9375786	Standard	NM_001446	NM_001446	NA	Approved	B-FABP, BLBP	uc003pzf.3	O15540	OTTHUMG00000015489	ENST00000368444.3:c.348+388C>T	chr6.hg19:g.123102727C>T		NA	B2R4L1|O14951|Q6IAU7|Q9H047	hg19	CCDS5127.1	0.02	2.024599	TCTxAGA	COVERED																																																																																			NOVEL	FABP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042037.1	5	11.437275	KEEP	0	0	0	38	1353	CC	1	0.999726	0		+	29	60	1020	0	0	91.79105	58	60	2184	145	ENST00000368444.3	0.333333	0.999726
SMPDL3A	10924	__UNKNOWN__	__UNKNOWN__	6	123110513	123110513	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs560776858		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:123110513G>C	ENST00000368440.4	+	1	199	c.22G>C	c.(22-24)Gtc>Ctc	p.V8L	SMPDL3A_ENST00000539041.1_5'UTR|SMPDL3A_ENST00000487215.1_3'UTR	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	8		NA			sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|cervix(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(226;0.236)		GCGCGCACTCGTCTGCTGCCT	0.721	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	11833	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													6	6	6	NA		NA	NA	6		NA											NA				123110513		1716	3155	4871	SO:0001583	missense			AK000184	CCDS5128.1, CCDS69190.1	6q22.32	2006-04-12			ENSG00000172594	ENSG00000172594	10924			17389	protein-coding gene	gene with protein product	acid sphingomyelinase-like phosphodiesterase 3a	610728			NA	12442002	Standard	NM_006714	XM_005266798	NA	Approved	FLJ20177, ASM3A, ASML3a, yR36GH4.1	uc003pzg.3	Q92484	OTTHUMG00000015490	ENST00000368440.4:c.22G>C	chr6.hg19:g.123110513G>C	ENSP00000357425:p.Val8Leu	NA	B7Z729|Q8WV13	hg19	CCDS5128.1	0.02	7.253623	CTCxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	5.189	0.220334	0.09863	.	.	ENSG00000172594	ENST00000368440	T	0.09723	2.95	3.93	-0.203	0.13204	.	1.112990	0.06948	N	0.814129	T	0.01592	0.0051	N	0.08118	0	0.28966	N	0.889554	B	0.06786	0.001	B	0.04013	0.001	T	0.48115	-0.9063	10	0.24483	T	0.36	-0.0817	9.6252	0.39746	0.0:0.5131:0.3471:0.1398	.	8	Q92484	ASM3A_HUMAN	L	8	ENSP00000357425:V8L	ENSP00000357425:V8L	V	+	1	0	SMPDL3A	123152212	0.009000	0.17119	0.079000	0.20413	0.013000	0.08279	-0.412000	0.07132	-0.057000	0.13199	0.561000	0.74099	GTC	NOVEL	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042039.1	2	76.421772	KEEP	0	0	0	254	8125	GG	1	1	0		+	62	60	2208	0	0	201.558358	110	60	3675	526	ENST00000368440.4	0.360465	1
KIAA0408	9729	__UNKNOWN__	__UNKNOWN__	6	127768592	127768592	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:127768592T>C	ENST00000483725.3	-	5	1208	c.872A>G	c.(871-873)gAa>gGa	p.E291G	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	291		NA								endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		GTCTAACCTTTCCTTCCATCT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													127	126	126	NA		NA	NA	6		NA											NA				127768592		2203	4300	6503	SO:0001583	missense			AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367	9729			21636	protein-coding gene	gene with protein product		NA			NA		Standard	NM_014702	NM_014702	NA	Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.872A>G	chr6.hg19:g.127768592T>C	ENSP00000435150:p.Glu291Gly	NA	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	hg19	CCDS34531.1	0.02	7.151459	CTTxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	T	7.480	0.648443	0.14516	.	.	ENSG00000189367	ENST00000483725	T	0.35789	1.29	5.32	-1.54	0.08584	.	0.608369	0.13862	U	0.357604	T	0.14098	0.0341	M	0.61703	1.905	0.09310	N	1	B	0.11235	0.004	B	0.11329	0.006	T	0.35201	-0.9798	10	0.59425	D	0.04	0.1544	6.6025	0.22708	0.0:0.4433:0.1442:0.4125	.	291	Q6ZU52	K0408_HUMAN	G	291	ENSP00000435150:E291G	ENSP00000435150:E291G	E	-	2	0	KIAA0408	127810285	0.000000	0.05858	0.010000	0.14722	0.283000	0.27025	-0.102000	0.10956	-0.255000	0.09486	0.528000	0.53228	GAA	NOVEL	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042145.3	1	14.137709	KEEP	0	0	0	47	1446	TT	1	1	0		-	52	60	1869	0	0	167.848687	108	60	3901	261	ENST00000483725.3	0.325	1
LAMA2	3908	__UNKNOWN__	__UNKNOWN__	6	129581935	129581935	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:129581935T>C	ENST00000421865.2	+	15	2225	c.2176T>C	c.(2176-2178)Tgc>Cgc	p.C726R		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	726	Laminin EGF-like 5; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.	NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AGTGTGTCAGTGCCCACCAGG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													195	175	182	NA		NA	NA	6		NA											NA				129581935		2203	4300	6503	SO:0001583	missense			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569	3908		Laminins	6482	protein-coding gene	gene with protein product	merosin, congenital muscular dystrophy	156225		LAMM	NA	2185464, 8294519	Standard		NM_000426	NA	Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.2176T>C	chr6.hg19:g.129581935T>C	ENSP00000400365:p.Cys726Arg	NA	Q14736|Q5VUM2|Q93022	hg19	CCDS5138.1	0.02	4.746832	CAGxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	T	16.12	3.031957	0.54790	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.72282	-0.64	5.58	5.58	0.84498	EGF-like, laminin (1);	0.000000	0.85682	D	0.000000	D	0.85396	0.5687	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89209	0.3563	10	0.87932	D	0	.	14.7315	0.69386	0.0:0.0:0.0:1.0	.	726;726	A6NF00;P24043	.;LAMA2_HUMAN	R	726	ENSP00000400365:C726R	ENSP00000346769:C726R	C	+	1	0	LAMA2	129623628	1.000000	0.71417	0.999000	0.59377	0.234000	0.25298	6.215000	0.72206	2.120000	0.65058	0.528000	0.53228	TGC	NOVEL	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042180.1	1	21.345584	KEEP	0	0	0	71	2142	TT	1	1	0		+	36	60	1274	0	0	109.924018	104	60	3757	271	ENST00000421865.2	0.257143	1
VNN2	8875	__UNKNOWN__	__UNKNOWN__	6	133078882	133078882	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:133078882C>A	ENST00000326499.6	-	1	265	c.141G>T	c.(139-141)caG>caT	p.Q47H	VNN2_ENST00000526192.1_5'UTR|VNN2_ENST00000525289.1_Missense_Mutation_p.Q47H|VNN2_ENST00000525270.1_De_novo_Start_OutOfFrame	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	47	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.	NA			cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		AGGCATCCTCCTGAGAAACTG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													132	130	131	NA		NA	NA	6		NA											NA				133078882		2203	4300	6503	SO:0001583	missense			AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	8875	3.5.1.92	Vanins	12706	protein-coding gene	gene with protein product	pantetheinase	603571			NA	9790769, 11491533	Standard		NM_078488	NA	Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.141G>T	chr6.hg19:g.133078882C>A	ENSP00000322276:p.Gln47His	NA	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	hg19	CCDS5161.1	0.02	17.046938	CTCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	c	8.631	0.893618	0.17613	.	.	ENSG00000112303	ENST00000326499;ENST00000525289;ENST00000524919;ENST00000532012	D;D;D;T	0.88124	-2.34;-2.23;-1.67;-1.38	5.59	-5.51	0.02568	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (2);	1.075010	0.07178	N	0.853493	T	0.56062	0.1960	N	0.04880	-0.145	0.09310	N	1	P;B	0.41569	0.755;0.001	P;B	0.48141	0.568;0.004	T	0.58896	-0.7555	10	0.41790	T	0.15	0.2594	0.6013	0.00745	0.228:0.1622:0.2407:0.3691	.	47;47	O95498-2;O95498	.;VNN2_HUMAN	H	47	ENSP00000322276:Q47H;ENSP00000436935:Q47H;ENSP00000431451:Q47H;ENSP00000431680:Q47H	ENSP00000322276:Q47H	Q	-	3	2	VNN2	133120575	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.335000	0.02662	-1.036000	0.03287	-0.215000	0.12644	CAG	NOVEL	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042264.2	6	27.386768	KEEP	0	0	0	91	3195	CC	1	1	0		-	13	60	475	0	0	28.581608	404	60	15013	618	ENST00000326499.6	0.031175	1
BCLAF1	9774	__UNKNOWN__	__UNKNOWN__	6	136582092	136582092	__UNKNOWN__	3'UTR	SNP	C	C	A	rs62431280	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:136582092C>A	ENST00000531224.1	-	0	3171				BCLAF1_ENST00000031135.9_3'UTR|BCLAF1_ENST00000527536.1_3'UTR|BCLAF1_ENST00000527759.1_3'UTR|BCLAF1_ENST00000530767.1_3'UTR|BCLAF1_ENST00000353331.4_3'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	NA		NA			apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		TCTACTATTTCTCAAGATATT	0.239	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(142;1534 1789 5427 7063 28491)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363	9774			16863	protein-coding gene	gene with protein product		612588			NA	8724849, 10330179	Standard	NM_014739	NM_001077440	NA	Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.*156G>T	chr6.hg19:g.136582092C>A		NA	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	hg19	CCDS5177.1	0.02	8.539796	TTTxTCA	COVERED																																																																																			NOVEL	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042375.2	9	13.246474	KEEP	0	3	94	77	2672	CC	1	1	0		-	42	60	1472	0	0	120.966183	175	60	6618	324	ENST00000531224.1	0.193548	1
UTRN	7402	__UNKNOWN__	__UNKNOWN__	6	145120481	145120481	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:145120481A>G	ENST00000367545.3	+	63	9245				UTRN_ENST00000367526.4_Intron	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	NA		NA			aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CCTTGCTGCTATGCATTCTAA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818	7402			12635	protein-coding gene	gene with protein product		128240	utrophin (homologous to dystrophin)	DMDL	NA	1426262	Standard		NM_007124	NA	Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.9245+1355A>G	chr6.hg19:g.145120481A>G		NA	Q5SYY1|Q5SZ57|Q9UJ40	hg19	CCDS34547.1	0.02	11.980941	GCTxTGC	COVERED																																																																																			NOVEL	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042551.1	2	28.276123	KEEP	0	0	0	94	2931	AA	1	1	0		+	10	60	388	0	0	24.842818	270	60	9794	470	ENST00000367545.3	0.035714	1
SYNE1	23345	__UNKNOWN__	__UNKNOWN__	6	152605306	152605306	__UNKNOWN__	Splice_Site	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:152605306G>A	ENST00000367255.5	-	96	18615	c.18014C>T	c.(18013-18015)gCa>gTa	p.A6005V	SYNE1_ENST00000448038.1_Splice_Site_p.A5934V|SYNE1_ENST00000341594.5_Splice_Site_p.A5617V|SYNE1_ENST00000356820.4_Splice_Site_p.A529V|SYNE1_ENST00000423061.1_Splice_Site_p.A5934V|SYNE1_ENST00000265368.4_Splice_Site_p.A6005V	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	6005		NA			cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ATCCATCAATGCCTGGAGGAA	0.493	NA	NA								HNSCC(10;0.0054)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													62	53	56	NA		NA	NA	6		NA											NA				152605306		2203	4300	6503	SO:0001630	splice_region_variant			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018	23345			17089	protein-coding gene	gene with protein product	myocyte nuclear envelope protein 1, nuclear envelope spectrin repeat-1	608441	chromosome 6 open reading frame 98	C6orf98	NA	9872452, 10878022	Standard	NM_182961	NM_182961	NA	Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.18013-1C>T	chr6.hg19:g.152605306G>A		NA	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	hg19	CCDS5236.2	0.02	6.498487	AATxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126447	0.56721	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000540663	T;T;T;T;T;T;T	0.46819	1.2;1.2;1.2;1.2;1.2;0.86;1.2	5.84	5.84	0.93424	.	0.098768	0.44285	N	0.000467	T	0.38374	0.1038	L	0.35723	1.085	0.32684	N	0.515109	D;B;B;P	0.54964	0.969;0.003;0.003;0.909	P;B;B;P	0.48627	0.584;0.005;0.005;0.48	T	0.20974	-1.0259	10	0.41790	T	0.15	.	20.2031	0.98269	0.0:0.0:1.0:0.0	.	420;6005;6005;5934	B7ZBD0;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	V	6005;5934;6005;5934;5617;529;180	ENSP00000356224:A6005V;ENSP00000396024:A5934V;ENSP00000265368:A6005V;ENSP00000390975:A5934V;ENSP00000341887:A5617V;ENSP00000349276:A529V;ENSP00000437411:A180V	ENSP00000265368:A6005V	A	-	2	0	SYNE1	152646999	0.999000	0.42202	0.967000	0.41034	0.994000	0.84299	2.522000	0.45572	2.785000	0.95823	0.650000	0.86243	GCA	NOVEL	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334755.2	2	16.548329	KEEP	0	0	0	55	1977	GG	1	1	0	Missense_Mutation	-	62	60	2153	0	0	197.034485	105	60	4003	290	ENST00000367255.5	0.371257	1
TULP4	56995	__UNKNOWN__	__UNKNOWN__	6	158902234	158902234	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:158902234G>A	ENST00000367097.3	+	8	2756	c.1399G>A	c.(1399-1401)Ggg>Agg	p.G467R	TULP4_ENST00000367094.2_Missense_Mutation_p.G467R	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	467		NA			intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GTACCTGGGCGGGCTTGTGCC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	47	47	NA		NA	NA	6		NA											NA				158902234		2203	4300	6503	SO:0001583	missense				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338	56995		WD repeat domain containing	15530	protein-coding gene	gene with protein product		NA			NA	11595174	Standard	NM_020245	NM_020245	NA	Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1399G>A	chr6.hg19:g.158902234G>A	ENSP00000356064:p.Gly467Arg	NA	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	hg19	CCDS34561.1	0.02	7.30065	GGCxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	36	5.681670	0.96774	.	.	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.70164	-0.46;-0.46	5.31	5.31	0.75309	Tumour necrosis factor-like (1);	0.000000	0.85682	D	0.000000	T	0.79106	0.4390	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.81309	-0.0991	10	0.87932	D	0	-29.1374	18.9788	0.92747	0.0:0.0:1.0:0.0	.	467;467;467	B4E202;Q9NRJ4-2;Q9NRJ4	.;.;TULP4_HUMAN	R	467	ENSP00000356064:G467R;ENSP00000356061:G467R	ENSP00000356061:G467R	G	+	1	0	TULP4	158822222	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	9.275000	0.95738	2.491000	0.84063	0.561000	0.74099	GGG	NOVEL	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042869.1	2	40.009614	KEEP	0	0	0	133	4390	GG	1	1	0		+	32	60	1205	0	0	99.357593	146	60	5007	374	ENST00000367097.3	0.179775	1
QKI	9444	__UNKNOWN__	__UNKNOWN__	6	163996418	163996418	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:163996418T>A	ENST00000361752.3	+	0	6253					NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	NA		NA			long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		ACATTACAGATTTCATTTTTA	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531	9444			21100	protein-coding gene	gene with protein product		609590	quaking homolog, KH domain RNA binding (mouse)		NA	10535969	Standard	NM_006775	NM_006775	NA	Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.*4676T>A	chr6.hg19:g.163996418T>A		NA	Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	hg19	CCDS5285.1	0.02	2.02688	AGAxTTC	COVERED																																																																																			NOVEL	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043016.2	4	6.018273	KEEP	0	0	0	20	646	TT	0.999863	0.992789	0		+	15	60	525	0	0	44.528319	49	60	1750	99	ENST00000361752.3	0.234375	0.992926
FGFR1OP	11116	__UNKNOWN__	__UNKNOWN__	6	167454694	167454694	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:167454694G>A	ENST00000366847.4	+	0	2659				RP11-517H2.6_ENST00000609590.1_RNA	NM_007045.2	NP_008976.1	O95684	FR1OP_HUMAN	FGFR1 oncogene partner	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein tyrosine kinase activity (GO:0061099)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|protein tyrosine kinase inhibitor activity (GO:0030292)			large_intestine(2)|ovary(1)|stomach(1)	4		Breast(66;1.48e-05)|Ovarian(120;0.0607)		OV - Ovarian serous cystadenocarcinoma(33;1.73e-19)|BRCA - Breast invasive adenocarcinoma(81;5.1e-06)|GBM - Glioblastoma multiforme(31;0.00231)		CTTGTGTAATGCCAGTTTCTC	0.343	NA	NA	T	FGFR1	MPD, NHL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		6	6q27	11116	FGFR1 oncogene partner (FOP)		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Y18046	CCDS5296.1, CCDS5297.1, CCDS75550.1	6q27	2008-02-05			ENSG00000213066	ENSG00000213066	11116			17012	protein-coding gene	gene with protein product		605392			NA	9949182, 10373756	Standard	NM_007045	NM_007045	NA	Approved	FOP	uc003qvj.3	O95684	OTTHUMG00000016011	ENST00000366847.4:c.*1228G>A	chr6.hg19:g.167454694G>A		NA	A8K1D1|B2R705|Q49AI0|Q5R3F6|Q96EW1	hg19	CCDS5296.1	0.02	4.445559	AATxCCA	COVERED																																																																																			NOVEL	FGFR1OP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043099.2	0	13.845656	KEEP	0	0	0	46	1678	GG	1	0.999989	0		+	11	60	395	0	0	29.408535	95	60	3609	187	ENST00000366847.4	0.103774	0.999989
TCP10L2	401285	__UNKNOWN__	__UNKNOWN__	6	167592285	167592285	__UNKNOWN__	Intron	SNP	G	G	T	rs372881768		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:167592285G>T	ENST00000366832.2	+	6	788					NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	NA		NA								endometrium(1)|kidney(2)|lung(3)	6						TCAATTACTTGCCCGAGCTCC	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984	401285			21254	protein-coding gene	gene with protein product		NA	t-complex 10-like 2 (mouse)		NA		Standard	XR_040749	NM_001145121	NA	Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.658-214G>T	chr6.hg19:g.167592285G>T		NA		hg19	CCDS47514.1	0.02	-0.368214	CTTxCCC	COVERED																																																																																			NOVEL	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043112.5	2	7.519304	KEEP	6	0	0	25	870	GG	0.999931	0.899252	0		+	9	40	300	0	0	24.821063	33	50	1252	90	ENST00000366832.2	0.214286	0.899314
MLLT4	4301	__UNKNOWN__	__UNKNOWN__	6	168325755	168325755	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:168325755G>T	ENST00000447894.2	+	22	3062	c.3062G>T	c.(3061-3063)aGc>aTc	p.S1021I	MLLT4_ENST00000351017.4_Missense_Mutation_p.S1028I|MLLT4_ENST00000392108.3_Missense_Mutation_p.S1021I|MLLT4_ENST00000400822.3_Missense_Mutation_p.S1020I|MLLT4_ENST00000366806.2_Missense_Mutation_p.S1021I|MLLT4_ENST00000344191.4_Missense_Mutation_p.S1021I|MLLT4_ENST00000392112.1_Missense_Mutation_p.S1005I			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1021	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.	NA			adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATGGGCCTTAGCATTGTTGCA	0.438	NA	NA	T	MLL	AL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		6	6q27	4301	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)		L	0													156	141	146	NA		NA	NA	6		NA											NA				168325755		2203	4300	6503	SO:0001583	missense			AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396	4301			7137	protein-coding gene	gene with protein product		159559	myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4		NA	8242616	Standard	NM_005936	NM_001040000	NA	Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3062G>T	chr6.hg19:g.168325755G>T	ENSP00000404595:p.Ser1021Ile	NA	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	hg19		0.02	4.522399	TTAxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	33	5.204931	0.95033	.	.	ENSG00000130396	ENST00000344191;ENST00000351017;ENST00000392108;ENST00000366806;ENST00000392112;ENST00000341575;ENST00000400822;ENST00000447894	T;T;T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44;1.44;1.44	5.65	5.65	0.86999	PDZ/DHR/GLGF (4);	0.099910	0.64402	D	0.000002	T	0.61527	0.2354	M	0.92459	3.31	0.80722	D	1	D;D;D;D	0.69078	0.986;0.997;0.996;0.99	D;D;D;D	0.66716	0.943;0.931;0.946;0.915	T	0.70568	-0.4836	10	0.87932	D	0	-12.5219	20.0965	0.97849	0.0:0.0:1.0:0.0	.	1021;1020;1021;1005	P55196;P55196-5;P55196-6;P55196-2	AFAD_HUMAN;.;.;.	I	1021;1028;1021;1021;1005;1021;1020;1021	ENSP00000341118:S1021I;ENSP00000252692:S1028I;ENSP00000375956:S1021I;ENSP00000355771:S1021I;ENSP00000375960:S1005I;ENSP00000383623:S1020I;ENSP00000404595:S1021I	ENSP00000345834:S1021I	S	+	2	0	MLLT4	168068604	1.000000	0.71417	0.995000	0.50966	0.970000	0.65996	9.088000	0.94132	2.824000	0.97209	0.655000	0.94253	AGC	NOVEL	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000372077.1	2	15.049033	KEEP	0	0	0	50	1810	GG	1	0.999999	0		+	41	60	1506	0	0	136.695627	79	60	3024	229	ENST00000447894.2	0.341667	0.999999
FRMD1	79981	__UNKNOWN__	__UNKNOWN__	6	168467749	168467749	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr6:168467749C>G	ENST00000283309.6	-	4	449				FRMD1_ENST00000537786.1_5'UTR|FRMD1_ENST00000440994.2_Intron	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	NA		NA				cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		GCGGGCACACCTGCTTGCAGC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303	79981			21240	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024919	NM_001122841	NA	Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.385-238G>C	chr6.hg19:g.168467749C>G		NA	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	hg19	CCDS5306.1	0.02	7.621041	CACxTGC	COVERED																																																																																			NOVEL	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362513.2	1	20.459891	KEEP	0	0	0	68	2376	CC	1	1	0		-	45	60	1530	0	0	134.34367	107	60	3919	297	ENST00000283309.6	0.296053	1
RSPH10B	222967	__UNKNOWN__	__UNKNOWN__	7	5998609	5998609	__UNKNOWN__	Intron	SNP	G	G	A	rs200932037		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:5998609G>A	ENST00000405415.1	-	6	1046				RSPH10B_ENST00000535104.1_Intron|RSPH10B_ENST00000337579.3_Intron|RSPH10B_ENST00000404406.1_Intron|RSPH10B_ENST00000539903.1_Intron|RSPH10B_ENST00000441023.2_Intron			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	NA		NA								breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		CAAGCGCGGCGGTGGTCATAC	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													139	97	112	NA		NA	NA	7		NA											NA				5998609		2109	3684	5793	SO:0001627	intron_variant				CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026	222967			27362	protein-coding gene	gene with protein product		NA			NA	16507594	Standard	NM_173565	NM_173565	NA	Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.659+14C>T	chr7.hg19:g.5998609G>A		NA	A6NMW7|Q86ST9|Q8NE68	hg19	CCDS34598.1	0.02	2.044149	GGCxGTG	COVERED																																																																																			NOVEL	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325465.2	0	3.679473	KEEP	50	2	59	33	1102	GG	0.999998	0.990962	0		-	12	33	394	0	0	31.899168	50	51	1694	175	ENST00000405415.1	0.193548	0.990964
C7orf26	79034	__UNKNOWN__	__UNKNOWN__	7	6639938	6639938	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:6639938G>A	ENST00000344417.5	+	4	1326	c.1059G>A	c.(1057-1059)gcG>gcA	p.A353A	C7orf26_ENST00000359073.5_Silent_p.A256A|C7orf26_ENST00000472693.1_3'UTR	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	353		NA								endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		ACCGGCTGGCGCAGGCTCTGC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													31	30	30	NA		NA	NA	7		NA											NA				6639938		2203	4300	6503	SO:0001819	synonymous_variant			BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576	79034			21702	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024067	NM_024067	NA	Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.1059G>A	chr7.hg19:g.6639938G>A		NA	Q9BQ43	hg19	CCDS5353.1	0.02	1.838245	GGCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	g	9.029	0.986733	0.18889	.	.	ENSG00000146576	ENST00000445375	T	0.65178	-0.14	5.2	-10.4	0.00318	.	0.000000	0.85682	D	0.000000	T	0.51975	0.1706	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62950	-0.6745	7	0.72032	D	0.01	-15.3557	2.6079	0.04883	0.2286:0.3434:0.2885:0.1395	.	.	.	.	T	91	ENSP00000390166:A91T	ENSP00000390166:A91T	A	+	1	0	C7orf26	6606463	0.000000	0.05858	0.460000	0.27093	0.953000	0.61014	-2.582000	0.00905	-2.126000	0.00820	-1.200000	0.01667	GCA	NOVEL	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246844.2	1	11.730537	KEEP	0	0	0	39	1298	GG	1	0.99994	0		+	9	60	329	0	0	24.189666	88	60	3170	178	ENST00000344417.5	0.092784	0.99994
ZNF12	7559	__UNKNOWN__	__UNKNOWN__	7	6730053	6730053	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:6730053T>C	ENST00000404360.1	-	0	2484				ZNF12_ENST00000405858.1_3'UTR|AC073343.13_ENST00000366167.2_RNA			P17014	ZNF12_HUMAN	zinc finger protein 12	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(3)	16		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		ACAAGAAGTATGTTTATTCAC	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X52334, AB021643	CCDS47538.1, CCDS47539.1	7p21.1	2013-01-08	2005-06-09		ENSG00000164631	ENSG00000164631	7559		Zinc fingers, C2H2-type, -	12902	protein-coding gene	gene with protein product		194536	zinc finger protein 325	ZNF325	NA		Standard	NM_016265	NM_016265	NA	Approved	KOX3, GIOT-3	uc003sqt.1	P17014	OTTHUMG00000151910	ENST00000404360.1:c.*426A>G	chr7.hg19:g.6730053T>C		NA	A8MYC4|A8WFQ8|B2RNQ7|B4DF45|Q6N016|Q8NHZ0|Q9H9P0|Q9ULZ6	hg19		0.02	4.712262	GTAxGTT	COVERED																																																																																			NOVEL	ZNF12-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000324374.1	1	20.461731	KEEP	0	0	0	68	2144	TT	1	1	0		-	95	60	3244	0	0	330.017575	48	60	1709	275	ENST00000404360.1	0.664336	1
DNAH11	8701	__UNKNOWN__	__UNKNOWN__	7	21603765	21603765	__UNKNOWN__	Intron	SNP	C	C	A	rs72655981|rs374963183	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:21603765C>A	ENST00000409508.3	+	6	1013				DNAH11_ENST00000328843.6_Intron	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						AAAAAAAAAACAAACCAGAAT	0.373	NA	NA							Kartagener syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	32	33	NA		NA	NA	7		NA											NA				21603765		1837	4080	5917	SO:0001627	intron_variant	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04				8701		Axonemal dyneins	2942	protein-coding gene	gene with protein product	dynein, ciliary, heavy chain 11, dynein, heavy chain beta-like	603339	dynein, axonemal, heavy polypeptide 11		NA	9256245	Standard	NM_003777	NM_001277115	NA	Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.983-39C>A	chr7.hg19:g.21603765C>A		NA	Q9UJ82	hg19		0.02	-0.242752	AAAxAAA	COVERED																																																																																			NOVEL	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000326582.6	0	2.282765	KEEP	0	0	0	8	215	CC	0.99257	0.636582	0		+	5	60	96	1	0	6.341814	23	60	633	48	ENST00000409508.3	0.178571	0.641347
DNAH11	8701	__UNKNOWN__	__UNKNOWN__	7	21781776	21781776	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs368833424	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:21781776G>C	ENST00000409508.3	+	49	8177	c.8146G>C	c.(8146-8148)Gtc>Ctc	p.V2716L	DNAH11_ENST00000328843.6_Missense_Mutation_p.V2723L	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2723	AAA 3. {ECO:0000250}.	NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						TTTATCAAACGTCTTCCAGGT	0.353	NA	NA							Kartagener syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													90	83	85	NA		NA	NA	7		NA											NA				21781776		1837	4099	5936	SO:0001583	missense	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04				8701		Axonemal dyneins	2942	protein-coding gene	gene with protein product	dynein, ciliary, heavy chain 11, dynein, heavy chain beta-like	603339	dynein, axonemal, heavy polypeptide 11		NA	9256245	Standard	NM_003777	NM_001277115	NA	Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.8146G>C	chr7.hg19:g.21781776G>C	ENSP00000475939:p.Val2716Leu	NA	Q9UJ82	hg19		0.02	7.158949	AACxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.37	1.619464	0.28801	.	.	ENSG00000105877	ENST00000328843	T	0.38240	1.15	5.58	-1.28	0.09318	.	0.348063	0.34110	N	0.004242	T	0.28995	0.0720	.	.	.	0.23628	N	0.997258	B	0.23891	0.093	B	0.29524	0.103	T	0.37430	-0.9706	9	0.62326	D	0.03	.	12.4375	0.55608	0.5219:0.0:0.4781:0.0	.	2723	Q96DT5	DYH11_HUMAN	L	2723	ENSP00000330671:V2723L	ENSP00000330671:V2723L	V	+	1	0	DNAH11	21748301	0.398000	0.25279	0.213000	0.23690	0.617000	0.37484	-0.176000	0.09811	-0.126000	0.11682	-0.345000	0.07892	GTC	NOVEL	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000326582.6	3	12.037735	KEEP	0	0	0	40	1364	GG	1	1	0		+	45	60	1695	1	0	149.688954	115	60	4221	251	ENST00000409508.3	0.28125	1
HOXA2	3199	__UNKNOWN__	__UNKNOWN__	7	27139790	27139790	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:27139790T>C	ENST00000222718.5	-	0	1996				HOTAIRM1_ENST00000593300.1_RNA	NM_006735.3	NP_006726.1	O43364	HXA2_HUMAN	homeobox A2	NA		NA			anterior/posterior pattern specification (GO:0009952)|brain segmentation (GO:0035284)|cell fate determination (GO:0001709)|dorsal/ventral pattern formation (GO:0009953)|embryonic viscerocranium morphogenesis (GO:0048703)|middle ear morphogenesis (GO:0042474)|motor neuron axon guidance (GO:0008045)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast development (GO:0002076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|rhombomere 2 development (GO:0021568)|rhombomere 3 morphogenesis (GO:0021658)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|cervix(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	22						TTAGAAGCCCTAGTCATTTTT	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5403.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105996	ENSG00000105996	3199		Homeoboxes / ANTP class : HOXL subclass	5103	protein-coding gene	gene with protein product		604685	homeo box A2	HOX1K	NA	1358459	Standard		NM_006735	NA	Approved		uc003syh.3	O43364	OTTHUMG00000023208	ENST00000222718.5:c.*555A>G	chr7.hg19:g.27139790T>C		NA	A1L4K3|B2RMW3	hg19	CCDS5403.1	0.02	2.136334	CCCxAGT	COVERED																																																																																			NOVEL	HOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358508.2	2	18.050843	KEEP	0	0	0	60	1887	TT	1	0.99994	0		-	14	60	553	0	0	44.593336	83	60	3099	208	ENST00000222718.5	0.14433	0.99994
RP11-89N17.1	0	__UNKNOWN__	__UNKNOWN__	7	33768040	33768040	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:33768040G>T	ENST00000311067.3	+	0	1030										NA		NA									NA						TCTTCTCCTGGGGCCTTGCAA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000311067.3:c.*163G>T	chr7.hg19:g.33768040G>T		NA		hg19		0.02	4.730935	CTGxGGC	COVERED																																																																																			NOVEL	RP11-89N17.1-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000343608.1	2	12.62993	KEEP	0	0	0	42	1426	GG	1	0.999998	0		+	43	60	1599	0	0	146.607544	76	60	2693	208	ENST00000311067.3	0.361345	0.999998
BMPER	168667	__UNKNOWN__	__UNKNOWN__	7	33976939	33976939	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:33976939G>A	ENST00000297161.2	+	4	632	c.258G>A	c.(256-258)gtG>gtA	p.V86V	BMPER_ENST00000426693.1_Silent_p.V86V	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	86	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.	NA			blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						AGTGCCCCGTGCTGTCCCGAG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													122	112	116	NA		NA	NA	7		NA											NA				33976939		2203	4300	6503	SO:0001819	synonymous_variant				CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619	168667			24154	protein-coding gene	gene with protein product	crossveinless-2	608699			NA	12897139, 14766204	Standard	NM_133468	NM_133468	NA	Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.258G>A	chr7.hg19:g.33976939G>A		NA	A8K1P8|Q8TF36	hg19	CCDS5442.1	0.02	2.135071	CGTxCTG	COVERED																																																																																			NOVEL	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250570.2	1	9.029149	KEEP	0	0	0	30	1061	GG	0.999997	0.992091	0		+	23	60	796	0	0	72.616317	40	60	1523	111	ENST00000297161.2	0.365079	0.992094
DPY19L1	23333	__UNKNOWN__	__UNKNOWN__	7	34971263	34971263	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:34971263C>T	ENST00000310974.4	-	22	2094	c.1950G>A	c.(1948-1950)ttG>ttA	p.L650L		NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	650		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						AATCCTTCACCAAGAGGTTAC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	43	46	NA		NA	NA	7		NA											NA				34971263		1795	4043	5838	SO:0001819	synonymous_variant			AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852	23333			22205	protein-coding gene	gene with protein product		613892			NA		Standard		NM_015283	NA	Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1950G>A	chr7.hg19:g.34971263C>T		NA	O94954|Q4G151	hg19	CCDS43567.1	0.02	6.838136	CACxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.185	0.794762	0.16327	.	.	ENSG00000173852	ENST00000428054	.	.	.	5.26	4.32	0.51571	.	.	.	.	.	T	0.63710	0.2534	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61544	-0.7041	4	.	.	.	-12.766	12.4834	0.55856	0.0:0.9144:0.0:0.0856	.	.	.	.	S	58	.	.	G	-	1	0	DPY19L1	34937788	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.120000	0.41968	1.110000	0.41699	0.643000	0.83706	GGT	NOVEL	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337506.1	2	24.680407	KEEP	100	0	0	82	2912	CC	1	1	0		-	51	40	1822	0	0	160.838839	123	40	4535	378	ENST00000310974.4	0.293103	1
NME8	51314	__UNKNOWN__	__UNKNOWN__	7	37905094	37905094	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:37905094A>G	ENST00000199447.4	+	10	900				EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Intron	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	NA		NA			cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)				NA						TGATCCCACGACACCTGGATT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	61	61	NA		NA	NA	7		NA											NA				37905094		2203	4300	6503	SO:0001627	intron_variant			AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288	51314			16473	protein-coding gene	gene with protein product	sperm-specific thioredoxin 2	607421	thioredoxin domain containing 3 (spermatozoa)	TXNDC3	NA	11737268, 11768308, 19852809	Standard	NM_016616	NM_016616	NA	Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.529-33A>G	chr7.hg19:g.37905094A>G		NA	Q9NZH1	hg19	CCDS5452.1	0.02	4.948708	ACGxCAC	COVERED																																																																																			NOVEL	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219946.1	1	9.327994	KEEP	0	0	0	31	992	AA	0.999997	0.999995	0		+	32	60	1149	0	0	100.356221	85	60	3004	189	ENST00000199447.4	0.273504	0.999998
POLR2J4	84820	__UNKNOWN__	__UNKNOWN__	7	44026248	44026248	__UNKNOWN__	RNA	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:44026248C>G	ENST00000427076.1	-	0	845				RP5-1165K10.2_ENST00000454572.1_RNA	NR_003655.2				polymerase (RNA) II (DNA directed) polypeptide J4, pseudogene	NA		NA									NA						GCCACGGGTCCTTTGTCATTC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							7p13	2008-08-21			ENSG00000214783	ENSG00000214783	84820			28195	pseudogene	pseudogene		NA			NA	15586814	Standard	NR_003655	NR_003655	NA	Approved	MGC13098	uc010kxw.2		OTTHUMG00000155253	ENST00000427076.1:	chr7.hg19:g.44026248C>G		NA		hg19		0.02	2.145277	GTCxTTT	COVERED																																																																																			NOVEL	POLR2J4-002	KNOWN	basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000473169.1	0	16.552298	KEEP	5	0	0	55	1908	CC	1	0.99993	0		-	60	60	2041	0	0	205.123611	36	60	1332	218	ENST00000427076.1	0.625	0.99993
FIGNL1	63979	__UNKNOWN__	__UNKNOWN__	7	50513579	50513579	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:50513579G>T	ENST00000419119.1	-	2	2960	c.1407C>A	c.(1405-1407)tcC>tcA	p.S469S	FIGNL1_ENST00000395556.2_Silent_p.S469S|FIGNL1_ENST00000433017.1_Silent_p.S469S|FIGNL1_ENST00000356889.4_Silent_p.S469S			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	469		NA			ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				TAGAAGTTAAGGATGAAGCAG	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	72	73	NA		NA	NA	7		NA											NA				50513579		2203	4300	6503	SO:0001819	synonymous_variant			AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436	63979		ATPases / AAA-type	13286	protein-coding gene	gene with protein product		615383			NA		Standard	NM_001042762	XM_005271783	NA	Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.1407C>A	chr7.hg19:g.50513579G>T		NA	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	hg19	CCDS5510.1	0.02	10.123044	TAAxGAT	COVERED																																																																																			NOVEL	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342579.1	0	28.29008	KEEP	0	0	0	94	3269	GG	1	1	0		-	9	60	307	0	0	17.861659	278	60	10439	482	ENST00000419119.1	0.031359	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56368290	56368290	__UNKNOWN__	IGR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:56368290G>A			NA	NA				AC073136.1 (30746 upstream) : RNU6-1335P (39633 downstream)						NA		NA									NA						TAACAGACATGTCATTCTCAT	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56368290G>A		NA		hg19		0.02	6.836232	CATxTCA	COVERED																																																																																			NOVEL					0			0	10.834962	KEEP	0	0	0	36	1284	GG	0.999999	0.999999	0			48	60	1734	0	0	151.793264	126	60	4847	266		0.275862	1
ZNF273	10793	__UNKNOWN__	__UNKNOWN__	7	64363807	64363807	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:64363807C>T	ENST00000476120.1	+	1	173				ZNF273_ENST00000319636.5_Intron|ZNF273_ENST00000527278.1_Intron|ZNF273_ENST00000545510.1_Intron	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				GGTGAGAGTGCCGGGTCCCAG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)					NA		NA				0													68	69	69	NA		NA	NA	7		NA											NA				64363807		2203	4300	6503	SO:0001627	intron_variant			X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039	10793		Zinc fingers, C2H2-type, -	13067	protein-coding gene	gene with protein product		604756			NA	7865130	Standard		NR_003099	NA	Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.102+10C>T	chr7.hg19:g.64363807C>T		NA	B3KQZ5|Q6P3V4	hg19	CCDS5528.2	0.02	12.764526	GTGxCGG	COVERED																																																																																			NOVEL	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313502.1	2	34.001432	KEEP	0	0	0	113	3896	CC	1	1	0		+	57	60	1919	0	0	152.560882	281	60	10027	599	ENST00000476120.1	0.168639	1
ZNF92	168374	__UNKNOWN__	__UNKNOWN__	7	64864254	64864254	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:64864254C>T	ENST00000431504.1	+	2	1163	c.999C>T	c.(997-999)tcC>tcT	p.S333S	ZNF92_ENST00000357512.2_Silent_p.S377S|ZNF92_ENST00000328747.7_Silent_p.S409S|ZNF92_ENST00000450302.2_Silent_p.S340S			Q03936	ZNF92_HUMAN	zinc finger protein 92	409		NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				TTAAACAGTCCTCAACCCTTA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	41	40	NA		NA	NA	7		NA											NA				64864254		2187	4292	6479	SO:0001819	synonymous_variant			M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757	168374		Zinc fingers, C2H2-type, -	13168	protein-coding gene	gene with protein product		603974	zinc finger protein 92 (HTF12)		NA	8467795	Standard	NM_152626	NM_001287533	NA	Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000431504.1:c.999C>T	chr7.hg19:g.64864254C>T		NA	A6NNF9|Q8N492|Q8NB35	hg19		0.02	9.287503	GTCxTCA	COVERED																																																																																			NOVEL	ZNF92-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345490.1	4	18.358509	KEEP	0	0	0	61	2122	CC	1	1	0		+	28	60	1040	0	0	82.191489	172	60	6341	321	ENST00000431504.1	0.14	1
ZNF92	168374	__UNKNOWN__	__UNKNOWN__	7	64865298	64865298	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:64865298G>A	ENST00000431504.1	+	0	2207				ZNF92_ENST00000357512.2_3'UTR|ZNF92_ENST00000328747.7_3'UTR|ZNF92_ENST00000450302.2_3'UTR			Q03936	ZNF92_HUMAN	zinc finger protein 92	NA		NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|skin(1)|stomach(1)	13		Lung NSC(55;0.159)				GAAAAACCCTGCAAATGTAAT	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M61872	CCDS34646.1, CCDS47596.1, CCDS75608.1, CCDS75609.1	7q11.21	2013-01-08	2006-05-12		ENSG00000146757	ENSG00000146757	168374		Zinc fingers, C2H2-type, -	13168	protein-coding gene	gene with protein product		603974	zinc finger protein 92 (HTF12)		NA	8467795	Standard	NM_152626	NM_001287533	NA	Approved	HPF12, TF12	uc003ttz.3	Q03936	OTTHUMG00000156557	ENST00000431504.1:c.*510G>A	chr7.hg19:g.64865298G>A		NA	A6NNF9|Q8N492|Q8NB35	hg19		0.02	6.335297	CCTxCAA	COVERED																																																																																			NOVEL	ZNF92-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345490.1	2	11.136804	KEEP	0	0	0	37	1354	GG	1	1	0		+	35	60	1252	0	0	101.881274	162	60	6183	292	ENST00000431504.1	0.177665	1
POM121	9883	__UNKNOWN__	__UNKNOWN__	7	72420467	72420467	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:72420467G>A	ENST00000395270.1	+	0	5499				NSUN5P2_ENST00000388955.4_RNA	NM_001257190.1	NP_001244119.1	Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	NA		NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				GGAGCCTGGCGGGGGTCCAGC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	39	38	NA		NA	NA	7		NA											NA				72420467		2203	4300	6503	SO:0001624	3_prime_UTR_variant			AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313	9883		-	19702	protein-coding gene	gene with protein product		615753	POM121 membrane glycoprotein (rat), POM121 membrane glycoprotein		NA	8335683, 9734811, 17900573	Standard		NM_172020	NA	Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000395270.1:c.*1458G>A	chr7.hg19:g.72420467G>A		NA	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	hg19	CCDS59059.1	0.02	17.688013	GGCxGGG	COVERED																																																																																			NOVEL	POM121-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252020.1	13	11.740539	KEEP	7	3	97	73	2457	GG	1	1	0		+	15	49	541	0	0	33.031579	419	60	14486	582	ENST00000395270.1	0.034562	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	72712121	72712121	__UNKNOWN__	IGR	SNP	T	T	C	rs62465079	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:72712121T>C			NA	NA				GTF2IRD2P1 (26463 upstream) : NSUN5 (4392 downstream)						NA		NA									NA						CCACCAGCTCTGGCTTTGGAG	0.657	NA	NA											.|||	3425	0.683906	0.8986	0.6484	5008	,	,	NA	5978	0.372	NA	0.7127	False	NA	,,,	NA	NA	NA	2504	0.7106	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.72712121T>C		NA		hg19		0.02	3.075655	CTCxGGC	COVERED																																																																																			NOVEL					0			1	8.124438	KEEP	0	0	0	27	848	TT	0.999988	0.999987	0			7	37	218	0	0	13.415447	119	60	4322	181		0.055556	1
NSUN5	55695	__UNKNOWN__	__UNKNOWN__	7	72717439	72717439	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs189692650	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:72717439G>A	ENST00000310326.8	-	10	1394	c.1369C>T	c.(1369-1371)Cgg>Tgg	p.R457W	NSUN5_ENST00000252594.6_3'UTR|NSUN5_ENST00000428206.1_3'UTR|NSUN5_ENST00000438747.2_Silent_p.A458A			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	215		NA			rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.A458A(1)		breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				TGCAAGCACCGGCTGCGGCTC	0.602	NA	NA											.|||	5	0.000998403	0	0	5008	,	,	NA	16952	0.005	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	stomach(1)						G	TRP/ARG,,,	1,4405		0,1,2202	82	88	86	NA	1369,,,1374	-2.3	0	7		86	0,8596		0,0,4298	no	missense,utr-3,utr-3,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	101,,,	0,1,6500	AA,AG,GG	NA	0.0,0.0227,0.0077	,,,	457/471,,,458/467	72717439	1,13001	2203	4298	6501	SO:0001583	missense			AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305	55695		NOP2/Sun domain containing	16385	protein-coding gene	gene with protein product	NOP2/Sun domain family, member 5A	615732	Williams Beuren syndrome chromosome region 20A, NOL1/NOP2/Sun domain family, member 5	WBSCR20, WBSCR20A	NA	11978965, 12073013	Standard	NM_148956	NM_148956	NA	Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000310326.8:c.1369C>T	chr7.hg19:g.72717439G>A	ENSP00000309126:p.Arg457Trp	NA	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	hg19	CCDS55119.1	0.02	25.482472	ACCxGCT	COVERED	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	.	10.09	1.254195	0.22965	2.27E-4	0.0	ENSG00000130305	ENST00000310326	T	0.12255	2.7	3.85	-2.33	0.06724	.	.	.	.	.	T	0.05777	0.0151	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34254	-0.9836	8	0.62326	D	0.03	.	4.2765	0.10811	0.4307:0.2305:0.3388:0.0	.	457	B4DP79	.	W	457	ENSP00000309126:R457W	ENSP00000309126:R457W	R	-	1	2	NSUN5	72355375	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.024000	0.13555	-0.422000	0.07405	-0.768000	0.03414	CGG	NOVEL	NSUN5-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345916.1	7	17.447109	KEEP	18	0	0	58	1858	GG	1	1	0		-	16	49	595	0	0	34.709531	620	50	20744	786	ENST00000310326.8	0.025157	1
LIMK1	3984	__UNKNOWN__	__UNKNOWN__	7	73523403	73523403	__UNKNOWN__	Intron	SNP	G	G	T	rs558731034		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:73523403G>T	ENST00000418310.1	+	10	1476				LIMK1_ENST00000538333.3_Intron|LIMK1_ENST00000336180.2_Intron			P53667	LIMK1_HUMAN	LIM domain kinase 1	NA		NA			actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	cccgctgtgcggccccgggca	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													29	25	26	NA		NA	NA	7		NA											NA				73523403		2203	4298	6501	SO:0001627	intron_variant			D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683	3984			6613	protein-coding gene	gene with protein product		601329			NA	8673124, 8812460	Standard	NM_002314	NM_002314	NA	Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000418310.1:c.1374+37G>T	chr7.hg19:g.73523403G>T		NA	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	hg19		0.02	9.315561	TGCxGCC	COVERED																																																																																			NOVEL	LIMK1-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000348344.1	0	14.440511	KEEP	0	0	0	48	1530	GG	1	1	0		+	38	60	1328	0	0	106.028617	194	60	6501	343	ENST00000418310.1	0.163793	1
HIP1	3092	__UNKNOWN__	__UNKNOWN__	7	75203144	75203144	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:75203144C>T	ENST00000434438.2	-	8	687	c.667G>A	c.(667-669)Gcc>Acc	p.A223T	HIP1_ENST00000336926.6_Missense_Mutation_p.A223T	NM_001243198.1	NP_001230127.1	O00291	HIP1_HUMAN	huntingtin interacting protein 1	223		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						ATCAGCGGGGCGAGGCGGCAC	0.552	NA	NA	T	PDGFRB	CMML									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	0													74	76	75	NA		NA	NA	7		NA											NA				75203144		2203	4300	6503	SO:0001583	missense			AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946	3092			4913	protein-coding gene	gene with protein product		601767			NA	9140394, 9147654	Standard	NM_005338	NM_005338	NA	Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000434438.2:c.667G>A	chr7.hg19:g.75203144C>T	ENSP00000410300:p.Ala223Thr	NA	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	hg19	CCDS59060.1	0.02	9.086334	GGGxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.3	4.135443	0.77662	.	.	ENSG00000127946	ENST00000336926;ENST00000434438	T;T	0.29397	1.57;1.57	5.67	4.78	0.61160	ANTH (1);Armadillo-type fold (1);	0.045818	0.85682	D	0.000000	T	0.50990	0.1648	M	0.62088	1.915	0.58432	D	0.999997	P;D	0.89917	0.706;1.0	B;D	0.75020	0.166;0.985	T	0.52495	-0.8568	10	0.59425	D	0.04	-18.8615	12.8561	0.57886	0.2964:0.7036:0.0:0.0	.	223;223	E7ES17;O00291	.;HIP1_HUMAN	T	223	ENSP00000336747:A223T;ENSP00000410300:A223T	ENSP00000336747:A223T	A	-	1	0	HIP1	75041080	1.000000	0.71417	0.775000	0.31657	0.670000	0.39368	4.725000	0.61979	1.379000	0.46325	0.591000	0.81541	GCC	NOVEL	HIP1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342864.2	4	22.56329	KEEP	0	0	0	75	2476	CC	1	1	0		-	51	60	1670	0	0	136.752756	196	60	6860	424	ENST00000434438.2	0.206478	1
SRCRB4D	0	__UNKNOWN__	__UNKNOWN__	7	76024547	76024547	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:76024547G>A	ENST00000275560.3	-	7	1294					NM_080744.1	NP_542782.1				NA		NA								autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						TACCATTCCCGCCTGGAGGGC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	63	64	NA		NA	NA	7		NA											NA				76024547		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000275560.3:c.946+22C>T	chr7.hg19:g.76024547G>A		NA		hg19	CCDS5585.1	0.02	-0.236859	CCCxCCT	COVERED																																																																																			NOVEL	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253001.3	0	4.514326	KEEP	0	0	0	15	513	GG	0.99649	0.610258	0		-	10	60	343	0	0	31.341367	17	60	596	55	ENST00000275560.3	0.37037	0.612407
ZP3	7784	__UNKNOWN__	__UNKNOWN__	7	76069902	76069902	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs1804905		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:76069902G>C	ENST00000394857.3	+	7	1092	c.1034G>C	c.(1033-1035)aGg>aCg	p.R345T	ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.R169T|ZP3_ENST00000336517.4_Missense_Mutation_p.R294T	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	345		NA		R -> T (in Ref. 2; CAA40095). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						CAGTGGTCCAGGTCTGCTTCC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													135	127	130	NA		NA	NA	7		NA											NA				76069902		2203	4300	6503	SO:0001583	missense			M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372	7784		Zona pellucida glycoproteins	13189	protein-coding gene	gene with protein product		182889	zona pellucida glycoprotein 3A (sperm receptor)	ZP3A, ZP3B	NA	1478648	Standard		NM_007155	NA	Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.1034G>C	chr7.hg19:g.76069902G>C	ENSP00000378326:p.Arg345Thr	NA	Q06633|Q29RW0	hg19	CCDS47618.1	0.02	8.821797	CCAxGTC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	8.608|8.608	0.888351|0.888351	0.17540|0.17540	.|.	.|.	ENSG00000188372|ENSG00000188372	ENST00000394860|ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	.|T;T;T	.|0.25250	.|2.41;2.63;1.81	4.64|4.64	-8.56|-8.56	0.00904|0.00904	.|.	.|0.754812	.|0.12103	.|U	.|0.499355	T|T	0.12518|0.12518	0.0304|0.0304	L|L	0.28115|0.28115	0.83|0.83	0.09310|0.09310	N|N	1|1	.|B;B	.|0.19817	.|0.002;0.039	.|B;B	.|0.17722	.|0.004;0.019	T|T	0.33292|0.33292	-0.9874|-0.9874	5|10	.|0.13108	.|T	.|0.6	-0.2921|-0.2921	12.2107|12.2107	0.54377|0.54377	0.1994:0.1279:0.6727:0.0|0.1994:0.1279:0.6727:0.0	rs1804905|rs1804905	.|294;345	.|P21754-3;P21754	.|.;ZP3_HUMAN	R|T	179|294;345;345;169	.|ENSP00000337310:R294T;ENSP00000378326:R345T;ENSP00000411955:R169T	.|ENSP00000337310:R294T	G|R	+|+	1|2	0|0	ZP3|ZP3	75907838|75907838	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.592000|-0.592000	0.05747|0.05747	-1.616000|-1.616000	0.01572|0.01572	-0.291000|-0.291000	0.09656|0.09656	GGT|AGG	NOVEL	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253004.1	5	6.456243	KEEP	0	1	33	33	1170	GG	0.999998	0.999998	0		+	9	21	319	0	0	19.997838	205	60	7514	301	ENST00000394857.3	0.042056	1
CCDC146	57639	__UNKNOWN__	__UNKNOWN__	7	76796928	76796928	__UNKNOWN__	Intron	SNP	A	A	G	rs28502738	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:76796928A>G	ENST00000285871.4	+	2	116				RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	NA		NA								breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				TTACTTTATAAGTGAAGACAC	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205	57639			29296	protein-coding gene	gene with protein product		NA			NA	10819331	Standard	NM_020879	NM_020879	NA	Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.-11-47A>G	chr7.hg19:g.76796928A>G		NA	A8K8X6|Q9P223	hg19	CCDS34671.1	0.02	9.399119	ATAxGTG	COVERED																																																																																			NOVEL	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341449.1	0	15.947613	KEEP	2	0	0	53	1707	AA	1	1	0		+	30	40	1100	0	0	86.98318	179	60	6458	284	ENST00000285871.4	0.143541	1
FGL2	10875	__UNKNOWN__	__UNKNOWN__	7	76824491	76824491	__UNKNOWN__	3'UTR	SNP	C	C	A	rs569471735|rs3093283|rs3093282|rs201063287	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:76824491C>A	ENST00000248598.5	-	0	2457				RP11-467H10.2_ENST00000459742.1_RNA|CCDC146_ENST00000431197.1_Intron|CCDC146_ENST00000285871.4_Intron	NM_006682.2	NP_006673.1	Q14314	FGL2_HUMAN	fibrinogen-like 2	NA		NA				extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	13						CCACCCCCCCCAAAAAAACCT	0.373	NA	NA											c|||	9	0.00179712	0.0061	0	5008	,	,	NA	10528	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Z36531	CCDS5591.1	7q11.23	2013-02-06			ENSG00000127951	ENSG00000127951	10875		Fibrinogen C domain containing	3696	protein-coding gene	gene with protein product		605351			NA	7642106	Standard	NM_006682	NM_006682	NA	Approved	pT49, T49	uc003ugb.3	Q14314	OTTHUMG00000130681	ENST00000248598.5:c.*1105G>T	chr7.hg19:g.76824491C>A		NA		hg19	CCDS5591.1	0.02	2.318233	CCCxAAA	COVERED																																																																																			NOVEL	FGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253176.1	1	5.355543	KEEP	0	0	0	18	613	CC	0.999859	0.993563	0		-	5	60	186	0	0	13.335983	60	60	2189	96	ENST00000248598.5	0.076923	0.993703
PHTF2	57157	__UNKNOWN__	__UNKNOWN__	7	77539661	77539661	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:77539661A>G	ENST00000307305.8	+	7	799	c.597A>G	c.(595-597)acA>acG	p.T199T	PHTF2_ENST00000415251.2_Silent_p.T199T|PHTF2_ENST00000248550.7_Silent_p.T237T|PHTF2_ENST00000450574.1_Silent_p.T203T|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000422959.2_Silent_p.T203T|PHTF2_ENST00000424760.1_Silent_p.T199T|PHTF2_ENST00000275575.7_Silent_p.T199T|PHTF2_ENST00000416283.2_Silent_p.T203T	NM_001127358.1	NP_001120830.1	Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	237		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						ACCACGGTACAAGCACCTCTC	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													118	118	118	NA		NA	NA	7		NA											NA				77539661		2001	4170	6171	SO:0001819	synonymous_variant			AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576	57157			13411	protein-coding gene	gene with protein product		NA			NA	10729229	Standard	NM_020432	NM_020432	NA	Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000307305.8:c.597A>G	chr7.hg19:g.77539661A>G		NA	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	hg19	CCDS47622.1	0.02	4.685392	TACxAGC	COVERED																																																																																			NOVEL	PHTF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344297.1	0	15.947246	KEEP	0	0	0	53	1644	AA	1	1	0		+	51	60	1870	0	0	170.129988	96	60	3513	257	ENST00000307305.8	0.346939	1
MAGI2	9863	__UNKNOWN__	__UNKNOWN__	7	77998517	77998517	__UNKNOWN__	Silent	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:77998517G>C	ENST00000354212.4	-	7	1312	c.1059C>G	c.(1057-1059)ggC>ggG	p.G353G	MAGI2_ENST00000535697.1_Silent_p.G190G|MAGI2_ENST00000522391.1_Silent_p.G353G|MAGI2_ENST00000419488.1_Silent_p.G353G|MAGI2_ENST00000536571.1_Silent_p.G185G	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	353	Interaction with DDN.|WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.	NA			cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TTTTTTCCCAGCCATATGGAA	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	60	60	NA		NA	NA	7		NA											NA				77998517		2203	4300	6503	SO:0001819	synonymous_variant			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391	9863			18957	protein-coding gene	gene with protein product		606382			NA	10681527, 9734811	Standard	NM_012301	XM_005250725	NA	Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1059C>G	chr7.hg19:g.77998517G>C		NA	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	hg19	CCDS5594.1	0.02	-0.228042	CCAxCCA	COVERED																																																																																			NOVEL	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253197.3	0	4.213831	KEEP	0	0	0	14	510	GG	0.99649	0.580884	0		-	9	60	324	0	0	29.411891	17	60	626	50	ENST00000354212.4	0.346154	0.58293
DBF4	10926	__UNKNOWN__	__UNKNOWN__	7	87517436	87517436	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:87517436A>G	ENST00000265728.1	+	6	1101					NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	NA		NA			DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				ACGTATTTGCAAAGTTTTCCT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													50	47	48	NA		NA	NA	7		NA											NA				87517436		692	1588	2280	SO:0001627	intron_variant			AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634	10926		Zinc fingers, DBF-type	17364	protein-coding gene	gene with protein product	activator of S phase kinase, chiffon homolog (Drosophila), zinc finger, DBF-type containing 1, DBF4 zinc finger A	604281	DBF4 homolog (S. cerevisiae)		NA	10373557, 10517317	Standard	NM_006716	NM_006716	NA	Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.597+62A>G	chr7.hg19:g.87517436A>G		NA	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	hg19	CCDS5611.1	0.02	-0.227494	TGCxAAG	COVERED																																																																																			NOVEL	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253678.1	0	3.610542	KEEP	0	0	0	12	372	AA	0.993634	0.579219	0		+	8	60	246	0	0	21.428188	18	60	654	53	ENST00000265728.1	0.307692	0.58293
ADAM22	53616	__UNKNOWN__	__UNKNOWN__	7	87761781	87761781	__UNKNOWN__	Intron	SNP	T	T	C	rs34674771		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:87761781T>C	ENST00000265727.7	+	12	1071				ADAM22_ENST00000398209.3_Intron|ADAM22_ENST00000315984.7_Intron|ADAM22_ENST00000439864.1_3'UTR|ADAM22_ENST00000398204.4_Intron|ADAM22_ENST00000398201.4_Intron			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	NA		NA			adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell adhesion (GO:0007162)	integral component of membrane (GO:0016021)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(4)|large_intestine(7)|liver(2)|lung(20)|ovary(6)|prostate(4)|skin(3)	53	Esophageal squamous(14;0.00202)		STAD - Stomach adenocarcinoma(171;0.215)			tcctcagctttcctttgtcta	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB009671	CCDS43608.1, CCDS43609.1, CCDS43610.1, CCDS47637.1	7q21	2008-07-18	2005-08-18		ENSG00000008277	ENSG00000008277	53616		ADAM metallopeptidase domain containing	201	protein-coding gene	gene with protein product	metalloproteinase-like, disintegrin-like, and cysteine-rich protein 2	603709	a disintegrin and metalloproteinase domain 22		NA	9693107, 10524237	Standard	NM_021723	NM_021723	NA	Approved	MDC2	uc003ujn.3	Q9P0K1	OTTHUMG00000137417	ENST00000265727.7:c.993-401T>C	chr7.hg19:g.87761781T>C		NA	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	hg19	CCDS47637.1	0.02	4.904741	CTTxCCT	COVERED																																																																																			NOVEL	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268370.2	2	12.937436	KEEP	0	0	0	43	1403	TT	1	0.999999	0		+	29	60	1042	0	0	88.985584	93	60	3307	201	ENST00000265727.7	0.237705	0.999999
FZD1	8321	__UNKNOWN__	__UNKNOWN__	7	90896411	90896411	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:90896411C>A	ENST00000287934.2	+	0	2629					NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	NA		NA			autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			TGTAAATAGCCTGTGTAAGAT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240	8321		GPCR / Class F : Frizzled receptors	4038	protein-coding gene	gene with protein product	Wnt receptor, frizzled, Drosophila, homolog of, 1	603408	frizzled (Drosophila) homolog 1, frizzled homolog 1 (Drosophila), frizzled 1, seven transmembrane spanning receptor, frizzled family receptor 1		NA	9813155	Standard	NM_003505	NM_003505	NA	Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.*272C>A	chr7.hg19:g.90896411C>A		NA	A4D1E8|O94815|Q549T8	hg19	CCDS5620.1	0.02	2.138486	AGCxTGT	COVERED																																																																																			NOVEL	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059367.2	1	6.019674	KEEP	0	0	0	20	716	CC	0.999863	0.998064	0		+	5	60	156	0	0	10.080486	69	60	2540	123	ENST00000287934.2	0.067568	0.9982
GATAD1	57798	__UNKNOWN__	__UNKNOWN__	7	92088075	92088075	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:92088075G>A	ENST00000287957.3	+	0	3286				AC007566.10_ENST00000427458.1_RNA	NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	NA		NA				nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAAGGGTATAGTAAAATTGAT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259	57798		GATA zinc finger domain containing	29941	protein-coding gene	gene with protein product	ocular development associated gene	614518			NA	12062807	Standard	NM_021167	NM_021167	NA	Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.*2199G>A	chr7.hg19:g.92088075G>A		NA	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	hg19	CCDS5625.1	0.02	7.02922	ATAxTAA	COVERED																																																																																			NOVEL	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253929.2	0	7.825799	KEEP	0	0	0	26	950	GG	0.999988	0.999988	0		+	30	60	1120	0	0	93.524767	122	60	4721	227	ENST00000287957.3	0.197368	1
PEX1	5189	__UNKNOWN__	__UNKNOWN__	7	92157803	92157803	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:92157803G>T	ENST00000248633.4	-	0	42					NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	NA		NA			ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			AAGGACCCGGGACCCGGCAGG	0.761	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980	5189		ATPases / AAA-type	8850	protein-coding gene	gene with protein product		602136	peroxisome biogenesis factor 1, Zellweger syndrome 1, Zellweger syndrome	ZWS1, ZWS	NA	9398848	Standard	NM_000466	NM_001282677	NA	Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.-54C>A	chr7.hg19:g.92157803G>T		NA	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	hg19	CCDS5627.1	0.02	1.941452	CGGxACC	COVERED																																																																																			NOVEL	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254066.3	0	7.519586	KEEP	0	0	0	25	778	GG	0.999931	0.963707	0		-	12	60	358	0	0	29.445674	39	60	1311	98	ENST00000248633.4	0.235294	0.963774
BET1	10282	__UNKNOWN__	__UNKNOWN__	7	93625616	93625616	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:93625616G>A	ENST00000222547.3	-	3	320	c.162C>T	c.(160-162)ggC>ggT	p.G54G	BET1_ENST00000471446.1_5'UTR|BET1_ENST00000425626.1_Silent_p.G54G|AC006378.2_ENST00000426634.1_RNA|AC006378.2_ENST00000426193.2_RNA|BET1_ENST00000433727.1_Silent_p.G54G	NM_005868.4	NP_005859.1	O15155	BET1_HUMAN	Bet1 golgi vesicular membrane trafficking protein	54	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.	NA			ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)|vesicle fusion with Golgi apparatus (GO:0048280)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				large_intestine(2)|lung(1)|prostate(1)|skin(1)	5	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			TAACTTCATGGCCTATTTCAA	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													86	99	95	NA		NA	NA	7		NA											NA				93625616		2202	4294	6496	SO:0001819	synonymous_variant			AF007551	CCDS5635.1	7q21.1-q22	2013-03-08	2013-03-08		ENSG00000105829	ENSG00000105829	10282			14562	protein-coding gene	gene with protein product	Golgi vesicular membrane trafficking protein p18, Bet1p homolog	605456	Bet1 (S. cerevisiae) homolog, BET1 homolog (S. cerevisiae), blocked early in transport 1 homolog (S. cerevisiae)		NA	9382863, 10449330	Standard	NM_005868	XM_005250109	NA	Approved	hbet1	uc003unf.1	O15155	OTTHUMG00000023487	ENST00000222547.3:c.162C>T	chr7.hg19:g.93625616G>A		NA	Q96EA0	hg19	CCDS5635.1	0.02	4.091761	ATGxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.161	1.018720	0.19355	.	.	ENSG00000105829	ENST00000457139	.	.	.	4.74	2.77	0.32553	.	.	.	.	.	T	0.55832	0.1945	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51710	-0.8671	4	.	.	.	.	7.369	0.26790	0.0:0.1402:0.526:0.3338	.	.	.	.	S	69	.	.	P	-	1	0	BET1	93463552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.208000	0.42797	1.346000	0.45694	0.643000	0.83706	CCA	NOVEL	BET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255181.2	2	9.631283	KEEP	0	0	0	32	1123	GG	0.999997	0.999997	0		-	5	60	185	0	0	11.602283	130	60	4792	197	ENST00000222547.3	0.037037	1
PEG10	23089	__UNKNOWN__	__UNKNOWN__	7	94294927	94294927	__UNKNOWN__	3'UTR	SNP	A	A	C	rs199593658		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:94294927A>C	ENST00000482108.1	+	0	2538				PEG10_ENST00000488574.1_3'UTR|PEG10_ENST00000465184.1_Intron	NM_001040152.1|NM_001172438.1|NM_001184962.1	NP_001035242.1|NP_001165909.1|NP_001171891.1	Q86TG7	PEG10_HUMAN	paternally expressed 10	NA		NA			apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|placenta development (GO:0001890)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(9)|prostate(3)|skin(1)	21	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			GTACCACAGTACccgccgcca	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	17	15	NA		NA	NA	7		NA											NA				94294927		690	1579	2269	SO:0001624	3_prime_UTR_variant			AB049834	CCDS55126.1, CCDS75636.1, CCDS75637.1	7q21	2007-12-07			ENSG00000242265	ENSG00000242265	23089			14005	protein-coding gene	gene with protein product		609810			NA	11318613, 15716091, 16093683	Standard	NM_015068	NM_001172437	NA	Approved	KIAA1051, HB-1, MEF3L, RGAG3, Mar2, Mart2	uc011kie.2	Q86TG7	OTTHUMG00000155578	ENST00000482108.1:c.*1081A>C	chr7.hg19:g.94294927A>C		NA	Q96A68|Q9UPV1	hg19	CCDS55126.1	0.02	2.326597	AGTxCCC	COVERED																																																																																			NOVEL	PEG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340751.1	3	5.035777	KEEP	0	2	11	21	563	AA	0.999892	0.999892	0		+	13	60	222	0	0	10.024058	132	60	3399	250	ENST00000482108.1	0.089655	1
PDK4	5166	__UNKNOWN__	__UNKNOWN__	7	95217112	95217112	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:95217112T>A	ENST00000005178.5	-	8	994	c.797A>T	c.(796-798)cAc>cTc	p.H266L		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	266	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.	NA			cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			ATTTTCCTGGTGTTCAACTGT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													83	81	82	NA		NA	NA	7		NA											NA				95217112		2203	4300	6503	SO:0001583	missense			U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799	5166			8812	protein-coding gene	gene with protein product		602527	pyruvate dehydrogenase kinase, isoenzyme 4		NA	7499431	Standard	NM_002612	NM_002612	NA	Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.797A>T	chr7.hg19:g.95217112T>A	ENSP00000005178:p.His266Leu	NA		hg19	CCDS5643.1	0.02	12.383953	TGGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	10.88	1.474396	0.26423	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.53640	0.61	5.61	4.43	0.53597	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.332397	0.34725	N	0.003734	T	0.28532	0.0706	L	0.28115	0.83	0.40595	D	0.981521	B	0.02656	0.0	B	0.08055	0.003	T	0.08391	-1.0724	10	0.09590	T	0.72	.	7.0661	0.25154	0.2431:0.0:0.1223:0.6346	.	266	Q16654	PDK4_HUMAN	L	266;230	ENSP00000005178:H266L	ENSP00000005178:H266L	H	-	2	0	PDK4	95055048	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	1.682000	0.37628	1.035000	0.39972	0.482000	0.46254	CAC	NOVEL	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333298.1	5	27.377016	KEEP	0	0	0	91	2844	TT	1	1	0		-	59	60	2280	0	0	192.535988	231	70	8459	513	ENST00000005178.5	0.203448	1
BRI3	25798	__UNKNOWN__	__UNKNOWN__	7	97920910	97920910	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:97920910C>T	ENST00000539286.1	+	3	374					NM_001159491.1	NP_001152963.1	Q9NQX7	ITM2C_HUMAN	brain protein I3	NA		NA			negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)	4	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)					ATCGCTCCCCCGGCCAGTCCT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF106966	CCDS5656.1, CCDS55133.1	7q21.3	2008-09-05			ENSG00000164713	ENSG00000164713	25798			1109	protein-coding gene	gene with protein product		615628			NA	14592447	Standard	NM_015379	NM_015379	NA	Approved		uc003upi.2	O95415	OTTHUMG00000154275	ENST00000539286.1:c.246-1041C>T	chr7.hg19:g.97920910C>T		NA	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	hg19	CCDS55133.1	0.02	7.160331	CCCxGGC	COVERED																																																																																			NOVEL	BRI3-008	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438227.1	4	15.895333	KEEP	0	0	0	53	1717	CC	1	1	0		+	37	60	1388	0	0	115.404955	157	60	5383	315	ENST00000539286.1	0.190722	1
ARPC1A	10552	__UNKNOWN__	__UNKNOWN__	7	98930925	98930925	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:98930925C>T	ENST00000262942.5	+	2	95				ARPC1A_ENST00000432884.2_Intron	NM_001190996.1|NM_006409.3	NP_001177925.1|NP_006400.2	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex, subunit 1A, 41kDa	NA		NA			actin cytoskeleton organization (GO:0030036)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of actin filament polymerization (GO:0030833)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|liver(2)|lung(7)|ovary(1)|prostate(1)	19	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			GTATAAAATGCTTTTTGTTAT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	67	71	NA		NA	NA	7		NA											NA				98930925		1568	3582	5150	SO:0001627	intron_variant			Y08999	CCDS5660.1	7q22.1	2013-03-14	2002-08-29		ENSG00000241685	ENSG00000241685	10552		Actin related protein 2/3 complex subunits, WD repeat domain containing	703	protein-coding gene	gene with protein product	actin binding protein (Schizosaccharomyces pombe sop2-like), SOP2-like protein	604220	actin related protein 2/3 complex, subunit 1A (41 kD)		NA	8978670, 9230079	Standard	NM_006409	NM_006409	NA	Approved	SOP2Hs, SOP2L, Arc40	uc003upx.2	Q92747	OTTHUMG00000154553	ENST00000262942.5:c.-29-23C>T	chr7.hg19:g.98930925C>T		NA	A4D276|B4DLQ7|D6W5S1|Q7Z5U8|Q86WU5|Q8IXQ0	hg19	CCDS5660.1	0.02	9.001313	ATGxTTT	COVERED																																																																																			NOVEL	ARPC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335908.1	3	15.028799	KEEP	0	0	0	50	1790	CC	1	1	0		+	54	60	1928	0	0	162.453913	191	60	7056	341	ENST00000262942.5	0.220408	1
ATP5J2-PTCD1	100526740	__UNKNOWN__	__UNKNOWN__	7	99036643	99036643	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:99036643T>G	ENST00000413834.1	-	3	144				PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000436336.2_5'UTR|CPSF4_ENST00000451876.1_5'UTR|ATP5J2-PTCD1_ENST00000437572.1_Intron					ATP5J2-PTCD1 readthrough	NA		NA									NA						CGGCGGCGGGTAAAGGCGAGA	0.761	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56496.1	7q22.1	2011-02-21			ENSG00000248919	ENSG00000248919	100526740			38844	other	readthrough		NA			NA		Standard	NM_001198879.1	NM_001198879	NA	Approved		uc011kiw.2		OTTHUMG00000160779	ENST00000413834.1:c.122-3752A>C	chr7.hg19:g.99036643T>G		NA		hg19	CCDS56496.1	0.02	2.993209	GGGxAAA	COVERED																																																																																			NOVEL	ATP5J2-PTCD1-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362258.1	2	19.457651	KEEP	0	13	112	107	2419	TT	1	0.999999	0		-	14	60	252	0	0	13.390376	111	60	2589	337	ENST00000413834.1	0.112	0.999999
GS1-259H13.10	0	__UNKNOWN__	__UNKNOWN__	7	99202126	99202126	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:99202126C>T	ENST00000455905.1	+	4	452	c.332C>T	c.(331-333)gCg>gTg	p.A111V	GS1-259H13.2_ENST00000431679.1_lincRNA						NA		NA									NA						CTTCTGGGTGCGACTGACAAA	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000455905.1:c.332C>T	chr7.hg19:g.99202126C>T	ENSP00000401282:p.Ala111Val	NA		hg19		0.02	4.476638	GTGxGAC	COVERED																																																																																			NOVEL	GS1-259H13.10-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000344945.1	2	3.912314	KEEP	0	0	0	13	457	CC	0.995343	0.995343	0		+	15	60	559	0	0	41.976699	133	60	4600	205	ENST00000455905.1	0.101351	1
AGFG2	3268	__UNKNOWN__	__UNKNOWN__	7	100151923	100151923	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:100151923G>A	ENST00000300176.4	+	5	873				AGFG2_ENST00000262935.4_Intron|AGFG2_ENST00000474713.1_Intron	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	NA		NA			regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAGCGTATATGCTTACAACAT	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	37	37	NA		NA	NA	7		NA											NA				100151923		2203	4300	6503	SO:0001627	intron_variant			AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351	3268		ADP-ribosylation factor GTPase activating proteins	5177	protein-coding gene	gene with protein product		604019	HIV-1 Rev binding protein-like	HRBL	NA	9799793	Standard	NM_006076	XM_005250306	NA	Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.751+42G>A	chr7.hg19:g.100151923G>A		NA	O75429|Q96AB9|Q96GL4	hg19	CCDS5697.1	0.02	1.473229	TATxCTT	COVERED																																																																																			NOVEL	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342769.1	2	5.712958	KEEP	0	0	0	19	617	GG	0.99986	0.999754	0		+	6	60	184	0	0	11.683112	86	60	3237	132	ENST00000300176.4	0.065217	0.999895
COL26A1	136227	__UNKNOWN__	__UNKNOWN__	7	101188724	101188724	__UNKNOWN__	RNA	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:101188724G>C	ENST00000397927.3	+	0	1022				COL26A1_ENST00000313669.7_RNA|COL26A1_ENST00000528707.1_RNA	NM_001278563.1	NP_001265492.1	Q96A83	COQA1_HUMAN	collagen, type XXVI, alpha 1	NA		NA			collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)					NA						TCACCAAACAGCCCCCAGGGC	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													17	22	20	NA		NA	NA	7		NA											NA				101188724		1846	4069	5915					AJ416091	CCDS64739.1	7q22.1	2013-01-16	2013-01-16	2013-01-16	ENSG00000160963	ENSG00000160963	136227		Collagens, EMI domain containing	18038	protein-coding gene	gene with protein product	Emu2 gene	608927	EMI domain containing 2	EMID2	NA	12221002, 12145293	Standard	NM_133457	NM_001278563	NA	Approved	Emu2, EMI6	uc003uyo.1	Q96A83	OTTHUMG00000150033	ENST00000397927.3:	chr7.hg19:g.101188724G>C		NA	Q32M90	hg19		0.02	1.933625	ACAxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.357	-0.941709	0.02322	.	.	ENSG00000160963	ENST00000313669	D	0.90563	-2.69	4.82	1.59	0.23543	.	1.277310	0.05851	N	0.621182	T	0.78848	0.4348	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.63954	-0.6520	10	0.12766	T	0.61	.	2.1461	0.03788	0.1109:0.1602:0.479:0.2499	.	270;270	Q96A83;C9JPW4	EMID2_HUMAN;.	T	270	ENSP00000318234:S270T	ENSP00000318234:S270T	S	+	2	0	EMID2	100975444	0.074000	0.21230	0.019000	0.16419	0.210000	0.24377	0.794000	0.26958	0.441000	0.26529	0.555000	0.69702	AGC	NOVEL	COL26A1-002	KNOWN	basic	polymorphic_pseudogene	NA	polymorphic_pseudogene	OTTHUMT00000315898.2	0	8.424584	KEEP	0	0	0	28	961	GG	0.999997	0.999675	0		+	5	60	160	0	0	10.14995	81	60	2951	147	ENST00000397927.3	0.05814	0.999678
CUX1	1523	__UNKNOWN__	__UNKNOWN__	7	101895304	101895304	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:101895304A>G	ENST00000560541.1	+	15	1843				CUX1_ENST00000547394.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000360264.3_3'UTR|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000292535.7_3'UTR			P39880	CUX1_HUMAN	cut-like homeobox 1	NA		NA			auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						GTTGGTTCCCATTCTGTCTTT	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923	1523		Homeoboxes / CUT class	2557	protein-coding gene	gene with protein product	golgi integral membrane protein 6	116896	cut (Drosophila)-like 1 (CCAAT displacement protein), cut-like 1, CCAAT displacement protein (Drosophila)	CUTL1	NA	8468066, 9799793, 15004235	Standard	NM_001913	NM_001202543	NA	Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000560541.1:c.1844-21333A>G	chr7.hg19:g.101895304A>G		NA	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	hg19		0.02	7.628838	CCCxTTC	COVERED																																																																																			NOVEL	CUX1-019	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000418419.1	0	8.124327	KEEP	0	0	0	27	849	AA	0.999988	0.999988	0		+	34	60	1204	0	0	101.541248	118	60	4374	235	ENST00000560541.1	0.223684	1
SH2B2	10603	__UNKNOWN__	__UNKNOWN__	7	101944350	101944350	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:101944350C>T	ENST00000536178.1	+	2	690	c.645C>T	c.(643-645)cgC>cgT	p.R215R	SH2B2_ENST00000306803.8_Silent_p.R172R			O14492	SH2B2_HUMAN	SH2B adaptor protein 2	172	PH. {ECO:0000255|PROSITE- ProRule:PRU00145, ECO:0000305}.	NA			actin cytoskeleton organization (GO:0030036)|antigen receptor-mediated signaling pathway (GO:0050851)|B-1 B cell homeostasis (GO:0001922)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cytokine-mediated signaling pathway (GO:0019221)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|regulation of JAK-STAT cascade (GO:0046425)|regulation of metabolic process (GO:0019222)|regulation of Ras protein signal transduction (GO:0046578)|signal transduction (GO:0007165)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stress fiber (GO:0001725)	JAK pathway signal transduction adaptor activity (GO:0008269)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	9						CCGAGCCCCGCGACAAGTGGA	0.736	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													2	2	2	NA		NA	NA	7		NA											NA				101944350		1376	3046	4422	SO:0001819	synonymous_variant			AB000520		7q22.1	2013-02-14			ENSG00000160999	ENSG00000160999	10603		Pleckstrin homology (PH) domain containing, SH2 domain containing	17381	protein-coding gene	gene with protein product	adaptor protein with pleckstrin homology and src	605300			NA	9233773	Standard	NM_020979	XM_005276976	NA	Approved	APS	uc011kko.2	O14492	OTTHUMG00000150652	ENST00000536178.1:c.645C>T	chr7.hg19:g.101944350C>T		NA	A6ND74	hg19		0.02	2.194634	CCGxGAC	COVERED																																																																																			NOVEL	SH2B2-202	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding		2	8.727515	KEEP	0	0	0	29	977	CC	0.999997	0.999107	0		+	13	60	418	0	0	32.757695	65	60	2193	137	ENST00000536178.1	0.166667	0.99911
RASA4B	100271927	__UNKNOWN__	__UNKNOWN__	7	102136604	102136604	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs746316	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:102136604C>T	ENST00000465829.1	-	11	1124	c.1054G>A	c.(1054-1056)Gtg>Atg	p.V352M	RASA4B_ENST00000306682.6_Missense_Mutation_p.V280M|RP11-514P8.8_ENST00000481893.1_RNA|RASA4B_ENST00000541662.1_Missense_Mutation_p.V352M			C9J798	RAS4B_HUMAN	RAS p21 protein activator 4B	352	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.	NA			intracellular signal transduction (GO:0035556)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)	p.V352M(1)		skin(1)	1						AAAGACTCCACGGACTTTGAG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	kidney(1)											NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS59506.1	7q22.1	2013-01-10			ENSG00000170667	ENSG00000170667	100271927		Pleckstrin homology (PH) domain containing	35202	protein-coding gene	gene with protein product		NA			NA		Standard	XM_003118600	NM_001277335	NA	Approved		uc003uzu.2	C9J798	OTTHUMG00000022944	ENST00000465829.1:c.1054G>A	chr7.hg19:g.102136604C>T	ENSP00000417895:p.Val352Met	NA		hg19		0.02	10.910075	CCAxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.627428	0.00813	.	.	ENSG00000170667	ENST00000541662;ENST00000465829;ENST00000481893;ENST00000306682	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	4.05	4.05	0.47172	Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.000000	0.85682	N	0.000000	T	0.39989	0.1099	N	0.00538	-1.39	0.20873	N	0.999832	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.004;0.003;0.0	T	0.42292	-0.9460	10	0.02654	T	1	.	8.9242	0.35630	0.0:0.0917:0.0:0.9083	rs746316;rs11547192	280;352;352	F8W6L0;F5GXT2;C9J798	.;.;RAS4B_HUMAN	M	352;352;280;280	ENSP00000440982:V352M;ENSP00000417895:V352M;ENSP00000419967:V280M;ENSP00000303968:V280M	ENSP00000303968:V280M	V	-	1	0	RASA4B	101923609	1.000000	0.71417	1.000000	0.80357	0.082000	0.17680	4.925000	0.63425	0.541000	0.28827	-0.556000	0.04195	GTG	NOVEL	RASA4B-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000059600.6	7	7.669918	KEEP	30	7	218	102	3598	CC	1	1	0		-	10	27	349	0	0	21.018416	266	60	9638	550	ENST00000465829.1	0.036232	1
KMT2E	55904	__UNKNOWN__	__UNKNOWN__	7	104748122	104748122	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:104748122G>A	ENST00000311117.3	+	22	3763	c.3218G>A	c.(3217-3219)aGa>aAa	p.R1073K	KMT2E_ENST00000257745.4_Missense_Mutation_p.R1073K|KMT2E_ENST00000334877.4_Missense_Mutation_p.R1073K|KMT2E_ENST00000334914.7_Missense_Mutation_p.R128K	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1073		NA		R -> S (in Ref. 1; AAM74947). {ECO:0000305}.	cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)				NA						AGCCCTGACAGAACAGGAGTT	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													78	80	79	NA		NA	NA	7		NA											NA				104748122		2203	4300	6503	SO:0001583	missense			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483	55904		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	18541	protein-coding gene	gene with protein product		608444	myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)	MLL5	NA	9218106, 7672722	Standard		XM_005250493	NA	Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3218G>A	chr7.hg19:g.104748122G>A	ENSP00000312379:p.Arg1073Lys	NA	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	hg19	CCDS34723.1	0.02	18.580878	ACAxAAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	35	5.587989	0.96590	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914	D;D;D;T	0.95554	-3.74;-3.01;-3.74;-0.04	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.96355	0.8811	L	0.34521	1.04	0.48830	D	0.999715	D	0.64830	0.994	D	0.70716	0.97	D	0.95982	0.8978	10	0.49607	T	0.09	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	1073	Q8IZD2	MLL5_HUMAN	K	1073;1073;1073;993;1073;128	ENSP00000312379:R1073K;ENSP00000335599:R1073K;ENSP00000257745:R1073K;ENSP00000333986:R128K	ENSP00000257745:R1073K	R	+	2	0	MLL5	104535358	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.188000	0.94921	2.854000	0.98071	0.655000	0.94253	AGA	NOVEL	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348697.1	3	26.72027	KEEP	0	1	26	98	3463	GG	1	1	0		+	89	60	3224	0	0	270.354751	334	60	12683	622	ENST00000311117.3	0.210402	1
KMT2E	55904	__UNKNOWN__	__UNKNOWN__	7	104753240	104753240	__UNKNOWN__	Silent	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:104753240A>C	ENST00000311117.3	+	27	5582	c.5037A>C	c.(5035-5037)ccA>ccC	p.P1679P	KMT2E_ENST00000257745.4_Silent_p.P1679P|KMT2E_ENST00000334877.4_Silent_p.P1637P|SRPK2_ENST00000493638.1_Intron	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1679	Pro-rich. {ECO:0000255}.	NA			cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.P1679P(1)			NA						ACTTACCCCCACCCCCACCCC	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	kidney(1)											NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483	55904		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	18541	protein-coding gene	gene with protein product		608444	myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)	MLL5	NA	9218106, 7672722	Standard		XM_005250493	NA	Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.5037A>C	chr7.hg19:g.104753240A>C		NA	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	hg19	CCDS34723.1	0.02	3.537943	CCCxCCC	COVERED																																																																																			NOVEL	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348697.1	9	6.828515	KEEP	0	11	108	63	1534	AA	1	1	0		+	23	60	317	0	0	16.702391	114	60	2771	324	ENST00000311117.3	0.167883	1
BCAP29	55973	__UNKNOWN__	__UNKNOWN__	7	107224384	107224384	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:107224384G>T	ENST00000445771.2	+	3	201	c.150G>T	c.(148-150)aaG>aaT	p.K50N	BCAP29_ENST00000379119.2_Missense_Mutation_p.K50N|BCAP29_ENST00000494086.1_3'UTR|BCAP29_ENST00000379117.2_Missense_Mutation_p.K50N|BCAP29_ENST00000005259.4_Missense_Mutation_p.K50N|BCAP29_ENST00000465919.1_5'UTR			Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	50		NA			apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						TTTGGAACAAGGCTTTCCTTA	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													125	128	127	NA		NA	NA	7		NA											NA				107224384		2201	4297	6498	SO:0001583	missense				CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790	55973			24131	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018844	NM_018844	NA	Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000445771.2:c.150G>T	chr7.hg19:g.107224384G>T	ENSP00000400718:p.Lys50Asn	NA	G5E9L4|O95003	hg19	CCDS34730.1	0.02	26.746304	CAAxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.35	3.603854	0.66445	.	.	ENSG00000075790	ENST00000005259;ENST00000445771;ENST00000479917;ENST00000421217;ENST00000457837;ENST00000379117;ENST00000473124;ENST00000379119;ENST00000491150	.	.	.	5.75	3.61	0.41365	.	0.000000	0.85682	D	0.000000	T	0.75781	0.3896	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.996;0.996	T	0.73515	-0.3958	9	0.48119	T	0.1	-41.5006	8.6376	0.33957	0.3707:0.0:0.6293:0.0	.	50;50;50	G5E9L4;C9JTE9;Q9UHQ4	.;.;BAP29_HUMAN	N	50;50;50;50;50;50;50;50;7	.	ENSP00000005259:K50N	K	+	3	2	BCAP29	107011620	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.594000	0.36697	0.490000	0.27771	0.585000	0.79938	AAG	NOVEL	BCAP29-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337022.2	3	75.525962	KEEP	0	0	0	251	8851	GG	1	1	0		+	92	60	3501	1	0	284.462291	480	60	18117	1167	ENST00000445771.2	0.160839	1
BCAP29	55973	__UNKNOWN__	__UNKNOWN__	7	107259810	107259810	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:107259810A>G	ENST00000005259.4	+	0	2067				BCAP29_ENST00000379119.2_3'UTR|BCAP29_ENST00000379117.2_3'UTR	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	NA		NA			apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						TATAATATTAATATGATTTCA	0.254	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790	55973			24131	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018844	NM_018844	NA	Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.*1002A>G	chr7.hg19:g.107259810A>G		NA	G5E9L4|O95003	hg19	CCDS34731.1	0.02	2.303036	TTAxTAT	COVERED																																																																																			NOVEL	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337011.2	5	5.115408	KEEP	0	0	0	17	556	AA	0.999366	0.99836	0		+	6	60	226	0	0	16.27804	72	60	2654	111	ENST00000005259.4	0.076923	0.998993
DLD	1738	__UNKNOWN__	__UNKNOWN__	7	107533751	107533751	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:107533751C>A	ENST00000205402.5	+	2	399				DLD_ENST00000437604.2_Intron|DLD_ENST00000440410.1_Intron|DLD_ENST00000494441.1_Intron|DLD_ENST00000537148.1_Intron	NM_000108.3	NP_000099.2	P09622	DLDH_HUMAN	dihydrolipoamide dehydrogenase	NA		NA			branched-chain amino acid catabolic process (GO:0009083)|cell redox homeostasis (GO:0045454)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|gastrulation (GO:0007369)|lysine catabolic process (GO:0006554)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|proteolysis (GO:0006508)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of membrane potential (GO:0042391)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|tricarboxylic acid cycle (GO:0006099)	acrosomal matrix (GO:0043159)|cilium (GO:0005929)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dihydrolipoyl dehydrogenase activity (GO:0004148)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(1)|kidney(5)|large_intestine(1)|lung(10)|prostate(1)	20					Flavin adenine dinucleotide(DB03147)	ACATTTTTTTCATCACATTAG	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													70	68	69	NA		NA	NA	7		NA											NA				107533751		2203	4300	6503	SO:0001627	intron_variant			AB209703	CCDS5749.1	7q31-q32	2006-05-22	2006-05-22		ENSG00000091140	ENSG00000091140	1738	1.8.1.4		2898	protein-coding gene	gene with protein product	E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex	238331	dihydrolipoamide dehydrogenase (E3 component of pyruvate dehydrogenase complex, 2-oxo-glutarate complex, branched chain keto acid dehydrogenase complex)	LAD, GCSL	NA		Standard	NM_000108	NM_000108	NA	Approved	DLDH	uc003vet.3	P09622	OTTHUMG00000154813	ENST00000205402.5:c.118+28C>A	chr7.hg19:g.107533751C>A		NA	B2R5X0|B4DHG0|B4DT69|Q14131|Q14167|Q59EV8|Q8WTS4	hg19	CCDS5749.1	0.02	8.765455	TTTxATC	COVERED																																																																																			NOVEL	DLD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337194.3	1	29.49679	KEEP	0	0	0	98	3576	CC	1	1	0		+	12	60	447	0	0	30.32932	203	60	7824	408	ENST00000205402.5	0.055814	1
LAMB1	3912	__UNKNOWN__	__UNKNOWN__	7	107615893	107615893	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:107615893G>T	ENST00000222399.6	-	11	1420				LAMB1_ENST00000393560.1_Intron|LAMB1_ENST00000393561.1_Intron	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TTAAAATCAGGAGGAAACTCA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													23	21	22	NA		NA	NA	7		NA											NA				107615893		2203	4300	6503	SO:0001627	intron_variant			M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136	3912		Laminins	6486	protein-coding gene	gene with protein product		150240	cutis laxa with marfanoid phenotype	CLM	NA	2563160, 2704655, 1864606	Standard	NM_002291	NM_002291	NA	Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1190-35C>A	chr7.hg19:g.107615893G>T		NA	Q14D91	hg19	CCDS5750.1	0.02	9.038402	CAGxAGG	COVERED																																																																																			NOVEL	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000314584.1	3	21.06598	KEEP	0	0	0	70	2412	GG	1	1	0		-	49	60	1747	0	0	147.635575	169	60	6331	344	ENST00000222399.6	0.224771	1
LAMB1	3912	__UNKNOWN__	__UNKNOWN__	7	107615894	107615894	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:107615894A>T	ENST00000222399.6	-	11	1420				LAMB1_ENST00000393560.1_Intron|LAMB1_ENST00000393561.1_Intron	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TAAAATCAGGAGGAAACTCAA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													23	21	21	NA		NA	NA	7		NA											NA				107615894		2203	4300	6503	SO:0001627	intron_variant			M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136	3912		Laminins	6486	protein-coding gene	gene with protein product		150240	cutis laxa with marfanoid phenotype	CLM	NA	2563160, 2704655, 1864606	Standard	NM_002291	NM_002291	NA	Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1190-36T>A	chr7.hg19:g.107615894A>T		NA	Q14D91	hg19	CCDS5750.1	0.02	9.463862	AGGxGGA	COVERED																																																																																			NOVEL	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000314584.1	3	20.758397	KEEP	0	0	0	69	2188	AA	1	1	0		-	46	60	1728	0	0	146.275805	169	60	6364	339	ENST00000222399.6	0.213953	1
GPR85	54329	__UNKNOWN__	__UNKNOWN__	7	112723032	112723032	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:112723032G>C	ENST00000297146.3	-	0	2348				GPR85_ENST00000424100.1_3'UTR|GPR85_ENST00000501255.2_3'UTR	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	NA		NA			signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						GATGAGGAAAGTGGTATTTAG	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604	54329		GPCR / Class A : Orphans	4536	protein-coding gene	gene with protein product		605188			NA	10978537, 10833454	Standard		NM_018970	NA	Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.*632C>G	chr7.hg19:g.112723032G>C		NA	Q9JHI6|Q9NPD1	hg19	CCDS5758.1	0.02	7.350117	AAAxTGG	COVERED																																																																																			NOVEL	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346650.2	2	6.019199	KEEP	0	0	0	20	714	GG	0.999863	0.999863	0		-	11	60	404	0	0	28.22911	150	60	5657	208	ENST00000297146.3	0.068323	1
CTTNBP2	83992	__UNKNOWN__	__UNKNOWN__	7	117364771	117364771	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:117364771G>A	ENST00000160373.3	-	19	4368	c.4277C>T	c.(4276-4278)aCa>aTa	p.T1426I		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1426		NA			brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GAAATCAGCTGTATGCTGGTC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	83	84	NA		NA	NA	7		NA											NA				117364771		2203	4300	6503	SO:0001583	missense				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063	83992		Ankyrin repeat domain containing	15679	protein-coding gene	gene with protein product		609772	cortactin binding protein 2	CORTBP2, C7orf8	NA	11707066	Standard	NM_033427	XM_005250635	NA	Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4277C>T	chr7.hg19:g.117364771G>A	ENSP00000160373:p.Thr1426Ile	NA	O43389|Q7LG11|Q9C0A5	hg19	CCDS5774.1	0.02	7.029401	GCTxTAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.280	-0.986703	0.02180	.	.	ENSG00000077063	ENST00000160373	D	0.88277	-2.36	5.45	-1.67	0.08238	.	0.856016	0.10773	N	0.635726	T	0.64227	0.2579	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.56739	-0.7929	10	0.18710	T	0.47	-6.802	8.2759	0.31873	0.722:0.1357:0.1423:0.0	.	1426	Q8WZ74	CTTB2_HUMAN	I	1426	ENSP00000160373:T1426I	ENSP00000160373:T1426I	T	-	2	0	CTTNBP2	117152007	0.052000	0.20516	0.018000	0.16275	0.686000	0.39977	1.398000	0.34554	-0.448000	0.07128	-0.819000	0.03115	ACA	NOVEL	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059201.4	0	9.029282	KEEP	0	0	0	30	1078	GG	0.999997	0.999997	0		-	37	60	1377	0	0	118.720905	115	60	4388	228	ENST00000160373.3	0.243421	1
FAM3C	10447	__UNKNOWN__	__UNKNOWN__	7	120989278	120989278	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:120989278T>C	ENST00000359943.3	-	0	2134					NM_001040020.1|NM_014888.2	NP_001035109.1|NP_055703.1	Q92520	FAM3C_HUMAN	family with sequence similarity 3, member C	NA		NA			multicellular organismal development (GO:0007275)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	cytokine activity (GO:0005125)			kidney(1)|lung(8)	9	all_neural(327;0.117)					AAACTTTAGGTTCGAAATTTA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D87120	CCDS5782.1	7q22.1-q31.1	2014-08-14			ENSG00000196937	ENSG00000196937	10447			18664	protein-coding gene	gene with protein product	predicted osteoblast protein, interleukin-like EMT inducer, interleukin-like epithelial-mesenchymal transition inducer	608618			NA	12160727	Standard	NM_001040020	NM_014888	NA	Approved	GS3876, ILEI	uc010lkm.3	Q92520	OTTHUMG00000156979	ENST00000359943.3:c.*1237A>G	chr7.hg19:g.120989278T>C		NA	A6NDN2|A8K3R7	hg19	CCDS5782.1	0.02	18.364704	AGGxTCG	COVERED																																																																																			NOVEL	FAM3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346945.1	6	29.1869	KEEP	16	0	0	97	3106	TT	1	1	0		-	13	49	458	0	0	27.014365	413	50	14732	628	ENST00000359943.3	0.030516	1
LRRC4	64101	__UNKNOWN__	__UNKNOWN__	7	127669518	127669518	__UNKNOWN__	Silent	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:127669518G>C	ENST00000249363.3	-	2	1433	c.1176C>G	c.(1174-1176)ctC>ctG	p.L392L	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	392	Ig-like.	NA			postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		AGGCGTGGCTGAGCACTGTCC	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													102	85	91	NA		NA	NA	7		NA											NA				127669518		2203	4300	6503	SO:0001819	synonymous_variant			AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594	64101		Immunoglobulin superfamily / I-set domain containing	15586	protein-coding gene	gene with protein product		610486	leucine-rich repeat-containing 4		NA	12969517	Standard	NM_022143	NM_022143	NA	Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.1176C>G	chr7.hg19:g.127669518G>C		NA	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	hg19	CCDS5799.1	0.02	22.8777	GCTxAGC	COVERED																																																																																			NOVEL	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349170.1	5	28.55966	KEEP	0	0	0	95	3264	GG	1	1	0		-	93	60	3420	0	0	286.124302	364	60	13621	709	ENST00000249363.3	0.203501	1
KCP	375616	__UNKNOWN__	__UNKNOWN__	7	128526804	128526804	__UNKNOWN__	RNA	SNP	C	C	T	rs375854442	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:128526804C>T	ENST00000476647.2	-	0	2732							Q6ZWJ8	KCP_HUMAN	kielin/chordin-like protein	NA		NA				extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)	4						GTGGGGGACACACCTCCTGGG	0.677	NA	NA											C|||	2	0.000399361	0.0015	0	5008	,	,	NA	14073	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								C		4,1380		0,4,688	54	50	51	NA		-7	0	7		51	0,3182		0,0,1591	no	intron	KCP	NM_001135914.1		0,4,2279	TT,TC,CC	NA	0.0,0.289,0.0876			128526804	4,4562	692	1591	2283					AK122706		7q32.3	2009-11-06	2009-02-18	2009-02-18	ENSG00000135253	ENSG00000135253	375616			17585	protein-coding gene	gene with protein product	kielin	609344	cysteine rich BMP regulator 2 (chordin-like)	CRIM2	NA	15793581	Standard	NM_199349	NM_001135914	NA	Approved	FLJ33365, NET67	uc011kor.2	Q6ZWJ8	OTTHUMG00000158363	ENST00000476647.2:	chr7.hg19:g.128526804C>T		NA	Q8NBE0	hg19		0.02	10.564372	ACAxACC	COVERED																																																																																			NOVEL	KCP-006	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000403051.1	5	21.363079	KEEP	0	0	0	71	2353	CC	1	1	0		-	21	60	669	0	0	44.890907	250	60	8672	431	ENST00000476647.2	0.077491	1
SMO	6608	__UNKNOWN__	__UNKNOWN__	7	128845518	128845518	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:128845518C>T	ENST00000249373.3	+	4	1095	c.815C>T	c.(814-816)gCg>gTg	p.A272V		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	272		NA			adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	TACGTCAATGCGTGCTTCTTT	0.567	NA	NA	Mis		skin basal cell									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	0													106	102	104	NA		NA	NA	7		NA											NA				128845518		2203	4300	6503	SO:0001583	missense			U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602	6608		GPCR / Class F : Frizzled receptors	11119	protein-coding gene	gene with protein product	frizzled family member 11	601500	smoothened (Drosophila) homolog, smoothened homolog (Drosophila), smoothened, seven transmembrane spanning receptor, smoothened, frizzled family receptor	SMOH	NA	9628830	Standard	NM_005631	NM_005631	NA	Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.815C>T	chr7.hg19:g.128845518C>T	ENSP00000249373:p.Ala272Val	NA	A4D1K5	hg19	CCDS5811.1	0.02	19.800696	ATGxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160927	0.78226	.	.	ENSG00000128602	ENST00000249373	D	0.81579	-1.51	5.57	5.57	0.84162	GPCR, family 2-like (1);	0.144727	0.64402	D	0.000007	T	0.79293	0.4421	L	0.45228	1.405	0.80722	D	1	D	0.58268	0.982	P	0.48425	0.577	T	0.75051	-0.3454	10	0.16420	T	0.52	.	18.5223	0.90958	0.0:1.0:0.0:0.0	.	272	Q99835	SMO_HUMAN	V	272	ENSP00000249373:A272V	ENSP00000249373:A272V	A	+	2	0	SMO	128632754	1.000000	0.71417	0.942000	0.38095	0.963000	0.63663	7.762000	0.85270	2.620000	0.88729	0.491000	0.48974	GCG	NOVEL	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350986.1	5	24.488599	KEEP	0	1	12	86	2885	CC	1	1	0		+	45	60	1640	0	0	120.774792	432	60	14456	720	ENST00000249373.3	0.09434	1
AHCYL2	23382	__UNKNOWN__	__UNKNOWN__	7	129066388	129066388	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:129066388A>G	ENST00000325006.3	+	16	1867	c.1813A>G	c.(1813-1815)Aag>Gag	p.K605E	AHCYL2_ENST00000490911.1_Missense_Mutation_p.K502E|AHCYL2_ENST00000446212.1_Missense_Mutation_p.K503E|AHCYL2_ENST00000446544.2_Missense_Mutation_p.K604E|AHCYL2_ENST00000474594.1_Missense_Mutation_p.K502E|AHCYL2_ENST00000531335.2_Missense_Mutation_p.K524E	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	605		NA			one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						TGGGCCCTTCAAGCCTAATTA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(160;1736 1964 29875 40941 45605)					NA		NA				0													104	91	95	NA		NA	NA	7		NA											NA				129066388		2203	4300	6503	SO:0001583	missense			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467	23382			22204	protein-coding gene	gene with protein product		NA	S-adenosylhomocysteine hydrolase-like 2		NA		Standard		NM_001130720	NA	Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.1813A>G	chr7.hg19:g.129066388A>G	ENSP00000315931:p.Lys605Glu	NA	B4DIZ5|D9N155|O94917	hg19	CCDS5812.1	0.02	4.604733	TTCxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	22.6	4.313378	0.81358	.	.	ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911	D;D;D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65;-1.65;-1.65	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.94699	0.8290	H	0.98446	4.235	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.998	D	0.96585	0.9433	10	0.87932	D	0	-19.6331	14.7107	0.69229	1.0:0.0:0.0:0.0	.	502;503;605;502;604	B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2	.;.;SAHH3_HUMAN;.;.	E	605;604;524;502;503;502	ENSP00000315931:K605E;ENSP00000413639:K604E;ENSP00000431787:K524E;ENSP00000420459:K502E;ENSP00000405267:K503E;ENSP00000420801:K502E	ENSP00000315931:K605E	K	+	1	0	AHCYL2	128853624	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.313000	0.96297	2.151000	0.67156	0.460000	0.39030	AAG	NOVEL	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354065.1	1	8.725375	KEEP	0	0	0	29	882	AA	0.999997	0.999996	0		+	19	60	704	0	0	56.550303	103	60	3781	190	ENST00000325006.3	0.155738	0.999999
MEST	4232	__UNKNOWN__	__UNKNOWN__	7	130139738	130139738	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:130139738T>C	ENST00000223215.4	+	7	779	c.558T>C	c.(556-558)cgT>cgC	p.R186R	MEST_ENST00000437945.1_Silent_p.R186R|MEST_ENST00000416162.2_Silent_p.R177R|MEST_ENST00000393187.1_Silent_p.R177R|MEST_ENST00000341441.5_Silent_p.R177R|MEST_ENST00000462132.1_3'UTR|MEST_ENST00000378576.4_Silent_p.R177R	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	186		NA			mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					AGACTCACCGTCCACTCCTTC	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(126;2182 2305 6517 35181)					NA		NA				0													101	90	93	NA		NA	NA	7		NA											NA				130139738		2203	4300	6503	SO:0001819	synonymous_variant				CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484	4232			7028	protein-coding gene	gene with protein product	Paternally-expressed gene 1	601029	mesoderm specific transcript (mouse) homolog, mesoderm specific transcript homolog (mouse)		NA	8884280	Standard	NM_002402	NM_002402	NA	Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.558T>C	chr7.hg19:g.130139738T>C		NA	B2R6S1|O14973|O15007|Q6AI49|Q92571	hg19	CCDS5822.1	0.02	4.966069	CCGxCCA	COVERED																																																																																			NOVEL	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345183.2	0	6.620464	KEEP	0	0	0	22	718	TT	0.999879	0.999875	0		+	12	60	458	0	0	34.821546	103	60	3652	189	ENST00000223215.4	0.104348	0.999997
MEST	4232	__UNKNOWN__	__UNKNOWN__	7	130144686	130144686	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:130144686T>C	ENST00000223215.4	+	12	1111				MEST_ENST00000437945.1_Intron|MEST_ENST00000416162.2_Intron|MEST_ENST00000393187.1_Intron|MEST_ENST00000341441.5_Intron|MEST_ENST00000378576.4_Intron	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	NA		NA			mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					TCCAGTGTGGTGTGTCCACAG	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(126;2182 2305 6517 35181)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484	4232			7028	protein-coding gene	gene with protein product	Paternally-expressed gene 1	601029	mesoderm specific transcript (mouse) homolog, mesoderm specific transcript homolog (mouse)		NA	8884280	Standard	NM_002402	NM_002402	NA	Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.891-94T>C	chr7.hg19:g.130144686T>C		NA	B2R6S1|O14973|O15007|Q6AI49|Q92571	hg19	CCDS5822.1	0.02	15.005818	TGGxGTG	COVERED																																																																																			NOVEL	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345183.2	2	12.030063	KEEP	0	0	0	40	1183	TT	1	1	0		+	80	60	2852	0	0	243.780284	252	60	8691	448	ENST00000223215.4	0.240964	1
AKR1B10	57016	__UNKNOWN__	__UNKNOWN__	7	134226071	134226071	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:134226071C>T	ENST00000359579.4	+	0	1501					NM_020299.4	NP_064695.3	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10 (aldose reductase)	NA		NA			cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	aldo-keto reductase (NADP) activity (GO:0004033)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|retinal dehydrogenase activity (GO:0001758)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(9)|skin(5)	20						ATTTTTTCCACTTATCTGATC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF052577	CCDS5832.1	7q33	2010-04-08			ENSG00000198074	ENSG00000198074	57016		Aldo-keto reductases	382	protein-coding gene	gene with protein product	aldose reductase-like 1, aldo-keto reductase family 1, member B11 (aldose reductase-like), aldose reductase-like peptide, aldose reductase-related protein, small intestine reductase	604707		AKR1B11	NA	9765596, 9565553	Standard	NM_020299	NM_020299	NA	Approved	AKR1B12, ARL-1, HIS, ARL1, HSI, ALDRLn	uc003vrr.3	O60218	OTTHUMG00000155356	ENST00000359579.4:c.*230C>T	chr7.hg19:g.134226071C>T		NA	A4D1P1|O75890|Q6FHF3|Q8IWZ1	hg19	CCDS5832.1	0.02	15.108602	CCAxTTA	COVERED																																																																																			NOVEL	AKR1B10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339615.1	2	18.957977	KEEP	0	0	0	63	2254	CC	1	1	0		+	10	60	368	0	0	21.537523	367	60	14046	573	ENST00000359579.4	0.026525	1
AGBL3	340351	__UNKNOWN__	__UNKNOWN__	7	134819672	134819672	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:134819672C>A	ENST00000436302.2	+	17	2675	c.2422C>A	c.(2422-2424)Caa>Aaa	p.Q808K	AGBL3_ENST00000435976.2_Intron|C7orf49_ENST00000459937.1_Intron|AGBL3_ENST00000458078.1_Missense_Mutation_p.Q863K	NM_178563.3	NP_848658.3	Q8NEM8	CBPC3_HUMAN	ATP/GTP binding protein-like 3	889		NA				cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|lung(2)|skin(3)	10						TTTTGTAATCCAAGGGGATGT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													96	83	87	NA		NA	NA	7		NA											NA				134819672		692	1591	2283	SO:0001583	missense			BC030651	CCDS47718.1	7q33	2014-06-23			ENSG00000146856	ENSG00000146856	340351			27981	protein-coding gene	gene with protein product		NA			NA		Standard	NM_178563	NM_178563	NA	Approved	MGC32955, CCP3	uc011kpw.2	Q8NEM8	OTTHUMG00000155406	ENST00000436302.2:c.2422C>A	chr7.hg19:g.134819672C>A	ENSP00000388275:p.Gln808Lys	NA	B7Z827|Q9H965	hg19	CCDS47718.1	0.02	12.466559	ATCxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.16	3.044098	0.55110	.	.	ENSG00000146856	ENST00000436302;ENST00000458078	T;T	0.13307	2.6;2.8	5.19	2.31	0.28768	.	.	.	.	.	T	0.09069	0.0224	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.33394	-0.9870	9	0.27785	T	0.31	-7.5442	5.5011	0.16829	0.3586:0.5495:0.0:0.0919	.	808	Q8NEM8-4	.	K	808;863	ENSP00000388275:Q808K;ENSP00000395969:Q863K	ENSP00000388275:Q808K	Q	+	1	0	AGBL3	134470212	0.001000	0.12720	0.005000	0.12908	0.032000	0.12392	0.704000	0.25661	0.825000	0.34637	-0.282000	0.10007	CAA	NOVEL	AGBL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376655.1	3	15.951263	KEEP	0	0	0	53	1873	CC	1	1	0		+	10	60	351	0	0	20.225929	339	60	12522	505	ENST00000436302.2	0.028653	1
ATP6V0A4	50617	__UNKNOWN__	__UNKNOWN__	7	138437399	138437399	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs202070044		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:138437399G>A	ENST00000310018.2	-	11	1282	c.1000C>T	c.(1000-1002)Cgt>Tgt	p.R334C	ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.R334C|ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.R334C	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	334		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						CTCTTGATACGTGTGGCATCT	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													84	67	73	NA		NA	NA	7		NA											NA				138437399		2203	4300	6503	SO:0001583	missense			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929	50617		ATPases / V-type	866	protein-coding gene	gene with protein product		605239	ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B, ATPase, H+ transporting, lysosomal V0 subunit a isoform 4, ATPase, H+ transporting, lysosomal V0 subunit A4	ATP6N1B, ATP6N2, RTA1C	NA	10577919, 10973252	Standard	NM_020632	XM_005250393	NA	Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1000C>T	chr7.hg19:g.138437399G>A	ENSP00000308122:p.Arg334Cys	NA	A4D1R4|A8KA80|Q32M47	hg19	CCDS5849.1	0.02	2.296647	TACxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.84	2.356461	0.41700	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.86497	-2.13;-2.13;-2.13	5.44	4.54	0.55810	.	0.523214	0.19944	N	0.102589	D	0.90998	0.7169	M	0.81802	2.56	0.40211	D	0.977629	D	0.67145	0.996	P	0.60473	0.875	D	0.90671	0.4598	10	0.56958	D	0.05	-13.9579	7.1564	0.25639	0.1394:0.0:0.6509:0.2097	.	334	Q9HBG4	VPP4_HUMAN	C	334	ENSP00000308122:R334C;ENSP00000376774:R334C;ENSP00000253856:R334C	ENSP00000308122:R334C	R	-	1	0	ATP6V0A4	138087939	0.544000	0.26441	0.924000	0.36721	0.037000	0.13140	1.124000	0.31320	2.717000	0.92951	0.655000	0.94253	CGT	NOVEL	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347514.1	0	3.912162	KEEP	0	0	0	13	432	GG	0.994391	0.974032	0		-	12	60	433	0	0	36.3986	44	60	1450	82	ENST00000310018.2	0.214286	0.979526
PRSS1	5644	__UNKNOWN__	__UNKNOWN__	7	142458486	142458486	__UNKNOWN__	Silent	SNP	C	C	T	rs369646357		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:142458486C>T	ENST00000311737.7	+	2	127	c.121C>T	c.(121-123)Ctg>Ttg	p.L41L	PRSS1_ENST00000486171.1_Silent_p.L41L	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	41	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	CCAGGTGTCCCTGAATTCTGG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													125	121	122	NA		NA	NA	7		NA											NA				142458486		2203	4300	6503	SO:0001819	synonymous_variant			M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	5644	3.4.21.4	Serine peptidases / Serine peptidases	9475	protein-coding gene	gene with protein product		276000		TRY1	NA		Standard		NM_002769	NA	Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.121C>T	chr7.hg19:g.142458486C>T		NA	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	hg19	CCDS5872.1	0.02	8.966314	TCCxTGA	COVERED																																																																																			NOVEL	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352538.2	11	7.740743	KEEP	4	1	32	37	1259	CC	1	1	0		+	12	49	428	0	0	28.343518	207	60	7659	363	ENST00000311737.7	0.054795	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	142478815	142478815	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:142478815C>T			NA	NA				PRSS1 (17894 upstream) : PRSS3P2 (24 downstream)						NA		NA									NA						GGCCTTCCACCACCAGACAGG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.142478815C>T		NA		hg19		0.02	10.004702	CACxACC	COVERED																																																																																			NOVEL					0			2	6.319742	KEEP	1	0	0	21	713	CC	0.999869	0.999869	0			26	60	958	0	0	74.749196	173	70	6178	286		0.130653	1
CASP2	835	__UNKNOWN__	__UNKNOWN__	7	143002039	143002039	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:143002039G>A	ENST00000310447.5	+	11	1475	c.1234G>A	c.(1234-1236)Gca>Aca	p.A412T	CASP2_ENST00000493642.1_3'UTR	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase	412		NA			aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|ectopic germ cell programmed cell death (GO:0035234)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|luteolysis (GO:0001554)|neural retina development (GO:0003407)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron apoptotic process (GO:0043525)|protein processing (GO:0016485)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(164;0.059)					CCAGGTGAACGCACTTATCAA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													83	73	77	NA		NA	NA	7		NA											NA				143002039		2203	4300	6503	SO:0001583	missense			AK096245, BC002427, BM998653, BX537669, CB988674, U13021	CCDS5879.1, CCDS47733.1	7q34-q35	2014-01-20	2008-08-01		ENSG00000106144	ENSG00000106144	835		Caspases, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	1503	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 57	600639	neural precursor cell expressed, developmentally down-regulated 2	NEDD2	NA	7789948, 8780721	Standard	NM_032982	NM_032982	NA	Approved	ICH1, PPP1R57, MGC2181	uc003wco.3	P42575	OTTHUMG00000023641	ENST00000310447.5:c.1234G>A	chr7.hg19:g.143002039G>A	ENSP00000312664:p.Ala412Thr	NA	A8K5F9|D3DXD6|E9PDN0|P42576|Q59F21|Q7KZL6|Q86UJ3|Q9BUP7|Q9BZK9|Q9BZL0	hg19	CCDS5879.1	0.02	10.835758	AACxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.95	2.390658	0.42410	.	.	ENSG00000106144	ENST00000310447	T	0.20881	2.04	5.27	5.27	0.74061	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.493222	0.23587	N	0.046600	T	0.16085	0.0387	L	0.57536	1.79	0.30934	N	0.726615	P	0.42961	0.795	B	0.31245	0.126	T	0.13282	-1.0515	10	0.18276	T	0.48	.	10.1669	0.42886	0.1219:0.0:0.8781:0.0	.	412	P42575	CASP2_HUMAN	T	412	ENSP00000312664:A412T	ENSP00000312664:A412T	A	+	1	0	CASP2	142712161	0.963000	0.33076	0.662000	0.29724	0.958000	0.62258	3.949000	0.56668	2.478000	0.83669	0.650000	0.86243	GCA	NOVEL	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059962.3	6	23.474607	KEEP	0	0	0	78	2674	GG	1	1	0		+	18	60	667	0	0	46.456924	256	60	8886	432	ENST00000310447.5	0.065693	1
EPHA1	2041	__UNKNOWN__	__UNKNOWN__	7	143096958	143096958	__UNKNOWN__	Silent	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:143096958G>C	ENST00000275815.3	-	4	707	c.621C>G	c.(619-621)acC>acG	p.T207T		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	207	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.	NA			activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				AGCCATTCAGGGTCTCAGGAC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													36	33	34	NA		NA	NA	7		NA											NA				143096958		2199	4296	6495	SO:0001819	synonymous_variant			M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2041	2.7.10.1	EPH receptors, Sterile alpha motif (SAM) domain containing, Fibronectin type III domain containing	3385	protein-coding gene	gene with protein product		179610	EphA1	EPHT, EPHT1	NA	9267020	Standard		NM_005232	NA	Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.621C>G	chr7.hg19:g.143096958G>C		NA	A1L3V3|B5A966|B5A967|Q15405	hg19	CCDS5884.1	0.02	6.938605	CAGxGTC	COVERED																																																																																			NOVEL	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342154.1	1	21.304671	KEEP	0	0	0	71	2354	GG	1	1	0		-	12	60	440	1	0	30.83815	160	60	5575	311	ENST00000275815.3	0.069767	1
FAM115C	285966	__UNKNOWN__	__UNKNOWN__	7	143426678	143426678	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:143426678C>G	ENST00000441159.2	+	0	4744				FAM115C_ENST00000409703.3_3'UTR			A6NFQ2	F115C_HUMAN	family with sequence similarity 115, member C	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)					endometrium(2)|large_intestine(4)|lung(2)|prostate(1)	9						AAATTCAACTCCAGAACTGAT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY167570	CCDS34769.1, CCDS47735.1, CCDS47735.2	7q35	2010-08-03	2008-06-12	2008-06-12	ENSG00000170379	ENSG00000170379	285966			26878	protein-coding gene	gene with protein product		NA	family with sequence similarity 139, member A	FAM139A	NA		Standard	NM_173678	NM_173678	NA	Approved	FLJ40722	uc003wdf.3	A6NFQ2	OTTHUMG00000153232	ENST00000441159.2:c.*1918C>G	chr7.hg19:g.143426678C>G		NA	B4DK02|Q14D25|Q17RQ4|Q8IWQ0|Q8NF84	hg19		0.02	2.399578	ACTxCAG	COVERED																																																																																			NOVEL	FAM115C-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000330287.1	1	3.009815	KEEP	0	0	0	10	350	CC	0.992708	0.987827	0		+	6	60	229	0	0	16.99118	61	60	2137	94	ENST00000441159.2	0.089552	0.995084
CNTNAP2	26047	__UNKNOWN__	__UNKNOWN__	7	148114865	148114865	__UNKNOWN__	3'UTR	SNP	A	A	G	rs1062072	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:148114865A>G	ENST00000361727.3	+	0	6669				CNTNAP2_ENST00000463592.2_3'UTR	NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	NA		NA			adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TGCAATTCCCATGATAGCTCT	0.343	NA	NA								HNSCC(39;0.1)			a|||	2690	0.537141	0.5182	0.6988	5008	,	,	NA	19467	0.629	NA	0.4583	False	NA	,,,	NA	NA	NA	2504	0.4346	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469	26047			13830	protein-coding gene	gene with protein product		604569			NA	10624965, 10048485	Standard		NM_014141	NA	Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.*2157A>G	chr7.hg19:g.148114865A>G		NA	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	hg19	CCDS5889.1	0.02	2.110109	CCCxTGA	COVERED																																																																																			NOVEL	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327668.1	3	2.406102	KEEP	0	0	0	8	236	AA	0.99257	0.992533	0		+	93	60	3278	0	0	362.323193	6	60	222	115	ENST00000361727.3	0.939394	0.999962
ZNF783	100289678	__UNKNOWN__	__UNKNOWN__	7	148964293	148964293	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:148964293G>A	ENST00000434415.1	+	4	816	c.653G>A	c.(652-654)cGt>cAt	p.R218H		NM_001195220.1	NP_001182149.1	Q6ZMS7	ZN783_HUMAN	zinc finger family member 783	218		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)	22	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.0014)			GAGGTGGGACGTCCAAGGATG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													58	59	58	NA		NA	NA	7		NA											NA				148964293		2078	4213	6291	SO:0001583	missense			AK131504	CCDS56519.1	7q36.1	2013-01-08	2008-05-28		ENSG00000204946	ENSG00000204946	100289678		Zinc fingers, C2H2-type, -	27222	protein-coding gene	gene with protein product		NA			NA	8619474, 9110174	Standard	NM_001195220	NM_001195220	NA	Approved	DKFZp667J212	uc011kuo.2	Q6ZMS7	OTTHUMG00000158969	ENST00000434415.1:c.653G>A	chr7.hg19:g.148964293G>A	ENSP00000410890:p.Arg218His	NA	C9J9J2	hg19	CCDS56519.1	0.02	6.018256	GACxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.158	0.585159	0.13749	.	.	ENSG00000204946	ENST00000434415	T	0.06449	3.3	4.86	2.09	0.27110	.	1.973700	0.02812	N	0.124489	T	0.06508	0.0167	N	0.19112	0.55	0.09310	N	0.999997	.	.	.	.	.	.	T	0.46693	-0.9173	8	0.18276	T	0.48	-0.1089	11.6234	0.51132	0.1684:0.0:0.8316:0.0	.	.	.	.	H	218	ENSP00000410890:R218H	ENSP00000367291:R218H	R	+	2	0	ZNF783	148595226	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.238000	0.08977	0.269000	0.21961	-1.175000	0.01729	CGT	NOVEL	ZNF783-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352715.1	1	10.533141	KEEP	0	0	0	35	1206	GG	0.999999	0.999999	0		+	7	60	255	0	0	15.684966	192	60	6902	291	ENST00000434415.1	0.035176	1
SSPO	23145	__UNKNOWN__	__UNKNOWN__	7	149522107	149522107	__UNKNOWN__	RNA	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:149522107A>T	ENST00000378016.2	+	0	13894							A2VEC9	SSPO_HUMAN	SCO-spondin	NA		NA			cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)				NA	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GGTGCCCTGCAGTGGGGGGTT	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	16	15	NA		NA	NA	7		NA											NA				149522107		1921	4124	6045					AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558	23145			21998	protein-coding gene	gene with protein product	subcommissural organ spondin, SCO protein, thrombospondin domain containing	NA	SCO-spondin homolog (Bos taurus)		NA	8743952, 11008217	Standard		NM_198455	NA	Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884	ENST00000378016.2:	chr7.hg19:g.149522107A>T		NA	Q76B61	hg19		0.02	2.063109	TGCxGTG	COVERED																																																																																			NOVEL	SSPO-202	KNOWN	basic	processed_transcript	NA	processed_transcript		0	3.309535	KEEP	0	0	0	11	336	AA	0.993072	0.99298	0		+	20	60	743	0	0	62.71848	74	60	2691	122	ENST00000378016.2	0.212766	0.999907
ATG9B	285973	__UNKNOWN__	__UNKNOWN__	7	150715660	150715660	__UNKNOWN__	Intron	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:150715660T>A	ENST00000494791.1	-	6	1794				ATG9B_ENST00000605938.1_Intron|ATG9B_ENST00000377974.2_Intron|ATG9B_ENST00000444312.1_Intron			Q674R7	ATG9B_HUMAN	autophagy related 9B	NA		NA			autophagic vacuole assembly (GO:0000045)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(4)|prostate(1)	14	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGCCCCAGATCAGAGAAACC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													19	22	21	NA		NA	NA	7		NA											NA				150715660		1905	4016	5921	SO:0001627	intron_variant			AK027791		7q36	2014-02-12	2012-06-06	2005-09-11	ENSG00000181652	ENSG00000181652	285973			21899	protein-coding gene	gene with protein product		612205	nitric oxide synthase 3 antisense, ATG9 autophagy related 9 homolog B (S. cerevisiae)	NOS3AS	NA	15234981, 15755735	Standard	NM_173681	NM_173681	NA	Approved	FLJ14885, APG9L2, SONE	uc011kvc.2	Q674R7	OTTHUMG00000158634	ENST00000494791.1:c.2777+46A>T	chr7.hg19:g.150715660T>A		NA	A1A5D3|Q6JRW5|Q8N8I8	hg19		0.02	8.746212	AGAxCAG	COVERED																																																																																			NOVEL	ATG9B-001	KNOWN	non_canonical_U12|basic	processed_transcript	NA	protein_coding	OTTHUMT00000351543.2	3	36.083153	KEEP	0	0	0	120	3545	TT	1	1	0		-	79	70	2765	0	0	248.342676	160	60	5581	450	ENST00000494791.1	0.330544	1
AGAP3	116988	__UNKNOWN__	__UNKNOWN__	7	150820860	150820860	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:150820860G>A	ENST00000463381.1	+	9	940				AGAP3_ENST00000397238.2_Intron	NM_001281300.1	NP_001268229.1	Q96P47	AGAP3_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 3	NA		NA			cellular response to reactive oxygen species (GO:0034614)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein import into nucleus, translocation (GO:0000060)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|liver(2)|lung(9)|ovary(2)|prostate(3)|urinary_tract(1)	28						TCTTTAACACGCCTCTTGTTT	0.657	NA	NA									OREG0018449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	80	77	NA		NA	NA	7		NA											NA				150820860		1990	4147	6137	SO:0001627	intron_variant			AF413079	CCDS43681.1, CCDS55185.1, CCDS64802.1	7q36.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000133612	ENSG00000133612	116988		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16923	protein-coding gene	gene with protein product		NA	centaurin, gamma 3	CENTG3	NA		Standard	NM_031946	NM_001042535	NA	Approved		uc003wjg.1	Q96P47	OTTHUMG00000158724	ENST00000463381.1:c.445-21G>A	chr7.hg19:g.150820860G>A		1735	B3KNZ8|E9PAL8|Q59EN0|Q96RK3	hg19		0.02	6.089491	CACxCCT	COVERED																																																																																			NOVEL	AGAP3-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351909.2	1	25.275916	KEEP	0	0	0	84	2861	GG	1	1	0		+	9	60	297	1	0	19.043484	148	60	5185	309	ENST00000463381.1	0.057325	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151945330	151945330	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs200264581		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:151945330G>T	ENST00000262189.6	-	14	2407	c.2189C>A	c.(2188-2190)tCt>tAt	p.S730Y	KMT2C_ENST00000355193.2_Missense_Mutation_p.S730Y	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	730		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						AGAAAGTTCAGAATTTTCTTT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	73	74	NA		NA	NA	7		NA											NA				151945330		2203	4300	6503	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2189C>A	chr7.hg19:g.151945330G>T	ENSP00000262189:p.Ser730Tyr	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	7.93216	TCAxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	4.321	0.058847	0.08339	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84070	-1.8;-1.8	5.33	3.43	0.39272	.	0.893834	0.09361	N	0.812799	T	0.69351	0.3101	L	0.29908	0.895	0.43503	D	0.995759	P	0.44877	0.845	B	0.34536	0.185	T	0.63655	-0.6588	10	0.37606	T	0.19	.	6.5725	0.22547	0.0681:0.2397:0.5684:0.1238	.	730	Q8NEZ4	MLL3_HUMAN	Y	730	ENSP00000262189:S730Y;ENSP00000347325:S730Y	ENSP00000262189:S730Y	S	-	2	0	MLL3	151576263	0.008000	0.16893	0.053000	0.19242	0.077000	0.17291	0.344000	0.19962	1.224000	0.43551	-0.182000	0.12963	TCT	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	0	20.465931	KEEP	22	0	0	68	2415	GG	1	1	0		-	8	40	288	0	1	17.847041	203	60	7709	369	ENST00000262189.6	0.037915	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962257	151962257	__UNKNOWN__	Silent	SNP	C	C	T	rs62478357		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:151962257C>T	ENST00000262189.6	-	8	1268	c.1050G>A	c.(1048-1050)ccG>ccA	p.P350P	KMT2C_ENST00000355193.2_Silent_p.P350P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	350		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						AGAGGTCTCCCGGGCTGTCGC	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													146	134	138	NA		NA	NA	7		NA											NA				151962257		2203	4296	6499	SO:0001819	synonymous_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1050G>A	chr7.hg19:g.151962257C>T		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	21.883158	TCCxGGG	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	8	18.773084	KEEP	192	15	463	225	7560	CC	1	1	0		-	20	49	735	0	0	46.199844	503	60	17034	1129	ENST00000262189.6	0.038241	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962265	151962265	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201834857		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:151962265C>T	ENST00000262189.6	-	8	1260	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	KMT2C_ENST00000355193.2_Missense_Mutation_p.D348N	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	348		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D348N(2)			NA						CCCGGGCTGTCGCACACTGCA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	skin(2)											112	101	104	NA		NA	NA	7		NA											NA				151962265		2203	4296	6499	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1042G>A	chr7.hg19:g.151962265C>T	ENSP00000262189:p.Asp348Asn	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	18.416055	TGTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730606	0.48939	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98807	-5.15;-5.15	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.43919	U	0.000512	D	0.98516	0.9505	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98479	1.0604	10	0.23302	T	0.38	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	348	Q8NEZ4	MLL3_HUMAN	N	348	ENSP00000262189:D348N;ENSP00000347325:D348N	ENSP00000262189:D348N	D	-	1	0	MLL3	151593198	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAC	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	8	35.620891	KEEP	203	9	287	219	7338	CC	1	1	0		-	18	49	645	0	0	39.495371	480	60	16379	1079	ENST00000262189.6	0.036145	1
ACTR3B	57180	__UNKNOWN__	__UNKNOWN__	7	152497656	152497656	__UNKNOWN__	Silent	SNP	T	T	C	rs201991209		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr7:152497656T>C	ENST00000256001.8	+	3	275	c.141T>C	c.(139-141)gcT>gcC	p.A47A	ACTR3B_ENST00000377776.3_Silent_p.A47A|ACTR3B_ENST00000397282.2_5'UTR|ACTR3B_ENST00000537264.1_Intron	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)	47		NA				cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	13		all_hematologic(28;0.0592)|Prostate(32;0.191)	OV - Ovarian serous cystadenocarcinoma(82;0.0287)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0434)		TTGACCAAGCTCAAAGGAGAG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													134	124	128	NA		NA	NA	7		NA											NA				152497656		2203	4300	6503	SO:0001819	synonymous_variant				CCDS5934.1, CCDS34782.1	7q36.1	2010-07-20			ENSG00000133627	ENSG00000133627	57180			17256	protein-coding gene	gene with protein product		NA			NA	10806390	Standard	NM_020445	NM_001040135	NA	Approved	ARP11, ARP3beta	uc003wle.2	Q9P1U1	OTTHUMG00000151463	ENST00000256001.8:c.141T>C	chr7.hg19:g.152497656T>C		NA	A8MTG1|B4DFW4|Q7Z526|Q96BT2	hg19	CCDS5934.1	0.02	4.062394	AGCxCAA	COVERED																																																																																			NOVEL	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322803.1	2	4.681342	KEEP	5	2	58	36	1157	TT	0.999999	0.999999	0		+	8	27	279	0	0	18.755987	119	60	4369	211	ENST00000256001.8	0.062992	1
ARHGEF10	9639	__UNKNOWN__	__UNKNOWN__	8	1876560	1876560	__UNKNOWN__	Intron	SNP	G	G	A	rs369649127		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:1876560G>A	ENST00000349830.3	+	24	2882				ARHGEF10_ENST00000398564.1_Intron|ARHGEF10_ENST00000520359.1_Intron|ARHGEF10_ENST00000262112.6_Intron|ARHGEF10_ENST00000518288.1_Intron	NM_014629.2	NP_055444.2	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	NA		NA			centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CCACATGGTCGTTTTCTTCTT	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G		1,4405	2.1+/-5.4	0,1,2202	86	90	88	NA		-9	0	8		88	0,8600		0,0,4300	no	intron	ARHGEF10	NM_014629.2		0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077			1876560	1,13005	2203	4300	6503	SO:0001627	intron_variant			AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728	9639		Rho guanine nucleotide exchange factors	14103	protein-coding gene	gene with protein product		608136			NA	9205841, 16896804	Standard		XM_005266039	NA	Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000349830.3:c.2698-33G>A	chr8.hg19:g.1876560G>A		NA	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	hg19	CCDS34794.1	0.02	6.901388	GTCxTTT	COVERED																																																																																			NOVEL	ARHGEF10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374589.1	2	19.522507	KEEP	0	0	0	65	2050	GG	1	1	0		+	17	60	635	0	0	47.266857	161	60	5303	289	ENST00000349830.3	0.095506	1
KBTBD11	9920	__UNKNOWN__	__UNKNOWN__	8	1952918	1952918	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:1952918A>G	ENST00000320248.3	+	0	4526					NM_014867.2	NP_055682.1	O94819	KBTBB_HUMAN	kelch repeat and BTB (POZ) domain containing 11	NA		NA								lung(1)|pancreas(1)	2		Ovarian(12;0.0563)|Colorectal(14;0.0815)|Hepatocellular(245;0.0831)		BRCA - Breast invasive adenocarcinoma(11;7.72e-05)|READ - Rectum adenocarcinoma(644;0.0929)|COAD - Colon adenocarcinoma(149;0.134)		AAAGAAAAACAGACTTCATAT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB018254	CCDS34795.1	8p23.3	2014-08-12			ENSG00000176595	ENSG00000176595	9920		BTB/POZ domain containing	29104	protein-coding gene	gene with protein product		NA			NA		Standard	NM_014867	NM_014867	NA	Approved	KIAA0711, KLHDC7C	uc003wpw.4	O94819	OTTHUMG00000163629	ENST00000320248.3:c.*1688A>G	chr8.hg19:g.1952918A>G		NA	Q3L1I0	hg19	CCDS34795.1	0.02	6.628164	AACxGAC	COVERED																																																																																			NOVEL	KBTBD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374601.1	2	13.239573	KEEP	0	0	0	44	1381	AA	1	1	0		+	47	60	1598	0	0	135.126401	151	60	5608	291	ENST00000320248.3	0.237374	1
CSMD1	64478	__UNKNOWN__	__UNKNOWN__	8	3045372	3045372	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:3045372G>T	ENST00000520002.1	-	37	6179				CSMD1_ENST00000602557.1_Intron|CSMD1_ENST00000539096.1_Intron|CSMD1_ENST00000523387.1_Intron|CSMD1_ENST00000537824.1_Intron|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	NA		NA				integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CACAGGTGAGGAAATTGACTC	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													44	45	45	NA		NA	NA	8		NA											NA				3045372		1903	4135	6038	SO:0001627	intron_variant					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117	64478		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	14026	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 24	608397			NA		Standard	NM_033225	NM_033225	NA	Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5623+18C>A	chr8.hg19:g.3045372G>T		NA	Q0H0J5|Q96QU9|Q96RM4	hg19		0.02	1.672436	GAGxAAA	COVERED																																																																																			NOVEL	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000374500.2	0	5.417647	KEEP	0	0	0	18	632	GG	0.999859	0.999754	0		-	5	60	177	0	0	11.629658	88	60	3145	131	ENST00000520002.1	0.053763	0.999895
MFHAS1	9258	__UNKNOWN__	__UNKNOWN__	8	8641187	8641187	__UNKNOWN__	3'UTR	SNP	T	T	C	rs183437943		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:8641187T>C	ENST00000276282.6	-	0	6090					NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	NA		NA								endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		TTGGAGGGCATTTGTTTGAGA	0.463	NA	NA											T|||	1	0.000199681	0	0.0014	5008	,	,	NA	18552	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA	Melanoma(103;1201 2045 17515 28966)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324	9258			16982	protein-coding gene	gene with protein product	leucine rich repeat containing 65, malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1	605352			NA	9973190	Standard	NM_004225	NM_004225	NA	Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.*2345A>G	chr8.hg19:g.8641187T>C		NA	Q96CI0	hg19	CCDS34844.1	0.02	2.152791	GCAxTTG	COVERED																																																																																			NOVEL	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374724.2	1	6.017892	KEEP	0	0	0	20	630	TT	0.999863	0.989407	0		-	11	60	408	0	0	33.637247	49	60	1786	96	ENST00000276282.6	0.183333	0.989542
SLC7A2	6542	__UNKNOWN__	__UNKNOWN__	8	17400978	17400978	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs143701037	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:17400978G>A	ENST00000494857.1	+	3	348	c.130G>A	c.(130-132)Gtt>Att	p.V44I	SLC7A2_ENST00000398090.3_Missense_Mutation_p.V84I|SLC7A2_ENST00000470360.1_Missense_Mutation_p.V84I|SLC7A2_ENST00000522656.1_Missense_Mutation_p.V44I|SLC7A2_ENST00000004531.10_Missense_Mutation_p.V84I	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	44		NA			amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|macrophage activation (GO:0042116)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide production involved in inflammatory response (GO:0002537)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	basic amino acid transmembrane transporter activity (GO:0015174)|high-affinity arginine transmembrane transporter activity (GO:0005289)|L-lysine transmembrane transporter activity (GO:0015189)|L-ornithine transmembrane transporter activity (GO:0000064)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	25				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	L-Lysine(DB00123)|L-Ornithine(DB00129)	TGCCCTGGGCGTTGGAAGCAC	0.587	NA	NA											G|||	12	0.00239617	0.0091	0	5008	,	,	NA	18751	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	ILE/VAL,ILE/VAL,ILE/VAL	33,4373	38.4+/-70.7	2,29,2172	79	69	72	NA	130,250,250	5.4	0.2	8	dbSNP_134	72	0,8600		0,0,4300	yes	missense,missense,missense	SLC7A2	NM_001008539.3,NM_001164771.1,NM_003046.5	29,29,29	2,29,6472	AA,AG,GG	NA	0.0,0.749,0.2537	probably-damaging,probably-damaging,probably-damaging	44/659,84/699,84/698	17400978	33,12973	2203	4300	6503	SO:0001583	missense			D29990	CCDS6002.2, CCDS34852.1, CCDS55203.1	8p22	2013-05-22			ENSG00000003989	ENSG00000003989	6542		Solute carriers	11060	protein-coding gene	gene with protein product		601872		ATRC2	NA	8954799	Standard	NM_003046	NM_001164771	NA	Approved	CAT-2, HCAT2	uc011kye.2	P52569	OTTHUMG00000130819	ENST00000494857.1:c.130G>A	chr8.hg19:g.17400978G>A	ENSP00000419140:p.Val44Ile	NA	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	hg19	CCDS34852.1	0.02	9.327753	GGCxTTG	COVERED	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	20.3	3.961506	0.74016	0.00749	0.0	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42	5.4	5.4	0.78164	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.83801	0.5333	L	0.45137	1.4	0.80722	D	1	D;D;D	0.76494	0.999;0.985;0.997	D;P;D	0.72625	0.978;0.555;0.954	D	0.87728	0.2577	10	0.59425	D	0.04	.	19.5642	0.95386	0.0:0.0:1.0:0.0	.	84;84;44	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	I	44;44;84;84;84	ENSP00000419140:V44I;ENSP00000430464:V44I;ENSP00000419873:V84I;ENSP00000004531:V84I;ENSP00000381164:V84I	ENSP00000004531:V84I	V	+	1	0	SLC7A2	17445357	1.000000	0.71417	0.164000	0.22755	0.211000	0.24417	9.823000	0.99369	2.717000	0.92951	0.655000	0.94253	GTT	NOVEL	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253367.3	3	35.184831	KEEP	0	0	0	117	3967	GG	1	1	0		+	86	60	3085	0	0	281.161059	156	60	5550	444	ENST00000494857.1	0.355372	1
SORBS3	10174	__UNKNOWN__	__UNKNOWN__	8	22424297	22424297	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:22424297C>A	ENST00000240123.7	+	15	1526				SORBS3_ENST00000428103.1_Intron|RP11-582J16.3_ENST00000517384.1_RNA|SORBS3_ENST00000523740.1_Intron	NM_005775.4	NP_005766.3	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3	NA		NA			actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of stress fiber assembly (GO:0051496)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)	18		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		GCCACCCGCCCAACTGAGAGA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	40	39	NA		NA	NA	8		NA											NA				22424297		2203	4300	6503	SO:0001627	intron_variant				CCDS6031.1	8p21.3	2008-02-05			ENSG00000120896	ENSG00000120896	10174			30907	protein-coding gene	gene with protein product		610795			NA	9885244, 12510380	Standard	NM_005775	NM_001018003	NA	Approved	SCAM-1, SH3D4, vinexin	uc003xbv.3	O60504	OTTHUMG00000131728	ENST00000240123.7:c.1144-38C>A	chr8.hg19:g.22424297C>A		NA	Q5BJE4|Q6NX54|Q96FY4|Q9UQE4	hg19	CCDS6031.1	0.02	4.643354	GCCxAAC	COVERED																																																																																			NOVEL	SORBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254647.3	5	34.304399	KEEP	0	0	0	114	4033	CC	1	1	0		+	14	60	534	0	0	40.843073	115	60	4249	323	ENST00000240123.7	0.108527	1
KIF13B	23303	__UNKNOWN__	__UNKNOWN__	8	29023235	29023235	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:29023235G>A	ENST00000524189.1	-	12	1251	c.1213C>T	c.(1213-1215)Cag>Tag	p.Q405*	KIF13B_ENST00000521515.1_Nonsense_Mutation_p.Q405*	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	405		NA			metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		GTCATTTCCTGGATTAGCTTC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													134	128	130	NA		NA	NA	8		NA											NA				29023235		1862	4112	5974	SO:0001587	stop_gained			AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892	23303		Kinesins	14405	protein-coding gene	gene with protein product		607350			NA	9734811, 10859302, 16864656	Standard		NM_015254	NA	Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.1213C>T	chr8.hg19:g.29023235G>A	ENSP00000427900:p.Gln405*	NA	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	hg19	CCDS55217.1	0.02	10.016919	CCTxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	37	6.160661	0.97334	.	.	ENSG00000197892	ENST00000524189;ENST00000521515	.	.	.	5.26	4.38	0.52667	.	0.054356	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	15.4179	0.74987	0.0:0.0:0.86:0.14	.	.	.	.	X	405	.	ENSP00000429201:Q405X	Q	-	1	0	KIF13B	29079154	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	5.251000	0.65438	1.433000	0.47394	0.655000	0.94253	CAG	NOVEL	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376878.1	4	26.786917	KEEP	0	0	0	89	3180	GG	1	1	0		-	67	60	2387	0	0	213.690657	142	60	5326	387	ENST00000524189.1	0.320574	1
DUSP4	1846	__UNKNOWN__	__UNKNOWN__	8	29194084	29194084	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:29194084C>T	ENST00000240101.2	-	0	2930				DUSP4_ENST00000240100.2_3'UTR	NM_057158.3	NP_476499.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	NA		NA			endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		ATTCCTTTAACTACAACAACG	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875	1846		Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases	3070	protein-coding gene	gene with protein product	VH1 homologous phosphatase 2, MAP kinase phosphatase 2	602747			NA	7535768, 9205128	Standard	NM_001394	NM_001394	NA	Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240101.2:c.*459G>A	chr8.hg19:g.29194084C>T		NA	B2RBU5|D3DSU4|G5E930|Q13524	hg19	CCDS6073.1	0.02	4.57508	TAAxTAC	COVERED																																																																																			NOVEL	DUSP4-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257250.1	1	8.728171	KEEP	0	0	0	29	1011	CC	0.999997	0.999993	0		-	35	60	1273	0	0	113.467135	79	60	2953	174	ENST00000240101.2	0.307018	0.999996
UNC5D	137970	__UNKNOWN__	__UNKNOWN__	8	35631796	35631796	__UNKNOWN__	Intron	SNP	C	C	T	rs369100742		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:35631796C>T	ENST00000287272.2	+	15	2291				UNC5D_ENST00000449677.1_Intron|UNC5D_ENST00000453357.2_Intron|UNC5D_ENST00000404895.2_Intron|UNC5D_ENST00000420357.1_Intron|UNC5D_ENST00000416672.1_Intron			Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	NA		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		TCTGATCATGCGTTCCTTATT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C		2,4404	4.2+/-10.8	0,2,2201	93	96	95	NA		-3	0	8		95	0,8600		0,0,4300	no	intron	UNC5D	NM_080872.2		0,2,6501	TT,TC,CC	NA	0.0,0.0454,0.0154			35631796	2,13004	2203	4300	6503	SO:0001627	intron_variant			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687	137970		Immunoglobulin superfamily / I-set domain containing	18634	protein-coding gene	gene with protein product		NA			NA	18402767	Standard		NM_080872	NA	Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000287272.2:c.2272-21C>T	chr8.hg19:g.35631796C>T		NA	Q8WYP7	hg19		0.02	1.945749	ATGxGTT	COVERED																																																																																			NOVEL	UNC5D-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000347597.1	2	4.207689	KEEP	0	0	0	14	465	CC	0.995343	0.995273	0		+	34	60	1213	0	0	110.432074	62	60	2238	127	ENST00000287272.2	0.354167	0.99993
ADAM2	2515	__UNKNOWN__	__UNKNOWN__	8	39691488	39691488	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:39691488G>A	ENST00000379853.2	-	3	187	c.163C>T	c.(163-165)Cca>Tca	p.P55S	ADAM2_ENST00000521880.1_Missense_Mutation_p.P55S|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000265708.4_Missense_Mutation_p.P55S|ADAM2_ENST00000347580.4_Missense_Mutation_p.P55S			Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	55		NA			adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		ACAGTATATGGTTTCCCTTCA	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													69	70	70	NA		NA	NA	8		NA											NA				39691488		2203	4293	6496	SO:0001583	missense			U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755	2515		ADAM metallopeptidase domain containing	198	protein-coding gene	gene with protein product	cancer/testis antigen 15	601533	fertilin beta	FTNB	NA	8702389, 9070941	Standard	NM_001464	NM_001278113	NA	Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000379853.2:c.163C>T	chr8.hg19:g.39691488G>A	ENSP00000369182:p.Pro55Ser	NA	P78326|Q9UQQ8	hg19		0.02	-0.394794	ATGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.457	-0.890844	0.02491	.	.	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.05580	3.42;3.42;3.42;3.42	4.72	-0.615	0.11587	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.05823	0.0152	L	0.33792	1.035	0.09310	N	1	B;B;B;B	0.31752	0.218;0.0;0.338;0.218	B;B;B;B	0.42030	0.196;0.002;0.373;0.271	T	0.44907	-0.9297	8	.	.	.	.	0.8471	0.01164	0.3204:0.0982:0.1812:0.4003	.	55;55;55;55	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	S	55	ENSP00000343854:P55S;ENSP00000369182:P55S;ENSP00000265708:P55S;ENSP00000429352:P55S	.	P	-	1	0	ADAM2	39810645	0.261000	0.24063	0.000000	0.03702	0.000000	0.00434	0.029000	0.13666	0.085000	0.17107	-1.069000	0.02264	CCA	NOVEL	ADAM2-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000376925.1	0	2.407968	KEEP	0	0	0	8	292	GG	0.99257	0.919755	0		-	3	60	113	0	0	7.945566	42	60	1551	71	ENST00000379853.2	0.066667	0.92664
AGPAT6	137964	__UNKNOWN__	__UNKNOWN__	8	41479296	41479296	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:41479296G>A	ENST00000396987.3	+	0	3074					NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	NA		NA			acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			aaaGTGCTGCGGGTGAGTGAA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	137964	2.3.1.15	1-acylglycerol-3-phosphate O-acyltransferases	20880	protein-coding gene	gene with protein product	lysophosphatidic acid acyltransferase, zeta	608143	1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)		NA	12938015	Standard	NM_178819	NM_178819	NA	Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.*776G>A	chr8.hg19:g.41479296G>A		NA	Q86V89	hg19	CCDS6117.1	0.02	7.127691	TGCxGGT	COVERED																																																																																			NOVEL	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377158.1	2	10.232658	KEEP	0	0	0	34	1150	GG	0.999998	0.999998	0		+	11	60	416	0	0	29.012687	164	60	5560	261	ENST00000396987.3	0.062857	1
ANK1	286	__UNKNOWN__	__UNKNOWN__	8	41754191	41754191	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:41754191C>T	ENST00000265709.8	-	0	89					NM_001142446.1	NP_001135918.1	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	NA		NA			axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CGAGGGGCGGCTGCCCGCGGC	0.801	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534	286		Ankyrin repeat domain containing	492	protein-coding gene	gene with protein product		612641		ANK	NA	1689849	Standard	NM_020475	NM_001142445	NA	Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000265709.8:c.-193G>A	chr8.hg19:g.41754191C>T		NA	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	hg19	CCDS47849.1	0.02	-0.33247	CGGxTGC	COVERED																																																																																			NOVEL	ANK1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377171.1	0	2.707692	KEEP	0	0	0	9	277	CC	0.99254	0.845628	0		-	3	60	99	0	0	6.780965	35	60	1165	57	ENST00000265709.8	0.078947	0.851984
HGSNAT	138050	__UNKNOWN__	__UNKNOWN__	8	43056095	43056095	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:43056095C>A	ENST00000379644.4	+	0	3333				HGSNAT_ENST00000458501.2_3'UTR	NM_152419.2	NP_689632.2	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			CAGCCCTAGCCTCTTCTCCTC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	138050	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	transmembrane protein 76	TMEM76	NA	17033958, 16960811	Standard	XM_372038	NM_152419	NA	Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000379644.4:c.*1383C>A	chr8.hg19:g.43056095C>A		NA	B4E2V0	hg19	CCDS47852.1	0.02	13.453535	AGCxTCT	COVERED																																																																																			NOVEL	HGSNAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377293.1	6	26.486588	KEEP	0	0	0	88	3171	CC	1	1	0		+	39	60	1390	0	0	105.149021	299	60	11105	537	ENST00000379644.4	0.115385	1
UBE2V2	7336	__UNKNOWN__	__UNKNOWN__	8	48975516	48975516	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:48975516C>G	ENST00000523111.2	+	0	2621					NM_003350.2	NP_003341.1	Q15819	UB2V2_HUMAN	ubiquitin-conjugating enzyme E2 variant 2	NA		NA			cell proliferation (GO:0008283)|DNA double-strand break processing (GO:0000729)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of DNA repair (GO:0045739)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of synapse assembly (GO:0051965)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of DNA repair (GO:0006282)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|UBC13-MMS2 complex (GO:0031372)	acid-amino acid ligase activity (GO:0016881)			large_intestine(1)|lung(2)	3		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00171)|all_lung(136;0.00196)				TTGAATGAAACTGTAGTCTAA	0.279	NA	NA						Rad6 pathway						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X98091	CCDS43738.1	8q11.21	2008-02-05			ENSG00000169139	ENSG00000169139	7336		Ubiquitin-conjugating enzymes E2	12495	protein-coding gene	gene with protein product		603001			NA	9418904, 9199207	Standard	NM_003350	NM_003350	NA	Approved	UEV-2, DDVit-1, EDPF-1, MMS2	uc003xqm.3	Q15819	OTTHUMG00000164206	ENST00000523111.2:c.*2128C>G	chr8.hg19:g.48975516C>G		NA		hg19	CCDS43738.1	0.02	10.045617	AAAxTGT	COVERED																																																																																			NOVEL	UBE2V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377808.3	1	12.34071	KEEP	0	0	0	41	1494	CC	1	1	0		+	41	60	1564	0	0	130.287985	176	60	6653	312	ENST00000523111.2	0.18894	1
SNTG1	54212	__UNKNOWN__	__UNKNOWN__	8	51465619	51465619	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:51465619C>A	ENST00000522124.1	+	12	1351	c.690C>A	c.(688-690)gcC>gcA	p.A230A	SNTG1_ENST00000518864.1_Silent_p.A230A|SNTG1_ENST00000276467.5_Silent_p.A230A|SNTG1_ENST00000517473.1_Silent_p.A230A	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	230		NA			cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				GGCAGAATGCCTTTCAAGTCA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													138	119	125	NA		NA	NA	8		NA											NA				51465619		2203	4300	6503	SO:0001819	synonymous_variant			AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481	54212			13740	protein-coding gene	gene with protein product		608714			NA	10747910	Standard		NM_018967	NA	Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.690C>A	chr8.hg19:g.51465619C>A		NA	Q2M3Q0|Q9NY98	hg19	CCDS6147.1	0.02	6.962005	TGCxTTT	COVERED																																																																																			NOVEL	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377964.1	0	6.922427	KEEP	0	0	0	23	804	CC	0.999892	0.999892	0		+	36	60	1337	0	0	110.491287	158	60	5868	260	ENST00000522124.1	0.185567	1
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52731235	52731235	__UNKNOWN__	3'UTR	SNP	A	A	G	rs146733619		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:52731235A>G	ENST00000360540.5	-	0	3156				PCMTD1_ENST00000544451.1_3'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	NA		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CAATTCCACCATCCCAGCCAC	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.*1676T>C	chr8.hg19:g.52731235A>G		NA	Q96FK9	hg19	CCDS6148.1	0.02	12.893154	ACCxTCC	COVERED																																																																																			NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	9	6.679174	KEEP	3	2	65	45	1322	AA	1	1	0		-	26	70	928	1	0	66.147385	295	70	10069	460	ENST00000360540.5	0.080997	1
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52731564	52731564	__UNKNOWN__	3'UTR	SNP	T	T	C	rs113180269		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:52731564T>C	ENST00000360540.5	-	0	2827				PCMTD1_ENST00000544451.1_3'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	NA		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				ATATGTTACATTGTACACTTT	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.*1347A>G	chr8.hg19:g.52731564T>C		NA	Q96FK9	hg19	CCDS6148.1	0.02	11.282005	ACAxTGT	COVERED																																																																																			NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	5	2.405966	KEEP	5	3	112	47	1465	TT	1	1	0		-	11	60	425	0	0	28.299243	232	60	8510	396	ENST00000360540.5	0.045267	1
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52733228	52733228	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs73592211		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:52733228G>A	ENST00000360540.5	-	7	1163	c.757C>T	c.(757-759)Cgc>Tgc	p.R253C	PCMTD1_ENST00000544451.1_Missense_Mutation_p.R177C|PCMTD1_ENST00000522514.1_Missense_Mutation_p.R253C|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	253		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CTAAGTGTGCGTCGAATGTAA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.757C>T	chr8.hg19:g.52733228G>A	ENSP00000353739:p.Arg253Cys	NA	Q96FK9	hg19	CCDS6148.1	0.02	4.205658	TGCxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044757	0.75732	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.47869	1.43;0.83;1.43	5.76	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.62060	0.2397	L	0.60455	1.87	0.80722	D	1	D;B;B	0.89917	1.0;0.333;0.231	P;B;B	0.62184	0.899;0.061;0.081	T	0.64300	-0.6440	10	0.52906	T	0.07	-15.7151	14.8982	0.70659	0.0689:0.0:0.9311:0.0	.	123;177;253	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	C	253;177;253	ENSP00000353739:R253C;ENSP00000444026:R177C;ENSP00000428099:R253C	ENSP00000353739:R253C	R	-	1	0	PCMTD1	52895781	1.000000	0.71417	0.985000	0.45067	0.970000	0.65996	8.903000	0.92573	1.438000	0.47492	0.650000	0.86243	CGC	NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	2	3.545203	KEEP	0	1	32	23	745	GG	0.999909	0.999908	0		-	15	49	554	0	0	43.40693	97	60	3311	174	ENST00000360540.5	0.133929	0.999999
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52733231	52733231	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A	rs75748152		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:52733231G>A	ENST00000360540.5	-	7	1160	c.754C>T	c.(754-756)Cga>Tga	p.R252*	PCMTD1_ENST00000544451.1_Nonsense_Mutation_p.R176*|PCMTD1_ENST00000522514.1_Nonsense_Mutation_p.R252*|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	252		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.R252*(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				AGTGTGCGTCGAATGTAAATA	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Nonsense(1)	skin(1)											61	63	62	NA		NA	NA	8		NA											NA				52733231		2203	4300	6503	SO:0001587	stop_gained				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.754C>T	chr8.hg19:g.52733231G>A	ENSP00000353739:p.Arg252*	NA	Q96FK9	hg19	CCDS6148.1	0.02	4.068528	GTCxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531859	0.85706	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	.	.	.	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.1963	14.672	0.68951	0.0:0.0:0.8201:0.1799	.	.	.	.	X	252;176;252	.	ENSP00000353739:R252X	R	-	1	2	PCMTD1	52895784	1.000000	0.71417	0.980000	0.43619	0.959000	0.62525	6.706000	0.74649	2.722000	0.93159	0.655000	0.94253	CGA	NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	2	7.217674	KEEP	0	0	0	24	763	GG	0.999909	0.999906	0		-	9	49	319	0	0	22.787221	98	60	3362	171	ENST00000360540.5	0.084112	0.999997
XKR4	114786	__UNKNOWN__	__UNKNOWN__	8	56436288	56436288	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:56436288C>T	ENST00000327381.6	+	3	1555	c.1455C>T	c.(1453-1455)gaC>gaT	p.D485D		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	485		NA				integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			AGATTGCAGACGCATTTGCCA	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													108	97	101	NA		NA	NA	8		NA											NA				56436288		2203	4300	6503	SO:0001819	synonymous_variant			AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579	114786			29394	protein-coding gene	gene with protein product		NA	X Kell blood group precursor-related family, member 4		NA		Standard	NM_052898	NM_052898	NA	Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1455C>T	chr8.hg19:g.56436288C>T		NA	Q96PZ8	hg19	CCDS34893.1	0.02	6.737192	AGAxGCA	COVERED																																																																																			NOVEL	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378129.2	1	7.223122	KEEP	0	0	0	24	823	CC	0.999909	0.999909	0		+	16	60	590	0	0	42.547819	181	60	6381	256	ENST00000327381.6	0.081218	1
IMPAD1	54928	__UNKNOWN__	__UNKNOWN__	8	57872930	57872930	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:57872930C>A	ENST00000262644.4	-	0	4760					NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	NA		NA			chondrocyte development (GO:0002063)|chondroitin sulfate metabolic process (GO:0030204)|embryonic digit morphogenesis (GO:0042733)|endochondral ossification (GO:0001958)|inositol biosynthetic process (GO:0006021)|phosphatidylinositol phosphorylation (GO:0046854)|post-embryonic development (GO:0009791)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|3'-nucleotidase activity (GO:0008254)|inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				CCTGACCTCCCTCTAGCTTCT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6169.1	8q12.1	2013-05-16			ENSG00000104331	ENSG00000104331	54928			26019	protein-coding gene	gene with protein product		614010			NA	21549340	Standard	NM_017813	NM_017813	NA	Approved	FLJ20421, IMPA3, gPAPP	uc003xte.4	Q9NX62	OTTHUMG00000164415	ENST00000262644.4:c.*3422G>T	chr8.hg19:g.57872930C>A		NA	Q6NVY7	hg19	CCDS6169.1	0.02	7.141265	TCCxTCT	COVERED																																																																																			NOVEL	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378665.1	9	23.777798	KEEP	0	0	0	79	2830	CC	1	1	0		-	42	60	1566	0	0	136.37761	120	60	4424	323	ENST00000262644.4	0.259259	1
YTHDF3	253943	__UNKNOWN__	__UNKNOWN__	8	64099653	64099653	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:64099653G>T	ENST00000521674.1	+	0	1408				YTHDF3_ENST00000517371.1_Intron|YTHDF3_ENST00000542911.2_Missense_Mutation_p.A172S|YTHDF3_ENST00000539294.1_Missense_Mutation_p.A361S			Q7Z739	YTHD3_HUMAN	YTH domain family, member 3	NA		NA					N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)				NA	Breast(64;0.0716)	all_cancers(86;0.169)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.146)	BRCA - Breast invasive adenocarcinoma(89;0.161)			TAACAGGGGAGCAGGCTTCAA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	91	90	NA		NA	NA	8		NA											NA				64099653		2093	4229	6322	SO:0001624	3_prime_UTR_variant			BC052970	CCDS75747.1, CCDS75748.1, CCDS75749.1	8q12.3	2013-06-07	2004-11-16		ENSG00000185728	ENSG00000185728	253943			26465	protein-coding gene	gene with protein product		NA	YTH domain family 3		NA	12477932	Standard	NM_152758	NM_152758	NA	Approved	FLJ31657	uc003xuz.4	Q7Z739	OTTHUMG00000164369	ENST00000521674.1:c.*1405G>T	chr8.hg19:g.64099653G>T		NA	B3KXL4|Q63Z37|Q659A3	hg19		0.02	13.658839	GGAxCAG	COVERED																																																																																			NOVEL	YTHDF3-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000378462.2	8	28.886608	KEEP	0	0	0	96	3421	GG	1	1	0		+	32	60	1197	0	0	89.489485	295	60	10947	458	ENST00000521674.1	0.097859	1
ARFGEF1	10565	__UNKNOWN__	__UNKNOWN__	8	68214690	68214690	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:68214690C>T	ENST00000262215.3	-	2	525	c.136G>A	c.(136-138)Gcg>Acg	p.A46T		NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	46	DCB; DCB:DCB domain and DCB:HUS domain interaction.	NA			endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TCAGTTTCCGCTTTTATTTCC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	36	35	NA		NA	NA	8		NA											NA				68214690		2197	4283	6480	SO:0001583	missense			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777	10565			15772	protein-coding gene	gene with protein product		604141			NA	10212200, 8917509	Standard	NM_006421	NM_006421	NA	Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.136G>A	chr8.hg19:g.68214690C>T	ENSP00000262215:p.Ala46Thr	NA	Q9NV46|Q9UFV2|Q9UNL0	hg19	CCDS6199.1	0.02	2.340155	CCGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.15	1.851527	0.32699	.	.	ENSG00000066777	ENST00000262215;ENST00000519436	T	0.20200	2.09	5.83	5.83	0.93111	.	0.446525	0.26673	N	0.023094	T	0.13756	0.0333	L	0.31804	0.96	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.16541	-1.0399	10	0.19147	T	0.46	.	7.9216	0.29850	0.1612:0.759:0.0:0.0798	.	46	Q9Y6D6	BIG1_HUMAN	T	46	ENSP00000262215:A46T	ENSP00000262215:A46T	A	-	1	0	ARFGEF1	68377244	0.559000	0.26562	0.995000	0.50966	0.977000	0.68977	0.787000	0.26858	2.759000	0.94783	0.650000	0.86243	GCG	NOVEL	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379441.4	0	6.318577	KEEP	0	0	0	21	732	CC	0.999869	0.963648	0		-	8	60	284	0	0	22.595932	43	60	1623	86	ENST00000262215.3	0.156863	0.963774
SULF1	23213	__UNKNOWN__	__UNKNOWN__	8	70517204	70517204	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:70517204G>A	ENST00000260128.4	+	13	2094				SULF1_ENST00000402687.4_Intron|SULF1_ENST00000458141.2_Intron|SULF1_ENST00000419716.3_Intron|SULF1_ENST00000521946.1_Intron	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	NA		NA			apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			CCACTCATGTGCTTCTCCATC	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													54	54	54	NA		NA	NA	8		NA											NA				70517204		2203	4300	6503	SO:0001627	intron_variant			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573	23213			20391	protein-coding gene	gene with protein product		610012			NA	12368295	Standard	NM_015170	NM_015170	NA	Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.1377+37G>A	chr8.hg19:g.70517204G>A		NA	Q86YV8|Q8NCA2|Q9UPS5	hg19	CCDS6204.1	0.02	6.449096	TGTxCTT	COVERED																																																																																			NOVEL	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378885.2	3	14.747659	KEEP	0	0	0	49	1744	GG	1	1	0		+	54	60	1891	0	0	166.498501	130	60	4914	292	ENST00000260128.4	0.293478	1
PMP2	5375	__UNKNOWN__	__UNKNOWN__	8	82354103	82354103	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:82354103T>C	ENST00000256103.2	-	0	2065				RP11-157I4.4_ENST00000524085.2_RNA	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	NA		NA			membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			ttgcccttgctttggaatcat	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588	5375		Fatty acid binding protein family	9117	protein-coding gene	gene with protein product		170715			NA	1720307, 8288226	Standard	NM_002677	NM_002677	NA	Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.*1530A>G	chr8.hg19:g.82354103T>C		NA	Q6FHL4	hg19	CCDS6229.1	0.02	2.080442	TGCxTTG	COVERED																																																																																			NOVEL	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379365.1	1	4.815436	KEEP	0	0	0	16	543	TT	0.997832	0.997726	0		-	11	60	403	0	0	30.926915	81	60	3033	133	ENST00000256103.2	0.119565	0.999895
SLC7A13	157724	__UNKNOWN__	__UNKNOWN__	8	87242181	87242181	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:87242181G>A	ENST00000297524.3	-	1	429	c.326C>T	c.(325-327)gCt>gTt	p.A109V	SLC7A13_ENST00000520624.1_Intron|SLC7A13_ENST00000419776.2_Missense_Mutation_p.A109V	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	109		NA				integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						AGCTTGGCCAGCAACTACCCC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	61	62	NA		NA	NA	8		NA											NA				87242181		2203	4300	6503	SO:0001583	missense			AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893	157724		Solute carriers	23092	protein-coding gene	gene with protein product		NA			NA	11907033, 11943479	Standard	NM_138817	XM_005250804	NA	Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.326C>T	chr8.hg19:g.87242181G>A	ENSP00000297524:p.Ala109Val	NA	Q05C37|Q08AH9|Q96N84	hg19	CCDS34917.1	0.02	13.348995	CCAxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.91	1.779176	0.31502	.	.	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.90133	-2.62;-2.62	4.33	3.41	0.39046	Amino acid permease domain (1);	0.215592	0.32258	N	0.006343	D	0.94624	0.8267	M	0.85710	2.77	0.20196	N	0.999923	D;D	0.76494	0.994;0.999	D;D	0.72982	0.944;0.979	D	0.87874	0.2673	10	0.87932	D	0	.	9.5385	0.39237	0.1105:0.0:0.8895:0.0	.	109;109	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	V	109	ENSP00000297524:A109V;ENSP00000410982:A109V	ENSP00000297524:A109V	A	-	2	0	SLC7A13	87311297	0.995000	0.38212	0.029000	0.17559	0.031000	0.12232	1.959000	0.40412	1.105000	0.41606	0.514000	0.50259	GCT	NOVEL	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374704.1	4	8.42665	KEEP	0	0	0	28	970	GG	0.999997	0.999997	0		-	44	60	1554	0	0	120.281281	284	60	10775	418	ENST00000297524.3	0.134146	1
WWP1	11059	__UNKNOWN__	__UNKNOWN__	8	87423811	87423811	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:87423811G>A	ENST00000517970.1	+	9	1076	c.769G>A	c.(769-771)Gtc>Atc	p.V257I	WWP1_ENST00000349423.2_Missense_Mutation_p.V39I|WWP1_ENST00000341922.2_Missense_Mutation_p.V127I|WWP1_ENST00000265428.4_Missense_Mutation_p.V257I	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	257		NA			central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						TAATGCGTCTGTCACGGGTAC	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													121	116	118	NA		NA	NA	8		NA											NA				87423811		2203	4300	6503	SO:0001583	missense			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124	11059			17004	protein-coding gene	gene with protein product		602307			NA	9169421, 9647693	Standard	NM_007013	NM_007013	NA	Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.769G>A	chr8.hg19:g.87423811G>A	ENSP00000427793:p.Val257Ile	NA	O00307|Q5YLC1|Q96BP4	hg19	CCDS6242.1	0.02	6.146431	TCTxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.029	0.560225	0.13498	.	.	ENSG00000123124	ENST00000517970;ENST00000265428;ENST00000341922;ENST00000349423	T;T;T;T	0.52754	0.93;0.93;0.65;0.94	5.46	-2.82	0.05787	.	2.098940	0.01600	N	0.021998	T	0.28863	0.0716	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11817	-1.0572	10	0.38643	T	0.18	.	4.6323	0.12507	0.4621:0.0:0.2958:0.242	.	39;257	Q9H0M0-6;Q9H0M0	.;WWP1_HUMAN	I	257;257;127;39	ENSP00000427793:V257I;ENSP00000265428:V257I;ENSP00000340564:V127I;ENSP00000342665:V39I	ENSP00000265428:V257I	V	+	1	0	WWP1	87492927	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.436000	0.06922	-0.661000	0.05345	0.650000	0.86243	GTC	NOVEL	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374755.1	4	6.468395	KEEP	0	1	12	26	953	GG	0.999988	0.999988	0		+	10	60	348	0	0	22.984691	163	60	6249	254	ENST00000517970.1	0.057803	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	87480857	87480857	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:87480857C>T			NA	NA				WWP1 (125 upstream) : RMDN1 (3721 downstream)						NA		NA									NA						CTGAAGAAGGCAGCTTTCCAG	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.87480857C>T		NA		hg19		0.02	31.249881	AGGxAGC	COVERED																																																																																			NOVEL					0			8	36.405766	KEEP	0	0	0	121	4302	CC	1	1	0			21	60	727	0	0	40.275457	808	60	30279	1133		0.025332	1
CPNE3	8895	__UNKNOWN__	__UNKNOWN__	8	87571281	87571281	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:87571281A>G	ENST00000521271.1	+	0	2419				CPNE3_ENST00000198765.4_3'UTR	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	NA		NA			lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						TGTACAATCAACAAGTAAAAA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719	8895			2316	protein-coding gene	gene with protein product		604207			NA	9430674	Standard		NM_003909	NA	Approved		uc003ydv.2	O75131		ENST00000521271.1:c.*643A>G	chr8.hg19:g.87571281A>G		NA	A8KA47|Q8IYA1	hg19	CCDS6243.1	0.02	14.286288	TCAxCAA	COVERED																																																																																			NOVEL	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374994.1	3	13.835659	KEEP	0	0	0	46	1409	AA	1	1	0		+	19	60	721	0	0	49.484938	316	60	11386	461	ENST00000521271.1	0.056716	1
MMP16	4325	__UNKNOWN__	__UNKNOWN__	8	89046960	89046960	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:89046960T>A	ENST00000286614.6	-	0	8834					NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	NA		NA			chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	AGGTTCAAATTGGCATTATGT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103	4325			7162	protein-coding gene	gene with protein product		602262	matrix metalloproteinase 16 (membrane-inserted), chromosome 8 open reading frame 57	C8orf57	NA	7559440	Standard	NM_005941	NM_005941	NA	Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.*6729A>T	chr8.hg19:g.89046960T>A		NA	B2RAN7|Q14824|Q52H48	hg19	CCDS6246.1	0.02	14.667963	AATxGGC	COVERED																																																																																			NOVEL	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375304.2	8	12.033177	KEEP	0	0	0	40	1217	TT	1	1	0		-	39	60	1433	0	0	109.581247	296	60	10736	444	ENST00000286614.6	0.116418	1
MMP16	4325	__UNKNOWN__	__UNKNOWN__	8	89052952	89052952	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:89052952C>T	ENST00000286614.6	-	0	2842					NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	NA		NA			chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	ACACTGAGGACATAGCTGAGA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103	4325			7162	protein-coding gene	gene with protein product		602262	matrix metalloproteinase 16 (membrane-inserted), chromosome 8 open reading frame 57	C8orf57	NA	7559440	Standard	NM_005941	NM_005941	NA	Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.*737G>A	chr8.hg19:g.89052952C>T		NA	B2RAN7|Q14824|Q52H48	hg19	CCDS6246.1	0.02	6.506639	GGAxATA	COVERED																																																																																			NOVEL	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375304.2	4	9.029656	KEEP	0	0	0	30	1078	CC	0.999997	0.999997	0		-	9	60	302	0	0	18.952422	180	60	6781	256	ENST00000286614.6	0.047619	1
FSBP	100861412	__UNKNOWN__	__UNKNOWN__	8	95444663	95444663	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:95444663A>G	ENST00000481490.2	-	2	669	c.596T>C	c.(595-597)gTt>gCt	p.V199A	RAD54B_ENST00000336148.5_Intron|RAD54B_ENST00000297592.5_3'UTR	NM_001256141.1	NP_001243070.1	O95073	FSBP_HUMAN	fibrinogen silencer binding protein	199		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)					NA						TCTCATATCAACAGAGGAAAG	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS59106.1	8q22.1	2012-08-13			ENSG00000265817	ENSG00000265817	100861412			43653	protein-coding gene	gene with protein product		NA			NA	20531236	Standard	NM_001256141	NM_001256141	NA	Approved		uc003ygm.3	O95073	OTTHUMG00000178341	ENST00000481490.2:c.596T>C	chr8.hg19:g.95444663A>G	ENSP00000420405:p.Val199Ala	NA	Q8N4S5	hg19	CCDS59106.1	0.02	40.491726	TCAxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	A	18.78	3.696552	0.68386	.	.	ENSG00000197275	ENST00000543299;ENST00000481490	T	0.59083	0.29	5.45	5.45	0.79879	.	0.073487	0.53938	D	0.000044	T	0.59445	0.2194	.	.	.	0.80722	D	1	D	0.55172	0.97	P	0.45474	0.482	T	0.64976	-0.6280	9	0.59425	D	0.04	-5.3391	15.4928	0.75624	1.0:0.0:0.0:0.0	.	199	O95073	FSBP_HUMAN	A	58;199	ENSP00000420405:V199A	ENSP00000420405:V199A	V	-	2	0	RAD54B	95513839	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.281000	0.65609	2.059000	0.61396	0.482000	0.46254	GTT	NOVEL	FSBP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000441631.1	6	35.806689	KEEP	0	0	0	119	3779	AA	1	1	0		-	117	60	4408	0	0	351.376358	693	60	24888	1088	ENST00000481490.2	0.144444	1
KIAA1429	25962	__UNKNOWN__	__UNKNOWN__	8	95538703	95538703	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:95538703G>A	ENST00000297591.5	-	8	1844	c.1769C>T	c.(1768-1770)aCa>aTa	p.T590I	KIAA1429_ENST00000437199.1_Missense_Mutation_p.T590I|KIAA1429_ENST00000421249.2_Missense_Mutation_p.T590I	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	590		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TCCAGCATCTGTGTCGTGATC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													154	150	152	NA		NA	NA	8		NA											NA				95538703		2203	4300	6503	SO:0001583	missense			AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944	25962			24500	protein-coding gene	gene with protein product	functional spliceosome-associated protein 121	NA			NA	10718198	Standard	NM_015496	NM_015496	NA	Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.1769C>T	chr8.hg19:g.95538703G>A	ENSP00000297591:p.Thr590Ile	NA	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	hg19	CCDS34923.1	0.02	36.103601	TCTxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.26	1.585273	0.28268	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.47869	0.83;0.83;0.83	5.95	5.95	0.96441	.	0.658638	0.15772	N	0.245378	T	0.35364	0.0929	N	0.14661	0.345	0.26904	N	0.967047	B;B	0.21905	0.062;0.018	B;B	0.21917	0.037;0.032	T	0.26608	-1.0098	10	0.46703	T	0.11	-0.3856	16.0062	0.80363	0.0:0.0:0.8575:0.1425	.	590;590	Q69YN4-4;Q69YN4	.;VIR_HUMAN	I	590	ENSP00000297591:T590I;ENSP00000395600:T590I;ENSP00000398390:T590I	ENSP00000297591:T590I	T	-	2	0	KIAA1429	95607879	0.984000	0.35163	0.999000	0.59377	0.988000	0.76386	3.757000	0.55212	2.817000	0.96982	0.563000	0.77884	ACA	NOVEL	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378720.2	8	53.137903	KEEP	0	1	9	180	6472	GG	1	1	0		-	135	60	4760	0	0	381.139734	686	60	26172	1248	ENST00000297591.5	0.164434	1
MTDH	92140	__UNKNOWN__	__UNKNOWN__	8	98737120	98737120	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:98737120G>T	ENST00000519934.1	+	0	1833				MTDH_ENST00000336273.3_3'UTR			Q86UE4	LYRIC_HUMAN	metadherin	NA		NA			lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			ACTTGGGAAAGTCTTTTTAAT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649	92140			29608	protein-coding gene	gene with protein product	astrocyte elevated gene 1	610323			NA	15093543	Standard		NM_178812	NA	Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000519934.1:c.*222G>T	chr8.hg19:g.98737120G>T		NA	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	hg19		0.02	6.865171	AAAxTCT	COVERED																																																																																			NOVEL	MTDH-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000379773.2	4	10.233641	KEEP	0	0	0	34	1227	GG	0.999998	0.999998	0		+	31	60	1117	0	0	91.384844	140	60	5270	254	ENST00000519934.1	0.181287	1
PABPC1	26986	__UNKNOWN__	__UNKNOWN__	8	101724606	101724606	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs202060459		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:101724606G>A	ENST00000318607.5	-	7	2084	c.956C>T	c.(955-957)aCa>aTa	p.T319I	PABPC1_ENST00000519004.1_Missense_Mutation_p.T274I|PABPC1_ENST00000522387.1_Missense_Mutation_p.T287I|PABPC1_ENST00000519596.1_5'UTR	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	319	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)	p.T319I(2)		breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ACTAGTGATTGTACCAAATGG	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(1)|endometrium(1)											154	166	162	NA		NA	NA	8		NA											NA				101724606		2203	4298	6501	SO:0001583	missense			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756	26986		RNA binding motif (RRM) containing	8554	protein-coding gene	gene with protein product		604679	poly(A)-binding protein, cytoplasmic 2	PAB1, PABPC2	NA	2885805	Standard	NM_002568	XM_005250861	NA	Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.956C>T	chr8.hg19:g.101724606G>A	ENSP00000313007:p.Thr319Ile	NA	Q15097|Q93004	hg19	CCDS6289.1	0.02	6.284628	ATTxTAC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.8|26.8	4.768189|4.768189	0.90020|0.90020	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.16196	.|2.36;2.36;2.36	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.64402	.|D	.|0.000009	.|T	.|0.37652	.|0.1011	M|M	0.62154|0.62154	1.92|1.92	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.54964	.|0.917;0.784;0.969	.|P;B;P	.|0.56916	.|0.747;0.442;0.809	.|T	.|0.03784	.|-1.1004	.|10	.|0.87932	.|D	.|0	.|.	20.0919|20.0919	0.97823|0.97823	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|287;319;319	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	X|I	188|319;319;274;287	.|ENSP00000313007:T319I;ENSP00000429594:T274I;ENSP00000429395:T287I	.|ENSP00000313007:T319I	Q|T	-|-	1|2	0|0	PABPC1|PABPC1	101793782|101793782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.776000|9.776000	0.99001|0.99001	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	CAA|ACA	NOVEL	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380217.1	8	10.533764	KEEP	1	0	0	35	1247	GG	0.999999	0.999999	0		-	8	50	289	0	0	18.509679	172	60	6579	261	ENST00000318607.5	0.044444	1
GRHL2	79977	__UNKNOWN__	__UNKNOWN__	8	102679908	102679908	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:102679908C>T	ENST00000251808.3	+	0	3193					NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	NA		NA			brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			TGCGCTGTCTCGTGGGAAAGG	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307	79977			2799	protein-coding gene	gene with protein product		608576	deafness, autosomal dominant 28, transcription factor CP2-like 3	DFNA28, TFCP2L3	NA	12393799	Standard	NM_024915	NM_024915	NA	Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.*977C>T	chr8.hg19:g.102679908C>T		NA	A1L303|Q6NT03|Q9H8B8	hg19	CCDS34931.1	0.02	16.370621	TCTxGTG	COVERED																																																																																			NOVEL	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313882.1	3	12.339208	KEEP	0	0	0	41	1404	CC	1	1	0		+	57	60	2071	0	1	164.477348	324	60	11407	518	ENST00000251808.3	0.149606	1
UBR5	51366	__UNKNOWN__	__UNKNOWN__	8	103283341	103283341	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:103283341A>G	ENST00000521922.1	-	49	7592				UBR5_ENST00000520539.1_Intron|UBR5_ENST00000518205.1_Intron|UBR5_ENST00000220959.4_Intron			O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	NA		NA			cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			ggtggtattgaatcaaagata	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(131;96 1741 5634 7352 27489)					NA		NA				0													80	75	77	NA		NA	NA	8		NA											NA				103283341		2203	4300	6503	SO:0001627	intron_variant			AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517	51366		Ubiquitin protein ligase E3 component n-recognins	16806	protein-coding gene	gene with protein product		608413	E3 ubiquitin protein ligase, HECT domain containing, 1	EDD1	NA	10030672, 16055722	Standard	NM_015902	NM_015902	NA	Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000521922.1:c.7067+20T>C	chr8.hg19:g.103283341A>G		NA	B2RP24|J3KMW7|O94970|Q9NPL3	hg19		0.02	14.435976	TTGxATC	COVERED																																																																																			NOVEL	UBR5-003	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380199.1	4	24.074618	KEEP	0	0	0	80	2628	AA	1	1	0		-	39	60	1381	0	0	105.369918	279	60	10174	498	ENST00000521922.1	0.122642	1
FZD6	8323	__UNKNOWN__	__UNKNOWN__	8	104342055	104342055	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:104342055G>A	ENST00000358755.4	+	6	2031	c.1714G>A	c.(1714-1716)Gca>Aca	p.A572T	FZD6_ENST00000522566.1_Missense_Mutation_p.A572T|FZD6_ENST00000523739.1_Missense_Mutation_p.A540T|FZD6_ENST00000540287.1_Missense_Mutation_p.A267T	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	572		NA			angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TGGCACTTCTGCAGTAGCAAT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													70	64	66	NA		NA	NA	8		NA											NA				104342055		2203	4300	6503	SO:0001583	missense			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930	8323		GPCR / Class F : Frizzled receptors	4044	protein-coding gene	gene with protein product		603409	frizzled (Drosophila) homolog 6, frizzled homolog 6 (Drosophila), frizzled 6, seven transmembrane spanning receptor, frizzled family receptor 6		NA	9480858, 14747478	Standard	NM_003506	NM_003506	NA	Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.1714G>A	chr8.hg19:g.104342055G>A	ENSP00000351605:p.Ala572Thr	NA	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	hg19	CCDS6298.1	0.02	15.396805	TCTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.50	1.957434	0.34565	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000540287;ENST00000539487	T;T;T;T	0.78003	-1.08;-1.08;-1.11;-1.14	5.54	3.71	0.42584	.	0.100896	0.64402	D	0.000002	T	0.62466	0.2430	L	0.34521	1.04	0.39391	D	0.966412	B;B;B	0.12013	0.002;0.005;0.002	B;B;B	0.18263	0.016;0.01;0.021	T	0.53315	-0.8456	10	0.05620	T	0.96	.	10.8343	0.46677	0.0679:0.0:0.8011:0.131	.	517;267;572	B4E236;F5H831;O60353	.;.;FZD6_HUMAN	T	572;572;540;267;517	ENSP00000429055:A572T;ENSP00000351605:A572T;ENSP00000429528:A540T;ENSP00000443757:A267T	ENSP00000351605:A572T	A	+	1	0	FZD6	104411231	1.000000	0.71417	0.132000	0.22025	0.984000	0.73092	3.897000	0.56273	0.781000	0.33589	0.655000	0.94253	GCA	NOVEL	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380560.1	2	16.547942	KEEP	0	0	0	55	1943	GG	1	1	0		+	39	60	1347	0	0	99.427297	327	60	12330	489	ENST00000358755.4	0.106557	1
RP11-127H5.1	0	__UNKNOWN__	__UNKNOWN__	8	105839668	105839668	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:105839668G>A	ENST00000521923.1	+	3	250	c.90G>A	c.(88-90)ggG>ggA	p.G30G							NA		NA									NA						aagtagctgggcctacaagTC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000521923.1:c.90G>A	chr8.hg19:g.105839668G>A		NA		hg19		0.02	4.557613	TGGxCCT	COVERED																																																																																			NOVEL	RP11-127H5.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380421.1	3	6.320176	KEEP	0	0	0	21	727	GG	0.999869	0.999866	0		+	14	60	504	0	0	38.530548	102	60	3741	176	ENST00000521923.1	0.12069	0.999997
ZFPM2	23414	__UNKNOWN__	__UNKNOWN__	8	106430876	106430876	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:106430876T>C	ENST00000407775.2	+	2	290				ZFPM2_ENST00000520492.1_Intron	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	NA		NA			blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			AATGAAATCTTTTCTCAGAAT	0.244	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	51	50	NA		NA	NA	8		NA											NA				106430876		875	1991	2866	SO:0001627	intron_variant			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946	23414		Zinc fingers, C2H2-type, Zinc fingers, C2HC-type containing	16700	protein-coding gene	gene with protein product		603693	zinc finger protein, multitype 2		NA	9927675, 10438528	Standard		NM_012082	NA	Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.41-496T>C	chr8.hg19:g.106430876T>C		NA	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	hg19	CCDS47908.1	0.02	4.825397	TCTxTTC	COVERED																																																																																			NOVEL	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380614.1	2	9.027527	KEEP	0	0	0	30	990	TT	0.999997	0.999997	0		+	37	60	1407	0	0	124.489276	94	60	3462	199	ENST00000407775.2	0.282443	1
ZFPM2	23414	__UNKNOWN__	__UNKNOWN__	8	106816490	106816490	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:106816490A>T	ENST00000407775.2	+	0	4430				RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000521622.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	NA		NA			blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			GCAATACTTTATAAAGAATGA	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946	23414		Zinc fingers, C2H2-type, Zinc fingers, C2HC-type containing	16700	protein-coding gene	gene with protein product		603693	zinc finger protein, multitype 2		NA	9927675, 10438528	Standard		NM_012082	NA	Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.*724A>T	chr8.hg19:g.106816490A>T		NA	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	hg19	CCDS47908.1	0.02	6.625007	TTTxTAA	COVERED																																																																																			NOVEL	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380614.1	1	6.31916	KEEP	0	0	0	21	661	AA	0.999869	0.999869	0		+	27	60	960	0	0	77.03647	137	60	4967	214	ENST00000407775.2	0.164634	1
NUDCD1	84955	__UNKNOWN__	__UNKNOWN__	8	110255472	110255472	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:110255472C>T	ENST00000239690.4	-	10	1892	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S	NUDCD1_ENST00000427660.2_Silent_p.S477S	NM_032869.3	NP_116258.2			NudC domain containing 1	NA		NA								breast(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(2)|skin(1)	25	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;1.56e-12)			GGGCTGCATACGAGTAATTTG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													155	163	160	NA		NA	NA	8		NA											NA				110255472		2203	4300	6503	SO:0001819	synonymous_variant			AF283302	CCDS6312.1, CCDS47910.1	8q23	2005-02-07			ENSG00000120526	ENSG00000120526	84955			24306	protein-coding gene	gene with protein product		606109			NA	11416219	Standard	NM_032869	NM_032869	NA	Approved	CML66, FLJ14991	uc003ynb.4	Q96RS6	OTTHUMG00000164931	ENST00000239690.4:c.1518G>A	chr8.hg19:g.110255472C>T		NA		hg19	CCDS6312.1	0.02	14.823099	ATAxGAG	COVERED																																																																																			NOVEL	NUDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380996.1	4	21.66952	KEEP	0	0	0	72	2470	CC	1	1	0		-	16	60	563	0	0	35.448466	348	60	12178	562	ENST00000239690.4	0.043956	1
CSMD3	114788	__UNKNOWN__	__UNKNOWN__	8	113293526	113293526	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:113293526C>T	ENST00000297405.5	-	59	9629	c.9385G>A	c.(9385-9387)Gat>Aat	p.D3129N	CSMD3_ENST00000455883.2_Missense_Mutation_p.D2960N|CSMD3_ENST00000343508.3_Missense_Mutation_p.D3089N|CSMD3_ENST00000352409.3_Missense_Mutation_p.D3059N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3129	Sushi 23. {ECO:0000255|PROSITE- ProRule:PRU00302}.	NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTTGTGCCATCAATTCGGAAG	0.408	NA	NA								HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													120	103	109	NA		NA	NA	8		NA											NA				113293526		2203	4300	6503	SO:0001583	missense			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796	114788			19291	protein-coding gene	gene with protein product		608399			NA		Standard	NM_052900	NM_052900	NA	Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9385G>A	chr8.hg19:g.113293526C>T	ENSP00000297405:p.Asp3129Asn	NA	Q96PZ3	hg19	CCDS6315.1	0.02	15.605078	CATxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	32	5.185442	0.94885	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	5.72	5.72	0.89469	Complement control module (2);Sushi/SCR/CCP (3);	0.065417	0.64402	D	0.000016	T	0.70343	0.3213	L	0.41906	1.305	0.58432	D	0.999999	P;P;D	0.53151	0.944;0.955;0.958	P;P;P	0.60236	0.747;0.871;0.783	T	0.64123	-0.6481	10	0.26408	T	0.33	.	19.8765	0.96875	0.0:1.0:0.0:0.0	.	2960;3129;3089	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	N	3089;3129;2399;2960;3059	ENSP00000345799:D3089N;ENSP00000297405:D3129N;ENSP00000341558:D2399N;ENSP00000412263:D2960N;ENSP00000343124:D3059N	ENSP00000297405:D3129N	D	-	1	0	CSMD3	113362702	1.000000	0.71417	1.000000	0.80357	0.724000	0.41520	5.907000	0.69908	2.695000	0.91970	0.650000	0.86243	GAT	NOVEL	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347141.1	1	14.72822	KEEP	0	0	0	49	1750	CC	1	1	0		-	33	60	1140	0	0	80.395996	367	60	14091	536	ENST00000297405.5	0.0825	1
TRPS1	7227	__UNKNOWN__	__UNKNOWN__	8	116422724	116422724	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:116422724C>A	ENST00000395715.3	-	0	7989					NM_001282902.1|NM_001282903.1|NM_014112.2	NP_001269831.1|NP_001269832.1|NP_054831.2	Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	NA		NA			chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AAAAAAATCTCAATATGTCAT	0.313	NA	NA							Langer-Giedion syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447	7227		GATA zinc finger domain containing, Zinc fingers, C2H2-type	12340	protein-coding gene	gene with protein product		604386			NA	8530105, 10615131, 10647898	Standard	NM_014112	NM_001282903	NA	Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000395715.3:c.*3527G>T	chr8.hg19:g.116422724C>A		NA	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	hg19	CCDS6318.2	0.02	3.678389	TCTxAAT	COVERED																																																																																			NOVEL	TRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286435.3	4	7.223756	KEEP	0	0	0	24	869	CC	0.999909	0.999909	0		-	8	60	277	0	0	18.009411	140	60	5274	198	ENST00000395715.3	0.054054	1
DERL1	79139	__UNKNOWN__	__UNKNOWN__	8	124054241	124054241	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:124054241A>T	ENST00000259512.4	-	1	422	c.122T>A	c.(121-123)cTc>cAc	p.L41H	DERL1_ENST00000405944.3_Missense_Mutation_p.L41H|DERL1_ENST00000419562.2_Missense_Mutation_p.L41H	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	41		NA			endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TTCGGGCCAGAGGAAGAGGTA	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													56	51	53	NA		NA	NA	8		NA											NA				124054241		2203	4300	6503	SO:0001583	missense			BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986	79139			28454	protein-coding gene	gene with protein product		608813	Der1-like domain family, member 1		NA	12975309, 15215855	Standard	NM_024295	NM_024295	NA	Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.122T>A	chr8.hg19:g.124054241A>T	ENSP00000259512:p.Leu41His	NA	B3KW41|E9PH19	hg19	CCDS6337.1	0.02	20.545823	CAGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	18.26	3.585460	0.66105	.	.	ENSG00000136986	ENST00000259512;ENST00000405944;ENST00000419562	T;T;T	0.38077	1.3;1.3;1.16	5.27	5.27	0.74061	.	0.059205	0.64402	D	0.000002	T	0.67850	0.2937	M	0.91249	3.19	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.998	T	0.75551	-0.3278	10	0.59425	D	0.04	.	15.35	0.74376	1.0:0.0:0.0:0.0	.	41;41;41	B4E1G1;Q9BUN8-2;Q9BUN8	.;.;DERL1_HUMAN	H	41	ENSP00000259512:L41H;ENSP00000384289:L41H;ENSP00000389965:L41H	ENSP00000259512:L41H	L	-	2	0	DERL1	124123422	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	6.345000	0.72995	2.214000	0.71695	0.372000	0.22366	CTC	NOVEL	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381714.2	3	93.8354	KEEP	0	0	0	312	9998	AA	1	1	0		-	100	60	3495	0	0	292.633398	360	60	12715	968	ENST00000259512.4	0.217391	1
MIR4663	100616260	__UNKNOWN__	__UNKNOWN__	8	124228063	124228063	__UNKNOWN__	RNA	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:124228063C>A	ENST00000582039.1	-	0	40					NR_039808.1				microRNA 4663	NA		NA									NA						GCAGCAATGACAGATGCCACT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							8	2011-09-12				ENSG00000266324	100616260		ncRNAs / Micro RNAs	41623	non-coding RNA	RNA, micro		NA			NA		Standard	NR_039808	NR_039808	NA	Approved	hsa-mir-4663	uc022baj.1			ENST00000582039.1:	chr8.hg19:g.124228063C>A		NA		hg19		0.02	6.831319	TGAxAGA	COVERED																																																																																			NOVEL	MIR4663-201	KNOWN	basic	miRNA	NA	miRNA		0	8.423815	KEEP	0	0	0	28	972	CC	0.999997	0.999997	0		-	9	60	338	0	0	23.263871	143	60	5360	239	ENST00000582039.1	0.059211	1
FAM91A1	157769	__UNKNOWN__	__UNKNOWN__	8	124827187	124827187	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:124827187T>C	ENST00000334705.7	+	0	5006					NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	NA		NA								breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TTCATTTGGCTTTTTACCATG	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853	157769			26306	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_144963	XM_005250806	NA	Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.*2243T>C	chr8.hg19:g.124827187T>C		NA	B6YY23|Q658T5|Q8TE89	hg19	CCDS6346.2	0.02	4.652313	GGCxTTT	COVERED																																																																																			NOVEL	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256607.1	4	8.725606	KEEP	0	0	0	29	918	TT	0.999997	0.999997	0		+	16	60	589	0	0	45.594657	112	60	4105	190	ENST00000334705.7	0.125	1
TMEM65	157378	__UNKNOWN__	__UNKNOWN__	8	125324591	125324591	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:125324591C>A	ENST00000297632.6	-	0	2867					NM_194291.2	NP_919267.2	Q6PI78	TMM65_HUMAN	transmembrane protein 65	NA		NA				integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	6	Lung NSC(37;1.18e-11)|Ovarian(258;0.00438)|all_neural(195;0.0779)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			GCTTTCTCTCCTCAAAGTCTA	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC032396	CCDS6348.1	8q24.13	2006-11-24			ENSG00000164983	ENSG00000164983	157378			25203	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_194291	NM_194291	NA	Approved		uc010mdl.3	Q6PI78	OTTHUMG00000165021	ENST00000297632.6:c.*1610G>T	chr8.hg19:g.125324591C>A		NA	Q8N5G8|Q8WVK5	hg19	CCDS6348.1	0.02	4.692455	CTCxTCA	COVERED																																																																																			NOVEL	TMEM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381464.1	1	7.223297	KEEP	0	0	0	24	835	CC	0.999909	0.999904	0		-	21	60	784	0	0	64.948221	91	60	3335	151	ENST00000297632.6	0.1875	0.999995
SQLE	6713	__UNKNOWN__	__UNKNOWN__	8	126011742	126011742	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:126011742C>T	ENST00000265896.5	+	1	995	c.97C>T	c.(97-99)Ctg>Ttg	p.L33L	SQLE_ENST00000523430.1_Intron	NM_003129.3	NP_003120.2	Q14534	ERG1_HUMAN	squalene epoxidase	33		NA			cellular aromatic compound metabolic process (GO:0006725)|cholesterol biosynthetic process (GO:0006695)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|squalene monooxygenase activity (GO:0004506)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)		Butenafine(DB01091)|Naftifine(DB00735)|Terbinafine(DB00857)	GTTGTGCGTGCTGGTGTTCCT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													62	66	64	NA		NA	NA	8		NA											NA				126011742		2023	4174	6197	SO:0001819	synonymous_variant			D78130	CCDS47918.1	8q24.1	2014-06-23			ENSG00000104549	ENSG00000104549	6713	1.14.13.132		11279	protein-coding gene	gene with protein product	squalene monooxygenase	602019			NA	9286711	Standard	NM_003129	NM_003129	NA	Approved		uc011liq.2	Q14534	OTTHUMG00000164990	ENST00000265896.5:c.97C>T	chr8.hg19:g.126011742C>T		NA	Q9UEK6	hg19	CCDS47918.1	0.02	14.677312	GTGxTGG	COVERED																																																																																			NOVEL	SQLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381362.1	6	39.726922	KEEP	0	0	0	132	4618	CC	1	1	0		+	11	60	398	0	0	23.299978	380	60	14169	606	ENST00000265896.5	0.028133	1
OC90	729330	__UNKNOWN__	__UNKNOWN__	8	133041233	133041233	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:133041233C>A	ENST00000254627.3	-	13	1225				OC90_ENST00000443356.2_Intron|OC90_ENST00000262283.5_Intron|OC90_ENST00000603859.1_Intron	NM_001080399.2	NP_001073868.2	Q02509	OC90_HUMAN	otoconin 90	NA		NA			lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CAGTTAAGTGCTTGGGAAACC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117	729330			8100	protein-coding gene	gene with protein product		601658		PLA2L	NA	10329003, 9860971	Standard	NM_001080399	NM_001080399	NA	Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000254627.3:c.1138+86G>T	chr8.hg19:g.133041233C>A		NA	B4DNG8	hg19	CCDS47919.1	0.02	6.619054	GTGxTTG	COVERED																																																																																			NOVEL	OC90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379693.1	4	6.311094	KEEP	0	0	0	21	738	CC	0.999869	0.999869	0		-	20	60	717	0	0	54.670431	147	60	5543	231	ENST00000254627.3	0.11976	1
OC90	729330	__UNKNOWN__	__UNKNOWN__	8	133044204	133044204	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:133044204A>G	ENST00000254627.3	-	12	1041	c.955T>C	c.(955-957)Tgc>Cgc	p.C319R	OC90_ENST00000443356.2_Missense_Mutation_p.C335R|OC90_ENST00000262283.5_Missense_Mutation_p.C531R|OC90_ENST00000603859.1_Missense_Mutation_p.C319R	NM_001080399.2	NP_001073868.2	Q02509	OC90_HUMAN	otoconin 90	335		NA			lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TCCTCCGGGCACCGGGATGTC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	83	83	NA		NA	NA	8		NA											NA				133044204		2024	4180	6204	SO:0001583	missense			Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117	729330			8100	protein-coding gene	gene with protein product		601658		PLA2L	NA	10329003, 9860971	Standard	NM_001080399	NM_001080399	NA	Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000254627.3:c.955T>C	chr8.hg19:g.133044204A>G	ENSP00000254627:p.Cys319Arg	NA	B4DNG8	hg19	CCDS47919.1	0.02	9.69042	GGCxCCG	COVERED	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681770	0.68042	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.25414	1.8;1.8;1.8	5.91	5.91	0.95273	Phospholipase A2 (3);	0.000000	0.85682	D	0.000000	T	0.46444	0.1393	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.40794	-0.9544	10	0.72032	D	0.01	-18.4309	15.1723	0.72884	1.0:0.0:0.0:0.0	.	319;335	Q02509-2;Q02509	.;OC90_HUMAN	R	319;335;531	ENSP00000254627:C319R;ENSP00000390050:C335R;ENSP00000262283:C531R	ENSP00000254627:C319R	C	-	1	0	RP11-240B13.2;OC90	133113386	1.000000	0.71417	0.998000	0.56505	0.606000	0.37113	7.511000	0.81718	2.254000	0.74563	0.533000	0.62120	TGC	NOVEL	OC90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379693.1	0	6.316226	KEEP	0	0	0	21	640	AA	0.999869	0.999869	0		-	16	60	567	0	0	39.710894	196	60	7021	294	ENST00000254627.3	0.075472	1
HHLA1	10086	__UNKNOWN__	__UNKNOWN__	8	133100030	133100030	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:133100030G>A	ENST00000434736.2	-	11	783				HHLA1_ENST00000414222.1_Intron			C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	NA		NA				extracellular region (GO:0005576)				endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						GGTTTCATCTGCTGGACAGTT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													164	147	152	NA		NA	NA	8		NA											NA				133100030		692	1591	2283	SO:0001627	intron_variant			AF110315		8q24	2011-03-01			ENSG00000132297	ENSG00000132297	10086			4904	protein-coding gene	gene with protein product		604109		PLA2L	NA	10329003	Standard	XR_017860	NM_001145095	NA	Approved		uc011liy.1	C9JL84	OTTHUMG00000140390	ENST00000434736.2:c.698-44C>T	chr8.hg19:g.133100030G>A		NA		hg19		0.02	13.346239	TCTxCTG	COVERED																																																																																			NOVEL	HHLA1-001	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000277163.2	4	7.825864	KEEP	0	0	0	26	956	GG	0.999957	0.999957	0		-	105	60	3692	0	0	332.039349	211	60	8114	443	ENST00000434736.2	0.332278	1
TG	7038	__UNKNOWN__	__UNKNOWN__	8	133882073	133882073	__UNKNOWN__	Splice_Site	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:133882073T>G	ENST00000220616.4	+	3	314		c.e3+2		TG_ENST00000377869.1_Splice_Site	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	NA		NA			hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CTGTGGCTTGTAAGTGGGAGT	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													42	41	41	NA		NA	NA	8		NA											NA				133882073		2203	4300	6503	SO:0001630	splice_region_variant			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832	7038			11764	protein-coding gene	gene with protein product		188450			NA		Standard	NM_003235	NM_003235	NA	Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.274+2T>G	chr8.hg19:g.133882073T>G		NA	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	hg19	CCDS34944.1	0.02	5.063981	TTGxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	16.79	3.220675	0.58560	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7594	0.57354	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TG	133951255	1.000000	0.71417	0.964000	0.40570	0.634000	0.38068	5.899000	0.69846	1.952000	0.56665	0.379000	0.24179	.	NOVEL	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379606.1	0	7.521677	KEEP	0	0	0	25	765	TT	0.999931	0.999912	0	Intron	+	17	60	581	0	0	46.262697	86	60	2846	150	ENST00000220616.4	0.165049	0.999981
TG	7038	__UNKNOWN__	__UNKNOWN__	8	133900416	133900416	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:133900416G>T	ENST00000220616.4	+	10	2404	c.2364G>T	c.(2362-2364)tgG>tgT	p.W788C	TG_ENST00000377869.1_Missense_Mutation_p.W788C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	788	Thyroglobulin type-1 7. {ECO:0000255|PROSITE-ProRule:PRU00500}.	NA			hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ACCAACGATGGGAGGCTCAGA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	64	68	NA		NA	NA	8		NA											NA				133900416		2203	4300	6503	SO:0001583	missense			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832	7038			11764	protein-coding gene	gene with protein product		188450			NA		Standard	NM_003235	NM_003235	NA	Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2364G>T	chr8.hg19:g.133900416G>T	ENSP00000220616:p.Trp788Cys	NA	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	hg19	CCDS34944.1	0.02	19.926921	ATGxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.96	2.392817	0.42410	.	.	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.78924	-1.22;-0.4	5.8	5.8	0.92144	Thyroglobulin type-1 (2);	0.096463	0.47455	D	0.000239	D	0.87752	0.6256	M	0.79258	2.445	0.58432	D	0.999997	D	0.62365	0.991	P	0.62382	0.901	D	0.88545	0.3112	10	0.87932	D	0	.	19.0314	0.92959	0.0:0.0:1.0:0.0	.	788	P01266	THYG_HUMAN	C	788	ENSP00000367100:W788C;ENSP00000220616:W788C	ENSP00000220616:W788C	W	+	3	0	TG	133969598	1.000000	0.71417	0.414000	0.26521	0.006000	0.05464	7.808000	0.86044	2.740000	0.93945	0.650000	0.86243	TGG	NOVEL	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379606.1	1	21.648941	KEEP	0	0	0	72	2433	GG	1	1	0		+	37	60	1303	0	0	91.612071	437	60	15417	618	ENST00000220616.4	0.078059	1
ST3GAL1	6482	__UNKNOWN__	__UNKNOWN__	8	134471745	134471745	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:134471745G>A	ENST00000319914.5	-	0	2312				ST3GAL1_ENST00000521180.1_3'UTR|ST3GAL1_ENST00000522652.1_3'UTR|ST3GAL1_ENST00000399640.2_3'UTR			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			CTTTCCCAGCGTCTCCCCAGC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	6482	2.4.99.4	Sialyltransferases	10862	protein-coding gene	gene with protein product	ST3Gal I	607187	sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)	SIAT4A	NA	10504389, 7655169	Standard	NM_003033	NM_003033	NA	Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.*262C>T	chr8.hg19:g.134471745G>A		NA	O60677|Q9UN51	hg19	CCDS6373.1	0.02	16.422029	AGCxTCT	COVERED																																																																																			NOVEL	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379132.1	6	12.340037	KEEP	0	0	0	41	1426	GG	1	1	0		-	67	60	2405	0	0	194.181854	331	60	11633	529	ENST00000319914.5	0.168342	1
ZFAT	57623	__UNKNOWN__	__UNKNOWN__	8	135725158	135725158	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:135725158C>T	ENST00000377838.3	-	0	123				ZFAT_ENST00000523399.1_5'UTR	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			TCCGGGCCCCCTCCCGTGCCG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	4	4	NA		NA	NA	8		NA											NA				135725158		689	1688	2377	SO:0001623	5_prime_UTR_variant			BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827	57623		Zinc fingers, C2H2-type	19899	protein-coding gene	gene with protein product		610931	zinc finger protein 406	ZNF406, ZFAT1	NA	10819331, 18329245	Standard	NM_001029939	NM_020863	NA	Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.-52G>A	chr8.hg19:g.135725158C>T		NA	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	hg19	CCDS47924.1	0.02	4.495196	CCCxTCC	COVERED																																																																																			NOVEL	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378272.1	6	87.704139	KEEP	0	1	24	300	10371	CC	1	1	0		-	21	60	708	0	0	55.038469	121	60	4267	668	ENST00000377838.3	0.147887	1
KHDRBS3	10656	__UNKNOWN__	__UNKNOWN__	8	136635951	136635951	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:136635951G>A	ENST00000355849.5	+	7	1300				KHDRBS3_ENST00000520981.1_Intron	NM_006558.1	NP_006549.1	O75525	KHDR3_HUMAN	KH domain containing, RNA binding, signal transduction associated 3	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	26	all_epithelial(106;2.85e-16)|all_neural(2;2.72e-06)|Lung NSC(106;3.95e-06)|all_lung(105;1.11e-05)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.247)			CTAAAAGGCCGCAAAAGAGAA	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF069681	CCDS6374.1	8q24.23	2008-05-15			ENSG00000131773	ENSG00000131773	10656			18117	protein-coding gene	gene with protein product		610421			NA	10332027, 10564820	Standard		XR_242372	NA	Approved	T-STAR, Etle, etoile, SALP, SLM2, SLM-2	uc003yuv.3	O75525	OTTHUMG00000164164	ENST00000355849.5:c.890+16671G>A	chr8.hg19:g.136635951G>A		NA	Q6NUL8|Q9UPA8	hg19	CCDS6374.1	0.02	16.514325	GCCxCAA	COVERED																																																																																			NOVEL	KHDRBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377529.1	2	18.055612	KEEP	0	0	0	60	2047	GG	1	1	0		+	65	60	2375	0	0	193.342038	311	60	11002	527	ENST00000355849.5	0.172872	1
FAM135B	51059	__UNKNOWN__	__UNKNOWN__	8	139143476	139143476	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:139143476C>T	ENST00000395297.1	-	0	5751					NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	NA		NA								NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TTTGCAGAAGCAGGAGCTTTC	0.428	NA	NA								HNSCC(54;0.14)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724	51059			28029	protein-coding gene	gene with protein product		NA			NA	8619474, 9110174	Standard	NM_015912	NM_015912	NA	Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.*1360G>A	chr8.hg19:g.139143476C>T		NA	B5MDB3|O95879|Q2WGJ7|Q3KP46	hg19	CCDS6375.2	0.02	6.630161	AAGxAGG	COVERED																																																																																			NOVEL	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313590.3	1	3.608231	KEEP	0	0	0	12	415	CC	0.993634	0.993634	0		-	21	60	739	0	0	57.544887	129	60	4949	189	ENST00000395297.1	0.14	1
COL22A1	169044	__UNKNOWN__	__UNKNOWN__	8	139672682	139672682	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:139672682C>G	ENST00000303045.6	-	44	3728	c.3282G>C	c.(3280-3282)aaG>aaC	p.K1094N	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.K1074N	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1094	Collagen-like 9.|Gly-rich.|Pro-rich.	NA			extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GACATACCGGCTTGCCAGGAG	0.428	NA	NA								HNSCC(7;0.00092)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													68	58	61	NA		NA	NA	8		NA											NA				139672682		2203	4300	6503	SO:0001583	missense			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436	169044		Collagens	22989	protein-coding gene	gene with protein product		610026			NA		Standard	XM_291257	NM_152888	NA	Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3282G>C	chr8.hg19:g.139672682C>G	ENSP00000303153:p.Lys1094Asn	NA	B7ZMH0|C9K0G4|Q8IVT9	hg19	CCDS6376.1	0.02	7.251316	CGGxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.12	1.544267	0.27563	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.93366	-3.21;-3.21	4.68	-8.44	0.00950	.	0.000000	0.52532	U	0.000067	D	0.90096	0.6906	N	0.16266	0.395	0.33827	D	0.629712	D;D	0.76494	0.999;0.999	D;D	0.85130	0.994;0.997	D	0.89531	0.3785	10	0.17832	T	0.49	.	15.0859	0.72151	0.0:0.7137:0.0:0.2863	.	1074;1094	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	N	1094;1074;787	ENSP00000303153:K1094N;ENSP00000387655:K1074N	ENSP00000303153:K1094N	K	-	3	2	COL22A1	139741864	0.457000	0.25752	0.808000	0.32385	0.834000	0.47266	-1.171000	0.03115	-1.640000	0.01525	-0.271000	0.10264	AAG	NOVEL	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315905.2	1	10.2317	KEEP	0	0	0	34	1222	CC	0.999998	0.999998	0		-	20	60	762	0	0	58.029172	169	60	6407	288	ENST00000303045.6	0.10582	1
COL22A1	169044	__UNKNOWN__	__UNKNOWN__	8	139791885	139791885	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:139791885G>T	ENST00000303045.6	-	14	2097				COL22A1_ENST00000435777.1_Intron	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	NA		NA			extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			AGTCTCCCAGGGCCTCTGCTT	0.547	NA	NA								HNSCC(7;0.00092)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436	169044		Collagens	22989	protein-coding gene	gene with protein product		610026			NA		Standard	XM_291257	NM_152888	NA	Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1651-80C>A	chr8.hg19:g.139791885G>T		NA	B7ZMH0|C9K0G4|Q8IVT9	hg19	CCDS6376.1	0.02	4.597464	CAGxGCC	COVERED																																																																																			NOVEL	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315905.2	1	4.750775	KEEP	0	0	0	16	495	GG	0.997832	0.997831	0		-	18	60	649	0	0	51.272208	105	60	3733	172	ENST00000303045.6	0.146341	0.999999
C8orf17	100507249	__UNKNOWN__	__UNKNOWN__	8	140943842	140943842	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:140943842G>T	ENST00000507535.3	+	0	427				TRAPPC9_ENST00000438773.2_Intron|TRAPPC9_ENST00000389328.4_Intron|TRAPPC9_ENST00000389327.3_Intron			Q9NRJ1	MOST1_HUMAN	chromosome 8 open reading frame 17	NA		NA				endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)					NA						CCCGCGGTCTGGAAAGTGCTC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF220264		8q24.3	2012-05-16			ENSG00000250733	ENSG00000250733	100507249			17737	protein-coding gene	gene with protein product		NA			NA	17143515	Standard			NA	Approved	MOST-1		Q9NRJ1	OTTHUMG00000140391	ENST00000507535.3:c.-688G>T	chr8.hg19:g.140943842G>T		NA		hg19		0.02	11.369954	TCTxGAA	COVERED																																																																																			NOVEL	C8orf17-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000277164.2	2	7.208041	KEEP	0	0	0	24	780	GG	0.999909	0.999909	0		+	37	60	1353	0	0	106.111791	233	60	8579	338	ENST00000507535.3	0.137037	1
JRK	8629	__UNKNOWN__	__UNKNOWN__	8	143746441	143746441	__UNKNOWN__	RNA	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:143746441G>T	ENST00000507178.2	-	0	1369							O75564	JERKY_HUMAN	Jrk homolog (mouse)	NA		NA				nucleus (GO:0005634)	DNA binding (GO:0003677)				NA	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ggggaccggagggttaatgaa	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													11	13	12	NA		NA	NA	8		NA											NA				143746441		1960	4029	5989					AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616	8629			6199	protein-coding gene	gene with protein product		603210	jerky (mouse) homolog, jerky homolog (mouse)		NA	9675132	Standard	NM_003724	NM_003724	NA	Approved	JH8, jerky	uc003ywo.3	O75564		ENST00000507178.2:	chr8.hg19:g.143746441G>T		NA	O75565	hg19		0.02	18.250461	GGAxGGT	COVERED																																																																																			NOVEL	JRK-003	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000362914.1	2	19.25852	KEEP	0	0	0	64	2193	GG	1	1	0		-	47	60	1722	0	0	129.755891	392	60	14163	638	ENST00000507178.2	0.107062	1
GML	2765	__UNKNOWN__	__UNKNOWN__	8	143921856	143921856	__UNKNOWN__	Start_Codon_SNP	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:143921856G>C	ENST00000220940.1	+	2	93	c.3G>C	c.(1-3)atG>atC	p.M1I		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	1		NA			apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GTGAAGTGATGCTCCTCTTTG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													154	134	141	NA		NA	NA	8		NA											NA				143921856		2203	4300	6503	SO:0001582	initiator_codon_variant			D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02				2765			4375	protein-coding gene	gene with protein product		602370	GPI anchored molecule like protein, glycosylphosphatidylinositol anchored molecule like protein		NA	8934543, 9169150	Standard	NM_002066	NM_002066	NA	Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.3G>C	chr8.hg19:g.143921856G>C	ENSP00000220940:p.Met1Ile	NA	A0AVF6|O00686|O00731	hg19	CCDS6391.1	0.02	30.348921	GATxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	N	10.83	1.462325	0.26248	.	.	ENSG00000104499	ENST00000522728;ENST00000220940	T;T	0.49432	0.78;0.93	2.97	2.97	0.34412	.	0.000000	0.39544	N	0.001328	T	0.45597	0.1350	.	.	.	0.09310	N	0.999995	P	0.50156	0.932	P	0.47470	0.548	T	0.38824	-0.9643	9	0.59425	D	0.04	.	9.6455	0.39865	0.0:0.0:1.0:0.0	.	1	Q99445	GML_HUMAN	I	1	ENSP00000430799:M1I;ENSP00000220940:M1I	ENSP00000220940:M1I	M	+	3	0	GML	143918858	0.089000	0.21612	0.078000	0.20375	0.009000	0.06853	0.825000	0.27393	1.955000	0.56771	0.650000	0.86243	ATG	NOVEL	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379659.1	2	12.03936	KEEP	0	0	0	40	1438	GG	1	1	0	Missense_Mutation	+	182	60	6661	0	0	588.890405	445	60	16876	880	ENST00000220940.1	0.290271	1
TOP1MT	116447	__UNKNOWN__	__UNKNOWN__	8	144403338	144403338	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:144403338C>T	ENST00000523676.1	-	9	1258				TOP1MT_ENST00000329245.4_Intron|TOP1MT_ENST00000519148.1_Intron|TOP1MT_ENST00000521193.1_Intron			Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	NA		NA			DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	ATACGTGTCACATAGCGGGGG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													30	31	31	NA		NA	NA	8		NA											NA				144403338		2174	4269	6443	SO:0001627	intron_variant			AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428	116447			29787	protein-coding gene	gene with protein product		606387			NA	11526219	Standard	NM_052963	NM_052963	NA	Approved		uc003yxz.4	Q969P6		ENST00000523676.1:c.852+32G>A	chr8.hg19:g.144403338C>T		NA	B7ZAR5|E7ES89|Q86ST4|Q86V82	hg19	CCDS59115.1	0.02	14.59734	TCAxATA	COVERED																																																																																			NOVEL	TOP1MT-005	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381295.1	1	12.929291	KEEP	0	0	0	43	1481	CC	1	1	0		-	11	60	395	0	0	23.315956	355	60	13252	472	ENST00000523676.1	0.030055	1
RHPN1	114822	__UNKNOWN__	__UNKNOWN__	8	144466070	144466070	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:144466070G>T	ENST00000289013.6	+	0	3363					NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	NA		NA			signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			AGTCCCTTCCGAGGGTCCGCA	0.672	NA	NA									OREG0019045	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106	114822			19973	protein-coding gene	gene with protein product		601031			NA	11572484	Standard		NM_052924	NA	Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.*1249G>T	chr8.hg19:g.144466070G>T		1687	Q8TAV1|Q96PV9	hg19	CCDS47927.1	0.02	25.975351	TCCxAGG	COVERED																																																																																			NOVEL	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381417.1	6	27.083762	KEEP	0	0	0	90	3018	GG	1	1	0		+	58	60	2074	0	0	153.350205	520	60	18323	843	ENST00000289013.6	0.100346	1
GSDMD	79792	__UNKNOWN__	__UNKNOWN__	8	144644420	144644420	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:144644420C>G	ENST00000526406.1	+	12	1921	c.1038C>G	c.(1036-1038)gaC>gaG	p.D346E	GSDMD_ENST00000533063.1_Missense_Mutation_p.D394E|GSDMD_ENST00000262580.4_Missense_Mutation_p.D346E	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	346		NA			cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						AGCCCCTGGACGGTCCAGCAG	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													24	22	23	NA		NA	NA	8		NA											NA				144644420		2165	4271	6436	SO:0001583	missense			AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518	79792			25697	protein-coding gene	gene with protein product		NA	gasdermin domain containing 1	GSDMDC1	NA	15289881, 17350798	Standard	NM_024736	NM_024736	NA	Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.1038C>G	chr8.hg19:g.144644420C>G	ENSP00000433209:p.Asp346Glu	NA	D3DWJ9|Q96Q98	hg19	CCDS34956.1	0.02	11.756334	GGAxGGT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.700|1.700	-0.501737|-0.501737	0.04261|0.04261	.|.	.|.	ENSG00000104518|ENSG00000104518	ENST00000526406;ENST00000533063;ENST00000262580|ENST00000525208	T;T;T|.	0.22539|.	1.95;1.95;1.95|.	4.39|4.39	-8.77|-8.77	0.00827|0.00827	.|.	0.955169|.	0.08732|.	N|.	0.901965|.	T|T	0.22820|0.22820	0.0551|0.0551	L|L	0.32530|0.32530	0.975|0.975	0.09310|0.09310	N|N	1|1	B;B;B|.	0.28324|.	0.102;0.102;0.207|.	B;B;B|.	0.25291|.	0.058;0.058;0.059|.	T|T	0.16041|0.16041	-1.0416|-1.0416	10|5	0.18710|.	T|.	0.47|.	-5.797|-5.797	4.2154|4.2154	0.10531|0.10531	0.2011:0.1042:0.1363:0.5585|0.2011:0.1042:0.1363:0.5585	.|.	346;346;394|.	A8K702;P57764;G3V1A6|.	.;GSDMD_HUMAN;.|.	E|G	346;394;346|42	ENSP00000433209:D346E;ENSP00000433958:D394E;ENSP00000262580:D346E|.	ENSP00000262580:D346E|.	D|R	+|+	3|1	2|2	GSDMD|GSDMD	144715563|144715563	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-9.053000|-9.053000	0.00014|0.00014	-5.828000|-5.828000	0.00009|0.00009	-1.079000|-1.079000	0.02226|0.02226	GAC|CGG	NOVEL	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382046.3	2	12.326627	KEEP	0	0	0	41	1377	CC	1	1	0		+	34	60	1263	0	0	97.40768	249	60	8715	418	ENST00000526406.1	0.120141	1
ZNF623	9831	__UNKNOWN__	__UNKNOWN__	8	144735517	144735517	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:144735517G>C	ENST00000501748.2	+	0	3564					NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TCAAAAAAGAGATCTACATTT	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309	9831		Zinc fingers, C2H2-type	29084	protein-coding gene	gene with protein product		NA			NA	9734811	Standard	NM_014789	NM_014789	NA	Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.*1864G>C	chr8.hg19:g.144735517G>C		NA	A4FU80|B4DGP3|E7ENV5	hg19	CCDS34957.1	0.02	10.04591	AGAxATC	COVERED																																																																																			NOVEL	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382522.3	6	6.92255	KEEP	0	0	0	23	820	GG	0.999892	0.999892	0		+	62	60	2361	0	0	209.306536	155	60	5849	275	ENST00000501748.2	0.285714	1
FAM83H	286077	__UNKNOWN__	__UNKNOWN__	8	144810406	144810406	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:144810406G>A	ENST00000388913.3	-	5	1350	c.1225C>T	c.(1225-1227)Cgg>Tgg	p.R409W		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	409		NA			biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			AAGCTGTGCCGCTTGAAGGCG	0.756	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													7	10	9	NA		NA	NA	8		NA											NA				144810406		1838	4016	5854	SO:0001583	missense			AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921	286077			24797	protein-coding gene	gene with protein product		611927			NA	18252228	Standard	NM_198488	NM_198488	NA	Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1225C>T	chr8.hg19:g.144810406G>A	ENSP00000373565:p.Arg409Trp	NA	A0JLS2|Q8N4W0	hg19	CCDS6410.2	0.02	8.832819	GCCxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	g	17.47	3.396995	0.62177	.	.	ENSG00000180921	ENST00000388913	T	0.34275	1.37	4.97	3.05	0.35203	.	3.420360	0.01402	N	0.013623	T	0.55337	0.1914	L	0.36672	1.1	0.42732	D	0.993719	D	0.89917	1.0	D	0.81914	0.995	T	0.27226	-1.0080	10	0.87932	D	0	.	12.634	0.56673	0.0:0.0:0.4409:0.5591	.	409	Q6ZRV2	FA83H_HUMAN	W	409	ENSP00000373565:R409W	ENSP00000373565:R409W	R	-	1	2	FAM83H	144882394	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	0.891000	0.28309	1.036000	0.39998	0.561000	0.74099	CGG	NOVEL	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257632.2	0	7.82497	KEEP	0	0	0	26	891	GG	0.999957	0.999957	0		-	17	60	607	0	0	42.872829	202	60	7257	295	ENST00000388913.3	0.077626	1
NRBP2	340371	__UNKNOWN__	__UNKNOWN__	8	144916621	144916621	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:144916621G>A	ENST00000442628.2	-	0	2856				NRBP2_ENST00000327830.5_3'UTR	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2	NA		NA								central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			agaacctccaggaaggaaggc	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24					340371			19339	protein-coding gene	gene with protein product		615563			NA	14702039	Standard	NM_178564	NM_178564	NA	Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.*1211C>T	chr8.hg19:g.144916621G>A		NA		hg19	CCDS34959.2	0.02	18.36371	CCAxGAA	COVERED																																																																																			NOVEL	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382247.1	3	15.651165	KEEP	0	0	0	52	1863	GG	1	1	0		-	24	60	886	0	0	59.402536	425	60	15804	604	ENST00000442628.2	0.053452	1
PARP10	84875	__UNKNOWN__	__UNKNOWN__	8	145058554	145058554	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs201826623	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:145058554G>A	ENST00000524918.1	-	6	1590	c.1504C>T	c.(1504-1506)Cgg>Tgg	p.R502W	PARP10_ENST00000525773.1_Missense_Mutation_p.R514W|PARP10_ENST00000313028.7_Missense_Mutation_p.R502W			Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	502		NA			negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGCAGGCTCCGCAGAAACTCC	0.617	NA	NA											G|||	3	0.000599042	0.0023	0	5008	,	,	NA	18097	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													21	25	24	NA		NA	NA	8		NA											NA				145058554		2202	4298	6500	SO:0001583	missense			AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685	84875		Poly (ADP-ribose) polymerases	25895	protein-coding gene	gene with protein product		609564			NA	15273990	Standard	NM_032789	NM_032789	NA	Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000524918.1:c.1504C>T	chr8.hg19:g.145058554G>A	ENSP00000431620:p.Arg502Trp	NA	Q8N2I0|Q8WV05|Q96CH7|Q96K72	hg19		0.02	21.006299	TCCxCAG	COVERED	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	18.84	3.708495	0.68615	.	.	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773	T;T;T	0.11063	2.82;2.82;2.81	4.21	4.21	0.49690	.	0.158906	0.29293	N	0.012579	T	0.04363	0.0120	N	0.08118	0	0.27279	N	0.958161	D;D	0.64830	0.994;0.992	B;B	0.41299	0.353;0.332	T	0.14839	-1.0458	10	0.87932	D	0	.	14.1138	0.65139	0.0:0.0:1.0:0.0	.	514;502	E9PNI7;Q53GL7	.;PAR10_HUMAN	W	502;208;502;514	ENSP00000431620:R502W;ENSP00000325618:R502W;ENSP00000434776:R514W	ENSP00000325618:R502W	R	-	1	2	PARP10	145130542	0.984000	0.35163	0.949000	0.38748	0.630000	0.37929	2.348000	0.44045	1.902000	0.55061	0.550000	0.68814	CGG	NOVEL	PARP10-004	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000383865.1	9	19.56054	KEEP	0	0	0	65	2178	GG	1	1	0		-	18	60	634	0	0	37.852989	515	60	17452	683	ENST00000524918.1	0.033771	1
OPLAH	26873	__UNKNOWN__	__UNKNOWN__	8	145113351	145113351	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:145113351C>A	ENST00000534424.1	-	7	887				OPLAH_ENST00000426825.1_Intron			O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	NA		NA			glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGGCCAAGGCCCAGGCCCAGG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	16	15	NA		NA	NA	8		NA											NA				145113351		2052	4159	6211	SO:0001627	intron_variant			AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	26873	3.5.2.9		8149	protein-coding gene	gene with protein product		614243			NA	14993790	Standard	NM_017570	NM_017570	NA	Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000534424.1:c.3147-44G>T	chr8.hg19:g.145113351C>A		NA	A5PKY8|Q75W65|Q9Y4Q0	hg19		0.02	11.137695	GGCxCAG	COVERED																																																																																			NOVEL	OPLAH-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000384059.2	3	4.513481	KEEP	0	0	0	15	497	CC	0.99649	0.99649	0		-	23	60	793	0	0	56.908144	228	60	7847	300	ENST00000534424.1	0.091633	1
SCRT1	83482	__UNKNOWN__	__UNKNOWN__	8	145556708	145556708	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:145556708G>T	ENST00000332135.4	-	0	1297					NM_031309.4	NP_112599.2	Q9BWW7	SCRT1_HUMAN	scratch family zinc finger 1	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron migration (GO:2001222)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|upper_aerodigestive_tract(1)	3	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;1.35e-39)|all cancers(56;1.37e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			CGGGCGGGGCGGGGTGGGACC	0.766	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC014675	CCDS6421.1	8q24.3	2013-10-09	2013-10-09		ENSG00000170616	ENSG00000261678	83482		Zinc fingers, C2H2-type	15950	protein-coding gene	gene with protein product		605858	scratch (drosophila homolog) 1, zinc finger protein, scratch homolog 1, zinc finger protein (Drosophila)		NA	11274425	Standard	NM_031309	NM_031309	NA	Approved	DKFZp547F072, ZNF898	uc003zbw.1	Q9BWW7	OTTHUMG00000165229	ENST00000332135.4:c.*139C>A	chr8.hg19:g.145556708G>T		NA	A8MX66|Q96C52	hg19	CCDS6421.1	0.02	2.422598	GGCxGGG	COVERED																																																																																			NOVEL	SCRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382800.2	0	5.715733	KEEP	0	0	0	19	576	GG	0.99986	0.970684	0		-	8	60	280	0	0	22.052521	45	60	1408	92	ENST00000332135.4	0.150943	0.97082
VPS28	51160	__UNKNOWN__	__UNKNOWN__	8	145650258	145650258	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:145650258A>G	ENST00000526054.1	-	6	338				VPS28_ENST00000529182.1_Intron|VPS28_ENST00000292510.4_Intron|VPS28_ENST00000377348.2_Intron			Q9UK41	VPS28_HUMAN	vacuolar protein sorting 28 homolog (S. cerevisiae)	NA		NA			endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|negative regulation of protein ubiquitination (GO:0031397)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			CCAGGTGGCCAGAGCCCTCTG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF316887	CCDS6425.1, CCDS34967.1	8q24.3	2014-08-12	2006-04-04		ENSG00000160948	ENSG00000160948	51160			18178	protein-coding gene	gene with protein product		611952	vacuolar protein sorting 28 (yeast)		NA		Standard		NM_183057	NA	Approved		uc003zct.1	Q9UK41	OTTHUMG00000165209	ENST00000526054.1:c.301-56T>C	chr8.hg19:g.145650258A>G		NA	Q86VK0	hg19	CCDS6425.1	0.02	24.12889	GCCxGAG	COVERED																																																																																			NOVEL	VPS28-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382694.1	0	18.652768	KEEP	0	0	0	62	1906	AA	1	1	0		-	53	60	1802	0	0	129.384858	507	60	18738	758	ENST00000526054.1	0.094643	1
PPP1R16A	84988	__UNKNOWN__	__UNKNOWN__	8	145724155	145724155	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr8:145724155C>T	ENST00000292539.4	+	3	1179	c.262C>T	c.(262-264)Cgc>Tgc	p.R88C	CTD-2517M14.5_ENST00000569326.1_RNA|CTD-2517M22.14_ENST00000532766.1_RNA|PPP1R16A_ENST00000435887.1_Missense_Mutation_p.R88C			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	88		NA				plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TTTTGCAGTCCGCCAGTTCCT	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													49	48	48	NA		NA	NA	8		NA											NA				145724155		2202	4300	6502	SO:0001583	missense				CCDS6429.1	8q24.3	2013-01-10	2011-10-04		ENSG00000160972	ENSG00000160972	84988		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Ankyrin repeat domain containing	14941	protein-coding gene	gene with protein product		609172	protein phosphatase 1, regulatory (inhibitor) subunit 16A		NA	11948623	Standard	NM_032902	NM_032902	NA	Approved	MGC14333, MYPT3	uc003zdf.3	Q96I34	OTTHUMG00000165173	ENST00000292539.4:c.262C>T	chr8.hg19:g.145724155C>T	ENSP00000292539:p.Arg88Cys	NA	D3DWM5	hg19	CCDS6429.1	0.02	39.809324	GTCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.60	1.688159	0.29962	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.67345	-0.26;-0.26	4.65	2.82	0.32997	Ankyrin repeat-containing domain (4);	0.199760	0.40302	N	0.001134	T	0.62405	0.2425	M	0.69823	2.125	0.58432	D	0.999999	B	0.25351	0.124	B	0.27170	0.077	T	0.61969	-0.6953	10	0.48119	T	0.1	.	8.275	0.31866	0.0:0.8035:0.0:0.1965	.	88	Q96I34	PP16A_HUMAN	C	88	ENSP00000292539:R88C;ENSP00000391126:R88C	ENSP00000292539:R88C	R	+	1	0	PPP1R16A	145694963	0.005000	0.15991	0.996000	0.52242	0.385000	0.30292	0.365000	0.20348	1.095000	0.41419	0.462000	0.41574	CGC	NOVEL	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382459.1	4	43.934427	KEEP	0	0	0	146	4892	CC	1	1	0		+	73	60	2745	0	0	202.48885	746	60	25631	1179	ENST00000292539.4	0.089133	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	14810	14810	__UNKNOWN__	IGR	SNP	C	C	G	rs71509922	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:14810C>G			NA	NA				None (None upstream) : MIR1302-2 (12846 downstream)						NA		NA									NA						GAGCCCCCTACGATTCCCAGT	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													6	9	8	NA		NA	NA	9		NA											NA				14810		1371	3648	5019	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.14810C>G		NA		hg19		0.02	-0.219107	CTAxGAT	UNCOVERED																																																																																			NOVEL					0			0	2.406434	KEEP	12	0	0	8	257	CT	0	0	0			3	31	108	0	0	8.249605	22	50	703	58		0.12	0.552887
DOCK8	81704	__UNKNOWN__	__UNKNOWN__	9	376312	376312	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:376312A>G	ENST00000469391.1	+	18	2080				DOCK8_ENST00000382331.1_Intron|DOCK8_ENST00000453981.1_Intron|DOCK8_ENST00000382329.1_Intron|DOCK8_ENST00000432829.2_Intron	NM_001190458.1|NM_001193536.1	NP_001177387.1|NP_001180465.1	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	NA		NA			blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		CCAGGTAAGGAATGTCAAGGT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													105	101	102	NA		NA	NA	9		NA											NA				376312		2203	4300	6503	SO:0001627	intron_variant			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099	81704			19191	protein-coding gene	gene with protein product		611432			NA	11214971	Standard	XM_036307	NM_203447	NA	Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000469391.1:c.2001+7A>G	chr9.hg19:g.376312A>G		NA	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	hg19	CCDS55284.1	0.02	12.638508	AGGxATG	COVERED																																																																																			NOVEL	DOCK8-012	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354646.1	3	30.091616	KEEP	0	0	0	100	3241	AA	1	1	0		+	41	60	1520	0	0	122.213336	221	60	8012	473	ENST00000469391.1	0.156489	1
CD274	29126	__UNKNOWN__	__UNKNOWN__	9	5468886	5468886	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:5468886G>C	ENST00000381577.3	+	0	1983				CD274_ENST00000381573.4_3'UTR	NM_014143.3	NP_054862.1	Q9NZQ7	PD1L1_HUMAN	CD274 molecule	NA		NA			cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		aagtgcccttgcaatatcaat	0.368	NA	NA	T	CIITA	PMBL, Hodgkin Lymphona, 									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		9	9p24	29126	CD274 molecule		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF177937	CCDS6464.1, CCDS59118.1	9p24.1	2014-01-30	2006-03-28	2005-02-25	ENSG00000120217	ENSG00000120217	29126		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Endogenous ligands	17635	protein-coding gene	gene with protein product	B7 homolog 1	605402	programmed cell death 1 ligand 1, CD274 antigen	PDCD1LG1	NA	11015443, 10581077	Standard	NM_014143	NM_014143	NA	Approved	B7-H, B7H1, PD-L1, PDL1, B7-H1	uc003zje.3	Q9NZQ7	OTTHUMG00000019503	ENST00000381577.3:c.*1024G>C	chr9.hg19:g.5468886G>C		NA	B2RBA2|B4DU27|Q14CJ2|Q2V8D5|Q66RK1|Q6WEX4|Q9NUZ5	hg19	CCDS6464.1	0.02	4.814588	CTTxCAA	COVERED																																																																																			NOVEL	CD274-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051631.2	3	9.631909	KEEP	0	0	0	32	1180	GG	0.999997	0.999996	0		+	36	60	1292	0	0	114.35628	85	60	3299	185	ENST00000381577.3	0.297521	0.999999
PTPRD	5789	__UNKNOWN__	__UNKNOWN__	9	8376093	8376093	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:8376093G>A	ENST00000381196.4	-	36	5050				PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000356435.5_Intron|PTPRD_ENST00000360074.4_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000358503.5_Intron|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000540109.1_Intron|PTPRD_ENST00000537002.1_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	NA		NA			heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GAACCATTCTGTGAAATAGGA	0.408	NA	NA								TSP Lung(15;0.13)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	67	69	NA		NA	NA	9		NA											NA				8376093		2203	4299	6502	SO:0001627	intron_variant			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707	5789		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	9668	protein-coding gene	gene with protein product		601598			NA	7896816, 8355697	Standard		NM_002839	NA	Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4507-3C>T	chr9.hg19:g.8376093G>A		NA	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	hg19	CCDS43786.1	0.02	6.925045	TCTxTGA	COVERED																																																																																			NOVEL	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055395.3	0	17.45688	KEEP	0	0	0	58	2092	GG	1	1	0		-	46	60	1710	0	0	150.698784	118	60	4514	290	ENST00000381196.4	0.280488	1
MPDZ	8777	__UNKNOWN__	__UNKNOWN__	9	13247743	13247743	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:13247743C>A	ENST00000541718.1	-	3	295	c.74G>T	c.(73-75)gGg>gTg	p.G25V	MPDZ_ENST00000381015.4_Missense_Mutation_p.G25V|MPDZ_ENST00000447879.1_Missense_Mutation_p.G25V|MPDZ_ENST00000319217.7_Missense_Mutation_p.G25V|MPDZ_ENST00000536827.1_Missense_Mutation_p.G25V|MPDZ_ENST00000381022.2_Missense_Mutation_p.G25V|MPDZ_ENST00000546205.1_Missense_Mutation_p.G25V	NM_001261407.1|NM_003829.4	NP_001248336.1|NP_003820.2	O75970	MPDZ_HUMAN	multiple PDZ domain protein	25	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.	NA			cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TGCTACATCCCCACGTTCTCG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													269	261	264	NA		NA	NA	9		NA											NA				13247743		1950	4148	6098	SO:0001583	missense			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186	8777			7208	protein-coding gene	gene with protein product		603785			NA		Standard	NM_003829	NM_003829	NA	Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000541718.1:c.74G>T	chr9.hg19:g.13247743C>A	ENSP00000439807:p.Gly25Val	NA	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	hg19	CCDS47951.1	0.02	1.99471	TCCxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334918	0.81801	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.19669	2.17;2.13;2.13;2.13;2.16;2.17;2.18	5.68	5.68	0.88126	.	0.000000	0.46442	D	0.000300	T	0.46908	0.1417	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.37731	-0.9693	10	0.87932	D	0	.	18.7628	0.91860	0.0:1.0:0.0:0.0	.	25;25;25	B7ZMI4;O75970-3;O75970-2	.;.;.	V	25	ENSP00000320006:G25V;ENSP00000439807:G25V;ENSP00000370410:G25V;ENSP00000444151:G25V;ENSP00000415208:G25V;ENSP00000370403:G25V;ENSP00000446358:G25V	ENSP00000320006:G25V	G	-	2	0	MPDZ	13237743	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.328000	0.79160	2.690000	0.91761	0.491000	0.48974	GGG	NOVEL	MPDZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401076.1	1	11.734319	KEEP	0	0	0	39	1342	CC	1	0.99911	0		-	12	60	418	0	0	32.912357	67	60	2388	142	ENST00000541718.1	0.151899	0.99911
SNAPC3	6619	__UNKNOWN__	__UNKNOWN__	9	15460800	15460800	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:15460800A>G	ENST00000380821.3	+	0	2348					NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	NA		NA			gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		TGAATTTAAAAAGATCTTGAG	0.269	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975	6619			11136	protein-coding gene	gene with protein product		602348	small nuclear RNA activating complex, polypeptide 3, 50kD		NA	9003788	Standard	NM_001039697	XR_428427	NA	Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.*936A>G	chr9.hg19:g.15460800A>G		NA	D3DRI8|Q2VPI6|Q5T285	hg19	CCDS6478.1	0.02	2.215301	AAAxAGA	COVERED																																																																																			NOVEL	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051763.2	1	8.124353	KEEP	0	0	0	27	853	AA	0.999988	0.999756	0		+	41	60	1568	0	0	149.959396	47	60	1723	145	ENST00000380821.3	0.465909	0.999768
RP11-145E5.5	0	__UNKNOWN__	__UNKNOWN__	9	21967846	21967846	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:21967846G>C	ENST00000404796.2	+	5	460				CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000304494.5_3'UTR|CDKN2A_ENST00000579755.1_3'UTR						NA		NA						p.0?(198)|p.0(1)			NA						acccccctgagcttccctagt	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				199	Whole gene deletion(199)	haematopoietic_and_lymphoid_tissue(34)|central_nervous_system(31)|lung(31)|skin(16)|kidney(14)|oesophagus(11)|bone(10)|pancreas(10)|urinary_tract(7)|breast(6)|soft_tissue(5)|thyroid(4)|pleura(4)|large_intestine(3)|stomach(3)|liver(3)|ovary(3)|upper_aerodigestive_tract(1)|vulva(1)|biliary_tract(1)|autonomic_ganglia(1)											NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000404796.2:c.348-61586G>C	chr9.hg19:g.21967846G>C		NA		hg19		0.02	2.452198	TGAxCTT	COVERED																																																																																			NOVEL	RP11-145E5.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000445913.1	1	3.309826	KEEP	0	0	0	11	360	GG	0.993072	0.982687	0		+	25	60	904	0	0	84.395692	36	60	1375	79	ENST00000404796.2	0.409836	0.989542
B4GALT1	2683	__UNKNOWN__	__UNKNOWN__	9	33112082	33112082	__UNKNOWN__	3'UTR	SNP	C	C	T	rs150168782	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:33112082C>T	ENST00000379731.4	-	0	2753				B4GALT1_ENST00000535206.1_Intron	NM_001497.3	NP_001488.2	P15291	B4GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	NA		NA			acute inflammatory response (GO:0002526)|angiogenesis involved in wound healing (GO:0060055)|binding of sperm to zona pellucida (GO:0007339)|branching morphogenesis of an epithelial tube (GO:0048754)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|development of secondary sexual characteristics (GO:0045136)|epithelial cell development (GO:0002064)|extracellular matrix organization (GO:0030198)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|lactose biosynthetic process (GO:0005989)|leukocyte migration (GO:0050900)|mammary gland development (GO:0030879)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|oligosaccharide biosynthetic process (GO:0009312)|penetration of zona pellucida (GO:0007341)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|regulation of acrosome reaction (GO:0060046)|regulation of cellular component movement (GO:0051270)|single fertilization (GO:0007338)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|desmosome (GO:0030057)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|glycocalyx (GO:0030112)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-tubulin binding (GO:0043014)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|beta-tubulin binding (GO:0048487)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|manganese ion binding (GO:0030145)|N-acetyllactosamine synthase activity (GO:0003945)|protein homodimerization activity (GO:0042803)|UDP-galactosyltransferase activity (GO:0035250)			endometrium(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)	14			LUSC - Lung squamous cell carcinoma(29;0.0084)	GBM - Glioblastoma multiforme(74;0.121)	N-Acetyl-D-glucosamine(DB00141)	AAAAGGGAGACGAAGGAAGGA	0.517	NA	NA											c|||	18	0.00359425	0.0121	0.0014	5008	,	,	NA	4109	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X14085	CCDS6535.1	9p13	2013-02-19			ENSG00000086062	ENSG00000086062	2683	2.4.1.22	Beta 4-glycosyltransferases	924	protein-coding gene	gene with protein product		137060		GGTB2	NA	9597550	Standard	NM_001497	NM_001497	NA	Approved	beta4Gal-T1	uc003zsg.2	P15291	OTTHUMG00000019764	ENST00000379731.4:c.*1370G>A	chr9.hg19:g.33112082C>T		NA	B2R710|D3DRL2|Q12909|Q12910|Q12911|Q14456|Q14509|Q14523	hg19	CCDS6535.1	0.02	4.462805	AGAxGAA	COVERED																																																																																			NOVEL	B4GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052039.1	5	12.338186	KEEP	0	0	0	41	1366	CC	1	1	0		-	20	60	704	0	0	56.016399	106	60	3703	217	ENST00000379731.4	0.15873	1
NFX1	4799	__UNKNOWN__	__UNKNOWN__	9	33366681	33366681	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:33366681C>T	ENST00000379540.3	+	22	3156	c.3094C>T	c.(3094-3096)Cgg>Tgg	p.R1032W	NFX1_ENST00000463421.1_3'UTR	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	1032	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.	NA			inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		AGACCACCGCCGGATCATCCA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													101	89	93	NA		NA	NA	9		NA											NA				33366681		2203	4300	6503	SO:0001583	missense			U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102	4799			7803	protein-coding gene	gene with protein product		603255			NA	7964459, 2511169	Standard		NM_002504	NA	Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.3094C>T	chr9.hg19:g.33366681C>T	ENSP00000368856:p.Arg1032Trp	NA	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	hg19	CCDS6538.1	0.02	15.076044	CGCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.8	4.336512	0.81801	.	.	ENSG00000086102	ENST00000379540	T	0.44482	0.92	6.07	4.07	0.47477	Single-stranded nucleic acid binding R3H (3);	0.114346	0.64402	D	0.000009	T	0.67552	0.2905	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.74222	-0.3735	10	0.66056	D	0.02	-4.5729	11.5512	0.50721	0.4781:0.5219:0.0:0.0	.	1032	Q12986	NFX1_HUMAN	W	1032	ENSP00000368856:R1032W	ENSP00000368856:R1032W	R	+	1	2	NFX1	33356681	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.534000	0.53568	1.553000	0.49476	0.655000	0.94253	CGG	NOVEL	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052069.1	3	24.974097	KEEP	0	0	0	83	2803	CC	1	1	0		+	66	60	2426	0	0	205.249198	236	60	8204	499	ENST00000379540.3	0.218543	1
AQP7	364	__UNKNOWN__	__UNKNOWN__	9	33395108	33395108	__UNKNOWN__	Silent	SNP	G	G	A	rs2381003	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:33395108G>A	ENST00000539936.1	-	3	350	c.112C>T	c.(112-114)Ctg>Ttg	p.L38L	AQP7_ENST00000537089.1_5'UTR|AQP7_ENST00000377425.4_Intron|AQP7_ENST00000541274.1_5'UTR			O14520	AQP7_HUMAN	aquaporin 7	38		NA	L -> V (in dbSNP:rs2381003).		excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		AACTCGGCCAGGAACTCTCGC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													129	86	101	NA		NA	NA	9		NA											NA				33395108		2203	4300	6503	SO:0001819	synonymous_variant			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269	364		Ion channels / Aquaporins	640	protein-coding gene	gene with protein product		602974		AQP7L	NA	9252401	Standard	NM_001170	NM_001170	NA	Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000539936.1:c.112C>T	chr9.hg19:g.33395108G>A		NA	Q08E94|Q5T5L9|Q8NHM3	hg19		0.02	6.91523	CCAxGAA	COVERED																																																																																			NOVEL	AQP7-203	KNOWN	basic	protein_coding	NA	protein_coding		11	3.080119	KEEP	0	2	62	32	1151	GG	0.999998	0.999998	0		-	11	60	398	0	0	27.940936	140	60	5195	241	ENST00000539936.1	0.072848	1
FAM205B	389715	__UNKNOWN__	__UNKNOWN__	9	34834840	34834840	__UNKNOWN__	RNA	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:34834840A>C	ENST00000455647.2	-	0	1553							Q63HN1	F205B_HUMAN	family with sequence similarity 205, member B	NA		NA									NA						GGTGGGGCTGACTGGGGTGAA	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							9p13.3	2013-05-22	2011-08-15	2011-08-15	ENSG00000257198	ENSG00000257198	389715			24504	other	unknown		NA	chromosome 9 open reading frame 144	C9orf144	NA		Standard	NR_024481	NR_024481	NA	Approved	DKFZp434J193, C9orf144A	uc003zvp.4	Q63HN1	OTTHUMG00000019839	ENST00000455647.2:	chr9.hg19:g.34834840A>C		NA	Q6ZRJ7	hg19		0.02	23.43255	CTGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	12.47	1.948097	0.34377	.	.	ENSG00000257198	ENST00000455647	.	.	.	4.1	1.57	0.23409	.	1.240650	0.05910	N	0.631481	T	0.23572	0.0570	.	.	.	0.09310	N	0.999999	B	0.31705	0.336	B	0.27796	0.083	T	0.22591	-1.0212	8	0.40728	T	0.16	.	4.454	0.11635	0.5927:0.2164:0.0:0.1909	.	217	Q63HN1	F205B_HUMAN	A	217	.	ENSP00000398718:S217A	S	-	1	0	AL589645.1	34824840	0.001000	0.12720	0.009000	0.14445	0.072000	0.16883	-0.036000	0.12185	0.209000	0.20645	0.449000	0.29647	TCA	NOVEL	FAM205B-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000052246.5	11	17.749864	KEEP	4	0	0	59	1819	AA	1	1	0		-	30	60	1074	0	0	72.088298	485	60	16870	720	ENST00000455647.2	0.058252	1
TLN1	7094	__UNKNOWN__	__UNKNOWN__	9	35697744	35697744	__UNKNOWN__	3'UTR	SNP	G	G	A	rs373116877		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:35697744G>A	ENST00000314888.9	-	0	8023				TLN1_ENST00000540444.1_3'UTR	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GTAGTGGCACGCACAGTCTCT	0.597	NA	NA									OREG0019174	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G		0,4406		0,0,2203	50	54	52	NA		5.2	1	9		52	1,8599	1.2+/-3.3	0,1,4299	no	utr-3	TLN1	NM_006289.3		0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077			35697744	1,13005	2203	4300	6503	SO:0001624	3_prime_UTR_variant			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076	7094			11845	protein-coding gene	gene with protein product		186745		TLN	NA	7635475, 10610730	Standard	NM_006289	NM_006289	NA	Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.*44C>T	chr9.hg19:g.35697744G>A		857	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	hg19	CCDS35009.1	0.02	11.138649	CACxCAC	COVERED																																																																																			NOVEL	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052353.2	2	25.113386	KEEP	0	1	33	95	3216	GG	1	1	0		-	60	60	2173	0	0	182.237715	225	60	7612	488	ENST00000314888.9	0.210526	1
TLN1	7094	__UNKNOWN__	__UNKNOWN__	9	35715137	35715137	__UNKNOWN__	Silent	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:35715137C>G	ENST00000314888.9	-	21	3026	c.2673G>C	c.(2671-2673)cgG>cgC	p.R891R	TLN1_ENST00000540444.1_Silent_p.R891R	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	891		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGCTGCCTCCCGCAGCCGCT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	38	36	NA		NA	NA	9		NA											NA				35715137		2201	4295	6496	SO:0001819	synonymous_variant			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076	7094			11845	protein-coding gene	gene with protein product		186745		TLN	NA	7635475, 10610730	Standard	NM_006289	NM_006289	NA	Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.2673G>C	chr9.hg19:g.35715137C>G		NA	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	hg19	CCDS35009.1	0.02	2.135509	CTCxCGC	COVERED																																																																																			NOVEL	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052353.2	0	5.718608	KEEP	0	0	0	19	671	CC	0.999863	0.991958	0		-	10	60	326	0	0	25.40683	53	60	1867	101	ENST00000314888.9	0.15873	0.992094
GNE	10020	__UNKNOWN__	__UNKNOWN__	9	36218254	36218254	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:36218254T>C	ENST00000539208.1	-	9	1666	c.1529A>G	c.(1528-1530)gAg>gGg	p.E510G	GNE_ENST00000377902.5_Missense_Mutation_p.E620G|GNE_ENST00000543356.2_Missense_Mutation_p.E615G|GNE_ENST00000396594.3_Missense_Mutation_p.E651G|GNE_ENST00000447283.2_Missense_Mutation_p.E546G|GNE_ENST00000539815.1_Missense_Mutation_p.E620G	NM_001190384.1	NP_001177313.1	Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	620	N-acetylmannosamine kinase.	NA			carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			ACCCACAGCCTCATCTTTTGG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(184;106 2118 20004 35750 50727)					NA		NA				0													142	116	125	NA		NA	NA	9		NA											NA				36218254		2203	4300	6503	SO:0001583	missense			AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921	10020			23657	protein-coding gene	gene with protein product		603824	UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase	IBM2	NA	9305887, 9305888	Standard	NM_005476	NM_005476	NA	Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539208.1:c.1529A>G	chr9.hg19:g.36218254T>C	ENSP00000445117:p.Glu510Gly	NA	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	hg19	CCDS55308.1	0.02	13.752605	GCCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	16.74	3.205535	0.58234	.	.	ENSG00000159921	ENST00000377902;ENST00000396594;ENST00000339267;ENST00000539815;ENST00000543356;ENST00000539208;ENST00000447283	D;D;D;D;D	0.99698	-6.43;-6.44;-6.43;-6.22;-6.31	5.58	5.58	0.84498	.	0.044896	0.85682	D	0.000000	D	0.99369	0.9778	L	0.43152	1.355	0.58432	D	0.999999	P;P;P;P;D	0.57899	0.72;0.925;0.925;0.877;0.981	B;P;P;B;D	0.65140	0.429;0.526;0.621;0.326;0.932	D	0.98556	1.0639	10	0.52906	T	0.07	-11.0426	13.69	0.62539	0.0:0.0:0.0:1.0	.	510;579;651;620;546	F5H499;Q9Y223-3;Q9Y223-2;Q9Y223;A7UNU7	.;.;.;GLCNE_HUMAN;.	G	620;651;615;620;592;510;546	ENSP00000367134:E620G;ENSP00000379839:E651G;ENSP00000439155:E620G;ENSP00000445117:E510G;ENSP00000414760:E546G	ENSP00000340770:E615G	E	-	2	0	GNE	36208254	1.000000	0.71417	0.806000	0.32338	0.465000	0.32709	6.609000	0.74173	2.123000	0.65237	0.459000	0.35465	GAG	NOVEL	GNE-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052413.2	1	39.114996	KEEP	0	0	0	130	4272	TT	1	1	0		-	40	60	1430	0	0	108.775764	298	60	11067	641	ENST00000539208.1	0.118343	1
ZBTB5	9925	__UNKNOWN__	__UNKNOWN__	9	37438547	37438547	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:37438547G>A	ENST00000307750.4	-	0	4190					NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		GCAGAGGTAAGCGGGCAGGCT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795	9925		-, BTB/POZ domain containing, Zinc fingers, C2H2-type	23836	protein-coding gene	gene with protein product		NA			NA	9205841	Standard	NM_014872	NM_014872	NA	Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.*1968C>T	chr9.hg19:g.37438547G>A		NA		hg19	CCDS6610.1	0.02	11.001422	TAAxCGG	COVERED																																																																																			NOVEL	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052462.1	2	22.51195	KEEP	0	0	0	75	2641	GG	1	1	0		-	72	60	2515	1	0	216.817584	206	60	7777	453	ENST00000307750.4	0.258993	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	38194377	38194377	__UNKNOWN__	IGR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:38194377C>G			NA	NA				snoU13 (3873 upstream) : RP11-113O24.3 (166046 downstream)						NA		NA									NA						GTAAGAAAAGCTACAGTCATT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.38194377C>G		NA		hg19		0.02	9.823032	AAGxTAC	COVERED																																																																																			NOVEL					0			3	12.039096	KEEP	0	0	0	40	1434	CC	1	1	0			51	60	1871	0	0	158.478948	180	60	6891	327		0.220779	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415292	68415292	__UNKNOWN__	IGR	SNP	C	C	T	rs4928838		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:68415292C>T			NA	NA				RP11-764K9.1 (5399 upstream) : MIR4477B (15 downstream)						NA		NA									NA						accattaatcctttcatgata	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415292C>T		NA		hg19		0.02	4.21744	ATCxTTT	COVERED																																																																																			NOVEL					0			3	3.745649	KEEP	0	1	30	23	827	CC	0.999909	0.999909	0			5	60	190	0	0	12.380009	114	60	4358	224		0.042017	1
TMEM252	169693	__UNKNOWN__	__UNKNOWN__	9	71152436	71152436	__UNKNOWN__	Intron	SNP	C	C	T	rs200184315		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:71152436C>T	ENST00000377311.3	-	2	331					NM_153237.1	NP_694969.1	Q8N6L7	TM252_HUMAN	transmembrane protein 252	NA		NA				integral component of membrane (GO:0016021)					NA						CATAAACATGCGTGCGTTATT	0.463	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	19654	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC029780	CCDS35040.1	9q21.13	2012-07-19	2012-07-19	2012-07-19	ENSG00000181778	ENSG00000181778	169693			28537	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 71	C9orf71	NA	12477932	Standard	NM_153237	NM_153237	NA	Approved	MGC34760	uc004agt.3	Q8N6L7	OTTHUMG00000019967	ENST00000377311.3:c.279-27G>A	chr9.hg19:g.71152436C>T		NA		hg19	CCDS35040.1	0.02	-0.403514	ATGxGTG	COVERED																																																																																			NOVEL	TMEM252-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052551.1	0	4.815152	KEEP	0	0	0	16	543	CC	0.997832	0.932466	0		-	4	60	134	0	0	9.408906	42	60	1419	77	ENST00000377311.3	0.086957	0.934492
TMEM2	23670	__UNKNOWN__	__UNKNOWN__	9	74300299	74300299	__UNKNOWN__	Silent	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:74300299T>A	ENST00000377044.4	-	24	4505	c.3966A>T	c.(3964-3966)atA>atT	p.I1322I	TMEM2_ENST00000377066.5_Silent_p.I1259I|TMEM2_ENST00000396272.3_Silent_p.I315I	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	1322		NA		I -> V (in Ref. 7; BAC11574). {ECO:0000305}.	multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ATCCCAAAAATATGGTACTCC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													38	35	36	NA		NA	NA	9		NA											NA				74300299		2203	4300	6503	SO:0001819	synonymous_variant				CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048	23670			11869	protein-coding gene	gene with protein product		605835			NA		Standard	NM_013390	NM_013390	NA	Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.3966A>T	chr9.hg19:g.74300299T>A		NA	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	hg19	CCDS6638.1	0.02	0.094079	AAAxATG	COVERED																																																																																			NOVEL	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052618.2	5	5.515071	KEEP	0	4	40	34	906	TT	1	0.998867	0		-	15	70	176	0	0	8.491068	62	60	1960	169	ENST00000377044.4	0.194805	0.998867
GNAQ	2776	__UNKNOWN__	__UNKNOWN__	9	80333235	80333235	__UNKNOWN__	3'UTR	SNP	G	G	A	rs78763022		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:80333235G>A	ENST00000286548.4	-	0	4306					NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	NA		NA			action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						AAAGAATCCCGTCCCGCCCCT	0.388	NA	NA	Mis		uveal melanoma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		9	9q21	2776	guanine nucleotide binding protein (G protein), q polypeptide		E	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052	2776			4390	protein-coding gene	gene with protein product		600998			NA	8825633	Standard	NM_002072	NM_002072	NA	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.*3004C>T	chr9.hg19:g.80333235G>A		NA	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	hg19	CCDS6658.1	0.02	12.108875	CCCxTCC	COVERED																																																																																			NOVEL	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052761.1	7	30.861571	KEEP	4	7	204	175	5452	GG	1	1	0		-	43	49	1521	0	0	121.902999	219	60	6899	607	ENST00000286548.4	0.164122	1
GNAQ	2776	__UNKNOWN__	__UNKNOWN__	9	80645987	80645987	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:80645987G>A	ENST00000286548.4	-	1	359					NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	NA		NA			action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						GGGGCGCAGAGGCCCGGCGGG	0.781	NA	NA	Mis		uveal melanoma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		9	9q21	2776	guanine nucleotide binding protein (G protein), q polypeptide		E	0													4	5	5	NA		NA	NA	9		NA											NA				80645987		2027	4015	6042	SO:0001627	intron_variant				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052	2776			4390	protein-coding gene	gene with protein product		600998			NA	8825633	Standard	NM_002072	NM_002072	NA	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.136+28C>T	chr9.hg19:g.80645987G>A		NA	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	hg19	CCDS6658.1	0.02	-0.350904	AGAxGCC	COVERED																																																																																			NOVEL	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052761.1	2	16.251596	KEEP	0	0	0	54	1893	GG	1	0.877708	0		-	4	60	145	0	0	10.808744	35	60	1254	131	ENST00000286548.4	0.102564	0.877708
GNAQ	2776	__UNKNOWN__	__UNKNOWN__	9	80646047	80646047	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:80646047G>A	ENST00000286548.4	-	1	327	c.105C>T	c.(103-105)gaC>gaT	p.D35D		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	35		NA			action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						CCCGGCGGGCGTCCCGCTTGT	0.716	NA	NA	Mis		uveal melanoma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		9	9q21	2776	guanine nucleotide binding protein (G protein), q polypeptide		E	0													10	11	11	NA		NA	NA	9		NA											NA				80646047		2164	4251	6415	SO:0001819	synonymous_variant				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052	2776			4390	protein-coding gene	gene with protein product		600998			NA	8825633	Standard	NM_002072	NM_002072	NA	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.105C>T	chr9.hg19:g.80646047G>A		NA	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	hg19	CCDS6658.1	0.02	-0.366993	GGCxTCC	COVERED																																																																																			NOVEL	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052761.1	0	14.137219	KEEP	1	0	0	47	1485	GG	1	0.899314	0		-	3	27	100	0	0	6.746071	39	60	1207	125	ENST00000286548.4	0.071429	0.899314
FRMD3	257019	__UNKNOWN__	__UNKNOWN__	9	85863318	85863318	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:85863318C>G	ENST00000304195.3	-	14	1515	c.1309G>C	c.(1309-1311)Gaa>Caa	p.E437Q	FRMD3_ENST00000376438.1_Missense_Mutation_p.E437Q|FRMD3_ENST00000465485.1_5'UTR|FRMD3_ENST00000328788.1_Missense_Mutation_p.E94Q|FRMD3_ENST00000376434.1_Missense_Mutation_p.E243Q	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	437		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						AAAGGTTCTTCTTTTATTTTA	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													107	105	106	NA		NA	NA	9		NA											NA				85863318		1905	4120	6025	SO:0001583	missense			AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159	257019			24125	protein-coding gene	gene with protein product		607619			NA	12601556	Standard	NM_174938	NM_174938	NA	Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.1309G>C	chr9.hg19:g.85863318C>G	ENSP00000303508:p.Glu437Gln	NA	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	hg19	CCDS43840.1	0.02	5.001429	CTTxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.64	2.594880	0.46318	.	.	ENSG00000172159	ENST00000376438;ENST00000376434;ENST00000328788;ENST00000304195	D;D;T;D	0.86956	-1.78;-2.19;0.75;-1.77	5.68	5.68	0.88126	.	0.153666	0.64402	D	0.000015	D	0.91106	0.7200	M	0.63843	1.955	0.45087	D	0.998107	B;B;D	0.53619	0.291;0.138;0.961	B;B;P	0.54590	0.067;0.022;0.756	D	0.91207	0.4996	10	0.62326	D	0.03	.	19.8666	0.96804	0.0:1.0:0.0:0.0	.	437;437;94	A2A2Y4;A2A2Y4-2;A2A2Y4-4	FRMD3_HUMAN;.;.	Q	437;243;94;437	ENSP00000365621:E437Q;ENSP00000365617:E243Q;ENSP00000328615:E94Q;ENSP00000303508:E437Q	ENSP00000303508:E437Q	E	-	1	0	FRMD3	85053138	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	3.764000	0.55264	2.707000	0.92482	0.650000	0.86243	GAA	NOVEL	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157355.1	2	10.827234	KEEP	0	0	0	36	1245	CC	0.999999	0.999993	0		-	39	60	1472	0	0	134.571232	72	60	2651	176	ENST00000304195.3	0.351351	0.999994
S1PR3	1903	__UNKNOWN__	__UNKNOWN__	9	91608734	91608734	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:91608734C>A	ENST00000358157.2	+	1	249				C9orf47_ENST00000375851.2_3'UTR|C9orf47_ENST00000334490.5_3'UTR	NM_005226.3	NP_005217.2	Q99500	S1PR3_HUMAN	sphingosine-1-phosphate receptor 3	NA		NA			adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|anatomical structure morphogenesis (GO:0009653)|cytokine production (GO:0001816)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of establishment of endothelial barrier (GO:1903141)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of interleukin-1 beta production (GO:0032651)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|skin(1)	34						GACAATAGGCCAGTTGGGTTA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF022139	CCDS6680.1	9q22.1-q22.2	2012-08-08	2008-04-30	2008-04-30	ENSG00000213694	ENSG00000213694	1903		GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate	3167	protein-coding gene	gene with protein product	sphingosine-1-phosphate receptor 3	601965	endothelial differentiation, sphingolipid G-protein-coupled receptor, 3	EDG3	NA	8878560, 9409733	Standard	NM_005226	NM_005226	NA	Approved	EDG-3	uc004aqe.4	Q99500	OTTHUMG00000020173	ENST00000358157.2:c.-148+2124C>A	chr9.hg19:g.91608734C>A		NA	Q5SQD8|Q7Z5I2	hg19	CCDS6680.1	0.02	4.534644	GGCxAGT	COVERED																																																																																			NOVEL	S1PR3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355971.1	1	29.487831	KEEP	0	0	0	98	3441	CC	1	1	0		+	22	60	766	1	0	61.439941	108	60	4024	281	ENST00000358157.2	0.169231	1
HIATL1	84641	__UNKNOWN__	__UNKNOWN__	9	97203312	97203312	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:97203312G>A	ENST00000375344.3	+	5	710	c.441G>A	c.(439-441)acG>acA	p.T147T	HIATL1_ENST00000428393.2_Silent_p.T82T	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	147		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				TCTCGGTCACGTTTTCTGTTA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(77;1260 1915 1973 10423)					NA		NA				0													136	129	131	NA		NA	NA	9		NA											NA				97203312		2203	4300	6503	SO:0001819	synonymous_variant			AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110	84641			23376	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032558	XM_005252277	NA	Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.441G>A	chr9.hg19:g.97203312G>A		NA	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	hg19	CCDS6710.2	0.02	6.847408	CACxTTT	COVERED																																																																																			NOVEL	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053184.1	3	30.096143	KEEP	0	0	0	100	3471	GG	1	1	0		+	22	60	801	0	0	62.054519	150	60	5465	372	ENST00000375344.3	0.127907	1
C9orf3	84909	__UNKNOWN__	__UNKNOWN__	9	97690814	97690814	__UNKNOWN__	Splice_Site	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:97690814G>T	ENST00000277198.2	+	7	1847		c.e7+1		C9orf3_ENST00000375315.2_Splice_Site|C9orf3_ENST00000297979.5_Intron|C9orf3_ENST00000473778.1_Splice_Site|C9orf3_ENST00000395357.2_Splice_Site	NM_001193331.2	NP_001180260.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	NA		NA			leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		AGGTGTTAAGGTAAAGCTGCA	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001630	splice_region_variant			AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120	84909			1361	protein-coding gene	gene with protein product	aminopeptidase O	NA			NA	15687497	Standard	NM_032823	NM_001193329	NA	Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000277198.2:c.1661+1G>T	chr9.hg19:g.97690814G>T		NA	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	hg19	CCDS55327.1	0.02	4.285702	AAGxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.12	2.141491	0.37825	.	.	ENSG00000148120	ENST00000277198;ENST00000375315;ENST00000428313;ENST00000395357	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.1628	0.93541	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C9orf3	96730635	1.000000	0.71417	1.000000	0.80357	0.109000	0.19521	7.684000	0.84104	2.837000	0.97791	0.655000	0.94253	.	NOVEL	C9orf3-004	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053199.1	3	33.937728	KEEP	0	1	35	125	4320	GG	1	1	0	Intron	+	47	60	1684	0	0	150.811234	100	60	3676	363	ENST00000277198.2	0.319728	1
NUTM2G	441457	__UNKNOWN__	__UNKNOWN__	9	99694397	99694397	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs199759392	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:99694397C>G	ENST00000372322.3	+	2	431	c.410C>G	c.(409-411)tCt>tGt	p.S137C	NUTM2G_ENST00000354649.3_Missense_Mutation_p.S137C|HIATL2_ENST00000506067.1_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	137		NA									NA						CCCGTTACCTCTGCCCAGGTG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	6	6	NA		NA	NA	9		NA											NA				99694397		1634	3695	5329	SO:0001583	missense				CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152	441457			23449	protein-coding gene	gene with protein product		NA	family with sequence similarity 22, member G	FAM22G	NA		Standard	NM_001170741	NM_001045477	NA	Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.410C>G	chr9.hg19:g.99694397C>G	ENSP00000361397:p.Ser137Cys	NA	A6NNI5|Q5VZR3	hg19	CCDS55329.1	0.02	-0.289512	CCTxTGC	UNCOVERED	.	.	.	.	.	.	.	.	.	.	.	10.57	1.388583	0.25118	.	.	ENSG00000188152	ENST00000354649;ENST00000372322;ENST00000417159;ENST00000375230	T;T	0.23552	1.9;1.9	1.03	1.03	0.20045	.	0.988350	0.08238	N	0.976439	T	0.19604	0.0471	N	0.22421	0.69	0.80722	P	0.0	P	0.36315	0.547	B	0.41036	0.346	T	0.35301	-0.9794	9	0.72032	D	0.01	.	5.4622	0.16624	0.0:1.0:0.0:0.0	.	137	Q5VZR2-2	.	C	137;137;137;18	ENSP00000346670:S137C;ENSP00000361397:S137C	ENSP00000346670:S137C	S	+	2	0	FAM22G	98734218	0.002000	0.14202	0.005000	0.12908	0.008000	0.06430	0.408000	0.21065	0.892000	0.36259	0.479000	0.44913	TCT	NOVEL	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053291.2	0	3.611554	KEEP	43	0	0	12	411	CC	0	0	0		+	14	27	524	0	0	49.310222	19	40	712	103	ENST00000372322.3	0.424242	0.760887
HIATL2	84278	__UNKNOWN__	__UNKNOWN__	9	99702566	99702566	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:99702566G>A	ENST00000506067.1	-	2	181							Q5VZR4	HIAL2_HUMAN	hippocampus abundant transcript-like 2	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)				NA						TGTGGCACTGGCTGTCTGGAA	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005058		9q22.33	2008-09-12	2008-09-12		ENSG00000196312	ENSG00000196312	84278			23672	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032318	NR_002894	NA	Approved	MGC12945	uc004aws.3	Q5VZR4	OTTHUMG00000020317	ENST00000506067.1:c.367+2318C>T	chr9.hg19:g.99702566G>A		NA	Q9BSG7	hg19		0.02	-0.438596	CTGxCTG	COVERED																																																																																			NOVEL	HIATL2-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000470418.1	4	6.012094	KEEP	2	0	0	20	686	GG	0.99986	0.959724	0		-	11	60	358	0	0	29.60879	39	60	1429	86	ENST00000506067.1	0.22	0.959859
HIATL2	84278	__UNKNOWN__	__UNKNOWN__	9	99711203	99711203	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:99711203C>T	ENST00000602917.1	-	4	609				HIATL2_ENST00000375223.4_Splice_Site|HIATL2_ENST00000506067.1_Intron			Q5VZR4	HIAL2_HUMAN	hippocampus abundant transcript-like 2	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)				NA						tcacgcctggctgattttcgt	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005058		9q22.33	2008-09-12	2008-09-12		ENSG00000196312	ENSG00000196312	84278			23672	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032318	NR_002894	NA	Approved	MGC12945	uc004aws.3	Q5VZR4	OTTHUMG00000020317	ENST00000602917.1:c.395+633G>A	chr9.hg19:g.99711203C>T		NA	Q9BSG7	hg19		0.02	-0.429882	TGGxTGA	COVERED																																																																																			NOVEL	HIATL2-001	PUTATIVE	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000053305.3	8	14.748086	KEEP	0	0	0	49	1765	CC	1	0.954491	0		-	8	60	285	0	0	22.847327	41	60	1544	127	ENST00000602917.1	0.163265	0.954491
ANKS6	203286	__UNKNOWN__	__UNKNOWN__	9	101552497	101552497	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:101552497G>T	ENST00000375019.2	-	2	282				ANKS6_ENST00000375018.1_Missense_Mutation_p.P251T|ANKS6_ENST00000540940.1_Missense_Mutation_p.P56T|ANKS6_ENST00000353234.4_Missense_Mutation_p.P251T|ANKS6_ENST00000471846.1_5'UTR			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	NA		NA				cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				AGGTGGTCAGGGTTGGCGCCC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													64	69	67	NA		NA	NA	9		NA											NA				101552497		2131	4234	6365	SO:0001627	intron_variant			AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138	203286		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	26724	protein-coding gene	gene with protein product		615370	sterile alpha motif domain containing 6, ankyrin repeat domain 14	SAMD6, ANKRD14	NA	23793029	Standard	NM_173551	XM_005251793	NA	Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000375019.2:c.41-5339C>A	chr9.hg19:g.101552497G>T		NA	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	hg19		0.02	4.2965	CAGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289321	0.40494	.	.	ENSG00000165138	ENST00000375018;ENST00000353234;ENST00000540940	T;T;T	0.66815	-0.23;-0.23;0.59	5.48	4.57	0.56435	Ankyrin repeat-containing domain (4);	0.103999	0.64402	D	0.000002	T	0.58609	0.2134	L	0.45051	1.395	0.45150	D	0.998168	P	0.41131	0.739	B	0.38985	0.287	T	0.56792	-0.7920	10	0.30078	T	0.28	-4.8463	14.1453	0.65347	0.0:0.1512:0.8488:0.0	.	251	Q68DC2	ANKS6_HUMAN	T	251;251;56	ENSP00000364158:P251T;ENSP00000297837:P251T;ENSP00000442189:P56T	ENSP00000297837:P251T	P	-	1	0	ANKS6	100592318	1.000000	0.71417	0.944000	0.38274	0.242000	0.25591	6.361000	0.73070	1.301000	0.44836	-0.304000	0.09214	CCT	NOVEL	ANKS6-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000053378.2	3	42.665556	KEEP	0	0	0	142	4711	GG	1	0.999999	0		-	27	60	951	0	0	79.979564	95	60	3323	349	ENST00000375019.2	0.221311	0.999999
ANKS6	203286	__UNKNOWN__	__UNKNOWN__	9	101552498	101552498	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:101552498G>T	ENST00000375019.2	-	2	282				ANKS6_ENST00000375018.1_Missense_Mutation_p.N250K|ANKS6_ENST00000540940.1_Missense_Mutation_p.N55K|ANKS6_ENST00000353234.4_Missense_Mutation_p.N250K|ANKS6_ENST00000471846.1_5'UTR			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	NA		NA				cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				GGTGGTCAGGGTTGGCGCCCT	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	68	67	NA		NA	NA	9		NA											NA				101552498		2130	4236	6366	SO:0001627	intron_variant			AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138	203286		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	26724	protein-coding gene	gene with protein product		615370	sterile alpha motif domain containing 6, ankyrin repeat domain 14	SAMD6, ANKRD14	NA	23793029	Standard	NM_173551	XM_005251793	NA	Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000375019.2:c.41-5340C>A	chr9.hg19:g.101552498G>T		NA	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	hg19		0.02	4.20558	AGGxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.45	2.539438	0.45176	.	.	ENSG00000165138	ENST00000375018;ENST00000353234;ENST00000540940	T;T;T	0.65178	0.48;0.48;-0.14	5.48	3.62	0.41486	Ankyrin repeat-containing domain (4);	0.248821	0.48767	D	0.000180	T	0.62332	0.2419	L	0.35414	1.06	0.40636	D	0.9819	D	0.63046	0.992	D	0.63283	0.913	T	0.61372	-0.7076	10	0.48119	T	0.1	-17.7065	5.801	0.18414	0.1698:0.1608:0.6694:0.0	.	250	Q68DC2	ANKS6_HUMAN	K	250;250;55	ENSP00000364158:N250K;ENSP00000297837:N250K;ENSP00000442189:N55K	ENSP00000297837:N250K	N	-	3	2	ANKS6	100592319	1.000000	0.71417	0.982000	0.44146	0.193000	0.23685	2.112000	0.41892	0.668000	0.31126	-0.258000	0.10820	AAC	NOVEL	ANKS6-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000053378.2	3	42.848203	KEEP	0	0	0	143	4788	GG	1	0.999999	0		-	27	60	938	0	0	78.790171	94	60	3344	350	ENST00000375019.2	0.22314	0.999999
GALNT12	79695	__UNKNOWN__	__UNKNOWN__	9	101594180	101594180	__UNKNOWN__	Silent	SNP	G	G	C	rs202039153		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:101594180G>C	ENST00000375011.3	+	4	858	c.858G>C	c.(856-858)acG>acC	p.T286T		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	286		NA			cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				TGGTGTTCACGTGGCACACAG	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	57	61	NA		NA	NA	9		NA											NA				101594180		2203	4300	6503	SO:0001819	synonymous_variant			AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	79695	2.4.1.41	Glycosyltransferase family 2 domain containing	19877	protein-coding gene	gene with protein product	polypeptide GalNAc transferase 12	610290	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)		NA	12135769	Standard	NM_024642	NM_024642	NA	Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.858G>C	chr9.hg19:g.101594180G>C		NA	Q5TCF7|Q8NG54|Q96CT9|Q9H771	hg19	CCDS6737.1	0.02	7.165906	CACxTGG	COVERED																																																																																			NOVEL	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053382.1	1	21.65365	KEEP	0	0	0	72	2466	GG	1	1	0		+	8	60	303	0	0	19.890951	173	60	6104	335	ENST00000375011.3	0.044199	1
BAAT	570	__UNKNOWN__	__UNKNOWN__	9	104124330	104124330	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:104124330T>C	ENST00000395051.3	-	0	1707				BAAT_ENST00000259407.2_3'UTR			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	NA		NA			acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	TGCTCTAATCTGATAAATTCT	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	570	2.3.1.65		932	protein-coding gene	gene with protein product	glycine N-choloyltransferase	602938	bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase), bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)		NA		Standard		NM_001701	NA	Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.*380A>G	chr9.hg19:g.104124330T>C		NA	Q3B7W9|Q96L31	hg19	CCDS6752.1	0.02	4.469805	ATCxGAT	COVERED																																																																																			NOVEL	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053433.1	1	7.218162	KEEP	0	0	0	24	735	TT	0.999909	0.999909	0		-	67	60	2333	0	0	227.443433	59	60	2198	177	ENST00000395051.3	0.531746	1
BAAT	570	__UNKNOWN__	__UNKNOWN__	9	104124376	104124376	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:104124376T>G	ENST00000395051.3	-	0	1661				BAAT_ENST00000259407.2_3'UTR			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	NA		NA			acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	TATTTGGTTTTATATCTGTTA	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	570	2.3.1.65		932	protein-coding gene	gene with protein product	glycine N-choloyltransferase	602938	bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase), bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)		NA		Standard		NM_001701	NA	Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.*334A>C	chr9.hg19:g.104124376T>G		NA	Q3B7W9|Q96L31	hg19	CCDS6752.1	0.02	5.045465	TTTxATA	COVERED																																																																																			NOVEL	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053433.1	2	6.920728	KEEP	0	0	0	23	716	TT	0.999892	0.999879	0		-	64	60	2484	0	0	248.0772	42	60	1458	157	ENST00000395051.3	0.603774	0.999987
OR13C2	392376	__UNKNOWN__	__UNKNOWN__	9	107367629	107367629	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs200685389	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:107367629G>A	ENST00000542196.1	-	1	322	c.280C>T	c.(280-282)Ctt>Ttt	p.L94F		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	94		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CAGCCAGAAAGGGAAATGGTC	0.522	NA	NA											G|||	66	0.0131789	0.0386	0.0014	5008	,	,	NA	22699	0.005	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0092	NA	NA	NA						NA		NA				0													93	91	91	NA		NA	NA	9		NA											NA				107367629		2202	4300	6502	SO:0001583	missense				CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119	392376		GPCR / Class A : Olfactory receptors	14701	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004481	NM_001004481	NA	Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.280C>T	chr9.hg19:g.107367629G>A	ENSP00000438815:p.Leu94Phe	NA	B9EGV8|Q6IF54	hg19	CCDS35092.1	0.02	15.267256	AAAxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.222118	0.00283	.	.	ENSG00000257019	ENST00000542196	T	0.00485	7.07	3.53	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	0.196320	0.24628	N	0.036909	T	0.00109	0.0003	N	0.00186	-1.895	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.39035	-0.9633	10	0.02654	T	1	.	6.7531	0.23497	0.8793:0.0:0.1207:0.0	.	94	Q8NGS9	O13C2_HUMAN	F	94	ENSP00000438815:L94F	ENSP00000438815:L94F	L	-	1	0	OR13C2	106407450	0.000000	0.05858	0.179000	0.23059	0.504000	0.33889	0.886000	0.28241	0.432000	0.26286	-0.672000	0.03802	CTT	NOVEL	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053489.2	5	9.801915	KEEP	125	2	67	56	1981	GG	1	1	0		-	16	47	596	2	0	38.452819	363	60	13299	692	ENST00000542196.1	0.042216	1
SLC44A1	23446	__UNKNOWN__	__UNKNOWN__	9	108154772	108154772	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:108154772G>A	ENST00000374720.3	+	0	5656				SLC44A1_ENST00000374724.1_Intron|SLC44A1_ENST00000343170.7_Intron|SLC44A1_ENST00000374723.1_3'UTR	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	NA		NA			choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	CTTGGTATCTGCCAAGGGCTT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214	23446		CD molecules, Solute carriers	18798	protein-coding gene	gene with protein product		606105	CDW92 antigen	CDW92	NA	11698453, 10677542	Standard	NM_080546	NM_080546	NA	Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.*3435G>A	chr9.hg19:g.108154772G>A		NA	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	hg19	CCDS6763.1	0.02	1.982625	TCTxCCA	COVERED																																																																																			NOVEL	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053500.1	2	4.213943	KEEP	0	0	0	14	511	GG	0.995343	0.991593	0		+	7	60	260	0	0	19.50463	62	60	2371	110	ENST00000374720.3	0.101449	0.996233
FSD1L	83856	__UNKNOWN__	__UNKNOWN__	9	108313234	108313234	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:108313234G>A	ENST00000374707.1	+	0	5582				FSD1L_ENST00000374710.3_3'UTR			Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing 1-like	NA		NA								NS(1)|endometrium(1)	2						TTCACAGTATGTAGAGCAGAA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF316830	CCDS6765.2, CCDS47999.1, CCDS6765.3, CCDS75870.1	9q31	2013-02-11	2006-03-10	2006-03-10	ENSG00000106701	ENSG00000106701	83856		Fibronectin type III domain containing	13753	protein-coding gene	gene with protein product		609829	cystatin and DUF19 domain containing 1, coiled-coil domain containing 10	CSDUFD1, CCDC10, FSD1NL, FSD1CL	NA	11267680	Standard	NM_207647	XM_005252254	NA	Approved		uc004bcq.2	Q9BXM9	OTTHUMG00000020426	ENST00000374707.1:c.*4470G>A	chr9.hg19:g.108313234G>A		NA	A2A338|A6NKH7|B7Z5S6|B7Z5W3|Q5T879|Q5T880	hg19		0.02	9.061936	TATxTAG	COVERED																																																																																			NOVEL	FSD1L-001	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000053511.1	5	10.233798	KEEP	0	0	0	34	1242	GG	0.999998	0.999998	0		+	18	60	673	0	0	49.495977	185	60	6975	286	ENST00000374707.1	0.08867	1
TNC	3371	__UNKNOWN__	__UNKNOWN__	9	117786439	117786439	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:117786439C>A	ENST00000341037.4	-	24	5914				TNC_ENST00000350763.4_Intron|TNC_ENST00000542877.1_Intron|TNC_ENST00000423613.2_Intron|TNC_ENST00000535648.1_Intron|TNC_ENST00000340094.3_Intron|TNC_ENST00000537320.1_Intron|TNC_ENST00000345230.3_Intron|TNC_ENST00000346706.3_Intron			P24821	TENA_HUMAN	tenascin C	NA		NA			bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						AAAATATGGACCTGAGAAATC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													83	80	81	NA		NA	NA	9		NA											NA				117786439		2203	4300	6503	SO:0001627	intron_variant				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982	3371		Fibrinogen C domain containing, Fibronectin type III domain containing	5318	protein-coding gene	gene with protein product	hexabrachion (tenascin)	187380	hexabrachion (tenascin C, cytotactin), deafness, autosomal dominant 56	HXB, DFNA56	NA	1704365, 1707164, 23936043	Standard	NM_002160	NM_002160	NA	Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000341037.4:c.5786-24G>T	chr9.hg19:g.117786439C>A		NA	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	hg19		0.02	3.991709	GGAxCTG	COVERED																																																																																			NOVEL	TNC-011	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000397659.2	1	7.824993	KEEP	0	0	0	26	892	CC	0.999957	0.999957	0		-	27	60	943	0	0	77.847951	108	60	3831	180	ENST00000341037.4	0.2	1
ASTN2	23245	__UNKNOWN__	__UNKNOWN__	9	119373879	119373879	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:119373879G>T	ENST00000361209.2	-	18	3334				ASTN2_ENST00000361477.3_Intron|ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000288520.5_Intron|ASTN2_ENST00000373996.3_Intron|ASTN2_ENST00000341734.4_Intron|ASTN2_ENST00000358637.4_3'UTR	NM_014010.4	NP_054729.3	O75129	ASTN2_HUMAN	astrotactin 2	NA		NA			negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						gatttcaaaagaatagtaacg	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219	23245			17021	protein-coding gene	gene with protein product		612856			NA	9734811	Standard	NM_014010	NM_014010	NA	Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000361209.2:c.3202+6723C>A	chr9.hg19:g.119373879G>T		NA	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	hg19	CCDS6815.1	0.02	4.270096	AAAxAAT	COVERED																																																																																			NOVEL	ASTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055428.2	5	8.124854	KEEP	0	0	0	27	953	GG	0.999988	0.999987	0		-	28	60	1020	0	0	86.374718	98	60	3740	177	ENST00000361209.2	0.222222	1
DAB2IP	153090	__UNKNOWN__	__UNKNOWN__	9	124536556	124536556	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:124536556C>T	ENST00000309989.1	+	11	2760	c.2613C>T	c.(2611-2613)agC>agT	p.S871S	DAB2IP_ENST00000259371.2_Silent_p.S967S|DAB2IP_ENST00000408936.3_Silent_p.S995S	NM_138709.1	NP_619723.1	Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	995	Necessary for interaction with AKT1.	NA			activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CACCTGTGAGCCCCAATGCCC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	41	43	NA		NA	NA	9		NA											NA				124536556		2203	4300	6503	SO:0001819	synonymous_variant			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848	153090			17294	protein-coding gene	gene with protein product	nGAP-like protein, DOC-2/DAB2 interactive protein, ASK-interacting protein, ASK1-interacting protein 1	609205			NA	11944990, 11812785	Standard	NM_032552	XM_005251721	NA	Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000309989.1:c.2613C>T	chr9.hg19:g.124536556C>T		NA	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	hg19	CCDS6832.1	0.02	3.858091	GAGxCCC	COVERED																																																																																			NOVEL	DAB2IP-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053898.1	3	21.970919	KEEP	0	0	0	73	2583	CC	1	1	0		+	12	60	419	0	0	29.890913	127	60	4631	280	ENST00000309989.1	0.086331	1
GOLGA1	2800	__UNKNOWN__	__UNKNOWN__	9	127693701	127693701	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:127693701C>G	ENST00000373555.4	-	4	469					NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	NA		NA			protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						GAGGTAGACACAAGGAAGGTC	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	78	80	NA		NA	NA	9		NA											NA				127693701		2203	4300	6503	SO:0001627	intron_variant			U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935	2800			4424	protein-coding gene	gene with protein product		602502	golgi autoantigen, golgin subfamily a, 1		NA	9324025	Standard	NM_002077	NM_002077	NA	Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.136-16G>C	chr9.hg19:g.127693701C>G		NA	Q5T164|Q8IYZ9	hg19	CCDS6860.1	0.02	2.26996	ACAxAAG	COVERED																																																																																			NOVEL	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054049.1	0	9.932567	KEEP	0	0	0	33	1189	CC	0.999998	0.986152	0		-	10	60	379	0	0	31.011272	49	60	1892	117	ENST00000373555.4	0.169492	0.986153
SCAI	286205	__UNKNOWN__	__UNKNOWN__	9	127734078	127734078	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:127734078G>T	ENST00000336505.6	-	16	1503	c.1445C>A	c.(1444-1446)cCt>cAt	p.P482H	SCAI_ENST00000373549.4_Missense_Mutation_p.P505H	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	482		NA			negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						GGCCATTAGAGGATTGTTCAA	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													106	94	98	NA		NA	NA	9		NA											NA				127734078		1839	4092	5931	SO:0001583	missense			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611	286205			26709	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 126	C9orf126	NA		Standard	NM_173690	NM_173690	NA	Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.1445C>A	chr9.hg19:g.127734078G>T	ENSP00000336756:p.Pro482His	NA	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	hg19	CCDS48017.1	0.02	4.564367	AGAxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	22.2	4.261084	0.80246	.	.	ENSG00000173611	ENST00000336505;ENST00000373549	T;T	0.67171	-0.25;-0.22	5.1	5.1	0.69264	.	0.050618	0.85682	D	0.000000	D	0.84460	0.5477	M	0.87682	2.9	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.87279	0.2291	10	0.87932	D	0	-12.0668	17.8998	0.88900	0.0:0.0:1.0:0.0	.	482;505	Q8N9R8;Q8N9R8-2	SCAI_HUMAN;.	H	482;505	ENSP00000336756:P482H;ENSP00000362650:P505H	ENSP00000336756:P482H	P	-	2	0	SCAI	126773899	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.920000	0.92779	2.543000	0.85770	0.655000	0.94253	CCT	NOVEL	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054055.3	1	13.481506	KEEP	0	0	0	45	1576	GG	1	1	0		-	27	60	1001	0	0	83.45506	110	60	4065	232	ENST00000336505.6	0.19708	1
DNM1	1759	__UNKNOWN__	__UNKNOWN__	9	131001724	131001724	__UNKNOWN__	Splice_Site	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:131001724G>T	ENST00000372923.3	+	12	1515	c.1423G>T	c.(1423-1425)Gtc>Ttc	p.V475F	DNM1_ENST00000486160.1_Splice_Site_p.V475F|DNM1_ENST00000341179.7_Splice_Site_p.V475F|DNM1_ENST00000393594.3_Splice_Site_p.V475F|DNM1_ENST00000475805.1_Splice_Site_p.V475F	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	475		NA			endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						ATCCTTGAAGGTCATGCTTCT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(113;146 1575 2722 28670 29921)					NA		NA				0													378	380	380	NA		NA	NA	9		NA											NA				131001724		2203	4300	6503	SO:0001630	splice_region_variant			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976	1759		Pleckstrin homology (PH) domain containing	2972	protein-coding gene	gene with protein product		602377		DNM	NA	2144893, 9143509	Standard	NM_004408	XM_005251763	NA	Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.1423-1G>T	chr9.hg19:g.131001724G>T		NA	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	hg19	CCDS6895.1	0.02	11.7102	AAGxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.8	4.204106	0.79127	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393589;ENST00000393594;ENST00000486160;ENST00000543158	T;T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29;-1.29	4.54	4.54	0.55810	Dynamin central domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.91446	0.7300	M	0.91920	3.255	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;P;D	0.68483	0.958;0.905;0.948	D	0.93275	0.6655	9	.	.	.	-8.2808	17.8257	0.88665	0.0:0.0:1.0:0.0	.	475;475;475	Q05193;Q05193-3;Q05193-2	DYN1_HUMAN;.;.	F	475;475;475;470;475;475;20	ENSP00000419225:V475F;ENSP00000345680:V475F;ENSP00000362014:V475F;ENSP00000377219:V475F;ENSP00000420045:V475F	.	V	+	1	0	DNM1	130041545	1.000000	0.71417	1.000000	0.80357	0.532000	0.34746	4.154000	0.58125	2.503000	0.84419	0.563000	0.77884	GTC	NOVEL	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054367.1	5	23.475738	KEEP	0	0	0	78	2731	GG	1	1	0	Missense_Mutation	+	83	60	2961	0	0	265.996934	171	60	6189	447	ENST00000372923.3	0.326772	1
ODF2	4957	__UNKNOWN__	__UNKNOWN__	9	131221857	131221857	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:131221857G>A	ENST00000434106.3	+	3	407	c.44G>A	c.(43-45)tGt>tAt	p.C15Y	ODF2_ENST00000372814.3_Missense_Mutation_p.C59Y|ODF2_ENST00000393533.2_Missense_Mutation_p.C15Y|ODF2_ENST00000604420.1_Missense_Mutation_p.C15Y|ODF2_ENST00000546203.1_Missense_Mutation_p.C15Y|ODF2_ENST00000393527.3_5'UTR|ODF2_ENST00000535026.1_5'UTR|ODF2_ENST00000351030.3_5'UTR|ODF2_ENST00000448249.3_5'UTR|ODF2_ENST00000372791.3_Missense_Mutation_p.C15Y	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	15		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						TTTCCATCGTGTGGGAAGAAC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													132	107	115	NA		NA	NA	9		NA											NA				131221857		2203	4300	6503	SO:0001583	missense			AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811	4957			8114	protein-coding gene	gene with protein product	cancer/testis antigen 134	602015	outer dense fibre of sperm tails 2		NA	9045620, 10072582	Standard		NM_153435	NA	Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.44G>A	chr9.hg19:g.131221857G>A	ENSP00000403453:p.Cys15Tyr	NA	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	hg19	CCDS56588.1	0.02	1.863162	CGTxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.0	4.079671	0.76528	.	.	ENSG00000136811	ENST00000393533;ENST00000372814;ENST00000372796;ENST00000434106;ENST00000546203;ENST00000446274;ENST00000432065;ENST00000372791	T;T;T;T;T;T	0.66280	0.82;0.55;1.32;1.32;-0.14;-0.2	5.65	5.65	0.86999	.	0.288132	0.38164	N	0.001789	T	0.67439	0.2893	N	0.24115	0.695	0.80722	D	1	D;D;D;D;D	0.60575	0.988;0.988;0.988;0.988;0.988	D;D;D;D;D	0.74348	0.983;0.983;0.983;0.983;0.983	T	0.67964	-0.5534	10	0.52906	T	0.07	-8.6859	15.093	0.72211	0.0:0.0:1.0:0.0	.	15;15;59;15;15	Q5BJF6-8;B4DX73;Q5BJF6-7;Q5BJF6-5;Q5BJF6	.;.;.;.;ODFP2_HUMAN	Y	15;59;15;15;15;15;15;15	ENSP00000377166:C15Y;ENSP00000361901:C59Y;ENSP00000361882:C15Y;ENSP00000403453:C15Y;ENSP00000437579:C15Y;ENSP00000361877:C15Y	ENSP00000361877:C15Y	C	+	2	0	ODF2	130261678	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.852000	0.48310	2.941000	0.99782	0.655000	0.94253	TGT	NOVEL	ODF2-011	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054449.3	0	7.223611	KEEP	0	0	0	24	867	GG	0.999909	0.999817	0		+	5	60	188	0	0	12.704442	89	60	3307	148	ENST00000434106.3	0.053191	0.999907
ZER1	10444	__UNKNOWN__	__UNKNOWN__	9	131492888	131492888	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:131492888C>A	ENST00000291900.2	-	0	3435				RP11-545E17.3_ENST00000443631.1_RNA	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	NA		NA			protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TTTCCACAGCCTGGGACCTGG	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445	10444		ZYG11 cell cycle regulator family	30960	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 60, zyg-11 homolog B (C. elegans)-like, zer-1 homolog (C. elegans)	C9orf60, ZYG11BL	NA	11719588	Standard	NM_006336	NM_006336	NA	Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.*728G>T	chr9.hg19:g.131492888C>A		NA	O00156|Q5T272|Q5T273	hg19	CCDS6910.1	0.02	4.405125	AGCxTGG	COVERED																																																																																			NOVEL	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054491.1	3	12.337262	KEEP	0	0	0	41	1385	CC	1	0.999999	0		-	15	60	562	0	0	43.724304	105	60	3805	190	ENST00000291900.2	0.125	0.999999
TOR1A	1861	__UNKNOWN__	__UNKNOWN__	9	132575466	132575466	__UNKNOWN__	3'UTR	SNP	C	C	G	rs147959623	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:132575466C>G	ENST00000351698.4	-	0	1832					NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	NA		NA			ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				TTTTGCAAAACGGAGTGACTG	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827	1861			3098	protein-coding gene	gene with protein product		605204	dystonia 1, torsion (autosomal dominant; torsin A)	DYT1	NA	10644435	Standard	NM_000113	NM_000113	NA	Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.*785G>C	chr9.hg19:g.132575466C>G		NA	B2RB58|Q53Y64|Q96CA0	hg19	CCDS6930.1	0.02	2.124203	AAAxGGA	COVERED																																																																																			NOVEL	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054611.1	1	6.318302	KEEP	0	0	0	21	701	CC	0.999869	0.999595	0		-	31	60	1155	0	0	105.683781	56	60	2006	127	ENST00000351698.4	0.356322	0.999726
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	133072374	133072374	__UNKNOWN__	IGR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:133072374C>A			NA	NA				NCS1 (72791 upstream) : HMCN2 (187461 downstream)						NA		NA									NA						CTCCCCTGCCCATTCCCCTTT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	43	41	NA		NA	NA	9		NA											NA				133072374		2052	4177	6229	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.133072374C>A		NA		hg19		0.02	4.853985	GCCxATT	COVERED																																																																																			NOVEL					0			1	10.531696	KEEP	0	0	0	35	1248	CC	0.999999	0.999983	0			33	60	1184	0	0	105.749873	72	60	2681	173		0.314286	0.999984
SETX	23064	__UNKNOWN__	__UNKNOWN__	9	135224644	135224644	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:135224644G>A	ENST00000224140.5	-	3	354	c.172C>T	c.(172-174)Cat>Tat	p.H58Y	SETX_ENST00000372169.2_Missense_Mutation_p.H58Y|SETX_ENST00000393220.1_Missense_Mutation_p.H58Y	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	58		NA			cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TTTACCTCATGCAAGAATGGC	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	82	84	NA		NA	NA	9		NA											NA				135224644		2203	4300	6503	SO:0001583	missense			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290	23064			445	protein-coding gene	gene with protein product		608465	amyotrophic lateral sclerosis 4, spinocerebellar ataxia, recessive, non-Friedreich type 1	ALS4, SCAR1	NA	9497266, 11022012	Standard	NM_015046	NM_015046	NA	Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.172C>T	chr9.hg19:g.135224644G>A	ENSP00000224140:p.His58Tyr	NA	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	hg19	CCDS6947.1	0.02	2.196497	CATxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969794	0.74246	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.83591	-1.74;-1.74;-1.74	5.41	5.41	0.78517	.	0.066547	0.64402	D	0.000017	D	0.87394	0.6166	L	0.32530	0.975	0.38599	D	0.950619	D	0.76494	0.999	D	0.83275	0.996	D	0.89600	0.3834	10	0.87932	D	0	.	18.1834	0.89786	0.0:0.0:1.0:0.0	.	58	Q7Z333	SETX_HUMAN	Y	58	ENSP00000224140:H58Y;ENSP00000361242:H58Y;ENSP00000376913:H58Y	ENSP00000224140:H58Y	H	-	1	0	SETX	134214465	1.000000	0.71417	0.998000	0.56505	0.680000	0.39746	7.141000	0.77330	2.530000	0.85305	0.591000	0.81541	CAT	NOVEL	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054774.3	0	3.611644	KEEP	0	0	0	12	432	GG	0.993634	0.975704	0		-	19	60	672	0	0	60.686627	37	60	1390	76	ENST00000224140.5	0.339286	0.981955
C9orf171	389799	__UNKNOWN__	__UNKNOWN__	9	135448029	135448029	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:135448029T>C	ENST00000343036.2	+	0	1143				C9orf171_ENST00000393216.2_3'UTR	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	NA		NA								large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						CAGATTCAAGTCTTAGGCTAA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523	389799			33776	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207417	NM_207417	NA	Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.*132T>C	chr9.hg19:g.135448029T>C		NA	Q147X1	hg19	CCDS6949.1	0.02	17.321652	AAGxCTT	COVERED																																																																																			NOVEL	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254589.1	4	22.26922	KEEP	0	0	0	74	2401	TT	1	1	0		+	145	60	5158	0	0	471.551533	253	60	9032	592	ENST00000343036.2	0.364322	1
CEL	1056	__UNKNOWN__	__UNKNOWN__	9	135937412	135937412	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:135937412T>G	ENST00000372080.4	+	1	48	c.32T>G	c.(31-33)gTg>gGg	p.V11G	CEL_ENST00000351304.7_Missense_Mutation_p.V8G	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	8		NA			cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CAACTGGTTGTGTTGGGCCTC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	9	8	NA		NA	NA	9		NA											NA				135937412		1654	3740	5394	SO:0001583	missense			M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	1056	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	bile salt-stimulated lipase	114840			NA	1676983	Standard		NM_001807	NA	Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.32T>G	chr9.hg19:g.135937412T>G	ENSP00000361151:p.Val11Gly	NA	Q16398|Q5T7U7|Q9UCH1|Q9UP41	hg19	CCDS43896.1	0.02	4.484278	TTGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	13.96	2.392253	0.42410	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.69175	-0.38;-0.38	5.04	3.86	0.44501	Carboxylesterase, type B (1);	0.753253	0.12676	N	0.448361	T	0.52757	0.1754	L	0.27053	0.805	0.25972	N	0.982489	B	0.13145	0.007	B	0.14578	0.011	T	0.45556	-0.9253	10	0.48119	T	0.1	.	9.2508	0.37554	0.0:0.0:0.3544:0.6456	.	8	P19835	CEL_HUMAN	G	11;8;11	ENSP00000361151:V11G;ENSP00000342217:V8G	ENSP00000304021:V11G	V	+	2	0	CEL	134927233	0.048000	0.20356	0.181000	0.23098	0.347000	0.29111	1.903000	0.39858	0.736000	0.32559	0.402000	0.26972	GTG	NOVEL	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054823.1	2	11.12643	KEEP	6	0	0	37	1107	TT	0.999998	0.999993	0		+	26	49	869	0	0	72.840729	87	50	3126	195	ENST00000372080.4	0.230088	0.999995
RXRA	6256	__UNKNOWN__	__UNKNOWN__	9	137328445	137328445	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:137328445G>A	ENST00000481739.1	+	10	1426	c.1374G>A	c.(1372-1374)ccG>ccA	p.P458P	RXRA_ENST00000356384.4_3'UTR|RXRA_ENST00000540193.1_Silent_p.P361P	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	458	Ligand-binding.	NA			camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	TGGAGGCGCCGCACCAAATGA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													88	79	82	NA		NA	NA	9		NA											NA				137328445		2203	4300	6503	SO:0001819	synonymous_variant			X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350	6256		Nuclear hormone receptors	10477	protein-coding gene	gene with protein product	nuclear receptor subfamily 2 group B member 1	180245			NA	2159111	Standard	NM_002957	XM_005263409	NA	Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.1374G>A	chr9.hg19:g.137328445G>A		NA	B3KY83|Q2NL52|Q2V504	hg19	CCDS35172.1	0.02	14.456675	GCCxCAC	COVERED																																																																																			NOVEL	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054949.1	4	56.87501	KEEP	0	0	0	189	6504	GG	1	1	0		+	115	60	4032	0	0	365.964788	212	60	7445	683	ENST00000481739.1	0.351682	1
NSMF	26012	__UNKNOWN__	__UNKNOWN__	9	140348325	140348325	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:140348325T>C	ENST00000371472.2	-	7	1026				NSMF_ENST00000371482.1_Intron|NSMF_ENST00000392812.4_Intron|NSMF_ENST00000541195.1_Intron|NSMF_ENST00000339554.3_Intron|NSMF_ENST00000371468.1_Intron|NSMF_ENST00000371473.3_Intron|NSMF_ENST00000371474.3_Intron|NSMF_ENST00000265663.7_Intron|NSMF_ENST00000371475.3_Intron|NSMF_ENST00000484316.1_Intron|NSMF_ENST00000437259.1_Intron			Q6X4W1	NSMF_HUMAN	NMDA receptor synaptonuclear signaling and neuronal migration factor	NA		NA			cellular response to amino acid stimulus (GO:0071230)|cellular response to electrical stimulus (GO:0071257)|cellular response to gonadotropin stimulus (GO:0071371)|positive regulation of neuron migration (GO:2001224)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of dendrite morphogenesis (GO:0048814)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuronal synaptic plasticity (GO:0048168)	apical dendrite (GO:0097440)|cell junction (GO:0030054)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuron projection (GO:0043005)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium-dependent protein binding (GO:0048306)				NA						GCCTCGGGAGTCTCAGACCCC	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													4	5	5	NA		NA	NA	9		NA											NA				140348325		655	1520	2175	SO:0001627	intron_variant				CCDS7044.1, CCDS48067.1, CCDS48068.1, CCDS48069.1, CCDS55357.1	9q34.3	2013-01-14	2013-01-14	2013-01-14	ENSG00000165802	ENSG00000165802	26012			29843	protein-coding gene	gene with protein product		608137	nasal embryonic LHRH factor	NELF	NA	11230166, 10898796	Standard	NM_015537	NM_015537	NA	Approved		uc004cna.3	Q6X4W1	OTTHUMG00000020989	ENST00000371472.2:c.827-53A>G	chr9.hg19:g.140348325T>C		NA	Q2TB96|Q6X4V7|Q6X4V8|Q6X4V9|Q8N2M2|Q96SY1|Q9NPM4|Q9NPP3|Q9NPS3	hg19	CCDS7044.1	0.02	2.198112	GAGxCTC	COVERED																																																																																			NOVEL	NSMF-002	PUTATIVE	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055331.2	2	12.329932	KEEP	0	0	0	41	1257	TT	1	0.979526	0		-	7	60	197	0	0	14.043897	49	60	1637	127	ENST00000371472.2	0.125	0.979526
DPH7	92715	__UNKNOWN__	__UNKNOWN__	9	140459602	140459602	__UNKNOWN__	Silent	SNP	G	G	A	rs373555595		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:140459602G>A	ENST00000277540.2	-	6	802	c.645C>T	c.(643-645)ggC>ggT	p.G215G	DPH7_ENST00000479650.1_5'UTR	NM_138778.2	NP_620133.1	Q9BTV6	DPH7_HUMAN	diphthamide biosynthesis 7	215		NA			peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)						NA						GGCCATCGTCGCCCCCTGTGT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0										0,4406		0,0,2203	69	72	71	NA	645	-8.1	0.8	9		71	1,8599		0,1,4299	no	coding-synonymous	WDR85	NM_138778.2		0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077		215/453	140459602	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			AK075115	CCDS7047.1	9q34.3	2013-06-20	2013-06-20	2013-06-20	ENSG00000148399	ENSG00000148399	92715		WD repeat domain containing	25199	protein-coding gene	gene with protein product		613210	chromosome 9 open reading frame 112, WD repeat domain 85	C9orf112, WDR85	NA	23486472	Standard	NM_138778	NM_138778	NA	Approved	FLJ90634, RRT2	uc004cnk.1	Q9BTV6	OTTHUMG00000020991	ENST00000277540.2:c.645C>T	chr9.hg19:g.140459602G>A		NA	Q96AB7	hg19	CCDS7047.1	0.02	3.979634	GTCxCCC	COVERED																																																																																			NOVEL	DPH7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055350.1	1	9.929368	KEEP	0	0	0	33	1144	GG	0.999998	0.999997	0		-	6	60	205	0	0	12.914691	119	60	4276	205	ENST00000277540.2	0.048	0.999999
ZMYND19	116225	__UNKNOWN__	__UNKNOWN__	9	140477176	140477176	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr9:140477176T>C	ENST00000298585.2	-	6	767					NM_138462.2	NP_612471.1	Q96E35	ZMY19_HUMAN	zinc finger, MYND-type containing 19	NA		NA				cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|synapse (GO:0045202)	metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	13	all_cancers(76;0.106)			OV - Ovarian serous cystadenocarcinoma(145;0.000275)|Epithelial(140;0.00047)		CCATCATGCCTGGGACGCAGT	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													20	21	21	NA		NA	NA	9		NA											NA				140477176		2203	4298	6501	SO:0001627	intron_variant			BC012948	CCDS7048.1	9q34.3	2008-02-05			ENSG00000165724	ENSG00000165724	116225		Zinc fingers, MYND-type	21146	protein-coding gene	gene with protein product		611424			NA		Standard	NM_138462	NM_138462	NA	Approved	MIZIP	uc004cno.1	Q96E35	OTTHUMG00000020992	ENST00000298585.2:c.541-38A>G	chr9.hg19:g.140477176T>C		NA	Q5T366	hg19	CCDS7048.1	0.02	1.937161	GCCxGGG	COVERED																																																																																			NOVEL	ZMYND19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055356.1	0	12.034567	KEEP	0	0	0	40	1241	TT	1	0.99994	0		-	21	60	735	0	0	61.520129	76	60	2805	172	ENST00000298585.2	0.216495	0.99994
PFKP	5214	__UNKNOWN__	__UNKNOWN__	10	3162113	3162113	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:3162113C>T	ENST00000381125.4	+	16	1636	c.1560C>T	c.(1558-1560)gcC>gcT	p.A520A	PFKP_ENST00000381075.2_Silent_p.A512A	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	520	C-terminal regulatory PFK domain 2.	NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)	p.A520A(1)|p.A512A(1)		breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		AGCTGTCAGCCGCCCGGGAGA	0.622	NA	NA									OREG0019976	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - coding silent(2)	lung(2)											86	72	77	NA		NA	NA	10		NA											NA				3162113		2203	4300	6503	SO:0001819	synonymous_variant			AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	5214	2.7.1.11		8878	protein-coding gene	gene with protein product	Phosphofructokinase, platelet type	171840			NA		Standard	NM_002627	NM_002627	NA	Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1560C>T	chr10.hg19:g.3162113C>T		609	B3KS15|Q5VSR7|Q5VSR8	hg19	CCDS7059.1	0.02	7.271412	AGCxGCC	COVERED																																																																																			NOVEL	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046454.1	1	15.949946	KEEP	0	0	0	53	1771	CC	1	1	0		+	20	60	747	1	0	56.400024	172	60	5990	296	ENST00000381125.4	0.104167	1
PFKP	5214	__UNKNOWN__	__UNKNOWN__	10	3177936	3177936	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:3177936T>A	ENST00000381125.4	+	21	2207	c.2131T>A	c.(2131-2133)Ttt>Att	p.F711I	PFKP_ENST00000381075.2_Missense_Mutation_p.F703I|PFKP_ENST00000381072.1_Missense_Mutation_p.F129I	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	711	C-terminal regulatory PFK domain 2.	NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		AGGAAAAAAATTTACCACCGA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													52	55	54	NA		NA	NA	10		NA											NA				3177936		2203	4300	6503	SO:0001583	missense			AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	5214	2.7.1.11		8878	protein-coding gene	gene with protein product	Phosphofructokinase, platelet type	171840			NA		Standard	NM_002627	NM_002627	NA	Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.2131T>A	chr10.hg19:g.3177936T>A	ENSP00000370517:p.Phe711Ile	NA	B3KS15|Q5VSR7|Q5VSR8	hg19	CCDS7059.1	0.02	8.957486	AAAxTTA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	13.56|13.56	2.272864|2.272864	0.40194|0.40194	.|.	.|.	ENSG00000067057|ENSG00000067057	ENST00000381125;ENST00000397834;ENST00000381075;ENST00000381072|ENST00000433193	T;T;T|.	0.80033|.	-1.32;-1.33;-1.01|.	5.21|5.21	4.05|4.05	0.47172|0.47172	Phosphofructokinase domain (1);|.	0.051743|.	0.85682|.	D|.	0.000000|.	T|T	0.56514|0.56514	0.1990|0.1990	L|L	0.55990|0.55990	1.75|1.75	0.33517|0.33517	D|D	0.591855|0.591855	D;D;D|.	0.89917|.	0.957;0.957;1.0|.	B;B;D|.	0.83275|.	0.438;0.438;0.996|.	T|T	0.65117|0.65117	-0.6246|-0.6246	10|5	0.37606|.	T|.	0.19|.	.|.	12.1349|12.1349	0.53966|0.53966	0.0:0.0:0.1434:0.8566|0.0:0.0:0.1434:0.8566	.|.	703;703;711|.	B3KS15;Q5VSR7;Q01813|.	.;.;K6PP_HUMAN|.	I|K	711;700;703;129|63	ENSP00000370517:F711I;ENSP00000370465:F703I;ENSP00000370462:F129I|.	ENSP00000370462:F129I|.	F|N	+|+	1|3	0|2	PFKP|PFKP	3167936|3167936	1.000000|1.000000	0.71417|0.71417	0.002000|0.002000	0.10522|0.10522	0.018000|0.018000	0.09664|0.09664	6.836000|6.836000	0.75349|0.75349	0.785000|0.785000	0.33685|0.33685	0.460000|0.460000	0.39030|0.39030	TTT|AAT	NOVEL	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046454.1	5	24.955154	KEEP	0	0	0	83	2545	TT	1	1	0		+	46	60	1695	0	0	139.622956	204	60	7376	418	ENST00000381125.4	0.184	1
AKR1C2	1646	__UNKNOWN__	__UNKNOWN__	10	5030956	5030956	__UNKNOWN__	3'UTR	SNP	A	A	G	rs11252868	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:5030956A>G	ENST00000380753.4	-	0	2391					NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	NA		NA			cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	GATCATTAAGACATGAGATTA	0.343	NA	NA											a|||	971	0.19389	0.2156	0.2017	5008	,	,	NA	17414	0.0268	NA	0.3052	False	NA	,,,	NA	NA	NA	2504	0.2168	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1646	1.3.1.20, 1.1.1.213	Aldo-keto reductases	385	protein-coding gene	gene with protein product	dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III	600450	aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III), testicular 17,20-desmolase deficiency	DDH2, TDD	NA	9716498, 21802064	Standard	NM_001354	NM_001354	NA	Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.*1232T>C	chr10.hg19:g.5030956A>G		NA	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	hg19	CCDS7062.1	0.02	15.649196	AAGxCAT	COVERED																																																																																			NOVEL	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046531.1	2	7.791282	KEEP	2	2	69	50	1554	AA	1	1	0		-	12	40	440	0	0	27.129116	332	60	11868	492	ENST00000380753.4	0.034884	1
USP6NL	9712	__UNKNOWN__	__UNKNOWN__	10	11505640	11505640	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:11505640C>T	ENST00000609104.1	-	15	1681	c.1287G>A	c.(1285-1287)caG>caA	p.Q429Q	USP6NL_ENST00000277575.5_Silent_p.Q446Q|USP6NL_ENST00000379237.2_Silent_p.Q452Q	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	429		NA			Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						GTCTTGGCGGCTGTGCTCTCT	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	63	63	NA		NA	NA	10		NA											NA				11505640		1917	4111	6028	SO:0001819	synonymous_variant			BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429	9712			16858	protein-coding gene	gene with protein product	related to the N terminus of tre	605405	USP6NL intronic transcript 1 (non-protein coding)	USP6NL-IT1	NA	8700515, 8700527, 12399475	Standard	NM_014688	XR_247492	NA	Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1287G>A	chr10.hg19:g.11505640C>T		NA	A8KA79|Q15400|Q5VV10|Q7L0K9	hg19	CCDS53492.1	0.02	17.467679	CGGxTGT	COVERED																																																																																			NOVEL	USP6NL-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046764.3	5	46.381995	KEEP	0	1	16	160	5614	CC	1	1	0		-	38	60	1327	0	0	96.222652	364	60	13580	715	ENST00000609104.1	0.094527	1
CAMK1D	57118	__UNKNOWN__	__UNKNOWN__	10	12873321	12873321	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:12873321G>C	ENST00000378847.3	+	0	3930					NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	NA		NA			inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		AGTTCATACAGTGCATGACAA	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049	57118			19341	protein-coding gene	gene with protein product		607957			NA	11050006	Standard	NM_020397	XM_006717481	NA	Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.*2435G>C	chr10.hg19:g.12873321G>C		NA	B0YIY0|Q9HD31	hg19	CCDS7091.1	0.02	5.01106	ACAxTGC	COVERED																																																																																			NOVEL	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046820.1	0	4.514472	KEEP	0	0	0	15	527	GG	0.99649	0.996483	0		+	25	60	951	0	0	81.445264	85	60	3203	153	ENST00000378847.3	0.227273	0.999993
ITGA8	8516	__UNKNOWN__	__UNKNOWN__	10	15658576	15658576	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:15658576A>C	ENST00000378076.3	-	14	1753					NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	NA		NA			brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						AGACAAAAACACAGAACACAT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													94	83	87	NA		NA	NA	10		NA											NA				15658576		2203	4300	6503	SO:0001627	intron_variant			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943	8516		Integrins	6144	protein-coding gene	gene with protein product		604063			NA	7768999	Standard	NM_003638	XM_005252633	NA	Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1400-18T>G	chr10.hg19:g.15658576A>C		NA	B0YJ31|Q5VX94	hg19	CCDS31155.1	0.02	4.355852	AACxCAG	COVERED																																																																																			NOVEL	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046987.1	0	16.245628	KEEP	0	0	0	54	1636	AA	1	1	0		-	44	60	1534	0	0	136.710816	95	60	3434	250	ENST00000378076.3	0.316547	1
CUBN	8029	__UNKNOWN__	__UNKNOWN__	10	17127586	17127586	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:17127586G>T	ENST00000377833.4	-	16	2176					NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	NA		NA			cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CCAACTGGTAGGTTACTTACA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													101	108	106	NA		NA	NA	10		NA											NA				17127586		2203	4300	6503	SO:0001627	intron_variant			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611	8029			2548	protein-coding gene	gene with protein product		602997		MGA1	NA	9572993, 9478979	Standard	NM_001081	NM_001081	NA	Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2110+9C>A	chr10.hg19:g.17127586G>T		NA	B0YIZ4|Q5VTA6|Q96RU9	hg19	CCDS7113.1	0.02	2.299644	GTAxGTT	COVERED																																																																																			NOVEL	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047009.1	1	6.62122	KEEP	0	0	0	22	764	GG	0.999879	0.994963	0		-	24	60	885	0	0	80.967719	43	60	1645	113	ENST00000377833.4	0.358209	0.995084
CACNB2	783	__UNKNOWN__	__UNKNOWN__	10	18830101	18830101	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:18830101T>A	ENST00000396576.2	+	0	3767				RP11-499P20.2_ENST00000425669.1_RNA	NM_000724.3	NP_000715.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	NA		NA			axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TACCTACCATTCCTCCCCACC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995	783		Calcium channel subunits	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2	NA	9254841, 8494331	Standard	NM_000724	NM_201596	NA	Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000396576.2:c.*1448T>A	chr10.hg19:g.18830101T>A		NA	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	hg19	CCDS7128.1	0.02	8.821703	CATxCCT	COVERED																																																																																			NOVEL	CACNB2-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047074.2	4	15.94269	KEEP	0	0	0	53	1571	TT	1	1	0		+	53	60	1756	0	0	148.266215	166	60	5966	366	ENST00000396576.2	0.242009	1
SKIDA1	387640	__UNKNOWN__	__UNKNOWN__	10	21807709	21807709	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:21807709G>A	ENST00000449193.2	-	0	1295					NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	NA		NA				nucleus (GO:0005634)					NA						CCGGCTGGGAGCTCCAAAGTT	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592	387640			32697	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 140	C10orf140	NA		Standard	NM_207371	NM_207371	NA	Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.-958C>T	chr10.hg19:g.21807709G>A		NA	B1ANA5|Q6ZMX4|Q8N3C3	hg19	CCDS44363.1	0.02	1.915066	GGAxCTC	COVERED																																																																																			NOVEL	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286950.2	1	9.329508	KEEP	0	0	0	31	1062	GG	0.999997	0.973963	0		-	10	60	315	0	0	25.041788	44	60	1524	99	ENST00000449193.2	0.185185	0.973965
MLLT10	8028	__UNKNOWN__	__UNKNOWN__	10	22016821	22016821	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:22016821G>A	ENST00000307729.7	+	16	2205	c.2027G>A	c.(2026-2028)gGc>gAc	p.G676D	MLLT10_ENST00000377072.3_Missense_Mutation_p.G692D|MLLT10_ENST00000446906.2_Missense_Mutation_p.G676D|MLLT10_ENST00000377059.3_Missense_Mutation_p.G676D			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	676		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						AACCTAGTTGGCAGAGGAAGC	0.418	NA	NA	T	MLL, PICALM, CDK6	AL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		10	10p12	8028	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)		L	0													65	62	63	NA		NA	NA	10		NA											NA				22016821		2203	4300	6503	SO:0001583	missense			U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403	8028		Zinc fingers, PHD-type	16063	protein-coding gene	gene with protein product		602409	myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10		NA	7888665	Standard		NM_004641	NA	Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.2027G>A	chr10.hg19:g.22016821G>A	ENSP00000307411:p.Gly676Asp	NA	B1ANA8|Q5JT37|Q5VX90|Q66K63	hg19	CCDS55708.1	0.02	8.971598	TTGxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.63	3.664444	0.67700	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059;ENST00000438473;ENST00000538639	T;T;T;T	0.09073	3.02;3.02;3.02;3.02	5.82	5.82	0.92795	.	0.048911	0.85682	D	0.000000	T	0.22166	0.0534	L	0.44542	1.39	0.52099	D	0.999947	D;D;P;D	0.89917	1.0;0.998;0.917;0.998	D;D;P;D	0.74023	0.982;0.928;0.502;0.928	T	0.00042	-1.2227	10	0.66056	D	0.02	.	15.5728	0.76354	0.0:0.1371:0.8629:0.0	.	371;676;676;692	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	D	692;676;676;511;676;335;334	ENSP00000366272:G692D;ENSP00000401406:G676D;ENSP00000307411:G676D;ENSP00000366258:G676D	ENSP00000307411:G676D	G	+	2	0	MLLT10	22056827	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.680000	0.68168	2.745000	0.94114	0.650000	0.86243	GGC	NOVEL	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047136.1	0	30.988434	KEEP	0	0	0	103	3572	GG	1	1	0		+	29	60	1071	0	0	82.69527	208	60	7464	447	ENST00000307729.7	0.122363	1
OTUD1	220213	__UNKNOWN__	__UNKNOWN__	10	23730227	23730227	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:23730227C>T	ENST00000376495.3	+	0	2030					NM_001145373.2	NP_001138845.1	Q5VV17	OTUD1_HUMAN	OTU deubiquitinase 1	NA		NA			protein K63-linked deubiquitination (GO:0070536)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						AGCTTTCAGGCGTAAATCCAG	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096389	CCDS44366.1	10p12.31	2014-02-24	2014-02-24		ENSG00000165312	ENSG00000165312	220213		OTU domain containing	27346	protein-coding gene	gene with protein product		612022	OTU domain containing 1	OTDC1	NA	23827681	Standard	XM_166659	NM_001145373	NA	Approved	DUBA7	uc001irr.2	Q5VV17	OTTHUMG00000017819	ENST00000376495.3:c.*395C>T	chr10.hg19:g.23730227C>T		NA		hg19	CCDS44366.1	0.02	7.077558	AGGxGTA	COVERED																																																																																			NOVEL	OTUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047215.1	1	24.97759	KEEP	0	0	0	83	2872	CC	1	1	0		+	34	60	1234	0	0	103.905956	124	60	4451	315	ENST00000376495.3	0.21519	1
KIAA1217	56243	__UNKNOWN__	__UNKNOWN__	10	24835154	24835154	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:24835154G>T	ENST00000376454.3	+	21	5763	c.5733G>T	c.(5731-5733)aaG>aaT	p.K1911N	KIAA1217_ENST00000458595.1_Missense_Mutation_p.K1317N|KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Missense_Mutation_p.K1342N|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376462.1_Missense_Mutation_p.K1232N	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1911		NA			embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AAGGTGCCAAGGGCACCAGGA	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													86	77	80	NA		NA	NA	10		NA											NA				24835154		2203	4300	6503	SO:0001583	missense			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549	56243			25428	protein-coding gene	gene with protein product	sickle tail	NA			NA	10574462	Standard	NM_019590	XM_005252500	NA	Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5733G>T	chr10.hg19:g.24835154G>T	ENSP00000365637:p.Lys1911Asn	NA	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	hg19	CCDS31165.1	0.02	33.288356	CAAxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274444	0.40194	.	.	ENSG00000120549	ENST00000376462;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000450158	T;T;T;T	0.45276	0.92;0.9;1.28;0.92	4.17	3.26	0.37387	.	0.126115	0.52532	D	0.000079	T	0.52041	0.1710	L	0.59436	1.845	0.29285	N	0.869738	P;D;D;P	0.59357	0.933;0.974;0.985;0.933	P;P;P;P	0.58873	0.732;0.632;0.847;0.732	T	0.49652	-0.8917	10	0.30078	T	0.28	.	11.7106	0.51623	0.0875:0.0:0.9125:0.0	.	1317;1342;1911;1312	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	N	1232;1317;1911;1342;1500	ENSP00000365645:K1232N;ENSP00000392625:K1317N;ENSP00000365637:K1911N;ENSP00000365635:K1342N	ENSP00000365635:K1342N	K	+	3	2	KIAA1217	24875160	1.000000	0.71417	0.956000	0.39512	0.932000	0.56968	7.530000	0.81962	0.729000	0.32403	0.655000	0.94253	AAG	NOVEL	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047223.2	33	68.232486	KEEP	0	0	0	227	7861	GG	1	1	0		+	45	60	1626	0	0	109.161195	744	60	27360	1263	ENST00000376454.3	0.057034	1
CUL2	8453	__UNKNOWN__	__UNKNOWN__	10	35317808	35317808	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:35317808G>A	ENST00000374748.1	-	17	1860	c.1547C>T	c.(1546-1548)gCg>gTg	p.A516V	CUL2_ENST00000537177.1_Missense_Mutation_p.A535V|CUL2_ENST00000602371.1_Missense_Mutation_p.A459V|CUL2_ENST00000374742.1_Missense_Mutation_p.A516V|CUL2_ENST00000374751.3_Missense_Mutation_p.A516V|CUL2_ENST00000374749.3_Missense_Mutation_p.A516V|CUL2_ENST00000374746.1_Missense_Mutation_p.A516V			Q13617	CUL2_HUMAN	cullin 2	516		NA			cell cycle arrest (GO:0007050)|cellular response to hypoxia (GO:0071456)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|VCB complex (GO:0030891)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|prostate(2)|skin(1)|urinary_tract(2)	31						AAGAGGCCACGCACCAGCCTA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	37	36	NA		NA	NA	10		NA											NA				35317808		2203	4300	6503	SO:0001583	missense			U83410	CCDS7179.1, CCDS73086.1	10p11.2	2011-05-24			ENSG00000108094	ENSG00000108094	8453			2552	protein-coding gene	gene with protein product		603135			NA	8681378	Standard	NM_003591	NM_003591	NA	Approved		uc021ppa.1	Q13617	OTTHUMG00000017950	ENST00000374748.1:c.1547C>T	chr10.hg19:g.35317808G>A	ENSP00000363880:p.Ala516Val	NA	B3KT95|B7Z6K8|D3DRY6|G3V1S2|O00200|Q5T2B6|Q9UNF9	hg19	CCDS7179.1	0.02	4.690236	CACxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	35	5.511389	0.96386	.	.	ENSG00000108094	ENST00000374751;ENST00000374748;ENST00000374746;ENST00000374749;ENST00000374754;ENST00000374742;ENST00000537177	T;T;T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77;-0.77;-0.77	5.77	5.77	0.91146	Cullin, N-terminal (1);Cullin homology (3);	0.000000	0.85682	D	0.000000	D	0.84745	0.5540	L	0.56280	1.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.992;0.995	D	0.84150	0.0422	10	0.59425	D	0.04	-21.1493	20.3626	0.98863	0.0:0.0:1.0:0.0	.	516;535;516	Q5T2B5;G3V1S2;Q13617	.;.;CUL2_HUMAN	V	516;516;516;516;459;516;535	ENSP00000363883:A516V;ENSP00000363880:A516V;ENSP00000363878:A516V;ENSP00000363881:A516V;ENSP00000363874:A516V;ENSP00000444856:A535V	ENSP00000363874:A516V	A	-	2	0	CUL2	35357814	1.000000	0.71417	0.975000	0.42487	0.987000	0.75469	9.864000	0.99589	2.885000	0.99019	0.655000	0.94253	GCG	NOVEL	CUL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047538.1	0	13.842154	KEEP	0	0	0	46	1606	GG	1	0.999999	0		-	26	60	947	0	0	79.492999	98	60	3594	227	ENST00000374748.1	0.209677	0.999999
GJD4	219770	__UNKNOWN__	__UNKNOWN__	10	35896585	35896585	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:35896585G>A	ENST00000321660.1	+	2	302	c.144G>A	c.(142-144)gaG>gaA	p.E48E	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	48		NA			cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						ACCAGGACGAGCAGGAGAGGT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													121	101	108	NA		NA	NA	10		NA											NA				35896585		2203	4300	6503	SO:0001819	synonymous_variant			AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291	219770		Ion channels / Gap junction proteins (connexins)	23296	protein-coding gene	gene with protein product	connexin 40.1	611922			NA	12477932	Standard	NM_153368	NM_153368	NA	Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.144G>A	chr10.hg19:g.35896585G>A		NA	Q8N2R7	hg19	CCDS7191.1	0.02	13.317062	CGAxCAG	COVERED																																																																																			NOVEL	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047576.1	2	27.066509	KEEP	0	0	0	90	3057	GG	1	1	0		+	75	60	2486	0	0	210.032465	234	60	8325	533	ENST00000321660.1	0.242718	1
CCNYL2	414194	__UNKNOWN__	__UNKNOWN__	10	42905549	42905549	__UNKNOWN__	RNA	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:42905549A>G	ENST00000483242.3	-	0	1377					NR_103829.1		Q5T2Q4	CCYL2_HUMAN	cyclin Y-like 2	NA		NA			regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					breast(2)|endometrium(1)|lung(3)|ovary(1)	7						GGATGGCCTTAGCACGCTGAA	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					BC039000		10q11.21	2007-02-09	2007-02-09	2007-02-09	ENSG00000182632	ENSG00000182632	414194			23495	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 21	C10orf21	NA		Standard	XM_936368	NR_103829	NA	Approved	bA178A10.2		Q5T2Q4	OTTHUMG00000018009	ENST00000483242.3:	chr10.hg19:g.42905549A>G		NA		hg19		0.02	4.804621	CTTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.038	-1.295160	0.01375	.	.	ENSG00000182632	ENST00000431603	.	.	.	2.0	0.852	0.18995	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25117	-1.0141	4	.	.	.	.	3.722	0.08460	0.8004:0.0:0.1996:0.0	.	.	.	.	P	282	.	.	L	-	2	0	CCNYL2	42225555	1.000000	0.71417	0.999000	0.59377	0.050000	0.14768	1.623000	0.37008	0.232000	0.21100	0.248000	0.18094	CTA	NOVEL	CCNYL2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000047670.5	1	7.522891	KEEP	0	0	0	25	799	AA	0.999931	0.99993	0		-	29	60	1067	0	0	91.482262	93	60	3424	183	ENST00000483242.3	0.237705	0.999999
RET	5979	__UNKNOWN__	__UNKNOWN__	10	43622756	43622756	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:43622756A>G	ENST00000355710.3	+	19	3419				RET_ENST00000340058.5_3'UTR	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CCCTGGGAGGACGCACCCCCA	0.582	NA	1	T, Mis, N, F	H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6	medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC	medullary thyroid,  papillary thyroid, pheochromocytoma	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	E, O	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731	5979		Cadherins / Cadherin-related	9967	protein-coding gene	gene with protein product	cadherin-related family member 16	164761	multiple endocrine neoplasia and medullary thyroid carcinoma 1, Hirschsprung disease 1	HSCR1, MEN2A, MTC1, MEN2B	NA	2687772, 1611909	Standard	NM_020975	NM_020975	NA	Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.3187+586A>G	chr10.hg19:g.43622756A>G		NA	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	hg19	CCDS7200.1	0.02	6.778152	AGGxCGC	COVERED																																																																																			NOVEL	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047694.2	3	25.253257	KEEP	0	0	0	84	2529	AA	1	1	0		+	26	60	892	0	0	71.021391	131	60	4344	301	ENST00000355710.3	0.165605	1
RASSF4	83937	__UNKNOWN__	__UNKNOWN__	10	45479463	45479463	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:45479463T>C	ENST00000340258.5	+	5	394				RASSF4_ENST00000472561.1_Intron|RASSF4_ENST00000334940.6_Missense_Mutation_p.V101A|RASSF4_ENST00000374417.2_Intron	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	NA		NA			endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						CAGTTGTCTGTTTTCAGAAAG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													34	31	32	NA		NA	NA	10		NA											NA				45479463		2198	4294	6492	SO:0001627	intron_variant			BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551	83937			20793	protein-coding gene	gene with protein product		610559			NA		Standard	NM_032023	NM_032023	NA	Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.282-7T>C	chr10.hg19:g.45479463T>C		NA	Q00425|Q5TFT8|Q9BQL3|Q9H071	hg19	CCDS7208.1	0.02	4.965787	CTGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.889	1.203744	0.22121	.	.	ENSG00000107551	ENST00000334940;ENST00000427758	T;T	0.31510	2.58;1.49	4.98	0.0701	0.14377	.	.	.	.	.	T	0.16642	0.0400	.	.	.	0.51233	D	0.999916	.	.	.	.	.	.	T	0.09997	-1.0649	6	0.08599	T	0.76	.	7.193	0.25837	0.0:0.3909:0.0:0.6091	.	.	.	.	A	101;119	ENSP00000334543:V101A;ENSP00000409767:V119A	ENSP00000334543:V101A	V	+	2	0	RASSF4	44799469	0.073000	0.21202	0.317000	0.25265	0.467000	0.32768	-0.085000	0.11250	0.104000	0.17725	0.533000	0.62120	GTT	NOVEL	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047745.2	2	21.3524	KEEP	0	0	0	71	2244	TT	1	0.999997	0		+	25	60	946	0	0	80.379825	90	60	3241	250	ENST00000340258.5	0.217391	0.999997
GDF10	2662	__UNKNOWN__	__UNKNOWN__	10	48426116	48426116	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:48426116T>A	ENST00000224605.2	-	0	2156					NM_004962.3	NP_004953.1	P55107	BMP3B_HUMAN	growth differentiation factor 10	NA		NA			fat cell differentiation (GO:0045444)|growth (GO:0040007)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(20)|skin(1)	31						AAACACTCATTTACACCACGA	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L42113	CCDS73117.1	10q11.22	2014-04-10			ENSG00000107623	ENSG00000266524	2662		Endogenous ligands	4215	protein-coding gene	gene with protein product		601361			NA	8679252	Standard	NM_004962	NM_004962	NA	Approved	BMP-3b	uc001jfb.3	P55107	OTTHUMG00000188319	ENST00000224605.2:c.*454A>T	chr10.hg19:g.48426116T>A		NA	Q5VSQ8|Q9UCX6	hg19	CCDS7220.1	0.02	1.994685	CATxTAC	COVERED																																																																																			NOVEL	GDF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047884.1	1	6.619434	KEEP	0	0	0	22	698	TT	0.999879	0.999097	0		-	30	60	1076	0	0	99.133651	49	60	1804	128	ENST00000224605.2	0.379747	0.999218
DRGX	644168	__UNKNOWN__	__UNKNOWN__	10	50594948	50594948	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:50594948G>C	ENST00000374139.2	-	4	245				DRGX_ENST00000434016.1_Intron			A6NNA5	DRGX_HUMAN	dorsal root ganglia homeobox	NA		NA			axon guidance (GO:0007411)|detection of chemical stimulus (GO:0009593)|detection of temperature stimulus (GO:0016048)|dorsal spinal cord development (GO:0021516)|neuron migration (GO:0001764)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of mechanical stimulus (GO:0050954)|transcription, DNA-templated (GO:0006351)|trigeminal nerve development (GO:0021559)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	11						AATCAAACAGGAGGAAGAAGC	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													70	77	75	NA		NA	NA	10		NA											NA				50594948		2023	4193	6216	SO:0001627	intron_variant				CCDS44388.1, CCDS44388.2	10q11.23	2011-06-20	2007-07-26	2007-07-26	ENSG00000165606	ENSG00000165606	644168		Homeoboxes / PRD class	21536	protein-coding gene	gene with protein product	paired-like homeodomain trancription factor DRG11	606701	paired related homeobox-like 1	PRRXL1	NA	7496632	Standard	XM_060970	NM_001276451	NA	Approved	DRG11	uc021pqd.2	A6NNA5	OTTHUMG00000018192	ENST00000374139.2:c.235-44C>G	chr10.hg19:g.50594948G>C		NA		hg19		0.02	2.056112	CAGxAGG	COVERED																																																																																			NOVEL	DRGX-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000047987.2	0	2.708842	KEEP	0	0	0	9	319	GG	0.99254	0.990111	0		-	7	60	247	0	0	18.069597	65	60	2383	93	ENST00000374139.2	0.097222	0.997553
OGDHL	55753	__UNKNOWN__	__UNKNOWN__	10	50957858	50957858	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:50957858T>G	ENST00000374103.4	-	8	986	c.901A>C	c.(901-903)Agg>Cgg	p.R301R	OGDHL_ENST00000432695.1_Silent_p.R92R|OGDHL_ENST00000419399.1_Silent_p.R244R	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	301		NA			glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						ACGTTCAGCCTTCCCCTGGAG	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	43	44	NA		NA	NA	10		NA											NA				50957858		2202	4299	6501	SO:0001819	synonymous_variant			AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444	55753			25590	protein-coding gene	gene with protein product		NA			NA	10574462	Standard	NM_018245	NM_018245	NA	Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.901A>C	chr10.hg19:g.50957858T>G		NA	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	hg19	CCDS7234.1	0.02	2.054336	GCCxTCC	COVERED																																																																																			NOVEL	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048007.1	0	6.017592	KEEP	0	0	0	20	634	TT	0.999863	0.999782	0		-	5	60	176	0	0	11.483605	90	60	3194	139	ENST00000374103.4	0.052632	0.999919
SGMS1	259230	__UNKNOWN__	__UNKNOWN__	10	52066289	52066289	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:52066289G>C	ENST00000361781.2	-	0	2814					NM_147156.3	NP_671512.1	Q86VZ5	SMS1_HUMAN	sphingomyelin synthase 1	NA		NA			apoptotic process (GO:0006915)|cell growth (GO:0016049)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|Golgi trans cisterna (GO:0000138)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GAAATACTTAGAAAATCACTT	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY280959	CCDS7240.1	10q11.2	2013-01-10	2007-03-16	2007-03-16	ENSG00000198964	ENSG00000198964	259230	2.7.8.27	Sterile alpha motif (SAM) domain containing	29799	protein-coding gene	gene with protein product		611573	transmembrane protein 23	TMEM23	NA	11841947, 14976195	Standard	NM_147156	NM_147156	NA	Approved	MOB, MGC17342, SMS1	uc001jje.3	Q86VZ5	OTTHUMG00000018231	ENST00000361781.2:c.*613C>G	chr10.hg19:g.52066289G>C		NA	Q68U43|Q6EKK0|Q75SP1	hg19	CCDS7240.1	0.02	10.03341	TTAxAAA	COVERED																																																																																			NOVEL	SGMS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048074.2	2	17.731965	KEEP	0	0	0	59	2103	GG	1	1	0		-	53	60	1987	0	0	172.976529	153	60	5811	304	ENST00000361781.2	0.257282	1
CTNNA3	29119	__UNKNOWN__	__UNKNOWN__	10	68688218	68688218	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:68688218C>T	ENST00000433211.2	-	8	1222				CTNNA3_ENST00000373744.4_Intron|LRRTM3_ENST00000361320.4_Intron	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						GAGGTATGAACCATTGTGATA	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													31	33	32	NA		NA	NA	10		NA											NA				68688218		2175	4269	6444	SO:0001627	intron_variant			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230	29119			2511	protein-coding gene	gene with protein product		607667			NA	12596047, 11590244	Standard	NM_013266	XM_005269717	NA	Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1048-152936G>A	chr10.hg19:g.68688218C>T		NA		hg19	CCDS7269.1	0.02	4.007821	GAAxCAT	COVERED																																																																																			NOVEL	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048282.2	2	10.224553	KEEP	0	0	0	34	1111	CC	0.999998	0.999997	0		-	9	60	319	0	0	22.256045	113	60	3922	174	ENST00000433211.2	0.07377	0.999999
PPA1	5464	__UNKNOWN__	__UNKNOWN__	10	71973369	71973369	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:71973369G>T	ENST00000373232.3	-	6	484				PPA1_ENST00000608321.1_Intron	NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	NA		NA			diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						GCCAAAGTCAGGACAACATTA	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													55	49	51	NA		NA	NA	10		NA											NA				71973369		2203	4300	6503	SO:0001627	intron_variant			AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	5464	3.6.1.1		9226	protein-coding gene	gene with protein product	cytosolic inorganic pyrophosphatase, inorganic pyrophosphatase 1, pyrophosphate phospho-hydrolase	179030	pyrophosphatase (inorganic)	PP	NA	10542310, 975879	Standard	NM_021129	NM_021129	NA	Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.385-24C>A	chr10.hg19:g.71973369G>T		NA	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	hg19	CCDS7299.1	0.02	16.941139	TCAxGAC	COVERED																																																																																			NOVEL	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048490.2	3	37.922878	KEEP	0	0	0	126	4507	GG	1	1	0		-	93	60	3525	0	0	306.173282	278	60	10393	657	ENST00000373232.3	0.250674	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	72813323	72813323	__UNKNOWN__	IGR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:72813323G>T			NA	NA				RP11-432J9.6 (97925 upstream) : UNC5B (159003 downstream)						NA		NA									NA						TGGGGAAGGTGGGGTGTGAGT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	32	32	NA		NA	NA	10		NA											NA				72813323		876	1991	2867	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.72813323G>T		NA		hg19		0.02	6.912373	GGTxGGG	COVERED																																																																																			NOVEL					0			2	8.728168	KEEP	0	0	0	29	1007	GG	0.999997	0.999997	0			13	60	457	0	0	33.161768	126	60	4533	242		0.093525	1
PSAP	5660	__UNKNOWN__	__UNKNOWN__	10	73579642	73579642	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:73579642C>T	ENST00000394936.3	-	10	1168	c.1021G>A	c.(1021-1023)Gct>Act	p.A341T	PSAP_ENST00000394934.1_Missense_Mutation_p.A343T			P07602	SAP_HUMAN	prosaposin	341	Saposin B-type 3. {ECO:0000255|PROSITE- ProRule:PRU00415}.	NA			blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TTGTCAAAAGCGTCGAGTATT	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													34	37	36	NA		NA	NA	10		NA											NA				73579642		2203	4300	6503	SO:0001583	missense			BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746	5660		Endogenous ligands	9498	protein-coding gene	gene with protein product	variant Gaucher disease and variant metachromatic leukodystrophy	176801	sphingolipid activator protein-1	SAP1, GLBA	NA	2717620	Standard	NM_002778	NM_001042465	NA	Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.1021G>A	chr10.hg19:g.73579642C>T	ENSP00000378394:p.Ala341Thr	NA	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	hg19	CCDS7311.1	0.02	4.247566	AAGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.42	1.634026	0.29068	.	.	ENSG00000197746	ENST00000394936;ENST00000373120;ENST00000357471;ENST00000394934;ENST00000404083;ENST00000394940	D;D	0.85955	-2.05;-2.05	5.67	-1.25	0.09405	Saposin-like (2);Saposin-like type B, 1 (1);Saposin B (2);	0.792273	0.12523	N	0.461446	T	0.72875	0.3515	N	0.20574	0.59	0.09310	N	1	B	0.21606	0.058	B	0.21708	0.036	T	0.53535	-0.8425	10	0.30078	T	0.28	-3.0132	11.487	0.50358	0.0:0.5654:0.0:0.4346	.	341	P07602	SAP_HUMAN	T	341;341;344;343;347;267	ENSP00000378394:A341T;ENSP00000378392:A343T	ENSP00000350063:A344T	A	-	1	0	PSAP	73249648	0.029000	0.19370	0.000000	0.03702	0.014000	0.08584	0.718000	0.25866	-0.910000	0.03847	-0.797000	0.03246	GCT	NOVEL	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048553.1	3	16.852538	KEEP	0	0	0	56	1900	CC	1	0.999987	0		-	8	60	252	0	0	16.749731	98	60	3406	210	ENST00000394936.3	0.075472	0.999987
MRPS16	51021	__UNKNOWN__	__UNKNOWN__	10	75010693	75010693	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A	rs104894168		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:75010693G>A	ENST00000372945.3	-	3	541	c.331C>T	c.(331-333)Cga>Tga	p.R111*	DNAJC9-AS1_ENST00000440197.2_RNA|MRPS16_ENST00000416782.2_Intron|MRPS16_ENST00000479005.1_5'UTR|MRPS16_ENST00000372940.3_Intron	NM_016065.3	NP_057149.1	Q9Y3D3	RT16_HUMAN	mitochondrial ribosomal protein S16	111		NA			translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)	4	Prostate(51;0.0119)					CGTTTCCTTCGCAGTCTCTCA	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0			GRCh37	CM043302	MRPS16	M	rs104894168						149	136	141	NA		NA	NA	10		NA											NA				75010693		2203	4300	6503	SO:0001587	stop_gained			AB051351	CCDS7323.1	10q22.1	2012-09-13			ENSG00000182180	ENSG00000182180	51021		Mitochondrial ribosomal proteins / small subunits	14048	protein-coding gene	gene with protein product		609204			NA	10810093	Standard		NM_016065	NA	Approved	CGI-132	uc001jts.1	Q9Y3D3	OTTHUMG00000018454	ENST00000372945.3:c.331C>T	chr10.hg19:g.75010693G>A	ENSP00000362036:p.Arg111*	NA	B4E032|Q96Q60	hg19	CCDS7323.1	0.02	8.957985	TTCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	31	5.068005	0.93950	.	.	ENSG00000182180	ENST00000372945	.	.	.	5.7	3.79	0.43588	.	0.246662	0.33772	U	0.004573	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.2191	11.9028	0.52692	0.0:0.0:0.5404:0.4596	.	.	.	.	X	111	.	ENSP00000362036:R111X	R	-	1	2	MRPS16	74680699	0.999000	0.42202	1.000000	0.80357	0.962000	0.63368	1.883000	0.39658	0.706000	0.31912	-0.182000	0.12963	CGA	NOVEL	MRPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048616.1	2	28.225188	KEEP	0	1	32	105	3654	GG	1	1	0		-	33	60	1183	0	0	91.696708	217	60	7776	446	ENST00000372945.3	0.132	1
DLG5	9231	__UNKNOWN__	__UNKNOWN__	10	79555888	79555888	__UNKNOWN__	Silent	SNP	G	G	A	rs141030163		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:79555888G>A	ENST00000372391.2	-	29	5372	c.5367C>T	c.(5365-5367)gtC>gtT	p.V1789V	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Silent_p.V1449V	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1789	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.	NA			apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GCTTATAGTCGACAAACAGGC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G		1,4405	2.1+/-5.4	0,1,2202	124	115	118	NA	5367	-6.1	0.9	10	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	DLG5	NM_004747.3		0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077		1789/1920	79555888	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208	9231			2904	protein-coding gene	gene with protein product		604090	discs, large (Drosophila) homolog 5		NA	9738934	Standard		XM_005270276	NA	Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.5367C>T	chr10.hg19:g.79555888G>A		NA	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	hg19	CCDS7353.2	0.02	4.775703	GTCxACA	COVERED																																																																																			NOVEL	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048900.2	0	6.921983	KEEP	0	0	0	23	779	GG	0.999892	0.999888	0		-	21	60	791	0	0	65.479903	93	60	3282	174	ENST00000372391.2	0.184211	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	81286316	81286316	__UNKNOWN__	IGR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:81286316G>A			NA	NA				EIF5AL1 (10128 upstream) : SFTPA2 (29291 downstream)						NA		NA									NA						ACATGCTTCTGCAGCTCCTTG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.81286316G>A		NA		hg19		0.02	3.868895	TCTxCAG	COVERED																																																																																			NOVEL					0			2	6.019779	KEEP	0	0	0	20	724	GG	0.999863	0.999863	0			11	60	393	0	0	27.507236	138	60	5225	216		0.073826	1
CCSER2	54462	__UNKNOWN__	__UNKNOWN__	10	86132019	86132019	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:86132019C>A	ENST00000224756.8	+	2	1396	c.1211C>A	c.(1210-1212)tCt>tAt	p.S404Y	CCSER2_ENST00000372088.2_Missense_Mutation_p.S404Y|CCSER2_ENST00000359979.4_Missense_Mutation_p.S404Y	NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	404		NA			microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)					NA						TCTTTGTCATCTTCTGATAAG	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													105	103	104	NA		NA	NA	10		NA											NA				86132019		2203	4299	6502	SO:0001583	missense				CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771	54462			29197	protein-coding gene	gene with protein product		NA	KIAA1128, family with sequence similarity 190, member B	KIAA1128, FAM190B	NA	10574461	Standard	NM_018999	XM_005269905	NA	Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.1211C>A	chr10.hg19:g.86132019C>A	ENSP00000224756:p.Ser404Tyr	NA	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	hg19	CCDS31235.1	0.02	8.982867	CATxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.44	3.388925	0.61956	.	.	ENSG00000107771	ENST00000359979;ENST00000224756;ENST00000372088	T;T;T	0.69561	-0.41;1.02;0.89	5.73	5.73	0.89815	.	0.000000	0.64402	D	0.000002	T	0.80565	0.4647	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	T	0.81577	-0.0869	10	0.87932	D	0	-16.3948	17.4071	0.87476	0.0:1.0:0.0:0.0	.	404;404;404	Q9H7U1-3;Q9H7U1;Q9H7U1-2	.;F190B_HUMAN;.	Y	404	ENSP00000353068:S404Y;ENSP00000224756:S404Y;ENSP00000361160:S404Y	ENSP00000224756:S404Y	S	+	2	0	FAM190B	86121999	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.705000	0.74644	2.721000	0.93114	0.655000	0.94253	TCT	NOVEL	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049132.2	3	12.941215	KEEP	0	0	0	43	1488	CC	1	1	0		+	29	60	1054	0	0	82.437111	184	60	6782	279	ENST00000224756.8	0.13615	1
LDB3	11155	__UNKNOWN__	__UNKNOWN__	10	88466439	88466439	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:88466439A>G	ENST00000361373.4	+	7	1069	c.1048A>G	c.(1048-1050)Acc>Gcc	p.T350A	LDB3_ENST00000458213.2_Intron|LDB3_ENST00000429277.2_Intron|LDB3_ENST00000263066.6_Intron|LDB3_ENST00000352360.5_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3	NA		NA								breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						CTCCGCCTCCACCACAGCCCC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													36	29	31	NA		NA	NA	10		NA											NA				88466439		2203	4300	6503	SO:0001583	missense			AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367	11155			15710	protein-coding gene	gene with protein product	cypher, oracle, Z-band alternatively spliced PDZ motif protein	605906	cardiomyopathy, dilated 1C (autosomal dominant)	CMD1C	NA	10427098, 23271734, 23996002, 14662268	Standard		NM_001080114	NA	Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1048A>G	chr10.hg19:g.88466439A>G	ENSP00000355296:p.Thr350Ala	NA		hg19	CCDS7377.1	0.02	1.972183	TCCxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.784477	0.00004	.	.	ENSG00000122367	ENST00000361373	D	0.82081	-1.57	0.235	-0.47	0.12131	.	.	.	.	.	T	0.48429	0.1499	N	0.00926	-1.1	0.09310	N	0.999998	P	0.34587	0.458	B	0.36092	0.217	T	0.51387	-0.8712	9	0.05959	T	0.93	.	1.5335	0.02540	0.3081:0.0:0.3634:0.3285	.	350	O75112	LDB3_HUMAN	A	350	ENSP00000355296:T350A	ENSP00000355296:T350A	T	+	1	0	LDB3	88456419	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	-0.168000	0.09925	-0.761000	0.04670	-0.765000	0.03448	ACC	NOVEL	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049160.2	1	9.018364	KEEP	0	0	0	30	845	AA	0.999997	0.999905	0		+	12	60	436	0	0	33.800657	81	60	2592	151	ENST00000361373.4	0.129032	0.999907
PDE6C	5146	__UNKNOWN__	__UNKNOWN__	10	95394516	95394516	__UNKNOWN__	Splice_Site	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:95394516A>T	ENST00000371447.3	+	9	1259	c.1121A>T	c.(1120-1122)aAa>aTa	p.K374I		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	374	GAF 2.	NA			phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	CGTTTGTAGAAAGGACCTGTA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													120	98	106	NA		NA	NA	10		NA											NA				95394516		2203	4300	6503	SO:0001630	splice_region_variant			U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	5146	3.1.4.17	Phosphodiesterases	8787	protein-coding gene	gene with protein product		600827			NA		Standard	NM_006204	NM_006204	NA	Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1120-1A>T	chr10.hg19:g.95394516A>T		NA	A6NCR6|Q5VY29	hg19	CCDS7429.1	0.02	9.167884	AGAxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	21.1	4.104944	0.77096	.	.	ENSG00000095464	ENST00000371447	T	0.65178	-0.14	4.63	4.63	0.57726	GAF (2);	0.000000	0.85682	D	0.000000	T	0.75737	0.3890	M	0.62723	1.935	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.77210	-0.2671	10	0.51188	T	0.08	.	14.4937	0.67670	1.0:0.0:0.0:0.0	.	374	P51160	PDE6C_HUMAN	I	374	ENSP00000360502:K374I	ENSP00000360502:K374I	K	+	2	0	PDE6C	95384506	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.709000	0.91379	2.072000	0.62099	0.533000	0.62120	AAA	NOVEL	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049437.1	1	3.911994	KEEP	0	0	0	13	417	AA	0.994391	0.994391	0	Missense_Mutation	+	24	60	865	1	0	64.737979	202	60	7329	281	ENST00000371447.3	0.106195	1
SORBS1	10580	__UNKNOWN__	__UNKNOWN__	10	97116822	97116822	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:97116822A>G	ENST00000361941.3	-	21	2155				SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000393949.1_Intron|SORBS1_ENST00000371246.2_Intron|SORBS1_ENST00000354106.3_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371247.2_Intron|SORBS1_ENST00000347291.4_Intron|SORBS1_ENST00000607232.1_Silent_p.S490S|SORBS1_ENST00000371227.4_Intron|SORBS1_ENST00000277982.5_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000474353.2_Intron	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1	NA		NA								NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TATGGACTGAAGATGAAGAAA	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637	10580			14565	protein-coding gene	gene with protein product	c-Cbl-associated protein	605264	SH3-domain protein 5 (ponsin)	SH3D5	NA	10085297, 11001060	Standard		XM_005269405	NA	Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.2128+565T>C	chr10.hg19:g.97116822A>G		NA		hg19	CCDS31255.1	0.02	4.813642	TGAxGAT	COVERED																																																																																			NOVEL	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049517.1	1	11.737029	KEEP	0	0	0	39	1297	AA	1	0.999999	0		-	24	60	866	0	0	71.986976	96	60	3601	206	ENST00000361941.3	0.2	0.999999
DNTT	1791	__UNKNOWN__	__UNKNOWN__	10	98078227	98078227	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:98078227A>T	ENST00000371174.2	+	2	424	c.322A>T	c.(322-324)Atc>Ttc	p.I108F	DNTT_ENST00000419175.1_Missense_Mutation_p.I108F			P04053	TDT_HUMAN	DNA nucleotidylexotransferase	108	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.	NA			DNA modification (GO:0006304)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA nucleotidylexotransferase activity (GO:0003912)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		CTCCTGGCTGATCGAATGCAT	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													145	133	137	NA		NA	NA	10		NA											NA				98078227		2203	4300	6503	SO:0001583	missense			AB046378	CCDS7447.1	10q23-q24	2013-05-21	2013-05-21		ENSG00000107447	ENSG00000107447	1791	2.7.7.31	DNA polymerases	2983	protein-coding gene	gene with protein product	Terminal deoxynucleotidyltransferase	187410	deoxynucleotidyltransferase, terminal		NA		Standard	NM_004088	NM_004088	NA	Approved	TDT	uc001kmf.3	P04053	OTTHUMG00000018832	ENST00000371174.2:c.322A>T	chr10.hg19:g.98078227A>T	ENSP00000360216:p.Ile108Phe	NA	Q53FH1|Q5W103|Q96E50	hg19	CCDS7447.1	0.02	8.977383	CTGxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	A	16.57	3.158912	0.57368	.	.	ENSG00000107447	ENST00000419175;ENST00000371174	T;T	0.79454	-1.27;-1.27	5.61	3.28	0.37604	BRCT (4);	0.101616	0.64402	D	0.000003	T	0.80819	0.4696	L	0.57536	1.79	0.40914	D	0.984255	P;P	0.47762	0.878;0.9	P;P	0.55965	0.683;0.788	T	0.79804	-0.1649	10	0.87932	D	0	0.0937	8.2493	0.31708	0.8361:0.0:0.1639:0.0	.	108;108	P04053-2;P04053	.;TDT_HUMAN	F	108	ENSP00000401169:I108F;ENSP00000360216:I108F	ENSP00000360216:I108F	I	+	1	0	DNTT	98068217	1.000000	0.71417	0.992000	0.48379	0.494000	0.33585	4.030000	0.57260	0.422000	0.26005	0.455000	0.32223	ATC	NOVEL	DNTT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049607.1	2	14.744771	KEEP	0	0	0	49	1562	AA	1	1	0		+	30	60	1061	0	0	82.055646	195	60	6911	332	ENST00000371174.2	0.133333	1
TLL2	7093	__UNKNOWN__	__UNKNOWN__	10	98146671	98146671	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:98146671T>C	ENST00000357947.3	-	14	2078					NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	NA		NA			cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		ACTTGTCCCATATACCCTCTC	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													110	95	100	NA		NA	NA	10		NA											NA				98146671		2203	4300	6503	SO:0001627	intron_variant			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587	7093			11844	protein-coding gene	gene with protein product		606743			NA	10516436	Standard		NM_012465	NA	Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.1852+38A>G	chr10.hg19:g.98146671T>C		NA	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	hg19	CCDS7449.1	0.02	17.724415	CCAxATA	COVERED																																																																																			NOVEL	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049608.1	7	27.679747	KEEP	0	0	0	92	2806	TT	1	1	0		-	76	60	2815	0	0	238.031164	276	60	9761	561	ENST00000357947.3	0.215909	1
PIK3AP1	118788	__UNKNOWN__	__UNKNOWN__	10	98416753	98416753	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:98416753A>T	ENST00000339364.5	-	3	550				PIK3AP1_ENST00000468783.1_Intron|PIK3AP1_ENST00000371110.2_Intron	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	NA		NA			negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		GACATGTTCCACCCCATGAGA	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629	118788			30034	protein-coding gene	gene with protein product		607942			NA	1251844, 11163197	Standard	NM_152309	NM_152309	NA	Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.431-62T>A	chr10.hg19:g.98416753A>T		NA	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	hg19	CCDS31259.1	0.02	6.745496	TCCxCCC	COVERED																																																																																			NOVEL	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049619.2	0	10.219818	KEEP	0	0	0	34	970	AA	0.999998	0.999998	0		-	15	60	556	0	0	40.608892	158	60	5460	238	ENST00000339364.5	0.086705	1
C10orf12	26148	__UNKNOWN__	__UNKNOWN__	10	98745474	98745474	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:98745474G>C	ENST00000286067.2	+	0	4434					NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	NA		NA								NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		TACTATTTCTGTTACCCCCTT	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640	26148			23420	protein-coding gene	gene with protein product		NA			NA	24550272	Standard	NM_015652	NM_015652	NA	Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.*583G>C	chr10.hg19:g.98745474G>C		NA	Q9H945|Q9Y457	hg19	CCDS7452.1	0.02	7.558317	TCTxTTA	COVERED																																																																																			NOVEL	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049627.1	2	9.63113	KEEP	0	0	0	32	1137	GG	0.999997	0.999997	0		+	80	60	3035	0	0	293.503657	80	60	3022	238	ENST00000286067.2	0.5	1
PI4K2A	55361	__UNKNOWN__	__UNKNOWN__	10	99410781	99410781	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:99410781G>A	ENST00000370631.3	+	2	576	c.519G>A	c.(517-519)ctG>ctA	p.L173L	PI4K2A_ENST00000370649.3_Silent_p.L143L|PI4K2A_ENST00000555577.1_Silent_p.L143L	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	173	PI3K/PI4K.	NA			basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TGCAGAAGCTGTGCTGTCCTT	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													90	77	82	NA		NA	NA	10		NA											NA				99410781		2203	4300	6503	SO:0001819	synonymous_variant			AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252	55361			30031	protein-coding gene	gene with protein product		609763			NA	11244087, 11279162	Standard	NM_018425	NM_018425	NA	Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.519G>A	chr10.hg19:g.99410781G>A		NA	D3DR59|Q9NSG8	hg19	CCDS7469.1	0.02	4.475356	GCTxTGC	COVERED																																																																																			NOVEL	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049735.1	0	9.631409	KEEP	0	0	0	32	1158	GG	0.999997	0.999994	0		+	9	60	341	0	0	24.722842	105	60	3984	191	ENST00000370631.3	0.078947	0.999996
DNMBP	23268	__UNKNOWN__	__UNKNOWN__	10	101689816	101689816	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:101689816A>G	ENST00000324109.4	-	5	2352				DNMBP_ENST00000342239.3_Intron|DNMBP_ENST00000543621.1_5'UTR|DNMBP-AS1_ENST00000434409.1_RNA	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	NA		NA			intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TGTCCCCTTCATGGTATTTGA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554	23268		Rho guanine nucleotide exchange factors	30373	protein-coding gene	gene with protein product	scaffold protein TUBA	611282			NA	10231032, 14506234	Standard	NM_015221	NM_015221	NA	Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2261-20913T>C	chr10.hg19:g.101689816A>G		NA	Q8IVY3|Q9Y2L3	hg19	CCDS7485.1	0.02	12.725994	TTCxTGG	COVERED																																																																																			NOVEL	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049832.2	3	29.185554	KEEP	0	0	0	97	3016	AA	1	1	0		-	53	60	1840	0	0	152.999349	199	60	7360	414	ENST00000324109.4	0.210317	1
NFKB2	4791	__UNKNOWN__	__UNKNOWN__	10	104157984	104157984	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:104157984G>A	ENST00000369966.3	+	10	1032	c.782G>A	c.(781-783)cGg>cAg	p.R261Q	NFKB2_ENST00000189444.6_Missense_Mutation_p.R261Q|NFKB2_ENST00000428099.1_Missense_Mutation_p.R261Q|NFKB2_ENST00000336486.5_3'UTR	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	261	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.	NA			extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	ATTGAGGTTCGGTTCTATGAG	0.562	NA	NA	T	IGH@	B-NHL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	0													117	116	117	NA		NA	NA	10		NA											NA				104157984		1889	4111	6000	SO:0001583	missense			X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150	4791		Ankyrin repeat domain containing	7795	protein-coding gene	gene with protein product		164012			NA	1876189	Standard		XM_005269860	NA	Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.782G>A	chr10.hg19:g.104157984G>A	ENSP00000358983:p.Arg261Gln	NA	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	hg19	CCDS41564.1	0.02	12.342788	TTCxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744417	0.69418	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	D;D;D	0.91631	-2.88;-2.88;-2.88	5.15	5.15	0.70609	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92067	0.7486	M	0.90542	3.125	0.80722	D	1	P;P;P	0.47762	0.9;0.872;0.648	B;B;B	0.30716	0.119;0.04;0.057	D	0.93758	0.7064	10	0.56958	D	0.05	.	18.6063	0.91266	0.0:0.0:1.0:0.0	.	261;261;261	D3DR86;Q00653;A8K9D9	.;NFKB2_HUMAN;.	Q	261	ENSP00000410256:R261Q;ENSP00000358983:R261Q;ENSP00000189444:R261Q	ENSP00000189444:R261Q	R	+	2	0	NFKB2	104147974	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.346000	0.97056	2.401000	0.81631	0.561000	0.74099	CGG	NOVEL	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050080.2	2	31.894861	KEEP	0	0	0	106	3521	GG	1	1	0		+	37	60	1337	0	0	104.435004	235	60	8030	474	ENST00000369966.3	0.136029	1
CNNM2	54805	__UNKNOWN__	__UNKNOWN__	10	104828454	104828454	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:104828454C>T	ENST00000369878.4	+	5	2330	c.2142C>T	c.(2140-2142)ggC>ggT	p.G714G	CNNM2_ENST00000475511.1_3'UTR|CNNM2_ENST00000433628.2_Silent_p.G714G	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	714		NA			magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CATACTATGGCGTGATGGCCC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													81	82	82	NA		NA	NA	10		NA											NA				104828454		1964	4158	6122	SO:0001819	synonymous_variant			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842	54805			103	protein-coding gene	gene with protein product		607803	cyclin M2	ACDP2	NA	21393841, 24699222	Standard	NM_017649	NM_017649	NA	Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.2142C>T	chr10.hg19:g.104828454C>T		NA	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	hg19	CCDS44474.1	0.02	4.159546	TGGxGTG	COVERED																																																																																			NOVEL	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050113.3	3	16.55193	KEEP	0	0	0	55	1871	CC	1	1	0		+	16	60	594	0	0	44.922326	134	60	4544	255	ENST00000369878.4	0.106667	1
TAF5	6877	__UNKNOWN__	__UNKNOWN__	10	105138232	105138232	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:105138232G>A	ENST00000369839.3	+	3	1061	c.1038G>A	c.(1036-1038)ccG>ccA	p.P346P	TAF5_ENST00000351396.4_Silent_p.P346P	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	346		NA			chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		ATGGGATGCCGCGTAGTAAGC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	70	71	NA		NA	NA	10		NA											NA				105138232		2203	4300	6503	SO:0001819	synonymous_variant			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835	6877		WD repeat domain containing	11539	protein-coding gene	gene with protein product		601787	TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD	TAF2D	NA	8884287, 8942982	Standard		NM_006951	NA	Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.1038G>A	chr10.hg19:g.105138232G>A		NA	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	hg19	CCDS7547.1	0.02	20.32035	GCCxCGT	COVERED																																																																																			NOVEL	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050144.1	10	23.17327	KEEP	0	0	0	77	2655	GG	1	1	0		+	30	60	1107	0	0	76.107149	457	60	16482	683	ENST00000369839.3	0.061602	1
TAF5	6877	__UNKNOWN__	__UNKNOWN__	10	105145185	105145185	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:105145185G>T	ENST00000369839.3	+	8	1790	c.1767G>T	c.(1765-1767)tgG>tgT	p.W589C	TAF5_ENST00000351396.4_Intron	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	589		NA			chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		ATCCAGTATGGGACACACAAT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	87	91	NA		NA	NA	10		NA											NA				105145185		2203	4300	6503	SO:0001583	missense			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835	6877		WD repeat domain containing	11539	protein-coding gene	gene with protein product		601787	TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD	TAF2D	NA	8884287, 8942982	Standard		NM_006951	NA	Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.1767G>T	chr10.hg19:g.105145185G>T	ENSP00000358854:p.Trp589Cys	NA	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	hg19	CCDS7547.1	0.02	6.831864	ATGxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.9	4.219790	0.79464	.	.	ENSG00000148835	ENST00000369839	T	0.60040	0.22	5.41	5.41	0.78517	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78880	0.4353	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81141	-0.1068	10	0.87932	D	0	-6.6708	19.5716	0.95423	0.0:0.0:1.0:0.0	.	589	Q15542	TAF5_HUMAN	C	589	ENSP00000358854:W589C	ENSP00000358854:W589C	W	+	3	0	TAF5	105135175	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	9.403000	0.97302	2.688000	0.91661	0.650000	0.86243	TGG	NOVEL	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050144.1	0	9.866552	KEEP	0	0	0	33	1071	GG	0.999998	0.999998	0		+	37	60	1375	0	0	116.007177	138	60	4831	249	ENST00000369839.3	0.211429	1
CALHM1	255022	__UNKNOWN__	__UNKNOWN__	10	105213377	105213377	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:105213377T>G	ENST00000329905.5	-	0	2819				RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	NA		NA			ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						agtggctgggtgactggccac	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933	255022			23494	protein-coding gene	gene with protein product		612234	family with sequence similarity 26, member C	FAM26C	NA	18585350	Standard	NM_001001412	NM_001001412	NA	Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.*1642A>C	chr10.hg19:g.105213377T>G		NA	Q5W091	hg19	CCDS7550.1	0.02	2.303581	GGGxGAC	COVERED																																																																																			NOVEL	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050165.1	1	2.429465	KEEP	0	4	43	24	600	TT	0.999997	0.999975	0		-	12	60	186	0	0	9.005977	91	60	2484	168	ENST00000329905.5	0.116505	0.999978
KIAA1598	57698	__UNKNOWN__	__UNKNOWN__	10	118666226	118666226	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:118666226G>A	ENST00000497044.1	-	0	1595				ENO4_ENST00000369207.2_Intron|KIAA1598_ENST00000392903.2_Silent_p.S464S|KIAA1598_ENST00000392901.4_Silent_p.S404S|KIAA1598_ENST00000260777.10_Intron|KIAA1598_ENST00000355371.4_Silent_p.S464S			A0MZ66	SHOT1_HUMAN	KIAA1598	NA		NA			axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		GGGATTTTAAGCTTCTTGAAC	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													89	82	85	NA		NA	NA	10		NA											NA				118666226		1568	3582	5150	SO:0001623	5_prime_UTR_variant			BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164	57698			29319	protein-coding gene	gene with protein product		611171			NA	10997877, 17030985	Standard	NM_018330	NM_001127211	NA	Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000497044.1:c.-2052C>T	chr10.hg19:g.118666226G>A		NA	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	hg19		0.02	17.631707	TAAxCTT	COVERED																																																																																			NOVEL	KIAA1598-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000050554.1	4	20.467473	KEEP	0	0	0	68	2476	GG	1	1	0		-	38	60	1317	0	0	94.15672	391	60	14845	620	ENST00000497044.1	0.088578	1
TACC2	10579	__UNKNOWN__	__UNKNOWN__	10	123845889	123845889	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs371332642		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:123845889G>A	ENST00000369005.1	+	4	4214	c.3874G>A	c.(3874-3876)Gcc>Acc	p.A1292T	TACC2_ENST00000515603.1_Missense_Mutation_p.A1292T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.A1292T|TACC2_ENST00000515273.1_Missense_Mutation_p.A1292T|TACC2_ENST00000334433.3_Missense_Mutation_p.A1292T|TACC2_ENST00000358010.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1292		NA			astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGGCTCCCTCGCCCCCCTGTT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	34	35	35	NA	,3874	-1.8	0	10		35	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	0,2,6501	AA,AG,GG	NA	0.0116,0.0227,0.0154	,benign	,1292/2949	123845889	2,13004	2203	4300	6503	SO:0001583	missense			AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162	10579			11523	protein-coding gene	gene with protein product		605302			NA	14767476	Standard		XM_005269388	NA	Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3874G>A	chr10.hg19:g.123845889G>A	ENSP00000358001:p.Ala1292Thr	NA	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	hg19	CCDS7626.1	0.02	8.795277	CTCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	2.236	-0.374998	0.05034	2.27E-4	1.16E-4	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02737	4.21;4.19;4.18;4.21;4.19	4.68	-1.84	0.07809	.	0.686468	0.11513	N	0.556503	T	0.01421	0.0046	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.47837	-0.9086	10	0.23302	T	0.38	-1.0114	4.9486	0.14002	0.5613:0.0:0.2483:0.1903	.	1292;1292;1292	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1292;1292;1292;1292;1292;1282	ENSP00000358001:A1292T;ENSP00000424467:A1292T;ENSP00000427618:A1292T;ENSP00000334280:A1292T;ENSP00000395048:A1292T	ENSP00000334280:A1292T	A	+	1	0	TACC2	123835879	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.419000	0.07071	-0.221000	0.09973	-1.101000	0.02118	GCC	NOVEL	TACC2-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090004.1	1	9.427988	KEEP	0	1	33	43	1423	GG	1	1	0		+	23	60	721	0	0	50.998168	200	60	6839	337	ENST00000369005.1	0.103139	1
GPR26	2849	__UNKNOWN__	__UNKNOWN__	10	125426338	125426338	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:125426338G>A	ENST00000284674.1	+	1	468	c.415G>A	c.(415-417)Gcc>Acc	p.A139T		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	139		NA			adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				CACCTTCCCAGCCGCCGCGCT	0.716	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	11	11	NA		NA	NA	10		NA											NA				125426338		2183	4254	6437	SO:0001583	missense				CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478	2849		GPCR / Class A : Orphans	4481	protein-coding gene	gene with protein product		604847			NA		Standard		NM_153442	NA	Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.415G>A	chr10.hg19:g.125426338G>A	ENSP00000284674:p.Ala139Thr	NA	Q2M2E2	hg19	CCDS7636.1	0.02	8.273222	CCAxCCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.180	0.589394	0.13812	.	.	ENSG00000154478	ENST00000284674	T	0.72394	-0.65	4.02	3.01	0.34805	GPCR, rhodopsin-like superfamily (1);	0.278519	0.32563	N	0.005926	T	0.36248	0.0960	N	0.01482	-0.84	0.09310	N	0.999992	B	0.12013	0.005	B	0.06405	0.002	T	0.12604	-1.0541	10	0.46703	T	0.11	-14.7691	3.2998	0.06979	0.4032:0.0:0.5968:0.0	.	139	Q8NDV2	GPR26_HUMAN	T	139	ENSP00000284674:A139T	ENSP00000284674:A139T	A	+	1	0	GPR26	125416328	0.892000	0.30473	0.218000	0.23776	0.029000	0.11900	2.911000	0.48774	2.067000	0.61834	0.655000	0.94253	GCC	NOVEL	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050850.1	2	8.727542	KEEP	0	0	0	29	1023	GG	0.999997	0.999997	0		+	14	60	421	0	0	26.815449	187	60	6713	291	ENST00000284674.1	0.069652	1
FAM175B	23172	__UNKNOWN__	__UNKNOWN__	10	126517483	126517483	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:126517483A>G	ENST00000298492.5	+	6	623					NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	NA		NA			cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						TTCTTTTGTCAGCAATATTTC	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													54	54	54	NA		NA	NA	10		NA											NA				126517483		2203	4299	6502	SO:0001627	intron_variant			D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660	23172			28975	protein-coding gene	gene with protein product	Abraxas brother	611144	KIAA0157	KIAA0157	NA	8590280	Standard	NM_032182	NM_032182	NA	Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.578+39A>G	chr10.hg19:g.126517483A>G		NA	B4DKR2|Q96H11	hg19	CCDS31308.2	0.02	6.304451	GTCxGCA	COVERED																																																																																			NOVEL	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050891.2	1	9.930023	KEEP	0	0	0	33	1033	AA	0.999998	0.999998	0		+	12	60	422	0	0	29.593437	143	60	5381	210	ENST00000298492.5	0.077419	1
FOXI2	399823	__UNKNOWN__	__UNKNOWN__	10	129539143	129539143	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:129539143A>G	ENST00000388920.4	+	0	2910					NM_207426.2	NP_997309.2	Q6ZQN5	FOXI2_HUMAN	forkhead box I2	NA		NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(3)	4		all_epithelial(44;0.0021)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)				AGGAGCCAGGAGTTGGGATAA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(54;1038 1280 2528 31583)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK128865	CCDS7655.2	10q26.2	2008-04-10			ENSG00000186766	ENSG00000186766	399823		Forkhead boxes	32448	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207426	NM_207426	NA	Approved	FLJ46831	uc009yas.2	Q6ZQN5	OTTHUMG00000019250	ENST00000388920.4:c.*1914A>G	chr10.hg19:g.129539143A>G		NA		hg19	CCDS7655.2	0.02	2.323157	AGGxGTT	COVERED																																																																																			NOVEL	FOXI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050984.2	0	3.912096	KEEP	0	0	0	13	420	AA	0.994391	0.965375	0		+	25	60	854	0	0	81.416275	28	60	1013	83	ENST00000388920.4	0.471698	0.97082
AL450307.1	0	__UNKNOWN__	__UNKNOWN__	10	133608302	133608302	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:133608302G>A	ENST00000341866.3	-	3	662	c.74C>T	c.(73-75)tCa>tTa	p.S25L							NA		NA									NA						TCTGCACAGTGACGGCCCGCC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000341866.3:c.74C>T	chr10.hg19:g.133608302G>A	ENSP00000340261:p.Ser25Leu	NA		hg19		0.02	8.058644	AGTxACG	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.143	-0.175809	0.06421	.	.	ENSG00000189275	ENST00000341866	.	.	.	0.867	-1.73	0.08081	.	.	.	.	.	T	0.28499	0.0705	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34229	-0.9837	5	0.87932	D	0	.	1.4846	0.02444	0.3024:0.0:0.3568:0.3408	.	.	.	.	L	25	.	ENSP00000340261:S25L	S	-	2	0	AL450307.1	133458292	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.924000	0.01565	-0.846000	0.04174	0.313000	0.20887	TCA	NOVEL	AL450307.1-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		1	12.940468	KEEP	0	0	0	43	1457	GG	1	1	0		-	9	60	273	0	0	16.88939	139	60	4940	311	ENST00000341866.3	0.060811	1
GPR123	84435	__UNKNOWN__	__UNKNOWN__	10	134942423	134942423	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:134942423T>C	ENST00000392607.3	+	7	1527	c.1091T>C	c.(1090-1092)aTg>aCg	p.M364T	GPR123_ENST00000607359.1_Missense_Mutation_p.M1083T|GPR123_ENST00000392606.2_Missense_Mutation_p.M267T	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	364		NA			G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CCCTGCAAGATGACCAACCTG	0.746	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													4	4	4	NA		NA	NA	10		NA											NA				134942423		1872	3737	5609	SO:0001583	missense			AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177	84435		-, GPCR / Class B : Orphans	13838	protein-coding gene	gene with protein product		612302			NA	12565841	Standard		XM_005252695	NA	Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.1091T>C	chr10.hg19:g.134942423T>C	ENSP00000376384:p.Met364Thr	NA	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	hg19	CCDS41580.1	0.02	7.2771	AGAxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	.	12.17	1.857439	0.32791	.	.	ENSG00000197177	ENST00000368577;ENST00000392607;ENST00000392606	T	0.03772	3.81	4.56	3.42	0.39159	.	0.217672	0.30940	N	0.008579	T	0.07954	0.0199	M	0.63428	1.95	0.26474	N	0.975224	B;B	0.24882	0.029;0.113	B;B	0.33196	0.01;0.159	T	0.14783	-1.0460	10	0.62326	D	0.03	-37.4112	8.5157	0.33244	0.0:0.0939:0.0:0.9061	.	364;1083	Q86SQ6;Q86SQ6-1	GP123_HUMAN;.	T	1083;364;268	ENSP00000376384:M364T	ENSP00000357566:M1083T	M	+	2	0	GPR123	134792413	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	3.503000	0.53340	0.890000	0.36211	0.459000	0.35465	ATG	NOVEL	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051113.2	2	14.427311	KEEP	0	0	0	48	1410	TT	1	1	0		+	19	60	670	0	0	50.918762	139	60	4888	255	ENST00000392607.3	0.120253	1
TUBGCP2	10844	__UNKNOWN__	__UNKNOWN__	10	135094800	135094800	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:135094800G>A	ENST00000252936.3	-	16	2589	c.2550C>T	c.(2548-2550)caC>caT	p.H850H	TUBGCP2_ENST00000368562.1_Silent_p.H443H|TUBGCP2_ENST00000417178.2_Silent_p.H720H|TUBGCP2_ENST00000368563.2_Silent_p.H850H|TUBGCP2_ENST00000543663.1_Silent_p.H878H			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	850		NA			G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		TGGCCATGCCGTGCTCACAGT	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													89	77	81	NA		NA	NA	10		NA											NA				135094800		2203	4300	6503	SO:0001819	synonymous_variant			AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640	10844			18599	protein-coding gene	gene with protein product		NA			NA	9566967	Standard		NM_001256617	NA	Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.2550C>T	chr10.hg19:g.135094800G>A		NA	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	hg19	CCDS7676.1	0.02	-0.350868	GCCxTGC	COVERED																																																																																			NOVEL	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051148.1	1	2.406623	KEEP	0	0	0	8	249	GG	0.99254	0.87116	0		-	10	60	369	0	0	31.903779	30	60	989	58	ENST00000252936.3	0.25	0.877708
ZNF511	118472	__UNKNOWN__	__UNKNOWN__	10	135125759	135125759	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr10:135125759G>A	ENST00000361518.5	+	5	1149				ZNF511_ENST00000463816.2_Intron|ZNF511_ENST00000359035.3_3'UTR|ZNF511_ENST00000368554.4_Intron	NM_145806.2	NP_665805.2	Q8NB15	ZN511_HUMAN	zinc finger protein 511	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		all cancers(32;7.56e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.15e-06)|Epithelial(32;9.99e-06)		GACCTGTGCCGTCTGCCTTTC	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091711	CCDS7677.1	10q26.3	2010-04-12			ENSG00000198546	ENSG00000198546	118472		Zinc fingers, C2H2-type	28445	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_145806	NM_145806	NA	Approved	MGC30006	uc001lmj.1	Q8NB15	OTTHUMG00000019317	ENST00000361518.5:c.680+414G>A	chr10.hg19:g.135125759G>A		NA	A8K8L5|Q8WUP1|Q96BV2	hg19	CCDS7677.1	0.02	22.400441	GCCxTCT	COVERED																																																																																			NOVEL	ZNF511-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051142.1	6	38.955054	KEEP	0	2	55	149	5076	GG	1	1	0		+	41	60	1464	0	0	104.05729	469	60	16167	893	ENST00000361518.5	0.080392	1
BET1L	51272	__UNKNOWN__	__UNKNOWN__	11	203766	203766	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:203766G>C	ENST00000382762.3	-	0	1978				RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000410108.1_Intron|BET1L_ENST00000325147.9_3'UTR	NM_001098787.1|NM_016526.4	NP_001092257.1|NP_057610.2			Bet1 golgi vesicular membrane trafficking protein-like	NA		NA									NA		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;4.2e-27)|Epithelial(43;2.8e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.7e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		AAGCCCCAGAGACATGGAGGC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF234160	CCDS7689.1, CCDS41582.1	11p15.5	2013-03-08	2013-03-08		ENSG00000177951	ENSG00000177951	51272			19348	protein-coding gene	gene with protein product	golgi integral membrane protein 3	615417	blocked early in transport 1 homolog (S. cerevisiae) like, blocked early in transport 1 homolog (S. cerevisiae)-like		NA	9242691, 15004235	Standard	NM_016526	NM_016526	NA	Approved	GS15, GOLIM3	uc001loe.2	Q9NYM9	OTTHUMG00000119071	ENST00000382762.3:c.*1536C>G	chr11.hg19:g.203766G>C		NA		hg19	CCDS41582.1	0.02	4.755236	AGAxACA	COVERED																																																																																			NOVEL	BET1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239285.1	3	15.349099	KEEP	0	0	0	51	1783	GG	1	1	0		-	49	60	1865	0	0	170.70178	90	60	3413	240	ENST00000382762.3	0.352518	1
PHRF1	57661	__UNKNOWN__	__UNKNOWN__	11	598591	598591	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:598591A>G	ENST00000416188.2	+	9	1117				PHRF1_ENST00000264555.5_Intron|PHRF1_ENST00000413872.2_Intron|PHRF1_ENST00000533464.1_Intron			Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	NA		NA			mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGCTGTGGGCATTTCCATTTC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047	57661		RING-type (C3HC4) zinc fingers, Zinc fingers, PHD-type	24351	protein-coding gene	gene with protein product	CTD binding SR like protein rA9, protein phosphatase 1, regulatory subunit 125	611780		RNF221	NA		Standard	NM_020901	XM_005253027	NA	Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000416188.2:c.1024+89A>G	chr11.hg19:g.598591A>G		NA	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	hg19	CCDS44507.1	0.02	7.429316	GGCxTTT	COVERED																																																																																			NOVEL	PHRF1-008	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398149.1	0	18.045153	KEEP	0	0	0	60	1780	AA	1	1	0		+	144	60	5109	0	0	543.841694	31	60	1062	258	ENST00000416188.2	0.822857	1
TSPAN4	7106	__UNKNOWN__	__UNKNOWN__	11	864429	864429	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:864429C>A	ENST00000397404.1	+	5	514				TSPAN4_ENST00000409543.2_Intron|TSPAN4_ENST00000409531.1_Intron|TSPAN4_ENST00000397406.1_Intron|TSPAN4_ENST00000525201.1_Intron|TSPAN4_ENST00000397396.1_Intron|TSPAN4_ENST00000397397.2_Intron|TSPAN4_ENST00000346501.4_Intron|TSPAN4_ENST00000397411.2_Intron|TSPAN4_ENST00000397408.1_Intron	NM_001025237.1	NP_001020408.1	O14817	TSN4_HUMAN	tetraspanin 4	NA		NA			protein complex assembly (GO:0006461)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	antigen binding (GO:0003823)|integrin binding (GO:0005178)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)	3		all_cancers(49;2.64e-08)|all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)		all cancers(45;4.32e-25)|Epithelial(43;3.29e-24)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCCTGCCCCCTCCACAGTTC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	87	87	NA		NA	NA	11		NA											NA				864429		2203	4299	6502	SO:0001627	intron_variant			AF022813	CCDS7721.1, CCDS41589.1	11p15.5	2013-02-14	2005-03-21	2005-03-21	ENSG00000214063	ENSG00000214063	7106		Tetraspanins	11859	protein-coding gene	gene with protein product		602644	transmembrane 4 superfamily member 7	TM4SF7	NA	9360996	Standard		XM_005253102	NA	Approved	NAG-2, TSPAN-4, TETRASPAN	uc001lsf.1	O14817	OTTHUMG00000133305	ENST00000397404.1:c.256-8C>A	chr11.hg19:g.864429C>A		NA	Q6IAP6	hg19	CCDS7721.1	0.02	6.968309	CCCxTCC	COVERED																																																																																			NOVEL	TSPAN4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257102.2	1	20.161527	KEEP	0	0	0	67	2308	CC	1	1	0		+	40	60	1415	0	0	121.637259	119	60	4301	282	ENST00000397404.1	0.251572	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016819	1016819	__UNKNOWN__	Silent	SNP	G	G	T	rs369828826		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:1016819G>T	ENST00000421673.2	-	31	6032	c.5982C>A	c.(5980-5982)acC>acA	p.T1994T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1994	Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTTGGATAGGTAGTGGTGG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													1471	1465	1467	NA		NA	NA	11		NA											NA				1016819		2203	4298	6501	SO:0001819	synonymous_variant			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5982C>A	chr11.hg19:g.1016819G>T		NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	37.741969	ATAxGTA	COVERED																																																																																			NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	172	32.260315	KEEP	42	32	987	454	15994	GG	1	1	0		-	73	60	2589	0	0	206.898162	380	60	13789	1668	ENST00000421673.2	0.161148	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1213367	1213367	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:1213367G>A	ENST00000358378.6	+	0	608							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		AAAATCTGCCGCCGACCTGAG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													196	204	202	NA		NA	NA	11		NA											NA				1213367		875	1990	2865	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*605G>A	chr11.hg19:g.1213367G>A		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	37.544217	GCCxCCG	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	14	17.669763	KEEP	0	30	874	367	12231	GG	1	1	0		+	22	60	764	0	0	49.66656	389	60	13048	1565	ENST00000358378.6	0.053528	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1213460	1213460	__UNKNOWN__	3'UTR	SNP	G	G	A	rs200307483		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:1213460G>A	ENST00000358378.6	+	0	701							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		CAGTGCAGCCGTGAAGAGGGC	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													397	389	392	NA		NA	NA	11		NA											NA				1213460		875	1990	2865	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*698G>A	chr11.hg19:g.1213460G>A		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	41.078737	GCCxTGA	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	13	38.397459	KEEP	0	21	641	353	11943	GG	1	1	0		+	23	60	856	0	0	59.562801	333	60	11387	1514	ENST00000358378.6	0.064607	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1221129	1221129	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:1221129G>A	ENST00000358378.6	+	0	3245							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		CAGCAGCAGGGCTGCAGCTCC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													24	24	24	NA		NA	NA	11		NA											NA				1221129		867	1985	2852	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*3242G>A	chr11.hg19:g.1221129G>A		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	15.639873	AGGxCTG	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	2	20.459693	KEEP	0	0	0	68	2344	GG	1	1	0		+	35	60	1244	0	0	91.676128	316	60	11473	512	ENST00000358378.6	0.099715	1
INS	3630	__UNKNOWN__	__UNKNOWN__	11	2181196	2181196	__UNKNOWN__	Silent	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:2181196A>C	ENST00000397262.1	-	2	451	c.219T>G	c.(217-219)ggT>ggG	p.G73G	INS-IGF2_ENST00000397270.1_Intron|INS_ENST00000512523.1_Intron|INS_ENST00000250971.3_Silent_p.G73G|INS_ENST00000381330.4_Silent_p.G73G	NM_001185098.1	NP_001172027.1	P01308	INS_HUMAN	insulin	73		NA			activation of protein kinase B activity (GO:0032148)|acute-phase response (GO:0006953)|alpha-beta T cell activation (GO:0046631)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of fatty acid metabolic process (GO:0045922)|negative regulation of feeding behavior (GO:2000252)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of glycogen catabolic process (GO:0045818)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of protein secretion (GO:0050709)|negative regulation of proteolysis (GO:0045861)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|negative regulation of vasodilation (GO:0045908)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of respiratory burst (GO:0060267)|positive regulation of vasodilation (GO:0045909)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of insulin secretion (GO:0050796)|regulation of protein localization (GO:0032880)|regulation of protein secretion (GO:0050708)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transmembrane transporter activity (GO:0022898)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	endoplasmic reticulum lumen (GO:0005788)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)|identical protein binding (GO:0042802)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protease binding (GO:0002020)			haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		Lung NSC(207;8.94e-06)|all_epithelial(84;3.17e-05)|all_lung(207;3.67e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.14)		GGCTGCCTGCACCAGGGCCCC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													31	28	29	NA		NA	NA	11		NA											NA				2181196		2173	4279	6452	SO:0001819	synonymous_variant			X70508	CCDS7729.1	11p15.5	2014-02-03			ENSG00000254647	ENSG00000254647	3630			6081	protein-coding gene	gene with protein product		176730	insulin-dependent diabetes mellitus 2	IDDM2, IDDM1	NA	6243748, 7773291	Standard	NM_000207	NM_000207	NA	Approved			P01308	OTTHUMG00000009558	ENST00000397262.1:c.219T>G	chr11.hg19:g.2181196A>C		NA	Q5EEX2	hg19	CCDS7729.1	0.02	1.683972	TGCxCCA	COVERED																																																																																			NOVEL	INS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026395.3	0	3.607577	KEEP	0	0	0	12	329	AA	0.993634	0.98989	0		-	5	60	164	0	0	11.00097	64	60	2033	90	ENST00000397262.1	0.072464	0.996233
NUP98	4928	__UNKNOWN__	__UNKNOWN__	11	3794882	3794882	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:3794882A>T	ENST00000324932.7	-	6	1003	c.583T>A	c.(583-585)Tat>Aat	p.Y195N	NUP98_ENST00000355260.3_Missense_Mutation_p.Y195N|NUP98_ENST00000397004.4_Missense_Mutation_p.Y195N|NUP98_ENST00000359171.4_Missense_Mutation_p.Y195N|NUP98_ENST00000397007.4_Missense_Mutation_p.Y195N	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	195	GLEBS; interaction with RAE1.|Gly/Thr-rich.	NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TTGCTTTCATATTCTTTCATA	0.348	NA	NA	T	HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11	AML									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	0													130	112	118	NA		NA	NA	11		NA											NA				3794882		2201	4298	6499	SO:0001583	missense			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713	4928			8068	protein-coding gene	gene with protein product		601021	nucleoporin 98kD		NA	9166830	Standard	NM_016320	NM_139131	NA	Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.583T>A	chr11.hg19:g.3794882A>T	ENSP00000316032:p.Tyr195Asn	NA	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	hg19	CCDS7746.1	0.02	4.540578	CATxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	26.6	4.752802	0.89753	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.84543	0.5495	M	0.91140	3.18	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.993;0.994;1.0;1.0	D;P;P;D;D	0.76575	0.972;0.885;0.839;0.988;0.988	D	0.86086	0.1547	9	0.38643	T	0.18	.	14.6811	0.69017	1.0:0.0:0.0:0.0	.	195;195;195;195;195	P52948;P52948-3;P52948-4;P52948-2;P52948-5	NUP98_HUMAN;.;.;.;.	N	195	.	ENSP00000316032:Y195N	Y	-	1	0	NUP98	3751458	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.060000	0.93907	2.151000	0.67156	0.533000	0.62120	TAT	NOVEL	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032766.3	1	5.112044	KEEP	0	0	0	17	526	AA	0.999366	0.999365	0		-	22	60	792	0	0	65.055004	96	60	3396	158	ENST00000324932.7	0.186441	0.999998
OR52I2	143502	__UNKNOWN__	__UNKNOWN__	11	4608262	4608262	__UNKNOWN__	Missense_Mutation	SNP	A	A	C	rs12793957	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:4608262A>C	ENST00000312614.4	+	1	242	c.220A>C	c.(220-222)Atc>Ctc	p.I74L		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	74		NA	I -> L (in dbSNP:rs12793957). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		AGGAAACACCATCATCGTGAC	0.502	NA	NA											A|||	1130	0.225639	0.1626	0.2839	5008	,	,	NA	24024	0.127	NA	0.2992	False	NA	,,,	NA	NA	NA	2504	0.2955	NA	NA	NA						NA		NA				0								A	LEU/ILE	390,4012		24,342,1835	258	229	239	NA	220	-0.5	0.6	11	dbSNP_121	239	2193,6399		321,1551,2424	no	missense	OR52I2	NM_001005170.2	5	345,1893,4259	CC,CA,AA	NA	25.5237,8.8596,19.8784	benign	74/351	4608262	2583,10411	2201	4296	6497	SO:0001583	missense			BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288	143502		GPCR / Class A : Olfactory receptors	15221	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001005170	NM_001005170	NA	Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.220A>C	chr11.hg19:g.4608262A>C	ENSP00000308764:p.Ile74Leu	NA	B2RNJ5|B9EKV8|Q6IFJ8	hg19	CCDS31355.1	0.02	13.191476	ACCxTCA	COVERED	243	0.11126373626373626	29	0.05894308943089431	62	0.1712707182320442	4	0.006993006993006993	148	0.19525065963060687	A	0.011	-1.704217	0.00719	0.088596	0.255237	ENSG00000226288	ENST00000312614	T	0.00570	6.51	4.1	-0.464	0.12160	GPCR, rhodopsin-like superfamily (1);	0.385935	0.18907	N	0.127868	T	0.00012	0.0000	N	0.00377	-1.585	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.08638	-1.0712	9	0.23302	T	0.38	-3.6158	13.6107	0.62076	0.6266:0.3734:0.0:0.0	rs12793957	74	Q8NH67	O52I2_HUMAN	L	74	ENSP00000308764:I74L	ENSP00000308764:I74L	I	+	1	0	OR52I2	4564838	0.000000	0.05858	0.559000	0.28332	0.088000	0.18126	-1.650000	0.01991	0.046000	0.15833	-0.244000	0.11960	ATC	NOVEL	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385946.1	7	3.558668	KEEP	19	2	72	37	1102	AA	1	1	0		+	28	39	990	0	0	70.185315	317	60	11510	458	ENST00000312614.4	0.081159	1
OR52A5	390054	__UNKNOWN__	__UNKNOWN__	11	5153512	5153512	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:5153512C>G	ENST00000307388.1	-	1	360	c.361G>C	c.(361-363)Gcc>Ccc	p.A121P		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	121		NA			detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		CGATCCAGGGCCATTGCCAGA	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													70	60	63	NA		NA	NA	11		NA											NA				5153512		2201	4298	6499	SO:0001583	missense			BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944	390054		GPCR / Class A : Olfactory receptors	19580	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001005160	NM_001005160	NA	Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.361G>C	chr11.hg19:g.5153512C>G	ENSP00000303469:p.Ala121Pro	NA		hg19	CCDS31373.1	0.02	7.388356	GGGxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.7	4.329268	0.81690	.	.	ENSG00000171944	ENST00000307388	T	0.56103	0.48	5.22	5.22	0.72569	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000272	T	0.80722	0.4677	H	0.94925	3.6	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85964	0.1472	10	0.87932	D	0	.	17.5151	0.87771	0.0:1.0:0.0:0.0	.	121	Q9H2C5	O52A5_HUMAN	P	121	ENSP00000303469:A121P	ENSP00000303469:A121P	A	-	1	0	OR52A5	5110088	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	3.376000	0.52417	2.707000	0.92482	0.655000	0.94253	GCC	NOVEL	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000142823.1	7	4.213346	KEEP	0	0	0	14	489	CC	0.995343	0.995343	0		-	61	60	2237	0	0	205.003581	107	60	3857	219	ENST00000307388.1	0.363095	1
HBB	3043	__UNKNOWN__	__UNKNOWN__	11	5247037	5247037	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:5247037A>G	ENST00000335295.4	-	3	365					NM_000518.4	NP_000509.1	P68871	HBB_HUMAN	hemoglobin, beta	NA		NA			bicarbonate transport (GO:0015701)|blood coagulation (GO:0007596)|hydrogen peroxide catabolic process (GO:0042744)|nitric oxide transport (GO:0030185)|oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|platelet aggregation (GO:0070527)|positive regulation of cell death (GO:0010942)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein heterooligomerization (GO:0051291)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|renal absorption (GO:0070293)|response to hydrogen peroxide (GO:0042542)|small molecule metabolic process (GO:0044281)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|hemoglobin binding (GO:0030492)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|skin(1)	15		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Iron Dextran(DB00893)	CCTTATCCCAACCATAAAATA	0.398	NA	NA							Sickle Cell Trait					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database		J00173	CCDS7753.1	11p15.5	2014-05-19			ENSG00000244734	ENSG00000244734	3043			4827	protein-coding gene	gene with protein product		141900			NA	2649166	Standard	NM_000518	NM_000518	NA	Approved	CD113t-C, HBD, beta-globin	uc001mae.1	P68871	OTTHUMG00000066678	ENST00000335295.4:c.316-81T>C	chr11.hg19:g.5247037A>G		NA	A4GX73|B2ZUE0|P02023|Q13852|Q14481|Q14510|Q45KT0|Q549N7|Q6FI08|Q6R7N2|Q8IZI1|Q9BX96|Q9UCD6|Q9UCP8|Q9UCP9	hg19	CCDS7753.1	0.02	2.136368	CCAxCCA	COVERED																																																																																			NOVEL	HBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000142977.2	0	3.3099	KEEP	0	0	0	11	343	AA	0.993072	0.993012	0		-	11	60	424	0	0	32.755418	86	60	3039	117	ENST00000335295.4	0.113402	0.99994
HBG1	3047	__UNKNOWN__	__UNKNOWN__	11	5269572	5269572	__UNKNOWN__	3'UTR	SNP	A	A	C	rs201642811	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:5269572A>C	ENST00000330597.3	-	0	548					NM_000559.2	NP_000550.2	P69891	HBG1_HUMAN	hemoglobin, gamma A	NA		NA			blood coagulation (GO:0007596)	cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			large_intestine(1)|lung(3)|skin(1)	5		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAAAGCTCTGAATCATGGGCA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(117;2080 2193 33416 49679)					NA		NA				0													47	51	50	NA		NA	NA	11		NA											NA				5269572		2201	4298	6499	SO:0001624	3_prime_UTR_variant			M91036	CCDS7754.1	11p15.5	2014-05-19			ENSG00000213934	ENSG00000213934	3047			4831	protein-coding gene	gene with protein product		142200			NA	2649166	Standard	NM_000559	NM_000559	NA	Approved	HBG-T2	uc001mah.1	P69891	OTTHUMG00000066681	ENST00000330597.3:c.*17T>G	chr11.hg19:g.5269572A>C		NA	P02096|P62027|Q549G1|Q8TDA1|Q96FH7	hg19	CCDS7754.1	0.02	22.545151	CTGxATC	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.871	-0.732124	0.03135	.	.	ENSG00000213934	ENST00000380256	.	.	.	1.04	-2.08	0.07254	.	.	.	.	.	T	0.11537	0.0281	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.23440	-1.0188	5	0.05959	T	0.93	.	3.6785	0.08301	0.1996:0.4964:0.0:0.304	rs11546324;rs11548394	.	.	.	M	153	.	ENSP00000369606:I153M	I	-	3	3	HBG1	5226148	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	-0.827000	0.04424	-1.623000	0.01558	-1.286000	0.01371	ATT	NOVEL	HBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000142982.1	1	12.669263	KEEP	1	1	37	55	1789	AA	1	1	0		-	28	33	1063	0	0	85.656874	155	60	5696	716	ENST00000330597.3	0.153005	1
OR52E8	390079	__UNKNOWN__	__UNKNOWN__	11	5878088	5878088	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:5878088G>C	ENST00000537935.1	-	1	876	c.845C>G	c.(844-846)gCc>gGc	p.A282G	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	282		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATACAGGTTGGCTAATATAAT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	117	111	NA		NA	NA	11		NA											NA				5878088		2144	4296	6440	SO:0001583	missense			BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269	390079		GPCR / Class A : Olfactory receptors	15217	protein-coding gene	gene with protein product		NA	olfactory receptor, family 52, subfamily E, member 8 pseudogene		NA		Standard	NM_001005168	NM_001005168	NA	Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.845C>G	chr11.hg19:g.5878088G>C	ENSP00000444054:p.Ala282Gly	NA	B9EH38	hg19	CCDS31400.1	0.02	17.365579	TTGxCTA	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398204	0.25205	.	.	ENSG00000183269	ENST00000537935	T	0.00207	8.55	4.12	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000068	T	0.00384	0.0012	M	0.83774	2.66	0.09310	N	1	P	0.40180	0.705	P	0.46975	0.533	T	0.12293	-1.0553	10	0.72032	D	0.01	.	11.9845	0.53140	0.0:0.0:0.825:0.175	.	282	Q6IFG1	O52E8_HUMAN	G	282	ENSP00000444054:A282G	ENSP00000444054:A282G	A	-	2	0	OR52E8	5834664	0.003000	0.15002	0.005000	0.12908	0.001000	0.01503	0.960000	0.29253	1.044000	0.40200	0.549000	0.68633	GCC	NOVEL	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401145.1	5	12.331339	KEEP	0	0	0	41	1382	GG	1	1	0		-	301	60	10658	1	0	1116.332344	92	60	3343	484	ENST00000537935.1	0.765903	1
TPP1	1200	__UNKNOWN__	__UNKNOWN__	11	6637624	6637624	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:6637624T>C	ENST00000299427.6	-	8	1057	c.997A>G	c.(997-999)Agc>Ggc	p.S333G	TPP1_ENST00000533371.1_Missense_Mutation_p.S90G	NM_000391.3	NP_000382.3	P49638	TTPA_HUMAN	tripeptidyl peptidase I	0		NA			embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)	Vitamin E(DB00163)	TAGGCGCTGCTGAGGGAGTCC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	82	84	NA		NA	NA	11		NA											NA				6637624		2201	4296	6497	SO:0001583	missense			AF017456	CCDS7770.1	11p15.4	2014-09-17	2004-12-09	2004-12-10	ENSG00000166340	ENSG00000166340	1200			2073	protein-coding gene	gene with protein product	TPP I	607998	ceroid-lipofuscinosis, neuronal 2, late infantile (Jansky-Bielschowsky disease), spinocerebellar ataxia, autosomal recessive 7	CLN2, SCAR7	NA	9653647, 23418007	Standard		NM_000391	NA	Approved		uc001mel.1	O14773	OTTHUMG00000133404	ENST00000299427.6:c.997A>G	chr11.hg19:g.6637624T>C	ENSP00000299427:p.Ser333Gly	NA	Q71V64	hg19	CCDS7770.1	0.02	1.924572	TGCxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	8.401	0.841876	0.16963	.	.	ENSG00000166340	ENST00000299427;ENST00000533371	D;D	0.93133	-3.17;-3.17	5.27	5.27	0.74061	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.098709	0.64402	D	0.000001	D	0.87708	0.6245	L	0.43152	1.355	0.80722	D	1	B	0.33135	0.399	B	0.27262	0.078	D	0.84243	0.0473	10	0.23891	T	0.37	-7.3569	8.7273	0.34478	0.1808:0.0:0.0:0.8192	.	333	O14773	TPP1_HUMAN	G	333;90	ENSP00000299427:S333G;ENSP00000437066:S90G	ENSP00000299427:S333G	S	-	1	0	TPP1	6594200	1.000000	0.71417	1.000000	0.80357	0.062000	0.15995	3.837000	0.55820	2.007000	0.58848	0.454000	0.30748	AGC	NOVEL	TPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257261.2	1	8.726648	KEEP	0	0	0	29	925	TT	0.999997	0.999723	0		-	4	60	147	0	0	9.564887	83	60	3080	143	ENST00000299427.6	0.045977	0.999726
DCHS1	8642	__UNKNOWN__	__UNKNOWN__	11	6647834	6647834	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:6647834T>C	ENST00000299441.3	-	15	6724	c.6313A>G	c.(6313-6315)Agc>Ggc	p.S2105G		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2105	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGAGAATGCTGTAGGTGATG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													196	186	189	NA		NA	NA	11		NA											NA				6647834		2201	4296	6497	SO:0001583	missense			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341	8642		Cadherins / Cadherin-related	13681	protein-coding gene	gene with protein product	cadherin-related family member 6	603057	protocadherin 16, dachsous 1 (Drosophila)	CDH25, PCDH16	NA	9199196	Standard	NM_003737	XM_005253207	NA	Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.6313A>G	chr11.hg19:g.6647834T>C	ENSP00000299441:p.Ser2105Gly	NA	O15098	hg19	CCDS7771.1	0.02	4.082704	TGCxGTA	COVERED	.	.	.	.	.	.	.	.	.	.	T	20.0	3.929743	0.73327	.	.	ENSG00000166341	ENST00000299441	T	0.55760	0.5	4.93	4.93	0.64822	Cadherin (4);Cadherin-like (1);	0.000000	0.53938	D	0.000051	T	0.73055	0.3538	M	0.82193	2.58	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.75379	-0.3338	10	0.44086	T	0.13	.	13.5556	0.61757	0.0:0.0:0.0:1.0	.	2105	Q96JQ0	PCD16_HUMAN	G	2105	ENSP00000299441:S2105G	ENSP00000299441:S2105G	S	-	1	0	DCHS1	6604410	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.317000	0.79018	2.080000	0.62538	0.460000	0.39030	AGC	NOVEL	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257258.1	6	10.531177	KEEP	0	0	0	35	1096	TT	0.999999	0.999999	0		-	29	60	989	0	0	82.131163	107	60	4027	207	ENST00000299441.3	0.213235	1
TRIM66	9866	__UNKNOWN__	__UNKNOWN__	11	8646062	8646062	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:8646062G>T	ENST00000402157.2	-	14	2862	c.2422C>A	c.(2422-2424)Ctg>Atg	p.L808M	TRIM66_ENST00000299550.6_Intron			O15016	TRI66_HUMAN	tripartite motif containing 66	799		NA				aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						CCTTGTCCCAGTAAGTCAGTG	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436	9866		Tripartite motif containing / Tripartite motif containing, Zinc fingers, PHD-type	29005	protein-coding gene	gene with protein product		612000	chromosome 11 open reading frame 29, tripartite motif-containing 66	C11orf29	NA	9205841	Standard	XM_084529	NM_014818	NA	Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000402157.2:c.2422C>A	chr11.hg19:g.8646062G>T	ENSP00000384876:p.Leu808Met	NA	Q9BQQ4	hg19		0.02	6.088695	CCAxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.39	1.924504	0.34002	.	.	ENSG00000166436	ENST00000402157	T	0.73363	-0.74	5.7	0.44	0.16572	.	.	.	.	.	T	0.68495	0.3007	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58685	-0.7593	6	0.30078	T	0.28	-0.0468	6.3235	0.21231	0.25:0.3305:0.4195:0.0	.	.	.	.	M	808	ENSP00000384876:L808M	ENSP00000384876:L808M	L	-	1	2	TRIM66	8602638	1.000000	0.71417	0.997000	0.53966	0.350000	0.29205	0.914000	0.28624	0.111000	0.17947	0.655000	0.94253	CTG	NOVEL	TRIM66-001	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000318299.2	3	10.233182	KEEP	0	0	0	34	1206	GG	0.999998	0.999998	0		-	8	60	266	0	0	16.082605	183	60	6916	276	ENST00000402157.2	0.041885	1
MRVI1	10335	__UNKNOWN__	__UNKNOWN__	11	10631360	10631360	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:10631360C>A	ENST00000423302.2	-	11	1635	c.1486G>T	c.(1486-1488)Gag>Tag	p.E496*	MRVI1_ENST00000541483.1_Nonsense_Mutation_p.E290*|MRVI1_ENST00000545852.1_Nonsense_Mutation_p.E181*|MRVI1_ENST00000527509.2_Nonsense_Mutation_p.E405*|MRVI1_ENST00000552103.1_Nonsense_Mutation_p.E405*|MRVI1_ENST00000421747.1_Nonsense_Mutation_p.E487*|MRVI1_ENST00000424001.1_Nonsense_Mutation_p.E181*|MRVI1_ENST00000436272.1_Nonsense_Mutation_p.E469*|MRVI1_ENST00000531107.1_Nonsense_Mutation_p.E488*|MRVI1_ENST00000534266.2_Nonsense_Mutation_p.E181*|MRVI1_ENST00000558540.1_Nonsense_Mutation_p.E181*|MRVI1_ENST00000547195.1_Nonsense_Mutation_p.E405*|LYVE1_ENST00000531706.1_Intron	NM_001206880.1|NM_130385.3	NP_001193809.1|NP_569056.4	Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	469		NA			blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		CTCTTTGACTCTTCTTCCTCA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													54	55	55	NA		NA	NA	11		NA											NA				10631360		1880	4100	5980	SO:0001587	stop_gained			AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952	10335			7237	protein-coding gene	gene with protein product	inositol 1,4,5-triphosphate-associated cGMP kinase substrate, IP3R-associated cGMP kinase substrate	604673			NA	10321731	Standard	NM_001098579	NM_001098579	NA	Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000423302.2:c.1486G>T	chr11.hg19:g.10631360C>A	ENSP00000412130:p.Glu496*	NA	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	hg19	CCDS55746.1	0.02	8.334241	ACTxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	38	6.804897	0.97853	.	.	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000545852;ENST00000424001;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509	.	.	.	6.17	6.17	0.99709	.	0.126578	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-14.5025	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	487;470;469;405;405;181;181;496;290;488;405	.	ENSP00000307885:E470X	E	-	1	0	MRVI1	10587936	1.000000	0.71417	0.980000	0.43619	0.903000	0.53119	6.581000	0.74045	2.941000	0.99782	0.655000	0.94253	GAG	NOVEL	MRVI1-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386137.2	4	27.087895	KEEP	0	0	0	90	3238	CC	1	1	0		-	8	60	290	0	0	17.744292	222	60	8548	415	ENST00000423302.2	0.034783	1
USP47	55031	__UNKNOWN__	__UNKNOWN__	11	11941998	11941998	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:11941998C>T	ENST00000399455.2	+	11	1355	c.1235C>T	c.(1234-1236)cCc>cTc	p.P412L	USP47_ENST00000339865.5_Missense_Mutation_p.P324L|USP47_ENST00000539466.1_5'UTR|USP47_ENST00000527733.1_Missense_Mutation_p.P392L	NM_001282659.1	NP_001269588.1	Q96K76	UBP47_HUMAN	ubiquitin specific peptidase 47	412	USP.	NA			base-excision repair (GO:0006284)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell growth (GO:0030307)|response to drug (GO:0042493)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-specific protease activity (GO:0004843)|WD40-repeat domain binding (GO:0071987)			breast(4)|endometrium(7)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46				Epithelial(150;0.000339)		ATGACATTTCCCGAGGAACTA	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													105	99	101	NA		NA	NA	11		NA											NA				11941998		1829	4073	5902	SO:0001583	missense			AK027362	CCDS41619.1, CCDS60725.1	11p15.2	2008-02-05	2005-08-08		ENSG00000170242	ENSG00000170242	55031		Ubiquitin-specific peptidases	20076	protein-coding gene	gene with protein product		614460	Trf (TATA binding protein-related factor)-proximal homolog (Drosophila), ubiquitin specific protease 47		NA	12838346	Standard	NM_017944	XM_005252997	NA	Approved		uc001mjr.3	Q96K76	OTTHUMG00000165685	ENST00000399455.2:c.1235C>T	chr11.hg19:g.11941998C>T	ENSP00000382382:p.Pro412Leu	NA	B3KXF5|E9PM46|Q658U0|Q86Y73|Q8TEP6|Q9BWI0|Q9NWN1	hg19		0.02	6.125906	TTCxCGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	29.0	4.964793	0.92791	.	.	ENSG00000170242	ENST00000339865;ENST00000527733;ENST00000399455;ENST00000535588	T;T;T	0.11495	2.77;2.77;2.77	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.54415	0.1857	H	0.99026	4.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74942	-0.3492	10	0.87932	D	0	.	18.9869	0.92775	0.0:1.0:0.0:0.0	.	392;324	E9PM46;Q96K76-2	.;.	L	324;392;412;412	ENSP00000339957:P324L;ENSP00000433146:P392L;ENSP00000382382:P412L	ENSP00000339957:P324L	P	+	2	0	USP47	11898574	1.000000	0.71417	0.977000	0.42913	0.980000	0.70556	7.818000	0.86416	2.591000	0.87537	0.563000	0.77884	CCC	NOVEL	USP47-003	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000385853.2	2	12.037986	KEEP	0	0	0	40	1367	CC	1	1	0		+	7	60	241	0	0	14.886673	157	60	5574	247	ENST00000399455.2	0.042683	1
MICAL2	9645	__UNKNOWN__	__UNKNOWN__	11	12183988	12183988	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:12183988C>G	ENST00000256194.4	+	3	552				MICAL2_ENST00000342902.5_Intron|MICAL2_ENST00000527546.1_Intron|MICAL2_ENST00000379612.3_Intron|MICAL2_ENST00000537344.1_Intron	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	NA		NA			actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CCCTCCTAGTCTTACCTTTGC	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													42	40	41	NA		NA	NA	11		NA											NA				12183988		2201	4293	6494	SO:0001627	intron_variant			AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816	9645			24693	protein-coding gene	gene with protein product		608881			NA	12110185	Standard	NM_014632	XM_005253249	NA	Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.264+22C>G	chr11.hg19:g.12183988C>G		NA	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	hg19	CCDS7809.1	0.02	7.28635	AGTxTTA	COVERED																																																																																			NOVEL	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385993.1	7	21.633747	KEEP	0	0	0	72	2518	CC	1	1	0		+	70	60	2623	0	0	241.193343	121	60	4624	335	ENST00000256194.4	0.366492	1
KCNJ11	3767	__UNKNOWN__	__UNKNOWN__	11	17407603	17407603	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:17407603A>G	ENST00000339994.4	-	0	2603				KCNJ11_ENST00000528731.1_3'UTR	NM_000525.3	NP_000516.3	Q14654	KCJ11_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 11	NA		NA			cellular response to glucose stimulus (GO:0071333)|cellular response to nicotine (GO:0071316)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|negative regulation of insulin secretion (GO:0046676)|neurological system process (GO:0050877)|positive regulation of cation channel activity (GO:2001259)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ischemia (GO:0002931)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	ATP-sensitive potassium channel complex (GO:0008282)|axolemma (GO:0030673)|cell body fiber (GO:0070852)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|ion channel binding (GO:0044325)|potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(3)|skin(2)	16				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)	Diazoxide(DB01119)|Glimepiride(DB00222)|Glyburide(DB01016)|Ibutilide(DB00308)|Levosimendan(DB00922)|Thiamylal(DB01154)|Verapamil(DB00661)|Yohimbine(DB01392)	CCCCCAAGCCACCTTCTGGAC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D50582	CCDS31436.1, CCDS53606.1	11p15.1	2011-07-05					3767		Potassium channels, Voltage-gated ion channels / Potassium channels, Inwardly rectifying	6257	protein-coding gene	gene with protein product		600937			NA	7502040, 16382105	Standard	NM_000525	NM_001166290	NA	Approved	Kir6.2, BIR	uc001mna.3	Q14654		ENST00000339994.4:c.*863T>C	chr11.hg19:g.17407603A>G		NA	B4DWI4|E9PNK0|Q2M1H7|Q58EX3|Q8IW96	hg19	CCDS31436.1	0.02	29.58613	GCCxCCT	COVERED																																																																																			NOVEL	KCNJ11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387037.1	7	36.992215	KEEP	0	0	0	123	3693	AA	1	1	0		-	103	60	3627	0	0	290.730325	519	60	18026	969	ENST00000339994.4	0.165595	1
SPTY2D1	144108	__UNKNOWN__	__UNKNOWN__	11	18636362	18636362	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs139020346		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:18636362G>A	ENST00000336349.5	-	3	1694	c.1459C>T	c.(1459-1461)Cgg>Tgg	p.R487W		NM_194285.2	NP_919261.2	Q68D10	SPT2_HUMAN	SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae)	487	Ser-rich.	NA								breast(4)|cervix(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|skin(1)|stomach(1)	30						CTGACAGACCGCCCCGGGGGG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	TRP/ARG	2,4396	4.2+/-10.8	0,2,2197	27	30	29	NA	1459	3.3	0	11	dbSNP_134	29	1,8585	1.2+/-3.3	0,1,4292	no	missense	SPTY2D1	NM_194285.2	101	0,3,6489	AA,AG,GG	NA	0.0116,0.0455,0.0231	probably-damaging	487/686	18636362	3,12981	2199	4293	6492	SO:0001583	missense			BX647798	CCDS31441.1	11p15.1	2005-10-28			ENSG00000179119	ENSG00000179119	144108			26818	protein-coding gene	gene with protein product		NA			NA		Standard	NM_194285	NM_194285	NA	Approved	FLJ39441, DKFZp686I068	uc001moy.3	Q68D10	OTTHUMG00000167733	ENST00000336349.5:c.1459C>T	chr11.hg19:g.18636362G>A	ENSP00000337991:p.Arg487Trp	NA	Q6AWA5|Q6MZI5|Q7Z390|Q7Z470|Q86VG8|Q8N3E7|Q8N417|Q8N8I3	hg19	CCDS31441.1	0.02	19.505035	ACCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.887	1.203079	0.22121	4.55E-4	1.16E-4	ENSG00000179119	ENST00000336349	T	0.26957	1.7	5.24	3.29	0.37713	.	0.440532	0.21768	N	0.069418	T	0.41534	0.1163	M	0.77820	2.39	0.09310	N	0.999999	D	0.65815	0.995	P	0.52424	0.698	T	0.35475	-0.9787	10	0.66056	D	0.02	-7.2126	12.7057	0.57060	0.0:0.0:0.7002:0.2998	.	487	Q68D10	SPT2_HUMAN	W	487	ENSP00000337991:R487W	ENSP00000337991:R487W	R	-	1	2	SPTY2D1	18592938	0.000000	0.05858	0.007000	0.13788	0.075000	0.17131	0.395000	0.20850	0.806000	0.34183	0.655000	0.94253	CGG	NOVEL	SPTY2D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395941.1	4	54.14784	KEEP	0	0	0	180	5776	GG	1	1	0		-	67	60	2257	0	0	179.529879	330	60	10315	780	ENST00000336349.5	0.168766	1
IGSF22	283284	__UNKNOWN__	__UNKNOWN__	11	18727451	18727451	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:18727451A>G	ENST00000513874.1	-	22	3962	c.3823T>C	c.(3823-3825)Tgc>Cgc	p.C1275R	IGSF22_ENST00000510673.1_5'UTR	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	670		NA								NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TTGAGCGTGCAGGTGGGGATG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													53	49	50	NA		NA	NA	11		NA											NA				18727451		692	1591	2283	SO:0001583	missense			AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057	283284		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	26750	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173588	NM_173588	NA	Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.3823T>C	chr11.hg19:g.18727451A>G	ENSP00000421191:p.Cys1275Arg	NA	A6NNA0|D6RGV7	hg19	CCDS41625.2	0.02	6.440866	TGCxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	A	20.7	4.040580	0.75732	.	.	ENSG00000179057	ENST00000513874	T	0.66815	-0.23	5.49	5.49	0.81192	.	.	.	.	.	T	0.77458	0.4133	L	0.59436	1.845	0.44181	D	0.996993	D	0.71674	0.998	D	0.68943	0.961	T	0.79448	-0.1799	9	0.66056	D	0.02	.	13.0882	0.59153	1.0:0.0:0.0:0.0	.	1275	D6RGV7	.	R	1275	ENSP00000421191:C1275R	ENSP00000421191:C1275R	C	-	1	0	IGSF22	18684027	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.956000	0.29202	2.072000	0.62099	0.528000	0.53228	TGC	NOVEL	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360850.2	0	26.780113	KEEP	0	0	0	89	2787	AA	1	1	0		-	42	60	1392	0	0	116.212464	143	60	5081	333	ENST00000513874.1	0.227027	1
LUZP2	338645	__UNKNOWN__	__UNKNOWN__	11	25004699	25004699	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:25004699A>T	ENST00000336930.6	+	9	691	c.625A>T	c.(625-627)Act>Tct	p.T209S	LUZP2_ENST00000533227.1_Missense_Mutation_p.T123S			Q86TE4	LUZP2_HUMAN	leucine zipper protein 2	209		NA				extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(11)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	32						AATGAAAGAGACTGTGCAGCT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													207	176	187	NA		NA	NA	11		NA											NA				25004699		2203	4300	6503	SO:0001583	missense			AL832641	CCDS31446.1, CCDS58128.1	11p14.3	2005-09-18			ENSG00000187398	ENSG00000187398	338645			23206	protein-coding gene	gene with protein product		608178			NA	12856284	Standard	NM_001009909	NM_001009909	NA	Approved		uc001mqs.3	Q86TE4	OTTHUMG00000166109	ENST00000336930.6:c.625A>T	chr11.hg19:g.25004699A>T	ENSP00000336817:p.Thr209Ser	NA	A2RUB8|E9PN53|Q6UXE7|Q6ZS65	hg19	CCDS31446.1	0.02	6.577591	GAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614917	0.87359	.	.	ENSG00000187398	ENST00000336930;ENST00000529015;ENST00000533227	T;T;T	0.24538	1.85;1.85;1.85	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.40067	0.1102	L	0.34521	1.04	0.36434	D	0.865089	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.49173	-0.8967	10	0.87932	D	0	-15.9794	13.8993	0.63792	1.0:0.0:0.0:0.0	.	123;209	E9PN53;Q86TE4	.;LUZP2_HUMAN	S	209;167;123	ENSP00000336817:T209S;ENSP00000437032:T167S;ENSP00000432952:T123S	ENSP00000336817:T209S	T	+	1	0	LUZP2	24961275	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	7.068000	0.76748	2.236000	0.73375	0.528000	0.53228	ACT	NOVEL	LUZP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387861.1	0	3.544044	KEEP	0	1	26	21	692	AA	0.999879	0.999879	0		+	18	60	633	0	0	47.612413	139	60	5011	214	ENST00000336930.6	0.11465	1
SLC5A12	159963	__UNKNOWN__	__UNKNOWN__	11	26725107	26725107	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:26725107G>A	ENST00000396005.3	-	6	1101	c.792C>T	c.(790-792)atC>atT	p.I264I	SLC5A12_ENST00000280467.6_Silent_p.I264I	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	264		NA			sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TTTTGCAAGAGATGCATCGCT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													127	122	124	NA		NA	NA	11		NA											NA				26725107		2203	4299	6502	SO:0001819	synonymous_variant			BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942	159963		Solute carriers	28750	protein-coding gene	gene with protein product		612455	solute carrier family 5 (sodium/glucose cotransporter), member 12		NA	12477932	Standard	NM_178498	NM_178498	NA	Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.792C>T	chr11.hg19:g.26725107G>A		NA	Q86UC7	hg19	CCDS7860.2	0.02	9.282267	AGAxATG	COVERED																																																																																			NOVEL	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319681.1	7	10.53434	KEEP	0	0	0	35	1269	GG	0.999999	0.999999	0		-	51	60	1867	0	0	160.1271	162	60	6191	300	ENST00000396005.3	0.239437	1
LGR4	55366	__UNKNOWN__	__UNKNOWN__	11	27393862	27393862	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:27393862C>A	ENST00000379214.4	-	16	1906	c.1463G>T	c.(1462-1464)aGc>aTc	p.S488I	LGR4_ENST00000389858.4_Missense_Mutation_p.S464I	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	488		NA			bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						GTCCTGGAGGCTGTTATCTTC	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													129	123	125	NA		NA	NA	11		NA											NA				27393862		2202	4299	6501	SO:0001583	missense			AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213	55366		GPCR / Class A : Orphans	13299	protein-coding gene	gene with protein product		606666	G protein-coupled receptor 48, leucine-rich repeat-containing G protein-coupled receptor 4	GPR48	NA	10894923	Standard	NM_018490	NM_018490	NA	Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.1463G>T	chr11.hg19:g.27393862C>A	ENSP00000368516:p.Ser488Ile	NA	A6NCH3|G5E9B3|Q8N537|Q9NYD1	hg19	CCDS31449.1	0.02	18.468476	AGGxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.47	3.131674	0.56828	.	.	ENSG00000205213	ENST00000379214;ENST00000389858	T;T	0.60672	0.17;0.29	5.78	4.87	0.63330	.	0.377742	0.31847	N	0.006962	T	0.53932	0.1827	L	0.60455	1.87	0.80722	D	1	B;B	0.30021	0.265;0.029	B;B	0.25405	0.06;0.01	T	0.55933	-0.8062	10	0.54805	T	0.06	.	14.7979	0.69891	0.0:0.9309:0.0:0.0691	.	464;488	G5E9B3;Q9BXB1	.;LGR4_HUMAN	I	488;464	ENSP00000368516:S488I;ENSP00000374508:S464I	ENSP00000368516:S488I	S	-	2	0	LGR4	27350438	0.455000	0.25736	1.000000	0.80357	0.913000	0.54294	0.796000	0.26986	1.461000	0.47929	-0.136000	0.14681	AGC	NOVEL	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257467.1	5	18.292937	KEEP	0	1	32	72	2596	CC	1	1	0		-	107	60	3958	0	0	341.242065	330	60	12719	658	ENST00000379214.4	0.244851	1
BDNF	627	__UNKNOWN__	__UNKNOWN__	11	27677289	27677289	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:27677289A>T	ENST00000525528.1	-	0	3916				BDNF_ENST00000420794.1_3'UTR|BDNF_ENST00000533246.1_3'UTR|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000395981.3_3'UTR|BDNF_ENST00000395980.2_3'UTR|BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000395978.3_3'UTR|BDNF_ENST00000395986.2_3'UTR|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000525950.1_3'UTR|BDNF-AS_ENST00000501176.2_RNA|BDNF_ENST00000314915.6_3'UTR|BDNF_ENST00000532997.1_3'UTR|BDNF_ENST00000439476.2_3'UTR|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000533131.1_3'UTR|BDNF_ENST00000418212.1_3'UTR|BDNF_ENST00000438929.1_3'UTR|BDNF_ENST00000395983.3_3'UTR|BDNF_ENST00000356660.4_3'UTR|BDNF_ENST00000530861.1_3'UTR|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000584049.1_5'UTR|BDNF-AS_ENST00000530686.1_RNA	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	NA		NA			axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						AGATGCAGCAATTGCTTGGGG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697	627		Endogenous ligands	1033	protein-coding gene	gene with protein product	neurotrophin	113505			NA	2236018, 1889806, 17942328, 17493809	Standard	NM_170735	NM_170731	NA	Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.*2079T>A	chr11.hg19:g.27677289A>T		NA	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	hg19	CCDS7866.1	0.02	14.006491	GCAxTTG	COVERED																																																																																			NOVEL	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388135.1	5	9.629301	KEEP	0	0	0	32	1038	AA	0.999997	0.999997	0		-	184	60	6633	0	0	660.100313	126	60	4587	393	ENST00000525528.1	0.593548	1
KIF18A	81930	__UNKNOWN__	__UNKNOWN__	11	28119374	28119374	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:28119374T>C	ENST00000263181.6	-	2	411	c.121A>G	c.(121-123)Atc>Gtc	p.I41V		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	41	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						AAAACTAGGATATGTTTATCC	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													120	119	119	NA		NA	NA	11		NA											NA				28119374		2202	4299	6501	SO:0001583	missense			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621	81930		Kinesins	29441	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 99	611271			NA	11230166	Standard	NM_031217	NM_031217	NA	Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.121A>G	chr11.hg19:g.28119374T>C	ENSP00000263181:p.Ile41Val	NA	Q4VPE3|Q86VS5|Q9H0F3	hg19	CCDS7867.1	0.02	29.71706	GGAxATG	COVERED	.	.	.	.	.	.	.	.	.	.	T	11.87	1.766188	0.31228	.	.	ENSG00000121621	ENST00000263181	T	0.72051	-0.62	5.53	4.34	0.51931	Kinesin, motor domain (4);	0.081869	0.85682	D	0.000000	T	0.42854	0.1221	N	0.05383	-0.06	0.43814	D	0.99637	B;B	0.12013	0.005;0.005	B;B	0.17098	0.017;0.017	T	0.40757	-0.9546	10	0.02654	T	1	.	8.2658	0.31813	0.1202:0.0689:0.0:0.8109	.	41;41	B2R6H3;Q8NI77	.;KI18A_HUMAN	V	41	ENSP00000263181:I41V	ENSP00000263181:I41V	I	-	1	0	KIF18A	28075950	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	3.914000	0.56401	2.236000	0.73375	0.528000	0.53228	ATC	NOVEL	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388328.3	13	24.35647	KEEP	0	0	0	81	2402	TT	1	1	0		-	18	60	692	0	0	41.4958	680	60	25019	925	ENST00000263181.6	0.025788	1
METTL15	196074	__UNKNOWN__	__UNKNOWN__	11	28352120	28352120	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:28352120T>C	ENST00000407364.3	+	7	1308	c.956T>C	c.(955-957)cTc>cCc	p.L319P	METTL15_ENST00000303459.6_3'UTR|METTL15_ENST00000406787.3_3'UTR|METTL15_ENST00000342303.5_3'UTR			A6NJ78	MET15_HUMAN	methyltransferase like 15	319		NA					methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						CTTGTTGCCCTCTCCTTCCAT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													93	81	85	NA		NA	NA	11		NA											NA				28352120		692	1591	2283	SO:0001583	missense			AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519	196074			26606	protein-coding gene	gene with protein product		NA	methyltransferase 5 domain containing 1	METT5D1	NA	12477932	Standard	NM_152636	NM_152636	NA	Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.956T>C	chr11.hg19:g.28352120T>C	ENSP00000384369:p.Leu319Pro	NA	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	hg19	CCDS44559.1	0.02	19.274817	CCCxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	T	22.0	4.226976	0.79576	.	.	ENSG00000169519	ENST00000407364	T	0.34667	1.35	5.32	5.32	0.75619	.	0.146536	0.47093	D	0.000250	T	0.66742	0.2820	M	0.91920	3.255	0.80722	D	1	D	0.64830	0.994	D	0.69307	0.963	T	0.75348	-0.3349	9	.	.	.	.	14.4582	0.67431	0.0:0.0:0.0:1.0	.	319	A6NJ78	MET15_HUMAN	P	319	ENSP00000384369:L319P	.	L	+	2	0	METTL15	28308696	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.579000	0.82511	2.013000	0.59113	0.533000	0.62120	CTC	NOVEL	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318135.2	4	23.771558	KEEP	38	0	0	79	2505	TT	1	1	0		+	20	49	707	0	0	44.587713	438	50	16382	695	ENST00000407364.3	0.043668	1
KCNA4	3739	__UNKNOWN__	__UNKNOWN__	11	30032008	30032008	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:30032008A>G	ENST00000328224.6	-	0	3451					NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	NA		NA			potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	CATCTTTTCCAGTTAATGTGC	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255	3739		Potassium channels, Voltage-gated ion channels / Potassium channels	6222	protein-coding gene	gene with protein product		176266	potassium voltage-gated channel, shaker-related subfamily, member 4-like	KCNA4L	NA	2263489, 16382104	Standard	NM_002233	NM_002233	NA	Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.*256T>C	chr11.hg19:g.30032008A>G		NA		hg19	CCDS41629.1	0.02	2.138425	TCCxGTT	COVERED																																																																																			NOVEL	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388074.2	3	3.309925	KEEP	0	0	0	11	353	AA	0.993072	0.991285	0		-	8	60	277	0	0	20.511382	66	60	2465	105	ENST00000328224.6	0.108108	0.9982
DCDC1	341019	__UNKNOWN__	__UNKNOWN__	11	30937209	30937209	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs375684196		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:30937209C>T	ENST00000597505.1	-	25	3501	c.3502G>A	c.(3502-3504)Gaa>Aaa	p.E1168K	DCDC1_ENST00000339794.5_Missense_Mutation_p.E247K|DCDC1_ENST00000406071.2_5'UTR			P59894	DCDC1_HUMAN	doublecortin domain containing 1	0		NA			intracellular signal transduction (GO:0035556)					central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|pancreas(2)|prostate(1)|skin(1)|stomach(1)	31	Lung SC(675;0.225)					TCTCTGTATTCGAACTGCTGA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C	LYS/GLU	0,4404		0,0,2202	127	96	106	NA	823	4.5	1	11		106	1,8597	1.2+/-3.3	0,1,4298	no	missense	DCDC5	NM_020869.3	56	0,1,6500	TT,TC,CC	NA	0.0116,0.0,0.0077	possibly-damaging	275/891	30937209	1,13001	2202	4299	6501	SO:0001583	missense			AY247970	CCDS7872.1	11p14.1	2013-05-22			ENSG00000170959	ENSG00000170959	341019			20625	protein-coding gene	gene with protein product		608062			NA	12820024	Standard	NM_181807	NM_181807	NA	Approved		uc001msv.3	P59894	OTTHUMG00000150144	ENST00000597505.1:c.3502G>A	chr11.hg19:g.30937209C>T	ENSP00000472625:p.Glu1168Lys	NA	A6PVL6|B7WNX6|Q6ZU04	hg19		0.02	6.604813	ATTxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.28	2.189802	0.38707	0.0	1.16E-4	ENSG00000170959	ENST00000339794	T	0.47869	0.83	5.44	4.54	0.55810	Ricin B-related lectin (1);Ricin B lectin (2);	0.120618	0.36703	N	0.002452	T	0.32704	0.0838	L	0.34521	1.04	0.26119	N	0.980574	P	0.41214	0.742	B	0.34138	0.176	T	0.14643	-1.0465	10	0.33141	T	0.24	-9.9669	11.4103	0.49921	0.0:0.915:0.0:0.085	.	247	Q6ZRR9	DCDC5_HUMAN	K	247	ENSP00000341700:E247K	ENSP00000341700:E247K	E	-	1	0	DCDC5	30893785	1.000000	0.71417	1.000000	0.80357	0.113000	0.19764	3.170000	0.50816	1.307000	0.44944	-0.136000	0.14681	GAA	NOVEL	DCDC1-010	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000463167.1	1	4.815667	KEEP	0	0	0	16	562	CC	0.997832	0.997832	0		-	8	60	288	0	0	18.945544	147	60	4962	198	ENST00000597505.1	0.051613	1
CCDC73	493860	__UNKNOWN__	__UNKNOWN__	11	32703752	32703752	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:32703752G>T	ENST00000335185.5	-	7	473				CCDC73_ENST00000534415.1_Intron|CCDC73_ENST00000531481.1_3'UTR	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73	NA		NA								NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TCTTTAACTTGTAGCCTTATC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714	493860			23261	protein-coding gene	gene with protein product		612328			NA		Standard	NM_001008391	NM_001008391	NA	Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279	ENST00000335185.5:c.429+1329C>A	chr11.hg19:g.32703752G>T		NA	Q6P5Q7|Q6ZMW0|Q86WE7	hg19	CCDS41630.1	0.02	6.94225	CTTxTAG	COVERED																																																																																			NOVEL	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388874.2	1	5.417724	KEEP	0	0	0	18	637	GG	0.999859	0.999859	0		-	33	60	1185	0	0	98.692339	129	60	4858	204	ENST00000335185.5	0.203704	1
TRIM44	54765	__UNKNOWN__	__UNKNOWN__	11	35756936	35756936	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:35756936G>T	ENST00000299413.5	+	4	1294				TRIM44_ENST00000532066.1_Intron	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	NA		NA				intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				TGTACCAACAGTGATTTCTAA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													201	175	183	NA		NA	NA	11		NA											NA				35756936		2202	4298	6500	SO:0001627	intron_variant			BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326	54765		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	19016	protein-coding gene	gene with protein product		612298	tripartite motif-containing 44		NA		Standard	NM_017583	NM_017583	NA	Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.988-38G>T	chr11.hg19:g.35756936G>T		NA	D3DR14|Q96QY2|Q9UGK0	hg19	CCDS31461.1	0.02	6.794696	ACAxTGA	COVERED																																																																																			NOVEL	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389081.1	0	9.932622	KEEP	0	0	0	33	1187	GG	0.999998	0.999998	0		+	18	60	664	0	0	50.763787	138	60	5266	231	ENST00000299413.5	0.115385	1
TP53I11	9537	__UNKNOWN__	__UNKNOWN__	11	44955267	44955267	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:44955267G>C	ENST00000533940.1	-	0	2342				TP53I11_ENST00000525680.1_3'UTR|TP53I11_ENST00000308212.5_3'UTR|TP53I11_ENST00000395648.3_3'UTR	NM_001258320.1	NP_001245249.1	O14683	P5I11_HUMAN	tumor protein p53 inducible protein 11	NA		NA			negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5						GACAGGGCGGGGAAGATGAGG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF010315	CCDS7911.1	11p11.2	2005-09-22				ENSG00000175274	9537			16842	protein-coding gene	gene with protein product		NA			NA	9305847	Standard	NM_006034	NM_006034	NA	Approved	PIG11	uc001myk.3	O14683		ENST00000533940.1:c.*1168C>G	chr11.hg19:g.44955267G>C		NA	Q3ZCS0	hg19	CCDS7911.1	0.02	4.500617	CGGxGAA	COVERED																																																																																			NOVEL	TP53I11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389909.1	3	12.323794	KEEP	0	0	0	41	1379	GG	1	1	0		-	28	60	965	0	0	80.163516	105	60	3718	220	ENST00000533940.1	0.210526	1
CHST1	8534	__UNKNOWN__	__UNKNOWN__	11	45671765	45671765	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:45671765G>A	ENST00000308064.2	-	4	1379	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C		NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	237		NA			carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		AGAATGCCGCGGGGGTCTCGG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													44	45	45	NA		NA	NA	11		NA											NA				45671765		2203	4299	6502	SO:0001583	missense			U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264	8534		Sulfotransferases, membrane-bound	1969	protein-coding gene	gene with protein product		603797			NA	9405439, 9639683	Standard	NM_003654	NM_003654	NA	Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.709C>T	chr11.hg19:g.45671765G>A	ENSP00000309270:p.Arg237Cys	NA	D3DQP2	hg19	CCDS7913.1	0.02	18.711174	CGCxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.93	3.727601	0.69074	.	.	ENSG00000175264	ENST00000308064	D	0.85171	-1.95	4.98	4.98	0.66077	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.93943	0.8061	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95072	0.8205	10	0.66056	D	0.02	-15.6808	14.0439	0.64693	0.0:0.0:0.8485:0.1515	.	237	O43916	CHST1_HUMAN	C	237	ENSP00000309270:R237C	ENSP00000309270:R237C	R	-	1	0	CHST1	45628341	1.000000	0.71417	0.405000	0.26409	0.920000	0.55202	4.254000	0.58798	2.310000	0.77875	0.462000	0.41574	CGC	NOVEL	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390127.1	4	43.583501	KEEP	0	0	0	145	4787	GG	1	1	0		-	26	60	968	0	0	66.575187	405	60	13784	729	ENST00000308064.2	0.060325	1
PHF21A	51317	__UNKNOWN__	__UNKNOWN__	11	45986887	45986887	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs188195248		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:45986887G>T	ENST00000418153.2	-	9	1171	c.972C>A	c.(970-972)agC>agA	p.S324R	PHF21A_ENST00000257821.4_Missense_Mutation_p.S325R|PHF21A_ENST00000527753.1_5'UTR|PHF21A_ENST00000323180.6_Missense_Mutation_p.S325R			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	324		NA			blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						GACTTGGCTTGCTAAGCTGTA	0.512	NA	NA									OREG0020936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													62	52	55	NA		NA	NA	11		NA											NA				45986887		2202	4299	6501	SO:0001583	missense			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365	51317		Zinc fingers, PHD-type	24156	protein-coding gene	gene with protein product		608325			NA	11214970, 12032298	Standard	NM_016621	NM_001101802	NA	Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.972C>A	chr11.hg19:g.45986887G>T	ENSP00000398824:p.Ser324Arg	935	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	hg19	CCDS44578.1	0.02	1.785957	CTTxCTA	COVERED	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021758	0.75275	.	.	ENSG00000135365	ENST00000257821;ENST00000323180;ENST00000418153	T;T;T	0.53206	0.63;0.63;0.63	6.17	6.17	0.99709	.	0.300523	0.43260	D	0.000596	T	0.52901	0.1763	L	0.56769	1.78	0.49915	D	0.999839	D;D;D	0.56968	0.978;0.967;0.958	P;P;P	0.53689	0.719;0.732;0.663	T	0.43653	-0.9378	10	0.22706	T	0.39	-6.987	10.4929	0.44760	0.0688:0.1344:0.7967:0.0	.	324;325;325	Q96BD5;Q96BD5-2;Q96BD5-3	PF21A_HUMAN;.;.	R	325;325;324	ENSP00000257821:S325R;ENSP00000323152:S325R;ENSP00000398824:S324R	ENSP00000257821:S325R	S	-	3	2	PHF21A	45943463	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.058000	0.57463	2.941000	0.99782	0.655000	0.94253	AGC	NOVEL	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000392583.1	1	7.531465	KEEP	0	3	39	40	1001	GG	1	0.999989	0		-	11	60	186	0	0	8.873047	94	60	2673	212	ENST00000418153.2	0.104762	0.999989
CKAP5	9793	__UNKNOWN__	__UNKNOWN__	11	46811966	46811966	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:46811966T>C	ENST00000529230.1	-	14	1811				CKAP5_ENST00000312055.5_Intron|CKAP5_ENST00000354558.3_Intron|CKAP5_ENST00000415402.1_Intron			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	NA		NA			centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						AGTCTTCTCATTGGTCTCACT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(4;85 273 2202 4844 13323)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216	9793			28959	protein-coding gene	gene with protein product		611142			NA	7788527, 8536682	Standard	NM_014756	NM_014756	NA	Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.1764+53A>G	chr11.hg19:g.46811966T>C		NA	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	hg19	CCDS31477.1	0.02	7.444309	TCAxTGG	COVERED																																																																																			NOVEL	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390679.1	0	12.335501	KEEP	0	0	0	41	1277	TT	1	1	0		-	24	60	905	0	0	71.768663	148	60	5414	263	ENST00000529230.1	0.139535	1
LRP4	4038	__UNKNOWN__	__UNKNOWN__	11	46880163	46880163	__UNKNOWN__	3'UTR	SNP	G	G	A	rs546660220	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:46880163G>A	ENST00000378623.1	-	0	6331				LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	NA		NA			dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GGGGCAGAGCGCAGTCCTGGG	0.567	NA	NA											G|||	8	0.00159744	0	0.0014	5008	,	,	NA	19306	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569	4038		Low density lipoprotein receptors	6696	protein-coding gene	gene with protein product		604270			NA	9693030	Standard	NM_002334	NM_002334	NA	Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.*371C>T	chr11.hg19:g.46880163G>A		NA	B2RN39|Q4AC85|Q5KTZ5	hg19	CCDS31478.1	0.02	6.587483	AGCxCAG	COVERED																																																																																			NOVEL	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391133.1	0	9.028326	KEEP	0	0	0	30	1031	GG	0.999997	0.999997	0		-	41	60	1459	0	0	122.327527	150	60	5387	251	ENST00000378623.1	0.21466	1
RAPSN	5913	__UNKNOWN__	__UNKNOWN__	11	47463329	47463329	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:47463329G>A	ENST00000524487.1	-	4	719				RAPSN_ENST00000298854.2_Intron|RAPSN_ENST00000529341.1_Intron|RAPSN_ENST00000352508.3_Intron			Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	NA		NA			positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						TATCAGGCCTGTGCCCCTGCC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													17	17	17	NA		NA	NA	11		NA											NA				47463329		2195	4296	6491	SO:0001627	intron_variant				CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917	5913		RING-type (C3HC4) zinc fingers	9863	protein-coding gene	gene with protein product	rapsyn	601592	receptor-associated protein of the synapse, 43kD		NA	8812503	Standard		NM_005055	NA	Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000524487.1:c.631-44C>T	chr11.hg19:g.47463329G>A		NA	Q8TDF3|Q9BTD9	hg19		0.02	1.960345	CCTxTGC	COVERED																																																																																			NOVEL	RAPSN-004	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000391729.1	0	6.319236	KEEP	0	0	0	21	701	GG	0.999869	0.999357	0		-	6	60	224	0	0	15.945464	76	60	2762	115	ENST00000524487.1	0.073171	0.999487
C1QTNF4	114900	__UNKNOWN__	__UNKNOWN__	11	47612327	47612327	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:47612327C>T	ENST00000302514.3	-	2	552	c.36G>A	c.(34-36)gcG>gcA	p.A12A		NM_031909.2	NP_114115.2	Q9BXJ3	C1QT4_HUMAN	C1q and tumor necrosis factor related protein 4	12		NA				extracellular space (GO:0005615)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						CCCAGCAGGCCGCTGGGCCCA	0.746	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	4	4	NA		NA	NA	11		NA											NA				47612327		1517	3212	4729	SO:0001819	synonymous_variant			AF329838	CCDS7942.1	11q11	2008-07-18				ENSG00000172247	114900			14346	protein-coding gene	gene with protein product	complement-c1q tumor necrosis factor-related protein 4	614911			NA	16094384	Standard	NM_031909	NM_031909	NA	Approved	CTRP4, ZACRP4	uc001ngc.2	Q9BXJ3		ENST00000302514.3:c.36G>A	chr11.hg19:g.47612327C>T		NA	Q8IV25	hg19	CCDS7942.1	0.02	4.177819	GGCxGCT	COVERED																																																																																			NOVEL	C1QTNF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391772.1	4	10.457393	KEEP	0	1	29	45	1411	CC	1	0.999996	0		-	9	60	294	0	0	20.10567	105	60	3311	175	ENST00000302514.3	0.078947	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	55890789	55890789	__UNKNOWN__	IGR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:55890789T>A			NA	NA				OR8H3 (2 upstream) : OR8J3 (13457 downstream)						NA		NA									NA						TCCAGGTAGTTAAAATAGCAG	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	70	69	NA		NA	NA	11		NA											NA				55890789		2196	4295	6491	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.55890789T>A		NA		hg19		0.02	24.930297	AGTxAAA	COVERED																																																																																			NOVEL					0			9	18.355806	KEEP	0	0	0	61	1932	TT	1	1	0			63	60	2252	0	0	169.083517	510	60	18442	804		0.109948	1
UBE2L6	9246	__UNKNOWN__	__UNKNOWN__	11	57319556	57319556	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:57319556C>A	ENST00000287156.4	-	0	932				UBE2L6_ENST00000340573.4_3'UTR	NM_004223.4	NP_004214.1	O14933	UB2L6_HUMAN	ubiquitin-conjugating enzyme E2L 6	NA		NA			cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|ovary(1)	5						GAGAACTGGCCTGTAACTGCA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF031141, AK093462, BC032491	CCDS7960.1, CCDS7961.1	11q12.1	2008-02-01			ENSG00000156587	ENSG00000156587	9246		Ubiquitin-conjugating enzymes E2	12490	protein-coding gene	gene with protein product		603890			NA	9153201	Standard	NM_004223	NM_004223	NA	Approved	UBCH8	uc001nkn.2	O14933	OTTHUMG00000167047	ENST00000287156.4:c.*275G>T	chr11.hg19:g.57319556C>A		NA	A6NDM6|A8MY53|Q8N5D8|Q9UEZ0	hg19	CCDS7960.1	0.02	8.863138	GGCxTGT	COVERED																																																																																			NOVEL	UBE2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000392657.1	4	7.223588	KEEP	0	0	0	24	855	CC	0.999909	0.999909	0		-	11	60	374	0	0	23.473294	227	60	8356	291	ENST00000287156.4	0.046218	1
CLP1	10978	__UNKNOWN__	__UNKNOWN__	11	57424651	57424651	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:57424651G>T	ENST00000533682.1	+	0	22				CLP1_ENST00000529430.1_Intron			Q5KU26	COL12_HUMAN	cleavage and polyadenylation factor I subunit 1	NA		NA			carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|stomach(1)	15						GTAGCTGGAAGAAATCATCGG	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC000446	CCDS7964.1, CCDS44600.1	11q12.1	2012-10-02	2012-10-02		ENSG00000172409	ENSG00000172409	10978	2.7.1.78		16999	protein-coding gene	gene with protein product	ATP/GTPbinding protein, polyribonucleotide 5'-hydroxyl-kinase	608757	CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)		NA	8896421, 11060040	Standard	NM_006831	NM_006831	NA	Approved	HEAB, hClp1	uc001nkw.3	Q92989	OTTHUMG00000167146	ENST00000533682.1:c.-704G>T	chr11.hg19:g.57424651G>T		NA	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	hg19	CCDS7964.1	0.02	21.020272	GAAxAAA	COVERED																																																																																			NOVEL	CLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393462.3	7	39.425071	KEEP	0	0	0	131	4543	GG	1	1	0		+	31	60	1065	0	0	70.327416	489	60	18266	741	ENST00000533682.1	0.059615	1
C11orf31	280636	__UNKNOWN__	__UNKNOWN__	11	57509459	57509459	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:57509459C>T	ENST00000388857.4	+	2	292				C11orf31_ENST00000534355.1_Intron|TMX2-CTNND1_ENST00000528395.1_Intron			Q8IZQ5	SELH_HUMAN	chromosome 11 open reading frame 31	NA		NA			cell redox homeostasis (GO:0045454)		poly(A) RNA binding (GO:0044822)|selenium binding (GO:0008430)				NA						GGGAGAGGGACGTGGGTGAAA	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ276249	CCDS44602.1	11q12.1	2012-03-01			ENSG00000211450	ENSG00000211450	280636			18251	protein-coding gene	gene with protein product	selenoprotein H	607914			NA	12775843	Standard	NM_170746	NM_170746	NA	Approved	SELH	uc021qjj.1	Q8IZQ5	OTTHUMG00000167202	ENST00000388857.4:c.268+33C>T	chr11.hg19:g.57509459C>T		NA	Q8N672	hg19	CCDS44602.1	0.02	7.129973	GGAxGTG	COVERED																																																																																			NOVEL	C11orf31-004	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS|seleno	protein_coding	NA	protein_coding	OTTHUMT00000393934.3	1	19.830015	KEEP	0	0	0	66	2038	CC	1	1	0		+	39	60	1402	0	0	118.641735	135	60	4232	253	ENST00000388857.4	0.224138	1
INCENP	3619	__UNKNOWN__	__UNKNOWN__	11	61916015	61916015	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:61916015A>G	ENST00000394818.3	+	16	2474	c.2272A>G	c.(2272-2274)Aag>Gag	p.K758E	INCENP_ENST00000278849.4_Missense_Mutation_p.K754E	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	758		NA			chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ACTGGAGGAGAAGAAGAAGAA	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													11	14	13	NA		NA	NA	11		NA											NA				61916015		2190	4286	6476	SO:0001583	missense			AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503	3619			6058	protein-coding gene	gene with protein product		604411	inner centromere protein antigens (135kD, 155kD)		NA	1860899, 11453556	Standard	NM_020238	NM_001040694	NA	Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.2272A>G	chr11.hg19:g.61916015A>G	ENSP00000378295:p.Lys758Glu	NA	A8MQD2|Q5Y192	hg19	CCDS44624.1	0.02	2.278865	GAGxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	13.48	2.249370	0.39797	.	.	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.17054	2.3;2.32	4.86	4.86	0.63082	.	0.000000	0.56097	D	0.000023	T	0.15089	0.0364	L	0.50333	1.59	0.32885	D	0.511056	P;P	0.50156	0.932;0.888	B;B	0.43508	0.422;0.242	T	0.06770	-1.0808	10	0.10111	T	0.7	.	8.7764	0.34765	0.8091:0.1909:0.0:0.0	.	754;758	Q9NQS7-2;Q9NQS7	.;INCE_HUMAN	E	758;754	ENSP00000378295:K758E;ENSP00000278849:K754E	ENSP00000278849:K754E	K	+	1	0	INCENP	61672591	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.044000	0.41241	1.815000	0.52974	0.454000	0.30748	AAG	NOVEL	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394723.2	1	5.115078	KEEP	0	0	0	17	517	AA	0.999366	0.983538	0		+	9	60	332	0	0	26.625298	49	60	1681	84	ENST00000394818.3	0.155172	0.984161
TAF6L	10629	__UNKNOWN__	__UNKNOWN__	11	62545495	62545495	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs201081654		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:62545495G>A	ENST00000294168.3	+	4	481	c.280G>A	c.(280-282)Gcc>Acc	p.A94T	TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	94		NA			chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						CATGCGCCCCGCCAGGGAGGG	0.592	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	20255	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													88	80	83	NA		NA	NA	11		NA											NA				62545495		2201	4299	6500	SO:0001583	missense			BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227	10629			17305	protein-coding gene	gene with protein product		602946	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD		NA	9674425	Standard	NM_006473	NM_006473	NA	Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.280G>A	chr11.hg19:g.62545495G>A	ENSP00000294168:p.Ala94Thr	NA	B2RAT0|Q96HA6	hg19	CCDS8035.1	0.02	6.915855	CCCxCCA	COVERED	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.53	2.564119	0.45694	.	.	ENSG00000162227	ENST00000294168;ENST00000529509	T;T	0.49139	0.79;0.8	5.78	4.88	0.63580	.	0.553031	0.17873	N	0.159120	T	0.24699	0.0599	N	0.04508	-0.205	0.42923	D	0.994291	B;B	0.09022	0.001;0.002	B;B	0.01281	0.0;0.0	T	0.06917	-1.0800	10	0.34782	T	0.22	-1.5531	8.7162	0.34411	0.1695:0.0:0.8305:0.0	.	94;94	B4DVM4;Q9Y6J9	.;TAF6L_HUMAN	T	94	ENSP00000294168:A94T;ENSP00000434662:A94T	ENSP00000294168:A94T	A	+	1	0	TAF6L	62302071	0.001000	0.12720	0.862000	0.33874	0.901000	0.52897	0.218000	0.17622	1.459000	0.47892	0.455000	0.32223	GCC	NOVEL	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395352.1	2	11.870909	KEEP	0	1	33	51	1728	GG	1	1	0		+	10	60	345	0	0	22.909661	155	60	5477	273	ENST00000294168.3	0.060606	1
PLA2G16	11145	__UNKNOWN__	__UNKNOWN__	11	63341845	63341845	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:63341845C>T	ENST00000323646.5	-	0	1415					NM_007069.3	NP_009000.2	P53816	HRSL3_HUMAN	phospholipase A2, group XVI	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|negative regulation of cell cycle (GO:0045786)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	1-acyl-2-lysophosphatidylserine acylhydrolase activity (GO:0052740)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phosphatidylserine 1-acylhydrolase activity (GO:0052739)|phospholipase A2 activity (GO:0004623)			kidney(2)|lung(1)|ovary(1)|skin(1)	5						agcaacaaggcaaaggaaaga	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X92814	CCDS8047.1	11q12.3	2014-03-14	2008-09-19	2008-09-19	ENSG00000176485	ENSG00000176485	11145	3.1.1.4		17825	protein-coding gene	gene with protein product	adipose-specific PLA2	613867	HRAS-like suppressor 3	HRASLS3	NA	9771974, 18614531	Standard	NM_001128203	NM_007069	NA	Approved	HREV107, H-REV107-1, HREV107-3, MGC118754., AdPLA	uc009you.1	P53816	OTTHUMG00000167852	ENST00000323646.5:c.*572G>A	chr11.hg19:g.63341845C>T		NA	B2R7Q4|B7XAK5|Q3SYI3|Q9HDD1	hg19	CCDS8047.1	0.02	4.140787	AGGxAAA	COVERED																																																																																			NOVEL	PLA2G16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396632.1	10	21.971994	KEEP	0	0	0	73	2655	CC	1	0.999998	0		-	14	60	461	0	0	34.177678	103	60	3947	245	ENST00000323646.5	0.119658	0.999998
NAALADL1	10004	__UNKNOWN__	__UNKNOWN__	11	64815663	64815663	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:64815663G>A	ENST00000355721.3	-	9	1185	c.1186C>T	c.(1186-1188)Cgc>Tgc	p.R396C	NAALADL1_ENST00000356632.3_Missense_Mutation_p.R402C|NAALADL1_ENST00000526799.1_5'UTR|NAALADL1_ENST00000340252.4_Missense_Mutation_p.R488C|NAALADL1_ENST00000355369.2_Missense_Mutation_p.R437C|NAALADL1_ENST00000528884.1_5'UTR|NAALADL1_ENST00000339885.2_Missense_Mutation_p.R437C|NAALADL1_ENST00000358658.3_Missense_Mutation_p.R437C			Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	437	NAALADase.	NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GCCACCGTGCGCTCCTGCAGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													118	118	118	NA		NA	NA	11		NA											NA				64815663		2201	4297	6498	SO:0001583	missense			AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060	10004			23536	protein-coding gene	gene with protein product	ileal peptidase I100	602640			NA	10085079	Standard	NM_005468	NM_005468	NA	Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000355721.3:c.1186C>T	chr11.hg19:g.64815663G>A	ENSP00000347955:p.Arg396Cys	NA	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	hg19	CCDS31604.1	0.02	30.302508	TGCxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.1	4.096115	0.76870	.	.	ENSG00000168060	ENST00000358658;ENST00000355369;ENST00000339885;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	4.13	4.13	0.48395	Peptidase M28 (1);	0.000000	0.85682	D	0.000000	T	0.70378	0.3217	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76852	-0.2806	10	0.87932	D	0	-25.646	9.4775	0.38880	0.0:0.0:0.7887:0.2113	.	437	Q9UQQ1	NALDL_HUMAN	C	437;437;437;437;488;396;402	ENSP00000351484:R437C;ENSP00000347530:R437C;ENSP00000340111:R437C;ENSP00000344244:R488C;ENSP00000347955:R396C;ENSP00000349045:R402C	ENSP00000340111:R437C	R	-	1	0	NAALADL1	64572239	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.700000	0.61803	2.313000	0.78055	0.561000	0.74099	CGC	NOVEL	NAALADL1-021	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385167.1	8	75.085686	KEEP	0	1	20	257	8601	GG	1	1	0		-	87	60	2916	0	0	219.249805	612	60	20994	1262	ENST00000355721.3	0.124464	1
MALAT1	378938	__UNKNOWN__	__UNKNOWN__	11	65266348	65266348	__UNKNOWN__	lincRNA	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:65266348T>A	ENST00000534336.1	+	0	1116					NR_002819.2		Q9UHZ2	MALAT_HUMAN	metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)	NA		NA									NA						GTAGTTTGCATTCAAGTTCCA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	87	85	NA		NA	NA	11		NA											NA				65266348		874	1988	2862					AF001540		11q13.1	2013-12-11	2007-11-20		ENSG00000251562	ENSG00000251562	378938		Long non-coding RNAs, -	29665	non-coding RNA	RNA, long non-coding	metastasis associated in lung adenocarcinoma transcript 1, non-protein coding RNA 47, hepcarcin, nuclear enriched abundant transcript 2, nuclear paraspeckle assembly transcript 2 (non-protein coding), long intergenic non-protein coding RNA 47	607924			NA	12970751, 22560368	Standard	NR_002819	NR_002819	NA	Approved	PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA	uc010roh.3	Q9UHZ2	OTTHUMG00000166322	ENST00000534336.1:	chr11.hg19:g.65266348T>A		NA		hg19		0.02	6.836264	GCAxTCA	COVERED																																																																																			NOVEL	MALAT1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000389143.1	1	46.340861	KEEP	0	0	0	154	5000	TT	1	1	0		+	43	60	1585	0	0	136.764385	131	60	4808	399	ENST00000534336.1	0.247126	1
RP11-867G23.13	0	__UNKNOWN__	__UNKNOWN__	11	66084534	66084534	__UNKNOWN__	RNA	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:66084534C>A	ENST00000534065.1	+	0	140										NA		NA									NA						CCCGGGCTGGCGGCAGCTCTT	0.786	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000534065.1:	chr11.hg19:g.66084534C>A		NA		hg19		0.02	-0.182835	TGGxGGC	COVERED																																																																																			NOVEL	RP11-867G23.13-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000392921.1	0	6.608653	KEEP	0	0	0	22	659	CC	0.999879	0.423426	0		+	6	60	228	0	0	20.23329	15	60	444	56	ENST00000534065.1	0.285714	0.423478
PELI3	246330	__UNKNOWN__	__UNKNOWN__	11	66244504	66244504	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:66244504C>T	ENST00000349459.6	+	0	2488				PELI3_ENST00000320740.7_3'UTR|CTD-3074O7.5_ENST00000533502.1_RNA|CTD-3074O7.5_ENST00000527092.1_RNA	NM_001098510.1	NP_001091980.1	Q8N2H9	PELI3_HUMAN	pellino E3 ubiquitin protein ligase family member 3	NA		NA			defense response to Gram-negative bacterium (GO:0050829)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Toll signaling pathway (GO:0045751)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon production (GO:0032480)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|protein K63-linked ubiquitination (GO:0070534)|regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070428)|Toll signaling pathway (GO:0008063)	cytosol (GO:0005829)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)	15						ggcctgtgcacaggctcaggt	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL834395	CCDS31615.1, CCDS41675.1, CCDS73328.1	11q13.2	2012-02-23	2012-02-23		ENSG00000174516	ENSG00000174516	246330		Pellino homologs	30010	protein-coding gene	gene with protein product		609827	pellino homolog 3 (Drosophila)		NA	12874243, 15917247	Standard	NM_145065	NM_145065	NA	Approved	MGC35521	uc001oic.4	Q8N2H9	OTTHUMG00000167109	ENST00000349459.6:c.*866C>T	chr11.hg19:g.66244504C>T		NA	Q8N3E1|Q8N9Q6|Q8TAW7|Q8TED5	hg19	CCDS41675.1	0.02	10.511274	GCAxAGG	COVERED																																																																																			NOVEL	PELI3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393225.1	7	19.865004	KEEP	0	0	0	66	2377	CC	1	1	0		+	12	60	435	0	0	27.781924	265	60	10012	418	ENST00000349459.6	0.043321	1
CTD-3074O7.11	0	__UNKNOWN__	__UNKNOWN__	11	66276884	66276884	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:66276884C>A	ENST00000419755.3	+	1	236				DPP3_ENST00000532677.1_3'UTR|DPP3_ENST00000541961.1_3'UTR|DPP3_ENST00000531863.1_3'UTR|DPP3_ENST00000453114.1_3'UTR|DPP3_ENST00000360510.2_3'UTR						NA		NA									NA						tttgtcagcactttccagcct	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000419755.3:c.158+99C>A	chr11.hg19:g.66276884C>A		NA		hg19		0.02	18.254366	GCAxTTT	COVERED																																																																																			NOVEL	CTD-3074O7.11-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000395848.2	6	44.222449	KEEP	0	0	0	147	5118	CC	1	1	0		+	82	60	2822	0	0	231.807432	333	60	12225	752	ENST00000419755.3	0.19759	1
TPCN2	219931	__UNKNOWN__	__UNKNOWN__	11	68816493	68816493	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:68816493C>T	ENST00000294309.3	+	1	129	c.28C>T	c.(28-30)Ccc>Tcc	p.P10S	TPCN2_ENST00000542467.1_Missense_Mutation_p.P10S	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	10		NA			calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGAGTCGGAGCCCCTGCTGGG	0.746	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													2	3	3	NA		NA	NA	11		NA											NA				68816493		1360	2558	3918	SO:0001583	missense			AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341	219931		Voltage-gated ion channels / Two-pore channels	20820	protein-coding gene	gene with protein product		612163			NA	16382101	Standard	NM_139075	NM_139075	NA	Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.28C>T	chr11.hg19:g.68816493C>T	ENSP00000294309:p.Pro10Ser	NA	Q9NT82	hg19	CCDS8189.1	0.02	2.179455	GAGxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799514	0.70567	.	.	ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.97598	-4.41;-4.45	3.84	3.84	0.44239	.	0.455984	0.15845	U	0.241846	D	0.97739	0.9258	M	0.64997	1.995	0.20307	N	0.999915	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.992;0.996	D	0.92828	0.6278	10	0.87932	D	0	-19.7112	11.9659	0.53035	0.0:1.0:0.0:0.0	.	10;10;10	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	S	10	ENSP00000294309:P10S;ENSP00000445551:P10S	ENSP00000294309:P10S	P	+	1	0	TPCN2	68573069	0.165000	0.22948	0.059000	0.19551	0.063000	0.16089	3.030000	0.49720	2.070000	0.61991	0.305000	0.20034	CCC	NOVEL	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396878.2	0	24.323665	KEEP	0	0	0	81	2622	CC	1	0.984161	0		+	24	60	764	0	0	70.73067	34	60	1201	177	ENST00000294309.3	0.413793	0.984161
CLPB	81570	__UNKNOWN__	__UNKNOWN__	11	72145515	72145515	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs139584512		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:72145515G>T	ENST00000538039.1	-	1	126	c.4C>A	c.(4-6)Ctg>Atg	p.L2M	CLPB_ENST00000294053.3_Missense_Mutation_p.L2M|CLPB_ENST00000543042.1_De_novo_Start_OutOfFrame|CLPB_ENST00000445069.2_Missense_Mutation_p.L2M|CLPB_ENST00000340729.5_Missense_Mutation_p.L2M	NM_001258392.1	NP_001245321.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	2		NA			cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						AGGGACCCCAGCATCTTGACA	0.667	NA	NA									OREG0021194	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	50	49	NA		NA	NA	11		NA											NA				72145515		2200	4293	6493	SO:0001583	missense			BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129	81570		Ankyrin repeat domain containing	30664	protein-coding gene	gene with protein product	suppressor of potassium transport defect 3	NA			NA	11230166, 7835694	Standard	NM_030813	NM_030813	NA	Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000538039.1:c.4C>A	chr11.hg19:g.72145515G>T	ENSP00000441518:p.Leu2Met	1135	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	hg19	CCDS58154.1	0.02	4.199937	CCAxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.05	2.120015	0.37436	.	.	ENSG00000162129	ENST00000294053;ENST00000538039;ENST00000340729	T;T;T	0.73258	1.45;0.7;-0.73	5.16	2.22	0.28083	.	0.260054	0.24332	N	0.039446	T	0.50956	0.1646	N	0.08118	0	0.80722	D	1	B;P;P	0.39250	0.354;0.665;0.535	P;P;B	0.45428	0.48;0.48;0.287	T	0.34378	-0.9831	10	0.28530	T	0.3	-2.8625	5.7429	0.18104	0.1649:0.1649:0.6702:0.0	.	2;2;2	F8W7P6;Q9H078-2;Q9H078	.;.;CLPB_HUMAN	M	2	ENSP00000294053:L2M;ENSP00000441518:L2M;ENSP00000340385:L2M	ENSP00000294053:L2M	L	-	1	2	CLPB	71823163	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	0.892000	0.28322	0.267000	0.21916	0.655000	0.94253	CTG	NOVEL	CLPB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396890.2	2	44.509559	KEEP	0	0	0	148	5218	GG	1	1	0		-	21	60	747	0	0	59.455474	113	60	4210	353	ENST00000538039.1	0.156716	1
RNF169	254225	__UNKNOWN__	__UNKNOWN__	11	74547794	74547794	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:74547794C>A	ENST00000299563.4	+	0	2159					NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						GAAGTGTTACCTATTTTTAAA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													22	23	23	NA		NA	NA	11		NA											NA				74547794		1874	4078	5952	SO:0001624	3_prime_UTR_variant			AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439	254225		RING-type (C3HC4) zinc fingers	26961	protein-coding gene	gene with protein product		NA			NA	12056414	Standard	XM_495886	NM_001098638	NA	Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.*19C>A	chr11.hg19:g.74547794C>A		NA	Q6N015	hg19	CCDS41691.1	0.02	13.468987	TACxTAT	COVERED																																																																																			NOVEL	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384741.1	5	25.556086	KEEP	0	0	0	85	2937	CC	1	1	0		+	22	60	819	0	0	58.148949	281	60	10573	470	ENST00000299563.4	0.072607	1
NEU3	10825	__UNKNOWN__	__UNKNOWN__	11	74716779	74716779	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs562313920		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:74716779C>A	ENST00000294064.4	+	3	1555	c.628C>A	c.(628-630)Cct>Act	p.P210T	NEU3_ENST00000532963.1_3'UTR|NEU3_ENST00000545272.1_Missense_Mutation_p.P101T|NEU3_ENST00000531509.1_Missense_Mutation_p.P210T|NEU3_ENST00000544263.1_Missense_Mutation_p.P177T|NEU3_ENST00000529024.1_Intron	NM_006656.5	NP_006647.3	Q9UQ49	NEUR3_HUMAN	sialidase 3 (membrane sialidase)	177		NA			carbohydrate metabolic process (GO:0005975)|ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-sialidase activity (GO:0016997)|exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(2)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						ACTGGTCATCCCTGCGTATAC	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													132	129	130	NA		NA	NA	11		NA											NA				74716779		2054	4199	6253	SO:0001583	missense			AB008185	CCDS44682.1	11q13.5	2008-02-05				ENSG00000162139	10825			7760	protein-coding gene	gene with protein product		604617			NA	10405317	Standard	NM_006656	NM_006656	NA	Approved		uc001ovw.3	Q9UQ49		ENST00000294064.4:c.628C>A	chr11.hg19:g.74716779C>A	ENSP00000294064:p.Pro210Thr	NA	A8K327|Q9NQE1	hg19	CCDS44682.1	0.02	14.492875	ATCxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	23.0	4.356797	0.82243	.	.	ENSG00000162139	ENST00000294064;ENST00000531509;ENST00000544263;ENST00000545272	D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55	5.24	5.24	0.73138	Neuraminidase (2);	0.000000	0.85682	D	0.000000	D	0.94453	0.8215	M	0.81341	2.54	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.94646	0.7835	10	0.66056	D	0.02	-13.6186	16.3645	0.83312	0.0:1.0:0.0:0.0	.	177;210	Q9UQ49;A8K327	NEUR3_HUMAN;.	T	210;210;177;101	ENSP00000294064:P210T;ENSP00000432097:P210T;ENSP00000445591:P177T;ENSP00000439908:P101T	ENSP00000294064:P210T	P	+	1	0	NEU3	74394427	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.651000	0.83577	2.726000	0.93360	0.655000	0.94253	CCT	NOVEL	NEU3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384595.1	5	15.931438	KEEP	0	0	0	53	1822	CC	1	1	0		+	153	60	5487	0	0	524.723773	170	60	6001	455	ENST00000294064.4	0.473684	1
SERPINH1	871	__UNKNOWN__	__UNKNOWN__	11	75277632	75277632	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:75277632C>T	ENST00000524558.1	+	2	1673	c.238C>T	c.(238-240)Ctc>Ttc	p.L80F	SERPINH1_ENST00000358171.3_Missense_Mutation_p.L80F|SERPINH1_ENST00000533603.1_Missense_Mutation_p.L80F|SERPINH1_ENST00000530284.1_Missense_Mutation_p.L80F			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	80		NA			chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GTCGCTAGGGCTCGTGTCGCT	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	31	35	NA		NA	NA	11		NA											NA				75277632		2199	4291	6490	SO:0001583	missense			X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257	871		Serine (or cysteine) peptidase inhibitors	1546	protein-coding gene	gene with protein product		600943	serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2, serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	CBP1, CBP2, SERPINH2	NA	7656593, 9533029, 24172014	Standard	NM_004353	NM_001207014	NA	Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.238C>T	chr11.hg19:g.75277632C>T	ENSP00000434412:p.Leu80Phe	NA	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	hg19	CCDS8239.1	0.02	2.191092	GGGxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.59	3.426232	0.62733	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526242;ENST00000526397;ENST00000421448;ENST00000529643;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000528990;ENST00000533449;ENST00000525611;ENST00000528760	D;D;D;D;D;D;D;D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11;-2.11	5.28	5.28	0.74379	Serpin domain (3);	0.112402	0.64402	D	0.000015	D	0.90607	0.7055	L	0.45581	1.43	0.80722	D	1	D;D	0.61080	0.989;0.989	P;D	0.63793	0.9;0.918	D	0.91566	0.5268	10	0.87932	D	0	.	16.4242	0.83809	0.0:1.0:0.0:0.0	.	80;80	E9PPV6;P50454	.;SERPH_HUMAN	F	80;80;55;80;80;80;80;80;80;80;80;80;80	ENSP00000434657:L80F;ENSP00000350894:L80F;ENSP00000431384:L55F;ENSP00000434964:L80F;ENSP00000435936:L80F;ENSP00000436305:L80F;ENSP00000436040:L80F;ENSP00000434412:L80F;ENSP00000431827:L80F;ENSP00000435452:L80F;ENSP00000437108:L80F	ENSP00000350894:L80F	L	+	1	0	SERPINH1	74955280	0.588000	0.26799	0.997000	0.53966	0.666000	0.39218	1.102000	0.31050	2.470000	0.83445	0.563000	0.77884	CTC	NOVEL	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383610.1	2	4.81488	KEEP	0	0	0	16	545	CC	0.997832	0.993528	0		+	13	60	436	0	0	35.398315	55	60	2024	93	ENST00000524558.1	0.191176	0.995687
MOGAT2	80168	__UNKNOWN__	__UNKNOWN__	11	75431161	75431161	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:75431161G>C	ENST00000198801.5	+	2	286	c.216G>C	c.(214-216)caG>caC	p.Q72H	MOGAT2_ENST00000526712.1_5'UTR	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	72		NA			diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)			NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					GGCACATCCAGGCCATCAGGT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													162	167	165	NA		NA	NA	11		NA											NA				75431161		2200	4293	6493	SO:0001583	missense			AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391	80168			23248	protein-coding gene	gene with protein product		610270			NA	14970677	Standard	NM_025098	NM_025098	NA	Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.216G>C	chr11.hg19:g.75431161G>C	ENSP00000198801:p.Gln72His	NA	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	hg19	CCDS8240.1	0.02	24.880915	CCAxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331243	0.41297	.	.	ENSG00000166391	ENST00000198801	T	0.14640	2.49	5.04	0.844	0.18943	.	0.843991	0.10944	N	0.616898	T	0.08891	0.0220	L	0.31804	0.96	0.19945	N	0.999948	B;B	0.17268	0.003;0.021	B;B	0.16722	0.014;0.016	T	0.36016	-0.9765	10	0.46703	T	0.11	0.3559	2.8679	0.05607	0.1602:0.3675:0.3413:0.131	.	72;72	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	H	72	ENSP00000198801:Q72H	ENSP00000198801:Q72H	Q	+	3	2	MOGAT2	75108809	0.000000	0.05858	0.000000	0.03702	0.828000	0.46876	-0.828000	0.04419	0.001000	0.14605	0.561000	0.74099	CAG	NOVEL	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383520.1	2	26.475093	KEEP	0	0	0	88	3012	GG	1	1	0		+	157	60	5398	0	0	474.699404	374	60	13469	781	ENST00000198801.5	0.295669	1
UVRAG	7405	__UNKNOWN__	__UNKNOWN__	11	75694451	75694451	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:75694451G>A	ENST00000533454.1	+	0	180				UVRAG_ENST00000528420.1_Silent_p.L139L|UVRAG_ENST00000532130.1_5'UTR|UVRAG_ENST00000531818.1_5'UTR|UVRAG_ENST00000356136.3_Silent_p.L240L			Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	NA		NA			DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						GTGAATGCCTGCAGTTAAAAA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													57	55	56	NA		NA	NA	11		NA											NA				75694451		2200	4293	6493	SO:0001623	5_prime_UTR_variant			X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382	7405			12640	protein-coding gene	gene with protein product	beclin 1 binding protein	602493	UV radiation resistance associated gene		NA	9169138, 16799551, 18843052	Standard	NM_003369	NM_003369	NA	Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000533454.1:c.-573G>A	chr11.hg19:g.75694451G>A		NA	B3KTC1|O00392	hg19		0.02	4.009961	CCTxCAG	COVERED																																																																																			NOVEL	UVRAG-005	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000383434.1	0	10.533698	KEEP	0	0	0	35	1239	GG	0.999999	0.999999	0		+	15	60	501	0	0	37.035505	118	60	4415	204	ENST00000533454.1	0.112782	1
MYO7A	4647	__UNKNOWN__	__UNKNOWN__	11	76905157	76905157	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:76905157C>A	ENST00000458637.2	+	32	4418				MYO7A_ENST00000409619.2_Intron|MYO7A_ENST00000409709.3_Intron	NM_001127180.1	NP_001120652.1	Q13402	MYO7A_HUMAN	myosin VIIA	NA		NA			actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGTCCAGCTCCATGCCAGTGC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474	4647		A-kinase anchor proteins, Myosins / Myosin superfamily : Class VII	7606	protein-coding gene	gene with protein product		276903	myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))	USH1B, DFNB2, DFNA11	NA	8884266	Standard	NM_000260	NM_000260	NA	Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000458637.2:c.4153-242C>A	chr11.hg19:g.76905157C>A		NA	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	hg19	CCDS53684.1	0.02	9.036016	CTCxATG	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.366	-0.587416	0.03799	.	.	ENSG00000137474	ENST00000544424	.	.	.	2.99	-4.5	0.03493	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34950	-0.9808	5	0.59425	D	0.04	.	1.1089	0.01700	0.1737:0.3546:0.1774:0.2942	.	.	.	.	N	28	.	ENSP00000443609:H28N	H	+	1	0	MYO7A	76582805	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.570000	0.05895	-1.009000	0.03400	-1.768000	0.00664	CAT	NOVEL	MYO7A-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328134.2	2	12.039699	KEEP	0	0	0	40	1447	CC	1	1	0		+	54	60	1953	0	0	165.384913	187	60	7101	356	ENST00000458637.2	0.224066	1
AQP11	282679	__UNKNOWN__	__UNKNOWN__	11	77320918	77320918	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:77320918T>A	ENST00000313578.3	+	0	1670				AQP11_ENST00000528638.1_3'UTR	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	NA		NA			endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			GGAAAGTTGCTTTTAGAAGTA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301	282679		Ion channels / Aquaporins	19940	protein-coding gene	gene with protein product		609914			NA	16107722	Standard	NM_173039	NM_173039	NA	Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.*496T>A	chr11.hg19:g.77320918T>A		NA		hg19	CCDS8251.1	0.02	6.948583	TGCxTTT	COVERED																																																																																			NOVEL	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382582.1	7	4.212554	KEEP	0	0	0	14	449	TT	0.995343	0.995343	0		+	12	60	452	0	0	31.665729	172	60	6259	224	ENST00000313578.3	0.065217	1
AAMDC	28971	__UNKNOWN__	__UNKNOWN__	11	77589801	77589801	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:77589801G>T	ENST00000532481.1	+	3	318				INTS4_ENST00000534064.1_3'UTR|AAMDC_ENST00000304716.8_Intron|INTS4_ENST00000535943.1_3'UTR|AAMDC_ENST00000527134.1_Splice_Site_p.G128W			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	NA		NA			negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)					NA						GACAGGAGAAGGGTAAGTAGA	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884	28971			30205	protein-coding gene	gene with protein product		NA	chromosome 11 open reading frame 67	C11orf67	NA	12477932	Standard	NM_024684	NM_024684	NA	Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000532481.1:c.228+8938G>T	chr11.hg19:g.77589801G>T		NA	Q96AQ4|Q9Y6B1	hg19		0.02	39.20713	GAAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.256	0.604273	0.14002	.	.	ENSG00000087884	ENST00000527134	.	.	.	4.66	-7.45	0.01374	.	.	.	.	.	T	0.37625	0.1010	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.53344	-0.8452	5	0.87932	D	0	.	9.1288	0.36833	0.7276:0.0:0.1661:0.1063	.	.	.	.	W	128	.	ENSP00000433281:G128W	G	+	1	0	C11orf67	77267449	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.134000	0.10436	-1.685000	0.01441	-0.150000	0.13652	GGG	NOVEL	AAMDC-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000390974.1	2	41.521953	KEEP	0	0	0	138	4822	GG	1	1	0		+	41	60	1482	0	0	94.794377	891	60	32378	1207	ENST00000532481.1	0.043991	1
NARS2	79731	__UNKNOWN__	__UNKNOWN__	11	78152193	78152193	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:78152193G>A	ENST00000528850.1	-	13	1518				RP11-452H21.1_ENST00000534168.1_RNA|NARS2_ENST00000281038.5_Intron			Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	NA		NA			asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	ATTCTTTCAGGGAACGGCAAT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													77	78	78	NA		NA	NA	11		NA											NA				78152193		2200	4292	6492	SO:0001627	intron_variant			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	79731	6.1.1.22	Aminoacyl tRNA synthetases / Class II	26274	protein-coding gene	gene with protein product	asparagine tRNA ligase 2, mitochondrial (putative)	612803			NA	15779907	Standard	NM_024678	NM_024678	NA	Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000528850.1:c.582-30C>T	chr11.hg19:g.78152193G>A		NA	G3V178	hg19	CCDS58164.1	0.02	31.322322	CAGxGAA	COVERED																																																																																			NOVEL	NARS2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391139.1	2	5.952914	KEEP	0	1	26	29	1008	GG	0.999997	0.999997	0		-	32	60	1210	0	0	79.010479	710	60	25372	871	ENST00000528850.1	0.043127	1
NARS2	79731	__UNKNOWN__	__UNKNOWN__	11	78270625	78270625	__UNKNOWN__	De_novo_Start_OutOfFrame	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:78270625G>C	ENST00000528850.1	-	0	809				NARS2_ENST00000281038.5_Missense_Mutation_p.S185C			Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	NA		NA			asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	AGAGTCATTGGATGTGATTAT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													146	145	145	NA		NA	NA	11		NA											NA				78270625		2200	4292	6492					BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	79731	6.1.1.22	Aminoacyl tRNA synthetases / Class II	26274	protein-coding gene	gene with protein product	asparagine tRNA ligase 2, mitochondrial (putative)	612803			NA	15779907	Standard	NM_024678	NM_024678	NA	Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000528850.1:c.-128C>G	chr11.hg19:g.78270625G>C		NA	G3V178	hg19	CCDS58164.1	0.02	36.428087	TTGxATG	COVERED	.	.	.	.	.	.	.	.	.	.	G	23.2	4.385401	0.82792	.	.	ENSG00000137513	ENST00000281038;ENST00000529880	T;T	0.80214	-1.35;-1.35	5.57	5.57	0.84162	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.000000	0.85682	D	0.000000	D	0.91831	0.7415	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93121	0.6525	10	0.87932	D	0	-12.3544	18.3183	0.90229	0.0:0.0:1.0:0.0	.	185	Q96I59	SYNM_HUMAN	C	185	ENSP00000281038:S185C;ENSP00000432240:S185C	ENSP00000281038:S185C	S	-	2	0	NARS2	77948273	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.888000	0.92464	2.606000	0.88127	0.563000	0.77884	TCC	NOVEL	NARS2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391139.1	1	23.777037	KEEP	0	0	0	79	2785	GG	1	1	0		-	32	60	1207	0	0	77.529687	775	60	28590	1095	ENST00000528850.1	0.039653	1
TENM4	26011	__UNKNOWN__	__UNKNOWN__	11	78565277	78565277	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201191369	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:78565277C>T	ENST00000278550.7	-	12	2015	c.1553G>A	c.(1552-1554)cGg>cAg	p.R518Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	518		NA			cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)				NA						CACAGTTCCCCGAGACTGGCG	0.557	NA	NA											C|||	2	0.000399361	0	0	5008	,	,	NA	17593	0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								C	GLN/ARG	1,1383		0,1,691	25	28	27	NA	1553	5.1	1	11		27	3,3179		0,3,1588	yes	missense	ODZ4	NM_001098816.2	43	0,4,2279	TT,TC,CC	NA	0.0943,0.0723,0.0876	probably-damaging	518/2770	78565277	4,4562	692	1591	2283	SO:0001583	missense			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256	26011			29945	protein-coding gene	gene with protein product		610084	odz, odd Oz/ten-m homolog 4 (Drosophila)	ODZ4	NA	12000766, 10625539	Standard		NM_001098816	NA	Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.1553G>A	chr11.hg19:g.78565277C>T	ENSP00000278550:p.Arg518Gln	NA	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	hg19	CCDS44688.1	0.02	4.612173	CCCxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	33	5.254336	0.95336	7.23E-4	9.43E-4	ENSG00000149256	ENST00000278550	T	0.27256	1.68	5.07	5.07	0.68467	.	0.133460	0.48767	D	0.000178	T	0.37571	0.1008	L	0.47716	1.5	0.51767	D	0.999932	D	0.76494	0.999	P	0.58820	0.846	T	0.02184	-1.1199	9	.	.	.	.	12.9951	0.58642	0.0:0.9229:0.0:0.0771	.	518	Q6N022	TEN4_HUMAN	Q	518	ENSP00000278550:R518Q	.	R	-	2	0	ODZ4	78242925	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	4.805000	0.62561	2.631000	0.89168	0.561000	0.74099	CGG	NOVEL	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391406.2	0	24.036709	KEEP	0	0	0	80	2634	CC	1	1	0		-	53	60	1901	0	0	174.211509	91	60	3077	305	ENST00000278550.7	0.368056	1
FOLH1B	219595	__UNKNOWN__	__UNKNOWN__	11	89403531	89403531	__UNKNOWN__	RNA	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:89403531A>T	ENST00000532352.1	+	0	908							Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B	NA		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(26)|ovary(4)|skin(4)|urinary_tract(2)	48						GTTTTTTTTCAAAGAATGTCT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													68	66	67	NA		NA	NA	11		NA											NA				89403531		2201	4299	6500					AF261715		11q14.3	2014-03-18			ENSG00000134612	ENSG00000134612	219595			13636	protein-coding gene	gene with protein product	prostate specific membrane antigen like protein, Cell growth-inhibiting gene 26 protein, glutamate carboxypeptidase III	609020	folate hydrolase 2	FOLH2, FOLHP	NA	9838072, 14716746	Standard	NM_153696	NM_153696	NA	Approved	PSMAL, GCPIII	uc001pda.3	Q9HBA9	OTTHUMG00000167376	ENST00000532352.1:	chr11.hg19:g.89403531A>T		NA		hg19		0.02	1.704481	TTCxAAG	COVERED																																																																																			NOVEL	FOLH1B-004	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000395421.1	0	4.661202	KEEP	0	1	12	20	638	AA	0.999869	0.998862	0		+	5	60	138	0	0	8.207278	73	60	2689	120	ENST00000532352.1	0.064103	0.998993
GPR83	10888	__UNKNOWN__	__UNKNOWN__	11	94112656	94112656	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:94112656G>A	ENST00000243673.2	-	0	2102					NM_016540.3	NP_057624.3	Q9NYM4	GPR83_HUMAN	G protein-coupled receptor 83	NA		NA			response to glucocorticoid (GO:0051384)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			NS(1)|breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAAATGGATGGGATAAGAGAG	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF236081	CCDS8297.1	11q21	2012-08-21	2003-07-30	2003-08-01	ENSG00000123901	ENSG00000123901	10888		GPCR / Class A : Orphans	4523	protein-coding gene	gene with protein product		605569	G protein-coupled receptor 72	GPR72	NA	10760605, 11060465	Standard	NM_016540	NM_016540	NA	Approved		uc001pet.2	Q9NYM4	OTTHUMG00000167779	ENST00000243673.2:c.*659C>T	chr11.hg19:g.94112656G>A		NA	B0M0K5|Q6NWR4|Q9P1Y8	hg19	CCDS8297.1	0.02	2.287542	ATGxGAT	COVERED																																																																																			NOVEL	GPR83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396232.1	2	3.310725	KEEP	0	0	0	11	382	GG	0.993072	0.975153	0		-	18	60	658	0	0	58.949986	39	60	1373	83	ENST00000243673.2	0.315789	0.981955
MAML2	84441	__UNKNOWN__	__UNKNOWN__	11	95826380	95826380	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:95826380G>A	ENST00000524717.1	-	2	2099	c.815C>T	c.(814-816)aCt>aTt	p.T272I		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	272		NA			gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				GCAAGACAGAGTCTCTCCTGG	0.483	NA	NA	T	MECT1, CRTC3	salivary gland mucoepidermoid									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	0													110	104	106	NA		NA	NA	11		NA											NA				95826380		1930	4130	6060	SO:0001583	missense			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384	84441			16259	protein-coding gene	gene with protein product		607537	mastermind (Drosophila)-like 2		NA	12370315, 12386158	Standard		NM_032427	NA	Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.815C>T	chr11.hg19:g.95826380G>A	ENSP00000434552:p.Thr272Ile	NA	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	hg19	CCDS44714.1	0.02	4.354551	AGAxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269026	0.40095	.	.	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.45668	0.89;0.89	5.42	5.42	0.78866	.	0.162027	0.42821	D	0.000649	T	0.40909	0.1136	L	0.42245	1.32	0.32315	N	0.563188	P	0.48764	0.915	B	0.42386	0.386	T	0.49579	-0.8925	10	0.33940	T	0.23	-8.8892	19.2175	0.93783	0.0:0.0:1.0:0.0	.	272	Q8IZL2	MAML2_HUMAN	I	272	ENSP00000434552:T272I;ENSP00000412394:T272I	ENSP00000412394:T272I	T	-	2	0	MAML2	95466028	1.000000	0.71417	0.985000	0.45067	0.987000	0.75469	5.688000	0.68227	2.536000	0.85505	0.455000	0.32223	ACT	NOVEL	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395540.1	4	13.24353	KEEP	0	0	0	44	1598	GG	1	0.999984	0		-	10	60	361	0	0	26.533069	95	60	3612	188	ENST00000524717.1	0.095238	0.999984
CCDC82	79780	__UNKNOWN__	__UNKNOWN__	11	96118030	96118030	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:96118030A>G	ENST00000423339.2	-	0	124				CCDC82_ENST00000542662.1_Intron|CCDC82_ENST00000278520.5_Intron			Q8N4S0	CCD82_HUMAN	coiled-coil domain containing 82	NA		NA								endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)	19		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.154)		aatggtccacaaacacaaaat	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF245436	CCDS8307.1	11q21	2006-03-09			ENSG00000149231	ENSG00000149231	79780			26282	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024725	NM_024725	NA	Approved	FLJ23518	uc001pfx.4	Q8N4S0	OTTHUMG00000167678	ENST00000423339.2:c.-119T>C	chr11.hg19:g.96118030A>G		NA	B3KPU7|Q8WV71|Q9H2Q5|Q9H5E3	hg19	CCDS8307.1	0.02	1.906997	CACxAAC	COVERED																																																																																			NOVEL	CCDC82-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395543.1	2	12.337984	KEEP	0	0	0	41	1300	AA	1	0.999804	0		-	13	60	437	0	0	33.834047	76	60	2767	167	ENST00000423339.2	0.146067	0.999804
CASP12	100506742	__UNKNOWN__	__UNKNOWN__	11	104769241	104769241	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:104769241G>A	ENST00000441710.1	-	0	156				CASP12_ENST00000433738.1_5'UTR|CASP12_ENST00000446862.1_5'UTR|CASP12_ENST00000494737.1_5'UTR|CASP12_ENST00000447913.1_5'UTR|CASP12_ENST00000375726.2_5'UTR|CASP12_ENST00000448103.1_5'UTR			Q6UXS9	CASPC_HUMAN	caspase 12 (gene/pseudogene)	NA		NA			endoplasmic reticulum unfolded protein response (GO:0030968)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)			breast(1)	1						ATATTACCCTGAATGGAAAAT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF464191		11q22.3	2011-02-14	2007-12-17	2006-02-17	ENSG00000204403	ENSG00000204403	100506742		Caspases	19004	protein-coding gene	gene with protein product		608633	caspase 12 pseudogene 1, caspase 12	CASP12P1	NA	12054529, 9038361, 16917906, 16532395	Standard	NM_001191016	NM_001191016	NA	Approved		uc031qdo.1	Q6UXS9	OTTHUMG00000154965	ENST00000441710.1:c.-100C>T	chr11.hg19:g.104769241G>A		NA	D6RBN7	hg19		0.02	2.165226	CCTxAAT	COVERED																																																																																			NOVEL	CASP12-005	NOVEL	non_canonical_genome_sequence_error|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000337829.1	3	8.125091	KEEP	0	0	0	27	922	GG	0.999988	0.997151	0		-	21	60	700	0	0	61.282419	50	60	1881	111	ENST00000441710.1	0.295775	0.997163
CASP1	834	__UNKNOWN__	__UNKNOWN__	11	104905208	104905208	__UNKNOWN__	Intron	SNP	A	A	G	rs2509650	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:104905208A>G	ENST00000528974.1	-	2	41				CASP1_ENST00000526568.1_Intron|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000598974.1_Intron|CASP1_ENST00000527979.1_5'UTR|CASP1_ENST00000393136.4_Intron|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000525825.1_Intron|CASP1_ENST00000534497.1_Intron|CASP1_ENST00000593315.1_Intron|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000533400.1_Intron|CASP1_ENST00000436863.3_Intron|CASP1_ENST00000446369.1_Intron|CASP1_ENST00000353247.5_Intron			P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TTGTCTGTTTAGAGCACAAGG	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(41;1246 1743 4934)					NA		NA				0													232	224	227	NA		NA	NA	11		NA											NA				104905208		2202	4299	6501	SO:0001627	intron_variant			U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752	834		Caspases	1499	protein-coding gene	gene with protein product	caspase-1, interleukin 1, beta, convertase	147678	caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase), caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)	IL1BC	NA	1373520, 9250871	Standard	NM_033292	NM_033292	NA	Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000528974.1:c.24-93T>C	chr11.hg19:g.104905208A>G		NA	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	hg19		0.02	20.457214	TTTxGAG	COVERED																																																																																			NOVEL	CASP1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000388122.1	8	29.957619	KEEP	13	8	276	196	6151	AA	1	1	0		-	27	52	991	0	0	67.097518	444	60	16606	833	ENST00000528974.1	0.057325	1
ACAT1	38	__UNKNOWN__	__UNKNOWN__	11	108014696	108014696	__UNKNOWN__	Intron	SNP	C	C	T	rs376661693|rs12801620		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:108014696C>T	ENST00000265838.4	+	10	1031					NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	NA		NA			adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	CCCCCCCCCCCTTTTTTTAAA	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	56	53	NA		NA	NA	11		NA											NA				108014696		2201	4298	6499	SO:0001627	intron_variant			D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	38	2.3.1.9		93	protein-coding gene	gene with protein product	acetoacetyl Coenzyme A thiolase	607809	acetyl-Coenzyme A acetyltransferase 1	ACAT	NA	1979337	Standard	NM_000019	NM_000019	NA	Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.941-14C>T	chr11.hg19:g.108014696C>T		NA	B2R6H1|G3XAB4|Q96FG8	hg19	CCDS8339.1	0.02	-0.338956	CCCxTTT	COVERED																																																																																			NOVEL	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389474.1	0	7.992823	KEEP	0	0	0	27	777	CC	0.999988	0.865735	0		+	10	70	320	0	1	27.705207	25	60	759	82	ENST00000265838.4	0.285714	0.865745
EXPH5	23086	__UNKNOWN__	__UNKNOWN__	11	108378184	108378184	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:108378184A>T	ENST00000265843.4	-	0	8160				EXPH5_ENST00000428840.1_3'UTR|EXPH5_ENST00000443411.1_3'UTR	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	NA		NA			intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AATATAAACCAAGCAAGATAA	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723	23086			30578	protein-coding gene	gene with protein product	synaptotagmin-like homologue lacking C2 domains b	612878			NA	9734811, 11773082	Standard	NM_015065	NM_015065	NA	Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.*2080T>A	chr11.hg19:g.108378184A>T		NA	Q2KHM1|Q9Y4D6	hg19	CCDS8341.1	0.02	4.825464	ACCxAGC	COVERED																																																																																			NOVEL	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390279.1	0	13.540234	KEEP	0	0	0	45	1396	AA	1	1	0		-	45	60	1659	0	0	150.766014	86	60	3169	221	ENST00000265843.4	0.343511	1
BTG4	54766	__UNKNOWN__	__UNKNOWN__	11	111367656	111367656	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:111367656G>T	ENST00000356018.2	-	4	710				BTG4_ENST00000525791.1_3'UTR	NM_017589.3	NP_060059.1	Q9NY30	BTG4_HUMAN	B-cell translocation gene 4	NA		NA			cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|neuron differentiation (GO:0030182)					large_intestine(2)|upper_aerodigestive_tract(1)	3		all_cancers(61;3.78e-13)|all_epithelial(67;5.29e-08)|Melanoma(852;3.15e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0204)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.22e-06)|BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|all cancers(92;2.18e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0509)		TGATTCTGTAGGAATTTAAGT	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ271351	CCDS8346.1	11q23	2008-05-27				ENSG00000137707	54766			13862	protein-coding gene	gene with protein product		605673			NA	10995567	Standard		NM_017589	NA	Approved	PC3B	uc001plj.3	Q9NY30		ENST00000356018.2:c.510+279C>A	chr11.hg19:g.111367656G>T		NA	Q8NEH7	hg19	CCDS8346.1	0.02	2.054153	GTAxGAA	COVERED																																																																																			NOVEL	BTG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391177.1	2	9.330298	KEEP	0	0	0	31	1092	GG	0.999997	0.999916	0		-	11	60	379	0	0	28.394213	84	70	3115	157	ENST00000356018.2	0.115789	0.999919
SIK3	23387	__UNKNOWN__	__UNKNOWN__	11	116728911	116728911	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:116728911G>A	ENST00000446921.2	-	20	2967	c.2946C>T	c.(2944-2946)cgC>cgT	p.R982R	SIK3_ENST00000375300.1_Silent_p.R1042R|SIK3_ENST00000375288.1_Silent_p.R319R|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000542607.1_Silent_p.R924R|SIK3_ENST00000434315.2_Silent_p.R823R|SIK3_ENST00000292055.4_Silent_p.R984R	NM_001281749.1	NP_001268678.1	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	984		NA			protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						ATAAAGCCTGGCGCTCTGTCA	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													105	100	102	NA		NA	NA	11		NA											NA				116728911		2201	4296	6497	SO:0001819	synonymous_variant			AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584	23387			29165	protein-coding gene	gene with protein product		614776			NA	10231032, 8889548	Standard	NM_025164	NM_025164	NA	Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000446921.2:c.2946C>T	chr11.hg19:g.116728911G>A		NA	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	hg19		0.02	3.869579	CTGxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	6.644	0.487217	0.12641	.	.	ENSG00000160584	ENST00000445177;ENST00000446921	.	.	.	5.54	4.61	0.57282	.	.	.	.	.	T	0.55924	0.1951	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53627	-0.8412	4	.	.	.	.	6.3757	0.21505	0.0715:0.1315:0.661:0.136	.	.	.	.	S	1084;947	.	.	P	-	1	0	SIK3	116234121	1.000000	0.71417	0.996000	0.52242	0.900000	0.52787	1.347000	0.33975	1.262000	0.44165	0.563000	0.77884	CCA	NOVEL	SIK3-014	KNOWN	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000319396.2	8	19.262343	KEEP	0	0	0	64	2262	GG	1	1	0		-	27	60	891	0	0	71.396025	122	60	4384	270	ENST00000446921.2	0.181208	1
BCL9L	283149	__UNKNOWN__	__UNKNOWN__	11	118768357	118768357	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:118768357A>C	ENST00000334801.3	-	0	6231				CXCR5_ENST00000292174.4_3'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	NA		NA			canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TCCCTTAGGGACCCAGAGACA	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174	283149			23688	protein-coding gene	gene with protein product		609004			NA	12964048	Standard	NM_182557	NM_182557	NA	Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.*767T>G	chr11.hg19:g.118768357A>C		NA	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	hg19	CCDS8403.1	0.02	4.971757	GGGxCCC	COVERED																																																																																			NOVEL	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389653.1	4	6.31488	KEEP	0	0	0	21	627	AA	0.999869	0.999847	0		-	74	60	2617	0	0	270.425283	29	60	1000	132	ENST00000334801.3	0.718447	0.999978
CCDC84	338657	__UNKNOWN__	__UNKNOWN__	11	118882809	118882809	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:118882809A>T	ENST00000334418.1	+	7	634				CCDC84_ENST00000580556.1_Intron	NM_198489.1	NP_940891.1	Q86UT8	CCD84_HUMAN	coiled-coil domain containing 84	NA		NA								breast(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		AATCTTTACCACCCTCATGGC	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													65	56	59	NA		NA	NA	11		NA											NA				118882809		2200	4295	6495	SO:0001627	intron_variant			AB094093	CCDS8405.1	11q23.3	2006-03-13			ENSG00000186166	ENSG00000186166	338657			30460	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198489	NM_198489	NA	Approved	DLNB14	uc001pul.3	Q86UT8	OTTHUMG00000166348	ENST00000334418.1:c.579-50A>T	chr11.hg19:g.118882809A>T		NA		hg19	CCDS8405.1	0.02	9.434496	ACCxCCC	COVERED																																																																																			NOVEL	CCDC84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389315.1	2	20.156994	KEEP	0	0	0	67	2029	AA	1	1	0		+	17	60	629	0	0	45.532228	189	60	6555	338	ENST00000334418.1	0.082524	1
HMBS	3145	__UNKNOWN__	__UNKNOWN__	11	118962164	118962164	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:118962164G>A	ENST00000278715.3	+	9	691	c.540G>A	c.(538-540)caG>caA	p.Q180Q	HMBS_ENST00000392841.1_Silent_p.Q163Q|HMBS_ENST00000542729.1_Silent_p.Q163Q|HMBS_ENST00000442944.2_Silent_p.Q163Q|HMBS_ENST00000544387.1_Silent_p.Q180Q|HMBS_ENST00000534956.1_Intron|HMBS_ENST00000543090.1_Silent_p.Q162Q|HMBS_ENST00000537841.1_Silent_p.Q163Q	NM_000190.3	NP_000181.2	P08397	HEM3_HUMAN	hydroxymethylbilane synthase	180		NA			heme biosynthetic process (GO:0006783)|peptidyl-pyrromethane cofactor linkage (GO:0018160)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	hydroxymethylbilane synthase activity (GO:0004418)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	15	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		TGGACGAGCAGCAGGAGTTCA	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	38	42	NA		NA	NA	11		NA											NA				118962164		1976	3743	5719	SO:0001819	synonymous_variant			X04808	CCDS8409.1, CCDS41726.1, CCDS58186.1, CCDS58187.1	11q23.3	2013-07-10			ENSG00000256269	ENSG00000256269	3145	2.5.1.61		4982	protein-coding gene	gene with protein product		609806	uroporphyrinogen I synthase, porphobilinogen deaminase, porphyria, acute; Chester type	PBGD, UPS, PORC	NA	8432552, 17298217	Standard	NM_000190	NM_001258208	NA	Approved		uc001puz.1	P08397	OTTHUMG00000168295	ENST00000278715.3:c.540G>A	chr11.hg19:g.118962164G>A		NA	A8K2L0|G3V1P4|G5EA58|P08396|Q16012	hg19	CCDS8409.1	0.02	4.522425	GCAxCAG	COVERED																																																																																			NOVEL	HMBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399188.1	1	27.088376	KEEP	0	0	0	90	3217	GG	1	0.999999	0		+	21	60	748	0	0	60.654911	99	60	3696	253	ENST00000278715.3	0.175	0.999999
TRIM29	23650	__UNKNOWN__	__UNKNOWN__	11	119983210	119983210	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:119983210C>T	ENST00000528870.1	-	6	2150				TRIM29_ENST00000341846.5_Intron|TRIM29_ENST00000541857.1_Intron|TRIM29_ENST00000529044.1_Intron|TRIM29_ENST00000524816.3_Intron|TRIM29_ENST00000525887.1_Intron			Q14134	TRI29_HUMAN	tripartite motif containing 29	NA		NA			negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		GAGTGGTCAGCGAGGCCAGAC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													128	110	116	NA		NA	NA	11		NA											NA				119983210		2199	4295	6494	SO:0001627	intron_variant			AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699	23650		Tripartite motif containing / Tripartite motif containing	17274	protein-coding gene	gene with protein product	tripartite motif protein TRIM29, ataxia-telangiectasia group D-associated protein	610658	tripartite motif-containing 29		NA	11331580	Standard	NM_012101	NM_012101	NA	Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000528870.1:c.304-26G>A	chr11.hg19:g.119983210C>T		NA	Q96AA9|Q9BZY7	hg19		0.02	26.781144	CAGxGAG	COVERED																																																																																			NOVEL	TRIM29-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000388022.1	6	14.111706	KEEP	0	2	54	66	2270	CC	1	1	0		-	59	60	2058	0	1	149.879318	553	60	19010	868	ENST00000528870.1	0.096405	1
TRIM29	23650	__UNKNOWN__	__UNKNOWN__	11	119999311	119999311	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:119999311T>C	ENST00000341846.5	-	2	1226				TRIM29_ENST00000541857.1_Intron|TRIM29_ENST00000529044.1_Intron	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	NA		NA			negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		CCAGGGCTCATCACTCATCTA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699	23650		Tripartite motif containing / Tripartite motif containing	17274	protein-coding gene	gene with protein product	tripartite motif protein TRIM29, ataxia-telangiectasia group D-associated protein	610658	tripartite motif-containing 29		NA	11331580	Standard	NM_012101	NM_012101	NA	Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.805-108A>G	chr11.hg19:g.119999311T>C		NA	Q96AA9|Q9BZY7	hg19	CCDS8428.1	0.02	27.717999	TCAxCAC	COVERED																																																																																			NOVEL	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277108.2	3	35.481608	KEEP	0	0	0	118	3588	TT	1	1	0		-	31	60	1146	1	0	75.721304	600	60	21494	878	ENST00000341846.5	0.049128	1
C11orf63	79864	__UNKNOWN__	__UNKNOWN__	11	122805826	122805826	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:122805826G>T	ENST00000531316.1	+	4	1726				C11orf63_ENST00000227349.2_Intron			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	NA		NA			axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		GAGGAGAAAGGAGAGACTGCT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													17	18	17	NA		NA	NA	11		NA											NA				122805826		2188	4275	6463	SO:0001627	intron_variant			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944	79864			26288	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024806	NM_024806	NA	Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.1634+43G>T	chr11.hg19:g.122805826G>T		NA	A8K6G0|Q96GB5|Q9H5D6	hg19	CCDS8438.1	0.02	10.386228	AAGxAGA	COVERED																																																																																			NOVEL	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387511.1	7	6.320592	KEEP	0	0	0	21	738	GG	0.999869	0.999869	0		+	21	60	707	0	0	49.175077	236	60	8700	337	ENST00000531316.1	0.081712	1
TMEM225	338661	__UNKNOWN__	__UNKNOWN__	11	123755983	123755983	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:123755983C>T	ENST00000375026.2	-	1	366	c.150G>A	c.(148-150)tgG>tgA	p.W50*		NM_001013743.1	NP_001013765.1	Q6GV28	TM225_HUMAN	transmembrane protein 225	50		NA			negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(12)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	28						AACACATCATCCAAGGACTGT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													156	137	143	NA		NA	NA	11		NA											NA				123755983		2202	4299	6501	SO:0001587	stop_gained			AY634366	CCDS31697.1	11q24.1	2014-06-13			ENSG00000204300	ENSG00000204300	338661			32390	protein-coding gene	gene with protein product	PMP22 claudin domain containing, protein phosphatase 1, regulatory subunit 154	NA			NA		Standard	NM_001013743	XM_006718832	NA	Approved	PMP22CD, PPP1R154	uc001pzi.3	Q6GV28	OTTHUMG00000165959	ENST00000375026.2:c.150G>A	chr11.hg19:g.123755983C>T	ENSP00000364166:p.Trp50*	NA		hg19	CCDS31697.1	0.02	13.683744	CATxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.5	4.304748	0.81247	.	.	ENSG00000204300	ENST00000375026	.	.	.	4.87	4.87	0.63330	.	0.000000	0.45867	D	0.000337	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.298	13.6897	0.62537	0.0:1.0:0.0:0.0	.	.	.	.	X	50	.	ENSP00000364166:W50X	W	-	3	0	TMEM225	123261193	0.999000	0.42202	0.987000	0.45799	0.130000	0.20726	2.934000	0.48956	2.686000	0.91538	0.655000	0.94253	TGG	NOVEL	TMEM225-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387260.1	2	4.514232	KEEP	0	0	0	15	505	CC	0.99649	0.99649	0		-	51	60	1871	0	0	150.184396	273	60	10197	418	ENST00000375026.2	0.157407	1
VWA5A	4013	__UNKNOWN__	__UNKNOWN__	11	123989867	123989867	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:123989867C>T	ENST00000392744.4	+	6	2136				VWA5A_ENST00000449321.1_Intron|VWA5A_ENST00000392748.1_Intron|VWA5A_ENST00000361352.5_Intron|VWA5A_ENST00000456829.2_Intron|VWA5A_ENST00000360334.4_Intron			O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	NA		NA								autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						TGTCGAATTACTCTCTTTTCT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002	4013			6658	protein-coding gene	gene with protein product		602929	loss of heterozygosity, 11, chromosomal region 2, gene A	LOH11CR2A	NA	9417908, 14504409	Standard	NM_014622	NM_001130142	NA	Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000392744.4:c.808+71C>T	chr11.hg19:g.123989867C>T		NA	Q6UN19|Q6UN20|Q9BVF8	hg19		0.02	6.601472	TTAxTCT	COVERED																																																																																			NOVEL	VWA5A-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000387278.1	2	7.825161	KEEP	0	0	0	26	918	CC	0.999957	0.999957	0		+	20	60	740	0	0	56.379767	158	60	6055	253	ENST00000392744.4	0.11236	1
SPA17	53340	__UNKNOWN__	__UNKNOWN__	11	124543778	124543778	__UNKNOWN__	5'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:124543778A>T	ENST00000532692.1	+	0	39				SPA17_ENST00000227135.2_5'UTR|SIAE_ENST00000525730.1_Intron			Q15506	SP17_HUMAN	sperm autoantigenic protein 17	NA		NA			binding of sperm to zona pellucida (GO:0007339)|epithelial cilium movement (GO:0003351)|single fertilization (GO:0007338)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|primary cilium (GO:0072372)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	5	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0223)		TTTTTTTTTTAAAGAAAAAAC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF334735	CCDS8450.1	11q24.2	2009-03-12			ENSG00000064199	ENSG00000064199	53340			11210	protein-coding gene	gene with protein product	cancer/testis antigen 22	608621			NA	8688458	Standard	NM_017425	NM_017425	NA	Approved	SP17, CT22	uc001qap.3	Q15506	OTTHUMG00000165927	ENST00000532692.1:c.-1383A>T	chr11.hg19:g.124543778A>T		NA	B2R4F2|Q9BXF7	hg19	CCDS8450.1	0.02	9.901211	TTTxAAG	COVERED																																																																																			NOVEL	SPA17-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387075.1	1	37.003521	KEEP	0	2	34	136	3580	AA	1	1	0		+	12	70	339	2	0	18.816975	254	60	7565	528	ENST00000532692.1	0.045113	1
SLC37A2	219855	__UNKNOWN__	__UNKNOWN__	11	124956190	124956190	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:124956190C>T	ENST00000308074.4	+	18	1579				SLC37A2_ENST00000525837.1_3'UTR|SLC37A2_ENST00000403796.2_Intron|SLC37A2_ENST00000298280.5_Intron	NM_198277.2	NP_938018.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	NA		NA			carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		GACTCGAGTGCCATTTGAGTG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(11;373 620 21213 26083 47768)					NA		NA				0													172	135	147	NA		NA	NA	11		NA											NA				124956190		692	1591	2283	SO:0001627	intron_variant			AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955	219855		Solute carriers	20644	protein-coding gene	gene with protein product		NA	solute carrier family 37 (glycerol-3-phosphate transporter), member 2		NA		Standard	XM_166184	NM_198277	NA	Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000308074.4:c.1515+34C>T	chr11.hg19:g.124956190C>T		NA	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	hg19	CCDS31714.1	0.02	20.234851	GTGxCAT	COVERED																																																																																			NOVEL	SLC37A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386840.1	3	8.403399	KEEP	0	0	0	28	907	CC	0.999997	0.999997	0		+	52	60	1897	0	0	142.824523	432	60	15560	620	ENST00000308074.4	0.107438	1
PKNOX2	63876	__UNKNOWN__	__UNKNOWN__	11	125280694	125280694	__UNKNOWN__	Silent	SNP	G	G	A	rs370466867		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:125280694G>A	ENST00000298282.9	+	9	1009	c.738G>A	c.(736-738)ccG>ccA	p.P246P	PKNOX2_ENST00000530517.1_3'UTR|PKNOX2_ENST00000542175.1_Silent_p.P182P	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	246		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(14)|ovary(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	29		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TATACCAACCGGTTACCATGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G		1,3911		0,1,1955	96	94	94	NA	738	-2	1	11		94	0,8292		0,0,4146	no	coding-synonymous	PKNOX2	NM_022062.2		0,1,6101	AA,AG,GG	NA	0.0,0.0256,0.0082		246/473	125280694	1,12203	1956	4146	6102	SO:0001819	synonymous_variant			AK023136	CCDS41730.1	11q24.2	2014-09-04			ENSG00000165495	ENSG00000165495	63876		Homeoboxes / TALE class	16714	protein-coding gene	gene with protein product		613066			NA	11549286	Standard		NM_022062	NA	Approved		uc001qbu.3	Q96KN3	OTTHUMG00000165884	ENST00000298282.9:c.738G>A	chr11.hg19:g.125280694G>A		NA	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	hg19	CCDS41730.1	0.02	10.048624	ACCxGTT	COVERED																																																																																			NOVEL	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386866.3	3	5.71693	KEEP	0	0	0	19	608	GG	0.99986	0.99986	0		+	28	60	1034	0	0	80.607048	188	60	6018	278	ENST00000298282.9	0.12963	1
EI24	9538	__UNKNOWN__	__UNKNOWN__	11	125453536	125453536	__UNKNOWN__	3'UTR	SNP	G	G	A	rs377515763		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:125453536G>A	ENST00000530985.1	+	0	1408				STT3A-AS1_ENST00000532714.1_RNA|EI24_ENST00000343678.4_3'UTR|STT3A-AS1_ENST00000530526.1_RNA|EI24_ENST00000278903.6_Silent_p.P326P			O14681	EI24_HUMAN	etoposide induced 2.4	NA		NA			apoptotic process (GO:0006915)|autophagy (GO:0006914)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of cell growth (GO:0030308)|neuromuscular process controlling balance (GO:0050885)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|response to drug (GO:0042493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(1)|lung(9)|ovary(1)	11	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.64e-07)|OV - Ovarian serous cystadenocarcinoma(99;0.0975)		TCCCTTCACCGCATCCGTCGC	0.547	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	18345	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													45	44	44	NA		NA	NA	11		NA											NA				125453536		1935	4126	6061	SO:0001624	3_prime_UTR_variant			AF010313	CCDS73410.1	11q24.2	2012-11-19	2012-11-16		ENSG00000149547	ENSG00000149547	9538			13276	protein-coding gene	gene with protein product	ectopic P-granules autophagy protein 4 homolog (C. elegans)	605170	etoposide induced 2.4 mRNA		NA	10594026, 9305847	Standard	NM_004879	NM_001290135	NA	Approved	PIG8, TP53I8, EPG4	uc001qcb.3	O14681	OTTHUMG00000165851	ENST00000530985.1:c.*1405G>A	chr11.hg19:g.125453536G>A		NA	A8K7D6|B4DKL6|Q9BUQ1	hg19		0.02	9.65183	ACCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369086	0.24771	.	.	ENSG00000149547	ENST00000526081	.	.	.	5.21	-9.43	0.00607	.	.	.	.	.	T	0.65238	0.2672	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.77310	-0.2635	5	0.87932	D	0	.	12.3463	0.55122	0.6878:0.0:0.2106:0.1016	.	.	.	.	T	26	.	ENSP00000437106:A26T	A	+	1	0	EI24	124958746	0.001000	0.12720	0.363000	0.25875	0.978000	0.69477	-1.511000	0.02260	-1.586000	0.01632	-0.140000	0.14226	GCA	NOVEL	EI24-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000386671.1	3	2.541648	KEEP	0	1	30	19	631	GG	0.999863	0.999863	0		+	39	60	1435	0	0	118.79574	166	60	5551	268	ENST00000530985.1	0.190244	1
RP11-680F20.5	0	__UNKNOWN__	__UNKNOWN__	11	125810349	125810349	__UNKNOWN__	lincRNA	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:125810349C>A	ENST00000530834.1	+	0	148										NA		NA									NA						ctcttcctctctgctctaact	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000530834.1:	chr11.hg19:g.125810349C>A		NA		hg19		0.02	13.333456	TCTxTGC	COVERED																																																																																			NOVEL	RP11-680F20.5-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000386742.1	4	11.436944	KEEP	0	0	0	38	1327	CC	1	1	0		+	39	60	1390	0	0	106.858361	268	60	10170	432	ENST00000530834.1	0.127036	1
ADAMTS8	11095	__UNKNOWN__	__UNKNOWN__	11	130275404	130275404	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:130275404C>A	ENST00000257359.6	-	0	3425					NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	NA		NA			negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		TTGTCTGCACCTCAGTACCGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	34	33	NA		NA	NA	11		NA											NA				130275404		2044	4193	6237	SO:0001624	3_prime_UTR_variant			AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917	11095		ADAM metallopeptidases with thrombospondin type 1 motif	224	protein-coding gene	gene with protein product		605175	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8		NA	10438512	Standard	NM_007037	NM_007037	NA	Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.*49G>T	chr11.hg19:g.130275404C>A		NA	Q9NZS0	hg19	CCDS41732.1	0.02	13.044539	CACxTCA	COVERED																																																																																			NOVEL	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385636.1	4	12.27548	KEEP	0	0	0	41	1379	CC	1	1	0		-	29	60	1037	0	0	75.900926	277	60	10273	416	ENST00000257359.6	0.094771	1
SNX19	399979	__UNKNOWN__	__UNKNOWN__	11	130786159	130786159	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr11:130786159G>A	ENST00000265909.4	-	0	245				SNX19_ENST00000530356.1_Intron|SNX19_ENST00000533214.1_5'UTR|SNX19_ENST00000528555.1_Intron|SNX19_ENST00000539184.1_Intron|SNX19_ENST00000533318.1_Intron	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	NA		NA			protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		AGGCCCTGGGGCCCACGGACA	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451	399979		Sorting nexins	21532	protein-coding gene	gene with protein product		NA			NA		Standard	NM_014758	NM_014758	NA	Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.-325C>T	chr11.hg19:g.130786159G>A		NA	E9PKB9|Q8IV55	hg19	CCDS31721.1	0.02	13.352657	GGGxCCC	COVERED																																																																																			NOVEL	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385649.1	5	49.354122	KEEP	0	0	0	164	5664	GG	1	1	0		-	20	60	654	0	0	41.711421	329	60	11541	671	ENST00000265909.4	0.057307	1
IQSEC3	440073	__UNKNOWN__	__UNKNOWN__	12	176120	176120	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs2650190		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:176120C>G	ENST00000538872.1	+	1	190	c.72C>G	c.(70-72)aaC>aaG	p.N24K	IQSEC3_ENST00000326261.4_Missense_Mutation_p.N24K			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	24		NA			actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		TCGTGCAGAACCAGCAGAGCC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													4	5	5	NA		NA	NA	12		NA											NA				176120		1422	3317	4739	SO:0001583	missense			AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645	440073			29193	protein-coding gene	gene with protein product		612118			NA	10470851	Standard	XM_495902	NM_001170738	NA	Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.72C>G	chr12.hg19:g.176120C>G	ENSP00000437554:p.Asn24Lys	NA	A6NIF2|A6NKV9|Q8TB43	hg19	CCDS53728.1	0.02	4.846132	GAAxCAG	COVERED	101	0.04624542124542125	33	0.06707317073170732	19	0.052486187845303865	18	0.03146853146853147	31	0.040897097625329816	c	16.55	3.154730	0.57259	.	.	ENSG00000120645	ENST00000538872;ENST00000326261	T;T	0.36699	1.24;1.24	3.68	2.77	0.32553	.	204.329000	0.01193	U	0.007372	T	0.06280	0.0162	L	0.53249	1.67	0.44275	D	0.99713	.	.	.	.	.	.	T	0.02437	-1.1159	8	0.72032	D	0.01	.	10.0887	0.42434	0.2025:0.7975:0.0:0.0	rs2650190	.	.	.	K	24	ENSP00000437554:N24K;ENSP00000315662:N24K	ENSP00000315662:N24K	N	+	3	2	IQSEC3	46381	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	4.047000	0.57383	0.732000	0.32470	0.456000	0.33151	AAC	NOVEL	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397382.3	2	9.302603	KEEP	5	2	72	56	1948	CC	1	0.999987	0		+	17	45	626	0	0	50.532257	88	60	3088	217	ENST00000538872.1	0.161905	0.999987
SLC6A13	6540	__UNKNOWN__	__UNKNOWN__	12	330742	330742	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:330742T>G	ENST00000343164.4	-	14	1568				SLC6A13_ENST00000445055.2_Intron	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	NA		NA			neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			AGAAAGGGGTTGGGGGGCGGG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													25	32	30	NA		NA	NA	12		NA											NA				330742		2202	4298	6500	SO:0001627	intron_variant			U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379	6540		Solute carriers	11046	protein-coding gene	gene with protein product	GABA transporter 2	615097	solute carrier family 6 (neurotransmitter transporter, GABA), member 13		NA		Standard	NM_016615	NM_001243392	NA	Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1516-30A>C	chr12.hg19:g.330742T>G		NA	B4DJL1|Q8TCC2|Q8WW56	hg19	CCDS8502.1	0.02	2.120551	GGTxGGG	COVERED																																																																																			NOVEL	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397801.1	1	6.884297	KEEP	0	3	18	30	771	TT	0.999998	0.9937	0		-	7	60	144	0	0	8.449561	57	60	1705	132	ENST00000343164.4	0.109375	0.993703
CACNA2D4	93589	__UNKNOWN__	__UNKNOWN__	12	2019190	2019190	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:2019190A>T	ENST00000382722.5	-	4	789				CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000587995.1_Intron	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	NA		NA			calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		gtgggttttcagcaagtgaaa	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(2;101 179 21030 23310 28141)					NA		NA				0													27	30	29	NA		NA	NA	12		NA											NA				2019190		692	1591	2283	SO:0001627	intron_variant			AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062	93589		Calcium channel subunits	20202	protein-coding gene	gene with protein product		608171			NA	12181424	Standard		NM_172364	NA	Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.427-59T>A	chr12.hg19:g.2019190A>T		NA	Q7Z3S8|Q86XZ5|Q8IZS9	hg19	CCDS44785.1	0.02	2.229467	TTCxGCA	COVERED																																																																																			NOVEL	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398230.2	1	5.115294	KEEP	0	0	0	17	537	AA	0.999366	0.997833	0		-	25	60	940	0	0	85.19548	50	60	1882	114	ENST00000382722.5	0.333333	0.998465
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2795019	2795019	__UNKNOWN__	Intron	SNP	C	C	T	rs66611965	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:2795019C>T	ENST00000347598.4	+	46	5824				CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000399606.1_Intron|CACNA1C_ENST00000335762.5_Intron|CACNA1C_ENST00000327702.7_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000399595.1_Intron|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399597.1_Intron|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399621.1_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	NA		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GTAAATGCACCGCTCGCTCTC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													36	36	36	NA		NA	NA	12		NA											NA				2795019		1966	4163	6129	SO:0001627	intron_variant			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5824+11C>T	chr12.hg19:g.2795019C>T		NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	1.91813	CACxGCT	COVERED																																																																																			NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	1	8.424515	KEEP	0	0	0	28	901	CC	0.999997	0.9937	0		+	4	27	143	0	0	9.685235	61	60	2004	114	ENST00000347598.4	0.061538	0.993703
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2795043	2795043	__UNKNOWN__	Intron	SNP	C	C	T	rs373603282		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:2795043C>T	ENST00000347598.4	+	46	5824				CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000399606.1_Intron|CACNA1C_ENST00000335762.5_Intron|CACNA1C_ENST00000327702.7_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000399595.1_Intron|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399597.1_Intron|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399621.1_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	NA		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGTGGTCGGCGGTTACTCCC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													22	22	22	NA		NA	NA	12		NA											NA				2795043		1933	4149	6082	SO:0001627	intron_variant			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5824+35C>T	chr12.hg19:g.2795043C>T		NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	2.225348	CGGxGGT	COVERED																																																																																			NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	2	6.615347	KEEP	0	0	0	22	682	CC	0.999879	0.970703	0		+	4	27	147	0	0	10.46127	49	60	1561	88	ENST00000347598.4	0.075472	0.97082
TULP3	7289	__UNKNOWN__	__UNKNOWN__	12	3049830	3049830	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:3049830C>A	ENST00000397132.2	+	12	1485	c.1444C>A	c.(1444-1446)Ctt>Att	p.L482I	TULP3_ENST00000448120.2_3'UTR	NM_001160408.1	NP_001153880.1	O75386	TULP3_HUMAN	tubby like protein 3	0		NA			anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TCAGACCTCCCTTCTGTGGAC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													107	103	104	NA		NA	NA	12		NA											NA				3049830		692	1591	2283	SO:0001583	missense			AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246	7289		Intraflagellar transport homologs	12425	protein-coding gene	gene with protein product		604730			NA	9828123	Standard	NM_003324	NM_003324	NA	Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000397132.2:c.1444C>A	chr12.hg19:g.3049830C>A	ENSP00000380321:p.Leu482Ile	NA	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	hg19	CCDS53737.1	0.02	13.282158	TCCxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.71	2.615799	0.46631	.	.	ENSG00000078246	ENST00000397132	D	0.92752	-3.1	4.32	1.38	0.22167	.	.	.	.	.	D	0.83949	0.5365	N	0.22421	0.69	0.09310	N	0.999998	B	0.28291	0.206	B	0.28139	0.086	T	0.74225	-0.3734	9	0.87932	D	0	.	4.689	0.12771	0.0:0.6138:0.1794:0.2068	.	482	F8WBZ9	.	I	482	ENSP00000380321:L482I	ENSP00000380321:L482I	L	+	1	0	TULP3	2920091	0.015000	0.18098	0.002000	0.10522	0.038000	0.13279	0.459000	0.21908	0.054000	0.16065	0.549000	0.68633	CTT	NOVEL	TULP3-004	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398469.1	3	30.097458	KEEP	0	0	0	100	3530	CC	1	1	0		+	46	60	1638	0	0	126.809072	301	60	11178	569	ENST00000397132.2	0.132565	1
ANO2	57101	__UNKNOWN__	__UNKNOWN__	12	5841926	5841926	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:5841926C>T	ENST00000356134.5	-	15	1509				ANO2_ENST00000546188.1_Intron|ANO2_ENST00000327087.8_Intron|ANO2_ENST00000538154.1_Intron	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	NA		NA			chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						AACTGCCCCACCACACACAAT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617	57101		Ion channels / Chloride channels : Calcium activated : Anoctamins	1183	protein-coding gene	gene with protein product	transmembrane protein 16B (eight membrane-spanning domains)	610109	chromosome 12 open reading frame 3, transmembrane protein 16B, anoctamin 2	C12orf3, TMEM16B	NA	12739008, 15067359, 24692353	Standard	NM_020373	NM_001278596	NA	Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1437+105G>A	chr12.hg19:g.5841926C>T		NA	C4N787|Q9H847	hg19		0.02	10.351818	CCAxCAC	COVERED																																																																																			NOVEL	ANO2-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000399019.4	5	18.02384	KEEP	0	0	0	60	2070	CC	1	1	0		-	10	60	353	0	0	21.660507	251	60	9268	407	ENST00000356134.5	0.038314	1
CD4	920	__UNKNOWN__	__UNKNOWN__	12	6924062	6924062	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs200162977		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:6924062G>A	ENST00000541982.1	+	4	540	c.346G>A	c.(346-348)Gtg>Atg	p.V116M	CD4_ENST00000011653.4_Missense_Mutation_p.V171M|CD4_ENST00000538827.1_3'UTR			P01730	CD4_HUMAN	CD4 molecule	171	Ig-like V-type.	NA			cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cytokine production (GO:0001816)|defense response to Gram-negative bacterium (GO:0050829)|entry into host cell (GO:0030260)|enzyme linked receptor protein signaling pathway (GO:0007167)|immune response (GO:0006955)|induction by virus of host cell-cell fusion (GO:0006948)|innate immune response (GO:0045087)|maintenance of protein location in cell (GO:0032507)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase activity (GO:0045860)|protein palmitoleylation (GO:0045234)|regulation of defense response to virus by virus (GO:0050690)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|T cell selection (GO:0045058)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|enzyme binding (GO:0019899)|extracellular matrix structural constituent (GO:0005201)|glycoprotein binding (GO:0001948)|MHC class II protein binding (GO:0042289)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	23		Myeloproliferative disorder(1001;0.0122)			Antithymocyte globulin(DB00098)	GACCCTCTCCGTGTCTCAGCT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	MET/VAL,,,,	1,4405		0,1,2202	88	77	81	NA	511,,,,	-2.2	0	12		81	0,8600		0,0,4300	no	missense,utr-5,utr-5,utr-5,utr-5	CD4	NM_000616.4,NM_001195014.2,NM_001195015.2,NM_001195016.2,NM_001195017.2	21,,,,	0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077	possibly-damaging,,,,	171/459,,,,	6924062	1,13005	2203	4300	6503	SO:0001583	missense			M35160	CCDS8562.1	12p13.31	2013-01-11	2006-03-28		ENSG00000010610	ENSG00000010610	920		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing	1678	protein-coding gene	gene with protein product		186940	CD4 antigen (p55), T-cell surface glycoprotein CD4		NA		Standard	NM_000616	NM_000616	NA	Approved		uc001qqv.2	P01730	OTTHUMG00000168514	ENST00000541982.1:c.346G>A	chr12.hg19:g.6924062G>A	ENSP00000445167:p.Val116Met	NA	B2R737|D3DUS5|Q4ZGK2|Q5U066|Q9UDE5	hg19		0.02	2.027733	TCCxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	6.758	0.508645	0.12883	2.27E-4	0.0	ENSG00000010610	ENST00000011653;ENST00000541982	T;T	0.26660	1.72;1.72	3.81	-2.19	0.07015	Immunoglobulin subtype (1);Immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	2.019350	0.02673	N	0.108791	T	0.10809	0.0264	N	0.14661	0.345	0.09310	N	1	P;P	0.44877	0.845;0.832	B;B	0.32724	0.137;0.151	T	0.13872	-1.0493	10	0.38643	T	0.18	-0.3726	1.8262	0.03121	0.4769:0.1887:0.211:0.1234	.	116;171	F5H480;P01730	.;CD4_HUMAN	M	171;116	ENSP00000011653:V171M;ENSP00000445167:V116M	ENSP00000011653:V171M	V	+	1	0	CD4	6794323	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.173000	0.09854	-0.202000	0.10268	-0.657000	0.03884	GTG	NOVEL	CD4-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399982.1	1	3.91193	KEEP	0	0	0	13	428	GG	0.994391	0.994339	0		+	33	60	1200	0	0	108.91655	63	60	2244	130	ENST00000541982.1	0.34375	0.999948
NANOG	79923	__UNKNOWN__	__UNKNOWN__	12	7948517	7948517	__UNKNOWN__	3'UTR	SNP	C	C	T	rs34237790		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:7948517C>T	ENST00000229307.4	+	0	1963					NM_024865.2	NP_079141.2	Q9H9S0	NANOG_HUMAN	Nanog homeobox	NA		NA			cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|embryo development (GO:0009790)|embryonic pattern specification (GO:0009880)|endodermal cell fate specification (GO:0001714)|gonad development (GO:0008406)|mesodermal cell fate commitment (GO:0001710)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to retinoic acid (GO:0032526)|somatic stem cell maintenance (GO:0035019)|stem cell division (GO:0017145)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14				Kidney(36;0.0872)		AAAGAGGTCTCGTATTTGCTG	0.333	NA	NA											C|||	2826	0.564297	0.354	0.6715	5008	,	,	NA	-128	0.369	NA	0.7962	False	NA	,,,	NA	NA	NA	2504	0.7352	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB093576	CCDS31736.1, CCDS73436.1	12p13.31	2011-06-20			ENSG00000111704	ENSG00000111704	79923		Homeoboxes / ANTP class : NKL subclass	20857	protein-coding gene	gene with protein product		607937			NA	12787505, 12787504	Standard	NM_024865	XM_005253484	NA	Approved	FLJ12581, FLJ40451	uc009zfy.1	Q9H9S0		ENST00000229307.4:c.*826C>T	chr12.hg19:g.7948517C>T		NA	D3DUU4|Q2TTG0|Q6JZS5	hg19	CCDS31736.1	0.02	4.593915	TCTxGTA	COVERED																																																																																			NOVEL	NANOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387480.2	7	11.906614	KEEP	105	2	58	60	2060	CC	1	0.999995	0		+	27	40	955	0	0	86.940542	49	50	1710	307	ENST00000229307.4	0.355263	0.999995
PZP	5858	__UNKNOWN__	__UNKNOWN__	12	9311143	9311143	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:9311143G>A	ENST00000261336.2	-	26	3195	c.3167C>T	c.(3166-3168)gCc>gTc	p.A1056V	PZP_ENST00000381997.2_Missense_Mutation_p.A842V	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1056		NA			female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						TCGAGCCTGGGCGAAAGTCTT	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(125;1402 1695 4685 34487 38571)					NA		NA				0													124	116	118	NA		NA	NA	12		NA											NA				9311143		2203	4300	6503	SO:0001583	missense			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838	5858			9750	protein-coding gene	gene with protein product		176420			NA		Standard	NM_002864	NM_002864	NA	Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.3167C>T	chr12.hg19:g.9311143G>A	ENSP00000261336:p.Ala1056Val	NA	A6ND27|Q15273|Q2NKL2|Q7M4N7	hg19	CCDS8600.1	0.02	4.35731	TGGxCGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.75	1.732811	0.30684	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.39406	1.08;1.08	4.44	2.59	0.31030	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	0.405089	0.22135	N	0.064137	T	0.52964	0.1767	M	0.82823	2.61	0.19300	N	0.99998	B;D	0.57899	0.029;0.981	B;P	0.52823	0.023;0.71	T	0.49214	-0.8963	10	0.87932	D	0	.	6.4841	0.22079	0.1683:0.149:0.6827:0.0	.	842;1056	P20742-2;P20742	.;PZP_HUMAN	V	1056;842	ENSP00000261336:A1056V;ENSP00000371427:A842V	ENSP00000261336:A1056V	A	-	2	0	PZP	9202410	0.000000	0.05858	0.025000	0.17156	0.075000	0.17131	0.870000	0.28010	0.573000	0.29400	-0.251000	0.11542	GCC	NOVEL	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337624.1	2	8.664068	KEEP	0	1	17	35	1236	GG	0.999999	0.999983	0		-	14	60	502	0	0	39.059073	90	60	3272	179	ENST00000261336.2	0.134615	0.999984
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9580280	9580280	__UNKNOWN__	IGR	SNP	A	A	G	rs201256560	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:9580280A>G			NA	NA				RP13-735L24.1 (30067 upstream) : SNORA75 (17373 downstream)						NA		NA									NA						AGTCGTTGATAGTCTTCAGCT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													244	231	235	NA		NA	NA	12		NA											NA				9580280		689	1590	2279	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9580280A>G		NA		hg19		0.02	10.386633	GATxGTC	COVERED																																																																																			NOVEL					0			0	4.216873	KEEP	24	3	103	50	1578	AA	1	1	0			23	40	818	0	0	59.14864	234	60	8740	390		0.089494	1
CLEC2D	29121	__UNKNOWN__	__UNKNOWN__	12	9845745	9845745	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:9845745C>G	ENST00000261340.7	+	5	565				CLEC2D_ENST00000543300.1_Intron|CLEC2D_ENST00000545918.1_Intron|CLEC2D_ENST00000290855.6_Intron|CLEC2D_ENST00000261339.6_Intron	NM_001004419.4	NP_001004419.1	Q9UHP7	CLC2D_HUMAN	C-type lectin domain family 2, member D	NA		NA			cell surface receptor signaling pathway (GO:0007166)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|stomach(1)	9						tggctccaggcttatctatgt	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													93	94	94	NA		NA	NA	12		NA											NA				9845745		2203	4300	6503	SO:0001627	intron_variant			AF133299	CCDS8602.1, CCDS31741.1, CCDS55800.1, CCDS55801.1, CCDS55802.1	12p13.31	2011-05-24	2005-09-29		ENSG00000069493	ENSG00000069493	29121		C-type lectin domain containing	14351	protein-coding gene	gene with protein product	C-type lectin related f, lectin-like transcript 1	605659	C-type lectin superfamily 2, member D		NA		Standard	NM_013269	NM_013269	NA	Approved	LLT1, CLAX, OCIL	uc001qwf.3	Q9UHP7	OTTHUMG00000168369	ENST00000261340.7:c.543+34C>G	chr12.hg19:g.9845745C>G		NA	D6CI39|D6CI40|D6CI41|Q6YID5|Q8WUP7|Q9HD37|Q9HD38	hg19	CCDS31741.1	0.02	20.382252	AGGxTTA	COVERED																																																																																			NOVEL	CLEC2D-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335428.2	4	37.016436	KEEP	0	0	0	123	4434	CC	1	1	0		+	125	60	4613	0	0	412.904441	276	60	10579	665	ENST00000261340.7	0.311721	1
CLEC1A	51267	__UNKNOWN__	__UNKNOWN__	12	10228233	10228233	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:10228233G>A	ENST00000457018.2	-	3	405	c.314C>T	c.(313-315)aCa>aTa	p.T105I	CLEC1A_ENST00000315330.4_Missense_Mutation_p.T138I|CLEC1A_ENST00000420265.2_Missense_Mutation_p.T46I			Q8NC01	CLC1A_HUMAN	C-type lectin domain family 1, member A	138		NA			cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	23						CCATTGTTCTGTACAAGGGCT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													125	119	121	NA		NA	NA	12		NA											NA				10228233		2203	4300	6503	SO:0001583	missense			AY358587	CCDS8612.1, CCDS73443.1	12p13.31	2005-02-09				ENSG00000150048	51267		C-type lectin domain containing	24355	protein-coding gene	gene with protein product		606782			NA	10671229, 11745369	Standard	NM_016511	XM_005253383	NA	Approved	CLEC1, MGC34328	uc001qxb.3	Q8NC01		ENST00000457018.2:c.314C>T	chr12.hg19:g.10228233G>A	ENSP00000415048:p.Thr105Ile	NA	Q8IUW7|Q9NZH3	hg19		0.02	11.481771	TCTxTAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.18	1.563908	0.27915	.	.	ENSG00000150048	ENST00000315330;ENST00000457018;ENST00000420265	T;T;T	0.17370	2.28;2.28;2.28	5.06	5.06	0.68205	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	0.114107	0.40222	N	0.001143	T	0.10208	0.0250	N	0.08118	0	0.19575	N	0.999967	B;B;B	0.28971	0.229;0.165;0.084	B;B;B	0.26614	0.063;0.069;0.071	T	0.26224	-1.0109	10	0.72032	D	0.01	.	14.2934	0.66295	0.0:0.0:1.0:0.0	.	46;105;138	E7ESV9;E9PFB4;Q8NC01	.;.;CLC1A_HUMAN	I	138;105;46	ENSP00000326407:T138I;ENSP00000415048:T105I;ENSP00000417010:T46I	ENSP00000326407:T138I	T	-	2	0	CLEC1A	10119500	1.000000	0.71417	0.901000	0.35422	0.246000	0.25737	4.628000	0.61282	2.520000	0.84964	0.655000	0.94253	ACA	NOVEL	CLEC1A-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399925.1	5	28.293096	KEEP	0	0	0	94	3425	GG	1	1	0		-	85	60	3097	0	0	275.60761	195	60	7450	493	ENST00000457018.2	0.303571	1
TMEM52B	120939	__UNKNOWN__	__UNKNOWN__	12	10339117	10339117	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:10339117G>A	ENST00000298530.3	+	3	754	c.176G>A	c.(175-177)gGg>gAg	p.G59E	TMEM52B_ENST00000381923.2_Missense_Mutation_p.G79E|TMEM52B_ENST00000536952.1_Missense_Mutation_p.G79E	NM_153022.2	NP_694567.1	Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	79		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)					NA						GGGGAAGATGGGGGCCCACCA	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													98	87	91	NA		NA	NA	12		NA											NA				10339117		2203	4300	6503	SO:0001583	missense			AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685	120939			26438	protein-coding gene	gene with protein product		NA	chromosome 12 open reading frame 59	C12orf59	NA	12975309	Standard	NM_153022	XM_005253299	NA	Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000298530.3:c.176G>A	chr12.hg19:g.10339117G>A	ENSP00000298530:p.Gly59Glu	NA	Q96NA7	hg19	CCDS8619.1	0.02	4.734734	ATGxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.376458	0.01214	.	.	ENSG00000165685	ENST00000381923;ENST00000298530;ENST00000543484;ENST00000536952	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.21	0.582	0.17412	.	0.762624	0.12203	N	0.490117	T	0.08179	0.0204	N	0.02802	-0.49	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.33828	-0.9853	10	0.02654	T	1	-0.8471	1.0346	0.01545	0.2705:0.1599:0.388:0.1817	.	79;59	Q4KMG9;Q4KMG9-2	CL059_HUMAN;.	E	79;59;79;79	ENSP00000371348:G79E;ENSP00000298530:G59E;ENSP00000445582:G79E;ENSP00000446102:G79E	ENSP00000298530:G59E	G	+	2	0	C12orf59	10230384	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	0.794000	0.26958	0.250000	0.21479	0.650000	0.86243	GGG	NOVEL	TMEM52B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399648.1	1	9.327014	KEEP	0	0	0	31	1005	GG	0.999997	0.999997	0		+	44	60	1556	0	0	140.440055	86	60	3047	205	ENST00000298530.3	0.338462	1
YBX3	8531	__UNKNOWN__	__UNKNOWN__	12	10854778	10854778	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:10854778G>A	ENST00000228251.4	-	8	1079				YBX3_ENST00000546164.1_Intron|YBX3_ENST00000279550.7_Intron	NM_003651.4	NP_003642.3	P16989	YBOX3_HUMAN	Y box binding protein 3	NA		NA			3'-UTR-mediated mRNA stabilization (GO:0070935)|cellular hyperosmotic response (GO:0071474)|cellular response to tumor necrosis factor (GO:0071356)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of necroptotic process (GO:0060546)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoplasmic translation (GO:2000767)|positive regulation of organ growth (GO:0046622)|response to cold (GO:0009409)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|tight junction (GO:0005923)	double-stranded DNA binding (GO:0003690)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|Rho GTPase binding (GO:0017048)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)				NA						CAACAGGACAGGGCTTCTCCA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													22	21	21	NA		NA	NA	12		NA											NA				10854778		2202	4300	6502	SO:0001627	intron_variant			L29064	CCDS8630.1, CCDS44831.1	12p13.1	2013-03-13	2013-03-13	2013-03-13	ENSG00000060138	ENSG00000060138	8531			2428	protein-coding gene	gene with protein product	cold-shock domain containing A1	603437	cold shock domain protein A	CSDA	NA	2977358, 8710501	Standard	NM_003651	NM_003651	NA	Approved	dbpA, ZONAB, CSDA1	uc001qyt.3	P16989	OTTHUMG00000168409	ENST00000228251.4:c.879-45C>T	chr12.hg19:g.10854778G>A		NA	B2RBW6|Q14121|Q969N6|Q96B76	hg19	CCDS8630.1	0.02	4.757699	ACAxGGC	COVERED																																																																																			NOVEL	YBX3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399628.1	0	16.251445	KEEP	0	0	0	54	1843	GG	1	0.999997	0		-	19	60	693	0	0	55.909813	97	60	3431	207	ENST00000228251.4	0.163793	0.999997
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	10954102	10954102	__UNKNOWN__	IGR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:10954102T>C			NA	NA				RP13-81N3.2 (24115 upstream) : TAS2R7 (28 downstream)						NA		NA									NA						CAATTACAGATACACTAATTA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.10954102T>C		NA		hg19		0.02	4.818681	AGAxACA	COVERED																																																																																			NOVEL					0			3	6.618272	KEEP	0	0	0	22	688	TT	0.999879	0.999871	0			19	60	719	0	0	59.065942	90	60	3280	159		0.174312	0.999992
PRB4	5545	__UNKNOWN__	__UNKNOWN__	12	11461549	11461549	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs11054243	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:11461549G>C	ENST00000535904.1	-	3	401	c.368C>G	c.(367-369)cCa>cGa	p.P123R	PRB4_ENST00000445719.2_Intron|PRB4_ENST00000279575.1_Missense_Mutation_p.P123R			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	144	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.	NA	Missing (in allele M and allele S).	SR -> RP (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TTGTGGGGGTGGTCTTTCTGG	0.607	NA	NA								HNSCC(22;0.051)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													144	161	155	NA		NA	NA	12		NA											NA				11461549		2203	4300	6503	SO:0001583	missense				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657	5545			9340	protein-coding gene	gene with protein product		180990			NA		Standard	NM_002723	NM_002723	NA	Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.368C>G	chr12.hg19:g.11461549G>C	ENSP00000442834:p.Pro123Arg	NA	A1L439|O00600|P02813|P10161|P10162|P81489	hg19	CCDS8641.1	0.02	2.150075	GGTxGTC	COVERED	143	0.06547619047619048	27	0.054878048780487805	36	0.09944751381215469	34	0.05944055944055944	46	0.06068601583113457	.	0.005	-2.169667	0.00315	.	.	ENSG00000230657	ENST00000279575;ENST00000535904	T;T	0.08102	3.13;3.13	0.796	-0.165	0.13355	.	.	.	.	.	T	0.00241	0.0007	M	0.66439	2.03	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.39099	-0.9630	9	0.25751	T	0.34	.	4.6253	0.12476	0.0:0.4116:0.5884:0.0	rs11054243;rs57631612;rs11054243	123	E9PAL0	.	R	123	ENSP00000279575:P123R;ENSP00000442834:P123R	ENSP00000279575:P123R	P	-	2	0	PRB4	11352816	0.651000	0.27340	0.007000	0.13788	0.004000	0.04260	-0.320000	0.08028	-0.098000	0.12285	-1.091000	0.02175	CCA	NOVEL	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402308.1	2	3.606798	KEEP	1	0	0	12	353	GG	0.993634	0.991846	0		-	5	60	186	0	0	13.112072	67	60	2190	119	ENST00000535904.1	0.069444	0.9982
PRB4	5545	__UNKNOWN__	__UNKNOWN__	12	11461553	11461553	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs71057722|rs11054244	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:11461553T>C	ENST00000535904.1	-	3	397	c.364A>G	c.(364-366)Aga>Gga	p.R122G	PRB4_ENST00000445719.2_Intron|PRB4_ENST00000279575.1_Missense_Mutation_p.R122G			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	143	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.	NA	Missing (in allele M and allele S).	SR -> RP (in Ref. 7; CAA30542). {ECO:0000305}.		extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						GGGGGTGGTCTTTCTGGCTTT	0.607	NA	NA								HNSCC(22;0.051)			C|||	23	0.00459265	0.0061	0.0058	5008	,	,	NA	15782	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0102	NA	NA	NA						NA		NA				0													147	164	159	NA		NA	NA	12		NA											NA				11461553		2203	4300	6503	SO:0001583	missense				CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657	5545			9340	protein-coding gene	gene with protein product		180990			NA		Standard	NM_002723	NM_002723	NA	Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.364A>G	chr12.hg19:g.11461553T>C	ENSP00000442834:p.Arg122Gly	NA	A1L439|O00600|P02813|P10161|P10162|P81489	hg19	CCDS8641.1	0.02	1.722794	GTCxTTC	COVERED	399	0.18269230769230768	88	0.17886178861788618	81	0.22375690607734808	105	0.18356643356643357	125	0.16490765171503957	.	0.008	-1.881129	0.00532	.	.	ENSG00000230657	ENST00000279575;ENST00000535904	T;T	0.01947	4.54;4.54	0.678	0.678	0.17969	.	.	.	.	.	T	0.00012	0.0000	N	0.00405	-1.535	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41645	-0.9497	7	0.02654	T	1	.	.	.	.	rs11054244;rs60322575	122	E9PAL0	.	G	122	ENSP00000279575:R122G;ENSP00000442834:R122G	ENSP00000279575:R122G	R	-	1	2	PRB4	11352820	0.015000	0.18098	0.003000	0.11579	0.001000	0.01503	-1.128000	0.03247	-0.174000	0.10743	-1.042000	0.02369	AGA	NOVEL	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402308.1	2	3.611139	KEEP	1	0	0	12	391	TT	0.993634	0.992337	0		-	5	60	154	0	0	9.902766	70	60	2355	120	ENST00000535904.1	0.066667	0.998696
GPRC5A	9052	__UNKNOWN__	__UNKNOWN__	12	13061218	13061218	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:13061218G>A	ENST00000014914.5	+	2	925	c.35G>A	c.(34-36)gGc>gAc	p.G12D	GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	12		NA			signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	TGCCGCAATGGCCTGAAATCC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	62	62	NA		NA	NA	12		NA											NA				13061218		2203	4300	6503	SO:0001583	missense			AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588	9052		GPCR / Class C : Orphans	9836	protein-coding gene	gene with protein product		604138	retinoic acid induced 3, G protein-coupled receptor, family C, group 5, member A	RAI3, GPCR5A	NA	9857033	Standard		NM_003979	NA	Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.35G>A	chr12.hg19:g.13061218G>A	ENSP00000014914:p.Gly12Asp	NA	B3KV45|O95357	hg19	CCDS8657.1	0.02	10.560816	ATGxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.954	-0.705530	0.03255	.	.	ENSG00000013588	ENST00000014914;ENST00000534831	T;T	0.14893	2.47;2.47	5.34	-2.84	0.05751	.	1.543730	0.03148	N	0.167549	T	0.07458	0.0188	N	0.04203	-0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38824	-0.9643	10	0.02654	T	1	-4.9077	11.7216	0.51685	0.4847:0.0:0.5153:0.0	.	12;12	Q8NFJ5;A8K556	RAI3_HUMAN;.	D	12	ENSP00000014914:G12D;ENSP00000441627:G12D	ENSP00000014914:G12D	G	+	2	0	GPRC5A	12952485	0.000000	0.05858	0.021000	0.16686	0.000000	0.00434	-0.683000	0.05179	-0.192000	0.10432	-1.105000	0.02106	GGC	NOVEL	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400682.1	2	30.696681	KEEP	0	0	0	102	3523	GG	1	1	0		+	16	60	583	0	0	38.960899	278	60	10086	490	ENST00000014914.5	0.054422	1
GPRC5A	9052	__UNKNOWN__	__UNKNOWN__	12	13065131	13065131	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:13065131G>A	ENST00000014914.5	+	3	1871				GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	NA		NA			signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	CAGGAACACTGATCCTTTGGA	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													102	82	88	NA		NA	NA	12		NA											NA				13065131		692	1591	2283	SO:0001627	intron_variant			AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588	9052		GPCR / Class C : Orphans	9836	protein-coding gene	gene with protein product		604138	retinoic acid induced 3, G protein-coupled receptor, family C, group 5, member A	RAI3, GPCR5A	NA	9857033	Standard		NM_003979	NA	Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.981+55G>A	chr12.hg19:g.13065131G>A		NA	B3KV45|O95357	hg19	CCDS8657.1	0.02	11.709554	ACTxATC	COVERED																																																																																			NOVEL	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400682.1	3	23.108062	KEEP	0	1	29	87	3105	GG	1	1	0		+	89	60	3251	0	0	296.115619	165	60	6283	425	ENST00000014914.5	0.350394	1
ERGIC2	51290	__UNKNOWN__	__UNKNOWN__	12	29510581	29510581	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:29510581T>C	ENST00000360150.4	-	7	526	c.451A>G	c.(451-453)Agt>Ggt	p.S151G		NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2	151		NA			vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)				endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)					GTTGATGTACTTTTAAAAGCA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													132	130	131	NA		NA	NA	12		NA											NA				29510581		1831	4091	5922	SO:0001583	missense			AF216751	CCDS41765.1	12p11.22	2006-02-08					51290			30208	protein-coding gene	gene with protein product		612236			NA	11445006, 12932305	Standard	NM_016570	NM_016570	NA	Approved	PTX1, Erv41	uc001riv.3	Q96RQ1		ENST00000360150.4:c.451A>G	chr12.hg19:g.29510581T>C	ENSP00000353270:p.Ser151Gly	NA	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	hg19	CCDS41765.1	0.02	-0.271967	TACxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.645	1.140097	0.21205	.	.	ENSG00000087502	ENST00000360150;ENST00000201023;ENST00000552155;ENST00000546839;ENST00000550353;ENST00000552132	.	.	.	5.6	4.46	0.54185	.	0.198563	0.56097	N	0.000021	T	0.24431	0.0592	N	0.02539	-0.55	0.38568	D	0.949867	B	0.02656	0.0	B	0.06405	0.002	T	0.07731	-1.0757	9	0.18276	T	0.48	.	9.5726	0.39438	0.0:0.083:0.0:0.917	.	151	Q96RQ1	ERGI2_HUMAN	G	151;159;151;151;133;151	.	ENSP00000201023:S159G	S	-	1	0	ERGIC2	29401848	1.000000	0.71417	0.977000	0.42913	0.989000	0.77384	3.545000	0.53648	0.963000	0.38082	0.482000	0.46254	AGT	NOVEL	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403489.1	0	7.522491	KEEP	0	0	0	25	817	TT	0.999957	0.717285	0		-	10	60	362	0	0	32.505616	21	60	774	74	ENST00000360150.4	0.322581	0.717315
TMTC1	83857	__UNKNOWN__	__UNKNOWN__	12	29920915	29920915	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:29920915G>T	ENST00000551659.1	-	2	541	c.396C>A	c.(394-396)acC>acA	p.T132T	TMTC1_ENST00000552618.1_Silent_p.T132T|TMTC1_ENST00000381224.2_Silent_p.T24T|TMTC1_ENST00000256062.5_Silent_p.T24T|TMTC1_ENST00000539277.1_Silent_p.T132T			Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	132		NA				integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TTTTATCACAGGTGTACATCA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													123	106	112	NA		NA	NA	12		NA											NA				29920915		2203	4300	6503	SO:0001819	synonymous_variant				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687	83857		Tetratricopeptide (TTC) repeat domain containing	24099	protein-coding gene	gene with protein product		615855			NA	24764305	Standard	NM_031920	NM_001193451	NA	Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000551659.1:c.396C>A	chr12.hg19:g.29920915G>T		NA	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	hg19		0.02	12.156248	ACAxGTG	COVERED																																																																																			NOVEL	TMTC1-010	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000403505.1	2	38.222505	KEEP	0	0	0	127	4458	GG	1	1	0		-	77	60	2849	0	0	253.03457	183	60	6831	489	ENST00000551659.1	0.296154	1
DENND5B	160518	__UNKNOWN__	__UNKNOWN__	12	31632690	31632690	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:31632690T>G	ENST00000389082.5	-	3	1001	c.737A>C	c.(736-738)aAa>aCa	p.K246T	DENND5B_ENST00000306833.6_Missense_Mutation_p.K281T|DENND5B_ENST00000536562.1_Missense_Mutation_p.K281T|DENND5B_ENST00000354285.4_Missense_Mutation_p.K268T|DENND5B_ENST00000545147.1_Intron	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	246	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.	NA			positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ACCATAAAATTTCAGTGACCT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													74	70	71	NA		NA	NA	12		NA											NA				31632690		1859	4101	5960	SO:0001583	missense			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456	160518		DENN/MADD domain containing	28338	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_144973	NM_144973	NA	Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.737A>C	chr12.hg19:g.31632690T>G	ENSP00000373734:p.Lys246Thr	NA	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	hg19	CCDS44857.1	0.02	4.816645	AATxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	T	18.73	3.685440	0.68157	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76	4.8	4.8	0.61643	DENN (3);	0.000000	0.85682	D	0.000000	T	0.15869	0.0382	L	0.28556	0.865	0.58432	D	0.999999	P;P;D;P;P	0.59357	0.823;0.753;0.985;0.571;0.516	P;B;P;P;P	0.55260	0.535;0.373;0.772;0.588;0.452	T	0.04229	-1.0967	10	0.30854	T	0.27	-24.5487	14.533	0.67939	0.0:0.0:0.0:1.0	.	281;168;268;246;281	Q6ZUT9-2;Q6ZUT9-3;Q6ZUT9-4;Q6ZUT9;G3V1S3	.;.;.;DEN5B_HUMAN;.	T	246;281;281;268;198	ENSP00000373734:K246T;ENSP00000306482:K281T;ENSP00000444889:K281T;ENSP00000346238:K268T;ENSP00000442938:K198T	ENSP00000306482:K281T	K	-	2	0	DENND5B	31523957	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	5.933000	0.70130	2.016000	0.59253	0.533000	0.62120	AAA	NOVEL	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402040.1	0	9.628476	KEEP	0	0	0	32	1002	TT	0.999997	0.999997	0		-	34	60	1279	0	0	111.94449	94	60	3416	195	ENST00000389082.5	0.265625	1
DENND5B	160518	__UNKNOWN__	__UNKNOWN__	12	31632692	31632692	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:31632692C>T	ENST00000389082.5	-	3	999	c.735G>A	c.(733-735)ctG>ctA	p.L245L	DENND5B_ENST00000306833.6_Silent_p.L280L|DENND5B_ENST00000536562.1_Silent_p.L280L|DENND5B_ENST00000354285.4_Silent_p.L267L|DENND5B_ENST00000545147.1_Intron	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	245	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.	NA			positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						CATAAAATTTCAGTGACCTCC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													74	69	71	NA		NA	NA	12		NA											NA				31632692		1861	4102	5963	SO:0001819	synonymous_variant			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456	160518		DENN/MADD domain containing	28338	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_144973	NM_144973	NA	Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.735G>A	chr12.hg19:g.31632692C>T		NA	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	hg19	CCDS44857.1	0.02	4.299767	TTTxAGT	COVERED																																																																																			NOVEL	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402040.1	0	9.330481	KEEP	0	0	0	31	1106	CC	0.999997	0.999997	0		-	36	60	1285	0	0	112.3655	94	60	3561	195	ENST00000389082.5	0.276923	1
KIF21A	55605	__UNKNOWN__	__UNKNOWN__	12	39731022	39731022	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:39731022A>G	ENST00000361418.5	-	17	2326				KIF21A_ENST00000541463.2_Intron|KIF21A_ENST00000361961.3_Intron|KIF21A_ENST00000544797.2_Intron|KIF21A_ENST00000395670.3_Intron			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	NA		NA			ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				AATTAGGTATAGACATCTATT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													104	92	96	NA		NA	NA	12		NA											NA				39731022		2203	4297	6500	SO:0001627	intron_variant			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10					55605		Kinesins, WD repeat domain containing	19349	protein-coding gene	gene with protein product		608283	fibrosis of the extraocular muscles, congenital, 1	FEOM1	NA	10225949	Standard	NM_017641	NM_017641	NA	Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2311-17T>C	chr12.hg19:g.39731022A>G		NA	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	hg19	CCDS53776.1	0.02	2.164736	TATxGAC	COVERED																																																																																			NOVEL	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403581.1	0	7.221594	KEEP	0	0	0	24	753	AA	0.999909	0.997073	0		-	12	60	446	0	0	36.318119	59	60	2217	111	ENST00000361418.5	0.169014	0.997163
LRRK2	120892	__UNKNOWN__	__UNKNOWN__	12	40749929	40749929	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:40749929T>A	ENST00000298910.7	+	46	6841	c.6783T>A	c.(6781-6783)aaT>aaA	p.N2261K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2261		NA	N -> I (in dbSNP:rs12581902). {ECO:0000269|PubMed:16172858}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				AACAAAAAAATTTTCTTTTGG	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													49	49	49	NA		NA	NA	12		NA											NA				40749929		2202	4295	6497	SO:0001583	missense			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906	120892		Parkinson disease	18618	protein-coding gene	gene with protein product		609007	Parkinson disease (autosomal dominant) 8	PARK8	NA	15541308	Standard	XM_058513	NM_198578	NA	Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6783T>A	chr12.hg19:g.40749929T>A	ENSP00000298910:p.Asn2261Lys	NA	A6NJU2|Q6ZS50|Q8NCX9	hg19	CCDS31774.1	0.02	2.278747	AAAxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	15.00	2.703303	0.48412	.	.	ENSG00000188906	ENST00000298910	T	0.36340	1.26	5.96	2.32	0.28847	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.368511	0.36200	N	0.002727	T	0.25121	0.0610	L	0.47716	1.5	0.30953	N	0.724568	B;B	0.32717	0.381;0.381	B;B	0.26969	0.075;0.075	T	0.16188	-1.0411	10	0.44086	T	0.13	.	5.9319	0.19144	0.1229:0.1356:0.0:0.7415	.	2261;2261	Q17RV3;Q5S007	.;LRRK2_HUMAN	K	2261	ENSP00000298910:N2261K	ENSP00000298910:N2261K	N	+	3	2	LRRK2	39036196	1.000000	0.71417	0.960000	0.40013	0.996000	0.88848	1.258000	0.32944	0.151000	0.19162	0.533000	0.62120	AAT	NOVEL	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277179.1	0	6.320011	KEEP	0	0	0	21	700	TT	0.999869	0.984032	0		+	7	60	273	0	0	21.363646	51	60	1866	104	ENST00000298910.7	0.12069	0.984161
COL2A1	1280	__UNKNOWN__	__UNKNOWN__	12	48376859	48376859	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:48376859G>A	ENST00000380518.3	-	32	2259				COL2A1_ENST00000337299.6_Intron|COL2A1_ENST00000493991.1_Intron	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	NA		NA			axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GCCCGCATTGGCCAACAGGAT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													50	58	55	NA		NA	NA	12		NA											NA				48376859		2202	4300	6502	SO:0001627	intron_variant			X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219	1280		Collagens	2200	protein-coding gene	gene with protein product		120140	collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital), arthroophthalmopathy, progressive (Stickler syndrome)	SEDC, AOM	NA	1677770	Standard	NM_001844	NM_033150	NA	Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.2094+16C>T	chr12.hg19:g.48376859G>A		NA	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	hg19	CCDS41778.1	0.02	8.989607	TTGxCCA	COVERED																																																																																			NOVEL	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313810.2	3	15.950803	KEEP	0	0	0	53	1843	GG	1	1	0		-	55	60	1969	0	0	167.623739	180	60	6471	356	ENST00000380518.3	0.234043	1
ADCY6	112	__UNKNOWN__	__UNKNOWN__	12	49166192	49166192	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs376944107		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:49166192C>A	ENST00000307885.4	-	17	3367	c.2673G>T	c.(2671-2673)agG>agT	p.R891S	ADCY6_ENST00000357869.3_Missense_Mutation_p.R838S|ADCY6_ENST00000550422.1_Missense_Mutation_p.R838S	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	891		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						TGAGGGCCACCCTCCCTGCAG	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													79	75	77	NA		NA	NA	12		NA											NA				49166192		2203	4300	6503	SO:0001583	missense				CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	112	4.6.1.1	Adenylate cyclases	237	protein-coding gene	gene with protein product		600294			NA		Standard	NM_020983	NM_015270	NA	Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.2673G>T	chr12.hg19:g.49166192C>A	ENSP00000311405:p.Arg891Ser	NA	Q9NR75|Q9UDB0	hg19	CCDS8767.1	0.02	6.839919	CACxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.37	1.918779	0.33908	.	.	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.78246	-1.16;-1.16;-1.15	5.61	4.72	0.59763	.	0.054038	0.64402	D	0.000001	T	0.62816	0.2459	L	0.31664	0.95	0.36672	D	0.878538	B;B;B	0.19331	0.035;0.007;0.004	B;B;B	0.13407	0.008;0.009;0.004	T	0.60712	-0.7209	10	0.22109	T	0.4	.	7.8926	0.29686	0.0:0.7594:0.0:0.2406	.	122;838;891	B4DG74;O43306-2;O43306	.;.;ADCY6_HUMAN	S	838;838;891	ENSP00000350536:R838S;ENSP00000446730:R838S;ENSP00000311405:R891S	ENSP00000311405:R891S	R	-	3	2	ADCY6	47452459	0.719000	0.27986	1.000000	0.80357	0.994000	0.84299	0.031000	0.13710	1.519000	0.48950	0.563000	0.77884	AGG	NOVEL	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408863.1	2	12.640291	KEEP	0	0	0	42	1449	CC	1	1	0		-	6	60	218	0	0	13.71437	145	60	5107	251	ENST00000307885.4	0.039735	1
RP11-302B13.5	0	__UNKNOWN__	__UNKNOWN__	12	49325195	49325195	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:49325195G>T	ENST00000398092.4	-	4	533				AC073610.5_ENST00000537495.1_Intron|CCDC65_ENST00000266984.5_Splice_Site						NA		NA									NA						TCCACCCACAGGCAGCACAAG	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000398092.4:c.384+8242C>A	chr12.hg19:g.49325195G>T		NA		hg19		0.02	6.117941	ACAxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089875	0.36855	.	.	ENSG00000139537	ENST00000266984	.	.	.	3.2	1.17	0.20885	.	.	.	.	.	.	.	.	.	.	.	0.19575	N	0.999963	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.87	0.09033	0.153:0.2488:0.5982:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC65	47611462	0.001000	0.12720	0.127000	0.21898	0.661000	0.39034	0.191000	0.17076	0.312000	0.23038	0.561000	0.74099	.	NOVEL	RP11-302B13.5-001	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000473246.1	1	16.850785	KEEP	0	0	0	56	1970	GG	1	1	0		-	6	60	215	0	0	12.684798	193	60	7315	305	ENST00000398092.4	0.030151	1
KMT2D	8085	__UNKNOWN__	__UNKNOWN__	12	49414631	49414631	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:49414631C>T	ENST00000301067.7	-	0	17545					NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	NA		NA			chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)				NA						GCCCCCATGTCCAGATGGAGA	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548	8085		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	7133	protein-coding gene	gene with protein product		602113	trinucleotide repeat containing 21, myeloid/lymphoid or mixed-lineage leukemia 2	TNRC21, MLL2	NA	9247308	Standard		NM_003482	NA	Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.*932G>A	chr12.hg19:g.49414631C>T		NA	O14687	hg19	CCDS44873.1	0.02	6.924489	TGTxCAG	COVERED																																																																																			NOVEL	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390183.2	5	16.852151	KEEP	0	0	0	56	1888	CC	1	1	0		-	34	60	1223	0	0	102.281576	129	60	4658	270	ENST00000301067.7	0.208589	1
KMT2D	8085	__UNKNOWN__	__UNKNOWN__	12	49444874	49444874	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:49444874A>G	ENST00000301067.7	-	10	2591	c.2592T>C	c.(2590-2592)ccT>ccC	p.P864P		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	864	Pro-rich.	NA		Missing (in Ref. 1; AAC51734). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)				NA						GGGGCTTTTCAGGCCGAGGGG	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													44	50	48	NA		NA	NA	12		NA											NA				49444874		1972	4140	6112	SO:0001819	synonymous_variant			AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548	8085		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	7133	protein-coding gene	gene with protein product		602113	trinucleotide repeat containing 21, myeloid/lymphoid or mixed-lineage leukemia 2	TNRC21, MLL2	NA	9247308	Standard		NM_003482	NA	Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.2592T>C	chr12.hg19:g.49444874A>G		NA	O14687	hg19	CCDS44873.1	0.02	11.023286	TTCxGGC	COVERED																																																																																			NOVEL	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390183.2	1	21.647815	KEEP	0	0	0	72	2195	AA	1	1	0		-	60	60	1953	0	0	162.486693	204	60	7469	388	ENST00000301067.7	0.227273	1
TUBA1C	84790	__UNKNOWN__	__UNKNOWN__	12	49658676	49658676	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:49658676G>C	ENST00000541364.1	+	2	241							Q9BQE3	TBA1C_HUMAN	tubulin, alpha 1c	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)	13						GGCTCCTTCCGACGAGTTTGG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004949	CCDS8782.1	12q13.12	2007-03-16	2007-02-12	2007-02-12		ENSG00000167553	84790		Tubulins	20768	protein-coding gene	gene with protein product		NA	tubulin, alpha 6	TUBA6	NA	7821789	Standard	NM_032704	NM_032704	NA	Approved	MGC14580, MGC10851, bcm948	uc001rtt.1	Q9BQE3		ENST00000541364.1:c.214-4572G>C	chr12.hg19:g.49658676G>C		NA		hg19		0.02	7.151351	TCCxACG	COVERED																																																																																			NOVEL	TUBA1C-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000404420.1	12	50.554051	KEEP	0	0	0	168	5588	GG	1	1	0		+	40	60	1458	0	0	125.83227	120	60	3947	471	ENST00000541364.1	0.25	1
AQP6	363	__UNKNOWN__	__UNKNOWN__	12	50367175	50367175	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:50367175C>G	ENST00000551733.1	+	3	378				AQP6_ENST00000315520.5_Silent_p.T73T			Q13520	AQP6_HUMAN	aquaporin 6, kidney specific	NA		NA			anion transport (GO:0006820)|excretion (GO:0007588)|odontogenesis (GO:0042476)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	integral component of plasma membrane (GO:0005887)|transport vesicle membrane (GO:0030658)	anion channel activity (GO:0005253)|water channel activity (GO:0015250)			endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(2)	13						TGCAGGTCACCTGGAAGGCCA	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	71	73	NA		NA	NA	12		NA											NA				50367175		2203	4300	6503	SO:0001627	intron_variant			AL137716	CCDS31798.1	12q13	2005-09-20			ENSG00000086159	ENSG00000086159	363		Ion channels / Aquaporins	639	protein-coding gene	gene with protein product		601383		AQP2L	NA	8812490	Standard	NM_001652, NM_053286	XM_006719375	NA	Approved		uc001rvr.1	Q13520	OTTHUMG00000133548	ENST00000551733.1:c.-121+857C>G	chr12.hg19:g.50367175C>G		NA		hg19		0.02	19.646813	CACxTGG	COVERED																																																																																			NOVEL	AQP6-004	PUTATIVE	upstream_ATG|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000407188.1	3	45.729442	KEEP	0	0	0	152	5043	CC	1	1	0		+	116	60	3875	0	0	327.248877	367	60	12828	816	ENST00000551733.1	0.240166	1
CERS5	91012	__UNKNOWN__	__UNKNOWN__	12	50538502	50538502	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:50538502G>A	ENST00000317551.6	-	2	322				CERS5_ENST00000422340.2_Intron	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)				NA						GCACTCTATCGTagtctcaga	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624		91012		Homeoboxes / CERS class	23749	protein-coding gene	gene with protein product		615335	LAG1 longevity assurance homolog 5 (S. cerevisiae), LAG1 homolog, ceramide synthase 5	LASS5	NA		Standard	NM_147190	NM_147190	NA	Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.198-662C>T	chr12.hg19:g.50538502G>A		NA	B4DV54	hg19	CCDS8801.1	0.02	1.971776	ATCxTAG	COVERED																																																																																			NOVEL	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406069.3	0	8.727001	KEEP	0	0	0	29	991	GG	0.999997	0.999892	0		-	8	60	303	0	0	22.275614	85	60	3022	167	ENST00000317551.6	0.086022	0.999895
KRT86	3892	__UNKNOWN__	__UNKNOWN__	12	52649316	52649316	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:52649316G>A	ENST00000544024.1	+	1	129				KRT121P_ENST00000529785.1_RNA			O43790	KRT86_HUMAN	keratin 86	NA		NA				extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		AAAAAGTGTTGGACTGAAGGG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442	3892		-, Intermediate filaments type II, keratins (basic)	6463	protein-coding gene	gene with protein product	hard keratin type II 6	601928	keratin, hair, basic, 6 (monilethrix)	KRTHB6	NA	9241275, 16831889	Standard	NM_002284	NM_002284	NA	Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000544024.1:c.-5+6104G>A	chr12.hg19:g.52649316G>A		NA	P78387	hg19	CCDS41785.1	0.02	5.089976	GTTxGAC	COVERED																																																																																			NOVEL	KRT86-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		0	6.62089	KEEP	0	0	0	22	756	GG	0.999879	0.999847	0		+	6	60	216	0	0	14.754471	89	60	3219	154	ENST00000544024.1	0.063158	0.999968
KRT75	9119	__UNKNOWN__	__UNKNOWN__	12	52825785	52825785	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:52825785C>G	ENST00000252245.5	-	3	995					NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		AACATCCCCACTCACCTTTTT	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	89	93	NA		NA	NA	12		NA											NA				52825785		2203	4300	6503	SO:0001627	intron_variant			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454	9119		-, Intermediate filaments type II, keratins (basic)	24431	protein-coding gene	gene with protein product		609025			NA	9856802, 10692104, 16831889	Standard	NM_004693	NM_004693	NA	Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.774+4G>C	chr12.hg19:g.52825785C>G		NA	B4DQU4|Q9NSA9	hg19	CCDS8827.1	0.02	5.918389	CCAxTCA	COVERED																																																																																			NOVEL	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404968.1	2	14.133965	KEEP	0	0	0	47	1624	CC	1	1	0		-	7	60	259	0	0	16.083	192	60	7196	298	ENST00000252245.5	0.035176	1
CALCOCO1	57658	__UNKNOWN__	__UNKNOWN__	12	54105712	54105712	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:54105712G>A	ENST00000550804.1	-	0	2152				CALCOCO1_ENST00000262059.4_3'UTR|CALCOCO1_ENST00000430117.2_3'UTR|CALCOCO1_ENST00000548263.1_3'UTR			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	NA		NA			intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						atttgtgcatgtACGAGGGAG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													149	116	127	NA		NA	NA	12		NA											NA				54105712		2203	4300	6503	SO:0001624	3_prime_UTR_variant			AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822	57658			29306	protein-coding gene	gene with protein product	coiled-coil leucine zipper coactivator 1, inorganic pyrophosphatase activator	NA			NA	10819331, 11230166	Standard	NM_020898	NM_020898	NA	Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.*16C>T	chr12.hg19:g.54105712G>A		NA	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	hg19	CCDS8864.1	0.02	15.741975	CATxTAC	COVERED																																																																																			NOVEL	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407233.2	26	33.108029	KEEP	0	0	0	110	3956	GG	1	1	0		-	49	60	1732	0	0	133.629665	324	60	12232	599	ENST00000550804.1	0.131367	1
CALCOCO1	57658	__UNKNOWN__	__UNKNOWN__	12	54116685	54116685	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:54116685T>G	ENST00000550804.1	-	4	511				CALCOCO1_ENST00000262059.4_Intron|CALCOCO1_ENST00000430117.2_Intron|CALCOCO1_ENST00000548263.1_Intron			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	NA		NA			intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						TTCACTTACGTGAGATATAAA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822	57658			29306	protein-coding gene	gene with protein product	coiled-coil leucine zipper coactivator 1, inorganic pyrophosphatase activator	NA			NA	10819331, 11230166	Standard	NM_020898	NM_020898	NA	Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.450+691A>C	chr12.hg19:g.54116685T>G		NA	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	hg19	CCDS8864.1	0.02	1.827999	ACGxGAG	COVERED																																																																																			NOVEL	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407233.2	13	20.159816	KEEP	0	0	0	67	2077	TT	1	0.999948	0		-	26	60	925	0	0	80.283023	72	60	2640	210	ENST00000550804.1	0.265306	0.999948
ERBB3	2065	__UNKNOWN__	__UNKNOWN__	12	56486591	56486591	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:56486591A>G	ENST00000267101.3	+	10	1610	c.1170A>G	c.(1168-1170)gtA>gtG	p.V390V	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Silent_p.V331V	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	390		NA			cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			TCCGGACAGTACGGGAGATCA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													101	100	100	NA		NA	NA	12		NA											NA				56486591		2203	4300	6503	SO:0001819	synonymous_variant			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361	2065			3431	protein-coding gene	gene with protein product		190151	lethal congenital contracture syndrome 2	LCCS2	NA		Standard		NM_001982	NA	Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.1170A>G	chr12.hg19:g.56486591A>G		NA	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	hg19	CCDS31833.1	0.02	4.501826	AGTxCGG	COVERED																																																																																			NOVEL	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407619.3	1	9.026335	KEEP	0	0	0	30	926	AA	0.999997	0.999991	0		+	11	60	417	0	0	31.376421	100	60	3523	173	ENST00000267101.3	0.099099	0.999994
STAT6	6778	__UNKNOWN__	__UNKNOWN__	12	57498459	57498459	__UNKNOWN__	Intron	SNP	C	C	A	rs12316334		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:57498459C>A	ENST00000537215.2	-	9	1204				STAT6_ENST00000543873.2_Intron|STAT6_ENST00000538913.2_Intron|STAT6_ENST00000556155.1_Intron|STAT6_ENST00000300134.3_Intron|STAT6_ENST00000454075.3_Intron	NM_001178080.1	NP_001171551.1	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	NA		NA			cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						CAAGGAGAGTCCCACAGTCTC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	61	62	NA		NA	NA	12		NA											NA				57498459		2203	4300	6503	SO:0001627	intron_variant			BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888	6778		SH2 domain containing	11368	protein-coding gene	gene with protein product		601512			NA	9605853, 8085155	Standard	NM_003153	NM_003153	NA	Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000537215.2:c.759+49G>T	chr12.hg19:g.57498459C>A		NA	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	hg19	CCDS53804.1	0.02	8.310146	AGTxCCA	COVERED																																																																																			NOVEL	STAT6-006	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412254.1	2	20.146458	KEEP	0	0	0	67	2197	CC	1	1	0		-	54	60	1848	0	0	155.932792	178	60	6358	375	ENST00000537215.2	0.232759	1
ARHGAP9	64333	__UNKNOWN__	__UNKNOWN__	12	57870878	57870878	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:57870878A>G	ENST00000393791.3	-	5	1009				ARHGAP9_ENST00000393797.2_Intron|ARHGAP9_ENST00000356411.2_Intron|ARHGAP9_ENST00000550454.1_Intron|ARHGAP9_ENST00000550288.1_Intron|ARHGAP9_ENST00000430041.2_Intron|ARHGAP9_ENST00000424809.2_Intron	NM_032496.2	NP_115885.2	Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	NA		NA			positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			CTTACACAAAACAGAAAGTCA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329	64333		Rho GTPase activating proteins, Pleckstrin homology (PH) domain containing	14130	protein-coding gene	gene with protein product		610576			NA	11396949	Standard	NM_032496	NM_032496	NA	Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000393791.3:c.870+60T>C	chr12.hg19:g.57870878A>G		NA	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	hg19	CCDS8941.2	0.02	6.897927	AAAxCAG	COVERED																																																																																			NOVEL	ARHGAP9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316537.1	5	19.254458	KEEP	0	0	0	64	1961	AA	1	1	0		-	9	60	339	0	0	23.0057	157	60	5517	285	ENST00000393791.3	0.054217	1
LEMD3	23592	__UNKNOWN__	__UNKNOWN__	12	65609716	65609716	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:65609716C>T	ENST00000308330.2	+	3	1586					NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	NA		NA			negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		TGTTTTTTTTCTTGTAATTGG	0.254	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													27	28	28	NA		NA	NA	12		NA											NA				65609716		2178	4249	6427	SO:0001627	intron_variant			AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106	23592			28887	protein-coding gene	gene with protein product		607844			NA	10671519, 15489854	Standard		NM_014319	NA	Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.1561-41C>T	chr12.hg19:g.65609716C>T		NA	Q9NT47|Q9NYA5	hg19	CCDS8972.1	0.02	-0.420359	TTTxTTG	COVERED																																																																																			NOVEL	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401312.2	0	2.438964	KEEP	0	1	10	12	378	CC	0.994391	0.943082	0		+	6	60	142	0	0	9.231686	42	60	1475	86	ENST00000308330.2	0.125	0.948402
HELB	92797	__UNKNOWN__	__UNKNOWN__	12	66704401	66704401	__UNKNOWN__	Intron	SNP	A	A	G	rs141898186	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:66704401A>G	ENST00000247815.4	+	4	1739					NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	NA		NA			DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		AAAACCTTTGACATTTCATCT	0.473	NA	NA											A|||	22	0.00439297	0.0166	0	5008	,	,	NA	19075	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								A		68,4338	59.9+/-96.7	1,66,2136	79	85	83	NA		-3.7	0	12	dbSNP_134	83	1,8599		0,1,4299	no	intron	HELB	NM_033647.2		1,67,6435	GG,GA,AA	NA	0.0116,1.5433,0.5305			66704401	69,12937	2203	4300	6503	SO:0001627	intron_variant			AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311	92797			17196	protein-coding gene	gene with protein product		614539			NA	12181327	Standard		NM_033647	NA	Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1680+13A>G	chr12.hg19:g.66704401A>G		NA	A8K4C9|Q4G0T2|Q9H7L5	hg19	CCDS8976.1	0.02	9.770792	TTGxCAT	COVERED																																																																																			NOVEL	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401919.1	1	11.431975	KEEP	0	0	0	38	1159	AA	1	1	0		+	62	60	2144	0	0	189.683187	141	60	4959	271	ENST00000247815.4	0.305419	1
BEST3	144453	__UNKNOWN__	__UNKNOWN__	12	70047953	70047953	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:70047953C>T	ENST00000330891.5	-	0	2967				BEST3_ENST00000331471.4_Intron|BEST3_ENST00000553096.1_3'UTR|BEST3_ENST00000488961.1_3'UTR	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	NA		NA			negative regulation of ion transport (GO:0043271)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(2)	12	Breast(13;2.31e-06)|Esophageal squamous(21;0.187)		Lung(24;0.000278)|OV - Ovarian serous cystadenocarcinoma(12;0.0019)|STAD - Stomach adenocarcinoma(21;0.00694)			CATGGCAAGACATAAGCAACA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF440758	CCDS8992.2, CCDS41810.1, CCDS61192.1, CCDS61193.1, CCDS73496.1	12q14.2-q15	2012-09-26	2006-10-18	2006-10-18	ENSG00000127325	ENSG00000127325	144453		Ion channels / Chloride channels : Calcium activated : Bestrophins	17105	protein-coding gene	gene with protein product		607337	vitelliform macular dystrophy 2-like 3	VMD2L3	NA	12032738	Standard	NM_152439	NM_032735	NA	Approved	MGC40411, MGC13168	uc001svg.3	Q8N1M1	OTTHUMG00000149919	ENST00000330891.5:c.*734G>A	chr12.hg19:g.70047953C>T		NA	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	hg19	CCDS8992.2	0.02	2.024407	AGAxATA	COVERED																																																																																			NOVEL	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313908.2	2	3.912972	KEEP	0	0	0	13	477	CC	0.994391	0.994118	0		-	22	60	798	0	0	68.931549	65	60	2467	122	ENST00000330891.5	0.252874	0.999726
ZFC3H1	196441	__UNKNOWN__	__UNKNOWN__	12	72028617	72028617	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:72028617A>C	ENST00000378743.3	-	11	2597					NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	NA		NA			RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						TAAAAAAAAAAAAACATTTGA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	42	42	NA		NA	NA	12		NA											NA				72028617		1802	4067	5869	SO:0001627	intron_variant			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858	196441		Zinc finger, C3H1-type containing	28328	protein-coding gene	gene with protein product		NA	proline/serine-rich coiled-coil 2, coiled-coil domain containing 131	PSRC2, CCDC131	NA	9628581	Standard	NM_144982	NM_144982	NA	Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.2239-12T>G	chr12.hg19:g.72028617A>C		NA	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	hg19	CCDS41813.1	0.02	2.267931	AAAxAAA	COVERED																																																																																			NOVEL	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404751.1	2	12.034717	KEEP	0	0	0	40	1232	AA	1	0.999407	0		-	29	60	1124	0	0	103.485039	51	60	1891	155	ENST00000378743.3	0.3625	0.999407
NAV3	89795	__UNKNOWN__	__UNKNOWN__	12	78593163	78593163	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:78593163C>T	ENST00000536525.2	+	36	6674	c.6501C>T	c.(6499-6501)ggC>ggT	p.G2167G	NAV3_ENST00000397909.2_Silent_p.G2189G|NAV3_ENST00000228327.6_Silent_p.G2167G|NAV3_ENST00000266692.7_Silent_p.G1990G|NAV3_ENST00000541270.1_Silent_p.G19G	NM_014903.4	NP_055718.4	Q8IVL0	NAV3_HUMAN	neuron navigator 3	2189		NA				membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCTTTTTAGGCAGATATCTTC	0.313	NA	NA								HNSCC(70;0.22)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													86	86	86	NA		NA	NA	12		NA											NA				78593163		1814	4072	5886	SO:0001819	synonymous_variant			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798	89795			15998	protein-coding gene	gene with protein product	pore membrane and/or filament interacting like protein 1, steerin 3	611629			NA	12079279, 12062803	Standard	NM_001024383	XM_005269215	NA	Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000536525.2:c.6501C>T	chr12.hg19:g.78593163C>T		NA	Q8NFW7|Q9Y2E7	hg19	CCDS41815.1	0.02	24.70623	AGGxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.773	1.173094	0.21704	.	.	ENSG00000067798	ENST00000552895;ENST00000551162	.	.	.	5.71	-1.96	0.07525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.4532	1.1052	0.01692	0.3093:0.2059:0.0975:0.3873	.	.	.	.	X	1062;57	.	.	Q	+	1	0	NAV3	77117294	0.147000	0.22687	0.975000	0.42487	0.987000	0.75469	-0.409000	0.07160	-0.318000	0.08665	0.650000	0.86243	CAG	NOVEL	NAV3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406811.1	8	66.512142	KEEP	0	0	0	221	8039	CC	1	1	0		+	136	60	4754	0	0	406.340849	417	70	16019	1012	ENST00000536525.2	0.245931	1
OTOGL	283310	__UNKNOWN__	__UNKNOWN__	12	80732959	80732959	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:80732959C>T	ENST00000547103.1	+	42	4908	c.4902C>T	c.(4900-4902)atC>atT	p.I1634I	OTOGL_ENST00000458043.2_Silent_p.I1646I			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1634	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.	NA			L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTGGACTAATCATAAAGTGGT	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													216	214	214	NA		NA	NA	12		NA											NA				80732959		1889	4101	5990	SO:0001819	synonymous_variant			AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899	283310			26901	protein-coding gene	gene with protein product		614925	chromosome 12 open reading frame 64	C12orf64	NA		Standard	NM_173591	NM_173591	NA	Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.4902C>T	chr12.hg19:g.80732959C>T		NA	F8W0C3|Q495U8|Q8N8G5|Q8NC28	hg19		0.02	8.992144	AATxATA	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.813	0.935772	0.18206	.	.	ENSG00000165899	ENST00000298820	.	.	.	5.72	0.151	0.14888	.	.	.	.	.	T	0.53738	0.1815	.	.	.	0.39166	D	0.962498	.	.	.	.	.	.	T	0.48758	-0.9007	4	.	.	.	.	7.5136	0.27587	0.1088:0.5787:0.0:0.3124	.	.	.	.	L	89	.	.	S	+	2	0	OTOGL	79257090	1.000000	0.71417	0.192000	0.23308	0.983000	0.72400	1.925000	0.40074	0.089000	0.17243	-0.806000	0.03193	TCA	NOVEL	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000407438.1	3	17.755921	KEEP	0	0	0	59	2064	CC	1	1	0		+	27	60	996	0	0	75.521873	219	60	8390	365	ENST00000547103.1	0.109756	1
MYF6	4618	__UNKNOWN__	__UNKNOWN__	12	81102939	81102939	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:81102939T>A	ENST00000228641.3	+	0	1151					NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	NA		NA			muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|muscle tissue morphogenesis (GO:0060415)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal muscle cell differentiation (GO:0035914)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						TGAAAACGCCTTTCGGCTTTG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS9019.1	12q21	2013-05-21				ENSG00000111046	4618		Basic helix-loop-helix proteins	7566	protein-coding gene	gene with protein product	muscle-specific regulatory factor 4	159991			NA	8978788	Standard	NM_002469	NM_002469	NA	Approved	MRF4, bHLHc4	uc001szf.2	P23409		ENST00000228641.3:c.*200T>A	chr12.hg19:g.81102939T>A		NA	B2R898|Q53X80|Q6FHI9	hg19	CCDS9019.1	0.02	4.731212	GCCxTTC	COVERED																																																																																			NOVEL	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407756.1	2	6.620237	KEEP	0	0	0	22	713	TT	0.999879	0.999877	0		+	27	60	982	0	0	83.413425	92	60	3435	175	ENST00000228641.3	0.226891	0.999998
CCER1	196477	__UNKNOWN__	__UNKNOWN__	12	91348829	91348829	__UNKNOWN__	5'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:91348829C>G	ENST00000358859.2	-	0	124				CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	NA		NA									NA						GACCCACTCCCGGGTCCCCAC	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651	196477			28373	protein-coding gene	gene with protein product		NA	chromosome 12 open reading frame 12	C12orf12	NA	17967063	Standard	NM_152638	NM_152638	NA	Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.-310G>C	chr12.hg19:g.91348829C>G		NA	Q8TC47	hg19	CCDS9036.1	0.02	2.218478	TCCxGGG	COVERED																																																																																			NOVEL	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407142.2	0	8.345169	KEEP	0	0	0	28	844	CC	0.999997	0.9937	0		-	13	60	450	0	1	37.092012	52	60	1611	111	ENST00000358859.2	0.2	0.993703
DCN	1634	__UNKNOWN__	__UNKNOWN__	12	91545383	91545383	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:91545383G>A	ENST00000052754.5	-	7	1387				DCN_ENST00000303320.3_Intron|DCN_ENST00000456569.2_Intron|DCN_ENST00000552962.1_Intron|DCN_ENST00000547568.2_Intron|DCN_ENST00000425043.1_Intron|DCN_ENST00000228329.5_Intron|DCN_ENST00000441303.2_Intron|DCN_ENST00000393155.1_Intron|DCN_ENST00000420120.2_Intron	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	NA		NA			aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						GCAGGGTGGGGGTCTTGCTTT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													61	54	56	NA		NA	NA	12		NA											NA				91545383		2203	4300	6503	SO:0001627	intron_variant			AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465	1634		Proteoglycans / Extracellular Matrix : Small leucine-rich repeats	2705	protein-coding gene	gene with protein product	decorin proteoglycan	125255			NA	8432526	Standard	NM_133507	NM_133507	NA	Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.885+47C>T	chr12.hg19:g.91545383G>A		NA	Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	hg19	CCDS9039.1	0.02	4.485264	GGGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	2.005	-0.428562	0.04701	.	.	ENSG00000011465	ENST00000550758	.	.	.	3.62	-4.28	0.03732	.	.	.	.	.	T	0.17280	0.0415	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26224	-1.0109	4	.	.	.	.	0.9173	0.01307	0.1482:0.1801:0.2594:0.4123	.	.	.	.	S	81	.	.	P	-	1	0	DCN	90069514	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	-0.678000	0.05209	-0.728000	0.04882	-1.239000	0.01543	CCC	NOVEL	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406799.3	1	17.919043	KEEP	0	0	0	60	1946	GG	1	1	0		-	26	60	940	0	0	77.627911	110	60	3739	250	ENST00000052754.5	0.191176	1
CLLU1	574028	__UNKNOWN__	__UNKNOWN__	12	92819432	92819432	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:92819432C>G	ENST00000378485.1	+	0	1698				CLLU1OS_ENST00000538965.1_Intron|CLLU1_ENST00000472839.2_3'UTR|RP11-693J15.4_ENST00000508671.1_RNA|CLLU1OS_ENST00000378487.2_Intron	NM_001025233.1	NP_001020404.1	Q5K131	CLLU1_HUMAN	chronic lymphocytic leukemia up-regulated 1	NA		NA				cytoplasm (GO:0005737)				NS(1)|breast(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						TAATGACCTACGATCCATTTC	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ845162		12q22	2012-04-19			ENSG00000257127	ENSG00000257127	574028			29841	protein-coding gene	gene with protein product		NA			NA	19726446	Standard	NM_001025233	NR_027932	NA	Approved		uc001tcg.1	Q5K131	OTTHUMG00000170103	ENST00000378485.1:c.*610C>G	chr12.hg19:g.92819432C>G		NA		hg19		0.02	2.217453	CTAxGAT	COVERED																																																																																			NOVEL	CLLU1-003	KNOWN	NMD_exception|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000366643.1	0	7.788177	KEEP	0	0	0	26	794	CC	0.999957	0.99366	0		+	4	60	148	1	0	10.241096	59	60	2038	124	ENST00000378485.1	0.063492	0.993703
NUDT4	11163	__UNKNOWN__	__UNKNOWN__	12	93792920	93792920	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:93792920C>T	ENST00000337179.5	+	5	783				NUDT4_ENST00000415493.2_Intron|NUDT4_ENST00000547014.1_Intron|NUDT4_ENST00000548662.1_Intron|NUDT4_ENST00000549992.1_Intron	NM_199040.2	NP_950241.1	Q9NZJ9	NUDT4_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 4	NA		NA			calcium-mediated signaling (GO:0019722)|cyclic nucleotide metabolic process (GO:0009187)|cyclic-nucleotide-mediated signaling (GO:0019935)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|regulation of RNA export from nucleus (GO:0046831)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)|snoRNA binding (GO:0030515)			endometrium(2)|kidney(1)|lung(2)	5						TTAAAATGGACTGTCTTGTAA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													40	39	39	NA		NA	NA	12		NA											NA				93792920		2203	4300	6503	SO:0001627	intron_variant			AF067803	CCDS9044.1, CCDS44952.1, CCDS73504.1	12q21	2008-09-04			ENSG00000173598	ENSG00000173598	11163		Nudix motif containing	8051	protein-coding gene	gene with protein product	diphosphoinositol polyphosphate phosphohydrolase type 2	609229			NA	10777568, 11376937	Standard	NM_019094	XM_005268595	NA	Approved	DIPP2, HDCMB47P, KIAA0487, DIPP2alpha, DIPP2beta	uc001tcm.3	Q9NZJ9	OTTHUMG00000170155	ENST00000337179.5:c.344-33C>T	chr12.hg19:g.93792920C>T		NA	B7Z916|Q4AEJ6|Q53EZ2|Q68DD7|Q9NPC5|Q9NS30|Q9NZK0|Q9NZK1	hg19	CCDS9044.1	0.02	1.910339	GGAxTGT	COVERED																																																																																			NOVEL	NUDT4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407701.1	2	15.94422	KEEP	0	0	0	53	1855	CC	1	0.999962	0		+	31	60	1139	0	0	101.805114	69	60	2558	184	ENST00000337179.5	0.31	0.999962
ELK3	2004	__UNKNOWN__	__UNKNOWN__	12	96661713	96661713	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:96661713A>C	ENST00000228741.3	+	0	2305					NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	NA		NA			angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					TCCCAGACAAAAATCTGAGAT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145	2004			3325	protein-coding gene	gene with protein product		600247			NA	7851904	Standard	NM_005230	NM_005230	NA	Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.*755A>C	chr12.hg19:g.96661713A>C		NA	B2R6S6|Q6FG57|Q6GU29|Q9UD17	hg19	CCDS9060.1	0.02	2.118784	CAAxAAT	COVERED																																																																																			NOVEL	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408694.1	1	14.143302	KEEP	0	0	0	47	1530	AA	1	0.999956	0		+	36	60	1399	0	0	128.894019	63	60	2344	185	ENST00000228741.3	0.363636	0.999956
C12orf55	0	__UNKNOWN__	__UNKNOWN__	12	96929420	96929420	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:96929420A>G	ENST00000524981.4	+	12	1814				C12orf55_ENST00000298953.3_Intron			Q96N23	CL055_HUMAN		NA		NA									NA						GTGTGGAAGGAGGTTTTTGTG	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000524981.4:c.1791+42A>G	chr12.hg19:g.96929420A>G		NA		hg19		0.02	2.007761	AGGxGGT	COVERED																																																																																			NOVEL	C12orf55-003	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000395046.4	0	6.921225	KEEP	0	0	0	23	734	AA	0.999892	0.999696	0		+	14	60	485	0	0	38.43907	75	60	2820	130	ENST00000524981.4	0.157303	0.999804
NR1H4	9971	__UNKNOWN__	__UNKNOWN__	12	100926225	100926225	__UNKNOWN__	Intron	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:100926225T>A	ENST00000392986.3	+	5	778				NR1H4_ENST00000549996.1_Intron|NR1H4_ENST00000188403.7_Intron|NR1H4_ENST00000551379.1_Intron|NR1H4_ENST00000548884.1_Intron			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	NA		NA			bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	TTTTCAGTGTTTCTCCCACAG	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	77	76	NA		NA	NA	12		NA											NA				100926225		2203	4300	6503	SO:0001627	intron_variant			U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504	9971		Nuclear hormone receptors	7967	protein-coding gene	gene with protein product		603826			NA	7774010, 9223286	Standard	NM_005123	NM_001206977	NA	Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000392986.3:c.446-11T>A	chr12.hg19:g.100926225T>A		NA	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	hg19	CCDS55873.1	0.02	2.060167	TGTxTCT	COVERED																																																																																			NOVEL	NR1H4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409135.1	1	5.716681	KEEP	0	0	0	19	576	TT	0.99986	0.999347	0		+	31	60	1068	0	0	97.75135	52	60	1847	115	ENST00000392986.3	0.373494	0.999487
ANO4	121601	__UNKNOWN__	__UNKNOWN__	12	101437325	101437325	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:101437325T>A	ENST00000392979.3	+	12	1419	c.1058T>A	c.(1057-1059)gTc>gAc	p.V353D	ANO4_ENST00000299222.9_De_novo_Start_OutOfFrame|ANO4_ENST00000392977.3_Missense_Mutation_p.V388D	NM_178826.3	NP_849148.2	Q32M45	ANO4_HUMAN	anoctamin 4	388		NA			chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						AGTAAAGAAGTCTGCCAAGCT	0.378	NA	NA								HNSCC(74;0.22)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													153	145	148	NA		NA	NA	12		NA											NA				101437325		2203	4300	6503	SO:0001583	missense			AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572	121601		Ion channels / Chloride channels : Calcium activated : Anoctamins	23837	protein-coding gene	gene with protein product		610111	transmembrane protein 16D	TMEM16D	NA	12739008, 15067359, 24692353	Standard	NM_178826	NM_178826	NA	Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392979.3:c.1058T>A	chr12.hg19:g.101437325T>A	ENSP00000376705:p.Val353Asp	NA	Q8NAJ0|Q8NB39|Q8NB53	hg19	CCDS31884.1	0.02	4.443466	AAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	24.4	4.523380	0.85600	.	.	ENSG00000151572	ENST00000392979;ENST00000392977	T;T	0.71103	-0.53;-0.54	5.48	5.48	0.80851	.	0.072973	0.56097	D	0.000040	T	0.79209	0.4407	L	0.50919	1.6	0.80722	D	1	D;P	0.56521	0.976;0.947	P;P	0.62089	0.864;0.898	T	0.81380	-0.0959	10	0.87932	D	0	.	15.8549	0.78968	0.0:0.0:0.0:1.0	.	388;353	Q32M45;Q32M45-2	ANO4_HUMAN;.	D	353;388	ENSP00000376705:V353D;ENSP00000376703:V388D	ENSP00000376703:V388D	V	+	2	0	ANO4	99961456	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.206000	0.71126	0.533000	0.62120	GTC	NOVEL	ANO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409294.2	2	18.055021	KEEP	0	0	0	60	1928	TT	1	1	0		+	42	60	1535	0	0	138.187923	87	60	3133	252	ENST00000392979.3	0.325581	1
IGF1	3479	__UNKNOWN__	__UNKNOWN__	12	102794723	102794723	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:102794723G>T	ENST00000337514.6	-	0	2287				IGF1_ENST00000456098.1_3'UTR	NM_000618.3	NP_000609.1	P05019	IGF1_HUMAN	insulin-like growth factor 1 (somatomedin C)	NA		NA			blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|bone mineralization involved in bone maturation (GO:0035630)|branching morphogenesis of an epithelial tube (GO:0048754)|cell activation (GO:0001775)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|DNA replication (GO:0006260)|exocrine pancreas development (GO:0031017)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|glial cell differentiation (GO:0010001)|glycolate metabolic process (GO:0009441)|inner ear development (GO:0048839)|insulin-like growth factor receptor signaling pathway (GO:0048009)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|mammary gland development (GO:0030879)|multicellular organism growth (GO:0035264)|muscle hypertrophy (GO:0014896)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|myoblast proliferation (GO:0051450)|myotube cell development (GO:0014904)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate gland growth (GO:0060736)|prostate gland stromal morphogenesis (GO:0060741)|proteoglycan biosynthetic process (GO:0030166)|Ras protein signal transduction (GO:0007265)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of multicellular organism growth (GO:0040014)|signal transduction (GO:0007165)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|skeletal system development (GO:0001501)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)|water homeostasis (GO:0030104)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|insulin-like growth factor binding protein complex (GO:0016942)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	hormone activity (GO:0005179)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|integrin binding (GO:0005178)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)	11						ATTTTGAAAAGTGTTTTAAGA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X00173	CCDS9091.1, CCDS44960.1, CCDS44961.1, CCDS44962.1	12q23.2	2014-09-16			ENSG00000017427	ENSG00000017427	3479		Endogenous ligands	5464	protein-coding gene	gene with protein product		147440			NA	2982726, 6358902	Standard	NM_000618	NM_001111283	NA	Approved	IGF1A, IGFI, IGF-I	uc001tjp.4	P05019	OTTHUMG00000149910	ENST00000337514.6:c.*1562C>A	chr12.hg19:g.102794723G>T		NA	B2RWM7|E9PD02|P01343|Q14620	hg19	CCDS9091.1	0.02	4.671723	AAAxTGT	COVERED																																																																																			NOVEL	IGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313854.1	2	12.039635	KEEP	0	0	0	40	1450	GG	1	0.999977	0		-	11	60	397	0	0	29.754463	92	60	3536	184	ENST00000337514.6	0.106796	0.999978
IGF1	3479	__UNKNOWN__	__UNKNOWN__	12	102794865	102794865	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:102794865C>A	ENST00000337514.6	-	0	2145				IGF1_ENST00000456098.1_3'UTR	NM_000618.3	NP_000609.1	P05019	IGF1_HUMAN	insulin-like growth factor 1 (somatomedin C)	NA		NA			blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|bone mineralization involved in bone maturation (GO:0035630)|branching morphogenesis of an epithelial tube (GO:0048754)|cell activation (GO:0001775)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|DNA replication (GO:0006260)|exocrine pancreas development (GO:0031017)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|glial cell differentiation (GO:0010001)|glycolate metabolic process (GO:0009441)|inner ear development (GO:0048839)|insulin-like growth factor receptor signaling pathway (GO:0048009)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|mammary gland development (GO:0030879)|multicellular organism growth (GO:0035264)|muscle hypertrophy (GO:0014896)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|myoblast proliferation (GO:0051450)|myotube cell development (GO:0014904)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate gland growth (GO:0060736)|prostate gland stromal morphogenesis (GO:0060741)|proteoglycan biosynthetic process (GO:0030166)|Ras protein signal transduction (GO:0007265)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of multicellular organism growth (GO:0040014)|signal transduction (GO:0007165)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|skeletal system development (GO:0001501)|Type I pneumocyte differentiation (GO:0060509)|Type II pneumocyte differentiation (GO:0060510)|water homeostasis (GO:0030104)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|insulin-like growth factor binding protein complex (GO:0016942)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	hormone activity (GO:0005179)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|integrin binding (GO:0005178)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)	11						TATAGAATTCCTTGCATCTCA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X00173	CCDS9091.1, CCDS44960.1, CCDS44961.1, CCDS44962.1	12q23.2	2014-09-16			ENSG00000017427	ENSG00000017427	3479		Endogenous ligands	5464	protein-coding gene	gene with protein product		147440			NA	2982726, 6358902	Standard	NM_000618	NM_001111283	NA	Approved	IGF1A, IGFI, IGF-I	uc001tjp.4	P05019	OTTHUMG00000149910	ENST00000337514.6:c.*1420G>T	chr12.hg19:g.102794865C>A		NA	B2RWM7|E9PD02|P01343|Q14620	hg19	CCDS9091.1	0.02	-0.306812	TTCxTTG	COVERED																																																																																			NOVEL	IGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313854.1	0	5.417579	KEEP	0	0	0	18	641	CC	0.999859	0.800133	0		-	3	60	114	0	0	8.386966	32	60	1179	63	ENST00000337514.6	0.085714	0.800245
STAB2	55576	__UNKNOWN__	__UNKNOWN__	12	104111601	104111601	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:104111601C>T	ENST00000388887.2	+	44	4869	c.4665C>T	c.(4663-4665)ctC>ctT	p.L1555L		NM_017564.9	NP_060034.9			stabilin 2	NA		NA								NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TCTGCACACTCATCAATGTCT	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													307	258	275	NA		NA	NA	12		NA											NA				104111601		2203	4300	6503	SO:0001819	synonymous_variant			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011	55576			18629	protein-coding gene	gene with protein product	hyaluronic acid receptor for endocytosis	608561			NA	11829752, 12077138	Standard		XR_429107	NA	Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4665C>T	chr12.hg19:g.104111601C>T		NA		hg19	CCDS31888.1	0.02	4.265291	ACTxATC	COVERED																																																																																			NOVEL	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407089.1	3	4.649232	KEEP	0	1	27	25	899	CC	0.999957	0.999957	0		+	47	60	1634	0	0	147.363148	91	60	3405	189	ENST00000388887.2	0.34058	1
C12orf23	0	__UNKNOWN__	__UNKNOWN__	12	107371671	107371671	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:107371671A>G	ENST00000551237.1	+	4	387				MTERFD3_ENST00000240050.4_Silent_p.F274F|MTERFD3_ENST00000552029.1_Silent_p.F274F|MTERFD3_ENST00000392830.2_Silent_p.F274F			Q8WUH6	TM263_HUMAN		NA		NA				integral component of membrane (GO:0016021)				endometrium(1)|lung(2)	3						CTGTGCATTTAAAAGCATTTT	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													71	77	75	NA		NA	NA	12		NA											NA				107371671		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000551237.1:c.388-457A>G	chr12.hg19:g.107371671A>G		NA	B3KMN9	hg19		0.02	4.710248	TTTxAAA	COVERED																																																																																			NOVEL	C12orf23-009	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000406864.1	0	15.945051	KEEP	0	0	0	53	1625	AA	1	0.999993	0		+	11	60	422	0	0	31.92158	99	60	3576	198	ENST00000551237.1	0.1	0.999993
C12orf76	400073	__UNKNOWN__	__UNKNOWN__	12	110486333	110486333	__UNKNOWN__	De_novo_Start_OutOfFrame	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:110486333T>A	ENST00000549724.1	-	0	571				C12orf76_ENST00000546651.2_De_novo_Start_OutOfFrame|C12orf76_ENST00000551185.2_De_novo_Start_OutOfFrame|C12orf76_ENST00000309050.5_Intron|C12orf76_ENST00000548936.1_Intron|C12orf76_ENST00000547573.1_De_novo_Start_OutOfFrame			Q8N812	CL076_HUMAN	chromosome 12 open reading frame 76	NA		NA								endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6						GAGAGGCCACTTCCGTCGCAA	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					BC041968	CCDS9141.1	12q24.11	2012-08-16			ENSG00000174456	ENSG00000174456	400073			33790	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207435	NM_207435	NA	Approved	FLJ40142	uc001tqe.2	Q8N812	OTTHUMG00000169315	ENST00000549724.1:c.-33A>T	chr12.hg19:g.110486333T>A		NA		hg19		0.02	2.238746	CACxTCC	COVERED																																																																																			NOVEL	C12orf76-003	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000403440.1	1	16.248455	KEEP	0	0	0	54	1714	TT	1	0.9982	0		-	28	60	943	0	0	86.349932	46	60	1617	162	ENST00000549724.1	0.378378	0.9982
BRAP	8315	__UNKNOWN__	__UNKNOWN__	12	112081544	112081544	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:112081544T>A	ENST00000419234.4	-	0	2431					NM_006768.3	NP_006759.3	Q6UWU4	CF089_HUMAN	BRCA1 associated protein	NA		NA			epithelial cell proliferation (GO:0050673)|positive regulation of cell cycle (GO:0045787)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	20						TCATAACTCCTTAATAGCCAA	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(146;846 1904 7830 25130 26065)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF035620	CCDS9154.1	12q24.12	2014-09-11			ENSG00000089234	ENSG00000089234	8315		RING-type (C3HC4) zinc fingers	1099	protein-coding gene	gene with protein product	impedes mitogenic signal propagation, galectin-2-binding protein	604986			NA	9497340, 19198608	Standard		XM_005253944	NA	Approved	BRAP2, RNF52, IMP	uc001tsn.4	Q7Z569	OTTHUMG00000169600	ENST00000419234.4:c.*459A>T	chr12.hg19:g.112081544T>A		NA	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	hg19	CCDS9154.1	0.02	-0.421039	TCCxTAA	COVERED																																																																																			NOVEL	BRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404993.2	0	6.921847	KEEP	0	0	0	23	759	TT	0.999892	0.9483	0		-	37	60	1335	0	0	139.92035	11	60	409	86	ENST00000419234.4	0.770833	0.948402
ACAD10	80724	__UNKNOWN__	__UNKNOWN__	12	112148232	112148232	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:112148232G>T	ENST00000313698.4	+	5	845				ACAD10_ENST00000549590.1_Intron|ACAD10_ENST00000392636.2_Intron|ACAD10_ENST00000413681.3_Intron|ACAD10_ENST00000455480.2_Intron	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	NA		NA				mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						CGAGCTGATGGGCCTGTAGGG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271	80724			21597	protein-coding gene	gene with protein product		611181	acyl-Coenzyme A dehydrogenase family, member 10		NA	15560374	Standard	NM_025247	NM_025247	NA	Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.690+744G>T	chr12.hg19:g.112148232G>T		NA	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	hg19	CCDS31903.1	0.02	4.300049	ATGxGCC	COVERED																																																																																			NOVEL	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368307.1	4	18.358573	KEEP	0	0	0	61	2081	GG	1	1	0		+	34	70	1187	0	0	101.964513	100	60	3536	272	ENST00000313698.4	0.253731	1
TPCN1	53373	__UNKNOWN__	__UNKNOWN__	12	113711150	113711150	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:113711150T>C	ENST00000392569.4	+	8	831				TPCN1_ENST00000335509.6_Intron|TPCN1_ENST00000541517.1_Intron|TPCN1_ENST00000550785.1_Intron			Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	NA		NA			calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						TGGGGTCTCTTTCTCTTTTCT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	34	36	NA		NA	NA	12		NA											NA				113711150		692	1591	2283	SO:0001627	intron_variant			AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815	53373		Voltage-gated ion channels / Two-pore channels	18182	protein-coding gene	gene with protein product		609666			NA	10574461, 10753632, 16382101	Standard	NM_017901	XM_005253905	NA	Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000392569.4:c.638+55T>C	chr12.hg19:g.113711150T>C		NA	A7E258|Q86XS9|Q8NC20	hg19		0.02	10.028197	TCTxTCT	COVERED																																																																																			NOVEL	TPCN1-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000405159.1	4	38.517851	KEEP	0	0	0	128	4185	TT	1	1	0		+	64	60	2467	0	0	219.930585	154	60	5546	413	ENST00000392569.4	0.293578	1
P2RX4	5025	__UNKNOWN__	__UNKNOWN__	12	121671830	121671830	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:121671830C>T	ENST00000337233.4	+	0	1953				P2RX4_ENST00000543171.1_3'UTR|P2RX4_ENST00000359949.7_3'UTR	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	NA		NA			apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGCAGCCATGCGGCAGAGCTG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124	5025		Purinergic receptors, Ligand-gated ion channels / Purinergic receptors, ionotropic	8535	protein-coding gene	gene with protein product		600846			NA	9016352	Standard	NM_175567	NM_002560	NA	Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.*478C>T	chr12.hg19:g.121671830C>T		NA	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	hg19	CCDS9214.1	0.02	6.16423	ATGxGGC	COVERED																																																																																			NOVEL	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402545.1	1	21.057757	KEEP	0	0	0	70	2237	CC	1	1	0		+	8	60	297	0	0	19.49073	163	60	5537	286	ENST00000337233.4	0.046784	1
BCL7A	605	__UNKNOWN__	__UNKNOWN__	12	122499638	122499638	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:122499638C>T	ENST00000538010.1	+	0	5935					NM_020993.3	NP_066273.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)					haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000202)|Epithelial(86;0.000386)|BRCA - Breast invasive adenocarcinoma(302;0.231)		GGGGAAGCTGCGGCTACACAT	0.582	NA	NA	T	MYC	BNHL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(17;197 467 16477 23242 44349)		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X89984	CCDS9226.1, CCDS53841.1	12q24.1	2008-07-03			ENSG00000110987	ENSG00000110987	605			1004	protein-coding gene	gene with protein product		601406		BCL7	NA	8605326, 9931421	Standard		NM_020993	NA	Approved		uc001ubo.3	Q4VC05	OTTHUMG00000168951	ENST00000538010.1:c.*2569C>T	chr12.hg19:g.122499638C>T		NA	B4DJN6|B7ZB21|Q13843|Q14CT7	hg19	CCDS9226.1	0.02	8.990854	CTGxGGC	COVERED																																																																																			NOVEL	BCL7A-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401711.1	1	43.372783	KEEP	0	1	31	155	5388	CC	1	1	0		+	26	60	926	0	0	69.525734	209	60	7459	534	ENST00000538010.1	0.110638	1
MLXIP	22877	__UNKNOWN__	__UNKNOWN__	12	122618534	122618534	__UNKNOWN__	Splice_Site	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:122618534G>T	ENST00000319080.7	+	9	1864	c.1732G>T	c.(1732-1734)Gct>Tct	p.A578S	MLXIP_ENST00000538698.1_Splice_Site_p.A185S|MLXIP_ENST00000377037.2_Missense_Mutation_p.G168C					MLX interacting protein	NA		NA								NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		TATCGCCCCAGGTGAGCCAGG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(105;787 1493 16200 18566 52466)					NA		NA				0													11	13	12	NA		NA	NA	12		NA											NA				122618534		1931	4123	6054	SO:0001630	splice_region_variant			AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727	22877		Basic helix-loop-helix proteins	17055	protein-coding gene	gene with protein product		608090			NA	10048485, 11073985	Standard	NM_014938	XM_006719290	NA	Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1732+1G>T	chr12.hg19:g.122618534G>T		NA		hg19		0.02	20.534403	CCAxGTG	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.1|21.1	4.093910|4.093910	0.76870|0.76870	.|.	.|.	ENSG00000175727|ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000539039|ENST00000377037	T;T|D	0.76448|0.85629	-1.02;-1.02|-2.01	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.382752|.	0.26727|.	N|.	0.022805|.	D|D	0.90731|0.90731	0.7091|0.7091	.|.	.|.	.|.	0.41925|0.41925	D|D	0.990539|0.990539	D|D	0.54601|0.58268	0.967|0.982	P|P	0.51806|0.57620	0.68|0.824	D|D	0.91945|0.91945	0.5566|0.5566	9|8	0.12103|0.87932	T|D	0.63|0	-13.0517|-13.0517	17.5193|17.5193	0.87783|0.87783	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	578|578	Q9HAP2|Q9HAP2-3	MLXIP_HUMAN|.	S|C	578;185;185|168	ENSP00000312834:A578S;ENSP00000440769:A185S|ENSP00000366236:G168C	ENSP00000312834:A578S|ENSP00000366236:G168C	A|G	+|+	1|1	0|0	MLXIP|MLXIP	121184487|121184487	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.564000|0.564000	0.35744|0.35744	6.311000|6.311000	0.72835|0.72835	2.553000|2.553000	0.86117|0.86117	0.655000|0.655000	0.94253|0.94253	GCT|GGT	NOVEL	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000401718.2	3	28.887994	KEEP	0	0	0	96	3362	GG	1	1	0	Missense_Mutation	+	52	60	1911	0	0	145.920553	399	70	14696	672	ENST00000319080.7	0.115299	1
VPS33A	65082	__UNKNOWN__	__UNKNOWN__	12	122726945	122726945	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:122726945C>A	ENST00000267199.4	-	8	1192	c.1080G>T	c.(1078-1080)ttG>ttT	p.L360F	RP11-512M8.5_ENST00000535844.1_Missense_Mutation_p.L321F	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	360		NA			lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		CATCTTTGATCAATTCTGCAA	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													155	133	141	NA		NA	NA	12		NA											NA				122726945		2203	4300	6503	SO:0001583	missense			AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719	65082			18179	protein-coding gene	gene with protein product		610034	vacuolar protein sorting 33A (yeast)		NA	11250079	Standard		NM_022916	NA	Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.1080G>T	chr12.hg19:g.122726945C>A	ENSP00000267199:p.Leu360Phe	NA	Q547V4|Q9H5Q0	hg19	CCDS9231.1	0.02	4.303124	GATxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719520	0.68844	.	.	ENSG00000139719	ENST00000267199	T	0.76578	-1.03	6.16	-10.1	0.00402	.	0.000000	0.64402	D	0.000003	T	0.77212	0.4097	L	0.60067	1.865	0.80722	D	1	D	0.53745	0.962	P	0.61874	0.895	D	0.85723	0.1326	10	0.30854	T	0.27	-6.5893	12.5412	0.56172	0.0:0.4808:0.4052:0.114	.	360	Q96AX1	VP33A_HUMAN	F	360	ENSP00000267199:L360F	ENSP00000446319:L321F	L	-	3	2	VPS33A	121292898	0.006000	0.16342	0.055000	0.19348	0.981000	0.71138	-1.451000	0.02387	-1.892000	0.01108	-0.355000	0.07637	TTG	NOVEL	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401607.2	2	12.640992	KEEP	0	0	0	42	1482	CC	1	1	0		-	116	60	4182	0	0	442.017886	29	60	1102	227	ENST00000267199.4	0.8	1
CLIP1	6249	__UNKNOWN__	__UNKNOWN__	12	122825966	122825966	__UNKNOWN__	Silent	SNP	C	C	T	rs192560335	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:122825966C>T	ENST00000540338.1	-	10	1826	c.1785G>A	c.(1783-1785)acG>acA	p.T595T	CLIP1_ENST00000358808.2_Silent_p.T584T|CLIP1_ENST00000361654.4_Silent_p.T549T|CLIP1_ENST00000302528.7_Silent_p.T584T|CLIP1_ENST00000537178.1_Silent_p.T549T|CLIP1_ENST00000545889.1_Silent_p.T285T			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	595		NA			microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		AAAGCTTTTCCGTGGCGGTAT	0.463	NA	NA											C|||	4	0.000798722	0	0.0043	5008	,	,	NA	18643	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													142	139	140	NA		NA	NA	12		NA											NA				122825966		2203	4300	6503	SO:0001819	synonymous_variant				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779	6249			10461	protein-coding gene	gene with protein product	restin	179838	restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)	RSN	NA	8222754	Standard	NM_002956	NM_001247997	NA	Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.1785G>A	chr12.hg19:g.122825966C>T		NA	A0AVD3|Q17RS4|Q29RG0	hg19	CCDS58285.1	0.02	9.218943	TTCxGTG	COVERED																																																																																			NOVEL	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401625.1	4	12.941062	KEEP	0	0	0	43	1459	CC	1	1	0		-	13	60	495	0	0	33.734171	228	60	7750	343	ENST00000540338.1	0.053942	1
HCAR2	338442	__UNKNOWN__	__UNKNOWN__	12	123186017	123186017	__UNKNOWN__	3'UTR	SNP	C	C	T	rs1055884	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:123186017C>T	ENST00000328880.5	-	0	1873				RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	NA		NA			negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	TTTTAACTGCCCAACCCTTAG	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782	338442		GPCR / Class A : Hydroxy-carboxylic acid receptors	24827	protein-coding gene	gene with protein product	niacin receptor 1	609163	G protein-coupled receptor 109A	GPR109A	NA	21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551	NM_177551	NA	Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.*722G>A	chr12.hg19:g.123186017C>T		NA	A0PJL5|A7LGG3	hg19	CCDS9235.1	0.02	33.511469	TGCxCAA	COVERED																																																																																			NOVEL	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370202.1	3	4.568323	KEEP	8	13	422	163	5567	CC	1	1	0		-	22	60	759	0	0	42.656893	822	60	29066	1224	ENST00000328880.5	0.026066	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123879666	123879666	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs61955119		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:123879666A>G	ENST00000402868.3	+	4	788	c.362A>G	c.(361-363)aAa>aGa	p.K121R	SETD8_ENST00000330479.4_Missense_Mutation_p.K121R|SETD8_ENST00000478781.2_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	162		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		GACGCCAGGAAAGGTCCCCTG	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	42	42	NA		NA	NA	12		NA											NA				123879666		2203	4299	6502	SO:0001583	missense			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.362A>G	chr12.hg19:g.123879666A>G	ENSP00000384629:p.Lys121Arg	NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	9.932342	GGAxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	5.623	0.299645	0.10622	.	.	ENSG00000183955	ENST00000402868;ENST00000330479;ENST00000437502	D;D	0.98135	-4.74;-4.74	5.57	4.68	0.58851	.	0.449979	0.25138	N	0.032848	D	0.87521	0.6198	N	0.00436	-1.5	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.79548	-0.1758	10	0.22109	T	0.4	-18.1838	8.9091	0.35541	0.227:0.0:0.773:0.0	rs61955119	162;121	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	R	121;121;112	ENSP00000384629:K121R;ENSP00000332995:K121R	ENSP00000332995:K121R	K	+	2	0	SETD8	122445619	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.905000	0.39878	0.751000	0.32900	-0.355000	0.07637	AAA	NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	7	7.766374	KEEP	0	7	256	115	3529	AA	1	1	0		+	23	60	895	0	0	68.102054	205	60	7360	456	ENST00000402868.3	0.100877	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123879668	123879668	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs61955120		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:123879668G>C	ENST00000402868.3	+	4	790	c.364G>C	c.(364-366)Ggt>Cgt	p.G122R	SETD8_ENST00000330479.4_Missense_Mutation_p.G122R|SETD8_ENST00000478781.2_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	163		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		CGCCAGGAAAGGTCCCCTGGT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	42	43	NA		NA	NA	12		NA											NA				123879668		2203	4299	6502	SO:0001583	missense			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.364G>C	chr12.hg19:g.123879668G>C	ENSP00000384629:p.Gly122Arg	NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	9.86848	AAAxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100201	0.56183	.	.	ENSG00000183955	ENST00000402868;ENST00000330479;ENST00000437502	D;D	0.98437	-4.93;-4.93	5.57	5.57	0.84162	.	0.436998	0.23989	N	0.042599	D	0.95940	0.8678	L	0.44542	1.39	0.37022	D	0.896266	P;P	0.49090	0.893;0.919	B;P	0.45506	0.416;0.483	D	0.94819	0.7985	10	0.09084	T	0.74	-8.6264	11.5132	0.50504	0.089:0.0:0.911:0.0	rs61955120	163;122	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	R	122;122;113	ENSP00000384629:G122R;ENSP00000332995:G122R	ENSP00000332995:G122R	G	+	1	0	SETD8	122445621	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.544000	0.45761	2.642000	0.89623	0.462000	0.41574	GGT	NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	6	9.077629	KEEP	0	7	240	114	3929	GG	1	1	0		+	23	60	834	0	0	62.220585	201	60	7242	450	ENST00000402868.3	0.102679	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123879769	123879769	__UNKNOWN__	Silent	SNP	A	A	G	rs139953522		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:123879769A>G	ENST00000402868.3	+	4	891	c.465A>G	c.(463-465)caA>caG	p.Q155Q	SETD8_ENST00000330479.4_Silent_p.Q155Q|SETD8_ENST00000478781.2_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	196		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		TCGCCAAGCAAGCCCTGAAAA	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													19	21	20	NA		NA	NA	12		NA											NA				123879769		2203	4296	6499	SO:0001819	synonymous_variant			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.465A>G	chr12.hg19:g.123879769A>G		NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	3.487791	GCAxGCC	COVERED																																																																																			NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	2	14.141293	KEEP	1	0	0	47	1478	AA	1	1	0		+	5	40	173	0	0	10.247331	140	60	5160	238	ENST00000402868.3	0.034483	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123893397	123893397	__UNKNOWN__	3'UTR	SNP	G	G	A	rs61953481		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:123893397G>A	ENST00000402868.3	+	0	2632				SETD8_ENST00000330479.4_Intron			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	NA		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		CCTCAGAAAGGCACCCAGGTG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.*1147G>A	chr12.hg19:g.123893397G>A		NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	4.001195	AAGxCAC	COVERED																																																																																			NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	1	7.478282	KEEP	0	0	0	25	837	GG	0.999931	0.999931	0		+	8	49	254	0	0	16.654042	107	60	3921	163	ENST00000402868.3	0.069565	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123893416	123893416	__UNKNOWN__	3'UTR	SNP	A	A	G	rs142906941		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:123893416A>G	ENST00000402868.3	+	0	2651				SETD8_ENST00000330479.4_Splice_Site			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	NA		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		TGTGCAGGGGAGCACACAGGG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.*1166A>G	chr12.hg19:g.123893416A>G		NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	4.000384	GGGxGCA	COVERED																																																																																			NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	3	2.54059	KEEP	0	1	36	21	632	AA	0.999879	0.999879	0		+	13	49	440	0	0	32.432094	105	60	3951	164	ENST00000402868.3	0.110169	1
FAM101A	144347	__UNKNOWN__	__UNKNOWN__	12	124796497	124796497	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:124796497G>A	ENST00000324038.3	+	2	317				FAM101A_ENST00000389727.3_Intron|FAM101A_ENST00000338359.4_Intron|FAM101A_ENST00000546355.1_Intron	NM_181709.4	NP_859060.3	Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	NA		NA								endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		TGGGCTCTGCGCGGGAGGAGG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	13	13	NA		NA	NA	12		NA											NA				124796497		2202	4291	6493	SO:0001627	intron_variant				CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882	144347			27051	protein-coding gene	gene with protein product		615927			NA	12477932	Standard	NM_181709	NM_181709	NA	Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000324038.3:c.74+24G>A	chr12.hg19:g.124796497G>A		NA	A5D8T5	hg19	CCDS9258.1	0.02	2.185836	TGCxCGG	COVERED																																																																																			NOVEL	FAM101A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400391.1	0	3.306024	KEEP	0	0	0	11	360	GG	0.993072	0.992296	0		+	30	60	1012	0	0	92.525719	50	60	1766	113	ENST00000324038.3	0.375	0.999218
NCOR2	9612	__UNKNOWN__	__UNKNOWN__	12	124812108	124812108	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:124812108T>C	ENST00000405201.1	-	45	7030	c.7030A>G	c.(7030-7032)Aga>Gga	p.R2344G	NCOR2_ENST00000397355.1_Missense_Mutation_p.R2335G|NCOR2_ENST00000404621.1_Missense_Mutation_p.R2334G|NCOR2_ENST00000429285.2_Missense_Mutation_p.R2334G|NCOR2_ENST00000356219.3_Missense_Mutation_p.R2351G|NCOR2_ENST00000404121.2_Missense_Mutation_p.R1905G			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	2355		NA			cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		AGTGCCTTTCTAATTATGGCC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													73	77	76	NA		NA	NA	12		NA											NA				124812108		1962	4157	6119	SO:0001583	missense			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498	9612			7673	protein-coding gene	gene with protein product		600848	nuclear receptor co-repressor 2		NA	7566127, 8813722	Standard	NM_006312	NM_001077261	NA	Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.7030A>G	chr12.hg19:g.124812108T>C	ENSP00000384018:p.Arg2344Gly	NA	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	hg19	CCDS41858.2	0.02	2.460958	TTCxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	15.03	2.713129	0.48517	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000447675;ENST00000429285	T;T;T;T;T;T	0.57752	0.38;0.77;0.38;0.77;0.49;0.66	5.18	2.76	0.32466	.	0.104471	0.64402	D	0.000005	T	0.67458	0.2895	M	0.76574	2.34	0.48511	D	0.999662	D;D	0.89917	0.994;1.0	D;D	0.91635	0.983;0.999	T	0.65689	-0.6107	10	0.87932	D	0	-18.4096	7.4547	0.27258	0.0:0.0748:0.1441:0.7812	.	2335;2344	C9J239;C9JFD3	.;.	G	2344;2334;2351;2335;2343;1905;436;2334	ENSP00000384018:R2344G;ENSP00000384202:R2334G;ENSP00000348551:R2351G;ENSP00000380513:R2335G;ENSP00000385618:R1905G;ENSP00000400281:R2334G	ENSP00000348551:R2351G	R	-	1	2	NCOR2	123378061	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	3.301000	0.51842	0.281000	0.22233	0.402000	0.26972	AGA	NOVEL	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318173.2	1	10.830894	KEEP	0	0	0	36	1101	TT	0.999999	0.987942	0		-	32	60	1195	0	0	116.763297	28	60	1011	126	ENST00000405201.1	0.533333	0.987943
NCOR2	9612	__UNKNOWN__	__UNKNOWN__	12	124835167	124835167	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:124835167G>A	ENST00000405201.1	-	28	3810	c.3810C>T	c.(3808-3810)taC>taT	p.Y1270Y	NCOR2_ENST00000397355.1_Silent_p.Y1261Y|NCOR2_ENST00000404621.1_Silent_p.Y1260Y|NCOR2_ENST00000429285.2_Silent_p.Y1260Y|NCOR2_ENST00000356219.3_Silent_p.Y1277Y|NCOR2_ENST00000404121.2_Silent_p.Y831Y			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1278		NA			cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TCTTGCCTTCGTAGATGACGT	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													103	109	107	NA		NA	NA	12		NA											NA				124835167		2172	4261	6433	SO:0001819	synonymous_variant			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498	9612			7673	protein-coding gene	gene with protein product		600848	nuclear receptor co-repressor 2		NA	7566127, 8813722	Standard	NM_006312	NM_001077261	NA	Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3810C>T	chr12.hg19:g.124835167G>A		NA	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	hg19	CCDS41858.2	0.02	25.591551	TTCxTAG	COVERED																																																																																			NOVEL	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318173.2	2	88.511249	KEEP	0	1	31	305	10380	GG	1	1	0		-	63	60	2300	0	0	174.192692	504	60	17925	1124	ENST00000405201.1	0.111111	1
SCARB1	949	__UNKNOWN__	__UNKNOWN__	12	125298849	125298849	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:125298849C>A	ENST00000261693.6	-	4	655	c.529G>T	c.(529-531)Ggt>Tgt	p.G177C	SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000546215.1_Missense_Mutation_p.G177C|SCARB1_ENST00000541205.1_Missense_Mutation_p.G136C|SCARB1_ENST00000540495.1_Missense_Mutation_p.G140C|SCARB1_ENST00000339570.5_Missense_Mutation_p.G177C|SCARB1_ENST00000544327.1_Missense_Mutation_p.G123C|SCARB1_ENST00000415380.2_Missense_Mutation_p.G177C|SCARB1_ENST00000376788.1_Missense_Mutation_p.G77C	NM_005505.4	NP_005496.4	Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	177		NA			adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	ATGATCTCACCCACAGTGCGG	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													159	132	141	NA		NA	NA	12		NA											NA				125298849		2203	4300	6503	SO:0001583	missense			Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060	949			1664	protein-coding gene	gene with protein product		601040	CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1	CD36L1	NA	7689561	Standard	NM_005505	NM_001082959	NA	Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000261693.6:c.529G>T	chr12.hg19:g.125298849C>A	ENSP00000261693:p.Gly177Cys	NA	F8W8N0|Q14016|Q52LZ5|Q6KFX4	hg19	CCDS9259.1	0.02	2.010185	CACxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.60	1.687978	0.29962	.	.	ENSG00000073060	ENST00000339570;ENST00000415380;ENST00000261693;ENST00000376788;ENST00000546215;ENST00000541205;ENST00000544327;ENST00000540495	T;T;T;T;T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73;-0.73	5.25	2.45	0.29901	.	0.326617	0.36932	N	0.002321	D	0.84261	0.5433	M	0.91510	3.215	0.27557	N	0.950315	D;D;D;D;D;D	0.76494	0.999;0.977;0.999;0.999;0.996;0.994	D;D;D;D;D;P	0.71870	0.963;0.914;0.975;0.975;0.938;0.902	T	0.76591	-0.2903	10	0.59425	D	0.04	-16.9015	9.3243	0.37984	0.0:0.7461:0.0:0.2539	.	136;177;177;177;177;177	B3KW46;B7ZKQ9;B4E3I1;Q8WTV0;F8W8N0;Q8WTV0-2	.;.;.;SCRB1_HUMAN;.;.	C	177;177;177;77;177;136;123;140	ENSP00000343795:G177C;ENSP00000414979:G177C;ENSP00000261693:G177C;ENSP00000365984:G77C;ENSP00000442862:G177C;ENSP00000446107:G136C;ENSP00000444851:G123C;ENSP00000443286:G140C	ENSP00000261693:G177C	G	-	1	0	SCARB1	123864802	0.025000	0.19082	0.006000	0.13384	0.044000	0.14063	1.869000	0.39519	0.617000	0.30160	0.561000	0.74099	GGT	NOVEL	SCARB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400166.1	0	7.523802	KEEP	0	0	0	25	849	CC	0.999931	0.999893	0		-	26	60	933	0	0	80.818402	74	60	2665	160	ENST00000261693.6	0.26	0.999962
DHX37	57647	__UNKNOWN__	__UNKNOWN__	12	125432578	125432578	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:125432578C>A	ENST00000544745.1	-	23	2910	c.2801G>T	c.(2800-2802)aGg>aTg	p.R934M	DHX37_ENST00000308736.2_Intron			Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	0		NA					ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		AAGCCCCTGCCTCAGTGACCC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													40	40	40	NA		NA	NA	12		NA											NA				125432578		1568	3582	5150	SO:0001583	missense			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990	57647		DEAH-boxes	17210	protein-coding gene	gene with protein product		NA	DEAD/DEAH box helicase DDX37	DDX37	NA	10819331	Standard	NM_032656	NM_032656	NA	Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000544745.1:c.2801G>T	chr12.hg19:g.125432578C>A	ENSP00000439009:p.Arg934Met	NA	Q9BUI7|Q9P211	hg19		0.02	6.88894	TGCxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.585	-0.530633	0.04112	.	.	ENSG00000150990	ENST00000544745	T	0.03212	4.01	2.45	1.53	0.23141	.	.	.	.	.	T	0.06050	0.0157	.	.	.	0.09310	N	1	P	0.50528	0.936	P	0.47162	0.54	T	0.33752	-0.9856	8	0.46703	T	0.11	.	9.8927	0.41300	0.0:0.8762:0.0:0.1238	.	934	F5H3Y4	.	M	934	ENSP00000439009:R934M	ENSP00000439009:R934M	R	-	2	0	DHX37	123998531	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.166000	0.09954	0.148000	0.19059	-1.598000	0.00824	AGG	NOVEL	DHX37-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000400197.1	0	10.233424	KEEP	0	0	0	34	1216	CC	0.999998	0.999998	0		-	22	60	796	1	0	61.779515	146	70	5383	258	ENST00000544745.1	0.130952	1
DHX37	57647	__UNKNOWN__	__UNKNOWN__	12	125438714	125438714	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:125438714G>A	ENST00000544745.1	-	16	1967	c.1858C>T	c.(1858-1860)Cgg>Tgg	p.R620W	DHX37_ENST00000308736.2_Missense_Mutation_p.R833W			Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	833	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.	NA					ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		ACCCGGGCCCGCTTGCTCTTC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	36	34	NA		NA	NA	12		NA											NA				125438714		2203	4300	6503	SO:0001583	missense			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990	57647		DEAH-boxes	17210	protein-coding gene	gene with protein product		NA	DEAD/DEAH box helicase DDX37	DDX37	NA	10819331	Standard	NM_032656	NM_032656	NA	Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000544745.1:c.1858C>T	chr12.hg19:g.125438714G>A	ENSP00000439009:p.Arg620Trp	NA	Q9BUI7|Q9P211	hg19		0.02	14.40819	CCCxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.95	3.732206	0.69189	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.30448	1.53;1.53	5.33	4.36	0.52297	Helicase-associated domain (2);	0.193729	0.46758	D	0.000273	T	0.49029	0.1533	M	0.66939	2.045	0.35486	D	0.798536	D	0.89917	1.0	D	0.65987	0.94	T	0.61720	-0.7005	10	0.87932	D	0	-5.9232	10.7681	0.46305	0.0:0.0:0.5726:0.4274	.	833	Q8IY37	DHX37_HUMAN	W	833;620	ENSP00000311135:R833W;ENSP00000439009:R620W	ENSP00000311135:R833W	R	-	1	2	DHX37	124004667	1.000000	0.71417	0.979000	0.43373	0.751000	0.42716	5.274000	0.65569	2.489000	0.83994	0.455000	0.32223	CGG	NOVEL	DHX37-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000400197.1	1	25.530737	KEEP	0	0	0	85	2843	GG	1	1	0		-	88	60	3079	0	0	270.053692	219	60	7534	497	ENST00000544745.1	0.286645	1
PIWIL1	9271	__UNKNOWN__	__UNKNOWN__	12	130839585	130839585	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:130839585T>C	ENST00000245255.3	+	11	1561					NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	NA		NA			gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		AGGGTTTCAGTTTTGTGTTTA	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													145	144	144	NA		NA	NA	12		NA											NA				130839585		2203	4300	6503	SO:0001627	intron_variant			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207	9271		Argonaute/PIWI family	9007	protein-coding gene	gene with protein product		605571	piwi (Drosophila)-like 1, piwi-like 1 (Drosophila)		NA	9851978, 12906857	Standard		NM_004764	NA	Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.1289+35T>C	chr12.hg19:g.130839585T>C		NA	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	hg19	CCDS9268.1	0.02	4.567622	CAGxTTT	COVERED																																																																																			NOVEL	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399510.1	7	7.52171	KEEP	0	0	0	25	807	TT	0.999957	0.999957	0		+	10	60	394	0	0	28.247916	139	60	5012	207	ENST00000245255.3	0.067114	1
RAN	5901	__UNKNOWN__	__UNKNOWN__	12	131357706	131357706	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:131357706A>T	ENST00000543796.1	+	4	505				RAN_ENST00000392367.3_Intron|RAN_ENST00000254675.3_Intron|RAN_ENST00000541630.1_Intron|RAN_ENST00000392369.2_Intron			P62826	RAN_HUMAN	RAN, member RAS oncogene family	NA		NA			actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		ACGGTTTTTGAGAGGTTTTGT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													85	96	92	NA		NA	NA	12		NA											NA				131357706		2203	4300	6503	SO:0001627	intron_variant			M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341	5901			9846	protein-coding gene	gene with protein product		601179			NA	8421051	Standard	NM_006325	XM_005253592	NA	Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.247+33A>T	chr12.hg19:g.131357706A>T		NA	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	hg19	CCDS9271.1	0.02	13.431529	TTGxGAG	COVERED																																																																																			NOVEL	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259441.2	4	53.565243	KEEP	0	0	0	178	5797	AA	1	1	0		+	27	60	997	0	0	72.08224	301	60	11293	656	ENST00000543796.1	0.082317	1
ULK1	8408	__UNKNOWN__	__UNKNOWN__	12	132399383	132399383	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:132399383G>C	ENST00000321867.4	+	17	1724					NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	NA		NA			autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GCCTTGGGTTGGCACCCCGGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169	8408			12558	protein-coding gene	gene with protein product	ATG1 autophagy related 1 homolog (S. cerevisiae)	603168	unc-51 (C. elegans)-like kinase 1, unc-51-like kinase 1 (C. elegans)		NA	9693035	Standard		NM_003565	NA	Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.1374-245G>C	chr12.hg19:g.132399383G>C		NA	Q9UQ28	hg19	CCDS9274.1	0.02	1.9684	GTTxGCA	COVERED																																																																																			NOVEL	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397769.3	2	5.355212	KEEP	0	0	0	18	599	GG	0.999859	0.999266	0		+	4	60	149	0	0	9.869786	78	60	2775	114	ENST00000321867.4	0.04878	0.999407
FBRSL1	57666	__UNKNOWN__	__UNKNOWN__	12	133151017	133151017	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:133151017G>C	ENST00000434748.2	+	12	2717	c.1697G>C	c.(1696-1698)aGt>aCt	p.S566T	FBRSL1_ENST00000261673.6_Missense_Mutation_p.S493T	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	566		NA					poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						GACAGCAGGAGTCTGCAGAAA	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													27	33	31	NA		NA	NA	12		NA											NA				133151017		692	1591	2283	SO:0001583	missense				CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787	57666			29308	protein-coding gene	gene with protein product		NA			NA	10997877	Standard		NM_001142641	NA	Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.1697G>C	chr12.hg19:g.133151017G>C	ENSP00000396160:p.Ser566Thr	NA	Q86XQ1	hg19	CCDS45010.1	0.02	9.820014	GGAxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.048	-1.260610	0.01445	.	.	ENSG00000112787	ENST00000434748;ENST00000261673	T;T	0.29397	1.57;1.57	3.23	-6.46	0.01908	.	1.049290	0.07559	U	0.916788	T	0.12817	0.0311	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34004	-0.9846	10	0.13108	T	0.6	13.0429	6.6342	0.22874	0.188:0.4701:0.342:0.0	.	566	Q9HCM7	FBSL_HUMAN	T	566;493	ENSP00000396160:S566T;ENSP00000261673:S493T	ENSP00000261673:S493T	S	+	2	0	FBRSL1	131661090	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.726000	0.00808	-1.223000	0.02584	-0.350000	0.07774	AGT	NOVEL	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397404.2	0	21.065391	KEEP	0	0	0	70	2410	GG	1	1	0		+	50	60	1773	0	0	149.958269	170	60	6107	355	ENST00000434748.2	0.227273	1
GOLGA3	2802	__UNKNOWN__	__UNKNOWN__	12	133360910	133360910	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr12:133360910A>T	ENST00000450791.2	-	15	3307				GOLGA3_ENST00000537452.1_Intron|GOLGA3_ENST00000204726.3_Intron|GOLGA3_ENST00000456883.2_Intron|GOLGA3_ENST00000545875.1_Intron			Q08378	GOGA3_HUMAN	golgin A3	NA		NA			intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GCCAAGATGGAACGGGCGCTT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													68	62	64	NA		NA	NA	12		NA											NA				133360910		2203	4300	6503	SO:0001627	intron_variant			AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615	2802			4426	protein-coding gene	gene with protein product	SY2/SY10 protein, Golgi complex-associated protein of 170 kD	602581	golgi autoantigen, golgin subfamily a, 3		NA	8315394, 15829563	Standard	NM_005895	NM_001172557	NA	Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.3124-17T>A	chr12.hg19:g.133360910A>T		NA	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	hg19	CCDS9281.1	0.02	4.202659	TGGxACG	COVERED																																																																																			NOVEL	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397569.2	2	7.216589	KEEP	0	0	0	24	688	AA	0.999909	0.999903	0		-	56	60	1845	0	0	177.802681	55	60	1917	150	ENST00000450791.2	0.504505	0.999994
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	19778601	19778601	__UNKNOWN__	IGR	SNP	G	G	A	rs141790008		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:19778601G>A			NA	NA				RP11-408E5.4 (17105 upstream) : RP11-408E5.5 (58335 downstream)						NA		NA									NA						ATTCATACCCGTCATTGGAGG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.19778601G>A		NA		hg19		0.02	6.619161	CCCxTCA	COVERED																																																																																			NOVEL					0			4	7.222042	KEEP	11	0	0	24	804	GG	0.999931	0.999931	0			30	40	1066	0	0	86.018807	146	51	5357	306		0.170455	1
TPTE2	93492	__UNKNOWN__	__UNKNOWN__	13	20077352	20077352	__UNKNOWN__	Intron	SNP	T	T	C	rs201812089	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:20077352T>C	ENST00000382978.1	-	1	54				TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000382977.4_Intron|TPTE2_ENST00000400103.2_Intron|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000400230.2_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GACACATGTATGCATAACTCA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													165	135	145	NA		NA	NA	13		NA											NA				20077352		2203	4300	6503	SO:0001627	intron_variant			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958	93492		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	17299	protein-coding gene	gene with protein product		606791			NA	11716755, 12717346, 15057823	Standard	NM_199254	NM_130785	NA	Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000382978.1:c.11+11A>G	chr13.hg19:g.20077352T>C		NA	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	hg19		0.02	19.343398	GTAxGCA	COVERED																																																																																			NOVEL	TPTE2-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000044022.1	7	10.999821	KEEP	1	2	70	61	1931	TT	1	1	0		-	16	52	567	0	0	34.495467	456	60	17046	711	ENST00000382978.1	0.033898	1
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20277061	20277061	__UNKNOWN__	3'UTR	SNP	G	G	A	rs151279350		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:20277061G>A	ENST00000338910.4	-	0	1985					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AGATTTCACAGTACTATGGAA	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.*254C>T	chr13.hg19:g.20277061G>A		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	8.983362	ACAxTAC	COVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	9	14.115608	KEEP	15	2	63	69	2433	GG	1	1	0		-	8	27	295	0	0	17.993802	239	60	9105	378	ENST00000338910.4	0.032389	1
ZMYM2	7750	__UNKNOWN__	__UNKNOWN__	13	20661521	20661521	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:20661521G>A	ENST00000382874.2	+	0	5691				ZMYM2_ENST00000382869.3_3'UTR	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		CAAAGTGCTAGCTGCAAATTA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741	7750		Zinc fingers, MYM type	12989	protein-coding gene	gene with protein product		602221	zinc finger protein 198	ZNF198	NA	9499416, 9425908	Standard	NM_003453	XM_005266517	NA	Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.*1367G>A	chr13.hg19:g.20661521G>A		NA	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	hg19	CCDS45016.1	0.02	6.612594	CTAxCTG	COVERED																																																																																			NOVEL	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044051.2	5	11.136536	KEEP	0	0	0	37	1333	GG	1	1	0		+	11	60	385	0	0	26.546708	143	60	5416	228	ENST00000382874.2	0.071429	1
C1QTNF9B	387911	__UNKNOWN__	__UNKNOWN__	13	24468329	24468329	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs4067961	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:24468329A>G	ENST00000382140.2	-	4	238	c.178T>C	c.(178-180)Tgt>Cgt	p.C60R	C1QTNF9B_ENST00000382057.3_Missense_Mutation_p.C60R|C1QTNF9B_ENST00000382137.3_Missense_Mutation_p.C60R|C1QTNF9B_ENST00000556521.1_5'UTR|C1QTNF9B_ENST00000382145.1_Missense_Mutation_p.C60R|C1QTNF9B-AS1_ENST00000417034.1_RNA			B2RNN3	C1T9B_HUMAN	C1q and tumor necrosis factor related protein 9B	60	Collagen-like 1.	NA				collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(1)	6						CTGCCAGGACATCCTGGTTCT	0.478	NA	NA											G|||	1779	0.355232	0.3903	0.3775	5008	,	,	NA	17613	0.4573	NA	0.3867	False	NA	,,,	NA	NA	NA	2504	0.1544	NA	NA	NA						NA		NA				0								G	ARG/CYS	677,3711		241,195,1758	109	103	105	NA	178	3.8	0.7	13	dbSNP_108	105	969,7593		354,261,3666	no	missense	C1QTNF9B	NM_001007537.1	180	595,456,5424	GG,GA,AA	NA	11.3174,15.4284,12.7104	benign	60/334	24468329	1646,11304	2194	4281	6475	SO:0001583	missense			BC110413	CCDS31947.1	13q12.12	2011-05-08			ENSG00000205863	ENSG00000205863	387911			34072	protein-coding gene	gene with protein product		614148			NA	17544811	Standard	NM_001007537	NM_001007537	NA	Approved	CTRP9B	uc010tcv.1	B2RNN3	OTTHUMG00000016570	ENST00000382140.2:c.178T>C	chr13.hg19:g.24468329A>G	ENSP00000371575:p.Cys60Arg	NA	A2A3T6|B9EH31|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	hg19	CCDS31947.1	0.02	6.523218	GACxTCC	COVERED	510	0.23351648351648352	125	0.2540650406504065	64	0.17679558011049723	180	0.3146853146853147	141	0.18601583113456466	N	0.018	-1.480394	0.01027	0.154284	0.113174	ENSG00000205863	ENST00000382145;ENST00000382137;ENST00000382140;ENST00000382057	D;D;D;D	0.93076	-3.16;-3.16;-3.16;-3.16	3.83	3.83	0.44106	.	0.566602	0.19325	N	0.117030	T	0.00012	0.0000	N	0.00521	-1.4	0.38100	P	0.06275399999999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14337	-1.0476	9	0.13470	T	0.59	.	7.0111	0.24863	0.0925:0.0:0.7391:0.1685	rs4067961;rs12866014	60;60	B2RNN3;B2RNN3-2	C1T9B_HUMAN;.	R	60	ENSP00000371580:C60R;ENSP00000371572:C60R;ENSP00000371575:C60R;ENSP00000371489:C60R	ENSP00000371489:C60R	C	-	1	0	C1QTNF9B	23366329	0.841000	0.29509	0.693000	0.30195	0.010000	0.07245	1.660000	0.37397	0.766000	0.33244	-0.665000	0.03846	TGT	NOVEL	C1QTNF9B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044162.3	1	10.530614	KEEP	15	0	0	35	1071	AA	0.999999	0.999999	0		-	37	40	1338	0	0	111.067854	150	60	5491	292	ENST00000382140.2	0.197861	1
RP11-307N16.6	0	__UNKNOWN__	__UNKNOWN__	13	24890337	24890337	__UNKNOWN__	Intron	SNP	C	C	G	rs9511193|rs386769039	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:24890337C>G	ENST00000382141.4	+	14	4058				C1QTNF9_ENST00000332018.4_Intron|C1QTNF9-AS1_ENST00000449656.1_RNA|C1QTNF9_ENST00000382071.2_Intron						NA		NA									NA						GGCTGCCTTTCAACTTCTCTC	0.517	NA	NA											C|||	1184	0.236422	0.2534	0.2522	5008	,	,	NA	19278	0.1905	NA	0.3072	False	NA	,,,	NA	NA	NA	2504	0.1769	NA	NA	NA						NA		NA				0													83	70	74	NA		NA	NA	13		NA											NA				24890337		2167	4250	6417	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000382141.4:c.3315+30C>G	chr13.hg19:g.24890337C>G		NA		hg19		0.02	4.255859	TTTxAAC	COVERED																																																																																			NOVEL	RP11-307N16.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000472022.1	3	3.009384	KEEP	0	0	0	10	341	CC	0.992708	0.992708	0		+	5	40	189	0	0	11.969064	132	60	5018	167	ENST00000382141.4	0.036496	1
ATP12A	479	__UNKNOWN__	__UNKNOWN__	13	25284942	25284942	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:25284942C>A	ENST00000381946.3	+	21	3077	c.2910C>A	c.(2908-2910)atC>atA	p.I970I	ATP12A_ENST00000218548.6_Silent_p.I976I			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	970		NA			ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		ATAAAGTCATCTGGGTGGGGA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(156;1582 1935 18898 22665 26498)					NA		NA				0													135	117	123	NA		NA	NA	13		NA											NA				25284942		2203	4300	6503	SO:0001819	synonymous_variant			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	479	3.6.3.10	ATPases / P-type	13816	protein-coding gene	gene with protein product	ATPase, Na+K+ transporting, alpha-1 polypeptide-like, potassium-transporting ATPase alpha chain 2, proton pump, non-gastric H(+)/K(+) ATPase alpha subunit, sodium/potassium ATPase, alpha polypeptide-like	182360	ATPase, Na+/K+ transporting, alpha polypeptide-like 1	ATP1AL1	NA	8838794, 2842249	Standard	NM_001676	NM_001676	NA	Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2910C>A	chr13.hg19:g.25284942C>A		NA	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	hg19	CCDS31948.1	0.02	4.320629	CATxTGG	COVERED																																																																																			NOVEL	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044199.1	0	6.62076	KEEP	0	0	0	22	766	CC	0.999879	0.999879	0		+	38	60	1372	0	0	119.374668	105	60	4054	218	ENST00000381946.3	0.265734	1
WASF3	10810	__UNKNOWN__	__UNKNOWN__	13	27260435	27260435	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:27260435T>A	ENST00000335327.5	+	0	2140				WASF3_ENST00000361042.4_3'UTR	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	NA		NA			actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		TTTGTTTTTTTAAAGGATGTG	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970	10810			12734	protein-coding gene	gene with protein product		605068			NA	10381382	Standard		NM_006646	NA	Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.*453T>A	chr13.hg19:g.27260435T>A		NA	O94974|Q86VQ2	hg19	CCDS9318.1	0.02	1.646489	TTTxAAA	COVERED																																																																																			NOVEL	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044258.1	5	5.115799	KEEP	0	0	0	17	542	TT	0.999859	0.999789	0		+	7	60	236	0	0	16.064615	89	60	3157	137	ENST00000335327.5	0.072917	0.99993
PAN3	255967	__UNKNOWN__	__UNKNOWN__	13	28834653	28834653	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:28834653G>A	ENST00000380958.3	+	8	1470	c.1318G>A	c.(1318-1320)Gca>Aca	p.A440T	PAN3_ENST00000282391.5_Missense_Mutation_p.A128T|PAN3_ENST00000399613.1_Missense_Mutation_p.A240T	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit	NA		NA						p.A240T(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GAAAGCAAACGCACCTTCCTT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	large_intestine(1)											161	139	146	NA		NA	NA	13		NA											NA				28834653		2203	4300	6503	SO:0001583	missense			AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520	255967			29991	protein-coding gene	gene with protein product		NA	PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)		NA	14583602	Standard	NM_175854	NM_175854	NA	Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.1318G>A	chr13.hg19:g.28834653G>A	ENSP00000370345:p.Ala440Thr	NA		hg19	CCDS9329.2	0.02	10.9963	AACxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	34	5.314056	0.95655	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.07567	3.18;3.18;3.18	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.19087	0.0458	L	0.31752	0.955	0.80722	D	1	P;D;D;D	0.76494	0.608;0.998;0.999;0.989	B;P;D;P	0.76575	0.245;0.748;0.988;0.668	T	0.07809	-1.0753	10	0.18710	T	0.47	-14.2913	19.8535	0.96748	0.0:0.0:1.0:0.0	.	440;440;128;386	Q58A45-4;Q58A45;Q58A45-2;Q58A45-3	.;PAN3_HUMAN;.;.	T	440;240;128	ENSP00000370345:A440T;ENSP00000382522:A240T;ENSP00000282391:A128T	ENSP00000282391:A128T	A	+	1	0	PAN3	27732653	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.605000	0.98321	2.686000	0.91538	0.585000	0.79938	GCA	NOVEL	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044318.4	3	20.766501	KEEP	0	0	0	69	2398	GG	1	1	0		+	9	60	336	0	0	20.980828	247	60	8710	430	ENST00000380958.3	0.035156	1
UBL3	5412	__UNKNOWN__	__UNKNOWN__	13	30340045	30340045	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:30340045C>T	ENST00000380680.4	-	0	2846					NM_007106.3	NP_009037.1	O95164	UBL3_HUMAN	ubiquitin-like 3	NA		NA				extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				large_intestine(3)|lung(1)	4		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		TGTCAGCCTGCAACTTCATTT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF044221	CCDS9334.1	13q12-q13	2008-07-18			ENSG00000122042	ENSG00000122042	5412			12504	protein-coding gene	gene with protein product		604711		PNSC1	NA	10375635	Standard	NM_007106	NM_007106	NA	Approved	HCG-1, DKFZP434K151, FLJ32018	uc001usp.3	O95164	OTTHUMG00000016661	ENST00000380680.4:c.*1347G>A	chr13.hg19:g.30340045C>T		NA	B2R4J1|Q5RL72|Q5VZS0|Q6FIG8|Q96SG7	hg19	CCDS9334.1	0.02	2.003441	CTGxAAC	COVERED																																																																																			NOVEL	UBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044342.1	4	7.17735	KEEP	0	0	0	24	827	CC	0.999909	0.998902	0		-	5	60	187	0	0	13.021356	73	70	2782	120	ENST00000380680.4	0.064103	0.998993
HMGB1	3146	__UNKNOWN__	__UNKNOWN__	13	31033915	31033915	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:31033915T>C	ENST00000405805.1	-	0	3167							P09429	HMGB1_HUMAN	high mobility group box 1	NA		NA			apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		TGCTAAGAGGTATTATTAGAA	0.259	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403	3146		High-mobility group / Canonical	4983	protein-coding gene	gene with protein product	high mobility group box 1, Sulfoglucuronyl carbohydrate binding protein, Amphoterin, high mobility group protein 1	163905	high-mobility group (nonhistone chromosomal) protein 1, high-mobility group box 1	HMG1	NA	8661151, 11279268	Standard	NM_002128	NM_002128	NA	Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.*1579A>G	chr13.hg19:g.31033915T>C		NA	A5D8W9|Q14321|Q5T7C3|Q6IBE1	hg19	CCDS9335.1	0.02	4.974635	AGGxATT	COVERED																																																																																			NOVEL	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000303998.2	1	17.146997	KEEP	0	0	0	57	1741	TT	1	0.999996	0		-	21	60	818	0	0	68.170356	93	60	3291	212	ENST00000405805.1	0.184211	0.999996
N4BP2L2	10443	__UNKNOWN__	__UNKNOWN__	13	33091315	33091315	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:33091315A>T	ENST00000267068.3	-	0	2540				N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Intron|N4BP2L2_ENST00000399396.3_Intron	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	NA		NA			negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		GATGATAACTATGTATGCATT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754	10443			26916	protein-coding gene	gene with protein product	phosphonoformate immuno-associated protein 5	615788			NA	8812419	Standard	NM_014887	NM_014887	NA	Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.*624T>A	chr13.hg19:g.33091315A>T		NA	A3KME8	hg19	CCDS9346.1	0.02	4.566354	ACTxTGT	COVERED																																																																																			NOVEL	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044421.1	3	7.220455	KEEP	0	0	0	24	725	AA	0.999909	0.999906	0		-	21	60	753	0	0	61.583054	94	60	3368	160	ENST00000267068.3	0.182609	0.999997
STARD13	90627	__UNKNOWN__	__UNKNOWN__	13	33678877	33678877	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:33678877G>A	ENST00000336934.5	-	0	4311				STARD13_ENST00000399365.3_3'UTR|STARD13_ENST00000255486.4_3'UTR	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		TTGACTTGGGGTCTGTAGTGA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121	90627		Rho GTPase activating proteins, StAR-related lipid transfer (START) domain containing	19164	protein-coding gene	gene with protein product		609866	START domain containing 13, long intergenic non-protein coding RNA 464	LINC00464	NA	8812419	Standard	NM_001243466	NM_178006	NA	Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.*853C>T	chr13.hg19:g.33678877G>A		NA	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	hg19	CCDS9348.1	0.02	4.240571	GGGxTCT	COVERED																																																																																			NOVEL	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276118.2	3	6.320329	KEEP	0	0	0	21	733	GG	0.999869	0.999867	0		-	10	60	344	0	0	24.305205	108	60	3955	172	ENST00000336934.5	0.084746	0.999998
SUPT20H	55578	__UNKNOWN__	__UNKNOWN__	13	37619329	37619329	__UNKNOWN__	Intron	SNP	G	G	A	rs567556501		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:37619329G>A	ENST00000350612.6	-	6	513				SUPT20H_ENST00000356185.3_Intron|SUPT20H_ENST00000475892.1_Intron|SUPT20H_ENST00000542180.1_Intron|SUPT20H_ENST00000464744.1_Intron|SUPT20H_ENST00000360252.4_Intron|SUPT20H_ENST00000470359.2_Intron	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	NA		NA			autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)				NA						TAAAAAAACCGCACATCCTGC	0.398	NA	NA											G|||	1	0.000199681	0	0.0014	5008	,	,	NA	16876	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710	55578			20596	protein-coding gene	gene with protein product	p38 interacting protein, transcription factor (p38 interacting protein)	613417	chromosome 13 open reading frame 19, family with sequence similarity 48, member A	C13orf19, FAM48A	NA	12070015 , 16685401	Standard	NM_017569	NM_001278480	NA	Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.292+54C>T	chr13.hg19:g.37619329G>A		NA	E7ER46|Q71RF3|Q9Y6A6	hg19	CCDS31959.1	0.02	4.259558	ACCxCAC	COVERED																																																																																			NOVEL	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354766.1	1	11.465766	KEEP	0	1	25	47	1497	GG	1	1	0		-	6	60	219	0	0	13.82942	144	70	4675	210	ENST00000350612.6	0.04	1
FREM2	341640	__UNKNOWN__	__UNKNOWN__	13	39433541	39433541	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:39433541G>A	ENST00000280481.7	+	14	7549	c.7333G>A	c.(7333-7335)Ggt>Agt	p.G2445S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2445		NA			cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GGGCCCTGACGGTGTGACCAG	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													162	139	147	NA		NA	NA	13		NA											NA				39433541		2203	4300	6503	SO:0001583	missense			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893	341640			25396	protein-coding gene	gene with protein product		608945			NA	15345741	Standard	NM_207361	NM_207361	NA	Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.7333G>A	chr13.hg19:g.39433541G>A	ENSP00000280481:p.Gly2445Ser	NA	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	hg19	CCDS31960.1	0.02	4.676334	GACxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	32	5.140013	0.94560	.	.	ENSG00000150893	ENST00000280481	D	0.85171	-1.95	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.92916	0.7746	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92017	0.5623	10	0.54805	T	0.06	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	2445;2445	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	S	2445	ENSP00000280481:G2445S	ENSP00000280481:G2445S	G	+	1	0	FREM2	38331541	1.000000	0.71417	0.956000	0.39512	0.450000	0.32258	7.987000	0.88182	2.890000	0.99128	0.650000	0.86243	GGT	NOVEL	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044599.2	0	4.95112	KEEP	0	1	33	28	966	GG	0.999997	0.999997	0		+	46	60	1735	0	0	155.776795	101	60	3492	220	ENST00000280481.7	0.312925	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	52396279	52396279	__UNKNOWN__	IGR	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:52396279T>G			NA	NA				RP11-327P2.5 (8923 upstream) : CCDC70 (39837 downstream)						NA		NA									NA						CATTCCTACATAGGGCAAACA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.52396279T>G		NA		hg19		0.02	2.303032	ACAxAGG	COVERED																																																																																			NOVEL					0			0	15.347029	KEEP	0	0	0	51	1628	TT	1	0.998993	0			41	60	1576	0	0	153.725569	37	60	1376	176		0.525641	0.998993
NEK3	4752	__UNKNOWN__	__UNKNOWN__	13	52722538	52722538	__UNKNOWN__	Intron	SNP	C	C	T	rs553893208		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:52722538C>T	ENST00000400357.2	-	7	1897				NEK3_ENST00000452082.2_Intron|NEK3_ENST00000378101.2_Intron|NEK3_ENST00000339406.3_Intron			P51956	NEK3_HUMAN	NIMA-related kinase 3	NA		NA			mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		CCATTTTGCACGCCATACTTA	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													168	150	156	NA		NA	NA	13		NA											NA				52722538		1921	4140	6061	SO:0001627	intron_variant			AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	4752	2.7.11.1		7746	protein-coding gene	gene with protein product	serine/threonine-protein kinase NEK3, phosphorylase B kinase kinase, glycogen synthase A kinase, hydroxyalkyl-protein kinase	604044	NIMA (never in mitosis gene a)-related kinase 3		NA	8274451, 7522034	Standard		NM_002498	NA	Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.603+11G>A	chr13.hg19:g.52722538C>T		NA	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	hg19	CCDS53871.1	0.02	7.232361	GCAxGCC	COVERED																																																																																			NOVEL	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045047.3	0	20.764724	KEEP	0	0	0	69	2369	CC	1	1	0		-	88	60	3304	0	0	323.543093	75	60	2682	295	ENST00000400357.2	0.539877	1
PCDH17	27253	__UNKNOWN__	__UNKNOWN__	13	58206837	58206837	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:58206837C>T	ENST00000377918.3	+	1	183	c.157C>T	c.(157-159)Cgc>Tgc	p.R53C		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	53	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		GCCTGCAGAGCGCGGCGGCGG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(72;952 1291 1619 12849 33676)					NA		NA				0													22	24	23	NA		NA	NA	13		NA											NA				58206837		2203	4299	6502	SO:0001583	missense			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946	27253		Cadherins / Protocadherins : Non-clustered	14267	protein-coding gene	gene with protein product		611760			NA	10835267	Standard	NM_001040429	NM_001040429	NA	Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.157C>T	chr13.hg19:g.58206837C>T	ENSP00000367151:p.Arg53Cys	NA	A8K1R5|Q5VVW9|Q5VVX0	hg19	CCDS31986.1	0.02	9.603331	GAGxGCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.09	2.133954	0.37630	.	.	ENSG00000118946	ENST00000377918	T	0.54071	0.59	5.55	4.69	0.59074	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.64402	D	0.000004	T	0.52058	0.1711	N	0.22421	0.69	0.53005	D	0.999965	D;D	0.65815	0.987;0.995	B;P	0.57548	0.254;0.823	T	0.49570	-0.8926	9	.	.	.	.	13.4978	0.61436	0.2842:0.7158:0.0:0.0	.	53;53	O14917-2;O14917	.;PCD17_HUMAN	C	53	ENSP00000367151:R53C	.	R	+	1	0	PCDH17	57104838	1.000000	0.71417	0.999000	0.59377	0.562000	0.35680	2.526000	0.45607	1.543000	0.49345	0.655000	0.94253	CGC	NOVEL	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045139.1	1	46.286253	KEEP	0	0	0	154	4997	CC	1	1	0		+	119	60	4103	0	0	400.470656	103	60	3422	491	ENST00000377918.3	0.536036	1
UCHL3	7347	__UNKNOWN__	__UNKNOWN__	13	76164052	76164052	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:76164052A>G	ENST00000377595.3	+	7	504				UCHL3_ENST00000606347.1_Intron|RP11-29G8.3_ENST00000563635.1_RNA	NM_001270952.1|NM_006002.4	NP_001257881.1|NP_005993.1	P15374	UCHL3_HUMAN	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	NA		NA			protein catabolic process (GO:0030163)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|large_intestine(2)|lung(3)|skin(1)	7				GBM - Glioblastoma multiforme(99;0.0125)		TAAGTAAAATATTCTCTTTTT	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M30496	CCDS9453.1, CCDS73586.1	13q21.33	2008-02-05			ENSG00000118939	ENSG00000118939	7347	3.2.1.15		12515	protein-coding gene	gene with protein product		603090			NA	2530630	Standard	NM_006002	NM_001270952	NA	Approved		uc001vjq.4	P15374	OTTHUMG00000017090	ENST00000377595.3:c.475-4999A>G	chr13.hg19:g.76164052A>G		NA	B2R970|Q5TBK8|Q6IBE9	hg19	CCDS9453.1	0.02	-0.421095	AATxTTC	COVERED																																																																																			NOVEL	UCHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045292.2	1	7.523291	KEEP	0	0	0	25	799	AA	0.999931	0.948336	0		+	10	60	382	0	0	32.304274	38	60	1331	91	ENST00000377595.3	0.208333	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	79888426	79888426	__UNKNOWN__	IGR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:79888426T>A			NA	NA				LINC00331 (521984 upstream) : RBM26 (5662 downstream)						NA		NA									NA						TGTGAAAAAATTATGTTAAGA	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.79888426T>A		NA		hg19		0.02	2.094529	AAAxTAT	COVERED																																																																																			NOVEL					0			1	13.53947	KEEP	0	0	0	45	1407	TT	1	0.99911	0			8	60	305	0	0	23.070005	71	60	2531	134		0.101266	0.99911
ABCC4	10257	__UNKNOWN__	__UNKNOWN__	13	95858879	95858879	__UNKNOWN__	Silent	SNP	C	C	T	rs374882007	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:95858879C>T	ENST00000376887.4	-	8	1182	c.1068G>A	c.(1066-1068)acG>acA	p.T356T	ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000431522.1_Silent_p.T356T|ABCC4_ENST00000536256.1_Silent_p.T281T|ABCC4_ENST00000412704.1_Silent_p.T356T	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	356	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.	NA	T -> M (in dbSNP:rs11568701).		blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CCCCATACAGCGTCACTGCCA	0.552	NA	NA											c|||	2	0.000399361	0	0	5008	,	,	NA	20964	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0								T	,	1,4405	2.1+/-5.4	0,1,2202	111	95	100	NA	1068,1068	-9	0	13		100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ABCC4	NM_001105515.1,NM_005845.3	,	0,1,6502	TT,TC,CC	NA	0.0,0.0227,0.0077	,	356/860,356/1326	95858879	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257	10257		ATP binding cassette transporters / subfamily C	55	protein-coding gene	gene with protein product	canalicular multispecific organic anion transporter (ABC superfamily), bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4), multidrug resistance-associated protein 4, multispecific organic anion transporter B	605250			NA	8894702, 9661885	Standard	NM_005845	NM_005845	NA	Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.1068G>A	chr13.hg19:g.95858879C>T		NA	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	hg19	CCDS9474.1	0.02	4.467768	CAGxGTC	COVERED																																																																																			NOVEL	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045478.2	2	5.65136	KEEP	0	1	29	29	960	CC	0.999997	0.999997	0		-	44	60	1549	0	0	136.626152	105	60	3773	197	ENST00000376887.4	0.295302	1
FARP1	10160	__UNKNOWN__	__UNKNOWN__	13	99020337	99020337	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:99020337T>C	ENST00000319562.6	+	5	584				FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	NA		NA			dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			CACAAATCAGTAAATGCTTTA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													46	43	44	NA		NA	NA	13		NA											NA				99020337		2203	4300	6503	SO:0001627	intron_variant			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767	10160		Rho guanine nucleotide exchange factors, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Pleckstrin homology (PH) domain containing	3591	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 75	602654			NA	9425278	Standard	NM_005766	NM_005766	NA	Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.320-34T>C	chr13.hg19:g.99020337T>C		NA	Q5JVI9|Q6IQ29	hg19	CCDS9487.1	0.02	6.769747	CAGxAAA	COVERED																																																																																			NOVEL	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045541.3	4	11.732667	KEEP	0	0	0	39	1160	TT	1	1	0		+	17	60	647	0	0	47.831263	176	60	6144	254	ENST00000319562.6	0.088083	1
SLC15A1	6564	__UNKNOWN__	__UNKNOWN__	13	99379215	99379215	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:99379215C>T	ENST00000376503.5	-	2	60					NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	NA		NA			digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	GTCAGAGGGGCCATTCACCAA	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386	6564		Solute carriers	10920	protein-coding gene	gene with protein product	peptide transporter HPEPT1, bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1), solute carrier family 15 oligopeptide transporter member 1	600544			NA	7896779	Standard	NM_005073	NM_005073	NA	Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.5-102G>A	chr13.hg19:g.99379215C>T		NA	Q5VW82	hg19	CCDS9489.1	0.02	6.494422	GGGxCAT	COVERED																																																																																			NOVEL	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045560.3	0	5.7023	KEEP	0	0	0	19	641	CC	0.99986	0.99986	0		-	6	60	227	0	0	14.159574	173	60	6286	258	ENST00000376503.5	0.03352	1
CCDC168	643677	__UNKNOWN__	__UNKNOWN__	13	103383985	103383985	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:103383985C>A	ENST00000322527.2	-	1	5174	c.5175G>T	c.(5173-5175)caG>caT	p.Q1725H		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1725		NA									NA						TATTTTTAACCTGGGACTCAG	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													81	63	68	NA		NA	NA	13		NA											NA				103383985		692	1591	2283	SO:0001583	missense				CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820	643677			26851	protein-coding gene	gene with protein product		NA	chromosome 13 open reading frame 40	C13orf40	NA		Standard	NM_001146197	NM_001146197	NA	Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.5175G>T	chr13.hg19:g.103383985C>A	ENSP00000320232:p.Gln1725His	NA	Q8N800	hg19		0.02	23.068811	AACxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	5.743	0.321581	0.10845	.	.	ENSG00000175820	ENST00000322527	T	0.04317	3.65	3.92	-0.351	0.12602	.	.	.	.	.	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B	0.23735	0.09	B	0.26310	0.068	T	0.44528	-0.9322	9	0.62326	D	0.03	.	11.5372	0.50645	0.7202:0.2798:0.0:0.0	.	1725	Q8NDH2	CC168_HUMAN	H	1725	ENSP00000320232:Q1725H	ENSP00000320232:Q1725H	Q	-	3	2	CCDC168	102181986	0.005000	0.15991	0.004000	0.12327	0.029000	0.11900	0.013000	0.13310	-0.101000	0.12219	-0.158000	0.13435	CAG	NOVEL	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		7	21.066983	KEEP	0	0	0	70	2412	CC	1	1	0		-	155	60	5592	0	0	491.389809	393	60	14617	711	ENST00000322527.2	0.282847	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	103393643	103393643	__UNKNOWN__	IGR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:103393643G>A			NA	NA				CCDC168 (4484 upstream) : LINC00283 (1696 downstream)						NA		NA									NA						TTTTCTTGCTGTATTCACTGC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	34	37	NA		NA	NA	13		NA											NA				103393643		692	1590	2282	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.103393643G>A		NA		hg19		0.02	11.490857	GCTxTAT	COVERED																																																																																			NOVEL					0			8	15.350212	KEEP	0	0	0	51	1826	GG	1	1	0			70	60	2540	0	0	219.154795	209	60	7942	394		0.250896	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	103401746	103401746	__UNKNOWN__	IGR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:103401746G>C			NA	NA				LINC00283 (4172 upstream) : TEX30 (16593 downstream)						NA		NA									NA						CATATCTTCAGTGACTAAATT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													128	107	113	NA		NA	NA	13		NA											NA				103401746		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.103401746G>C		NA		hg19		0.02	14.896006	TCAxTGA	COVERED																																																																																			NOVEL					0			4	15.951327	KEEP	0	0	0	53	1899	GG	1	1	0			21	60	830	0	0	59.638037	290	60	11001	444		0.067524	1
ARGLU1	55082	__UNKNOWN__	__UNKNOWN__	13	107211856	107211856	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:107211856C>T	ENST00000400198.3	-	2	741	c.497G>A	c.(496-498)cGc>cAc	p.R166H	ARGLU1_ENST00000375926.1_Missense_Mutation_p.A16T	NM_018011.3	NP_060481.3	Q9NWB6	ARGL1_HUMAN	arginine and glutamate rich 1	166	Glu-rich.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)				large_intestine(1)|lung(5)|pancreas(1)	7	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TTCCATGATGCGTTTGGCTTC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													153	152	152	NA		NA	NA	13		NA											NA				107211856		1920	4134	6054	SO:0001583	missense			BC071587	CCDS41906.1	13q33.3	2011-10-03	2007-11-28		ENSG00000134884	ENSG00000134884	55082			25482	protein-coding gene	gene with protein product		614046			NA	21454576	Standard	NM_018011	NM_018011	NA	Approved	FLJ10154	uc001vqk.4	Q9NWB6	OTTHUMG00000017321	ENST00000400198.3:c.497G>A	chr13.hg19:g.107211856C>T	ENSP00000383059:p.Arg166His	NA	B4E0Y3|Q5T257|Q6IQ34	hg19	CCDS41906.1	0.02	38.215828	ATGxGTT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.8|26.8	4.770213|4.770213	0.90108|0.90108	.|.	.|.	ENSG00000134884|ENSG00000134884	ENST00000375926;ENST00000360629|ENST00000400198;ENST00000426600	.|.	.|.	.|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71074|0.71074	0.3297|0.3297	L|L	0.46157|0.46157	1.445|1.445	0.35632|0.35632	D|D	0.810307|0.810307	.|D	.|0.76494	.|0.999	.|D	.|0.74674	.|0.984	T|T	0.73799|0.73799	-0.3869|-0.3869	6|9	0.87932|0.38643	D|T	0|0.18	-4.5113|-4.5113	19.451|19.451	0.94867|0.94867	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|166	.|Q9NWB6	.|ARGL1_HUMAN	T|H	16|166;116	.|.	ENSP00000353844:A16T|ENSP00000383059:R166H	A|R	-|-	1|2	0|0	ARGLU1|ARGLU1	106009857|106009857	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.398000|7.398000	0.79919|0.79919	2.593000|2.593000	0.87608|0.87608	0.655000|0.655000	0.94253|0.94253	GCA|CGC	NOVEL	ARGLU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045727.1	6	68.316923	KEEP	0	0	0	227	7858	CC	1	1	0		-	55	60	1965	0	0	133.278875	831	60	29905	1313	ENST00000400198.3	0.062077	1
TNFSF13B	10673	__UNKNOWN__	__UNKNOWN__	13	108922361	108922361	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:108922361C>T	ENST00000375887.4	+	1	296	c.118C>T	c.(118-120)Cga>Tga	p.R40*	TNFSF13B_ENST00000430559.1_Nonsense_Mutation_p.R40*|TNFSF13B_ENST00000542136.1_Nonsense_Mutation_p.R40*	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	40		NA			B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	CCCCTCTGTCCGATCCTCCAA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													139	144	142	NA		NA	NA	13		NA											NA				108922361		2203	4300	6503	SO:0001587	stop_gained			AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524	10673		Tumor necrosis factor (ligand) superfamily, CD molecules	11929	protein-coding gene	gene with protein product		603969		TNFSF20	NA	10331498, 10359578	Standard		NM_006573	NA	Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.118C>T	chr13.hg19:g.108922361C>T	ENSP00000365048:p.Arg40*	NA	E0ADT7|Q6FHD6|Q7Z5J2	hg19	CCDS9509.1	0.02	9.797728	GTCxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.59	3.426778	0.62733	.	.	ENSG00000102524	ENST00000430559;ENST00000375887;ENST00000542136	.	.	.	4.72	-1.69	0.08186	.	1.258710	0.05638	N	0.582872	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	0.1824	6.7447	0.23454	0.0:0.5308:0.1251:0.3441	.	.	.	.	X	40	.	ENSP00000365048:R40X	R	+	1	2	TNFSF13B	107720362	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	-0.019000	0.12546	-0.351000	0.08249	0.650000	0.86243	CGA	NOVEL	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045739.3	4	11.435701	KEEP	0	0	0	38	1299	CC	1	1	0		+	37	60	1385	0	0	111.805821	197	60	6716	340	ENST00000375887.4	0.15812	1
COL4A1	1282	__UNKNOWN__	__UNKNOWN__	13	110853168	110853168	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:110853168G>A	ENST00000375820.4	-	20	1242				COL4A1_ENST00000543140.1_Intron	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	NA		NA			axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			AGGTGTGCAAGTATGCTATAA	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													85	81	83	NA		NA	NA	13		NA											NA				110853168		2203	4300	6503	SO:0001627	intron_variant			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498	1282		Collagens	2202	protein-coding gene	gene with protein product		120130			NA	3691802	Standard		NM_001845	NA	Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.1120+32C>T	chr13.hg19:g.110853168G>A		NA	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	hg19	CCDS9511.1	0.02	8.082217	CAAxTAT	COVERED																																																																																			NOVEL	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045759.3	0	11.136091	KEEP	0	0	0	37	1312	GG	1	1	0		-	9	60	318	0	0	19.511484	227	60	8601	311	ENST00000375820.4	0.038136	1
ADPRHL1	113622	__UNKNOWN__	__UNKNOWN__	13	114107633	114107633	__UNKNOWN__	Silent	SNP	G	G	A	rs537275759	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:114107633G>A	ENST00000375418.3	-	1	206	c.120C>T	c.(118-120)tcC>tcT	p.S40S		NM_138430.3	NP_612439.2	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1	40		NA			protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	11	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)			CCAGGCCCCCGGAACGTTGCA	0.597	NA	NA											G|||	2	0.000399361	0.0015	0	5008	,	,	NA	19195	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													128	119	122	NA		NA	NA	13		NA											NA				114107633		2203	4300	6503	SO:0001819	synonymous_variant			AJ313429	CCDS9535.1, CCDS9536.1	13q34	2003-06-19			ENSG00000153531	ENSG00000153531	113622			21303	protein-coding gene	gene with protein product		610620			NA	12070318	Standard	NM_138430	NM_138430	NA	Approved	ARH2	uc001vtq.1	Q8NDY3	OTTHUMG00000017386	ENST00000375418.3:c.120C>T	chr13.hg19:g.114107633G>A		NA	Q5JUG2|Q96GD1	hg19	CCDS9535.1	0.02	22.10236	CCCxGAA	COVERED																																																																																			NOVEL	ADPRHL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045915.2	4	37.905443	KEEP	0	0	0	126	4140	GG	1	1	0		-	67	60	2510	0	0	197.458952	433	60	14708	809	ENST00000375418.3	0.134	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	114312503	114312503	__UNKNOWN__	IGR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr13:114312503A>G			NA	NA				ATP4B (2 upstream) : GRK1 (8966 downstream)						NA		NA									NA						TGCACCCTCTACGCCCAGACT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													26	25	25	NA		NA	NA	13		NA											NA				114312503		2198	4298	6496	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.114312503A>G		NA		hg19		0.02	15.204833	TCTxCGC	COVERED																																																																																			NOVEL					0			8	20.15524	KEEP	0	0	0	67	2003	AA	1	1	0			71	60	2721	0	0	233.540308	239	60	8269	515		0.229032	1
PARP2	10038	__UNKNOWN__	__UNKNOWN__	14	20825687	20825687	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:20825687C>T	ENST00000429687.3	+	15	1613				PARP2_ENST00000527915.1_3'UTR|PARP2_ENST00000250416.5_Intron			Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	NA		NA			base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		CCTGTAAGTACTCAGAACCAG	0.493	NA	NA						Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													61	58	59	NA		NA	NA	14		NA											NA				20825687		1913	4132	6045	SO:0001627	intron_variant			AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484	10038		Poly (ADP-ribose) polymerases	272	protein-coding gene	gene with protein product		607725	ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2, poly (ADP-ribose) polymerase family, member 2	ADPRTL2	NA	10329013, 18353725	Standard		NM_005484	NA	Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000429687.3:c.1553+8C>T	chr14.hg19:g.20825687C>T		NA	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	hg19	CCDS45077.1	0.02	11.525369	GTAxTCA	COVERED																																																																																			NOVEL	PARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387845.2	2	19.824228	KEEP	0	0	0	66	2255	CC	1	1	0		+	105	60	3847	0	0	355.591225	169	60	6383	411	ENST00000429687.3	0.383212	1
TEP1	7011	__UNKNOWN__	__UNKNOWN__	14	20864064	20864064	__UNKNOWN__	Silent	SNP	G	G	A	rs558347552		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:20864064G>A	ENST00000556935.1	-	9	1419	c.1380C>T	c.(1378-1380)aaC>aaT	p.N460N	TEP1_ENST00000262715.5_Silent_p.N568N			Q99973	TEP1_HUMAN	telomerase-associated protein 1	568	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.	NA			RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.N568N(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		CATCATGGGCGTTAAGAAATC	0.507	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	17664	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	ovary(1)											131	127	129	NA		NA	NA	14		NA											NA				20864064		2203	4300	6503	SO:0001819	synonymous_variant				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566	7011		WD repeat domain containing	11726	protein-coding gene	gene with protein product	TROVE domain family, member 1	601686			NA	9403057	Standard	NM_007110	NM_007110	NA	Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000556935.1:c.1380C>T	chr14.hg19:g.20864064G>A		NA	A0AUV9	hg19		0.02	4.581888	GGCxTTA	COVERED																																																																																			NOVEL	TEP1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000410689.1	6	17.450958	KEEP	0	0	0	58	1976	GG	1	1	0		-	37	60	1376	0	0	120.685901	99	60	3514	254	ENST00000556935.1	0.272059	1
DHRS4	10901	__UNKNOWN__	__UNKNOWN__	14	24424346	24424346	__UNKNOWN__	Silent	SNP	G	G	A	rs4981491		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:24424346G>A	ENST00000313250.5	+	2	434	c.231G>A	c.(229-231)caG>caA	p.Q77Q	DHRS4_ENST00000397075.3_Silent_p.Q77Q|DHRS4_ENST00000543741.2_Silent_p.Q77Q|DHRS4_ENST00000558263.1_Silent_p.Q77Q|DHRS4_ENST00000308178.8_Silent_p.Q59Q|DHRS4_ENST00000382761.3_Silent_p.Q59Q|DHRS4_ENST00000559632.1_Silent_p.Q77Q|DHRS4_ENST00000421831.1_Silent_p.Q59Q|DHRS4_ENST00000558581.1_Silent_p.Q77Q|DHRS4_ENST00000397074.3_Silent_p.Q77Q|DHRS4_ENST00000397073.2_Silent_p.Q59Q	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	77		NA			alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CCACGCTGCAGGGGGAGGGGC	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													37	42	40	NA		NA	NA	14		NA											NA				24424346		2203	4299	6502	SO:0001819	synonymous_variant			AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	10901	1.1.1.184	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1	16985	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 25C, member 2	611596			NA	10333503, 19027726	Standard		NM_021004	NA	Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.231G>A	chr14.hg19:g.24424346G>A		NA	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	hg19	CCDS9605.1	0.02	4.456119	GCAxGGG	COVERED																																																																																			NOVEL	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000071857.3	1	26.132093	KEEP	0	5	163	144	4902	GG	1	1	0		+	5	49	196	0	0	12.63677	134	60	4843	361	ENST00000313250.5	0.035971	1
NYNRIN	57523	__UNKNOWN__	__UNKNOWN__	14	24877504	24877504	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:24877504G>A	ENST00000382554.3	+	3	946	c.628G>A	c.(628-630)Ggc>Agc	p.G210S		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	210		NA			DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						CAGCCGCTTCGGCATCTCTGA	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	42	39	NA		NA	NA	14		NA											NA				24877504		2082	4219	6301	SO:0001583	missense			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978	57523			20165	protein-coding gene	gene with protein product	Cousin of GIN1	NA	KIAA1305	KIAA1305	NA	19561090, 17114934	Standard		NM_025081	NA	Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.628G>A	chr14.hg19:g.24877504G>A	ENSP00000371994:p.Gly210Ser	NA	Q6P153|Q86TR3|Q9HAC4	hg19	CCDS45090.1	0.02	9.437765	TTCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.04	3.288007	0.59976	.	.	ENSG00000205978	ENST00000382554	T	0.13420	2.59	5.06	4.17	0.49024	.	0.462149	0.16728	N	0.201970	T	0.08313	0.0207	L	0.27053	0.805	0.30874	N	0.732166	P	0.41546	0.754	B	0.29862	0.108	T	0.07868	-1.0750	10	0.87932	D	0	.	9.4667	0.38817	0.0958:0.0:0.9042:0.0	.	210	Q9P2P1	NYNRI_HUMAN	S	210	ENSP00000371994:G210S	ENSP00000371994:G210S	G	+	1	0	NYNRIN	23947344	0.982000	0.34865	0.992000	0.48379	0.434000	0.31775	2.166000	0.42406	1.354000	0.45846	-0.150000	0.13652	GGC	NOVEL	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412939.1	4	34.125122	KEEP	0	1	33	125	4004	GG	1	1	0		+	31	60	1148	0	0	89.45249	210	60	7014	468	ENST00000382554.3	0.128631	1
GZMB	3002	__UNKNOWN__	__UNKNOWN__	14	25100241	25100241	__UNKNOWN__	3'UTR	SNP	T	T	C	rs545182439		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:25100241T>C	ENST00000216341.4	-	0	886				RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000415355.3_3'UTR|GZMB_ENST00000382542.1_3'UTR|GZMB_ENST00000382540.1_3'UTR|RP11-104E19.1_ENST00000557736.1_RNA			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	NA		NA			apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		AGAGAAGGTGTTTCATTACAG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													182	179	180	NA		NA	NA	14		NA											NA				25100241		2203	4300	6503	SO:0001624	3_prime_UTR_variant			BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453	3002			4709	protein-coding gene	gene with protein product	fragmentin 2, cytotoxic serine protease B, cathepsin G-like 1, T-cell serine protease 1-3E	123910		CTLA1, CSPB	NA	2323780	Standard	NM_004131	NM_004131	NA	Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.*36A>G	chr14.hg19:g.25100241T>C		NA	Q8N1D2|Q9UCC1	hg19	CCDS9633.1	0.02	7.418232	GTGxTTC	COVERED																																																																																			NOVEL	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276540.3	2	9.628472	KEEP	0	0	0	32	1005	TT	0.999997	0.999997	0		-	59	60	2241	0	0	203.493825	117	60	4165	269	ENST00000216341.4	0.335227	1
HECTD1	25831	__UNKNOWN__	__UNKNOWN__	14	31626207	31626207	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:31626207C>G	ENST00000399332.1	-	12	2259	c.1771G>C	c.(1771-1773)Gat>Cat	p.D591H	HECTD1_ENST00000553700.1_Missense_Mutation_p.D591H	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	591		NA			neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		AAGTGGCCATCATCATCATCC	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	62	65	NA		NA	NA	14		NA											NA				31626207		1839	4095	5934	SO:0001583	missense			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148	25831		Ankyrin repeat domain containing	20157	protein-coding gene	gene with protein product		NA	HECT domain containing 1		NA	10574461	Standard		XM_005267502	NA	Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.1771G>C	chr14.hg19:g.31626207C>G	ENSP00000382269:p.Asp591His	NA	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	hg19	CCDS41939.1	0.02	4.971152	CATxATC	COVERED	.	.	.	.	.	.	.	.	.	.	C	25.8	4.672833	0.88445	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957;ENST00000556224	T;T;T;T	0.66638	-0.22;-0.22;1.04;-0.22	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81706	0.4879	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.77557	0.97;0.99	T	0.82368	-0.0492	10	0.87932	D	0	-19.1888	20.024	0.97514	0.0:1.0:0.0:0.0	.	591;591	D3DS86;Q9ULT8	.;HECD1_HUMAN	H	591;591;591;65;591	ENSP00000450697:D591H;ENSP00000382269:D591H;ENSP00000451860:D65H;ENSP00000452015:D591H	ENSP00000261312:D591H	D	-	1	0	HECTD1	30695958	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.732000	0.84908	2.809000	0.96659	0.655000	0.94253	GAT	NOVEL	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409942.1	0	7.524908	KEEP	0	0	0	25	914	CC	0.999931	0.999908	0		-	37	60	1389	0	0	127.344236	66	60	2513	147	ENST00000399332.1	0.359223	0.999978
AKAP6	9472	__UNKNOWN__	__UNKNOWN__	14	33016011	33016011	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:33016011A>G	ENST00000280979.4	+	4	2322	c.2152A>G	c.(2152-2154)Agt>Ggt	p.S718G	AKAP6_ENST00000557272.1_Missense_Mutation_p.S718G|AKAP6_ENST00000557354.1_Missense_Mutation_p.S718G	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	718		NA			action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TGGGCCCCTGAGTGACATTCT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(49;821 1200 7288 13647 42351)					NA		NA				0													74	68	70	NA		NA	NA	14		NA											NA				33016011		2203	4300	6503	SO:0001583	missense			AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320	9472		A-kinase anchor proteins	376	protein-coding gene	gene with protein product	protein kinase A anchoring protein 6	604691			NA	7721854, 9205841	Standard	NM_004274	NM_004274	NA	Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.2152A>G	chr14.hg19:g.33016011A>G	ENSP00000280979:p.Ser718Gly	NA	A7E242|A7E2D4|O15028	hg19	CCDS9644.1	0.02	4.372215	CTGxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	20.1	3.934929	0.73442	.	.	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272	T;T;T	0.37235	1.21;1.21;1.21	6.17	6.17	0.99709	.	0.156172	0.53938	D	0.000053	T	0.58018	0.2093	M	0.64997	1.995	0.50039	D	0.99984	D;D	0.76494	0.997;0.999	D;D	0.80764	0.985;0.994	T	0.58457	-0.7633	10	0.56958	D	0.05	-15.28	15.3933	0.74767	1.0:0.0:0.0:0.0	.	718;718	A7E242;Q13023	.;AKAP6_HUMAN	G	718	ENSP00000280979:S718G;ENSP00000450531:S718G;ENSP00000451247:S718G	ENSP00000280979:S718G	S	+	1	0	AKAP6	32085762	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.751000	0.85126	2.371000	0.80710	0.533000	0.62120	AGT	NOVEL	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276617.2	0	7.824215	KEEP	0	0	0	26	832	AA	0.999957	0.999934	0		+	13	60	441	0	0	33.348904	90	60	3311	137	ENST00000280979.4	0.126214	0.999978
LRFN5	145581	__UNKNOWN__	__UNKNOWN__	14	42356858	42356858	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:42356858A>T	ENST00000298119.4	+	3	2219	c.1030A>T	c.(1030-1032)Att>Ttt	p.I344F	LRFN5_ENST00000554171.1_Missense_Mutation_p.I344F|LRFN5_ENST00000554120.1_Missense_Mutation_p.I344F	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	344	Ig-like.	NA				integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		AACACTTGACATTCTTATCAC	0.423	NA	NA								HNSCC(30;0.082)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	114	115	NA		NA	NA	14		NA											NA				42356858		2203	4300	6503	SO:0001583	missense			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379	145581		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	20360	protein-coding gene	gene with protein product	fibronectin type III, immunoglobulin and leucine rich repeat domains 8	612811	chromosome 14 open reading frame 146	C14orf146	NA	16828986	Standard	NM_152447	NM_152447	NA	Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1030A>T	chr14.hg19:g.42356858A>T	ENSP00000298119:p.Ile344Phe	NA	B3KU78|Q86XL2	hg19	CCDS9678.1	0.02	9.896852	GACxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	17.96	3.516323	0.64634	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	T;T;T	0.79247	-1.25;-1.25;-1.25	5.4	5.4	0.78164	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.56097	D	0.000024	D	0.84188	0.5417	M	0.73430	2.235	0.80722	D	1	B;P	0.44195	0.308;0.828	B;P	0.53912	0.333;0.737	D	0.84430	0.0576	10	0.44086	T	0.13	.	13.6708	0.62424	1.0:0.0:0.0:0.0	.	344;344	G3V364;Q96NI6	.;LRFN5_HUMAN	F	344	ENSP00000298119:I344F;ENSP00000451897:I344F;ENSP00000451067:I344F	ENSP00000298119:I344F	I	+	1	0	LRFN5	41426608	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.287000	0.95975	2.165000	0.68154	0.460000	0.39030	ATT	NOVEL	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276786.1	2	25.573595	KEEP	0	0	0	85	2647	AA	1	1	0		+	76	60	2794	0	0	251.585945	158	60	5860	407	ENST00000298119.4	0.324786	1
MGAT2	4247	__UNKNOWN__	__UNKNOWN__	14	50089769	50089769	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:50089769C>T	ENST00000305386.2	+	0	2281				RP11-649E7.5_ENST00000555043.1_RNA	NM_002408.3	NP_002399.1	Q10469	MGAT2_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	NA		NA			cellular protein metabolic process (GO:0044267)|oligosaccharide biosynthetic process (GO:0009312)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0008455)|carbohydrate binding (GO:0030246)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)	11	all_epithelial(31;0.0021)|Breast(41;0.0124)					TCTCTTGACACACTTATTAGG	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U15128	CCDS9690.1	14q21	2013-02-25			ENSG00000168282	ENSG00000168282	4247	2.4.1.143	Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases	7045	protein-coding gene	gene with protein product		602616			NA	7635144	Standard	NM_002408	NM_002408	NA	Approved	GNT-II	uc001wwr.3	Q10469	OTTHUMG00000140271	ENST00000305386.2:c.*439C>T	chr14.hg19:g.50089769C>T		NA	B3KPC5|B3KQM0	hg19	CCDS9690.1	0.02	6.985575	ACAxACT	COVERED																																																																																			NOVEL	MGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276807.1	2	25.88501	KEEP	0	0	0	86	3123	CC	1	1	0		+	50	60	1802	0	0	161.384343	107	60	4066	327	ENST00000305386.2	0.318471	1
ERO1L	30001	__UNKNOWN__	__UNKNOWN__	14	53118885	53118885	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:53118885T>C	ENST00000395686.3	-	13	1349					NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	NA		NA			4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					TCTACTTCTATGAGTACTATA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930	30001			13280	protein-coding gene	gene with protein product		615435	ERO1 (S. cerevisiae)-like		NA	10671517	Standard	NM_014584	NM_014584	NA	Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.1125+71A>G	chr14.hg19:g.53118885T>C		NA	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	hg19	CCDS9709.1	0.02	-0.228107	CTAxGAG	COVERED																																																																																			NOVEL	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276892.1	1	3.310075	KEEP	0	0	0	11	345	TT	0.993072	0.578892	0		-	5	60	188	0	0	15.658095	21	60	788	41	ENST00000395686.3	0.192308	0.58293
RHOJ	57381	__UNKNOWN__	__UNKNOWN__	14	63747811	63747811	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:63747811G>A	ENST00000316754.3	+	3	822	c.360G>A	c.(358-360)aaG>aaA	p.K120K	RHOJ_ENST00000555125.1_Silent_p.K120K	NM_020663.4	NP_065714.1	Q9H4E5	RHOJ_HUMAN	ras homolog family member J	120		NA			actin cytoskeleton organization (GO:0030036)|GTP catabolic process (GO:0006184)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.00326)|all cancers(60;0.031)|BRCA - Breast invasive adenocarcinoma(234;0.119)		CCGAGCTCAAGGACTGCATGC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													150	112	125	NA		NA	NA	14		NA											NA				63747811		2203	4300	6503	SO:0001819	synonymous_variant			AK027351	CCDS9757.1	14q23.1	2012-02-27	2012-02-27	2004-03-24	ENSG00000126785	ENSG00000126785	57381			688	protein-coding gene	gene with protein product		607653	RAS-like, family 7, member B, ras homolog gene family, member J	RASL7B, ARHJ	NA	10967094	Standard		NM_020663	NA	Approved	FLJ14445, TCL	uc001xgb.2	Q9H4E5	OTTHUMG00000140342	ENST00000316754.3:c.360G>A	chr14.hg19:g.63747811G>A		NA	Q96KC1	hg19	CCDS9757.1	0.02	4.751833	CAAxGAC	COVERED																																																																																			NOVEL	RHOJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276975.3	0	16.252001	KEEP	0	0	0	54	1877	GG	1	1	0		+	21	60	794	0	0	64.609326	107	60	3955	230	ENST00000316754.3	0.164062	1
SPTB	6710	__UNKNOWN__	__UNKNOWN__	14	65220308	65220308	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:65220308G>T	ENST00000556626.1	-	33	6691	c.6549C>A	c.(6547-6549)ggC>ggA	p.G2183G	SPTB_ENST00000342835.4_5'UTR|SPTB_ENST00000389722.3_Silent_p.G2183G			P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	0		NA			actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GGCCCAGGTAGCCTTCCATCT	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													85	86	86	NA		NA	NA	14		NA											NA				65220308		2203	4300	6503	SO:0001819	synonymous_variant				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182	6710		Pleckstrin homology (PH) domain containing	11274	protein-coding gene	gene with protein product	spherocytosis, clinical type I	182870			NA	2209094	Standard		NM_001024858	NA	Approved		uc001xhr.3	P11277		ENST00000556626.1:c.6549C>A	chr14.hg19:g.65220308G>T		NA	Q15510|Q15519	hg19	CCDS32099.1	0.02	4.130018	GTAxCCT	COVERED																																																																																			NOVEL	SPTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414076.1	1	23.505031	KEEP	0	1	10	82	2859	GG	1	1	0		-	52	60	1826	0	0	166.90202	90	60	3333	282	ENST00000556626.1	0.366197	1
SPTB	6710	__UNKNOWN__	__UNKNOWN__	14	65271710	65271710	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:65271710G>A	ENST00000556626.1	-	3	389	c.247C>T	c.(247-249)Cgg>Tgg	p.R83W	SPTB_ENST00000389720.3_Missense_Mutation_p.R83W|SPTB_ENST00000389721.5_Missense_Mutation_p.R83W|SPTB_ENST00000389722.3_Missense_Mutation_p.R83W|SPTB_ENST00000542895.1_Missense_Mutation_p.R83W			P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	83	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.	NA			actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CGCCCATCCCGCAGGTCCTTG	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	84	85	NA		NA	NA	14		NA											NA				65271710		2203	4300	6503	SO:0001583	missense				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182	6710		Pleckstrin homology (PH) domain containing	11274	protein-coding gene	gene with protein product	spherocytosis, clinical type I	182870			NA	2209094	Standard		NM_001024858	NA	Approved		uc001xhr.3	P11277		ENST00000556626.1:c.247C>T	chr14.hg19:g.65271710G>A	ENSP00000451752:p.Arg83Trp	NA	Q15510|Q15519	hg19	CCDS32099.1	0.02	4.853781	CCCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.8	4.209073	0.79240	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	4.67	3.75	0.43078	Calponin homology domain (5);	0.090781	0.51477	D	0.000083	D	0.82568	0.5065	M	0.92412	3.305	0.51767	D	0.999935	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.86754	0.1962	10	0.87932	D	0	.	13.2537	0.60066	0.0:0.0:0.8396:0.1604	.	83;87	P11277;Q59FP5	SPTB1_HUMAN;.	W	87;83;83;83;83;83	ENSP00000374372:R83W;ENSP00000451752:R83W;ENSP00000374371:R83W;ENSP00000443882:R83W;ENSP00000374370:R83W	ENSP00000374370:R83W	R	-	1	2	SPTB	64341463	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.440000	0.52886	1.293000	0.44690	0.650000	0.86243	CGG	NOVEL	SPTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414076.1	1	6.620142	KEEP	0	0	0	22	750	GG	0.999879	0.999863	0		-	39	60	1432	0	0	131.724432	66	60	2280	162	ENST00000556626.1	0.371429	0.999984
TMEM229B	161145	__UNKNOWN__	__UNKNOWN__	14	67939710	67939710	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:67939710A>G	ENST00000557006.1	-	0	1213				TMEM229B_ENST00000357461.2_3'UTR			Q8NBD8	T229B_HUMAN	transmembrane protein 229B	NA		NA				integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GCACCTGAATATTGCCTAATG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK090706	CCDS9783.1	14q23.3-q24.1	2009-09-22	2009-09-22	2009-09-22	ENSG00000198133	ENSG00000198133	161145			20130	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 83	C14orf83	NA		Standard	NM_182526	NM_182526	NA	Approved	FLJ33387	uc001xjk.3	Q8NBD8		ENST00000557006.1:c.*427T>C	chr14.hg19:g.67939710A>G		NA		hg19	CCDS9783.1	0.02	7.14857	AATxTTG	COVERED																																																																																			NOVEL	TMEM229B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412718.2	3	12.936559	KEEP	0	0	0	43	1302	AA	1	1	0		-	61	60	2277	0	0	206.042316	123	60	4339	268	ENST00000557006.1	0.331522	1
RBM25	58517	__UNKNOWN__	__UNKNOWN__	14	73578436	73578436	__UNKNOWN__	Missense_Mutation	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:73578436A>C	ENST00000261973.7	+	16	2503	c.2218A>C	c.(2218-2220)Agt>Cgt	p.S740R	RBM25_ENST00000532483.1_3'UTR|RBM25_ENST00000527432.1_Missense_Mutation_p.S740R	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	740		NA			mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		ACACATTAAGAGTCTCATTGA	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													147	142	143	NA		NA	NA	14		NA											NA				73578436		2203	4300	6503	SO:0001583	missense			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707	58517		RNA binding motif (RRM) containing	23244	protein-coding gene	gene with protein product	functional spliceosome-associated protein 94	612427	RNA-binding region (RNP1, RRM) containing 7	RNPC7	NA	9847074, 7596406	Standard	XM_027330	NM_021239	NA	Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.2218A>C	chr14.hg19:g.73578436A>C	ENSP00000261973:p.Ser740Arg	NA	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	hg19	CCDS32113.1	0.02	12.392652	AAGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	22.6	4.305212	0.81247	.	.	ENSG00000119707	ENST00000261973;ENST00000527432	T;T	0.12879	2.64;2.64	5.7	5.7	0.88788	.	0.035827	0.85682	D	0.000000	T	0.22166	0.0534	M	0.73962	2.25	0.80722	D	1	B	0.33777	0.425	B	0.37346	0.247	T	0.02161	-1.1203	10	0.26408	T	0.33	.	15.9596	0.79918	1.0:0.0:0.0:0.0	.	740	P49756	RBM25_HUMAN	R	740	ENSP00000261973:S740R;ENSP00000431150:S740R	ENSP00000261973:S740R	S	+	1	0	RBM25	72648189	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.339000	0.96797	2.171000	0.68590	0.402000	0.26972	AGT	NOVEL	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394966.1	6	32.496413	KEEP	0	0	0	108	3473	AA	1	1	0		+	50	60	1789	1	0	144.871574	240	60	8979	506	ENST00000261973.7	0.172414	1
ISCA2	122961	__UNKNOWN__	__UNKNOWN__	14	74960516	74960516	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:74960516G>A	ENST00000554924.1	+	1	49	c.39G>A	c.(37-39)acG>acA	p.T13T	ISCA2_ENST00000556816.1_Silent_p.T13T|ISCA2_ENST00000298818.8_Silent_p.T13T			Q86U28	ISCA2_HUMAN	iron-sulfur cluster assembly 2	13		NA			iron-sulfur cluster assembly (GO:0016226)	mitochondrion (GO:0005739)	iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			lung(1)	1				BRCA - Breast invasive adenocarcinoma(234;0.00146)		CGGCCGCGACGCAGAGAGCGG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	12	11	NA		NA	NA	14		NA											NA				74960516		2174	4242	6416	SO:0001819	synonymous_variant				CCDS32122.1, CCDS61504.1	14q24.2	2013-08-06	2013-08-06	2007-01-18	ENSG00000165898	ENSG00000165898	122961			19857	protein-coding gene	gene with protein product		615317	HesB like domain containing 1, iron-sulfur cluster assembly 2 homolog (S. cerevisiae)	HBLD1	NA	22323289	Standard	NM_194279	NM_194279	NA	Approved	ISA2	uc001xpz.3	Q86U28		ENST00000554924.1:c.39G>A	chr14.hg19:g.74960516G>A		NA	A6NFF1|A8K3W3|G3V291|Q8IYZ0|Q96BB2	hg19		0.02	2.143222	GACxCAG	COVERED																																																																																			NOVEL	ISCA2-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000412356.1	1	27.468865	KEEP	0	1	7	94	3041	GG	1	0.999622	0		+	13	60	472	0	0	37.628247	72	60	2504	240	ENST00000554924.1	0.152941	0.999622
PGF	5228	__UNKNOWN__	__UNKNOWN__	14	75409430	75409430	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:75409430G>A	ENST00000555567.1	-	7	1033	c.492C>T	c.(490-492)ggC>ggT	p.G164G	PGF_ENST00000553716.1_Silent_p.G143G|PGF_ENST00000238607.6_Silent_p.G163G|PGF_ENST00000405431.2_Silent_p.G215G	NM_002632.5	NP_002623.2	P49763	PLGF_HUMAN	placental growth factor	0		NA			branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|regulation of morphogenesis of a branching structure (GO:0060688)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.00668)	Aflibercept(DB08885)	GAACAGCATCGCCGCACCTGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(127;389 2301 5452 48547)					NA		NA				0													42	41	42	NA		NA	NA	14		NA											NA				75409430		2203	4298	6501	SO:0001819	synonymous_variant			S72960	CCDS9835.1, CCDS55932.1, CCDS73664.1	14q24.3	2013-02-18	2008-03-20		ENSG00000119630	ENSG00000119630	5228			8893	protein-coding gene	gene with protein product	placenta growth factor	601121	placental growth factor-like, placental growth factor, vascular endothelial growth factor-related protein	PGFL	NA	7681160	Standard	NM_002632	NM_002632	NA	Approved	PLGF, PlGF-2, PlGF, SHGC-10760, D12S1900	uc001xqz.3	P49763	OTTHUMG00000171496	ENST00000555567.1:c.492C>T	chr14.hg19:g.75409430G>A		NA	Q07101|Q9BV78|Q9Y6S8	hg19	CCDS9835.1	0.02	9.657868	ATCxCCG	COVERED																																																																																			NOVEL	PGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413746.2	0	38.738947	KEEP	0	0	0	129	4244	GG	1	1	0		-	79	60	2701	0	0	246.258722	137	60	4789	446	ENST00000555567.1	0.365741	1
DIO2	1734	__UNKNOWN__	__UNKNOWN__	14	80677810	80677810	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:80677810G>A	ENST00000557010.1	-	3	391	c.6C>T	c.(4-6)ggC>ggT	p.G2G	DIO2_ENST00000557125.1_Silent_p.G2G|DIO2_ENST00000422005.3_Silent_p.G2G|DIO2-AS1_ENST00000553979.1_RNA|DIO2_ENST00000438257.4_Silent_p.G2G|DIO2_ENST00000555750.1_Silent_p.G2G	NM_000793.5|NM_001242502.1|NM_001242503.1	NP_000784.2|NP_001229431.1|NP_001229432.1	Q92813	IOD2_HUMAN	deiodinase, iodothyronine, type II	2		NA			cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|selenocysteine incorporation (GO:0001514)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|thyroid hormone metabolic process (GO:0042403)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	selenium binding (GO:0008430)|thyroxine 5'-deiodinase activity (GO:0004800)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(14)|skin(1)|stomach(1)	25				BRCA - Breast invasive adenocarcinoma(234;0.0281)		CGCTGAGGATGCCCATCTTCT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													28	30	29	NA		NA	NA	14		NA											NA				80677810		2047	4197	6244	SO:0001819	synonymous_variant			AF007144	CCDS45146.1, CCDS55934.1	14q24.2-q24.3	2014-05-02			ENSG00000211448	ENSG00000211448	1734	1.97.1.10		2884	protein-coding gene	gene with protein product	thyroxine deiodinase, type II, deiodonase-2, deiodinase-2	601413			NA	8755651, 10343107	Standard		NM_001007023	NA	Approved	TXDI2, SelY	uc021rxb.1	Q92813	OTTHUMG00000171443	ENST00000557010.1:c.6C>T	chr14.hg19:g.80677810G>A		NA	B9EGK0|G3V315|Q6B0A3|Q9HCP8|Q9P1W4|Q9UDZ1	hg19	CCDS45146.1	0.02	8.530829	GATxCCC	COVERED																																																																																			NOVEL	DIO2-001	KNOWN	basic|appris_principal|CCDS|seleno	protein_coding	NA	protein_coding	OTTHUMT00000413428.2	1	41.768811	KEEP	0	1	23	147	5270	GG	1	1	0		-	32	60	1080	0	0	83.729513	187	60	7009	498	ENST00000557010.1	0.146119	1
FLRT2	23768	__UNKNOWN__	__UNKNOWN__	14	86088573	86088573	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:86088573C>T	ENST00000330753.4	+	2	1482	c.715C>T	c.(715-717)Cgt>Tgt	p.R239C	FLRT2_ENST00000554746.1_Missense_Mutation_p.R239C	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	239		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTCAATTGTACGTAATTCGCT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													86	85	85	NA		NA	NA	14		NA											NA				86088573		2203	4300	6503	SO:0001583	missense			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070	23768		Fibronectin type III domain containing	3761	protein-coding gene	gene with protein product		604807			NA	10644439, 16872596	Standard		XM_005267490	NA	Approved		uc001xvr.3	O43155		ENST00000330753.4:c.715C>T	chr14.hg19:g.86088573C>T	ENSP00000332879:p.Arg239Cys	NA	A0AV84|B7ZLP3	hg19	CCDS9877.1	0.02	11.99229	GTAxGTA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.16	2.752457	0.49362	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.57907	0.37;0.37	5.78	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.64832	0.2634	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65018	-0.6270	10	0.42905	T	0.14	-16.9625	14.4373	0.67290	0.2907:0.7093:0.0:0.0	.	239	O43155	FLRT2_HUMAN	C	239	ENSP00000332879:R239C;ENSP00000451050:R239C	ENSP00000332879:R239C	R	+	1	0	FLRT2	85158326	0.994000	0.37717	0.692000	0.30179	0.564000	0.35744	3.215000	0.51169	1.359000	0.45940	0.650000	0.86243	CGT	NOVEL	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413193.1	6	13.908613	KEEP	0	2	62	68	2271	CC	1	1	0		+	60	60	2193	0	0	187.517028	195	60	6870	391	ENST00000330753.4	0.235294	1
TDP1	55775	__UNKNOWN__	__UNKNOWN__	14	90442111	90442111	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:90442111C>T	ENST00000335725.4	+	7	1006				TDP1_ENST00000555565.1_Intron|TDP1_ENST00000393452.3_Intron|TDP1_ENST00000555880.1_Intron|TDP1_ENST00000393454.2_Intron|TDP1_ENST00000357382.3_Intron	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	NA		NA			cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		TAAATGACTTCTTTTTCATCC	0.333	NA	NA						Repair of DNA-protein crosslinks						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													170	166	167	NA		NA	NA	14		NA											NA				90442111		2203	4300	6503	SO:0001627	intron_variant			AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088	55775			18884	protein-coding gene	gene with protein product		607198			NA	11839309, 12244316	Standard	NM_018319	XM_005267847	NA	Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.757-14C>T	chr14.hg19:g.90442111C>T		NA	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	hg19	CCDS9888.1	0.02	4.285533	CTTxTTT	COVERED																																																																																			NOVEL	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411239.1	0	11.436955	KEEP	0	0	0	38	1345	CC	1	1	0		+	41	60	1471	0	0	128.873741	106	60	3975	235	ENST00000335725.4	0.278912	1
ATG2B	55102	__UNKNOWN__	__UNKNOWN__	14	96829173	96829173	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:96829173G>T	ENST00000359933.4	-	1	1034	c.141C>A	c.(139-141)gcC>gcA	p.A47A		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	47		NA			autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AGGGGACCTGGGCGAGGGACC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													36	38	37	NA		NA	NA	14		NA											NA				96829173		1860	4091	5951	SO:0001819	synonymous_variant			AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739	55102			20187	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 103, ATG2 autophagy related 2 homolog B (S. cerevisiae)	C14orf103	NA	22350415	Standard	NM_018036	NM_018036	NA	Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.141C>A	chr14.hg19:g.96829173G>T		NA	Q6ZRE7|Q96DQ3|Q9NW80	hg19	CCDS9944.2	0.02	4.275702	CTGxGCG	COVERED																																																																																			NOVEL	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000314037.1	0	30.925816	KEEP	0	0	0	103	3509	GG	1	0.999996	0		-	7	60	229	0	0	14.839343	107	60	3799	287	ENST00000359933.4	0.061404	0.999996
PAPOLA	10914	__UNKNOWN__	__UNKNOWN__	14	97027020	97027020	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:97027020T>C	ENST00000392990.2	+	20	2039				PAPOLA_ENST00000216277.8_Missense_Mutation_p.L680S			P51003	PAPOA_HUMAN	poly(A) polymerase alpha	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|RNA polyadenylation (GO:0043631)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0555)|all_epithelial(191;0.149)|Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.213)		TGTCTTGCTTTGAGTGGACAT	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(19;254 734 11908 35501 39234)					NA		NA				0													102	105	104	NA		NA	NA	14		NA											NA				97027020		2203	4288	6491	SO:0001627	intron_variant			X76770	CCDS9946.1, CCDS58334.1, CCDS58335.1	14q32.1-q32.2	2008-02-08				ENSG00000090060	10914	2.7.7.19		14981	protein-coding gene	gene with protein product		605553			NA	8302877, 10429366	Standard		NM_032632	NA	Approved	PAP	uc001yfq.3	P51003		ENST00000392990.2:c.2005-2136T>C	chr14.hg19:g.97027020T>C		NA	Q86SX4|Q86TV0|Q8IYF5|Q9BVU2	hg19		0.02	4.930693	CTTxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	5.067	0.197943	0.09652	.	.	ENSG00000090060	ENST00000216277;ENST00000555626	.	.	.	5.66	5.66	0.87406	.	0.285381	0.28712	N	0.014394	T	0.37210	0.0995	N	0.05383	-0.06	0.80722	D	1	B;B	0.20052	0.041;0.02	B;B	0.19391	0.025;0.011	T	0.24941	-1.0146	9	0.18710	T	0.47	.	14.1459	0.65351	0.0:0.0:0.0:1.0	.	696;680	B4DYF4;P51003	.;PAPOA_HUMAN	S	680;430	.	ENSP00000216277:L680S	L	+	2	0	PAPOLA	96096773	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.387000	0.44389	2.160000	0.67779	0.528000	0.53228	TTG	NOVEL	PAPOLA-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000413479.1	0	15.045025	KEEP	0	0	0	50	1586	TT	1	0.999998	0		+	34	60	1248	0	0	110.250438	84	60	3095	221	ENST00000392990.2	0.288136	0.999998
BCL11B	64919	__UNKNOWN__	__UNKNOWN__	14	99642453	99642453	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:99642453C>T	ENST00000357195.3	-	4	729	c.720G>A	c.(718-720)gcG>gcA	p.A240A	BCL11B_ENST00000443726.2_Silent_p.A46A|BCL11B_ENST00000345514.2_Silent_p.A169A	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	240		NA			alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		GCGTGTTCTGCGCGTGCTGCA	0.657	NA	NA	T	TLX3	T-ALL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	0													29	28	28	NA		NA	NA	14		NA											NA				99642453		2201	4295	6496	SO:0001819	synonymous_variant			AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152	64919		Zinc fingers, C2H2-type	13222	protein-coding gene	gene with protein product		606558		ZNF856B	NA	11719382, 16950772	Standard	NM_138576	NM_138576	NA	Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.720G>A	chr14.hg19:g.99642453C>T		NA	Q9H162	hg19	CCDS9950.1	0.02	9.514981	CTGxGCG	COVERED																																																																																			NOVEL	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000072332.2	2	47.242482	KEEP	0	0	0	157	5284	CC	1	1	0		-	66	60	2377	0	0	209.025649	166	60	5718	495	ENST00000357195.3	0.284483	1
EML1	2009	__UNKNOWN__	__UNKNOWN__	14	100406993	100406993	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:100406993A>G	ENST00000262233.6	+	0	3131				EML1_ENST00000334192.4_3'UTR	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	NA		NA			brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				GTTTCATTGCATTCTCCCTTG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629	2009		WD repeat domain containing	3330	protein-coding gene	gene with protein product		602033		EMAPL	NA	9226380, 10521658	Standard	NM_001008707	XM_005267397	NA	Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.*544A>G	chr14.hg19:g.100406993A>G		NA	Q86U15|Q8N536|Q8N5C4|Q8WWL6	hg19	CCDS32155.1	0.02	7.272412	TGCxTTC	COVERED																																																																																			NOVEL	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413943.1	1	7.519013	KEEP	0	0	0	25	743	AA	0.999931	0.999931	0		+	50	60	1677	0	0	146.815926	120	60	4318	216	ENST00000262233.6	0.294118	1
HSP90AA1	3320	__UNKNOWN__	__UNKNOWN__	14	102548528	102548528	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:102548528G>A	ENST00000216281.8	-	10	2214	c.2009C>T	c.(2008-2010)gCg>gTg	p.A670V	HSP90AA1_ENST00000334701.7_Missense_Mutation_p.A792V	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	670		NA			ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	AGACAGGAGCGCAGTTTCATA	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	93	95	NA		NA	NA	14		NA											NA				102548528		2203	4300	6503	SO:0001583	missense			M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824	3320		Heat shock proteins / HSPC	5253	protein-coding gene	gene with protein product		140571	heat shock 90kD protein 1, alpha, heat shock 90kDa protein 1, alpha	HSPC1, HSPCA	NA	2527334, 16269234	Standard	NM_005348	NM_001017963	NA	Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.2009C>T	chr14.hg19:g.102548528G>A	ENSP00000216281:p.Ala670Val	NA	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	hg19	CCDS9967.1	0.02	9.459848	AGCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	g	31	5.101001	0.94245	.	.	ENSG00000080824	ENST00000216281;ENST00000334701	T;T	0.67345	-0.26;-0.26	4.47	4.47	0.54385	.	0.000000	0.85682	U	0.000000	D	0.84215	0.5423	M	0.93106	3.38	0.80722	D	1	D;D	0.89917	1.0;0.999	P;P	0.60173	0.797;0.87	D	0.89205	0.3560	10	0.87932	D	0	-27.9222	17.5686	0.87928	0.0:0.0:1.0:0.0	.	792;670	P07900-2;P07900	.;HS90A_HUMAN	V	670;792	ENSP00000216281:A670V;ENSP00000335153:A792V	ENSP00000216281:A670V	A	-	2	0	HSP90AA1	101618281	1.000000	0.71417	0.061000	0.19648	0.953000	0.61014	9.466000	0.97665	2.224000	0.72417	0.580000	0.79431	GCG	NOVEL	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414952.2	3	24.077392	KEEP	0	0	0	80	2793	GG	1	1	0		-	45	60	1674	0	0	139.800085	182	60	6566	411	ENST00000216281.8	0.198238	1
CTD-3051D23.1	0	__UNKNOWN__	__UNKNOWN__	14	105310821	105310821	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:105310821G>A	ENST00000556430.1	+	0	1822										NA		NA									NA						gaggggccacgtaactcttcc	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000556430.1:	chr14.hg19:g.105310821G>A		NA		hg19		0.02	12.18308	CACxTAA	COVERED																																																																																			NOVEL	CTD-3051D23.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000410286.1	2	23.771646	KEEP	0	0	0	79	2611	GG	1	1	0		+	81	60	2970	0	0	266.266774	175	60	5948	424	ENST00000556430.1	0.316406	1
AHNAK2	113146	__UNKNOWN__	__UNKNOWN__	14	105406621	105406621	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:105406621C>T	ENST00000557457.1	-	3	404	c.161G>A	c.(160-162)gGt>gAt	p.G54D	AHNAK2_ENST00000333244.5_Missense_Mutation_p.G5056D			Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5056		NA				costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTGAAAGCTACCCCCTGCTGT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													109	115	113	NA		NA	NA	14		NA											NA				105406621		2050	4191	6241	SO:0001583	missense			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567	113146			20125	protein-coding gene	gene with protein product		608570	chromosome 14 open reading frame 78	C14orf78	NA	15007166	Standard	NM_138420	NM_138420	NA	Approved		uc010axc.1	Q8IVF2		ENST00000557457.1:c.161G>A	chr14.hg19:g.105406621C>T	ENSP00000450998:p.Gly54Asp	NA	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	hg19		0.02	16.129227	CTAxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	10.79	1.448468	0.26074	.	.	ENSG00000185567	ENST00000557457;ENST00000333244	T;T	0.02446	4.29;5.28	2.85	1.8	0.24995	.	0.576865	0.12445	U	0.468277	T	0.08714	0.0216	L	0.57536	1.79	0.09310	N	1	D	0.65815	0.995	D	0.63877	0.919	T	0.28267	-1.0049	10	0.30078	T	0.28	.	8.6712	0.34152	0.0:0.7645:0.2355:0.0	.	5056	Q8IVF2	AHNK2_HUMAN	D	54;5056	ENSP00000450998:G54D;ENSP00000353114:G5056D	ENSP00000353114:G5056D	G	-	2	0	AHNAK2	104477666	0.000000	0.05858	0.003000	0.11579	0.008000	0.06430	0.190000	0.17057	1.311000	0.45024	0.561000	0.74099	GGT	NOVEL	AHNAK2-003	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000410299.1	5	26.481567	KEEP	0	0	0	88	3079	CC	1	1	0		-	99	60	3553	0	0	307.119116	287	60	10356	613	ENST00000557457.1	0.256477	1
AHNAK2	113146	__UNKNOWN__	__UNKNOWN__	14	105409359	105409359	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:105409359G>A	ENST00000557457.1	-	2	24				AHNAK2_ENST00000333244.5_Silent_p.F4143F			Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	NA		NA				costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCGACACCCCGAATGATGGCA	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													286	295	292	NA		NA	NA	14		NA											NA				105409359		1979	4135	6114	SO:0001627	intron_variant			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567	113146			20125	protein-coding gene	gene with protein product		608570	chromosome 14 open reading frame 78	C14orf78	NA	15007166	Standard	NM_138420	NM_138420	NA	Approved		uc010axc.1	Q8IVF2		ENST00000557457.1:c.220-2044C>T	chr14.hg19:g.105409359G>A		NA	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	hg19		0.02	11.384819	CCCxAAT	COVERED																																																																																			NOVEL	AHNAK2-003	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000410299.1	5	16.989396	KEEP	0	1	33	68	2337	GG	1	1	0		-	11	47	401	0	0	25.656661	245	60	8678	413	ENST00000557457.1	0.042969	1
CRIP2	1397	__UNKNOWN__	__UNKNOWN__	14	105940884	105940884	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:105940884G>A	ENST00000483017.3	+	1	551				CRIP2_ENST00000329146.4_5'UTR	NM_001270837.1	NP_001257766.1	P52943	CRIP2_HUMAN	cysteine-rich protein 2	NA		NA			hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	cell cortex (GO:0005938)	zinc ion binding (GO:0008270)			lung(2)	2		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.235)		cggccccgACGTCGCCATGGA	0.816	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10003.1, CCDS59246.1	14q32.3	2008-08-11			ENSG00000182809	ENSG00000182809	1397			2361	protein-coding gene	gene with protein product		601183			NA	8843343, 10681529	Standard	NM_001312	NM_001312	NA	Approved	CRP2, ESP1	uc031qqr.1	P52943	OTTHUMG00000029906	ENST00000483017.3:c.265+1035G>A	chr14.hg19:g.105940884G>A		NA	A1A4U1|B7Z6C0|E9PD13	hg19	CCDS59246.1	0.02	-0.131546	GACxTCG	COVERED																																																																																			NOVEL	CRIP2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000074599.3	1	3.310443	KEEP	0	0	0	11	368	GG	0.993072	0.227586	0		+	4	60	121	0	0	10.230743	11	60	375	31	ENST00000483017.3	0.266667	0.229173
IGHA1	3493	__UNKNOWN__	__UNKNOWN__	14	106173808	106173808	__UNKNOWN__	RNA	SNP	G	G	A	rs371291470		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:106173808G>A	ENST00000390547.2	-	0	758							P01876	IGHA1_HUMAN	immunoglobulin heavy constant alpha 1	NA		NA			antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|positive regulation of respiratory burst (GO:0060267)|protein-chromophore linkage (GO:0018298)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)				NA						GGCTGAAGCCGCGTGCCAGGC	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													36	47	43	NA		NA	NA	14		NA											NA				106173808		2139	4256	6395					J00220		14q32.33	2012-10-02			ENSG00000211895	ENSG00000211895	3493		Immunoglobulins / IGH locus	5478	other	immunoglobulin gene		146900			NA		Standard	NG_001019	NG_001019	NA	Approved			P01876	OTTHUMG00000152494	ENST00000390547.2:	chr14.hg19:g.106173808G>A		NA		hg19		0.02	8.369368	GCCxCGT	COVERED																																																																																			NOVEL	IGHA1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	NA	IG_C_gene	OTTHUMT00000326459.1	4	2.274628	KEEP	3	5	143	58	1972	GG	1	1	0		-	54	40	1835	0	0	155.300327	172	50	6120	384	ENST00000390547.2	0.238938	1
IGHV4-31	28396	__UNKNOWN__	__UNKNOWN__	14	106805350	106805350	__UNKNOWN__	RNA	SNP	G	G	A	rs141108390	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:106805350G>A	ENST00000438142.2	-	0	284									immunoglobulin heavy variable 4-31	NA		NA									NA						TGTAATAGATGTACCCAATCC	0.542	NA	NA											N|||	490	0.0978435	0.2421	0.0389	5008	,	,	NA	10639	0.0377	NA	0.0249	False	NA	,,,	NA	NA	NA	2504	0.0818	NA	NA	NA						NA		NA				0								A		180,3578		22,136,1721	156	226	204	NA		-6.3	0	14	dbSNP_134	204	159,8083		4,151,3966	no	intergenic				26,287,5687	AA,AG,GG	NA	1.9291,4.7898,2.825			106805350	339,11661	1879	4121	6000					L10098		14q32.33	2012-02-08			ENSG00000231475	ENSG00000231475	28396		Immunoglobulins / IGH locus	5649	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000152097	ENST00000438142.2:	chr14.hg19:g.106805350G>A		NA		hg19		0.02	10.86614	GATxTAC	COVERED																																																																																			NOVEL	IGHV4-31-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000325194.1	1	4.88493	KEEP	1	2	59	37	1301	GG	1	1	0		-	12	59	438	0	0	30.990798	149	60	5654	410	ENST00000438142.2	0.074534	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	106866383	106866383	__UNKNOWN__	IGR	SNP	G	G	A	rs76297373	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr14:106866383G>A			NA	NA				IGHV3-35 (20594 upstream) : IGHV3-38 (22 downstream)						NA		NA									NA						GTGTCTGGGCGCACAATGACT	0.562	NA	NA											G|||	170	0.0339457	0.1188	0.013	5008	,	,	NA	15101	0.001	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0													82	72	76	NA		NA	NA	14		NA											NA				106866383		2072	4211	6283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.106866383G>A		NA		hg19		0.02	4.466742	GGCxCAC	COVERED																																																																																			NOVEL					0			2	3.009345	KEEP	0	0	0	10	325	GG	0.992708	0.992708	0			13	40	475	0	0	35.05116	124	60	3945	168		0.094891	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20444702	20444702	__UNKNOWN__	IGR	SNP	C	C	T	rs201397924		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:20444702C>T			NA	NA				RP11-173D3.1 (91496 upstream) : CHEK2P2 (43294 downstream)						NA		NA									NA						ATCTCGATCTCGTCCTCACCA	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20444702C>T		NA		hg19		0.02	26.618252	TCTxGTC	COVERED																																																																																			NOVEL					0			7	18.387864	KEEP	5	4	116	102	3460	CC	1	1	0			37	49	1328	0	0	89.338271	593	60	21638	971		0.05873	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20454011	20454011	__UNKNOWN__	IGR	SNP	G	G	A	rs199504918		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:20454011G>A			NA	NA				RP11-173D3.1 (100805 upstream) : CHEK2P2 (33985 downstream)						NA		NA									NA						CACTTCTCCTGGTGGTCCAGA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20454011G>A		NA		hg19		0.02	6.240935	CCTxGTG	COVERED																																																																																			NOVEL					0			1	3.947778	KEEP	4	1	31	24	862	GG	0.999909	0.999909	0			6	40	223	0	0	13.787669	171	60	6288	264		0.033898	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20456743	20456743	__UNKNOWN__	IGR	SNP	G	G	A	rs566357797	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:20456743G>A			NA	NA				RP11-173D3.1 (103537 upstream) : CHEK2P2 (31253 downstream)						NA		NA									NA						TTTCACCAGCGCCTGGCTCAT	0.622	NA	NA											N|||	98	0.0195687	0.0061	0.0173	5008	,	,	NA	50178	0.005	NA	0.0547	False	NA	,,,	NA	NA	NA	2504	0.0184	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20456743G>A		NA		hg19		0.02	6.440449	AGCxCCT	COVERED																																																																																			NOVEL					0			0	4.885508	KEEP	2	2	65	39	1350	GG	1	1	0			8	60	295	0	0	19.333224	161	60	5691	300		0.047337	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20462613	20462613	__UNKNOWN__	IGR	SNP	G	G	C	rs28374902	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:20462613G>C			NA	NA				RP11-173D3.1 (109407 upstream) : CHEK2P2 (25383 downstream)						NA		NA									NA						GTCCCAATCTGGGTGTAGAGG	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20462613G>C		NA		hg19		0.02	4.869852	TCTxGGT	COVERED																																																																																			NOVEL					0			0	3.912697	KEEP	0	0	0	13	461	GG	0.994391	0.99439	0			19	60	727	0	0	58.566165	107	60	4015	163		0.150794	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22440731	22440731	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:22440731C>T			NA	NA				RP11-2F9.4 (4554 upstream) : IGHV1OR15-1 (7650 downstream)						NA		NA									NA						GCGGCGGGGGCCAGTCTTGGT	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22440731C>T		NA		hg19		0.02	6.119435	GGGxCAG	COVERED																																																																																			NOVEL					0			0	11.379583	KEEP	0	0	0	38	1157	CC	1	1	0			15	60	439	0	0	29.380248	149	60	4649	256		0.091463	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22489900	22489900	__UNKNOWN__	IGR	SNP	T	T	C	rs113115466		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:22489900T>C			NA	NA				IGHV4OR15-8 (16547 upstream) : MIR1268A (23328 downstream)						NA		NA									NA						CTAAATACTGTTTTCTTCAGG	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													40	35	37	NA		NA	NA	15		NA											NA				22489900		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22489900T>C		NA		hg19		0.02	2.232891	CTGxTTT	COVERED																																																																																			NOVEL					0			1	3.309271	KEEP	0	0	0	11	338	TT	0.993072	0.992752	0			6	60	227	0	0	16.750819	62	60	2207	129		0.088235	0.999678
TRPM1	4308	__UNKNOWN__	__UNKNOWN__	15	31327931	31327931	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:31327931A>C	ENST00000256552.6	-	21	2719				TRPM1_ENST00000542188.1_Intron|RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000397795.2_Intron	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1	NA		NA								NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		TAGCAATCAAATTTTGAAACG	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160	4308		Voltage-gated ion channels / Transient receptor potential cation channels	7146	protein-coding gene	gene with protein product		603576	melastatin 1	MLSN1	NA	9806836, 9537257, 16382100	Standard	NM_002420	NM_001252020	NA	Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2572-54T>G	chr15.hg19:g.31327931A>C		NA		hg19	CCDS58346.1	0.02	7.511589	CAAxTTT	COVERED																																																																																			NOVEL	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417166.2	1	12.33543	KEEP	0	0	0	41	1308	AA	1	1	0		-	10	60	390	0	0	27.701727	144	60	5257	240	ENST00000256552.6	0.064935	1
KLF13	51621	__UNKNOWN__	__UNKNOWN__	15	31667896	31667896	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:31667896A>G	ENST00000307145.3	+	0	4619					NM_015995.2	NP_057079.2	Q9Y2Y9	KLF13_HUMAN	Kruppel-like factor 13	NA		NA			negative regulation of cell proliferation (GO:0008285)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)	2		all_lung(180;3.71e-11)		all cancers(64;1.11e-18)|Epithelial(43;1.73e-14)|GBM - Glioblastoma multiforme(186;0.00016)|Colorectal(1;0.00158)|BRCA - Breast invasive adenocarcinoma(123;0.00255)|COAD - Colon adenocarcinoma(236;0.0446)|READ - Rectum adenocarcinoma(1;0.13)|Lung(196;0.171)		AGCTCCCCAAATGCCTACTGG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF132599	CCDS10025.1	15q13.3	2013-01-08			ENSG00000169926	ENSG00000169926	51621		Kruppel-like transcription factors, Zinc fingers, C2H2-type	13672	protein-coding gene	gene with protein product		605328			NA	10415854, 10023774	Standard	NM_015995	NM_015995	NA	Approved	RFLAT-1, BTEB3, NSLP1, FKLF-2	uc001zfo.3	Q9Y2Y9	OTTHUMG00000172224	ENST00000307145.3:c.*3394A>G	chr15.hg19:g.31667896A>G		NA	Q9Y356	hg19	CCDS10025.1	0.02	4.913495	CAAxTGC	COVERED																																																																																			NOVEL	KLF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251381.1	2	12.03608	KEEP	0	0	0	40	1274	AA	1	0.999999	0		+	20	60	756	0	0	61.588139	101	60	3627	200	ENST00000307145.3	0.165289	0.999999
CHRNA7	1139	__UNKNOWN__	__UNKNOWN__	15	32462832	32462832	__UNKNOWN__	3'UTR	SNP	T	T	A	rs71220246	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:32462832T>A	ENST00000306901.3	+	0	3779					NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	NA		NA			activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)			endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	TCAAATAACTTCTCTGTCCTT	0.318	NA	NA											A|||	1064	0.21246	0.0741	0.2565	5008	,	,	NA	10555	0.12	NA	0.3728	False	NA	,,,	NA	NA	NA	2504	0.2986	NA	NA	NA	Esophageal Squamous(193;529 2900 40232 43193)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344	1139		Cholinergic receptors, Ligand-gated ion channels / Acetylcholine receptors, nicotinic	1960	protein-coding gene	gene with protein product	acetylcholine receptor, nicotinic, alpha 7 (neuronal)	118511	cholinergic receptor, nicotinic, alpha polypeptide 7		NA	8188270	Standard		NM_001190455	NA	Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.*2173T>A	chr15.hg19:g.32462832T>A		NA	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	hg19	CCDS10027.1	0.02	-0.219294	ACTxCTC	COVERED																																																																																			NOVEL	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251410.2	1	2.708378	KEEP	0	0	0	9	293	TT	0.99254	0.548763	0		+	4	40	138	0	0	10.935795	21	50	770	44	ENST00000306901.3	0.16	0.552887
FMN1	342184	__UNKNOWN__	__UNKNOWN__	15	33261055	33261055	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:33261055T>G	ENST00000559047.1	-	5	2846	c.2847A>C	c.(2845-2847)ccA>ccC	p.P949P	FMN1_ENST00000334528.9_Silent_p.P726P|FMN1_ENST00000561249.1_Silent_p.P851P			Q68DA7	FMN1_HUMAN	formin 1	949	FH1.|Pro-rich.	NA			actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		GTGCAAGTCCTGGGGGTGGTG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													26	27	27	NA		NA	NA	15		NA											NA				33261055		1775	3996	5771	SO:0001819	synonymous_variant			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905	342184			3768	protein-coding gene	gene with protein product	limb deformity protein	136535	formin (limb deformity)	LD, FMN	NA	1673046	Standard	NM_001103184	NM_001277313	NA	Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2847A>C	chr15.hg19:g.33261055T>G		NA	Q3B7I6|Q3ZAR4|Q6ZSY1	hg19		0.02	-0.20033	TCCxGGG	COVERED																																																																																			NOVEL	FMN1-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417414.1	3	3.549504	KEEP	0	1	14	17	498	TT	0.999859	0.490475	0		-	5	60	93	0	1	6.485271	18	60	584	53	ENST00000559047.1	0.217391	0.490544
AQR	9716	__UNKNOWN__	__UNKNOWN__	15	35261775	35261775	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:35261775T>C	ENST00000156471.5	-	1	265	c.40A>G	c.(40-42)Acg>Gcg	p.T14A		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	14		NA			mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TGGGACACCGTAGGGGCCACG	0.632	NA	NA									OREG0023038	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	44	42	NA		NA	NA	15		NA											NA				35261775		2046	4178	6224	SO:0001583	missense			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776	9716			29513	protein-coding gene	gene with protein product	functional spliceosome-associated protein 164	610548	aquarius homolog (mouse)		NA	9626505, 16949364	Standard	NM_014691	NM_014691	NA	Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.40A>G	chr15.hg19:g.35261775T>C	ENSP00000156471:p.Thr14Ala	854	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	hg19	CCDS42013.1	0.02	9.800749	CCGxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	T	17.61	3.432872	0.62844	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.95103	-3.61	4.86	4.86	0.63082	.	0.143965	0.56097	D	0.000033	D	0.94398	0.8198	M	0.89163	3.01	0.42050	D	0.991115	P	0.35411	0.5	B	0.33960	0.173	D	0.94750	0.7926	10	0.72032	D	0.01	-11.6385	11.947	0.52934	0.0:0.0:0.0:1.0	.	14	O60306	AQR_HUMAN	A	14	ENSP00000156471:T14A	ENSP00000156471:T14A	T	-	1	0	AQR	33049067	0.981000	0.34729	0.695000	0.30226	0.257000	0.26127	2.661000	0.46758	2.048000	0.60808	0.460000	0.39030	ACG	NOVEL	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417526.2	2	50.772099	KEEP	0	0	0	169	4986	TT	1	1	0		-	168	60	6176	0	0	632.039189	76	60	2491	501	ENST00000156471.5	0.688525	1
BAHD1	22893	__UNKNOWN__	__UNKNOWN__	15	40750864	40750864	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:40750864C>A	ENST00000416165.1	+	2	272	c.201C>A	c.(199-201)ccC>ccA	p.P67P	BAHD1_ENST00000561234.1_Silent_p.P67P|BAHD1_ENST00000560846.1_Silent_p.P67P	NM_014952.3	NP_055767.3	Q8TBE0	BAHD1_HUMAN	bromo adjacent homology domain containing 1	67		NA			heterochromatin assembly (GO:0031507)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|chromosome (GO:0005694)	chromatin binding (GO:0003682)			NS(1)|endometrium(6)|kidney(3)|large_intestine(3)|lung(10)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	28		all_cancers(109;8.28e-19)|all_epithelial(112;2.64e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.46e-06)|BRCA - Breast invasive adenocarcinoma(123;0.08)		CTGAGAAGCCCAAGGCCTGCA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													65	61	62	NA		NA	NA	15		NA											NA				40750864		2203	4300	6503	SO:0001819	synonymous_variant			AL833923	CCDS10058.1, CCDS73705.1	15q14	2005-11-10			ENSG00000140320	ENSG00000140320	22893			29153	protein-coding gene	gene with protein product		613880			NA	10231032	Standard	NM_014952	XM_005254229	NA	Approved	KIAA0945	uc001zlu.2	Q8TBE0	OTTHUMG00000129982	ENST00000416165.1:c.201C>A	chr15.hg19:g.40750864C>A		NA	Q8NDF7|Q9Y2F4	hg19	CCDS10058.1	0.02	4.573111	GCCxAAG	COVERED																																																																																			NOVEL	BAHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252248.1	3	20.764567	KEEP	0	0	0	69	2388	CC	1	1	0		+	20	60	709	0	0	55.723527	117	60	4304	246	ENST00000416165.1	0.145985	1
MGA	23269	__UNKNOWN__	__UNKNOWN__	15	42046649	42046649	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:42046649A>G	ENST00000570161.1	+	17	7023	c.7023A>G	c.(7021-7023)gaA>gaG	p.E2341E	MGA_ENST00000389936.4_Silent_p.E2302E|MGA_ENST00000545763.1_Silent_p.E2132E|MGA_ENST00000566586.1_Silent_p.E2132E|MGA_ENST00000219905.7_Silent_p.E2341E			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0		NA			carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ACTGTGTAGAATACATTGAGG	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													57	58	57	NA		NA	NA	15		NA											NA				42046649		1957	4140	6097	SO:0001819	synonymous_variant			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197	23269		MAX dimerization proteins, T-boxes	14010	protein-coding gene	gene with protein product		NA	MAX gene associated		NA		Standard	NM_001164273.1	NM_001080541	NA	Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7023A>G	chr15.hg19:g.42046649A>G		NA	Q0VAX6|Q75ME7|Q86UM5	hg19	CCDS55959.1	0.02	2.232927	AGAxTAC	COVERED																																																																																			NOVEL	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000420229.1	4	9.620614	KEEP	0	0	0	32	1034	AA	0.999997	0.999675	0		+	34	60	1264	0	0	117.559245	52	60	1890	138	ENST00000570161.1	0.395349	0.999678
GANC	2595	__UNKNOWN__	__UNKNOWN__	15	42570201	42570201	__UNKNOWN__	Intron	SNP	A	A	G	rs12916523	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:42570201A>G	ENST00000566442.1	+	4	793				GANC_ENST00000318010.8_Intron|GANC_ENST00000440615.2_Intron			Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	NA		NA			carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GCTTTCTAACATATTCCCTCT	0.289	NA	NA											A|||	4481	0.894768	0.7126	0.9813	5008	,	,	NA	17827	0.9415	NA	0.997	False	NA	,,,	NA	NA	NA	2504	0.9264	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	2595	3.2.1.20		4139	protein-coding gene	gene with protein product		104180			NA	6995030, 12370436	Standard	NM_198141	NM_198141	NA	Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000566442.1:c.93-479A>G	chr15.hg19:g.42570201A>G		NA	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	hg19		0.02	-0.228093	AACxTAT	COVERED																																																																																			NOVEL	GANC-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420684.1	0	2.407172	KEEP	0	0	0	8	247	AA	0.99257	0.578599	0		+	18	60	615	0	0	63.64769	7	60	259	41	ENST00000566442.1	0.72	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	45118177	45118177	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:45118177C>T			NA	NA				TRIM69 (58150 upstream) : CTD-2008A1.1 (560 downstream)						NA		NA									NA						AGGTCCAAATCTTACCAGAAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.45118177C>T		NA		hg19		0.02	18.423298	AATxTTA	COVERED																																																																																			NOVEL					0			5	32.204505	KEEP	23	0	0	107	3816	CC	1	1	0			140	49	5107	0	0	457.632961	302	50	11440	693		0.316742	1
CTD-2008A1.2	0	__UNKNOWN__	__UNKNOWN__	15	45123796	45123796	__UNKNOWN__	RNA	SNP	A	A	T	rs147030370	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:45123796A>T	ENST00000561384.2	-	0	831										NA		NA									NA						GCACCCCAGCAGACCTTCTAC	0.577	NA	NA											A|||	127	0.0253594	0.0038	0.036	5008	,	,	NA	15417	0.0069	NA	0.0467	False	NA	,,,	NA	NA	NA	2504	0.044	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000561384.2:	chr15.hg19:g.45123796A>T		NA		hg19		0.02	4.381374	AGCxGAC	COVERED																																																																																			NOVEL	CTD-2008A1.2-002	PUTATIVE	basic	processed_transcript	NA	pseudogene	OTTHUMT00000416181.2	2	10.661665	KEEP	0	1	24	44	1350	AA	1	0.999973	0		-	6	21	207	1	0	13.661407	96	60	3396	176	ENST00000561384.2	0.058824	0.999973
BLOC1S6	26258	__UNKNOWN__	__UNKNOWN__	15	45899556	45899556	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:45899556T>C	ENST00000568816.1	+	0	1661				BLOC1S6_ENST00000220531.3_3'UTR|RP11-96O20.4_ENST00000564080.1_Intron			Q9UL45	BL1S6_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	NA		NA			anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|endosome to melanosome transport (GO:0035646)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of pigment cell differentiation (GO:0050942)|post-Golgi vesicle-mediated transport (GO:0006892)|secretion of lysosomal enzymes (GO:0033299)|synaptic vesicle docking involved in exocytosis (GO:0016081)	BLOC-1 complex (GO:0031083)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|transport vesicle (GO:0030133)	actin filament binding (GO:0051015)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)				NA						TATATATTCCTAAAGCTTGGT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF080470	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164	26258		Biogenesis of lysosomal organelles complex-1 subunits	8549	protein-coding gene	gene with protein product		604310	pallid (mouse) homolog, pallidin, pallidin homolog (mouse)	PA, PLDN	NA	10610180	Standard	NM_012388	NM_012388	NA	Approved	HPS9	uc001zvq.3	Q9UL45	OTTHUMG00000131477	ENST00000568816.1:c.*844T>C	chr15.hg19:g.45899556T>C		NA		hg19		0.02	2.369833	TCCxAAA	COVERED																																																																																			NOVEL	BLOC1S6-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420260.1	2	6.604	KEEP	0	0	0	22	673	TT	0.999879	0.986034	0		+	8	60	311	0	0	24.748311	51	60	1875	109	ENST00000568816.1	0.135593	0.986153
FBN1	2200	__UNKNOWN__	__UNKNOWN__	15	48787830	48787830	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:48787830G>T	ENST00000316623.5	-	21	2875					NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	NA		NA			extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		TCTAGTCTTGGGCCTAAAAGA	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													81	88	86	NA		NA	NA	15		NA											NA				48787830		2195	4296	6491	SO:0001627	intron_variant			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147	2200			3603	protein-coding gene	gene with protein product	Marfan syndrome	134797	fibrillin 1 (Marfan syndrome)	FBN, MFS1, WMS	NA	10036187, 12525539	Standard		NM_000138	NA	Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.2420-45C>A	chr15.hg19:g.48787830G>T		NA	B2RUU0|D2JYH6|Q15972|Q75N87	hg19	CCDS32232.1	0.02	1.868586	TTGxGCC	COVERED																																																																																			NOVEL	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417355.1	3	12.932692	KEEP	0	0	0	43	1427	GG	1	0.999407	0		-	4	60	146	0	0	9.569962	78	60	2842	150	ENST00000316623.5	0.04878	0.999407
FBN1	2200	__UNKNOWN__	__UNKNOWN__	15	48936934	48936934	__UNKNOWN__	Silent	SNP	C	C	T	rs397515785		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:48936934C>T	ENST00000316623.5	-	2	488	c.33G>A	c.(31-33)ctG>ctA	p.L11L	FBN1_ENST00000560355.1_Silent_p.L11L	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	11		NA			extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CGGTAAATCCCAGGGCGATCT	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	63	64	NA		NA	NA	15		NA											NA				48936934		2197	4296	6493	SO:0001819	synonymous_variant			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147	2200			3603	protein-coding gene	gene with protein product	Marfan syndrome	134797	fibrillin 1 (Marfan syndrome)	FBN, MFS1, WMS	NA	10036187, 12525539	Standard		NM_000138	NA	Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.33G>A	chr15.hg19:g.48936934C>T		NA	B2RUU0|D2JYH6|Q15972|Q75N87	hg19	CCDS32232.1	0.02	4.344421	TCCxAGG	COVERED																																																																																			NOVEL	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417355.1	3	20.141817	KEEP	0	0	0	67	2233	CC	1	1	0		-	32	60	1023	0	0	86.189734	97	60	3472	242	ENST00000316623.5	0.248062	1
SHC4	399694	__UNKNOWN__	__UNKNOWN__	15	49255465	49255465	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:49255465T>C	ENST00000332408.4	-	0	176					NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	NA		NA			apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		CGCCTTGGAATCCTTGTCGGG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634	399694		SH2 domain containing	16743	protein-coding gene	gene with protein product	rai-like protein	NA			NA		Standard	NM_203349	NM_203349	NA	Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.-253A>G	chr15.hg19:g.49255465T>C		NA	Q6UXQ3|Q8IYW3	hg19	CCDS10130.1	0.02	2.008957	GAAxCCT	COVERED																																																																																			NOVEL	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254371.1	3	10.797446	KEEP	0	0	0	36	1024	TT	0.999999	0.994421	0		-	7	60	250	0	0	18.697218	58	60	2112	121	ENST00000332408.4	0.107692	0.994422
AP4E1	23431	__UNKNOWN__	__UNKNOWN__	15	51289792	51289792	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:51289792G>A	ENST00000261842.5	+	18	2722	c.2616G>A	c.(2614-2616)ctG>ctA	p.L872L	AP4E1_ENST00000560508.1_Silent_p.L797L	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	872		NA			intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ATTGTAGTCTGTCTACACCTT	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													115	111	113	NA		NA	NA	15		NA											NA				51289792		2196	4294	6490	SO:0001819	synonymous_variant			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014	23431			573	protein-coding gene	gene with protein product		607244			NA	10436028, 21620353	Standard		NM_007347	NA	Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2616G>A	chr15.hg19:g.51289792G>A		NA	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	hg19	CCDS32240.1	0.02	10.39573	TCTxTCT	COVERED																																																																																			NOVEL	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418656.1	7	26.405209	KEEP	0	1	23	96	3406	GG	1	1	0		+	12	60	442	0	0	28.232702	278	60	10606	497	ENST00000261842.5	0.041379	1
LYSMD2	256586	__UNKNOWN__	__UNKNOWN__	15	52029590	52029590	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:52029590G>T	ENST00000558126.1	-	2	167				LYSMD2_ENST00000267838.3_Missense_Mutation_p.A77E|LYSMD2_ENST00000454181.2_Intron|LYSMD2_ENST00000560491.1_Intron			Q8IV50	LYSM2_HUMAN	LysM, putative peptidoglycan-binding, domain containing 2	NA		NA								lung(2)|upper_aerodigestive_tract(1)	3				all cancers(107;0.00258)		CGTGTCGCCCGCGCGGACCCG	0.766	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													2	2	2	NA		NA	NA	15		NA											NA				52029590		1296	2841	4137	SO:0001627	intron_variant			AY125955	CCDS10143.1, CCDS45259.1	15q21.2	2005-08-09			ENSG00000140280	ENSG00000140280	256586			28571	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_153374	NM_153374	NA	Approved	MGC35274	uc002abi.3	Q8IV50	OTTHUMG00000131804	ENST00000558126.1:c.83-12402C>A	chr15.hg19:g.52029590G>T		NA	Q5CZ88|Q8WTV3	hg19		0.02	-0.298166	CCCxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831410	0.91036	.	.	ENSG00000140280	ENST00000267838	T	0.39592	1.07	4.22	4.22	0.49857	Peptidoglycan-binding Lysin subgroup (1);Peptidoglycan-binding lysin domain (1);	0.314447	0.33161	N	0.005215	T	0.27731	0.0682	N	0.11818	0.18	0.80722	D	1	D	0.54601	0.967	B	0.43916	0.436	T	0.05321	-1.0892	10	0.14656	T	0.56	.	16.8192	0.85741	0.0:0.0:1.0:0.0	.	77	Q8IV50	LYSM2_HUMAN	E	77	ENSP00000267838:A77E	ENSP00000267838:A77E	A	-	2	0	LYSMD2	49816882	1.000000	0.71417	0.998000	0.56505	0.960000	0.62799	4.609000	0.61148	2.199000	0.70637	0.281000	0.19383	GCG	NOVEL	LYSMD2-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000419219.1	0	25.578833	KEEP	0	0	0	85	2898	GG	1	0.78106	0		-	11	60	380	0	0	33.955384	23	60	790	183	ENST00000558126.1	0.323529	0.78106
RAB27A	5873	__UNKNOWN__	__UNKNOWN__	15	55496052	55496052	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:55496052C>T	ENST00000396307.2	-	0	2570				RAB27A_ENST00000336787.1_3'UTR	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		ATTTTACCAACCATGGATAAG	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974	5873		RAB, member RAS oncogene	9766	protein-coding gene	gene with protein product		603868			NA	7592656	Standard	NM_004580, NM_183236	NM_183235	NA	Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.*1653G>A	chr15.hg19:g.55496052C>T		NA	O00195|Q6FI40|Q9UIR9|Q9Y5U3	hg19	CCDS10153.1	0.02	2.226264	CAAxCAT	COVERED																																																																																			NOVEL	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254918.1	1	7.462156	KEEP	0	0	0	25	845	CC	0.999931	0.992857	0		-	20	60	734	0	0	65.683148	44	60	1586	117	ENST00000396307.2	0.3125	0.992926
NEDD4	4734	__UNKNOWN__	__UNKNOWN__	15	56243808	56243808	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:56243808A>G	ENST00000435532.3	-	3	310					NM_006154.2	NP_006145.2	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	NA		NA			adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		aaaaaaaaaaaagaaagaaaa	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													9	10	10	NA		NA	NA	15		NA											NA				56243808		1634	3660	5294	SO:0001627	intron_variant			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869	4734			7727	protein-coding gene	gene with protein product	receptor-potentiating factor 1	602278	neural precursor cell expressed, developmentally down-regulated 4		NA	9073511, 8649367	Standard	NM_198400	XR_243101	NA	Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000435532.3:c.120-21T>C	chr15.hg19:g.56243808A>G		NA	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	hg19	CCDS45265.1	0.02	-0.131599	AAAxAGA	COVERED																																																																																			NOVEL	NEDD4-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359821.2	0	2.407199	KEEP	0	0	0	8	245	AA	0.99257	0.22747	0		-	5	60	197	0	0	18.323931	8	60	298	26	ENST00000435532.3	0.384615	0.229173
POLR2M	81488	__UNKNOWN__	__UNKNOWN__	15	58009404	58009404	__UNKNOWN__	3'UTR	SNP	C	C	T	rs2414518		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:58009404C>T	ENST00000299638.3	+	0	3848				POLR2M_ENST00000380557.4_3'UTR|POLR2M_ENST00000380563.2_Intron	NM_015532.3	NP_056347.1	P0CAP2	GRL1A_HUMAN	polymerase (RNA) II (DNA directed) polypeptide M	NA		NA			maintenance of ER location (GO:0051685)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)	DNA-directed RNA polymerase activity (GO:0003899)				NA						GTTTTTTCTACACTGTCAATA	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF326773	CCDS32252.1, CCDS42045.1	15q21.3	2013-01-21	2011-11-07	2011-11-07		ENSG00000255529	81488		RNA polymerase subunits	14862	protein-coding gene	gene with protein product		606485	glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A	GRINL1A	NA	16769904, 22850672	Standard		NM_015532	NA	Approved	Gdown, Gdown1, GCOM1	uc002aev.1	P0CAP2	OTTHUMG00000166486	ENST00000299638.3:c.*2527C>T	chr15.hg19:g.58009404C>T		NA	Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5|Q9Y3V6	hg19	CCDS32252.1	0.02	18.811222	CTAxACT	COVERED																																																																																			NOVEL	POLR2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255719.2	11	9.910183	KEEP	1	9	267	127	4574	CC	1	1	0		+	31	60	1084	0	0	73.079499	457	60	17359	767	ENST00000299638.3	0.063525	1
TLN2	83660	__UNKNOWN__	__UNKNOWN__	15	63084965	63084965	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:63084965C>T	ENST00000561311.1	+	45	6092	c.5862C>T	c.(5860-5862)tgC>tgT	p.C1954C	TLN2_ENST00000306829.6_Silent_p.C1954C			Q9Y4G6	TLN2_HUMAN	talin 2	1954		NA			cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						TGATCGAATGCGCCCGTGCCG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	43	43	NA		NA	NA	15		NA											NA				63084965		2203	4300	6503	SO:0001819	synonymous_variant			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914	83660			15447	protein-coding gene	gene with protein product		607349			NA	9205841, 11527381	Standard		NM_015059	NA	Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.5862C>T	chr15.hg19:g.63084965C>T		NA	A6NLB8	hg19	CCDS32261.1	0.02	1.82833	ATGxGCC	COVERED																																																																																			NOVEL	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257878.2	0	13.841955	KEEP	0	0	0	46	1554	CC	1	0.999948	0		+	5	60	187	0	0	12.512501	93	60	3205	180	ENST00000561311.1	0.05102	0.999948
TPM1	7168	__UNKNOWN__	__UNKNOWN__	15	63363244	63363244	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:63363244C>A	ENST00000357980.4	+	10	977				TPM1_ENST00000267996.7_Intron|TPM1_ENST00000358278.3_Intron|TPM1_ENST00000559556.1_Intron|TPM1_ENST00000559397.1_Intron|TPM1_ENST00000404484.4_Intron|RP11-244F12.2_ENST00000558905.1_RNA			P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	NA		NA			cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						ACCATTGTGTCCAAAGCACAG	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													69	64	66	NA		NA	NA	15		NA											NA				63363244		2203	4300	6503	SO:0001627	intron_variant			AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416	7168		Tropomyosins	12010	protein-coding gene	gene with protein product		191010	chromosome 15 open reading frame 13, cardiomyopathy, hypertrophic 3	C15orf13, CMH3	NA	10343096, 8205619	Standard	NM_001018004	XM_005254637	NA	Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000357980.4:c.899-45C>A	chr15.hg19:g.63363244C>A		NA	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	hg19		0.02	17.888787	TGTxCAA	COVERED																																																																																			NOVEL	TPM1-008	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000417087.2	6	44.244962	KEEP	0	0	0	147	5239	CC	1	1	0		+	40	60	1410	0	0	103.10067	372	60	13667	747	ENST00000357980.4	0.097087	1
HERC1	8925	__UNKNOWN__	__UNKNOWN__	15	64048854	64048854	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:64048854C>A	ENST00000443617.2	-	5	1402	c.1315G>T	c.(1315-1317)Gac>Tac	p.D439Y		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	439		NA			cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TTATTGGAGTCTCCAAGGCCC	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	31	32	NA		NA	NA	15		NA											NA				64048854		1877	4110	5987	SO:0001583	missense			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657	8925		WD repeat domain containing	4867	protein-coding gene	gene with protein product		605109	hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1		NA	8861955, 9233772	Standard	NM_003922	NM_003922	NA	Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.1315G>T	chr15.hg19:g.64048854C>A	ENSP00000390158:p.Asp439Tyr	NA	Q8IW65	hg19	CCDS45277.1	0.02	6.370729	AGTxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815594	0.90790	.	.	ENSG00000103657	ENST00000443617	D	0.82081	-1.57	5.24	5.24	0.73138	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	U	0.000000	D	0.91043	0.7182	M	0.75615	2.305	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.80764	0.983;0.994	D	0.91333	0.5091	10	0.59425	D	0.04	.	19.1806	0.93622	0.0:1.0:0.0:0.0	.	439;439	C9JUT5;Q15751	.;HERC1_HUMAN	Y	439	ENSP00000390158:D439Y	ENSP00000390158:D439Y	D	-	1	0	HERC1	61835907	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.750000	0.85110	2.611000	0.88343	0.561000	0.74099	GAC	NOVEL	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418523.1	2	14.145935	KEEP	0	0	0	47	1667	CC	1	1	0		-	18	60	622	0	0	44.94462	175	60	6519	285	ENST00000443617.2	0.093264	1
PLEKHO2	80301	__UNKNOWN__	__UNKNOWN__	15	65134096	65134096	__UNKNOWN__	5'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:65134096C>G	ENST00000323544.4	+	0	9					NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	NA		NA								NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						TTCTTGGGCCCCCGGCAGCCG	0.831	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839	80301		Pleckstrin homology (PH) domain containing	30026	protein-coding gene	gene with protein product		NA	pleckstrin homology domain containing, family Q member 1	PLEKHQ1	NA	12477932	Standard	NM_025201	NM_025201	NA	Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.-120C>G	chr15.hg19:g.65134096C>G		NA	Q7L4H4|Q8WYS8	hg19	CCDS10196.1	0.02	-0.078696	GCCxCCG	UNCOVERED																																																																																			NOVEL	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256659.1	0	2.406861	KEEP	0	0	0	8	252	CC	0.99257	0.076761	0		+	3	60	83	0	0	7.429014	5	60	168	18	ENST00000323544.4	0.375	0.077336
RPL4	6124	__UNKNOWN__	__UNKNOWN__	15	66794372	66794372	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:66794372C>T	ENST00000568588.1	-	6	917				SNORD18B_ENST00000365659.1_RNA|RPL4_ENST00000307961.6_Intron			P36578	RL4_HUMAN	ribosomal protein L4	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						TCAGAATTTCCACAAATATCA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													102	101	101	NA		NA	NA	15		NA											NA				66794372		876	1991	2867	SO:0001627	intron_variant			AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444	6124		L ribosomal proteins	10353	protein-coding gene	gene with protein product	60S ribosomal protein L4	180479			NA	9582194, 8268230	Standard	NM_000968	NM_000968	NA	Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000568588.1:c.140-122G>A	chr15.hg19:g.66794372C>T		NA	A8K502|P39029|Q4VBR0|Q969Z9	hg19		0.02	-0.333226	TTCxACA	COVERED																																																																																			NOVEL	RPL4-020	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420737.1	1	5.417691	KEEP	0	0	0	18	656	CC	0.999859	0.851864	0		-	5	60	181	0	0	14.061797	33	60	1206	75	ENST00000568588.1	0.131579	0.851984
SMAD3	4088	__UNKNOWN__	__UNKNOWN__	15	67457340	67457340	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:67457340C>T	ENST00000439724.3	+	2	208	c.182C>T	c.(181-183)gCc>gTc	p.A61V	SMAD3_ENST00000540846.2_5'UTR|SMAD3_ENST00000559092.1_Missense_Mutation_p.P87S|SMAD3_ENST00000327367.4_Missense_Mutation_p.A105V	NM_001145103.1	NP_001138575.1	P84022	SMAD3_HUMAN	SMAD family member 3	105	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.	NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GAGCTACGGGCCATGGAGCTG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													104	106	106	NA		NA	NA	15		NA											NA				67457340		2201	4299	6500	SO:0001583	missense			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949	4088		SMADs	6769	protein-coding gene	gene with protein product		603109	MAD, mothers against decapentaplegic homolog 3 (Drosophila), SMAD, mothers against DPP homolog 3 (Drosophila)	MADH3	NA	8774881, 8673135	Standard	NM_005902	NM_001145102	NA	Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000439724.3:c.182C>T	chr15.hg19:g.67457340C>T	ENSP00000401133:p.Ala61Val	NA	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	hg19	CCDS45288.1	0.02	6.542276	GGGxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872339	0.51695	.	.	ENSG00000166949	ENST00000327367;ENST00000535241;ENST00000439724	T;T	0.78003	-1.14;-1.14	4.39	4.39	0.52855	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.89466	0.6723	M	0.88640	2.97	0.80722	D	1	D;P	0.71674	0.998;0.932	D;P	0.70016	0.967;0.854	D	0.91822	0.5468	10	0.72032	D	0.01	.	17.1514	0.86779	0.0:1.0:0.0:0.0	.	61;105	B7Z4Z5;P84022	.;SMAD3_HUMAN	V	105;105;61	ENSP00000332973:A105V;ENSP00000401133:A61V	ENSP00000332973:A105V	A	+	2	0	SMAD3	65244394	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.471000	0.80985	2.270000	0.75569	0.561000	0.74099	GCC	NOVEL	SMAD3-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417462.1	2	27.984383	KEEP	0	0	0	93	3259	CC	1	1	0		+	21	60	691	0	0	50.850809	163	60	5852	363	ENST00000439724.3	0.11413	1
IQCH	64799	__UNKNOWN__	__UNKNOWN__	15	67692501	67692501	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:67692501G>A	ENST00000335894.4	+	14	2021	c.1955G>A	c.(1954-1956)cGt>cAt	p.R652H	IQCH_ENST00000358767.3_Missense_Mutation_p.R388H|IQCH_ENST00000360277.4_Missense_Mutation_p.R313H|IQCH_ENST00000546225.1_Missense_Mutation_p.R309H	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	652		NA						p.R652H(2)		NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(2)|pancreas(2)|skin(5)|upper_aerodigestive_tract(1)	33				Colorectal(3;0.0856)		CAAATACAGCGTTGGCTCTTT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)											102	96	98	NA		NA	NA	15		NA											NA				67692501		2201	4299	6500	SO:0001583	missense			AY014282	CCDS10223.1, CCDS32273.1, CCDS10223.2, CCDS61680.1, CCDS61681.1	15q23	2005-10-24			ENSG00000103599	ENSG00000103599	64799			25721	protein-coding gene	gene with protein product		612523			NA	12477932	Standard	NM_022784	NM_022784	NA	Approved	FLJ12476	uc002aqo.2	Q86VS3	OTTHUMG00000133231	ENST00000335894.4:c.1955G>A	chr15.hg19:g.67692501G>A	ENSP00000336861:p.Arg652His	NA	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	hg19	CCDS32273.1	0.02	9.612662	AGCxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407769	0.83340	.	.	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.55760	0.61;0.61;0.5;0.61	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.75019	0.3793	M	0.80183	2.485	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.989;0.993	T	0.78003	-0.2374	10	0.59425	D	0.04	-24.1551	18.8189	0.92088	0.0:0.0:1.0:0.0	.	309;313;652	Q86VS3-2;Q86VS3-4;Q86VS3	.;.;IQCH_HUMAN	H	388;309;652;313	ENSP00000351617:R388H;ENSP00000444118:R309H;ENSP00000336861:R652H;ENSP00000353419:R313H	ENSP00000336861:R652H	R	+	2	0	IQCH	65479555	1.000000	0.71417	1.000000	0.80357	0.394000	0.30568	8.872000	0.92352	2.436000	0.82500	0.655000	0.94253	CGT	NOVEL	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256969.1	1	13.543284	KEEP	0	0	0	45	1561	GG	1	1	0		+	57	60	2116	0	0	184.427277	161	60	5629	334	ENST00000335894.4	0.261468	1
CORO2B	10391	__UNKNOWN__	__UNKNOWN__	15	69018255	69018255	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:69018255G>A	ENST00000543950.1	+	12	1724	c.1370G>A	c.(1369-1371)cGc>cAc	p.R457H	CORO2B_ENST00000540068.1_Missense_Mutation_p.R457H|CORO2B_ENST00000566799.1_Missense_Mutation_p.R462H|CORO2B_ENST00000261861.5_Missense_Mutation_p.R457H	NM_001190457.1	NP_001177386.1	Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	462		NA			actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						AAGGACATCCGCATTCGGCAG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	66	66	NA		NA	NA	15		NA											NA				69018255		2200	4298	6498	SO:0001583	missense			AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647	10391		Coronins, WD repeat domain containing	2256	protein-coding gene	gene with protein product	clipin C, coronin, actin-binding, 2B	605002	coronin, actin-binding protein, 2B		NA	10224093, 10231032	Standard	NM_006091	NM_001190456	NA	Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000543950.1:c.1370G>A	chr15.hg19:g.69018255G>A	ENSP00000443819:p.Arg457His	NA	A8K0W3|O94767|Q8TAN1	hg19	CCDS53952.1	0.02	12.990176	TCCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.83	2.651404	0.47362	.	.	ENSG00000103647	ENST00000261861;ENST00000540068;ENST00000543950	T;T	0.62364	0.03;0.03	3.62	3.62	0.41486	.	0.648478	0.16147	N	0.227460	T	0.52141	0.1716	L	0.41824	1.3	0.37482	D	0.916024	B	0.20261	0.043	B	0.21151	0.033	T	0.58999	-0.7536	10	0.87932	D	0	-17.6714	9.7615	0.40534	0.0:0.0:0.7933:0.2067	.	462	Q9UQ03	COR2B_HUMAN	H	462;457;457	ENSP00000446250:R457H;ENSP00000443819:R457H	ENSP00000261861:R462H	R	+	2	0	CORO2B	66805309	0.430000	0.25538	1.000000	0.80357	0.978000	0.69477	2.763000	0.47605	1.732000	0.51606	0.442000	0.29010	CGC	NOVEL	CORO2B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257068.3	3	22.497535	KEEP	0	1	32	86	2816	GG	1	1	0		+	12	60	451	0	0	28.370154	323	60	10937	525	ENST00000543950.1	0.035821	1
TMEM202	338949	__UNKNOWN__	__UNKNOWN__	15	72700048	72700048	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:72700048C>A	ENST00000567679.1	+	0	266				TMEM202_ENST00000341689.3_Silent_p.L212L			A6NGA9	TM202_HUMAN	transmembrane protein 202	NA		NA				integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	18						TCTCTCTTCTCAACTACTTAA	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													74	75	74	NA		NA	NA	15		NA											NA				72700048		2199	4297	6496	SO:0001624	3_prime_UTR_variant				CCDS32287.1	15q24.1	2007-12-18				ENSG00000187806	338949			33733	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080462	NM_001080462	NA	Approved	FLJ27523	uc002auq.3	A6NGA9		ENST00000567679.1:c.*62C>A	chr15.hg19:g.72700048C>A		NA		hg19		0.02	4.293225	TCTxAAC	COVERED																																																																																			NOVEL	TMEM202-001	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420204.2	1	5.718329	KEEP	0	0	0	19	657	CC	0.99986	0.999854	0		+	12	60	425	0	0	31.666771	100	60	3850	170	ENST00000567679.1	0.107143	0.999995
PML	5371	__UNKNOWN__	__UNKNOWN__	15	74327745	74327745	__UNKNOWN__	Intron	SNP	G	G	A	rs377501404		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:74327745G>A	ENST00000268058.3	+	7	1806				PML_ENST00000569477.1_3'UTR|PML_ENST00000564428.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Missense_Mutation_p.R648H|PML_ENST00000565898.1_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Missense_Mutation_p.R600H|PML_ENST00000563500.1_3'UTR|PML_ENST00000435786.2_3'UTR|PML_ENST00000359928.4_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						CACCAGGAGCGCCCTGCCGTC	0.667	NA	NA	T	RARA, PAX5	APL, ALL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		15	15q22	5371	promyelocytic leukemia		L	0								G	,,HIS/ARG,,,,,,HIS/ARG	1,4395	2.1+/-5.4	0,1,2197	73	69	71	NA	,,1943,,,,,,1799	-6	0	15		71	0,8594		0,0,4297	no	intron,intron,missense,utr-3,utr-3,intron,intron,intron,missense	PML	NM_002675.3,NM_033238.2,NM_033239.2,NM_033240.2,NM_033244.3,NM_033246.2,NM_033247.2,NM_033249.2,NM_033250.2	,,29,,,,,,29	0,1,6494	AA,AG,GG	NA	0.0,0.0227,0.0077	,,,,,,,,	,,648/830,,,,,,600/782	74327745	1,12989	2198	4297	6495	SO:0001627	intron_variant			AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464	5371		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	9113	protein-coding gene	gene with protein product		102578			NA		Standard	NM_002675	NM_033244	NA	Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+874G>A	chr15.hg19:g.74327745G>A		NA	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	hg19	CCDS10255.1	0.02	17.51715	AGCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.499	0.652237	0.14580	2.27E-4	0.0	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	3.02	-6.03	0.02185	.	.	.	.	.	T	0.14184	0.0343	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19549	-1.0302	8	0.72032	D	0.01	.	2.5459	0.04736	0.2036:0.27:0.3933:0.1331	.	600;648	P29590-13;P29590-8	.;.	H	648;600	.	ENSP00000268059:R648H	R	+	2	0	PML	72114798	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-3.477000	0.00458	-2.366000	0.00606	-1.587000	0.00848	CGC	NOVEL	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269021.3	4	64.094863	KEEP	0	2	59	234	7737	GG	1	1	0		+	38	60	1299	0	0	91.778641	405	60	13761	856	ENST00000268058.3	0.085779	1
PML	5371	__UNKNOWN__	__UNKNOWN__	15	74327990	74327990	__UNKNOWN__	Intron	SNP	C	C	T	rs115552704		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:74327990C>T	ENST00000268058.3	+	7	1806				PML_ENST00000564428.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Nonsense_Mutation_p.R730*|PML_ENST00000565898.1_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Nonsense_Mutation_p.R682*|PML_ENST00000563500.1_3'UTR|PML_ENST00000435786.2_3'UTR|PML_ENST00000359928.4_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						AGGGGCTGTGCGATCCCGCAG	0.617	NA	NA	T	RARA, PAX5	APL, ALL								C|||	1	0.000199681	8e-04	0	5008	,	,	NA	16011	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA			Dom	yes		15	15q22	5371	promyelocytic leukemia		L	0													55	60	58	NA		NA	NA	15		NA											NA				74327990		2197	4296	6493	SO:0001627	intron_variant			AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464	5371		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	9113	protein-coding gene	gene with protein product		102578			NA		Standard	NM_002675	NM_033244	NA	Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1710+1119C>T	chr15.hg19:g.74327990C>T		NA	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	hg19	CCDS10255.1	0.02	15.855625	GTGxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934804	0.73442	.	.	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	2.93	1.02	0.19986	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.4884	0.07629	0.25:0.6127:0.0:0.1373	.	.	.	.	X	730;682	.	ENSP00000268059:R730X	R	+	1	2	PML	72115043	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.259000	0.08721	0.281000	0.22233	-0.475000	0.04921	CGA	NOVEL	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269021.3	3	49.944194	KEEP	0	0	0	166	5427	CC	1	1	0		+	88	60	3039	0	0	256.268137	295	60	10047	680	ENST00000268058.3	0.229765	1
UBE2Q2	92912	__UNKNOWN__	__UNKNOWN__	15	76192505	76192505	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:76192505G>A	ENST00000267938.4	+	0	2216				UBE2Q2_ENST00000569423.1_3'UTR|UBE2Q2_ENST00000338677.4_3'UTR	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	NA		NA			protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						TGTTGGTTCAGTGTTTCTTAT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367	92912		Ubiquitin-conjugating enzymes E2	19248	protein-coding gene	gene with protein product		612501	ubiquitin-conjugating enzyme E2Q (putative) 2		NA	16300736	Standard	NM_173469	NM_001145335	NA	Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.*706G>A	chr15.hg19:g.76192505G>A		NA	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	hg19	CCDS10286.1	0.02	1.903726	TCAxTGT	COVERED																																																																																			NOVEL	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286475.1	2	8.126442	KEEP	0	0	0	27	966	GG	0.999988	0.99898	0		+	10	60	364	0	0	28.2007	68	60	2544	127	ENST00000267938.4	0.128205	0.998993
CHRNA3	1136	__UNKNOWN__	__UNKNOWN__	15	78894053	78894053	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:78894053T>C	ENST00000348639.3	-	5	1431	c.931A>G	c.(931-933)Acc>Gcc	p.T311A	CHRNA3_ENST00000326828.5_Missense_Mutation_p.T311A	NM_001166694.1	NP_001160166.1	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	311		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	AAAATCATGGTGAACAGGAGG	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													137	117	124	NA		NA	NA	15		NA											NA				78894053		2196	4293	6489	SO:0001583	missense				CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644	1136		Cholinergic receptors, Ligand-gated ion channels / Acetylcholine receptors, nicotinic	1957	protein-coding gene	gene with protein product	acetylcholine receptor, nicotinic, alpha 3 (neuronal)	118503	cholinergic receptor, nicotinic, alpha polypeptide 3		NA	2004777	Standard		NM_000743	NA	Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000348639.3:c.931A>G	chr15.hg19:g.78894053T>C	ENSP00000267951:p.Thr311Ala	NA	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	hg19	CCDS53964.1	0.02	7.067197	TGGxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	T	23.9	4.465656	0.84425	.	.	ENSG00000080644	ENST00000348639;ENST00000326828;ENST00000326858	T;T	0.72505	-0.66;-0.66	6.02	6.02	0.97574	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.83954	0.5366	M	0.75777	2.31	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.85130	0.997;0.995	D	0.84563	0.0651	10	0.51188	T	0.08	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	311;311	P32297;P32297-3	ACHA3_HUMAN;.	A	311;311;175	ENSP00000267951:T311A;ENSP00000315602:T311A	ENSP00000315602:T311A	T	-	1	0	CHRNA3	76681108	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.033000	0.88852	2.311000	0.77944	0.533000	0.62120	ACC	NOVEL	CHRNA3-002	KNOWN	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000290112.2	3	9.628644	KEEP	0	0	0	32	1001	TT	0.999997	0.999997	0		-	36	60	1248	0	0	102.712151	146	60	5197	282	ENST00000348639.3	0.197802	1
UNC45A	55898	__UNKNOWN__	__UNKNOWN__	15	91496998	91496998	__UNKNOWN__	3'UTR	SNP	G	G	A	rs565197531		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:91496998G>A	ENST00000418476.2	+	0	2927				AC068831.6_ENST00000553321.1_RNA|UNC45A_ENST00000394275.2_3'UTR	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	NA		NA			cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			ATTGTGGCACGGAGAGTAAGG	0.562	NA	NA											G|||	1	0.000199681	8e-04	0	5008	,	,	NA	22981	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													19	15	16	NA		NA	NA	15		NA											NA				91496998		1321	2305	3626	SO:0001624	3_prime_UTR_variant				CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553	55898			30594	protein-coding gene	gene with protein product	smooth muscle cell associated protein-1	611219			NA	12356907	Standard	NM_018671	XM_005254963	NA	Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.*52G>A	chr15.hg19:g.91496998G>A		NA	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	hg19	CCDS10367.1	0.02	9.088923	CACxGAG	COVERED																																																																																			NOVEL	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280406.2	3	21.295878	KEEP	0	0	0	71	2349	GG	1	1	0		+	8	60	309	0	0	19.563559	227	60	7944	397	ENST00000418476.2	0.034043	1
NR2F2	7026	__UNKNOWN__	__UNKNOWN__	15	96882091	96882091	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:96882091G>A	ENST00000394166.3	+	0	3874				NR2F2_ENST00000394171.2_3'UTR	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	NA		NA			anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			GAGCCCCTGTGAGCTCTCGCT	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551	7026		Nuclear hormone receptors	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2	NA	8530078, 11544252	Standard		NM_021005	NA	Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.*1240G>A	chr15.hg19:g.96882091G>A		NA	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	hg19	CCDS10375.1	0.02	2.240563	TGTxAGC	COVERED																																																																																			NOVEL	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313534.1	2	18.931802	KEEP	0	0	0	63	2183	GG	1	0.963774	0		+	22	60	769	0	0	72.257429	29	60	1056	158	ENST00000394166.3	0.431373	0.963774
IGF1R	3480	__UNKNOWN__	__UNKNOWN__	15	99507441	99507441	__UNKNOWN__	3'UTR	SNP	A	A	T	rs3825952	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:99507441A>T	ENST00000558762.1	+	0	11409				IGF1R_ENST00000268035.6_3'UTR|RP11-654A16.3_ENST00000559468.1_RNA			P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	NA		NA			axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)	TTAAAAAAAAATTTTTTTAAG	0.289	NA	NA											T|||	12	0.00239617	0	0	5008	,	,	NA	14879	0.0089	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443	3480		CD molecules, Fibronectin type III domain containing	5465	protein-coding gene	gene with protein product		147370			NA	1316909	Standard	NM_000875	XM_006720486	NA	Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000558762.1:c.*6770A>T	chr15.hg19:g.99507441A>T		NA	B1B5Y2|Q14CV2|Q9UCC0	hg19		0.02	2.1877	AAAxTTT	COVERED																																																																																			NOVEL	IGF1R-002	NOVEL	NAGNAG_splice_site|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000415271.1	0	10.217855	KEEP	0	0	0	34	1038	AA	0.999998	0.981954	0		+	8	60	300	0	0	23.777464	49	60	1787	114	ENST00000558762.1	0.140351	0.981955
DNM1P47	100216544	__UNKNOWN__	__UNKNOWN__	15	102312207	102312207	__UNKNOWN__	RNA	SNP	A	A	G	rs75381810	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr15:102312207A>G	ENST00000561463.1	+	0	13575									DNM1 pseudogene 47	NA		NA									NA						CTCCTGGACCAGGCTCATCAG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660	100216544			35200	pseudogene	pseudogene		NA		DNM1DN14@	NA		Standard	NG_009149	NG_009149	NA	Approved	DNM1DN14-3			OTTHUMG00000172265	ENST00000561463.1:	chr15.hg19:g.102312207A>G		NA		hg19		0.02	1.900524	ACCxGGC	COVERED																																																																																			NOVEL	DNM1P47-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417589.1	1	4.798333	KEEP	0	0	0	16	449	AA	0.997832	0.992926	0		+	4	49	138	0	0	9.131798	63	50	2297	107	ENST00000561463.1	0.059701	0.995084
RAB11FIP3	9727	__UNKNOWN__	__UNKNOWN__	16	553092	553092	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:553092G>C	ENST00000262305.4	+	7	1778	c.1390G>C	c.(1390-1392)Gac>Cac	p.D464H	RAB11FIP3_ENST00000457159.1_Missense_Mutation_p.D509H|RAB11FIP3_ENST00000450428.1_Missense_Mutation_p.D168H	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	464		NA			cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				GGACATTGCTGACAAGGTAGG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(160;2366 2595 4474 8099)					NA		NA				0													62	64	63	NA		NA	NA	16		NA											NA				553092		2201	4300	6501	SO:0001583	missense			AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565	9727		EF-hand domain containing	17224	protein-coding gene	gene with protein product		608738			NA	9734811, 11481332	Standard	NM_014700	NM_014700	NA	Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.1390G>C	chr16.hg19:g.553092G>C	ENSP00000262305:p.Asp464His	NA	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	hg19	CCDS32351.1	0.02	2.241736	GCTxACA	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.46	3.130821	0.56828	.	.	ENSG00000090565	ENST00000262305;ENST00000457159;ENST00000434585;ENST00000450428;ENST00000452814;ENST00000448401	.	.	.	5.7	5.7	0.88788	.	.	.	.	.	T	0.76492	0.3995	L	0.60455	1.87	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.998	T	0.76677	-0.2871	8	0.56958	D	0.05	-53.4506	16.5532	0.84477	0.0:0.0:1.0:0.0	.	509;168;464	O75154-3;O75154-2;O75154	.;.;RFIP3_HUMAN	H	464;509;385;168;154;168	.	ENSP00000262305:D464H	D	+	1	0	RAB11FIP3	493093	1.000000	0.71417	0.996000	0.52242	0.937000	0.57800	7.508000	0.81686	2.703000	0.92315	0.585000	0.79938	GAC	NOVEL	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109066.4	1	3.31084	KEEP	0	0	0	11	394	GG	0.993072	0.992697	0		+	22	60	839	0	0	73.290492	63	60	2359	113	ENST00000262305.4	0.258824	0.999622
WDR24	84219	__UNKNOWN__	__UNKNOWN__	16	734971	734971	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:734971C>A	ENST00000293883.4	-	8	2964				WDR24_ENST00000248142.6_Intron	NM_032259.2	NP_115635.1	Q96S15	WDR24_HUMAN	WD repeat domain 24	NA		NA								breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				CCTGCCCCACCTCCCGACCCC	0.731	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													7	8	8	NA		NA	NA	16		NA											NA				734971		2006	3906	5912	SO:0001627	intron_variant			AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580	84219		WD repeat domain containing	20852	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 21	C16orf21	NA	11230166	Standard	NM_032259	NM_032259	NA	Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000293883.4:c.2204+20G>T	chr16.hg19:g.734971C>A		NA	A2IDB8|D3DU59|Q96GC7|Q9H0B7	hg19	CCDS10420.1	0.02	2.170708	CACxTCC	COVERED																																																																																			NOVEL	WDR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206852.1	2	9.834071	KEEP	0	0	0	33	1040	CC	0.999998	0.986152	0		-	14	60	469	0	0	39.547389	45	60	1510	106	ENST00000293883.4	0.237288	0.986153
WDR24	84219	__UNKNOWN__	__UNKNOWN__	16	737968	737968	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:737968C>T	ENST00000293883.4	-	2	1241				WDR24_ENST00000248142.6_Missense_Mutation_p.A271T	NM_032259.2	NP_115635.1	Q96S15	WDR24_HUMAN	WD repeat domain 24	NA		NA								breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				TACTCCCGGGCGTCATTTGCC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580	84219		WD repeat domain containing	20852	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 21	C16orf21	NA	11230166	Standard	NM_032259	NM_032259	NA	Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000293883.4:c.482-229G>A	chr16.hg19:g.737968C>T		NA	A2IDB8|D3DU59|Q96GC7|Q9H0B7	hg19	CCDS10420.1	0.02	4.573462	GGGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	2.979	-0.210768	0.06140	.	.	ENSG00000127580	ENST00000248142	T	0.77229	-1.08	2.5	0.52	0.17040	.	1.509350	0.05273	U	0.517843	T	0.63698	0.2533	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.50508	-0.8820	7	0.27785	T	0.31	.	3.0693	0.06225	0.2655:0.5835:0.0:0.151	.	.	.	.	T	271	ENSP00000248142:A271T	ENSP00000248142:A271T	A	-	1	0	WDR24	677969	0.015000	0.18098	0.000000	0.03702	0.001000	0.01503	1.044000	0.30329	0.179000	0.19938	-0.652000	0.03908	GCC	NOVEL	WDR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206852.1	2	9.026358	KEEP	0	0	0	30	995	CC	0.999997	0.999997	0		-	38	60	1377	0	0	120.706546	99	60	3354	187	ENST00000293883.4	0.277372	1
TPSAB1	7177	__UNKNOWN__	__UNKNOWN__	16	1291355	1291355	__UNKNOWN__	Intron	SNP	G	G	C	rs112842602		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:1291355G>C	ENST00000338844.3	+	3	266				TPSAB1_ENST00000461509.2_Intron	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	NA		NA			defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				GAGGGGTGGGGAAGGGCTGGA	0.711	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	34	33	NA		NA	NA	16		NA											NA				1291355		2197	4296	6493	SO:0001627	intron_variant			M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236	7177			12019	protein-coding gene	gene with protein product	tryptase alpha II, tryptase beta I, tryptase-I, tryptase-II, tryptase-III	191080	tryptase beta 1	TPSB1, TPS1, TPS2	NA	2203827, 9920877	Standard	NM_003294	NM_003294	NA	Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.233+30G>C	chr16.hg19:g.1291355G>C		NA	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	hg19	CCDS10431.1	0.02	2.370036	GGGxAAG	COVERED																																																																																			NOVEL	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206914.1	1	4.815238	KEEP	1	0	0	16	543	GG	0.997832	0.984015	0		+	4	40	155	0	0	11.430774	44	50	1598	91	ENST00000338844.3	0.083333	0.986153
MAPK8IP3	23162	__UNKNOWN__	__UNKNOWN__	16	1798297	1798297	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:1798297G>A	ENST00000250894.4	+	7	1201	c.1044G>A	c.(1042-1044)acG>acA	p.T348T	MAPK8IP3_ENST00000356010.5_Silent_p.T348T|MAPK8IP3_ENST00000568271.1_3'UTR	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	348		NA			activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						TTGACTCCACGCCAGAGCTGG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	60	60	NA		NA	NA	16		NA											NA				1798297		2009	4174	6183	SO:0001819	synonymous_variant			AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834	23162			6884	protein-coding gene	gene with protein product	homolog of Drosophila Sunday driver 2	605431			NA	10523642, 10629060	Standard	NM_001040439	XM_005255187	NA	Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.1044G>A	chr16.hg19:g.1798297G>A		NA	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	hg19	CCDS10442.2	0.02	4.539494	CACxCCA	COVERED																																																																																			NOVEL	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250508.2	0	9.322785	KEEP	0	0	0	31	1018	GG	0.999997	0.999997	0		+	39	60	1412	0	0	123.726349	102	60	3435	224	ENST00000250894.4	0.276596	1
PDPK1	5170	__UNKNOWN__	__UNKNOWN__	16	2652467	2652467	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:2652467C>T	ENST00000342085.4	+	0	6519					NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	TATGAAGAAACACCAAACTAT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													71	55	60	NA		NA	NA	16		NA											NA				2652467		692	1591	2283	SO:0001624	3_prime_UTR_variant			AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992	5170			8816	protein-coding gene	gene with protein product	PkB kinase	605213			NA	9094314, 9445477	Standard		NM_002613	NA	Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.*4699C>T	chr16.hg19:g.2652467C>T		NA	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	hg19	CCDS10472.1	0.02	23.134005	AAAxACC	COVERED																																																																																			NOVEL	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250831.3	8	91.183739	KEEP	4	0	0	303	10627	CC	1	1	0		+	32	49	1123	0	0	73.991311	542	60	20208	1068	ENST00000342085.4	0.055749	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	2730882	2730882	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:2730882C>T			NA	NA				ERVK13-1 (7440 upstream) : KCTD5 (1593 downstream)						NA		NA									NA						TATGAAGAAACACCAAACTAT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.2730882C>T		NA		hg19		0.02	13.397492	AAAxACC	COVERED																																																																																			NOVEL					0			4	46.348199	KEEP	5	0	0	154	5359	CC	1	1	0			43	60	1563	0	0	121.137677	291	60	10832	577		0.128743	1
ZSCAN10	84891	__UNKNOWN__	__UNKNOWN__	16	3142319	3142319	__UNKNOWN__	Splice_Site	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:3142319T>C	ENST00000252463.2	-	2	319		c.e2-2		ZSCAN10_ENST00000538082.2_Intron|ZSCAN10_ENST00000575108.1_Splice_Site|ZSCAN10_ENST00000572548.1_Intron	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(3)|endometrium(3)|kidney(1)|lung(8)|ovary(2)|prostate(1)|skin(4)|urinary_tract(1)	24						ACTAAAATCCTGTTCAAAACA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													41	46	44	NA		NA	NA	16		NA											NA				3142319		2192	4296	6488	SO:0001630	splice_region_variant			AA206569	CCDS10493.1, CCDS61813.1, CCDS61814.1	16p13.3	2013-01-08	2007-02-20	2007-02-20		ENSG00000130182	84891		-, Zinc fingers, C2H2-type	12997	protein-coding gene	gene with protein product		NA	zinc finger protein 206	ZNF206	NA	9653642	Standard	NM_032805	NM_032805	NA	Approved		uc002ctv.1	Q96SZ4		ENST00000252463.2:c.232-2A>G	chr16.hg19:g.3142319T>C		NA	B3KQD3|H0YFS6|Q1WWM2	hg19	CCDS10493.1	0.02	7.891472	TCCxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	7.611	0.674760	0.14841	.	.	ENSG00000130182	ENST00000252463	.	.	.	4.23	3.14	0.36123	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.7937	0.18375	0.0:0.1187:0.0:0.8813	.	.	.	.	.	-1	.	.	.	-	.	.	ZSCAN10	3082320	0.994000	0.37717	0.999000	0.59377	0.855000	0.48748	2.808000	0.47963	1.923000	0.55706	0.459000	0.35465	.	NOVEL	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000437124.2	3	16.847887	KEEP	0	0	0	56	1749	TT	1	1	0	Intron	-	7	60	245	0	0	14.656004	194	60	7220	327	ENST00000252463.2	0.034826	1
SRL	6345	__UNKNOWN__	__UNKNOWN__	16	4257902	4257902	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:4257902C>T	ENST00000399609.3	-	2	74				SRL_ENST00000537996.1_Intron	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	NA		NA				sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						TCGGGGCCCGCGCTGGCGGCA	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739	6345			11295	protein-coding gene	gene with protein product		604992			NA	2762314	Standard	XM_064152	NM_001098814	NA	Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.62-3267G>A	chr16.hg19:g.4257902C>T		NA		hg19	CCDS42113.1	0.02	4.591064	CCGxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.70	2.017299	0.35606	.	.	ENSG00000185739	ENST00000330063	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	T	0.71039	0.3293	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71758	-0.4496	5	0.51188	T	0.08	-0.6944	12.2274	0.54468	0.0:0.1714:0.8286:0.0	.	.	.	.	T	89	.	ENSP00000333285:A89T	A	-	1	0	SRL	4197903	0.238000	0.23825	0.728000	0.30774	0.083000	0.17756	0.986000	0.29590	1.272000	0.44329	-0.231000	0.12243	GCG	NOVEL	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438087.1	0	18.657787	KEEP	0	0	0	62	2087	CC	1	1	0		-	20	60	670	0	0	52.03132	114	60	3873	267	ENST00000399609.3	0.149254	1
PPL	5493	__UNKNOWN__	__UNKNOWN__	16	4953986	4953986	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:4953986T>G	ENST00000345988.2	-	3	307	c.218A>C	c.(217-219)cAg>cCg	p.Q73P	PPL_ENST00000590782.2_Missense_Mutation_p.Q73P	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	73		NA			keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CAACACCTTCTGCAGGGTCAC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													65	50	55	NA		NA	NA	16		NA											NA				4953986		2197	4300	6497	SO:0001583	missense			AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898	5493			9273	protein-coding gene	gene with protein product		602871			NA	9570964, 9521878	Standard	NM_002705	NM_002705	NA	Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.218A>C	chr16.hg19:g.4953986T>G	ENSP00000340510:p.Gln73Pro	NA	O60314|O60454|Q14C98	hg19	CCDS10526.1	0.02	7.86035	TTCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	T	18.25	3.582893	0.65992	.	.	ENSG00000118898	ENST00000345988	T	0.66815	-0.23	5.28	5.28	0.74379	.	0.063344	0.64402	D	0.000005	T	0.67449	0.2894	M	0.62723	1.935	0.40991	D	0.984855	P	0.49961	0.93	P	0.44860	0.462	T	0.73886	-0.3841	10	0.72032	D	0.01	.	13.7765	0.63057	0.0:0.0:0.0:1.0	.	73	O60437	PEPL_HUMAN	P	73	ENSP00000340510:Q73P	ENSP00000340510:Q73P	Q	-	2	0	PPL	4893987	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	4.559000	0.60796	1.986000	0.57962	0.533000	0.62120	CAG	NOVEL	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251715.1	3	34.566957	KEEP	0	0	0	115	3541	TT	1	1	0		-	9	60	317	0	0	19.207571	239	60	8763	492	ENST00000345988.2	0.03629	1
SEC14L5	9717	__UNKNOWN__	__UNKNOWN__	16	5057340	5057340	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:5057340C>A	ENST00000251170.7	+	13	1617					NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	NA		NA				integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						TGCCCTTTATCTCTGACCTGC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	39	39	NA		NA	NA	16		NA											NA				5057340		2011	4173	6184	SO:0001627	intron_variant			AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184	9717			29032	protein-coding gene	gene with protein product		NA			NA	9455477	Standard		NM_014692	NA	Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1438-13C>A	chr16.hg19:g.5057340C>A		NA		hg19	CCDS45403.1	0.02	2.077226	TATxTCT	COVERED																																																																																			NOVEL	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434379.1	0	7.213583	KEEP	0	0	0	24	820	CC	0.999931	0.999248	0		+	34	60	1212	0	0	113.472628	47	60	1798	143	ENST00000251170.7	0.419753	0.999317
TMEM114	283953	__UNKNOWN__	__UNKNOWN__	16	8622156	8622156	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:8622156C>A	ENST00000568335.1	-	1	70	c.71G>T	c.(70-72)gGt>gTt	p.G24V		NM_001146336.1	NP_001139808.1			transmembrane protein 114	NA		NA								endometrium(1)|skin(1)	2						AGCTCAGAAACCCCGTCATCC	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													110	115	114	NA		NA	NA	16		NA											NA				8622156		692	1591	2283	SO:0001583	missense			BC150511	CCDS73825.1	16p13.2	2012-04-20			ENSG00000232258	ENSG00000232258	283953			33227	protein-coding gene	gene with protein product		611579			NA	17492639	Standard	NM_001146336	NM_001146336	NA	Approved		uc010uyd.2	B3SHH9	OTTHUMG00000172868	ENST00000568335.1:c.71G>T	chr16.hg19:g.8622156C>A	ENSP00000454261:p.Gly24Val	NA		hg19		0.02	2.095203	AAAxCCC	COVERED																																																																																			NOVEL	TMEM114-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000420965.1	3	4.814213	KEEP	0	0	0	16	525	CC	0.997832	0.996943	0		-	25	60	868	0	0	77.326844	54	60	1894	126	ENST00000568335.1	0.316456	0.99911
USP7	7874	__UNKNOWN__	__UNKNOWN__	16	9002211	9002211	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:9002211T>C	ENST00000344836.4	-	12	1456	c.1258A>G	c.(1258-1260)Aag>Gag	p.K420E	USP7_ENST00000535863.1_Missense_Mutation_p.K321E|USP7_ENST00000381886.4_Missense_Mutation_p.K404E	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	420	USP.	NA			maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						TCATTGATCTTGATATTTTGG	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													148	137	140	NA		NA	NA	16		NA											NA				9002211		2197	4300	6497	SO:0001583	missense			Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555	7874		Ubiquitin-specific peptidases	12630	protein-coding gene	gene with protein product		602519	ubiquitin specific protease 7 (herpes virus-associated)	HAUSP	NA	12838346, 9925944	Standard		NM_003470	NA	Approved		uc002czl.2	Q93009		ENST00000344836.4:c.1258A>G	chr16.hg19:g.9002211T>C	ENSP00000343535:p.Lys420Glu	NA	A6NMY8|B7Z815|H0Y3G8	hg19	CCDS32385.1	0.02	-0.280735	TCTxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	28.6	4.930747	0.92389	.	.	ENSG00000187555	ENST00000344836;ENST00000381886;ENST00000535863;ENST00000544549;ENST00000542333	T;T;T	0.28895	1.59;1.59;1.59	5.7	5.7	0.88788	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.69886	0.3161	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81362	-0.0967	10	0.87932	D	0	.	15.9662	0.79974	0.0:0.0:0.0:1.0	.	420;404	Q93009;B7Z815	UBP7_HUMAN;.	E	420;428;321;321;362	ENSP00000343535:K420E;ENSP00000443646:K321E;ENSP00000439272:K362E	ENSP00000343535:K420E	K	-	1	0	USP7	8909712	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.842000	0.86851	2.170000	0.68504	0.533000	0.62120	AAG	NOVEL	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434268.2	0	3.606793	KEEP	0	0	0	12	325	TT	0.993634	0.734962	0		-	8	60	295	0	0	25.502369	24	60	848	50	ENST00000344836.4	0.25	0.739671
GRIN2A	2903	__UNKNOWN__	__UNKNOWN__	16	9858293	9858293	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:9858293C>T	ENST00000396573.2	-	14	3417	c.3108G>A	c.(3106-3108)gaG>gaA	p.E1036E	GRIN2A_ENST00000535259.1_Silent_p.E879E|GRIN2A_ENST00000562109.1_Silent_p.E1036E|GRIN2A_ENST00000330684.3_Silent_p.E1036E|GRIN2A_ENST00000404927.2_Silent_p.E1036E|GRIN2A_ENST00000396575.2_Silent_p.E1036E	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1036		NA			directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTGCTGTTGCCTCATCCCTCT	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													133	141	138	NA		NA	NA	16		NA											NA				9858293		2197	4300	6497	SO:0001819	synonymous_variant				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454	2903		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4585	protein-coding gene	gene with protein product		138253		NMDAR2A	NA	9480759	Standard		XM_005255267	NA	Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3108G>A	chr16.hg19:g.9858293C>T		NA	O00669|Q17RZ6	hg19	CCDS10539.1	0.02	4.273733	TGCxTCA	COVERED																																																																																			NOVEL	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251930.3	3	10.534141	KEEP	0	0	0	35	1240	CC	0.999999	0.999998	0		-	6	60	222	0	0	14.368179	131	60	4825	203	ENST00000396573.2	0.043796	1
NDE1	54820	__UNKNOWN__	__UNKNOWN__	16	15737284	15737284	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:15737284G>T	ENST00000396355.1	+	0	161				NDE1_ENST00000396353.2_5'UTR	NM_001143979.1	NP_001137451.1	Q9NXR1	NDE1_HUMAN	nudE neurodevelopment protein 1	NA		NA			centrosome duplication (GO:0051298)|cerebral cortex development (GO:0021987)|establishment of chromosome localization (GO:0051303)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuroblast proliferation (GO:0007405)|neuron migration (GO:0001764)|vesicle transport along microtubule (GO:0047496)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole centrosome (GO:0031616)	microtubule binding (GO:0008017)			endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						GGAGTCGAAAGGAACCTTGAA	0.527	NA	NA									OREG0023635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													29	30	30	NA		NA	NA	16		NA											NA				15737284		692	1591	2283	SO:0001623	5_prime_UTR_variant			AF124431	CCDS10564.1	16p13.11	2013-08-06	2013-08-06		ENSG00000072864	ENSG00000072864	54820			17619	protein-coding gene	gene with protein product		609449	nudE nuclear distribution gene E homolog 1 (A. nidulans), nudE nuclear distribution E homolog 1 (A. nidulans)		NA	10940388, 12427674	Standard	NM_017668	NM_017668	NA	Approved	nudE, FLJ20101, NDE	uc002dds.3	Q9NXR1	OTTHUMG00000129885	ENST00000396355.1:c.-666G>T	chr16.hg19:g.15737284G>T		705	Q49AQ2	hg19	CCDS10564.1	0.02	4.584155	AAAxGAA	COVERED																																																																																			NOVEL	NDE1-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252133.1	0	49.648245	KEEP	0	0	0	165	5754	GG	1	0.999995	0		+	17	60	621	0	0	49.434335	96	60	3513	383	ENST00000396355.1	0.150442	0.999995
ACSM2B	348158	__UNKNOWN__	__UNKNOWN__	16	20548442	20548442	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:20548442G>T	ENST00000329697.6	-	0	2040				ACSM2B_ENST00000565322.1_3'UTR	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	NA		NA			fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						AATGTTTTGTGCTAATAACCA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813	348158		Acyl-CoA synthetase family	30931	protein-coding gene	gene with protein product	xenobiotic/medium chain fatty acid:CoA ligase	614359	acyl-CoA synthetase medium-chain family member 2	ACSM2	NA	12616642	Standard	NM_182617	NM_182617	NA	Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.*138C>A	chr16.hg19:g.20548442G>T		NA	Q86YT1	hg19	CCDS10586.1	0.02	11.57933	TGTxCTA	COVERED																																																																																			NOVEL	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254417.2	0	11.429142	KEEP	0	0	0	38	1323	GG	1	1	0		-	80	60	2898	0	0	257.046612	188	60	7107	364	ENST00000329697.6	0.298507	1
ERI2	112479	__UNKNOWN__	__UNKNOWN__	16	20810256	20810256	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:20810256G>T	ENST00000564349.1	-	10	1062	c.587C>A	c.(586-588)cCt>cAt	p.P196H	ERI2_ENST00000357967.4_Missense_Mutation_p.P289H|ERI2_ENST00000569729.1_Intron|ERI2_ENST00000389345.5_Missense_Mutation_p.P24H|ERI2_ENST00000563117.1_Missense_Mutation_p.P196H|ERI2_ENST00000300005.3_Intron			A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	289	Exonuclease.	NA					exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						TTTTTCATGAGGATTTATTAT	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													52	41	45	NA		NA	NA	16		NA											NA				20810256		692	1589	2281	SO:0001583	missense			BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678	112479		Enhanced RNAi three prime mRNA exonucleases	30541	protein-coding gene	gene with protein product	enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans), exoribonuclease 2, zinc finger, GRF-type containing 5	NA	exonuclease domain containing 1	EXOD1	NA	10819331	Standard	NM_080663	NM_080663	NA	Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000564349.1:c.587C>A	chr16.hg19:g.20810256G>T	ENSP00000455982:p.Pro196His	NA	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	hg19		0.02	1.74266	TGAxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.252	1.040888	0.19669	.	.	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.19394	2.19;2.15	6.17	3.15	0.36227	.	1.388450	0.04458	N	0.373916	T	0.24236	0.0587	L	0.46157	1.445	0.09310	N	1	B	0.29805	0.257	B	0.32149	0.141	T	0.33574	-0.9863	10	0.54805	T	0.06	1.6958	8.6724	0.34159	0.1278:0.0:0.7373:0.1349	.	289	A8K979	ERI2_HUMAN	H	289;24	ENSP00000350651:P289H;ENSP00000373996:P24H	ENSP00000350651:P289H	P	-	2	0	ERI2	20717757	0.026000	0.19158	0.000000	0.03702	0.621000	0.37620	2.187000	0.42602	0.443000	0.26582	-0.136000	0.14681	CCT	NOVEL	ERI2-014	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000436146.1	1	8.426477	KEEP	0	0	0	28	976	GG	0.999997	0.999619	0		-	5	60	181	0	0	12.22997	80	60	2923	136	ENST00000564349.1	0.058824	0.999622
ANKS4B	257629	__UNKNOWN__	__UNKNOWN__	16	21261692	21261692	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:21261692C>G	ENST00000311620.5	+	2	878	c.805C>G	c.(805-807)Cca>Gca	p.P269A		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	269		NA			response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|lung(11)|ovary(2)	20				GBM - Glioblastoma multiforme(48;0.0565)		TCTCAATCGTCCAGGTCTAGG	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													95	100	98	NA		NA	NA	16		NA											NA				21261692		2036	4201	6237	SO:0001583	missense			AK096138	CCDS42130.1	16p12.2	2013-01-10				ENSG00000175311	257629		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	26795	protein-coding gene	gene with protein product		609901			NA		Standard	NM_145865	NM_145865	NA	Approved	FLJ38819, HARP	uc010bwp.1	Q8N8V4		ENST00000311620.5:c.805C>G	chr16.hg19:g.21261692C>G	ENSP00000308772:p.Pro269Ala	NA		hg19	CCDS42130.1	0.02	4.746672	CGTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885404	0.72410	.	.	ENSG00000175311	ENST00000311620	D	0.87179	-2.22	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.93719	0.7993	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93736	0.7046	10	0.66056	D	0.02	-12.8089	18.9594	0.92671	0.0:1.0:0.0:0.0	.	269	Q8N8V4	ANS4B_HUMAN	A	269	ENSP00000308772:P269A	ENSP00000308772:P269A	P	+	1	0	ANKS4B	21169193	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	7.789000	0.85783	2.726000	0.93360	0.591000	0.81541	CCA	NOVEL	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000436535.1	1	9.33032	KEEP	0	0	0	31	1081	CC	0.999997	0.999997	0		+	44	60	1658	0	0	148.94167	96	60	3471	205	ENST00000311620.5	0.314286	1
PDZD9	255762	__UNKNOWN__	__UNKNOWN__	16	21995780	21995780	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:21995780G>A	ENST00000424898.2	-	4	665	c.603C>T	c.(601-603)gaC>gaT	p.D201D	PDZD9_ENST00000537222.2_Silent_p.D141D|PDZD9_ENST00000286143.6_Silent_p.D139D			Q8IXQ8	PDZD9_HUMAN	PDZ domain containing 9	201		NA								breast(3)|endometrium(2)|lung(3)|pancreas(1)	9						CACAATTAATGTCTTTTCCTA	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													214	195	202	NA		NA	NA	16		NA											NA				21995780		2198	4300	6498	SO:0001819	synonymous_variant			BC039562	CCDS10602.1, CCDS10602.2	16p12.1	2010-04-14	2010-04-14	2010-04-14	ENSG00000155714	ENSG00000155714	255762			28740	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 65	C16orf65	NA	12477932	Standard	NM_173806	NM_173806	NA	Approved	MGC50721	uc021ter.1	Q8IXQ8	OTTHUMG00000131586	ENST00000424898.2:c.603C>T	chr16.hg19:g.21995780G>A		NA	F5GWW8	hg19		0.02	6.733129	AATxTCT	COVERED																																																																																			NOVEL	PDZD9-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000381652.1	1	10.834975	KEEP	0	0	0	36	1262	GG	0.999999	0.999999	0		-	13	60	476	0	0	34.11563	150	60	5675	231	ENST00000424898.2	0.079755	1
RP11-368J21.3	0	__UNKNOWN__	__UNKNOWN__	16	22588087	22588087	__UNKNOWN__	RNA	SNP	G	G	C	rs371946225	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:22588087G>C	ENST00000550753.1	+	0	2562					NR_003676.2					NA		NA									NA						GTGGGACACCGTTCCCTGGAT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550753.1:	chr16.hg19:g.22588087G>C		NA		hg19		0.02	8.458608	ACCxTTC	COVERED																																																																																			NOVEL	RP11-368J21.3-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409041.1	1	5.488253	KEEP	18	2	68	42	1428	GG	1	1	0		+	9	27	325	0	0	20.575558	206	60	7334	347	ENST00000550753.1	0.04186	1
IL21R	50615	__UNKNOWN__	__UNKNOWN__	16	27460177	27460177	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:27460177A>G	ENST00000337929.3	+	9	1663	c.1190A>G	c.(1189-1191)gAc>gGc	p.D397G	IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Missense_Mutation_p.D397G|IL21R_ENST00000395754.4_Missense_Mutation_p.D397G|IL21R_ENST00000395755.1_Missense_Mutation_p.D397G	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	397		NA			interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						TGTGAGGATGACGGCTACCCA	0.627	NA	NA	T	BCL6	NHL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		16	16p11	50615	interleukin 21 receptor		L	0													56	56	56	NA		NA	NA	16		NA											NA				27460177		2197	4300	6497	SO:0001583	missense			AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522	50615		Interleukins and interleukin receptors, CD molecules	6006	protein-coding gene	gene with protein product		605383			NA	11081504	Standard	NM_181078	NM_181078	NA	Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1190A>G	chr16.hg19:g.27460177A>G	ENSP00000338010:p.Asp397Gly	NA	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	hg19	CCDS10630.1	0.02	9.227442	ATGxCGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	16.77	3.216047	0.58452	.	.	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.42513	0.97;0.97;0.97	5.19	5.19	0.71726	.	0.143972	0.32287	N	0.006309	T	0.46756	0.1409	M	0.67953	2.075	0.23712	N	0.997043	P	0.49559	0.925	P	0.47075	0.536	T	0.46428	-0.9192	10	0.37606	T	0.19	-23.345	11.4742	0.50288	1.0:0.0:0.0:0.0	.	397	Q9HBE5	IL21R_HUMAN	G	397	ENSP00000338010:D397G;ENSP00000379104:D397G;ENSP00000379103:D397G	ENSP00000338010:D397G	D	+	2	0	IL21R	27367678	0.291000	0.24352	0.257000	0.24404	0.959000	0.62525	3.220000	0.51207	1.966000	0.57179	0.459000	0.35465	GAC	NOVEL	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254578.2	3	17.450638	KEEP	0	0	0	58	1801	AA	1	1	0		+	7	60	268	0	0	16.393378	234	60	8283	374	ENST00000337929.3	0.029046	1
GTF3C1	2975	__UNKNOWN__	__UNKNOWN__	16	27517391	27517391	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:27517391G>T	ENST00000356183.4	-	10	1614	c.1599C>A	c.(1597-1599)ccC>ccA	p.P533P	GTF3C1_ENST00000561623.1_Silent_p.P533P	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	533		NA			5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CTGGGAAGGAGGGCGGCTGCT	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													85	77	80	NA		NA	NA	16		NA											NA				27517391		2197	4300	6497	SO:0001819	synonymous_variant			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235	2975		General transcription factors	4664	protein-coding gene	gene with protein product		603246	general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )		NA	8164661, 8127861	Standard	NM_001520	NM_001520	NA	Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.1599C>A	chr16.hg19:g.27517391G>T		NA	B2RP21|Q12838|Q6DKN9|Q9Y4W9	hg19	CCDS32414.1	0.02	1.968732	GGAxGGC	COVERED																																																																																			NOVEL	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000433856.1	0	4.815558	KEEP	0	0	0	16	558	GG	0.997832	0.99724	0		-	7	60	238	0	0	16.782636	75	60	2688	114	ENST00000356183.4	0.085366	0.999407
SBK1	388228	__UNKNOWN__	__UNKNOWN__	16	28332541	28332541	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:28332541C>T	ENST00000341901.4	+	0	2363					NM_001024401.2	NP_001019572.1	Q52WX2	SBK1_HUMAN	SH3 domain binding kinase 1	NA		NA				cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(3)|ovary(1)	5						cacacacacacacacacacac	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS32416.1	16p11.2	2013-09-27	2013-09-27			ENSG00000188322	388228			17699	protein-coding gene	gene with protein product		NA	SH3-binding domain kinase 1		NA		Standard	XM_370948	XM_005255315	NA	Approved	Sbk	uc002dpd.3	Q52WX2		ENST00000341901.4:c.*299C>T	chr16.hg19:g.28332541C>T		NA		hg19	CCDS32416.1	0.02	4.028125	ACAxACA	COVERED																																																																																			NOVEL	SBK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387677.1	5	9.188888	KEEP	0	2	58	51	1678	CC	1	1	0		+	10	60	363	2	0	25.875544	117	60	4217	212	ENST00000341901.4	0.07874	1
SULT1A2	6799	__UNKNOWN__	__UNKNOWN__	16	28603721	28603721	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs141581853	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:28603721C>T	ENST00000533150.1	-	3	1655	c.539G>A	c.(538-540)cGc>cAc	p.R180H	SULT1A2_ENST00000335715.4_Missense_Mutation_p.R213H|SULT1A2_ENST00000395630.1_Missense_Mutation_p.R213H			P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	213		NA			3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)	p.R213H(4)		NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						TGGCAGGGAGCGCCCCACAAA	0.532	NA	NA											.|||	134	0.0267572	0.0363	0.0677	5008	,	,	NA	20273	0.005	NA	0.0268	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA						NA		NA				4	Substitution - Missense(4)	skin(2)|large_intestine(1)|NS(1)											132	119	123	NA		NA	NA	16		NA											NA				28603721		2197	4300	6497	SO:0001583	missense			U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	6799	2.8.2.1	Sulfotransferases, cytosolic	11454	protein-coding gene	gene with protein product		601292		STP2	NA	8661000, 8912648	Standard	NM_001054	NM_001054	NA	Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000533150.1:c.539G>A	chr16.hg19:g.28603721C>T	ENSP00000435271:p.Arg180His	NA	A9QY25|P78393|Q14CJ7	hg19		0.02	10.820312	GAGxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	c	15.21	2.765812	0.49574	.	.	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630	D;D;D	0.82526	-1.62;-1.62;-1.62	4.98	3.0	0.34707	Sulfotransferase domain (1);	0.265029	0.30329	N	0.009878	T	0.81307	0.4795	M	0.85462	2.755	0.22081	N	0.999373	B	0.12013	0.005	B	0.06405	0.002	T	0.73867	-0.3847	10	0.62326	D	0.03	.	6.5172	0.22254	0.0:0.7359:0.0:0.2641	.	213	P50226	ST1A2_HUMAN	H	180;213;213	ENSP00000435271:R180H;ENSP00000338742:R213H;ENSP00000378992:R213H	ENSP00000338742:R213H	R	-	2	0	SULT1A2	28511222	0.000000	0.05858	1.000000	0.80357	0.908000	0.53690	-0.149000	0.10204	2.300000	0.77407	0.456000	0.33151	CGC	NOVEL	SULT1A2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000395195.1	4	8.853474	KEEP	1	1	30	40	1365	CC	1	1	0		-	12	60	409	0	0	25.253335	262	60	9174	410	ENST00000533150.1	0.043796	1
SULT1A2	6799	__UNKNOWN__	__UNKNOWN__	16	28603796	28603796	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs189792619		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:28603796T>C	ENST00000533150.1	-	3	1580	c.464A>G	c.(463-465)cAa>cGa	p.Q155R	SULT1A2_ENST00000335715.4_Intron|SULT1A2_ENST00000395630.1_Intron			P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	177		NA			3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine biosynthetic process (GO:0009309)|catecholamine metabolic process (GO:0006584)|phenol-containing compound metabolic process (GO:0018958)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|sulfotransferase activity (GO:0008146)			NS(2)|breast(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|skin(2)	14						AGTGGAGGCTTGGATTGCTGA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	46	46	NA		NA	NA	16		NA											NA				28603796		2197	4300	6497	SO:0001583	missense			U34804	CCDS10636.1	16p12.1	2008-02-05			ENSG00000197165	ENSG00000197165	6799	2.8.2.1	Sulfotransferases, cytosolic	11454	protein-coding gene	gene with protein product		601292		STP2	NA	8661000, 8912648	Standard	NM_001054	NM_001054	NA	Approved	HAST4	uc002dqh.2	P50226	OTTHUMG00000048082	ENST00000533150.1:c.464A>G	chr16.hg19:g.28603796T>C	ENSP00000435271:p.Gln155Arg	NA	A9QY25|P78393|Q14CJ7	hg19		0.02	9.379762	GCTxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	-	3.766	-0.048628	0.07407	.	.	ENSG00000197165	ENST00000533150	T	0.02067	4.47	3.17	-6.34	0.01982	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.30090	-0.9990	6	0.35671	T	0.21	.	1.2793	0.02037	0.4094:0.0892:0.2211:0.2803	.	.	.	.	R	155	ENSP00000435271:Q155R	ENSP00000435271:Q155R	Q	-	2	0	SULT1A2	28511297	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.421000	0.01031	-3.509000	0.00150	-4.208000	0.00009	CAA	NOVEL	SULT1A2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000395195.1	3	8.559225	KEEP	1	1	33	40	1242	TT	1	1	0		-	17	60	585	0	0	40.096078	219	60	8006	348	ENST00000533150.1	0.072034	1
ATP2A1	487	__UNKNOWN__	__UNKNOWN__	16	28895814	28895814	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:28895814G>C	ENST00000395503.4	+	6	647				ATP2A1_ENST00000357084.3_Intron|ATP2A1_ENST00000536376.1_Intron	NM_004320.4	NP_004311.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	NA		NA			apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AGGAGAACGAGTCAGACACAG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	487	3.6.3.8	ATPases / P-type	811	protein-coding gene	gene with protein product	sarcoplasmic/endoplasmic reticulum calcium ATPase 1, calcium pump 1	108730		ATP2A	NA		Standard	NM_004320	NM_004320	NA	Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000395503.4:c.464-82G>C	chr16.hg19:g.28895814G>C		NA	A8K5J9|B3KY17|O14984	hg19	CCDS42139.1	0.02	4.63884	CGAxTCA	COVERED																																																																																			NOVEL	ATP2A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254687.2	0	5.416937	KEEP	0	0	0	18	624	GG	0.999859	0.999859	0		+	30	60	1066	0	0	89.445207	109	60	3966	169	ENST00000395503.4	0.215827	1
CDIPT	10423	__UNKNOWN__	__UNKNOWN__	16	29874775	29874775	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:29874775C>T	ENST00000219789.6	-	0	282					NM_006319.3	NP_006310.1	O14735	CDIPT_HUMAN	CDP-diacylglycerol--inositol 3-phosphatidyltransferase	NA		NA			CDP-diacylglycerol metabolic process (GO:0046341)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alcohol binding (GO:0043178)|carbohydrate binding (GO:0030246)|CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity (GO:0003881)|diacylglycerol binding (GO:0019992)|manganese ion binding (GO:0030145)			endometrium(1)|lung(3)	4						AAAGATAAGGCGATAAAATTC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF014807	CCDS10657.1, CCDS67002.1	16p11.2	2012-11-19	2010-04-29		ENSG00000103502	ENSG00000103502	10423	2.7.8.11		1769	protein-coding gene	gene with protein product	phosphatidylinositol synthase	605893	CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase)		NA	9407135	Standard	NM_006319	NM_006319	NA	Approved	PIS1, PIS	uc002dum.3	O14735	OTTHUMG00000177144	ENST00000219789.6:c.-597G>A	chr16.hg19:g.29874775C>T		NA	B4DUV0|H3BTV1|Q6FGU1|Q6ZN70	hg19	CCDS10657.1	0.02	7.250345	AGGxGAT	COVERED																																																																																			NOVEL	CDIPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255147.3	2	24.929577	KEEP	0	0	0	83	2775	CC	1	1	0		-	33	60	1093	0	0	89.59244	128	60	4483	303	ENST00000219789.6	0.204969	1
ALDOA	226	__UNKNOWN__	__UNKNOWN__	16	30080715	30080715	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:30080715A>T	ENST00000395240.3	+	6	808				ALDOA_ENST00000564546.1_Intron|ALDOA_ENST00000569545.1_Intron|ALDOA_ENST00000412304.2_Intron|ALDOA_ENST00000566897.1_Intron|ALDOA_ENST00000338110.5_Intron|ALDOA_ENST00000563060.2_Intron|ALDOA_ENST00000569798.1_Intron|ALDOA_ENST00000564595.2_Intron|ALDOA_ENST00000395248.1_Intron	NM_184041.2	NP_908930.1	P04075	ALDOA_HUMAN	aldolase A, fructose-bisphosphate	NA		NA			actin filament organization (GO:0007015)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|fructose 1,6-bisphosphate metabolic process (GO:0030388)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homotetramerization (GO:0051289)|regulation of cell shape (GO:0008360)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|membrane (GO:0016020)|nucleus (GO:0005634)|platelet alpha granule lumen (GO:0031093)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|fructose binding (GO:0070061)|fructose-bisphosphate aldolase activity (GO:0004332)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|tubulin binding (GO:0015631)			breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	17						GAGAAGGTAAATGGCTACCTG	0.617	NA	NA									OREG0023729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													109	100	103	NA		NA	NA	16		NA											NA				30080715		2197	4300	6497	SO:0001627	intron_variant			X05236	CCDS10668.1, CCDS58450.1	16p11.2	2008-03-06			ENSG00000149925	ENSG00000149925	226	4.1.2.13		414	protein-coding gene	gene with protein product		103850			NA	3570299	Standard	NM_000034	NM_000034	NA	Approved		uc010veg.2	P04075	OTTHUMG00000132107	ENST00000395240.3:c.636+5A>T	chr16.hg19:g.30080715A>T		814	B4DXI7|Q6FH76|Q6FI10|Q96B15|Q9BWD9|Q9UCN2	hg19		0.02	16.416672	TAAxTGG	COVERED																																																																																			NOVEL	ALDOA-011	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000435374.1	8	51.721607	KEEP	0	0	0	172	5405	AA	1	1	0		+	83	60	2986	0	0	254.598328	270	60	9708	669	ENST00000395240.3	0.235127	1
MAPK3	5595	__UNKNOWN__	__UNKNOWN__	16	30134157	30134157	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:30134157C>T	ENST00000395200.1	-	1	111				MAPK3_ENST00000263025.4_Intron|MAPK3_ENST00000484663.1_5'UTR|MAPK3_ENST00000322266.5_Intron|MAPK3_ENST00000395199.3_Intron|MAPK3_ENST00000403394.1_Intron|MAPK3_ENST00000395202.1_Intron			P27361	MK03_HUMAN	mitogen-activated protein kinase 3	NA		NA			activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage induced protein phosphorylation (GO:0006975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-1-mediated signaling pathway (GO:0070498)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apolipoprotein binding (GO:2000657)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to exogenous dsRNA (GO:0043330)|sensory perception of pain (GO:0019233)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)				NA					Arsenic trioxide(DB01169)|Sulindac(DB00605)	TCCAAGCCTGCTCCCCTGAGG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M84490	CCDS10672.1, CCDS42148.1, CCDS42149.1	16p11.2	2011-06-10			ENSG00000102882	ENSG00000102882	5595	2.7.11.1	Mitogen-activated protein kinase cascade / Kinases	6877	protein-coding gene	gene with protein product		601795		PRKM3	NA	9628824	Standard		NM_001109891	NA	Approved	ERK1, p44mapk, p44erk1	uc002dws.3	P27361	OTTHUMG00000132149	ENST00000395200.1:c.83+203G>A	chr16.hg19:g.30134157C>T		NA	A8CZ58|B0LPG3|Q8NHX1	hg19		0.02	8.693095	CTGxTCC	COVERED																																																																																			NOVEL	MAPK3-011	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000268291.1	2	57.119088	KEEP	0	0	0	190	6461	CC	1	1	0		-	42	60	1463	0	0	117.623322	203	60	7396	583	ENST00000395200.1	0.171429	1
ZNF688	146542	__UNKNOWN__	__UNKNOWN__	16	30581349	30581349	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:30581349C>G	ENST00000223459.6	-	3	1823	c.719G>C	c.(718-720)cGg>cCg	p.R240P	ZNF688_ENST00000395219.1_Missense_Mutation_p.R226P	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	240		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						CCGGCCCCGCCGCCCCCCGGA	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	13	12	NA		NA	NA	16		NA											NA				30581349		2159	4243	6402	SO:0001583	missense			AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809	146542		Zinc fingers, C2H2-type, -	30489	protein-coding gene	gene with protein product		NA			NA	10493829	Standard	NM_145271	XM_005255139	NA	Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.719G>C	chr16.hg19:g.30581349C>G	ENSP00000223459:p.Arg240Pro	NA	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	hg19	CCDS10684.1	0.02	2.236032	CGCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.95	3.920877	0.73213	.	.	ENSG00000229809	ENST00000395219;ENST00000223459	T;T	0.04454	3.62;3.87	4.42	4.42	0.53409	.	.	.	.	.	T	0.11239	0.0274	L	0.27053	0.805	0.35083	D	0.76356	D;D	0.76494	0.999;0.999	D;D	0.79108	0.992;0.992	T	0.18272	-1.0342	9	0.48119	T	0.1	.	12.694	0.56992	0.0:1.0:0.0:0.0	.	240;226	P0C7X2;A8MV39	ZN688_HUMAN;.	P	226;240	ENSP00000378645:R226P;ENSP00000223459:R240P	ENSP00000223459:R240P	R	-	2	0	ZNF688	30488850	0.987000	0.35691	0.992000	0.48379	0.986000	0.74619	2.982000	0.49337	2.439000	0.82584	0.467000	0.42956	CGG	NOVEL	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255544.2	2	18.316638	KEEP	0	0	0	61	1906	CC	1	0.992094	0		-	11	60	339	0	0	26.539756	52	60	1671	145	ENST00000223459.6	0.174603	0.992094
RNF40	9810	__UNKNOWN__	__UNKNOWN__	16	30786178	30786178	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:30786178C>A	ENST00000563683.1	+	0	3739				RNF40_ENST00000324685.6_3'UTR|RNF40_ENST00000357890.5_3'UTR			O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	NA		NA			histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			CATCCCAAGGCTCTACTGGGT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549	9810		RING-type (C3HC4) zinc fingers	16867	protein-coding gene	gene with protein product	BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)	607700	ring finger protein 40		NA	9734811, 10944455, 12121982	Standard	NM_014771	NM_014771	NA	Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000563683.1:c.*743C>A	chr16.hg19:g.30786178C>A		NA	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	hg19		0.02	14.041619	AGGxTCT	COVERED																																																																																			NOVEL	RNF40-011	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000434279.1	5	43.019362	KEEP	0	0	0	143	5125	CC	1	1	0		+	75	60	2704	0	0	232.18764	231	60	8734	597	ENST00000563683.1	0.245098	1
ITGAX	3687	__UNKNOWN__	__UNKNOWN__	16	31391254	31391254	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:31391254G>T	ENST00000268296.4	+	26	3097				ITGAX_ENST00000562522.1_Intron	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	NA		NA			blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GCCCCATGTGGGTCCCTGATG	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	38	39	NA		NA	NA	16		NA											NA				31391254		2197	4300	6497	SO:0001627	intron_variant			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678	3687		CD molecules, Complement system, Integrins	6152	protein-coding gene	gene with protein product		151510	integrin, alpha X (antigen CD11C (p150), alpha polypeptide)	CD11C	NA	3284962, 2303426	Standard	NM_000887	NM_001286375	NA	Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.2977-49G>T	chr16.hg19:g.31391254G>T		NA	Q8IVA6	hg19	CCDS10711.1	0.02	12.501818	GTGxGTC	COVERED																																																																																			NOVEL	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255628.2	2	13.543161	KEEP	0	0	0	45	1554	GG	1	1	0		+	12	60	436	0	0	26.714131	333	60	11944	497	ENST00000268296.4	0.034783	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33781448	33781448	__UNKNOWN__	IGR	SNP	A	A	G	rs201825813	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:33781448A>G			NA	NA				RP11-812E19.3 (3704 upstream) : AC136932.2 (164500 downstream)						NA		NA									NA						GCTGACCGCCAGTCCCCTGTC	0.607	NA	NA											.|||	563	0.11242	0.1369	0.0965	5008	,	,	NA	21004	0.0873	NA	0.1491	False	NA	,,,	NA	NA	NA	2504	0.0787	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33781448A>G		NA		hg19		0.02	2.196564	GCCxGTC	COVERED																																																																																			NOVEL					0			0	3.00837	KEEP	27	0	0	10	308	AA	0.99254	0.972219	0			8	25	284	0	0	22.245364	48	50	1741	115		0.142857	0.979526
ZNF423	23090	__UNKNOWN__	__UNKNOWN__	16	49671213	49671213	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs141893384	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:49671213C>T	ENST00000561648.1	-	4	1903	c.1850G>A	c.(1849-1851)cGg>cAg	p.R617Q	ZNF423_ENST00000567169.1_Missense_Mutation_p.R500Q|ZNF423_ENST00000562871.1_Missense_Mutation_p.R557Q|ZNF423_ENST00000262383.2_Missense_Mutation_p.R617Q|ZNF423_ENST00000535559.1_Missense_Mutation_p.R500Q|ZNF423_ENST00000563137.2_Missense_Mutation_p.R557Q|ZNF423_ENST00000562520.1_Missense_Mutation_p.R557Q	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	617		NA			cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GAGCCGCTGCCGCTTCGGGGA	0.557	NA	NA											C|||	2	0.000399361	0.0015	0	5008	,	,	NA	22369	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								C	GLN/ARG	12,4384	19.1+/-41.9	0,12,2186	87	74	78	NA	1850	4.8	1	16	dbSNP_134	78	0,8600		0,0,4300	yes	missense	ZNF423	NM_015069.2	43	0,12,6486	TT,TC,CC	NA	0.0,0.273,0.0923	probably-damaging	617/1285	49671213	12,12984	2198	4300	6498	SO:0001583	missense			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935	23090		Zinc fingers, C2H2-type	16762	protein-coding gene	gene with protein product	OLF-1/EBF associated zinc finger gene,  Smad- and Olf-interacting zinc finger protein, early B-cell factor associated zinc finger protein	604557			NA	9872452, 10660046	Standard	NM_015069	NM_001271620	NA	Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1850G>A	chr16.hg19:g.49671213C>T	ENSP00000455426:p.Arg617Gln	NA	O94860|Q76N04|Q9NZ13	hg19	CCDS32445.1	0.02	12.638607	TGCxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.66	3.185061	0.57909	0.00273	0.0	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.09445	2.98;3.02	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.10594	0.0259	N	0.24115	0.695	0.54753	D	0.99998	D	0.56746	0.977	P	0.44860	0.462	T	0.23013	-1.0200	9	.	.	.	.	17.8389	0.88709	0.0:1.0:0.0:0.0	.	617	Q2M1K9	ZN423_HUMAN	Q	617;500	ENSP00000262383:R617Q;ENSP00000442321:R500Q	.	R	-	2	0	ZNF423	48228714	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	7.487000	0.81328	2.208000	0.71279	0.561000	0.74099	CGG	NOVEL	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000423258.1	2	33.993861	KEEP	0	0	0	113	3771	CC	1	1	0		-	78	60	2870	0	0	254.931717	184	70	6228	437	ENST00000561648.1	0.29771	1
PAPD5	64282	__UNKNOWN__	__UNKNOWN__	16	50257268	50257268	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:50257268A>G	ENST00000561678.1	+	6	1050	c.976A>G	c.(976-978)Atg>Gtg	p.M326V	PAPD5_ENST00000357464.3_Missense_Mutation_p.M357V|PAPD5_ENST00000573002.1_3'UTR|PAPD5_ENST00000436909.3_Missense_Mutation_p.M436V			Q8NDF8	PAPD5_HUMAN	PAP associated domain containing 5	357	PAP-associated.	NA			histone mRNA catabolic process (GO:0071044)|mitotic nuclear division (GO:0007067)|mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)			endometrium(1)|kidney(1)|lung(2)	4		all_cancers(37;0.0452)		BRCA - Breast invasive adenocarcinoma(181;0.0843)|GBM - Glioblastoma multiforme(240;0.231)		CAGGCCATCAATGCTTTATAT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	43	44	NA		NA	NA	16		NA											NA				50257268		1854	4097	5951	SO:0001583	missense			AF089897	CCDS54006.1	16q12.1	2010-11-18				ENSG00000121274	64282			30758	protein-coding gene	gene with protein product	TUTase3	605540			NA	10066793	Standard	NM_022447	NM_001040284	NA	Approved	TRF4-2	uc010vgo.2	Q8NDF8		ENST00000561678.1:c.976A>G	chr16.hg19:g.50257268A>G	ENSP00000455837:p.Met326Val	NA	B4DV38|Q9NW67|Q9Y6C0	hg19		0.02	2.531206	TCAxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	14.12	2.439973	0.43326	.	.	ENSG00000121274	ENST00000436909;ENST00000357464	T;T	0.53423	0.62;0.62	5.87	4.78	0.61160	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	T	0.42675	0.1213	L	0.45137	1.4	0.58432	D	0.999999	B;B	0.25904	0.137;0.05	B;B	0.30401	0.115;0.055	T	0.29761	-1.0001	10	0.45353	T	0.12	.	12.3605	0.55201	0.9339:0.0:0.0661:0.0	.	436;357	B4DV38;Q8NDF8	.;PAPD5_HUMAN	V	436;357	ENSP00000396995:M436V;ENSP00000350054:M357V	ENSP00000350054:M357V	M	+	1	0	PAPD5	48814769	1.000000	0.71417	0.845000	0.33349	0.993000	0.82548	5.956000	0.70315	1.142000	0.42291	0.533000	0.62120	ATG	NOVEL	PAPD5-002	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000423150.1	0	8.425987	KEEP	0	0	0	28	899	AA	0.999997	0.967422	0		+	20	60	769	0	0	71.397906	32	60	1184	102	ENST00000561678.1	0.384615	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	51098526	51098526	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:51098526C>T			NA	NA				RP11-883G14.4 (8216 upstream) : SALL1 (71359 downstream)						NA		NA									NA						ttgtttcattcagcaatcaca	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.51098526C>T		NA		hg19		0.02	2.348923	ATTxAGC	COVERED																																																																																			NOVEL					0			0	2.708984	KEEP	0	0	0	9	331	CC	0.99254	0.956584	0			17	60	613	0	0	55.490778	33	60	1279	78		0.34	0.963774
FTO	79068	__UNKNOWN__	__UNKNOWN__	16	54150020	54150020	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:54150020C>T	ENST00000471389.1	+	0	5933					NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	NA		NA			adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						CATCACTCCACTGAATCCAGG	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718	79068		Alkylation repair homologs	24678	protein-coding gene	gene with protein product	AlkB homolog 9, alpha-ketoglutarate-dependent dioxygenase	610966			NA	17434869, 17991826, 22002720	Standard	NM_001080432	NM_001080432	NA	Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.*4193C>T	chr16.hg19:g.54150020C>T		NA	A2RUH1|B2RNS0|Q0P676|Q7Z785	hg19	CCDS32448.1	0.02	2.138368	CCAxTGA	COVERED																																																																																			NOVEL	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352196.1	3	6.320757	KEEP	0	0	0	21	756	CC	0.999869	0.99807	0		+	25	60	918	0	0	83.353316	48	60	1821	115	ENST00000471389.1	0.342466	0.9982
IRX5	10265	__UNKNOWN__	__UNKNOWN__	16	54966029	54966029	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:54966029G>A	ENST00000560154.1	+	2	313	c.313G>A	c.(313-315)Gtc>Atc	p.V105I	IRX5_ENST00000558597.1_5'UTR|IRX5_ENST00000320990.5_Intron|IRX5_ENST00000394636.4_Intron			P78411	IRX5_HUMAN	iroquois homeobox 5	329		NA			embryonic cranial skeleton morphogenesis (GO:0048701)|gonad development (GO:0008406)|neuron maturation (GO:0042551)|regulation of heart rate (GO:0002027)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|vitamin D binding (GO:0005499)			kidney(3)|large_intestine(6)|lung(4)|prostate(1)	14						CCCAACGTGCGTCCGCTCCCC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			U90309	CCDS10751.1, CCDS58462.1	16q12.2	2011-06-20	2007-07-13		ENSG00000176842	ENSG00000176842	10265		Homeoboxes / TALE class	14361	protein-coding gene	gene with protein product		606195			NA		Standard		NM_005853	NA	Approved	IRX-2a	uc002ehv.3	P78411	OTTHUMG00000133201	ENST00000560154.1:c.313G>A	chr16.hg19:g.54966029G>A	ENSP00000453660:p.Val105Ile	NA	H0YMS7|P78416|Q7Z2E1	hg19		0.02	24.480391	TGCxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.198	-0.164308	0.06502	.	.	ENSG00000176842	ENST00000447390	.	.	.	4.06	-1.13	0.09775	.	.	.	.	.	T	0.26484	0.0647	.	.	.	0.19775	N	0.999952	B	0.23316	0.083	B	0.18263	0.021	T	0.28744	-1.0034	7	0.87932	D	0	.	3.1928	0.06623	0.3581:0.0:0.441:0.2008	.	105	A2RRB5	.	I	105	.	ENSP00000411820:V105I	V	+	1	0	IRX5	53523530	0.000000	0.05858	0.006000	0.13384	0.037000	0.13140	-1.166000	0.03129	0.024000	0.15214	0.313000	0.20887	GTC	NOVEL	IRX5-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417440.1	5	143.895736	KEEP	0	0	0	479	15086	GG	1	1	0		+	165	60	5614	0	0	502.224196	337	70	10610	1371	ENST00000560154.1	0.328685	1
NLRC5	84166	__UNKNOWN__	__UNKNOWN__	16	57060331	57060331	__UNKNOWN__	Silent	SNP	C	C	T	rs557863238	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:57060331C>T	ENST00000262510.6	+	6	1701	c.1476C>T	c.(1474-1476)agC>agT	p.S492S	NLRC5_ENST00000539144.1_Silent_p.S492S|NLRC5_ENST00000436936.1_Silent_p.S492S|NLRC5_ENST00000308149.7_Silent_p.S492S	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	492	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.	NA			defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				CCACTCACAGCCTGCTGACTT	0.582	NA	NA											C|||	2	0.000399361	0	0	5008	,	,	NA	21559	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0													49	48	48	NA		NA	NA	16		NA											NA				57060331		2198	4300	6498	SO:0001819	synonymous_variant			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853	84166		Nucleotide-binding domain and leucine rich repeat containing	29933	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5, NOD-like receptor C5	613537			NA	12615073	Standard	NM_032206	NM_032206	NA	Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1476C>T	chr16.hg19:g.57060331C>T		NA	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	hg19	CCDS10773.1	0.02	15.719961	CAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.625	-0.520518	0.04171	.	.	ENSG00000140853	ENST00000538805	.	.	.	5.4	2.36	0.29203	.	.	.	.	.	T	0.31765	0.0807	.	.	.	0.20307	N	0.999916	.	.	.	.	.	.	T	0.20571	-1.0271	4	.	.	.	.	6.0439	0.19750	0.1237:0.5973:0.0:0.279	.	.	.	.	S	245	.	.	P	+	1	0	NLRC5	55617832	0.000000	0.05858	0.374000	0.26016	0.446000	0.32137	-0.377000	0.07456	0.663000	0.31027	-0.254000	0.11334	CCT	NOVEL	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257346.1	1	21.969396	KEEP	0	0	0	73	2553	CC	1	1	0		+	36	60	1223	0	0	92.152911	256	60	9400	561	ENST00000262510.6	0.123288	1
COQ9	57017	__UNKNOWN__	__UNKNOWN__	16	57495052	57495052	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:57495052C>T	ENST00000567072.1	+	0	1380				COQ9_ENST00000262507.6_3'UTR|AC009052.12_ENST00000567090.1_RNA			O75208	COQ9_HUMAN	coenzyme Q9	NA		NA			mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CAGAAAACTGCCTCACCTGAG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682	57017			25302	protein-coding gene	gene with protein product		612837	chromosome 16 open reading frame 49, coenzyme Q9 homolog (yeast), coenzyme Q9 homolog (S. cerevisiae)	C16orf49	NA	19375058	Standard	NM_020312	NM_020312	NA	Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000567072.1:c.*516C>T	chr16.hg19:g.57495052C>T		NA	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	hg19		0.02	-0.280741	CTGxCTC	COVERED																																																																																			NOVEL	COQ9-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000432601.1	2	3.605802	KEEP	0	0	0	12	401	CC	0.993634	0.734962	0		+	4	60	130	0	0	9.673844	28	60	1056	53	ENST00000567072.1	0.125	0.739671
GPR97	222487	__UNKNOWN__	__UNKNOWN__	16	57702196	57702196	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:57702196C>T	ENST00000333493.4	+	0	98				GPR97_ENST00000327655.6_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	NA		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GCCAGCTCAGCAGAGCCTGGG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	12	10	NA		NA	NA	16		NA											NA				57702196		655	1516	2171	SO:0001623	5_prime_UTR_variant			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885	222487		-, GPCR / Class B : Orphans	13728	protein-coding gene	gene with protein product		NA			NA	12435584, 222487	Standard	NM_170776	NM_170776	NA	Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.-64C>T	chr16.hg19:g.57702196C>T		NA	Q6ZMF4|Q86SL9|Q8IZF1	hg19	CCDS10786.1	0.02	-0.429882	CAGxAGA	COVERED																																																																																			NOVEL	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257333.2	1	9.028776	KEEP	0	0	0	30	1023	CC	0.999997	0.954488	0		+	3	60	101	0	0	6.632669	46	60	1694	91	ENST00000333493.4	0.061224	0.954491
GPR97	222487	__UNKNOWN__	__UNKNOWN__	16	57713135	57713135	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs149201757		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:57713135G>A	ENST00000333493.4	+	5	700	c.539G>A	c.(538-540)cGc>cAc	p.R180H	GPR97_ENST00000450388.3_Missense_Mutation_p.R60H|GPR97_ENST00000327655.6_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	180		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTGAACAATCGCCTGGTGGGT	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	HIS/ARG	1,4395	2.1+/-5.4	0,1,2197	128	117	121	NA	539	-3.5	0	16	dbSNP_134	121	0,8600		0,0,4300	no	missense	GPR97	NM_170776.4	29	0,1,6497	AA,AG,GG	NA	0.0,0.0227,0.0077	benign	180/550	57713135	1,12995	2198	4300	6498	SO:0001583	missense			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885	222487		-, GPCR / Class B : Orphans	13728	protein-coding gene	gene with protein product		NA			NA	12435584, 222487	Standard	NM_170776	NM_170776	NA	Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.539G>A	chr16.hg19:g.57713135G>A	ENSP00000332900:p.Arg180His	NA	Q6ZMF4|Q86SL9|Q8IZF1	hg19	CCDS10786.1	0.02	9.039568	ATCxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.941	-0.014258	0.07681	2.27E-4	0.0	ENSG00000182885	ENST00000333493;ENST00000450388	T;T	0.29655	1.56;1.6	4.99	-3.51	0.04696	.	0.503929	0.18229	N	0.147623	T	0.24661	0.0598	M	0.72118	2.19	0.21782	N	0.999542	B	0.11235	0.004	B	0.04013	0.001	T	0.31336	-0.9947	10	0.20046	T	0.44	.	7.9057	0.29761	0.4323:0.1057:0.4619:0.0	.	180	Q86Y34	GPR97_HUMAN	H	180;60	ENSP00000332900:R180H;ENSP00000404803:R60H	ENSP00000332900:R180H	R	+	2	0	GPR97	56270636	0.001000	0.12720	0.033000	0.17914	0.092000	0.18411	-0.145000	0.10265	-0.681000	0.05204	-1.855000	0.00564	CGC	NOVEL	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257333.2	3	24.709844	KEEP	0	1	31	93	3198	GG	1	1	0		+	82	60	2770	0	0	253.454015	136	60	4667	420	ENST00000333493.4	0.376147	1
NDRG4	65009	__UNKNOWN__	__UNKNOWN__	16	58528752	58528752	__UNKNOWN__	Intron	SNP	G	G	A	rs375448238		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:58528752G>A	ENST00000394282.4	+	3	539				NDRG4_ENST00000258187.5_Intron|NDRG4_ENST00000394279.2_Intron	NM_001130487.1	NP_001123959.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	NA		NA			cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						aaaaaaaaaagaaaAGAAAAG	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034	65009			14466	protein-coding gene	gene with protein product		614463			NA	11352569, 16408304	Standard		NM_020465	NA	Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000394282.4:c.133-116G>A	chr16.hg19:g.58528752G>A		NA	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	hg19	CCDS45500.1	0.02	1.7835	AAAxAAA	COVERED																																																																																			NOVEL	NDRG4-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257383.5	5	4.669745	KEEP	0	1	11	20	523	GG	0.999869	0.984032	0		+	7	60	153	1	0	9.604426	49	70	1473	98	ENST00000394282.4	0.125	0.984161
CDH11	1009	__UNKNOWN__	__UNKNOWN__	16	64980855	64980855	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:64980855G>C	ENST00000268603.4	-	0	3657				CDH11_ENST00000394156.3_3'UTR	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	NA		NA			adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TGTACAAATAGATACATTAAA	0.284	NA	NA	T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		16	16q22.1	1009	cadherin 11, type 2, OB-cadherin (osteoblast)		M	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937	1009		Cadherins / Major cadherins	1750	protein-coding gene	gene with protein product	OB-Cadherin	600023			NA	9615235	Standard	NM_033664	NM_001797	NA	Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.*651C>G	chr16.hg19:g.64980855G>C		NA	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	hg19	CCDS10803.1	0.02	2.171645	ATAxATA	COVERED																																																																																			NOVEL	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268755.1	2	12.339964	KEEP	0	0	0	41	1459	GG	1	0.999894	0		-	15	60	551	0	0	44.417563	78	60	2949	168	ENST00000268603.4	0.16129	0.999895
DPEP2	64174	__UNKNOWN__	__UNKNOWN__	16	68021570	68021570	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:68021570G>T	ENST00000572888.1	-	10	1950	c.1300C>A	c.(1300-1302)Cgt>Agt	p.R434S	DPEP2_ENST00000412757.2_Missense_Mutation_p.R434S|DPEP2_ENST00000393847.1_Missense_Mutation_p.R434S			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	434		NA			arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		TGTCTCTGACGCAGACGTGAG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													112	102	105	NA		NA	NA	16		NA											NA				68021570		2198	4300	6498	SO:0001583	missense			AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	64174	3.4.13.19		23028	protein-coding gene	gene with protein product		609925			NA		Standard	NM_022355	NM_022355	NA	Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.1300C>A	chr16.hg19:g.68021570G>T	ENSP00000458977:p.Arg434Ser	NA	B2RCF8|Q6UX92|Q8TC95	hg19	CCDS10857.1	0.02	15.223235	GACxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.022	0.985248	0.18889	.	.	ENSG00000167261	ENST00000393847;ENST00000412757;ENST00000322384	T;T	0.16897	2.31;2.31	3.52	2.55	0.30701	.	1.847310	0.02185	N	0.060816	T	0.16471	0.0396	L	0.40543	1.245	0.09310	N	1	B;B	0.16603	0.002;0.018	B;B	0.15870	0.006;0.014	T	0.26538	-1.0100	10	0.19147	T	0.46	1.7932	8.2335	0.31612	0.0:0.0:0.7624:0.2376	.	434;347	Q9H4A9;Q9H4A9-2	DPEP2_HUMAN;.	S	434;434;347	ENSP00000377430:R434S;ENSP00000412549:R434S	ENSP00000314702:R347S	R	-	1	0	DPEP2	66579071	0.004000	0.15560	0.001000	0.08648	0.006000	0.05464	1.477000	0.35431	1.045000	0.40225	-0.311000	0.09066	CGT	NOVEL	DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000437026.1	2	25.58169	KEEP	0	0	0	85	2975	GG	1	1	0		-	101	60	3737	0	0	337.460905	206	60	7357	496	ENST00000572888.1	0.32899	1
IL34	146433	__UNKNOWN__	__UNKNOWN__	16	70693884	70693884	__UNKNOWN__	Intron	SNP	C	C	T	rs201952472		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:70693884C>T	ENST00000288098.2	+	6	921				IL34_ENST00000566361.1_Intron|IL34_ENST00000429149.2_Intron	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	NA		NA			inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						TTTTTTTTTTCCCCTATCTCT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													136	162	153	NA		NA	NA	16		NA											NA				70693884		2198	4300	6498	SO:0001627	intron_variant			BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368	146433		Interleukins and interleukin receptors	28529	protein-coding gene	gene with protein product		612081	chromosome 16 open reading frame 77	C16orf77	NA	18467591	Standard	NM_152456	NM_152456	NA	Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.539-16C>T	chr16.hg19:g.70693884C>T		NA	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	hg19	CCDS10895.1	0.02	8.31614	TTTxCCC	COVERED																																																																																			NOVEL	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268971.3	1	9.08725	KEEP	0	2	44	46	1523	CC	1	1	0		+	9	60	278	0	1	16.118793	206	70	7229	345	ENST00000288098.2	0.04186	1
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	71166771	71166771	__UNKNOWN__	Intron	SNP	G	G	A	rs11647627	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:71166771G>A	ENST00000393567.2	-	9	1194				HYDIN_ENST00000448089.2_Intron|HYDIN_ENST00000321489.5_Intron|HYDIN_ENST00000538248.1_Intron|HYDIN_ENST00000393550.2_Intron|HYDIN_ENST00000448691.1_Intron|HYDIN_ENST00000288168.10_Intron|HYDIN_ENST00000541601.1_Intron	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TCCAACAAGGGCTTCCATAGA	0.483	NA	NA											g|||	1472	0.29393	0.0386	0.281	5008	,	,	NA	22862	0.379	NA	0.4543	False	NA	,,,	NA	NA	NA	2504	0.3957	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.1044-3045C>T	chr16.hg19:g.71166771G>A		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	7.021146	AGGxCTT	COVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	5	3.009197	KEEP	0	0	0	10	339	GG	0.992708	0.992708	0		-	53	60	1862	0	0	168.630515	100	60	3624	202	ENST00000393567.2	0.346405	1
TAT	6898	__UNKNOWN__	__UNKNOWN__	16	71602123	71602123	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:71602123G>A	ENST00000355962.4	-	12	1422	c.1289C>T	c.(1288-1290)gCg>gTg	p.A430V	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	430		NA			2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	CCGGCTGCACGCCTCCAGCAT	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)					NA		NA				0													77	62	67	NA		NA	NA	16		NA											NA				71602123		2198	4300	6498	SO:0001583	missense				CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	6898	2.6.1.5		11573	protein-coding gene	gene with protein product		613018			NA		Standard		NM_000353	NA	Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1289C>T	chr16.hg19:g.71602123G>A	ENSP00000348234:p.Ala430Val	NA	B2R8I1|D3DWS2	hg19	CCDS10903.1	0.02	9.661542	CACxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	35	5.514348	0.96402	.	.	ENSG00000198650	ENST00000355962	D	0.91894	-2.93	6.17	6.17	0.99709	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.96889	0.8984	M	0.87827	2.91	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96545	0.9403	10	0.87932	D	0	-23.6921	20.8794	0.99867	0.0:0.0:1.0:0.0	.	430	P17735	ATTY_HUMAN	V	430	ENSP00000348234:A430V	ENSP00000348234:A430V	A	-	2	0	TAT	70159624	1.000000	0.71417	1.000000	0.80357	0.664000	0.39144	9.599000	0.98280	2.941000	0.99782	0.655000	0.94253	GCG	NOVEL	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268989.1	0	10.830941	KEEP	0	0	0	36	1201	GG	0.999999	0.999999	0		-	42	60	1441	0	0	119.316463	160	60	5766	298	ENST00000355962.4	0.207921	1
PHLPP2	23035	__UNKNOWN__	__UNKNOWN__	16	71724649	71724649	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:71724649A>T	ENST00000393524.2	-	3	1152				PHLPP2_ENST00000567016.1_Intron|PHLPP2_ENST00000356272.3_Intron|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000568954.1_Intron			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment membrane (GO:0042622)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37						CCACCATTAAAGTAGTGTAAG	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	30	31	NA		NA	NA	16		NA											NA				71724649		2198	4300	6498	SO:0001627	intron_variant			BX647823	CCDS32479.1, CCDS73910.1	16q22.2	2013-01-11	2009-05-26	2009-05-26	ENSG00000040199	ENSG00000040199	23035		Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent, Pleckstrin homology (PH) domain containing	29149	protein-coding gene	gene with protein product		611066	PH domain and leucine rich repeat protein phosphatase-like	PHLPPL	NA	17386267	Standard	NM_015020	NM_001289003	NA	Approved	KIAA0931	uc002fax.3	Q6ZVD8		ENST00000393524.2:c.419-37T>A	chr16.hg19:g.71724649A>T		NA	A1L374|Q9NV17|Q9Y2E3	hg19		0.02	4.648556	TAAxGTA	COVERED																																																																																			NOVEL	PHLPP2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000434140.1	0	9.328309	KEEP	0	0	0	31	998	AA	0.999997	0.999995	0		-	24	60	913	0	0	76.968316	93	60	3541	178	ENST00000393524.2	0.205128	0.999998
HPR	3250	__UNKNOWN__	__UNKNOWN__	16	72097230	72097230	__UNKNOWN__	Intron	SNP	C	C	G	rs12917768	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:72097230C>G	ENST00000540303.2	+	1	37				HPR_ENST00000561690.1_Intron|HPR_ENST00000356967.5_Intron	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	NA		NA				blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				TACATTGGTACAGATGCAGAA	0.418	NA	NA											A|||	1570	0.313498	0.3548	0.2363	5008	,	,	NA	20586	0.2579	NA	0.2704	False	NA	,,,	NA	NA	NA	2504	0.4141	NA	NA	NA						NA		NA				0													241	133	164	NA		NA	NA	16		NA											NA				72097230		554	1390	1944	SO:0001627	intron_variant			BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701	3250			5156	protein-coding gene	gene with protein product		140210			NA	2987228, 16778136	Standard	NM_020995	NM_020995	NA	Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.5+71C>G	chr16.hg19:g.72097230C>G		NA	Q7LE20|Q92658|Q92659|Q9ULB0	hg19	CCDS42193.1	0.02	4.077135	GTAxAGA	COVERED																																																																																			NOVEL	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421696.1	0	2.709003	KEEP	2	0	0	9	333	CC	0.99254	0.99254	0		+	5	40	179	0	0	10.801245	143	60	5468	196	ENST00000540303.2	0.033784	1
LDHD	197257	__UNKNOWN__	__UNKNOWN__	16	75147462	75147462	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs375237795		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:75147462C>T	ENST00000450168.2	-	8	1107	c.1057G>A	c.(1057-1059)Gca>Aca	p.A353T	LDHD_ENST00000300051.4_Missense_Mutation_p.A376T	NM_194436.2	NP_919417.1			lactate dehydrogenase D	NA		NA								endometrium(1)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	16						GCCAGGGCTGCGTACCAGGCA	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C	THR/ALA,THR/ALA	1,4377		0,1,2188	19	22	21	NA	1126,1057	4.1	0.9	16		21	0,8584		0,0,4292	no	missense,missense	LDHD	NM_153486.3,NM_194436.2	58,58	0,1,6480	TT,TC,CC	NA	0.0,0.0228,0.0077	possibly-damaging,possibly-damaging	376/508,353/485	75147462	1,12961	2189	4292	6481	SO:0001583	missense			AY092767	CCDS10913.1, CCDS45529.1	16q22.3	2011-01-27			ENSG00000166816	ENSG00000166816	197257			19708	protein-coding gene	gene with protein product		607490			NA	12127981	Standard	NM_153486	NM_153486	NA	Approved		uc002fdm.3	Q86WU2	OTTHUMG00000137605	ENST00000450168.2:c.1057G>A	chr16.hg19:g.75147462C>T	ENSP00000417011:p.Ala353Thr	NA		hg19	CCDS45529.1	0.02	7.006729	CTGxGTA	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530095	0.45073	2.28E-4	0.0	ENSG00000166816	ENST00000450168;ENST00000300051	D;D	0.90069	-2.61;-2.61	5.09	4.11	0.48088	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.182978	0.46758	D	0.000264	D	0.89536	0.6743	M	0.82433	2.59	0.58432	D	0.999996	B;B	0.34349	0.395;0.45	B;B	0.38194	0.113;0.267	D	0.88791	0.3278	10	0.87932	D	0	-14.5135	9.8936	0.41304	0.1389:0.7868:0.0:0.0744	.	353;376	Q86WU2-2;Q86WU2	.;LDHD_HUMAN	T	353;376	ENSP00000417011:A353T;ENSP00000300051:A376T	ENSP00000300051:A376T	A	-	1	0	LDHD	73704963	0.998000	0.40836	0.854000	0.33618	0.028000	0.11728	3.937000	0.56575	1.083000	0.41159	0.462000	0.41574	GCA	NOVEL	LDHD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434651.1	0	17.109476	KEEP	0	0	0	57	1973	CC	1	1	0		-	45	60	1559	0	0	135.249242	121	60	4370	267	ENST00000450168.2	0.271084	1
BCAR1	9564	__UNKNOWN__	__UNKNOWN__	16	75300517	75300517	__UNKNOWN__	Intron	SNP	C	C	T	rs533142324		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:75300517C>T	ENST00000393422.2	-	1	139				BCAR1_ENST00000420641.3_Intron	NM_001170715.1	NP_001164186.1	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	NA		NA			actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		AGCCACTGGGCACGTGCATGT	0.587	NA	NA											C|||	1	0.000199681	0	0.0014	5008	,	,	NA	19363	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820	9564		Cas scaffolding proteins	971	protein-coding gene	gene with protein product	Crk-associated substrate, Cas scaffolding protein family member 1	602941			NA	8413311, 10639512	Standard	NM_014567	NM_001170714	NA	Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000393422.2:c.66+1295G>A	chr16.hg19:g.75300517C>T		NA	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	hg19	CCDS54043.1	0.02	10.245133	GGGxACG	COVERED																																																																																			NOVEL	BCAR1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269016.2	2	28.868864	KEEP	0	0	0	96	3386	CC	1	1	0		-	26	60	872	0	0	62.836583	236	60	8734	404	ENST00000393422.2	0.099237	1
MON1B	22879	__UNKNOWN__	__UNKNOWN__	16	77229452	77229452	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:77229452A>G	ENST00000439557.2	+	4	1066	c.989A>G	c.(988-990)tAc>tGc	p.Y330C	MON1B_ENST00000248248.3_Missense_Mutation_p.Y439C|MON1B_ENST00000320859.6_Intron|MON1B_ENST00000545553.1_Missense_Mutation_p.Y293C			Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	439		NA								breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						GAGGCCCCCTACAGCAGAGAG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	41	44	NA		NA	NA	16		NA											NA				77229452		2198	4300	6498	SO:0001583	missense			BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111	22879			25020	protein-coding gene	gene with protein product		608954	MON1 homolog B (yeast)		NA	10048485	Standard	NM_014940	NM_014940	NA	Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000439557.2:c.989A>G	chr16.hg19:g.77229452A>G	ENSP00000404053:p.Tyr330Cys	NA	B4DDZ0|O94949	hg19		0.02	4.807984	CCTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	A	25.1	4.603292	0.87157	.	.	ENSG00000103111	ENST00000248248;ENST00000439557;ENST00000545553	.	.	.	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.84920	0.5579	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.999	D	0.88306	0.2953	9	0.72032	D	0.01	.	13.1287	0.59369	1.0:0.0:0.0:0.0	.	293;330;319;439	B4DDZ0;E7EW32;Q6ZR87;Q7L1V2	.;.;.;MON1B_HUMAN	C	439;330;293	.	ENSP00000248248:Y439C	Y	+	2	0	MON1B	75786953	1.000000	0.71417	0.993000	0.49108	0.978000	0.69477	9.135000	0.94478	2.142000	0.66516	0.533000	0.62120	TAC	NOVEL	MON1B-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000433886.1	2	16.822895	KEEP	0	0	0	56	1708	AA	1	1	0		+	15	60	562	0	0	43.064214	117	60	4074	250	ENST00000439557.2	0.113636	1
ADAMTS18	170692	__UNKNOWN__	__UNKNOWN__	16	77316822	77316822	__UNKNOWN__	3'UTR	SNP	T	T	C	rs4038556|rs191089565		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:77316822T>C	ENST00000282849.5	-	0	5115				RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	NA		NA			eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						ttttttttttttGCTGTTAGC	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873	170692		ADAM metallopeptidases with thrombospondin type 1 motif	17110	protein-coding gene	gene with protein product		607512	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18	ADAMTS21	NA	11867212, 17546048	Standard		NM_199355	NA	Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.*1031A>G	chr16.hg19:g.77316822T>C		NA	Q6P4R5|Q6ZWJ9	hg19	CCDS10926.1	0.02	-0.253983	TTTxTGC	COVERED																																																																																			NOVEL	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269037.1	2	2.703008	KEEP	0	0	0	9	255	TT	0.99254	0.663536	0		-	5	60	156	2	0	12.872429	17	60	593	48	ENST00000282849.5	0.227273	0.668523
PKD1L2	114780	__UNKNOWN__	__UNKNOWN__	16	81214783	81214783	__UNKNOWN__	RNA	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:81214783C>T	ENST00000527937.1	-	0	149				PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000531391.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2	NA		NA			ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGTCCAAATACCAGCTGAACA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													150	147	148	NA		NA	NA	16		NA											NA				81214783		2075	4215	6290					AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473	114780			21715	protein-coding gene	gene with protein product		607894			NA	12782129	Standard		NM_052892	NA	Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126	ENST00000527937.1:	chr16.hg19:g.81214783C>T		NA	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	hg19		0.02	6.818758	ATAxCAG	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.400844|5.400844	0.96030|0.96030	.|.	.|.	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000531391;ENST00000337114;ENST00000527937	.|.	.|.	.|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.205228	.|0.32357	.|N	.|0.006201	T|.	0.37376|.	0.1001|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.30937|.	-0.9961|.	3|.	.|0.02654	.|T	.|1	-10.2268|-10.2268	15.517|15.517	0.75833|0.75833	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	I|X	225|12;697;12	.|.	.|ENSP00000337397:W697X	V|W	-|-	1|3	0|0	PKD1L2|PKD1L2	79772284|79772284	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.423000|0.423000	0.31445|0.31445	2.475000|2.475000	0.45162|0.45162	2.467000|2.467000	0.83353|0.83353	0.563000|0.563000	0.77884|0.77884	GTA|TGG	NOVEL	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	NA	polymorphic_pseudogene	OTTHUMT00000387978.1	0	11.713064	KEEP	0	1	8	42	1476	CC	1	1	0		-	29	60	1080	0	0	87.714236	146	60	5427	287	ENST00000527937.1	0.165714	1
PKD1L2	114780	__UNKNOWN__	__UNKNOWN__	16	81219188	81219188	__UNKNOWN__	RNA	SNP	G	G	A	rs200865153		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:81219188G>A	ENST00000525539.1	-	0	1905				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2	NA		NA			ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ACAGCCAGGCGCAGGGTGACA	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	CYS/ARG,CYS/ARG	0,4152		0,0,2076	35	45	41	NA	1906,1906	2.7	0.6	16		41	1,8425		0,1,4212	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	180,180	0,1,6288	AA,AG,GG	NA	0.0119,0.0,0.0080	probably-damaging,probably-damaging	636/992,636/2460	81219188	1,12577	2076	4213	6289					AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473	114780			21715	protein-coding gene	gene with protein product		607894			NA	12782129	Standard		NM_052892	NA	Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126	ENST00000525539.1:	chr16.hg19:g.81219188G>A		NA	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	hg19		0.02	6.978219	GGCxCAG	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.17|16.17	3.047752|3.047752	0.55110|0.55110	0.0|0.0	1.19E-4|1.19E-4	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|T	.|0.70986	.|-0.53	4.83|4.83	2.68|2.68	0.31781|0.31781	.|Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	.|1.252640	.|0.05331	.|N	.|0.528415	T|T	0.82254|0.82254	0.4997|0.4997	.|.	.|.	.|.	0.22050|0.22050	N|N	0.999391|0.999391	.|D;D	.|0.89917	.|0.998;1.0	.|P;D	.|0.65773	.|0.804;0.938	T|T	0.64149|0.64149	-0.6475|-0.6475	4|9	.|0.87932	.|D	.|0	-3.9833|-3.9833	10.5621|10.5621	0.45152|0.45152	0.0:0.0:0.456:0.544|0.0:0.0:0.456:0.544	.|.	.|636;636	.|Q7Z442-3;Q7Z442	.|.;PK1L2_HUMAN	V|C	163|636	.|ENSP00000337397:R636C	.|ENSP00000337397:R636C	A|R	-|-	2|1	0|0	PKD1L2|PKD1L2	79776689|79776689	0.229000|0.229000	0.23729|0.23729	0.631000|0.631000	0.29282|0.29282	0.634000|0.634000	0.38068|0.38068	0.368000|0.368000	0.20399|0.20399	0.991000|0.991000	0.38814|0.38814	0.551000|0.551000	0.68910|0.68910	GCG|CGC	NOVEL	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	NA	polymorphic_pseudogene	OTTHUMT00000387972.2	0	12.173037	KEEP	0	1	33	52	1749	GG	1	1	0		-	39	60	1437	0	0	120.230042	153	60	5696	291	ENST00000525539.1	0.203125	1
PLCG2	5336	__UNKNOWN__	__UNKNOWN__	16	81991617	81991617	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:81991617T>A	ENST00000359376.3	+	0	4026					NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	NA		NA			B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CTGGGGTATGTGTGTAAGGGT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													143	145	145	NA		NA	NA	16		NA											NA				81991617		1993	4168	6161	SO:0001624	3_prime_UTR_variant				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	5336	3.1.4.11	SH2 domain containing	9066	protein-coding gene	gene with protein product		600220			NA	7835906	Standard		XR_248240	NA	Approved		uc002fgt.3	P16885		ENST00000359376.3:c.*14T>A	chr16.hg19:g.81991617T>A		NA	D3DUL3|Q3ZTS2|Q59H45|Q969T5	hg19	CCDS42204.1	0.02	4.585193	ATGxGTG	COVERED																																																																																			NOVEL	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000432429.1	3	8.426034	KEEP	0	0	0	28	894	TT	0.999997	0.999997	0		+	26	60	976	0	0	80.218757	121	60	4435	211	ENST00000359376.3	0.176871	1
MBTPS1	8720	__UNKNOWN__	__UNKNOWN__	16	84108228	84108228	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:84108228C>A	ENST00000343411.3	-	12	2062	c.1567G>T	c.(1567-1569)Gga>Tga	p.G523*	MBTPS1_ENST00000569770.1_Intron	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	523		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CCTGTGACTCCCATGCCGTTG	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													119	96	104	NA		NA	NA	16		NA											NA				84108228		2200	4300	6500	SO:0001587	stop_gained			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943	8720			15456	protein-coding gene	gene with protein product		603355	membrane-bound transcription factor protease, site 1		NA	9809072, 10944850	Standard	NM_003791	NM_003791	NA	Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1567G>T	chr16.hg19:g.84108228C>A	ENSP00000344223:p.Gly523*	NA	A8K6V8|Q24JQ2|Q9UF67	hg19	CCDS10941.1	0.02	4.557808	CTCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	44	11.266675	0.99539	.	.	ENSG00000140943	ENST00000343411	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-16.9363	18.9448	0.92618	0.0:1.0:0.0:0.0	.	.	.	.	X	523	.	ENSP00000344223:G523X	G	-	1	0	MBTPS1	82665729	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.790000	0.85794	2.477000	0.83638	0.650000	0.86243	GGA	NOVEL	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269080.2	1	8.427197	KEEP	0	0	0	28	972	CC	0.999997	0.999997	0		-	25	60	924	0	0	75.912144	114	60	4026	225	ENST00000343411.3	0.179856	1
MBTPS1	8720	__UNKNOWN__	__UNKNOWN__	16	84115514	84115514	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:84115514C>T	ENST00000343411.3	-	11	1782		c.e11-1		MBTPS1_ENST00000569770.1_Splice_Site	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CTGGACTGTGCTGGAGGAAAA	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	47	46	NA		NA	NA	16		NA											NA				84115514		2200	4300	6500	SO:0001630	splice_region_variant			D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943	8720			15456	protein-coding gene	gene with protein product		603355	membrane-bound transcription factor protease, site 1		NA	9809072, 10944850	Standard	NM_003791	NM_003791	NA	Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1287-1G>A	chr16.hg19:g.84115514C>T		NA	A8K6V8|Q24JQ2|Q9UF67	hg19	CCDS10941.1	0.02	16.202007	GTGxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416254	0.83449	.	.	ENSG00000140943	ENST00000343411	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2823	0.94057	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MBTPS1	82673015	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.803000	0.85983	2.554000	0.86153	0.561000	0.74099	.	NOVEL	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269080.2	2	27.385039	KEEP	0	0	0	91	3205	CC	1	1	0	Intron	-	78	60	2763	0	0	230.115528	299	60	10914	617	ENST00000343411.3	0.206897	1
HSDL1	83693	__UNKNOWN__	__UNKNOWN__	16	84156324	84156324	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:84156324G>T	ENST00000219439.4	-	0	3080				HSDL1_ENST00000565275.1_5'UTR	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	NA		NA				mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						TTAGCTCTGGGGAAAAAAATA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160	83693		Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	16475	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 12C, member 3	NA			NA	12153137, 19027726	Standard	NM_031463	NM_031463	NA	Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.*1911C>A	chr16.hg19:g.84156324G>T		NA	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	hg19	CCDS10942.1	0.02	1.949058	TGGxGAA	COVERED																																																																																			NOVEL	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269076.3	1	5.116403	KEEP	0	0	0	17	582	GG	0.999366	0.999296	0		-	23	60	783	0	0	66.372772	73	60	2509	132	ENST00000219439.4	0.239583	0.99993
TAF1C	9013	__UNKNOWN__	__UNKNOWN__	16	84212613	84212613	__UNKNOWN__	Silent	SNP	G	G	T	rs138100695		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:84212613G>T	ENST00000566732.1	-	15	2676	c.2466C>A	c.(2464-2466)tcC>tcA	p.S822S	TAF1C_ENST00000541676.1_Silent_p.S755S|TAF1C_ENST00000341690.6_Silent_p.S754S|TAF1C_ENST00000567759.1_Silent_p.S848S|TAF1C_ENST00000570117.1_Silent_p.S516S|TAF1C_ENST00000378541.4_Silent_p.S848S	NM_001243156.1	NP_001230085	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	848		NA			gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.S848S(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TGTGCTGCTGGGAGCGAGTGG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	lung(1)											62	62	62	NA		NA	NA	16		NA											NA				84212613		2200	4300	6500	SO:0001819	synonymous_variant			L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168	9013			11534	protein-coding gene	gene with protein product		604905	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD		NA	7801123	Standard	NM_139353	NM_005679	NA	Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000566732.1:c.2466C>A	chr16.hg19:g.84212613G>T		NA	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	hg19	CCDS58489.1	0.02	8.181064	CTGxGAG	COVERED																																																																																			NOVEL	TAF1C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000433047.1	5	18.658417	KEEP	0	0	0	62	2086	GG	1	1	0		-	21	60	705	0	0	51.305058	180	60	6285	320	ENST00000566732.1	0.104478	1
KLHDC4	54758	__UNKNOWN__	__UNKNOWN__	16	87741588	87741588	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:87741588G>A	ENST00000270583.5	-	0	1716				KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_3'UTR|KLHDC4_ENST00000347925.5_3'UTR	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	NA		NA								breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		TGTGCGTCAGGACGCACGCTG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731	54758			25272	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017566	NM_001184854	NA	Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.*95C>T	chr16.hg19:g.87741588G>A		NA	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	hg19	CCDS10963.1	0.02	9.204541	CAGxACG	COVERED	.	.	.	.	.	.	.	.	.	.	G	4.603	0.112122	0.08831	.	.	ENSG00000104731	ENST00000316853	.	.	.	2.21	0.166	0.14999	.	.	.	.	.	T	0.24275	0.0588	.	.	.	0.09310	N	1	B	0.23058	0.079	B	0.19391	0.025	T	0.20505	-1.0273	7	0.27082	T	0.32	.	5.7866	0.18336	0.2926:0.0:0.7074:0.0	.	237	Q9UF94	.	S	237	.	ENSP00000326148:P237S	P	-	1	0	KLHDC4	86299089	0.004000	0.15560	0.001000	0.08648	0.002000	0.02628	1.353000	0.34045	0.081000	0.16988	0.511000	0.50034	CCT	NOVEL	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269109.2	2	17.150766	KEEP	0	0	0	57	1917	GG	1	1	0		-	111	60	4046	0	0	390.758082	111	60	3968	372	ENST00000270583.5	0.5	1
MVD	4597	__UNKNOWN__	__UNKNOWN__	16	88718381	88718381	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:88718381G>A	ENST00000301012.3	-	0	1784					NM_002461.1	NP_002452.1	P53602	MVD1_HUMAN	mevalonate (diphospho) decarboxylase	NA		NA			cellular protein metabolic process (GO:0044267)|cholesterol biosynthetic process (GO:0006695)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|isoprenoid biosynthetic process (GO:0008299)|positive regulation of cell proliferation (GO:0008284)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|diphosphomevalonate decarboxylase activity (GO:0004163)|Hsp70 protein binding (GO:0030544)|protein homodimerization activity (GO:0042803)			endometrium(3)|large_intestine(1)|lung(7)|ovary(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.0478)		CATGGCCACCGGGGCCGCACT	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U49260	CCDS10968.1	16q24.3	2010-04-29			ENSG00000167508	ENSG00000167508	4597	4.1.1.33		7529	protein-coding gene	gene with protein product	mevalonate pyrophosphate decarboxylase	603236			NA	8626466	Standard	NM_002461	NM_002461	NA	Approved	MPD	uc002flg.1	P53602	OTTHUMG00000137865	ENST00000301012.3:c.*552C>T	chr16.hg19:g.88718381G>A		NA	Q53Y65	hg19	CCDS10968.1	0.02	1.943591	ACCxGGG	COVERED																																																																																			NOVEL	MVD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269547.2	0	14.442912	KEEP	0	0	0	48	1543	GG	1	0.999622	0		-	14	60	498	0	0	39.980977	71	60	2262	170	ENST00000301012.3	0.164706	0.999622
ACSF3	197322	__UNKNOWN__	__UNKNOWN__	16	89220642	89220642	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:89220642G>C	ENST00000378345.4	+	0	1187				ACSF3_ENST00000317447.4_3'UTR|ACSF3_ENST00000537116.1_3'UTR|ACSF3_ENST00000406948.3_3'UTR			Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	NA		NA			fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		TGCGGGTCTGGTGGGGAGCAG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													55	44	47	NA		NA	NA	16		NA											NA				89220642		2197	4300	6497	SO:0001624	3_prime_UTR_variant			AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715	197322		Acyl-CoA synthetase family	27288	protein-coding gene	gene with protein product	malonyl-CoA synthetase	614245			NA	17762044, 21846720	Standard	NM_174917	XM_005256293	NA	Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000378345.4:c.*27G>C	chr16.hg19:g.89220642G>C		NA	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	hg19		0.02	21.078955	CTGxTGG	COVERED																																																																																			NOVEL	ACSF3-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000395755.1	4	31.901392	KEEP	0	0	0	106	3649	GG	1	1	0		+	46	60	1693	0	0	125.533258	432	60	15414	732	ENST00000378345.4	0.096234	1
CDK10	8558	__UNKNOWN__	__UNKNOWN__	16	89762715	89762715	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:89762715G>A	ENST00000331006.8	+	0	3298				CDK10_ENST00000353379.7_3'UTR			Q15131	CDK10_HUMAN	cyclin-dependent kinase 10	NA		NA			negative regulation of cell proliferation (GO:0008285)|traversing start control point of mitotic cell cycle (GO:0007089)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			ovary(1)	1		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0276)		TGGCTCTGATGCTGAGCGAAG	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L33264	CCDS10984.2, CCDS32514.1, CCDS32514.2	16q24.3	2011-11-08	2007-11-21		ENSG00000185324	ENSG00000185324	8558		Cyclin-dependent kinases	1770	protein-coding gene	gene with protein product		603464	cyclin-dependent kinase (CDC2-like) 10		NA	8208557, 8084611	Standard		NM_052988	NA	Approved	PISSLRE	uc010cio.3	Q15131	OTTHUMG00000138049	ENST00000331006.8:c.*615G>A	chr16.hg19:g.89762715G>A		NA	A8K370|A8K8I6|A8MXU6|B3KQJ3|B7Z420|D3DX82|D3DX83|Q0VGZ7|Q15130|Q6PJC0	hg19		0.02	12.967065	GATxCTG	COVERED																																																																																			NOVEL	CDK10-016	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000423068.1	5	21.365992	KEEP	0	0	0	71	2543	GG	1	1	0		+	167	60	5741	0	0	548.846705	182	60	6873	498	ENST00000331006.8	0.47851	1
DBNDD1	79007	__UNKNOWN__	__UNKNOWN__	16	90086463	90086463	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr16:90086463G>A	ENST00000568838.1	-	1	73	c.64C>T	c.(64-66)Caa>Taa	p.Q22*	GAS8_ENST00000536122.1_Intron			Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	0		NA				cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		ttcagcgattgccagctcctg	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001587	stop_gained			AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249	79007			28455	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024043	NM_001288708	NA	Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000568838.1:c.64C>T	chr16.hg19:g.90086463G>A	ENSP00000457625:p.Gln22*	NA	B4DQS3|Q69YT2|Q9BW25	hg19		0.02	6.19942	ATTxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.19	2.759077	0.49468	.	.	ENSG00000003249	ENST00000392973	.	.	.	1.41	0.167	0.15006	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999981	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.566	0.02605	0.4932:0.0:0.2064:0.3004	.	.	.	.	X	22	.	.	Q	-	1	0	DBNDD1	88613964	0.001000	0.12720	0.000000	0.03702	0.031000	0.12232	0.262000	0.18460	-0.386000	0.07821	-1.094000	0.02160	CAA	NOVEL	DBNDD1-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000420936.1	3	22.270313	KEEP	0	0	0	74	2645	GG	1	1	0		-	13	60	470	0	0	33.374393	154	60	5841	321	ENST00000568838.1	0.077844	1
WDR81	124997	__UNKNOWN__	__UNKNOWN__	17	1630301	1630301	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:1630301G>A	ENST00000409644.1	+	1	2048	c.2048G>A	c.(2047-2049)aGt>aAt	p.S683N	WDR81_ENST00000419248.1_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000437219.2_Intron|WDR81_ENST00000446363.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	683		NA			negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GGCTCCTCCAGTCAAGCGTCC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	15	14	NA		NA	NA	17		NA											NA				1630301		691	1588	2279	SO:0001583	missense			AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716	124997		WD repeat domain containing	26600	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 166	614218			NA		Standard	NM_152348	NM_001163673	NA	Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.2048G>A	chr17.hg19:g.1630301G>A	ENSP00000386609:p.Ser683Asn	NA	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	hg19	CCDS54062.1	0.02	9.255888	CCAxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.529695	0.00951	.	.	ENSG00000167716	ENST00000409644	T	0.54279	0.58	5.5	2.2	0.27929	.	.	.	.	.	T	0.38746	0.1052	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.28364	-1.0046	6	0.35671	T	0.21	.	2.5267	0.04693	0.1411:0.1281:0.4666:0.2642	.	.	.	.	N	683	ENSP00000386609:S683N	ENSP00000386609:S683N	S	+	2	0	WDR81	1577051	0.035000	0.19736	0.082000	0.20525	0.007000	0.05969	1.518000	0.35877	0.640000	0.30582	0.561000	0.74099	AGT	NOVEL	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333118.2	3	25.861173	KEEP	0	0	0	86	2971	GG	1	1	0		+	67	60	2407	0	0	214.743159	148	60	5500	364	ENST00000409644.1	0.311628	1
ATP2A3	489	__UNKNOWN__	__UNKNOWN__	17	3850769	3850769	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:3850769C>T	ENST00000397043.3	-	8	1134	c.1011G>A	c.(1009-1011)ccG>ccA	p.P337P	ATP2A3_ENST00000309890.7_Silent_p.P337P|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000397035.3_Silent_p.P337P|ATP2A3_ENST00000352011.3_Silent_p.P337P|ATP2A3_ENST00000359983.3_Silent_p.P337P|ATP2A3_ENST00000397041.3_Silent_p.P337P			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	337		NA			blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TCTCCACGGACGGCAGGCTTC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(32;29 774 15719 37967)					NA		NA				0													93	74	80	NA		NA	NA	17		NA											NA				3850769		2203	4300	6503	SO:0001819	synonymous_variant				CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	489	3.6.3.8	ATPases / P-type	813	protein-coding gene	gene with protein product	sarcoplasmic/endoplasmic reticulum calcium ATPase 3, calcium pump 3	601929			NA	8809064	Standard	NM_174953	NM_005173	NA	Approved	SERCA3	uc002fwy.2	Q93084		ENST00000397043.3:c.1011G>A	chr17.hg19:g.3850769C>T		NA	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	hg19	CCDS45580.1	0.02	6.605524	GGAxGGC	COVERED																																																																																			NOVEL	ATP2A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438402.1	1	28.880154	KEEP	0	0	0	96	3174	CC	1	1	0		-	37	60	1301	0	0	107.185458	152	60	5262	369	ENST00000397043.3	0.195767	1
CAMTA2	23125	__UNKNOWN__	__UNKNOWN__	17	4883287	4883287	__UNKNOWN__	Missense_Mutation	SNP	T	T	G	rs148874211		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:4883287T>G	ENST00000572543.1	-	9	1457	c.1345A>C	c.(1345-1347)Atc>Ctc	p.I449L	CAMTA2_ENST00000358183.4_Missense_Mutation_p.I444L|CAMTA2_ENST00000381311.5_Missense_Mutation_p.I446L|CAMTA2_ENST00000414043.3_Missense_Mutation_p.I467L|CAMTA2_ENST00000348066.3_Missense_Mutation_p.I444L|CAMTA2_ENST00000361571.5_Missense_Mutation_p.I443L			O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	444		NA			cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						TCATCTTGGATGAAGAAGCAG	0.637	NA	NA											T|||	1	0.000199681	8e-04	0	5008	,	,	NA	13811	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								T	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE	2,4396		0,2,2197	63	63	63	NA	1336,1399,1327,1330	4.4	1	17	dbSNP_134	63	0,8580		0,0,4290	no	missense,missense,missense,missense	CAMTA2	NM_001171166.1,NM_001171167.1,NM_001171168.1,NM_015099.3	5,5,5,5	0,2,6487	GG,GT,TT	NA	0.0,0.0455,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	446/1198,467/1242,443/1202,444/1203	4883287	2,12976	2199	4290	6489	SO:0001583	missense			AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509	23125			18807	protein-coding gene	gene with protein product		611508			NA	11925432	Standard	NM_015099	NM_015099	NA	Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000572543.1:c.1345A>C	chr17.hg19:g.4883287T>G	ENSP00000460779:p.Ile449Leu	NA	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	hg19		0.02	4.320842	GGAxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	T	18.71	3.683158	0.68157	4.55E-4	0.0	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.33865	2.61;1.65;1.39;1.66;1.43	4.45	4.45	0.53987	.	0.176616	0.40222	N	0.001142	T	0.35770	0.0943	N	0.14661	0.345	0.26071	N	0.981226	P;P;P;P;P	0.44090	0.734;0.734;0.826;0.734;0.65	P;P;P;P;P	0.57009	0.651;0.651;0.811;0.651;0.743	T	0.15378	-1.0439	10	0.33141	T	0.24	-9.4808	11.7258	0.51708	0.0:0.0:0.0:1.0	.	420;467;446;444;443	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	L	467;446;443;444;444	ENSP00000412886:I467L;ENSP00000370712:I446L;ENSP00000354828:I443L;ENSP00000350910:I444L;ENSP00000321813:I444L	ENSP00000321813:I444L	I	-	1	0	CAMTA2	4824011	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.355000	0.44107	1.879000	0.54435	0.459000	0.35465	ATC	NOVEL	CAMTA2-007	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000438757.1	1	17.476639	KEEP	0	1	5	60	1816	TT	1	1	0		-	44	60	1586	0	0	141.25971	99	60	3573	248	ENST00000572543.1	0.307692	1
USP6	9098	__UNKNOWN__	__UNKNOWN__	17	5037195	5037195	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs74900103		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:5037195G>A	ENST00000574788.1	+	15	2628	c.398G>A	c.(397-399)aGg>aAg	p.R133K	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Missense_Mutation_p.R133K|USP6_ENST00000332776.4_Missense_Mutation_p.R133K			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	133	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.	NA			cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ATGAAGGAGAGGGGCAAGAGG	0.547	NA	NA	T	COL1A1, CDH11, ZNF9, OMD	aneurysmal bone cysts									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	0													185	166	173	NA		NA	NA	17		NA											NA				5037195		2203	4300	6503	SO:0001583	missense			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	9098	3.4.19.12	Ubiquitin-specific peptidases	12629	protein-coding gene	gene with protein product	ubiquitin carboxyl-terminal hydrolase 6, TBC1D3 and USP32 fusion, Tre-2 oncogene	604334	ubiquitin specific protease 6 (Tre-2 oncogene), TRE oncogene, Smith Magenis syndrome chromosome region, ubiquitin specific peptidase 6 (Tre-2 oncogene)	HRP1, TRESMCR	NA	12838346, 1349106	Standard	NM_004505	NM_004505	NA	Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.398G>A	chr17.hg19:g.5037195G>A	ENSP00000460380:p.Arg133Lys	NA	Q15634|Q86WP6|Q8IWT4	hg19	CCDS11069.2	0.02	4.256496	AGAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.090	-1.168985	0.01660	.	.	ENSG00000129204	ENST00000332776;ENST00000250066	T;T	0.26373	1.74;1.74	0.862	-1.72	0.08107	Rab-GAP/TBC domain (4);	0.104487	0.64402	N	0.000003	T	0.05135	0.0137	N	0.01576	-0.805	0.34807	D	0.737346	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40459	-0.9562	10	0.05351	T	0.99	.	2.1908	0.03898	0.3285:0.3345:0.337:0.0	.	133;133	B9A6N0;P35125	.;UBP6_HUMAN	K	133	ENSP00000328010:R133K;ENSP00000250066:R133K	ENSP00000250066:R133K	R	+	2	0	USP6	4977919	0.068000	0.21057	0.092000	0.20876	0.093000	0.18481	0.731000	0.26058	-1.381000	0.02112	-1.368000	0.01194	AGG	NOVEL	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438990.1	3	4.514717	KEEP	0	0	0	15	535	GG	0.99649	0.996475	0		+	5	37	187	0	0	12.362254	100	60	3664	148	ENST00000574788.1	0.047619	0.999984
TXNDC17	84817	__UNKNOWN__	__UNKNOWN__	17	6544375	6544375	__UNKNOWN__	5'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:6544375C>A	ENST00000570330.1	+	0	40				TXNDC17_ENST00000574838.1_5'UTR|TXNDC17_ENST00000250101.5_5'UTR			Q9BRA2	TXD17_HUMAN	thioredoxin domain containing 17	NA		NA			oxidation-reduction process (GO:0055114)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	electron carrier activity (GO:0009055)|peroxidase activity (GO:0004601)|protein-disulfide reductase activity (GO:0047134)			endometrium(1)|kidney(1)|ovary(1)	3						GACGTGCACTCCTCCAGTAGC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													11	12	12	NA		NA	NA	17		NA											NA				6544375		2176	4255	6431	SO:0001623	5_prime_UTR_variant			BC006405	CCDS11077.1	17p13.2	2007-08-16	2007-08-16	2007-08-16	ENSG00000129235	ENSG00000129235	84817			28218	protein-coding gene	gene with protein product	thioredoxin (Trx)-related protein, 14 kDa	NA	thioredoxin-like 5	TXNL5	NA	14607844, 14607843	Standard	NM_032731	NM_032731	NA	Approved	MGC14353, TRP14	uc002gdf.4	Q9BRA2	OTTHUMG00000102053	ENST00000570330.1:c.-28C>A	chr17.hg19:g.6544375C>A		NA	A8K7E8	hg19		0.02	1.825047	ACTxCTC	COVERED																																																																																			NOVEL	TXNDC17-010	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000439248.1	0	21.665606	KEEP	0	0	0	72	2444	CC	1	0.999726	0		+	29	60	939	0	0	83.685136	58	60	2068	190	ENST00000570330.1	0.333333	0.999726
NLGN2	57555	__UNKNOWN__	__UNKNOWN__	17	7311805	7311805	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:7311805G>A	ENST00000302926.2	+	1	304	c.231G>A	c.(229-231)ccG>ccA	p.P77P	NLGN2_ENST00000575301.1_Silent_p.P77P|NLGN2_ENST00000572893.1_3'UTR	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	77		NA			cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				ACGCCACGCCGCCCCTGGGCG	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													4	4	4	NA		NA	NA	17		NA											NA				7311805		1864	3663	5527	SO:0001819	synonymous_variant			AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992	57555			14290	protein-coding gene	gene with protein product		606479			NA	10767552, 10819331	Standard	NM_020795	NM_020795	NA	Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.231G>A	chr17.hg19:g.7311805G>A		NA	Q9P2I1	hg19	CCDS11103.1	0.02	2.267341	GCCxCCC	COVERED																																																																																			NOVEL	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000226941.2	0	13.622633	KEEP	0	1	30	56	1654	GG	1	0.997553	0		+	22	60	751	0	0	66.557605	49	60	1534	180	ENST00000302926.2	0.309859	0.997553
TP53	7157	__UNKNOWN__	__UNKNOWN__	17	7578265	7578265	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:7578265A>G	ENST00000269305.4	-	6	773	c.584T>C	c.(583-585)aTc>aCc	p.I195T	TP53_ENST00000413465.2_Missense_Mutation_p.I195T|TP53_ENST00000574684.1_Intron|TP53_ENST00000455263.2_Missense_Mutation_p.I195T|TP53_ENST00000445888.2_Missense_Mutation_p.I195T|TP53_ENST00000420246.2_Missense_Mutation_p.I195T|TP53_ENST00000359597.4_Missense_Mutation_p.I195T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	195	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.	NA	I -> F (in sporadic cancers; somatic mutation).|I -> L (in a sporadic cancer; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation).|I -> T (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074, ECO:0000269|PubMed:9450901}.|I -> V (in a sporadic cancer; somatic mutation).|I -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.I195T(69)|p.I195N(12)|p.I195S(10)|p.0?(8)|p.I195fs*14(5)|p.?(5)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.I102S(2)|p.I102T(2)|p.I63T(2)|p.I63S(2)|p.P191fs*6(1)|p.H193_I195delHLI(1)|p.P59_E66>Q(1)|p.I102fs*14(1)|p.I195fs*12(1)|p.I195fs*50(1)|p.I195_G199delIRVEG(1)|p.P98_E105>Q(1)|p.I63fs*14(1)|p.H193_I195>AP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TTCCACTCGGATAAGATGCTG	0.552	NA	111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	134	Substitution - Missense(99)|Whole gene deletion(8)|Insertion - Frameshift(7)|Deletion - In frame(6)|Complex - deletion inframe(6)|Unknown(5)|Deletion - Frameshift(2)|Complex - frameshift(1)	ovary(37)|breast(21)|large_intestine(18)|lung(10)|central_nervous_system(8)|biliary_tract(6)|haematopoietic_and_lymphoid_tissue(5)|skin(5)|stomach(4)|oesophagus(4)|bone(4)|endometrium(3)|urinary_tract(3)|upper_aerodigestive_tract(2)|liver(2)|pancreas(2)											100	89	93	NA		NA	NA	17		NA											NA				7578265		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510	7157			11998	protein-coding gene	gene with protein product	Li-Fraumeni syndrome	191170			NA	6396087, 3456488, 2047879	Standard	NM_000546	NM_001126115	NA	Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.584T>C	chr17.hg19:g.7578265A>G	ENSP00000269305:p.Ile195Thr	NA	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	hg19	CCDS11118.1	0.02	7.400908	CGGxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324656	0.41197	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	D;D;D;D;D;D;D;D	0.99823	-6.95;-6.95;-6.95;-6.95;-6.95;-6.95;-6.95;-6.95	5.41	3.21	0.36854	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.103171	0.64402	N	0.000004	D	0.99785	0.9910	M	0.90019	3.08	0.52099	D	0.999943	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.991;0.989;0.998;0.997;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.995;0.953;0.979;0.995;0.993;0.996	D	0.98429	1.0581	10	0.87932	D	0	-18.4587	8.2743	0.31864	0.8356:0.0:0.1644:0.0	.	156;195;195;102;195;195;195	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	T	195;195;195;195;195;195;184;102;63;102;63	ENSP00000410739:I195T;ENSP00000352610:I195T;ENSP00000269305:I195T;ENSP00000398846:I195T;ENSP00000391127:I195T;ENSP00000391478:I195T;ENSP00000425104:I63T;ENSP00000423862:I102T	ENSP00000269305:I195T	I	-	2	0	TP53	7518990	1.000000	0.71417	0.946000	0.38457	0.026000	0.11368	9.287000	0.95975	0.456000	0.26937	-0.256000	0.11100	ATC	NOVEL	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367397.1	2	21.363546	KEEP	0	0	0	71	2245	AA	1	1	0		-	129	60	4679	0	0	483.90056	49	60	1737	307	ENST00000269305.4	0.724719	1
DNAH2	146754	__UNKNOWN__	__UNKNOWN__	17	7674139	7674139	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs146759071	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:7674139G>A	ENST00000572933.1	+	27	5710	c.4250G>A	c.(4249-4251)cGc>cAc	p.R1417H	DNAH2_ENST00000389173.2_Missense_Mutation_p.R1417H			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1417	Stem. {ECO:0000250}.	NA			cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				AAGGCATCACGCTTTGTCAAG	0.483	NA	NA											G|||	17	0.00339457	0.0121	0	5008	,	,	NA	22332	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	HIS/ARG	39,4367	43.8+/-77.6	0,39,2164	187	165	173	NA	4250	3.9	0.9	17	dbSNP_134	173	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DNAH2	NM_020877.2	29	0,41,6462	AA,AG,GG	NA	0.0233,0.8852,0.3152	benign	1417/4428	7674139	41,12965	2203	4300	6503	SO:0001583	missense			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914	146754		Axonemal dyneins	2948	protein-coding gene	gene with protein product		603333	dynein, axonemal, heavy polypeptide 2, dynein heavy chain domain 3	DNHD3	NA	9256245	Standard	NM_020877	XM_005256470	NA	Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.4250G>A	chr17.hg19:g.7674139G>A	ENSP00000458355:p.Arg1417His	NA	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	hg19	CCDS32551.1	0.02	2.255844	CACxCTT	COVERED	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	14.49	2.551776	0.45487	0.008852	2.33E-4	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.62498	0.02	4.84	3.86	0.44501	Dynein heavy chain, domain-2 (1);	0.219630	0.37053	N	0.002279	T	0.52386	0.1731	M	0.78456	2.415	0.80722	D	1	B	0.16166	0.016	B	0.20955	0.032	T	0.59461	-0.7450	10	0.51188	T	0.08	.	8.4322	0.32764	0.0845:0.155:0.7605:0.0	.	1417	Q9P225	DYH2_HUMAN	H	1417	ENSP00000373825:R1417H	ENSP00000353818:R1417H	R	+	2	0	DNAH2	7614864	0.994000	0.37717	0.876000	0.34364	0.987000	0.75469	2.871000	0.48459	1.389000	0.46526	0.557000	0.71058	CGC	NOVEL	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440241.1	1	8.125941	KEEP	0	0	0	27	940	GG	0.999988	0.997541	0		+	10	60	364	0	0	28.574954	62	60	2201	132	ENST00000572933.1	0.138889	0.997553
CHD3	1107	__UNKNOWN__	__UNKNOWN__	17	7792121	7792121	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:7792121G>C	ENST00000380358.4	+	2	278				CHD3_ENST00000358181.4_5'UTR	NM_001005271.2	NP_001005271.2	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	NA		NA			centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				CTTTGTTTGGGTCTCCCATAC	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004	1107		Zinc fingers, PHD-type	1918	protein-coding gene	gene with protein product		602120			NA	9326634, 7560064	Standard	NM_001005273	NM_001005271	NA	Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000380358.4:c.278-861G>C	chr17.hg19:g.7792121G>C		NA	D3DTQ9|E9PG89|Q9Y4I0	hg19	CCDS32553.2	0.02	6.951746	TGGxTCT	COVERED																																																																																			NOVEL	CHD3-003	NOVEL	not_organism_supported|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318052.1	6	29.730723	KEEP	0	1	17	105	3683	GG	1	1	0		+	10	60	379	0	0	26.405891	151	60	5535	348	ENST00000380358.4	0.062112	1
MYH10	4628	__UNKNOWN__	__UNKNOWN__	17	8421975	8421975	__UNKNOWN__	Silent	SNP	G	G	A	rs199975844	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:8421975G>A	ENST00000269243.4	-	19	2523	c.2385C>T	c.(2383-2385)gcC>gcT	p.A795A	MYH10_ENST00000379980.4_Silent_p.A811A|MYH10_ENST00000360416.3_Silent_p.A826A|MYH10_ENST00000396239.1_Silent_p.A816A	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	795	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.	NA			actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CTCTGCAAACGGCCTGGAAGA	0.423	NA	NA											g|||	2	0.000399361	0.0015	0	5008	,	,	NA	20054	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													88	80	82	NA		NA	NA	17		NA											NA				8421975		2203	4300	6503	SO:0001819	synonymous_variant			M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026	4628		Myosins / Myosin superfamily : Class II	7568	protein-coding gene	gene with protein product		160776	myosin, heavy polypeptide 10, non-muscle		NA	1860190	Standard		NM_001256012	NA	Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2385C>T	chr17.hg19:g.8421975G>A		NA	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	hg19	CCDS11144.1	0.02	4.869777	AACxGCC	COVERED																																																																																			NOVEL	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000227001.2	2	18.356006	KEEP	0	0	0	61	2030	GG	1	1	0		-	16	60	591	0	0	45.938273	110	60	3778	248	ENST00000269243.4	0.126984	1
MYH13	8735	__UNKNOWN__	__UNKNOWN__	17	10222449	10222449	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:10222449G>A	ENST00000418404.3	-	26	3559	c.3396C>T	c.(3394-3396)ctC>ctT	p.L1132L	MYH13_ENST00000252172.4_Silent_p.L1132L			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1132		NA			cellular response to starvation (GO:0009267)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)	extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.L1132L(2)		breast(3)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(21)|lung(48)|ovary(7)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	108						TCTTGGCTCTGAGCGTGTGTT	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - coding silent(2)	lung(2)											52	56	55	NA		NA	NA	17		NA											NA				10222449		2201	4299	6500	SO:0001819	synonymous_variant			AF075248	CCDS45613.1	17p13	2011-09-27	2006-09-29			ENSG00000006788	8735		Myosins / Myosin superfamily : Class II	7571	protein-coding gene	gene with protein product	extraocular muscle myosin heavy chain, extraocular myosin heavy chain	603487	myosin, heavy polypeptide 13, skeletal muscle		NA	9806854	Standard	NM_003802	NM_003802	NA	Approved	MyHC-eo	uc002gmk.1	Q9UKX3		ENST00000418404.3:c.3396C>T	chr17.hg19:g.10222449G>A		NA	O95252|Q9P0U8	hg19	CCDS45613.1	0.02	6.889554	TCTxAGC	COVERED																																																																																			NOVEL	MYH13-003	KNOWN	alternative_3_UTR|alternative_5_UTR|NMD_exception|not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442255.1	5	21.065074	KEEP	0	0	0	70	2487	GG	1	1	0		-	62	60	2207	0	0	202.239213	106	60	4020	308	ENST00000418404.3	0.369048	1
MYH3	4621	__UNKNOWN__	__UNKNOWN__	17	10538678	10538678	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:10538678G>A	ENST00000583535.1	-	30	4260				MYH3_ENST00000226209.7_Intron	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	NA		NA			actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AAACAGAGCTGCGCACTTGGC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													100	99	99	NA		NA	NA	17		NA											NA				10538678		2203	4300	6503	SO:0001627	intron_variant				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063	4621		Myosins / Myosin superfamily : Class II	7573	protein-coding gene	gene with protein product	myosin, skeletal, heavy chain, embryonic 1, muscle embryonic myosin heavy chain 3	160720	myosin, heavy polypeptide 3, skeletal muscle, embryonic		NA	2726495	Standard	NM_002470	NM_002470	NA	Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4172+5C>T	chr17.hg19:g.10538678G>A		NA	Q15492	hg19	CCDS11157.1	0.02	1.933617	GCTxCGC	COVERED																																																																																			NOVEL	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252734.2	0	8.125007	KEEP	0	0	0	27	971	GG	0.999988	0.999665	0		-	21	60	710	0	0	60.264096	65	60	2412	152	ENST00000583535.1	0.244186	0.999678
COX10	1352	__UNKNOWN__	__UNKNOWN__	17	13977770	13977770	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:13977770C>T	ENST00000261643.3	+	2	251	c.174C>T	c.(172-174)cgC>cgT	p.R58R	COX10_ENST00000429152.2_Silent_p.R58R|COX10_ENST00000536205.1_5'UTR|COX10_ENST00000537334.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	58		NA			aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TCCTCAAACGCATGGTATGTT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													182	178	179	NA		NA	NA	17		NA											NA				13977770		2203	4300	6503	SO:0001819	synonymous_variant			U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695	1352		Mitochondrial respiratory chain complex assembly factors	2260	protein-coding gene	gene with protein product	heme A: farnesyltransferase, protoheme IX farnesyltransferase, mitochondrial, heme O synthase	602125	COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase), COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)		NA	9177788, 12928484	Standard	NM_001303	NM_001303	NA	Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.174C>T	chr17.hg19:g.13977770C>T		NA	B2R6U5|B4DJ50|O15334|Q969F7	hg19	CCDS11166.1	0.02	1.977235	ACGxATG	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.597	1.127782	0.20959	.	.	ENSG00000006695	ENST00000429152	.	.	.	5.33	3.34	0.38264	.	.	.	.	.	T	0.52289	0.1725	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44787	-0.9305	4	.	.	.	-15.4661	4.7144	0.12887	0.1517:0.6065:0.0:0.2419	.	.	.	.	Y	19	.	.	H	+	1	0	COX10	13918495	0.997000	0.39634	1.000000	0.80357	0.974000	0.67602	0.354000	0.20146	0.745000	0.32763	-0.198000	0.12761	CAT	NOVEL	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130003.1	1	9.932696	KEEP	0	0	0	33	1199	CC	0.999998	0.999315	0		+	54	70	1903	0	0	193.658393	27	60	1039	135	ENST00000261643.3	0.666667	0.999317
COX10	1352	__UNKNOWN__	__UNKNOWN__	17	14095195	14095195	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:14095195A>G	ENST00000261643.3	+	6	772				COX10_ENST00000536205.1_Intron|COX10_ENST00000537334.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	NA		NA			aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		CCAGATCAGTACTGCCTCTAC	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695	1352		Mitochondrial respiratory chain complex assembly factors	2260	protein-coding gene	gene with protein product	heme A: farnesyltransferase, protoheme IX farnesyltransferase, mitochondrial, heme O synthase	602125	COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase), COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)		NA	9177788, 12928484	Standard	NM_001303	NM_001303	NA	Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.696-111A>G	chr17.hg19:g.14095195A>G		NA	B2R6U5|B4DJ50|O15334|Q969F7	hg19	CCDS11166.1	0.02	9.194954	AGTxCTG	COVERED																																																																																			NOVEL	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130003.1	5	17.526841	KEEP	13	3	82	87	2721	AA	1	1	0		+	7	40	260	0	0	15.835914	216	60	7525	374	ENST00000261643.3	0.03139	1
CDRT1	374286	__UNKNOWN__	__UNKNOWN__	17	15522759	15522759	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs201445711		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:15522759A>T	ENST00000395906.3	-	1	67	c.68T>A	c.(67-69)aTc>aAc	p.I23N	RP11-385D13.1_ENST00000455584.2_Intron	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	23		NA								endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GCATAGAGGGATGGAATCGGT	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													215	229	224	NA		NA	NA	17		NA											NA				15522759		2202	4300	6502	SO:0001583	missense			U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322	374286		F-boxes / WD-40 domains, WD repeat domain containing	14379	protein-coding gene	gene with protein product		604596	F-box and WD repeat domain containing 10 pseudogene 1, F-box and WD-40 domain protein 10 pseudogene 1	FBXW10P1	NA	9787083, 11381029	Standard	NM_006382	NM_006382	NA	Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.68T>A	chr17.hg19:g.15522759A>T	ENSP00000379242:p.Ile23Asn	NA	O43848|O95611	hg19	CCDS45619.1	0.02	16.943039	GGGxTGG	COVERED	195	0.08928571428571429	32	0.06504065040650407	40	0.11049723756906077	28	0.04895104895104895	95	0.12532981530343007	.	6.026	0.373201	0.11409	.	.	ENSG00000251537	ENST00000261644;ENST00000395906	T	0.24723	1.84	5.01	3.92	0.45320	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.41745	D	0.989634	P	0.36438	0.553	B	0.32465	0.146	T	0.35025	-0.9805	9	0.66056	D	0.02	.	10.5666	0.45175	0.8552:0.0:0.0:0.1448	.	23	O95170	CDRT1_HUMAN	N	23	ENSP00000379242:I23N	ENSP00000261644:I23N	I	-	2	0	RP11-385D13.1	15463484	0.022000	0.18835	0.015000	0.15790	0.003000	0.03518	1.621000	0.36986	0.847000	0.35167	-0.456000	0.05471	ATC	NOVEL	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000448127.1	1	2.847543	KEEP	32	10	303	116	3628	AA	1	1	0		-	38	50	1263	0	0	88.827149	391	50	13944	704	ENST00000395906.3	0.088578	1
ZNF286A	57335	__UNKNOWN__	__UNKNOWN__	17	15621841	15621841	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:15621841G>A	ENST00000464847.2	+	0	3356				ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000578920.1_Intron|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000421016.1_3'UTR|ZNF286A_ENST00000413242.2_Intron|ZNF286A_ENST00000593105.1_Intron			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		GGTTCAGTGTGTTATTATATT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607	57335		Zinc fingers, C2H2-type, -	13501	protein-coding gene	gene with protein product		NA	zinc finger protein 286	ZNF286	NA	11347906	Standard	NM_020652	NM_020652	NA	Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.*1237G>A	chr17.hg19:g.15621841G>A		NA	B4DKF9|Q96JF3	hg19	CCDS11172.1	0.02	6.644327	TGTxTTA	COVERED																																																																																			NOVEL	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130696.4	5	32.504229	KEEP	268	0	0	108	3833	GG	1	1	0		+	50	50	1649	0	0	142.690635	129	50	4836	634	ENST00000464847.2	0.27933	1
NCOR1	9611	__UNKNOWN__	__UNKNOWN__	17	15995255	15995255	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:15995255G>A	ENST00000268712.3	-	22	3195	c.2938C>T	c.(2938-2940)Caa>Taa	p.Q980*	NCOR1_ENST00000395848.1_Nonsense_Mutation_p.Q887*|NCOR1_ENST00000395851.1_Nonsense_Mutation_p.Q996*	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	980		NA			CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ATCTGTTCTTGTCTCTGCCGC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													156	145	149	NA		NA	NA	17		NA											NA				15995255		2203	4300	6503	SO:0001587	stop_gained			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027	9611			7672	protein-coding gene	gene with protein product	thyroid hormone- and retinoic acid receptor-associated corepressor 1, protein phosphatase 1, regulatory subunit 109	600849	nuclear receptor co-repressor 1		NA	7566114, 9724795	Standard	NM_006311	NM_006311	NA	Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.2938C>T	chr17.hg19:g.15995255G>A	ENSP00000268712:p.Gln980*	NA	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	hg19	CCDS11175.1	0.02	2.182241	CTTxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	40	8.455611	0.98820	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	.	.	.	5.02	5.02	0.67125	.	0.163752	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-9.3373	17.6965	0.88282	0.0:0.0:1.0:0.0	.	.	.	.	X	980;996;887;887	.	ENSP00000268712:Q980X	Q	-	1	0	NCOR1	15935980	1.000000	0.71417	0.998000	0.56505	0.910000	0.53928	8.596000	0.90844	2.485000	0.83878	0.650000	0.86243	CAA	NOVEL	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131751.5	1	7.825548	KEEP	0	0	0	26	927	GG	0.999957	0.99619	0		-	23	60	828	0	0	74.69948	46	60	1753	113	ENST00000268712.3	0.333333	0.996233
FAM211A	0	__UNKNOWN__	__UNKNOWN__	17	16350226	16350226	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:16350226G>A	ENST00000409083.3	-	3	538				C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|FAM211A_ENST00000470794.1_Intron	NM_207387.3	NP_997270.2				NA		NA								lung(1)	1						CGCCTCTCCAGGATCCATCTC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409083.3:c.376-2781C>T	chr17.hg19:g.16350226G>A		NA		hg19	CCDS11178.2	0.02	-0.298242	CCAxGAT	COVERED																																																																																			NOVEL	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130461.2	0	4.815788	KEEP	0	0	0	16	573	GG	0.997832	0.779366	0		-	8	60	291	0	0	24.86177	26	60	957	64	ENST00000409083.3	0.235294	0.78106
TOM1L2	146691	__UNKNOWN__	__UNKNOWN__	17	17750675	17750675	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:17750675C>A	ENST00000379504.3	-	0	1881				TOM1L2_ENST00000318094.10_3'UTR|TOM1L2_ENST00000395739.4_3'UTR|TOM1L2_ENST00000581396.1_3'UTR|TOM1L2_ENST00000478943.1_3'UTR	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	NA		NA			intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GGCTGGGCCACTCTGCCCGCT	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(192;2505 2909 14455 25269)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662	146691			11984	protein-coding gene	gene with protein product		615519	target of myb1 (chicken) homolog-like 1		NA	10036180	Standard		NM_001082968	NA	Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.*274G>T	chr17.hg19:g.17750675C>A		NA	B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	hg19	CCDS42270.1	0.02	2.231619	CCAxTCT	COVERED																																																																																			NOVEL	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131928.1	2	6.858391	KEEP	0	0	0	23	742	CC	0.999892	0.967321	0		-	8	60	295	0	0	23.622905	44	60	1661	90	ENST00000379504.3	0.153846	0.967425
GID4	79018	__UNKNOWN__	__UNKNOWN__	17	17970453	17970453	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:17970453G>A	ENST00000268719.4	+	0	2972				GID4_ENST00000579871.1_Intron	NM_024052.4	NP_076957.3	Q8IVV7	GID4_HUMAN	GID complex subunit 4	NA		NA									NA						TGATGGACAAGTGAAGGAGGC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK127580	CCDS11190.1	17p11.2	2013-07-31	2013-07-31	2012-07-20	ENSG00000141034	ENSG00000141034	79018			28453	protein-coding gene	gene with protein product	vacuolar import and degradation 24	NA	chromosome 17 open reading frame 39, GID complex subunit 4, VID24 homolog (S. cerevisiae)	C17orf39	NA	11997338	Standard	NM_024052	NM_024052	NA	Approved	VID24	uc002gsg.1	Q8IVV7	OTTHUMG00000059398	ENST00000268719.4:c.*1896G>A	chr17.hg19:g.17970453G>A		NA	Q8TEB5|Q9BW50	hg19	CCDS11190.1	0.02	4.347048	CAAxTGA	COVERED																																																																																			NOVEL	GID4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132071.2	4	14.441929	KEEP	0	0	0	48	1665	GG	1	1	0		+	21	60	756	1	0	59.993313	118	60	4399	230	ENST00000268719.4	0.151079	1
ZNF286B	729288	__UNKNOWN__	__UNKNOWN__	17	18564721	18564721	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:18564721G>T	ENST00000285274.5	-	0	2165				ZNF286B_ENST00000545289.1_3'UTR			P0CG31	Z286B_HUMAN	zinc finger protein 286B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						GGAAGGGAATGCTAAGGACTT	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459	729288		Zinc fingers, C2H2-type	33241	protein-coding gene	gene with protein product	zinc finger protein 590	NA	zinc finger protein 286-like, zinc finger 286C pseudogene	ZNF286L, ZNF286C	NA		Standard	XM_001723047	NM_001145045	NA	Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000285274.5:c.*1748C>A	chr17.hg19:g.18564721G>T		NA		hg19		0.02	13.205312	AATxCTA	COVERED																																																																																			NOVEL	ZNF286B-003	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000131052.3	12	12.513069	KEEP	24	8	225	121	4371	GG	1	1	0		-	24	45	829	0	0	55.877736	343	60	12895	635	ENST00000285274.5	0.065395	1
TVP23B	51030	__UNKNOWN__	__UNKNOWN__	17	18694197	18694197	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:18694197T>G	ENST00000307767.8	+	3	394				TVP23B_ENST00000574226.1_Intron|TVP23B_ENST00000476139.1_Intron|TVP23B_ENST00000581733.1_Intron	NM_016078.4	NP_057162.4	Q9NYZ1	TV23B_HUMAN	trans-golgi network vesicle protein 23 homolog B (S. cerevisiae)	NA		NA				integral component of membrane (GO:0016021)					NA						TTCATTGTGTTTTGGTTTTCA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	68	66	NA		NA	NA	17		NA											NA				18694197		2193	4282	6475	SO:0001627	intron_variant			AF151906	CCDS42274.1	17p11.2	2012-11-29	2012-11-29	2012-11-29	ENSG00000171928	ENSG00000171928	51030			20399	protein-coding gene	gene with protein product		NA	family with sequence similarity 18, member B, family with sequence similarity 18, member B1	FAM18B, FAM18B1	NA	10810093	Standard	NM_016078	NM_016078	NA	Approved	CGI-148, YDR084C	uc002gum.2	Q9NYZ1	OTTHUMG00000059052	ENST00000307767.8:c.96-12T>G	chr17.hg19:g.18694197T>G		NA	A8K448|Q96HK5|Q9Y3E6	hg19	CCDS42274.1	0.02	10.159703	TGTxTTG	COVERED																																																																																			NOVEL	TVP23B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130667.2	8	39.720588	KEEP	118	0	0	132	4246	TT	1	1	0		+	137	49	5251	0	0	534.369109	67	60	2417	527	ENST00000307767.8	0.671569	1
AKAP10	11216	__UNKNOWN__	__UNKNOWN__	17	19809122	19809122	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:19809122C>A	ENST00000225737.6	-	0	2564					NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	NA		NA			blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					AGCAAACCACCTCTGGCACCT	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599	11216		A-kinase anchor proteins	368	protein-coding gene	gene with protein product	dual-specificity A-kinase anchoring protein 2, protein kinase A anchoring protein 10, mitochondrial A kinase PPKA anchor protein 10	604694			NA	9326583	Standard	NM_007202	NM_007202	NA	Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.*418G>T	chr17.hg19:g.19809122C>A		NA	B2R650|Q96AJ7	hg19	CCDS11214.1	0.02	4.569767	CACxTCT	COVERED																																																																																			NOVEL	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132380.2	0	13.840442	KEEP	0	0	0	46	1602	CC	1	1	0		-	39	60	1418	0	0	126.547204	87	60	3170	215	ENST00000225737.6	0.309524	1
CCDC144NL	339184	__UNKNOWN__	__UNKNOWN__	17	20768691	20768691	__UNKNOWN__	3'UTR	SNP	C	C	T	rs75640454		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:20768691C>T	ENST00000327925.5	-	0	822				CCDC144NL_ENST00000539484.1_Intron	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	NA		NA								large_intestine(3)|lung(3)|skin(1)	7						TTCTTAAAGGCAAAAGTTAAT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													65	60	62	NA		NA	NA	17		NA											NA				20768691		2203	4300	6503	SO:0001624	3_prime_UTR_variant				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212	339184			33735	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004306	NM_001004306	NA	Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.*37G>A	chr17.hg19:g.20768691C>T		NA		hg19	CCDS32591.1	0.02	16.275924	AGGxAAA	COVERED																																																																																			NOVEL	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255361.2	6	9.537354	KEEP	5	3	98	66	2387	CC	1	1	0		-	24	59	861	0	0	59.854641	317	60	12017	539	ENST00000327925.5	0.070381	1
CCDC144NL	339184	__UNKNOWN__	__UNKNOWN__	17	20768692	20768692	__UNKNOWN__	3'UTR	SNP	A	A	G	rs4629022		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:20768692A>G	ENST00000327925.5	-	0	821				CCDC144NL_ENST00000539484.1_Intron	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	NA		NA								large_intestine(3)|lung(3)|skin(1)	7						TCTTAAAGGCAAAAGTTAATA	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													66	61	62	NA		NA	NA	17		NA											NA				20768692		2203	4300	6503	SO:0001624	3_prime_UTR_variant				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212	339184			33735	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004306	NM_001004306	NA	Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.*36T>C	chr17.hg19:g.20768692A>G		NA		hg19	CCDS32591.1	0.02	17.313611	GGCxAAA	COVERED																																																																																			NOVEL	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255361.2	6	7.930516	KEEP	5	3	114	66	2079	AA	1	1	0		-	41	60	1486	0	0	113.328651	309	60	11450	546	ENST00000327925.5	0.117143	1
KCNJ12	3768	__UNKNOWN__	__UNKNOWN__	17	21318781	21318781	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs41284970		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:21318781C>T	ENST00000583088.1	+	3	1022	c.127C>T	c.(127-129)Cgc>Tgc	p.R43C	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R43C	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	43		NA		R -> H (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GCGCAGGTGCCGCAACCGCTT	0.602	NA	NA								Prostate(3;0.18)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C	CYS/ARG	1,4405		0,1,2202	135	98	111	NA	127	5.3	1	17	dbSNP_127	111	0,8600		0,0,4300	no	missense	KCNJ12	NM_021012.4	180	0,1,6502	TT,TC,CC	NA	0.0,0.0227,0.0077	probably-damaging	43/434	21318781	1,13005	2203	4300	6503	SO:0001583	missense			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185	3768		Potassium channels, Voltage-gated ion channels / Potassium channels, Inwardly rectifying	6258	protein-coding gene	gene with protein product		602323	potassium inwardly-rectifying channel, subfamily J, inhibitor 1	KCNJN1	NA	7859381, 12417321, 16382105	Standard	NM_021012	NM_021012	NA	Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.127C>T	chr17.hg19:g.21318781C>T	ENSP00000463778:p.Arg43Cys	NA	O43401|Q15756|Q8NG63	hg19	CCDS11219.1	0.02	29.074458	TGCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.70	3.876575	0.72180	2.27E-4	0.0	ENSG00000184185	ENST00000331718	T	0.38240	1.15	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	P	0.62885	0.908	T	0.56318	-0.7999	10	0.87932	D	0	.	13.1369	0.59413	0.2687:0.7312:0.0:0.0	rs41284970	43	Q14500	IRK12_HUMAN	C	43	ENSP00000328150:R43C	ENSP00000328150:R43C	R	+	1	0	KCNJ12	21259374	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.900000	0.56295	2.506000	0.84524	0.591000	0.81541	CGC	NOVEL	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255060.2	10	7.587596	KEEP	0	16	476	193	6383	CC	1	1	0		+	25	60	785	0	0	48.038918	448	60	15659	977	ENST00000583088.1	0.052854	1
KCNJ12	3768	__UNKNOWN__	__UNKNOWN__	17	21320350	21320350	__UNKNOWN__	3'UTR	SNP	G	G	A	rs73981226	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:21320350G>A	ENST00000583088.1	+	0	2591				KCNJ12_ENST00000331718.5_3'UTR	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	NA		NA			muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GAGAAACACCGGGTTTCAGCT	0.468	NA	NA								Prostate(3;0.18)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185	3768		Potassium channels, Voltage-gated ion channels / Potassium channels, Inwardly rectifying	6258	protein-coding gene	gene with protein product		602323	potassium inwardly-rectifying channel, subfamily J, inhibitor 1	KCNJN1	NA	7859381, 12417321, 16382105	Standard	NM_021012	NM_021012	NA	Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.*394G>A	chr17.hg19:g.21320350G>A		NA	O43401|Q15756|Q8NG63	hg19	CCDS11219.1	0.02	4.48888	ACCxGGT	COVERED																																																																																			NOVEL	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255060.2	4	5.984331	KEEP	0	0	0	20	643	GG	0.999863	0.999862	0		+	39	70	1427	0	0	127.9719	84	60	2870	175	ENST00000583088.1	0.317073	0.999999
KSR1	8844	__UNKNOWN__	__UNKNOWN__	17	25952255	25952255	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:25952255C>A	ENST00000398988.3	+	0	6028				AC015688.3_ENST00000584605.1_Intron	NM_014238.1	NP_055053.1	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	NA		NA			Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		ACTGGTGAGCCCCACAGTTGG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(88;1120 1336 6324 10502 16832)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068	8844			6465	protein-coding gene	gene with protein product		601132	kinase suppressor of ras	KSR	NA	8521512	Standard	NM_014238	XM_006722151	NA	Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000398988.3:c.*3294C>A	chr17.hg19:g.25952255C>A		NA	F8WEA9|H7BYU0|Q13476	hg19	CCDS58532.1	0.02	4.669671	AGCxCCA	COVERED																																																																																			NOVEL	KSR1-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255074.2	1	9.018585	KEEP	0	0	0	30	986	CC	0.999997	0.999997	0		+	33	60	1189	0	0	103.180488	93	60	3272	198	ENST00000398988.3	0.261905	1
SUZ12P	0	__UNKNOWN__	__UNKNOWN__	17	29061941	29061941	__UNKNOWN__	RNA	SNP	T	T	C	rs112064181		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:29061941T>C	ENST00000582557.1	+	0	861										NA		NA									NA						TAGATTTCTTTGAACTCGGAA	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000582557.1:	chr17.hg19:g.29061941T>C		NA		hg19		0.02	1.792017	CTTxGAA	COVERED																																																																																			NOVEL	SUZ12P-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000444260.1	0	7.220394	KEEP	0	0	0	24	732	TT	0.999909	0.995596	0		+	5	21	168	0	0	11.431896	63	50	2347	117	ENST00000582557.1	0.073529	0.995687
CRLF3	51379	__UNKNOWN__	__UNKNOWN__	17	29119491	29119491	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:29119491G>A	ENST00000324238.6	-	6	1050	c.926C>T	c.(925-927)cCg>cTg	p.P309L	CTD-2349P21.9_ENST00000580085.1_lincRNA|CRLF3_ENST00000577725.1_Intron|CRLF3_ENST00000544695.1_Missense_Mutation_p.P193L	NM_015986.3	NP_057070.3	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	309		NA			G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of cell growth (GO:0030308)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	17		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				GAAATAAGTCGGAGCTCTGGA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(30;346 881 29244 33464 41299)					NA		NA				0													141	136	138	NA		NA	NA	17		NA											NA				29119491		2203	4300	6503	SO:0001583	missense			AF120151	CCDS32607.1	17q11.2	2008-05-02				ENSG00000176390	51379			17177	protein-coding gene	gene with protein product		614853			NA		Standard		NM_015986	NA	Approved	CREME9, CYTOR4	uc002hfr.4	Q8IUI8		ENST00000324238.6:c.926C>T	chr17.hg19:g.29119491G>A	ENSP00000318804:p.Pro309Leu	NA	A6NJF3|B2R8C3|Q2MLY7|Q9UNI3|Q9Y6M8	hg19	CCDS32607.1	0.02	11.059731	GTCxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031719	0.93575	.	.	ENSG00000176390	ENST00000324238;ENST00000544695	T;T	0.61158	0.13;0.13	5.22	5.22	0.72569	.	0.048925	0.85682	D	0.000000	T	0.64349	0.2590	M	0.61703	1.905	0.80722	D	1	D	0.63880	0.993	P	0.48400	0.576	T	0.67381	-0.5685	10	0.48119	T	0.1	-12.5322	18.7625	0.91858	0.0:0.0:1.0:0.0	.	309	Q8IUI8	CRLF3_HUMAN	L	309;193	ENSP00000318804:P309L;ENSP00000444188:P193L	ENSP00000318804:P309L	P	-	2	0	CRLF3	26143617	1.000000	0.71417	0.982000	0.44146	0.984000	0.73092	9.391000	0.97249	2.409000	0.81822	0.591000	0.81541	CCG	NOVEL	CRLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444354.1	2	21.593788	KEEP	0	0	0	72	2354	GG	1	1	0		-	8	60	300	0	0	18.310926	252	60	8593	408	ENST00000324238.6	0.030769	1
ACACA	31	__UNKNOWN__	__UNKNOWN__	17	35620815	35620815	__UNKNOWN__	Intron	SNP	G	G	A	rs538782041|rs538493742|rs111738937|rs553598219	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:35620815G>A	ENST00000394406.2	-	11	1199				ACACA_ENST00000335166.5_Intron|ACACA_ENST00000360679.3_Intron|ACACA_ENST00000353139.5_Intron	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	NA		NA			acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGAAAAGGGGGAAAAAAAAAA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)					NA		NA				0													50	50	50	NA		NA	NA	17		NA											NA				35620815		2203	4300	6503	SO:0001627	intron_variant			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	31	6.4.1.2		84	protein-coding gene	gene with protein product	acetyl-CoA carboxylase 1	200350	acetyl-Coenzyme A carboxylase alpha	ACAC, ACC	NA		Standard	NM_198836	NM_198837	NA	Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.1009-18C>T	chr17.hg19:g.35620815G>A		NA	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	hg19	CCDS11317.1	0.02	2.164796	GGGxAAA	COVERED																																																																																			NOVEL	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256696.1	1	3.31925	KEEP	0	1	13	16	517	GG	0.999366	0.996531	0		-	22	60	784	2	0	69.812326	49	60	1791	108	ENST00000394406.2	0.309859	0.997163
PLXDC1	57125	__UNKNOWN__	__UNKNOWN__	17	37262111	37262111	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:37262111C>T	ENST00000315392.4	-	7	1018	c.807G>A	c.(805-807)gtG>gtA	p.V269V	PLXDC1_ENST00000493200.1_5'UTR|PLXDC1_ENST00000394316.2_Silent_p.V269V|PLXDC1_ENST00000539608.1_Silent_p.V196V|PLXDC1_ENST00000444911.2_Silent_p.V229V	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	269		NA			angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)			kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						ACTCACCTGGCACATCCGGGG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													127	126	126	NA		NA	NA	17		NA											NA				37262111		2203	4300	6503	SO:0001819	synonymous_variant			AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381	57125			20945	protein-coding gene	gene with protein product	tumor endothelial marker 7 precursor	606826			NA	10947988, 11559528	Standard	NM_020405	NM_020405	NA	Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.807G>A	chr17.hg19:g.37262111C>T		NA	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	hg19	CCDS11333.1	0.02	6.335973	TGGxACA	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.528	0.870279	0.17322	.	.	ENSG00000161381	ENST00000444435	.	.	.	4.99	1.7	0.24286	.	.	.	.	.	T	0.43722	0.1260	.	.	.	0.54753	D	0.999989	.	.	.	.	.	.	T	0.20874	-1.0262	4	.	.	.	-4.0089	2.4827	0.04591	0.1965:0.501:0.1904:0.1121	.	.	.	.	Y	53	.	.	C	-	2	0	PLXDC1	34515637	0.000000	0.05858	0.498000	0.27564	0.891000	0.51852	-1.594000	0.02094	0.070000	0.16634	0.561000	0.74099	TGC	NOVEL	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256892.2	1	10.834721	KEEP	0	0	0	36	1289	CC	0.999999	0.999999	0		-	56	60	1851	0	0	160.885171	140	60	5241	318	ENST00000315392.4	0.285714	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	37399513	37399513	__UNKNOWN__	IGR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:37399513C>A			NA	NA				STAC2 (17388 upstream) : RP11-690G19.4 (702 downstream)						NA		NA									NA						AGATCGACACCTTCAGGCCCA	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.37399513C>A		NA		hg19		0.02	4.519276	CACxTTC	COVERED																																																																																			NOVEL					0			1	7.524577	KEEP	0	0	0	25	889	CC	0.999931	0.999923	0			18	60	640	0	0	51.381888	91	60	3347	179		0.165138	0.999992
RARA	5914	__UNKNOWN__	__UNKNOWN__	17	38512948	38512948	__UNKNOWN__	3'UTR	SNP	A	A	C	rs371896486		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:38512948A>C	ENST00000425707.3	+	0	2094				RARA_ENST00000254066.5_3'UTR|RARA_ENST00000394081.3_3'UTR|RARA_ENST00000394086.3_3'UTR	NM_001145302.2	NP_001138774.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	NA		NA			apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	CCCTGTACATACCCTGCCATA	0.468	NA	NA	T	PML, ZNF145, TIF1, NUMA1, NPM1	APL									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		17	17q12	5914	retinoic acid receptor, alpha		L	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759	5914		Nuclear hormone receptors	9864	protein-coding gene	gene with protein product		180240			NA	2825036, 8244378	Standard		NM_001145301	NA	Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000425707.3:c.*470A>C	chr17.hg19:g.38512948A>C		NA	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	hg19	CCDS45671.1	0.02	1.891805	CATxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	24.6	4.551035	0.86127	.	.	ENSG00000131759	ENST00000319149	.	.	.	5.25	4.16	0.48862	.	.	.	.	.	T	0.55033	0.1895	.	.	.	0.09310	P	0.999999999948796	.	.	.	.	.	.	T	0.67699	-0.5603	4	0.87932	D	0	.	7.2046	0.25899	0.901:0.0:0.099:0.0	.	.	.	.	P	612	.	ENSP00000316769:T612P	T	+	1	0	RARA	35766474	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.596000	0.36718	2.094000	0.63399	0.459000	0.35465	ACC	NOVEL	RARA-007	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447443.1	3	3.81686	KEEP	0	17	148	68	1633	AA	1	1	0		+	28	60	348	0	0	13.541323	188	60	4761	403	ENST00000425707.3	0.12963	1
SMARCE1	6605	__UNKNOWN__	__UNKNOWN__	17	38781541	38781541	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:38781541T>C	ENST00000348513.6	-	0	5512					NM_003079.4	NP_003070.3	Q969G3	SMCE1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|metabolic process (GO:0008152)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|N-acetyltransferase activity (GO:0008080)|protein N-terminus binding (GO:0047485)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)			large_intestine(1)	1		Breast(137;0.000812)				ATTATTGCAGTAAGCCACATT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF035262	CCDS11370.1	17q21.2	2006-09-20			ENSG00000073584	ENSG00000073584	6605			11109	protein-coding gene	gene with protein product		603111			NA	9435219	Standard	NM_003079	NM_003079	NA	Approved	BAF57	uc002hux.2	Q969G3	OTTHUMG00000133367	ENST00000348513.6:c.*3496A>G	chr17.hg19:g.38781541T>C		NA	B3KMC1|B4DFR4|C0IMW4|C0IMW5|C0IMW7|H7C3F6|O43539	hg19	CCDS11370.1	0.02	8.518568	CAGxAAG	COVERED																																																																																			NOVEL	SMARCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257203.1	1	15.041387	KEEP	0	0	0	50	1567	TT	1	1	0		-	8	60	275	0	0	16.714711	201	60	7187	311	ENST00000348513.6	0.038278	1
KRTAP4-4	84616	__UNKNOWN__	__UNKNOWN__	17	39316965	39316965	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:39316965T>C	ENST00000390661.3	-	0	18					NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	NA		NA				keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GTGGAGGTTCTGGGTGGGTTT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	50	48	NA		NA	NA	17		NA											NA				39316965		2200	4296	6496	SO:0001623	5_prime_UTR_variant			AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396	84616		Keratin associated proteins	16928	protein-coding gene	gene with protein product		NA	keratin associated protein 4-13	KRTAP4-13	NA	11279113	Standard		NM_032524	NA	Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.-22A>G	chr17.hg19:g.39316965T>C		NA	Q9BYU7	hg19	CCDS11383.1	0.02	18.774274	TTCxGGG	COVERED																																																																																			NOVEL	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257291.1	6	29.490478	KEEP	3	0	0	98	3121	TT	1	1	0		-	197	60	6812	0	0	654.178449	205	60	7739	637	ENST00000390661.3	0.49005	1
STAT3	6774	__UNKNOWN__	__UNKNOWN__	17	40500498	40500498	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:40500498G>T	ENST00000264657.5	-	2	349	c.37C>A	c.(37-39)Cgg>Agg	p.R13R	STAT3_ENST00000404395.3_Silent_p.R13R|STAT3_ENST00000585517.1_Silent_p.R13R|STAT3_ENST00000588969.1_Silent_p.R13R|STAT3_ENST00000389272.3_Intron	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	13		NA			acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		TCCAGGTACCGTGTGTCAAGC	0.512	NA	NA							Hyperimmunoglobulin E Recurrent Infection Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													104	96	99	NA		NA	NA	17		NA											NA				40500498		2203	4300	6503	SO:0001819	synonymous_variant	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610	6774		SH2 domain containing	11364	protein-coding gene	gene with protein product		102582			NA	7512451	Standard	NM_139276, NM_003150	NM_139276	NA	Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.37C>A	chr17.hg19:g.40500498G>T		NA	A8K7B8|K7ENL3|O14916|Q9BW54	hg19	CCDS32656.1	0.02	9.777901	ACCxTGT	COVERED																																																																																			NOVEL	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319353.3	4	19.224625	KEEP	0	0	0	64	2108	GG	1	1	0		-	36	60	1321	0	0	108.166525	166	60	5577	322	ENST00000264657.5	0.178218	1
RUNDC1	146923	__UNKNOWN__	__UNKNOWN__	17	41143301	41143301	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:41143301G>A	ENST00000361677.1	+	5	1422	c.1410G>A	c.(1408-1410)atG>atA	p.M470I		NM_173079.2	NP_775102	Q96C34	RUND1_HUMAN	RUN domain containing 1	470	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.	NA								breast(1)|large_intestine(2)|lung(4)|prostate(1)	8		Breast(137;0.00499)		BRCA - Breast invasive adenocarcinoma(366;0.161)		CAGAGGCCATGCACCCGTGGG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													61	60	60	NA		NA	NA	17		NA											NA				41143301		2203	4300	6503	SO:0001583	missense			AL831813	CCDS11448.1	17q21.31	2004-02-27				ENSG00000198863	146923			25418	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173079	NM_173079	NA	Approved	DKFZp761H0421	uc002ici.1	Q96C34		ENST00000361677.1:c.1410G>A	chr17.hg19:g.41143301G>A	ENSP00000354622:p.Met470Ile	NA	Q6Y2K8|Q8IXT9|Q8N3W1	hg19	CCDS11448.1	0.02	14.509863	CATxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457532	0.43634	.	.	ENSG00000198863	ENST00000361677	T	0.19250	2.16	4.92	4.92	0.64577	RUN (2);	0.087810	0.85682	D	0.000000	T	0.17959	0.0431	L	0.28115	0.83	0.54753	D	0.999983	B	0.29232	0.238	B	0.29267	0.1	T	0.04427	-1.0952	10	0.33141	T	0.24	-35.5706	18.3135	0.90208	0.0:0.0:1.0:0.0	.	470	Q96C34	RUND1_HUMAN	I	470	ENSP00000354622:M470I	ENSP00000354622:M470I	M	+	3	0	RUNDC1	38396827	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.289000	0.65656	2.551000	0.86045	0.655000	0.94253	ATG	NOVEL	RUNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452464.1	3	33.409893	KEEP	0	0	0	111	4008	GG	1	1	0		+	12	60	413	0	0	23.091227	432	60	16025	664	ENST00000361677.1	0.027027	1
ETV4	2118	__UNKNOWN__	__UNKNOWN__	17	41607555	41607555	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:41607555G>T	ENST00000545089.1	-	7	745				ETV4_ENST00000319349.5_Intron|ETV4_ENST00000591713.1_Intron|ETV4_ENST00000393664.2_Intron|ETV4_ENST00000586826.1_5'UTR|ETV4_ENST00000545954.1_Intron|ETV4_ENST00000538265.1_Intron			P43268	ETV4_HUMAN	ets variant 4	NA		NA			branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|motor neuron axon guidance (GO:0008045)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)		EWSR1/ETV4(6)|CANT1/ETV4(3)|TMPRSS2/ETV4(13)|DDX5_ENST00000540698/ETV4(2)|KLK2/ETV4(2)	ovary(2)|upper_aerodigestive_tract(1)	3		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		GACATCTGTGGGGGAAGAAGG	0.602	NA	NA	T	EWSR1, TMPRSS2, DDX5, KLK2, CANT1	Ewing sarcoma, Prostate carcinoma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(116;1540 1611 12927 31103 34118)		Dom	yes		17	17q21	2118	ets variant gene 4 (E1A enhancer binding protein, E1AF)		M, E	0													37	37	37	NA		NA	NA	17		NA											NA				41607555		2133	4179	6312	SO:0001627	intron_variant			U18018	CCDS11465.1, CCDS58553.1, CCDS59292.1	17q21	2014-04-30	2008-09-12			ENSG00000175832	2118			3493	protein-coding gene	gene with protein product	E1A enhancer binding protein	600711	ets variant gene 4 (E1A enhancer-binding protein, E1AF)		NA	8530053, 1547944	Standard	NM_001986	NM_001986	NA	Approved	E1A-F, E1AF, PEA3	uc002idw.3	P43268		ENST00000545089.1:c.650-6C>A	chr17.hg19:g.41607555G>T		NA	A8K314|B7Z5J3|B7Z9J6|Q96AW9	hg19		0.02	13.590706	GTGxGGG	COVERED																																																																																			NOVEL	ETV4-004	NOVEL	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000453492.1	5	25.830795	KEEP	0	1	11	90	3070	GG	1	1	0		-	27	60	954	0	0	68.407595	285	60	10165	524	ENST00000545089.1	0.086538	1
DBF4B	80174	__UNKNOWN__	__UNKNOWN__	17	42824475	42824475	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:42824475C>T	ENST00000315005.3	+	11	993	c.855C>T	c.(853-855)agC>agT	p.S285S	DBF4B_ENST00000393547.2_Silent_p.S285S	NM_145663.2	NP_663696.1	Q8NFT6	DBF4B_HUMAN	DBF4 zinc finger B	285		NA			cell cycle (GO:0007049)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of protein kinase activity (GO:0045860)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)	7		Prostate(33;0.0322)				GAGAGCCAAGCCCACGATCAG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													159	136	144	NA		NA	NA	17		NA											NA				42824475		2203	4300	6503	SO:0001819	synonymous_variant			AF465820	CCDS11485.1, CCDS45706.1, CCDS45706.2	17q21.31	2014-02-17	2014-02-17		ENSG00000161692	ENSG00000161692	80174		Zinc fingers, DBF-type	17883	protein-coding gene	gene with protein product	chiffon homolog B (Drosophila), zinc finger, DBF-type containing 1B	611661	DBF4 homolog B (S. cerevisiae)		NA	15668232	Standard	NM_025104	NM_145663	NA	Approved	FLJ13087, DRF1, ASKL1, chifb, ZDBF1B	uc002ihf.3	Q8NFT6	OTTHUMG00000165717	ENST00000315005.3:c.855C>T	chr17.hg19:g.42824475C>T		NA	D3DX56|Q8TEX0|Q96B19|Q9H912	hg19	CCDS11485.1	0.02	11.123509	AAGxCCA	COVERED																																																																																			NOVEL	DBF4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385930.1	5	13.492861	KEEP	0	0	0	45	1507	CC	1	1	0		+	53	60	1892	0	0	157.105922	210	60	7468	402	ENST00000315005.3	0.201521	1
HEXIM1	10614	__UNKNOWN__	__UNKNOWN__	17	43227040	43227040	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:43227040G>A	ENST00000332499.2	+	1	2357	c.483G>A	c.(481-483)aaG>aaA	p.K161K		NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	161	Basic region; mediates nuclear localization and interaction with 7SK snRNA and NR3C1.	NA			heart development (GO:0007507)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			breast(1)|kidney(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						CCAAGAAGAAGCGGCATTGGA	0.552	NA	NA									OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													50	58	55	NA		NA	NA	17		NA											NA				43227040		2203	4300	6503	SO:0001819	synonymous_variant			AB021179	CCDS11495.1	17q21.31	2006-03-28				ENSG00000186834	10614			24953	protein-coding gene	gene with protein product		607328			NA	12119119, 12832472	Standard	NM_006460	NM_006460	NA	Approved	CLP-1, HIS1, MAQ1, EDG1	uc002iig.3	O94992		ENST00000332499.2:c.483G>A	chr17.hg19:g.43227040G>A		914	B2R8Y5	hg19	CCDS11495.1	0.02	19.847921	GAAxCGG	COVERED																																																																																			NOVEL	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449821.2	8	104.418429	KEEP	0	0	0	347	12204	GG	1	1	0		+	104	60	3696	0	0	308.720062	391	60	14565	1019	ENST00000332499.2	0.210101	1
ARL17B	100506084	__UNKNOWN__	__UNKNOWN__	17	44363353	44363353	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:44363353C>T	ENST00000570618.1	-	5	505							Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)			pancreas(1)	1						TGTTGACTGGCACTGTGGACA	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696	100506084		ADP-ribosylation factors-like, ADP-ribosylation factors	32387	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 17	ARL17	NA		Standard	NM_001039083	NM_001039083	NA	Approved			Q8IVW1	OTTHUMG00000178031	ENST00000570618.1:c.376-10569G>A	chr17.hg19:g.44363353C>T		NA	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	hg19	CCDS54137.1	0.02	23.606098	TGGxACT	COVERED																																																																																			NOVEL	ARL17B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440291.1	5	41.532441	KEEP	0	0	0	138	4911	CC	1	1	0		-	30	60	1067	0	0	69.835301	547	60	20715	852	ENST00000570618.1	0.051993	1
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45214564	45214564	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs201184967		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:45214564A>T	ENST00000531206.1	-	14	1888	c.1885T>A	c.(1885-1887)Tgt>Agt	p.C629S	CDC27_ENST00000446365.2_Missense_Mutation_p.C562S|CDC27_ENST00000527547.1_Missense_Mutation_p.C622S|CDC27_ENST00000066544.3_Missense_Mutation_p.C623S			P30260	CDC27_HUMAN	cell division cycle 27	623		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTCGAAAACAAGCTAATGCT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	61	60	NA		NA	NA	17		NA											NA				45214564		2203	4300	6503	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.1885T>A	chr17.hg19:g.45214564A>T	ENSP00000434614:p.Cys629Ser	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	32.027139	AACxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.90	2.968854	0.53614	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.42245	0.1194	L	0.33485	1.01	0.80722	D	1	D;P;P;P	0.55172	0.97;0.698;0.698;0.936	P;B;B;P	0.56751	0.805;0.112;0.112;0.491	T	0.12889	-1.0530	10	0.25751	T	0.34	-10.7595	14.1085	0.65107	1.0:0.0:0.0:0.0	.	562;622;629;623	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	623;629;562;622	ENSP00000066544:C623S;ENSP00000434614:C629S;ENSP00000392802:C562S;ENSP00000437339:C622S	ENSP00000066544:C623S	C	-	1	0	CDC27	42569563	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.529000	0.81952	2.228000	0.72767	0.477000	0.44152	TGT	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	68	34.181056	KEEP	3	3	98	148	4598	AA	1	1	0		-	15	60	550	0	0	43.457448	90	60	3275	1144	ENST00000531206.1	0.142857	1
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45234303	45234303	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs200611688		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:45234303G>C	ENST00000531206.1	-	7	821	c.818C>G	c.(817-819)gCa>gGa	p.A273G	CDC27_ENST00000446365.2_Missense_Mutation_p.A212G|CDC27_ENST00000527547.1_Missense_Mutation_p.A273G|CDC27_ENST00000066544.3_Missense_Mutation_p.A273G			P30260	CDC27_HUMAN	cell division cycle 27	273		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						ACTAAGAGCTGCTGGTCCTCC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													62	66	65	NA		NA	NA	17		NA											NA				45234303		2201	4293	6494	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.818C>G	chr17.hg19:g.45234303G>C	ENSP00000434614:p.Ala273Gly	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	10.219555	GCTxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.95	2.983381	0.53827	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.69175	-0.37;-0.38;-0.11;-0.36;0.76	5.64	5.64	0.86602	.	0.116892	0.56097	D	0.000021	T	0.54647	0.1871	L	0.29908	0.895	0.51233	D	0.999911	B;P;P;B	0.43094	0.304;0.629;0.799;0.304	B;B;B;B	0.36092	0.15;0.213;0.217;0.046	T	0.57911	-0.7729	10	0.40728	T	0.16	-26.4879	17.2083	0.86924	0.0:0.0:1.0:0.0	.	212;273;273;273	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	G	273;273;212;273;273	ENSP00000066544:A273G;ENSP00000434614:A273G;ENSP00000392802:A212G;ENSP00000437339:A273G;ENSP00000432105:A273G	ENSP00000066544:A273G	A	-	2	0	CDC27	42589302	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.260000	0.95568	2.665000	0.90641	0.460000	0.39030	GCA	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	16	19.369931	KEEP	3	3	99	99	3588	GG	1	1	0		-	7	60	254	0	0	17.486558	101	60	3761	497	ENST00000531206.1	0.064815	1
CDK5RAP3	80279	__UNKNOWN__	__UNKNOWN__	17	46048807	46048807	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:46048807G>A	ENST00000338399.4	+	2	158				RP11-6N17.9_ENST00000582262.1_RNA|CDK5RAP3_ENST00000536708.2_Intron	NM_176096.1	NP_788276.1	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	NA		NA			brain development (GO:0007420)|protein ufmylation (GO:0071569)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of neuron differentiation (GO:0045664)	membrane (GO:0016020)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(2)|cervix(3)|endometrium(3)|large_intestine(2)|lung(5)|prostate(1)|skin(1)	18						GCTGGCTGTCGGGGGGAGGCC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													12	13	13	NA		NA	NA	17		NA											NA				46048807		2028	4153	6181	SO:0001627	intron_variant			AF110322	CCDS42356.1, CCDS62232.1	17q21.2	2008-07-18				ENSG00000108465	80279			18673	protein-coding gene	gene with protein product	ischemic heart CDK5 activator-binding protein C53, LXXLL/leucine-zipper-containing ARFbinding protein	608202			NA	10721722	Standard	NM_176096	NM_176096	NA	Approved	MST016, FLJ13660, C53, IC53, HSF-27, OK/SW-cl.114, LZAP	uc010wlc.3	Q96JB5		ENST00000338399.4:c.52+34G>A	chr17.hg19:g.46048807G>A		NA	B7Z6N4|D3DTU1|D3DTU2|F5H3I5|Q53FA2|Q9H3F8|Q9H8G0|Q9HBR9	hg19	CCDS42356.1	0.02	12.160561	GTCxGGG	COVERED																																																																																			NOVEL	CDK5RAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442913.1	4	61.984835	KEEP	0	0	0	206	6983	GG	1	1	0		+	31	60	1171	0	0	90.42744	233	60	7939	640	ENST00000338399.4	0.117424	1
COL1A1	1277	__UNKNOWN__	__UNKNOWN__	17	48275214	48275214	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:48275214G>T	ENST00000225964.5	-	9	761					NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	NA		NA			blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	TGGGATTGAAGGGAAGAGGTA	0.483	NA	NA	T	PDGFB, USP6	dermatofibrosarcoma protuberans, aneurysmal bone cyst 		Osteogenesis imperfecta							NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		17	17q21.31-q22	1277	collagen, type I, alpha 1	yes	M	0													62	59	60	NA		NA	NA	17		NA											NA				48275214		692	1591	2283	SO:0001627	intron_variant			Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821	1277		Collagens	2197	protein-coding gene	gene with protein product		120150			NA	3178743, 2857713	Standard		NM_000088	NA	Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.643-68C>A	chr17.hg19:g.48275214G>T		NA	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	hg19	CCDS11561.1	0.02	4.680443	GAAxGGA	COVERED																																																																																			NOVEL	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309036.2	1	16.249471	KEEP	0	0	0	54	1911	GG	1	0.999973	0		-	9	60	335	1	0	25.424273	74	70	2699	197	ENST00000225964.5	0.108434	0.999973
LRRC59	55379	__UNKNOWN__	__UNKNOWN__	17	48462704	48462704	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:48462704G>A	ENST00000225972.7	-	6	738					NM_018509.3	NP_060979.2	Q96AG4	LRC59_HUMAN	leucine rich repeat containing 59	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CACTCCAGCAGTTTGCTTTCC	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													21	19	20	NA		NA	NA	17		NA											NA				48462704		1327	2308	3635	SO:0001627	intron_variant			AK025328	CCDS11566.1	17q21.33	2014-02-12	2006-01-12		ENSG00000108829	ENSG00000108829	55379			28817	protein-coding gene	gene with protein product		614854			NA	12477932	Standard	NM_018509	NM_018509	NA	Approved	PRO1855, FLJ21675	uc002iqt.3	Q96AG4	OTTHUMG00000162079	ENST00000225972.7:c.503-52C>T	chr17.hg19:g.48462704G>A		NA	B2RE83|D3DTX8|Q9P189	hg19	CCDS11566.1	0.02	6.713438	GCAxTTT	COVERED																																																																																			NOVEL	LRRC59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367117.2	4	15.94421	KEEP	0	0	0	53	1876	GG	1	1	0		-	45	60	1608	0	0	137.33832	143	60	5496	298	ENST00000225972.7	0.239362	1
SPAG9	9043	__UNKNOWN__	__UNKNOWN__	17	49064459	49064459	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:49064459G>A	ENST00000357122.4	-	21	3106				SPAG9_ENST00000505279.1_Intron|SPAG9_ENST00000262013.7_Intron|SPAG9_ENST00000510283.1_Intron	NM_003971.5	NP_003962.3	O60271	JIP4_HUMAN	sperm associated antigen 9	NA		NA			activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			AATGTTAAAAGCATTGACACC	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													115	103	107	NA		NA	NA	17		NA											NA				49064459		2203	4300	6503	SO:0001627	intron_variant			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294	9043			14524	protein-coding gene	gene with protein product	sperm surface protein, JNK/SAPK-associated protein, JNK interacting protein, sperm specific protein, c-Jun NH2-terminal kinase-associated leucine zipper protein, Max-binding protein, JNK-associated leucine-zipper protein, HLC-4 protein, lung cancer oncogene 4, proliferation-inducing gene 6, cancer/testis antigen 89	605430			NA	9480848, 11106729	Standard	NM_003971	NM_003971	NA	Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000357122.4:c.2897+13C>T	chr17.hg19:g.49064459G>A		NA	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	hg19	CCDS11577.1	0.02	12.15727	AAAxCAT	COVERED																																																																																			NOVEL	SPAG9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368544.1	2	24.070839	KEEP	0	0	0	80	2827	GG	1	1	0		-	11	60	403	0	0	24.486079	328	60	12236	526	ENST00000357122.4	0.032448	1
BCAS3	54828	__UNKNOWN__	__UNKNOWN__	17	58952118	58952118	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:58952118T>C	ENST00000390652.5	+	9	692				BCAS3_ENST00000408905.3_Intron|BCAS3_ENST00000588462.1_Intron|BCAS3_ENST00000589222.1_Intron|BCAS3_ENST00000407086.3_Intron	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3	NA		NA								NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			CAATTTTTTTTCCCTTCTTAT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													84	79	81	NA		NA	NA	17		NA											NA				58952118		1833	4081	5914	SO:0001627	intron_variant			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376	54828		WD repeat domain containing	14347	protein-coding gene	gene with protein product		607470			NA	12378525	Standard	NM_017679	NM_017679	NA	Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.661+19T>C	chr17.hg19:g.58952118T>C		NA		hg19	CCDS45749.1	0.02	1.812823	TTTxCCC	COVERED																																																																																			NOVEL	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449578.1	2	4.51358	KEEP	0	0	0	15	488	TT	0.99649	0.995362	0		+	7	60	224	0	0	15.586082	70	60	2567	116	ENST00000390652.5	0.090909	0.998867
TBX2	6909	__UNKNOWN__	__UNKNOWN__	17	59482155	59482155	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:59482155C>T	ENST00000240328.3	+	5	1332				RP11-332H18.4_ENST00000592009.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	NA		NA			aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						GGAGGAGGGACAGGGAGGTGG	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(3;187 253 11467 14965 23079)					NA		NA				0													2	3	3	NA		NA	NA	17		NA											NA				59482155		1551	3391	4942	SO:0001627	intron_variant			AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068	6909		T-boxes	11597	protein-coding gene	gene with protein product		600747			NA	8530034	Standard	NM_005994	NM_005994	NA	Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.1051+25C>T	chr17.hg19:g.59482155C>T		NA	Q16424|Q7Z647	hg19	CCDS11627.2	0.02	3.614336	GGAxAGG	COVERED																																																																																			NOVEL	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346977.2	1	15.302751	KEEP	0	0	0	51	1673	CC	1	1	0		+	6	70	201	0	0	12.529418	119	70	3988	209	ENST00000240328.3	0.048	1
RP11-51L5.5	0	__UNKNOWN__	__UNKNOWN__	17	60374316	60374316	__UNKNOWN__	RNA	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:60374316C>T	ENST00000602493.1	-	0	71										NA		NA									NA						TGGCAGGCTGCTGTCTCAGGA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000602493.1:	chr17.hg19:g.60374316C>T		NA		hg19		0.02	11.256166	CTGxTGT	COVERED																																																																																			NOVEL	RP11-51L5.5-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000467668.1	2	11.730979	KEEP	1	0	0	39	1397	CC	1	1	0		-	65	49	2314	0	0	196.193838	218	50	8195	425	ENST00000602493.1	0.229682	1
SCN4A	6329	__UNKNOWN__	__UNKNOWN__	17	62020279	62020279	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:62020279C>G	ENST00000578147.1	-	23	4271	c.4195G>C	c.(4195-4197)Gag>Cag	p.E1399Q	SCN4A_ENST00000435607.1_Missense_Mutation_p.E1399Q			P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1399		NA			membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGCACGCACTCCCCTGTGAAG	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													205	194	198	NA		NA	NA	17		NA											NA				62020279		2203	4300	6503	SO:0001583	missense			U24693		17q23.3	2012-02-26	2007-01-23				6329		Sodium channels, Voltage-gated ion channels / Sodium channels	10591	protein-coding gene	gene with protein product		603967		HYKPP	NA	1654742, 1659948, 16382098	Standard	NM_000334	XM_005257566	NA	Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000578147.1:c.4195G>C	chr17.hg19:g.62020279C>G	ENSP00000463963:p.Glu1399Gln	NA	Q15478|Q16447|Q7Z6B1	hg19		0.02	17.616295	ACTxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	23.7	4.451990	0.84209	.	.	ENSG00000007314	ENST00000435607	D	0.98807	-5.15	3.87	3.87	0.44632	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99569	0.9845	H	0.99675	4.695	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97240	0.9890	10	0.87932	D	0	.	15.3689	0.74548	0.0:1.0:0.0:0.0	.	1399	P35499	SCN4A_HUMAN	Q	1399	ENSP00000396320:E1399Q	ENSP00000396320:E1399Q	E	-	1	0	SCN4A	59374011	1.000000	0.71417	0.998000	0.56505	0.905000	0.53344	7.609000	0.82925	2.165000	0.68154	0.462000	0.41574	GAG	NOVEL	SCN4A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000444562.1	2	16.853979	KEEP	0	0	0	56	1939	CC	1	1	0		-	73	60	2665	0	0	223.223452	280	60	10072	515	ENST00000578147.1	0.206799	1
ERN1	2081	__UNKNOWN__	__UNKNOWN__	17	62144100	62144100	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:62144100C>A	ENST00000433197.3	-	8	868	c.773G>T	c.(772-774)gGg>gTg	p.G258V		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1	NA		NA								central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						CCCCACCTCCCCAGACATGAA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													54	58	56	NA		NA	NA	17		NA											NA				62144100		2096	4221	6317	SO:0001583	missense			AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607	2081			3449	protein-coding gene	gene with protein product	inositol-requiring enzyme 1	604033	ER to nucleus signalling 1		NA	9637683	Standard	NM_001433	NM_001433	NA	Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.773G>T	chr17.hg19:g.62144100C>A	ENSP00000401445:p.Gly258Val	NA		hg19	CCDS45762.1	0.02	12.183702	TCCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	23.0	4.360495	0.82353	.	.	ENSG00000178607	ENST00000433197	T	0.19806	2.12	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.45558	0.1348	M	0.79258	2.445	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	T	0.38415	-0.9662	10	0.52906	T	0.07	-31.2759	12.8347	0.57767	0.0:0.9255:0.0:0.0745	.	258	O75460	ERN1_HUMAN	V	258	ENSP00000401445:G258V	ENSP00000401445:G258V	G	-	2	0	ERN1	59497832	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.704000	0.54815	2.619000	0.88677	0.561000	0.74099	GGG	NOVEL	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000443734.2	5	25.255564	KEEP	0	0	0	84	2845	CC	1	1	0		-	55	60	2008	0	0	169.213206	201	60	7165	416	ENST00000433197.3	0.214844	1
CEP95	90799	__UNKNOWN__	__UNKNOWN__	17	62530857	62530857	__UNKNOWN__	Splice_Site	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:62530857T>C	ENST00000556440.2	+	17	2580		c.e17+2		CEP95_ENST00000553412.1_Splice_Site	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	NA		NA				centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						GAAGAAATGGTAAGTCTGACT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													71	71	71	NA		NA	NA	17		NA											NA				62530857		1872	4093	5965	SO:0001630	splice_region_variant			AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890	90799			25141	protein-coding gene	gene with protein product		NA	coiled-coil domain containing 45	CCDC45	NA	21399614	Standard	NM_138363	NM_138363	NA	Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2070+2T>C	chr17.hg19:g.62530857T>C		NA	B4DMD2|Q96M81	hg19	CCDS45763.1	0.02	17.762258	TGGxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	16.54	3.151331	0.57151	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0416	0.80687	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP95	59961319	1.000000	0.71417	0.979000	0.43373	0.543000	0.35085	6.706000	0.74649	2.235000	0.73313	0.533000	0.62120	.	NOVEL	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000445100.2	4	26.460767	KEEP	0	0	0	88	2632	TT	1	1	0	Intron	+	78	60	2945	0	0	250.223337	280	60	9865	557	ENST00000556440.2	0.217877	1
hsa-mir-6080	0	__UNKNOWN__	__UNKNOWN__	17	62776956	62776956	__UNKNOWN__	RNA	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:62776956C>T	ENST00000400873.3	-	0	523					NR_026899.1					NA		NA									NA						CATTGGCACCCTGAATCACCC	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000400873.3:	chr17.hg19:g.62776956C>T		NA		hg19		0.02	19.677149	ACCxTGA	COVERED																																																																																			NOVEL	hsa-mir-6080.1-201	KNOWN	basic	processed_transcript	NA	processed_transcript		3	49.944191	KEEP	0	0	0	166	5791	CC	1	1	0		-	86	60	3166	0	0	265.892901	327	60	11943	784	ENST00000400873.3	0.208232	1
CACNG1	786	__UNKNOWN__	__UNKNOWN__	17	65051225	65051225	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:65051225G>T	ENST00000226021.3	+	3	382	c.311G>T	c.(310-312)aGc>aTc	p.S104I		NM_000727.3	NP_000718.1	Q06432	CCG1_HUMAN	calcium channel, voltage-dependent, gamma subunit 1	104		NA			muscle contraction (GO:0006936)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transport (GO:0006810)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	8	all_cancers(12;1.04e-10)|Breast(2;1.45e-16)|all_epithelial(3;4.81e-12)				Diltiazem(DB00343)|Fluspirilene(DB04842)|Ibutilide(DB00308)|Lercanidipine(DB00528)|Magnesium Sulfate(DB00653)|Nitrendipine(DB01054)|Spironolactone(DB00421)	GCAGAGTACAGCATCTCGGCA	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													142	116	125	NA		NA	NA	17		NA											NA				65051225		2203	4300	6503	SO:0001583	missense			L07738	CCDS11668.1	17q24	2008-05-02				ENSG00000108878	786		Calcium channel subunits	1405	protein-coding gene	gene with protein product		114209		CACNLG	NA	8395940	Standard		NM_000727	NA	Approved		uc002jfu.3	Q06432		ENST00000226021.3:c.311G>T	chr17.hg19:g.65051225G>T	ENSP00000226021:p.Ser104Ile	NA	B2R9N3|Q14D59	hg19	CCDS11668.1	0.02	8.859796	ACAxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.9	4.214128	0.79352	.	.	ENSG00000108878	ENST00000226021	T	0.68181	-0.31	4.59	4.59	0.56863	.	0.118844	0.64402	D	0.000018	T	0.79730	0.4496	M	0.76838	2.35	0.48135	D	0.999599	D	0.55385	0.971	P	0.58780	0.845	T	0.82080	-0.0634	10	0.51188	T	0.08	.	17.8192	0.88645	0.0:0.0:1.0:0.0	.	104	Q06432	CCG1_HUMAN	I	104	ENSP00000226021:S104I	ENSP00000226021:S104I	S	+	2	0	CACNG1	62481687	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.550000	0.82173	2.285000	0.76669	0.456000	0.33151	AGC	NOVEL	CACNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447039.1	2	10.534403	KEEP	0	0	0	35	1254	GG	0.999999	0.999999	0		+	19	60	667	0	0	47.51301	207	60	7730	330	ENST00000226021.3	0.084071	1
AMZ2	51321	__UNKNOWN__	__UNKNOWN__	17	66246420	66246420	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:66246420C>A	ENST00000359904.3	+	2	1224	c.92C>A	c.(91-93)gCt>gAt	p.A31D	AMZ2_ENST00000577985.1_Missense_Mutation_p.A31D|AMZ2_ENST00000359783.4_Missense_Mutation_p.A31D|AMZ2_ENST00000580753.1_Missense_Mutation_p.A31D|AMZ2_ENST00000392720.2_Missense_Mutation_p.A31D|AMZ2_ENST00000577866.1_Missense_Mutation_p.A31D|AMZ2_ENST00000585050.1_Intron|AMZ2_ENST00000577273.1_Missense_Mutation_p.A31D	NM_016627.4	NP_057711.3	Q86W34	AMZ2_HUMAN	archaelysin family metallopeptidase 2	31		NA					metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	all_cancers(12;1.12e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)			AAATTAAATGCTGGGGAACAA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													119	115	116	NA		NA	NA	17		NA											NA				66246420		2203	4300	6503	SO:0001583	missense			CR609550	CCDS11674.1, CCDS32714.1	17q24.2	2010-04-08			ENSG00000196704	ENSG00000196704	51321			28041	protein-coding gene	gene with protein product	archaemetzincin-2	615169			NA	15972818	Standard	NM_016627	XM_005257436	NA	Approved		uc002jgr.1	Q86W34		ENST00000359904.3:c.92C>A	chr17.hg19:g.66246420C>A	ENSP00000352976:p.Ala31Asp	NA	A6NLD9|B3KR44|Q5XKF1|Q9NZE2	hg19	CCDS11674.1	0.02	4.60141	ATGxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	6.477	0.456092	0.12283	.	.	ENSG00000196704	ENST00000359904;ENST00000359783;ENST00000392720	T;T;T	0.32988	1.43;2.18;1.43	3.58	3.58	0.41010	.	0.366500	0.22614	N	0.057793	T	0.29684	0.0741	L	0.54323	1.7	0.09310	N	1	P;P	0.49961	0.791;0.93	B;B	0.42319	0.198;0.383	T	0.17715	-1.0360	10	0.33940	T	0.23	-21.0433	13.1124	0.59281	0.0:1.0:0.0:0.0	.	31;31	A6NLD9;Q86W34	.;AMZ2_HUMAN	D	31	ENSP00000352976:A31D;ENSP00000352831:A31D;ENSP00000376481:A31D	ENSP00000352831:A31D	A	+	2	0	AMZ2	63758015	0.000000	0.05858	0.036000	0.18154	0.783000	0.44284	0.724000	0.25954	1.991000	0.58162	0.306000	0.20318	GCT	NOVEL	AMZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000448261.1	3	6.922396	KEEP	0	0	0	23	816	CC	0.999892	0.999887	0		+	23	60	826	0	0	68.979543	88	60	3315	153	ENST00000359904.3	0.207207	0.999995
CASKIN2	57513	__UNKNOWN__	__UNKNOWN__	17	73503041	73503041	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:73503041G>A	ENST00000321617.3	-	5	977				CASKIN2_ENST00000581870.1_Intron|CASKIN2_ENST00000433559.2_Intron	NM_020753.3	NP_065804.2	Q8WXE0	CSKI2_HUMAN	CASK interacting protein 2	NA		NA				cytoplasm (GO:0005737)				endometrium(1)|kidney(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCTGCGCCACGCCCCTGTGGG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													50	49	49	NA		NA	NA	17		NA											NA				73503041		2203	4298	6501	SO:0001627	intron_variant			AB032965	CCDS11723.1, CCDS45775.1	17q25.1	2014-09-04			ENSG00000177303	ENSG00000177303	57513		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	18200	protein-coding gene	gene with protein product		612185			NA	12040031	Standard	NM_020753	NM_020753	NA	Approved	KIAA1139, FLJ21609, ANKS5B	uc002joc.4	Q8WXE0	OTTHUMG00000179683	ENST00000321617.3:c.390+23C>T	chr17.hg19:g.73503041G>A		NA	B4DTT3|B7Z9H1|Q7LG69|Q9ULT1	hg19	CCDS11723.1	0.02	18.237053	CACxCCC	COVERED																																																																																			NOVEL	CASKIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447609.1	8	47.803431	KEEP	0	0	0	159	5446	GG	1	1	0		-	86	60	2829	0	0	231.72044	332	60	11522	770	ENST00000321617.3	0.205742	1
MYO15B	80022	__UNKNOWN__	__UNKNOWN__	17	73610987	73610987	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:73610987C>T	ENST00000578382.2	+	31	5308					NR_003587.2		Q96JP2	MY15B_HUMAN	myosin XVB pseudogene	NA		NA				cytoplasm (GO:0005737)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)				NA						GCCTCTGCTGCCCCTTCCATT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					17q25.1	2014-07-16			ENSG00000266714	ENSG00000266714	80022		Myosins / Myosin superfamily : Class XV	14083	pseudogene	pseudogene		NA			NA	11294886	Standard	NR_003587	NR_003587	NA	Approved	MYO15BP	uc002jon.1	Q96JP2	OTTHUMG00000179794	ENST00000578382.2:c.5309-55C>T	chr17.hg19:g.73610987C>T		NA		hg19		0.02	6.668536	CTGxCCC	COVERED																																																																																			NOVEL	MYO15B-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000448172.2	6	15.646944	KEEP	0	0	0	52	1731	CC	1	1	0		+	15	60	554	0	0	40.984863	144	60	5119	256	ENST00000578382.2	0.09434	1
MYO15B	80022	__UNKNOWN__	__UNKNOWN__	17	73620968	73620968	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:73620968C>T	ENST00000578382.2	+	0	8333					NR_003587.2		Q96JP2	MY15B_HUMAN	myosin XVB pseudogene	NA		NA				cytoplasm (GO:0005737)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)				NA						TTCGATAACTCCACCTACATC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					17q25.1	2014-07-16			ENSG00000266714	ENSG00000266714	80022		Myosins / Myosin superfamily : Class XV	14083	pseudogene	pseudogene		NA			NA	11294886	Standard	NR_003587	NR_003587	NA	Approved	MYO15BP	uc002jon.1	Q96JP2	OTTHUMG00000179794	ENST00000578382.2:c.*8330C>T	chr17.hg19:g.73620968C>T		NA		hg19		0.02	11.222755	ACTxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.28	3.077652	0.55753	.	.	ENSG00000188126	ENST00000293201	T	0.72505	-0.66	4.91	2.78	0.32641	.	.	.	.	.	T	0.64659	0.2618	.	.	.	0.09310	N	1	P;P	0.46656	0.786;0.882	B;P	0.45343	0.254;0.477	T	0.56780	-0.7922	8	0.62326	D	0.03	-2.851	6.1399	0.20253	0.3414:0.5614:0.0:0.0972	.	278;252	Q9H614;Q8TCJ6	.;.	F	278	ENSP00000293201:S278F	ENSP00000293201:S278F	S	+	2	0	MYO15B	71132563	0.015000	0.18098	0.030000	0.17652	0.130000	0.20726	2.693000	0.47027	1.302000	0.44855	0.561000	0.74099	TCC	NOVEL	MYO15B-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000448172.2	3	21.367739	KEEP	0	0	0	71	2425	CC	1	1	0		+	25	60	821	0	0	58.152162	239	60	8653	434	ENST00000578382.2	0.094697	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74559687	74559687	__UNKNOWN__	IGR	SNP	C	C	G	rs201470689		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:74559687C>G			NA	NA				SNHG16 (1900 upstream) : ST6GALNAC2 (1773 downstream)						NA		NA									NA						CCGCAGAGTGCCTTCCAGGAA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74559687C>G		NA		hg19		0.02	22.169697	GTGxCTT	COVERED																																																																																			NOVEL					0			8	9.200452	KEEP	5	9	292	133	4591	CC	1	1	0			29	42	1003	0	0	65.738287	485	60	17730	729		0.05642	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74559818	74559818	__UNKNOWN__	IGR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:74559818A>T			NA	NA				SNHG16 (2031 upstream) : ST6GALNAC2 (1642 downstream)						NA		NA									NA						ttttttttttaacattttata	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74559818A>T		NA		hg19		0.02	11.262094	TTTxACA	COVERED																																																																																			NOVEL					0			10	15.002055	KEEP	1	8	245	136	3981	AA	1	1	0			13	60	443	2	0	26.64044	323	70	11375	586		0.03869	1
TNRC6C	57690	__UNKNOWN__	__UNKNOWN__	17	76099513	76099513	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:76099513C>T	ENST00000588847.1	+	22	5426	c.4699C>T	c.(4699-4701)Cgg>Tgg	p.R1567W	TNRC6C_ENST00000588061.1_Missense_Mutation_p.R1531W|TNRC6C_ENST00000335749.4_Missense_Mutation_p.R1567W|TNRC6C_ENST00000541771.1_Missense_Mutation_p.R1531W|TNRC6C_ENST00000301624.4_Missense_Mutation_p.R1531W|TNRC6C_ENST00000544502.1_Missense_Mutation_p.R1567W			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	1531	RRM.|Silencing domain; interaction with CNOT1 and PAN3.|Sufficient for translational repression when tethered to a target mRNA.	NA			embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			TTCTACACTGCGGACATTGTG	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													91	88	89	NA		NA	NA	17		NA											NA				76099513		1962	4160	6122	SO:0001583	missense			AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687	57690		Trinucleotide (CAG) repeat containing	29318	protein-coding gene	gene with protein product		610741			NA		Standard	NM_018996	NM_018996	NA	Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588847.1:c.4699C>T	chr17.hg19:g.76099513C>T	ENSP00000467154:p.Arg1567Trp	NA	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	hg19	CCDS45799.1	0.02	12.200269	CTGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856920	0.71834	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	4.34	1.94	0.25998	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.66346	0.2780	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.71748	-0.4499	10	0.87932	D	0	-16.9324	13.7816	0.63085	0.2913:0.7087:0.0:0.0	.	1567;1531	G3XAB8;Q9HCJ0	.;TNR6C_HUMAN	W	1531;1567;1567;1531;1531;1567	ENSP00000336783:R1567W;ENSP00000301624:R1531W;ENSP00000440310:R1531W;ENSP00000442421:R1567W	ENSP00000301624:R1531W	R	+	1	2	TNRC6C	73611108	1.000000	0.71417	0.980000	0.43619	0.988000	0.76386	3.919000	0.56439	0.757000	0.33036	0.561000	0.74099	CGG	NOVEL	TNRC6C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255891.4	1	12.939356	KEEP	0	0	0	43	1443	CC	1	1	0		+	42	60	1488	0	0	119.305308	213	60	7666	373	ENST00000588847.1	0.164706	1
TK1	7083	__UNKNOWN__	__UNKNOWN__	17	76170610	76170610	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:76170610C>T	ENST00000301634.7	-	0	1173				TK1_ENST00000405273.1_Intron|TK1_ENST00000588734.1_3'UTR	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble	NA		NA			deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	CAGCTCCAGCCTGGGCGATCG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	7083	2.7.1.21		11830	protein-coding gene	gene with protein product		188300			NA		Standard	NM_003258	NM_003258	NA	Approved		uc002juw.2	P04183	OTTHUMG00000150674	ENST00000301634.7:c.*230G>A	chr17.hg19:g.76170610C>T		NA	B2RC58|Q969V0|Q9UMG9	hg19	CCDS11754.1	0.02	6.944092	AGCxTGG	COVERED																																																																																			NOVEL	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319577.1	4	16.25142	KEEP	0	0	0	54	1893	CC	1	1	0		-	15	60	506	0	0	34.827072	181	60	6535	313	ENST00000301634.7	0.076531	1
DNAH17	8632	__UNKNOWN__	__UNKNOWN__	17	76440788	76440788	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:76440788G>T	ENST00000585328.1	-	71	11535	c.11411C>A	c.(11410-11412)cCc>cAc	p.P3804H	DNAH17_ENST00000389840.5_Missense_Mutation_p.P3795H|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3795		NA			cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CTCCTTCTCGGGGGCTTCCGA	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													74	54	61	NA		NA	NA	17		NA											NA				76440788		2203	4300	6503	SO:0001583	missense			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775	8632		Axonemal dyneins	2946	protein-coding gene	gene with protein product		610063	dynein, axonemal, heavy polypeptide 17, dynein, axonemal, heavy chain like 1, dynein, axonemal, heavy like 1	DNAHL1	NA	9545504	Standard	NM_173628	NM_173628	NA	Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.11411C>A	chr17.hg19:g.76440788G>T	ENSP00000465516:p.Pro3804His	NA	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	hg19		0.02	28.265773	TCGxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	24.8	4.566535	0.86439	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.15139	2.45	4.99	4.99	0.66335	.	0.910489	0.09408	N	0.806164	T	0.68696	0.3029	H	0.99820	4.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.79176	-0.1911	10	0.87932	D	0	.	18.2779	0.90089	0.0:0.0:1.0:0.0	.	3804	E7EUM8	.	H	3804;3795	ENSP00000374490:P3795H	ENSP00000300671:P3804H	P	-	2	0	DNAH17	73952383	1.000000	0.71417	0.863000	0.33907	0.910000	0.53928	9.591000	0.98241	2.309000	0.77851	0.561000	0.74099	CCC	NOVEL	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000318962.2	3	30.681454	KEEP	0	0	0	102	3493	GG	1	1	0		-	96	60	3438	0	0	274.019804	518	60	18280	895	ENST00000585328.1	0.156352	1
DNAH17	8632	__UNKNOWN__	__UNKNOWN__	17	76446417	76446417	__UNKNOWN__	Silent	SNP	C	C	T	rs185361296		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:76446417C>T	ENST00000585328.1	-	68	11068	c.10944G>A	c.(10942-10944)ccG>ccA	p.P3648P	DNAH17_ENST00000389840.5_Silent_p.P3639P|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3639		NA			cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TCTCCGCAGCCGGGCGGTAGT	0.522	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	21493	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								C		1,4405	2.1+/-5.4	0,1,2202	127	103	111	NA	10959	-9.5	0	17		111	0,8600		0,0,4300	no	coding-synonymous	DNAH17	NM_173628.3		0,1,6502	TT,TC,CC	NA	0.0,0.0227,0.0077		3653/4463	76446417	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775	8632		Axonemal dyneins	2946	protein-coding gene	gene with protein product		610063	dynein, axonemal, heavy polypeptide 17, dynein, axonemal, heavy chain like 1, dynein, axonemal, heavy like 1	DNAHL1	NA	9545504	Standard	NM_173628	NM_173628	NA	Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.10944G>A	chr17.hg19:g.76446417C>T		NA	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	hg19		0.02	9.637592	AGCxGGG	COVERED																																																																																			NOVEL	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000318962.2	2	6.620958	KEEP	0	0	0	22	744	CC	0.999879	0.999879	0		-	11	60	414	0	0	27.732939	207	60	7197	305	ENST00000585328.1	0.050459	1
ENGASE	64772	__UNKNOWN__	__UNKNOWN__	17	77079583	77079583	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs200896035	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:77079583C>T	ENST00000579016.1	+	9	1162	c.1162C>T	c.(1162-1164)Cgt>Tgt	p.R388C	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	388		NA				cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						CCGACTGGAGCGTTATCTGCC	0.612	NA	NA											C|||	2	0.000399361	0	0	5008	,	,	NA	20560	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0								C	CYS/ARG	1,4259		0,1,2129	103	112	109	NA	1162	3.4	0.1	17		109	1,8471		0,1,4235	no	missense	ENGASE	NM_001042573.1	180	0,2,6364	TT,TC,CC	NA	0.0118,0.0235,0.0157	probably-damaging	388/744	77079583	2,12730	2130	4236	6366	SO:0001583	missense			AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	64772	3.2.1.96		24622	protein-coding gene	gene with protein product	Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase, Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase	611898			NA	12114544, 18586680	Standard	NM_022759	NM_001042573	NA	Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1162C>T	chr17.hg19:g.77079583C>T	ENSP00000462333:p.Arg388Cys	NA	Q659F0|Q8TB86|Q9H6U4	hg19	CCDS42394.1	0.02	25.639033	GAGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.00	2.106980	0.37145	2.35E-4	1.18E-4	ENSG00000167280	ENST00000545583	.	.	.	5.47	3.38	0.38709	Glycoside hydrolase, family 85 (1);	0.541931	0.21223	N	0.078113	T	0.56717	0.2004	M	0.71581	2.175	0.09310	N	0.999993	D	0.76494	0.999	D	0.63703	0.917	T	0.45775	-0.9238	9	0.54805	T	0.06	-17.9742	8.8697	0.35309	0.3457:0.4862:0.1681:0.0	.	388	Q8NFI3	ENASE_HUMAN	C	388	.	ENSP00000438577:R388C	R	+	1	0	ENGASE	74591178	0.001000	0.12720	0.083000	0.20561	0.112000	0.19704	0.813000	0.27225	1.279000	0.44446	0.561000	0.74099	CGT	NOVEL	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395807.1	4	38.822863	KEEP	0	0	0	129	4401	CC	1	1	0		+	22	60	760	0	0	45.34231	595	60	20725	985	ENST00000579016.1	0.035656	1
ENGASE	64772	__UNKNOWN__	__UNKNOWN__	17	77082064	77082064	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:77082064T>C	ENST00000579016.1	+	14	1865	c.1865T>C	c.(1864-1866)gTc>gCc	p.V622A		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	622		NA				cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						GTGCAGGCCGTCACCATCTCT	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													25	30	29	NA		NA	NA	17		NA											NA				77082064		2099	4219	6318	SO:0001583	missense			AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	64772	3.2.1.96		24622	protein-coding gene	gene with protein product	Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase, Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase	611898			NA	12114544, 18586680	Standard	NM_022759	NM_001042573	NA	Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1865T>C	chr17.hg19:g.77082064T>C	ENSP00000462333:p.Val622Ala	NA	Q659F0|Q8TB86|Q9H6U4	hg19	CCDS42394.1	0.02	7.16037	CCGxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.986	1.229359	0.22542	.	.	ENSG00000167280	ENST00000545583	.	.	.	4.5	3.43	0.39272	.	0.329212	0.27891	N	0.017435	T	0.48390	0.1497	M	0.63428	1.95	0.42183	D	0.991693	B	0.34015	0.435	B	0.27262	0.078	T	0.43475	-0.9389	9	0.37606	T	0.19	-15.7921	8.5729	0.33581	0.0:0.0883:0.0:0.9117	.	622	Q8NFI3	ENASE_HUMAN	A	622	.	ENSP00000438577:V622A	V	+	2	0	ENGASE	74593659	0.506000	0.26139	0.029000	0.17559	0.009000	0.06853	4.277000	0.58939	0.757000	0.33036	0.383000	0.25322	GTC	NOVEL	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395807.1	1	12.634968	KEEP	0	0	0	42	1260	TT	1	1	0		+	28	60	1037	0	0	82.28992	166	60	5700	278	ENST00000579016.1	0.14433	1
SGSH	6448	__UNKNOWN__	__UNKNOWN__	17	78185908	78185908	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:78185908C>G	ENST00000326317.6	-	7	997	c.911G>C	c.(910-912)cGc>cCc	p.R304P	SGSH_ENST00000570923.1_3'UTR|SGSH_ENST00000534910.1_Missense_Mutation_p.R101P	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	304		NA	R -> L. {ECO:0000269|PubMed:17128482}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|metal ion binding (GO:0046872)|N-sulfoglucosamine sulfohydrolase activity (GO:0016250)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TTGGCCCCAGCGTTTTGGGTG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	62	66	NA		NA	NA	17		NA											NA				78185908		2203	4300	6503	SO:0001583	missense			BC047318	CCDS11770.1	17q25.3	2011-11-08	2008-07-31			ENSG00000181523	6448	3.10.1.1		10818	protein-coding gene	gene with protein product	sulfamidase, mucopolysaccharidosis type IIIA	605270			NA	7493035	Standard	NM_000199	NM_000199	NA	Approved	HSS, MPS3A, SFMD	uc002jxz.4	P51688		ENST00000326317.6:c.911G>C	chr17.hg19:g.78185908C>G	ENSP00000314606:p.Arg304Pro	NA	A8K5E2	hg19	CCDS11770.1	0.02	16.921773	CAGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.5	4.293290	0.80914	.	.	ENSG00000181523	ENST00000326317;ENST00000534910	D;D	0.98280	-4.84;-4.84	4.62	4.62	0.57501	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.97932	0.9320	L	0.38838	1.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97326	0.9947	10	0.20519	T	0.43	-40.3214	17.0355	0.86474	0.0:1.0:0.0:0.0	.	304	P51688	SPHM_HUMAN	P	304;101	ENSP00000314606:R304P;ENSP00000437778:R101P	ENSP00000314606:R304P	R	-	2	0	SGSH	75800503	1.000000	0.71417	0.991000	0.47740	0.590000	0.36582	7.594000	0.82698	2.115000	0.64714	0.557000	0.71058	CGC	NOVEL	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000437695.1	1	25.877622	KEEP	0	0	0	86	2942	CC	1	1	0		-	27	60	916	0	0	61.158936	393	60	13990	653	ENST00000326317.6	0.064286	1
NPTX1	4884	__UNKNOWN__	__UNKNOWN__	17	78449374	78449374	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:78449374C>A	ENST00000306773.4	-	2	746	c.589G>T	c.(589-591)Gag>Tag	p.E197*	NPTX1_ENST00000575212.1_5'UTR	NM_002522.3	NP_002513.2	Q15818	NPTX1_HUMAN	neuronal pentraxin I	197		NA			axonogenesis involved in innervation (GO:0060385)|cellular response to glucose stimulus (GO:0071333)|cellular response to potassium ion (GO:0035865)|central nervous system development (GO:0007417)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial transport (GO:0006839)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)	11	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0487)			TTGACCCTCTCCTCGGTGTCG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													53	40	45	NA		NA	NA	17		NA											NA				78449374		2202	4299	6501	SO:0001587	stop_gained			U61849	CCDS32762.1	17q25.3	2008-05-14				ENSG00000171246	4884			7952	protein-coding gene	gene with protein product		602367			NA	8884281	Standard		NM_002522	NA	Approved		uc002jyp.1	Q15818		ENST00000306773.4:c.589G>T	chr17.hg19:g.78449374C>A	ENSP00000307549:p.Glu197*	NA	B3KXH3|Q5FWE6	hg19	CCDS32762.1	0.02	5.786376	TCTxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	38	6.707614	0.97780	.	.	ENSG00000171246	ENST00000306773	.	.	.	3.6	3.6	0.41247	.	0.062223	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	-19.3081	10.7066	0.45958	0.0:0.8048:0.1952:0.0	.	.	.	.	X	197	.	ENSP00000307549:E197X	E	-	1	0	NPTX1	76063969	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.884000	0.56175	2.010000	0.58986	0.561000	0.74099	GAG	NOVEL	NPTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438051.1	2	17.757151	KEEP	0	0	0	59	2037	CC	1	1	0		-	7	60	234	0	0	13.999484	171	60	6383	317	ENST00000306773.4	0.039326	1
FSCN2	25794	__UNKNOWN__	__UNKNOWN__	17	79503900	79503900	__UNKNOWN__	Splice_Site	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:79503900G>A	ENST00000417245.2	+	5	1409		c.e5-1		FSCN2_ENST00000334850.7_Splice_Site	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	NA		NA			actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			CCGTCCCCCAGGCCGCGACGG	0.761	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													6	7	7	NA		NA	NA	17		NA											NA				79503900		1699	3791	5490	SO:0001630	splice_region_variant			AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765	25794		Fascins	3960	protein-coding gene	gene with protein product		607643	fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal), fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)		NA	10234509	Standard	NM_012418	NM_012418	NA	Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.1274-1G>A	chr17.hg19:g.79503900G>A		NA	A0AVC4|A8MRA6	hg19	CCDS45811.1	0.02	13.909922	CCAxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.95	2.984966	0.53934	.	.	ENSG00000186765	ENST00000417245;ENST00000334850	.	.	.	4.67	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3387	0.83075	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FSCN2	77114376	1.000000	0.71417	0.998000	0.56505	0.333000	0.28666	5.788000	0.69020	2.134000	0.65973	0.484000	0.47621	.	NOVEL	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394746.1	2	30.986757	KEEP	0	0	0	103	3462	GG	1	1	0	Intron	+	58	60	1969	0	1	157.276547	281	60	9677	586	ENST00000417245.2	0.171091	1
MYADML2	255275	__UNKNOWN__	__UNKNOWN__	17	79899161	79899161	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:79899161G>A	ENST00000409745.2	-	3	811	c.457C>T	c.(457-459)Ccc>Tcc	p.P153S	MYADML2_ENST00000330655.3_Missense_Mutation_p.P153S	NM_001145113.2	NP_001138585.2	A6NDP7	MADL2_HUMAN	myeloid-associated differentiation marker-like 2	153	MARVEL 1. {ECO:0000255|PROSITE- ProRule:PRU00581}.	NA				cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(1)	1						ACCTGGCCGGGCCGGGCCCGC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													7	13	11	NA		NA	NA	17		NA											NA				79899161		673	1543	2216	SO:0001583	missense			AC137723, BC029306	CCDS45815.1	17q25.3	2008-10-15			ENSG00000185105	ENSG00000185105	255275			34548	protein-coding gene	gene with protein product		NA			NA		Standard	XR_041347	NM_001145113	NA	Approved	LOC255275	uc010wvf.1	A6NDP7	OTTHUMG00000154388	ENST00000409745.2:c.457C>T	chr17.hg19:g.79899161G>A	ENSP00000386702:p.Pro153Ser	NA		hg19	CCDS45815.1	0.02	9.952211	CGGxCCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843028	0.91197	.	.	ENSG00000185105	ENST00000409745;ENST00000330655	.	.	.	4.95	4.95	0.65309	Marvel (1);	0.054916	0.85682	D	0.000000	T	0.79452	0.4448	M	0.75085	2.285	0.58432	D	0.999996	D	0.89917	1.0	D	0.85130	0.997	T	0.80306	-0.1438	9	0.51188	T	0.08	-0.1305	18.3629	0.90380	0.0:0.0:1.0:0.0	.	153	A6NDP7	MADL2_HUMAN	S	153	.	ENSP00000327718:P153S	P	-	1	0	MYADML2	77492452	1.000000	0.71417	0.998000	0.56505	0.935000	0.57460	6.179000	0.71974	2.577000	0.86979	0.561000	0.74099	CCC	NOVEL	MYADML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335008.2	3	21.082972	KEEP	0	1	34	82	2692	GG	1	1	0		-	12	60	392	0	1	24.088925	236	60	7806	442	ENST00000409745.2	0.048387	1
NOTUM	147111	__UNKNOWN__	__UNKNOWN__	17	79910618	79910618	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:79910618C>T	ENST00000409678.3	-	0	2093					NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)	NA		NA				extracellular region (GO:0005576)	hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	15	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GACCCCCAGGCCACAGATGGG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC060882	CCDS32771.2	17q25.3	2008-02-05			ENSG00000185269	ENSG00000185269	147111			27106	protein-coding gene	gene with protein product		609847			NA		Standard	NM_178493	NM_178493	NA	Approved		uc010wvg.2	Q6P988	OTTHUMG00000154416	ENST00000409678.3:c.*219G>A	chr17.hg19:g.79910618C>T		NA	Q8N410|Q8NI82	hg19	CCDS32771.2	0.02	1.991773	AGGxCAC	COVERED																																																																																			NOVEL	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335123.2	2	2.398159	KEEP	0	0	0	8	253	CC	0.99257	0.988289	0		-	4	60	138	0	0	9.106054	64	60	2286	97	ENST00000409678.3	0.058824	0.995687
CSNK1D	1453	__UNKNOWN__	__UNKNOWN__	17	80210894	80210894	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:80210894A>T	ENST00000314028.6	-	4	912	c.563T>A	c.(562-564)aTt>aAt	p.I188N	CSNK1D_ENST00000398519.5_Missense_Mutation_p.I188N|CSNK1D_ENST00000392334.2_Missense_Mutation_p.I188N|CSNK1D_ENST00000578904.1_5'UTR	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	188	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			GGGCTCACCAATTCCAAGGTG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													136	98	111	NA		NA	NA	17		NA											NA				80210894		2203	4300	6503	SO:0001583	missense				CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551	1453			2452	protein-coding gene	gene with protein product		600864			NA	7797465	Standard	NM_139062	NM_001893	NA	Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.563T>A	chr17.hg19:g.80210894A>T	ENSP00000324464:p.Ile188Asn	NA	A2I2P2|Q96KZ6|Q9BTN5	hg19	CCDS11805.1	0.02	8.833952	CCAxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.72	2.916028	0.52546	.	.	ENSG00000141551	ENST00000314028;ENST00000392334;ENST00000398519;ENST00000269361	T;T	0.08720	3.06;3.06	5.64	5.64	0.86602	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.33702	0.0872	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.17198	-1.0377	10	0.87932	D	0	.	15.0541	0.71897	1.0:0.0:0.0:0.0	.	188;188;131	P48730;P48730-2;B4E0G1	KC1D_HUMAN;.;.	N	188;188;131;80	ENSP00000324464:I188N;ENSP00000376146:I188N	ENSP00000269361:I80N	I	-	2	0	CSNK1D	77804183	1.000000	0.71417	0.899000	0.35326	0.985000	0.73830	9.262000	0.95591	2.155000	0.67459	0.533000	0.62120	ATT	NOVEL	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442632.1	3	26.757169	KEEP	0	0	0	89	2769	AA	1	1	0		-	43	60	1519	0	0	124.321507	187	60	6627	391	ENST00000314028.6	0.186957	1
CSNK1D	1453	__UNKNOWN__	__UNKNOWN__	17	80223672	80223672	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:80223672C>T	ENST00000314028.6	-	2	426	c.77G>A	c.(76-78)gGt>gAt	p.G26D	CSNK1D_ENST00000392334.2_Splice_Site_p.G26D|CSNK1D_ENST00000398519.5_Splice_Site_p.G26D	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	26	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			AATGTCCGTACCTTGGCAAAG	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													169	145	153	NA		NA	NA	17		NA											NA				80223672		2203	4300	6503	SO:0001630	splice_region_variant				CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551	1453			2452	protein-coding gene	gene with protein product		600864			NA	7797465	Standard	NM_139062	NM_001893	NA	Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.77-1G>A	chr17.hg19:g.80223672C>T		NA	A2I2P2|Q96KZ6|Q9BTN5	hg19	CCDS11805.1	0.02	11.029867	GTAxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	34	5.372077	0.95923	.	.	ENSG00000141551	ENST00000314028;ENST00000392334;ENST00000403276	T;T;T	0.24151	1.87;1.87;1.87	5.85	5.85	0.93711	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.68586	0.3017	H	0.97659	4.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79990	-0.1570	10	0.87932	D	0	.	19.1551	0.93507	0.0:1.0:0.0:0.0	.	26;26	P48730;P48730-2	KC1D_HUMAN;.	D	26	ENSP00000324464:G26D;ENSP00000376146:G26D;ENSP00000385769:G26D	ENSP00000324464:G26D	G	-	2	0	CSNK1D	77816961	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.484000	0.81180	2.770000	0.95276	0.650000	0.86243	GGT	NOVEL	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442632.1	2	23.172376	KEEP	0	0	0	77	2665	CC	1	1	0	Missense_Mutation	-	53	60	1918	0	0	157.645743	232	60	8438	452	ENST00000314028.6	0.185965	1
C17orf62	79415	__UNKNOWN__	__UNKNOWN__	17	80405441	80405441	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:80405441C>T	ENST00000583617.1	-	3	183				C17orf62_ENST00000585064.1_Intron|C17orf62_ENST00000342572.8_Intron|C17orf62_ENST00000583359.1_Intron|C17orf62_ENST00000578919.1_Intron|C17orf62_ENST00000585080.1_Intron|C17orf62_ENST00000578913.1_Intron|C17orf62_ENST00000577732.1_Intron|C17orf62_ENST00000437807.2_Intron|C17orf62_ENST00000336995.7_Intron|C17orf62_ENST00000306645.5_Intron|C17orf62_ENST00000434650.2_Intron|C17orf62_ENST00000577436.1_Intron			Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62	NA		NA				integral component of membrane (GO:0016021)				breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			GGGGGTGGGGCGGGGGGTGCT	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													10	12	11	NA		NA	NA	17		NA											NA				80405441		2194	4283	6477	SO:0001627	intron_variant			AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927	79415			28672	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001033046	NM_001100407	NA	Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000583617.1:c.127+14G>A	chr17.hg19:g.80405441C>T		NA	E1B6X3|Q96NR1	hg19		0.02	1.901372	GGGxGGG	COVERED																																																																																			NOVEL	C17orf62-037	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000443265.1	0	6.013165	KEEP	0	0	0	20	646	CC	0.999863	0.994947	0		-	10	60	259	0	0	18.43824	57	60	1849	131	ENST00000583617.1	0.149254	0.995084
NARF	26502	__UNKNOWN__	__UNKNOWN__	17	80416598	80416598	__UNKNOWN__	5'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:80416598G>C	ENST00000457415.3	+	0	20				NARF_ENST00000345415.7_5'UTR|NARF_ENST00000412079.2_5'UTR|NARF_ENST00000309794.11_5'UTR|NARF_ENST00000581743.1_3'UTR|NARF_ENST00000390006.4_Intron			Q9UHQ1	NARF_HUMAN	nuclear prelamin A recognition factor	NA		NA				lamin filament (GO:0005638)|nuclear lamina (GO:0005652)|nuclear lumen (GO:0031981)|nucleus (GO:0005634)	lamin binding (GO:0005521)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACAAAGGGCCGCGGGCGGCGG	0.716	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													1	3	2	NA		NA	NA	17		NA											NA				80416598		429	1153	1582	SO:0001623	5_prime_UTR_variant			BC000438	CCDS32777.1, CCDS42403.1, CCDS42404.1	17q25.3	2011-12-19			ENSG00000141562	ENSG00000141562	26502			29916	protein-coding gene	gene with protein product	iron-only hydrogenase-like protein 2	605349			NA	10514485, 15667261	Standard	NM_031968	NM_031968	NA	Approved	FLJ10067, DKFZp434G0420, IOP2	uc002kfg.4	Q9UHQ1		ENST00000457415.3:c.-82G>C	chr17.hg19:g.80416598G>C		NA	A6NCJ3|B3KPX2|K4DI98|Q96AY9|Q9BWC6	hg19		0.02	4.080418	GCCxCGG	COVERED																																																																																			NOVEL	NARF-018	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000443578.1	5	32.753454	KEEP	0	0	0	109	3449	GG	1	0.999999	0		+	10	60	321	0	0	21.758779	115	60	3685	302	ENST00000457415.3	0.08	0.999999
METRNL	284207	__UNKNOWN__	__UNKNOWN__	17	81052032	81052032	__UNKNOWN__	Silent	SNP	C	C	T	rs142053233	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr17:81052032C>T	ENST00000320095.7	+	4	773	c.648C>T	c.(646-648)caC>caT	p.H216H	METRNL_ENST00000570778.1_Silent_p.H134H|METRNL_ENST00000571814.1_Silent_p.H134H|METRNL_ENST00000571940.1_3'UTR	NM_001004431.1	NP_001004431.1	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation regulator-like	216		NA			brown fat cell differentiation (GO:0050873)|fat cell differentiation (GO:0045444)|negative regulation of inflammatory response (GO:0050728)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of energy homeostasis (GO:2000507)|response to cold (GO:0009409)|response to muscle activity (GO:0014850)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)		BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			AAGTTACCCACGAGCCTGAGC	0.632	NA	NA											c|||	21	0.00419329	0.003	0	5008	,	,	NA	16425	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0174	NA	NA	NA						NA		NA				0								C		4,4402	8.1+/-20.4	0,4,2199	74	72	73	NA	648	-10	0	17	dbSNP_134	73	0,8592		0,0,4296	no	coding-synonymous	METRNL	NM_001004431.1		0,4,6495	TT,TC,CC	NA	0.0,0.0908,0.0308		216/312	81052032	4,12994	2203	4296	6499	SO:0001819	synonymous_variant			AK093748	CCDS32779.1	17q25.3	2004-12-01				ENSG00000176845	284207			27584	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004431	NM_001004431	NA	Approved		uc002kgh.3	Q641Q3		ENST00000320095.7:c.648C>T	chr17.hg19:g.81052032C>T		NA	B3KSJ5|Q86VM0	hg19	CCDS32779.1	0.02	28.44041	CCAxGAG	COVERED																																																																																			NOVEL	METRNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438902.1	5	58.715583	KEEP	0	1	31	206	7006	CC	1	1	0		+	18	60	672	1	0	39.836491	651	60	23209	1158	ENST00000320095.7	0.026906	1
YES1	7525	__UNKNOWN__	__UNKNOWN__	18	724236	724236	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:724236A>T	ENST00000584307.1	-	0	1990				YES1_ENST00000577961.1_3'UTR|YES1_ENST00000314574.4_3'UTR			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	NA		NA			blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	TGATAAATTCATCATTGGTAC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105	7525		SH2 domain containing	12841	protein-coding gene	gene with protein product		164880	v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1		NA	2983418	Standard	NM_005433	NM_005433	NA	Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.*188T>A	chr18.hg19:g.724236A>T		NA	A6NLB3|D3DUH1	hg19	CCDS11824.1	0.02	4.869304	TTCxTCA	COVERED																																																																																			NOVEL	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440827.2	3	13.84072	KEEP	0	0	0	46	1435	AA	1	1	0		-	36	60	1367	0	0	121.140049	90	60	3327	229	ENST00000584307.1	0.285714	1
EMILIN2	84034	__UNKNOWN__	__UNKNOWN__	18	2913120	2913120	__UNKNOWN__	Silent	SNP	C	C	T	rs376259104		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:2913120C>T	ENST00000254528.3	+	8	3039	c.2880C>T	c.(2878-2880)ccC>ccT	p.P960P	EMILIN2_ENST00000308080.5_3'UTR	NM_032048.2	NP_114437.2	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	960	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.	NA			cell adhesion (GO:0007155)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix constituent conferring elasticity (GO:0030023)			breast(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(4)	48				READ - Rectum adenocarcinoma(2;0.1)		CCCTCACCCCCGAGAGAGACG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C		0,4406		0,0,2203	57	59	58	NA	2880	-10.9	0	18		58	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EMILIN2	NM_032048.2		0,1,6502	TT,TC,CC	NA	0.0116,0.0,0.0077		960/1054	2913120	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			AF270513	CCDS11828.1	18p11.3	2008-02-05			ENSG00000132205	ENSG00000132205	84034		EMI domain containing	19881	protein-coding gene	gene with protein product		608928			NA		Standard	NM_032048	NM_032048	NA	Approved	FLJ33200, FOAP-10	uc002kln.3	Q9BXX0	OTTHUMG00000128525	ENST00000254528.3:c.2880C>T	chr18.hg19:g.2913120C>T		NA	B2RMY3|Q8NBH3|Q96JQ4	hg19	CCDS11828.1	0.02	7.056959	CCCxGAG	COVERED																																																																																			NOVEL	EMILIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250337.2	1	21.368082	KEEP	0	0	0	71	2412	CC	1	1	0		+	39	60	1444	0	0	121.838649	144	60	5078	331	ENST00000254528.3	0.213115	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	5132988	5132988	__UNKNOWN__	IGR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:5132988T>C			NA	NA				RP11-92G19.2 (47512 upstream) : C18orf42 (12295 downstream)						NA		NA									NA						CTTTTGTGCATCGTAGGATTC	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.5132988T>C		NA		hg19		0.02	10.036917	GCAxCGT	COVERED	.	.	.	.	.	.	.	.	.	.	T	2.548	-0.304725	0.05495	.	.	ENSG00000215368	ENST00000400144	.	.	.	0.605	-1.21	0.09524	.	.	.	.	.	T	0.37812	0.1017	.	.	.	.	.	.	.	.	.	.	.	.	T	0.40997	-0.9533	4	0.37606	T	0.19	.	5.2419	0.15477	0.0:0.3618:0.0:0.6382	.	.	.	.	V	62	.	ENSP00000444229:M62V	M	-	1	0	AP005380.1	5122988	0.911000	0.30947	0.019000	0.16419	0.013000	0.08279	1.268000	0.33062	-0.980000	0.03524	-0.779000	0.03376	ATG	NOVEL					0			2	11.433352	KEEP	0	0	0	38	1221	TT	1	1	0			80	60	2971	0	0	273.43722	136	60	4980	327		0.37037	1
LAMA1	284217	__UNKNOWN__	__UNKNOWN__	18	7032977	7032977	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:7032977C>A	ENST00000389658.3	-	15	2257					NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	NA		NA			axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AAGAGAGAAGCGTCACCTCAC	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													92	71	78	NA		NA	NA	18		NA											NA				7032977		2203	4300	6503	SO:0001627	intron_variant			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680	284217		Laminins	6481	protein-coding gene	gene with protein product		150320		LAMA	NA	2591971	Standard	NM_005559	NM_005559	NA	Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.2163+5G>T	chr18.hg19:g.7032977C>A		NA		hg19	CCDS32787.1	0.02	2.189005	AAGxGTC	COVERED																																																																																			NOVEL	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257369.1	2	9.028905	KEEP	0	0	0	30	1053	CC	0.999997	0.999859	0		-	25	60	953	0	0	83.994788	66	60	2375	161	ENST00000389658.3	0.274725	0.999862
LRRC30	339291	__UNKNOWN__	__UNKNOWN__	18	7231537	7231537	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:7231537C>T	ENST00000383467.2	+	1	415	c.401C>T	c.(400-402)gCc>gTc	p.A134V		NM_001105581.1	NP_001099051.1	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	134		NA								central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						GAGGTGCCGGCCGAGCTGAGC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													38	44	42	NA		NA	NA	18		NA											NA				7231537		2052	4204	6256	SO:0001583	missense				CCDS42409.1	18p11.23	2005-01-06				ENSG00000206422	339291			30219	protein-coding gene	gene with protein product		NA			NA		Standard	XM_292678	NM_001105581	NA	Approved		uc010wzk.2	A6NM36		ENST00000383467.2:c.401C>T	chr18.hg19:g.7231537C>T	ENSP00000372959:p.Ala134Val	NA		hg19	CCDS42409.1	0.02	8.225845	CGGxCGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417583	0.62622	.	.	ENSG00000206422	ENST00000383467	T	0.25085	1.82	5.65	4.73	0.59995	.	0.264284	0.42294	D	0.000725	T	0.22781	0.0550	L	0.55103	1.725	0.09310	N	1	B	0.28713	0.22	B	0.21708	0.036	T	0.08953	-1.0697	10	0.30854	T	0.27	.	11.4374	0.50076	0.1399:0.7251:0.135:0.0	.	134	A6NM36	LRC30_HUMAN	V	134	ENSP00000372959:A134V	ENSP00000372959:A134V	A	+	2	0	LRRC30	7221537	0.998000	0.40836	0.027000	0.17364	0.985000	0.73830	4.784000	0.62411	2.827000	0.97445	0.650000	0.86243	GCC	NOVEL	LRRC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442140.1	0	17.155054	KEEP	0	0	0	57	1976	CC	1	1	0		+	11	60	388	0	0	24.874809	219	60	7916	345	ENST00000383467.2	0.047826	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	7232110	7232110	__UNKNOWN__	IGR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:7232110T>C			NA	NA				LRRC30 (65 upstream) : SNORA48 (68907 downstream)						NA		NA									NA						ACTTCTCTCGTCTCAGCTTTC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.7232110T>C		NA		hg19		0.02	10.150992	TCGxCTC	COVERED																																																																																			NOVEL					0			1	14.144225	KEEP	0	0	0	47	1564	TT	1	1	0			62	60	2321	0	0	207.116519	143	60	5130	325		0.302439	1
NDUFV2	4729	__UNKNOWN__	__UNKNOWN__	18	9105108	9105108	__UNKNOWN__	Intron	SNP	C	C	T	rs1396740	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:9105108C>T	ENST00000318388.6	+	1	168				NDUFV2_ENST00000400033.1_Intron|RP11-21J18.1_ENST00000579126.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	NA		NA			cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						attacttatacaaccaggccc	0.343	NA	NA											T|||	3720	0.742812	0.6233	0.7896	5008	,	,	NA	18856	0.6915	NA	0.826	False	NA	,,,	NA	NA	NA	2504	0.8384	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	4729	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7717	protein-coding gene	gene with protein product	complex I 24kDa subunit, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	600532	NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)		NA	9763677, 7607668	Standard	NM_021074	NM_021074	NA	Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.54+2313C>T	chr18.hg19:g.9105108C>T		NA	Q9BV41	hg19	CCDS11842.1	0.02	-0.175451	ATAxAAC	COVERED																																																																																			NOVEL	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254475.2	0	2.407355	KEEP	0	0	0	8	269	CC	0.99257	0.384528	0		+	16	60	567	0	0	59.98599	4	60	139	32	ENST00000318388.6	0.8	0.387407
SPIRE1	56907	__UNKNOWN__	__UNKNOWN__	18	12446776	12446776	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:12446776A>G	ENST00000409402.4	-	0	5399				RP11-861E21.2_ENST00000588197.1_RNA|RP11-861E21.2_ENST00000589795.1_RNA|SPIRE1_ENST00000410092.3_3'UTR	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1	NA		NA								breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						CCAGTCCTACAGTAATATAGT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278	56907			30622	protein-coding gene	gene with protein product		609216	spire homolog 1 (Drosophila), spire family actin nucleation factor 1		NA	10574461, 11747823	Standard	XM_290818	NM_001128626	NA	Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.*2861T>C	chr18.hg19:g.12446776A>G		NA		hg19	CCDS45829.1	0.02	1.936625	TACxGTA	COVERED																																																																																			NOVEL	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333109.2	1	8.124828	KEEP	0	0	0	27	859	AA	0.999988	0.999927	0		-	30	60	1025	0	0	90.756528	67	60	2501	139	ENST00000409402.4	0.309278	0.99994
FAM210A	125228	__UNKNOWN__	__UNKNOWN__	18	13664713	13664713	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:13664713A>T	ENST00000322247.3	-	0	2972				FAM210A_ENST00000402563.1_3'UTR	NM_001098801.1	NP_001092271.1	Q96ND0	F210A_HUMAN	family with sequence similarity 210, member A	NA		NA				integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)					NA						TTTAAAAAGCATTCTAATATA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK055618	CCDS11866.1	18p11.21	2011-11-24	2011-11-24	2011-11-24	ENSG00000177150	ENSG00000177150	125228			28346	protein-coding gene	gene with protein product		NA	chromosome 18 open reading frame 19	C18orf19	NA	14702039	Standard	NM_152352	NM_152352	NA	Approved	MGC24180, HsT2329	uc010dli.3	Q96ND0	OTTHUMG00000131719	ENST00000322247.3:c.*1766T>A	chr18.hg19:g.13664713A>T		NA	D3DUJ4	hg19	CCDS11866.1	0.02	5.08863	AGCxTTC	COVERED																																																																																			NOVEL	FAM210A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254637.1	2	13.23934	KEEP	0	0	0	44	1390	AA	1	0.999968	0		-	22	60	826	0	0	70.107733	79	60	2901	189	ENST00000322247.3	0.217822	0.999968
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	14392844	14392844	__UNKNOWN__	IGR	SNP	C	C	G	rs200563073	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:14392844C>G			NA	NA				CYP4F35P (50321 upstream) : CXADRP3 (85109 downstream)						NA		NA									NA						GCGCCTCCAGCTCCTCGGTGG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.14392844C>G		NA		hg19		0.02	-0.184233	CAGxTCC	COVERED																																																																																			NOVEL					0			1	3.009292	KEEP	1	0	0	10	343	CC	0.992708	0.42039	0			5	49	187	0	0	16.080045	16	60	607	46		0.238095	0.423478
CTAGE1	64693	__UNKNOWN__	__UNKNOWN__	18	19997740	19997740	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:19997740C>T	ENST00000391403.2	-	1	138	c.35G>A	c.(34-36)tGg>tAg	p.W12*		NM_172241.2	NP_758441.2	Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1	0		NA				integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					CACCAATTCCCATGGAAAACC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													89	81	84	NA		NA	NA	18		NA											NA				19997740		2203	4300	6503	SO:0001587	stop_gained			AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710	64693			24346	protein-coding gene	gene with protein product	cutaneous T-cell lymphoma-associated antigen 1, cutaneous T-cell lymphoma-associated antigen 2, cancer/testis antigen family 21, member 1, cancer/testis antigen family 21, member 2	608856			NA	11149944, 12839582	Standard	NM_022663, NM_172241	NM_172241	NA	Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6		ENST00000391403.2:c.35G>A	chr18.hg19:g.19997740C>T	ENSP00000375220:p.Trp12*	NA	B0YIZ3	hg19	CCDS45837.1	0.02	17.044889	TCCxATG	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.53	2.266080	0.40095	.	.	ENSG00000212710	ENST00000391403	.	.	.	0.949	-0.0782	0.13716	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3891	0.07282	0.0:0.6836:0.0:0.3164	.	.	.	.	X	12	.	.	W	-	2	0	CTAGE1	18251738	1.000000	0.71417	0.000000	0.03702	0.002000	0.02628	2.223000	0.42936	-0.063000	0.13065	0.455000	0.32223	TGG	NOVEL	CTAGE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386768.3	2	18.056613	KEEP	0	0	0	60	2047	CC	1	1	0		-	28	60	1058	0	0	75.661355	355	60	12955	498	ENST00000391403.2	0.073107	1
TAF4B	6875	__UNKNOWN__	__UNKNOWN__	18	23872360	23872360	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:23872360A>G	ENST00000269142.5	+	8	2724				TAF4B_ENST00000400466.2_Intron|TAF4B_ENST00000578121.1_Intron	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	NA		NA			gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			ATGCTGGTCCATCTCAGTCCC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													129	120	123	NA		NA	NA	18		NA											NA				23872360		1917	4134	6051	SO:0001627	intron_variant			Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384	6875			11538	protein-coding gene	gene with protein product	TATA box binding protein (TBP)-associated factor 4B	601689	TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD	TAF2C2	NA	8858156, 10849440	Standard	NM_005640	XM_005258339	NA	Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1726+15A>G	chr18.hg19:g.23872360A>G		NA	Q29YA4|Q29YA5	hg19	CCDS42421.1	0.02	11.802739	TCCxTCT	COVERED																																																																																			NOVEL	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000446260.3	2	8.72563	KEEP	0	0	0	29	917	AA	0.999997	0.999997	0		+	11	60	381	0	0	24.146793	244	60	8996	345	ENST00000269142.5	0.043137	1
DSC1	1823	__UNKNOWN__	__UNKNOWN__	18	28711548	28711548	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:28711548G>T	ENST00000257198.5	-	15	2749				DSC1_ENST00000257197.3_Intron|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	NA		NA			homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CAAAGACAGTGGAACTTACTT	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													104	86	92	NA		NA	NA	18		NA											NA				28711548		2203	4300	6503	SO:0001627	intron_variant			AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765	1823		Cadherins / Major cadherins	3035	protein-coding gene	gene with protein product		125643			NA	8486729	Standard	NM_004948, NM_024421	NM_024421	NA	Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2487+8C>A	chr18.hg19:g.28711548G>T		NA	Q9HB01	hg19	CCDS11894.1	0.02	30.698454	AGTxGAA	COVERED																																																																																			NOVEL	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254946.1	0	8.126515	KEEP	0	0	0	27	958	GG	0.999988	0.999988	0		-	98	60	3555	0	0	281.615281	566	60	21091	808	ENST00000257198.5	0.14759	1
DSG4	147409	__UNKNOWN__	__UNKNOWN__	18	28991215	28991215	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:28991215C>T	ENST00000308128.4	+	15	2294	c.2159C>T	c.(2158-2160)gCa>gTa	p.A720V	RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.A739V|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	720		NA			anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AACACCTATGCAGCCGGGGGC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													83	78	80	NA		NA	NA	18		NA											NA				28991215		2203	4300	6503	SO:0001583	missense			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065	147409		Cadherins / Major cadherins	21307	protein-coding gene	gene with protein product		607892			NA	12648213	Standard	NM_177986	NM_001134453	NA	Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.2159C>T	chr18.hg19:g.28991215C>T	ENSP00000311859:p.Ala720Val	NA	A2RUI1|Q6Y9L9|Q8IXV4	hg19	CCDS11897.1	0.02	32.849684	ATGxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.37	3.373608	0.61624	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.59906	0.23;0.23	5.96	5.96	0.96718	.	0.000000	0.34603	N	0.003835	T	0.66046	0.2750	M	0.62723	1.935	0.37831	D	0.928731	D;D	0.63046	0.992;0.974	P;P	0.61722	0.893;0.717	T	0.63550	-0.6612	10	0.15066	T	0.55	.	10.4644	0.44598	0.1398:0.7075:0.1526:0.0	.	739;720	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	V	720;739	ENSP00000311859:A720V;ENSP00000352785:A739V	ENSP00000311859:A720V	A	+	2	0	DSG4	27245213	0.943000	0.32029	0.962000	0.40283	0.470000	0.32858	1.866000	0.39489	2.815000	0.96918	0.650000	0.86243	GCA	NOVEL	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254941.1	5	26.481959	KEEP	0	0	0	88	3098	CC	1	1	0		+	159	60	5507	0	0	455.111482	623	60	23426	1075	ENST00000308128.4	0.203325	1
RNF125	54941	__UNKNOWN__	__UNKNOWN__	18	29649603	29649603	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:29649603T>C	ENST00000217740.3	+	0	2447				RP11-53I6.2_ENST00000583184.1_RNA	NM_017831.3	NP_060301.2	Q96EQ8	RN125_HUMAN	ring finger protein 125, E3 ubiquitin protein ligase	NA		NA			innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						ACTGCTAGACTGATTTAAATG	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000463	CCDS11902.1	18q12.1	2013-01-09	2012-02-23		ENSG00000101695	ENSG00000101695	54941		RING-type (C3HC4) zinc fingers	21150	protein-coding gene	gene with protein product		610432	ring finger protein 125		NA		Standard	NM_017831	NM_017831	NA	Approved	FLJ20456	uc002kxf.1	Q96EQ8	OTTHUMG00000132266	ENST00000217740.3:c.*1256T>C	chr18.hg19:g.29649603T>C		NA	Q9NX39	hg19	CCDS11902.1	0.02	11.006548	GACxGAT	COVERED																																																																																			NOVEL	RNF125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255354.1	2	9.364452	KEEP	0	1	34	43	1395	TT	1	1	0		+	34	60	1154	0	0	85.593143	266	60	10100	439	ENST00000217740.3	0.113333	1
CCDC178	374864	__UNKNOWN__	__UNKNOWN__	18	30936271	30936271	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:30936271G>C	ENST00000383096.3	-	7	554				CCDC178_ENST00000402325.1_Intron|CCDC178_ENST00000403303.1_Intron|CCDC178_ENST00000583930.1_Intron|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000579947.1_Intron|CCDC178_ENST00000300227.8_Intron|CCDC178_ENST00000406524.2_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	NA		NA									NA						GTTTTAAAAAGCATGAAATTT	0.234	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													11	11	11	NA		NA	NA	18		NA											NA				30936271		1965	3999	5964	SO:0001627	intron_variant			AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960	374864			29588	protein-coding gene	gene with protein product		NA	chromosome 18 open reading frame 34	C18orf34	NA		Standard	NM_198995	NM_198995	NA	Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.371+16C>G	chr18.hg19:g.30936271G>C		NA	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	hg19	CCDS42424.1	0.02	4.581969	AAAxCAT	COVERED																																																																																			NOVEL	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255373.2	1	5.1169	KEEP	0	0	0	17	626	GG	0.999366	0.999366	0		-	9	60	331	0	0	23.008865	127	60	4889	201	ENST00000383096.3	0.066176	1
ZNF397	84307	__UNKNOWN__	__UNKNOWN__	18	32823204	32823204	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:32823204A>G	ENST00000355632.4	+	3	638	c.503A>G	c.(502-504)cAg>cGg	p.Q168R	ZNF397_ENST00000592264.1_Missense_Mutation_p.Q168R|ZNF397_ENST00000589420.1_3'UTR|ZNF397_ENST00000585800.1_Missense_Mutation_p.Q168R|ZNF397_ENST00000330501.7_Missense_Mutation_p.Q168R|ZNF397_ENST00000591206.1_Missense_Mutation_p.Q168R|ZNF397_ENST00000261333.6_Missense_Mutation_p.Q168R			Q8NF99	ZN397_HUMAN	zinc finger protein 397	168		NA			transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	12						ATCCACCTCCAGCCCTTAAAG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													123	116	119	NA		NA	NA	18		NA											NA				32823204		2203	4300	6503	SO:0001583	missense			BC006172	CCDS32814.1, CCDS45852.1	18p12	2013-01-09	2003-07-22			ENSG00000186812	84307		-, Zinc fingers, C2H2-type	18818	protein-coding gene	gene with protein product		609601	zinc finger protein 47	ZNF47	NA		Standard	NM_032347	NM_032347	NA	Approved	ZSCAN15, MGC13250	uc010dmp.3	Q8NF99		ENST00000355632.4:c.503A>G	chr18.hg19:g.32823204A>G	ENSP00000347850:p.Gln168Arg	NA	Q9BRM2	hg19		0.02	10.389165	TCCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	10.18	1.278298	0.23307	.	.	ENSG00000186812	ENST00000261333;ENST00000330501;ENST00000355632	T;T;T	0.07908	4.26;3.15;4.16	4.93	2.61	0.31194	.	0.295721	0.18571	N	0.137344	T	0.07279	0.0184	L	0.42245	1.32	0.09310	N	1	B;B;B;B	0.13594	0.006;0.001;0.008;0.008	B;B;B;B	0.13407	0.007;0.001;0.009;0.006	T	0.25187	-1.0139	10	0.46703	T	0.11	.	5.6024	0.17361	0.7883:0.0:0.2117:0.0	.	168;168;168;168	Q96K65;Q8NF99;Q8NF99-2;Q8NF99-3	.;ZN397_HUMAN;.;.	R	168	ENSP00000261333:Q168R;ENSP00000331577:Q168R;ENSP00000347850:Q168R	ENSP00000261333:Q168R	Q	+	2	0	ZNF397	31077202	0.004000	0.15560	0.699000	0.30290	0.482000	0.33219	0.155000	0.16362	0.983000	0.38602	0.477000	0.44152	CAG	NOVEL	ZNF397-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000442401.1	5	29.489116	KEEP	0	0	0	98	3115	AA	1	1	0		+	11	60	358	0	0	21.188789	280	60	10516	490	ENST00000355632.4	0.037801	1
ZNF24	7572	__UNKNOWN__	__UNKNOWN__	18	32914955	32914955	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:32914955T>C	ENST00000589881.1	-	0	4654				ZNF24_ENST00000261332.6_3'UTR|ZNF24_ENST00000399061.3_3'UTR			P17028	ZNF24_HUMAN	zinc finger protein 24	NA		NA			myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	15						TTTTCTACACTCACATTACCA	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(42;769 913 8916 19469 46270)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF016052	CCDS11912.1	18q12	2013-01-09	2006-05-10		ENSG00000172466	ENSG00000172466	7572		-, Zinc fingers, C2H2-type	13032	protein-coding gene	gene with protein product		194534	zinc finger protein 24 (KOX 17)	ZNF191	NA		Standard	NM_006965	NM_006965	NA	Approved	ZSCAN3, Zfp191, KOX17	uc002kys.2	P17028	OTTHUMG00000132565	ENST00000589881.1:c.*4069A>G	chr18.hg19:g.32914955T>C		NA	O14754|Q53YE4|Q6ICR5|Q8IZN4	hg19		0.02	10.738891	CACxCAC	COVERED																																																																																			NOVEL	ZNF24-003	KNOWN	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000442598.2	4	18.655864	KEEP	0	0	0	62	2012	TT	1	1	0		-	13	60	438	0	0	27.859226	238	60	8782	395	ENST00000589881.1	0.051793	1
MOCOS	55034	__UNKNOWN__	__UNKNOWN__	18	33851128	33851128	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:33851128C>A	ENST00000261326.5	+	0	5168					NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase	NA		NA								breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CTctcctttacagcactatta	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643	55034			18234	protein-coding gene	gene with protein product		613274			NA	11302742	Standard		NM_017947	NA	Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.*2480C>A	chr18.hg19:g.33851128C>A		NA		hg19	CCDS11919.1	0.02	4.627685	TTAxAGC	COVERED																																																																																			NOVEL	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255801.1	0	2.708559	KEEP	0	0	0	9	320	CC	0.99254	0.992531	0		+	44	60	1601	0	0	149.38971	64	60	2416	142	ENST00000261326.5	0.407407	0.999991
LOXHD1	125336	__UNKNOWN__	__UNKNOWN__	18	44229231	44229231	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:44229231C>T	ENST00000441551.2	-	2	131	c.132G>A	c.(130-132)gtG>gtA	p.V44V	LOXHD1_ENST00000536736.1_Splice_Site_p.V44V			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	898	PLAT 1. {ECO:0000255|PROSITE- ProRule:PRU00152}.	NA			calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						CCACTTCATACACTGGAGGAG	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													77	79	78	NA		NA	NA	18		NA											NA				44229231		692	1591	2283	SO:0001630	splice_region_variant			AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210	125336			26521	protein-coding gene	gene with protein product		613072	deafness, autosomal recessive 77	DFNB77	NA	19732867	Standard	NM_144612	NM_144612	NA	Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000441551.2:c.131-1G>A	chr18.hg19:g.44229231C>T		NA	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	hg19		0.02	2.085748	ATAxACT	COVERED	.	.	.	.	.	.	.	.	.	.	C	5.515	0.280035	0.10458	.	.	ENSG00000167210	ENST00000441551	.	.	.	4.28	1.34	0.21922	.	.	.	.	.	T	0.41949	0.1181	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.14364	-1.0475	5	0.26408	T	0.33	.	2.964	0.05902	0.1333:0.3128:0.3911:0.1628	.	.	.	.	I	25	.	ENSP00000387621:V25I	V	-	1	0	LOXHD1	42483229	1.000000	0.71417	0.923000	0.36655	0.218000	0.24690	1.275000	0.33144	0.021000	0.15133	-0.291000	0.09656	GTA	NOVEL	LOXHD1-013	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000446054.1	0	3.912758	KEEP	0	0	0	13	466	CC	0.994391	0.993613	0	Silent	-	14	60	499	0	0	40.469988	66	60	2485	114	ENST00000441551.2	0.175	0.999218
KATNAL2	83473	__UNKNOWN__	__UNKNOWN__	18	44561631	44561631	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:44561631G>A	ENST00000592005.1	+	3	724				TCEB3B_ENST00000332567.4_Missense_Mutation_p.A2V|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron					katanin p60 subunit A-like 2	NA		NA								central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						GGACCCTGCCGCCATCTCACC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	43	44	NA		NA	NA	18		NA											NA				44561631		2201	4297	6498	SO:0001627	intron_variant			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216	83473		ATPases / AAA-type	25387	protein-coding gene	gene with protein product		614697			NA	12477932	Standard	NM_031303	NM_031303	NA	Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.51+34745G>A	chr18.hg19:g.44561631G>A		NA		hg19		0.02	-0.438636	GCCxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.46	1.643954	0.29246	.	.	ENSG00000206181	ENST00000332567	T	0.09163	3.01	2.13	0.266	0.15617	Transcription factor IIS, N-terminal (1);	0.601202	0.11580	N	0.549814	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	D	0.57899	0.981	B	0.35859	0.212	T	0.37079	-0.9721	10	0.62326	D	0.03	-1.0932	2.8357	0.05515	0.1626:0.0:0.5654:0.272	.	2	Q8IYF1	ELOA2_HUMAN	V	2	ENSP00000331302:A2V	ENSP00000331302:A2V	A	-	2	0	TCEB3B	42815629	0.026000	0.19158	0.006000	0.13384	0.008000	0.06430	0.852000	0.27764	0.067000	0.16545	-0.269000	0.10298	GCG	NOVEL	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446324.2	0	6.319996	KEEP	0	0	0	21	725	GG	0.999869	0.959733	0		+	14	60	515	0	0	45.304634	36	60	1258	99	ENST00000592005.1	0.28	0.959859
KATNAL2	83473	__UNKNOWN__	__UNKNOWN__	18	44595595	44595595	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:44595595C>T	ENST00000592005.1	+	4	724				KATNAL2_ENST00000245121.5_Missense_Mutation_p.P205L|KATNAL2_ENST00000356157.7_Missense_Mutation_p.P277L					katanin p60 subunit A-like 2	NA		NA								central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						CCTTAGTATCCACAGCTATTT	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													194	167	176	NA		NA	NA	18		NA											NA				44595595		2203	4300	6503	SO:0001627	intron_variant			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216	83473		ATPases / AAA-type	25387	protein-coding gene	gene with protein product		614697			NA	12477932	Standard	NM_031303	NM_031303	NA	Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.52-6053C>T	chr18.hg19:g.44595595C>T		NA		hg19		0.02	11.021612	ATCxACA	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719731	0.68844	.	.	ENSG00000167216	ENST00000356157;ENST00000245121;ENST00000454462	D;D	0.94723	-3.5;-3.5	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.98216	0.9410	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98880	1.0769	10	0.87932	D	0	-0.6436	19.8154	0.96566	0.0:1.0:0.0:0.0	.	277	Q8IYT4	KATL2_HUMAN	L	277;205;45	ENSP00000348478:P277L;ENSP00000245121:P205L	ENSP00000245121:P205L	P	+	2	0	KATNAL2	42849593	1.000000	0.71417	0.996000	0.52242	0.064000	0.16182	7.325000	0.79124	2.699000	0.92147	0.655000	0.94253	CCA	NOVEL	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446324.2	0	13.844976	KEEP	0	0	0	46	1648	CC	1	1	0		+	8	60	297	0	0	17.666411	279	60	10292	418	ENST00000592005.1	0.027875	1
ZBTB7C	201501	__UNKNOWN__	__UNKNOWN__	18	45691511	45691511	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:45691511A>G	ENST00000588982.1	-	0	426				ZBTB7C_ENST00000586438.1_5'UTR|ZBTB7C_ENST00000590800.1_Intron			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	NA		NA					metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						ccaacccttcattttacagag	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828	201501		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	31700	protein-coding gene	gene with protein product		NA	zinc finger and BTB domain containing 36	ZBTB36	NA		Standard	NM_001039360	NM_001039360	NA	Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.-76T>C	chr18.hg19:g.45691511A>G		NA	O73453	hg19	CCDS32830.1	0.02	2.311832	TTCxTTT	COVERED																																																																																			NOVEL	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450731.1	1	8.12243	KEEP	0	0	0	27	818	AA	0.999988	0.99898	0		-	33	60	1132	0	0	106.104801	44	60	1651	133	ENST00000588982.1	0.428571	0.998993
ONECUT2	9480	__UNKNOWN__	__UNKNOWN__	18	55104066	55104066	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:55104066G>A	ENST00000491143.2	+	1	1150	c.1118G>A	c.(1117-1119)cGg>cAg	p.R373Q		NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	373		NA			cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		GACCTGCTCCGGAATCCAAAA	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													28	33	31	NA		NA	NA	18		NA											NA				55104066		2136	4262	6398	SO:0001583	missense			Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547	9480		Homeoboxes / CUT class	8139	protein-coding gene	gene with protein product		604894	one cut domain, family member 2		NA	9915796	Standard		NM_004852	NA	Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.1118G>A	chr18.hg19:g.55104066G>A	ENSP00000419185:p.Arg373Gln	NA		hg19	CCDS42440.1	0.02	11.561822	TCCxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	29.3	4.994160	0.93167	.	.	ENSG00000119547	ENST00000491143;ENST00000262095	.	.	.	4.88	4.88	0.63580	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.64402	D	0.000001	D	0.84906	0.5576	M	0.90483	3.12	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	D	0.88546	0.3113	9	0.87932	D	0	-20.9939	16.8063	0.85706	0.0:0.0:1.0:0.0	.	373	O95948	ONEC2_HUMAN	Q	354;373	.	ENSP00000262095:R373Q	R	+	2	0	ONECUT2	53255064	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.715000	0.98748	2.282000	0.76494	0.462000	0.41574	CGG	NOVEL	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357264.3	3	20.703157	KEEP	0	0	0	69	2273	GG	1	1	0		+	25	60	933	0	0	68.108652	269	60	9329	435	ENST00000491143.2	0.085034	1
ZCCHC2	54877	__UNKNOWN__	__UNKNOWN__	18	60190897	60190897	__UNKNOWN__	Silent	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:60190897T>G	ENST00000269499.5	+	1	658	c.240T>G	c.(238-240)ggT>ggG	p.G80G		NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	80		NA				cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						cgggggcgggtatgccgggcg	0.826	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664	54877		Zinc fingers, CCHC domain containing	22916	protein-coding gene	gene with protein product		NA	chromosome 18 open reading frame 49	C18orf49	NA	11214970	Standard	NM_017742	NM_017742	NA	Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.240T>G	chr18.hg19:g.60190897T>G		NA	B2RPG6|Q8N3S1|Q9NXF6	hg19	CCDS45880.1	0.02	-0.192296	GGGxATG	COVERED																																																																																			NOVEL	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450083.1	0	2.347846	KEEP	0	3	16	14	317	TT	0.999366	0.457467	0		+	6	60	121	0	0	9.799713	13	60	384	68	ENST00000269499.5	0.315789	0.457757
SERPINB3	6317	__UNKNOWN__	__UNKNOWN__	18	61323286	61323286	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:61323286T>C	ENST00000283752.5	-	8	921	c.778A>G	c.(778-780)Aaa>Gaa	p.K260E	SERPINB3_ENST00000332821.8_Missense_Mutation_p.K208E|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	260		NA			negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GCAGTGAGTTTCTCTTCAAGC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													62	59	60	NA		NA	NA	18		NA											NA				61323286		2203	4297	6500	SO:0001583	missense			U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149	6317		Serine (or cysteine) peptidase inhibitors	10569	protein-coding gene	gene with protein product		600517	serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3	SCC, SCCA1	NA	7724531, 24172014	Standard	NM_006919	NM_006919	NA	Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.778A>G	chr18.hg19:g.61323286T>C	ENSP00000283752:p.Lys260Glu	NA	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	hg19	CCDS11987.1	0.02	14.151932	GTTxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.331	1.060619	0.19987	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.85088	-1.94;-1.94	3.07	-6.15	0.02105	Serpin domain (3);	0.700883	0.12329	N	0.478591	T	0.73055	0.3538	L	0.34521	1.04	0.09310	N	1	B;B	0.25521	0.128;0.023	B;B	0.29077	0.098;0.021	T	0.56914	-0.7900	10	0.11485	T	0.65	.	12.3263	0.55013	0.0:0.2161:0.666:0.1179	.	208;260	P29508-2;P29508	.;SPB3_HUMAN	E	260;208	ENSP00000283752:K260E;ENSP00000329498:K208E	ENSP00000283752:K260E	K	-	1	0	SERPINB3	59474266	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	-0.501000	0.06398	-2.586000	0.00459	0.369000	0.22263	AAA	NOVEL	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133791.1	3	14.442272	KEEP	1	0	0	48	1510	TT	1	1	0		-	49	60	1808	0	0	143.37151	290	60	10471	471	ENST00000283752.5	0.144543	1
SERPINB2	5055	__UNKNOWN__	__UNKNOWN__	18	61558595	61558595	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr18:61558595C>A	ENST00000299502.4	+	2	71				SERPINB2_ENST00000457692.1_Intron	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	NA		NA			blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	GCAGCCTGTCCTACTGTTGCT	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632	5055		Serine (or cysteine) peptidase inhibitors	8584	protein-coding gene	gene with protein product		173390	serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2	PLANH2, PAI2	NA	24172014	Standard	NM_002575	NM_002575	NA	Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.-9-75C>A	chr18.hg19:g.61558595C>A		NA	Q96E96	hg19	CCDS11989.1	0.02	26.668004	GTCxTAC	COVERED																																																																																			NOVEL	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000134009.1	4	24.680493	KEEP	0	0	0	82	2912	CC	1	1	0		+	141	60	5185	0	0	448.800849	417	60	15405	800	ENST00000299502.4	0.252688	1
HMHA1	23526	__UNKNOWN__	__UNKNOWN__	19	1073329	1073329	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:1073329C>T	ENST00000586866.1	+	3	652				HMHA1_ENST00000536472.1_Intron|HMHA1_ENST00000543365.1_Intron|HMHA1_ENST00000539243.2_Intron|HMHA1_ENST00000590214.1_Intron|HMHA1_ENST00000313093.2_Intron			Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCTCTCTGCCTAgaagggca	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	32	32	NA		NA	NA	19		NA											NA				1073329		2202	4300	6502	SO:0001627	intron_variant			D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448	23526		Rho GTPase activating proteins	17102	protein-coding gene	gene with protein product		601155			NA	9820596, 9039502	Standard		NM_012292	NA	Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000586866.1:c.577+38C>T	chr19.hg19:g.1073329C>T		NA	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	hg19		0.02	4.463206	TGCxTAG	COVERED																																																																																			NOVEL	HMHA1-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000458031.2	1	11.738668	KEEP	0	0	0	39	1410	CC	1	0.999984	0		+	5	60	189	0	0	12.579458	99	60	3658	185	ENST00000586866.1	0.048077	0.999984
MUM1	84939	__UNKNOWN__	__UNKNOWN__	19	1358631	1358631	__UNKNOWN__	Intron	SNP	G	G	A	rs376184873	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:1358631G>A	ENST00000415183.3	+	3	243				MUM1_ENST00000344663.3_Intron|MUM1_ENST00000311401.5_5'UTR|MUM1_ENST00000591806.1_Intron			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	NA		NA			chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AAATGGATCCGCTTTCTTAAA	0.483	NA	NA											G|||	3	0.000599042	0	0	5008	,	,	NA	19266	0.003	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953	84939			29641	protein-coding gene	gene with protein product		NA			NA	11042152, 7644523	Standard	NM_032853	NM_032853	NA	Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.217+168G>A	chr19.hg19:g.1358631G>A		NA	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	hg19		0.02	9.462281	TCCxCTT	COVERED																																																																																			NOVEL	MUM1-016	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000449510.1	5	30.42945	KEEP	0	1	16	107	3685	GG	1	1	0		+	62	60	2193	0	0	189.602451	176	60	6219	450	ENST00000415183.3	0.260504	1
ABHD17A	81926	__UNKNOWN__	__UNKNOWN__	19	1880087	1880087	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:1880087A>G	ENST00000292577.7	-	3	793	c.360T>C	c.(358-360)aaT>aaC	p.N120N	ABHD17A_ENST00000250974.9_Silent_p.N171N|ABHD17A_ENST00000590661.1_Intron	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	120		NA				extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)				NA						GGTCCACGGCATTGCCGTGCG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													45	50	48	NA		NA	NA	19		NA											NA				1880087		2201	4299	6500	SO:0001819	synonymous_variant			BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968	81926		Abhydrolase domain containing	28756	protein-coding gene	gene with protein product		NA	chromosome 19 open reading frame 27, family with sequence similarity 108, member A1	C19orf27, FAM108A1	NA	14702039	Standard	NM_031213	NM_031213	NA	Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.360T>C	chr19.hg19:g.1880087A>G		NA	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	hg19	CCDS45902.1	0.02	2.009655	GGCxTTG	COVERED																																																																																			NOVEL	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415556.2	1	9.022772	KEEP	5	0	0	30	877	AA	0.999997	0.994419	0		-	7	40	260	0	0	19.651334	59	60	1998	130	ENST00000292577.7	0.106061	0.994422
TMPRSS9	360200	__UNKNOWN__	__UNKNOWN__	19	2413752	2413752	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:2413752G>A	ENST00000332578.3	+	9	1207	c.1207G>A	c.(1207-1209)Gct>Act	p.A403T		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	403	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTTCTTTCTGGCTGGCATCGT	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	80	77	NA		NA	NA	19		NA											NA				2413752		2203	4300	6503	SO:0001583	missense			AJ488946	CCDS12088.1	19p13.3	2010-04-13					360200		Serine peptidases / Transmembrane	30079	protein-coding gene	gene with protein product	polyserase 1	610477			NA	12886014	Standard	NM_182973	NM_182973	NA	Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1207G>A	chr19.hg19:g.2413752G>A	ENSP00000330264:p.Ala403Thr	NA	Q6ZND6|Q7Z411	hg19	CCDS12088.1	0.02	3.922187	CTGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669400	0.47677	.	.	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88586	-2.4	4.08	1.86	0.25419	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.285134	0.24504	N	0.037947	D	0.88905	0.6564	L	0.28458	0.855	0.42564	D	0.993154	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.982	D	0.86326	0.1695	10	0.66056	D	0.02	.	7.7318	0.28791	0.0945:0.165:0.7406:0.0	.	403;437	Q7Z410;E7EMP4	TMPS9_HUMAN;.	T	437;403	ENSP00000330264:A403T	ENSP00000330264:A403T	A	+	1	0	TMPRSS9	2364752	1.000000	0.71417	0.236000	0.24074	0.015000	0.08874	6.548000	0.73896	0.203000	0.20529	0.555000	0.69702	GCT	NOVEL	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451330.3	2	17.089062	KEEP	0	0	0	57	1902	GG	1	1	0		+	17	60	566	0	0	42.197159	125	70	4404	245	ENST00000332578.3	0.119718	1
SAFB	6294	__UNKNOWN__	__UNKNOWN__	19	5661746	5661746	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:5661746C>T	ENST00000588852.1	+	15	2133	c.2080C>T	c.(2080-2082)Ctg>Ttg	p.L694L	SAFB_ENST00000433404.1_Silent_p.L524L|SAFB_ENST00000592224.1_Silent_p.L693L|SAFB_ENST00000454510.1_Silent_p.L625L|SAFB_ENST00000538656.1_Silent_p.L536L|SAFB_ENST00000292123.5_Silent_p.L694L			Q15424	SAFB1_HUMAN	scaffold attachment factor B	694	Arg-rich.|Glu-rich.|Interaction with POLR2A.|Interaction with SAFB2.	NA			chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		GCGCGAGGAGCTGAGGCGCCA	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(88;338 1345 6184 8214 20897)					NA		NA				0													8	9	9	NA		NA	NA	19		NA											NA				5661746		2136	4188	6324	SO:0001819	synonymous_variant			L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633	6294		RNA binding motif (RRM) containing	10520	protein-coding gene	gene with protein product	Hsp27 ERE-TATA binding protein	602895			NA	9605873, 8600450	Standard		NM_002967	NA	Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000588852.1:c.2080C>T	chr19.hg19:g.5661746C>T		NA	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	hg19	CCDS59339.1	0.02	8.316575	GAGxTGA	COVERED																																																																																			NOVEL	SAFB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451645.1	3	33.70256	KEEP	0	0	0	112	3864	CC	1	1	0		+	41	60	1374	0	0	111.055587	179	60	6499	390	ENST00000588852.1	0.186364	1
HSD11B1L	374875	__UNKNOWN__	__UNKNOWN__	19	5687676	5687676	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:5687676T>A	ENST00000581521.1	+	9	1140	c.665T>A	c.(664-666)gTc>gAc	p.V222D	HSD11B1L_ENST00000411793.2_Missense_Mutation_p.V88D|HSD11B1L_ENST00000301382.4_Missense_Mutation_p.V141D|HSD11B1L_ENST00000423665.2_Missense_Mutation_p.V222D|RPL36_ENST00000582380.2_Intron|HSD11B1L_ENST00000577917.1_Missense_Mutation_p.V141D|RPL36_ENST00000577222.1_Intron|HSD11B1L_ENST00000342970.2_Missense_Mutation_p.V135D|HSD11B1L_ENST00000581893.1_Missense_Mutation_p.V88D|HSD11B1L_ENST00000583928.1_Missense_Mutation_p.V88D|HSD11B1L_ENST00000339423.2_Missense_Mutation_p.V222D|RPL36_ENST00000579649.1_Intron|HSD11B1L_ENST00000581773.1_Missense_Mutation_p.V222D			Q7Z5J1	DHI1L_HUMAN	hydroxysteroid (11-beta) dehydrogenase 1-like	222		NA				extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)				NA						GCCGAGGCAGTCAGGTGAGGC	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													7	9	8	NA		NA	NA	19		NA											NA				5687676		2143	4207	6350	SO:0001583	missense			AY268353	CCDS12144.1, CCDS12145.1, CCDS12146.1, CCDS45931.1, CCDS45932.1, CCDS58641.1, CCDS58642.1, CCDS74266.1	19p13.3	2011-09-20				ENSG00000167733	374875	1.1.1.-	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	30419	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase 10, short chain dehydrogenase/reductase family 26C, member 2	NA			NA	12477932	Standard	NM_198706	NM_001267868	NA	Approved	SCDR10, SDR26C2	uc010dug.4	Q7Z5J1		ENST00000581521.1:c.665T>A	chr19.hg19:g.5687676T>A	ENSP00000463794:p.Val222Asp	NA	Q05D45|Q52LF4|Q7Z5I9|Q7Z5J0|Q7Z5P5|Q7Z5P6|Q7Z5P7|Q7Z5P8	hg19	CCDS12145.1	0.02	2.050889	CAGxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991746	0.54041	.	.	ENSG00000167733	ENST00000411793;ENST00000301382;ENST00000423665;ENST00000342970;ENST00000339423	D;T;D;T;T	0.88201	-1.66;0.71;-2.35;0.71;0.71	2.78	1.55	0.23275	.	0.275476	0.28718	U	0.014376	D	0.85128	0.5626	L	0.27053	0.805	0.35500	D	0.799731	D;D;D;D;D;D	0.71674	0.996;0.984;0.998;0.958;0.99;0.996	D;B;D;P;P;P	0.66497	0.944;0.388;0.91;0.658;0.537;0.806	T	0.82192	-0.0579	10	0.20519	T	0.43	.	2.3369	0.04250	0.0:0.2291:0.3004:0.4705	.	135;88;141;222;141;222	Q7Z5J1-5;Q7Z5J1-7;Q7Z5J1-6;Q7Z5J1-2;Q7Z5J1-3;Q7Z5J1	.;.;.;.;.;DHI1L_HUMAN	D	88;141;222;135;222	ENSP00000398955:V88D;ENSP00000301382:V141D;ENSP00000407154:V222D;ENSP00000343451:V135D;ENSP00000340436:V222D	ENSP00000301382:V141D	V	+	2	0	HSD11B1L	5638676	0.996000	0.38824	0.782000	0.31804	0.591000	0.36615	2.649000	0.46656	1.228000	0.43614	0.454000	0.30748	GTC	NOVEL	HSD11B1L-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442581.1	2	22.264815	KEEP	0	0	0	74	2266	TT	1	0.999559	0		+	39	60	1336	0	0	127.27922	44	60	1488	210	ENST00000581521.1	0.46988	0.999559
LONP1	9361	__UNKNOWN__	__UNKNOWN__	19	5692085	5692085	__UNKNOWN__	Silent	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:5692085G>T	ENST00000360614.3	-	18	2995	c.2838C>A	c.(2836-2838)gcC>gcA	p.A946A	LONP1_ENST00000540670.2_Silent_p.A750A|LONP1_ENST00000593119.1_Silent_p.A882A|LONP1_ENST00000585374.1_Silent_p.A832A|LONP1_ENST00000590729.1_Silent_p.A816A	NM_004793.2	NP_004784.2			lon peptidase 1, mitochondrial	NA		NA								breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CGTCCGGGAAGGCGATGTCGA	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													127	107	113	NA		NA	NA	19		NA											NA				5692085		2203	4300	6503	SO:0001819	synonymous_variant			U02389	CCDS12148.1, CCDS62507.1, CCDS62508.1	19p13.2	2014-01-28	2006-10-20	2006-10-20	ENSG00000196365	ENSG00000196365	9361		ATPases / AAA-type, Serine peptidases / Serine peptidases	9479	protein-coding gene	gene with protein product		605490	protease, serine, 15	PRSS15	NA	8248235, 8119403	Standard	NM_004793	NM_004793	NA	Approved	LonHS, hLON, PIM1	uc002mcx.4	P36776		ENST00000360614.3:c.2838C>A	chr19.hg19:g.5692085G>T		NA		hg19	CCDS12148.1	0.02	11.664075	GAAxGCG	COVERED																																																																																			NOVEL	LONP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451662.1	2	58.208852	KEEP	0	1	30	204	7187	GG	1	1	0		-	37	60	1293	0	0	99.496327	243	60	8970	668	ENST00000360614.3	0.132143	1
LONP1	9361	__UNKNOWN__	__UNKNOWN__	19	5712033	5712033	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:5712033G>T	ENST00000360614.3	-	4	796				LONP1_ENST00000540670.2_Intron|LONP1_ENST00000593119.1_Intron|LONP1_ENST00000585374.1_Intron|LONP1_ENST00000590729.1_Intron	NM_004793.2	NP_004784.2			lon peptidase 1, mitochondrial	NA		NA								breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GAGCAAGGCAGGTGTGAATCA	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													12	13	13	NA		NA	NA	19		NA											NA				5712033		2196	4290	6486	SO:0001627	intron_variant			U02389	CCDS12148.1, CCDS62507.1, CCDS62508.1	19p13.2	2014-01-28	2006-10-20	2006-10-20	ENSG00000196365	ENSG00000196365	9361		ATPases / AAA-type, Serine peptidases / Serine peptidases	9479	protein-coding gene	gene with protein product		605490	protease, serine, 15	PRSS15	NA	8248235, 8119403	Standard	NM_004793	NM_004793	NA	Approved	LonHS, hLON, PIM1	uc002mcx.4	P36776		ENST00000360614.3:c.639-20C>A	chr19.hg19:g.5712033G>T		NA		hg19	CCDS12148.1	0.02	8.538518	GCAxGTG	COVERED																																																																																			NOVEL	LONP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451662.1	3	25.281352	KEEP	0	0	0	84	2934	GG	1	1	0		-	14	60	489	0	0	32.497341	227	60	8312	426	ENST00000360614.3	0.058091	1
KHSRP	8570	__UNKNOWN__	__UNKNOWN__	19	6418750	6418750	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:6418750A>G	ENST00000398148.3	-	8	835	c.743T>C	c.(742-744)gTc>gCc	p.V248A		NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	248	Gly-rich.|KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.	NA			gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of miRNA metabolic process (GO:2000628)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|transcription, DNA-templated (GO:0006351)	cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CTTGCCAATGACCAGGCCGGC	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(55;593 1006 2067 9135 22980)					NA		NA				0													48	55	53	NA		NA	NA	19		NA											NA				6418750		2087	4212	6299	SO:0001583	missense			U94832	CCDS45936.1	19p13.3	2010-11-23	2008-02-04		ENSG00000088247	ENSG00000088247	8570			6316	protein-coding gene	gene with protein product	FUSE binding protein 2	603445			NA	9136930, 8940189	Standard		NM_003685	NA	Approved	KSRP, FBP2, FUBP2	uc002mer.4	Q92945		ENST00000398148.3:c.743T>C	chr19.hg19:g.6418750A>G	ENSP00000381216:p.Val248Ala	NA	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	hg19	CCDS45936.1	0.02	4.681685	ATGxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	17.27	3.346318	0.61073	.	.	ENSG00000088247	ENST00000398148;ENST00000201886;ENST00000424942	T	0.40225	1.04	5.01	5.01	0.66863	K Homology (1);K Homology, type 1, subgroup (1);K Homology, type 1 (1);	0.126265	0.51477	D	0.000088	T	0.68118	0.2966	M	0.87180	2.865	0.50467	D	0.999878	P	0.49185	0.92	D	0.68192	0.956	T	0.74386	-0.3682	10	0.87932	D	0	.	13.7366	0.62821	1.0:0.0:0.0:0.0	.	248	Q92945	FUBP2_HUMAN	A	248;248;204	ENSP00000381216:V248A	ENSP00000201886:V248A	V	-	2	0	KHSRP	6369750	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	9.047000	0.93823	1.889000	0.54706	0.533000	0.62120	GTC	NOVEL	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453305.1	3	12.447641	KEEP	0	2	12	46	1476	AA	1	0.999973	0		-	21	60	726	0	0	60.1324	81	60	2638	191	ENST00000398148.3	0.205882	0.999973
DENND1C	79958	__UNKNOWN__	__UNKNOWN__	19	6471327	6471327	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:6471327G>C	ENST00000381480.2	-	17	1362				DENND1C_ENST00000543576.1_Intron	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	NA		NA			positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CTGGGGTAAGGAGAGAGTGTG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	47	48	NA		NA	NA	19		NA											NA				6471327		1949	4143	6092	SO:0001627	intron_variant			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744	79958		DENN/MADD domain containing	26225	protein-coding gene	gene with protein product		613634	family with sequence similarity 31, member C	FAM31C	NA	12477932	Standard	NM_024898	XM_005259646	NA	Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1250-11C>G	chr19.hg19:g.6471327G>C		NA	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	hg19	CCDS45938.1	0.02	4.896171	AAGxAGA	COVERED																																																																																			NOVEL	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453332.2	0	5.65538	KEEP	0	0	0	19	603	GG	0.99986	0.999859	0		-	38	60	1403	0	0	125.417391	85	60	3039	158	ENST00000381480.2	0.308943	0.999999
MCOLN1	57192	__UNKNOWN__	__UNKNOWN__	19	7592443	7592443	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:7592443G>A	ENST00000264079.6	+	5	734	c.609G>A	c.(607-609)ccG>ccA	p.P203P		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	203		NA		P -> S (in Ref. 1; CAC08215). {ECO:0000305}.	calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GGCCCCCTCCGCCCCCCAGCG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	102	95	NA		NA	NA	19		NA											NA				7592443		2203	4300	6503	SO:0001819	synonymous_variant			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674	57192		Voltage-gated ion channels / Transient receptor potential cation channels	13356	protein-coding gene	gene with protein product		605248			NA	16382100	Standard	NM_020533	NM_020533	NA	Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.609G>A	chr19.hg19:g.7592443G>A		NA	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	hg19	CCDS12180.1	0.02	9.227845	TCCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.381	1.072896	0.20147	.	.	ENSG00000090674	ENST00000394321	.	.	.	4.51	-6.83	0.01693	.	.	.	.	.	T	0.22282	0.0537	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.30327	-0.9982	7	0.87932	D	0	.	1.2942	0.02066	0.204:0.3665:0.1934:0.2361	.	90	Q9GZU1-2	.	H	90	.	ENSP00000377856:R90H	R	+	2	0	MCOLN1	7498443	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.816000	0.04477	-1.258000	0.02471	-0.218000	0.12543	CGC	NOVEL	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458974.2	3	23.693289	KEEP	0	1	28	89	2833	GG	1	1	0		+	75	60	2425	0	0	219.194768	133	60	4466	396	ENST00000264079.6	0.360577	1
C19orf59	0	__UNKNOWN__	__UNKNOWN__	19	7743288	7743288	__UNKNOWN__	Splice_Site	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:7743288T>A	ENST00000333598.3	+	4	827		c.e4+2		C19orf59_ENST00000597445.1_Splice_Site	NM_174918.2	NP_777578.2	Q8IX19	MCEM1_HUMAN		NA		NA				integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)|stomach(1)	5						TTTGGAATGGTGAGCGGAGGG	0.572	NA	NA									OREG0025208	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													157	157	157	NA		NA	NA	19		NA											NA				7743288		2203	4300	6503	SO:0001630	splice_region_variant											NA			NA				NA			NA					NA						ENST00000333598.3:c.373+2T>A	chr19.hg19:g.7743288T>A		644	Q8IX20	hg19	CCDS12183.1	0.02	4.660802	TGGxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	12.18	1.859295	0.32884	.	.	ENSG00000183019	ENST00000333598	.	.	.	3.34	3.34	0.38264	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3869	0.32505	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	C19orf59	7649288	1.000000	0.71417	0.934000	0.37439	0.086000	0.17979	2.935000	0.48963	1.753000	0.51906	0.533000	0.62120	.	NOVEL	C19orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000461248.1	2	5.115131	KEEP	0	0	0	17	531	TT	0.999366	0.999366	0	Intron	+	44	60	1652	0	0	150.608302	83	60	2902	173	ENST00000333598.3	0.346457	1
ICAM3	3385	__UNKNOWN__	__UNKNOWN__	19	10449357	10449357	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:10449357C>T	ENST00000160262.5	-	2	552		c.e2+1		ICAM3_ENST00000589261.1_Splice_Site	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	NA		NA			extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			CGTCGACTCACTGTACACGGT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													76	59	65	NA		NA	NA	19		NA											NA				10449357		2203	4300	6503	SO:0001630	splice_region_variant				CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662	3385		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	5346	protein-coding gene	gene with protein product		146631			NA	1448174	Standard		NM_002162	NA	Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.343+1G>A	chr19.hg19:g.10449357C>T		NA	Q6PD68	hg19	CCDS12235.1	0.02	2.208559	TCAxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.48	1.950963	0.34471	.	.	ENSG00000076662	ENST00000160262	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4418	0.75190	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ICAM3	10310357	0.987000	0.35691	0.888000	0.34837	0.181000	0.23173	3.563000	0.53784	2.720000	0.93068	0.655000	0.94253	.	NOVEL	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451234.1	1	3.009915	KEEP	0	0	0	10	361	CC	0.992708	0.987171	0	Intron	-	22	60	791	0	0	71.351634	44	60	1668	88	ENST00000160262.5	0.333333	0.994422
ZNF433	163059	__UNKNOWN__	__UNKNOWN__	19	12125942	12125942	__UNKNOWN__	Silent	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:12125942A>G	ENST00000344980.6	-	4	1910	c.1740T>C	c.(1738-1740)caT>caC	p.H580H	CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000406892.2_RNA|ZNF433_ENST00000419886.2_Silent_p.H545H	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	580		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						GAGTCCTTCCATGCATTTGAA	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													109	112	111	NA		NA	NA	19		NA											NA				12125942		2202	4298	6500	SO:0001819	synonymous_variant			AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647	163059		Zinc fingers, C2H2-type, -	20811	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152602	NM_001080411	NA	Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.1740T>C	chr19.hg19:g.12125942A>G		NA	Q86VX3	hg19	CCDS45983.1	0.02	14.626065	TCCxTGC	COVERED																																																																																			NOVEL	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403716.1	3	39.112339	KEEP	0	0	0	130	3982	AA	1	1	0		-	56	60	1994	0	0	161.765755	263	60	9818	562	ENST00000344980.6	0.175549	1
ZNF490	57474	__UNKNOWN__	__UNKNOWN__	19	12720034	12720034	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:12720034G>C	ENST00000311437.6	-	2	240				ZNF490_ENST00000465656.1_Intron	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						GAAACAAGAGGATGCATTTTG	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													178	127	144	NA		NA	NA	19		NA											NA				12720034		2203	4300	6503	SO:0001627	intron_variant			AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033	57474		Zinc fingers, C2H2-type, -	23705	protein-coding gene	gene with protein product		NA			NA		Standard	NM_020714	NM_020714	NA	Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.118-18C>G	chr19.hg19:g.12720034G>C		NA		hg19	CCDS12272.1	0.02	-0.307031	GAGxATG	COVERED																																																																																			NOVEL	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344073.1	0	5.710419	KEEP	0	0	0	19	608	GG	0.99986	0.800133	0		-	13	60	496	0	0	45.775678	22	60	810	58	ENST00000311437.6	0.371429	0.800245
ILVBL	10994	__UNKNOWN__	__UNKNOWN__	19	15230777	15230777	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:15230777A>C	ENST00000263383.3	-	7	956				ILVBL_ENST00000534378.1_Intron|ILVBL_ENST00000531635.1_Intron	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	NA		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						TCAGACACAAAAGAGAGGCAA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													26	23	24	NA		NA	NA	19		NA											NA				15230777		1923	3633	5556	SO:0001627	intron_variant			U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135	10994			6041	protein-coding gene	gene with protein product	acetolactate synthase homolog	605770			NA	8954801	Standard	NM_006844	NM_006844	NA	Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.816+15T>G	chr19.hg19:g.15230777A>C		NA	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	hg19	CCDS12325.1	0.02	2.189014	CAAxAGA	COVERED																																																																																			NOVEL	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385439.1	1	5.717878	KEEP	0	0	0	19	620	AA	0.99986	0.999721	0		-	38	60	1406	0	0	131.875826	53	60	1903	144	ENST00000263383.3	0.417582	0.999862
PGLYRP2	114770	__UNKNOWN__	__UNKNOWN__	19	15590124	15590124	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:15590124G>A	ENST00000340880.4	-	1	539	c.59C>T	c.(58-60)aCa>aTa	p.T20I	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.T20I	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	20		NA			defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						TGACTCACCTGTCCCTGGGTC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													110	86	94	NA		NA	NA	19		NA											NA				15590124		2203	4300	6503	SO:0001583	missense			AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	114770	3.5.1.28		30013	protein-coding gene	gene with protein product	peptidoglycan recognition protein L precursor, peptidoglycan recognition protein-like, N-acetylmuramoyl-L-alanine amidase	608199			NA	11461926, 12669421, 14506276	Standard	NM_052890	NM_052890	NA	Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.59C>T	chr19.hg19:g.15590124G>A	ENSP00000345968:p.Thr20Ile	NA	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	hg19	CCDS12330.2	0.02	8.959218	CCTxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.00	2.106155	0.37145	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.06218	3.4;3.33	4.76	3.7	0.42460	.	0.305630	0.29233	N	0.012756	T	0.13670	0.0331	M	0.71581	2.175	0.23899	N	0.996523	D;P	0.55172	0.97;0.868	P;B	0.49708	0.62;0.383	T	0.04495	-1.0947	10	0.66056	D	0.02	-2.8695	11.2257	0.48882	0.0:0.1844:0.8156:0.0	.	20;20	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	I	20	ENSP00000345968:T20I;ENSP00000292609:T20I	ENSP00000292609:T20I	T	-	2	0	PGLYRP2	15451124	0.982000	0.34865	0.891000	0.34965	0.191000	0.23601	1.522000	0.35921	1.337000	0.45525	0.655000	0.94253	ACA	NOVEL	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319626.1	1	7.223242	KEEP	0	0	0	24	852	GG	0.999909	0.999909	0		-	60	60	2104	0	0	182.093241	167	60	6317	297	ENST00000340880.4	0.264317	1
AP1M1	8907	__UNKNOWN__	__UNKNOWN__	19	16344428	16344428	__UNKNOWN__	Splice_Site	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:16344428A>G	ENST00000429941.2	+	9	1129	c.1013A>G	c.(1012-1014)cAg>cGg	p.Q338R	AP1M1_ENST00000291439.3_Splice_Site_p.Q391R|AP1M1_ENST00000590756.1_Splice_Site_p.Q319R|AP1M1_ENST00000541844.1_Splice_Site_p.Q319R|AP1M1_ENST00000444449.2_Splice_Site_p.Q403R			Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	391	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						TCCGGCATCCAGGTACGTAAG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													53	47	49	NA		NA	NA	19		NA											NA				16344428		2203	4300	6503	SO:0001630	splice_region_variant				CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23					8907			13667	protein-coding gene	gene with protein product		603535			NA	9653655, 17988225	Standard	NM_032493	NM_032493	NA	Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000429941.2:c.1014+1A>G	chr19.hg19:g.16344428A>G		NA	Q4TTY5	hg19		0.02	7.561086	TCCxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	A	16.90	3.249128	0.59103	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844;ENST00000429941	T;T;T;T	0.19669	2.13;2.13;2.13;2.16	3.74	3.74	0.42951	Clathrin adaptor, mu subunit, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.43055	0.1230	M	0.73372	2.23	0.80722	D	1	B;D;D	0.89917	0.359;1.0;1.0	B;D;D	0.91635	0.261;0.999;0.999	T	0.34925	-0.9809	10	0.48119	T	0.1	-37.6109	12.0827	0.53680	1.0:0.0:0.0:0.0	.	338;403;391	E7ENJ6;Q4TTY5;Q9BXS5	.;.;AP1M1_HUMAN	R	403;391;319;338	ENSP00000388996:Q403R;ENSP00000291439:Q391R;ENSP00000445682:Q319R;ENSP00000411498:Q338R	ENSP00000291439:Q391R	Q	+	2	0	AP1M1	16205428	1.000000	0.71417	1.000000	0.80357	0.484000	0.33280	8.855000	0.92236	1.699000	0.51192	0.460000	0.39030	CAG	NOVEL	AP1M1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000460495.1	3	22.869007	KEEP	0	0	0	76	2410	AA	1	1	0	Missense_Mutation	+	7	60	248	0	0	14.283788	243	60	9075	443	ENST00000429941.2	0.028	1
CTD-3222D19.2	0	__UNKNOWN__	__UNKNOWN__	19	16611868	16611868	__UNKNOWN__	Intron	SNP	C	C	T	rs200336566		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:16611868C>T	ENST00000409035.1	-	8	1924				C19orf44_ENST00000594035.1_Nonsense_Mutation_p.R89*|C19orf44_ENST00000221671.3_Nonsense_Mutation_p.R89*						NA		NA									NA						CTCCAGGATCCGAGCCAATGC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	111	107	NA		NA	NA	19		NA											NA				16611868		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409035.1:c.1282-5205G>A	chr19.hg19:g.16611868C>T		NA		hg19		0.02	14.985658	ATCxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.16	3.774132	0.69992	.	.	ENSG00000105072	ENST00000221671	.	.	.	5.11	0.36	0.16097	.	0.196265	0.35525	N	0.003148	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.5685	15.5164	0.75828	0.2745:0.7255:0.0:0.0	.	.	.	.	X	89	.	ENSP00000221671:R89X	R	+	1	2	C19orf44	16472868	0.193000	0.23313	0.001000	0.08648	0.006000	0.05464	0.415000	0.21181	-0.267000	0.09325	-0.262000	0.10625	CGA	NOVEL	CTD-3222D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000461092.1	2	28.816245	KEEP	0	0	0	96	3039	CC	1	1	0		-	41	60	1545	0	0	120.71916	282	60	9204	554	ENST00000409035.1	0.126935	1
CTD-3222D19.2	0	__UNKNOWN__	__UNKNOWN__	19	16617557	16617557	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:16617557T>C	ENST00000409035.1	-	8	1924				C19orf44_ENST00000594035.1_Missense_Mutation_p.V374A|C19orf44_ENST00000221671.3_Missense_Mutation_p.V374A						NA		NA									NA						GCTCCAGCTGTCAGTGAGAAC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	52	51	NA		NA	NA	19		NA											NA				16617557		2202	4300	6502	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409035.1:c.1282-10894A>G	chr19.hg19:g.16617557T>C		NA		hg19		0.02	2.522378	CTGxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	14.40	2.522994	0.44866	.	.	ENSG00000105072	ENST00000221671	.	.	.	4.18	1.99	0.26369	.	0.767287	0.11447	N	0.563163	T	0.46190	0.1380	M	0.67953	2.075	0.09310	N	1	P;P;D	0.54964	0.884;0.932;0.969	P;P;P	0.50934	0.503;0.558;0.654	T	0.33650	-0.9860	9	0.54805	T	0.06	-13.3703	3.997	0.09563	0.1893:0.1038:0.0:0.7069	.	374;47;374	Q9H6X5;B4DN63;Q9H6X5-2	CS044_HUMAN;.;.	A	374	.	ENSP00000221671:V374A	V	+	2	0	C19orf44	16478557	0.008000	0.16893	0.006000	0.13384	0.074000	0.17049	1.420000	0.34804	0.112000	0.17975	0.459000	0.35465	GTC	NOVEL	CTD-3222D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000461092.1	0	8.125366	KEEP	0	0	0	27	886	TT	0.999988	0.970808	0		-	4	60	144	0	0	10.152296	49	60	1770	114	ENST00000409035.1	0.075472	0.97082
MAST3	23031	__UNKNOWN__	__UNKNOWN__	19	18249809	18249809	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:18249809C>T	ENST00000262811.6	+	19	2008					NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	NA		NA					ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(6)|ovary(4)|pancreas(1)|stomach(1)	31						GCTGCATGTGCCTCTCCCTCC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													39	43	42	NA		NA	NA	19		NA											NA				18249809		2141	4249	6390	SO:0001627	intron_variant			AB011133	CCDS46014.1	19p13	2008-02-05				ENSG00000099308	23031			19036	protein-coding gene	gene with protein product		612258			NA		Standard	XM_038150	NM_015016	NA	Approved	KIAA0561	uc002nhz.4	O60307		ENST00000262811.6:c.2009-16C>T	chr19.hg19:g.18249809C>T		NA	Q7LDZ8|Q9UPI0	hg19	CCDS46014.1	0.02	7.959526	GTGxCTC	COVERED																																																																																			NOVEL	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466526.2	5	9.027932	KEEP	0	0	0	30	1025	CC	0.999997	0.999997	0		+	7	60	251	1	0	14.595565	242	60	8945	333	ENST00000262811.6	0.028112	1
PIK3R2	5296	__UNKNOWN__	__UNKNOWN__	19	18266954	18266954	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:18266954C>T	ENST00000593731.1	+	2	825	c.265C>T	c.(265-267)Cgc>Tgc	p.R89C	PIK3R2_ENST00000222254.8_Missense_Mutation_p.R89C			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	89		NA			blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	gcccggccctcgcccacgggg	0.746	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													4	5	5	NA		NA	NA	19		NA											NA				18266954		1967	3877	5844	SO:0001583	missense				CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647	5296		SH2 domain containing	8980	protein-coding gene	gene with protein product		603157			NA	1314371	Standard	NM_005027	NM_005027	NA	Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.265C>T	chr19.hg19:g.18266954C>T	ENSP00000471914:p.Arg89Cys	NA	Q5EAT5|Q9UPH9	hg19	CCDS12371.1	0.02	6.581359	CCTxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028682	0.54790	.	.	ENSG00000105647	ENST00000222254	T	0.07800	3.16	4.44	4.44	0.53790	.	0.065216	0.64402	D	0.000004	T	0.14614	0.0353	L	0.39898	1.24	0.50632	D	0.999887	D	0.76494	0.999	P	0.51806	0.68	T	0.01367	-1.1373	10	0.87932	D	0	-10.1184	16.4683	0.84092	0.0:1.0:0.0:0.0	.	89	O00459	P85B_HUMAN	C	89	ENSP00000222254:R89C	ENSP00000222254:R89C	R	+	1	0	PIK3R2	18127954	0.985000	0.35326	0.848000	0.33437	0.125000	0.20455	1.616000	0.36933	2.197000	0.70478	0.561000	0.74099	CGC	NOVEL	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000466386.2	0	47.230834	KEEP	0	0	0	157	4912	CC	1	1	0		+	45	70	1574	0	0	137.026754	119	60	3916	436	ENST00000593731.1	0.27439	1
MPV17L2	84769	__UNKNOWN__	__UNKNOWN__	19	18304034	18304034	__UNKNOWN__	5'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:18304034C>G	ENST00000599612.2	+	0	43					NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	NA		NA				integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						CAGTGACTCGCGACTGGTCGG	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858	84769			28177	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032683	NM_032683	NA	Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.-58C>G	chr19.hg19:g.18304034C>G		NA	Q96P34|Q96QA0|Q9BSG4	hg19	CCDS42522.1	0.02	-0.210516	TCGxGAC	COVERED																																																																																			NOVEL	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466294.2	1	5.712834	KEEP	0	0	0	19	610	CC	0.99986	0.522088	0		+	3	60	102	0	0	7.706012	21	60	710	60	ENST00000599612.2	0.125	0.522161
TMEM59L	25789	__UNKNOWN__	__UNKNOWN__	19	18729109	18729109	__UNKNOWN__	Intron	SNP	A	A	G	rs112435133		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:18729109A>G	ENST00000600490.1	+	7	967				TMEM59L_ENST00000262817.3_Intron			Q9UK28	TM59L_HUMAN	transmembrane protein 59-like	NA		NA				Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(2)	13						TGGGGGTGGGAGGGGGGTGGG	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF186264	CCDS12383.1	19p12	2008-02-05	2007-03-14	2007-03-14		ENSG00000105696	25789			13237	protein-coding gene	gene with protein product		NA	chromosome 19 open reading frame 4	C19orf4	NA	10527841	Standard		NM_012109	NA	Approved	BSMAP	uc002njy.4	Q9UK28		ENST00000600490.1:c.782+27A>G	chr19.hg19:g.18729109A>G		NA		hg19	CCDS12383.1	0.02	-0.355092	GGGxGGG	COVERED																																																																																			NOVEL	TMEM59L-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465143.2	1	3.619364	KEEP	0	1	5	14	355	AA	0.99649	0.885755	0		+	5	60	104	0	0	6.475254	34	60	947	72	ENST00000600490.1	0.128205	0.888875
MEF2BNB	729991	__UNKNOWN__	__UNKNOWN__	19	19303111	19303111	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:19303111C>T	ENST00000462790.3	-	0	287				MEF2BNB_ENST00000477565.3_5'UTR|MEF2B_ENST00000602424.2_5'UTR|MEF2BNB_ENST00000494489.2_Intron|RFXANK_ENST00000353145.1_5'UTR|RFXANK_ENST00000303088.4_5'UTR|RFXANK_ENST00000456252.3_5'UTR	NM_001145784.1	NP_001139256.1	Q96FH0	MF2NB_HUMAN	MEF2B neighbor	NA		NA			heart development (GO:0007507)						NA						GGGAAGGAGGCACACCCGGGG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS46025.1, CCDS54235.1	19p13.11	2011-04-19			ENSG00000254901	ENSG00000254901	729991			37247	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001145783	NA	Approved		uc002nlq.3	Q96FH0	OTTHUMG00000166546	ENST00000462790.3:c.-185G>A	chr19.hg19:g.19303111C>T		NA	B2RXF9|Q9BT01	hg19	CCDS46025.1	0.02	-0.385272	AGGxACA	COVERED																																																																																			NOVEL	MEF2BNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336091.4	1	9.310006	KEEP	0	0	0	31	987	CC	0.999997	0.918168	0		-	4	60	112	0	0	7.365188	40	60	1414	92	ENST00000462790.3	0.090909	0.918171
RFXANK	8625	__UNKNOWN__	__UNKNOWN__	19	19309406	19309406	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:19309406G>T	ENST00000303088.4	+	8	1038				RFXANK_ENST00000392324.4_Intron|RFXANK_ENST00000407360.3_Intron|RFXANK_ENST00000353145.1_Intron|RFXANK_ENST00000456252.3_Intron	NM_003721.2	NP_003712.1	O14593	RFXK_HUMAN	regulatory factor X-associated ankyrin-containing protein	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			NS(1)|breast(1)|endometrium(1)|lung(8)|ovary(2)|prostate(1)	14			Epithelial(12;0.00228)			gagagtacaaggCATTTTGAG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													56	56	56	NA		NA	NA	19		NA											NA				19309406		692	1591	2283	SO:0001627	intron_variant			AF094760	CCDS12395.1, CCDS12396.1, CCDS62611.1	19p12	2014-09-17			ENSG00000064490	ENSG00000064490	8625		Ankyrin repeat domain containing	9987	protein-coding gene	gene with protein product	ankyrin repeat-containing regulatory factor X-associated protein, regulatory factor X subunit B, RFX-Bdelta4, DNA-binding protein RFXANK	603200			NA	9806546, 10072068	Standard	NM_003721	NM_003721	NA	Approved	BLS, RFX-B, ANKRA1, F14150_1, MGC138628	uc002nls.3	O14593	OTTHUMG00000169224	ENST00000303088.4:c.565-60G>T	chr19.hg19:g.19309406G>T		NA	O95839|Q24JQ1|Q6FGA8	hg19	CCDS12395.1	0.02	9.366819	CAAxGCA	COVERED																																																																																			NOVEL	RFXANK-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402923.2	4	13.24345	KEEP	0	0	0	44	1600	GG	1	1	0		+	53	60	1932	0	0	162.525939	196	60	7262	361	ENST00000303088.4	0.212851	1
CILP2	148113	__UNKNOWN__	__UNKNOWN__	19	19656180	19656180	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:19656180G>T	ENST00000291495.5	+	8	2911	c.2826G>T	c.(2824-2826)aaG>aaT	p.K942N	CILP2_ENST00000586018.1_Missense_Mutation_p.K948N	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	942		NA				extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						GCTTCCTCAAGGTGAAGATCC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													22	20	21	NA		NA	NA	19		NA											NA				19656180		2202	4300	6502	SO:0001583	missense			AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161	148113		Immunoglobulin superfamily / Immunoglobulin-like domain containing	24213	protein-coding gene	gene with protein product		612419			NA	12477932	Standard	NM_153221	NM_153221	NA	Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.2826G>T	chr19.hg19:g.19656180G>T	ENSP00000291495:p.Lys942Asn	NA	Q6NV88|Q8N4A6|Q8WV21	hg19	CCDS12405.1	0.02	8.185431	CAAxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.29	3.082590	0.55861	.	.	ENSG00000160161	ENST00000291495	T	0.10477	2.87	5.79	1.26	0.21427	.	0.048642	0.85682	D	0.000000	T	0.25827	0.0629	M	0.69358	2.11	0.41786	D	0.98984	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.01143	-1.1438	10	0.87932	D	0	-40.221	8.4499	0.32864	0.3882:0.0:0.6118:0.0	.	942;942	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	N	942	ENSP00000291495:K942N	ENSP00000291495:K942N	K	+	3	2	CILP2	19517180	0.998000	0.40836	0.994000	0.49952	0.750000	0.42670	0.406000	0.21032	0.389000	0.25086	0.555000	0.69702	AAG	NOVEL	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459738.3	1	17.755652	KEEP	0	0	0	59	2022	GG	1	1	0		+	9	60	318	0	0	19.327134	238	60	8730	357	ENST00000291495.5	0.036437	1
ZNF492	57615	__UNKNOWN__	__UNKNOWN__	19	22846680	22846680	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs12975335	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:22846680G>C	ENST00000456783.2	+	4	453	c.209G>C	c.(208-210)aGa>aCa	p.R70T		NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	70		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ATACTGAGAAGATATAAAAAA	0.313	NA	NA											N|||	414	0.0826677	0.1815	0.0447	5008	,	,	NA	12389	0.0585	NA	0.0487	False	NA	,,,	NA	NA	NA	2504	0.0358	NA	NA	NA						NA		NA				0													36	43	41	NA		NA	NA	19		NA											NA				22846680		1758	4091	5849	SO:0001583	missense			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676	57615		Zinc fingers, C2H2-type	23707	protein-coding gene	gene with protein product		NA	zinc finger protein 115 (Y20)	ZNF115	NA	10819331	Standard	NM_020855	NM_020855	NA	Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.209G>C	chr19.hg19:g.22846680G>C	ENSP00000413660:p.Arg70Thr	NA	Q08EI7|Q08EI8	hg19	CCDS46032.1	0.02	4.843203	GAAxATA	COVERED	151	0.06913919413919414	63	0.12804878048780488	16	0.04419889502762431	32	0.055944055944055944	40	0.052770448548812667	.	2.536	-0.307310	0.05458	.	.	ENSG00000229676	ENST00000456783	T	0.08102	3.13	1.17	-0.293	0.12835	.	.	.	.	.	T	0.00073	0.0002	L	0.60012	1.86	0.09310	N	0.999994	B	0.14012	0.009	B	0.15484	0.013	T	0.38178	-0.9673	9	0.45353	T	0.12	.	3.706	0.08401	0.2972:0.0:0.7028:0.0	rs12975335	70	Q9P255	ZN492_HUMAN	T	70	ENSP00000413660:R70T	ENSP00000413660:R70T	R	+	2	0	ZNF492	22638520	0.038000	0.19896	0.053000	0.19242	0.132000	0.20833	0.691000	0.25467	-0.205000	0.10219	0.460000	0.39030	AGA	NOVEL	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464581.1	2	4.213617	KEEP	5	0	0	14	493	GG	0.99649	0.99649	0		+	13	40	459	0	0	33.941787	113	60	4296	179	ENST00000456783.2	0.103175	1
ZNF492	57615	__UNKNOWN__	__UNKNOWN__	19	22846697	22846697	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs62118831	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:22846697T>C	ENST00000456783.2	+	4	470	c.226T>C	c.(226-228)Tgt>Cgt	p.C76R		NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	76		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				AAAATGTGGATGTGAAAATTT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													42	51	48	NA		NA	NA	19		NA											NA				22846697		1869	4136	6005	SO:0001583	missense			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676	57615		Zinc fingers, C2H2-type	23707	protein-coding gene	gene with protein product		NA	zinc finger protein 115 (Y20)	ZNF115	NA	10819331	Standard	NM_020855	NM_020855	NA	Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.226T>C	chr19.hg19:g.22846697T>C	ENSP00000413660:p.Cys76Arg	NA	Q08EI7|Q08EI8	hg19	CCDS46032.1	0.02	3.871108	GGAxGTG	COVERED	142	0.06501831501831502	55	0.11178861788617886	18	0.049723756906077346	31	0.05419580419580419	38	0.05013192612137203	.	1.077	-0.668120	0.03428	.	.	ENSG00000229676	ENST00000456783	T	0.07444	3.19	0.769	-0.852	0.10713	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	8	0.56958	D	0.05	.	4.6246	0.12472	0.0:0.2798:0.0:0.7202	rs62118831	76	Q9P255	ZN492_HUMAN	R	76	ENSP00000413660:C76R	ENSP00000413660:C76R	C	+	1	0	ZNF492	22638537	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.635000	0.02018	-1.043000	0.03258	-1.309000	0.01313	TGT	NOVEL	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464581.1	2	5.716527	KEEP	4	0	0	19	579	TT	0.99986	0.999859	0		+	10	40	352	0	0	24.880409	114	60	4200	181	ENST00000456783.2	0.080645	1
TSHZ3	57616	__UNKNOWN__	__UNKNOWN__	19	31766462	31766462	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:31766462A>T	ENST00000240587.4	-	0	4564					NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	NA		NA			in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					AATAGTTCTGATGCCTGCCAG	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297	57616		Teashirt zinc fingers, Homeoboxes / ZF class, Zinc fingers, C2H2-type	30700	protein-coding gene	gene with protein product	teashirt 3	614119	zinc finger protein 537, teashirt family zinc finger 3	ZNF537	NA		Standard	NM_020856	NM_020856	NA	Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.*991T>A	chr19.hg19:g.31766462A>T		NA	Q9H0G6|Q9P254	hg19	CCDS12421.2	0.02	4.241	CTGxTGC	COVERED																																																																																			NOVEL	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316743.2	2	5.650312	KEEP	0	1	29	29	928	AA	0.999997	0.999995	0		-	17	60	607	0	0	47.689778	101	60	3603	188	ENST00000240587.4	0.144068	0.999998
AC011525.2	0	__UNKNOWN__	__UNKNOWN__	19	32083761	32083761	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:32083761A>G	ENST00000562167.1	-	0	860				AC011525.4_ENST00000590611.2_lincRNA						NA		NA									NA						ACCAGCCCACATGTCCATGCA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000562167.1:	chr19.hg19:g.32083761A>G		NA		hg19		0.02	20.228592	CACxTGT	COVERED																																																																																			NOVEL	AC011525.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000431043.3	5	18.050257	KEEP	0	0	0	60	1790	AA	1	1	0		-	61	60	2216	0	0	176.465088	340	60	12259	542	ENST00000562167.1	0.15212	1
AC011525.2	0	__UNKNOWN__	__UNKNOWN__	19	32083780	32083780	__UNKNOWN__	lincRNA	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:32083780G>C	ENST00000562167.1	-	0	841				AC011525.4_ENST00000590611.2_lincRNA						NA		NA									NA						CAGCCCTCCCGCTGGCTGTGT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000562167.1:	chr19.hg19:g.32083780G>C		NA		hg19		0.02	15.929538	CCCxCTG	COVERED																																																																																			NOVEL	AC011525.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000431043.3	5	17.153998	KEEP	0	0	0	57	1961	GG	1	1	0		-	56	60	2005	0	0	160.023125	299	60	10664	497	ENST00000562167.1	0.157746	1
CEP89	84902	__UNKNOWN__	__UNKNOWN__	19	33424478	33424478	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:33424478T>C	ENST00000305768.5	-	8	853	c.765A>G	c.(763-765)caA>caG	p.Q255Q	CEP89_ENST00000590597.2_Silent_p.Q255Q	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	255		NA			cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						GGGTAAGGCTTTGATTCATAT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													274	248	257	NA		NA	NA	19		NA											NA				33424478		2203	4300	6503	SO:0001819	synonymous_variant			AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289	84902			25907	protein-coding gene	gene with protein product		615470	coiled-coil domain containing 123	CCDC123	NA	16395595	Standard	NM_032816	NM_032816	NA	Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.765A>G	chr19.hg19:g.33424478T>C		NA	B9EGA6|Q8N5J8	hg19	CCDS32987.1	0.02	11.003418	GCTxTGA	COVERED																																																																																			NOVEL	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451300.2	2	9.027007	KEEP	0	0	0	30	962	TT	0.999997	0.999997	0		-	10	60	372	0	0	23.104282	279	60	10093	354	ENST00000305768.5	0.034602	1
GPI	2821	__UNKNOWN__	__UNKNOWN__	19	34859644	34859644	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:34859644G>T	ENST00000356487.5	+	4	643				GPI_ENST00000586425.1_Intron|GPI_ENST00000415930.3_Intron	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	NA		NA			aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					CCTTGGCCGTGTGTGTGAGTT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													73	59	64	NA		NA	NA	19		NA											NA				34859644		2203	4300	6503	SO:0001627	intron_variant			M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	2821	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	glucose phosphate isomerase		NA	2387591, 8575767	Standard		NM_001184722	NA	Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.402+37G>T	chr19.hg19:g.34859644G>T		NA	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	hg19	CCDS12437.1	0.02	13.329316	CGTxTGT	COVERED																																																																																			NOVEL	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451693.3	2	18.355968	KEEP	0	0	0	61	2080	GG	1	1	0		+	61	60	2172	1	0	176.790279	280	60	10309	483	ENST00000356487.5	0.178886	1
GPI	2821	__UNKNOWN__	__UNKNOWN__	19	34868644	34868644	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:34868644C>T	ENST00000356487.5	+	6	732	c.491C>T	c.(490-492)cCc>cTc	p.P164L	GPI_ENST00000586425.1_Missense_Mutation_p.P164L|GPI_ENST00000415930.3_Missense_Mutation_p.P175L	NM_000175.3	NP_000166.2	P06744	G6PI_HUMAN	glucose-6-phosphate isomerase	164		NA			aldehyde catabolic process (GO:0046185)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|hemostasis (GO:0007599)|humoral immune response (GO:0006959)|learning or memory (GO:0007611)|methylglyoxal biosynthetic process (GO:0019242)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glucose-6-phosphate isomerase activity (GO:0004347)|intramolecular transferase activity (GO:0016866)|monosaccharide binding (GO:0048029)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	25	Esophageal squamous(110;0.162)					CCGCAGGGACCCCTCATGGTG	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	73	73	NA		NA	NA	19		NA											NA				34868644		2203	4300	6503	SO:0001583	missense			M61214	CCDS12437.1, CCDS54246.1	19q13.1	2012-10-02	2010-05-11			ENSG00000105220	2821	5.3.1.9		4458	protein-coding gene	gene with protein product		172400	glucose phosphate isomerase		NA	2387591, 8575767	Standard		NM_001184722	NA	Approved	AMF, NLK	uc002nvg.2	P06744		ENST00000356487.5:c.491C>T	chr19.hg19:g.34868644C>T	ENSP00000348877:p.Pro164Leu	NA	B4DG39|Q9BRD3|Q9BSK5|Q9UHE6	hg19	CCDS12437.1	0.02	8.763713	GACxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	34	5.333073	0.95758	.	.	ENSG00000105220	ENST00000415930;ENST00000356487	D;D	0.94828	-3.53;-3.53	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.98626	0.9540	H	0.98507	4.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.998;0.999	D	0.99211	1.0876	10	0.87932	D	0	-1.705	20.0893	0.97812	0.0:1.0:0.0:0.0	.	136;175;147;164	B4DE36;B4DG39;B4DVJ0;P06744	.;.;.;G6PI_HUMAN	L	175;164	ENSP00000405573:P175L;ENSP00000348877:P164L	ENSP00000348877:P164L	P	+	2	0	GPI	39560484	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.818000	0.86416	2.761000	0.94854	0.655000	0.94253	CCC	NOVEL	GPI-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451693.3	0	6.313382	KEEP	0	0	0	21	683	CC	0.999869	0.999869	0		+	34	60	1206	0	0	94.46651	204	60	7139	298	ENST00000356487.5	0.142857	1
WTIP	126374	__UNKNOWN__	__UNKNOWN__	19	34985465	34985465	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:34985465A>T	ENST00000590071.2	+	6	1368				WTIP_ENST00000270288.6_Intron	NM_001080436.1	NP_001073905.1	A6NIX2	WTIP_HUMAN	Wilms tumor 1 interacting protein	NA		NA			cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|negative regulation of hippo signaling (GO:0035331)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)	4	all_lung(56;5.94e-07)|Lung NSC(56;9.35e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.211)			TCAGCTGATCACTTCTGGTTT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	70	69	NA		NA	NA	19		NA											NA				34985465		1995	4165	6160	SO:0001627	intron_variant			AK130059	CCDS59375.1	19q13.11	2012-03-16			ENSG00000142279	ENSG00000142279	126374			20964	protein-coding gene	gene with protein product	WT1-interacting protein	614790			NA	14736876	Standard	XM_059037	NM_001080436	NA	Approved		uc002nvm.3	A6NIX2		ENST00000590071.2:c.1032-26A>T	chr19.hg19:g.34985465A>T		NA		hg19	CCDS59375.1	0.02	9.966983	ATCxCTT	COVERED																																																																																			NOVEL	WTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459381.3	4	9.026208	KEEP	0	0	0	30	926	AA	0.999997	0.999997	0		+	126	60	4699	0	0	463.354725	98	60	3540	327	ENST00000590071.2	0.5625	1
GRAMD1A	57655	__UNKNOWN__	__UNKNOWN__	19	35491420	35491420	__UNKNOWN__	Intron	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:35491420C>G	ENST00000411896.2	+	1	61				GRAMD1A_ENST00000424536.2_Intron|GRAMD1A_ENST00000504615.2_Intron|GRAMD1A_ENST00000317991.5_Intron|GRAMD1A_ENST00000599564.1_Intron	NM_001136199.1	NP_001129671.1	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	NA		NA				integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AGCTCAGGGACCGGGCGCGCG	0.776	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													2	2	2	NA		NA	NA	19		NA											NA				35491420		922	2255	3177	SO:0001627	intron_variant			AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351	57655			29305	protein-coding gene	gene with protein product		NA	KIAA1533	KIAA1533	NA	10819331	Standard	NM_020895	NM_020895	NA	Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000411896.2:c.8+30C>G	chr19.hg19:g.35491420C>G		NA	A6NKY7|Q8NC77|Q9P1Z5	hg19	CCDS46046.1	0.02	-0.306981	GGAxCGG	COVERED																																																																																			NOVEL	GRAMD1A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000461559.1	0	8.663194	KEEP	0	0	0	29	928	CC	0.999997	0.800243	0		+	5	70	181	0	0	14.253145	30	70	998	102	ENST00000411896.2	0.142857	0.800245
CD22	933	__UNKNOWN__	__UNKNOWN__	19	35831960	35831960	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:35831960G>A	ENST00000085219.5	+	7	1492	c.1426G>A	c.(1426-1428)Ggc>Agc	p.G476S	CD22_ENST00000594250.1_Missense_Mutation_p.G299S|CD22_ENST00000341773.6_Missense_Mutation_p.G299S|CD22_ENST00000419549.2_Missense_Mutation_p.G304S|CD22_ENST00000270311.6_Missense_Mutation_p.G356S|CD22_ENST00000544992.2_Missense_Mutation_p.G476S|CD22_ENST00000536635.2_Missense_Mutation_p.G388S	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	476	Ig-like C2-type 4.	NA			cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCAAAACGTTGGCTGGGACAA	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(42;1009 1133 23674 26041)					NA		NA				0													98	87	91	NA		NA	NA	19		NA											NA				35831960		2203	4300	6503	SO:0001583	missense			X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124	933		CD molecules, Sialic acid binding Ig-like lectins, Immunoglobulin superfamily / C2-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	1643	protein-coding gene	gene with protein product	sialic acid binding Ig-like lectin 2	107266	CD22 antigen		NA	8496602, 1691828	Standard	NM_001771	NM_001185099	NA	Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1426G>A	chr19.hg19:g.35831960G>A	ENSP00000085219:p.Gly476Ser	NA	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	hg19	CCDS12457.1	0.02	19.583327	GTTxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	7.050	0.564352	0.13498	.	.	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	D;D;D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94;-1.94;-1.94	5.47	-10.9	0.00192	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.108200	0.06794	N	0.787608	T	0.57066	0.2028	N	0.12182	0.205	0.09310	N	0.999999	B;B;B;B;B	0.26363	0.003;0.003;0.011;0.005;0.147	B;B;B;B;B	0.19666	0.013;0.005;0.018;0.013;0.026	T	0.52675	-0.8544	10	0.10636	T	0.68	.	0.327	0.00312	0.2343:0.1904:0.2227:0.3526	.	304;476;388;476;299	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	S	476;388;299;476;356;304	ENSP00000085219:G476S;ENSP00000442279:G388S;ENSP00000339349:G299S;ENSP00000441237:G476S;ENSP00000270311:G356S;ENSP00000403822:G304S	ENSP00000085219:G476S	G	+	1	0	CD22	40523800	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.781000	0.01774	-1.675000	0.01459	-0.310000	0.09108	GGC	NOVEL	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466099.1	1	10.20663	KEEP	0	0	0	34	1150	GG	0.999998	0.999998	0		+	75	60	2772	0	0	226.155624	360	60	13112	573	ENST00000085219.5	0.172414	1
DMKN	93099	__UNKNOWN__	__UNKNOWN__	19	35993785	35993785	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:35993785G>C	ENST00000339686.3	-	10	1314	c.1138C>G	c.(1138-1140)Cag>Gag	p.Q380E	DMKN_ENST00000462126.1_5'UTR|DMKN_ENST00000472252.2_Missense_Mutation_p.Q27E|DMKN_ENST00000443640.1_Missense_Mutation_p.Q143E|DMKN_ENST00000480502.1_Intron|DMKN_ENST00000467637.1_Missense_Mutation_p.Q105E|DMKN_ENST00000429837.1_Missense_Mutation_p.Q339E|DMKN_ENST00000492341.2_Missense_Mutation_p.Q27E|DMKN_ENST00000436012.1_Missense_Mutation_p.Q76E|DMKN_ENST00000402589.2_Missense_Mutation_p.Q93E|DMKN_ENST00000419602.1_Missense_Mutation_p.Q369E|DMKN_ENST00000602781.1_Missense_Mutation_p.Q93E|DMKN_ENST00000414866.2_Missense_Mutation_p.Q93E	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	380		NA				extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGCGGGACCTGGTTCTGTGGA	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													31	35	34	NA		NA	NA	19		NA											NA				35993785		2203	4300	6503	SO:0001583	missense			BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249	93099			25063	protein-coding gene	gene with protein product		NA			NA	16374476	Standard	NM_033317	NM_001035516	NA	Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1138C>G	chr19.hg19:g.35993785G>C	ENSP00000342012:p.Gln380Glu	NA	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	hg19	CCDS12463.1	0.02	7.10861	CCTxGTT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.55|13.55	2.271978|2.271978	0.40194|0.40194	.|.	.|.	ENSG00000161249|ENSG00000161249	ENST00000434389|ENST00000402589;ENST00000339686;ENST00000436012;ENST00000414866;ENST00000429837;ENST00000419602;ENST00000443640	.|T;T;T;T;T;T;T	.|0.34667	.|1.35;1.35;1.35;1.35;1.35;1.35;1.35	5.85|5.85	2.49|2.49	0.30216|0.30216	.|.	.|0.836654	.|0.10179	.|N	.|0.706103	T|T	0.45357|0.45357	0.1338|0.1338	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;P;P;B;B;B	.|0.42941	.|0.073;0.021;0.167;0.01;0.01;0.01;0.794;0.794;0.328;0.073;0.073	.|B;B;B;B;B;B;P;P;B;B;B	.|0.49226	.|0.033;0.033;0.085;0.011;0.033;0.033;0.603;0.524;0.124;0.033;0.033	T|T	0.27020|0.27020	-1.0086|-1.0086	5|9	.|.	.|.	.|.	-0.0925|-0.0925	9.9831|9.9831	0.41826|0.41826	0.0727:0.0:0.7147:0.2126|0.0727:0.0:0.7147:0.2126	.|.	.|76;27;36;36;56;74;369;339;380;93;143	.|B4E3D1;B7ZB10;Q6E0U4-12;Q6E0U4-11;Q6E0U4-10;Q6E0U4-9;C9J4P6;Q6E0U4-4;Q6E0U4;Q6E0U4-8;C9IYI1	.|.;.;.;.;.;.;.;.;DMKN_HUMAN;.;.	R|E	90|93;380;76;93;339;369;143	.|ENSP00000384509:Q93E;ENSP00000342012:Q380E;ENSP00000412075:Q76E;ENSP00000392222:Q93E;ENSP00000405503:Q339E;ENSP00000391036:Q369E;ENSP00000406864:Q143E	.|.	P|Q	-|-	2|1	0|0	DMKN|DMKN	40685625|40685625	0.011000|0.011000	0.17503|0.17503	0.221000|0.221000	0.23827|0.23827	0.004000|0.004000	0.04260|0.04260	1.470000|1.470000	0.35354|0.35354	0.383000|0.383000	0.24910|0.24910	-2.023000|-2.023000	0.00429|0.00429	CCA|CAG	NOVEL	DMKN-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109461.2	1	6.317531	KEEP	0	0	0	21	694	GG	0.999869	0.999869	0		-	29	60	966	0	0	77.20024	136	60	4895	234	ENST00000339686.3	0.175758	1
SBSN	374897	__UNKNOWN__	__UNKNOWN__	19	36017727	36017727	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:36017727T>G	ENST00000452271.2	-	1	1485	c.1457A>C	c.(1456-1458)cAg>cCg	p.Q486P	SBSN_ENST00000518157.1_Missense_Mutation_p.Q143P	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	486	Ala/Gly/His-rich.	NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CTTCCCAGCCTGGTGGACCCC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													107	90	96	NA		NA	NA	19		NA											NA				36017727		2203	4300	6503	SO:0001583	missense			AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05					374897			24950	protein-coding gene	gene with protein product		609969			NA	12228223	Standard	NM_198538	NM_198538	NA	Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.1457A>C	chr19.hg19:g.36017727T>G	ENSP00000430242:p.Gln486Pro	NA	A8K5J0|E9PBV3	hg19	CCDS54253.1	0.02	19.139605	GCCxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	t	13.13	2.146618	0.37923	.	.	ENSG00000189001	ENST00000452271;ENST00000518157	T;T	0.61627	0.09;0.48	4.46	4.46	0.54185	.	0.000000	0.39341	U	0.001397	T	0.68476	0.3005	M	0.73962	2.25	0.29095	N	0.881866	B;D	0.69078	0.268;0.997	B;D	0.63793	0.157;0.918	T	0.63690	-0.6580	10	0.31617	T	0.26	.	7.6513	0.28350	0.189:0.0:0.0:0.811	.	143;486	Q6UWP8;E9PBV3	SBSN_HUMAN;.	P	486;143	ENSP00000430242:Q486P;ENSP00000428771:Q143P	ENSP00000430242:Q486P	Q	-	2	0	SBSN	40709567	.	.	0.999000	0.59377	0.350000	0.29205	.	.	1.758000	0.51981	0.375000	0.23000	CAG	NOVEL	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109463.3	5	17.752575	KEEP	0	0	0	59	1860	TT	1	1	0		-	62	60	2075	0	0	158.006591	400	60	14962	642	ENST00000452271.2	0.134199	1
ATP4A	495	__UNKNOWN__	__UNKNOWN__	19	36041947	36041947	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:36041947G>A	ENST00000262623.3	-	20	2980	c.2952C>T	c.(2950-2952)ccC>ccT	p.P984P		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	984		NA			ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	TGGGCATGCCGGGGCAGTAGC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	64	70	NA		NA	NA	19		NA											NA				36041947		2203	4300	6503	SO:0001819	synonymous_variant				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	495	3.6.3.10	ATPases / P-type	819	protein-coding gene	gene with protein product	gastric H,K-ATPase alpha subunit, H(+)-K(+)-ATPase alpha subunit, proton pump	137216			NA	1330887	Standard	NM_000704	NM_000704	NA	Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.2952C>T	chr19.hg19:g.36041947G>A		NA	O00738	hg19	CCDS12467.1	0.02	15.405556	GCCxGGG	COVERED																																																																																			NOVEL	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109470.2	6	12.038982	KEEP	0	0	0	40	1394	GG	1	1	0		-	11	60	406	0	0	24.429655	354	60	12320	514	ENST00000262623.3	0.030137	1
ATP4A	495	__UNKNOWN__	__UNKNOWN__	19	36049633	36049633	__UNKNOWN__	Intron	SNP	C	C	T	rs566221157		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:36049633C>T	ENST00000262623.3	-	9	1284					NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	NA		NA			ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	GCGGCTCTCCCGGACCAGAAC	0.701	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	14239	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0													5	7	6	NA		NA	NA	19		NA											NA				36049633		2088	4143	6231	SO:0001627	intron_variant				CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	495	3.6.3.10	ATPases / P-type	819	protein-coding gene	gene with protein product	gastric H,K-ATPase alpha subunit, H(+)-K(+)-ATPase alpha subunit, proton pump	137216			NA	1330887	Standard	NM_000704	NM_000704	NA	Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.1256-45G>A	chr19.hg19:g.36049633C>T		NA	O00738	hg19	CCDS12467.1	0.02	11.89952	TCCxGGA	COVERED																																																																																			NOVEL	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109470.2	1	17.153322	KEEP	0	0	0	57	1898	CC	1	1	0		-	41	60	1493	0	0	118.373027	237	60	7834	421	ENST00000262623.3	0.147482	1
ARHGAP33	115703	__UNKNOWN__	__UNKNOWN__	19	36278038	36278038	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:36278038C>A	ENST00000314737.5	+	21	2203				ARHGAP33_ENST00000007510.4_Intron|ARHGAP33_ENST00000378944.5_Intron	NM_052948.3	NP_443180.2	O14559	RHG33_HUMAN	Rho GTPase activating protein 33	NA		NA			protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						GGGCCTGGCCCCAGCTGAACC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													32	41	38	NA		NA	NA	19		NA											NA				36278038		2201	4295	6496	SO:0001627	intron_variant			AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777	115703		Rho GTPase activating proteins	23085	protein-coding gene	gene with protein product		614902	sorting nexin 26	SNX26	NA	12297274, 12461558	Standard	NM_052948	NM_052948	NA	Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000314737.5:c.2120-32C>A	chr19.hg19:g.36278038C>A		NA	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	hg19	CCDS12477.1	0.02	15.611471	GCCxCAG	COVERED																																																																																			NOVEL	ARHGAP33-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459120.1	3	16.852527	KEEP	0	0	0	56	1878	CC	1	1	0		+	15	60	553	0	0	35.108627	361	70	12781	540	ENST00000314737.5	0.039894	1
ARHGAP33	115703	__UNKNOWN__	__UNKNOWN__	19	36278842	36278842	__UNKNOWN__	Silent	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:36278842A>C	ENST00000314737.5	+	21	2976	c.2892A>C	c.(2890-2892)tcA>tcC	p.S964S	ARHGAP33_ENST00000007510.4_Silent_p.S1125S|ARHGAP33_ENST00000378944.5_Silent_p.S961S	NM_052948.3	NP_443180.2	O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1125		NA			protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TTGGCCAATCACCCCCACTCC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													20	24	22	NA		NA	NA	19		NA											NA				36278842		2203	4298	6501	SO:0001819	synonymous_variant			AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777	115703		Rho GTPase activating proteins	23085	protein-coding gene	gene with protein product		614902	sorting nexin 26	SNX26	NA	12297274, 12461558	Standard	NM_052948	NM_052948	NA	Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000314737.5:c.2892A>C	chr19.hg19:g.36278842A>C		NA	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	hg19	CCDS12477.1	0.02	1.466263	ATCxCCC	COVERED																																																																																			NOVEL	ARHGAP33-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459120.1	11	3.39401	KEEP	0	4	20	19	472	AA	0.999909	0.999908	0		+	12	60	197	0	0	9.748911	98	60	2549	208	ENST00000314737.5	0.109091	0.999999
ZNF568	374900	__UNKNOWN__	__UNKNOWN__	19	37427633	37427633	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:37427633A>T	ENST00000333987.7	+	5	641				ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000415168.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTAATTAGCATTATGTTTTT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													63	63	63	NA		NA	NA	19		NA											NA				37427633		2157	4287	6444	SO:0001627	intron_variant			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453	374900		Zinc fingers, C2H2-type, -	25392	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198539	NM_198539	NA	Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.136-15A>T	chr19.hg19:g.37427633A>T		NA	B4DS92|E7ER33|Q6N060|Q8NA64	hg19	CCDS42558.1	0.02	19.13357	AGCxTTA	COVERED																																																																																			NOVEL	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109572.2	6	20.153839	KEEP	0	0	0	67	2080	AA	1	1	0		+	20	60	775	1	0	52.195229	397	60	14610	602	ENST00000333987.7	0.047962	1
AC016582.2	0	__UNKNOWN__	__UNKNOWN__	19	38314758	38314758	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:38314758A>G	ENST00000592640.1	-	0	1319				CTD-2554C21.2_ENST00000590433.1_lincRNA	NR_040015.1					NA		NA									NA						GCTATCCTTGAAGTGACAAAA	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000592640.1:	chr19.hg19:g.38314758A>G		NA		hg19		0.02	7.191907	TTGxAGT	COVERED																																																																																			NOVEL	AC016582.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000109619.2	4	5.998546	KEEP	0	0	0	20	634	AA	0.999863	0.999863	0		-	16	60	590	0	0	43.231588	163	60	6048	272	ENST00000592640.1	0.089385	1
RASGRP4	115727	__UNKNOWN__	__UNKNOWN__	19	38910667	38910667	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:38910667G>A	ENST00000587738.1	-	6	580				RASGRP4_ENST00000454404.2_Intron|RASGRP4_ENST00000293062.9_Intron|RASGRP4_ENST00000586305.1_Intron|RASGRP4_ENST00000587753.1_Intron|RASGRP4_ENST00000426920.2_Intron|RASGRP4_ENST00000433821.2_Intron			Q8TDF6	GRP4_HUMAN	RAS guanyl releasing protein 4	NA		NA			activation of phospholipase C activity (GO:0007202)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|myeloid cell differentiation (GO:0030099)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to extracellular stimulus (GO:0009991)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|GTP-dependent protein binding (GO:0030742)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			cervix(1)|kidney(1)|large_intestine(4)|lung(12)|pancreas(1)|prostate(3)|skin(1)	23	all_cancers(60;4.21e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GGGGCCAAGAGGGGCAGGGTA	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													27	30	29	NA		NA	NA	19		NA											NA				38910667		1981	4155	6136	SO:0001627	intron_variant			AY048119	CCDS46068.1, CCDS54262.1, CCDS54263.1, CCDS54264.1	19q13.1	2013-01-10					115727		EF-hand domain containing	18958	protein-coding gene	gene with protein product		607320			NA	11956218	Standard	NM_170604	NM_170604	NA	Approved		uc021uub.1	Q8TDF6		ENST00000587738.1:c.510-14C>T	chr19.hg19:g.38910667G>A		NA	A6H8M4|C0LTP2|C0LTP3|C0LTP4|C0LTP5|C0LTP7|C9J416|C9JHZ1|Q8N858|Q96QN5|Q96QN6|Q96QN7	hg19	CCDS46068.1	0.02	14.559489	AGAxGGG	COVERED																																																																																			NOVEL	RASGRP4-013	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460540.1	4	15.648696	KEEP	0	0	0	52	1785	GG	1	1	0		-	50	60	1823	0	0	144.645722	288	60	10569	469	ENST00000587738.1	0.147929	1
EIF3K	27335	__UNKNOWN__	__UNKNOWN__	19	39123338	39123338	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:39123338G>A	ENST00000538434.1	+	5	473				EIF3K_ENST00000588934.1_Intron|EIF3K_ENST00000248342.4_Intron|EIF3K_ENST00000593149.1_Intron|EIF3K_ENST00000592558.1_Intron|EIF3K_ENST00000545173.2_Intron					eukaryotic translation initiation factor 3, subunit K	NA		NA							EIF3K/CYP39A1(2)	central_nervous_system(1)|endometrium(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCTGGGTCCTGGTGCACATCT	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													47	39	41	NA		NA	NA	19		NA											NA				39123338		2203	4300	6503	SO:0001627	intron_variant			AB019392	CCDS12517.1, CCDS74360.1	19q13.2	2012-05-28	2007-07-27	2007-07-27	ENSG00000178982	ENSG00000178982	27335			24656	protein-coding gene	gene with protein product		609596	eukaryotic translation initiation factor 3, subunit 12	EIF3S12	NA	11042152, 14519125	Standard	NM_013234	XM_006723147	NA	Approved	eIF3k, PRO1474, HSPC029, PTD001, PLAC-24, M9, ARG134	uc002oiz.1	Q9UBQ5		ENST00000538434.1:c.238+20G>A	chr19.hg19:g.39123338G>A		NA		hg19		0.02	4.83431	CCTxGTG	COVERED																																																																																			NOVEL	EIF3K-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000453409.1	0	4.814542	KEEP	0	0	0	16	506	GG	0.997832	0.997831	0		+	39	60	1453	0	0	129.422648	91	60	3154	163	ENST00000538434.1	0.3	1
PAF1	54623	__UNKNOWN__	__UNKNOWN__	19	39879196	39879196	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:39879196G>A	ENST00000221265.3	-	10	1188				PAF1_ENST00000221266.7_Intron|PAF1_ENST00000595564.1_Intron	NM_019088.3	NP_061961.2	P28328	PEX2_HUMAN	Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)	NA		NA			bile acid biosynthetic process (GO:0006699)|cholesterol homeostasis (GO:0042632)|fatty acid beta-oxidation (GO:0006635)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|peroxisome organization (GO:0007031)|protein destabilization (GO:0031648)|protein import into peroxisome matrix (GO:0016558)|regulation of cholesterol biosynthetic process (GO:0045540)|very long-chain fatty acid metabolic process (GO:0000038)	Cdc73/Paf1 complex (GO:0016593)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)|urinary_tract(2)	17	all_cancers(60;9.14e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.88e-06)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			CGCAACCCACGCACACATCAT	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													170	170	170	NA		NA	NA	19		NA											NA				39879196		2203	4300	6503	SO:0001627	intron_variant				CCDS12533.1, CCDS59387.1	19q13.1	2008-02-05				ENSG00000006712	54623			25459	protein-coding gene	gene with protein product		610506			NA	15632063	Standard	NM_019088	NM_019088	NA	Approved	PD2, F23149_1, FLJ11123	uc002old.4	Q8N7H5		ENST00000221265.3:c.857+3C>T	chr19.hg19:g.39879196G>A		NA	Q567S6|Q9BW41	hg19	CCDS12533.1	0.02	27.636537	CACxCAC	COVERED																																																																																			NOVEL	PAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464477.1	5	38.941439	KEEP	0	1	9	133	4591	GG	1	1	0		-	88	60	3135	0	0	245.088023	539	60	18982	953	ENST00000221265.3	0.140351	1
SUPT5H	6829	__UNKNOWN__	__UNKNOWN__	19	39964849	39964849	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:39964849G>A	ENST00000599117.1	+	28	3018				SUPT5H_ENST00000402194.2_Intron|SUPT5H_ENST00000598725.1_Intron|SUPT5H_ENST00000359191.6_Intron|SUPT5H_ENST00000432763.2_Intron			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TCCAACAAATGCCCCCTTCTC	0.632	NA	NA									OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													118	121	120	NA		NA	NA	19		NA											NA				39964849		2203	4300	6503	SO:0001627	intron_variant			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235	6829			11469	protein-coding gene	gene with protein product		602102	suppressor of Ty (S.cerevisiae) 5 homolog		NA	8975720	Standard	NM_003169	NM_003169	NA	Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2652-25G>A	chr19.hg19:g.39964849G>A		889	O43279|Q59G52|Q99639	hg19	CCDS12536.1	0.02	28.485506	AATxCCC	COVERED																																																																																			NOVEL	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464918.1	69	81.217215	KEEP	0	1	28	280	9784	GG	1	1	0		+	96	60	2832	0	0	206.968137	617	60	22688	1321	ENST00000599117.1	0.134642	1
TIMM50	92609	__UNKNOWN__	__UNKNOWN__	19	39976301	39976301	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:39976301C>T	ENST00000607714.1	+	6	394				TIMM50_ENST00000599794.1_Intron|TIMM50_ENST00000544017.1_Intron|TIMM50_ENST00000314349.4_Intron			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	NA		NA			cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTTGTCTGAGCGCCCCCATCC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	76	78	NA		NA	NA	19		NA											NA				39976301		2203	4300	6503	SO:0001627	intron_variant			BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197	92609		Serine/threonine phosphatases / CTD aspartate-based phosphatases	23656	protein-coding gene	gene with protein product		607381	translocase of inner mitochondrial membrane 50 homolog (yeast)		NA	12437925	Standard	NM_001001563	NM_001001563	NA	Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.373-27C>T	chr19.hg19:g.39976301C>T		NA	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	hg19		0.02	19.677455	GAGxGCC	COVERED																																																																																			NOVEL	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000470728.1	9	26.180032	KEEP	0	0	0	87	2984	CC	1	1	0		+	64	60	2247	0	0	172.690406	428	60	15072	719	ENST00000607714.1	0.130081	1
AKT2	208	__UNKNOWN__	__UNKNOWN__	19	40740872	40740872	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:40740872C>A	ENST00000392038.2	-	13	1665				AKT2_ENST00000579047.1_Missense_Mutation_p.K420N|AKT2_ENST00000424901.1_Intron|AKT2_ENST00000311278.6_Intron	NM_001243027.1|NM_001243028.1|NM_001626.4	NP_001229956.1|NP_001229957.1|NP_001617.1	P31751	AKT2_HUMAN	v-akt murine thymoma viral oncogene homolog 2	NA		NA			activation of Ral GTPase activity (GO:0032859)|apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|fat cell differentiation (GO:0045444)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transmembrane transport (GO:0065002)|mammary gland epithelial cell differentiation (GO:0060644)|membrane organization (GO:0061024)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of cell motility (GO:2000147)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)|protein localization to plasma membrane (GO:0072659)|regulation of cell cycle arrest (GO:0071156)|regulation of cell migration (GO:0030334)|regulation of translation (GO:0006417)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			GAGGGCCCTCCTTGAGAAGTG	0.627	NA	NA	A		ovarian, pancreatic 									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		19	19q13.1-q13.2	208	v-akt murine thymoma viral oncogene homolog 2		E	0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M77198	CCDS12552.1	19q13.1-q13.2	2013-01-10			ENSG00000105221	ENSG00000105221	208	2.7.11.1	Pleckstrin homology (PH) domain containing	392	protein-coding gene	gene with protein product		164731			NA	1409633	Standard	NM_001626	NM_001626	NA	Approved		uc002onf.3	P31751	OTTHUMG00000137375	ENST00000392038.2:c.1366+79G>T	chr19.hg19:g.40740872C>A		NA	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	hg19	CCDS12552.1	0.02	17.830661	CTCxTTG	COVERED																																																																																			NOVEL	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268029.1	3	23.776828	KEEP	0	0	0	79	2796	CC	1	1	0		-	67	60	2319	0	0	183.170802	363	60	13207	651	ENST00000392038.2	0.155814	1
LTBP4	8425	__UNKNOWN__	__UNKNOWN__	19	41122916	41122916	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:41122916C>T	ENST00000602240.1	+	0	3024				LTBP4_ENST00000243562.9_Intron|LTBP4_ENST00000396819.3_Silent_p.G978G|LTBP4_ENST00000308370.7_Silent_p.G1045G|LTBP4_ENST00000204005.9_Silent_p.G1008G|LTBP4_ENST00000545697.1_Intron			Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding protein 4	NA		NA			extracellular matrix organization (GO:0030198)|growth hormone secretion (GO:0030252)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|regulation of cell differentiation (GO:0045595)|regulation of cell growth (GO:0001558)|regulation of proteolysis (GO:0030162)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|glycosaminoglycan binding (GO:0005539)|integrin binding (GO:0005178)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CGCCAGGGGGCGGATGCCAGG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													53	56	55	NA		NA	NA	19		NA											NA				41122916		1979	4132	6111	SO:0001624	3_prime_UTR_variant			Y13622	CCDS74368.1, CCDS74369.1, CCDS74370.1	19q13.1-q13.2	2011-10-20				ENSG00000090006	8425		Latent transforming growth factor, beta binding proteins	6717	protein-coding gene	gene with protein product		604710			NA	9660815, 9271198	Standard	NM_003573	NM_003573	NA	Approved	LTBP-4, LTBP-4L, FLJ46318, FLJ90018	uc002ooh.1	Q8N2S1		ENST00000602240.1:c.*3021C>T	chr19.hg19:g.41122916C>T		NA	O00508|O75412|O75413	hg19		0.02	32.111299	GGGxGGA	COVERED																																																																																			NOVEL	LTBP4-002	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000462815.2	2	33.093568	KEEP	0	0	0	110	3659	CC	1	1	0		+	104	60	3471	0	0	268.820032	600	60	21209	929	ENST00000602240.1	0.147727	1
C19orf54	284325	__UNKNOWN__	__UNKNOWN__	19	41246907	41246907	__UNKNOWN__	3'UTR	SNP	C	C	T	rs62621363	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:41246907C>T	ENST00000378313.2	-	0	2606				C19orf54_ENST00000598485.2_Missense_Mutation_p.E67K|C19orf54_ENST00000594163.1_5'UTR|C19orf54_ENST00000470681.1_3'UTR	NM_198476.3	NP_940878.3	Q5BKX5	CS054_HUMAN	chromosome 19 open reading frame 54	NA		NA								breast(1)|lung(1)|urinary_tract(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			ggcggctattcttgtgcctgg	0.582	NA	NA											C|||	65	0.0129792	0	0.0202	5008	,	,	NA	17798	0	NA	0.0358	False	NA	,,,	NA	NA	NA	2504	0.0153	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK123126	CCDS12564.2	19q13.2	2012-10-26			ENSG00000188493	ENSG00000188493	284325			24758	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198476	NM_198476	NA	Approved	FLJ41131	uc002oou.1	Q5BKX5	OTTHUMG00000150174	ENST00000378313.2:c.*1431G>A	chr19.hg19:g.41246907C>T		NA	A8MSZ5|B4DNU7	hg19	CCDS12564.2	0.02	4.444885	ATTxTTG	COVERED																																																																																			NOVEL	C19orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316701.1	3	10.534654	KEEP	0	0	0	35	1269	CC	0.999999	0.999998	0		-	35	60	1261	0	0	110.21455	93	60	3445	205	ENST00000378313.2	0.273437	1
PHLDB3	653583	__UNKNOWN__	__UNKNOWN__	19	43990978	43990978	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs547222779		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:43990978C>T	ENST00000292140.5	-	11	1654	c.1294G>A	c.(1294-1296)Ggc>Agc	p.G432S		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	432		NA					enzyme binding (GO:0019899)	p.G432C(1)		breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGGTATCTGCCGGAGTCCCCC	0.602	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	16423	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	lung(1)											25	26	26	NA		NA	NA	19		NA											NA				43990978		2011	4188	6199	SO:0001583	missense				CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531	653583		Pleckstrin homology (PH) domain containing	30499	protein-coding gene	gene with protein product		NA			NA		Standard		NM_198850	NA	Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1294G>A	chr19.hg19:g.43990978C>T	ENSP00000292140:p.Gly432Ser	NA	Q8N7Z4	hg19	CCDS12621.2	0.02	9.786831	TGCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.50	2.853100	0.51270	.	.	ENSG00000176531	ENST00000292140	T	0.54866	0.55	3.99	-1.09	0.09904	.	.	.	.	.	T	0.24005	0.0581	L	0.27053	0.805	0.09310	N	1	B;P	0.52842	0.127;0.956	B;B	0.36134	0.009;0.218	T	0.29027	-1.0025	9	0.02654	T	1	.	4.3352	0.11083	0.0:0.4126:0.3682:0.2192	.	136;432	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	S	432	ENSP00000292140:G432S	ENSP00000292140:G432S	G	-	1	0	PHLDB3	48682818	0.079000	0.21365	0.327000	0.25402	0.895000	0.52256	0.071000	0.14594	0.116000	0.18110	-0.385000	0.06624	GGC	NOVEL	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319643.2	2	19.857891	KEEP	0	0	0	66	2184	CC	1	1	0		-	36	60	1352	0	0	109.51706	188	60	6275	360	ENST00000292140.5	0.160714	1
KCNN4	3783	__UNKNOWN__	__UNKNOWN__	19	44278650	44278650	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:44278650G>T	ENST00000262888.3	-	3	772	c.377C>A	c.(376-378)cCg>cAg	p.P126Q		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	126		NA			calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	CTGCACGCACGGCGGGCCCCG	0.746	NA	NA									OREG0025535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	7	6	NA		NA	NA	19		NA											NA				44278650		1993	3956	5949	SO:0001583	missense			AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783	3783		Potassium channels, Voltage-gated ion channels / Potassium channels, calcium-activated	6293	protein-coding gene	gene with protein product		602754			NA	9380751, 9407042, 16382103	Standard	NM_002250	NM_002250	NA	Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.377C>A	chr19.hg19:g.44278650G>T	ENSP00000262888:p.Pro126Gln	922	Q53XR4	hg19	CCDS12630.1	0.02	4.159587	CACxGCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	5.214	0.224924	0.09916	.	.	ENSG00000104783	ENST00000262888	D	0.99846	-7.13	3.77	0.0597	0.14333	.	0.796730	0.11809	N	0.527369	D	0.97926	0.9318	N	0.08118	0	0.09310	N	1	B	0.27380	0.177	B	0.26202	0.067	D	0.99989	1.3821	10	0.30078	T	0.28	-15.2422	5.4825	0.16731	0.1027:0.0:0.3765:0.5208	.	126	O15554	KCNN4_HUMAN	Q	126	ENSP00000262888:P126Q	ENSP00000262888:P126Q	P	-	2	0	KCNN4	48970490	0.000000	0.05858	0.710000	0.30468	0.157000	0.22087	0.091000	0.15046	-0.095000	0.12351	-0.335000	0.08231	CCG	NOVEL	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463598.1	0	23.126843	KEEP	0	0	0	77	2479	GG	1	1	0		-	5	60	178	0	0	10.846261	134	60	4362	276	ENST00000262888.3	0.035971	1
CLASRP	11129	__UNKNOWN__	__UNKNOWN__	19	45567360	45567360	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:45567360T>G	ENST00000221455.3	+	12	1094	c.996T>G	c.(994-996)ttT>ttG	p.F332L	CLASRP_ENST00000544944.2_Missense_Mutation_p.F332L|CLASRP_ENST00000391953.4_Missense_Mutation_p.F270L	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	332		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						TCACCAGTTTTGGGGGCAGCG	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													15	20	18	NA		NA	NA	19		NA											NA				45567360		2201	4294	6495	SO:0001583	missense			AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859	11129			17731	protein-coding gene	gene with protein product	Clk4 associating SR-related protein	NA	splicing factor, arginine/serine-rich 16	SFRS16	NA	12169693	Standard	NM_007056	NM_007056	NA	Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.996T>G	chr19.hg19:g.45567360T>G	ENSP00000221455:p.Phe332Leu	NA	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	hg19	CCDS12652.2	0.02	9.11198	TTTxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	T	20.3	3.961631	0.74016	.	.	ENSG00000104859	ENST00000221455;ENST00000391952;ENST00000391953;ENST00000544944	T;T;T;T	0.10573	3.01;2.86;3.01;3.01	4.7	2.57	0.30868	.	0.000000	0.37012	U	0.002287	T	0.25754	0.0627	M	0.74467	2.265	0.58432	D	0.999997	P;D;D	0.67145	0.75;0.995;0.996	B;D;P	0.63957	0.222;0.92;0.835	T	0.00926	-1.1512	10	0.66056	D	0.02	-5.9955	7.7318	0.28791	0.0:0.1844:0.0:0.8156	.	270;332;332	F8WAG9;F5H0Q6;Q8N2M8	.;.;CLASR_HUMAN	L	332;332;270;332	ENSP00000221455:F332L;ENSP00000375814:F332L;ENSP00000375815:F270L;ENSP00000438702:F332L	ENSP00000221455:F332L	F	+	3	2	CLASRP	50259200	0.448000	0.25681	1.000000	0.80357	0.871000	0.50021	-0.277000	0.08502	0.665000	0.31066	0.383000	0.25322	TTT	NOVEL	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316749.1	0	27.520995	KEEP	0	11	134	141	4061	TT	1	1	0		+	56	60	1956	0	0	165.495969	186	60	6385	582	ENST00000221455.3	0.231405	1
KLC3	147700	__UNKNOWN__	__UNKNOWN__	19	45850092	45850092	__UNKNOWN__	Intron	SNP	C	C	A	rs372686045		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:45850092C>A	ENST00000391946.2	+	3	591				KLC3_ENST00000585434.1_Intron|KLC3_ENST00000470402.1_Intron	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	NA		NA			axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		CACAGTCCCCCAGACCCTCCT	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892	147700		Tetratricopeptide (TTC) repeat domain containing	20717	protein-coding gene	gene with protein product		601334			NA		Standard	NM_145275	XM_005258536	NA	Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.489+60C>A	chr19.hg19:g.45850092C>A		NA	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	hg19	CCDS12660.2	0.02	4.156233	CCCxAGA	COVERED																																																																																			NOVEL	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000289776.1	1	13.531947	KEEP	1	0	0	45	1581	CC	1	1	0		+	6	60	204	0	0	12.947572	113	70	4185	271	ENST00000391946.2	0.05042	1
KLC3	147700	__UNKNOWN__	__UNKNOWN__	19	45850096	45850096	__UNKNOWN__	Intron	SNP	C	C	T	rs56146951|rs113906887	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:45850096C>T	ENST00000391946.2	+	3	591				KLC3_ENST00000585434.1_Intron|KLC3_ENST00000470402.1_Intron	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	NA		NA			axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GTCCCCCAGACCCTCCTTAGA	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892	147700		Tetratricopeptide (TTC) repeat domain containing	20717	protein-coding gene	gene with protein product		601334			NA		Standard	NM_145275	XM_005258536	NA	Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.489+64C>T	chr19.hg19:g.45850096C>T		NA	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	hg19	CCDS12660.2	0.02	4.07405	AGAxCCT	COVERED																																																																																			NOVEL	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000289776.1	1	13.21983	KEEP	1	0	0	44	1435	CC	1	1	0		+	8	60	260	0	0	17.259425	106	70	3660	269	ENST00000391946.2	0.070175	1
PPP1R13L	10848	__UNKNOWN__	__UNKNOWN__	19	45899174	45899174	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:45899174G>T	ENST00000418234.2	-	7	982				PPP1R13L_ENST00000360957.5_Intron	NM_001142502.1	NP_001135974.1	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13 like	NA		NA			apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic camera-type eye development (GO:0031076)|hair cycle (GO:0042633)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle tissue development (GO:0003229)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		gaaggggatcgggtgagagag	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(61;1447 1663 31419 50578)					NA		NA				0													5	6	5	NA		NA	NA	19		NA											NA				45899174		2077	4118	6195	SO:0001627	intron_variant			AF078036	CCDS33050.1	19q13.32	2013-01-10	2011-10-04		ENSG00000104881	ENSG00000104881	10848		Ankyrin repeat domain containing	18838	protein-coding gene	gene with protein product		607463	protein phosphatase 1, regulatory (inhibitor) subunit 13 like		NA	10336463	Standard	NM_006663	NM_006663	NA	Approved	RAI, IASPP	uc002pbo.3	Q8WUF5		ENST00000418234.2:c.904-30C>A	chr19.hg19:g.45899174G>T		NA	Q2PNZ9|Q5DU71|Q5I1X4|Q6P1R7|Q6PKF8|Q9Y290	hg19	CCDS33050.1	0.02	2.382081	ATCxGGT	COVERED																																																																																			NOVEL	PPP1R13L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000457586.1	5	11.12525	KEEP	0	0	0	37	1231	GG	1	0.996232	0		-	10	60	368	0	0	29.173127	59	60	1998	141	ENST00000418234.2	0.144928	0.996233
GPR4	2828	__UNKNOWN__	__UNKNOWN__	19	46094520	46094520	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:46094520C>T	ENST00000323040.4	-	2	1549	c.605G>A	c.(604-606)cGg>cAg	p.R202Q	OPA3_ENST00000544371.1_Intron	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	202		NA			G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		CAGGATGCCCCGGTACGACAG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(117;181 1612 1673 14956 42937)					NA		NA				0													47	43	45	NA		NA	NA	19		NA											NA				46094520		2203	4300	6503	SO:0001583	missense			BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464	2828		GPCR / Class A : Orphans	4497	protein-coding gene	gene with protein product		600551			NA	8595909	Standard	NM_005282	NM_005282	NA	Approved		uc002pcm.3	P46093		ENST00000323040.4:c.605G>A	chr19.hg19:g.46094520C>T	ENSP00000319744:p.Arg202Gln	NA	A8K3T3|B0M0K1|Q6NWM4	hg19	CCDS12669.1	0.02	12.038632	CCCxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.70	2.314499	0.40996	.	.	ENSG00000177464	ENST00000323040	T	0.71817	-0.6	5.33	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.085190	0.45606	D	0.000342	T	0.46946	0.1419	N	0.24115	0.695	0.31524	N	0.662071	P	0.37207	0.587	B	0.27500	0.08	T	0.53085	-0.8488	10	0.27082	T	0.32	.	6.7783	0.23632	0.0:0.7264:0.1803:0.0933	.	202	P46093	GPR4_HUMAN	Q	202	ENSP00000319744:R202Q	ENSP00000319744:R202Q	R	-	2	0	GPR4	50786360	0.010000	0.17322	0.967000	0.41034	0.870000	0.49936	1.610000	0.36869	2.501000	0.84356	0.455000	0.32223	CGG	NOVEL	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459603.1	2	28.23231	KEEP	0	0	0	94	3100	CC	1	1	0		-	151	60	5431	0	0	529.565399	134	60	4641	458	ENST00000323040.4	0.529825	1
SYMPK	8189	__UNKNOWN__	__UNKNOWN__	19	46326664	46326664	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:46326664C>G	ENST00000245934.7	-	20	2910	c.2666G>C	c.(2665-2667)cGc>cCc	p.R889P	SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	889		NA			cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GATGAGGAAGCGGACGTCTGG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													95	83	87	NA		NA	NA	19		NA											NA				46326664		2203	4300	6503	SO:0001583	missense			U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755	8189			22935	protein-coding gene	gene with protein product		602388			NA	9330635	Standard	NM_004819	NM_004819	NA	Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.2666G>C	chr19.hg19:g.46326664C>G	ENSP00000245934:p.Arg889Pro	NA	O00521|O00689|O00733|Q59GT5|Q8N2U5	hg19	CCDS12676.2	0.02	13.381566	AAGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746575	0.89663	.	.	ENSG00000125755	ENST00000245934	T	0.65732	-0.17	4.67	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.81828	0.4905	M	0.88241	2.94	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85663	0.1290	10	0.87932	D	0	.	15.1866	0.73006	0.0:1.0:0.0:0.0	.	904;889	Q4LE61;Q92797	.;SYMPK_HUMAN	P	889	ENSP00000245934:R889P	ENSP00000245934:R889P	R	-	2	0	SYMPK	51018504	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.962000	0.76048	2.425000	0.82216	0.650000	0.86243	CGC	NOVEL	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316581.1	3	34.304229	KEEP	0	0	0	114	3907	CC	1	1	0		-	40	60	1450	0	0	110.906577	295	60	10269	600	ENST00000245934.7	0.119403	1
DHX34	9704	__UNKNOWN__	__UNKNOWN__	19	47884094	47884094	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:47884094C>T	ENST00000328771.4	+	15	3353	c.3004C>T	c.(3004-3006)Ctc>Ttc	p.L1002F		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	1002		NA			negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CCTCCGGCGGCTCACAGGGCT	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													87	83	84	NA		NA	NA	19		NA											NA				47884094		2203	4300	6503	SO:0001583	missense			D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815	9704		DEAH-boxes	16719	protein-coding gene	gene with protein product		615475	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34	DDX34	NA	10708517, 8590280	Standard	NM_014681	NM_014681	NA	Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.3004C>T	chr19.hg19:g.47884094C>T	ENSP00000331907:p.Leu1002Phe	NA	B4DMY8	hg19	CCDS12700.1	0.02	10.191293	CGGxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	13.16	2.153911	0.38021	.	.	ENSG00000134815	ENST00000328771	T	0.03982	3.74	4.76	4.76	0.60689	.	0.286062	0.23465	N	0.047890	T	0.11537	0.0281	L	0.52011	1.625	0.49687	D	0.999818	D	0.65815	0.995	P	0.60345	0.873	T	0.00406	-1.1759	10	0.87932	D	0	-23.5866	7.0734	0.25191	0.0:0.8148:0.0:0.1851	.	1002	Q14147	DHX34_HUMAN	F	1002	ENSP00000331907:L1002F	ENSP00000331907:L1002F	L	+	1	0	DHX34	52575925	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	2.268000	0.43338	2.474000	0.83562	0.462000	0.41574	CTC	NOVEL	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000314313.3	8	23.477047	KEEP	0	0	0	78	2827	CC	1	1	0		+	9	60	324	0	0	19.613424	258	60	9698	456	ENST00000328771.4	0.033708	1
SLC8A2	6543	__UNKNOWN__	__UNKNOWN__	19	47933272	47933272	__UNKNOWN__	3'UTR	SNP	C	C	T	rs555421520		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:47933272C>T	ENST00000236877.6	-	0	3235				SLC8A2_ENST00000539381.1_3'UTR|SLC8A2_ENST00000542837.1_3'UTR	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	NA		NA			blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		GAAAAGGAGACCAGGGTCCAA	0.677	NA	NA											.|||	1	0.000199681	8e-04	0	5008	,	,	NA	12821	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160	6543		Solute carriers	11069	protein-coding gene	gene with protein product		601901			NA	8021246	Standard		NM_015063	NA	Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.*74G>A	chr19.hg19:g.47933272C>T		NA	B4DYQ9	hg19	CCDS33065.1	0.02	1.809252	AGAxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.858	0.946316	0.18356	.	.	ENSG00000118160	ENST00000391903	.	.	.	2.99	-0.981	0.10269	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.8454	0.08933	0.0:0.4772:0.2405:0.2823	.	.	.	.	X	801	.	ENSP00000375772:W801X	W	-	3	0	SLC8A2	52625084	0.000000	0.05858	0.000000	0.03702	0.210000	0.24377	-0.680000	0.05197	-0.178000	0.10672	0.449000	0.29647	TGG	NOVEL	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466997.1	3	18.955616	KEEP	0	0	0	63	2100	CC	1	0.999804	0		-	11	60	403	0	0	31.107579	78	70	2699	206	ENST00000236877.6	0.123596	0.999804
FAM83E	54854	__UNKNOWN__	__UNKNOWN__	19	49106985	49106985	__UNKNOWN__	Silent	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:49106985C>T	ENST00000263266.3	-	4	1131	c.942G>A	c.(940-942)gtG>gtA	p.V314V		NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	314		NA								NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GGCGGCGGGACACGCGGTGCG	0.796	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													3	3	3	NA		NA	NA	19		NA											NA				49106985		1474	3297	4771	SO:0001819	synonymous_variant			AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523	54854			25972	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017708	NM_017708	NA	Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.942G>A	chr19.hg19:g.49106985C>T		NA	Q9NXK1	hg19	CCDS42587.1	0.02	-0.252787	GGAxACG	COVERED																																																																																			NOVEL	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466145.1	1	4.513379	KEEP	0	0	0	15	480	CC	0.99649	0.666177	0		-	10	60	294	0	0	26.064363	19	60	573	50	ENST00000263266.3	0.344828	0.668523
TRPM4	54795	__UNKNOWN__	__UNKNOWN__	19	49675285	49675285	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs144328631		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:49675285G>T	ENST00000252826.5	+	9	1196	c.1070G>T	c.(1069-1071)cGg>cTg	p.R357L	TRPM4_ENST00000427978.2_Missense_Mutation_p.R357L|TRPM4_ENST00000601347.1_3'UTR|TRPM4_ENST00000355712.5_Intron	NM_017636.3	NP_060106.2	Q8TD43	TRPM4_HUMAN	transient receptor potential cation channel, subfamily M, member 4	357		NA			calcium ion transmembrane transport (GO:0070588)|cardiac conduction (GO:0061337)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|protein sumoylation (GO:0016925)|regulation of membrane potential (GO:0042391)|regulation of T cell cytokine production (GO:0002724)|transmembrane transport (GO:0055085)|vasoconstriction (GO:0042310)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)			breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(18)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	49		all_lung(116;8.54e-05)|Lung NSC(112;0.000139)|all_neural(266;0.0506)|Ovarian(192;0.15)		all cancers(93;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000222)|GBM - Glioblastoma multiforme(486;0.00339)|Epithelial(262;0.00751)		ATTATGACCCGGAAGGAGCTC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													112	120	118	NA		NA	NA	19		NA											NA				49675285		2203	4300	6503	SO:0001583	missense			AK000048	CCDS33073.1, CCDS56098.1	19q13.3	2011-12-14				ENSG00000130529	54795		Voltage-gated ion channels / Transient receptor potential cation channels	17993	protein-coding gene	gene with protein product		606936			NA	11535825, 16382100	Standard	NM_017636	NM_017636	NA	Approved	FLJ20041	uc002pmw.3	Q8TD43		ENST00000252826.5:c.1070G>T	chr19.hg19:g.49675285G>T	ENSP00000252826:p.Arg357Leu	NA	A2RU25|Q7Z5D9|Q96L84|Q9NXV1	hg19	CCDS33073.1	0.02	2.326159	CCCxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.62	2.290626	0.40494	.	.	ENSG00000130529	ENST00000252826;ENST00000427978	T;T	0.35789	1.29;1.29	4.77	3.73	0.42828	.	0.657181	0.14202	N	0.334610	T	0.32823	0.0842	M	0.63843	1.955	0.80722	D	1	B;B;B	0.28026	0.198;0.028;0.004	B;B;B	0.25759	0.063;0.035;0.002	T	0.15780	-1.0425	10	0.46703	T	0.11	-31.7794	6.308	0.21149	0.0961:0.0:0.7219:0.182	.	183;357;357	Q8TD43-2;Q8TD43-3;Q8TD43	.;.;TRPM4_HUMAN	L	357	ENSP00000252826:R357L;ENSP00000407492:R357L	ENSP00000252826:R357L	R	+	2	0	TRPM4	54367097	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.382000	0.34374	1.135000	0.42183	0.591000	0.81541	CGG	NOVEL	TRPM4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465543.2	1	5.416732	KEEP	0	0	0	18	594	GG	0.999859	0.992786	0		+	27	60	994	0	0	93.34602	37	60	1250	109	ENST00000252826.5	0.421875	0.992926
EMC10	284361	__UNKNOWN__	__UNKNOWN__	19	50983481	50983481	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:50983481G>A	ENST00000334976.6	+	4	448				EMC10_ENST00000598585.1_Intron|EMC10_ENST00000376918.3_Intron|CTD-2545M3.2_ENST00000598194.1_RNA	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	NA		NA				ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)					NA						CGGTGAGTTGGTGTCGGGGAT	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	69	70	NA		NA	NA	19		NA											NA				50983481		2203	4300	6503	SO:0001627	intron_variant			BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671	284361			27609	protein-coding gene	gene with protein product	hematopoietic signal peptide-containing secreted 1, hematopoietic signal peptide-containing membrane domain-containing 1	614545	chromosome 19 open reading frame 63	C19orf63	NA	12975309, 22119785	Standard	NM_175063	NM_175063	NA	Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.402+9G>A	chr19.hg19:g.50983481G>A		NA	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	hg19	CCDS12796.1	0.02	17.804189	TTGxTGT	COVERED																																																																																			NOVEL	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464760.2	4	42.727255	KEEP	0	0	0	142	4837	GG	1	1	0		+	12	60	454	0	0	27.310984	421	60	15124	751	ENST00000334976.6	0.027714	1
SIGLEC8	27181	__UNKNOWN__	__UNKNOWN__	19	51960936	51960936	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:51960936C>A	ENST00000321424.3	-	2	578	c.512G>T	c.(511-513)aGg>aTg	p.R171M	SIGLEC8_ENST00000430817.1_Intron|SIGLEC8_ENST00000340550.5_Intron|SIGLEC8_ENST00000597352.1_5'UTR	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	171	Ig-like C2-type 1.	NA			cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GGTCAGGTTCCTGGAGTGGCC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													79	87	84	NA		NA	NA	19		NA											NA				51960936		2203	4300	6503	SO:0001583	missense			AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366	27181		Sialic acid binding Ig-like lectins, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	10877	protein-coding gene	gene with protein product		605639			NA	10625619	Standard	NM_014442	XR_243922	NA	Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.512G>T	chr19.hg19:g.51960936C>A	ENSP00000321077:p.Arg171Met	NA	Q7Z728	hg19	CCDS33086.1	0.02	4.446884	TTCxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	.	8.804	0.933715	0.18206	.	.	ENSG00000105366	ENST00000321424	T	0.20069	2.1	2.69	-3.71	0.04424	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	1.150320	0.06565	N	0.747307	T	0.15912	0.0383	L	0.41824	1.3	0.09310	N	1	B	0.29571	0.249	B	0.36030	0.216	T	0.43261	-0.9402	10	0.54805	T	0.06	.	0.9902	0.01454	0.3907:0.2774:0.1933:0.1386	.	171	Q9NYZ4	SIGL8_HUMAN	M	171	ENSP00000321077:R171M	ENSP00000321077:R171M	R	-	2	0	SIGLEC8	56652748	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-0.866000	0.04245	-0.336000	0.08438	0.502000	0.49764	AGG	NOVEL	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463648.2	1	5.718659	KEEP	0	0	0	19	677	CC	0.99986	0.99986	0		-	36	60	1323	0	0	114.818395	104	60	3778	203	ENST00000321424.3	0.257143	1
CACNG8	59283	__UNKNOWN__	__UNKNOWN__	19	54493399	54493399	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:54493399C>T	ENST00000270458.2	+	0	8677					NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	NA		NA			calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		TCTGTCCCTGCTCCTGGGGGA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408	59283		Calcium channel subunits	13628	protein-coding gene	gene with protein product		606900			NA	11170751	Standard		NM_031895	NA	Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.*7296C>T	chr19.hg19:g.54493399C>T		NA	Q9BXT0|Q9BY23	hg19	CCDS33104.1	0.02	1.839128	CTGxTCC	COVERED																																																																																			NOVEL	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139361.3	0	6.922515	KEEP	0	0	0	23	813	CC	0.999892	0.998093	0		+	4	60	144	0	0	9.552981	70	60	2558	120	ENST00000270458.2	0.054054	0.9982
LILRA6	79168	__UNKNOWN__	__UNKNOWN__	19	54744435	54744435	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs199737866		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:54744435C>T	ENST00000396365.2	-	6	1012	c.973G>A	c.(973-975)Gtc>Atc	p.V325I	LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.V325I|LILRA6_ENST00000245621.5_Missense_Mutation_p.V325I	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	325	Ig-like C2-type 2.	NA			immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GACAGGGAGACGGTGTCATAG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								C	ILE/VAL	1,4171		0,1,2085	13	19	17	NA	973	-0.2	0	19		17	4,8496		0,4,4246	no	missense	LILRA6	NM_024318.2	29	0,5,6331	TT,TC,CC	NA	0.0471,0.024,0.0395		325/482	54744435	5,12667	2086	4250	6336	SO:0001583	missense			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482	79168		Leukocyte immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	15495	protein-coding gene	gene with protein product		NA	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6	LILRB6	NA	10941842	Standard	NM_024318	NM_024318	NA	Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.973G>A	chr19.hg19:g.54744435C>T	ENSP00000379651:p.Val325Ile	NA		hg19	CCDS42610.1	0.02	2.188038	AGAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	7.108	0.575482	0.13623	2.4E-4	4.71E-4	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00717	5.79;5.79;5.79	2.16	-0.167	0.13347	Immunoglobulin-like fold (1);	0.435149	0.17144	N	0.185360	T	0.00875	0.0029	L	0.38531	1.155	0.09310	N	1	B;P;P	0.47034	0.127;0.889;0.501	B;B;B	0.42422	0.022;0.387;0.041	T	0.53507	-0.8429	10	0.66056	D	0.02	.	8.9816	0.35968	0.0:0.2362:0.7638:0.0	.	325;325;325	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	I	325	ENSP00000411227:V325I;ENSP00000379651:V325I;ENSP00000245621:V325I	ENSP00000245621:V325I	V	-	1	0	LILRA6	59436247	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.386000	0.07370	0.042000	0.15717	-1.112000	0.02068	GTC	NOVEL	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313725.1	3	9.326397	KEEP	58	0	0	31	974	CC	0.999988	0.981943	0		-	11	40	355	0	0	28.621471	46	60	1533	169	ENST00000396365.2	0.192982	0.981955
CTD-2105E13.6	0	__UNKNOWN__	__UNKNOWN__	19	55866106	55866106	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:55866106G>T	ENST00000591954.3	-	0	1815				COX6B2_ENST00000326529.4_5'UTR						NA		NA									NA						GTCCCACCCGGGTCAGGAGAA	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000591954.3:c.*398C>A	chr19.hg19:g.55866106G>T		NA		hg19		0.02	-0.280687	CCGxGTC	COVERED																																																																																			NOVEL	CTD-2105E13.6-002	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000466459.2	0	6.284445	KEEP	0	0	0	21	671	GG	0.999869	0.739575	0		-	6	60	175	0	0	13.751005	25	60	876	69	ENST00000591954.3	0.193548	0.739671
RFPL4A	342931	__UNKNOWN__	__UNKNOWN__	19	56273155	56273155	__UNKNOWN__	Intron	SNP	T	T	C	rs62126990		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:56273155T>C	ENST00000434937.2	+	2	162					NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	NA		NA					zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TTTTTTTCTATAGACATTTGC	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													7	5	6	NA		NA	NA	19		NA											NA				56273155		608	1394	2002	SO:0001627	intron_variant				CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638	342931		RING-type (C3HC4) zinc fingers	16449	protein-coding gene	gene with protein product		612601	ret finger protein-like 4	RFPL4	NA	11850190	Standard	XM_292796	NM_001145014	NA	Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.-9-3T>C	chr19.hg19:g.56273155T>C		NA		hg19	CCDS46201.1	0.02	4.974554	CTAxAGA	COVERED																																																																																			NOVEL	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384184.1	1	5.386621	KEEP	1	2	72	43	1346	TT	1	0.999996	0		+	42	50	1611	0	0	148.556157	72	60	2651	200	ENST00000434937.2	0.368421	0.999996
ZNF71	58491	__UNKNOWN__	__UNKNOWN__	19	57133382	57133382	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:57133382G>A	ENST00000328070.6	+	3	961	c.727G>A	c.(727-729)Gcg>Acg	p.A243T		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	243		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GAAGCCCTACGCGTGCGGGGA	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													52	49	50	NA		NA	NA	19		NA											NA				57133382		2203	4300	6503	SO:0001583	missense			X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951	58491		Zinc fingers, C2H2-type	13141	protein-coding gene	gene with protein product		194545	zinc finger protein 71 (Cos26)		NA	1639391	Standard	NM_021216	NM_021216	NA	Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.727G>A	chr19.hg19:g.57133382G>A	ENSP00000328245:p.Ala243Thr	NA	Q15919|Q9UC09|Q9UQD3	hg19	CCDS12947.1	0.02	17.697737	TACxCGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.29	3.081543	0.55753	.	.	ENSG00000197951	ENST00000328070	T	0.35973	1.28	3.82	-1.04	0.10068	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17916	0.0430	N	0.05554	-0.025	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.23084	-1.0198	9	0.66056	D	0.02	.	8.2461	0.31689	0.6706:0.0:0.3294:0.0	.	243	Q9NQZ8	ZNF71_HUMAN	T	243	ENSP00000328245:A243T	ENSP00000328245:A243T	A	+	1	0	ZNF71	61825194	0.000000	0.05858	0.936000	0.37596	0.984000	0.73092	-1.689000	0.01923	-0.049000	0.13379	-0.258000	0.10820	GCG	NOVEL	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459798.2	9	56.903242	KEEP	0	1	28	199	6705	GG	1	1	0		+	26	60	937	0	0	64.038212	385	60	13417	754	ENST00000328070.6	0.06326	1
ZNF71	58491	__UNKNOWN__	__UNKNOWN__	19	57133462	57133462	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:57133462G>A	ENST00000328070.6	+	3	1041	c.807G>A	c.(805-807)ccG>ccA	p.P269P		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	269		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GGGAGAAGCCGTACGTGTGCC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	54	53	NA		NA	NA	19		NA											NA				57133462		2203	4300	6503	SO:0001819	synonymous_variant			X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951	58491		Zinc fingers, C2H2-type	13141	protein-coding gene	gene with protein product		194545	zinc finger protein 71 (Cos26)		NA	1639391	Standard	NM_021216	NM_021216	NA	Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.807G>A	chr19.hg19:g.57133462G>A		NA	Q15919|Q9UC09|Q9UQD3	hg19	CCDS12947.1	0.02	18.5641	GCCxTAC	COVERED																																																																																			NOVEL	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459798.2	8	67.956531	KEEP	0	2	60	247	8156	GG	1	1	0		+	122	60	4267	0	0	370.875824	327	60	11170	923	ENST00000328070.6	0.271715	1
DUXA	503835	__UNKNOWN__	__UNKNOWN__	19	57665661	57665661	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:57665661C>A	ENST00000554048.2	-	0	733					NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)		tggccAAGTCCTTTACCATCT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS33126.1	19q13.43	2012-10-04			ENSG00000258873	ENSG00000258873	503835		Homeoboxes / PRD class	32179	protein-coding gene	gene with protein product		611168			NA		Standard	NM_001012729	NM_001012729	NA	Approved		uc002qoa.1	A6NLW8	OTTHUMG00000170714	ENST00000554048.2:c.*119G>T	chr19.hg19:g.57665661C>A		NA		hg19	CCDS33126.1	0.02	9.742643	GTCxTTT	COVERED																																																																																			NOVEL	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410075.3	7	10.233213	KEEP	0	0	0	34	1213	CC	0.999999	0.999999	0		-	151	60	5588	0	0	578.915951	55	60	1985	296	ENST00000554048.2	0.73301	1
ZNF547	284306	__UNKNOWN__	__UNKNOWN__	19	57889224	57889224	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:57889224A>G	ENST00000282282.3	+	4	1030	c.880A>G	c.(880-882)Agg>Ggg	p.R294G	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	294		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TACAGGAAAAAGGTCTTATGG	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	116	116	NA		NA	NA	19		NA											NA				57889224		2203	4300	6503	SO:0001583	missense			AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433	284306		Zinc fingers, C2H2-type, -	26432	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173631	NM_173631	NA	Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.880A>G	chr19.hg19:g.57889224A>G	ENSP00000282282:p.Arg294Gly	NA	A8K5Z9|Q96NC4	hg19	CCDS33131.1	0.02	11.200324	AAAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	A	20.2	3.950086	0.73787	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.16457	2.34	1.87	0.839	0.18907	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.28532	0.0706	L	0.61218	1.895	0.23681	N	0.997126	P;D;B	0.63046	0.884;0.992;0.229	P;P;B	0.58172	0.484;0.834;0.049	T	0.09207	-1.0685	9	0.87932	D	0	.	6.2209	0.20681	0.8567:0.0:0.1433:0.0	.	294;294;294	Q8IVP9-2;C9JTQ3;Q8IVP9	.;.;ZN547_HUMAN	G	294	ENSP00000282282:R294G	ENSP00000282282:R294G	R	+	1	2	ZNF547	62581036	0.990000	0.36364	0.002000	0.10522	0.947000	0.59692	4.096000	0.57734	0.197000	0.20387	0.402000	0.26972	AGG	NOVEL	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465787.1	5	12.33101	KEEP	0	0	0	41	1318	AA	1	1	0		+	26	60	904	0	0	65.491994	250	60	9202	364	ENST00000282282.3	0.094203	1
AC004076.7	0	__UNKNOWN__	__UNKNOWN__	19	57929440	57929440	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:57929440C>T	ENST00000597410.1	+	2	41				ZNF17_ENST00000595206.1_Intron|ZNF17_ENST00000601808.1_Intron|ZNF17_ENST00000307658.7_Intron|AC003002.6_ENST00000596400.1_Intron						NA		NA									NA						GTGTCTTGTGCTGGGCAATGT	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													120	115	116	NA		NA	NA	19		NA											NA				57929440		2201	4299	6500	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000597410.1:c.42-10387C>T	chr19.hg19:g.57929440C>T		NA		hg19		0.02	6.563359	GTGxTGG	COVERED																																																																																			NOVEL	AC004076.7-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000466421.1	2	11.134067	KEEP	0	0	0	37	1299	CC	1	1	0		+	32	60	1149	0	0	94.375018	139	60	5269	246	ENST00000597410.1	0.187135	1
VN1R1	57191	__UNKNOWN__	__UNKNOWN__	19	57967698	57967698	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:57967698G>T	ENST00000321039.3	-	1	156	c.157C>A	c.(157-159)Ctc>Atc	p.L53I	AC004076.9_ENST00000415705.3_Intron|AC004076.9_ENST00000596831.1_Intron	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	53		NA			response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		GTCTGAATGAGGAAGCTAATC	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													55	56	55	NA		NA	NA	19		NA											NA				57967698		2203	4300	6503	SO:0001583	missense			AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201	57191		Vomeronasal receptors / Type 1, GPCR / Unclassified : Vomeronasal receptors, type 1	13548	protein-coding gene	gene with protein product		605234	vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1	VNR19I1	NA	10973240	Standard	NM_020633	NM_020633	NA	Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.157C>A	chr19.hg19:g.57967698G>T	ENSP00000322339:p.Leu53Ile	NA	B3KSV5|Q7Z5H8|Q7Z5H9	hg19	CCDS12951.1	0.02	12.068648	TGAxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.28	2.786463	0.49997	.	.	ENSG00000178201	ENST00000321039	T	0.40756	1.02	4.18	-3.91	0.04168	.	.	.	.	.	T	0.37544	0.1007	L	0.31578	0.945	0.09310	N	1	D	0.63046	0.992	P	0.56088	0.791	T	0.35895	-0.9770	9	0.72032	D	0.01	.	5.3558	0.16059	0.3448:0.256:0.3992:0.0	.	53	Q9GZP7	VN1R1_HUMAN	I	53	ENSP00000322339:L53I	ENSP00000322339:L53I	L	-	1	0	VN1R1	62659510	0.996000	0.38824	0.003000	0.11579	0.004000	0.04260	1.045000	0.30341	-0.311000	0.08754	0.644000	0.83932	CTC	NOVEL	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466464.1	3	15.35003	KEEP	0	0	0	51	1817	GG	1	1	0		-	42	60	1546	0	0	124.039869	227	60	8365	412	ENST00000321039.3	0.156134	1
ZIK1	284307	__UNKNOWN__	__UNKNOWN__	19	58102327	58102327	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:58102327A>G	ENST00000597850.1	+	4	1363	c.1148A>G	c.(1147-1149)cAg>cGg	p.Q383R	ZIK1_ENST00000307468.4_3'UTR|ZIK1_ENST00000599456.1_Missense_Mutation_p.Q328R|ZIK1_ENST00000536878.2_Missense_Mutation_p.Q370R	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	383		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GAGTGTGGCCAGTGTGGGAAA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													65	64	64	NA		NA	NA	19		NA											NA				58102327		2203	4300	6503	SO:0001583	missense			AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649	284307		Zinc fingers, C2H2-type, -	33104	protein-coding gene	gene with protein product		NA	zinc finger protein interacting with K protein 1 homolog (mouse)		NA		Standard	NM_001010879	XM_005258769	NA	Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.1148A>G	chr19.hg19:g.58102327A>G	ENSP00000472867:p.Gln383Arg	NA	O43339|Q3SY51|Q3SY53	hg19	CCDS33135.1	0.02	12.295514	GCCxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	11.26	1.584971	0.28268	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.01005	5.45	3.37	3.37	0.38596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01976	0.0062	L	0.55481	1.735	0.09310	N	1	B;P	0.49185	0.063;0.92	B;P	0.47603	0.037;0.551	T	0.48490	-0.9031	9	0.62326	D	0.03	.	11.1978	0.48724	1.0:0.0:0.0:0.0	.	370;383	F5H435;Q3SY52	.;ZIK1_HUMAN	R	370;336;383	ENSP00000438487:Q370R	ENSP00000303820:Q383R	Q	+	2	0	ZIK1	62794139	0.000000	0.05858	0.008000	0.14137	0.453000	0.32348	0.144000	0.16135	1.533000	0.49186	0.533000	0.62120	CAG	NOVEL	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466791.1	3	17.452809	KEEP	0	0	0	58	1837	AA	1	1	0		+	14	60	501	0	0	31.762358	309	60	11619	463	ENST00000597850.1	0.043344	1
ZNF132	7691	__UNKNOWN__	__UNKNOWN__	19	58948384	58948384	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:58948384A>T	ENST00000254166.3	-	2	633					NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		GGCATAAGGTAGTCATCACCA	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													123	85	98	NA		NA	NA	19		NA											NA				58948384		2203	4300	6503	SO:0001627	intron_variant			U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849	7691		Zinc fingers, C2H2-type, -	12916	protein-coding gene	gene with protein product		604074	zinc finger protein 132 (clone pHZ-12)		NA	7557990	Standard	NM_003433	NM_003433	NA	Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.232+29T>A	chr19.hg19:g.58948384A>T		NA	Q32MI9	hg19	CCDS12980.1	0.02	16.915922	GGTxGTC	COVERED																																																																																			NOVEL	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467035.1	2	18.354593	KEEP	0	0	0	61	1905	AA	1	1	0		-	65	60	2343	0	0	190.25612	310	60	10894	551	ENST00000254166.3	0.173333	1
ZNF132	7691	__UNKNOWN__	__UNKNOWN__	19	58948485	58948485	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr19:58948485A>T	ENST00000254166.3	-	2	561	c.161T>A	c.(160-162)cTc>cAc	p.L54H		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	54	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		TGCATCAAGGAGCTCCCACTC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													126	94	105	NA		NA	NA	19		NA											NA				58948485		2203	4300	6503	SO:0001583	missense			U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849	7691		Zinc fingers, C2H2-type, -	12916	protein-coding gene	gene with protein product		604074	zinc finger protein 132 (clone pHZ-12)		NA	7557990	Standard	NM_003433	NM_003433	NA	Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.161T>A	chr19.hg19:g.58948485A>T	ENSP00000254166:p.Leu54His	NA	Q32MI9	hg19	CCDS12980.1	0.02	14.087138	AGGxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.53	2.861400	0.51482	.	.	ENSG00000131849	ENST00000254166;ENST00000391695	T	0.02177	4.41	3.41	2.26	0.28386	Krueppel-associated box (4);	.	.	.	.	T	0.06690	0.0171	L	0.53780	1.695	0.09310	N	0.999998	D	0.89917	1.0	D	0.79784	0.993	T	0.36915	-0.9728	9	0.16896	T	0.51	.	7.2447	0.26115	0.7748:0.2252:0.0:0.0	.	54	P52740	ZN132_HUMAN	H	54;23	ENSP00000254166:L54H	ENSP00000254166:L54H	L	-	2	0	ZNF132	63640297	0.023000	0.18921	0.967000	0.41034	0.970000	0.65996	0.315000	0.19451	1.319000	0.45190	0.460000	0.39030	CTC	NOVEL	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467035.1	2	14.134623	KEEP	0	0	0	47	1472	AA	1	1	0		-	57	60	1994	0	0	160.265528	278	60	10249	448	ENST00000254166.3	0.170149	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	168436	168436	__UNKNOWN__	IGR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:168436C>T			NA	NA				DEFB127 (28632 upstream) : DEFB128 (57 downstream)						NA		NA									NA						CAGAAGGAAGCAGATGAATCT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.168436C>T		NA		hg19		0.02	17.534798	AAGxAGA	COVERED																																																																																			NOVEL					0			1	13.844533	KEEP	0	0	0	46	1643	CC	1	1	0			76	60	2625	0	0	210.84722	364	60	13662	570		0.172727	1
C20orf96	140680	__UNKNOWN__	__UNKNOWN__	20	256730	256730	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:256730G>T	ENST00000360321.2	-	10	1051				C20orf96_ENST00000382369.5_Intron	NM_080571.1|NM_153269.2	NP_542138.1|NP_695001.2	Q9NUD7	CT096_HUMAN	chromosome 20 open reading frame 96	NA		NA								endometrium(3)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12		all_cancers(10;0.00959)|Lung NSC(37;0.227)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			TCAATAATCTGAGAGGAAAGG	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													60	63	62	NA		NA	NA	20		NA											NA				256730		2203	4300	6503	SO:0001627	intron_variant			AL034548	CCDS12994.1, CCDS74685.1	20p13	2012-10-30			ENSG00000196476	ENSG00000196476	140680			16227	protein-coding gene	gene with protein product		NA			NA		Standard	NM_153269	NM_153269	NA	Approved	dJ1103G7.2	uc002wde.2	Q9NUD7	OTTHUMG00000031626	ENST00000360321.2:c.913-3C>A	chr20.hg19:g.256730G>T		NA	A3KPE0|B2RPH9|Q8N840|Q8NAX5	hg19	CCDS12994.1	0.02	1.968372	TCTxAGA	COVERED																																																																																			NOVEL	C20orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077439.2	0	3.31077	KEEP	0	0	0	11	384	GG	0.993072	0.992484	0		-	20	60	707	0	0	60.459438	62	60	2319	106	ENST00000360321.2	0.243902	0.999407
SOX12	6666	__UNKNOWN__	__UNKNOWN__	20	310744	310744	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:310744G>T	ENST00000342665.2	+	0	4506				RP5-1103G7.4_ENST00000442637.1_RNA	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	NA		NA			cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			ctcccagcaggcccaggccag	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U35612	CCDS12995.1	20p13	2008-07-28	2002-07-22	2002-07-26	ENSG00000177732	ENSG00000177732	6666		SRY (sex determining region Y)-boxes	11198	protein-coding gene	gene with protein product		601947	SRY (sex determining region Y)-box 22	SOX22	NA	9215677	Standard	NM_006943	NM_006943	NA	Approved		uc002wdh.4	O15370	OTTHUMG00000031623	ENST00000342665.2:c.*3228G>T	chr20.hg19:g.310744G>T		NA	Q5D038|Q9NUD4	hg19	CCDS12995.1	0.02	11.25079	CAGxCCC	COVERED																																																																																			NOVEL	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077435.2	2	30.999895	KEEP	0	0	0	103	3615	GG	1	1	0		+	46	60	1618	0	0	130.997292	215	70	7719	470	ENST00000342665.2	0.176245	1
SNPH	9751	__UNKNOWN__	__UNKNOWN__	20	1286596	1286596	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:1286596G>A	ENST00000381873.3	+	6	1619	c.1383G>A	c.(1381-1383)ctG>ctA	p.L461L	SNPH_ENST00000381867.1_Silent_p.L505L	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	461		NA			brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						GCTCCCTGCTGCGGGGCTGCT	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													8	6	7	NA		NA	NA	20		NA											NA				1286596		2022	4042	6064	SO:0001819	synonymous_variant				CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298	9751			15931	protein-coding gene	gene with protein product		604942			NA	10707983	Standard	NM_014723	NM_014723	NA	Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.1383G>A	chr20.hg19:g.1286596G>A		NA	Q8IYI3	hg19	CCDS13012.1	0.02	4.094756	GCTxCGG	COVERED																																																																																			NOVEL	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000145240.2	2	18.658389	KEEP	0	0	0	62	2168	GG	1	1	0		+	30	60	1016	0	0	83.915739	114	60	4314	294	ENST00000381873.3	0.208333	1
NOP56	10528	__UNKNOWN__	__UNKNOWN__	20	2635587	2635587	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs371285710		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:2635587G>A	ENST00000329276.5	+	5	1079	c.563G>A	c.(562-564)cGt>cAt	p.R188H		NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	188		NA			cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TTCTCTATGCGTGTCAGGTAA	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	HIS/ARG	0,4406		0,0,2203	103	103	103	NA	563	4.9	1	20		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	NOP56	NM_006392.3	29	0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077	probably-damaging	188/595	2635587	1,13005	2203	4300	6503	SO:0001583	missense			Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361	10528			15911	protein-coding gene	gene with protein product	spinocerebellar ataxia 36	614154	nucleolar protein 5A (56kD with KKE/D repeat), nucleolar protein 5A (56kDa with KKE/D repeat), NOP56 ribonucleoprotein homolog (yeast)	NOL5A	NA	9372940, 21683323	Standard	NM_006392	NR_027700	NA	Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.563G>A	chr20.hg19:g.2635587G>A	ENSP00000370589:p.Arg188His	NA	Q2M3T6|Q9NQ05	hg19	CCDS13030.1	0.02	4.384866	TGCxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	26.2	4.715437	0.89112	0.0	1.16E-4	ENSG00000101361	ENST00000329276;ENST00000445139	D;D	0.86769	-2.17;-2.17	5.89	4.94	0.65067	NOSIC (2);	0.000000	0.85682	D	0.000000	D	0.96134	0.8740	H	0.98849	4.35	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97134	0.9820	10	0.87932	D	0	-9.7591	12.8657	0.57937	0.0786:0.0:0.9214:0.0	.	188	O00567	NOP56_HUMAN	H	188	ENSP00000370589:R188H;ENSP00000388497:R188H	ENSP00000370589:R188H	R	+	2	0	NOP56	2583587	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	9.603000	0.98315	1.494000	0.48533	-0.266000	0.10368	CGT	NOVEL	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077631.2	3	11.136145	KEEP	0	0	0	37	1289	GG	1	0.999995	0		+	13	60	474	0	0	36.093858	100	60	3408	183	ENST00000329276.5	0.115044	0.999995
PTPRA	5786	__UNKNOWN__	__UNKNOWN__	20	3018621	3018621	__UNKNOWN__	Intron	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:3018621A>G	ENST00000216877.6	+	23	2707				PTPRA_ENST00000358719.4_Intron|PTPRA_ENST00000399903.2_Intron|PTPRA_ENST00000356147.3_Intron|PTPRA_ENST00000318266.5_Intron|PTPRA_ENST00000380393.3_Intron|PTPRA_ENST00000425918.2_Intron	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	NA		NA			axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TTCCATCTTCAACAAAAAAAT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670	5786		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA	NA	2172030, 2169617	Standard		NM_080840	NA	Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.2308-84A>G	chr20.hg19:g.3018621A>G		NA	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	hg19	CCDS13039.1	0.02	5.957481	TTCxACA	COVERED																																																																																			NOVEL	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077682.3	1	8.114315	KEEP	0	0	0	27	821	AA	0.999988	0.999988	0		+	8	60	270	0	0	16.777185	164	60	5984	220	ENST00000216877.6	0.046512	1
UBOX5	22888	__UNKNOWN__	__UNKNOWN__	20	3090864	3090864	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:3090864C>T	ENST00000217173.2	-	5	1985	c.1514G>A	c.(1513-1515)gGc>gAc	p.G505D	UBOX5_ENST00000348031.2_Missense_Mutation_p.G451D|UBOX5-AS1_ENST00000446537.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5	NA		NA								endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						CAGGAGGTGGCCGCAGGGCAG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													68	76	73	NA		NA	NA	20		NA											NA				3090864		2203	4300	6503	SO:0001583	missense			AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019	22888		RING-type (C3HC4) zinc fingers, U-box domain containing	17777	protein-coding gene	gene with protein product		NA			NA	11274149	Standard	NM_014948	NM_014948	NA	Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.1514G>A	chr20.hg19:g.3090864C>T	ENSP00000217173:p.Gly505Asp	NA		hg19	CCDS13046.1	0.02	4.5898	TGGxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.8	4.197122	0.79015	.	.	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.67523	-0.12;-0.27	5.04	5.04	0.67666	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);	0.182346	0.47093	U	0.000251	T	0.81034	0.4739	M	0.72894	2.215	0.44789	D	0.997793	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.961	T	0.80489	-0.1360	10	0.41790	T	0.15	-12.2613	18.7495	0.91809	0.0:1.0:0.0:0.0	.	451;505	Q86X87;O94941	.;RNF37_HUMAN	D	505;451	ENSP00000217173:G505D;ENSP00000311726:G451D	ENSP00000217173:G505D	G	-	2	0	UBOX5	3038864	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	4.788000	0.62439	2.497000	0.84241	0.561000	0.74099	GGC	NOVEL	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077706.2	0	10.231617	KEEP	0	0	0	34	1158	CC	0.999998	0.999966	0		-	21	60	676	1	0	55.210087	80	60	2798	174	ENST00000217173.2	0.207921	0.999968
DDRGK1	65992	__UNKNOWN__	__UNKNOWN__	20	3172396	3172396	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:3172396C>T	ENST00000354488.3	-	7	787				DDRGK1_ENST00000380201.2_Silent_p.T248T	NM_023935.1	NP_076424.1	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1	NA		NA				endoplasmic reticulum (GO:0005783)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7						CAGCAGGCCACGTTCCAGGGC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	33	36	NA		NA	NA	20		NA											NA				3172396		2202	4300	6502	SO:0001627	intron_variant			AL121891	CCDS13050.1	20p13	2011-08-18	2008-10-03	2008-10-03	ENSG00000198171	ENSG00000198171	65992			16110	protein-coding gene	gene with protein product	Dashurin	NA	chromosome 20 open reading frame 116	C20orf116	NA	20036718, 20228063, 21494687	Standard	NM_023935	NM_023935	NA	Approved	dJ1187M17.3	uc002wic.3	Q96HY6	OTTHUMG00000031732	ENST00000354488.3:c.729+14G>A	chr20.hg19:g.3172396C>T		NA	A6NIU5|C9JSZ5|Q9BW47	hg19	CCDS13050.1	0.02	9.374716	CCAxGTT	COVERED																																																																																			NOVEL	DDRGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077709.2	6	14.107863	KEEP	0	0	0	47	1540	CC	1	1	0		-	39	60	1439	0	0	115.675312	209	60	6922	355	ENST00000354488.3	0.157258	1
CDC25B	994	__UNKNOWN__	__UNKNOWN__	20	3784181	3784181	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs200957584		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:3784181G>A	ENST00000245960.5	+	14	2184	c.1487G>A	c.(1486-1488)cGc>cAc	p.R496H	CDC25B_ENST00000340833.4_Missense_Mutation_p.R455H|CDC25B_ENST00000379598.5_Missense_Mutation_p.R405H|CDC25B_ENST00000344256.6_Missense_Mutation_p.R432H|CDC25B_ENST00000439880.2_Missense_Mutation_p.R482H|CDC25B_ENST00000467519.1_3'UTR	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	496	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.	NA			female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						CGTGGGCCCCGCATGTGAGTC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	67	71	NA		NA	NA	20		NA											NA				3784181		2203	4300	6503	SO:0001583	missense				CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224	994		Protein tyrosine phosphatases / Class III Cys-based PTPs	1726	protein-coding gene	gene with protein product		116949	cell division cycle 25B, cell division cycle 25 homolog B (S. cerevisiae), cell division cycle 25 homolog B (S. pombe)		NA	1836978	Standard	NM_021874	NM_021873	NA	Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.1487G>A	chr20.hg19:g.3784181G>A	ENSP00000245960:p.Arg496His	NA	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	hg19	CCDS13067.1	0.02	18.905501	CCCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	32	5.119412	0.94385	.	.	ENSG00000101224	ENST00000344256;ENST00000379598;ENST00000245960;ENST00000439880;ENST00000340833	T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47	5.55	4.6	0.57074	Rhodanese-like (5);	0.000000	0.85682	D	0.000000	T	0.48892	0.1525	L	0.54863	1.705	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.77004	0.989;0.989;0.989;0.982;0.982;0.985	T	0.48790	-0.9004	10	0.59425	D	0.04	-10.8351	12.379	0.55295	0.0821:0.0:0.9179:0.0	.	405;418;432;455;482;496	B4DQZ3;B4DRC3;B4DIG0;P30305-3;P30305-2;P30305	.;.;.;.;.;MPIP2_HUMAN	H	432;405;496;482;455	ENSP00000339125:R432H;ENSP00000368918:R405H;ENSP00000245960:R496H;ENSP00000405972:R482H;ENSP00000339170:R455H	ENSP00000245960:R496H	R	+	2	0	CDC25B	3732181	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	4.073000	0.57570	1.495000	0.48549	0.655000	0.94253	CGC	NOVEL	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077779.2	5	33.741307	KEEP	0	2	38	126	4415	GG	1	1	0		+	79	60	2796	0	0	230.070034	331	60	11903	708	ENST00000245960.5	0.192683	1
PROKR2	128674	__UNKNOWN__	__UNKNOWN__	20	5294763	5294763	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs141090506	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:5294763G>A	ENST00000217270.3	-	1	252	c.253C>T	c.(253-255)Cgc>Tgc	p.R85C	PROKR2_ENST00000546004.1_Missense_Mutation_p.R85C	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	85		NA	R -> C (in HH3; uncertain pathological significance). {ECO:0000269|PubMed:17054399}.|R -> H (in HH3; phenotype consistent with Kallmann syndrome; dbSNP:rs74315418). {ECO:0000269|PubMed:17054399}.		circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.R85C(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						GTGAGGTTGCGCAACTTCTTA	0.547	NA	NA								HNSCC(71;0.22)			G|||	3	0.000599042	8e-04	0.0014	5008	,	,	NA	22073	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	ovary(1)	GRCh37	CM083840	PROKR2	M	rs141090506						191	149	163	NA		NA	NA	20		NA											NA				5294763		2203	4300	6503	SO:0001583	missense			AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292	128674		GPCR / Class A : Prokineticin receptors	15836	protein-coding gene	gene with protein product		607123	G protein-coupled receptor 73-like 1, Kallmann syndrome 3 (autosomal dominant)	GPR73L1, KAL3	NA	11886876, 17054399	Standard	NM_144773	NM_144773	NA	Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.253C>T	chr20.hg19:g.5294763G>A	ENSP00000217270:p.Arg85Cys	NA	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	hg19	CCDS13089.1	0.02	12.716237	TGCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809204	0.70797	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.46063	0.88;0.88	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72993	0.3530	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80455	-0.1375	10	0.87932	D	0	.	10.8357	0.46685	0.0:0.0:0.8114:0.1886	.	85	Q8NFJ6	PKR2_HUMAN	C	85	ENSP00000440790:R85C;ENSP00000217270:R85C	ENSP00000217270:R85C	R	-	1	0	PROKR2	5242763	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.002000	0.49496	2.347000	0.79759	0.655000	0.94253	CGC	NOVEL	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077854.1	0	10.53291	KEEP	0	0	0	35	1208	GG	0.999999	0.999999	0		-	11	60	404	0	0	24.685966	321	60	11265	439	ENST00000217270.3	0.033133	1
PLCB1	23236	__UNKNOWN__	__UNKNOWN__	20	8702997	8702997	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:8702997A>T	ENST00000338037.6	+	15	1540				PLCB1_ENST00000494924.1_Intron|PLCB1_ENST00000378641.3_Intron|PLCB1_ENST00000378637.2_Intron	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	NA		NA			activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TTAAAATTTGACAGGAGAAGC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													170	146	155	NA		NA	NA	20		NA											NA				8702997		2203	4300	6503	SO:0001627	intron_variant			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	23236	3.1.4.11		15917	protein-coding gene	gene with protein product		607120			NA	10760467, 11118617	Standard		NM_015192	NA	Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1514-4A>T	chr20.hg19:g.8702997A>T		NA	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	hg19	CCDS13102.1	0.02	13.62774	TTGxCAG	COVERED																																																																																			NOVEL	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077938.3	3	27.678223	KEEP	0	0	0	92	3014	AA	1	1	0		+	51	60	1803	0	0	143.915464	266	60	9585	525	ENST00000338037.6	0.160883	1
PLCB4	5332	__UNKNOWN__	__UNKNOWN__	20	9460657	9460657	__UNKNOWN__	3'UTR	SNP	C	C	A	rs536773247	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:9460657C>A	ENST00000378501.2	+	0	4601				PLCB4_ENST00000334005.3_3'UTR|PLCB4_ENST00000378473.3_3'UTR|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378493.1_3'UTR|PLCB4_ENST00000278655.4_3'UTR	NM_000933.3	NP_000924.3	Q15147	PLCB4_HUMAN	phospholipase C, beta 4	NA		NA			inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						AACCCTCTCTCTATATATATA	0.254	NA	NA											C|||	2	0.000399361	0.0015	0	5008	,	,	NA	16859	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	5332	3.1.4.11		9059	protein-coding gene	gene with protein product		600810			NA	8530101	Standard		NM_000933	NA	Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378501.2:c.*1001C>A	chr20.hg19:g.9460657C>A		NA	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	hg19	CCDS13104.1	0.02	6.583913	TCTxTAT	COVERED																																																																																			NOVEL	PLCB4-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077958.2	4	10.835412	KEEP	0	0	0	36	1284	CC	0.999999	0.999999	0		+	15	60	557	0	0	40.438503	165	60	6310	268	ENST00000378501.2	0.083333	1
SPTLC3	55304	__UNKNOWN__	__UNKNOWN__	20	13029668	13029668	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:13029668T>A	ENST00000399002.2	+	2	467	c.193T>A	c.(193-195)Ttc>Atc	p.F65I	SPTLC3_ENST00000476791.1_3'UTR|SPTLC3_ENST00000378194.4_Missense_Mutation_p.F65I	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	65		NA			small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						TGTTATGGTTTTCACTTACAT	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													153	158	157	NA		NA	NA	20		NA											NA				13029668		2203	4300	6503	SO:0001583	missense			AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	55304	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	chromosome 20 open reading frame 38, serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)	C20orf38, SPTLC2L	NA	17023427	Standard	NM_018327	NM_018327	NA	Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.193T>A	chr20.hg19:g.13029668T>A	ENSP00000381968:p.Phe65Ile	NA	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	hg19	CCDS13115.2	0.02	24.872192	GTTxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	T	14.53	2.564403	0.45694	.	.	ENSG00000172296	ENST00000434210;ENST00000399002;ENST00000378194;ENST00000450297	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.63	3.31	0.37934	.	0.634955	0.17796	N	0.161730	T	0.64951	0.2645	L	0.40543	1.245	0.25201	N	0.990053	B;P	0.51537	0.001;0.946	B;P	0.51453	0.007;0.67	T	0.54761	-0.8245	10	0.38643	T	0.18	-13.4756	4.2777	0.10816	0.1541:0.1513:0.0:0.6946	.	65;65	Q9NUV7;Q9NUV7-2	SPTC3_HUMAN;.	I	65;65;65;38	ENSP00000389749:F65I;ENSP00000381968:F65I;ENSP00000367436:F65I;ENSP00000409125:F38I	ENSP00000367436:F65I	F	+	1	0	SPTLC3	12977668	0.998000	0.40836	0.993000	0.49108	0.948000	0.59901	0.707000	0.25704	1.025000	0.39708	0.533000	0.62120	TTC	NOVEL	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254544.1	5	37.613468	KEEP	0	0	0	125	4030	TT	1	1	0		+	47	60	1705	0	0	121.789208	545	60	19775	907	ENST00000399002.2	0.079392	1
DZANK1	55184	__UNKNOWN__	__UNKNOWN__	20	18435880	18435880	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:18435880T>G	ENST00000358866.6	-	3	401				DZANK1_ENST00000329494.5_Intron|DZANK1_ENST00000262547.5_Intron|DZANK1_ENST00000357236.4_Intron			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	NA		NA					zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						GATTATAGTTTCATTACTTGC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													106	95	98	NA		NA	NA	20		NA											NA				18435880		1889	4120	6009	SO:0001627	intron_variant			AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091	55184		Ankyrin repeat domain containing	15858	protein-coding gene	gene with protein product	ankyrin repeat domain 64	NA	chromosome 20 open reading frame 12	C20orf84, C20orf12	NA		Standard	NM_001099407	NM_001099407	NA	Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.378+10A>C	chr20.hg19:g.18435880T>G		NA	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	hg19	CCDS46582.1	0.02	10.036891	GTTxCAT	COVERED																																																																																			NOVEL	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471926.1	3	10.532392	KEEP	0	0	0	35	1143	TT	0.999999	0.999999	0		-	48	60	1821	0	0	155.097975	170	60	6160	312	ENST00000358866.6	0.220183	1
RALGAPA2	57186	__UNKNOWN__	__UNKNOWN__	20	20452874	20452874	__UNKNOWN__	Intron	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:20452874T>A	ENST00000202677.7	-	37	5503					NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	NA		NA			activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AGAGAAAATATCAATGATTTG	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559	57186			16207	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 74	C20orf74	NA	16490346, 19520869	Standard	NM_020343	NM_020343	NA	Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.5495+598A>T	chr20.hg19:g.20452874T>A		NA	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	hg19	CCDS46584.1	0.02	8.959391	ATAxCAA	COVERED																																																																																			NOVEL	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471941.1	5	12.337483	KEEP	0	0	0	41	1326	TT	1	1	0		-	30	60	1077	0	0	83.526638	197	60	7156	301	ENST00000202677.7	0.132159	1
CD93	22918	__UNKNOWN__	__UNKNOWN__	20	23063205	23063205	__UNKNOWN__	3'UTR	SNP	T	T	A	rs6113931		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:23063205T>A	ENST00000246006.4	-	0	3488					NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	NA		NA			macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					tgtgtgtgtgtgagagagaga	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810	22918		CD molecules	15855	protein-coding gene	gene with protein product		120577	matrix-remodelling associated 4, complement component 1, q subcomponent, receptor 1, CD93 antigen	MXRA4, C1QR1	NA	9047234, 10648005	Standard	NM_012072	NM_012072	NA	Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.*1382A>T	chr20.hg19:g.23063205T>A		NA	O00274	hg19	CCDS13149.1	0.02	2.068269	GTGxGAG	COVERED																																																																																			NOVEL	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078312.2	5	2.943173	KEEP	2	1	32	21	662	TT	0.999869	0.999276	0		-	6	60	218	2	0	15.65876	67	60	2366	117	ENST00000246006.4	0.082192	0.999407
GZF1	64412	__UNKNOWN__	__UNKNOWN__	20	23345607	23345607	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:23345607T>C	ENST00000338121.5	+	2	664	c.587T>C	c.(586-588)tTg>tCg	p.L196S	GZF1_ENST00000542987.1_Intron|GZF1_ENST00000377051.2_Missense_Mutation_p.L196S|GZF1_ENST00000544236.1_Intron			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	196		NA			branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					TCTTCAGATTTGCCACCGAAG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	50	49	NA		NA	NA	20		NA											NA				23345607		2203	4300	6503	SO:0001583	missense			AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812	64412		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	15808	protein-coding gene	gene with protein product		613842	zinc finger protein 336	ZNF336	NA	14522971, 16049025	Standard	NM_022482	NM_022482	NA	Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.587T>C	chr20.hg19:g.23345607T>C	ENSP00000338290:p.Leu196Ser	NA	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	hg19	CCDS13151.1	0.02	9.889111	ATTxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	T	1.506	-0.550886	0.03996	.	.	ENSG00000125812	ENST00000338121;ENST00000377051	T;T	0.11063	2.81;2.81	4.08	-2.57	0.06248	.	1.609080	0.03765	N	0.258750	T	0.06781	0.0173	N	0.19112	0.55	0.09310	N	1	B	0.20887	0.049	B	0.16722	0.016	T	0.38672	-0.9650	10	0.09590	T	0.72	.	8.9893	0.36014	0.0:0.5427:0.1307:0.3266	.	196	Q9H116	GZF1_HUMAN	S	196	ENSP00000338290:L196S;ENSP00000366250:L196S	ENSP00000338290:L196S	L	+	2	0	GZF1	23293607	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.087000	0.03383	-0.406000	0.07588	-0.436000	0.05848	TTG	NOVEL	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078333.1	1	18.948258	KEEP	0	0	0	63	1919	TT	1	1	0		+	40	60	1376	0	0	110.259105	194	60	7088	358	ENST00000338121.5	0.17094	1
NANP	140838	__UNKNOWN__	__UNKNOWN__	20	25596964	25596964	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:25596964T>C	ENST00000304788.3	-	2	570	c.344A>G	c.(343-345)aAa>aGa	p.K115R		NM_152667.2	NP_689880.1	Q8TBE9	NANP_HUMAN	N-acetylneuraminic acid phosphatase	115		NA			carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate biosynthetic process (GO:0046380)		N-acylneuraminate-9-phosphatase activity (GO:0050124)			endometrium(2)|lung(2)|prostate(1)	5						AAGCATGGCTTTGACGTCTTC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	114	115	NA		NA	NA	20		NA											NA				25596964		2203	4300	6503	SO:0001583	missense			AL031673	CCDS13173.1	20p11.1	2006-10-24	2006-01-24	2006-01-24	ENSG00000170191	ENSG00000170191	140838			16140	protein-coding gene	gene with protein product		610763	chromosome 20 open reading frame 147, haloacid dehalogenase-like hydrolase domain containing 4	C20orf147, HDHD4	NA	16237198	Standard	NM_152667	NM_152667	NA	Approved	dJ694B14.3, MGC26833	uc002wuy.3	Q8TBE9	OTTHUMG00000032132	ENST00000304788.3:c.344A>G	chr20.hg19:g.25596964T>C	ENSP00000302441:p.Lys115Arg	NA	B3KP12|Q5JYN8|Q8TE97|Q9Y3N0	hg19	CCDS13173.1	0.02	7.493945	GCTxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	T	9.044	0.990364	0.18966	.	.	ENSG00000170191	ENST00000304788	T	0.05258	3.47	5.4	4.3	0.51218	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.271680	0.40554	N	0.001062	T	0.03348	0.0097	N	0.11106	0.095	0.29027	N	0.885911	B	0.11235	0.004	B	0.16722	0.016	T	0.40627	-0.9553	10	0.09843	T	0.71	-15.4183	9.3743	0.38272	0.0:0.085:0.0:0.915	.	115	Q8TBE9	NANP_HUMAN	R	115	ENSP00000302441:K115R	ENSP00000302441:K115R	K	-	2	0	NANP	25544964	0.981000	0.34729	1.000000	0.80357	0.828000	0.46876	1.755000	0.38379	0.895000	0.36342	-0.425000	0.05940	AAA	NOVEL	NANP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078457.2	3	9.027454	KEEP	0	0	0	30	976	TT	0.999997	0.999997	0		-	27	60	977	0	0	79.393389	129	60	4670	244	ENST00000304788.3	0.173077	1
FAM182A	284800	__UNKNOWN__	__UNKNOWN__	20	26063993	26063993	__UNKNOWN__	RNA	SNP	A	A	G	rs202066058		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:26063993A>G	ENST00000376398.2	+	0	1510					NR_026713.1		Q5T1J6	F182A_HUMAN	family with sequence similarity 182, member A	NA		NA								breast(1)|endometrium(2)|kidney(1)	4						CTGAGACTTGATGTTTAATAT	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AL391119		20p11	2013-03-18	2008-08-05	2008-08-05	ENSG00000125804	ENSG00000125804	284800			16222	other	unknown		NA	chromosome 20 open reading frame 91	C20orf91	NA		Standard		NR_026713	NA	Approved	bB329D4.1, C20orf91A	uc010gdq.3	Q5T1J6	OTTHUMG00000032144	ENST00000376398.2:	chr20.hg19:g.26063993A>G		NA	A2RRD0|Q8N947	hg19		0.02	7.248384	TTGxTGT	COVERED																																																																																			NOVEL	FAM182A-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000078473.2	8	9.963901	KEEP	24	1	37	46	1464	AA	1	1	0		+	8	49	301	0	0	21.672995	96	60	3447	350	ENST00000376398.2	0.076923	1
FAM182A	284800	__UNKNOWN__	__UNKNOWN__	20	26064021	26064021	__UNKNOWN__	RNA	SNP	G	G	T	rs76817215		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:26064021G>T	ENST00000376398.2	+	0	1538					NR_026713.1		Q5T1J6	F182A_HUMAN	family with sequence similarity 182, member A	NA		NA								breast(1)|endometrium(2)|kidney(1)	4						AGTTCTTTTGGGGCCTGTTGT	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AL391119		20p11	2013-03-18	2008-08-05	2008-08-05	ENSG00000125804	ENSG00000125804	284800			16222	other	unknown		NA	chromosome 20 open reading frame 91	C20orf91	NA		Standard		NR_026713	NA	Approved	bB329D4.1, C20orf91A	uc010gdq.3	Q5T1J6	OTTHUMG00000032144	ENST00000376398.2:	chr20.hg19:g.26064021G>T		NA	A2RRD0|Q8N947	hg19		0.02	6.27031	TTGxGGC	COVERED																																																																																			NOVEL	FAM182A-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000078473.2	11	10.205372	KEEP	30	1	34	46	1590	GG	1	1	0		+	8	49	289	0	0	20.585785	93	60	3172	372	ENST00000376398.2	0.079208	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628251	29628251	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29628251A>G	ENST00000278882.3	+	6	633	c.253A>G	c.(253-255)Aat>Gat	p.N85D	FRG1B_ENST00000358464.4_Missense_Mutation_p.N85D|FRG1B_ENST00000439954.2_Missense_Mutation_p.N90D			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	85		NA						p.N85D(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTTGGCCTCAAATAGCTGCTT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)											NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.253A>G	chr20.hg19:g.29628251A>G	ENSP00000278882:p.Asn85Asp	NA	C4AME5	hg19		0.02	39.701339	TCAxATA	COVERED	.	.	.	.	.	.	.	.	.	.	a	15.78	2.933773	0.52866	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.50277	0.75	2.08	2.08	0.27032	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	.	.	.	0.45390	D	0.998378	B;B	0.26809	0.086;0.16	B;B	0.40329	0.326;0.253	T	0.51553	-0.8691	9	0.66056	D	0.02	.	8.0833	0.30758	1.0:0.0:0.0:0.0	.	90;85	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	D	85;90;85	ENSP00000408863:N90D	ENSP00000278882:N85D	N	+	1	0	FRG1B	28241912	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	8.047000	0.89440	1.208000	0.43306	0.347000	0.21830	AAT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	14	8.717585	KEEP	48	25	898	342	11216	AA	1	1	0		+	39	60	1475	0	0	103.699974	553	60	20223	1571	ENST00000278882.3	0.065878	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628254	29628254	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29628254A>G	ENST00000278882.3	+	6	636	c.256A>G	c.(256-258)Agc>Ggc	p.S86G	FRG1B_ENST00000358464.4_Missense_Mutation_p.S86G|FRG1B_ENST00000439954.2_Missense_Mutation_p.S91G			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	86		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGCCTCAAATAGCTGCTTTAT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.256A>G	chr20.hg19:g.29628254A>G	ENSP00000278882:p.Ser86Gly	NA	C4AME5	hg19		0.02	39.328663	AATxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	a	4.173	0.030659	0.08101	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.42900	0.96	2.08	2.08	0.27032	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.17704	0.0425	.	.	.	0.41329	D	0.987223	B;B	0.17268	0.021;0.013	B;B	0.20384	0.029;0.018	T	0.15983	-1.0418	9	0.02654	T	1	.	8.0833	0.30758	1.0:0.0:0.0:0.0	.	91;86	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	G	86;91;86	ENSP00000408863:S91G	ENSP00000278882:S86G	S	+	1	0	FRG1B	28241915	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.159000	0.58157	1.208000	0.43306	0.347000	0.21830	AGC	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	14	12.49246	KEEP	48	24	853	339	10979	AA	1	1	0		+	23	59	862	0	0	54.9931	567	60	20931	1570	ENST00000278882.3	0.038983	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632643	29632643	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs143379667		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29632643T>C	ENST00000278882.3	+	8	838	c.458T>C	c.(457-459)cTt>cCt	p.L153P	FRG1B_ENST00000358464.4_Missense_Mutation_p.L153P			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	153		NA						p.L153P(10)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GACCACAAACTTAAAATAAGT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				10	Substitution - Missense(10)	endometrium(6)|kidney(4)											NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.458T>C	chr20.hg19:g.29632643T>C	ENSP00000278882:p.Leu153Pro	NA	C4AME5	hg19		0.02	38.920367	AACxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	t	12.77	2.038665	0.35989	.	.	ENSG00000149531	ENST00000278882;ENST00000358464	.	.	.	1.44	1.44	0.22558	.	0.000000	0.64402	U	0.000001	T	0.50463	0.1617	.	.	.	0.80722	D	1	P	0.35033	0.481	B	0.40038	0.317	T	0.53187	-0.8474	8	0.87932	D	0	.	6.9831	0.24713	0.0:0.0:0.0:1.0	.	153	Q9BZ01	FRG1B_HUMAN	P	153	.	ENSP00000278882:L153P	L	+	2	0	FRG1B	28246304	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.723000	0.74742	0.925000	0.37094	0.327000	0.21459	CTT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	18	30.764558	KEEP	102	19	685	341	11274	TT	1	1	0		+	58	60	2138	0	0	157.677489	566	70	21656	1542	ENST00000278882.3	0.092949	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632680	29632680	__UNKNOWN__	Silent	SNP	G	G	A	rs4892355		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29632680G>A	ENST00000278882.3	+	8	875	c.495G>A	c.(493-495)aaG>aaA	p.K165K	FRG1B_ENST00000358464.4_Silent_p.K165K			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	165		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTCTTAAAAAGGCTCAGAAAG	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.495G>A	chr20.hg19:g.29632680G>A		NA	C4AME5	hg19		0.02	39.41481	AAAxGCT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	19	67.618997	KEEP	69	11	340	344	12285	GG	1	1	0		+	52	54	1941	1	1	143.38644	518	70	19121	1510	ENST00000278882.3	0.091228	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633983	29633983	__UNKNOWN__	3'UTR	SNP	A	A	G	rs76742789	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29633983A>G	ENST00000278882.3	+	0	1002				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTTTCTGAATAAAATATTCAG	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*73A>G	chr20.hg19:g.29633983A>G		NA	C4AME5	hg19		0.02	41.931275	AATxAAA	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	20	40.83653	KEEP	35	13	426	285	8774	AA	1	1	0		+	38	60	1429	1	0	98.291095	608	70	21468	1429	ENST00000278882.3	0.058824	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633987	29633987	__UNKNOWN__	3'UTR	SNP	T	T	A	rs4006817	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29633987T>A	ENST00000278882.3	+	0	1006				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CTGAATAAAATATTCAGAGGA	0.308	NA	NA											.|||	743	0.148363	0.0446	0.1657	5008	,	,	NA	33780	0.1984	NA	0.166	False	NA	,,,	NA	NA	NA	2504	0.2065	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*77T>A	chr20.hg19:g.29633987T>A		NA	C4AME5	hg19		0.02	38.109889	AAAxATT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	21	40.24961	KEEP	32	16	469	299	9270	TT	1	1	0		+	21	60	768	0	0	46.449383	638	70	22999	1456	ENST00000278882.3	0.031866	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633992	29633992	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29633992A>G	ENST00000278882.3	+	0	1011				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAAAATATTCAGAGGAAATGC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*82A>G	chr20.hg19:g.29633992A>G		NA	C4AME5	hg19		0.02	35.92498	TTCxGAG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	21	40.340531	KEEP	32	15	491	306	9771	AA	1	1	0		+	37	60	1280	0	0	83.261581	644	70	24129	1467	ENST00000278882.3	0.054332	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29652138	29652138	__UNKNOWN__	IGR	SNP	C	C	T	rs71273513|rs77358300		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:29652138C>T			NA	NA				AL441988.1 (14838 upstream) : DEFB115 (193328 downstream)						NA		NA									NA						tcagtcatagcctgccttcat	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29652138C>T		NA		hg19		0.02	38.907505	TAGxCTG	COVERED																																																																																			NOVEL					0			16	16.425163	KEEP	0	11	343	175	6264	CC	1	1	0			23	60	823	0	0	56.514302	325	60	12091	1308		0.066092	1
PLAGL2	5326	__UNKNOWN__	__UNKNOWN__	20	30783212	30783212	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:30783212G>T	ENST00000246229.4	-	0	2798					NM_002657.3	NP_002648.1	Q9UPG8	PLAL2_HUMAN	pleiomorphic adenoma gene-like 2	NA		NA			chylomicron assembly (GO:0034378)|lipid metabolic process (GO:0006629)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|post-embryonic development (GO:0009791)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|liver(1)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TCAAGGTGGGGACTAGGGGAT	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(163;15 1893 11280 16306 47518)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13197.1	20q11.21	2013-01-08			ENSG00000126003	ENSG00000126003	5326		Zinc fingers, C2H2-type	9047	protein-coding gene	gene with protein product	C2H2-type zinc finger protein	604866			NA	15585652, 17950244	Standard	NM_002657	NM_002657	NA	Approved	ZNF900	uc002wxn.2	Q9UPG8	OTTHUMG00000032210	ENST00000246229.4:c.*1043C>A	chr20.hg19:g.30783212G>T		NA	A8K8T5|E1P5M3|Q92584	hg19	CCDS13197.1	0.02	8.80048	GGGxACT	COVERED																																																																																			NOVEL	PLAGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078615.2	4	12.640513	KEEP	0	0	0	42	1449	GG	1	1	0		-	46	60	1510	0	0	124.90616	165	60	5986	301	ENST00000246229.4	0.218009	1
EFCAB8	388795	__UNKNOWN__	__UNKNOWN__	20	31455420	31455420	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:31455420G>T	ENST00000400522.4	+	3	169	c.75G>T	c.(73-75)gaG>gaT	p.E25D				A8MWE9	EFCB8_HUMAN	EF-hand calcium binding domain 8	25		NA					calcium ion binding (GO:0005509)			endometrium(2)	2						AGAACAAGGAGGCTGCTAGCT	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													91	84	86	NA		NA	NA	20		NA											NA				31455420		692	1591	2283	SO:0001583	missense					20q11.21	2013-01-10			ENSG00000215529	ENSG00000215529	388795		WD repeat domain containing, EF-hand domain containing	34532	protein-coding gene	gene with protein product		NA			NA		Standard	XM_371397	XM_006710086	NA	Approved			A8MWE9	OTTHUMG00000153693	ENST00000400522.4:c.75G>T	chr20.hg19:g.31455420G>T	ENSP00000383366:p.Glu25Asp	NA		hg19		0.02	4.634937	GGAxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.59	1.684044	0.29872	.	.	ENSG00000215529	ENST00000400522	.	.	.	3.77	2.77	0.32553	.	.	.	.	.	T	0.40372	0.1114	L	0.34521	1.04	0.22489	N	0.999055	.	.	.	.	.	.	T	0.50311	-0.8843	4	.	.	.	.	9.012	0.36146	0.0:0.2266:0.7734:0.0	.	.	.	.	M	33	.	.	R	+	2	0	EFCAB8	30919081	0.031000	0.19500	0.057000	0.19452	0.088000	0.18126	1.460000	0.35244	1.103000	0.41568	0.561000	0.74099	AGG	NOVEL	EFCAB8-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000332144.2	0	6.319648	KEEP	0	0	0	21	713	GG	0.999869	0.999869	0		+	52	60	1903	0	0	177.088915	78	60	2830	189	ENST00000400522.4	0.4	1
BPIFB1	92747	__UNKNOWN__	__UNKNOWN__	20	31887810	31887810	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:31887810G>T	ENST00000253354.1	+	8	908				BPIFB1_ENST00000464032.1_Intron	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	NA		NA			innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)				NA						CCAGGACCTTGAGGGTGAAGT	0.537	NA	NA									OREG0025869	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	75	83	NA		NA	NA	20		NA											NA				31887810		2203	4300	6503	SO:0001627	intron_variant			BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999	92747		BPI fold containing	16108	protein-coding gene	gene with protein product	von Ebner minor salivary gland protein	NA	chromosome 20 open reading frame 114	C20orf114	NA	11971875, 21787333	Standard	NM_033197	NM_033197	NA	Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.747+20G>T	chr20.hg19:g.31887810G>T		828	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	hg19	CCDS13218.1	0.02	6.635114	CTTxAGG	COVERED																																																																																			NOVEL	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000106499.2	0	8.126453	KEEP	0	0	0	27	952	GG	0.999988	0.999988	0		+	34	60	1173	2	0	94.386416	161	60	6100	276	ENST00000253354.1	0.174359	1
PHF20	51230	__UNKNOWN__	__UNKNOWN__	20	34459685	34459685	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:34459685G>A	ENST00000374012.3	+	9	1345	c.1216G>A	c.(1216-1218)Gaa>Aaa	p.E406K	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	406		NA			chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					ATCAATGGGAGAAAACACGAT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													124	125	125	NA		NA	NA	20		NA											NA				34459685		2203	4300	6503	SO:0001583	missense			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293	51230		Tudor domain containing, Zinc fingers, PHD-type	16098	protein-coding gene	gene with protein product	tudor domain containing 20A	610335	chromosome 20 open reading frame 104	C20orf104	NA		Standard	NM_016436	NM_016436	NA	Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1216G>A	chr20.hg19:g.34459685G>A	ENSP00000363124:p.Glu406Lys	NA	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	hg19	CCDS13268.1	0.02	2.191017	GGAxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087691	0.76642	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.50277	1.43;0.75;0.76	5.56	5.56	0.83823	.	0.570348	0.19927	N	0.102957	T	0.40619	0.1124	L	0.36672	1.1	0.80722	D	1	P;P	0.44734	0.734;0.842	B;B	0.40165	0.321;0.321	T	0.28554	-1.0040	10	0.42905	T	0.14	.	15.0108	0.71547	0.0:0.0:1.0:0.0	.	406;406	Q9BVI0;Q66K49	PHF20_HUMAN;.	K	406	ENSP00000363124:E406K;ENSP00000341900:E406K;ENSP00000363112:E406K	ENSP00000341900:E406K	E	+	1	0	PHF20	33923099	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	3.103000	0.50298	2.617000	0.88574	0.591000	0.81541	GAA	NOVEL	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078949.2	1	2.708599	KEEP	0	0	0	9	305	GG	0.99254	0.988259	0		+	5	60	193	0	0	13.929527	63	60	2359	85	ENST00000374012.3	0.073529	0.995687
EPB41L1	2036	__UNKNOWN__	__UNKNOWN__	20	34818331	34818331	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:34818331G>A	ENST00000338074.2	+	0	3876				EPB41L1_ENST00000373946.3_3'UTR|EPB41L1_ENST00000441639.1_3'UTR	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	NA		NA			cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CACTGAACTGGCCCAGCTAAG	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367	2036			3378	protein-coding gene	gene with protein product		602879			NA	9570967, 9828140	Standard	NM_012156	NM_012156	NA	Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.*1069G>A	chr20.hg19:g.34818331G>A		NA	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	hg19	CCDS13271.1	0.02	11.164882	CTGxCCC	COVERED																																																																																			NOVEL	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078978.3	4	12.94078	KEEP	0	0	0	43	1471	GG	1	1	0		+	31	60	1096	0	0	82.000174	251	60	9120	405	ENST00000338074.2	0.109929	1
TTI1	9675	__UNKNOWN__	__UNKNOWN__	20	36640940	36640940	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:36640940G>A	ENST00000373448.2	-	3	1517	c.1279C>T	c.(1279-1281)Cgg>Tgg	p.R427W	TTI1_ENST00000449821.1_Missense_Mutation_p.R427W|TTI1_ENST00000487362.1_5'UTR|TTI1_ENST00000373447.3_Missense_Mutation_p.R427W	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	427		NA			regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)		p.R427R(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						TTGGAAAGCCGCTGGAGATGG	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	prostate(1)											57	55	56	NA		NA	NA	20		NA											NA				36640940		2203	4300	6503	SO:0001583	missense			BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407	9675			29029	protein-coding gene	gene with protein product	smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)	614425	KIAA0406, Tel2 interacting protein 1 homolog (S. pombe)	KIAA0406	NA	9455477, 20427287, 20371770	Standard	NM_014657	NM_014657	NA	Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.1279C>T	chr20.hg19:g.36640940G>A	ENSP00000362547:p.Arg427Trp	NA	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	hg19	CCDS13300.1	0.02	10.330138	GCCxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.48	3.633491	0.67015	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.67523	-0.27;-0.27;-0.27	5.5	5.5	0.81552	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80834	0.4699	M	0.77103	2.36	0.80722	D	1	D	0.71674	0.998	P	0.60345	0.873	T	0.82456	-0.0448	10	0.72032	D	0.01	-0.9474	18.5685	0.91126	0.0:0.0:1.0:0.0	.	427	O43156	TTI1_HUMAN	W	427	ENSP00000362547:R427W;ENSP00000362546:R427W;ENSP00000407270:R427W	ENSP00000362546:R427W	R	-	1	2	TTI1	36074354	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.490000	0.60319	2.861000	0.98227	0.655000	0.94253	CGG	NOVEL	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079138.2	5	14.078345	KEEP	0	1	29	57	1954	GG	1	1	0		-	9	60	293	0	0	16.645941	265	60	9186	385	ENST00000373448.2	0.032847	1
PPP1R16B	26051	__UNKNOWN__	__UNKNOWN__	20	37546919	37546919	__UNKNOWN__	Silent	SNP	G	G	A	rs143948877	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:37546919G>A	ENST00000299824.1	+	11	1503	c.1314G>A	c.(1312-1314)gcG>gcA	p.A438A	PPP1R16B_ENST00000373331.2_Silent_p.A396A	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	438		NA			regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				ACCAGTATGCGCTGGCCAACG	0.617	NA	NA											G|||	11	0.00219649	0.0076	0.0014	5008	,	,	NA	19158	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0								G	,	14,4392	22.3+/-47.3	0,14,2189	157	150	152	NA	1188,1314	-7	0.9	20	dbSNP_134	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PPP1R16B	NM_001172735.1,NM_015568.2	,	0,15,6488	AA,AG,GG	NA	0.0116,0.3177,0.1153	,	396/526,438/568	37546919	15,12991	2203	4300	6503	SO:0001819	synonymous_variant			AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445	26051		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Ankyrin repeat domain containing	15850	protein-coding gene	gene with protein product	TGF-beta-inhibited membrane-associated protein, ankyrin repeat domain protein 4	613275	protein phosphatase 1, regulatory (inhibitor) subunit 16B		NA	10048485, 12055102	Standard	NM_015568	NM_001172735	NA	Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1314G>A	chr20.hg19:g.37546919G>A		NA	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	hg19	CCDS13309.1	0.02	16.742544	TGCxCTG	COVERED	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	7.476	0.647746	0.14516	0.003177	1.16E-4	ENSG00000101445	ENST00000438192	.	.	.	5.3	-6.96	0.01622	.	.	.	.	.	T	0.39036	0.1063	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51244	-0.8730	4	.	.	.	.	7.1848	0.25793	0.1667:0.1055:0.5763:0.1514	.	.	.	.	H	339	.	.	R	+	2	0	PPP1R16B	36980333	0.025000	0.19082	0.946000	0.38457	0.828000	0.46876	-1.223000	0.02962	-0.886000	0.03966	-1.152000	0.01820	CGC	NOVEL	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079220.2	7	21.059962	KEEP	0	0	0	70	2348	GG	1	1	0		+	71	60	2539	0	0	211.127845	279	60	9810	525	ENST00000299824.1	0.202857	1
SEMG2	6407	__UNKNOWN__	__UNKNOWN__	20	43851542	43851542	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:43851542G>C	ENST00000372769.3	+	2	1359	c.1269G>C	c.(1267-1269)aaG>aaC	p.K423N		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	423	4 X 60 AA tandem repeats, type I.|Repeat-rich region.	NA			sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				GTGGAGAAAAGGATGTACAGA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													81	77	78	NA		NA	NA	20		NA											NA				43851542		2203	4300	6503	SO:0001583	missense				CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157	6407			10743	protein-coding gene	gene with protein product	Semenogelin 2	182141			NA	1517240, 9523691	Standard	NM_003008	NM_003008	NA	Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.1269G>C	chr20.hg19:g.43851542G>C	ENSP00000361855:p.Lys423Asn	NA	Q53ZU2|Q6X2M5|Q6X2M6	hg19	CCDS13346.1	0.02	19.963408	AAAxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	5.935	0.356461	0.11239	.	.	ENSG00000124157	ENST00000372769	T	0.07114	3.22	0.964	-0.265	0.12946	.	.	.	.	.	T	0.08044	0.0201	N	0.05554	-0.025	0.09310	N	1	B;D	0.76494	0.001;0.999	B;D	0.85130	0.01;0.997	T	0.30650	-0.9971	9	0.15952	T	0.53	.	2.8884	0.05668	0.6556:0.0:0.3444:0.0	.	423;423	A8K6Z6;Q02383	.;SEMG2_HUMAN	N	423	ENSP00000361855:K423N	ENSP00000361855:K423N	K	+	3	2	SEMG2	43284956	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.409000	0.07160	-0.109000	0.12044	-0.492000	0.04666	AAG	NOVEL	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079417.1	7	14.748345	KEEP	0	0	0	49	1770	GG	1	1	0		+	89	60	3131	0	0	260.881445	336	60	12399	566	ENST00000372769.3	0.209412	1
MATN4	8785	__UNKNOWN__	__UNKNOWN__	20	43926730	43926730	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:43926730G>C	ENST00000372756.1	-	7	1435				MATN4_ENST00000342716.4_Intron|MATN4_ENST00000537548.1_Intron|MATN4_ENST00000360607.6_Intron|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000353917.5_Intron|MATN4_ENST00000372754.1_Intron			O95460	MATN4_HUMAN	matrilin 4	NA		NA			extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CGGGGTCTCAGAGGGTGCCCC	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													26	28	28	NA		NA	NA	20		NA											NA				43926730		2203	4298	6501	SO:0001627	intron_variant			AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159	8785			6910	protein-coding gene	gene with protein product		603897			NA	9827539, 9027493	Standard		NM_003833	NA	Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372756.1:c.1427-20C>G	chr20.hg19:g.43926730G>C		NA	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	hg19	CCDS13348.1	0.02	14.941884	TCAxAGG	COVERED																																																																																			NOVEL	MATN4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080334.1	6	40.929843	KEEP	0	0	0	136	4675	GG	1	1	0		-	71	60	2668	0	0	225.13919	268	60	10183	608	ENST00000372756.1	0.20944	1
WFDC3	140686	__UNKNOWN__	__UNKNOWN__	20	44418669	44418669	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:44418669G>A	ENST00000372632.2	-	0	20				WFDC3_ENST00000372630.2_5'UTR|WFDC3_ENST00000481847.1_Intron|WFDC3_ENST00000243938.4_Intron			Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				TGTACACCTTGCCCAGAGTAT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	34	37	NA		NA	NA	20		NA											NA				44418669		692	1591	2283	SO:0001623	5_prime_UTR_variant			AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116	140686		WAP four-disulfide core domain containing	15957	protein-coding gene	gene with protein product		NA			NA	12206714, 10680116	Standard		NM_080614	NA	Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000372632.2:c.-55C>T	chr20.hg19:g.44418669G>A		NA	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	hg19		0.02	22.281091	CTTxCCC	COVERED																																																																																			NOVEL	WFDC3-014	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000316865.1	3	38.523228	KEEP	0	0	0	128	4609	GG	1	1	0		-	96	60	3362	0	0	273.659553	428	60	16228	829	ENST00000372632.2	0.183206	1
STAU1	6780	__UNKNOWN__	__UNKNOWN__	20	47730927	47730927	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:47730927C>T	ENST00000371856.2	-	0	2632				STAU1_ENST00000371828.3_3'UTR|STAU1_ENST00000347458.5_3'UTR|STAU1_ENST00000371792.1_3'UTR|STAU1_ENST00000371802.1_3'UTR|STAU1_ENST00000360426.4_3'UTR|STAU1_ENST00000340954.7_3'UTR	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	NA		NA			intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			AGTTGGGTCACGCTGAGTAGG	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214	6780			11370	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 150	601716	staufen (Drosophila, RNA-binding protein), staufen, RNA binding protein (Drosophila), staufen, RNA binding protein, homolog 1 (Drosophila)	STAU	NA	8884277, 15680326	Standard	NM_017453	XM_005260524	NA	Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.*488G>A	chr20.hg19:g.47730927C>T		NA	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	hg19	CCDS13414.1	0.02	6.840812	TCAxGCT	COVERED																																																																																			NOVEL	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079633.1	12	14.445875	KEEP	0	0	0	48	1640	CC	1	1	0		-	16	60	582	0	0	42.236036	169	60	5985	280	ENST00000371856.2	0.086486	1
BCAS1	8537	__UNKNOWN__	__UNKNOWN__	20	52602019	52602019	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:52602019G>C	ENST00000395961.3	-	7	1113	c.947C>G	c.(946-948)aCc>aGc	p.T316S	BCAS1_ENST00000371440.3_Missense_Mutation_p.T361S|BCAS1_ENST00000371435.2_Missense_Mutation_p.T316S|BCAS1_ENST00000434986.2_Missense_Mutation_p.T74S	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	316		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			AGCTGAAGTGGTGGGTGACTT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													128	124	125	NA		NA	NA	20		NA											NA				52602019		2203	4300	6503	SO:0001583	missense			AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787	8537			974	protein-coding gene	gene with protein product		602968			NA	9671742	Standard	NM_003657	NM_003657	NA	Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.947C>G	chr20.hg19:g.52602019G>C	ENSP00000379290:p.Thr316Ser	NA	A0AVG5|Q68CZ3	hg19	CCDS13444.1	0.02	4.743134	GTGxTGG	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.103|6.103	0.387339|0.387339	0.11581|0.11581	.|.	.|.	ENSG00000064787|ENSG00000064787	ENST00000422805|ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986	.|T;T;T;T;T	.|0.07114	.|3.22;3.22;3.22;3.22;3.22	6.03|6.03	1.84|1.84	0.25277|0.25277	.|.	.|0.952207	.|0.08792	.|N	.|0.893011	T|T	0.05227|0.05227	0.0139|0.0139	N|N	0.21448|0.21448	0.665|0.665	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B	.|0.33171	.|0.019;0.4;0.019;0.035;0.023;0.023	.|B;B;B;B;B;B	.|0.31101	.|0.019;0.124;0.019;0.041;0.016;0.016	T|T	0.42766|0.42766	-0.9432|-0.9432	5|10	.|0.33141	.|T	.|0.24	0.3888|0.3888	3.0781|3.0781	0.06253|0.06253	0.1525:0.1391:0.5643:0.1441|0.1525:0.1391:0.5643:0.1441	.|.	.|316;74;361;316;316;316	.|B2RCQ5;B4DFL4;O75363-2;G3XAF7;A0AVG7;O75363	.|.;.;.;.;.;BCAS1_HUMAN	A|S	35|223;361;194;316;316;74	.|ENSP00000396361:T223S;ENSP00000360495:T361S;ENSP00000379290:T316S;ENSP00000360490:T316S;ENSP00000409956:T74S	.|ENSP00000360490:T316S	P|T	-|-	1|2	0|0	BCAS1|BCAS1	52035426|52035426	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.947000|0.947000	0.59692|0.59692	0.162000|0.162000	0.16501|0.16501	0.122000|0.122000	0.18314|0.18314	0.655000|0.655000	0.94253|0.94253	CCA|ACC	NOVEL	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079766.2	0	15.939467	KEEP	0	0	0	53	1842	GG	1	1	0		-	8	60	315	0	0	22.294897	121	60	4565	232	ENST00000395961.3	0.062016	1
CBLN4	140689	__UNKNOWN__	__UNKNOWN__	20	54579927	54579927	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:54579927C>T	ENST00000064571.2	-	0	601					NM_080617.5	NP_542184.1	Q9NTU7	CBLN4_HUMAN	cerebellin 4 precursor	NA		NA			protein secretion (GO:0009306)	cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(1)|lung(10)|ovary(3)|pancreas(1)	17			Colorectal(105;0.202)			AGGTCCAGGGCGCCGGGCGCA	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AY358527	CCDS13448.1	20q13	2004-08-19	2004-08-19	2004-08-19	ENSG00000054803	ENSG00000054803	140689			16231	protein-coding gene	gene with protein product		615029	cerebellin precursor-like 1	CBLNL1	NA		Standard	NM_080617	NM_080617	NA	Approved	dJ885A10.1	uc002xxa.4	Q9NTU7	OTTHUMG00000032782	ENST00000064571.2:c.-700G>A	chr20.hg19:g.54579927C>T		NA	A8K0S5	hg19	CCDS13448.1	0.02	21.970149	GGGxGCC	COVERED																																																																																			NOVEL	CBLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079783.2	2	49.866905	KEEP	0	1	23	174	5620	CC	1	1	0		-	103	60	3437	0	0	280.069122	422	60	14309	875	ENST00000064571.2	0.19619	1
TFAP2C	7022	__UNKNOWN__	__UNKNOWN__	20	55206987	55206987	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:55206987G>A	ENST00000201031.2	+	3	829				TFAP2C_ENST00000544508.1_Intron	NM_003222.3	NP_003213.1	Q92754	AP2C_HUMAN	transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma)	NA		NA			cell-cell signaling (GO:0007267)|cerebral cortex development (GO:0021987)|dichotomous subdivision of terminal units involved in mammary gland duct morphogenesis (GO:0060598)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|forebrain neuron fate commitment (GO:0021877)|germ-line stem cell maintenance (GO:0030718)|hair follicle development (GO:0001942)|keratinocyte development (GO:0003334)|male gonad development (GO:0008584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epidermis development (GO:0045682)|regulation of gene expression, epigenetic (GO:0040029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sebaceous gland development (GO:0048733)|somatic stem cell maintenance (GO:0035019)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	13			Colorectal(105;0.229)			AAGGTTGGGGGTATTTGGTGG	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													35	30	31	NA		NA	NA	20		NA											NA				55206987		692	1591	2283	SO:0001627	intron_variant				CCDS13454.1	20q13.2	2008-07-17	2001-11-28		ENSG00000087510	ENSG00000087510	7022			11744	protein-coding gene	gene with protein product	estrogen receptor factor 1	601602	transcription factor AP-2 gamma (activating enhancer-binding protein 2 gamma)		NA	8661133	Standard	NM_003222	NM_003222	NA	Approved	AP2-GAMMA, ERF1, TFAP2G, hAP-2g	uc002xya.3	Q92754	OTTHUMG00000032805	ENST00000201031.2:c.586+75G>A	chr20.hg19:g.55206987G>A		NA	B4DWK3|O00685|O00730|Q86V30|Q8IVB6|Q9P1X2	hg19	CCDS13454.1	0.02	11.501682	GGGxTAT	COVERED																																																																																			NOVEL	TFAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079823.2	5	28.530324	KEEP	0	0	0	95	3298	GG	1	1	0		+	54	60	1961	0	0	164.69857	201	60	7457	402	ENST00000201031.2	0.211765	1
ZNF831	128611	__UNKNOWN__	__UNKNOWN__	20	57767415	57767415	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:57767415C>A	ENST00000371030.2	+	1	1341	c.1341C>A	c.(1339-1341)acC>acA	p.T447T		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	447		NA					metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CGCCCTACACCTACAAGGACT	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													33	40	38	NA		NA	NA	20		NA											NA				57767415		2072	4185	6257	SO:0001819	synonymous_variant			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203	128611			16167	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 174	C20orf174	NA		Standard	NM_178457	NM_178457	NA	Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.1341C>A	chr20.hg19:g.57767415C>A		NA	Q5TDR4|Q8TCP0	hg19	CCDS42894.1	0.02	23.762035	CACxTAC	COVERED																																																																																			NOVEL	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079916.2	4	44.477974	KEEP	0	0	0	148	5008	CC	1	1	0		+	22	60	791	0	0	48.983037	560	60	20180	901	ENST00000371030.2	0.037801	1
RP11-429E11.3	0	__UNKNOWN__	__UNKNOWN__	20	60293473	60293473	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:60293473C>T	ENST00000317652.1	-	0	1088				CDH4_ENST00000360469.5_Intron|CDH4_ENST00000543233.1_Intron						NA		NA									NA						AAAAGGAATGCTCCTCTCTGG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000317652.1:c.*331G>A	chr20.hg19:g.60293473C>T		NA		hg19		0.02	13.143231	ATGxTCC	COVERED																																																																																			NOVEL	RP11-429E11.3-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000079962.1	4	8.124956	KEEP	0	0	0	27	935	CC	0.999988	0.999988	0		-	17	60	615	0	0	41.109415	289	60	10816	385	ENST00000317652.1	0.055556	1
LAMA5	3911	__UNKNOWN__	__UNKNOWN__	20	60887073	60887073	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs6089728		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:60887073G>T	ENST00000252999.3	-	70	9604	c.9538C>A	c.(9538-9540)Cgt>Agt	p.R3180S		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3180	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.	NA			angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AGGCTCACACGGCCCTGCTGC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													53	56	55	NA		NA	NA	20		NA											NA				60887073		2202	4298	6500	SO:0001583	missense			AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702	3911		Laminins	6485	protein-coding gene	gene with protein product		601033			NA	9271224	Standard	NM_005560	NM_005560	NA	Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.9538C>A	chr20.hg19:g.60887073G>T	ENSP00000252999:p.Arg3180Ser	NA	Q8TDF8|Q8WZA7|Q9H1P1	hg19	CCDS33502.1	0.02	13.461165	CACxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	g	12.75	2.031304	0.35797	.	.	ENSG00000130702	ENST00000252999	T	0.78481	-1.18	4.44	3.41	0.39046	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.484707	0.23491	N	0.047604	T	0.69169	0.3081	L	0.44542	1.39	0.80722	D	1	B	0.13594	0.008	B	0.15052	0.012	T	0.68146	-0.5486	10	0.45353	T	0.12	.	11.7469	0.51825	0.0:0.0:0.7065:0.2935	.	3180	O15230	LAMA5_HUMAN	S	3180	ENSP00000252999:R3180S	ENSP00000252999:R3180S	R	-	1	0	LAMA5	60320468	0.973000	0.33851	0.862000	0.33874	0.042000	0.13812	2.074000	0.41529	2.014000	0.59158	0.556000	0.70494	CGT	NOVEL	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080014.2	2	24.252478	KEEP	0	0	0	81	2496	GG	1	1	0		-	18	60	634	0	0	41.86028	308	60	9950	487	ENST00000252999.3	0.055215	1
SLCO4A1	28231	__UNKNOWN__	__UNKNOWN__	20	61299509	61299509	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:61299509G>A	ENST00000370507.1	+	8	1880	c.1784G>A	c.(1783-1785)aGc>aAc	p.S595N	SLCO4A1_ENST00000217159.1_Missense_Mutation_p.S595N|SLCO4A1_ENST00000470412.1_3'UTR			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	595		NA			sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TTCCTCAGCAGCATTCCTGCA	0.512	NA	NA									OREG0026115	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(168;741 2006 10379 40139 45334)					NA		NA				0													135	134	135	NA		NA	NA	20		NA											NA				61299509		2203	4300	6503	SO:0001583	missense			AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187	28231		Solute carriers	10953	protein-coding gene	gene with protein product		612436	solute carrier family 21 (organic anion transporter), member 12	SLC21A12	NA	10873595	Standard	NM_016354	NM_016354	NA	Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.1784G>A	chr20.hg19:g.61299509G>A	ENSP00000359538:p.Ser595Asn	1052	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	hg19	CCDS13501.1	0.02	13.626624	GCAxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154090	0.78114	.	.	ENSG00000101187	ENST00000217159;ENST00000370507;ENST00000342674	T;T	0.58797	0.31;0.31	4.94	4.94	0.65067	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.144020	0.06737	N	0.777659	T	0.61388	0.2343	M	0.63843	1.955	0.58432	D	0.999993	B	0.14012	0.009	B	0.19148	0.024	T	0.46148	-0.9212	10	0.23891	T	0.37	.	18.1323	0.89605	0.0:0.0:1.0:0.0	.	595	Q96BD0	SO4A1_HUMAN	N	595;595;447	ENSP00000217159:S595N;ENSP00000359538:S595N	ENSP00000217159:S595N	S	+	2	0	SLCO4A1	60769954	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.538000	0.90634	2.270000	0.75569	0.491000	0.48974	AGC	NOVEL	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080048.2	1	23.166129	KEEP	0	0	0	77	2750	GG	1	1	0		+	67	60	2354	0	0	194.011988	274	60	10335	485	ENST00000370507.1	0.196481	1
MRGBP	55257	__UNKNOWN__	__UNKNOWN__	20	61431359	61431359	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:61431359C>T	ENST00000370487.3	+	0	1050					NM_018270.4	NP_060740.1	Q9NV56	MRGBP_HUMAN	MRG/MORF4L binding protein	NA		NA			chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	H4/H2A histone acetyltransferase complex (GO:0043189)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)					NA						AGAGGGGCATCGGGCCAGGGA	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001776	CCDS13503.1	20q13.33	2012-10-29	2012-10-29	2012-10-29	ENSG00000101189	ENSG00000101189	55257			15866	protein-coding gene	gene with protein product		611157	chromosome 20 open reading frame 20	C20orf20	NA	12963728	Standard	NM_018270	NM_018270	NA	Approved	FLJ10914, MRG15BP, Eaf7	uc002ydi.3	Q9NV56	OTTHUMG00000032940	ENST00000370487.3:c.*364C>T	chr20.hg19:g.61431359C>T		NA	A8C4L5	hg19	CCDS13503.1	0.02	11.603361	CATxGGG	COVERED																																																																																			NOVEL	MRGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080080.1	2	13.539184	KEEP	0	0	0	45	1482	CC	1	1	0		+	62	60	2243	0	0	188.651296	227	60	8068	402	ENST00000370487.3	0.214533	1
DIDO1	11083	__UNKNOWN__	__UNKNOWN__	20	61511360	61511360	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:61511360G>A	ENST00000266070.4	-	16	6273	c.5948C>T	c.(5947-5949)gCg>gTg	p.A1983V	DIDO1_ENST00000395343.1_Missense_Mutation_p.A1983V	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	1983	Pro-rich.	NA			apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGGTGCAGGCGCCCTTTGGTT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)					NA		NA				0													119	140	133	NA		NA	NA	20		NA											NA				61511360		2203	4299	6502	SO:0001583	missense			AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191	11083		Zinc fingers, PHD-type	2680	protein-coding gene	gene with protein product		604140	chromosome 20 open reading frame 158, death associated transcription factor 1	C20orf158, DATF1	NA	10393935	Standard	NM_080796	NM_033081	NA	Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.5948C>T	chr20.hg19:g.61511360G>A	ENSP00000266070:p.Ala1983Val	NA	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	hg19	CCDS33506.1	0.02	14.829738	GGCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.60	1.394350	0.25205	.	.	ENSG00000101191	ENST00000266070;ENST00000395343	T;T	0.08984	3.03;3.03	4.91	3.87	0.44632	.	0.169768	0.26931	N	0.021774	T	0.08313	0.0207	L	0.51422	1.61	0.80722	D	1	P	0.35155	0.487	B	0.27076	0.076	T	0.13202	-1.0518	10	0.49607	T	0.09	-15.6707	12.1388	0.53986	0.0:0.4288:0.5711:0.0	.	1983	Q9BTC0	DIDO1_HUMAN	V	1983	ENSP00000266070:A1983V;ENSP00000378752:A1983V	ENSP00000266070:A1983V	A	-	2	0	DIDO1	60981805	0.996000	0.38824	0.600000	0.28864	0.133000	0.20885	3.067000	0.50010	2.414000	0.81942	0.561000	0.74099	GCG	NOVEL	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080091.2	2	41.522295	KEEP	0	0	0	138	4651	GG	1	1	0		-	27	60	951	0	0	65.897681	348	60	11799	663	ENST00000266070.4	0.072	1
PTK6	5753	__UNKNOWN__	__UNKNOWN__	20	62164981	62164981	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs372528046		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:62164981C>T	ENST00000217185.2	-	4	620	c.593G>A	c.(592-594)gGg>gAg	p.G198E	PTK6_ENST00000542869.1_Missense_Mutation_p.G97E	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6	198	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|intestinal epithelial cell differentiation (GO:0060575)|negative regulation of growth (GO:0045926)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(1)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)		Vandetanib(DB05294)	GTAGCCGGACCCCAGCTTCCT	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													91	95	93	NA		NA	NA	20		NA											NA				62164981		2203	4300	6503	SO:0001583	missense			U61412	CCDS13524.1, CCDS74750.1	20q13.3	2013-02-18	2013-02-18		ENSG00000101213	ENSG00000101213	5753	2.7.10.1	SH2 domain containing	9617	protein-coding gene	gene with protein product		602004	PTK6 protein tyrosine kinase 6		NA	8247543, 9284935	Standard		NM_005975	NA	Approved	BRK	uc002yfg.4	Q13882	OTTHUMG00000033039	ENST00000217185.2:c.593G>A	chr20.hg19:g.62164981C>T	ENSP00000217185:p.Gly198Glu	NA	B2RCR3|B4DW46|Q58F01	hg19	CCDS13524.1	0.02	22.215422	GACxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	c	20.6	4.017495	0.75161	.	.	ENSG00000101213	ENST00000217185;ENST00000542869	D;D	0.94966	-3.57;-3.57	4.32	4.32	0.51571	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.42821	U	0.000642	D	0.98400	0.9468	H	0.98407	4.225	0.53005	D	0.999969	D	0.89917	1.0	D	0.97110	1.0	D	0.99806	1.1038	10	0.87932	D	0	.	15.5905	0.76523	0.0:1.0:0.0:0.0	.	198	Q13882	PTK6_HUMAN	E	198;97	ENSP00000217185:G198E;ENSP00000442460:G97E	ENSP00000217185:G198E	G	-	2	0	PTK6	61635425	1.000000	0.71417	0.894000	0.35097	0.352000	0.29268	5.333000	0.65917	1.964000	0.57103	0.486000	0.48141	GGG	NOVEL	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080313.1	3	35.809555	KEEP	0	0	0	119	4065	CC	1	1	0		-	43	60	1563	1	0	115.126496	410	60	14341	747	ENST00000217185.2	0.094923	1
STMN3	50861	__UNKNOWN__	__UNKNOWN__	20	62272046	62272046	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:62272046G>T	ENST00000370053.1	-	0	1269					NM_001276310.1|NM_015894.2	NP_001263239.1|NP_056978.2	Q9NZ72	STMN3_HUMAN	stathmin-like 3	NA		NA			cytoplasmic microtubule organization (GO:0031122)|negative regulation of Rac protein signal transduction (GO:0035021)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|regulation of cytoskeleton organization (GO:0051493)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of Rac GTPase activity (GO:0032314)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	protein domain specific binding (GO:0019904)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)	8	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			CTCCCCAGCAGACTCAGGGCA	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF069709	CCDS13529.1, CCDS63330.1	20q13.3	2007-01-22			ENSG00000197457	ENSG00000197457	50861			15926	protein-coding gene	gene with protein product		608362			NA	9603203, 10655513	Standard	NM_015894	NM_001276310	NA	Approved	SCLIP	uc002yfr.2	Q9NZ72	OTTHUMG00000032985	ENST00000370053.1:c.*645C>A	chr20.hg19:g.62272046G>T		NA	B3KSQ5|B7WP52|B7Z5G4|O75527|Q969Y4	hg19	CCDS13529.1	0.02	1.610967	GCAxACT	COVERED																																																																																			NOVEL	STMN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080163.1	1	14.446356	KEEP	5	0	0	48	1659	GG	1	0.999962	0		-	12	60	419	0	0	31.693675	88	60	3288	187	ENST00000370053.1	0.12	0.999962
RP4-583P15.15	0	__UNKNOWN__	__UNKNOWN__	20	62369909	62369909	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:62369909G>A	ENST00000490623.2	+	11	2613				RP4-583P15.14_ENST00000476221.1_Intron|LIME1_ENST00000309546.3_Intron|LIME1_ENST00000490824.1_Intron|RP4-583P15.14_ENST00000467211.1_Intron						NA		NA									NA						TCAGCAGGTTGGATGGTGCTG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													13	16	15	NA		NA	NA	20		NA											NA				62369909		2173	4268	6441	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000490623.2:c.1251-42G>A	chr20.hg19:g.62369909G>A		NA		hg19		0.02	9.811264	GTTxGAT	COVERED																																																																																			NOVEL	RP4-583P15.15-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000473237.1	4	25.21853	KEEP	0	0	0	84	2890	GG	1	1	0		+	40	60	1445	0	0	118.385454	179	60	6402	364	ENST00000490623.2	0.182648	1
ZBTB46	140685	__UNKNOWN__	__UNKNOWN__	20	62376706	62376706	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:62376706G>A	ENST00000245663.4	-	0	3497				RP4-583P15.10_ENST00000447343.2_RNA|ZBTB46_ENST00000395104.1_3'UTR|ZBTB46_ENST00000302995.2_Intron	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	NA		NA			negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					AAAAACAAAAGCCGTGACTCC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584	140685		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	16094	protein-coding gene	gene with protein product	BTB-ZF protein expressed in effector lymphocytes	614639	BTB (POZ) domain containing 4	ZNF340, BTBD4	NA		Standard	NM_025224	NM_025224	NA	Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.*1577C>T	chr20.hg19:g.62376706G>A		NA	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	hg19	CCDS13538.1	0.02	4.326148	AAAxCCG	COVERED																																																																																			NOVEL	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080232.2	1	19.560195	KEEP	0	0	0	65	2241	GG	1	1	0		-	23	60	819	0	0	66.444217	108	60	3997	281	ENST00000245663.4	0.175573	1
ABHD16B	140701	__UNKNOWN__	__UNKNOWN__	20	62493374	62493374	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:62493374C>T	ENST00000369916.3	+	1	809	c.481C>T	c.(481-483)Cgc>Tgc	p.R161C		NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	161		NA					hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						CATGGACCGCCGCCAGCACCC	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													18	20	20	NA		NA	NA	20		NA											NA				62493374		2197	4295	6492	SO:0001583	missense				CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260	140701		Abhydrolase domain containing	16128	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 135	C20orf135	NA		Standard		NM_080622	NA	Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.481C>T	chr20.hg19:g.62493374C>T	ENSP00000358932:p.Arg161Cys	NA		hg19	CCDS13539.1	0.02	17.743951	CGCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.87	2.664153	0.47572	.	.	ENSG00000183260	ENST00000369916	T	0.43294	0.95	4.59	4.59	0.56863	.	0.000000	0.85682	U	0.000000	T	0.63604	0.2525	M	0.82823	2.61	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.67960	-0.5535	10	0.87932	D	0	-10.7627	8.6832	0.34221	0.0:0.8941:0.0:0.1059	.	161	Q9H3Z7	ABHGB_HUMAN	C	161	ENSP00000358932:R161C	ENSP00000358932:R161C	R	+	1	0	ABHD16B	61963818	1.000000	0.71417	0.997000	0.53966	0.400000	0.30750	2.756000	0.47549	2.096000	0.63516	0.491000	0.48974	CGC	NOVEL	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080254.1	3	52.561611	KEEP	0	0	0	175	5757	CC	1	1	0		+	31	60	1108	0	0	77.02516	406	60	13653	786	ENST00000369916.3	0.070938	1
UCKL1	54963	__UNKNOWN__	__UNKNOWN__	20	62572283	62572283	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr20:62572283G>A	ENST00000369908.5	-	10	1371				UCKL1_ENST00000369892.3_Intron|UCKL1_ENST00000354216.6_Intron|UCKL1_ENST00000358711.3_Intron	NM_001193379.1	NP_001180308.1	Q9NWZ5	UCKL1_HUMAN	uridine-cytidine kinase 1-like 1	NA		NA			CTP salvage (GO:0044211)|UMP salvage (GO:0044206)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|uridine kinase activity (GO:0004849)			endometrium(3)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CCTCCACCTCGCGGGCTACGG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													42	43	42	NA		NA	NA	20		NA											NA				62572283		2198	4294	6492	SO:0001627	intron_variant			AK000524	CCDS13547.1, CCDS54479.1	20q13.33	2012-09-20	2004-07-13	2004-07-13	ENSG00000198276	ENSG00000198276	54963			15938	protein-coding gene	gene with protein product		610866	uridine kinase-like 1	URKL1	NA		Standard	NM_017859	NM_017859	NA	Approved	FLJ20517	uc010gkn.3	Q9NWZ5	OTTHUMG00000033003	ENST00000369908.5:c.1071+19C>T	chr20.hg19:g.62572283G>A		NA	B7Z8N2|Q5JWV0|Q70AQ5|Q8N524|Q9H3Z2	hg19	CCDS54479.1	0.02	11.916742	CTCxCGG	COVERED																																																																																			NOVEL	UCKL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000470249.1	1	26.433968	KEEP	0	0	0	88	2889	GG	1	1	0		-	35	60	1231	0	0	94.2765	241	60	8206	456	ENST00000369908.5	0.126812	1
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9909124	9909124	__UNKNOWN__	RNA	SNP	C	C	T	rs527258031	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:9909124C>T	ENST00000416067.1	-	0	282					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						AGGTTCACGGCGTCACACTGG	0.682	NA	NA											.|||	17	0.00339457	0.0061	0	5008	,	,	NA	16010	0.002	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9909124C>T		NA		hg19		0.02	8.769364	CGGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	.	5.400	0.259063	0.10239	.	.	ENSG00000227328	ENST00000416067	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.17280	0.0415	.	.	.	.	.	.	P	0.44521	0.837	B	0.31812	0.136	T	0.19128	-1.0315	5	.	.	.	.	5.9913	0.19465	0.0:0.9994:0.0:6.0E-4	.	71	B7WNX9	.	T	71	.	.	A	-	1	0	TEKT4P2	.	0.012000	0.17670	0.027000	0.17364	0.028000	0.11728	0.915000	0.28638	0.181000	0.19994	0.184000	0.17185	GCC	NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	0	8.417892	KEEP	1	6	179	91	3045	CC	1	1	0		-	21	60	716	0	0	54.263594	145	60	5199	409	ENST00000416067.1	0.126506	1
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	10943003	10943003	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs1810856	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:10943003C>T	ENST00000361285.4	-	12	913	c.584G>A	c.(583-585)cGa>cAa	p.R195Q	TPTE_ENST00000298232.7_Missense_Mutation_p.R177Q|TPTE_ENST00000342420.5_Missense_Mutation_p.R157Q|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	195		NA	R -> Q (in dbSNP:rs1810856).		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCGTAGAAGTCGAAGTAAATG	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													72	67	69	NA		NA	NA	21		NA											NA				10943003		2203	4299	6502	SO:0001583	missense			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.584G>A	chr21.hg19:g.10943003C>T	ENSP00000355208:p.Arg195Gln	NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19	CCDS13560.2	0.02	4.564254	AGTxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	.	10.95	1.494560	0.26774	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.98028	-4.67;-4.67;-4.67	2.07	1.16	0.20824	Ion transport (1);	0.072998	0.56097	U	0.000040	D	0.97368	0.9139	M	0.75615	2.305	0.45733	D	0.998638	D;D;D	0.65815	0.995;0.995;0.994	P;P;P	0.56788	0.795;0.795;0.806	D	0.95693	0.8742	10	0.72032	D	0.01	-5.7066	6.6713	0.23070	0.0:0.836:0.0:0.164	rs1810856;rs59194479	157;177;195	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	Q	177;195;157	ENSP00000298232:R177Q;ENSP00000355208:R195Q;ENSP00000344441:R157Q	ENSP00000298232:R177Q	R	-	2	0	TPTE	9964874	0.005000	0.15991	0.035000	0.18076	0.042000	0.13812	0.889000	0.28282	0.423000	0.26033	0.194000	0.17425	CGA	NOVEL	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157413.1	1	5.417485	KEEP	0	0	0	18	627	CC	0.999859	0.999859	0		-	20	70	734	0	0	58.213711	117	60	4223	207	ENST00000361285.4	0.145985	1
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	10943038	10943038	__UNKNOWN__	Intron	SNP	C	C	A	rs2020014	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:10943038C>A	ENST00000361285.4	-	12	896				TPTE_ENST00000298232.7_Intron|TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_Intron	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAAATTTAAACGATCCATTTT	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													43	40	41	NA		NA	NA	21		NA											NA				10943038		2203	4298	6501	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.567-18G>T	chr21.hg19:g.10943038C>A		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19	CCDS13560.2	0.02	4.921971	AAAxGAT	COVERED																																																																																			NOVEL	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157413.1	4	5.716406	KEEP	0	0	0	19	653	CC	0.99986	0.999858	0		-	16	60	611	0	0	48.272385	104	60	3671	179	ENST00000361285.4	0.133333	0.999999
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11038748	11038748	__UNKNOWN__	RNA	SNP	C	C	T	rs75164355	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:11038748C>T	ENST00000470054.1	-	0	1455							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CGAGGTCTACCAGGAGAAAAT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11038748C>T		NA	A8K925|Q08ER0	hg19		0.02	16.76232	TACxAGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	5	13.931359	KEEP	31	1	33	58	1967	CC	1	1	0		-	12	27	463	0	0	28.874109	370	60	13487	566	ENST00000470054.1	0.031414	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11058248	11058248	__UNKNOWN__	RNA	SNP	G	G	A	rs8130203	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:11058248G>A	ENST00000470054.1	-	0	399							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GCAGCACAAGGATAATGATAC	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													80	67	71	NA		NA	NA	21		NA											NA				11058248		692	1591	2283					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11058248G>A		NA	A8K925|Q08ER0	hg19		0.02	27.803206	AAGxATA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	6	2.430327	KEEP	130	15	491	180	6195	GG	1	1	0		-	33	49	1173	1	0	77.25115	591	60	21701	1163	ENST00000470054.1	0.052885	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11058282	11058282	__UNKNOWN__	RNA	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:11058282G>A	ENST00000470054.1	-	0	365							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCTCTTCACAGCATTTGATAG	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													112	87	94	NA		NA	NA	21		NA											NA				11058282		692	1591	2283					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11058282G>A		NA	A8K925|Q08ER0	hg19		0.02	30.211505	ACAxCAT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	8	29.611339	KEEP	57	6	205	170	6262	GG	1	1	0		-	23	49	841	0	0	51.288847	668	60	25802	1257	ENST00000470054.1	0.033285	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11059849	11059849	__UNKNOWN__	RNA	SNP	G	G	T	rs11183999	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:11059849G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gccggacgtggtggcaggcac	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11059849G>T		NA	A8K925|Q08ER0	hg19		0.02	4.479309	GTGxTGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	10	19.831614	KEEP	0	2	63	88	3019	GG	1	0.999999	0		-	8	60	294	0	0	21.705192	77	60	2795	285	ENST00000470054.1	0.094118	0.999999
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11059897	11059897	__UNKNOWN__	RNA	SNP	A	A	G	rs6582758	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:11059897A>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aagcaggagaaGCTTCTAAAT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11059897A>G		NA	A8K925|Q08ER0	hg19		0.02	4.711485	AGAxGCT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	12	6.732704	KEEP	0	6	196	91	3021	AA	1	1	0		-	9	60	360	0	0	26.586537	106	60	4009	376	ENST00000470054.1	0.078261	1
GABPA	2551	__UNKNOWN__	__UNKNOWN__	21	27142914	27142914	__UNKNOWN__	3'UTR	SNP	C	C	T	rs375897808		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:27142914C>T	ENST00000354828.3	+	0	3263				GABPA_ENST00000400075.3_3'UTR	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa	NA		NA			cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						AATATTTATGCACCTTCTCCT	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727	2551			4071	protein-coding gene	gene with protein product	human nuclear respiratory factor-2 subunit alpha, nuclear respiratory factor 2 alpha subunit	600609	GA-binding protein transcription factor, alpha subunit (60kD)		NA	8441384	Standard	NM_002040	NM_002040	NA	Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.*1371C>T	chr21.hg19:g.27142914C>T		NA	Q12939	hg19	CCDS13575.1	0.02	8.477012	ATGxACC	COVERED																																																																																			NOVEL	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000171365.1	5	10.939276	KEEP	4	3	99	71	2557	CC	1	1	0		+	9	49	331	0	0	20.606916	239	60	8931	403	ENST00000354828.3	0.03629	1
MAP3K7CL	56911	__UNKNOWN__	__UNKNOWN__	21	30458150	30458150	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:30458150G>A	ENST00000399935.2	+	0	98				MAP3K7CL_ENST00000399947.2_5'UTR|MAP3K7CL_ENST00000399934.1_5'UTR|MAP3K7CL_ENST00000496779.1_3'UTR|MAP3K7CL_ENST00000341618.4_5'UTR|MAP3K7CL_ENST00000545939.1_5'UTR|MAP3K7CL_ENST00000286791.5_5'UTR			P57077	M3KCL_HUMAN	MAP3K7 C-terminal like	NA		NA				cytosol (GO:0005829)|nucleus (GO:0005634)					NA						GACAACTTGAGTGGTTAAATT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													143	118	126	NA		NA	NA	21		NA											NA				30458150		2203	4300	6503	SO:0001623	5_prime_UTR_variant			AF269161	CCDS13584.1, CCDS68182.1, CCDS74775.1	21q22.3	2013-02-22	2013-02-22	2013-02-22	ENSG00000156265	ENSG00000156265	56911			16457	protein-coding gene	gene with protein product		611110	chromosome 21 open reading frame 7	C21orf7	NA		Standard	NM_020152	NM_020152	NA	Approved	TAKL, TAK1L, TAKL-1, TAKL-2, TAKL-4	uc002ynf.3	P57077	OTTHUMG00000078806	ENST00000399935.2:c.-570G>A	chr21.hg19:g.30458150G>A		NA	D3DSE0|Q8TCL9	hg19		0.02	25.803675	TGAxTGG	COVERED																																																																																			NOVEL	MAP3K7CL-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000171867.2	6	39.424856	KEEP	0	0	0	131	4718	GG	1	1	0		+	154	60	5594	0	0	490.817611	399	60	15251	869	ENST00000399935.2	0.278481	1
CLDN8	9073	__UNKNOWN__	__UNKNOWN__	21	31587637	31587637	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs367879638		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:31587637G>A	ENST00000399899.1	-	1	754	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C	CLDN8_ENST00000286809.1_Missense_Mutation_p.R203C	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	203		NA			calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						TGGGTTGTGCGATGGGAAGGT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0								G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	151	137	141	NA	607	5.2	0.8	21		141	0,8600		0,0,4300	no	missense	CLDN8	NM_199328.2	180	0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077	benign	203/226	31587637	1,13005	2203	4300	6503	SO:0001583	missense			AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284	9073		Claudins	2050	protein-coding gene	gene with protein product		611231			NA	9892664	Standard	NM_199328	NM_199328	NA	Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.607C>T	chr21.hg19:g.31587637G>A	ENSP00000382783:p.Arg203Cys	NA	D3DSE3|Q53EX7	hg19	CCDS13587.1	0.02	24.278041	TGCxATG	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.61	1.689819	0.29962	2.27E-4	0.0	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.84442	-1.85;-1.85	5.15	5.15	0.70609	.	38.239000	0.02435	U	0.083955	T	0.79028	0.4377	N	0.08118	0	0.38649	D	0.951807	B	0.20780	0.048	B	0.12156	0.007	T	0.40553	-0.9557	10	0.38643	T	0.18	.	18.7903	0.91971	0.0:0.0:1.0:0.0	.	203	P56748	CLD8_HUMAN	C	203	ENSP00000382783:R203C;ENSP00000286809:R203C	ENSP00000286809:R203C	R	-	1	0	CLDN8	30509508	0.473000	0.25878	0.795000	0.32087	0.098000	0.18820	2.471000	0.45127	2.855000	0.98099	0.650000	0.86243	CGC	NOVEL	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000182260.1	4	32.108921	KEEP	0	2	63	129	4282	GG	1	1	0		-	264	60	9619	0	0	930.090632	260	60	9271	824	ENST00000399899.1	0.503817	1
TIAM1	7074	__UNKNOWN__	__UNKNOWN__	21	32491779	32491779	__UNKNOWN__	3'UTR	SNP	T	T	C	rs17551019	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:32491779T>C	ENST00000286827.3	-	0	6154					NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	NA		NA			apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CAAATATAGATTCAAACATTA	0.428	NA	NA											T|||	54	0.0107827	8e-04	0.0115	5008	,	,	NA	14995	0	NA	0.0278	False	NA	,,,	NA	NA	NA	2504	0.0174	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299	7074		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11805	protein-coding gene	gene with protein product		600687			NA	8595894, 15340013	Standard	NM_003253	NM_003253	NA	Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.*907A>G	chr21.hg19:g.32491779T>C		NA	B7ZLR6|F5GZ53|Q17RT7	hg19	CCDS13609.1	0.02	2.120846	AGAxTCA	COVERED																																																																																			NOVEL	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000192552.1	0	3.909684	KEEP	0	0	0	13	366	TT	0.994391	0.993094	0		-	13	60	482	0	0	39.383988	62	60	2249	104	ENST00000286827.3	0.173333	0.998696
IFNAR2	3455	__UNKNOWN__	__UNKNOWN__	21	34614351	34614351	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:34614351G>A	ENST00000342136.4	+	2	381				IFNAR2_ENST00000404220.3_Intron|IFNAR2_ENST00000382264.3_Intron|IFNAR2_ENST00000382241.3_Intron|IFNAR2_ENST00000420068.1_Intron|IFNAR2_ENST00000413881.1_Intron|IFNAR2_ENST00000342101.3_Intron			P48551	INAR2_HUMAN	interferon (alpha, beta and omega) receptor 2	NA		NA			cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|type I interferon binding (GO:0019962)|type I interferon receptor activity (GO:0004905)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	11					"Interferon Alfa-2a(DB00034)|"Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)	GAGAGCACTGGCAGGAAGTCG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													124	96	105	NA		NA	NA	21		NA											NA				34614351		692	1591	2283	SO:0001627	intron_variant				CCDS13621.1, CCDS13622.1, CCDS74782.1	21q22.1	2010-08-17			ENSG00000159110	ENSG00000159110	3455		Interferons	5433	protein-coding gene	gene with protein product		602376		IFNABR	NA	8181059	Standard		NM_207585	NA	Approved		uc002yrd.3	P48551	OTTHUMG00000065127	ENST00000342136.4:c.55+69G>A	chr21.hg19:g.34614351G>A		NA	A8KAJ4|D3DSE8|D3DSE9|Q15467|Q6FHD7	hg19	CCDS13621.1	0.02	9.035341	CTGxCAG	COVERED																																																																																			NOVEL	IFNAR2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139825.1	0	14.430654	KEEP	0	0	0	48	1666	GG	1	1	0		+	48	60	1714	0	0	145.627531	159	60	5934	299	ENST00000342136.4	0.231884	1
IFNAR1	3454	__UNKNOWN__	__UNKNOWN__	21	34731734	34731734	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:34731734G>A	ENST00000270139.3	+	0	5705					NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	NA		NA			cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"Interferon Alfa-2a(DB00034)|"Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)	GCCCAGGGTTGAGCATCCTGA	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(73;817 1211 32990 35667 42746)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166	3454		Interferons	5432	protein-coding gene	gene with protein product		107450		IFNAR	NA	8181059	Standard		NM_000629	NA	Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.*3879G>A	chr21.hg19:g.34731734G>A		NA	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	hg19	CCDS13624.1	0.02	4.496396	GTTxAGC	COVERED																																																																																			NOVEL	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139823.4	1	7.823616	KEEP	0	0	0	26	890	GG	0.999957	0.999956	0		+	22	60	766	0	0	62.015047	101	60	3658	173	ENST00000270139.3	0.178862	0.999999
DNAJC28	54943	__UNKNOWN__	__UNKNOWN__	21	34860967	34860967	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:34860967C>T	ENST00000314399.3	-	2	1172	c.734G>A	c.(733-735)cGa>cAa	p.R245Q	DNAJC28_ENST00000381947.3_Missense_Mutation_p.R245Q|DNAJC28_ENST00000402202.1_Missense_Mutation_p.R245Q	NM_017833.3	NP_060303.2	Q9NX36	DJC28_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 28	245		NA						p.R245Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(5)|skin(1)|urinary_tract(1)	18						GATCAGTATTCGGTTCAGGTT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	endometrium(1)											212	209	210	NA		NA	NA	21		NA											NA				34860967		2203	4300	6503	SO:0001583	missense			AK000468	CCDS13626.1	21q22.11	2011-09-02	2008-06-17	2008-06-17	ENSG00000177692	ENSG00000177692	54943		Heat shock proteins / DNAJ (HSP40)	1297	protein-coding gene	gene with protein product	Orf28	NA	chromosome 21 open reading frame 55	C21orf55	NA		Standard		NM_017833	NA	Approved	C21orf78	uc002yrw.3	Q9NX36	OTTHUMG00000065531	ENST00000314399.3:c.734G>A	chr21.hg19:g.34860967C>T	ENSP00000320303:p.Arg245Gln	NA	D3DSF2	hg19	CCDS13626.1	0.02	21.924188	ATTxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935146	0.92458	.	.	ENSG00000177692	ENST00000381947;ENST00000314399;ENST00000402202	.	.	.	5.26	5.26	0.73747	DnaJ homologue, subfamily C, member 28, conserved domain (1);	0.000000	0.85682	D	0.000000	T	0.80465	0.4628	M	0.79805	2.47	0.46279	D	0.998961	D	0.89917	1.0	D	0.91635	0.999	T	0.81473	-0.0917	9	0.48119	T	0.1	-22.5028	17.6336	0.88116	0.0:1.0:0.0:0.0	.	245	Q9NX36	DJC28_HUMAN	Q	245	.	ENSP00000320303:R245Q	R	-	2	0	DNAJC28	33782837	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.113000	0.77095	2.454000	0.82982	0.650000	0.86243	CGA	NOVEL	DNAJC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000140454.3	5	37.618814	KEEP	0	0	0	125	4272	CC	1	1	0		-	17	60	630	0	0	38.330052	523	60	18946	810	ENST00000314399.3	0.031481	1
GART	2618	__UNKNOWN__	__UNKNOWN__	21	34897104	34897104	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:34897104G>A	ENST00000381831.3	-	11	1533	c.1270C>T	c.(1270-1272)Cgt>Tgt	p.R424C	GART_ENST00000361093.5_Missense_Mutation_p.R424C|GART_ENST00000381839.3_Missense_Mutation_p.R424C|GART_ENST00000381815.4_Missense_Mutation_p.R424C	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	424		NA			'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)			NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	GCTATGGCACGAAAGCCGACG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													99	96	97	NA		NA	NA	21		NA											NA				34897104		2203	4300	6503	SO:0001583	missense			M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2618	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT	NA	2050105	Standard	NM_000819	NM_001136005	NA	Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.1270C>T	chr21.hg19:g.34897104G>A	ENSP00000371253:p.Arg424Cys	NA	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	hg19	CCDS13627.1	0.02	4.376753	CACxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.21	3.331898	0.60853	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000361093	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	6.03	5.08	0.68730	Rudiment single hybrid motif (1);Phosphoribosylglycinamide synthetase, C-domain (2);	0.000000	0.85682	D	0.000000	T	0.75874	0.3909	H	0.96430	3.82	0.80722	D	1	D	0.69078	0.997	P	0.57720	0.826	D	0.84151	0.0423	10	0.87932	D	0	-18.1128	18.0638	0.89385	0.0:0.0:0.8714:0.1286	.	424	P22102	PUR2_HUMAN	C	424	ENSP00000371236:R424C;ENSP00000371253:R424C;ENSP00000371261:R424C;ENSP00000354388:R424C	ENSP00000354388:R424C	R	-	1	0	GART	33818974	1.000000	0.71417	0.140000	0.22221	0.539000	0.34962	4.893000	0.63199	2.868000	0.98415	0.557000	0.71058	CGT	NOVEL	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000140626.3	1	5.717535	KEEP	0	0	0	19	617	GG	0.99986	0.99986	0		-	16	60	588	0	0	44.42127	132	60	4480	182	ENST00000381831.3	0.108108	1
GART	2618	__UNKNOWN__	__UNKNOWN__	21	34900539	34900539	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:34900539C>T	ENST00000381831.3	-	10	1263	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T	GART_ENST00000361093.5_Missense_Mutation_p.A334T|GART_ENST00000381839.3_Missense_Mutation_p.A334T|GART_ENST00000381815.4_Missense_Mutation_p.A334T	NM_001136005.1	NP_001129477.1	P22102	PUR2_HUMAN	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	334		NA			'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|glycine metabolic process (GO:0006544)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|phosphoribosylamine-glycine ligase activity (GO:0004637)|phosphoribosylformylglycinamidine cyclo-ligase activity (GO:0004641)|phosphoribosylglycinamide formyltransferase activity (GO:0004644)	p.A334T(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(13)|ovary(3)|prostate(5)|urinary_tract(1)	31					Pemetrexed(DB00642)	ACAGTTAGGGCGGTGTGGTTT	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	lung(1)											170	155	160	NA		NA	NA	21		NA											NA				34900539		2203	4300	6503	SO:0001583	missense			M32082	CCDS13627.1, CCDS13628.1	21q22.11	2012-10-02			ENSG00000159131	ENSG00000159131	2618	2.1.2.2, 6.3.3.1, 6.3.4.13		4163	protein-coding gene	gene with protein product		138440		PRGS, PGFT	NA	2050105	Standard	NM_000819	NM_001136005	NA	Approved		uc002yrx.3	P22102	OTTHUMG00000065628	ENST00000381831.3:c.1000G>A	chr21.hg19:g.34900539C>T	ENSP00000371253:p.Ala334Thr	NA	A8K945|A8KA32|D3DSF3|D3DSF4|O14659|Q52M77	hg19	CCDS13627.1	0.02	4.48329	GGGxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.9	4.356172	0.82243	.	.	ENSG00000159131	ENST00000381815;ENST00000381831;ENST00000381839;ENST00000361093	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.57	5.57	0.84162	Rudiment single hybrid motif (1);Phosphoribosylglycinamide synthetase, C-domain (2);	0.000000	0.85682	D	0.000000	T	0.75102	0.3804	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.78605	-0.2139	10	0.56958	D	0.05	-17.2212	19.5479	0.95307	0.0:1.0:0.0:0.0	.	334	P22102	PUR2_HUMAN	T	334	ENSP00000371236:A334T;ENSP00000371253:A334T;ENSP00000371261:A334T;ENSP00000354388:A334T	ENSP00000354388:A334T	A	-	1	0	GART	33822409	1.000000	0.71417	0.136000	0.22124	0.370000	0.29829	7.053000	0.76641	2.636000	0.89361	0.555000	0.69702	GCC	NOVEL	GART-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000140626.3	0	11.3912	KEEP	0	0	0	38	1306	CC	1	1	0		-	11	60	396	0	0	28.267369	125	60	4560	231	ENST00000381831.3	0.080882	1
SON	6651	__UNKNOWN__	__UNKNOWN__	21	34930102	34930102	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:34930102G>A	ENST00000381679.4	+	0	6600				SON_ENST00000290239.6_Intron|SON_ENST00000300278.4_Intron|SON_ENST00000381692.2_Intron|SON_ENST00000356577.4_Intron			P18583	SON_HUMAN	SON DNA binding protein	NA		NA			cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						TCAACATTTCGGGTTTTGGCT	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140	6651		G patch domain containing	11183	protein-coding gene	gene with protein product	NRE-binding protein, negative regulatory element-binding protein, Bax antagonist selected in Saccharomyces 1	182465		C21orf50	NA	8318737, 21551269	Standard	NM_138927	NM_032195	NA	Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000381679.4:c.*245G>A	chr21.hg19:g.34930102G>A		NA	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	hg19		0.02	4.689194	TTCxGGT	COVERED																																																																																			NOVEL	SON-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000140982.3	0	4.848268	KEEP	0	1	22	24	794	GG	0.999931	0.999899	0		+	7	60	262	0	0	18.496303	94	60	3251	141	ENST00000381679.4	0.069307	0.999968
KCNE1	3753	__UNKNOWN__	__UNKNOWN__	21	35820090	35820090	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:35820090G>A	ENST00000337385.3	-	0	2218				KCNE1_ENST00000432085.1_3'UTR|KCNE1_ENST00000399289.3_3'UTR	NM_001270402.1|NM_001270403.1	NP_001257331.1|NP_001257332.1	P15382	KCNE1_HUMAN	potassium voltage-gated channel, Isk-related family, member 1	NA		NA			cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular response to cAMP (GO:0071320)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|protein N-linked glycosylation (GO:0006487)|protein O-linked glycosylation (GO:0006493)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	potassium channel regulator activity (GO:0015459)|telethonin binding (GO:0031433)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(4)|lung(1)|ovary(2)	7					Indapamide(DB00808)	ATACTGTATGGCAGTAggctg	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L28168	CCDS13636.1	21q22.1-q22.2	2014-09-17			ENSG00000180509	ENSG00000180509	3753		Potassium channels	6240	protein-coding gene	gene with protein product		176261			NA	8432548	Standard		NM_001127670	NA	Approved	minK, ISK, JLNS2, LQT5	uc010gmp.4	P15382	OTTHUMG00000086236	ENST00000337385.3:c.*1453C>T	chr21.hg19:g.35820090G>A		NA	A5H1P2|Q8N709|Q91Z94	hg19	CCDS13636.1	0.02	6.976899	ATGxCAG	COVERED																																																																																			NOVEL	KCNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194155.1	3	6.320378	KEEP	0	0	0	21	728	GG	0.999869	0.999869	0		-	43	60	1538	0	0	134.284521	114	70	4109	214	ENST00000337385.3	0.273885	1
DSCAM	1826	__UNKNOWN__	__UNKNOWN__	21	41384336	41384336	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:41384336G>A	ENST00000400454.1	-	0	7141					NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	NA		NA			cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				AGCAGACATGGAAATAAAGGC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(134;970 1778 1785 21664 32388)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587	1826		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	3039	protein-coding gene	gene with protein product		602523			NA	9426258	Standard	NM_001389	NM_001271534	NA	Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.*625C>T	chr21.hg19:g.41384336G>A		NA	O60468	hg19	CCDS42929.1	0.02	4.575341	ATGxAAA	COVERED																																																																																			NOVEL	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195029.1	1	13.177851	KEEP	0	0	0	44	1442	GG	1	0.999996	0		-	70	60	2515	1	0	251.897562	44	60	1551	193	ENST00000400454.1	0.614035	0.999996
ABCG1	9619	__UNKNOWN__	__UNKNOWN__	21	43717251	43717251	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:43717251G>T	ENST00000398449.3	+	0	2895				ABCG1_ENST00000398437.1_3'UTR|ABCG1_ENST00000361802.2_3'UTR|ABCG1_ENST00000398457.2_3'UTR|ABCG1_ENST00000347800.2_3'UTR|ABCG1_ENST00000340588.4_3'UTR|ABCG1_ENST00000343687.3_3'UTR|ABCG1_ENST00000462050.1_3'UTR	NM_016818.2	NP_058198.2	P45844	ABCG1_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 1	NA		NA			amyloid precursor protein catabolic process (GO:0042987)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|detection of hormone stimulus (GO:0009720)|glycoprotein transport (GO:0034436)|high-density lipoprotein particle remodeling (GO:0034375)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of cholesterol efflux (GO:0010875)|regulation of cholesterol esterification (GO:0010872)|regulation of transcription, DNA-templated (GO:0006355)|response to high density lipoprotein particle (GO:0055099)|response to lipid (GO:0033993)|response to organic substance (GO:0010033)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|glycoprotein transporter activity (GO:0034437)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sterol-transporting ATPase activity (GO:0034041)|toxin transporter activity (GO:0019534)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|ovary(3)|prostate(2)|stomach(1)	29					Adenosine triphosphate(DB00171)	ATTTTTAAAAGCTATACAAAA	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U34919	CCDS13681.1, CCDS13682.1, CCDS13683.1, CCDS42937.1, CCDS42938.1	21q22.3	2012-03-14			ENSG00000160179	ENSG00000160179	9619		ATP binding cassette transporters / subfamily G	73	protein-coding gene	gene with protein product	ATP-binding cassette transporter 8	603076			NA	8659545, 16870176	Standard	NM_207174	NM_016818	NA	Approved	ABC8	uc002zaq.3	P45844	OTTHUMG00000086791	ENST00000398449.3:c.*749G>T	chr21.hg19:g.43717251G>T		NA	Q86SU8|Q96L76|Q9BXK6|Q9BXK7|Q9BXK8|Q9BXK9|Q9BXL0|Q9BXL1|Q9BXL2|Q9BXL3|Q9BXL4	hg19	CCDS42938.1	0.02	2.147564	AAAxCTA	COVERED																																																																																			NOVEL	ABCG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195313.2	0	5.116349	KEEP	0	0	0	17	590	GG	0.999366	0.997265	0		+	23	60	826	0	0	73.804277	50	60	1893	99	ENST00000398449.3	0.315068	0.997898
AGPAT3	56894	__UNKNOWN__	__UNKNOWN__	21	45404574	45404574	__UNKNOWN__	3'UTR	SNP	T	T	G	rs200193131|rs573954296	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:45404574T>G	ENST00000398063.2	+	0	3924				AGPAT3_ENST00000291572.8_3'UTR	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	NA		NA			CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		TTTTTTTTTTTGGGGGGGGGA	0.383	NA	NA											T|||	374	0.0746805	0.1732	0.0519	5008	,	,	NA	13142	0.0268	NA	0.0288	False	NA	,,,	NA	NA	NA	2504	0.0542	NA	NA	NA	Pancreas(60;623 1650 5574 52796)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	56894	2.3.1.51	1-acylglycerol-3-phosphate O-acyltransferases	326	protein-coding gene	gene with protein product		614794			NA		Standard	NM_020132	XM_005261159	NA	Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.*2301T>G	chr21.hg19:g.45404574T>G		NA	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	hg19	CCDS13703.1	0.02	4.58199	TTTxGGG	COVERED																																																																																			NOVEL	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195722.1	2	5.712521	KEEP	0	0	0	19	526	TT	0.99986	0.999833	0		+	6	60	188	2	0	12.001812	90	60	3084	149	ENST00000398063.2	0.0625	0.999973
AGPAT3	56894	__UNKNOWN__	__UNKNOWN__	21	45404584	45404584	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:45404584A>G	ENST00000398063.2	+	0	3934				AGPAT3_ENST00000291572.8_3'UTR	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	NA		NA			CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		TGGGGGGGGGAGGGTGGATTT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(60;623 1650 5574 52796)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	56894	2.3.1.51	1-acylglycerol-3-phosphate O-acyltransferases	326	protein-coding gene	gene with protein product		614794			NA		Standard	NM_020132	XM_005261159	NA	Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.*2311A>G	chr21.hg19:g.45404584A>G		NA	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	hg19	CCDS13703.1	0.02	1.090935	GGGxGGG	COVERED																																																																																			NOVEL	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195722.1	2	2.572896	KEEP	0	3	16	15	299	AA	0.999859	0.999754	0		+	9	60	154	0	0	7.580575	81	70	1839	167	ENST00000398063.2	0.1	0.999895
ICOSLG	23308	__UNKNOWN__	__UNKNOWN__	21	45648657	45648657	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:45648657T>C	ENST00000407780.3	-	0	1296				ICOSLG_ENST00000400377.3_3'UTR|ICOSLG_ENST00000344330.4_Intron|ICOSLG_ENST00000400379.3_3'UTR	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	NA		NA			B cell activation (GO:0042113)|defense response (GO:0006952)|hyperosmotic response (GO:0006972)|positive regulation of activated T cell proliferation (GO:0042104)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(2)|lung(1)|stomach(1)|urinary_tract(1)	5				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		AGTCCCTTCCTGTGGGTGACT	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB014553	CCDS42952.1, CCDS63377.1, CCDS63379.1	21q22.3	2014-01-30		2005-01-12	ENSG00000160223	ENSG00000160223	23308		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Endogenous ligands	17087	protein-coding gene	gene with protein product	B7-related protein 1, B7 homologue 2, B7 homolog 2	605717		ICOSL	NA	9734811, 11007762	Standard	NM_015259	NM_001283050	NA	Approved	KIAA0653, GL50, B7-H2, B7RP-1, B7H2, B7RP1, ICOS-L, CD275	uc002zee.3	O75144	OTTHUMG00000086920	ENST00000407780.3:c.*260A>G	chr21.hg19:g.45648657T>C		NA	A8MUZ1|Q9HD18|Q9NRQ1	hg19	CCDS42952.1	0.02	6.534684	TCCxGTG	COVERED																																																																																			NOVEL	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195838.1	0	12.030882	KEEP	0	0	0	40	1244	TT	1	1	0		-	41	60	1417	0	0	117.508763	156	60	5859	307	ENST00000407780.3	0.208122	1
C21orf2	755	__UNKNOWN__	__UNKNOWN__	21	45751955	45751955	__UNKNOWN__	Intron	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:45751955G>A	ENST00000339818.4	-	5	581				C21orf2_ENST00000397956.3_Intron|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000325223.7_Intron|C21orf2_ENST00000496321.1_Intron	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	NA		NA			cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		CAGGCCACATGCACTGCAGCT	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226	755			1260	protein-coding gene	gene with protein product	nuclear encoded mitochondrial protein, leucine rich repeat containing 76	603191			NA	9465297	Standard	NM_004928	NM_004928	NA	Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.374-58C>T	chr21.hg19:g.45751955G>A		NA	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	hg19	CCDS13709.1	0.02	4.141297	CATxCAC	COVERED																																																																																			NOVEL	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195799.1	2	18.960621	KEEP	0	0	0	63	2255	GG	1	1	0		-	46	60	1630	0	0	146.341564	95	60	3525	270	ENST00000339818.4	0.326241	1
TSPEAR	54084	__UNKNOWN__	__UNKNOWN__	21	45953664	45953664	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr21:45953664C>T	ENST00000397916.1	-	3	400	c.242G>A	c.(241-243)aGc>aAc	p.S81N	TSPEAR_ENST00000323084.4_Missense_Mutation_p.S149N			Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	149	Laminin G-like.	NA			sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CAGGGCCGGGCTGCGGAAGGA	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													29	29	29	NA		NA	NA	21		NA											NA				45953664		2195	4288	6483	SO:0001583	missense			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894	54084			1268	protein-coding gene	gene with protein product		612920	chromosome 21 open reading frame 29, deafness, autosomal recessive 98	C21orf29, DFNB98	NA	12095917, 22678063	Standard	NM_144991	NM_144991	NA	Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000397916.1:c.242G>A	chr21.hg19:g.45953664C>T	ENSP00000381012:p.Ser81Asn	NA		hg19		0.02	4.282296	GGGxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	c	0.113	-1.135577	0.01742	.	.	ENSG00000175894	ENST00000323084;ENST00000397916;ENST00000341581	T;T	0.02085	4.46;4.46	4.9	1.43	0.22495	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.567389	0.19436	N	0.114313	T	0.01730	0.0055	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48525	-0.9028	10	0.18276	T	0.48	-6.6525	6.6709	0.23068	0.0:0.4357:0.0:0.5643	.	149	Q8WU66	TSEAR_HUMAN	N	149;81;149	ENSP00000321987:S149N;ENSP00000381012:S81N	ENSP00000321987:S149N	S	-	2	0	TSPEAR	44778092	0.000000	0.05858	0.005000	0.12908	0.052000	0.14988	0.041000	0.13927	0.409000	0.25649	-0.142000	0.14014	AGC	NOVEL	TSPEAR-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000195865.1	0	27.988203	KEEP	0	0	0	93	3286	CC	1	1	0		-	49	60	1667	0	0	151.666533	86	60	3194	316	ENST00000397916.1	0.362963	1
MICAL3	57553	__UNKNOWN__	__UNKNOWN__	22	18271092	18271092	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:18271092G>T	ENST00000441493.2	-	0	8767				XXbac-B461K10.4_ENST00000476405.1_RNA	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	NA		NA			actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GTGCTGTGGAGGATGCCACAG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156	57553			24694	protein-coding gene	gene with protein product		608882			NA	12110185	Standard		NM_015241	NA	Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.*2406C>A	chr22.hg19:g.18271092G>T		NA	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	hg19	CCDS46659.1	0.02	8.936716	GGAxGAT	COVERED																																																																																			NOVEL	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447351.1	2	13.23935	KEEP	0	0	0	44	1529	GG	1	1	0		-	23	60	801	0	0	58.185164	218	60	8014	358	ENST00000441493.2	0.095436	1
MICAL3	57553	__UNKNOWN__	__UNKNOWN__	22	18272729	18272729	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:18272729G>A	ENST00000441493.2	-	0	7130				XXbac-B461K10.4_ENST00000476405.1_RNA	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	NA		NA			actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		GACAATGCCTGTCTGCCAACT	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156	57553			24694	protein-coding gene	gene with protein product		608882			NA	12110185	Standard		NM_015241	NA	Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.*769C>T	chr22.hg19:g.18272729G>A		NA	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	hg19	CCDS46659.1	0.02	8.932878	CCTxTCT	COVERED																																																																																			NOVEL	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447351.1	0	9.932768	KEEP	0	0	0	33	1204	GG	0.999998	0.999998	0		-	49	60	1781	0	0	149.744164	181	60	6815	304	ENST00000441493.2	0.213043	1
PEX26	55670	__UNKNOWN__	__UNKNOWN__	22	18573308	18573308	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:18573308G>A	ENST00000329627.7	+	0	3591					NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	NA		NA			protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GTTTCATATCGCTTCTGTGGT	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193	55670			22965	protein-coding gene	gene with protein product		608666	peroxisome biogenesis factor 26		NA	12717447, 12851857	Standard	NM_017929	NM_017929	NA	Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.*2467G>A	chr22.hg19:g.18573308G>A		NA	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	hg19	CCDS13750.1	0.02	20.785141	ATCxCTT	COVERED																																																																																			NOVEL	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000314644.3	8	29.787789	KEEP	0	0	0	99	3423	GG	1	1	0		+	83	60	2840	0	0	228.738843	384	60	13637	710	ENST00000329627.7	0.17773	1
PRODH	5625	__UNKNOWN__	__UNKNOWN__	22	18908629	18908629	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:18908629C>T	ENST00000357068.6	-	8	1277				PRODH_ENST00000334029.2_Intron|PRODH_ENST00000420436.1_Intron	NM_016335.4	NP_057419	O43272	PROD_HUMAN	proline dehydrogenase (oxidase) 1	NA		NA			4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)	FAD binding (GO:0071949)|proline dehydrogenase activity (GO:0004657)			breast(1)|endometrium(3)|lung(4)|upper_aerodigestive_tract(1)	9					L-Proline(DB00172)	CTTGTGGTGTCTTAAGGCTCC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF010310	CCDS13754.1, CCDS56223.1	22q11.2	2014-07-10	2001-12-05		ENSG00000100033	ENSG00000100033	5625	1.5.5.2		9453	protein-coding gene	gene with protein product		606810	proline dehydrogenase (proline oxidase )		NA	9385373, 10192398	Standard	NM_016335	NM_001195226	NA	Approved	HSPOX2, PRODH1, PIG6, PRODH2, TP53I6	uc002zok.4	O43272	OTTHUMG00000150163	ENST00000357068.6:c.1011+225G>A	chr22.hg19:g.18908629C>T		NA	A6NF53|O14680|Q0P507|Q147W8|Q504W1|Q59FI8|Q6NV86|Q9UF13	hg19	CCDS13754.1	0.02	7.836692	TGTxTTA	COVERED																																																																																			NOVEL	PRODH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316637.2	2	4.789306	KEEP	0	0	0	16	545	CC	0.997832	0.997832	0		-	7	47	252	0	0	14.95327	222	60	8079	276	ENST00000357068.6	0.030568	1
GSC2	2928	__UNKNOWN__	__UNKNOWN__	22	19137330	19137330	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:19137330G>A	ENST00000086933.2	-	2	358	c.359C>T	c.(358-360)cCg>cTg	p.P120L		NM_005315.1	NP_005306.1	O15499	GSC2_HUMAN	goosecoid homeobox 2	120		NA			anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(2)	4	Colorectal(54;0.0993)					CTGCGAACCCGGGCCGACCGC	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													6	7	7	NA		NA	NA	22		NA											NA				19137330		1993	4013	6006	SO:0001583	missense				CCDS13757.1	22q11.21	2011-06-20	2007-08-28	2007-08-28	ENSG00000063515	ENSG00000063515	2928		Homeoboxes / PRD class	4613	protein-coding gene	gene with protein product		601845	goosecoid-like	GSCL	NA	9150167	Standard	NM_005315	NM_005315	NA	Approved		uc011ags.2	O15499	OTTHUMG00000150122	ENST00000086933.2:c.359C>T	chr22.hg19:g.19137330G>A	ENSP00000086933:p.Pro120Leu	NA		hg19	CCDS13757.1	0.02	6.98558	CCCxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	g	14.01	2.408890	0.42715	.	.	ENSG00000063515	ENST00000086933	D	0.95412	-3.7	4.16	1.94	0.25998	Homeodomain-related (1);Homeodomain-like (1);	0.285799	0.31071	N	0.008318	D	0.91945	0.7449	N	0.19112	0.55	0.45129	D	0.998148	D	0.63880	0.993	P	0.53954	0.738	D	0.87434	0.2390	10	0.27785	T	0.31	-12.2582	8.3541	0.32321	0.0:0.2035:0.5269:0.2696	.	120	O15499	GSC2_HUMAN	L	120	ENSP00000086933:P120L	ENSP00000086933:P120L	P	-	2	0	GSC2	17517330	0.354000	0.24912	0.107000	0.21349	0.035000	0.12851	0.311000	0.19380	0.295000	0.22570	-0.887000	0.02937	CCG	NOVEL	GSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316440.2	0	16.849383	KEEP	0	0	0	56	1861	GG	1	1	0		-	31	60	1166	0	0	97.613828	125	60	4314	264	ENST00000086933.2	0.198718	1
GNB1L	54584	__UNKNOWN__	__UNKNOWN__	22	19772320	19772320	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:19772320G>T	ENST00000329517.6	-	0	5132					NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					AATCAGAGGGGCCCACTCCAC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838	54584		WD repeat domain containing	4397	protein-coding gene	gene with protein product		610778			NA	11072084	Standard		NM_053004	NA	Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.*3912C>A	chr22.hg19:g.19772320G>T		NA	Q9H2S2|Q9H4M4	hg19	CCDS13768.1	0.02	10.215283	GGGxCCC	COVERED																																																																																			NOVEL	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075202.1	2	8.118108	KEEP	0	0	0	27	837	GG	0.999988	0.999988	0		-	37	60	1251	0	0	97.125702	215	60	7490	320	ENST00000329517.6	0.146825	1
TXNRD2	10587	__UNKNOWN__	__UNKNOWN__	22	19863493	19863493	__UNKNOWN__	Intron	SNP	G	G	A	rs565397993	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:19863493G>A	ENST00000400521.1	-	18	1647				TXNRD2_ENST00000400518.1_Intron|TXNRD2_ENST00000400519.1_3'UTR|TXNRD2_ENST00000542719.1_Intron|TXNRD2_ENST00000535882.1_3'UTR	NM_006440.3	NP_006431.2	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2	NA		NA			cell redox homeostasis (GO:0045454)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|response to oxygen radical (GO:0000305)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|urinary_tract(2)	30	Colorectal(54;0.0993)					AGGGAGCGACGCGGTGCTACA	0.498	NA	NA											G|||	3	0.000599042	0	0	5008	,	,	NA	16397	0.003	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF106697	CCDS42981.1, CCDS63402.1	22q11.21	2014-09-17			ENSG00000184470	ENSG00000184470	10587			18155	protein-coding gene	gene with protein product	thioredoxin reductase beta, selenoprotein Z	606448			NA	9923614, 10215850, 11012661	Standard	NM_006440	NM_006440	NA	Approved	TR, TRXR2, TR3	uc021wlj.1	Q9NNW7	OTTHUMG00000149975	ENST00000400521.1:c.1573-163C>T	chr22.hg19:g.19863493G>A		NA	O95840|Q96IJ2|Q9H2Z5|Q9NZV3|Q9NZV4|Q9P2Y0|Q9P2Y1|Q9UQU8	hg19	CCDS42981.1	0.02	10.51329	GACxCGG	COVERED																																																																																			NOVEL	TXNRD2-003	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS|seleno	protein_coding	NA	protein_coding	OTTHUMT00000314903.3	5	13.540804	KEEP	0	0	0	45	1471	GG	1	1	0		-	15	60	535	0	0	35.077867	273	60	9375	363	ENST00000400521.1	0.052083	1
ARVCF	421	__UNKNOWN__	__UNKNOWN__	22	19967634	19967634	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:19967634G>A	ENST00000263207.3	-	6	1319	c.1028C>T	c.(1027-1029)tCg>tTg	p.S343L	ARVCF_ENST00000401994.1_Missense_Mutation_p.S280L|ARVCF_ENST00000406259.1_Missense_Mutation_p.S343L|ARVCF_ENST00000344269.3_Missense_Mutation_p.S280L|ARVCF_ENST00000406522.1_Missense_Mutation_p.S280L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	343		NA			calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CACTGAGGGCGAGCGCCGCAC	0.736	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													5	7	6	NA		NA	NA	22		NA											NA				19967634		1827	3710	5537	SO:0001583	missense				CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889	421		Armadillo repeat containing	728	protein-coding gene	gene with protein product		602269			NA	9126485, 15456900	Standard	NM_001670	NM_001670	NA	Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1028C>T	chr22.hg19:g.19967634G>A	ENSP00000263207:p.Ser343Leu	NA	B7WNV2	hg19	CCDS13771.1	0.02	4.705144	GGCxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	34	5.323590	0.95708	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.70399	-0.48;-0.45;-0.45;-0.42;-0.47	5.35	5.35	0.76521	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.67011	0.2848	L	0.54323	1.7	0.80722	D	1	P	0.47677	0.899	B	0.38803	0.282	T	0.68655	-0.5351	9	.	.	.	-20.1456	19.4432	0.94831	0.0:0.0:1.0:0.0	.	343	O00192	ARVC_HUMAN	L	343;280;280;280;343	ENSP00000263207:S343L;ENSP00000342042:S280L;ENSP00000384341:S280L;ENSP00000384732:S280L;ENSP00000385444:S343L	.	S	-	2	0	ARVCF	18347634	1.000000	0.71417	0.951000	0.38953	0.865000	0.49528	7.076000	0.76806	2.676000	0.91093	0.655000	0.94253	TCG	NOVEL	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075314.5	2	5.413868	KEEP	0	0	0	18	558	GG	0.999859	0.999858	0		-	23	60	801	0	0	65.435712	99	60	3089	191	ENST00000263207.3	0.188525	0.999999
PI4KAP2	375133	__UNKNOWN__	__UNKNOWN__	22	21829555	21829555	__UNKNOWN__	RNA	SNP	T	T	G	rs377578228		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:21829555T>G	ENST00000450651.1	-	0	1783							A4QPH2	PI4P2_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha pseudogene 2	NA		NA			phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)	p.I530L(4)		endometrium(3)|urinary_tract(1)	4						TCCAACATGATAGTGACCAGG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				4	Substitution - Missense(4)	endometrium(3)|urinary_tract(1)											26	21	23	NA		NA	NA	22		NA											NA				21829555		692	1582	2274							22q11.21	2014-03-20	2007-08-14		ENSG00000183506	ENSG00000183506	375133			33577	pseudogene	pseudogene		NA			NA		Standard		NR_003700	NA	Approved		uc011aie.1	A4QPH2	OTTHUMG00000150827	ENST00000450651.1:	chr22.hg19:g.21829555T>G		NA	Q6ICJ0|Q6ZT68|Q8WUK7	hg19		0.02	2.059575	TGAxAGT	COVERED																																																																																			NOVEL	PI4KAP2-005	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000334908.1	2	7.520281	KEEP	19	0	0	25	747	TT	0.999863	0.999422	0		-	5	27	184	0	0	12.583129	78	50	2712	150	ENST00000450651.1	0.060241	0.999559
TOP3B	8940	__UNKNOWN__	__UNKNOWN__	22	22330266	22330266	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:22330266A>T	ENST00000398793.2	-	2	337				TOP3B_ENST00000357179.5_Intron|TOP3B_ENST00000413067.2_Intron	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	NA		NA			chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CAAAGAAAAAACAAGACCAAC	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038	8940			11993	protein-coding gene	gene with protein product		603582			NA	9786842, 9074928	Standard	NM_003935	XM_005261811	NA	Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.98-87T>A	chr22.hg19:g.22330266A>T		NA	A0M8Q3|Q9BUP5	hg19	CCDS13797.1	0.02	2.313855	AAAxCAA	COVERED																																																																																			NOVEL	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320251.1	2	4.212714	KEEP	0	0	0	14	440	AA	0.995343	0.972316	0		-	9	60	328	0	0	26.528754	45	60	1612	84	ENST00000398793.2	0.166667	0.976865
TOP3B	8940	__UNKNOWN__	__UNKNOWN__	22	22330267	22330267	__UNKNOWN__	Intron	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:22330267C>A	ENST00000398793.2	-	2	337				TOP3B_ENST00000357179.5_Intron|TOP3B_ENST00000413067.2_Intron	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	NA		NA			chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		AAAGAAAAAACAAGACCAACC	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038	8940			11993	protein-coding gene	gene with protein product		603582			NA	9786842, 9074928	Standard	NM_003935	XM_005261811	NA	Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.98-88G>T	chr22.hg19:g.22330267C>A		NA	A0M8Q3|Q9BUP5	hg19	CCDS13797.1	0.02	2.305401	AAAxAAG	COVERED																																																																																			NOVEL	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320251.1	2	4.213915	KEEP	0	0	0	14	509	CC	0.995343	0.972316	0		-	10	60	341	0	0	27.567919	45	60	1697	84	ENST00000398793.2	0.181818	0.976865
IGLV7-43	28776	__UNKNOWN__	__UNKNOWN__	22	22749479	22749479	__UNKNOWN__	RNA	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:22749479G>C	ENST00000390298.2	+	0	80									immunoglobulin lambda variable 7-43	NA		NA									NA						GGATCCTTCTGTCTGCCCTTC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					X14614		22q11.2	2012-02-08			ENSG00000211652	ENSG00000211652	28776		Immunoglobulins / IGL locus	5929	other	immunoglobulin gene		NA			NA		Standard	NG_000002	NG_000002	NA	Approved				OTTHUMG00000151053	ENST00000390298.2:	chr22.hg19:g.22749479G>C		NA		hg19		0.02	7.330454	TCTxTCT	COVERED																																																																																			NOVEL	IGLV7-43-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000321113.1	2	11.437131	KEEP	0	0	0	38	1349	GG	1	1	0		+	151	60	5803	0	0	613.242212	35	60	1321	279	ENST00000390298.2	0.811828	1
IGLV3-25	28793	__UNKNOWN__	__UNKNOWN__	22	23029718	23029718	__UNKNOWN__	RNA	SNP	A	A	T	rs199561156	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:23029718A>T	ENST00000390305.2	+	0	363									immunoglobulin lambda variable 3-25	NA		NA									NA						TATTACTGTCAATCAGCAGAC	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													84	83	83	NA		NA	NA	22		NA											NA				23029718		2047	4207	6254					X97474		22q11.2	2012-02-08			ENSG00000211659	ENSG00000211659	28793		Immunoglobulins / IGL locus	5908	other	immunoglobulin gene		NA			NA		Standard	NG_000002	NG_000002	NA	Approved				OTTHUMG00000151221	ENST00000390305.2:	chr22.hg19:g.23029718A>T		NA		hg19		0.02	13.524902	GTCxATC	COVERED																																																																																			NOVEL	IGLV3-25-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000321825.1	4	8.948737	KEEP	0	1	32	41	1257	AA	1	1	0		+	22	60	796	0	0	56.254558	269	60	9769	435	ENST00000390305.2	0.075601	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	23029767	23029767	__UNKNOWN__	IGR	SNP	G	G	A	rs373289152		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:23029767G>A			NA	NA				IGLV3-25 (32 upstream) : LL22NC03-102D1.18 (5495 downstream)						NA		NA									NA						AAGCAGACAGGGAAGTGAGAC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													71	69	70	NA		NA	NA	22		NA											NA				23029767		2051	4208	6259	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.23029767G>A		NA		hg19		0.02	12.507029	CAGxGAA	COVERED																																																																																			NOVEL					0			21	5.109894	KEEP	0	2	45	33	1144	GG	0.999999	0.999999	0			63	60	2376	0	0	203.849517	208	60	7346	405		0.232472	1
RTDR1	0	__UNKNOWN__	__UNKNOWN__	22	23479767	23479767	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:23479767C>T	ENST00000216036.4	-	3	499				RTDR1_ENST00000406876.1_Intron	NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN		NA		NA								breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)		TGTTTTTTTTCCCTTCAAATC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000216036.4:c.302+1259G>A	chr22.hg19:g.23479767C>T		NA		hg19	CCDS13803.1	0.02	4.444509	TTTxCCT	COVERED																																																																																			NOVEL	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319049.1	6	2.708689	KEEP	0	0	0	9	310	CC	0.99254	0.99254	0		-	38	60	1347	0	0	118.865416	91	60	3164	161	ENST00000216036.4	0.294574	1
RGL4	266747	__UNKNOWN__	__UNKNOWN__	22	24040069	24040069	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:24040069C>T	ENST00000401461.1	+	10	1965				KB-1572G7.2_ENST00000421064.1_RNA|RGL4_ENST00000290691.5_Intron			Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	NA		NA			small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						GGGGCACTCACGTTGGATGAG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													70	52	58	NA		NA	NA	22		NA											NA				24040069		2203	4300	6503	SO:0001627	intron_variant				CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496	266747			31911	protein-coding gene	gene with protein product	RalGDS related oncogene	612214			NA	9178890, 10851075	Standard	NM_153615	NM_153615	NA	Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000401461.1:c.852+21C>T	chr22.hg19:g.24040069C>T		NA	Q495L8	hg19		0.02	2.299756	TCAxGTT	COVERED																																																																																			NOVEL	RGL4-003	PUTATIVE	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000319712.2	2	4.81233	KEEP	0	0	0	16	520	CC	0.997832	0.992926	0		+	15	60	522	0	0	43.886434	52	60	1941	104	ENST00000401461.1	0.223881	0.995084
KIAA1671	85379	__UNKNOWN__	__UNKNOWN__	22	25574693	25574693	__UNKNOWN__	Intron	SNP	G	G	A	rs4049527	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:25574693G>A	ENST00000406486.4	+	10	5461				KIAA1671_ENST00000358431.3_Intron|KIAA1671_ENST00000401395.1_Intron			Q9BY89	K1671_HUMAN	KIAA1671	NA		NA								autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						ACCTCAGGCCGGGTGGTCTCA	0.647	NA	NA											A|||	119	0.023762	0.0401	0.0331	5008	,	,	NA	13020	0.004	NA	0.0268	False	NA	,,,	NA	NA	NA	2504	0.0123	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077	85379			29345	protein-coding gene	gene with protein product		NA			NA	15289310	Standard	NM_001145206	NM_001145206	NA	Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5074+1204G>A	chr22.hg19:g.25574693G>A		NA	B0QYF2|B7ZW08|Q5THZ5	hg19	CCDS46676.1	0.02	1.933343	GCCxGGT	COVERED																																																																																			NOVEL	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320306.6	3	7.821601	KEEP	0	0	0	26	822	GG	0.999957	0.999683	0		+	4	33	154	0	0	10.390904	77	60	2664	142	ENST00000406486.4	0.049383	0.999726
HPS4	89781	__UNKNOWN__	__UNKNOWN__	22	26862177	26862177	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:26862177C>T	ENST00000398145.2	-	9	1323				HPS4_ENST00000402105.3_Intron|HPS4_ENST00000336873.5_Intron|HPS4_ENST00000398141.1_Intron	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	NA		NA			blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GGCAACCATGCGCCTCACTAC	0.512	NA	NA							Hermansky-Pudlak syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													129	93	105	NA		NA	NA	22		NA											NA				26862177		2203	4300	6503	SO:0001627	intron_variant	Familial Cancer Database	HPS, HPS1-8		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099	89781			15844	protein-coding gene	gene with protein product		606682			NA	11836498, 12663659	Standard	NM_022081	NM_022081	NA	Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.706+14G>A	chr22.hg19:g.26862177C>T		NA	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	hg19	CCDS13835.1	0.02	6.772683	ATGxGCC	COVERED																																																																																			NOVEL	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320778.1	2	6.742891	KEEP	0	1	33	34	1133	CC	0.999999	0.999999	0		-	28	60	981	0	0	79.679463	127	60	4274	254	ENST00000398145.2	0.180645	1
TTC28	23331	__UNKNOWN__	__UNKNOWN__	22	28397383	28397383	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:28397383G>A	ENST00000397906.2	-	15	4518	c.4377C>T	c.(4375-4377)cgC>cgT	p.R1459R	TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000428584.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	1459		NA			mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CGCTGAGGGAGCGGATGGAAG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													57	60	59	NA		NA	NA	22		NA											NA				28397383		692	1591	2283	SO:0001819	synonymous_variant			AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154	23331		Tetratricopeptide (TTC) repeat domain containing	29179	protein-coding gene	gene with protein product		615098			NA	10470851	Standard	XM_929318	NM_001145418	NA	Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.4377C>T	chr22.hg19:g.28397383G>A		NA	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	hg19	CCDS46678.1	0.02	2.103282	GGAxCGG	COVERED																																																																																			NOVEL	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320930.2	0	7.523833	KEEP	0	0	0	25	857	GG	0.999931	0.998924	0		-	4	60	148	0	0	9.85879	74	60	2757	124	ENST00000397906.2	0.051282	0.998993
ZNRF3	84133	__UNKNOWN__	__UNKNOWN__	22	29446285	29446285	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:29446285G>A	ENST00000544604.2	+	8	2291	c.2116G>A	c.(2116-2118)Gag>Aag	p.E706K	ZNRF3_ENST00000332811.4_Missense_Mutation_p.E606K|ZNRF3_ENST00000406323.3_Missense_Mutation_p.E606K|ZNRF3_ENST00000402174.1_Missense_Mutation_p.E606K	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	706		NA			canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						GGGGGGCCACGAGTTGCCGTC	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													12	14	14	NA		NA	NA	22		NA											NA				29446285		1931	4101	6032	SO:0001583	missense			AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579	84133		RING-type (C3HC4) zinc fingers	18126	protein-coding gene	gene with protein product		612062			NA	10574461	Standard	XM_290972	NM_032173	NA	Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.2116G>A	chr22.hg19:g.29446285G>A	ENSP00000443824:p.Glu706Lys	NA	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	hg19	CCDS56225.1	0.02	6.223876	CACxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.29	1.308072	0.23821	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55	5.01	5.01	0.66863	.	0.750628	0.13015	N	0.420542	T	0.72128	0.3422	L	0.44542	1.39	0.29553	N	0.851213	P	0.42375	0.778	B	0.32465	0.146	T	0.71087	-0.4694	10	0.49607	T	0.09	-23.4737	6.4393	0.21841	0.086:0.0:0.6075:0.3065	.	706	Q9ULT6	ZNRF3_HUMAN	K	706;606;413;606;606	ENSP00000443824:E706K;ENSP00000328614:E606K;ENSP00000384456:E606K;ENSP00000384553:E606K	ENSP00000328614:E606K	E	+	1	0	ZNRF3	27776285	1.000000	0.71417	0.855000	0.33649	0.071000	0.16799	3.097000	0.50251	2.317000	0.78254	0.655000	0.94253	GAG	NOVEL	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320943.2	1	25.606848	KEEP	0	1	31	96	3188	GG	1	1	0		+	7	60	258	0	0	16.177364	180	60	6340	334	ENST00000544604.2	0.037433	1
ZNRF3	84133	__UNKNOWN__	__UNKNOWN__	22	29449548	29449548	__UNKNOWN__	Intron	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:29449548T>G	ENST00000544604.2	+	9	2942				ZNRF3_ENST00000332811.4_Intron|ZNRF3_ENST00000406323.3_Intron|ZNRF3_ENST00000402174.1_Intron	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	NA		NA			canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						CCCTGATGATTGTTCTCTCTC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													94	103	100	NA		NA	NA	22		NA											NA				29449548		2004	4190	6194	SO:0001627	intron_variant			AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579	84133		RING-type (C3HC4) zinc fingers	18126	protein-coding gene	gene with protein product		612062			NA	10574461	Standard	XM_290972	NM_032173	NA	Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.2768-19T>G	chr22.hg19:g.29449548T>G		NA	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	hg19	CCDS56225.1	0.02	7.144697	GATxGTT	COVERED																																																																																			NOVEL	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320943.2	5	24.057574	KEEP	0	0	0	80	2322	TT	1	1	0		+	24	60	926	0	0	73.801998	149	60	5348	308	ENST00000544604.2	0.138728	1
MTMR3	8897	__UNKNOWN__	__UNKNOWN__	22	30422596	30422596	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:30422596C>T	ENST00000323630.5	+	0	4615				CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000401950.2_3'UTR|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000333027.3_3'UTR			Q13615	MTMR3_HUMAN	myotubularin related protein 3	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CACCCTCAGGCATGAGTACAG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330	8897		Zinc fingers, FYVE domain containing, Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins	7451	protein-coding gene	gene with protein product		603558			NA	8640223, 9736772	Standard	NM_021090	NM_153050	NA	Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000323630.5:c.*806C>T	chr22.hg19:g.30422596C>T		NA	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	hg19		0.02	4.144081	AGGxATG	COVERED																																																																																			NOVEL	MTMR3-004	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000322069.1	0	19.86381	KEEP	0	0	0	66	2326	CC	1	1	0		+	35	60	1202	0	0	104.288969	93	60	3466	231	ENST00000323630.5	0.273437	1
RNF215	200312	__UNKNOWN__	__UNKNOWN__	22	30780437	30780437	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:30780437G>A	ENST00000382363.3	-	5	709	c.635C>T	c.(634-636)gCc>gTc	p.A212V		NM_001017981.1	NP_001017981.1	Q9Y6U7	RN215_HUMAN	ring finger protein 215	212		NA				integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)	6						CTCGATATTGGCAGACAGGGA	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													117	91	100	NA		NA	NA	22		NA											NA				30780437		2203	4300	6503	SO:0001583	missense				CCDS33633.1	22q12.2	2013-01-09			ENSG00000099999	ENSG00000099999	200312		RING-type (C3HC4) zinc fingers	33434	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001017981	NM_001017981	NA	Approved		uc003ahp.3	Q9Y6U7	OTTHUMG00000151016	ENST00000382363.3:c.635C>T	chr22.hg19:g.30780437G>A	ENSP00000371800:p.Ala212Val	NA	A6NEL1	hg19	CCDS33633.1	0.02	4.00078	TTGxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.96	2.690253	0.48097	.	.	ENSG00000099999	ENST00000382363	T	0.46063	0.88	4.67	3.59	0.41128	.	0.224337	0.37623	N	0.002004	T	0.23886	0.0578	N	0.19112	0.55	0.80722	D	1	B	0.22346	0.068	B	0.20767	0.031	T	0.06954	-1.0798	10	0.28530	T	0.3	-19.8804	6.9701	0.24644	0.0:0.1756:0.6165:0.2079	.	212	Q9Y6U7	RN215_HUMAN	V	212	ENSP00000371800:A212V	ENSP00000371800:A212V	A	-	2	0	RNF215	29110437	0.996000	0.38824	0.998000	0.56505	0.194000	0.23727	1.606000	0.36826	2.410000	0.81850	0.561000	0.74099	GCC	NOVEL	RNF215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320960.1	2	9.631482	KEEP	0	0	0	32	1148	GG	0.999997	0.999997	0		-	6	60	213	0	0	13.528464	128	60	4745	186	ENST00000382363.3	0.044776	1
CBX7	23492	__UNKNOWN__	__UNKNOWN__	22	39548544	39548544	__UNKNOWN__	5'UTR	SNP	T	T	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:39548544T>G	ENST00000216133.5	-	0	111					NM_175709.3	NP_783640.1	O95931	CBX7_HUMAN	chromobox homolog 7	NA		NA			chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sebaceous gland development (GO:0048733)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|single-stranded RNA binding (GO:0003727)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7	Melanoma(58;0.04)					GCTGGCGGGGTCCCCGTCACC	0.806	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(46;845 904 3560 9866 23971)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS13986.1	22q13.1	2010-07-06			ENSG00000100307	ENSG00000100307	23492			1557	protein-coding gene	gene with protein product		608457			NA		Standard	NM_175709	NM_175709	NA	Approved		uc003axb.3	O95931	OTTHUMG00000150418	ENST00000216133.5:c.-95A>C	chr22.hg19:g.39548544T>G		NA	Q86T17	hg19	CCDS13986.1	0.02	1.184303	GGGxCCC	COVERED																																																																																			NOVEL	CBX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318020.1	2	10.366238	KEEP	0	22	214	114	2726	TT	1	0.997163	0		-	10	60	164	0	0	9.209068	57	60	1410	291	ENST00000216133.5	0.149254	0.997163
SYNGR1	9145	__UNKNOWN__	__UNKNOWN__	22	39773627	39773627	__UNKNOWN__	Intron	SNP	C	C	G	rs140460321		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:39773627C>G	ENST00000328933.5	+	3	498				SYNGR1_ENST00000318801.4_Missense_Mutation_p.R170G|SYNGR1_ENST00000381535.4_Missense_Mutation_p.R171G	NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	NA		NA			protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					CCTGGCCGTGCGGAGATTCAA	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													67	58	61	NA		NA	NA	22		NA											NA				39773627		2203	4300	6503	SO:0001627	intron_variant			AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321	9145			11498	protein-coding gene	gene with protein product		603925			NA	9760194, 10595519	Standard	NM_004711	NM_004711	NA	Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.483+1425C>G	chr22.hg19:g.39773627C>G		NA	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	hg19	CCDS13989.1	0.02	13.968175	GTGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	.	16.03	3.005848	0.54254	.	.	ENSG00000100321	ENST00000318801;ENST00000381535	T	0.47528	0.84	5.93	3.78	0.43462	.	.	.	.	.	T	0.43255	0.1239	.	.	.	0.23886	N	0.996569	P;P	0.39060	0.657;0.657	B;B	0.36922	0.236;0.122	T	0.29305	-1.0016	8	0.66056	D	0.02	.	15.2566	0.73591	0.2565:0.7435:0.0:0.0	.	171;170	O43759-3;O43759-2	.;.	G	170;171	ENSP00000318845:R170G	ENSP00000318845:R170G	R	+	1	2	SYNGR1	38103573	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.577000	0.53885	0.784000	0.33661	0.655000	0.94253	CGG	NOVEL	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075866.2	1	59.819152	KEEP	0	0	0	199	6786	CC	1	1	0		+	41	60	1425	0	0	109.955411	262	60	9313	642	ENST00000328933.5	0.135314	1
CYP2D6	1565	__UNKNOWN__	__UNKNOWN__	22	42523558	42523558	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs202102799		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:42523558T>C	ENST00000360608.5	-	7	1178	c.1064A>G	c.(1063-1065)tAc>tGc	p.Y355C	NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.Y355C|CYP2D6_ENST00000359033.4_Missense_Mutation_p.Y304C|NDUFA6-AS1_ENST00000416037.2_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	355		NA			alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGCAGTGGTGTAGGGCATGTG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													106	82	90	NA		NA	NA	22		NA											NA				42523558		2202	4300	6502	SO:0001583	missense			M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197	1565		Cytochrome P450s	2625	protein-coding gene	gene with protein product		124030	cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6, cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2, cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2, cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2, cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP	NA	8449513	Standard		NM_000106	NA	Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1064A>G	chr22.hg19:g.42523558T>C	ENSP00000353820:p.Tyr355Cys	NA	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	hg19	CCDS46721.1	0.02	7.074608	GTGxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884011	0.51908	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.76186	-1.0;-1.0;-1.0	4.93	-8.43	0.00953	.	0.656947	0.15234	N	0.273223	D	0.88265	0.6390	H	0.96518	3.835	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.995;0.976;0.995	D	0.91542	0.5250	10	0.87932	D	0	.	18.217	0.89889	0.1595:0.0:0.0:0.8405	.	355;304;355	C1ID54;Q6NXU8;Q6NWU0	.;.;.	C	355;355;301;304;304	ENSP00000353820:Y355C;ENSP00000374620:Y355C;ENSP00000351927:Y304C	ENSP00000351927:Y304C	Y	-	2	0	CYP2D6	40853502	0.995000	0.38212	0.872000	0.34217	0.407000	0.30961	0.270000	0.18607	-1.565000	0.01676	-0.509000	0.04479	TAC	NOVEL	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320525.1	0	3.980546	KEEP	1	2	68	37	1132	TT	1	1	0		-	6	40	236	0	0	15.224375	162	60	5588	274	ENST00000360608.5	0.035714	1
SERHL	94009	__UNKNOWN__	__UNKNOWN__	22	42905119	42905119	__UNKNOWN__	RNA	SNP	G	G	A	rs79689977	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:42905119G>A	ENST00000359906.2	+	0	697					NR_027786.1		Q9NQF3	SERHL_HUMAN	serine hydrolase-like	NA		NA					hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)	2						TTGATCAAGTGAGTCTGGACC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													158	113	128	NA		NA	NA	22		NA											NA				42905119		2203	4300	6503					AL365513		22q13.2-q13.31	2009-10-06				ENSG00000172250	94009			14408	protein-coding gene	gene with protein product	kraken-like	607979			NA	11352564	Standard	NM_170694	NR_027786	NA	Approved	HS126B42, BK126B4.1, dJ222E13.1	uc021wql.1	Q9NQF3		ENST00000359906.2:	chr22.hg19:g.42905119G>A		NA	Q5JZ95|Q9UH21	hg19		0.02	6.78585	AGTxAGT	COVERED																																																																																			NOVEL	SERHL-001	KNOWN	basic	antisense	NA	processed_transcript	OTTHUMT00000320498.2	3	3.460972	KEEP	3	2	64	34	1175	GG	0.999998	0.999998	0		+	28	49	991	0	0	80.496907	129	60	4902	261	ENST00000359906.2	0.178344	1
RRP7A	27341	__UNKNOWN__	__UNKNOWN__	22	42910760	42910760	__UNKNOWN__	Silent	SNP	A	A	G	rs28430278	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:42910760A>G	ENST00000323013.6	-	5	501	c.486T>C	c.(484-486)tcT>tcC	p.S162S		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	162		NA					nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						GGTCGGGCACAGAGTCTGCGT	0.647	NA	NA											A|||	129	0.0257588	0.0817	0.013	5008	,	,	NA	21046	0.005	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0													40	43	42	NA		NA	NA	22		NA											NA				42910760		2201	4299	6500	SO:0001819	synonymous_variant			BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306	27341			24286	protein-coding gene	gene with protein product		NA			NA	10810093, 12087473	Standard	NM_015703	NM_015703	NA	Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.486T>C	chr22.hg19:g.42910760A>G		NA	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	hg19	CCDS14036.1	0.02	1.906064	CACxGAG	COVERED																																																																																			NOVEL	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320451.1	1	11.466632	KEEP	9	1	31	49	1538	AA	1	0.976865	0		-	5	27	175	0	0	12.610835	50	50	1896	143	ENST00000323013.6	0.090909	0.976865
RRP7A	27341	__UNKNOWN__	__UNKNOWN__	22	42911257	42911257	__UNKNOWN__	Silent	SNP	A	A	G	rs1137212	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:42911257A>G	ENST00000323013.6	-	4	375	c.360T>C	c.(358-360)taT>taC	p.Y120Y		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	120		NA					nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						GGAACACCACATAGGCTACCT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													14	27	23	NA		NA	NA	22		NA											NA				42911257		1720	4093	5813	SO:0001819	synonymous_variant			BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306	27341			24286	protein-coding gene	gene with protein product		NA			NA	10810093, 12087473	Standard	NM_015703	NM_015703	NA	Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.360T>C	chr22.hg19:g.42911257A>G		NA	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	hg19	CCDS14036.1	0.02	-0.10527	CACxTAG	UNCOVERED																																																																																			NOVEL	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320451.1	0	3.9123	KEEP	1	0	0	13	423	AA	0.994391	0.139048	0		-	3	40	92	0	0	7.700846	9	50	334	38	ENST00000323013.6	0.25	0.139832
GRAMD4	23151	__UNKNOWN__	__UNKNOWN__	22	47074896	47074896	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:47074896A>G	ENST00000406902.1	+	0	3698				GRAMD4_ENST00000361034.3_3'UTR|GRAMD4_ENST00000408031.1_3'UTR			Q6IC98	GRAM4_HUMAN	GRAM domain containing 4	NA		NA			apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	12		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)		TGGCTCCTGTAGGGGACTGGC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS33672.1	22q13.31	2008-03-03			ENSG00000075240	ENSG00000075240	23151			29113	protein-coding gene	gene with protein product	death-inducing-protein	613691			NA	15565177	Standard	NM_015124	NM_015124	NA	Approved	KIAA0767, DIP	uc003bhx.3	Q6IC98	OTTHUMG00000150402	ENST00000406902.1:c.*1748A>G	chr22.hg19:g.47074896A>G		NA	A9IN51|A9IN57|Q68EN0|Q9UGE6|Q9Y4B9	hg19	CCDS33672.1	0.02	6.898432	TGTxGGG	COVERED																																																																																			NOVEL	GRAMD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317969.1	3	31.566192	KEEP	0	0	0	105	3182	AA	1	1	0		+	36	60	1313	0	0	110.684846	131	60	4642	344	ENST00000406902.1	0.215569	1
BRD1	23774	__UNKNOWN__	__UNKNOWN__	22	50192174	50192174	__UNKNOWN__	Intron	SNP	C	C	T	rs6009878	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chr22:50192174C>T	ENST00000216267.8	-	4	2272				BRD1_ENST00000404760.1_Intron|BRD1_ENST00000404034.1_Intron|BRD1_ENST00000342989.5_Intron|BRD1_ENST00000457780.2_Intron|BRD1_ENST00000542442.1_Intron	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	NA		NA			histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GTCACACATGCGGCAGGACAG	0.522	NA	NA											C|||	680	0.135783	0.3306	0.0519	5008	,	,	NA	17410	0.0913	NA	0.0189	False	NA	,,,	NA	NA	NA	2504	0.0982	NA	NA	NA						NA		NA				0								C		1110,3296	393.1+/-328.7	141,828,1234	77	67	70	NA		-3.2	0	22	dbSNP_114	70	263,8337	100.1+/-161.6	6,251,4043	no	intron	BRD1	NM_014577.1		147,1079,5277	TT,TC,CC	NA	3.0581,25.1929,10.5567			50192174	1373,11633	2203	4300	6503	SO:0001627	intron_variant			AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425	23774			1102	protein-coding gene	gene with protein product	BR140-like	604589	bromodomain-containing 1		NA	10591208, 10602503	Standard	NM_014577	NM_014577	NA	Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.1785+31G>A	chr22.hg19:g.50192174C>T		NA	A6ZJA4	hg19	CCDS14080.1	0.02	14.798009	ATGxGGC	COVERED																																																																																			NOVEL	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317402.1	7	65.149561	KEEP	0	3	80	245	8462	CC	1	1	0		-	13	60	468	0	0	28.615314	354	60	12477	829	ENST00000216267.8	0.035422	1
TBL1X	6907	__UNKNOWN__	__UNKNOWN__	X	9656074	9656074	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:9656074C>A	ENST00000380961.1	+	7	699	c.222C>A	c.(220-222)gaC>gaA	p.D74E	TBL1X_ENST00000536365.1_Missense_Mutation_p.D74E|TBL1X_ENST00000424279.1_Missense_Mutation_p.D74E|TBL1X_ENST00000217964.7_Missense_Mutation_p.D125E|TBL1X_ENST00000407597.2_Missense_Mutation_p.D125E	NM_001139468.1	NP_001132940.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	125	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.	NA			canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				CAGTGTTCGACGGCCGCCCCA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													46	43	44	NA		NA	NA	X		NA											NA				9656074		2203	4300	6503	SO:0001583	missense			Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849	6907		WD repeat domain containing	11585	protein-coding gene	gene with protein product		300196	transducin (beta)-like 1	TBL1	NA	10330347	Standard	NM_005647	NM_005647	NA	Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000380961.1:c.222C>A	chrX.hg19:g.9656074C>A	ENSP00000370348:p.Asp74Glu	NA	A8K044|A8K4J7|Q86UY2	hg19	CCDS48078.1	0.02	10.511393	CGAxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509668	0.44660	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000415293;ENST00000217964	T;T;T;T;T	0.57273	0.41;0.54;0.54;0.54;0.41	4.89	-4.24	0.03777	.	0.000000	0.85682	D	0.000000	T	0.27559	0.0677	N	0.12527	0.23	0.47905	D	0.999542	B;B	0.17268	0.021;0.021	B;B	0.21708	0.036;0.036	T	0.01734	-1.1285	10	0.30854	T	0.27	.	9.8313	0.40944	0.0:0.1253:0.1217:0.753	.	88;125	Q59F53;O60907	.;TBL1X_HUMAN	E	125;74;74;74;74;125	ENSP00000385988:D125E;ENSP00000394097:D74E;ENSP00000445317:D74E;ENSP00000370348:D74E;ENSP00000217964:D125E	ENSP00000217964:D125E	D	+	3	2	TBL1X	9616074	0.870000	0.30015	0.711000	0.30485	0.927000	0.56198	-0.084000	0.11268	-0.985000	0.03503	-1.166000	0.01754	GAC	NOVEL	TBL1X-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055708.1	5	45.120949	KEEP	0	0	0	150	5053	CC	1	1	0		+	8	60	289	0	0	17.004454	268	60	9634	550	ENST00000380961.1	0.028986	1
OFD1	8481	__UNKNOWN__	__UNKNOWN__	X	13787112	13787112	__UNKNOWN__	Intron	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:13787112A>C	ENST00000340096.6	+	23	3323				OFD1_ENST00000380567.1_Intron|OFD1_ENST00000490265.1_Intron|OFD1_ENST00000380550.3_Intron	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	NA		NA			axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						GAAGGAATTGAGAACATTATG	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													34	30	31	NA		NA	NA	X		NA											NA				13787112		692	1590	2282	SO:0001627	intron_variant			Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651	8481			2567	protein-coding gene	gene with protein product		300170	retinitis pigmentosa 23 (X-linked recessive)	CXorf5, RP23	NA	9722947, 9215688, 22619378	Standard	NM_003611	NM_003611	NA	Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.2997-73A>C	chrX.hg19:g.13787112A>C		NA	B9ZVU5|O75666|Q4VAK4	hg19	CCDS14157.1	0.02	4.75735	TTGxGAA	COVERED																																																																																			NOVEL	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055808.1	5	6.61989	KEEP	0	0	0	22	713	AA	0.999879	0.999876	0		+	33	60	1224	0	0	108.064732	83	60	3028	150	ENST00000340096.6	0.284483	0.999997
FANCB	2187	__UNKNOWN__	__UNKNOWN__	X	14868685	14868685	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:14868685A>G	ENST00000324138.3	-	6	1591	c.1438T>C	c.(1438-1440)Tat>Cat	p.Y480H	FANCB_ENST00000398334.1_Missense_Mutation_p.Y480H	NM_152633.2	NP_689846.1	Q8NB91	FANCB_HUMAN	Fanconi anemia, complementation group B	480		NA			DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	24	Hepatocellular(33;0.183)					ATTACACGATACCATATCTTC	0.353	NA	NA						Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													170	139	149	NA		NA	NA	X		NA											NA				14868685		2203	4299	6502	SO:0001583	missense	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AK091383	CCDS14161.1	Xp22.2	2014-09-17			ENSG00000181544	ENSG00000181544	2187		Fanconi anemia, complementation groups	3583	protein-coding gene	gene with protein product		300515			NA	9382107, 15502827	Standard	NM_152633	NM_152633	NA	Approved	FAB, FLJ34064, FAAP95	uc004cwh.1	Q8NB91	OTTHUMG00000021168	ENST00000324138.3:c.1438T>C	chrX.hg19:g.14868685A>G	ENSP00000326819:p.Tyr480His	NA	B2RMZ4|Q7Z2U2|Q86XG1	hg19	CCDS14161.1	0.02	1.874217	GATxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	a	11.55	1.673587	0.29693	.	.	ENSG00000181544	ENST00000324138;ENST00000398334;ENST00000452869	.	.	.	5.85	4.7	0.59300	.	0.185090	0.47455	D	0.000222	T	0.26738	0.0654	L	0.43152	1.355	0.25975	N	0.98246	P	0.44380	0.834	B	0.41666	0.363	T	0.10800	-1.0614	9	0.17369	T	0.5	-8.5665	6.3459	0.21349	0.7614:0.0:0.2386:0.0	.	480	Q8NB91	FANCB_HUMAN	H	480	.	ENSP00000326819:Y480H	Y	-	1	0	FANCB	14778606	1.000000	0.71417	0.985000	0.45067	0.923000	0.55619	3.335000	0.52105	1.980000	0.57719	0.433000	0.28618	TAT	NOVEL	FANCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055835.1	0	3.910229	KEEP	0	0	0	13	388	AA	0.994391	0.991133	0		-	4	60	138	0	0	9.053256	66	60	2338	94	ENST00000324138.3	0.057143	0.996724
EIF1AX	1964	__UNKNOWN__	__UNKNOWN__	X	20145968	20145968	__UNKNOWN__	3'UTR	SNP	C	C	A	rs138669696		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:20145968C>A	ENST00000379607.5	-	0	1094					NM_001412.3	NP_001403.1	P47813	IF1AX_HUMAN	eukaryotic translation initiation factor 1A, X-linked	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(2)|lung(1)|ovary(1)|prostate(1)	5						TTTTCTTCAACTGCAGACTTC	0.348	NA	NA											A|||	1179	0.312318	0.6104	0.1873	3775	,	,	NA	10158	0.0188	NA	0.1551	False	NA	,,,	NA	NA	NA	2504	0.0685	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L18960	CCDS14196.1	Xp22.13	2014-02-19	2002-11-28	2004-05-26	ENSG00000173674	ENSG00000173674	1964			3250	protein-coding gene	gene with protein product		300186	eukaryotic translation initiation factor 1A, X chromosome	EIF4C, EIF1A	NA	8106356, 9381176	Standard		NM_001412	NA	Approved	eIF-1A, eIF-4C	uc004czt.3	P47813	OTTHUMG00000022704	ENST00000379607.5:c.*456G>T	chrX.hg19:g.20145968C>A		NA	B2R5U5|Q0VGC2|Q5JPS5|Q5JPS6	hg19	CCDS14196.1	0.02	13.515598	CAAxTGC	COVERED																																																																																			NOVEL	EIF1AX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058913.1	4	9.28259	KEEP	2	16	478	199	7073	CC	1	1	0		-	33	33	1187	0	0	88.86091	276	50	10437	638	ENST00000379607.5	0.106796	1
TM4SF2	0	__UNKNOWN__	__UNKNOWN__	X	37981467	37981467	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:37981467G>T	ENST00000465127.1	+	4	278				SYTL5_ENST00000456733.2_Splice_Site_p.G636C|SYTL5_ENST00000297875.2_Splice_Site_p.G614C|SYTL5_ENST00000357972.5_Splice_Site_p.G614C						NA		NA								haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	11						CTTTGTGAAGGGGTAACTTTG	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													122	104	110	NA		NA	NA	X		NA											NA				37981467		2202	4300	6502	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000465127.1:c.172-543908G>T	chrX.hg19:g.37981467G>T		NA		hg19		0.02	4.456824	AAGxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637327	0.87760	.	.	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.68765	-0.35;-0.35;-0.35	5.44	5.44	0.79542	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.74718	0.3753	L	0.35341	1.055	0.80722	D	1	D;P	0.89917	1.0;0.938	D;P	0.97110	1.0;0.651	T	0.73512	-0.3959	10	0.35671	T	0.21	-6.3849	18.3378	0.90294	0.0:0.0:1.0:0.0	.	636;614	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	C	614;614;636	ENSP00000297875:G614C;ENSP00000350657:G614C;ENSP00000395220:G636C	ENSP00000297875:G614C	G	+	1	0	SYTL5	37866411	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.462000	0.80851	2.270000	0.75569	0.600000	0.82982	GGC	NOVEL	TM4SF2-001	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000363378.1	1	15.650039	KEEP	0	0	0	52	1794	GG	1	1	0		+	59	60	2113	0	0	198.328988	80	60	2836	244	ENST00000465127.1	0.42446	1
SRPX	8406	__UNKNOWN__	__UNKNOWN__	X	38080134	38080134	__UNKNOWN__	5'UTR	SNP	C	C	T	rs376943677		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:38080134C>T	ENST00000378533.3	-	0	18				TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000544439.1_5'UTR|SRPX_ENST00000343800.6_Intron|SRPX_ENST00000538295.1_5'UTR|SRPX_ENST00000432886.2_5'UTR	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	NA		NA			autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						TGCGTGCTAGCGGGCGGGCGA	0.711	NA	NA									OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955	8406			11309	protein-coding gene	gene with protein product		300187	sushi-repeat-containing protein, X chromosome, sushi-repeat-containing protein, X-linked		NA	8634708, 8634709	Standard	NM_006307	NM_006307	NA	Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.-89G>A	chrX.hg19:g.38080134C>T		875	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	hg19	CCDS14245.1	0.02	4.047315	TAGxGGG	COVERED																																																																																			NOVEL	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056243.1	4	41.202149	KEEP	0	0	0	137	4638	CC	1	1	0		-	5	60	172	0	0	10.412518	124	60	4201	386	ENST00000378533.3	0.03876	1
GPR34	2857	__UNKNOWN__	__UNKNOWN__	X	41554848	41554848	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:41554848T>C	ENST00000378142.4	+	0	246				CASK_ENST00000378166.4_Intron|GPR34_ENST00000378138.5_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						GAGGAATATGTCATTTAGCAC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	49	52	NA		NA	NA	X		NA											NA				41554848		2203	4300	6503	SO:0001623	5_prime_UTR_variant			AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659	2857		GPCR / Class A : Orphans	4490	protein-coding gene	gene with protein product		300241			NA	10395919, 10036181	Standard	NM_005300	NM_005300	NA	Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.-39T>C	chrX.hg19:g.41554848T>C		NA	O95853	hg19	CCDS14258.1	0.02	12.342432	ATGxCAT	COVERED																																																																																			NOVEL	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056264.1	2	38.206895	KEEP	0	0	0	127	3971	TT	1	1	0		+	73	60	2712	0	0	237.604843	197	60	7002	505	ENST00000378142.4	0.27037	1
KCND1	3750	__UNKNOWN__	__UNKNOWN__	X	48824560	48824560	__UNKNOWN__	Intron	SNP	A	A	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:48824560A>T	ENST00000218176.3	-	1	2419				KCND1_ENST00000376477.1_De_novo_Start_OutOfFrame	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	NA		NA			protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	AGCAAACCCAATTCATTCAGt	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057	3750		Potassium channels, Voltage-gated ion channels / Potassium channels	6237	protein-coding gene	gene with protein product		300281			NA	10729221, 16382104	Standard	NM_004979	NM_004979	NA	Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1121+997T>A	chrX.hg19:g.48824560A>T		NA	A6NEF1|B2RCG0|O75671	hg19	CCDS14314.1	0.02	2.006832	CCAxTTC	COVERED																																																																																			NOVEL	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060774.1	3	4.814793	KEEP	0	0	0	16	519	AA	0.997832	0.997636	0		-	25	60	916	0	0	80.577795	64	60	2312	119	ENST00000218176.3	0.280899	0.999804
USP27X	389856	__UNKNOWN__	__UNKNOWN__	X	49645475	49645475	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs373156118		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:49645475G>A	ENST00000508866.2	+	1	1006	c.565G>A	c.(565-567)Gcc>Acc	p.A189T		NM_001145073.1	NP_001138545.1	A6NNY8	UBP27_HUMAN	ubiquitin specific peptidase 27, X-linked	189	USP.	NA			ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			endometrium(7)	7						CGGGAAGGCGGCCAACAATCC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													128	96	105	NA		NA	NA	X		NA											NA				49645475		692	1591	2283	SO:0001583	missense			AW851065	CCDS65260.1	Xp11.23	2007-10-05	2005-08-08			ENSG00000273820	389856		Ubiquitin-specific peptidases	13486	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 27, X chromosome, ubiquitin specific protease 27, X-linked		NA	12838346	Standard	XM_372213	NM_001145073	NA	Approved	USP27	uc004dop.3	A6NNY8		ENST00000508866.2:c.565G>A	chrX.hg19:g.49645475G>A	ENSP00000475071:p.Ala189Thr	NA		hg19		0.02	9.264765	GCGxCCA	COVERED																																																																																			NOVEL	USP27X-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000060837.3	4	14.744567	KEEP	0	0	0	49	1695	GG	1	1	0		+	86	60	3038	0	0	281.992017	129	60	4491	306	ENST00000508866.2	0.4	1
HUWE1	10075	__UNKNOWN__	__UNKNOWN__	X	53563431	53563431	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:53563431C>T	ENST00000342160.3	-	78	12792	c.12335G>A	c.(12334-12336)cGc>cAc	p.R4112H	HUWE1_ENST00000262854.6_Missense_Mutation_p.R4112H			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4112	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.	NA			base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GGCCACAATGCGTCCGACAAA	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													211	176	188	NA		NA	NA	X		NA											NA				53563431		2203	4300	6503	SO:0001583	missense			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758	10075			30892	protein-coding gene	gene with protein product		300697	HECT, UBA and WWE domain containing 1		NA	9205841, 10998601	Standard	XM_497119	NM_031407	NA	Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12335G>A	chrX.hg19:g.53563431C>T	ENSP00000340648:p.Arg4112His	NA	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	hg19	CCDS35301.1	0.02	7.049288	ATGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.69	3.192028	0.58017	.	.	ENSG00000086758	ENST00000342160;ENST00000262854	T;T	0.59224	0.28;0.28	5.42	5.42	0.78866	HECT (4);	0.143577	0.50627	D	0.000103	T	0.81861	0.4912	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.971;0.988	D	0.86502	0.1804	10	0.87932	D	0	.	17.2029	0.86910	0.0:1.0:0.0:0.0	.	4112;4096	Q7Z6Z7;Q7Z6Z7-2	HUWE1_HUMAN;.	H	4112	ENSP00000340648:R4112H;ENSP00000262854:R4112H	ENSP00000262854:R4112H	R	-	2	0	HUWE1	53580156	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.232000	0.78116	2.415000	0.81967	0.594000	0.82650	CGC	NOVEL	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056766.1	2	11.135521	KEEP	0	0	0	37	1285	CC	1	1	0		-	68	60	2508	0	0	230.637602	116	60	3905	271	ENST00000342160.3	0.369565	1
HUWE1	10075	__UNKNOWN__	__UNKNOWN__	X	53644044	53644044	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:53644044G>A	ENST00000342160.3	-	20	2301	c.1844C>T	c.(1843-1845)gCc>gTc	p.A615V	HUWE1_ENST00000262854.6_Missense_Mutation_p.A615V|HUWE1_ENST00000218328.8_Missense_Mutation_p.A615V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	615		NA			base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						AAGACCTCGGGCATTCAAACA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													62	56	58	NA		NA	NA	X		NA											NA				53644044		2203	4300	6503	SO:0001583	missense			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758	10075			30892	protein-coding gene	gene with protein product		300697	HECT, UBA and WWE domain containing 1		NA	9205841, 10998601	Standard	XM_497119	NM_031407	NA	Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.1844C>T	chrX.hg19:g.53644044G>A	ENSP00000340648:p.Ala615Val	NA	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	hg19	CCDS35301.1	0.02	4.487395	CGGxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	34	5.298923	0.95574	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.64260	0.9;0.9;-0.09	5.45	5.45	0.79879	E3 ubiquitin ligase, domain of unknown function DUF913 (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000001	T	0.71451	0.3341	L	0.44542	1.39	0.58432	D	0.999999	D	0.64830	0.994	P	0.62885	0.908	T	0.71738	-0.4502	10	0.46703	T	0.11	.	17.0476	0.86508	0.0:0.0:1.0:0.0	.	615	Q7Z6Z7	HUWE1_HUMAN	V	615	ENSP00000340648:A615V;ENSP00000262854:A615V;ENSP00000218328:A615V	ENSP00000218328:A615V	A	-	2	0	HUWE1	53660769	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.346000	0.97056	2.289000	0.77006	0.594000	0.82650	GCC	NOVEL	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056766.1	0	12.339457	KEEP	0	0	0	41	1436	GG	1	0.999999	0		-	39	60	1374	0	0	122.472551	85	60	3143	201	ENST00000342160.3	0.314516	0.999999
WNK3	65267	__UNKNOWN__	__UNKNOWN__	X	54222540	54222540	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:54222540A>C	ENST00000375169.3	-	0	7887				WNK3_ENST00000354646.2_3'UTR	NM_001002838.3	NP_001002838.1	Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	NA		NA			intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						GCAGTTTTAAAGAATTAGGGA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632	65267			14543	protein-coding gene	gene with protein product		300358	protein kinase, lysine deficient 3	PRKWNK3	NA		Standard	NM_020922	NM_020922	NA	Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375169.3:c.*2217T>G	chrX.hg19:g.54222540A>C		NA	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	hg19	CCDS35302.1	0.02	2.31401	TAAxGAA	COVERED																																																																																			NOVEL	WNK3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056798.2	2	3.611098	KEEP	0	0	0	12	386	AA	0.993634	0.967765	0		-	19	60	660	0	0	59.858031	35	60	1240	73	ENST00000375169.3	0.351852	0.973965
WNK3	65267	__UNKNOWN__	__UNKNOWN__	X	54224855	54224855	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:54224855C>T	ENST00000375159.2	-	23	5304	c.5305G>A	c.(5305-5307)Gcc>Acc	p.A1769T	WNK3_ENST00000354646.2_Missense_Mutation_p.A1769T|WNK3_ENST00000375169.3_Missense_Mutation_p.A1712T			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1769		NA			intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						CCAGATTGGGCGGGAATTACT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													90	74	79	NA		NA	NA	X		NA											NA				54224855		2203	4300	6503	SO:0001583	missense			AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632	65267			14543	protein-coding gene	gene with protein product		300358	protein kinase, lysine deficient 3	PRKWNK3	NA		Standard	NM_020922	NM_020922	NA	Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.5305G>A	chrX.hg19:g.54224855C>T	ENSP00000364301:p.Ala1769Thr	NA	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	hg19	CCDS14357.1	0.02	3.956985	GGGxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	2.190	-0.385492	0.04966	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.28666	1.6;1.6;1.6	5.45	0.233	0.15386	.	0.611954	0.15328	N	0.268176	T	0.09113	0.0225	N	0.03608	-0.345	0.09310	N	0.999991	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.35176	-0.9799	10	0.02654	T	1	-0.0297	4.8679	0.13618	0.0:0.3396:0.3159:0.3445	.	1712;1769	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	T	1712;1769;1769	ENSP00000364312:A1712T;ENSP00000346667:A1769T;ENSP00000364301:A1769T	ENSP00000346667:A1769T	A	-	1	0	WNK3	54241580	0.052000	0.20516	0.989000	0.46669	0.934000	0.57294	-1.320000	0.02700	-0.072000	0.12864	-0.499000	0.04595	GCC	NOVEL	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056799.2	1	11.115953	KEEP	0	0	0	37	1185	CC	1	1	0		-	14	60	438	0	0	30.798192	125	60	4161	217	ENST00000375159.2	0.100719	1
ITIH6	347365	__UNKNOWN__	__UNKNOWN__	X	54775729	54775729	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:54775729T>C	ENST00000218436.6	-	0	4570					NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	NA		NA			hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)				NA						tccagacaagtaaacagatga	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313	347365			28907	protein-coding gene	gene with protein product		NA	inter-alpha (globulin) inhibitor H5-like	ITIH5L	NA	12975309	Standard	NM_198510	NM_198510	NA	Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.*599A>G	chrX.hg19:g.54775729T>C		NA	A6NN03	hg19	CCDS14361.1	0.02	2.285507	AAGxAAA	COVERED																																																																																			NOVEL	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056814.2	1	3.309243	KEEP	0	0	0	11	330	TT	0.993072	0.992296	0		-	27	60	1030	0	0	93.669227	53	60	1870	105	ENST00000218436.6	0.3375	0.999218
PAGE2B	389860	__UNKNOWN__	__UNKNOWN__	X	55102559	55102559	__UNKNOWN__	Splice_Site	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:55102559G>A	ENST00000374971.1	+	2	136		c.e2+1		PAGE2B_ENST00000374974.3_Splice_Site	NM_001015038.1	NP_001015038.1	Q5JRK9	GGEE3_HUMAN	P antigen family, member 2B	NA		NA								lung(3)	3						ATCTGTGATTGTGAGTCCTTT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													126	104	112	NA		NA	NA	X		NA											NA				55102559		2203	4300	6503	SO:0001630	splice_region_variant				CCDS35304.1	Xp11.22	2009-06-17			ENSG00000238269	ENSG00000238269	389860			31805	protein-coding gene	gene with protein product		NA			NA		Standard	XM_372224	NM_001015038	NA	Approved	CT16.5	uc004due.4	Q5JRK9	OTTHUMG00000021645	ENST00000374971.1:c.84+1G>A	chrX.hg19:g.55102559G>A		NA	A1L414	hg19	CCDS35304.1	0.02	4.496102	ATTxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	g	2.829	-0.243044	0.05906	.	.	ENSG00000238269	ENST00000374974;ENST00000374971;ENST00000453343	.	.	.	1.29	0.38	0.16222	.	.	.	.	.	.	.	.	.	.	.	0.19945	N	0.999948	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.239	0.06774	0.3051:0.0:0.6949:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PAGE2B	55119284	0.811000	0.29063	0.042000	0.18584	0.085000	0.17905	1.457000	0.35212	0.066000	0.16515	0.287000	0.19450	.	NOVEL	PAGE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056849.1	1	9.631772	KEEP	0	0	0	32	1164	GG	0.999997	0.999997	0	Intron	+	47	60	1718	0	0	158.695836	76	60	2884	179	ENST00000374971.1	0.382114	0.999999
FAM104B	90736	__UNKNOWN__	__UNKNOWN__	X	55172521	55172521	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:55172521G>T	ENST00000477847.2	-	3	468	c.335C>A	c.(334-336)aCa>aAa	p.T112K	FAM104B_ENST00000332132.4_Intron|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_Missense_Mutation_p.T114K|FAM104B_ENST00000425133.2_Missense_Mutation_p.T116K|FAM104B_ENST00000358460.4_Intron	NM_001166702.1	NP_001160174.1	Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	0		NA								endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						AATTCATCATGTTGGAGCTTG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													29	20	22	NA		NA	NA	X		NA											NA				55172521		692	1590	2282	SO:0001583	missense			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518	90736			25085	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 44	CXorf44	NA	12477932	Standard	NM_138362	NM_138362	NA	Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000477847.2:c.335C>A	chrX.hg19:g.55172521G>T	ENSP00000421161:p.Thr112Lys	NA	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	hg19	CCDS55423.1	0.02	41.149514	CATxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	g	8.588	0.883807	0.17467	.	.	ENSG00000182518	ENST00000425133;ENST00000477847;ENST00000489298	T;T;T	0.54866	0.55;0.55;0.55	1.6	1.6	0.23607	.	.	.	.	.	T	0.30070	0.0753	N	0.19112	0.55	0.09310	N	1	P	0.41524	0.753	B	0.32022	0.139	T	0.17137	-1.0379	9	0.87932	D	0	.	6.0913	0.19995	0.0:0.0:1.0:0.0	.	116	Q5XKR9-3	.	K	116;112;114	ENSP00000397188:T116K;ENSP00000421161:T112K;ENSP00000423164:T114K	ENSP00000397188:T116K	T	-	2	0	FAM104B	55189246	0.987000	0.35691	0.006000	0.13384	0.065000	0.16274	1.636000	0.37144	1.084000	0.41184	0.436000	0.28706	ACA	NOVEL	FAM104B-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056853.2	54	30.704384	KEEP	0	23	730	358	12882	GG	1	1	0		-	115	60	4053	0	0	314.101315	732	60	27528	1548	ENST00000477847.2	0.135773	1
FAM104B	90736	__UNKNOWN__	__UNKNOWN__	X	55172586	55172586	__UNKNOWN__	Silent	SNP	G	G	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:55172586G>A	ENST00000477847.2	-	3	403	c.270C>T	c.(268-270)tcC>tcT	p.S90S	FAM104B_ENST00000332132.4_Intron|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_Silent_p.S92S|FAM104B_ENST00000425133.2_Silent_p.S94S|FAM104B_ENST00000358460.4_Intron	NM_001166702.1	NP_001160174.1	Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	93		NA						p.S94S(1)		endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						GGTTGATATGGGAGTAAAGAC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - coding silent(1)	endometrium(1)											78	66	70	NA		NA	NA	X		NA											NA				55172586		2203	4297	6500	SO:0001819	synonymous_variant			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518	90736			25085	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 44	CXorf44	NA	12477932	Standard	NM_138362	NM_138362	NA	Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000477847.2:c.270C>T	chrX.hg19:g.55172586G>A		NA	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	hg19	CCDS55423.1	0.02	48.400801	ATGxGAG	COVERED																																																																																			NOVEL	FAM104B-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056853.2	97	27.592266	KEEP	0	26	855	391	13278	GG	1	1	0		-	148	60	5402	0	0	441.009686	692	60	24071	1553	ENST00000477847.2	0.17619	1
EDA	1896	__UNKNOWN__	__UNKNOWN__	X	68835966	68835966	__UNKNOWN__	5'UTR	SNP	A	A	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:68835966A>C	ENST00000374552.4	+	0	56				EDA_ENST00000374553.2_5'UTR|EDA_ENST00000525810.1_5'UTR|EDA_ENST00000338901.3_5'UTR|EDA_ENST00000502251.1_3'UTR|EDA_ENST00000524573.1_5'UTR|EDA_ENST00000527388.1_5'UTR	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	NA		NA			cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						tccctttcccacccctcGGAG	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813	1896		Tumor necrosis factor (ligand) superfamily	3157	protein-coding gene	gene with protein product		300451	ectodermal dysplasia 1, anhidrotic, oligodontia 1	ED1, EDA2, ODT1	NA	8696334, 18657636, 16583127	Standard	NM_001399	NM_001005612	NA	Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.-187A>C	chrX.hg19:g.68835966A>C		NA	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	hg19	CCDS14394.1	0.02	3.025261	CCCxCCC	COVERED																																																																																			NOVEL	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057048.2	11	16.585061	KEEP	0	22	188	125	3354	AA	1	1	0		+	16	60	244	0	0	9.773972	178	70	5182	453	ENST00000374552.4	0.082474	1
EDA	1896	__UNKNOWN__	__UNKNOWN__	X	69080745	69080745	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:69080745T>C	ENST00000374552.4	+	2	638				EDA_ENST00000524573.1_Intron|EDA_ENST00000525810.1_3'UTR|EDA_ENST00000374553.2_Intron|EDA_ENST00000502251.1_Intron|EDA_ENST00000527388.1_3'UTR	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	NA		NA			cell differentiation (GO:0030154)|cell-matrix adhesion (GO:0007160)|ectoderm development (GO:0007398)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|immune response (GO:0006955)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|salivary gland cavitation (GO:0060662)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	apical part of cell (GO:0045177)|collagen trimer (GO:0005581)|cytoskeleton (GO:0005856)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						actctgaagatctgttaaaag	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													77	74	75	NA		NA	NA	X		NA											NA				69080745		1061	2140	3201	SO:0001627	intron_variant			U59227	CCDS14394.1, CCDS35318.1, CCDS35319.1, CCDS43966.1, CCDS35318.2, CCDS35319.2, CCDS55436.1	Xq12-q13.1	2013-05-22	2004-08-09	2004-08-12	ENSG00000158813	ENSG00000158813	1896		Tumor necrosis factor (ligand) superfamily	3157	protein-coding gene	gene with protein product		300451	ectodermal dysplasia 1, anhidrotic, oligodontia 1	ED1, EDA2, ODT1	NA	8696334, 18657636, 16583127	Standard	NM_001399	NM_001005612	NA	Approved	EDA1, XLHED, HED, XHED, ED1-A1, ED1-A2, EDA-A1, EDA-A2	uc004dxs.3	Q92838	OTTHUMG00000021764	ENST00000374552.4:c.397-96132T>C	chrX.hg19:g.69080745T>C		NA	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	hg19	CCDS14394.1	0.02	9.963327	AGAxCTG	COVERED																																																																																			NOVEL	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057048.2	2	21.960281	KEEP	0	0	0	73	2250	TT	1	1	0		+	79	60	2912	0	0	267.492704	136	60	4927	365	ENST00000374552.4	0.367442	1
DGAT2L6	347516	__UNKNOWN__	__UNKNOWN__	X	69424889	69424889	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs142158168		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:69424889G>A	ENST00000333026.3	+	7	1047	c.947G>A	c.(946-948)cGc>cAc	p.R316H		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	316		NA			lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(2)|large_intestine(3)|lung(5)|ovary(1)	12						AGTGCCCTGCGCAAGCTCTTT	0.473	NA	NA											G|||	21	0.00556291	0	0	3775	,	,	NA	14161	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0215	NA	NA	NA						NA		NA				0								G	HIS/ARG	0,3835		0,0,1632,571	91	71	78	NA	947	-0.3	0.4	X	dbSNP_134	78	1,6727		0,1,2427,1872	no	missense	DGAT2L6	NM_198512.1	29	0,1,4059,2443	AA,AG,GG,G	NA	0.0149,0.0,0.0095	benign	316/338	69424889	1,10562	2203	4300	6503	SO:0001583	missense			AK129500	CCDS14397.1	Xq13.1	2008-02-05			ENSG00000184210	ENSG00000184210	347516			23250	protein-coding gene	gene with protein product		300926			NA	15671038	Standard	NM_198512	NM_198512	NA	Approved	DC3, FLJ25989	uc004dxx.1	Q6ZPD8	OTTHUMG00000021774	ENST00000333026.3:c.947G>A	chrX.hg19:g.69424889G>A	ENSP00000328036:p.Arg316His	NA	Q6IEE2	hg19	CCDS14397.1	0.02	4.722226	TGCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	1.103	-0.660381	0.03454	0.0	1.49E-4	ENSG00000184210	ENST00000333026	D	0.93366	-3.21	4.74	-0.289	0.12851	.	0.877007	0.09912	N	0.739650	D	0.89884	0.6844	L	0.55481	1.735	0.09310	N	0.999998	B	0.12630	0.006	B	0.14578	0.011	T	0.77765	-0.2465	10	0.44086	T	0.13	-11.8955	8.8441	0.35159	0.6236:0.0:0.3764:0.0	.	316	Q6ZPD8	DG2L6_HUMAN	H	316	ENSP00000328036:R316H	ENSP00000328036:R316H	R	+	2	0	DGAT2L6	69341614	0.000000	0.05858	0.422000	0.26621	0.525000	0.34531	-0.295000	0.08298	-0.438000	0.07232	-0.912000	0.02778	CGC	NOVEL	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057067.1	1	9.93244	KEEP	0	0	0	33	1188	GG	0.999998	0.999996	0		+	31	60	1103	0	0	95.318656	89	60	3203	199	ENST00000333026.3	0.258333	0.999999
HDAC8	55869	__UNKNOWN__	__UNKNOWN__	X	71787529	71787529	__UNKNOWN__	Intron	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:71787529G>C	ENST00000373573.3	-	4	779				HDAC8_ENST00000478743.1_Intron|HDAC8_ENST00000373571.1_Intron|HDAC8_ENST00000373554.1_3'UTR|HDAC8_ENST00000373560.2_Intron|HDAC8_ENST00000373556.3_3'UTR|HDAC8_ENST00000373589.4_Intron|HDAC8_ENST00000429103.2_Intron|HDAC8_ENST00000373583.1_Intron|HDAC8_ENST00000373559.4_Intron|HDAC8_ENST00000439122.2_Intron|HDAC8_ENST00000373561.4_Intron	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	NA		NA			chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cohesin localization to chromatin (GO:0071922)|sister chromatid cohesion (GO:0007062)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|transcription factor binding (GO:0008134)			breast(3)|cervix(1)|endometrium(1)|lung(4)|prostate(1)	10	Renal(35;0.156)				Vorinostat(DB02546)	actaggtgtagagcccaggtg	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													300	219	243	NA		NA	NA	X		NA											NA				71787529		692	1591	2283	SO:0001627	intron_variant			AF230097	CCDS14420.1, CCDS55448.1, CCDS55449.1, CCDS55450.1, CCDS55451.1, CCDS55452.1	Xq13	2014-01-29	2002-09-02	2002-09-06	ENSG00000147099	ENSG00000147099	55869			13315	protein-coding gene	gene with protein product		300269	histone deacetylase-like 1, Wilson-Turner X-linked mental retardation syndrome	HDACL1, WTS, MRXS6	NA	10756090, 10922473, 22889856	Standard	NM_018486	NM_001166448	NA	Approved	RPD3	uc004eau.3	Q9BY41	OTTHUMG00000021814	ENST00000373573.3:c.437+209C>G	chrX.hg19:g.71787529G>C		NA	A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	hg19	CCDS14420.1	0.02	2.513586	GTAxAGC	COVERED																																																																																			NOVEL	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057193.2	2	3.912889	KEEP	0	0	0	13	468	GG	0.994391	0.968502	0		-	20	60	750	0	0	69.083665	34	60	1313	83	ENST00000373573.3	0.37037	0.973965
BRWD3	254065	__UNKNOWN__	__UNKNOWN__	X	79984422	79984422	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:79984422C>T	ENST00000373275.4	-	14	1449					NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	NA		NA			cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)					breast(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(39)|ovary(4)|prostate(2)|skin(3)	87						AAACAATTTGCAGTATTCATA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													61	53	56	NA		NA	NA	X		NA											NA				79984422		2202	4299	6501	SO:0001627	intron_variant				CCDS14447.1	Xq21.1	2013-01-09			ENSG00000165288	ENSG00000165288	254065		WD repeat domain containing	17342	protein-coding gene	gene with protein product		300553			NA	15543602, 16094372	Standard	NM_153252	NM_153252	NA	Approved	FLJ38568, MRX93	uc004edt.3	Q6RI45	OTTHUMG00000021908	ENST00000373275.4:c.1233-18G>A	chrX.hg19:g.79984422C>T		NA	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	hg19	CCDS14447.1	0.02	-0.438638	TTGxAGT	COVERED																																																																																			NOVEL	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057344.1	0	5.41779	KEEP	0	0	0	18	649	CC	0.999859	0.959724	0		-	18	60	645	0	0	58.899418	32	60	1208	79	ENST00000373275.4	0.36	0.959859
APOOL	139322	__UNKNOWN__	__UNKNOWN__	X	84301507	84301507	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:84301507A>G	ENST00000373173.2	+	2	158	c.71A>G	c.(70-72)cAt>cGt	p.H24R		NM_198450.5	NP_940852.3	Q6UXV4	MIC27_HUMAN	apolipoprotein O-like	24		NA				integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8						GTAAGTGTACATGCAGCCAAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	75	77	NA		NA	NA	X		NA											NA				84301507		1867	4089	5956	SO:0001583	missense			AK130506	CCDS48138.1	Xq21.1	2007-01-17	2007-01-17	2007-01-17	ENSG00000155008	ENSG00000155008	139322			24009	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 33, family with sequence similarity 121A	CXorf33, FAM121A	NA	12975309	Standard	NM_198450	NM_198450	NA	Approved	UNQ8193, AAIR8193	uc004eem.3	Q6UXV4	OTTHUMG00000021930	ENST00000373173.2:c.71A>G	chrX.hg19:g.84301507A>G	ENSP00000362268:p.His24Arg	NA	Q3KNU7|Q5H9D1	hg19	CCDS48138.1	0.02	1.815953	TACxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.023	-1.405722	0.01155	.	.	ENSG00000155008	ENST00000373173;ENST00000373169	.	.	.	4.53	-4.31	0.03698	.	0.766226	0.12814	N	0.436977	T	0.24509	0.0594	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11470	-1.0586	9	0.32370	T	0.25	-21.9967	7.9471	0.29993	0.4287:0.1209:0.4504:0.0	.	24	Q6UXV4	APOOL_HUMAN	R	24	.	ENSP00000362264:H24R	H	+	2	0	APOOL	84188163	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	0.251000	0.18257	-1.169000	0.02772	-0.377000	0.06932	CAT	NOVEL	APOOL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057385.2	1	11.435326	KEEP	0	0	0	38	1212	AA	1	0.999768	0		+	4	60	142	0	0	9.04532	84	60	3131	167	ENST00000373173.2	0.045455	0.999768
SATL1	340562	__UNKNOWN__	__UNKNOWN__	X	84363582	84363582	__UNKNOWN__	Silent	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:84363582T>C	ENST00000509231.1	-	1	472	c.393A>G	c.(391-393)caA>caG	p.Q131Q	SATL1_ENST00000332921.5_5'UTR|SATL1_ENST00000395409.3_5'UTR			Q86VE3	SATL1_HUMAN	spermidine/spermine N1-acetyl transferase-like 1	186	Gln-rich.	NA					N-acetyltransferase activity (GO:0008080)			NS(1)|breast(5)|endometrium(2)|large_intestine(3)|lung(13)|skin(3)|stomach(1)|urinary_tract(1)	29						TCATACCTGATTGGTTCGTGC	0.552	NA	NA									OREG0019887	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													255	150	182	NA		NA	NA	X		NA											NA				84363582		692	1591	2283	SO:0001819	synonymous_variant			BC043215	CCDS35343.1, CCDS35343.2	Xq21	2008-02-05			ENSG00000184788	ENSG00000184788	340562			27992	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	XM_291339	NM_001012980	NA	Approved		uc004een.3	Q86VE3	OTTHUMG00000021931	ENST00000509231.1:c.393A>G	chrX.hg19:g.84363582T>C		1228	A0AVK7|E9PB72|Q5H8V9	hg19	CCDS35343.2	0.02	15.113826	TGAxTGG	COVERED																																																																																			NOVEL	SATL1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057386.2	6	19.55527	KEEP	0	0	0	65	2011	TT	1	1	0		-	88	60	3302	0	0	292.164924	220	60	7877	449	ENST00000509231.1	0.285714	1
ZNF711	7552	__UNKNOWN__	__UNKNOWN__	X	84520106	84520106	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:84520106C>T	ENST00000360700.4	+	6	1664				ZNF711_ENST00000542798.1_Intron|ZNF711_ENST00000276123.3_Intron|ZNF711_ENST00000395402.1_Intron|ZNF711_ENST00000373165.3_Intron			Q9Y462	ZN711_HUMAN	zinc finger protein 711	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(3)|skin(4)	28						TATTTTAATGCGTGTTTTAAT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													48	48	48	NA		NA	NA	X		NA											NA				84520106		2202	4299	6501	SO:0001627	intron_variant			BC006349	CCDS35344.1	Xq21.1	2014-02-19	2006-06-29	2006-06-29	ENSG00000147180	ENSG00000147180	7552		Zinc fingers, C2H2-type	13128	protein-coding gene	gene with protein product		314990	zinc finger protein 6 (CMPX1), zinc finger protein 6	ZNF6	NA	19377476	Standard	NM_021998	XM_005262186	NA	Approved	CMPX1, ZNF4, ZNF5, dJ75N13.1, Zfp711, MRX97	uc004eeo.3	Q9Y462	OTTHUMG00000021933	ENST00000360700.4:c.779-18C>T	chrX.hg19:g.84520106C>T		NA	B4DSV4|Q6NX42|Q9Y4J6	hg19		0.02	1.991819	ATGxGTG	COVERED																																																																																			NOVEL	ZNF711-003	NOVEL	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000057390.2	0	6.912631	KEEP	0	0	0	23	777	CC	0.999892	0.996125	0		+	7	60	243	0	0	17.854917	61	60	2220	101	ENST00000360700.4	0.102941	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	89177952	89177952	__UNKNOWN__	IGR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:89177952T>C			NA	NA				TGIF2LX (70 upstream) : RNU6-555P (674281 downstream)						NA		NA									NA						CAATCTTAATTATTGGGACTA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.89177952T>C		NA		hg19		0.02	10.950946	AATxATT	COVERED																																																																																			NOVEL					0			2	13.469816	KEEP	1	1	20	52	1579	TT	1	1	0			22	60	841	0	0	60.611876	273	60	9836	411		0.074576	1
PCDH11X	27328	__UNKNOWN__	__UNKNOWN__	X	91875570	91875570	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:91875570T>C	ENST00000373094.1	+	0	6520				PCDH11X_ENST00000373097.1_3'UTR	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	NA		NA			homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GATTAAACTGTGTGTAAATTT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(38;925 1092 2571 38200 45895)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290	27328		Cadherins / Protocadherins : Non-clustered	8656	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 119	300246	protocadherin 11	PCDH11	NA	10644456	Standard	NM_032969	NM_001168360	NA	Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.*1631T>C	chrX.hg19:g.91875570T>C		NA	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	hg19	CCDS14461.1	0.02	13.481922	CTGxGTG	COVERED																																																																																			NOVEL	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057436.1	5	18.052474	KEEP	0	0	0	60	1840	TT	1	1	0		+	18	60	642	0	0	42.061806	329	60	11792	468	ENST00000373094.1	0.051873	1
CHRDL1	91851	__UNKNOWN__	__UNKNOWN__	X	109922588	109922588	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:109922588T>C	ENST00000372042.1	-	11	1323	c.1222A>G	c.(1222-1224)Aag>Gag	p.K408E	CHRDL1_ENST00000372045.1_Missense_Mutation_p.K400E|CHRDL1_ENST00000434224.1_Missense_Mutation_p.K327E|CHRDL1_ENST00000394797.4_Missense_Mutation_p.K406E|CHRDL1_ENST00000482160.1_Missense_Mutation_p.K328E|CHRDL1_ENST00000444321.2_Missense_Mutation_p.K407E|CHRDL1_ENST00000218054.4_Missense_Mutation_p.K406E			Q9BU40	CRDL1_HUMAN	chordin-like 1	400		NA			BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						GTCACCAGCTTGAAGTGAGGA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													180	142	155	NA		NA	NA	X		NA											NA				109922588		2203	4300	6503	SO:0001583	missense			AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938	91851			29861	protein-coding gene	gene with protein product		300350	megalocornea 1 (X-linked)	MGC1	NA	11441185, 11118896, 22284829	Standard	NM_145234	NM_001143981	NA	Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372042.1:c.1222A>G	chrX.hg19:g.109922588T>C	ENSP00000361112:p.Lys408Glu	NA	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	hg19	CCDS48149.1	0.02	5.035966	GCTxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	T	21.1	4.100910	0.76983	.	.	ENSG00000101938	ENST00000372045;ENST00000434224;ENST00000218054;ENST00000394797;ENST00000372042;ENST00000482160;ENST00000444321	T;T;T;T;T;T;T	0.32988	2.17;1.43;2.17;2.17;2.43;1.43;2.17	5.03	5.03	0.67393	.	0.098405	0.64402	D	0.000002	T	0.40619	0.1124	L	0.27053	0.805	0.45390	D	0.998374	D;D;D;D;D;D	0.63880	0.986;0.993;0.993;0.993;0.993;0.993	D;D;D;D;D;D	0.70935	0.965;0.971;0.971;0.971;0.971;0.956	T	0.16394	-1.0404	9	.	.	.	-15.7162	14.3831	0.66923	0.0:0.0:0.0:1.0	.	328;407;387;400;408;327	B4DMP3;E9PGS5;Q59FB2;Q9BU40;D3DUY6;D3YTA8	.;.;.;CRDL1_HUMAN;.;.	E	400;327;406;406;408;328;407	ENSP00000361115:K400E;ENSP00000389627:K327E;ENSP00000218054:K406E;ENSP00000378276:K406E;ENSP00000361112:K408E;ENSP00000418443:K328E;ENSP00000399739:K407E	.	K	-	1	0	CHRDL1	109809244	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.251000	0.65438	1.932000	0.55993	0.481000	0.45027	AAG	NOVEL	CHRDL1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057913.3	2	9.02767	KEEP	0	0	0	30	948	TT	0.999997	0.999986	0		-	15	60	550	0	0	43.325213	92	60	3422	170	ENST00000372042.1	0.140187	0.999989
UBE2A	7319	__UNKNOWN__	__UNKNOWN__	X	118716633	118716633	__UNKNOWN__	Silent	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:118716633C>A	ENST00000371558.2	+	5	498	c.324C>A	c.(322-324)tcC>tcA	p.S108S	UBE2A_ENST00000346330.3_Silent_p.S78S|UBE2A_ENST00000371569.5_Silent_p.S33S	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A	108		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						TTCTAACATCCATACAGGTGA	0.318	NA	NA						Rad6 pathway						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													187	160	169	NA		NA	NA	X		NA											NA				118716633		2203	4300	6503	SO:0001819	synonymous_variant			AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721	7319		Ubiquitin-conjugating enzymes E2	12472	protein-coding gene	gene with protein product		312180	ubiquitin-conjugating enzyme E2A (RAD6 homolog)		NA	1559696	Standard	NM_003336	NM_003336	NA	Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.324C>A	chrX.hg19:g.118716633C>A		NA	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	hg19	CCDS14580.1	0.02	1.919052	ATCxATA	COVERED																																																																																			NOVEL	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058036.1	1	10.534223	KEEP	0	0	0	35	1251	CC	0.999999	0.999954	0		+	4	60	140	0	0	8.638505	95	60	3592	160	ENST00000371558.2	0.040404	0.999956
LAMP2	3920	__UNKNOWN__	__UNKNOWN__	X	119572319	119572319	__UNKNOWN__	Intron	SNP	T	T	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:119572319T>A	ENST00000434600.2	-	8	1289				LAMP2_ENST00000538785.1_Intron|LAMP2_ENST00000200639.4_Intron|LAMP2_ENST00000371335.4_3'UTR	NM_001122606.1|NM_002294.2	NP_001116078.1|NP_002285.1	P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	NA		NA			blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						CCAGTTTTTTTAAAAAAAAGA	0.249	NA	NA												4	0.0010596	0.003	0	3775	,	,	NA	10503	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893	3920		CD molecules	6501	protein-coding gene	gene with protein product		309060			NA		Standard		NM_002294	NA	Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000434600.2:c.1093+3265A>T	chrX.hg19:g.119572319T>A		NA	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	hg19	CCDS48159.1	0.02	-0.333373	TTTxAAA	COVERED																																																																																			NOVEL	LAMP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058102.2	1	4.511036	KEEP	0	0	0	15	436	TT	0.99649	0.848994	0		-	12	60	430	0	0	38.433327	26	60	929	60	ENST00000434600.2	0.315789	0.851984
XPNPEP2	7512	__UNKNOWN__	__UNKNOWN__	X	128893123	128893123	__UNKNOWN__	Intron	SNP	G	G	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:128893123G>T	ENST00000371106.3	+	15	1559					NM_003399.5	NP_003390.4	O43895	XPP2_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 2, membrane-bound	NA		NA				anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(3)|kidney(3)|large_intestine(5)|liver(1)|lung(20)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	37						CCTAGCCCCAGGCATTTGGCA	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	67	72	NA		NA	NA	X		NA											NA				128893123		2203	4300	6503	SO:0001627	intron_variant			U90724	CCDS14613.1	Xq25	2008-02-05			ENSG00000122121	ENSG00000122121	7512	3.4.11.9		12823	protein-coding gene	gene with protein product		300145			NA	9375790, 9628831	Standard	NM_003399	NM_003399	NA	Approved		uc004eut.1	O43895	OTTHUMG00000022373	ENST00000371106.3:c.1368-33G>T	chrX.hg19:g.128893123G>T		NA	A0AV16|O75994	hg19	CCDS14613.1	0.02	9.318594	CCAxGCA	COVERED																																																																																			NOVEL	XPNPEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058210.1	7	20.465739	KEEP	0	0	0	68	2385	GG	1	1	0		+	36	60	1345	0	0	107.416156	207	60	7618	394	ENST00000371106.3	0.148148	1
CCDC160	347475	__UNKNOWN__	__UNKNOWN__	X	133378914	133378914	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:133378914G>C	ENST00000517294.1	+	3	467	c.84G>C	c.(82-84)gaG>gaC	p.E28D	CCDC160_ENST00000370809.4_Missense_Mutation_p.E28D			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	28		NA								endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						AGACTTCTGAGCCTGAATCTT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													25	23	24	NA		NA	NA	X		NA											NA				133378914		1815	4074	5889	SO:0001583	missense			BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952	347475			37286	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001101357	NM_001101357	NA	Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.84G>C	chrX.hg19:g.133378914G>C	ENSP00000427951:p.Glu28Asp	NA		hg19	CCDS48171.1	0.02	9.775965	TGAxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.636	1.137670	0.21123	.	.	ENSG00000203952	ENST00000517294;ENST00000370809	.	.	.	5.16	-0.0902	0.13666	.	0.456851	0.18461	N	0.140512	T	0.13372	0.0324	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.22034	-1.0228	9	0.15499	T	0.54	-10.6733	3.2259	0.06731	0.1527:0.3776:0.3382:0.1316	.	28	A6NGH7	CC160_HUMAN	D	28	.	ENSP00000359845:E28D	E	+	3	2	CCDC160	133206580	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.813000	0.04491	-0.418000	0.07450	-0.213000	0.12676	GAG	NOVEL	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377679.1	5	21.97076	KEEP	0	0	0	73	2595	GG	1	1	0		+	76	60	2713	0	0	245.073306	149	60	5638	347	ENST00000517294.1	0.337778	1
RBMX	27316	__UNKNOWN__	__UNKNOWN__	X	135955996	135955996	__UNKNOWN__	3'UTR	SNP	G	G	A	rs850		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:135955996G>A	ENST00000320676.7	-	0	1635				RBMX_ENST00000496459.2_5'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000570135.1_3'UTR	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	NA		NA			cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TGCCTCATTTGCTGGGAAAAA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274	27316		RNA binding motif (RRM) containing	9910	protein-coding gene	gene with protein product	heterogeneous nuclear ribonucleoprotein G	300199	RNA binding motif protein, X chromosome		NA	10391206, 10391207	Standard	NM_002139	NM_002139	NA	Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.*305C>T	chrX.hg19:g.135955996G>A		NA	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	hg19	CCDS14661.1	0.02	16.963668	TTTxCTG	COVERED																																																																																			NOVEL	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058507.1	4	45.741485	KEEP	7	0	0	152	5534	GG	1	1	0		-	22	40	751	0	0	48.341159	393	60	15128	732	ENST00000320676.7	0.053012	1
RBMX	27316	__UNKNOWN__	__UNKNOWN__	X	135960230	135960230	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs199717308		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:135960230C>T	ENST00000320676.7	-	4	386	c.232G>A	c.(232-234)Gcc>Acc	p.A78T	RBMX_ENST00000565438.1_5'UTR|RBMX_ENST00000562646.1_Missense_Mutation_p.A78T|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000570135.1_Intron	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	78	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A78T(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					ACCTTGATGGCTTTTCCATCT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	prostate(1)											30	27	28	NA		NA	NA	X		NA											NA				135960230		2203	4300	6503	SO:0001583	missense				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274	27316		RNA binding motif (RRM) containing	9910	protein-coding gene	gene with protein product	heterogeneous nuclear ribonucleoprotein G	300199	RNA binding motif protein, X chromosome		NA	10391206, 10391207	Standard	NM_002139	NM_002139	NA	Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.232G>A	chrX.hg19:g.135960230C>T	ENSP00000359645:p.Ala78Thr	NA	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	hg19	CCDS14661.1	0.02	-0.315822	TGGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	.	11.06	1.528254	0.27299	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.15139	2.45	5.15	4.19	0.49359	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.364756	0.24165	U	0.040949	T	0.06781	0.0173	N	0.01168	-0.975	0.80722	D	1	B;B	0.11235	0.001;0.004	B;B	0.14023	0.01;0.01	T	0.28170	-1.0052	10	0.35671	T	0.21	.	13.8269	0.63357	0.1641:0.8359:0.0:0.0	.	78;65	P38159;Q8N8Y7	HNRPG_HUMAN;.	T	78;65	ENSP00000359645:A78T	ENSP00000359645:A78T	A	-	1	0	RBMX	135787896	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	3.150000	0.50662	2.132000	0.65825	0.504000	0.49776	GCC	NOVEL	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058507.1	2	3.009658	KEEP	0	0	0	10	350	CC	0.992708	0.812496	0		-	3	42	104	0	0	7.348196	33	60	1215	52	ENST00000320676.7	0.083333	0.818465
RBMX	27316	__UNKNOWN__	__UNKNOWN__	X	135961560	135961560	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs80321628		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:135961560C>G	ENST00000320676.7	-	2	181	c.27G>C	c.(25-27)aaG>aaC	p.K9N	RBMX_ENST00000565438.1_Intron|RBMX_ENST00000562646.1_Missense_Mutation_p.K9N|RBMX_ENST00000431446.3_Missense_Mutation_p.K9N|RBMX_ENST00000570135.1_5'UTR	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	9	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K9N(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAATGAAGAGCTTTCCTGGGC	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	pancreas(1)											109	103	105	NA		NA	NA	X		NA											NA				135961560		2203	4300	6503	SO:0001583	missense				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274	27316		RNA binding motif (RRM) containing	9910	protein-coding gene	gene with protein product	heterogeneous nuclear ribonucleoprotein G	300199	RNA binding motif protein, X chromosome		NA	10391206, 10391207	Standard	NM_002139	NM_002139	NA	Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.27G>C	chrX.hg19:g.135961560C>G	ENSP00000359645:p.Lys9Asn	NA	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	hg19	CCDS14661.1	0.02	3.975484	GAGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	.	19.30	3.801463	0.70682	.	.	ENSG00000147274	ENST00000431446;ENST00000320676;ENST00000449161	D;D	0.89050	-2.46;-2.46	4.66	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	U	0.000000	D	0.88507	0.6455	L	0.56340	1.77	0.09310	P	0.9999999999999992	P;B;P	0.46656	0.882;0.278;0.868	P;B;B	0.50270	0.636;0.142;0.311	D	0.91729	0.5395	9	0.72032	D	0.01	.	8.8627	0.35267	0.0:0.7507:0.0:0.2493	.	9;9;9	B4E3U4;P38159;Q8N8Y7	.;HNRPG_HUMAN;.	N	9	ENSP00000411989:K9N;ENSP00000359645:K9N	ENSP00000359645:K9N	K	-	3	2	RBMX	135789226	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.970000	0.29383	1.905000	0.55150	0.508000	0.49915	AAG	NOVEL	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058507.1	10	26.012647	KEEP	1	1	33	98	3397	CC	1	1	0		-	6	39	223	0	0	14.569085	126	60	4669	303	ENST00000320676.7	0.045455	1
MIR513A1	574509	__UNKNOWN__	__UNKNOWN__	X	146295067	146295067	__UNKNOWN__	RNA	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:146295067C>G	ENST00000385138.1	-	0	42					NR_030231.1				microRNA 513a-1	NA		NA									NA						tgacacctccctgtgaaaggc	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													109	87	94	NA		NA	NA	X		NA											NA				146295067		1568	3582	5150							Xq27.3	2011-09-12	2008-01-07	2008-12-18	ENSG00000207873	ENSG00000207873	574509		ncRNAs / Micro RNAs	32141	non-coding RNA	RNA, micro		NA	microRNA 513-1	MIRN513-1, MIRN513A1	NA		Standard	NR_030231	NR_030231	NA	Approved	hsa-mir-513-1, hsa-mir-513a-1				ENST00000385138.1:	chrX.hg19:g.146295067C>G		NA		hg19		0.02	12.551241	TCCxTGT	COVERED																																																																																			NOVEL	MIR513A1-201	KNOWN	basic	miRNA	NA	miRNA		2	12.339694	KEEP	0	0	0	41	1433	CC	1	1	0		-	87	60	2984	0	0	265.84146	185	60	6971	388	ENST00000385138.1	0.319853	1
FMR1NB	158521	__UNKNOWN__	__UNKNOWN__	X	147062883	147062883	__UNKNOWN__	5'UTR	SNP	G	G	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:147062883G>C	ENST00000370467.3	+	0	35					NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	NA		NA				integral component of membrane (GO:0016021)|nucleolus (GO:0005730)				breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					CGGACCGTTGGGCTGTGAGGC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													54	46	49	NA		NA	NA	X		NA											NA				147062883		2203	4300	6503	SO:0001623	5_prime_UTR_variant				CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988	158521			26372	protein-coding gene	gene with protein product	cancer/testis antigen 37	NA			NA	12601173	Standard	NM_152578	NM_152578	NA	Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.-40G>C	chrX.hg19:g.147062883G>C		NA	D3DWT3	hg19	CCDS14683.1	0.02	2.469857	TTGxGCT	COVERED																																																																																			NOVEL	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058667.1	0	6.621185	KEEP	0	0	0	22	753	GG	0.999879	0.986034	0		+	21	60	766	0	0	69.940589	38	60	1276	97	ENST00000370467.3	0.355932	0.986153
IDS	3423	__UNKNOWN__	__UNKNOWN__	X	148562469	148562469	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:148562469C>A	ENST00000340855.6	-	0	3670					NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	NA		NA			carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					AGAGAGATTTCTACAAATAAA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3423	3.1.6.13		5389	protein-coding gene	gene with protein product	Hunter syndrome	300823		SIDS	NA		Standard		NM_006123	NA	Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.*1808G>T	chrX.hg19:g.148562469C>A		NA	D3DWT4|Q14604|Q9BRM3	hg19	CCDS14685.1	0.02	-0.438665	TTTxTAC	COVERED																																																																																			NOVEL	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058677.3	3	2.40749	KEEP	0	0	0	8	274	CC	0.99257	0.952727	0		-	14	60	511	0	0	44.904019	36	60	1366	74	ENST00000340855.6	0.28	0.959859
NSDHL	50814	__UNKNOWN__	__UNKNOWN__	X	152037528	152037528	__UNKNOWN__	Silent	SNP	A	A	C	rs369318994		LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:152037528A>C	ENST00000370274.3	+	8	1184	c.990A>C	c.(988-990)gcA>gcC	p.A330A	NSDHL_ENST00000440023.1_Silent_p.A330A	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	330		NA			cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					TGCGGGTCGCACTGGCTGGCA	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													75	58	64	NA		NA	NA	X		NA											NA				152037528		2203	4300	6503	SO:0001819	synonymous_variant			X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	50814	1.1.1.170	Short chain dehydrogenase/reductase superfamily / Extended SDR fold	13398	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 31E, member 1	300275			NA	10710235, 12837764, 19027726	Standard	NM_015922	NM_015922	NA	Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.990A>C	chrX.hg19:g.152037528A>C		NA	D3DWT6|O00344	hg19	CCDS14717.1	0.02	9.083957	CGCxCTG	COVERED																																																																																			NOVEL	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060927.1	3	15.642889	KEEP	0	0	0	52	1572	AA	1	1	0		+	76	60	2608	0	0	236.734793	137	60	4750	326	ENST00000370274.3	0.356808	1
ATP2B3	492	__UNKNOWN__	__UNKNOWN__	X	152807350	152807350	__UNKNOWN__	Silent	SNP	G	G	A	rs147526826	byFrequency	LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:152807350G>A	ENST00000349466.2	+	4	956	c.630G>A	c.(628-630)gcG>gcA	p.A210A	ATP2B3_ENST00000370186.1_Silent_p.A210A|ATP2B3_ENST00000393842.1_Silent_p.A210A|ATP2B3_ENST00000359149.3_Silent_p.A210A|ATP2B3_ENST00000263519.4_Silent_p.A210A|ATP2B3_ENST00000370181.2_Silent_p.A210A			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	210		NA			blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.A210A(4)		NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCGTGGCTGCGCTGGTGGTGG	0.632	NA	NA											G|||	9	0.00238411	0.0068	0	3775	,	,	NA	10536	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				4	Substitution - coding silent(4)	endometrium(4)						G	,	28,3807		0,22,6,1610,565	76	73	74	NA	630,630	-11	0	X	dbSNP_134	74	1,6727		0,1,0,2427,1872	no	coding-synonymous,coding-synonymous	ATP2B3	NM_001001344.2,NM_021949.3	,	0,23,6,4037,2437	AA,AG,A,GG,G	NA	0.0149,0.7301,0.2745	,	210/1221,210/1174	152807350	29,10534	2203	4300	6503	SO:0001819	synonymous_variant			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	492	3.6.3.8	ATPases / P-type	816	protein-coding gene	gene with protein product	plasma membrane calcium-transporting ATPase 3, cilia and flagella associated protein 39	300014	spinocerebellar ataxia, X-linked 1, cerebellar ataxia 2 (X-linked)	SCAX1, CLA2	NA	8187550, 22912398	Standard	NM_021949	NM_021949	NA	Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.630G>A	chrX.hg19:g.152807350G>A		NA	B7WNR8|B7WNY5|Q12995|Q16858	hg19	CCDS35440.1	0.02	6.860604	TGCxCTG	COVERED																																																																																			NOVEL	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060957.1	1	11.693768	KEEP	0	0	0	39	1332	GG	1	1	0		+	51	60	1771	0	0	157.951181	109	60	3946	247	ENST00000349466.2	0.31875	1
L1CAM	3897	__UNKNOWN__	__UNKNOWN__	X	153133303	153133303	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:153133303C>G	ENST00000370060.1	-	16	2080	c.1891G>C	c.(1891-1893)Gtg>Ctg	p.V631L	L1CAM_ENST00000370055.1_Missense_Mutation_p.V626L|L1CAM_ENST00000543994.1_Missense_Mutation_p.V633L|L1CAM_ENST00000361981.3_Missense_Mutation_p.V626L|L1CAM_ENST00000361699.4_Missense_Mutation_p.V631L|L1CAM_ENST00000370057.3_Missense_Mutation_p.V631L|L1CAM_ENST00000538883.1_Missense_Mutation_p.V633L	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	631	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GACACGCGCACCTGGCTCTGC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													51	46	48	NA		NA	NA	X		NA											NA				153133303		2189	4246	6435	SO:0001583	missense			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910	3897		CD molecules, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	6470	protein-coding gene	gene with protein product		308840	antigen identified by monoclonal antibody R1	HSAS1, SPG1, HSAS, MASA, MIC5, S10	NA		Standard	NM_024003	NM_001278116	NA	Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.1891G>C	chrX.hg19:g.153133303C>G	ENSP00000359077:p.Val631Leu	NA	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	hg19	CCDS14733.1	0.02	4.870698	GCAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972308	0.74246	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47;0.47;0.47	4.67	4.67	0.58626	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.113273	0.38663	N	0.001615	T	0.63721	0.2535	L	0.52126	1.63	0.45676	D	0.998599	D;P;D	0.65815	0.984;0.843;0.995	P;P;D	0.66351	0.905;0.66;0.943	T	0.66440	-0.5923	10	0.72032	D	0.01	.	11.7755	0.51983	0.0:1.0:0.0:0.0	.	626;631;631	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	L	631;633;631;633;626;626;631	ENSP00000359077:V631L;ENSP00000438430:V633L;ENSP00000359074:V631L;ENSP00000439645:V633L;ENSP00000354712:V626L;ENSP00000359072:V626L;ENSP00000355380:V631L	ENSP00000355380:V631L	V	-	1	0	L1CAM	152786497	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.384000	0.44362	2.162000	0.67917	0.529000	0.55759	GTG	NOVEL	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000061094.2	1	13.190815	KEEP	0	1	11	48	1604	CC	1	1	0		-	84	60	3119	0	0	317.265027	42	60	1490	212	ENST00000370060.1	0.666667	1
FLNA	2316	__UNKNOWN__	__UNKNOWN__	X	153578476	153578476	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:153578476C>T	ENST00000344736.4	-	42	7178	c.7136G>A	c.(7135-7137)cGa>cAa	p.R2379Q	FLNA_ENST00000360319.4_Missense_Mutation_p.R2411Q|FLNA_ENST00000369850.3_Missense_Mutation_p.R2419Q|FLNA_ENST00000498491.1_5'UTR|FLNA_ENST00000369856.3_Missense_Mutation_p.R552Q|FLNA_ENST00000422373.1_Missense_Mutation_p.R2411Q			P21333	FLNA_HUMAN	filamin A, alpha	2419		NA			actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTCCCCAACTCGGATCTTGAA	0.582	NA	NA									OREG0003592	type=REGULATORY REGION|Gene=FLNA|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													116	120	119	NA		NA	NA	X		NA											NA				153578476		2030	4169	6199	SO:0001583	missense			X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924	2316			3754	protein-coding gene	gene with protein product	actin binding protein 280	300017	filamin A, alpha (actin binding protein 280)	FLN1, FLN, OPD2, OPD1	NA	8406501, 12612583	Standard		NM_001456	NA	Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000344736.4:c.7136G>A	chrX.hg19:g.153578476C>T	ENSP00000358863:p.Arg2379Gln	1756	E9KL45|Q5HY53|Q5HY55|Q8NF52	hg19		0.02	8.960351	ACTxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	29.8	5.041099	0.93685	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736	D;D;D;T;D	0.88277	-2.36;-2.36;-2.36;-0.63;-2.36	5.67	5.67	0.87782	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.93871	0.8039	M	0.69185	2.1	0.58432	D	0.999998	D;D;D;D	0.89917	0.997;1.0;0.999;0.999	D;D;D;D	0.75484	0.986;0.955;0.944;0.944	D	0.93568	0.6901	10	0.49607	T	0.09	.	18.7977	0.92001	0.0:1.0:0.0:0.0	.	552;2411;2419;2419	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	Q	2411;2087;2411;2419;552;2379	ENSP00000353467:R2411Q;ENSP00000416926:R2411Q;ENSP00000358866:R2419Q;ENSP00000358872:R552Q;ENSP00000358863:R2379Q	ENSP00000358863:R2379Q	R	-	2	0	FLNA	153231670	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.046000	0.71029	2.385000	0.81259	0.529000	0.55759	CGA	NOVEL	FLNA-010	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000130295.1	0	24.073996	KEEP	0	0	0	80	2653	CC	1	1	0		-	7	60	269	0	0	16.677179	220	60	7715	393	ENST00000344736.4	0.030837	1
TAZ	6901	__UNKNOWN__	__UNKNOWN__	X	153641527	153641527	__UNKNOWN__	Intron	SNP	C	C	T			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:153641527C>T	ENST00000350743.4	+	3	527				TAZ_ENST00000369790.4_Intron|TAZ_ENST00000475699.1_Intron|TAZ_ENST00000369776.4_Intron|TAZ_ENST00000299328.5_Intron|TAZ_ENST00000351413.4_Intron	NM_181311.2	NP_851828.1	Q9GZV5	WWTR1_HUMAN	tafazzin	NA		NA			cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			lung(1)	1	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGGCATGAAGCCTTTCCTGTC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													82	62	69	NA		NA	NA	X		NA											NA				153641527		2202	4299	6501	SO:0001627	intron_variant			X92762	CCDS14748.1, CCDS14749.1, CCDS14750.1, CCDS35450.1	Xq28	2014-09-17	2008-07-29		ENSG00000102125	ENSG00000102125	6901			11577	protein-coding gene	gene with protein product	Barth syndrome	300394	endocardial fibroelastosis 2, cardiomyopathy, dilated 3A (X-linked)	CMD3A, EFE2, EFE	NA	8042670	Standard		NM_000116	NA	Approved	BTHS, XAP-2, G4.5	uc004fkx.3	Q16635	OTTHUMG00000033190	ENST00000350743.4:c.239-17C>T	chrX.hg19:g.153641527C>T		NA	D3DNH7|Q8N3P2|Q9Y3W6	hg19	CCDS14749.1	0.02	4.472172	AAGxCTT	COVERED																																																																																			NOVEL	TAZ-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080939.1	1	19.198757	KEEP	0	0	0	64	2253	CC	1	1	0		+	50	60	1821	0	0	169.273285	76	60	2690	257	ENST00000350743.4	0.396825	1
BRCC3	79184	__UNKNOWN__	__UNKNOWN__	X	154348456	154348456	__UNKNOWN__	Intron	SNP	T	T	C			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:154348456T>C	ENST00000340647.4	+	10	1005				BRCC3_ENST00000369459.2_Intron|BRCC3_ENST00000369462.1_Intron|MTCP1_ENST00000362018.2_Intron|BRCC3_ENST00000330045.7_Intron			P46736	BRCC3_HUMAN	BRCA1/BRCA2-containing complex, subunit 3	NA		NA			double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|regulation of catalytic activity (GO:0050790)|response to ionizing radiation (GO:0010212)|response to X-ray (GO:0010165)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|nuclear ubiquitin ligase complex (GO:0000152)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	enzyme regulator activity (GO:0030234)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|polyubiquitin binding (GO:0031593)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|pancreas(1)|skin(1)	22	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					AAAAAACTTCTTTTTCAATTT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0													59	58	58	NA		NA	NA	X		NA											NA				154348456		1894	4119	6013	SO:0001627	intron_variant			X64643	CCDS56610.1, CCDS56611.1, CCDS56612.1	Xq28	2013-05-29	2005-11-21	2005-11-21	ENSG00000185515	ENSG00000185515	79184			24185	protein-coding gene	gene with protein product	Lys-63-specific deubiquitinase	300617	chromosome X open reading frame 53	CXorf53	NA	1303175, 14636569	Standard	NM_024332	NM_024332	NA	Approved	C6.1A, BRCC36	uc004fna.3	P46736	OTTHUMG00000022658	ENST00000340647.4:c.876+13T>C	chrX.hg19:g.154348456T>C		NA	A6QRF8|A6QRF9|A8MUX5|A8MWH0|A9Z1Y0|A9Z1Y5|B1B062|B4DQN7|Q16107|Q53YX5|Q9BTZ6	hg19	CCDS56610.1	0.02	15.999442	TTCxTTT	COVERED																																																																																			NOVEL	BRCC3-006	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316164.1	7	30.395599	KEEP	0	0	0	101	3354	TT	1	1	0		+	12	60	460	0	0	28.957884	343	60	13033	594	ENST00000340647.4	0.033803	1
CLIC2	1193	__UNKNOWN__	__UNKNOWN__	X	154505823	154505823	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-017_T	LTS-017_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-017_FF_T	LTS-017_FFPE1_N	g.chrX:154505823C>G	ENST00000369449.2	-	0	2331					NM_001289.4	NP_001280.3	O15247	CLIC2_HUMAN	chloride intracellular channel 2	NA		NA			chloride transmembrane transport (GO:1902476)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|oxidation-reduction process (GO:0055114)|positive regulation of binding (GO:0051099)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|signal transduction (GO:0007165)|transport (GO:0006810)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|glutathione peroxidase activity (GO:0004602)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	18	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ctttctctccctagcccctgg	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(108;581 1592 2289 21669 28822)					NA		NA				0													NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ000217	CCDS14767.1	Xq28	2012-09-26			ENSG00000155962	ENSG00000155962	1193		Ion channels / Chloride channels : Intracellular	2063	protein-coding gene	gene with protein product		300138			NA	9339381	Standard	NM_001289	NM_001289	NA	Approved	XAP121	uc004fnf.3	O15247	OTTHUMG00000022660	ENST00000369449.2:c.*1369G>C	chrX.hg19:g.154505823C>G		NA	A8K9S0|O15174|Q5JT80|Q8TCE3	hg19	CCDS14767.1	0.02	5.072446	TCCxTAG	COVERED																																																																																			NOVEL	CLIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058793.1	6	11.709038	KEEP	0	0	0	39	1327	CC	1	0.999977	0		-	70	60	2549	0	0	260.106417	33	60	1253	174	ENST00000369449.2	0.679612	0.999978
MT-RNR2	4550	__UNKNOWN__	__UNKNOWN__	M	2692	2692	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrM:2692G>A	ENST00000387347.2	+	0	1022					NR_039705.1				mitochondrially encoded 16S RNA	NA		NA									NA						tgacctgcccgtgaagaggcg	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							mitochondria	2014-01-30	2005-02-15	2005-02-16	ENSG00000210082	ENSG00000210082	4550		ncRNAs / Ribosomal RNA genes, Endogenous ligands	7471	non-coding RNA	RNA, ribosomal	humanin, formyl-humanin	561010		MTRNR2	NA	12009529, 12445508	Standard	NC_012920		NA	Approved	HN		Q8IVG9		ENST00000387347.2:	chrM.hg19:g.2692G>A		NA		hg19		0.02	3.760357	CCCxTGA	COVERED																																																																																			NOVEL	MT-RNR2-201	KNOWN	basic	Mt_rRNA	NA	Mt_rRNA		4	9.310043	KEEP	0	0	0	31	1066	GG	0.999997	0.999997	0		+	7	60	260	0	0	17.058826	143	60	5107	220	ENST00000387347.2	0.046667	1
MT-ND6	4541	__UNKNOWN__	__UNKNOWN__	M	14372	14372	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrM:14372T>C	ENST00000361681.2	-	1	301	c.302A>G	c.(301-303)gAa>gGa	p.E101G				P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	101		NA			cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						ACAGCACCAATCCTACCTCCA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	4541	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7462	protein-coding gene	gene with protein product	complex I ND6 subunit, NADH-ubiquinone oxidoreductase chain 6	516006	NADH dehydrogenase 6	MTND6	NA		Standard	YP_003024037		NA	Approved	NAD6, ND6		P03923		ENST00000361681.2:c.302A>G	chrM.hg19:g.14372T>C	ENSP00000354665:p.Glu101Gly	NA	Q34774|Q8HG30	hg19		0.02	7.347886	CAAxCCT	COVERED																																																																																			NOVEL	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		7	6.786833	KEEP	0	2	70	47	1410	TT	1	1	0		-	150	60	5544	0	0	587.724271	34	60	1181	303	ENST00000361681.2	0.815217	1
SCNN1D	6339	__UNKNOWN__	__UNKNOWN__	1	1225443	1225443	__UNKNOWN__	Intron	SNP	T	T	C	rs201111157		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:1225443T>C	ENST00000379116.5	+	13	1888				SCNN1D_ENST00000338555.2_Intron|SCNN1D_ENST00000400928.3_Intron|SCNN1D_ENST00000325425.8_Intron	NM_001130413.3	NP_001123885.2	P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	NA		NA			ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	gtcccgtgtctctgctccgtc	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572	6339		Ion channels / Sodium channel, nonvoltage-gated, Sodium channels	10601	protein-coding gene	gene with protein product		601328	sodium channel, nonvoltage-gated 1, delta, sodium channel, non-voltage-gated 1, delta		NA	8661065	Standard	NM_002978	NM_001130413	NA	Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000379116.5:c.1663-208T>C	chr1.hg19:g.1225443T>C		NA	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	hg19	CCDS44037.2	0.02	-0.419736	GTCxCTG	COVERED																																																																																			NOVEL	SCNN1D-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407296.1	1	4.204234	KEEP	3	0	0	14	370	TT	0.993634	0.942364	0		+	3	20	99	0	0	6.711912	37	60	1278	74	ENST00000379116.5	0.075	0.948402
DVL1	1855	__UNKNOWN__	__UNKNOWN__	1	1275264	1275264	__UNKNOWN__	Intron	SNP	A	A	G	rs59153307|rs12037363		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:1275264A>G	ENST00000378888.5	-	9	1194				DVL1_ENST00000378891.5_Intron			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	NA		NA			axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		AGACCCACCCACAGCCGCATG	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404	1855		Dishevelled homologs	3084	protein-coding gene	gene with protein product		601365	dishevelled 1 (homologous to Drosophila dsh), dishevelled, dsh homolog 1 (Drosophila)		NA	8817329	Standard	NM_004421	NM_004421	NA	Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.910-72T>C	chr1.hg19:g.1275264A>G		NA	Q5TA33|Q5TA35	hg19		0.02	3.629506	CCCxCAG	COVERED																																																																																			NOVEL	DVL1-004	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000008490.1	1	9.33572	KEEP	0	1	37	44	1175	AA	1	1	0		-	7	60	196	0	0	11.684214	116	60	3829	191	ENST00000378888.5	0.056911	1
VWA1	64856	__UNKNOWN__	__UNKNOWN__	1	1378235	1378235	__UNKNOWN__	3'UTR	SNP	A	A	G	rs70949589|rs2411340		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:1378235A>G	ENST00000476993.1	+	0	4484				VWA1_ENST00000404702.3_3'UTR	NM_022834.4	NP_073745.2	Q6PCB0	VWA1_HUMAN	von Willebrand factor A domain containing 1	NA		NA			behavioral response to pain (GO:0048266)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interstitial matrix (GO:0005614)				NS(1)|breast(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TAGTGACGGTAATAAACCAAG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC059409	CCDS27.1, CCDS28.1, CCDS28.2	1p36.33	2013-02-11			ENSG00000179403	ENSG00000179403	64856		Fibronectin type III domain containing	30910	protein-coding gene	gene with protein product		611901			NA	14527666, 12062410	Standard	NM_022834	NM_022834	NA	Approved	FLJ22215, VWA-1, WARP	uc001afs.3	Q6PCB0	OTTHUMG00000002975	ENST00000476993.1:c.*3068A>G	chr1.hg19:g.1378235A>G		NA	A8K692|B3KUA1|E9PB53|Q7L5D7|Q9H6J5	hg19	CCDS27.1	0.02	2.324043	GGTxATA	COVERED																																																																																			NOVEL	VWA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000008291.1	1	4.54322	KEEP	1	1	28	25	707	AA	0.999957	0.999683	0		+	5	60	197	0	0	13.777061	82	60	2889	134	ENST00000476993.1	0.057471	0.999726
ATAD3C	219293	__UNKNOWN__	__UNKNOWN__	1	1387891	1387891	__UNKNOWN__	Intron	SNP	A	A	G	rs1624483	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:1387891A>G	ENST00000378785.2	+	3	1217					NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	NA		NA					ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CACAGGTCCTATCCCTGCTGG	0.622	NA	NA											N|||	3403	0.679513	0.888	0.5634	5008	,	,	NA	17241	0.9911	NA	0.1938	False	NA	,,,	NA	NA	NA	2504	0.6585	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915	219293		ATPases / AAA-type	32151	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001039211	NM_001039211	NA	Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.222+77A>G	chr1.hg19:g.1387891A>G		NA	Q8N1Z5	hg19	CCDS44039.1	0.02	2.479259	CCTxTCC	COVERED																																																																																			NOVEL	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001279.3	4	2.40692	KEEP	0	0	0	8	241	AA	0.99257	0.976849	0		+	14	60	490	0	0	41.763654	44	60	1585	75	ENST00000378785.2	0.241379	0.984161
CDK11B	984	__UNKNOWN__	__UNKNOWN__	1	1572709	1572709	__UNKNOWN__	Intron	SNP	G	G	A	rs28498915	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:1572709G>A	ENST00000407249.3	-	15	1579				CDK11B_ENST00000340677.5_Intron|CDK11B_ENST00000341832.6_Intron|CDK11B_ENST00000317673.7_Intron			P21127	CD11B_HUMAN	cyclin-dependent kinase 11B	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(3)|lung(4)|skin(1)|stomach(2)	12						CTGTCACCGCGGGGGTGACCA	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000081	CCDS72682.1, CCDS72683.1, CCDS72684.1	1p36.33	2013-09-24	2009-12-16	2009-12-16	ENSG00000248333	ENSG00000248333	984		Cyclin-dependent kinases	1729	protein-coding gene	gene with protein product		176873	cell division cycle 2-like 1 (PITSLRE proteins)	CDC2L1	NA	1774066, 14511641, 19884882	Standard	NM_001787	XM_006711061	NA	Approved	CDK11-p110, CDK11-p58, CDK11-p46	uc001agv.1	P21127	OTTHUMG00000078638	ENST00000407249.3:c.1579+60C>T	chr1.hg19:g.1572709G>A		NA	O95265|Q12817|Q12818|Q12819|Q12820|Q12822|Q8N530|Q9NZS5|Q9UBJ0|Q9UBQ1|Q9UBR0|Q9UNY2|Q9UP57|Q9UP58|Q9UP59	hg19		0.02	6.633607	CGCxGGG	COVERED																																																																																			NOVEL	CDK11B-204	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding		0	3.945971	KEEP	9	4	119	55	1759	GG	1	1	0		-	10	49	345	0	0	22.984056	152	60	4959	257	ENST00000407249.3	0.061728	1
CDK11B	984	__UNKNOWN__	__UNKNOWN__	1	1582641	1582641	__UNKNOWN__	Intron	SNP	T	T	C	rs115373564		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:1582641T>C	ENST00000407249.3	-	3	227				CDK11B_ENST00000340677.5_Intron|CDK11B_ENST00000341832.6_Intron|CDK11B_ENST00000317673.7_Intron			P21127	CD11B_HUMAN	cyclin-dependent kinase 11B	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(3)|lung(4)|skin(1)|stomach(2)	12						ttcctcagtatgggtcacact	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000081	CCDS72682.1, CCDS72683.1, CCDS72684.1	1p36.33	2013-09-24	2009-12-16	2009-12-16	ENSG00000248333	ENSG00000248333	984		Cyclin-dependent kinases	1729	protein-coding gene	gene with protein product		176873	cell division cycle 2-like 1 (PITSLRE proteins)	CDC2L1	NA	1774066, 14511641, 19884882	Standard	NM_001787	XM_006711061	NA	Approved	CDK11-p110, CDK11-p58, CDK11-p46	uc001agv.1	P21127	OTTHUMG00000078638	ENST00000407249.3:c.228-1232A>G	chr1.hg19:g.1582641T>C		NA	O95265|Q12817|Q12818|Q12819|Q12820|Q12822|Q8N530|Q9NZS5|Q9UBJ0|Q9UBQ1|Q9UBR0|Q9UNY2|Q9UP57|Q9UP58|Q9UP59	hg19		0.02	4.09694	GTAxGGG	COVERED																																																																																			NOVEL	CDK11B-204	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding		4	3.611011	KEEP	2	0	0	12	379	TT	0.993634	0.993633	0		-	8	39	252	0	0	16.185153	115	60	4187	141	ENST00000407249.3	0.065041	0.999999
TTC34	100287898	__UNKNOWN__	__UNKNOWN__	1	2585401	2585401	__UNKNOWN__	Intron	SNP	A	A	C	rs201903230|rs6692051	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:2585401A>C	ENST00000401094.6	-	5	524				TTC34_ENST00000401095.3_Intron			A8MYJ7	TTC34_HUMAN	tetratricopeptide repeat domain 34	NA		NA									NA						CTGGAGCAGCACCCACAACCA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS55565.1	1p36.32	2013-01-11			ENSG00000215912	ENSG00000215912	100287898		Tetratricopeptide (TTC) repeat domain containing	34297	protein-coding gene	gene with protein product		NA			NA		Standard	XM_002342015	NM_001242672	NA	Approved		uc021oey.1	A8MYJ7	OTTHUMG00000000539	ENST00000401094.6:c.97-8399T>G	chr1.hg19:g.2585401A>C		NA	A8MXL8	hg19		0.02	2.335432	AGCxCCC	UNCOVERED																																																																																			NOVEL	TTC34-001	NOVEL	NMD_exception|basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000438565.2	13	3.007864	KEEP	11	0	0	10	294	AA	0	0	0		-	5	60	171	0	0	14.264733	18	60	600	100	ENST00000401094.6	0.217391	0.992094
TTC34	100287898	__UNKNOWN__	__UNKNOWN__	1	2585583	2585583	__UNKNOWN__	Intron	SNP	C	C	G	rs6678990		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:2585583C>G	ENST00000401094.6	-	5	524				TTC34_ENST00000401095.3_Intron			A8MYJ7	TTC34_HUMAN	tetratricopeptide repeat domain 34	NA		NA									NA						AGGCGAGCATCTGAACGCACG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS55565.1	1p36.32	2013-01-11			ENSG00000215912	ENSG00000215912	100287898		Tetratricopeptide (TTC) repeat domain containing	34297	protein-coding gene	gene with protein product		NA			NA		Standard	XM_002342015	NM_001242672	NA	Approved		uc021oey.1	A8MYJ7	OTTHUMG00000000539	ENST00000401094.6:c.97-8581G>C	chr1.hg19:g.2585583C>G		NA	A8MXL8	hg19		0.02	2.311824	CATxTGA	COVERED																																																																																			NOVEL	TTC34-001	NOVEL	NMD_exception|basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000438565.2	9	3.611655	KEEP	3	0	0	12	414	CC	0.993072	0.992072	0		-	4	60	158	0	0	13.462244	15	60	551	122	ENST00000401094.6	0.210526	0.998993
TTC34	100287898	__UNKNOWN__	__UNKNOWN__	1	2586397	2586397	__UNKNOWN__	Intron	SNP	G	G	C	rs200036373		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:2586397G>C	ENST00000401094.6	-	5	524				TTC34_ENST00000401095.3_Intron			A8MYJ7	TTC34_HUMAN	tetratricopeptide repeat domain 34	NA		NA									NA						TGACAGCCTGGAACAGCACCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS55565.1	1p36.32	2013-01-11			ENSG00000215912	ENSG00000215912	100287898		Tetratricopeptide (TTC) repeat domain containing	34297	protein-coding gene	gene with protein product		NA			NA		Standard	XM_002342015	NM_001242672	NA	Approved		uc021oey.1	A8MYJ7	OTTHUMG00000000539	ENST00000401094.6:c.97-9395C>G	chr1.hg19:g.2586397G>C		NA	A8MXL8	hg19		0.02	-0.29829	CTGxAAC	COVERED																																																																																			NOVEL	TTC34-001	NOVEL	NMD_exception|basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000438565.2	5	2.407771	KEEP	2	0	0	8	276	GG	0.99257	0.775257	0		-	6	47	222	0	0	20.086927	12	60	443	58	ENST00000401094.6	0.333333	0.78106
MEGF6	1953	__UNKNOWN__	__UNKNOWN__	1	3414888	3414888	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:3414888C>A	ENST00000356575.4	-	26	3579				MEGF6_ENST00000294599.4_Intron	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	NA		NA				extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GATGCCACCCCTTCCCAGCAG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(73;978 3658)					NA		NA				0							NA						6	8	7	NA		NA	NA	1		NA											NA				3414888		1792	3893	5685	SO:0001627	intron_variant			AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591	1953			3232	protein-coding gene	gene with protein product		604266	EGF-like-domain, multiple 3	EGFL3	NA	9693030	Standard	NM_001409	NM_001409	NA	Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3352+46G>T	chr1.hg19:g.3414888C>A		NA	Q4AC86|Q5VV39	hg19	CCDS41237.1	0.02	2.305817	CCCxTTC	COVERED																																																																																			NOVEL	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354866.1	0	6.319702	KEEP	0	0	0	21	699	CC	0.999869	0.976737	0		-	18	60	628	0	0	56.258704	37	60	1305	92	ENST00000356575.4	0.327273	0.976865
LRRC47	57470	__UNKNOWN__	__UNKNOWN__	1	3699155	3699155	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:3699155C>A	ENST00000378251.1	-	5	1441					NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	NA		NA					phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		caccacgccccgcAGACTTGT	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764	57470			29207	protein-coding gene	gene with protein product		NA			NA	10574461	Standard	NM_020710	NM_020710	NA	Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.1413+69G>T	chr1.hg19:g.3699155C>A		NA	Q9ULN5	hg19	CCDS51.1	0.02	4.373309	CCCxGCA	COVERED																																																																																			NOVEL	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009744.1	0	4.210911	KEEP	0	0	0	14	426	CC	0.995343	0.995343	0		-	38	60	1403	0	0	123.301464	99	60	3481	158	ENST00000378251.1	0.277372	1
CAMTA1	23261	__UNKNOWN__	__UNKNOWN__	1	7809757	7809757	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:7809757A>T	ENST00000303635.7	+	20	4896				CAMTA1_ENST00000439411.2_Intron|CAMTA1_ENST00000476864.1_Intron	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TGGGAGTTTTATTGATTCTGG	0.308	NA	NA	T	WWTR1	epitheliod hemangioendothelioma									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735	23261			18806	protein-coding gene	gene with protein product		611501			NA	11925432	Standard	NM_015215	NM_001195563	NA	Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.4690-1502A>T	chr1.hg19:g.7809757A>T		NA	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	hg19	CCDS30576.1	0.02	2.760706	TTTxTTG	COVERED																																																																																			NOVEL	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003588.3	0	3.541693	KEEP	0	1	11	16	408	AA	0.999366	0.999366	0		+	18	60	333	0	0	19.906594	112	60	3152	179	ENST00000303635.7	0.138462	1
MTHFR	4524	__UNKNOWN__	__UNKNOWN__	1	11863606	11863606	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:11863606G>A	ENST00000376590.3	-	2	171				MTHFR_ENST00000376585.1_5'UTR	NM_005957.4	NP_005948.3	P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	NA		NA			blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CGTGGGGAGGGAACAGAGGCA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						10	10	10	NA		NA	NA	1		NA											NA				11863606		872	1980	2852	SO:0001627	intron_variant			BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	4524	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	5,10-methylenetetrahydrofolate reductase (NADPH)		NA	7920641	Standard	NM_005957	NM_005957	NA	Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376590.3:c.13-420C>T	chr1.hg19:g.11863606G>A		NA	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	hg19	CCDS137.1	0.02	6.69588	AGGxAAC	COVERED																																																																																			NOVEL	MTHFR-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006539.1	3	29.09883	KEEP	0	1	23	105	3558	GG	1	1	0		-	45	60	1637	0	0	140.002387	145	60	5413	372	ENST00000376590.3	0.236842	1
VPS13D	55187	__UNKNOWN__	__UNKNOWN__	1	12320683	12320683	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:12320683T>G	ENST00000358136.3	+	11	1240				VPS13D_ENST00000356315.4_Intron	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)	NA		NA								NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CTTGTGAGGGTGTCCAGTGTC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707	55187			23595	protein-coding gene	gene with protein product		608877	vacuolar protein sorting 13D (yeast)		NA		Standard	NM_015378	NM_015378	NA	Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.1111-67T>G	chr1.hg19:g.12320683T>G		NA		hg19	CCDS30588.1	0.02	0.961996	GGGxGTC	COVERED																																																																																			NOVEL	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000036897.2	0	2.703786	KEEP	0	0	0	9	235	TT	0.99254	0.956584	0		+	14	60	198	0	0	13.40224	37	60	1009	117	ENST00000358136.3	0.27451	0.963774
C1orf158	93190	__UNKNOWN__	__UNKNOWN__	1	12822232	12822232	__UNKNOWN__	3'UTR	SNP	A	A	G	rs111347003	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:12822232A>G	ENST00000288048.5	+	0	2149					NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	NA		NA								central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		tggatgagtgaatGACAGGAG	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330	93190			28567	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152290	NM_152290	NA	Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.*1348A>G	chr1.hg19:g.12822232A>G		NA	Q5VUY4	hg19	CCDS147.1	0.02	3.874331	GTGxATG	COVERED																																																																																			NOVEL	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005325.1	2	2.70545	KEEP	6	0	0	9	269	AA	0.99254	0.99254	0		+	5	40	183	0	0	11.385812	131	60	4792	169	ENST00000288048.5	0.036765	1
PRAMEF1	65121	__UNKNOWN__	__UNKNOWN__	1	12854414	12854414	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs1063769	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:12854414G>A	ENST00000332296.7	+	3	741	c.638G>A	c.(637-639)cGc>cAc	p.R213H		NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	213		NA	R -> H (in dbSNP:rs1063769).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGAAATTCGCAACATGTCC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						332	303	313	NA		NA	NA	1		NA											NA				12854414		2203	4300	6503	SO:0001583	missense			AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721	65121		-	28840	protein-coding gene	gene with protein product		NA			NA		Standard	NM_023013	NM_023013	NA	Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.638G>A	chr1.hg19:g.12854414G>A	ENSP00000332134:p.Arg213His	NA	Q9UQP2	hg19	CCDS148.1	0.02	7.120796	TTCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	.	2.614	-0.290146	0.05568	.	.	ENSG00000116721	ENST00000332296	T	0.01025	5.43	1.61	-3.22	0.05125	.	0.000000	0.49916	U	0.000135	T	0.00666	0.0022	L	0.34521	1.04	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.48514	-0.9029	9	0.16420	T	0.52	.	3.4737	0.07577	0.1852:0.0:0.2519:0.5629	rs1063769	213	O95521	PRAM1_HUMAN	H	213	ENSP00000332134:R213H	ENSP00000332134:R213H	R	+	2	0	PRAMEF1	12777001	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.869000	0.01643	-1.558000	0.01690	-0.446000	0.05623	CGC	NOVEL	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005458.1	1	3.610903	KEEP	3	0	0	12	386	GG	0.993634	0.993634	0		+	7	25	269	0	0	18.085989	137	60	4546	179	ENST00000332296.7	0.048611	1
HNRNPCL1	343069	__UNKNOWN__	__UNKNOWN__	1	12907843	12907843	__UNKNOWN__	Silent	SNP	T	T	G	rs2982093		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:12907843T>G	ENST00000317869.6	-	2	525	c.300A>C	c.(298-300)tcA>tcC	p.S100S		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	100		NA				nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						TCTCCGCTGCTGATCGTTTCA	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						133	126	129	NA		NA	NA	1		NA											NA				12907843		2203	4300	6503	SO:0001819	synonymous_variant			BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172	343069		RNA binding motif (RRM) containing	29295	protein-coding gene	gene with protein product		NA		HNRPCL1	NA		Standard	NM_001013631	NM_001013631	NA	Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.300A>C	chr1.hg19:g.12907843T>G		NA	B2RP44	hg19	CCDS30591.1	0.02	17.926109	TGCxGAT	COVERED																																																																																			NOVEL	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005462.1	6	8.731085	KEEP	9	3	82	58	1771	TT	1	1	0		-	42	60	1375	0	0	99.60276	350	60	13137	630	ENST00000317869.6	0.107143	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	13183631	13183631	__UNKNOWN__	IGR	SNP	A	A	T	rs80009603	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:13183631A>T			NA	NA				RP13-221M14.3 (19163 upstream) : PRAMEF26 (32724 downstream)						NA		NA									NA						CAGGTTAATAACTGCAACCTG	0.502	NA	NA											.|||	165	0.0329473	0.0053	0.0173	5008	,	,	NA	17952	0.0903	NA	0.0348	False	NA	,,,	NA	NA	NA	2504	0.0204	NA	NA	NA						NA		NA				0							NA						59	45	49	NA		NA	NA	1		NA											NA				13183631		691	1587	2278	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.13183631A>T		NA		hg19		0.02	4.459011	ATAxCTG	COVERED																																																																																			NOVEL					0			3	4.210422	KEEP	15	0	0	14	429	AA	0.995343	0.995343	0			51	47	1847	0	0	168.571193	92	60	3310	200		0.356643	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	13183634	13183634	__UNKNOWN__	IGR	SNP	G	G	A	rs2982225	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:13183634G>A			NA	NA				RP13-221M14.3 (19166 upstream) : PRAMEF26 (32721 downstream)						NA		NA									NA						GTTAATAACTGCAACCTGGCT	0.493	NA	NA											.|||	165	0.0329473	0.0053	0.0173	5008	,	,	NA	17919	0.0903	NA	0.0348	False	NA	,,,	NA	NA	NA	2504	0.0204	NA	NA	NA						NA		NA				0							NA						59	45	49	NA		NA	NA	1		NA											NA				13183634		691	1583	2274	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.13183634G>A		NA		hg19		0.02	4.095161	ACTxCAA	COVERED																																																																																			NOVEL					0			2	4.207879	KEEP	15	0	0	14	479	GG	0.995343	0.995343	0			49	40	1719	0	0	155.731656	92	60	3441	198		0.347518	1
TMEM82	388595	__UNKNOWN__	__UNKNOWN__	1	16071035	16071035	__UNKNOWN__	Silent	SNP	G	G	A	rs554348940		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16071035G>A	ENST00000375782.1	+	4	855	c.717G>A	c.(715-717)ccG>ccA	p.P239P	RP11-169K16.4_ENST00000418525.1_RNA|TMEM82_ENST00000465575.1_3'UTR	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	239	Leu-rich.	NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCTGGACACCGCTCACCATCT	0.622	NA	NA											G|||	1	0.000199681	8e-04	0	5008	,	,	NA	18822	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						53	38	43	NA		NA	NA	1		NA											NA				16071035		2202	4298	6500	SO:0001819	synonymous_variant				CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460	388595			32350	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013641	NM_001013641	NA	Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.717G>A	chr1.hg19:g.16071035G>A		NA	B2RP27|Q5VVD4	hg19	CCDS30608.1	0.02	6.752654	ACCxCTC	COVERED																																																																																			NOVEL	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000008471.2	1	21.969642	KEEP	0	0	0	73	2546	GG	1	1	0		+	45	60	1552	0	0	130.935703	150	60	5495	344	ENST00000375782.1	0.230769	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16362543	16362543	__UNKNOWN__	IGR	SNP	C	C	G	rs61772376		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16362543C>G			NA	NA				CLCNKA (1998 upstream) : CLCNKB (7728 downstream)						NA		NA									NA						TGTGCTcactctctccttcct	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16362543C>G		NA		hg19		0.02	4.359277	ACTxTCT	COVERED																																																																																			NOVEL					0			1	3.546218	KEEP	1	1	38	25	790	CC	0.999957	0.999957	0			7	54	245	0	0	15.587801	142	60	5312	181		0.04698	1
FAM131C	348487	__UNKNOWN__	__UNKNOWN__	1	16385874	16385874	__UNKNOWN__	Intron	SNP	T	T	C	rs3978464		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16385874T>C	ENST00000375662.4	-	6	746				FAM131C_ENST00000494078.1_Intron	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	NA		NA								large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		tgaagaaacttaggctgagaa	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519	348487			26717	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 117	C1orf117	NA	12477932	Standard	NM_182623	NM_182623	NA	Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.562+114A>G	chr1.hg19:g.16385874T>C		NA	Q5T5Q5|Q8N3X3|Q8N9P9	hg19	CCDS41270.1	0.02	14.615768	ACTxAGG	COVERED																																																																																			NOVEL	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026319.1	5	3.178829	KEEP	2	8	282	109	3160	TT	1	1	0		-	14	49	552	0	0	37.175372	293	60	10549	552	ENST00000375662.4	0.045603	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16862273	16862273	__UNKNOWN__	IGR	SNP	C	C	A	rs76517011		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16862273C>A			NA	NA				U1 (1554 upstream) : AL355149.2 (3287 downstream)						NA		NA									NA						CATAAGGAATCAGACGGATGC	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16862273C>A		NA		hg19		0.02	10.416663	AATxAGA	COVERED																																																																																			NOVEL					0			7	3.513696	KEEP	26	3	92	44	1440	CC	1	1	0			28	60	978	0	0	72.400178	236	60	8739	342		0.106061	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16862282	16862282	__UNKNOWN__	IGR	SNP	G	G	A	rs11260784	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16862282G>A			NA	NA				U1 (1563 upstream) : AL355149.2 (3278 downstream)						NA		NA									NA						TCAGACGGATGCGGAAACCGA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16862282G>A		NA		hg19		0.02	12.375531	GATxCGG	COVERED	.	.	.	.	.	.	.	.	.	.	g	2.407	-0.336138	0.05278	.	.	ENSG00000197511	ENST00000357301	.	.	.	0.311	0.311	0.15831	.	.	.	.	.	T	0.54902	0.1887	.	.	.	.	.	.	.	.	.	.	.	.	T	0.64927	-0.6292	3	0.87932	D	0	.	.	.	.	rs11260784	.	.	.	I	1	.	ENSP00000349853:M1I	M	+	3	0	AL355149.1	16734869	0.005000	0.15991	0.045000	0.18777	0.059000	0.15707	0.514000	0.22786	0.392000	0.25172	0.398000	0.26397	ATG	NOVEL					0			7	11.136745	KEEP	34	3	85	67	2247	GG	1	1	0			22	60	744	0	0	50.381226	290	60	10778	427		0.070513	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16862294	16862294	__UNKNOWN__	IGR	SNP	A	A	G	rs71259516		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16862294A>G			NA	NA				U1 (1575 upstream) : AL355149.2 (3266 downstream)						NA		NA									NA						GGAAACCGAGACGGGCTGGAT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16862294A>G		NA		hg19		0.02	17.026315	GAGxCGG	COVERED																																																																																			NOVEL					0			6	4.215259	KEEP	40	6	203	85	2597	AA	1	1	0			39	51	1376	0	0	101.558194	343	60	12030	531		0.102094	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16862472	16862472	__UNKNOWN__	IGR	SNP	G	G	C	rs200621127		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16862472G>C			NA	NA				U1 (1753 upstream) : AL355149.2 (3088 downstream)						NA		NA									NA						tttttcctcagatccaagagc	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16862472G>C		NA		hg19		0.02	43.068015	TCAxATC	COVERED	.	.	.	.	.	.	.	.	.	.	g	3.046	-0.196522	0.06259	.	.	ENSG00000197511	ENST00000357301	.	.	.	0.425	-0.851	0.10716	.	.	.	.	.	T	0.18045	0.0433	N	0.08118	0	.	.	.	.	.	.	.	.	.	T	0.23226	-1.0194	4	0.87932	D	0	.	.	.	.	.	.	.	.	H	65	.	ENSP00000349853:D65H	D	+	1	0	AL355149.1	16735059	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.886000	0.04157	-0.571000	0.06014	-1.277000	0.01392	GAT	NOVEL					0			6	21.193409	KEEP	62	37	1292	521	18323	GG	1	1	0			38	49	1459	0	0	100.949909	624	50	23829	1746		0.057402	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16877444	16877444	__UNKNOWN__	IGR	SNP	T	T	A	rs79270280		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16877444T>A			NA	NA				AL355149.1 (1962 upstream) : NBPF1 (11369 downstream)						NA		NA									NA						CCAGACTAGATGAATAATCAC	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16877444T>A		NA		hg19		0.02	5.148047	AGAxGAA	COVERED																																																																																			NOVEL					0			0	3.245173	KEEP	7	1	35	23	725	TT	0.999892	0.99989	0			11	49	421	0	0	31.553647	105	60	3948	187		0.094828	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16877479	16877479	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16877479G>A			NA	NA				AL355149.1 (1997 upstream) : NBPF1 (11334 downstream)						NA		NA									NA						GACTGGACCCGGCTCTTGAAG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16877479G>A		NA		hg19		0.02	4.987374	CCCxGCT	COVERED																																																																																			NOVEL					0			0	7.157491	KEEP	3	0	0	24	785	GG	0.999892	0.999891	0			13	49	484	0	0	36.586138	110	60	3806	188		0.105691	0.999999
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16889529	16889529	__UNKNOWN__	3'UTR	SNP	T	T	C	rs698877		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16889529T>C	ENST00000430580.2	-	0	5216					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		aaTGCAGCTATATTATCTTTT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.*909A>G	chr1.hg19:g.16889529T>C		NA	Q8N4E8|Q9C0H0	hg19		0.02	6.440812	CTAxATT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	7	9.024755	KEEP	8	0	0	30	889	TT	0.999997	0.999997	0		-	28	40	1018	0	0	81.025486	157	60	5646	257	ENST00000430580.2	0.151351	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16890441	16890441	__UNKNOWN__	Silent	SNP	C	C	T	rs3863779	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16890441C>T	ENST00000430580.2	-	29	4304	c.3417G>A	c.(3415-3417)caG>caA	p.Q1139Q		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	1214	NBPF 8. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GGGCTGCTTACTGTGGGAATA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	T		403,4003		0,403,1800	561	489	513	NA	3366	0.6	0	1	dbSNP_108	513	1034,7566		0,1034,3266	no	coding-synonymous	NBPF1	NM_017940.3		0,1437,5066	TT,TC,CC	NA	12.0233,9.1466,11.0487		1122/1123	16890441	1437,11569	2203	4300	6503	SO:0001819	synonymous_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3417G>A	chr1.hg19:g.16890441C>T		NA	Q8N4E8|Q9C0H0	hg19		0.02	13.898668	TTAxTGT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	6	4.119733	KEEP	2	3	98	48	1753	CC	1	1	0		-	45	60	1635	0	0	126.963353	300	60	11463	499	ENST00000430580.2	0.130435	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16891333	16891333	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16891333C>T	ENST00000430580.2	-	28	4032	c.3145G>A	c.(3145-3147)Ggg>Agg	p.G1049R		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	1029	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		tcttcttccccttcttttctt	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						58	26	41	NA		NA	NA	1		NA											NA				16891333		619	665	1284	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3145G>A	chr1.hg19:g.16891333C>T	ENSP00000474456:p.Gly1049Arg	NA	Q8N4E8|Q9C0H0	hg19		0.02	2.047321	CCCxTTC	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	3	3.446942	KEEP	2	1	33	23	840	CC	0.999892	0.99779	0		-	13	60	466	0	0	37.952468	60	60	2293	132	ENST00000430580.2	0.178082	0.997898
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16891340	16891340	__UNKNOWN__	Missense_Mutation	SNP	T	T	A	rs3962237	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16891340T>A	ENST00000430580.2	-	28	4025	c.3138A>T	c.(3136-3138)agA>agT	p.R1046S		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	1026	NBPF 7. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ccccttcttttcttccccttc	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						59	26	42	NA		NA	NA	1		NA											NA				16891340		621	667	1288	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3138A>T	chr1.hg19:g.16891340T>A	ENSP00000474456:p.Arg1046Ser	NA	Q8N4E8|Q9C0H0	hg19		0.02	1.748161	TTTxCTT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	4	3.545512	KEEP	2	1	32	23	739	TT	0.999892	0.99779	0		-	10	60	342	0	0	26.37379	62	60	2249	131	ENST00000430580.2	0.138889	0.997898
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16891956	16891956	__UNKNOWN__	Intron	SNP	C	C	T	rs3872312	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16891956C>T	ENST00000430580.2	-	27	3952					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CTGACCCATCCCATGTCTGGG	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3064+171G>A	chr1.hg19:g.16891956C>T		NA	Q8N4E8|Q9C0H0	hg19		0.02	15.840591	ATCxCAT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	2	13.914212	KEEP	3	2	65	69	2339	CC	1	1	0		-	15	60	571	0	0	36.554397	381	60	14006	595	ENST00000430580.2	0.037879	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16892010	16892010	__UNKNOWN__	Intron	SNP	T	T	C	rs375255056		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16892010T>C	ENST00000430580.2	-	27	3952					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CATGTGCCTATAGGTCCTCAC	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3064+117A>G	chr1.hg19:g.16892010T>C		NA	Q8N4E8|Q9C0H0	hg19		0.02	25.346684	CTAxAGG	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	7	18.329921	KEEP	6	5	178	123	3773	TT	1	1	0		-	20	60	766	0	0	48.496551	552	60	20366	917	ENST00000430580.2	0.034965	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16892060	16892060	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16892060G>C	ENST00000430580.2	-	27	3952					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TGGCCACTTGGAGCAGGAATA	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3064+67C>G	chr1.hg19:g.16892060G>C		NA	Q8N4E8|Q9C0H0	hg19		0.02	17.933278	TTGxAGC	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	3	10.876435	KEEP	9	4	134	83	2859	GG	1	1	0		-	18	40	680	0	0	43.941755	423	60	15846	688	ENST00000430580.2	0.040816	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16892547	16892547	__UNKNOWN__	Intron	SNP	G	G	A	rs374244631		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16892547G>A	ENST00000430580.2	-	27	3779					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CGAATTGGCCGGGTGACACAC	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						41	34	37	NA		NA	NA	1		NA											NA				16892547		1427	2504	3931	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2892-247C>T	chr1.hg19:g.16892547G>A		NA	Q8N4E8|Q9C0H0	hg19		0.02	2.422486	GCCxGGT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	6	3.611658	KEEP	7	0	0	12	410	GG	0.993072	0.964095	0		-	5	60	193	0	0	14.494366	48	60	1714	93	ENST00000430580.2	0.09434	0.97082
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16892565	16892565	__UNKNOWN__	Intron	SNP	G	G	A	rs202086630	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16892565G>A	ENST00000430580.2	-	27	3779					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CACTGACGAAGGGGTCAAAGG	0.473	NA	NA											.|||	129	0.0257588	8e-04	0.0231	5008	,	,	NA	138365	0.0079	NA	0.0467	False	NA	,,,	NA	NA	NA	2504	0.0583	NA	NA	NA						NA		NA				0							NA						33	28	30	NA		NA	NA	1		NA											NA				16892565		1380	2431	3811	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2892-265C>T	chr1.hg19:g.16892565G>A		NA	Q8N4E8|Q9C0H0	hg19		0.02	-0.412343	GAAxGGG	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	7	3.309748	KEEP	8	0	0	11	355	GG	0.992708	0.934874	0		-	4	41	138	0	0	9.769403	43	60	1638	82	ENST00000430580.2	0.085106	0.941741
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16893489	16893489	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16893489C>T	ENST00000430580.2	-	25	3727				NBPF1_ENST00000432949.1_Intron|NBPF1_ENST00000420031.2_Intron	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GAGAGCCCTGCTCACTGACCC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2839+184G>A	chr1.hg19:g.16893489C>T		NA	Q8N4E8|Q9C0H0	hg19		0.02	10.778882	CTGxTCA	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	4	6.846022	KEEP	0	2	63	45	1568	CC	1	1	0		-	16	60	573	0	0	38.014463	276	60	10254	384	ENST00000430580.2	0.054795	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16893721	16893721	__UNKNOWN__	Missense_Mutation	SNP	A	A	C	rs201533998		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16893721A>C	ENST00000430580.2	-	25	3679	c.2792T>G	c.(2791-2793)tTt>tGt	p.F931C	NBPF1_ENST00000432949.1_3'UTR|NBPF1_ENST00000420031.2_3'UTR	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	931	NBPF 5. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CAATATGTAAAAGGCACTTCT	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	A	CYS/PHE	79,4327		0,79,2124	1081	917	973	NA	2792	0.4	0	1	dbSNP_134	973	175,8425		0,175,4125	no	missense	NBPF1	NM_017940.3	205	0,254,6249	CC,CA,AA	NA	2.0349,1.793,1.9529		931/1123	16893721	254,12752	2203	4300	6503	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2792T>G	chr1.hg19:g.16893721A>C	ENSP00000474456:p.Phe931Cys	NA	Q8N4E8|Q9C0H0	hg19		0.02	12.393476	TAAxAGG	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	13	6.956721	KEEP	0	1	37	36	1147	AA	1	1	0		-	22	60	839	0	0	60.653934	266	60	9596	394	ENST00000430580.2	0.076389	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16901021	16901021	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs200611498		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16901021A>G	ENST00000430580.2	-	21	3246	c.2359T>C	c.(2359-2361)Tct>Cct	p.S787P	NBPF1_ENST00000432949.1_Missense_Mutation_p.S245P|NBPF1_ENST00000287968.8_Missense_Mutation_p.S152P|NBPF1_ENST00000420031.2_Missense_Mutation_p.S5P	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	787	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCAACATGAGAGGATGAGCCA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						2	3	2	NA		NA	NA	1		NA											NA				16901021		1003	1827	2830	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2359T>C	chr1.hg19:g.16901021A>G	ENSP00000474456:p.Ser787Pro	NA	Q8N4E8|Q9C0H0	hg19		0.02	2.029793	GAGxGGA	UNCOVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	0	4.212499	KEEP	56	0	0	14	436	AA	0	0	0		-	4	40	143	0	0	9.429643	71	40	2593	152	ENST00000430580.2	0.053333	0.998465
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16902844	16902844	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs199969012		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16902844G>T	ENST00000430580.2	-	19	2924	c.2037C>A	c.(2035-2037)gaC>gaA	p.D679E	NBPF1_ENST00000432949.1_Missense_Mutation_p.D137E|NBPF1_ENST00000287968.8_Missense_Mutation_p.D44E	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	679		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CCTGGGACTTGTCTGGCTCAT	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						373	406	394	NA		NA	NA	1		NA											NA				16902844		1511	2708	4219	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2037C>A	chr1.hg19:g.16902844G>T	ENSP00000474456:p.Asp679Glu	NA	Q8N4E8|Q9C0H0	hg19		0.02	6.818693	CTTxTCT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	5	8.696967	KEEP	13	2	69	53	1921	GG	1	1	0		-	16	47	597	0	0	44.305577	154	60	5871	330	ENST00000430580.2	0.094118	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16907164	16907164	__UNKNOWN__	Intron	SNP	C	C	T	rs201839566		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16907164C>T	ENST00000430580.2	-	16	2479					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ACAATATGTGCGTATACAGCC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.1591+75G>A	chr1.hg19:g.16907164C>T		NA	Q8N4E8|Q9C0H0	hg19		0.02	4.149588	GTGxGTA	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	1	4.514661	KEEP	1	0	0	15	522	CC	0.99649	0.996488	0		-	7	39	231	0	0	15.104572	105	60	3832	137	ENST00000430580.2	0.0625	0.999998
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16907303	16907303	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs681623	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16907303C>T	ENST00000430580.2	-	16	2415	c.1528G>A	c.(1528-1530)Gct>Act	p.A510T		NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	510	NBPF 2. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA	A -> T (in dbSNP:rs681623). {ECO:0000269|PubMed:11214970}.			cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ACAACCAGAGCTGAGTTGACT	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						1179	1182	1181	NA		NA	NA	1		NA											NA				16907303		2203	4300	6503	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.1528G>A	chr1.hg19:g.16907303C>T	ENSP00000474456:p.Ala510Thr	NA	Q8N4E8|Q9C0H0	hg19		0.02	9.366377	GAGxTGA	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	0	4.917215	KEEP	8	3	74	43	1380	CC	1	1	0		-	9	39	300	0	0	17.197595	262	60	9916	358	ENST00000430580.2	0.03321	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16914139	16914139	__UNKNOWN__	Intron	SNP	C	C	A	rs3098812	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16914139C>A	ENST00000430580.2	-	10	1454					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TTTGGCCCATCATAGATGCCA	0.507	NA	NA											.|||	1235	0.246605	0.093	0.3012	5008	,	,	NA	49263	0.4673	NA	0.2306	False	NA	,,,	NA	NA	NA	2504	0.2045	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.566+80G>T	chr1.hg19:g.16914139C>A		NA	Q8N4E8|Q9C0H0	hg19		0.02	2.440061	CATxATA	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	0	3.611638	KEEP	12	0	0	12	412	CC	0.99254	0.956584	0		-	7	60	258	0	0	20.550655	40	60	1511	78	ENST00000430580.2	0.148936	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16940140	16940140	__UNKNOWN__	IGR	SNP	G	G	C	rs9726502	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16940140G>C			NA	NA				NBPF1 (158 upstream) : RP5-1182A14.5 (3745 downstream)						NA		NA									NA						AAAGGGACCCGGCGGCCTCTT	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16940140G>C		NA		hg19		0.02	-0.104269	CCCxGCG	UNCOVERED																																																																																			NOVEL					0			0	2.639829	KEEP	0	0	0	9	231	GG	0.99254	0.138789	0			5	60	160	0	0	15.023766	6	60	205	31		0.454545	0.139832
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16945452	16945452	__UNKNOWN__	lincRNA	SNP	C	C	T	rs11260834	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16945452C>T	ENST00000412962.1	-	0	2067							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						CTCCCTACGACGGCAGGCCTA	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16945452C>T		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	2.203172	CGAxGGC	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	0	2.444989	KEEP	0	4	122	51	1763	CC	1	0.998993	0		-	21	60	759	0	0	66.188534	57	60	2074	189	ENST00000412962.1	0.269231	0.998993
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16945570	16945570	__UNKNOWN__	lincRNA	SNP	A	A	G	rs28552760	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16945570A>G	ENST00000412962.1	-	0	1949							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						TGACAGCGCCATCTTCTCAGA	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16945570A>G		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.412336	GCCxTCT	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	0	5.708538	KEEP	0	0	0	19	543	AA	0.99986	0.941609	0		-	8	40	298	0	0	24.305469	39	60	1436	74	ENST00000412962.1	0.170213	0.941741
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16949215	16949215	__UNKNOWN__	lincRNA	SNP	G	G	A	rs372364	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16949215G>A	ENST00000412962.1	-	0	1000							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						ggctgggcgcggtggctcatg	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16949215G>A		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.297526	CGCxGTG	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	7	6.319668	KEEP	1	0	0	21	697	GG	0.999863	0.780953	0		-	6	60	206	0	0	16.593505	28	60	958	66	ENST00000412962.1	0.176471	0.78106
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16950889	16950889	__UNKNOWN__	lincRNA	SNP	G	G	A	rs12045375	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16950889G>A	ENST00000412962.1	-	0	1000							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						TTGCCCCAGCGTCTCCACCTG	0.697	NA	NA											.|||	1177	0.235024	0.0174	0.2738	5008	,	,	NA	56460	0.4712	NA	0.2495	False	NA	,,,	NA	NA	NA	2504	0.2434	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16950889G>A		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	1.871999	AGCxTCT	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	1	9.078905	KEEP	0	4	112	70	2262	GG	1	0.999895	0		-	8	60	290	0	0	20.976973	85	60	2944	224	ENST00000412962.1	0.086022	0.999895
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16952102	16952102	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16952102G>A	ENST00000412962.1	-	0	1000							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						ctgaggtatgggaggttgggc	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16952102G>A		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.244658	ATGxGAG	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	7	3.911485	KEEP	0	0	0	13	418	GG	0.994391	0.63775	0		-	7	60	231	0	0	19.602012	21	60	758	47	ENST00000412962.1	0.25	0.641347
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16954981	16954981	__UNKNOWN__	lincRNA	SNP	C	C	A	rs10157498	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16954981C>A	ENST00000412962.1	-	0	458							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						AAGCTCCCGGCGAACCCGTGC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16954981C>A		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	8.987986	CGGxGAA	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	1	2.240963	KEEP	0	11	337	126	4393	CC	1	1	0		-	16	60	582	0	0	41.591788	185	60	6743	456	ENST00000412962.1	0.079602	1
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16956467	16956467	__UNKNOWN__	lincRNA	SNP	A	A	T	rs1762950	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16956467A>T	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						gcaattttttaaatttttagt	0.567	NA	NA											.|||	2275	0.454273	0.4803	0.4207	5008	,	,	NA	61852	0.504	NA	0.4364	False	NA	,,,	NA	NA	NA	2504	0.41	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16956467A>T		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.289512	TTTxAAT	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	0	3.90972	KEEP	0	0	0	13	376	AA	0.994391	0.756619	0		-	3	60	112	0	0	8.266095	30	60	1082	54	ENST00000412962.1	0.090909	0.760887
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16956468	16956468	__UNKNOWN__	lincRNA	SNP	A	A	T	rs1762951	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16956468A>T	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						caattttttaaatttttagta	0.567	NA	NA											.|||	2275	0.454273	0.4803	0.4207	5008	,	,	NA	60432	0.504	NA	0.4364	False	NA	,,,	NA	NA	NA	2504	0.41	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16956468A>T		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.289514	TTAxATT	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	0	3.91187	KEEP	0	0	0	13	414	AA	0.994391	0.756619	0		-	3	60	112	0	0	8.266087	30	60	1080	54	ENST00000412962.1	0.090909	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16965337	16965337	__UNKNOWN__	IGR	SNP	G	G	C	rs9660436	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16965337G>C			NA	NA				CROCCP2 (4283 upstream) : RNU1-3 (27942 downstream)						NA		NA									NA						TACAggccaagcatggtggct	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16965337G>C		NA		hg19		0.02	-0.254426	CAAxCAT	UNCOVERED																																																																																			NOVEL					0			1	2.708972	KEEP	3	0	0	9	332	GG	0	0	0			7	60	266	0	0	22.979536	22	60	839	48		0.241379	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16969145	16969145	__UNKNOWN__	IGR	SNP	T	T	C	rs11580567	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16969145T>C			NA	NA				CROCCP2 (8091 upstream) : RNU1-3 (24134 downstream)						NA		NA									NA						AGGAGCACAGTGAGAACAGAG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16969145T>C		NA		hg19		0.02	2.199818	CAGxGAG	COVERED																																																																																			NOVEL					0			0	3.90733	KEEP	5	0	0	13	341	TT	0.994391	0.990101	0			7	49	262	0	0	19.799127	60	50	2050	88		0.104478	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16971674	16971674	__UNKNOWN__	IGR	SNP	G	G	A	rs9727306	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16971674G>A			NA	NA				CROCCP2 (10620 upstream) : RNU1-3 (21605 downstream)						NA		NA									NA						GCAGCAAAAGGGTGGAGGGGA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16971674G>A		NA		hg19		0.02	4.457699	AAGxGTG	COVERED																																																																																			NOVEL					0			1	2.962924	KEEP	3	2	66	33	1074	GG	0.999998	0.999995	0			8	49	289	0	0	20.078818	108	52	3935	159		0.068966	0.999997
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16973519	16973519	__UNKNOWN__	IGR	SNP	G	G	A	rs2501762	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16973519G>A			NA	NA				CROCCP2 (12465 upstream) : RNU1-3 (19760 downstream)						NA		NA									NA						AACTTCTGCCGTAACCCTGAT	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16973519G>A		NA		hg19		0.02	27.352554	GCCxTAA	COVERED																																																																																			NOVEL					0			2	91.370043	KEEP	337	14	439	458	15482	GG	1	1	0			46	50	1709	0	0	121.454113	581	50	20226	1648		0.073365	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16973784	16973784	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16973784C>T			NA	NA				CROCCP2 (12730 upstream) : RNU1-3 (19495 downstream)						NA		NA									NA						ATCTTCAGCACCCGCACCAGC	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16973784C>T		NA		hg19		0.02	4.689109	GCAxCCG	COVERED																																																																																			NOVEL					0			3	6.217931	KEEP	51	3	86	51	1673	CC	0.999997	0.999971	0			16	40	577	0	0	46.16672	85	40	3115	193		0.158416	0.999973
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16973855	16973855	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16973855G>A			NA	NA				CROCCP2 (12801 upstream) : RNU1-3 (19424 downstream)						NA		NA									NA						CCGGGCTAGGGAAGGTCCAGG	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16973855G>A		NA		hg19		0.02	6.216708	AGGxAAG	COVERED																																																																																			NOVEL					0			5	6.186538	KEEP	44	8	252	109	3693	GG	1	1	0			10	49	363	0	0	24.692591	155	50	5784	383		0.060606	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16974312	16974312	__UNKNOWN__	IGR	SNP	G	G	C	rs368199873		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16974312G>C			NA	NA				CROCCP2 (13258 upstream) : RNU1-3 (18967 downstream)						NA		NA									NA						GAGGCCACAAGTGTCAGCTGC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16974312G>C		NA		hg19		0.02	8.378609	CAAxTGT	COVERED																																																																																			NOVEL					0			0	2.490252	KEEP	4	5	183	72	2577	GG	1	1	0			16	42	571	0	0	39.778222	206	60	7730	338		0.072072	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16974511	16974511	__UNKNOWN__	IGR	SNP	G	G	A	rs58679574	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16974511G>A			NA	NA				CROCCP2 (13457 upstream) : RNU1-3 (18768 downstream)						NA		NA									NA						GGGTAGTCACGGGCTTAGGGC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16974511G>A		NA		hg19		0.02	18.104773	CACxGGC	COVERED																																																																																			NOVEL					0			8	4.654697	KEEP	4	19	519	199	6666	GG	1	1	0			27	60	980	0	0	68.995614	348	60	12310	758		0.072	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16975289	16975289	__UNKNOWN__	IGR	SNP	T	T	A	rs200220176		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16975289T>A			NA	NA				CROCCP2 (14235 upstream) : RNU1-3 (17990 downstream)						NA		NA									NA						CCCCCCCAGGTTAGGAGTTGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16975289T>A		NA		hg19		0.02	36.841051	AGGxTAG	COVERED																																																																																			NOVEL					0			6	30.314732	KEEP	89	32	922	426	13107	TT	1	1	0			39	49	1435	0	0	93.987088	784	60	27852	1613		0.047388	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16976896	16976896	__UNKNOWN__	IGR	SNP	A	A	G	rs374493848		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16976896A>G			NA	NA				CROCCP2 (15842 upstream) : RNU1-3 (16383 downstream)						NA		NA									NA						aaacagtaataaagaagagaa	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16976896A>G		NA		hg19		0.02	31.54191	AATxAAG	COVERED																																																																																			NOVEL					0			10	19.325043	KEEP	10	2	74	90	2713	AA	1	1	0			34	49	1284	0	0	85.255223	681	60	24730	984		0.047552	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16977482	16977482	__UNKNOWN__	IGR	SNP	T	T	C	rs397834305		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16977482T>C			NA	NA				CROCCP2 (16428 upstream) : RNU1-3 (15797 downstream)						NA		NA									NA						AAATAAATTATTTGTCCTCTG	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16977482T>C		NA		hg19		0.02	39.273807	TTAxTTG	COVERED																																																																																			NOVEL					0			7	36.592923	KEEP	49	6	195	190	5878	TT	1	1	0			37	60	1407	0	0	92.690756	793	60	29251	1251		0.044578	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16978054	16978054	__UNKNOWN__	IGR	SNP	T	T	G	rs201137396		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:16978054T>G			NA	NA				CROCCP2 (17000 upstream) : RNU1-3 (15225 downstream)						NA		NA									NA						CATCTGAGAGTGGGCTTCCTT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16978054T>G		NA		hg19		0.02	42.285603	GAGxGGG	COVERED																																																																																			NOVEL					0			16	39.597045	KEEP	53	13	389	268	8030	TT	1	1	0			63	49	2255	0	0	157.443119	815	60	28693	1393		0.071754	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17077100	17077100	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17077100G>C			NA	NA				RNU1-4 (9926 upstream) : MST1L (4304 downstream)						NA		NA									NA						GTGGGTGCCAGGGTGGGGCAG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17077100G>C		NA		hg19		0.02	-0.280744	CCAxGGT	COVERED																																																																																			NOVEL					0			0	3.147226	KEEP	18	1	39	24	868	GG	0.999869	0.739575	0			5	49	169	0	0	13.263412	27	50	1031	95		0.15625	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17077171	17077171	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17077171G>A			NA	NA				RNU1-4 (9997 upstream) : MST1L (4233 downstream)						NA		NA									NA						CACCCAGGACGCAGAGCACAG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17077171G>A		NA		hg19		0.02	-0.429749	GACxCAG	COVERED																																																																																			NOVEL					0			2	7.825461	KEEP	8	0	0	26	914	GG	0.999931	0.954425	0			5	49	173	0	0	12.675253	44	50	1537	104		0.102041	0.954491
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17083031	17083031	__UNKNOWN__	RNA	SNP	A	A	C	rs1759201	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17083031A>C	ENST00000455405.2	-	0	1557							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						TAGGCATCCCATTGTCAGTCT	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17083031A>C		NA	B7WPB1|Q13209	hg19		0.02	24.064228	CCCxTTG	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	7	7.799977	KEEP	105	5	175	87	2749	AA	1	1	0		-	26	37	957	0	0	61.813011	565	60	21177	991	ENST00000455405.2	0.043993	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17083919	17083919	__UNKNOWN__	RNA	SNP	G	G	A	rs143067724	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17083919G>A	ENST00000455405.2	-	0	700							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						TGAGGGCCCCGGGCCACAGCA	0.572	NA	NA											.|||	668	0.133387	0.1989	0.0908	5008	,	,	NA	54748	0.006	NA	0.1889	False	NA	,,,	NA	NA	NA	2504	0.1493	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17083919G>A		NA	B7WPB1|Q13209	hg19		0.02	4.340628	CCCxGGC	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	6	2.640618	KEEP	39	1	26	18	564	GG	0.999859	0.999857	0		-	7	40	246	0	0	16.716876	100	50	3372	194	ENST00000455405.2	0.065421	0.999998
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17084021	17084021	__UNKNOWN__	RNA	SNP	C	C	G	rs2446543	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17084021C>G	ENST00000455405.2	-	0	691							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.A634P(1)			NA						ACCTCACAGGCCCCCACAGGG	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	kidney(1)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17084021C>G		NA	B7WPB1|Q13209	hg19		0.02	11.670918	AGGxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	.	9.021	0.984781	0.18889	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41938	D	0.000787	T	0.57431	0.2053	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.61426	-0.7065	6	0.15499	T	0.54	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	rs2446543	634;660	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	P	634;660	.	ENSP00000439273:A634P	A	-	1	0	MST1P9	16956608	0.997000	0.39634	0.867000	0.34043	0.000000	0.00434	4.380000	0.59581	0.502000	0.28037	0.000000	0.15137	GCC	NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	4	7.56448	KEEP	66	4	131	71	2452	CC	1	1	0		-	39	50	1350	0	0	105.223483	231	50	8420	424	ENST00000455405.2	0.144444	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17085028	17085028	__UNKNOWN__	RNA	SNP	G	G	A	rs2761534		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17085028G>A	ENST00000455405.2	-	0	160							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.R483C(1)|p.R452C(1)			NA						AGCTTGGAACGACGCTGATCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17085028G>A		NA	B7WPB1|Q13209	hg19		0.02	20.065143	AACxACG	COVERED	.	.	.	.	.	.	.	.	.	.	.	9.858	1.195618	0.22037	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);	.	.	.	.	T	0.40956	0.1138	.	.	.	.	.	.	D;D	0.67145	0.996;0.981	P;P	0.53549	0.729;0.613	T	0.44221	-0.9342	5	0.39692	T	0.17	.	2.6507	0.04998	0.5:0.0:0.5:0.0	rs2761534;rs3882324;rs3981970;rs3982159	483;483	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	C	452;483;483	.	ENSP00000439273:R483C	R	-	1	0	MST1P9	16957615	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.159000	0.16442	-0.000000	0.14550	0.000000	0.15137	CGT	NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	6	25.22774	KEEP	26	19	503	262	8550	GG	1	1	0		-	16	45	571	0	0	33.486896	522	60	17557	1085	ENST00000455405.2	0.02974	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17087530	17087530	__UNKNOWN__	IGR	SNP	C	C	T	rs200218107	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17087530C>T			NA	NA				MST1L (2163 upstream) : RP11-108M9.1 (90285 downstream)						NA		NA									NA						CGGGCACCACCGCATGTAGCA	0.632	NA	NA											.|||	131	0.0261581	0.0106	0.0389	5008	,	,	NA	50160	0	NA	0.0646	False	NA	,,,	NA	NA	NA	2504	0.0256	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17087530C>T		NA		hg19		0.02	23.118681	CACxGCA	COVERED																																																																																			NOVEL					0			2	85.603518	KEEP	17	1	15	290	9763	CC	1	1	0			36	49	1383	0	0	99.863408	447	60	15664	1030		0.074534	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17197409	17197409	__UNKNOWN__	IGR	SNP	G	G	A	rs201203798		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17197409G>A			NA	NA				RP11-108M9.2 (11630 upstream) : U1 (2793 downstream)						NA		NA									NA						CCATTGTGTCGGCTTTGTCTG	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17197409G>A		NA		hg19		0.02	1.842691	GTCxGCT	COVERED																																																																																			NOVEL					0			2	3.009232	KEEP	14	0	0	10	317	GG	0.99257	0.992195	0			4	39	142	0	0	9.194124	77	60	2468	109		0.049383	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17197685	17197685	__UNKNOWN__	IGR	SNP	G	G	A	rs7513766		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:17197685G>A			NA	NA				RP11-108M9.2 (11906 upstream) : U1 (2517 downstream)						NA		NA									NA						GGGCCTGGGCGTCTCTGGAGC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17197685G>A		NA		hg19		0.02	21.20457	GGCxTCT	COVERED																																																																																			NOVEL					0			6	8.221813	KEEP	7	16	461	190	6505	GG	1	1	0			71	60	2553	0	0	231.757251	134	60	4764	843		0.346341	1
ALDH4A1	8659	__UNKNOWN__	__UNKNOWN__	1	19199156	19199156	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:19199156G>A	ENST00000375341.3	-	0	2132				RP13-279N23.2_ENST00000494072.3_Intron|ALDH4A1_ENST00000290597.5_Intron|ALDH4A1_ENST00000538839.1_3'UTR|ALDH4A1_ENST00000538309.1_3'UTR	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	NA		NA			4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TCCCCAGCACGATCTCAAACC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	8659	1.5.1.12	Aldehyde dehydrogenases	406	protein-coding gene	gene with protein product		606811		ALDH4	NA	8621661	Standard		NM_003748	NA	Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.*183C>T	chr1.hg19:g.19199156G>A		NA	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	hg19	CCDS188.1	0.02	6.838587	CACxATC	COVERED																																																																																			NOVEL	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006954.1	2	5.250337	KEEP	0	1	27	27	934	GG	0.999997	0.999997	0		-	11	60	399	0	0	28.040671	140	60	5183	218	ENST00000375341.3	0.072848	1
RAP1GAP	5909	__UNKNOWN__	__UNKNOWN__	1	21935901	21935901	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:21935901T>G	ENST00000374765.4	-	15	1272				RAP1GAP_ENST00000290101.4_Intron|RAP1GAP_ENST00000374761.2_Intron|RAP1GAP_ENST00000374763.2_Intron|RAP1GAP_ENST00000542643.2_Intron	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	NA		NA			GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		AAAAAAAAGGTGTTTTCAAGA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864	5909			9858	protein-coding gene	gene with protein product		600278	RAP1, GTPase activating protein 1	RAP1GA1	NA	1904317	Standard	NM_002885	NM_001145657	NA	Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1071+166A>C	chr1.hg19:g.21935901T>G		NA	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	hg19	CCDS218.1	0.02	1.761166	AGGxGTT	COVERED																																																																																			NOVEL	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019759.2	2	3.587638	KEEP	0	0	0	12	264	TT	0.993634	0.991202	0		-	22	60	402	0	0	31.551102	49	60	1195	115	ENST00000374765.4	0.309859	0.997553
CELA3A	10136	__UNKNOWN__	__UNKNOWN__	1	22332008	22332008	__UNKNOWN__	Silent	SNP	T	T	C	rs56968853		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:22332008T>C	ENST00000290122.3	+	3	217	c.198T>C	c.(196-198)gaT>gaC	p.D66D	CELA3A_ENST00000374663.1_Silent_p.D66D	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	66	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCGCCCCCGATTGGGTTGTGA	0.617	NA	NA									OREG0013211	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						81	95	90	NA		NA	NA	1		NA											NA				22332008		2197	4300	6497	SO:0001819	synonymous_variant			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789	10136			15944	protein-coding gene	gene with protein product	protease E	NA	elastase 3A, pancreatic (protease E), elastase 3A, pancreatic	ELA3A	NA	2826474, 2460440	Standard	NM_005747	NM_005747	NA	Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.198T>C	chr1.hg19:g.22332008T>C		755	B1AQ53|Q9BRW4	hg19	CCDS220.1	0.02	4.564329	CGAxTGG	COVERED																																																																																			NOVEL	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007791.1	1	8.714701	KEEP	0	0	0	29	801	TT	0.999997	0.999997	0		+	5	49	199	0	0	12.951715	133	60	4773	199	ENST00000290122.3	0.036232	1
CELA3A	10136	__UNKNOWN__	__UNKNOWN__	1	22332608	22332608	__UNKNOWN__	Intron	SNP	T	T	A	rs77328205		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:22332608T>A	ENST00000290122.3	+	4	381					NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	NA		NA			cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCTTCCCCCATATCCGAGGGT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789	10136			15944	protein-coding gene	gene with protein product	protease E	NA	elastase 3A, pancreatic (protease E), elastase 3A, pancreatic	ELA3A	NA	2826474, 2460440	Standard	NM_005747	NM_005747	NA	Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.362+319T>A	chr1.hg19:g.22332608T>A		NA	B1AQ53|Q9BRW4	hg19	CCDS220.1	0.02	8.102027	CCAxATC	COVERED																																																																																			NOVEL	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007791.1	1	8.117816	KEEP	1	0	0	27	755	TT	0.999988	0.999988	0		+	7	39	249	0	0	14.978492	199	60	7103	299	ENST00000290122.3	0.033981	1
CELA3A	10136	__UNKNOWN__	__UNKNOWN__	1	22332610	22332610	__UNKNOWN__	Intron	SNP	T	T	G	rs76694312		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:22332610T>G	ENST00000290122.3	+	4	381					NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	NA		NA			cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTCCCCCATATCCGAGGGTTT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789	10136			15944	protein-coding gene	gene with protein product	protease E	NA	elastase 3A, pancreatic (protease E), elastase 3A, pancreatic	ELA3A	NA	2826474, 2460440	Standard	NM_005747	NM_005747	NA	Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.362+321T>G	chr1.hg19:g.22332610T>G		NA	B1AQ53|Q9BRW4	hg19	CCDS220.1	0.02	8.891347	ATAxCCG	COVERED																																																																																			NOVEL	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007791.1	1	7.821864	KEEP	1	0	0	26	794	TT	0.999957	0.999957	0		+	7	39	260	0	0	16.061468	200	60	7162	300	ENST00000290122.3	0.033816	1
BSDC1	55108	__UNKNOWN__	__UNKNOWN__	1	32846897	32846897	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:32846897G>A	ENST00000455895.2	-	5	391				BSDC1_ENST00000419121.2_Intron|BSDC1_ENST00000449308.1_Intron|BSDC1_ENST00000341071.7_Intron|BSDC1_ENST00000526031.1_Intron|BSDC1_ENST00000446293.2_Intron|BSDC1_ENST00000413080.1_Intron	NM_001143888.1|NM_018045.6	NP_001137360.1|NP_060515.3	Q9NW68	BSDC1_HUMAN	BSD domain containing 1	NA		NA								breast(1)|central_nervous_system(2)|kidney(1)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GAGGAAAACAGAAATTCTGAG	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						46	47	47	NA		NA	NA	1		NA											NA				32846897		2203	4300	6503	SO:0001627	intron_variant			BX641056	CCDS363.2, CCDS44101.1, CCDS44102.1, CCDS44103.1, CCDS72752.1	1p35.1	2008-02-05			ENSG00000160058	ENSG00000160058	55108			25501	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018045	XM_005270985	NA	Approved	FLJ10276, RP4-811H24.7	uc010ohg.2	Q9NW68	OTTHUMG00000007588	ENST00000455895.2:c.358-28C>T	chr1.hg19:g.32846897G>A		NA	B4DMS7|B4DTI7|B4DTP7|B4E2X8|Q49AT8|Q68DY6|Q6IAA3|Q6MZK1|Q6UXS1|Q9HAL9	hg19	CCDS363.2	0.02	2.2261	ACAxAAA	COVERED																																																																																			NOVEL	BSDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020056.3	0	6.019348	KEEP	0	0	0	20	717	GG	0.999863	0.992789	0		-	9	60	330	0	0	26.007945	55	60	2097	112	ENST00000455895.2	0.140625	0.992926
AK2	204	__UNKNOWN__	__UNKNOWN__	1	33475556	33475556	__UNKNOWN__	3'UTR	SNP	A	A	C	rs201880820		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:33475556A>C	ENST00000373449.2	-	0	1614				RP1-117O3.2_ENST00000427524.1_RNA	NM_001199199.1|NM_013411.4	NP_001186128.1|NP_037543.1			adenylate kinase 2	NA		NA								kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TTTAGGGGCCAAACAAGGCAG	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	204	2.7.4.3	Adenylate kinases	362	protein-coding gene	gene with protein product		103020			NA	8843353, 6961883	Standard	NM_001625	NM_013411	NA	Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000373449.2:c.*874T>G	chr1.hg19:g.33475556A>C		NA		hg19	CCDS373.1	0.02	2.038978	GCCxAAC	COVERED																																																																																			NOVEL	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011884.1	2	3.610234	KEEP	5	0	0	12	360	AA	0.993634	0.991846	0		-	5	40	174	0	0	11.903832	67	60	2397	98	ENST00000373449.2	0.069444	0.9982
SFPQ	6421	__UNKNOWN__	__UNKNOWN__	1	35652686	35652686	__UNKNOWN__	Silent	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:35652686T>C	ENST00000357214.5	-	9	2000	c.1902A>G	c.(1900-1902)ctA>ctG	p.L634L		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	634		NA			alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				CACCACCTCCTAGAGGTGGAA	0.443	NA	NA	T	TFE3	papillary renal cell									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	0							NA						101	95	97	NA		NA	NA	1		NA											NA				35652686		2203	4300	6503	SO:0001819	synonymous_variant			X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560	6421		RNA binding motif (RRM) containing	10774	protein-coding gene	gene with protein product	polypyrimidine tract binding protein associated, protein phosphatase 1, regulatory subunit 140	605199	splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)		NA	8449401	Standard	NM_005066	NM_005066	NA	Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.1902A>G	chr1.hg19:g.35652686T>C		NA	P30808|Q5SZ71	hg19	CCDS388.1	0.02	4.74339	TCCxAGA	COVERED																																																																																			NOVEL	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011984.4	2	7.517742	KEEP	0	0	0	25	714	TT	0.999931	0.999931	0		-	6	60	227	0	0	15.02828	123	60	4515	167	ENST00000357214.5	0.046512	1
RIMS3	9783	__UNKNOWN__	__UNKNOWN__	1	41086730	41086730	__UNKNOWN__	3'UTR	SNP	C	C	T	rs148341793	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:41086730C>T	ENST00000372684.3	-	0	6855					NM_014747.2	NP_055562.2	Q9UJD0	RIMS3_HUMAN	regulating synaptic membrane exocytosis 3	NA		NA			calcium ion-dependent exocytosis (GO:0017156)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.47e-17)			GAAGCAGCTGCCCCACCTTCT	0.448	NA	NA											C|||	8	0.00159744	0	0.0043	5008	,	,	NA	21322	0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC003103	CCDS30687.1	1p34.2	2013-09-19			ENSG00000117016	ENSG00000117016	9783			21292	protein-coding gene	gene with protein product		611600			NA	12620390, 10748113	Standard	NM_014747	NM_014747	NA	Approved	RIM3, NIM3	uc001cfu.1	Q9UJD0	OTTHUMG00000007453	ENST00000372684.3:c.*5459G>A	chr1.hg19:g.41086730C>T		NA	D3DPV8|Q92511|X5D7U7	hg19	CCDS30687.1	0.02	2.047327	CTGxCCC	COVERED																																																																																			NOVEL	RIMS3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019585.1	2	2.407815	KEEP	0	0	0	8	280	CC	0.99257	0.990484	0		-	47	60	1675	0	0	169.276267	26	60	973	93	ENST00000372684.3	0.643836	0.997898
CYP4B1	1580	__UNKNOWN__	__UNKNOWN__	1	47265000	47265000	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:47265000A>G	ENST00000371919.4	+	1	180				CYP4B1_ENST00000271153.4_Intron|CYP4B1_ENST00000546128.1_Intron|CYP4B1_ENST00000371923.4_Intron			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	NA		NA			biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	AATCAGGCCTAATTCCCAGGG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973	1580		Cytochrome P450s	2644	protein-coding gene	gene with protein product		124075	cytochrome P450, subfamily IVB, polypeptide 1		NA		Standard	NM_000779	NM_000779	NA	Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000371919.4:c.180+67A>G	chr1.hg19:g.47265000A>G		NA	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	hg19	CCDS542.1	0.02	5.288521	CCTxATT	COVERED																																																																																			NOVEL	CYP4B1-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021913.2	1	5.7127	KEEP	0	0	0	19	525	AA	0.99986	0.999828	0		+	18	60	665	0	0	54.53544	83	60	2949	144	ENST00000371919.4	0.178218	0.999968
TTC39A	22996	__UNKNOWN__	__UNKNOWN__	1	51778588	51778588	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:51778588C>T	ENST00000262676.5	-	3	325	c.165G>A	c.(163-165)ctG>ctA	p.L55L	TTC39A_ENST00000413473.2_Silent_p.L62L|TTC39A_ENST00000371750.5_Silent_p.L59L|TTC39A_ENST00000262675.7_Silent_p.L31L|TTC39A_ENST00000447632.2_Silent_p.L59L|TTC39A_ENST00000371747.3_Silent_p.L58L|TTC39A_ENST00000451380.1_Silent_p.L58L			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	59		NA						p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						TGGCATATGTCAGTGAGTGGT	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)					NA						265	262	263	NA		NA	NA	1		NA											NA				51778588		2132	4243	6375	SO:0001819	synonymous_variant			AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831	22996		Tetratricopeptide (TTC) repeat domain containing	18657	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 34	C1orf34	NA	9455484, 9461476	Standard		XM_005270643	NA	Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000262676.5:c.165G>A	chr1.hg19:g.51778588C>T		NA	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	hg19		0.02	4.865912	TGTxAGT	COVERED																																																																																			NOVEL	TTC39A-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000022432.2	0	9.932341	KEEP	0	0	0	33	1167	CC	0.999998	0.999994	0		-	39	60	1440	0	0	130.621234	76	60	2911	195	ENST00000262676.5	0.33913	0.999997
ACOT11	26027	__UNKNOWN__	__UNKNOWN__	1	55014160	55014160	__UNKNOWN__	Intron	SNP	C	C	T	rs299872	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:55014160C>T	ENST00000343744.2	+	1	115				ACOT11_ENST00000371316.3_Intron|ACOT11_ENST00000481208.1_Intron	NM_147161.3	NP_671517.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	NA		NA			fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						AAGGAGAAATCGCAGAACCCC	0.517	NA	NA											C|||	3150	0.628994	0.2163	0.7983	5008	,	,	NA	15358	0.756	NA	0.7256	False	NA	,,,	NA	NA	NA	2504	0.8364	NA	NA	NA	Ovarian(148;1440 1861 22015 32453 51933)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	26027	3.1.2.-	Acyl CoA thioesterases, StAR-related lipid transfer (START) domain containing	18156	protein-coding gene	gene with protein product	StAR-related lipid transfer (START) domain containing 14	606803	thioesterase, adipose associated	THEA	NA	11696000, 16103133, 16940157	Standard	NM_015547	NM_015547	NA	Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000343744.2:c.33+145C>T	chr1.hg19:g.55014160C>T		NA	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	hg19	CCDS593.1	0.02	-0.385973	AATxGCA	COVERED																																																																																			NOVEL	ACOT11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027351.1	0	5.416261	KEEP	0	0	0	18	577	CC	0.999859	0.918042	0		+	9	60	349	0	0	31.559361	19	60	632	82	ENST00000343744.2	0.321429	0.918171
LRRC7	57554	__UNKNOWN__	__UNKNOWN__	1	70504368	70504368	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:70504368C>T	ENST00000035383.5	+	19	2777	c.2747C>T	c.(2746-2748)cCg>cTg	p.P916L	LRRC7_ENST00000310961.5_Missense_Mutation_p.P921L|LRRC7_ENST00000415775.2_Missense_Mutation_p.P200L	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	916		NA				cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CACTGCCGCCCGGAATCTTCT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						53	52	52	NA		NA	NA	1		NA											NA				70504368		2203	4300	6503	SO:0001583	missense				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122	57554			18531	protein-coding gene	gene with protein product		614453			NA	12525888	Standard	NM_020794	NM_020794	NA	Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2747C>T	chr1.hg19:g.70504368C>T	ENSP00000035383:p.Pro916Leu	NA	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	hg19	CCDS645.1	0.02	12.721055	GCCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.21	1.869317	0.32977	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000415775;ENST00000370957	T;T;T	0.37411	1.2;1.27;2.37	5.67	5.67	0.87782	.	0.197539	0.45606	D	0.000346	T	0.31420	0.0796	L	0.47716	1.5	0.52501	D	0.999957	D;P;P	0.58620	0.983;0.938;0.897	B;P;B	0.46510	0.41;0.519;0.32	T	0.08411	-1.0723	10	0.62326	D	0.03	.	18.7487	0.91804	0.0:1.0:0.0:0.0	.	200;916;916	F8WE45;Q96NW7-2;Q96NW7	.;.;LRRC7_HUMAN	L	921;916;200;739	ENSP00000309245:P921L;ENSP00000035383:P916L;ENSP00000394867:P200L	ENSP00000035383:P916L	P	+	2	0	LRRC7	70276956	1.000000	0.71417	0.995000	0.50966	0.271000	0.26615	4.256000	0.58810	2.686000	0.91538	0.467000	0.42956	CCG	NOVEL	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131261.1	3	16.251884	KEEP	0	0	0	54	1835	CC	1	1	0		+	15	60	588	0	0	40.954498	249	60	8722	400	ENST00000035383.5	0.056818	1
LPHN2	23266	__UNKNOWN__	__UNKNOWN__	1	81969189	81969189	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:81969189A>T	ENST00000370728.1	+	2	398				LPHN2_ENST00000370727.1_Intron|LPHN2_ENST00000370723.1_Intron|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370725.1_Intron|LPHN2_ENST00000370730.1_Intron|LPHN2_ENST00000370721.1_Intron			O95490	LPHN2_HUMAN	latrophilin 2	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		GCCACTCTCCAGTCGAGAGTG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114	23266		-, GPCR / Class B : Orphans	18582	protein-coding gene	gene with protein product		607018	latrophilin 1	LPHH1	NA	10760572	Standard	NM_012302	XR_248786	NA	Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.-248+58415A>T	chr1.hg19:g.81969189A>T		NA	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	hg19		0.02	6.584325	TCCxGTC	COVERED																																																																																			NOVEL	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000027188.1	2	4.178728	KEEP	13	5	145	65	2011	AA	1	1	0		+	7	27	254	0	0	15.914979	172	60	6482	320	ENST00000370728.1	0.039106	1
RBMXL1	494115	__UNKNOWN__	__UNKNOWN__	1	89448623	89448623	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs141468346		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:89448623A>G	ENST00000321792.5	-	2	1314	c.887T>C	c.(886-888)cTt>cCt	p.L296P	CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.L296P|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	296	Ser-rich.	NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)				NA						CCCTCGTGTAAGTGGAGCACT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						179	176	177	NA		NA	NA	1		NA											NA				89448623		2203	4300	6503	SO:0001583	missense			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516	494115		RNA binding motif (RRM) containing	25073	protein-coding gene	gene with protein product	kynurenine aminotransferase III	NA			NA	10441733	Standard	NM_019610	NM_019610	NA	Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.887T>C	chr1.hg19:g.89448623A>G	ENSP00000318415:p.Leu296Pro	NA		hg19	CCDS716.1	0.02	2.455606	GTAxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.070	-1.203792	0.01581	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.71461	-0.57;-0.57	1.89	0.914	0.19360	.	0.000000	0.85682	N	0.000000	T	0.07279	0.0184	N	0.00075	-2.25	0.41802	D	0.989928	B	0.02656	0.0	B	0.01281	0.0	T	0.44817	-0.9303	10	0.02654	T	1	-8.7659	6.5352	0.22350	0.1727:0.0:0.8273:0.0	.	296	Q96E39	RBMXL_HUMAN	P	296	ENSP00000318415:L296P;ENSP00000446099:L296P	ENSP00000318415:L296P	L	-	2	0	RBMXL1	89221211	1.000000	0.71417	0.995000	0.50966	0.881000	0.50899	4.582000	0.60957	0.129000	0.18514	-0.814000	0.03130	CTT	NOVEL	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029403.3	7	2.406935	KEEP	0	0	0	8	243	AA	0.99257	0.990141	0		-	6	49	239	0	0	17.794839	66	60	2448	83	ENST00000321792.5	0.083333	0.997553
RBMXL1	494115	__UNKNOWN__	__UNKNOWN__	1	89449399	89449399	__UNKNOWN__	Silent	SNP	T	T	C	rs77567101	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:89449399T>C	ENST00000321792.5	-	2	538	c.111A>G	c.(109-111)gtA>gtG	p.V37V	CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000399794.2_Silent_p.V37V|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	37	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)				NA						TTATCAAGAGTACTTCCACTA	0.428	NA	NA									OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	T	,,,	1667,2739		0,1667,536	209	198	202	NA	,,111,111	0.4	1	1	dbSNP_131	202	2526,6074		0,2526,1774	no	intron,intron,coding-synonymous,coding-synonymous	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,,	0,4193,2310	CC,CT,TT	NA	29.3721,37.8348,32.239	,,,	,,37/391,37/391	89449399	4193,8813	2203	4300	6503	SO:0001819	synonymous_variant			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516	494115		RNA binding motif (RRM) containing	25073	protein-coding gene	gene with protein product	kynurenine aminotransferase III	NA			NA	10441733	Standard	NM_019610	NM_019610	NA	Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.111A>G	chr1.hg19:g.89449399T>C		1267		hg19	CCDS716.1	0.02	2.587332	GAGxACT	COVERED																																																																																			NOVEL	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029403.3	2	2.83841	KEEP	1	1	30	20	544	TT	0.999869	0.984032	0		-	4	40	166	0	0	12.420396	47	60	1562	80	ENST00000321792.5	0.078431	0.984161
RBMXL1	494115	__UNKNOWN__	__UNKNOWN__	1	89449434	89449434	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs2893084	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:89449434T>C	ENST00000321792.5	-	2	503	c.76A>G	c.(76-78)Aca>Gca	p.T26A	CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.T26A|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	26	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)				NA						CCAAATACTGTTTCAAGAGCT	0.413	NA	NA									OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						184	183	183	NA		NA	NA	1		NA											NA				89449434		2203	4300	6503	SO:0001583	missense			BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516	494115		RNA binding motif (RRM) containing	25073	protein-coding gene	gene with protein product	kynurenine aminotransferase III	NA			NA	10441733	Standard	NM_019610	NM_019610	NA	Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.76A>G	chr1.hg19:g.89449434T>C	ENSP00000318415:p.Thr26Ala	1267		hg19	CCDS716.1	0.02	2.27142	CTGxTTC	COVERED	.	.	.	.	.	.	.	.	.	.	T	3.554	-0.091124	0.07053	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.85171	-1.95;-1.95	1.28	-2.56	0.06268	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.275039	0.28382	N	0.015553	T	0.30885	0.0779	N	0.03224	-0.385	0.20873	N	0.999835	B	0.02656	0.0	B	0.06405	0.002	T	0.49818	-0.8899	10	0.02654	T	1	7.3308	6.0529	0.19794	0.0:0.6607:0.0:0.3393	rs2893084	26	Q96E39	RBMXL_HUMAN	A	26	ENSP00000318415:T26A;ENSP00000446099:T26A	ENSP00000318415:T26A	T	-	1	0	RBMXL1	89222022	1.000000	0.71417	0.482000	0.27366	0.917000	0.54804	1.281000	0.33214	-0.855000	0.04125	-0.760000	0.03462	ACA	NOVEL	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029403.3	1	6.55294	KEEP	0	2	43	37	1038	TT	1	0.999894	0		-	12	40	431	0	0	33.670283	75	60	2641	144	ENST00000321792.5	0.137931	0.999895
CNN3	1266	__UNKNOWN__	__UNKNOWN__	1	95392286	95392286	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:95392286C>G	ENST00000370206.4	-	1	441				CNN3_ENST00000538964.1_Intron|CNN3_ENST00000394202.4_Intron	NM_001839.3	NP_001830.1	Q15417	CNN3_HUMAN	calponin 3, acidic	NA		NA			actomyosin structure organization (GO:0031032)|epithelial cell differentiation (GO:0030855)	focal adhesion (GO:0005925)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(1)|stomach(1)|urinary_tract(2)	18		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		CGGCCCCTCTCCAGGAAAACG	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC025372	CCDS30775.1, CCDS65592.1, CCDS65593.1	1p22-p21	2010-07-08			ENSG00000117519	ENSG00000117519	1266			2157	protein-coding gene	gene with protein product		602374			NA	8526917	Standard	NM_001839	NM_001839	NA	Approved		uc001dqz.4	Q15417	OTTHUMG00000010783	ENST00000370206.4:c.57+107G>C	chr1.hg19:g.95392286C>G		NA	B4DFK6|B4DP09|F8WA86|Q6FHA7	hg19	CCDS30775.1	0.02	2.044079	TCTxCAG	COVERED																																																																																			NOVEL	CNN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029702.2	2	24.640836	KEEP	0	0	0	82	2623	CC	1	0.990964	0		-	10	60	329	0	0	25.779968	52	60	1908	156	ENST00000370206.4	0.16129	0.990964
ALX3	257	__UNKNOWN__	__UNKNOWN__	1	110603166	110603166	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:110603166C>T	ENST00000369792.4	-	0	1308				RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	NA		NA			embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|pattern specification process (GO:0007389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(81;2.35e-05)|all_epithelial(167;7.69e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.015)|all cancers(265;0.0706)|Epithelial(280;0.0758)|Colorectal(144;0.113)|LUSC - Lung squamous cell carcinoma(189;0.135)		TTCGAAGCCCCTTCTCCTAGG	0.592	NA	NA									OREG0013648	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF008203	CCDS819.1	1p13.3	2014-02-04	2008-11-04		ENSG00000156150	ENSG00000156150	257		Homeoboxes / PRD class	449	protein-coding gene	gene with protein product		606014	aristaless-like homeobox 3, frontonasal dysplasia	FND	NA	15226305, 11807986, 19409524	Standard	NM_006492	NM_006492	NA	Approved		uc001dzb.3	O95076	OTTHUMG00000011650	ENST00000369792.4:c.*189G>A	chr1.hg19:g.110603166C>T		1428	O95075|Q5T8M4	hg19	CCDS819.1	0.02	4.590632	CCCxTTC	COVERED																																																																																			NOVEL	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032232.2	0	11.738426	KEEP	0	0	0	39	1393	CC	1	1	0		-	33	60	1200	0	0	103.26212	101	60	3754	211	ENST00000369792.4	0.246269	1
NRAS	4893	__UNKNOWN__	__UNKNOWN__	1	115251319	115251319	__UNKNOWN__	Intron	SNP	C	C	T	rs9724641	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:115251319C>T	ENST00000369535.4	-	5	704					NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)			NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTAGCTCAACGGACACAATC	0.333	NA	50	Mis		melanoma, MM, AML, thyroid				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			C|||	242	0.0483227	0.174	0.0173	5008	,	,	NA	20379	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA			Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		L, E	0							NA	C		739,3667	300.4+/-286.3	66,607,1530	65	60	61	NA		-1.8	0	1	dbSNP_119	61	4,8596	3.7+/-12.6	0,4,4296	no	intron	NRAS	NM_002524.4		66,611,5826	TT,TC,CC	NA	0.0465,16.7726,5.7127			115251319	743,12263	2203	4300	6503	SO:0001627	intron_variant	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281	4893			7989	protein-coding gene	gene with protein product		164790			NA		Standard	NM_002524	NM_002524	NA	Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.451-44G>A	chr1.hg19:g.115251319C>T		NA	Q14971|Q15104|Q15282	hg19	CCDS877.1	0.02	12.747895	CAAxGGA	COVERED																																																																																			NOVEL	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033395.2	48	10.531513	KEEP	0	0	0	35	1121	CC	0.999999	0.999999	0		-	16	60	529	0	0	32.584841	323	60	10145	418	ENST00000369535.4	0.047198	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120389857	120389857	__UNKNOWN__	IGR	SNP	T	T	C	rs78696614		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120389857T>C			NA	NA				REG4 (35574 upstream) : ADAM30 (46298 downstream)						NA		NA									NA						GGAACACTTTTCCTTTTTAGG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120389857T>C		NA		hg19		0.02	3.774628	TTTxCCT	COVERED																																																																																			NOVEL					0			1	5.412012	KEEP	5	0	0	18	483	TT	0.999859	0.999859	0			12	40	415	0	0	29.564457	125	60	4418	162		0.087591	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120389866	120389866	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120389866G>A			NA	NA				REG4 (35583 upstream) : ADAM30 (46289 downstream)						NA		NA									NA						TTCCTTTTTAGGGGTCTGTTC	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120389866G>A		NA		hg19		0.02	6.323363	TTAxGGG	COVERED																																																																																			NOVEL					0			1	5.357425	KEEP	5	1	14	23	792	GG	0.999909	0.999909	0			33	60	1125	0	0	90.49402	153	60	5651	230		0.177419	1
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120534283	120534283	__UNKNOWN__	Intron	SNP	C	C	T	rs201430695		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120534283C>T	ENST00000256646.2	-	5	971					NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	NA		NA			apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		aaccccatctctactaaaaat	0.517	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.752-4578G>A	chr1.hg19:g.120534283C>T		NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	6.378997	TCTxTAC	COVERED																																																																																			NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	9	2.806193	KEEP	14	3	90	41	1424	CC	1	1	0		-	35	27	1209	0	0	98.013495	157	50	5850	253	ENST00000256646.2	0.182292	1
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120535935	120535935	__UNKNOWN__	Intron	SNP	A	A	T	rs1690030		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120535935A>T	ENST00000256646.2	-	4	971				NOTCH2_ENST00000602566.1_3'UTR	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	NA		NA			apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		GATTTGATTCAATTAGTTCTC	0.338	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.751+3684T>A	chr1.hg19:g.120535935A>T		NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	29.745847	TTCxATT	COVERED																																																																																			NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	8	8.953542	KEEP	58	16	484	200	6041	AA	1	1	0		-	46	44	1647	0	0	112.200545	681	60	25142	1175	ENST00000256646.2	0.063274	1
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120590571	120590571	__UNKNOWN__	Intron	SNP	C	C	A	rs199848465		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120590571C>A	ENST00000256646.2	-	2	293				NOTCH2_ENST00000602566.1_Intron	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	NA		NA			apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		catttttttccgtagagacgg	0.537	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.74-17961G>T	chr1.hg19:g.120590571C>A		NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	-0.070184	TTCxGTA	UNCOVERED																																																																																			NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	2	2.407575	KEEP	0	0	0	8	264	CC	0.99257	0.053735	0		-	2	27	74	0	0	6.400598	6	60	206	17	ENST00000256646.2	0.25	0.054137
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120611960	120611960	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs2603926		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120611960C>T	ENST00000256646.2	-	1	280	c.61G>A	c.(61-63)Gcc>Acc	p.A21T		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	21		NA		A -> T (in Ref. 2; AAG37073). {ECO:0000305}.	apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCGCGGGGGCCGCGCAGCAC	0.766	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0							NA						6	8	8	NA		NA	NA	1		NA											NA				120611960		1705	3725	5430	SO:0001583	missense	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.61G>A	chr1.hg19:g.120611960C>T	ENSP00000256646:p.Ala21Thr	NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	2.106135	GGGxCGC	COVERED	338	0.15476190476190477	115	0.23373983739837398	62	0.1712707182320442	66	0.11538461538461539	95	0.12532981530343007	c	6.410	0.443770	0.12164	.	.	ENSG00000134250	ENST00000256646	T	0.57752	0.38	3.09	2.14	0.27477	.	.	.	.	.	T	0.07324	0.0185	N	0.01874	-0.695	0.18873	N	0.999985	B;B	0.18461	0.0;0.028	B;B	0.11329	0.0;0.006	T	0.40813	-0.9543	9	0.13470	T	0.59	.	6.5614	0.22489	0.0:0.8575:0.0:0.1425	.	21;21	Q6IQ50;Q04721	.;NOTC2_HUMAN	T	21	ENSP00000256646:A21T	ENSP00000256646:A21T	A	-	1	0	NOTCH2	120413483	0.972000	0.33761	0.995000	0.50966	0.349000	0.29174	0.433000	0.21477	0.641000	0.30601	0.184000	0.17185	GCC	NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	5	5.80209	KEEP	3	5	111	59	1933	CC	1	0.998993	0		-	14	40	398	0	0	30.625542	64	70	2287	181	ENST00000256646.2	0.179487	0.998993
NOTCH2	4853	__UNKNOWN__	__UNKNOWN__	1	120612034	120612034	__UNKNOWN__	5'UTR	SNP	T	T	G	rs201668322		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:120612034T>G	ENST00000256646.2	-	0	206					NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	NA		NA			apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCGGTCGCCTCCTCCTccgc	0.721	NA	NA	N, F, Mis		marginal zone lymphoma, DLBCL				Alagille Syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0							NA						4	6	5	NA		NA	NA	1		NA											NA				120612034		1749	3728	5477	SO:0001623	5_prime_UTR_variant	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250	4853		Ankyrin repeat domain containing	7882	protein-coding gene	gene with protein product		600275	Notch (Drosophila) homolog 2, Notch homolog 2 (Drosophila)		NA	7698746	Standard	NM_024408	NM_001200001	NA	Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.-14A>C	chr1.hg19:g.120612034T>G		NA	Q5T3X7|Q99734|Q9H240	hg19	CCDS908.1	0.02	1.681367	GCCxCCT	COVERED																																																																																			NOVEL	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033679.1	11	12.631915	KEEP	6	4	137	90	2546	TT	1	0.999881	0		-	17	39	531	0	0	42.556033	70	70	2528	248	ENST00000256646.2	0.195402	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121355222	121355222	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121355222A>G			NA	NA				RP11-344P13.1 (32900 upstream) : None (None downstream)						NA		NA									NA						cgaaatcctcagagaggtcca	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121355222A>G		NA		hg19		0.02	-0.289521	CTCxGAG	COVERED																																																																																			NOVEL					0			24	4.548234	KEEP	23	1	31	26	829	AA	0.994391	0.756619	0			3	60	105	0	0	9.278393	7	60	265	85		0.3	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121355250	121355250	__UNKNOWN__	IGR	SNP	T	T	G	rs202163559|rs545819298	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121355250T>G			NA	NA				RP11-344P13.1 (32928 upstream) : None (None downstream)						NA		NA									NA						acttgcagattctacaaaaag	0.388	NA	NA											.|||	280	0.0559105	0.0507	0.0403	5008	,	,	NA	59878	0.0506	NA	0.0915	False	NA	,,,	NA	NA	NA	2504	0.0429	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121355250T>G		NA		hg19		0.02	-0.254425	GATxCTA	COVERED																																																																																			NOVEL					0			18	2.542858	KEEP	18	1	36	21	658	TT	0.992708	0.663648	0			9	60	337	0	0	36.581715	1	22	36	72		0.9	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121359045	121359045	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121359045T>A			NA	NA				RP11-344P13.1 (36723 upstream) : None (None downstream)						NA		NA									NA						gtgacttgaatgcaatcatca	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121359045T>A		NA		hg19		0.02	-0.263205	GAAxGCA	UNCOVERED																																																																																			NOVEL					0			19	3.911885	KEEP	32	0	0	13	411	TT	0	0	0			2	27	86	0	0	6.827433	16	31	620	94		0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121483309	121483309	__UNKNOWN__	IGR	SNP	C	C	G	rs28857589		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121483309C>G			NA	NA				RP11-344P13.1 (160987 upstream) : None (None downstream)						NA		NA									NA						aaggaatgttcagctctgtga	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121483309C>G		NA		hg19		0.02	2.015781	GTTxAGC	COVERED																																																																																			NOVEL					0			17	5.718861	KEEP	22	0	0	19	689	CC	0.994391	0.994196	0			4	60	152	0	0	10.985053	48	60	1856	177		0.076923	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121483810	121483810	__UNKNOWN__	IGR	SNP	A	A	G	rs151286364		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121483810A>G			NA	NA				RP11-344P13.1 (161488 upstream) : None (None downstream)						NA		NA									NA						ctgctgtatcaaaaggaatct	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121483810A>G		NA		hg19		0.02	2.068184	ATCxAAA	COVERED																																																																																			NOVEL					0			3	5.416623	KEEP	7	0	0	18	569	AA	0.995343	0.994904	0			4	60	148	0	0	10.76842	43	60	1595	129		0.085106	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121483897	121483897	__UNKNOWN__	IGR	SNP	T	T	C	rs199621103		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121483897T>C			NA	NA				RP11-344P13.1 (161575 upstream) : None (None downstream)						NA		NA									NA						tgtgaagatatttccttttcc	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121483897T>C		NA		hg19		0.02	2.522367	ATAxTTC	COVERED																																																																																			NOVEL					0			7	6.018645	KEEP	22	0	0	20	641	AT	0.994391	0.974032	0			4	49	157	0	0	12.621753	24	60	873	118		0.142857	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485152	121485152	__UNKNOWN__	IGR	SNP	C	C	G	rs74189293|rs74222610|rs4092802|rs67605471	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121485152C>G			NA	NA				RP11-344P13.1 (162830 upstream) : None (None downstream)						NA		NA									NA						atcctttacacagagcagact	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485152C>G		NA		hg19		0.02	46.434996	ACAxAGA	COVERED																																																																																			NOVEL					0			214	4.715499	KEEP	22	62	2185	778	27418	CC	1	1	0			30	60	1141	0	0	79.305697	464	60	17752	1980		0.060729	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485318	121485318	__UNKNOWN__	IGR	SNP	T	T	G	rs1138166|rs6600659		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:121485318T>G			NA	NA				RP11-344P13.1 (162996 upstream) : None (None downstream)						NA		NA									NA						taacctttcttttcatagagc	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485318T>G		NA		hg19		0.02	43.952192	TCTxTTC	COVERED																																																																																			NOVEL					0			298	53.493289	KEEP	39	52	1773	797	24536	TT	1	1	0			40	60	1510	1	0	110.046049	447	60	16115	1984		0.082136	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142536715	142536715	__UNKNOWN__	IGR	SNP	T	T	C	rs11578605		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142536715T>C			NA	NA				None (None upstream) : RP11-417J8.1 (16577 downstream)						NA		NA									NA						tagaatggaatggaatggaat	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142536715T>C		NA		hg19		0.02	-0.157915	GAAxGGA	UNCOVERED																																																																																			NOVEL					0			18	2.406901	KEEP	19	0	0	8	239	TT	0	0	0			5	60	169	0	0	18.110591	1	60	36	56		0.833333	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142601524	142601524	__UNKNOWN__	IGR	SNP	G	G	T	rs200823855		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142601524G>T			NA	NA				RP11-417J8.2 (13291 upstream) : RP11-417J8.3 (17598 downstream)						NA		NA									NA						ggaggccaaggttggtggctc	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142601524G>T		NA		hg19		0.02	-0.078959	AAGxTTG	UNCOVERED																																																																																			NOVEL					0			3	2.708916	KEEP	1	0	0	9	323	GG	0.99257	0.076761	0			3	60	108	0	0	9.743421	6	60	221	21		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142601557	142601557	__UNKNOWN__	IGR	SNP	C	C	A	rs4847812	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142601557C>A			NA	NA				RP11-417J8.2 (13324 upstream) : RP11-417J8.3 (17565 downstream)						NA		NA									NA						gagctcaagaccagcctgatc	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142601557C>A		NA		hg19		0.02	-0.070183	AGAxCAG	UNCOVERED																																																																																			NOVEL					0			2	2.407572	KEEP	1	0	0	8	267	CC	0	0	0			5	60	183	0	0	18.387123	3	60	101	18		0.625	0.054137
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142634852	142634852	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142634852A>G	ENST00000610091.1	-	0	5682				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						agctcagaggagacctgcagt	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142634852A>G		NA		hg19		0.02	2.287524	AGGxGAC	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	2	3.008002	KEEP	0	0	0	10	300	AA	0.992708	0.974795	0		-	5	45	182	0	0	13.482649	46	60	1711	88	ENST00000610091.1	0.098039	0.981955
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142634865	142634865	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142634865G>A	ENST00000610091.1	-	0	5669				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						cctgcagtgggtagctccttt	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142634865G>A		NA		hg19		0.02	-0.412342	TGGxTAG	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	2	3.009749	KEEP	0	0	0	10	346	GG	0.992708	0.934874	0		-	5	45	195	0	0	15.283789	36	60	1342	69	ENST00000610091.1	0.121951	0.941741
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142693933	142693933	__UNKNOWN__	lincRNA	SNP	G	G	A	rs199895209		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142693933G>A	ENST00000610091.1	-	0	3506										NA		NA									NA						AAAGTGTAGAGCCAGTGAAAA	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142693933G>A		NA		hg19		0.02	4.346971	AGAxCCA	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	0	2.84404	KEEP	38	1	30	20	733	GG	0.99649	0.99649	0		-	18	47	652	0	0	51.021687	113	50	4359	254	ENST00000610091.1	0.137405	1
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142729698	142729698	__UNKNOWN__	lincRNA	SNP	G	G	A	rs9328999		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142729698G>A	ENST00000610091.1	-	0	82										NA		NA									NA						acaggcacccgccaccatgcc	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142729698G>A		NA		hg19		0.02	-0.105281	CCCxCCA	UNCOVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	3	2.708744	KEEP	3	0	0	9	311	GG	0.99257	0.138793	0		-	2	47	74	0	0	6.400538	6	60	227	26	ENST00000610091.1	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142796607	142796607	__UNKNOWN__	IGR	SNP	G	G	A	rs79595519	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142796607G>A			NA	NA				RP11-417J8.6 (66640 upstream) : RP11-423O2.5 (6616 downstream)						NA		NA									NA						ggatcacgaggtcaggagatc	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142796607G>A		NA		hg19		0.02	-0.228076	GAGxTCA	COVERED																																																																																			NOVEL					0			3	4.045996	KEEP	3	1	21	21	725	GT	0.999909	0.582877	0			5	60	151	0	0	11.95972	21	60	780	73		0.192308	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142799560	142799560	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142799560A>T			NA	NA				RP11-417J8.6 (69593 upstream) : RP11-423O2.5 (3663 downstream)						NA		NA									NA						TTTTCTCTCCATAGGGAGCTT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142799560A>T		NA		hg19		0.02	9.354065	TCCxTAG	COVERED																																																																																			NOVEL					0			6	4.373827	KEEP	6	2	67	38	1161	AA	1	1	0			16	52	575	0	0	39.966649	213	60	8006	361		0.069869	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142799568	142799568	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142799568C>T			NA	NA				RP11-417J8.6 (69601 upstream) : RP11-423O2.5 (3655 downstream)						NA		NA									NA						CCATAGGGAGCTTATAGCTTC	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142799568C>T		NA		hg19		0.02	9.582605	GAGxTTA	COVERED																																																																																			NOVEL					0			6	7.192167	KEEP	7	2	57	44	1608	CC	1	1	0			24	60	891	0	0	66.810798	213	60	8194	402		0.101266	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142799657	142799657	__UNKNOWN__	IGR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142799657T>G			NA	NA				RP11-417J8.6 (69690 upstream) : RP11-423O2.5 (3566 downstream)						NA		NA									NA						GCTATGAAGATTGCACACAGG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142799657T>G		NA		hg19		0.02	6.631622	AGAxTGC	COVERED																																																																																			NOVEL					0			2	4.571909	KEEP	11	2	74	41	1239	TT	1	1	0			7	24	257	1	0	16.317625	166	50	6005	288		0.040462	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142823851	142823851	__UNKNOWN__	IGR	SNP	G	G	T	rs61814349		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142823851G>T			NA	NA				RP11-423O2.5 (7847 upstream) : RP11-423O2.7 (127133 downstream)						NA		NA									NA						gggtttacaggaatgagccac	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142823851G>T		NA		hg19		0.02	-0.131597	CAGxAAT	COVERED																																																																																			NOVEL					0			2	3.310401	KEEP	1	0	0	11	378	GG	0.992708	0.227502	0			3	47	108	0	0	8.971757	12	48	432	37		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142868373	142868373	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142868373C>T			NA	NA				RP11-423O2.5 (52369 upstream) : RP11-423O2.7 (82611 downstream)						NA		NA									NA						gtggctcatgcctgtaatctg	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142868373C>T		NA		hg19		0.02	-0.193013	ATGxCTG	UNCOVERED																																																																																			NOVEL					0			0	2.407835	KEEP	14	0	0	8	281	CC	0	0	0			3	27	108	0	0	8.491441	18	27	670	45		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142868606	142868606	__UNKNOWN__	IGR	SNP	G	G	T	rs148605275		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142868606G>T			NA	NA				RP11-423O2.5 (52602 upstream) : RP11-423O2.7 (82378 downstream)						NA		NA									NA						actacagtctgggtgacagaa	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142868606G>T		NA		hg19		0.02	-0.193009	TCTxGGT	UNCOVERED																																																																																			NOVEL					0			0	2.708803	KEEP	2	0	0	9	316	GG	0	0	0			5	40	195	0	0	16.76505	17	50	609	38		0.227273	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142917423	142917423	__UNKNOWN__	IGR	SNP	T	T	G	rs144645959		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142917423T>G			NA	NA				RP11-423O2.5 (101419 upstream) : RP11-423O2.7 (33561 downstream)						NA		NA									NA						atgggggtgatgaagtccggc	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142917423T>G		NA		hg19		0.02	2.405213	TGAxGAA	UNCOVERED																																																																																			NOVEL					0			2	2.706644	KEEP	24	0	0	9	245	TT	0	0	0			11	52	388	0	0	32.108038	44	57	1569	95		0.2	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142917512	142917512	__UNKNOWN__	IGR	SNP	A	A	T	rs140057021		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142917512A>T			NA	NA				RP11-423O2.5 (101508 upstream) : RP11-423O2.7 (33472 downstream)						NA		NA									NA						gagtctgcaaagtccccaagc	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142917512A>T		NA		hg19		0.02	4.335021	CAAxGTC	COVERED																																																																																			NOVEL					0			3	10.531783	KEEP	129	0	0	35	1133	AA	0.99254	0.99254	0			7	27	256	0	0	17.835847	96	40	3520	336		0.067961	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142917549	142917549	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:142917549G>C			NA	NA				RP11-423O2.5 (101545 upstream) : RP11-423O2.7 (33435 downstream)						NA		NA									NA						atttgttggtgctcaaacaaa	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142917549G>C		NA		hg19		0.02	4.338611	GGTxCTC	COVERED																																																																																			NOVEL					0			2	2.679868	KEEP	124	2	66	32	1165	GG	0.993634	0.993634	0			6	27	200	0	0	12.674849	108	47	4014	356		0.052632	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119078	143119078	__UNKNOWN__	lincRNA	SNP	T	T	C	rs201036514		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143119078T>C	ENST00000412204.2	-	0	5409				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						TCCAGTGTCCTCTGGGTGTTT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119078T>C		NA		hg19		0.02	18.929348	TCCxCTG	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	10	25.250415	KEEP	208	5	169	143	4611	TT	1	1	0		-	25	46	889	0	0	59.472051	403	48	15078	1110	ENST00000412204.2	0.058411	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119202	143119202	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143119202A>G	ENST00000412204.2	-	0	5308				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						AAGGaaaagtagaaataagta	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119202A>G		NA		hg19		0.02	5.833051	AGTxGAA	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	1	7.047884	KEEP	42	1	30	34	937	AA	0.999998	0.999998	0		-	20	40	693	0	0	51.477668	162	46	5933	263	ENST00000412204.2	0.10989	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143185486	143185486	__UNKNOWN__	lincRNA	SNP	A	A	G	rs374199073		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143185486A>G	ENST00000412204.2	-	0	2503				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						CCAGGCCAACATTCTGGACAT	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143185486A>G		NA		hg19		0.02	-0.254424	AACxTTC	UNCOVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	0	3.9061	KEEP	34	0	0	13	360	AA	0	0	0		-	6	40	217	0	0	18.142243	23	40	855	87	ENST00000412204.2	0.206897	0.668523
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143188456	143188456	__UNKNOWN__	lincRNA	SNP	A	A	C	rs192025180		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143188456A>C	ENST00000412204.2	-	0	2503				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						GCCAGGGACCACATGAGGACT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143188456A>C		NA		hg19		0.02	2.361063	ACCxCAT	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	0	2.7082	KEEP	2	0	0	9	283	AA	0.99254	0.980573	0		-	6	47	214	0	0	16.135241	47	48	1730	92	ENST00000412204.2	0.113208	0.987943
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143188506	143188506	__UNKNOWN__	lincRNA	SNP	T	T	C	rs112091998		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143188506T>C	ENST00000412204.2	-	0	2503				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						AGTTTCTTGGTACCTCAGTGG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143188506T>C		NA		hg19		0.02	2.403052	TGGxACC	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	0	3.911013	KEEP	1	0	0	13	383	TT	0.994391	0.993389	0		-	5	47	189	0	0	13.339788	69	48	2408	128	ENST00000412204.2	0.067568	0.998993
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143189180	143189180	__UNKNOWN__	lincRNA	SNP	G	G	T	rs200239537		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143189180G>T	ENST00000412204.2	-	0	2503				RP11-782C8.3_ENST00000425124.1_lincRNA|RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						CAATAATACTGGTTTTCATTT	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143189180G>T		NA		hg19		0.02	2.28348	ACTxGTT	UNCOVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	3	2.708813	KEEP	24	0	0	9	314	GG	0	0	0		-	8	40	302	0	0	23.330334	60	40	2172	119	ENST00000412204.2	0.117647	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143237037	143237037	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143237037C>T			NA	NA				RP11-782C8.1 (3620 upstream) : RP11-435B5.3 (110932 downstream)						NA		NA									NA						TGCTGCCAAACAGGACCCAAA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143237037C>T		NA		hg19		0.02	9.129143	AAAxAGG	COVERED																																																																																			NOVEL					0			8	9.667146	KEEP	7	1	31	43	1597	CC	1	1	0			7	45	266	0	0	16.557525	207	60	8024	403		0.03271	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143264835	143264835	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143264835C>A			NA	NA				RP11-782C8.1 (31418 upstream) : RP11-435B5.3 (83134 downstream)						NA		NA									NA						gccagatatgctggtacaggc	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143264835C>A		NA		hg19		0.02	2.269967	ATGxTGG	COVERED																																																																																			NOVEL					0			6	2.443197	KEEP	14	1	31	19	713	CC	0.997832	0.984015	0			5	41	187	0	0	14.169349	42	48	1600	116		0.106383	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143264844	143264844	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143264844G>A			NA	NA				RP11-782C8.1 (31427 upstream) : RP11-435B5.3 (83125 downstream)						NA		NA									NA						gctggtacaggcctataatct	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143264844G>A		NA		hg19		0.02	2.131777	CAGxCCT	COVERED																																																																																			NOVEL					0			6	2.441215	KEEP	14	1	31	19	671	GG	0.997832	0.965327	0			4	42	147	0	0	10.830111	39	48	1455	105		0.093023	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143278802	143278802	__UNKNOWN__	IGR	SNP	C	C	T	rs539194249	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143278802C>T			NA	NA				RP11-782C8.1 (45385 upstream) : RP11-435B5.3 (69167 downstream)						NA		NA									NA						GCAGGGACGCCGACCTGCTGG	0.622	NA	NA											.|||	3	0.000599042	0	0	5008	,	,	NA	59110	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143278802C>T		NA		hg19		0.02	4.99235	CGCxGAC	COVERED																																																																																			NOVEL					0			4	10.091526	KEEP	7	3	98	68	2292	CC	1	0.999996	0			6	47	216	0	0	16.048312	53	50	1894	262		0.101695	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143283257	143283257	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143283257G>A			NA	NA				RP11-782C8.1 (49840 upstream) : RP11-435B5.3 (64712 downstream)						NA		NA									NA						TGGACTTGGAGCTCACAGCGT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143283257G>A		NA		hg19		0.02	1.980468	GGAxCTC	COVERED																																																																																			NOVEL					0			2	6.80939	KEEP	32	5	140	72	2560	GG	1	0.999881	0			12	40	434	0	0	33.905562	76	51	2887	250		0.136364	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143283645	143283645	__UNKNOWN__	IGR	SNP	A	A	C	rs74348929		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143283645A>C			NA	NA				RP11-782C8.1 (50228 upstream) : RP11-435B5.3 (64324 downstream)						NA		NA									NA						TCAGAAACTCAGGCTTAAGGG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143283645A>C		NA		hg19		0.02	2.613504	CTCxGGC	COVERED																																																																																			NOVEL					0			4	2.542335	KEEP	9	1	36	21	663	AA	0.999863	0.973832	0			12	45	408	0	0	36.232827	26	46	989	113		0.315789	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143283801	143283801	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143283801C>T			NA	NA				RP11-782C8.1 (50384 upstream) : RP11-435B5.3 (64168 downstream)						NA		NA									NA						TGGGCTCTCCCGTGTCCTCCT	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143283801C>T		NA		hg19		0.02	2.298805	TCCxGTG	COVERED																																																																																			NOVEL					0			2	5.718205	KEEP	8	0	0	19	647	CC	0.999366	0.999202	0			4	35	154	0	0	10.992369	54	50	1849	141		0.068966	0.999835
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143441902	143441902	__UNKNOWN__	lincRNA	SNP	G	G	A	rs7412315		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143441902G>A	ENST00000423249.1	-	0	59										NA		NA									NA						gtttctccacgttggtcagac	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143441902G>A		NA		hg19		0.02	-0.087732	CACxTTG	UNCOVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	2	3.608141	KEEP	3	0	0	12	407	GG	0.993072	0.09903	0		-	4	45	143	0	0	13.523257	5	50	185	29	ENST00000423249.1	0.444444	0.099721
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143451412	143451412	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143451412C>T	ENST00000423249.1	-	0	59										NA		NA									NA						atccacctcccttggcctccc	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143451412C>T		NA		hg19		0.02	-0.359686	TCCxTTG	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	1	3.310905	KEEP	8	0	0	11	402	CC	0.99254	0.882244	0		-	4	60	150	0	0	11.455458	32	60	1181	77	ENST00000423249.1	0.111111	0.888875
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143451450	143451450	__UNKNOWN__	lincRNA	SNP	A	A	T	rs112189225		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143451450A>T	ENST00000423249.1	-	0	59										NA		NA									NA						agcataagccaccatgcccag	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143451450A>T		NA		hg19		0.02	-0.289376	GCCxCCA	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	1	3.006128	KEEP	4	0	0	10	282	AA	0.992708	0.755338	0		-	3	60	99	0	0	7.194421	25	60	810	57	ENST00000423249.1	0.107143	0.760887
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143460758	143460758	__UNKNOWN__	lincRNA	SNP	C	C	A	rs147875616		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143460758C>A	ENST00000423249.1	-	0	59										NA		NA									NA						gttccccgatcccccaataat	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143460758C>A		NA		hg19		0.02	-0.114053	GATxCCC	UNCOVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	3	2.398186	KEEP	2	0	0	8	251	CC	0	0	0		-	5	47	180	0	0	16.623789	8	27	299	27	ENST00000423249.1	0.384615	0.162467
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143460857	143460857	__UNKNOWN__	lincRNA	SNP	T	T	C	rs372512642		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143460857T>C	ENST00000423249.1	-	0	59										NA		NA									NA						ggccggtggatcacttgaggt	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143460857T>C		NA		hg19		0.02	-0.078958	GGAxCAC	UNCOVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	3	3.602696	KEEP	10	0	0	12	345	TT	0	0	0		-	2	25	77	0	0	6.583925	7	31	258	35	ENST00000423249.1	0.222222	0.077336
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143463001	143463001	__UNKNOWN__	lincRNA	SNP	C	C	T	rs2048001		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143463001C>T	ENST00000423249.1	-	0	59										NA		NA									NA						catgagccaccgtgcccagcc	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143463001C>T		NA		hg19		0.02	-0.087733	CACxGTG	UNCOVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	2	2.240892	KEEP	4	1	33	19	639	CC	0.999859	0.099707	0		-	2	60	77	0	0	6.583894	7	50	262	42	ENST00000423249.1	0.222222	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143468212	143468212	__UNKNOWN__	IGR	SNP	G	G	A	rs199925365		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143468212G>A			NA	NA				RP11-435B5.4 (2774 upstream) : RP11-435B5.6 (30131 downstream)						NA		NA									NA						ctcgtgatccgccctcctagg	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143468212G>A		NA		hg19		0.02	-0.261483	TCCxCCC	COVERED																																																																																			NOVEL					0			2	5.718753	KEEP	5	0	0	19	685	GG	0.999366	0.693229	0			4	47	162	0	0	13.204403	23	47	775	66		0.148148	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143468249	143468249	__UNKNOWN__	IGR	SNP	G	G	A	rs372502620	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143468249G>A			NA	NA				RP11-435B5.4 (2811 upstream) : RP11-435B5.6 (30094 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.443	NA	NA											.|||	123	0.0245607	0.0015	0.0187	5008	,	,	NA	35314	0.0546	NA	0.0348	False	NA	,,,	NA	NA	NA	2504	0.0184	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143468249G>A		NA		hg19		0.02	-0.28951	GGCxTGA	COVERED																																																																																			NOVEL					0			4	3.646933	KEEP	7	1	34	24	842	GG	0.999879	0.760795	0			3	40	116	0	0	8.796424	27	48	980	83		0.1	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143468310	143468310	__UNKNOWN__	IGR	SNP	A	A	C	rs181650963		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143468310A>C			NA	NA				RP11-435B5.4 (2872 upstream) : RP11-435B5.6 (30033 downstream)						NA		NA									NA						AGCATGAAAAAAATCATGTCT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143468310A>C		NA		hg19		0.02	-0.254401	AAAxAAT	COVERED																																																																																			NOVEL					0			2	5.113559	KEEP	2	0	0	17	509	AA	0.997832	0.667074	0			3	47	114	0	1	8.741571	24	48	863	62		0.111111	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143485945	143485945	__UNKNOWN__	IGR	SNP	G	G	A	rs1712090		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143485945G>A			NA	NA				RP11-435B5.4 (20507 upstream) : RP11-435B5.6 (12398 downstream)						NA		NA									NA						catgcctattgtcccagctac	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143485945G>A		NA		hg19		0.02	-0.438671	ATTxTCC	COVERED																																																																																			NOVEL					0			9	8.126734	KEEP	16	0	0	27	972	GG	0.999859	0.959724	0			4	49	150	0	0	11.262003	36	50	1387	99		0.1	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143486499	143486499	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:143486499T>C			NA	NA				RP11-435B5.4 (21061 upstream) : RP11-435B5.6 (11844 downstream)						NA		NA									NA						tgtgcacctgtagtcccagct	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143486499T>C		NA		hg19		0.02	-0.096493	CTGxAGT	UNCOVERED																																																																																			NOVEL					0			1	2.406884	KEEP	1	0	0	8	239	TT	0.99257	0.119541	0			2	60	78	0	0	6.489433	9	60	310	22		0.181818	0.120436
SRGAP2B	647135	__UNKNOWN__	__UNKNOWN__	1	144016820	144016820	__UNKNOWN__	RNA	SNP	C	C	T	rs4844759	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144016820C>T	ENST00000467933.1	+	0	1108							P0DMP2	SRG2B_HUMAN	SLIT-ROBO Rho GTPase activating protein 2B	NA		NA			nervous system development (GO:0007399)						NA						agaatgaggccgcggaccctc	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA						CCDS72854.1	1q21.1	2014-07-10	2013-02-13	2012-05-08	ENSG00000196369	ENSG00000196369	647135			35237	protein-coding gene	gene with protein product		614703	SLIT-ROBO Rho GTPase activating protein 2 pseudogene 2, SLIT-ROBO Rho GTPase activating protein 2B (pseudogene)	SRGAP2P2	NA	22559943, 22559944	Standard	NM_001271870	NM_001271870	NA	Approved		uc010oxm.1	P0DMP2	OTTHUMG00000041442	ENST00000467933.1:	chr1.hg19:g.144016820C>T		NA		hg19		0.02	-0.192969	GGCxGCG	COVERED																																																																																			NOVEL	SRGAP2B-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000352915.1	2	3.610609	KEEP	1	0	0	12	388	CC	0.993072	0.454585	0		+	6	60	221	0	0	19.365167	16	60	551	42	ENST00000467933.1	0.272727	0.457757
SRGAP2B	647135	__UNKNOWN__	__UNKNOWN__	1	144016830	144016830	__UNKNOWN__	RNA	SNP	C	C	T	rs4844758	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144016830C>T	ENST00000467933.1	+	0	1108							P0DMP2	SRG2B_HUMAN	SLIT-ROBO Rho GTPase activating protein 2B	NA		NA			nervous system development (GO:0007399)						NA						cgcggaccctcgcggtgagtg	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA						CCDS72854.1	1q21.1	2014-07-10	2013-02-13	2012-05-08	ENSG00000196369	ENSG00000196369	647135			35237	protein-coding gene	gene with protein product		614703	SLIT-ROBO Rho GTPase activating protein 2 pseudogene 2, SLIT-ROBO Rho GTPase activating protein 2B (pseudogene)	SRGAP2P2	NA	22559943, 22559944	Standard	NM_001271870	NM_001271870	NA	Approved		uc010oxm.1	P0DMP2	OTTHUMG00000041442	ENST00000467933.1:	chr1.hg19:g.144016830C>T		NA		hg19		0.02	-0.157902	CCTxGCG	COVERED																																																																																			NOVEL	SRGAP2B-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000352915.1	2	3.611602	KEEP	1	0	0	12	412	CC	0.993072	0.32057	0		+	6	60	225	0	0	20.387363	12	60	397	33	ENST00000467933.1	0.333333	0.322807
SRGAP2B	647135	__UNKNOWN__	__UNKNOWN__	1	144036042	144036042	__UNKNOWN__	RNA	SNP	G	G	A	rs587677180	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144036042G>A	ENST00000467933.1	+	0	1108							P0DMP2	SRG2B_HUMAN	SLIT-ROBO Rho GTPase activating protein 2B	NA		NA			nervous system development (GO:0007399)						NA						gtgtaatggcgccatcttggc	0.512	NA	NA											G|||	6	0.00119808	0	0.0043	5008	,	,	NA	27584	0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA						CCDS72854.1	1q21.1	2014-07-10	2013-02-13	2012-05-08	ENSG00000196369	ENSG00000196369	647135			35237	protein-coding gene	gene with protein product		614703	SLIT-ROBO Rho GTPase activating protein 2 pseudogene 2, SLIT-ROBO Rho GTPase activating protein 2B (pseudogene)	SRGAP2P2	NA	22559943, 22559944	Standard	NM_001271870	NM_001271870	NA	Approved		uc010oxm.1	P0DMP2	OTTHUMG00000041442	ENST00000467933.1:	chr1.hg19:g.144036042G>A		NA		hg19		0.02	-0.149126	GGCxCCA	UNCOVERED																																																																																			NOVEL	SRGAP2B-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000352915.1	1	2.407683	KEEP	8	0	0	8	275	GG	0	0	0		+	3	54	112	0	0	9.191364	14	55	494	38	ENST00000467933.1	0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144582128	144582128	__UNKNOWN__	IGR	SNP	C	C	A	rs148575358	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144582128C>A			NA	NA				RNU1-59P (47929 upstream) : RP11-640M9.2 (11916 downstream)						NA		NA									NA						ttggagaccaccctgatcaac	0.512	NA	NA											c|||	2558	0.510783	0.2368	0.5908	5008	,	,	NA	15719	0.7212	NA	0.6501	False	NA	,,,	NA	NA	NA	2504	0.4642	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144582128C>A		NA		hg19		0.02	-0.05264	CCAxCCT	UNCOVERED																																																																																			NOVEL					0			2	2.407846	KEEP	3	0	0	8	280	CC	0	0	0			2	40	73	0	0	6.595601	4	60	157	19		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144686304	144686304	__UNKNOWN__	IGR	SNP	C	C	T	rs75923987		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144686304C>T			NA	NA				RP11-640M9.2 (80413 upstream) : NBPF9 (125439 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144686304C>T		NA		hg19		0.02	-0.114005	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			2	2.407678	KEEP	1	0	0	8	273	CC	0.99257	0.16126	0			3	60	95	0	0	8.000847	9	60	326	26		0.25	0.162467
NBPF9	400818	__UNKNOWN__	__UNKNOWN__	1	144828860	144828860	__UNKNOWN__	3'UTR	SNP	C	C	T	rs201650621		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144828860C>T	ENST00000468645.1	+	0	2203				NBPF9_ENST00000440491.2_3'UTR|NBPF9_ENST00000281815.8_3'UTR|NBPF9_ENST00000338347.4_3'UTR			Q3BBW0	NBPF9_HUMAN	neuroblastoma breakpoint family, member 9	NA		NA				cytoplasm (GO:0005737)				NS(2)|prostate(1)	3						AATGAAACTACAGTTCCATTT	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS72895.1, CCDS72896.1	1q21.1	2013-01-17			ENSG00000168614	ENSG00000269713	400818		neuroblastoma breakpoint family	31991	protein-coding gene	gene with protein product		613999			NA	16079250	Standard	NM_001037675	NM_001037675	NA	Approved	AE01		Q3BBW0	OTTHUMG00000013845	ENST00000468645.1:c.*2200C>T	chr1.hg19:g.144828860C>T		NA		hg19		0.02	6.047158	CTAxAGT	COVERED																																																																																			NOVEL	NBPF9-002	KNOWN	not_best_in_genome_evidence|basic	processed_transcript	NA	protein_coding	OTTHUMT00000038846.1	3	3.611959	KEEP	2	0	0	12	445	CC	0.993634	0.993634	0		+	11	40	376	0	0	25.136763	160	60	6097	226	ENST00000468645.1	0.064327	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144991243	144991243	__UNKNOWN__	Intron	SNP	C	C	T	rs1664013	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144991243C>T	ENST00000530740.1	-	4	591				PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369354.3_Intron|PDE4DIP_ENST00000369347.4_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313382.9_Intron|AL590452.1_ENST00000596396.1_3'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGAACTGTggctgggtgtggt	0.478	NA	NA	T	PDGFRB	MPD									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.552+3347G>A	chr1.hg19:g.144991243C>T		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.201783	TGGxTGG	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	0	2.407882	KEEP	0	0	0	8	285	CC	0.99257	0.4869	0		-	6	60	210	0	0	18.129658	17	60	644	37	ENST00000530740.1	0.26087	0.490544
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144991278	144991278	__UNKNOWN__	Intron	SNP	T	T	A	rs1778596	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:144991278T>A	ENST00000530740.1	-	4	591				PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369354.3_Intron|PDE4DIP_ENST00000369347.4_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313382.9_Intron|AL590452.1_ENST00000596396.1_3'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		atcccagcaatttaggaggcc	0.458	NA	NA	T	PDGFRB	MPD									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.552+3312A>T	chr1.hg19:g.144991278T>A		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.175449	CAAxTTA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	1	2.708307	KEEP	0	0	0	9	285	TT	0.99254	0.384517	0		-	3	60	103	0	0	8.060536	17	60	613	35	ENST00000530740.1	0.15	0.387407
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145015554	145015554	__UNKNOWN__	Intron	SNP	T	T	C	rs12563129	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145015554T>C	ENST00000530740.1	-	3	480				PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000493130.2_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		taacatttaatttataaatta	0.284	NA	NA	T	PDGFRB	MPD								T|||	960	0.191693	0.0764	0.1729	5008	,	,	NA	69679	0.3492	NA	0.2038	False	NA	,,,	NA	NA	NA	2504	0.1861	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.441+305A>G	chr1.hg19:g.145015554T>C		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	4.179111	TAAxTTA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	2	5.711068	KEEP	0	0	0	19	514	TT	0.99986	0.999859	0		-	13	60	476	0	0	35.685961	112	60	4065	152	ENST00000530740.1	0.104	0.999999
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145056222	145056222	__UNKNOWN__	Intron	SNP	G	G	A	rs373930085	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145056222G>A	ENST00000530740.1	-	1	272				PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000369348.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		atctagggatggtagtgcaaa	0.478	NA	NA	T	PDGFRB	MPD								G|||	447	0.0892572	0.1369	0.0634	5008	,	,	NA	62509	0.0417	NA	0.0845	False	NA	,,,	NA	NA	NA	2504	0.0971	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.233+19407C>T	chr1.hg19:g.145056222G>A		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.166689	GATxGTA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	4	2.706984	KEEP	0	0	0	9	297	GG	0.99254	0.351306	0		-	6	60	213	0	0	19.186837	12	60	440	31	ENST00000530740.1	0.333333	0.353947
SEC22B	9554	__UNKNOWN__	__UNKNOWN__	1	145109456	145109456	__UNKNOWN__	RNA	SNP	C	C	T	rs7553975	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145109456C>T	ENST00000453618.1	+	0	512							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)					NA						TACAGAGATTCTGCTTTAAAC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380		9554			10700	protein-coding gene	gene with protein product		604029	SEC22, vesicle trafficking protein (S. cerevisiae)-like 1, SEC22 vesicle trafficking protein-like 1 (S. cerevisiae), SEC22 vesicle trafficking protein homolog B (S. cerevisiae)	SEC22L1	NA	9094723, 16354670	Standard	NM_004892	NM_004892	NA	Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745	ENST00000453618.1:	chr1.hg19:g.145109456C>T		NA	A8K1G0	hg19		0.02	23.187422	ATTxTGC	COVERED																																																																																			NOVEL	SEC22B-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000038523.5	7	3.11063	KEEP	0	3	81	39	1305	CC	1	1	0		+	124	60	4352	0	0	373.371706	371	60	13714	618	ENST00000453618.1	0.250505	1
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145209366	145209366	__UNKNOWN__	5'UTR	SNP	A	A	G	rs856450	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145209366A>G	ENST00000468030.1	+	0	222				NOTCH2NL_ENST00000344859.3_5'UTR|NOTCH2NL_ENST00000362074.6_5'UTR						NA		NA									NA						CCGAGAAGATACCCGCCCTGC	0.736	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						6	7	7	NA		NA	NA	1		NA											NA				145209366		817	1891	2708	SO:0001623	5_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.-115A>G	chr1.hg19:g.145209366A>G		NA		hg19		0.02	6.603215	GATxCCC	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	4	22.468671	KEEP	4	5	172	135	3540	AA	1	1	0		+	6	40	230	0	0	14.649408	161	60	4952	411	ENST00000468030.1	0.035928	1
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145238045	145238045	__UNKNOWN__	Intron	SNP	C	C	T	rs200297196	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145238045C>T	ENST00000468030.1	+	2	292				NOTCH2NL_ENST00000369340.3_Intron|NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000362074.6_Intron						NA		NA									NA						tgagccaccgcgcctggccGT	0.468	NA	NA											C|||	2046	0.408546	0.4107	0.4179	5008	,	,	NA	30655	0.3938	NA	0.4115	False	NA	,,,	NA	NA	NA	2504	0.411	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.-44-10768C>T	chr1.hg19:g.145238045C>T		NA		hg19		0.02	-0.043864	CCGxGCC	UNCOVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	0	2.407923	KEEP	14	0	0	8	288	CC	0	0	0		+	2	40	75	0	0	6.992876	3	40	100	31	ENST00000468030.1	0.4	0.024074
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145290723	145290723	__UNKNOWN__	Intron	SNP	G	G	A	rs55865362		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145290723G>A	ENST00000468030.1	+	5	970				NOTCH2NL_ENST00000344859.3_Intron|NBPF10_ENST00000369339.3_Intron|NOTCH2NL_ENST00000479995.2_Intron						NA		NA									NA						ACTCTACAGTGTGGGTTGCCT	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.635-2391G>A	chr1.hg19:g.145290723G>A		NA		hg19		0.02	16.726446	AGTxTGG	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	1	3.296685	KEEP	4	0	0	11	324	GG	0.993072	0.993072	0		+	61	60	2191	0	0	177.74822	291	60	10757	383	ENST00000468030.1	0.173295	1
NBPF10	100132406	__UNKNOWN__	__UNKNOWN__	1	145323656	145323656	__UNKNOWN__	Intron	SNP	A	A	T	rs75252120	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145323656A>T	ENST00000369339.3	+	10	1293				NBPF10_ENST00000342960.5_Missense_Mutation_p.I1165F|NBPF10_ENST00000369338.1_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	NA		NA				cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.I1165F(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TATTGCAGGAATTAAAAAGGA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				3	Substitution - Missense(3)	endometrium(2)|kidney(1)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425	100132406		neuroblastoma breakpoint family	31992	protein-coding gene	gene with protein product		614000			NA	16079250	Standard	NM_001039703	NM_001039703	NA	Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.1040+12502A>T	chr1.hg19:g.145323656A>T		NA	Q5RHC0|Q9NWN6	hg19		0.02	8.628239	GGAxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	.	7.524	0.657305	0.14580	.	.	ENSG00000163386	ENST00000342960	T	0.03441	3.93	.	.	.	.	.	.	.	.	T	0.02342	0.0072	M	0.67953	2.075	0.09310	N	1	.	.	.	.	.	.	T	0.44065	-0.9352	5	0.28530	T	0.3	.	.	.	.	.	.	.	.	F	1165	ENSP00000345684:I1165F	ENSP00000345684:I1165F	I	+	1	0	NBPF10	144035013	0.353000	0.24904	0.005000	0.12908	0.123000	0.20343	1.122000	0.31295	0.386000	0.24997	0.128000	0.15822	ATT	NOVEL	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	NA	protein_coding	OTTHUMT00000038550.3	2	6.585429	KEEP	15	2	57	42	1296	AA	1	1	0		+	12	60	444	0	0	29.396765	230	60	8281	360	ENST00000369339.3	0.049587	1
NBPF10	100132406	__UNKNOWN__	__UNKNOWN__	1	145323666	145323666	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145323666A>G	ENST00000369339.3	+	10	1293				NBPF10_ENST00000342960.5_Missense_Mutation_p.D1168G|NBPF10_ENST00000369338.1_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	NA		NA				cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.D1168G(2)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ATTAAAAAGGACGAAGAAGAG	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	endometrium(1)|kidney(1)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425	100132406		neuroblastoma breakpoint family	31992	protein-coding gene	gene with protein product		614000			NA	16079250	Standard	NM_001039703	NM_001039703	NA	Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.1040+12512A>G	chr1.hg19:g.145323666A>G		NA	Q5RHC0|Q9NWN6	hg19		0.02	11.948234	AGGxCGA	COVERED	.	.	.	.	.	.	.	.	.	.	.	8.978	0.974738	0.18736	.	.	ENSG00000163386	ENST00000342960	T	0.03524	3.9	.	.	.	.	.	.	.	.	T	0.02380	0.0073	L	0.60455	1.87	0.09310	N	1	.	.	.	.	.	.	T	0.42965	-0.9420	5	0.45353	T	0.12	.	.	.	.	.	.	.	.	G	1168	ENSP00000345684:D1168G	ENSP00000345684:D1168G	D	+	2	0	NBPF10	144035023	0.002000	0.14202	0.003000	0.11579	0.095000	0.18619	-0.338000	0.07842	0.386000	0.24997	0.128000	0.15822	GAC	NOVEL	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	NA	protein_coding	OTTHUMT00000038550.3	3	4.215656	KEEP	12	3	97	48	1504	AA	1	1	0		+	15	60	561	0	0	38.332082	246	60	8816	392	ENST00000369339.3	0.057471	1
RP11-458D21.1	0	__UNKNOWN__	__UNKNOWN__	1	145374875	145374875	__UNKNOWN__	lincRNA	SNP	T	T	C	rs6692019		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:145374875T>C	ENST00000433081.2	-	0	1596										NA		NA									NA						accccatctctactaaaaata	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000433081.2:	chr1.hg19:g.145374875T>C		NA		hg19		0.02	-0.087621	CTCxACT	UNCOVERED																																																																																			NOVEL	RP11-458D21.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000100475.2	3	3.007523	KEEP	2	0	0	10	286	TT	0.99254	0.098977	0		-	2	40	77	0	0	6.482503	8	55	242	24	ENST00000433081.2	0.2	0.099721
NBPF14	25832	__UNKNOWN__	__UNKNOWN__	1	148009141	148009141	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148009141A>G	ENST00000369219.1	-	16	1980							Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	NA		NA				cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					ATGGCCTGAGACTAGGAAGAG	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092351		1q21.1	2013-01-17			ENSG00000122497		25832		neuroblastoma breakpoint family	25232	protein-coding gene	gene with protein product		614003			NA	8619474, 9110174, 16079250	Standard	NM_015383	NM_015383	NA	Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1963+202T>C	chr1.hg19:g.148009141A>G		NA	Q5TI23|Q8IX76|Q9UJI9	hg19		0.02	-0.315831	GAGxCTA	COVERED																																																																																			NOVEL	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		2	2.406568	KEEP	2	0	0	8	240	AA	0.99257	0.812384	0		-	4	60	142	0	0	10.655631	32	60	1151	47	ENST00000369219.1	0.111111	0.818465
NBPF20	100288142	__UNKNOWN__	__UNKNOWN__	1	148251607	148251607	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148251607G>A	ENST00000369202.1	-	0	14331							Q3BBV1	NBPFK_HUMAN	neuroblastoma breakpoint family, member 20	NA		NA				cytoplasm (GO:0005737)				breast(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	27						TAGCTACCCAGAGATACGTGG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS72856.1	1q21.2	2014-01-16			ENSG00000203832		100288142		neuroblastoma breakpoint family	32000	protein-coding gene	gene with protein product		614007			NA	16079250	Standard		NM_001278267	NA	Approved			Q3BBV1	OTTHUMG00000042439	ENST00000369202.1:c.*268C>T	chr1.hg19:g.148251607G>A		NA		hg19		0.02	4.562915	CCAxAGA	COVERED																																																																																			NOVEL	NBPF20-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000100689.2	2	7.223752	KEEP	93	0	0	24	875	GG	0.993072	0.993054	0		-	5	22	188	0	0	12.479278	99	40	3841	259	ENST00000369202.1	0.048077	0.999981
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148347670	148347670	__UNKNOWN__	IGR	SNP	G	G	A	rs202081375		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148347670G>A			NA	NA				NBPF20 (619 upstream) : NBPF15 (208308 downstream)						NA		NA									NA						ctgccgcctcggcctcccaaa	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148347670G>A		NA		hg19		0.02	-0.087725	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			1	2.407788	KEEP	0	0	0	8	278	GG	0.99257	0.09898	0			2	24	78	0	0	6.581223	8	60	287	23		0.2	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148853906	148853906	__UNKNOWN__	IGR	SNP	T	T	A	rs2907982		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148853906T>A			NA	NA				RP11-763B22.6 (189 upstream) : RNA5SP59 (59366 downstream)						NA		NA									NA						GGTCTGTATCTCCTGCTGGGT	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148853906T>A		NA		hg19		0.02	-0.236832	ATCxCCT	COVERED																																																																																			NOVEL					0			0	2.407558	KEEP	0	0	0	8	260	TT	0.99257	0.607857	0			5	37	164	0	0	13.556629	18	49	660	43		0.217391	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148853997	148853997	__UNKNOWN__	IGR	SNP	C	C	T	rs61813066		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148853997C>T			NA	NA				RP11-763B22.6 (280 upstream) : RNA5SP59 (59275 downstream)						NA		NA									NA						TGGAGCTGCCCGCACTGCTGC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148853997C>T		NA		hg19		0.02	-0.14914	GCCxGCA	UNCOVERED																																																																																			NOVEL					0			0	2.407955	KEEP	8	0	0	8	289	CG	0	0	0			3	46	114	0	0	9.478319	13	47	461	43		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148864513	148864513	__UNKNOWN__	IGR	SNP	T	T	C	rs371418194		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148864513T>C			NA	NA				RP11-763B22.6 (10796 upstream) : RNA5SP59 (48759 downstream)						NA		NA									NA						GGGCTGTGCCTGCTGGTCCTG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148864513T>C		NA		hg19		0.02	-0.350915	GCCxGCT	COVERED																																																																																			NOVEL					0			1	2.959309	KEEP	14	1	11	14	411	TT	0.992708	0.871307	0			6	27	218	0	0	17.320457	34	27	1241	68		0.15	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148864581	148864581	__UNKNOWN__	IGR	SNP	C	C	T	rs201005596		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148864581C>T			NA	NA				RP11-763B22.6 (10864 upstream) : RNA5SP59 (48691 downstream)						NA		NA									NA						CCAGGGCAGGCGGGGCAGGGC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148864581C>T		NA		hg19		0.02	2.159312	AGGxGGG	COVERED																																																																																			NOVEL					0			0	4.350484	KEEP	11	1	15	20	671	CC	0.999859	0.999347	0			10	49	346	0	0	26.113447	73	50	2660	141		0.120482	0.999487
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148864642	148864642	__UNKNOWN__	IGR	SNP	G	G	T	rs111609219		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148864642G>T			NA	NA				RP11-763B22.6 (10925 upstream) : RNA5SP59 (48630 downstream)						NA		NA									NA						CTTCTGGGGCGCCTGGCATCC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148864642G>T		NA		hg19		0.02	4.923354	GGCxCCT	COVERED																																																																																			NOVEL					0			0	5.407222	KEEP	3	1	34	30	1014	GG	0.999997	0.999996	0			13	49	492	0	0	37.537144	107	50	3824	204		0.108333	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148878111	148878111	__UNKNOWN__	IGR	SNP	C	C	T	rs2494564		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148878111C>T			NA	NA				RP11-763B22.6 (24394 upstream) : RNA5SP59 (35161 downstream)						NA		NA									NA						ccttggcctcccaaagtgttg	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148878111C>T		NA		hg19		0.02	-0.210556	CTCxCAA	COVERED																																																																																			NOVEL					0			1	3.310073	KEEP	3	0	0	11	366	CC	0.992708	0.518353	0			3	27	128	0	0	10.30448	21	60	770	45		0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148878167	148878167	__UNKNOWN__	IGR	SNP	G	G	A	rs9727292		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148878167G>A			NA	NA				RP11-763B22.6 (24450 upstream) : RNA5SP59 (35105 downstream)						NA		NA									NA						gtgcagtggcgtgatctctgc	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148878167G>A		NA		hg19		0.02	-0.184228	GGCxTGA	COVERED																																																																																			NOVEL					0			3	3.611641	KEEP	9	0	0	12	412	GG	0.99254	0.420319	0			3	33	111	0	0	8.932738	16	48	573	51		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148881296	148881296	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148881296G>A			NA	NA				RP11-763B22.6 (27579 upstream) : RNA5SP59 (31976 downstream)						NA		NA									NA						gctgggcatggtggtggacaa	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148881296G>A		NA		hg19		0.02	-0.114044	ATGxTGG	UNCOVERED																																																																																			NOVEL					0			1	2.407931	KEEP	8	0	0	8	289	GG	0	0	0			4	27	136	0	0	12.023359	9	50	334	36		0.307692	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148902406	148902406	__UNKNOWN__	IGR	SNP	C	C	T	rs151005		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:148902406C>T			NA	NA				RP11-763B22.6 (48689 upstream) : RNA5SP59 (10866 downstream)						NA		NA									NA						CAGCAGCTGGCGCAGGGGAAT	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148902406C>T		NA		hg19		0.02	10.231117	TGGxGCA	COVERED																																																																																			NOVEL					0			1	3.723077	KEEP	61	9	248	100	3297	CC	1	1	0			10	27	355	0	0	22.067196	239	60	8201	469		0.040161	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149049485	149049485	__UNKNOWN__	IGR	SNP	G	G	T	rs12741994	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:149049485G>T			NA	NA				AL732363.1 (13108 upstream) : RNU1-114P (97228 downstream)						NA		NA									NA						CCACCTTCAAGAGCTGGAAAA	0.502	NA	NA											g|||	1179	0.235423	0.2315	0.2536	5008	,	,	NA	18244	0.1577	NA	0.2078	False	NA	,,,	NA	NA	NA	2504	0.3364	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149049485G>T		NA		hg19		0.02	4.792376	CAAxAGC	COVERED																																																																																			NOVEL					0			0	2.407458	KEEP	0	0	0	8	275	GG	0.99257	0.992565	0			29	60	1054	0	0	91.417787	83	60	3170	153		0.258929	0.999995
RP11-403I13.8	0	__UNKNOWN__	__UNKNOWN__	1	149288143	149288143	__UNKNOWN__	lincRNA	SNP	C	C	A	rs587641049		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:149288143C>A	ENST00000433084.1	+	0	693										NA		NA									NA						ATGGCTACTTCGGGGTGGGGG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000433084.1:	chr1.hg19:g.149288143C>A		NA		hg19		0.02	10.575929	CTTxGGG	COVERED																																																																																			NOVEL	RP11-403I13.8-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000099633.1	3	4.81538	KEEP	5	3	97	50	1625	CC	1	1	0		+	20	60	668	0	0	45.492292	249	60	8151	411	ENST00000433084.1	0.074349	1
RP11-403I13.9	0	__UNKNOWN__	__UNKNOWN__	1	149311786	149311786	__UNKNOWN__	lincRNA	SNP	C	C	A	rs77863507		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:149311786C>A	ENST00000449024.1	-	0	187										NA		NA									NA						AGATCAAAACCCATTATGggc	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000449024.1:	chr1.hg19:g.149311786C>A		NA		hg19		0.02	-0.228095	AACxCAT	COVERED																																																																																			NOVEL	RP11-403I13.9-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000099634.1	0	3.310838	KEEP	1	0	0	11	388	CC	0.992708	0.578679	0		-	5	60	191	0	0	15.958173	21	60	808	51	ENST00000449024.1	0.192308	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149339713	149339713	__UNKNOWN__	IGR	SNP	G	G	T	rs28526228		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:149339713G>T			NA	NA				CR812485.1 (16291 upstream) : FCGR1C (29614 downstream)						NA		NA									NA						TAGGAGAGAGGTGCAGGGCCT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149339713G>T		NA		hg19		0.02	4.27899	GAGxTGC	COVERED																																																																																			NOVEL					0			0	5.112559	KEEP	17	0	0	17	538	GG	0.993634	0.993633	0			15	60	518	0	0	39.043884	110	60	4004	171		0.12	0.999999
OAZ3	51686	__UNKNOWN__	__UNKNOWN__	1	151739253	151739253	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:151739253G>T	ENST00000479764.1	+	0	3200				OAZ3_ENST00000577465.1_3'UTR|OAZ3_ENST00000315067.8_Intron|OAZ3_ENST00000400999.1_5'UTR|OAZ3_ENST00000321531.5_Intron|OAZ3_ENST00000453029.2_Intron|RP11-98D18.16_ENST00000596133.1_RNA|RP11-98D18.3_ENST00000512280.1_RNA			Q9UMX2	OAZ3_HUMAN	ornithine decarboxylase antizyme 3	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of polyamine transmembrane transport (GO:1902268)|polyamine biosynthetic process (GO:0006596)|positive regulation of protein catabolic process (GO:0045732)|putrescine transport (GO:0015847)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of phosphoprotein phosphatase activity (GO:0043666)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)	ornithine decarboxylase inhibitor activity (GO:0008073)|putrescine transmembrane transporter activity (GO:0015489)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)		L-Ornithine(DB00129)	ATCAAGAGGGGAAAAACACGT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						187	146	159	NA		NA	NA	1		NA											NA				151739253		692	1591	2283	SO:0001623	5_prime_UTR_variant			AF175296	CCDS58028.1	1q21.3	2008-02-05			ENSG00000143450	ENSG00000143450	51686			8097	protein-coding gene	gene with protein product		605138			NA	10781085	Standard	NM_016178	NM_016178	NA	Approved		uc010pdm.2	Q9UMX2	OTTHUMG00000013061	ENST00000479764.1:c.-317G>T	chr1.hg19:g.151739253G>T		NA	E7EUE7|Q6GMR0	hg19		0.02	8.4277	GGGxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	23.3	4.394988	0.83011	.	.	ENSG00000143450	ENST00000321531	.	.	.	5.06	4.11	0.48088	.	.	.	.	.	T	0.59376	0.2189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63703	-0.6577	5	0.87932	D	0	.	10.9237	0.47180	0.0:0.0:0.8144:0.1856	.	.	.	.	V	19	.	ENSP00000313922:G19V	G	+	2	0	OAZ3	150005877	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.261000	0.43276	2.648000	0.89879	0.561000	0.74099	GGA	NOVEL	OAZ3-001	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000036642.2	3	10.533467	KEEP	0	0	0	35	1193	GG	0.999999	0.999999	0		+	26	60	861	0	0	64.498444	182	60	6680	301	ENST00000479764.1	0.125	1
HRNR	388697	__UNKNOWN__	__UNKNOWN__	1	152187588	152187588	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201071455	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:152187588C>T	ENST00000368801.2	-	3	6592	c.6517G>A	c.(6517-6519)Ggc>Agc	p.G2173S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2173		NA			establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTTGTCGGCCGTGGCCCGAA	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						105	129	121	NA		NA	NA	1		NA											NA				152187588		1574	3256	4830	SO:0001583	missense			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915	388697		EF-hand domain containing	20846	protein-coding gene	gene with protein product	filaggrin family member 3	NA			NA		Standard	XM_373868	NM_001009931	NA	Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6517G>A	chr1.hg19:g.152187588C>T	ENSP00000357791:p.Gly2173Ser	NA	Q5DT20|Q5U1F4	hg19	CCDS30859.1	0.02	8.862117	GGCxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	-	9.554	1.116776	0.20795	.	.	ENSG00000197915	ENST00000368801	T	0.01527	4.8	3.22	-0.994	0.10225	.	.	.	.	.	T	0.00328	0.0010	N	0.16743	0.435	0.80722	P	0.0	B	0.27264	0.173	B	0.11329	0.006	T	0.35076	-0.9803	8	0.06494	T	0.89	.	7.4135	0.27032	0.0:0.5254:0.0:0.4746	.	2173	Q86YZ3	HORN_HUMAN	S	2173	ENSP00000357791:G2173S	ENSP00000357791:G2173S	G	-	1	0	HRNR	150454212	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.789000	0.00768	-0.075000	0.12798	-0.131000	0.14894	GGC	NOVEL	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034016.1	6	13.133617	KEEP	69	6	177	106	3493	CC	1	1	0		-	14	46	479	0	0	32.29042	198	47	6934	475	ENST00000368801.2	0.066038	1
HRNR	388697	__UNKNOWN__	__UNKNOWN__	1	152187619	152187619	__UNKNOWN__	Silent	SNP	A	A	G	rs80264994	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:152187619A>G	ENST00000368801.2	-	3	6561	c.6486T>C	c.(6484-6486)caT>caC	p.H2162H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2162		NA			establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCCAGACCCATGCTGACCAT	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	A		152,4244		0,152,2046	275	318	303	NA	6486	-7.7	0	1	dbSNP_131	303	178,8378		0,178,4100	no	coding-synonymous	HRNR	NM_001009931.1		0,330,6146	GG,GA,AA	NA	2.0804,3.4577,2.5479		2162/2851	152187619	330,12622	2198	4278	6476	SO:0001819	synonymous_variant			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915	388697		EF-hand domain containing	20846	protein-coding gene	gene with protein product	filaggrin family member 3	NA			NA		Standard	XM_373868	NM_001009931	NA	Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6486T>C	chr1.hg19:g.152187619A>G		NA	Q5DT20|Q5U1F4	hg19	CCDS30859.1	0.02	16.639106	CCCxTGC	COVERED																																																																																			NOVEL	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034016.1	13	8.955285	KEEP	43	10	314	140	4215	AA	1	1	0		-	30	46	991	0	0	67.687958	356	48	13128	737	ENST00000368801.2	0.07772	1
FLG	2312	__UNKNOWN__	__UNKNOWN__	1	152284478	152284478	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs199888588		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:152284478A>G	ENST00000368799.1	-	3	2919	c.2884T>C	c.(2884-2886)Tgg>Cgg	p.W962R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	962	Ser-rich.	NA			establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACCCAGACCACCTCTCAGAG	0.577	NA	NA							Ichthyosis					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631	2312		EF-hand domain containing	3748	protein-coding gene	gene with protein product		135940			NA	2740331, 2248957, 16444271	Standard	NM_002016	NM_002016	NA	Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2884T>C	chr1.hg19:g.152284478A>G	ENSP00000357789:p.Trp962Arg	NA	Q01720|Q5T583|Q9UC71	hg19	CCDS30860.1	0.02	14.306358	ACCxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	-	1.826	-0.471074	0.04445	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01560	4.77	2.55	-5.09	0.02920	.	.	.	.	.	T	0.00271	0.0008	N	0.13043	0.29	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46610	-0.9179	9	0.24483	T	0.36	.	0.3349	0.00325	0.227:0.281:0.2108:0.2812	.	962	P20930	FILA_HUMAN	R	962;169	ENSP00000357789:W962R	ENSP00000357789:W962R	W	-	1	0	FLG	150551102	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.820000	0.04457	-2.271000	0.00683	-1.668000	0.00747	TGG	NOVEL	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033742.1	11	9.259273	KEEP	21	1	32	42	1262	AA	1	1	0		-	15	40	480	0	0	29.554241	277	60	9927	414	ENST00000368799.1	0.05137	1
LCE1B	353132	__UNKNOWN__	__UNKNOWN__	1	152784701	152784701	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:152784701A>G	ENST00000360090.3	+	0	255					NM_178349.1	NP_848126.1	Q5T7P3	LCE1B_HUMAN	late cornified envelope 1B	NA		NA			keratinization (GO:0031424)					breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|skin(2)	18	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTATAAGTATATAAAAAGCAT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BI670515	CCDS1027.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000196734	ENSG00000196734	353132		Late cornified envelopes	16611	protein-coding gene	gene with protein product		612604	small proline rich-like (epidermal differentiation complex) 2A	SPRL2A	NA	11698679	Standard	NM_178349	NM_178349	NA	Approved	LEP2	uc001faq.3	Q5T7P3	OTTHUMG00000014402	ENST00000360090.3:c.-222A>G	chr1.hg19:g.152784701A>G		NA	A4IF40	hg19	CCDS1027.1	0.02	4.702905	TATxTAA	COVERED																																																																																			NOVEL	LCE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040060.1	2	3.910277	KEEP	0	0	0	13	387	AA	0.994391	0.994391	0		+	47	60	1766	0	0	159.362442	98	60	3506	182	ENST00000360090.3	0.324138	1
S100A7A	338324	__UNKNOWN__	__UNKNOWN__	1	153395663	153395663	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:153395663T>G	ENST00000368729.4	+	0	4241					NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	NA		NA				cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)			cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			TTTACCATTATTTTCAATTTC	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330	338324		S100 calcium binding proteins, EF-hand domain containing	21657	protein-coding gene	gene with protein product		NA	S100 calcium binding protein A15, S100 calcium binding protein A7-like 1	S100A15, S100A7L1	NA	11230159	Standard	NM_176823	NM_176823	NA	Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.*3878T>G	chr1.hg19:g.153395663T>G		NA	D3DV38|Q5SY69	hg19	CCDS30872.1	0.02	2.31181	TTAxTTT	COVERED																																																																																			NOVEL	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000036786.2	1	2.407382	KEEP	0	0	0	8	253	TT	0.99257	0.991446	0		+	31	60	1157	0	0	107.949759	46	60	1688	96	ENST00000368729.4	0.402597	0.998867
IFI16	3428	__UNKNOWN__	__UNKNOWN__	1	158985756	158985756	__UNKNOWN__	Silent	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:158985756A>G	ENST00000368131.4	+	3	650	c.360A>G	c.(358-360)gcA>gcG	p.A120A	IFI16_ENST00000359709.3_Silent_p.A120A|IFI16_ENST00000340979.6_Silent_p.A120A|IFI16_ENST00000295809.7_Silent_p.A120A|IFI16_ENST00000368132.3_Silent_p.A120A|IFI16_ENST00000430894.2_Silent_p.A124A|IFI16_ENST00000448393.2_Silent_p.A120A	NM_005531.2	NP_005522.2	Q16666	IF16_HUMAN	interferon, gamma-inducible protein 16	120	Lys-rich.	NA			activation of cysteine-type endopeptidase activity (GO:0097202)|activation of innate immune response (GO:0002218)|autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular response to glucose starvation (GO:0042149)|cellular response to ionizing radiation (GO:0071479)|defense response to virus (GO:0051607)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|monocyte differentiation (GO:0030224)|myeloid cell differentiation (GO:0030099)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|negative regulation of DNA binding (GO:0043392)|negative regulation of innate immune response (GO:0045824)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|positive regulation of cytokine production (GO:0001819)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of autophagy (GO:0010506)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0429)					CTGAAGGAGCAGAGGCAACTC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						72	65	67	NA		NA	NA	1		NA											NA				158985756		2203	4300	6503	SO:0001819	synonymous_variant			M63838	CCDS1180.3, CCDS58039.1	1q22	2008-02-05			ENSG00000163565	ENSG00000163565	3428			5395	protein-coding gene	gene with protein product		147586			NA	1526658, 7959953	Standard	NM_005531	NM_005531	NA	Approved	IFNGIP1, PYHIN2	uc010pis.2	Q16666	OTTHUMG00000037108	ENST00000368131.4:c.360A>G	chr1.hg19:g.158985756A>G		NA	B4DJT8|H3BLV7|Q59GX0|Q5T3W7|Q5T3W8|Q5T3X0|Q5T3X1|Q5T3X2|Q8N9E5|Q8NEQ7|Q96AJ5|Q9UH78	hg19	CCDS1180.3	0.02	6.962879	AGCxGAG	COVERED																																																																																			NOVEL	IFI16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090101.3	1	6.919523	KEEP	0	0	0	23	690	AA	0.999892	0.999892	0		+	6	60	226	0	0	14.179356	165	60	6193	236	ENST00000368131.4	0.035088	1
FCGR2A	2212	__UNKNOWN__	__UNKNOWN__	1	161488539	161488539	__UNKNOWN__	3'UTR	SNP	G	G	C	rs6427601		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:161488539G>C	ENST00000271450.6	+	0	1593				RP11-25K21.6_ENST00000537821.2_RNA	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	NA		NA			Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	gctgggattagaggcatgtgc	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226	2212		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	3616	protein-coding gene	gene with protein product	Immunoglobulin G Fc receptor II	146790	Fc fragment of IgG, low affinity IIa, receptor for (CD32)	FCG2, FCGR2A1, FCGR2	NA	2139735	Standard	NM_021642	NM_021642	NA	Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.*601G>C	chr1.hg19:g.161488539G>C		NA	Q8WUN1|Q8WW64	hg19	CCDS44264.1	0.02	9.374585	TTAxAGG	COVERED																																																																																			NOVEL	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083318.3	14	5.095804	KEEP	12	0	0	17	558	GG	0.999366	0.999366	0		+	44	47	1616	0	0	132.533854	201	60	7371	285	ENST00000271450.6	0.179592	1
FCGR2A	2212	__UNKNOWN__	__UNKNOWN__	1	161488557	161488557	__UNKNOWN__	3'UTR	SNP	C	C	A	rs6427602		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:161488557C>A	ENST00000271450.6	+	0	1611				RP11-25K21.6_ENST00000537821.2_RNA	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	NA		NA			Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	tgccatcatacccagctaatt	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226	2212		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	3616	protein-coding gene	gene with protein product	Immunoglobulin G Fc receptor II	146790	Fc fragment of IgG, low affinity IIa, receptor for (CD32)	FCG2, FCGR2A1, FCGR2	NA	2139735	Standard	NM_021642	NM_021642	NA	Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.*619C>A	chr1.hg19:g.161488557C>A		NA	Q8WUN1|Q8WW64	hg19	CCDS44264.1	0.02	7.759535	ATAxCCA	COVERED																																																																																			NOVEL	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083318.3	10	7.222426	KEEP	3	0	0	24	794	CC	0.999909	0.999909	0		+	19	39	645	0	0	45.764459	194	60	6929	251	ENST00000271450.6	0.089202	1
FCGR2A	2212	__UNKNOWN__	__UNKNOWN__	1	161488928	161488928	__UNKNOWN__	3'UTR	SNP	A	A	T	rs55798332		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:161488928A>T	ENST00000271450.6	+	0	1982				RP11-25K21.6_ENST00000537821.2_RNA	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	NA		NA			Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TATTTCCTGGACTAAATTCCC	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226	2212		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	3616	protein-coding gene	gene with protein product	Immunoglobulin G Fc receptor II	146790	Fc fragment of IgG, low affinity IIa, receptor for (CD32)	FCG2, FCGR2A1, FCGR2	NA	2139735	Standard	NM_021642	NM_021642	NA	Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.*990A>T	chr1.hg19:g.161488928A>T		NA	Q8WUN1|Q8WW64	hg19	CCDS44264.1	0.02	26.246375	TGGxCTA	COVERED																																																																																			NOVEL	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083318.3	8	8.521295	KEEP	6	3	84	58	1787	AA	1	1	0		+	22	48	737	1	0	42.297197	642	60	22804	855	ENST00000271450.6	0.033133	1
FCGR2B	2213	__UNKNOWN__	__UNKNOWN__	1	161643025	161643025	__UNKNOWN__	Intron	SNP	C	C	A	rs145835719	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:161643025C>A	ENST00000236937.9	+	4	741				FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000367961.4_Intron|FCGR2B_ENST00000403078.3_Intron|RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000358671.5_Intron|FCGR2B_ENST00000367962.4_Intron	NM_001002273.2|NM_001002274.2	NP_001002273.1|NP_001002274.1	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)					NA	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCAAGGTATGCGGAGTCTGCC	0.522	NA	NA	T	?	ALL								c|||	209	0.0417332	0.0915	0.0317	5008	,	,	NA	20261	0.0188	NA	0.0258	False	NA	,,,	NA	NA	NA	2504	0.0215	NA	NA	NA			Dom	yes		1	1q23	2213	Fc fragment of IgG, low affinity IIb, receptor for (CD32)		L	0							NA						66	64	64	NA		NA	NA	1		NA											NA				161643025		2131	4287	6418	SO:0001627	intron_variant			BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694	2213		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	3618	protein-coding gene	gene with protein product		604590	Fc fragment of IgG, low affinity IIb, receptor for (CD32)	FCG2, FCGR2	NA	2139735	Standard	NM_004001	NM_004001	NA	Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000236937.9:c.646+6C>A	chr1.hg19:g.161643025C>A		NA	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	hg19	CCDS30925.1	0.02	1.773031	ATGxGGA	COVERED																																																																																			NOVEL	FCGR2B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157309.1	0	4.240424	KEEP	48	1	31	25	830	CC	0.999863	0.999782	0		+	5	40	173	0	0	11.233447	88	60	2885	187	ENST00000236937.9	0.053763	0.999919
XCL1	6375	__UNKNOWN__	__UNKNOWN__	1	168550512	168550512	__UNKNOWN__	3'UTR	SNP	G	G	C	rs200980747	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:168550512G>C	ENST00000367818.3	+	0	564					NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	NA		NA			cell-cell signaling (GO:0007267)|cellular response to interleukin-4 (GO:0071353)|cellular response to transforming growth factor beta stimulus (GO:0071560)|immune response (GO:0006955)|mature natural killer cell chemotaxis (GO:0035782)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T-helper 1 cell activation (GO:2000518)|negative regulation of T-helper 1 type immune response (GO:0002826)|negative regulation of transcription, DNA-templated (GO:0045892)|neutrophil chemotaxis (GO:0030593)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000566)|positive regulation of granzyme A production (GO:2000513)|positive regulation of granzyme B production (GO:0071663)|positive regulation of immunoglobulin production in mucosal tissue (GO:2000558)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 cell cytokine production (GO:2000556)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of thymocyte migration (GO:2000412)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of inflammatory response (GO:0050727)|release of sequestered calcium ion into cytosol (GO:0051209)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|protein homodimerization activity (GO:0042803)			kidney(2)|lung(7)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.208)					CACTTTACACGCTCATGGACT	0.413	NA	NA											G|||	747	0.149161	0.1679	0.1527	5008	,	,	NA	18432	0.1915	NA	0.1014	False	NA	,,,	NA	NA	NA	2504	0.1268	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D43768	CCDS1274.1	1q24.2	2014-01-30	2002-08-22	2002-08-23	ENSG00000143184	ENSG00000143184	6375		Endogenous ligands	10645	protein-coding gene	gene with protein product		600250	small inducible cytokine subfamily C, member 1 (lymphotactin)	LTN, SCYC1	NA	7602097, 7875320	Standard	NM_002995	NM_002995	NA	Approved	LPTN, ATAC, SCM-1a, SCM-1, lymphotactin	uc001gfo.2	P47992	OTTHUMG00000034548	ENST00000367818.3:c.*54G>C	chr1.hg19:g.168550512G>C		NA	Q52MA8	hg19	CCDS1274.1	0.02	20.174201	CACxCTC	COVERED																																																																																			NOVEL	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083612.1	6	9.41054	KEEP	47	5	180	94	3270	GG	1	1	0		+	24	27	827	0	0	50.741462	558	60	20407	916	ENST00000367818.3	0.041237	1
F5	2153	__UNKNOWN__	__UNKNOWN__	1	169510367	169510367	__UNKNOWN__	Missense_Mutation	SNP	T	T	G	rs112331368		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:169510367T>G	ENST00000367797.3	-	13	4162	c.3961A>C	c.(3961-3963)Att>Ctt	p.I1321L	F5_ENST00000367796.3_Missense_Mutation_p.I1326L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1321	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.	NA			blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	TCTGGAGAAATGGGCATCTGA	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						241	263	256	NA		NA	NA	1		NA											NA				169510367		2203	4300	6503	SO:0001583	missense			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734	2153			3542	protein-coding gene	gene with protein product		612309			NA		Standard	NM_000130	NM_000130	NA	Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.3961A>C	chr1.hg19:g.169510367T>G	ENSP00000356771:p.Ile1321Leu	NA	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	hg19	CCDS1281.1	0.02	17.658441	AAAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.030	-1.339000	0.01287	.	.	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.27402	1.67;1.67	4.43	-1.86	0.07760	.	1.363260	0.04512	N	0.383023	T	0.01222	0.0040	N	0.00408	-1.53	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.24512	-1.0158	9	0.02654	T	1	0.3928	0.6533	0.00830	0.2782:0.1115:0.2426:0.3678	.	1321	P12259	FA5_HUMAN	L	1321;1326	ENSP00000356771:I1321L;ENSP00000356770:I1326L	ENSP00000356770:I1326L	I	-	1	0	F5	167776991	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.185000	0.03073	-0.636000	0.05524	-2.880000	0.00097	ATT	NOVEL	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083712.1	6	10.560832	KEEP	5	1	37	48	1458	TT	1	1	0		-	13	40	439	0	0	24.512666	458	60	16249	644	ENST00000367797.3	0.027601	1
CACNA1E	777	__UNKNOWN__	__UNKNOWN__	1	181548452	181548452	__UNKNOWN__	Intron	SNP	A	A	G	rs544033384		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:181548452A>G	ENST00000367570.1	+	5	934				CACNA1E_ENST00000360108.3_Intron|CACNA1E_ENST00000367573.2_Intron|CACNA1E_ENST00000526775.1_Intron|CACNA1E_ENST00000357570.5_Intron|CACNA1E_ENST00000358338.5_Intron|CACNA1E_ENST00000367567.4_Intron	NM_000721.3	NP_000712.2	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	NA		NA			calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						TTGGAAAAGTATGTCCTATTC	0.433	NA	NA											A|||	1	0.000199681	0	0	5008	,	,	NA	21599	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216	777		Calcium channel subunits, Voltage-gated ion channels / Calcium channels, EF-hand domain containing	1392	protein-coding gene	gene with protein product		601013		CACNL1A6	NA	8388125, 16382099	Standard	NM_000721	NM_001205293	NA	Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367570.1:c.769+92A>G	chr1.hg19:g.181548452A>G		NA	B1AM12|B1AM13|B1AM14|Q14580|Q14581	hg19	CCDS53443.1	0.02	7.204058	AGTxTGT	COVERED																																																																																			NOVEL	CACNA1E-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090791.2	1	4.809952	KEEP	0	0	0	16	449	AA	0.997832	0.997832	0		+	7	60	278	0	0	18.140307	182	60	6681	214	ENST00000367570.1	0.037037	1
CRB1	23418	__UNKNOWN__	__UNKNOWN__	1	197313530	197313530	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:197313530C>A	ENST00000367399.2	+	3	652				CRB1_ENST00000543483.1_5'UTR|CRB1_ENST00000535699.1_Missense_Mutation_p.H189N|CRB1_ENST00000538660.1_Missense_Mutation_p.H258N|CRB1_ENST00000367400.3_Missense_Mutation_p.H258N	NM_001193640.1	NP_001180569.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	NA		NA			cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						CCTGGGGGATCACTGTGAACT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						246	221	230	NA		NA	NA	1		NA											NA				197313530		2203	4300	6503	SO:0001627	intron_variant				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376	23418			2343	protein-coding gene	gene with protein product		604210	crumbs (Drosophila) homolog 1, crumbs homolog 1 (Drosophila)	RP12	NA	10373321, 10508521	Standard	NM_201253	NM_201253	NA	Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367399.2:c.653-12431C>A	chr1.hg19:g.197313530C>A		NA	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	hg19	CCDS53454.1	0.02	9.346428	GATxACT	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.937	-0.444513	0.04604	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400	D;D;D	0.91464	-2.85;-2.85;-2.85	5.35	1.2	0.21068	EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.77896	0.4199	N	0.05441	-0.05	0.09310	N	1	B;B;B;B	0.28178	0.077;0.181;0.202;0.014	B;B;B;B	0.32090	0.024;0.055;0.14;0.005	T	0.65425	-0.6171	9	0.27785	T	0.31	.	4.1544	0.10254	0.1402:0.5998:0.12:0.1399	.	258;189;258;283	B7Z5T2;F5H0L2;P82279;Q59H36	.;.;CRUM1_HUMAN;.	N	189;258;258	ENSP00000438786:H189N;ENSP00000438091:H258N;ENSP00000356370:H258N	ENSP00000356370:H258N	H	+	1	0	CRB1	195580153	0.000000	0.05858	0.006000	0.13384	0.151000	0.21798	0.466000	0.22019	-0.046000	0.13446	0.650000	0.86243	CAC	NOVEL	CRB1-005	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280653.1	0	7.524784	KEEP	0	0	0	25	903	CC	0.999931	0.999931	0		+	43	60	1572	0	0	130.802117	174	60	6707	303	ENST00000367399.2	0.198157	1
PKP1	5317	__UNKNOWN__	__UNKNOWN__	1	201286950	201286950	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:201286950A>C	ENST00000367324.3	+	5	1305				PKP1_ENST00000263946.3_Intron|PKP1_ENST00000352845.3_Intron|PKP1_ENST00000475988.1_Intron	NM_001005337.2	NP_001005337.1	Q13835	PKP1_HUMAN	plakophilin 1	NA		NA			apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						AGGGCTGTGCAAGGCCACTGG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						12	13	12	NA		NA	NA	1		NA											NA				201286950		2188	4279	6467	SO:0001627	intron_variant			X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277	5317		Armadillo repeat containing	9023	protein-coding gene	gene with protein product	ectodermal dysplasia/skin fragility syndrome	601975	plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)		NA	9272178	Standard	NM_000299	NM_001005337	NA	Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000367324.3:c.1054+43A>C	chr1.hg19:g.201286950A>C		NA	O00645|Q14CA0|Q15152	hg19	CCDS30967.1	0.02	-0.315823	TGCxAGG	COVERED																																																																																			NOVEL	PKP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086894.1	1	4.209887	KEEP	0	0	0	14	382	AA	0.995343	0.814653	0		+	4	60	136	0	0	10.056656	32	60	1127	51	ENST00000367324.3	0.111111	0.818465
IPO9	55705	__UNKNOWN__	__UNKNOWN__	1	201851033	201851033	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:201851033G>T	ENST00000361565.4	+	0	9046					NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	NA		NA			protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						aaagtcagtaggacttAAAGA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700	55705		Importins	19425	protein-coding gene	gene with protein product		NA			NA	11823430, 10574461	Standard	NM_018085	NM_018085	NA	Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.*5851G>T	chr1.hg19:g.201851033G>T		NA	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	hg19	CCDS1415.1	0.02	6.918647	GTAxGAC	COVERED																																																																																			NOVEL	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087088.1	1	5.116617	KEEP	0	0	0	17	598	GG	0.999366	0.999366	0		+	35	60	1309	0	0	109.475569	141	60	5139	211	ENST00000361565.4	0.198864	1
SRGAP2	23380	__UNKNOWN__	__UNKNOWN__	1	206575069	206575069	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:206575069A>C	ENST00000414007.1	+	4	636				SRGAP2_ENST00000419187.2_Intron			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	NA		NA			actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					GATTAATTACACAGAAGGCAC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028	23380		Rho GTPase activating proteins	19751	protein-coding gene	gene with protein product		606524	formin binding protein 2	FNBP2	NA	15046868, 11672528	Standard	NM_015326	XM_005277510	NA	Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.636+65A>C	chr1.hg19:g.206575069A>C		NA		hg19		0.02	15.220336	TACxCAG	COVERED																																																																																			NOVEL	SRGAP2-201	KNOWN	basic	protein_coding	NA	protein_coding		4	9.926459	KEEP	15	0	0	33	955	AA	0.999998	0.999998	0		+	32	27	1141	0	0	81.435098	355	50	12189	448	ENST00000414007.1	0.082687	1
YOD1	55432	__UNKNOWN__	__UNKNOWN__	1	207219115	207219115	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:207219115G>T	ENST00000315927.4	-	0	4343				YOD1_ENST00000367084.1_3'UTR|YOD1_ENST00000391927.1_3'UTR	NM_018566.3	NP_061036.3	Q5VVQ6	OTU1_HUMAN	YOD1 deubiquitinase	NA		NA			cellular amino acid metabolic process (GO:0006520)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)		Lys48-specific deubiquitinase activity (GO:1990380)|metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11	Prostate(682;0.19)					GGCATTTAGGGACACAGACAA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS31002.1, CCDS60402.1	1q32.2	2013-06-04	2013-06-04		ENSG00000180667	ENSG00000180667	55432		OTU domain containing	25035	protein-coding gene	gene with protein product		612023	YOD1 OTU deubiquinating enzyme 1 homolog ( yeast), YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)		NA		Standard	NM_018566	NM_001276320	NA	Approved	DKFZp451J1719, OTUD2, DUBA8	uc001hfe.1	Q5VVQ6	OTTHUMG00000036032	ENST00000315927.4:c.*3250C>A	chr1.hg19:g.207219115G>T		NA	B2RNX3|Q5VVQ5|Q6ZRS6|Q86T63|Q9P1L8	hg19	CCDS31002.1	0.02	6.246207	AGGxACA	COVERED																																																																																			NOVEL	YOD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087837.1	3	8.426663	KEEP	0	0	0	28	950	GG	0.999997	0.999997	0		-	17	60	616	0	0	45.578739	156	60	5809	235	ENST00000315927.4	0.098266	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	208480641	208480641	__UNKNOWN__	IGR	SNP	C	C	T	rs5023225	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:208480641C>T			NA	NA				PLXNA2 (62976 upstream) : RP11-565N2.1 (299803 downstream)						NA		NA									NA						cctcccaaagcgctgggatta	0.498	NA	NA											-|||	2001	0.399561	0.7844	0.2738	5008	,	,	NA	23510	0.3938	NA	0.1809	False	NA	,,,	NA	NA	NA	2504	0.1994	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.208480641C>T		NA		hg19		0.02	-0.313835	AAGxGCT	COVERED																																																																																			NOVEL					0			40	4.180068	KEEP	32	2	66	37	1237	CC	0.999957	0.818429	0			3	60	104	0	0	7.395511	32	60	1108	134		0.085714	0.818465
VASH2	79805	__UNKNOWN__	__UNKNOWN__	1	213124073	213124073	__UNKNOWN__	5'UTR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:213124073C>A	ENST00000366968.4	+	0	138				VASH2_ENST00000366964.3_5'UTR|VASH2_ENST00000366966.2_5'UTR|VASH2_ENST00000271776.4_3'UTR|VASH2_ENST00000366967.2_5'UTR|VASH2_ENST00000366965.2_5'UTR	NM_001136474.1	NP_001129946.1	Q86V25	VASH2_HUMAN	vasohibin 2	NA		NA			positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		ATGAAGCCAACCGTCCCGAGG	0.716	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494	79805			25723	protein-coding gene	gene with protein product		610471			NA	16528006	Standard	NM_024749	XR_247041	NA	Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000366968.4:c.-213C>A	chr1.hg19:g.213124073C>A		NA	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	hg19	CCDS44315.1	0.02	-0.052632	CAAxCGT	UNCOVERED																																																																																			NOVEL	VASH2-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089682.2	1	2.407553	KEEP	0	0	0	8	270	CC	0.99257	0.036492	0		+	4	60	132	0	0	13.448768	2	60	75	17	ENST00000366968.4	0.666667	0.036766
PTPN14	5784	__UNKNOWN__	__UNKNOWN__	1	214656066	214656066	__UNKNOWN__	Intron	SNP	C	C	T	rs77576710	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:214656066C>T	ENST00000366956.5	-	2	41					NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	NA		NA			lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		AGACTCTCCTCCTCTATTTTT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(92;557 1424 24372 34121 40073)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104	5784		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	9647	protein-coding gene	gene with protein product		603155			NA	7733990	Standard	NM_005401	NM_005401	NA	Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.154-17766G>A	chr1.hg19:g.214656066C>T		NA	Q5VSI0	hg19	CCDS1514.1	0.02	9.238189	CCTxCTC	COVERED																																																																																			NOVEL	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089918.2	1	13.630107	KEEP	26	1	33	57	1931	CC	1	1	0		-	9	40	309	0	0	17.694553	288	60	10770	477	ENST00000366956.5	0.030303	1
EPRS	2058	__UNKNOWN__	__UNKNOWN__	1	220152718	220152718	__UNKNOWN__	Intron	SNP	G	G	T	rs565797137	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:220152718G>T	ENST00000366923.3	-	27	4179					NM_004446.2	NP_004437.2	P07814	SYEP_HUMAN	glutamyl-prolyl-tRNA synthetase	NA		NA			cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|glutamyl-tRNA aminoacylation (GO:0006424)|negative regulation of translation (GO:0017148)|prolyl-tRNA aminoacylation (GO:0006433)|protein complex assembly (GO:0006461)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|GAIT complex (GO:0097452)|membrane (GO:0016020)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|glutamate-tRNA ligase activity (GO:0004818)|proline-tRNA ligase activity (GO:0004827)|RNA stem-loop binding (GO:0035613)			breast(2)|endometrium(11)|kidney(2)|large_intestine(13)|lung(24)|ovary(1)|prostate(3)|skin(2)|stomach(2)|urinary_tract(3)	63				GBM - Glioblastoma multiforme(131;0.0735)	L-Proline(DB00172)	AATATGGCTTGTATTTTATAA	0.368	NA	NA											G|||	1540	0.307508	0.298	0.3055	5008	,	,	NA	15182	0.3611	NA	0.2873	False	NA	,,,	NA	NA	NA	2504	0.2873	NA	NA	NA						NA		NA				0							NA						20	20	20	NA		NA	NA	1		NA											NA				220152718		2202	4300	6502	SO:0001627	intron_variant			X54326	CCDS31027.1	1q41	2011-07-01			ENSG00000136628	ENSG00000136628	2058	6.1.1.15, 6.1.1.17	Aminoacyl tRNA synthetases / Class I, Aminoacyl tRNA synthetases / Class II	3418	protein-coding gene	gene with protein product	glutamate tRNA ligase, proline tRNA ligase	138295		QPRS, QARS	NA	1988429	Standard	NM_004446	NM_004446	NA	Approved	EARS, PARS, GLUPRORS	uc001hly.1	P07814	OTTHUMG00000037433	ENST00000366923.3:c.3909+41C>A	chr1.hg19:g.220152718G>T		NA	A0AVA9|B9EGH3|Q05BP6|Q05DF8|Q5DSM1|Q5H9S5|Q6PD57|Q86X73	hg19	CCDS31027.1	0.02	1.124817	CTTxTAT	COVERED																																																																																			NOVEL	EPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091133.2	1	3.001928	KEEP	0	0	0	10	282	GG	0.992708	0.99267	0		-	15	60	237	0	0	13.106918	84	60	2062	130	ENST00000366923.3	0.151515	0.999962
PSEN2	5664	__UNKNOWN__	__UNKNOWN__	1	227068322	227068322	__UNKNOWN__	5'UTR	SNP	A	A	C	rs200137699		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:227068322A>C	ENST00000366782.1	+	0	476				PSEN2_ENST00000366783.3_Intron|PSEN2_ENST00000422240.2_Intron|PSEN2_ENST00000340188.4_Intron			P49810	PSN2_HUMAN	presenilin 2	NA		NA			amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				GGACAGCGATAACTCAGCCTC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						179	161	166	NA		NA	NA	1		NA											NA				227068322		876	1991	2867	SO:0001623	5_prime_UTR_variant			BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801	5664			9509	protein-coding gene	gene with protein product		600759	Alzheimer disease 4	AD4	NA	7638621	Standard	NM_000447	NM_000447	NA	Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366782.1:c.-25A>C	chr1.hg19:g.227068322A>C		NA	A8K8D4|B1AP21|Q96P32	hg19		0.02	19.769362	GATxACT	COVERED																																																																																			NOVEL	PSEN2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000091540.1	4	6.706488	KEEP	0	8	253	111	3150	AA	1	1	0		+	22	60	839	0	0	57.099499	391	60	13855	717	ENST00000366782.1	0.053269	1
CDC42BPA	8476	__UNKNOWN__	__UNKNOWN__	1	227178103	227178103	__UNKNOWN__	3'UTR	SNP	A	A	G	rs562976671		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:227178103A>G	ENST00000366769.3	-	0	10317				CDC42BPA_ENST00000366767.3_3'UTR|CDC42BPA_ENST00000366764.2_3'UTR|CDC42BPA_ENST00000334218.5_3'UTR|CDC42BPA_ENST00000366766.2_3'UTR	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)	NA		NA								NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCTGGACTTGAGTAACAAAGT	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776	8476			1737	protein-coding gene	gene with protein product	myotonic dystrophy kinase-related Cdc42-binding kinase	603412	CDC42-binding protein kinase alpha (DMPK-like)		NA		Standard	NM_014826	NM_003607	NA	Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.*3866T>C	chr1.hg19:g.227178103A>G		NA		hg19	CCDS1558.1	0.02	4.842954	TTGxGTA	COVERED																																																																																			NOVEL	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091696.1	1	11.433977	KEEP	0	0	0	38	1183	AA	1	1	0		-	28	60	1005	0	0	84.551994	101	60	3752	193	ENST00000366769.3	0.217054	1
PGBD5	79605	__UNKNOWN__	__UNKNOWN__	1	230493095	230493095	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:230493095C>T	ENST00000525115.1	-	2	148				PGBD5_ENST00000321327.2_Intron|PGBD5_ENST00000391860.1_Intron			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	NA		NA				integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		GTGGAGTGTTCCTTAGGACGG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						19	19	19	NA		NA	NA	1		NA											NA				230493095		2203	4300	6503	SO:0001627	intron_variant			AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614	79605			19405	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024554	NM_001258311	NA	Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.125-28G>A	chr1.hg19:g.230493095C>T		NA	A0PJF3|B9EK58|Q5SR37|Q6PJN2	hg19		0.02	12.219319	GTTxCTT	COVERED																																																																																			NOVEL	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000382617.1	5	28.578845	KEEP	0	0	0	95	3118	CC	1	1	0		-	70	60	2306	0	0	189.789831	262	60	9217	567	ENST00000525115.1	0.210843	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	232259468	232259468	__UNKNOWN__	IGR	SNP	A	A	T	rs12064215	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:232259468A>T			NA	NA				DISC1 (82450 upstream) : RP5-865N13.2 (36368 downstream)						NA		NA									NA						ctcaaaaagcacccccactga	0.483	NA	NA											A|||	3428	0.684505	0.8026	0.6268	5008	,	,	NA	18436	0.7768	NA	0.5209	False	NA	,,,	NA	NA	NA	2504	0.6391	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.232259468A>T		NA		hg19		0.02	-0.087726	AGCxCCC	UNCOVERED																																																																																			NOVEL					0			1	3.007124	KEEP	17	0	0	10	311	AA	0	0	0			3	40	118	0	0	10.578619	7	40	244	46		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	232259487	232259487	__UNKNOWN__	IGR	SNP	C	C	T	rs200843226		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:232259487C>T			NA	NA				DISC1 (82469 upstream) : RP5-865N13.2 (36349 downstream)						NA		NA									NA						gagcaccttgcgacccccact	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.232259487C>T		NA		hg19		0.02	-0.070178	TTGxGAC	UNCOVERED																																																																																			NOVEL					0			1	3.009758	KEEP	17	0	0	10	358	CC	0	0	0			3	40	107	0	0	9.833025	5	40	177	42		0.375	0.054137
CEP170	9859	__UNKNOWN__	__UNKNOWN__	1	243327939	243327939	__UNKNOWN__	Missense_Mutation	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:243327939A>C	ENST00000366542.1	-	13	3374	c.3323T>G	c.(3322-3324)cTt>cGt	p.L1108R	CEP170_ENST00000366544.1_Missense_Mutation_p.L1010R|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.L1010R	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1108	Targeting to microtubules.	NA				centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			AGCTTCACCAAGTCGTGCTCT	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						66	61	63	NA		NA	NA	1		NA											NA				243327939		1951	4144	6095	SO:0001583	missense			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702	9859			28920	protein-coding gene	gene with protein product	KARP 1 binding protein, XRCC5 binding protein	613023	KIAA0470	KIAA0470	NA	15616186	Standard	NM_014812	NM_014812	NA	Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.3323T>G	chr1.hg19:g.243327939A>C	ENSP00000355500:p.Leu1108Arg	NA	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	hg19	CCDS44339.1	0.02	10.055315	CCAxGTC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.95|13.95	2.389291|2.389291	0.42410|0.42410	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000532008|ENST00000336415	T;T;T|T	0.75938|0.69806	-0.48;-0.51;-0.98|-0.43	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.77032|0.77032	0.4071|0.4071	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	B;D;D;D|.	0.76494|.	0.005;0.999;0.999;0.999|.	B;D;D;D|.	0.85130|.	0.021;0.996;0.996;0.997|.	T|T	0.78272|0.78272	-0.2268|-0.2268	10|8	0.37606|0.46703	T|T	0.19|0.11	-10.3616|-10.3616	13.9643|13.9643	0.64199|0.64199	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1071;1010;1010;1108|.	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79|.	.;.;.;CE170_HUMAN|.	R|V	1108;1010;1010;69|1072	ENSP00000355500:L1108R;ENSP00000355502:L1010R;ENSP00000355501:L1010R|ENSP00000338161:L1072V	ENSP00000355500:L1108R|ENSP00000338161:L1072V	L|L	-|-	2|1	0|2	CEP170|CEP170	241394562|241394562	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	8.663000|8.663000	0.91134|0.91134	1.879000|1.879000	0.54435|0.54435	0.454000|0.454000	0.30748|0.30748	CTT|TTG	NOVEL	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096178.2	2	6.553313	KEEP	16	1	26	31	996	AA	0.999997	0.999997	0		-	13	27	444	0	0	27.942101	259	60	9572	376	ENST00000366542.1	0.047794	1
CEP170	9859	__UNKNOWN__	__UNKNOWN__	1	243332731	243332731	__UNKNOWN__	Intron	SNP	G	G	A	rs201349181		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:243332731G>A	ENST00000366542.1	-	12	1895				CEP170_ENST00000366544.1_Intron|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Intron	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	NA		NA				centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CTTATAAAATGAATTCATTTA	0.244	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702	9859			28920	protein-coding gene	gene with protein product	KARP 1 binding protein, XRCC5 binding protein	613023	KIAA0470	KIAA0470	NA	15616186	Standard	NM_014812	NM_014812	NA	Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.1843+198C>T	chr1.hg19:g.243332731G>A		NA	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	hg19	CCDS44339.1	0.02	-0.386027	AATxAAT	COVERED																																																																																			NOVEL	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096178.2	1	2.708938	KEEP	1	0	0	9	326	GG	0.99254	0.911321	0		-	9	60	318	0	0	26.413361	35	60	1344	61	ENST00000366542.1	0.204545	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	243419304	243419304	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:243419304G>A			NA	NA				CEP170 (681 upstream) : SDCCAG8 (15 downstream)						NA		NA									NA						CAAAGCGAGGGCCAGTGGGTG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.243419304G>A		NA		hg19		0.02	1.970714	AGGxCCA	COVERED																																																																																			NOVEL					0			2	8.422829	KEEP	0	0	0	28	898	GG	0.999997	0.986151	0			6	60	212	0	0	15.640221	53	60	1893	88		0.101695	0.986153
OR2W5	441932	__UNKNOWN__	__UNKNOWN__	1	247654794	247654794	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:247654794G>A	ENST00000522351.1	+	0	425							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			TCCCATGACCGCTATGTGGCC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						99	87	91	NA		NA	NA	1		NA											NA				247654794		2203	4300	6503							1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664	441932		GPCR / Class A : Olfactory receptors	15424	other	unknown		NA		OR2W5P	NA	12213199	Standard	NM_001004698	NM_001004698	NA	Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573	ENST00000522351.1:	chr1.hg19:g.247654794G>A		NA	B9EH85	hg19		0.02	9.365763	ACCxCTA	COVERED																																																																																			NOVEL	OR2W5-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000375789.1	5	16.338028	KEEP	0	1	30	65	2122	GG	1	1	0		+	85	60	3032	0	0	274.343555	164	60	5596	348	ENST00000522351.1	0.341365	1
OR2L8	391190	__UNKNOWN__	__UNKNOWN__	1	248112554	248112554	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs202165563		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:248112554T>C	ENST00000357191.3	+	1	395	c.395T>C	c.(394-396)cTc>cCc	p.L132P	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	132		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L132P(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CTCCACTATCTCATCCGCATG	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	skin(1)					NA						294	255	269	NA		NA	NA	1		NA											NA				248112554		2203	4300	6503	SO:0001583	missense			BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936	391190		GPCR / Class A : Olfactory receptors	15014	protein-coding gene	gene with protein product		NA	olfactory receptor, family 2, subfamily L, member 8		NA		Standard		NM_001001963	NA	Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.395T>C	chr1.hg19:g.248112554T>C	ENSP00000349719:p.Leu132Pro	NA	Q6IF03	hg19	CCDS31101.1	0.02	24.390905	ATCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	.	0	-2.779851	0.00079	.	.	ENSG00000196936	ENST00000357191	T	0.00648	5.99	1.64	-3.28	0.05033	GPCR, rhodopsin-like superfamily (1);	0.569254	0.13211	N	0.405136	T	0.00210	0.0006	N	0.00554	-1.385	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32402	-0.9908	10	0.02654	T	1	.	2.9738	0.05930	0.1117:0.4051:0.1115:0.3717	.	132	Q8NGY9	OR2L8_HUMAN	P	132	ENSP00000349719:L132P	ENSP00000349719:L132P	L	+	2	0	OR2L8	246179177	0.000000	0.05858	0.002000	0.10522	0.242000	0.25591	-4.646000	0.00204	-2.286000	0.00670	-2.951000	0.00084	CTC	NOVEL	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096853.2	8	4.182013	KEEP	19	5	154	68	2133	TT	1	1	0		+	18	40	666	0	0	40.384714	561	60	20623	792	ENST00000357191.3	0.031088	1
ZNF692	55657	__UNKNOWN__	__UNKNOWN__	1	249149969	249149969	__UNKNOWN__	Missense_Mutation	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr1:249149969A>C	ENST00000306601.4	-	7	1002	c.836T>G	c.(835-837)cTc>cGc	p.L279R	ZNF692_ENST00000366469.5_Missense_Mutation_p.L278R|ZNF692_ENST00000451251.1_Missense_Mutation_p.L284R|ZNF692_ENST00000427146.1_Missense_Mutation_p.L234R|ZNF692_ENST00000366471.3_Missense_Mutation_p.L234R	NM_017865.3	NP_060335.2	Q9BU19	ZN692_HUMAN	zinc finger protein 692	279		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(6)|lung(7)|stomach(1)	17	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GGTCCTGCTGAGCTGTGGCTG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						57	62	60	NA		NA	NA	1		NA											NA				249149969		2203	4300	6503	SO:0001583	missense			BC002948	CCDS31127.1, CCDS44348.1, CCDS53487.1	1q44	2013-01-08			ENSG00000171163	ENSG00000171163	55657		Zinc fingers, C2H2-type	26049	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_017865	NM_001136036	NA	Approved	FLJ20531, Zfp692	uc001ifc.2	Q9BU19	OTTHUMG00000040423	ENST00000306601.4:c.836T>G	chr1.hg19:g.249149969A>C	ENSP00000305483:p.Leu279Arg	NA	B4DXZ0|Q5SRA5|Q5SRA6|Q9HBC9|Q9NW93|Q9NWY6|Q9UF97	hg19	CCDS31127.1	0.02	7.442707	CTGxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	A	12.13	1.845845	0.32606	.	.	ENSG00000171163	ENST00000306601;ENST00000427146;ENST00000366470;ENST00000366471;ENST00000366469;ENST00000451251	T;T;T;T;T	0.08634	3.09;3.12;3.12;3.07;3.07	4.27	1.89	0.25635	.	0.270289	0.26324	N	0.025025	T	0.07548	0.0190	L	0.56769	1.78	0.09310	N	1	P;P;P;P	0.45902	0.868;0.703;0.703;0.868	B;B;B;B	0.40228	0.23;0.323;0.323;0.23	T	0.26643	-1.0097	10	0.42905	T	0.14	-5.4812	2.744	0.05262	0.6023:0.0:0.2071:0.1905	.	284;234;107;279	B4DXZ0;Q9BU19-2;Q9BU19-3;Q9BU19	.;.;.;ZN692_HUMAN	R	279;234;107;234;278;284	ENSP00000305483:L279R;ENSP00000390044:L234R;ENSP00000355427:L234R;ENSP00000355425:L278R;ENSP00000391200:L284R	ENSP00000305483:L279R	L	-	2	0	ZNF692	247116592	0.012000	0.17670	0.000000	0.03702	0.018000	0.09664	0.528000	0.23002	0.282000	0.22254	0.379000	0.24179	CTC	NOVEL	ZNF692-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097298.1	2	26.975103	KEEP	0	1	6	92	2779	AA	1	1	0		-	7	60	233	0	0	14.555012	154	60	5679	304	ENST00000306601.4	0.043478	1
TRAPPC12	51112	__UNKNOWN__	__UNKNOWN__	2	3391442	3391442	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:3391442G>A	ENST00000324266.5	+	2	243	c.48G>A	c.(46-48)ccG>ccA	p.P16P	TRAPPC12_ENST00000382110.2_Silent_p.P16P	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	16		NA			vesicle-mediated transport (GO:0016192)						NA						CGGAGGCCCCGCACCCCCCTC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						10	10	10	NA		NA	NA	2		NA											NA				3391442		2142	4212	6354	SO:0001819	synonymous_variant			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853	51112		Trafficking protein particle complex, Tetratricopeptide (TTC) repeat domain containing	24284	protein-coding gene	gene with protein product		614139	tetratricopeptide repeat domain 15	TTC15	NA	10810093, 21525244, 20562859	Standard	NM_016030	NM_016030	NA	Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.48G>A	chr2.hg19:g.3391442G>A		NA	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	hg19	CCDS1652.1	0.02	10.431526	CCCxCAC	COVERED																																																																																			NOVEL	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206693.2	2	63.4697	KEEP	0	0	0	211	6878	GG	1	1	0		+	12	60	424	0	0	26.515864	274	60	9198	591	ENST00000324266.5	0.041958	1
MFSD2B	388931	__UNKNOWN__	__UNKNOWN__	2	24239933	24239933	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:24239933T>C	ENST00000406420.3	+	4	487				MFSD2B_ENST00000338315.4_Intron	NM_001080473.1	NP_001073942.1	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing 2B	NA		NA			transport (GO:0006810)	integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10						GCTGCCGCCCTCCCCACCCGC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46228.1	2p23.3	2010-05-11			ENSG00000205639	ENSG00000205639	388931			37207	protein-coding gene	gene with protein product		NA			NA	18694395	Standard	NM_001080473	NM_001080473	NA	Approved		uc002reo.2	A6NFX1	OTTHUMG00000090819	ENST00000406420.3:c.471+95T>C	chr2.hg19:g.24239933T>C		NA	B5MC32	hg19	CCDS46228.1	0.02	1.430043	CCCxCCC	COVERED																																																																																			NOVEL	MFSD2B-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324307.1	1	4.941445	KEEP	0	1	24	25	729	TT	0.999957	0.994379	0		+	12	60	171	0	0	9.766411	53	60	1557	166	ENST00000406420.3	0.184615	0.994422
MFSD2B	388931	__UNKNOWN__	__UNKNOWN__	2	24239938	24239938	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:24239938A>C	ENST00000406420.3	+	4	487				MFSD2B_ENST00000338315.4_Intron	NM_001080473.1	NP_001073942.1	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing 2B	NA		NA			transport (GO:0006810)	integral component of membrane (GO:0016021)				cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10						CGCCCTCCCCACCCGCCTGTG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46228.1	2p23.3	2010-05-11			ENSG00000205639	ENSG00000205639	388931			37207	protein-coding gene	gene with protein product		NA			NA	18694395	Standard	NM_001080473	NM_001080473	NA	Approved		uc002reo.2	A6NFX1	OTTHUMG00000090819	ENST00000406420.3:c.471+100A>C	chr2.hg19:g.24239938A>C		NA	B5MC32	hg19	CCDS46228.1	0.02	1.596973	CCCxCCC	COVERED																																																																																			NOVEL	MFSD2B-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324307.1	1	3.528778	KEEP	0	1	23	20	497	AA	0.999869	0.981827	0		+	10	60	151	0	0	8.682103	46	60	1177	150	ENST00000406420.3	0.178571	0.981955
HEATR5B	54497	__UNKNOWN__	__UNKNOWN__	2	37267652	37267652	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:37267652G>A	ENST00000233099.5	-	20	2961	c.2866C>T	c.(2866-2868)Ctt>Ttt	p.L956F	HEATR5B_ENST00000354531.2_Missense_Mutation_p.L956F	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	956		NA				extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AGTGAATGAAGAGACCAAGTC	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						67	61	63	NA		NA	NA	2		NA											NA				37267652		2203	4300	6503	SO:0001583	missense			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869	54497			29273	protein-coding gene	gene with protein product		NA			NA	10718198	Standard	NM_019024	XM_005264379	NA	Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.2866C>T	chr2.hg19:g.37267652G>A	ENSP00000233099:p.Leu956Phe	NA	B5MDU8|Q7Z3B2|Q9NVL7	hg19	CCDS33181.1	0.02	11.456183	GAAxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	29.1	4.978158	0.92982	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.70282	-0.47;-0.47	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.86552	0.5960	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.88281	0.2936	10	0.87932	D	0	-16.3817	19.3907	0.94581	0.0:0.0:1.0:0.0	.	956	Q9P2D3	HTR5B_HUMAN	F	956	ENSP00000233099:L956F;ENSP00000346531:L956F	ENSP00000233099:L956F	L	-	1	0	HEATR5B	37121156	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.766000	0.98957	2.569000	0.86673	0.655000	0.94253	CTT	NOVEL	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325492.1	0	9.928516	KEEP	0	0	0	33	1135	GG	0.999998	0.999998	0		-	158	60	5633	0	0	554.226053	125	60	4710	362	ENST00000233099.5	0.558304	1
EML4	27436	__UNKNOWN__	__UNKNOWN__	2	42509973	42509973	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:42509973C>T	ENST00000318522.5	+	8	1064	c.802C>T	c.(802-804)Cga>Tga	p.R268*	EML4_ENST00000401738.3_Nonsense_Mutation_p.R279*|EML4_ENST00000402711.2_Nonsense_Mutation_p.R210*	NM_019063.3	NP_061936	Q9HC35	EMAL4_HUMAN	echinoderm microtubule associated protein like 4	268		NA			microtubule-based process (GO:0007017)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|mitotic spindle (GO:0072686)			EML4/ALK(543)	NS(2)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	12						ATATGGTTATCGAGGAAAGGA	0.328	NA	NA	T	ALK	NSCLC									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		2	2p21	27436	echinoderm microtubule associated protein like 4		E	0							NA						125	126	126	NA		NA	NA	2		NA											NA				42509973		2203	4300	6503	SO:0001587	stop_gained			AF177377	CCDS1807.1, CCDS46266.1	2p21	2013-01-10		2002-02-15	ENSG00000143924	ENSG00000143924	27436		WD repeat domain containing	1316	protein-coding gene	gene with protein product		607442		C2orf2	NA		Standard	NM_019063	NM_019063	NA	Approved	ROPP120, ELP120	uc002rsi.3	Q9HC35	OTTHUMG00000128603	ENST00000318522.5:c.802C>T	chr2.hg19:g.42509973C>T	ENSP00000320663:p.Arg268*	NA	A6H8Y6|B2RBK3|B2RTW7|B5MCW9|Q3SWW0|Q53R29|Q53TW8|Q6PJ45|Q9NV40	hg19	CCDS1807.1	0.02	6.578643	TATxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	39	7.760972	0.98474	.	.	ENSG00000143924	ENST00000318522;ENST00000402711;ENST00000401738	.	.	.	5.7	1.55	0.23275	.	0.106578	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0406	11.2704	0.49136	0.3813:0.5085:0.1102:0.0	.	.	.	.	X	268;210;279	.	ENSP00000320663:R268X	R	+	1	2	EML4	42363477	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.719000	0.54926	-0.005000	0.14395	0.650000	0.86243	CGA	NOVEL	EML4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250463.3	1	9.330036	KEEP	0	0	0	31	1059	CC	0.999997	0.999997	0		+	19	60	676	0	0	49.756877	173	60	6366	260	ENST00000318522.5	0.098958	1
LHCGR	3973	__UNKNOWN__	__UNKNOWN__	2	48946233	48946233	__UNKNOWN__	Intron	SNP	G	G	A	rs10203717	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:48946233G>A	ENST00000294954.7	-	6	558				LHCGR_ENST00000403273.1_Intron|LHCGR_ENST00000405626.1_Intron|LHCGR_ENST00000401907.1_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000344775.3_Intron	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	NA		NA			activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	aggctgaggcgggcggatcac	0.498	NA	NA											a|||	473	0.0944489	0.0038	0.0375	5008	,	,	NA	17489	0.2083	NA	0.0726	False	NA	,,,	NA	NA	NA	2504	0.1626	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039	3973		GPCR / Class A : Gonadotropin and TSH receptors	6585	protein-coding gene	gene with protein product		152790	hypergonadotropic hypogonadism	HHG	NA		Standard	NM_000233.3	NM_000233	NA	Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.536+4361C>T	chr2.hg19:g.48946233G>A		NA	Q14751|Q15996|Q9UEW9	hg19	CCDS1842.1	0.02	-0.043866	GGCxGGC	UNCOVERED																																																																																			NOVEL	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251364.4	5	2.407849	KEEP	1	0	0	8	282	GG	0	0	0		-	2	49	75	0	0	6.992816	3	60	108	17	ENST00000294954.7	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	67049232	67049232	__UNKNOWN__	IGR	SNP	C	C	T	rs66679284	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:67049232C>T			NA	NA				AC007392.4 (118873 upstream) : AC007403.2 (82335 downstream)						NA		NA									NA						TGCTGGCCACCGGCAGGACTT	0.517	NA	NA											C|||	655	0.130791	0.1112	0.0937	5008	,	,	NA	19067	0.1746	NA	0.0885	False	NA	,,,	NA	NA	NA	2504	0.182	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.67049232C>T		NA		hg19		0.02	-0.36839	CACxGGC	COVERED																																																																																			NOVEL					0			1	3.009469	KEEP	0	0	0	10	331	CC	0.992708	0.892756	0			24	60	906	0	0	89.596595	18	60	610	56		0.571429	0.899314
ASPRV1	151516	__UNKNOWN__	__UNKNOWN__	2	70187827	70187827	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:70187827G>C	ENST00000320256.4	-	1	1570	c.994C>G	c.(994-996)Ccc>Gcc	p.P332A		NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1	NA		NA								endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						TCTGAGGAGGGGTCCTCCTCT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						85	89	88	NA		NA	NA	2		NA											NA				70187827		2203	4300	6503	SO:0001583	missense			AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617	151516			26321	protein-coding gene	gene with protein product	Skin ASpartic Protease	611765			NA	16098038, 16565508	Standard	NM_152792	NM_152792	NA	Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.994C>G	chr2.hg19:g.70187827G>C	ENSP00000315383:p.Pro332Ala	NA		hg19	CCDS1897.1	0.02	13.017466	AGGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.70	2.016725	0.35606	.	.	ENSG00000244617	ENST00000320256	T	0.44881	0.91	4.85	0.565	0.17309	.	1.486130	0.04976	N	0.464693	T	0.23727	0.0574	N	0.14661	0.345	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.18745	-1.0327	10	0.38643	T	0.18	-3.2168	1.9081	0.03281	0.1963:0.1564:0.4875:0.1597	.	332	Q53RT3	APRV1_HUMAN	A	332	ENSP00000315383:P332A	ENSP00000315383:P332A	P	-	1	0	ASPRV1	70041331	0.005000	0.15991	0.022000	0.16811	0.752000	0.42762	-0.171000	0.09883	0.179000	0.19938	0.655000	0.94253	CCC	NOVEL	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334161.1	2	17.154301	KEEP	0	0	0	57	1924	GG	1	1	0		-	81	60	2947	0	0	260.851083	195	60	7100	419	ENST00000320256.4	0.293478	1
TIA1	7072	__UNKNOWN__	__UNKNOWN__	2	70457825	70457825	__UNKNOWN__	Intron	SNP	C	C	A	rs111976691	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:70457825C>A	ENST00000415783.2	-	3	452				TIA1_ENST00000433529.2_Intron|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000416149.2_Intron|TIA1_ENST00000445587.1_Intron|TIA1_ENST00000282574.4_Intron	NM_022037.2	NP_071320.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	NA		NA			apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						AAAAAGGAAACAAAATCATAT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001	7072		RNA binding motif (RRM) containing	11802	protein-coding gene	gene with protein product	T-cell-restricted intracellular antigen-1, nucleolysin TIA-1 isoform p40	603518	TIA1 cytotoxic granule-associated RNA-binding protein		NA	8176212, 12486009	Standard	NM_022037	NM_022173	NA	Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000415783.2:c.222+62G>T	chr2.hg19:g.70457825C>A		NA	Q53SS9	hg19	CCDS1900.1	0.02	1.879385	AAAxAAA	COVERED																																																																																			NOVEL	TIA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251843.1	2	7.524318	KEEP	0	0	0	25	869	CC	0.999931	0.999931	0		-	14	60	239	0	0	12.271719	115	60	3768	179	ENST00000415783.2	0.108527	1
RETSAT	54884	__UNKNOWN__	__UNKNOWN__	2	85570978	85570978	__UNKNOWN__	Intron	SNP	A	A	G	rs28619418	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:85570978A>G	ENST00000295802.4	-	10	1646				RETSAT_ENST00000475624.2_Intron|RETSAT_ENST00000263854.6_Intron|RETSAT_ENST00000457495.2_Intron	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	NA		NA			oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	TCCCTCTTCCACTCTTTCCCA	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	54884	1.3.99.23		25991	protein-coding gene	gene with protein product		NA			NA	12975309, 15358783	Standard	NM_017750	NM_017750	NA	Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1534-57T>C	chr2.hg19:g.85570978A>G		NA	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	hg19	CCDS1972.1	0.02	-0.412176	TCCxCTC	COVERED																																																																																			NOVEL	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252489.1	1	2.70486	KEEP	0	0	0	9	243	AA	0.99254	0.934716	0		-	6	40	222	0	0	17.390673	39	60	1288	58	ENST00000295802.4	0.133333	0.941741
C2orf68	388969	__UNKNOWN__	__UNKNOWN__	2	85838575	85838575	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:85838575T>C	ENST00000306336.5	-	2	271				USP39_ENST00000459775.1_Intron|C2orf68_ENST00000478626.1_5'UTR|C2orf68_ENST00000409734.3_3'UTR	NM_001013649.3	NP_001013671.2	Q2NKX9	CB068_HUMAN	chromosome 2 open reading frame 68	NA		NA								breast(1)|central_nervous_system(1)|endometrium(1)	3						GGCTCCCCGATACTCTGACAG	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42704.1	2p11.2	2008-07-18			ENSG00000168887	ENSG00000168887	388969			34353	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013649	NM_001013649	NA	Approved		uc002sqc.2	Q2NKX9	OTTHUMG00000153088	ENST00000306336.5:c.226+215A>G	chr2.hg19:g.85838575T>C		NA	B4DT10|Q4G0J7|Q6ZVA6	hg19	CCDS42704.1	0.02	8.393916	CGAxACT	COVERED																																																																																			NOVEL	C2orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329451.1	2	21.032794	KEEP	0	0	0	70	1952	TT	1	1	0		-	8	60	288	0	0	17.833874	204	60	7239	319	ENST00000306336.5	0.037736	1
C2orf68	388969	__UNKNOWN__	__UNKNOWN__	2	85838591	85838591	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:85838591C>G	ENST00000306336.5	-	2	271				USP39_ENST00000459775.1_Intron|C2orf68_ENST00000478626.1_5'UTR|C2orf68_ENST00000409734.3_3'UTR	NM_001013649.3	NP_001013671.2	Q2NKX9	CB068_HUMAN	chromosome 2 open reading frame 68	NA		NA								breast(1)|central_nervous_system(1)|endometrium(1)	3						GACAGCGATGCTTAACTGGGG	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42704.1	2p11.2	2008-07-18			ENSG00000168887	ENSG00000168887	388969			34353	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013649	NM_001013649	NA	Approved		uc002sqc.2	Q2NKX9	OTTHUMG00000153088	ENST00000306336.5:c.226+199G>C	chr2.hg19:g.85838591C>G		NA	B4DT10|Q4G0J7|Q6ZVA6	hg19	CCDS42704.1	0.02	8.622393	ATGxTTA	COVERED																																																																																			NOVEL	C2orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329451.1	3	25.912487	KEEP	0	1	5	88	3156	CC	1	1	0		-	9	60	319	0	0	19.885955	211	60	7930	357	ENST00000306336.5	0.040909	1
RMND5A	64795	__UNKNOWN__	__UNKNOWN__	2	86980488	86980488	__UNKNOWN__	Intron	SNP	G	G	T	rs200296332	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:86980488G>T	ENST00000283632.4	+	4	915					NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	NA		NA								kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						TTAATGGCTTGCCCCATATTT	0.388	NA	NA											G|||	989	0.197484	0.1732	0.1873	5008	,	,	NA	17623	0.2917	NA	0.1869	False	NA	,,,	NA	NA	NA	2504	0.1513	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561	64795			25850	protein-coding gene	gene with protein product	GID complex subunit 2 homolog A	NA			NA	12477932	Standard	NM_022780	NM_022780	NA	Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.421-93G>T	chr2.hg19:g.86980488G>T		NA	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	hg19	CCDS1991.1	0.02	-0.32261	CTTxCCC	COVERED																																																																																			NOVEL	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252591.2	0	2.390474	KEEP	0	0	0	8	190	GG	0.99257	0.829507	0		+	7	60	112	0	0	6.827402	30	60	875	48	ENST00000283632.4	0.189189	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87355846	87355846	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:87355846T>C			NA	NA				PLGLB1 (106871 upstream) : MIR4771-2 (66062 downstream)						NA		NA									NA						CAATTTTTTTTGTTCTTCACC	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87355846T>C		NA		hg19		0.02	4.778173	TTTxGTT	COVERED																																																																																			NOVEL					0			2	4.244532	KEEP	1	1	31	25	729	TT	0.999957	0.999956	0			12	37	454	0	0	33.962265	113	60	4074	174		0.096	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87410070	87410070	__UNKNOWN__	IGR	SNP	T	T	C	rs200989520	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:87410070T>C			NA	NA				PLGLB1 (161095 upstream) : MIR4771-2 (11838 downstream)						NA		NA									NA						AAATTCATTCTTTTTCTTTCA	0.408	NA	NA											C|||	1883	0.375998	0.6248	0.196	5008	,	,	NA	10960	0.3859	NA	0.2823	False	NA	,,,	NA	NA	NA	2504	0.2536	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87410070T>C		NA		hg19		0.02	1.707433	TTCxTTT	COVERED																																																																																			NOVEL					0			0	5.113465	KEEP	14	0	0	17	507	TT	0.999366	0.999171	0			7	47	245	0	0	17.195706	82	60	3072	136		0.078652	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87575902	87575902	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:87575902G>A			NA	NA				IGKV3OR2-268 (9744 upstream) : LINC00152 (178984 downstream)						NA		NA									NA						cctctccgccgctgtccgtct	0.806	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87575902G>A		NA		hg19		0.02	-0.140353	GCCxCTG	COVERED																																																																																			NOVEL					0			0	4.213775	KEEP	2	0	0	14	495	GG	0.995343	0.25975	0			2	60	79	0	0	6.361006	12	60	404	42		0.142857	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87584501	87584501	__UNKNOWN__	IGR	SNP	C	C	T	rs367776845		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:87584501C>T			NA	NA				IGKV3OR2-268 (18343 upstream) : LINC00152 (170385 downstream)						NA		NA									NA						ctggtcttgcctttgccctgc	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87584501C>T		NA		hg19		0.02	-0.140359	TGCxTTT	COVERED																																																																																			NOVEL					0			0	4.514602	KEEP	4	0	0	15	524	CC	0.995343	0.25975	0			2	49	79	0	0	6.430656	11	50	399	42		0.153846	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87644457	87644457	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:87644457C>T			NA	NA				IGKV3OR2-268 (78299 upstream) : LINC00152 (110429 downstream)						NA		NA									NA						agccatccagccagctaagcc	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87644457C>T		NA		hg19		0.02	-0.254384	CAGxCAG	COVERED																																																																																			NOVEL					0			15	5.716307	KEEP	7	0	0	19	654	CC	0.997832	0.667074	0			3	27	105	0	0	9.855165	4	27	148	62		0.428571	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87644462	87644462	__UNKNOWN__	IGR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:87644462T>G			NA	NA				IGKV3OR2-268 (78304 upstream) : LINC00152 (110424 downstream)						NA		NA									NA						tccagccagctaagccagccg	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87644462T>G		NA		hg19		0.02	-0.228089	AGCxAAG	COVERED																																																																																			NOVEL					0			15	5.714947	KEEP	6	0	0	19	562	TT	0.997832	0.639957	0			3	27	89	0	0	8.868217	2	27	81	63		0.6	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	89868298	89868298	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:89868298C>G			NA	NA				IGKV2-40 (238112 upstream) : IGKV2D-40 (22697 downstream)						NA		NA									NA						ccattccattccattccattc	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.89868298C>G		NA		hg19		0.02	-0.280741	ATTxCAT	COVERED																																																																																			NOVEL					0			31	8.728263	KEEP	29	0	0	29	1013	CC	0.99986	0.76078	0			2	28	71	0	0	8.053914	0	0	0	121		1	0.760887
IGKV2D-24	28885	__UNKNOWN__	__UNKNOWN__	2	90044427	90044427	__UNKNOWN__	RNA	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90044427T>C	ENST00000462693.1	+	0	378									immunoglobulin kappa variable 2D-24 (non-functional)	NA		NA									NA						GCACGCAAGCTACACAATTTC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						144	138	140	NA		NA	NA	2		NA											NA				90044427		1920	4123	6043					X63401		2p11.2	2012-02-08	2008-09-10		ENSG00000241566	ENSG00000241566	28885		Immunoglobulins / IGK locus	5797	other	immunoglobulin gene		NA	immunoglobulin kappa variable 2D-24		NA		Standard	NG_000833	NG_000833	NA	Approved				OTTHUMG00000151618	ENST00000462693.1:	chr2.hg19:g.90044427T>C		NA		hg19		0.02	7.10085	AGCxACA	COVERED																																																																																			NOVEL	IGKV2D-24-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000323290.1	1	9.62533	KEEP	0	0	0	32	933	TT	0.999997	0.999997	0		+	16	60	606	0	0	44.871253	162	60	5894	251	ENST00000462693.1	0.089888	1
IGKV1D-17	28900	__UNKNOWN__	__UNKNOWN__	2	90121732	90121732	__UNKNOWN__	RNA	SNP	A	A	G	rs368378296		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90121732A>G	ENST00000483379.1	+	0	236									immunoglobulin kappa variable 1D-17	NA		NA									NA						GAGAACACTAACAGTTTACTC	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						100	92	95	NA		NA	NA	2		NA											NA				90121732		1884	4122	6006					X63392		2p11.2	2012-02-08			ENSG00000242766	ENSG00000242766	28900		Immunoglobulins / IGK locus	5749	other	immunoglobulin gene		NA			NA		Standard	NG_000833	NG_000833	NA	Approved				OTTHUMG00000151610	ENST00000483379.1:	chr2.hg19:g.90121732A>G		NA		hg19		0.02	2.2627	CTAxCAG	COVERED																																																																																			NOVEL	IGKV1D-17-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000323282.1	1	2.700475	KEEP	1	0	0	9	261	AA	0.99254	0.992448	0		+	16	40	601	0	0	49.111998	78	50	2727	114	ENST00000483379.1	0.170213	0.999907
CH17-132F21.1	0	__UNKNOWN__	__UNKNOWN__	2	90458606	90458606	__UNKNOWN__	Silent	SNP	C	C	T	rs368855200		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90458606C>T	ENST00000603238.1	+	2	282	c.282C>T	c.(280-282)acC>acT	p.T94T							NA		NA									NA						ACACTCTCACCATCCGCAGCC	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000603238.1:c.282C>T	chr2.hg19:g.90458606C>T		NA		hg19		0.02	31.922681	CACxATC	COVERED																																																																																			NOVEL	CH17-132F21.1-001	PUTATIVE	not_best_in_genome_evidence|mRNA_end_NF|cds_end_NF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000468882.1	11	13.59752	KEEP	116	5	138	94	3233	CC	1	1	0		+	42	49	1562	0	0	106.177503	700	51	25781	1100	ENST00000603238.1	0.056604	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90458676	90458676	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90458676G>A			NA	NA				CH17-132F21.1 (5 upstream) : RP11-685N3.1 (79162 downstream)						NA		NA									NA						CCCTCCCACAGCGTTACAAGT	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90458676G>A		NA		hg19		0.02	26.510757	ACAxCGT	COVERED																																																																																			NOVEL					0			5	4.446956	KEEP	98	8	254	104	3735	GG	1	1	0			53	49	1883	0	0	134.601358	578	51	22150	1040		0.083994	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90458801	90458801	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90458801T>A			NA	NA				CH17-132F21.1 (130 upstream) : RP11-685N3.1 (79037 downstream)						NA		NA									NA						GGAAAGTCATTGGGAGATTTT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90458801T>A		NA		hg19		0.02	4.576413	CATxGGG	UNCOVERED																																																																																			NOVEL					0			2	3.310279	KEEP	113	0	0	11	352	TT	0	0	0			5	20	202	0	0	13.096819	143	27	5221	288		0.033784	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90468276	90468276	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90468276A>G			NA	NA				CH17-132F21.1 (9605 upstream) : RP11-685N3.1 (69562 downstream)						NA		NA									NA						cacccctgtaatcctagcact	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90468276A>G		NA		hg19		0.02	-0.087733	GTAxTCC	UNCOVERED																																																																																			NOVEL					0			6	3.910973	KEEP	5	0	0	13	394	AA	0.992708	0.098994	0			3	40	113	0	0	10.07846	7	60	260	34		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90481805	90481805	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:90481805G>A			NA	NA				CH17-132F21.1 (23134 upstream) : RP11-685N3.1 (56033 downstream)						NA		NA									NA						tggcttggctggctgggtggc	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90481805G>A		NA		hg19		0.02	-0.096487	GCTxGCT	UNCOVERED																																																																																			NOVEL					0			2	3.009509	KEEP	8	0	0	10	330	GG	0	0	0			2	60	72	0	0	6.495902	4	40	125	31		0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91687652	91687652	__UNKNOWN__	IGR	SNP	G	G	A	rs2637044	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91687652G>A			NA	NA				None (None upstream) : RP11-575H3.1 (80740 downstream)						NA		NA									NA						aatcagccaggcatggtggca	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91687652G>A		NA		hg19		0.02	-0.298289	CAGxCAT	COVERED																																																																																			NOVEL					0			2	3.310929	KEEP	10	0	0	11	397	GG	0.99254	0.775233	0			4	27	145	0	0	11.060862	30	49	1135	68		0.117647	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91692517	91692517	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91692517G>A			NA	NA				None (None upstream) : RP11-575H3.1 (75875 downstream)						NA		NA									NA						atagctcaccgcagcctcgaa	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91692517G>A		NA		hg19		0.02	-0.210543	ACCxCAG	COVERED																																																																																			NOVEL					0			4	3.310491	KEEP	0	0	0	11	365	GG	0.993072	0.518544	0			3	27	107	0	0	8.204987	21	50	765	42		0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91705032	91705032	__UNKNOWN__	IGR	SNP	G	G	A	rs62146253|rs201611085		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91705032G>A			NA	NA				None (None upstream) : RP11-575H3.1 (63360 downstream)						NA		NA									NA						ggagtgcagtggtacaatctt	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91705032G>A		NA		hg19		0.02	-0.043865	AGTxGTA	UNCOVERED																																																																																			NOVEL					0			1	2.708649	KEEP	8	0	0	9	304	GG	0	0	0			2	39	73	0	0	6.792799	3	40	105	23		0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91744210	91744210	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91744210A>G			NA	NA				None (None upstream) : RP11-575H3.1 (24182 downstream)						NA		NA									NA						GGGCACAAgcagggcaggcta	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91744210A>G		NA		hg19		0.02	-0.201762	AGCxGGG	COVERED																																																																																			NOVEL					0			0	3.910796	KEEP	6	0	0	13	394	AA	0.993072	0.487146	0			3	27	101	0	0	7.664532	20	50	741	49		0.130435	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91750635	91750635	__UNKNOWN__	IGR	SNP	A	A	C	rs62146768		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91750635A>C			NA	NA				None (None upstream) : RP11-575H3.1 (17757 downstream)						NA		NA									NA						gctgaggagaacgcagctccg	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91750635A>C		NA		hg19		0.02	-0.096499	AGAxCGC	UNCOVERED																																																																																			NOVEL					0			0	2.704538	KEEP	3	0	0	9	257	AA	0.99254	0.119538	0			6	40	203	0	0	19.870492	5	47	177	25		0.545455	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91766566	91766566	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91766566G>A			NA	NA				None (None upstream) : RP11-575H3.1 (1826 downstream)						NA		NA									NA						ATGTGTGGTCGTTTTTCACTC	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91766566G>A		NA		hg19		0.02	41.473419	GTCxTTT	COVERED																																																																																			NOVEL					0			12	20.58554	KEEP	2	9	248	156	5399	GG	1	1	0			58	60	2114	0	0	146.638929	810	60	28064	1238		0.06682	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91766609	91766609	__UNKNOWN__	IGR	SNP	G	G	A	rs2433883		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91766609G>A			NA	NA				None (None upstream) : RP11-575H3.1 (1783 downstream)						NA		NA									NA						TATGGGGGTTGTAATGTTTAT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91766609G>A		NA		hg19		0.02	40.147534	GTTxTAA	COVERED																																																																																			NOVEL					0			9	9.878208	KEEP	1	13	378	166	5897	GG	1	1	0			89	60	3295	0	0	246.892892	790	60	29732	1261		0.101251	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91766632	91766632	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91766632A>G			NA	NA				None (None upstream) : RP11-575H3.1 (1760 downstream)						NA		NA									NA						CACTCCTTGGATGATTTCCGA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91766632A>G		NA		hg19		0.02	42.564646	TGGxTGA	COVERED																																																																																			NOVEL					0			8	28.546883	KEEP	5	5	157	150	4511	AA	1	1	0			58	60	2159	0	0	150.691091	834	70	30438	1215		0.065022	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91766893	91766893	__UNKNOWN__	IGR	SNP	C	C	T	rs56152219		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91766893C>T			NA	NA				None (None upstream) : RP11-575H3.1 (1499 downstream)						NA		NA									NA						gcagccttgaccacctggggg	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91766893C>T		NA		hg19		0.02	4.519127	TGAxCAC	COVERED																																																																																			NOVEL					0			10	2.361968	KEEP	0	0	0	8	262	CC	0.99257	0.992562	0			7	60	248	0	0	17.256771	89	60	3158	120		0.072917	0.999992
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91771677	91771677	__UNKNOWN__	IGR	SNP	C	C	T	rs2936283		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91771677C>T			NA	NA				RP11-575H3.1 (2757 upstream) : AC027612.6 (33508 downstream)						NA		NA									NA						aaacctggacctcccaggctc	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91771677C>T		NA		hg19		0.02	-0.28952	GACxTCC	COVERED																																																																																			NOVEL					0			3	2.70889	KEEP	0	0	0	9	321	CC	0.99254	0.755211	0			6	60	230	0	0	19.067882	27	60	1024	54		0.181818	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91774454	91774454	__UNKNOWN__	IGR	SNP	C	C	T	rs4927507		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91774454C>T			NA	NA				RP11-575H3.1 (5534 upstream) : AC027612.6 (30731 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91774454C>T		NA		hg19		0.02	-0.149144	AGAxGGG	COVERED																																																																																			NOVEL					0			1	2.708797	KEEP	0	0	0	9	315	CC	0.99254	0.289823	0			3	60	113	0	0	9.378294	13	60	478	31		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91777946	91777946	__UNKNOWN__	IGR	SNP	T	T	C	rs6757163		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91777946T>C			NA	NA				RP11-575H3.1 (9026 upstream) : AC027612.6 (27239 downstream)						NA		NA									NA						CACCGGCTGGTGAGTCCAGGC	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91777946T>C		NA		hg19		0.02	6.359391	TGGxGAG	COVERED																																																																																			NOVEL					0			0	11.518458	KEEP	0	3	105	75	2048	TT	1	1	0			10	60	342	0	0	22.237716	169	60	5278	358		0.055866	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91783215	91783215	__UNKNOWN__	IGR	SNP	G	G	A	rs2580502		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91783215G>A			NA	NA				RP11-575H3.1 (14295 upstream) : AC027612.6 (21970 downstream)						NA		NA									NA						tgctcctcccgcctcagcctc	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91783215G>A		NA		hg19		0.02	-0.15791	CCCxCCT	COVERED																																																																																			NOVEL					0			4	3.909134	KEEP	0	0	0	13	445	GG	0.995343	0.321303	0			3	60	104	0	0	8.309899	15	60	550	50		0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91785244	91785244	__UNKNOWN__	IGR	SNP	G	G	A	rs140082746		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91785244G>A			NA	NA				RP11-575H3.1 (16324 upstream) : AC027612.6 (19941 downstream)						NA		NA									NA						tgcccatcttggcctcccaaa	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91785244G>A		NA		hg19		0.02	-0.184181	CTTxGCC	COVERED																																																																																			NOVEL					0			3	3.611675	KEEP	1	0	0	12	417	GG	0.993072	0.420544	0			3	60	113	0	0	9.060574	17	60	631	45		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91801784	91801784	__UNKNOWN__	IGR	SNP	C	C	A	rs13400002	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91801784C>A			NA	NA				RP11-575H3.1 (32864 upstream) : AC027612.6 (3401 downstream)						NA		NA									NA						ttgcctcagcctccagaatag	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91801784C>A		NA		hg19		0.02	-0.254391	AGCxTCC	COVERED																																																																																			NOVEL					0			3	2.708789	KEEP	0	0	0	9	316	CC	0.99254	0.663536	0			3	60	114	0	0	8.793811	23	60	863	46		0.115385	0.668523
AC027612.6	0	__UNKNOWN__	__UNKNOWN__	2	91809292	91809292	__UNKNOWN__	RNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91809292C>T	ENST00000609777.1	-	0	199										NA		NA									NA						TTGGATACCTCCCGCTTTTGG	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000609777.1:	chr2.hg19:g.91809292C>T		NA		hg19		0.02	34.745122	CCTxCCG	COVERED																																																																																			NOVEL	AC027612.6-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000471986.1	3	28.72368	KEEP	56	4	115	136	4642	CC	1	1	0		-	50	60	1785	0	0	121.047924	754	60	28506	1200	ENST00000609777.1	0.062189	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91872069	91872069	__UNKNOWN__	IGR	SNP	C	C	T	rs2537164	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91872069C>T			NA	NA				RNA5SP100 (9077 upstream) : AC027612.3 (2058 downstream)						NA		NA									NA						CATCACTGCACACACACAAAA	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91872069C>T		NA		hg19		0.02	40.279112	GCAxACA	COVERED																																																																																			NOVEL					0			19	4.622105	KEEP	75	15	412	161	5647	CC	1	1	0			163	49	5948	1	0	491.881576	690	50	26172	1234		0.19109	1
AC027612.3	0	__UNKNOWN__	__UNKNOWN__	2	91886002	91886002	__UNKNOWN__	RNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91886002C>T	ENST00000436174.1	-	0	797										NA		NA									NA						AGTGAAGATCCACAGCAGTCT	0.269	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000436174.1:	chr2.hg19:g.91886002C>T		NA		hg19		0.02	11.724013	ATCxACA	COVERED																																																																																			NOVEL	AC027612.3-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000338339.1	1	3.951381	KEEP	30	4	122	56	1974	CC	1	1	0		-	30	40	1126	0	0	84.661564	268	60	9658	520	ENST00000436174.1	0.100671	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91916093	91916093	__UNKNOWN__	IGR	SNP	T	T	C	rs372280320		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91916093T>C			NA	NA				AC027612.3 (15957 upstream) : AC027612.2 (35857 downstream)						NA		NA									NA						actaggattataggcatgacc	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91916093T>C		NA		hg19		0.02	-0.096504	TTAxAGG	UNCOVERED																																																																																			NOVEL					0			0	2.406802	KEEP	18	0	0	8	240	TT	0	0	0			3	27	117	0	0	10.332249	8	27	285	38		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91916904	91916904	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91916904A>G			NA	NA				AC027612.3 (16768 upstream) : AC027612.2 (35046 downstream)						NA		NA									NA						tggtgcaatcatggctcactg	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91916904A>G		NA		hg19		0.02	-0.289508	ATCxTGG	COVERED																																																																																			NOVEL					0			8	5.115567	KEEP	0	0	0	17	536	AA	0.999366	0.760405	0			3	39	107	0	0	7.943293	26	60	954	64		0.103448	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91917376	91917376	__UNKNOWN__	IGR	SNP	G	G	A	rs2659427	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91917376G>A			NA	NA				AC027612.3 (17240 upstream) : AC027612.2 (34574 downstream)						NA		NA									NA						actaagctgtgattgagccac	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91917376G>A		NA		hg19		0.02	-0.254099	TGTxATT	COVERED																																																																																			NOVEL					0			2	2.70891	KEEP	1	0	0	9	323	GG	0.99257	0.663556	0			7	60	247	0	0	21.908508	16	60	621	48		0.304348	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91935064	91935064	__UNKNOWN__	IGR	SNP	G	G	A	rs74968405		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91935064G>A			NA	NA				AC027612.3 (34928 upstream) : AC027612.2 (16886 downstream)						NA		NA									NA						TTTATTTTTGGTTAGAGTACC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91935064G>A		NA		hg19		0.02	3.605302	TTGxTTA	COVERED																																																																																			NOVEL					0			2	6.620899	KEEP	1	0	0	22	754	GG	0.999879	0.999873	0			6	40	198	0	0	12.534515	105	60	3698	157		0.054054	0.999995
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91935093	91935093	__UNKNOWN__	IGR	SNP	G	G	A	rs77045622		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91935093G>A			NA	NA				AC027612.3 (34957 upstream) : AC027612.2 (16857 downstream)						NA		NA									NA						TCTCTTCTACGAAAAGCAAAA	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91935093G>A		NA		hg19		0.02	1.740258	TACxAAA	COVERED																																																																																			NOVEL					0			3	4.51426	KEEP	1	0	0	15	500	GG	0.99649	0.994697	0			6	40	198	0	0	13.634256	68	60	2369	97		0.081081	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91944003	91944003	__UNKNOWN__	IGR	SNP	T	T	C	rs76159807	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91944003T>C			NA	NA				AC027612.3 (43867 upstream) : AC027612.2 (7947 downstream)						NA		NA									NA						TCACCCGGGATGGAGGGGTCC	0.607	NA	NA											t|||	11	0.00219649	0.0053	0.0014	5008	,	,	NA	17874	0.002	NA	0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91944003T>C		NA		hg19		0.02	2.040833	GGAxGGA	COVERED																																																																																			NOVEL					0			0	6.24214	KEEP	1	1	35	33	942	TT	0.999998	0.963772	0			7	40	251	0	0	19.582643	44	60	1612	104		0.137255	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91960848	91960848	__UNKNOWN__	IGR	SNP	G	G	A	rs62144303		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91960848G>A			NA	NA				AC027612.2 (8804 upstream) : SLC9B1P2 (119649 downstream)						NA		NA									NA						CCTCCCCAGCGGGTGCAGCCC	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91960848G>A		NA		hg19		0.02	-0.228046	AGCxGGT	COVERED																																																																																			NOVEL					0			0	2.406988	KEEP	0	0	0	8	255	GG	0.99257	0.578599	0			7	50	253	0	0	22.063745	19	60	641	42		0.269231	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91987242	91987242	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:91987242G>T			NA	NA				AC027612.2 (35198 upstream) : SLC9B1P2 (93255 downstream)						NA		NA									NA						aaggaaggaaggagaaaaaaa	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91987242G>T		NA		hg19		0.02	-0.096492	GAAxGAG	UNCOVERED																																																																																			NOVEL					0			2	2.75238	KEEP	4	1	13	14	506	GG	0.993634	0.119669	0			2	24	73	0	0	6.435776	5	45	170	37		0.285714	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92308508	92308508	__UNKNOWN__	IGR	SNP	A	A	G	rs2172570		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:92308508A>G			NA	NA				SLC9B1P2 (206270 upstream) : None (None downstream)						NA		NA									NA						attctcagaaacttcattggg	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92308508A>G		NA		hg19		0.02	2.047321	GAAxCTT	COVERED																																																																																			NOVEL					0			22	9.965564	KEEP	94	1	37	46	1495	AA	0.999892	0.99779	0			3	40	112	0	0	11.654406	1	40	35	268		0.75	0.997898
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92313018	92313018	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:92313018A>G			NA	NA				SLC9B1P2 (210780 upstream) : None (None downstream)						NA		NA									NA						gcaagtggatatttgtctagc	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92313018A>G		NA		hg19		0.02	7.423376	GATxTTT	COVERED																																																																																			NOVEL					0			29	30.226653	KEEP	129	2	67	124	3748	AA	1	1	0			5	47	195	1	1	14.00082	67	49	2509	519		0.069444	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92313089	92313089	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:92313089A>T			NA	NA				SLC9B1P2 (210851 upstream) : None (None downstream)						NA		NA									NA						attcccagaaacttctttgtg	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92313089A>T		NA		hg19		0.02	1.669225	GAAxCTT	COVERED																																																																																			NOVEL					0			17	13.528216	KEEP	93	3	100	80	2272	AA	1	0.999407	0			5	24	173	0	0	14.565178	17	40	599	249		0.227273	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92320435	92320435	__UNKNOWN__	IGR	SNP	T	T	G	rs4393208		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:92320435T>G			NA	NA				SLC9B1P2 (218197 upstream) : None (None downstream)						NA		NA									NA						gtgttgaacattccctttcat	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92320435T>G		NA		hg19		0.02	12.242035	ACAxTCC	COVERED																																																																																			NOVEL					0			50	6.765709	KEEP	89	4	148	74	2425	TT	1	1	0			16	40	592	0	0	53.740897	31	60	1093	618		0.340426	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325170	92325170	__UNKNOWN__	IGR	SNP	T	T	C	rs150440252		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:92325170T>C			NA	NA				SLC9B1P2 (222932 upstream) : None (None downstream)						NA		NA									NA						gatgtttcaattgaagtcaca	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325170T>C		NA		hg19		0.02	7.113338	CAAxTGA	COVERED																																																																																			NOVEL					0			13	24.972244	KEEP	175	0	0	83	2573	TT	1	1	0			6	40	233	0	0	15.888296	111	40	4068	497		0.051282	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325274	92325274	__UNKNOWN__	IGR	SNP	A	A	T	rs7425659		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:92325274A>T			NA	NA				SLC9B1P2 (223036 upstream) : None (None downstream)						NA		NA									NA						actacggtgaaaaaggaaata	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325274A>T		NA		hg19		0.02	4.190174	TGAxAAA	COVERED																																																																																			NOVEL					0			8	5.214209	KEEP	133	3	93	50	1512	AA	0.997832	0.9978	0			4	40	147	0	0	10.96218	36	40	1258	306		0.1	0.999968
ANKRD36C	400986	__UNKNOWN__	__UNKNOWN__	2	96521138	96521138	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs5005871		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:96521138T>C	ENST00000456556.1	-	63	4955	c.4871A>G	c.(4870-4872)aAc>aGc	p.N1624S	ANKRD36C_ENST00000419039.2_Missense_Mutation_p.N651S|ANKRD36C_ENST00000420871.2_Missense_Mutation_p.N875S			Q5JPF3	AN36C_HUMAN	ankyrin repeat domain 36C	1624		NA					ion channel inhibitor activity (GO:0008200)			breast(1)|endometrium(8)|kidney(5)|lung(4)	18						AGCTTGAAGGTTTTCTACTCT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AL832836		2q11.1	2013-01-10			ENSG00000174501	ENSG00000174501	400986		Ankyrin repeat domain containing	32946	protein-coding gene	gene with protein product	protein immuno-reactive with anti-PTH polyclonal antibodies	NA			NA		Standard	NM_001010914	XR_251121	NA	Approved	DKFZp667P0924	uc002suz.1	Q5JPF3	OTTHUMG00000155211	ENST00000456556.1:c.4871A>G	chr2.hg19:g.96521138T>C	ENSP00000403302:p.Asn1624Ser	NA	C9JZ08|Q15694|Q53S06|Q658V2	hg19		0.02	2.499557	AGGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	t	9.645	1.140111	0.21205	.	.	ENSG00000174501	ENST00000420871;ENST00000456556;ENST00000419039	T;T;T	0.13778	2.56;2.56;2.56	2.64	-5.28	0.02755	.	.	.	.	.	T	0.07863	0.0197	L	0.42245	1.32	0.09310	N	1	.	.	.	.	.	.	T	0.42413	-0.9453	7	0.13108	T	0.6	.	0.7715	0.01024	0.3266:0.1273:0.3289:0.2173	rs5005871	.	.	.	S	875;1624;651	ENSP00000415231:N875S;ENSP00000403302:N1624S;ENSP00000407838:N651S	ENSP00000407838:N651S	N	-	2	0	AC073995.2	95884865	0.155000	0.22806	0.000000	0.03702	0.007000	0.05969	0.150000	0.16263	-1.321000	0.02281	-0.736000	0.03550	AAC	NOVEL	ANKRD36C-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000338799.2	5	3.911215	KEEP	4	0	0	13	399	TT	0.994391	0.989502	0		-	11	25	441	0	0	36.936036	49	60	1717	104	ENST00000456556.1	0.183333	0.995084
ANKRD36C	400986	__UNKNOWN__	__UNKNOWN__	2	96619873	96619873	__UNKNOWN__	Intron	SNP	C	C	A	rs111807008		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:96619873C>A	ENST00000456556.1	-	14	1221							Q5JPF3	AN36C_HUMAN	ankyrin repeat domain 36C	NA		NA					ion channel inhibitor activity (GO:0008200)			breast(1)|endometrium(8)|kidney(5)|lung(4)	18						TCTGAGGAAACTCAGTTATCT	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832836		2q11.1	2013-01-10			ENSG00000174501	ENSG00000174501	400986		Ankyrin repeat domain containing	32946	protein-coding gene	gene with protein product	protein immuno-reactive with anti-PTH polyclonal antibodies	NA			NA		Standard	NM_001010914	XR_251121	NA	Approved	DKFZp667P0924	uc002suz.1	Q5JPF3	OTTHUMG00000155211	ENST00000456556.1:c.1137-120G>T	chr2.hg19:g.96619873C>A		NA	C9JZ08|Q15694|Q53S06|Q658V2	hg19		0.02	2.036651	AAAxTCA	COVERED																																																																																			NOVEL	ANKRD36C-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000338799.2	2	2.70875	KEEP	2	0	0	9	312	CC	0.99254	0.99248	0		-	12	60	456	0	0	40.412899	30	60	1146	108	ENST00000456556.1	0.285714	0.99994
SEMA4C	54910	__UNKNOWN__	__UNKNOWN__	2	97525768	97525768	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:97525768A>C	ENST00000305476.5	-	0	3229					NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	NA		NA			cell migration in hindbrain (GO:0021535)|cerebellum development (GO:0021549)|muscle cell differentiation (GO:0042692)|neural tube closure (GO:0001843)|positive regulation of stress-activated MAPK cascade (GO:0032874)|semaphorin-plexin signaling pathway (GO:0071526)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle membrane (GO:0030672)	receptor activity (GO:0004872)			NS(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	17						CCCTCCCCCCACCCTGAAAAC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB051526	CCDS2029.1	2q11.2	2013-01-11			ENSG00000168758	ENSG00000168758	54910		Semaphorins, Immunoglobulin superfamily / Immunoglobulin-like domain containing	10731	protein-coding gene	gene with protein product	M-Sema F	604462		SEMAI	NA	7656991	Standard	NM_017789	NM_017789	NA	Approved	Semacl1, Semaf	uc002sxh.4	Q9C0C4	OTTHUMG00000130535	ENST00000305476.5:c.*595T>G	chr2.hg19:g.97525768A>C		NA	Q32MJ3|Q7Z5X0	hg19	CCDS2029.1	0.02	1.699258	CCCxCCC	COVERED																																																																																			NOVEL	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252957.1	1	2.515824	KEEP	0	4	71	34	855	AA	1	0.981955	0		-	11	60	200	1	0	13.763659	41	60	1204	107	ENST00000305476.5	0.211538	0.981955
ANKRD36	375248	__UNKNOWN__	__UNKNOWN__	2	97828864	97828864	__UNKNOWN__	Intron	SNP	C	C	T	rs62153882	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:97828864C>T	ENST00000461153.2	+	18	1673				ANKRD36_ENST00000420699.2_Intron			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	NA		NA								endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						gttagccaggcgtggtggcat	0.552	NA	NA											.|||	1726	0.344649	0.0877	0.4467	5008	,	,	NA	16405	0.246	NA	0.7793	False	NA	,,,	NA	NA	NA	2504	0.274	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976	375248		Ankyrin repeat domain containing	24079	protein-coding gene	gene with protein product		NA			NA	12975309	Standard		NM_001164315	NA	Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.1429+989C>T	chr2.hg19:g.97828864C>T		NA	B4E3I8|Q6UX02|Q86X62|Q9HCD1	hg19	CCDS54379.1	0.02	-0.289466	AGGxGTG	COVERED																																																																																			NOVEL	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339154.5	3	3.009398	KEEP	0	0	0	10	335	CC	0.992708	0.755338	0		+	4	60	117	0	0	8.382587	28	60	1044	43	ENST00000461153.2	0.125	0.760887
TMEM131	23505	__UNKNOWN__	__UNKNOWN__	2	98444708	98444708	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:98444708T>G	ENST00000186436.5	-	11	1303				TMEM131_ENST00000425805.2_Intron	NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	NA		NA				integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						CTTTAAAAAATAATTACAATA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568	23505			30366	protein-coding gene	gene with protein product		615659			NA	9039502, 10996388	Standard	XM_371542	NM_015348	NA	Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.1074+5119A>C	chr2.hg19:g.98444708T>G		NA		hg19	CCDS46368.1	0.02	1.935579	AAAxAAT	COVERED																																																																																			NOVEL	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329285.2	3	4.212546	KEEP	0	0	0	14	430	TT	0.995343	0.987474	0		-	6	40	222	0	0	16.459596	57	60	2001	82	ENST00000186436.5	0.095238	0.992094
WASH2P	375260	__UNKNOWN__	__UNKNOWN__	2	114355769	114355769	__UNKNOWN__	RNA	SNP	T	T	G	rs11490601		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:114355769T>G	ENST00000538033.2	+	0	2154							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene	NA		NA			Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)				NA						cctggccctgtccccgaggtg	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556	375260		WAS protein homologs	33145	pseudogene	pseudogene		NA	family with sequence similarity 39, member B	FAM39B	NA	18159949	Standard	NM_198943	NR_024077	NA	Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822	ENST00000538033.2:	chr2.hg19:g.114355769T>G		NA		hg19		0.02	-0.105273	CTGxCCC	UNCOVERED																																																																																			NOVEL	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	NA	pseudogene	OTTHUMT00000467782.1	1	2.707776	KEEP	11	0	0	9	276	TT	0	0	0		+	5	46	185	0	0	17.34592	7	60	243	30	ENST00000538033.2	0.416667	0.139832
EN1	2019	__UNKNOWN__	__UNKNOWN__	2	119600860	119600860	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:119600860T>G	ENST00000295206.6	-	2	1373				EN1_ENST00000546667.1_Intron	NM_001426.3	NP_001417.3	Q05925	HME1_HUMAN	engrailed homeobox 1	NA		NA			anatomical structure morphogenesis (GO:0009653)|dorsal/ventral pattern formation (GO:0009953)|embryonic forelimb morphogenesis (GO:0035115)|hindbrain development (GO:0030902)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|multicellular organism growth (GO:0035264)|neuron development (GO:0048666)|pigmentation (GO:0043473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|response to cocaine (GO:0042220)|skeletal system development (GO:0001501)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	9						CGGGGTGGGGTGGGGGTGGGG	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						1	1	1	NA		NA	NA	2		NA											NA				119600860		1269	2562	3831	SO:0001627	intron_variant			L12699	CCDS2123.1	2q14.2	2011-06-20	2007-02-15		ENSG00000163064	ENSG00000163064	2019		Homeoboxes / ANTP class : NKL subclass	3342	protein-coding gene	gene with protein product		131290			NA	8094370	Standard		NM_001426	NA	Approved		uc002tlm.3	Q05925	OTTHUMG00000131401	ENST00000295206.6:c.863-30A>C	chr2.hg19:g.119600860T>G		NA	Q4ZG44	hg19	CCDS2123.1	0.02	-0.338471	GGGxGGG	COVERED																																																																																			NOVEL	EN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254191.3	0	6.013276	KEEP	0	0	0	20	543	TT	0.999863	0.865627	0		-	4	60	108	0	0	7.135579	35	60	1092	64	ENST00000295206.6	0.102564	0.865745
HS6ST1	9394	__UNKNOWN__	__UNKNOWN__	2	129024915	129024915	__UNKNOWN__	3'UTR	SNP	C	C	T	rs4662595		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:129024915C>T	ENST00000259241.6	-	0	2070					NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	NA		NA			angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		AAGGGCCAGCCGCGGACTCAC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720	9394		Sulfotransferases, membrane-bound	5201	protein-coding gene	gene with protein product		604846		HS6ST	NA	9535912	Standard	NM_004807	NM_004807	NA	Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.*821G>A	chr2.hg19:g.129024915C>T		NA	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	hg19	CCDS42748.1	0.02	2.145292	AGCxGCG	COVERED																																																																																			NOVEL	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331572.1	1	2.348388	KEEP	23	3	88	39	1293	CC	1	0.99993	0		-	4	40	165	0	0	11.244904	89	60	3100	176	ENST00000259241.6	0.043011	0.99993
HS6ST1	9394	__UNKNOWN__	__UNKNOWN__	2	129075961	129075961	__UNKNOWN__	5'UTR	SNP	T	T	C	rs61732881	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:129075961T>C	ENST00000494089.1	-	0	85				HS6ST1_ENST00000259241.6_Silent_p.T59T			O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	NA		NA			angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		GGGGGTCGGGTGTGGGGAACA	0.667	NA	NA											C|||	3623	0.723442	0.8971	0.7839	5008	,	,	NA	8563	0.8304	NA	0.6044	False	NA	,,,	NA	NA	NA	2504	0.4581	NA	NA	NA						NA		NA				0							NA						7	15	12	NA		NA	NA	2		NA											NA				129075961		1621	3941	5562	SO:0001623	5_prime_UTR_variant			AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720	9394		Sulfotransferases, membrane-bound	5201	protein-coding gene	gene with protein product		604846		HS6ST	NA	9535912	Standard	NM_004807	NM_004807	NA	Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000494089.1:c.-500A>G	chr2.hg19:g.129075961T>C		NA	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	hg19		0.02	3.440796	GGGxGTG	COVERED																																																																																			NOVEL	HS6ST1-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000331573.1	1	9.021276	KEEP	12	4	119	72	1959	TT	1	0.999989	0		-	5	33	163	0	0	10.006836	98	60	3333	229	ENST00000494089.1	0.048544	0.999989
RAB6C	84084	__UNKNOWN__	__UNKNOWN__	2	130739950	130739950	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:130739950T>G	ENST00000410061.2	+	0	2716					NM_032144.2	NP_115520.2	Q9H0N0	RAB6C_HUMAN	RAB6C, member RAS oncogene family	NA		NA			cell cycle process (GO:0022402)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of centrosome duplication (GO:0010824)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	5	Colorectal(110;0.1)					GCTGAATTTATGTTGTAAACG	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF124200	CCDS46408.1	2q21.1	2012-07-02			ENSG00000222014	ENSG00000222014	84084		RAB, member RAS oncogene	16525	protein-coding gene	gene with protein product		612909			NA	11054569, 17426708	Standard	NM_032144	NM_032144	NA	Approved	WTH3	uc002tpx.1	Q9H0N0	OTTHUMG00000153487	ENST00000410061.2:c.*1497T>G	chr2.hg19:g.130739950T>G		NA	Q53RU3|Q6FIF7|Q9P128	hg19	CCDS46408.1	0.02	7.500408	TTAxGTT	COVERED																																																																																			NOVEL	RAB6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331384.1	7	6.919733	KEEP	0	0	0	23	702	TT	0.999892	0.999892	0		+	48	60	1664	0	0	144.239675	130	60	4792	216	ENST00000410061.2	0.269663	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	130751353	130751353	__UNKNOWN__	IGR	SNP	G	G	A	rs371030660		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:130751353G>A			NA	NA				RAB6C (11042 upstream) : AC018865.8 (33064 downstream)						NA		NA									NA						ATCCGGTGCCGCCTGGAGGCA	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.130751353G>A		NA		hg19		0.02	-0.342087	GCCxCCT	COVERED																																																																																			NOVEL					0			1	3.577127	KEEP	1	0	0	12	395	GG	0.993634	0.87212	0			4	43	114	0	0	7.91747	31	60	1121	63		0.114286	0.877708
PLEKHB2	55041	__UNKNOWN__	__UNKNOWN__	2	132021542	132021542	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:132021542C>T	ENST00000404460.1	+	7	477				POTEE_ENST00000358087.5_3'UTR|POTEE_ENST00000356920.5_Silent_p.A838A|PLEKHB2_ENST00000303908.3_Intron			Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	NA		NA				endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		CCATCCAGGCCGTGCCGTCCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						153	155	154	NA		NA	NA	2		NA											NA				132021542		2203	4300	6503	SO:0001627	intron_variant				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762	55041		Pleckstrin homology (PH) domain containing	19236	protein-coding gene	gene with protein product		NA			NA	10200314	Standard	NM_017958	NM_017958	NA	Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000404460.1:c.424-89051C>T	chr2.hg19:g.132021542C>T		NA	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	hg19		0.02	4.393262	GGCxGTG	COVERED																																																																																			NOVEL	PLEKHB2-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000318943.2	3	9.931538	KEEP	16	0	0	33	1111	CC	0.999988	0.999982	0		+	5	25	181	0	0	11.65716	105	60	3677	177	ENST00000404460.1	0.045455	0.999995
PLEKHB2	55041	__UNKNOWN__	__UNKNOWN__	2	132021884	132021884	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:132021884C>T	ENST00000404460.1	+	7	477				POTEE_ENST00000358087.5_3'UTR|POTEE_ENST00000356920.5_Silent_p.N952N|PLEKHB2_ENST00000303908.3_Intron			Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	NA		NA				endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		CCATCGGCAACGAGCGGTTCC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762	55041		Pleckstrin homology (PH) domain containing	19236	protein-coding gene	gene with protein product		NA			NA	10200314	Standard	NM_017958	NM_017958	NA	Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000404460.1:c.424-88709C>T	chr2.hg19:g.132021884C>T		NA	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	hg19		0.02	4.662919	CAAxGAG	COVERED																																																																																			NOVEL	PLEKHB2-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000318943.2	1	13.540272	KEEP	56	0	0	45	1484	CC	0.999997	0.999978	0		+	6	49	231	0	0	16.054657	96	50	3307	221	ENST00000404460.1	0.058824	0.999981
TUBA3D	113457	__UNKNOWN__	__UNKNOWN__	2	132237643	132237643	__UNKNOWN__	Splice_Site	SNP	C	C	T	rs72992288	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:132237643C>T	ENST00000321253.6	+	4	484	c.377C>T	c.(376-378)gCg>gTg	p.A126V	TUBA3D_ENST00000409047.2_3'UTR	NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	126		NA			'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		TTCTCTCAGGCGGATCTGTGC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(137;2059 2432 35543 39401)					NA		NA				0							NA						42	47	45	NA		NA	NA	2		NA											NA				132237643		2203	4300	6503	SO:0001630	splice_region_variant			K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886	113457		Tubulins	24071	protein-coding gene	gene with protein product	alpha-tubulin isotype H2-alpha	NA			NA	3785200	Standard	NM_080386	NM_080386	NA	Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.376-1C>T	chr2.hg19:g.132237643C>T		NA	A6NJQ0|Q5W099|Q6PEY3|Q96F18	hg19	CCDS33290.1	0.02	-0.438586	AGGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	c	3.775	-0.046823	0.07407	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	T	0.66638	-0.22	2.24	1.33	0.21861	Tubulin/FtsZ, GTPase domain (4);	0.356468	0.19523	U	0.112234	T	0.54663	0.1872	L	0.41415	1.275	0.80722	D	1	B	0.26363	0.147	B	0.31191	0.125	T	0.51348	-0.8717	10	0.87932	D	0	.	6.8167	0.23835	0.0:0.8406:0.0:0.1594	.	126	Q13748	TBA3C_HUMAN	V	126	ENSP00000326042:A126V	ENSP00000326042:A126V	A	+	2	0	TUBA3D	131954113	1.000000	0.71417	0.989000	0.46669	0.080000	0.17528	4.780000	0.62382	0.267000	0.21916	0.194000	0.17425	GCG	NOVEL	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331800.2	0	5.717976	KEEP	1	0	0	19	641	CC	0.99986	0.959724	0	Missense_Mutation	+	7	27	244	0	0	18.948303	43	60	1527	90	ENST00000321253.6	0.14	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	132292791	132292791	__UNKNOWN__	IGR	SNP	T	T	C	rs3101988		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:132292791T>C			NA	NA				CCDC74A (1552 upstream) : RNU6-617P (67571 downstream)						NA		NA									NA						GTGGATGCTCTGGGCACAGGT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.132292791T>C		NA		hg19		0.02	-0.342155	CTCxGGG	COVERED																																																																																			NOVEL					0			2	2.706778	KEEP	2	0	0	9	260	TT	0.99254	0.859287	0			7	57	259	0	0	21.26947	32	60	1181	53		0.179487	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	132292905	132292905	__UNKNOWN__	IGR	SNP	G	G	A	rs3101987		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:132292905G>A			NA	NA				CCDC74A (1666 upstream) : RNU6-617P (67457 downstream)						NA		NA									NA						CAACAGAACAGTGGGCATGAG	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.132292905G>A		NA		hg19		0.02	2.243681	ACAxTGG	COVERED																																																																																			NOVEL					0			0	9.029469	KEEP	0	0	0	30	1100	GG	0.999997	0.990961	0			4	27	154	0	0	10.868505	58	50	2211	120		0.064516	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	132769532	132769532	__UNKNOWN__	IGR	SNP	C	C	T	rs370361122		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:132769532C>T			NA	NA				RP1-156L9.1 (17798 upstream) : ANKRD30BL (135631 downstream)						NA		NA									NA						tttgaggcaccgcgatcagcc	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.132769532C>T		NA		hg19		0.02	-0.105273	CACxGCG	UNCOVERED																																																																																			NOVEL					0			4	2.7088	KEEP	1	0	0	9	312	CC	0.99257	0.138793	0			5	60	179	0	0	16.993995	6	60	207	23		0.454545	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133016519	133016519	__UNKNOWN__	IGR	SNP	C	C	T	rs62165016		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133016519C>T			NA	NA				ANKRD30BL (977 upstream) : AC097532.2 (26848 downstream)						NA		NA									NA						atcgcttgaacacgggaggtg	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133016519C>T		NA		hg19		0.02	6.78519	GAAxACG	COVERED																																																																																			NOVEL					0			38	14.43201	KEEP	26	12	340	168	5744	CC	1	1	0			5	60	176	0	0	15.512966	12	60	440	504		0.294118	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133016909	133016909	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133016909C>G			NA	NA				ANKRD30BL (1367 upstream) : AC097532.2 (26458 downstream)						NA		NA									NA						ACGTCTTAACCACACACCCAT	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133016909C>G		NA		hg19		0.02	37.437994	AACxACA	COVERED																																																																																			NOVEL					0			31	133.106679	KEEP	18	3	98	477	16106	CC	1	1	0			25	48	837	0	0	75.463484	47	60	1609	1590		0.347222	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133018665	133018665	__UNKNOWN__	IGR	SNP	G	G	A	rs62165048	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133018665G>A			NA	NA				ANKRD30BL (3123 upstream) : AC097532.2 (24702 downstream)						NA		NA									NA						ATGAGCTGAGGCTGGCAAGGC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133018665G>A		NA		hg19		0.02	-0.342081	GAGxCTG	COVERED																																																																																			NOVEL					0			4	10.834295	KEEP	0	0	0	36	1213	GG	0.999999	0.865745	0			2	57	76	0	0	7.350096	2	60	72	78		0.5	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133018929	133018929	__UNKNOWN__	IGR	SNP	A	A	G	rs111556001		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133018929A>G			NA	NA				ANKRD30BL (3387 upstream) : AC097532.2 (24438 downstream)						NA		NA									NA						GGCCTATAAAACATATAGACT	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133018929A>G		NA		hg19		0.02	30.931431	AAAxCAT	COVERED																																																																																			NOVEL					0			59	11.634322	KEEP	10	9	325	152	4497	AA	1	1	0			14	60	541	0	0	51.25759	18	60	604	934		0.4375	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133019578	133019578	__UNKNOWN__	IGR	SNP	C	C	G	rs112681737		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133019578C>G			NA	NA				ANKRD30BL (4036 upstream) : AC097532.2 (23789 downstream)						NA		NA									NA						GGAGGACCAGCAGCTCTTAGT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133019578C>G		NA		hg19		0.02	22.805349	CAGxAGC	COVERED																																																																																			NOVEL					0			15	24.69809	KEEP	8	6	212	156	5668	CC	1	1	0			24	60	910	1	0	86.340032	30	60	1109	862		0.444444	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133019948	133019948	__UNKNOWN__	IGR	SNP	T	T	A	rs148551384		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133019948T>A			NA	NA				ANKRD30BL (4406 upstream) : AC097532.2 (23419 downstream)						NA		NA									NA						AAATTAAAAATGAAGTTTCCA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133019948T>A		NA		hg19		0.02	6.604873	AAAxGAA	COVERED																																																																																			NOVEL					0			35	10.162573	KEEP	5	1	26	43	1338	TT	1	1	0			8	60	286	0	0	24.246601	27	60	988	260		0.228571	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020363	133020363	__UNKNOWN__	IGR	SNP	G	G	A	rs62165969	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133020363G>A			NA	NA				ANKRD30BL (4821 upstream) : AC097532.2 (23004 downstream)						NA		NA									NA						TCGAAGGCATGGAAATCTACT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020363G>A		NA		hg19		0.02	10.375639	CATxGAA	COVERED																																																																																			NOVEL					0			11	6.69089	KEEP	12	2	56	42	1506	GG	1	1	0			10	60	369	0	0	32.726765	24	60	881	389		0.294118	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020542	133020542	__UNKNOWN__	IGR	SNP	G	G	A	rs80203822		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133020542G>A			NA	NA				ANKRD30BL (5000 upstream) : AC097532.2 (22825 downstream)						NA		NA									NA						CTATCCAAGTGGATCCAAATT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020542G>A		NA		hg19		0.02	7.77921	AGTxGAT	COVERED																																																																																			NOVEL					0			3	2.407833	KEEP	3	0	0	8	280	GG	0.99257	0.99257	0			19	60	699	0	0	58.324188	76	60	2787	194		0.2	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020549	133020549	__UNKNOWN__	IGR	SNP	A	A	G	rs143254731		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133020549A>G			NA	NA				ANKRD30BL (5007 upstream) : AC097532.2 (22818 downstream)						NA		NA									NA						AGTGGATCCAAATTATGCTTA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020549A>G		NA		hg19		0.02	6.534589	CCAxATT	COVERED																																																																																			NOVEL					0			3	3.008374	KEEP	5	0	0	10	300	AA	0.992708	0.992708	0			8	42	301	0	0	21.780868	93	60	3257	188		0.079208	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020763	133020763	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133020763T>C			NA	NA				ANKRD30BL (5221 upstream) : AC097532.2 (22604 downstream)						NA		NA									NA						ATGAATTTGGTTACTAATACT	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020763T>C		NA		hg19		0.02	16.724704	TGGxTAC	COVERED																																																																																			NOVEL					0			17	8.260391	KEEP	4	1	39	41	1292	TT	1	1	0			16	60	588	0	0	44.13165	138	60	5015	486		0.103896	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020801	133020801	__UNKNOWN__	IGR	SNP	T	T	C	rs112432912		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133020801T>C			NA	NA				ANKRD30BL (5259 upstream) : AC097532.2 (22566 downstream)						NA		NA									NA						GGTCAATAACTTCAAACTAAC	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020801T>C		NA		hg19		0.02	11.981872	AACxTCA	COVERED																																																																																			NOVEL					0			12	5.753073	KEEP	1	1	37	32	1017	TT	0.999998	0.999998	0			24	60	896	0	0	73.552014	112	60	3944	326		0.176471	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133025664	133025664	__UNKNOWN__	IGR	SNP	C	C	A	rs62166690		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133025664C>A			NA	NA				ANKRD30BL (10122 upstream) : AC097532.2 (17703 downstream)						NA		NA									NA						GGGGAAGAAACCCACAACTGC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133025664C>A		NA		hg19		0.02	3.695783	AAAxCCA	COVERED																																																																																			NOVEL					0			4	13.611845	KEEP	0	2	62	67	2339	CC	1	0.999995	0			5	60	171	1	1	17.18686	3	60	103	210		0.625	0.999995
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133025842	133025842	__UNKNOWN__	IGR	SNP	G	G	C	rs147011479		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133025842G>C			NA	NA				ANKRD30BL (10300 upstream) : AC097532.2 (17525 downstream)						NA		NA									NA						CGCCGGCAAGGGGTGGGGGAA	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133025842G>C		NA		hg19		0.02	7.529362	AAGxGGT	COVERED																																																																																			NOVEL					0			16	21.330548	KEEP	0	3	106	108	3717	GG	1	1	0			6	60	226	1	0	15.635913	93	60	3468	385		0.060606	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133026513	133026513	__UNKNOWN__	IGR	SNP	C	C	T	rs62166707		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133026513C>T			NA	NA				ANKRD30BL (10971 upstream) : AC097532.2 (16854 downstream)						NA		NA									NA						ggcacctgccccaccgctcct	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133026513C>T		NA		hg19		0.02	2.264562	GCCxCAC	COVERED																																																																																			NOVEL					0			3	6.310589	KEEP	2	0	0	21	684	CC	0.999863	0.997026	0			4	60	150	0	0	14.500197	4	60	144	98		0.5	0.997163
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133029118	133029118	__UNKNOWN__	IGR	SNP	G	G	A	rs565158524|rs373303682	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133029118G>A			NA	NA				ANKRD30BL (13576 upstream) : AC097532.2 (14249 downstream)						NA		NA									NA						aacagagacagagagagacac	0.483	NA	NA											.|||	32	0.00638978	8e-04	0.0029	5008	,	,	NA	19108	0	NA	0.0099	False	NA	,,,	NA	NA	NA	2504	0.0194	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133029118G>A		NA		hg19		0.02	-0.298252	ACAxAGA	COVERED																																																																																			NOVEL					0			17	2.557607	KEEP	20	2	61	30	1043	GG	0.999859	0.78095	0			2	60	69	1	1	7.024868	1	3	31	81		0.666667	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133029307	133029307	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133029307C>T			NA	NA				ANKRD30BL (13765 upstream) : AC097532.2 (14060 downstream)						NA		NA									NA						aagacagagacgaacagagag	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133029307C>T		NA		hg19		0.02	9.288975	AGAxGAA	COVERED																																																																																			NOVEL					0			121	52.654582	KEEP	5	8	223	254	8516	CC	1	1	0			12	60	441	1	0	34.608378	76	60	2635	627		0.136364	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133034054	133034054	__UNKNOWN__	IGR	SNP	G	G	A	rs2176439	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133034054G>A			NA	NA				ANKRD30BL (18512 upstream) : AC097532.2 (9313 downstream)						NA		NA									NA						tccaccctgggcgtcaagagt	0.468	NA	NA											.|||	3679	0.734625	0.4554	0.6542	5008	,	,	NA	12260	0.8938	NA	0.9165	False	NA	,,,	NA	NA	NA	2504	0.818	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133034054G>A		NA		hg19		0.02	1.968485	TGGxCGT	COVERED																																																																																			NOVEL					0			1	9.330488	KEEP	4	0	0	31	1102	GG	0.999997	0.999404	0			3	60	111	0	0	12.531085	0	0	0	144		1	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133037512	133037512	__UNKNOWN__	IGR	SNP	C	C	T	rs3099921	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133037512C>T			NA	NA				ANKRD30BL (21970 upstream) : AC097532.2 (5855 downstream)						NA		NA									NA						gagcactgggcagaaatcact	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133037512C>T		NA		hg19		0.02	-0.03509	GGGxAGA	UNCOVERED																																																																																			NOVEL					0			0	3.912049	KEEP	2	0	0	13	430	CC	0.993072	0.019843	0			2	60	66	0	0	7.55376	0	0	0	17		1	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133118660	133118660	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:133118660C>G			NA	NA				RP11-725P16.2 (13790 upstream) : RNU6-175P (45664 downstream)						NA		NA									NA						GGACCCTGCTCTCTGGGCGGT	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133118660C>G		NA		hg19		0.02	-0.114056	GCTxTCT	UNCOVERED																																																																																			NOVEL					0			0	2.4074	KEEP	3	0	0	8	265	CC	0.99257	0.16126	0			2	25	81	0	0	8.224882	1	60	42	32		0.666667	0.162467
ACVR2A	92	__UNKNOWN__	__UNKNOWN__	2	148686407	148686407	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:148686407G>A	ENST00000241416.7	+	0	3742					NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	NA		NA			activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGAATTTCCAGATTACCAATC	0.259	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989	92			173	protein-coding gene	gene with protein product		102581	activin A receptor, type II	ACVR2	NA	1314589, 10702675	Standard	NM_001616	NM_001278579	NA	Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.*1564G>A	chr2.hg19:g.148686407G>A		NA	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	hg19	CCDS33301.1	0.02	4.651923	CCAxATT	COVERED																																																																																			NOVEL	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319051.1	2	7.825508	KEEP	0	0	0	26	937	GG	0.999957	0.999957	0		+	35	60	1277	0	0	111.788151	93	60	3555	186	ENST00000241416.7	0.273437	1
RIF1	55183	__UNKNOWN__	__UNKNOWN__	2	152320014	152320014	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:152320014A>G	ENST00000243326.5	+	29	4463	c.3980A>G	c.(3979-3981)aAc>aGc	p.N1327S	RIF1_ENST00000444746.2_Missense_Mutation_p.N1327S|RIF1_ENST00000453091.2_Missense_Mutation_p.N1327S|RIF1_ENST00000430328.2_Missense_Mutation_p.N1327S|RIF1_ENST00000428287.2_Missense_Mutation_p.N1327S			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0		NA			fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTAGAAAATAACCCACCTGGT	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						72	79	77	NA		NA	NA	2		NA											NA				152320014		2203	4300	6503	SO:0001583	missense			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345	55183			23207	protein-coding gene	gene with protein product		608952	RAP1 interacting factor homolog (yeast)		NA	15342490, 15042697, 22850674	Standard		NM_018151	NA	Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.3980A>G	chr2.hg19:g.152320014A>G	ENSP00000243326:p.Asn1327Ser	NA	A0AVS0|Q9NS16	hg19	CCDS2194.1	0.02	13.102961	ATAxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	11.71	1.721158	0.30503	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.10288	2.89;2.92;2.92;2.89;2.92	4.92	3.78	0.43462	.	0.559095	0.20832	N	0.084873	T	0.11836	0.0288	L	0.50333	1.59	0.80722	D	1	B;P	0.39696	0.047;0.683	B;B	0.39465	0.034;0.3	T	0.05616	-1.0874	10	0.40728	T	0.16	-8.4107	10.137	0.42712	0.9209:0.0:0.0791:0.0	.	1327;1327	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	S	1327	ENSP00000390181:N1327S;ENSP00000414615:N1327S;ENSP00000415691:N1327S;ENSP00000243326:N1327S;ENSP00000416123:N1327S	ENSP00000243326:N1327S	N	+	2	0	RIF1	152028260	0.570000	0.26651	0.753000	0.31225	0.312000	0.27988	1.024000	0.30077	0.924000	0.37069	0.455000	0.32223	AAC	NOVEL	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254836.3	3	15.638212	KEEP	0	0	0	52	1547	AA	1	1	0		+	80	60	3043	0	0	271.835045	186	60	6493	379	ENST00000243326.5	0.300752	1
SCN3A	6328	__UNKNOWN__	__UNKNOWN__	2	166019052	166019052	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:166019052G>A	ENST00000283254.7	-	8	1435				SCN3A_ENST00000409101.3_Intron|SCN3A_ENST00000360093.3_Intron	NM_001081676.1|NM_006922.3	NP_001075145.1|NP_008853.3	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	NA		NA			membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTAACATAATGTAATACTTCT	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						99	102	101	NA		NA	NA	2		NA											NA				166019052		2203	4300	6503	SO:0001627	intron_variant			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253	6328		Sodium channels, Voltage-gated ion channels / Sodium channels	10590	protein-coding gene	gene with protein product		182391	sodium channel, voltage-gated, type III, alpha polypeptide		NA	9589372, 16382098	Standard	NM_006922	NM_001081676	NA	Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000283254.7:c.967+13C>T	chr2.hg19:g.166019052G>A		NA	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	hg19	CCDS33312.1	0.02	8.817873	AATxTAA	COVERED																																																																																			NOVEL	SCN3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000102655.2	3	5.115757	KEEP	0	0	0	17	575	GG	0.999366	0.999366	0		-	59	60	2095	0	0	183.636875	150	60	5653	237	ENST00000283254.7	0.282297	1
STK39	27347	__UNKNOWN__	__UNKNOWN__	2	169023818	169023818	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:169023818G>A	ENST00000355999.4	-	3	1126	c.421C>T	c.(421-423)Cta>Tta	p.L141L		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	141	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						CCTCCACTTAGTAATTTCATG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						93	86	89	NA		NA	NA	2		NA											NA				169023818		1909	4131	6040	SO:0001819	synonymous_variant			AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648	27347			17717	protein-coding gene	gene with protein product	STE20/SPS1 homolog (yeast)	607648			NA	10980603	Standard	NM_013233	NM_013233	NA	Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.421C>T	chr2.hg19:g.169023818G>A		NA	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	hg19	CCDS42770.1	0.02	12.635176	TTAxTAA	COVERED																																																																																			NOVEL	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258112.2	1	10.23343	KEEP	0	0	0	34	1232	GG	0.999998	0.999998	0		-	9	60	331	0	0	19.75623	298	60	11459	433	ENST00000355999.4	0.029316	1
STK39	27347	__UNKNOWN__	__UNKNOWN__	2	169023819	169023819	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:169023819T>A	ENST00000355999.4	-	3	1125	c.420A>T	c.(418-420)ttA>ttT	p.L140F		NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	140	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						CTCCACTTAGTAATTTCATGA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						94	87	89	NA		NA	NA	2		NA											NA				169023819		1907	4132	6039	SO:0001583	missense			AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648	27347			17717	protein-coding gene	gene with protein product	STE20/SPS1 homolog (yeast)	607648			NA	10980603	Standard	NM_013233	NM_013233	NA	Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.420A>T	chr2.hg19:g.169023819T>A	ENSP00000348278:p.Leu140Phe	NA	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	hg19	CCDS42770.1	0.02	12.519261	TAGxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	17.61	3.432389	0.62844	.	.	ENSG00000198648	ENST00000355999	T	0.23348	1.91	6.03	-1.18	0.09617	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.25457	0.0619	N	0.05199	-0.095	0.53688	D	0.999978	D	0.89917	1.0	D	0.97110	1.0	T	0.01688	-1.1295	10	0.41790	T	0.15	-24.1534	13.6016	0.62022	0.0:0.5043:0.0:0.4957	.	140	Q9UEW8	STK39_HUMAN	F	140	ENSP00000348278:L140F	ENSP00000348278:L140F	L	-	3	2	STK39	168732065	0.843000	0.29541	0.989000	0.46669	0.994000	0.84299	-0.027000	0.12371	-0.375000	0.07955	0.533000	0.62120	TTA	NOVEL	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258112.2	1	10.222806	KEEP	0	0	0	34	964	TT	0.999998	0.999998	0		-	10	60	336	0	0	19.720521	299	60	10730	439	ENST00000355999.4	0.032362	1
LRP2	4036	__UNKNOWN__	__UNKNOWN__	2	170097899	170097899	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:170097899T>C	ENST00000443831.1	-	23	3391				LRP2_ENST00000263816.3_Intron			P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	NA		NA			cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)	ATGGGGTAAATCGGCTTGTGA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						78	84	82	NA		NA	NA	2		NA											NA				170097899		2203	4300	6503	SO:0001627	intron_variant				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479	4036		Low density lipoprotein receptors	6694	protein-coding gene	gene with protein product	megalin	600073			NA	7959795	Standard	NM_004525	NM_004525	NA	Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000443831.1:c.3257-24A>G	chr2.hg19:g.170097899T>C		NA	O00711|Q16215	hg19		0.02	7.880902	AAAxCGG	COVERED																																																																																			NOVEL	LRP2-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000337306.1	1	6.319434	KEEP	0	0	0	21	674	TT	0.999869	0.999869	0		-	7	60	254	0	0	14.922969	240	60	8709	323	ENST00000443831.1	0.02834	1
MYO3B	140469	__UNKNOWN__	__UNKNOWN__	2	171264205	171264205	__UNKNOWN__	Intron	SNP	G	G	A	rs377388181	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:171264205G>A	ENST00000408978.4	+	22	2663				MYO3B_ENST00000409044.3_Intron|MYO3B_ENST00000334231.6_Intron|MYO3B_ENST00000602629.1_Intron	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	NA		NA			peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CTAATTTGCCGTTTGCTATTC	0.423	NA	NA											G|||	8	0.00159744	0.0061	0	5008	,	,	NA	20089	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA	G	,,	19,3765		0,19,1873	213	200	204	NA	,,	-4.2	0	2		204	1,8253		0,1,4126	no	intron,intron,intron	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	0,20,5999	AA,AG,GG	NA	0.0121,0.5021,0.1661	,,	,,	171264205	20,12018	1892	4127	6019	SO:0001627	intron_variant				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909	140469		Myosins / Myosin superfamily : Class III	15576	protein-coding gene	gene with protein product		610040			NA		Standard		NM_001083615	NA	Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2521-20G>A	chr2.hg19:g.171264205G>A		NA	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	hg19	CCDS42773.1	0.02	16.864598	GCCxTTT	COVERED																																																																																			NOVEL	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333410.1	2	18.35738	KEEP	0	0	0	61	2085	GG	1	1	0		+	85	60	3177	0	0	269.143549	308	60	10633	562	ENST00000408978.4	0.216285	1
CHRNA1	1134	__UNKNOWN__	__UNKNOWN__	2	175614809	175614809	__UNKNOWN__	Missense_Mutation	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:175614809A>C	ENST00000409219.1	-	7	884	c.867T>G	c.(865-867)agT>agG	p.S289R	CHRNA1_ENST00000348749.5_Missense_Mutation_p.S289R|CHRNA1_ENST00000409542.1_Missense_Mutation_p.S207R|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000261007.5_Missense_Mutation_p.S314R			P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	314		NA			cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	AGGGCACAGCACTGGACGTGG	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						192	147	162	NA		NA	NA	2		NA											NA				175614809		2203	4300	6503	SO:0001583	missense			Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435	1134		Cholinergic receptors, Ligand-gated ion channels / Acetylcholine receptors, nicotinic	1955	protein-coding gene	gene with protein product	acetylcholine receptor, nicotinic, alpha 1 (muscle)	100690	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)	CHRNA	NA		Standard		NM_001039523	NA	Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000409219.1:c.867T>G	chr2.hg19:g.175614809A>C	ENSP00000386611:p.Ser289Arg	NA	B4DRV6|D3DPE8	hg19		0.02	10.08953	AGCxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	12.88	2.070069	0.36566	.	.	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542;ENST00000409219	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.5	-7.99	0.01131	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.072602	0.85682	D	0.000000	D	0.86230	0.5883	L	0.41961	1.31	0.80722	D	1	P;D	0.76494	0.707;0.999	P;D	0.77557	0.517;0.99	D	0.88211	0.2890	10	0.56958	D	0.05	.	16.5509	0.84472	0.6247:0.0:0.3753:0.0	.	289;314	Q53SH4;P02708	.;ACHA_HUMAN	R	289;314;207;289	ENSP00000261008:S289R;ENSP00000261007:S314R;ENSP00000387026:S207R;ENSP00000386611:S289R	ENSP00000261007:S314R	S	-	3	2	CHRNA1	175323055	0.000000	0.05858	0.031000	0.17742	0.759000	0.43091	-1.295000	0.02764	-1.940000	0.01043	-0.290000	0.09829	AGT	NOVEL	CHRNA1-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000334119.1	1	12.633094	KEEP	0	0	0	42	1210	AA	1	1	0		-	62	60	2222	0	0	192.893504	173	60	6261	343	ENST00000409219.1	0.26383	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	184472912	184472912	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:184472912G>A			NA	NA				RP11-438L19.1 (392784 upstream) : AC093639.1 (296343 downstream)						NA		NA									NA						GAAACGCCGCGCCAAGCCCTC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.184472912G>A		NA		hg19		0.02	4.738347	CGCxCCA	COVERED																																																																																			NOVEL					0			1	11.131907	KEEP	0	0	0	37	1253	GG	1	0.999989	0			31	60	1017	0	0	88.709113	75	60	2744	155		0.292453	0.999989
STAT1	6772	__UNKNOWN__	__UNKNOWN__	2	191875240	191875240	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:191875240T>C	ENST00000392323.2	-	3	334				STAT1_ENST00000392322.3_Intron|STAT1_ENST00000361099.3_Intron|STAT1_ENST00000540176.1_Intron|STAT1_ENST00000409465.1_Intron			P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	NA		NA			apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			GTTTGTGATTTTATCAAATAA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415	6772		SH2 domain containing	11362	protein-coding gene	gene with protein product	transcription factor ISGF-3 components p91/p84	600555	signal transducer and activator of transcription 1, 91kD		NA	7885841	Standard	NM_007315	NM_139266	NA	Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000392323.2:c.78-65A>G	chr2.hg19:g.191875240T>C		NA	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	hg19		0.02	7.149152	ATTxTAT	COVERED																																																																																			NOVEL	STAT1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000257868.2	2	10.231355	KEEP	0	0	0	34	1089	TT	0.999998	0.999998	0		-	59	60	2177	0	0	195.675865	125	60	4484	232	ENST00000392323.2	0.320652	1
CFLAR	8837	__UNKNOWN__	__UNKNOWN__	2	202003344	202003344	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:202003344T>C	ENST00000342795.5	+	5	903				CFLAR_ENST00000340870.5_Intron|CFLAR_ENST00000341222.6_Intron|CFLAR_ENST00000479953.2_Intron|CFLAR_ENST00000457277.1_Intron|CFLAR_ENST00000309955.3_Intron|CFLAR_ENST00000341582.6_Intron|CFLAR_ENST00000494258.1_Intron|CFLAR_ENST00000440180.1_Intron|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000423241.2_Intron|CFLAR_ENST00000395148.2_3'UTR			O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						GGTACCCGTCTCAGTGATGGG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(16;548 657 22190 32864 42338)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402	8837		Endogenous ligands	1876	protein-coding gene	gene with protein product		603599		CASP8AP1	NA	9208847, 9217161	Standard	NM_003879	NM_003879	NA	Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000342795.5:c.524-1736T>C	chr2.hg19:g.202003344T>C		NA	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	hg19		0.02	5.754327	GTCxCAG	COVERED																																																																																			NOVEL	CFLAR-007	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336701.1	5	11.130433	KEEP	0	0	0	37	1123	TT	1	1	0		+	9	60	313	0	0	20.53238	152	60	5540	216	ENST00000342795.5	0.055901	1
RPE	6120	__UNKNOWN__	__UNKNOWN__	2	210867311	210867311	__UNKNOWN__	5'UTR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:210867311A>T	ENST00000359429.6	+	0	23				RPE_ENST00000436630.2_5'UTR	NM_199229.1	NP_954699.1	Q96AT9	RPE_HUMAN	ribulose-5-phosphate-3-epimerase	NA		NA			carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|ribulose-phosphate 3-epimerase activity (GO:0004750)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	9				Epithelial(149;0.00241)|Lung(261;0.041)|all cancers(144;0.0429)|LUSC - Lung squamous cell carcinoma(261;0.0431)		CGGGGCCAAAACTGCGCGCCC	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS2388.1, CCDS42810.1, CCDS63107.1, CCDS63108.1	2q32-q33.3	2012-10-02			ENSG00000197713	ENSG00000197713	6120	5.1.3.1		10293	protein-coding gene	gene with protein product		180480			NA		Standard	NM_006916	NM_199229	NA	Approved		uc002vdn.4	Q96AT9	OTTHUMG00000154690	ENST00000359429.6:c.-75A>T	chr2.hg19:g.210867311A>T		NA	A8K4S0|B4E016|C9JPQ7|O43767|Q53TV9|Q8N215|Q96N34|Q9BSB5	hg19	CCDS2388.1	0.02	6.649101	AAAxCTG	COVERED																																																																																			NOVEL	RPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336574.2	2	34.598685	KEEP	0	0	0	115	3481	AA	1	1	0		+	51	60	1773	0	0	154.47227	133	60	4646	412	ENST00000359429.6	0.277174	1
ERBB4	2066	__UNKNOWN__	__UNKNOWN__	2	212566230	212566230	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:212566230C>T	ENST00000342788.4	-	12	1800				ERBB4_ENST00000436443.1_Intron|ERBB4_ENST00000402597.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	NA		NA			cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	gcctgtaatcccagcactttg	0.527	NA	NA								TSP Lung(8;0.080)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568	2066			3432	protein-coding gene	gene with protein product		600543	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4		NA	7700649, 17018285	Standard	NM_001042599	NM_001042599	NA	Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1489+461G>A	chr2.hg19:g.212566230C>T		NA	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	hg19	CCDS2394.1	0.02	-0.061413	ATCxCAG	UNCOVERED																																																																																			NOVEL	ERBB4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256597.1	3	3.248565	KEEP	0	0	0	11	353	CC	0.993072	0.043483	0		-	2	47	76	0	0	6.735504	5	60	189	21	ENST00000342788.4	0.285714	0.043787
ERBB4	2066	__UNKNOWN__	__UNKNOWN__	2	212566238	212566238	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:212566238T>G	ENST00000342788.4	-	12	1800				ERBB4_ENST00000436443.1_Intron|ERBB4_ENST00000402597.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	NA		NA			cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	tcccagcactttgggaggcca	0.512	NA	NA								TSP Lung(8;0.080)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568	2066			3432	protein-coding gene	gene with protein product		600543	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4		NA	7700649, 17018285	Standard	NM_001042599	NM_001042599	NA	Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1489+453A>C	chr2.hg19:g.212566238T>G		NA	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	hg19	CCDS2394.1	0.02	-0.061413	ACTxTGG	UNCOVERED																																																																																			NOVEL	ERBB4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256597.1	3	3.009088	KEEP	0	0	0	10	314	TT	0.992708	0.043467	0		-	2	47	82	0	0	7.335529	5	60	181	22	ENST00000342788.4	0.285714	0.043787
FN1	2335	__UNKNOWN__	__UNKNOWN__	2	216272059	216272059	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:216272059G>A	ENST00000354785.4	-	18	2888				FN1_ENST00000323926.6_Intron|FN1_ENST00000432072.2_Intron|FN1_ENST00000443816.1_Intron|FN1_ENST00000357867.4_Intron|FN1_ENST00000359671.1_Intron|FN1_ENST00000346544.3_Intron|FN1_ENST00000357009.2_Intron|FN1_ENST00000336916.4_Intron|FN1_ENST00000421182.1_Intron|FN1_ENST00000356005.4_Intron|FN1_ENST00000345488.5_Intron|FN1_ENST00000446046.1_Intron			P02751	FINC_HUMAN	fibronectin 1	NA		NA			acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	AGATTCATGAGCAAAAGTAAG	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						128	124	125	NA		NA	NA	2		NA											NA				216272059		2203	4300	6503	SO:0001627	intron_variant				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414	2335		Fibronectin type III domain containing, Endogenous ligands	3778	protein-coding gene	gene with protein product	migration-stimulating factor, cold-insoluble globulin	135600			NA	2992939, 3003095	Standard	NM_212476	NM_054034	NA	Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000354785.4:c.2519-15C>T	chr2.hg19:g.216272059G>A		NA	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	hg19	CCDS42814.1	0.02	7.291778	TGAxCAA	COVERED																																																																																			NOVEL	FN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256667.2	0	8.728373	KEEP	0	0	0	29	1045	GG	0.999997	0.999997	0		-	44	60	1579	0	0	135.541581	135	60	5134	267	ENST00000354785.4	0.24581	1
CTDSP1	58190	__UNKNOWN__	__UNKNOWN__	2	219267971	219267971	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:219267971C>G	ENST00000273062.2	+	6	824	c.488C>G	c.(487-489)gCt>gGt	p.A163G	CTDSP1_ENST00000488627.1_3'UTR|CTDSP1_ENST00000443891.1_Missense_Mutation_p.A162G	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	163	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.	NA			negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GACCCAGTAGCTGACCTGCTG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						44	52	50	NA		NA	NA	2		NA											NA				219267971		2202	4300	6502	SO:0001583	missense			AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579	58190		Serine/threonine phosphatases / CTD aspartate-based phosphatases	21614	protein-coding gene	gene with protein product	nuclear LIM interactor-interacting factor, small CTD phosphatase 1	605323			NA	11950066, 12721286	Standard	NM_182642, NM_021198	NM_021198	NA	Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.488C>G	chr2.hg19:g.219267971C>G	ENSP00000273062:p.Ala163Gly	NA	C9IYG0|Q7Z5Q3|Q7Z5Q4	hg19	CCDS2416.1	0.02	15.737368	TAGxTGA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.0|22.0	4.234724|4.234724	0.79800|0.79800	.|.	.|.	ENSG00000144579|ENSG00000144579	ENST00000443891;ENST00000273062|ENST00000452977;ENST00000428361	T;T|.	0.18016|.	2.24;2.24|.	4.64|4.64	4.64|4.64	0.57946|0.57946	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);|.	0.198000|.	0.44097|.	D|.	0.000489|.	T|T	0.79770|0.79770	0.4503|0.4503	M|M	0.86805|0.86805	2.84|2.84	0.80722|0.80722	D|D	1|1	P;B|.	0.51537|.	0.946;0.175|.	P;P|.	0.59171|.	0.853;0.474|.	T|T	0.83328|0.83328	-0.0014|-0.0014	10|5	0.87932|.	D|.	0|.	-13.4146|-13.4146	16.2821|16.2821	0.82697|0.82697	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	163;162|.	Q9GZU7;C9IYG0|.	CTDS1_HUMAN;.|.	G|V	162;163|156;164	ENSP00000392248:A162G;ENSP00000273062:A163G|.	ENSP00000273062:A163G|.	A|L	+|+	2|1	0|2	CTDSP1|CTDSP1	218976215|218976215	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	7.764000|7.764000	0.85297|0.85297	2.121000|2.121000	0.65114|0.65114	0.491000|0.491000	0.48974|0.48974	GCT|CTG	NOVEL	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256774.1	1	69.821554	KEEP	0	0	0	232	8310	CC	1	1	0		+	16	60	585	0	0	37.244883	369	60	13907	771	ENST00000273062.2	0.041558	1
TTLL4	9654	__UNKNOWN__	__UNKNOWN__	2	219610500	219610500	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs370491335		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:219610500C>T	ENST00000392102.1	+	7	2213	c.1873C>T	c.(1873-1875)Cgg>Tgg	p.R625W	TTLL4_ENST00000457313.1_Missense_Mutation_p.R460W|TTLL4_ENST00000258398.4_Missense_Mutation_p.R625W|TTLL4_ENST00000442769.1_Missense_Mutation_p.R625W	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	625	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.	NA			protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)			endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GACCATTGGACGGTCCCACTT	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(172;1818 2053 15407 20943 49753)					NA		NA				0							NA	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	67	61	63	NA	1873	4.6	1	2		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	TTLL4	NM_014640.4	101	0,2,6501	TT,TC,CC	NA	0.0116,0.0227,0.0154	possibly-damaging	625/1200	219610500	2,13004	2203	4300	6503	SO:0001583	missense				CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912	9654		Tubulin tyrosine ligase-like family	28976	protein-coding gene	gene with protein product		NA			NA	11054573	Standard	NM_014640	NM_014640	NA	Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.1873C>T	chr2.hg19:g.219610500C>T	ENSP00000375951:p.Arg625Trp	NA	A8K6V5|Q8WW29	hg19	CCDS2422.1	0.02	7.215029	GGAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.55	3.153584	0.57259	2.27E-4	1.16E-4	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.05513	3.68;3.93;3.43;3.93	5.5	4.62	0.57501	.	0.249544	0.27402	N	0.019536	T	0.19287	0.0463	L	0.50333	1.59	0.51482	D	0.999928	D;D;P	0.89917	0.983;1.0;0.956	P;D;B	0.97110	0.492;1.0;0.256	T	0.00316	-1.1823	10	0.66056	D	0.02	.	13.2787	0.60202	0.3031:0.6969:0.0:0.0	.	460;625;625	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	W	460;625;625;625	ENSP00000393332:R460W;ENSP00000375951:R625W;ENSP00000396555:R625W;ENSP00000258398:R625W	ENSP00000258398:R625W	R	+	1	2	TTLL4	219318744	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.280000	0.43443	1.294000	0.44707	0.655000	0.94253	CGG	NOVEL	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256726.1	0	8.728227	KEEP	0	0	0	29	1023	CC	0.999997	0.999997	0		+	37	60	1365	0	0	116.021708	128	60	4665	262	ENST00000392102.1	0.224242	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	220197989	220197989	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:220197989C>T			NA	NA				RESP18 (90 upstream) : DNPEP (40278 downstream)						NA		NA									NA						aacctccgctcgacctctact	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						61	50	54	NA		NA	NA	2		NA											NA				220197989		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.220197989C>T		NA		hg19		0.02	2.352334	GCTxGAC	COVERED																																																																																			NOVEL					0			0	3.309389	KEEP	0	0	0	11	351	CC	0.993072	0.982687	0			21	60	800	0	0	73.532185	37	60	1232	72		0.362069	0.989542
SLC4A3	6508	__UNKNOWN__	__UNKNOWN__	2	220502830	220502830	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:220502830A>T	ENST00000358055.3	+	18	3278				SLC4A3_ENST00000373760.2_Intron|SLC4A3_ENST00000273063.6_Intron|SLC4A3_ENST00000317151.3_Intron|SLC4A3_ENST00000373762.3_Intron			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	NA		NA			bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCCCCGTGTTAGTCTGCTGAC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						49	42	44	NA		NA	NA	2		NA											NA				220502830		692	1591	2283	SO:0001627	intron_variant				CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923	6508		Solute carriers	11029	protein-coding gene	gene with protein product	Anion exchanger 3, neuronal	106195	solute carrier family 4, anion exchanger, member 3		NA	8001971	Standard	NM_005070	NM_005070	NA	Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2767-56A>T	chr2.hg19:g.220502830A>T		NA	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	hg19	CCDS2445.1	0.02	21.778011	GTTxGTC	COVERED																																																																																			NOVEL	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316472.1	1	41.475035	KEEP	0	0	0	138	4056	AA	1	1	0		+	123	60	4527	0	0	392.78905	357	60	12989	797	ENST00000358055.3	0.25625	1
EPHA4	2043	__UNKNOWN__	__UNKNOWN__	2	222431695	222431695	__UNKNOWN__	Intron	SNP	A	A	G	rs147387638	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:222431695A>G	ENST00000409854.1	-	2	194				EPHA4_ENST00000281821.2_Intron|EPHA4_ENST00000409938.1_Intron|EPHA4_ENST00000392071.4_Intron			P54764	EPHA4_HUMAN	EPH receptor A4	NA		NA			adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		aagaggaagaagaagaagaag	0.408	NA	NA											A|||	430	0.0858626	0.0227	0.0692	5008	,	,	NA	13345	0.129	NA	0.1421	False	NA	,,,	NA	NA	NA	2504	0.0808	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2043	2.7.10.1	EPH receptors, Sterile alpha motif (SAM) domain containing, Fibronectin type III domain containing	3388	protein-coding gene	gene with protein product		602188	EphA4	TYRO1	NA	9267020	Standard		NM_004438	NA	Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000409854.1:c.159+1742T>C	chr2.hg19:g.222431695A>G		NA	A8K2P1|B2R601|B7Z6Q8|Q2M380	hg19		0.02	-0.350924	AGAxGAA	COVERED																																																																																			NOVEL	EPHA4-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000332696.2	4	4.814235	KEEP	1	0	0	16	504	AA	0.99649	0.874627	0		-	4	60	136	0	0	10.108063	31	70	1136	61	ENST00000409854.1	0.114286	0.877708
CUL3	8452	__UNKNOWN__	__UNKNOWN__	2	225346684	225346684	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:225346684C>G	ENST00000264414.4	-	14	2292	c.1954G>C	c.(1954-1956)Gaa>Caa	p.E652Q	CUL3_ENST00000409096.1_Missense_Mutation_p.E628Q|CUL3_ENST00000409777.1_Missense_Mutation_p.E628Q|CUL3_ENST00000344951.4_Missense_Mutation_p.E586Q	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	652		NA			cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TTTTCTATTTCCTTTGATTTG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						123	123	123	NA		NA	NA	2		NA											NA				225346684		2203	4300	6503	SO:0001583	missense			U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257	8452			2553	protein-coding gene	gene with protein product		603136			NA	8681378, 17192413	Standard		NM_003590	NA	Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1954G>C	chr2.hg19:g.225346684C>G	ENSP00000264414:p.Glu652Gln	NA	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	hg19	CCDS2462.1	0.02	2.622277	TTTxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.48	3.834788	0.71373	.	.	ENSG00000036257	ENST00000264414;ENST00000344951;ENST00000409096;ENST00000409777	T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89	5.85	5.85	0.93711	Cullin, N-terminal (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Cullin homology (1);	0.000000	0.85682	D	0.000000	T	0.78291	0.4260	M	0.67397	2.05	0.80722	D	1	P;P;B	0.41008	0.69;0.735;0.362	B;B;B	0.42495	0.316;0.389;0.22	T	0.80094	-0.1526	10	0.72032	D	0.01	.	20.1649	0.98147	0.0:1.0:0.0:0.0	.	586;630;652	Q13618-3;Q53S54;Q13618	.;.;CUL3_HUMAN	Q	652;586;628;628	ENSP00000264414:E652Q;ENSP00000343601:E586Q;ENSP00000387200:E628Q;ENSP00000386525:E628Q	ENSP00000264414:E652Q	E	-	1	0	CUL3	225054928	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.042000	0.70996	2.753000	0.94483	0.655000	0.94253	GAA	NOVEL	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256871.2	0	2.407481	KEEP	0	0	0	8	259	CC	0.99257	0.963607	0		-	14	60	526	0	0	45.990598	39	60	1475	74	ENST00000264414.4	0.264151	0.97082
IRS1	3667	__UNKNOWN__	__UNKNOWN__	2	227659840	227659840	__UNKNOWN__	Silent	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:227659840T>G	ENST00000305123.5	-	1	4635	c.3615A>C	c.(3613-3615)ccA>ccC	p.P1205P	IRS1_ENST00000498335.1_5'UTR	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	1205	Pro-rich.	NA			cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GATGAGGGGGTGGGGGTGGGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047	3667		Pleckstrin homology (PH) domain containing	6125	protein-coding gene	gene with protein product		147545			NA	1648180	Standard	NM_005544	NM_005544	NA	Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.3615A>C	chr2.hg19:g.227659840T>G		NA		hg19	CCDS2463.1	0.02	2.308268	GGGxGGG	COVERED																																																																																			NOVEL	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256886.3	1	3.829795	KEEP	0	11	157	70	1678	TT	1	1	0		-	13	60	210	0	0	9.477016	120	60	3079	279	ENST00000305123.5	0.097744	1
ITM2C	81618	__UNKNOWN__	__UNKNOWN__	2	231740559	231740559	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:231740559A>G	ENST00000409704.2	+	3	466				ITM2C_ENST00000326407.6_Intron|ITM2C_ENST00000335005.6_Intron|ITM2C_ENST00000326427.6_Intron|ITM2C_ENST00000492029.1_Intron			Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	NA		NA			negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GGGGGGTGGGAGGGTGTCCCG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						14	19	17	NA		NA	NA	2		NA											NA				231740559		2142	4177	6319	SO:0001627	intron_variant			AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916	81618		BRICHOS domain containing	6175	protein-coding gene	gene with protein product	BRICHOS domain containing 2C	609554			NA	9653160	Standard	NM_030926	NM_030926	NA	Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000409704.2:c.264+36A>G	chr2.hg19:g.231740559A>G		NA	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	hg19		0.02	1.968108	GGGxGGG	COVERED																																																																																			NOVEL	ITM2C-008	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000397049.1	0	3.77938	KEEP	0	4	47	30	767	AA	0.999999	0.987942	0		+	9	60	203	1	1	14.741679	38	60	1065	127	ENST00000409704.2	0.191489	0.987943
ALPP	250	__UNKNOWN__	__UNKNOWN__	2	233244861	233244861	__UNKNOWN__	Intron	SNP	G	G	C	rs2853375	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:233244861G>C	ENST00000392027.2	+	6	926				AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	NA		NA			dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GCCAGCCAGGGCCCCAAATCC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						61	60	60	NA		NA	NA	2		NA											NA				233244861		2203	4300	6503	SO:0001627	intron_variant			M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	250	3.1.3.1		439	protein-coding gene	gene with protein product	Regan isozyme	171800	alkaline phosphatase, placental (Regan isozyme)		NA	3001717, 3461452	Standard	NM_001632	XM_005246439	NA	Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.658-35G>C	chr2.hg19:g.233244861G>C		NA	P05188|P06861|Q53S78|Q96DB7	hg19	CCDS2490.1	0.02	4.5628	AGGxCCC	COVERED																																																																																			NOVEL	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257032.3	1	6.251208	KEEP	0	1	38	34	1112	GG	0.999999	0.999998	0		+	8	40	304	0	1	21.343441	116	60	4137	186	ENST00000392027.2	0.064516	1
ALPPL2	251	__UNKNOWN__	__UNKNOWN__	2	233273291	233273291	__UNKNOWN__	Intron	SNP	C	C	T	rs186417264	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:233273291C>T	ENST00000295453.3	+	7	908					NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	NA		NA			dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	TGGGTAATGACCCCCTTCCTG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						61	57	58	NA		NA	NA	2		NA											NA				233273291		2192	4279	6471	SO:0001627	intron_variant			J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286	251			441	protein-coding gene	gene with protein product		171810			NA		Standard	NM_031313	NM_031313	NA	Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.856+8C>T	chr2.hg19:g.233273291C>T		NA	A8KAF2|Q16727|Q53S81|Q96CM1	hg19	CCDS2491.1	0.02	3.642451	TGAxCCC	COVERED																																																																																			NOVEL	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257034.2	3	7.647443	KEEP	17	1	33	37	1267	CC	0.999997	0.999995	0		+	5	27	168	0	0	10.203549	113	60	4148	210	ENST00000295453.3	0.042373	0.999998
AC104667.3	0	__UNKNOWN__	__UNKNOWN__	2	238499866	238499866	__UNKNOWN__	3'UTR	SNP	C	C	T	rs114742872|rs3830542		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:238499866C>T	ENST00000470375.1	+	0	204				AC104667.3_ENST00000452801.1_Missense_Mutation_p.P19S						NA		NA									NA						TCTTCCCAAGCCATGAAACTT	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000470375.1:c.*201C>T	chr2.hg19:g.238499866C>T		NA		hg19		0.02	-0.193013	AAGxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	T	2.779	-0.253891	0.05829	.	.	ENSG00000234949	ENST00000452801	.	.	.	1.64	-2.87	0.05700	.	.	.	.	.	T	0.21881	0.0527	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.22836	-1.0205	4	.	.	.	.	4.4361	0.11550	0.0:0.4843:0.2182:0.2975	.	.	.	.	S	19	.	.	P	+	1	0	AC104667.3	238164605	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.274000	0.01163	-1.415000	0.02022	-0.369000	0.07265	CCA	NOVEL	AC104667.3-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000328853.1	0	3.912605	KEEP	0	0	0	13	454	CC	0.994391	0.455189	0		+	9	60	326	0	0	30.429987	13	60	495	41	ENST00000470375.1	0.409091	0.457757
OR6B2	389090	__UNKNOWN__	__UNKNOWN__	2	240969640	240969640	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:240969640C>T	ENST00000402971.2	-	1	266	c.207G>A	c.(205-207)ctG>ctA	p.L69L		NM_001005853.1	NP_001005853.1	Q6IFH4	OR6B2_HUMAN	olfactory receptor, family 6, subfamily B, member 2	69		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)	15		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.4e-29)|all cancers(36;2.08e-27)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)		ACCAGATCTCCAGGAAAGACA	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						118	128	125	NA		NA	NA	2		NA											NA				240969640		2116	4237	6353	SO:0001819	synonymous_variant				CCDS46559.1	2q37.3	2012-08-09	2004-10-07	2004-10-07	ENSG00000182083	ENSG00000182083	389090		GPCR / Class A : Olfactory receptors	15041	protein-coding gene	gene with protein product		NA	olfactory receptor, family 6, subfamily B, member 2 pseudogene	OR6B2P	NA		Standard	NM_001005853	XM_005247004	NA	Approved		uc010zoc.2	Q6IFH4	OTTHUMG00000152400	ENST00000402971.2:c.207G>A	chr2.hg19:g.240969640C>T		NA	B2RPR3|Q8NGW0	hg19	CCDS46559.1	0.02	12.468637	CTCxAGG	COVERED																																																																																			NOVEL	OR6B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326079.1	1	13.311655	KEEP	24	2	62	66	2280	CC	1	1	0		-	20	44	699	0	0	46.805013	306	60	11554	505	ENST00000402971.2	0.06135	1
AC131097.3	0	__UNKNOWN__	__UNKNOWN__	2	242946503	242946503	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:242946503G>A	ENST00000415434.1	+	0	310										NA		NA									NA						GAATGTCCTCGGCACTGCCCT	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000415434.1:	chr2.hg19:g.242946503G>A		NA		hg19		0.02	1.97326	CTCxGCA	COVERED																																																																																			NOVEL	AC131097.3-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000322318.1	1	10.22913	KEEP	8	0	0	34	1111	GG	0.999998	0.999892	0		+	7	40	231	0	0	15.867686	86	60	2762	158	ENST00000415434.1	0.075269	0.999895
AC131097.3	0	__UNKNOWN__	__UNKNOWN__	2	242946516	242946516	__UNKNOWN__	RNA	SNP	G	G	A	rs540495953	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr2:242946516G>A	ENST00000415434.1	+	0	310										NA		NA									NA						ACTGCCCTCCGTGGGGACGTC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000415434.1:	chr2.hg19:g.242946516G>A		NA		hg19		0.02	4.466764	TCCxTGG	COVERED																																																																																			NOVEL	AC131097.3-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000322318.1	1	11.434468	KEEP	7	0	0	38	1266	GG	1	0.999996	0		+	6	21	220	0	0	14.660358	108	60	3694	204	ENST00000415434.1	0.052632	0.999997
FANCD2	2177	__UNKNOWN__	__UNKNOWN__	3	10091153	10091153	__UNKNOWN__	Silent	SNP	C	C	T	rs35652360	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:10091153C>T	ENST00000419585.1	+	17	1670	c.1509C>T	c.(1507-1509)aaC>aaT	p.N503N	FANCD2_ENST00000287647.3_Silent_p.N503N|FANCD2_ENST00000383806.1_Silent_p.N503N|FANCD2_ENST00000383807.1_Silent_p.N503N			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	503		NA			DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TAGTGTTAAACCCATCTGCTA	0.408	NA	NA	D, Mis, N, F			AML, leukemia		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA		yes	Rec		Fanconi anaemia D2	3	3p26	2177	Fanconi anemia, complementation group D2		L	0							NA						237	256	249	NA		NA	NA	3		NA											NA				10091153		2201	4296	6497	SO:0001819	synonymous_variant	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554	2177		Fanconi anemia, complementation groups	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD	NA	7581463, 11239453, 18475298	Standard		XM_005264946	NA	Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1509C>T	chr3.hg19:g.10091153C>T		NA	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	hg19	CCDS33696.1	0.02	1.847807	AAAxCCA	COVERED																																																																																			NOVEL	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339873.1	1	3.458274	KEEP	10	1	12	16	568	CC	0.997832	0.995734	0		+	6	27	204	0	0	14.25977	67	60	2492	126	ENST00000419585.1	0.082192	0.997898
LSM3	27258	__UNKNOWN__	__UNKNOWN__	3	14225608	14225608	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:14225608G>C	ENST00000306024.3	+	3	731					NM_014463.2	NP_055278.1	P62310	LSM3_HUMAN	LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)	NA		NA			exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|large_intestine(2)|ovary(1)	4						CATATTTATGGGAAGCCTGTC	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF182289	CCDS2619.1	3p25.1	2012-08-15			ENSG00000170860	ENSG00000170860	27258			17874	protein-coding gene	gene with protein product		607283			NA	10369684	Standard	NM_014463	NM_014463	NA	Approved	YLR438C, SMX4, USS2	uc003byn.3	P62310	OTTHUMG00000129838	ENST00000306024.3:c.228+76G>C	chr3.hg19:g.14225608G>C		NA	Q6IAH0|Q9Y4Z1	hg19	CCDS2619.1	0.02	-0.377247	ATGxGAA	COVERED																																																																																			NOVEL	LSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252078.3	0	3.009819	KEEP	0	0	0	10	353	GG	0.992708	0.90244	0		+	4	60	135	0	0	9.631387	39	60	1462	74	ENST00000306024.3	0.093023	0.909069
C3orf20	84077	__UNKNOWN__	__UNKNOWN__	3	14745899	14745899	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T	rs146642906	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:14745899C>T	ENST00000253697.3	+	7	1386	c.934C>T	c.(934-936)Cga>Tga	p.R312*	C3orf20_ENST00000495387.1_3'UTR|C3orf20_ENST00000435614.1_Nonsense_Mutation_p.R190*|C3orf20_ENST00000412910.1_Nonsense_Mutation_p.R190*	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	312		NA				cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CATGATCTTACGAAACTACAA	0.493	NA	NA											C|||	3	0.000599042	0	0.0014	5008	,	,	NA	20247	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA	C	stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	109	113	112	NA	568,568,934	4.9	0.4	3	dbSNP_134	112	2,8598	3.0+/-9.4	0,2,4298	no	stop-gained,stop-gained,stop-gained	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	,,	0,2,6501	TT,TC,CC	NA	0.0233,0.0,0.0154	,,	190/783,190/783,312/905	14745899	2,13004	2203	4300	6503	SO:0001587	stop_gained			AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379	84077			25320	protein-coding gene	gene with protein product		NA			NA	11230166	Standard	NM_032137	NM_032137	NA	Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.934C>T	chr3.hg19:g.14745899C>T	ENSP00000253697:p.Arg312*	NA	Q7L0U6|Q8NCP2|Q9H0I7	hg19	CCDS33706.1	0.02	4.599371	TTAxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	38	6.971027	0.97971	0.0	2.33E-4	ENSG00000131379	ENST00000253697;ENST00000435614;ENST00000412910	.	.	.	4.91	4.91	0.64330	.	0.149471	0.31589	N	0.007385	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.8772	13.6102	0.62074	0.0:1.0:0.0:0.0	.	.	.	.	X	312;190;190	.	ENSP00000253697:R312X	R	+	1	2	C3orf20	14720903	0.716000	0.27956	0.382000	0.26119	0.050000	0.14768	2.073000	0.41519	2.276000	0.75962	0.585000	0.79938	CGA	NOVEL	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340586.1	1	7.825748	KEEP	0	0	0	26	933	CC	0.999957	0.999957	0		+	7	60	274	0	0	18.80891	127	60	4609	209	ENST00000253697.3	0.052239	1
AC144521.1	0	__UNKNOWN__	__UNKNOWN__	3	18952245	18952245	__UNKNOWN__	RNA	SNP	A	A	G	rs111238918		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:18952245A>G	ENST00000425799.2	+	0	569										NA		NA									NA						CAGAGGACAAATAATTTATTT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000425799.2:	chr3.hg19:g.18952245A>G		NA		hg19		0.02	15.142938	CAAxTAA	COVERED																																																																																			NOVEL	AC144521.1-022	KNOWN	basic	antisense	NA	processed_transcript	OTTHUMT00000339554.2	7	6.96506	KEEP	44	4	152	76	2412	AA	1	1	0		+	33	50	1279	0	0	97.956754	278	60	10376	595	ENST00000425799.2	0.106109	1
ZNF385D	79750	__UNKNOWN__	__UNKNOWN__	3	21461733	21461733	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:21461733C>T	ENST00000281523.2	-	0	2679					NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	NA		NA				nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						CAACATTCTCCGTTTTTACTG	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789	79750			26191	protein-coding gene	gene with protein product		NA	zinc finger protein 659	ZNF659	NA	12477932	Standard	NM_024697	NM_024697	NA	Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.*973G>A	chr3.hg19:g.21461733C>T		NA		hg19	CCDS2636.1	0.02	2.262665	CTCxGTT	COVERED																																																																																			NOVEL	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252884.1	2	3.611248	KEEP	0	0	0	12	398	CC	0.993634	0.993541	0		-	20	60	769	0	0	65.314399	74	60	2524	124	ENST00000281523.2	0.212766	0.999907
LTF	4057	__UNKNOWN__	__UNKNOWN__	3	46480994	46480994	__UNKNOWN__	Intron	SNP	A	A	G	rs55787894	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:46480994A>G	ENST00000417439.1	-	15	1718				LTF_ENST00000493056.1_Intron|LTF_ENST00000426532.2_Intron|LTF_ENST00000231751.4_Intron			P02788	TRFL_HUMAN	lactotransferrin	NA		NA			antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		AGAAGGTGGCATCATCCACGC	0.537	NA	NA											A|||	520	0.103834	0.003	0.1066	5008	,	,	NA	20660	0.0893	NA	0.1471	False	NA	,,,	NA	NA	NA	2504	0.2086	NA	NA	NA						NA		NA				0							NA	A	,	111,4295	85.3+/-124.0	1,109,2093	53	49	50	NA	,	3.9	0.1	3	dbSNP_129	50	1184,7416	237.5+/-269.3	92,1000,3208	no	intron,intron	LTF	NM_001199149.1,NM_002343.3	,	93,1109,5301	GG,GA,AA	NA	13.7674,2.5193,9.9569	,	,	46480994	1295,11711	2203	4300	6503	SO:0001627	intron_variant				CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223	4057			6720	protein-coding gene	gene with protein product		150210			NA	17476971, 3356163	Standard	NM_002343	NM_001199149	NA	Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000417439.1:c.1718-23T>C	chr3.hg19:g.46480994A>G		NA	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	hg19		0.02	2.334743	GGCxTCA	COVERED																																																																																			NOVEL	LTF-003	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000343953.1	1	3.609279	KEEP	0	0	0	12	351	AA	0.993634	0.985778	0		-	34	60	1247	0	0	122.041772	29	60	1076	80	ENST00000417439.1	0.539683	0.992094
LRRC2	79442	__UNKNOWN__	__UNKNOWN__	3	46559359	46559359	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:46559359G>T	ENST00000395905.3	-	0	2653					NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	NA		NA								breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		GTTGTCCTGTGGTACCCACAA	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827	79442			14676	protein-coding gene	gene with protein product		607180	leucine-rich repeat-containing 2		NA	11896456	Standard		NM_024512	NA	Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.*1145C>A	chr3.hg19:g.46559359G>T		NA	B2RDQ7|Q96LT5	hg19	CCDS2741.1	0.02	7.150303	TGTxGTA	COVERED																																																																																			NOVEL	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257375.2	2	10.534459	KEEP	0	0	0	35	1240	GG	0.999999	0.999999	0		-	36	60	1338	0	0	113.823993	125	60	4597	243	ENST00000395905.3	0.223602	1
NME6	10201	__UNKNOWN__	__UNKNOWN__	3	48336203	48336203	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:48336203C>T	ENST00000421967.1	-	6	554	c.509G>A	c.(508-510)cGc>cAc	p.R170H	NME6_ENST00000415053.1_Missense_Mutation_p.R162H|NME6_ENST00000426723.1_Missense_Mutation_p.R95H|NME6_ENST00000451657.1_Missense_Mutation_p.A149T|NME6_ENST00000435684.1_Missense_Mutation_p.A149T|NME6_ENST00000442597.1_Missense_Mutation_p.R162H|NME6_ENST00000415644.1_Missense_Mutation_p.R95H|NME6_ENST00000444069.1_5'UTR|NME6_ENST00000426689.2_Missense_Mutation_p.R162H|NME6_ENST00000452211.1_Missense_Mutation_p.R162H|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000450160.1_Missense_Mutation_p.A149T|NME6_ENST00000447314.1_Missense_Mutation_p.R117H	NM_005793.3	NP_005784.1	O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	162		NA			apoptotic process (GO:0006915)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|negative regulation of cell growth (GO:0030308)|negative regulation of mitosis (GO:0045839)|UTP biosynthetic process (GO:0006228)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.R170H(1)		breast(1)|large_intestine(5)	6				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		AGGGCCACAGCGCAACTGGGG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	large_intestine(1)					NA						100	92	95	NA		NA	NA	3		NA											NA				48336203		2203	4300	6503	SO:0001583	missense			AF051941	CCDS2763.1	3p21.31	2012-05-18	2012-05-18		ENSG00000172113	ENSG00000172113	10201			20567	protein-coding gene	gene with protein product		608294	non-metastatic cells 6, protein expressed in (nucleoside-diphosphate kinase)		NA	10453732, 19852809	Standard	NM_005793	NM_005793	NA	Approved	NM23-H6, IPIA-ALPHA	uc003cso.3	O75414	OTTHUMG00000133531	ENST00000421967.1:c.509G>A	chr3.hg19:g.48336203C>T	ENSP00000416658:p.Arg170His	NA	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	hg19	CCDS2763.1	0.02	9.618451	CAGxGCA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.298969|5.298969	0.95574|0.95574	.|.	.|.	ENSG00000172113|ENSG00000172113	ENST00000450160;ENST00000451657;ENST00000435684|ENST00000421967;ENST00000426689;ENST00000452211;ENST00000426723;ENST00000415644;ENST00000415053;ENST00000442597;ENST00000447314;ENST00000425930	.|T;T;T;T;T;T;T	.|0.66638	.|0.35;0.36;0.36;0.36;0.36;-0.22;0.38	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72566|0.72566	0.3476|0.3476	L|L	0.29908|0.29908	0.895|0.895	0.30258|0.30258	N|N	0.793406|0.793406	P|D;D;D	0.46327|0.89917	0.876|1.0;1.0;0.998	B|D;P;P	0.39738|0.87578	0.308|0.998;0.894;0.799	T|T	0.71839|0.71839	-0.4471|-0.4471	8|10	0.87932|0.62326	D|D	0|0.03	-3.3845|-3.3845	15.0702|15.0702	0.72030|0.72030	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	149|95;162;162	O75414-3|O75414-2;O75414;C9J9V6	.|.;NDK6_HUMAN;.	T|H	149|170;162;162;95;95;162;162;117;162	.|ENSP00000416658:R170H;ENSP00000440286:R162H;ENSP00000392352:R162H;ENSP00000399582:R162H;ENSP00000406642:R162H;ENSP00000414842:R117H;ENSP00000411116:R162H	ENSP00000393261:A149T|ENSP00000399582:R162H	A|R	-|-	1|2	0|0	NME6|NME6	48311207|48311207	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.916000|0.916000	0.54674|0.54674	4.866000|4.866000	0.63005|0.63005	2.494000|2.494000	0.84150|0.84150	0.561000|0.561000	0.74099|0.74099	GCT|CGC	NOVEL	NME6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257506.3	0	10.525819	KEEP	0	0	0	35	1179	CC	0.999999	0.999999	0		-	11	60	381	0	0	24.787323	197	60	6893	284	ENST00000421967.1	0.052885	1
IMPDH2	3615	__UNKNOWN__	__UNKNOWN__	3	49066167	49066167	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:49066167G>C	ENST00000326739.4	-	2	187					NM_000884.2	NP_000875.2			IMP (inosine 5'-monophosphate) dehydrogenase 2	NA		NA								breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(2)|stomach(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGATGTTCAGGACCCAATTCC	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						118	95	103	NA		NA	NA	3		NA											NA				49066167		2203	4300	6503	SO:0001627	intron_variant				CCDS2786.1	3p21.2	2014-05-15	2010-04-29		ENSG00000178035	ENSG00000178035	3615	1.1.1.205		6053	protein-coding gene	gene with protein product		146691			NA	9858805, 1969416	Standard		XM_006713128	NA	Approved		uc003cvt.3	P12268	OTTHUMG00000156771	ENST00000326739.4:c.147+23C>G	chr3.hg19:g.49066167G>C		NA		hg19	CCDS2786.1	0.02	4.669607	CAGxACC	COVERED																																																																																			NOVEL	IMPDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345657.1	0	14.445767	KEEP	0	0	0	48	1631	GG	1	1	0		-	7	60	267	0	0	18.301761	119	60	4382	208	ENST00000326739.4	0.055556	1
MST1	4485	__UNKNOWN__	__UNKNOWN__	3	49722468	49722468	__UNKNOWN__	Silent	SNP	A	A	C	rs572177192		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:49722468A>C	ENST00000449682.2	-	14	1960	c.1599T>G	c.(1597-1599)acT>acG	p.T533T		NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth factor-like)	519	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			embryo implantation (GO:0007566)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		ACTGCCGGGCAGTCAGTATCC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(110;181 1524 8005 22865 46297)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			M74178	CCDS33757.2	3p21	2008-09-05			ENSG00000173531	ENSG00000173531	4485			7380	protein-coding gene	gene with protein product	hepatocyte growth factor-like protein homolog	142408		D3F15S2, HGFL, DNF15S2	NA	2902784, 8393443	Standard	NM_020998	NM_020998	NA	Approved	MSP, NF15S2	uc003cxg.3	P26927	OTTHUMG00000155918	ENST00000449682.2:c.1599T>G	chr3.hg19:g.49722468A>C		NA	A6NLA3|A8MSX3|Q13350|Q14870|Q6GTN4	hg19	CCDS33757.2	0.02	1.805302	GGCxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	12.65	2.002529	0.35320	.	.	ENSG00000173531	ENST00000448220	.	.	.	4.8	-8.04	0.01110	.	.	.	.	.	T	0.32912	0.0845	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43507	-0.9387	4	.	.	.	.	1.0069	0.01488	0.1621:0.3277:0.1909:0.3193	.	.	.	.	R	19	.	.	L	-	2	0	MST1	49697472	0.886000	0.30341	0.960000	0.40013	0.991000	0.79684	-0.074000	0.11450	-1.041000	0.03266	0.533000	0.62120	CTG	NOVEL	MST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342315.3	4	6.61896	KEEP	22	0	0	22	660	AA	0.997832	0.996826	0		-	5	27	139	1	0	8.570211	73	50	2746	133	ENST00000449682.2	0.064103	0.998993
SEMA3F	6405	__UNKNOWN__	__UNKNOWN__	3	50220902	50220902	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:50220902C>T	ENST00000002829.3	+	12	1622	c.1138C>T	c.(1138-1140)Cgc>Tgc	p.R380C	SEMA3F_ENST00000434342.1_Missense_Mutation_p.R349C|SEMA3F_ENST00000413852.1_Missense_Mutation_p.R281C	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	380	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.	NA			axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		GGCTGATATTCGCATGGTCTT	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						86	74	78	NA		NA	NA	3		NA											NA				50220902		2203	4300	6503	SO:0001583	missense			U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617	6405		Semaphorins, Immunoglobulin superfamily / Immunoglobulin-like domain containing	10728	protein-coding gene	gene with protein product	sema IV	601124			NA	8786119, 8649831	Standard	NM_004186	NM_004186	NA	Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.1138C>T	chr3.hg19:g.50220902C>T	ENSP00000002829:p.Arg380Cys	NA	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	hg19	CCDS2811.1	0.02	4.76646	ATTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888829	0.91814	.	.	ENSG00000001617	ENST00000450338;ENST00000413852;ENST00000002829;ENST00000434342	T;T;T;T	0.12147	2.71;2.71;2.71;2.71	5.45	5.45	0.79879	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.45458	0.1343	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.53865	-0.8378	10	0.87932	D	0	.	14.8537	0.70319	0.1443:0.8557:0.0:0.0	.	349;380	C9JQ85;Q13275	.;SEM3F_HUMAN	C	349;281;380;349	ENSP00000398399:R349C;ENSP00000388931:R281C;ENSP00000002829:R380C;ENSP00000409859:R349C	ENSP00000002829:R380C	R	+	1	0	SEMA3F	50195906	0.998000	0.40836	0.986000	0.45419	0.995000	0.86356	3.939000	0.56591	2.542000	0.85734	0.511000	0.50034	CGC	NOVEL	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345929.1	3	14.746293	KEEP	0	0	0	49	1659	CC	1	0.999997	0		+	40	60	1481	0	0	134.928869	75	60	2683	207	ENST00000002829.3	0.347826	0.999997
TEX264	51368	__UNKNOWN__	__UNKNOWN__	3	51738069	51738069	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:51738069G>A	ENST00000415259.1	+	0	2060				TEX264_ENST00000416589.1_3'UTR|TEX264_ENST00000463857.1_3'UTR|TEX264_ENST00000395057.1_3'UTR|TEX264_ENST00000341333.5_3'UTR|TEX264_ENST00000457573.1_3'UTR			Q9Y6I9	TX264_HUMAN	testis expressed 264	NA		NA				extracellular vesicular exosome (GO:0070062)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(193;8.53e-05)|Kidney(197;0.000594)|KIRC - Kidney renal clear cell carcinoma(197;0.000759)		CAGTTGCTGAGGAACTGagca	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						5	6	6	NA		NA	NA	3		NA											NA				51738069		2095	4169	6264	SO:0001624	3_prime_UTR_variant			AF072733	CCDS2833.1, CCDS74945.1	3p21	2007-03-13	2007-03-13		ENSG00000164081	ENSG00000164081	51368			30247	protein-coding gene	gene with protein product		NA	testis expressed gene 264, testis expressed sequence 264		NA	12975309	Standard	NM_015926	NM_001243725	NA	Approved	ZSIG11, FLJ13935	uc003dbm.4	Q9Y6I9	OTTHUMG00000156901	ENST00000415259.1:c.*37G>A	chr3.hg19:g.51738069G>A		NA	B3KN87|Q9UKD7	hg19	CCDS2833.1	0.02	10.350779	TGAxGAA	COVERED																																																																																			NOVEL	TEX264-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346530.1	1	17.155771	KEEP	0	0	0	57	2033	GG	1	1	0		+	48	60	1793	0	0	153.751434	157	60	5799	322	ENST00000415259.1	0.234146	1
DNAH1	25981	__UNKNOWN__	__UNKNOWN__	3	52393946	52393946	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:52393946G>A	ENST00000420323.2	+	27	4683	c.4422G>A	c.(4420-4422)gtG>gtA	p.V1474V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1474	Stem. {ECO:0000250}.	NA			cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTGATCTGGTGGCCCTTGTGC	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						155	163	160	NA		NA	NA	3		NA											NA				52393946		2141	4245	6386	SO:0001819	synonymous_variant			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841	25981		Axonemal dyneins	2940	protein-coding gene	gene with protein product		603332	dynein, axonemal, heavy polypeptide 1		NA	8812413, 9256245	Standard	NM_015512	NM_015512	NA	Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.4422G>A	chr3.hg19:g.52393946G>A		NA	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	hg19	CCDS46842.1	0.02	15.413408	GGTxGCC	COVERED																																																																																			NOVEL	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350816.1	4	38.517273	KEEP	0	0	0	128	4428	GG	1	1	0		+	75	60	2726	0	0	234.139335	233	60	8767	520	ENST00000420323.2	0.243506	1
FAM86DP	692099	__UNKNOWN__	__UNKNOWN__	3	75471400	75471400	__UNKNOWN__	RNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75471400C>T	ENST00000459803.1	-	0	1741					NR_024241.1				family with sequence similarity 86, member D, pseudogene	NA		NA									NA						TGGCCAGAAGCTGAAATGACG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					BC016686		3p12.3	2010-06-04	2010-06-04	2010-06-04	ENSG00000244026	ENSG00000244026	692099			32659	pseudogene	pseudogene		NA	family with sequence similarity 86, member D	FAM86D	NA		Standard	NR_024241	NR_024241	NA	Approved		uc003dpp.4		OTTHUMG00000158855	ENST00000459803.1:	chr3.hg19:g.75471400C>T		NA		hg19		0.02	2.040036	AAGxTGA	COVERED																																																																																			NOVEL	FAM86DP-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000352425.1	2	2.744943	KEEP	2	1	34	21	773	CC	0.999869	0.99807	0		-	4	43	137	0	0	8.86869	70	60	2646	125	ENST00000459803.1	0.054054	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75679872	75679872	__UNKNOWN__	IGR	SNP	C	C	T	rs200814675		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75679872C>T			NA	NA				CTD-2026G6.3 (50722 upstream) : MIR1324 (41 downstream)						NA		NA									NA						TCCATGCACACAGAGGATGCA	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						4	3	3	NA		NA	NA	3		NA											NA				75679872		1038	2542	3580	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75679872C>T		NA		hg19		0.02	9.369548	ACAxAGA	COVERED																																																																																			NOVEL					0			0	4.20707	KEEP	17	0	0	14	424	CC	0.99649	0.99649	0			19	40	672	0	0	56.018257	72	48	2673	266		0.208791	1
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75679993	75679993	__UNKNOWN__	RNA	SNP	C	C	T	rs202177109	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75679993C>T	ENST00000408868.1	+	0	80					NR_031714.1				microRNA 1324	NA		NA									NA						ATTCTATGCACTTTCCTGGAG	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						60	61	61	NA		NA	NA	3		NA											NA				75679993		1568	3575	5143							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75679993C>T		NA		hg19		0.02	32.04908	GCAxTTT	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		6	35.714114	KEEP	18	8	236	202	7173	CC	1	1	0		+	17	60	618	0	0	39.312767	387	60	14616	1299	ENST00000408868.1	0.042079	1
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75680006	75680006	__UNKNOWN__	RNA	SNP	T	T	C	rs58827088	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75680006T>C	ENST00000408868.1	+	0	93					NR_031714.1				microRNA 1324	NA		NA									NA						TCCTGGAGGCTCCATGCTGGT	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						52	50	51	NA		NA	NA	3		NA											NA				75680006		1568	3573	5141							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75680006T>C		NA		hg19		0.02	40.312378	GGCxCCA	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		7	26.631087	KEEP	21	10	351	211	6747	TT	1	1	0		+	69	60	2469	0	0	199.330039	339	60	12762	1330	ENST00000408868.1	0.169118	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75680122	75680122	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75680122C>A			NA	NA				MIR1324 (113 upstream) : FRG2C (33358 downstream)						NA		NA									NA						CCTCCCTAGTCCCTTTGCAGA	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75680122C>A		NA		hg19		0.02	12.548233	AGTxCCT	COVERED																																																																																			NOVEL					0			3	10.567395	KEEP	61	1	28	45	1521	CC	1	1	0			59	50	1961	0	0	169.956721	152	50	5349	429		0.279621	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75692896	75692896	__UNKNOWN__	IGR	SNP	C	C	T	rs62248974	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75692896C>T			NA	NA				MIR1324 (12887 upstream) : FRG2C (20584 downstream)						NA		NA									NA						cactgaaacacccctgggatg	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75692896C>T		NA		hg19		0.02	4.258296	ACAxCCC	COVERED																																																																																			NOVEL					0			3	8.363196	KEEP	12	1	35	40	1422	CC	1	0.999997	0			10	60	366	0	0	29.400459	53	60	1997	217		0.15873	0.999997
FRG2C	100288801	__UNKNOWN__	__UNKNOWN__	3	75714185	75714185	__UNKNOWN__	Intron	SNP	C	C	T	rs73840322		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75714185C>T	ENST00000464571.1	+	3	303				FRG2C_ENST00000308062.3_Intron			A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	NA		NA				nucleus (GO:0005634)				breast(2)|ovary(1)	3						TGGGGTTTGGCGGTAACCTCA	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969	100288801			33626	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001124759.1	NM_001124759	NA	Approved			A6NGY1	OTTHUMG00000158963	ENST00000464571.1:c.254-92C>T	chr3.hg19:g.75714185C>T		NA		hg19		0.02	3.850459	TGGxGGT	COVERED																																																																																			NOVEL	FRG2C-002	NOVEL	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352695.1	2	3.306104	KEEP	10	0	0	11	360	CC	0.993072	0.99307	0		+	7	40	211	0	0	14.223668	71	60	2636	139	ENST00000464571.1	0.089744	0.999998
FRG2C	100288801	__UNKNOWN__	__UNKNOWN__	3	75714895	75714895	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75714895G>A	ENST00000464571.1	+	4	599	c.549G>A	c.(547-549)tcG>tcA	p.S183S	FRG2C_ENST00000308062.3_Silent_p.S184S			A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	184		NA				nucleus (GO:0005634)				breast(2)|ovary(1)	3						GAGCTATGTCGGAGGCTGTTT	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969	100288801			33626	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001124759.1	NM_001124759	NA	Approved			A6NGY1	OTTHUMG00000158963	ENST00000464571.1:c.549G>A	chr3.hg19:g.75714895G>A		NA		hg19		0.02	33.181191	GTCxGAG	COVERED																																																																																			NOVEL	FRG2C-002	NOVEL	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352695.1	7	31.436482	KEEP	9	4	124	148	5018	GG	1	1	0		+	31	40	1155	0	0	83.556273	352	60	12406	1043	ENST00000464571.1	0.08094	1
FRG2C	100288801	__UNKNOWN__	__UNKNOWN__	3	75716051	75716051	__UNKNOWN__	3'UTR	SNP	C	C	T	rs73840340	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75716051C>T	ENST00000464571.1	+	0	1755				FRG2C_ENST00000308062.3_3'UTR			A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	NA		NA				nucleus (GO:0005634)				breast(2)|ovary(1)	3						TATTCATCTGCCTCATGTTTT	0.234	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969	100288801			33626	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001124759.1	NM_001124759	NA	Approved			A6NGY1	OTTHUMG00000158963	ENST00000464571.1:c.*859C>T	chr3.hg19:g.75716051C>T		NA		hg19		0.02	10.343349	CTGxCTC	COVERED																																																																																			NOVEL	FRG2C-002	NOVEL	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352695.1	22	2.294778	KEEP	0	2	46	24	836	CC	0.999957	0.999957	0		+	50	60	1793	0	0	146.018211	231	60	8456	368	ENST00000464571.1	0.177936	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75718973	75718973	__UNKNOWN__	IGR	SNP	T	T	G	rs377680734		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75718973T>G			NA	NA				FRG2C (2602 upstream) : LINC00960 (4590 downstream)						NA		NA									NA						GGGCAAGGTGTGCTTGCGCCA	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75718973T>G		NA		hg19		0.02	-0.37725	GTGxGCT	COVERED																																																																																			NOVEL					0			1	5.714036	KEEP	2	0	0	19	548	TT	0.99986	0.908941	0			3	60	104	0	0	9.178393	7	60	263	85		0.3	0.909069
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75786623	75786623	__UNKNOWN__	Silent	SNP	G	G	T	rs112829115		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75786623G>T	ENST00000478296.1	-	4	2277	c.2001C>A	c.(1999-2001)atC>atA	p.I667I	ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Silent_p.I710I|ZNF717_ENST00000422325.1_Silent_p.I717I|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	707		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGCTTCTGAAGATTTGCCTTC	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						17	17	17	NA		NA	NA	3		NA											NA				75786623		654	1494	2148	SO:0001819	synonymous_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2001C>A	chr3.hg19:g.75786623G>T		NA		hg19		0.02	14.365265	GAAxATT	COVERED																																																																																			NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	10	6.752178	KEEP	0	1	30	33	1130	GG	0.999998	0.999998	0		-	43	60	1591	0	0	139.04214	118	60	4379	392	ENST00000478296.1	0.267081	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75786687	75786687	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs80214016	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75786687A>T	ENST00000478296.1	-	4	2213	c.1937T>A	c.(1936-1938)cTc>cAc	p.L646H	ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.L689H|ZNF717_ENST00000422325.1_Missense_Mutation_p.L696H|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	686		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CCCCGGTGTGAGTTCTCTGAT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						4	4	4	NA		NA	NA	3		NA											NA				75786687		576	1439	2015	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1937T>A	chr3.hg19:g.75786687A>T	ENSP00000419377:p.Leu646His	NA		hg19		0.02	18.287138	GTGxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	.	5.999	0.368292	0.11352	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.07688	3.17;3.33;3.32	1.63	-1.62	0.08372	.	.	.	.	.	T	0.03959	0.0111	N	0.11756	0.17	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.40534	-0.9558	9	0.72032	D	0.01	.	2.2385	0.04014	0.4226:0.0:0.338:0.2395	rs6668837;rs52802391;rs6668837	696	C9JSV9	.	H	646;696;689	ENSP00000419377:L646H;ENSP00000409514:L696H;ENSP00000383643:L689H	ENSP00000383643:L689H	L	-	2	0	ZNF717	75869377	0.001000	0.12720	0.003000	0.11579	0.001000	0.01503	-0.548000	0.06048	-0.465000	0.06953	-0.721000	0.03606	CTC	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	9	2.472757	KEEP	0	5	147	60	1877	AA	1	1	0		-	23	60	823	0	0	61.679874	189	60	6726	593	ENST00000478296.1	0.108491	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788031	75788031	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75788031T>C	ENST00000478296.1	-	4	869	c.593A>G	c.(592-594)aAc>aGc	p.N198S	ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.N241S|ZNF717_ENST00000422325.1_Missense_Mutation_p.N248S|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	241		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						AACAGCTGAGTTATTACAGGC	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						21	16	18	NA		NA	NA	3		NA											NA				75788031		266	677	943	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.593A>G	chr3.hg19:g.75788031T>C	ENSP00000419377:p.Asn198Ser	NA		hg19		0.02	36.61045	GAGxTAT	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.014	-1.581289	0.00879	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.05786	3.39;3.55;3.54	2.2	-3.06	0.05379	.	.	.	.	.	T	0.02649	0.0080	N	0.13272	0.32	0.09310	N	1	B	0.28324	0.207	B	0.23852	0.049	T	0.46679	-0.9174	9	0.17832	T	0.49	.	2.8263	0.05486	0.3808:0.1327:0.0:0.4865	.	248	C9JSV9	.	S	198;248;241	ENSP00000419377:N198S;ENSP00000409514:N248S;ENSP00000383643:N241S	ENSP00000383643:N241S	N	-	2	0	ZNF717	75870721	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.725000	0.04942	-0.541000	0.06257	0.367000	0.22151	AAC	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	9	27.339503	KEEP	0	0	0	91	2735	TT	1	1	0		-	66	60	2446	0	0	213.95395	180	60	6326	949	ENST00000478296.1	0.268293	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788489	75788489	__UNKNOWN__	Silent	SNP	C	C	T	rs111354562		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:75788489C>T	ENST00000478296.1	-	4	411	c.135G>A	c.(133-135)caG>caA	p.Q45Q	ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000400845.3_Silent_p.Q88Q|ZNF717_ENST00000422325.1_Silent_p.Q95Q|ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	88	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CATCAATGATCTGGACAGCTG	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						1	1	1	NA		NA	NA	3		NA											NA				75788489		349	773	1122	SO:0001819	synonymous_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.135G>A	chr3.hg19:g.75788489C>T		NA		hg19		0.02	9.289192	GATxTGG	COVERED																																																																																			NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	8	3.279704	KEEP	0	2	57	31	1133	CC	0.999998	0.999998	0		-	15	60	535	0	0	39.047788	145	60	5517	324	ENST00000478296.1	0.09375	1
IMPG2	50939	__UNKNOWN__	__UNKNOWN__	3	100963325	100963325	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:100963325C>T	ENST00000193391.7	-	13	2037	c.1850G>A	c.(1849-1851)aGt>aAt	p.S617N		NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	617		NA			visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	TGAAGTCTCACTCCATGGCCA	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						139	129	132	NA		NA	NA	3		NA											NA				100963325		2203	4300	6503	SO:0001583	missense			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148	50939			18362	protein-coding gene	gene with protein product		607056			NA	10542133	Standard		NM_016247	NA	Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.1850G>A	chr3.hg19:g.100963325C>T	ENSP00000193391:p.Ser617Asn	NA	A8MWT5|Q9UKD4|Q9UKK5	hg19	CCDS2940.1	0.02	24.560222	TCAxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.01	2.406348	0.42715	.	.	ENSG00000081148	ENST00000193391	T	0.24723	1.84	5.88	3.13	0.36017	.	0.567532	0.20198	N	0.097147	T	0.17066	0.0410	L	0.32530	0.975	0.21105	N	0.999783	B;B	0.15473	0.013;0.013	B;B	0.10450	0.005;0.005	T	0.20571	-1.0271	10	0.54805	T	0.06	-2.7547	4.7047	0.12844	0.0:0.5556:0.1568:0.2876	.	617;617	F1T0J3;Q9BZV3	.;IMPG2_HUMAN	N	617	ENSP00000193391:S617N	ENSP00000193391:S617N	S	-	2	0	IMPG2	102446015	0.015000	0.18098	0.971000	0.41717	0.969000	0.65631	-0.077000	0.11394	0.396000	0.25283	0.655000	0.94253	AGT	NOVEL	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353256.3	4	16.553991	KEEP	0	0	0	55	1990	CC	1	1	0		-	30	60	1096	0	0	72.612999	552	60	20918	779	ENST00000193391.7	0.051546	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	107046624	107046624	__UNKNOWN__	IGR	SNP	T	T	A	rs539907774	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:107046624T>A			NA	NA				RP11-446H18.5 (5033 upstream) : RP11-446H18.6 (1652 downstream)						NA		NA									NA						AAAATATACATTTTTTTAAGG	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.107046624T>A		NA		hg19		0.02	12.380381	ACAxTTT	COVERED																																																																																			NOVEL					0			2	13.540608	KEEP	0	0	0	45	1416	TT	1	1	0			57	60	2109	0	0	176.653503	223	60	8300	417		0.203571	1
GAP43	2596	__UNKNOWN__	__UNKNOWN__	3	115342277	115342277	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:115342277C>T	ENST00000305124.6	+	0	107					NM_002045.3	NP_002036.1	P17677	NEUM_HUMAN	growth associated protein 43	NA		NA			axon choice point recognition (GO:0016198)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of filopodium assembly (GO:0051489)|regulation of growth (GO:0040008)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	32				GBM - Glioblastoma multiforme(114;0.164)		ggagagagagcaccagagaga	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS33830.1, CCDS46890.1	3q13.31	2013-09-19			ENSG00000172020	ENSG00000172020	2596			4140	protein-coding gene	gene with protein product	neuron growth-associated protein 43, neuromodulin, nerve growth-related peptide GAP43, axonal membrane protein GAP-43, protein F1, calmodulin-binding protein P-57, neural phosphoprotein B-50	162060			NA	3272162, 8231732	Standard	NM_002045	NM_002045	NA	Approved	B-50, PP46	uc003ebr.2	P17677	OTTHUMG00000133758	ENST00000305124.6:c.-260C>T	chr3.hg19:g.115342277C>T		NA	A8K0Y4	hg19	CCDS33830.1	0.02	1.991424	GAGxACC	COVERED																																																																																			NOVEL	GAP43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258216.2	3	3.605539	KEEP	0	0	0	12	385	CC	0.993634	0.989348	0		+	12	60	401	0	0	32.065752	56	60	2077	98	ENST00000305124.6	0.176471	0.995687
GAP43	2596	__UNKNOWN__	__UNKNOWN__	3	115380557	115380557	__UNKNOWN__	Intron	SNP	G	G	A	rs34445778	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:115380557G>A	ENST00000393780.3	+	2	210				GAP43_ENST00000305124.6_Intron	NM_001130064.1	NP_001123536.1	P17677	NEUM_HUMAN	growth associated protein 43	NA		NA			axon choice point recognition (GO:0016198)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of filopodium assembly (GO:0051489)|regulation of growth (GO:0040008)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	32				GBM - Glioblastoma multiforme(114;0.164)		ggatggtctcgatctcctgac	0.537	NA	NA											G|||	692	0.138179	0.0333	0.2378	5008	,	,	NA	13281	0.1706	NA	0.1899	False	NA	,,,	NA	NA	NA	2504	0.1227	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33830.1, CCDS46890.1	3q13.31	2013-09-19			ENSG00000172020	ENSG00000172020	2596			4140	protein-coding gene	gene with protein product	neuron growth-associated protein 43, neuromodulin, nerve growth-related peptide GAP43, axonal membrane protein GAP-43, protein F1, calmodulin-binding protein P-57, neural phosphoprotein B-50	162060			NA	3272162, 8231732	Standard	NM_002045	NM_002045	NA	Approved	B-50, PP46	uc003ebr.2	P17677	OTTHUMG00000133758	ENST00000393780.3:c.-258-1811G>A	chr3.hg19:g.115380557G>A		NA	A8K0Y4	hg19	CCDS46890.1	0.02	-0.02632	CTCxATC	UNCOVERED																																																																																			NOVEL	GAP43-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258217.2	2	2.387234	KEEP	2	0	0	8	238	GG	0	0	0		+	2	42	75	0	0	7.624924	1	40	34	14	ENST00000393780.3	0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	119396349	119396349	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:119396349T>C			NA	NA				COX17 (99 upstream) : MAATS1 (25519 downstream)						NA		NA									NA						AACGAGAGGGTGCCCCCTTCA	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.119396349T>C		NA		hg19		0.02	2.128394	GGGxGCC	COVERED																																																																																			NOVEL					0			2	10.810353	KEEP	0	0	0	36	1028	TT	0.999999	0.999947	0			23	60	765	0	0	64.296166	75	60	2677	158		0.234694	0.999948
KALRN	8997	__UNKNOWN__	__UNKNOWN__	3	124438600	124438600	__UNKNOWN__	3'UTR	SNP	C	C	T	rs190672607	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:124438600C>T	ENST00000291478.5	+	0	4316				KALRN_ENST00000428018.2_3'UTR|KALRN_ENST00000360013.3_3'UTR	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	NA		NA			apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TTAGCTGTTACGAAATTTTAA	0.373	NA	NA											T|||	2	0.000399361	0	0.0014	5008	,	,	NA	19451	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145	8997		Rho guanine nucleotide exchange factors, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	4814	protein-coding gene	gene with protein product	serine/threonine kinase with Dbl and pleckstrin homology domains	604605	huntingtin-associated protein interacting protein (duo)	HAPIP	NA	9285789, 10023074	Standard	NM_003947	NM_001024660	NA	Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.*283C>T	chr3.hg19:g.124438600C>T		NA	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	hg19	CCDS3028.1	0.02	6.408814	TTAxGAA	COVERED																																																																																			NOVEL	KALRN-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246891.5	2	7.220207	KEEP	0	0	0	24	815	CC	0.999909	0.999909	0		+	9	60	336	0	0	21.9592	191	60	6884	270	ENST00000291478.5	0.045	1
SNX4	8723	__UNKNOWN__	__UNKNOWN__	3	125238797	125238797	__UNKNOWN__	Intron	SNP	A	A	G	rs545176634|rs149129314	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:125238797A>G	ENST00000251775.4	-	1	166				SNX4_ENST00000536067.1_Intron|SNX4_ENST00000473417.1_Intron	NM_003794.2	NP_003785.1	O95219	SNX4_HUMAN	sorting nexin 4	NA		NA			endocytic recycling (GO:0032456)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|early endosome membrane (GO:0031901)|membrane (GO:0016020)|protein complex (GO:0043234)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(2)|central_nervous_system(1)|lung(6)|ovary(1)|skin(1)	11						ggcccggcccagcccagccca	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF065485	CCDS3032.1	3q21.2	2014-02-12			ENSG00000114520	ENSG00000114520	8723		Sorting nexins	11175	protein-coding gene	gene with protein product		605931			NA	9819414	Standard	NM_003794	NM_003794	NA	Approved	ATG24B	uc003eib.4	O95219	OTTHUMG00000159575	ENST00000251775.4:c.141+78T>C	chr3.hg19:g.125238797A>G		NA	B3KMH0|B4DQV4|D3DNA3	hg19	CCDS3032.1	0.02	1.930728	CCCxGCC	COVERED																																																																																			NOVEL	SNX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356299.1	2	4.899494	KEEP	0	3	84	46	1294	AA	1	0.998465	0		-	4	60	131	0	0	8.308905	68	60	2256	151	ENST00000251775.4	0.055556	0.998465
SLC41A3	54946	__UNKNOWN__	__UNKNOWN__	3	125775536	125775536	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:125775536C>A	ENST00000360370.4	-	3	317				SLC41A3_ENST00000514023.1_Intron|SLC41A3_ENST00000508835.1_Intron|SLC41A3_ENST00000346785.5_Intron|SLC41A3_ENST00000383598.2_5'UTR|SLC41A3_ENST00000315891.6_Intron			Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		GTGCCCTGTGCCTGCAGAGAG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544	54946		Solute carriers	31046	protein-coding gene	gene with protein product		610803			NA		Standard	NM_017836	NM_001164475	NA	Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000360370.4:c.274-5643G>T	chr3.hg19:g.125775536C>A		NA	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	hg19	CCDS43144.1	0.02	2.042447	GTGxCTG	COVERED																																																																																			NOVEL	SLC41A3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370519.1	1	9.26196	KEEP	0	0	0	31	1027	CC	0.999997	0.999619	0		-	15	60	500	0	0	39.99329	70	60	2601	143	ENST00000360370.4	0.176471	0.999622
ACAD9	28976	__UNKNOWN__	__UNKNOWN__	3	128616492	128616492	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:128616492C>T	ENST00000308982.7	+	6	653	c.572C>T	c.(571-573)tCa>tTa	p.S191L		NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	191		NA				dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						GATGCAGCCTCAATCCGGAGC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						139	100	113	NA		NA	NA	3		NA											NA				128616492		2203	4300	6503	SO:0001583	missense			AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646	28976		Mitochondrial respiratory chain complex assembly factors	21497	protein-coding gene	gene with protein product		611103	acyl-Coenzyme A dehydrogenase family, member 9		NA	12359260, 21057504, 20816094	Standard	NM_014049	NM_014049	NA	Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.572C>T	chr3.hg19:g.128616492C>T	ENSP00000312618:p.Ser191Leu	NA	D3DNB8|Q8WXX3	hg19	CCDS3053.1	0.02	13.712991	CCTxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067941	0.76301	.	.	ENSG00000177646	ENST00000308982;ENST00000334167	D	0.99121	-5.45	5.67	5.67	0.87782	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, conserved site (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.000000	0.85682	D	0.000000	D	0.99124	0.9698	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.97110	0.989;1.0	D	0.99844	1.1064	10	0.72032	D	0.01	.	17.2634	0.87078	0.0:1.0:0.0:0.0	.	68;191	Q9H9W4;Q9H845	.;ACAD9_HUMAN	L	191;58	ENSP00000312618:S191L	ENSP00000312618:S191L	S	+	2	0	ACAD9	130099182	1.000000	0.71417	0.991000	0.47740	0.291000	0.27294	6.946000	0.75953	2.688000	0.91661	0.555000	0.69702	TCA	NOVEL	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358405.1	2	13.844434	KEEP	0	0	0	46	1621	CC	1	1	0		+	61	60	2206	0	0	180.932014	271	60	10417	460	ENST00000308982.7	0.183735	1
CPNE4	131034	__UNKNOWN__	__UNKNOWN__	3	131869423	131869423	__UNKNOWN__	Intron	SNP	G	G	C	rs370474239|rs3916420|rs546005707|rs375699732	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:131869423G>C	ENST00000512055.1	-	3	299							Q96A23	CPNE4_HUMAN	copine IV	NA		NA				extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						ctgtctgtctgtctctctctc	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353	131034			2317	protein-coding gene	gene with protein product	copine 8	604208			NA	9430674, 12670487	Standard	NM_130808	XM_005247107	NA	Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1828-110258C>G	chr3.hg19:g.131869423G>C		NA	D3DNC5|Q8TEX1	hg19	CCDS3072.1	0.02	-0.070183	TCTxTCT	UNCOVERED																																																																																			NOVEL	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356583.4	14	2.40769	KEEP	9	0	0	8	279	GG	0	0	0		-	2	60	78	0	0	7.924861	1	60	39	26	ENST00000512055.1	0.666667	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	134369922	134369922	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:134369922T>C			NA	NA				KY (58 upstream) : RNU6-1174P (129446 downstream)						NA		NA									NA						AAGAGGGCGCTCCCCCGCCGC	0.716	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.134369922T>C		NA		hg19		0.02	1.866149	CGCxCCC	COVERED																																																																																			NOVEL					0			1	2.620684	KEEP	0	2	39	23	558	TT	0.999931	0.999553	0			15	60	189	0	0	9.620229	70	60	1789	251		0.176471	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	156429646	156429646	__UNKNOWN__	IGR	SNP	G	G	A	rs2129908		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:156429646G>A			NA	NA				TIPARP (5087 upstream) : LINC00886 (35488 downstream)						NA		NA									NA						tccacctcccgggttcgagtg	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.156429646G>A		NA		hg19		0.02	-0.403542	CCCxGGT	COVERED																																																																																			NOVEL					0			3	8.427067	KEEP	0	0	0	28	957	GG	0.999997	0.934489	0			3	21	116	0	0	8.215891	43	60	1561	99		0.065217	0.934492
KPNA4	3840	__UNKNOWN__	__UNKNOWN__	3	160219829	160219829	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:160219829C>T	ENST00000334256.4	-	0	1934					NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			tatatatatacacacacacat	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432	3840		Importins, Armadillo repeat containing	6397	protein-coding gene	gene with protein product		602970			NA	9168958, 9395085	Standard	NM_002268	NM_002268	NA	Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.*63G>A	chr3.hg19:g.160219829C>T		NA	A8K4S6|D3DNM2|O00190	hg19	CCDS3191.1	0.02	5.89854	ATAxACA	COVERED																																																																																			NOVEL	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352960.1	2	8.071308	KEEP	0	2	57	47	1580	CC	1	1	0		-	8	60	286	1	0	18.076502	179	60	6628	301	ENST00000334256.4	0.042781	1
KPNA4	3840	__UNKNOWN__	__UNKNOWN__	3	160219839	160219839	__UNKNOWN__	3'UTR	SNP	T	T	C	rs372756786|rs537249690	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:160219839T>C	ENST00000334256.4	-	0	1924					NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			cacacacacatatatatatat	0.343	NA	NA											T|||	376	0.0750799	0.0711	0.0764	5008	,	,	NA	9305	0.0655	NA	0.0646	False	NA	,,,	NA	NA	NA	2504	0.1002	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432	3840		Importins, Armadillo repeat containing	6397	protein-coding gene	gene with protein product		602970			NA	9168958, 9395085	Standard	NM_002268	NM_002268	NA	Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.*53A>G	chr3.hg19:g.160219839T>C		NA	A8K4S6|D3DNM2|O00190	hg19	CCDS3191.1	0.02	8.839721	ACAxATA	COVERED																																																																																			NOVEL	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352960.1	2	8.590221	KEEP	0	2	73	54	1564	TT	1	1	0		-	12	60	433	2	0	28.958765	202	60	7327	345	ENST00000334256.4	0.056075	1
PIK3CA	5290	__UNKNOWN__	__UNKNOWN__	3	178927345	178927345	__UNKNOWN__	Intron	SNP	T	T	C	rs3729682	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:178927345T>C	ENST00000263967.3	+	7	1302					NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGAAGACTTTTCTTGATGTA	0.328	NA	57	Mis		colorectal, gastric, gliobastoma, breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			T|||	513	0.102436	0.1407	0.1153	5008	,	,	NA	15598	0.1042	NA	0.0557	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	phosphoinositide-3-kinase, catalytic, alpha polypeptide		E, O	0							NA	T		404,3232		29,346,1443	93	89	90	NA		0.6	0	3	dbSNP_107	90	493,7665		22,449,3608	no	intron	PIK3CA	NM_006218.2		51,795,5051	CC,CT,TT	NA	6.0431,11.1111,7.6056			178927345	897,10897	1818	4079	5897	SO:0001627	intron_variant				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	5290	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	phosphoinositide-3-kinase, catalytic, alpha polypeptide		NA	1322797	Standard		NM_006218	NA	Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1146-38T>C	chr3.hg19:g.178927345T>C		NA	Q14CW1|Q99762	hg19	CCDS43171.1	0.02	17.016154	CTTxTCT	COVERED																																																																																			NOVEL	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348409.2	61	8.121213	KEEP	0	0	0	27	791	TT	0.999988	0.999988	0		+	37	60	1332	0	0	99.469122	316	60	11159	439	ENST00000263967.3	0.104816	1
PIK3CA	5290	__UNKNOWN__	__UNKNOWN__	3	178937877	178937877	__UNKNOWN__	Intron	SNP	A	A	G	rs11918324	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:178937877A>G	ENST00000263967.3	+	13	2172					NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTCTTAAGGTACATATTACTT	0.259	NA	57	Mis		colorectal, gastric, gliobastoma, breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			A|||	512	0.102236	0.1407	0.1153	5008	,	,	NA	14302	0.1042	NA	0.0557	False	NA	,,,	NA	NA	NA	2504	0.0869	NA	NA	NA	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	phosphoinositide-3-kinase, catalytic, alpha polypeptide		E, O	0							NA	A		380,3132		21,338,1397	16	16	16	NA		-4.3	0	3	dbSNP_120	16	461,7429		20,421,3504	no	intron	PIK3CA	NM_006218.2		41,759,4901	GG,GA,AA	NA	5.8428,10.82,7.3759			178937877	841,10561	1756	3945	5701	SO:0001627	intron_variant				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	5290	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	phosphoinositide-3-kinase, catalytic, alpha polypeptide		NA	1322797	Standard		NM_006218	NA	Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2015+37A>G	chr3.hg19:g.178937877A>G		NA	Q14CW1|Q99762	hg19	CCDS43171.1	0.02	4.484279	GGTxCAT	UNCOVERED																																																																																			NOVEL	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348409.2	18	5.414436	KEEP	134	0	0	18	518	AA	0	0	0		+	7	40	256	0	0	17.544768	106	49	3631	287	ENST00000263967.3	0.061947	0.999995
PIK3CA	5290	__UNKNOWN__	__UNKNOWN__	3	178938747	178938747	__UNKNOWN__	Intron	SNP	A	A	T	rs6443625	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:178938747A>T	ENST00000263967.3	+	14	2172					NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	atatatatatatttttaattt	0.294	NA	57	Mis		colorectal, gastric, gliobastoma, breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			A|||	1367	0.272963	0.4713	0.2565	5008	,	,	NA	14994	0.1091	NA	0.1958	False	NA	,,,	NA	NA	NA	2504	0.2648	NA	NA	NA	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	phosphoinositide-3-kinase, catalytic, alpha polypeptide		E, O	0							NA	A		1420,2116		322,776,670	12	11	11	NA		-5.8	0	3	dbSNP_116	11	1459,6617		164,1131,2743	no	intron	PIK3CA	NM_006218.2		486,1907,3413	TT,TA,AA	NA	18.0659,40.1584,24.7933			178938747	2879,8733	1768	4038	5806	SO:0001627	intron_variant				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	5290	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	phosphoinositide-3-kinase, catalytic, alpha polypeptide		NA	1322797	Standard		NM_006218	NA	Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.2016-27A>T	chr3.hg19:g.178938747A>T		NA	Q14CW1|Q99762	hg19	CCDS43171.1	0.02	9.33671	TATxTTT	COVERED																																																																																			NOVEL	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348409.2	42	6.618268	KEEP	0	0	0	22	646	AA	0.999879	0.999879	0		+	19	60	614	0	0	43.145388	185	60	6404	271	ENST00000263967.3	0.093137	1
PIK3CA	5290	__UNKNOWN__	__UNKNOWN__	3	178957371	178957371	__UNKNOWN__	3'UTR	SNP	T	T	C	rs397840435	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:178957371T>C	ENST00000263967.3	+	0	8583					NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TTCAGTGTGATTCAGTCCTCA	0.343	NA	57	Mis		colorectal, gastric, gliobastoma, breast					HNSCC(19;0.045)|TSP Lung(28;0.18)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	phosphoinositide-3-kinase, catalytic, alpha polypeptide		E, O	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	5290	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	phosphoinositide-3-kinase, catalytic, alpha polypeptide		NA	1322797	Standard		NM_006218	NA	Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.*5219T>C	chr3.hg19:g.178957371T>C		NA	Q14CW1|Q99762	hg19	CCDS43171.1	0.02	28.110006	TGAxTCA	COVERED																																																																																			NOVEL	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348409.2	8	4.247879	KEEP	16	4	137	62	1909	TT	1	1	0		+	54	50	1993	0	0	144.553663	589	60	21702	846	ENST00000263967.3	0.083981	1
PARL	55486	__UNKNOWN__	__UNKNOWN__	3	183558492	183558492	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:183558492C>T	ENST00000317096.4	-	7	818				PARL_ENST00000311101.5_Intron|PARL_ENST00000435888.1_Intron	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	NA		NA			membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ttttttttttcttttcttttt	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						38	31	33	NA		NA	NA	3		NA											NA				183558492		692	1587	2279	SO:0001627	intron_variant			AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193	55486			18253	protein-coding gene	gene with protein product	rhomboid 7 homolog 1 (Drosophila)	607858		PSARL	NA		Standard	NM_018622	XM_005247587	NA	Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.758-64G>A	chr3.hg19:g.183558492C>T		NA	Q96CQ4|Q9BTJ6|Q9P1E3	hg19	CCDS3248.1	0.02	-0.360751	TTTxTTT	COVERED																																																																																			NOVEL	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346465.1	2	3.608693	KEEP	1	0	0	12	376	CC	0.993072	0.893084	0		-	10	70	155	0	0	10.325868	32	60	923	69	ENST00000317096.4	0.238095	0.899314
TMEM41A	90407	__UNKNOWN__	__UNKNOWN__	3	185208773	185208773	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:185208773C>T	ENST00000421852.1	-	0	1442				TMEM41A_ENST00000475480.1_Intron	NM_080652.3	NP_542383.1	Q96HV5	TM41A_HUMAN	transmembrane protein 41A	NA		NA				integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)|skin(1)	4	all_cancers(143;7.78e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			ACAGCATTTTCtttttttctc	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC019884	CCDS3271.1	3q27.2	2006-04-12			ENSG00000163900	ENSG00000163900	90407			30544	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_080652	NM_080652	NA	Approved	MGC15397	uc003fpj.2	Q96HV5	OTTHUMG00000156660	ENST00000421852.1:c.*552G>A	chr3.hg19:g.185208773C>T		NA	A8K4B3|D3DNU2|Q6ZMJ0	hg19	CCDS3271.1	0.02	4.057248	TTTxTTT	COVERED																																																																																			NOVEL	TMEM41A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345174.1	3	4.507181	KEEP	0	0	0	15	507	CC	0.99649	0.99648	0		-	13	60	201	0	0	10.464493	88	60	2897	151	ENST00000421852.1	0.128713	0.999989
TRA2B	6434	__UNKNOWN__	__UNKNOWN__	3	185649692	185649692	__UNKNOWN__	Intron	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:185649692T>A	ENST00000453386.2	-	2	312				TRA2B_ENST00000382191.4_Intron|TRA2B_ENST00000342294.4_Intron|TRA2B_ENST00000471134.1_Intron	NM_004593.2	NP_004584.1	P62995	TRA2B_HUMAN	transformer 2 beta homolog (Drosophila)	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing, via transesterification reactions (GO:0000375)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(3)|prostate(1)|urinary_tract(1)	18						CAGGATAAAATCCAGTGCCAA	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF057159	CCDS33905.1, CCDS58872.1	3q26.2-q27	2014-06-13	2009-02-27	2009-02-27	ENSG00000136527	ENSG00000136527	6434		RNA binding motif (RRM) containing	10781	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 156	602719	splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)	SFRS10	NA	9790768	Standard	NM_004593	NM_004593	NA	Approved	Htra2-beta, PPP1R156	uc003fpv.3	P62995	OTTHUMG00000156641	ENST00000453386.2:c.37-5170A>T	chr3.hg19:g.185649692T>A		NA	B4DVK2|D3DNU3|O15449|Q15815|Q64283	hg19	CCDS33905.1	0.02	1.313663	AAAxCCA	COVERED																																																																																			NOVEL	TRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344984.1	1	3.898832	KEEP	0	0	0	13	352	TT	0.994391	0.994196	0		-	6	60	144	0	0	7.807458	83	60	2657	112	ENST00000453386.2	0.067416	0.999804
ATP13A3	79572	__UNKNOWN__	__UNKNOWN__	3	194211601	194211601	__UNKNOWN__	Intron	SNP	A	A	G	rs112819430	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:194211601A>G	ENST00000439040.1	-	2	746				LINC00884_ENST00000448892.1_RNA			Q9H7F0	AT133_HUMAN	ATPase type 13A3	NA		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		gaggctgggcatggtggctca	0.522	NA	NA											g|||	339	0.0676917	0.177	0.0187	5008	,	,	NA	19350	0.0486	NA	0.0189	False	NA	,,,	NA	NA	NA	2504	0.0245	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657	79572		ATPases / P-type	24113	protein-coding gene	gene with protein product	ATPase family homolog up regulated in senescence cells	610232			NA	11867234	Standard	NM_024524	NM_024524	NA	Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.45+3177T>C	chr3.hg19:g.194211601A>G		NA	Q8NC11|Q96KS1	hg19	CCDS43187.1	0.02	-0.096503	GGCxTGG	UNCOVERED																																																																																			NOVEL	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342799.2	2	2.407259	KEEP	0	0	0	8	248	AA	0.99257	0.119541	0		-	6	60	208	0	0	20.370559	5	60	188	23	ENST00000439040.1	0.545455	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195366734	195366734	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195366734T>C			NA	NA				APOD (55658 upstream) : RP11-141C7.4 (126 downstream)						NA		NA									NA						ttcgtacttttctctcgctac	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195366734T>C		NA		hg19		0.02	9.656274	TTTxCTC	COVERED																																																																																			NOVEL					0			4	12.624318	KEEP	4	0	0	42	1268	TT	1	1	0			8	40	321	0	0	20.643887	235	60	8610	362		0.032922	1
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195395663	195395663	__UNKNOWN__	lincRNA	SNP	C	C	T	rs13060386		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195395663C>T	ENST00000445430.1	+	0	919									long intergenic non-protein coding RNA 969	NA		NA									NA						aatgtcatttccttaaggaga	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195395663C>T		NA		hg19		0.02	2.069585	TTTxCTT	UNCOVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	1	2.708793	KEEP	27	0	0	9	310	CC	0	0	0		+	11	49	404	0	0	32.592695	57	60	2009	117	ENST00000445430.1	0.161765	0.999407
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195398245	195398245	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195398245G>A	ENST00000445430.1	+	0	1088									long intergenic non-protein coding RNA 969	NA		NA									NA						TTTCAGCACCGCTCGCCCTCA	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195398245G>A		NA		hg19		0.02	13.059619	ACCxCTC	COVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	5	21.035127	KEEP	30	4	107	108	3693	GG	1	1	0		+	14	27	446	0	0	25.099104	380	60	13753	561	ENST00000445430.1	0.035533	1
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195400654	195400654	__UNKNOWN__	lincRNA	SNP	T	T	C	rs9682586	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195400654T>C	ENST00000445430.1	+	0	1284									long intergenic non-protein coding RNA 969	NA		NA									NA						GGAATGGGCATCTTGACATTT	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195400654T>C		NA		hg19		0.02	2.040844	GCAxCTT	UNCOVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	0	3.60973	KEEP	19	0	0	12	356	TT	0	0	0		+	5	40	175	0	0	12.7831	46	50	1653	81	ENST00000445430.1	0.098039	0.963774
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195509318	195509318	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195509318C>T	ENST00000346145.4	-	2	122				MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Missense_Mutation_p.D3045N|MUC4_ENST00000475231.1_Missense_Mutation_p.D3045N	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						13	8	9	NA		NA	NA	3		NA											NA				195509318		626	1528	2154	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-3992G>A	chr3.hg19:g.195509318C>T		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.298188	TGTxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	N	10.26	1.300829	0.23650	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.5;1.5	1.18	-0.252	0.12999	.	.	.	.	.	T	0.11623	0.0283	N	0.19112	0.55	0.09310	N	1	P	0.47841	0.901	B	0.28991	0.097	T	0.19353	-1.0308	8	.	.	.	.	4.04	0.09746	0.0:0.5204:0.0:0.4796	.	2917	E7ESK3	.	N	3045	ENSP00000417498:D3045N;ENSP00000420243:D3045N	.	D	-	1	0	MUC4	196994097	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.209000	0.00273	-0.382000	0.07870	0.000000	0.15137	GAC	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	2	2.707232	KEEP	0	0	0	9	269	CC	0.99254	0.794276	0		-	5	60	187	0	0	15.063869	27	60	870	52	ENST00000346145.4	0.15625	0.800245
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195511897	195511897	__UNKNOWN__	Intron	SNP	G	G	A	rs71187736		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195511897G>A	ENST00000346145.4	-	2	122				MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Missense_Mutation_p.A2185V|MUC4_ENST00000475231.1_Missense_Mutation_p.A2185V	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						8	13	12	NA		NA	NA	3		NA											NA				195511897		616	1525	2141	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-6571C>T	chr3.hg19:g.195511897G>A		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.42111	GATxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	5.008	0.187161	0.09547	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.27104	1.69;1.71	.	.	.	.	.	.	.	.	T	0.07279	0.0184	N	0.02539	-0.55	0.09310	N	1	B	0.17465	0.022	B	0.14578	0.011	T	0.31447	-0.9943	7	.	.	.	.	4.2517	0.10698	0.5493:0.0:0.4507:0.0	.	2185	E7ESK3	.	V	2185	ENSP00000417498:A2185V;ENSP00000420243:A2185V	.	A	-	2	0	MUC4	196996292	0.000000	0.05858	0.003000	0.11579	0.046000	0.14306	0.252000	0.18278	-1.752000	0.01325	-2.092000	0.00371	GCA	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	4	2.708261	KEEP	7	0	0	9	300	GG	0.99254	0.941327	0		-	6	25	219	0	0	17.028158	40	60	1470	80	ENST00000346145.4	0.130435	0.948402
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195511945	195511945	__UNKNOWN__	Intron	SNP	G	G	A	rs201304037	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195511945G>A	ENST00000346145.4	-	2	122				MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Missense_Mutation_p.A2169V|MUC4_ENST00000475231.1_Missense_Mutation_p.A2169V	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A2169V(4)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				4	Substitution - Missense(4)	endometrium(2)|skin(2)					NA						13	15	14	NA		NA	NA	3		NA											NA				195511945		661	1548	2209	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-6619C>T	chr3.hg19:g.195511945G>A		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.377245	GATxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	5.257	0.232852	0.09969	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.57;1.59	.	.	.	.	.	.	.	.	T	0.14570	0.0352	N	0.19112	0.55	0.09310	N	1	B	0.27997	0.197	B	0.23018	0.043	T	0.25537	-1.0129	6	.	.	.	.	.	.	.	.	2169	E7ESK3	.	V	2169	ENSP00000417498:A2169V;ENSP00000420243:A2169V	.	A	-	2	0	MUC4	196996340	0.000000	0.05858	0.001000	0.08648	0.066000	0.16364	-1.488000	0.02308	-0.417000	0.07461	0.064000	0.15345	GCA	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	4	2.407856	KEEP	9	0	0	8	281	GG	0.99257	0.902315	0		-	4	20	142	0	0	10.556303	34	60	1261	72	ENST00000346145.4	0.105263	0.909069
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195513173	195513173	__UNKNOWN__	Intron	SNP	G	G	A	rs77448757	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195513173G>A	ENST00000346145.4	-	2	122				MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Missense_Mutation_p.P1760S|MUC4_ENST00000475231.1_Missense_Mutation_p.P1760S	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGAGGGGTGGCCTGA	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						53	49	50	NA		NA	NA	3		NA											NA				195513173		692	1591	2283	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-7847C>T	chr3.hg19:g.195513173G>A		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.193004	GAGxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	-	3.212	-0.161316	0.06502	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29142	1.58;1.58	.	.	.	.	.	.	.	.	T	0.08935	0.0221	N	0.02539	-0.55	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.27872	-1.0061	7	.	.	.	.	4.5334	0.12017	0.332:0.0:0.668:0.0	.	1760	E7ESK3	.	S	1760	ENSP00000417498:P1760S;ENSP00000420243:P1760S	.	P	-	1	0	MUC4	196997568	0.080000	0.21391	0.007000	0.13788	0.007000	0.05969	2.260000	0.43267	-1.764000	0.01305	-1.783000	0.00646	CCT	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	3	2.963678	KEEP	0	0	0	10	310	GG	0.992708	0.454419	0		-	4	60	140	0	0	11.468205	17	60	617	35	ENST00000346145.4	0.190476	0.457757
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195513180	195513180	__UNKNOWN__	Intron	SNP	C	C	G	rs77724343	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195513180C>G	ENST00000346145.4	-	2	122				MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Missense_Mutation_p.Q1757H|MUC4_ENST00000475231.1_Missense_Mutation_p.Q1757H	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.Q1757H(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCCTGACCTGTGG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	stomach(2)					NA						49	44	45	NA		NA	NA	3		NA											NA				195513180		692	1590	2282	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-7854G>C	chr3.hg19:g.195513180C>G		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.19145	GGCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	-	1.229	-0.624622	0.03636	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38722	1.23;1.12	.	.	.	.	.	.	.	.	T	0.12347	0.0300	N	0.02539	-0.55	0.09310	N	1	B	0.14438	0.01	B	0.01281	0.0	T	0.15838	-1.0423	7	.	.	.	.	2.2036	0.03930	0.0:0.3333:0.3352:0.3315	.	1757	E7ESK3	.	H	1757	ENSP00000417498:Q1757H;ENSP00000420243:Q1757H	.	Q	-	3	2	MUC4	196997575	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-3.644000	0.00405	-1.916000	0.01075	-1.964000	0.00472	CAG	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	3	3.00981	KEEP	0	0	0	10	348	CC	0.992708	0.454419	0		-	4	60	140	0	0	11.479711	17	60	587	36	ENST00000346145.4	0.190476	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195723581	195723581	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:195723581C>T			NA	NA				SDHAP1 (6431 upstream) : TFRC (52573 downstream)						NA		NA									NA						CGGAGGGAGGCGGAGGCTGTG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195723581C>T		NA		hg19		0.02	2.049635	AGGxGGA	COVERED																																																																																			NOVEL					0			1	6.319993	KEEP	8	0	0	21	712	CC	0.999859	0.990825	0			5	25	147	0	0	9.692901	57	60	1806	108		0.080645	0.990964
SENP5	205564	__UNKNOWN__	__UNKNOWN__	3	196625691	196625691	__UNKNOWN__	Intron	SNP	A	A	T	rs12487121		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:196625691A>T	ENST00000323460.5	+	3	1762				SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		agaccattcgatgattgcatt	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(47;891 1095 11174 13858 51271)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231	205564			28407	protein-coding gene	gene with protein product		612845	SUMO1/sentrin specific protease 5		NA	12477932	Standard	NM_152699	NM_152699	NA	Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1514-846A>T	chr3.hg19:g.196625691A>T		NA	B4DY82|Q96SA5	hg19	CCDS3322.1	0.02	9.762185	TCGxTGA	COVERED																																																																																			NOVEL	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340524.1	96	32.40867	KEEP	89	6	201	178	5760	AA	1	1	0		+	11	49	420	0	0	31.119788	113	60	4286	819	ENST00000323460.5	0.08871	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	197376962	197376962	__UNKNOWN__	IGR	SNP	A	A	G	rs1058628	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:197376962A>G			NA	NA				RP11-496H1.2 (4074 upstream) : AC024560.2 (10473 downstream)						NA		NA									NA						AGGAAAGTACAAAAACATGAG	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.197376962A>G		NA		hg19		0.02	4.899025	TACxAAA	COVERED																																																																																			NOVEL					0			3	4.212314	KEEP	6	0	0	14	428	AA	0.995343	0.995343	0			22	60	830	0	0	68.157288	104	60	3855	192		0.174603	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	197376981	197376981	__UNKNOWN__	IGR	SNP	A	A	G	rs1058626		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:197376981A>G			NA	NA				RP11-496H1.2 (4093 upstream) : AC024560.2 (10454 downstream)						NA		NA									NA						AGCCCCCACGATGAGGAAAAA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.197376981A>G		NA		hg19		0.02	4.595937	ACGxTGA	COVERED																																																																																			NOVEL					0			2	4.212193	KEEP	6	0	0	14	431	AA	0.995343	0.995342	0			14	40	531	0	0	41.227532	102	60	3809	180		0.12069	0.999999
LMLN	89782	__UNKNOWN__	__UNKNOWN__	3	197768920	197768920	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr3:197768920G>T	ENST00000330198.4	+	0	5372					NM_033029.3	NP_149018.2	Q96KR4	LMLN_HUMAN	leishmanolysin-like (metallopeptidase M8 family)	NA		NA			cell adhesion (GO:0007155)|mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;9.84e-24)|all cancers(36;3.18e-22)|OV - Ovarian serous cystadenocarcinoma(49;5.35e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.111)		CTGGACAAATGTGAAACTGGA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ312398	CCDS3332.1, CCDS46988.1	3q29	2008-02-04			ENSG00000185621	ENSG00000185621	89782	3.4.24.36		15991	protein-coding gene	gene with protein product		609380			NA		Standard	NM_033029	NM_033029	NA	Approved	Gp63, Msp	uc010iar.3	Q96KR4	OTTHUMG00000155375	ENST00000330198.4:c.*3382G>T	chr3.hg19:g.197768920G>T		NA	B3LDG9|B3LDH0|C9J796|F8WB28|Q96KR5	hg19	CCDS3332.1	0.02	4.546646	AATxTGA	COVERED																																																																																			NOVEL	LMLN-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339701.1	1	5.116442	KEEP	0	0	0	17	591	GG	0.999366	0.999366	0		+	33	60	1199	0	0	102.443346	107	60	4083	190	ENST00000330198.4	0.235714	1
GAK	2580	__UNKNOWN__	__UNKNOWN__	4	843633	843633	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:843633G>C	ENST00000314167.4	-	27	3945				GAK_ENST00000511163.1_Intron|GAK_ENST00000509566.1_Intron	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	NA		NA			cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		ccccccccccgccccgccccT	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						5	6	6	NA		NA	NA	4		NA											NA				843633		1951	3948	5899	SO:0001627	intron_variant			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950	2580		Heat shock proteins / DNAJ (HSP40)	4113	protein-coding gene	gene with protein product	auxilin-2	602052			NA	9299234	Standard	NM_005255	NM_005255	NA	Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3834+46C>G	chr4.hg19:g.843633G>C		NA	Q5U4P5|Q9BVY6	hg19	CCDS3340.1	0.02	2.432584	CCCxCCC	COVERED																																																																																			NOVEL	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239188.1	2	16.617211	KEEP	0	6	101	92	2941	GG	1	0.998465	0		-	4	60	139	1	0	9.199209	65	60	2162	239	ENST00000314167.4	0.057971	0.998465
CTBP1	1487	__UNKNOWN__	__UNKNOWN__	4	1230670	1230670	__UNKNOWN__	Intron	SNP	G	G	A	rs13108428		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:1230670G>A	ENST00000382952.3	-	3	547				CTBP1_ENST00000510568.1_3'UTR|CTBP1_ENST00000290921.6_Intron|CTBP1_ENST00000515690.1_Intron	NM_001012614.1	NP_001012632.1	Q13363	CTBP1_HUMAN	C-terminal binding protein 1	NA		NA			Golgi organization (GO:0007030)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone deacetylation (GO:0031065)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of transcription by chromatin organization (GO:0034401)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		AGGGCAAACCGAATGTCCACC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U37408	CCDS3348.1, CCDS43203.1	4p16	2008-02-05			ENSG00000159692	ENSG00000159692	1487			2494	protein-coding gene	gene with protein product	brefeldin A-ribosylated substrate	602618			NA	9479502	Standard	NM_001328	XM_005272261	NA	Approved	BARS	uc003gcv.1	Q13363	OTTHUMG00000089259	ENST00000382952.3:c.162+1300C>T	chr4.hg19:g.1230670G>A		NA	Q4W5N3|Q7Z2Q5	hg19	CCDS43203.1	0.02	4.172241	ACCxAAT	COVERED																																																																																			NOVEL	CTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359459.1	2	16.207123	KEEP	2	0	0	54	1717	GG	1	1	0		-	18	60	620	0	0	48.940589	97	60	3185	232	ENST00000382952.3	0.156522	1
MSANTD1	345222	__UNKNOWN__	__UNKNOWN__	4	3250227	3250227	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:3250227G>A	ENST00000507492.1	+	4	859				MSANTD1_ENST00000438480.2_De_novo_Start_OutOfFrame			Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	NA		NA								endometrium(1)|lung(2)	3						CTCACCGGCCGGTGCCAGAGG	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981	345222			33741	protein-coding gene	gene with protein product		NA	chromosome 4 open reading frame 44	C4orf44	NA		Standard	NM_001012982	NM_001042690	NA	Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000507492.1:c.17-778G>A	chr4.hg19:g.3250227G>A		NA	C9J6V0	hg19		0.02	9.954675	GCCxGTG	COVERED																																																																																			NOVEL	MSANTD1-001	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000358238.2	2	28.998509	KEEP	0	1	33	108	3589	GG	1	1	0		+	9	60	359	0	0	24.005637	204	60	7192	396	ENST00000507492.1	0.042254	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	3575939	3575939	__UNKNOWN__	IGR	SNP	A	A	G	rs77709452	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:3575939A>G			NA	NA				RP11-529E10.7 (25624 upstream) : LINC00955 (2656 downstream)						NA		NA									NA						tgaaccaaggaggcagaggtt	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.3575939A>G		NA		hg19		0.02	-0.061412	AGGxGGC	UNCOVERED																																																																																			NOVEL					0			0	2.700985	KEEP	0	0	0	9	271	AA	0.99254	0.04346	0			2	39	78	0	0	7.095687	4	60	155	24		0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	3575986	3575986	__UNKNOWN__	IGR	SNP	T	T	G	rs73199326	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:3575986T>G			NA	NA				RP11-529E10.7 (25671 upstream) : LINC00955 (2609 downstream)						NA		NA									NA						actccagccttggtgacagag	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.3575986T>G		NA		hg19		0.02	-0.052641	CCTxGGT	UNCOVERED																																																																																			NOVEL					0			0	2.707775	KEEP	0	0	0	9	271	TT	0.99254	0.036491	0			2	39	84	0	0	7.695666	4	60	151	21		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	24612688	24612688	__UNKNOWN__	IGR	SNP	A	A	G	rs4697462		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:24612688A>G			NA	NA				DHX15 (26515 upstream) : RP11-496D24.2 (48790 downstream)						NA		NA									NA						aagaggaagaagaagaagaag	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.24612688A>G		NA		hg19		0.02	-0.096507	AGAxGAA	UNCOVERED																																																																																			NOVEL					0			16	2.407372	KEEP	2	0	0	8	255	AA	0.99257	0.119541	0			3	60	109	0	0	12.33101	0	0	0	20		1	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	33103784	33103784	__UNKNOWN__	IGR	SNP	C	C	T	rs375996861|rs111775503	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:33103784C>T			NA	NA				RP11-240A16.1 (748942 upstream) : RP11-802H3.2 (331347 downstream)						NA		NA									NA						tccttccttccttctttcttt	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.33103784C>T		NA		hg19		0.02	-0.052641	TTCxTTC	UNCOVERED																																																																																			NOVEL					0			2	3.009903	KEEP	0	0	0	10	366	CC	0.992708	0.036498	0			2	60	77	0	2	6.995642	4	60	151	25		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	42399786	42399786	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:42399786G>A			NA	NA				RP11-63A11.1 (6501 upstream) : SHISA3 (69 downstream)						NA		NA									NA						TGAGCCGGGCGAAGGGCGGCA	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.42399786G>A		NA		hg19		0.02	-0.236838	GGCxAAG	COVERED																																																																																			NOVEL					0			2	5.415604	KEEP	0	0	0	18	551	GG	0.999859	0.612321	0			9	60	329	0	0	29.911345	17	60	535	48		0.346154	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49099316	49099316	__UNKNOWN__	IGR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49099316T>G			NA	NA				CWH43 (35220 upstream) : AC118282.3 (99903 downstream)						NA		NA									NA						tccattccattccattccatt	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49099316T>G		NA		hg19		0.02	-0.412324	CATxCCA	COVERED																																																																																			NOVEL					0			21	4.081023	KEEP	31	2	76	40	1234	TT	0.999999	0.948401	0			2	46	75	0	0	6.635801	5	25	167	163		0.285714	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49100275	49100275	__UNKNOWN__	IGR	SNP	C	C	G	rs78593584|rs373492417		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49100275C>G			NA	NA				CWH43 (36179 upstream) : AC118282.3 (98944 downstream)						NA		NA									NA						ccattccactcctttccattc	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49100275C>G		NA		hg19		0.02	-0.043867	ACTxCTT	UNCOVERED																																																																																			NOVEL					0			3	3.009672	KEEP	7	0	0	10	342	CC	0.99257	0.023895	0			2	33	76	0	0	7.724894	1	10	36	29		0.666667	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49111553	49111553	__UNKNOWN__	IGR	SNP	C	C	T	rs56651379		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49111553C>T			NA	NA				CWH43 (47457 upstream) : AC118282.3 (87666 downstream)						NA		NA									NA						gattccattccattccattcc	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49111553C>T		NA		hg19		0.02	1.994705	TTCxATT	COVERED																																																																																			NOVEL					0			34	2.406703	KEEP	45	3	88	39	1339	CC	0.999957	0.999175	0			6	48	218	0	0	19.516874	13	43	459	199		0.315789	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49122177	49122177	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49122177C>G			NA	NA				CWH43 (58081 upstream) : AC118282.3 (77042 downstream)						NA		NA									NA						ccattccattccactccattc	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49122177C>G		NA		hg19		0.02	-0.1316	ATTxCAC	UNCOVERED																																																																																			NOVEL					0			5	3.00978	KEEP	6	0	0	10	348	CC	0	0	0			2	46	69	1	0	6.392647	3	47	118	36		0.4	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49122206	49122206	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49122206T>C			NA	NA				CWH43 (58110 upstream) : AC118282.3 (77013 downstream)						NA		NA									NA						tacattccactcgggttgaat	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49122206T>C		NA		hg19		0.02	-0.140369	CACxCGG	COVERED																																																																																			NOVEL					0			8	4.211548	KEEP	7	0	0	14	422	TT	0.992708	0.259062	0			2	46	76	0	0	6.483928	7	47	255	43		0.222222	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49142586	49142586	__UNKNOWN__	IGR	SNP	G	G	C	rs201060859		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49142586G>C			NA	NA				CWH43 (78490 upstream) : AC118282.3 (56633 downstream)						NA		NA									NA						gttccgttccgttccattcca	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49142586G>C		NA		hg19		0.02	2.196513	TCCxTTC	COVERED																																																																																			NOVEL					0			72	6.957184	KEEP	38	1	31	34	1179	AG	0.999957	0.990921	0			3	40	112	0	0	9.1095	15	43	533	153		0.166667	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49240002	49240002	__UNKNOWN__	IGR	SNP	T	T	A	rs201851340		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49240002T>A			NA	NA				AC118282.4 (28537 upstream) : AC119751.5 (345039 downstream)						NA		NA									NA						TCTTTAAGACTTTATGGTTAA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49240002T>A		NA		hg19		0.02	2.287507	GACxTTA	UNCOVERED																																																																																			NOVEL					0			0	2.407234	KEEP	8	0	0	8	247	TT	0	0	0			5	27	189	0	0	14.418513	41	60	1550	89		0.108696	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49263448	49263448	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49263448G>A			NA	NA				AC118282.4 (51983 upstream) : AC119751.5 (321593 downstream)						NA		NA									NA						agcttagccgggcatggtgac	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49263448G>A		NA		hg19		0.02	-0.254359	CCGxGCA	COVERED																																																																																			NOVEL					0			2	4.514392	KEEP	2	0	0	15	518	GG	0.994391	0.664773	0			3	27	107	0	0	8.148587	22	50	768	52		0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49268900	49268900	__UNKNOWN__	IGR	SNP	C	C	T	rs4358367		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49268900C>T			NA	NA				AC118282.4 (57435 upstream) : AC119751.5 (316141 downstream)						NA		NA									NA						gactgggtttcgctatgttgg	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49268900C>T		NA		hg19		0.02	-0.035093	TTTxGCT	UNCOVERED																																																																																			NOVEL					0			3	2.407823	KEEP	1	0	0	8	278	CC	0	0	0			2	27	70	0	0	7.124756	1	27	38	12		0.666667	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49268904	49268904	__UNKNOWN__	IGR	SNP	A	A	T	rs4342169		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49268904A>T			NA	NA				AC118282.4 (57439 upstream) : AC119751.5 (316137 downstream)						NA		NA									NA						gggtttcgctatgttggccag	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49268904A>T		NA		hg19		0.02	-0.043865	GCTxTGT	UNCOVERED																																																																																			NOVEL					0			3	2.407163	KEEP	1	0	0	8	245	AA	0	0	0			2	27	70	0	0	7.124783	1	27	36	14		0.666667	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49273044	49273044	__UNKNOWN__	IGR	SNP	C	C	T	rs4555605	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49273044C>T			NA	NA				AC118282.4 (61579 upstream) : AC119751.5 (311997 downstream)						NA		NA									NA						GGCTGAGGGCCGGTTCCCGCC	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49273044C>T		NA		hg19		0.02	-0.349553	GGCxGGT	COVERED																																																																																			NOVEL					0			1	6.319321	KEEP	7	0	0	21	689	CC	0.99986	0.88875	0			4	40	152	0	0	11.715818	31	60	1066	93		0.114286	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49273093	49273093	__UNKNOWN__	IGR	SNP	C	C	T	rs6823104	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49273093C>T			NA	NA				AC118282.4 (61628 upstream) : AC119751.5 (311948 downstream)						NA		NA									NA						CTGGCTTGGCCACAGCCACAG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49273093C>T		NA		hg19		0.02	-0.385961	GGCxACA	COVERED																																																																																			NOVEL					0			1	6.319832	KEEP	9	0	0	21	714	CC	0.99986	0.918042	0			6	60	215	0	0	16.951605	35	60	1280	93		0.146341	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49273173	49273173	__UNKNOWN__	IGR	SNP	C	C	A	rs58655579		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49273173C>A			NA	NA				AC118282.4 (61708 upstream) : AC119751.5 (311868 downstream)						NA		NA									NA						AGGCTGCTGCCTGCACGCAGA	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49273173C>A		NA		hg19		0.02	-0.307067	TGCxTGC	COVERED																																																																																			NOVEL					0			0	3.91264	KEEP	3	0	0	13	458	CC	0.993634	0.795151	0			3	49	112	0	0	8.39648	27	60	1035	68		0.1	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49273559	49273559	__UNKNOWN__	IGR	SNP	G	G	A	rs6822670		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49273559G>A			NA	NA				AC118282.4 (62094 upstream) : AC119751.5 (311482 downstream)						NA		NA									NA						CATGGTTTGGGTGGCCTCTGG	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49273559G>A		NA		hg19		0.02	-0.087734	TGGxTGG	UNCOVERED																																																																																			NOVEL					0			0	3.247966	KEEP	8	0	0	11	340	GG	0	0	0			2	49	76	0	0	6.483885	7	47	263	36		0.222222	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49294431	49294431	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49294431G>A			NA	NA				AC118282.4 (82966 upstream) : AC119751.5 (290610 downstream)						NA		NA									NA						caatgtgggcgtggttggaga	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49294431G>A		NA		hg19		0.02	-0.192946	GGCxTGG	UNCOVERED																																																																																			NOVEL					0			3	4.514602	KEEP	24	0	0	15	519	GG	0	0	0			3	22	101	0	0	8.272955	12	25	405	63		0.2	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49315688	49315688	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49315688C>A			NA	NA				AC118282.4 (104223 upstream) : AC119751.5 (269353 downstream)						NA		NA									NA						gcatgctgggcttaataccta	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49315688C>A		NA		hg19		0.02	-0.271972	GGGxTTA	COVERED																																																																																			NOVEL					0			4	3.040341	KEEP	14	1	34	22	757	CC	0.994391	0.713292	0			3	21	104	0	0	7.596981	27	52	1003	66		0.1	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49324292	49324292	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49324292G>C			NA	NA				AC118282.4 (112827 upstream) : AC119751.5 (260749 downstream)						NA		NA									NA						CCAAGGGGCAGCTCCTCACCA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49324292G>C		NA		hg19		0.02	-0.385989	GCAxCTC	UNCOVERED																																																																																			NOVEL					0			1	3.913009	KEEP	36	0	0	13	490	GG	0	0	0			3	22	117	0	0	8.471476	38	40	1392	107		0.073171	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49512298	49512298	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49512298C>T			NA	NA				AC118282.4 (300833 upstream) : AC119751.5 (72743 downstream)						NA		NA									NA						gtagcaactacctagtgcgat	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49512298C>T		NA		hg19		0.02	2.352284	CTAxCTA	COVERED																																																																																			NOVEL					0			5	5.1163	KEEP	2	0	0	17	592	CC	0.999366	0.988916	0			5	60	191	1	0	14.569115	42	60	1579	108		0.106383	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49512590	49512590	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49512590A>G			NA	NA				AC118282.4 (301125 upstream) : AC119751.5 (72451 downstream)						NA		NA									NA						ccttcctCCTATTTCTCTCTT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49512590A>G		NA		hg19		0.02	2.294317	CCTxTTT	COVERED																																																																																			NOVEL					0			27	5.583548	KEEP	13	2	70	43	1259	AA	1	0.99911	0			6	60	232	0	0	17.83279	49	60	1793	181		0.109091	0.99911
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49515855	49515855	__UNKNOWN__	IGR	SNP	T	T	A	rs374280136	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49515855T>A			NA	NA				AC118282.4 (304390 upstream) : AC119751.5 (69186 downstream)						NA		NA									NA						CTCGGGAGAATATGAGCGGTC	0.622	NA	NA											N|||	114	0.0227636	0.0628	0.0072	5008	,	,	NA	335117	0.003	NA	0.0119	False	NA	,,,	NA	NA	NA	2504	0.0112	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49515855T>A		NA		hg19		0.02	4.881561	GAAxATG	COVERED																																																																																			NOVEL					0			2	6.618958	KEEP	21	0	0	22	662	TT	0.999863	0.999836	0			7	44	272	0	0	19.795294	85	46	2988	183		0.076087	0.999973
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49515856	49515856	__UNKNOWN__	IGR	SNP	A	A	G	rs368039405	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49515856A>G			NA	NA				AC118282.4 (304391 upstream) : AC119751.5 (69185 downstream)						NA		NA									NA						TCGGGAGAATATGAGCGGTCC	0.622	NA	NA											N|||	114	0.0227636	0.0628	0.0072	5008	,	,	NA	327454	0.003	NA	0.0119	False	NA	,,,	NA	NA	NA	2504	0.0112	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49515856A>G		NA		hg19		0.02	2.210181	AATxTGA	COVERED																																																																																			NOVEL					0			2	6.618287	KEEP	23	0	0	22	647	AA	0.999863	0.999825	0			7	44	286	0	0	21.259317	83	46	2956	182		0.077778	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49531959	49531959	__UNKNOWN__	IGR	SNP	G	G	A	rs61796716	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49531959G>A			NA	NA				AC118282.4 (320494 upstream) : AC119751.5 (53082 downstream)						NA		NA									NA						caaatttctgggctcacatga	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49531959G>A		NA		hg19		0.02	-0.324546	CTGxGCT	COVERED																																																																																			NOVEL					0			6	6.01901	KEEP	9	0	0	20	689	GG	0.999366	0.835186	0			9	60	326	0	0	28.361776	25	60	896	86		0.264706	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49558510	49558510	__UNKNOWN__	IGR	SNP	C	C	G	rs113194539		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:49558510C>G			NA	NA				AC118282.4 (347045 upstream) : AC119751.5 (26531 downstream)						NA		NA									NA						CACACTGAAACGATTCTCAGA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49558510C>G		NA		hg19		0.02	-0.315796	AAAxGAT	UNCOVERED																																																																																			NOVEL					0			2	2.70858	KEEP	12	0	0	9	307	CC	0	0	0			3	27	115	0	0	8.447596	33	48	1151	70		0.083333	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	68416409	68416409	__UNKNOWN__	IGR	SNP	G	G	A	rs199660231|rs368878906		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:68416409G>A			NA	NA				CENPC (5085 upstream) : STAP1 (8036 downstream)						NA		NA									NA						aaaaaaaaaagaaagctatca	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.68416409G>A		NA		hg19		0.02	-0.422534	AAAxAAA	COVERED																																																																																			NOVEL					0			0	2.833781	KEEP	0	1	12	14	388	GG	0.99649	0.951141	0			8	60	132	0	0	7.670334	41	60	1046	95		0.163265	0.954491
YTHDC1	91746	__UNKNOWN__	__UNKNOWN__	4	69215348	69215348	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:69215348A>C	ENST00000344157.4	-	1	364				YTHDC1_ENST00000355665.3_Intron|YTHDC1_ENST00000579690.1_Intron	NM_001031732.2	NP_001026902.1	Q96MU7	YTDC1_HUMAN	YTH domain containing 1	NA		NA			mRNA splice site selection (GO:0006376)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	30						TAACCTCCCCAACCCCCACCC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098515	CCDS3522.2, CCDS33992.1	4q13.3	2009-01-14			ENSG00000083896	ENSG00000083896	91746			30626	protein-coding gene	gene with protein product		NA			NA	12368078, 10564280	Standard	NM_133370	XM_005265706	NA	Approved	YT521, KIAA1966, YT521-B	uc003hdx.3	Q96MU7	OTTHUMG00000129306	ENST00000344157.4:c.28+95T>G	chr4.hg19:g.69215348A>C		NA	Q4W5Q3|Q7Z622|Q8TF35	hg19	CCDS33992.1	0.02	1.62524	CCCxACC	COVERED																																																																																			NOVEL	YTHDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251437.1	1	17.250464	KEEP	0	10	126	104	2699	AA	1	0.999768	0		-	8	60	175	0	0	10.405398	70	60	1996	280	ENST00000344157.4	0.102564	0.999768
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	70047633	70047633	__UNKNOWN__	IGR	SNP	A	A	G	rs113854028	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:70047633A>G			NA	NA				UGT2B7 (68928 upstream) : RP11-704M14.1 (184 downstream)						NA		NA									NA						TAAAACAGAAAAAAATGAAAT	0.358	NA	NA											G|||	1726	0.344649	0.3343	0.281	5008	,	,	NA	19680	0.4752	NA	0.2485	False	NA	,,,	NA	NA	NA	2504	0.3681	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.70047633A>G		NA		hg19		0.02	2.091198	GAAxAAA	COVERED																																																																																			NOVEL					0			4	4.513856	KEEP	1	0	0	15	482	AA	0.99649	0.992192	0			4	31	155	0	0	10.802833	64	60	2302	108		0.058824	0.995687
ART3	419	__UNKNOWN__	__UNKNOWN__	4	77021843	77021843	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:77021843T>G	ENST00000355810.4	+	7	996				ART3_ENST00000349321.3_Intron|ART3_ENST00000341029.5_Intron	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	NA		NA			protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CCTTTACAGGTGGGAATATTT	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219	419			725	protein-coding gene	gene with protein product		603086			NA	9119374	Standard	NM_001179	NM_001130017	NA	Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.878-105T>G	chr4.hg19:g.77021843T>G		NA	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	hg19	CCDS47079.1	0.02	0.965185	AGGxGGG	COVERED																																																																																			NOVEL	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252416.2	1	3.033029	KEEP	0	1	5	12	323	TT	0.994391	0.983992	0		+	6	60	130	0	0	7.403441	55	60	1778	94	ENST00000355810.4	0.098361	0.989542
ANTXR2	118429	__UNKNOWN__	__UNKNOWN__	4	80824525	80824525	__UNKNOWN__	3'UTR	SNP	T	T	A	rs75657044		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:80824525T>A	ENST00000403729.2	-	0	6050					NM_058172.5	NP_477520.2	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	NA		NA			reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						tctctctctctcACACACACA	0.353	NA	NA							Juvenile Hyaline Fibromatosis					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297	118429			21732	protein-coding gene	gene with protein product	capillary morphogenesis protein 2	608041			NA	11683410, 12700348	Standard	NM_058172	NM_058172	NA	Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000403729.2:c.*4058A>T	chr4.hg19:g.80824525T>A		NA	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	hg19	CCDS47085.1	0.02	-0.429853	CTCxCAC	COVERED																																																																																			NOVEL	ANTXR2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324666.2	2	2.708383	KEEP	0	0	0	9	288	TT	0.99254	0.947371	0		-	3	60	105	0	0	7.033595	46	60	1629	64	ENST00000403729.2	0.061224	0.954491
ANTXR2	118429	__UNKNOWN__	__UNKNOWN__	4	80824581	80824581	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:80824581G>A	ENST00000403729.2	-	0	5994					NM_058172.5	NP_477520.2	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	NA		NA			reproductive process (GO:0022414)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	13						ATCTAAACAAGCATATTTTTA	0.338	NA	NA							Juvenile Hyaline Fibromatosis					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	AY040326	CCDS47085.1, CCDS47086.1, CCDS68733.1	4q21.3	2004-01-15			ENSG00000163297	ENSG00000163297	118429			21732	protein-coding gene	gene with protein product	capillary morphogenesis protein 2	608041			NA	11683410, 12700348	Standard	NM_058172	NM_058172	NA	Approved	CMG2, CMG-2, FLJ31074	uc003hlz.4	P58335	OTTHUMG00000151982	ENST00000403729.2:c.*4002C>T	chr4.hg19:g.80824581G>A		NA	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	hg19	CCDS47085.1	0.02	2.478524	CAAxCAT	COVERED																																																																																			NOVEL	ANTXR2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324666.2	3	4.213883	KEEP	0	0	0	14	508	GG	0.995343	0.979578	0		-	37	60	1318	0	0	132.959205	21	60	799	87	ENST00000403729.2	0.637931	0.984161
PLAC8	51316	__UNKNOWN__	__UNKNOWN__	4	84029139	84029139	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:84029139T>G	ENST00000509973.1	-	2	71				PLAC8_ENST00000411416.2_Intron|PLAC8_ENST00000515389.1_Intron|PLAC8_ENST00000311507.4_Intron|PLAC8_ENST00000426923.2_Intron|PLAC8_ENST00000505406.1_Intron			Q9UHV8	PP13_HUMAN	placenta-specific 8	NA		NA			apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			large_intestine(2)|lung(3)|ovary(1)	6		Hepatocellular(203;0.114)				ATCTctgttgtggggtggggg	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF208846	CCDS3601.1	4q21.22	2006-05-20			ENSG00000145287	ENSG00000145287	51316			19254	protein-coding gene	gene with protein product		607515			NA	12758124, 12384430	Standard	NM_016619	NM_016619	NA	Approved	onzin, C15	uc003hoe.3	Q9NZF1	OTTHUMG00000130294	ENST00000509973.1:c.53-2966A>C	chr4.hg19:g.84029139T>G		NA	C5HZ15	hg19		0.02	1.824203	TTGxGGG	COVERED																																																																																			NOVEL	PLAC8-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363078.1	0	5.063253	KEEP	0	2	54	36	961	TT	1	0.97082	0		-	5	60	134	0	0	8.711425	46	60	1608	135	ENST00000509973.1	0.098039	0.97082
MAPK10	5602	__UNKNOWN__	__UNKNOWN__	4	86938364	86938364	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:86938364C>T	ENST00000395169.3	-	0	2018				MAPK10_ENST00000359221.3_3'UTR|MAPK10_ENST00000395160.3_3'UTR|MAPK10_ENST00000449047.2_3'UTR|MAPK10_ENST00000395157.3_3'UTR|MAPK10_ENST00000361569.2_3'UTR|MAPK10_ENST00000395166.1_3'UTR	NM_138980.2|NM_138982.2	NP_620446.1|NP_620448.1	P53779	MK10_HUMAN	mitogen-activated protein kinase 10	NA		NA			activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		CGCTGGGTTTCGCAGGCAGGC	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						66	71	69	NA		NA	NA	4		NA											NA				86938364		2203	4300	6503	SO:0001624	3_prime_UTR_variant			U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	5602	2.7.11.1	Mitogen-activated protein kinase cascade / Kinases	6872	protein-coding gene	gene with protein product		602897		PRKM10	NA	8654373, 12436199	Standard		NM_002753	NA	Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000395169.3:c.*17G>A	chr4.hg19:g.86938364C>T		NA	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	hg19	CCDS3612.1	0.02	2.016014	TTTxGCA	COVERED																																																																																			NOVEL	MAPK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253054.3	1	12.038534	KEEP	0	0	0	40	1354	CC	1	0.999768	0		-	39	60	1350	0	0	127.3303	49	60	1767	156	ENST00000395169.3	0.443182	0.999768
CISD2	493856	__UNKNOWN__	__UNKNOWN__	4	103810174	103810174	__UNKNOWN__	3'UTR	SNP	G	G	A	rs372309407		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:103810174G>A	ENST00000273986.4	+	0	2102				SLC9B1_ENST00000394789.3_Intron	NM_001008388.4	NP_001008389.1	Q8N5K1	CISD2_HUMAN	CDGSH iron sulfur domain 2	NA		NA			mitochondrion degradation (GO:0000422)|multicellular organismal aging (GO:0010259)|regulation of autophagy (GO:0010506)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)	4				OV - Ovarian serous cystadenocarcinoma(123;1.97e-08)		attgttattgggcacttgtat	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX537971	CCDS34040.1	4q24	2009-03-25	2007-08-10	2007-08-10	ENSG00000145354	ENSG00000145354	493856		CDGSH iron sulfur domain containing	24212	protein-coding gene	gene with protein product	mitoNEET related 1, endoplasmic reticulum intermembrane small protein	611507	zinc finger, CDGSH-type domain 2, Wolfram syndrome 2	ZCD2, WFS2	NA	17376863, 17584744, 17846994	Standard	NM_001008388	NM_001008388	NA	Approved	Miner1, ERIS	uc003hwt.4	Q8N5K1	OTTHUMG00000161014	ENST00000273986.4:c.*1587G>A	chr4.hg19:g.103810174G>A		NA	Q7Z3D5	hg19	CCDS34040.1	0.02	3.619211	TTGxGCA	COVERED																																																																																			NOVEL	CISD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363417.2	2	9.631158	KEEP	0	0	0	32	1117	GG	0.999997	0.999997	0		+	5	40	179	0	0	11.06919	126	60	4495	197	ENST00000273986.4	0.038168	1
CISD2	493856	__UNKNOWN__	__UNKNOWN__	4	103810176	103810176	__UNKNOWN__	3'UTR	SNP	C	C	A	rs375157177		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:103810176C>A	ENST00000273986.4	+	0	2104				SLC9B1_ENST00000394789.3_Intron	NM_001008388.4	NP_001008389.1	Q8N5K1	CISD2_HUMAN	CDGSH iron sulfur domain 2	NA		NA			mitochondrion degradation (GO:0000422)|multicellular organismal aging (GO:0010259)|regulation of autophagy (GO:0010506)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)	4				OV - Ovarian serous cystadenocarcinoma(123;1.97e-08)		tgttattgggcacttgtatgt	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX537971	CCDS34040.1	4q24	2009-03-25	2007-08-10	2007-08-10	ENSG00000145354	ENSG00000145354	493856		CDGSH iron sulfur domain containing	24212	protein-coding gene	gene with protein product	mitoNEET related 1, endoplasmic reticulum intermembrane small protein	611507	zinc finger, CDGSH-type domain 2, Wolfram syndrome 2	ZCD2, WFS2	NA	17376863, 17584744, 17846994	Standard	NM_001008388	NM_001008388	NA	Approved	Miner1, ERIS	uc003hwt.4	Q8N5K1	OTTHUMG00000161014	ENST00000273986.4:c.*1589C>A	chr4.hg19:g.103810176C>A		NA	Q7Z3D5	hg19	CCDS34040.1	0.02	3.636678	GGGxACT	COVERED																																																																																			NOVEL	CISD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363417.2	2	9.029449	KEEP	0	0	0	30	1087	CC	0.999997	0.999997	0		+	5	40	169	0	0	10.110077	124	60	4654	191	ENST00000273986.4	0.03876	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	106448079	106448079	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:106448079C>T			NA	NA				PPA2 (52841 upstream) : AC004066.3 (13267 downstream)						NA		NA									NA						GGCGGTGATGCTCCTTCTCCC	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.106448079C>T		NA		hg19		0.02	-0.227372	ATGxTCC	COVERED																																																																																			NOVEL					0			0	6.015997	KEEP	0	0	0	20	657	CC	0.999863	0.612323	0			13	60	481	0	0	46.509952	13	60	463	53		0.5	0.612407
COL25A1	84570	__UNKNOWN__	__UNKNOWN__	4	109805320	109805320	__UNKNOWN__	Intron	SNP	C	C	T	rs187162153		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:109805320C>T	ENST00000399132.1	-	19	1551				COL25A1_ENST00000399126.1_Intron|COL25A1_ENST00000399127.1_Intron	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1	NA		NA								NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CGAGACTGTCCGTGCAGTATT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						76	72	73	NA		NA	NA	4		NA											NA				109805320		1852	4092	5944	SO:0001627	intron_variant			AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517	84570		Collagens	18603	protein-coding gene	gene with protein product		610004			NA	11927537	Standard	NM_032518	NM_001256074	NA	Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1020+13G>A	chr4.hg19:g.109805320C>T		NA		hg19	CCDS43258.1	0.02	10.342087	GTCxGTG	COVERED																																																																																			NOVEL	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315938.2	1	11.374126	KEEP	0	0	0	38	1259	CC	1	1	0		-	56	60	2081	0	0	182.47657	150	60	5356	306	ENST00000399132.1	0.271845	1
GYPE	2996	__UNKNOWN__	__UNKNOWN__	4	144801497	144801497	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:144801497C>T	ENST00000358615.4	-	2	188				GYPE_ENST00000437468.2_Intron	NM_198682.2	NP_941391.2	P15421	GLPE_HUMAN	glycophorin E (MNS blood group)	NA		NA				integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_hematologic(180;0.158)					GACAGGTCCCCTAAAATAGGG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47138.1	4q31.21	2010-01-19	2010-01-19		ENSG00000197465	ENSG00000197465	2996		Blood group antigens	4705	protein-coding gene	gene with protein product		138590	glycophorin E		NA		Standard	NM_002102	NM_198682	NA	Approved	GPE, MNS	uc003ijj.3	P15421	OTTHUMG00000161402	ENST00000358615.4:c.136+66G>A	chr4.hg19:g.144801497C>T		NA	D3DNZ5	hg19	CCDS47138.1	0.02	2.329387	CCCxTAA	COVERED																																																																																			NOVEL	GYPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364780.1	0	2.406895	KEEP	0	0	0	8	255	CC	0.99257	0.991047	0		-	5	40	199	1	0	14.464094	65	60	2314	83	ENST00000358615.4	0.071429	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	175321990	175321990	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:175321990T>C			NA	NA				RP11-51M24.1 (24394 upstream) : MIR4276 (22955 downstream)						NA		NA									NA						cattttgttctgtactaagaa	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.175321990T>C		NA		hg19		0.02	-0.114056	TTCxGTA	UNCOVERED																																																																																			NOVEL					0			0	2.407317	KEEP	2	0	0	8	251	TT	0	0	0			2	20	83	0	0	6.830451	11	60	432	28		0.153846	0.162467
SORBS2	8470	__UNKNOWN__	__UNKNOWN__	4	186508517	186508517	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:186508517C>T	ENST00000437304.2	-	0	3322				SORBS2_ENST00000448662.2_3'UTR|SORBS2_ENST00000418609.1_3'UTR|SORBS2_ENST00000284776.7_3'UTR|SORBS2_ENST00000449407.2_3'UTR|SORBS2_ENST00000431808.1_3'UTR|SORBS2_ENST00000319471.9_3'UTR|SORBS2_ENST00000355634.5_3'UTR|SORBS2_ENST00000393528.3_3'UTR	NM_001145673.1	NP_001139145.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	NA		NA			actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TGATTTTTTTCTTTCTGATCC	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(153;41 2433 9491 36028)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556	8470			24098	protein-coding gene	gene with protein product	Arg/Abl interacting protein	NA			NA	9211900, 9872452	Standard	NM_003603	NM_021069	NA	Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000437304.2:c.*264G>A	chr4.hg19:g.186508517C>T		NA	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	hg19	CCDS47175.1	0.02	0.799173	TTTxTTT	COVERED																																																																																			NOVEL	SORBS2-009	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347952.2	3	5.248477	KEEP	0	4	73	44	1492	CC	1	0.999862	0		-	6	60	143	0	0	7.658658	84	70	3093	196	ENST00000437304.2	0.066667	0.999862
AF146191.4	0	__UNKNOWN__	__UNKNOWN__	4	190804834	190804834	__UNKNOWN__	lincRNA	SNP	G	G	A	rs3884604	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190804834G>A	ENST00000511785.1	-	0	231				RP11-463J17.1_ENST00000503609.1_lincRNA						NA		NA									NA						CATCAGAGATGCTGGTTTTCA	0.333	NA	NA											.|||	1821	0.363618	0.4561	0.2767	5008	,	,	NA	16610	0.3185	NA	0.3976	False	NA	,,,	NA	NA	NA	2504	0.3119	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000511785.1:	chr4.hg19:g.190804834G>A		NA		hg19		0.02	2.196454	GATxCTG	COVERED																																																																																			NOVEL	AF146191.4-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000361301.1	1	2.646684	KEEP	2	0	0	9	292	GG	0.99254	0.972219	0		-	9	60	325	0	0	31.085505	10	60	395	82	ENST00000511785.1	0.473684	0.979526
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878419	190878419	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190878419T>C	ENST00000226798.4	+	6	654				FRG1_ENST00000514482.1_Intron	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		tcttgtattatatttttcagg	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.433-134T>C	chr4.hg19:g.190878419T>C		NA	A8K775	hg19	CCDS34121.1	0.02	12.600291	TTAxATT	COVERED																																																																																			NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	8	3.005533	KEEP	8	0	0	10	257	TT	0.992708	0.992708	0		+	9	40	322	0	0	20.543549	192	60	6863	330	ENST00000226798.4	0.044776	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878487	190878487	__UNKNOWN__	Intron	SNP	C	C	G	rs184174635		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190878487C>G	ENST00000226798.4	+	6	654				FRG1_ENST00000514482.1_Intron	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TTAATTCAGTCTAAACACTTA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.433-66C>G	chr4.hg19:g.190878487C>G		NA	A8K775	hg19	CCDS34121.1	0.02	29.333538	AGTxTAA	COVERED																																																																																			NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	13	6.858752	KEEP	12	1	38	36	1255	CC	0.999999	0.999999	0		+	20	56	690	0	0	47.422716	259	70	9943	702	ENST00000226798.4	0.071685	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878494	190878494	__UNKNOWN__	Intron	SNP	C	C	T	rs202170867		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190878494C>T	ENST00000226798.4	+	6	654				FRG1_ENST00000514482.1_Intron	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		AGTCTAAACACTTAATGTTTC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.433-59C>T	chr4.hg19:g.190878494C>T		NA	A8K775	hg19	CCDS34121.1	0.02	25.426515	ACAxTTA	COVERED																																																																																			NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	13	4.984039	KEEP	15	2	58	37	1325	CC	1	1	0		+	20	37	773	0	0	55.654196	257	70	9841	716	ENST00000226798.4	0.072202	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878577	190878577	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs200267221		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190878577A>G	ENST00000226798.4	+	6	679	c.457A>G	c.(457-459)Aat>Gat	p.N153D	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	153		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GTTGGCCTCAAATAGCTGCTT	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						14	18	17	NA		NA	NA	4		NA											NA				190878577		2154	4261	6415	SO:0001583	missense			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.457A>G	chr4.hg19:g.190878577A>G	ENSP00000226798:p.Asn153Asp	NA	A8K775	hg19	CCDS34121.1	0.02	39.690831	TCAxATA	COVERED	.	.	.	.	.	.	.	.	.	.	.	16.34	3.096595	0.56075	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.50548	1.75;0.74	4.19	2.99	0.34606	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.88105	2.93	0.58432	D	0.999994	P	0.35033	0.481	P	0.49085	0.6	T	0.60182	-0.7313	10	0.38643	T	0.18	-7.9248	8.2154	0.31507	0.9006:0.0:0.0994:0.0	.	153	Q14331	FRG1_HUMAN	D	153;25;90	ENSP00000226798:N153D;ENSP00000435943:N90D	ENSP00000226798:N153D	N	+	1	0	FRG1	191115571	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	9.035000	0.93752	0.593000	0.29745	-0.580000	0.04137	AAT	NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	19	19.863879	KEEP	75	6	215	141	4379	AA	1	1	0		+	41	49	1545	0	0	105.691885	682	60	24300	1178	ENST00000226798.4	0.056708	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878626	190878626	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190878626G>A	ENST00000226798.4	+	6	728	c.506G>A	c.(505-507)aGt>aAt	p.S169N	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	169		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.S169N(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GAAGCAAAAAGTAAAACAGCA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	skin(1)					NA						49	46	47	NA		NA	NA	4		NA											NA				190878626		2184	4282	6466	SO:0001583	missense			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.506G>A	chr4.hg19:g.190878626G>A	ENSP00000226798:p.Ser169Asn	NA	A8K775	hg19	CCDS34121.1	0.02	34.830861	AAAxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	.	14.80	2.642895	0.47153	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.48522	1.77;0.81	4.19	2.41	0.29592	Actin cross-linking (1);	0.160510	0.64402	N	0.000002	T	0.36552	0.0971	N	0.17723	0.515	0.45777	D	0.998661	P	0.35982	0.531	P	0.45406	0.479	T	0.07578	-1.0765	10	0.30854	T	0.27	0.1847	7.6816	0.28518	0.219:0.0:0.781:0.0	.	169	Q14331	FRG1_HUMAN	N	169;41;106	ENSP00000226798:S169N;ENSP00000435943:S106N	ENSP00000226798:S169N	S	+	2	0	FRG1	191115620	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	1.784000	0.38674	0.340000	0.23745	0.454000	0.30748	AGT	NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	20	43.380527	KEEP	43	7	225	223	8166	GG	1	1	0		+	31	60	1112	0	1	70.822213	673	60	25825	1359	ENST00000226798.4	0.044034	1
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190881021	190881021	__UNKNOWN__	Intron	SNP	C	C	A	rs373303976		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190881021C>A	ENST00000226798.4	+	7	759				FRG1_ENST00000514482.1_Intron	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TCTCTGTCAGCCCTTCACCTT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.538-882C>A	chr4.hg19:g.190881021C>A		NA	A8K775	hg19	CCDS34121.1	0.02	17.919661	CAGxCCT	COVERED																																																																																			NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	3	7.400225	KEEP	6	5	158	80	2902	CC	1	1	0		+	41	60	1430	0	0	113.220965	221	60	8217	721	ENST00000226798.4	0.156489	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	190904645	190904645	__UNKNOWN__	IGR	SNP	G	G	A	rs9995127	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr4:190904645G>A			NA	NA				FRG1 (20286 upstream) : RNA5SP174 (31647 downstream)						NA		NA						p.T112M(1)			NA						CACTGACTCCGTCAGCTCCGC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	prostate(1)					NA						6	9	8	NA		NA	NA	4		NA											NA				190904645		1930	4175	6105	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.190904645G>A		NA		hg19		0.02	-0.070186	TCCxTCA	UNCOVERED																																																																																			NOVEL					0			0	2.407721	KEEP	1	0	0	8	278	GG	0	0	0			5	40	185	0	0	18.586904	3	40	111	20		0.625	0.054137
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	801252	801252	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs142091140	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:801252C>T	ENST00000283441.8	-	12	1592	c.1209G>A	c.(1207-1209)atG>atA	p.M403I	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.M403I|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	403		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.M403I(2)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TGTCAGTTTTCATGGGCTCTG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	prostate(2)					NA	C	ILE/MET	6,4398		0,6,2196	147	108	121	NA	1209	-0.4	0	5	dbSNP_134	121	6,8584		0,6,4289	no	missense	ZDHHC11	NM_024786.2	10	0,12,6485	TT,TC,CC	NA	0.0698,0.1362,0.0924	benign	403/413	801252	12,12982	2202	4295	6497	SO:0001583	missense			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1209G>A	chr5.hg19:g.801252C>T	ENSP00000283441:p.Met403Ile	NA	Q6UWR9	hg19	CCDS3857.1	0.02	34.072752	TTTxATG	COVERED	.	.	.	.	.	.	.	.	.	.	N	6.779	0.512644	0.12944	0.001362	6.98E-4	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.36520	1.25;1.25	1.57	-0.362	0.12560	.	.	.	.	.	T	0.14098	0.0341	N	0.08118	0	0.09310	N	1	B	0.18968	0.032	B	0.09377	0.004	T	0.29549	-1.0008	9	0.14656	T	0.56	-9.9532	3.9839	0.09507	0.0:0.5594:0.0:0.4406	.	403	Q9H8X9	ZDH11_HUMAN	I	403	ENSP00000397719:M403I;ENSP00000283441:M403I	ENSP00000283441:M403I	M	-	3	0	ZDHHC11	854252	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.366000	0.07563	-0.120000	0.11809	0.384000	0.25694	ATG	NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	6	14.990176	KEEP	4	4	129	95	3411	CC	1	1	0		-	39	49	1450	0	0	96.398205	741	60	28575	1057	ENST00000283441.8	0.05	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	801339	801339	__UNKNOWN__	Intron	SNP	A	A	C	rs372948613		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:801339A>C	ENST00000283441.8	-	12	1565				ZDHHC11_ENST00000424784.2_Intron|ZDHHC11_ENST00000503758.2_Intron	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			ACTTGTTATAATGCCAAAGTG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						84	47	58	NA		NA	NA	5		NA											NA				801339		692	1588	2280	SO:0001627	intron_variant			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1182-60T>G	chr5.hg19:g.801339A>C		NA	Q6UWR9	hg19	CCDS3857.1	0.02	14.742237	ATAxTGC	COVERED																																																																																			NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	5	4.947719	KEEP	11	1	36	29	840	AA	0.999997	0.999997	0		-	10	33	371	0	0	21.618744	386	60	14009	440	ENST00000283441.8	0.025253	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	837673	837673	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:837673A>G	ENST00000283441.8	-	6	1168				ZDHHC11_ENST00000424784.2_Intron|ZDHHC11_ENST00000503758.2_Intron	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			AGCTCAGCAGAGTGGCCAGTG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.785-78T>C	chr5.hg19:g.837673A>G		NA	Q6UWR9	hg19	CCDS3857.1	0.02	7.361917	CAGxGTG	COVERED																																																																																			NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	0	3.076532	KEEP	12	2	59	31	969	AA	0.999997	0.999997	0		-	13	27	475	0	0	33.738793	158	60	6027	245	ENST00000283441.8	0.076023	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840299	840299	__UNKNOWN__	Intron	SNP	G	G	T	rs3822814	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:840299G>T	ENST00000283441.8	-	5	1168				ZDHHC11_ENST00000424784.2_Intron|ZDHHC11_ENST00000503758.2_Intron|ZDHHC11_ENST00000511539.1_3'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			ccattccattgtctctgaaca	0.428	NA	NA											G|||	198	0.0395367	0.1248	0.0173	5008	,	,	NA	32468	0.0109	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.784+310C>A	chr5.hg19:g.840299G>T		NA	Q6UWR9	hg19	CCDS3857.1	0.02	33.164559	ATTxTCT	COVERED																																																																																			NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	9	13.626729	KEEP	7	8	262	137	4904	GG	1	1	0		-	42	54	1462	0	0	93.226156	827	60	31494	1200	ENST00000283441.8	0.048331	1
ZDHHC11	79844	__UNKNOWN__	__UNKNOWN__	5	840644	840644	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs200038670		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:840644G>C	ENST00000283441.8	-	5	1133	c.750C>G	c.(748-750)caC>caG	p.H250Q	ZDHHC11_ENST00000424784.2_Missense_Mutation_p.H250Q|ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000511539.1_Missense_Mutation_p.H37Q	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	250		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.H250Q(2)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCTGGCCCAGGTGCACCAAGC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	lung(2)					NA						137	146	143	NA		NA	NA	5		NA											NA				840644		2203	4300	6503	SO:0001583	missense			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818	79844		Zinc fingers, DHHC-type	19158	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024786	NM_024786	NA	Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.750C>G	chr5.hg19:g.840644G>C	ENSP00000283441:p.His250Gln	NA	Q6UWR9	hg19	CCDS3857.1	0.02	22.390636	CAGxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	g	5.277	0.236438	0.10023	.	.	ENSG00000188818	ENST00000424784;ENST00000283441;ENST00000511193;ENST00000511539	T;T;T;T	0.43688	1.86;1.86;0.99;0.94	2.74	-0.394	0.12434	.	642.914000	0.00961	U	0.003101	T	0.25494	0.0620	N	0.03608	-0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.15870	0.014;0.001	T	0.27606	-1.0069	10	0.29301	T	0.29	-6.9343	13.336	0.60518	0.0:0.2548:0.7452:0.0	.	250;37	Q9H8X9;Q6UWR9	ZDH11_HUMAN;.	Q	250;250;25;37	ENSP00000397719:H250Q;ENSP00000283441:H250Q;ENSP00000426873:H25Q;ENSP00000427067:H37Q	ENSP00000283441:H250Q	H	-	3	2	ZDHHC11	893644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.474000	0.06607	-0.110000	0.12022	-2.048000	0.00412	CAC	NOVEL	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206681.3	7	19.561979	KEEP	3	5	170	125	4096	GG	1	1	0		-	45	60	1592	0	0	114.178848	476	60	17300	769	ENST00000283441.8	0.086372	1
SLC12A7	10723	__UNKNOWN__	__UNKNOWN__	5	1051666	1051666	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:1051666A>T	ENST00000264930.5	-	0	4104					NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	NA		NA			cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TTATGAAAAGAAGTGGCTGGT	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504	10723		Solute carriers	10915	protein-coding gene	gene with protein product		604879			NA	10347194	Standard	NM_006598	NM_006598	NA	Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.*809T>A	chr5.hg19:g.1051666A>T		NA	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	hg19	CCDS34129.1	0.02	9.656512	AAGxAGT	COVERED																																																																																			NOVEL	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366446.2	2	26.15787	KEEP	0	0	0	87	2603	AA	1	1	0		-	8	60	280	0	0	16.155596	264	60	9529	449	ENST00000264930.5	0.029412	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	1576408	1576408	__UNKNOWN__	IGR	SNP	C	C	T	rs201115947		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:1576408C>T			NA	NA				CTD-2245E15.3 (24583 upstream) : SDHAP3 (12734 downstream)						NA		NA									NA						CCACCAGGTCCGTGTTCCAGA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.1576408C>T		NA		hg19		0.02	2.376779	GTCxGTG	COVERED																																																																																			NOVEL					0			2	2.242273	KEEP	7	1	33	19	639	CC	0.999859	0.999177	0			7	27	289	0	0	21.97257	72	60	2440	134		0.088608	0.999317
IRX4	50805	__UNKNOWN__	__UNKNOWN__	5	1878599	1878599	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:1878599C>T	ENST00000505790.1	-	6	1500	c.1044G>A	c.(1042-1044)gaG>gaA	p.E348E	IRX4_ENST00000231357.2_Silent_p.E348E|IRX4_ENST00000513692.1_Silent_p.E348E	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	348		NA			establishment of organ orientation (GO:0048561)|heart development (GO:0007507)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|lung(7)|ovary(1)|prostate(1)	10				GBM - Glioblastoma multiforme(108;0.242)		CCAGCTTGGCCTCGCAGACCT	0.771	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						2	3	2	NA		NA	NA	5		NA											NA				1878599		1347	2837	4184	SO:0001819	synonymous_variant			AF124733	CCDS3867.1, CCDS75225.1	5p15.33	2011-06-20	2007-07-13		ENSG00000113430	ENSG00000113430	50805		Homeoboxes / TALE class	6129	protein-coding gene	gene with protein product		606199	iroquois homeobox protein 4		NA	10625552	Standard	NM_016358	NM_016358	NA	Approved		uc003jcz.2	P78413	OTTHUMG00000090411	ENST00000505790.1:c.1044G>A	chr5.hg19:g.1878599C>T		NA	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	hg19	CCDS3867.1	0.02	7.186969	GGCxTCG	COVERED																																																																																			NOVEL	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365500.1	4	24.980404	KEEP	0	0	0	83	2889	CC	1	1	0		-	35	60	1245	0	0	102.056823	152	60	5548	316	ENST00000505790.1	0.187166	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	3276373	3276373	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:3276373G>C			NA	NA				CTD-2029E14.1 (95027 upstream) : LINC01019 (140892 downstream)						NA		NA									NA						ggagggaggggaggaaggagg	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.3276373G>C		NA		hg19		0.02	-0.061409	GGGxAGG	UNCOVERED																																																																																			NOVEL					0			6	3.6114	KEEP	13	0	0	12	404	GG	0	0	0			3	26	100	0	0	9.354872	4	29	146	27		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	3611544	3611544	__UNKNOWN__	IGR	SNP	A	A	T	rs542479950		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:3611544A>T			NA	NA				IRX1 (10027 upstream) : CTD-2287N17.1 (401277 downstream)						NA		NA									NA						CACAAAACCCAGGAGACCTTT	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.3611544A>T		NA		hg19		0.02	7.66511	CCCxGGA	COVERED																																																																																			NOVEL					0			1	6.31879	KEEP	0	0	0	21	655	AA	0.999869	0.999869	0			37	60	1400	0	0	117.746261	145	60	5512	245		0.203297	1
KIAA0947	0	__UNKNOWN__	__UNKNOWN__	5	5422800	5422800	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:5422800G>T	ENST00000512608.1	+	1	29							Q9Y2F5	ICE1_HUMAN		NA		NA			positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GGACTGCGTCGCGCTCGGGGG	0.741	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000512608.1:c.29+1995G>T	chr5.hg19:g.5422800G>T		NA	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	hg19		0.02	4.535844	GTCxCGC	COVERED																																																																																			NOVEL	KIAA0947-005	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000365579.1	2	39.101359	KEEP	0	0	0	130	4189	GG	1	1	0		+	21	60	747	0	0	59.845121	108	60	3442	330	ENST00000512608.1	0.162791	1
FBXL7	23194	__UNKNOWN__	__UNKNOWN__	5	15937696	15937696	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:15937696G>T	ENST00000504595.1	+	0	2358					NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	NA		NA			cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						TAGAGCAGCAGCGAGGATCCA	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580	23194		F-boxes / Leucine-rich repeats	13604	protein-coding gene	gene with protein product		605656			NA	10048485, 10531035	Standard	NM_012304	NM_012304	NA	Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.*401G>T	chr5.hg19:g.15937696G>T		NA	B9EGF1|D6RDY7|O94926	hg19	CCDS54833.1	0.02	4.580937	GCAxCGA	COVERED																																																																																			NOVEL	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366117.1	3	7.82305	KEEP	0	0	0	26	898	GG	0.999957	0.99993	0		+	17	60	569	0	0	45.07244	85	70	3061	143	ENST00000504595.1	0.166667	0.999973
FBXL7	23194	__UNKNOWN__	__UNKNOWN__	5	15937697	15937697	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:15937697C>G	ENST00000504595.1	+	0	2359					NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	NA		NA			cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						AGAGCAGCAGCGAGGATCCAT	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580	23194		F-boxes / Leucine-rich repeats	13604	protein-coding gene	gene with protein product		605656			NA	10048485, 10531035	Standard	NM_012304	NM_012304	NA	Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.*402C>G	chr5.hg19:g.15937697C>G		NA	B9EGF1|D6RDY7|O94926	hg19	CCDS54833.1	0.02	4.755335	CAGxGAG	COVERED																																																																																			NOVEL	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366117.1	3	7.822384	KEEP	0	0	0	26	855	CC	0.999957	0.999941	0		+	17	60	591	0	0	47.052464	88	70	3042	147	ENST00000504595.1	0.161905	0.999984
GDNF	2668	__UNKNOWN__	__UNKNOWN__	5	37812837	37812837	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:37812837A>G	ENST00000326524.2	-	0	3751				GDNF_ENST00000344622.4_3'UTR	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor	NA		NA			adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					ACAAAAATAAAGTCTGTAGAG	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621	2668		Endogenous ligands	4232	protein-coding gene	gene with protein product	astrocyte-derived trophic factor, glial cell line derived neurotrophic factor, glial derived neurotrophic factor	600837			NA	8493557	Standard	NM_000514	NM_199231	NA	Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.*2916T>C	chr5.hg19:g.37812837A>G		NA	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	hg19	CCDS3922.1	0.02	2.20998	TAAxGTC	COVERED																																																																																			NOVEL	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207606.1	1	3.610696	KEEP	0	0	0	12	382	AA	0.993634	0.993596	0		-	24	60	890	0	0	76.519299	76	60	2774	139	ENST00000326524.2	0.24	0.999962
OXCT1	5019	__UNKNOWN__	__UNKNOWN__	5	41794174	41794174	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:41794174G>C	ENST00000196371.5	-	13	1339	c.1179C>G	c.(1177-1179)caC>caG	p.H393Q	OXCT1_ENST00000513081.1_5'UTR|OXCT1_ENST00000512084.1_5'UTR|OXCT1_ENST00000509987.1_Missense_Mutation_p.H207Q|OXCT1_ENST00000510634.1_5'UTR	NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	393		NA			adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	TCAGATCGACGTGTCCACTGA	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						109	106	107	NA		NA	NA	5		NA											NA				41794174		2203	4300	6503	SO:0001583	missense			U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720	5019			8527	protein-coding gene	gene with protein product		601424	3-oxoacid CoA transferase	OXCT	NA	8751852	Standard	NM_000436	NM_000436	NA	Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.1179C>G	chr5.hg19:g.41794174G>C	ENSP00000196371:p.His393Gln	NA	B2R5V2|B7Z528	hg19	CCDS3937.1	0.02	26.189563	GACxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	g	14.46	2.542754	0.45280	.	.	ENSG00000083720	ENST00000196371;ENST00000509987	D;D	0.88201	-2.35;-2.35	5.87	0.643	0.17770	3-oxoacid CoA-transferase, subunit B (1);	0.098157	0.64402	D	0.000001	D	0.95840	0.8646	H	0.97829	4.085	0.52501	D	0.999952	D	0.89917	1.0	D	0.97110	1.0	D	0.94263	0.7504	10	0.72032	D	0.01	-17.3231	10.2122	0.43147	0.5668:0.0:0.4332:0.0	.	393	P55809	SCOT1_HUMAN	Q	393;207	ENSP00000196371:H393Q;ENSP00000425348:H207Q	ENSP00000196371:H393Q	H	-	3	2	OXCT1	41829931	1.000000	0.71417	0.985000	0.45067	0.383000	0.30230	1.737000	0.38197	-0.108000	0.12066	-0.295000	0.09555	CAC	NOVEL	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211594.2	5	31.602694	KEEP	0	0	0	105	3727	GG	1	1	0		-	113	60	4321	0	0	366.35903	421	60	15029	842	ENST00000196371.5	0.21161	1
C5orf28	64417	__UNKNOWN__	__UNKNOWN__	5	43445076	43445076	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:43445076G>T	ENST00000500337.2	-	0	2227				C5orf28_ENST00000537319.1_3'UTR|C5orf28_ENST00000397080.3_3'UTR			Q0VDI3	CE028_HUMAN	chromosome 5 open reading frame 28	NA		NA				integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(2)|lung(5)	9	Lung NSC(6;2.07e-05)					TGTGGATAAGGCATTGCTTTA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK025310	CCDS3945.1	5p12	2011-01-25			ENSG00000151881	ENSG00000151881	64417			26139	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_022483	NM_022483	NA	Approved	FLJ21657	uc003jny.3	Q0VDI3	OTTHUMG00000131150	ENST00000500337.2:c.*1248C>A	chr5.hg19:g.43445076G>T		NA	B2RDA6|Q9H6Z2	hg19	CCDS3945.1	0.02	8.671857	AAGxCAT	COVERED																																																																																			NOVEL	C5orf28-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368003.1	1	13.845014	KEEP	0	0	0	46	1632	GG	1	1	0		-	52	60	1885	0	0	159.157587	185	60	6785	349	ENST00000500337.2	0.219409	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	49410230	49410230	__UNKNOWN__	IGR	SNP	A	A	C	rs141946569		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:49410230A>C			NA	NA				None (None upstream) : EMB (281795 downstream)						NA		NA									NA						agattctccaaaaacagtgtt	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.49410230A>C		NA		hg19		0.02	-0.245649	CCAxAAA	UNCOVERED																																																																																			NOVEL					0			3	2.40726	KEEP	15	0	0	8	255	AA	0	0	0			3	21	117	0	0	9.691148	14	40	499	66		0.176471	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	49410286	49410286	__UNKNOWN__	IGR	SNP	T	T	C	rs372241016		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:49410286T>C			NA	NA				None (None upstream) : EMB (281739 downstream)						NA		NA									NA						gtgagttgaatggacagatca	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.49410286T>C		NA		hg19		0.02	-0.263196	GAAxGGA	UNCOVERED																																																																																			NOVEL					0			3	2.708398	KEEP	13	0	0	9	287	TT	0	0	0			4	21	128	0	0	10.362569	16	37	620	63		0.2	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	49440797	49440797	__UNKNOWN__	IGR	SNP	T	T	G	rs142556023		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:49440797T>G			NA	NA				None (None upstream) : EMB (251228 downstream)						NA		NA									NA						ttgctgagaatgcttcagtct	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.49440797T>G		NA		hg19		0.02	2.387394	GAAxGCT	UNCOVERED																																																																																			NOVEL					0			4	3.911819	KEEP	30	0	0	13	406	TT	0	0	0			3	49	118	0	0	8.710147	34	50	1246	110		0.081081	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	64446717	64446717	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:64446717C>T			NA	NA				Y_RNA (27416 upstream) : ADAMTS6 (637 downstream)						NA		NA									NA						GGGCAGAAGCCGTGCTGTGGC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.64446717C>T		NA		hg19		0.02	2.346977	AGCxGTG	COVERED																																																																																			NOVEL					0			0	3.611642	KEEP	0	0	0	12	412	CC	0.993634	0.991545	0			18	60	661	0	0	56.981988	55	60	1929	112		0.246575	0.997898
ADAMTS6	11174	__UNKNOWN__	__UNKNOWN__	5	64596005	64596005	__UNKNOWN__	Intron	SNP	C	C	A	rs566762938		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:64596005C>A	ENST00000536360.1	-	10	2037							Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	NA		NA				proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		AAGAAAAAAACCCCAACACAT	0.343	NA	NA											c|||	1	0.000199681	0	0.0014	5008	,	,	NA	18465	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						29	30	30	NA		NA	NA	5		NA											NA				64596005		2202	4298	6500	SO:0001627	intron_variant			AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192	11174		ADAM metallopeptidases with thrombospondin type 1 motif	222	protein-coding gene	gene with protein product	a disintegrin and metalloproteinase with thrombospondin motifs 6	605008	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6		NA	10464288	Standard	NM_197941	NM_197941	NA	Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.1224-47G>T	chr5.hg19:g.64596005C>A		NA	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	hg19		0.02	2.032142	AAAxCCC	COVERED																																																																																			NOVEL	ADAMTS6-201	KNOWN	basic	protein_coding	NA	protein_coding		0	3.009345	KEEP	0	0	0	10	338	CC	0.992708	0.96037	0		-	11	60	358	0	0	29.399364	41	60	1438	64	ENST00000536360.1	0.211538	0.967425
TRAPPC13	80006	__UNKNOWN__	__UNKNOWN__	5	64920561	64920561	__UNKNOWN__	5'UTR	SNP	T	T	A	rs5023817		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:64920561T>A	ENST00000399438.3	+	0	19					NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	NA		NA									NA						tttttttttttAAAAAAAAAA	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597	80006			25828	protein-coding gene	gene with protein product	Trs65-related	NA	chromosome 5 open reading frame 44	C5orf44	NA	12477932	Standard	NM_024941	NM_024941	NA	Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.-327T>A	chr5.hg19:g.64920561T>A		NA	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	hg19	CCDS47222.1	0.02	-0.147714	TTTxAAA	COVERED																																																																																			NOVEL	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370113.1	12	2.693293	KEEP	2	0	0	9	221	TT	0.99257	0.289832	0		+	5	60	161	0	1	15.194929	6	60	191	34	ENST00000399438.3	0.454545	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	68309958	68309958	__UNKNOWN__	IGR	SNP	C	C	T	rs201196305		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:68309958C>T			NA	NA				RP11-141O11.1 (46286 upstream) : 7SK (12623 downstream)						NA		NA						p.0?(1)			NA						cttcctcttcctcttcttcct	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Whole gene deletion(1)	large_intestine(1)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.68309958C>T		NA		hg19		0.02	-0.052637	TTCxTCT	UNCOVERED																																																																																			NOVEL					0			3	2.407394	KEEP	1	0	0	8	270	CC	0	0	0			2	60	70	0	0	6.750091	2	60	67	20		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	71146749	71146749	__UNKNOWN__	IGR	SNP	C	C	T	rs10462545	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:71146749C>T			NA	NA				CARTPT (129874 upstream) : MAP1B (256311 downstream)						NA		NA									NA						tcttccagtgcggtaacgtga	0.502	NA	NA											-|||	2302	0.459665	0.4228	0.5821	5008	,	,	NA	14420	0.3839	NA	0.5954	False	NA	,,,	NA	NA	NA	2504	0.3609	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.71146749C>T		NA		hg19		0.02	6.641561	GTGxGGT	COVERED																																																																																			NOVEL					0			189	35.807298	KEEP	0	4	122	162	5297	CC	1	1	0			8	60	274	0	0	18.794689	106	60	3772	411		0.070175	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	83999798	83999798	__UNKNOWN__	IGR	SNP	G	G	A	rs10038766	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:83999798G>A			NA	NA				CTD-2269F5.1 (213215 upstream) : CTC-384G19.1 (408361 downstream)						NA		NA									NA						ggctcaaaaagcacccccact	0.493	NA	NA											T|||	3590	0.716853	0.8101	0.7882	5008	,	,	NA	15708	0.621	NA	0.7525	False	NA	,,,	NA	NA	NA	2504	0.6022	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.83999798G>A		NA		hg19		0.02	-0.140372	AAAxCAC	COVERED																																																																																			NOVEL					0			0	2.708869	KEEP	2	0	0	9	319	GG	0.99254	0.259018	0			6	44	215	0	0	19.76551	10	48	379	37		0.375	0.260965
ARRDC3	57561	__UNKNOWN__	__UNKNOWN__	5	90679088	90679088	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:90679088C>T	ENST00000265138.3	-	0	88					NM_020801.2	NP_065852.1	Q96B67	ARRD3_HUMAN	arrestin domain containing 3	NA		NA			fat pad development (GO:0060613)|negative regulation of heat generation (GO:0031651)|negative regulation of locomotion involved in locomotory behavior (GO:0090327)|negative regulation of multicellular organismal metabolic process (GO:0044252)|positive regulation of adrenergic receptor signaling pathway (GO:0071879)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|skin development (GO:0043588)|temperature homeostasis (GO:0001659)	endosome (GO:0005768)|plasma membrane (GO:0005886)	beta-3 adrenergic receptor binding (GO:0031699)			breast(2)|endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	18		all_cancers(142;2.22e-05)|all_epithelial(76;1.58e-07)|all_lung(232;0.000521)|Lung NSC(167;0.000548)|Ovarian(174;0.0798)|Colorectal(57;0.207)		OV - Ovarian serous cystadenocarcinoma(54;4.56e-30)|Epithelial(54;7.55e-26)|all cancers(79;3.63e-22)		GCAGCAGAGGCTGCTGCTCCG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AB037797	CCDS34202.1	5q14.3	2013-10-11			ENSG00000113369	ENSG00000113369	57561			29263	protein-coding gene	gene with protein product	alpha-arrestin 3	612464			NA	10718198, 19605364	Standard	NM_020801	NM_020801	NA	Approved	KIAA1376	uc003kjz.2	Q96B67	OTTHUMG00000162616	ENST00000265138.3:c.-179G>A	chr5.hg19:g.90679088C>T		NA	A8K6T8|Q9P2H1	hg19	CCDS34202.1	0.02	-0.18422	AGGxTGC	COVERED																																																																																			NOVEL	ARRDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369763.2	1	3.912448	KEEP	0	0	0	13	444	CC	0.994391	0.421102	0		-	7	60	241	0	0	21.633806	14	60	540	41	ENST00000265138.3	0.333333	0.423478
CTD-2215E18.1	0	__UNKNOWN__	__UNKNOWN__	5	96478160	96478160	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:96478160T>C	ENST00000509481.1	+	3	573				LIX1_ENST00000274382.4_Intron						NA		NA								urinary_tract(1)	1						AGGACTATTTTCTAAAAAGTC	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						64	60	61	NA		NA	NA	5		NA											NA				96478160		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000509481.1:c.32+39362T>C	chr5.hg19:g.96478160T>C		NA		hg19		0.02	6.496283	TTTxCTA	COVERED																																																																																			NOVEL	CTD-2215E18.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370857.1	0	5.414052	KEEP	0	0	0	18	522	TT	0.999859	0.999859	0		+	13	60	485	1	0	34.116548	177	60	6265	229	ENST00000509481.1	0.068421	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	99715833	99715833	__UNKNOWN__	IGR	SNP	T	T	A	rs78916689		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:99715833T>A			NA	NA				RNU6-1119P (226350 upstream) : RP11-346J10.1 (21311 downstream)						NA		NA									NA						AATAGAAAGGTTTCCCGCTGA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.99715833T>A		NA		hg19		0.02	-0.289498	AGGxTTC	COVERED																																																																																			NOVEL					0			0	3.007342	KEEP	1	0	0	10	292	TT	0.99254	0.755211	0			15	60	552	0	0	52.482424	18	60	632	58		0.454545	0.760887
ST8SIA4	7903	__UNKNOWN__	__UNKNOWN__	5	100146904	100146904	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:100146904C>T	ENST00000231461.5	-	0	2037					NM_005668.4	NP_005659.1	Q92187	SIA8D_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	NA		NA			axon guidance (GO:0007411)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(11)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	25		all_cancers(142;1.5e-07)|all_epithelial(76;1.43e-10)|Prostate(80;0.000644)|Lung NSC(167;0.0059)|all_lung(232;0.00914)|Ovarian(225;0.024)|Colorectal(57;0.09)|Breast(839;0.203)		COAD - Colon adenocarcinoma(37;0.00402)		TGTGTGATAGCTTTTAAAAAG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L41680	CCDS4091.1, CCDS47252.1	5q21	2013-03-01	2003-01-14	2005-02-07	ENSG00000113532	ENSG00000113532	7903		Sialyltransferases	10871	protein-coding gene	gene with protein product	ST8Sia IV	602547	sialyltransferase 8 (alpha-2, 8-polysialytransferase) D	SIAT8D	NA	7624364	Standard	NM_005668	NM_005668	NA	Approved	PST, PST1	uc003knk.3	Q92187	OTTHUMG00000128727	ENST00000231461.5:c.*647G>A	chr5.hg19:g.100146904C>T		NA	A8KA07|G3V104|Q8N1F4|Q92693	hg19	CCDS4091.1	0.02	-0.362672	TAGxTTT	COVERED																																																																																			NOVEL	ST8SIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250632.3	4	3.827111	KEEP	0	0	0	13	371	CC	0.994391	0.894269	0		-	5	60	118	0	0	7.816863	33	60	1026	68	ENST00000231461.5	0.131579	0.899314
AP3S1	1176	__UNKNOWN__	__UNKNOWN__	5	115249078	115249078	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs7733604	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:115249078C>T	ENST00000316788.7	+	6	1030	c.473C>T	c.(472-474)cCa>cTa	p.P158L	AP3S1_ENST00000505423.1_3'UTR	NM_001284.2	NP_001275.1	Q92572	AP3S1_HUMAN	adaptor-related protein complex 3, sigma 1 subunit	158		NA	P -> L (in dbSNP:rs7733604).		anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|insulin receptor signaling pathway (GO:0008286)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|AP-type membrane coat adaptor complex (GO:0030119)|Golgi apparatus (GO:0005794)|transport vesicle (GO:0030133)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	12		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;1.08e-07)|Epithelial(69;1.11e-06)|all cancers(49;5.2e-05)		GCAGGAGCTCCAGCCCGTGCT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						58	60	59	NA		NA	NA	5		NA											NA				115249078		2202	4300	6502	SO:0001583	missense			D63643	CCDS4123.1	5q22	2010-06-29			ENSG00000177879	ENSG00000177879	1176			2013	protein-coding gene	gene with protein product		601507		CLAPS3	NA	8697810, 9118953	Standard		NM_001284	NA	Approved		uc003krl.3	Q92572	OTTHUMG00000128887	ENST00000316788.7:c.473C>T	chr5.hg19:g.115249078C>T	ENSP00000325369:p.Pro158Leu	NA	O00647|O00676|O00721|O00727|Q53XL4|Q6ICQ2	hg19	CCDS4123.1	0.02	8.753049	CTCxAGC	COVERED	494	0.2261904761904762	130	0.26422764227642276	77	0.212707182320442	99	0.17307692307692307	188	0.24802110817941952	C	15.31	2.795436	0.50208	.	.	ENSG00000177879	ENST00000316788	T	0.46063	0.88	6.05	5.17	0.71159	.	0.161410	0.56097	D	0.000028	T	0.00012	0.0000	M	0.75777	2.31	0.09310	P	0.99999999918701	B;B	0.20671	0.047;0.047	B;B	0.20384	0.029;0.029	T	0.04268	-1.0964	9	0.48119	T	0.1	-15.07	16.3644	0.83308	0.1331:0.8669:0.0:0.0	rs7733604;rs13163962;rs61457466;rs7733604	158;158	B2R4I8;Q92572	.;AP3S1_HUMAN	L	158	ENSP00000325369:P158L	ENSP00000325369:P158L	P	+	2	0	AP3S1	115276977	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.728000	0.84847	1.540000	0.49301	0.650000	0.86243	CCA	NOVEL	AP3S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250847.2	6	3.414343	KEEP	0	3	90	43	1518	CC	1	1	0		+	9	60	333	0	0	21.580488	195	60	7336	296	ENST00000316788.7	0.044118	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	131409409	131409409	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:131409409G>A			NA	NA				IL3 (10512 upstream) : CSF2 (73 downstream)						NA		NA									NA						TAGTTCCCCCGCCTCCCTGGC	0.493	NA	NA									OREG0003477	type=REGULATORY REGION|Gene=CSF2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.131409409G>A		1587		hg19		0.02	2.138665	CCCxCCT	COVERED																																																																																			NOVEL					0			0	5.394313	KEEP	0	0	0	18	552	GG	0.999859	0.99806	0			12	60	429	0	0	34.389152	62	60	2126	120		0.162162	0.9982
AFF4	27125	__UNKNOWN__	__UNKNOWN__	5	132227522	132227522	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:132227522C>T	ENST00000265343.5	-	13	3017				AFF4_ENST00000378595.3_3'UTR	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	NA		NA			spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ttttaaagttcttttacagac	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(126;889 1733 2942 10745 11605)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364	27125			17869	protein-coding gene	gene with protein product	ALL1 fused gene from 5q31	604417			NA	10588740	Standard	NM_014423	XM_005271963	NA	Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2637+333G>A	chr5.hg19:g.132227522C>T		NA	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	hg19	CCDS4164.1	0.02	3.062233	GTTxTTT	COVERED																																																																																			NOVEL	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133049.1	1	2.25225	KEEP	0	1	9	11	355	CC	0.993634	0.993621	0		-	17	60	230	0	0	11.642721	86	60	2830	133	ENST00000265343.5	0.165049	0.999987
LECT2	3950	__UNKNOWN__	__UNKNOWN__	5	135273154	135273154	__UNKNOWN__	Intron	SNP	T	T	C	rs561382129		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:135273154T>C	ENST00000522943.1	-	3	418				FBXL21_ENST00000467490.1_RNA|FBXL21_ENST00000297158.9_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2	NA		NA			chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)			large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCCTGTGATATACTCTCTCAG	0.408	NA	NA											T|||	1	0.000199681	8e-04	0	5008	,	,	NA	17228	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						91	90	90	NA		NA	NA	5		NA											NA				135273154		1882	4121	6003	SO:0001627	intron_variant			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826	3950			6550	protein-coding gene	gene with protein product		602882			NA	9545637	Standard	NM_002302	NM_002302	NA	Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000522943.1:c.289+13757A>G	chr5.hg19:g.135273154T>C		NA	B2RA90|O14565|Q52M49	hg19		0.02	12.186191	ATAxACT	COVERED																																																																																			NOVEL	LECT2-005	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000381629.1	2	9.62754	KEEP	0	0	0	32	949	TT	0.999997	0.999997	0		-	14	60	541	0	0	36.919127	254	60	9205	380	ENST00000522943.1	0.052239	1
FAM13B	51306	__UNKNOWN__	__UNKNOWN__	5	137281734	137281734	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:137281734T>C	ENST00000033079.3	-	19	2630				FAM13B_ENST00000420893.2_Intron|FAM13B_ENST00000425075.2_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						AAATCTAAAATGTCCAAAACA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						54	50	51	NA		NA	NA	5		NA											NA				137281734		2202	4300	6502	SO:0001627	intron_variant			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003	51306		Rho GTPase activating proteins	1335	protein-coding gene	gene with protein product		609371	chromosome 5 open reading frame 5, family with sequence similarity 13, member B1	C5orf5, FAM13B1	NA	11087669, 11161817	Standard		NM_016603	NA	Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.2179-48A>G	chr5.hg19:g.137281734T>C		NA	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	hg19	CCDS4195.1	0.02	2.189142	AAAxGTC	COVERED																																																																																			NOVEL	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251279.1	4	6.615767	KEEP	0	0	0	22	686	TT	0.999879	0.999741	0		-	14	60	512	0	0	40.988787	76	60	2769	139	ENST00000033079.3	0.155556	0.999862
PCDHA10	56139	__UNKNOWN__	__UNKNOWN__	5	140235919	140235919	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:140235919G>A	ENST00000307360.5	+	1	286	c.286G>A	c.(286-288)Ggg>Agg	p.G96R	PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.G96R|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	96	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGCTGTGCGGGCGGAGCGT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						126	132	130	NA		NA	NA	5		NA											NA				140235919		2198	4277	6475	SO:0001583	missense			AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120	56139		Cadherins / Protocadherins : Clustered	8664	other	complex locus constituent	KIAA0345-like 4, ortholog to mouse CNR8	606316		CNRS8	NA	10380929	Standard	NM_018901	NM_018901	NA	Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.286G>A	chr5.hg19:g.140235919G>A	ENSP00000304234:p.Gly96Arg	NA	A1L493|O75280|Q9NRU2	hg19	CCDS54921.1	0.02	6.69723	TGCxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.11	1.838307	0.32513	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.30981	1.51;1.51	4.27	3.4	0.38934	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.33789	0.0875	M	0.74647	2.275	0.24514	N	0.994192	D;P;P	0.56521	0.976;0.896;0.876	B;B;B	0.41374	0.32;0.355;0.242	T	0.25847	-1.0120	9	0.52906	T	0.07	.	10.6279	0.45519	0.1588:0.0:0.8412:0.0	.	96;96;96	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	R	96	ENSP00000421030:G96R;ENSP00000304234:G96R	ENSP00000304234:G96R	G	+	1	0	PCDHA10	140216103	0.657000	0.27393	1.000000	0.80357	0.961000	0.63080	1.693000	0.37742	1.137000	0.42214	-0.347000	0.07816	GGG	NOVEL	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372895.2	2	11.434908	KEEP	0	0	0	38	1236	GG	1	1	0		+	9	60	335	0	0	22.06715	181	60	6092	250	ENST00000307360.5	0.047368	1
NR3C1	2908	__UNKNOWN__	__UNKNOWN__	5	142680219	142680219	__UNKNOWN__	Silent	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:142680219T>C	ENST00000231509.3	-	5	2072	c.1581A>G	c.(1579-1581)ccA>ccG	p.P527P	NR3C1_ENST00000424646.2_Silent_p.P500P|NR3C1_ENST00000504572.1_Silent_p.P527P|NR3C1_ENST00000394466.2_Silent_p.P527P|NR3C1_ENST00000415690.2_Silent_p.P526P|NR3C1_ENST00000503201.1_Silent_p.P526P|NR3C1_ENST00000394464.2_Silent_p.P526P|NR3C1_ENST00000416954.2_Silent_p.P129P|NR3C1_ENST00000504336.1_5'UTR|NR3C1_ENST00000343796.2_Silent_p.P526P			P04150	GCR_HUMAN	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)	526	Hinge.|Interaction with CLOCK.	NA			adrenal gland development (GO:0030325)|chromatin modification (GO:0016568)|gene expression (GO:0010467)|glucocorticoid metabolic process (GO:0008211)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of glucocorticoid mediated signaling pathway (GO:1900170)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucocorticoid biosynthetic process (GO:0031946)|regulation of gluconeogenesis (GO:0006111)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	glucocorticoid receptor activity (GO:0004883)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|zinc ion binding (GO:0008270)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	35		Acute lymphoblastic leukemia(2;3.2e-05)|all_hematologic(2;0.000361)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)		Alclometasone(DB00240)|Amcinonide(DB00288)|Beclomethasone(DB00394)|Betamethasone(DB00443)|Budesonide(DB01222)|Ciclesonide(DB01410)|Clobetasol propionate(DB01013)|Clocortolone(DB00838)|Cortisone acetate(DB01380)|Desonide(DB01260)|Desoximetasone(DB00547)|Dexamethasone(DB01234)|Diflorasone(DB00223)|Difluprednate(DB06781)|Fludrocortisone(DB00687)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Fluoxymesterone(DB01185)|Flurandrenolide(DB00846)|Fluticasone furoate(DB08906)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Loteprednol(DB00873)|Medrysone(DB00253)|Megestrol acetate(DB00351)|Methylprednisolone(DB00959)|Mifepristone(DB00834)|Mometasone(DB00764)|Paramethasone(DB01384)|Prednicarbate(DB01130)|Prednisolone(DB00860)|Prednisone(DB00635)|Rimexolone(DB00896)|Spironolactone(DB00421)|Triamcinolone(DB00620)	GGGTGAGTTGTGGTAACGTTG	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						214	195	201	NA		NA	NA	5		NA											NA				142680219		2203	4300	6503	SO:0001819	synonymous_variant			X03225	CCDS4278.1, CCDS34258.1, CCDS47298.1	5q31-q32	2013-01-16	2002-08-27		ENSG00000113580	ENSG00000113580	2908		Nuclear hormone receptors	7978	protein-coding gene	gene with protein product		138040	nuclear receptor subfamily 3, group C, member 1	GRL	NA	2867473	Standard		NM_001204258	NA	Approved	GR	uc003lnb.3	P04150	OTTHUMG00000129677	ENST00000231509.3:c.1581A>G	chr5.hg19:g.142680219T>C		NA	A0ZXF9|B0LPG8|D3DQF4|P04151|Q53EP5|Q6N0A4	hg19	CCDS34258.1	0.02	14.452711	TTGxGGT	COVERED																																																																																			NOVEL	NR3C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251879.1	5	14.435457	KEEP	0	0	0	48	1439	TT	1	1	0		-	56	60	1981	0	0	160.718898	260	60	9698	459	ENST00000231509.3	0.177215	1
PDGFRB	5159	__UNKNOWN__	__UNKNOWN__	5	149513611	149513611	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:149513611A>C	ENST00000261799.4	-	5	1101					NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	NA		NA			adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGAAGTCACCACCAGCCACTA	0.488	NA	NA	T	ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP	MPD, AML, CMML, CML									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		5	5q31-q32	5159	platelet-derived growth factor receptor, beta polypeptide		L	0							NA						74	68	70	NA		NA	NA	5		NA											NA				149513611		2203	4300	6503	SO:0001627	intron_variant			M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721	5159		CD molecules, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	8804	protein-coding gene	gene with protein product		173410		PDGFR	NA		Standard	NM_002609	XM_005268464	NA	Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.632-40T>G	chr5.hg19:g.149513611A>C		NA	B5A957|Q8N5L4	hg19	CCDS4303.1	0.02	3.143801	ACCxCCA	COVERED																																																																																			NOVEL	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252332.1	4	2.632204	KEEP	0	6	43	25	671	AA	0.999997	0.999997	0		-	16	60	272	0	0	9.844866	245	60	6988	367	ENST00000261799.4	0.061303	1
CCDC69	26112	__UNKNOWN__	__UNKNOWN__	5	150603312	150603312	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:150603312T>G	ENST00000355417.2	-	1	223				CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	NA		NA								haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CGGGCCGGGGTAAAGGGCGCC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624	26112			24487	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_015621	NM_015621	NA	Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.48+171A>C	chr5.hg19:g.150603312T>G		NA	A8K9X6	hg19	CCDS4312.1	0.02	2.081573	GGGxAAA	COVERED																																																																																			NOVEL	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252435.1	0	2.804855	KEEP	0	5	56	30	685	TT	0.999999	0.986152	0		-	12	60	164	0	0	9.544192	46	60	1231	123	ENST00000355417.2	0.206897	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	150632415	150632415	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:150632415G>A			NA	NA				CCDC69 (28709 upstream) : GM2A (37 downstream)						NA		NA									NA						tcccgcgcgcgcagctccgcc	0.766	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.150632415G>A		NA		hg19		0.02	-0.40107	CGCxCAG	COVERED																																																																																			NOVEL					0			3	8.715494	KEEP	0	0	0	29	860	GG	0.999997	0.934489	0			11	60	289	0	0	23.178963	35	60	1043	80		0.23913	0.934492
NMUR2	56923	__UNKNOWN__	__UNKNOWN__	5	151775035	151775035	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs200217677		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:151775035C>T	ENST00000255262.3	-	3	1087	c.922G>A	c.(922-924)Gtc>Atc	p.V308I		NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	308		NA			activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			ACCACATGGACGAGGTTGAAC	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						161	138	146	NA		NA	NA	5		NA											NA				151775035		2203	4300	6503	SO:0001583	missense			AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911	56923		GPCR / Class A : Neuromedin U receptors	16454	protein-coding gene	gene with protein product		605108		NMU2R	NA	8940772, 10894543	Standard	NM_020167	NM_020167	NA	Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.922G>A	chr5.hg19:g.151775035C>T	ENSP00000255262:p.Val308Ile	NA	Q7LC54|Q96AM5|Q9NRA6	hg19	CCDS4321.1	0.02	9.218248	GGAxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	3.194	-0.165148	0.06461	.	.	ENSG00000132911	ENST00000255262	T	0.37058	1.22	5.8	-1.33	0.09172	GPCR, rhodopsin-like superfamily (1);	0.288600	0.34088	N	0.004277	T	0.21631	0.0521	L	0.31420	0.93	0.20196	N	0.999928	B	0.16166	0.016	B	0.12156	0.007	T	0.24905	-1.0147	10	0.16896	T	0.51	-20.6769	11.7365	0.51767	0.0:0.3467:0.0:0.6533	.	308	Q9GZQ4	NMUR2_HUMAN	I	308	ENSP00000255262:V308I	ENSP00000255262:V308I	V	-	1	0	NMUR2	151755228	0.989000	0.36119	0.946000	0.38457	0.108000	0.19459	1.557000	0.36299	-0.395000	0.07715	-2.086000	0.00376	GTC	NOVEL	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252439.1	3	9.326364	KEEP	0	0	0	31	1062	CC	0.999997	0.999997	0		-	12	60	447	0	0	29.675282	231	60	8462	352	ENST00000255262.3	0.049383	1
DOCK2	1794	__UNKNOWN__	__UNKNOWN__	5	169108734	169108734	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:169108734T>C	ENST00000256935.8	+	7	550					NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	NA		NA			actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TCACCTCCAGTTTTTGCTTTA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						129	125	127	NA		NA	NA	5		NA											NA				169108734		2203	4300	6503	SO:0001627	intron_variant			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516	1794			2988	protein-coding gene	gene with protein product		603122	dedicator of cyto-kinesis 2		NA		Standard	NM_004946	NM_004946	NA	Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.471-14T>C	chr5.hg19:g.169108734T>C		NA	Q2M3I0|Q96AK7	hg19	CCDS4371.1	0.02	17.760026	CAGxTTT	COVERED																																																																																			NOVEL	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252828.2	2	9.626492	KEEP	0	0	0	32	968	TT	0.999997	0.999997	0		+	63	60	2384	0	0	194.267908	318	60	11369	512	ENST00000256935.8	0.165354	1
RP11-91H12.4	0	__UNKNOWN__	__UNKNOWN__	5	175353584	175353584	__UNKNOWN__	RNA	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:175353584A>T	ENST00000502813.1	-	0	87										NA		NA									NA						atgtatttttaaaaaactaca	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502813.1:	chr5.hg19:g.175353584A>T		NA		hg19		0.02	18.520879	TTTxAAA	COVERED																																																																																			NOVEL	RP11-91H12.4-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000470921.1	6	8.490948	KEEP	78	2	59	49	1491	AA	1	1	0		-	16	40	582	0	0	35.793603	437	60	15761	690	ENST00000502813.1	0.03532	1
FAM153C	653316	__UNKNOWN__	__UNKNOWN__	5	177474257	177474257	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:177474257G>A	ENST00000511189.1	+	10	591				FAM153C_ENST00000507848.1_Intron|FAM153C_ENST00000398106.2_3'UTR			Q494X1	F153C_HUMAN	family with sequence similarity 153, member C	NA		NA								kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGTGCTGGTCGCACCCCCATG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC101338		5q35.3	2008-01-09				ENSG00000204677	653316			33936	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001079527	NR_038353	NA	Approved	NY-REN-7-like	uc011dge.2	Q494X1		ENST00000511189.1:c.519+123G>A	chr5.hg19:g.177474257G>A		NA	A4IF33|B2RUV5|B7ZW12	hg19		0.02	-0.412319	GTCxCAC	COVERED																																																																																			NOVEL	FAM153C-005	NOVEL	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000373559.1	2	4.502029	KEEP	20	0	0	15	496	GG	0.994391	0.936459	0		+	4	31	143	0	0	10.268885	43	60	1555	95	ENST00000511189.1	0.085106	0.941741
COL23A1	91522	__UNKNOWN__	__UNKNOWN__	5	178012707	178012707	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr5:178012707C>A	ENST00000390654.3	-	1	652					NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	NA		NA			collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		GCCCTACAGCCCTGGATGGCG	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767	91522		Collagens	22990	protein-coding gene	gene with protein product		610043			NA	12644459	Standard	NM_173465	NM_173465	NA	Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.294+4197G>T	chr5.hg19:g.178012707C>A		NA	Q8IVR4|Q9NT93	hg19	CCDS4436.1	0.02	-0.429751	AGCxCTG	COVERED																																																																																			NOVEL	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253475.1	2	5.718418	KEEP	4	0	0	19	654	CC	0.99986	0.954357	0		-	3	60	103	0	0	7.927488	19	60	659	122	ENST00000390654.3	0.136364	0.954491
IRF4	3662	__UNKNOWN__	__UNKNOWN__	6	397027	397027	__UNKNOWN__	Intron	SNP	C	C	T	rs4959828		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:397027C>T	ENST00000380956.4	+	5	618				IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CCAGTGCTTCCTATCTCAGCC	0.542	NA	NA	T	IGH@	MM									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265	3662			6119	protein-coding gene	gene with protein product		601900		MUM1	NA	8921401, 18417578	Standard		NM_002460	NA	Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.493-81C>T	chr6.hg19:g.397027C>T		NA	Q5VUI7|Q99660	hg19	CCDS4469.1	0.02	12.317534	TTCxTAT	COVERED																																																																																			NOVEL	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043638.1	2	8.425884	KEEP	6	0	0	28	928	CC	0.999997	0.999997	0		+	10	30	392	0	0	25.307992	266	60	9348	332	ENST00000380956.4	0.036232	1
IRF4	3662	__UNKNOWN__	__UNKNOWN__	6	397079	397079	__UNKNOWN__	Intron	SNP	T	T	C	rs6941792		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:397079T>C	ENST00000380956.4	+	5	618				IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CCAGTGCTTCTTATCTCAGCC	0.577	NA	NA	T	IGH@	MM									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	0							NA						81	85	84	NA		NA	NA	6		NA											NA				397079		2203	4300	6503	SO:0001627	intron_variant			U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265	3662			6119	protein-coding gene	gene with protein product		601900		MUM1	NA	8921401, 18417578	Standard		NM_002460	NA	Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.493-29T>C	chr6.hg19:g.397079T>C		NA	Q5VUI7|Q99660	hg19	CCDS4469.1	0.02	24.752937	TTCxTAT	COVERED																																																																																			NOVEL	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043638.1	2	15.317457	KEEP	5	5	181	114	3465	TT	1	1	0		+	21	40	820	0	0	54.117684	483	60	18106	713	ENST00000380956.4	0.041667	1
TMEM14B	81853	__UNKNOWN__	__UNKNOWN__	6	10756728	10756728	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs72821581	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:10756728C>T	ENST00000379542.5	+	6	489	c.322C>T	c.(322-324)Cgt>Tgt	p.R108C	TMEM14B_ENST00000473276.1_Missense_Mutation_p.S48L|RP11-637O19.3_ENST00000480294.1_Intron|SYCP2L_ENST00000543878.1_Intron|TMEM14B_ENST00000491103.1_3'UTR|TMEM14B_ENST00000467317.1_Intron|TMEM14B_ENST00000379530.3_Missense_Mutation_p.R74C|TMEM14B_ENST00000481240.1_Intron	NM_030969.3	NP_112231.3	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B	108		NA				integral component of membrane (GO:0016021)		p.R108C(4)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(2)|skin(2)	11	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				AGTTGGAGTTCGTATGTTGAT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				4	Substitution - Missense(4)	skin(2)|NS(1)|prostate(1)					NA						162	139	147	NA		NA	NA	6		NA											NA				10756728		2203	4300	6503	SO:0001583	missense			AL024498	CCDS4515.1, CCDS47372.1, CCDS75395.1, CCDS75396.1, CCDS75397.1	6p25.1-p23	2008-08-12			ENSG00000137210	ENSG00000137210	81853			21384	protein-coding gene	gene with protein product		NA			NA		Standard	NM_030969	NM_030969	NA	Approved	MGC1223	uc003mzk.4	Q9NUH8	OTTHUMG00000014246	ENST00000379542.5:c.322C>T	chr6.hg19:g.10756728C>T	ENSP00000368858:p.Arg108Cys	NA	Q5THN7|Q5THN8|Q96IX7|Q9BVN8	hg19	CCDS4515.1	0.02	7.902754	GTTxGTA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.745|5.745	0.321925|0.321925	0.10900|0.10900	.|.	.|.	ENSG00000137210|ENSG00000137210	ENST00000472062;ENST00000379542;ENST00000379530|ENST00000473276	T;T|T	0.26660|0.56941	2.12;1.72|0.43	3.75|3.75	1.3|1.3	0.21679|0.21679	.|.	0.473115|.	0.27366|.	N|.	0.019688|.	T|T	0.39517|0.39517	0.1081|0.1081	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	P;P|.	0.49635|.	0.926;0.917|.	B;B|.	0.42653|.	0.226;0.394|.	T|T	0.36359|0.36359	-0.9751|-0.9751	10|7	0.56958|0.87932	D|D	0.05|0	.|.	9.9351|9.9351	0.41545|0.41545	0.4256:0.5744:0.0:0.0|0.4256:0.5744:0.0:0.0	.|.	74;108|.	Q5THN7;Q9NUH8|.	.;TM14B_HUMAN|.	C|L	108;108;74|48	ENSP00000368858:R108C;ENSP00000368845:R74C|ENSP00000420580:S48L	ENSP00000368845:R74C|ENSP00000420580:S48L	R|S	+|+	1|2	0|0	TMEM14B|TMEM14B	10864714|10864714	0.007000|0.007000	0.16637|0.16637	0.210000|0.210000	0.23637|0.23637	0.087000|0.087000	0.18053|0.18053	1.323000|1.323000	0.33701|0.33701	0.291000|0.291000	0.22468|0.22468	-1.051000|-1.051000	0.02340|0.02340	CGT|TCG	NOVEL	TMEM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039836.1	4	7.524341	KEEP	0	0	0	25	870	CC	0.999931	0.999931	0		+	7	60	242	0	0	14.210597	204	60	7297	304	ENST00000379542.5	0.033175	1
DTNBP1	84062	__UNKNOWN__	__UNKNOWN__	6	15595459	15595459	__UNKNOWN__	Intron	SNP	G	G	A	rs148020371		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:15595459G>A	ENST00000344537.5	-	7	661				DTNBP1_ENST00000355917.3_Intron|DTNBP1_ENST00000338950.5_Intron	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	NA		NA			actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			TTGGTTTAAAGAAAAAAATCA	0.348	NA	NA							Hermansky-Pudlak syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	HPS, HPS1-8	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579	84062		Biogenesis of lysosomal organelles complex-1 subunits	17328	protein-coding gene	gene with protein product	dysbindin-1, biogenesis of lysosomal organelles complex-1, subunit 8	607145			NA	11316798	Standard	NM_032122	NM_032122	NA	Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.489-2147C>T	chr6.hg19:g.15595459G>A		NA	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	hg19	CCDS4534.1	0.02	5.050464	AAAxAAA	COVERED																																																																																			NOVEL	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039933.2	0	3.579241	KEEP	0	2	48	29	1015	GG	0.999997	0.999997	0		-	16	60	352	0	0	18.496247	201	60	7233	296	ENST00000344537.5	0.073733	1
DTNBP1	84062	__UNKNOWN__	__UNKNOWN__	6	15662932	15662932	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:15662932T>G	ENST00000344537.5	-	1	229				DTNBP1_ENST00000355917.3_Intron|DTNBP1_ENST00000338950.5_Intron	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	NA		NA			actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			ggcggggaggtgcgggacagg	0.731	NA	NA							Hermansky-Pudlak syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	HPS, HPS1-8	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579	84062		Biogenesis of lysosomal organelles complex-1 subunits	17328	protein-coding gene	gene with protein product	dysbindin-1, biogenesis of lysosomal organelles complex-1, subunit 8	607145			NA	11316798	Standard	NM_032122	NM_032122	NA	Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.56+112A>C	chr6.hg19:g.15662932T>G		NA	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	hg19	CCDS4534.1	0.02	0.412538	AGGxGCG	COVERED																																																																																			NOVEL	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039933.2	2	5.21398	KEEP	0	7	43	34	754	TT	1	0.99994	0		-	28	60	207	0	0	8.451018	67	60	1637	189	ENST00000344537.5	0.294737	0.99994
ATXN1	6310	__UNKNOWN__	__UNKNOWN__	6	16306794	16306794	__UNKNOWN__	Silent	SNP	G	G	A	rs377559897		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:16306794G>A	ENST00000244769.4	-	9	3150	c.2214C>T	c.(2212-2214)ctC>ctT	p.L738L	ATXN1_ENST00000436367.1_Silent_p.L738L	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	738	Interaction with USP7.|RNA-binding.	NA			adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				CATTCTCAGAGAGCATCTGGG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						86	83	84	NA		NA	NA	6		NA											NA				16306794		2203	4300	6503	SO:0001819	synonymous_variant			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788	6310		Ataxins	10548	protein-coding gene	gene with protein product		601556	spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)	SCA1	NA	1582256	Standard	NM_000332	NM_000332	NA	Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.2214C>T	chr6.hg19:g.16306794G>A		NA	Q17S02|Q9UJG2|Q9Y4J1	hg19	CCDS34342.1	0.02	26.351658	AGAxAGC	COVERED																																																																																			NOVEL	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039943.3	2	74.929762	KEEP	0	0	0	249	8869	GG	1	1	0		-	96	60	3522	0	0	284.019447	497	60	19254	1057	ENST00000244769.4	0.161889	1
FAM65B	9750	__UNKNOWN__	__UNKNOWN__	6	24843660	24843660	__UNKNOWN__	Silent	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:24843660G>C	ENST00000259698.4	-	14	1525	c.1350C>G	c.(1348-1350)tcC>tcG	p.S450S	FAM65B_ENST00000510784.2_Silent_p.S434S|FAM65B_ENST00000378023.4_Silent_p.S400S|FAM65B_ENST00000538035.1_Silent_p.S429S|FAM65B_ENST00000540914.1_Silent_p.S400S	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	450		NA			cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						AGTTGGAAGGGGAGCCTGTTG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						90	90	90	NA		NA	NA	6		NA											NA				24843660		1994	4156	6150	SO:0001819	synonymous_variant			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913	9750			13872	protein-coding gene	gene with protein product	myogenesis-related and NCAM-associated protein homolog (chicken)	611410	chromosome 6 open reading frame 32	C6orf32	NA	9205841, 17150207, 17825087	Standard		NM_001286447	NA	Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.1350C>G	chr6.hg19:g.24843660G>C		NA	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	hg19	CCDS47383.1	0.02	4.722296	AGGxGAG	COVERED																																																																																			NOVEL	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040024.2	3	6.319529	KEEP	0	0	0	21	694	GG	0.999869	0.999868	0		-	28	60	956	0	0	80.765783	91	60	3285	158	ENST00000259698.4	0.235294	0.999999
RP11-367G6.3	0	__UNKNOWN__	__UNKNOWN__	6	25042253	25042253	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:25042253G>A	ENST00000606385.1	-	0	145				RP3-425P12.5_ENST00000428903.1_RNA						NA		NA									NA						AAATGAAAAAGAAAACTTAAC	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000606385.1:	chr6.hg19:g.25042253G>A		NA		hg19		0.02	3.578418	AAAxAAA	COVERED																																																																																			NOVEL	RP11-367G6.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000471007.1	3	2.297184	KEEP	0	2	25	17	573	GG	0.99986	0.999841	0		-	7	70	187	0	0	11.148099	96	70	3097	141	ENST00000606385.1	0.067961	0.999981
HIST1H2BK	85236	__UNKNOWN__	__UNKNOWN__	6	27114425	27114425	__UNKNOWN__	Silent	SNP	G	G	A	rs202101103		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:27114425G>A	ENST00000356950.1	-	1	152	c.153C>T	c.(151-153)ccC>ccT	p.P51P	HIST1H2BK_ENST00000396891.4_Silent_p.P51P			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	51		NA			antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						TGCCGGTGTCGGGGTGGACCT	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						111	97	102	NA		NA	NA	6		NA											NA				27114425		2203	4295	6498	SO:0001819	synonymous_variant			AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903	85236		Histones / Replication-dependent	13954	protein-coding gene	gene with protein product		615045	H2B histone family, member T, histone 1, H2bk	H2BFT	NA	12408966	Standard	NM_080593	NM_080593	NA	Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.153C>T	chr6.hg19:g.27114425G>A		NA	A8K7P7|Q2VPI7	hg19	CCDS4621.1	0.02	13.068131	GTCxGGG	COVERED																																																																																			NOVEL	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040141.1	4	9.905186	KEEP	26	14	448	190	6306	GG	1	1	0		-	31	50	1221	0	0	95.206477	237	60	8258	621	ENST00000356950.1	0.115672	1
DHX16	8449	__UNKNOWN__	__UNKNOWN__	6	30633177	30633177	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:30633177C>T	ENST00000376442.3	-	5	1117					NM_001164239.1|NM_003587.4	NP_001157711.1|NP_003578.2	O60231	DHX16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 16	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			kidney(2)|ovary(2)	4						GGATGACCCACGTGTTGCCCA	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB001601	CCDS4685.1	6p21.3	2010-02-17	2003-06-13	2003-06-20	ENSG00000204560	ENSG00000204560	8449		DEAH-boxes	2739	protein-coding gene	gene with protein product		603405	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 16	DDX16	NA	9547260	Standard	NM_003587	NM_003587	NA	Approved	DBP2, Prp2, PRPF2	uc003nqz.3	O60231	OTTHUMG00000031060	ENST00000376442.3:c.921+78G>A	chr6.hg19:g.30633177C>T		NA	O60322|Q5JP45|Q969X7|Q96QC1	hg19	CCDS4685.1	0.02	2.112078	CCAxGTG	COVERED																																																																																			NOVEL	DHX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076076.2	5	5.115872	KEEP	0	0	0	17	569	CC	0.999366	0.998235	0		-	29	60	1035	0	0	95.185089	48	60	1752	97	ENST00000376442.3	0.376623	0.998867
C4A	720	__UNKNOWN__	__UNKNOWN__	6	31964228	31964228	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs577596183		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:31964228A>G	ENST00000428956.2	+	28	3611	c.3527A>G	c.(3526-3528)aAc>aGc	p.N1176S	C4A_ENST00000498271.1_Missense_Mutation_p.N1176S	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1176		NA	N -> S (in allotype C4A1; dbSNP:rs17874654). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:3696167, ECO:0000269|Ref.3, ECO:0000269|Ref.8}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)				NA					Intravenous Immunoglobulin(DB00028)	TCAAAGGCAAACTCATTTTTG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						90	102	98	NA		NA	NA	6		NA											NA				31964228		1555	3540	5095	SO:0001583	missense			L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731	720		Blood group antigens, Complement system	1323	protein-coding gene	gene with protein product		120810	complement component 4A		NA		Standard	NM_007293	NM_001252204	NA	Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3527A>G	chr6.hg19:g.31964228A>G	ENSP00000396688:p.Asn1176Ser	NA	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	hg19	CCDS47404.1	0.02	1.950878	CAAxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	a	1.772	-0.484018	0.04383	.	.	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.36340	1.26;1.26	3.47	2.24	0.28232	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.09247	0.0228	L	0.48642	1.525	0.09310	P	0.999999896602	B;B	0.11235	0.004;0.004	B;B	0.23150	0.044;0.044	T	0.30001	-0.9993	8	0.05351	T	0.99	.	6.9466	0.24522	0.7642:0.2358:0.0:0.0	rs2746414	1176;1176	A6H8M8;P0C0L4	.;CO4A_HUMAN	S	1176	ENSP00000396688:N1176S;ENSP00000420212:N1176S	ENSP00000396688:N1176S	N	+	2	0	C4A	32072207	0.016000	0.18221	0.755000	0.31263	0.803000	0.45373	1.116000	0.31221	0.338000	0.23692	0.338000	0.21704	AAC	NOVEL	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076364.3	0	4.448825	KEEP	0	1	38	28	879	AA	0.999997	0.999556	0		+	6	40	228	0	0	16.277431	78	60	2723	125	ENST00000428956.2	0.071429	0.999559
CYP21A2	1589	__UNKNOWN__	__UNKNOWN__	6	32008123	32008123	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:32008123C>T	ENST00000418967.2	+	8	1097				CYP21A2_ENST00000435122.2_Intron	NM_000500.7	NP_000491.4	P08686	CP21A_HUMAN	cytochrome P450, family 21, subfamily A, polypeptide 2	NA		NA			glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 21-monooxygenase activity (GO:0004509)|steroid binding (GO:0005496)|steroid hydroxylase activity (GO:0008395)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	11					Ketoconazole(DB01026)	GCTGAGGGAGCGGCTGGAGGC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(174;1669 1998 3915 34700 46447)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X58906	CCDS4735.1, CCDS47406.1	6p21.3	2014-09-17	2003-01-14		ENSG00000231852	ENSG00000231852	1589	1.14.99.10	Cytochrome P450s	2600	protein-coding gene	gene with protein product	Steroid 21-monooxygenase	613815	cytochrome P450, subfamily XXIA (steroid 21-hydroxylase, congenital adrenal hyperplasia), polypeptide 2	CYP21, CYP21B	NA		Standard	NM_000500	NM_000500	NA	Approved	P450c21B, CA21H, CPS1, CAH1	uc021yvd.1	P08686	OTTHUMG00000031069	ENST00000418967.2:c.940-60C>T	chr6.hg19:g.32008123C>T		NA	A2BHY6|P04033|Q01204|Q08AG8|Q16749|Q16806|Q5ST44|Q96NU8	hg19	CCDS4735.1	0.02	4.123335	GAGxGGC	COVERED																																																																																			NOVEL	CYP21A2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268768.2	2	11.663756	KEEP	12	1	23	47	1503	CC	1	0.999999	0		+	8	27	281	0	0	19.157513	112	50	3999	191	ENST00000418967.2	0.066667	0.999999
PPT2	9374	__UNKNOWN__	__UNKNOWN__	6	32121459	32121459	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:32121459T>G	ENST00000395523.1	+	1	60				PPT2_ENST00000361568.2_Intron			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	NA		NA			cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						GTGGGGTGGGTGTTGAGGGGC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	9374	3.1.2.22		9326	protein-coding gene	gene with protein product		603298			NA	9341199, 10051407	Standard	NM_138717	NM_138717	NA	Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000395523.1:c.-415+46T>G	chr6.hg19:g.32121459T>G		NA	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	hg19	CCDS4742.1	0.02	1.402982	GGGxGTT	COVERED																																																																																			NOVEL	PPT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076549.2	0	6.659586	KEEP	0	7	66	47	1216	TT	1	0.981955	0		+	8	60	141	0	0	8.306928	49	60	1285	144	ENST00000395523.1	0.140351	0.981955
HLA-DRB5	3127	__UNKNOWN__	__UNKNOWN__	6	32497905	32497905	__UNKNOWN__	Silent	SNP	G	G	T	rs71549219	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:32497905G>T	ENST00000374975.3	-	1	159	c.97C>A	c.(97-99)Cga>Aga	p.R33R		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5	NA		NA								NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CACTTACGTCGGGTGTCCCCA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						102	104	103	NA		NA	NA	6		NA											NA				32497905		2203	4300	6503	SO:0001819	synonymous_variant				CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502	3127		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4953	protein-coding gene	gene with protein product		604776			NA		Standard	NM_002125	NM_002125	NA	Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.97C>A	chr6.hg19:g.32497905G>T		NA		hg19	CCDS4751.1	0.02	7.404686	GTCxGGT	COVERED																																																																																			NOVEL	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076022.2	3	3.344992	KEEP	3	1	28	21	737	AG	0.999998	0.999998	0		-	16	60	605	0	0	57.660694	19	60	613	284	ENST00000374975.3	0.457143	1
HLA-DQA2	3118	__UNKNOWN__	__UNKNOWN__	6	32713784	32713784	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs62619945	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:32713784C>A	ENST00000374940.3	+	3	650	c.548C>A	c.(547-549)gCt>gAt	p.A183D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	183	Alpha-2.|Ig-like C1-type.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"Insulin(DB00071)	CTCCCTTCTGCTGATGAGATT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						190	211	203	NA		NA	NA	6		NA											NA				32713784		1511	2707	4218	SO:0001583	missense				CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541	3118		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4943	protein-coding gene	gene with protein product		613503		HLA-DXA	NA		Standard	NM_020056	NM_020056	NA	Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.548C>A	chr6.hg19:g.32713784C>A	ENSP00000364076:p.Ala183Asp	NA	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	hg19	CCDS4753.1	0.02	9.155635	CTGxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	.	3.489	-0.104314	0.06967	.	.	ENSG00000237541	ENST00000374940	T	0.02890	4.12	3.06	-0.376	0.12505	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.680175	0.13893	N	0.355519	T	0.00695	0.0023	N	0.21324	0.655	0.22112	N	0.999352	B	0.14805	0.011	B	0.20184	0.028	T	0.42258	-0.9462	10	0.19590	T	0.45	.	10.1342	0.42697	0.7082:0.2918:0.0:0.0	rs62619945	183	P01906	DQA2_HUMAN	D	183	ENSP00000364076:A183D	ENSP00000364076:A183D	A	+	2	0	HLA-DQA2	32821762	0.000000	0.05858	0.960000	0.40013	0.740000	0.42216	-1.389000	0.02530	-0.242000	0.09667	0.174000	0.16983	GCT	NOVEL	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076179.2	17	2.276763	KEEP	6	2	61	29	1020	CC	0.999997	0.999997	0		+	11	49	403	0	0	27.465718	173	60	6324	296	ENST00000374940.3	0.059783	1
FGD2	221472	__UNKNOWN__	__UNKNOWN__	6	36982409	36982409	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:36982409C>G	ENST00000274963.8	+	7	994					NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	NA		NA			actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						AACTCCGGCCCTGCCCCTTTC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						58	61	60	NA		NA	NA	6		NA											NA				36982409		2203	4300	6503	SO:0001627	intron_variant			AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192	221472		Zinc fingers, FYVE domain containing, Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	3664	protein-coding gene	gene with protein product		605091	FGD1 family, member 2		NA	10458911	Standard	NM_173558	NM_173558	NA	Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.824-13C>G	chr6.hg19:g.36982409C>G		NA	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	hg19	CCDS4829.1	0.02	10.786228	GCCxTGC	COVERED																																																																																			NOVEL	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040398.2	1	33.706798	KEEP	0	0	0	112	4000	CC	1	1	0		+	14	60	489	0	1	31.219092	277	60	10455	545	ENST00000274963.8	0.04811	1
TFAP2D	83741	__UNKNOWN__	__UNKNOWN__	6	50719059	50719059	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:50719059G>T	ENST00000008391.3	+	7	1367					NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)	NA		NA								NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					TTTCCAGTTTGCTCAAATTCT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						71	61	64	NA		NA	NA	6		NA											NA				50719059		2203	4299	6502	SO:0001627	intron_variant			AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197	83741			15581	protein-coding gene	gene with protein product		610161	transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1	TFAP2BL1	NA	11733187	Standard	NM_172238	NM_172238	NA	Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.1139+22G>T	chr6.hg19:g.50719059G>T		NA		hg19	CCDS4933.1	0.02	16.113719	TTTxCTC	COVERED																																																																																			NOVEL	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040881.1	3	14.447622	KEEP	0	0	0	48	1747	GG	1	1	0		+	23	60	847	0	0	57.496375	376	60	14063	532	ENST00000008391.3	0.057644	1
PRIM2	5558	__UNKNOWN__	__UNKNOWN__	6	57415804	57415804	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:57415804T>C	ENST00000389488.2	+	10	1107				PRIM2_ENST00000607273.1_Intron			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	NA		NA			DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		caggcttgtctggaactcctg	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143	5558			9370	protein-coding gene	gene with protein product		176636	primase, polypeptide 2A (58kD), primase, polypeptide 2A, 58kDa	PRIM2A	NA	8530050, 20675616	Standard	NM_000947	NM_001282487	NA	Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.1107+17487T>C	chr6.hg19:g.57415804T>C		NA	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	hg19		0.02	-0.122809	GTCxGGA	COVERED																																																																																			NOVEL	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000043468.3	0	2.406203	KEEP	0	0	0	8	238	TT	0.99257	0.194853	0		+	5	60	173	0	0	15.722062	9	60	334	30	ENST00000389488.2	0.357143	0.196312
PRIM2	5558	__UNKNOWN__	__UNKNOWN__	6	57512974	57512974	__UNKNOWN__	3'UTR	SNP	G	G	A	rs74695174	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:57512974G>A	ENST00000389488.2	+	0	1889				PRIM2_ENST00000607273.1_3'UTR			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	NA		NA			DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		agactgctgggctcaagcgat	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143	5558			9370	protein-coding gene	gene with protein product		176636	primase, polypeptide 2A (58kD), primase, polypeptide 2A, 58kDa	PRIM2A	NA	8530050, 20675616	Standard	NM_000947	NM_001282487	NA	Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.*1886G>A	chr6.hg19:g.57512974G>A		NA	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	hg19		0.02	-0.236835	TGGxCTC	COVERED																																																																																			NOVEL	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000043468.3	5	3.912794	KEEP	0	0	0	13	460	GG	0.994391	0.608972	0		+	3	60	106	0	0	8.872924	11	60	395	47	ENST00000389488.2	0.214286	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58776517	58776517	__UNKNOWN__	IGR	SNP	G	G	C	rs9500442	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58776517G>C			NA	NA				RP11-143A22.1 (262657 upstream) : None (None downstream)						NA		NA									NA						tgtttttgtagtatttccaag	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58776517G>C		NA		hg19		0.02	6.925521	GTAxTAT	COVERED																																																																																			NOVEL					0			16	5.364837	KEEP	17	4	153	71	2542	GG	1	1	0			10	60	345	0	0	22.206026	185	60	7135	363		0.051282	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58776555	58776555	__UNKNOWN__	IGR	SNP	T	T	C	rs4928523	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58776555T>C			NA	NA				RP11-143A22.1 (262695 upstream) : None (None downstream)						NA		NA									NA						ttgaagcctatgctagaaatg	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58776555T>C		NA		hg19		0.02	7.926689	CTAxGCT	COVERED																																																																																			NOVEL					0			13	10.527231	KEEP	0	3	112	74	2236	TT	1	1	0			7	60	246	0	0	14.327598	224	60	8334	390		0.030303	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777160	58777160	__UNKNOWN__	IGR	SNP	C	C	G	rs28821267		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58777160C>G			NA	NA				RP11-143A22.1 (263300 upstream) : None (None downstream)						NA		NA									NA						tgaaacctcccttttcacaga	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777160C>G		NA		hg19		0.02	6.29343	TCCxTTT	COVERED																																																																																			NOVEL					0			11	10.068646	KEEP	0	1	36	46	1628	CC	1	1	0			8	60	290	0	0	19.581839	129	60	4845	291		0.058394	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777451	58777451	__UNKNOWN__	IGR	SNP	T	T	A	rs4388317		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58777451T>A			NA	NA				RP11-143A22.1 (263591 upstream) : None (None downstream)						NA		NA									NA						agaagcaatctcagaaactac	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777451T>A		NA		hg19		0.02	6.091954	ATCxCAG	COVERED																																																																																			NOVEL					0			13	8.74663	KEEP	0	4	116	70	2151	TT	1	1	0			7	60	255	0	0	16.247664	159	60	5892	313		0.042169	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777790	58777790	__UNKNOWN__	IGR	SNP	C	C	G	rs4928379	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58777790C>G			NA	NA				RP11-143A22.1 (263930 upstream) : None (None downstream)						NA		NA									NA						tagaatcattctcagaaacaa	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777790C>G		NA		hg19		0.02	4.676251	ATTxTCA	COVERED																																																																																			NOVEL					0			5	2.479539	KEEP	1	2	71	33	1147	CC	0.999998	0.999998	0			8	60	303	0	0	20.803264	132	60	4948	225		0.057143	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58778718	58778718	__UNKNOWN__	IGR	SNP	T	T	C	rs9638017	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58778718T>C			NA	NA				RP11-143A22.1 (264858 upstream) : None (None downstream)						NA		NA									NA						tttgaaacactgtttttgtag	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58778718T>C		NA		hg19		0.02	5.744607	CACxGTT	COVERED																																																																																			NOVEL					0			13	4.615505	KEEP	2	3	102	51	1569	TT	1	1	0			8	60	272	0	0	17.344399	147	60	5503	258		0.051613	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58779131	58779131	__UNKNOWN__	IGR	SNP	A	A	G	rs4304197		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:58779131A>G			NA	NA				RP11-143A22.1 (265271 upstream) : None (None downstream)						NA		NA									NA						cttcccataaaacctagacgg	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58779131A>G		NA		hg19		0.02	6.625815	TAAxACC	COVERED																																																																																			NOVEL					0			12	12.925777	KEEP	1	3	109	81	2446	AA	1	1	0			13	60	500	1	0	35.493916	181	60	6511	355		0.06701	1
EYS	346007	__UNKNOWN__	__UNKNOWN__	6	65300847	65300847	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:65300847C>G	ENST00000503581.1	-	26	5450	c.4913G>C	c.(4912-4914)aGa>aCa	p.R1638T	EYS_ENST00000370621.3_Missense_Mutation_p.R1638T|EYS_ENST00000370616.2_Missense_Mutation_p.R1638T	NM_001142800.1	NP_001136272.1	Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1638		NA			detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TAAAATTGTTCTTTTTGCACT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						89	83	85	NA		NA	NA	6		NA											NA				65300847		692	1590	2282	SO:0001583	missense				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107	346007			21555	protein-coding gene	gene with protein product		612424	chromosome 6 open reading frame 180, EGF-like-domain, multiple 11, retinitis pigmentosa 25 (autosomal recessive), EGF-like-domain, multiple 10, chromosome 6 open reading frame 178, chromosome 6 open reading frame 179	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179	NA	18836446, 18976725	Standard	XM_294050	NM_001142800	NA	Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000503581.1:c.4913G>C	chr6.hg19:g.65300847C>G	ENSP00000424243:p.Arg1638Thr	NA	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	hg19	CCDS47445.1	0.02	4.655401	GTTxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.902	1.207126	0.22205	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84589	-1.87;-1.85;-1.85	5.32	3.53	0.40419	.	.	.	.	.	T	0.49795	0.1578	N	0.08118	0	0.09310	N	0.999998	P;B	0.36535	0.557;0.421	B;B	0.35971	0.215;0.107	T	0.49504	-0.8933	9	0.72032	D	0.01	.	2.7258	0.05213	0.1515:0.5434:0.1462:0.1588	.	1638;1638	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	T	1638	ENSP00000424243:R1638T;ENSP00000359655:R1638T;ENSP00000359650:R1638T	ENSP00000359650:R1638T	R	-	2	0	EYS	65357568	0.530000	0.26330	0.574000	0.28523	0.966000	0.64601	0.591000	0.23969	0.746000	0.32786	0.591000	0.81541	AGA	NOVEL	EYS-012	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359944.1	1	2.407301	KEEP	0	0	0	8	271	CC	0.99257	0.99257	0		-	11	60	416	0	0	30.150836	128	60	4777	167	ENST00000503581.1	0.079137	1
PGM3	5238	__UNKNOWN__	__UNKNOWN__	6	83885570	83885570	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:83885570A>G	ENST00000283977.4	-	8	1012				PGM3_ENST00000512866.1_Intron|PGM3_ENST00000513973.1_Intron|PGM3_ENST00000506587.1_Intron					phosphoglucomutase 3	NA		NA								NS(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	18		all_cancers(76;0.000504)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.068)		BRCA - Breast invasive adenocarcinoma(397;0.0478)		TTTTTGTCACATCCAATTATT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001258	CCDS4997.1, CCDS56435.1, CCDS56436.1, CCDS75487.1	6q14.1-q15	2012-10-02			ENSG00000013375	ENSG00000013375	5238	5.4.2.3		8907	protein-coding gene	gene with protein product	acetylglucosamine phosphomutase	172100			NA	12174217, 10721701	Standard	NM_015599	NM_001199917	NA	Approved	AGM1, DKFZP434B187, PAGM	uc011dyz.2	O95394	OTTHUMG00000015110	ENST00000283977.4:c.885+110T>C	chr6.hg19:g.83885570A>G		NA		hg19		0.02	1.455638	CACxTCC	COVERED																																																																																			NOVEL	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000366385.2	1	3.007722	KEEP	0	0	0	10	288	AA	0.992708	0.992627	0		-	16	60	493	0	0	38.236318	79	60	2887	105	ENST00000283977.4	0.168421	0.999919
RNGTT	8732	__UNKNOWN__	__UNKNOWN__	6	89633891	89633891	__UNKNOWN__	Intron	SNP	C	C	A	rs16881113	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:89633891C>A	ENST00000369485.4	-	4	554				RNGTT_ENST00000369475.3_Intron|RNGTT_ENST00000538899.1_Intron|RNGTT_ENST00000265607.6_Intron	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		CAACCCAGAACTGAACTGACA	0.498	NA	NA											C|||	485	0.096845	0.1687	0.072	5008	,	,	NA	17079	0.0784	NA	0.0905	False	NA	,,,	NA	NA	NA	2504	0.0429	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	8732	2.7.7.50	Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases	10073	protein-coding gene	gene with protein product		603512			NA	9828141, 9512541	Standard		NM_001286428	NA	Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.367+4812G>T	chr6.hg19:g.89633891C>A		NA	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	hg19	CCDS5017.1	0.02	-0.245652	GAAxTGA	COVERED																																																																																			NOVEL	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041469.1	0	2.708691	KEEP	0	0	0	9	316	CC	0.99254	0.636563	0		-	14	60	521	0	0	50.350309	14	60	529	43	ENST00000369485.4	0.5	0.641347
PM20D2	135293	__UNKNOWN__	__UNKNOWN__	6	89864639	89864639	__UNKNOWN__	Intron	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:89864639T>A	ENST00000275072.4	+	4	1007					NM_001010853.1	NP_001010853.1	Q8IYS1	P20D2_HUMAN	peptidase M20 domain containing 2	NA		NA				extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|skin(1)	12		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		CTTTTAAAAGTTAATCTAAGT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						49	51	50	NA		NA	NA	6		NA											NA				89864639		2203	4300	6503	SO:0001627	intron_variant			BC035036	CCDS34499.1	6q15	2014-07-14	2007-11-14	2007-11-14	ENSG00000146281	ENSG00000146281	135293			21408	protein-coding gene	gene with protein product	&#946;-alanyl-lysine dipeptidase	615913	aminoacylase 1-like 2	ACY1L2	NA	24891507	Standard	NM_001010853	NM_001010853	NA	Approved	bA63L7.3	uc003pmz.4	Q8IYS1	OTTHUMG00000015193	ENST00000275072.4:c.912+18T>A	chr6.hg19:g.89864639T>A		NA	B4DYJ2|Q5T7J9|Q6MZV2|Q86XD9	hg19	CCDS34499.1	0.02	4.461071	AAGxTAA	COVERED																																																																																			NOVEL	PM20D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041477.1	0	8.723458	KEEP	0	0	0	29	911	TT	0.999997	0.999997	0		+	30	60	1110	0	0	95.163412	97	60	3511	206	ENST00000275072.4	0.23622	1
BACH2	60468	__UNKNOWN__	__UNKNOWN__	6	90660341	90660341	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:90660341C>T	ENST00000257749.4	-	7	2191	c.1484G>A	c.(1483-1485)cGg>cAg	p.R495Q	RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000343122.3_Missense_Mutation_p.R495Q|BACH2_ENST00000537989.1_Missense_Mutation_p.R495Q|RP3-512E2.2_ENST00000445838.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	495		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.R495Q(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		GGTGTTGGGCCGCATCCTTCC	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	large_intestine(2)					NA						49	58	55	NA		NA	NA	6		NA											NA				90660341		2203	4300	6503	SO:0001583	missense			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182	60468		BTB/POZ domain containing, basic leucine zipper proteins	14078	protein-coding gene	gene with protein product		605394			NA	10949928, 12829606	Standard	NM_021813	NM_001170794	NA	Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1484G>A	chr6.hg19:g.90660341C>T	ENSP00000257749:p.Arg495Gln	NA	E1P518|Q59H70|Q5T793|Q9NTS5	hg19	CCDS5026.1	0.02	7.449753	GGCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805616	0.70682	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.43294	0.95;0.95;0.95	5.21	5.21	0.72293	.	0.052557	0.85682	D	0.000000	T	0.33990	0.0882	L	0.29908	0.895	0.51012	D	0.999902	D	0.76494	0.999	P	0.61275	0.886	T	0.07158	-1.0787	10	0.07030	T	0.85	-26.5095	18.7663	0.91874	0.0:1.0:0.0:0.0	.	495	Q9BYV9	BACH2_HUMAN	Q	495	ENSP00000257749:R495Q;ENSP00000437473:R495Q;ENSP00000345642:R495Q	ENSP00000257749:R495Q	R	-	2	0	BACH2	90717062	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.291000	0.78721	2.428000	0.82296	0.557000	0.71058	CGG	NOVEL	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041522.2	4	27.686862	KEEP	0	0	0	92	3091	CC	1	1	0		-	37	60	1364	0	0	116.365461	124	60	4333	302	ENST00000257749.4	0.229814	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	93044300	93044300	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:93044300C>A			NA	NA				U3 (214951 upstream) : RP1-149C7.1 (53258 downstream)						NA		NA									NA						TGAACCTGCACTCAAAAAATC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.93044300C>A		NA		hg19		0.02	11.825456	GCAxTCA	COVERED																																																																																			NOVEL					0			1	11.136518	KEEP	0	0	0	37	1333	CC	1	1	0			72	60	2602	0	0	226.02897	202	60	7512	383		0.262774	1
EPHA7	2045	__UNKNOWN__	__UNKNOWN__	6	93969084	93969084	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:93969084C>A	ENST00000369303.4	-	10	2096	c.1912G>T	c.(1912-1914)Gtg>Ttg	p.V638L		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	638	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		GCACCAATCACACGCTCAATT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						163	147	153	NA		NA	NA	6		NA											NA				93969084		2203	4300	6503	SO:0001583	missense			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333	2045		EPH receptors, Sterile alpha motif (SAM) domain containing, Fibronectin type III domain containing	3390	protein-coding gene	gene with protein product		602190	EphA7		NA	9267020	Standard		NM_004440	NA	Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1912G>T	chr6.hg19:g.93969084C>A	ENSP00000358309:p.Val638Leu	NA	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	hg19	CCDS5031.1	0.02	4.487345	TCAxACG	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.48	2.847084	0.51164	.	.	ENSG00000135333	ENST00000369303	T	0.61859	0.07	5.9	5.9	0.94986	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.51975	0.1706	L	0.29908	0.895	0.80722	D	1	B;B;B	0.27416	0.178;0.024;0.029	B;B;B	0.43478	0.421;0.007;0.012	T	0.57481	-0.7804	10	0.87932	D	0	.	20.2821	0.98520	0.0:1.0:0.0:0.0	.	634;633;638	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	L	638	ENSP00000358309:V638L	ENSP00000358309:V638L	V	-	1	0	EPHA7	94025805	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.786000	0.95864	0.563000	0.77884	GTG	NOVEL	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041545.1	1	6.003887	KEEP	0	0	0	20	684	CC	0.999863	0.999862	0		-	32	60	1172	0	0	101.718599	92	60	3439	163	ENST00000369303.4	0.258065	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	98227584	98227584	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:98227584T>C			NA	NA				RP1-104O17.2 (46996 upstream) : RP11-436D23.1 (37000 downstream)						NA		NA									NA						tcctggctcatcctggctcaa	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.98227584T>C		NA		hg19		0.02	-0.254424	TCAxCCT	UNCOVERED																																																																																			NOVEL					0			3	2.407169	KEEP	18	0	0	8	252	TT	0	0	0			17	22	664	0	0	65.969483	12	43	433	75		0.586207	0.668523
USP45	85015	__UNKNOWN__	__UNKNOWN__	6	99956681	99956681	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:99956681T>G	ENST00000327681.6	-	3	633				USP45_ENST00000500704.2_Intron|USP45_ENST00000369233.2_Intron|USP45_ENST00000369231.3_Intron|USP45_ENST00000392738.2_Intron|USP45_ENST00000329966.6_Intron|USP45_ENST00000369232.2_Intron|USP45_ENST00000472914.2_Intron	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	NA		NA			protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		AAACAAAATCTCAACATTTTC	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						41	36	38	NA		NA	NA	6		NA											NA				99956681		2203	4300	6503	SO:0001627	intron_variant			AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552	85015		Ubiquitin-specific peptidases	20080	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 45		NA	12838346	Standard	NM_032929	NM_001080481	NA	Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.101-23A>C	chr6.hg19:g.99956681T>G		NA	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	hg19	CCDS34501.1	0.02	2.317198	ATCxCAA	COVERED																																																																																			NOVEL	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041609.2	0	3.911526	KEEP	0	0	0	13	410	TT	0.994391	0.988129	0		-	16	60	598	0	0	51.680774	49	60	1777	83	ENST00000327681.6	0.246154	0.993703
BVES-AS1	154442	__UNKNOWN__	__UNKNOWN__	6	105585519	105585519	__UNKNOWN__	RNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:105585519A>G	ENST00000580511.1	+	0	325				BVES-AS1_ENST00000580854.1_RNA			Q5T3Y7	BVAS1_HUMAN	BVES antisense RNA 1	NA		NA									NA						GTGGCGGGGGAGGCTGAACGT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AL137368		6q21	2012-10-12	2012-08-15	2012-02-06	ENSG00000203808	ENSG00000203808	154442		Long non-coding RNAs	21223	non-coding RNA	RNA, long non-coding		NA	chromosome 6 open reading frame 112, BVES antisense RNA 1 (non-protein coding)	C6orf112	NA		Standard	NR_037157	NR_037157	NA	Approved	bA99L11.2	uc003pqz.3	Q5T3Y7	OTTHUMG00000015292	ENST00000580511.1:	chr6.hg19:g.105585519A>G		NA	Q5T552	hg19		0.02	-0.430704	GGGxGGC	COVERED																																																																																			NOVEL	BVES-AS1-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000444424.1	0	5.411691	KEEP	0	0	0	18	489	AA	0.999859	0.959724	0		+	10	60	146	0	0	8.717099	40	60	1194	110	ENST00000580511.1	0.2	0.959859
LAMA2	3908	__UNKNOWN__	__UNKNOWN__	6	129477922	129477922	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:129477922T>C	ENST00000421865.2	+	8	1255					NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TAAACTTCTTTTGGCCTTGGC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569	3908		Laminins	6482	protein-coding gene	gene with protein product	merosin, congenital muscular dystrophy	156225		LAMM	NA	2185464, 8294519	Standard		NM_000426	NA	Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.1206+2094T>C	chr6.hg19:g.129477922T>C		NA	Q14736|Q5VUM2|Q93022	hg19	CCDS5138.1	0.02	4.411778	CTTxTGG	COVERED																																																																																			NOVEL	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042180.1	1	6.05269	KEEP	43	1	34	32	1000	TT	0.999892	0.999892	0		+	5	25	190	0	0	11.959471	139	60	5121	271	ENST00000421865.2	0.034722	1
RAET1L	154064	__UNKNOWN__	__UNKNOWN__	6	150342396	150342396	__UNKNOWN__	Intron	SNP	G	G	C	rs9479414|rs200545240	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:150342396G>C	ENST00000367341.1	-	3	349				RAET1L_ENST00000286380.2_Intron			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	NA		NA			antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		CTTACAATTTGCTGGCCTTAC	0.463	NA	NA											C|||	2298	0.458866	0.6059	0.5908	5008	,	,	NA	18465	0.2361	NA	0.4245	False	NA	,,,	NA	NA	NA	2504	0.4315	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918	154064			16798	protein-coding gene	gene with protein product		611047			NA	11827464	Standard	NM_130900	NM_130900	NA	Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.350-74C>G	chr6.hg19:g.150342396G>C		NA	A3KME4|Q8TE74	hg19	CCDS5224.1	0.02	5.056916	TTTxCTG	UNCOVERED																																																																																			NOVEL	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042676.1	3	2.407766	KEEP	23	0	0	8	276	GG	0	0	0		-	51	49	1853	0	0	175.079718	65	60	2429	153	ENST00000367341.1	0.439655	0.999997
TMEM181	57583	__UNKNOWN__	__UNKNOWN__	6	159050654	159050654	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:159050654T>G	ENST00000367090.3	+	15	1614					NM_020823.1	NP_065874.1	Q9P2C4	TM181_HUMAN	transmembrane protein 181	NA		NA			pathogenesis (GO:0009405)	integral component of membrane (GO:0016021)	toxic substance binding (GO:0015643)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)	22		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		CACTGGCGGGTGCTTGGCACT	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037844	CCDS43520.1	6q25.3	2012-08-10	2006-10-19	2006-10-19	ENSG00000146433	ENSG00000146433	57583			20958	protein-coding gene	gene with protein product		613209	G protein-coupled receptor 178, KIAA1423	KIAA1423, GPR178	NA	16452613	Standard	NM_020823	NM_020823	NA	Approved		uc003qrm.4	Q9P2C4	OTTHUMG00000015913	ENST00000367090.3:c.1604-108T>G	chr6.hg19:g.159050654T>G		NA	Q5VTU1	hg19	CCDS43520.1	0.02	-0.30967	GGGxGCT	COVERED																																																																																			NOVEL	TMEM181-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042873.1	2	2.395437	KEEP	0	0	0	8	195	TT	0.99257	0.812384	0		+	10	60	136	0	0	9.102912	26	60	687	70	ENST00000367090.3	0.277778	0.818465
SOD2	6648	__UNKNOWN__	__UNKNOWN__	6	160132105	160132105	__UNKNOWN__	Intron	SNP	T	T	C	rs372251214		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:160132105T>C	ENST00000546087.1	-	4	1713							P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	NA		NA			age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		caaccaccactcacattgctc	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	6648	1.15.1.1		11180	protein-coding gene	gene with protein product		147460			NA		Standard	NM_000636	NM_000636	NA	Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.115-18210A>G	chr6.hg19:g.160132105T>C		NA	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	hg19		0.02	8.599088	CACxCAC	COVERED																																																																																			NOVEL	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399943.1	11	21.698709	KEEP	121	1	34	84	2605	TT	1	1	0		-	8	21	279	0	0	16.939744	204	50	7200	501	ENST00000546087.1	0.037736	1
SOD2	6648	__UNKNOWN__	__UNKNOWN__	6	160132166	160132166	__UNKNOWN__	Intron	SNP	A	A	C	rs76479338		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:160132166A>C	ENST00000546087.1	-	4	1713							P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	NA		NA			age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		tctgatcaccataaccacctc	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	6648	1.15.1.1		11180	protein-coding gene	gene with protein product		147460			NA		Standard	NM_000636	NM_000636	NA	Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.115-18271T>G	chr6.hg19:g.160132166A>C		NA	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	hg19		0.02	14.908538	ACCxTAA	COVERED																																																																																			NOVEL	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399943.1	22	12.706823	KEEP	117	8	250	130	4001	AA	1	1	0		-	24	40	811	0	0	53.614697	370	50	13702	904	ENST00000546087.1	0.060914	1
SOD2	6648	__UNKNOWN__	__UNKNOWN__	6	160132440	160132440	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:160132440T>C	ENST00000546087.1	-	4	1713							P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	NA		NA			age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		caaccaccactcacattgctc	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	6648	1.15.1.1		11180	protein-coding gene	gene with protein product		147460			NA		Standard	NM_000636	NM_000636	NA	Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.115-18545A>G	chr6.hg19:g.160132440T>C		NA	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	hg19		0.02	4.064113	CACxCAC	COVERED																																																																																			NOVEL	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399943.1	17	6.141788	KEEP	154	4	130	66	1993	TT	0.999859	0.99984	0		-	5	24	171	0	0	10.850373	96	40	3512	324	ENST00000546087.1	0.049505	0.999981
SOD2	6648	__UNKNOWN__	__UNKNOWN__	6	160132487	160132487	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:160132487T>C	ENST00000546087.1	-	4	1713							P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	NA		NA			age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		accactcacattgctctgatc	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	6648	1.15.1.1		11180	protein-coding gene	gene with protein product		147460			NA		Standard	NM_000636	NM_000636	NA	Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.115-18592A>G	chr6.hg19:g.160132487T>C		NA	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	hg19		0.02	7.421473	ACAxTGC	COVERED																																																																																			NOVEL	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399943.1	25	11.379667	KEEP	178	5	178	100	3001	TT	1	1	0		-	12	27	447	0	0	31.107816	174	49	6254	534	ENST00000546087.1	0.064516	1
MPC1	51660	__UNKNOWN__	__UNKNOWN__	6	166779477	166779477	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:166779477C>T	ENST00000360961.6	-	4	411	c.290G>A	c.(289-291)cGg>cAg	p.R97Q	MPC1_ENST00000487218.1_5'UTR|MPC1_ENST00000341756.6_Missense_Mutation_p.R97Q	NM_001270879.1|NM_016098.3	NP_001257808.1|NP_057182.1	Q9Y5U8	MPC1_HUMAN	mitochondrial pyruvate carrier 1	97		NA	R -> W (in MPYCD; inactive). {ECO:0000269|PubMed:22628558}.		cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	pyruvate transmembrane transporter activity (GO:0050833)				NA						TTTGATAAGCCGCCCTCCCTG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						93	85	88	NA		NA	NA	6		NA											NA				166779477		2203	4300	6503	SO:0001583	missense			AF125101	CCDS5293.1, CCDS75547.1	6q27	2012-08-01	2012-07-30	2012-07-30	ENSG00000060762	ENSG00000060762	51660			21606	protein-coding gene	gene with protein product		614738	brain protein 44-like	BRP44L	NA	22628558	Standard	NM_016098	NM_016098	NA	Approved	dJ68L15.3, CGI-129	uc031sra.1	Q9Y5U8	OTTHUMG00000015999	ENST00000360961.6:c.290G>A	chr6.hg19:g.166779477C>T	ENSP00000354223:p.Arg97Gln	NA	B2R5I7|Q5TI66|Q9HB67|Q9UQN4	hg19	CCDS5293.1	0.02	4.748726	AGCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.9	4.351094	0.82132	.	.	ENSG00000060762	ENST00000360961;ENST00000341756;ENST00000392123	D;D	0.84146	-1.81;-1.81	6.17	3.47	0.39725	.	0.162341	0.56097	D	0.000037	D	0.93032	0.7782	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.93113	0.6518	10	0.87932	D	0	-16.6049	9.8676	0.41154	0.0:0.7891:0.0:0.2109	.	97	Q9Y5U8	BR44L_HUMAN	Q	97;97;54	ENSP00000354223:R97Q;ENSP00000340784:R97Q	ENSP00000340784:R97Q	R	-	2	0	BRP44L	166699467	1.000000	0.71417	0.027000	0.17364	0.708000	0.40852	7.002000	0.76304	0.494000	0.27859	0.655000	0.94253	CGG	NOVEL	MPC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043052.1	0	6.320268	KEEP	0	0	0	21	714	CC	0.999869	0.999867	0		-	23	60	837	0	0	69.502184	94	60	3286	174	ENST00000360961.6	0.196581	0.999998
CCR6	1235	__UNKNOWN__	__UNKNOWN__	6	167551351	167551351	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:167551351G>C	ENST00000341935.5	+	0	2185				CCR6_ENST00000349984.4_3'UTR|RP11-517H2.6_ENST00000609590.1_RNA|CCR6_ENST00000400926.2_3'UTR	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	NA		NA			cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|humoral immune response (GO:0006959)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)|receptor activity (GO:0004872)			endometrium(3)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	14		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;8.21e-20)|BRCA - Breast invasive adenocarcinoma(81;4.55e-06)|GBM - Glioblastoma multiforme(31;0.00507)		TGGCCGGCTAGTGTTTCCTCT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U68030	CCDS5298.1	6q27	2012-08-08			ENSG00000112486	ENSG00000112486	1235		GPCR / Class A : Chemokine receptors : C-C motif, CD molecules	1607	protein-coding gene	gene with protein product		601835		STRL22	NA	8886020	Standard		NM_031409	NA	Approved	CKR-L3, GPR-CY4, CMKBR6, GPR29, DRY-6, DCR2, BN-1, CD196	uc010kkm.3	P51684	OTTHUMG00000016015	ENST00000341935.5:c.*508G>C	chr6.hg19:g.167551351G>C		NA	E1P5C6|P78553|Q92846	hg19	CCDS5298.1	0.02	4.893614	CTAxTGT	COVERED																																																																																			NOVEL	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043118.1	4	4.815483	KEEP	0	0	0	16	560	GG	0.997832	0.997832	0		+	10	60	394	0	0	28.339606	136	60	5141	188	ENST00000341935.5	0.068493	1
SMOC2	64094	__UNKNOWN__	__UNKNOWN__	6	168924034	168924034	__UNKNOWN__	Intron	SNP	C	C	T	rs113032838	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr6:168924034C>T	ENST00000356284.2	+	3	476				SMOC2_ENST00000354536.5_Intron	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	NA		NA			extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		tcccaaagtgctgggattaca	0.527	NA	NA											-|||	700	0.139776	0.1831	0.1311	5008	,	,	NA	11038	0.0694	NA	0.0696	False	NA	,,,	NA	NA	NA	2504	0.2321	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562	64094		EF-hand domain containing	20323	protein-coding gene	gene with protein product		607223			NA	12031507	Standard		NM_022138	NA	Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.257-2992C>T	chr6.hg19:g.168924034C>T		NA	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	hg19	CCDS55076.1	0.02	-0.017546	GTGxTGG	UNCOVERED																																																																																			NOVEL	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043201.1	2	2.407925	KEEP	4	0	0	8	291	CC	0	0	0		+	2	60	71	0	0	8.053956	0	0	0	18	ENST00000356284.2	1	0
BRAT1	221927	__UNKNOWN__	__UNKNOWN__	7	2579433	2579433	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:2579433C>T	ENST00000340611.4	-	11	1741	c.1485G>A	c.(1483-1485)ccG>ccA	p.P495P	BRAT1_ENST00000473879.1_5'UTR	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	495		NA			response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						TGAGGAACTGCGGGATGAGGG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						25	27	27	NA		NA	NA	7		NA											NA				2579433		2200	4298	6498	SO:0001819	synonymous_variant			BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009	221927			21701	protein-coding gene	gene with protein product	BRCA1-associated protein required for ATM activation protein 1	614506	chromosome 7 open reading frame 27	C7orf27, BAAT1	NA	16452482	Standard	NM_152743	NM_152743	NA	Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1485G>A	chr7.hg19:g.2579433C>T		NA	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	hg19	CCDS5334.1	0.02	2.150572	CTGxGGG	COVERED																																																																																			NOVEL	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239305.2	1	16.854126	KEEP	0	0	0	56	1937	CC	1	0.999559	0		-	6	60	226	0	0	16.077725	78	60	2762	174	ENST00000340611.4	0.071429	0.999559
AIMP2	7965	__UNKNOWN__	__UNKNOWN__	7	6062926	6062926	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:6062926C>T	ENST00000400479.2	+	5	714				AIMP2_ENST00000223029.3_Intron|AIMP2_ENST00000395236.2_Intron|EIF2AK1_ENST00000199389.6_3'UTR			Q13155	AIMP2_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	NA		NA			apoptotic process (GO:0006915)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|tRNA aminoacylation for protein translation (GO:0006418)|Type II pneumocyte differentiation (GO:0060510)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						CGTGTTTTTTCTTTTCAGTGC	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						72	69	70	NA		NA	NA	7		NA											NA				6062926		2203	4300	6503	SO:0001627	intron_variant			U24169	CCDS5344.1	7p22.1	2009-05-29			ENSG00000106305	ENSG00000106305	7965			20609	protein-coding gene	gene with protein product		600859			NA	8666379, 18695251	Standard	NM_006303	NM_006303	NA	Approved	p38, PRO0992, JTV-1, JTV1	uc003spo.3	Q13155	OTTHUMG00000122077	ENST00000400479.2:c.341-8C>T	chr7.hg19:g.6062926C>T		NA	Q75MR1|Q96CZ5|Q9P1L2	hg19		0.02	2.452912	TTTxTTT	COVERED																																																																																			NOVEL	AIMP2-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325473.2	4	4.754178	KEEP	0	2	27	26	759	CC	0.999997	0.999997	0		+	11	60	269	0	0	15.776758	128	60	4310	180	ENST00000400479.2	0.079137	1
C7orf31	136895	__UNKNOWN__	__UNKNOWN__	7	25218528	25218528	__UNKNOWN__	Intron	SNP	T	T	C	rs7793893	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:25218528T>C	ENST00000409280.1	-	2	443				C7orf31_ENST00000283905.3_Intron			Q8N865	CG031_HUMAN	chromosome 7 open reading frame 31	NA		NA								autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|stomach(1)	14						ggcatggtggtgcatgcctgt	0.517	NA	NA											C|||	3004	0.59984	0.8064	0.5231	5008	,	,	NA	15992	0.4196	NA	0.6113	False	NA	,,,	NA	NA	NA	2504	0.5491	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK097248	CCDS5394.1	7p15.2	2011-11-24			ENSG00000153790	ENSG00000153790	136895			21722	protein-coding gene	gene with protein product		NA			NA		Standard	NM_138811	NM_138811	NA	Approved		uc003sxn.1	Q8N865	OTTHUMG00000128497	ENST00000409280.1:c.134+265A>G	chr7.hg19:g.25218528T>C		NA	A4D165|Q6MZV8|Q6P989|Q7LE28|Q86XK1|Q8N1H5|Q96BN4	hg19	CCDS5394.1	0.02	-0.04386	TGGxGCA	UNCOVERED																																																																																			NOVEL	C7orf31-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326929.1	3	3.005485	KEEP	2	0	0	10	285	TT	0.99257	0.023895	0		-	3	60	96	0	0	9.569431	2	60	70	17	ENST00000409280.1	0.6	0.024074
CBX3	11335	__UNKNOWN__	__UNKNOWN__	7	26252959	26252959	__UNKNOWN__	3'UTR	SNP	T	T	A	rs13247806		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:26252959T>A	ENST00000337620.4	+	0	2111				CBX3_ENST00000409747.1_3'UTR|CBX3_ENST00000396386.2_3'UTR	NM_007276.4	NP_009207.2	Q13185	CBX3_HUMAN	chromobox homolog 3	NA		NA			chromatin remodeling (GO:0006338)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome, centromeric region (GO:0000779)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nuclear pericentric heterochromatin (GO:0031618)|nucleus (GO:0005634)|spindle (GO:0005819)	enzyme binding (GO:0019899)|histone methyltransferase binding (GO:1990226)|identical protein binding (GO:0042802)|protein domain specific binding (GO:0019904)			endometrium(4)|large_intestine(2)|lung(2)|ovary(1)	9						ATAAATAGTTTTATATTCCTT	0.269	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U26312	CCDS5398.1	7p15.2	2010-07-06	2010-06-24		ENSG00000122565	ENSG00000122565	11335			1553	protein-coding gene	gene with protein product	HP1 gamma homolog (Drosophila)	604477	chromobox homolog 3 (Drosophila HP1 gamma)		NA	8663349	Standard	NM_007276	NM_016587	NA	Approved	HP1Hs-gamma	uc003sxu.3	Q13185	OTTHUMG00000022911	ENST00000337620.4:c.*1131T>A	chr7.hg19:g.26252959T>A		NA	Q96CD7|Q99409|Q9BVS3|Q9P0Z6	hg19	CCDS5398.1	0.02	3.991634	GTTxTAT	COVERED																																																																																			NOVEL	CBX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214117.1	1	3.945173	KEEP	0	1	25	22	706	TT	0.999892	0.999892	0		+	7	60	250	0	0	16.411973	127	60	4629	177	ENST00000337620.4	0.052239	1
HOTAIRM1	100506311	__UNKNOWN__	__UNKNOWN__	7	27135648	27135648	__UNKNOWN__	RNA	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:27135648C>G	ENST00000495032.1	+	0	26									HOXA transcript antisense RNA, myeloid-specific 1	NA		NA									NA						AGAGGGGGGGCGGGAGGGCGG	0.602	NA	NA									OREG0003739|OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay|type=REGULATORY REGION|Gene=HOXA1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							7p15.2	2012-10-19	2012-08-15		ENSG00000233429	ENSG00000233429	100506311		Long non-coding RNAs, -	37117	non-coding RNA	RNA, long non-coding	HOXA cluster antisense RNA 1 (non-protein coding), non-protein coding RNA 179	NA	hox transcript antisense RNA, myeloid-specific 1 (non-protein coding), HOXA transcript antisense RNA, myeloid-specific 1 (non-protein coding)		NA	19144990	Standard		NR_038366	NA	Approved	HOXA-AS1, NCRNA00179, HOXA1-AS1	uc003syg.3		OTTHUMG00000158089	ENST00000495032.1:	chr7.hg19:g.27135648C>G		792		hg19		0.02	-0.241542	GGGxGGG	COVERED																																																																																			NOVEL	HOTAIRM1-005	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000350154.1	0	4.041667	KEEP	0	3	25	23	594	CC	0.999957	0.64132	0		+	7	60	121	0	0	8.871076	19	60	497	68	ENST00000495032.1	0.269231	0.641347
HOXA3	3200	__UNKNOWN__	__UNKNOWN__	7	27147481	27147481	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:27147481G>A	ENST00000396352.4	-	0	1584				HOXA-AS2_ENST00000518088.1_RNA|HOXA3_ENST00000317201.2_3'UTR	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	NA		NA			angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						agcaaccaaagaaaaaaGGTG	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(136;1368 1743 5685 7935 50360)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997	3200		Homeoboxes / ANTP class : HOXL subclass	5104	protein-coding gene	gene with protein product		142954	homeo box A3	HOX1E, HOX1	NA	1973146, 1358459	Standard		XM_005249730	NA	Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.*53C>T	chr7.hg19:g.27147481G>A		NA	A4D181	hg19	CCDS5404.1	0.02	0.570518	AAAxAAA	COVERED																																																																																			NOVEL	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358708.2	2	8.002115	KEEP	0	5	80	56	1780	GG	1	0.99994	0		-	18	60	182	0	1	7.742016	72	60	2347	187	ENST00000396352.4	0.2	0.99994
NT5C3A	51251	__UNKNOWN__	__UNKNOWN__	7	33054388	33054388	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs79747830	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:33054388T>C	ENST00000610140.1	-	9	1023	c.950A>G	c.(949-951)gAt>gGt	p.D317G	AVL9_ENST00000404479.1_Intron|NT5C3A_ENST00000381626.2_Missense_Mutation_p.D271G|NT5C3A_ENST00000405342.1_Missense_Mutation_p.D283G|NT5C3A_ENST00000409467.1_Missense_Mutation_p.D271G|NT5C3A_ENST00000242210.7_Missense_Mutation_p.D322G|NT5C3A_ENST00000396152.2_Missense_Mutation_p.D283G			Q9H0P0	5NT3A_HUMAN	5'-nucleotidase, cytosolic IIIA	322		NA			dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside metabolic process (GO:0006213)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	2'-phosphotransferase activity (GO:0008665)|5'-nucleotidase activity (GO:0008253)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)	p.D322G(1)			NA						TAATGATTCATCTTGTACTAA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	skin(1)					NA						103	105	104	NA		NA	NA	7		NA											NA				33054388		2203	4298	6501	SO:0001583	missense			AF312735	CCDS34616.1, CCDS34617.1, CCDS55101.1	7p14.3	2013-03-06	2013-03-06	2013-03-06	ENSG00000122643	ENSG00000122643	51251	3.1.3.5		17820	protein-coding gene	gene with protein product	lupin	606224	5'-nucleotidase, cytosolic III	NT5C3	NA	11042152, 10942414	Standard	NM_016489	NM_001002010	NA	Approved	UMPH1, PSN1, PN-I, UMPH, P5'N-1, cN-III, p36, POMP, hUMP1	uc003tdk.4	Q9H0P0	OTTHUMG00000152983	ENST00000610140.1:c.950A>G	chr7.hg19:g.33054388T>C	ENSP00000476480:p.Asp317Gly	NA	A8K253|B2RAA5|B8ZZC4|Q6IPZ1|Q6NXS6|Q7L3G6|Q9P0P5|Q9UC42|Q9UC43|Q9UC44|Q9UC45	hg19		0.02	12.336714	TCAxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	T	26.2	4.714928	0.89112	.	.	ENSG00000122643	ENST00000381626;ENST00000396152;ENST00000242210;ENST00000405342;ENST00000409467	D;D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5;-2.5	5.94	5.94	0.96194	HAD-like domain (1);	0.323125	0.35646	N	0.003065	D	0.95564	0.8558	M	0.93197	3.39	0.80722	D	1	P;P	0.50369	0.934;0.553	P;P	0.60949	0.881;0.531	D	0.96469	0.9347	10	0.87932	D	0	.	16.4075	0.83691	0.0:0.0:0.0:1.0	.	322;283	Q9H0P0;Q9H0P0-1	5NT3_HUMAN;.	G	271;283;322;283;271	ENSP00000371039:D271G;ENSP00000379456:D283G;ENSP00000242210:D322G;ENSP00000385261:D283G;ENSP00000387166:D271G	ENSP00000242210:D322G	D	-	2	0	NT5C3	33020913	1.000000	0.71417	0.960000	0.40013	0.989000	0.77384	8.040000	0.89188	2.275000	0.75901	0.528000	0.53228	GAT	NOVEL	NT5C3A-011	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000473102.1	4	13.374295	KEEP	0	1	36	57	1778	TT	1	1	0		-	11	49	370	0	0	21.88687	319	60	11606	446	ENST00000610140.1	0.033333	1
TRGV4	6977	__UNKNOWN__	__UNKNOWN__	7	38393632	38393632	__UNKNOWN__	RNA	SNP	A	A	G	rs185377428	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:38393632A>G	ENST00000390345.2	-	0	377									T cell receptor gamma variable 4	NA		NA									NA						ACTGGCTGCAATGGGAACAAC	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						44	41	42	NA		NA	NA	7		NA											NA				38393632		1758	3849	5607					X15272		7p14	2013-12-13			ENSG00000211698	ENSG00000211698	6977		T cell receptors / TRG locus	12289	other	T cell receptor gene	T-cell receptor, gamma, variable region V4	NA		TCRGV4	NA	2969332	Standard	NG_001336	NG_001336	NA	Approved	V1S4			OTTHUMG00000155099	ENST00000390345.2:	chr7.hg19:g.38393632A>G		NA		hg19		0.02	9.082841	GCAxTGG	COVERED																																																																																			NOVEL	TRGV4-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	NA	TR_V_gene	OTTHUMT00000338400.4	5	5.554048	KEEP	1	1	39	32	1036	AA	0.999998	0.999998	0		-	7	40	267	0	0	16.673571	206	60	7545	305	ENST00000390345.2	0.032864	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	38397930	38397930	__UNKNOWN__	IGR	SNP	A	A	G	rs2392550	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:38397930A>G			NA	NA				TRGV4 (3812 upstream) : TRGV3 (182 downstream)						NA		NA									NA						GGGGAACAGGATGCAGCTGCT	0.517	NA	NA											N|||	1885	0.376398	0.6657	0.3429	5008	,	,	NA	22147	0.2738	NA	0.3191	False	NA	,,,	NA	NA	NA	2504	0.1738	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.38397930A>G		NA		hg19		0.02	5.071092	AGGxTGC	COVERED																																																																																			NOVEL					0			2	5.717266	KEEP	11	0	0	19	591	AA	0.99986	0.999837	0			38	47	1393	0	0	127.977464	65	60	2384	169		0.368932	0.999978
BLVRA	644	__UNKNOWN__	__UNKNOWN__	7	43827573	43827573	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:43827573G>A	ENST00000402924.1	+	4	246	c.83G>A	c.(82-84)cGg>cAg	p.R28Q	BLVRA_ENST00000265523.4_Missense_Mutation_p.R28Q	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	28		NA			heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						AGGGACTTGCGGAATCCACAC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						263	200	222	NA		NA	NA	7		NA											NA				43827573		2203	4300	6503	SO:0001583	missense			BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	644	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR	NA		Standard	NM_000712	NM_001253823	NA	Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.83G>A	chr7.hg19:g.43827573G>A	ENSP00000385757:p.Arg28Gln	NA	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	hg19	CCDS5472.1	0.02	17.944852	TGCxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859159	0.32884	.	.	ENSG00000106605	ENST00000265523;ENST00000402924;ENST00000424330	T;T;T	0.21734	1.99;1.99;1.99	5.06	-3.89	0.04193	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.709765	0.14068	N	0.343600	T	0.06188	0.0160	N	0.02296	-0.605	0.09310	N	0.999998	B	0.10296	0.003	B	0.06405	0.002	T	0.26573	-1.0099	10	0.37606	T	0.19	.	5.6097	0.17398	0.5675:0.0:0.1817:0.2508	.	28	P53004	BIEA_HUMAN	Q	28	ENSP00000265523:R28Q;ENSP00000385757:R28Q;ENSP00000412005:R28Q	ENSP00000265523:R28Q	R	+	2	0	BLVRA	43794098	0.995000	0.38212	0.098000	0.21074	0.945000	0.59286	0.036000	0.13819	-0.601000	0.05783	-0.367000	0.07326	CGG	NOVEL	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339006.1	4	38.159789	KEEP	0	0	0	127	4316	GG	1	1	0		+	54	60	2022	0	0	161.860581	307	60	10866	600	ENST00000402924.1	0.149584	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	48882469	48882469	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:48882469A>G			NA	NA				AC091770.3 (179568 upstream) : AC004899.1 (4892 downstream)						NA		NA									NA						GGGAAAAGGGAGGGCTCCAGG	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.48882469A>G		NA		hg19		0.02	-0.40357	GGGxGGG	COVERED																																																																																			NOVEL					0			1	3.336719	KEEP	0	1	5	13	409	AA	0.995343	0.93014	0			16	60	606	0	0	55.32665	30	60	1124	75		0.347826	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	53932942	53932942	__UNKNOWN__	IGR	SNP	G	G	T	rs372635045		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:53932942G>T			NA	NA				GS1-179L18.1 (53318 upstream) : RP11-806J6.1 (61426 downstream)						NA		NA									NA						TAATTCTTAAGCTCGAGAAAG	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.53932942G>T		NA		hg19		0.02	17.190237	TAAxCTC	COVERED																																																																																			NOVEL					0			6	14.146314	KEEP	2	0	0	47	1709	GG	1	1	0			31	60	1149	0	0	80.851998	414	60	15709	575		0.069663	1
EGFR	1956	__UNKNOWN__	__UNKNOWN__	7	55218903	55218903	__UNKNOWN__	Intron	SNP	T	T	C	rs2075109	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:55218903T>C	ENST00000455089.1	+	4	681				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000420316.2_Intron|EGFR_ENST00000344576.2_Intron|EGFR_ENST00000275493.2_Intron|EGFR_ENST00000342916.3_Intron			P00533	EGFR_HUMAN	epidermal growth factor receptor	NA		NA			activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	ATTTATTGAATGTGCTTAACT	0.393	NA	8	A, O, Mis		glioma, NSCLC	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	2522	0.503594	0.584	0.513	5008	,	,	NA	21517	0.3522	NA	0.4841	False	NA	,,,	NA	NA	NA	2504	0.5644	NA	NA	NA		yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)		E, O	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648	1956			3236	protein-coding gene	gene with protein product	erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)	131550	epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)	ERBB	NA	1505215	Standard	NM_005228	NM_201282	NA	Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000455089.1:c.425-84T>C	chr7.hg19:g.55218903T>C		NA	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	hg19		0.02	4.186961	GAAxGTG	COVERED																																																																																			NOVEL	EGFR-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000343056.1	15	3.909992	KEEP	0	0	0	13	375	TT	0.994391	0.994391	0		+	8	60	223	0	0	12.960367	139	60	4987	178	ENST00000455089.1	0.054422	1
EGFR	1956	__UNKNOWN__	__UNKNOWN__	7	55238087	55238087	__UNKNOWN__	Intron	SNP	C	C	T	rs10258429	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:55238087C>T	ENST00000455089.1	+	15	2002				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H|EGFR_ENST00000275493.2_Intron			P00533	EGFR_HUMAN	epidermal growth factor receptor	NA		NA			activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GCGTGTCCCACCAGAGCGGGA	0.512	NA	8	A, O, Mis		glioma, NSCLC	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,	NA	20745	0.0496	NA	0.0736	False	NA	,,,	NA	NA	NA	2504	0.09	NA	NA	NA		yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)		E, O	0							NA	C	,	922,3484	352.1+/-311.5	101,720,1382	108	89	95	NA	,1968	2.4	0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC	NA	7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648	1956			3236	protein-coding gene	gene with protein product	erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)	131550	epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)	ERBB	NA	1505215	Standard	NM_005228	NM_201282	NA	Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000455089.1:c.1746-781C>T	chr7.hg19:g.55238087C>T		NA	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	hg19		0.02	10.725257	CCAxCAG	COVERED																																																																																			NOVEL	EGFR-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000343056.1	81	14.747204	KEEP	0	0	0	49	1698	CC	1	1	0		+	16	60	464	0	0	27.043863	296	60	10406	467	ENST00000455089.1	0.051282	1
EGFR	1956	__UNKNOWN__	__UNKNOWN__	7	55241836	55241836	__UNKNOWN__	Intron	SNP	C	C	T	rs17290336	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:55241836C>T	ENST00000455089.1	+	17	2306				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000275493.2_Intron			P00533	EGFR_HUMAN	epidermal growth factor receptor	NA		NA			activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCATCATCTACTTTACTCTTT	0.493	NA	8	A, O, Mis		glioma, NSCLC	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	219	0.04373	0.0946	0.0389	5008	,	,	NA	18923	0.001	NA	0.0497	False	NA	,,,	NA	NA	NA	2504	0.0164	NA	NA	NA		yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)		E, O	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648	1956			3236	protein-coding gene	gene with protein product	erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)	131550	epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)	ERBB	NA	1505215	Standard	NM_005228	NM_201282	NA	Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000455089.1:c.2049+100C>T	chr7.hg19:g.55241836C>T		NA	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	hg19		0.02	1.964687	CTAxTTT	COVERED																																																																																			NOVEL	EGFR-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000343056.1	39	3.912648	KEEP	0	0	0	13	466	CC	0.994391	0.994299	0		+	4	60	152	0	0	9.930428	90	60	3184	126	ENST00000455089.1	0.042553	0.999907
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56441150	56441150	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:56441150G>C			NA	NA				RNU6-1335P (33120 upstream) : RNU6-1052P (28612 downstream)						NA		NA									NA						CTTGGCTCGAGAAAGTTCGGG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56441150G>C		NA		hg19		0.02	1.822851	CGAxAAA	COVERED																																																																																			NOVEL					0			1	9.3297	KEEP	24	0	0	31	1061	GG	0.999957	0.998652	0			4	45	144	0	0	9.508952	72	48	2426	147		0.052632	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56441319	56441319	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:56441319A>G			NA	NA				RNU6-1335P (33289 upstream) : RNU6-1052P (28443 downstream)						NA		NA									NA						CCGACCGGAGACCGTTTGGGG	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56441319A>G		NA		hg19		0.02	4.66086	GAGxCCG	COVERED																																																																																			NOVEL					0			2	18.578241	KEEP	76	1	29	72	2091	AA	1	1	0			5	47	189	0	0	12.13767	122	48	4260	342		0.03937	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	57068848	57068848	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:57068848G>A			NA	NA				RN7SL816P (35634 upstream) : ZNF479 (118472 downstream)						NA		NA									NA						CTTGACCACCGTGGAGTCTGA	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.57068848G>A		NA		hg19		0.02	-0.342139	ACCxTGG	UNCOVERED																																																																																			NOVEL					0			1	2.407697	KEEP	5	0	0	8	270	GG	0	0	0			13	60	491	0	0	44.522153	26	60	915	61		0.333333	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	57077383	57077383	__UNKNOWN__	IGR	SNP	C	C	T	rs1717917	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:57077383C>T			NA	NA				RN7SL816P (44169 upstream) : ZNF479 (109937 downstream)						NA		NA									NA						GGCCTCCCACCGTGCATGGGA	0.647	NA	NA											N|||	2786	0.55631	0.5492	0.598	5008	,	,	NA	8121	0.4464	NA	0.5507	False	NA	,,,	NA	NA	NA	2504	0.6554	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.57077383C>T		NA		hg19		0.02	2.061622	CACxGTG	COVERED																																																																																			NOVEL					0			0	3.0096	KEEP	1	0	0	10	337	CC	0.992708	0.980739	0			6	39	211	0	0	15.494029	54	50	1913	86		0.1	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61968711	61968711	__UNKNOWN__	IGR	SNP	T	T	G	rs10949867	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61968711T>G			NA	NA				None (None upstream) : RNU6-417P (503129 downstream)						NA		NA									NA						ttctttgtgttgtgtgcattc	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61968711T>G		NA		hg19		0.02	2.069103	TGTxGTG	COVERED																																																																																			NOVEL					0			7	4.442141	KEEP	38	1	35	27	749	TT	0.994391	0.993801	0			7	46	272	0	0	20.615418	64	40	2156	143		0.098592	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61968970	61968970	__UNKNOWN__	IGR	SNP	G	G	A	rs74187916|rs66812331|rs12375237	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61968970G>A			NA	NA				None (None upstream) : RNU6-417P (502870 downstream)						NA		NA									NA						gtggatatatggaccgcattg	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61968970G>A		NA		hg19		0.02	34.423682	TATxGAC	COVERED																																																																																			NOVEL					0			65	54.306463	KEEP	6	10	309	289	10146	GG	1	1	0			18	60	697	0	0	41.597617	716	60	26599	1328		0.024523	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969037	61969037	__UNKNOWN__	IGR	SNP	T	T	C	rs71300101|rs4409238	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61969037T>C			NA	NA				None (None upstream) : RNU6-417P (502803 downstream)						NA		NA									NA						gaattctcagtaacttctttg	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969037T>C		NA		hg19		0.02	33.06656	CAGxAAC	COVERED																																																																																			NOVEL					0			48	63.562097	KEEP	10	6	220	288	8486	TT	1	1	0			18	60	691	1	0	41.060592	710	60	25506	1390		0.024725	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969268	61969268	__UNKNOWN__	IGR	SNP	G	G	C	rs71204446|rs4275109	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61969268G>C			NA	NA				None (None upstream) : RNU6-417P (502572 downstream)						NA		NA									NA						tcttagagcagtttagaaaca	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969268G>C		NA		hg19		0.02	33.905332	GCAxTTT	COVERED																																																																																			NOVEL					0			37	22.885253	KEEP	7	17	596	284	10296	GG	1	1	0			32	60	1194	0	0	77.77831	691	60	26034	1353		0.04426	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969415	61969415	__UNKNOWN__	IGR	SNP	T	T	C	rs2100384	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61969415T>C			NA	NA				None (None upstream) : RNU6-417P (502425 downstream)						NA		NA									NA						actcacagagttgaaccttgc	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969415T>C		NA		hg19		0.02	36.707724	GAGxTGA	COVERED																																																																																			NOVEL					0			58	16.937632	KEEP	6	17	592	263	8053	TT	1	1	0			22	60	814	0	0	48.958505	716	60	25717	1378		0.02981	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969461	61969461	__UNKNOWN__	IGR	SNP	G	G	A	rs71267899|rs4337988|rs71280882		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61969461G>A			NA	NA				None (None upstream) : RNU6-417P (502379 downstream)						NA		NA									NA						tcttgctgtggcattttcagg	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969461G>A		NA		hg19		0.02	33.149889	GTGxCAT	COVERED																																																																																			NOVEL					0			69	60.789133	KEEP	2	6	179	265	9168	GG	1	1	0			21	60	768	0	0	44.592775	784	60	28560	1351		0.026087	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969487	61969487	__UNKNOWN__	IGR	SNP	A	A	T	rs71246290|rs372527282|rs4374877	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61969487A>T			NA	NA				None (None upstream) : RNU6-417P (502353 downstream)						NA		NA									NA						atttcaagcgatttgaggaca	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969487A>T		NA		hg19		0.02	30.024445	GCGxTTT	COVERED																																																																																			NOVEL					0			64	59.187262	KEEP	7	4	126	241	7487	AA	1	1	0			22	60	784	0	0	45.609464	743	60	27006	1312		0.028758	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969600	61969600	__UNKNOWN__	IGR	SNP	T	T	C	rs3919785	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61969600T>C			NA	NA				None (None upstream) : RNU6-417P (502240 downstream)						NA		NA									NA						acctttcttttcatagaggag	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969600T>C		NA		hg19		0.02	20.311733	TTTxCAT	COVERED																																																																																			NOVEL					0			31	8.428577	KEEP	41	9	309	136	4273	TT	1	1	0			19	60	724	0	0	49.413394	331	60	12039	717		0.054286	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970251	61970251	__UNKNOWN__	IGR	SNP	G	G	A	rs4318939		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61970251G>A			NA	NA				None (None upstream) : RNU6-417P (501589 downstream)						NA		NA									NA						tgatgtgtgcgttcaactcac	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970251G>A		NA		hg19		0.02	6.684147	TGCxTTC	COVERED																																																																																			NOVEL					0			8	2.344214	KEEP	29	4	126	52	1742	GG	1	1	0			9	48	329	0	0	22.387282	142	50	4637	311		0.059603	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970285	61970285	__UNKNOWN__	IGR	SNP	G	G	A	rs4318941	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61970285G>A			NA	NA				None (None upstream) : RNU6-417P (501555 downstream)						NA		NA									NA						tcttttcatagaggagtttgg	0.378	NA	NA											.|||	25	0.00499201	0	0.0072	5008	,	,	NA	1694949	0.005	NA	0.007	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970285G>A		NA		hg19		0.02	12.987509	ATAxAGG	COVERED																																																																																			NOVEL					0			15	18.499249	KEEP	38	4	124	105	3774	GG	1	1	0			9	49	326	0	0	19.825181	257	60	9734	562		0.033835	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970383	61970383	__UNKNOWN__	IGR	SNP	A	A	G	rs4294068		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61970383A>G			NA	NA				None (None upstream) : RNU6-417P (501457 downstream)						NA		NA									NA						tgaatgctagacggaagaatt	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970383A>G		NA		hg19		0.02	29.608349	TAGxCGG	COVERED																																																																																			NOVEL					0			81	69.635162	KEEP	27	1	36	244	7631	AA	1	1	0			18	60	653	0	0	37.781629	665	60	24029	1237		0.026354	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970413	61970413	__UNKNOWN__	IGR	SNP	T	T	G	rs2219031		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61970413T>G			NA	NA				None (None upstream) : RNU6-417P (501427 downstream)						NA		NA									NA						ttctttgtgttgtgtgcattc	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970413T>G		NA		hg19		0.02	28.181499	TGTxGTG	COVERED																																																																																			NOVEL					0			76	27.458727	KEEP	50	11	371	221	6784	TT	1	1	0			25	60	940	0	0	60.594604	587	60	21620	1173		0.04085	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970534	61970534	__UNKNOWN__	IGR	SNP	T	T	C	rs2167819		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:61970534T>C			NA	NA				None (None upstream) : RNU6-417P (501306 downstream)						NA		NA									NA						gaaagggaaatatcttcaaat	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970534T>C		NA		hg19		0.02	6.439238	AAAxATC	COVERED																																																																																			NOVEL					0			24	4.249985	KEEP	137	4	146	65	1941	TT	0.999869	0.999869	0			11	40	406	0	0	28.87373	136	40	4834	364		0.07483	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63040467	63040467	__UNKNOWN__	IGR	SNP	G	G	A	rs1860493		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:63040467G>A			NA	NA				RP11-340I6.3 (158043 upstream) : RN7SL855P (31355 downstream)						NA		NA									NA						CTCGGACCACGGTGCCTGGGT	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63040467G>A		NA		hg19		0.02	-0.263165	CACxGTG	COVERED																																																																																			NOVEL					0			1	2.407427	KEEP	0	0	0	8	264	GG	0.99257	0.688515	0			7	60	251	0	0	21.362416	23	60	795	45		0.233333	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63210060	63210060	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:63210060C>G			NA	NA				MIR4283-2 (128513 upstream) : RP11-340I6.7 (138517 downstream)						NA		NA									NA						GACCCACTTGCAGCCTCCCGG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63210060C>G		NA		hg19		0.02	-0.228089	TTGxAGC	COVERED																																																																																			NOVEL					0			1	4.21343	KEEP	10	0	0	14	492	CC	0.992708	0.578679	0			4	40	136	0	0	10.662538	22	46	799	60		0.153846	0.58293
TYW1	55253	__UNKNOWN__	__UNKNOWN__	7	66648091	66648091	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:66648091C>G	ENST00000359626.5	+	14	1862					NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	NA		NA			tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				TAACAACGAACTTGGCTTTTC	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						82	64	70	NA		NA	NA	7		NA											NA				66648091		2203	4300	6503	SO:0001627	intron_variant			AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874	55253			25598	protein-coding gene	gene with protein product	tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)	611243	radical S-adenosyl methionine and flavodoxin domains 1	RSAFD1	NA	16162496, 17150819	Standard	NM_018264	NM_018264	NA	Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1699-22C>G	chr7.hg19:g.66648091C>G		NA	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	hg19	CCDS5538.1	0.02	8.625756	GAAxTTG	COVERED																																																																																			NOVEL	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251932.2	2	3.401939	KEEP	14	3	105	48	1657	CC	1	1	0		+	9	33	330	0	0	20.787482	222	60	8373	359	ENST00000359626.5	0.038961	1
POM121	9883	__UNKNOWN__	__UNKNOWN__	7	72413593	72413593	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs71554688	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:72413593T>C	ENST00000395270.1	+	14	3307	c.2266T>C	c.(2266-2268)Tac>Cac	p.Y756H	POM121_ENST00000358357.3_Missense_Mutation_p.Y756H|POM121_ENST00000446813.1_Missense_Mutation_p.Y756H|POM121_ENST00000434423.2_Missense_Mutation_p.Y1021H|POM121_ENST00000257622.4_Missense_Mutation_p.Y756H	NM_001257190.1	NP_001244119.1	Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1021	Pore side. {ECO:0000255}.|Thr-rich.	NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CGTGCCTGCGTACGTGCCTAC	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						93	90	91	NA		NA	NA	7		NA											NA				72413593		2203	4300	6503	SO:0001583	missense			AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313	9883		-	19702	protein-coding gene	gene with protein product		615753	POM121 membrane glycoprotein (rat), POM121 membrane glycoprotein		NA	8335683, 9734811, 17900573	Standard		NM_172020	NA	Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000395270.1:c.2266T>C	chr7.hg19:g.72413593T>C	ENSP00000378687:p.Tyr756His	NA	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	hg19	CCDS59059.1	0.02	11.760467	GCGxACG	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.046599	0.00398	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.05382	3.45;3.46;3.45;3.46;3.7	0.1	-0.2	0.13216	.	.	.	.	.	T	0.01558	0.0050	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41378	-0.9512	8	0.15066	T	0.55	.	.	.	.	.	756;1021	A8MXF9;Q96HA1	.;P121A_HUMAN	H	756;756;756;756;1021	ENSP00000393020:Y756H;ENSP00000257622:Y756H;ENSP00000378687:Y756H;ENSP00000351124:Y756H;ENSP00000405562:Y1021H	ENSP00000257622:Y756H	Y	+	1	0	POM121	72051529	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	-0.232000	0.09055	-1.887000	0.01115	-1.904000	0.00526	TAC	NOVEL	POM121-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252020.1	2	17.044011	KEEP	24	12	425	205	5920	TT	1	1	0		+	12	49	436	0	0	28.03659	257	60	9013	685	ENST00000395270.1	0.04461	1
EIF4H	7458	__UNKNOWN__	__UNKNOWN__	7	73610430	73610430	__UNKNOWN__	3'UTR	SNP	G	G	A	rs533293491		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:73610430G>A	ENST00000265753.8	+	0	1678				EIF4H_ENST00000353999.6_3'UTR	NM_022170.1	NP_071496.1	Q15056	IF4H_HUMAN	eukaryotic translation initiation factor 4H	NA		NA			cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|gene expression (GO:0010467)|regulation of translational initiation (GO:0006446)|sexual reproduction (GO:0019953)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|lung(2)|prostate(1)	4						TCCTTTCGCCGTGCGTGGTGG	0.602	NA	NA											G|||	1	0.000199681	0	0	5008	,	,	NA	19042	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5564.1, CCDS5565.1	7q11.23	2013-02-12	2006-11-27	2006-11-27	ENSG00000106682	ENSG00000106682	7458		RNA binding motif (RRM) containing	12741	protein-coding gene	gene with protein product		603431	Williams-Beuren syndrome chromosome region 1	WBSCR1	NA	9516461, 15078951	Standard	NM_022170	NM_022170	NA	Approved	WSCR1, KIAA0038	uc003uad.1	Q15056	OTTHUMG00000023025	ENST00000265753.8:c.*792G>A	chr7.hg19:g.73610430G>A		NA	A8K3R1|D3DXF6|D3DXF8	hg19	CCDS5564.1	0.02	4.84541	GCCxTGC	COVERED																																																																																			NOVEL	EIF4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252375.2	3	17.45501	KEEP	5	0	0	58	1988	GG	1	0.999987	0		+	41	60	1485	0	0	137.317086	65	60	2328	200	ENST00000265753.8	0.386792	0.999987
HGF	3082	__UNKNOWN__	__UNKNOWN__	7	81386479	81386479	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:81386479A>G	ENST00000222390.5	-	4	709				HGF_ENST00000423064.2_Intron|HGF_ENST00000444829.2_Intron|HGF_ENST00000453411.1_Intron|HGF_ENST00000354224.6_Intron|HGF_ENST00000453018.1_3'UTR|HGF_ENST00000457544.2_Intron	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	NA		NA			activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CAGAGGCTTCATCTCTTTTCT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						124	116	119	NA		NA	NA	7		NA											NA				81386479		2203	4300	6503	SO:0001627	intron_variant				CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991	3082			4893	protein-coding gene	gene with protein product	hepatopoietin A, fibroblast-derived tumor cytotoxic factor, scatter factor, lung fibroblast-derived mitogen	142409	deafness, autosomal recessive 39	DFNB39	NA	1837206, 19576567	Standard	NM_000601	XM_006715956	NA	Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.482+25T>C	chr7.hg19:g.81386479A>G		NA	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	hg19	CCDS5597.1	0.02	9.879896	TTCxTCT	COVERED																																																																																			NOVEL	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253315.2	1	15.643984	KEEP	0	0	0	52	1583	AA	1	1	0		-	125	60	4252	0	0	413.966858	111	60	4053	360	ENST00000222390.5	0.529661	1
PCLO	27445	__UNKNOWN__	__UNKNOWN__	7	82585401	82585401	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:82585401G>A	ENST00000333891.9	-	5	5205	c.4868C>T	c.(4867-4869)gCa>gTa	p.A1623V	PCLO_ENST00000423517.2_Missense_Mutation_p.A1623V	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein	NA		NA								breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						ACGTCTTCCTGCATCTTCATC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						316	304	308	NA		NA	NA	7		NA											NA				82585401		2072	4193	6265	SO:0001583	missense			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472	27445			13406	protein-coding gene	gene with protein product	aczonin	604918	piccolo (presynaptic cytomatrix protein)		NA	8900486, 9628581	Standard	NM_014510	NM_014510	NA	Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4868C>T	chr7.hg19:g.82585401G>A	ENSP00000334319:p.Ala1623Val	NA		hg19	CCDS47630.1	0.02	23.708152	CCTxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.675	-0.066720	0.07273	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.28;2.28	5.15	2.32	0.28847	.	.	.	.	.	T	0.16811	0.0404	L	0.51422	1.61	0.30203	N	0.798435	B;B	0.17667	0.023;0.023	B;B	0.16722	0.016;0.016	T	0.10989	-1.0606	9	0.87932	D	0	.	8.6396	0.33970	0.2031:0.1122:0.6847:0.0	.	1623;1623	Q9Y6V0-5;Q9Y6V0-6	.;.	V	1554;1623;1623	ENSP00000334319:A1623V;ENSP00000388393:A1623V	ENSP00000334319:A1623V	A	-	2	0	PCLO	82423337	0.140000	0.22579	0.002000	0.10522	0.856000	0.48823	2.088000	0.41663	-0.037000	0.13646	-0.797000	0.03246	GCA	NOVEL	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337368.5	4	21.669598	KEEP	0	0	0	72	2586	GG	1	1	0		-	23	60	841	0	0	53.532697	531	60	20248	776	ENST00000333891.9	0.041516	1
SEMA3E	9723	__UNKNOWN__	__UNKNOWN__	7	83277718	83277718	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:83277718C>A	ENST00000307792.3	-	1	583					NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	NA		NA			axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				tttttttAAACAAAAGGATCT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						38	37	37	NA		NA	NA	7		NA											NA				83277718		2203	4299	6502	SO:0001627	intron_variant			AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381	9723		Semaphorins, Immunoglobulin superfamily / Immunoglobulin-like domain containing	10727	protein-coding gene	gene with protein product	M-sema H	608166		SEMAH	NA	9205841, 9515811	Standard	NM_012431	NM_012431	NA	Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.115+25G>T	chr7.hg19:g.83277718C>A		NA	B4E1P1|Q75M94|Q75M97	hg19	CCDS34674.1	0.02	2.402779	AAAxAAA	COVERED																																																																																			NOVEL	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336606.1	1	4.788044	KEEP	0	1	12	21	624	CC	0.999879	0.999856	0		-	11	60	181	1	0	9.089004	89	70	2653	158	ENST00000307792.3	0.11	0.999978
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	84320490	84320490	__UNKNOWN__	IGR	SNP	C	C	A	rs375669147|rs200292955		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:84320490C>A			NA	NA				AC092022.1 (25166 upstream) : AC074183.4 (248174 downstream)						NA		NA									NA						gaagaagaagcagaagaagaa	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.84320490C>A		NA		hg19		0.02	-0.052639	AAGxAGA	UNCOVERED																																																																																			NOVEL					0			3	2.407794	KEEP	4	0	0	8	277	CC	0	0	0			2	33	71	1	0	7.224879	1	34	33	23		0.666667	0.036766
SRI	6717	__UNKNOWN__	__UNKNOWN__	7	87837888	87837888	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:87837888A>C	ENST00000265729.2	-	7	564				SRI_ENST00000394641.3_Intron|SRI_ENST00000431660.1_Intron|SRI_ENST00000490437.1_Intron|SRI_ENST00000419179.1_Intron	NM_003130.3	NP_003121.1	P30626	SORCN_HUMAN	sorcin	NA		NA			action potential (GO:0001508)|calcium ion transport (GO:0006816)|cytoplasmic sequestering of transcription factor (GO:0042994)|heart development (GO:0007507)|intracellular sequestering of iron ion (GO:0006880)|muscle organ development (GO:0007517)|negative regulation of heart rate (GO:0010459)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|proteolysis (GO:0006508)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart contraction (GO:0008016)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of relaxation of muscle (GO:1901077)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of striated muscle contraction (GO:0006942)|signal transduction (GO:0007165)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|ion channel binding (GO:0044325)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5	Esophageal squamous(14;0.00202)					TGTCTGTAAAACAACACAGTA	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						86	84	85	NA		NA	NA	7		NA											NA				87837888		2203	4300	6503	SO:0001627	intron_variant			M32886	CCDS5612.1, CCDS47638.1, CCDS59063.1	7q21.1	2014-09-17			ENSG00000075142	ENSG00000075142	6717		EF-hand domain containing	11292	protein-coding gene	gene with protein product		182520			NA	2901906	Standard	NM_003130	NM_001256891	NA	Approved		uc003ujq.2	P30626	OTTHUMG00000157267	ENST00000265729.2:c.512-8T>G	chr7.hg19:g.87837888A>C		NA	A8MTH6|B4DKK2|D6W5Q0	hg19	CCDS5612.1	0.02	11.928286	AAAxCAA	COVERED																																																																																			NOVEL	SRI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253680.1	4	18.948629	KEEP	0	0	0	63	1863	AA	1	1	0		-	61	60	2228	0	0	187.534853	225	60	8086	414	ENST00000265729.2	0.213287	1
STEAP1	26872	__UNKNOWN__	__UNKNOWN__	7	89790339	89790339	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs201266997		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:89790339A>G	ENST00000297205.2	+	3	505	c.305A>G	c.(304-306)cAt>cGt	p.H102R	STEAP2-AS1_ENST00000478318.2_RNA	NM_012449.2	NP_036581.1	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the prostate 1	102		NA			ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|transmembrane transport (GO:0055085)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	channel activity (GO:0015267)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	14	all_hematologic(106;0.112)					GCAACTTCCCATCAACAATAT	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						66	68	67	NA		NA	NA	7		NA											NA				89790339		2203	4297	6500	SO:0001583	missense			AF186249	CCDS5614.1	7q21	2011-08-31	2005-02-21	2005-02-24	ENSG00000164647	ENSG00000164647	26872		Serine peptidases / Serine peptidases	11378	protein-coding gene	gene with protein product		604415	six transmembrane epithelial antigen of the prostate	STEAP	NA		Standard	NM_012449	NM_012449	NA	Approved	PRSS24	uc003ujx.3	Q9UHE8	OTTHUMG00000023006	ENST00000297205.2:c.305A>G	chr7.hg19:g.89790339A>G	ENSP00000297205:p.His102Arg	NA	A4D1E0|O95034	hg19	CCDS5614.1	0.02	15.493388	CCCxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.411946	0.01145	.	.	ENSG00000164647	ENST00000297205	T	0.05996	3.36	5.02	1.36	0.22044	.	0.596018	0.16571	N	0.208613	T	0.06050	0.0157	L	0.50993	1.605	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42327	-0.9458	10	0.15066	T	0.55	-9.4356	8.8478	0.35181	0.6689:0.0:0.3311:0.0	.	102;102	B4E221;Q9UHE8	.;STEA1_HUMAN	R	102	ENSP00000297205:H102R	ENSP00000297205:H102R	H	+	2	0	STEAP1	89628275	0.142000	0.22610	0.020000	0.16555	0.307000	0.27823	1.518000	0.35877	0.398000	0.25338	0.533000	0.62120	CAT	NOVEL	STEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059327.3	1	7.684231	KEEP	48	2	67	49	1460	AA	1	1	0		+	16	40	533	0	0	31.240338	419	60	15478	598	ENST00000297205.2	0.036782	1
STEAP1	26872	__UNKNOWN__	__UNKNOWN__	7	89791240	89791240	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs199817828		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:89791240A>G	ENST00000297205.2	+	4	810	c.610A>G	c.(610-612)Aaa>Gaa	p.K204E	STEAP2-AS1_ENST00000478318.2_RNA	NM_012449.2	NP_036581.1	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the prostate 1	204	Ferric oxidoreductase.	NA			ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|transmembrane transport (GO:0055085)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	channel activity (GO:0015267)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|transporter activity (GO:0005215)			kidney(2)|large_intestine(3)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	14	all_hematologic(106;0.112)					CCAACAAAATAAAGAAGATGC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						43	44	44	NA		NA	NA	7		NA											NA				89791240		2203	4296	6499	SO:0001583	missense			AF186249	CCDS5614.1	7q21	2011-08-31	2005-02-21	2005-02-24	ENSG00000164647	ENSG00000164647	26872		Serine peptidases / Serine peptidases	11378	protein-coding gene	gene with protein product		604415	six transmembrane epithelial antigen of the prostate	STEAP	NA		Standard	NM_012449	NM_012449	NA	Approved	PRSS24	uc003ujx.3	Q9UHE8	OTTHUMG00000023006	ENST00000297205.2:c.610A>G	chr7.hg19:g.89791240A>G	ENSP00000297205:p.Lys204Glu	NA	A4D1E0|O95034	hg19	CCDS5614.1	0.02	17.852684	AATxAAG	COVERED	38	0.0173992673992674	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	15.81	2.941792	0.53079	.	.	ENSG00000164647	ENST00000297205	T	0.07444	3.19	5.61	5.61	0.85477	Flavoprotein transmembrane component (1);	0.250346	0.33005	N	0.005400	T	0.01940	0.0061	L	0.51914	1.62	0.36302	D	0.857104	P;P	0.36683	0.565;0.477	B;B	0.41946	0.282;0.371	T	0.07558	-1.0766	10	0.48119	T	0.1	-6.2003	15.8022	0.78463	1.0:0.0:0.0:0.0	.	204;204	B4E221;Q9UHE8	.;STEA1_HUMAN	E	204	ENSP00000297205:K204E	ENSP00000297205:K204E	K	+	1	0	STEAP1	89629176	0.941000	0.31946	0.991000	0.47740	0.976000	0.68499	3.801000	0.55545	2.133000	0.65898	0.533000	0.62120	AAA	NOVEL	STEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059327.3	1	9.533879	KEEP	70	3	113	71	2161	AA	1	1	0		+	13	27	496	0	0	30.688942	403	50	14639	650	ENST00000297205.2	0.03125	1
LMTK2	22853	__UNKNOWN__	__UNKNOWN__	7	97822041	97822041	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:97822041C>G	ENST00000297293.5	+	11	2557	c.2264C>G	c.(2263-2265)aCt>aGt	p.T755S		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	755		NA			early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GCTGGTTTTACTGAAGCTATG	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						67	70	69	NA		NA	NA	7		NA											NA				97822041		2203	4300	6503	SO:0001583	missense			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715	22853			17880	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 100	610989			NA	15005709	Standard	NM_014916	NM_014916	NA	Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2264C>G	chr7.hg19:g.97822041C>G	ENSP00000297293:p.Thr755Ser	NA	A4D272|Q75MG7|Q9UPS3	hg19	CCDS5654.1	0.02	9.102239	TTAxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	6.618	0.482387	0.12581	.	.	ENSG00000164715	ENST00000297293	T	0.77098	-1.07	5.66	1.75	0.24633	.	0.725072	0.14620	N	0.308473	T	0.60418	0.2267	L	0.31664	0.95	0.09310	N	1	B	0.18863	0.031	B	0.15870	0.014	T	0.39542	-0.9609	10	0.12766	T	0.61	.	6.7552	0.23510	0.0:0.6541:0.1303:0.2157	.	755	Q8IWU2	LMTK2_HUMAN	S	755	ENSP00000297293:T755S	ENSP00000297293:T755S	T	+	2	0	LMTK2	97659977	0.000000	0.05858	0.000000	0.03702	0.504000	0.33889	0.831000	0.27476	0.104000	0.17725	0.655000	0.94253	ACT	NOVEL	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334560.1	5	10.534594	KEEP	0	0	0	35	1271	CC	0.999999	0.999999	0		+	17	60	628	0	0	44.289458	228	60	8542	321	ENST00000297293.5	0.069388	1
FBXO24	26261	__UNKNOWN__	__UNKNOWN__	7	100183926	100183926	__UNKNOWN__	5'Flank	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:100183926C>G	ENST00000241071.6	+	0	0				FBXO24_ENST00000498195.1_Intron	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	NA		NA			protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CGGAGTCTGACGAGAGAAGGG	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001631	upstream_gene_variant			AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336	26261		F-boxes /  other	13595	protein-coding gene	gene with protein product		609097	F-box only protein 24		NA	10531035, 10531037	Standard		NM_012172	NA	Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:	chr7.hg19:g.100183926C>G	Exception_encountered	NA	A4D2D4|B4DX91|B4DY42|Q9H0G1	hg19	CCDS5698.1	0.02	4.944591	TGAxGAG	COVERED																																																																																			NOVEL	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356104.1	1	44.818697	KEEP	0	0	0	149	4963	CC	1	1	0		+	27	60	1000	0	0	84.164295	102	60	3512	365	ENST00000241071.6	0.209302	1
PRKRIP1	79706	__UNKNOWN__	__UNKNOWN__	7	102023242	102023242	__UNKNOWN__	Intron	SNP	G	G	A	rs61652290	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:102023242G>A	ENST00000462601.1	+	1	104				PRKRIP1_ENST00000496391.1_Intron|PRKRIP1_ENST00000482465.1_Intron			Q9H875	PKRI1_HUMAN	PRKR interacting protein 1 (IL11 inducible)	NA		NA			negative regulation of phosphorylation (GO:0042326)|negative regulation of protein kinase activity (GO:0006469)|renal system process (GO:0003014)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|lung(4)|ovary(1)	6						TAGGTTTGGCGATCCAGCTGG	0.562	NA	NA											g|||	3815	0.761781	0.7421	0.8501	5008	,	,	NA	10091	0.7292	NA	0.826	False	NA	,,,	NA	NA	NA	2504	0.6933	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023964	CCDS34714.1	7q22.1	2013-01-09			ENSG00000128563	ENSG00000128563	79706		Zinc fingers, C2H2-type, -	21894	protein-coding gene	gene with protein product	likely ortholog of mouse C114 dsRNA-binding protein, KRAB box domain containing 3	NA			NA	12679338	Standard	NM_024653	NM_024653	NA	Approved	C114, FLJ13902, KRBOX3	uc003uzh.2	Q9H875	OTTHUMG00000157717	ENST00000462601.1:c.34+6473G>A	chr7.hg19:g.102023242G>A		NA	B4DGM2|Q8NDM6|Q96CF8	hg19		0.02	6.743274	GGCxATC	COVERED																																																																																			NOVEL	PRKRIP1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000349487.1	3	5.851897	KEEP	22	1	27	29	959	GG	0.999988	0.999988	0		+	8	40	300	0	0	19.306853	188	50	6884	306	ENST00000462601.1	0.040816	1
RP11-514P8.6	0	__UNKNOWN__	__UNKNOWN__	7	102270836	102270836	__UNKNOWN__	Intron	SNP	T	T	C	rs386626900		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:102270836T>C	ENST00000519541.1	-	6	811										NA		NA									NA						tctctccccctccctttcttt	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000519541.1:c.684-6038A>G	chr7.hg19:g.102270836T>C		NA		hg19		0.02	-0.131591	CCCxCCC	COVERED																																																																																			NOVEL	RP11-514P8.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000453067.1	2	2.400635	KEEP	1	0	0	8	223	TT	0.99257	0.22747	0		-	4	60	147	2	1	12.830892	11	60	381	32	ENST00000519541.1	0.266667	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	102319079	102319079	__UNKNOWN__	IGR	SNP	G	G	A	rs368279784		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:102319079G>A			NA	NA				POLR2J2 (6991 upstream) : FAM185A (70338 downstream)						NA		NA									NA						TGTGAGATGCGTGTGAAAATG	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.102319079G>A		NA		hg19		0.02	4.202266	TGCxTGT	COVERED																																																																																			NOVEL					0			1	2.708832	KEEP	29	0	0	9	325	GG	0.99254	0.992534	0			16	40	551	0	0	42.857651	95	40	3533	152		0.144144	0.999994
KMT2E	55904	__UNKNOWN__	__UNKNOWN__	7	104750897	104750897	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:104750897T>G	ENST00000311117.3	+	25	4389				KMT2E_ENST00000257745.4_Intron|KMT2E_ENST00000334877.4_Intron|KMT2E_ENST00000334914.7_Intron	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	NA		NA			cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)				NA						TAATGTTCTCTTTGGGTCTGC	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						225	216	219	NA		NA	NA	7		NA											NA				104750897		2203	4300	6503	SO:0001627	intron_variant			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483	55904		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	18541	protein-coding gene	gene with protein product		608444	myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)	MLL5	NA	9218106, 7672722	Standard		XM_005250493	NA	Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3845-27T>G	chr7.hg19:g.104750897T>G		NA	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	hg19	CCDS34723.1	0.02	18.361922	CTCxTTG	COVERED																																																																																			NOVEL	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348697.1	9	22.55706	KEEP	0	0	0	75	2375	TT	1	1	0		+	29	60	1015	0	0	68.680114	420	60	15619	608	ENST00000311117.3	0.064588	1
SYPL1	6856	__UNKNOWN__	__UNKNOWN__	7	105733138	105733138	__UNKNOWN__	Intron	SNP	G	G	A	rs371973286		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:105733138G>A	ENST00000011473.2	-	5	692				SYPL1_ENST00000470347.1_Intron|SYPL1_ENST00000455385.2_Intron	NM_006754.3	NP_006745.1	Q16563	SYPL1_HUMAN	synaptophysin-like 1	NA		NA			synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|integral component of synaptic vesicle membrane (GO:0030285)|secretory granule (GO:0030141)	transporter activity (GO:0005215)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	7						aaaaaaaaaagaaaTTAATCT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5736.1, CCDS47685.1	7q22.2	2005-05-24	2005-05-24	2005-05-24	ENSG00000008282	ENSG00000008282	6856			11507	protein-coding gene	gene with protein product		NA	synaptophysin-like protein	SYPL	NA		Standard		NM_006754	NA	Approved		uc003vdp.4	Q16563	OTTHUMG00000157587	ENST00000011473.2:c.645+256C>T	chr7.hg19:g.105733138G>A		NA	A4D0R2|Q96AR8	hg19	CCDS5736.1	0.02	-0.278695	AAAxAAA	COVERED																																																																																			NOVEL	SYPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349221.1	2	4.77875	KEEP	0	0	0	16	454	GG	0.997832	0.738068	0		-	5	60	101	2	0	6.502299	27	60	888	67	ENST00000011473.2	0.15625	0.739671
KCND2	3751	__UNKNOWN__	__UNKNOWN__	7	120381654	120381654	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs561063026		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:120381654C>T	ENST00000331113.4	+	3	2310	c.1345C>T	c.(1345-1347)Cgg>Tgg	p.R449W		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	449		NA			action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	GCAGAGCAAACGGAATGGTTT	0.373	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	17606	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						96	103	101	NA		NA	NA	7		NA											NA				120381654		2203	4300	6503	SO:0001583	missense			AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408	3751		Potassium channels, Voltage-gated ion channels / Potassium channels	6238	protein-coding gene	gene with protein product		605410			NA	10551270, 16382104	Standard	NM_012281	NM_012281	NA	Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1345C>T	chr7.hg19:g.120381654C>T	ENSP00000333496:p.Arg449Trp	NA	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	hg19	CCDS5776.1	0.02	13.901185	AAAxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.6	4.175352	0.78564	.	.	ENSG00000184408	ENST00000331113	D	0.84800	-1.9	5.26	4.35	0.52113	Potassium channel, voltage dependent, Kv4, C-terminal (1);	0.080350	0.50627	D	0.000104	D	0.89238	0.6658	L	0.55990	1.75	0.38843	D	0.956104	D	0.76494	0.999	D	0.64877	0.93	D	0.89283	0.3613	9	.	.	.	.	14.9473	0.71042	0.144:0.856:0.0:0.0	.	449	Q9NZV8	KCND2_HUMAN	W	449	ENSP00000333496:R449W	.	R	+	1	2	KCND2	120168890	1.000000	0.71417	0.985000	0.45067	0.956000	0.61745	4.276000	0.58933	1.165000	0.42670	0.650000	0.86243	CGG	NOVEL	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346996.1	0	17.456219	KEEP	0	0	0	58	2024	CC	1	1	0		+	18	60	672	0	0	45.657252	304	60	10808	486	ENST00000331113.4	0.055901	1
GRM8	2918	__UNKNOWN__	__UNKNOWN__	7	126698170	126698170	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:126698170G>A	ENST00000339582.2	-	3	1536				GRM8_ENST00000444921.2_Intron|GRM8_ENST00000358373.3_Intron|MIR592_ENST00000384959.1_RNA|GRM8_ENST00000480995.1_Intron|GRM8_ENST00000405249.1_Intron			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	NA		NA			adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				ATGATGTTGCGTCACCACGTG	0.398	NA	NA								HNSCC(24;0.065)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						85	72	76	NA		NA	NA	7		NA											NA				126698170		1568	3582	5150	SO:0001627	intron_variant				CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603	2918		GPCR / Class C : Glutamate receptors, metabotropic, Glutamate receptors	4600	protein-coding gene	gene with protein product		601116			NA	8824806	Standard		NM_000845	NA	Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.727+48379C>T	chr7.hg19:g.126698170G>A		NA	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	hg19	CCDS5794.1	0.02	4.810052	TGCxTCA	COVERED																																																																																			NOVEL	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059209.4	0	3.611517	KEEP	0	0	0	12	405	GG	0.993634	0.993627	0		-	27	60	995	0	0	85.763494	83	60	2745	134	ENST00000339582.2	0.245455	0.999994
C7orf55-LUC7L2	100996928	__UNKNOWN__	__UNKNOWN__	7	139056271	139056271	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:139056271C>T	ENST00000354926.4	+	2	415				C7orf55-LUC7L2_ENST00000541170.3_Intron|LUC7L2_ENST00000541515.3_Intron	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough	NA		NA									NA						GATTTGGTTTCTTGTTTGTAT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963	100996928			44671	other	readthrough		NA			NA		Standard		NM_001244584	NA	Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.62-4537C>T	chr7.hg19:g.139056271C>T		NA		hg19	CCDS43656.1	0.02	6.880149	TTTxTTG	COVERED																																																																																			NOVEL	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323618.2	4	10.533968	KEEP	0	0	0	35	1226	CC	0.999999	0.999999	0		+	75	60	2682	0	0	253.572652	94	60	3495	229	ENST00000354926.4	0.443787	1
BRAF	673	__UNKNOWN__	__UNKNOWN__	7	140434604	140434604	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:140434604A>G	ENST00000288602.6	-	18	2188					NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	NA		NA			activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	aaagaaaaaaaaagaaaaaag	0.328	NA	61	Mis, T, O	AKAP9, KIAA1549	melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0							NA						8	9	9	NA		NA	NA	7		NA											NA				140434604		1948	4047	5995	SO:0001627	intron_variant	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764	673			1097	protein-coding gene	gene with protein product		164757	v-raf murine sarcoma viral oncogene homolog B		NA	2284096, 1565476	Standard	NM_004333	NM_004333	NA	Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.2128-34T>C	chr7.hg19:g.140434604A>G		NA	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	hg19	CCDS5863.1	0.02	1.965239	AAAxAAG	COVERED																																																																																			NOVEL	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348886.1	10	4.511252	KEEP	0	0	0	15	419	AA	0.99649	0.993663	0		-	6	60	200	0	0	14.584857	50	60	1769	99	ENST00000288602.6	0.107143	0.997163
BRAF	673	__UNKNOWN__	__UNKNOWN__	7	140454123	140454123	__UNKNOWN__	Intron	SNP	A	A	T	rs71645987	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:140454123A>T	ENST00000288602.6	-	14	1755					NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	NA		NA			activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	GTAAAGACTTATTTAGAATCA	0.318	NA	61	Mis, T, O	AKAP9, KIAA1549	melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				A|||	174	0.0347444	0.1271	0.0086	5008	,	,	NA	18185	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA	Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764	673			1097	protein-coding gene	gene with protein product		164757	v-raf murine sarcoma viral oncogene homolog B		NA	2284096, 1565476	Standard	NM_004333	NM_004333	NA	Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1695-90T>A	chr7.hg19:g.140454123A>T		NA	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	hg19	CCDS5863.1	0.02	6.82457	CTTxTTT	COVERED																																																																																			NOVEL	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348886.1	18	4.812993	KEEP	0	0	0	16	459	AA	0.997832	0.997832	0		-	17	60	584	0	0	42.853356	146	60	5137	195	ENST00000288602.6	0.104294	1
RP11-1220K2.2	0	__UNKNOWN__	__UNKNOWN__	7	141857988	141857988	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:141857988A>G	ENST00000477922.3	+	19	2132										NA		NA								endometrium(1)|lung(5)	6						TTGTTACATAATGTGCCATTG	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000477922.3:c.2079-60A>G	chr7.hg19:g.141857988A>G		NA		hg19		0.02	9.614422	ATAxTGT	COVERED																																																																																			NOVEL	RP11-1220K2.2-003	PUTATIVE	not_best_in_genome_evidence|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351325.3	1	6.92129	KEEP	0	0	0	23	739	AA	0.999892	0.999892	0		+	38	60	1435	0	0	116.70707	194	60	7057	302	ENST00000477922.3	0.163793	1
TRBV11-1	28582	__UNKNOWN__	__UNKNOWN__	7	142223845	142223845	__UNKNOWN__	RNA	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:142223845T>C	ENST00000390367.3	-	0	338									T cell receptor beta variable 11-1	NA		NA									NA						CAGAGATACATGGCCGAGTCC	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						80	80	80	NA		NA	NA	7		NA											NA				142223845		1988	4171	6159					M33233		7q34	2012-02-07			ENSG00000211720	ENSG00000211720	28582		T cell receptors / TRB locus	12180	other	T cell receptor gene		NA			NA	8650574	Standard	NG_001333	NG_001333	NA	Approved	TRBV111, TCRBV11S1, TCRBV21S1			OTTHUMG00000158505	ENST00000390367.3:	chr7.hg19:g.142223845T>C		NA		hg19		0.02	2.135051	ACAxGGC	COVERED																																																																																			NOVEL	TRBV11-1-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	NA	TR_V_gene	OTTHUMT00000351211.1	4	2.707677	KEEP	0	0	0	9	265	TT	0.99254	0.984693	0		-	8	60	286	0	0	22.064295	54	60	2009	80	ENST00000390367.3	0.129032	0.992094
PRSS1	5644	__UNKNOWN__	__UNKNOWN__	7	142459679	142459679	__UNKNOWN__	Silent	SNP	G	G	A	rs376671702	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:142459679G>A	ENST00000311737.7	+	3	261	c.255G>A	c.(253-255)gaG>gaA	p.E85E	PRSS1_ENST00000486171.1_Silent_p.E99E	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	85	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	AGGGGAATGAGCAGTTCATCA	0.537	NA	NA											G|||	2	0.000399361	0.0015	0	5008	,	,	NA	19152	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						232	216	221	NA		NA	NA	7		NA											NA				142459679		2203	4300	6503	SO:0001819	synonymous_variant			M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	5644	3.4.21.4	Serine peptidases / Serine peptidases	9475	protein-coding gene	gene with protein product		276000		TRY1	NA		Standard		NM_002769	NA	Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.255G>A	chr7.hg19:g.142459679G>A		NA	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	hg19	CCDS5872.1	0.02	15.820525	TGAxCAG	COVERED																																																																																			NOVEL	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352538.2	6	18.9324	KEEP	3	2	69	87	3100	GG	1	1	0		+	13	49	481	0	0	30.035212	346	60	13220	541	ENST00000311737.7	0.036212	1
WDR86	349136	__UNKNOWN__	__UNKNOWN__	7	151074006	151074006	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151074006C>T	ENST00000463000.1	-	0	369				NUB1_ENST00000568733.1_Intron|NUB1_ENST00000355851.4_Intron|NUB1_ENST00000566856.1_Intron|NUB1_ENST00000413040.2_Intron			Q86TI4	WDR86_HUMAN	WD repeat domain 86	NA		NA								breast(1)|endometrium(2)|kidney(1)|lung(6)	10			OV - Ovarian serous cystadenocarcinoma(82;0.00419)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CGTCCCCTGACGTCACCGGGC	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK125347	CCDS5925.2, CCDS64805.1, CCDS64806.1, CCDS75680.1	7q36.1	2013-01-09			ENSG00000187260	ENSG00000187260	349136		WD repeat domain containing	28020	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_198285	NM_198285	NA	Approved		uc003wkb.2	Q86TI4	OTTHUMG00000150764	ENST00000463000.1:c.-1012G>A	chr7.hg19:g.151074006C>T		NA	B4DJF1|C9JAJ5|C9JXE3|Q3KNT1|Q6ZUS8	hg19		0.02	-0.350907	TGAxGTC	COVERED																																																																																			NOVEL	WDR86-005	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000348551.1	1	4.513025	KEEP	0	0	0	15	474	CC	0.99649	0.874627	0		-	16	60	597	0	0	55.643073	24	60	839	55	ENST00000463000.1	0.4	0.877708
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962257	151962257	__UNKNOWN__	Silent	SNP	C	C	T	rs62478357		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151962257C>T	ENST00000262189.6	-	8	1268	c.1050G>A	c.(1048-1050)ccG>ccA	p.P350P	KMT2C_ENST00000355193.2_Silent_p.P350P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	350		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						AGAGGTCTCCCGGGCTGTCGC	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						146	134	138	NA		NA	NA	7		NA											NA				151962257		2203	4296	6499	SO:0001819	synonymous_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1050G>A	chr7.hg19:g.151962257C>T		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	28.027717	TCCxGGG	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	6	30.501128	KEEP	199	9	278	199	6840	CC	1	1	0		-	35	49	1253	0	0	82.669506	624	60	21374	1297	ENST00000262189.6	0.053111	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962265	151962265	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201834857		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151962265C>T	ENST00000262189.6	-	8	1260	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	KMT2C_ENST00000355193.2_Missense_Mutation_p.D348N	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	348		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D348N(2)			NA						CCCGGGCTGTCGCACACTGCA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	skin(2)					NA						112	101	104	NA		NA	NA	7		NA											NA				151962265		2203	4296	6499	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1042G>A	chr7.hg19:g.151962265C>T	ENSP00000262189:p.Asp348Asn	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	25.039439	TGTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730606	0.48939	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98807	-5.15;-5.15	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.43919	U	0.000512	D	0.98516	0.9505	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98479	1.0604	10	0.23302	T	0.38	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	348	Q8NEZ4	MLL3_HUMAN	N	348	ENSP00000262189:D348N;ENSP00000347325:D348N	ENSP00000262189:D348N	D	-	1	0	MLL3	151593198	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAC	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	5	27.198498	KEEP	210	9	278	188	6426	CC	1	1	0		-	31	49	1122	0	0	73.454843	594	60	20630	1216	ENST00000262189.6	0.0496	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151970758	151970758	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151970758G>A	ENST00000262189.6	-	7	1231				KMT2C_ENST00000355193.2_Intron	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	NA		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						TACATTGGTTGAAGTTTAAAA	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						206	191	196	NA		NA	NA	7		NA											NA				151970758		2203	4300	6503	SO:0001627	intron_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1012+31C>T	chr7.hg19:g.151970758G>A		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	20.918279	GTTxAAG	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	4	8.960025	KEEP	41	4	117	71	2389	GG	1	1	0		-	33	60	1182	0	0	80.025866	507	60	19010	677	ENST00000262189.6	0.061111	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151970877	151970877	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs138627563		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151970877G>A	ENST00000262189.6	-	7	1143	c.925C>T	c.(925-927)Cct>Tct	p.P309S	KMT2C_ENST00000355193.2_Missense_Mutation_p.P309S	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	309		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						GCAGCACAAGGATAATGATAC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						204	190	195	NA		NA	NA	7		NA											NA				151970877		2203	4300	6503	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.925C>T	chr7.hg19:g.151970877G>A	ENSP00000262189:p.Pro309Ser	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	30.1762	AAGxATA	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.24	3.790455	0.70337	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.70045	-0.45;-0.45	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.44483	D	0.000455	D	0.83403	0.5247	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85377	0.1117	10	0.54805	T	0.06	.	18.3751	0.90433	0.0:0.0:1.0:0.0	.	309	Q8NEZ4	MLL3_HUMAN	S	309	ENSP00000262189:P309S;ENSP00000347325:P309S	ENSP00000262189:P309S	P	-	1	0	MLL3	151601810	1.000000	0.71417	0.804000	0.32291	0.996000	0.88848	9.781000	0.99029	2.423000	0.82170	0.650000	0.86243	CCT	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	5	31.765244	KEEP	76	11	349	228	7834	GG	1	1	0		-	25	49	895	0	0	54.631918	674	60	25415	1268	ENST00000262189.6	0.035765	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151970951	151970951	__UNKNOWN__	Splice_Site	SNP	C	C	T	rs201009236		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151970951C>T	ENST00000262189.6	-	7	1069	c.851G>A	c.(850-852)cGa>cAa	p.R284Q	KMT2C_ENST00000355193.2_Splice_Site_p.R284Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	284		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						AAATGCACATCGCTGAAAGGG	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						54	51	52	NA		NA	NA	7		NA											NA				151970951		2202	4299	6501	SO:0001630	splice_region_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.850-1G>A	chr7.hg19:g.151970951C>T		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	16.165101	CATxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.49	2.551821	0.45487	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.70631	-0.5;-0.5	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.258206	0.20689	N	0.087494	T	0.78381	0.4274	M	0.69463	2.115	0.80722	D	1	D	0.58970	0.984	P	0.52159	0.691	T	0.81093	-0.1089	10	0.59425	D	0.04	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	284	Q8NEZ4	MLL3_HUMAN	Q	284	ENSP00000262189:R284Q;ENSP00000347325:R284Q	ENSP00000262189:R284Q	R	-	2	0	MLL3	151601884	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.773000	0.55333	2.423000	0.82170	0.650000	0.86243	CGA	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	1	16.648928	KEEP	186	3	75	82	2642	CC	1	1	0	Missense_Mutation	-	19	49	698	0	0	47.034636	322	60	10631	656	ENST00000262189.6	0.055718	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151971006	151971006	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:151971006C>T	ENST00000262189.6	-	7	1068				KMT2C_ENST00000355193.2_Intron	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	NA		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						AAGGAATATTCAAATATAAGC	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.850-54G>A	chr7.hg19:g.151971006C>T		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	8.798203	ATTxAAA	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	4	7.524386	KEEP	36	0	0	25	870	CC	0.999879	0.999879	0		-	11	49	387	0	0	25.126052	203	60	7772	298	ENST00000262189.6	0.051402	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	152105058	152105058	__UNKNOWN__	Intron	SNP	T	T	C	rs113828391		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:152105058T>C	ENST00000262189.6	-	1	380				KMT2C_ENST00000355193.2_Intron	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	NA		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						TACTTCAGTATTATTTAGCTT	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.161+27652A>G	chr7.hg19:g.152105058T>C		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	-0.228092	GTAxTAT	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	10	3.610059	KEEP	0	0	0	12	352	TT	0.993634	0.579219	0		-	3	60	116	0	0	9.164018	20	60	724	46	ENST00000262189.6	0.130435	0.58293
PTPRN2	5799	__UNKNOWN__	__UNKNOWN__	7	158066718	158066718	__UNKNOWN__	Intron	SNP	C	C	A	rs113350652		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr7:158066718C>A	ENST00000389418.4	-	3	287				PTPRN2_ENST00000389413.3_Intron|PTPRN2_ENST00000389416.4_Intron|PTPRN2_ENST00000404321.2_Intron|PTPRN2_ENST00000409483.1_Intron	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	NA		NA			negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		ACAGGGGGAGCCGCAGACACA	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093	5799		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like	9677	protein-coding gene	gene with protein product	IAR PTPRP	601698			NA	8954911, 9220540	Standard		NM_130842	NA	Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.277+42792G>T	chr7.hg19:g.158066718C>A		NA	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	hg19	CCDS5947.1	0.02	-0.184192	GAGxCGC	COVERED																																																																																			NOVEL	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353214.1	0	3.003325	KEEP	0	0	0	10	310	CC	0.992708	0.42039	0		-	4	33	128	0	0	10.268918	17	60	568	49	ENST00000389418.4	0.190476	0.423478
CSMD1	64478	__UNKNOWN__	__UNKNOWN__	8	2949256	2949256	__UNKNOWN__	Intron	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:2949256T>A	ENST00000520002.1	-	49	7697				CSMD1_ENST00000537824.1_Intron|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000602557.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	NA		NA				integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		AGGTTTAGCTTTTGATTACAC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117	64478		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	14026	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 24	608397			NA		Standard	NM_033225	NM_033225	NA	Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.7142-72A>T	chr8.hg19:g.2949256T>A		NA	Q0H0J5|Q96QU9|Q96RM4	hg19		0.02	-0.429889	GCTxTTG	COVERED																																																																																			NOVEL	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000374500.2	0	2.708263	KEEP	0	0	0	9	289	TT	0.99254	0.947371	0		-	28	60	1033	0	0	102.125601	21	60	776	65	ENST00000520002.1	0.571429	0.954491
CSMD1	64478	__UNKNOWN__	__UNKNOWN__	8	3047704	3047704	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:3047704G>A	ENST00000520002.1	-	35	5753				CSMD1_ENST00000537824.1_Intron|CSMD1_ENST00000602723.1_Intron|CSMD1_ENST00000400186.3_Intron|CSMD1_ENST00000523387.1_Intron|CSMD1_ENST00000542608.1_Intron|CSMD1_ENST00000539096.1_Intron|CSMD1_ENST00000602557.1_Intron			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	NA		NA				integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TGCGTGGAACGTGGGTTTAAG	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117	64478		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	14026	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 24	608397			NA		Standard	NM_033225	NM_033225	NA	Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.5198-67C>T	chr8.hg19:g.3047704G>A		NA	Q0H0J5|Q96QU9|Q96RM4	hg19		0.02	-0.368391	AACxTGG	COVERED																																																																																			NOVEL	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000374500.2	0	4.815198	KEEP	0	0	0	16	538	GG	0.997832	0.897364	0		-	20	60	719	0	0	68.821305	22	60	808	62	ENST00000520002.1	0.47619	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	7915650	7915650	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:7915650G>C			NA	NA				FAM90A24P (35737 upstream) : MIR548I3 (30812 downstream)						NA		NA									NA						agcctcccctgcctcccctgc	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.7915650G>C		NA		hg19		0.02	-0.052639	CCTxCCT	UNCOVERED																																																																																			NOVEL					0			1	2.708886	KEEP	11	0	0	9	322	GG	0	0	0			3	25	115	0	0	11.124931	3	23	114	29		0.5	0.036766
SLC35G5	83650	__UNKNOWN__	__UNKNOWN__	8	11188922	11188922	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs76944947	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:11188922T>C	ENST00000382435.4	+	1	526	c.307T>C	c.(307-309)Tgg>Cgg	p.W103R		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	103	EamA 1.	NA				integral component of membrane (GO:0016021)		p.W103R(1)			NA						CATCCGAGGCTGGGCCTGCTT	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	pancreas(1)					NA						216	216	216	NA		NA	NA	8		NA											NA				11188922		2203	4300	6503	SO:0001583	missense			AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710	83650		Solute carriers	15546	protein-coding gene	gene with protein product		615199	acyl-malonyl condensing enzyme 1-like 2	AMAC, AMAC1L2	NA		Standard	NM_054028	NM_054028	NA	Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.307T>C	chr8.hg19:g.11188922T>C	ENSP00000371872:p.Trp103Arg	NA	A2RRL6	hg19	CCDS5980.1	0.02	7.770475	GGCxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	t	0	-2.642709	0.00112	.	.	ENSG00000177710	ENST00000382435	T	0.69306	-0.39	0.34	-0.68	0.11346	.	0.244821	0.21560	N	0.072582	T	0.30665	0.0772	N	0.01168	-0.975	0.18873	N	0.999984	B	0.02656	0.0	B	0.01281	0.0	T	0.14062	-1.0486	10	0.23891	T	0.37	-0.4591	6.793	0.23709	0.0:0.7448:0.0:0.2552	.	103	Q96KT7	S35G5_HUMAN	R	103	ENSP00000371872:W103R	ENSP00000371872:W103R	W	+	1	0	SLC35G5	11226332	0.010000	0.17322	0.030000	0.17652	0.042000	0.13812	0.106000	0.15354	-2.178000	0.00768	-2.006000	0.00442	TGG	NOVEL	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207313.2	0	13.212665	KEEP	2	8	281	142	4323	TT	1	1	0		+	8	25	323	0	0	22.1105	162	60	6129	427	ENST00000382435.4	0.047059	1
GATA4	2626	__UNKNOWN__	__UNKNOWN__	8	11565851	11565851	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:11565851C>A	ENST00000335135.4	+	2	588	c.30C>A	c.(28-30)aaC>aaA	p.N10K	GATA4_ENST00000532059.1_Missense_Mutation_p.N10K|GATA4_ENST00000528712.1_Intron	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	10		NA			atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		TGGCCGCCAACCACGGGCCGC	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						5	6	6	NA		NA	NA	8		NA											NA				11565851		2048	4086	6134	SO:0001583	missense			AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574	2626		GATA zinc finger domain containing	4173	protein-coding gene	gene with protein product		600576	GATA-binding protein 4		NA	7665171	Standard	NM_002052	NM_002052	NA	Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.30C>A	chr8.hg19:g.11565851C>A	ENSP00000334458:p.Asn10Lys	NA	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	hg19	CCDS5983.1	0.02	2.187795	CAAxCAC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.9|21.9	4.211222|4.211222	0.79240|0.79240	.|.	.|.	ENSG00000136574|ENSG00000136574	ENST00000335135;ENST00000528027;ENST00000532059|ENST00000259090	D;D;D|.	0.98296|.	-4.85;-4.85;-4.85|.	3.37|3.37	2.45|2.45	0.29901|0.29901	GATA-type transcription activator, N-terminal (1);|.	0.000000|.	0.64402|.	D|.	0.000008|.	T|T	0.50701|0.50701	0.1631|0.1631	L|L	0.55213|0.55213	1.73|1.73	0.58432|0.58432	D|D	0.999997|0.999997	D;D|.	0.76494|.	0.972;0.999|.	P;D|.	0.87578|.	0.802;0.998|.	T|T	0.44267|0.44267	-0.9339|-0.9339	10|6	0.62326|0.02654	D|T	0.03|1	-16.7359|-16.7359	10.0712|10.0712	0.42335|0.42335	0.0:0.895:0.0:0.105|0.0:0.895:0.0:0.105	.|.	10;10|.	B7ZKZ4;P43694|.	.;GATA4_HUMAN|.	K|N	10|10	ENSP00000334458:N10K;ENSP00000432278:N10K;ENSP00000435712:N10K|.	ENSP00000334458:N10K|ENSP00000259090:T10N	N|T	+|+	3|2	2|0	GATA4|GATA4	11603260|11603260	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.902000|0.902000	0.53008|0.53008	3.969000|3.969000	0.56816|0.56816	1.710000|1.710000	0.51325|0.51325	0.505000|0.505000	0.49811|0.49811	AAC|ACC	NOVEL	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207587.2	0	21.364212	KEEP	0	0	0	71	2398	CC	1	0.981955	0		+	32	60	1056	0	0	103.887957	25	60	901	179	ENST00000335135.4	0.561404	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12407064	12407064	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:12407064G>A			NA	NA				AC130352.1 (22714 upstream) : AC068587.2 (28449 downstream)						NA		NA									NA						tccacctcccgggttcaagcg	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12407064G>A		NA		hg19		0.02	-0.096504	CCCxGGT	UNCOVERED																																																																																			NOVEL					0			4	2.708568	KEEP	0	0	0	9	301	GG	0.99254	0.138789	0			7	60	256	0	0	25.807962	4	60	146	22		0.636364	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12521775	12521775	__UNKNOWN__	IGR	SNP	A	A	G	rs79193063	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:12521775A>G			NA	NA				AC068587.1 (28014 upstream) : MIR5692A2 (54860 downstream)						NA		NA									NA						acaccaccatacctggcttta	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12521775A>G		NA		hg19		0.02	-0.070186	CATxCCT	UNCOVERED																																																																																			NOVEL					0			3	3.008574	KEEP	0	0	0	10	298	AA	0.992708	0.053742	0			2	60	79	0	0	7.195697	4	60	141	22		0.333333	0.054137
VPS37A	137492	__UNKNOWN__	__UNKNOWN__	8	17125957	17125957	__UNKNOWN__	Intron	SNP	G	G	C	rs73200948	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:17125957G>C	ENST00000324849.4	+	3	989				VPS37A_ENST00000324815.3_Intron|VPS37A_ENST00000521829.1_Intron	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	NA		NA			cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		TTAGAAATCTGAAATGCATTT	0.249	NA	NA											G|||	495	0.0988419	0.0197	0.0764	5008	,	,	NA	16435	0.1042	NA	0.1054	False	NA	,,,	NA	NA	NA	2504	0.2096	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975	137492			24928	protein-coding gene	gene with protein product	hepatocellular carcinoma related protein 1	609927	vacuolar protein sorting 37A (yeast), polyglutamine binding protein 2	PQBP2	NA	15240819, 15218037, 22717650	Standard	NM_152415	NM_152415	NA	Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.315+76G>C	chr8.hg19:g.17125957G>C		NA	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	hg19	CCDS6001.1	0.02	-0.315766	TCTxAAA	COVERED																																																																																			NOVEL	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253301.2	1	2.40784	KEEP	0	0	0	8	281	GG	0.99257	0.812384	0		+	25	60	951	0	0	97.394936	11	60	403	51	ENST00000324849.4	0.694444	0.818465
ASAH1	427	__UNKNOWN__	__UNKNOWN__	8	17915036	17915036	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:17915036C>T	ENST00000262097.6	-	0	1506				ASAH1_ENST00000314146.10_3'UTR|ASAH1_ENST00000520781.1_3'UTR|ASAH1_ENST00000417108.2_3'UTR|ASAH1_ENST00000381733.4_3'UTR	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	NA		NA			cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		GTAGGCCAGACGTGTGCTCAC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						100	87	92	NA		NA	NA	8		NA											NA				17915036		2203	4300	6503	SO:0001624	3_prime_UTR_variant			U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763	427			735	protein-coding gene	gene with protein product		613468	N-acylsphingosine amidohydrolase (acid ceramidase)	ASAH	NA	8955159, 10610716	Standard	NM_004315	NM_004315	NA	Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.*7G>A	chr8.hg19:g.17915036C>T		NA	E9PDS0|Q6W898|Q96AS2	hg19	CCDS6006.1	0.02	4.634655	AGAxGTG	COVERED																																																																																			NOVEL	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214077.2	0	9.542209	KEEP	0	1	23	40	1345	CC	1	1	0		-	88	60	3270	0	0	333.431674	42	60	1526	211	ENST00000262097.6	0.676923	1
GPR124	25960	__UNKNOWN__	__UNKNOWN__	8	37686177	37686177	__UNKNOWN__	Intron	SNP	G	G	T	rs368070981|rs372209670		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:37686177G>T	ENST00000412232.2	+	3	351				GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	NA		NA			central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			ttttttttttgtatttttagt	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181	25960		-, GPCR / Class B : Orphans, Immunoglobulin superfamily / Immunoglobulin-like domain containing	17849	protein-coding gene	gene with protein product	tumor endothelial marker 5	606823			NA	11559528, 12565841	Standard		NM_032777	NA	Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.339-229G>T	chr8.hg19:g.37686177G>T		NA	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	hg19	CCDS6097.2	0.02	-0.174353	TTTxTAT	COVERED																																																																																			NOVEL	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343331.2	1	4.185928	KEEP	0	0	0	14	362	GG	0.995343	0.385603	0		+	5	60	89	2	0	6.4154	15	60	458	43	ENST00000412232.2	0.25	0.387407
POLB	5423	__UNKNOWN__	__UNKNOWN__	8	42227787	42227787	__UNKNOWN__	Intron	SNP	T	T	G	rs3136806	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:42227787T>G	ENST00000265421.4	+	13	1083				POLB_ENST00000538005.1_Intron|POLB_ENST00000521492.1_Intron	NM_002690.2	NP_002681.1	P06746	DPOLB_HUMAN	polymerase (DNA directed), beta	NA		NA			base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neuron apoptotic process (GO:0051402)|pyrimidine dimer repair (GO:0006290)|response to ethanol (GO:0045471)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|enzyme binding (GO:0019899)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)|microtubule binding (GO:0008017)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(1)	16	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;2.58e-12)|Lung NSC(13;4.24e-11)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.1)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.18e-11)|Lung(22;0.00467)|OV - Ovarian serous cystadenocarcinoma(14;0.00523)|LUSC - Lung squamous cell carcinoma(45;0.024)		Cytarabine(DB00987)	Gtttttttttttttttttttt	0.338	NA	NA						DNA polymerases (catalytic subunits)					t|||	1121	0.223842	0.416	0.1744	5008	,	,	NA	19276	0.1369	NA	0.0964	False	NA	,,,	NA	NA	NA	2504	0.2198	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6129.1	8p12-p11	2012-10-02			ENSG00000070501	ENSG00000070501	5423	2.7.7.7	DNA polymerases	9174	protein-coding gene	gene with protein product		174760			NA		Standard	NM_002690	NM_002690	NA	Approved		uc003xoz.2	P06746	OTTHUMG00000164093	ENST00000265421.4:c.913+281T>G	chr8.hg19:g.42227787T>G		NA	B2RC78|Q3KP48|Q6FI34	hg19	CCDS6129.1	0.02	2.183736	TTTxTTT	COVERED																																																																																			NOVEL	POLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377242.1	1	2.706436	KEEP	0	0	0	9	259	TT	0.99254	0.988801	0		+	24	60	808	1	0	74.535284	37	60	1181	82	ENST00000265421.4	0.393443	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	43822429	43822429	__UNKNOWN__	IGR	SNP	T	T	G	rs28865586		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:43822429T>G			NA	NA				AC134698.1 (406513 upstream) : None (None downstream)						NA		NA									NA						gatatttggatagatttgagg	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.43822429T>G		NA		hg19		0.02	5.201261	GGAxAGA	COVERED																																																																																			NOVEL					0			106	23.333106	KEEP	122	1	9	81	2465	TT	1	0.999994	0			6	44	244	0	0	17.783956	81	45	2910	368		0.068966	0.999994
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	43822531	43822531	__UNKNOWN__	IGR	SNP	A	A	G	rs202236829		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:43822531A>G			NA	NA				AC134698.1 (406615 upstream) : None (None downstream)						NA		NA									NA						tcagagttgaacattcccttt	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.43822531A>G		NA		hg19		0.02	2.411755	TGAxCAT	COVERED																																																																																			NOVEL					0			0	7.821633	KEEP	18	0	0	26	786	AA	0.999892	0.99876	0			4	22	150	0	0	10.178239	69	34	2551	166		0.054795	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	43838636	43838636	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:43838636A>T			NA	NA				AC134698.1 (422720 upstream) : None (None downstream)						NA		NA									NA						ctcagaaaatactttgccata	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.43838636A>T		NA		hg19		0.02	-0.412327	AATxCTT	COVERED																																																																																			NOVEL					0			0	5.415034	KEEP	35	0	0	18	529	AA	0.992708	0.934874	0			6	23	225	0	0	17.568174	41	42	1468	119		0.12766	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46844190	46844190	__UNKNOWN__	IGR	SNP	C	C	T	rs138982836	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:46844190C>T			NA	NA				None (None upstream) : RNU6-656P (898481 downstream)						NA		NA									NA						tatctacctacagaaactaga	0.413	NA	NA											.|||	1472	0.29393	0.3245	0.2594	5008	,	,	NA	4053787	0.2758	NA	0.3062	False	NA	,,,	NA	NA	NA	2504	0.2832	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46844190C>T		NA		hg19		0.02	1.637245	CTAxAGA	COVERED																																																																																			NOVEL					0			5	6.019907	KEEP	38	0	0	20	731	CC	0.993072	0.993012	0			5	20	175	0	0	11.478233	86	23	3241	178		0.054945	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46844220	46844220	__UNKNOWN__	IGR	SNP	A	A	T	rs372039098		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:46844220A>T			NA	NA				None (None upstream) : RNU6-656P (898451 downstream)						NA		NA									NA						tctgagaatcacgtttgtgat	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46844220A>T		NA		hg19		0.02	4.390853	ATCxCGT	COVERED																																																																																			NOVEL					0			10	5.347382	KEEP	56	1	32	29	845	AA	0.999859	0.999859	0			9	22	306	0	0	20.684138	122	24	4520	257		0.068702	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46849336	46849336	__UNKNOWN__	IGR	SNP	T	T	C	rs76425519		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:46849336T>C			NA	NA				None (None upstream) : RNU6-656P (893335 downstream)						NA		NA									NA						gtgtctgcattcaagtcacag	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46849336T>C		NA		hg19		0.02	6.322347	CATxCAA	COVERED																																																																																			NOVEL					0			6	12.337466	KEEP	79	0	0	41	1305	TT	0.999892	0.999892	0			6	40	212	0	0	13.274725	136	41	4986	326		0.042254	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46856218	46856218	__UNKNOWN__	IGR	SNP	C	C	T	rs4317583		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:46856218C>T			NA	NA				None (None upstream) : RNU6-656P (886453 downstream)						NA		NA									NA						acatttggagcgctttcaggc	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46856218C>T		NA		hg19		0.02	-0.289512	GAGxGCT	COVERED																																																																																			NOVEL					0			38	9.028883	KEEP	81	0	0	30	1060	CC	0.992708	0.755338	0			3	22	111	0	0	8.548033	22	44	807	182		0.12	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	58118588	58118588	__UNKNOWN__	IGR	SNP	C	C	T	rs10111007		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:58118588C>T			NA	NA				AC025674.1 (22309 upstream) : RP11-513O17.2 (13059 downstream)						NA		NA									NA						agagcaggggcgaaagttcct	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.58118588C>T		NA		hg19		0.02	1.856712	GGGxGAA	COVERED																																																																																			NOVEL					0			4	2.708589	KEEP	0	0	0	9	301	CC	0.99254	0.990111	0			7	60	222	0	0	15.686327	63	60	2249	93		0.1	0.997553
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	58118698	58118698	__UNKNOWN__	IGR	SNP	A	A	T	rs28716836		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:58118698A>T			NA	NA				AC025674.1 (22419 upstream) : RP11-513O17.2 (12949 downstream)						NA		NA									NA						tggaccttggactcagggtct	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.58118698A>T		NA		hg19		0.02	2.173486	TGGxCTC	COVERED																																																																																			NOVEL					0			1	3.308663	KEEP	1	0	0	11	327	AA	0.993072	0.989819	0			8	60	292	0	0	22.21487	62	60	2194	103		0.114286	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	58118735	58118735	__UNKNOWN__	IGR	SNP	C	C	T	rs28483335		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:58118735C>T			NA	NA				AC025674.1 (22456 upstream) : RP11-513O17.2 (12912 downstream)						NA		NA									NA						cgctgcctgtcctctgatgct	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.58118735C>T		NA		hg19		0.02	2.214005	TGTxCTC	COVERED																																																																																			NOVEL					0			1	3.912486	KEEP	1	0	0	13	446	CC	0.994391	0.968502	0			7	60	248	0	0	19.096627	47	60	1821	96		0.12963	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	58124235	58124235	__UNKNOWN__	IGR	SNP	G	G	A	rs145398737		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:58124235G>A			NA	NA				AC025674.1 (27956 upstream) : RP11-513O17.2 (7412 downstream)						NA		NA									NA						ggcgtgaggcggagtgaaaga	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.58124235G>A		NA		hg19		0.02	-0.280713	GGCxGAG	COVERED																																																																																			NOVEL					0			1	4.212962	KEEP	7	0	0	14	473	GG	0.993634	0.734962	0			4	27	146	0	0	11.273391	28	50	982	62		0.125	0.739671
C8orf34	116328	__UNKNOWN__	__UNKNOWN__	8	69445629	69445629	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:69445629G>A	ENST00000518698.1	+	7	1396				C8orf34_ENST00000337103.4_Intron|C8orf34_ENST00000539993.1_Intron|C8orf34_ENST00000348340.2_3'UTR	NM_052958.2	NP_443190.2	Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	NA		NA								NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			TTTACCTTCTGACTACGTAAT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084	116328			30905	protein-coding gene	gene with protein product	vestibule 1	NA			NA		Standard	NM_052958	NM_052958	NA	Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000518698.1:c.1105+245G>A	chr8.hg19:g.69445629G>A		NA	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	hg19	CCDS6203.2	0.02	16.952096	TCTxACT	COVERED																																																																																			NOVEL	C8orf34-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378765.2	7	7.222405	KEEP	0	0	0	24	851	GG	0.999909	0.999909	0		+	17	60	614	0	0	38.890658	388	60	14851	525	ENST00000518698.1	0.041975	1
RP11-257P3.3	0	__UNKNOWN__	__UNKNOWN__	8	82434521	82434521	__UNKNOWN__	RNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:82434521A>G	ENST00000523380.1	+	0	200				RP11-257P3.3_ENST00000518637.1_RNA						NA		NA									NA						CGGCGGGGGGACCTTGGGGCG	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000523380.1:	chr8.hg19:g.82434521A>G		NA		hg19		0.02	1.260472	GGGxCCT	COVERED																																																																																			NOVEL	RP11-257P3.3-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000379716.1	0	2.979364	KEEP	0	0	0	10	213	AA	0.992708	0.956746	0		+	10	60	151	0	0	9.268177	40	60	1027	68	ENST00000523380.1	0.2	0.963774
MMP16	4325	__UNKNOWN__	__UNKNOWN__	8	89050030	89050030	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:89050030T>A	ENST00000286614.6	-	0	5764					NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	NA		NA			chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	ATGGTCATTTTACATGAAGAC	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103	4325			7162	protein-coding gene	gene with protein product		602262	matrix metalloproteinase 16 (membrane-inserted), chromosome 8 open reading frame 57	C8orf57	NA	7559440	Standard	NM_005941	NM_005941	NA	Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.*3659A>T	chr8.hg19:g.89050030T>A		NA	B2RAN7|Q14824|Q52H48	hg19	CCDS6246.1	0.02	10.824503	TTTxACA	COVERED																																																																																			NOVEL	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375304.2	2	5.113425	KEEP	0	0	0	17	496	TT	0.999366	0.999366	0		-	41	60	1472	0	0	114.930272	257	60	9158	348	ENST00000286614.6	0.137584	1
KCNS2	3788	__UNKNOWN__	__UNKNOWN__	8	99441108	99441108	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs114019607	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:99441108C>T	ENST00000287042.4	+	2	1251	c.901C>T	c.(901-903)Cgg>Tgg	p.R301W	KCNS2_ENST00000521839.1_Missense_Mutation_p.R301W	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	301		NA			protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R301W(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			GAGGCTGATGCGGATCTTCCG	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(138;844 2489 9202 24627)					NA		NA				1	Substitution - Missense(1)	endometrium(1)					NA						119	110	113	NA		NA	NA	8		NA											NA				99441108		2203	4300	6503	SO:0001583	missense			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486	3788		Potassium channels, Voltage-gated ion channels / Potassium channels	6301	protein-coding gene	gene with protein product		602906			NA	9305895, 16382104	Standard	NM_020697	NM_020697	NA	Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.901C>T	chr8.hg19:g.99441108C>T	ENSP00000287042:p.Arg301Trp	NA	A8KAN1	hg19	CCDS6279.1	0.02	13.416539	ATGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.27	2.784282	0.49997	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	D;D	0.99652	-6.3;-6.3	5.83	1.38	0.22167	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99750	0.9900	H	0.97214	3.96	0.46774	D	0.999195	D	0.89917	1.0	D	0.91635	0.999	D	0.97924	1.0316	10	0.87932	D	0	.	15.2029	0.73153	0.612:0.388:0.0:0.0	.	301	Q9ULS6	KCNS2_HUMAN	W	301	ENSP00000287042:R301W;ENSP00000430712:R301W	ENSP00000287042:R301W	R	+	1	2	KCNS2	99510284	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.392000	0.34486	0.319000	0.23209	0.655000	0.94253	CGG	NOVEL	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000103134.1	3	16.850232	KEEP	0	0	0	56	1868	CC	1	1	0		+	12	60	456	0	0	28.918716	320	60	10792	429	ENST00000287042.4	0.036145	1
PABPC1	26986	__UNKNOWN__	__UNKNOWN__	8	101717832	101717832	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs75035099	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:101717832G>C	ENST00000318607.5	-	12	2800	c.1672C>G	c.(1672-1674)Caa>Gaa	p.Q558E	PABPC1_ENST00000519004.1_Missense_Mutation_p.Q513E|PABPC1_ENST00000522387.1_Missense_Mutation_p.Q526E	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	558	PABC. {ECO:0000255|PROSITE- ProRule:PRU00641}.	NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			ATTTGCTTTTGCTCTTGAGGA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						59	51	54	NA		NA	NA	8		NA											NA				101717832		2203	4300	6503	SO:0001583	missense			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756	26986		RNA binding motif (RRM) containing	8554	protein-coding gene	gene with protein product		604679	poly(A)-binding protein, cytoplasmic 2	PAB1, PABPC2	NA	2885805	Standard	NM_002568	XM_005250861	NA	Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1672C>G	chr8.hg19:g.101717832G>C	ENSP00000313007:p.Gln558Glu	NA	Q15097|Q93004	hg19	CCDS6289.1	0.02	10.784178	TTTxCTC	COVERED	245|245	0.11217948717948718|0.11217948717948718	94|94	0.1910569105691057|0.1910569105691057	30|30	0.08287292817679558|0.08287292817679558	48|48	0.08391608391608392|0.08391608391608392	73|73	0.09630606860158311|0.09630606860158311	G|G	28.4|28.4	4.918584|4.918584	0.92249|0.92249	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000517990;ENST00000522658|ENST00000520868	T;T;T;T;T|.	0.55760|.	0.5;0.5;0.5;0.5;0.5|.	5.75|5.75	5.75|5.75	0.90469|0.90469	Polyadenylate-binding protein/Hyperplastic disc protein (5);|.	0.000000|.	0.64402|.	D|.	0.000007|.	T|T	0.00724|0.00724	0.0024|0.0024	H|H	0.94183|0.94183	3.505|3.505	0.80722|0.80722	D|D	1|1	D;P;B|.	0.63880|.	0.993;0.573;0.316|.	D;P;P|.	0.71414|.	0.973;0.453;0.453|.	T|T	0.43048|0.43048	-0.9415|-0.9415	10|5	0.87932|.	D|.	0|.	.|.	19.907|19.907	0.97012|0.97012	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	526;558;558|.	E7ERJ7;B3KT93;P11940|.	.;.;PABP1_HUMAN|.	E|R	558;469;513;526;67;105|90	ENSP00000313007:Q558E;ENSP00000429594:Q513E;ENSP00000429395:Q526E;ENSP00000428030:Q67E;ENSP00000428840:Q105E|.	ENSP00000313007:Q558E|.	Q|S	-|-	1|3	0|2	PABPC1|PABPC1	101787008|101787008	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.789000|9.789000	0.99068|0.99068	2.880000|2.880000	0.98712|0.98712	0.655000|0.655000	0.94253|0.94253	CAA|AGC	NOVEL	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380217.1	14	2.618013	KEEP	0	3	110	47	1663	GG	1	1	0		-	9	60	335	0	0	20.564471	268	60	10183	399	ENST00000318607.5	0.032491	1
PABPC1	26986	__UNKNOWN__	__UNKNOWN__	8	101721899	101721899	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A	rs142985461	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:101721899C>A	ENST00000318607.5	-	8	2161	c.1033G>T	c.(1033-1035)Gaa>Taa	p.E345*	PABPC1_ENST00000519004.1_Nonsense_Mutation_p.E300*|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Nonsense_Mutation_p.E313*	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	345	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TTAGTGGCTTCTTCTGGGGAG	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						74	69	71	NA		NA	NA	8		NA											NA				101721899		2203	4298	6501	SO:0001587	stop_gained			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756	26986		RNA binding motif (RRM) containing	8554	protein-coding gene	gene with protein product		604679	poly(A)-binding protein, cytoplasmic 2	PAB1, PABPC2	NA	2885805	Standard	NM_002568	XM_005250861	NA	Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1033G>T	chr8.hg19:g.101721899C>A	ENSP00000313007:p.Glu345*	NA	Q15097|Q93004	hg19	CCDS6289.1	0.02	21.170106	CTTxTTC	COVERED	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	41|41|41	8.575894|8.575894|8.575894	0.98870|0.98870|0.98870	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519100|ENST00000519596	.|.|.	.|.|.	.|.|.	4.92|4.92|4.92	4.92|4.92|4.92	0.64577|0.64577|0.64577	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000008|.|.	.|T|T	.|0.74412|0.74412	.|0.3713|0.3713	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|T|T	.|0.73987|0.73987	.|-0.3809|-0.3809	.|3|3	0.87932|.|.	D|.|.	0|.|.	.|.|.	18.4911|18.4911|18.4911	0.90848|0.90848|0.90848	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	X|N|I	345;345;300;313|213|177	.|.|.	ENSP00000313007:E345X|.|.	E|K|R	-|-|-	1|3|2	0|2|0	PABPC1|PABPC1|PABPC1	101791075|101791075|101791075	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.998000|0.998000|0.998000	0.95712|0.95712|0.95712	7.748000|7.748000|7.748000	0.85085|0.85085|0.85085	2.426000|2.426000|2.426000	0.82243|0.82243|0.82243	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|AAG|AGA	NOVEL	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380217.1	3	3.51207	KEEP	17	6	174	73	2551	CC	1	1	0		-	27	46	1015	0	0	70.929799	391	60	14755	688	ENST00000318607.5	0.064593	1
PABPC1	26986	__UNKNOWN__	__UNKNOWN__	8	101725000	101725000	__UNKNOWN__	Silent	SNP	G	G	A	rs62513925	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:101725000G>A	ENST00000318607.5	-	6	1884	c.756C>T	c.(754-756)aaC>aaT	p.N252N	PABPC1_ENST00000519004.1_Silent_p.N207N|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Silent_p.N220N	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	252	CSDE1-binding.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			GCTCCTTTCCGTTCATCTCAT	0.368	NA	NA											G|||	4	0.000798722	8e-04	0	5008	,	,	NA	17072	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA						NA		NA				0							NA						89	81	84	NA		NA	NA	8		NA											NA				101725000		2203	4300	6503	SO:0001819	synonymous_variant			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756	26986		RNA binding motif (RRM) containing	8554	protein-coding gene	gene with protein product		604679	poly(A)-binding protein, cytoplasmic 2	PAB1, PABPC2	NA	2885805	Standard	NM_002568	XM_005250861	NA	Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.756C>T	chr8.hg19:g.101725000G>A		NA	Q15097|Q93004	hg19	CCDS6289.1	0.02	6.48812	TCCxTTC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.541|8.541	0.873172|0.873172	0.17322|0.17322	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000519100	.|.	.|.	.|.	5.57|5.57	1.83|1.83	0.25207|0.25207	.|.	.|.	.|.	.|.	.|.	T|T	0.58119|0.58119	0.2100|0.2100	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.50311|0.50311	-0.8843|-0.8843	4|4	.|.	.|.	.|.	.|.	9.6713|9.6713	0.40015|0.40015	0.8007:0.0:0.1993:0.0|0.8007:0.0:0.1993:0.0	rs62513925|rs62513925	.|.	.|.	.|.	W|M	85|121	.|.	.|.	R|T	-|-	1|2	2|0	PABPC1|PABPC1	101794176|101794176	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.651000|0.651000	0.24873|0.24873	0.140000|0.140000	0.18849|0.18849	-0.238000|-0.238000	0.12139|0.12139	CGG|ACG	NOVEL	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380217.1	6	8.361368	KEEP	1	0	0	28	922	GG	0.999997	0.999997	0		-	7	54	241	0	0	15.105679	147	70	4980	233	ENST00000318607.5	0.045455	1
PABPC1	26986	__UNKNOWN__	__UNKNOWN__	8	101725003	101725003	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs62513926	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:101725003C>A	ENST00000318607.5	-	6	1881	c.753G>T	c.(751-753)atG>atT	p.M251I	PABPC1_ENST00000519004.1_Missense_Mutation_p.M206I|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Missense_Mutation_p.M219I	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	251	CSDE1-binding.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			CCTTTCCGTTCATCTCATCCA	0.363	NA	NA											C|||	4	0.000798722	8e-04	0	5008	,	,	NA	16420	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA						NA		NA				0							NA						87	79	82	NA		NA	NA	8		NA											NA				101725003		2203	4300	6503	SO:0001583	missense			Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756	26986		RNA binding motif (RRM) containing	8554	protein-coding gene	gene with protein product		604679	poly(A)-binding protein, cytoplasmic 2	PAB1, PABPC2	NA	2885805	Standard	NM_002568	XM_005250861	NA	Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.753G>T	chr8.hg19:g.101725003C>A	ENSP00000313007:p.Met251Ile	NA	Q15097|Q93004	hg19	CCDS6289.1	0.02	3.904641	GTTxATC	COVERED	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	19.31|19.31|19.31	3.802199|3.802199|3.802199	0.70682|0.70682|0.70682	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000519596|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519100	.|T;T;T|.	.|0.17528|.	.|2.27;2.27;2.27|.	5.57|5.57|5.57	5.57|5.57|5.57	0.84162|0.84162|0.84162	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	.|T|.	.|0.77718|.	.|0.4172|.	M|M|M	0.75884|0.75884|0.75884	2.315|2.315|2.315	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B;B;B|.	.|0.34264|.	.|0.047;0.446;0.26|.	.|B;P;B|.	.|0.46940|.	.|0.103;0.532;0.186|.	.|T|.	.|0.76179|.	.|-0.3054|.	.|10|.	.|0.72032|.	.|D|.	.|0.01|.	.|.|.	19.9103|19.9103|19.9103	0.97024|0.97024|0.97024	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs62513926|rs62513926|rs62513926	.|219;251;251|.	.|E7ERJ7;B3KT93;P11940|.	.|.;.;PABP1_HUMAN|.	X|I|L	84|251;251;206;219|120	.|ENSP00000313007:M251I;ENSP00000429594:M206I;ENSP00000429395:M219I|.	.|ENSP00000313007:M251I|.	E|M|X	-|-|-	1|3|2	0|0|2	PABPC1|PABPC1|PABPC1	101794179|101794179|101794179	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.995000|0.995000|0.995000	0.86356|0.86356|0.86356	7.789000|7.789000|7.789000	0.85783|0.85783|0.85783	2.779000|2.779000|2.779000	0.95612|0.95612|0.95612	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GAA|ATG|TGA	NOVEL	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380217.1	6	8.108479	KEEP	1	0	0	27	879	CC	0.999988	0.999988	0		-	7	54	234	0	2	14.650065	135	70	4669	221	ENST00000318607.5	0.049296	1
TAF2	6873	__UNKNOWN__	__UNKNOWN__	8	120770298	120770298	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:120770298A>G	ENST00000378164.2	-	21	3067				TAF2_ENST00000519355.1_Intron	NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			ATAGCATCATAGCACATAAAC	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						135	135	135	NA		NA	NA	8		NA											NA				120770298		2203	4299	6502	SO:0001627	intron_variant			AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313	6873			11536	protein-coding gene	gene with protein product		604912	TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD	TAF2B	NA	9774672, 9418870	Standard	NM_003184	NM_003184	NA	Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2768+14T>C	chr8.hg19:g.120770298A>G		NA	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	hg19	CCDS34937.1	0.02	4.685057	CATxGCA	COVERED																																																																																			NOVEL	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381436.1	0	8.726608	KEEP	0	0	0	29	912	AA	0.999997	0.999997	0		-	16	60	600	0	0	45.669861	131	60	4953	229	ENST00000378164.2	0.108844	1
FBXO32	114907	__UNKNOWN__	__UNKNOWN__	8	124553388	124553388	__UNKNOWN__	5'UTR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:124553388C>A	ENST00000517956.1	-	0	58				FBXO32_ENST00000443022.2_5'UTR	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	NA		NA			cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)				autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			cggcgcggggcaccctgcggg	0.781	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804	114907		F-boxes /  other	16731	protein-coding gene	gene with protein product		606604	F-box only protein 32		NA	11679633, 11717410	Standard		NM_058229	NA	Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.-134G>T	chr8.hg19:g.124553388C>A		NA	A4KYM0	hg19	CCDS6345.1	0.02	-0.368273	GGGxACC	COVERED																																																																																			NOVEL	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381281.1	0	10.473813	KEEP	0	0	0	35	1032	CC	0.999999	0.899313	0		-	7	60	211	0	0	16.230076	35	60	1171	107	ENST00000517956.1	0.166667	0.899314
TG	7038	__UNKNOWN__	__UNKNOWN__	8	133909949	133909949	__UNKNOWN__	Silent	SNP	C	C	T	rs116032324	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:133909949C>T	ENST00000220616.4	+	12	3097	c.3057C>T	c.(3055-3057)tcC>tcT	p.S1019S	TG_ENST00000377869.1_Silent_p.S1019S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1019	Thyroglobulin type-1 8. {ECO:0000255|PROSITE-ProRule:PRU00500}.	NA			hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CTGGAGCATCCGCCCTTCTGC	0.587	NA	NA											C|||	11	0.00219649	0	0.0043	5008	,	,	NA	16462	0	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA						NA		NA				0							NA	C		0,4406		0,0,2203	77	80	79	NA	3057	-8.3	0	8	dbSNP_132	79	15,8585	11.9+/-42.8	0,15,4285	no	coding-synonymous	TG	NM_003235.4		0,15,6488	TT,TC,CC	NA	0.1744,0.0,0.1153		1019/2769	133909949	15,12991	2203	4300	6503	SO:0001819	synonymous_variant			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832	7038			11764	protein-coding gene	gene with protein product		188450			NA		Standard	NM_003235	NM_003235	NA	Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.3057C>T	chr8.hg19:g.133909949C>T		NA	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	hg19	CCDS34944.1	0.02	12.860057	ATCxGCC	COVERED																																																																																			NOVEL	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379606.1	3	19.896196	KEEP	0	1	31	77	2540	CC	1	1	0		+	14	60	521	0	0	33.684955	313	60	10789	514	ENST00000220616.4	0.042813	1
COL22A1	169044	__UNKNOWN__	__UNKNOWN__	8	139668038	139668038	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:139668038C>G	ENST00000303045.6	-	45	3780				COL22A1_ENST00000435777.1_Intron|COL22A1_ENST00000341807.4_Intron	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	NA		NA			extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ATCGTTAATACTACCAAATAG	0.418	NA	NA								HNSCC(7;0.00092)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436	169044		Collagens	22989	protein-coding gene	gene with protein product		610026			NA		Standard	XM_291257	NM_152888	NA	Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3333+101G>C	chr8.hg19:g.139668038C>G		NA	B7ZMH0|C9K0G4|Q8IVT9	hg19	CCDS6376.1	0.02	4.872731	ATAxTAC	COVERED																																																																																			NOVEL	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315905.2	1	3.912535	KEEP	0	0	0	13	442	CC	0.994391	0.994391	0		-	36	60	1306	0	0	113.510437	101	60	3694	160	ENST00000303045.6	0.262774	1
EPPK1	83481	__UNKNOWN__	__UNKNOWN__	8	144940267	144940267	__UNKNOWN__	Silent	SNP	G	G	A	rs28441354		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr8:144940267G>A	ENST00000525985.1	-	2	7226	c.7155C>T	c.(7153-7155)ggC>ggT	p.G2385G				P58107	EPIPL_HUMAN	epiplakin 1	2385		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GGTCGAAGAAGCCCTTGGTGT	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						274	257	263	NA		NA	NA	8		NA											NA				144940267		2190	4273	6463	SO:0001819	synonymous_variant			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150	83481			15577	protein-coding gene	gene with protein product	epidermal autoantigen 450K	607553			NA	11278896, 15671067	Standard	NM_031308	NM_031308	NA	Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7155C>T	chr8.hg19:g.144940267G>A		NA	Q76E58|Q9NSU9	hg19		0.02	36.180143	GAAxCCC	COVERED																																																																																			NOVEL	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000382675.1	12	23.477984	KEEP	21	16	513	258	9232	GG	1	1	0		-	53	60	1788	0	0	124.425349	596	60	22428	1385	ENST00000525985.1	0.081664	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	10395	10395	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:10395C>T			NA	NA				None (None upstream) : MIR1302-2 (17261 downstream)						NA		NA									NA						cgaacccgaacccgaacccga	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.10395C>T		NA		hg19		0.02	-0.184214	GAAxCCG	COVERED																																																																																			NOVEL					0			48	17.220763	KEEP	27	2	62	79	2611	CC	1	0.423478	0			2	48	80	0	0	6.530704	11	60	391	187		0.153846	0.423478
MPDZ	8777	__UNKNOWN__	__UNKNOWN__	9	13119623	13119623	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:13119623C>T	ENST00000541718.1	-	39	5478	c.5257G>A	c.(5257-5259)Gac>Aac	p.D1753N	MPDZ_ENST00000447879.1_Missense_Mutation_p.D1720N|MPDZ_ENST00000541093.1_5'UTR|MPDZ_ENST00000319217.7_Missense_Mutation_p.D1753N|MPDZ_ENST00000381015.4_Missense_Mutation_p.D1753N|MPDZ_ENST00000381022.2_Missense_Mutation_p.D1753N|MPDZ_ENST00000536827.1_Missense_Mutation_p.D1720N|MPDZ_ENST00000546205.1_Missense_Mutation_p.D1767N|MPDZ_ENST00000538841.1_Missense_Mutation_p.D612N	NM_001261407.1|NM_003829.4	NP_001248336.1|NP_003820.2	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1753	PDZ 11. {ECO:0000255|PROSITE- ProRule:PRU00143}.	NA			cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TTGACAATGTCTGACACAAAT	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						113	111	112	NA		NA	NA	9		NA											NA				13119623		1926	4127	6053	SO:0001583	missense			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186	8777			7208	protein-coding gene	gene with protein product		603785			NA		Standard	NM_003829	NM_003829	NA	Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000541718.1:c.5257G>A	chr9.hg19:g.13119623C>T	ENSP00000439807:p.Asp1753Asn	NA	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	hg19	CCDS47951.1	0.02	27.383699	TGTxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	36	5.904323	0.97087	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000438511;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T;T;T;T	0.26067	1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76;1.76	6.02	6.02	0.97574	PDZ/DHR/GLGF (4);	0.000000	0.49305	D	0.000148	T	0.40067	0.1102	N	0.20610	0.595	0.80722	D	1	D;P;D;D;D;D;D;D	0.76494	0.996;0.91;0.996;0.995;0.999;0.998;0.996;0.988	D;P;D;D;D;D;D;P	0.77004	0.957;0.728;0.938;0.928;0.989;0.928;0.955;0.904	T	0.22626	-1.0211	10	0.56958	D	0.05	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	1720;612;458;1720;1633;1753;1753;446	B7ZMI4;B7ZB24;B4DGX5;O75970-3;E7EPZ1;O75970-2;O75970;B3KRN5	.;.;.;.;.;.;MPDZ_HUMAN;.	N	1753;1753;1753;294;689;612;1720;1720;1753;1633;1767	ENSP00000320006:D1753N;ENSP00000439807:D1753N;ENSP00000370410:D1753N;ENSP00000415964:D294N;ENSP00000444230:D689N;ENSP00000444717:D612N;ENSP00000444151:D1720N;ENSP00000415208:D1720N;ENSP00000370403:D1753N;ENSP00000446358:D1767N	ENSP00000320006:D1753N	D	-	1	0	MPDZ	13109623	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	7.818000	0.86416	2.857000	0.98124	0.650000	0.86243	GAC	NOVEL	MPDZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401076.1	3	23.16867	KEEP	0	0	0	77	2779	CC	1	1	0		-	100	60	3631	0	0	297.049538	456	60	17444	758	ENST00000541718.1	0.179856	1
HAUS6	54801	__UNKNOWN__	__UNKNOWN__	9	19055523	19055523	__UNKNOWN__	3'UTR	SNP	A	A	G	rs3800829		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:19055523A>G	ENST00000380502.3	-	0	4153					NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	NA		NA			centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AAACCCAACAACAAAACAGAC	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874	54801		HAUS augmin-like complex subunits	25948	protein-coding gene	gene with protein product		613433	family with sequence similarity 29, member A	FAM29A	NA	10997877, 19427217	Standard	NM_017645	NM_001270890	NA	Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.*818T>C	chr9.hg19:g.19055523A>G		NA	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	hg19	CCDS6489.1	0.02	13.739933	ACAxCAA	COVERED																																																																																			NOVEL	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051825.1	8	11.603408	KEEP	8	2	76	65	1991	AA	1	1	0		-	12	49	466	0	0	29.993066	315	60	11141	484	ENST00000380502.3	0.036697	1
HAUS6	54801	__UNKNOWN__	__UNKNOWN__	9	19055569	19055569	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:19055569T>C	ENST00000380502.3	-	0	4107					NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	NA		NA			centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						tgttaaaatataaaaGTAGCA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874	54801		HAUS augmin-like complex subunits	25948	protein-coding gene	gene with protein product		613433	family with sequence similarity 29, member A	FAM29A	NA	10997877, 19427217	Standard	NM_017645	NM_001270890	NA	Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.*772A>G	chr9.hg19:g.19055569T>C		NA	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	hg19	CCDS6489.1	0.02	12.13677	ATAxAAA	COVERED																																																																																			NOVEL	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051825.1	9	4.102449	KEEP	66	3	110	52	1503	TT	1	1	0		-	17	49	663	0	0	46.443434	268	50	9673	431	ENST00000380502.3	0.059649	1
LINGO2	158038	__UNKNOWN__	__UNKNOWN__	9	28189483	28189483	__UNKNOWN__	Intron	SNP	A	A	G	rs375953714		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:28189483A>G	ENST00000379992.2	-	4	364				LINGO2_ENST00000493941.1_Intron	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		gggagggaggaaggaaggaag	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482	158038		Immunoglobulin superfamily / I-set domain containing	21207	protein-coding gene	gene with protein product		609793	leucine rich repeat neuronal 6C	LRRN6C	NA	14686891	Standard	NM_152570	NM_152570	NA	Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.85+105722T>C	chr9.hg19:g.28189483A>G		NA	A8K4K7|B2RPM5|Q6ZMD0	hg19	CCDS6524.1	0.02	-0.175446	AGGxAGG	COVERED																																																																																			NOVEL	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051978.2	8	4.511179	KEEP	7	0	0	15	427	AA	0.993072	0.384723	0		-	3	31	107	0	0	8.872015	12	43	408	62	ENST00000379992.2	0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	35103314	35103314	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:35103314G>T			NA	NA				STOML2 (160 upstream) : FAM214B (794 downstream)						NA		NA									NA						GAAGGCTGTGGTTGTTCTGGG	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.35103314G>T		NA		hg19		0.02	-0.236833	GTGxTTG	COVERED																																																																																			NOVEL					0			2	3.91235	KEEP	0	0	0	13	457	GG	0.994391	0.608972	0			9	60	316	0	0	28.431246	18	60	646	41		0.333333	0.612407
RP11-204M4.2	0	__UNKNOWN__	__UNKNOWN__	9	41967130	41967130	__UNKNOWN__	lincRNA	SNP	T	T	C	rs201860860		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:41967130T>C	ENST00000454645.1	-	0	653					NR_003670.1					NA		NA									NA						TGGGGAGTGATGTTCCTTTCA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000454645.1:	chr9.hg19:g.41967130T>C		NA		hg19		0.02	-0.043866	TGAxGTT	UNCOVERED																																																																																			NOVEL	RP11-204M4.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000143738.1	2	2.406698	KEEP	0	0	0	8	238	TT	0.99257	0.023895	0		-	2	49	70	0	0	6.492708	3	60	115	19	ENST00000454645.1	0.4	0.024074
RP11-204M4.2	0	__UNKNOWN__	__UNKNOWN__	9	41967144	41967144	__UNKNOWN__	lincRNA	SNP	T	T	C	rs199993853		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:41967144T>C	ENST00000454645.1	-	0	653					NR_003670.1					NA		NA									NA						CCTTTCAATATGCACAAATAT	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000454645.1:	chr9.hg19:g.41967144T>C		NA		hg19		0.02	-0.043867	ATAxGCA	UNCOVERED																																																																																			NOVEL	RP11-204M4.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000143738.1	2	2.407221	KEEP	0	0	0	8	249	TT	0.99257	0.023895	0		-	2	49	78	0	0	7.292802	3	60	115	20	ENST00000454645.1	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	43315996	43315996	__UNKNOWN__	IGR	SNP	G	G	A	rs2874508		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:43315996G>A			NA	NA				RP11-327I22.8 (126585 upstream) : SPATA31A6 (308510 downstream)						NA		NA									NA						AGGGTTGTACGTTGGCCTTGC	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.43315996G>A		NA		hg19		0.02	3.879985	TACxTTG	COVERED																																																																																			NOVEL					0			2	4.213295	KEEP	2	0	0	14	475	GG	0.995343	0.995343	0			11	47	394	0	0	28.603325	111	60	3756	160		0.090164	0.999999
CNTNAP3B	728577	__UNKNOWN__	__UNKNOWN__	9	43816735	43816735	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs200986004	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:43816735G>C	ENST00000377564.3	+	6	1234	c.841G>C	c.(841-843)Gac>Cac	p.D281H	CNTNAP3B_ENST00000276974.6_Missense_Mutation_p.D281H	NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	281	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.	NA			cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						CGAGCTCCTCGACACGCAGGT	0.488	NA	NA											g|||	100	0.0199681	0.0166	0.0101	5008	,	,	NA	22562	0.0466	NA	0.008	False	NA	,,,	NA	NA	NA	2504	0.0164	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529	728577			32035	protein-coding gene	gene with protein product		NA			NA	15820314	Standard		XM_006716853	NA	Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.841G>C	chr9.hg19:g.43816735G>C	ENSP00000366787:p.Asp281His	NA	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	hg19	CCDS55312.1	0.02	11.9854	CTCxACA	COVERED	.	.	.	.	.	.	.	.	.	.	g	14.89	2.671567	0.47781	.	.	ENSG00000154529	ENST00000377564;ENST00000276974;ENST00000341990;ENST00000403166	T;T	0.78246	-1.16;-1.16	2.77	-4.35	0.03656	.	.	.	.	.	T	0.60907	0.2305	N	0.14661	0.345	0.09310	N	1	.	.	.	.	.	.	T	0.56492	-0.7970	7	0.62326	D	0.03	.	8.1029	0.30868	0.5769:0.0:0.4231:0.0	.	.	.	.	H	281	ENSP00000366787:D281H;ENSP00000276974:D281H	ENSP00000276974:D281H	D	+	1	0	CNTNAP3B	43756731	0.000000	0.05858	0.000000	0.03702	0.466000	0.32739	0.894000	0.28350	-0.920000	0.03799	-0.506000	0.04501	GAC	NOVEL	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000036930.3	3	14.56148	KEEP	38	6	208	121	4191	GG	1	1	0		+	20	40	683	0	0	44.685155	327	50	12023	678	ENST00000377564.3	0.057637	1
RP11-374M1.3	0	__UNKNOWN__	__UNKNOWN__	9	45039064	45039064	__UNKNOWN__	lincRNA	SNP	G	G	A	rs1741046	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:45039064G>A	ENST00000441101.1	-	0	285										NA		NA									NA						CACATACATggccgggtgcag	0.567	NA	NA											g|||	1944	0.388179	0.3404	0.3746	5008	,	,	NA	32327	0.37	NA	0.4592	False	NA	,,,	NA	NA	NA	2504	0.408	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000441101.1:	chr9.hg19:g.45039064G>A		NA		hg19		0.02	-0.122808	ATGxCCG	COVERED																																																																																			NOVEL	RP11-374M1.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037010.1	1	2.708799	KEEP	5	0	0	9	324	GG	0.99257	0.194853	0		-	3	27	110	0	0	9.632495	8	50	278	37	ENST00000441101.1	0.272727	0.196312
RP11-374M1.3	0	__UNKNOWN__	__UNKNOWN__	9	45039066	45039066	__UNKNOWN__	lincRNA	SNP	C	C	T	rs1741047	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:45039066C>T	ENST00000441101.1	-	0	285										NA		NA									NA						CATACATggccgggtgcagtg	0.567	NA	NA											c|||	1944	0.388179	0.3404	0.3746	5008	,	,	NA	31349	0.37	NA	0.4592	False	NA	,,,	NA	NA	NA	2504	0.408	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000441101.1:	chr9.hg19:g.45039066C>T		NA		hg19		0.02	-0.131593	GGCxGGG	COVERED																																																																																			NOVEL	RP11-374M1.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037010.1	1	2.708726	KEEP	5	0	0	9	311	CC	0.99257	0.22747	0		-	3	27	122	0	0	10.700948	9	50	309	38	ENST00000441101.1	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	45362692	45362692	__UNKNOWN__	IGR	SNP	G	G	T	rs74791779	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:45362692G>T			NA	NA				RP11-449H15.2 (150191 upstream) : RP11-187C18.5 (31152 downstream)						NA		NA									NA						CCGACCTGTTGTTCACTTTGC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.45362692G>T		NA		hg19		0.02	2.152623	GTTxTTC	COVERED																																																																																			NOVEL					0			1	3.04559	KEEP	37	1	34	22	785	GG	0.999366	0.988916	0			5	47	186	0	0	14.560565	33	48	1247	145		0.131579	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	45362703	45362703	__UNKNOWN__	IGR	SNP	T	T	C	rs199890896		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:45362703T>C			NA	NA				RP11-449H15.2 (150202 upstream) : RP11-187C18.5 (31141 downstream)						NA		NA									NA						TTCACTTTGCTGGTGAGCCAG	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.45362703T>C		NA		hg19		0.02	2.178909	TGCxGGT	COVERED																																																																																			NOVEL					0			1	3.045175	KEEP	40	1	37	23	727	TT	0.999366	0.983538	0			5	47	175	0	0	13.400745	34	48	1325	143		0.128205	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	45363590	45363590	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:45363590G>C			NA	NA				RP11-449H15.2 (151089 upstream) : RP11-187C18.5 (30254 downstream)						NA		NA									NA						TCGGGCTCAGGGCCGGGAGCC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.45363590G>C		NA		hg19		0.02	-0.421077	CAGxGCC	COVERED																																																																																			NOVEL					0			1	14.082029	KEEP	75	0	0	47	1552	GG	0.99649	0.945073	0			11	49	379	0	0	35.69937	14	50	541	165		0.44	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	45363959	45363959	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:45363959G>C			NA	NA				RP11-449H15.2 (151458 upstream) : RP11-187C18.5 (29885 downstream)						NA		NA									NA						TGTGTCCCTTGATGGGTGCCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.45363959G>C		NA		hg19		0.02	2.496036	CTTxATG	UNCOVERED																																																																																			NOVEL					0			0	3.611414	KEEP	22	0	0	12	398	GG	0	0	0			4	25	156	0	0	11.455855	46	40	1743	93		0.08	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66455746	66455746	__UNKNOWN__	IGR	SNP	C	C	A	rs374442991		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66455746C>A			NA	NA				RP11-118H15.1 (571861 upstream) : RP11-262H14.1 (1542 downstream)						NA		NA									NA						GAGTGCGCCCCTCACTGTGGC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66455746C>A		NA		hg19		0.02	4.234673	CCCxTCA	COVERED																																																																																			NOVEL					0			2	2.775557	KEEP	2	2	59	30	1028	CG	0.999998	0.999966	0			4	57	149	0	0	10.723169	47	60	1712	150		0.078431	0.999968
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66457259	66457259	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66457259G>T			NA	NA				RP11-118H15.1 (573374 upstream) : RP11-262H14.1 (29 downstream)						NA		NA									NA						gagCACCACAGTagagcgcga	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66457259G>T		NA		hg19		0.02	9.919657	ACAxTAG	COVERED																																																																																			NOVEL					0			6	7.527485	KEEP	1	3	91	57	1992	GG	1	1	0			11	60	373	0	0	26.312296	116	60	4190	371		0.086614	1
RP11-262H14.1	0	__UNKNOWN__	__UNKNOWN__	9	66457330	66457330	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66457330G>T	ENST00000424345.1	+	0	42										NA		NA									NA						cagcgacagagccttggagag	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424345.1:	chr9.hg19:g.66457330G>T		NA		hg19		0.02	13.251231	AGAxCCT	COVERED																																																																																			NOVEL	RP11-262H14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000128851.1	5	14.284178	KEEP	28	4	121	90	3193	GG	1	1	0		+	12	49	429	0	0	29.793937	158	60	5897	507	ENST00000424345.1	0.070588	1
RP11-262H14.1	0	__UNKNOWN__	__UNKNOWN__	9	66457628	66457628	__UNKNOWN__	lincRNA	SNP	G	G	A	rs10907851	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66457628G>A	ENST00000424345.1	+	0	67										NA		NA									NA						CACGGGGCGAGGCCTGGGTCT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424345.1:	chr9.hg19:g.66457628G>A		NA		hg19		0.02	6.719145	CGAxGCC	COVERED																																																																																			NOVEL	RP11-262H14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000128851.1	2	6.485338	KEEP	9	4	114	62	2000	GG	1	1	0		+	6	49	222	0	0	15.710546	77	60	2627	296	ENST00000424345.1	0.072289	1
RP11-262H14.1	0	__UNKNOWN__	__UNKNOWN__	9	66457977	66457977	__UNKNOWN__	lincRNA	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66457977G>C	ENST00000424345.1	+	0	67										NA		NA									NA						GCCGCGAGTCGGAAGAGGTGG	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424345.1:	chr9.hg19:g.66457977G>C		NA		hg19		0.02	-0.289485	GTCxGAA	COVERED																																																																																			NOVEL	RP11-262H14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000128851.1	1	2.541211	KEEP	2	1	33	20	638	GG	0.999863	0.780953	0		+	4	42	141	0	0	11.161557	22	60	750	74	ENST00000424345.1	0.153846	0.78106
RP11-262H14.1	0	__UNKNOWN__	__UNKNOWN__	9	66458102	66458102	__UNKNOWN__	lincRNA	SNP	C	C	T	rs4471149	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66458102C>T	ENST00000424345.1	+	0	67										NA		NA									NA						TTGGGAAGCACGGAGACAAAA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424345.1:	chr9.hg19:g.66458102C>T		NA		hg19		0.02	-0.192983	GCAxGGA	COVERED																																																																																			NOVEL	RP11-262H14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000128851.1	1	5.052011	KEEP	2	0	0	17	494	CC	0.999366	0.457467	0		+	2	60	77	0	0	6.481423	8	60	251	49	ENST00000424345.1	0.2	0.457757
RP11-262H14.1	0	__UNKNOWN__	__UNKNOWN__	9	66461066	66461066	__UNKNOWN__	lincRNA	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66461066G>C	ENST00000424345.1	+	0	224										NA		NA									NA						tgctgttttggttactatggt	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424345.1:	chr9.hg19:g.66461066G>C		NA		hg19		0.02	-0.078961	TTGxTTA	UNCOVERED																																																																																			NOVEL	RP11-262H14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000128851.1	3	2.708445	KEEP	2	0	0	9	308	GG	0.99254	0.076759	0		+	2	25	79	0	0	7.392815	3	50	113	28	ENST00000424345.1	0.4	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66470010	66470010	__UNKNOWN__	IGR	SNP	G	G	A	rs4395999	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66470010G>A			NA	NA				RP11-262H14.1 (700 upstream) : RP11-262H14.7 (47195 downstream)						NA		NA									NA						acaggcgtgagccactgtgcc	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66470010G>A		NA		hg19		0.02	-0.087734	TGAxCCA	UNCOVERED																																																																																			NOVEL					0			4	2.70887	KEEP	6	0	0	9	319	GG	0.99257	0.09898	0			2	49	78	0	0	6.935513	5	50	186	31		0.285714	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66486224	66486224	__UNKNOWN__	IGR	SNP	G	G	A	rs199766004		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66486224G>A			NA	NA				RP11-262H14.1 (16914 upstream) : RP11-262H14.7 (30981 downstream)						NA		NA									NA						CCTGGTGCTGGGTCCTTCCAC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66486224G>A		NA		hg19		0.02	-0.175451	CTGxGTC	UNCOVERED																																																																																			NOVEL					0			0	3.611808	KEEP	18	0	0	12	422	GG	0	0	0			3	40	111	0	0	10.043524	6	40	210	49		0.333333	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66493571	66493571	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66493571G>T			NA	NA				RP11-262H14.1 (24261 upstream) : RP11-262H14.7 (23634 downstream)						NA		NA									NA						CTAGCCAAGGGCCCTCTGCAG	0.716	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66493571G>T		NA		hg19		0.02	-0.217966	AGGxCCC	COVERED																																																																																			NOVEL					0			3	9.869978	KEEP	15	0	0	33	1027	GG	0.999931	0.552849	0			3	27	106	0	0	8.057218	22	50	776	82		0.12	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66499180	66499180	__UNKNOWN__	IGR	SNP	T	T	C	rs2633108		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66499180T>C			NA	NA				RP11-262H14.1 (29870 upstream) : RP11-262H14.7 (18025 downstream)						NA		NA									NA						ACTGGGGCCGTTACACGTGAC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66499180T>C		NA		hg19		0.02	4.946338	CCGxTAC	COVERED																																																																																			NOVEL					0			1	7.319002	KEEP	5	3	111	63	1792	TT	1	1	0			8	42	319	0	0	22.40388	132	60	4682	237		0.057143	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66499218	66499218	__UNKNOWN__	IGR	SNP	C	C	T	rs538963479		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66499218C>T			NA	NA				RP11-262H14.1 (29908 upstream) : RP11-262H14.7 (17987 downstream)						NA		NA									NA						AGGCAAAGGGCGCGGAGATGC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66499218C>T		NA		hg19		0.02	4.732408	GGGxGCG	COVERED																																																																																			NOVEL					0			1	13.946267	KEEP	18	6	127	92	3230	CC	1	1	0			7	27	215	0	0	11.810782	185	60	6789	396		0.036458	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66499337	66499337	__UNKNOWN__	IGR	SNP	G	G	A	rs372955429		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66499337G>A			NA	NA				RP11-262H14.1 (30027 upstream) : RP11-262H14.7 (17868 downstream)						NA		NA									NA						ATACTAGGGAGCTACCTTTCC	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66499337G>A		NA		hg19		0.02	9.294852	GGAxCTA	COVERED																																																																																			NOVEL					0			2	6.770547	KEEP	26	3	92	55	1876	GG	1	1	0			8	49	289	0	0	18.398224	178	50	6616	370		0.043011	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66499385	66499385	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66499385G>T			NA	NA				RP11-262H14.1 (30075 upstream) : RP11-262H14.7 (17820 downstream)						NA		NA									NA						AGATAGGCTGGGGGGAGGAAG	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66499385G>T		NA		hg19		0.02	4.202561	CTGxGGG	COVERED																																																																																			NOVEL					0			3	4.810201	KEEP	26	0	0	16	500	GG	0.997832	0.997825	0			10	40	340	0	0	24.896089	85	40	2986	155		0.105263	0.999994
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66499694	66499694	__UNKNOWN__	IGR	SNP	A	A	G	rs111388370		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66499694A>G			NA	NA				RP11-262H14.1 (30384 upstream) : RP11-262H14.7 (17511 downstream)						NA		NA									NA						TCCCAGGCCAATGTGTCCTTG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66499694A>G		NA		hg19		0.02	2.214104	CCAxTGT	COVERED																																																																																			NOVEL					0			1	3.008691	KEEP	0	0	0	10	301	AA	0.992708	0.966863	0			10	47	374	0	0	31.117317	42	55	1449	71		0.192308	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66800792	66800792	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:66800792G>C			NA	NA				RP11-318K12.2 (41420 upstream) : AL353626.1 (57744 downstream)						NA		NA									NA						tgttgaaaaaggaaatatctt	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66800792G>C		NA		hg19		0.02	4.464712	AAAxGAA	COVERED																																																																																			NOVEL					0			116	29.644365	KEEP	67	3	110	137	4951	GG	1	1	0			5	44	171	0	1	12.94301	35	60	1304	474		0.125	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	67047230	67047230	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:67047230G>T			NA	NA				RP11-381O7.3 (15158 upstream) : AL591379.1 (47702 downstream)						NA		NA									NA						GACCGGTCCCGTTGCTACAGC	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.67047230G>T		NA		hg19		0.02	2.341531	CCCxTTG	COVERED																																																																																			NOVEL					0			3	3.479691	KEEP	55	2	58	32	1117	GG	0.999892	0.999514	0			6	23	221	0	0	15.743614	73	25	2739	194		0.075949	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	67273546	67273546	__UNKNOWN__	IGR	SNP	T	T	C	rs12238799	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:67273546T>C			NA	NA				AL845321.1 (48094 upstream) : RP11-236F9.2 (16023 downstream)						NA		NA									NA						CAGTGCACAGTTAGTGAAGCT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.67273546T>C		NA		hg19		0.02	7.433552	CAGxTAG	COVERED																																																																																			NOVEL					0			0	7.388695	KEEP	20	5	191	91	2902	TT	1	1	0			24	47	954	0	0	75.264251	171	60	6213	426		0.123077	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	67273568	67273568	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:67273568T>C			NA	NA				AL845321.1 (48116 upstream) : RP11-236F9.2 (16001 downstream)						NA		NA									NA						ACAGCTGCGTTCATGTGGGCT	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.67273568T>C		NA		hg19		0.02	7.553046	CGTxCAT	COVERED																																																																																			NOVEL					0			0	5.987949	KEEP	19	5	160	76	2399	TT	1	1	0			18	47	664	0	0	50.051817	152	60	5506	345		0.105882	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	67283582	67283582	__UNKNOWN__	IGR	SNP	A	A	T	rs12236708	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:67283582A>T			NA	NA				AL845321.1 (58130 upstream) : RP11-236F9.2 (5987 downstream)						NA		NA									NA						caaaaaaaaaatacaaaaatt	0.512	NA	NA											A|||	2427	0.484625	0.497	0.4294	5008	,	,	NA	29064	0.4742	NA	0.4642	False	NA	,,,	NA	NA	NA	2504	0.5389	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.67283582A>T		NA		hg19		0.02	-0.157915	AAAxTAC	COVERED																																																																																			NOVEL					0			4	2.707232	KEEP	3	0	0	9	261	AA	0.99257	0.320408	0			5	54	184	0	0	16.313134	12	55	435	33		0.294118	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	67335967	67335967	__UNKNOWN__	IGR	SNP	T	T	C	rs71251472|rs4043431		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:67335967T>C			NA	NA				RP11-236F9.2 (37335 upstream) : RP11-38P6.1 (243839 downstream)						NA		NA									NA						gccataattgtgtcactgaac	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.67335967T>C		NA		hg19		0.02	-0.1316	TTGxGTC	COVERED																																																																																			NOVEL					0			1	2.708423	KEEP	1	0	0	9	288	TT	0.99254	0.259018	0			6	40	230	0	0	21.710517	8	60	298	31		0.428571	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	67335968	67335968	__UNKNOWN__	IGR	SNP	G	G	A	rs71251472|rs3882292		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:67335968G>A			NA	NA				RP11-236F9.2 (37336 upstream) : RP11-38P6.1 (243838 downstream)						NA		NA									NA						ccataattgtgtcactgaact	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.67335968G>A		NA		hg19		0.02	-0.140359	TGTxTCA	COVERED																																																																																			NOVEL					0			1	2.708943	KEEP	1	0	0	9	328	GG	0.99254	0.259018	0			6	40	212	0	0	19.910308	8	60	294	31		0.428571	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68357664	68357664	__UNKNOWN__	IGR	SNP	A	A	G	rs113923126	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68357664A>G			NA	NA				RP11-149F8.5 (17020 upstream) : RP11-764K9.1 (40213 downstream)						NA		NA									NA						TCCTCAAGCTAACTTATATTG	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68357664A>G		NA		hg19		0.02	-0.412311	GCTxACT	COVERED																																																																																			NOVEL					0			1	3.910597	KEEP	2	0	0	13	382	AA	0.994391	0.936459	0			3	37	122	0	0	8.81566	43	60	1520	71		0.065217	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68372223	68372223	__UNKNOWN__	IGR	SNP	C	C	T	rs183510740		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68372223C>T			NA	NA				RP11-149F8.5 (31579 upstream) : RP11-764K9.1 (25654 downstream)						NA		NA									NA						CCTCCCATTCCTCTTCCTCCC	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68372223C>T		NA		hg19		0.02	1.991414	TTCxTCT	UNCOVERED																																																																																			NOVEL					0			3	2.698912	KEEP	54	0	0	9	273	CC	0	0	0			6	40	219	0	0	16.909671	42	40	1537	133		0.125	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68372229	68372229	__UNKNOWN__	IGR	SNP	C	C	T	rs372709317		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68372229C>T			NA	NA				RP11-149F8.5 (31585 upstream) : RP11-764K9.1 (25648 downstream)						NA		NA									NA						ATTCCTCTTCCTCCCCCCAGC	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68372229C>T		NA		hg19		0.02	2.191024	TTCxTCC	UNCOVERED																																																																																			NOVEL					0			2	2.704001	KEEP	53	0	0	9	282	CC	0	0	0			6	40	219	0	0	17.028527	40	40	1459	133		0.130435	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68380450	68380450	__UNKNOWN__	IGR	SNP	C	C	T	rs113547259		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68380450C>T			NA	NA				RP11-149F8.5 (39806 upstream) : RP11-764K9.1 (17427 downstream)						NA		NA									NA						CTGCCCTGGGCGAGGGAGCCT	0.736	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68380450C>T		NA		hg19		0.02	-0.350866	GGGxGAG	COVERED																																																																																			NOVEL					0			0	5.110197	KEEP	3	0	0	17	552	CC	0.997832	0.875805	0			4	60	145	0	0	12.9245	9	60	284	72		0.307692	0.877708
RP11-764K9.1	0	__UNKNOWN__	__UNKNOWN__	9	68405065	68405065	__UNKNOWN__	lincRNA	SNP	C	C	A	rs4401986		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68405065C>A	ENST00000417843.2	-	0	224										NA		NA									NA						ggcagtgacacaacaaaaaaa	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417843.2:	chr9.hg19:g.68405065C>A		NA		hg19		0.02	-0.289515	ACAxAAC	COVERED																																																																																			NOVEL	RP11-764K9.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000129817.2	0	2.708961	KEEP	0	0	0	9	330	CC	0.99254	0.755211	0		-	3	27	113	0	0	9.378318	13	60	471	50	ENST00000417843.2	0.1875	0.760887
RP11-764K9.1	0	__UNKNOWN__	__UNKNOWN__	9	68405126	68405126	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68405126C>T	ENST00000417843.2	-	0	224										NA		NA									NA						taatccacaacaaaatacttg	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417843.2:	chr9.hg19:g.68405126C>T		NA		hg19		0.02	-0.140373	CAAxAAA	COVERED																																																																																			NOVEL	RP11-764K9.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000129817.2	0	2.407818	KEEP	1	0	0	8	289	CC	0.99257	0.320408	0		-	3	49	114	0	0	9.781593	10	60	383	34	ENST00000417843.2	0.230769	0.322807
RP11-764K9.1	0	__UNKNOWN__	__UNKNOWN__	9	68409304	68409304	__UNKNOWN__	lincRNA	SNP	C	C	T	rs62545662		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68409304C>T	ENST00000417843.2	-	0	67										NA		NA									NA						TCACGCTCCCCGGACTCCCAG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417843.2:	chr9.hg19:g.68409304C>T		NA		hg19		0.02	-0.184183	CCCxGGA	COVERED																																																																																			NOVEL	RP11-764K9.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000129817.2	3	4.513582	KEEP	2	0	0	15	490	CC	0.99649	0.421991	0		-	3	60	112	0	0	11.654294	1	27	43	52	ENST00000417843.2	0.75	0.423478
RP11-764K9.1	0	__UNKNOWN__	__UNKNOWN__	9	68409370	68409370	__UNKNOWN__	lincRNA	SNP	C	C	T	rs62545663		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68409370C>T	ENST00000417843.2	-	0	67										NA		NA									NA						GTGGAAGGGGCGAGCAGGGGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417843.2:	chr9.hg19:g.68409370C>T		NA		hg19		0.02	-0.192986	GGGxGAG	COVERED																																																																																			NOVEL	RP11-764K9.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000129817.2	0	2.70842	KEEP	1	0	0	9	298	CC	0.99254	0.454342	0		-	3	60	107	0	0	9.332211	8	58	286	39	ENST00000417843.2	0.272727	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68414257	68414257	__UNKNOWN__	IGR	SNP	G	G	A	rs147144293		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68414257G>A			NA	NA				RP11-764K9.1 (4364 upstream) : MIR4477B (1050 downstream)						NA		NA									NA						aaccacagtggcctcaaagaa	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68414257G>A		NA		hg19		0.02	-0.271933	GTGxCCT	COVERED																																																																																			NOVEL					0			1	2.662685	KEEP	0	0	0	9	285	GG	0.99254	0.711964	0			3	60	85	0	0	7.44192	6	60	220	52		0.333333	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415593	68415593	__UNKNOWN__	IGR	SNP	A	A	G	rs74873739		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68415593A>G			NA	NA				MIR4477B (205 upstream) : CR786580.2 (96752 downstream)						NA		NA									NA						gttgcttcttatggacgagca	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415593A>G		NA		hg19		0.02	2.408349	CTTxTGG	COVERED																																																																																			NOVEL					0			1	3.609095	KEEP	0	0	0	12	345	AA	0.993634	0.988091	0			3	60	120	0	0	8.738437	39	60	1407	78		0.071429	0.994422
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415736	68415736	__UNKNOWN__	IGR	SNP	C	C	T	rs79090368		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68415736C>T			NA	NA				MIR4477B (348 upstream) : CR786580.2 (96609 downstream)						NA		NA									NA						agagggtttactccaattttg	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415736C>T		NA		hg19		0.02	6.936071	TTAxTCC	COVERED																																																																																			NOVEL					0			8	2.414471	KEEP	1	3	100	43	1577	CC	1	1	0			10	60	366	0	0	26.621381	105	60	4060	290		0.086957	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415758	68415758	__UNKNOWN__	IGR	SNP	A	A	G	rs148226791		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68415758A>G			NA	NA				MIR4477B (370 upstream) : CR786580.2 (96587 downstream)						NA		NA									NA						aagaagttctactgttgataa	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415758A>G		NA		hg19		0.02	8.059886	TCTxCTG	COVERED																																																																																			NOVEL					0			3	4.847522	KEEP	0	1	37	29	842	AA	0.999997	0.999997	0			15	60	580	0	0	47.392346	77	60	2737	229		0.163043	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415809	68415809	__UNKNOWN__	IGR	SNP	T	T	G	rs76710627		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68415809T>G			NA	NA				MIR4477B (421 upstream) : CR786580.2 (96536 downstream)						NA		NA									NA						ggaaatcttttgtgaaaggaa	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415809T>G		NA		hg19		0.02	2.34691	TTTxGTG	COVERED																																																																																			NOVEL					0			1	2.407061	KEEP	1	0	0	8	241	TT	0.99257	0.990484	0			4	60	140	0	0	10.616279	29	60	1050	85		0.121212	0.997898
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68427854	68427854	__UNKNOWN__	IGR	SNP	C	C	T	rs140372562		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68427854C>T			NA	NA				MIR4477B (12466 upstream) : CR786580.2 (84491 downstream)						NA		NA									NA						AAACAAAAATCCCAGTCATTT	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68427854C>T		NA		hg19		0.02	34.102585	AATxCCA	COVERED																																																																																			NOVEL					0			9	24.437742	KEEP	39	11	329	197	6830	CC	1	1	0			21	40	745	0	0	44.759051	596	70	21837	1243		0.034036	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68429234	68429234	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68429234A>G			NA	NA				MIR4477B (13846 upstream) : CR786580.2 (83111 downstream)						NA		NA									NA						GATTATACATATTTACTATTA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68429234A>G		NA		hg19		0.02	8.99238	CATxTTT	COVERED																																																																																			NOVEL					0			36	12.791391	KEEP	14	2	73	68	1925	AA	1	1	0			11	60	414	0	0	27.870105	201	60	7358	366		0.051887	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68433379	68433379	__UNKNOWN__	IGR	SNP	A	A	G	rs1825863		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68433379A>G			NA	NA				MIR4477B (17991 upstream) : CR786580.2 (78966 downstream)						NA		NA									NA						CTTTAAAGTGACAGTAAATGA	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68433379A>G		NA		hg19		0.02	29.026851	GTGxCAG	COVERED																																																																																			NOVEL					0			15	4.018976	KEEP	14	6	208	86	2688	AA	1	1	0			63	60	2210	0	0	166.06758	487	60	17056	856		0.114545	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68433511	68433511	__UNKNOWN__	IGR	SNP	C	C	T	rs372742056|rs202018667		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68433511C>T			NA	NA				MIR4477B (18123 upstream) : CR786580.2 (78834 downstream)						NA		NA									NA						TTCTATGTCCCCTGCTTCATT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68433511C>T		NA		hg19		0.02	28.672529	TCCxCTG	COVERED																																																																																			NOVEL					0			3	6.586149	KEEP	68	5	157	77	2556	CC	1	1	0			15	40	567	0	0	39.52278	224	60	8128	835		0.062762	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68433657	68433657	__UNKNOWN__	IGR	SNP	A	A	C	rs141211711		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68433657A>C			NA	NA				MIR4477B (18269 upstream) : CR786580.2 (78688 downstream)						NA		NA									NA						TTCCTCCCTGATTTAAAAATC	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68433657A>C		NA		hg19		0.02	27.167842	CTGxTTT	COVERED																																																																																			NOVEL					0			19	6.48525	KEEP	8	2	79	49	1381	AA	1	1	0			18	60	679	0	0	44.23592	402	60	14802	657		0.042857	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68452821	68452821	__UNKNOWN__	IGR	SNP	G	G	A	rs112219831		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68452821G>A			NA	NA				MIR4477B (37433 upstream) : CR786580.2 (59524 downstream)						NA		NA									NA						TAATATTTAAGCACTTTAAGA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68452821G>A		NA		hg19		0.02	10.345832	TAAxCAC	COVERED																																																																																			NOVEL					0			4	2.443546	KEEP	12	1	34	20	707	GG	0.99986	0.99986	0			48	46	1701	0	0	139.089804	211	48	7980	310		0.185328	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68454404	68454404	__UNKNOWN__	IGR	SNP	A	A	G	rs75574725		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68454404A>G			NA	NA				MIR4477B (39016 upstream) : CR786580.2 (57941 downstream)						NA		NA									NA						AAAAAGAAGCAGGGATATGAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68454404A>G		NA		hg19		0.02	6.359376	AGCxGGG	COVERED																																																																																			NOVEL					0			3	2.739243	KEEP	51	1	28	19	554	AA	0.99649	0.99649	0			10	54	353	0	0	27.609668	60	60	2218	264		0.142857	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68484625	68484625	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68484625C>T			NA	NA				MIR4477B (69237 upstream) : CR786580.2 (27720 downstream)						NA		NA									NA						cttccaactcctggcctcaag	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68484625C>T		NA		hg19		0.02	2.143908	CTCxTGG	COVERED																																																																																			NOVEL					0			9	5.553613	KEEP	0	1	33	30	1077	CC	0.999997	0.990961	0			3	47	114	0	0	8.904937	21	60	760	119		0.125	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68484698	68484698	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68484698C>T			NA	NA				MIR4477B (69310 upstream) : CR786580.2 (27647 downstream)						NA		NA									NA						ccatgcTGGTCCTGATGTCAT	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68484698C>T		NA		hg19		0.02	2.296325	GGTxCTG	COVERED																																																																																			NOVEL					0			2	3.611446	KEEP	3	0	0	12	408	CC	0.993634	0.97329	0			6	47	224	0	0	19.279913	19	55	675	82		0.24	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68504849	68504849	__UNKNOWN__	IGR	SNP	G	G	T	rs111648802		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68504849G>T			NA	NA				MIR4477B (89461 upstream) : CR786580.2 (7496 downstream)						NA		NA									NA						AGAGAGGGATGATTTCCTTCC	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68504849G>T		NA		hg19		0.02	2.088178	GATxATT	COVERED																																																																																			NOVEL					0			7	3.912941	KEEP	1	0	0	13	473	GG	0.994391	0.976447	0			3	47	112	0	0	8.492814	25	55	937	106		0.107143	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68681913	68681913	__UNKNOWN__	IGR	SNP	C	C	T	rs373813873		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68681913C>T			NA	NA				CR786580.1 (168726 upstream) : AL353763.2 (315495 downstream)						NA		NA									NA						cttggcctcccaaagtgctgg	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68681913C>T		NA		hg19		0.02	-0.403574	TCCxAAA	COVERED																																																																																			NOVEL					0			8	2.277711	KEEP	4	2	64	30	1068	CC	0.999997	0.93449	0			6	27	228	0	0	17.927892	40	50	1525	116		0.130435	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68681947	68681947	__UNKNOWN__	IGR	SNP	C	C	A	rs367656476		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68681947C>A			NA	NA				CR786580.1 (168760 upstream) : AL353763.2 (315461 downstream)						NA		NA									NA						agccaccatgcccagtcctaa	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68681947C>A		NA		hg19		0.02	-0.298262	ATGxCCA	COVERED																																																																																			NOVEL					0			5	7.824791	KEEP	10	0	0	26	914	CC	0.999957	0.800211	0			4	27	145	0	0	11.061031	30	50	1118	102		0.117647	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68681948	68681948	__UNKNOWN__	IGR	SNP	C	C	T	rs371385362		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68681948C>T			NA	NA				CR786580.1 (168761 upstream) : AL353763.2 (315460 downstream)						NA		NA									NA						gccaccatgcccagtcctaaa	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68681948C>T		NA		hg19		0.02	-0.30706	TGCxCAG	COVERED																																																																																			NOVEL					0			5	8.426938	KEEP	10	0	0	28	968	CC	0.999957	0.800211	0			3	27	101	0	0	7.126685	31	50	1145	102		0.088235	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68726259	68726259	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68726259C>G			NA	NA				CR786580.1 (213072 upstream) : AL353763.2 (271149 downstream)						NA		NA									NA						GCCCGCAGCTCTAGCGGGAGG	0.756	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68726259C>G		NA		hg19		0.02	-0.297868	GCTxTAG	COVERED																																																																																			NOVEL					0			3	5.552337	KEEP	26	1	36	31	1048	CC	0.999909	0.780989	0			4	49	146	0	0	12.738285	11	50	383	111		0.266667	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728799	68728799	__UNKNOWN__	IGR	SNP	A	A	T	rs4928724	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68728799A>T			NA	NA				CR786580.1 (215612 upstream) : AL353763.2 (268609 downstream)						NA		NA									NA						ACACAAATCAATATACTTAAA	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728799A>T		NA		hg19		0.02	11.419816	TCAxTAT	COVERED																																																																																			NOVEL					0			2	4.803907	KEEP	7	3	85	46	1406	AA	1	1	0			11	60	366	0	0	29.445259	49	60	1714	309		0.183333	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728952	68728952	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68728952T>C			NA	NA				CR786580.1 (215765 upstream) : AL353763.2 (268456 downstream)						NA		NA									NA						TTAACATTTCTTGAGATCTCA	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728952T>C		NA		hg19		0.02	20.71687	TTCxTGA	COVERED																																																																																			NOVEL					0			2	16.431101	KEEP	48	8	291	156	5064	TT	1	1	0			32	59	1228	0	0	87.822449	422	60	15536	870		0.070485	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728997	68728997	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:68728997T>C			NA	NA				CR786580.1 (215810 upstream) : AL353763.2 (268411 downstream)						NA		NA									NA						ATTTATGATGTATTCATATTT	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728997T>C		NA		hg19		0.02	8.613083	ATGxATT	COVERED																																																																																			NOVEL					0			1	5.403379	KEEP	32	3	94	51	1474	TT	1	1	0			7	40	266	0	0	16.616404	203	50	7057	300		0.033333	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69065535	69065535	__UNKNOWN__	IGR	SNP	C	C	A	rs79836909	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:69065535C>A			NA	NA				MIR1299 (63214 upstream) : PGM5P2 (14704 downstream)						NA		NA									NA						GACAGACCTACGCTGTCGGGG	0.602	NA	NA											.|||	2299	0.459065	0.525	0.379	5008	,	,	NA	16232	0.5069	NA	0.3519	False	NA	,,,	NA	NA	NA	2504	0.4877	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69065535C>A		NA		hg19		0.02	24.586426	CTAxGCT	COVERED																																																																																			NOVEL					0			9	17.423945	KEEP	146	12	372	189	6248	CC	1	1	0			40	60	1522	0	0	150.896406	29	60	1047	1083		0.57971	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69067824	69067824	__UNKNOWN__	IGR	SNP	A	A	T	rs371906163		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:69067824A>T			NA	NA				MIR1299 (65503 upstream) : PGM5P2 (12415 downstream)						NA		NA									NA						ACACAAATCAATATACTTAAA	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69067824A>T		NA		hg19		0.02	6.868046	TCAxTAT	COVERED																																																																																			NOVEL					0			5	7.22131	KEEP	35	0	0	24	745	AA	0.999869	0.999869	0			14	55	526	0	0	44.787901	49	60	1762	220		0.222222	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69067973	69067973	__UNKNOWN__	IGR	SNP	C	C	G	rs377553662		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:69067973C>G			NA	NA				MIR1299 (65652 upstream) : PGM5P2 (12266 downstream)						NA		NA									NA						GTTAACATTTCTTGAGATCTC	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69067973C>G		NA		hg19		0.02	11.35871	TTTxTTG	COVERED																																																																																			NOVEL					0			6	11.91205	KEEP	103	2	73	65	2364	CC	1	1	0			11	40	423	0	0	27.408466	269	50	10324	567		0.039286	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69067974	69067974	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:69067974T>C			NA	NA				MIR1299 (65653 upstream) : PGM5P2 (12265 downstream)						NA		NA									NA						TTAACATTTCTTGAGATCTCA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69067974T>C		NA		hg19		0.02	11.103839	TTCxTGA	COVERED																																																																																			NOVEL					0			6	7.331136	KEEP	103	3	111	63	2062	TT	1	1	0			9	40	333	0	0	20.429146	264	50	9725	560		0.032967	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69634664	69634664	__UNKNOWN__	IGR	SNP	G	G	C	rs113223844	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:69634664G>C			NA	NA				AL445665.2 (47220 upstream) : AL445665.1 (15598 downstream)						NA		NA									NA						GTGAAGATGCGGGGGGGGCAG	0.567	NA	NA											G|||	1493	0.298123	0.3442	0.2205	5008	,	,	NA	34516	0.3065	NA	0.2078	False	NA	,,,	NA	NA	NA	2504	0.3753	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69634664G>C		NA		hg19		0.02	4.508349	TGCxGGG	COVERED																																																																																			NOVEL					0			1	2.576427	KEEP	6	2	67	32	1051	GG	0.999998	0.999998	0			18	31	633	0	1	51.000612	87	60	3143	222		0.171429	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69830318	69830318	__UNKNOWN__	IGR	SNP	G	G	A	rs4507870	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:69830318G>A			NA	NA				AL359955.1 (8477 upstream) : RNU6-1293P (62468 downstream)						NA		NA									NA						GGATGTAGCCGTAGAATTCTG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69830318G>A		NA		hg19		0.02	1.874209	GCCxTAG	COVERED																																																																																			NOVEL					0			1	2.407467	KEEP	0	0	0	8	273	GG	0.99257	0.989319	0			4	25	136	0	0	8.853674	66	60	2273	92		0.057143	0.996724
PCSK5	5125	__UNKNOWN__	__UNKNOWN__	9	78790187	78790187	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs10118321	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:78790187G>C	ENST00000376767.3	+	14	2554	c.2042G>C	c.(2041-2043)tGg>tCg	p.W681S	PCSK5_ENST00000545128.1_Intron|PCSK5_ENST00000376752.4_Intron			Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	0	CRM (Cys-rich motif).	NA			anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ggaatggaatggaatcgaatc	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139	5125			8747	protein-coding gene	gene with protein product		600488			NA	7782070	Standard		NM_001190482	NA	Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000376767.3:c.2042G>C	chr9.hg19:g.78790187G>C	ENSP00000365958:p.Trp681Ser	NA	F5H2G7|Q13527|Q96EP4	hg19		0.02	1.716245	AATxGAA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	0.135|0.135	-1.109232|-1.109232	0.01813|0.01813	.|.	.|.	ENSG00000099139|ENSG00000099139	ENST00000396108|ENST00000376767	.|T	.|0.78126	.|-1.15	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.69043|0.69043	0.3067|0.3067	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|P	.|0.44006	.|0.824	.|B	.|0.42959	.|0.403	T|T	0.60073|0.60073	-0.7334|-0.7334	4|7	0.14252|0.72032	T|D	0.57|0.01	.|.	4.6597|4.6597	0.12636|0.12636	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs10118321|rs10118321	.|681	.|B1AMG5	.|.	I|S	679|681	.|ENSP00000365958:W681S	ENSP00000379415:M679I|ENSP00000365958:W681S	M|W	+|+	3|2	0|0	PCSK5|PCSK5	77980007|77980007	0.006000|0.006000	0.16342|0.16342	0.095000|0.095000	0.20976|0.20976	0.096000|0.096000	0.18686|0.18686	-1.253000|-1.253000	0.02877|0.02877	-0.000000|-0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	ATG|TGG	NOVEL	PCSK5-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000052718.1	19	6.320594	KEEP	15	0	0	21	746	GG	0.999366	0.999135	0		+	14	60	467	0	0	38.673679	51	60	1785	132	ENST00000376767.3	0.215385	0.999768
PCSK5	5125	__UNKNOWN__	__UNKNOWN__	9	78790207	78790207	__UNKNOWN__	Silent	SNP	C	C	A	rs55947300|rs10124596|rs71372053	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:78790207C>A	ENST00000376767.3	+	14	2574	c.2062C>A	c.(2062-2064)Cga>Aga	p.R688R	PCSK5_ENST00000545128.1_Intron|PCSK5_ENST00000376752.4_Intron			Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	0	CRM (Cys-rich motif).	NA			anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						cgaatcgaatcgaatagaata	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139	5125			8747	protein-coding gene	gene with protein product		600488			NA	7782070	Standard		NM_001190482	NA	Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000376767.3:c.2062C>A	chr9.hg19:g.78790207C>A		NA	F5H2G7|Q13527|Q96EP4	hg19		0.02	2.208606	AATxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	N	0.971	-0.700223	0.03279	.	.	ENSG00000099139	ENST00000396108	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	1.4193	0.02309	0.3429:0.3282:0.0:0.3289	rs10124596	.	.	.	X	686	.	ENSP00000379415:S686X	S	+	2	0	PCSK5	77980027	0.000000	0.05858	0.006000	0.13384	0.010000	0.07245	-3.492000	0.00453	-2.375000	0.00598	-2.399000	0.00225	TCG	NOVEL	PCSK5-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000052718.1	6	3.310383	KEEP	1	0	0	11	362	CC	0.993072	0.98819	0		+	26	60	947	0	0	93.073179	21	60	685	79	ENST00000376767.3	0.553191	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	94788927	94788927	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:94788927C>T			NA	NA				ROR2 (76483 upstream) : SPTLC1 (5353 downstream)						NA		NA									NA						CTCGCGGCCGCGCGTCCTGTG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.94788927C>T		NA		hg19		0.02	4.382368	CCGxGCG	COVERED																																																																																			NOVEL					0			3	48.753216	KEEP	0	0	0	162	5547	CC	1	1	0			13	60	445	0	0	32.11496	123	60	4379	436		0.095588	1
HIATL1	84641	__UNKNOWN__	__UNKNOWN__	9	97190662	97190662	__UNKNOWN__	Intron	SNP	G	G	A	rs117399794	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:97190662G>A	ENST00000375344.3	+	3	473				HIATL1_ENST00000428393.2_Intron	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				AGTACAGGCAGGTAGAGTTCA	0.289	NA	NA											N|||	3762	0.751198	0.9796	0.7536	5008	,	,	NA	9324	0.6567	NA	0.6421	False	NA	,,,	NA	NA	NA	2504	0.6503	NA	NA	NA	Pancreas(77;1260 1915 1973 10423)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110	84641			23376	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032558	XM_005252277	NA	Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.205-809G>A	chr9.hg19:g.97190662G>A		NA	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	hg19	CCDS6710.2	0.02	-0.2632	GCAxGTA	COVERED																																																																																			NOVEL	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053184.1	0	4.213912	KEEP	6	0	0	14	508	GG	0.995343	0.690438	0		+	6	40	218	0	0	18.143437	24	50	923	61	ENST00000375344.3	0.2	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	99961638	99961638	__UNKNOWN__	IGR	SNP	C	C	G	rs41316516	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:99961638C>G			NA	NA				RP11-498P14.3 (1669 upstream) : RP11-498P14.4 (33844 downstream)						NA		NA									NA						AGTTTTCACACAAGTTTTGCT	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						151	219	197	NA		NA	NA	9		NA											NA				99961638		1908	4226	6134	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.99961638C>G		NA		hg19		0.02	2.138359	ACAxAAG	COVERED	507	0.23214285714285715	160	0.3252032520325203	102	0.281767955801105	136	0.23776223776223776	109	0.1437994722955145	N	0.920	-0.716024	0.03206	.	.	ENSG00000188801	ENST00000375210	.	.	.	.	.	.	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.310936	0.23389	N	0.048720	T	0.00012	0.0000	.	.	.	0.20489	N	0.999891	B	0.02656	0.0	B	0.01281	0.0	T	0.42050	-0.9474	5	.	.	.	-1.6877	3.5811	0.07954	2.0E-4:0.4998:0.4998:2.0E-4	rs41316516	52	Q5SYY0	Z322B_HUMAN	F	52	.	.	L	-	3	2	ZNF322P1	99001459	0.066000	0.20996	0.000000	0.03702	0.000000	0.00434	0.073000	0.14640	-0.000000	0.14550	0.000000	0.15137	TTG	NOVEL					0			0	11.437832	KEEP	20	0	0	38	1393	CC	1	0.9982	0			6	40	214	0	0	15.221552	68	50	2611	159		0.081081	0.9982
COL27A1	85301	__UNKNOWN__	__UNKNOWN__	9	117073858	117073858	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:117073858C>A	ENST00000356083.3	+	0	6857					NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	NA		NA			extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						aaaacaaaaacaaaaacaaaa	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739	85301		Collagens	22986	protein-coding gene	gene with protein product		608461			NA	12766169	Standard	NM_032888	NM_032888	NA	Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.*883C>A	chr9.hg19:g.117073858C>A		NA	Q66K43|Q96JF7	hg19	CCDS6802.1	0.02	-0.329263	AAAxAAA	COVERED																																																																																			NOVEL	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053763.1	0	3.804616	KEEP	0	0	0	13	404	CC	0.994391	0.847205	0		+	7	60	138	0	0	9.607426	28	70	906	54	ENST00000356083.3	0.2	0.851984
LRSAM1	90678	__UNKNOWN__	__UNKNOWN__	9	130235930	130235930	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:130235930C>T	ENST00000323301.4	+	10	1223				LRSAM1_ENST00000300417.6_Intron|LRSAM1_ENST00000373324.4_Intron|LRSAM1_ENST00000373322.1_Intron	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	NA		NA			cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						gggctaggaccggtgaaaaac	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356	90678		Sterile alpha motif (SAM) domain containing	25135	protein-coding gene	gene with protein product		610933			NA	12975309	Standard	NM_138361	NM_001005373	NA	Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.620-150C>T	chr9.hg19:g.130235930C>T		NA	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	hg19	CCDS6873.1	0.02	2.340186	GACxGGT	COVERED																																																																																			NOVEL	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054164.1	2	3.30993	KEEP	0	0	0	11	346	CC	0.993072	0.957097	0		+	4	60	151	0	0	10.920411	47	60	1647	63	ENST00000323301.4	0.078431	0.963774
CEL	1056	__UNKNOWN__	__UNKNOWN__	9	135946015	135946015	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs77696629	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:135946015T>C	ENST00000372080.4	+	10	1479	c.1463T>C	c.(1462-1464)aTc>aCc	p.I488T	CEL_ENST00000351304.7_Intron	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	485		NA			cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		AAGGCCATGATCGCCTACTGG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						76	86	83	NA		NA	NA	9		NA											NA				135946015		2018	4177	6195	SO:0001583	missense			M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	1056	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	bile salt-stimulated lipase	114840			NA	1676983	Standard		NM_001807	NA	Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1463T>C	chr9.hg19:g.135946015T>C	ENSP00000361151:p.Ile488Thr	NA	Q16398|Q5T7U7|Q9UCH1|Q9UP41	hg19	CCDS43896.1	0.02	14.506694	TGAxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234627	0.79800	.	.	ENSG00000170835	ENST00000372080;ENST00000303626	T	0.68025	-0.3	5.72	4.57	0.56435	Carboxylesterase, type B (1);	0.094910	0.64402	D	0.000001	T	0.72993	0.3530	L	0.38175	1.15	0.80722	D	1	D	0.54047	0.964	D	0.75020	0.985	T	0.74463	-0.3657	10	0.87932	D	0	.	11.5416	0.50669	0.134:0.0:0.0:0.866	.	485	P19835	CEL_HUMAN	T	488;487	ENSP00000361151:I488T	ENSP00000304021:I487T	I	+	2	0	CEL	134935836	1.000000	0.71417	0.959000	0.39883	0.951000	0.60555	7.622000	0.83099	0.976000	0.38417	0.391000	0.25812	ATC	NOVEL	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054823.1	2	19.55914	KEEP	3	0	0	65	2060	TT	1	1	0		+	9	39	351	0	0	21.326898	333	60	11853	438	ENST00000372080.4	0.026316	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	135957837	135957837	__UNKNOWN__	IGR	SNP	T	T	G	rs1734945|rs386739102	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:135957837T>G			NA	NA				CEL (10589 upstream) : CELP (88 downstream)						NA		NA									NA						CACCTGAGGGTGTAGAGGGGA	0.597	NA	NA											g|||	966	0.192891	0.1112	0.3357	5008	,	,	NA	16382	0.1736	NA	0.341	False	NA	,,,	NA	NA	NA	2504	0.0695	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.135957837T>G		NA		hg19		0.02	-0.105214	GGGxGTA	UNCOVERED																																																																																			NOVEL					0			0	5.109415	KEEP	2	0	0	17	464	TT	0.999366	0.139743	0			2	40	78	0	0	6.40694	10	57	310	33		0.166667	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	135957917	135957917	__UNKNOWN__	IGR	SNP	A	A	G	rs1633754	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:135957917A>G			NA	NA				CEL (10669 upstream) : CELP (8 downstream)						NA		NA									NA						CGAGGCCCAGAGGGAGGGCCA	0.612	NA	NA											A|||	695	0.138778	0.0386	0.2565	5008	,	,	NA	14351	0.1389	NA	0.2674	False	NA	,,,	NA	NA	NA	2504	0.0583	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.135957917A>G		NA		hg19		0.02	-0.11405	CAGxGGG	UNCOVERED																																																																																			NOVEL					0			0	5.717187	KEEP	0	0	0	19	595	AA	0.99986	0.162444	0			3	40	103	0	0	8.681634	10	57	364	37		0.230769	0.162467
MIR3689A	100500846	__UNKNOWN__	__UNKNOWN__	9	137741344	137741344	__UNKNOWN__	RNA	SNP	C	C	T	rs149892846		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:137741344C>T	ENST00000578854.1	-	0	66					NR_037460.1				microRNA 3689a	NA		NA									NA						CCAGGAACCACGATATCACAC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							9	2011-09-12				ENSG00000265872	100500846		ncRNAs / Micro RNAs	38904	non-coding RNA	RNA, micro		NA			NA		Standard	NR_037460	NR_037460	NA	Approved	hsa-mir-3689a	uc022bpb.1			ENST00000578854.1:	chr9.hg19:g.137741344C>T		NA		hg19		0.02	-0.393739	CCAxGAT	COVERED																																																																																			NOVEL	MIR3689A-201	KNOWN	basic	miRNA	NA	miRNA		0	8.5488	KEEP	3	1	27	38	1247	CC	1	0.92664	0		-	11	49	404	0	0	35.047115	32	60	1054	102	ENST00000578854.1	0.255814	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	137741452	137741452	__UNKNOWN__	IGR	SNP	T	T	A	rs112586586	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:137741452T>A			NA	NA				MIR3689A (42 upstream) : MIR3689D1 (2 downstream)						NA		NA									NA						GGATCACACCTCTCAGGAAGA	0.592	NA	NA											t|||	1368	0.273163	0.1649	0.2911	5008	,	,	NA	9065	0.1954	NA	0.4473	False	NA	,,,	NA	NA	NA	2504	0.3078	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.137741452T>A		NA		hg19		0.02	-0.298225	ACCxCTC	COVERED																																																																																			NOVEL					0			0	9.921615	KEEP	17	0	0	33	954	TT	0.999892	0.780976	0			5	39	141	0	0	10.543466	26	49	926	92		0.16129	0.78106
KCNT1	57582	__UNKNOWN__	__UNKNOWN__	9	138594276	138594276	__UNKNOWN__	Intron	SNP	T	T	C	rs35105977		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:138594276T>C	ENST00000371757.2	+	1	177				KCNT1_ENST00000298480.5_Intron|KCNT1_ENST00000487664.1_Intron	NM_020822.2	NP_065873.2	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	NA		NA			potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		ACCCCCAAGTTCCCCCTCAGG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147	57582		Potassium channels, Voltage-gated ion channels / Potassium channels, calcium-activated	18865	protein-coding gene	gene with protein product		608167			NA	10718198, 16382103	Standard	NM_020822	NM_020822	NA	Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000371757.2:c.110+62T>C	chr9.hg19:g.138594276T>C		NA	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	hg19	CCDS35175.2	0.02	0.671768	AGTxCCC	COVERED																																																																																			NOVEL	KCNT1-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055021.2	0	6.658956	KEEP	0	2	10	26	712	TT	0.999997	0.992091	0		+	16	70	223	0	0	14.48606	47	70	1336	116	ENST00000371757.2	0.253968	0.992094
KCNT1	57582	__UNKNOWN__	__UNKNOWN__	9	138594294	138594294	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:138594294A>C	ENST00000371757.2	+	1	177				KCNT1_ENST00000298480.5_Intron|KCNT1_ENST00000487664.1_Intron	NM_020822.2	NP_065873.2	Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	NA		NA			potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		AGGCTCCCGCACCCTCCAGGA	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147	57582		Potassium channels, Voltage-gated ion channels / Potassium channels, calcium-activated	18865	protein-coding gene	gene with protein product		608167			NA	10718198, 16382103	Standard	NM_020822	NM_020822	NA	Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000371757.2:c.110+80A>C	chr9.hg19:g.138594294A>C		NA	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	hg19	CCDS35175.2	0.02	-0.284671	CGCxCCC	COVERED																																																																																			NOVEL	KCNT1-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055021.2	0	2.301674	KEEP	0	1	6	10	234	AA	0.993072	0.755616	0		+	12	70	177	0	0	13.913221	21	60	534	76	ENST00000371757.2	0.363636	0.760887
NOTCH1	4851	__UNKNOWN__	__UNKNOWN__	9	139395046	139395046	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:139395046C>T	ENST00000277541.6	-	31	5967	c.5892G>A	c.(5890-5892)ccG>ccA	p.P1964P		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1964		NA			anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CCGCATGCAGCGGGGTGCGGC	0.677	NA	NA	T, Mis, O	TRB@	T-ALL					HNSCC(8;0.001)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		9	9q34.3	4851	Notch homolog 1, translocation-associated (Drosophila) (TAN1)		L	0							NA						66	82	76	NA		NA	NA	9		NA											NA				139395046		2193	4294	6487	SO:0001819	synonymous_variant			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400	4851		Ankyrin repeat domain containing	7881	protein-coding gene	gene with protein product		190198	Notch (Drosophila) homolog 1 (translocation-associated), Notch homolog 1, translocation-associated (Drosophila)	TAN1	NA	1831692	Standard	NM_017617	NM_017617	NA	Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5892G>A	chr9.hg19:g.139395046C>T		NA	Q59ED8|Q5SXM3	hg19	CCDS43905.1	0.02	9.532095	CAGxGGG	COVERED																																																																																			NOVEL	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055087.1	2	38.781419	KEEP	0	0	0	129	4432	CC	1	1	0		-	77	60	2727	0	0	245.753344	153	60	5692	450	ENST00000277541.6	0.334783	1
LCN6	158062	__UNKNOWN__	__UNKNOWN__	9	139635852	139635852	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:139635852A>C	ENST00000435202.1	-	9	826				LCN10_ENST00000497771.1_Intron|LCN10_ENST00000527229.1_Intron|LCN10_ENST00000474369.1_Intron			P62502	LCN6_HUMAN	lipocalin 6	NA		NA			single fertilization (GO:0007338)	extracellular region (GO:0005576)				lung(3)|upper_aerodigestive_tract(1)	4	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.32e-06)|Epithelial(140;7.83e-05)		AGACCAGGGAACCCCTCCTCC	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(172;919 2704 37090 48131)					NA		NA				0							NA						21	23	22	NA		NA	NA	9		NA											NA				139635852		1875	4087	5962	SO:0001627	intron_variant			AF303084	CCDS7005.1	9q34.3	2012-10-08			ENSG00000267206	ENSG00000267206	158062		Lipocalins	17337	protein-coding gene	gene with protein product		609379			NA		Standard	NM_198946	NM_198946	NA	Approved		uc004ciy.2	P62502	OTTHUMG00000020941	ENST00000435202.1:c.460-457T>G	chr9.hg19:g.139635852A>C		NA	B0QZ80|Q71SF6	hg19		0.02	3.016394	GGAxCCC	COVERED																																																																																			NOVEL	LCN6-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000055104.2	0	2.680066	KEEP	0	8	83	40	963	AA	1	1	0		-	31	60	310	0	0	11.260902	156	60	4224	281	ENST00000435202.1	0.165775	1
ENTPD2	954	__UNKNOWN__	__UNKNOWN__	9	139943536	139943536	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:139943536C>T	ENST00000355097.2	-	8	1197				ENTPD2_ENST00000312665.5_Intron|ENTPD2_ENST00000460614.1_5'UTR	NM_001246.3|NM_203468.2	NP_001237.1|NP_982293.1	Q9Y5L3	ENTP2_HUMAN	ectonucleoside triphosphate diphosphohydrolase 2	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(3)	12	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		AGCTGGGACGCGGGCGGGACA	0.741	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						3	3	3	NA		NA	NA	9		NA											NA				139943536		1774	3575	5349	SO:0001627	intron_variant			U91510	CCDS7025.1, CCDS7026.1	9q34	2008-07-21			ENSG00000054179	ENSG00000054179	954			3364	protein-coding gene	gene with protein product	CD39-like-1, ecto-ATPase	602012		CD39L1	NA	9271669	Standard	NM_203468	NM_203468	NA	Approved	NTPDase-2	uc004ckw.2	Q9Y5L3	OTTHUMG00000020953	ENST00000355097.2:c.1150-9G>A	chr9.hg19:g.139943536C>T		NA	O15464|Q5SPY6|Q5SPY7	hg19	CCDS7026.1	0.02	4.23189	ACGxGGG	COVERED																																																																																			NOVEL	ENTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055169.1	1	17.74888	KEEP	0	0	0	59	1944	CC	1	0.999998	0		-	42	60	1445	0	0	131.175178	76	60	2636	201	ENST00000355097.2	0.355932	0.999998
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139997541	139997541	__UNKNOWN__	Intron	SNP	G	G	A	rs112370753		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:139997541G>A	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		ACTTGCAGGCGTGCAGGTCGG	0.537	NA	NA											-|||	1	0.000199681	8e-04	0	5008	,	,	NA	27775	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1417G>A	chr9.hg19:g.139997541G>A		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	35.292005	GGCxTGC	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	124	5.579831	KEEP	54	27	772	291	9715	GG	1	1	0		+	106	60	3712	0	0	296.08595	547	60	18867	1428	ENST00000371589.4	0.162328	1
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139997873	139997873	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:139997873C>T	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000540391.1_3'UTR|MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		GTTACATTCACGCTGGTGCAG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1749C>T	chr9.hg19:g.139997873C>T		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	18.748018	TCAxGCT	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	14	22.173581	KEEP	9	10	296	178	5948	CC	1	1	0		+	16	40	537	0	0	32.676111	358	60	12454	848	ENST00000371589.4	0.042781	1
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139998039	139998039	__UNKNOWN__	Intron	SNP	G	G	A	rs201745335	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:139998039G>A	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000540391.1_3'UTR|MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		ACTTGCAGGCGTGCGGGTCGG	0.552	NA	NA											-|||	8	0.00159744	0	0	5008	,	,	NA	29870	0.0079	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1915G>A	chr9.hg19:g.139998039G>A		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	26.298594	GGCxTGC	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	101	31.497355	KEEP	18	9	268	200	6572	GG	1	1	0		+	36	60	1185	0	0	78.832733	497	60	17394	1073	ENST00000371589.4	0.067542	1
PNPLA7	375775	__UNKNOWN__	__UNKNOWN__	9	140403897	140403897	__UNKNOWN__	Intron	SNP	T	T	C	rs546371418	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:140403897T>C	ENST00000277531.4	-	12	1337				PNPLA7_ENST00000406427.1_Intron|PNPLA7_ENST00000371457.1_Intron	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	NA		NA			lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TTAGCTGGTATGAATGAGTTT	0.463	NA	NA											C|||	24	0.00479233	0.0174	0	5008	,	,	NA	25433	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653	375775		Patatin-like phospholipase domain containing	24768	protein-coding gene	gene with protein product		612122	chromosome 9 open reading frame 111	C9orf111	NA	16799181, 12640454, 19029121	Standard	NM_152286	XM_005266082	NA	Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.1151-3362A>G	chr9.hg19:g.140403897T>C		NA	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	hg19	CCDS7045.1	0.02	1.717697	GTAxGAA	COVERED																																																																																			NOVEL	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254787.1	2	2.708226	KEEP	1	0	0	9	286	TT	0.99254	0.99231	0		-	6	40	210	0	0	14.358831	82	60	2919	116	ENST00000277531.4	0.068182	0.999768
PNPLA7	375775	__UNKNOWN__	__UNKNOWN__	9	140403935	140403935	__UNKNOWN__	Intron	SNP	C	C	T	rs77333050	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:140403935C>T	ENST00000277531.4	-	12	1337				PNPLA7_ENST00000406427.1_Intron|PNPLA7_ENST00000371457.1_Intron	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	NA		NA			lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TTAGCTGGTACGAGTGAGTTT	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653	375775		Patatin-like phospholipase domain containing	24768	protein-coding gene	gene with protein product		612122	chromosome 9 open reading frame 111	C9orf111	NA	16799181, 12640454, 19029121	Standard	NM_152286	XM_005266082	NA	Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.1151-3400G>A	chr9.hg19:g.140403935C>T		NA	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	hg19	CCDS7045.1	0.02	4.256405	GTAxGAG	COVERED																																																																																			NOVEL	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254787.1	2	3.912495	KEEP	1	0	0	13	445	CC	0.994391	0.994375	0		-	6	40	216	0	0	14.48304	99	60	3445	132	ENST00000277531.4	0.057143	0.999984
PNPLA7	375775	__UNKNOWN__	__UNKNOWN__	9	140440242	140440242	__UNKNOWN__	Intron	SNP	C	C	T	rs201713279	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr9:140440242C>T	ENST00000277531.4	-	3	385				AL365502.1_ENST00000580317.1_RNA|PNPLA7_ENST00000406427.1_Intron	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	NA		NA			lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		ctgttatgcccggacagggcc	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653	375775		Patatin-like phospholipase domain containing	24768	protein-coding gene	gene with protein product		612122	chromosome 9 open reading frame 111	C9orf111	NA	16799181, 12640454, 19029121	Standard	NM_152286	XM_005266082	NA	Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.198+1039G>A	chr9.hg19:g.140440242C>T		NA	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	hg19	CCDS7045.1	0.02	2.231596	GCCxGGA	COVERED																																																																																			NOVEL	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254787.1	2	3.74743	KEEP	1	1	33	24	831	CC	0.999909	0.967338	0		-	4	40	144	0	0	10.220884	47	60	1633	94	ENST00000277531.4	0.078431	0.967425
AKR1C1	1645	__UNKNOWN__	__UNKNOWN__	10	5005941	5005941	__UNKNOWN__	Intron	SNP	C	C	A	rs28464583		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:5005941C>A	ENST00000380872.4	+	1	276				AKR1C1_ENST00000477661.1_Intron|AKR1C1_ENST00000434459.2_Intron	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	NA		NA			bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	AGAGTCTATACAACTCAGCAG	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Colon(130;2054 2316 13360 15380)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1645	1.3.1.20, 1.1.1.149, 1.1.1.112	Aldo-keto reductases	384	protein-coding gene	gene with protein product	dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase	600449	aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)	DDH1	NA	8011662	Standard	NM_001353	NM_001353	NA	Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.84+221C>A	chr10.hg19:g.5005941C>A		NA	P52896|Q5SR15|Q7M4N2|Q9UCX2	hg19	CCDS7061.1	0.02	1.721842	ATAxAAC	COVERED																																																																																			NOVEL	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046523.2	2	4.815656	KEEP	2	0	0	16	570	CC	0.997832	0.99653	0		+	7	40	237	0	0	16.899429	69	60	2577	105	ENST00000380872.4	0.092105	0.998696
AKR1C2	1646	__UNKNOWN__	__UNKNOWN__	10	5045545	5045545	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:5045545C>T	ENST00000380753.4	-	1	272				AKR1C2_ENST00000407674.1_Intron|AKR1C2_ENST00000455190.1_Intron|AKR1C2_ENST00000421196.3_Intron	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	NA		NA			cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	GTGATACTCTCCCAACAGATT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1646	1.3.1.20, 1.1.1.213	Aldo-keto reductases	385	protein-coding gene	gene with protein product	dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III	600450	aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III), testicular 17,20-desmolase deficiency	DDH2, TDD	NA	9716498, 21802064	Standard	NM_001354	NM_001354	NA	Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.84+398G>A	chr10.hg19:g.5045545C>T		NA	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	hg19	CCDS7062.1	0.02	2.261228	TCTxCCA	UNCOVERED																																																																																			NOVEL	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046531.1	4	3.009412	KEEP	35	0	0	10	326	CC	0	0	0		-	23	40	804	0	0	74.027387	37	40	1369	104	ENST00000380753.4	0.383333	0.987943
C1QL3	389941	__UNKNOWN__	__UNKNOWN__	10	16563336	16563336	__UNKNOWN__	5'UTR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:16563336T>G	ENST00000298943.3	-	0	668					NM_001010908.1	NP_001010908.1	Q5VWW1	C1QL3_HUMAN	complement component 1, q subcomponent-like 3	NA		NA			regulation of synapse organization (GO:0050807)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				breast(1)|endometrium(3)|kidney(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GAgcccggggtgggggccggg	0.811	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS31156.1	10p13	2012-03-26			ENSG00000165985	ENSG00000165985	389941			19359	protein-coding gene	gene with protein product		615227			NA	21378161	Standard	XM_372305	NM_001010908	NA	Approved	K100, C1ql, C1QTNF13, CTRP13	uc001ioj.1	Q5VWW1	OTTHUMG00000017738	ENST00000298943.3:c.-272A>C	chr10.hg19:g.16563336T>G		NA	A0PJY4|A0PJY5	hg19	CCDS31156.1	0.02	-0.353411	GGGxGGG	COVERED																																																																																			NOVEL	C1QL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047003.1	0	4.457707	KEEP	0	1	11	19	506	TT	0.999869	0.888759	0		-	4	60	110	0	0	7.413166	36	60	1030	80	ENST00000298943.3	0.1	0.888875
EPC1	80314	__UNKNOWN__	__UNKNOWN__	10	32636216	32636216	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:32636216A>C	ENST00000375110.2	-	1	308					NM_001272019.2|NM_001282391.1	NP_001258948.1|NP_001269320.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	NA		NA			chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				AACCCCCGGCACCCGCCGGCC	0.831	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616	80314			19876	protein-coding gene	gene with protein product		610999			NA	10976108	Standard		NM_025209	NA	Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000375110.2:c.3+31202T>G	chr10.hg19:g.32636216A>C		NA	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	hg19		0.02	2.302537	GGCxCCC	COVERED																																																																																			NOVEL	EPC1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000047481.2	3	8.688569	KEEP	0	5	26	39	887	AA	1	0.999998	0		-	44	60	397	0	0	26.404622	68	60	1600	226	ENST00000375110.2	0.392857	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42360866	42360866	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42360866C>A			NA	NA				None (None upstream) : AL031601.1 (369484 downstream)						NA		NA									NA						ccattccattccattccattc	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42360866C>A		NA		hg19		0.02	3.804147	ATTxCAT	COVERED																																																																																			NOVEL					0			75	4.834062	KEEP	184	14	411	161	5569	CC	1	1	0			4	35	146	0	1	12.162353	16	60	576	551		0.2	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385044	42385044	__UNKNOWN__	IGR	SNP	T	T	A	rs28877678		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42385044T>A			NA	NA				None (None upstream) : AL031601.1 (345306 downstream)						NA		NA									NA						tggaatcgaatggcatcattg	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385044T>A		NA		hg19		0.02	13.773435	GAAxGGC	COVERED																																																																																			NOVEL					0			41	31.889116	KEEP	181	0	0	106	3221	TT	1	1	0			10	40	351	0	0	27.405388	60	49	2179	695		0.142857	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385255	42385255	__UNKNOWN__	IGR	SNP	G	G	A	rs71230978		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42385255G>A			NA	NA				None (None upstream) : AL031601.1 (345095 downstream)						NA		NA									NA						ttatcaaatggaatcgaatgg	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385255G>A		NA		hg19		0.02	31.880902	ATGxAAT	COVERED																																																																																			NOVEL					0			108	11.319098	KEEP	26	31	895	353	12233	GG	1	1	0			18	60	659	2	0	41.201696	460	60	17044	1506		0.037657	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385558	42385558	__UNKNOWN__	IGR	SNP	C	C	A	rs9665006		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42385558C>A			NA	NA				None (None upstream) : AL031601.1 (344792 downstream)						NA		NA									NA						tcaaaaataaccatcatcaat	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385558C>A		NA		hg19		0.02	19.216547	TAAxCAT	COVERED																																																																																			NOVEL					0			85	14.396293	KEEP	95	11	350	171	5891	CC	1	1	0			12	40	426	1	0	26.097908	309	60	11268	977		0.037383	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385627	42385627	__UNKNOWN__	IGR	SNP	C	C	T	rs74206654|rs9703387	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42385627C>T			NA	NA				None (None upstream) : AL031601.1 (344723 downstream)						NA		NA									NA						caaatggaaccgaatggaatc	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385627C>T		NA		hg19		0.02	24.525262	AACxGAA	COVERED																																																																																			NOVEL					0			99	42.386001	KEEP	190	8	251	229	7722	CC	1	1	0			23	50	882	0	0	59.660928	431	60	14991	1238		0.050661	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42388344	42388344	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42388344T>A			NA	NA				None (None upstream) : AL031601.1 (342006 downstream)						NA		NA									NA						atcatgaaattgaaatggatg	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42388344T>A		NA		hg19		0.02	19.488629	AATxGAA	COVERED																																																																																			NOVEL					0			64	5.920455	KEEP	282	15	465	183	5615	TT	1	1	0			31	45	1133	0	0	84.385231	278	48	10209	1216		0.100324	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42390381	42390381	__UNKNOWN__	IGR	SNP	A	A	T	rs140407384	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42390381A>T			NA	NA				None (None upstream) : AL031601.1 (339969 downstream)						NA		NA									NA						atcaaatggaatcgaatagaa	0.363	NA	NA											.|||	93	0.0185703	0.0613	0.0086	5008	,	,	NA	73142	0	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42390381A>T		NA		hg19		0.02	4.572814	GGAxTCG	COVERED																																																																																			NOVEL					0			30	7.150774	KEEP	16	1	32	35	1088	AA	0.999997	0.999975	0			5	42	185	0	0	13.036615	66	60	2436	201		0.070423	0.999978
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42392336	42392336	__UNKNOWN__	IGR	SNP	A	A	G	rs138629488		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42392336A>G			NA	NA				None (None upstream) : AL031601.1 (338014 downstream)						NA		NA									NA						attgaaacgaatggaattatc	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42392336A>G		NA		hg19		0.02	9.208235	CGAxTGG	COVERED																																																																																			NOVEL					0			48	26.346516	KEEP	132	2	70	112	3469	AA	1	1	0			7	42	259	0	0	17.577577	116	60	4321	602		0.056911	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42392678	42392678	__UNKNOWN__	IGR	SNP	G	G	A	rs143302300		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42392678G>A			NA	NA				None (None upstream) : AL031601.1 (337672 downstream)						NA		NA									NA						gaatagaatcgaatggaacaa	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42392678G>A		NA		hg19		0.02	12.284767	ATCxAAT	COVERED																																																																																			NOVEL					0			80	33.299119	KEEP	44	3	92	143	4767	GG	1	1	0			18	60	639	0	0	43.261816	270	60	9361	738		0.0625	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42392729	42392729	__UNKNOWN__	IGR	SNP	C	C	G	rs143507773		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42392729C>G			NA	NA				None (None upstream) : AL031601.1 (337621 downstream)						NA		NA									NA						caaatggaatcgaatggaatt	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42392729C>G		NA		hg19		0.02	17.15773	AATxGAA	COVERED																																																																																			NOVEL					0			111	7.317913	KEEP	50	11	398	163	5682	CC	1	1	0			21	49	780	0	0	54.795263	285	60	10495	860		0.068627	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42395987	42395987	__UNKNOWN__	IGR	SNP	A	A	T	rs151117385|rs200485205		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42395987A>T			NA	NA				None (None upstream) : AL031601.1 (334363 downstream)						NA		NA									NA						atcaaatggaattatcaaatg	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42395987A>T		NA		hg19		0.02	19.286171	GGAxTTA	COVERED																																																																																			NOVEL					0			4	13.808613	KEEP	41	5	151	99	3129	AA	1	1	0			11	40	396	0	1	28.116299	129	59	4605	629		0.078571	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42400337	42400337	__UNKNOWN__	IGR	SNP	G	G	T	rs74221624		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42400337G>T			NA	NA				None (None upstream) : AL031601.1 (330013 downstream)						NA		NA									NA						agagcagtttggaaacactct	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42400337G>T		NA		hg19		0.02	20.426974	TTTxGAA	COVERED																																																																																			NOVEL					0			46	10.629159	KEEP	46	6	166	94	3310	CG	1	1	0			11	50	380	0	0	35.100239	17	60	653	764		0.392857	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42528017	42528017	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42528017A>G			NA	NA				None (None upstream) : AL031601.1 (202333 downstream)						NA		NA									NA						tcttctgtctagcattatatg	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42528017A>G		NA		hg19		0.02	24.097667	TCTxGCA	COVERED																																																																																			NOVEL					0			270	40.014777	KEEP	135	12	436	285	8848	AA	1	1	0			17	26	617	0	2	56.45512	30	60	1076	1258		0.361702	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42534602	42534602	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42534602A>T			NA	NA				None (None upstream) : AL031601.1 (195748 downstream)						NA		NA									NA						ttgaacgcacacatcacaaac	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42534602A>T		NA		hg19		0.02	-0.333376	CACxCAT	COVERED																																																																																			NOVEL					0			23	8.722103	KEEP	60	0	0	29	859	AA	0.992708	0.845771	0			2	23	74	0	0	7.150006	2	21	75	127		0.5	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42544697	42544697	__UNKNOWN__	IGR	SNP	A	A	G	rs151337506		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42544697A>G			NA	NA				None (None upstream) : AL031601.1 (185653 downstream)						NA		NA									NA						cgaaggcctcaaaaaggtcca	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42544697A>G		NA		hg19		0.02	-0.070183	CTCxAAA	UNCOVERED																																																																																			NOVEL					0			4	3.008621	KEEP	11	0	0	10	302	AA	0.99257	0.053735	0			2	49	74	0	0	6.695664	4	25	141	33		0.333333	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42680864	42680864	__UNKNOWN__	IGR	SNP	A	A	G	rs10751397	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42680864A>G			NA	NA				None (None upstream) : AL031601.1 (49486 downstream)						NA		NA									NA						TGTGCTCAGTACTGTCTGGAA	0.483	NA	NA											a|||	2090	0.417332	0.4561	0.3415	5008	,	,	NA	28055	0.3323	NA	0.3837	False	NA	,,,	NA	NA	NA	2504	0.5409	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42680864A>G		NA		hg19		0.02	2.373305	AGTxCTG	COVERED																																																																																			NOVEL					0			2	3.00896	KEEP	31	0	0	10	306	AA	0.992708	0.989456	0			10	31	360	0	0	28.306377	60	45	2124	127		0.142857	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42681108	42681108	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42681108C>A			NA	NA				None (None upstream) : AL031601.1 (49242 downstream)						NA		NA									NA						ATGCTGCATCCAGTCTGCAAA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42681108C>A		NA		hg19		0.02	14.377538	ATCxAGT	COVERED																																																																																			NOVEL					0			3	7.526139	KEEP	194	3	97	59	2061	CC	0.999998	0.999998	0			55	29	2077	0	0	170.021672	267	43	10149	713		0.170807	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42681152	42681152	__UNKNOWN__	IGR	SNP	C	C	T	rs111787724		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:42681152C>T			NA	NA				None (None upstream) : AL031601.1 (49198 downstream)						NA		NA									NA						GACAGTGGATCTGGGACAGAT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42681152C>T		NA		hg19		0.02	18.80183	GATxTGG	COVERED																																																																																			NOVEL					0			6	10.773499	KEEP	122	4	120	78	2739	CC	1	1	0			23	40	845	1	0	56.761221	397	60	15161	709		0.054762	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	48001538	48001538	__UNKNOWN__	IGR	SNP	C	C	T	rs190927558	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:48001538C>T			NA	NA				FAM21B (52685 upstream) : ASAH2C (64 downstream)						NA		NA									NA						GCAAGATATACGGGACAAACc	0.473	NA	NA											T|||	3211	0.641174	0.7542	0.5908	5008	,	,	NA	1809	0.7867	NA	0.4314	False	NA	,,,	NA	NA	NA	2504	0.59	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.48001538C>T		NA		hg19		0.02	2.199897	ATAxGGG	COVERED																																																																																			NOVEL					0			5	5.417108	KEEP	0	0	0	18	628	CC	0.999859	0.994943	0			6	60	218	0	0	16.060803	57	60	2029	119		0.095238	0.995084
ERCC6	2074	__UNKNOWN__	__UNKNOWN__	10	50740753	50740753	__UNKNOWN__	Silent	SNP	G	G	A	rs114369077		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:50740753G>A	ENST00000355832.5	-	2	336	c.258C>T	c.(256-258)agC>agT	p.S86S	PGBD3_ENST00000603152.1_Silent_p.S86S|ERCC6-PGBD3_ENST00000447839.2_Silent_p.S86S|ERCC6-PGBD3_ENST00000515869.1_Silent_p.S86S	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	86		NA			activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						GGGCCTGGGCGCTAGGCTCTA	0.622	NA	NA						Direct reversal of damage;Nucleotide excision repair (NER)					G|||	1	0.000199681	0	0	5008	,	,	NA	19985	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						122	108	113	NA		NA	NA	10		NA											NA				50740753		2203	4300	6503	SO:0001819	synonymous_variant			L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830	2074			3438	protein-coding gene	gene with protein product	Cockayne syndrome B protein	609413	excision repair cross-complementing rodent repair deficiency, complementation group 6	CKN2	NA	1339317, 19179336	Standard	NM_000124	NM_000124	NA	Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.258C>T	chr10.hg19:g.50740753G>A		NA	D3DX94|Q5W0L9	hg19	CCDS7229.1	0.02	15.112516	GGCxCTA	COVERED																																																																																			NOVEL	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047990.1	6	67.992613	KEEP	0	0	0	226	7642	GG	1	1	0		-	27	60	979	0	0	68.239569	361	60	12872	739	ENST00000355832.5	0.069588	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	52422479	52422479	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:52422479T>A			NA	NA				RP11-564C4.6 (2451 upstream) : ASAH2B (76598 downstream)						NA		NA									NA						ACAAGAAGACTCTAAGCCCTG	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.52422479T>A		NA		hg19		0.02	2.114214	GACxCTA	COVERED																																																																																			NOVEL					0			1	3.009225	KEEP	2	0	0	10	320	TT	0.992708	0.966863	0			4	49	149	0	0	10.617102	50	60	1912	83		0.074074	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	52445761	52445761	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:52445761A>T			NA	NA				RP11-564C4.6 (25733 upstream) : ASAH2B (53316 downstream)						NA		NA									NA						GGCCGGCCCCACTCTTTCCTC	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.52445761A>T		NA		hg19		0.02	-0.280125	CCCxCTC	COVERED																																																																																			NOVEL					0			1	6.914184	KEEP	8	0	0	23	640	AA	0.999863	0.73957	0			3	23	115	0	0	8.611205	29	47	964	67		0.09375	0.739671
ANK3	288	__UNKNOWN__	__UNKNOWN__	10	61898939	61898939	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:61898939C>T	ENST00000280772.2	-	24	2806				ANK3_ENST00000460468.1_Intron|ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	NA		NA			axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						AGCAAATCCCCCAATATCTCA	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150	288		Ankyrin repeat domain containing	494	protein-coding gene	gene with protein product	ankyrin-3, node of Ranvier, ankyrin-G	600465			NA	7665168	Standard	NM_020987	NM_020987	NA	Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.2615-94G>A	chr10.hg19:g.61898939C>T		NA	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	hg19	CCDS7258.1	0.02	12.035567	CCCxCAA	COVERED																																																																																			NOVEL	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048201.4	0	11.436979	KEEP	0	0	0	38	1308	CC	1	1	0		-	52	60	1889	0	0	158.100469	199	60	7139	312	ENST00000280772.2	0.207171	1
HK1	3098	__UNKNOWN__	__UNKNOWN__	10	71139768	71139768	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:71139768G>C	ENST00000359426.6	+	9	1286	c.1182G>C	c.(1180-1182)ttG>ttC	p.L394F	HK1_ENST00000448642.2_Missense_Mutation_p.L429F|HK1_ENST00000360289.2_Missense_Mutation_p.L382F|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000404387.2_Missense_Mutation_p.L398F|HK1_ENST00000298649.3_Missense_Mutation_p.L393F	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	394	Hexokinase type-2 1.|Regulatory.	NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GCGCCATCTTGAACCGCCTGC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						150	118	129	NA		NA	NA	10		NA											NA				71139768		2203	4300	6503	SO:0001583	missense			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	3098	2.7.1.1		4922	protein-coding gene	gene with protein product		142600			NA		Standard	NM_000188	NM_033496	NA	Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1182G>C	chr10.hg19:g.71139768G>C	ENSP00000352398:p.Leu394Phe	NA	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	hg19	CCDS7292.1	0.02	12.906228	CTTxAAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.50	3.838412	0.71373	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16;-4.16	5.39	3.36	0.38483	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.97990	0.9338	M	0.91249	3.19	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.999;0.999	D;D;D;D;D;D	0.87578	0.996;0.997;0.998;0.986;0.97;0.929	D	0.97427	1.0013	10	0.87932	D	0	-1.7568	8.3712	0.32417	0.0909:0.2947:0.6144:0.0	.	394;394;393;429;398;382	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	F	382;429;398;393;394;394	ENSP00000353433:L382F;ENSP00000402103:L429F;ENSP00000384774:L398F;ENSP00000298649:L393F;ENSP00000352398:L394F	ENSP00000298649:L393F	L	+	3	2	HK1	70809774	0.971000	0.33674	0.996000	0.52242	0.753000	0.42808	1.592000	0.36676	2.525000	0.85131	0.462000	0.41574	TTG	NOVEL	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048429.2	2	42.388616	KEEP	0	0	0	141	4861	GG	1	1	0		+	24	60	934	0	0	69.403726	253	60	9647	523	ENST00000359426.6	0.086643	1
AGAP5	729092	__UNKNOWN__	__UNKNOWN__	10	75435673	75435673	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs200986858	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:75435673G>A	ENST00000443782.2	-	7	801	c.676C>T	c.(676-678)Cgc>Tgc	p.R226C	RP11-464F9.1_ENST00000399449.3_RNA|AGAP5_ENST00000374094.4_Missense_Mutation_p.R249C			A6NIR3	AGAP5_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 5	249		NA			regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(5)|skin(1)	12						TTGGACCAGCGCATGGACCGC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						9	8	8	NA		NA	NA	10		NA											NA				75435673		689	1571	2260	SO:0001583	missense				CCDS44439.1	10q22.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000172650	ENSG00000172650	729092		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	23467	protein-coding gene	gene with protein product		NA	centaurin, gamma-like family, member 2	CTGLF2	NA		Standard	XM_001132585	NM_001144000	NA	Approved	Em:AC073389.1	uc009xri.3	A6NIR3	OTTHUMG00000018473	ENST00000443782.2:c.676C>T	chr10.hg19:g.75435673G>A	ENSP00000402792:p.Arg226Cys	NA	A8MSN5	hg19		0.02	4.389852	AGCxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210413	0.39003	.	.	ENSG00000172650	ENST00000374094;ENST00000443782	T;T	0.48522	0.81;0.81	.	.	.	.	0.065932	0.64402	D	0.000008	T	0.40498	0.1119	M	0.66939	2.045	0.58432	D	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.26395	-1.0104	9	0.72032	D	0.01	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	249	A6NIR3	AGAP5_HUMAN	C	249;226	ENSP00000363207:R249C;ENSP00000402792:R226C	ENSP00000363207:R249C	R	-	1	0	AGAP5	75105679	1.000000	0.71417	0.204000	0.23530	0.205000	0.24178	4.667000	0.61561	0.064000	0.16427	0.064000	0.15345	CGC	NOVEL	AGAP5-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000048673.1	0	14.01075	KEEP	163	2	61	68	2262	GG	0.999879	0.999847	0		-	5	22	188	0	0	12.544806	96	45	3328	356	ENST00000443782.2	0.049505	0.999968
KCNMA1	3778	__UNKNOWN__	__UNKNOWN__	10	79398274	79398274	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:79398274A>G	ENST00000286627.5	-	0	79					NM_001271519.1|NM_002247.3	NP_001258448.1|NP_002238.2	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	NA		NA			blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	CCCAGGCGGGAGGGGAGGAGG	0.791	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113	3778		Potassium channels, Voltage-gated ion channels / Potassium channels, calcium-activated	6284	protein-coding gene	gene with protein product	BK channel alpha subunit	600150		SLO	NA	7987297, 16382103	Standard	NM_002247	NM_002247	NA	Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286627.5:c.-874T>C	chr10.hg19:g.79398274A>G		NA	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	hg19	CCDS7352.1	0.02	-0.277077	GGGxGGG	COVERED																																																																																			NOVEL	KCNMA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048877.3	1	5.113794	KEEP	0	0	0	17	509	AA	0.999366	0.739203	0		-	7	60	103	0	0	6.407728	25	60	811	62	ENST00000286627.5	0.21875	0.739671
EIF5AL1	143244	__UNKNOWN__	__UNKNOWN__	10	81276176	81276176	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:81276176C>T	ENST00000520547.2	+	0	3820					NM_001099692.1	NP_001093162.1	Q6IS14	IF5AL_HUMAN	eukaryotic translation initiation factor 5A-like 1	NA		NA			mRNA transport (GO:0051028)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of translational elongation (GO:0045901)|positive regulation of translational termination (GO:0045905)|protein transport (GO:0015031)|translational frameshifting (GO:0006452)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)	ribosome binding (GO:0043022)|translation elongation factor activity (GO:0003746)			endometrium(1)	1	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			ACATACTCCCCCTTCCCTTGA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS53546.1	10q22.3	2012-04-19			ENSG00000253626	ENSG00000253626	143244			17419	protein-coding gene	gene with protein product		NA	eukaryotic translation initiation factor 5A pseudogene 1	EIF5AP1	NA		Standard	NM_001099692	NM_001099692	NA	Approved	bA342M3.3	uc009xrx.3	Q6IS14	OTTHUMG00000018563	ENST00000520547.2:c.*3306C>T	chr10.hg19:g.81276176C>T		NA		hg19	CCDS53546.1	0.02	6.477642	CCCxCTT	COVERED																																																																																			NOVEL	EIF5AL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048954.4	5	9.630261	KEEP	9	0	0	32	1083	CC	0.999997	0.999997	0		+	10	27	357	0	0	24.289062	148	50	5319	220	ENST00000520547.2	0.063291	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	81800046	81800046	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:81800046G>C			NA	NA				RP11-479O17.10 (67077 upstream) : TMEM254-AS1 (6569 downstream)						NA		NA									NA						ATTGAAAATAGTACAAATATT	0.299	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.81800046G>C		NA		hg19		0.02	2.044038	ATAxTAC	COVERED																																																																																			NOVEL					0			1	3.912745	KEEP	2	0	0	13	456	GG	0.994391	0.985406	0			8	39	286	0	0	22.064294	54	60	2037	87		0.129032	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	81800111	81800111	__UNKNOWN__	IGR	SNP	G	G	A	rs201954311		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:81800111G>A			NA	NA				RP11-479O17.10 (67142 upstream) : TMEM254-AS1 (6504 downstream)						NA		NA									NA						GTACTTGCAAGACTGACCTAT	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.81800111G>A		NA		hg19		0.02	4.011435	CAAxACT	COVERED																																																																																			NOVEL					0			1	6.621708	KEEP	3	0	0	22	801	GG	0.999879	0.999872	0			12	39	434	0	0	32.66513	98	60	3734	172		0.109091	0.999993
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	82006880	82006880	__UNKNOWN__	IGR	SNP	G	G	A	rs2573329	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:82006880G>A			NA	NA				LINC00857 (27467 upstream) : AL359195.1 (2585 downstream)						NA		NA									NA						GAGGAGTCCAGCCTAGGACCA	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.82006880G>A		NA		hg19		0.02	1.973841	CCAxCCT	COVERED																																																																																			NOVEL					0			2	8.426489	KEEP	4	0	0	28	986	GG	0.999988	0.996712	0			4	39	139	0	0	9.1527	66	50	2540	117		0.057143	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	82006964	82006964	__UNKNOWN__	IGR	SNP	T	T	C	rs373076531		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:82006964T>C			NA	NA				LINC00857 (27551 upstream) : AL359195.1 (2501 downstream)						NA		NA									NA						CACTGCCACCTTGGGAGCCAG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.82006964T>C		NA		hg19		0.02	2.19777	ACCxTGG	COVERED																																																																																			NOVEL					0			1	3.580069	KEEP	33	2	66	35	1109	TT	0.999957	0.999792	0			6	40	208	0	0	14.154645	82	50	3023	169		0.068182	0.999835
BMPR1A	657	__UNKNOWN__	__UNKNOWN__	10	88684422	88684422	__UNKNOWN__	3'UTR	SNP	A	A	G	rs61856966		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:88684422A>G	ENST00000372037.3	+	0	3082					NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	NA		NA			BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						ACCATGTTCTATATTCTTTAT	0.323	NA	NA	Mis, N, F			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(190;603 2086 22044 30335 47971)	yes	Rec		Juvenile polyposis	10	10q22.3	657	bone morphogenetic protein receptor, type IA		E	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779	657		CD molecules	1076	protein-coding gene	gene with protein product		601299		ACVRLK3	NA	8397373, 9730621	Standard	NM_004329	NM_004329	NA	Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.*946A>G	chr10.hg19:g.88684422A>G		NA	A8K6U9|Q8NEN8	hg19	CCDS7378.1	0.02	14.678779	TCTxTAT	COVERED																																																																																			NOVEL	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049170.3	3	3.910855	KEEP	23	3	109	51	1507	AA	1	1	0		+	23	40	866	0	0	61.891129	290	60	10513	425	ENST00000372037.3	0.073482	1
NUTM2A-AS1	728190	__UNKNOWN__	__UNKNOWN__	10	89013351	89013351	__UNKNOWN__	RNA	SNP	C	C	T	rs376604860		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:89013351C>T	ENST00000446751.1	-	0	572				NUTM2A-AS1_ENST00000451940.2_RNA|NUTM2A-AS1_ENST00000447424.1_RNA|NUTM2A-AS1_ENST00000433530.1_RNA|NUTM2A-AS1_ENST00000456104.1_RNA|NUTM2A-AS1_ENST00000433920.1_RNA					NUTM2A antisense RNA 1	NA		NA									NA						ctttgggaggccgaggtgggc	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AK311174, AK309777		10q23.2	2013-03-14	2013-03-14	2013-03-14	ENSG00000223482	ENSG00000223482	728190		Long non-coding RNAs	45161	non-coding RNA	RNA, long non-coding		NA	FAM22A antisense RNA 1	FAM22A-AS1	NA		Standard	NR_024397	NR_024397	NA	Approved		uc001kem.3		OTTHUMG00000018671	ENST00000446751.1:	chr10.hg19:g.89013351C>T		NA		hg19		0.02	-0.043867	AGGxCGA	UNCOVERED																																																																																			NOVEL	NUTM2A-AS1-012	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000049210.1	1	2.407772	KEEP	7	0	0	8	283	CC	0	0	0		-	2	47	71	0	0	6.592709	3	25	128	21	ENST00000446751.1	0.4	0.024074
NUTM2D	728130	__UNKNOWN__	__UNKNOWN__	10	89127071	89127071	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:89127071A>T	ENST00000412718.1	+	7	2181							Q5VT03	NTM2D_HUMAN	NUT family member 2D	NA		NA									NA						GGCCGGCCCCACTCTTTCCTC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						20	26	24	NA		NA	NA	10		NA											NA				89127071		1894	3969	5863	SO:0001627	intron_variant					10q23.31	2013-03-14	2013-03-14	2013-03-14	ENSG00000214562	ENSG00000214562	728130			23447	protein-coding gene	gene with protein product		NA	family with sequence similarity 22, member D	FAM22D	NA		Standard	NR_075100	NR_075100	NA	Approved		uc001kes.3	Q5VT03	OTTHUMG00000018672	ENST00000412718.1:c.1636-20A>T	chr10.hg19:g.89127071A>T		NA	A6NGV9	hg19	CCDS41546.1	0.02	-0.393969	CCCxCTC	COVERED																																																																																			NOVEL	NUTM2D-005	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471068.1	1	3.610584	KEEP	3	0	0	12	364	AA	0.993634	0.920741	0		+	4	27	127	0	0	8.921041	38	50	1280	66	ENST00000412718.1	0.095238	0.92664
NUTM2D	728130	__UNKNOWN__	__UNKNOWN__	10	89127086	89127086	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:89127086C>T	ENST00000412718.1	+	7	2181							Q5VT03	NTM2D_HUMAN	NUT family member 2D	NA		NA									NA						TTCCTCCTGACGTAGGGAGCC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						18	22	21	NA		NA	NA	10		NA											NA				89127086		1863	3905	5768	SO:0001627	intron_variant					10q23.31	2013-03-14	2013-03-14	2013-03-14	ENSG00000214562	ENSG00000214562	728130			23447	protein-coding gene	gene with protein product		NA	family with sequence similarity 22, member D	FAM22D	NA		Standard	NR_075100	NR_075100	NA	Approved		uc001kes.3	Q5VT03	OTTHUMG00000018672	ENST00000412718.1:c.1636-5C>T	chr10.hg19:g.89127086C>T		NA	A6NGV9	hg19	CCDS41546.1	0.02	-0.412311	TGAxGTA	COVERED																																																																																			NOVEL	NUTM2D-005	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471068.1	1	3.611499	KEEP	7	0	0	12	408	CC	0.993634	0.935746	0		+	6	27	203	0	0	15.491734	39	50	1372	72	ENST00000412718.1	0.133333	0.941741
PTEN	5728	__UNKNOWN__	__UNKNOWN__	10	89717778	89717778	__UNKNOWN__	Splice_Site	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:89717778T>G	ENST00000371953.3	+	7	2158		c.e7+2		PTEN_ENST00000472832.1_Splice_Site	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	NA		NA			activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.M264fs*8(2)|p.G165_*404del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		CTAAAAAAGGTTTGTACTTTA	0.323	NA	31	D, Mis, N, F, S		glioma,  prostate, endometrial	harmartoma, glioma,  prostate, endometrial			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA		yes	Rec	yes	Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome	10	10q23.3	5728	phosphatase and tensin homolog gene		L, E, M, O	51	Whole gene deletion(37)|Deletion - Frameshift(11)|Unknown(2)|Deletion - In frame(1)	prostate(16)|central_nervous_system(10)|skin(6)|lung(4)|ovary(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	GRCh37	CS982334	PTEN	S	NA						79	74	76	NA		NA	NA	10		NA											NA				89717778		2203	4300	6503	SO:0001630	splice_region_variant	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862	5728		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	9588	protein-coding gene	gene with protein product	mutated in multiple advanced cancers 1	601728		BZS, MHAM	NA	9090379	Standard	NM_000314	NM_000314	NA	Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.801+2T>G	chr10.hg19:g.89717778T>G		NA	B2R904|F2YHV0|O00633|O02679|Q6ICT7	hg19	CCDS31238.1	0.02	2.145139	AGGxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	20.2	3.955754	0.73902	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.15	5.15	0.70609	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9657	0.71193	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTEN	89707758	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	7.661000	0.83786	1.928000	0.55862	0.477000	0.44152	.	NOVEL	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049241.1	1	4.213125	KEEP	0	0	0	14	452	TT	0.995343	0.995273	0	Intron	+	7	60	264	0	0	18.855416	89	60	3154	124	ENST00000371953.3	0.072917	0.99993
MYOF	26509	__UNKNOWN__	__UNKNOWN__	10	95093661	95093661	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs201634420	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:95093661G>C	ENST00000359263.4	-	42	4572	c.4573C>G	c.(4573-4575)Cgg>Ggg	p.R1525G	MYOF_ENST00000371501.4_Missense_Mutation_p.R1525G|MYOF_ENST00000358334.5_Missense_Mutation_p.R1512G|MYOF_ENST00000371502.4_Missense_Mutation_p.R1544G	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1525		NA			blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GGGTAGATCCGAAAGGAGCCC	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						28	29	28	NA		NA	NA	10		NA											NA				95093661		1993	4183	6176	SO:0001583	missense			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119	26509			3656	protein-coding gene	gene with protein product	fer-1-like family member 3	604603	fer-1 (C.elegans)-like 3 (myoferlin), fer-1-like 3, myoferlin (C. elegans)	FER1L3	NA	10607832, 10995573, 17702744	Standard	NM_013451	NM_013451	NA	Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4573C>G	chr10.hg19:g.95093661G>C	ENSP00000352208:p.Arg1525Gly	NA	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	hg19	CCDS41551.1	0.02	4.817448	TCCxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.19	1.566352	0.27915	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.79	5.13	-1.22	0.09494	C2 calcium/lipid-binding domain, CaLB (1);	0.106892	0.64402	D	0.000016	D	0.84570	0.5501	M	0.80982	2.52	0.21416	N	0.999697	B;P	0.38617	0.382;0.64	B;B	0.36335	0.222;0.132	T	0.78996	-0.1983	10	0.72032	D	0.01	-15.0647	17.7131	0.88327	0.0:0.0:0.5782:0.4218	.	1512;1525	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	G	1512;1525;1525;1544	ENSP00000351094:R1512G;ENSP00000352208:R1525G;ENSP00000360556:R1525G;ENSP00000360557:R1544G	ENSP00000351094:R1512G	R	-	1	2	MYOF	95083651	0.997000	0.39634	0.043000	0.18650	0.724000	0.41520	1.120000	0.31271	-0.341000	0.08376	0.650000	0.86243	CGG	NOVEL	MYOF-005	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049423.2	2	12.339882	KEEP	0	0	0	41	1418	GG	1	1	0		-	34	60	1266	0	0	110.2519	97	60	3567	205	ENST00000359263.4	0.259542	1
SORBS1	10580	__UNKNOWN__	__UNKNOWN__	10	97073554	97073554	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:97073554C>G	ENST00000371227.4	-	0	5252				SORBS1_ENST00000371249.2_3'UTR|SORBS1_ENST00000393949.1_3'UTR|SORBS1_ENST00000347291.4_3'UTR|SORBS1_ENST00000306402.6_3'UTR|SORBS1_ENST00000353505.5_3'UTR|SORBS1_ENST00000371246.2_3'UTR|SORBS1_ENST00000371247.2_3'UTR					sorbin and SH3 domain containing 1	NA		NA								NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GTATTTGTCTCACTCAGGATC	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637	10580			14565	protein-coding gene	gene with protein product	c-Cbl-associated protein	605264	SH3-domain protein 5 (ponsin)	SH3D5	NA	10085297, 11001060	Standard		XM_005269405	NA	Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000371227.4:c.*1262G>C	chr10.hg19:g.97073554C>G		NA		hg19		0.02	9.99994	TCTxACT	COVERED																																																																																			NOVEL	SORBS1-015	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000049528.2	2	14.14236	KEEP	0	0	0	47	1625	CC	1	1	0		-	52	60	1955	0	0	165.314664	193	60	7251	346	ENST00000371227.4	0.212245	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	98561359	98561359	__UNKNOWN__	IGR	SNP	G	G	C	rs560124785	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:98561359G>C			NA	NA				RNU6-1274P (58329 upstream) : MIR607 (27066 downstream)						NA		NA									NA						GAGAGAGACAGACagacagag	0.398	NA	NA											G|||	22	0.00439297	0.0076	0.0043	5008	,	,	NA	26328	0.002	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.98561359G>C		NA		hg19		0.02	7.407056	ACAxACA	COVERED																																																																																			NOVEL					0			212	15.159122	KEEP	14	14	513	229	8064	GG	1	1	0			5	60	191	2	0	14.675032	40	60	1470	493		0.111111	1
LCOR	84458	__UNKNOWN__	__UNKNOWN__	10	98720980	98720980	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:98720980G>T	ENST00000498444.1	+	2	248				LCOR_ENST00000540664.1_3'UTR			Q96JN0	LCOR_HUMAN	ligand dependent nuclear receptor corepressor	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(1)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|urinary_tract(1)	13		Colorectal(252;0.162)		Epithelial(162;4.43e-09)|all cancers(201;2.96e-07)		ATGTTGATTTGACAATAGAAC	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7451.1, CCDS53561.1	10q24	2006-06-28			ENSG00000196233	ENSG00000196233	84458			29503	protein-coding gene	gene with protein product		607698			NA	12535528, 15193453	Standard		NM_001170765	NA	Approved	MLR2, FLJ38026, KIAA1795		Q96JN0	OTTHUMG00000018841	ENST00000498444.1:c.248+9027G>T	chr10.hg19:g.98720980G>T		NA	D3DR47|Q5VW16|Q7Z723|Q86T32|Q86T33|Q8N3L6	hg19		0.02	4.667614	TTTxACA	COVERED																																																																																			NOVEL	LCOR-014	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000049634.1	1	11.135858	KEEP	0	0	0	37	1297	GG	1	1	0		+	43	60	1552	0	0	136.836039	106	60	4104	230	ENST00000498444.1	0.288591	1
HOGA1	112817	__UNKNOWN__	__UNKNOWN__	10	99371776	99371776	__UNKNOWN__	3'UTR	SNP	C	C	T	rs114372258		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:99371776C>T	ENST00000370646.4	+	0	1705				PI4K2A_ENST00000555577.1_Intron|PI4K2A_ENST00000370649.3_Intron|HOGA1_ENST00000370647.4_3'UTR	NM_138413.3	NP_612422.2	Q86XE5	HOGA1_HUMAN	4-hydroxy-2-oxoglutarate aldolase 1	NA		NA			4-hydroxyproline catabolic process (GO:0019470)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|oxalate metabolic process (GO:0033609)|pyruvate biosynthetic process (GO:0042866)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	4-hydroxy-2-oxoglutarate aldolase activity (GO:0008700)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|stomach(1)	14						Attttcttttctttttttttt	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC011916	CCDS7467.1, CCDS44469.1	10q24.1	2010-12-19	2010-12-19	2010-12-19	ENSG00000241935	ENSG00000241935	112817			25155	protein-coding gene	gene with protein product	dihydrodipicolinate synthetase homolog 2 (E. coli), N-acetylneuraminate pyruvate lyase 2 (putative)	613597	chromosome 10 open reading frame 65, dihydrodipicolinate synthase-like, mitochondrial	C10orf65, DHDPSL	NA	20797690	Standard	NM_138413	NM_001134670	NA	Approved	FLJ37472, DHDPS2, NPL2		Q86XE5	OTTHUMG00000018859	ENST00000370646.4:c.*360C>T	chr10.hg19:g.99371776C>T		NA	A8K075|Q5T680|Q5T684|Q711P0|Q8N9F2|Q96EV5	hg19	CCDS7467.1	0.02	-0.29582	TTTxTTT	COVERED																																																																																			NOVEL	HOGA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049726.1	1	2.394965	KEEP	0	0	0	8	201	CC	0.99257	0.775257	0		+	8	60	205	2	1	16.913052	21	60	565	47	ENST00000370646.4	0.275862	0.78106
NDUFB8	4714	__UNKNOWN__	__UNKNOWN__	10	102288991	102288991	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:102288991A>C	ENST00000299166.4	-	2	225				SEC31B_ENST00000535773.1_Intron|NDUFB8_ENST00000557395.1_Intron|NDUFB8_ENST00000370322.1_Intron|NDUFB8_ENST00000531258.1_Intron|NDUFB8_ENST00000370320.4_Intron	NM_005004.2	NP_004995.1	O95169	NDUB8_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(2)|lung(2)	4		Colorectal(252;0.234)		Epithelial(162;5.68e-10)|all cancers(201;4.05e-08)		CCCCCCTCCCACCTCCCTCCA	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF044958	CCDS7497.1, CCDS65916.1, CCDS65917.1	10q24.31	2011-07-04	2002-08-29		ENSG00000166136	ENSG00000166136	4714		Mitochondrial respiratory chain complex / Complex I	7703	protein-coding gene	gene with protein product	complex I ASHI subunit	602140	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8 (19kD, ASHI)		NA	9763676	Standard	NM_005004	NM_001284368	NA	Approved	ASHI, CI-ASHI	uc001kri.1	O95169	OTTHUMG00000019346	ENST00000299166.4:c.212+145T>G	chr10.hg19:g.102288991A>C		NA	A8K0L4|Q5W143|Q5W144|Q5W145|Q9UG53|Q9UJR4|Q9UQF3	hg19	CCDS7497.1	0.02	-0.408775	CCCxCCT	COVERED																																																																																			NOVEL	NDUFB8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051225.1	0	2.746801	KEEP	0	2	10	13	332	AA	0.99649	0.945073	0		-	12	60	225	0	0	16.670153	36	60	826	71	ENST00000299166.4	0.25	0.948402
NDUFB8	4714	__UNKNOWN__	__UNKNOWN__	10	102288994	102288994	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:102288994T>C	ENST00000299166.4	-	2	225				SEC31B_ENST00000535773.1_Intron|NDUFB8_ENST00000557395.1_Intron|NDUFB8_ENST00000370322.1_Intron|NDUFB8_ENST00000531258.1_Intron|NDUFB8_ENST00000370320.4_Intron	NM_005004.2	NP_004995.1	O95169	NDUB8_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(2)|lung(2)	4		Colorectal(252;0.234)		Epithelial(162;5.68e-10)|all cancers(201;4.05e-08)		CCCTCCCACCTCCCTCCACAG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF044958	CCDS7497.1, CCDS65916.1, CCDS65917.1	10q24.31	2011-07-04	2002-08-29		ENSG00000166136	ENSG00000166136	4714		Mitochondrial respiratory chain complex / Complex I	7703	protein-coding gene	gene with protein product	complex I ASHI subunit	602140	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8 (19kD, ASHI)		NA	9763676	Standard	NM_005004	NM_001284368	NA	Approved	ASHI, CI-ASHI	uc001kri.1	O95169	OTTHUMG00000019346	ENST00000299166.4:c.212+142A>G	chr10.hg19:g.102288994T>C		NA	A8K0L4|Q5W143|Q5W144|Q5W145|Q9UG53|Q9UJR4|Q9UQF3	hg19	CCDS7497.1	0.02	-0.431276	ACCxCCC	COVERED																																																																																			NOVEL	NDUFB8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051225.1	0	2.241579	KEEP	0	3	17	14	373	TT	0.999366	0.959251	0		-	10	60	140	0	0	8.112682	40	60	1127	74	ENST00000299166.4	0.2	0.959859
NDUFB8	4714	__UNKNOWN__	__UNKNOWN__	10	102288998	102288998	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:102288998T>C	ENST00000299166.4	-	2	225				SEC31B_ENST00000535773.1_Intron|NDUFB8_ENST00000557395.1_Intron|NDUFB8_ENST00000370322.1_Intron|NDUFB8_ENST00000531258.1_Intron|NDUFB8_ENST00000370320.4_Intron	NM_005004.2	NP_004995.1	O95169	NDUB8_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(2)|lung(2)	4		Colorectal(252;0.234)		Epithelial(162;5.68e-10)|all cancers(201;4.05e-08)		CCCACCTCCCTCCACAGAGAA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF044958	CCDS7497.1, CCDS65916.1, CCDS65917.1	10q24.31	2011-07-04	2002-08-29		ENSG00000166136	ENSG00000166136	4714		Mitochondrial respiratory chain complex / Complex I	7703	protein-coding gene	gene with protein product	complex I ASHI subunit	602140	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8 (19kD, ASHI)		NA	9763676	Standard	NM_005004	NM_001284368	NA	Approved	ASHI, CI-ASHI	uc001kri.1	O95169	OTTHUMG00000019346	ENST00000299166.4:c.212+138A>G	chr10.hg19:g.102288998T>C		NA	A8K0L4|Q5W143|Q5W144|Q5W145|Q9UG53|Q9UJR4|Q9UQF3	hg19	CCDS7497.1	0.02	-0.373654	CCCxCCA	COVERED																																																																																			NOVEL	NDUFB8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051225.1	0	2.46265	KEEP	0	2	21	16	417	TT	0.999859	0.908941	0		-	9	60	166	0	0	11.399039	34	60	1035	76	ENST00000299166.4	0.209302	0.909069
C10orf76	79591	__UNKNOWN__	__UNKNOWN__	10	103766337	103766337	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:103766337G>A	ENST00000370033.4	-	14	1127	c.1008C>T	c.(1006-1008)acC>acT	p.T336T		NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	336		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		GTGTGACTGGGGTTGTAGGAG	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						136	145	142	NA		NA	NA	10		NA											NA				103766337		1966	4158	6124	SO:0001819	synonymous_variant			AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029	79591			25788	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_024541	NM_024541	NA	Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.1008C>T	chr10.hg19:g.103766337G>A		NA	Q2TB87|Q9H8Z9	hg19	CCDS41563.1	0.02	2.394199	TGGxGTT	COVERED																																																																																			NOVEL	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050007.1	2	5.410912	KEEP	0	0	0	18	573	GG	0.999859	0.998969	0		-	20	60	720	0	0	62.259076	58	60	2167	116	ENST00000370033.4	0.25641	0.99911
C10orf32-ASMT	100528007	__UNKNOWN__	__UNKNOWN__	10	104625178	104625178	__UNKNOWN__	Intron	SNP	T	T	C	rs10786716	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:104625178T>C	ENST00000299353.6	+	5	344									C10orf32-ASMT readthrough (NMD candidate)	NA		NA									NA						CCTggccgggtgtggtggctc	0.493	NA	NA											C|||	2141	0.427516	0.3283	0.4092	5008	,	,	NA	16048	0.5942	NA	0.3698	False	NA	,,,	NA	NA	NA	2504	0.4622	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					10q24.32	2013-09-25			ENSG00000270316	ENSG00000270316	100528007			49183	other	readthrough		NA			NA		Standard		NR_037644	NA	Approved				OTTHUMG00000184175	ENST00000299353.6:c.318+2489T>C	chr10.hg19:g.104625178T>C		NA		hg19	CCDS7542.2	0.02	-0.070109	GGGxGTG	UNCOVERED																																																																																			NOVEL	C10orf32-ASMT-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000468206.2	0	2.406745	KEEP	0	0	0	8	239	TT	0.99257	0.053735	0		+	3	60	88	0	0	7.928036	5	60	174	21	ENST00000299353.6	0.375	0.054137
C10orf32-ASMT	100528007	__UNKNOWN__	__UNKNOWN__	10	104625237	104625237	__UNKNOWN__	Intron	SNP	A	A	G	rs10786717	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:104625237A>G	ENST00000299353.6	+	5	344									C10orf32-ASMT readthrough (NMD candidate)	NA		NA									NA						cggatcacagagtcaggagtt	0.517	NA	NA											G|||	1926	0.384585	0.3275	0.402	5008	,	,	NA	15120	0.5437	NA	0.3499	False	NA	,,,	NA	NA	NA	2504	0.3211	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					10q24.32	2013-09-25			ENSG00000270316	ENSG00000270316	100528007			49183	other	readthrough		NA			NA		Standard		NR_037644	NA	Approved				OTTHUMG00000184175	ENST00000299353.6:c.318+2548A>G	chr10.hg19:g.104625237A>G		NA		hg19	CCDS7542.2	0.02	-0.052639	CAGxGTC	UNCOVERED																																																																																			NOVEL	C10orf32-ASMT-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000468206.2	0	2.707045	KEEP	0	0	0	9	263	AA	0.99254	0.036491	0		+	3	60	109	0	0	10.52494	3	60	118	20	ENST00000299353.6	0.5	0.036766
SORCS1	114815	__UNKNOWN__	__UNKNOWN__	10	108339086	108339086	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:108339086A>G	ENST00000263054.6	-	25	3379				SORCS1_ENST00000369698.1_Intron|SORCS1_ENST00000344440.6_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	NA		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		GGGAGAAGGAAGAGGTCAGGG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						109	87	95	NA		NA	NA	10		NA											NA				108339086		2203	4300	6503	SO:0001627	intron_variant			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018	114815			16697	protein-coding gene	gene with protein product		606283			NA	11499680	Standard	NM_052918	NM_001206570	NA	Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3371+40T>C	chr10.hg19:g.108339086A>G		NA	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	hg19	CCDS7559.1	0.02	7.764386	GGAxGAG	COVERED																																																																																			NOVEL	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050232.4	1	6.318856	KEEP	0	0	0	21	650	AA	0.999869	0.999869	0		-	46	60	1690	0	0	147.756856	125	60	4594	221	ENST00000263054.6	0.269006	1
NRAP	4892	__UNKNOWN__	__UNKNOWN__	10	115370156	115370156	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:115370156C>A	ENST00000359988.3	-	31	3848				NRAP_ENST00000369358.4_Intron|NRAP_ENST00000369360.3_Intron|NRAP_ENST00000360478.3_Intron	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein	NA		NA								autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AGGAAAGAAACAAACTGATTA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893	4892			7988	protein-coding gene	gene with protein product		602873			NA	12789664, 10320340	Standard	NM_006175	NM_006175	NA	Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3603+61G>T	chr10.hg19:g.115370156C>A		NA		hg19	CCDS7579.1	0.02	2.641228	AAAxAAA	COVERED																																																																																			NOVEL	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050425.2	5	9.56795	KEEP	0	0	0	32	1072	CC	0.999997	0.999997	0		-	13	60	230	0	0	10.441557	152	60	5303	281	ENST00000359988.3	0.078788	1
ABLIM1	3983	__UNKNOWN__	__UNKNOWN__	10	116209984	116209984	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:116209984C>A	ENST00000277895.5	-	14	1692				ABLIM1_ENST00000533213.2_Intron|ABLIM1_ENST00000369252.4_Intron|ABLIM1_ENST00000392952.3_Intron|ABLIM1_ENST00000369266.3_Intron|ABLIM1_ENST00000369253.2_Intron	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	NA		NA			axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		AAAAAAAAAACAAAAACAATG	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204	3983			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM	NA	9245787	Standard		NM_002313	NA	Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1594+1398G>T	chr10.hg19:g.116209984C>A		NA	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	hg19	CCDS7590.1	0.02	4.476634	AAAxAAA	COVERED																																																																																			NOVEL	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050469.3	0	2.322754	KEEP	0	3	47	25	846	CC	0.999997	0.999993	0		-	12	60	439	1	0	33.370034	94	70	3507	159	ENST00000277895.5	0.113208	0.999996
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127585238	127585238	__UNKNOWN__	Intron	SNP	G	G	T	rs148621471		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:127585238G>T	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				AGGgaggcccgggctggagct	0.751	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						7	11	10	NA		NA	NA	10		NA											NA				127585238		2155	4236	6391	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+14G>T	chr10.hg19:g.127585238G>T		NA	Q6UXY9|Q6X7T6	hg19		0.02	10.732617	CCCxGGC	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	1	15.975377	KEEP	0	12	348	176	5793	GG	1	1	0		+	12	60	429	0	0	31.921141	103	60	3807	527	ENST00000368695.1	0.104348	1
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127585302	127585302	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:127585302C>T	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				TGTGGGCGCCCCGCGCGCGAC	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						6	13	11	NA		NA	NA	10		NA											NA				127585302		673	1574	2247	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+78C>T	chr10.hg19:g.127585302C>T		NA	Q6UXY9|Q6X7T6	hg19		0.02	6.5218	GCCxCGC	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	2	13.259173	KEEP	0	1	34	56	1822	CC	1	1	0		+	9	60	276	0	0	19.573494	74	60	2707	239	ENST00000368695.1	0.108434	1
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127588059	127588059	__UNKNOWN__	Intron	SNP	C	C	T	rs77736321		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:127588059C>T	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				agattacaggcgtgagccagc	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+2835C>T	chr10.hg19:g.127588059C>T		NA	Q6UXY9|Q6X7T6	hg19		0.02	-0.219324	AGGxGTG	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	3	4.815662	KEEP	1	0	0	16	564	CC	0.99649	0.550947	0		+	4	50	152	0	0	14.185887	6	60	201	60	ENST00000368695.1	0.4	0.552887
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127607936	127607936	__UNKNOWN__	Intron	SNP	G	G	T	rs76570938		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:127607936G>T	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				caccacacccggctgattttt	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+22712G>T	chr10.hg19:g.127607936G>T		NA	Q6UXY9|Q6X7T6	hg19		0.02	-0.175443	CCCxGCT	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	8	2.707784	KEEP	1	0	0	9	282	GG	0.99257	0.384528	0		+	7	60	264	0	0	27.669473	2	60	66	33	ENST00000368695.1	0.777778	0.387407
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127608054	127608054	__UNKNOWN__	Intron	SNP	T	T	G	rs77002387		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:127608054T>G	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				ggattacaggtgtgagccact	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+22830T>G	chr10.hg19:g.127608054T>G		NA	Q6UXY9|Q6X7T6	hg19		0.02	-0.184227	AGGxGTG	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	5	3.9107	KEEP	1	0	0	13	394	TT	0.994391	0.421102	0		+	6	60	223	0	0	21.010594	8	60	285	50	ENST00000368695.1	0.428571	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	133772553	133772553	__UNKNOWN__	IGR	SNP	C	C	G	rs11146348		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:133772553C>G			NA	NA				PPP2R2D (2534 upstream) : BNIP3 (9024 downstream)						NA		NA									NA						GGCGTGTGCTCATCCCCCATC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.133772553C>G		NA		hg19		0.02	5.089083	GCTxATC	COVERED																																																																																			NOVEL					0			0	5.796453	KEEP	9	3	90	51	1692	CC	1	1	0			11	47	251	0	0	12.517174	181	60	6265	322		0.057292	1
TUBGCP2	10844	__UNKNOWN__	__UNKNOWN__	10	135104007	135104007	__UNKNOWN__	Intron	SNP	G	G	A	rs201672112|rs148460658		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:135104007G>A	ENST00000252936.3	-	8	1254				TUBGCP2_ENST00000368562.1_5'UTR|TUBGCP2_ENST00000368563.2_Intron|TUBGCP2_ENST00000543663.1_Intron|TUBGCP2_ENST00000417178.2_Intron			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		aaaaaaaaaagaaaaaaaaaa	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640	10844			18599	protein-coding gene	gene with protein product		NA			NA	9566967	Standard		NM_001256617	NA	Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1215-534C>T	chr10.hg19:g.135104007G>A		NA	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	hg19	CCDS7676.1	0.02	-0.236745	AAAxAAA	COVERED																																																																																			NOVEL	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051148.1	2	2.386452	KEEP	0	0	0	8	231	GG	0.99257	0.607857	0		-	3	60	96	2	2	7.113919	21	60	702	35	ENST00000252936.3	0.125	0.612407
RP11-108K14.8	0	__UNKNOWN__	__UNKNOWN__	10	135233516	135233516	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:135233516C>T	ENST00000468317.2	+	12	1135				MTG1_ENST00000317502.6_Intron|MTG1_ENST00000477902.2_Intron						NA		NA									NA						TCACTGAACCCTCCCGTCCCC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						104	76	85	NA		NA	NA	10		NA											NA				135233516		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468317.2:c.881-14C>T	chr10.hg19:g.135233516C>T		NA		hg19		0.02	9.632139	ACCxTCC	COVERED																																																																																			NOVEL	RP11-108K14.8-001	PUTATIVE	non_canonical_U12|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000390432.1	2	30.392963	KEEP	0	0	0	101	3467	CC	1	1	0		+	17	60	630	0	0	44.78276	213	60	7860	411	ENST00000468317.2	0.073913	1
FRG2B	441581	__UNKNOWN__	__UNKNOWN__	10	135438810	135438810	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:135438810G>A	ENST00000425520.1	-	4	682	c.630C>T	c.(628-630)ctC>ctT	p.L210L	FRG2B_ENST00000443774.1_Silent_p.L211L	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	210		NA				nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGAGCCGAGTGAGCAGTGTCA	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						9	11	10	NA		NA	NA	10		NA											NA				135438810		1770	3917	5687	SO:0001819	synonymous_variant			AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899	441581			33518	protein-coding gene	gene with protein product		NA			NA	15520407	Standard	NM_001080998	NM_001080998	NA	Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.630C>T	chr10.hg19:g.135438810G>A		NA	Q5VSQ1	hg19	CCDS44502.1	0.02	5.974059	AGTxAGC	COVERED																																																																																			NOVEL	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467780.1	3	2.629038	KEEP	38	1	20	16	477	GG	0.994391	0.994391	0		-	8	25	257	0	0	16.085477	139	42	4834	248	ENST00000425520.1	0.054422	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	135455233	135455233	__UNKNOWN__	IGR	SNP	C	C	T	rs113001163		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:135455233C>T			NA	NA				FRG2B (14934 upstream) : AL845259.1 (17850 downstream)						NA		NA									NA						AAAAAAAAGCCAAAATAGGCA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.135455233C>T		NA		hg19		0.02	-0.3762	AGCxAAA	COVERED																																																																																			NOVEL					0			2	2.407994	KEEP	0	0	0	8	296	CC	0.99257	0.902315	0			6	60	233	0	0	19.29312	28	60	998	69		0.176471	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	135470778	135470778	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr10:135470778T>A			NA	NA				FRG2B (30479 upstream) : AL845259.1 (2305 downstream)						NA		NA									NA						TGTGACAGGCTCAGGGCCATA	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.135470778T>A		NA		hg19		0.02	-0.131522	GGCxCAG	UNCOVERED																																																																																			NOVEL					0			0	2.407206	KEEP	27	0	0	8	249	TT	0	0	0			3	37	86	0	0	7.539776	6	39	226	57		0.333333	0.229173
BET1L	51272	__UNKNOWN__	__UNKNOWN__	11	189669	189669	__UNKNOWN__	Intron	SNP	A	A	C	rs546609209		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:189669A>C	ENST00000410108.1	-	4	230									Bet1 golgi vesicular membrane trafficking protein-like	NA		NA									NA		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;4.2e-27)|Epithelial(43;2.8e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.7e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		agacgggttgaacctcagtaa	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF234160	CCDS7689.1, CCDS41582.1	11p15.5	2013-03-08	2013-03-08		ENSG00000177951	ENSG00000177951	51272			19348	protein-coding gene	gene with protein product	golgi integral membrane protein 3	615417	blocked early in transport 1 homolog (S. cerevisiae) like, blocked early in transport 1 homolog (S. cerevisiae)-like		NA	9242691, 15004235	Standard	NM_016526	NM_016526	NA	Approved	GS15, GOLIM3	uc001loe.2	Q9NYM9	OTTHUMG00000119071	ENST00000410108.1:c.169-9265T>G	chr11.hg19:g.189669A>C		NA		hg19		0.02	-0.035093	TTGxACC	UNCOVERED																																																																																			NOVEL	BET1L-005	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000335359.1	0	2.40368	KEEP	0	0	0	8	211	AA	0.99257	0.019833	0		-	2	60	81	0	0	9.054152	0	0	0	17	ENST00000410108.1	1	0.019982
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016819	1016819	__UNKNOWN__	Silent	SNP	G	G	T	rs369828826		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1016819G>T	ENST00000421673.2	-	31	6032	c.5982C>A	c.(5980-5982)acC>acA	p.T1994T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1994	Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTTGGATAGGTAGTGGTGG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						1471	1465	1467	NA		NA	NA	11		NA											NA				1016819		2203	4298	6501	SO:0001819	synonymous_variant			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5982C>A	chr11.hg19:g.1016819G>T		NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	40.316755	ATAxGTA	COVERED																																																																																			NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	78	40.153101	KEEP	17	18	551	327	11609	GG	1	1	0		-	65	60	2417	0	0	191.751527	389	60	14339	1493	ENST00000421673.2	0.143172	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016960	1016960	__UNKNOWN__	Silent	SNP	G	G	T	rs113980831		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1016960G>T	ENST00000421673.2	-	31	5891	c.5841C>A	c.(5839-5841)acC>acA	p.T1947T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1947	Approximate repeats.|Thr-rich.	NA		NITPKHTSTGTRTPV -> KITTNPTSIGSSTPM (in Ref. 5; AAA35866). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGGGGTTCTGGTGCCTGTAC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						516	536	529	NA		NA	NA	11		NA											NA				1016960		2200	4292	6492	SO:0001819	synonymous_variant			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5841C>A	chr11.hg19:g.1016960G>T		NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	39.052697	TCTxGTG	COVERED																																																																																			NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	29	13.769705	KEEP	17	21	611	261	8937	GG	1	1	0		-	37	60	1319	0	0	98.384709	311	60	11535	1310	ENST00000421673.2	0.106322	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1092910	1092910	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1092910G>A	ENST00000441003.2	+	30	4756	c.4729G>A	c.(4729-4731)Ggc>Agc	p.G1577S	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.G1578S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.G1577S(1)|p.G1578S(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccggcacacagac	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	prostate(2)					NA						85	125	111	NA		NA	NA	11		NA											NA				1092910		1937	3603	5540	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4729G>A	chr11.hg19:g.1092910G>A	ENSP00000415183:p.Gly1577Ser	NA	Q14878	hg19		0.02	19.339963	ACCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	g	2.787	-0.252217	0.05829	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11169	2.8;2.9	1.49	-2.97	0.05530	.	1.221530	0.07178	U	0.853623	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.24882	0.113	B	0.11329	0.006	T	0.37798	-0.9690	9	0.07175	T	0.84	.	4.8921	0.13731	0.6336:0.1684:0.198:0.0	.	1577	E7EUV1	.	S	1577;1578	ENSP00000415183:G1577S;ENSP00000351956:G1578S	ENSP00000351956:G1578S	G	+	1	0	MUC2	1082910	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.266000	0.02842	-2.620000	0.00440	-1.713000	0.00713	GGC	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	42	34.482553	KEEP	124	24	729	371	12303	GG	1	1	0		+	15	58	487	0	0	28.509366	382	60	12871	1528	ENST00000441003.2	0.037783	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1092948	1092948	__UNKNOWN__	Silent	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1092948C>G	ENST00000441003.2	+	30	4794	c.4767C>G	c.(4765-4767)acC>acG	p.T1589T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1590T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1590T(2)|p.T1589T(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tcaccaccaccactacggtga	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				4	Substitution - coding silent(4)	endometrium(2)|kidney(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4767C>G	chr11.hg19:g.1092948C>G		NA	Q14878	hg19		0.02	13.349428	CACxACT	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	30	85.01655	KEEP	160	5	158	338	11425	CC	1	1	0		+	12	44	376	1	0	20.314287	363	60	13063	1305	ENST00000441003.2	0.032	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093066	1093066	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs56365200	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1093066C>A	ENST00000441003.2	+	30	4912	c.4885C>A	c.(4885-4887)Cca>Aca	p.P1629T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1596T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaaccccaacagccat	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						123	163	149	NA		NA	NA	11		NA											NA				1093066		1876	3602	5478	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4885C>A	chr11.hg19:g.1093066C>A	ENSP00000415183:p.Pro1629Thr	NA	Q14878	hg19		0.02	8.939302	ACCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.903	-0.721580	0.03182	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12879	2.64;3.49	1.75	-3.49	0.04724	.	16.324000	0.00424	N	0.000074	T	0.04407	0.0121	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25502	-1.0130	9	0.05620	T	0.96	.	2.5689	0.04790	0.221:0.4621:0.0:0.317	rs56365200	1629	E7EUV1	.	T	1629;1596	ENSP00000415183:P1629T;ENSP00000351956:P1596T	ENSP00000351956:P1596T	P	+	1	0	MUC2	1083066	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.774000	0.00187	-0.960000	0.03613	-3.899000	0.00016	CCA	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	4	15.90193	KEEP	27	5	152	107	3469	CC	1	1	0		+	10	48	298	0	0	19.854698	109	60	3675	450	ENST00000441003.2	0.084034	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093204	1093204	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs56299570		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1093204C>A	ENST00000441003.2	+	30	5050	c.5023C>A	c.(5023-5025)Cca>Aca	p.P1675T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1642T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.P1675T(1)|p.P1642T(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gtccccaaccccaacagccat	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5023C>A	chr11.hg19:g.1093204C>A	ENSP00000415183:p.Pro1675Thr	NA	Q14878	hg19		0.02	4.082523	ACCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.954	-0.705464	0.03255	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.09073	3.02;3.53	1.75	-3.49	0.04724	.	0.575351	0.10542	U	0.662513	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	9	0.16896	T	0.51	.	6.9769	0.24681	0.6778:0.3222:0.0:0.0	rs56299570	1675	E7EUV1	.	T	1675;1642	ENSP00000415183:P1675T;ENSP00000351956:P1642T	ENSP00000351956:P1642T	P	+	1	0	MUC2	1083204	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.268000	0.00533	-1.450000	0.01936	0.184000	0.17185	CCA	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	3	7.917539	KEEP	7	2	64	49	1553	CC	1	0.999973	0		+	7	58	251	0	0	17.690884	85	60	3039	211	ENST00000441003.2	0.076087	0.999973
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093274	1093274	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs11245949	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1093274C>T	ENST00000441003.2	+	30	5120	c.5093C>T	c.(5092-5094)tCg>tTg	p.S1698L	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.S1665L	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accccaacatcgacacccatc	0.637	NA	NA											N|||	2435	0.486222	0.4826	0.4899	5008	,	,	NA	22392	0.631	NA	0.3608	False	NA	,,,	NA	NA	NA	2504	0.4683	NA	NA	NA						NA		NA				0							NA						129	167	154	NA		NA	NA	11		NA											NA				1093274		1842	3364	5206	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5093C>T	chr11.hg19:g.1093274C>T	ENSP00000415183:p.Ser1698Leu	NA	Q14878	hg19		0.02	10.461088	CATxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	T	1.748	-0.490089	0.04322	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.08370	3.13;3.1	0.851	-1.7	0.08159	.	227.466000	0.04577	U	0.394340	T	0.06005	0.0156	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40979	-0.9534	9	0.30854	T	0.27	.	5.5277	0.16967	0.0:0.5285:0.0:0.4715	rs11245949;rs59265712	1698	E7EUV1	.	L	1698;1665	ENSP00000415183:S1698L;ENSP00000351956:S1665L	ENSP00000351956:S1665L	S	+	2	0	MUC2	1083274	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.256000	0.18351	-1.248000	0.02503	-2.819000	0.00109	TCG	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	7	14.306393	KEEP	100	11	313	158	5137	CC	1	1	0		+	22	60	696	0	0	49.812535	185	60	6198	680	ENST00000441003.2	0.10628	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093295	1093295	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs200837746|rs200145328		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1093295C>T	ENST00000441003.2	+	30	5141	c.5114C>T	c.(5113-5115)aCt>aTt	p.T1705I	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1672I	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1705I(1)|p.T1672I(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccaccactacggtgacc	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	large_intestine(2)					NA						113	161	144	NA		NA	NA	11		NA											NA				1093295		1882	3466	5348	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5114C>T	chr11.hg19:g.1093295C>T	ENSP00000415183:p.Thr1705Ile	NA	Q14878	hg19		0.02	14.222236	CCAxTAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.775	-0.764347	0.02996	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11277	3.02;2.79	1.6	-0.698	0.11280	.	0.547305	0.11728	U	0.535177	T	0.05868	0.0153	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38457	-0.9660	9	0.34782	T	0.22	.	3.0673	0.06219	0.0:0.5189:0.2842:0.1969	.	1705	E7EUV1	.	I	1705;1672	ENSP00000415183:T1705I;ENSP00000351956:T1672I	ENSP00000351956:T1672I	T	+	2	0	MUC2	1083295	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.065000	0.14466	-0.392000	0.07751	-1.238000	0.01547	ACT	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	12	36.465105	KEEP	129	12	315	233	7951	CC	1	1	0		+	14	60	464	0	0	29.133433	259	60	9446	924	ENST00000441003.2	0.051282	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093323	1093323	__UNKNOWN__	Silent	SNP	C	C	T	rs7948036		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1093323C>T	ENST00000441003.2	+	30	5169	c.5142C>T	c.(5140-5142)acC>acT	p.T1714T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.T2T|MUC2_ENST00000359061.5_Silent_p.T1681T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	caacacccaccggcacacaga	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	C		29,3837		0,29,1904	171	218	202	NA	5139	-0.5	0	11	dbSNP_116	202	60,7230		0,60,3585	no	coding-synonymous	MUC2	NM_002457.2		0,89,5489	TT,TC,CC	NA	0.823,0.7501,0.7978		1713/2813	1093323	89,11067	1933	3645	5578	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5142C>T	chr11.hg19:g.1093323C>T		NA	Q14878	hg19		0.02	17.155548	CACxGGC	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	23	5.404468	KEEP	133	26	709	269	8743	CC	1	1	0		+	21	60	688	0	0	45.524845	295	60	10047	1166	ENST00000441003.2	0.066456	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093368	1093368	__UNKNOWN__	Silent	SNP	G	G	A	rs111440994		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1093368G>A	ENST00000441003.2	+	30	5214	c.5187G>A	c.(5185-5187)acG>acA	p.T1729T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.T17T|MUC2_ENST00000359061.5_Silent_p.T1696T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1696T(3)|p.T1729T(3)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				6	Substitution - coding silent(6)	prostate(6)					NA						175	224	207	NA		NA	NA	11		NA											NA				1093368		1971	3826	5797	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5187G>A	chr11.hg19:g.1093368G>A		NA	Q14878	hg19		0.02	20.419102	TACxGTG	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	39	30.549541	KEEP	127	23	703	349	11283	GG	1	1	0		+	21	60	704	2	0	45.197971	376	60	12656	1394	ENST00000441003.2	0.052897	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1212895	1212895	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1212895C>G	ENST00000358378.6	+	0	136							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		aacctctggtcctggaactac	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*133C>G	chr11.hg19:g.1212895C>G		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	34.758439	GGTxCTG	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	43	64.481233	KEEP	50	23	768	483	16300	CC	1	1	0		+	26	60	958	0	0	68.342989	314	60	11468	1574	ENST00000358378.6	0.076471	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1213119	1213119	__UNKNOWN__	3'UTR	SNP	C	C	T	rs200209677		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1213119C>T	ENST00000358378.6	+	0	360							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		CTCCTACAACCAGCACGACCT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						119	115	116	NA		NA	NA	11		NA											NA				1213119		875	1990	2865	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*357C>T	chr11.hg19:g.1213119C>T		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	34.893015	AACxAGC	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	47	24.317621	KEEP	41	13	396	220	7606	CC	1	1	0		+	21	22	725	1	0	47.349614	356	60	13251	1252	ENST00000358378.6	0.055703	1
BRSK2	9024	__UNKNOWN__	__UNKNOWN__	11	1466576	1466576	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:1466576A>T	ENST00000528841.1	+	10	1249	c.865A>T	c.(865-867)Atc>Ttc	p.I289F	BRSK2_ENST00000544817.1_5'UTR|BRSK2_ENST00000308230.5_Missense_Mutation_p.I289F|BRSK2_ENST00000528710.1_Missense_Mutation_p.I229F|BRSK2_ENST00000531197.1_Missense_Mutation_p.I289F|BRSK2_ENST00000526678.1_Missense_Mutation_p.I289F|BRSK2_ENST00000308219.9_Missense_Mutation_p.I289F|BRSK2_ENST00000382179.1_Missense_Mutation_p.I335F			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	289		NA			actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CAAGGTGCAGATCCGCTCGCT	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						36	45	42	NA		NA	NA	11		NA											NA				1466576		2150	4261	6411	SO:0001583	missense			AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672	9024			11405	protein-coding gene	gene with protein product	serine/threonine kinase 29	609236	chromsosome 11 open reading frame 7	C11orf7, STK29	NA	9852686, 9929968	Standard	NM_003957	NM_001256629	NA	Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.865A>T	chr11.hg19:g.1466576A>T	ENSP00000432000:p.Ile289Phe	NA	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	hg19	CCDS58107.1	0.02	4.445932	CAGxTCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	14.81	2.647601	0.47258	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528710;ENST00000382179	T;T;T;T;T;T;T	0.72835	-0.69;-0.69;-0.68;-0.69;-0.68;-0.49;-0.53	3.85	3.85	0.44370	Protein kinase-like domain (1);	0.129000	0.50627	U	0.000101	T	0.63402	0.2508	L	0.36672	1.1	0.80722	D	1	P;P;B;B;B	0.49090	0.609;0.919;0.246;0.286;0.409	B;P;B;B;B	0.51229	0.36;0.663;0.255;0.091;0.123	T	0.58177	-0.7682	10	0.13108	T	0.6	.	7.7142	0.28694	0.9038:0.0:0.0962:0.0	.	289;335;289;289;289	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	F	289;289;289;289;289;229;335	ENSP00000310697:I289F;ENSP00000431152:I289F;ENSP00000310805:I289F;ENSP00000432000:I289F;ENSP00000433370:I289F;ENSP00000433235:I229F;ENSP00000371614:I335F	ENSP00000310697:I289F	I	+	1	0	BRSK2	1423152	1.000000	0.71417	1.000000	0.80357	0.822000	0.46500	1.690000	0.37711	1.621000	0.50320	0.379000	0.24179	ATC	NOVEL	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393033.1	1	27.54193	KEEP	0	2	55	111	3375	AA	1	0.999987	0		+	38	60	1282	0	0	116.291938	68	60	2404	280	ENST00000528841.1	0.358491	0.999987
RP13-726E6.2	0	__UNKNOWN__	__UNKNOWN__	11	3569010	3569010	__UNKNOWN__	RNA	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:3569010C>G	ENST00000527970.1	-	0	285										NA		NA									NA						AGTCTCTTGCCTCTCAAGCAC	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000527970.1:	chr11.hg19:g.3569010C>G		NA		hg19		0.02	2.005722	TGCxTCT	COVERED																																																																																			NOVEL	RP13-726E6.2-002	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000392273.1	0	3.611472	KEEP	5	0	0	12	426	CC	0.993634	0.970646	0		-	6	27	209	0	0	15.533569	49	60	1868	96	ENST00000527970.1	0.109091	0.976865
RP13-726E6.2	0	__UNKNOWN__	__UNKNOWN__	11	3569056	3569056	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:3569056G>A	ENST00000527970.1	-	0	285										NA		NA									NA						TTTGGGATTCGTTGCAGAGAA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000527970.1:	chr11.hg19:g.3569056G>A		NA		hg19		0.02	2.340154	TTCxTTG	COVERED																																																																																			NOVEL	RP13-726E6.2-002	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000392273.1	0	3.310693	KEEP	5	0	0	11	384	GG	0.993072	0.957097	0		-	5	30	189	0	0	14.182205	46	50	1728	82	ENST00000527970.1	0.098039	0.963774
OR51A4	401666	__UNKNOWN__	__UNKNOWN__	11	4967651	4967651	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs28673258		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:4967651A>G	ENST00000380373.2	-	1	705	c.680T>C	c.(679-681)cTg>cCg	p.L227P	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	227		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGCAATTCCCAGTACAGTCTT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						115	98	104	NA		NA	NA	11		NA											NA				4967651		2195	4284	6479	SO:0001583	missense			AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497	401666		GPCR / Class A : Olfactory receptors	14795	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001005329	NM_001005329	NA	Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.680T>C	chr11.hg19:g.4967651A>G	ENSP00000369731:p.Leu227Pro	NA		hg19	CCDS31367.1	0.02	13.743878	CCCxGTA	COVERED	406	0.1858974358974359	68	0.13821138211382114	84	0.23204419889502761	91	0.1590909090909091	163	0.21503957783641162	A	14.25	2.480485	0.44044	.	.	ENSG00000205497	ENST00000380373	T	0.41758	0.99	3.44	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	H	0.98612	4.28	0.48975	P	2.6599999999998847E-4	D	0.64830	0.994	D	0.73708	0.981	T	0.33650	-0.9860	8	0.72032	D	0.01	.	11.2274	0.48892	1.0:0.0:0.0:0.0	rs28673258	227	Q8NGJ6	O51A4_HUMAN	P	227	ENSP00000369731:L227P	ENSP00000369731:L227P	L	-	2	0	OR51A4	4924227	0.044000	0.20184	0.036000	0.18154	0.966000	0.64601	3.521000	0.53472	1.571000	0.49722	0.392000	0.25879	CTG	NOVEL	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000142821.1	7	12.916861	KEEP	20	0	0	43	1280	AA	1	1	0		-	10	33	361	0	0	21.312677	329	60	12192	450	ENST00000380373.2	0.029499	1
TRIM6-TRIM34	445372	__UNKNOWN__	__UNKNOWN__	11	5654041	5654041	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:5654041A>C	ENST00000354852.5	+	8	1658				TRIM6-TRIM34_ENST00000457787.2_Intron|TRIM34_ENST00000514226.1_Intron|TRIM34_ENST00000429814.2_Intron|HBG2_ENST00000380259.2_Intron	NM_001003819.3	NP_001003819.1			TRIM6-TRIM34 readthrough	NA		NA								NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(9)|ovary(1)|prostate(2)|stomach(2)|urinary_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;1.01e-08)|BRCA - Breast invasive adenocarcinoma(625;0.145)		GGAAAATCTCACCTTTTCATC	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB039903	CCDS31388.1	11p15.4	2014-03-14	2011-01-25		ENSG00000258588	ENSG00000258588	445372			33440	other	readthrough		NA			NA		Standard	NM_001003819	NM_001003819	NA	Approved		uc001mbf.3		OTTHUMG00000066899	ENST00000354852.5:c.1485+57A>C	chr11.hg19:g.5654041A>C		NA		hg19	CCDS31388.1	0.02	-0.245516	CTCxCCT	COVERED																																																																																			NOVEL	TRIM6-TRIM34-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000143374.3	2	3.60787	KEEP	0	0	0	12	337	AA	0.993634	0.637264	0		+	4	60	99	0	0	6.832178	24	60	759	62	ENST00000354852.5	0.142857	0.641347
OR56A1	120796	__UNKNOWN__	__UNKNOWN__	11	6048438	6048438	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:6048438A>G	ENST00000316650.5	-	1	533	c.497T>C	c.(496-498)aTt>aCt	p.I166T		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	166		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGGATAGGAATGGGTGCAGT	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						135	120	125	NA		NA	NA	11		NA											NA				6048438		2201	4296	6497	SO:0001583	missense			AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934	120796		GPCR / Class A : Olfactory receptors	14781	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001001917	NM_001001917	NA	Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.497T>C	chr11.hg19:g.6048438A>G	ENSP00000321246:p.Ile166Thr	NA	B2RNI2|Q6IFL0	hg19	CCDS31405.1	0.02	4.902898	GGAxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.428	-0.904925	0.02453	.	.	ENSG00000180934	ENST00000316650	T	0.00123	8.7	4.27	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.161017	0.28736	N	0.014303	T	0.00178	0.0005	M	0.62088	1.915	0.09310	N	1	B	0.14438	0.01	B	0.23150	0.044	T	0.30851	-0.9964	10	0.54805	T	0.06	.	8.2834	0.31913	0.8231:0.0:0.0:0.1769	.	166	Q8NGH5	O56A1_HUMAN	T	166	ENSP00000321246:I166T	ENSP00000321246:I166T	I	-	2	0	OR56A1	6005014	0.001000	0.12720	0.021000	0.16686	0.017000	0.09413	1.025000	0.30090	1.914000	0.55421	0.533000	0.62120	ATT	NOVEL	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383757.1	2	8.724214	KEEP	0	0	0	29	881	AA	0.999997	0.999997	0		-	44	60	1695	0	0	151.854614	101	60	3649	208	ENST00000316650.5	0.303448	1
SYT9	143425	__UNKNOWN__	__UNKNOWN__	11	7487027	7487027	__UNKNOWN__	Intron	SNP	A	A	G	rs201053383		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:7487027A>G	ENST00000318881.6	+	7	1704				CTD-2516F10.2_ENST00000530169.1_RNA|CTD-2516F10.2_ENST00000526706.1_RNA|CTD-2516F10.2_ENST00000526695.1_RNA	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	NA		NA			positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		ggcaggaggcaaaaggcactt	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743	143425		Synaptotagmins	19265	protein-coding gene	gene with protein product		613528			NA	11543631	Standard	NM_175733	NM_175733	NA	Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.1468-996A>G	chr11.hg19:g.7487027A>G		NA		hg19	CCDS7778.1	0.02	-0.087709	GGCxAAA	UNCOVERED																																																																																			NOVEL	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384483.1	7	4.211127	KEEP	7	0	0	14	409	AA	0.993072	0.09903	0		+	4	24	117	0	0	10.685047	6	60	206	37	ENST00000318881.6	0.4	0.099721
ANO3	63982	__UNKNOWN__	__UNKNOWN__	11	26465484	26465484	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:26465484A>G	ENST00000256737.3	+	3	1165				ANO3_ENST00000525139.1_Intron|ANO3_ENST00000531646.1_Intron|ANO3_ENST00000537978.1_Intron	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	NA		NA			calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						GAAAAAGTTCATGTTTGGTTT	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343	63982		Ion channels / Chloride channels : Calcium activated : Anoctamins	14004	protein-coding gene	gene with protein product	transmembrane protein 16C (eight membrane-spanning domains)	610110	chromosome 11 open reading frame 25, transmembrane protein 16C	C11orf25, TMEM16C	NA	12739008, 15067359, 23200863, 24692353	Standard	NM_031418	NM_031418	NA	Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.313+101A>G	chr11.hg19:g.26465484A>G		NA	B7Z3F5	hg19	CCDS31447.1	0.02	-0.289518	TTCxTGT	COVERED																																																																																			NOVEL	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387806.1	0	4.210484	KEEP	0	0	0	14	400	AA	0.995343	0.757343	0		+	10	60	373	0	0	33.280145	23	60	857	51	ENST00000256737.3	0.30303	0.760887
KCNA4	3739	__UNKNOWN__	__UNKNOWN__	11	30033191	30033191	__UNKNOWN__	Silent	SNP	G	G	A	rs3802914	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:30033191G>A	ENST00000328224.6	-	2	2268	c.1035C>T	c.(1033-1035)ggC>ggT	p.G345G		NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	345		NA			potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	CACCATGCCCGCCAGCACTCA	0.498	NA	NA											g|||	855	0.170727	0.3154	0.1801	5008	,	,	NA	19509	0.0357	NA	0.171	False	NA	,,,	NA	NA	NA	2504	0.1074	NA	NA	NA						NA		NA				0							NA	A		1191,2871		182,827,1022	84	77	79	NA	1035	-10.9	0.1	11	dbSNP_107	79	1368,7020		118,1132,2944	no	coding-synonymous	KCNA4	NM_002233.3		300,1959,3966	AA,AG,GG	NA	16.309,29.3205,20.5542		345/654	30033191	2559,9891	2031	4194	6225	SO:0001819	synonymous_variant			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255	3739		Potassium channels, Voltage-gated ion channels / Potassium channels	6222	protein-coding gene	gene with protein product		176266	potassium voltage-gated channel, shaker-related subfamily, member 4-like	KCNA4L	NA	2263489, 16382104	Standard	NM_002233	NM_002233	NA	Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1035C>T	chr11.hg19:g.30033191G>A		NA		hg19	CCDS41629.1	0.02	7.021863	CCCxCCA	COVERED																																																																																			NOVEL	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388074.2	0	7.823782	KEEP	0	0	0	26	860	GG	0.999957	0.999957	0		-	56	60	1980	0	0	175.456837	129	60	4761	235	ENST00000328224.6	0.302703	1
PRDM11	56981	__UNKNOWN__	__UNKNOWN__	11	45234313	45234313	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:45234313C>T	ENST00000424263.2	+	6	799				PRDM11_ENST00000528980.1_Intron|PRDM11_ENST00000263765.4_Intron|PRDM11_ENST00000530656.1_Intron	NM_001256695.1|NM_001256696.1	NP_001243624.1|NP_001243625.1	Q9NQV5	PRD11_HUMAN	PR domain containing 11	NA		NA					methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GCAGTTCTGCCAGGAGCTGGT	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(118;1511 1736 6472 36603 43224)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485	56981			13996	protein-coding gene	gene with protein product	PR-domain containing protein 11	NA			NA		Standard	NM_020229	NM_001256695	NA	Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000424263.2:c.555-6808C>T	chr11.hg19:g.45234313C>T		NA	Q8N9F1	hg19	CCDS58130.1	0.02	6.526351	TGCxAGG	COVERED																																																																																			NOVEL	PRDM11-002	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389930.1	0	69.823373	KEEP	0	0	0	232	8035	CC	1	1	0		+	9	60	336	0	0	21.999576	189	60	7090	575	ENST00000424263.2	0.045455	1
DGKZ	8525	__UNKNOWN__	__UNKNOWN__	11	46388921	46388921	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:46388921G>A	ENST00000454345.1	+	3	934	c.809G>A	c.(808-810)cGg>cAg	p.R270Q	DGKZ_ENST00000343674.6_Missense_Mutation_p.R98Q|DGKZ_ENST00000532868.2_Missense_Mutation_p.R86Q|DGKZ_ENST00000318201.8_Missense_Mutation_p.R81Q|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000421244.2_Missense_Mutation_p.R81Q|DGKZ_ENST00000456247.2_Missense_Mutation_p.R81Q|DGKZ_ENST00000527911.1_Missense_Mutation_p.R81Q|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000395574.3_Missense_Mutation_p.R47Q|DGKZ_ENST00000543978.1_Intron	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	270		NA			blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		GAGTCAGAGCGGCAGATCCGG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						32	34	33	NA		NA	NA	11		NA											NA				46388921		2196	4298	6494	SO:0001583	missense			U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	8525	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	diacylglycerol kinase, zeta 104kDa		NA	8626588	Standard	NM_001105540	NM_003646	NA	Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.809G>A	chr11.hg19:g.46388921G>A	ENSP00000412178:p.Arg270Gln	NA	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	hg19	CCDS41640.1	0.02	2.307085	AGCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	16.20	3.054913	0.55325	.	.	ENSG00000149091	ENST00000343674;ENST00000395574;ENST00000532868;ENST00000527911;ENST00000456247;ENST00000421244;ENST00000318201;ENST00000454345	T;T;T;T;T;T;T;T	0.25085	2.26;2.5;2.62;3.48;2.3;2.36;2.49;1.82	5.04	4.11	0.48088	.	0.746320	0.12845	N	0.434428	T	0.25606	0.0623	L	0.47016	1.485	0.35014	D	0.757161	B;P;B;B;B;P;B;B;D;B	0.57257	0.265;0.544;0.029;0.091;0.155;0.673;0.147;0.091;0.979;0.124	B;B;B;B;B;B;B;B;P;B	0.46049	0.042;0.055;0.004;0.011;0.026;0.197;0.024;0.006;0.502;0.042	T	0.34129	-0.9841	10	0.52906	T	0.07	.	6.3229	0.21227	0.0728:0.1301:0.6628:0.1343	.	81;47;47;81;270;81;81;47;47;98	B7Z2M9;B7Z6M3;B7Z8F6;E9PPW4;Q13574;Q13574-2;G3V0F6;A8MVN1;Q6ZWA5;Q6ZVG7	.;.;.;.;DGKZ_HUMAN;.;.;.;.;.	Q	98;47;47;81;81;81;81;270	ENSP00000343065:R98Q;ENSP00000378941:R47Q;ENSP00000436273:R47Q;ENSP00000436291:R81Q;ENSP00000395684:R81Q;ENSP00000391021:R81Q;ENSP00000320340:R81Q;ENSP00000412178:R270Q	ENSP00000320340:R81Q	R	+	2	0	DGKZ	46345497	1.000000	0.71417	0.996000	0.52242	0.980000	0.70556	3.977000	0.56874	1.231000	0.43661	0.555000	0.69702	CGG	NOVEL	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389772.1	1	17.149391	KEEP	0	0	0	57	1904	GG	1	0.999804	0		+	23	60	877	0	0	76.599248	66	60	2330	192	ENST00000454345.1	0.258427	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	49913558	49913558	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:49913558C>G			NA	NA				RP11-707M1.1 (81587 upstream) : OR4C13 (60384 downstream)						NA		NA									NA						TGGCCACTGTCCTTGGTGCTG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.49913558C>G		NA		hg19		0.02	-0.061411	TGTxCTT	UNCOVERED																																																																																			NOVEL					0			0	4.491829	KEEP	0	0	0	15	464	CC	0.99649	0.043633	0			3	60	107	0	0	10.055163	4	60	147	31		0.428571	0.043787
TNKS1BP1	85456	__UNKNOWN__	__UNKNOWN__	11	57067934	57067934	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:57067934T>C	ENST00000532437.1	-	10	5514				TNKS1BP1_ENST00000358252.3_Intron			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	NA		NA			gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				AGAAGGGGCATGAGGCCTCCG	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115	85456			19081	protein-coding gene	gene with protein product		607104			NA	11854288	Standard	NM_033396	NM_033396	NA	Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.5187+67A>G	chr11.hg19:g.57067934T>C		NA	A7E2F8|Q6PJ35|Q6ZV74	hg19	CCDS7951.1	0.02	4.273775	GCAxGAG	COVERED																																																																																			NOVEL	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000392455.1	1	13.533147	KEEP	0	0	0	45	1258	TT	1	1	0		-	10	60	368	0	0	26.028207	127	60	4614	199	ENST00000532437.1	0.072993	1
RP11-142C4.6	0	__UNKNOWN__	__UNKNOWN__	11	58817625	58817625	__UNKNOWN__	RNA	SNP	A	A	G	rs564404	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:58817625A>G	ENST00000533954.1	-	0	507				RP11-142C4.6_ENST00000532098.1_RNA	NR_033853.1					NA		NA									NA						GAGGGGATAAAAGCAGCTGCA	0.413	NA	NA											-|||	3161	0.63119	0.5053	0.5504	5008	,	,	NA	14918	0.7887	NA	0.5964	False	NA	,,,	NA	NA	NA	2504	0.7321	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000533954.1:	chr11.hg19:g.58817625A>G		NA		hg19		0.02	-0.307065	TAAxAGC	COVERED																																																																																			NOVEL	RP11-142C4.6-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000394603.1	2	2.407314	KEEP	0	0	0	8	258	AA	0.99257	0.7943	0		-	10	40	379	0	0	33.577552	25	60	924	50	ENST00000533954.1	0.285714	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	61735433	61735433	__UNKNOWN__	IGR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:61735433T>G			NA	NA				FTH1 (301 upstream) : AP003733.1 (19 downstream)						NA		NA									NA						GGGGGAAGGGTGCGGGGGCGC	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.61735433T>G		NA		hg19		0.02	-0.137458	GGGxGCG	COVERED																																																																																			NOVEL					0			2	2.402885	KEEP	0	0	0	8	206	TT	0.99257	0.259026	0			6	60	105	0	0	8.63383	10	60	291	26		0.375	0.260965
RARRES3	5920	__UNKNOWN__	__UNKNOWN__	11	63310670	63310670	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:63310670A>G	ENST00000255688.3	+	3	166				RARRES3_ENST00000439013.2_Intron|RARRES3_ENST00000537871.1_Intron|RARRES3_ENST00000354445.2_Intron	NM_004585.3	NP_004576.2	Q9UL19	HRSL4_HUMAN	retinoic acid receptor responder (tazarotene induced) 3	NA		NA			lipid catabolic process (GO:0016042)|negative regulation of cell proliferation (GO:0008285)|phospholipid metabolic process (GO:0006644)	integral component of membrane (GO:0016021)	phospholipase A2 activity (GO:0004623)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	6						ggggtccccaaccctgggctg	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41662.1	11q23	2008-05-02			ENSG00000133321	ENSG00000133321	5920			9869	protein-coding gene	gene with protein product		605092			NA	9270552	Standard		NM_004585	NA	Approved	TIG3, HRASLS4	uc001nxf.4	Q9UL19	OTTHUMG00000167850	ENST00000255688.3:c.119-1423A>G	chr11.hg19:g.63310670A>G		NA	B2R599|B4DDW2|E7ENZ7|O95200	hg19	CCDS41662.1	0.02	4.046751	CCAxCCC	COVERED																																																																																			NOVEL	RARRES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396629.1	1	7.210054	KEEP	2	0	0	24	688	AA	0.999909	0.999896	0		+	8	33	286	0	0	20.103543	98	60	3245	146	ENST00000255688.3	0.075472	0.999987
PCNXL3	399909	__UNKNOWN__	__UNKNOWN__	11	65391933	65391933	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:65391933C>G	ENST00000355703.3	+	15	3255					NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CGTGTCCCCTCCCTGCCAGTG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						47	59	55	NA		NA	NA	11		NA											NA				65391933		2064	4187	6251	SO:0001627	intron_variant			BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136	399909			18760	protein-coding gene	gene with protein product		NA			NA	15146197	Standard	NM_032223	NM_032223	NA	Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2717-9C>G	chr11.hg19:g.65391933C>G		NA	Q6MZN8	hg19	CCDS44650.1	0.02	4.807902	CCTxCCT	COVERED																																																																																			NOVEL	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390321.1	1	21.065388	KEEP	0	0	0	70	2378	CC	1	1	0		+	38	60	1378	0	0	121.374518	95	60	3563	251	ENST00000355703.3	0.285714	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	65418431	65418431	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:65418431G>A			NA	NA				SIPA1 (30 upstream) : RELA (2635 downstream)						NA		NA									NA						AGGGCAAGGGGTTTTGCCTCC	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.65418431G>A		NA		hg19		0.02	1.912447	GGGxTTT	COVERED																																																																																			NOVEL					0			0	10.005286	KEEP	0	1	33	45	1558	GG	1	0.998867	0			5	60	170	0	0	11.355621	72	60	2709	166		0.064935	0.998867
TBX10	347853	__UNKNOWN__	__UNKNOWN__	11	67399030	67399030	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:67399030G>A	ENST00000335385.3	-	0	1291					NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	NA		NA			anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						TCCCACACCCGGTGTAAGGTC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800	347853		T-boxes	11593	protein-coding gene	gene with protein product		604648	T-box 7	TBX7	NA	9545502	Standard	NM_005995	NM_005995	NA	Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.*46C>T	chr11.hg19:g.67399030G>A		NA	Q14D64|Q86XS3	hg19	CCDS31621.1	0.02	2.368027	CCCxGTG	COVERED																																																																																			NOVEL	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394034.1	2	12.639462	KEEP	0	0	0	42	1420	GG	1	0.999407	0		-	29	60	1100	0	0	100.704475	53	60	1888	158	ENST00000335385.3	0.353659	0.999407
SUV420H1	51111	__UNKNOWN__	__UNKNOWN__	11	67925502	67925502	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:67925502C>T	ENST00000304363.4	-	11	2664	c.2311G>A	c.(2311-2313)Ggc>Agc	p.G771S		NM_017635.3	NP_060105	Q4FZB7	SV421_HUMAN	suppressor of variegation 4-20 homolog 1 (Drosophila)	771		NA			histone H4-K20 trimethylation (GO:0034773)|muscle organ development (GO:0007517)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)|histone-lysine N-methyltransferase activity (GO:0018024)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(15)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	46						GAACTACTGCCTGATCCTGAG	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						181	195	190	NA		NA	NA	11		NA											NA				67925502		2200	4294	6494	SO:0001583	missense			AL512763	CCDS31623.1, CCDS44660.1	11q13.2	2011-07-01			ENSG00000110066	ENSG00000110066	51111		Chromatin-modifying enzymes / K-methyltransferases	24283	protein-coding gene	gene with protein product		610881			NA	10810093, 11401438	Standard	NM_017635	NM_016028	NA	Approved	CGI-85, KMT5B	uc001onm.1	Q4FZB7	OTTHUMG00000150484	ENST00000304363.4:c.2311G>A	chr11.hg19:g.67925502C>T	ENSP00000305899:p.Gly771Ser	NA	B7WNX7|Q3SX56|Q4V775|Q6P150|Q96E44|Q9BUL0|Q9H022|Q9H2K3|Q9NXV3|Q9Y393	hg19	CCDS31623.1	0.02	23.399891	TGCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904161	0.33628	.	.	ENSG00000110066	ENST00000304363	T	0.46819	0.86	5.32	4.41	0.53225	.	0.211965	0.49916	N	0.000138	T	0.33962	0.0881	L	0.27053	0.805	0.80722	D	1	B	0.24576	0.106	B	0.20767	0.031	T	0.13098	-1.0522	10	0.46703	T	0.11	-10.7877	11.0389	0.47818	0.0:0.8502:0.0:0.1498	.	771	Q4FZB7	SV421_HUMAN	S	771	ENSP00000305899:G771S	ENSP00000305899:G771S	G	-	1	0	SUV420H1	67682078	0.983000	0.35010	0.169000	0.22859	0.966000	0.64601	4.002000	0.57053	1.252000	0.44001	0.313000	0.20887	GGC	NOVEL	SUV420H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318319.1	4	19.55807	KEEP	0	0	0	65	2313	CC	1	1	0		-	197	60	7345	0	0	683.146497	302	60	11225	637	ENST00000304363.4	0.39479	1
KRTAP5-7	440050	__UNKNOWN__	__UNKNOWN__	11	71238705	71238705	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs536797652		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:71238705G>A	ENST00000398536.4	+	1	393	c.359G>A	c.(358-360)tGc>tAc	p.C120Y		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	120	7 X 4 AA repeats of C-C-X-P.	NA				keratin filament (GO:0045095)		p.C120Y(2)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						tgtaagccctgctgctgccag	0.607	NA	NA											g|||	1	0.000199681	8e-04	0	5008	,	,	NA	20154	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)					NA						129	139	136	NA		NA	NA	11		NA											NA				71238705		2200	4294	6494	SO:0001583	missense			AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411	440050		Keratin associated proteins	23602	protein-coding gene	gene with protein product		NA			NA	15144888	Standard		NM_001012503	NA	Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.359G>A	chr11.hg19:g.71238705G>A	ENSP00000417330:p.Cys120Tyr	NA	B2RNM3|Q701N5	hg19	CCDS41682.1	0.02	5.933029	CCTxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	N	4.462	0.085611	0.08583	.	.	ENSG00000244411	ENST00000398536	T	0.01304	5.03	1.87	1.87	0.25490	.	.	.	.	.	T	0.01421	0.0046	L	0.60455	1.87	0.26143	N	0.980242	B	0.12630	0.006	B	0.08055	0.003	T	0.51733	-0.8668	9	0.02654	T	1	.	4.3831	0.11304	0.201:0.0:0.799:0.0	.	120	Q6L8G8	KRA57_HUMAN	Y	120	ENSP00000417330:C120Y	ENSP00000417330:C120Y	C	+	2	0	KRTAP5-7	70916353	0.718000	0.27976	0.999000	0.59377	0.075000	0.17131	2.143000	0.42187	1.367000	0.46095	0.289000	0.19496	TGC	NOVEL	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000127953.1	1	7.927969	KEEP	0	3	84	56	1988	GG	1	1	0		+	6	39	211	0	0	12.488464	178	60	6627	309	ENST00000398536.4	0.032609	1
KRTAP5-10	387273	__UNKNOWN__	__UNKNOWN__	11	71279877	71279877	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:71279877G>A	ENST00000376536.4	+	3	441							Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	NA		NA				keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						tgctgttcccggtccagctgc	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572	387273		Keratin associated proteins	23605	protein-coding gene	gene with protein product		NA			NA	15144888	Standard		NM_001012710	NA	Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000376536.4:c.442-32G>A	chr11.hg19:g.71279877G>A		NA	B9EHA4	hg19		0.02	4.863077	CCCxGTC	COVERED																																																																																			NOVEL	KRTAP5-10-201	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding		0	7.759009	KEEP	0	1	32	37	1235	GG	1	0.999981	0		+	6	70	224	2	0	15.304576	98	60	3295	173	ENST00000376536.4	0.057692	0.999981
RAB6A	5870	__UNKNOWN__	__UNKNOWN__	11	73441744	73441744	__UNKNOWN__	Intron	SNP	A	A	T	rs541100474		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:73441744A>T	ENST00000310653.6	-	2	631				RAB6A_ENST00000536566.1_Intron|RAB6A_ENST00000336083.3_Intron|RAB6A_ENST00000541588.1_Intron	NM_001077637.1|NM_002869.4	NP_001071105.1|NP_002860.2	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						ataattttttaaaaatatCTT	0.269	NA	NA											A|||	1	0.000199681	0	0	5008	,	,	NA	16373	0.001	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						30	26	27	NA		NA	NA	11		NA											NA				73441744		692	1583	2275	SO:0001627	intron_variant			AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582	5870		RAB, member RAS oncogene	9786	protein-coding gene	gene with protein product		179513		RAB6	NA		Standard		NM_001243718	NA	Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000310653.6:c.129+65T>A	chr11.hg19:g.73441744A>T		NA	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	hg19	CCDS8223.1	0.02	-0.324602	TTTxAAA	COVERED																																																																																			NOVEL	RAB6A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259240.3	2	5.715367	KEEP	0	0	0	19	552	AA	0.99986	0.835599	0		-	7	60	255	0	0	21.046352	30	60	1068	63	ENST00000310653.6	0.189189	0.835716
SESN3	143686	__UNKNOWN__	__UNKNOWN__	11	94906296	94906296	__UNKNOWN__	3'UTR	SNP	C	C	A	rs375839799		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:94906296C>A	ENST00000536441.1	-	0	1938				RP11-712B9.2_ENST00000534891.1_RNA|RP11-712B9.2_ENST00000534864.1_RNA	NM_001271594.1|NM_144665.2	NP_001258523.1|NP_653266.2	P58005	SESN3_HUMAN	sestrin 3	NA		NA			glucose homeostasis (GO:0042593)|regulation of protein kinase B signaling (GO:0051896)|regulation of response to reactive oxygen species (GO:1901031)|response to insulin (GO:0032868)	nucleus (GO:0005634)				endometrium(5)|large_intestine(6)|lung(3)|skin(1)|stomach(1)	16		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)		BRCA - Breast invasive adenocarcinoma(274;0.234)		AAAAAAAAAACAAACGGCTAA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096300	CCDS8303.1, CCDS60938.1	11q21	2005-09-18			ENSG00000149212	ENSG00000149212	143686			23060	protein-coding gene	gene with protein product		607768			NA	12607115	Standard	NM_144665	NM_144665	NA	Approved	SEST3, MGC29667	uc001pfj.4	P58005	OTTHUMG00000167829	ENST00000536441.1:c.*123G>T	chr11.hg19:g.94906296C>A		NA	B7Z7P9|Q96AD1	hg19	CCDS8303.1	0.02	2.377777	AAAxAAA	COVERED																																																																																			NOVEL	SESN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396475.3	1	2.773564	KEEP	0	1	20	17	494	CC	0.999859	0.999859	0		-	11	60	197	2	0	9.049093	128	60	3771	204	ENST00000536441.1	0.079137	1
TMPRSS5	80975	__UNKNOWN__	__UNKNOWN__	11	113569982	113569982	__UNKNOWN__	Intron	SNP	T	T	C	rs11214709		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:113569982T>C	ENST00000536856.1	-	2	85				TMPRSS5_ENST00000545579.1_Intron|TMPRSS5_ENST00000299882.5_Intron|TMPRSS5_ENST00000538955.1_Intron|TMPRSS5_ENST00000540540.1_Intron|TMPRSS5_ENST00000544634.1_Intron|TMPRSS5_ENST00000544476.1_Intron			Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	NA		NA			proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	peptidase activity (GO:0008233)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		tctctctctctctctctctct	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028140	CCDS44735.1, CCDS73390.1, CCDS73391.1, CCDS73392.1, CCDS73393.1	11q	2010-04-13	2008-07-31		ENSG00000166682	ENSG00000166682	80975		Serine peptidases / Transmembrane	14908	protein-coding gene	gene with protein product	spinesin	606751			NA		Standard	NM_030770	NM_030770	NA	Approved	MGC141886, MGC148044	uc001poc.4	Q9H3S3	OTTHUMG00000168186	ENST00000536856.1:c.572-233A>G	chr11.hg19:g.113569982T>C		NA		hg19		0.02	-0.102922	CTCxCTC	UNCOVERED																																																																																			NOVEL	TMPRSS5-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000398650.1	13	2.406143	KEEP	10	0	0	8	236	TT	0	0	0		-	4	60	142	1	0	13.808322	4	60	79	26	ENST00000536856.1	0.5	0.139832
ZNF259	0	__UNKNOWN__	__UNKNOWN__	11	116650617	116650617	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:116650617C>G	ENST00000227322.3	-	13	1239					NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		NA		NA			apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		GAGGCTATgtcgggggagggg	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						41	35	37	NA		NA	NA	11		NA											NA				116650617		692	1591	2283	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000227322.3:c.1180-64G>C	chr11.hg19:g.116650617C>G		NA	Q2TAA0	hg19	CCDS8375.1	0.02	-0.400513	TGTxGGG	COVERED																																																																																			NOVEL	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000106283.2	2	3.305795	KEEP	0	0	0	11	347	CC	0.993072	0.928018	0		-	8	60	129	0	0	7.653379	38	60	1230	106	ENST00000227322.3	0.173913	0.934492
ZNF259	0	__UNKNOWN__	__UNKNOWN__	11	116650623	116650623	__UNKNOWN__	Intron	SNP	A	A	G	rs182845671		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:116650623A>G	ENST00000227322.3	-	13	1239					NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		NA		NA			apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		ATgtcgggggaggggggaggg	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000227322.3:c.1180-70T>C	chr11.hg19:g.116650623A>G		NA	Q2TAA0	hg19	CCDS8375.1	0.02	1.319105	GGGxGGG	COVERED																																																																																			NOVEL	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000106283.2	2	3.052146	KEEP	0	2	10	14	362	AA	0.997832	0.996826	0		-	16	60	221	0	0	14.032199	49	60	1311	119	ENST00000227322.3	0.246154	0.998993
ARHGEF12	23365	__UNKNOWN__	__UNKNOWN__	11	120359500	120359500	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr11:120359500A>G	ENST00000397843.2	+	0	8515				ARHGEF12_ENST00000532993.1_3'UTR|ARHGEF12_ENST00000356641.3_3'UTR	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	NA		NA			apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		AATATCTGGAACTATCTTTAA	0.249	NA	NA	T	MLL	AML									NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA			Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914	23365		Rho guanine nucleotide exchange factors	14193	protein-coding gene	gene with protein product		604763			NA	10681437, 9205841	Standard	NM_015313	NM_001198665	NA	Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.*3714A>G	chr11.hg19:g.120359500A>G		NA	O15086|Q6P526	hg19	CCDS41727.1	0.02	4.98275	GGAxCTA	COVERED																																																																																			NOVEL	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388052.1	3	3.610413	KEEP	0	0	0	12	363	AA	0.993634	0.993633	0		+	30	60	1114	1	0	94.574038	106	60	3770	162	ENST00000397843.2	0.220588	1
IQSEC3	440073	__UNKNOWN__	__UNKNOWN__	12	176120	176120	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs2650190		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:176120C>G	ENST00000538872.1	+	1	190	c.72C>G	c.(70-72)aaC>aaG	p.N24K	IQSEC3_ENST00000326261.4_Missense_Mutation_p.N24K			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	24		NA			actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		TCGTGCAGAACCAGCAGAGCC	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						4	5	5	NA		NA	NA	12		NA											NA				176120		1422	3317	4739	SO:0001583	missense			AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645	440073			29193	protein-coding gene	gene with protein product		612118			NA	10470851	Standard	XM_495902	NM_001170738	NA	Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.72C>G	chr12.hg19:g.176120C>G	ENSP00000437554:p.Asn24Lys	NA	A6NIF2|A6NKV9|Q8TB43	hg19	CCDS53728.1	0.02	1.962945	GAAxCAG	COVERED	101	0.04624542124542125	33	0.06707317073170732	19	0.052486187845303865	18	0.03146853146853147	31	0.040897097625329816	c	16.55	3.154730	0.57259	.	.	ENSG00000120645	ENST00000538872;ENST00000326261	T;T	0.36699	1.24;1.24	3.68	2.77	0.32553	.	204.329000	0.01193	U	0.007372	T	0.06280	0.0162	L	0.53249	1.67	0.44275	D	0.99713	.	.	.	.	.	.	T	0.02437	-1.1159	8	0.72032	D	0.01	.	10.0887	0.42434	0.2025:0.7975:0.0:0.0	rs2650190	.	.	.	K	24	ENSP00000437554:N24K;ENSP00000315662:N24K	ENSP00000315662:N24K	N	+	3	2	IQSEC3	46381	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	4.047000	0.57383	0.732000	0.32470	0.456000	0.33151	AAC	NOVEL	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397382.3	0	24.967407	KEEP	2	0	0	83	2846	CC	1	0.999907	0		+	4	27	154	0	0	10.145297	89	60	3295	254	ENST00000538872.1	0.043011	0.999907
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2786435	2786435	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:2786435G>T	ENST00000347598.4	+	42	5100				CACNA1C_ENST00000399606.1_Intron|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399621.1_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000327702.7_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399595.1_Intron|CACNA1C_ENST00000399597.1_Intron|CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000335762.5_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	NA		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTGGTCATTGCCTCTGACCT	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						15	17	16	NA		NA	NA	12		NA											NA				2786435		1946	4135	6081	SO:0001627	intron_variant			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5100+48G>T	chr12.hg19:g.2786435G>T		NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	1.584905	ATTxCCT	COVERED																																																																																			NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	3	5.498023	KEEP	0	2	40	33	840	GG	0.999999	0.997162	0		+	8	60	147	0	0	8.243843	63	60	1345	118	ENST00000347598.4	0.112676	0.997163
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2794921	2794921	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs200231105	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:2794921G>A	ENST00000347598.4	+	46	5737	c.5737G>A	c.(5737-5739)Gaa>Aaa	p.E1913K	CACNA1C_ENST00000399606.1_Missense_Mutation_p.E1885K|CACNA1C_ENST00000399644.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399638.1_Missense_Mutation_p.E1893K|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399634.1_Missense_Mutation_p.E1936K|CACNA1C_ENST00000399621.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399649.1_Missense_Mutation_p.E1871K|CACNA1C_ENST00000399601.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399591.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000402845.3_Missense_Mutation_p.E1884K|CACNA1C_ENST00000327702.7_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399637.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000406454.3_Missense_Mutation_p.E1936K|CACNA1C_ENST00000344100.3_Missense_Mutation_p.E1906K|CACNA1C_ENST00000399655.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399603.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399641.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399595.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000399597.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399617.1_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399629.1_Missense_Mutation_p.E1882K|CACNA1C_ENST00000335762.5_Missense_Mutation_p.E1890K	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1948		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E1913K(2)|p.E1906K(2)|p.E1978K(2)|p.E1900K(2)|p.E1400K(2)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CCAGGATGACGAAAATCGGCA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				10	Substitution - Missense(10)	kidney(5)|endometrium(5)					NA						47	48	48	NA		NA	NA	12		NA											NA				2794921		2013	4164	6177	SO:0001583	missense			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5737G>A	chr12.hg19:g.2794921G>A	ENSP00000266376:p.Glu1913Lys	NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	2.141805	GACxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988512	0.53934	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39	4.26	3.35	0.38373	.	1.675690	0.03914	N	0.282339	T	0.64427	0.2597	L	0.39633	1.23	0.24214	N	0.99546	P;D;P;B;D;P;P;D;B;B;D;P;P;B;P;B;P;B;D;P;P;D;D;P;P	0.76494	0.801;0.999;0.941;0.097;0.999;0.921;0.953;0.961;0.11;0.33;0.978;0.941;0.757;0.432;0.902;0.306;0.757;0.062;0.978;0.588;0.769;0.961;0.961;0.882;0.941	B;P;B;B;D;B;B;P;B;B;P;B;B;B;B;B;B;B;P;B;B;P;P;B;B	0.78314	0.21;0.858;0.304;0.03;0.991;0.308;0.378;0.485;0.04;0.071;0.485;0.304;0.122;0.099;0.114;0.033;0.122;0.024;0.485;0.172;0.172;0.485;0.485;0.172;0.304	T	0.56056	-0.8042	10	0.07030	T	0.85	.	14.0749	0.64885	0.0:0.1521:0.8479:0.0	.	556;1906;1862;1948;1900;1884;1865;1882;1893;1865;1885;1865;1896;1913;1865;1900;1936;1873;1871;1873;1854;1884;1884;1865;1865	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	K	1890;1865;1865;1893;1865;1884;1884;1873;1865;1913;1885;1865;1906;1882;1900;1871;1884;1865;1936;1900;1936;1873;1766	ENSP00000336982:E1890K;ENSP00000382563:E1865K;ENSP00000382552:E1865K;ENSP00000382547:E1893K;ENSP00000382506:E1865K;ENSP00000382530:E1884K;ENSP00000382546:E1884K;ENSP00000382500:E1873K;ENSP00000382549:E1865K;ENSP00000266376:E1913K;ENSP00000382515:E1885K;ENSP00000382510:E1865K;ENSP00000341092:E1906K;ENSP00000382537:E1882K;ENSP00000329877:E1900K;ENSP00000382557:E1871K;ENSP00000385724:E1884K;ENSP00000382512:E1865K;ENSP00000382542:E1936K;ENSP00000382526:E1900K;ENSP00000385896:E1936K;ENSP00000382504:E1873K	ENSP00000323129:E1766K	E	+	1	0	CACNA1C	2665182	1.000000	0.71417	0.943000	0.38184	0.802000	0.45316	5.486000	0.66856	0.981000	0.38548	0.449000	0.29647	GAA	NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	1	4.380606	KEEP	1	2	55	34	1137	GG	0.999999	0.999621	0		+	5	57	191	0	0	13.255639	79	60	2836	158	ENST00000347598.4	0.059524	0.999622
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2794937	2794937	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201777030		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:2794937C>T	ENST00000347598.4	+	46	5753	c.5753C>T	c.(5752-5754)aCg>aTg	p.T1918M	CACNA1C_ENST00000399606.1_Missense_Mutation_p.T1890M|CACNA1C_ENST00000399644.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399638.1_Missense_Mutation_p.T1898M|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399634.1_Missense_Mutation_p.T1941M|CACNA1C_ENST00000399621.1_Missense_Mutation_p.T1889M|CACNA1C_ENST00000399649.1_Missense_Mutation_p.T1876M|CACNA1C_ENST00000399601.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399591.1_Missense_Mutation_p.T1878M|CACNA1C_ENST00000402845.3_Missense_Mutation_p.T1889M|CACNA1C_ENST00000327702.7_Missense_Mutation_p.T1905M|CACNA1C_ENST00000399637.1_Missense_Mutation_p.T1889M|CACNA1C_ENST00000406454.3_Missense_Mutation_p.T1941M|CACNA1C_ENST00000344100.3_Missense_Mutation_p.T1911M|CACNA1C_ENST00000399655.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399603.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399641.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399595.1_Missense_Mutation_p.T1878M|CACNA1C_ENST00000399597.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399617.1_Missense_Mutation_p.T1905M|CACNA1C_ENST00000399629.1_Missense_Mutation_p.T1887M|CACNA1C_ENST00000335762.5_Missense_Mutation_p.T1895M	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1953		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.T1911M(1)|p.T1983M(1)|p.T1405M(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGGCAACTGACGCTCCCAGAG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				3	Substitution - Missense(3)	skin(3)					NA						49	49	49	NA		NA	NA	12		NA											NA				2794937		2012	4159	6171	SO:0001583	missense			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5753C>T	chr12.hg19:g.2794937C>T	ENSP00000266376:p.Thr1918Met	NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	2.081347	TGAxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.33	2.802724	0.50315	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55	4.26	4.26	0.50523	.	29.029300	0.00550	N	0.000258	T	0.70133	0.3189	L	0.56769	1.78	0.34775	D	0.734153	P;P;D;P;P;D;D;P;P;D;P;D;P;P;D;P;P;B;P;P;D;P;P;D;D	0.65815	0.863;0.922;0.995;0.664;0.934;0.988;0.992;0.869;0.638;0.966;0.922;0.989;0.927;0.783;0.992;0.677;0.927;0.317;0.922;0.485;0.985;0.869;0.869;0.981;0.995	B;P;P;B;P;P;P;P;B;P;P;P;P;P;P;B;P;B;P;B;P;P;P;P;P	0.56916	0.238;0.595;0.809;0.146;0.756;0.647;0.795;0.595;0.282;0.553;0.595;0.736;0.521;0.595;0.65;0.391;0.521;0.299;0.595;0.229;0.542;0.595;0.595;0.46;0.809	T	0.60281	-0.7294	10	0.38643	T	0.18	.	16.9179	0.86156	0.0:1.0:0.0:0.0	.	561;1911;1867;1953;1905;1889;1870;1887;1898;1870;1890;1870;1901;1918;1870;1905;1941;1878;1876;1878;1859;1889;1889;1870;1870	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	M	1895;1870;1870;1898;1870;1889;1889;1878;1870;1918;1890;1870;1911;1887;1905;1876;1889;1870;1941;1905;1941;1878;1771	ENSP00000336982:T1895M;ENSP00000382563:T1870M;ENSP00000382552:T1870M;ENSP00000382547:T1898M;ENSP00000382506:T1870M;ENSP00000382530:T1889M;ENSP00000382546:T1889M;ENSP00000382500:T1878M;ENSP00000382549:T1870M;ENSP00000266376:T1918M;ENSP00000382515:T1890M;ENSP00000382510:T1870M;ENSP00000341092:T1911M;ENSP00000382537:T1887M;ENSP00000329877:T1905M;ENSP00000382557:T1876M;ENSP00000385724:T1889M;ENSP00000382512:T1870M;ENSP00000382542:T1941M;ENSP00000382526:T1905M;ENSP00000385896:T1941M;ENSP00000382504:T1878M	ENSP00000323129:T1771M	T	+	2	0	CACNA1C	2665198	1.000000	0.71417	0.106000	0.21319	0.488000	0.33401	5.733000	0.68571	2.202000	0.70862	0.449000	0.29647	ACG	NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	1	4.28362	KEEP	1	2	62	36	1267	CC	1	0.999881	0		+	5	40	149	0	0	9.21774	86	60	3102	164	ENST00000347598.4	0.054945	0.999881
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2794977	2794977	__UNKNOWN__	Silent	SNP	G	G	A	rs56270948	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:2794977G>A	ENST00000347598.4	+	46	5793	c.5793G>A	c.(5791-5793)ccG>ccA	p.P1931P	CACNA1C_ENST00000399606.1_Silent_p.P1903P|CACNA1C_ENST00000399644.1_Silent_p.P1883P|CACNA1C_ENST00000399638.1_Silent_p.P1911P|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399634.1_Silent_p.P1954P|CACNA1C_ENST00000399621.1_Silent_p.P1902P|CACNA1C_ENST00000399649.1_Silent_p.P1889P|CACNA1C_ENST00000399601.1_Silent_p.P1883P|CACNA1C_ENST00000399591.1_Silent_p.P1891P|CACNA1C_ENST00000402845.3_Silent_p.P1902P|CACNA1C_ENST00000327702.7_Silent_p.P1918P|CACNA1C_ENST00000399637.1_Silent_p.P1902P|CACNA1C_ENST00000406454.3_Silent_p.P1954P|CACNA1C_ENST00000344100.3_Silent_p.P1924P|CACNA1C_ENST00000399655.1_Silent_p.P1883P|CACNA1C_ENST00000399603.1_Silent_p.P1883P|CACNA1C_ENST00000399641.1_Silent_p.P1883P|CACNA1C_ENST00000399595.1_Silent_p.P1891P|CACNA1C_ENST00000399597.1_Silent_p.P1883P|CACNA1C_ENST00000399617.1_Silent_p.P1918P|CACNA1C_ENST00000399629.1_Silent_p.P1900P|CACNA1C_ENST00000335762.5_Silent_p.P1908P	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1966		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GGCAATCTCCGAAGAGGGGTT	0.567	NA	NA											a|||	180	0.0359425	0.0575	0.0317	5008	,	,	NA	20996	0.0446	NA	0.0249	False	NA	,,,	NA	NA	NA	2504	0.0123	NA	NA	NA						NA		NA				0							NA						48	49	49	NA		NA	NA	12		NA											NA				2794977		1989	4164	6153	SO:0001819	synonymous_variant			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5793G>A	chr12.hg19:g.2794977G>A		NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	1.88065	TCCxAAG	COVERED																																																																																			NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	0	11.13595	KEEP	0	0	0	37	1270	GG	1	0.999881	0		+	6	40	229	0	0	16.16127	85	60	3127	169	ENST00000347598.4	0.065934	0.999881
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2795043	2795043	__UNKNOWN__	Intron	SNP	C	C	T	rs373603282		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:2795043C>T	ENST00000347598.4	+	46	5824				CACNA1C_ENST00000399606.1_Intron|CACNA1C_ENST00000399644.1_Intron|CACNA1C_ENST00000399638.1_Intron|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399621.1_Intron|CACNA1C_ENST00000399649.1_Intron|CACNA1C_ENST00000399601.1_Intron|CACNA1C_ENST00000399591.1_Intron|CACNA1C_ENST00000402845.3_Intron|CACNA1C_ENST00000327702.7_Intron|CACNA1C_ENST00000399637.1_Intron|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000344100.3_Intron|CACNA1C_ENST00000399655.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399595.1_Intron|CACNA1C_ENST00000399597.1_Intron|CACNA1C_ENST00000399617.1_Intron|CACNA1C_ENST00000399629.1_Intron|CACNA1C_ENST00000335762.5_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	NA		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATGTGGTCGGCGGTTACTCCC	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						22	22	22	NA		NA	NA	12		NA											NA				2795043		1933	4149	6082	SO:0001627	intron_variant			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5824+35C>T	chr12.hg19:g.2795043C>T		NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44788.1	0.02	2.287871	CGGxGGT	COVERED																																																																																			NOVEL	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317035.1	0	6.018882	KEEP	0	0	0	20	688	CC	0.999863	0.981821	0		+	4	40	153	0	0	10.920845	53	60	1755	89	ENST00000347598.4	0.070175	0.981955
CACNA1C	775	__UNKNOWN__	__UNKNOWN__	12	2801890	2801890	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:2801890G>A	ENST00000399655.1	+	0	8207					NM_000719.6|NM_001129829.1|NM_001129834.1	NP_000710.5|NP_001123301.1|NP_001123306.1	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	NA		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AATATATTCCGTGTAATGTTT	0.269	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067	775		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1	NA	1650913, 16382099	Standard	NM_000719	NM_001129832	NA	Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000399655.1:c.*1525G>A	chr12.hg19:g.2801890G>A		NA	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	hg19	CCDS44794.1	0.02	2.171479	TCCxTGT	COVERED																																																																																			NOVEL	CACNA1C-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317019.2	2	6.621681	KEEP	0	0	0	22	786	GG	0.999879	0.999773	0		+	33	60	1247	0	0	114.177146	60	60	2154	131	ENST00000399655.1	0.354839	0.999895
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	5279381	5279381	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:5279381C>T			NA	NA				KCNA5 (123432 upstream) : RP11-319E16.1 (63781 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.5279381C>T		NA		hg19		0.02	-0.070188	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			3	2.708737	KEEP	1	0	0	9	314	CC	0.99257	0.053735	0			7	60	268	0	0	28.830429	1	60	41	23		0.875	0.054137
CLSTN3	9746	__UNKNOWN__	__UNKNOWN__	12	7295339	7295339	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:7295339A>C	ENST00000266546.6	+	11	1990				CLSTN3_ENST00000537408.1_Intron	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	NA		NA			homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						tttGGTTTCCACATttctcct	0.428	NA	NA									OREG0021650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182	9746		Cadherins / Cadherin-related	18371	protein-coding gene	gene with protein product	cadherin-related family member 14	611324			NA	12498782	Standard	NM_014718	NM_014718	NA	Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1541-126A>C	chr12.hg19:g.7295339A>C		640	D3DUT6|O94831|Q2T9J5|Q5UE57	hg19	CCDS8575.1	0.02	1.360677	TCCxCAT	COVERED																																																																																			NOVEL	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398560.2	2	2.536621	KEEP	0	2	26	18	433	AA	0.999863	0.998064	0		+	13	60	172	2	0	9.53381	54	60	1587	118	ENST00000266546.6	0.19403	0.9982
CLSTN3	9746	__UNKNOWN__	__UNKNOWN__	12	7295356	7295356	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:7295356C>T	ENST00000266546.6	+	11	1990				CLSTN3_ENST00000537408.1_Intron	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	NA		NA			homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						tcctttttttctttctcaact	0.448	NA	NA									OREG0021650	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182	9746		Cadherins / Cadherin-related	18371	protein-coding gene	gene with protein product	cadherin-related family member 14	611324			NA	12498782	Standard	NM_014718	NM_014718	NA	Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.1541-109C>T	chr12.hg19:g.7295356C>T		640	D3DUT6|O94831|Q2T9J5|Q5UE57	hg19	CCDS8575.1	0.02	3.354235	TTTxTTT	COVERED																																																																																			NOVEL	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398560.2	6	5.831371	KEEP	0	1	30	30	967	CC	0.999997	0.999995	0		+	13	60	326	0	0	21.372648	101	60	3595	173	ENST00000266546.6	0.114035	0.999998
FOXJ2	55810	__UNKNOWN__	__UNKNOWN__	12	8207199	8207199	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:8207199A>G	ENST00000162391.3	+	0	4623					NM_018416.2	NP_060886.1	Q9P0K8	FOXJ2_HUMAN	forkhead box J2	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			autonomic_ganglia(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	16				Kidney(36;0.0944)		TTAACTAAAGAGCACTTTATT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF155132	CCDS8587.1	12p13.31	2006-12-15				ENSG00000065970	55810		Forkhead boxes	24818	protein-coding gene	gene with protein product		NA			NA	10777590, 10966786	Standard	NM_018416	NM_018416	NA	Approved	FHX	uc001qtu.3	Q9P0K8		ENST00000162391.3:c.*1753A>G	chr12.hg19:g.8207199A>G		NA	A0AVK4|B2RMP3|Q96PS9|Q9NSN5	hg19	CCDS8587.1	0.02	2.341543	AAGxGCA	COVERED																																																																																			NOVEL	FOXJ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400088.1	0	3.309867	KEEP	0	0	0	11	341	AA	0.993072	0.992697	0		+	58	60	2109	0	0	215.494033	27	60	991	105	ENST00000162391.3	0.682353	0.999622
CLEC4E	26253	__UNKNOWN__	__UNKNOWN__	12	8691590	8691590	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:8691590T>G	ENST00000446457.2	-	3	375				CLEC4E_ENST00000545274.1_Intron|CLEC4E_ENST00000299663.3_Intron			Q9ULY5	CLC4E_HUMAN	C-type lectin domain family 4, member E	NA		NA			immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Lung SC(5;0.184)					CTTCCAGATTTACTGTTCAGA	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB024718	CCDS8594.1	12p13.31	2005-02-09		2005-02-09	ENSG00000166523	ENSG00000166523	26253		C-type lectin domain containing	14555	protein-coding gene	gene with protein product		609962	C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 9	CLECSF9	NA	10528209	Standard	NM_014358	NM_014358	NA	Approved	mincle	uc001quo.1	Q9ULY5	OTTHUMG00000168675	ENST00000446457.2:c.276+147A>C	chr12.hg19:g.8691590T>G		NA	B2R6Q6	hg19		0.02	5.0165	ATTxACT	COVERED																																																																																			NOVEL	CLEC4E-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000400567.1	0	3.609712	KEEP	0	0	0	12	343	TT	0.993634	0.993633	0		-	9	60	345	0	0	24.529235	123	60	4360	160	ENST00000446457.2	0.068182	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9446495	9446495	__UNKNOWN__	IGR	SNP	G	G	A	rs2429878		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:9446495G>A			NA	NA				SNORA75 (7077 upstream) : RP13-735L24.1 (73564 downstream)						NA		NA									NA						GGACCTGGTGGACCGACTGAA	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9446495G>A		NA		hg19		0.02	-0.324604	GTGxACC	COVERED																																																																																			NOVEL					0			1	15.948837	KEEP	10	0	0	53	1809	GG	1	0.835716	0			3	27	109	0	0	7.810549	34	50	1295	137		0.081081	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9573223	9573223	__UNKNOWN__	IGR	SNP	C	C	A	rs4763936	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:9573223C>A			NA	NA				RP13-735L24.1 (23010 upstream) : SNORA75 (24430 downstream)						NA		NA									NA						AGAAACCACACCGCACAGGTT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						125	129	128	NA		NA	NA	12		NA											NA				9573223		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9573223C>A		NA		hg19		0.02	2.129587	ACAxCGC	COVERED																																																																																			NOVEL					0			3	8.295729	KEEP	0	1	29	38	1296	CC	1	0.998465	0			10	49	359	0	0	27.945181	64	60	2457	147		0.135135	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9586651	9586651	__UNKNOWN__	IGR	SNP	T	T	C	rs71248976		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:9586651T>C			NA	NA				RP13-735L24.1 (36438 upstream) : SNORA75 (11002 downstream)						NA		NA									NA						GCCCAGCCCATAGCCCCCAGC	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						387	335	351	NA		NA	NA	12		NA											NA				9586651		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9586651T>C		NA		hg19		0.02	6.389891	CCAxAGC	COVERED																																																																																			NOVEL					0			1	20.754382	KEEP	9	0	0	69	2039	TT	1	1	0			9	33	326	2	0	21.658851	159	60	5795	330		0.053571	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9586746	9586746	__UNKNOWN__	IGR	SNP	T	T	A	rs201559465		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:9586746T>A			NA	NA				RP13-735L24.1 (36533 upstream) : SNORA75 (10907 downstream)						NA		NA									NA						TCTGTGTGTGTGAGAGAGAAC	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9586746T>A		NA		hg19		0.02	4.757231	GTGxGAG	COVERED																																																																																			NOVEL					0			2	7.153783	KEEP	14	1	32	35	1066	TT	0.999998	0.999995	0			11	47	428	0	0	32.253324	105	50	3811	197		0.094828	0.999997
TAS2R46	259292	__UNKNOWN__	__UNKNOWN__	12	11214535	11214535	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs74198939	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:11214535T>C	ENST00000533467.1	-	1	358	c.359A>G	c.(358-360)cAc>cGc	p.H120R	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	120		NA			detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		CCTCTTTAAGTGAAGAAAAAT	0.368	NA	NA											.|||	5	0.000998403	0	0	5008	,	,	NA	20555	0.005	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						88	93	91	NA		NA	NA	12		NA											NA				11214535		2027	4203	6230	SO:0001583	missense			AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761	259292		Taste receptors / Type 2, GPCR / Unclassified : Taste receptors	18877	protein-coding gene	gene with protein product		612774			NA	12379855	Standard	NM_176887	NM_176887	NA	Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.359A>G	chr12.hg19:g.11214535T>C	ENSP00000436450:p.His120Arg	NA	P59548|Q645X6	hg19	CCDS53748.1	0.02	3.868849	AAGxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	t	1.867	-0.461270	0.04508	.	.	ENSG00000226761	ENST00000533467	T	0.00730	5.77	2.54	-1.43	0.08884	.	.	.	.	.	T	0.00906	0.0030	L	0.48642	1.525	0.09310	N	1	B	0.06786	0.001	B	0.17722	0.019	T	0.40001	-0.9586	9	0.31617	T	0.26	.	8.2925	0.31965	0.0:0.5775:0.0:0.4225	.	120	P59540	T2R46_HUMAN	R	120	ENSP00000436450:H120R	ENSP00000436450:H120R	H	-	2	0	TAS2R46	11105802	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-1.211000	0.02997	-0.536000	0.06298	-3.032000	0.00072	CAC	NOVEL	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383559.1	2	8.42314	KEEP	1	0	0	28	843	TT	0.999997	0.999997	0		-	6	40	200	0	0	12.031182	139	60	4953	194	ENST00000533467.1	0.041379	1
TAS2R46	259292	__UNKNOWN__	__UNKNOWN__	12	11214601	11214601	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:11214601A>G	ENST00000533467.1	-	1	292	c.293T>C	c.(292-294)cTt>cCt	p.L98P	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	98		NA			detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		GCTAGTAGCAAGCCAGTTGCT	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761	259292		Taste receptors / Type 2, GPCR / Unclassified : Taste receptors	18877	protein-coding gene	gene with protein product		612774			NA	12379855	Standard	NM_176887	NM_176887	NA	Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.293T>C	chr12.hg19:g.11214601A>G	ENSP00000436450:p.Leu98Pro	NA	P59548|Q645X6	hg19	CCDS53748.1	0.02	3.687235	GCAxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	8.952	0.968336	0.18659	.	.	ENSG00000226761	ENST00000533467	T	0.01240	5.12	2.54	1.27	0.21489	.	.	.	.	.	T	0.06508	0.0167	H	0.95611	3.695	0.54753	D	0.999982	B	0.34399	0.452	P	0.44477	0.451	T	0.00324	-1.1817	9	0.72032	D	0.01	.	6.7411	0.23437	0.7592:0.2408:0.0:0.0	.	98	P59540	T2R46_HUMAN	P	98	ENSP00000436450:L98P	ENSP00000436450:L98P	L	-	2	0	TAS2R46	11105868	0.211000	0.23529	0.973000	0.42090	0.213000	0.24496	1.762000	0.38451	0.195000	0.20347	0.163000	0.16589	CTT	NOVEL	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383559.1	1	7.823596	KEEP	1	0	0	26	842	AA	0.999957	0.999957	0		-	6	40	207	0	0	12.701549	140	60	5205	217	ENST00000533467.1	0.041096	1
GRIN2B	2904	__UNKNOWN__	__UNKNOWN__	12	13719980	13719980	__UNKNOWN__	Silent	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:13719980G>T	ENST00000609686.1	-	12	2786	c.2577C>A	c.(2575-2577)ggC>ggA	p.G859G		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	859		NA			behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AGAAGACCATGCCAGGCTTGC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						98	82	88	NA		NA	NA	12		NA											NA				13719980		2203	4300	6503	SO:0001819	synonymous_variant				CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079		2904		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4586	protein-coding gene	gene with protein product		138252		NMDAR2B	NA	1350383	Standard		NM_000834	NA	Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2577C>A	chr12.hg19:g.13719980G>T		NA	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	hg19	CCDS8662.1	0.02	4.825385	CATxCCA	COVERED																																																																																			NOVEL	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268014.2	1	8.427821	KEEP	0	0	0	28	1026	GG	0.999997	0.999997	0		-	36	60	1334	0	0	117.125093	95	60	3652	199	ENST00000609686.1	0.274809	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	18891016	18891016	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:18891016C>T			NA	NA				PLCZ1 (25 upstream) : CAPZA3 (28 downstream)						NA		NA									NA						TTCCACACTTCACAAGGAAAG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.18891016C>T		NA		hg19		0.02	4.771425	CTTxACA	COVERED																																																																																			NOVEL					0			1	5.116391	KEEP	0	0	0	17	584	CC	0.999366	0.999344	0			9	60	319	0	0	22.939856	94	60	3507	131		0.087379	0.999978
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	18891017	18891017	__UNKNOWN__	IGR	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:18891017A>C			NA	NA				PLCZ1 (26 upstream) : CAPZA3 (27 downstream)						NA		NA									NA						TCCACACTTCACAAGGAAAGC	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.18891017A>C		NA		hg19		0.02	4.971473	TTCxCAA	COVERED																																																																																			NOVEL					0			1	5.416018	KEEP	0	0	0	18	557	AA	0.999859	0.999837	0			9	60	314	0	0	22.514141	94	60	3454	132		0.087379	0.999978
PLEKHA5	54477	__UNKNOWN__	__UNKNOWN__	12	19441055	19441055	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:19441055T>G	ENST00000429027.2	+	13	1895				PLEKHA5_ENST00000309364.4_Intron|PLEKHA5_ENST00000424268.1_Intron|PLEKHA5_ENST00000317589.4_Intron|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000510738.2_Intron|PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000543806.1_Intron|PLEKHA5_ENST00000299275.6_Intron|PLEKHA5_ENST00000538714.1_Intron	NM_001256470.1	NP_001243399.1	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	NA		NA			reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					ATGAACTAGGTGGGTTTCTTT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(196;329 2193 11246 14234 19524)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126	54477		Pleckstrin homology (PH) domain containing	30036	protein-coding gene	gene with protein product		607770			NA	11214970, 11001876	Standard	NM_019012	NM_001143821	NA	Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000429027.2:c.1863+565T>G	chr12.hg19:g.19441055T>G		NA	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	hg19	CCDS58213.1	0.02	1.134411	AGGxGGG	COVERED																																																																																			NOVEL	PLEKHA5-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397012.1	2	4.238708	KEEP	0	1	5	16	456	TT	0.999366	0.992297	0		+	7	60	141	0	0	8.001003	56	70	1799	98	ENST00000429027.2	0.111111	0.992926
PDE3A	5139	__UNKNOWN__	__UNKNOWN__	12	20705617	20705617	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:20705617G>A	ENST00000359062.3	+	2	1000					NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	NA		NA			blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	AGCCTCATCAGAGAGGACAAG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	5139	3.1.4.17	Phosphodiesterases	8778	protein-coding gene	gene with protein product		123805			NA	1315035, 10679291	Standard		NM_000921	NA	Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.961-3977G>A	chr12.hg19:g.20705617G>A		NA	O60865|Q13348|Q17RD1	hg19	CCDS31754.1	0.02	10.92083	TCAxAGA	COVERED																																																																																			NOVEL	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401756.2	5	62.678897	KEEP	54	8	259	299	10619	GG	1	1	0		+	15	45	557	0	0	37.295986	272	60	10592	851	ENST00000359062.3	0.052265	1
KRAS	3845	__UNKNOWN__	__UNKNOWN__	12	25362854	25362854	__UNKNOWN__	Intron	SNP	C	C	T	rs12313763	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:25362854C>T	ENST00000256078.4	-	6	638				KRAS_ENST00000557334.1_Intron|KRAS_ENST00000311936.3_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)		UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CCCTGAAATACATAAAAAGTA	0.284	NA	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			C|||	419	0.0836661	0.2897	0.0447	5008	,	,	NA	17844	0	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	0							NA	C	,	1093,3305	362.1+/-316.0	129,835,1235	44	46	45	NA	,	-1	0.2	12	dbSNP_120	45	42,8534	26.3+/-74.7	0,42,4246	no	intron,intron	KRAS	NM_004985.3,NM_033360.2	,	129,877,5481	TT,TC,CC	NA	0.4897,24.8522,8.7483	,	,	25362854	1135,11839	2199	4288	6487	SO:0001627	intron_variant	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703	3845			6407	protein-coding gene	gene with protein product		190070	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog, v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	KRAS2	NA		Standard	NM_033360	NM_004985	NA	Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.568-9G>A	chr12.hg19:g.25362854C>T		NA	A8K8Z5|B0LPF9|P01118|Q96D10	hg19	CCDS8703.1	0.02	13.110522	ATAxATA	COVERED																																																																																			NOVEL	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412232.1	70	11.738267	KEEP	0	0	0	39	1403	CC	1	1	0		-	51	60	1744	0	0	136.160437	292	60	10805	490	ENST00000256078.4	0.148688	1
RP11-443N24.2	0	__UNKNOWN__	__UNKNOWN__	12	25957147	25957147	__UNKNOWN__	lincRNA	SNP	C	C	T	rs76082602	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:25957147C>T	ENST00000536949.1	-	0	91										NA		NA									NA						GAACGAAATACGGACGTTCAA	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000536949.1:	chr12.hg19:g.25957147C>T		NA		hg19		0.02	4.844956	ATAxGGA	COVERED																																																																																			NOVEL	RP11-443N24.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000402337.1	12	3.310731	KEEP	0	0	0	11	386	CC	0.993072	0.993059	0		-	14	60	530	0	0	44.092452	60	60	2204	149	ENST00000536949.1	0.189189	0.999987
RP11-443N24.2	0	__UNKNOWN__	__UNKNOWN__	12	25957532	25957532	__UNKNOWN__	lincRNA	SNP	C	C	T	rs111520978	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:25957532C>T	ENST00000536949.1	-	0	91										NA		NA									NA						AGAACCTCAGCTTGCTAACTG	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000536949.1:	chr12.hg19:g.25957532C>T		NA		hg19		0.02	10.675297	CAGxTTG	COVERED																																																																																			NOVEL	RP11-443N24.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000402337.1	2	16.855326	KEEP	2	0	0	56	2027	CC	1	1	0		-	9	40	330	0	0	20.008548	272	60	10274	388	ENST00000536949.1	0.032028	1
STK38L	23012	__UNKNOWN__	__UNKNOWN__	12	27432385	27432385	__UNKNOWN__	Intron	SNP	T	T	C	rs4963688	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:27432385T>C	ENST00000389032.3	+	2	158				STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like	NA		NA								breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					Aggctgggcttggtggctcac	0.488	NA	NA											t|||	3755	0.7498	0.7088	0.7392	5008	,	,	NA	13887	0.7113	NA	0.8241	False	NA	,,,	NA	NA	NA	2504	0.7761	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455	23012			17848	protein-coding gene	gene with protein product	nuclear Dbf2-related 2	615836			NA	16488889	Standard	NM_015000	NM_015000	NA	Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.-11-18258T>C	chr12.hg19:g.27432385T>C		NA		hg19	CCDS31761.1	0.02	-0.026321	GCTxGGT	UNCOVERED																																																																																			NOVEL	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403297.1	0	2.406753	KEEP	0	0	0	8	238	TT	0.99257	0	0		+	3	60	118	0	0	13.231186	0	0	0	11	ENST00000389032.3	1	0
DDX11	1663	__UNKNOWN__	__UNKNOWN__	12	31241852	31241852	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:31241852C>T	ENST00000542838.1	+	7	935				DDX11_ENST00000350437.4_Intron|DDX11_ENST00000545668.1_Intron|DDX11_ENST00000407793.2_Intron|DDX11_ENST00000251758.5_Intron|DDX11_ENST00000228264.6_Intron			Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TGTCCTGCCTCGGCTTTGTGC	0.552	NA	NA								Multiple Myeloma(12;0.14)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573	1663		DEAD-boxes	2736	protein-coding gene	gene with protein product	CHL1-like helicase homolog (S. cerevisiae)	601150	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase), DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11		NA		Standard	NM_030653	NM_030653	NA	Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000542838.1:c.685-126C>T	chr12.hg19:g.31241852C>T		NA	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	hg19	CCDS41767.1	0.02	4.566749	CCTxGGC	COVERED																																																																																			NOVEL	DDX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399721.1	1	3.310054	KEEP	4	0	0	11	356	CC	0.993072	0.993069	0		+	11	25	394	0	0	28.901002	104	48	3700	132	ENST00000542838.1	0.095652	0.999997
DDX11	1663	__UNKNOWN__	__UNKNOWN__	12	31241956	31241956	__UNKNOWN__	Intron	SNP	C	C	T	rs77175335		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:31241956C>T	ENST00000542838.1	+	7	935				DDX11_ENST00000350437.4_Intron|DDX11_ENST00000545668.1_Intron|DDX11_ENST00000407793.2_Intron|DDX11_ENST00000251758.5_Intron|DDX11_ENST00000228264.6_Intron			Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CTCTTTGAAGCGCCTTTCTTT	0.512	NA	NA								Multiple Myeloma(12;0.14)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						67	63	64	NA		NA	NA	12		NA											NA				31241956		2203	4300	6503	SO:0001627	intron_variant			U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573	1663		DEAD-boxes	2736	protein-coding gene	gene with protein product	CHL1-like helicase homolog (S. cerevisiae)	601150	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase), DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11		NA		Standard	NM_030653	NM_030653	NA	Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000542838.1:c.685-22C>T	chr12.hg19:g.31241956C>T		NA	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	hg19	CCDS41767.1	0.02	11.936058	AAGxGCC	COVERED																																																																																			NOVEL	DDX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399721.1	6	7.441555	KEEP	21	7	196	94	3209	CC	1	1	0		+	12	45	387	0	0	21.71428	341	60	12292	579	ENST00000542838.1	0.033994	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	38008639	38008639	__UNKNOWN__	IGR	SNP	G	G	T	rs200540541		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:38008639G>T			NA	NA				None (None upstream) : RNA5SP358 (546628 downstream)						NA		NA									NA						gttgcctatggtggaaaaaga	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.38008639G>T		NA		hg19		0.02	2.238229	ATGxTGG	COVERED																																																																																			NOVEL					0			33	3.009914	KEEP	12	0	0	10	358	GG	0.992708	0.990921	0			4	60	153	0	0	16.121769	1	9	35	131		0.8	0.9982
NR4A1	3164	__UNKNOWN__	__UNKNOWN__	12	52449770	52449770	__UNKNOWN__	Intron	SNP	A	A	C	rs201978713		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:52449770A>C	ENST00000243050.1	+	4	1190				NR4A1_ENST00000550082.1_Intron|NR4A1_ENST00000394825.1_Intron|NR4A1_ENST00000360284.3_Intron|NR4A1_ENST00000545748.1_Intron|NR4A1_ENST00000394824.2_Intron	NM_002135.4	NP_002126.2	P22736	NR4A1_HUMAN	nuclear receptor subfamily 4, group A, member 1	NA		NA			cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell chemotaxis (GO:0035767)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)	16				BRCA - Breast invasive adenocarcinoma(357;0.0967)		CCCCCTCCCCACCCCACACTC	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L13740	CCDS8818.1, CCDS55828.1, CCDS73471.1	12q13	2013-01-16			ENSG00000123358	ENSG00000123358	3164		Nuclear hormone receptors	7980	protein-coding gene	gene with protein product		139139		HMR, GFRP1	NA	2626032	Standard		NM_002135	NA	Approved	TR3, N10, NAK-1, NGFIB, NUR77	uc001rzt.3	P22736	OTTHUMG00000150393	ENST00000243050.1:c.877-44A>C	chr12.hg19:g.52449770A>C		NA	B4DML7|Q15627|Q53Y00|Q6IBU8	hg19	CCDS8818.1	0.02	-0.372666	CCCxCCC	COVERED																																																																																			NOVEL	NR4A1-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317922.2	0	4.436968	KEEP	0	2	39	29	739	AA	0.999997	0.909066	0		+	7	60	118	0	0	7.067489	35	60	940	83	ENST00000243050.1	0.166667	0.909069
KRT84	3890	__UNKNOWN__	__UNKNOWN__	12	52773597	52773597	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:52773597C>T	ENST00000257951.3	-	8	1523					NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	NA		NA			hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CAGTGTGAGCCTGAGTTTAAA	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						94	81	85	NA		NA	NA	12		NA											NA				52773597		692	1591	2283	SO:0001627	intron_variant			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849	3890		-, Intermediate filaments type II, keratins (basic)	6461	protein-coding gene	gene with protein product	hard keratin type II 4	602766	keratin, hair, basic, 4	KRTHB4	NA	2431943, 16831889	Standard	NM_033045	NM_033045	NA	Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1456+62G>A	chr12.hg19:g.52773597C>T		NA	B2RA43|Q6ISB0|Q701L6	hg19	CCDS8825.1	0.02	4.854056	AGCxTGA	COVERED																																																																																			NOVEL	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405187.1	2	8.725783	KEEP	0	0	0	29	1044	CC	0.999997	0.999981	0		-	31	60	1138	0	0	100.926297	74	60	2717	178	ENST00000257951.3	0.295238	0.999984
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	53242796	53242796	__UNKNOWN__	IGR	SNP	C	C	G	rs371854851		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:53242796C>G			NA	NA				KRT78 (18 upstream) : KRT8 (48180 downstream)						NA		NA									NA						GGCCCCAGCACGAGACTTTTA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.53242796C>G		NA		hg19		0.02	1.884718	GCAxGAG	COVERED																																																																																			NOVEL					0			0	5.109884	KEEP	0	0	0	17	533	CC	0.999366	0.995602	0			4	60	141	0	0	9.383474	65	60	2207	105		0.057971	0.996233
CSAD	51380	__UNKNOWN__	__UNKNOWN__	12	53573510	53573510	__UNKNOWN__	Intron	SNP	C	C	T	rs77274322		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:53573510C>T	ENST00000444623.1	-	2	178				CSAD_ENST00000267085.4_Intron|CSAD_ENST00000379843.3_Intron|CSAD_ENST00000453446.2_Intron|CSAD_ENST00000379846.1_Intron|CSAD_ENST00000542115.1_Intron	NM_001244705.1	NP_001231634.1	Q9Y600	CSAD_HUMAN	cysteine sulfinic acid decarboxylase	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|taurine biosynthetic process (GO:0042412)		pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(4)	14					L-Cysteine(DB00151)	TTTTTTTTTTCTTTTGGTATC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(109;252 1546 16882 28524 44645)					NA		NA				0							NA						71	55	60	NA		NA	NA	12		NA											NA				53573510		692	1591	2283	SO:0001627	intron_variant			AB044561	CCDS8848.2, CCDS58235.1	12q13.11-q14.3	2008-08-04			ENSG00000139631	ENSG00000139631	51380			18966	protein-coding gene	gene with protein product	P-selectin cytoplasmic tail-associated protein	NA			NA	15489334	Standard	NM_015989	NM_015989	NA	Approved	PCAP, CSD	uc001sbz.3	Q9Y600	OTTHUMG00000048076	ENST00000444623.1:c.90-584G>A	chr12.hg19:g.53573510C>T		NA	A8K0U4|Q4QQH9|Q9UNJ5|Q9Y601	hg19	CCDS58235.1	0.02	4.233004	TTTxTTT	COVERED																																																																																			NOVEL	CSAD-017	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343697.1	1	8.558449	KEEP	0	2	43	44	1352	CC	1	1	0		-	29	70	479	0	0	25.249723	208	60	6421	300	ENST00000444623.1	0.122363	1
NCKAP1L	3071	__UNKNOWN__	__UNKNOWN__	12	54913208	54913208	__UNKNOWN__	Intron	SNP	G	G	T	rs375680240|rs201644490		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:54913208G>T	ENST00000293373.6	+	16	1704				NCKAP1L_ENST00000545638.2_Intron	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	NA		NA			actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						AAAGAATTTTGTTTAATTTTT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338	3071			4862	protein-coding gene	gene with protein product		141180	hematopoietic protein 1	HEM1	NA	1932118	Standard	NM_005337	NM_005337	NA	Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.1625+92G>T	chr12.hg19:g.54913208G>T		NA	B4DUT5|Q52LW0	hg19	CCDS31813.1	0.02	-0.334926	TTTxTTT	COVERED																																																																																			NOVEL	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406195.1	0	2.219434	KEEP	0	0	0	8	125	GG	0.99257	0.859313	0		+	9	70	150	2	0	10.441087	28	60	817	50	ENST00000293373.6	0.243243	0.865745
WIBG	84305	__UNKNOWN__	__UNKNOWN__	12	56320843	56320843	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:56320843G>C	ENST00000398213.4	-	1	37				WIBG_ENST00000302533.6_Intron|WIBG_ENST00000408946.2_Intron|WIBG_ENST00000557259.1_Intron|WIBG_ENST00000547925.1_Intron|WIBG_ENST00000454792.2_Intron	NM_001143853.1	NP_001137325.1	Q9BRP8	WIBG_HUMAN	within bgcn homolog (Drosophila)	NA		NA			nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|exon-exon junction complex (GO:0035145)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						AAGCGGCTCCGCGCCTCCCGC	0.701	NA	NA									OREG0021911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014976	CCDS41795.1, CCDS44916.1	12q13.2	2008-02-05				ENSG00000170473	84305			30258	protein-coding gene	gene with protein product		NA			NA	12438415, 12483225	Standard	NM_032345	NM_032345	NA	Approved	PYM	uc001sif.1	Q9BRP8	OTTHUMG00000170220	ENST00000398213.4:c.34+16C>G	chr12.hg19:g.56320843G>C		1014	B6ZDM5|Q8IXJ8|Q8N8E7	hg19	CCDS44916.1	0.02	-0.347727	TCCxCGC	COVERED																																																																																			NOVEL	WIBG-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408080.1	1	2.223363	KEEP	0	7	106	46	1268	GG	1	0.877708	0		-	5	60	107	0	0	6.767041	33	60	968	124	ENST00000398213.4	0.131579	0.877708
STAT6	6778	__UNKNOWN__	__UNKNOWN__	12	57496730	57496730	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:57496730C>T	ENST00000537215.2	-	11	1327				STAT6_ENST00000300134.3_Intron|STAT6_ENST00000538913.2_Intron|STAT6_ENST00000543873.2_Intron|STAT6_ENST00000556155.1_Intron|STAT6_ENST00000454075.3_Intron	NM_001178080.1	NP_001171551.1	P42226	STAT6_HUMAN	signal transducer and activator of transcription 6, interleukin-4 induced	NA		NA			cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|mammary gland epithelial cell proliferation (GO:0033598)|mammary gland morphogenesis (GO:0060443)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|T-helper 1 cell lineage commitment (GO:0002296)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein phosphatase binding (GO:0019903)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(2)|lung(8)|ovary(4)|skin(1)	28						ACAGGGGtttcttttctttct	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						54	51	52	NA		NA	NA	12		NA											NA				57496730		2203	4300	6503	SO:0001627	intron_variant			BC005823, BQ028928	CCDS8931.1, CCDS53804.1	12q13	2013-02-14				ENSG00000166888	6778		SH2 domain containing	11368	protein-coding gene	gene with protein product		601512			NA	9605853, 8085155	Standard	NM_003153	NM_003153	NA	Approved	D12S1644, IL-4-STAT	uc001sna.3	P42226		ENST00000537215.2:c.883-26G>A	chr12.hg19:g.57496730C>T		NA	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	hg19	CCDS53804.1	0.02	1.060406	TTTxTTT	COVERED																																																																																			NOVEL	STAT6-006	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412254.1	1	7.822055	KEEP	0	0	0	26	875	CC	0.999957	0.999954	0		-	15	60	210	0	0	9.565949	99	60	3515	151	ENST00000537215.2	0.131579	0.999997
DPY19L2	283417	__UNKNOWN__	__UNKNOWN__	12	63964498	63964498	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:63964498T>C	ENST00000324472.4	-	20	2184				DPY19L2_ENST00000413230.2_Intron	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	NA		NA			multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AATTGGGAGTTGCCAAGTGAG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						46	37	40	NA		NA	NA	12		NA											NA				63964498		2203	4300	6503	SO:0001627	intron_variant				CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990	283417			19414	protein-coding gene	gene with protein product	spermatogenesis associated 34	613893			NA	12975309	Standard	NM_173812	XM_006719348	NA	Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2000+39A>G	chr12.hg19:g.63964498T>C		NA	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	hg19	CCDS31851.1	0.02	1.711327	AGTxGCC	COVERED																																																																																			NOVEL	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400689.2	1	5.113801	KEEP	4	0	0	17	497	TT	0.999366	0.999329	0		-	12	45	418	1	0	31.65695	87	60	2990	143	ENST00000324472.4	0.121212	0.999962
DPY19L2	283417	__UNKNOWN__	__UNKNOWN__	12	63964600	63964600	__UNKNOWN__	Silent	SNP	G	G	A	rs577993411	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:63964600G>A	ENST00000324472.4	-	20	2121	c.1938C>T	c.(1936-1938)agC>agT	p.S646S	DPY19L2_ENST00000413230.2_Silent_p.S93S	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	646		NA			multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.S646>?(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		ACAGCTTGATGCTTGCCATTG	0.373	NA	NA											G|||	19	0.00379393	0.0061	0.0072	5008	,	,	NA	17290	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA						NA		NA				1	Complex(1)	skin(1)					NA						99	80	87	NA		NA	NA	12		NA											NA				63964600		2203	4300	6503	SO:0001819	synonymous_variant				CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990	283417			19414	protein-coding gene	gene with protein product	spermatogenesis associated 34	613893			NA	12975309	Standard	NM_173812	XM_006719348	NA	Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.1938C>T	chr12.hg19:g.63964600G>A		NA	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	hg19	CCDS31851.1	0.02	12.386938	GATxCTT	COVERED																																																																																			NOVEL	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400689.2	1	2.782712	KEEP	6	5	153	63	2239	GG	1	1	0		-	30	49	1082	0	0	81.743804	238	60	8938	441	ENST00000324472.4	0.11194	1
TRHDE	29953	__UNKNOWN__	__UNKNOWN__	12	73057797	73057797	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:73057797T>G	ENST00000261180.4	+	0	3993					NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	NA		NA			cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						TATCTCAACATTATTCTTTCT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	29953	3.4.19.6		30748	protein-coding gene	gene with protein product	pyroglutamyl-peptidase II, pyroglutamyl aminopeptidase II, TRH-specific aminopeptidase	606950			NA	10491199, 12975309	Standard	NM_013381	NM_013381	NA	Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.*822T>G	chr12.hg19:g.73057797T>G		NA	A5PL19|Q6UWJ4	hg19	CCDS9004.1	0.02	2.050644	ACAxTAT	COVERED																																																																																			NOVEL	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405380.1	5	4.812978	KEEP	0	0	0	16	483	TT	0.997832	0.997392	0		+	7	60	271	0	0	19.977243	77	60	2835	120	ENST00000261180.4	0.083333	0.999559
KITLG	4254	__UNKNOWN__	__UNKNOWN__	12	88899024	88899024	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:88899024T>G	ENST00000228280.5	-	9	965				KITLG_ENST00000378535.4_Intron|KITLG_ENST00000357116.4_Intron|KITLG_ENST00000347404.5_Intron	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	NA		NA			cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						TGAAAAACAATAAGAAAAAAT	0.348	NA	NA							Testicular Cancer, Familial Clustering of					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						67	66	66	NA		NA	NA	12		NA											NA				88899024		2202	4299	6501	SO:0001627	intron_variant	Familial Cancer Database		M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130	4254			6343	protein-coding gene	gene with protein product	mast cell growth factor, stem cell factor, steel factor, familial progressive hyperpigmentation 2	184745		MGF	NA	2208279, 1707188, 19375057	Standard	NM_003994	NM_003994	NA	Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.783-12A>C	chr12.hg19:g.88899024T>G		NA	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	hg19	CCDS31868.1	0.02	12.813187	CAAxAAG	COVERED																																																																																			NOVEL	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406424.2	2	27.680483	KEEP	0	0	0	92	2797	TT	1	1	0		-	113	60	4290	0	0	396.8114	186	60	6859	489	ENST00000228280.5	0.377926	1
PLXNC1	10154	__UNKNOWN__	__UNKNOWN__	12	94620285	94620285	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:94620285C>T	ENST00000258526.4	+	8	2039					NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTTTTGCCTTCTTTTAAATGC	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040	10154		CD molecules, Plexins	9106	protein-coding gene	gene with protein product		604259			NA		Standard		NR_037687	NA	Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.1791-96C>T	chr12.hg19:g.94620285C>T		NA	Q59H25	hg19	CCDS9049.1	0.02	1.08948	CTTxTTT	COVERED																																																																																			NOVEL	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408126.2	1	2.967552	KEEP	0	0	0	10	284	CC	0.992708	0.989456	0		+	10	60	152	1	0	7.988686	60	60	1780	94	ENST00000258526.4	0.142857	0.996724
DRAM1	55332	__UNKNOWN__	__UNKNOWN__	12	102284749	102284749	__UNKNOWN__	Intron	SNP	G	G	T	rs4764829	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:102284749G>T	ENST00000544152.1	+	2	238				DRAM1_ENST00000258534.8_Intron			Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	NA		NA			apoptotic process (GO:0006915)|autophagy (GO:0006914)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12						ggatggtctcgatctcttgac	0.577	NA	NA											G|||	3630	0.72484	0.8805	0.585	5008	,	,	NA	10688	0.9127	NA	0.5149	False	NA	,,,	NA	NA	NA	2504	0.636	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC018435, DA721965	CCDS41823.1	12q23.2	2014-02-12	2009-06-12		ENSG00000136048	ENSG00000136048	55332			25645	protein-coding gene	gene with protein product	damage-regulated autophagy modulator	610776			NA	16839881	Standard	NM_018370	NM_018370	NA	Approved	FLJ11259, DRAM	uc001tix.3	Q8N682		ENST00000544152.1:c.132-6892G>T	chr12.hg19:g.102284749G>T		NA	B7Z4T0|Q7L3E3|Q9NUN1	hg19		0.02	-0.306795	CTCxATC	COVERED																																																																																			NOVEL	DRAM1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409196.1	12	9.612347	KEEP	44	4	92	65	2050	GG	1	0.800245	0		+	3	60	103	0	0	10.770095	1	60	14	190	ENST00000544152.1	0.75	0.800245
TDG	6996	__UNKNOWN__	__UNKNOWN__	12	104359763	104359763	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:104359763C>T	ENST00000392872.3	+	0	182				TDG_ENST00000544861.1_5'UTR|TDG_ENST00000266775.9_5'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	NA		NA			base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CTACAGAGACCGGCTGCCCGT	0.677	NA	NA						Base excision repair (BER), DNA glycosylases						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						3	7	6	NA		NA	NA	12		NA											NA				104359763		559	1341	1900	SO:0001623	5_prime_UTR_variant			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	6996	3.2.2.29		11700	protein-coding gene	gene with protein product	G/T mismatch-specific thymine DNA glycosylase	601423			NA	8662714, 9299239	Standard		NM_003211	NA	Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.-53C>T	chr12.hg19:g.104359763C>T		NA	Q8IUZ6|Q8IZM3	hg19	CCDS9095.1	0.02	5.144841	GACxGGC	COVERED																																																																																			NOVEL	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399673.2	8	10.852499	KEEP	0	7	210	110	3629	CC	1	0.999987	0		+	11	60	418	0	0	31.708289	95	60	3310	268	ENST00000392872.3	0.103774	0.999987
TDG	6996	__UNKNOWN__	__UNKNOWN__	12	104359779	104359779	__UNKNOWN__	5'UTR	SNP	C	C	T	rs372823872		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:104359779C>T	ENST00000392872.3	+	0	198				TDG_ENST00000544861.1_5'UTR|TDG_ENST00000266775.9_5'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	NA		NA			base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CCCGTGTGCCCGGCAGGTGGA	0.687	NA	NA						Base excision repair (BER), DNA glycosylases						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						5	7	6	NA		NA	NA	12		NA											NA				104359779		2049	4006	6055	SO:0001623	5_prime_UTR_variant			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	6996	3.2.2.29		11700	protein-coding gene	gene with protein product	G/T mismatch-specific thymine DNA glycosylase	601423			NA	8662714, 9299239	Standard		NM_003211	NA	Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.-37C>T	chr12.hg19:g.104359779C>T		NA	Q8IUZ6|Q8IZM3	hg19	CCDS9095.1	0.02	4.510746	GCCxGGC	COVERED																																																																																			NOVEL	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399673.2	2	20.632308	KEEP	0	5	149	121	4011	CC	1	0.999993	0		+	5	60	189	0	0	12.455666	105	60	3632	302	ENST00000392872.3	0.045455	0.999993
HCFC2	29915	__UNKNOWN__	__UNKNOWN__	12	104481785	104481785	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:104481785G>A	ENST00000229330.4	+	9	1357	c.1253G>A	c.(1252-1254)aGa>aAa	p.R418K		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	418	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GACCCTCACAGACAAGGCAGT	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(184;1814 2036 4771 6974 15702)					NA		NA				0							NA						121	110	114	NA		NA	NA	12		NA											NA				104481785		2203	4300	6503	SO:0001583	missense			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727	29915			24972	protein-coding gene	gene with protein product		607926			NA	10196288	Standard	NM_013320	NM_013320	NA	Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1253G>A	chr12.hg19:g.104481785G>A	ENSP00000229330:p.Arg418Lys	NA	B2R8Q5|C0H5X3	hg19	CCDS9097.1	0.02	3.962022	ACAxACA	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.51	2.854630	0.51376	.	.	ENSG00000111727	ENST00000229330	T	0.01629	4.72	5.82	5.82	0.92795	Fibronectin, type III (3);	0.140166	0.48767	D	0.000167	T	0.04452	0.0122	L	0.38531	1.155	0.37424	D	0.913768	P	0.52842	0.956	P	0.62184	0.899	T	0.53373	-0.8448	10	0.06365	T	0.9	-26.0087	15.5852	0.76475	0.0:0.0:1.0:0.0	.	418	Q9Y5Z7	HCFC2_HUMAN	K	418	ENSP00000229330:R418K	ENSP00000229330:R418K	R	+	2	0	HCFC2	103005915	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.053000	0.64269	2.758000	0.94735	0.650000	0.86243	AGA	NOVEL	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407780.1	2	15.350635	KEEP	0	0	0	51	1870	GG	1	1	0		+	9	60	327	1	0	22.884712	118	60	4543	242	ENST00000229330.4	0.070866	1
HCFC2	29915	__UNKNOWN__	__UNKNOWN__	12	104481786	104481786	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:104481786A>T	ENST00000229330.4	+	9	1358	c.1254A>T	c.(1252-1254)agA>agT	p.R418S		NM_013320.2	NP_037452.1	Q9Y5Z7	HCFC2_HUMAN	host cell factor C2	418	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						ACCCTCACAGACAAGGCAGTA	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(184;1814 2036 4771 6974 15702)					NA		NA				0							NA						121	110	114	NA		NA	NA	12		NA											NA				104481786		2203	4300	6503	SO:0001583	missense			AF117210	CCDS9097.1	12q23.3	2011-03-30			ENSG00000111727	ENSG00000111727	29915			24972	protein-coding gene	gene with protein product		607926			NA	10196288	Standard	NM_013320	NM_013320	NA	Approved	HCF-2	uc001tkj.4	Q9Y5Z7	OTTHUMG00000170175	ENST00000229330.4:c.1254A>T	chr12.hg19:g.104481786A>T	ENSP00000229330:p.Arg418Ser	NA	B2R8Q5|C0H5X3	hg19	CCDS9097.1	0.02	4.343628	CAGxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	A	16.97	3.269369	0.59540	.	.	ENSG00000111727	ENST00000229330	T	0.01647	4.71	5.82	4.68	0.58851	Fibronectin, type III (3);	0.140166	0.48767	D	0.000167	T	0.04452	0.0122	L	0.47716	1.5	0.37314	D	0.909233	D	0.57899	0.981	D	0.67231	0.95	T	0.54866	-0.8229	10	0.10111	T	0.7	-26.0087	7.7922	0.29127	0.9091:0.0:0.0909:0.0	.	418	Q9Y5Z7	HCFC2_HUMAN	S	418	ENSP00000229330:R418S	ENSP00000229330:R418S	R	+	3	2	HCFC2	103005916	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.222000	0.42926	2.225000	0.72522	0.528000	0.53228	AGA	NOVEL	HCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407780.1	2	15.34593	KEEP	0	0	0	51	1620	AA	1	1	0		+	9	60	326	1	0	22.723067	120	60	4372	244	ENST00000229330.4	0.069767	1
RP11-144F15.1	0	__UNKNOWN__	__UNKNOWN__	12	107155118	107155118	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:107155118G>A	ENST00000551505.1	-	1	229				RFX4_ENST00000357881.4_Silent_p.A702A|RFX4_ENST00000392842.1_Silent_p.A693A|RFX4_ENST00000229387.5_Silent_p.A599A						NA		NA									NA						TGCATTCTGCGAGGTACGGAA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						112	101	105	NA		NA	NA	12		NA											NA				107155118		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000551505.1:c.209+13349C>T	chr12.hg19:g.107155118G>A		NA		hg19		0.02	11.240806	TGCxAGG	COVERED																																																																																			NOVEL	RP11-144F15.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000407171.1	1	17.185891	KEEP	0	1	25	66	2151	GG	1	1	0		-	10	60	377	0	0	24.053448	251	60	8954	371	ENST00000551505.1	0.038314	1
FOXN4	121643	__UNKNOWN__	__UNKNOWN__	12	109723305	109723305	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:109723305G>A	ENST00000299162.5	-	8	809	c.705C>T	c.(703-705)gaC>gaT	p.D235D	FOXN4_ENST00000355216.1_Silent_p.D55D	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	235		NA			amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(9)|ovary(2)	16						TCTTCCACCCGTCGGGGGCCG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						60	58	59	NA		NA	NA	12		NA											NA				109723305		2203	4300	6503	SO:0001819	synonymous_variant			AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445	121643		Forkhead boxes	21399	protein-coding gene	gene with protein product		609429			NA		Standard	XM_062735	NM_213596	NA	Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.705C>T	chr12.hg19:g.109723305G>A		NA	Q6ZMR4|Q96NZ0	hg19	CCDS9126.2	0.02	6.969201	CCCxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	4.573	0.106351	0.08780	.	.	ENSG00000139445	ENST00000266856	.	.	.	4.71	-3.75	0.04372	.	.	.	.	.	T	0.68769	0.3037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73248	-0.4043	5	0.87932	D	0	-5.8988	12.5965	0.56472	0.7974:0.0:0.2026:0.0	.	.	.	.	W	194	.	ENSP00000266856:R194W	R	-	1	2	FOXN4	108207688	0.041000	0.20044	0.703000	0.30354	0.047000	0.14425	-0.579000	0.05834	-0.624000	0.05611	-1.202000	0.01658	CGG	NOVEL	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328306.1	0	21.066129	KEEP	0	0	0	70	2418	GG	1	1	0		-	61	60	2235	0	0	200.313528	132	60	4852	352	ENST00000299162.5	0.316062	1
KCTD10	83892	__UNKNOWN__	__UNKNOWN__	12	109915194	109915194	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:109915194C>T	ENST00000228495.6	-	0	155					NM_031954.3	NP_114160.1	Q9H3F6	BACD3_HUMAN	potassium channel tetramerization domain containing 10	NA		NA			proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	10						CCCACTTCCGCCCCGCAGAGG	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC040062	CCDS9128.1	12q24.12	2013-06-20	2013-06-20		ENSG00000110906	ENSG00000110906	83892		BTB/POZ domain containing	23236	protein-coding gene	gene with protein product		613421	potassium channel tetramerisation domain containing 10		NA	12477932	Standard	NM_031954	XM_005253946	NA	Approved	MSTP028, BTBD28	uc001toi.1	Q9H3F6	OTTHUMG00000169253	ENST00000228495.6:c.-127G>A	chr12.hg19:g.109915194C>T		NA	Q53HN2|Q59FV1|Q6PL47|Q96SU0	hg19	CCDS9128.1	0.02	4.330196	CCGxCCC	COVERED																																																																																			NOVEL	KCTD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403099.1	1	39.651577	KEEP	0	0	0	132	4357	CC	1	1	0		-	47	60	1663	0	0	149.589356	95	60	3407	305	ENST00000228495.6	0.330986	1
ATXN2	6311	__UNKNOWN__	__UNKNOWN__	12	111912762	111912762	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:111912762A>C	ENST00000542287.2	-	19	2366				ATXN2_ENST00000377617.3_Intron|ATXN2_ENST00000389153.4_Intron|ATXN2_ENST00000550104.1_Intron|ATXN2_ENST00000535949.1_Intron|ATXN2_ENST00000608853.1_Intron			Q99700	ATX2_HUMAN	ataxin 2	NA		NA			cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						tcacacctgtaatcccagcac	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842	6311		Ataxins	10555	protein-coding gene	gene with protein product	trinucleotide repeat containing 13	601517	spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)	SCA2, TNRC13	NA	8358438, 9225980	Standard	NM_002973	NM_002973	NA	Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000542287.2:c.2204-4216T>G	chr12.hg19:g.111912762A>C		NA	A6NLD4|Q6ZQZ7|Q99493	hg19		0.02	-0.070185	TGTxATC	UNCOVERED																																																																																			NOVEL	ATXN2-011	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000404980.1	4	3.008145	KEEP	0	0	0	10	286	AA	0.992708	0.053742	0		-	3	47	108	0	0	9.932822	5	60	181	20	ENST00000542287.2	0.375	0.054137
HCAR2	338442	__UNKNOWN__	__UNKNOWN__	12	123186168	123186168	__UNKNOWN__	3'UTR	SNP	T	T	C	rs584219	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:123186168T>C	ENST00000328880.5	-	0	1722				HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	NA		NA			negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	AACACAGATATTAACCAAAGC	0.463	NA	NA											T|||	6	0.00119808	0.0023	0	5008	,	,	NA	22730	0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782	338442		GPCR / Class A : Hydroxy-carboxylic acid receptors	24827	protein-coding gene	gene with protein product	niacin receptor 1	609163	G protein-coupled receptor 109A	GPR109A	NA	21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551	NM_177551	NA	Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.*571A>G	chr12.hg19:g.123186168T>C		NA	A0PJL5|A7LGG3	hg19	CCDS9235.1	0.02	41.27498	ATAxTAA	COVERED																																																																																			NOVEL	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370202.1	7	47.273841	KEEP	30	1	31	168	5318	TT	1	1	0		-	118	51	4519	0	0	359.840961	727	60	26760	1228	ENST00000328880.5	0.139645	1
HCAR3	8843	__UNKNOWN__	__UNKNOWN__	12	123199640	123199640	__UNKNOWN__	3'UTR	SNP	A	A	G	rs141997200	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:123199640A>G	ENST00000528880.2	-	0	1799				HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	TAACCAAAGCATGTGAGTCTC	0.458	NA	NA											N|||	91	0.0181709	0.0681	0	5008	,	,	NA	21300	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398	8843		GPCR / Class A : Hydroxy-carboxylic acid receptors	16824	protein-coding gene	gene with protein product		606039	G protein-coupled receptor 109B	GPR109B	NA	7505609, 9205127, 18983141, 21454438	Standard	NM_006018	NM_006018	NA	Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.*481T>C	chr12.hg19:g.123199640A>G		NA	A8K4G5|B2R830|E9PI97|Q8NGE4	hg19	CCDS53842.1	0.02	28.544833	AGCxTGT	COVERED																																																																																			NOVEL	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387549.2	10	30.990034	KEEP	27	0	0	103	3170	AA	1	1	0		-	41	47	1448	0	0	97.740255	619	60	23138	960	ENST00000528880.2	0.062121	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123875311	123875311	__UNKNOWN__	Silent	SNP	C	C	T	rs74356260		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:123875311C>T	ENST00000402868.3	+	3	693	c.267C>T	c.(265-267)gcC>gcT	p.A89A	SETD8_ENST00000478781.2_3'UTR|SETD8_ENST00000330479.4_Silent_p.A89A			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	130		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)	p.A89A(4)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AACCATTAGCCGGAATCTACA	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				4	Substitution - coding silent(4)	prostate(3)|central_nervous_system(1)					NA						105	100	101	NA		NA	NA	12		NA											NA				123875311		2203	4300	6503	SO:0001819	synonymous_variant			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.267C>T	chr12.hg19:g.123875311C>T		NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	8.998375	AGCxGGA	COVERED																																																																																			NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	9	14.292561	KEEP	2	2	61	69	2281	CC	1	1	0		+	11	60	418	0	0	27.784771	223	60	7840	380	ENST00000402868.3	0.047009	1
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123892264	123892264	__UNKNOWN__	3'UTR	SNP	T	T	C	rs61955129		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:123892264T>C	ENST00000402868.3	+	0	1499				SETD8_ENST00000330479.4_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	NA		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		GTGGGCCCCGTGCCCTCCCCG	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						13	13	13	NA		NA	NA	12		NA											NA				123892264		2201	4297	6498	SO:0001624	3_prime_UTR_variant			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.*14T>C	chr12.hg19:g.123892264T>C		NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	12.151296	CCGxGCC	COVERED																																																																																			NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	1	3.336291	KEEP	35	7	216	87	2509	TT	1	1	0		+	48	40	1607	0	0	129.341321	215	50	7412	481	ENST00000402868.3	0.18251	1
ATP6V0A2	23545	__UNKNOWN__	__UNKNOWN__	12	124209098	124209098	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:124209098C>A	ENST00000330342.3	+	4	542					NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		aagaaaaaaacaaaacaaAAA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344	23545		ATPases / V-type	18481	protein-coding gene	gene with protein product	infantile malignant osteopetrosis	611716	infantile malignant osteopetrosis, ATPase, H+ transporting, lysosomal V0 subunit a isoform 2, ATPase, H+ transporting, lysosomal V0 subunit A2		NA	2247090, 18157129	Standard	NM_012463	NM_012463	NA	Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.295-103C>A	chr12.hg19:g.124209098C>A		NA	A8K026|Q6NUM0	hg19	CCDS9254.1	0.02	3.572688	AAAxAAA	COVERED																																																																																			NOVEL	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400765.2	13	8.751286	KEEP	0	5	78	58	1923	CC	1	1	0		+	17	60	273	0	0	12.216641	167	70	5020	310	ENST00000330342.3	0.092391	1
TMEM132B	114795	__UNKNOWN__	__UNKNOWN__	12	126144787	126144787	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:126144787C>G	ENST00000299308.3	+	0	8776					NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	NA		NA				integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		aagagcgagactttgtctcaa	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02					114795			29397	protein-coding gene	gene with protein product		NA			NA	11572484	Standard	NM_052907	NM_001286219	NA	Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.*5531C>G	chr12.hg19:g.126144787C>G		NA	A2RRG8|Q8NA73|Q96JN9|Q96PY1	hg19	CCDS41859.1	0.02	-0.333368	AGAxTTT	COVERED																																																																																			NOVEL	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400043.1	2	2.40802	KEEP	0	0	0	8	303	CC	0.99257	0.845654	0		+	14	60	529	0	0	48.719224	24	60	873	52	ENST00000299308.3	0.368421	0.851984
ANKLE2	23141	__UNKNOWN__	__UNKNOWN__	12	133331901	133331901	__UNKNOWN__	Intron	SNP	G	G	A	rs563959431	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr12:133331901G>A	ENST00000357997.5	-	2	271				ANKLE2_ENST00000337516.5_Intron|ANKLE2_ENST00000539605.1_5'UTR	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	NA		NA			mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		aggctgaggcgggcggatcat	0.498	NA	NA											G|||	2	0.000399361	0	0.0029	5008	,	,	NA	13357	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915	23141		Ankyrin repeat domain containing	29101	protein-coding gene	gene with protein product	LEM domain containing 7	NA	KIAA0692	KIAA0692	NA	9734811	Standard		XM_005266159	NA	Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.182-182C>T	chr12.hg19:g.133331901G>A		NA	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	hg19	CCDS41869.1	0.02	2.525784	GGCxGGC	COVERED																																																																																			NOVEL	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397712.1	0	5.112156	KEEP	0	0	0	17	541	GG	0.999366	0.992297	0		-	22	60	825	0	0	75.110734	42	60	1540	83	ENST00000357997.5	0.34375	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	19385544	19385544	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:19385544A>G			NA	NA				LINC00418 (91675 upstream) : RP11-38M15.11 (48422 downstream)						NA		NA									NA						ggggaattggagcatcagaat	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.19385544A>G		NA		hg19		0.02	1.798513	TGGxGCA	COVERED																																																																																			NOVEL					0			5	2.342725	KEEP	22	1	35	20	648	AA	0.999859	0.999694	0			8	23	273	0	0	19.408108	82	50	2904	138		0.088889	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	19385612	19385612	__UNKNOWN__	IGR	SNP	G	G	A	rs199805857		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:19385612G>A			NA	NA				LINC00418 (91743 upstream) : RP11-38M15.11 (48354 downstream)						NA		NA									NA						gaacaaagaagagaataagaa	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.19385612G>A		NA		hg19		0.02	7.567057	GAAxAGA	COVERED																																																																																			NOVEL					0			12	5.791776	KEEP	28	2	71	44	1625	GG	1	1	0			20	45	760	0	0	59.422494	139	46	5405	361		0.125786	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	19385645	19385645	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:19385645T>A			NA	NA				LINC00418 (91776 upstream) : RP11-38M15.11 (48321 downstream)						NA		NA									NA						gcaaccatcatagtaataatt	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.19385645T>A		NA		hg19		0.02	6.660047	TCAxAGT	COVERED																																																																																			NOVEL					0			7	3.508848	KEEP	18	3	80	40	1215	TT	1	1	0			10	34	364	0	0	24.931124	150	50	5497	294		0.0625	1
TPTE2	93492	__UNKNOWN__	__UNKNOWN__	13	20000609	20000609	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs141691551	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:20000609C>T	ENST00000382978.1	-	17	1273	c.1231G>A	c.(1231-1233)Ggt>Agt	p.G411S	TPTE2_ENST00000255310.6_Missense_Mutation_p.G374S|TPTE2_ENST00000382975.4_Missense_Mutation_p.G411S|TPTE2_ENST00000457266.2_Missense_Mutation_p.G340S|TPTE2_ENST00000390680.2_Missense_Mutation_p.G374S|TPTE2_ENST00000382977.4_Missense_Mutation_p.G451S|TPTE2_ENST00000400230.2_Missense_Mutation_p.G451S|TPTE2_ENST00000400103.2_Missense_Mutation_p.G340S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	451	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.	NA			phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.G451S(1)|p.G374R(1)|p.G374S(1)|p.G451R(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AGAGGTGGACCGTCATATACA	0.338	NA	NA											c|||	18	0.00359425	0.0129	0.0014	5008	,	,	NA	17308	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				4	Substitution - Missense(4)	prostate(2)|lung(2)					NA	C	SER/GLY,SER/GLY,SER/GLY	59,4347	53.6+/-89.4	0,59,2144	115	115	115	NA	1018,1120,1351	0.8	0	13	dbSNP_134	115	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	TPTE2	NM_001141968.1,NM_130785.3,NM_199254.2	56,56,56	0,60,6443	TT,TC,CC	NA	0.0116,1.3391,0.4613	benign,benign,benign	340/412,374/446,451/523	20000609	60,12946	2203	4300	6503	SO:0001583	missense			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958	93492		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	17299	protein-coding gene	gene with protein product		606791			NA	11716755, 12717346, 15057823	Standard	NM_199254	NM_130785	NA	Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000382978.1:c.1231G>A	chr13.hg19:g.20000609C>T	ENSP00000372438:p.Gly411Ser	NA	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	hg19		0.02	15.123907	GACxGTC	COVERED	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	c	2.177	-0.388580	0.04932	0.013391	1.16E-4	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548	D;D;D;D;D;D;D;D	0.84873	-1.91;-1.91;-1.91;-1.91;-1.91;-1.91;-1.91;-1.91	2.06	0.84	0.18912	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.174692	0.50627	D	0.000101	T	0.56673	0.2001	N	0.12746	0.255	0.09310	N	1	B;B;B	0.32829	0.124;0.101;0.386	B;B;B	0.29524	0.064;0.024;0.103	T	0.51803	-0.8659	9	.	.	.	-15.6776	4.9604	0.14063	0.6673:0.3327:0.0:0.0	.	340;374;451	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	S	411;340;451;374;374;451;411;340;451	ENSP00000372438:G411S;ENSP00000382974:G340S;ENSP00000383089:G451S;ENSP00000255310:G374S;ENSP00000375098:G374S;ENSP00000372437:G451S;ENSP00000372435:G411S;ENSP00000442218:G340S	.	G	-	1	0	TPTE2	18898609	0.779000	0.28652	0.004000	0.12327	0.004000	0.04260	1.504000	0.35726	0.231000	0.21079	0.194000	0.17425	GGT	NOVEL	TPTE2-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000044022.1	4	7.493302	KEEP	8	2	63	47	1604	CC	1	1	0		-	11	42	389	0	0	22.872922	345	60	12211	540	ENST00000382978.1	0.030899	1
TPTE2	93492	__UNKNOWN__	__UNKNOWN__	13	20077352	20077352	__UNKNOWN__	Intron	SNP	T	T	C	rs201812089	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:20077352T>C	ENST00000382978.1	-	1	54				TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000382977.4_Intron|TPTE2_ENST00000400230.2_Intron|TPTE2_ENST00000400103.2_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GACACATGTATGCATAACTCA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						165	135	145	NA		NA	NA	13		NA											NA				20077352		2203	4300	6503	SO:0001627	intron_variant			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958	93492		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	17299	protein-coding gene	gene with protein product		606791			NA	11716755, 12717346, 15057823	Standard	NM_199254	NM_130785	NA	Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000382978.1:c.11+11A>G	chr13.hg19:g.20077352T>C		NA	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	hg19		0.02	20.872078	GTAxGCA	COVERED																																																																																			NOVEL	TPTE2-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000044022.1	4	16.183465	KEEP	0	1	38	67	2089	TT	1	1	0		-	13	52	477	0	0	27.606303	499	60	18662	730	ENST00000382978.1	0.025391	1
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20277061	20277061	__UNKNOWN__	3'UTR	SNP	G	G	A	rs151279350		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:20277061G>A	ENST00000338910.4	-	0	1985					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AGATTTCACAGTACTATGGAA	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.*254C>T	chr13.hg19:g.20277061G>A		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	13.26003	ACAxTAC	COVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	2	17.757441	KEEP	16	0	0	59	2097	GG	1	1	0		-	14	27	521	0	0	34.156405	289	60	10845	426	ENST00000338910.4	0.046205	1
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20280025	20280025	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:20280025A>T	ENST00000338910.4	-	8	1376					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		AGTAAACATTAACAATTTAAC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.1217-54T>A	chr13.hg19:g.20280025A>T		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	5.809914	ATTxACA	COVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	0	4.638518	KEEP	37	1	30	26	708	AA	0.999931	0.999931	0		-	10	27	364	0	0	23.956603	189	60	6713	265	ENST00000338910.4	0.050251	1
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20280027	20280027	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:20280027C>A	ENST00000338910.4	-	8	1376					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TAAACATTAACAATTTAACAA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.1217-56G>T	chr13.hg19:g.20280027C>A		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	5.710208	TAAxAAT	COVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	1	4.548265	KEEP	36	1	28	25	860	CC	0.999909	0.999909	0		-	10	27	357	0	0	23.25749	189	60	7119	262	ENST00000338910.4	0.050251	1
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20354156	20354156	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:20354156T>C	ENST00000338910.4	-	1	532					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		gtggggggggtcagcccccct	0.836	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.372+2369A>G	chr13.hg19:g.20354156T>C		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	-0.043861	GGGxCAG	UNCOVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	0	2.690452	KEEP	10	0	0	9	213	TT	0	0	0		-	2	20	79	0	0	7.39303	3	40	93	27	ENST00000338910.4	0.4	0.024074
FGF9	2254	__UNKNOWN__	__UNKNOWN__	13	22275880	22275880	__UNKNOWN__	3'UTR	SNP	A	A	G	rs75400485		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:22275880A>G	ENST00000382353.5	+	0	1463				FGF9_ENST00000478546.1_3'UTR	NM_002010.2	NP_002001.1	P31371	FGF9_HUMAN	fibroblast growth factor 9	NA		NA			angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic digestive tract development (GO:0048566)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein import into nucleus (GO:0006606)|regulation of timing of cell differentiation (GO:0048505)|signal transduction (GO:0007165)|substantia nigra development (GO:0021762)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|skin(2)	9		all_cancers(29;1.23e-20)|all_epithelial(30;9.83e-19)|all_lung(29;9.64e-17)|Lung SC(185;0.0262)|Breast(139;0.106)		all cancers(112;3.92e-05)|Epithelial(112;0.000166)|OV - Ovarian serous cystadenocarcinoma(117;0.00314)|Lung(94;0.163)		gtgtgtgtgtatgtgtgtAGC	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(195;1939 2127 12623 13963 52730)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D14838	CCDS9298.1	13q11-q12	2014-01-30	2013-06-18		ENSG00000102678	ENSG00000102678	2254		Endogenous ligands	3687	protein-coding gene	gene with protein product	glia-activating factor	600921	fibroblast growth factor 9 (glia-activating factor)		NA	8321227	Standard		NM_002010	NA	Approved		uc001uog.2	P31371	OTTHUMG00000017412	ENST00000382353.5:c.*306A>G	chr13.hg19:g.22275880A>G		NA	A8K427|Q3SY32	hg19	CCDS9298.1	0.02	2.066171	TGTxTGT	COVERED																																																																																			NOVEL	FGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046002.2	2	2.369556	KEEP	0	0	0	8	178	AA	0.99257	0.992062	0		+	9	60	181	0	0	10.357933	74	70	2329	99	ENST00000382353.5	0.108434	0.999487
RP11-307N16.6	0	__UNKNOWN__	__UNKNOWN__	13	24890339	24890339	__UNKNOWN__	Intron	SNP	A	A	G	rs9511194|rs386769039	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:24890339A>G	ENST00000382141.4	+	14	4058				C1QTNF9_ENST00000332018.4_Intron|C1QTNF9-AS1_ENST00000449656.1_RNA|C1QTNF9_ENST00000382071.2_Intron						NA		NA									NA						CTGCCTTTCAACTTCTCTCTT	0.512	NA	NA											A|||	1180	0.235623	0.2526	0.2522	5008	,	,	NA	19310	0.1875	NA	0.3062	False	NA	,,,	NA	NA	NA	2504	0.1779	NA	NA	NA						NA		NA				0							NA	A		259,4025		75,109,1958	82	70	74	NA		-0.6	0	13	dbSNP_119	74	570,7798		163,244,3777	no	intron	C1QTNF9	NM_178540.3		238,353,5735	GG,GA,AA	NA	6.8117,6.0458,6.5523			24890339	829,11823	2142	4184	6326	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000382141.4:c.3315+32A>G	chr13.hg19:g.24890339A>G		NA		hg19		0.02	2.402984	TCAxCTT	COVERED																																																																																			NOVEL	RP11-307N16.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000472022.1	1	6.615233	KEEP	1	0	0	22	609	AA	0.999879	0.998872	0		+	8	40	291	0	0	22.011261	64	60	2218	110	ENST00000382141.4	0.111111	0.998993
RP11-307N16.6	0	__UNKNOWN__	__UNKNOWN__	13	24890354	24890354	__UNKNOWN__	Intron	SNP	C	C	A	rs28661531	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:24890354C>A	ENST00000382141.4	+	14	4058				C1QTNF9_ENST00000332018.4_Intron|C1QTNF9-AS1_ENST00000449656.1_RNA|C1QTNF9_ENST00000382071.2_Intron						NA		NA									NA						TCTCTTCATTCCTTTCATCTC	0.512	NA	NA											C|||	933	0.186302	0.1437	0.17	5008	,	,	NA	20169	0.2768	NA	0.17	False	NA	,,,	NA	NA	NA	2504	0.1789	NA	NA	NA						NA		NA				0							NA	C		44,4294		1,42,2126	70	60	63	NA		-1.6	0	13	dbSNP_125	63	134,8350		3,128,4111	no	intron	C1QTNF9	NM_178540.3		4,170,6237	AA,AC,CC	NA	1.5794,1.0143,1.3882			24890354	178,12644	2169	4242	6411	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000382141.4:c.3315+47C>A	chr13.hg19:g.24890354C>A		NA		hg19		0.02	2.10004	ATTxCTT	COVERED																																																																																			NOVEL	RP11-307N16.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000472022.1	1	4.513568	KEEP	0	0	0	15	486	CC	0.99649	0.991591	0		+	12	60	424	0	0	34.992083	49	60	1715	89	ENST00000382141.4	0.196721	0.995084
PARP4	143	__UNKNOWN__	__UNKNOWN__	13	25052393	25052393	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs79107024	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:25052393G>T	ENST00000381989.3	-	13	1575	c.1470C>A	c.(1468-1470)caC>caA	p.H490Q		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	490	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.	NA			cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.H490Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTCTCCCGGGTGTGAGTACT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	lung(1)					NA						106	86	92	NA		NA	NA	13		NA											NA				25052393		2203	4300	6503	SO:0001583	missense			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699	143		Poly (ADP-ribose) polymerases	271	protein-coding gene	gene with protein product	von Willebrand factor A domain containing 5C	607519	ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1	ADPRTL1	NA	10644454	Standard	NM_006437	NM_006437	NA	Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1470C>A	chr13.hg19:g.25052393G>T	ENSP00000371419:p.His490Gln	NA	O75903|Q14682|Q5QNZ9|Q9H1M6	hg19	CCDS9307.1	0.02	4.19668	CGGxTGT	COVERED	285	0.1304945054945055	99	0.20121951219512196	44	0.12154696132596685	36	0.06293706293706294	106	0.13984168865435356	G	3.333	-0.136204	0.06711	.	.	ENSG00000102699	ENST00000381989	T	0.13420	2.59	3.91	-0.744	0.11101	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.898333	0.09533	N	0.789209	T	0.00012	0.0000	L	0.60067	1.865	0.24090	N	0.995918	B	0.14805	0.011	B	0.13407	0.009	T	0.44314	-0.9336	10	0.16896	T	0.51	-1.9083	3.6715	0.08276	0.2177:0.0:0.3285:0.4537	.	490	Q9UKK3	PARP4_HUMAN	Q	490	ENSP00000371419:H490Q	ENSP00000371419:H490Q	H	-	3	2	PARP4	23950393	0.588000	0.26799	0.018000	0.16275	0.865000	0.49528	-0.111000	0.10807	-0.008000	0.14320	0.644000	0.83932	CAC	NOVEL	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044189.1	1	4.851171	KEEP	2	1	34	28	989	GG	0.999997	0.999996	0		-	11	60	404	0	0	29.684381	109	60	4058	206	ENST00000381989.3	0.091667	0.999999
PARP4	143	__UNKNOWN__	__UNKNOWN__	13	25052423	25052423	__UNKNOWN__	Intron	SNP	G	G	A	rs200378131	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:25052423G>A	ENST00000381989.3	-	13	1554					NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	NA		NA			cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TACTACATGCGAAAGGAAATA	0.393	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						75	63	67	NA		NA	NA	13		NA											NA				25052423		2203	4300	6503	SO:0001627	intron_variant			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699	143		Poly (ADP-ribose) polymerases	271	protein-coding gene	gene with protein product	von Willebrand factor A domain containing 5C	607519	ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1	ADPRTL1	NA	10644454	Standard	NM_006437	NM_006437	NA	Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1449-9C>T	chr13.hg19:g.25052423G>A		NA	O75903|Q14682|Q5QNZ9|Q9H1M6	hg19	CCDS9307.1	0.02	4.809915	TGCxAAA	COVERED																																																																																			NOVEL	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044189.1	1	3.546318	KEEP	3	1	32	23	787	GG	0.999892	0.999885	0		-	11	57	416	0	0	31.460213	96	60	3480	172	ENST00000381989.3	0.102804	0.999993
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	25600042	25600042	__UNKNOWN__	IGR	SNP	T	T	A	rs3002236	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:25600042T>A			NA	NA				LSP1 (8367 upstream) : PABPC3 (70257 downstream)						NA		NA									NA						AACAATAGCCTCTTCTAAGGA	0.398	NA	NA											N|||	2456	0.490415	0.6293	0.4553	5008	,	,	NA	16444	0.4563	NA	0.3966	False	NA	,,,	NA	NA	NA	2504	0.4591	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.25600042T>A		NA		hg19		0.02	3.9393	GCCxCTT	COVERED																																																																																			NOVEL					0			0	6.016932	KEEP	31	0	0	20	609	TT	0.999863	0.999863	0			11	40	362	0	0	24.688391	130	60	4768	220		0.078014	1
AMER2	219287	__UNKNOWN__	__UNKNOWN__	13	25739600	25739600	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:25739600C>T	ENST00000357816.2	-	0	6276							Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	NA		NA			ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)				NA						TTCCAAACTGCTTCATAAATA	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566	219287		-	26360	protein-coding gene	gene with protein product		614659	family with sequence similarity 123A	FAM123A	NA	20843316	Standard	NM_152704	XM_005266279	NA	Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000357816.2:c.*4142G>A	chr13.hg19:g.25739600C>T		NA	Q5RL80|Q5VX56|Q8N593|Q96NN5	hg19	CCDS9312.1	0.02	3.478759	CTGxTTC	COVERED																																																																																			NOVEL	AMER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044221.2	3	5.417958	KEEP	4	0	0	18	665	CC	0.999859	0.999859	0		-	9	42	307	0	0	20.270356	139	60	5230	200	ENST00000357816.2	0.060811	1
NBEA	26960	__UNKNOWN__	__UNKNOWN__	13	36241629	36241629	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:36241629C>A	ENST00000379939.2	+	55	8672	c.8511C>A	c.(8509-8511)taC>taA	p.Y2837*	NBEA_ENST00000540320.1_Nonsense_Mutation_p.Y2840*|NBEA_ENST00000379922.3_Nonsense_Mutation_p.Y418*|NBEA_ENST00000310336.4_Nonsense_Mutation_p.Y2840*|NBEA_ENST00000537702.1_Nonsense_Mutation_p.Y633*|NBEA_ENST00000400445.3_Nonsense_Mutation_p.Y2840*			Q8NFP9	NBEA_HUMAN	neurobeachin	2840		NA			protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		GTATCATATACTATGAACGAG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						169	166	167	NA		NA	NA	13		NA											NA				36241629		1898	4128	6026	SO:0001587	stop_gained			AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915	26960		A-kinase anchor proteins, WD repeat domain containing	7648	protein-coding gene	gene with protein product		604889			NA	10501977	Standard	NM_015678	NM_015678	NA	Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000379939.2:c.8511C>A	chr13.hg19:g.36241629C>A	ENSP00000369271:p.Tyr2837*	NA	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	hg19		0.02	12.384288	ATAxTAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	41	9.075267	0.99057	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518;ENST00000402346;ENST00000537702;ENST00000379922	.	.	.	5.73	4.87	0.63330	.	0.111998	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.2668	0.49114	0.0:0.8583:0.0:0.1417	.	.	.	.	X	2840;2840;2837;2840;1469;418;633;418	.	ENSP00000308534:Y2840X	Y	+	3	2	NBEA	35139629	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.056000	0.41355	1.390000	0.46547	0.655000	0.94253	TAC	NOVEL	NBEA-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000044460.1	3	15.044158	KEEP	0	0	0	50	1760	CC	1	1	0		+	89	60	3240	0	0	288.658113	202	60	7639	410	ENST00000379939.2	0.305842	1
RB1	5925	__UNKNOWN__	__UNKNOWN__	13	48916895	48916895	__UNKNOWN__	Intron	SNP	C	C	T	rs520342	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:48916895C>T	ENST00000267163.4	+	3	518					NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	NA		NA			androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(5)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"Insulin(DB00071)|Insulin Regular(DB00030)	TAAAAGGAAACGAATTCTGGA	0.328	NA	6	D, Mis, N, F, S		retinoblastoma, sarcoma, breast, small cell lung	retinoblastoma, sarcoma, breast, small cell lung			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			C|||	1005	0.200679	0.1256	0.1801	5008	,	,	NA	16479	0.2371	NA	0.2455	False	NA	,,,	NA	NA	NA	2504	0.2331	NA	NA	NA		yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		L, E, M, O	20	Whole gene deletion(15)|Unknown(5)	bone(10)|breast(6)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)					NA	C		650,3746		60,530,1608	33	35	35	NA		-0.6	0	13	dbSNP_83	35	2096,6492		264,1568,2462	no	intron	RB1	NM_000321.2		324,2098,4070	TT,TC,CC	NA	24.4061,14.7862,21.1491			48916895	2746,10238	2198	4294	6492	SO:0001627	intron_variant	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687	5925		Endogenous ligands	9884	protein-coding gene	gene with protein product	prepro-retinoblastoma-associated protein, protein phosphatase 1, regulatory subunit 130	614041	osteosarcoma	OSRC	NA	1857421, 15057823	Standard		NM_000321	NA	Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.380+45C>T	chr13.hg19:g.48916895C>T		NA	A8K5E3|P78499|Q5VW46|Q8IZL4	hg19	CCDS31973.1	0.02	-0.289475	AAAxGAA	COVERED																																																																																			NOVEL	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044884.1	0	2.708831	KEEP	0	0	0	9	320	CC	0.99254	0.755211	0		+	16	60	589	0	0	56.607632	17	60	576	54	ENST00000267163.4	0.484848	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	79424353	79424353	__UNKNOWN__	IGR	SNP	A	A	G	rs73243103	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:79424353A>G			NA	NA				LINC00331 (57911 upstream) : RBM26 (469735 downstream)						NA		NA									NA						TTAATACATCAAAAGGTCATA	0.343	NA	NA											A|||	90	0.0179712	8e-04	0.0159	5008	,	,	NA	20278	0.0208	NA	0.0437	False	NA	,,,	NA	NA	NA	2504	0.0133	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.79424353A>G		NA		hg19		0.02	2.329797	ATCxAAA	COVERED																																																																																			NOVEL					0			3	3.008908	KEEP	0	0	0	10	308	AA	0.992708	0.991184	0			24	60	834	0	0	74.441734	51	60	1876	112		0.32	0.998465
FARP1	10160	__UNKNOWN__	__UNKNOWN__	13	98863606	98863606	__UNKNOWN__	Intron	SNP	A	A	G	rs4772050	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:98863606A>G	ENST00000319562.6	+	2	242				FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Intron	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	NA		NA			dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			ggaactgcgcatgcgagggat	0.522	NA	NA											A|||	1867	0.372804	0.1089	0.5274	5008	,	,	NA	20365	0.3085	NA	0.5815	False	NA	,,,	NA	NA	NA	2504	0.4714	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767	10160		Rho guanine nucleotide exchange factors, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Pleckstrin homology (PH) domain containing	3591	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 75	602654			NA	9425278	Standard	NM_005766	NM_005766	NA	Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.-23-1868A>G	chr13.hg19:g.98863606A>G		NA	Q5JVI9|Q6IQ29	hg19	CCDS9487.1	0.02	-0.052637	CGCxTGC	UNCOVERED																																																																																			NOVEL	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045541.3	0	2.407355	KEEP	0	0	0	8	251	AA	0.99257	0.036492	0		+	2	60	80	0	0	7.295749	4	60	138	19	ENST00000319562.6	0.333333	0.036766
ERCC5	2073	__UNKNOWN__	__UNKNOWN__	13	103498610	103498610	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:103498610C>T	ENST00000355739.4	+	0	1417				ERCC5_ENST00000535557.1_5'UTR|BIVM-ERCC5_ENST00000602836.1_Intron	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	NA		NA			DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TAGGACGCAGCCGCCTCATGG	0.642	NA	NA	Mis, N, F			skin basal cell, skin squamous cell, melanoma		Nucleotide excision repair (NER)	Xeroderma Pigmentosum					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA		yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))		E	0							NA						25	27	26	NA		NA	NA	13		NA											NA				103498610		2203	4299	6502	SO:0001623	5_prime_UTR_variant	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899	2073			3437	protein-coding gene	gene with protein product	Cockayne syndrome	133530	xeroderma pigmentosum, complementation group G, excision repair cross-complementing rodent repair deficiency, complementation group 5	ERCM2, XPGC	NA	8088806	Standard		NM_000123	NA	Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.-7C>T	chr13.hg19:g.103498610C>T		NA	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	hg19	CCDS32004.1	0.02	6.615444	CAGxCGC	COVERED																																																																																			NOVEL	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045708.1	1	45.399583	KEEP	0	0	0	151	5211	CC	1	1	0		+	98	60	3379	0	0	328.035415	90	60	3301	429	ENST00000355739.4	0.521277	1
ING1	3621	__UNKNOWN__	__UNKNOWN__	13	111371444	111371444	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:111371444T>G	ENST00000333219.7	+	2	1008				ING1_ENST00000464141.1_Intron|ING1_ENST00000375775.3_Intron|ING1_ENST00000338450.7_Intron|ING1_ENST00000375774.3_Intron	NM_001267728.1|NM_198219.2	NP_001254657.1|NP_937862.1	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	NA		NA			cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CTGTGGCTGGTGGGCTTTGTT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487	3621		Zinc fingers, PHD-type	6062	protein-coding gene	gene with protein product	inhibitor of growth 1, tumor suppressor ING1, growth inhibitor ING1, growth inhibitory protein ING1	601566			NA	8944021, 9186514	Standard	NM_005537	NM_198219	NA	Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000333219.7:c.137-132T>G	chr13.hg19:g.111371444T>G		NA	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	hg19	CCDS9516.1	0.02	1.033453	TGGxGGG	COVERED																																																																																			NOVEL	ING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045767.1	2	7.217531	KEEP	0	5	37	38	922	TT	1	0.999768	0		+	9	60	164	0	0	8.466745	78	60	2118	163	ENST00000333219.7	0.103448	0.999768
ATP11A	23250	__UNKNOWN__	__UNKNOWN__	13	113505578	113505578	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:113505578C>T	ENST00000487903.1	+	18	2079				ATP11A_ENST00000283558.8_Intron|ATP11A_ENST00000375645.3_Intron|ATP11A_ENST00000375630.2_Intron			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	NA		NA			phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				AACTGGGATGCAGGCCGACGG	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						43	36	39	NA		NA	NA	13		NA											NA				113505578		2203	4300	6503	SO:0001627	intron_variant			AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	23250	3.6.3.1	ATPases / P-type	13552	protein-coding gene	gene with protein product	potential phospholipid-transporting ATPase IH, phospholipid-translocating ATPase	605868	ATPase, Class VI, type 11A		NA	11015572	Standard	NM_015205	NM_032189	NA	Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.1991+46C>T	chr13.hg19:g.113505578C>T		NA	Q5VXT2	hg19	CCDS32011.1	0.02	4.158371	ATGxAGG	COVERED																																																																																			NOVEL	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045834.3	0	11.551875	KEEP	0	1	18	45	1560	CC	1	0.999997	0		+	6	60	216	0	0	14.211762	110	60	4105	187	ENST00000487903.1	0.051724	0.999997
MCF2L	23263	__UNKNOWN__	__UNKNOWN__	13	113718079	113718079	__UNKNOWN__	Intron	SNP	C	C	T	rs370706500	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr13:113718079C>T	ENST00000535094.2	+	6	648				MCF2L_ENST00000423482.2_Intron|MCF2L_ENST00000397030.1_Intron|MCF2L_ENST00000442652.2_Intron|MCF2L_ENST00000375597.4_Intron|MCF2L_ENST00000375608.3_Intron|MCF2L_ENST00000421756.1_Intron|MCF2L_ENST00000434480.2_Intron|MCF2L_ENST00000375604.2_Intron|MCF2L_ENST00000375601.3_Intron	NM_001112732.2	NP_001106203.2	O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	NA		NA			apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CTCCTTTCTACGGCTGAGTTC	0.517	NA	NA											C|||	7	0.00139776	8e-04	0.0029	5008	,	,	NA	18702	0.001	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217	23263		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	14576	protein-coding gene	gene with protein product		609499			NA	9205841	Standard		NM_001112732	NA	Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000535094.2:c.490-539C>T	chr13.hg19:g.113718079C>T		NA	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	hg19	CCDS45070.2	0.02	4.08489	CTAxGGC	COVERED																																																																																			NOVEL	MCF2L-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045853.4	1	2.407706	KEEP	13	0	0	8	274	CC	0.99257	0.992566	0		+	6	27	209	0	0	13.583067	107	60	3902	160	ENST00000535094.2	0.053097	0.999995
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19110082	19110082	__UNKNOWN__	IGR	SNP	A	A	G	rs370986604		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19110082A>G			NA	NA				None (None upstream) : RP11-754I20.1 (220 downstream)						NA		NA									NA						GAAGAAGGGCAAGGGCGAGCG	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19110082A>G		NA		hg19		0.02	4.153238	GGCxAGG	COVERED																																																																																			NOVEL					0			0	9.374509	KEEP	0	2	68	55	1570	AA	1	1	0			5	40	186	0	0	11.854854	121	60	4282	239		0.039683	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19110105	19110105	__UNKNOWN__	IGR	SNP	A	A	G	rs201277721		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19110105A>G			NA	NA				None (None upstream) : RP11-754I20.1 (197 downstream)						NA		NA									NA						GGGGACTGGGAAAGGGCGAGC	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19110105A>G		NA		hg19		0.02	2.189037	GGGxAAG	COVERED																																																																																			NOVEL					0			0	4.092932	KEEP	0	3	75	40	1099	AA	1	0.999862	0			5	49	187	0	0	12.727333	84	60	2955	166		0.05618	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19400637	19400637	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19400637G>A			NA	NA				OR11H12 (22031 upstream) : RP11-536C10.7 (6157 downstream)						NA		NA									NA						GTCTGGGTTTGAAGCTTTGGG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19400637G>A		NA		hg19		0.02	2.003466	TTTxAAG	COVERED																																																																																			NOVEL					0			0	2.40769	KEEP	11	0	0	8	273	GG	0.99257	0.99157	0			17	47	594	0	0	49.751749	61	48	2262	107		0.217949	0.998993
RP11-536C10.16	0	__UNKNOWN__	__UNKNOWN__	14	19413007	19413007	__UNKNOWN__	lincRNA	SNP	A	A	T	rs58290770		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19413007A>T	ENST00000550928.1	+	0	225										NA		NA									NA						TCCCGGTGTCACTGCCGAGTG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550928.1:	chr14.hg19:g.19413007A>T		NA		hg19		0.02	2.429271	GTCxCTG	COVERED																																																																																			NOVEL	RP11-536C10.16-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000408569.1	2	9.621856	KEEP	74	0	0	32	946	AA	0.997832	0.9963	0		+	5	27	202	0	0	15.038037	57	49	2073	203	ENST00000550928.1	0.080645	0.998465
RP11-536C10.16	0	__UNKNOWN__	__UNKNOWN__	14	19413013	19413013	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19413013G>A	ENST00000550928.1	+	0	225										NA		NA									NA						TGTCACTGCCGAGTGCTCCGG	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550928.1:	chr14.hg19:g.19413013G>A		NA		hg19		0.02	2.238278	GCCxAGT	COVERED																																																																																			NOVEL	RP11-536C10.16-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000408569.1	2	3.646683	KEEP	75	2	50	30	956	GG	0.997832	0.996036	0		+	6	27	232	0	0	17.547726	55	50	1900	204	ENST00000550928.1	0.098361	0.9982
RP11-536C10.16	0	__UNKNOWN__	__UNKNOWN__	14	19413323	19413323	__UNKNOWN__	lincRNA	SNP	C	C	T	rs2073410		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19413323C>T	ENST00000550928.1	+	0	225										NA		NA									NA						CGCCTCCACACTAGAACTTCC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550928.1:	chr14.hg19:g.19413323C>T		NA		hg19		0.02	1.863077	ACAxTAG	COVERED																																																																																			NOVEL	RP11-536C10.16-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000408569.1	3	3.310985	KEEP	29	0	0	11	407	CC	0.992708	0.992616	0		+	17	40	627	0	0	51.515859	77	50	2891	153	ENST00000550928.1	0.180851	0.999907
RP11-536C10.16	0	__UNKNOWN__	__UNKNOWN__	14	19413410	19413410	__UNKNOWN__	lincRNA	SNP	G	G	C	rs2845303		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19413410G>C	ENST00000550928.1	+	0	225										NA		NA									NA						ATCAGGGGTTGTTTTGGAAGC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550928.1:	chr14.hg19:g.19413410G>C		NA		hg19		0.02	1.728294	GTTxTTT	COVERED																																																																																			NOVEL	RP11-536C10.16-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000408569.1	2	4.514325	KEEP	14	0	0	15	526	GG	0.99649	0.996446	0		+	5	40	172	0	0	11.02867	93	50	3441	156	ENST00000550928.1	0.05102	0.999956
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19422299	19422299	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19422299G>A			NA	NA				RP11-536C10.16 (8401 upstream) : MED15P1 (77546 downstream)						NA		NA									NA						TGCATGCGGTGAGGGCAGTGA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19422299G>A		NA		hg19		0.02	-0.394788	GGTxAGG	COVERED																																																																																			NOVEL					0			0	2.241158	KEEP	2	1	27	17	595	GG	0.999366	0.926053	0			3	27	108	0	0	7.445983	42	60	1567	69		0.066667	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19422704	19422704	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19422704G>T			NA	NA				RP11-536C10.16 (8806 upstream) : MED15P1 (77141 downstream)						NA		NA									NA						AACATGGTTTGCAGGGAAGAG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19422704G>T		NA		hg19		0.02	-0.412076	TTTxCAG	COVERED																																																																																			NOVEL					0			1	8.727897	KEEP	4	0	0	29	1001	GG	0.999997	0.941738	0			5	47	159	0	0	11.382922	42	60	1515	96		0.106383	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19422756	19422756	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19422756C>G			NA	NA				RP11-536C10.16 (8858 upstream) : MED15P1 (77089 downstream)						NA		NA									NA						CCGGCTCTCCCGAGCTGCCCC	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19422756C>G		NA		hg19		0.02	-0.324577	TCCxGAG	COVERED																																																																																			NOVEL					0			0	2.877966	KEEP	3	2	61	31	1054	CC	0.999998	0.835714	0			6	47	221	0	0	17.841361	31	60	1153	100		0.162162	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19433927	19433927	__UNKNOWN__	IGR	SNP	A	A	T	rs28556795	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19433927A>T			NA	NA				RP11-536C10.16 (20029 upstream) : MED15P1 (65918 downstream)						NA		NA									NA						ACCCAAGCAAAATCTATTGCT	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19433927A>T		NA		hg19		0.02	2.033122	CAAxATC	COVERED																																																																																			NOVEL					0			3	3.30914	KEEP	0	0	0	11	329	AA	0.993072	0.992752	0			25	60	919	0	0	81.315728	61	60	2158	104		0.290698	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19444744	19444744	__UNKNOWN__	IGR	SNP	T	T	C	rs28658467		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19444744T>C			NA	NA				RP11-536C10.16 (30846 upstream) : MED15P1 (55101 downstream)						NA		NA									NA						GCACAACCCATGTGGGGTACA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19444744T>C		NA		hg19		0.02	7.440957	CCAxGTG	COVERED																																																																																			NOVEL					0			1	4.513601	KEEP	0	0	0	15	475	TT	0.99649	0.99649	0			7	40	278	0	0	18.63752	154	60	5661	230		0.043478	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19474764	19474764	__UNKNOWN__	IGR	SNP	G	G	T	rs74961150		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19474764G>T			NA	NA				RP11-536C10.16 (60866 upstream) : MED15P1 (25081 downstream)						NA		NA									NA						TTAAAACTATGCAGTGAGTGC	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19474764G>T		NA		hg19		0.02	2.113401	TATxCAG	UNCOVERED																																																																																			NOVEL					0			2	2.40798	KEEP	8	0	0	8	293	GG	0	0	0			5	31	144	0	0	9.305853	64	60	2490	105		0.072464	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19499526	19499526	__UNKNOWN__	IGR	SNP	C	C	T	rs111459074		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19499526C>T			NA	NA				RP11-536C10.16 (85628 upstream) : MED15P1 (319 downstream)						NA		NA									NA						TGGCCTGCCCCGCCTCACAGC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19499526C>T		NA		hg19		0.02	-0.342114	CCCxGCC	COVERED																																																																																			NOVEL					0			4	4.848047	KEEP	41	1	28	26	848	CC	0.992708	0.859432	0			4	27	147	0	0	11.008729	35	27	1152	103		0.102564	0.865745
MED15P1	326615	__UNKNOWN__	__UNKNOWN__	14	19500170	19500170	__UNKNOWN__	RNA	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19500170T>A	ENST00000552968.1	-	0	488									mediator complex subunit 15 pseudogene 1	NA		NA									NA						CCAGCCCAGCTGGATGTATGT	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							14q11.2	2013-06-03	2010-02-25	2010-02-25	ENSG00000257853	ENSG00000257853	326615			19271	pseudogene	pseudogene		NA	PCQAP pseudogene, mediator complex subunit 15 pseudogene	PCQAPP, MED15P	NA		Standard	NG_002605	NG_002605	NA	Approved				OTTHUMG00000170337	ENST00000552968.1:	chr14.hg19:g.19500170T>A		NA		hg19		0.02	4.525963	AGCxGGA	COVERED																																																																																			NOVEL	MED15P1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000408573.1	0	20.160261	KEEP	38	0	0	67	2094	TT	1	1	0		-	7	47	267	0	0	18.180082	124	50	4747	290	ENST00000552968.1	0.053435	1
POTEG	404785	__UNKNOWN__	__UNKNOWN__	14	19553524	19553524	__UNKNOWN__	Silent	SNP	G	G	A	rs142702316	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19553524G>A	ENST00000409832.3	+	1	160	c.108G>A	c.(106-108)agG>agA	p.R36R		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	36		NA								cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						CCTGGTGCAGGGGGAGCGGCA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						18	29	25	NA		NA	NA	14		NA											NA				19553524		1543	3281	4824	SO:0001819	synonymous_variant				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036	404785		POTE ankyrin domain containing, Ankyrin repeat domain containing	33896	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 4	608916	ANKRD26-like family C, member 2	A26C2	NA		Standard	NM_001005356	NR_027480	NA	Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.108G>A	chr14.hg19:g.19553524G>A		NA	A1L153|A6NMI9|Q6S5H6|Q6S8J2	hg19	CCDS32018.1	0.02	7.116427	CAGxGGG	COVERED																																																																																			NOVEL	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408579.1	0	13.683877	KEEP	75	4	127	90	3123	GG	1	1	0		+	16	46	539	0	0	37.396469	183	48	6824	424	ENST00000409832.3	0.080402	1
POTEG	404785	__UNKNOWN__	__UNKNOWN__	14	19554578	19554578	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19554578G>A	ENST00000409832.3	+	1	573					NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	NA		NA								cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						tggctaacacggtgaaacccc	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036	404785		POTE ankyrin domain containing, Ankyrin repeat domain containing	33896	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 4	608916	ANKRD26-like family C, member 2	A26C2	NA		Standard	NM_001005356	NR_027480	NA	Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.521+641G>A	chr14.hg19:g.19554578G>A		NA	A1L153|A6NMI9|Q6S5H6|Q6S8J2	hg19	CCDS32018.1	0.02	-0.122824	CACxGTG	COVERED																																																																																			NOVEL	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408579.1	0	3.611612	KEEP	0	0	0	12	409	GG	0.993634	0.195062	0		+	3	44	116	0	0	9.872432	11	50	392	33	ENST00000409832.3	0.214286	0.196312
POTEG	404785	__UNKNOWN__	__UNKNOWN__	14	19585383	19585383	__UNKNOWN__	3'UTR	SNP	C	C	T	rs200075574	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19585383C>T	ENST00000409832.3	+	0	2367					NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	NA		NA								cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						CCTCACCGAGCGTGGCTATAG	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036	404785		POTE ankyrin domain containing, Ankyrin repeat domain containing	33896	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 4	608916	ANKRD26-like family C, member 2	A26C2	NA		Standard	NM_001005356	NR_027480	NA	Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.*788C>T	chr14.hg19:g.19585383C>T		NA	A1L153|A6NMI9|Q6S5H6|Q6S8J2	hg19	CCDS32018.1	0.02	5.845477	GAGxGTG	COVERED																																																																																			NOVEL	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408579.1	2	10.7411	KEEP	45	2	66	59	1950	CC	1	1	0		+	8	25	294	0	0	18.725823	187	53	6497	350	ENST00000409832.3	0.041026	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19719886	19719886	__UNKNOWN__	IGR	SNP	G	G	A	rs2716324		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19719886G>A			NA	NA				AL589743.1 (32321 upstream) : RP11-496I2.2 (20146 downstream)						NA		NA									NA						AGCTAGAGACGTGACAGTGCC	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19719886G>A		NA		hg19		0.02	-0.377144	GACxTGA	COVERED																																																																																			NOVEL					0			0	3.911811	KEEP	3	0	0	13	419	GG	0.994391	0.90397	0			3	25	111	0	0	7.807431	40	60	1344	66		0.069767	0.909069
CTD-2314B22.3	0	__UNKNOWN__	__UNKNOWN__	14	19882033	19882033	__UNKNOWN__	lincRNA	SNP	T	T	A	rs28432025		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:19882033T>A	ENST00000552602.1	-	0	2289										NA		NA									NA						aagatgtttttagagatgggg	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000552602.1:	chr14.hg19:g.19882033T>A		NA		hg19		0.02	-0.11405	TTTxAGA	UNCOVERED																																																																																			NOVEL	CTD-2314B22.3-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409412.1	2	2.406155	KEEP	8	0	0	8	233	TT	0	0	0		-	3	40	109	0	0	9.281628	10	48	357	30	ENST00000552602.1	0.230769	0.162467
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20136982	20136982	__UNKNOWN__	RNA	SNP	C	C	A	rs56248208		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:20136982C>A	ENST00000548261.1	+	0	391										NA		NA									NA						CTCTTCCCTGCAAACCATGTT	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20136982C>A		NA		hg19		0.02	1.968391	CTGxAAA	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	1	6.882575	KEEP	27	2	54	42	1429	CC	0.999998	0.999405	0		+	4	39	135	0	0	8.516851	76	60	2768	176	ENST00000548261.1	0.05	0.999407
RP11-597A11.6	0	__UNKNOWN__	__UNKNOWN__	14	20146388	20146388	__UNKNOWN__	lincRNA	SNP	G	G	A	rs199802754	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:20146388G>A	ENST00000555580.1	-	0	225										NA		NA									NA						ATGTGGAGGCGGAAGTTTTGG	0.473	NA	NA											.|||	795	0.158746	0.0673	0.196	5008	,	,	NA	41988	0.1766	NA	0.2018	False	NA	,,,	NA	NA	NA	2504	0.1933	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555580.1:	chr14.hg19:g.20146388G>A		NA		hg19		0.02	15.23979	GGCxGAA	COVERED																																																																																			NOVEL	RP11-597A11.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409767.1	4	6.974275	KEEP	3	3	93	56	1832	GG	1	1	0		-	43	60	1616	0	0	128.185265	263	60	9255	430	ENST00000555580.1	0.140523	1
RP11-597A11.6	0	__UNKNOWN__	__UNKNOWN__	14	20146601	20146601	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:20146601G>A	ENST00000555580.1	-	0	225										NA		NA									NA						CGTCAGTTACGCCCAGGACTT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555580.1:	chr14.hg19:g.20146601G>A		NA		hg19		0.02	12.416243	TACxCCC	COVERED																																																																																			NOVEL	RP11-597A11.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409767.1	2	17.463553	KEEP	4	7	219	135	4475	GG	1	1	0		-	13	49	446	0	0	27.041677	317	60	11148	596	ENST00000555580.1	0.039394	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	20147236	20147236	__UNKNOWN__	IGR	SNP	G	G	A	rs572115899	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:20147236G>A			NA	NA				RP11-597A11.6 (61 upstream) : RP11-597A11.2 (2342 downstream)						NA		NA									NA						AAGTGCAAAGGCCCTGTACGT	0.473	NA	NA											.|||	237	0.0473243	0.0499	0.0245	5008	,	,	NA	58412	0.0268	NA	0.0408	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.20147236G>A		NA		hg19		0.02	6.018004	AAGxCCC	COVERED																																																																																			NOVEL					0			3	2.210104	KEEP	0	3	81	36	1252	GG	1	1	0			11	60	360	0	0	23.245749	171	60	6224	277		0.06044	1
MYH6	4624	__UNKNOWN__	__UNKNOWN__	14	23853765	23853765	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:23853765C>T	ENST00000356287.3	-	35	5480	c.5451G>A	c.(5449-5451)ctG>ctA	p.L1817L	MYH6_ENST00000405093.3_Silent_p.L1817L			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1817		NA			adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCCGCGCTTCCAGCTTCTGCA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						79	79	79	NA		NA	NA	14		NA											NA				23853765		2203	4300	6503	SO:0001819	synonymous_variant			D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616	4624		Myosins / Myosin superfamily : Class II	7576	protein-coding gene	gene with protein product	cardiomyopathy, hypertrophic 1	160710	myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)		NA	2144212	Standard		NM_002471	NA	Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5451G>A	chr14.hg19:g.23853765C>T		NA	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	hg19	CCDS9600.1	0.02	-0.350927	TTCxAGC	COVERED																																																																																			NOVEL	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000071796.3	0	8.123387	KEEP	0	0	0	27	913	CC	0.999988	0.877697	0		-	16	60	564	0	0	52.341706	24	60	906	81	ENST00000356287.3	0.4	0.877708
IRF2BPL	64207	__UNKNOWN__	__UNKNOWN__	14	77491348	77491348	__UNKNOWN__	3'UTR	SNP	C	C	T	rs1059245		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:77491348C>T	ENST00000238647.3	-	0	3686					NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	NA		NA			development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						aaGTCTTTTTCTTTTGTGTGT	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669	64207			14282	protein-coding gene	gene with protein product	enhanced at puberty 1	611720	chromosome 14 open reading frame 4	C14orf4	NA	11095982, 17627301	Standard	NM_024496	NM_024496	NA	Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.*397G>A	chr14.hg19:g.77491348C>T		NA	Q8NDQ2|Q96JG2|Q9H3I7	hg19	CCDS9854.1	0.02	-0.315676	TTTxTTT	COVERED																																																																																			NOVEL	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414298.1	1	3.002302	KEEP	0	0	0	10	336	CC	0.992708	0.812496	0		-	5	60	117	0	0	7.867482	30	60	1042	49	ENST00000238647.3	0.142857	0.818465
TMEM63C	57156	__UNKNOWN__	__UNKNOWN__	14	77725476	77725476	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:77725476A>C	ENST00000298351.4	+	0	4972					NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	NA		NA			cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		CCCTCCCCCCACCTACTGCCA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548	57156			23787	protein-coding gene	gene with protein product	calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)	NA	chromosome 14 open reading frame 171	C14orf171	NA	24503647	Standard		NM_020431	NA	Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.*2407A>C	chr14.hg19:g.77725476A>C		NA	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	hg19	CCDS45141.1	0.02	1.353923	CCCxCCT	COVERED																																																																																			NOVEL	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414193.1	2	6.059409	KEEP	0	2	10	24	619	AA	0.999957	0.999634	0		+	16	60	239	0	0	14.067721	70	60	1765	160	ENST00000298351.4	0.186047	0.999678
FOXN3	1112	__UNKNOWN__	__UNKNOWN__	14	89622728	89622728	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:89622728C>T	ENST00000345097.4	-	0	7619				FOXN3_ENST00000261302.5_3'UTR	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	NA		NA			mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTCGGCTGATCGCGCCTGCCT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254	1112		Forkhead boxes	1928	protein-coding gene	gene with protein product		602628	chromosome 14 open reading frame 116, checkpoint suppressor 1	C14orf116, CHES1	NA	9154802	Standard	NM_005197	NM_005197	NA	Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.*6030G>A	chr14.hg19:g.89622728C>T		NA	Q96II7|Q9UIE7	hg19	CCDS41977.1	0.02	20.633217	GATxGCG	COVERED																																																																																			NOVEL	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410902.2	9	24.711623	KEEP	0	1	28	92	3144	CC	1	1	0		-	30	60	1108	0	0	77.239453	421	60	14927	711	ENST00000345097.4	0.066519	1
RP11-1127D7.1	0	__UNKNOWN__	__UNKNOWN__	14	99391901	99391901	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:99391901A>G	ENST00000554025.1	-	0	1423										NA		NA									NA						aactgaaatgaggaacctgaa	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554025.1:	chr14.hg19:g.99391901A>G		NA		hg19		0.02	2.311807	ATGxGGA	COVERED																																																																																			NOVEL	RP11-1127D7.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000413592.1	0	3.008545	KEEP	0	0	0	10	307	AA	0.992708	0.991583	0		-	29	60	1053	0	0	96.985201	48	60	1777	103	ENST00000554025.1	0.376623	0.998867
WDR20	91833	__UNKNOWN__	__UNKNOWN__	14	102675840	102675840	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:102675840A>G	ENST00000342702.3	+	3	1364	c.1333A>G	c.(1333-1335)Agc>Ggc	p.S445G	WDR20_ENST00000335263.5_Missense_Mutation_p.S445G|WDR20_ENST00000545563.1_Missense_Mutation_p.S272G|WDR20_ENST00000424963.2_Missense_Mutation_p.S321G|WDR20_ENST00000499851.2_Missense_Mutation_p.S188G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000454394.2_Missense_Mutation_p.S476G|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556807.1_Missense_Mutation_p.S384G|WDR20_ENST00000556511.2_Missense_Mutation_p.S384G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	445		NA								breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						AAATGCTGGCAGCAAAAGCAG	0.532	NA	NA									OREG0022939	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						101	103	102	NA		NA	NA	14		NA											NA				102675840		2203	4300	6503	SO:0001583	missense			BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153	91833		WD repeat domain containing	19667	protein-coding gene	gene with protein product		NA			NA		Standard	NM_181291	NM_181291	NA	Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.1333A>G	chr14.hg19:g.102675840A>G	ENSP00000341037:p.Ser445Gly	1368	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	hg19	CCDS9969.1	0.02	13.199764	GGCxGCA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.709|6.709	0.499566|0.499566	0.12762|0.12762	.|.	.|.	ENSG00000140153|ENSG00000140153	ENST00000556511|ENST00000335263;ENST00000299135;ENST00000424963;ENST00000342702;ENST00000556807;ENST00000499851;ENST00000454394;ENST00000401892;ENST00000545563	.|T;T;T;T;T;T;T	.|0.67698	.|-0.28;-0.28;-0.28;-0.28;-0.28;-0.28;-0.28	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.162599	.|0.64402	.|D	.|0.000002	T|T	0.56277|0.56277	0.1974|0.1974	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B;B;B	.|0.24882	.|0.001;0.113;0.001;0.0;0.0;0.043;0.0	.|B;B;B;B;B;B;B	.|0.24006	.|0.001;0.05;0.001;0.0;0.002;0.027;0.002	T|T	0.52087|0.52087	-0.8622|-0.8622	5|10	.|0.19590	.|T	.|0.45	.|.	16.0225|16.0225	0.80509|0.80509	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|476;457;384;445;384;321;445	.|E7EUY8;Q5JPH5;G3V2F8;Q8TBZ3-2;F8W9S4;B3KR43;Q8TBZ3	.|.;.;.;.;.;.;WDR20_HUMAN	R|G	375|445;384;321;445;384;188;476;375;272	.|ENSP00000335434:S445G;ENSP00000395793:S321G;ENSP00000341037:S445G;ENSP00000450636:S384G;ENSP00000443641:S188G;ENSP00000406084:S476G;ENSP00000437927:S272G	.|ENSP00000299135:S384G	Q|S	+|+	2|1	0|0	WDR20|WDR20	101745593|101745593	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.951000|0.951000	0.60555|0.60555	7.099000|7.099000	0.76981|0.76981	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	CAG|AGC	NOVEL	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414963.1	4	16.246743	KEEP	0	0	0	54	1652	AA	1	1	0		+	80	60	2787	0	0	247.958255	175	60	6562	351	ENST00000342702.3	0.313725	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	106134536	106134536	__UNKNOWN__	IGR	SNP	T	T	C	rs3211548		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:106134536T>C			NA	NA				RP11-731F5.2 (19142 upstream) : AL928768.3 (35764 downstream)						NA		NA									NA						AGCATCCTCGTGCGACCGCGA	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.106134536T>C		NA		hg19		0.02	-0.228097	TCGxGCG	COVERED																																																																																			NOVEL					0			1	3.238154	KEEP	1	1	35	23	638	TT	0.999892	0.582867	0			3	60	98	0	0	7.194498	23	60	839	68		0.115385	0.58293
IGHA1	3493	__UNKNOWN__	__UNKNOWN__	14	106174767	106174767	__UNKNOWN__	RNA	SNP	G	G	T	rs1128862	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:106174767G>T	ENST00000390547.2	-	0	235							P01876	IGHA1_HUMAN	immunoglobulin heavy constant alpha 1	NA		NA			antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|positive regulation of respiratory burst (GO:0060267)|protein-chromophore linkage (GO:0018298)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)				NA						GGACTTGCCGGCTAGGCACTG	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						60	71	67	NA		NA	NA	14		NA											NA				106174767		2123	4240	6363					J00220		14q32.33	2012-10-02			ENSG00000211895	ENSG00000211895	3493		Immunoglobulins / IGH locus	5478	other	immunoglobulin gene		146900			NA		Standard	NG_001019	NG_001019	NA	Approved			P01876	OTTHUMG00000152494	ENST00000390547.2:	chr14.hg19:g.106174767G>T		NA		hg19		0.02	1.689947	CCGxCTA	COVERED																																																																																			NOVEL	IGHA1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	NA	IG_C_gene	OTTHUMT00000326459.1	4	3.815257	KEEP	3	3	92	45	1578	GG	1	0.999862	0		-	9	54	301	0	0	21.647346	82	60	3006	178	ENST00000390547.2	0.098901	0.999862
IGHV4-4	28401	__UNKNOWN__	__UNKNOWN__	14	106478137	106478137	__UNKNOWN__	RNA	SNP	C	C	T	rs147818197		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:106478137C>T	ENST00000390596.2	-	0	384									immunoglobulin heavy variable 4-4	NA		NA									NA						CGGCCGTGTCCGCGGCGGTCA	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						157	106	122	NA		NA	NA	14		NA											NA				106478137		1929	4088	6017					X62112		14q32.33	2012-02-08			ENSG00000211936	ENSG00000276775	28401		Immunoglobulins / IGH locus	5652	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000152322	ENST00000390596.2:	chr14.hg19:g.106478137C>T		NA		hg19		0.02	-0.385966	GTCxGCG	COVERED																																																																																			NOVEL	IGHV4-4-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000325884.1	3	5.116485	KEEP	2	0	0	17	580	CC	0.999366	0.917589	0		-	4	29	155	0	0	11.67331	38	60	1348	73	ENST00000390596.2	0.095238	0.918171
IGHV3-7	28452	__UNKNOWN__	__UNKNOWN__	14	106518704	106518704	__UNKNOWN__	RNA	SNP	C	C	T	rs199995238		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:106518704C>T	ENST00000390598.2	-	0	125									immunoglobulin heavy variable 3-7	NA		NA									NA						ACACTGGACACCTGCAAACAA	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						151	143	145	NA		NA	NA	14		NA											NA				106518704		1885	4101	5986					M99649		14q32.33	2012-02-08			ENSG00000211938	ENSG00000211938	28452		Immunoglobulins / IGH locus	5620	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000152271	ENST00000390598.2:	chr14.hg19:g.106518704C>T		NA		hg19		0.02	6.408714	ACAxCTG	COVERED																																																																																			NOVEL	IGHV3-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000325659.1	19	13.574301	KEEP	6	1	28	55	1901	CC	1	1	0		-	7	27	262	0	0	16.367593	193	60	7086	308	ENST00000390598.2	0.035	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	106866383	106866383	__UNKNOWN__	IGR	SNP	G	G	A	rs76297373	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:106866383G>A			NA	NA				IGHV3-35 (20594 upstream) : IGHV3-38 (22 downstream)						NA		NA									NA						GTGTCTGGGCGCACAATGACT	0.562	NA	NA											G|||	170	0.0339457	0.1188	0.013	5008	,	,	NA	15101	0.001	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						82	72	76	NA		NA	NA	14		NA											NA				106866383		2072	4211	6283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.106866383G>A		NA		hg19		0.02	2.063203	GGCxCAC	COVERED																																																																																			NOVEL					0			1	3.310073	KEEP	0	0	0	11	363	GG	0.993072	0.99298	0			6	40	230	0	0	16.262965	85	60	2828	116		0.065934	0.999907
IGHV3-66	28412	__UNKNOWN__	__UNKNOWN__	14	107131110	107131110	__UNKNOWN__	RNA	SNP	C	C	G	rs200434308	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:107131110C>G	ENST00000390632.2	-	0	349									immunoglobulin heavy variable 3-66	NA		NA									NA						TTGGAATTGTCTCTGGAGATG	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	C		132,4148		0,132,2008	102	125	117	NA		1.7	0.8	14	dbSNP_134	117	257,8263		1,255,4004	no	intergenic				1,387,6012	GG,GC,CC	NA	3.0164,3.0841,3.0391			107131110	389,12411	2140	4260	6400					X92218		14q32.33	2012-02-08			ENSG00000211972	ENSG00000211972	28412		Immunoglobulins / IGH locus	5619	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151880	ENST00000390632.2:	chr14.hg19:g.107131110C>G		NA		hg19		0.02	6.716929	TGTxTCT	COVERED																																																																																			NOVEL	IGHV3-66-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324225.1	14	3.48447	KEEP	14	2	76	38	1313	CC	1	1	0		-	8	27	306	0	0	20.348872	165	60	6244	297	ENST00000390632.2	0.046243	1
IGHV1-69	28461	__UNKNOWN__	__UNKNOWN__	14	107170390	107170390	__UNKNOWN__	RNA	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:107170390G>T	ENST00000390633.2	-	0	38									immunoglobulin heavy variable 1-69	NA		NA									NA						TGCTCCCAGGGGCTTCTTCAG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						71	56	61	NA		NA	NA	14		NA											NA				107170390		1908	4110	6018					L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973	28461		Immunoglobulins / IGH locus	5558	other	immunoglobulin gene		NA		IGHV1-E	NA	8469934	Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151862	ENST00000390633.2:	chr14.hg19:g.107170390G>T		NA		hg19		0.02	1.84839	AGGxGCT	COVERED																																																																																			NOVEL	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324207.1	2	4.495437	KEEP	0	0	0	15	472	GG	0.99649	0.994395	0		-	4	60	145	0	0	9.805415	64	60	2248	100	ENST00000390633.2	0.058824	0.997898
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	107183741	107183741	__UNKNOWN__	IGR	SNP	G	G	T	rs111689989		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:107183741G>T			NA	NA				IGHV2-70 (4403 upstream) : IGHV3-72 (15190 downstream)						NA		NA									NA						GTCAGAAACTGCCACACAAAT	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.107183741G>T		NA		hg19		0.02	4.369906	ACTxCCA	COVERED																																																																																			NOVEL					0			4	3.616965	KEEP	0	3	94	45	1628	GG	1	1	0			9	60	331	0	0	23.381316	115	60	4383	213		0.072581	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	107183761	107183761	__UNKNOWN__	IGR	SNP	C	C	A	rs113533707		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr14:107183761C>A			NA	NA				IGHV2-70 (4423 upstream) : IGHV3-72 (15170 downstream)						NA		NA									NA						TCCACTGTTTCTCTCACTCTT	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.107183761C>A		NA		hg19		0.02	4.457634	TTTxTCT	COVERED																																																																																			NOVEL					0			4	2.513718	KEEP	0	3	96	42	1525	CC	1	0.999997	0			9	60	343	0	0	24.921993	105	60	4033	202		0.078947	0.999997
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20450052	20450052	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:20450052C>T			NA	NA				RP11-173D3.1 (96846 upstream) : CHEK2P2 (37944 downstream)						NA		NA									NA						GCAGCCCTCCCTGTGCCAAGC	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20450052C>T		NA		hg19		0.02	1.982726	TCCxTGT	COVERED																																																																																			NOVEL					0			1	7.221857	KEEP	0	0	0	24	793	CC	0.999909	0.996142	0			8	45	298	0	0	22.868161	61	60	2106	98		0.115942	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20563252	20563252	__UNKNOWN__	IGR	SNP	G	G	T	rs372580439	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:20563252G>T			NA	NA				RP11-509A17.3 (1459 upstream) : AC026495.1 (108 downstream)						NA		NA									NA						AGCACCTCAGGAGCCCAGAAG	0.682	NA	NA											.|||	32	0.00638978	0.0038	0.0086	5008	,	,	NA	49902	0.005	NA	0.0089	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20563252G>T		NA		hg19		0.02	-0.307035	CAGxAGC	COVERED																																																																																			NOVEL					0			0	3.009544	KEEP	0	0	0	10	333	GG	0.992708	0.79441	0			16	60	556	0	0	52.751493	19	60	692	51		0.457143	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22691690	22691690	__UNKNOWN__	IGR	SNP	G	G	A	rs368893326		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:22691690G>A			NA	NA				MIR4509-2 (16449 upstream) : GOLGA8DP (13030 downstream)						NA		NA									NA						GGAATGGAAAGGCTGAAATCC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22691690G>A		NA		hg19		0.02	4.969157	AAAxGCT	COVERED																																																																																			NOVEL					0			1	7.289892	KEEP	6	2	53	43	1556	GG	1	0.999999	0			10	47	382	0	0	27.804877	116	48	4551	229		0.079365	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22691729	22691729	__UNKNOWN__	IGR	SNP	G	G	C	rs71469079	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:22691729G>C			NA	NA				MIR4509-2 (16488 upstream) : GOLGA8DP (12991 downstream)						NA		NA									NA						GGGCAAGCGGGATCGGCAAAA	0.507	NA	NA											.|||	613	0.122404	0.1218	0.1138	5008	,	,	NA	49512	0.0109	NA	0.2107	False	NA	,,,	NA	NA	NA	2504	0.1534	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22691729G>C		NA		hg19		0.02	7.237837	CGGxATC	COVERED																																																																																			NOVEL					0			2	4.460902	KEEP	4	3	106	52	1808	GG	1	1	0			10	47	385	0	0	27.288321	141	48	5349	267		0.066225	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	23182197	23182197	__UNKNOWN__	IGR	SNP	C	C	T	rs28561424		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:23182197C>T			NA	NA				RP11-26F2.1 (50270 upstream) : WHAMMP3 (5530 downstream)						NA		NA									NA						GTCCTATAGACGGGAAGTCCA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.23182197C>T		NA		hg19		0.02	8.546146	AGAxGGG	COVERED																																																																																			NOVEL					0			2	4.619301	KEEP	1	3	96	49	1700	CC	1	1	0			14	44	514	0	0	34.939524	225	60	7902	366		0.058577	1
PWRN1	791114	__UNKNOWN__	__UNKNOWN__	15	24803687	24803687	__UNKNOWN__	lincRNA	SNP	C	C	T	rs200366213		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:24803687C>T	ENST00000568609.1	+	0	170					NR_026646.1				Prader-Willi region non-protein coding RNA 1	NA		NA									NA						tcatttagctcccacttataa	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AC139362, AC139147, AC100720		15q11.2	2014-07-18	2008-08-13			ENSG00000259905	791114		-	33235	non-coding RNA	RNA, long non-coding	non-protein coding RNA 198	611215			NA	17337158	Standard	NR_026646	NR_026646	NA	Approved	NCRNA00198	uc001ywn.3			ENST00000568609.1:	chr15.hg19:g.24803687C>T		NA		hg19		0.02	-0.166695	GCTxCCA	COVERED																																																																																			NOVEL	PWRN1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000422069.1	1	3.611557	KEEP	1	0	0	12	419	CC	0.993634	0.351693	0		+	3	31	110	0	0	9.078259	13	60	506	46	ENST00000568609.1	0.1875	0.353947
ATP10A	57194	__UNKNOWN__	__UNKNOWN__	15	26003856	26003856	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:26003856C>T	ENST00000356865.6	-	2	766					NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	NA		NA			ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		taactcattccgatcacctgc	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190	57194		ATPases / P-type	13542	protein-coding gene	gene with protein product		605855	ATPase, Class V, type 10C, ATPase, Class V, type 10A	ATP10C	NA	11015572, 9628581	Standard	NM_024490	NM_024490	NA	Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.654+22309G>A	chr15.hg19:g.26003856C>T		NA	Q4G0S9|Q969I4	hg19	CCDS32178.1	0.02	16.512921	TTCxGAT	COVERED																																																																																			NOVEL	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414830.1	19	29.695039	KEEP	266	8	218	176	5725	CC	1	1	0		-	15	34	565	0	0	36.609581	344	60	11357	1108	ENST00000356865.6	0.041783	1
GABRB3	2562	__UNKNOWN__	__UNKNOWN__	15	27017985	27017985	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:27017985A>C	ENST00000311550.5	-	1	192				GABRB3_ENST00000557641.1_Intron|GABRB3_ENST00000299267.4_Intron|GABRB3_ENST00000541819.2_Intron	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	NA		NA			cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	cgccccgcgcaccccgcgccc	0.721	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						10	11	10	NA		NA	NA	15		NA											NA				27017985		2039	3981	6020	SO:0001627	intron_variant				CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206	2562		GABA receptors, Ligand-gated ion channels / GABA(A) receptors	4083	protein-coding gene	gene with protein product	GABA(A) receptor, beta 3	137192			NA		Standard		NM_000814	NA	Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.80+44T>G	chr15.hg19:g.27017985A>C		NA	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	hg19	CCDS10019.1	0.02	-0.369443	CGCxCCC	COVERED																																																																																			NOVEL	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251352.2	0	8.979034	KEEP	0	3	35	43	1035	AA	1	0.918171	0		-	7	60	110	0	0	6.357335	37	60	845	121	ENST00000311550.5	0.159091	0.918171
RP11-483E23.2	0	__UNKNOWN__	__UNKNOWN__	15	28600002	28600002	__UNKNOWN__	RNA	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:28600002T>A	ENST00000568624.1	-	0	404										NA		NA									NA						TTCGTATGGTTTGAACCTGGG	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000568624.1:	chr15.hg19:g.28600002T>A		NA		hg19		0.02	-0.394752	GGTxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	.	5.336	0.247398	0.10130	.	.	ENSG00000237850	ENST00000454724;ENST00000424531	.	.	.	.	.	.	.	.	.	.	.	T	0.14270	0.0345	.	.	.	.	.	.	B	0.11235	0.004	B	0.01281	0.0	T	0.23476	-1.0187	4	0.18276	T	0.48	.	.	.	.	.	112	B4DY83	.	H	118;116	.	ENSP00000393266:Q116H	Q	-	3	2	AC091304.2	26273597	0.988000	0.35896	0.117000	0.21633	0.118000	0.20060	-1.015000	0.03637	-2.183000	0.00763	-2.300000	0.00261	CAA	NOVEL	RP11-483E23.2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000431212.1	0	3.608838	KEEP	1	0	0	12	335	TT	0.993072	0.920221	0		-	3	22	99	0	0	6.549565	42	60	1481	62	ENST00000568624.1	0.066667	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	31093647	31093647	__UNKNOWN__	IGR	SNP	T	T	G	rs183010080	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:31093647T>G			NA	NA				AC004460.1 (56 upstream) : FAN1 (102407 downstream)						NA		NA									NA						GCGGCACTGGTAGGAGGACAC	0.632	NA	NA											N|||	218	0.0435304	0.1165	0.0288	5008	,	,	NA	15113	0.004	NA	0.0278	False	NA	,,,	NA	NA	NA	2504	0.0123	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.31093647T>G		NA		hg19		0.02	-0.394783	TGGxAGG	COVERED																																																																																			NOVEL					0			0	4.810966	KEEP	0	0	0	16	453	TT	0.997832	0.924631	0			6	59	214	0	0	16.589791	39	60	1375	71		0.133333	0.92664
PLA2G4D	283748	__UNKNOWN__	__UNKNOWN__	15	42378650	42378650	__UNKNOWN__	Intron	SNP	A	A	G	rs77332371	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:42378650A>G	ENST00000290472.3	-	4	350					NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		TCATTATGCCACCACACGTCT	0.348	NA	NA											C|||	252	0.0503195	0.0431	0.0735	5008	,	,	NA	12111	0	NA	0.1024	False	NA	,,,	NA	NA	NA	2504	0.0419	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	283748	3.1.1.4		30038	protein-coding gene	gene with protein product		612864			NA	14709560	Standard	NM_178034	NM_178034	NA	Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.256-108T>C	chr15.hg19:g.42378650A>G		NA	Q8N176	hg19	CCDS32203.1	0.02	-0.210551	GCCxCCA	COVERED																																																																																			NOVEL	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419317.1	0	2.404937	KEEP	0	0	0	8	210	AA	0.99257	0.518282	0		-	22	60	800	0	0	87.504485	2	60	74	35	ENST00000290472.3	0.916667	0.522161
HAUS2	55142	__UNKNOWN__	__UNKNOWN__	15	42860232	42860232	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:42860232T>G	ENST00000260372.3	+	0	1989				RP11-265N6.2_ENST00000561902.1_RNA	NM_018097.2	NP_060567.1	Q9NVX0	HAUS2_HUMAN	HAUS augmin-like complex, subunit 2	NA		NA			centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|HAUS complex (GO:0070652)|microtubule (GO:0005874)|nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(1)	3						aaaaaaaaGGTGTTTCTGAAT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001322	CCDS10090.1, CCDS45247.1	15q15.1	2014-02-20	2009-04-20	2009-04-20	ENSG00000137814	ENSG00000137814	55142		HAUS augmin-like complex subunits	25530	protein-coding gene	gene with protein product		613429	chromosome 15 open reading frame 25, centrosomal protein 27kDa	C15orf25, CEP27	NA	14702039, 14654843, 19427217	Standard	NM_018097	NM_018097	NA	Approved	FLJ10460, HsT17025	uc001zqe.3	Q9NVX0	OTTHUMG00000130678	ENST00000260372.3:c.*1218T>G	chr15.hg19:g.42860232T>G		NA	C9JH36|Q9H9B3	hg19	CCDS10090.1	0.02	-0.357113	AGGxGTT	COVERED																																																																																			NOVEL	HAUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253173.1	3	3.895578	KEEP	0	0	0	13	318	TT	0.994391	0.883889	0		+	10	70	174	1	0	12.412583	30	70	840	80	ENST00000260372.3	0.25	0.888875
EPB42	2038	__UNKNOWN__	__UNKNOWN__	15	43512858	43512858	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:43512858A>C	ENST00000441366.2	-	1	236				EPB42_ENST00000540029.1_Intron|EPB42_ENST00000300215.3_Intron	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	NA		NA			cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		ccccccccccacagccacctc	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947	2038		Transglutaminases	3381	protein-coding gene	gene with protein product	Erythrocyte surface protein band 4.2	177070			NA	1284644	Standard	NM_000119	NM_000119	NA	Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.10+155T>G	chr15.hg19:g.43512858A>C		NA	Q4KKX0|Q4VB97	hg19	CCDS45249.1	0.02	-0.209603	CCCxCAG	COVERED																																																																																			NOVEL	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000432219.1	1	3.00772	KEEP	0	0	0	10	289	AA	0.992708	0.518353	0		-	4	60	97	1	0	6.931691	20	60	596	65	ENST00000441366.2	0.166667	0.522161
CATSPER2	117155	__UNKNOWN__	__UNKNOWN__	15	43920853	43920853	__UNKNOWN__	3'UTR	SNP	T	T	G	rs2442939	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:43920853T>G	ENST00000396879.1	-	0	3745				STRC_ENST00000541030.1_Intron	NM_001282309.1	NP_001269238.1	Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	NA		NA			calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAGCCCTTACTTAAGGTTGGG	0.448	NA	NA											t|||	1903	0.379992	0.6853	0.2493	5008	,	,	NA	14454	0.2629	NA	0.2406	False	NA	,,,	NA	NA	NA	2504	0.3241	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762	117155		Voltage-gated ion channels / Cation channels, sperm associated	18810	protein-coding gene	gene with protein product		607249			NA	11675491, 16382101	Standard	NM_054020	NM_172095	NA	Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000396879.1:c.*2046A>C	chr15.hg19:g.43920853T>G		NA	Q8NHT9|Q96P54|Q96P55	hg19	CCDS32216.1	0.02	4.801137	TACxTAA	COVERED																																																																																			NOVEL	CATSPER2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133150.2	0	7.45111	KEEP	9	1	35	37	1158	TT	1	0.999994	0		-	18	40	637	0	0	50.924488	93	60	3495	194	ENST00000396879.1	0.162162	0.999994
CATSPER2	117155	__UNKNOWN__	__UNKNOWN__	15	43920920	43920920	__UNKNOWN__	3'UTR	SNP	A	A	T	rs28525379		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:43920920A>T	ENST00000396879.1	-	0	3678				STRC_ENST00000541030.1_Intron	NM_001282309.1	NP_001269238.1	Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	NA		NA			calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		TTTCATCACAACCACCACCTT	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762	117155		Voltage-gated ion channels / Cation channels, sperm associated	18810	protein-coding gene	gene with protein product		607249			NA	11675491, 16382101	Standard	NM_054020	NM_172095	NA	Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000396879.1:c.*1979T>A	chr15.hg19:g.43920920A>T		NA	Q8NHT9|Q96P54|Q96P55	hg19	CCDS32216.1	0.02	1.543504	ACAxCCA	COVERED																																																																																			NOVEL	CATSPER2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133150.2	1	9.927425	KEEP	4	0	0	33	1003	AA	0.999998	0.99962	0		-	4	27	134	0	0	8.308562	81	60	2821	135	ENST00000396879.1	0.047059	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	50087827	50087827	__UNKNOWN__	IGR	SNP	A	A	C	rs2660965		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:50087827A>C			NA	NA				RP11-353B9.1 (139398 upstream) : ATP8B4 (62607 downstream)						NA		NA									NA						gttccagttcaagttccagtt	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.50087827A>C		NA		hg19		0.02	15.821443	TTCxAGT	COVERED																																																																																			NOVEL					0			8	7.620765	KEEP	3	3	108	63	1832	AA	1	1	0			9	40	358	0	0	22.949166	262	60	9632	512		0.03321	1
ZNF280D	54816	__UNKNOWN__	__UNKNOWN__	15	56991517	56991517	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:56991517C>A	ENST00000559000.1	-	11	2142				ZNF280D_ENST00000396245.1_Intron|ZNF280D_ENST00000267807.7_Intron|ZNF280D_ENST00000559237.1_Intron|ZNF280D_ENST00000558320.1_3'UTR			Q6N043	Z280D_HUMAN	zinc finger protein 280D	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		AGGAAAGAAGCAAATATAGCT	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20			54816			25953	protein-coding gene	gene with protein product		NA	suppressor of hairy wing homolog 4 (Drosophila)	SUHW4	NA	10997877	Standard	XM_370867	XM_005254481	NA	Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000559000.1:c.342+1613G>T	chr15.hg19:g.56991517C>A		NA	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	hg19		0.02	1.569606	AAGxAAA	COVERED																																																																																			NOVEL	ZNF280D-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000419442.2	0	7.194601	KEEP	4	2	66	47	1700	CC	1	0.999407	0		-	6	45	201	0	0	13.645026	76	60	2953	183	ENST00000559000.1	0.073171	0.999407
POLR2M	81488	__UNKNOWN__	__UNKNOWN__	15	58008419	58008419	__UNKNOWN__	3'UTR	SNP	T	T	C	rs12898359		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:58008419T>C	ENST00000299638.3	+	0	2863				POLR2M_ENST00000380563.2_Intron|POLR2M_ENST00000380557.4_3'UTR	NM_015532.3	NP_056347.1	P0CAP2	GRL1A_HUMAN	polymerase (RNA) II (DNA directed) polypeptide M	NA		NA			maintenance of ER location (GO:0051685)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)	DNA-directed RNA polymerase activity (GO:0003899)				NA						ATATTGTCAATATGTTCCCAT	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF326773	CCDS32252.1, CCDS42045.1	15q21.3	2013-01-21	2011-11-07	2011-11-07		ENSG00000255529	81488		RNA polymerase subunits	14862	protein-coding gene	gene with protein product		606485	glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A	GRINL1A	NA	16769904, 22850672	Standard		NM_015532	NA	Approved	Gdown, Gdown1, GCOM1	uc002aev.1	P0CAP2	OTTHUMG00000166486	ENST00000299638.3:c.*1542T>C	chr15.hg19:g.58008419T>C		NA	Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5|Q9Y3V6	hg19	CCDS32252.1	0.02	9.378309	CAAxATG	COVERED																																																																																			NOVEL	POLR2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255719.2	4	10.529608	KEEP	1	0	0	35	1064	TT	0.999999	0.999999	0		+	8	40	309	0	0	20.09847	194	60	7076	280	ENST00000299638.3	0.039604	1
GOLGA6A	342096	__UNKNOWN__	__UNKNOWN__	15	74364231	74364231	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:74364231C>T	ENST00000290438.3	-	15	1634					NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	NA		NA				Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						GCACAGCCTTCACACCTTCCG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289	342096			13567	protein-coding gene	gene with protein product		610288	golgi autoantigen, golgin subfamily a, member 6, golgi autoantigen, golgin subfamily a, 6, golgi autoantigen, golgin subfamily a, 6A	GOLGA6	NA	11161787	Standard	XM_292357	NM_001038640	NA	Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1594-234G>A	chr15.hg19:g.74364231C>T		NA	A8K959|Q9NYA7	hg19	CCDS32290.1	0.02	1.859801	CTTxACA	COVERED																																																																																			NOVEL	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421835.1	4	2.241628	KEEP	15	1	30	18	626	CC	0.999366	0.998854	0		-	5	27	185	0	0	12.709508	77	50	2877	128	ENST00000290438.3	0.060976	0.999487
GOLGA6A	342096	__UNKNOWN__	__UNKNOWN__	15	74364287	74364287	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:74364287A>G	ENST00000290438.3	-	14	1634					NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	NA		NA				Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TGGCTCCAGCAGAGGTGAAAA	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289	342096			13567	protein-coding gene	gene with protein product		610288	golgi autoantigen, golgin subfamily a, member 6, golgi autoantigen, golgin subfamily a, 6, golgi autoantigen, golgin subfamily a, 6A	GOLGA6	NA	11161787	Standard	XM_292357	NM_001038640	NA	Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1593+271T>C	chr15.hg19:g.74364287A>G		NA	A8K959|Q9NYA7	hg19	CCDS32290.1	0.02	-0.228059	AGCxGAG	UNCOVERED																																																																																			NOVEL	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421835.1	1	3.610492	KEEP	33	0	0	12	368	AA	0	0	0		-	5	25	164	0	0	13.259088	21	40	784	71	ENST00000290438.3	0.192308	0.58293
GOLGA6A	342096	__UNKNOWN__	__UNKNOWN__	15	74364291	74364291	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:74364291G>T	ENST00000290438.3	-	14	1634					NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	NA		NA				Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TCCAGCAGAGGTGAAAAATGC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289	342096			13567	protein-coding gene	gene with protein product		610288	golgi autoantigen, golgin subfamily a, member 6, golgi autoantigen, golgin subfamily a, 6, golgi autoantigen, golgin subfamily a, 6A	GOLGA6	NA	11161787	Standard	XM_292357	NM_001038640	NA	Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1593+267C>A	chr15.hg19:g.74364291G>T		NA	A8K959|Q9NYA7	hg19	CCDS32290.1	0.02	-0.227107	GAGxTGA	UNCOVERED																																																																																			NOVEL	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421835.1	0	3.310222	KEEP	34	0	0	11	371	GG	0	0	0		-	5	25	179	0	0	14.864926	20	40	703	72	ENST00000290438.3	0.2	0.58293
GOLGA6A	342096	__UNKNOWN__	__UNKNOWN__	15	74364535	74364535	__UNKNOWN__	Intron	SNP	C	C	T	rs200938195	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:74364535C>T	ENST00000290438.3	-	14	1634					NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	NA		NA				Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						GGTGGCAAAGCGGGGCAGGGA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						30	35	33	NA		NA	NA	15		NA											NA				74364535		1425	2480	3905	SO:0001627	intron_variant			AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289	342096			13567	protein-coding gene	gene with protein product		610288	golgi autoantigen, golgin subfamily a, member 6, golgi autoantigen, golgin subfamily a, 6, golgi autoantigen, golgin subfamily a, 6A	GOLGA6	NA	11161787	Standard	XM_292357	NM_001038640	NA	Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1593+23G>A	chr15.hg19:g.74364535C>T		NA	A8K959|Q9NYA7	hg19	CCDS32290.1	0.02	1.899802	AAGxGGG	COVERED																																																																																			NOVEL	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421835.1	2	5.846961	KEEP	33	1	24	28	934	CC	0.999366	0.999202	0		-	10	40	356	0	0	26.749462	80	60	2860	178	ENST00000290438.3	0.111111	0.999835
GOLGA6A	342096	__UNKNOWN__	__UNKNOWN__	15	74364603	74364603	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs142837205		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:74364603G>A	ENST00000290438.3	-	14	1589	c.1549C>T	c.(1549-1551)Ccc>Tcc	p.P517S		NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	517		NA				Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						TTTGGCGTGGGCCGAGGCGCC	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						33	59	50	NA		NA	NA	15		NA											NA				74364603		1403	2574	3977	SO:0001583	missense			AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289	342096			13567	protein-coding gene	gene with protein product		610288	golgi autoantigen, golgin subfamily a, member 6, golgi autoantigen, golgin subfamily a, 6, golgi autoantigen, golgin subfamily a, 6A	GOLGA6	NA	11161787	Standard	XM_292357	NM_001038640	NA	Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1549C>T	chr15.hg19:g.74364603G>A	ENSP00000290438:p.Pro517Ser	NA	A8K959|Q9NYA7	hg19	CCDS32290.1	0.02	1.923656	TGGxCCG	COVERED	.	.	.	.	.	.	.	.	.	.	g	3.605	-0.080767	0.07141	.	.	ENSG00000159289	ENST00000290438	T	0.21734	1.99	1.55	-3.11	0.05299	.	.	.	.	.	T	0.14013	0.0339	L	0.56124	1.755	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.38457	-0.9660	9	0.25751	T	0.34	.	0.3526	0.00351	0.3002:0.1942:0.3097:0.1959	.	517	Q9NYA3	GOG6A_HUMAN	S	517	ENSP00000290438:P517S	ENSP00000290438:P517S	P	-	1	0	GOLGA6A	72151656	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.254000	0.08781	-0.702000	0.05056	-1.597000	0.00832	CCC	NOVEL	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421835.1	0	6.857741	KEEP	38	1	32	34	1218	GG	0.999859	0.970684	0		-	5	40	171	0	0	12.295716	48	60	1738	135	ENST00000290438.3	0.09434	0.97082
GOLGA6A	342096	__UNKNOWN__	__UNKNOWN__	15	74364655	74364655	__UNKNOWN__	Intron	SNP	A	A	G	rs76120758	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:74364655A>G	ENST00000290438.3	-	14	1542					NM_001038640.2	NP_001033729.2	Q9NYA3	GOG6A_HUMAN	golgin A6 family, member A	NA		NA				Golgi apparatus (GO:0005794)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|liver(1)|lung(6)|prostate(1)|urinary_tract(1)	16						CATCTCCTGTAGGGAGGTGGC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						45	82	69	NA		NA	NA	15		NA											NA				74364655		1445	2638	4083	SO:0001627	intron_variant			AF263742	CCDS32290.1	15q24.1	2013-05-10	2010-02-12	2009-09-28	ENSG00000159289	ENSG00000159289	342096			13567	protein-coding gene	gene with protein product		610288	golgi autoantigen, golgin subfamily a, member 6, golgi autoantigen, golgin subfamily a, 6, golgi autoantigen, golgin subfamily a, 6A	GOLGA6	NA	11161787	Standard	XM_292357	NM_001038640	NA	Approved	GLP	uc002axa.1	Q9NYA3	OTTHUMG00000173035	ENST00000290438.3:c.1502-5T>C	chr15.hg19:g.74364655A>G		NA	A8K959|Q9NYA7	hg19	CCDS32290.1	0.02	2.639853	TGTxGGG	COVERED																																																																																			NOVEL	GOLGA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421835.1	1	5.347846	KEEP	15	1	20	25	748	AA	0.999869	0.963648	0		-	5	40	195	0	0	14.782286	46	60	1689	101	ENST00000290438.3	0.098039	0.963774
CSPG4	1464	__UNKNOWN__	__UNKNOWN__	15	75982329	75982329	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs200311411		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:75982329A>T	ENST00000308508.5	-	3	1169	c.1077T>A	c.(1075-1077)agT>agA	p.S359R		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	359	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.	NA			activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GGCCATTGACACTGAGGTCTT	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						11	12	12	NA		NA	NA	15		NA											NA				75982329		2175	4257	6432	SO:0001583	missense			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546	1464		Proteoglycans / Cell surface : Other	2466	protein-coding gene	gene with protein product	melanoma-associated chondroitin sulfate proteoglycan	601172	chondroitin sulfate proteoglycan 4 (melanoma-associated)		NA	8790396, 16407841	Standard	NM_001897	NM_001897	NA	Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1077T>A	chr15.hg19:g.75982329A>T	ENSP00000312506:p.Ser359Arg	NA	D3DW77|Q92675	hg19	CCDS10284.1	0.02	1.642971	GACxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	6.340	0.430847	0.12045	.	.	ENSG00000173546	ENST00000308508	T	0.75477	-0.94	5.26	-0.145	0.13436	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.250863	0.34386	N	0.004006	T	0.47581	0.1453	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18524	-1.0334	10	0.06757	T	0.87	.	1.3272	0.02128	0.3146:0.2414:0.3211:0.1229	.	359	Q6UVK1	CSPG4_HUMAN	R	359	ENSP00000312506:S359R	ENSP00000312506:S359R	S	-	3	2	CSPG4	73769384	0.003000	0.15002	0.430000	0.26722	0.911000	0.54048	-0.250000	0.08830	-0.057000	0.13199	-0.375000	0.07067	AGT	NOVEL	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286472.1	2	8.00245	KEEP	4	2	43	42	1214	AA	1	0.999622	0		-	6	40	216	0	0	15.046365	79	60	2756	142	ENST00000308508.5	0.070588	0.999622
RP11-24M17.4	0	__UNKNOWN__	__UNKNOWN__	15	76054552	76054552	__UNKNOWN__	RNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:76054552A>G	ENST00000569596.1	+	0	169										NA		NA									NA						CAAGCTGAGGAGTGAGCAGGC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000569596.1:	chr15.hg19:g.76054552A>G		NA		hg19		0.02	-0.385953	AGGxGTG	COVERED																																																																																			NOVEL	RP11-24M17.4-002	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000420499.1	0	7.220368	KEEP	0	0	0	24	738	AA	0.999909	0.918088	0		+	3	44	107	0	0	7.376561	41	60	1526	84	ENST00000569596.1	0.068182	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	84851949	84851949	__UNKNOWN__	IGR	SNP	G	G	A	rs151283447		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:84851949G>A			NA	NA				RP11-182J1.16 (963 upstream) : AC103965.1 (16113 downstream)						NA		NA									NA						CGCCTCTAGCGTTGGGAATCA	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.84851949G>A		NA		hg19		0.02	-0.30693	AGCxTTG	COVERED																																																																																			NOVEL					0			1	4.850367	KEEP	9	1	31	27	936	GG	0.999997	0.800243	0			18	22	642	0	0	62.257467	17	60	587	92		0.514286	0.800245
DNM1P47	100216544	__UNKNOWN__	__UNKNOWN__	15	102299954	102299954	__UNKNOWN__	RNA	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:102299954A>G	ENST00000561463.1	+	0	8000									DNM1 pseudogene 47	NA		NA									NA						TCATCTTCTCAGAGCTGCTGT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660	100216544			35200	pseudogene	pseudogene		NA		DNM1DN14@	NA		Standard	NG_009149	NG_009149	NA	Approved	DNM1DN14-3			OTTHUMG00000172265	ENST00000561463.1:	chr15.hg19:g.102299954A>G		NA		hg19		0.02	-0.245629	CTCxGAG	COVERED																																																																																			NOVEL	DNM1P47-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417589.1	2	11.132463	KEEP	21	0	0	37	1140	AA	0.999931	0.641303	0		+	3	22	99	0	0	7.195154	25	33	906	98	ENST00000561463.1	0.107143	0.641347
DNM1P47	100216544	__UNKNOWN__	__UNKNOWN__	15	102304515	102304515	__UNKNOWN__	RNA	SNP	G	G	A	rs111318154		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:102304515G>A	ENST00000561463.1	+	0	12561									DNM1 pseudogene 47	NA		NA									NA						CAGGCACAGCGGTGTGACGAG	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660	100216544			35200	pseudogene	pseudogene		NA		DNM1DN14@	NA		Standard	NG_009149	NG_009149	NA	Approved	DNM1DN14-3			OTTHUMG00000172265	ENST00000561463.1:	chr15.hg19:g.102304515G>A		NA		hg19		0.02	-0.184224	AGCxGTG	COVERED																																																																																			NOVEL	DNM1P47-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417589.1	0	3.912654	KEEP	2	0	0	13	449	GG	0.993634	0.454842	0		+	3	22	112	0	0	8.891484	18	48	633	47	ENST00000561463.1	0.142857	0.457757
DNM1P47	100216544	__UNKNOWN__	__UNKNOWN__	15	102306253	102306253	__UNKNOWN__	RNA	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:102306253G>C	ENST00000561463.1	+	0	13180									DNM1 pseudogene 47	NA		NA									NA						AGGGCCGCCGGAGCCCCCAGG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660	100216544			35200	pseudogene	pseudogene		NA		DNM1DN14@	NA		Standard	NG_009149	NG_009149	NA	Approved	DNM1DN14-3			OTTHUMG00000172265	ENST00000561463.1:	chr15.hg19:g.102306253G>C		NA		hg19		0.02	-0.070186	CCGxAGC	UNCOVERED																																																																																			NOVEL	DNM1P47-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417589.1	0	2.708681	KEEP	0	0	0	9	305	GG	0.99254	0.053733	0		+	2	49	81	0	0	7.100574	6	60	223	19	ENST00000561463.1	0.25	0.054137
WASH3P	374666	__UNKNOWN__	__UNKNOWN__	15	102516714	102516714	__UNKNOWN__	RNA	SNP	T	T	G	rs199625471		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:102516714T>G	ENST00000557932.1	+	0	1662							C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene	NA		NA			Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						GTTCTTCTCTTAAGAGGCTTC	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596	374666		WAS protein homologs	24362	pseudogene	pseudogene		NA	family with sequence similarity 39, member D pseudogene	FAM39DP	NA	11701968, 18159949	Standard	NM_199163	NR_003659	NA	Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275	ENST00000557932.1:	chr15.hg19:g.102516714T>G		NA		hg19		0.02	-0.210554	TCTxAAG	UNCOVERED																																																																																			NOVEL	WASH3P-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417608.1	1	3.008116	KEEP	10	0	0	10	284	TT	0	0	0		+	5	47	187	0	0	15.752061	19	48	677	46	ENST00000557932.1	0.208333	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	102516734	102516734	__UNKNOWN__	IGR	SNP	C	C	T	rs200346477		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr15:102516734C>T			NA	NA				WASH3P (3 upstream) : DDX11L9 (26 downstream)						NA		NA									NA						CCAGAGAAAACGGCACACCAA	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.102516734C>T		NA		hg19		0.02	-0.210529	AAAxGGC	UNCOVERED																																																																																			NOVEL					0			0	3.310309	KEEP	20	0	0	11	376	CC	0	0	0			6	47	206	0	0	17.601844	18	48	646	54		0.25	0.522161
CAPN15	6650	__UNKNOWN__	__UNKNOWN__	16	603676	603676	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:603676C>T	ENST00000219611.2	+	0	3784				LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	NA		NA			proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)				NA						CCCCCGCCCCCCTCCTTCCCC	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326	6650			11182	protein-coding gene	gene with protein product		603267	small optic lobes (Drosophila) homolog, small optic lobes homolog (Drosophila)	SOLH	NA	9722942	Standard	NM_005632	NM_005632	NA	Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.*160C>T	chr16.hg19:g.603676C>T		NA	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	hg19	CCDS10410.1	0.02	10.101996	CCCxCTC	COVERED																																																																																			NOVEL	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239271.1	6	38.021952	KEEP	0	1	21	134	4374	CC	1	1	0		+	121	60	4217	1	0	414.701725	96	60	3466	442	ENST00000219611.2	0.557604	1
PDPK1	5170	__UNKNOWN__	__UNKNOWN__	16	2652643	2652643	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:2652643T>C	ENST00000342085.4	+	0	6695					NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	TTACAGTATTTAGAGCTGCTG	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						113	93	99	NA		NA	NA	16		NA											NA				2652643		692	1591	2283	SO:0001624	3_prime_UTR_variant			AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992	5170			8816	protein-coding gene	gene with protein product	PkB kinase	605213			NA	9094314, 9445477	Standard		NM_002613	NA	Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.*4875T>C	chr16.hg19:g.2652643T>C		NA	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	hg19	CCDS10472.1	0.02	15.567366	ATTxAGA	COVERED																																																																																			NOVEL	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250831.3	6	15.276469	KEEP	0	1	38	64	1914	TT	1	1	0		+	160	60	6111	1	0	586.191902	177	60	6322	449	ENST00000342085.4	0.474777	1
ZSCAN10	84891	__UNKNOWN__	__UNKNOWN__	16	3141573	3141573	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:3141573G>A	ENST00000252463.2	-	4	677	c.590C>T	c.(589-591)cCa>cTa	p.P197L	ZSCAN10_ENST00000575108.1_5'UTR|ZSCAN10_ENST00000538082.2_Missense_Mutation_p.P115L|ZSCAN10_ENST00000572548.1_3'UTR	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	197		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(3)|endometrium(3)|kidney(1)|lung(8)|ovary(2)|prostate(1)|skin(4)|urinary_tract(1)	24						CTTATTCTCTGGCACATCCTC	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						83	82	82	NA		NA	NA	16		NA											NA				3141573		2197	4300	6497	SO:0001583	missense			AA206569	CCDS10493.1, CCDS61813.1, CCDS61814.1	16p13.3	2013-01-08	2007-02-20	2007-02-20		ENSG00000130182	84891		-, Zinc fingers, C2H2-type	12997	protein-coding gene	gene with protein product		NA	zinc finger protein 206	ZNF206	NA	9653642	Standard	NM_032805	NM_032805	NA	Approved		uc002ctv.1	Q96SZ4		ENST00000252463.2:c.590C>T	chr16.hg19:g.3141573G>A	ENSP00000252463:p.Pro197Leu	NA	B3KQD3|H0YFS6|Q1WWM2	hg19	CCDS10493.1	0.02	2.579397	TCTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.54	1.969013	0.34754	.	.	ENSG00000130182	ENST00000538082;ENST00000252463	T	0.05580	3.42	4.65	2.57	0.30868	.	0.503256	0.16962	N	0.192473	T	0.02970	0.0088	N	0.08118	0	0.09310	N	1	B;B	0.18461	0.028;0.028	B;B	0.16722	0.016;0.016	T	0.45469	-0.9259	10	0.22109	T	0.4	-5.1942	6.0823	0.19948	0.1039:0.0:0.7061:0.1901	.	130;197	Q1WWM2;Q96SZ4	.;ZSC10_HUMAN	L	130;197	ENSP00000252463:P197L	ENSP00000252463:P197L	P	-	2	0	ZSCAN10	3081574	0.014000	0.17966	0.097000	0.21041	0.228000	0.25075	0.508000	0.22692	1.045000	0.40225	0.561000	0.74099	CCA	NOVEL	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000437124.2	0	4.514048	KEEP	0	0	0	15	518	GG	0.99649	0.980707	0		-	30	60	1086	0	0	105.38473	28	60	1090	92	ENST00000252463.2	0.517241	0.984161
CREBBP	1387	__UNKNOWN__	__UNKNOWN__	16	3824775	3824775	__UNKNOWN__	Intron	SNP	G	G	A	rs540869886	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:3824775G>A	ENST00000262367.5	-	12	2968				CREBBP_ENST00000382070.3_Intron	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	NA		NA			cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AAACTCTTAAGTAAAATAAGA	0.368	NA	NA	T, N, F, Mis, O	MLL, MORF, RUNXBP2	ALL, AML, DLBCL, B-NHL 		Rubinstein-Taybi syndrome						G|||	2	0.000399361	0	0	5008	,	,	NA	23119	0.002	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339	1387		Chromatin-modifying enzymes / K-acetyltransferases	2348	protein-coding gene	gene with protein product		600140	Rubinstein-Taybi syndrome	RSTS	NA	8413673	Standard	NM_004380	NM_001079846	NA	Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.2159-81C>T	chr16.hg19:g.3824775G>A		NA	D3DUC9|O00147|Q16376|Q4LE28	hg19	CCDS10509.1	0.02	2.317249	TAAxTAA	COVERED																																																																																			NOVEL	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251591.2	1	8.727949	KEEP	0	0	0	29	1024	GG	0.999997	0.9937	0		-	9	60	325	0	0	25.516422	55	60	2074	108	ENST00000262367.5	0.140625	0.993703
SRL	6345	__UNKNOWN__	__UNKNOWN__	16	4254426	4254426	__UNKNOWN__	Intron	SNP	C	C	T	rs74003219	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:4254426C>T	ENST00000399609.3	-	2	176				SRL_ENST00000537996.1_Intron	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	NA		NA				sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						CCCCGGCCTCCAAGATACAGC	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739	6345			11295	protein-coding gene	gene with protein product		604992			NA	2762314	Standard	XM_064152	NM_001098814	NA	Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.163+107G>A	chr16.hg19:g.4254426C>T		NA		hg19	CCDS42113.1	0.02	2.49072	CTCxAAG	COVERED																																																																																			NOVEL	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438087.1	1	6.620713	KEEP	0	0	0	22	725	CC	0.999879	0.995566	0		-	4	60	166	0	0	12.126935	56	60	1932	92	ENST00000399609.3	0.066667	0.995687
NDE1	54820	__UNKNOWN__	__UNKNOWN__	16	15758530	15758530	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:15758530C>T	ENST00000396355.1	+	3	783				NDE1_ENST00000396354.1_Intron|NDE1_ENST00000396353.2_Intron	NM_001143979.1	NP_001137451.1	Q9NXR1	NDE1_HUMAN	nudE neurodevelopment protein 1	NA		NA			centrosome duplication (GO:0051298)|cerebral cortex development (GO:0021987)|establishment of chromosome localization (GO:0051303)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuroblast proliferation (GO:0007405)|neuron migration (GO:0001764)|vesicle transport along microtubule (GO:0047496)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole centrosome (GO:0031616)	microtubule binding (GO:0008017)			endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13						TTTTTTTTTTCTGTTAAAGGG	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF124431	CCDS10564.1	16p13.11	2013-08-06	2013-08-06		ENSG00000072864	ENSG00000072864	54820			17619	protein-coding gene	gene with protein product		609449	nudE nuclear distribution gene E homolog 1 (A. nidulans), nudE nuclear distribution E homolog 1 (A. nidulans)		NA	10940388, 12427674	Standard	NM_017668	NM_017668	NA	Approved	nudE, FLJ20101, NDE	uc002dds.3	Q9NXR1	OTTHUMG00000129885	ENST00000396355.1:c.-43-63C>T	chr16.hg19:g.15758530C>T		NA	Q49AQ2	hg19	CCDS10564.1	0.02	1.965605	TTTxTGT	COVERED																																																																																			NOVEL	NDE1-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252133.1	2	3.668182	KEEP	0	3	36	26	686	CC	0.999997	0.999997	0		+	14	60	208	1	0	8.937984	126	60	3413	218	ENST00000396355.1	0.1	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	18937995	18937995	__UNKNOWN__	IGR	SNP	C	C	T	rs150660539		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:18937995C>T			NA	NA				SMG1 (219 upstream) : CTD-2288F12.1 (189 downstream)						NA		NA									NA						TTCTCCCAAACGCTTCCCGGA	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.18937995C>T		NA		hg19		0.02	-0.412311	AAAxGCT	COVERED																																																																																			NOVEL					0			1	5.385735	KEEP	1	2	60	39	1338	CC	1	0.941741	0			3	27	114	0	0	7.987094	44	60	1584	115		0.06383	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	20729278	20729278	__UNKNOWN__	IGR	SNP	G	G	A	rs57719481		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:20729278G>A			NA	NA				ACSM1 (20212 upstream) : THUMPD1 (15707 downstream)						NA		NA									NA						aagaggaagaggaagaagaag	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.20729278G>A		NA		hg19		0.02	-0.078948	AGAxGAA	UNCOVERED																																																																																			NOVEL					0			7	3.002433	KEEP	4	0	0	10	344	GG	0.99257	0.076761	0			2	40	76	0	0	6.484053	7	60	243	22		0.222222	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	21396929	21396929	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:21396929A>T			NA	NA				CRYM-AS1 (67017 upstream) : NPIPB3 (16628 downstream)						NA		NA									NA						ACCAACATTAACTCATTTGAT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						72	65	67	NA		NA	NA	16		NA											NA				21396929		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.21396929A>T		NA		hg19		0.02	9.753841	TTAxCTC	COVERED																																																																																			NOVEL					0			1	3.301314	KEEP	0	3	91	43	1309	AA	1	1	0			14	42	487	0	0	30.934293	281	61	10033	461		0.047458	1
RRN3P2	653390	__UNKNOWN__	__UNKNOWN__	16	29110458	29110458	__UNKNOWN__	RNA	SNP	T	T	C	rs561841139		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:29110458T>C	ENST00000564580.1	+	0	1131							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2	NA		NA						p.W375R(25)			NA						GAATTTTGAGTGGATAGTGAT	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				25	Substitution - Missense(25)	endometrium(19)|kidney(4)|prostate(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472	653390			37619	pseudogene	pseudogene		NA			NA		Standard	NR_003369	NR_003369	NA	Approved		uc002dsf.4	A6NIE6		ENST00000564580.1:	chr16.hg19:g.29110458T>C		NA		hg19		0.02	4.47962	GAGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	N	5.632	0.301362	0.10678	.	.	ENSG00000103472	ENST00000427965	.	.	.	1.93	1.93	0.25924	.	0.000000	0.64402	N	0.000001	T	0.11239	0.0274	.	.	.	.	.	.	.	.	.	.	.	.	T	0.29701	-1.0003	5	0.02654	T	1	.	2.7527	0.05285	0.2724:0.5536:0.0:0.174	.	.	.	.	R	375	.	ENSP00000398611:W375R	W	+	1	0	AC009093.1	29017959	1.000000	0.71417	0.564000	0.28396	0.423000	0.31445	3.439000	0.52878	0.163000	0.19507	-1.160000	0.01791	TGG	NOVEL	RRN3P2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000433243.1	6	5.083825	KEEP	0	2	69	41	1258	TT	1	0.999999	0		+	5	21	180	0	0	11.278326	120	60	4318	236	ENST00000564580.1	0.04	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32190787	32190787	__UNKNOWN__	IGR	SNP	T	T	C	rs62042697		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:32190787T>C			NA	NA				HERC2P4 (7899 upstream) : RP11-17M15.1 (8866 downstream)						NA		NA									NA						TGACAACAACTGCCGTTTGTT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32190787T>C		NA		hg19		0.02	-0.377179	AACxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.213	-1.034729	0.02029	.	.	ENSG00000230267	ENST00000433784	.	.	.	2.36	-2.93	0.05598	.	.	.	.	.	T	0.11196	0.0273	.	.	.	.	.	.	.	.	.	.	.	.	T	0.32640	-0.9899	4	0.02654	T	1	.	4.3383	0.11097	0.1491:0.3104:0.0:0.5406	.	.	.	.	R	132	.	ENSP00000402538:Q132R	Q	-	2	0	AC133485.1	32098288	0.000000	0.05858	0.103000	0.21229	0.007000	0.05969	-2.269000	0.01168	-1.415000	0.02022	-1.033000	0.02402	CAG	NOVEL					0			0	2.405415	KEEP	0	0	0	8	222	TT	0.99257	0.902315	0			5	47	180	0	0	13.675554	38	60	1359	57		0.116279	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32403458	32403458	__UNKNOWN__	IGR	SNP	T	T	C	rs80131538		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:32403458T>C			NA	NA				RP11-17M15.2 (81582 upstream) : RP11-626K17.3 (62474 downstream)						NA		NA									NA						GCTGCTGTTTTTTCCCACTTC	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32403458T>C		NA		hg19		0.02	5.227062	TTTxTTC	COVERED																																																																																			NOVEL					0			2	3.345035	KEEP	5	1	34	23	738	TT	0.999892	0.999883	0			15	49	584	0	0	46.659649	93	60	3343	152		0.138889	0.999991
RP11-67H24.2	0	__UNKNOWN__	__UNKNOWN__	16	32833793	32833793	__UNKNOWN__	lincRNA	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:32833793C>G	ENST00000569859.1	+	0	373										NA		NA									NA						ttccttccctcatttcctcct	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000569859.1:	chr16.hg19:g.32833793C>G		NA		hg19		0.02	-0.166695	CCTxATT	UNCOVERED																																																																																			NOVEL	RP11-67H24.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000432377.1	6	3.00995	KEEP	5	0	0	10	365	CC	0	0	0		+	2	31	82	0	0	6.806228	10	60	389	42	ENST00000569859.1	0.166667	0.353947
SLC6A10P	386757	__UNKNOWN__	__UNKNOWN__	16	32889454	32889454	__UNKNOWN__	RNA	SNP	G	G	T	rs62044740		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:32889454G>T	ENST00000330048.5	-	0	3472					NR_003083.2				solute carrier family 6 (neurotransmitter transporter), member 10, pseudogene	NA		NA									NA						CTCTCAAGTTGTTATAAAATG	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U41163		16p11.2	2013-07-19	2013-07-19	2013-07-19	ENSG00000214617	ENSG00000214617	386757		Solute carriers	11043	pseudogene	pseudogene	creatine transporter-2	NA	solute carrier family 6 (neurotransmitter transporter, creatine), member 10	SLC6A10	NA	9154116	Standard		NR_003083	NA	Approved	CT-2	uc002edh.1		OTTHUMG00000132481	ENST00000330048.5:	chr16.hg19:g.32889454G>T		NA		hg19		0.02	16.817852	GTTxTTA	COVERED																																																																																			NOVEL	SLC6A10P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000432081.2	3	4.517349	KEEP	23	3	88	46	1619	GG	1	1	0		-	19	27	674	0	0	43.119997	389	60	14579	546	ENST00000330048.5	0.046569	1
SLC6A10P	386757	__UNKNOWN__	__UNKNOWN__	16	32890950	32890950	__UNKNOWN__	RNA	SNP	A	A	G	rs151263854		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:32890950A>G	ENST00000330048.5	-	0	3016					NR_003083.2				solute carrier family 6 (neurotransmitter transporter), member 10, pseudogene	NA		NA									NA						ATACACCCAGACCACCACCAC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					U41163		16p11.2	2013-07-19	2013-07-19	2013-07-19	ENSG00000214617	ENSG00000214617	386757		Solute carriers	11043	pseudogene	pseudogene	creatine transporter-2	NA	solute carrier family 6 (neurotransmitter transporter, creatine), member 10	SLC6A10	NA	9154116	Standard		NR_003083	NA	Approved	CT-2	uc002edh.1		OTTHUMG00000132481	ENST00000330048.5:	chr16.hg19:g.32890950A>G		NA		hg19		0.02	10.661903	CAGxCCA	COVERED																																																																																			NOVEL	SLC6A10P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000432081.2	3	5.617728	KEEP	15	6	186	84	2375	AA	1	1	0		-	10	47	365	0	0	22.894487	249	60	8505	419	ENST00000330048.5	0.03861	1
TP53TG3C	653550	__UNKNOWN__	__UNKNOWN__	16	33238000	33238000	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33238000C>A	ENST00000398667.4	+	2	1821							Q9ULZ0	T53G3_HUMAN	TP53 target 3C	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)					NA						ggctggctgactgggtggctt	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS58458.1	16p11.2	2012-01-12				ENSG00000205457	653550			42962	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001205259	XM_006721074	NA	Approved			Q9ULZ0		ENST00000398667.4:c.363-25683C>A	chr16.hg19:g.33238000C>A		NA	B2R5K6|Q4KN31|Q9ULY9	hg19		0.02	-0.087324	TGAxTGG	UNCOVERED																																																																																			NOVEL	TP53TG3C-202	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding		5	2.398008	KEEP	0	0	0	8	259	CC	0.99257	0.09898	0		+	3	60	86	0	1	7.942984	4	48	151	21	ENST00000398667.4	0.428571	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33294200	33294200	__UNKNOWN__	IGR	SNP	C	C	G	rs7498386		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33294200C>G			NA	NA				RP11-1437A8.5 (20044 upstream) : RP11-23E10.3 (42082 downstream)						NA		NA									NA						ggctggctggcaggcttggct	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33294200C>G		NA		hg19		0.02	-0.219318	TGGxAGG	COVERED																																																																																			NOVEL					0			7	4.504438	KEEP	2	0	0	15	467	CC	0.99649	0.550947	0			3	60	111	0	2	9.372571	11	60	380	46		0.214286	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33410777	33410777	__UNKNOWN__	IGR	SNP	G	G	T	rs74905055		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33410777G>T			NA	NA				RP11-23E10.4 (43964 upstream) : BMS1P8 (86385 downstream)						NA		NA									NA						ATAAATGACCGAAGGGGACAG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33410777G>T		NA		hg19		0.02	17.763571	ACCxAAG	COVERED																																																																																			NOVEL					0			4	4.920997	KEEP	12	3	99	51	1736	GG	1	1	0			15	40	552	0	0	33.841357	433	60	16114	630		0.033482	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33410780	33410780	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33410780G>T			NA	NA				RP11-23E10.4 (43967 upstream) : BMS1P8 (86382 downstream)						NA		NA									NA						AATGACCGAAGGGGACAGCTC	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33410780G>T		NA		hg19		0.02	18.614491	GAAxGGG	COVERED																																																																																			NOVEL					0			4	4.420375	KEEP	12	3	101	50	1772	GG	1	1	0			17	40	650	0	0	41.828221	425	60	15805	617		0.038462	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33544213	33544213	__UNKNOWN__	IGR	SNP	G	G	A	rs28592030	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33544213G>A			NA	NA				BMS1P8 (45121 upstream) : IGHV3OR16-12 (61017 downstream)						NA		NA									NA						TCTATCTTGAGTGTACATGAC	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33544213G>A		NA		hg19		0.02	2.071537	TGAxTGT	COVERED																																																																																			NOVEL					0			0	3.605894	KEEP	0	0	0	12	410	GG	0.993634	0.993529	0			4	60	137	0	0	11.079133	18	60	687	118		0.181818	0.999895
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33544292	33544292	__UNKNOWN__	IGR	SNP	A	A	G	rs12933436	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33544292A>G			NA	NA				BMS1P8 (45200 upstream) : IGHV3OR16-12 (60938 downstream)						NA		NA									NA						GGCTATGTTCAAAACAGAATC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33544292A>G		NA		hg19		0.02	4.056257	TTCxAAA	COVERED																																																																																			NOVEL					0			1	2.943508	KEEP	0	1	35	22	682	AA	0.999892	0.999892	0			6	60	223	0	0	14.910671	110	60	4051	214		0.051724	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33544302	33544302	__UNKNOWN__	IGR	SNP	C	C	G	rs2698634		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33544302C>G			NA	NA				BMS1P8 (45210 upstream) : IGHV3OR16-12 (60928 downstream)						NA		NA									NA						AAAACAGAATCTTTCTTGTCA	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33544302C>G		NA		hg19		0.02	4.981371	AATxTTT	COVERED																																																																																			NOVEL					0			1	2.745732	KEEP	0	1	37	22	802	CC	0.999892	0.999892	0			23	60	874	0	0	72.28428	104	60	4008	206		0.181102	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33661448	33661448	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33661448A>G			NA	NA				RP11-812E19.7 (117 upstream) : ARHGAP23P1 (77448 downstream)						NA		NA									NA						TTGTCTCTGGAGATGGTGAAT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33661448A>G		NA		hg19		0.02	4.94636	TGGxGAT	COVERED																																																																																			NOVEL					0			5	6.921059	KEEP	40	0	0	23	726	AA	0.995343	0.995343	0			65	48	2378	0	0	226.822339	75	48	2781	243		0.464286	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33741083	33741083	__UNKNOWN__	IGR	SNP	G	G	C	rs144847558		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33741083G>C			NA	NA				ARHGAP23P1 (1449 upstream) : RP11-812E19.3 (34295 downstream)						NA		NA									NA						CAAGGCCTCCGGCAGACTCCA	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33741083G>C		NA		hg19		0.02	5.886354	TCCxGCA	COVERED	266	0.12179487179487179	93	0.18902439024390244	30	0.08287292817679558	49	0.08566433566433566	94	0.12401055408970976	.	0.310	-0.968235	0.02232	.	.	ENSG00000226511	ENST00000450856	.	.	.	1.16	1.16	0.20824	.	.	.	.	.	T	0.00073	0.0002	.	.	.	.	.	.	.	.	.	.	.	.	T	0.12760	-1.0535	3	.	.	.	.	7.1189	0.25433	0.0:0.7143:0.2857:0.0	rs2549427	.	.	.	R	3	.	.	P	-	2	0	AC140658.1	33648584	0.081000	0.21417	0.312000	0.25196	0.134000	0.20937	-0.173000	0.09854	-0.283000	0.09115	-0.700000	0.03674	CCG	NOVEL					0			2	6.196149	KEEP	12	3	80	49	1619	GG	1	1	0			16	40	524	0	0	36.643302	163	50	5691	270		0.089385	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33934570	33934570	__UNKNOWN__	IGR	SNP	A	A	T	rs199701507		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33934570A>T			NA	NA				RP11-812E19.3 (156826 upstream) : AC136932.2 (11378 downstream)						NA		NA									NA						TGACCTTTGGACATCTCGTCT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33934570A>T		NA		hg19		0.02	4.469771	TGGxCAT	COVERED																																																																																			NOVEL					0			2	4.514215	KEEP	0	0	0	15	491	AA	0.99649	0.99649	0			4	49	145	0	0	10.856427	34	60	1222	188		0.105263	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33940265	33940265	__UNKNOWN__	IGR	SNP	A	A	G	rs76854017	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33940265A>G			NA	NA				RP11-812E19.3 (162521 upstream) : AC136932.2 (5683 downstream)						NA		NA									NA						CAATTCCACCATCCCAGCCAC	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33940265A>G		NA		hg19		0.02	19.084977	ACCxTCC	COVERED																																																																																			NOVEL					0			9	6.278797	KEEP	7	2	54	40	1124	AA	1	1	0			49	60	1743	0	0	140.732365	238	60	8101	549		0.170732	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33940348	33940348	__UNKNOWN__	IGR	SNP	A	A	G	rs146689645		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33940348A>G			NA	NA				RP11-812E19.3 (162604 upstream) : AC136932.2 (5600 downstream)						NA		NA									NA						ACTTGGAACAATTTCATGCTT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33940348A>G		NA		hg19		0.02	17.362991	ACAxTTT	COVERED																																																																																			NOVEL					0			13	5.716722	KEEP	0	0	0	19	587	AA	0.99986	0.99986	0			27	60	1025	0	0	77.643615	235	60	8433	388		0.103053	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33940664	33940664	__UNKNOWN__	IGR	SNP	G	G	A	rs79869205	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33940664G>A			NA	NA				RP11-812E19.3 (162920 upstream) : AC136932.2 (5284 downstream)						NA		NA									NA						ACAAACAATGGCAGTTACTAT	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33940664G>A		NA		hg19		0.02	36.846957	ATGxCAG	COVERED																																																																																			NOVEL					0			9	11.338073	KEEP	0	7	235	120	4317	GG	1	1	0			37	60	1337	0	0	94.238812	458	60	17365	1162		0.074747	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33941141	33941141	__UNKNOWN__	IGR	SNP	C	C	A	rs138676690		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33941141C>A			NA	NA				RP11-812E19.3 (163397 upstream) : AC136932.2 (4807 downstream)						NA		NA									NA						ATACAGTGAACTACAGAAAAA	0.318	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33941141C>A		NA		hg19		0.02	15.748378	GAAxTAC	COVERED																																																																																			NOVEL					0			6	6.088539	KEEP	3	2	59	41	1446	CC	1	1	0			19	48	662	0	0	47.274989	199	60	7411	474		0.087156	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33946320	33946320	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33946320T>A			NA	NA				AC136932.2 (299 upstream) : LINC00273 (14731 downstream)						NA		NA									NA						ggatttagaatattccataaa	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33946320T>A		NA		hg19		0.02	6.472237	GAAxATT	COVERED																																																																																			NOVEL					0			2	6.95085	KEEP	1	1	31	34	992	TT	0.999999	0.999999	0			5	55	186	0	0	12.864847	75	60	2813	265		0.0625	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33946493	33946493	__UNKNOWN__	IGR	SNP	C	C	T	rs10153106	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33946493C>T			NA	NA				AC136932.2 (472 upstream) : LINC00273 (14558 downstream)						NA		NA									NA						aggcacccaaccttcagcagc	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33946493C>T		NA		hg19		0.02	-0.393787	CAAxCTT	COVERED																																																																																			NOVEL					0			8	2.398015	KEEP	0	0	0	8	249	CC	0.99257	0.934744	0			5	60	149	0	0	12.077391	18	60	642	60		0.217391	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33947922	33947922	__UNKNOWN__	IGR	SNP	A	A	T	rs111854203		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33947922A>T			NA	NA				AC136932.2 (1901 upstream) : LINC00273 (13129 downstream)						NA		NA									NA						tggcatgatcatagctcactg	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33947922A>T		NA		hg19		0.02	-0.245439	ATCxTAG	COVERED																																																																																			NOVEL					0			8	3.911518	KEEP	0	0	0	13	401	AG	0.99649	0.639096	0			4	49	164	0	0	14.99619	8	60	277	60		0.333333	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33947926	33947926	__UNKNOWN__	IGR	SNP	C	C	T	rs7342697		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33947926C>T			NA	NA				AC136932.2 (1905 upstream) : LINC00273 (13125 downstream)						NA		NA									NA						atgatcatagctcactgcaac	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33947926C>T		NA		hg19		0.02	-0.245648	TAGxTCA	COVERED																																																																																			NOVEL					0			7	3.91289	KEEP	0	0	0	13	471	CC	0.994391	0.63775	0			4	60	145	0	0	12.770855	10	60	375	58		0.285714	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33950316	33950316	__UNKNOWN__	IGR	SNP	C	C	G	rs112095231	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33950316C>G			NA	NA				AC136932.2 (4295 upstream) : LINC00273 (10735 downstream)						NA		NA									NA						cccatcagaacctcttttctt	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33950316C>G		NA		hg19		0.02	2.141734	GAAxCTC	COVERED																																																																																			NOVEL					0			6	4.812665	KEEP	6	0	0	16	543	CC	0.99649	0.996114	0			3	60	121	0	0	11.725226	3	60	107	117		0.5	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33950352	33950352	__UNKNOWN__	IGR	SNP	C	C	T	rs4065499	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33950352C>T			NA	NA				AC136932.2 (4331 upstream) : LINC00273 (10699 downstream)						NA		NA									NA						acagATGAGACGCATGAGAGG	0.493	NA	NA											C|||	7	0.00139776	0	0	5008	,	,	NA	18525	0.001	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33950352C>T		NA		hg19		0.02	2.355733	AGAxGCA	UNCOVERED																																																																																			NOVEL					0			8	2.407827	KEEP	12	0	0	8	278	CC	0	0	0			4	49	151	0	0	14.932197	3	60	117	109		0.571429	0.997553
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33958900	33958900	__UNKNOWN__	IGR	SNP	C	C	A	rs111645276	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:33958900C>A			NA	NA				AC136932.2 (12879 upstream) : LINC00273 (2151 downstream)						NA		NA									NA						AGATCCAACCCTAAAATCTGG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33958900C>A		NA		hg19		0.02	-0.411902	ACCxTAA	COVERED																																																																																			NOVEL					0			4	2.708915	KEEP	1	0	0	9	327	CC	0.99254	0.934716	0			3	60	108	0	0	11.312506	1	19	9	66		0.75	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46386856	46386856	__UNKNOWN__	IGR	SNP	C	C	G	rs6422015|rs4250068	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46386856C>G			NA	NA				None (None upstream) : ANKRD26P1 (116396 downstream)						NA		NA									NA						cattggagtccacttagtgaa	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46386856C>G		NA		hg19		0.02	-0.184194	GTCxACT	UNCOVERED																																																																																			NOVEL					0			4	3.009731	KEEP	30	0	0	10	353	CC	0	0	0			4	49	133	0	0	10.76967	17	50	622	65		0.190476	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46387397	46387397	__UNKNOWN__	IGR	SNP	A	A	C	rs4468658		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46387397A>C			NA	NA				None (None upstream) : ANKRD26P1 (115855 downstream)						NA		NA									NA						cgatgattccatttgagcccg	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46387397A>C		NA		hg19		0.02	-0.333376	TCCxTTT	COVERED																																																																																			NOVEL					0			11	2.944036	KEEP	9	1	38	23	702	AA	0.999869	0.851873	0			3	43	106	0	0	7.70974	29	47	1063	93		0.09375	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46387554	46387554	__UNKNOWN__	IGR	SNP	G	G	T	rs28781625		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46387554G>T			NA	NA				None (None upstream) : ANKRD26P1 (115698 downstream)						NA		NA									NA						gtccattttaggatttgattc	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46387554G>T		NA		hg19		0.02	-0.175463	TTAxGAT	COVERED																																																																																			NOVEL					0			4	3.307256	KEEP	8	0	0	11	379	GG	0.99257	0.384528	0			4	23	151	0	0	12.662305	16	46	587	45		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46389721	46389721	__UNKNOWN__	IGR	SNP	A	A	T	rs4597497		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46389721A>T			NA	NA				None (None upstream) : ANKRD26P1 (113531 downstream)						NA		NA									NA						attccattcgattctattcaa	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46389721A>T		NA		hg19		0.02	-0.377234	TCGxTTC	COVERED																																																																																			NOVEL					0			5	6.016516	KEEP	32	0	0	20	605	AA	0.992708	0.911475	0			3	24	108	0	0	7.539046	39	25	1436	103		0.071429	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391233	46391233	__UNKNOWN__	IGR	SNP	G	G	C	rs4353504		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391233G>C			NA	NA				None (None upstream) : ANKRD26P1 (112019 downstream)						NA		NA									NA						gattccatttgattccattca	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391233G>C		NA		hg19		0.02	-0.307069	TTTxATT	UNCOVERED																																																																																			NOVEL					0			3	5.417495	KEEP	16	0	0	18	630	GG	0	0	0			3	47	117	0	0	8.725184	31	50	1176	69		0.088235	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391298	46391298	__UNKNOWN__	IGR	SNP	T	T	C	rs4605190	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391298T>C			NA	NA				None (None upstream) : ANKRD26P1 (111954 downstream)						NA		NA									NA						attcaatgattatccccttag	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391298T>C		NA		hg19		0.02	-0.429883	GATxATC	COVERED																																																																																			NOVEL					0			5	2.540242	KEEP	11	1	33	20	586	TT	0.99986	0.959724	0			5	49	198	0	0	15.269005	42	60	1510	96		0.106383	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391452	46391452	__UNKNOWN__	IGR	SNP	G	G	A	rs4232883		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391452G>A			NA	NA				None (None upstream) : ANKRD26P1 (111800 downstream)						NA		NA									NA						gattccattcgattgcattcg	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391452G>A		NA		hg19		0.02	1.930031	TTCxATT	COVERED																																																																																			NOVEL					0			10	15.950725	KEEP	13	0	0	53	1810	GG	1	0.998695	0			5	31	187	0	0	13.575296	56	48	2004	176		0.081967	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391488	46391488	__UNKNOWN__	IGR	SNP	G	G	A	rs4322693|rs67119531	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391488G>A			NA	NA				None (None upstream) : ANKRD26P1 (111764 downstream)						NA		NA									NA						tccattcaacgatgattccat	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391488G>A		NA		hg19		0.02	2.2592	AACxATG	COVERED																																																																																			NOVEL					0			14	7.694468	KEEP	6	2	67	49	1644	GG	1	0.999487	0			4	47	146	0	0	10.040386	59	48	2123	168		0.063492	0.999487
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391501	46391501	__UNKNOWN__	IGR	SNP	G	G	C	rs4452108		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391501G>C			NA	NA				None (None upstream) : ANKRD26P1 (111751 downstream)						NA		NA									NA						gattccattcgagtccattcg	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391501G>C		NA		hg19		0.02	2.15932	TTCxAGT	COVERED																																																																																			NOVEL					0			14	7.194886	KEEP	9	2	72	49	1648	GG	1	0.999487	0			5	46	188	0	0	13.463379	62	48	2211	168		0.074627	0.999487
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391651	46391651	__UNKNOWN__	IGR	SNP	A	A	G	rs61323778|rs4103653|rs146432508		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391651A>G			NA	NA				None (None upstream) : ANKRD26P1 (111601 downstream)						NA		NA									NA						attcgtgtccattcggtgatt	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391651A>G		NA		hg19		0.02	2.320589	TCCxTTC	COVERED																																																																																			NOVEL					0			16	3.310822	KEEP	3	3	103	47	1424	AA	1	0.998696	0			7	27	242	0	0	17.441765	68	50	2532	167		0.093333	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391717	46391717	__UNKNOWN__	IGR	SNP	A	A	T	rs61538226|rs60912433|rs61203268|rs4246390		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391717A>T			NA	NA				None (None upstream) : ANKRD26P1 (111535 downstream)						NA		NA									NA						gattccattcaattccattcg	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391717A>T		NA		hg19		0.02	-0.333374	TTCxATT	COVERED																																																																																			NOVEL					0			9	6.952266	KEEP	9	1	28	33	1000	AA	0.999997	0.851982	0			3	45	111	0	0	8.047646	33	48	1169	96		0.083333	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391857	46391857	__UNKNOWN__	IGR	SNP	C	C	G	rs4967673		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391857C>G			NA	NA				None (None upstream) : ANKRD26P1 (111395 downstream)						NA		NA									NA						ttcgatgattccattcgagtc	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391857C>G		NA		hg19		0.02	-0.368477	ATTxCAT	COVERED																																																																																			NOVEL					0			5	7.207173	KEEP	14	0	0	24	787	CC	0.999366	0.898744	0			3	47	111	0	0	7.871363	38	60	1409	90		0.073171	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46391911	46391911	__UNKNOWN__	IGR	SNP	G	G	T	rs4553793		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46391911G>T			NA	NA				None (None upstream) : ANKRD26P1 (111341 downstream)						NA		NA									NA						tgattacattggattccgttc	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46391911G>T		NA		hg19		0.02	2.097966	ATTxGAT	COVERED																																																																																			NOVEL					0			11	10.534329	KEEP	3	0	0	35	1246	GG	0.999998	0.999833	0			4	49	152	0	0	10.043875	84	60	3125	163		0.045455	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46392009	46392009	__UNKNOWN__	IGR	SNP	C	C	T	rs4372866	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46392009C>T			NA	NA				None (None upstream) : ANKRD26P1 (111243 downstream)						NA		NA									NA						ctattcgattctcttcgatgg	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46392009C>T		NA		hg19		0.02	4.405027	ATTxTCT	COVERED																																																																																			NOVEL					0			18	7.6546	KEEP	1	1	33	37	1305	CC	1	0.999999	0			8	60	287	0	0	19.847113	109	60	4061	198		0.068376	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46392210	46392210	__UNKNOWN__	IGR	SNP	A	A	T	rs4232887|rs375905212	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46392210A>T			NA	NA				None (None upstream) : ANKRD26P1 (111042 downstream)						NA		NA									NA						attcgattccattcgatgatt	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46392210A>T		NA		hg19		0.02	2.096753	TCCxTTC	COVERED																																																																																			NOVEL					0			4	2.475163	KEEP	55	2	68	32	968	AA	0.999863	0.979392	0			7	40	243	0	0	18.597041	47	60	1731	168		0.12963	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46393128	46393128	__UNKNOWN__	IGR	SNP	T	T	G	rs28827236	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46393128T>G			NA	NA				None (None upstream) : ANKRD26P1 (110124 downstream)						NA		NA									NA						cgattccatttgatgatttca	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46393128T>G		NA		hg19		0.02	-0.324558	ATTxGAT	COVERED																																																																																			NOVEL					0			13	6.620294	KEEP	6	0	0	22	698	CT	0.999869	0.835607	0			3	49	114	1	0	8.50844	29	50	1043	88		0.09375	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46395251	46395251	__UNKNOWN__	IGR	SNP	G	G	C	rs4292070	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46395251G>C			NA	NA				None (None upstream) : ANKRD26P1 (108001 downstream)						NA		NA									NA						tattccattagattccattcg	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46395251G>C		NA		hg19		0.02	1.994786	TTAxATT	COVERED																																																																																			NOVEL					0			5	14.145447	KEEP	11	0	0	47	1629	GG	1	0.99911	0			7	42	255	0	0	18.655534	70	48	2631	161		0.090909	0.99911
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46396781	46396781	__UNKNOWN__	IGR	SNP	C	C	T	rs4407222		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46396781C>T			NA	NA				None (None upstream) : ANKRD26P1 (106471 downstream)						NA		NA									NA						cgactccattcgatgattcca	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46396781C>T		NA		hg19		0.02	-0.175454	ATTxGAT	COVERED																																																																																			NOVEL					0			2	3.009668	KEEP	2	0	0	10	338	CC	0.99254	0.384517	0			4	49	147	0	0	12.701237	12	54	417	42		0.25	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46399506	46399506	__UNKNOWN__	IGR	SNP	G	G	C	rs146160236		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46399506G>C			NA	NA				None (None upstream) : ANKRD26P1 (103746 downstream)						NA		NA									NA						tattccatttgatgatgattc	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46399506G>C		NA		hg19		0.02	-0.254427	TTTxATG	UNCOVERED																																																																																			NOVEL					0			6	4.514532	KEEP	27	0	0	15	520	GG	0	0	0			5	24	189	0	0	15.667249	22	28	830	68		0.185185	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46400059	46400059	__UNKNOWN__	IGR	SNP	G	G	A	rs4271612		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46400059G>A			NA	NA				None (None upstream) : ANKRD26P1 (103193 downstream)						NA		NA									NA						attccattcagttccattcga	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46400059G>A		NA		hg19		0.02	-0.421115	TCAxTTC	COVERED																																																																																			NOVEL					0			8	3.045999	KEEP	1	1	34	22	820	GG	0.999879	0.948287	0			4	36	146	0	0	10.60748	42	60	1597	98		0.086957	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46401949	46401949	__UNKNOWN__	IGR	SNP	G	G	T	rs59196308|rs7188365		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46401949G>T			NA	NA				None (None upstream) : ANKRD26P1 (101303 downstream)						NA		NA									NA						gattccattcgattccattcg	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46401949G>T		NA		hg19		0.02	-0.254415	TTCxATT	UNCOVERED																																																																																			NOVEL					0			7	6.621088	KEEP	39	0	0	22	745	GG	0	0	0			3	25	108	0	0	8.09157	25	27	898	91		0.107143	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46403570	46403570	__UNKNOWN__	IGR	SNP	A	A	G	rs11247431	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46403570A>G			NA	NA				None (None upstream) : ANKRD26P1 (99682 downstream)						NA		NA									NA						attcgtgttcattcggtgatt	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46403570A>G		NA		hg19		0.02	-0.219326	TTCxTTC	COVERED																																																																																			NOVEL					0			1	3.007686	KEEP	2	0	0	10	292	AA	0.99254	0.548763	0			3	40	103	0	0	7.864295	20	40	734	36		0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46403717	46403717	__UNKNOWN__	IGR	SNP	A	A	T	rs150682234|rs6422043|rs71220399		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46403717A>T			NA	NA				None (None upstream) : ANKRD26P1 (99535 downstream)						NA		NA									NA						attcgattccattcgacgatt	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46403717A>T		NA		hg19		0.02	4.375378	TCCxTTC	COVERED																																																																																			NOVEL					0			16	9.286292	KEEP	6	2	60	52	1569	AA	1	0.999996	0			7	60	260	1	0	18.114079	100	60	3707	226		0.065421	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46405120	46405120	__UNKNOWN__	IGR	SNP	C	C	G	rs4380210	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46405120C>G			NA	NA				None (None upstream) : ANKRD26P1 (98132 downstream)						NA		NA									NA						cgattccattcgataatgatt	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46405120C>G		NA		hg19		0.02	2.087918	ATTxGAT	COVERED																																																																																			NOVEL					0			5	6.048076	KEEP	4	1	5	22	753	CC	0.999869	0.981827	0			6	55	223	0	0	17.309507	42	60	1513	116		0.125	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46405873	46405873	__UNKNOWN__	IGR	SNP	T	T	C	rs149627354|rs7198709		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46405873T>C			NA	NA				None (None upstream) : ANKRD26P1 (97379 downstream)						NA		NA									NA						atgattcctttcgattccatt	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46405873T>C		NA		hg19		0.02	2.425863	CTTxCGA	COVERED																																																																																			NOVEL					0			6	3.14475	KEEP	28	1	36	23	736	TT	0.99649	0.989441	0			8	46	312	0	0	24.663602	54	47	1964	151		0.129032	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46405920	46405920	__UNKNOWN__	IGR	SNP	C	C	A	rs6598649		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46405920C>A			NA	NA				None (None upstream) : ANKRD26P1 (97332 downstream)						NA		NA									NA						caatcattCCCTTTGATTCCA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46405920C>A		NA		hg19		0.02	2.087903	TCCxTTT	COVERED																																																																																			NOVEL					0			3	2.340233	KEEP	16	1	26	17	593	CC	0.99649	0.978509	0			6	45	224	0	0	17.03234	49	47	1820	115		0.109091	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46406575	46406575	__UNKNOWN__	IGR	SNP	G	G	T	rs4453526	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46406575G>T			NA	NA				None (None upstream) : ANKRD26P1 (96677 downstream)						NA		NA									NA						atgatttcctgtgattccctt	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46406575G>T		NA		hg19		0.02	-0.333374	CCTxTGA	COVERED																																																																																			NOVEL					0			6	6.019902	KEEP	8	0	0	20	730	GG	0.999366	0.851444	0			4	24	143	0	0	11.093124	26	48	968	76		0.133333	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46406785	46406785	__UNKNOWN__	IGR	SNP	A	A	G	rs7188643		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46406785A>G			NA	NA				None (None upstream) : ANKRD26P1 (96467 downstream)						NA		NA									NA						attcgtgtccattcgatgatt	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46406785A>G		NA		hg19		0.02	-0.42091	TCCxTTC	COVERED																																																																																			NOVEL					0			10	9.461081	KEEP	77	1	36	44	1345	AA	0.994391	0.943082	0			3	40	99	0	0	6.578125	41	40	1479	166		0.068182	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46407470	46407470	__UNKNOWN__	IGR	SNP	G	G	T	rs376985980|rs4459570		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46407470G>T			NA	NA				None (None upstream) : ANKRD26P1 (95782 downstream)						NA		NA									NA						gattctatttgattcaattgg	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46407470G>T		NA		hg19		0.02	-0.289509	TTTxATT	UNCOVERED																																																																																			NOVEL					0			1	2.708576	KEEP	10	0	0	9	312	GG	0	0	0			3	47	107	2	0	7.808486	29	52	1068	61		0.09375	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46407668	46407668	__UNKNOWN__	IGR	SNP	C	C	T	rs4249141		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46407668C>T			NA	NA				None (None upstream) : ANKRD26P1 (95584 downstream)						NA		NA									NA						tgattccattcgattccattt	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46407668C>T		NA		hg19		0.02	-0.324353	ATTxGAT	COVERED																																																																																			NOVEL					0			9	6.655124	KEEP	8	1	28	32	1082	CC	0.999997	0.835713	0			3	46	109	0	0	7.967501	30	47	1071	94		0.090909	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46408513	46408513	__UNKNOWN__	IGR	SNP	A	A	C	rs4451975	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46408513A>C			NA	NA				None (None upstream) : ANKRD26P1 (94739 downstream)						NA		NA									NA						attccattcgatgatgattcc	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46408513A>C		NA		hg19		0.02	-0.28049	TCGxTGA	UNCOVERED																																																																																			NOVEL					0			5	4.512738	KEEP	31	0	0	15	450	AA	0	0	0			3	30	113	0	0	8.544455	26	40	933	76		0.103448	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46420835	46420835	__UNKNOWN__	IGR	SNP	T	T	G	rs9746459		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:46420835T>G			NA	NA				None (None upstream) : ANKRD26P1 (82417 downstream)						NA		NA									NA						tggactctaatggaatcatca	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46420835T>G		NA		hg19		0.02	-0.175457	TAAxGGA	UNCOVERED																																																																																			NOVEL					0			6	3.309612	KEEP	10	0	0	11	334	TT	0	0	0			3	24	108	0	0	8.709592	15	60	548	48		0.166667	0.387407
CYLD	1540	__UNKNOWN__	__UNKNOWN__	16	50817044	50817044	__UNKNOWN__	Intron	SNP	C	C	T	rs3785140	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:50817044C>T	ENST00000398568.2	+	10	2117				CYLD_ENST00000569418.1_Intron|CYLD_ENST00000566206.1_Intron|CYLD_ENST00000427738.3_Intron|CYLD_ENST00000540145.1_Intron|CYLD_ENST00000568704.2_Intron|CYLD_ENST00000311559.9_Intron|CYLD_ENST00000564326.1_Intron	NM_001042412.1	NP_001035877.1	Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	NA		NA			cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				ggtttcaccacgttggccagg	0.532	NA	NA	Mis, N, F, S		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis				T|||	1270	0.253594	0.1921	0.3617	5008	,	,	NA	17881	0.1339	NA	0.4473	False	NA	,,,	NA	NA	NA	2504	0.184	NA	NA	NA		yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17					1540			2584	protein-coding gene	gene with protein product	ubiquitin specific peptidase like 2	605018		CYLD1	NA	7493027	Standard		NM_015247	NA	Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000398568.2:c.1817+667C>T	chr16.hg19:g.50817044C>T		NA	O94934|Q7L3N6|Q96EH0|Q9NZX9	hg19	CCDS42164.1	0.02	-0.280734	CCAxGTT	COVERED																																																																																			NOVEL	CYLD-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422997.1	94	11.736261	KEEP	45	0	0	39	1291	CC	0.999892	0.739592	0		+	2	60	73	0	0	8.254036	0	0	0	107	ENST00000398568.2	1	0.739671
CHD9	80205	__UNKNOWN__	__UNKNOWN__	16	53353826	53353826	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:53353826T>C	ENST00000566029.1	+	37	7874				CHD9_ENST00000447540.1_Intron|CHD9_ENST00000398510.3_Intron|CHD9_ENST00000564845.1_Intron			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	NA		NA			cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ATGAAGGAGATAATAAAAAAG	0.284	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200	80205			25701	protein-coding gene	gene with protein product		NA			NA	9205841	Standard	NM_025134	XM_005256168	NA	Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000566029.1:c.7665+1574T>C	chr16.hg19:g.53353826T>C		NA	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	hg19	CCDS45485.1	0.02	2.294762	AGAxAAT	COVERED																																																																																			NOVEL	CHD9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422338.1	0	6.918246	KEEP	0	0	0	23	672	TT	0.999892	0.999002	0		+	17	60	654	0	0	55.758153	61	60	2146	122	ENST00000566029.1	0.217949	0.99911
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	55754047	55754047	__UNKNOWN__	IGR	SNP	A	A	G	rs3874620		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:55754047A>G			NA	NA				SLC6A2 (13943 upstream) : CES1P1 (40463 downstream)						NA		NA									NA						TTTATTCAGCATCACGATCAG	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.55754047A>G		NA		hg19		0.02	-0.368457	AGCxTCA	COVERED																																																																																			NOVEL					0			4	3.009309	KEEP	1	0	0	10	320	AA	0.992708	0.892756	0			5	42	181	0	0	13.828922	37	50	1364	70		0.119048	0.899314
MTSS1L	92154	__UNKNOWN__	__UNKNOWN__	16	70711843	70711843	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:70711843A>C	ENST00000338779.6	-	9	899					NM_138383.2	NP_612392.1	Q765P7	MTSSL_HUMAN	metastasis suppressor 1-like	NA		NA			filopodium assembly (GO:0046847)|signal transduction (GO:0007165)					breast(1)|central_nervous_system(2)|endometrium(1)|liver(1)|lung(1)|skin(1)	7						CCTATCGCCCACCTGCCCGCC	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						17	11	13	NA		NA	NA	16		NA											NA				70711843		2117	4200	6317	SO:0001627	intron_variant				CCDS32476.1	16q22.1	2008-12-16				ENSG00000132613	92154			25094	protein-coding gene	gene with protein product	actin-bundling protein with BAIAP2 homology	NA			NA	12477932	Standard	NM_138383	XM_006721335	NA	Approved	ABBA-1, LOC92154	uc002ezj.3	Q765P7		ENST00000338779.6:c.625-41T>G	chr16.hg19:g.70711843A>C		NA	A6NJI7|Q9BUA8	hg19	CCDS32476.1	0.02	0.897005	CCCxCCT	COVERED																																																																																			NOVEL	MTSS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434927.3	0	9.57656	KEEP	0	2	31	43	1155	AA	1	0.984161	0		-	11	60	192	0	0	12.323805	47	60	1459	185	ENST00000338779.6	0.189655	0.984161
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	70894733	70894733	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:70894733C>A	ENST00000393567.2	-	70	11999	c.11849G>T	c.(11848-11850)tGc>tTc	p.C3950F		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3950		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATCAAAATGGCAGATGGGCAA	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						2	2	2	NA		NA	NA	16		NA											NA				70894733		1481	3338	4819	SO:0001583	missense			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11849G>T	chr16.hg19:g.70894733C>A	ENSP00000377197:p.Cys3950Phe	NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	20.879645	TGGxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.2	4.261116	0.80246	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01323	5.01	5.69	5.69	0.88448	.	0.000000	0.36482	U	0.002568	T	0.10423	0.0255	M	0.82323	2.585	0.80722	D	1	D	0.69078	0.997	D	0.71870	0.975	T	0.00164	-1.1968	10	0.66056	D	0.02	.	19.4183	0.94710	0.0:1.0:0.0:0.0	.	3949	F8WD23	.	F	3950;3949	ENSP00000377197:C3950F	ENSP00000313052:C3949F	C	-	2	0	HYDIN	69452234	1.000000	0.71417	0.998000	0.56505	0.716000	0.41182	4.651000	0.61447	2.689000	0.91719	0.407000	0.27541	TGC	NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	2	24.934919	KEEP	0	0	0	83	2938	CC	1	1	0		-	48	60	1724	0	0	128.716321	409	60	15981	688	ENST00000393567.2	0.105033	1
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	71103148	71103148	__UNKNOWN__	Intron	SNP	G	G	A	rs1398390	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:71103148G>A	ENST00000393567.2	-	14	2125				HYDIN_ENST00000393550.2_Intron|HYDIN_ENST00000538248.1_Intron|HYDIN_ENST00000288168.10_Intron|HYDIN_ENST00000541601.1_Intron|HYDIN_ENST00000448089.2_Intron|HYDIN_ENST00000321489.5_Intron|HYDIN_ENST00000448691.1_Intron	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AGCTGTGTGTGCAGGAAGGCC	0.512	NA	NA											G|||	2958	0.590655	0.798	0.5159	5008	,	,	NA	16667	0.7321	NA	0.3012	False	NA	,,,	NA	NA	NA	2504	0.5153	NA	NA	NA						NA		NA				0							NA						31	44	39	NA		NA	NA	16		NA											NA				71103148		2192	4299	6491	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.1974+21C>T	chr16.hg19:g.71103148G>A		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	6.624655	TGTxCAG	COVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	1	5.116226	KEEP	0	0	0	17	591	GG	0.999366	0.999366	0		-	31	60	1098	0	0	90.248991	131	60	4907	192	ENST00000393567.2	0.191358	1
RP11-252A24.2	0	__UNKNOWN__	__UNKNOWN__	16	74385121	74385121	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:74385121G>A	ENST00000429810.2	-	0	815										NA		NA									NA						GGCCTTGTTCGAGATTGAAAA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000429810.2:	chr16.hg19:g.74385121G>A		NA		hg19		0.02	1.848001	TTCxAGA	COVERED																																																																																			NOVEL	RP11-252A24.2-003	KNOWN	basic	retained_intron	NA	pseudogene	OTTHUMT00000434683.1	1	3.309937	KEEP	5	0	0	11	345	GG	0.993072	0.990985	0		-	5	27	182	0	0	12.671203	68	60	2195	89	ENST00000429810.2	0.068493	0.997898
RP11-252A24.2	0	__UNKNOWN__	__UNKNOWN__	16	74385202	74385202	__UNKNOWN__	RNA	SNP	A	A	G	rs11864336		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:74385202A>G	ENST00000429810.2	-	0	815										NA		NA									NA						CTATGGAGCAAAGAGGAGAGG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000429810.2:	chr16.hg19:g.74385202A>G		NA		hg19		0.02	6.417387	GCAxAGA	COVERED																																																																																			NOVEL	RP11-252A24.2-003	KNOWN	basic	retained_intron	NA	pseudogene	OTTHUMT00000434683.1	4	3.614581	KEEP	14	3	100	47	1489	AA	1	1	0		-	6	27	218	0	0	12.98017	193	60	7045	329	ENST00000429810.2	0.030151	1
NPIPB15	440348	__UNKNOWN__	__UNKNOWN__	16	74425902	74425902	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs141751158		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:74425902T>C	ENST00000429990.1	+	7	1352	c.1256T>C	c.(1255-1257)aTa>aCa	p.I419T				A6NHN6	NPB15_HUMAN	nuclear pore complex interacting protein family, member B15	419		NA				extracellular region (GO:0005576)					NA						gcctgggcaataagaataaat	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						3	3	3	NA		NA	NA	16		NA											NA				74425902		1357	2958	4315	SO:0001583	missense			BC160029		16q22.3	2013-06-11	2013-06-11	2013-06-11	ENSG00000196436	ENSG00000196436	440348			34409	protein-coding gene	gene with protein product		NA	nuclear pore complex interacting protein-like 2	NPIPL2	NA		Standard	NM_001018059	XM_005256273	NA	Approved	LOC440348	uc010vmt.1	A6NHN6	OTTHUMG00000156916	ENST00000429990.1:c.1256T>C	chr16.hg19:g.74425902T>C	ENSP00000411140:p.Ile419Thr	NA	C9J9U8	hg19		0.02	-0.333152	CAAxAAG	UNCOVERED	.	.	.	.	.	.	.	.	.	.	-	7.398	0.632084	0.14322	.	.	ENSG00000196436	ENST00000504746;ENST00000429990	T	0.53423	0.62	.	.	.	.	.	.	.	.	T	0.20941	0.0504	N	0.08118	0	0.21020	N	0.999804	B	0.30211	0.273	B	0.32762	0.152	T	0.23404	-1.0189	8	0.12430	T	0.62	.	2.6652	0.05046	0.0:0.5:0.0:0.5	.	358	A6NHN6	NPPL2_HUMAN	T	283;419	ENSP00000411140:I419T	ENSP00000411140:I419T	I	+	2	0	NPIPL2	72983403	0.026000	0.19158	0.000000	0.03702	0.000000	0.00434	0.065000	0.14466	0.000000	0.14550	0.000000	0.15137	ATA	NOVEL	NPIPB15-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000346597.2	1	5.105765	KEEP	32	0	0	17	484	TT	0	0	0		+	5	40	129	0	0	8.895464	33	40	1159	92	ENST00000429990.1	0.131579	0.851984
MON1B	22879	__UNKNOWN__	__UNKNOWN__	16	77235702	77235702	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:77235702T>A	ENST00000248248.3	+	0	5491				SYCE1L_ENST00000378644.4_Intron|RP11-538I12.2_ENST00000569032.1_RNA	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	NA		NA								breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						aagttctaatttaaatgtatt	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111	22879			25020	protein-coding gene	gene with protein product		608954	MON1 homolog B (yeast)		NA	10048485	Standard	NM_014940	NM_014940	NA	Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.*3497T>A	chr16.hg19:g.77235702T>A		NA	B4DDZ0|O94949	hg19	CCDS10925.1	0.02	-0.166686	AATxTAA	COVERED																																																																																			NOVEL	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269036.2	2	3.306771	KEEP	0	0	0	11	300	TT	0.993072	0.351495	0		+	4	60	148	0	0	12.462076	15	60	524	34	ENST00000248248.3	0.210526	0.353947
CLEC3A	10143	__UNKNOWN__	__UNKNOWN__	16	78056600	78056600	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:78056600G>T	ENST00000299642.4	+	1	189	c.104G>T	c.(103-105)aGa>aTa	p.R35I	CLEC3A_ENST00000575655.1_Missense_Mutation_p.R26I|RP11-281J9.2_ENST00000563114.1_RNA	NM_001244755.1	NP_001231684.1	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	26		NA			skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						CACACATCCAGATTAAAAGCC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						111	87	95	NA		NA	NA	16		NA											NA				78056600		2198	4300	6498	SO:0001583	missense			AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509	10143		C-type lectin domain containing	2052	protein-coding gene	gene with protein product		613588	C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)	CLECSF1	NA	10524194	Standard	NM_005752	NM_001244755	NA	Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000299642.4:c.104G>T	chr16.hg19:g.78056600G>T	ENSP00000299642:p.Arg35Ile	NA	B2R8C4|Q3SX91|Q6UXF5	hg19	CCDS10927.2	0.02	6.813248	CCAxATT	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.656	1.142951	0.21205	.	.	ENSG00000166509	ENST00000299642	.	.	.	5.71	1.17	0.20885	.	0.674999	0.14890	N	0.292464	T	0.31451	0.0797	N	0.14661	0.345	0.53005	D	0.999965	P	0.37955	0.612	B	0.32289	0.143	T	0.05273	-1.0895	9	0.49607	T	0.09	-8.5561	11.2364	0.48942	0.882:0.0:0.118:0.0	.	26	O75596	CLC3A_HUMAN	I	26	.	ENSP00000299642:R26I	R	+	2	0	CLEC3A	76614101	0.536000	0.26378	0.017000	0.16124	0.126000	0.20510	0.856000	0.27818	-0.021000	0.14009	-0.793000	0.03317	AGA	NOVEL	CLEC3A-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269041.2	2	10.233065	KEEP	0	0	0	34	1225	GG	0.999998	0.999998	0		+	64	60	2375	0	0	215.672945	124	60	4797	273	ENST00000299642.4	0.340426	1
CDH13	1012	__UNKNOWN__	__UNKNOWN__	16	83711799	83711799	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:83711799T>G	ENST00000268613.10	+	11	1518				CDH13_ENST00000428848.3_Intron|CDH13_ENST00000566620.1_Intron			P55290	CAD13_HUMAN	cadherin 13	NA		NA			adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		GAGACCCTTCTGTCTGCTTTC	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						36	38	37	NA		NA	NA	16		NA											NA				83711799		1951	4147	6098	SO:0001627	intron_variant			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945	1012		Cadherins / Major cadherins	1753	protein-coding gene	gene with protein product	T-cadherin, H-cadherin (heart)	601364			NA	8673923, 9468307	Standard	NM_001257	NM_001257	NA	Approved	CDHH	uc010vns.2	P55290		ENST00000268613.10:c.1426-14T>G	chr16.hg19:g.83711799T>G		NA	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	hg19	CCDS58485.1	0.02	7.646126	TTCxGTC	COVERED																																																																																			NOVEL	CDH13-009	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000432918.1	1	19.248525	KEEP	0	0	0	64	1910	TT	1	1	0		+	11	60	336	0	0	19.757064	218	60	7750	386	ENST00000268613.10	0.048035	1
ZDHHC7	55625	__UNKNOWN__	__UNKNOWN__	16	85009106	85009106	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:85009106A>G	ENST00000313732.4	-	0	2122					NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	NA		NA			peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						ATTTCTTTAAAAAATGAAAGC	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786	55625		Zinc fingers, DHHC-type	18459	protein-coding gene	gene with protein product	Sertoli cell gene with zinc finger domain-&#946;	614604			NA		Standard	NM_017740	NM_017740	NA	Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.*843T>C	chr16.hg19:g.85009106A>G		NA	D3DUM1|Q8WV42|Q9NVD8	hg19	CCDS10950.1	0.02	4.983949	TAAxAAA	COVERED																																																																																			NOVEL	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269087.1	1	7.822154	KEEP	0	0	0	26	778	AA	0.999957	0.999952	0		-	42	60	1462	0	0	134.021506	70	60	2511	152	ENST00000313732.4	0.375	0.999995
PIEZO1	9780	__UNKNOWN__	__UNKNOWN__	16	88789499	88789499	__UNKNOWN__	Intron	SNP	G	G	A	rs140520334	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:88789499G>A	ENST00000301015.9	-	33	4742					NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	NA		NA			cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CCGGGCCCACGTACCTGCCGC	0.731	NA	NA											G|||	8	0.00159744	0	0.0014	5008	,	,	NA	10586	0	NA	0.007	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA	G		2,1380		0,2,689	13	20	18	NA		-8	0	16	dbSNP_134	18	28,3144		0,28,1558	no	intron	PIEZO1	NM_001142864.2		0,30,2247	AA,AG,GG	NA	0.8827,0.1447,0.6588			88789499	30,4524	691	1586	2277	SO:0001627	intron_variant			D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335	9780			28993	protein-coding gene	gene with protein product		611184	family with sequence similarity 38, member A	FAM38A	NA	20813920, 21056836, 21299953, 21696149	Standard	NM_014745	NM_001142864	NA	Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.4495+3C>T	chr16.hg19:g.88789499G>A		NA	A6NHT9|A7E2B7|Q0KKZ9	hg19	CCDS54058.1	0.02	2.239918	CACxTAC	COVERED																																																																																			NOVEL	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345699.4	0	19.168363	KEEP	0	0	0	64	1979	GG	1	0.998465	0		-	20	60	702	0	0	61.018748	54	60	1707	182	ENST00000301015.9	0.27027	0.998465
DBNDD1	79007	__UNKNOWN__	__UNKNOWN__	16	90086080	90086080	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:90086080G>T	ENST00000568838.1	-	1	401				GAS8_ENST00000536122.1_5'UTR			Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	NA		NA				cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0275)		ACACCACCGGGACCTGGCTGC	0.806	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249	79007			28455	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024043	NM_001288708	NA	Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000568838.1:c.391+55C>A	chr16.hg19:g.90086080G>T		NA	B4DQS3|Q69YT2|Q9BW25	hg19		0.02	-0.263109	CGGxACC	COVERED																																																																																			NOVEL	DBNDD1-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000420936.1	0	6.308747	KEEP	0	0	0	21	639	GG	0.999869	0.693577	0		-	3	60	100	0	0	7.244408	26	60	890	55	ENST00000568838.1	0.103448	0.693668
TUBB8P7	197331	__UNKNOWN__	__UNKNOWN__	16	90161651	90161651	__UNKNOWN__	RNA	SNP	C	C	T	rs561420739	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr16:90161651C>T	ENST00000564451.1	+	0	1004				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7	NA		NA									NA						GCTGTGACTGCCTGCAGGGTT	0.602	NA	NA											.|||	84	0.0167732	0.059	0.0029	5008	,	,	NA	18646	0.003	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812	197331			42345	pseudogene	pseudogene		NA			NA		Standard	NG_002334	NG_002334	NA	Approved				OTTHUMG00000172847	ENST00000564451.1:	chr16.hg19:g.90161651C>T		NA		hg19		0.02	-0.228101	CTGxCTG	COVERED																																																																																			NOVEL	TUBB8P7-004	KNOWN	basic	processed_transcript	NA	polymorphic_pseudogene	OTTHUMT00000420856.1	0	2.708851	KEEP	7	0	0	9	316	CC	0.99257	0.578599	0		+	3	24	111	0	0	8.493692	23	47	845	51	ENST00000564451.1	0.115385	0.58293
ABR	29	__UNKNOWN__	__UNKNOWN__	17	910363	910363	__UNKNOWN__	Intron	SNP	G	G	A	rs112719182	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:910363G>A	ENST00000302538.5	-	22	2637				ABR_ENST00000572441.1_Intron|ABR_ENST00000536794.2_Intron|ABR_ENST00000544583.2_Intron|ABR_ENST00000291107.2_Intron|ABR_ENST00000543210.2_Intron|ABR_ENST00000574437.1_Intron	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	NA		NA			actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		TCATGGGACCGTCACCCTCCG	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(197;2016 2115 4129 29033 46447)					NA		NA				0							NA						11	8	9	NA		NA	NA	17		NA											NA				910363		1953	3978	5931	SO:0001627	intron_variant			L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842	29		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	81	protein-coding gene	gene with protein product		600365	active BCR-related gene		NA	2587217, 7479768	Standard		NM_001092	NA	Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.2490+41C>T	chr17.hg19:g.910363G>A		NA	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	hg19	CCDS10999.1	0.02	-0.297205	ACCxTCA	COVERED																																																																																			NOVEL	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206675.4	0	4.811668	KEEP	11	0	0	16	463	GG	0.997832	0.779366	0		-	5	40	139	0	0	10.214336	29	60	949	66	ENST00000302538.5	0.147059	0.78106
AC006435.1	0	__UNKNOWN__	__UNKNOWN__	17	2317730	2317730	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs185852688	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:2317730C>T	ENST00000609667.1	-	2	285	c.206G>A	c.(205-207)cGt>cAt	p.R69H							NA		NA									NA						caggtctgaacgtcgaagtct	0.537	NA	NA											C|||	6	0.00119808	0.0015	0	5008	,	,	NA	21214	0.004	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA	C		3,4061		0,3,2029	151	164	160	NA		0.3	0	17		160	0,8354		0,0,4177	no	near-gene-3				0,3,6206	TT,TC,CC	NA	0.0,0.0738,0.0242			2317730	3,12415	2032	4177	6209	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000609667.1:c.206G>A	chr17.hg19:g.2317730C>T	ENSP00000476359:p.Arg69His	NA		hg19		0.02	2.14184	GAAxGTC	COVERED	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	6.527	0.465461	0.12402	7.38E-4	0.0	ENSG00000205821	ENST00000381977	.	.	.	3.55	0.333	0.15943	.	.	.	.	.	T	0.26846	0.0657	.	.	.	.	.	.	D	0.58268	0.982	B	0.42738	0.396	T	0.32295	-0.9912	6	0.87932	D	0	.	3.7743	0.08654	0.0:0.562:0.2042:0.2338	.	69	Q4G0H6	.	H	69	.	ENSP00000371404:R69H	R	-	2	0	AC006435.1	2264480	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.143000	0.10296	0.126000	0.18424	0.563000	0.77884	CGT	NOVEL	AC006435.1-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		1	6.621329	KEEP	0	0	0	22	762	CC	0.999879	0.999501	0		-	7	60	252	0	0	18.054479	78	60	2728	127	ENST00000609667.1	0.082353	0.999622
RAP1GAP2	23108	__UNKNOWN__	__UNKNOWN__	17	2930465	2930465	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:2930465A>C	ENST00000254695.8	+	22	2197				RAP1GAP2_ENST00000542807.1_Intron|RAP1GAP2_ENST00000540393.2_Intron|RAP1GAP2_ENST00000366401.4_Intron	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	NA		NA			negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						GCCAGTTTTCACCCCTCCTCC	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359	23108			29176	protein-coding gene	gene with protein product		NA	GTPase activating RANGAP domain-like 4, GTPase activating Rap/RanGAP domain-like 4	GARNL4	NA	15632203	Standard		NM_015085	NA	Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.2107+101A>C	chr17.hg19:g.2930465A>C		NA	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	hg19	CCDS45573.1	0.02	-0.372779	TTCxCCC	COVERED																																																																																			NOVEL	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438208.2	0	4.18515	KEEP	0	0	0	14	313	AA	0.995343	0.904836	0		+	9	60	124	0	0	7.234695	34	60	1046	81	ENST00000254695.8	0.209302	0.909069
ALOX15	246	__UNKNOWN__	__UNKNOWN__	17	4545061	4545061	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:4545061C>T	ENST00000570836.1	-	2	72				ALOX15_ENST00000574640.1_5'UTR|ALOX15_ENST00000545513.1_Intron			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	NA		NA			apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		GGTGGCAGGTCTCCAATCAAC	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	246	1.13.11.33	Arachidonate lipoxygenases	433	protein-coding gene	gene with protein product		152392			NA	1570320	Standard		NM_001140	NA	Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.25-90G>A	chr17.hg19:g.4545061C>T		NA	A8K2P4|B7ZA11|Q8N6R7|Q99657	hg19	CCDS11049.1	0.02	-0.403553	GGTxTCC	COVERED																																																																																			NOVEL	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207487.2	0	3.006292	KEEP	0	0	0	10	313	CC	0.992708	0.927678	0		-	13	60	462	0	0	40.508334	33	70	1208	68	ENST00000570836.1	0.282609	0.934492
MINK1	50488	__UNKNOWN__	__UNKNOWN__	17	4796062	4796062	__UNKNOWN__	Splice_Site	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:4796062A>T	ENST00000355280.6	+	19	2506	c.2310A>T	c.(2308-2310)ggA>ggT	p.G770G	MINK1_ENST00000453408.3_Splice_Site_p.G750G|MINK1_ENST00000347992.7_Splice_Site_p.G733G	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1	NA		NA								central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						ACCGCGTGGGAGGTATGTGAG	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						13	15	14	NA		NA	NA	17		NA											NA				4796062		1985	4165	6150	SO:0001630	splice_region_variant			AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503	50488			17565	protein-coding gene	gene with protein product	misshapen/NIK-related kinase	609426	misshapen-like kinase 1 (zebrafish)		NA	10708748, 12087176	Standard	NM_015716	NM_015716	NA	Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2311+1A>T	chr17.hg19:g.4796062A>T		NA		hg19	CCDS45588.1	0.02	6.642824	GGGxGGT	COVERED																																																																																			NOVEL	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439801.1	1	30.383114	KEEP	0	0	0	101	2986	AA	1	1	0	Silent	+	8	60	296	0	0	19.606089	153	60	5602	278	ENST00000355280.6	0.049689	1
MINK1	50488	__UNKNOWN__	__UNKNOWN__	17	4798281	4798281	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:4798281G>A	ENST00000355280.6	+	25	3113				MINK1_ENST00000453408.3_Intron|MINK1_ENST00000347992.7_Intron	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1	NA		NA								central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						GTATTATGAGGTGCCAAGACC	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503	50488			17565	protein-coding gene	gene with protein product	misshapen/NIK-related kinase	609426	misshapen-like kinase 1 (zebrafish)		NA	10708748, 12087176	Standard	NM_015716	NM_015716	NA	Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2918-89G>A	chr17.hg19:g.4798281G>A		NA		hg19	CCDS45588.1	0.02	2.34019	GAGxTGC	COVERED																																																																																			NOVEL	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439801.1	0	4.442416	KEEP	0	0	0	15	455	GG	0.99649	0.960391	0		+	17	60	582	0	0	52.211947	34	60	1230	79	ENST00000355280.6	0.333333	0.963774
DLG4	1742	__UNKNOWN__	__UNKNOWN__	17	7117055	7117055	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:7117055C>T	ENST00000302955.6	-	1	230				DLG4_ENST00000399506.2_Intron|DLG4_ENST00000485100.1_Intron|DLG4_ENST00000399510.2_Intron	NM_001128827.1	NP_001122299.1	P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	NA		NA			alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	GGGGTCTCCTCAAATCGGCTG	0.463	NA	NA									OREG0024129	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535	1742			2903	protein-coding gene	gene with protein product		602887			NA	9286702	Standard	NM_001365	NM_001128827	NA	Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000302955.6:c.30+3381G>A	chr17.hg19:g.7117055C>T		639	B7Z1S1|G5E939|Q92941|Q9UKK8	hg19	CCDS45600.1	0.02	8.630182	CCTxAAA	COVERED																																																																																			NOVEL	DLG4-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259420.1	1	21.970751	KEEP	0	0	0	73	2530	CC	1	1	0		-	32	60	1123	0	0	88.01542	187	60	7120	334	ENST00000302955.6	0.146119	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	7439952	7439952	__UNKNOWN__	IGR	SNP	C	C	T	rs113823642	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:7439952C>T			NA	NA				POLR2A (22019 upstream) : Y_RNA (460 downstream)						NA		NA									NA						cacacccggccAAGATTTATT	0.537	NA	NA											C|||	286	0.0571086	0.205	0.0173	5008	,	,	NA	14831	0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.7439952C>T		NA		hg19		0.02	-0.087732	GGCxAAG	UNCOVERED																																																																																			NOVEL					0			4	2.407869	KEEP	0	0	0	8	283	CC	0.99257	0.09898	0			9	60	332	0	0	36.081939	1	60	34	20		0.9	0.099721
TP53	7157	__UNKNOWN__	__UNKNOWN__	17	7577141	7577141	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs193920774		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:7577141C>T	ENST00000269305.4	-	8	986	c.797G>A	c.(796-798)gGa>gAa	p.G266E	TP53_ENST00000420246.2_Missense_Mutation_p.G266E|TP53_ENST00000455263.2_Missense_Mutation_p.G266E|TP53_ENST00000359597.4_Missense_Mutation_p.G266E|TP53_ENST00000413465.2_Intron|TP53_ENST00000445888.2_Missense_Mutation_p.G266E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	266	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.	NA	G -> A (in sporadic cancers; somatic mutation).|G -> E (in sporadic cancers; somatic mutation).|G -> R (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G266E(50)|p.G266V(42)|p.0?(8)|p.?(3)|p.G266fs*79(3)|p.G262_F270delGNLLGRNSF(2)|p.G266A(2)|p.G266_E271delGRNSFE(2)|p.G262_S269delGNLLGRNS(2)|p.G266fs*4(1)|p.G266T(1)|p.L265_K305del41(1)|p.E258fs*71(1)|p.L265_R267delLGR(1)|p.G266_N268delGRN(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCTGTTCCGTCCCAGTAGATT	0.517	NA	111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	121	Substitution - Missense(95)|Deletion - In frame(9)|Whole gene deletion(8)|Deletion - Frameshift(6)|Unknown(3)	lung(23)|oesophagus(10)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(9)|breast(9)|upper_aerodigestive_tract(8)|ovary(8)|urinary_tract(7)|pancreas(6)|skin(5)|central_nervous_system(4)|stomach(4)|bone(4)|liver(4)|endometrium(3)|vulva(1)|kidney(1)|thyroid(1)|cervix(1)|eye(1)|genital_tract(1)|biliary_tract(1)					NA						50	44	46	NA		NA	NA	17		NA											NA				7577141		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510	7157			11998	protein-coding gene	gene with protein product	Li-Fraumeni syndrome	191170			NA	6396087, 3456488, 2047879	Standard	NM_000546	NM_001126115	NA	Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.797G>A	chr17.hg19:g.7577141C>T	ENSP00000269305:p.Gly266Glu	NA	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	hg19	CCDS11118.1	0.02	4.625764	CGTxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	25.2	4.614795	0.87359	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99898	-7.61;-7.61;-7.61;-7.61;-7.61;-7.61	5.13	5.13	0.70059	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99906	0.9955	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.998	D	0.96190	0.9137	10	0.87932	D	0	-13.0798	16.1198	0.81342	0.0:1.0:0.0:0.0	.	266;266;266;266	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	E	266;266;266;266;266;255;134	ENSP00000352610:G266E;ENSP00000269305:G266E;ENSP00000398846:G266E;ENSP00000391127:G266E;ENSP00000391478:G266E;ENSP00000425104:G134E	ENSP00000269305:G266E	G	-	2	0	TP53	7517866	1.000000	0.71417	0.996000	0.52242	0.744000	0.42396	7.587000	0.82613	2.667000	0.90743	0.462000	0.41574	GGA	NOVEL	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367397.1	2	11.415023	KEEP	0	0	0	38	1230	CC	1	1	0		-	100	60	3532	0	0	369.76667	31	60	1045	178	ENST00000269305.4	0.763359	1
LSMD1	0	__UNKNOWN__	__UNKNOWN__	17	7761502	7761502	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:7761502G>T	ENST00000576861.1	-	4	214				CYB5D1_ENST00000571846.1_Missense_Mutation_p.R17L|LSMD1_ENST00000570555.1_Intron|CYB5D1_ENST00000332439.4_Missense_Mutation_p.R17L|CYB5D1_ENST00000570446.1_Missense_Mutation_p.R17L			Q9BRA0	LSMD1_HUMAN		NA		NA			negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|lung(2)|ovary(1)	4		all_cancers(10;0.11)|Prostate(122;0.219)				TATTTTCAGCGTCGCTATTTC	0.587	NA	NA									OREG0024147	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(66;626 1401 29924 42527)					NA		NA				0							NA						76	82	80	NA		NA	NA	17		NA											NA				7761502		2203	4300	6503	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000576861.1:c.4-986C>A	chr17.hg19:g.7761502G>T		644	Q8N4M0	hg19		0.02	7.157277	AGCxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	27.2	4.809236	0.90707	.	.	ENSG00000182224	ENST00000332439;ENST00000541486	T	0.73789	-0.78	5.94	5.94	0.96194	Cytochrome b5 (3);	0.150704	0.46758	D	0.000280	T	0.72724	0.3496	L	0.54323	1.7	0.33207	D	0.552923	P;P	0.52577	0.753;0.954	B;P	0.45753	0.247;0.492	T	0.79212	-0.1896	10	0.35671	T	0.21	2.3156	13.8266	0.63354	0.0:0.2565:0.7434:0.0	.	17;17	Q6P9G0-2;Q6P9G0	.;CB5D1_HUMAN	L	17	ENSP00000331479:R17L	ENSP00000331479:R17L	R	+	2	0	CYB5D1	7702227	1.000000	0.71417	0.987000	0.45799	0.817000	0.46193	4.190000	0.58365	2.826000	0.97356	0.561000	0.74099	CGT	NOVEL	LSMD1-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000440836.1	6	38.192944	KEEP	0	0	0	127	4202	GG	1	1	0		-	13	60	487	0	0	34.538052	170	60	5683	366	ENST00000576861.1	0.071038	1
MYH8	4626	__UNKNOWN__	__UNKNOWN__	17	10323508	10323508	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:10323508C>T	ENST00000403437.2	-	3	131	c.37G>A	c.(37-39)Ggc>Agc	p.G13S	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	13		NA			ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GCAGCTTCGCCAAAAACAGCC	0.488	NA	NA							Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling					NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						94	88	90	NA		NA	NA	17		NA											NA				10323508		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020	4626		Myosins / Myosin superfamily : Class II	7578	protein-coding gene	gene with protein product		160741	myosin, heavy polypeptide 8, skeletal muscle, perinatal		NA	2373371	Standard	NM_002472	NM_002472	NA	Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.37G>A	chr17.hg19:g.10323508C>T	ENSP00000384330:p.Gly13Ser	NA	Q14910	hg19	CCDS11153.1	0.02	4.655484	CGCxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	33	5.289935	0.95546	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.86097	-2.07	4.59	4.59	0.56863	.	0.000000	0.42548	U	0.000699	D	0.90745	0.7095	M	0.75615	2.305	0.80722	D	1	P	0.47762	0.9	P	0.57152	0.814	D	0.92147	0.5725	10	0.87932	D	0	.	17.5857	0.87981	0.0:1.0:0.0:0.0	.	13	P13535	MYH8_HUMAN	S	13	ENSP00000384330:G13S	ENSP00000252173:G13S	G	-	1	0	MYH8	10264233	1.000000	0.71417	0.998000	0.56505	0.948000	0.59901	7.609000	0.82925	2.395000	0.81488	0.467000	0.42956	GGC	NOVEL	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252724.2	2	10.228044	KEEP	0	0	0	34	1160	CC	0.999998	0.999998	0		-	11	60	400	0	0	28.554936	128	60	4764	202	ENST00000403437.2	0.079137	1
MYH3	4621	__UNKNOWN__	__UNKNOWN__	17	10538600	10538600	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:10538600A>G	ENST00000583535.1	-	30	4260				MYH3_ENST00000226209.7_Intron	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	NA		NA			actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						AAGACACATGAGATGGGGAAA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063	4621		Myosins / Myosin superfamily : Class II	7573	protein-coding gene	gene with protein product	myosin, skeletal, heavy chain, embryonic 1, muscle embryonic myosin heavy chain 3	160720	myosin, heavy polypeptide 3, skeletal muscle, embryonic		NA	2726495	Standard	NM_002470	NM_002470	NA	Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.4172+83T>C	chr17.hg19:g.10538600A>G		NA	Q15492	hg19	CCDS11157.1	0.02	-0.37624	ATGxGAT	COVERED																																																																																			NOVEL	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252734.2	1	3.909899	KEEP	0	0	0	13	385	AA	0.994391	0.90397	0		-	6	60	209	0	0	16.225121	37	60	1314	63	ENST00000583535.1	0.139535	0.909069
SHISA6	388336	__UNKNOWN__	__UNKNOWN__	17	11455264	11455264	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:11455264C>T	ENST00000441885.3	+	4	1107	c.947C>T	c.(946-948)cCa>cTa	p.P316L	SHISA6_ENST00000432116.3_Intron|SHISA6_ENST00000409168.3_Intron	NM_207386.3	NP_997269.2	Q6ZSJ9	SHSA6_HUMAN	shisa family member 6	266		NA				alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)				breast(1)|endometrium(4)	5						CAGATCCCGCCACATGGTGAG	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						165	138	146	NA		NA	NA	17		NA											NA				11455264		692	1591	2283	SO:0001583	missense			AK127379, AK128003	CCDS45615.1, CCDS54089.1, CCDS54090.1	17p13.1-p12	2013-07-31	2013-07-31		ENSG00000188803	ENSG00000188803	388336		Shisa homologs	34491	protein-coding gene	gene with protein product		NA	shisa homolog 6 (Xenopus laevis)		NA		Standard	NM_207386	NM_207386	NA	Approved	FLJ45455	uc002gnc.2	Q6ZSJ9	OTTHUMG00000154121	ENST00000441885.3:c.947C>T	chr17.hg19:g.11455264C>T	ENSP00000390084:p.Pro316Leu	NA	B3KXV5|Q4PL63	hg19	CCDS45615.1	0.02	4.902395	CGCxACA	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754632	0.31046	.	.	ENSG00000188803	ENST00000441885	.	.	.	3.82	3.82	0.43975	.	.	.	.	.	T	0.52058	0.1711	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54262	-0.8320	7	0.56958	D	0.05	.	11.5005	0.50435	0.0:1.0:0.0:0.0	.	316	Q6ZSJ9-3	.	L	316	.	ENSP00000390084:P316L	P	+	2	0	SHISA6	11395989	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.534000	0.36051	2.431000	0.82371	0.467000	0.42956	CCA	NOVEL	SHISA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333969.3	2	12.339909	KEEP	0	0	0	41	1448	CC	1	1	0		+	49	60	1879	0	0	170.998638	96	60	3585	246	ENST00000441885.3	0.337931	1
COX10	1352	__UNKNOWN__	__UNKNOWN__	17	14095195	14095195	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:14095195A>G	ENST00000261643.3	+	6	772				COX10_ENST00000537334.1_Intron|COX10_ENST00000536205.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	NA		NA			aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		CCAGATCAGTACTGCCTCTAC	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695	1352		Mitochondrial respiratory chain complex assembly factors	2260	protein-coding gene	gene with protein product	heme A: farnesyltransferase, protoheme IX farnesyltransferase, mitochondrial, heme O synthase	602125	COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase), COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)		NA	9177788, 12928484	Standard	NM_001303	NM_001303	NA	Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.696-111A>G	chr17.hg19:g.14095195A>G		NA	B2R6U5|B4DJ50|O15334|Q969F7	hg19	CCDS11166.1	0.02	8.901609	AGTxCTG	COVERED																																																																																			NOVEL	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130003.1	4	7.289146	KEEP	12	2	77	51	1498	AA	1	1	0		+	13	40	465	0	0	30.778539	231	60	8209	353	ENST00000261643.3	0.053279	1
RP1-37N7.3	0	__UNKNOWN__	__UNKNOWN__	17	18314830	18314830	__UNKNOWN__	lincRNA	SNP	T	T	C	rs62074236	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:18314830T>C	ENST00000577684.1	+	0	358										NA		NA									NA						ttcttcctcatcccgcaccct	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000577684.1:	chr17.hg19:g.18314830T>C		NA		hg19		0.02	-0.412328	TCAxCCC	COVERED																																																																																			NOVEL	RP1-37N7.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000447480.1	1	2.405242	KEEP	1	0	0	8	220	TT	0.99257	0.934744	0		+	14	47	491	0	0	43.347918	33	60	1192	60	ENST00000577684.1	0.297872	0.941741
LGALS9C	654346	__UNKNOWN__	__UNKNOWN__	17	18380298	18380298	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:18380298T>C	ENST00000328114.6	+	1	120				LGALS9C_ENST00000412421.2_Intron|LGALS9C_ENST00000583322.1_Intron|LGALS9C_ENST00000584941.1_Intron|LGALS9C_ENST00000578983.1_Intron|LGALS9C_ENST00000581545.1_Intron	NM_001040078.2	NP_001035167.2	Q6DKI2	LEG9C_HUMAN	lectin, galactoside-binding, soluble, 9C	NA		NA					carbohydrate binding (GO:0030246)			NS(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	7						TGGCAGGAGATAGGGGTGGGG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32587.1	17p11.2	2011-08-04			ENSG00000171916	ENSG00000171916	654346		Lectins, galactoside-binding	33874	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001040078	NM_001040078	NA	Approved		uc002gtw.3	Q6DKI2	OTTHUMG00000059251	ENST00000328114.6:c.39+91T>C	chr17.hg19:g.18380298T>C		NA	B0AZM7	hg19	CCDS32587.1	0.02	-0.350892	AGAxAGG	COVERED																																																																																			NOVEL	LGALS9C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131456.2	0	2.406207	KEEP	1	0	0	8	228	TT	0.99257	0.871187	0		+	7	40	259	0	0	21.270018	32	60	1110	51	ENST00000328114.6	0.179487	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	20492720	20492720	__UNKNOWN__	IGR	SNP	C	C	T	rs373824829		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:20492720C>T			NA	NA				CDRT15L2 (8496 upstream) : AC087499.10 (23504 downstream)						NA		NA									NA						TGGCCCTCACCGGCCTCCCCA	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.20492720C>T		NA		hg19		0.02	-0.438625	CACxGGC	COVERED																																																																																			NOVEL					0			0	4.447547	KEEP	4	1	32	26	845	CC	0.999909	0.959772	0			5	39	188	0	0	14.127743	45	50	1572	97		0.1	0.959859
CCDC144NL	339184	__UNKNOWN__	__UNKNOWN__	17	20768912	20768912	__UNKNOWN__	Intron	SNP	C	C	G	rs186155723		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:20768912C>G	ENST00000327925.5	-	4	691				CCDC144NL_ENST00000539484.1_Intron	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	NA		NA								large_intestine(3)|lung(3)|skin(1)	7						GTGACTCTTGCATAGCTCCAG	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212	339184			33735	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004306	NM_001004306	NA	Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.572-90G>C	chr17.hg19:g.20768912C>G		NA		hg19	CCDS32591.1	0.02	4.328236	TTGxATA	COVERED																																																																																			NOVEL	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255361.2	1	2.407906	KEEP	6	0	0	8	286	CC	0.99257	0.992561	0		-	7	40	260	0	0	18.488399	88	60	3312	122	ENST00000327925.5	0.073684	0.999991
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21558073	21558073	__UNKNOWN__	IGR	SNP	C	C	T	rs375403224		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:21558073C>T			NA	NA				AC138710.1 (76902 upstream) : UBBP4 (171527 downstream)						NA		NA									NA						GCACATCACGCTCCAAGTGGA	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21558073C>T		NA		hg19		0.02	-0.24532	ACGxTCC	COVERED																																																																																			NOVEL					0			1	2.708959	KEEP	0	0	0	9	329	CC	0.99254	0.636563	0			3	40	107	0	0	8.043659	24	60	886	44		0.111111	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21558325	21558325	__UNKNOWN__	IGR	SNP	G	G	C	rs9894478		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:21558325G>C			NA	NA				AC138710.1 (77154 upstream) : UBBP4 (171275 downstream)						NA		NA									NA						CTGAACATCAGGCTCCAGGTG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21558325G>C		NA		hg19		0.02	-0.421099	TCAxGCT	COVERED																																																																																			NOVEL					0			0	3.611622	KEEP	1	0	0	12	419	GG	0.993634	0.942364	0			5	60	170	0	0	13.086907	31	60	1178	77		0.138889	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21561753	21561753	__UNKNOWN__	IGR	SNP	G	G	A	rs34621173		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:21561753G>A			NA	NA				AC138710.1 (80582 upstream) : UBBP4 (167847 downstream)						NA		NA									NA						TCTGGGACTGGGTCGTGGGCC	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21561753G>A		NA		hg19		0.02	2.408385	CTGxGTC	COVERED																																																																																			NOVEL					0			4	6.187953	KEEP	0	2	58	41	1389	GG	1	0.994422	0			5	60	195	0	0	16.65601	18	60	651	143		0.217391	0.994422
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	22253144	22253144	__UNKNOWN__	IGR	SNP	T	T	C	rs4107688		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:22253144T>C			NA	NA				RP11-285M22.1 (60204 upstream) : None (None downstream)						NA		NA									NA						cttgggcctctctgaggattt	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.22253144T>C		NA		hg19		0.02	6.925938	CTCxCTG	COVERED																																																																																			NOVEL					0			41	22.336057	KEEP	64	2	71	99	3078	TT	1	1	0			7	46	264	0	0	20.884272	44	47	1628	420		0.137255	1
LRRC37B	114659	__UNKNOWN__	__UNKNOWN__	17	30349792	30349792	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:30349792C>T	ENST00000543378.2	+	4	1716	c.1381C>T	c.(1381-1383)Cgc>Tgc	p.R461C	LRRC37B_ENST00000581786.1_3'UTR|LRRC37B_ENST00000327564.7_Missense_Mutation_p.R570C|LRRC37B_ENST00000584368.1_Missense_Mutation_p.R555C|LRRC37B_ENST00000394713.3_Missense_Mutation_p.R543C|LRRC37B_ENST00000341671.7_Missense_Mutation_p.R543C			Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	543		NA				cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				GCAGAGGCTCCGCCAAGTGCC	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						76	78	77	NA		NA	NA	17		NA											NA				30349792		2201	4296	6497	SO:0001583	missense			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158	114659			29070	protein-coding gene	gene with protein product	KIAA0563-related	NA			NA	11468690, 10843809	Standard	NM_052888	NM_052888	NA	Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000543378.2:c.1381C>T	chr17.hg19:g.30349792C>T	ENSP00000443345:p.Arg461Cys	NA	Q17RC9|Q5YKG6	hg19		0.02	5.188534	CTCxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	N	10.66	1.412391	0.25465	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.68181	-0.25;-0.31;0.77;-0.3	1.79	1.79	0.24919	.	.	.	.	.	T	0.57475	0.2056	L	0.37850	1.14	0.09310	N	0.999997	D;D	0.76494	0.966;0.999	P;B	0.46452	0.517;0.423	T	0.50516	-0.8819	9	0.72032	D	0.01	.	7.0848	0.25252	0.0:1.0:0.0:0.0	.	543;543	Q17RC9;Q96QE4	.;LR37B_HUMAN	C	461;570;543;543	ENSP00000443345:R461C;ENSP00000332536:R570C;ENSP00000378202:R543C;ENSP00000340519:R543C	ENSP00000332536:R570C	R	+	1	0	LRRC37B	27373905	0.086000	0.21541	0.209000	0.23619	0.216000	0.24613	0.615000	0.24329	1.312000	0.45043	0.299000	0.19835	CGC	NOVEL	LRRC37B-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446503.1	0	7.520465	KEEP	0	0	0	25	832	CC	0.999931	0.999899	0		+	35	49	1316	0	0	119.995026	66	50	2383	160	ENST00000543378.2	0.346535	0.999968
AC116407.1	0	__UNKNOWN__	__UNKNOWN__	17	30462790	30462790	__UNKNOWN__	RNA	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:30462790T>C	ENST00000583230.1	-	0	43										NA		NA									NA						tggccctgtctgggcataaca	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000583230.1:	chr17.hg19:g.30462790T>C		NA		hg19		0.02	-0.175466	GTCxGGG	COVERED																																																																																			NOVEL	AC116407.1-201	NOVEL	basic	miRNA	NA	miRNA		3	3.008732	KEEP	3	0	0	10	302	TT	0.99254	0.384517	0		-	5	40	199	0	0	17.813045	12	60	454	35	ENST00000583230.1	0.294118	0.387407
AC116407.1	0	__UNKNOWN__	__UNKNOWN__	17	30462791	30462791	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:30462791G>A	ENST00000583230.1	-	0	42										NA		NA									NA						ggccctgtctgggcataacag	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000583230.1:	chr17.hg19:g.30462791G>A		NA		hg19		0.02	-0.175465	TCTxGGC	COVERED																																																																																			NOVEL	AC116407.1-201	NOVEL	basic	miRNA	NA	miRNA		3	3.009294	KEEP	3	0	0	10	329	GG	0.99254	0.384517	0		-	5	40	198	0	0	17.712988	12	60	451	35	ENST00000583230.1	0.294118	0.387407
SPACA3	124912	__UNKNOWN__	__UNKNOWN__	17	31324395	31324395	__UNKNOWN__	Intron	SNP	T	T	A	rs538091519	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:31324395T>A	ENST00000580599.1	+	5	704				SPACA3_ENST00000394637.2_Intron|SPACA3_ENST00000394638.1_Intron|SPACA3_ENST00000269053.3_Intron			Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	NA		NA			cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			agatacacactcacacacaca	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316	124912			16260	protein-coding gene	gene with protein product	cancer/testis antigen 54, sperm lyzozyme-like acrosomal protein 1	612749			NA	12606493	Standard	NM_173847	NM_173847	NA	Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000580599.1:c.296-68T>A	chr17.hg19:g.31324395T>A		NA	Q7Z4Y5	hg19		0.02	4.212336	CACxCAC	COVERED																																																																																			NOVEL	SPACA3-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447512.1	1	4.94704	KEEP	0	1	21	24	725	TT	0.999931	0.999924	0		+	9	60	209	0	0	12.116169	97	60	3479	164	ENST00000580599.1	0.084906	0.999993
CTB-91J4.1	0	__UNKNOWN__	__UNKNOWN__	17	34491235	34491235	__UNKNOWN__	RNA	SNP	G	G	A	rs187827179		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:34491235G>A	ENST00000592460.1	+	0	157										NA		NA									NA						AACAGCAGCTGCTCCTCCTCC	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000592460.1:	chr17.hg19:g.34491235G>A		NA		hg19		0.02	2.187684	GCTxCTC	COVERED																																																																																			NOVEL	CTB-91J4.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000450617.1	0	5.417858	KEEP	10	0	0	18	655	GG	0.999366	0.981333	0		+	22	49	803	0	0	74.287057	35	50	1331	109	ENST00000592460.1	0.385965	0.981955
TBC1D3	729873	__UNKNOWN__	__UNKNOWN__	17	36349314	36349314	__UNKNOWN__	Intron	SNP	G	G	A	rs62072924		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:36349314G>A	ENST00000537432.1	-	6	488				RP11-1407O15.2_ENST00000544906.1_Intron			Q8IZP1	TBC3A_HUMAN	TBC1 domain family, member 3	NA		NA				plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGCTGAGTCTGCCTGTGCCAT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45658.1	17q12	2014-09-16			ENSG00000274611	ENSG00000274419	729873			19031	protein-coding gene	gene with protein product	prostate cancer gene 17	607741			NA	12604796, 12359748, 16863688	Standard	NM_001123391	NM_001123391	NA	Approved	TBC1D3A, DKFZp434P2235, PRC17	uc002hoo.2	Q8IZP1	OTTHUMG00000188487	ENST00000537432.1:c.1-2232C>T	chr17.hg19:g.36349314G>A		NA	A6NGX2|A8K007|Q6DCB4|Q9H0B9|Q9UDD4	hg19	CCDS45658.1	0.02	2.196459	TCTxCCT	COVERED																																																																																			NOVEL	TBC1D3-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding		0	3.611821	KEEP	1	0	0	12	434	GG	0.993634	0.97329	0		-	8	49	278	0	0	21.64514	48	60	1886	93	ENST00000537432.1	0.142857	0.979526
TBC1D3	729873	__UNKNOWN__	__UNKNOWN__	17	36351203	36351203	__UNKNOWN__	Intron	SNP	C	C	T	rs6503735	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:36351203C>T	ENST00000537432.1	-	5	488				RP11-1407O15.2_ENST00000544906.1_Intron			Q8IZP1	TBC3A_HUMAN	TBC1 domain family, member 3	NA		NA				plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ccaccacacccggccCAGACT	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45658.1	17q12	2014-09-16			ENSG00000274611	ENSG00000274419	729873			19031	protein-coding gene	gene with protein product	prostate cancer gene 17	607741			NA	12604796, 12359748, 16863688	Standard	NM_001123391	NM_001123391	NA	Approved	TBC1D3A, DKFZp434P2235, PRC17	uc002hoo.2	Q8IZP1	OTTHUMG00000188487	ENST00000537432.1:c.0+732G>A	chr17.hg19:g.36351203C>T		NA	A6NGX2|A8K007|Q6DCB4|Q9H0B9|Q9UDD4	hg19	CCDS45658.1	0.02	-0.19299	ACCxGGC	COVERED																																																																																			NOVEL	TBC1D3-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding		2	3.608086	KEEP	0	0	0	12	397	CC	0.993634	0.454842	0		-	6	60	225	0	0	19.764804	16	60	531	43	ENST00000537432.1	0.272727	0.457757
RP11-1407O15.2	0	__UNKNOWN__	__UNKNOWN__	17	36384810	36384810	__UNKNOWN__	Intron	SNP	A	A	G	rs7215771		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:36384810A>G	ENST00000312412.4	-	3	340										NA		NA								kidney(1)|lung(3)	4						gtgagactctatctctaTTAG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000312412.4:c.341-9633T>C	chr17.hg19:g.36384810A>G		NA		hg19		0.02	2.31261	TCTxTCT	COVERED																																																																																			NOVEL	RP11-1407O15.2-202	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		2	5.113833	KEEP	0	0	0	17	501	AA	0.999366	0.998235	0		-	28	60	1047	0	0	96.161429	49	60	1710	100	ENST00000312412.4	0.363636	0.998867
RP11-1407O15.2	0	__UNKNOWN__	__UNKNOWN__	17	36385370	36385370	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:36385370A>C	ENST00000312412.4	-	3	340										NA		NA								kidney(1)|lung(3)	4						atctctactaaaaaaaattag	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000312412.4:c.341-10193T>G	chr17.hg19:g.36385370A>C		NA		hg19		0.02	-0.210556	CTAxAAA	COVERED																																																																																			NOVEL	RP11-1407O15.2-202	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		5	3.909364	KEEP	0	0	0	13	378	AA	0.994391	0.519232	0		-	5	60	199	0	0	16.951989	19	60	686	46	ENST00000312412.4	0.208333	0.522161
PCGF2	7703	__UNKNOWN__	__UNKNOWN__	17	36896667	36896667	__UNKNOWN__	5'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:36896667C>G	ENST00000580830.1	-	0	690				PCGF2_ENST00000579882.1_5'UTR|PCGF2_ENST00000578109.1_Intron|PCGF2_ENST00000585100.1_5'UTR|PCGF2_ENST00000360797.2_5'UTR|PCGF2_ENST00000581345.1_5'UTR			P35227	PCGF2_HUMAN	polycomb group ring finger 2	NA		NA			anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					ATTCCGGGGTCGGGGGTGGGG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						33	37	36	NA		NA	NA	17		NA											NA				36896667		2203	4300	6503	SO:0001623	5_prime_UTR_variant			D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258	7703		RING-type (C3HC4) zinc fingers, Polycomb group ring fingers	12929	protein-coding gene	gene with protein product		600346	ring finger protein 110	ZNF144, RNF110	NA	8325509	Standard	NM_007144	NM_007144	NA	Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.-12G>C	chr17.hg19:g.36896667C>G		NA	A6NGD8	hg19	CCDS32638.1	0.02	0.785549	GGTxGGG	COVERED																																																																																			NOVEL	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442246.2	0	8.103154	KEEP	0	6	42	43	1218	CC	1	0.999407	0		-	8	60	143	0	0	7.309875	72	60	2045	189	ENST00000580830.1	0.1	0.999407
KRTAP1-1	81851	__UNKNOWN__	__UNKNOWN__	17	39197538	39197538	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs146863522		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:39197538G>T	ENST00000306271.4	-	1	175	c.112C>A	c.(112-114)Cgc>Agc	p.R38S		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	38		NA	Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.R38S(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TCACAGCAGCGTGGCTGGCAG	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	NS(1)					NA						54	68	63	NA		NA	NA	17		NA											NA				39197538		2019	4207	6226	SO:0001583	missense			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581	81851		Keratin associated proteins	16772	protein-coding gene	gene with protein product		608819			NA	11279113	Standard	NM_030967	NM_030967	NA	Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.112C>A	chr17.hg19:g.39197538G>T	ENSP00000305975:p.Arg38Ser	NA	A6NC32|Q96S60|Q96S67	hg19	CCDS42324.1	0.02	8.482904	AGCxTGG	COVERED	93	0.042582417582417584	46	0.09349593495934959	8	0.022099447513812154	30	0.05244755244755245	9	0.011873350923482849	g	0.001	-3.345547	0.00016	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.24723	1.84	2.68	-1.04	0.10068	.	.	.	.	.	T	0.00144	0.0004	N	0.00031	-2.6	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.27226	-1.0080	8	0.02654	T	1	.	0.9532	0.01380	0.2199:0.1031:0.2626:0.4145	.	38	Q07627	KRA11_HUMAN	S	38;28	ENSP00000305975:R38S	ENSP00000305975:R38S	R	-	1	0	KRTAP1-1	36451064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.060000	0.14342	-0.640000	0.05495	-3.131000	0.00060	CGC	NOVEL	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257696.1	29	6.049128	KEEP	3	7	222	98	3111	GG	1	1	0		-	24	60	853	0	0	63.437385	207	60	6874	380	ENST00000306271.4	0.103896	1
KRTAP1-1	81851	__UNKNOWN__	__UNKNOWN__	17	39197549	39197549	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:39197549G>C	ENST00000306271.4	-	1	164	c.101C>G	c.(100-102)tCc>tGc	p.S34C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	34		NA	Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)		p.S34C(6)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCTGGCAGGAGCTGGTCTC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				6	Substitution - Missense(6)	kidney(4)|lung(1)|prostate(1)					NA						49	62	58	NA		NA	NA	17		NA											NA				39197549		2018	4199	6217	SO:0001583	missense			AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581	81851		Keratin associated proteins	16772	protein-coding gene	gene with protein product		608819			NA	11279113	Standard	NM_030967	NM_030967	NA	Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.101C>G	chr17.hg19:g.39197549G>C	ENSP00000305975:p.Ser34Cys	NA	A6NC32|Q96S60|Q96S67	hg19	CCDS42324.1	0.02	8.593113	CAGxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.085	-1.176298	0.01646	.	.	ENSG00000188581	ENST00000306271	T	0.16196	2.36	3.91	1.65	0.23941	.	.	.	.	.	T	0.01835	0.0058	N	0.00010	-3.04	0.22552	N	0.998996	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	9	0.02654	T	1	.	7.8006	0.29172	0.1777:0.6415:0.1808:0.0	.	34	Q07627	KRA11_HUMAN	C	34	ENSP00000305975:S34C	ENSP00000305975:S34C	S	-	2	0	KRTAP1-1	36451075	1.000000	0.71417	0.987000	0.45799	0.816000	0.46133	1.227000	0.32576	0.919000	0.36945	-0.233000	0.12211	TCC	NOVEL	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257696.1	29	2.556139	KEEP	3	7	257	98	3189	GG	1	1	0		-	23	42	834	0	0	61.464131	217	60	7768	404	ENST00000306271.4	0.095833	1
KRTAP4-11	653240	__UNKNOWN__	__UNKNOWN__	17	39274416	39274416	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs408579	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:39274416C>T	ENST00000391413.2	-	1	190	c.152G>A	c.(151-153)aGg>aAg	p.R51K		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	51	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].	NA	Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.R51K(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCACTGGGGCCTGCAGCAGCT	0.672	NA	NA											t|||	242	0.0483227	0.1248	0.0202	5008	,	,	NA	19066	0.005	NA	0.0219	False	NA	,,,	NA	NA	NA	2504	0.0368	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	endometrium(1)					NA						9	15	13	NA		NA	NA	17		NA											NA				39274416		682	1579	2261	SO:0001583	missense			AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721	653240		Keratin associated proteins	18911	protein-coding gene	gene with protein product		NA	keratin associated protein 4-14	KRTAP4-14	NA		Standard		NM_033059	NA	Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.152G>A	chr17.hg19:g.39274416C>T	ENSP00000375232:p.Arg51Lys	NA	A0AUY2	hg19	CCDS45675.1	0.02	5.755847	GGCxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	.	4.205	0.036712	0.08148	.	.	ENSG00000212721	ENST00000391413	T	0.01455	4.87	3.47	-1.13	0.09775	.	2.855670	0.02563	U	0.096976	T	0.02610	0.0079	M	0.72118	2.19	0.09310	N	1	B	0.25441	0.126	B	0.28916	0.096	T	0.52283	-0.8596	10	0.05959	T	0.93	.	3.7627	0.08610	0.1684:0.4051:0.0:0.4265	rs408579	51	Q9BYQ6	KR411_HUMAN	K	51	ENSP00000375232:R51K	ENSP00000375232:R51K	R	-	2	0	KRTAP4-11	36527942	0.000000	0.05858	0.002000	0.10522	0.072000	0.16883	-0.738000	0.04871	-0.091000	0.12440	-0.208000	0.12717	AGG	NOVEL	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257690.1	38	3.240447	KEEP	0	4	117	52	1745	CC	1	1	0		-	9	41	290	0	0	17.608399	180	60	6351	287	ENST00000391413.2	0.047619	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	39382884	39382884	__UNKNOWN__	IGR	SNP	G	G	A	rs1817968	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:39382884G>A			NA	NA				KRTAP9-1 (35993 upstream) : KRTAP9-2 (15 downstream)						NA		NA									NA						CTGAACAGAAGCCCACCCTCC	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						152	163	160	NA		NA	NA	17		NA											NA				39382884		2203	4297	6500	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.39382884G>A		NA		hg19		0.02	1.845407	GAAxCCC	COVERED																																																																																			NOVEL					0			2	2.751888	KEEP	5	1	13	14	480	GG	0.995343	0.986349	0			6	40	166	0	0	11.059413	56	60	2089	96		0.096774	0.990964
KRTAP9-2	83899	__UNKNOWN__	__UNKNOWN__	17	39383027	39383027	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs71371478	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:39383027G>T	ENST00000377721.3	+	1	128	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.A41S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	41	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].	NA				keratin filament (GO:0045095)		p.A41S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCAGCCCGCCTGCTGTGT	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	skin(1)					NA						59	53	55	NA		NA	NA	17		NA											NA				39383027		2203	4300	6503	SO:0001583	missense			AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886	83899		Keratin associated proteins	16926	protein-coding gene	gene with protein product		NA			NA	11279113	Standard		NM_031961	NA	Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.121G>T	chr17.hg19:g.39383027G>T	ENSP00000366950:p.Ala41Ser	NA	Q17RK8|Q2TB15|Q6ISF6	hg19	CCDS32651.1	0.02	1.749772	CCCxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.020245	0.00418	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01192	5.2;5.4	2.86	-2.81	0.05805	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	5.0512	0.14508	0.3642:0.0:0.0934:0.5425	.	41	Q9BYQ4	KRA92_HUMAN	S	41	ENSP00000366950:A41S;ENSP00000398325:A41S	ENSP00000366950:A41S	A	+	1	0	KRTAP9-2	36636553	0.000000	0.05858	0.088000	0.20740	0.203000	0.24098	-1.973000	0.01500	-1.243000	0.02519	-4.519000	0.00005	GCC	NOVEL	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257717.1	6	2.241384	KEEP	3	1	33	19	623	GG	0.99986	0.997758	0		+	4	40	138	0	0	9.00729	68	60	2217	107	ENST00000377721.3	0.055556	0.997898
RUNDC3A	10900	__UNKNOWN__	__UNKNOWN__	17	42390866	42390866	__UNKNOWN__	Silent	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:42390866C>A	ENST00000426726.3	+	4	727	c.453C>A	c.(451-453)acC>acA	p.T151T	RUNDC3A_ENST00000225441.7_Silent_p.T151T|RUNDC3A_ENST00000590941.1_Silent_p.T146T|AC003102.3_ENST00000588097.1_RNA	NM_001144825.1	NP_001138297.1	Q59EK9	RUN3A_HUMAN	RUN domain containing 3A	151	Interaction with RAP2A. {ECO:0000250}.|RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.	NA			positive regulation of cGMP biosynthetic process (GO:0030828)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanylate cyclase activator activity (GO:0030250)|small GTPase regulator activity (GO:0005083)			large_intestine(1)|lung(1)|ovary(2)	4		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		ACACCCGGACCACCAGGTCAG	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(82;1061 1416 11136 20771 23901)					NA		NA				0							NA						47	51	50	NA		NA	NA	17		NA											NA				42390866		2107	4236	6343	SO:0001819	synonymous_variant			AF055026	CCDS45698.1, CCDS45699.1, CCDS59294.1	17q21.31	2008-02-05			ENSG00000108309	ENSG00000108309	10900			16984	protein-coding gene	gene with protein product		605448			NA	9523700	Standard	NM_006695	NM_006695	NA	Approved	RPIP8, RAP2IP	uc002igl.4	Q59EK9	OTTHUMG00000169259	ENST00000426726.3:c.453C>A	chr17.hg19:g.42390866C>A		NA	B2R974|O15483|O60651|Q7Z3S2|Q9UF50	hg19	CCDS45698.1	0.02	9.151402	GACxACC	COVERED																																																																																			NOVEL	RUNDC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403173.2	0	21.669451	KEEP	0	0	0	72	2526	CC	1	1	0		+	44	60	1527	0	0	125.162893	184	60	6981	363	ENST00000426726.3	0.192982	1
FMNL1	752	__UNKNOWN__	__UNKNOWN__	17	43320559	43320559	__UNKNOWN__	Silent	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:43320559C>G	ENST00000331495.3	+	17	2421	c.2085C>G	c.(2083-2085)ctC>ctG	p.L695L	FMNL1_ENST00000328118.3_Silent_p.L695L|FMNL1_ENST00000587489.1_Silent_p.L273L	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	695	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.	NA			actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						TCAGCGCTCTCAAGAGTAAGG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(164;1247 1997 8702 11086 51972)					NA		NA				0							NA						84	90	88	NA		NA	NA	17		NA											NA				43320559		2203	4300	6503	SO:0001819	synonymous_variant			AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922	752			1212	protein-coding gene	gene with protein product		604656	formin-like	C17orf1B, FMNL	NA	9799091	Standard	NM_005892	NM_005892	NA	Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.2085C>G	chr17.hg19:g.43320559C>G		NA	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	hg19	CCDS11497.1	0.02	10.260965	TCTxAAG	COVERED																																																																																			NOVEL	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450198.1	6	30.134898	KEEP	0	1	16	106	3752	CC	1	1	0		+	100	60	3902	0	0	367.589092	138	60	5359	462	ENST00000331495.3	0.420168	1
FMNL1	752	__UNKNOWN__	__UNKNOWN__	17	43323615	43323615	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:43323615C>T	ENST00000331495.3	+	25	3465	c.3129C>T	c.(3127-3129)atC>atT	p.I1043I	CTD-2020K17.4_ENST00000420431.2_RNA|FMNL1_ENST00000328118.3_Silent_p.I1043I|FMNL1_ENST00000587489.1_Silent_p.I621I	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	1043		NA			actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						TGGACCTCATCTCTGAGCTGA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(164;1247 1997 8702 11086 51972)					NA		NA				0							NA						81	82	82	NA		NA	NA	17		NA											NA				43323615		2203	4300	6503	SO:0001819	synonymous_variant			AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922	752			1212	protein-coding gene	gene with protein product		604656	formin-like	C17orf1B, FMNL	NA	9799091	Standard	NM_005892	NM_005892	NA	Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.3129C>T	chr17.hg19:g.43323615C>T		NA	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	hg19	CCDS11497.1	0.02	12.28332	CATxTCT	COVERED																																																																																			NOVEL	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450198.1	1	21.600438	KEEP	0	1	23	80	2791	CC	1	1	0		+	86	60	3038	0	0	273.652129	171	60	6474	423	ENST00000331495.3	0.33463	1
MAPT	4137	__UNKNOWN__	__UNKNOWN__	17	44084008	44084008	__UNKNOWN__	Intron	SNP	T	T	C	rs12946693	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:44084008T>C	ENST00000415613.2	+	11	1827				MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	NA		NA			adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	tagctgggcatggtggctcac	0.468	NA	NA											T|||	2409	0.48103	0.5295	0.4496	5008	,	,	NA	15436	0.495	NA	0.5746	False	NA	,,,	NA	NA	NA	2504	0.3272	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868	4137			6893	protein-coding gene	gene with protein product	G protein beta1/gamma2 subunit-interacting factor 1, microtubule-associated protein tau, isoform 4, protein phosphatase 1, regulatory subunit 103	157140		DDPAC, MAPTL	NA	7936241, 3131773	Standard	NM_016835	NM_001123067	NA	Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000415613.2:c.1828-3668T>C	chr17.hg19:g.44084008T>C		NA	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	hg19	CCDS45715.1	0.02	-0.043867	GCAxGGT	UNCOVERED																																																																																			NOVEL	MAPT-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401265.1	3	2.405985	KEEP	1	0	0	8	241	TT	0	0	0		+	5	60	186	0	0	20.985154	0	0	0	17	ENST00000415613.2	1	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44351743	44351743	__UNKNOWN__	IGR	SNP	G	G	A	rs2696541	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:44351743G>A			NA	NA				RP11-259G18.1 (6858 upstream) : ARL17B (406 downstream)						NA		NA									NA						ACCAGAGTCTGTAGTCCAGGA	0.363	NA	NA											G|||	392	0.0782748	0.0151	0.1441	5008	,	,	NA	25357	0.001	NA	0.2107	False	NA	,,,	NA	NA	NA	2504	0.0603	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44351743G>A		NA		hg19		0.02	2.138369	TCTxTAG	COVERED																																																																																			NOVEL					0			2	2.542495	KEEP	0	1	30	19	652	GG	0.999863	0.998064	0			6	60	210	0	0	15.092401	61	60	2290	102		0.089552	0.9982
ARL17B	100506084	__UNKNOWN__	__UNKNOWN__	17	44363276	44363276	__UNKNOWN__	Intron	SNP	G	G	A	rs373334752		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:44363276G>A	ENST00000570618.1	-	5	505							Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)			pancreas(1)	1						TGTAAGGAACGGAGCACCCTC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696	100506084		ADP-ribosylation factors-like, ADP-ribosylation factors	32387	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 17	ARL17	NA		Standard	NM_001039083	NM_001039083	NA	Approved			Q8IVW1	OTTHUMG00000178031	ENST00000570618.1:c.376-10492C>T	chr17.hg19:g.44363276G>A		NA	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	hg19	CCDS54137.1	0.02	8.793589	AACxGAG	COVERED																																																																																			NOVEL	ARL17B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440291.1	2	3.548025	KEEP	0	4	123	55	1824	GG	1	1	0		-	8	49	300	0	0	18.564522	234	50	7869	352	ENST00000570618.1	0.033058	1
ARL17B	100506084	__UNKNOWN__	__UNKNOWN__	17	44363594	44363594	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:44363594C>T	ENST00000570618.1	-	5	505							Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)			pancreas(1)	1						CTTTCAAGATCGACATTCCAG	0.274	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696	100506084		ADP-ribosylation factors-like, ADP-ribosylation factors	32387	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 17	ARL17	NA		Standard	NM_001039083	NM_001039083	NA	Approved			Q8IVW1	OTTHUMG00000178031	ENST00000570618.1:c.376-10810G>A	chr17.hg19:g.44363594C>T		NA	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	hg19	CCDS54137.1	0.02	1.78787	GATxGAC	COVERED																																																																																			NOVEL	ARL17B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440291.1	4	2.407569	KEEP	1	0	0	8	264	CC	0.99257	0.991794	0		-	10	47	357	0	0	27.393063	70	50	2315	89	ENST00000570618.1	0.125	0.999218
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45214564	45214564	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs201184967		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:45214564A>T	ENST00000531206.1	-	14	1888	c.1885T>A	c.(1885-1887)Tgt>Agt	p.C629S	CDC27_ENST00000446365.2_Missense_Mutation_p.C562S|CDC27_ENST00000527547.1_Missense_Mutation_p.C622S|CDC27_ENST00000066544.3_Missense_Mutation_p.C623S			P30260	CDC27_HUMAN	cell division cycle 27	623		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTCGAAAACAAGCTAATGCT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						59	61	60	NA		NA	NA	17		NA											NA				45214564		2203	4300	6503	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.1885T>A	chr17.hg19:g.45214564A>T	ENSP00000434614:p.Cys629Ser	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	24.038067	AACxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.90	2.968854	0.53614	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.42245	0.1194	L	0.33485	1.01	0.80722	D	1	D;P;P;P	0.55172	0.97;0.698;0.698;0.936	P;B;B;P	0.56751	0.805;0.112;0.112;0.491	T	0.12889	-1.0530	10	0.25751	T	0.34	-10.7595	14.1085	0.65107	1.0:0.0:0.0:0.0	.	562;622;629;623	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	623;629;562;622	ENSP00000066544:C623S;ENSP00000434614:C629S;ENSP00000392802:C562S;ENSP00000437339:C622S	ENSP00000066544:C623S	C	-	1	0	CDC27	42569563	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.529000	0.81952	2.228000	0.72767	0.477000	0.44152	TGT	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	52	12.792497	KEEP	3	8	255	132	4034	AA	1	1	0		-	18	60	639	0	0	50.186109	106	60	3831	881	ENST00000531206.1	0.145161	1
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45214606	45214606	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs79260965		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:45214606G>T	ENST00000531206.1	-	14	1846	c.1843C>A	c.(1843-1845)Cat>Aat	p.H615N	CDC27_ENST00000446365.2_Missense_Mutation_p.H548N|CDC27_ENST00000527547.1_Missense_Mutation_p.H608N|CDC27_ENST00000066544.3_Missense_Mutation_p.H609N			P30260	CDC27_HUMAN	cell division cycle 27	609		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						ACAAACTCATGCCCTAATAGA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						60	63	62	NA		NA	NA	17		NA											NA				45214606		2203	4300	6503	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.1843C>A	chr17.hg19:g.45214606G>T	ENSP00000434614:p.His615Asn	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	12.604989	CATxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	35	5.460249	0.96240	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72431	0.3459	M	0.93507	3.425	0.80722	D	1	D;D;P;D	0.59767	0.986;0.982;0.95;0.97	P;P;P;P	0.55260	0.772;0.662;0.728;0.705	T	0.79727	-0.1682	10	0.62326	D	0.03	-29.2384	17.5633	0.87913	0.0:0.0:1.0:0.0	.	548;608;615;609	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	N	609;615;548;608	ENSP00000066544:H609N;ENSP00000434614:H615N;ENSP00000392802:H548N;ENSP00000437339:H608N	ENSP00000066544:H609N	H	-	1	0	CDC27	42569605	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.869000	0.99810	2.761000	0.94854	0.585000	0.79938	CAT	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	28	13.92734	KEEP	3	3	96	80	2757	GG	1	1	0		-	18	60	640	0	0	53.544463	67	60	2477	466	ENST00000531206.1	0.211765	1
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45234303	45234303	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs200611688		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:45234303G>C	ENST00000531206.1	-	7	821	c.818C>G	c.(817-819)gCa>gGa	p.A273G	CDC27_ENST00000446365.2_Missense_Mutation_p.A212G|CDC27_ENST00000527547.1_Missense_Mutation_p.A273G|CDC27_ENST00000066544.3_Missense_Mutation_p.A273G			P30260	CDC27_HUMAN	cell division cycle 27	273		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						ACTAAGAGCTGCTGGTCCTCC	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						62	66	65	NA		NA	NA	17		NA											NA				45234303		2201	4293	6494	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.818C>G	chr17.hg19:g.45234303G>C	ENSP00000434614:p.Ala273Gly	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	9.04777	GCTxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.95	2.983381	0.53827	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.69175	-0.37;-0.38;-0.11;-0.36;0.76	5.64	5.64	0.86602	.	0.116892	0.56097	D	0.000021	T	0.54647	0.1871	L	0.29908	0.895	0.51233	D	0.999911	B;P;P;B	0.43094	0.304;0.629;0.799;0.304	B;B;B;B	0.36092	0.15;0.213;0.217;0.046	T	0.57911	-0.7729	10	0.40728	T	0.16	-26.4879	17.2083	0.86924	0.0:0.0:1.0:0.0	.	212;273;273;273	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	G	273;273;212;273;273	ENSP00000066544:A273G;ENSP00000434614:A273G;ENSP00000392802:A212G;ENSP00000437339:A273G;ENSP00000432105:A273G	ENSP00000066544:A273G	A	-	2	0	CDC27	42589302	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.260000	0.95568	2.665000	0.90641	0.460000	0.39030	GCA	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	16	12.372022	KEEP	1	1	34	53	1909	GG	1	1	0		-	11	60	412	0	0	31.158002	94	60	3561	360	ENST00000531206.1	0.104762	1
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45234417	45234417	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs193061947		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:45234417A>G	ENST00000531206.1	-	7	707	c.704T>C	c.(703-705)aTt>aCt	p.I235T	CDC27_ENST00000446365.2_Missense_Mutation_p.I174T|CDC27_ENST00000527547.1_Missense_Mutation_p.I235T|CDC27_ENST00000066544.3_Missense_Mutation_p.I235T			P30260	CDC27_HUMAN	cell division cycle 27	235		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AGCTGAATCAATATAAGACAC	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						36	41	39	NA		NA	NA	17		NA											NA				45234417		2182	4288	6470	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.704T>C	chr17.hg19:g.45234417A>G	ENSP00000434614:p.Ile235Thr	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	2.206648	TCAxTAT	COVERED	.	.	.	.	.	.	.	.	.	.	A	16.60	3.168932	0.57584	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68025	-0.3;-0.29;0.02;-0.3;0.81	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	N	0.24115	0.695	0.58432	D	0.999999	B;B;B;B	0.25667	0.004;0.131;0.032;0.008	B;B;B;B	0.23419	0.006;0.046;0.008;0.004	T	0.46830	-0.9163	10	0.14656	T	0.56	-16.8692	13.444	0.61129	1.0:0.0:0.0:0.0	.	174;235;235;235	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	T	235;235;174;235;235	ENSP00000066544:I235T;ENSP00000434614:I235T;ENSP00000392802:I174T;ENSP00000437339:I235T;ENSP00000432105:I235T	ENSP00000066544:I235T	I	-	2	0	CDC27	42589416	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.754000	0.91642	2.066000	0.61787	0.377000	0.23210	ATT	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	3	5.716203	KEEP	7	0	0	19	562	AA	0.999859	0.999663	0		-	3	20	119	0	0	8.810511	34	60	1220	119	ENST00000531206.1	0.081081	0.999804
NPEPPS	9520	__UNKNOWN__	__UNKNOWN__	17	45623441	45623441	__UNKNOWN__	Intron	SNP	A	A	T	rs200025451|rs181591349|rs200936566	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:45623441A>T	ENST00000322157.4	+	2	577				NPEPPS_ENST00000530173.1_Intron|NPEPPS_ENST00000525037.1_Intron|NPEPPS_ENST00000544660.1_Intron	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	NA		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						tgtgtgtgtgagagagagaga	0.438	NA	NA											A|||	2675	0.534145	0.5575	0.4841	5008	,	,	NA	16313	0.5942	NA	0.501	False	NA	,,,	NA	NA	NA	2504	0.5102	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	9520	3.4.11.2		7900	protein-coding gene	gene with protein product	puromycin-sensitive aminopeptidase, metalloproteinase MP100	606793			NA	9048733, 10329370	Standard	NM_006310	NM_006310	NA	Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.340+82A>T	chr17.hg19:g.45623441A>T		NA	B7Z463|Q6P145|Q9NP16|Q9UEM2	hg19	CCDS45721.1	0.02	1.959957	GTGxGAG	COVERED																																																																																			NOVEL	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384269.1	0	2.643283	KEEP	0	1	14	14	410	AA	0.99649	0.99598	0		+	26	60	916	0	0	82.429176	52	60	1878	112	ENST00000322157.4	0.333333	0.999487
NPEPPS	9520	__UNKNOWN__	__UNKNOWN__	17	45668087	45668087	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A	rs376523771		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:45668087G>A	ENST00000322157.4	+	10	1337	c.1100G>A	c.(1099-1101)tGg>tAg	p.W367*	NPEPPS_ENST00000530173.1_Nonsense_Mutation_p.W363*|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Nonsense_Mutation_p.W287*	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	367		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						TTTTAGGAATGGTGGACTCAT	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						78	71	73	NA		NA	NA	17		NA											NA				45668087		1824	4076	5900	SO:0001587	stop_gained			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	9520	3.4.11.2		7900	protein-coding gene	gene with protein product	puromycin-sensitive aminopeptidase, metalloproteinase MP100	606793			NA	9048733, 10329370	Standard	NM_006310	NM_006310	NA	Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1100G>A	chr17.hg19:g.45668087G>A	ENSP00000320324:p.Trp367*	NA	B7Z463|Q6P145|Q9NP16|Q9UEM2	hg19	CCDS45721.1	0.02	8.017333	AATxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	25.5	4.640414	0.87859	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660;ENST00000527964;ENST00000527360	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.9233	0.97095	0.0:0.0:1.0:0.0	.	.	.	.	X	363;367;354;287;50;64	.	ENSP00000320324:W367X	W	+	2	0	NPEPPS	43023086	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.703000	0.98714	2.704000	0.92352	0.591000	0.81541	TGG	NOVEL	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384269.1	2	15.348959	KEEP	79	0	0	51	1762	GG	0.999999	0.999999	0		+	13	27	464	0	0	30.856799	219	60	8325	365	ENST00000322157.4	0.056034	1
HOXB6	3216	__UNKNOWN__	__UNKNOWN__	17	46673026	46673026	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:46673026G>T	ENST00000484302.2	-	0	2046				HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000476204.1_RNA			P17509	HXB6_HUMAN	homeobox B6	NA		NA			anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						CGCCTTTGCTGAAGAATTCTG	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511	3216		Homeoboxes / ANTP class : HOXL subclass	5117	protein-coding gene	gene with protein product		142961	homeo box B6	HOX2, HOX2B	NA	1973146, 1358459	Standard		XM_005257284	NA	Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.*749C>A	chr17.hg19:g.46673026G>T		NA	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	hg19	CCDS11531.1	0.02	6.307774	GCTxAAG	COVERED																																																																																			NOVEL	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358146.2	3	13.611361	KEEP	0	1	7	48	1582	GG	1	1	0		-	48	60	1718	0	0	151.498169	117	60	4362	241	ENST00000484302.2	0.290909	1
HOXB6	3216	__UNKNOWN__	__UNKNOWN__	17	46673038	46673038	__UNKNOWN__	3'UTR	SNP	C	C	G	rs183318604		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:46673038C>G	ENST00000484302.2	-	0	2034				HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000476204.1_RNA			P17509	HXB6_HUMAN	homeobox B6	NA		NA			anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte homeostasis (GO:0034101)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(1)|lung(4)	7						AGAATTCTGGCTCAGGAAAGA	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS11531.1	17q21.32	2011-06-20	2005-12-22		ENSG00000108511	ENSG00000108511	3216		Homeoboxes / ANTP class : HOXL subclass	5117	protein-coding gene	gene with protein product		142961	homeo box B6	HOX2, HOX2B	NA	1973146, 1358459	Standard		XM_005257284	NA	Approved		uc002ins.1	P17509	OTTHUMG00000159912	ENST00000484302.2:c.*737G>C	chr17.hg19:g.46673038C>G		NA	A8K835|D3DTV5|P09068|Q9HB11|Q9UGH2	hg19	CCDS11531.1	0.02	7.207032	TGGxTCA	COVERED																																																																																			NOVEL	HOXB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358146.2	2	13.241438	KEEP	0	0	0	44	1524	CC	1	1	0		-	53	60	1951	0	0	175.423458	112	60	4167	228	ENST00000484302.2	0.321212	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	60530333	60530333	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:60530333T>C			NA	NA				METTL2A (2879 upstream) : TLK2 (5685 downstream)						NA		NA									NA						TTTCCATTACTGTATTTACTT	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.60530333T>C		NA		hg19		0.02	9.62433	TACxGTA	COVERED																																																																																			NOVEL					0			4	8.123469	KEEP	1	0	0	27	825	TT	0.999988	0.999988	0			23	49	763	1	0	53.829249	230	60	8692	348		0.090909	1
PRKCA	5578	__UNKNOWN__	__UNKNOWN__	17	64795065	64795065	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:64795065G>A	ENST00000413366.3	+	17	1880					NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	NA		NA			activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	ggtggtggtggtggtggtggt	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	5578	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA	NA		Standard		NM_002737	NA	Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1855-4926G>A	chr17.hg19:g.64795065G>A		NA	B5BU22|Q15137|Q32M72|Q96RE4	hg19	CCDS11664.1	0.02	-0.139589	GTGxTGG	COVERED																																																																																			NOVEL	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000446976.1	4	7.105208	KEEP	34	0	0	24	740	GG	0.994391	0.290363	0		+	3	24	72	0	0	6.503957	4	13	142	99	ENST00000413366.3	0.428571	0.292001
TMEM104	54868	__UNKNOWN__	__UNKNOWN__	17	72832671	72832671	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:72832671C>T	ENST00000417024.2	+	10	915				TMEM104_ENST00000582330.1_Missense_Mutation_p.R446C|TMEM104_ENST00000582773.1_Intron|TMEM104_ENST00000335464.5_Missense_Mutation_p.R446C			Q8NE00	TM104_HUMAN	transmembrane protein 104	NA		NA				integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					GTACCACTGCCGCAGGGACAC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						56	47	50	NA		NA	NA	17		NA											NA				72832671		2203	4300	6503	SO:0001627	intron_variant			AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066	54868			25984	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017728	NM_017728	NA	Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000417024.2:c.770-2355C>T	chr17.hg19:g.72832671C>T		NA	Q8TEU1|Q9NT56|Q9NXH1	hg19		0.02	10.306579	TGCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	23.1	4.370075	0.82573	.	.	ENSG00000109066	ENST00000335464	T	0.56776	0.44	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.78874	0.4352	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83318	-0.0019	10	0.72032	D	0.01	-31.4614	19.021	0.92916	0.0:1.0:0.0:0.0	.	446	Q8NE00	TM104_HUMAN	C	446	ENSP00000334849:R446C	ENSP00000334849:R446C	R	+	1	0	TMEM104	70344266	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.568000	0.53820	2.584000	0.87258	0.462000	0.41574	CGC	NOVEL	TMEM104-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000444438.1	2	18.6902	KEEP	0	1	28	72	2419	CC	1	1	0		+	108	60	3957	0	0	377.243177	125	60	4417	350	ENST00000417024.2	0.463519	1
MIF4GD	57409	__UNKNOWN__	__UNKNOWN__	17	73265611	73265611	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:73265611C>T	ENST00000578305.1	-	2	189				MIF4GD_ENST00000579297.1_Intron|MIF4GD_ENST00000577542.1_Intron|MIF4GD_ENST00000579119.1_Intron|MIF4GD_ENST00000580571.1_Intron|MIF4GD_ENST00000245551.5_Intron|MIF4GD_ENST00000325102.8_Intron			A9UHW6	MI4GD_HUMAN	MIF4G domain containing	NA		NA			regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)	10	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			GAGCCGTGTTCTTTTTTTTAT	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			CR605810	CCDS11719.1, CCDS56044.1, CCDS58598.1	17q25.1	2005-12-15		2005-12-15			57409			24030	protein-coding gene	gene with protein product		612072		MIFD	NA		Standard	NM_020679	NM_001242498	NA	Approved	AD023, MGC45027	uc002jnq.3	A9UHW6		ENST00000578305.1:c.82+583G>A	chr17.hg19:g.73265611C>T		NA	B4DUM7|Q8N4Q5|Q9HBL5	hg19		0.02	0.817055	GTTxTTT	COVERED																																																																																			NOVEL	MIF4GD-014	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446677.1	2	2.618418	KEEP	0	1	20	16	489	CC	0.999366	0.994453	0		-	6	60	140	0	0	8.135214	61	60	2048	117	ENST00000578305.1	0.089552	0.995084
QRICH2	84074	__UNKNOWN__	__UNKNOWN__	17	74286054	74286054	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:74286054T>G	ENST00000262765.5	-	5	3480					NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	NA		NA								breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						aaagacaaaGTGGGTTGACTC	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						102	117	112	NA		NA	NA	17		NA											NA				74286054		2203	4300	6503	SO:0001627	intron_variant			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646	84074			25326	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032134	NM_032134	NA	Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.3300+18A>C	chr17.hg19:g.74286054T>G		NA	A2RRE1|Q96LM3	hg19	CCDS32741.1	0.02	1.033608	AAGxGGG	COVERED																																																																																			NOVEL	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395140.1	9	7.600773	KEEP	0	3	15	31	910	TT	0.999998	0.999998	0		-	10	60	192	0	0	8.986496	116	60	3526	226	ENST00000262765.5	0.079365	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74559679	74559679	__UNKNOWN__	IGR	SNP	G	G	T	rs200359199		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:74559679G>T			NA	NA				SNHG16 (1892 upstream) : ST6GALNAC2 (1781 downstream)						NA		NA									NA						TGGTGTCTCCGCAGAGTGCCT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74559679G>T		NA		hg19		0.02	23.376805	TCCxCAG	COVERED																																																																																			NOVEL					0			10	7.391212	KEEP	3	5	137	73	2424	GG	1	1	0			34	52	1252	0	0	88.902514	422	60	14782	568		0.074561	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74559687	74559687	__UNKNOWN__	IGR	SNP	C	C	G	rs201470689		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:74559687C>G			NA	NA				SNHG16 (1900 upstream) : ST6GALNAC2 (1773 downstream)						NA		NA									NA						CCGCAGAGTGCCTTCCAGGAA	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74559687C>G		NA		hg19		0.02	18.396742	GTGxCTT	COVERED																																																																																			NOVEL					0			9	9.365841	KEEP	4	4	116	72	2527	CC	1	1	0			22	33	794	0	0	52.141658	411	60	15025	551		0.050808	1
CCDC40	55036	__UNKNOWN__	__UNKNOWN__	17	78058810	78058810	__UNKNOWN__	Intron	SNP	G	G	A	rs369919631		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:78058810G>A	ENST00000397545.4	+	13	2262				CCDC40_ENST00000374877.3_Intron	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	NA		NA			axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GCAGGGAGACGTGGTCCCCGG	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	G		0,3990		0,0,1995	26	27	26	NA		0.2	0	17		26	1,8315		0,1,4157	no	intron	CCDC40	NM_017950.3		0,1,6152	AA,AG,GG	NA	0.012,0.0,0.0081			78058810	1,12305	1995	4158	6153	SO:0001627	intron_variant			AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519	55036			26090	protein-coding gene	gene with protein product		613799			NA	21131974	Standard	XM_371082	NM_017950	NA	Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.2235+23G>A	chr17.hg19:g.78058810G>A		NA	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	hg19	CCDS42395.1	0.02	2.308446	GACxTGG	COVERED																																																																																			NOVEL	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256005.2	0	7.522873	KEEP	0	0	0	25	849	GG	0.999931	0.994354	0		+	23	60	817	0	0	74.140897	43	60	1619	94	ENST00000397545.4	0.348485	0.994422
RPTOR	57521	__UNKNOWN__	__UNKNOWN__	17	78897327	78897327	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:78897327C>A	ENST00000306801.3	+	23	3024	c.2662C>A	c.(2662-2664)Ctg>Atg	p.L888M	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Missense_Mutation_p.L730M	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	888		NA			cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CAGCTCCAGCCTGACCAACGA	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						42	46	45	NA		NA	NA	17		NA											NA				78897327		2201	4300	6501	SO:0001583	missense				CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564	57521		WD repeat domain containing	30287	protein-coding gene	gene with protein product	regulatory associated protein of mTOR	607130			NA	10718198, 12150926	Standard	NM_020761	NM_001163034	NA	Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.2662C>A	chr17.hg19:g.78897327C>A	ENSP00000307272:p.Leu888Met	NA	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	hg19	CCDS11773.1	0.02	14.349706	AGCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.8	4.195527	0.78902	.	.	ENSG00000141564	ENST00000306801;ENST00000544334	T;T	0.50001	0.77;0.76	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000012	T	0.63367	0.2505	M	0.63843	1.955	0.80722	D	1	D;P	0.69078	0.997;0.944	D;P	0.78314	0.991;0.496	T	0.61554	-0.7039	10	0.36615	T	0.2	.	12.7653	0.57388	0.0:0.9207:0.0:0.0793	.	730;888	F5H7J5;Q8N122	.;RPTOR_HUMAN	M	888;730	ENSP00000307272:L888M;ENSP00000442479:L730M	ENSP00000307272:L888M	L	+	1	2	RPTOR	76511922	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.310000	0.59141	2.313000	0.78055	0.655000	0.94253	CTG	NOVEL	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438125.1	2	63.495039	KEEP	0	0	0	211	7225	CC	1	1	0		+	145	60	5123	1	0	490.080365	159	60	5852	635	ENST00000306801.3	0.476974	1
FSCN2	25794	__UNKNOWN__	__UNKNOWN__	17	79496618	79496618	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:79496618G>C	ENST00000417245.2	+	1	962				FSCN2_ENST00000334850.7_Intron	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	NA		NA			actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			AGAGGCAAGGGTTCCTGGCCT	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765	25794		Fascins	3960	protein-coding gene	gene with protein product		607643	fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal), fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)		NA	10234509	Standard	NM_012418	NM_012418	NA	Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.826+235G>C	chr17.hg19:g.79496618G>C		NA	A0AVC4|A8MRA6	hg19	CCDS45811.1	0.02	7.329005	AGGxTTC	COVERED																																																																																			NOVEL	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394746.1	2	21.300895	KEEP	0	1	35	83	2905	GG	1	1	0		+	21	60	795	0	0	63.011647	131	60	4921	305	ENST00000417245.2	0.138158	1
PCYT2	5833	__UNKNOWN__	__UNKNOWN__	17	79866720	79866720	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:79866720C>G	ENST00000538936.2	-	3	449				PCYT2_ENST00000570391.1_Intron|PCYT2_ENST00000571105.1_Intron|PCYT2_ENST00000570388.1_Intron|PCYT2_ENST00000331285.3_Intron|PCYT2_ENST00000538721.2_Intron	NM_001256435.1|NM_002861.3	NP_001243364.1|NP_002852.1	Q99447	PCY2_HUMAN	phosphate cytidylyltransferase 2, ethanolamine	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)	ethanolamine-phosphate cytidylyltransferase activity (GO:0004306)			breast(2)|endometrium(1)|lung(4)|ovary(1)	8	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		Lamivudine(DB00709)	CCTGATGTCCCCAGGCCCCCA	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						42	49	47	NA		NA	NA	17		NA											NA				79866720		2201	4296	6497	SO:0001627	intron_variant			D84307	CCDS11791.1, CCDS54178.1, CCDS58610.1, CCDS62364.1	17q25.3	2008-07-18				ENSG00000185813	5833			8756	protein-coding gene	gene with protein product		602679			NA	9083101	Standard	NM_002861	XM_005256386	NA	Approved	ET	uc002kch.2	Q99447		ENST00000538936.2:c.340+31G>C	chr17.hg19:g.79866720C>G		NA	B7Z7A5|B7ZAS0|F5H8B1|Q6IBM3|Q96G08	hg19	CCDS11791.1	0.02	6.255702	TCCxCAG	COVERED																																																																																			NOVEL	PCYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439939.1	0	20.735033	KEEP	0	0	0	69	2264	CC	1	1	0		-	102	60	3285	0	0	326.62194	70	60	2487	314	ENST00000538936.2	0.593023	1
CCDC57	284001	__UNKNOWN__	__UNKNOWN__	17	80108891	80108891	__UNKNOWN__	Intron	SNP	T	T	A	rs74982371		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:80108891T>A	ENST00000389641.4	-	15	2278				CCDC57_ENST00000392346.2_Intron|CCDC57_ENST00000392347.1_Intron			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	NA		NA								endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			ACCCAGAACCTGGCACACACC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155	284001			27564	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_198082	XM_006722279	NA	Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2242-5162A>T	chr17.hg19:g.80108891T>A		NA	A6NP51|A8MQC7|Q8IWG2|Q8TER3	hg19		0.02	-0.052639	ACCxGGC	UNCOVERED																																																																																			NOVEL	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000277182.3	0	3.608419	KEEP	0	0	0	12	331	TT	0.993634	0.036532	0		-	2	40	73	0	0	6.595659	4	60	142	19	ENST00000389641.4	0.333333	0.036766
FOXK2	3607	__UNKNOWN__	__UNKNOWN__	17	80544191	80544191	__UNKNOWN__	Intron	SNP	A	A	T	rs200361741		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:80544191A>T	ENST00000335255.5	+	7	1750					NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			cgggggggaaaggaggagagg	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568	3607		Forkhead boxes	6036	protein-coding gene	gene with protein product		147685	interleukin enhancer binding factor 1	ILF, ILF1	NA	3260003	Standard	NM_181430	NM_004514	NA	Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1576+115A>T	chr17.hg19:g.80544191A>T		NA	A6NEP5|Q13622|Q13623|Q13624	hg19	CCDS11813.1	0.02	-0.287688	GAAxGGA	UNCOVERED																																																																																			NOVEL	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277099.2	3	2.234047	KEEP	36	1	30	18	515	AA	0	0	0		+	5	60	147	0	0	12.353716	14	34	414	106	ENST00000335255.5	0.263158	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	81083301	81083301	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr17:81083301C>T			NA	NA				AC144831.1 (19441 upstream) : AC139099.4 (8598 downstream)						NA		NA									NA						TGCCGGGCGACTCTCAGGGCA	0.697	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.81083301C>T		NA		hg19		0.02	2.387673	CGAxTCT	COVERED																																																																																			NOVEL					0			1	8.050084	KEEP	2	1	26	36	1174	CC	0.999999	0.981955	0			4	49	129	0	0	9.215106	35	60	1277	123		0.102564	0.981955
RP11-683L23.1	0	__UNKNOWN__	__UNKNOWN__	18	49125	49125	__UNKNOWN__	Silent	SNP	G	G	T	rs11875825	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:49125G>T	ENST00000573909.1	-	2	626	c.94C>A	c.(94-96)Cga>Aga	p.R32R	RP11-683L23.1_ENST00000308911.6_Intron						NA		NA									NA						GACGGGGGTCGCACCGCTGGC	0.692	NA	NA											.|||	3029	0.604832	0.4561	0.5663	5008	,	,	NA	11689	0.8839	NA	0.5288	False	NA	,,,	NA	NA	NA	2504	0.6237	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000573909.1:c.94C>A	chr18.hg19:g.49125G>T		NA		hg19		0.02	-0.061408	GTCxCAC	UNCOVERED																																																																																			NOVEL	RP11-683L23.1-002	PUTATIVE	not_best_in_genome_evidence|basic	protein_coding	NA	protein_coding	OTTHUMT00000439819.1	0	2.407706	KEEP	0	0	0	8	273	GG	0.99257	0.043461	0		-	2	24	75	0	0	6.795763	4	50	133	20	ENST00000573909.1	0.333333	0.043787
RP11-683L23.1	0	__UNKNOWN__	__UNKNOWN__	18	49208	49208	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:49208G>A	ENST00000573909.1	-	2	543	c.11C>T	c.(10-12)cCa>cTa	p.P4L	RP11-683L23.1_ENST00000308911.6_Silent_p.A29A						NA		NA									NA						CGGAGTCGATGGCATGTTCAT	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000573909.1:c.11C>T	chr18.hg19:g.49208G>A	ENSP00000459638:p.Pro4Leu	NA		hg19		0.02	-0.140361	GATxGCA	COVERED																																																																																			NOVEL	RP11-683L23.1-002	PUTATIVE	not_best_in_genome_evidence|basic	protein_coding	NA	protein_coding	OTTHUMT00000439819.1	1	5.415832	KEEP	1	0	0	18	618	GG	0.999859	0.260928	0		-	4	47	134	0	0	11.401117	12	60	440	47	ENST00000573909.1	0.25	0.260965
L3MBTL4	91133	__UNKNOWN__	__UNKNOWN__	18	5954738	5954738	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:5954738C>G	ENST00000284898.6	-	0	3553				L3MBTL4_ENST00000317931.7_3'UTR|L3MBTL4_ENST00000400105.2_3'UTR|L3MBTL4_ENST00000535782.1_3'UTR	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	NA		NA			chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				TGtttattatcatttaaaata	0.333	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(41;748 902 17366 28959 43175)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655	91133		Sterile alpha motif (SAM) domain containing	26677	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_173464	NM_173464	NA	Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.*1481G>C	chr18.hg19:g.5954738C>G		NA	A8MTL8|Q8IXS3	hg19	CCDS11839.2	0.02	-0.245654	TATxATT	COVERED																																																																																			NOVEL	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254448.2	0	2.708757	KEEP	0	0	0	9	312	CC	0.99254	0.636563	0		-	13	60	486	0	0	46.404322	15	70	581	45	ENST00000284898.6	0.464286	0.641347
L3MBTL4	91133	__UNKNOWN__	__UNKNOWN__	18	6125544	6125544	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:6125544C>A	ENST00000284898.6	-	14	1400				L3MBTL4_ENST00000317931.7_Intron|L3MBTL4_ENST00000400105.2_Intron|L3MBTL4_ENST00000400104.3_Intron|L3MBTL4_ENST00000535782.1_Intron	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)	NA		NA			chromatin modification (GO:0016568)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		Colorectal(10;0.0249)				cctcccacctcagcctgctga	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(41;748 902 17366 28959 43175)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039316	CCDS11839.2	18p11.31-p11.23	2013-01-10			ENSG00000154655	ENSG00000154655	91133		Sterile alpha motif (SAM) domain containing	26677	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_173464	NM_173464	NA	Approved	FLJ35936, HsT1031	uc010dkt.3	Q8NA19	OTTHUMG00000131573	ENST00000284898.6:c.1199+12648G>T	chr18.hg19:g.6125544C>A		NA	A8MTL8|Q8IXS3	hg19	CCDS11839.2	0.02	-0.096507	CCTxAGC	UNCOVERED																																																																																			NOVEL	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254448.2	2	2.407909	KEEP	0	0	0	8	290	CC	0.99257	0.119541	0		-	4	60	144	0	0	13.177	7	60	270	24	ENST00000284898.6	0.363636	0.120436
VAPA	9218	__UNKNOWN__	__UNKNOWN__	18	9944866	9944866	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:9944866A>T	ENST00000400000.2	+	5	672				VAPA_ENST00000584796.1_Intron|VAPA_ENST00000340541.4_Intron	NM_003574.5|NM_194434.2	NP_003565.4|NP_919415.2	Q9P0L0	VAPA_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein A, 33kDa	NA		NA			cell death (GO:0008219)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein localization to endoplasmic reticulum (GO:0070972)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	protein heterodimerization activity (GO:0046982)|signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(1)|lung(2)|prostate(1)	4						aatatcatgcagaagaaatca	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11847.2, CCDS11848.2	18p11.2	2008-07-28	2002-08-29		ENSG00000101558	ENSG00000101558	9218			12648	protein-coding gene	gene with protein product		605703	VAMP (vesicle-associated membrane protein)-associated protein A (33kD)		NA	9920726, 9657962	Standard		NM_003574	NA	Approved	hVAP-33, VAP-A	uc002koj.3	Q9P0L0	OTTHUMG00000131603	ENST00000400000.2:c.418-5526A>T	chr18.hg19:g.9944866A>T		NA	A6NDZ0|D3DUI3|O75453|Q5U0E7|Q9UBZ2	hg19	CCDS11848.2	0.02	4.219685	TGCxGAA	COVERED																																																																																			NOVEL	VAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254490.1	0	6.319182	KEEP	0	0	0	21	664	AA	0.999869	0.999861	0		+	8	60	300	0	0	21.40097	101	60	3781	151	ENST00000400000.2	0.073394	0.999992
IMPA2	3613	__UNKNOWN__	__UNKNOWN__	18	12029089	12029089	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:12029089A>C	ENST00000269159.3	+	7	993				IMPA2_ENST00000588927.1_Intron|IMPA2_ENST00000589238.1_Intron	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	NA		NA			inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	TGAATTTCCCACCTTCCCCAG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3613	3.1.3.25		6051	protein-coding gene	gene with protein product		605922			NA	9322233	Standard		NM_014214	NA	Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.751+97A>C	chr18.hg19:g.12029089A>C		NA	B0YJ29|Q9UJT3	hg19	CCDS11855.1	0.02	1.550897	CCCxCCT	COVERED																																																																																			NOVEL	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254601.1	6	3.99256	KEEP	0	3	46	30	777	AA	0.999998	0.999993	0		+	13	60	200	0	1	9.482953	97	60	3074	189	ENST00000269159.3	0.118182	0.999995
POTEC	388468	__UNKNOWN__	__UNKNOWN__	18	14543039	14543039	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs45570841	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:14543039T>C	ENST00000358970.5	-	1	106	c.107A>G	c.(106-108)aAg>aGg	p.K36R	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	36		NA	K -> R (in dbSNP:rs45570841).							NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GCCGCTCCCCTTGCAGCAGGG	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						114	96	101	NA		NA	NA	18		NA											NA				14543039		692	1591	2283	SO:0001583	missense			BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206	388468		POTE ankyrin domain containing, Ankyrin repeat domain containing	33894	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 6	NA	ANKRD26-like family B, member 2	A26B2	NA		Standard	XM_496269	NM_001137671	NA	Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.107A>G	chr18.hg19:g.14543039T>C	ENSP00000351856:p.Lys36Arg	NA		hg19	CCDS45835.1	0.02	9.074387	CCCxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.041299	0.00402	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.23950	1.88	0.722	-0.942	0.10398	.	.	.	.	.	T	0.04634	0.0126	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21930	-1.0231	8	0.02654	T	1	.	.	.	.	rs45570841	36	B2RU33	POTEC_HUMAN	R	36	ENSP00000351856:K36R	ENSP00000351856:K36R	K	-	2	0	POTEC	14533039	0.001000	0.12720	0.001000	0.08648	0.123000	0.20343	-1.546000	0.02188	-1.423000	0.02002	-1.128000	0.01989	AAG	NOVEL	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371179.1	2	10.302463	KEEP	1	2	77	61	1913	TT	1	1	0		-	16	44	556	0	0	38.60413	198	60	7382	349	ENST00000358970.5	0.074766	1
POTEC	388468	__UNKNOWN__	__UNKNOWN__	18	14543161	14543161	__UNKNOWN__	5'UTR	SNP	C	C	A	rs367913261|rs45446896	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:14543161C>A	ENST00000389891.4	-	0	331							B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	NA		NA								NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TTTAACAGCCCGGGGAGGCCG	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						90	73	79	NA		NA	NA	18		NA											NA				14543161		692	1590	2282	SO:0001623	5_prime_UTR_variant			BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206	388468		POTE ankyrin domain containing, Ankyrin repeat domain containing	33894	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 6	NA	ANKRD26-like family B, member 2	A26B2	NA		Standard	XM_496269	NM_001137671	NA	Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000389891.4:c.-1227G>T	chr18.hg19:g.14543161C>A		NA		hg19		0.02	2.271704	GCCxGGG	COVERED																																																																																			NOVEL	POTEC-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000443010.1	1	9.629529	KEEP	1	0	0	32	1040	CC	0.999997	0.999892	0		-	5	27	197	0	0	13.6286	88	60	2849	136	ENST00000389891.4	0.053763	0.999895
POTEC	388468	__UNKNOWN__	__UNKNOWN__	18	14543477	14543477	__UNKNOWN__	5'UTR	SNP	G	G	A	rs372286696		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:14543477G>A	ENST00000389891.4	-	0	15							B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	NA		NA								NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						tgcgagggaggaaacgccaat	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206	388468		POTE ankyrin domain containing, Ankyrin repeat domain containing	33894	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 6	NA	ANKRD26-like family B, member 2	A26B2	NA		Standard	XM_496269	NM_001137671	NA	Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000389891.4:c.-1543C>T	chr18.hg19:g.14543477G>A		NA		hg19		0.02	-0.315683	GAGxAAA	COVERED																																																																																			NOVEL	POTEC-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000443010.1	0	3.909482	KEEP	0	0	0	13	431	GG	0.994391	0.813874	0		-	3	21	108	0	0	7.748505	33	60	1215	68	ENST00000389891.4	0.083333	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	15224388	15224388	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:15224388G>A			NA	NA				RP11-454P7.3 (26660 upstream) : AP005901.1 (89166 downstream)						NA		NA									NA						tgcccaggctggagtgcaatg	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.15224388G>A		NA		hg19		0.02	-0.052635	GCTxGAG	UNCOVERED																																																																																			NOVEL					0			0	2.708925	KEEP	4	0	0	9	326	GG	0	0	0			2	22	72	0	0	6.495729	4	40	143	24		0.333333	0.036766
KATNAL2	83473	__UNKNOWN__	__UNKNOWN__	18	44555147	44555147	__UNKNOWN__	Intron	SNP	T	T	G	rs139717358	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:44555147T>G	ENST00000592005.1	+	3	724				TCEB3C_ENST00000330682.2_Missense_Mutation_p.E356A|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron					katanin p60 subunit A-like 2	NA		NA								central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						GGGGACCCCTTCCACGTCGCC	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	T	,ALA/GLU	71,3171		0,71,1550	233	223	226	NA	,1067	-1.6	0	18	dbSNP_134	226	595,6065		0,595,2735	no	intron,missense	KATNAL2,TCEB3C	NM_031303.2,NM_145653.3	,107	0,666,4285	GG,GT,TT	NA	8.9339,2.19,6.7259	,benign	,356/547	44555147	666,9236	1621	3330	4951	SO:0001627	intron_variant			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216	83473		ATPases / AAA-type	25387	protein-coding gene	gene with protein product		614697			NA	12477932	Standard	NM_031303	NM_031303	NA	Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.51+28261T>G	chr18.hg19:g.44555147T>G		NA		hg19		0.02	7.207513	CCTxCCA	COVERED	.	.	.	.	.	.	.	.	.	.	t	5.286	0.238258	0.10023	0.0219	0.089339	ENSG00000183791	ENST00000330682	T	0.29397	1.57	1.6	-1.61	0.08399	.	0.408249	0.20310	N	0.094854	T	0.00580	0.0019	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.10382	-1.0632	10	0.62326	D	0.03	-1.0576	6.2705	0.20951	0.0:0.6512:0.0:0.3488	.	356	Q8NG57	ELOA3_HUMAN	A	356	ENSP00000328232:E356A	ENSP00000328232:E356A	E	-	2	0	TCEB3C	42809145	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.045000	0.12003	-0.528000	0.06366	-1.744000	0.00683	GAA	NOVEL	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446324.2	4	8.114307	KEEP	83	9	309	135	4099	TT	1	1	0		+	15	50	557	0	0	39.726159	185	50	6685	504	ENST00000592005.1	0.075	1
CCDC102B	79839	__UNKNOWN__	__UNKNOWN__	18	66722099	66722099	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:66722099A>G	ENST00000360242.5	+	0	2384				CCDC102B_ENST00000319445.6_3'UTR	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	NA		NA								breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				CTAGGTAGAAATCAGGCCAAA	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636	79839			26295	protein-coding gene	gene with protein product		NA	chromosome 18 open reading frame 14, aminoacylase 1-like	C18orf14, ACY1L	NA	14702039	Standard	NM_024781	NM_001093729	NA	Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.*725A>G	chr18.hg19:g.66722099A>G		NA	Q7Z467|Q8NDK7|Q9H5C1	hg19	CCDS11996.2	0.02	4.728878	GAAxTCA	COVERED																																																																																			NOVEL	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256225.2	1	9.628848	KEEP	0	0	0	32	1008	AA	0.999997	0.999997	0		+	70	60	2691	0	0	259.756969	72	60	2678	225	ENST00000360242.5	0.492958	1
SALL3	27164	__UNKNOWN__	__UNKNOWN__	18	76754749	76754749	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr18:76754749C>T	ENST00000537592.2	+	2	2758	c.2758C>T	c.(2758-2760)Ccg>Tcg	p.P920S	SALL3_ENST00000575389.2_Missense_Mutation_p.P920S|SALL3_ENST00000536229.3_Missense_Mutation_p.P787S	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	920		NA			forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CTCCAAGTCCCCGGGCCTGGG	0.766	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						6	8	7	NA		NA	NA	18		NA											NA				76754749		1844	3827	5671	SO:0001583	missense			AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463	27164		Zinc fingers, C2H2-type	10527	protein-coding gene	gene with protein product		605079	sal (Drosophila)-like 3, sal-like 3 (Drosophila)		NA	10610715	Standard	NM_171999	NM_171999	NA	Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2758C>T	chr18.hg19:g.76754749C>T	ENSP00000441823:p.Pro920Ser	NA	Q9UGH1	hg19	CCDS12013.1	0.02	-0.403513	TCCxCGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.55	1.671683	0.29693	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.11930	2.73	5.49	5.49	0.81192	.	0.000000	0.56097	D	0.000026	T	0.40932	0.1137	M	0.80616	2.505	0.80722	D	1	P;D	0.89917	0.539;1.0	B;D	0.71414	0.284;0.973	T	0.11867	-1.0570	10	0.33141	T	0.24	-35.3838	19.4094	0.94662	0.0:1.0:0.0:0.0	.	652;920	F5GXY4;Q9BXA9	.;SALL3_HUMAN	S	920;920;652	ENSP00000441823:P920S	ENSP00000299466:P920S	P	+	1	0	SALL3	74855737	1.000000	0.71417	0.946000	0.38457	0.406000	0.30931	5.567000	0.67378	2.583000	0.87209	0.561000	0.74099	CCG	NOVEL	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256397.1	0	18.893338	KEEP	0	0	0	63	2077	CC	1	0.934492	0		+	27	60	974	0	0	96.732455	19	60	679	141	ENST00000537592.2	0.586957	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	156581	156581	__UNKNOWN__	IGR	SNP	T	T	C	rs199596742	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:156581T>C			NA	NA				OR4F17 (44885 upstream) : AC016626.2 (2779 downstream)						NA		NA									NA						ATTAGAAGTATGAAGAAAGTA	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.156581T>C		NA		hg19		0.02	2.522371	GTAxGAA	COVERED																																																																																			NOVEL					0			0	2.707275	KEEP	13	0	0	9	259	TT	0.99257	0.963607	0			19	40	688	0	0	62.844639	34	40	1262	74		0.358491	0.97082
PPAP2C	8612	__UNKNOWN__	__UNKNOWN__	19	282401	282401	__UNKNOWN__	Intron	SNP	C	C	T	rs112688465		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:282401C>T	ENST00000269812.3	-	5	590				PPAP2C_ENST00000327790.3_Intron|PPAP2C_ENST00000434325.2_Intron	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	NA		NA			dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCTGCCAGGCGCTCCCCCTC	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	8612	3.1.3.4		9230	protein-coding gene	gene with protein product		607126			NA	9570154, 9607309	Standard		NM_177543	NA	Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.541-91G>A	chr19.hg19:g.282401C>T		NA	A6NLV0|E9PAY8	hg19	CCDS12023.1	0.02	-0.306985	AGGxGCT	COVERED																																																																																			NOVEL	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451777.2	0	2.708218	KEEP	0	0	0	9	283	CC	0.99254	0.812359	0		-	3	60	110	0	0	7.986339	32	60	1008	48	ENST00000269812.3	0.085714	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	479771	479771	__UNKNOWN__	IGR	SNP	T	T	C	rs2392795	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:479771T>C			NA	NA				ODF3L2 (4788 upstream) : MADCAM1 (9404 downstream)						NA		NA									NA						ctcctgaccttgtgatccgcc	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.479771T>C		NA		hg19		0.02	-0.078949	CCTxGTG	UNCOVERED																																																																																			NOVEL					0			1	2.406742	KEEP	0	0	0	8	240	TT	0.99257	0.076761	0			3	60	92	0	0	8.143179	6	60	210	22		0.333333	0.077336
HCN2	610	__UNKNOWN__	__UNKNOWN__	19	603516	603516	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:603516C>T	ENST00000251287.2	+	2	685					NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	NA		NA			cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGGCACCGGCCTGAGGTGTG	0.672	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Melanoma(145;1175 2427 8056 36306)					NA		NA				0							NA						32	31	32	NA		NA	NA	19		NA											NA				603516		2190	4290	6480	SO:0001627	intron_variant			AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822	610		Voltage-gated ion channels / Cyclic nucleotide-regulated channels	4846	protein-coding gene	gene with protein product		602781		BCNG2	NA	9405696, 9630217, 16382102	Standard	NM_001194	NM_001194	NA	Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.633-28C>T	chr19.hg19:g.603516C>T		NA	O60742|O60743|O75267|Q9UBS2	hg19	CCDS12035.1	0.02	1.877446	CGGxCTG	COVERED																																																																																			NOVEL	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452100.1	1	5.417491	KEEP	0	0	0	18	631	CC	0.999859	0.999177	0		+	19	60	630	0	0	52.904799	62	60	2266	114	ENST00000251287.2	0.234568	0.999317
MED16	10025	__UNKNOWN__	__UNKNOWN__	19	879828	879828	__UNKNOWN__	Intron	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:879828C>A	ENST00000589119.1	-	7	1353				MED16_ENST00000395808.3_Intron|MED16_ENST00000269814.4_Intron|MED16_ENST00000325464.1_Intron|MED16_ENST00000606828.1_Intron|MED16_ENST00000312090.6_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	NA		NA			androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGCCAGCCCCACGTGCCCC	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221	10025		WD repeat domain containing	17556	protein-coding gene	gene with protein product		604062	thyroid hormone receptor associated protein 5	THRAP5	NA	10235266, 10198638	Standard	NM_005481	NM_005481	NA	Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1353+108G>T	chr19.hg19:g.879828C>A		NA	Q6PJT2|Q96AD4|Q96I35|Q9Y652	hg19	CCDS12047.1	0.02	-0.175385	GCCxCAC	COVERED																																																																																			NOVEL	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000457902.3	2	3.310156	KEEP	4	0	0	11	359	CC	0.992708	0.384582	0		-	3	60	105	0	0	8.410349	15	60	510	47	ENST00000589119.1	0.166667	0.387407
MED16	10025	__UNKNOWN__	__UNKNOWN__	19	879855	879855	__UNKNOWN__	Intron	SNP	C	C	G	rs199801344		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:879855C>G	ENST00000589119.1	-	7	1353				MED16_ENST00000395808.3_Intron|MED16_ENST00000269814.4_Intron|MED16_ENST00000325464.1_Intron|MED16_ENST00000606828.1_Intron|MED16_ENST00000312090.6_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	NA		NA			androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACCTTCCCCTGGTTGTCAA	0.692	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221	10025		WD repeat domain containing	17556	protein-coding gene	gene with protein product		604062	thyroid hormone receptor associated protein 5	THRAP5	NA	10235266, 10198638	Standard	NM_005481	NM_005481	NA	Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1353+81G>C	chr19.hg19:g.879855C>G		NA	Q6PJT2|Q96AD4|Q96I35|Q9Y652	hg19	CCDS12047.1	0.02	-0.131582	CCCxTGG	COVERED																																																																																			NOVEL	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000457902.3	0	2.700713	KEEP	2	0	0	9	288	CC	0.99254	0.227464	0		-	3	49	104	0	0	8.672667	11	60	389	32	ENST00000589119.1	0.214286	0.229173
NFIC	4782	__UNKNOWN__	__UNKNOWN__	19	3439880	3439880	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:3439880G>A	ENST00000443272.2	+	6	1009				NFIC_ENST00000589123.1_Intron|NFIC_ENST00000341919.3_Intron|NFIC_ENST00000586919.1_Intron|NFIC_ENST00000346156.5_Intron|NFIC_ENST00000395111.3_Intron|NFIC_ENST00000590282.1_Intron	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	NA		NA			DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		tagagacggggtttcaccgtg	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905	4782			7786	protein-coding gene	gene with protein product		600729		NFI	NA	3398920, 7590749	Standard	NM_005597	NM_205843	NA	Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.958+4675G>A	chr19.hg19:g.3439880G>A		NA	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	hg19	CCDS59330.1	0.02	-0.043844	GGGxTTT	UNCOVERED																																																																																			NOVEL	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452834.1	2	2.708388	KEEP	2	0	0	9	297	GG	0.99254	0.023894	0		+	2	30	73	0	0	7.424803	1	48	39	17	ENST00000443272.2	0.666667	0.024074
PIP5K1C	23396	__UNKNOWN__	__UNKNOWN__	19	3648561	3648561	__UNKNOWN__	Intron	SNP	C	C	T	rs34162087		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:3648561C>T	ENST00000589578.1	-	9	1211				PIP5K1C_ENST00000335312.3_Intron|PIP5K1C_ENST00000539785.1_Intron|PIP5K1C_ENST00000537021.1_Intron			O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	NA		NA			actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GACCCGGGCGCCCACCTGTGG	0.701	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(135;99 1744 12852 27186 39851)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111	23396			8996	protein-coding gene	gene with protein product		606102			NA	9535851	Standard	NM_012398	NM_001195733	NA	Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000589578.1:c.1211+61G>A	chr19.hg19:g.3648561C>T		NA	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	hg19		0.02	-0.39477	GCGxCCA	COVERED																																																																																			NOVEL	PIP5K1C-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000453628.1	0	2.641657	KEEP	0	1	23	17	576	CC	0.999859	0.926509	0		-	4	60	147	0	0	10.830328	39	60	1403	70	ENST00000589578.1	0.093023	0.92664
ACER1	125981	__UNKNOWN__	__UNKNOWN__	19	6306873	6306873	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:6306873G>A	ENST00000301452.4	-	6	724	c.647C>T	c.(646-648)aCc>aTc	p.T216I		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	216		NA			cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						ATAAGGGAAGGTGATGCTGAT	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						75	53	60	NA		NA	NA	19		NA											NA				6306873		2203	4300	6503	SO:0001583	missense			AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	125981	3.5.1.23	Alkaline ceramidase	18356	protein-coding gene	gene with protein product		613491	N-acylsphingosine amidohydrolase (alkaline ceramidase) 3	ASAH3	NA	12783875	Standard	NM_133492	NM_133492	NA	Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.647C>T	chr19.hg19:g.6306873G>A	ENSP00000301452:p.Thr216Ile	NA		hg19	CCDS12161.1	0.02	4.678684	AAGxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	20.2	3.945443	0.73672	.	.	ENSG00000167769	ENST00000301452	T	0.44881	0.91	5.49	3.32	0.38043	.	0.224020	0.46145	D	0.000301	T	0.45856	0.1363	M	0.63428	1.95	0.41201	D	0.986372	P	0.46327	0.876	P	0.47864	0.559	T	0.50575	-0.8812	10	0.72032	D	0.01	-34.5272	9.7205	0.40300	0.0796:0.1407:0.7797:0.0	.	216	Q8TDN7	ACER1_HUMAN	I	216	ENSP00000301452:T216I	ENSP00000301452:T216I	T	-	2	0	ACER1	6257873	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	4.128000	0.57951	1.311000	0.45024	0.655000	0.94253	ACC	NOVEL	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452982.1	1	13.240344	KEEP	0	0	0	44	1550	GG	1	0.999999	0		-	46	60	1680	0	0	154.244058	79	60	2958	201	ENST00000301452.4	0.368	0.999999
ADAMTS10	81794	__UNKNOWN__	__UNKNOWN__	19	8654577	8654577	__UNKNOWN__	Intron	SNP	G	G	A	rs74178113	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:8654577G>A	ENST00000597188.1	-	17	2171				ADAMTS10_ENST00000270328.4_Intron|ADAMTS10_ENST00000595838.1_Intron	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	NA		NA				extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CCAAGAGGAAGGGCAGCTTGG	0.667	NA	NA											G|||	748	0.149361	0.1172	0.1888	5008	,	,	NA	13734	0.125	NA	0.1978	False	NA	,,,	NA	NA	NA	2504	0.1401	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303	81794		ADAM metallopeptidases with thrombospondin type 1 motif	13201	protein-coding gene	gene with protein product		608990	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10		NA		Standard	NM_030957	XM_005272499	NA	Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.1901-108C>T	chr19.hg19:g.8654577G>A		NA	M0QZE4	hg19	CCDS12206.1	0.02	-0.298247	GAAxGGC	COVERED																																																																																			NOVEL	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460085.3	1	2.407868	KEEP	0	0	0	8	281	GG	0.99257	0.775257	0		-	13	60	468	0	0	43.180868	21	60	729	44	ENST00000597188.1	0.382353	0.78106
COL5A3	50509	__UNKNOWN__	__UNKNOWN__	19	10091280	10091280	__UNKNOWN__	Intron	SNP	A	A	T	rs58569966	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:10091280A>T	ENST00000264828.3	-	35	2690					NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	NA		NA			axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCTCTCTCTcacacacacaca	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573	50509		Collagens	14864	protein-coding gene	gene with protein product		120216			NA	10722718	Standard	NM_015719	NM_015719	NA	Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2604+43T>A	chr19.hg19:g.10091280A>T		NA	Q9NZQ6	hg19	CCDS12222.1	0.02	2.508294	CTCxCAC	COVERED																																																																																			NOVEL	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315788.1	0	4.813806	KEEP	0	0	0	16	493	AA	0.997832	0.992266	0		-	5	60	189	0	0	13.632192	60	60	2140	86	ENST00000264828.3	0.076923	0.994422
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	11380855	11380855	__UNKNOWN__	IGR	SNP	C	C	G	rs12971903	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:11380855C>G			NA	NA				DOCK6 (7727 upstream) : TSPAN16 (25968 downstream)						NA		NA									NA						aggccaaggccggtggatcaa	0.542	NA	NA											g|||	2651	0.529353	0.1142	0.6225	5008	,	,	NA	15386	0.6399	NA	0.7028	False	NA	,,,	NA	NA	NA	2504	0.7321	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.11380855C>G		NA		hg19		0.02	-0.412345	GGCxGGT	COVERED																																																																																			NOVEL					0			106	19.405675	KEEP	116	3	101	100	3445	CC	1	0.941741	0			5	60	182	0	0	20.585021	0	0	0	275		1	0.941741
ZNF44	51710	__UNKNOWN__	__UNKNOWN__	19	12382803	12382803	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:12382803G>A	ENST00000356109.5	-	0	2529					NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		CTATTTGAAAGAAATGGAAAC	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857	51710		Zinc fingers, C2H2-type, -	13110	protein-coding gene	gene with protein product		194542	zinc finger protein 58, zinc finger protein 44 (KOX 7), zinc finger protein 55	ZNF58, ZNF55	NA	1946370, 1505991	Standard	NM_016264	NM_016264	NA	Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.*419C>T	chr19.hg19:g.12382803G>A		NA	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	hg19	CCDS54223.1	0.02	0.905427	AAAxAAA	COVERED																																																																																			NOVEL	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344132.1	2	2.91986	KEEP	0	1	11	14	417	GG	0.997832	0.994072	0		-	15	60	169	0	0	8.676642	53	70	1554	101	ENST00000356109.5	0.220588	0.996233
MAN2B1	4125	__UNKNOWN__	__UNKNOWN__	19	12768825	12768825	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:12768825T>G	ENST00000456935.2	-	10	1350				MAN2B1_ENST00000221363.4_Intron|MAN2B1_ENST00000495617.1_Intron	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	NA		NA			cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGCCTAGGGGTGGTTTCCAAC	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						17	18	18	NA		NA	NA	19		NA											NA				12768825		1566	3576	5142	SO:0001627	intron_variant				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	4125	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB	NA		Standard		NM_000528	NA	Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.1309+51A>C	chr19.hg19:g.12768825T>G		NA	G5E928|O15330|Q16680|Q93094|Q9BW13	hg19	CCDS32919.1	0.02	3.889302	GGGxGGT	COVERED																																																																																			NOVEL	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344062.1	2	6.079347	KEEP	0	3	61	42	1009	TT	1	1	0		-	17	70	330	0	0	19.636551	119	60	3162	218	ENST00000456935.2	0.125	1
DHPS	1725	__UNKNOWN__	__UNKNOWN__	19	12792615	12792615	__UNKNOWN__	5'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:12792615C>G	ENST00000210060.7	-	0	101					NM_001930.3	NP_001921.1	P49366	DHYS_HUMAN	deoxyhypusine synthase	NA		NA			cellular protein metabolic process (GO:0044267)|deoxyhypusine biosynthetic process from spermidine (GO:0050983)|glucose homeostasis (GO:0042593)|peptidyl-lysine modification to peptidyl-hypusine (GO:0008612)|positive regulation of cell proliferation (GO:0008284)|positive regulation of T cell proliferation (GO:0042102)|post-translational protein modification (GO:0043687)|protein homotetramerization (GO:0051289)|translation (GO:0006412)	cytosol (GO:0005829)	deoxyhypusine synthase activity (GO:0034038)			central_nervous_system(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)	8						AAAGCTGCCCCTAGGCCGGGC	0.662	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						9	12	11	NA		NA	NA	19		NA											NA				12792615		2171	4262	6433	SO:0001623	5_prime_UTR_variant			U79262	CCDS12276.1, CCDS12277.1, CCDS59354.1	19p13.2	2011-11-24			ENSG00000095059	ENSG00000095059	1725			2869	protein-coding gene	gene with protein product	migration-inducing gene 13	600944			NA	7673224	Standard	NM_001930	NM_001930	NA	Approved	MIG13	uc002muh.2	P49366		ENST00000210060.7:c.-35G>C	chr19.hg19:g.12792615C>G		NA	A8K688|M0R1I5|Q13184|Q13276|Q9UDG0	hg19	CCDS12276.1	0.02	2.145122	CCCxTAG	COVERED																																																																																			NOVEL	DHPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462708.1	3	7.825139	KEEP	0	0	0	26	910	CC	0.999957	0.999887	0		-	14	60	513	0	0	40.6627	82	60	3054	126	ENST00000210060.7	0.145833	0.99993
C19orf43	79002	__UNKNOWN__	__UNKNOWN__	19	12845256	12845256	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:12845256C>T	ENST00000592273.1	-	1	224	c.216G>A	c.(214-216)aaG>aaA	p.K72K	C19orf43_ENST00000588213.1_Silent_p.K72K|C19orf43_ENST00000242784.4_Silent_p.K72K			Q9BQ61	CS043_HUMAN	chromosome 19 open reading frame 43	72		NA								endometrium(2)|large_intestine(2)	4						CCTCCTCCATCTTCCGCTTGA	0.726	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						7	5	6	NA		NA	NA	19		NA											NA				12845256		1921	3799	5720	SO:0001819	synonymous_variant			AK027588	CCDS12279.1	19p13.2	2011-11-24			ENSG00000123144	ENSG00000123144	79002			28424	protein-coding gene	gene with protein product	functional spliceosome-associated protein 18	NA			NA	12477932	Standard	NM_024038	NM_024038	NA	Approved	MGC2803, fSAP18	uc002muu.3	Q9BQ61		ENST00000592273.1:c.216G>A	chr19.hg19:g.12845256C>T		NA		hg19		0.02	36.843887	CATxTTC	COVERED																																																																																			NOVEL	C19orf43-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000450855.1	4	103.625053	KEEP	0	1	18	351	11939	CC	1	1	0		-	122	60	4385	0	0	347.304848	693	60	25894	1510	ENST00000592273.1	0.149693	1
ASNA1	439	__UNKNOWN__	__UNKNOWN__	19	12849502	12849502	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:12849502C>T	ENST00000591090.1	+	3	411				ASNA1_ENST00000357332.3_Intron					arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)	NA		NA								endometrium(1)|lung(6)|ovary(3)	10						GCCCCCACTTCTGGGAAAAGC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						46	41	43	NA		NA	NA	19		NA											NA				12849502		2203	4300	6503	SO:0001627	intron_variant			U60276	CCDS32920.1	19p13.13	2010-08-05	2001-12-04			ENSG00000198356	439			752	protein-coding gene	gene with protein product	golgi to ER traffic 3 homolog (S. cerevisiae), transmembrane domain recognition complex, 40kDa	601913	arsA (bacterial) arsenite transporter, ATP-binding, homolog 1		NA	8884272, 17382883	Standard	NM_004317	NM_004317	NA	Approved	ARSA-I, GET3, TRC40	uc002muv.3	O43681		ENST00000591090.1:c.309+30C>T	chr19.hg19:g.12849502C>T		NA		hg19	CCDS32920.1	0.02	6.440845	CTTxTGG	COVERED																																																																																			NOVEL	ASNA1-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450921.1	1	3.912773	KEEP	0	0	0	13	467	CC	0.994391	0.994391	0		+	22	60	783	0	0	59.499557	163	60	6153	238	ENST00000591090.1	0.118919	1
RAD23A	5886	__UNKNOWN__	__UNKNOWN__	19	13056888	13056888	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:13056888T>G	ENST00000586534.1	+	1	133				RAD23A_ENST00000316856.3_Intron|RAD23A_ENST00000588826.2_Intron|RAD23A_ENST00000541222.1_Intron|RAD23A_ENST00000592268.1_Intron			P54725	RD23A_HUMAN	RAD23 homolog A (S. cerevisiae)	NA		NA			nucleotide-excision repair (GO:0006289)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)|ubiquitin-specific protease binding (GO:1990381)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12						GGGGGTGGGGTGGGGGCGGGG	0.746	NA	NA						Nucleotide excision repair (NER)						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						1	1	1	NA		NA	NA	19		NA											NA				13056888		399	898	1297	SO:0001627	intron_variant				CCDS12289.1, CCDS59357.1, CCDS59358.1	19p13.2	2008-07-17	2001-11-28			ENSG00000179262	5886			9812	protein-coding gene	gene with protein product	RAD23, yeast homolog, A	600061	RAD23 (S. cerevisiae) homolog A		NA	7851894	Standard	NM_005053	NM_005053	NA	Approved	HHR23A, MGC111083	uc002mvw.2	P54725		ENST00000586534.1:c.72+54T>G	chr19.hg19:g.13056888T>G		NA	K7ESE3|Q59EU8|Q5M7Z1	hg19	CCDS12289.1	0.02	-0.390714	GGGxGGG	COVERED																																																																																			NOVEL	RAD23A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452752.1	0	3.091902	KEEP	0	3	45	27	680	TT	0.999997	0.926637	0		+	6	60	141	0	0	9.551257	36	60	1021	101	ENST00000586534.1	0.142857	0.92664
NACC1	112939	__UNKNOWN__	__UNKNOWN__	19	13249248	13249248	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:13249248A>C	ENST00000292431.4	+	0	1738					NM_052876.3	NP_443108.1	Q96RE7	NACC1_HUMAN	nucleus accumbens associated 1, BEN and BTB (POZ) domain containing	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear body (GO:0016604)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(3)|skin(1)	9						GGGGCCACACACTTCCCCTCC	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						24	22	23	NA		NA	NA	19		NA											NA				13249248		2202	4297	6499	SO:0001624	3_prime_UTR_variant			AF395817	CCDS12294.1	19p13.13	2013-01-09	2008-10-03	2008-10-03		ENSG00000160877	112939		BEN domain containing, BTB/POZ domain containing	20967	protein-coding gene	gene with protein product	nucleus accumbens associated 1, BEN domain containing 8	610672	BTB (POZ) domain containing 14B	BTBD14B	NA	12477932	Standard	NM_052876	NM_052876	NA	Approved	NAC1, NAC-1, BEND8, BTBD30	uc002mwm.4	Q96RE7		ENST00000292431.4:c.*28A>C	chr19.hg19:g.13249248A>C		NA		hg19	CCDS12294.1	0.02	11.827701	CACxCTT	COVERED																																																																																			NOVEL	NACC1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452879.1	4	14.730313	KEEP	0	0	0	49	1327	AA	1	1	0		+	25	60	880	0	0	64.605016	226	60	7553	315	ENST00000292431.4	0.099602	1
LPHN1	22859	__UNKNOWN__	__UNKNOWN__	19	14281301	14281301	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:14281301C>T	ENST00000340736.6	-	4	692				LPHN1_ENST00000591528.1_Intron|CTB-55O6.12_ENST00000592086.1_RNA|LPHN1_ENST00000361434.3_Intron|CTB-55O6.12_ENST00000588387.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	NA		NA			calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GTCTGTGAGGCGGGGGAGCAG	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071	22859		-, GPCR / Class B : Orphans	20973	protein-coding gene	gene with protein product		NA			NA	10994649	Standard	NM_014921	NM_014921	NA	Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.394+192G>A	chr19.hg19:g.14281301C>T		NA	Q96IE7|Q9BU07|Q9HAR3	hg19	CCDS32928.1	0.02	-0.307026	AGGxGGG	COVERED																																																																																			NOVEL	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459696.1	0	2.407796	KEEP	0	0	0	8	280	CC	0.99257	0.7943	0		-	12	60	368	0	0	32.751321	23	60	843	45	ENST00000340736.6	0.342857	0.800245
EMR2	30817	__UNKNOWN__	__UNKNOWN__	19	14876693	14876693	__UNKNOWN__	Intron	SNP	G	G	A	rs377051619		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:14876693G>A	ENST00000315576.3	-	8	1086				EMR2_ENST00000594076.1_Intron|EMR2_ENST00000353005.1_Intron|EMR2_ENST00000392964.3_Intron|EMR2_ENST00000392965.3_Intron|EMR2_ENST00000601345.1_Intron|EMR2_ENST00000353876.1_Intron|EMR2_ENST00000596991.2_Intron|EMR2_ENST00000392967.2_Intron|EMR2_ENST00000594294.1_Intron|EMR2_ENST00000346057.1_Intron|EMR2_ENST00000595839.1_Intron	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	NA		NA			cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						CCCCCAGCTCGTTCCTCCCGG	0.652	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507	30817		CD molecules, -, GPCR / Class B : Orphans	3337	protein-coding gene	gene with protein product		606100	egf-like module containing, mucin-like, hormone receptor-like sequence 2		NA		Standard		NM_013447	NA	Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.635-77C>T	chr19.hg19:g.14876693G>A		NA	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	hg19	CCDS32935.1	0.02	4.109546	CTCxTTC	COVERED																																																																																			NOVEL	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466502.2	3	5.41402	KEEP	0	0	0	18	614	GG	0.999859	0.999859	0		-	11	40	381	0	0	26.88124	122	60	4408	154	ENST00000315576.3	0.082707	1
EMR2	30817	__UNKNOWN__	__UNKNOWN__	19	14876724	14876724	__UNKNOWN__	Intron	SNP	A	A	T	rs372861785		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:14876724A>T	ENST00000315576.3	-	8	1086				EMR2_ENST00000594076.1_Intron|EMR2_ENST00000353005.1_Intron|EMR2_ENST00000392964.3_Intron|EMR2_ENST00000392965.3_Intron|EMR2_ENST00000601345.1_Intron|EMR2_ENST00000353876.1_Intron|EMR2_ENST00000596991.2_Intron|EMR2_ENST00000392967.2_Intron|EMR2_ENST00000594294.1_Intron|EMR2_ENST00000346057.1_Intron|EMR2_ENST00000595839.1_Intron	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	NA		NA			cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						CCCCTTGGAGAGGTGGACGCT	0.622	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507	30817		CD molecules, -, GPCR / Class B : Orphans	3337	protein-coding gene	gene with protein product		606100	egf-like module containing, mucin-like, hormone receptor-like sequence 2		NA		Standard		NM_013447	NA	Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.635-108T>A	chr19.hg19:g.14876724A>T		NA	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	hg19	CCDS32935.1	0.02	1.755905	GAGxGGT	COVERED																																																																																			NOVEL	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466502.2	6	2.406983	KEEP	0	0	0	8	244	AA	0.99257	0.99249	0		-	5	39	174	0	0	11.289623	90	60	3329	105	ENST00000315576.3	0.052632	0.999919
AKAP8L	26993	__UNKNOWN__	__UNKNOWN__	19	15512385	15512385	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15512385C>T	ENST00000397410.5	-	5	522	c.392G>A	c.(391-393)aGg>aAg	p.R131K	AKAP8L_ENST00000595465.2_Missense_Mutation_p.R70K	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	131		NA				cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(4)|kidney(2)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11						CAGGACGGCCCTCGAGTCGCA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						36	35	35	NA		NA	NA	19		NA											NA				15512385		2125	4225	6350	SO:0001583	missense			BC000713	CCDS46005.1	19p13.12	2013-10-16			ENSG00000011243	ENSG00000011243	26993			29857	protein-coding gene	gene with protein product	neighbor of A kinase anchoring protein 95	609475			NA	10748171, 10761695	Standard	NM_014371	XM_005259854	NA	Approved	NAKAP95, HAP95	uc002naw.1	Q9ULX6	OTTHUMG00000182446	ENST00000397410.5:c.392G>A	chr19.hg19:g.15512385C>T	ENSP00000380557:p.Arg131Lys	NA	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	hg19	CCDS46005.1	0.02	17.310407	GCCxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	19.54	3.846150	0.71603	.	.	ENSG00000011243	ENST00000397410	T	0.62941	-0.01	4.72	4.72	0.59763	.	0.059077	0.64402	D	0.000003	T	0.73892	0.3645	L	0.52905	1.665	0.30459	N	0.774505	P;D;P	0.61697	0.956;0.99;0.956	P;D;P	0.72982	0.899;0.979;0.899	T	0.73742	-0.3887	10	0.51188	T	0.08	-20.1741	14.5905	0.68362	0.0:1.0:0.0:0.0	.	70;131;131	B4DJ74;B3KMD4;Q9ULX6	.;.;AKP8L_HUMAN	K	131	ENSP00000380557:R131K	ENSP00000380557:R131K	R	-	2	0	AKAP8L	15373385	1.000000	0.71417	0.937000	0.37676	0.280000	0.26924	5.590000	0.67530	2.166000	0.68216	0.655000	0.94253	AGG	NOVEL	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000461301.2	6	32.503716	KEEP	0	0	0	108	3827	CC	1	1	0		-	60	60	2101	0	0	168.011551	304	60	11454	546	ENST00000397410.5	0.164835	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	15780321	15780321	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15780321G>A			NA	NA				CYP4F3 (6686 upstream) : CYP4F12 (3245 downstream)						NA		NA									NA						CTTCATGTTTGAGGGAGAGGA	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.15780321G>A		NA		hg19		0.02	2.099949	TTTxAGG	COVERED																																																																																			NOVEL					0			2	2.407685	KEEP	0	0	0	8	275	GG	0.99257	0.98769	0			13	60	466	0	0	38.487065	54	60	2080	88		0.19403	0.995084
CYP4F12	66002	__UNKNOWN__	__UNKNOWN__	19	15784026	15784026	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15784026G>A	ENST00000550308.1	+	1	379					NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	NA		NA			arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GTGGCTCCAAGATGCTGGCAT	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204	66002		Cytochrome P450s	18857	protein-coding gene	gene with protein product		611485	cytochrome P450, subfamily IVF, polypeptide 12		NA	11162607	Standard		NM_023944	NA	Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.-2+81G>A	chr19.hg19:g.15784026G>A		NA	E7ET51|O60389|Q5JPJ7|Q9HCS1	hg19	CCDS42517.1	0.02	11.349039	CAAxATG	COVERED																																																																																			NOVEL	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378938.9	1	13.243004	KEEP	0	0	0	44	1558	GG	1	1	0		+	15	60	547	0	0	37.38598	229	60	8685	366	ENST00000550308.1	0.061475	1
CYP4F12	66002	__UNKNOWN__	__UNKNOWN__	19	15784032	15784032	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15784032G>A	ENST00000550308.1	+	1	379					NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	NA		NA			arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CCAAGATGCTGGCATGGGAAA	0.602	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204	66002		Cytochrome P450s	18857	protein-coding gene	gene with protein product		611485	cytochrome P450, subfamily IVF, polypeptide 12		NA	11162607	Standard		NM_023944	NA	Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.-2+87G>A	chr19.hg19:g.15784032G>A		NA	E7ET51|O60389|Q5JPJ7|Q9HCS1	hg19	CCDS42517.1	0.02	11.951231	GCTxGCA	COVERED																																																																																			NOVEL	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378938.9	1	13.827789	KEEP	0	0	0	46	1582	GG	1	1	0		+	11	60	383	0	0	23.970089	239	60	9109	389	ENST00000550308.1	0.044	1
CYP4F12	66002	__UNKNOWN__	__UNKNOWN__	19	15784085	15784085	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15784085G>A	ENST00000550308.1	+	1	379					NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	NA		NA			arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	AACTCCCAAGGATTCAGGTGG	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204	66002		Cytochrome P450s	18857	protein-coding gene	gene with protein product		611485	cytochrome P450, subfamily IVF, polypeptide 12		NA	11162607	Standard		NM_023944	NA	Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.-2+140G>A	chr19.hg19:g.15784085G>A		NA	E7ET51|O60389|Q5JPJ7|Q9HCS1	hg19	CCDS42517.1	0.02	14.294696	AAGxATT	COVERED																																																																																			NOVEL	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378938.9	1	14.746325	KEEP	0	0	0	49	1684	GG	1	1	0		+	23	60	864	0	0	61.657829	291	60	10957	488	ENST00000550308.1	0.073248	1
CYP4F12	66002	__UNKNOWN__	__UNKNOWN__	19	15784106	15784106	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15784106G>T	ENST00000550308.1	+	1	379					NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	NA		NA			arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCCCTTCTGGACTCTAATCG	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204	66002		Cytochrome P450s	18857	protein-coding gene	gene with protein product		611485	cytochrome P450, subfamily IVF, polypeptide 12		NA	11162607	Standard		NM_023944	NA	Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.-2+161G>T	chr19.hg19:g.15784106G>T		NA	E7ET51|O60389|Q5JPJ7|Q9HCS1	hg19	CCDS42517.1	0.02	12.970876	CTGxACT	COVERED																																																																																			NOVEL	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378938.9	1	12.338373	KEEP	0	0	0	41	1405	GG	1	1	0		+	27	60	949	0	0	67.664856	291	60	10809	480	ENST00000550308.1	0.084906	1
CYP4F12	66002	__UNKNOWN__	__UNKNOWN__	19	15794651	15794651	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:15794651G>A	ENST00000550308.1	+	7	1298				CYP4F12_ENST00000324632.10_Intron	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	NA		NA			arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	AATTGGTTTTGATCCAAAGGG	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204	66002		Cytochrome P450s	18857	protein-coding gene	gene with protein product		611485	cytochrome P450, subfamily IVF, polypeptide 12		NA	11162607	Standard		NM_023944	NA	Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.918+78G>A	chr19.hg19:g.15794651G>A		NA	E7ET51|O60389|Q5JPJ7|Q9HCS1	hg19	CCDS42517.1	0.02	11.754877	TTTxATC	COVERED																																																																																			NOVEL	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378938.9	4	7.21396	KEEP	0	0	0	24	773	GG	0.999909	0.999909	0		+	46	60	1651	0	0	132.50162	237	60	8818	315	ENST00000550308.1	0.162544	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	16102865	16102865	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:16102865C>T			NA	NA				OR10H4 (42097 upstream) : LINC00661 (23578 downstream)						NA		NA									NA						GTTCTTTGATCTGACATTTGA	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.16102865C>T		NA		hg19		0.02	3.84478	GATxTGA	COVERED																																																																																			NOVEL					0			0	2.407783	KEEP	0	0	0	8	276	CC	0.99257	0.99257	0			18	60	628	0	0	48.751758	111	60	4155	144		0.139535	1
HSH2D	84941	__UNKNOWN__	__UNKNOWN__	19	16263283	16263283	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:16263283G>A	ENST00000593154.2	+	5	656				HSH2D_ENST00000397372.4_Intron|HSH2D_ENST00000588246.1_Intron|HSH2D_ENST00000253680.6_Intron	NM_032855.2	NP_116244.1	Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	NA		NA			negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						CTCCATGAATGATCCCATGGC	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684	84941		SH2 domain containing	24920	protein-coding gene	gene with protein product		608349			NA	11700021	Standard	NM_032855	NM_032855	NA	Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000593154.2:c.126-79G>A	chr19.hg19:g.16263283G>A		NA	B5ME72|Q6ZNG7	hg19		0.02	8.300955	AATxATC	COVERED																																																																																			NOVEL	HSH2D-009	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000460267.3	4	5.107213	KEEP	0	0	0	17	533	GG	0.999366	0.999366	0		+	32	60	1119	0	0	86.638877	202	60	7141	282	ENST00000593154.2	0.136752	1
MYO9B	4650	__UNKNOWN__	__UNKNOWN__	19	17306199	17306199	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:17306199C>T	ENST00000594824.1	+	22	4110	c.3963C>T	c.(3961-3963)gcC>gcT	p.A1321A	MYO9B_ENST00000595618.1_Silent_p.A1321A|MYO9B_ENST00000397274.2_Silent_p.A1321A			Q13459	MYO9B_HUMAN	myosin IXB	1321	Tail.	NA			actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						TGGTGGCCGCCGCCAGCCCTA	0.711	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						8	12	11	NA		NA	NA	19		NA											NA				17306199		1935	4060	5995	SO:0001819	synonymous_variant				CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331	4650		Myosins / Myosin superfamily : Class IX	7609	protein-coding gene	gene with protein product		602129		CELIAC4	NA	9226381	Standard		NM_004145	NA	Approved		uc010eak.3	Q13459		ENST00000594824.1:c.3963C>T	chr19.hg19:g.17306199C>T		NA	O75314|Q9NUJ2|Q9UHN0	hg19		0.02	12.056965	CGCxGCC	COVERED																																																																																			NOVEL	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000463236.1	2	34.47851	KEEP	0	0	0	115	3417	CC	1	1	0		+	52	60	1889	0	0	157.219003	208	60	6699	540	ENST00000594824.1	0.2	1
MAP1S	55201	__UNKNOWN__	__UNKNOWN__	19	17831042	17831042	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:17831042T>G	ENST00000324096.4	+	1	269				MAP1S_ENST00000544059.2_5'UTR|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	NA		NA			apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CGCCCGTGGGTGGAGATGGGT	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479	55201			15715	protein-coding gene	gene with protein product		607573	chromosome 19 open reading frame 5, VCY2 interacting protein 1, BPY2 interacting protein 1	C19orf5, VCY2IP1, BPY2IP1	NA	11827465, 15528209, 16297881, 14627543	Standard	NM_018174	NM_018174	NA	Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.118+613T>G	chr19.hg19:g.17831042T>G		NA	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	hg19	CCDS32954.1	0.02	-0.404275	GGGxGGA	COVERED																																																																																			NOVEL	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466027.1	0	3.006527	KEEP	0	0	0	10	270	TT	0.992708	0.934874	0		+	12	60	138	0	0	8.017552	34	60	1042	89	ENST00000324096.4	0.26087	0.941741
CILP2	148113	__UNKNOWN__	__UNKNOWN__	19	19651216	19651216	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:19651216T>G	ENST00000291495.5	+	3	452	c.367T>G	c.(367-369)Tgc>Ggc	p.C123G	CILP2_ENST00000586018.1_Missense_Mutation_p.C129G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	123		NA				extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CGGCTTCTGGTGCCTCAACCG	0.741	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						4	5	4	NA		NA	NA	19		NA											NA				19651216		1984	3981	5965	SO:0001583	missense			AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161	148113		Immunoglobulin superfamily / Immunoglobulin-like domain containing	24213	protein-coding gene	gene with protein product		612419			NA	12477932	Standard	NM_153221	NM_153221	NA	Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.367T>G	chr19.hg19:g.19651216T>G	ENSP00000291495:p.Cys123Gly	NA	Q6NV88|Q8N4A6|Q8WV21	hg19	CCDS12405.1	0.02	4.40931	TGGxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	T	23.6	4.430198	0.83776	.	.	ENSG00000160161	ENST00000291495	T	0.70986	-0.53	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.81508	0.4837	H	0.95004	3.61	0.53688	D	0.999978	P;P	0.41131	0.603;0.739	B;P	0.45881	0.427;0.496	D	0.85455	0.1163	10	0.72032	D	0.01	-6.3037	11.3897	0.49806	0.0:0.0:0.0:1.0	.	123;123	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	G	123	ENSP00000291495:C123G	ENSP00000291495:C123G	C	+	1	0	CILP2	19512216	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.832000	0.86757	1.576000	0.49790	0.254000	0.18369	TGC	NOVEL	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459738.3	0	18.034344	KEEP	0	0	0	60	1662	TT	1	1	0		+	7	60	246	0	0	16.038383	126	60	4294	271	ENST00000291495.5	0.052632	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	21567559	21567559	__UNKNOWN__	IGR	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:21567559G>T			NA	NA				ZNF738 (5455 upstream) : ZNF493 (12361 downstream)						NA		NA									NA						CCCTACAAATGTGAAGAATGT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.21567559G>T		NA		hg19		0.02	4.458933	AATxTGA	COVERED																																																																																			NOVEL					0			8	8.16773	KEEP	19	4	128	72	2607	GG	1	1	0			7	44	250	0	0	17.489125	88	60	3350	359		0.073684	1
ZNF676	163223	__UNKNOWN__	__UNKNOWN__	19	22363844	22363844	__UNKNOWN__	Silent	SNP	G	G	A	rs7252604		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:22363844G>A	ENST00000397121.2	-	3	992	c.675C>T	c.(673-675)taC>taT	p.Y225Y		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	225		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				CTTCACATTTGTAGGGTTTCT	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						55	60	58	NA		NA	NA	19		NA											NA				22363844		2134	4255	6389	SO:0001819	synonymous_variant			AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109	163223		Zinc fingers, C2H2-type	20429	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001001411	NM_001001411	NA	Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.675C>T	chr19.hg19:g.22363844G>A		NA	A8MVX5	hg19	CCDS42539.1	0.02	4.200643	TTTxTAG	COVERED																																																																																			NOVEL	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464392.1	31	3.949104	KEEP	5	4	110	52	1867	GG	1	1	0		-	13	49	448	0	0	33.023248	112	60	4213	230	ENST00000397121.2	0.104	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	22793195	22793195	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:22793195C>A			NA	NA				CTC-457E21.6 (1892 upstream) : AC011516.2 (5163 downstream)						NA		NA									NA						ATGTTTGCACCTTTTCCTTCC	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.22793195C>A		NA		hg19		0.02	7.092114	CACxTTT	COVERED																																																																																			NOVEL					0			3	9.325609	KEEP	0	0	0	31	1089	CC	0.999997	0.999997	0			59	60	2091	0	0	187.964826	120	60	4485	243		0.329609	1
ZNF492	57615	__UNKNOWN__	__UNKNOWN__	19	22836805	22836805	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs200144130		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:22836805G>A	ENST00000456783.2	+	3	362	c.118G>A	c.(118-120)Gct>Act	p.A40T		NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	40	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A40T(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				TGAGATGGTAGCTGAACCCCC	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	prostate(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676	57615		Zinc fingers, C2H2-type	23707	protein-coding gene	gene with protein product		NA	zinc finger protein 115 (Y20)	ZNF115	NA	10819331	Standard	NM_020855	NM_020855	NA	Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.118G>A	chr19.hg19:g.22836805G>A	ENSP00000413660:p.Ala40Thr	NA	Q08EI7|Q08EI8	hg19	CCDS46032.1	0.02	12.421448	GTAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	10.18	1.279365	0.23307	.	.	ENSG00000229676	ENST00000456783	T	0.07688	3.17	0.458	0.458	0.16670	Krueppel-associated box (1);	.	.	.	.	T	0.13372	0.0324	M	0.72576	2.205	0.09310	N	1	P	0.45011	0.848	P	0.46585	0.521	T	0.13899	-1.0492	8	0.42905	T	0.14	.	.	.	.	.	40	Q9P255	ZN492_HUMAN	T	40	ENSP00000413660:A40T	ENSP00000413660:A40T	A	+	1	0	ZNF492	22628645	0.064000	0.20934	0.002000	0.10522	0.002000	0.02628	1.318000	0.33643	0.482000	0.27582	0.484000	0.47621	GCT	NOVEL	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464581.1	5	11.642906	KEEP	1	3	89	70	2591	GG	1	1	0		+	12	27	422	0	0	25.716367	308	60	11795	511	ENST00000456783.2	0.0375	1
ZNF492	57615	__UNKNOWN__	__UNKNOWN__	19	22836848	22836848	__UNKNOWN__	Intron	SNP	T	T	C	rs3745117	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:22836848T>C	ENST00000456783.2	+	3	374					NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ATACAACAGATGACACAGATG	0.408	NA	NA											-|||	1122	0.224042	0.1679	0.2507	5008	,	,	NA	13723	0.2619	NA	0.2515	False	NA	,,,	NA	NA	NA	2504	0.2137	NA	NA	NA						NA		NA				0							NA						89	94	92	NA		NA	NA	19		NA											NA				22836848		2203	4300	6503	SO:0001627	intron_variant			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676	57615		Zinc fingers, C2H2-type	23707	protein-coding gene	gene with protein product		NA	zinc finger protein 115 (Y20)	ZNF115	NA	10819331	Standard	NM_020855	NM_020855	NA	Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.130+31T>C	chr19.hg19:g.22836848T>C		NA	Q08EI7|Q08EI8	hg19	CCDS46032.1	0.02	10.187885	AGAxGAC	COVERED																																																																																			NOVEL	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464581.1	5	3.063767	KEEP	1	4	119	52	1566	TT	1	1	0		+	18	39	562	0	0	35.831547	262	60	9305	433	ENST00000456783.2	0.064286	1
TSHZ3	57616	__UNKNOWN__	__UNKNOWN__	19	31769976	31769976	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:31769976G>A	ENST00000240587.4	-	2	1050	c.723C>T	c.(721-723)gaC>gaT	p.D241D		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	241		NA			in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CATGGTTGTCGTCGCGGTAAT	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						240	215	223	NA		NA	NA	19		NA											NA				31769976		2203	4300	6503	SO:0001819	synonymous_variant			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297	57616		Teashirt zinc fingers, Homeoboxes / ZF class, Zinc fingers, C2H2-type	30700	protein-coding gene	gene with protein product	teashirt 3	614119	zinc finger protein 537, teashirt family zinc finger 3	ZNF537	NA		Standard	NM_020856	NM_020856	NA	Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.723C>T	chr19.hg19:g.31769976G>A		NA	Q9H0G6|Q9P254	hg19	CCDS12421.2	0.02	29.373548	GTCxTCG	COVERED																																																																																			NOVEL	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316743.2	8	76.674454	KEEP	0	0	0	255	8613	GG	1	1	0		-	166	60	6091	0	0	528.566132	479	60	17278	1133	ENST00000240587.4	0.257364	1
ANKRD27	84079	__UNKNOWN__	__UNKNOWN__	19	33149768	33149768	__UNKNOWN__	Intron	SNP	G	G	A	rs259251	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:33149768G>A	ENST00000306065.4	-	2	261				ANKRD27_ENST00000587352.1_Intron	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	NA		NA			early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					AGTCTACCACGTCTCTGGAAC	0.537	NA	NA											G|||	1871	0.373602	0.1573	0.4712	5008	,	,	NA	18049	0.252	NA	0.6252	False	NA	,,,	NA	NA	NA	2504	0.4632	NA	NA	NA						NA		NA				0							NA	G		424,1328		57,310,509	37	35	36	NA		-0.1	0	19	dbSNP_79	36	2593,1389		827,939,225	no	intron	ANKRD27	NM_032139.2		884,1249,734	AA,AG,GG	NA	34.882,24.2009,47.384			33149768	3017,2717	876	1991	2867	SO:0001627	intron_variant			AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186	84079		Ankyrin repeat domain containing	25310	protein-coding gene	gene with protein product	Vps9 domain and ankyrin-repeat-containing protein	NA			NA	11230166, 16525121	Standard	NM_032139	NM_032139	NA	Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.102+51C>T	chr19.hg19:g.33149768G>A		NA	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	hg19	CCDS32986.1	0.02	2.038129	CACxTCT	COVERED																																																																																			NOVEL	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450329.1	2	2.406845	KEEP	0	0	0	8	248	GG	0.99257	0.99251	0		-	32	60	1192	0	0	107.794792	65	60	2059	108	ENST00000306065.4	0.329897	0.99994
GPATCH1	55094	__UNKNOWN__	__UNKNOWN__	19	33572124	33572124	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:33572124G>A	ENST00000170564.2	+	1	339	c.25G>A	c.(25-27)Gaa>Aaa	p.E9K		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	9		NA			mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CAGTGACAGCGAAGAAGATCT	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(67;88 1713 4567 18227)					NA		NA				0							NA						46	41	43	NA		NA	NA	19		NA											NA				33572124		2047	3990	6037	SO:0001583	missense			AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650	55094		G patch domain containing	24658	protein-coding gene	gene with protein product	evolutionarily conserved G patch domain containing	NA		GPATC1	NA	12477932	Standard	NM_018025	NM_018025	NA	Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.25G>A	chr19.hg19:g.33572124G>A	ENSP00000170564:p.Glu9Lys	NA	Q8IZV6|Q8N3B7|Q9NW94	hg19	CCDS12428.1	0.02	4.312019	AGCxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.0	4.084860	0.76642	.	.	ENSG00000076650	ENST00000170564	T	0.14640	2.49	5.4	5.4	0.78164	.	0.720110	0.13810	N	0.361153	T	0.16300	0.0392	M	0.64997	1.995	0.80722	D	1	P	0.46457	0.878	B	0.34242	0.178	T	0.14839	-1.0458	10	0.34782	T	0.22	-0.9512	17.7338	0.88387	0.0:0.0:1.0:0.0	.	9	Q9BRR8	GPTC1_HUMAN	K	9	ENSP00000170564:E9K	ENSP00000170564:E9K	E	+	1	0	GPATCH1	38263964	1.000000	0.71417	0.957000	0.39632	0.272000	0.26649	7.937000	0.87672	2.521000	0.84997	0.467000	0.42956	GAA	NOVEL	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450834.1	2	22.568736	KEEP	0	0	0	75	2508	GG	1	1	0		+	20	60	731	0	0	57.44727	124	60	4284	283	ENST00000170564.2	0.138889	1
ZNF302	55900	__UNKNOWN__	__UNKNOWN__	19	35169696	35169696	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:35169696G>A	ENST00000446502.2	+	0	195				ZNF302_ENST00000509528.1_5'UTR|ZNF302_ENST00000423823.2_5'UTR|ZNF302_ENST00000457781.2_5'UTR|ZNF302_ENST00000505365.2_5'UTR|ZNF302_ENST00000507959.1_5'UTR|ZNF302_ENST00000505242.1_5'UTR			Q9NR11	ZN302_HUMAN	zinc finger protein 302	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TTGGCCATTGGAAATTGCAGA	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						109	107	108	NA		NA	NA	19		NA											NA				35169696		1884	4114	5998	SO:0001623	5_prime_UTR_variant			AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335	55900		Zinc fingers, C2H2-type, -	13848	protein-coding gene	gene with protein product		NA			NA		Standard		NM_018675	NA	Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.-14G>A	chr19.hg19:g.35169696G>A		NA	Q658J3|Q9BZD8|Q9P0J4	hg19		0.02	27.767532	TTGxAAA	COVERED																																																																																			NOVEL	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000372731.1	6	35.440742	KEEP	0	1	20	125	4296	GG	1	1	0		+	92	60	3375	0	0	266.581078	554	60	20571	976	ENST00000446502.2	0.142415	1
ZNF302	55900	__UNKNOWN__	__UNKNOWN__	19	35174983	35174983	__UNKNOWN__	Intron	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:35174983G>T	ENST00000446502.2	+	6	554				ZNF302_ENST00000509528.1_Intron|ZNF302_ENST00000423823.2_Intron|ZNF302_ENST00000457781.2_Intron|ZNF302_ENST00000505365.2_Nonsense_Mutation_p.E101*|ZNF302_ENST00000507959.1_Nonsense_Mutation_p.E102*|ZNF302_ENST00000505242.1_Intron			Q9NR11	ZN302_HUMAN	zinc finger protein 302	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AGAAGTCACTGAAATATTTGA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335	55900		Zinc fingers, C2H2-type, -	13848	protein-coding gene	gene with protein product		NA			NA		Standard		NM_018675	NA	Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.347-174G>T	chr19.hg19:g.35174983G>T		NA	Q658J3|Q9BZD8|Q9P0J4	hg19		0.02	4.66294	ACTxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596817	0.46318	.	.	ENSG00000089335	ENST00000502743;ENST00000506901;ENST00000507959;ENST00000505365	.	.	.	0.967	0.967	0.19674	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999997	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	5.2771	0.15655	0.0:0.0:1.0:0.0	.	.	.	.	X	101;102;102;101	.	ENSP00000423460:E101X	E	+	1	0	ZNF302	39866823	0.924000	0.31332	0.098000	0.21074	0.034000	0.12701	1.486000	0.35530	0.822000	0.34565	0.467000	0.42956	GAA	NOVEL	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000372731.1	2	7.825733	KEEP	0	0	0	26	933	GG	0.999957	0.999938	0		+	14	60	525	0	0	41.402219	89	60	3377	169	ENST00000446502.2	0.135922	0.999981
SBSN	374897	__UNKNOWN__	__UNKNOWN__	19	36018413	36018413	__UNKNOWN__	Silent	SNP	T	T	A	rs368150998		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36018413T>A	ENST00000452271.2	-	1	799	c.771A>T	c.(769-771)gcA>gcT	p.A257A	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	257	Ala/Gly/His-rich.	NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CAAATCTCCCTGCCTCATTTC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						48	50	50	NA		NA	NA	19		NA											NA				36018413		692	1591	2283	SO:0001819	synonymous_variant			AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05					374897			24950	protein-coding gene	gene with protein product		609969			NA	12228223	Standard	NM_198538	NM_198538	NA	Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.771A>T	chr19.hg19:g.36018413T>A		NA	A8K5J0|E9PBV3	hg19	CCDS54253.1	0.02	24.164311	CCCxGCC	COVERED																																																																																			NOVEL	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109463.3	11	3.359083	KEEP	1	11	302	118	3426	TT	1	1	0		-	27	60	953	0	0	61.55696	532	60	19404	820	ENST00000452271.2	0.048301	1
ZBTB32	27033	__UNKNOWN__	__UNKNOWN__	19	36206871	36206871	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36206871G>T	ENST00000392197.2	+	5	1304	c.986G>T	c.(985-987)aGc>aTc	p.S329I	ZBTB32_ENST00000262630.3_Missense_Mutation_p.S329I			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	329		NA			DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCACAGCTCAGCCCTGGGGAG	0.647	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						26	31	29	NA		NA	NA	19		NA											NA				36206871		2201	4300	6501	SO:0001583	missense			AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590	27033		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	16763	protein-coding gene	gene with protein product	repressor of GATA	605859			NA	10572087	Standard	NM_014383	XM_005258739	NA	Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.986G>T	chr19.hg19:g.36206871G>T	ENSP00000376035:p.Ser329Ile	NA	Q8WVP2	hg19	CCDS12471.1	0.02	8.565823	TCAxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.53	3.844283	0.71488	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.10668	2.85;2.85	4.41	4.41	0.53225	.	0.116315	0.39615	N	0.001311	T	0.14830	0.0358	L	0.32530	0.975	0.35708	D	0.816186	D	0.58268	0.982	P	0.52758	0.708	T	0.08534	-1.0717	10	0.48119	T	0.1	-5.6577	12.3707	0.55254	0.0:0.0:1.0:0.0	.	329	Q9Y2Y4	ZBT32_HUMAN	I	329	ENSP00000262630:S329I;ENSP00000376035:S329I	ENSP00000262630:S329I	S	+	2	0	ZBTB32	40898711	0.040000	0.19996	1.000000	0.80357	0.987000	0.75469	1.573000	0.36472	2.290000	0.77057	0.655000	0.94253	AGC	NOVEL	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109491.3	2	25.577372	KEEP	0	0	0	85	2916	GG	1	1	0		+	14	60	508	0	0	35.029989	200	60	7413	361	ENST00000392197.2	0.065421	1
KMT2B	9757	__UNKNOWN__	__UNKNOWN__	19	36229219	36229219	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36229219G>A	ENST00000222270.7	+	37	7909	c.7909G>A	c.(7909-7911)Gat>Aat	p.D2637N	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.D2637N	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2637	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.	NA			chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)				NA						GGATGACTTTGATGTAGTGGA	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						73	81	78	NA		NA	NA	19		NA											NA				36229219		2192	4296	6488	SO:0001583	missense			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333	9757		Chromatin-modifying enzymes / K-methyltransferases	15840	protein-coding gene	gene with protein product	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4	606834			NA	10409430, 10637508	Standard	NM_014727	XM_006723513	NA	Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.7909G>A	chr19.hg19:g.36229219G>A	ENSP00000222270:p.Asp2637Asn	NA	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	hg19	CCDS46055.1	0.02	26.817647	TTTxATG	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.85	3.489671	0.64074	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	T;T	0.81415	-1.49;-1.49	5.42	5.42	0.78866	SET domain (3);	0.000000	0.46442	D	0.000300	T	0.81064	0.4745	N	0.12182	0.205	0.58432	D	0.999998	D	0.89917	1.0	D	0.77557	0.99	T	0.80582	-0.1318	10	0.28530	T	0.3	.	17.9826	0.89146	0.0:0.0:1.0:0.0	.	2637	Q9UMN6	MLL4_HUMAN	N	2637	ENSP00000222270:D2637N;ENSP00000398837:D2637N	ENSP00000222270:D2637N	D	+	1	0	AD000671.1	40921059	1.000000	0.71417	0.994000	0.49952	0.651000	0.38670	8.062000	0.89475	2.551000	0.86045	0.462000	0.41574	GAT	NOVEL	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		9	37.620526	KEEP	0	0	0	125	4309	GG	1	1	0		+	96	60	3493	0	0	282.488027	479	60	18301	813	ENST00000222270.7	0.166957	1
LIN37	55957	__UNKNOWN__	__UNKNOWN__	19	36243359	36243359	__UNKNOWN__	Silent	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36243359G>A	ENST00000301159.9	+	3	499	c.135G>A	c.(133-135)ggG>ggA	p.G45G	AC002398.9_ENST00000591613.2_3'UTR|AC002398.11_ENST00000591091.1_RNA	NM_019104.2	NP_061977	Q96GY3	LIN37_HUMAN	lin-37 DREAM MuvB core complex component	45		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				large_intestine(1)|lung(5)	6	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AGGAAGCTGGGAAAACACCCT	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						119	120	119	NA		NA	NA	19		NA											NA				36243359		1960	4144	6104	SO:0001819	synonymous_variant			BC008939	CCDS62642.1	19q13.12	2014-07-17	2014-07-17		ENSG00000267796	ENSG00000267796	55957			33234	protein-coding gene	gene with protein product		NA	lin-37 homolog (C. elegans)		NA	21498570	Standard	NM_019104	NM_019104	NA	Approved	ZK418.4, F25965, lin-37	uc021usw.1	Q96GY3	OTTHUMG00000182070	ENST00000301159.9:c.135G>A	chr19.hg19:g.36243359G>A		NA	A8KAQ1|O14557|Q7Z2T9	hg19		0.02	13.914906	TGGxAAA	COVERED																																																																																			NOVEL	LIN37-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000459109.2	2	25.279985	KEEP	0	0	0	84	2891	GG	1	1	0		+	44	60	1592	1	0	125.342792	264	60	9901	481	ENST00000301159.9	0.142857	1
LIN37	55957	__UNKNOWN__	__UNKNOWN__	19	36244295	36244295	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36244295G>A	ENST00000301159.9	+	6	808				AC002398.9_ENST00000591613.2_Intron|AC002398.11_ENST00000591091.1_RNA	NM_019104.2	NP_061977	Q96GY3	LIN37_HUMAN	lin-37 DREAM MuvB core complex component	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				large_intestine(1)|lung(5)	6	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TAGGCACACAGATGTGCACTC	0.552	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008939	CCDS62642.1	19q13.12	2014-07-17	2014-07-17		ENSG00000267796	ENSG00000267796	55957			33234	protein-coding gene	gene with protein product		NA	lin-37 homolog (C. elegans)		NA	21498570	Standard	NM_019104	NM_019104	NA	Approved	ZK418.4, F25965, lin-37	uc021usw.1	Q96GY3	OTTHUMG00000182070	ENST00000301159.9:c.444+141G>A	chr19.hg19:g.36244295G>A		NA	A8KAQ1|O14557|Q7Z2T9	hg19		0.02	14.023388	ACAxATG	COVERED																																																																																			NOVEL	LIN37-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000459109.2	1	20.158039	KEEP	0	0	0	67	2313	GG	1	1	0		+	62	60	2272	0	0	189.610536	246	60	9383	469	ENST00000301159.9	0.201299	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	36795827	36795827	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36795827C>T			NA	NA				ZNF565 (58668 upstream) : CTD-3162L10.1 (5432 downstream)						NA		NA									NA						aacccggcagcttcaggggct	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.36795827C>T		NA		hg19		0.02	-0.410975	CAGxTTC	COVERED																																																																																			NOVEL					0			2	3.912523	KEEP	30	0	0	13	450	CC	0.99257	0.934744	0			3	40	102	0	0	6.822246	43	40	1573	97		0.065217	0.941741
ZNF566	84924	__UNKNOWN__	__UNKNOWN__	19	36964383	36964383	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36964383G>A	ENST00000493391.1	-	2	444				ZNF566_ENST00000472909.2_Intron|ZNF566_ENST00000454319.1_Intron|ZNF566_ENST00000434377.2_Intron|ZNF566_ENST00000392170.2_Intron|ZNF566_ENST00000424129.2_Intron			Q969W8	ZN566_HUMAN	zinc finger protein 566	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					CCACGTATATGACTTCATTAA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						85	82	83	NA		NA	NA	19		NA											NA				36964383		2203	4300	6503	SO:0001627	intron_variant			AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08					84924		Zinc fingers, C2H2-type, -	25919	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032838	NM_001145343	NA	Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000493391.1:c.79+3067C>T	chr19.hg19:g.36964383G>A		NA	B7ZL95|Q2M3J1	hg19		0.02	19.169592	TATxACT	COVERED																																																																																			NOVEL	ZNF566-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341055.2	6	13.842195	KEEP	0	0	0	46	1606	GG	1	1	0		-	64	60	2312	0	0	181.955216	384	60	14514	570	ENST00000493391.1	0.142857	1
ZNF566	84924	__UNKNOWN__	__UNKNOWN__	19	36967379	36967379	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36967379G>C	ENST00000493391.1	-	2	444				ZNF566_ENST00000472909.2_Intron|ZNF566_ENST00000454319.1_Intron|ZNF566_ENST00000434377.2_Intron|ZNF566_ENST00000392170.2_Intron|ZNF566_ENST00000424129.2_Intron			Q969W8	ZN566_HUMAN	zinc finger protein 566	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					GCATCATCATGAGGAAAGCAA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						121	100	107	NA		NA	NA	19		NA											NA				36967379		692	1591	2283	SO:0001627	intron_variant			AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08					84924		Zinc fingers, C2H2-type, -	25919	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032838	NM_001145343	NA	Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000493391.1:c.79+71C>G	chr19.hg19:g.36967379G>C		NA	B7ZL95|Q2M3J1	hg19		0.02	4.63784	CATxAGG	COVERED																																																																																			NOVEL	ZNF566-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341055.2	2	4.514754	KEEP	0	0	0	15	537	GG	0.99649	0.99649	0		-	16	60	609	0	0	46.87694	125	70	4671	160	ENST00000493391.1	0.113475	1
ZNF566	84924	__UNKNOWN__	__UNKNOWN__	19	36967541	36967541	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:36967541G>C	ENST00000493391.1	-	2	376				ZNF566_ENST00000472909.2_Intron|ZNF566_ENST00000454319.1_Intron|ZNF566_ENST00000434377.2_Intron|ZNF566_ENST00000392170.2_Intron|ZNF566_ENST00000424129.2_Intron			Q969W8	ZN566_HUMAN	zinc finger protein 566	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					AAAGAAGATAGATAAGACCCC	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						71	62	65	NA		NA	NA	19		NA											NA				36967541		692	1591	2283	SO:0001627	intron_variant			AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08					84924		Zinc fingers, C2H2-type, -	25919	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032838	NM_001145343	NA	Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000493391.1:c.148-23C>G	chr19.hg19:g.36967541G>C		NA	B7ZL95|Q2M3J1	hg19		0.02	17.246772	ATAxATA	COVERED																																																																																			NOVEL	ZNF566-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341055.2	3	12.023477	KEEP	0	0	0	40	1397	GG	1	1	0		-	47	60	1758	0	0	135.709175	348	60	13258	542	ENST00000493391.1	0.118987	1
ZNF850	342892	__UNKNOWN__	__UNKNOWN__	19	37253567	37253567	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:37253567C>T	ENST00000591344.1	-	0	100				ZNF850_ENST00000589390.1_5'UTR	NM_001193552.1|NM_001267779.1	NP_001180481.1|NP_001254708.1	A8MQ14	ZN850_HUMAN	zinc finger protein 850	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						CCGAATATTCCATGGTTAGAG	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC052603	CCDS59379.1, CCDS74350.1	19q13.12	2013-01-08	2010-08-02	2010-08-02		ENSG00000267041	342892		Zinc fingers, C2H2-type, -	27994	protein-coding gene	gene with protein product		NA	zinc finger protein 850 pseudogene, zinc finger protein 850 (pseudogene)	ZNF850P	NA	12477932	Standard	XM_001720258	NM_001193552	NA	Approved		uc010efc.3	A8MQ14		ENST00000591344.1:c.-59G>A	chr19.hg19:g.37253567C>T		NA		hg19	CCDS59379.1	0.02	14.660437	TTCxATG	COVERED																																																																																			NOVEL	ZNF850-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453557.1	2	12.029897	KEEP	0	0	0	40	1416	CC	1	1	0		-	42	60	1564	0	0	121.360385	296	60	11129	497	ENST00000591344.1	0.12426	1
ZNF850	342892	__UNKNOWN__	__UNKNOWN__	19	37253614	37253614	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:37253614C>T	ENST00000591344.1	-	2	90				ZNF850_ENST00000589390.1_Intron	NM_001193552.1|NM_001267779.1	NP_001180481.1|NP_001254708.1	A8MQ14	ZN850_HUMAN	zinc finger protein 850	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						TATTATTTCCCAAATAAATGA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC052603	CCDS59379.1, CCDS74350.1	19q13.12	2013-01-08	2010-08-02	2010-08-02		ENSG00000267041	342892		Zinc fingers, C2H2-type, -	27994	protein-coding gene	gene with protein product		NA	zinc finger protein 850 pseudogene, zinc finger protein 850 (pseudogene)	ZNF850P	NA	12477932	Standard	XM_001720258	NM_001193552	NA	Approved		uc010efc.3	A8MQ14		ENST00000591344.1:c.69-37G>A	chr19.hg19:g.37253614C>T		NA		hg19	CCDS59379.1	0.02	9.358938	TCCxAAA	COVERED																																																																																			NOVEL	ZNF850-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453557.1	3	7.524749	KEEP	0	0	0	25	901	CC	0.999931	0.999931	0		-	35	60	1254	0	0	99.725276	192	60	7284	303	ENST00000591344.1	0.154185	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	37771916	37771916	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:37771916C>G			NA	NA				CTD-3220F14.1 (9496 upstream) : HKR1 (31822 downstream)						NA		NA									NA						AACCCACCCTCCGGCGCACAG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.37771916C>G		NA		hg19		0.02	-0.140375	CCTxCGG	UNCOVERED																																																																																			NOVEL					0			0	2.407811	KEEP	9	0	0	8	277	CC	0	0	0			2	22	84	0	0	6.736301	14	40	541	43		0.125	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	37771930	37771930	__UNKNOWN__	IGR	SNP	A	A	C	rs76876109		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:37771930A>C			NA	NA				CTD-3220F14.1 (9510 upstream) : HKR1 (31808 downstream)						NA		NA									NA						CGCACAGGGCACATGTGTCCC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.37771930A>C		NA		hg19		0.02	-0.184238	GGCxCAT	UNCOVERED																																																																																			NOVEL					0			0	2.707814	KEEP	8	0	0	9	270	AA	0	0	0			3	40	119	0	0	9.591311	18	40	663	46		0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	37772075	37772075	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:37772075C>A			NA	NA				CTD-3220F14.1 (9655 upstream) : HKR1 (31663 downstream)						NA		NA									NA						cacagacacgcactgcgcgcg	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.37772075C>A		NA		hg19		0.02	-0.20177	ACGxACT	UNCOVERED																																																																																			NOVEL					0			0	2.70749	KEEP	11	0	0	9	307	CC	0	0	0			4	40	136	0	0	10.894081	19	47	688	53		0.173913	0.490544
DPF1	8193	__UNKNOWN__	__UNKNOWN__	19	38701853	38701853	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:38701853C>G	ENST00000416611.1	-	0	2170				DPF1_ENST00000412732.1_3'UTR|DPF1_ENST00000420980.2_3'UTR			Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1	NA		NA			apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAAGAAACAACCACGCCCCCT	0.617	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332	8193		Zinc fingers, PHD-type	20225	protein-coding gene	gene with protein product		601670			NA	8812431	Standard		XM_005259288	NA	Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000416611.1:c.*850G>C	chr19.hg19:g.38701853C>G		NA	B3KSY8|Q08AJ0	hg19		0.02	17.835191	CAAxCAC	COVERED																																																																																			NOVEL	DPF1-003	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000347723.1	1	32.795588	KEEP	0	0	0	109	3696	CC	1	1	0		-	38	60	1367	0	0	102.648877	312	60	11005	641	ENST00000416611.1	0.108571	1
CATSPERG	57828	__UNKNOWN__	__UNKNOWN__	19	38831287	38831287	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:38831287T>G	ENST00000409235.3	+	4	439				CATSPERG_ENST00000215069.4_Intron|CATSPERG_ENST00000410018.1_Intron	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	NA		NA			cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						agagacagggtcttgcgctgt	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338	57828			25243	protein-coding gene	gene with protein product		613452	chromosome 19 open reading frame 15, cation channel, sperm-associated, gamma	C19orf15	NA	19516020	Standard	NM_021185	NM_021185	NA	Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.325-2933T>G	chr19.hg19:g.38831287T>G		NA	A6NEG6|Q659E1	hg19	CCDS12514.2	0.02	-0.096502	GGGxCTT	UNCOVERED																																																																																			NOVEL	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330204.1	2	2.406619	KEEP	0	0	0	8	243	TT	0.99257	0.119541	0		+	5	60	179	0	0	16.993845	6	60	214	24	ENST00000409235.3	0.454545	0.120436
SPTBN4	57731	__UNKNOWN__	__UNKNOWN__	19	41007935	41007935	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:41007935G>T	ENST00000352632.3	+	8	978	c.892G>T	c.(892-894)Ggg>Tgg	p.G298W	SPTBN4_ENST00000598249.1_Missense_Mutation_p.G298W|SPTBN4_ENST00000344104.3_Missense_Mutation_p.G298W|SPTBN4_ENST00000338932.3_Missense_Mutation_p.G298W|SPTBN4_ENST00000595535.1_Missense_Mutation_p.G298W			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	298		NA			actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GAAGCGTATCGGGAAGGTATA	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						97	93	94	NA		NA	NA	19		NA											NA				41007935		2203	4300	6503	SO:0001583	missense			AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460	57731		Pleckstrin homology (PH) domain containing	14896	protein-coding gene	gene with protein product		606214			NA	11086001	Standard		NM_020971	NA	Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.892G>T	chr19.hg19:g.41007935G>T	ENSP00000263373:p.Gly298Trp	NA	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	hg19	CCDS12559.1	0.02	10.011323	ATCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692052	0.68271	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.79141	-1.21;-1.19;-1.24	4.06	4.06	0.47325	.	0.000000	0.64402	U	0.000017	D	0.88727	0.6515	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	1.0;0.984	D;D	0.81914	0.995;0.932	D	0.89864	0.4018	10	0.48119	T	0.1	.	15.5271	0.75919	0.0:0.0:1.0:0.0	.	298;298	Q9H254;Q71S06	SPTN4_HUMAN;.	W	298	ENSP00000263373:G298W;ENSP00000340345:G298W;ENSP00000340741:G298W	ENSP00000340345:G298W	G	+	1	0	SPTBN4	45699775	1.000000	0.71417	0.993000	0.49108	0.693000	0.40251	9.616000	0.98359	2.276000	0.75962	0.467000	0.42956	GGG	NOVEL	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462559.2	1	9.930457	KEEP	0	0	0	33	1081	GG	0.999998	0.999998	0		+	39	60	1470	0	0	120.893296	182	60	6167	300	ENST00000352632.3	0.176471	1
ITPKC	80271	__UNKNOWN__	__UNKNOWN__	19	41235261	41235261	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:41235261G>C	ENST00000263370.2	+	3	1443	c.1410G>C	c.(1408-1410)atG>atC	p.M470I		NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	470		NA			inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TCAACCAGATGGAAGACCTCC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						56	51	53	NA		NA	NA	19		NA											NA				41235261		2203	4300	6503	SO:0001583	missense			Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	80271	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	inositol 1,4,5-trisphosphate 3-kinase C		NA	11085927	Standard	NM_025194	NM_025194	NA	Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.1410G>C	chr19.hg19:g.41235261G>C	ENSP00000263370:p.Met470Ile	NA	Q9UE25|Q9Y475	hg19	CCDS12563.1	0.02	7.611349	GATxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.86	3.905188	0.72868	.	.	ENSG00000086544	ENST00000263370	T	0.14266	2.52	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.32285	0.0824	L	0.58510	1.815	0.80722	D	1	D	0.56521	0.976	P	0.60949	0.881	T	0.00269	-1.1861	10	0.44086	T	0.13	-28.9639	18.5144	0.90930	0.0:0.0:1.0:0.0	.	470	Q96DU7	IP3KC_HUMAN	I	470	ENSP00000263370:M470I	ENSP00000263370:M470I	M	+	3	0	ITPKC	45927101	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.721000	0.98766	2.746000	0.94184	0.561000	0.74099	ATG	NOVEL	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463104.1	2	10.53335	KEEP	0	0	0	35	1189	GG	0.999999	0.999999	0		+	32	60	1042	0	0	85.304716	122	60	4491	211	ENST00000263370.2	0.207792	1
CYP2A6	1548	__UNKNOWN__	__UNKNOWN__	19	41354417	41354417	__UNKNOWN__	Intron	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:41354417G>C	ENST00000301141.5	-	3	514				CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	NA		NA			coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	AAGTGCGGGCGCCTTTCCCCA	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974	1548		Cytochrome P450s	2610	protein-coding gene	gene with protein product		122720	cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6	CYP2A3	NA	7668294, 2748347	Standard	NM_000762	NM_000762	NA	Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.493+101C>G	chr19.hg19:g.41354417G>C		NA	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	hg19	CCDS12568.1	0.02	1.795311	GGCxCCT	COVERED																																																																																			NOVEL	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463259.1	1	4.212739	KEEP	0	0	0	14	442	GG	0.995343	0.994457	0		-	4	47	141	0	0	9.137182	75	60	2514	96	ENST00000301141.5	0.050633	0.99911
ATP1A3	478	__UNKNOWN__	__UNKNOWN__	19	42473132	42473132	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:42473132C>T	ENST00000545399.1	-	20	2881				ATP1A3_ENST00000543770.1_Intron|ATP1A3_ENST00000302102.5_Intron|ATP1A3_ENST00000602133.1_Intron	NM_001256214.1	NP_001243143.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	NA		NA			adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|memory (GO:0007613)|potassium ion import (GO:0010107)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	axon (GO:0030424)|dendritic spine head (GO:0044327)|dendritic spine neck (GO:0044326)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(19)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	52						GCCGCCACCCCGACGTTCCGG	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12594.1, CCDS58663.1, CCDS58664.1	19q13.2	2012-10-22			ENSG00000105409	ENSG00000105409	478	3.6.3.9	ATPases / P-type	801	protein-coding gene	gene with protein product	sodium/potassium-transporting ATPase subunit alpha-3, sodium pump subunit alpha-3, sodium-potassium ATPase catalytic subunit alpha-3	182350	dystonia 12	DYT12	NA	17282997	Standard	NM_152296	NM_152296	NA	Approved		uc002osh.4	P13637	OTTHUMG00000137384	ENST00000545399.1:c.2728-65G>A	chr19.hg19:g.42473132C>T		NA	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	hg19	CCDS58664.1	0.02	5.046075	CCCxGAC	COVERED																																																																																			NOVEL	ATP1A3-008	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268114.2	1	4.813071	KEEP	0	0	0	16	486	CC	0.997832	0.997819	0		-	68	60	2462	0	0	248.530407	38	60	1159	125	ENST00000545399.1	0.641509	0.999987
TMEM145	284339	__UNKNOWN__	__UNKNOWN__	19	42818791	42818791	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:42818791C>T	ENST00000301204.3	+	4	341	c.300C>T	c.(298-300)atC>atT	p.I100I	TMEM145_ENST00000598766.1_Silent_p.I110I|TMEM145_ENST00000601020.1_3'UTR	NM_173633.2	NP_775904.2	Q8NBT3	TM145_HUMAN	transmembrane protein 145	100		NA			G-protein coupled receptor signaling pathway (GO:0007186)|response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	27		Prostate(69;0.00682)				AGTCAGTGATCCGGCCGGAGA	0.642	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						109	110	110	NA		NA	NA	19		NA											NA				42818791		2203	4300	6503	SO:0001819	synonymous_variant			AK075286	CCDS12603.1	19q13.2	2008-02-05				ENSG00000167619	284339			26912	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173633	NM_173633	NA	Approved	FLJ90805	uc002otk.1	Q8NBT3		ENST00000301204.3:c.300C>T	chr19.hg19:g.42818791C>T		NA		hg19	CCDS12603.1	0.02	10.553922	GATxCGG	COVERED																																																																																			NOVEL	TMEM145-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463737.1	4	16.248303	KEEP	0	0	0	54	1812	CC	1	1	0		+	9	60	330	0	0	20.136334	263	60	9776	393	ENST00000301204.3	0.033088	1
MEGF8	1954	__UNKNOWN__	__UNKNOWN__	19	42865015	42865015	__UNKNOWN__	Silent	SNP	C	C	T	rs151134622|rs34886828	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:42865015C>T	ENST00000334370.4	+	31	6011	c.5376C>T	c.(5374-5376)ttC>ttT	p.F1792F	MEGF8_ENST00000251268.6_Silent_p.F1859F	NM_001410.2	NP_001401.2	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1859		NA			BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CTGGGGGTTTCGGGGGAGTGG	0.662	NA	NA											c|||	2	0.000399361	0.0015	0	5008	,	,	NA	14689	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA	T		1,4397		0,1,2198	18	22	21	NA	5376	-6.5	0.9	19	dbSNP_134	21	0,8596		0,0,4298	no	coding-synonymous	MEGF8	NM_001410.2		0,1,6496	TT,TC,CC	NA	0.0,0.0227,0.0077		1792/2779	42865015	1,12993	2199	4298	6497	SO:0001819	synonymous_variant			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429	1954			3233	protein-coding gene	gene with protein product	HBV pre s2 binding protein 1	604267	EGF-like-domain, multiple 4, chromosome 19 open reading frame 49	EGFL4, C19orf49	NA	9693030	Standard	NM_001410	NM_001410	NA	Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000334370.4:c.5376C>T	chr19.hg19:g.42865015C>T		NA	A8KAY0|O75097	hg19	CCDS12604.2	0.02	6.524993	TTTxGGG	COVERED																																																																																			NOVEL	MEGF8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317695.1	1	16.673199	KEEP	0	1	12	60	1919	CC	1	1	0		+	7	60	255	0	0	16.283087	157	60	5515	261	ENST00000334370.4	0.042683	1
CEACAM16	388551	__UNKNOWN__	__UNKNOWN__	19	45207036	45207036	__UNKNOWN__	Intron	SNP	T	T	A	rs200629926|rs575937266|rs567755665		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:45207036T>A	ENST00000405314.2	+	2	479				CTB-171A8.1_ENST00000590796.1_RNA|CEACAM16_ENST00000587331.1_Intron			Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16	NA		NA			sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)				endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				TTCttttttttaaaaaaaaaa	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892	388551		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	31948	protein-coding gene	gene with protein product		614591			NA	21368133	Standard	XM_371177	NM_001039213	NA	Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000405314.2:c.382+73T>A	chr19.hg19:g.45207036T>A		NA	A7LI12	hg19	CCDS54278.1	0.02	-0.184136	TTTxAAA	COVERED																																																																																			NOVEL	CEACAM16-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding		0	2.385859	KEEP	0	0	0	8	206	TT	0.99257	0.420331	0		+	4	60	141	1	0	11.569281	17	60	506	32	ENST00000405314.2	0.190476	0.423478
HSD17B14	51171	__UNKNOWN__	__UNKNOWN__	19	49338554	49338554	__UNKNOWN__	Intron	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:49338554A>C	ENST00000263278.4	-	2	394				HSD17B14_ENST00000599157.1_Intron	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	NA		NA			steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		ggaggaggggatgggggcctg	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076	51171		Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1	23238	protein-coding gene	gene with protein product	retinal short-chain dehydrogenase/reductase 3, short chain dehydrogenase/reductase family 47C, member 1	612832	dehydrogenase/reductase (SDR family) member 10	DHRS10	NA	10800688, 17067289, 19027726	Standard	NM_016246	XM_005258969	NA	Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.127+507T>G	chr19.hg19:g.49338554A>C		NA	Q9UKU3	hg19	CCDS12736.1	0.02	-0.035092	GGGxTGG	UNCOVERED																																																																																			NOVEL	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466212.1	2	2.406722	KEEP	0	0	0	8	236	AA	0.99257	0.019833	0		-	2	40	80	0	0	7.750177	2	60	72	19	ENST00000263278.4	0.5	0.019982
HSD17B14	51171	__UNKNOWN__	__UNKNOWN__	19	49338587	49338587	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:49338587G>A	ENST00000263278.4	-	2	394				HSD17B14_ENST00000599157.1_Intron	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	NA		NA			steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		tgagggaggaggggctgggag	0.687	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076	51171		Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1	23238	protein-coding gene	gene with protein product	retinal short-chain dehydrogenase/reductase 3, short chain dehydrogenase/reductase family 47C, member 1	612832	dehydrogenase/reductase (SDR family) member 10	DHRS10	NA	10800688, 17067289, 19027726	Standard	NM_016246	XM_005258969	NA	Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.127+474C>T	chr19.hg19:g.49338587G>A		NA	Q9UKU3	hg19	CCDS12736.1	0.02	-0.070185	GGAxGGG	UNCOVERED																																																																																			NOVEL	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466212.1	3	2.407874	KEEP	0	0	0	8	283	GG	0.99257	0.053735	0		-	2	37	75	0	0	6.500579	6	60	217	24	ENST00000263278.4	0.25	0.054137
PRMT1	3276	__UNKNOWN__	__UNKNOWN__	19	50185182	50185182	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:50185182G>A	ENST00000391851.4	+	3	283	c.154G>A	c.(154-156)Gag>Aag	p.E52K	PRMT1_ENST00000454376.2_Missense_Mutation_p.E70K|PRMT1_ENST00000532489.1_Missense_Mutation_p.E24K	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	60	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.	NA			cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		GCTGAAGGACGAGGTGCGCAC	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						67	53	58	NA		NA	NA	19		NA											NA				50185182		2203	4300	6503	SO:0001583	missense			D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	3276	2.1.1.125	Protein arginine methyltransferases	5187	protein-coding gene	gene with protein product		602950	HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2, HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)	HRMT1L2	NA	9545638	Standard	NM_001536	NM_001207042	NA	Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.154G>A	chr19.hg19:g.50185182G>A	ENSP00000375724:p.Glu52Lys	NA	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	hg19	CCDS42592.1	0.02	2.010296	GACxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.93	2.086377	0.36855	.	.	ENSG00000126457	ENST00000529284;ENST00000532489;ENST00000527382;ENST00000528623;ENST00000534465;ENST00000391851;ENST00000449059;ENST00000454376;ENST00000529836;ENST00000526224;ENST00000527412	T;T;T;T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99	5.04	3.97	0.46021	.	0.000000	0.85682	D	0.000000	T	0.13200	0.0320	N	0.17594	0.5	0.58432	D	0.999999	B;B;B;B	0.15141	0.012;0.001;0.002;0.005	B;B;B;B	0.11329	0.006;0.001;0.004;0.006	T	0.05699	-1.0869	10	0.42905	T	0.14	-2.5421	11.7121	0.51630	0.0888:0.0:0.9112:0.0	.	60;24;52;46	Q99873;E9PKG1;G5E9B6;Q99873-2	ANM1_HUMAN;.;.;.	K	24;24;24;46;24;52;46;70;46;24;49	ENSP00000432349:E24K;ENSP00000433556:E24K;ENSP00000432538:E24K;ENSP00000431957:E24K;ENSP00000375724:E52K;ENSP00000406162:E70K;ENSP00000437273:E46K;ENSP00000432788:E24K;ENSP00000436732:E49K	ENSP00000375724:E52K	E	+	1	0	PRMT1	54876994	1.000000	0.71417	0.991000	0.47740	0.005000	0.04900	6.286000	0.72665	2.629000	0.89072	0.643000	0.83706	GAG	NOVEL	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395065.1	1	24.055806	KEEP	0	0	0	80	2571	GG	1	0.999962	0		+	41	60	1535	0	0	143.66933	59	60	1988	227	ENST00000391851.4	0.41	0.999962
PRMT1	3276	__UNKNOWN__	__UNKNOWN__	19	50191516	50191516	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:50191516C>T	ENST00000391851.4	+	0	1205				PRMT1_ENST00000454376.2_3'UTR|PRMT1_ENST00000527866.1_3'UTR|PRMT1_ENST00000532489.1_3'UTR	NM_198318.4	NP_938074.2	Q99873	ANM1_HUMAN	protein arginine methyltransferase 1	NA		NA			cell surface receptor signaling pathway (GO:0007166)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of megakaryocyte differentiation (GO:0045653)|neuron projection development (GO:0031175)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|protein methylation (GO:0006479)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|identical protein binding (GO:0042802)|methyltransferase activity (GO:0008168)|N-methyltransferase activity (GO:0008170)|poly(A) RNA binding (GO:0044822)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(2)	12		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00103)|GBM - Glioblastoma multiforme(134;0.012)		CCGGCTCTCCCGCCCTGCACG	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						54	48	50	NA		NA	NA	19		NA											NA				50191516		2203	4300	6503	SO:0001624	3_prime_UTR_variant			D66904	CCDS42592.1, CCDS46145.1, CCDS74425.1	19q13	2014-06-12	2006-02-16	2006-02-16	ENSG00000126457	ENSG00000126457	3276	2.1.1.125	Protein arginine methyltransferases	5187	protein-coding gene	gene with protein product		602950	HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 2, HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)	HRMT1L2	NA	9545638	Standard	NM_001536	NM_001207042	NA	Approved	HCP1, ANM1	uc010enf.2	Q99873	OTTHUMG00000167568	ENST00000391851.4:c.*14C>T	chr19.hg19:g.50191516C>T		NA	B4E3C3|G5E9B6|Q15529|Q2VP93|Q6LEU5|Q8WUW5|Q99872|Q99874|Q9NZ04|Q9NZ05|Q9NZ06	hg19	CCDS42592.1	0.02	6.26216	TCCxGCC	COVERED																																																																																			NOVEL	PRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395065.1	1	48.958218	KEEP	0	1	23	171	5554	CC	1	1	0		+	7	60	256	0	0	16.462442	153	60	5157	391	ENST00000391851.4	0.04375	1
CPT1C	126129	__UNKNOWN__	__UNKNOWN__	19	50204212	50204212	__UNKNOWN__	Intron	SNP	T	T	C	rs113828873|rs71180648		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:50204212T>C	ENST00000392518.4	+	5	825				CPT1C_ENST00000354199.5_Intron|CPT1C_ENST00000598293.1_Intron|CPT1C_ENST00000405931.2_Intron|CPT1C_ENST00000323446.5_Intron	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	NA		NA			carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		tctctgtccctctctctctgg	0.612	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169	126129			18540	protein-coding gene	gene with protein product		608846			NA	12376098, 11001805	Standard	NM_152359	NM_001136052	NA	Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.453+100T>C	chr19.hg19:g.50204212T>C		NA	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	hg19	CCDS12779.1	0.02	-0.359685	CCCxCTC	COVERED																																																																																			NOVEL	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465873.1	0	3.609981	KEEP	0	0	0	12	356	TT	0.993634	0.883216	0		+	5	60	176	0	0	13.384437	36	60	1260	55	ENST00000392518.4	0.121951	0.888875
PNKP	11284	__UNKNOWN__	__UNKNOWN__	19	50370425	50370425	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs201218221|rs371086920		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:50370425C>G	ENST00000322344.3	-	2	146	c.37G>C	c.(37-39)Gag>Cag	p.E13Q	PNKP_ENST00000596014.1_Missense_Mutation_p.E13Q|PNKP_ENST00000600910.1_Missense_Mutation_p.E13Q|PNKP_ENST00000595792.1_5'UTR|PNKP_ENST00000600573.1_Missense_Mutation_p.E13Q	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	13	FHA.	NA			dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		GGGGGGCTCTCGAGCCACAAG	0.711	NA	NA						Other BER factors						NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						9	12	11	NA		NA	NA	19		NA											NA				50370425		2019	4021	6040	SO:0001583	missense			AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650	11284			9154	protein-coding gene	gene with protein product		605610			NA	10446192, 10446193	Standard	NM_007254	NM_007254	NA	Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.37G>C	chr19.hg19:g.50370425C>G	ENSP00000323511:p.Glu13Gln	NA	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	hg19	CCDS12783.1	0.02	1.360903	TCTxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	3.736	-0.054620	0.07362	.	.	ENSG00000039650	ENST00000322344	T	0.23147	1.92	5.58	3.2	0.36748	SMAD/FHA domain (1);	0.404404	0.25099	N	0.033157	T	0.15219	0.0367	N	0.19112	0.55	0.22468	N	0.999075	B	0.11235	0.004	B	0.04013	0.001	T	0.18777	-1.0326	10	0.12766	T	0.61	-38.1299	13.2167	0.59865	0.0:0.6623:0.3377:0.0	.	13	Q96T60	PNKP_HUMAN	Q	13	ENSP00000323511:E13Q	ENSP00000323511:E13Q	E	-	1	0	PNKP	55062237	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	1.873000	0.39558	1.312000	0.45043	0.655000	0.94253	GAG	NOVEL	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465830.1	1	28.043598	KEEP	0	7	60	117	3046	CC	1	0.999973	0		-	13	60	176	0	0	7.826717	88	60	2005	306	ENST00000322344.3	0.128713	0.999973
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	52256656	52256656	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:52256656A>G			NA	NA				FPR1 (1494 upstream) : FPR2 (7447 downstream)						NA		NA									NA						catgccagggatctgggttgt	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.52256656A>G		NA		hg19		0.02	-0.289506	GGGxTCT	COVERED																																																																																			NOVEL					0			0	2.708231	KEEP	0	0	0	9	283	AA	0.99254	0.755211	0			12	60	438	0	0	40.1313	21	60	751	56		0.363636	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	52418589	52418589	__UNKNOWN__	IGR	SNP	C	C	T	rs533920002		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:52418589C>T			NA	NA				ZNF649 (10325 upstream) : ZNF613 (11883 downstream)						NA		NA									NA						TGCAGTGATACGGTTTCTCTC	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.52418589C>T		NA		hg19		0.02	2.325984	ATAxGGT	COVERED																																																																																			NOVEL					0			1	4.21364	KEEP	0	0	0	14	486	CC	0.995343	0.988302	0			4	60	142	0	0	9.614914	60	60	2173	97		0.0625	0.992926
ZNF525	170958	__UNKNOWN__	__UNKNOWN__	19	53878987	53878987	__UNKNOWN__	Intron	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:53878987C>T	ENST00000475179.1	+	3	129				ZNF525_ENST00000593918.1_Intron|ZNF525_ENST00000467003.1_Intron|ZNF525_ENST00000491101.1_Intron|ZNF525_ENST00000474037.1_Intron			Q8N782	ZN525_HUMAN	zinc finger protein 525	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(3)|lung(3)	9						AGAACTCCTCCCATAACCATT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075859		19q13.42	2013-01-16			ENSG00000203326	ENSG00000203326	170958		Zinc fingers, C2H2-type, -	29423	protein-coding gene	gene with protein product		NA			NA	11853319	Standard	NR_003699	NR_003699	NA	Approved	KIAA1979	uc010eqn.3	Q8N782	OTTHUMG00000158277	ENST00000475179.1:c.16-36C>T	chr19.hg19:g.53878987C>T		NA	Q8TF23	hg19		0.02	4.179107	CTCxCAT	COVERED																																																																																			NOVEL	ZNF525-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000350553.1	5	4.138037	KEEP	32	1	29	24	810	CC	0.99649	0.99649	0		+	9	24	331	0	0	23.348946	116	60	4212	209	ENST00000475179.1	0.072	0.999999
ZNF765	91661	__UNKNOWN__	__UNKNOWN__	19	53905282	53905282	__UNKNOWN__	Intron	SNP	C	C	T	rs200826571		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:53905282C>T	ENST00000396408.3	+	3	132				ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		AGAACTCCTCCCATAACCATT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						101	115	110	NA		NA	NA	19		NA											NA				53905282		1492	2637	4129	SO:0001627	intron_variant			BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417	91661		Zinc fingers, C2H2-type, -	25092	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_138372	XR_430215	NA	Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.16-36C>T	chr19.hg19:g.53905282C>T		NA	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	hg19	CCDS46171.1	0.02	3.836046	CTCxCAT	COVERED																																																																																			NOVEL	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371603.1	3	2.915166	KEEP	36	3	98	44	1535	CC	1	1	0		+	12	31	430	1	0	31.349	118	60	4206	238	ENST00000396408.3	0.092308	1
LILRA6	79168	__UNKNOWN__	__UNKNOWN__	19	54745665	54745665	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs1052966	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:54745665C>T	ENST00000396365.2	-	4	484	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRA6_ENST00000419410.2_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Missense_Mutation_p.G149R|LILRA6_ENST00000391735.3_Missense_Mutation_p.G149R|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.G149R|LILRA6_ENST00000440558.2_Missense_Mutation_p.G149R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	149		NA	G -> R (in dbSNP:rs1052966).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.G149R(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.582	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	large_intestine(2)					NA						25	40	35	NA		NA	NA	19		NA											NA				54745665		2106	4268	6374	SO:0001583	missense			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482	79168		Leukocyte immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	15495	protein-coding gene	gene with protein product		NA	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6	LILRB6	NA	10941842	Standard	NM_024318	NM_024318	NA	Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.445G>A	chr19.hg19:g.54745665C>T	ENSP00000379651:p.Gly149Arg	NA		hg19	CCDS42610.1	0.02	-0.34215	ATCxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825878	0.32237	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;3.85;2.76;2.76	3.1	-6.21	0.02065	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.12050	0.0293	L	0.39326	1.205	0.09310	N	1	P;B;P;P;B;P	0.41978	0.64;0.037;0.767;0.555;0.383;0.716	P;B;B;B;B;B	0.47044	0.535;0.085;0.444;0.211;0.344;0.276	T	0.27773	-1.0064	10	0.44086	T	0.13	.	4.765	0.13128	0.0:0.4155:0.3207:0.2638	rs1052966;rs3193450;rs13346484	149;149;149;149;149;149	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	R	149	ENSP00000390120:G149R;ENSP00000270464:G149R;ENSP00000411227:G149R;ENSP00000375615:G149R;ENSP00000379651:G149R;ENSP00000245621:G149R	ENSP00000245621:G149R	G	-	1	0	LILRA6	59437477	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-2.553000	0.00927	-1.315000	0.02297	0.162000	0.16502	GGA	NOVEL	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313725.1	2	3.310673	KEEP	9	0	0	11	375	CC	0.99254	0.859287	0		-	3	25	111	0	0	7.974482	35	60	1273	66	ENST00000396365.2	0.078947	0.865745
LILRA6	79168	__UNKNOWN__	__UNKNOWN__	19	54745775	54745775	__UNKNOWN__	Intron	SNP	G	G	A	rs13346528		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:54745775G>A	ENST00000396365.2	-	4	395				LILRA6_ENST00000419410.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000245621.5_Intron|LILRA6_ENST00000440558.2_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	NA		NA			immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AAGAGGCACCGTGTTAAATGG	0.632	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						50	84	73	NA		NA	NA	19		NA											NA				54745775		2134	4296	6430	SO:0001627	intron_variant			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482	79168		Leukocyte immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	15495	protein-coding gene	gene with protein product		NA	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6	LILRB6	NA	10941842	Standard	NM_024318	NM_024318	NA	Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.356-21C>T	chr19.hg19:g.54745775G>A		NA		hg19	CCDS42610.1	0.02	-0.271943	ACCxTGT	UNCOVERED																																																																																			NOVEL	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313725.1	2	2.407892	KEEP	2	0	0	8	285	GG	0	0	0		-	3	40	111	0	0	8.251744	28	60	1015	45	ENST00000396365.2	0.096774	0.717315
KIR2DL3	3804	__UNKNOWN__	__UNKNOWN__	19	55271927	55271927	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55271927G>A	ENST00000434419.2	+	5	693				KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron			P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CGGGCCCCACGGTTCTGGCAG	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772	3804		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6331	protein-coding gene	gene with protein product		604938			NA	7749980, 8662091	Standard		XM_006725426	NA	Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000434419.2:c.665-3416G>A	chr19.hg19:g.55271927G>A		NA	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	hg19		0.02	9.755972	CACxGTT	COVERED																																																																																			NOVEL	KIR2DL3-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		7	2.374241	KEEP	62	5	148	60	2015	GG	1	1	0		+	34	60	1283	0	0	105.349835	161	60	5767	437	ENST00000434419.2	0.174359	1
KIR2DL3	3804	__UNKNOWN__	__UNKNOWN__	19	55275386	55275386	__UNKNOWN__	Silent	SNP	C	C	T	rs593229	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55275386C>T	ENST00000434419.2	+	5	737	c.708C>T	c.(706-708)tcC>tcT	p.S236S	KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron			P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	236		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		AACCAAGCTCCAAAACCGGTG	0.498	NA	NA											.|||	2	0.000399361	0	0	5008	,	,	NA	16052	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772	3804		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6331	protein-coding gene	gene with protein product		604938			NA	7749980, 8662091	Standard		XM_006725426	NA	Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000434419.2:c.708C>T	chr19.hg19:g.55275386C>T		NA	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	hg19		0.02	9.574457	CTCxAAA	COVERED																																																																																			NOVEL	KIR2DL3-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		1	2.511179	KEEP	14	3	90	40	1374	CC	1	1	0		+	17	44	646	0	0	46.056932	223	60	8104	412	ENST00000434419.2	0.070833	1
KIR2DL3	3804	__UNKNOWN__	__UNKNOWN__	19	55281206	55281206	__UNKNOWN__	Intron	SNP	G	G	A	rs373223164		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55281206G>A	ENST00000434419.2	+	5	744				KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron			P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CCCATGATGTGGTCAACATGT	0.582	NA	NA									OREG0003674	type=REGULATORY REGION|Gene=KIR2DL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772	3804		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6331	protein-coding gene	gene with protein product		604938			NA	7749980, 8662091	Standard		XM_006725426	NA	Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000434419.2:c.715+5813G>A	chr19.hg19:g.55281206G>A		1006	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	hg19		0.02	1.795164	TGTxGTC	COVERED																																																																																			NOVEL	KIR2DL3-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		0	8.427405	KEEP	17	0	0	28	987	GG	0.999957	0.999067	0		+	4	31	138	0	0	8.883254	73	60	2824	166	ENST00000434419.2	0.051948	0.99911
KIR2DL3	3804	__UNKNOWN__	__UNKNOWN__	19	55281219	55281219	__UNKNOWN__	Intron	SNP	A	A	G	rs377462001		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55281219A>G	ENST00000434419.2	+	5	744				KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron			P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CAACATGTAAACTGCATGGGC	0.597	NA	NA									OREG0003674	type=REGULATORY REGION|Gene=KIR2DL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						35	31	33	NA		NA	NA	19		NA											NA				55281219		677	1534	2211	SO:0001627	intron_variant			L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772	3804		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6331	protein-coding gene	gene with protein product		604938			NA	7749980, 8662091	Standard		XM_006725426	NA	Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000434419.2:c.715+5826A>G	chr19.hg19:g.55281219A>G		1006	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	hg19		0.02	1.990323	TAAxCTG	COVERED																																																																																			NOVEL	KIR2DL3-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		0	8.726065	KEEP	17	0	0	29	903	AA	0.999988	0.999849	0		+	5	31	171	0	0	11.184041	83	60	2943	172	ENST00000434419.2	0.056818	0.999862
KIR2DL1	3802	__UNKNOWN__	__UNKNOWN__	19	55295190	55295190	__UNKNOWN__	Silent	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55295190A>T	ENST00000336077.6	+	8	1012	c.972A>T	c.(970-972)acA>acT	p.T324T	KIR2DL1_ENST00000291633.7_Silent_p.T350T|KIR2DL3_ENST00000434419.2_Silent_p.T324T|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron	NM_014218.2	NP_055033.2	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 1	324		NA			immune response (GO:0006955)|natural killer cell inhibitory signaling pathway (GO:0002769)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17				GBM - Glioblastoma multiforme(193;0.0192)		GGCCCAAGACACCCCCAACAG	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	GBM(72;624 1217 3963 34152 38303)					NA		NA				0							NA						7	7	7	NA		NA	NA	19		NA											NA				55295190		1798	3703	5501	SO:0001819	synonymous_variant			L41267	CCDS12904.1	19q13.4	2013-01-29			ENSG00000125498	ENSG00000125498	3802		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6329	protein-coding gene	gene with protein product		604936			NA	7749980, 7716543	Standard		NM_014218	NA	Approved	cl-42, nkat1, 47.11, p58.1, CD158A	uc002qhb.1	P43626	OTTHUMG00000065885	ENST00000336077.6:c.972A>T	chr19.hg19:g.55295190A>T		NA	O43470|Q32WE6|Q6IST4	hg19	CCDS12904.1	0.02	26.030562	GACxCCC	COVERED																																																																																			NOVEL	KIR2DL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000141148.2	3	22.754748	KEEP	4	2	22	84	2499	AA	1	1	0		+	23	60	826	0	0	52.204127	551	60	19040	840	ENST00000336077.6	0.04007	1
KIR3DL1	3811	__UNKNOWN__	__UNKNOWN__	19	55297822	55297822	__UNKNOWN__	Intron	SNP	G	G	A	rs371301192		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55297822G>A	ENST00000402254.2	+	2	67				KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GCTCATGGTCGTCAGCATGGC	0.627	NA	NA									OREG0003677	type=REGULATORY REGION|Gene=KIR3DL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay		NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633	3811		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6338	protein-coding gene	gene with protein product		604946		KIR	NA	7716543, 7749980	Standard	NM_013289	NM_013289	NA	Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000402254.2:c.35-31167G>A	chr19.hg19:g.55297822G>A		1006	O43473|Q14946|Q16541	hg19		0.02	6.523203	GTCxTCA	COVERED																																																																																			NOVEL	KIR3DL1-201	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding		31	9.343106	KEEP	21	9	285	131	4557	GG	1	1	0		+	23	60	843	0	0	65.117074	162	60	5813	451	ENST00000402254.2	0.124324	1
KIR3DL1	3811	__UNKNOWN__	__UNKNOWN__	19	55359837	55359837	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:55359837A>G	ENST00000402254.2	+	7	1033				KIR2DS4_ENST00000339924.8_RNA			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	NA		NA			immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ctgaggctgcaatcacactga	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633	3811		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6338	protein-coding gene	gene with protein product		604946		KIR	NA	7716543, 7749980	Standard	NM_013289	NM_013289	NA	Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000402254.2:c.1001-17423A>G	chr19.hg19:g.55359837A>G		NA	O43473|Q14946|Q16541	hg19		0.02	25.248676	TGCxATC	COVERED																																																																																			NOVEL	KIR3DL1-201	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding		4	13.637079	KEEP	25	3	102	81	2348	AA	1	1	0		+	17	40	634	0	0	38.103796	570	60	20651	824	ENST00000402254.2	0.028961	1
SSC5D	284297	__UNKNOWN__	__UNKNOWN__	19	56001337	56001337	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:56001337C>A	ENST00000389623.6	+	4	473	c.450C>A	c.(448-450)agC>agA	p.S150R	SSC5D_ENST00000587166.1_Missense_Mutation_p.S150R	NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	150		NA			defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						TGAGCCCCAGCACGGAGGAGC	0.706	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						32	40	37	NA		NA	NA	19		NA											NA				56001337		692	1590	2282	SO:0001583	missense				CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954	284297			26641	protein-coding gene	gene with protein product	soluble scavenger with 5 domains	NA	scavenger receptor cysteine rich domain containing (5 domains)		NA	19535143	Standard	XM_001718392	NM_001144950	NA	Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.450C>A	chr19.hg19:g.56001337C>A	ENSP00000374274:p.Ser150Arg	NA	B5MDQ5|C7S7T9|C7S7U0|K7EP70	hg19	CCDS46196.1	0.02	1.889803	CAGxACG	COVERED	.	.	.	.	.	.	.	.	.	.	.	11.89	1.775076	0.31411	.	.	ENSG00000179954	ENST00000389623;ENST00000541230	T	0.01252	5.1	4.26	2.05	0.26809	.	.	.	.	.	T	0.01124	0.0037	N	0.24115	0.695	0.09310	N	1	B	0.15141	0.012	B	0.14578	0.011	T	0.49303	-0.8954	9	0.16420	T	0.52	.	5.9304	0.19136	0.0:0.6765:0.2117:0.1118	.	150	A1L4H1	SRCRL_HUMAN	R	150	ENSP00000374274:S150R	ENSP00000374274:S150R	S	+	3	2	SSC5D	60693149	0.001000	0.12720	0.001000	0.08648	0.068000	0.16541	0.905000	0.28504	0.359000	0.24239	0.478000	0.44815	AGC	NOVEL	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453345.2	0	17.445188	KEEP	0	0	0	58	1919	CC	1	0.999862	0		+	31	60	1089	0	0	98.347702	60	60	2171	160	ENST00000389623.6	0.340659	0.999862
RFPL4A	342931	__UNKNOWN__	__UNKNOWN__	19	56274086	56274086	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs2616963	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:56274086G>A	ENST00000434937.2	+	3	580	c.409G>A	c.(409-411)Gcc>Acc	p.A137T		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	137	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA					zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GTTCGACACTGCCCTGTGCGT	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						23	19	20	NA		NA	NA	19		NA											NA				56274086		692	1577	2269	SO:0001583	missense				CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638	342931		RING-type (C3HC4) zinc fingers	16449	protein-coding gene	gene with protein product		612601	ret finger protein-like 4	RFPL4	NA	11850190	Standard	XM_292796	NM_001145014	NA	Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.409G>A	chr19.hg19:g.56274086G>A	ENSP00000392936:p.Ala137Thr	NA		hg19	CCDS46201.1	0.02	5.780584	ACTxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.918	-0.018800	0.07681	.	.	ENSG00000223638	ENST00000434937	T	0.10477	2.87	2.64	-1.13	0.09775	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.06280	0.0162	N	0.25485	0.75	0.09310	N	1	B	0.15141	0.012	B	0.19148	0.024	T	0.43278	-0.9401	9	0.22706	T	0.39	-27.0091	4.5168	0.11939	0.1218:0.0:0.3181:0.5601	.	137	A6NLU0	RFPLA_HUMAN	T	137	ENSP00000392936:A137T	ENSP00000392936:A137T	A	+	1	0	RFPL4A	60965898	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.357000	0.07651	-0.126000	0.11682	-0.119000	0.15052	GCC	NOVEL	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384184.1	6	9.356533	KEEP	193	7	204	103	3560	GG	1	1	0		+	33	27	1024	0	0	79.902399	159	40	5948	509	ENST00000434937.2	0.171875	1
RFPL4AL1	729974	__UNKNOWN__	__UNKNOWN__	19	56283978	56283978	__UNKNOWN__	Silent	SNP	C	C	G	rs116977548	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:56283978C>G	ENST00000341750.4	+	3	341	c.297C>G	c.(295-297)acC>acG	p.T99T		NM_001277397.1	NP_001264326.1	F8VTS6	RFAL1_HUMAN	ret finger protein-like 4A-like 1	99	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA					zinc ion binding (GO:0008270)				NA						TGGATATGACCTTCGATGTGG	0.458	NA	NA											c|||	2213	0.441893	0.6982	0.4352	5008	,	,	NA	17828	0.2659	NA	0.4384	False	NA	,,,	NA	NA	NA	2504	0.2853	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant				CCDS59425.1	19q13.42	2013-02-22			ENSG00000229292	ENSG00000229292	729974			45147	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001277397	NA	Approved		uc031rnc.1	F8VTS6	OTTHUMG00000165450	ENST00000341750.4:c.297C>G	chr19.hg19:g.56283978C>G		NA		hg19	CCDS59425.1	0.02	4.936944	GACxTTC	COVERED																																																																																			NOVEL	RFPL4AL1-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384186.1	5	9.163077	KEEP	5	1	21	38	1344	CC	1	1	0		+	8	40	251	0	0	14.630912	177	50	6544	277	ENST00000341750.4	0.043243	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	57828735	57828735	__UNKNOWN__	IGR	SNP	G	G	T	rs1559	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr19:57828735G>T			NA	NA				CTC-444N24.11 (8805 upstream) : ZNF543 (3141 downstream)						NA		NA									NA						AATTTAAATGGTTCTCCTAGT	0.363	NA	NA											t|||	1226	0.244808	0.3026	0.2061	5008	,	,	NA	13966	0.3482	NA	0.1223	False	NA	,,,	NA	NA	NA	2504	0.2137	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.57828735G>T		NA		hg19		0.02	-0.184236	ATGxTTC	COVERED																																																																																			NOVEL					0			1	3.009865	KEEP	0	0	0	10	354	GG	0.992708	0.42039	0			6	60	212	0	0	18.606472	15	60	549	41		0.285714	0.423478
PSMF1	9491	__UNKNOWN__	__UNKNOWN__	20	1106597	1106597	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:1106597C>G	ENST00000335877.6	+	2	458				PSMF1_ENST00000246015.4_Intron|PSMF1_ENST00000438768.2_Intron|PSMF1_ENST00000333082.3_Intron|PSMF1_ENST00000381898.4_Intron	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						tgggctacttcagttccttaa	0.443	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						8	8	8	NA		NA	NA	20		NA											NA				1106597		873	1984	2857	SO:0001627	intron_variant			D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818	9491		Proteasome (prosome, macropain) subunits	9571	protein-coding gene	gene with protein product	proteasome inhibitor hP131 subunit	NA			NA	10363639	Standard	NM_178578	NM_006814	NA	Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.282+304C>G	chr20.hg19:g.1106597C>G		NA	A0AVQ9|D3DVW3|Q9H4I1	hg19	CCDS13010.1	0.02	7.512469	CTTxAGT	COVERED																																																																																			NOVEL	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077504.2	2	9.631249	KEEP	0	0	0	32	1128	CC	0.999997	0.999997	0		+	14	60	551	0	0	40.142652	174	60	6656	267	ENST00000335877.6	0.074468	1
CDC25B	994	__UNKNOWN__	__UNKNOWN__	20	3783629	3783629	__UNKNOWN__	Intron	SNP	G	G	A	rs375745615		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:3783629G>A	ENST00000245960.5	+	12	1954				CDC25B_ENST00000467519.1_Intron|CDC25B_ENST00000379598.5_Intron|CDC25B_ENST00000439880.2_Intron|CDC25B_ENST00000344256.6_Intron|CDC25B_ENST00000340833.4_Intron	NM_004358.3|NM_021872.2|NM_021873.2	NP_004349.1|NP_068658.1|NP_068659.1	P30305	MPIP2_HUMAN	cell division cycle 25B	NA		NA			female meiosis I (GO:0007144)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|oocyte maturation (GO:0001556)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein kinase activity (GO:0045860)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(1)	18						GGTAAACAGCGTTGCGTCATT	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA	G	,,	1,4405	2.1+/-5.4	0,1,2202	139	95	110	NA	,,	-1	0	20		110	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron	CDC25B	NM_004358.3,NM_021872.2,NM_021873.2	,,	0,2,6501	AA,AG,GG	NA	0.0116,0.0227,0.0154	,,	,,	3783629	2,13004	2203	4300	6503	SO:0001627	intron_variant				CCDS13065.1, CCDS13066.1, CCDS13067.1, CCDS74700.1, CCDS74701.1	20p13	2013-01-17	2013-01-17		ENSG00000101224	ENSG00000101224	994		Protein tyrosine phosphatases / Class III Cys-based PTPs	1726	protein-coding gene	gene with protein product		116949	cell division cycle 25B, cell division cycle 25 homolog B (S. cerevisiae), cell division cycle 25 homolog B (S. pombe)		NA	1836978	Standard	NM_021874	NM_021873	NA	Approved		uc002wjn.3	P30305	OTTHUMG00000031764	ENST00000245960.5:c.1257+10G>A	chr20.hg19:g.3783629G>A		NA	D3DVY1|D3DVY2|D3DVY3|D3DVY4|O43551|Q13971|Q5JX77|Q6RSS1|Q9BRA6	hg19	CCDS13067.1	0.02	23.44073	AGCxTTG	COVERED																																																																																			NOVEL	CDC25B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077779.2	3	31.899561	KEEP	0	0	0	106	3580	GG	1	1	0		+	14	60	534	0	0	32.293005	492	60	16968	737	ENST00000245960.5	0.027668	1
PLCB4	5332	__UNKNOWN__	__UNKNOWN__	20	9460540	9460540	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:9460540A>G	ENST00000378501.2	+	0	4484				PLCB4_ENST00000334005.3_3'UTR|PLCB4_ENST00000278655.4_3'UTR|PLCB4_ENST00000378473.3_3'UTR|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378493.1_3'UTR	NM_000933.3	NP_000924.3	Q15147	PLCB4_HUMAN	phospholipase C, beta 4	NA		NA			inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						ACAAGCACCAATAAAGACTAA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	5332	3.1.4.11		9059	protein-coding gene	gene with protein product		600810			NA	8530101	Standard		NM_000933	NA	Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378501.2:c.*884A>G	chr20.hg19:g.9460540A>G		NA	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	hg19	CCDS13104.1	0.02	11.842537	CCAxTAA	COVERED																																																																																			NOVEL	PLCB4-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077958.2	3	6.619548	KEEP	0	0	0	22	687	AA	0.999879	0.999879	0		+	43	60	1622	0	0	131.085392	230	60	8465	343	ENST00000378501.2	0.157509	1
RALGAPA2	57186	__UNKNOWN__	__UNKNOWN__	20	20445797	20445797	__UNKNOWN__	Intron	SNP	A	A	T	rs557026555	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:20445797A>T	ENST00000202677.7	-	37	5503					NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	NA		NA			activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AGGCCTTcacacacacacaca	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559	57186			16207	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 74	C20orf74	NA	16490346, 19520869	Standard	NM_020343	NM_020343	NA	Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.5495+7675T>A	chr20.hg19:g.20445797A>T		NA	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	hg19	CCDS46584.1	0.02	-0.421083	CACxCAC	COVERED																																																																																			NOVEL	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471941.1	3	3.90246	KEEP	0	0	0	13	354	AA	0.994391	0.943082	0		-	5	60	195	0	2	15.522526	32	60	1139	67	ENST00000202677.7	0.135135	0.948402
CST2	1470	__UNKNOWN__	__UNKNOWN__	20	23805930	23805930	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs199856966		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:23805930T>C	ENST00000304725.2	-	2	329	c.259A>G	c.(259-261)Ata>Gta	p.I87V		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	87		NA			detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						CCCACCTCTATGTCGAAGAAG	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Pancreas(193;496 3017 22514 29918)					NA		NA				0							NA						314	240	265	NA		NA	NA	20		NA											NA				23805930		2203	4300	6503	SO:0001583	missense			M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369	1470			2474	protein-coding gene	gene with protein product	cystatin 2	123856			NA		Standard		NM_001322	NA	Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.259A>G	chr20.hg19:g.23805930T>C	ENSP00000307540:p.Ile87Val	NA	Q9UCQ7	hg19	CCDS13161.1	0.02	11.678288	CTAxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.007	-1.972408	0.00457	.	.	ENSG00000170369	ENST00000304725	T	0.11169	2.8	2.36	1.34	0.21922	Proteinase inhibitor I25, cystatin, conserved site (1);Proteinase inhibitor I25, cystatin (2);	0.163089	0.40818	N	0.001002	T	0.01523	0.0049	N	0.00150	-1.985	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43718	-0.9374	10	0.02654	T	1	.	5.1107	0.14808	0.0:0.6785:0.0:0.3215	.	87	P09228	CYTT_HUMAN	V	87	ENSP00000307540:I87V	ENSP00000307540:I87V	I	-	1	0	CST2	23753930	0.000000	0.05858	0.005000	0.12908	0.003000	0.03518	-0.283000	0.08433	-0.065000	0.13021	-0.665000	0.03846	ATA	NOVEL	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078352.2	5	14.735187	KEEP	2	0	0	49	1462	TT	1	1	0		-	14	40	430	0	0	23.694066	368	60	13561	553	ENST00000304725.2	0.036649	1
FAM182B	728882	__UNKNOWN__	__UNKNOWN__	20	25753853	25753853	__UNKNOWN__	Intron	SNP	A	A	G	rs76897919		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:25753853A>G	ENST00000478164.1	-	3	645				FAM182B_ENST00000376404.2_Intron			Q5T319	F182B_HUMAN	family with sequence similarity 182, member B	NA		NA								lung(1)	1						GACAGTGGACACCAGCTGAAC	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20p11.1	2010-07-14			ENSG00000175170	ENSG00000175170	728882			34503	pseudogene	pseudogene		NA			NA		Standard	NR_026714	NR_027061	NA	Approved			Q5T319	OTTHUMG00000032136	ENST00000478164.1:c.347+1892T>C	chr20.hg19:g.25753853A>G		NA	Q4G0Q1	hg19		0.02	13.481136	GACxCCA	COVERED																																																																																			NOVEL	FAM182B-005	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000316665.1	5	4.672713	KEEP	6	2	70	40	1158	AA	1	1	0		-	11	47	387	0	0	24.01175	265	60	9393	400	ENST00000478164.1	0.039855	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	26211052	26211052	__UNKNOWN__	IGR	SNP	T	T	G	rs534754392	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:26211052T>G			NA	NA				MIR663A (22138 upstream) : None (None downstream)						NA		NA									NA						GCAGAGGCATTACAATACCCT	0.338	NA	NA											t|||	89	0.0177716	0.0015	0.0274	5008	,	,	NA	19633	0	NA	0.0567	False	NA	,,,	NA	NA	NA	2504	0.0112	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.26211052T>G		NA		hg19		0.02	13.719299	CATxACA	COVERED																																																																																			NOVEL					0			8	4.44025	KEEP	2	1	38	28	772	TT	0.999997	0.999997	0			20	60	745	1	0	53.292492	244	60	8544	356		0.075758	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	26211059	26211059	__UNKNOWN__	IGR	SNP	C	C	A	rs201531362		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:26211059C>A			NA	NA				MIR663A (22145 upstream) : None (None downstream)						NA		NA									NA						CATTACAATACCCTGTAACAA	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.26211059C>A		NA		hg19		0.02	15.890847	ATAxCCT	COVERED																																																																																			NOVEL					0			7	4.361645	KEEP	0	2	55	34	1158	CC	0.999999	0.999999	0			19	60	663	0	0	45.305516	258	60	9426	402		0.068592	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	26254092	26254092	__UNKNOWN__	IGR	SNP	G	G	A	rs201752858		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:26254092G>A			NA	NA				MIR663A (65178 upstream) : None (None downstream)						NA		NA									NA						ctactcaggaggttgaggcaa	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.26254092G>A		NA		hg19		0.02	-0.070181	GGAxGTT	UNCOVERED																																																																																			NOVEL					0			0	2.407868	KEEP	0	0	0	8	285	GG	0.99257	0.053735	0			2	49	77	0	0	6.83563	5	60	182	20		0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29449691	29449691	__UNKNOWN__	IGR	SNP	A	A	G	rs113507639		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29449691A>G			NA	NA				None (None upstream) : RP4-610C12.4 (63890 downstream)						NA		NA									NA						TCAAAAATAAAAGATGAGTTT	0.303	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29449691A>G		NA		hg19		0.02	4.955739	TAAxAGA	COVERED																																																																																			NOVEL					0			2	3.600562	KEEP	0	0	0	12	345	AA	0.993634	0.993634	0			16	60	489	0	0	35.703191	112	60	3994	197		0.125	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29612980	29612980	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29612980A>G	ENST00000278882.3	+	1	257				FRG1B_ENST00000439954.2_Intron|FRG1B_ENST00000468180.2_3'UTR|FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GAAAGAAAGTATCAAGGAGTG	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.-124+867A>G	chr20.hg19:g.29612980A>G		NA	C4AME5	hg19		0.02	16.124469	AGTxTCA	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	1	8.058383	KEEP	176	4	147	78	2275	AA	1	1	0		+	20	40	733	0	0	56.966782	135	60	4950	677	ENST00000278882.3	0.129032	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29613055	29613055	__UNKNOWN__	Intron	SNP	G	G	A	rs73616389	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29613055G>A	ENST00000278882.3	+	1	257				FRG1B_ENST00000439954.2_Intron|FRG1B_ENST00000468180.2_3'UTR|FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GCCAGAATAAGTGGCAGGTAT	0.433	NA	NA											.|||	3	0.000599042	0	0.0014	5008	,	,	NA	17543	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.-124+942G>A	chr20.hg19:g.29613055G>A		NA	C4AME5	hg19		0.02	4.401728	TAAxTGG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	1	3.00959	KEEP	16	0	0	10	340	GG	0.992708	0.992702	0		+	12	40	434	0	0	33.536528	82	60	3042	138	ENST00000278882.3	0.12766	0.999994
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29625956	29625956	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs147809085		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29625956G>A	ENST00000278882.3	+	5	580	c.200G>A	c.(199-201)aGa>aAa	p.R67K	FRG1B_ENST00000439954.2_Missense_Mutation_p.R72K|FRG1B_ENST00000358464.4_Missense_Mutation_p.R67K			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	67		NA						p.R67K(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATTGGACCAAGAGAACAATGG	0.338	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.200G>A	chr20.hg19:g.29625956G>A	ENSP00000278882:p.Arg67Lys	NA	C4AME5	hg19		0.02	36.786535	CAAxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	g	9.648	1.140706	0.21205	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.46063	0.88	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.27241	0.0668	.	.	.	0.46901	D	0.99924	B	0.02656	0.0	B	0.15484	0.013	T	0.07986	-1.0744	9	0.28530	T	0.3	.	9.3557	0.38164	0.0:0.0:1.0:0.0	.	72	F5H5R5	.	K	67;72;67	ENSP00000408863:R72K	ENSP00000278882:R67K	R	+	2	0	FRG1B	28239617	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	6.360000	0.73064	1.250000	0.43966	0.184000	0.17185	AGA	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	3	39.325415	KEEP	69	6	162	188	6452	GG	1	1	0		+	19	54	720	0	0	45.357576	521	60	19599	1158	ENST00000278882.3	0.035185	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29625971	29625971	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs145033899		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29625971C>A	ENST00000278882.3	+	5	595	c.215C>A	c.(214-216)cCa>cAa	p.P72Q	FRG1B_ENST00000439954.2_Missense_Mutation_p.P77Q|FRG1B_ENST00000358464.4_Missense_Mutation_p.P72Q			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	72		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CAATGGGAACCAGTCTTTCAA	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.215C>A	chr20.hg19:g.29625971C>A	ENSP00000278882:p.Pro72Gln	NA	C4AME5	hg19		0.02	35.007131	AACxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	c	12.14	1.847531	0.32606	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.49720	0.77	1.68	1.68	0.24146	.	0.112402	0.64402	D	0.000009	T	0.63271	0.2497	.	.	.	0.49483	D	0.999795	D	0.63046	0.992	D	0.79784	0.993	T	0.65948	-0.6044	9	0.66056	D	0.02	.	9.3557	0.38164	0.0:1.0:0.0:0.0	.	77	F5H5R5	.	Q	72;77;72	ENSP00000408863:P77Q	ENSP00000278882:P72Q	P	+	2	0	FRG1B	28239632	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	6.442000	0.73443	1.250000	0.43966	0.184000	0.17185	CCA	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	7	26.917753	KEEP	44	4	121	132	4540	CC	1	1	0		+	25	54	935	0	0	61.602525	509	60	19471	1031	ENST00000278882.3	0.046816	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29626055	29626055	__UNKNOWN__	Intron	SNP	A	A	G	rs74373385	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29626055A>G	ENST00000278882.3	+	5	608				FRG1B_ENST00000439954.2_Intron|FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CAATCATAATATATTTAAAAA	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.228+71A>G	chr20.hg19:g.29626055A>G		NA	C4AME5	hg19		0.02	20.795759	AATxTAT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	15	9.320901	KEEP	2	0	0	31	852	AA	0.999997	0.999997	0		+	18	60	636	0	0	42.423362	290	60	10561	517	ENST00000278882.3	0.058442	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628251	29628251	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29628251A>G	ENST00000278882.3	+	6	633	c.253A>G	c.(253-255)Aat>Gat	p.N85D	FRG1B_ENST00000439954.2_Missense_Mutation_p.N90D|FRG1B_ENST00000358464.4_Missense_Mutation_p.N85D			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	85		NA						p.N85D(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTTGGCCTCAAATAGCTGCTT	0.358	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - Missense(2)	kidney(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.253A>G	chr20.hg19:g.29628251A>G	ENSP00000278882:p.Asn85Asp	NA	C4AME5	hg19		0.02	41.140915	TCAxATA	COVERED	.	.	.	.	.	.	.	.	.	.	a	15.78	2.933773	0.52866	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.50277	0.75	2.08	2.08	0.27032	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	.	.	.	0.45390	D	0.998378	B;B	0.26809	0.086;0.16	B;B	0.40329	0.326;0.253	T	0.51553	-0.8691	9	0.66056	D	0.02	.	8.0833	0.30758	1.0:0.0:0.0:0.0	.	90;85	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	D	85;90;85	ENSP00000408863:N90D	ENSP00000278882:N85D	N	+	1	0	FRG1B	28241912	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	8.047000	0.89440	1.208000	0.43306	0.347000	0.21830	AAT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	15	40.030192	KEEP	37	15	542	322	10198	AA	1	1	0		+	36	60	1398	0	0	96.932874	599	60	21793	1529	ENST00000278882.3	0.056693	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628263	29628263	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29628263A>G	ENST00000278882.3	+	6	645	c.265A>G	c.(265-267)Att>Gtt	p.I89V	FRG1B_ENST00000439954.2_Missense_Mutation_p.I94V|FRG1B_ENST00000358464.4_Missense_Mutation_p.I89V			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	89		NA						p.I89V(4)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAGCTGCTTTATTAGATGCAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				4	Substitution - Missense(4)	prostate(2)|kidney(2)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.265A>G	chr20.hg19:g.29628263A>G	ENSP00000278882:p.Ile89Val	NA	C4AME5	hg19		0.02	41.616116	TTTxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	a	8.196	0.797144	0.16327	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.44482	0.92	2.08	2.08	0.27032	Actin cross-linking (1);	0.052017	0.85682	D	0.000000	T	0.22666	0.0547	.	.	.	0.33862	D	0.633895	B;B	0.06786	0.0;0.001	B;B	0.20767	0.018;0.031	T	0.12041	-1.0563	9	0.22706	T	0.39	.	3.8663	0.09018	0.8139:0.0:0.1861:0.0	.	94;89	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	V	89;94;89	ENSP00000408863:I94V	ENSP00000278882:I89V	I	+	1	0	FRG1B	28241924	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.345000	0.59360	1.208000	0.43306	0.347000	0.21830	ATT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	14	59.765535	KEEP	42	9	328	313	9432	AA	1	1	0		+	24	60	941	0	0	61.507507	593	60	21782	1491	ENST00000278882.3	0.038898	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632559	29632559	__UNKNOWN__	Intron	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29632559T>C	ENST00000278882.3	+	8	805				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAATAGTAAATATGTGTAATC	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.426-52T>C	chr20.hg19:g.29632559T>C		NA	C4AME5	hg19		0.02	18.828807	AAAxATG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	1	21.34529	KEEP	77	3	106	108	2918	TT	1	1	0		+	21	31	776	0	0	52.557162	351	60	12647	667	ENST00000278882.3	0.056452	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632643	29632643	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs143379667		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29632643T>C	ENST00000278882.3	+	8	838	c.458T>C	c.(457-459)cTt>cCt	p.L153P	FRG1B_ENST00000358464.4_Missense_Mutation_p.L153P			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	153		NA						p.L153P(10)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GACCACAAACTTAAAATAAGT	0.294	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				10	Substitution - Missense(10)	endometrium(6)|kidney(4)					NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.458T>C	chr20.hg19:g.29632643T>C	ENSP00000278882:p.Leu153Pro	NA	C4AME5	hg19		0.02	39.513699	AACxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	t	12.77	2.038665	0.35989	.	.	ENSG00000149531	ENST00000278882;ENST00000358464	.	.	.	1.44	1.44	0.22558	.	0.000000	0.64402	U	0.000001	T	0.50463	0.1617	.	.	.	0.80722	D	1	P	0.35033	0.481	B	0.40038	0.317	T	0.53187	-0.8474	8	0.87932	D	0	.	6.9831	0.24713	0.0:0.0:0.0:1.0	.	153	Q9BZ01	FRG1B_HUMAN	P	153	.	ENSP00000278882:L153P	L	+	2	0	FRG1B	28246304	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.723000	0.74742	0.925000	0.37094	0.327000	0.21459	CTT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	23	35.183253	KEEP	104	19	692	358	11509	TT	1	1	0		+	55	60	2054	0	0	152.253612	535	70	20473	1561	ENST00000278882.3	0.09322	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632680	29632680	__UNKNOWN__	Silent	SNP	G	G	A	rs4892355		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29632680G>A	ENST00000278882.3	+	8	875	c.495G>A	c.(493-495)aaG>aaA	p.K165K	FRG1B_ENST00000358464.4_Silent_p.K165K			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	165		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTCTTAAAAAGGCTCAGAAAG	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.495G>A	chr20.hg19:g.29632680G>A		NA	C4AME5	hg19		0.02	40.235661	AAAxGCT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	27	56.1368	KEEP	70	16	482	356	12767	GG	1	1	0		+	47	60	1762	0	0	130.073684	474	70	17454	1532	ENST00000278882.3	0.090211	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632772	29632772	__UNKNOWN__	Intron	SNP	G	G	A	rs113430333		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29632772G>A	ENST00000278882.3	+	8	916				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATAGAAATGGCATGTAGAAA	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.536+51G>A	chr20.hg19:g.29632772G>A		NA	C4AME5	hg19		0.02	18.132377	ATGxCAT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	6	12.176105	KEEP	1	4	115	81	2842	GG	1	1	0		+	12	60	424	0	0	26.034269	301	70	11193	577	ENST00000278882.3	0.038339	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633983	29633983	__UNKNOWN__	3'UTR	SNP	A	A	G	rs76742789	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29633983A>G	ENST00000278882.3	+	0	1002				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTTTCTGAATAAAATATTCAG	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*73A>G	chr20.hg19:g.29633983A>G		NA	C4AME5	hg19		0.02	39.179784	AATxAAA	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	20	23.150549	KEEP	22	12	412	221	6576	AA	1	1	0		+	26	60	912	0	0	55.948649	651	70	23343	1324	ENST00000278882.3	0.038405	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633987	29633987	__UNKNOWN__	3'UTR	SNP	T	T	A	rs4006817	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29633987T>A	ENST00000278882.3	+	0	1006				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CTGAATAAAATATTCAGAGGA	0.308	NA	NA											.|||	743	0.148363	0.0446	0.1657	5008	,	,	NA	33780	0.1984	NA	0.166	False	NA	,,,	NA	NA	NA	2504	0.2065	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*77T>A	chr20.hg19:g.29633987T>A		NA	C4AME5	hg19		0.02	39.361324	AAAxATT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	19	23.327709	KEEP	20	14	422	226	6793	TT	1	1	0		+	36	60	1325	0	0	88.055986	665	70	24190	1339	ENST00000278882.3	0.051355	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633992	29633992	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29633992A>G	ENST00000278882.3	+	0	1011				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAAAATATTCAGAGGAAATGC	0.308	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*82A>G	chr20.hg19:g.29633992A>G		NA	C4AME5	hg19		0.02	38.289261	TTCxGAG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	19	41.404323	KEEP	19	8	285	237	7408	AA	1	1	0		+	40	60	1409	0	0	93.205788	670	70	25066	1352	ENST00000278882.3	0.056338	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29634031	29634031	__UNKNOWN__	IGR	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29634031A>C			NA	NA				FRG1B (21 upstream) : AL441988.1 (3130 downstream)						NA		NA									NA						TTGTTGTGAAATTATTGTTTA	0.313	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29634031A>C		NA		hg19		0.02	35.376778	GAAxTTA	COVERED																																																																																			NOVEL					0			13	11.478863	KEEP	13	13	485	207	6305	AA	1	1	0			19	49	725	0	0	43.461834	700	70	26020	1287		0.026426	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29637779	29637779	__UNKNOWN__	IGR	SNP	A	A	C	rs6141138		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29637779A>C			NA	NA				AL441988.1 (479 upstream) : DEFB115 (207687 downstream)						NA		NA									NA						CATAAGAGCAAATATTTTAAG	0.279	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29637779A>C		NA		hg19		0.02	1.936603	GCAxATA	COVERED																																																																																			NOVEL					0			1	3.009178	KEEP	0	0	0	10	329	AA	0.992708	0.992648	0			5	60	186	0	0	13.070338	68	60	2410	109		0.068493	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29637851	29637851	__UNKNOWN__	IGR	SNP	C	C	G	rs148007340		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29637851C>G			NA	NA				AL441988.1 (551 upstream) : DEFB115 (207615 downstream)						NA		NA									NA						TCTTGGATTTCTTTCAACACC	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29637851C>G		NA		hg19		0.02	7.474299	TTTxTTT	COVERED																																																																																			NOVEL					0			2	2.845615	KEEP	0	1	36	22	785	CC	0.999892	0.999892	0			9	60	349	0	0	25.977607	93	60	3526	242		0.088235	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29637936	29637936	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29637936A>T			NA	NA				AL441988.1 (636 upstream) : DEFB115 (207530 downstream)						NA		NA									NA						CTAGTCTCTGAAACATCTTTT	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29637936A>T		NA		hg19		0.02	8.557825	CTGxAAC	COVERED																																																																																			NOVEL					0			2	4.943462	KEEP	4	1	27	26	741	AA	0.999988	0.999988	0			8	60	286	0	0	20.655737	83	60	3059	326		0.087912	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29646275	29646275	__UNKNOWN__	IGR	SNP	G	G	T	rs73610077		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29646275G>T			NA	NA				AL441988.1 (8975 upstream) : DEFB115 (199191 downstream)						NA		NA									NA						gaaagcaagagcaggaggaag	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29646275G>T		NA		hg19		0.02	2.299647	AGAxCAG	COVERED																																																																																			NOVEL					0			4	2.94403	KEEP	0	1	29	20	732	GG	0.999869	0.994953	0			4	60	145	0	0	11.232477	27	60	1027	107		0.129032	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29648755	29648755	__UNKNOWN__	IGR	SNP	A	A	G	rs6087178	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29648755A>G			NA	NA				AL441988.1 (11455 upstream) : DEFB115 (196711 downstream)						NA		NA									NA						ctgggattacaggtgtgagtc	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29648755A>G		NA		hg19		0.02	1.555161	TACxGGT	COVERED																																																																																			NOVEL					0			9	4.881819	KEEP	0	2	65	39	1192	AA	1	0.999919	0			6	60	207	0	0	18.416549	13	60	477	170		0.315789	0.999919
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29652005	29652005	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29652005A>G			NA	NA				AL441988.1 (14705 upstream) : DEFB115 (193461 downstream)						NA		NA									NA						gggacttcttagcctccataa	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29652005A>G		NA		hg19		0.02	7.177946	CTTxGCC	COVERED																																																																																			NOVEL					0			3	2.406915	KEEP	0	0	0	8	239	AA	0.99257	0.99257	0			17	60	636	0	0	50.255693	106	60	3714	203		0.138211	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29652138	29652138	__UNKNOWN__	IGR	SNP	C	C	T	rs71273513|rs77358300		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:29652138C>T			NA	NA				AL441988.1 (14838 upstream) : DEFB115 (193328 downstream)						NA		NA									NA						tcagtcatagcctgccttcat	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29652138C>T		NA		hg19		0.02	39.592893	TAGxCTG	COVERED																																																																																			NOVEL					0			15	4.159896	KEEP	0	14	418	161	5685	CG	1	1	0			24	60	896	0	0	63.740202	305	60	11480	1272		0.072948	1
KIF3B	9371	__UNKNOWN__	__UNKNOWN__	20	30897799	30897799	__UNKNOWN__	Silent	SNP	C	C	T	rs200457491		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:30897799C>T	ENST00000375712.3	+	2	386	c.219C>T	c.(217-219)taC>taT	p.Y73Y		NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	73	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.	NA			anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)			NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			TTGAACTGTACGATGAGACGT	0.488	NA	NA											C|||	1	0.000199681	0	0	5008	,	,	NA	21535	0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA	C		0,4406		0,0,2203	159	138	145	NA	219	-3.3	1	20		145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIF3B	NM_004798.3		0,2,6501	TT,TC,CC	NA	0.0233,0.0,0.0154		73/748	30897799	2,13004	2203	4300	6503	SO:0001819	synonymous_variant			AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350	9371		Kinesins	6320	protein-coding gene	gene with protein product		603754			NA	9205841	Standard	NM_004798	NM_004798	NA	Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.219C>T	chr20.hg19:g.30897799C>T		NA	B2RMP4|B4DSR5|E1P5M5	hg19	CCDS13200.1	0.02	14.447522	GTAxGAT	COVERED																																																																																			NOVEL	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078619.1	3	7.476181	KEEP	0	0	0	25	813	CC	0.999957	0.999957	0		+	43	60	1614	0	0	126.592343	285	60	9905	398	ENST00000375712.3	0.131098	1
MYH7B	57644	__UNKNOWN__	__UNKNOWN__	20	33567129	33567129	__UNKNOWN__	Intron	SNP	C	C	T	rs529535821		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:33567129C>T	ENST00000262873.7	+	4	309					NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	NA		NA				membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGCTTGGGAACTCCAGCTAGA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814	57644		Myosins / Myosin superfamily : Class II	15906	protein-coding gene	gene with protein product		609928	myosin, heavy polypeptide 7B, cardiac muscle, beta		NA	11919279, 15014174	Standard	NM_020884	XM_006723839	NA	Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.218-64C>T	chr20.hg19:g.33567129C>T		NA	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	hg19	CCDS42869.1	0.02	4.271112	GAAxTCC	COVERED																																																																																			NOVEL	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078833.2	1	8.110439	KEEP	0	0	0	27	926	CC	0.999988	0.999987	0		+	6	60	215	0	0	13.893642	120	60	4270	188	ENST00000262873.7	0.047619	1
TOX2	84969	__UNKNOWN__	__UNKNOWN__	20	42693611	42693611	__UNKNOWN__	Intron	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:42693611C>G	ENST00000341197.4	+	6	988				TOX2_ENST00000372999.1_Intron|TOX2_ENST00000358131.5_Intron|TOX2_ENST00000423191.2_Intron|TOX2_ENST00000435864.2_Intron	NM_001098797.1	NP_001092267.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	NA		NA			female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			GAAAGAATGGCTCAGACCTAC	0.557	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20			84969			16095	protein-coding gene	gene with protein product	granulosa cell HMG box 1	611163	chromosome 20 open reading frame 100	C20orf100	NA	14764631	Standard		NM_001098796	NA	Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000341197.4:c.960+114C>G	chr20.hg19:g.42693611C>G		NA	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	hg19	CCDS46603.1	0.02	1.907588	TGGxTCA	COVERED																																																																																			NOVEL	TOX2-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079331.2	2	2.708428	KEEP	0	0	0	9	306	CC	0.99254	0.992346	0		+	20	60	734	0	0	62.357949	69	60	2564	102	ENST00000341197.4	0.224719	0.999804
MATN4	8785	__UNKNOWN__	__UNKNOWN__	20	43933117	43933117	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:43933117G>A	ENST00000372756.1	-	2	402	c.394C>T	c.(394-396)Cga>Tga	p.R132*	MATN4_ENST00000537548.1_Nonsense_Mutation_p.R132*|MATN4_ENST00000360607.6_Nonsense_Mutation_p.R132*|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000353917.5_Nonsense_Mutation_p.R132*|MATN4_ENST00000372754.1_Nonsense_Mutation_p.R132*|MATN4_ENST00000342716.4_Nonsense_Mutation_p.R132*			O95460	MATN4_HUMAN	matrilin 4	132	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.	NA			extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				TCTGGCGGTCGCGCGCCCTCG	0.731	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						9	9	9	NA		NA	NA	20		NA											NA				43933117		2150	4222	6372	SO:0001587	stop_gained			AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159	8785			6910	protein-coding gene	gene with protein product		603897			NA	9827539, 9027493	Standard		NM_003833	NA	Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372756.1:c.394C>T	chr20.hg19:g.43933117G>A	ENSP00000361842:p.Arg132*	NA	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	hg19	CCDS13348.1	0.02	4.118866	GTCxCGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	32	5.141764	0.94560	.	.	ENSG00000124159	ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132	.	.	.	4.81	4.81	0.61882	.	0.000000	0.44902	D	0.000415	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.0299	0.86458	0.0:0.0:1.0:0.0	.	.	.	.	X	132	.	ENSP00000255132:R132X	R	-	1	2	MATN4	43366531	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	8.060000	0.89464	2.506000	0.84524	0.462000	0.41574	CGA	NOVEL	MATN4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080334.1	1	6.913734	KEEP	0	0	0	23	734	GG	0.999892	0.999892	0		-	8	60	273	0	0	18.022454	124	60	3871	173	ENST00000372756.1	0.060606	1
NFATC2	4773	__UNKNOWN__	__UNKNOWN__	20	50007118	50007118	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:50007118C>T	ENST00000396009.3	-	0	3812				NFATC2_ENST00000371564.3_3'UTR|NFATC2_ENST00000609943.1_3'UTR	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	NA		NA			B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CAGCCTGGGTCAGCCCCCCAA	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096	4773		Nuclear factor of activated T-cells	7776	protein-coding gene	gene with protein product		600490			NA	8202141	Standard	NM_012340	NM_012340	NA	Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.*815G>A	chr20.hg19:g.50007118C>T		NA	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	hg19	CCDS13437.1	0.02	9.106777	GGTxAGC	COVERED																																																																																			NOVEL	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079730.2	1	10.233202	KEEP	0	0	0	34	1192	CC	0.999998	0.999998	0		-	51	60	1759	0	0	147.069824	182	60	6728	318	ENST00000396009.3	0.218884	1
ATP9A	10079	__UNKNOWN__	__UNKNOWN__	20	50281549	50281549	__UNKNOWN__	Intron	SNP	G	G	A	rs111554304	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:50281549G>A	ENST00000338821.5	-	13	1558				ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	NA		NA			phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						gattacaggcgtgagccacca	0.478	NA	NA											G|||	1232	0.246006	0.0522	0.2622	5008	,	,	NA	14700	0.503	NA	0.3141	False	NA	,,,	NA	NA	NA	2504	0.1616	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793	10079		ATPases / P-type	13540	protein-coding gene	gene with protein product		609126	ATPase, Class II, type 9A		NA	9734811, 11015572	Standard	NM_006045	NM_006045	NA	Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.1293+4986C>T	chr20.hg19:g.50281549G>A		NA	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	hg19	CCDS33489.1	0.02	-0.05264	GGCxTGA	UNCOVERED																																																																																			NOVEL	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000106494.1	6	2.407735	KEEP	3	0	0	8	276	GG	0	0	0		-	3	60	118	0	0	11.425179	3	60	110	16	ENST00000338821.5	0.5	0.036766
FAM209A	200232	__UNKNOWN__	__UNKNOWN__	20	55099744	55099744	__UNKNOWN__	5'UTR	SNP	A	A	G	rs2426630		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:55099744A>G	ENST00000371328.3	+	0	203				FAM209A_ENST00000481560.1_Intron|GCNT7_ENST00000243913.4_Intron	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)					NA						CAATGGCCAGAGTGGCCTCAG	0.597	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103	200232			16100	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 106	C20orf106	NA		Standard		NM_001012971	NA	Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.-121A>G	chr20.hg19:g.55099744A>G		NA	Q05C43	hg19	CCDS33493.1	0.02	24.086185	CAGxGTG	COVERED																																																																																			NOVEL	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079815.2	6	15.950678	KEEP	1	3	103	89	2774	AA	1	1	0		+	42	49	1508	0	0	107.815289	470	60	17049	686	ENST00000371328.3	0.082031	1
STX16-NPEPL1	100534593	__UNKNOWN__	__UNKNOWN__	20	57253740	57253740	__UNKNOWN__	Intron	SNP	T	T	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:57253740T>G	ENST00000530122.1	+	8	1446				STX16_ENST00000359617.4_3'UTR|STX16_ENST00000371132.4_3'UTR|STX16_ENST00000371141.4_3'UTR|STX16_ENST00000361830.3_3'UTR|STX16_ENST00000361770.5_3'UTR|STX16_ENST00000355957.5_3'UTR|STX16_ENST00000358029.4_3'UTR					STX16-NPEPL1 readthrough (NMD candidate)	NA		NA									NA						TTTCCCAAGGTGGGAGAGACA	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q13.32	2013-05-09	2013-05-09		ENSG00000254995	ENSG00000254995	100534593			41993	other	readthrough		NA			NA		Standard	NR_037945.1	NR_037945	NA	Approved				OTTHUMG00000167390	ENST00000530122.1:c.873+4973T>G	chr20.hg19:g.57253740T>G		NA		hg19		0.02	1.679037	AGGxGGG	COVERED																																																																																			NOVEL	STX16-NPEPL1-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000394467.1	5	5.41219	KEEP	0	0	0	18	496	TT	0.999859	0.999177	0		+	8	60	185	0	0	11.143676	72	70	2184	128	ENST00000530122.1	0.1	0.999317
PTK6	5753	__UNKNOWN__	__UNKNOWN__	20	62161006	62161006	__UNKNOWN__	Silent	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr20:62161006C>T	ENST00000217185.2	-	8	1266	c.1239G>A	c.(1237-1239)ccG>ccA	p.P413P	PTK6_ENST00000542869.1_Silent_p.P312P	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6	413	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|intestinal epithelial cell differentiation (GO:0060575)|negative regulation of growth (GO:0045926)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(1)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)		Vandetanib(DB05294)	GCACGCTGGGCGGGCACTCCA	0.657	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						20	19	19	NA		NA	NA	20		NA											NA				62161006		2130	4187	6317	SO:0001819	synonymous_variant			U61412	CCDS13524.1, CCDS74750.1	20q13.3	2013-02-18	2013-02-18		ENSG00000101213	ENSG00000101213	5753	2.7.10.1	SH2 domain containing	9617	protein-coding gene	gene with protein product		602004	PTK6 protein tyrosine kinase 6		NA	8247543, 9284935	Standard		NM_005975	NA	Approved	BRK	uc002yfg.4	Q13882	OTTHUMG00000033039	ENST00000217185.2:c.1239G>A	chr20.hg19:g.62161006C>T		NA	B2RCR3|B4DW46|Q58F01	hg19	CCDS13524.1	0.02	9.018201	GGGxGGG	COVERED																																																																																			NOVEL	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080313.1	2	32.474376	KEEP	0	0	0	108	3545	CC	1	1	0		-	10	60	371	0	0	24.441227	199	60	6474	386	ENST00000217185.2	0.047847	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9650059	9650059	__UNKNOWN__	IGR	SNP	A	A	T	rs77569291		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9650059A>T			NA	NA				None (None upstream) : CR381670.1 (33131 downstream)						NA		NA									NA						ATCTGGGACCACACCACACCA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9650059A>T		NA		hg19		0.02	4.520594	ACCxCAC	COVERED																																																																																			NOVEL					0			2	2.439382	KEEP	46	1	28	18	554	AA	0.995343	0.995343	0			6	40	220	0	0	14.390736	120	60	4395	236		0.047619	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9650060	9650060	__UNKNOWN__	IGR	SNP	C	C	T	rs376222179		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9650060C>T			NA	NA				None (None upstream) : CR381670.1 (33130 downstream)						NA		NA									NA						TCTGGGACCACACCACACCAG	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9650060C>T		NA		hg19		0.02	4.403671	CCAxACC	COVERED																																																																																			NOVEL					0			3	2.541867	KEEP	48	1	30	19	647	CC	0.99649	0.99649	0			19	60	702	0	0	55.927006	109	60	4065	239		0.148437	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9650070	9650070	__UNKNOWN__	IGR	SNP	G	G	A	rs80315236		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9650070G>A			NA	NA				None (None upstream) : CR381670.1 (33120 downstream)						NA		NA									NA						CACCACACCAGTTCTCTCCTT	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9650070G>A		NA		hg19		0.02	4.194446	CCAxTTC	COVERED																																																																																			NOVEL					0			2	2.643942	KEEP	50	1	32	20	727	GG	0.997832	0.997832	0			8	40	276	0	0	18.371945	122	60	4675	254		0.061538	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9650228	9650228	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9650228C>G			NA	NA				None (None upstream) : CR381670.1 (32962 downstream)						NA		NA									NA						TTATGGGTGTCTGTGAATTAA	0.323	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9650228C>G		NA		hg19		0.02	2.396215	TGTxTGT	UNCOVERED																																																																																			NOVEL					0			3	2.408045	KEEP	41	0	0	8	303	CC	0	0	0			8	40	300	0	0	24.122803	44	46	1613	103		0.153846	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9677028	9677028	__UNKNOWN__	IGR	SNP	C	C	A	rs372634257		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9677028C>A			NA	NA				None (None upstream) : CR381670.1 (6162 downstream)						NA		NA									NA						caggcgtgcgcccccacgcct	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9677028C>A		NA		hg19		0.02	-0.105277	GCGxCCC	UNCOVERED																																																																																			NOVEL					0			2	3.310753	KEEP	1	0	0	11	382	CC	0.992708	0.138812	0			2	57	71	0	0	6.592743	3	60	115	28		0.4	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9695901	9695901	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9695901C>T			NA	NA				CR381670.1 (12629 upstream) : MIR3648 (129930 downstream)						NA		NA									NA						ACGCTGTGAGCTCCAAGTCCA	0.572	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9695901C>T		NA		hg19		0.02	-0.280737	GAGxTCC	COVERED																																																																																			NOVEL					0			0	8.727671	KEEP	20	0	0	29	1000	CC	0.99986	0.739568	0			3	40	97	0	0	6.809794	29	48	1073	80		0.09375	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9699001	9699001	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9699001T>A			NA	NA				CR381670.1 (15729 upstream) : MIR3648 (126830 downstream)						NA		NA									NA						acatttcagctggagtcagtt	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9699001T>A		NA		hg19		0.02	2.429359	AGCxGGA	COVERED																																																																																			NOVEL					0			12	2.864085	KEEP	12	2	58	30	885	TT	0.999957	0.998422	0			6	55	223	0	0	16.69579	54	54	2032	148		0.1	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9699630	9699630	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9699630A>T			NA	NA				CR381670.1 (16358 upstream) : MIR3648 (126201 downstream)						NA		NA									NA						agactcacagacttcactgag	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9699630A>T		NA		hg19		0.02	1.851057	CAGxCTT	COVERED																																																																																			NOVEL					0			9	4.045567	KEEP	5	1	33	25	772	AA	0.999909	0.999468	0			5	49	178	0	0	12.497961	61	50	2174	141		0.075758	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9715898	9715898	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9715898G>A			NA	NA				CR381670.1 (32626 upstream) : MIR3648 (109933 downstream)						NA		NA									NA						atactaccatgcccagcTAAt	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9715898G>A		NA		hg19		0.02	-0.070177	CATxCCC	UNCOVERED																																																																																			NOVEL					0			0	2.708669	KEEP	7	0	0	9	322	GG	0	0	0			3	27	107	0	0	9.833042	5	40	175	22		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9825569	9825569	__UNKNOWN__	IGR	SNP	G	G	A	rs199605544		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9825569G>A			NA	NA				CR381670.1 (142297 upstream) : MIR3648 (262 downstream)						NA		NA									NA						CCTCTTCCCCGCCCGCCGCCC	0.761	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9825569G>A		NA		hg19		0.02	11.670722	CCCxCCC	COVERED																																																																																			NOVEL					0			117	96.552114	KEEP	0	3	90	355	10319	GG	1	1	0			11	60	360	2	0	20.644132	302	60	8601	1140		0.035144	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9825610	9825610	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9825610A>G			NA	NA				CR381670.1 (142338 upstream) : MIR3648 (221 downstream)						NA		NA									NA						CGAGCGGCTCACCGGCTTCAC	0.781	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9825610A>G		NA		hg19		0.02	17.737719	CTCxCCG	COVERED																																																																																			NOVEL					0			84	14.215239	KEEP	0	32	941	379	10631	AA	1	1	0			35	60	1162	0	0	82.268667	345	60	11657	1169		0.092105	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9825630	9825630	__UNKNOWN__	IGR	SNP	T	T	C	rs370253309		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9825630T>C			NA	NA				CR381670.1 (142358 upstream) : MIR3648 (201 downstream)						NA		NA									NA						CGTCCGTTGGTGGCCCCGCCT	0.791	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9825630T>C		NA		hg19		0.02	14.923823	TGGxGGC	COVERED																																																																																			NOVEL					0			59	15.910573	KEEP	0	28	842	349	10033	TT	1	1	0			23	60	776	0	0	51.872398	323	60	10919	1047		0.066474	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9826293	9826293	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9826293C>T			NA	NA				MIR3687 (30 upstream) : TEKT4P2 (80900 downstream)						NA		NA									NA						TTGCCGGTCGCTCGCCCTTTc	0.836	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9826293C>T		NA		hg19		0.02	24.953202	TCGxTCG	COVERED																																																																																			NOVEL					0			3	76.862174	KEEP	0	36	1062	630	21046	CC	1	1	0			36	60	1057	0	1	63.657483	615	60	21380	1786		0.0553	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9826698	9826698	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9826698T>C			NA	NA				MIR3687 (435 upstream) : TEKT4P2 (80495 downstream)						NA		NA									NA						cgggcgcgggtcgggccgtcc	0.866	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9826698T>C		NA		hg19		0.02	2.008702	GGGxCGG	COVERED																																																																																			NOVEL					0			0	11.652018	KEEP	0	1	38	52	1367	TT	1	0.976865	0			7	60	239	0	0	18.34331	45	60	1341	154		0.134615	0.976865
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9891891	9891891	__UNKNOWN__	IGR	SNP	A	A	G	rs552045926	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9891891A>G			NA	NA				MIR3687 (65628 upstream) : TEKT4P2 (15302 downstream)						NA		NA									NA						TCTGGAATCAAGATTTAACGC	0.373	NA	NA											.|||	1166	0.232827	0.1808	0.2882	5008	,	,	NA	31023	0.125	NA	0.3867	False	NA	,,,	NA	NA	NA	2504	0.2168	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9891891A>G		NA		hg19		0.02	2.23627	TCAxGAT	UNCOVERED																																																																																			NOVEL					0			2	2.40756	KEEP	12	0	0	8	261	AA	0	0	0			16	60	614	0	0	51.553059	65	60	2300	117		0.197531	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9896603	9896603	__UNKNOWN__	IGR	SNP	C	C	T	rs7442447		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9896603C>T			NA	NA				MIR3687 (70340 upstream) : TEKT4P2 (10590 downstream)						NA		NA									NA						cataacagaacaagaggtcat	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9896603C>T		NA		hg19		0.02	-0.3948	GAAxAAG	COVERED																																																																																			NOVEL					0			1	3.009897	KEEP	1	0	0	10	360	CC	0.99254	0.919727	0			16	49	608	0	0	55.714892	29	60	1092	74		0.355556	0.92664
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9911003	9911003	__UNKNOWN__	RNA	SNP	G	G	A	rs368106393		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9911003G>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						TCTGTGTGTAGGAACAAGCCT	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9911003G>A		NA		hg19		0.02	2.110115	GTAxGAA	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	3	2.738763	KEEP	10	1	31	20	693	GG	0.99986	0.999822	0		-	7	53	250	0	0	22.048891	17	60	608	134	ENST00000416067.1	0.291667	0.999962
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9911831	9911831	__UNKNOWN__	RNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9911831C>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						GCTGGTCTCCCGTGTGCTTGC	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9911831C>T		NA		hg19		0.02	-0.298271	TCCxGTG	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	2	2.407419	KEEP	1	0	0	8	264	CC	0.99257	0.775257	0		-	3	60	103	0	0	7.497786	27	60	939	46	ENST00000416067.1	0.1	0.78106
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9913816	9913816	__UNKNOWN__	RNA	SNP	C	C	T	rs374401025		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9913816C>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						TGCCCTCCTCCTGGACCTGAC	0.682	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9913816C>T		NA		hg19		0.02	-0.149143	CTCxTGG	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	1	2.40774	KEEP	0	0	0	8	279	CC	0.99257	0.289832	0		-	3	60	111	0	0	9.732272	8	60	289	32	ENST00000416067.1	0.272727	0.292001
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9943632	9943632	__UNKNOWN__	RNA	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9943632G>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						agttggggccgggcttggtgg	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9943632G>A		NA		hg19		0.02	-0.262959	GCCxGGC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	6	9.028786	KEEP	2	0	0	30	1020	GG	0.999997	0.693666	0		-	4	60	125	0	0	9.890233	18	60	613	81	ENST00000416067.1	0.181818	0.693668
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9943687	9943687	__UNKNOWN__	RNA	SNP	A	A	G	rs372236731		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9943687A>G	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						aggcacgtggatcacgaggtc	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9943687A>G		NA		hg19		0.02	-0.245656	TGGxTCA	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	4	4.146674	KEEP	1	1	35	26	802	AA	0.999988	0.641339	0		-	3	60	116	0	0	9.591096	14	60	532	82	ENST00000416067.1	0.176471	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9984239	9984239	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:9984239C>T			NA	NA				TEKT4P2 (15654 upstream) : CR381653.1 (215703 downstream)						NA		NA									NA						ccttagtatcccaagtagcca	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9984239C>T		NA		hg19		0.02	-0.096504	ATCxCAA	UNCOVERED																																																																																			NOVEL					0			7	2.407095	KEEP	1	0	0	8	261	CC	0	0	0			3	47	107	0	0	9.332194	8	55	288	22		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10019963	10019963	__UNKNOWN__	IGR	SNP	A	A	G	rs371086989		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10019963A>G			NA	NA				TEKT4P2 (51378 upstream) : CR381653.1 (179979 downstream)						NA		NA									NA						ctggagtgcaatggcatgatc	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10019963A>G		NA		hg19		0.02	-0.096506	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			5	4.513762	KEEP	16	0	0	15	473	AA	0	0	0			2	40	77	0	0	6.835516	5	27	181	36		0.285714	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10020096	10020096	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10020096G>A			NA	NA				TEKT4P2 (51511 upstream) : CR381653.1 (179846 downstream)						NA		NA									NA						tagtagagatggggtttcacc	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10020096G>A		NA		hg19		0.02	-0.193011	GATxGGG	COVERED																																																																																			NOVEL					0			4	2.442928	KEEP	5	1	31	19	680	GG	0.999863	0.457694	0			3	42	117	0	0	9.609434	15	47	548	54		0.166667	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10085558	10085558	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10085558A>G			NA	NA				TEKT4P2 (116973 upstream) : CR381653.1 (114384 downstream)						NA		NA									NA						gtgtaatggaatagaatggaa	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10085558A>G		NA		hg19		0.02	-0.236877	GGAxTAG	COVERED																																																																																			NOVEL					0			1	2.406867	KEEP	2	0	0	8	249	AA	0.99257	0.607857	0			2	49	77	0	0	6.306275	10	60	368	43		0.166667	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10085698	10085698	__UNKNOWN__	IGR	SNP	G	G	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10085698G>C			NA	NA				TEKT4P2 (117113 upstream) : CR381653.1 (114244 downstream)						NA		NA									NA						gaaaggagtggaatggaatgg	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10085698G>C		NA		hg19		0.02	2.038607	GTGxAAT	COVERED																																																																																			NOVEL					0			38	11.714548	KEEP	15	0	0	39	1291	GG	1	0.999218	0			3	52	115	2	0	10.278475	7	60	258	169		0.3	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10143250	10143250	__UNKNOWN__	IGR	SNP	C	C	T	rs369932148		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10143250C>T			NA	NA				TEKT4P2 (174665 upstream) : CR381653.1 (56692 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10143250C>T		NA		hg19		0.02	2.158111	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			2	2.708787	KEEP	8	0	0	9	313	CC	0	0	0			7	49	256	0	0	20.722271	35	50	1283	90		0.166667	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10144654	10144654	__UNKNOWN__	IGR	SNP	C	C	T	rs375919883		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10144654C>T			NA	NA				TEKT4P2 (176069 upstream) : CR381653.1 (55288 downstream)						NA		NA									NA						ctgttgcccacgctggagtgc	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10144654C>T		NA		hg19		0.02	-0.122727	CCAxGCT	UNCOVERED																																																																																			NOVEL					0			4	3.009097	KEEP	13	0	0	10	320	CG	0	0	0			4	53	155	0	0	13.772969	10	59	316	41		0.285714	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10145146	10145146	__UNKNOWN__	IGR	SNP	T	T	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10145146T>A			NA	NA				TEKT4P2 (176561 upstream) : CR381653.1 (54796 downstream)						NA		NA									NA						ttttgtattttcagtagagat	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10145146T>A		NA		hg19		0.02	-0.37715	TTTxCAG	COVERED																																																																																			NOVEL					0			7	2.373065	KEEP	3	2	48	25	796	TT	0.999931	0.909006	0			4	49	144	0	0	10.805875	33	60	1199	92		0.108108	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10145250	10145250	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10145250G>A			NA	NA				TEKT4P2 (176665 upstream) : CR381653.1 (54692 downstream)						NA		NA									NA						ttacatgaatgagccactgca	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10145250G>A		NA		hg19		0.02	-0.175466	AATxAGC	COVERED																																																																																			NOVEL					0			2	2.708647	KEEP	2	0	0	9	308	GG	0.99257	0.384528	0			3	49	112	0	0	9.472402	11	50	416	37		0.214286	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10146470	10146470	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10146470T>C			NA	NA				TEKT4P2 (177885 upstream) : CR381653.1 (53472 downstream)						NA		NA									NA						tttattttttttgtagagtca	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10146470T>C		NA		hg19		0.02	-0.228098	TTTxTGT	UNCOVERED																																																																																			NOVEL					0			3	2.406525	KEEP	7	0	0	8	234	TT	0	0	0			3	27	109	0	0	8.348771	22	50	797	40		0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10146504	10146504	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10146504G>A			NA	NA				TEKT4P2 (177919 upstream) : CR381653.1 (53438 downstream)						NA		NA									NA						tgctcaggctggtctcacgat	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10146504G>A		NA		hg19		0.02	-0.411612	GCTxGTC	COVERED																																																																																			NOVEL					0			7	3.043412	KEEP	8	1	28	20	692	GG	0.997832	0.939699	0			4	27	156	0	0	11.610686	42	50	1581	85		0.086957	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10157041	10157041	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10157041C>G			NA	NA				TEKT4P2 (188456 upstream) : CR381653.1 (42901 downstream)						NA		NA									NA						ggtccagccacagccttgtgg	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10157041C>G		NA		hg19		0.02	-0.149147	CCAxAGC	UNCOVERED																																																																																			NOVEL					0			1	2.407765	KEEP	17	0	0	8	278	CT	0	0	0			2	27	79	0	0	6.430514	11	27	409	52		0.153846	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10180625	10180625	__UNKNOWN__	IGR	SNP	C	C	T	rs372583252		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10180625C>T			NA	NA				TEKT4P2 (212040 upstream) : CR381653.1 (19317 downstream)						NA		NA									NA						ggtatgtgggcaagtagaagg	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10180625C>T		NA		hg19		0.02	-0.377214	GGGxAAG	COVERED																																																																																			NOVEL					0			1	3.61198	KEEP	10	0	0	12	443	CC	0.992708	0.90244	0			7	40	243	0	0	19.344671	36	48	1362	76		0.162791	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10207662	10207662	__UNKNOWN__	IGR	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10207662A>T			NA	NA				CR381653.1 (7637 upstream) : RN7SL52P (172717 downstream)						NA		NA									NA						ttgaactacaaaaagaaaatt	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10207662A>T		NA		hg19		0.02	1.929995	ACAxAAA	UNCOVERED																																																																																			NOVEL					0			1	3.309961	KEEP	48	0	0	11	350	AG	0	0	0			7	40	253	0	0	18.624795	66	40	2391	150		0.09589	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10211989	10211989	__UNKNOWN__	IGR	SNP	C	C	T	rs376998147		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10211989C>T			NA	NA				CR381653.1 (11964 upstream) : RN7SL52P (168390 downstream)						NA		NA									NA						accatcttggccaggctggtc	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10211989C>T		NA		hg19		0.02	-0.122826	TGGxCAG	UNCOVERED																																																																																			NOVEL					0			5	2.407846	KEEP	11	0	0	8	282	CC	0	0	0			3	52	109	0	0	9.172418	11	52	408	30		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10212919	10212919	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:10212919T>C			NA	NA				CR381653.1 (12894 upstream) : RN7SL52P (167460 downstream)						NA		NA									NA						CCTCGCCTTGTAGGAAGAGTG	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10212919T>C		NA		hg19		0.02	-0.254424	TTGxAGG	UNCOVERED																																																																																			NOVEL					0			0	2.707956	KEEP	45	0	0	9	274	TT	0	0	0			4	22	144	0	0	11.321978	24	29	880	99		0.142857	0.668523
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11012962	11012962	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11012962C>T	ENST00000415664.2	-	0	958							P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGTGAAGATCCACAGCAGTCT	0.264	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.-2378G>A	chr21.hg19:g.11012962C>T		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	8.74258	ATCxACA	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	1	7.38987	KEEP	1	2	58	45	1566	CC	1	1	0		-	8	21	278	0	0	16.765822	219	60	7717	378	ENST00000415664.2	0.035242	1
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11022381	11022381	__UNKNOWN__	Intron	SNP	T	T	C	rs635056		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11022381T>C	ENST00000415664.2	-	3	239				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TGAAAGAAGATTAACCAgctg	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3098-1170A>G	chr21.hg19:g.11022381T>C		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.193012	AGAxTAA	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	2	3.610533	KEEP	2	0	0	12	363	TT	0.992708	0.454419	0		-	6	49	232	0	0	21.269374	11	60	400	40	ENST00000415664.2	0.352941	0.457757
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11026921	11026921	__UNKNOWN__	Intron	SNP	T	T	C	rs12329741		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11026921T>C	ENST00000415664.2	-	2	122				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGATAAAACATTTTATTAAAT	0.289	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3215-82A>G	chr21.hg19:g.11026921T>C		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	2.064898	ACAxTTT	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	1	3.606316	KEEP	4	0	0	12	313	TT	0.993634	0.990815	0		-	14	60	523	0	0	43.768463	56	60	2030	90	ENST00000415664.2	0.2	0.997163
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11038882	11038882	__UNKNOWN__	RNA	SNP	C	C	T	rs12627085		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11038882C>T	ENST00000470054.1	-	0	1321							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GCATGTCATGCGAAGGCAAGT	0.438	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11038882C>T		NA	A8K925|Q08ER0	hg19		0.02	32.163105	ATGxGAA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	4	20.359576	KEEP	119	3	92	100	3411	CC	1	1	0		-	27	49	934	0	0	56.255591	699	60	24945	1129	ENST00000470054.1	0.03719	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11040214	11040214	__UNKNOWN__	RNA	SNP	G	G	C	rs626164	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11040214G>C	ENST00000470054.1	-	0	774							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgcagtagcagaaacatggct	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11040214G>C		NA	A8K925|Q08ER0	hg19		0.02	-0.122828	GCAxAAA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	0	2.402057	KEEP	0	0	0	8	272	GG	0.99257	0.194853	0		-	3	60	120	0	0	10.272366	11	60	423	26	ENST00000470054.1	0.214286	0.196312
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11043242	11043242	__UNKNOWN__	RNA	SNP	A	A	C	rs2740215		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11043242A>C	ENST00000470054.1	-	0	774							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gggtttcaccatgttggccag	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11043242A>C		NA	A8K925|Q08ER0	hg19		0.02	-0.24565	ACCxTGT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	0	2.406332	KEEP	0	0	0	8	230	AA	0.99257	0.636582	0		-	3	60	105	0	0	7.893914	23	60	853	43	ENST00000470054.1	0.115385	0.641347
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11049584	11049584	__UNKNOWN__	RNA	SNP	C	C	T	rs9808647		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11049584C>T	ENST00000470054.1	-	0	524							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGAGGTCTCCCGGGCTGTCGC	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						67	54	58	NA		NA	NA	21		NA											NA				11049584		692	1590	2282					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11049584C>T		NA	A8K925|Q08ER0	hg19		0.02	35.080134	TCCxGGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	6	20.646085	KEEP	137	8	255	158	5423	CC	1	1	0		-	36	59	1348	0	0	89.756188	692	60	24368	1234	ENST00000470054.1	0.049451	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11049592	11049592	__UNKNOWN__	RNA	SNP	C	C	T	rs3906134	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11049592C>T	ENST00000470054.1	-	0	516							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CCCGGGCTGTCGCACACTGCA	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						72	57	62	NA		NA	NA	21		NA											NA				11049592		692	1591	2283					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11049592C>T		NA	A8K925|Q08ER0	hg19		0.02	35.422358	TGTxGCA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	7	18.76828	KEEP	107	9	275	159	5389	CC	1	1	0		-	32	60	1195	0	0	77.669193	715	60	25812	1247	ENST00000470054.1	0.042838	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11058322	11058322	__UNKNOWN__	RNA	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11058322C>T	ENST00000470054.1	-	0	325							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAATGCACATCGCTGAAAGGG	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						92	70	77	NA		NA	NA	21		NA											NA				11058322		692	1591	2283					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11058322C>T		NA	A8K925|Q08ER0	hg19		0.02	34.419725	CATxGCT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	4	24.209479	KEEP	7	4	115	121	4071	CC	1	1	0		-	32	49	1215	0	0	79.335431	719	60	24738	1058	ENST00000470054.1	0.04261	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11058353	11058353	__UNKNOWN__	RNA	SNP	T	T	C	rs79433933		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11058353T>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GAAATCTCTTTATAAAACCTT	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						20	18	19	NA		NA	NA	21		NA											NA				11058353		692	1589	2281					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11058353T>C		NA	A8K925|Q08ER0	hg19		0.02	25.196937	CTTxATA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	1	5.552943	KEEP	17	4	139	67	1995	TT	1	1	0		-	23	49	840	0	0	53.743514	531	60	18953	671	ENST00000470054.1	0.041516	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11058377	11058377	__UNKNOWN__	RNA	SNP	C	C	T	rs74696585	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11058377C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAGGAATATTCAAATATAAGC	0.328	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11058377C>T		NA	A8K925|Q08ER0	hg19		0.02	13.825747	ATTxAAA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	3	7.752844	KEEP	20	1	20	33	1066	CC	0.999997	0.999997	0		-	16	49	561	0	0	35.284158	346	60	13029	421	ENST00000470054.1	0.044199	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11064808	11064808	__UNKNOWN__	RNA	SNP	G	G	T	rs4039860		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11064808G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aggatcacgaggtcatgagat	0.498	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11064808G>T		NA	A8K925|Q08ER0	hg19		0.02	-0.21933	CGAxGTC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	2	3.912552	KEEP	0	0	0	13	457	GG	0.994391	0.549786	0		-	3	60	111	0	0	8.860103	17	60	628	50	ENST00000470054.1	0.15	0.552887
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11064828	11064828	__UNKNOWN__	RNA	SNP	C	C	G	rs157522		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11064828C>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tcgagaccatcctggctaaca	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11064828C>G		NA	A8K925|Q08ER0	hg19		0.02	-0.210545	CATxCTG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	3	3.611441	KEEP	0	0	0	12	399	CC	0.993634	0.518837	0		-	3	60	110	0	0	9.17192	12	60	417	42	ENST00000470054.1	0.2	0.522161
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11077442	11077442	__UNKNOWN__	RNA	SNP	G	G	T	rs2979600		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11077442G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		caaaggtcaggctggggccac	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11077442G>T		NA	A8K925|Q08ER0	hg19		0.02	-0.279761	CAGxCTG	UNCOVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	1	2.407933	KEEP	2	0	0	8	289	GG	0	0	0		-	3	60	112	0	0	8.313112	29	60	1087	50	ENST00000470054.1	0.09375	0.739671
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11079932	11079932	__UNKNOWN__	RNA	SNP	G	G	A	rs283397		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11079932G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		acaaaaataagccaggcatgg	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11079932G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.184223	TAAxCCA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	4	2.708683	KEEP	1	0	0	9	318	GG	0.99257	0.420331	0		-	3	60	96	0	0	7.679092	13	60	478	35	ENST00000470054.1	0.1875	0.423478
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11080440	11080440	__UNKNOWN__	RNA	SNP	A	A	G	rs7281245		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11080440A>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aaaacaaacaaaaaTGGGCAA	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11080440A>G		NA	A8K925|Q08ER0	hg19		0.02	-0.271971	ACAxAAA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	3	3.30987	KEEP	0	0	0	11	343	AA	0.993072	0.712346	0		-	5	60	193	0	0	16.15805	21	60	770	51	ENST00000470054.1	0.192308	0.717315
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11080529	11080529	__UNKNOWN__	RNA	SNP	A	A	G	rs3954671	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11080529A>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gagctagaggatcacttgacc	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11080529A>G		NA	A8K925|Q08ER0	hg19		0.02	-0.219328	AGGxTCA	UNCOVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	1	2.407165	KEEP	1	0	0	8	247	AA	0	0	0		-	7	60	251	0	0	22.002086	18	60	662	39	ENST00000470054.1	0.28	0.552887
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11080699	11080699	__UNKNOWN__	RNA	SNP	G	G	A	rs11184036		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11080699G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGGAAGACAGggcagggcaca	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11080699G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.421099	CAGxGCA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	2	2.407478	KEEP	0	0	0	8	265	GG	0.99257	0.941356	0		-	6	60	208	0	0	15.990721	39	60	1393	61	ENST00000470054.1	0.133333	0.948402
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11080847	11080847	__UNKNOWN__	RNA	SNP	G	G	T	rs9637267		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11080847G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gctgggcatggtggctcacac	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11080847G>T		NA	A8K925|Q08ER0	hg19		0.02	1.765708	ATGxTGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	2	6.019627	KEEP	5	0	0	20	705	GG	0.999859	0.997023	0		-	4	39	138	0	0	9.21311	60	60	2207	113	ENST00000470054.1	0.0625	0.997163
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11080989	11080989	__UNKNOWN__	RNA	SNP	C	C	T	rs71220003|rs3954669	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11080989C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tggcagcatgcgcctgtagtc	0.512	NA	NA											c|||	1919	0.383187	0.3888	0.3847	5008	,	,	NA	67163	0.4226	NA	0.3618	False	NA	,,,	NA	NA	NA	2504	0.3558	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11080989C>T		NA	A8K925|Q08ER0	hg19		0.02	-0.254383	ATGxGCC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	0	2.407956	KEEP	0	0	0	8	291	CC	0.99257	0.663556	0		-	6	40	215	0	0	17.942756	23	60	810	42	ENST00000470054.1	0.206897	0.668523
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11089484	11089484	__UNKNOWN__	RNA	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11089484A>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gtgtcaccgcactccagcctg	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11089484A>T		NA	A8K925|Q08ER0	hg19		0.02	-0.192942	CGCxCTC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	2	3.608805	KEEP	0	0	0	12	337	AA	0.994391	0.455189	0		-	3	60	112	0	0	8.960972	17	60	577	43	ENST00000470054.1	0.15	0.457757
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11094656	11094656	__UNKNOWN__	RNA	SNP	G	G	A	rs4913583	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11094656G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTggccgagcgcagtggctca	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11094656G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.394727	AGCxCAG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	2	2.708778	KEEP	0	0	0	9	316	GG	0.99254	0.919727	0		-	5	60	179	0	0	13.470766	40	60	1405	68	ENST00000470054.1	0.111111	0.92664
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11097590	11097590	__UNKNOWN__	RNA	SNP	G	G	A	rs57543194		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11097590G>A	ENST00000470054.1	-	0	279							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tcaccacaggggactcctcct	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						65	84	77	NA		NA	NA	21		NA											NA				11097590		1439	2596	4035					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11097590G>A		NA	A8K925|Q08ER0	hg19		0.02	2.341551	AGGxGAC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	2	5.957284	KEEP	0	0	0	20	668	GG	0.999863	0.999485	0		-	5	53	189	0	0	13.136913	76	60	2761	129	ENST00000470054.1	0.061728	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11106405	11106405	__UNKNOWN__	IGR	SNP	G	G	A	rs4913776	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11106405G>A			NA	NA				BAGE2 (7480 upstream) : AP003900.6 (63382 downstream)						NA		NA									NA						cctgtaatccgagctacttag	0.522	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11106405G>A		NA		hg19		0.02	-0.201754	TCCxAGC	COVERED																																																																																			NOVEL					0			3	3.009581	KEEP	0	0	0	10	339	GG	0.993072	0.487146	0			5	60	181	0	0	15.480449	16	60	569	52		0.238095	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11112071	11112071	__UNKNOWN__	IGR	SNP	G	G	C	rs182435103		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11112071G>C			NA	NA				BAGE2 (13146 upstream) : AP003900.6 (57716 downstream)						NA		NA									NA						gcagagtcaggccacaaggcc	0.542	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11112071G>C		NA		hg19		0.02	2.43135	CAGxCCA	COVERED																																																																																			NOVEL					0			1	2.708329	KEEP	0	0	0	9	302	GG	0.99254	0.960208	0			14	60	498	0	0	43.602387	36	60	1296	71		0.28	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11112150	11112150	__UNKNOWN__	IGR	SNP	G	G	A	rs140426267		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11112150G>A			NA	NA				BAGE2 (13225 upstream) : AP003900.6 (57637 downstream)						NA		NA									NA						TAAATGCCACggctgggcgca	0.547	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11112150G>A		NA		hg19		0.02	2.390919	CACxGCT	COVERED																																																																																			NOVEL					0			5	10.232244	KEEP	0	0	0	34	1140	GG	0.999998	0.995685	0			4	60	153	0	0	10.82779	56	60	1946	131		0.066667	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114515	11114515	__UNKNOWN__	IGR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11114515A>G			NA	NA				BAGE2 (15590 upstream) : AP003900.6 (55272 downstream)						NA		NA									NA						AACAGACTCCATAACCTTCCA	0.353	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114515A>G		NA		hg19		0.02	27.441718	TCCxTAA	COVERED																																																																																			NOVEL					0			4	23.700991	KEEP	0	1	32	90	2806	AA	1	1	0			18	60	645	1	0	37.246223	643	60	24085	951		0.027231	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114613	11114613	__UNKNOWN__	IGR	SNP	C	C	T	rs545625602	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11114613C>T			NA	NA				BAGE2 (15688 upstream) : AP003900.6 (55174 downstream)						NA		NA									NA						CAGCAGCGGCCCAGGTGGAGT	0.502	NA	NA											c|||	89	0.0177716	0.0091	0.0101	5008	,	,	NA	111536	0.0129	NA	0.008	False	NA	,,,	NA	NA	NA	2504	0.0501	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114613C>T		NA		hg19		0.02	38.571396	GGCxCAG	COVERED																																																																																			NOVEL					0			4	40.5308	KEEP	0	3	92	167	5572	CC	1	1	0			29	60	998	0	0	59.873139	791	60	28513	1214		0.035366	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114909	11114909	__UNKNOWN__	IGR	SNP	G	G	C	rs9631382	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11114909G>C			NA	NA				BAGE2 (15984 upstream) : AP003900.6 (54878 downstream)						NA		NA									NA						CCCGGCTCCTGCTGGCTCCCA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114909G>C		NA		hg19		0.02	2.320571	CCTxCTG	COVERED																																																																																			NOVEL					0			3	3.009685	KEEP	0	0	0	10	353	GG	0.992708	0.991413	0			4	60	154	0	0	11.051459	52	60	1979	99		0.071429	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114910	11114910	__UNKNOWN__	IGR	SNP	C	C	A	rs10433193	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11114910C>A			NA	NA				BAGE2 (15985 upstream) : AP003900.6 (54877 downstream)						NA		NA									NA						CCGGCTCCTGCTGGCTCCCAC	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114910C>A		NA		hg19		0.02	2.220694	CTGxTGG	COVERED																																																																																			NOVEL					0			3	3.009566	KEEP	0	0	0	10	355	CC	0.992708	0.991413	0			21	60	757	0	0	69.629261	35	60	1351	100		0.375	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11119550	11119550	__UNKNOWN__	IGR	SNP	A	A	G	rs2740256		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11119550A>G			NA	NA				BAGE2 (20625 upstream) : AP003900.6 (50237 downstream)						NA		NA									NA						tctcaaacaaacaaacaaaTT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11119550A>G		NA		hg19		0.02	-0.342147	CAAxCAA	COVERED																																																																																			NOVEL					0			2	3.609091	KEEP	0	0	0	12	346	AA	0.993634	0.860234	0			8	60	296	0	0	24.823031	31	60	1103	59		0.205128	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11123781	11123781	__UNKNOWN__	IGR	SNP	T	T	C	rs9325305	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11123781T>C			NA	NA				BAGE2 (24856 upstream) : AP003900.6 (46006 downstream)						NA		NA									NA						gccGAGACTTTTTAATACATG	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11123781T>C		NA		hg19		0.02	-0.394788	CTTxTTA	COVERED																																																																																			NOVEL					0			2	4.814795	KEEP	0	0	0	16	511	TT	0.997832	0.924631	0			4	60	144	0	0	10.805391	33	60	1203	72		0.108108	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11124307	11124307	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11124307C>A			NA	NA				BAGE2 (25382 upstream) : AP003900.6 (45480 downstream)						NA		NA									NA						ttttccccttccccttcccct	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11124307C>A		NA		hg19		0.02	2.032096	CTTxCCC	COVERED																																																																																			NOVEL					0			16	7.170618	KEEP	1	2	54	43	1463	CC	1	0.967425	0			4	60	123	2	0	8.531247	37	60	1341	120		0.097561	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11138260	11138260	__UNKNOWN__	IGR	SNP	G	G	A	rs28468585	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11138260G>A			NA	NA				BAGE2 (39335 upstream) : AP003900.6 (31527 downstream)						NA		NA									NA						atgagccaccgtgtccggcca	0.512	NA	NA											g|||	2524	0.503994	0.5061	0.5029	5008	,	,	NA	60155	0.499	NA	0.507	False	NA	,,,	NA	NA	NA	2504	0.5041	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11138260G>A		NA		hg19		0.02	-0.394762	ACCxTGT	COVERED																																																																																			NOVEL					0			5	2.843861	KEEP	1	1	30	20	712	GG	0.999863	0.926513	0			5	60	176	0	0	13.753278	30	60	1090	89		0.142857	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11138265	11138265	__UNKNOWN__	IGR	SNP	C	C	T	rs28643537	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11138265C>T			NA	NA				BAGE2 (39340 upstream) : AP003900.6 (31522 downstream)						NA		NA									NA						ccaccgtgtccggccaggaag	0.493	NA	NA											c|||	2524	0.503994	0.5061	0.5029	5008	,	,	NA	55839	0.499	NA	0.507	False	NA	,,,	NA	NA	NA	2504	0.5041	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11138265C>T		NA		hg19		0.02	-0.403558	GTCxGGC	COVERED																																																																																			NOVEL					0			6	2.341874	KEEP	1	1	32	19	640	CC	0.999863	0.934364	0			5	60	182	0	0	14.160649	33	60	1179	93		0.131579	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11164162	11164162	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11164162C>G			NA	NA				BAGE2 (65237 upstream) : AP003900.6 (5625 downstream)						NA		NA									NA						gaactcccaacctcaggtgat	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11164162C>G		NA		hg19		0.02	-0.298287	CAAxCTC	COVERED																																																																																			NOVEL					0			4	5.718659	KEEP	0	0	0	19	679	CC	0.99986	0.78095	0			3	49	123	0	0	9.365802	30	60	1104	69		0.090909	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11168657	11168657	__UNKNOWN__	IGR	SNP	C	C	T	rs201613109		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11168657C>T			NA	NA				BAGE2 (69732 upstream) : AP003900.6 (1130 downstream)						NA		NA									NA						AGCCTCGCAGCCAGCATCCCC	0.736	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11168657C>T		NA		hg19		0.02	-0.201773	CAGxCAG	COVERED																																																																																			NOVEL					0			0	3.310164	KEEP	0	0	0	11	372	CC	0.993072	0.487146	0			3	60	110	0	0	8.691557	18	60	674	45		0.142857	0.490544
AP003900.6	0	__UNKNOWN__	__UNKNOWN__	21	11181017	11181017	__UNKNOWN__	lincRNA	SNP	A	A	G	rs10433250	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11181017A>G	ENST00000603265.1	+	0	231										NA		NA									NA						GCTGTGGAGCATGGTCTCGAA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603265.1:	chr21.hg19:g.11181017A>G		NA		hg19		0.02	4.343864	AGCxTGG	COVERED																																																																																			NOVEL	AP003900.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469752.1	2	5.115658	KEEP	0	0	0	17	538	AA	0.999366	0.999366	0		+	5	60	185	0	0	12.055412	105	60	3906	186	ENST00000603265.1	0.045455	1
AP003900.6	0	__UNKNOWN__	__UNKNOWN__	21	11181379	11181379	__UNKNOWN__	lincRNA	SNP	C	C	G	rs1811012		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11181379C>G	ENST00000603265.1	+	0	231										NA		NA									NA						TATGGCCGTTCTGGAGACTTG	0.532	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603265.1:	chr21.hg19:g.11181379C>G		NA		hg19		0.02	7.17781	GTTxTGG	COVERED																																																																																			NOVEL	AP003900.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469752.1	1	5.11687	KEEP	0	0	0	17	615	CC	0.999366	0.999366	0		+	8	60	302	0	0	19.679457	179	60	6857	269	ENST00000603265.1	0.042781	1
AP003900.6	0	__UNKNOWN__	__UNKNOWN__	21	11181475	11181475	__UNKNOWN__	lincRNA	SNP	T	T	G	rs146511569		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11181475T>G	ENST00000603265.1	+	0	231										NA		NA									NA						TGTCATGGCCTGCAGCGTACC	0.502	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603265.1:	chr21.hg19:g.11181475T>G		NA		hg19		0.02	5.218269	GCCxGCA	COVERED																																																																																			NOVEL	AP003900.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469752.1	1	2.708102	KEEP	0	0	0	9	278	TT	0.99254	0.992532	0		+	13	60	443	0	0	33.318797	94	60	3461	128	ENST00000603265.1	0.121495	0.999992
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11186615	11186615	__UNKNOWN__	IGR	SNP	T	T	C	rs2004948		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:11186615T>C			NA	NA				AP003900.6 (2569 upstream) : None (None downstream)						NA		NA									NA						ttaaaaaatatggatcttggc	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11186615T>C		NA		hg19		0.02	-0.228108	ATAxGGA	COVERED																																																																																			NOVEL					0			5	5.113005	KEEP	9	0	0	17	497	TT	0.993072	0.578892	0			3	60	108	0	0	10.155169	4	60	150	59		0.428571	0.58293
POTED	317754	__UNKNOWN__	__UNKNOWN__	21	14982904	14982904	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs374506316		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:14982904G>A	ENST00000299443.5	+	1	407	c.355G>A	c.(355-357)Gct>Act	p.A119T		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	119		NA				plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						CAACGTGGGCGCTTGGGGAGA	0.577	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351	317754		POTE ankyrin domain containing, Ankyrin repeat domain containing	23822	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 1	607549	ankyrin repeat domain 21, ANKRD26-like family B, member 3	ANKRD21, A26B3	NA	12475935, 15276201, 16364570	Standard	NM_174981	NM_174981	NA	Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.355G>A	chr21.hg19:g.14982904G>A	ENSP00000299443:p.Ala119Thr	NA	C9JCF7	hg19	CCDS13562.1	0.02	1.784253	GGCxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.447	-0.895470	0.02491	.	.	ENSG00000166351	ENST00000299443	T	0.27557	1.66	0.582	-1.16	0.09678	.	.	.	.	.	T	0.16342	0.0393	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	8	0.15499	T	0.54	.	.	.	.	.	119	Q86YR6	POTED_HUMAN	T	119	ENSP00000299443:A119T	ENSP00000299443:A119T	A	+	1	0	POTED	13904775	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-4.599000	0.00210	-2.251000	0.00700	-2.739000	0.00128	GCT	NOVEL	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157660.1	2	6.320468	KEEP	2	0	0	21	734	GG	0.999863	0.996096	0		+	5	24	163	0	0	10.970507	62	60	2262	112	ENST00000299443.5	0.074627	0.996233
POTED	317754	__UNKNOWN__	__UNKNOWN__	21	14982922	14982922	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs190840287		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:14982922C>G	ENST00000299443.5	+	1	425	c.373C>G	c.(373-375)Cac>Gac	p.H125D		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	125		NA				plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						AGACTACGACCACAGCGCCTT	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						36	55	51	NA		NA	NA	21		NA											NA				14982922		841	3164	4005	SO:0001583	missense			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351	317754		POTE ankyrin domain containing, Ankyrin repeat domain containing	23822	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 1	607549	ankyrin repeat domain 21, ANKRD26-like family B, member 3	ANKRD21, A26B3	NA	12475935, 15276201, 16364570	Standard	NM_174981	NM_174981	NA	Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.373C>G	chr21.hg19:g.14982922C>G	ENSP00000299443:p.His125Asp	NA	C9JCF7	hg19	CCDS13562.1	0.02	2.240331	GACxACA	COVERED	336	0.15384615384615385	69	0.1402439024390244	23	0.06353591160220995	126	0.2202797202797203	118	0.15567282321899736	c	0.001	-3.806688	0.00004	.	.	ENSG00000166351	ENST00000299443	T	0.24723	1.84	0.802	-1.6	0.08426	.	.	.	.	.	T	0.00012	0.0000	N	0.00230	-1.795	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08576	-1.0715	9	0.02654	T	1	.	1.5905	0.02653	0.1864:0.4449:0.1933:0.1755	.	125	Q86YR6	POTED_HUMAN	D	125	ENSP00000299443:H125D	ENSP00000299443:H125D	H	+	1	0	POTED	13904793	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.678000	0.00839	-4.527000	0.00044	-3.939000	0.00015	CAC	NOVEL	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157660.1	2	4.514426	KEEP	0	0	0	15	519	CC	0.99649	0.960391	0		+	4	24	149	0	0	10.720382	47	60	1758	74	ENST00000299443.5	0.078431	0.963774
POTED	317754	__UNKNOWN__	__UNKNOWN__	21	14982952	14982952	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs117112505	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:14982952A>G	ENST00000299443.5	+	1	455	c.403A>G	c.(403-405)Atc>Gtc	p.I135V		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	135		NA	I -> V (in dbSNP:rs6517870). {ECO:0000269|PubMed:12475935}.			plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						GAGGTACCACATCCGTCGAGA	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						42	58	55	NA		NA	NA	21		NA											NA				14982952		790	3147	3937	SO:0001583	missense			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351	317754		POTE ankyrin domain containing, Ankyrin repeat domain containing	23822	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 1	607549	ankyrin repeat domain 21, ANKRD26-like family B, member 3	ANKRD21, A26B3	NA	12475935, 15276201, 16364570	Standard	NM_174981	NM_174981	NA	Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.403A>G	chr21.hg19:g.14982952A>G	ENSP00000299443:p.Ile135Val	NA	C9JCF7	hg19	CCDS13562.1	0.02	-0.368472	CACxTCC	COVERED	164	0.07509157509157509	39	0.07926829268292683	12	0.03314917127071823	44	0.07692307692307693	69	0.09102902374670185	G	0.003	-2.565705	0.00134	.	.	ENSG00000166351	ENST00000299443	T	0.51817	0.69	1.29	-2.58	0.06228	.	.	.	.	.	T	0.00384	0.0012	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14699	-1.0463	8	0.02654	T	1	.	5.6284	0.17495	0.5692:0.0:0.4308:0.0	rs6517870;rs6517870	135	Q86YR6	POTED_HUMAN	V	135	ENSP00000299443:I135V	ENSP00000299443:I135V	I	+	1	0	POTED	13904823	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.921000	0.00693	-1.089000	0.03073	-2.766000	0.00121	ATC	NOVEL	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157660.1	2	2.406886	KEEP	1	0	0	8	238	AA	0.99257	0.892632	0		+	14	40	524	0	0	47.4696	28	60	1020	54	ENST00000299443.5	0.333333	0.899314
SIK1	150094	__UNKNOWN__	__UNKNOWN__	21	44836479	44836479	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:44836479A>G	ENST00000270162.6	-	0	2627					NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	NA		NA			cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	AAAATAAAACAAAAATAAACT	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178	150094			11142	protein-coding gene	gene with protein product	myocardial SNF1-like kinase	605705	SNF1-like kinase	SNF1LK	NA	7893599	Standard	NM_173354	NM_173354	NA	Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.*143T>C	chr21.hg19:g.44836479A>G		NA	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	hg19	CCDS33575.1	0.02	3.593214	AACxAAA	COVERED																																																																																			NOVEL	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195654.1	0	7.21878	KEEP	0	0	0	24	700	AA	0.999909	0.999909	0		-	8	60	264	0	0	17.040439	127	60	4640	167	ENST00000270162.6	0.059259	1
TSPEAR	54084	__UNKNOWN__	__UNKNOWN__	21	45941767	45941767	__UNKNOWN__	Splice_Site	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:45941767G>A	ENST00000397916.1	-	9	1519	c.1361C>T	c.(1360-1362)cCg>cTg	p.P454L	TSPEAR_ENST00000323084.4_Splice_Site_p.P522L|C21orf90_ENST00000465978.1_Intron			Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	522		NA			sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						GGGCCTTACCGGGAAGGACTG	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						64	62	63	NA		NA	NA	21		NA											NA				45941767		2203	4300	6503	SO:0001630	splice_region_variant			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894	54084			1268	protein-coding gene	gene with protein product		612920	chromosome 21 open reading frame 29, deafness, autosomal recessive 98	C21orf29, DFNB98	NA	12095917, 22678063	Standard	NM_144991	NM_144991	NA	Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000397916.1:c.1362+1C>T	chr21.hg19:g.45941767G>A		NA		hg19		0.02	4.838183	ACCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	11.73	1.725288	0.30593	.	.	ENSG00000175894	ENST00000323084;ENST00000397918;ENST00000397916;ENST00000341581	D;D	0.84298	-1.83;-1.83	5.18	-0.207	0.13189	.	0.557049	0.17810	N	0.161223	T	0.60274	0.2256	N	0.03238	-0.38	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.29243	-1.0018	10	0.21540	T	0.41	-22.0281	3.6438	0.08177	0.5725:0.0:0.1628:0.2647	.	522	Q8WU66	TSEAR_HUMAN	L	522;375;454;523	ENSP00000321987:P522L;ENSP00000381012:P454L	ENSP00000321987:P522L	P	-	2	0	TSPEAR	44766195	0.970000	0.33590	0.996000	0.52242	0.959000	0.62525	0.342000	0.19926	-0.202000	0.10268	0.563000	0.77884	CCG	NOVEL	TSPEAR-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000195865.1	0	10.530493	KEEP	0	0	0	35	1121	GG	0.999999	0.999998	0	Missense_Mutation	-	43	60	1569	0	0	139.768431	98	60	3153	196	ENST00000397916.1	0.304965	1
COL18A1	80781	__UNKNOWN__	__UNKNOWN__	21	46916032	46916032	__UNKNOWN__	Intron	SNP	A	A	T	rs62214270		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr21:46916032A>T	ENST00000359759.4	+	29	3774				COL18A1_ENST00000459895.1_Intron|COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	NA		NA			angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		atgccctccaagccctccatg	0.607	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871	80781		Collagens	2195	protein-coding gene	gene with protein product	endostatin	120328	Knobloch syndrome, type 1	KNO	NA	8188291, 8776601, 10942434, 17546652	Standard		NM_130445	NA	Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.3754-382A>T	chr21.hg19:g.46916032A>T		NA	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	hg19		0.02	6.403064	CCAxGCC	COVERED																																																																																			NOVEL	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000206827.1	1	5.917989	KEEP	0	3	92	52	1625	AA	1	1	0		+	8	60	240	0	0	14.262802	160	60	5954	282	ENST00000359759.4	0.047619	1
AP000525.9	0	__UNKNOWN__	__UNKNOWN__	22	16157982	16157982	__UNKNOWN__	RNA	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16157982G>T	ENST00000447898.1	-	0	293										NA		NA									NA						CCAAGCGGACGCGGCCAGAGG	0.677	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000447898.1:	chr22.hg19:g.16157982G>T		NA		hg19		0.02	-0.061414	GACxCGG	UNCOVERED																																																																																			NOVEL	AP000525.9-002	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000276780.1	0	3.611724	KEEP	9	0	0	12	423	GG	0.99257	0.043461	0		-	2	27	78	0	0	7.095665	4	27	149	27	ENST00000447898.1	0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16350245	16350245	__UNKNOWN__	IGR	SNP	C	C	A	rs2905295		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16350245C>A			NA	NA				POTEH (62308 upstream) : LA16c-2F2.8 (22835 downstream)						NA		NA									NA						GTTGCTTAGGCACAGCAGCAC	0.517	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16350245C>A		NA		hg19		0.02	2.147142	AGGxACA	COVERED																																																																																			NOVEL					0			0	3.912947	KEEP	0	0	0	13	477	CC	0.994391	0.9923	0			9	60	328	0	0	25.553323	59	60	2237	109		0.132353	0.997898
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16350293	16350293	__UNKNOWN__	IGR	SNP	C	C	T	rs61578976		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16350293C>T			NA	NA				POTEH (62356 upstream) : LA16c-2F2.8 (22787 downstream)						NA		NA									NA						GCGCACTGAGCATCCCACTGC	0.512	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16350293C>T		NA		hg19		0.02	1.781102	GAGxATC	COVERED																																																																																			NOVEL					0			0	3.61183	KEEP	0	0	0	12	433	CC	0.993634	0.993529	0			9	60	329	0	0	24.825342	74	60	2783	135		0.108434	0.999895
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16350338	16350338	__UNKNOWN__	IGR	SNP	C	C	T	rs58463599		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16350338C>T			NA	NA				POTEH (62401 upstream) : LA16c-2F2.8 (22742 downstream)						NA		NA									NA						GCAACAAAAACACCTCTCCCA	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16350338C>T		NA		hg19		0.02	2.212035	AAAxACC	COVERED																																																																																			NOVEL					0			0	3.009195	KEEP	0	0	0	10	332	CC	0.992708	0.991583	0			6	60	178	0	0	11.859746	62	60	2314	111		0.088235	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16366157	16366157	__UNKNOWN__	IGR	SNP	T	T	A	rs201337825		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16366157T>A			NA	NA				POTEH (78220 upstream) : LA16c-2F2.8 (6923 downstream)						NA		NA									NA						CCTGTCAGATTTTGAGAAAAA	0.478	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16366157T>A		NA		hg19		0.02	6.850577	GATxTTG	UNCOVERED																																																																																			NOVEL					0			1	3.911107	KEEP	44	0	0	13	402	TT	0	0	0			28	40	986	0	0	79.742033	132	50	4787	250		0.175	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16404760	16404760	__UNKNOWN__	IGR	SNP	G	G	A	rs199767078		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16404760G>A			NA	NA				LA16c-2F2.8 (27705 upstream) : LA16c-23H5.4 (12508 downstream)						NA		NA									NA						GGAAAAGTTAGCTTTATACGT	0.483	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16404760G>A		NA		hg19		0.02	1.836999	TTAxCTT	COVERED																																																																																			NOVEL					0			2	6.256013	KEEP	19	1	32	32	1176	GG	0.999957	0.999896	0			8	27	284	0	0	20.224753	89	50	3263	176		0.082474	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16888068	16888068	__UNKNOWN__	IGR	SNP	C	C	A	rs202154730		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16888068C>A			NA	NA				AP000539.2 (311877 upstream) : KB-67B5.17 (113880 downstream)						NA		NA									NA						TGGAAAAAATCCACCTCACCA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16888068C>A		NA		hg19		0.02	3.587635	AATxCAC	COVERED																																																																																			NOVEL					0			2	3.6118	KEEP	10	0	0	12	421	CC	0.993072	0.993072	0			7	40	249	0	0	17.229244	93	60	3359	169		0.07	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16914822	16914822	__UNKNOWN__	IGR	SNP	C	C	G	rs10212045		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:16914822C>G			NA	NA				AP000539.2 (338631 upstream) : KB-67B5.17 (87126 downstream)						NA		NA									NA						AAGTGCTGATCGTATCAAATA	0.383	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16914822C>G		NA		hg19		0.02	5.171411	GATxGTA	COVERED																																																																																			NOVEL					0			2	4.514136	KEEP	5	0	0	15	487	CC	0.99649	0.996468	0			15	47	565	0	0	45.89541	77	60	2802	143		0.163043	0.999978
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	17054332	17054332	__UNKNOWN__	IGR	SNP	T	T	C	rs143558414	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:17054332T>C			NA	NA				KB-67B5.17 (46205 upstream) : KCNMB3P1 (7634 downstream)						NA		NA									NA						ATATGAACAATATTTGGATAA	0.308	NA	NA											t|||	689	0.13758	0.0356	0.0865	5008	,	,	NA	13050	0.2024	NA	0.1372	False	NA	,,,	NA	NA	NA	2504	0.2454	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.17054332T>C		NA		hg19		0.02	11.329663	CAAxATT	COVERED																																																																																			NOVEL					0			62	9.023581	KEEP	102	0	0	30	891	TT	0.999869	0.999869	0			11	60	410	0	0	26.24351	262	60	9227	500		0.040293	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	17055569	17055569	__UNKNOWN__	IGR	SNP	T	T	G	rs3729688	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:17055569T>G			NA	NA				KB-67B5.17 (47442 upstream) : KCNMB3P1 (6397 downstream)						NA		NA									NA						TTCACTGCAGTGGGGCAGAGT	0.418	NA	NA											t|||	2141	0.427516	0.295	0.536	5008	,	,	NA	18928	0.4365	NA	0.5	False	NA	,,,	NA	NA	NA	2504	0.4458	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.17055569T>G		NA		hg19		0.02	4.28317	CAGxGGG	COVERED																																																																																			NOVEL					0			25	3.008625	KEEP	2	0	0	10	304	TT	0.992708	0.992708	0			17	60	570	0	0	42.928799	118	60	4132	160		0.125926	1
GGT3P	2679	__UNKNOWN__	__UNKNOWN__	22	18769650	18769650	__UNKNOWN__	RNA	SNP	A	A	G	rs62229901		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:18769650A>G	ENST00000412448.1	-	0	1027							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene	NA		NA			glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)				NA						CCACAGACATACCACAAGACA	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA							22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421	2679		Gamma-glutamyltransferases	4252	pseudogene	pseudogene		NA	gamma-glutamyltransferase 3	GGT3	NA	8104871, 18357469	Standard	NR_003267	NR_003267	NA	Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161	ENST00000412448.1:	chr22.hg19:g.18769650A>G		NA		hg19		0.02	-0.05264	CATxCCA	UNCOVERED																																																																																			NOVEL	GGT3P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000341281.1	0	3.00587	KEEP	7	0	0	10	286	AA	0	0	0		-	3	49	111	0	0	10.725109	3	49	109	23	ENST00000412448.1	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	18883922	18883922	__UNKNOWN__	IGR	SNP	G	G	C	rs5747920	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:18883922G>C			NA	NA				AC008132.13 (35360 upstream) : DGCR6 (9618 downstream)						NA		NA									NA						gggattacaggcctgagccaa	0.388	NA	NA											G|||	1950	0.389377	0.2133	0.428	5008	,	,	NA	27809	0.4782	NA	0.4493	False	NA	,,,	NA	NA	NA	2504	0.4468	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.18883922G>C		NA		hg19		0.02	-0.219324	CAGxCCT	COVERED																																																																																			NOVEL					0			3	3.611809	KEEP	12	0	0	12	426	GG	0.99257	0.54878	0			3	60	118	0	0	12.254514	1	40	34	51		0.75	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	20296729	20296729	__UNKNOWN__	IGR	SNP	T	T	C	rs58499303		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:20296729T>C			NA	NA				RTN4R (37459 upstream) : DGCR6L (5069 downstream)						NA		NA									NA						TGGGTCTGCCTTCGGCCTCCT	0.587	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.20296729T>C		NA		hg19		0.02	-0.210562	GCCxTCG	COVERED																																																																																			NOVEL					0			1	2.407216	KEEP	0	0	0	8	246	TT	0.99257	0.518282	0			3	27	114	0	0	8.904693	21	60	802	36		0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	20475067	20475067	__UNKNOWN__	IGR	SNP	C	C	T	rs10854564	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:20475067C>T			NA	NA				RIMBP3 (13281 upstream) : AC011718.2 (156955 downstream)						NA		NA									NA						GGCGCCACAGCGCATGGAGCA	0.637	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.20475067C>T		NA		hg19		0.02	-0.061413	CAGxGCA	UNCOVERED																																																																																			NOVEL					0			0	3.009459	KEEP	2	0	0	10	340	CC	0.992708	0.043467	0			2	40	74	0	0	6.892786	3	50	112	22		0.4	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	20502771	20502771	__UNKNOWN__	IGR	SNP	T	T	G	rs1659630	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:20502771T>G			NA	NA				RIMBP3 (40985 upstream) : AC011718.2 (129251 downstream)						NA		NA									NA						ACATTTTTGGTTCTCATGCTG	0.498	NA	NA											.|||	3325	0.663938	0.7224	0.7017	5008	,	,	NA	10362	0.6171	NA	0.7177	False	NA	,,,	NA	NA	NA	2504	0.5511	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.20502771T>G		NA		hg19		0.02	-0.228098	TGGxTCT	COVERED																																																																																			NOVEL					0			0	3.610915	KEEP	3	0	0	12	378	TT	0.993634	0.579219	0			11	40	383	0	0	35.855128	15	60	544	47		0.423077	0.58293
USP41	373856	__UNKNOWN__	__UNKNOWN__	22	20721058	20721058	__UNKNOWN__	Intron	SNP	C	C	T	rs71312755		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:20721058C>T	ENST00000486536.2	-	5	484				USP41_ENST00000454608.2_Intron			Q3LFD5	UBP41_HUMAN	ubiquitin specific peptidase 41	NA		NA			ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			endometrium(1)|kidney(1)|lung(2)|skin(1)	5						AGATGAAGTCCACTTGGAATG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ586979		22q11.22	2011-01-31	2005-08-08		ENSG00000161133	ENSG00000161133	373856		Ubiquitin-specific peptidases	20070	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 41		NA	12838346	Standard	XM_036729	XM_006710116	NA	Approved		uc011ahq.1	Q3LFD5	OTTHUMG00000151317	ENST00000486536.2:c.705-34G>A	chr22.hg19:g.20721058C>T		NA	A8MXD0|Q70BM7	hg19		0.02	6.836989	GTCxACT	COVERED																																																																																			NOVEL	USP41-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000319621.3	1	6.01934	KEEP	3	0	0	20	695	CC	0.999863	0.999863	0		-	24	45	817	0	0	62.847079	150	60	5491	216	ENST00000486536.2	0.137931	1
HIC2	23119	__UNKNOWN__	__UNKNOWN__	22	21803659	21803659	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:21803659G>A	ENST00000443632.2	+	0	4847				HIC2_ENST00000407464.2_3'UTR|HIC2_ENST00000407598.2_3'UTR			Q96JB3	HIC2_HUMAN	hypermethylated in cancer 2	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Melanoma(16;0.000465)|Ovarian(15;0.00438)|Colorectal(54;0.0968)	Lung SC(17;0.0262)|all_lung(157;0.205)				CAGAGAAACAGGAATCAGAAA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	NSCLC(23;437 858 2282 27947 40366)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB028943	CCDS13789.1	22q11.21	2013-01-09			ENSG00000169635	ENSG00000169635	23119		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	18595	protein-coding gene	gene with protein product		607712			NA	11554746	Standard		NM_015094	NA	Approved	KIAA1020, HRG22, ZBTB30, ZNF907	uc002zur.4	Q96JB3	OTTHUMG00000150781	ENST00000443632.2:c.*2627G>A	chr22.hg19:g.21803659G>A		NA	Q504T6|Q96KR3|Q9NSM9|Q9UPX9	hg19	CCDS13789.1	0.02	2.047327	ACAxGAA	COVERED																																																																																			NOVEL	HIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320061.2	2	4.81557	KEEP	0	0	0	16	570	GG	0.997832	0.995734	0		+	4	60	151	0	0	10.276409	69	60	2539	106	ENST00000443632.2	0.054795	0.997898
IGLV8-61	28774	__UNKNOWN__	__UNKNOWN__	22	22453499	22453499	__UNKNOWN__	RNA	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:22453499C>A	ENST00000390283.2	+	0	291									immunoglobulin lambda variable 8-61	NA		NA									NA						ACTCGCTCTTCTGGGGTCCCT	0.562	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						137	141	140	NA		NA	NA	22		NA											NA				22453499		1993	4168	6161					Z73650		22q11.2	2012-02-08			ENSG00000211638	ENSG00000211638	28774		Immunoglobulins / IGL locus	5931	other	immunoglobulin gene		NA			NA		Standard	NG_000002	NG_000002	NA	Approved				OTTHUMG00000150844	ENST00000390283.2:	chr22.hg19:g.22453499C>A		NA		hg19		0.02	16.631829	CTTxTGG	COVERED																																																																																			NOVEL	IGLV8-61-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000320321.1	3	25.882074	KEEP	0	0	0	86	3057	CC	1	1	0		+	152	60	5453	0	0	508.102396	222	60	8506	575	ENST00000390283.2	0.406417	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	22994603	22994603	__UNKNOWN__	IGR	SNP	C	C	A	rs78395647		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:22994603C>A			NA	NA				GGTLC2 (4392 upstream) : D86994.2 (12294 downstream)						NA		NA									NA						catctgcccacccatctgtcc	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.22994603C>A		NA		hg19		0.02	2.440019	CCAxCCA	COVERED																																																																																			NOVEL					0			0	4.815704	KEEP	1	0	0	16	572	CC	0.997832	0.961684	0			8	34	292	0	0	23.395787	43	60	1632	98		0.156863	0.963774
GGT1	2678	__UNKNOWN__	__UNKNOWN__	22	25023903	25023903	__UNKNOWN__	Silent	SNP	C	C	T	rs1041998		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:25023903C>T	ENST00000400382.1	+	13	2048	c.1293C>T	c.(1291-1293)aaC>aaT	p.N431N	GGT1_ENST00000401885.1_Silent_p.N87N|GGT1_ENST00000404920.1_Silent_p.N87N|GGT1_ENST00000400380.1_Silent_p.N431N|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Silent_p.N431N|GGT1_ENST00000248923.4_Silent_p.N431N|GGT1_ENST00000406383.2_Silent_p.N431N|GGT1_ENST00000404532.1_Silent_p.N87N|GGT1_ENST00000404223.1_Silent_p.N87N|GGT1_ENST00000403838.1_Silent_p.N87N			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	431		NA			arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GCATCACCAACGAGTTTGGGG	0.627	NA	NA											c|||	1	0.000199681	0	0.0014	5008	,	,	NA	10503	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA	C	,,,	1,4405		0,1,2202	72	79	77	NA	1293,1293,1293,1293	0.1	0	22	dbSNP_86	77	12,8588		0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGT1	NM_001032364.2,NM_001032365.2,NM_005265.2,NM_013430.2	,,,	0,13,6490	TT,TC,CC	NA	0.1395,0.0227,0.1	,,,	431/570,431/570,431/570,431/570	25023903	13,12993	2203	4300	6503	SO:0001819	synonymous_variant			M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2678	2.3.2.2	CD molecules, Gamma-glutamyltransferases	4250	protein-coding gene	gene with protein product		612346		GGT	NA	8104871, 18357469	Standard	NM_013430	NM_001288833	NA	Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1293C>T	chr22.hg19:g.25023903C>T		NA	Q08247|Q14404|Q8TBS1|Q9UMK1	hg19	CCDS42992.1	0.02	2.21767	CAAxGAG	COVERED																																																																																			NOVEL	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250797.1	0	5.895056	KEEP	2	2	43	35	1152	CC	0.999999	0.993702	0		+	7	52	262	0	0	19.898294	58	60	1938	134	ENST00000400382.1	0.107692	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	25716115	25716115	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:25716115C>G			NA	NA				RP3-462D8.2 (37857 upstream) : LRP5L (31272 downstream)						NA		NA									NA						GGAGGCGTCTCTCTCTGCATC	0.567	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.25716115C>G		NA		hg19		0.02	4.911254	TCTxTCT	COVERED																																																																																			NOVEL					0			0	10.231973	KEEP	0	0	0	34	1165	CC	0.999998	0.999998	0			107	60	4061	0	0	422.708175	35	60	1302	210		0.753521	1
MYO18B	84700	__UNKNOWN__	__UNKNOWN__	22	26193824	26193824	__UNKNOWN__	Intron	SNP	C	C	T	rs2877299	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:26193824C>T	ENST00000407587.2	+	12	2545				MYO18B_ENST00000536101.1_Intron|MYO18B_ENST00000335473.7_Intron			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						AAATGACCCCCGCATTCCTTC	0.468	NA	NA											C|||	2775	0.554113	0.261	0.6268	5008	,	,	NA	19779	0.6617	NA	0.6978	False	NA	,,,	NA	NA	NA	2504	0.6401	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454	84700		Myosins / Myosin superfamily : Class XVIII	18150	protein-coding gene	gene with protein product		607295			NA	12209013, 12547197	Standard	NM_032608	NM_032608	NA	Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.2377-96C>T	chr22.hg19:g.26193824C>T		NA	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	hg19		0.02	-0.38587	CCCxGCA	COVERED																																																																																			NOVEL	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000400691.1	1	2.407304	KEEP	0	0	0	8	260	CC	0.99257	0.911349	0		+	36	60	1349	0	0	142.99448	8	60	285	58	ENST00000407587.2	0.818182	0.918171
RFPL1	5988	__UNKNOWN__	__UNKNOWN__	22	29837847	29837847	__UNKNOWN__	Silent	SNP	G	G	C	rs61734564	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:29837847G>C	ENST00000354373.2	+	2	899	c.690G>C	c.(688-690)acG>acC	p.T230T	RFPL1S_ENST00000461286.3_RNA	NM_021026.2	NP_066306.2	O75677	RFPL1_HUMAN	ret finger protein-like 1	230	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA					zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(1)|lung(6)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	16						CTGCCAGCACGGTGCCGCTGA	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						120	106	111	NA		NA	NA	22		NA											NA				29837847		2203	4300	6503	SO:0001819	synonymous_variant			AJ010228	CCDS13857.2	22q12	2006-04-25			ENSG00000128250	ENSG00000128250	5988		RING-type (C3HC4) zinc fingers	9977	protein-coding gene	gene with protein product		605968			NA	10508838	Standard	NM_021026	NM_021026	NA	Approved	RNF78	uc003afn.3	O75677	OTTHUMG00000150516	ENST00000354373.2:c.690G>C	chr22.hg19:g.29837847G>C		NA	Q6IC06|Q9UJ97	hg19	CCDS13857.2	0.02	18.749615	CACxGTG	COVERED																																																																																			NOVEL	RFPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318719.1	7	14.419125	KEEP	2	5	175	109	3719	GG	1	1	0		+	20	60	662	0	0	40.151331	462	60	16714	742	ENST00000354373.2	0.041494	1
RNF185	91445	__UNKNOWN__	__UNKNOWN__	22	31602587	31602587	__UNKNOWN__	3'UTR	SNP	G	G	A	rs200090813		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:31602587G>A	ENST00000326132.6	+	0	2753				RNF185_ENST00000266252.7_3'UTR	NM_152267.3	NP_689480.2	Q96GF1	RN185_HUMAN	ring finger protein 185	NA		NA			autophagy (GO:0006914)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(3)|skin(1)	6						AATGGAGTGAGCCCAGGAGAG	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13890.1, CCDS46689.1	22q12.2	2013-01-09			ENSG00000138942	ENSG00000138942	91445		RING-type (C3HC4) zinc fingers	26783	protein-coding gene	gene with protein product	hypothetical protein FLJ38628	NA			NA	12477932	Standard	NM_152267	NM_152267	NA	Approved	FLJ38628	uc003akb.3	Q96GF1	OTTHUMG00000151253	ENST00000326132.6:c.*2015G>A	chr22.hg19:g.31602587G>A		NA	A8K5C1|A9X3T8|Q8N900	hg19	CCDS13890.1	0.02	17.750019	TGAxCCC	COVERED																																																																																			NOVEL	RNF185-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321927.2	5	12.580405	KEEP	1	4	123	85	3096	GG	1	1	0		+	25	46	900	0	0	61.499317	369	60	13959	615	ENST00000326132.6	0.063452	1
RNF185	91445	__UNKNOWN__	__UNKNOWN__	22	31602602	31602602	__UNKNOWN__	3'UTR	SNP	G	G	A	rs200997145		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:31602602G>A	ENST00000326132.6	+	0	2768				RNF185_ENST00000266252.7_3'UTR	NM_152267.3	NP_689480.2	Q96GF1	RN185_HUMAN	ring finger protein 185	NA		NA			autophagy (GO:0006914)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(3)|skin(1)	6						GGAGAGCTCAGCCAACAGAGG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13890.1, CCDS46689.1	22q12.2	2013-01-09			ENSG00000138942	ENSG00000138942	91445		RING-type (C3HC4) zinc fingers	26783	protein-coding gene	gene with protein product	hypothetical protein FLJ38628	NA			NA	12477932	Standard	NM_152267	NM_152267	NA	Approved	FLJ38628	uc003akb.3	Q96GF1	OTTHUMG00000151253	ENST00000326132.6:c.*2030G>A	chr22.hg19:g.31602602G>A		NA	A8K5C1|A9X3T8|Q8N900	hg19	CCDS13890.1	0.02	17.213402	TCAxCCA	COVERED																																																																																			NOVEL	RNF185-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321927.2	4	9.505818	KEEP	1	5	152	85	3129	GG	1	1	0		+	38	59	1346	0	0	97.443712	380	60	14450	649	ENST00000326132.6	0.090909	1
HMGXB4	10042	__UNKNOWN__	__UNKNOWN__	22	35683618	35683618	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:35683618A>G	ENST00000216106.5	+	8	1596				HMGXB4_ENST00000444518.2_Intron	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	NA		NA			endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GAAAATGCAAATcagaagtca	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281	10042		High mobility group / Non-canonical	5003	protein-coding gene	gene with protein product		604702	high-mobility group protein 2-like 1	HMG2L1	NA	10329004, 10591208, 20511232	Standard	NM_005487	NM_001003681	NA	Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1468+173A>G	chr22.hg19:g.35683618A>G		NA	O75672|O75673|Q9UMT5	hg19	CCDS33641.1	0.02	-0.228104	CAAxTCA	COVERED																																																																																			NOVEL	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318104.2	1	2.404054	KEEP	0	0	0	8	226	AA	0.99257	0.578599	0		+	3	60	111	0	0	8.493666	23	60	853	36	ENST00000216106.5	0.115385	0.58293
FOXRED2	80020	__UNKNOWN__	__UNKNOWN__	22	36884154	36884154	__UNKNOWN__	3'UTR	SNP	G	G	A	rs114424463		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:36884154G>A	ENST00000397224.4	-	0	4049					NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	NA		NA			ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						aaaaaaaaaagaaaaagaaaa	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350	80020			26264	protein-coding gene	gene with protein product		613777			NA	12477932	Standard	NM_024955	NM_024955	NA	Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.*1901C>T	chr22.hg19:g.36884154G>A		NA	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	hg19	CCDS13929.1	0.02	-0.319869	AAAxAAA	COVERED																																																																																			NOVEL	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000104098.2	4	4.322703	KEEP	0	1	12	19	519	GG	0.999863	0.835601	0		-	8	60	117	0	0	7.408298	27	70	794	74	ENST00000397224.4	0.228571	0.835716
CSNK1E	1454	__UNKNOWN__	__UNKNOWN__	22	38776466	38776466	__UNKNOWN__	Intron	SNP	A	A	G	rs370421077		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:38776466A>G	ENST00000400206.2	-	3	139				RP3-449O17.1_ENST00000457665.1_RNA			P49674	KC1E_HUMAN	casein kinase 1, epsilon	NA		NA			cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					GATAGGAGACACGATTCTAAA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923	1454			2453	protein-coding gene	gene with protein product		600863			NA	7797465, 10535959	Standard	NM_001894	NM_001894	NA	Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000400206.2:c.327-38T>C	chr22.hg19:g.38776466A>G		NA		hg19	CCDS13970.1	0.02	1.982703	GACxCGA	COVERED																																																																																			NOVEL	CSNK1E-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321460.1	1	6.317418	KEEP	17	0	0	21	631	AA	0.99986	0.996093	0		-	4	27	132	0	0	8.500256	65	60	2265	112	ENST00000400206.2	0.057971	0.996233
APOBEC3F	200316	__UNKNOWN__	__UNKNOWN__	22	39441197	39441197	__UNKNOWN__	Silent	SNP	G	G	A	rs200983508	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:39441197G>A	ENST00000308521.5	+	3	780	c.423G>A	c.(421-423)ggG>ggA	p.G141G	APOBEC3G_ENST00000452957.2_Intron|APOBEC3F_ENST00000491387.1_3'UTR	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	141		NA			base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.G141G(2)		breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					GTCAGGCAGGGGCCCGCGTGA	0.592	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				2	Substitution - coding silent(2)	lung(1)|endometrium(1)					NA						47	49	48	NA		NA	NA	22		NA											NA				39441197		2203	4300	6503	SO:0001819	synonymous_variant			BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394	200316		Apolipoprotein B mRNA editing enzymes	17356	protein-coding gene	gene with protein product		608993			NA	11863358, 17121840	Standard	NM_145298	NM_145298	NA	Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.423G>A	chr22.hg19:g.39441197G>A		NA	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	hg19	CCDS33648.1	0.02	6.09945	AGGxGCC	COVERED																																																																																			NOVEL	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321216.1	0	13.978836	KEEP	3	4	121	89	3065	GG	1	1	0		+	7	21	250	0	0	15.746174	159	60	5870	340	ENST00000308521.5	0.042169	1
XPNPEP3	63929	__UNKNOWN__	__UNKNOWN__	22	41323917	41323917	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chr22:41323917C>T	ENST00000357137.4	+	0	3086				XPNPEP3_ENST00000544094.1_Intron	NM_022098.3	NP_071381.1	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3, putative	NA		NA			glomerular filtration (GO:0003094)|protein processing (GO:0016485)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metallopeptidase activity (GO:0008237)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	17						agaaaGATTTCTTTCGCAGAT	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA	Ovarian(145;306 1841 7037 21878 30110)					NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS14007.1, CCDS74869.1	22q13.2	2010-07-20			ENSG00000196236	ENSG00000196236	63929			28052	protein-coding gene	gene with protein product		613553			NA	15708373, 20179356	Standard	NM_022098	NM_022098	NA	Approved	APP3, NPHPL1	uc003azh.3	Q9NQH7	OTTHUMG00000151312	ENST00000357137.4:c.*1478C>T	chr22.hg19:g.41323917C>T		NA	B2R9G1|B7Z790|B7Z7B2|Q6I9V9|Q8NDA6|Q9BV27|Q9BVH0	hg19	CCDS14007.1	0.02	-0.348736	TTTxTTT	COVERED																																																																																			NOVEL	XPNPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322201.2	2	3.293203	KEEP	0	0	0	11	344	CC	0.993072	0.871627	0		+	7	60	114	0	0	6.824011	33	60	1113	54	ENST00000357137.4	0.175	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	9373826	9373826	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:9373826G>A			NA	NA				GS1-519E5.1 (130580 upstream) : TBL1X (57508 downstream)						NA		NA									NA						GAACACCATTGCTTCCGGCTG	0.488	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.9373826G>A		NA		hg19		0.02	-0.254408	ATTxCTT	COVERED																																																																																			NOVEL					0			1	2.407562	KEEP	1	0	0	8	282	GG	0.99257	0.663556	0			3	60	110	0	0	8.564176	20	60	761	44		0.130435	0.668523
TBL1X	6907	__UNKNOWN__	__UNKNOWN__	X	9665368	9665368	__UNKNOWN__	Intron	SNP	C	C	A	rs2239411	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:9665368C>A	ENST00000380961.1	+	12	1377				TBL1X_ENST00000217964.7_Intron|TBL1X_ENST00000407597.2_Intron|TBL1X_ENST00000424279.1_Intron|TBL1X_ENST00000536365.1_Intron	NM_001139468.1	NP_001132940.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	NA		NA			canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				AAAACTTTGCCAGAATAGTTA	0.408	NA	NA											G|||	1244	0.329536	0.1407	0.3545	3775	,	,	NA	13293	0.1696	NA	0.335	False	NA	,,,	NA	NA	NA	2504	0.3108	NA	NA	NA						NA		NA				0							NA	G	,,,	835,3000		79,556,121,997,450	114	101	105	NA	,,,	-4.9	0	X	dbSNP_98	105	2844,3884		425,1186,808,817,1064	no	intron,intron,intron,intron	TBL1X	NM_001139466.1,NM_001139467.1,NM_001139468.1,NM_005647.3	,,,	504,1742,929,1814,1514	AA,AC,A,CC,C	NA	42.2711,21.7731,34.8291	,,,	,,,	9665368	3679,6884	2203	4300	6503	SO:0001627	intron_variant			Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849	6907		WD repeat domain containing	11585	protein-coding gene	gene with protein product		300196	transducin (beta)-like 1	TBL1	NA	10330347	Standard	NM_005647	NM_005647	NA	Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000380961.1:c.901-41C>A	chrX.hg19:g.9665368C>A		NA	A8K044|A8K4J7|Q86UY2	hg19	CCDS48078.1	0.02	-0.298296	TGCxAGA	COVERED																																																																																			NOVEL	TBL1X-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055708.1	1	3.912954	KEEP	0	0	0	13	475	CC	0.994391	0.776679	0		+	4	60	149	0	0	11.46075	30	60	1159	59	ENST00000380961.1	0.117647	0.78106
BMX	660	__UNKNOWN__	__UNKNOWN__	X	15574199	15574199	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:15574199C>A	ENST00000357607.2	+	19	2145	c.1957C>A	c.(1957-1959)Cca>Aca	p.P653T	BMX_ENST00000348343.6_Missense_Mutation_p.P653T|BMX_ENST00000342014.6_Missense_Mutation_p.P653T			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	653	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					TGTTTAGCTTCCAGAAAAGCG	0.343	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						194	189	191	NA		NA	NA	X		NA											NA				15574199		2203	4300	6503	SO:0001583	missense			AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010	660		Pleckstrin homology (PH) domain containing, SH2 domain containing	1079	protein-coding gene	gene with protein product	BTK-like on X chromosome	300101			NA	7970727	Standard	NM_001721	NM_203281	NA	Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1957C>A	chrX.hg19:g.15574199C>A	ENSP00000350224:p.Pro653Thr	NA	A6NIH9|O60564|Q12871	hg19	CCDS14168.1	0.02	8.990973	CTTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.44	3.625182	0.66901	.	.	ENSG00000102010	ENST00000357607;ENST00000348343;ENST00000342014	D;D;D	0.92446	-3.04;-3.04;-3.04	5.98	5.1	0.69264	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000016	D	0.96676	0.8915	M	0.92923	3.36	0.38863	D	0.956524	D	0.89917	1.0	D	0.97110	1.0	D	0.97612	1.0130	10	0.87932	D	0	.	11.8984	0.52669	0.0:0.8293:0.1707:0.0	.	653	P51813	BMX_HUMAN	T	653	ENSP00000350224:P653T;ENSP00000308774:P653T;ENSP00000340082:P653T	ENSP00000340082:P653T	P	+	1	0	BMX	15484120	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.929000	0.48916	1.239000	0.43787	0.600000	0.82982	CCA	NOVEL	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055877.1	5	17.189546	KEEP	0	1	31	68	2340	CC	1	1	0		+	22	60	785	0	0	58.319174	190	60	7143	357	ENST00000357607.2	0.103774	1
DMD	1756	__UNKNOWN__	__UNKNOWN__	X	31187648	31187648	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:31187648G>T	ENST00000357033.4	-	74	10671	c.10465C>A	c.(10465-10467)Cgt>Agt	p.R3489S	DMD_ENST00000359836.1_Missense_Mutation_p.R1016S|DMD_ENST00000343523.2_Intron|DMD_ENST00000378702.4_Missense_Mutation_p.R421S|DMD_ENST00000378677.2_Missense_Mutation_p.R3485S|DMD_ENST00000378680.2_Intron|DMD_ENST00000361471.4_Missense_Mutation_p.R408S|DMD_ENST00000378723.3_Missense_Mutation_p.R421S|DMD_ENST00000541735.1_Intron|DMD_ENST00000474231.1_Missense_Mutation_p.R1029S|DMD_ENST00000378707.3_Missense_Mutation_p.R1029S	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3489	Binds to SNTB1.	NA			cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GCAGGACTACGAGGCTGGCTC	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						52	47	48	NA		NA	NA	X		NA											NA				31187648		2202	4300	6502	SO:0001583	missense			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947	1756			2928	protein-coding gene	gene with protein product	muscular dystrophy, Duchenne and Becker types	300377	dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272, mental retardation, X-linked 85	MRX85	NA	3282674, 3607877, 23900271	Standard	NM_004006	NM_004019	NA	Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.10465C>A	chrX.hg19:g.31187648G>T	ENSP00000354923:p.Arg3489Ser	NA	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	hg19	CCDS14233.1	0.02	1.979412	TACxAGG	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.2|20.2	3.947105|3.947105	0.73672|0.73672	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000378702;ENST00000474231;ENST00000361471|ENST00000465285	D;D;D;D;D;D;D;D;D|.	0.83837|.	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77|.	5.29|5.29	4.43|4.43	0.53597|0.53597	.|.	0.000000|.	0.36893|.	U|.	0.002347|.	T|.	0.61098|.	0.2320|.	L|L	0.49126|0.49126	1.545|1.545	0.80722|0.80722	D|D	1|1	P;P;P;P;P;B;B;B;P;B;B;B;B|.	0.44090|.	0.544;0.826;0.826;0.826;0.826;0.213;0.124;0.038;0.706;0.081;0.174;0.038;0.116|.	B;B;B;B;B;B;B;B;B;B;B;B;B|.	0.43478|.	0.416;0.145;0.145;0.145;0.145;0.168;0.033;0.033;0.421;0.105;0.081;0.034;0.044|.	T|.	0.58261|.	-0.7667|.	9|.	.|.	.|.	.|.	.|.	13.2783|13.2783	0.60200|0.60200	0.0778:0.0:0.9222:0.0|0.0778:0.0:0.9222:0.0	.|.	3481;3489;3485;2148;2145;1016;1029;1029;3366;408;421;408;421|.	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1|.	.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.|.	S|X	3481;2148;2145;421;1172;3485;3489;1016;3489;3366;1029;421;1029;408|1217	ENSP00000367997:R421S;ENSP00000350765:R1172S;ENSP00000367948:R3485S;ENSP00000354923:R3489S;ENSP00000352894:R1016S;ENSP00000367979:R1029S;ENSP00000367974:R421S;ENSP00000417123:R1029S;ENSP00000354464:R408S|.	.|.	R|S	-|-	1|2	0|0	DMD|DMD	31097569|31097569	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.826000|7.826000	0.86716|0.86716	1.215000|1.215000	0.43411|0.43411	0.594000|0.594000	0.82650|0.82650	CGT|TCG	NOVEL	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056182.2	1	4.213742	KEEP	0	0	0	14	490	GG	0.995343	0.979578	0		-	5	60	171	0	0	12.091237	53	60	1952	91	ENST00000357033.4	0.086207	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	45842987	45842987	__UNKNOWN__	IGR	SNP	C	C	G	rs377236967		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:45842987C>G			NA	NA				RP5-1158E12.1 (66512 upstream) : RP1-30G7.2 (342371 downstream)						NA		NA									NA						GGGGGCCTGGCCACGGGGATG	0.667	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.45842987C>G		NA		hg19		0.02	-0.193009	TGGxCAC	COVERED																																																																																			NOVEL					0			3	6.018479	KEEP	0	0	0	20	671	CC	0.999863	0.457694	0			3	30	113	0	0	9.378336	13	60	471	57		0.1875	0.457757
GAGE2A	729447	__UNKNOWN__	__UNKNOWN__	X	49360741	49360741	__UNKNOWN__	Intron	SNP	A	A	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:49360741A>G	ENST00000362097.1	+	5	411					NM_001127212.1	NP_001120684.1	Q6NT46	GAG2A_HUMAN	G antigen 2A	NA		NA								endometrium(4)	4	Ovarian(276;0.236)					AGTGACTGAAATAAATATCAA	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U19143	CCDS48114.1	Xp11.23	2009-03-17	2007-07-23	2007-07-23	ENSG00000189064	ENSG00000189064	729447			4099	protein-coding gene	gene with protein product	cancer/testis antigen family 4, member 2	300720	G antigen 2	GAGE2	NA	7544395	Standard		NM_001127212	NA	Approved	CT4.2		Q6NT46	OTTHUMG00000024143	ENST00000362097.1:c.329-573A>G	chrX.hg19:g.49360741A>G		NA		hg19	CCDS48114.1	0.02	20.290986	GAAxTAA	COVERED																																																																																			NOVEL	GAGE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060827.3	15	11.712706	KEEP	143	11	405	180	5680	AA	1	1	0		+	40	40	1556	0	0	116.729544	394	41	14852	986	ENST00000362097.1	0.092166	1
FAM104B	90736	__UNKNOWN__	__UNKNOWN__	X	55172521	55172521	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:55172521G>T	ENST00000477847.2	-	3	468	c.335C>A	c.(334-336)aCa>aAa	p.T112K	FAM104B_ENST00000332132.4_Intron|FAM104B_ENST00000489298.1_Missense_Mutation_p.T114K|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000358460.4_Intron|FAM104B_ENST00000425133.2_Missense_Mutation_p.T116K	NM_001166702.1	NP_001160174.1	Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	0		NA								endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						AATTCATCATGTTGGAGCTTG	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						29	20	22	NA		NA	NA	X		NA											NA				55172521		692	1590	2282	SO:0001583	missense			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518	90736			25085	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 44	CXorf44	NA	12477932	Standard	NM_138362	NM_138362	NA	Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000477847.2:c.335C>A	chrX.hg19:g.55172521G>T	ENSP00000421161:p.Thr112Lys	NA	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	hg19	CCDS55423.1	0.02	42.778905	CATxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	g	8.588	0.883807	0.17467	.	.	ENSG00000182518	ENST00000425133;ENST00000477847;ENST00000489298	T;T;T	0.54866	0.55;0.55;0.55	1.6	1.6	0.23607	.	.	.	.	.	T	0.30070	0.0753	N	0.19112	0.55	0.09310	N	1	P	0.41524	0.753	B	0.32022	0.139	T	0.17137	-1.0379	9	0.87932	D	0	.	6.0913	0.19995	0.0:0.0:1.0:0.0	.	116	Q5XKR9-3	.	K	116;112;114	ENSP00000397188:T116K;ENSP00000421161:T112K;ENSP00000423164:T114K	ENSP00000397188:T116K	T	-	2	0	FAM104B	55189246	0.987000	0.35691	0.006000	0.13384	0.065000	0.16274	1.636000	0.37144	1.084000	0.41184	0.436000	0.28706	ACA	NOVEL	FAM104B-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056853.2	48	11.682855	KEEP	0	24	765	307	11117	GG	1	1	0		-	95	60	3373	0	0	258.761576	657	60	24893	1493	ENST00000477847.2	0.12633	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	56508246	56508246	__UNKNOWN__	IGR	SNP	C	C	T	rs5913944		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:56508246C>T			NA	NA				KLF8 (193924 upstream) : UBQLN2 (81779 downstream)						NA		NA									NA						cctcgtgatccgcccgcctcg	0.527	NA	NA											-|||	1214	0.321589	0.1944	0.3718	3775	,	,	NA	11110	0.2619	NA	0.2107	False	NA	,,,	NA	NA	NA	2504	0.228	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.56508246C>T		NA		hg19		0.02	-0.017547	ATCxGCC	UNCOVERED																																																																																			NOVEL					0			2	2.626018	KEEP	4	0	0	9	248	CC	0	0	0			2	60	73	0	0	8.254047	0	0	0	14		1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	61717857	61717857	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:61717857G>A			NA	NA				None (None upstream) : SPIN4 (849249 downstream)						NA		NA									NA						ccttcaaagaggtccaaatat	0.428	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.61717857G>A		NA		hg19		0.02	-0.342078	AGAxGTC	COVERED																																																																																			NOVEL					0			6	3.683074	KEEP	9	2	68	36	1296	GG	0.999997	0.865743	0			3	24	112	0	0	8.039245	36	40	1337	111		0.076923	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	61719733	61719733	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:61719733G>A			NA	NA				None (None upstream) : SPIN4 (847373 downstream)						NA		NA									NA						ttccaacacagtcctccaagc	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.61719733G>A		NA		hg19		0.02	-0.33339	ACAxTCC	COVERED																																																																																			NOVEL					0			3	6.019699	KEEP	11	0	0	20	719	GG	0.994391	0.847205	0			5	40	181	0	0	14.186484	31	40	1177	71		0.138889	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	61729264	61729264	__UNKNOWN__	IGR	SNP	T	T	C	rs75107860		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:61729264T>C			NA	NA				None (None upstream) : SPIN4 (837842 downstream)						NA		NA									NA						caaagcagtttctgagaatgc	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.61729264T>C		NA		hg19		0.02	-0.324611	GTTxCTG	COVERED																																																																																			NOVEL					0			13	3.611277	KEEP	12	0	0	12	395	TT	0.99254	0.829482	0			3	41	116	0	0	11.569897	2	30	72	85		0.6	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	65175748	65175748	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:65175748G>A			NA	NA				MSN (213957 upstream) : RP6-159A1.3 (43844 downstream)						NA		NA									NA						GCTTGTTTGTGTAGGTAGAAT	0.378	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.65175748G>A		NA		hg19		0.02	6.069925	TGTxTAG	COVERED																																																																																			NOVEL					0			1	3.846693	KEEP	9	1	29	23	809	GG	0.999909	0.999909	0			14	31	456	0	0	31.718462	145	60	5439	204		0.08805	1
KIAA2022	340533	__UNKNOWN__	__UNKNOWN__	X	73954393	73954393	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:73954393A>C	ENST00000055682.6	-	0	10009					NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	NA		NA			base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						TGAGACTCAGAAACCCCTGAG	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030	340533			29433	protein-coding gene	gene with protein product	XLMR-related protein, neurite extension	300524			NA	15466006, 23615299	Standard	NM_001008537	NM_001008537	NA	Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.*4847T>G	chrX.hg19:g.73954393A>C		NA	A7YY87|Q5JUX9|Q8IVE9	hg19	CCDS35337.1	0.02	-0.228067	CAGxAAC	COVERED																																																																																			NOVEL	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057270.2	0	3.609928	KEEP	0	0	0	12	355	AA	0.993634	0.579219	0		-	17	60	650	0	0	65.830487	9	60	306	43	ENST00000055682.6	0.653846	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	74802478	74802478	__UNKNOWN__	IGR	SNP	A	A	G	rs5938117	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:74802478A>G			NA	NA				ZDHHC15 (59141 upstream) : MAGEE2 (200344 downstream)						NA		NA									NA						ccagataaataaaaacatatg	0.493	NA	NA											G|||	1894	0.501722	0.3601	0.2767	3775	,	,	NA	12134	0.6696	NA	0.1471	False	NA	,,,	NA	NA	NA	2504	0.4121	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.74802478A>G		NA		hg19		0.02	-0.184222	AATxAAA	COVERED																																																																																			NOVEL					0			8	2.406012	KEEP	0	0	0	8	232	AA	0.99257	0.420331	0			2	60	82	0	0	6.330878	18	60	639	31		0.1	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	74803221	74803221	__UNKNOWN__	IGR	SNP	C	C	T	rs141172387		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:74803221C>T			NA	NA				ZDHHC15 (59884 upstream) : MAGEE2 (199601 downstream)						NA		NA									NA						TCCCAGAGTGCGGTGCTGTTT	0.478	NA	NA											C|||	51	0.0135099	0.0378	0.0014	3775	,	,	NA	13708	0	NA	0	False	NA	,,,	NA	NA	NA	2504	0	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.74803221C>T		NA		hg19		0.02	1.496437	GTGxGGT	COVERED																																																																																			NOVEL					0			20	3.009778	KEEP	0	0	0	10	349	CC	0.992708	0.988426	0			5	60	136	0	0	8.259632	63	60	2046	91		0.073529	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	74803898	74803898	__UNKNOWN__	IGR	SNP	T	T	C	rs5937404	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:74803898T>C			NA	NA				ZDHHC15 (60561 upstream) : MAGEE2 (198924 downstream)						NA		NA									NA						AGGACTTCAGTGAGAAAGGAA	0.473	NA	NA											C|||	432	0.114437	0.1891	0.0173	3775	,	,	NA	15062	0.0238	NA	0.0258	False	NA	,,,	NA	NA	NA	2504	0.1227	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.74803898T>C		NA		hg19		0.02	1.912719	CAGxGAG	COVERED																																																																																			NOVEL					0			11	3.307915	KEEP	0	0	0	11	312	TT	0.993072	0.991948	0			7	60	237	0	0	16.858774	70	60	2393	95		0.090909	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	79826338	79826338	__UNKNOWN__	IGR	SNP	A	A	G	rs73630393		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:79826338A>G			NA	NA				FAM46D (125528 upstream) : BRWD3 (100014 downstream)						NA		NA									NA						AGAAGCAACCACTTTGCCATT	0.507	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.79826338A>G		NA		hg19		0.02	1.522894	ACCxCTT	COVERED																																																																																			NOVEL					0			1	4.21174	KEEP	0	0	0	14	422	AA	0.99649	0.99519	0			4	21	128	0	0	7.909263	72	60	2526	110		0.052632	0.998696
DOCK11	139818	__UNKNOWN__	__UNKNOWN__	X	117676747	117676747	__UNKNOWN__	Silent	SNP	C	C	A	rs368102203		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:117676747C>A	ENST00000276202.7	+	2	225	c.162C>A	c.(160-162)acC>acA	p.T54T	DOCK11_ENST00000276204.6_Silent_p.T54T	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	54		NA			blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AAAGAAAAACCCAGATTTACA	0.373	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						128	125	126	NA		NA	NA	X		NA											NA				117676747		2203	4300	6503	SO:0001819	synonymous_variant			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251	139818		Pleckstrin homology (PH) domain containing	23483	protein-coding gene	gene with protein product	zizimin2	300681			NA	12432077, 16968698	Standard	NM_144658	NM_144658	NA	Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.162C>A	chrX.hg19:g.117676747C>A		NA	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	hg19	CCDS35373.1	0.02	2.343549	AACxCAG	COVERED																																																																																			NOVEL	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356002.1	1	3.050869	KEEP	0	1	13	15	485	CC	0.997832	0.988815	0		+	39	60	1475	0	0	148.353263	23	60	799	90	ENST00000276202.7	0.629032	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	128283443	128283443	__UNKNOWN__	IGR	SNP	A	A	G	rs2886115		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:128283443A>G			NA	NA				RP1-30E17.2 (548997 upstream) : RNA5SP513 (287063 downstream)						NA		NA									NA						tcaggagttcaagaccagcct	0.517	NA	NA											G|||	3307	0.876026	0.7526	0.634	3775	,	,	NA	13023	0.745	NA	0.4742	False	NA	,,,	NA	NA	NA	2504	0.6585	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.128283443A>G		NA		hg19		0.02	-0.035086	TTCxAGA	UNCOVERED																																																																																			NOVEL					0			6	2.406991	KEEP	0	0	0	8	243	AA	0.99257	0.019833	0			2	49	75	0	0	7.250456	2	60	59	15		0.5	0.019982
RP1-274L7.1	0	__UNKNOWN__	__UNKNOWN__	X	129630630	129630630	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:129630630T>C	ENST00000458525.1	-	0	1015										NA		NA									NA						aactttaatttctcctgagga	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000458525.1:	chrX.hg19:g.129630630T>C		NA		hg19		0.02	6.749006	ATTxCTC	COVERED																																																																																			NOVEL	RP1-274L7.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000058271.1	2	7.787564	KEEP	0	2	72	51	1519	TT	1	1	0		-	6	27	222	0	0	13.587469	178	51	6328	299	ENST00000458525.1	0.032609	1
FAM122C	159091	__UNKNOWN__	__UNKNOWN__	X	133948765	133948765	__UNKNOWN__	Intron	SNP	A	A	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:133948765A>T	ENST00000370785.3	+	2	515				FAM122C_ENST00000445123.1_Intron|FAM122C_ENST00000414371.2_Intron|FAM122C_ENST00000370784.4_Intron	NM_138819.3	NP_620174.1	Q6P4D5	F222C_HUMAN	family with sequence similarity 122C	NA		NA								endometrium(2)|kidney(1)|lung(2)	5	Acute lymphoblastic leukemia(192;0.000127)					TTTGTAATGGATTTTATATAA	0.363	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						26	27	27	NA		NA	NA	X		NA											NA				133948765		2179	4274	6453	SO:0001627	intron_variant			BC017868	CCDS14644.1, CCDS55500.1, CCDS55501.1, CCDS76028.1	Xq26.3	2008-02-05	2006-07-11		ENSG00000156500	ENSG00000156500	159091			25202	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_138819	NM_138819	NA	Approved	RP3-473B4.1	uc004exz.2	Q6P4D5	OTTHUMG00000022716	ENST00000370785.3:c.111-36A>T	chrX.hg19:g.133948765A>T		NA	F5H036|Q8WVK9	hg19	CCDS14644.1	0.02	1.193671	TGGxTTT	COVERED																																																																																			NOVEL	FAM122C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058955.1	3	6.876267	KEEP	0	0	0	23	594	AA	0.999892	0.99921	0		+	8	60	158	0	0	8.492513	72	60	2107	122	ENST00000370785.3	0.1	0.999317
ARHGEF6	9459	__UNKNOWN__	__UNKNOWN__	X	135767786	135767786	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:135767786G>A	ENST00000250617.6	-	12	2598				ARHGEF6_ENST00000370622.1_Intron|ARHGEF6_ENST00000370620.1_Intron|ARHGEF6_ENST00000535227.1_Intron	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					aaaaaaggaagaaaaaTACGA	0.403	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						51	50	50	NA		NA	NA	X		NA											NA				135767786		2202	4300	6502	SO:0001627	intron_variant			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675	9459		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	685	protein-coding gene	gene with protein product	Rac/Cdc42 guanine exchange factor (GEF) 6, PAK-interacting exchange factor, alpha, rho guanine nucleotide exchange factor 6	300267	mental retardation, X-linked 46	MRX46	NA	7584048, 9659915	Standard	NM_004840	NM_004840	NA	Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1392+49C>T	chrX.hg19:g.135767786G>A		NA	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	hg19	CCDS14660.1	0.02	0.820537	GAAxAAA	COVERED																																																																																			NOVEL	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058511.2	1	2.842151	KEEP	0	1	12	14	421	GG	0.99649	0.978509	0		-	14	60	165	0	0	9.853329	39	70	1153	77	ENST00000250617.6	0.264151	0.981955
RBMX	27316	__UNKNOWN__	__UNKNOWN__	X	135955996	135955996	__UNKNOWN__	3'UTR	SNP	G	G	A	rs850		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:135955996G>A	ENST00000320676.7	-	0	1635				RBMX_ENST00000570135.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000496459.2_5'UTR	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	NA		NA			cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TGCCTCATTTGCTGGGAAAAA	0.368	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274	27316		RNA binding motif (RRM) containing	9910	protein-coding gene	gene with protein product	heterogeneous nuclear ribonucleoprotein G	300199	RNA binding motif protein, X chromosome		NA	10391206, 10391207	Standard	NM_002139	NM_002139	NA	Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.*305C>T	chrX.hg19:g.135955996G>A		NA	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	hg19	CCDS14661.1	0.02	16.091582	TTTxCTG	COVERED																																																																																			NOVEL	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058507.1	3	16.491366	KEEP	17	4	108	93	3356	GG	1	1	0		-	85	50	3032	0	0	255.064269	304	60	11664	617	ENST00000320676.7	0.218509	1
RBMX	27316	__UNKNOWN__	__UNKNOWN__	X	135961560	135961560	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs80321628		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:135961560C>G	ENST00000320676.7	-	2	181	c.27G>C	c.(25-27)aaG>aaC	p.K9N	RBMX_ENST00000562646.1_Missense_Mutation_p.K9N|RBMX_ENST00000565438.1_Intron|RBMX_ENST00000570135.1_5'UTR|RBMX_ENST00000431446.3_Missense_Mutation_p.K9N	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	9	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.	NA			cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K9N(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAATGAAGAGCTTTCCTGGGC	0.413	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				1	Substitution - Missense(1)	pancreas(1)					NA						109	103	105	NA		NA	NA	X		NA											NA				135961560		2203	4300	6503	SO:0001583	missense				CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274	27316		RNA binding motif (RRM) containing	9910	protein-coding gene	gene with protein product	heterogeneous nuclear ribonucleoprotein G	300199	RNA binding motif protein, X chromosome		NA	10391206, 10391207	Standard	NM_002139	NM_002139	NA	Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.27G>C	chrX.hg19:g.135961560C>G	ENSP00000359645:p.Lys9Asn	NA	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	hg19	CCDS14661.1	0.02	4.62841	GAGxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	.	19.30	3.801463	0.70682	.	.	ENSG00000147274	ENST00000431446;ENST00000320676;ENST00000449161	D;D	0.89050	-2.46;-2.46	4.66	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	U	0.000000	D	0.88507	0.6455	L	0.56340	1.77	0.09310	P	0.9999999999999992	P;B;P	0.46656	0.882;0.278;0.868	P;B;B	0.50270	0.636;0.142;0.311	D	0.91729	0.5395	9	0.72032	D	0.01	.	8.8627	0.35267	0.0:0.7507:0.0:0.2493	.	9;9;9	B4E3U4;P38159;Q8N8Y7	.;HNRPG_HUMAN;.	N	9	ENSP00000411989:K9N;ENSP00000359645:K9N	ENSP00000359645:K9N	K	-	3	2	RBMX	135789226	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.970000	0.29383	1.905000	0.55150	0.508000	0.49915	AAG	NOVEL	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058507.1	6	10.633981	KEEP	0	1	36	48	1609	CC	1	0.999991	0		-	7	50	265	0	0	18.766328	95	60	3508	188	ENST00000320676.7	0.068627	0.999991
CXorf40B	541578	__UNKNOWN__	__UNKNOWN__	X	149100711	149100711	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:149100711C>T	ENST00000370406.3	-	0	1356				CXorf40B_ENST00000355203.2_3'UTR|CXorf40B_ENST00000370404.1_3'UTR|CXorf40B_ENST00000462691.1_Intron			Q96DE9	CX04B_HUMAN	chromosome X open reading frame 40B	NA		NA								endometrium(1)|lung(4)	5	Acute lymphoblastic leukemia(192;6.56e-05)					ATTGAAGGTGCCATGATTTAG	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						80	62	68	NA		NA	NA	X		NA											NA				149100711		2200	4299	6499	SO:0001624	3_prime_UTR_variant			BC009523	CCDS35426.1	Xq28	2012-11-28			ENSG00000197021	ENSG00000197021	541578			17402	protein-coding gene	gene with protein product		NA			NA		Standard	NP_001013867	XM_005274698	NA	Approved		uc004fdy.3	Q96DE9	OTTHUMG00000034327	ENST00000370406.3:c.*51G>A	chrX.hg19:g.149100711C>T		NA		hg19	CCDS35426.1	0.02	14.23216	GTGxCAT	COVERED																																																																																			NOVEL	CXorf40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000082896.2	1	8.196023	KEEP	18	5	123	71	2512	CC	1	1	0		-	15	47	495	0	0	28.239572	428	60	15564	645	ENST00000370406.3	0.03386	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	152200106	152200106	__UNKNOWN__	IGR	SNP	G	G	A	rs11094614	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:152200106G>A			NA	NA				RN7SL190P (36067 upstream) : PNMA3 (24659 downstream)						NA		NA									NA						TCCTGTAGTGGCTGTTTGCAG	0.547	NA	NA											G|||	868	0.229934	0.3306	0.0793	3775	,	,	NA	14308	0.1329	NA	0.0954	False	NA	,,,	NA	NA	NA	2504	0.1493	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.152200106G>A		NA		hg19		0.02	-0.149136	GTGxCTG	COVERED																																																																																			NOVEL					0			1	3.27596	KEEP	0	0	0	11	358	GG	0.993634	0.290142	0			10	60	346	0	0	34.368665	7	60	250	31		0.588235	0.292001
ATP2B3	492	__UNKNOWN__	__UNKNOWN__	X	152840380	152840380	__UNKNOWN__	Intron	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:152840380G>A	ENST00000349466.2	+	21	3668				ATP2B3_ENST00000359149.3_Intron|ATP2B3_ENST00000263519.4_Intron|ATP2B3_ENST00000370181.2_Intron|ATP2B3_ENST00000370186.1_Intron			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	NA		NA			blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCGCCCTGTGTAAGGCTCAG	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	492	3.6.3.8	ATPases / P-type	816	protein-coding gene	gene with protein product	plasma membrane calcium-transporting ATPase 3, cilia and flagella associated protein 39	300014	spinocerebellar ataxia, X-linked 1, cerebellar ataxia 2 (X-linked)	SCAX1, CLA2	NA	8187550, 22912398	Standard	NM_021949	NM_021949	NA	Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3343-5056G>A	chrX.hg19:g.152840380G>A		NA	B7WNR8|B7WNY5|Q12995|Q16858	hg19	CCDS35440.1	0.02	1.851027	TGTxTAA	COVERED																																																																																			NOVEL	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060957.1	3	13.23395	KEEP	0	0	0	44	1481	GG	1	0.999559	0		+	7	60	254	0	0	18.316185	76	60	2849	142	ENST00000349466.2	0.084337	0.999559
HCFC1	3054	__UNKNOWN__	__UNKNOWN__	X	153214289	153214289	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrX:153214289C>G	ENST00000369984.4	-	0	7095				HCFC1_ENST00000354233.3_3'UTR|HCFC1_ENST00000310441.7_3'UTR			P51610	HCFC1_HUMAN	host cell factor C1	NA		NA			cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGTCACTGAGCAGGGTGGGCC	0.527	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534	3054			4839	protein-coding gene	gene with protein product	VP16-accessory protein, protein phosphatase 1, regulatory subunit 89	300019	mental retardation, X-linked 3, host cell factor C1 (VP16-accessory protein)	HFC1, MRX3	NA	8392914, 23000143	Standard	NM_005334	XM_005274664	NA	Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000369984.4:c.*509G>C	chrX.hg19:g.153214289C>G		NA	Q6P4G5	hg19		0.02	2.390786	GAGxAGG	COVERED																																																																																			NOVEL	HCFC1-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000061101.3	1	16.553719	KEEP	0	0	0	55	1937	CC	1	0.995687	0		-	9	60	341	0	0	26.853331	59	60	2250	157	ENST00000369984.4	0.132353	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10008432	10008432	__UNKNOWN__	IGR	SNP	G	G	C	rs77384733		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10008432G>C			NA	NA				RNA5SP519 (77830 upstream) : AC010970.1 (25548 downstream)						NA		NA									NA						ccttccctctgttcttccttc	0.537	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10008432G>C		NA		hg19		0.02	-0.192587	TCTxTTC	COVERED																																																																																			NOVEL					0			3	2.407188	KEEP	0	0	0	8	270	GG	0.99257	0.454356	0			2	60	64	0	0	6.524578	1	60	33	36		0.666667	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10011033	10011033	__UNKNOWN__	IGR	SNP	G	G	T	rs111325982		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10011033G>T			NA	NA				RNA5SP519 (80431 upstream) : AC010970.1 (22947 downstream)						NA		NA									NA						AAATGTAAAGGGTCCATATAA	0.254	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10011033G>T		NA		hg19		0.02	15.939152	AAGxGTC	COVERED																																																																																			NOVEL					0			49	6.760334	KEEP	0	4	124	66	2285	GG	1	1	0			22	60	778	0	0	54.632146	264	60	9501	569		0.076923	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10011960	10011960	__UNKNOWN__	IGR	SNP	T	T	C	rs75651145	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10011960T>C			NA	NA				RNA5SP519 (81358 upstream) : AC010970.1 (22020 downstream)						NA		NA									NA						GTAACATAAATGATGTATTGA	0.269	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10011960T>C		NA		hg19		0.02	5.230081	AAAxGAT	COVERED																																																																																			NOVEL					0			6	5.415074	KEEP	0	0	0	18	544	TT	0.999859	0.999859	0			10	60	324	0	0	20.519276	166	60	6100	223		0.056818	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10019420	10019420	__UNKNOWN__	IGR	SNP	A	A	G	rs372926596		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10019420A>G			NA	NA				RNA5SP519 (88818 upstream) : AC010970.1 (14560 downstream)						NA		NA									NA						gtatgtttgaacaagaaatga	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10019420A>G		NA		hg19		0.02	-0.42106	TGAxCAA	COVERED																																																																																			NOVEL					0			19	4.212625	KEEP	13	0	0	14	442	AA	0.992708	0.941486	0			5	40	193	0	0	20.511493	1	49	35	82		0.833333	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10019497	10019497	__UNKNOWN__	IGR	SNP	C	C	G	rs111600006		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10019497C>G			NA	NA				RNA5SP519 (88895 upstream) : AC010970.1 (14483 downstream)						NA		NA									NA						AAACGAAACACCACCTCCTGG	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10019497C>G		NA		hg19		0.02	2.552187	ACAxCAC	COVERED																																																																																			NOVEL					0			64	6.683861	KEEP	24	2	74	48	1572	CC	1	0.989542	0			6	60	223	0	0	25.161866	0	0	0	139		1	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10028086	10028086	__UNKNOWN__	IGR	SNP	G	G	T	rs112967940		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10028086G>T			NA	NA				RNA5SP519 (97484 upstream) : AC010970.1 (5894 downstream)						NA		NA									NA						ACAAACTCATGCCCTAATAGA	0.348	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10028086G>T		NA		hg19		0.02	2.229759	CATxCCC	COVERED																																																																																			NOVEL					0			2	4.514549	KEEP	5	0	0	15	510	GG	0.995343	0.993815	0			5	60	183	0	0	18.38682	3	60	115	99		0.625	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10028116	10028116	__UNKNOWN__	IGR	SNP	T	T	C	rs112312281		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:10028116T>C			NA	NA				RNA5SP519 (97514 upstream) : AC010970.1 (5864 downstream)						NA		NA									NA						TAAGCATAATTTGGATCCACT	0.398	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10028116T>C		NA		hg19		0.02	7.787906	AATxTGG	COVERED																																																																																			NOVEL					0			3	14.439004	KEEP	17	0	0	48	1420	TT	1	1	0			5	60	172	0	0	17.28607	3	60	107	287		0.625	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13314236	13314236	__UNKNOWN__	IGR	SNP	G	G	A	rs75731131	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:13314236G>A			NA	NA				None (None upstream) : AC134878.2 (26122 downstream)						NA		NA									NA						GTCTCCACATGGTCACGCACA	0.627	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13314236G>A		NA		hg19		0.02	-0.210233	CATxGTC	COVERED																																																																																			NOVEL					0			2	2.94413	KEEP	10	1	32	21	721	GG	0.999366	0.52183	0			4	27	141	0	0	16.007564	0	0	0	60		1	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13439544	13439544	__UNKNOWN__	IGR	SNP	T	T	G	rs373936442		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:13439544T>G			NA	NA				AC134878.1 (98911 upstream) : SLC9B1P1 (56696 downstream)						NA		NA									NA						tcccagcactttgggaggctg	0.473	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13439544T>G		NA		hg19		0.02	-0.02632	ACTxTGG	UNCOVERED																																																																																			NOVEL					0			1	2.407406	KEEP	16	0	0	8	256	TT	0	0	0			2	40	78	0	0	7.924903	1	6	37	36		0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13467957	13467957	__UNKNOWN__	IGR	SNP	C	C	G			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:13467957C>G			NA	NA				AC134878.1 (127324 upstream) : SLC9B1P1 (28283 downstream)						NA		NA									NA						gtgatcagtgcagagatttgt	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13467957C>G		NA		hg19		0.02	-0.289521	GTGxAGA	UNCOVERED																																																																																			NOVEL					0			2	2.407986	KEEP	6	0	0	8	296	CT	0	0	0			2	24	84	0	0	7.006197	10	40	400	57		0.166667	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13482110	13482110	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:13482110G>A			NA	NA				AC134878.1 (141477 upstream) : SLC9B1P1 (14130 downstream)						NA		NA									NA						catcacctaagtgatcagtgc	0.433	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13482110G>A		NA		hg19		0.02	2.317178	TAAxTGA	COVERED																																																																																			NOVEL					0			16	3.045802	KEEP	18	1	34	22	797	GG	0.997832	0.993528	0			3	25	108	0	0	8.878381	13	60	505	156		0.1875	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13843959	13843959	__UNKNOWN__	IGR	SNP	G	G	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:13843959G>A			NA	NA				SLC9B1P1 (319242 upstream) : AC011293.1 (103483 downstream)						NA		NA									NA						ggaatggaatggaatggaatg	0.388	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13843959G>A		NA		hg19		0.02	-0.23688	AATxGAA	COVERED																																																																																			NOVEL					0			18	7.524574	KEEP	32	0	0	25	886	GG	0.997832	0.611079	0			2	33	76	0	1	7.350111	2	10	72	87		0.5	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13868444	13868444	__UNKNOWN__	IGR	SNP	T	T	C			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:13868444T>C			NA	NA				SLC9B1P1 (343727 upstream) : AC011293.1 (78998 downstream)						NA		NA									NA						tggaatggaatggaatggaat	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13868444T>C		NA		hg19		0.02	7.220966	GAAxGGA	COVERED																																																																																			NOVEL					0			157	3.574404	KEEP	56	11	390	148	4494	TT	1	1	0			7	39	218	0	1	14.446397	84	60	3091	542		0.076923	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58972893	58972893	__UNKNOWN__	IGR	SNP	C	C	T	rs146755545		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:58972893C>T			NA	NA				None (None upstream) : SPRY3 (127586 downstream)						NA		NA									NA						ccattccattccattcccttt	0.418	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58972893C>T		NA		hg19		0.02	-0.166597	ATTxCAT	COVERED																																																																																			NOVEL					0			12	3.611814	KEEP	6	0	0	12	424	CC	0.993634	0.38494	0			2	60	71	0	1	7.234087	1	60	15	43		0.666667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58980581	58980581	__UNKNOWN__	IGR	SNP	A	A	C	rs141355288		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:58980581A>C			NA	NA				None (None upstream) : SPRY3 (119898 downstream)						NA		NA									NA						attccattccactccattcca	0.458	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58980581A>C		NA		hg19		0.02	-0.105251	TCCxCTC	UNCOVERED																																																																																			NOVEL					0			4	3.309095	KEEP	11	0	0	11	333	AA	0.99257	0.138793	0			2	60	59	0	0	6.849823	0	0	0	36		1	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58996944	58996944	__UNKNOWN__	IGR	SNP	C	C	A			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:58996944C>A			NA	NA				None (None upstream) : SPRY3 (103535 downstream)						NA		NA									NA						tgatataccacttgtcaaggc	0.493	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58996944C>A		NA		hg19		0.02	-0.149143	CCAxTTG	UNCOVERED																																																																																			NOVEL					0			5	2.708812	KEEP	19	0	0	9	318	CC	0	0	0			2	25	76	0	0	6.895633	4	60	152	48		0.333333	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59002047	59002047	__UNKNOWN__	IGR	SNP	C	C	G	rs6568352		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59002047C>G			NA	NA				None (None upstream) : SPRY3 (98432 downstream)						NA		NA									NA						TCCCTTCAGTCTACAGGGACT	0.423	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59002047C>G		NA		hg19		0.02	6.851771	AGTxTAC	COVERED																																																																																			NOVEL					0			12	6.922341	KEEP	0	0	0	23	819	CC	0.999892	0.999892	0			9	60	337	0	0	27.758857	41	60	1543	255		0.18	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59002171	59002171	__UNKNOWN__	IGR	SNP	C	C	A	rs6568350	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59002171C>A			NA	NA				None (None upstream) : SPRY3 (98308 downstream)						NA		NA									NA						GGCTCCTGTACAGAGAAGCGT	0.408	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59002171C>A		NA		hg19		0.02	26.412776	GTAxAGA	COVERED																																																																																			NOVEL					0			11	3.37256	KEEP	3	10	298	116	4185	CC	1	1	0			46	60	1696	0	0	140.438038	196	60	7421	956		0.190083	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59007477	59007477	__UNKNOWN__	IGR	SNP	G	G	A	rs7067285		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59007477G>A			NA	NA				None (None upstream) : SPRY3 (93002 downstream)						NA		NA									NA						ctgtcaccccggctagagtgc	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59007477G>A		NA		hg19		0.02	-0.2544	CCCxGCT	COVERED																																																																																			NOVEL					0			2	3.009433	KEEP	0	0	0	10	335	GG	0.992708	0.663648	0			3	60	114	0	0	9.232683	16	60	551	44		0.157895	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59015741	59015741	__UNKNOWN__	IGR	SNP	T	T	C	rs370514953		LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59015741T>C			NA	NA				None (None upstream) : SPRY3 (84738 downstream)						NA		NA									NA						AGCTCTCATGTctgggtgtgg	0.448	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59015741T>C		NA		hg19		0.02	-0.429883	ATGxCTG	COVERED																																																																																			NOVEL					0			4	3.900428	KEEP	0	0	0	13	371	TT	0.994391	0.949137	0			6	60	225	0	0	18.091761	33	60	1186	80		0.153846	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59015755	59015755	__UNKNOWN__	IGR	SNP	C	C	T	rs78635756	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59015755C>T			NA	NA				None (None upstream) : SPRY3 (84724 downstream)						NA		NA									NA						ggtgtggtggctcatgcctgt	0.453	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59015755C>T		NA		hg19		0.02	-0.421121	TGGxTCA	COVERED																																																																																			NOVEL					0			3	4.167194	KEEP	1	0	0	14	455	CC	0.994391	0.943082	0			10	60	360	0	0	31.979981	23	60	893	82		0.30303	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59027271	59027271	__UNKNOWN__	IGR	SNP	C	C	T			LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59027271C>T			NA	NA				None (None upstream) : SPRY3 (73208 downstream)						NA		NA									NA						tgcactccagcctgggcgaca	0.468	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59027271C>T		NA		hg19		0.02	-0.201788	CAGxCTG	COVERED																																																																																			NOVEL					0			4	3.243791	KEEP	1	1	32	22	732	CC	0.999879	0.490485	0			4	60	152	0	0	12.762246	16	60	611	57		0.2	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59030445	59030445	__UNKNOWN__	IGR	SNP	G	G	T	rs12171825	byFrequency	LTS-018_T	LTS-018_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-018_FF_T	LTS-018_FFPE2_N	g.chrY:59030445G>T			NA	NA				None (None upstream) : SPRY3 (70034 downstream)						NA		NA									NA						ctgcagcctgggtaacaaagc	0.463	NA	NA												NA	NA	NA	NA	NA			NA	NA	NA	NA	NA		NA		NA	NA	NA	NA	NA	NA	NA	NA						NA		NA				0							NA						NA	NA	NA	NA		NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59030445G>T		NA		hg19		0.02	-0.1316	CTGxGTA	COVERED																																																																																			NOVEL					0			4	2.407458	KEEP	1	0	0	8	271	AG	0.99257	0.22747	0			2	60	78	0	0	6.406263	10	60	380	32		0.166667	0.229173
MT-TV	4577	__UNKNOWN__	__UNKNOWN__	M	1613	1613	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrM:1613G>A	ENST00000387342.1	+	0	12									mitochondrially encoded tRNA valine	NA		NA									NA						CCAGAGTGTAGCTTAACACAA	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000210077	ENSG00000210077	4577		ncRNAs / Transfer RNA, mitochondrial	7500	non-coding RNA	RNA, transfer		590105	tRNA valine	MTTV	NA		Standard			NA	Approved	trnV				ENST00000387342.1:	chrM.hg19:g.1613G>A		NA		hg19		0.02	-0.149125	GTAxCTT	COVERED																																																																																			NOVEL	MT-TV-201	KNOWN	basic	Mt_tRNA	NA	Mt_tRNA		4	2.698509	KEEP	1	0	0	9	257	GG	0.99257	0.289832	0		+	6	60	179	0	0	15.968493	11	60	383	38	ENST00000387342.1	0.352941	0.292001
AL645608.2	0	__UNKNOWN__	__UNKNOWN__	1	818484	818484	__UNKNOWN__	Intron	SNP	G	G	C	rs142231141		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:818484G>C	ENST00000594233.1	+	1	16										NA		NA									NA						taggattacaggcatgtgcca	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000594233.1:c.16+426G>C	chr1.hg19:g.818484G>C		NA		hg19		0.02	-0.184194	ACAxGCA	COVERED																																																																																			NOVEL	AL645608.2-201	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding		16	3.309533	KEEP	4	0	0	11	327	GG	0.992708	0.454419	0		+	3	60	101	0	0	8.732843	8	60	251	49	ENST00000594233.1	0.272727	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	825714	825714	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:825714C>G			NA	NA				AL645608.2 (5731 upstream) : RP11-54O7.16 (14499 downstream)						NA		NA									NA						cttgacttctcaattgatttc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.825714C>G		NA		hg19		0.02	-0.429863	TCTxAAT	COVERED																																																																																			NOVEL					0			27	7.22215	KEEP	2	0	0	24	756	CC	0.999892	0.954388	0			3	60	96	0	0	7.772003	12	60	409	114		0.2	0.954491
C1orf159	54991	__UNKNOWN__	__UNKNOWN__	1	1032835	1032835	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1032835T>C	ENST00000421241.2	-	2	39				C1orf159_ENST00000379319.1_Intron|C1orf159_ENST00000437760.1_Intron|C1orf159_ENST00000482816.1_Intron|C1orf159_ENST00000379339.1_Intron|C1orf159_ENST00000294576.5_Intron|C1orf159_ENST00000448924.1_Intron	NM_017891.4	NP_060361.4	Q96HA4	CA159_HUMAN	chromosome 1 open reading frame 159	NA		NA				integral component of membrane (GO:0016021)					NA	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.96e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.77e-22)|Colorectal(212;6.51e-05)|COAD - Colon adenocarcinoma(227;0.000214)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		ctctgtcgcctgggctggagt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128434	CCDS7.2	1p36.33	2008-02-05			ENSG00000131591	ENSG00000131591	54991			26062	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_017891	NM_017891	NA	Approved	FLJ20584	uc001acu.2	Q96HA4	OTTHUMG00000000745	ENST00000421241.2:c.135-5352A>G	chr1.hg19:g.1032835T>C		NA	B3KQ46|Q5T2W6|Q6UX67|Q6ZR77|Q9NWV0	hg19	CCDS7.2	0.02	-0.122802	GCCxGGG	COVERED																																																																																			NOVEL	C1orf159-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001852.2	1	2.406335	KEEP	0	0	0	8	225	TT	0.99257	0.194853	0		-	3	60	104	0	0	8.672761	11	60	337	34	ENST00000421241.2	0.214286	0.196312
C1orf159	54991	__UNKNOWN__	__UNKNOWN__	1	1032836	1032836	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1032836G>A	ENST00000421241.2	-	2	39				C1orf159_ENST00000379319.1_Intron|C1orf159_ENST00000437760.1_Intron|C1orf159_ENST00000482816.1_Intron|C1orf159_ENST00000379339.1_Intron|C1orf159_ENST00000294576.5_Intron|C1orf159_ENST00000448924.1_Intron	NM_017891.4	NP_060361.4	Q96HA4	CA159_HUMAN	chromosome 1 open reading frame 159	NA		NA				integral component of membrane (GO:0016021)					NA	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.96e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.77e-22)|Colorectal(212;6.51e-05)|COAD - Colon adenocarcinoma(227;0.000214)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		tctgtcgcctgggctggagtg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128434	CCDS7.2	1p36.33	2008-02-05			ENSG00000131591	ENSG00000131591	54991			26062	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_017891	NM_017891	NA	Approved	FLJ20584	uc001acu.2	Q96HA4	OTTHUMG00000000745	ENST00000421241.2:c.135-5353C>T	chr1.hg19:g.1032836G>A		NA	B3KQ46|Q5T2W6|Q6UX67|Q6ZR77|Q9NWV0	hg19	CCDS7.2	0.02	-0.122814	CCTxGGC	COVERED																																																																																			NOVEL	C1orf159-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001852.2	1	2.407096	KEEP	0	0	0	8	244	GG	0.99257	0.194853	0		-	4	60	122	0	0	10.470846	10	60	351	34	ENST00000421241.2	0.285714	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	1383237	1383237	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1383237T>C			NA	NA				VWA1 (4975 upstream) : ATAD3C (1831 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.1383237T>C		NA		hg19		0.02	-0.18418	TCAxGCC	COVERED																																																																																			NOVEL					0			6	5.113439	KEEP	4	0	0	17	476	TT	0.994391	0.421102	0			4	60	135	0	0	10.968857	17	60	495	58		0.190476	0.423478
ATAD3C	219293	__UNKNOWN__	__UNKNOWN__	1	1404813	1404813	__UNKNOWN__	3'UTR	SNP	T	T	C	rs2936657		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1404813T>C	ENST00000378785.2	+	0	3134					NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	NA		NA					ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		gcctggatgatagagtgagac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915	219293		ATPases / AAA-type	32151	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001039211	NM_001039211	NA	Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.*903T>C	chr1.hg19:g.1404813T>C		NA	Q8N1Z5	hg19	CCDS44039.1	0.02	-0.33323	TGAxAGA	COVERED																																																																																			NOVEL	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001279.3	11	6.013099	KEEP	0	0	0	20	523	TT	0.999869	0.877593	0		+	3	60	97	1	1	6.810132	29	60	817	83	ENST00000378785.2	0.09375	0.877708
SSU72	29101	__UNKNOWN__	__UNKNOWN__	1	1479923	1479923	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1479923G>A	ENST00000291386.3	-	3	676					NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	NA		NA			dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		acttgaacccgggaggcagag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075	29101			25016	protein-coding gene	gene with protein product		NA	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)		NA	15125841, 15659578	Standard	NM_014188	NM_014188	NA	Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.364+319C>T	chr1.hg19:g.1479923G>A		NA	Q9BZS6|Q9H933	hg19	CCDS32.1	0.02	-0.342032	CCCxGGA	COVERED																																																																																			NOVEL	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001366.1	4	2.811641	KEEP	3	4	109	48	1246	GG	1	0.865745	0		-	4	60	101	0	0	6.616863	31	60	945	97	ENST00000291386.3	0.114286	0.865745
SSU72	29101	__UNKNOWN__	__UNKNOWN__	1	1480003	1480003	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1480003C>A	ENST00000291386.3	-	3	676					NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	NA		NA			dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		tctcaaaaaacaaaacaaaaa	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075	29101			25016	protein-coding gene	gene with protein product		NA	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)		NA	15125841, 15659578	Standard	NM_014188	NM_014188	NA	Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.364+239G>T	chr1.hg19:g.1480003C>A		NA	Q9BZS6|Q9H933	hg19	CCDS32.1	0.02	2.824264	AAAxAAA	COVERED																																																																																			NOVEL	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001366.1	67	9.685873	KEEP	0	14	346	155	4811	CC	1	1	0		-	11	60	322	1	2	21.331739	113	60	3937	456	ENST00000291386.3	0.08871	1
SSU72	29101	__UNKNOWN__	__UNKNOWN__	1	1480008	1480008	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1480008C>A	ENST00000291386.3	-	3	676					NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	NA		NA			dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)			large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		aaaaacaaaacaaaaaaaCAC	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075	29101			25016	protein-coding gene	gene with protein product		NA	Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)		NA	15125841, 15659578	Standard	NM_014188	NM_014188	NA	Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.364+234G>T	chr1.hg19:g.1480008C>A		NA	Q9BZS6|Q9H933	hg19	CCDS32.1	0.02	2.736502	AAAxAAA	COVERED																																																																																			NOVEL	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001366.1	74	19.123267	KEEP	0	11	295	168	5248	CC	1	1	0		-	6	60	178	1	2	10.061226	127	60	4400	477	ENST00000291386.3	0.045113	1
SLC35E2B	728661	__UNKNOWN__	__UNKNOWN__	1	1599812	1599812	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs12729295		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1599812C>T	ENST00000378662.1	-	9	1694	c.934G>A	c.(934-936)Gtc>Atc	p.V312I	SLC35E2B_ENST00000234800.6_Missense_Mutation_p.V312I			P0CK96	S352B_HUMAN	solute carrier family 35, member E2B	312		NA		V -> I (in Ref. 1; BAA32292, 3; BAG54222 and 4; CAI56761). {ECO:0000305}.		integral component of membrane (GO:0016021)				kidney(1)|lung(1)	2						TACGCCGTGACGCTCTGAAGG	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													32	44	41			NA	NA	1		NA											NA				1599812		692	1578	2270	SO:0001583	missense				CCDS44041.1	1p36.33	2013-05-22			ENSG00000189339	ENSG00000189339	728661		Solute carriers	33941	protein-coding gene	gene with protein product		NA			NA		Standard		XM_006710870	NA	Approved		uc001ahg.4	P0CK96	OTTHUMG00000078639	ENST00000378662.1:c.934G>A	chr1.hg19:g.1599812C>T	ENSP00000367931:p.Val312Ile	NA	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q9Y3J8	hg19	CCDS44041.1	0.02	-0.350857	TGAxGCT	COVERED	1212	0.554945054945055	231	0.4695121951219512	225	0.6215469613259669	288	0.5034965034965035	468	0.6174142480211082	c	8.520	0.868488	0.17322	.	.	ENSG00000189339	ENST00000378662;ENST00000234800	T;T	0.62498	0.02;0.02	5.07	5.07	0.68467	Domain of unknown function DUF250 (1);	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	L	0.28014	0.82	0.22873	P	0.99862843	B	0.32781	0.384	B	0.25884	0.064	T	0.30297	-0.9983	9	0.02654	T	1	-59.6953	11.3121	0.49370	0.0:0.9165:0.0:0.0835	rs12729295	312	P0CK96	S352B_HUMAN	I	312	ENSP00000367931:V312I;ENSP00000234800:V312I	ENSP00000234800:V312I	V	-	1	0	SLC35E2B	1589675	0.998000	0.40836	0.998000	0.56505	0.212000	0.24457	3.705000	0.54823	2.518000	0.84900	0.563000	0.77884	GTC	NOVEL	SLC35E2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000171589.1	1	2.707816	KEEP	32	0	0	9	268	CC	0.99257	0.871187	0		-	6	40	158	0	0	11.325727	34	50	1131	110	ENST00000378662.1	0.15	0.877708
GNB1	2782	__UNKNOWN__	__UNKNOWN__	1	1724242	1724242	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1724242C>T	ENST00000378609.4	-	8	829					NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	NA		NA			adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		cggaggctcacgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369	2782		WD repeat domain containing	4396	protein-coding gene	gene with protein product		139380			NA		Standard	NM_002074	NM_002074	NA	Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.497+441G>A	chr1.hg19:g.1724242C>T		NA	B1AJZ7|P04697|P04901|Q1RMY8	hg19	CCDS34.1	0.02	-0.017536	TCAxGCC	UNCOVERED																																																																																			NOVEL	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000002762.3	2	2.405797	KEEP	0	0	0	8	227	CC	0.99257	0	0		-	2	51	54	0	0	6.352461	0	0	0	13	ENST00000378609.4	1	0
C1orf222	0	__UNKNOWN__	__UNKNOWN__	1	1931327	1931327	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:1931327G>A	ENST00000434971.2	-	1	14							Q69YW0	CA222_HUMAN		NA		NA								breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)	11	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		cctacaggccgggcgcggtgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000434971.2:c.18+3812C>T	chr1.hg19:g.1931327G>A		NA		hg19		0.02	-0.131559	GCCxGGC	COVERED																																																																																			NOVEL	C1orf222-201	KNOWN	basic	protein_coding	NA	protein_coding		6	4.211019	KEEP	4	0	0	14	402	GG	0.995343	0.228106	0		-	3	60	84	1	0	6.782161	10	60	313	44	ENST00000434971.2	0.230769	0.229173
ACOT7	11332	__UNKNOWN__	__UNKNOWN__	1	6431043	6431043	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6431043A>G	ENST00000377855.2	-	1	320				ACOT7_ENST00000545482.1_Intron|ACOT7_ENST00000608083.1_Intron|ACOT7_ENST00000361521.4_Intron	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	NA		NA			coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		gctaatttttatatttttagt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(74;673 1226 4974 11850 13190)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021	11332		Acyl CoA thioesterases	24157	protein-coding gene	gene with protein product	brain acyl CoA hydrolase	602587			NA	10578051, 16103133, 16940157	Standard	NM_007274	XM_005263427	NA	Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.173+14510T>C	chr1.hg19:g.6431043A>G		NA	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	hg19	CCDS65.1	0.02	-0.043858	TTTxTAT	UNCOVERED																																																																																			NOVEL	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003773.1	5	3.607958	KEEP	0	0	0	12	318	AA	0.993634	0.02392	0		-	2	40	68	0	0	6.550141	2	60	61	20	ENST00000377855.2	0.5	0.024074
NOL9	79707	__UNKNOWN__	__UNKNOWN__	1	6583739	6583739	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6583739G>A	ENST00000377705.5	-	0	4316					NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	NA		NA			maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		GGTCTGACCGGCACAAGCTAG	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408	79707			26265	protein-coding gene	gene with protein product	polynucleotide 5'-kinase	NA			NA	21063389	Standard	NM_024654	NM_024654	NA	Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.*2175C>T	chr1.hg19:g.6583739G>A		NA	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	hg19	CCDS80.1	0.02	0.763136	CCGxCAC	COVERED																																																																																			NOVEL	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000002625.1	18	13.238569	KEEP	0	0	0	44	1325	GG	1	0.999559	0		-	5	60	133	0	0	7.474169	79	60	2680	162	ENST00000377705.5	0.059524	0.999559
NOL9	79707	__UNKNOWN__	__UNKNOWN__	1	6597921	6597921	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6597921A>G	ENST00000377705.5	-	6	1108					NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	NA		NA			maturation of 5.8S rRNA (GO:0000460)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|polynucleotide 5'-hydroxyl-kinase activity (GO:0051731)|RNA binding (GO:0003723)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|skin(2)|urinary_tract(1)	19	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;2.46e-35)|all_epithelial(116;1.41e-22)|all_lung(118;7.59e-07)|Lung NSC(185;4.28e-06)|Colorectal(325;4.52e-05)|Breast(487;0.000353)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.47e-07)|COAD - Colon adenocarcinoma(227;1.47e-05)|Kidney(185;5.27e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|BRCA - Breast invasive adenocarcinoma(365;0.00113)|STAD - Stomach adenocarcinoma(132;0.0017)|READ - Rectum adenocarcinoma(331;0.0649)		ggtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091284	CCDS80.1	1p36.31	2012-05-02			ENSG00000162408	ENSG00000162408	79707			26265	protein-coding gene	gene with protein product	polynucleotide 5'-kinase	NA			NA	21063389	Standard	NM_024654	NM_024654	NA	Approved	FLJ23323, NET6, Grc3	uc001ans.3	Q5SY16	OTTHUMG00000000904	ENST00000377705.5:c.1075+3968T>C	chr1.hg19:g.6597921A>G		NA	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	hg19	CCDS80.1	0.02	-0.140336	CACxCCT	UNCOVERED																																																																																			NOVEL	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000002625.1	4	2.406475	KEEP	3	0	0	8	226	AA	0	0	0		-	3	60	99	0	0	8.072252	12	60	366	41	ENST00000377705.5	0.2	0.260965
ZBTB48	3104	__UNKNOWN__	__UNKNOWN__	1	6641580	6641580	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6641580C>T	ENST00000377674.4	+	2	848					NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	NA		NA			transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		aaaaattagccgggtgtggtg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(125;1449 1657 4031 29866 49542)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859	3104		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	4930	protein-coding gene	gene with protein product		165270	GLI-Kruppel family member HKR3	HKR3	NA	2850480, 8661141	Standard	NM_005341	NM_001278647	NA	Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.690+221C>T	chr1.hg19:g.6641580C>T		NA	Q5SY19	hg19	CCDS84.1	0.02	-0.140341	AGCxGGG	COVERED																																																																																			NOVEL	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000004193.1	3	2.40633	KEEP	0	0	0	8	230	CC	0.99257	0.259026	0		+	3	60	93	0	1	7.472295	12	60	375	35	ENST00000377674.4	0.2	0.260965
KLHL21	9903	__UNKNOWN__	__UNKNOWN__	1	6654866	6654866	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6654866G>A	ENST00000377658.4	-	3	1552				KLHL21_ENST00000463043.1_Intron|KLHL21_ENST00000377663.3_3'UTR|KLHL21_ENST00000467612.1_Intron	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	NA		NA			chromosome passenger complex localization to spindle midzone (GO:0035853)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|regulation of cytokinesis (GO:0032465)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|polar microtubule (GO:0005827)				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|prostate(2)	8	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.36e-07)|COAD - Colon adenocarcinoma(227;1.4e-05)|Kidney(185;4.95e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000528)|KIRC - Kidney renal clear cell carcinoma(229;0.000927)|STAD - Stomach adenocarcinoma(132;0.0172)|READ - Rectum adenocarcinoma(331;0.0644)		agacaggagggtcacttgagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK090472	CCDS30575.1	1p36	2013-01-30	2013-01-30		ENSG00000162413	ENSG00000162413	9903		Kelch-like, BTB/POZ domain containing	29041	protein-coding gene	gene with protein product		NA	kelch-like 21 (Drosophila)		NA		Standard	NM_014851	XM_005263542	NA	Approved	KIAA0469	uc001aoa.3	Q9UJP4	OTTHUMG00000001437	ENST00000377658.4:c.1500+678C>T	chr1.hg19:g.6654866G>A		NA	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	hg19	CCDS30575.1	0.02	1.155322	AGGxTCA	COVERED																																																																																			NOVEL	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000004188.1	18	3.229415	KEEP	0	7	181	75	2251	GG	1	0.999559	0		-	6	60	171	0	0	10.687555	75	60	2500	210	ENST00000377658.4	0.074074	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	6763720	6763720	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6763720G>A			NA	NA				DNAJC11 (1736 upstream) : RP11-242F24.1 (20976 downstream)						NA		NA									NA						tagtagagacggggtttcacc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.6763720G>A		NA		hg19		0.02	-0.149102	GACxGGG	COVERED																																																																																			NOVEL					0			4	3.308429	KEEP	7	0	0	11	312	GG	0.99257	0.289832	0			3	27	88	0	0	6.879343	13	60	400	35		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	6823054	6823054	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:6823054T>G			NA	NA				snoU13 (10173 upstream) : RP11-312B8.1 (20897 downstream)						NA		NA									NA						gattacaggcttgagccactg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.6823054T>G		NA		hg19		0.02	-0.07893	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			6	2.706597	KEEP	0	0	0	9	244	TT	0.99254	0.076759	0			3	60	99	0	0	8.843968	6	60	174	22		0.333333	0.077336
CAMTA1	23261	__UNKNOWN__	__UNKNOWN__	1	7002515	7002515	__UNKNOWN__	Intron	SNP	C	C	T	rs112801534	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:7002515C>T	ENST00000303635.7	+	3	441				CAMTA1_ENST00000439411.2_Intron	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		tccaggagttcgagagcagcc	0.478		NA	T	WWTR1	epitheliod hemangioendothelioma								C|||	112	0.0223642	0.0008	0.1254	5008	,	,	NA	13180	0.003	NA	0.0149	False	NA	,,,	NA	NA	NA	2504	0.0061	NA	NA	NA			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735	23261			18806	protein-coding gene	gene with protein product		611501			NA	11925432	Standard	NM_015215	NM_001195563	NA	Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.234+117245C>T	chr1.hg19:g.7002515C>T		NA	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	hg19	CCDS30576.1	0.02	-0.122795	GTTxGAG	COVERED																																																																																			NOVEL	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003588.3	7	2.707666	KEEP	0	0	0	9	268	CC	0.99254	0.194847	0		+	3	60	85	0	0	7.00098	9	60	296	36	ENST00000303635.7	0.25	0.196312
TNFRSF9	3604	__UNKNOWN__	__UNKNOWN__	1	7980457	7980457	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:7980457T>C	ENST00000377507.3	-	0	1372					NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	NA		NA			apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		gcagttcatgtctgtaatccc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249	3604		Tumor necrosis factor receptor superfamily, CD molecules	11924	protein-coding gene	gene with protein product		602250		ILA	NA	8262389, 8639902	Standard		NM_001561	NA	Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.*438A>G	chr1.hg19:g.7980457T>C		NA		hg19	CCDS92.1	0.02	-0.403381	ATGxCTG	COVERED																																																																																			NOVEL	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003622.1	7	12.324188	KEEP	1	0	0	41	1107	TT	1	0.934492	0		-	4	60	133	1	1	9.432053	39	60	1139	102	ENST00000377507.3	0.093023	0.934492
PARK7	11315	__UNKNOWN__	__UNKNOWN__	1	8038011	8038011	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:8038011A>G	ENST00000493678.1	+	6	476				PARK7_ENST00000377493.5_Intron|PARK7_ENST00000377491.1_Intron|PARK7_ENST00000377488.1_Intron|PARK7_ENST00000338639.5_Intron			Q99497	PARK7_HUMAN	parkinson protein 7	NA		NA			adult locomotory behavior (GO:0008344)|autophagy (GO:0006914)|cellular response to glyoxal (GO:0036471)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to oxidative stress (GO:0034599)|dopamine uptake involved in synaptic transmission (GO:0051583)|glycolate biosynthetic process (GO:0046295)|glyoxal catabolic process (GO:1903190)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|lactate biosynthetic process (GO:0019249)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|methylglyoxal catabolic process to D-lactate (GO:0019243)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001268)|negative regulation of death-inducing signaling complex assembly (GO:1903073)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein acetylation (GO:1901984)|negative regulation of protein binding (GO:0032091)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of protein K48-linked deubiquitination (GO:1903094)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of TRAIL-activated apoptotic signaling pathway (GO:1903122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|negative regulation of ubiquitin-specific protease activity (GO:2000157)|positive regulation of androgen receptor activity (GO:2000825)|positive regulation of dopamine biosynthetic process (GO:1903181)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of L-dopa biosynthetic process (GO:1903197)|positive regulation of L-dopa decarboxylase activity (GO:1903200)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of oxidative phosphorylation uncoupler activity (GO:2000277)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of pyrroline-5-carboxylate reductase activity (GO:1903168)|positive regulation of superoxide dismutase activity (GO:1901671)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine 3-monooxygenase activity (GO:1903178)|protein stabilization (GO:0050821)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of fibril organization (GO:1902903)|regulation of inflammatory response (GO:0050727)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of neuron apoptotic process (GO:0043523)|single fertilization (GO:0007338)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|cupric ion binding (GO:1903135)|cuprous ion binding (GO:1903136)|cytokine binding (GO:0019955)|enzyme binding (GO:0019899)|glyoxalase (glycolic acid-forming) activity (GO:1990422)|glyoxalase III activity (GO:0019172)|identical protein binding (GO:0042802)|L-dopa decarboxylase activator activity (GO:0036478)|mRNA binding (GO:0003729)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|peptidase activity (GO:0008233)|peroxidase activity (GO:0004601)|peroxiredoxin activity (GO:0051920)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|repressing transcription factor binding (GO:0070491)|RNA binding (GO:0003723)|scaffold protein binding (GO:0097110)|small protein activating enzyme binding (GO:0044388)|small protein conjugating enzyme binding (GO:0044390)|superoxide dismutase copper chaperone activity (GO:0016532)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|tyrosine 3-monooxygenase activator activity (GO:0036470)|ubiquitin-specific protease binding (GO:1990381)			large_intestine(1)	1	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;1.28e-70)|GBM - Glioblastoma multiforme(8;3.05e-36)|Colorectal(212;6.83e-08)|COAD - Colon adenocarcinoma(227;7.51e-06)|Kidney(185;5.22e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000414)|KIRC - Kidney renal clear cell carcinoma(229;0.000967)|STAD - Stomach adenocarcinoma(132;0.00102)|READ - Rectum adenocarcinoma(331;0.0649)		gtagagatggagtttcaccat	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D61380	CCDS93.1	1p36.23	2014-04-11	2011-07-21		ENSG00000116288	ENSG00000116288	11315		Parkinson disease	16369	protein-coding gene	gene with protein product		NA	Parkinson disease (autosomal recessive, early onset) 7		NA	11462174, 9070310	Standard	NM_007262	NM_007262	NA	Approved	DJ-1, DJ1	uc001aox.4	Q99497	OTTHUMG00000001210	ENST00000493678.1:c.409+213A>G	chr1.hg19:g.8038011A>G		NA	B2R4Z1|O14805|Q6DR95|Q7LFU2	hg19	CCDS93.1	0.02	-0.078938	TGGxGTT	UNCOVERED																																																																																			NOVEL	PARK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003577.1	10	2.405831	KEEP	1	0	0	8	218	AC	0.99257	0.076761	0		+	2	47	66	0	0	6.725493	1	60	25	19	ENST00000493678.1	0.666667	0.077336
GPR157	80045	__UNKNOWN__	__UNKNOWN__	1	9169172	9169172	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9169172T>C	ENST00000377411.4	-	2	740				GPR157_ENST00000414642.2_Intron	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		gatggagtcttgctctgtggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758	80045		GPCR / Class B : Orphans	23687	protein-coding gene	gene with protein product		NA			NA	10574461	Standard	NM_024980	XM_005263496	NA	Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.597+2162A>G	chr1.hg19:g.9169172T>C		NA	A2A334|Q8WWB8|Q9HA73	hg19	CCDS100.2	0.02	-0.096479	TCTxGCT	UNCOVERED																																																																																			NOVEL	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000127658.2	1	3.238402	KEEP	0	1	26	20	540	TT	0.999869	0.12042	0		-	3	45	88	0	0	7.743392	6	60	180	38	ENST00000377411.4	0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	9265523	9265523	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9265523C>T			NA	NA				RP3-510D11.1 (2845 upstream) : H6PD (29310 downstream)						NA		NA									NA						ccacgcctggctaattttgta	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.9265523C>T		NA		hg19		0.02	-0.114017	TGGxTAA	UNCOVERED																																																																																			NOVEL					0			8	2.406224	KEEP	3	0	0	8	233	CC	0	0	0			4	52	106	0	1	9.375803	7	60	236	25		0.363636	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	9287653	9287653	__UNKNOWN__	IGR	SNP	C	C	T	rs564891893	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9287653C>T			NA	NA				RP3-510D11.1 (24975 upstream) : H6PD (7180 downstream)						NA		NA									NA						gcagaggttgcggtgagccaa	0.483		NA											C|||	10	0.00199681	0.0008	0.0072	5008	,	,	NA	13579	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.9287653C>T		NA		hg19		0.02	-0.061387	TTGxGGT	UNCOVERED																																																																																			NOVEL					0			7	2.406824	KEEP	5	0	0	8	235	CG	0	0	0			3	46	77	0	0	7.667434	2	60	63	22		0.6	0.043787
SPSB1	80176	__UNKNOWN__	__UNKNOWN__	1	9359447	9359447	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9359447T>C	ENST00000328089.6	+	1	192					NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	NA		NA			intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		cctgtaatcctagcacttcag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621	80176			30628	protein-coding gene	gene with protein product		611657			NA	15713673, 12076535	Standard	NM_025106	NM_025106	NA	Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.-150+6317T>C	chr1.hg19:g.9359447T>C		NA	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	hg19	CCDS102.1	0.02	-0.201733	TCCxAGC	COVERED																																																																																			NOVEL	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000003727.2	9	3.007344	KEEP	0	0	0	10	273	TT	0.992708	0.486967	0		+	3	60	103	0	0	7.992069	18	60	538	52	ENST00000328089.6	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	9568493	9568493	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9568493A>C			NA	NA				RP13-392I16.1 (4963 upstream) : SLC25A33 (31047 downstream)						NA		NA									NA						atgatctcggatcactgcaac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.9568493A>C		NA		hg19		0.02	-0.078938	CGGxTCA	UNCOVERED																																																																																			NOVEL					0			6	2.673487	KEEP	2	0	0	9	215	AA	0.99257	0.076761	0			2	32	72	0	0	6.335842	5	60	145	27		0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	9587260	9587260	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9587260T>C			NA	NA				RP13-392I16.1 (23730 upstream) : SLC25A33 (12280 downstream)						NA		NA									NA						cctggccgggtgcggtggctc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.9587260T>C		NA		hg19		0.02	-0.289397	GGGxGCG	COVERED																																																																																			NOVEL					0			7	2.634083	KEEP	7	1	26	18	455	TT	0.995343	0.757343	0			3	60	105	0	0	7.567105	30	60	863	80		0.090909	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	9587300	9587300	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9587300C>T			NA	NA				RP13-392I16.1 (23770 upstream) : SLC25A33 (12240 downstream)						NA		NA									NA						tttgggaggccgaggcgggtg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.9587300C>T		NA		hg19		0.02	-0.210517	GGCxGAG	COVERED																																																																																			NOVEL					0			10	5.114283	KEEP	12	0	0	17	513	CC	0.993072	0.518544	0			4	60	111	0	0	8.314659	20	60	666	72		0.166667	0.522161
PIK3CD	5293	__UNKNOWN__	__UNKNOWN__	1	9788071	9788071	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9788071T>C	ENST00000377346.4	+	0	4297				PIK3CD_ENST00000536656.1_3'UTR	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	NA		NA			adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	ccatgttggctgggctggtct	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	5293	2.7.1.153		8977	protein-coding gene	gene with protein product	phosphatidylinositol 3-kinase, catalytic, delta polypeptide, phosphoinositide-3-kinase C	602839	phosphoinositide-3-kinase, catalytic, delta polypeptide		NA	9113989, 9455486	Standard	NM_005026	NM_005026	NA	Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.*967T>C	chr1.hg19:g.9788071T>C		NA	A6NCG0|G1FFP1|O15445|Q5SR49	hg19	CCDS104.1	0.02	-0.385875	GGCxGGG	COVERED																																																																																			NOVEL	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000004235.1	1	2.402506	KEEP	0	0	0	8	198	TT	0.99257	0.911349	0		+	3	60	98	0	0	6.509139	40	60	1169	56	ENST00000377346.4	0.069767	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	9898129	9898129	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:9898129T>C			NA	NA				CLSTN1 (13545 upstream) : CTNNBIP1 (10204 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.9898129T>C		NA		hg19		0.02	-0.166639	TCAxGCC	COVERED																																																																																			NOVEL					0			6	3.608953	KEEP	0	0	0	12	327	TT	0.993634	0.351693	0			3	60	101	0	0	8.091784	14	60	411	44		0.176471	0.353947
UBE4B	10277	__UNKNOWN__	__UNKNOWN__	1	10179208	10179208	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:10179208A>G	ENST00000253251.8	+	8	1790				UBE4B_ENST00000343090.6_Intron|UBE4B_ENST00000475795.1_Intron|UBE4B_ENST00000377157.3_Intron					ubiquitination factor E4B	NA		NA								NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		caaagtgctgagattacaggc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939	10277		U-box domain containing	12500	protein-coding gene	gene with protein product		613565	ubiquitination factor E4B (homologous to yeast UFD2), ubiquitination factor E4B (UFD2 homolog, yeast)		NA	9734811, 10089879	Standard	NM_006048	NM_006048	NA	Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.952-363A>G	chr1.hg19:g.10179208A>G		NA		hg19	CCDS110.1	0.02	-0.149121	CTGxGAT	COVERED																																																																																			NOVEL	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005017.1	5	2.406512	KEEP	0	0	0	8	228	AA	0.99254	0.289823	0		+	3	60	105	0	0	8.772733	11	60	337	40	ENST00000253251.8	0.214286	0.292001
KIF1B	23095	__UNKNOWN__	__UNKNOWN__	1	10360032	10360032	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:10360032C>T	ENST00000377081.1	+	21	2194				KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377093.4_Intron|KIF1B_ENST00000377086.1_Intron|KIF1B_ENST00000377083.1_Intron			O60333	KIF1B_HUMAN	kinesin family member 1B	NA		NA			anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		cggtggctcacgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523	23095		Kinesins, Pleckstrin homology (PH) domain containing	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2	NA	11389829, 10762626	Standard		NM_015074	NA	Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377081.1:c.2115+2728C>T	chr1.hg19:g.10360032C>T		NA	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	hg19		0.02	-0.131568	TCAxGCC	COVERED																																																																																			NOVEL	KIF1B-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000005106.1	5	5.114639	KEEP	0	0	0	17	510	CC	0.999366	0.229028	0		+	3	60	83	0	0	6.681983	10	60	335	47	ENST00000377081.1	0.230769	0.229173
KIF1B	23095	__UNKNOWN__	__UNKNOWN__	1	10361462	10361462	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:10361462C>A	ENST00000377081.1	+	21	2194				KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377093.4_Intron|KIF1B_ENST00000377086.1_Intron|KIF1B_ENST00000377083.1_Intron			O60333	KIF1B_HUMAN	kinesin family member 1B	NA		NA			anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		ggtggctcacccctgtaatcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523	23095		Kinesins, Pleckstrin homology (PH) domain containing	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2	NA	11389829, 10762626	Standard		NM_015074	NA	Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377081.1:c.2115+4158C>A	chr1.hg19:g.10361462C>A		NA	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	hg19		0.02	-0.09649	CACxCCT	UNCOVERED																																																																																			NOVEL	KIF1B-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000005106.1	5	2.708173	KEEP	0	0	0	9	280	CG	0.993072	0.119602	0		+	3	60	89	0	0	7.532163	8	60	268	29	ENST00000377081.1	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	10451565	10451565	__UNKNOWN__	IGR	SNP	C	C	T	rs528148605		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:10451565C>T			NA	NA				RN7SL721P (1212 upstream) : PGD (7560 downstream)						NA		NA									NA						ggtgaaaccccgtctctacta	0.552		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	13718	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.10451565C>T		NA		hg19		0.02	-0.122798	CCCxGTC	COVERED																																																																																			NOVEL					0			4	3.00717	KEEP	1	0	0	10	275	CC	0.992708	0.19488	0			3	60	89	0	0	7.172935	11	60	347	31		0.214286	0.196312
DFFA	1676	__UNKNOWN__	__UNKNOWN__	1	10520072	10520072	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:10520072T>C	ENST00000377038.3	-	0	2538					NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	NA		NA			apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		gaggctgaggtgggtggatca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049	1676			2772	protein-coding gene	gene with protein product	DNA fragmentation factor, 45 kD, alpha subunit	601882	DNA fragmentation factor, 45 kD, alpha polypeptide		NA	9605855, 9108473	Standard	NM_004401	NM_004401	NA	Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.*1475A>G	chr1.hg19:g.10520072T>C		NA	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	hg19	CCDS118.1	0.02	-0.245568	AGGxGGG	COVERED																																																																																			NOVEL	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005418.1	10	2.938661	KEEP	1	1	23	18	492	TT	0.999859	0.641257	0		-	3	60	96	0	0	6.892934	25	60	733	56	ENST00000377038.3	0.107143	0.641347
PEX14	5195	__UNKNOWN__	__UNKNOWN__	1	10649684	10649684	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:10649684G>A	ENST00000356607.4	+	4	249				PEX14_ENST00000538836.1_Intron	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	NA		NA			microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		tgcccaggctggtctcaaact	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655	5195			8856	protein-coding gene	gene with protein product		601791			NA	9653144	Standard		NM_004565	NA	Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.170-9611G>A	chr1.hg19:g.10649684G>A		NA	B2R7N1|B3KML6|B7Z1N2|Q8WX51	hg19	CCDS30582.1	0.02	-0.227988	GCTxGTC	COVERED																																																																																			NOVEL	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005414.1	14	5.416758	KEEP	1	0	0	18	573	GG	0.999859	0.582848	0		+	3	60	87	1	1	6.327788	19	60	653	67	ENST00000356607.4	0.136364	0.58293
TNFRSF8	943	__UNKNOWN__	__UNKNOWN__	1	12129284	12129284	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:12129284G>A	ENST00000263932.2	+	1	285				TNFRSF8_ENST00000417814.2_Intron	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	NA		NA			cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	tgcccaggctggagtgcaatg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949	943		Tumor necrosis factor receptor superfamily, CD molecules	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E	NA	1330892, 1310894	Standard		XM_006711049	NA	Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.63+5566G>A	chr1.hg19:g.12129284G>A		NA	B1AN79|B9EGD9|D3YTD8|Q6P4D9	hg19	CCDS144.1	0.02	-0.087721	GCTxGAG	UNCOVERED																																																																																			NOVEL	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005130.1	6	3.610351	KEEP	3	0	0	12	357	GG	0.99254	0.098977	0		+	3	32	90	0	0	7.943222	6	60	205	25	ENST00000263932.2	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	12800774	12800774	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:12800774T>C			NA	NA				snoU13 (978 upstream) : C1orf158 (5388 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.12800774T>C		NA		hg19		0.02	-0.166655	GTGxTGG	COVERED																																																																																			NOVEL					0			3	2.706854	KEEP	1	0	0	9	250	TT	0.99254	0.351306	0			3	60	99	0	0	7.810091	15	60	460	41		0.166667	0.353947
HNRNPCL1	343069	__UNKNOWN__	__UNKNOWN__	1	12907837	12907837	__UNKNOWN__	Silent	SNP	C	C	T	rs1736811	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:12907837C>T	ENST00000317869.6	-	2	531	c.306G>A	c.(304-306)gcG>gcA	p.A102A		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	102		NA				nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						CGTACATCTCCGCTGCTGATC	0.493		NA											.|||	37	0.00738818	0.0182	0.0072	5008	,	,	NA	19760	0.0	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172	343069		RNA binding motif (RRM) containing	29295	protein-coding gene	gene with protein product		NA		HNRPCL1	NA		Standard	NM_001013631	NM_001013631	NA	Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.306G>A	chr1.hg19:g.12907837C>T		NA	B2RP44	hg19	CCDS30591.1	0.02	1.432423	CTCxGCT	COVERED																																																																																			NOVEL	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005462.1	2	3.60955	KEEP	0	0	0	12	346	CC	0.993634	0.992109	0		-	25	60	714	0	0	65.164792	37	60	1213	122	ENST00000317869.6	0.403226	0.998465
HNRNPCL1	343069	__UNKNOWN__	__UNKNOWN__	1	12908311	12908311	__UNKNOWN__	5'UTR	SNP	C	C	G	rs6657053	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:12908311C>G	ENST00000317869.6	-	0	57					NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	NA		NA				nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						CAAAATGGCTCCCAACAAGAA	0.408		NA											.|||	62	0.0123802	0.0015	0.0259	5008	,	,	NA	18265	0.001	NA	0.0288	False	NA	,,,	NA	NA	NA	2504	0.0123	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172	343069		RNA binding motif (RRM) containing	29295	protein-coding gene	gene with protein product		NA		HNRPCL1	NA		Standard	NM_001013631	NM_001013631	NA	Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.-169G>C	chr1.hg19:g.12908311C>G		NA	B2RP44	hg19	CCDS30591.1	0.02	3.727674	GCTxCCA	COVERED																																																																																			NOVEL	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000005462.1	7	4.179062	KEEP	6	2	60	35	1056	CC	0.999999	0.999999	0		-	8	60	271	0	0	17.956405	119	60	3999	251	ENST00000317869.6	0.062992	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	12949755	12949755	__UNKNOWN__	IGR	SNP	C	C	G	rs28442077		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:12949755C>G			NA	NA				PRAMEF4 (3730 upstream) : PRAMEF10 (2971 downstream)						NA		NA									NA						ttagtagagacagagtttcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.12949755C>G		NA		hg19		0.02	-0.035092	AGAxAGA	UNCOVERED																																																																																			NOVEL					0			7	3.008782	KEEP	5	0	0	10	301	CC	0	0	0			2	30	70	0	0	6.750043	2	28	69	21		0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	13774341	13774341	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:13774341A>G			NA	NA				PRAMEF20 (26538 upstream) : LRRC38 (27103 downstream)						NA		NA									NA						cctgaccaacatggagaaacc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.13774341A>G		NA		hg19		0.02	-0.122794	AACxTGG	COVERED																																																																																			NOVEL					0			5	2.406063	KEEP	1	0	0	8	221	AA	0.99257	0.194853	0			3	25	108	0	0	9.432621	8	60	236	34		0.272727	0.196312
FHAD1	114827	__UNKNOWN__	__UNKNOWN__	1	15724484	15724484	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:15724484A>G	ENST00000358897.4	+	0	4952				FHAD1_ENST00000417793.1_3'UTR	NM_052929.1	NP_443161.1	B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	NA		NA								skin(1)|stomach(1)	2						aaaattagccaggtgtggtgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621	114827			29408	protein-coding gene	gene with protein product		NA			NA	11572484	Standard	NM_052929	NM_052929	NA	Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000358897.4:c.*575A>G	chr1.hg19:g.15724484A>G		NA	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	hg19		0.02	-0.140329	GCCxGGT	COVERED																																																																																			NOVEL	FHAD1-202	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding		6	5.413934	KEEP	0	0	0	18	500	AA	0.999859	0.260928	0		+	3	60	95	0	0	7.672388	12	60	350	38	ENST00000358897.4	0.2	0.260965
RP11-169K16.9	0	__UNKNOWN__	__UNKNOWN__	1	16167568	16167568	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16167568T>C	ENST00000317122.1	-	0	40					NR_024279.1					NA		NA									NA						tcccaaagtgttgggattaca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000317122.1:	chr1.hg19:g.16167568T>C		NA		hg19		0.02	-0.157866	GTGxTGG	COVERED																																																																																			NOVEL	RP11-169K16.9-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000025992.1	8	6.011742	KEEP	4	0	0	20	517	TT	0.999863	0.322762	0		-	3	60	94	0	0	7.479625	13	60	387	60	ENST00000317122.1	0.1875	0.322807
SPEN	23013	__UNKNOWN__	__UNKNOWN__	1	16211726	16211726	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16211726T>G	ENST00000375759.3	+	3	1085					NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		agatggagtctcgctctgttg	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526	23013		RNA binding motif (RRM) containing	17575	protein-coding gene	gene with protein product		613484	SPEN homolog, transcriptional regulator (Drosophila), spen homolog, transcriptional regulator (Drosophila)		NA	10451362, 11331609	Standard	NM_015001	NM_015001	NA	Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.881+8553T>G	chr1.hg19:g.16211726T>G		NA	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	hg19	CCDS164.1	0.02	-0.192957	GTCxCGC	COVERED																																																																																			NOVEL	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025993.1	22	6.615823	KEEP	0	0	0	22	597	TT	0.999879	0.457701	0		+	3	53	106	0	0	8.678834	13	60	382	63	ENST00000375759.3	0.1875	0.457757
SPEN	23013	__UNKNOWN__	__UNKNOWN__	1	16257159	16257159	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs141407539		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16257159G>A	ENST00000375759.3	+	11	4628	c.4424G>A	c.(4423-4425)cGa>cAa	p.R1475Q		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1475		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCAAATTTTCGAAACAACAAA	0.383		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	20471	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0								G	GLN/ARG	1,4397	2.1+/-5.4	0,1,2198	59	64	62		4424	5.3	1	1	dbSNP_134	62	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SPEN	NM_015001.2	43	0,4,6495	AA,AG,GG	NA	0.0349,0.0227,0.0308	probably-damaging	1475/3665	16257159	4,12994	2199	4300	6499	SO:0001583	missense				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526	23013		RNA binding motif (RRM) containing	17575	protein-coding gene	gene with protein product		613484	SPEN homolog, transcriptional regulator (Drosophila), spen homolog, transcriptional regulator (Drosophila)		NA	10451362, 11331609	Standard	NM_015001	NM_015001	NA	Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4424G>A	chr1.hg19:g.16257159G>A	ENSP00000364912:p.Arg1475Gln	NA	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	hg19	CCDS164.1	0.02	1.476256	TTCxAAA	COVERED	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.30	1.598566	0.28445	2.27E-4	3.49E-4	ENSG00000065526	ENST00000375759	T	0.11930	2.73	5.27	5.27	0.74061	.	.	.	.	.	T	0.11750	0.0286	N	0.20986	0.625	0.43439	D	0.99561	P	0.52577	0.954	B	0.40659	0.336	T	0.07947	-1.0746	9	0.33141	T	0.24	-8.5555	19.0911	0.93227	0.0:0.0:1.0:0.0	.	1475	Q96T58	MINT_HUMAN	Q	1475	ENSP00000364912:R1475Q	ENSP00000364912:R1475Q	R	+	2	0	SPEN	16129746	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.357000	0.52277	2.746000	0.94184	0.563000	0.77884	CGA	NOVEL	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025993.1	1	4.81299	KEEP	0	0	0	16	460	GG	0.997832	0.994563	0		+	5	60	145	0	0	9.105801	64	60	2019	119	ENST00000375759.3	0.072464	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16406755	16406755	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16406755G>A			NA	NA				FAM131C (6628 upstream) : EPHA2 (44076 downstream)						NA		NA									NA						cagaggttgcggtgagccgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16406755G>A		NA		hg19		0.02	-0.096475	TGCxGTG	UNCOVERED																																																																																			NOVEL					0			4	2.406654	KEEP	0	0	0	8	238	GG	0.99257	0.119541	0			4	60	113	0	1	10.284489	6	60	197	26		0.4	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16413688	16413688	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16413688A>G			NA	NA				FAM131C (13561 upstream) : EPHA2 (37143 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16413688A>G		NA		hg19		0.02	-0.175236	CACxCCT	COVERED																																																																																			NOVEL					0			9	3.006414	KEEP	0	0	0	10	262	AA	0.992708	0.384582	0			3	60	82	0	0	6.377113	12	60	331	41		0.2	0.387407
RP11-276H7.3	0	__UNKNOWN__	__UNKNOWN__	1	16487796	16487796	__UNKNOWN__	RNA	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16487796G>C	ENST00000426353.1	+	0	161										NA		NA									NA						cggggtttcagcatgttagcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000426353.1:	chr1.hg19:g.16487796G>C		NA		hg19		0.02	-0.096466	TCAxCAT	UNCOVERED																																																																																			NOVEL	RP11-276H7.3-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000085369.1	3	2.406851	KEEP	0	0	0	8	239	GG	0.99257	0.119541	0		+	3	60	101	0	0	8.732849	8	60	247	28	ENST00000426353.1	0.272727	0.120436
FBXO42	54455	__UNKNOWN__	__UNKNOWN__	1	16587410	16587410	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16587410A>G	ENST00000375592.3	-	5	719					NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	NA		NA								autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		tgttgcccagactggtcttaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637	54455		F-boxes /  other	29249	protein-coding gene	gene with protein product		609109			NA	10718198	Standard		XM_006710698	NA	Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.503-4156T>C	chr1.hg19:g.16587410A>G		NA	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	hg19	CCDS30613.1	0.02	-0.306952	CAGxCTG	COVERED																																																																																			NOVEL	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006285.1	16	6.315027	KEEP	0	0	0	21	563	AA	0.999869	0.800141	0		-	3	60	93	0	0	6.369107	30	60	876	81	ENST00000375592.3	0.090909	0.800245
FBXO42	54455	__UNKNOWN__	__UNKNOWN__	1	16625711	16625711	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16625711T>C	ENST00000375592.3	-	4	584				FBXO42_ENST00000478089.1_Intron	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	NA		NA								autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		tttcaccatgttggccaggct	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637	54455		F-boxes /  other	29249	protein-coding gene	gene with protein product		609109			NA	10718198	Standard		XM_006710698	NA	Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.368-4299A>G	chr1.hg19:g.16625711T>C		NA	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	hg19	CCDS30613.1	0.02	-0.32442	ATGxTGG	COVERED																																																																																			NOVEL	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006285.1	68	15.595553	KEEP	51	2	57	72	1886	TT	1	0.835716	0		-	3	40	97	0	0	6.853577	28	60	780	182	ENST00000375592.3	0.096774	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16685833	16685833	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16685833A>G			NA	NA				FBXO42 (6884 upstream) : SZRD1 (7744 downstream)						NA		NA									NA						cgcccgcctcagcctcccaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16685833A>G		NA		hg19		0.02	-0.131573	CTCxGCC	COVERED																																																																																			NOVEL					0			7	3.910606	KEEP	3	0	0	13	370	AA	0.993072	0.227586	0			3	60	101	0	0	8.372787	11	60	336	48		0.214286	0.229173
SPATA21	374955	__UNKNOWN__	__UNKNOWN__	1	16751687	16751687	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16751687G>A	ENST00000335496.1	-	4	517				SPATA21_ENST00000540400.1_Intron|SPATA21_ENST00000466212.1_Intron|SPATA21_ENST00000375577.1_Missense_Mutation_p.R170C	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	NA		NA					calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		attaacaggcgtgagccacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144	374955		EF-hand domain containing	28026	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198546	NM_198546	NA	Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.35-3221C>T	chr1.hg19:g.16751687G>A		NA	B9EK40|F5GXP5	hg19	CCDS172.1	0.02	-0.394686	GGCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	3.902	-0.021858	0.07634	.	.	ENSG00000187144	ENST00000375577	.	.	.	0.761	-0.274	0.12910	.	.	.	.	.	T	0.33323	0.0859	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32981	-0.9886	5	0.54805	T	0.06	.	3.3332	0.07092	0.3282:0.0:0.6718:0.0	.	.	.	.	C	170	.	ENSP00000364727:R170C	R	-	1	0	SPATA21	16624274	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.489000	0.06490	-0.137000	0.11455	-0.424000	0.05967	CGC	NOVEL	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006677.2	15	6.346952	KEEP	0	1	25	30	835	GG	0.999997	0.926637	0		-	5	60	144	0	0	10.303936	34	60	1081	99	ENST00000335496.1	0.128205	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16834064	16834064	__UNKNOWN__	IGR	SNP	G	G	C	rs7528338		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16834064G>C			NA	NA				CROCCP3 (14868 upstream) : RNU1-1 (6552 downstream)						NA		NA									NA						CAGAGTGAGGGGACAATTTGT	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16834064G>C		NA		hg19		0.02	-0.035089	AGGxGAC	UNCOVERED																																																																																			NOVEL					0			6	3.007208	KEEP	0	0	0	10	277	AG	0.995343	0.023962	0			4	37	132	0	0	15.107567	0	0	0	19		1	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16836491	16836491	__UNKNOWN__	IGR	SNP	G	G	C	rs371380050		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16836491G>C			NA	NA				CROCCP3 (17295 upstream) : RNU1-1 (4125 downstream)						NA		NA									NA						ATAATGTAATGggccaggtgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16836491G>C		NA		hg19		0.02	1.683729	AATxGGC	COVERED																																																																																			NOVEL					0			19	2.308791	KEEP	6	3	92	40	1237	GG	1	0.996724	0			9	60	288	0	0	21.617689	58	60	1963	164		0.134328	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16836607	16836607	__UNKNOWN__	IGR	SNP	C	C	G	rs374056388		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16836607C>G			NA	NA				CROCCP3 (17411 upstream) : RNU1-1 (4009 downstream)						NA		NA									NA						cccgtgtctactaaaaataca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16836607C>G		NA		hg19		0.02	-0.271949	CTAxTAA	COVERED																																																																																			NOVEL					0			5	6.619085	KEEP	4	0	0	22	654	CC	0.999863	0.717217	0			3	40	95	0	0	6.697919	27	60	919	67		0.1	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16836675	16836675	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16836675A>G			NA	NA				CROCCP3 (17479 upstream) : RNU1-1 (3941 downstream)						NA		NA									NA						ggaggctgagacaggagaatt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16836675A>G		NA		hg19		0.02	-0.254353	GAGxCAG	COVERED																																																																																			NOVEL					0			16	3.239582	KEEP	6	1	29	21	572	AA	0.999863	0.668432	0			3	60	97	0	0	7.206836	21	60	630	81		0.125	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16862294	16862294	__UNKNOWN__	IGR	SNP	A	A	G	rs71259516		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16862294A>G			NA	NA				U1 (1575 upstream) : AL355149.2 (3266 downstream)						NA		NA									NA						GGAAACCGAGACGGGCTGGAT	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16862294A>G		NA		hg19		0.02	1.669557	GAGxCGG	COVERED																																																																																			NOVEL					0			2	2.705599	KEEP	10	0	0	9	238	AA	0.99254	0.991952	0			6	46	195	0	0	13.080465	75	60	2214	104		0.074074	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16862472	16862472	__UNKNOWN__	IGR	SNP	G	G	C	rs200621127		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16862472G>C			NA	NA				U1 (1753 upstream) : AL355149.2 (3088 downstream)						NA		NA									NA						tttttcctcagatccaagagc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16862472G>C		NA		hg19		0.02	17.591401	TCAxATC	COVERED	.	.	.	.	.	.	.	.	.	.	g	3.046	-0.196522	0.06259	.	.	ENSG00000197511	ENST00000357301	.	.	.	0.425	-0.851	0.10716	.	.	.	.	.	T	0.18045	0.0433	N	0.08118	0	.	.	.	.	.	.	.	.	.	T	0.23226	-1.0194	4	0.87932	D	0	.	.	.	.	.	.	.	.	H	65	.	ENSP00000349853:D65H	D	+	1	0	AL355149.1	16735059	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.886000	0.04157	-0.571000	0.06014	-1.277000	0.01392	GAT	NOVEL					0			6	15.916195	KEEP	60	5	157	108	3302	GG	1	1	0			44	49	1462	0	0	104.341428	413	51	13788	891		0.09628	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16892010	16892010	__UNKNOWN__	Intron	SNP	T	T	C	rs375255056		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16892010T>C	ENST00000430580.2	-	27	3952					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CATGTGCCTATAGGTCCTCAC	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3064+117A>G	chr1.hg19:g.16892010T>C		NA	Q8N4E8|Q9C0H0	hg19		0.02	7.675115	CTAxAGG	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	9	9.022422	KEEP	1	0	0	30	822	TT	0.999997	0.999997	0		-	7	60	251	0	0	14.812499	225	60	6701	419	ENST00000430580.2	0.030172	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16892060	16892060	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16892060G>C	ENST00000430580.2	-	27	3952					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TGGCCACTTGGAGCAGGAATA	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.3064+67C>G	chr1.hg19:g.16892060G>C		NA	Q8N4E8|Q9C0H0	hg19		0.02	3.769159	TTGxAGC	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	6	5.416079	KEEP	1	0	0	18	551	GG	0.999859	0.999859	0		-	11	42	382	0	0	26.442034	137	60	4574	242	ENST00000430580.2	0.074324	1
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16902804	16902804	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs77427788	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16902804C>A	ENST00000430580.2	-	19	2964	c.2077G>T	c.(2077-2079)Ggg>Tgg	p.G693W	NBPF1_ENST00000287968.8_Missense_Mutation_p.G58W|NBPF1_ENST00000432949.1_Missense_Mutation_p.G151W	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	693		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		AGTCTACACCCCTCAGCCAGC	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													188	202	197			NA	NA	1		NA											NA				16902804		1509	2699	4208	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2077G>T	chr1.hg19:g.16902804C>A	ENSP00000474456:p.Gly693Trp	NA	Q8N4E8|Q9C0H0	hg19		0.02	3.145354	ACCxCTC	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	13	3.309339	KEEP	11	0	0	11	336	CC	0.992708	0.992706	0		-	9	42	276	0	0	18.091363	109	53	3686	199	ENST00000430580.2	0.076271	0.999998
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16902823	16902823	__UNKNOWN__	Silent	SNP	G	G	C	rs80271292		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16902823G>C	ENST00000430580.2	-	19	2945	c.2058C>G	c.(2056-2058)ctC>ctG	p.L686L	NBPF1_ENST00000287968.8_Silent_p.L51L|NBPF1_ENST00000432949.1_Silent_p.L144L	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	686		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		GCTGTTCTTGGAGGTCCTGCC	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													332	360	350			NA	NA	1		NA											NA				16902823		1510	2706	4216	SO:0001819	synonymous_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2058C>G	chr1.hg19:g.16902823G>C		NA	Q8N4E8|Q9C0H0	hg19		0.02	3.706977	TTGxAGG	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	15	3.309767	KEEP	11	0	0	11	333	GG	0.992708	0.992707	0		-	15	47	516	0	0	39.125992	105	60	3546	224	ENST00000430580.2	0.125	0.999999
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16902844	16902844	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs199969012		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16902844G>T	ENST00000430580.2	-	19	2924	c.2037C>A	c.(2035-2037)gaC>gaA	p.D679E	NBPF1_ENST00000287968.8_Missense_Mutation_p.D44E|NBPF1_ENST00000432949.1_Missense_Mutation_p.D137E	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	679		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CCTGGGACTTGTCTGGCTCAT	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													373	406	394			NA	NA	1		NA											NA				16902844		1511	2708	4219	SO:0001583	missense			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2037C>A	chr1.hg19:g.16902844G>T	ENSP00000474456:p.Asp679Glu	NA	Q8N4E8|Q9C0H0	hg19		0.02	3.011087	CTTxTCT	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	11	3.008913	KEEP	5	0	0	10	305	GG	0.992708	0.992707	0		-	9	47	273	0	0	17.791928	109	60	3800	219	ENST00000430580.2	0.076271	0.999999
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16902856	16902856	__UNKNOWN__	Silent	SNP	C	C	T	rs200172966		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16902856C>T	ENST00000430580.2	-	19	2912	c.2025G>A	c.(2023-2025)ccG>ccA	p.P675P	NBPF1_ENST00000287968.8_Silent_p.P40P|NBPF1_ENST00000432949.1_Silent_p.P133P	NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	675		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CTGGCTCATCCGGAGTGAGGA	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C		215,2807		0,215,1296	365	405	391		2025	-1.3	0	1	dbSNP_134	391	20,5398		0,20,2689	no	coding-synonymous	NBPF1	NM_017940.3		0,235,3985	TT,TC,CC	NA	0.3691,7.1145,2.7844		675/1123	16902856	235,8205	1511	2709	4220	SO:0001819	synonymous_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.2025G>A	chr1.hg19:g.16902856C>T		NA	Q8N4E8|Q9C0H0	hg19		0.02	2.964742	ATCxGGA	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	10	3.007354	KEEP	3	0	0	10	280	CC	0.992708	0.992705	0		-	12	42	370	0	0	26.173495	100	60	3286	197	ENST00000430580.2	0.107143	0.999997
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16913084	16913084	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16913084C>T	ENST00000430580.2	-	11	1666					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		cctcgtgatccacccgccccg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.778+460G>A	chr1.hg19:g.16913084C>T		NA	Q8N4E8|Q9C0H0	hg19		0.02	1.410087	ATCxACC	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	16	8.054465	KEEP	5	1	26	36	1052	CC	0.999998	0.976863	0		-	7	60	199	0	0	14.520616	42	60	1288	145	ENST00000430580.2	0.142857	0.976865
NBPF1	55672	__UNKNOWN__	__UNKNOWN__	1	16913162	16913162	__UNKNOWN__	Intron	SNP	A	A	G	rs142478291		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16913162A>G	ENST00000430580.2	-	11	1666					NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1	NA		NA				cytoplasm (GO:0005737)					NA				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		ATTAATAGCTAAGACAAGCCA	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481	55672		neuroblastoma breakpoint family	26088	protein-coding gene	gene with protein product		610501			NA	11214970, 16079250	Standard	NM_017940	NM_017940	NA	Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.778+382T>C	chr1.hg19:g.16913162A>G		NA	Q8N4E8|Q9C0H0	hg19		0.02	-0.263076	GCTxAGA	COVERED																																																																																			NOVEL	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000106436.3	6	5.110596	KEEP	4	0	0	17	436	AA	0.997832	0.692164	0		-	8	60	256	0	0	22.448997	18	60	494	73	ENST00000430580.2	0.307692	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16942975	16942975	__UNKNOWN__	IGR	SNP	A	A	G	rs2761553		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16942975A>G			NA	NA				NBPF1 (2993 upstream) : RP5-1182A14.5 (910 downstream)						NA		NA									NA						tgggtggatcacttgaggtca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16942975A>G		NA		hg19		0.02	-0.32442	ATCxCTT	COVERED																																																																																			NOVEL					0			13	5.243871	KEEP	6	1	33	29	793	AA	0.999997	0.835713	0			7	60	229	0	0	18.734896	27	60	757	111		0.205882	0.835716
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16949162	16949162	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16949162A>G	ENST00000412962.1	-	0	1000							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						ctgcactccaacctgggcgac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16949162A>G		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	1.844839	CCAxCCT	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	12	2.270787	KEEP	1	2	64	30	822	AA	0.999997	0.990961	0		-	4	51	138	0	0	9.453449	52	60	1549	130	ENST00000412962.1	0.071429	0.990964
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16949381	16949381	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16949381A>G	ENST00000412962.1	-	0	1000							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						agctacttggaaggctgaggc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16949381A>G		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.402459	TGGxAGG	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	6	3.040923	KEEP	0	1	31	21	593	AA	0.999879	0.934379	0		-	4	60	125	0	0	8.771411	36	60	1061	86	ENST00000412962.1	0.1	0.934492
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16952377	16952377	__UNKNOWN__	lincRNA	SNP	C	C	T	rs9658928	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16952377C>T	ENST00000412962.1	-	0	892							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						CCCTCCAGGCCCTGCCGTGCC	0.697		NA											.|||	849	0.169529	0.1452	0.0965	5008	,	,	NA	49550	0.2907	NA	0.1392	False	NA	,,,	NA	NA	NA	2504	0.1605	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16952377C>T		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	2.773468	GGCxCTG	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	3	3.441687	KEEP	0	1	24	20	595	CC	0.999869	0.99985	0		-	9	60	256	0	0	16.651184	94	60	3050	148	ENST00000412962.1	0.087379	0.999981
CROCCP2	84809	__UNKNOWN__	__UNKNOWN__	1	16956441	16956441	__UNKNOWN__	lincRNA	SNP	T	T	G	rs576464645		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16956441T>G	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2	NA		NA			centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)					NA						ttacaggcgttagccactgtg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908	84809			28170	pseudogene	pseudogene		NA	ciliary rootlet coiled-coil, rootletin-like 1	CROCCL1	NA	12477932	Standard	NR_026752.1	NR_026752	NA	Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884	ENST00000412962.1:	chr1.hg19:g.16956441T>G		NA	Q8NF65|Q96FR5|Q9BRE8	hg19		0.02	-0.306892	CGTxAGC	COVERED																																																																																			NOVEL	CROCCP2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000092784.1	12	3.006585	KEEP	0	0	0	10	263	TT	0.992708	0.79441	0		-	3	60	107	0	0	7.809163	29	60	821	62	ENST00000412962.1	0.09375	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16962892	16962892	__UNKNOWN__	IGR	SNP	T	T	C	rs71229319	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16962892T>C			NA	NA				CROCCP2 (1838 upstream) : RNU1-3 (30387 downstream)						NA		NA									NA						ccattcgcactttgtgaatgt	0.358		NA											.|||	878	0.175319	0.1732	0.2334	5008	,	,	NA	75790	0.0784	NA	0.1551	False	NA	,,,	NA	NA	NA	2504	0.2577	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16962892T>C		NA		hg19		0.02	-0.219257	CACxTTG	COVERED																																																																																			NOVEL					0			9	2.707001	KEEP	0	0	0	9	251	TT	0.99254	0.548763	0			5	60	166	0	0	13.653071	19	60	568	40		0.208333	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16967090	16967090	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16967090T>C			NA	NA				CROCCP2 (6036 upstream) : RNU1-3 (26189 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16967090T>C		NA		hg19		0.02	-0.228027	TCAxGCC	COVERED																																																																																			NOVEL					0			12	3.441309	KEEP	0	1	30	22	612	TT	0.999892	0.582867	0			3	60	100	0	0	7.565045	20	60	586	66		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16972134	16972134	__UNKNOWN__	IGR	SNP	C	C	T	rs4661404	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16972134C>T			NA	NA				CROCCP2 (11080 upstream) : RNU1-3 (21145 downstream)						NA		NA									NA						GGGGTGGCTCCCACTCCTGCT	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16972134C>T		NA		hg19		0.02	1.271927	CTCxCAC	COVERED																																																																																			NOVEL					0			2	6.317769	KEEP	17	0	0	21	638	CC	0.99986	0.999267	0			9	49	271	0	0	19.080788	73	60	2464	182		0.109756	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16974511	16974511	__UNKNOWN__	IGR	SNP	G	G	A	rs58679574	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16974511G>A			NA	NA				CROCCP2 (13457 upstream) : RNU1-3 (18768 downstream)						NA		NA									NA						GGGTAGTCACGGGCTTAGGGC	0.652		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16974511G>A		NA		hg19		0.02	5.542539	CACxGGC	COVERED																																																																																			NOVEL					0			23	7.250349	KEEP	5	4	107	62	1865	GG	1	1	0			10	60	294	0	0	16.382445	218	60	7104	417		0.04386	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16974592	16974592	__UNKNOWN__	IGR	SNP	C	C	T	rs201212576|rs71253919	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16974592C>T			NA	NA				CROCCP2 (13538 upstream) : RNU1-3 (18687 downstream)						NA		NA									NA						TGCCGGAACCCCGACGGCTCA	0.667		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16974592C>T		NA		hg19		0.02	4.432069	ACCxCGA	COVERED																																																																																			NOVEL					0			8	3.808475	KEEP	3	3	83	42	1257	CC	1	1	0			29	60	879	0	0	66.711941	158	60	5363	333		0.15508	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16975093	16975093	__UNKNOWN__	IGR	SNP	C	C	T	rs2095111	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16975093C>T			NA	NA				CROCCP2 (14039 upstream) : RNU1-3 (18186 downstream)						NA		NA									NA						TGGGGATAGCCATGGGCCCTG	0.622		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16975093C>T		NA		hg19		0.02	5.536095	AGCxATG	COVERED																																																																																			NOVEL					0			15	12.365378	KEEP	55	1	28	51	1498	CC	1	1	0			21	60	604	0	0	39.492088	220	60	7288	438		0.087137	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16975489	16975489	__UNKNOWN__	IGR	SNP	C	C	G	rs79648786	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16975489C>G			NA	NA				CROCCP2 (14435 upstream) : RNU1-3 (17790 downstream)						NA		NA									NA						AGTCAGCTTGCGGAATTGGTG	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16975489C>G		NA		hg19		0.02	1.55544	TTGxGGA	COVERED																																																																																			NOVEL					0			0	3.604383	KEEP	11	0	0	12	302	CC	0.992708	0.992627	0			6	27	179	0	0	11.118654	88	60	2737	156		0.06383	0.999919
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16975994	16975994	__UNKNOWN__	IGR	SNP	T	T	C	rs2261801	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16975994T>C			NA	NA				CROCCP2 (14940 upstream) : RNU1-3 (17285 downstream)						NA		NA									NA						CCTCAGGCTCTCAGCTTGTCC	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16975994T>C		NA		hg19		0.02	6.087862	CTCxCAG	COVERED																																																																																			NOVEL					0			4	3.609095	KEEP	7	0	0	12	332	TT	0.993634	0.993634	0			19	40	640	0	0	47.918378	138	60	4093	236		0.121019	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16977467	16977467	__UNKNOWN__	IGR	SNP	C	C	A	rs61182047		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16977467C>A			NA	NA				CROCCP2 (16413 upstream) : RNU1-3 (15812 downstream)						NA		NA									NA						GCCATACACCCCAAGAAATAA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16977467C>A		NA		hg19		0.02	4.412795	ACCxCAA	COVERED																																																																																			NOVEL					0			7	4.109666	KEEP	22	3	77	41	1230	CC	1	1	0			13	47	362	0	0	22.297502	163	60	5464	364		0.073864	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16977482	16977482	__UNKNOWN__	IGR	SNP	T	T	C	rs397834305		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16977482T>C			NA	NA				CROCCP2 (16428 upstream) : RNU1-3 (15797 downstream)						NA		NA									NA						AAATAAATTATTTGTCCTCTG	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16977482T>C		NA		hg19		0.02	5.288543	TTAxTTG	COVERED																																																																																			NOVEL					0			8	6.578561	KEEP	20	2	60	43	1160	TT	1	1	0			7	47	238	0	0	14.333293	171	60	5088	339		0.039326	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16978054	16978054	__UNKNOWN__	IGR	SNP	T	T	G	rs201137396		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16978054T>G			NA	NA				CROCCP2 (17000 upstream) : RNU1-3 (15225 downstream)						NA		NA									NA						CATCTGAGAGTGGGCTTCCTT	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16978054T>G		NA		hg19		0.02	6.642566	GAGxGGG	COVERED																																																																																			NOVEL					0			13	9.351649	KEEP	46	1	28	41	1094	TT	0.999999	0.999999	0			9	27	288	0	0	16.634672	220	60	6358	457		0.039301	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16984441	16984441	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16984441A>G			NA	NA				CROCCP2 (23387 upstream) : RNU1-3 (8838 downstream)						NA		NA									NA						ATTAATGCCCACTTCTggctg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16984441A>G		NA		hg19		0.02	-0.394699	CCCxCTT	COVERED																																																																																			NOVEL					0			19	6.918406	KEEP	6	0	0	23	651	AA	0.999869	0.941618	0			4	49	134	1	0	9.618358	37	60	1119	105		0.097561	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	16984471	16984471	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:16984471G>A			NA	NA				CROCCP2 (23417 upstream) : RNU1-3 (8808 downstream)						NA		NA									NA						gctcatgcctgtaatcccagc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.16984471G>A		NA		hg19		0.02	1.339543	CCTxTAA	COVERED																																																																																			NOVEL					0			25	4.981042	KEEP	7	2	55	36	1103	GG	0.999998	0.992092	0			4	49	120	0	0	7.789869	48	60	1620	153		0.076923	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17015884	17015884	__UNKNOWN__	IGR	SNP	T	T	G	rs61772159	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17015884T>G			NA	NA				AL021920.1 (8061 upstream) : ESPNP (1828 downstream)						NA		NA									NA						aatttttgtatttttagtaga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17015884T>G		NA		hg19		0.02	-0.166617	GTAxTTT	UNCOVERED																																																																																			NOVEL					0			5	2.405219	KEEP	3	0	0	8	209	TT	0	0	0			8	60	274	0	0	25.848758	10	50	280	34		0.444444	0.353947
ESPNP	284729	__UNKNOWN__	__UNKNOWN__	1	17022578	17022578	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17022578T>C	ENST00000492551.1	-	0	1938					NR_026567.1				espin pseudogene	NA		NA									NA						CAGTGGCTCATGCCTGTAATC	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869	284729			23285	pseudogene	pseudogene		NA			NA	15286153	Standard		NR_026567	NA	Approved		uc001azn.1		OTTHUMG00000000803	ENST00000492551.1:	chr1.hg19:g.17022578T>C		NA		hg19		0.02	-0.4034	TCAxGCC	COVERED																																																																																			NOVEL	ESPNP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000326311.1	12	5.71387	KEEP	0	0	0	19	523	TT	0.99986	0.934361	0		-	3	60	101	0	0	6.872875	38	60	1090	92	ENST00000492551.1	0.073171	0.934492
ESPNP	284729	__UNKNOWN__	__UNKNOWN__	1	17023110	17023110	__UNKNOWN__	RNA	SNP	G	G	A	rs11260887|rs201639447	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17023110G>A	ENST00000492551.1	-	0	1753					NR_026567.1				espin pseudogene	NA		NA									NA						GTTGAGCAGCGGCTGAAACCC	0.687		NA											g|||	1622	0.323882	0.1233	0.3703	5008	,	,	NA	35506	0.4792	NA	0.3429	False	NA	,,,	NA	NA	NA	2504	0.3824	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869	284729			23285	pseudogene	pseudogene		NA			NA	15286153	Standard		NR_026567	NA	Approved		uc001azn.1		OTTHUMG00000000803	ENST00000492551.1:	chr1.hg19:g.17023110G>A		NA		hg19		0.02	4.523744	AGCxGCT	COVERED																																																																																			NOVEL	ESPNP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000326311.1	1	3.309343	KEEP	0	0	0	11	327	GG	0.993072	0.993072	0		-	33	60	947	0	0	75.915889	119	60	3838	233	ENST00000492551.1	0.217105	1
ESPNP	284729	__UNKNOWN__	__UNKNOWN__	1	17032201	17032201	__UNKNOWN__	RNA	SNP	G	G	C	rs4661920	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17032201G>C	ENST00000492551.1	-	0	696					NR_026567.1				espin pseudogene	NA		NA									NA						tcaaagtgcaggcatgagcca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869	284729			23285	pseudogene	pseudogene		NA			NA	15286153	Standard		NR_026567	NA	Approved		uc001azn.1		OTTHUMG00000000803	ENST00000492551.1:	chr1.hg19:g.17032201G>C		NA		hg19		0.02	-0.236856	GCAxGCA	COVERED																																																																																			NOVEL	ESPNP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000326311.1	13	8.425204	KEEP	0	0	0	28	860	GG	0.999997	0.641345	0		-	6	60	198	0	0	16.679911	19	60	651	77	ENST00000492551.1	0.24	0.641347
ESPNP	284729	__UNKNOWN__	__UNKNOWN__	1	17032262	17032262	__UNKNOWN__	RNA	SNP	G	G	A	rs4661921	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17032262G>A	ENST00000492551.1	-	0	696					NR_026567.1				espin pseudogene	NA		NA									NA						atttttagacggagtcttgct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869	284729			23285	pseudogene	pseudogene		NA			NA	15286153	Standard		NR_026567	NA	Approved		uc001azn.1		OTTHUMG00000000803	ENST00000492551.1:	chr1.hg19:g.17032262G>A		NA		hg19		0.02	-0.210526	GACxGAG	COVERED																																																																																			NOVEL	ESPNP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000326311.1	12	3.942008	KEEP	1	1	31	24	697	GG	0.999931	0.522125	0		-	3	60	98	0	0	7.560697	17	60	561	72	ENST00000492551.1	0.15	0.522161
ESPNP	284729	__UNKNOWN__	__UNKNOWN__	1	17033805	17033805	__UNKNOWN__	RNA	SNP	C	C	T	rs59259153|rs373187758	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17033805C>T	ENST00000492551.1	-	0	673					NR_026567.1				espin pseudogene	NA		NA									NA						CGTGCGCAGGCAGTGGGTGCA	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869	284729			23285	pseudogene	pseudogene		NA			NA	15286153	Standard		NR_026567	NA	Approved		uc001azn.1		OTTHUMG00000000803	ENST00000492551.1:	chr1.hg19:g.17033805C>T		NA		hg19		0.02	2.324449	AGGxAGT	COVERED																																																																																			NOVEL	ESPNP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000326311.1	0	2.338643	KEEP	0	1	23	16	470	CC	0.999366	0.999366	0		-	37	59	973	0	0	79.576767	105	60	3614	244	ENST00000492551.1	0.260563	1
ESPNP	284729	__UNKNOWN__	__UNKNOWN__	1	17041447	17041447	__UNKNOWN__	RNA	SNP	G	G	A	rs57934216		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17041447G>A	ENST00000492551.1	-	0	194					NR_026567.1				espin pseudogene	NA		NA									NA						tttttgagacggagtcttgct	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869	284729			23285	pseudogene	pseudogene		NA			NA	15286153	Standard		NR_026567	NA	Approved		uc001azn.1		OTTHUMG00000000803	ENST00000492551.1:	chr1.hg19:g.17041447G>A		NA		hg19		0.02	-0.298235	GACxGAG	COVERED																																																																																			NOVEL	ESPNP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000326311.1	8	5.715753	KEEP	2	0	0	19	556	GG	0.999859	0.78095	0		-	4	60	123	0	0	8.862729	30	60	967	76	ENST00000492551.1	0.117647	0.78106
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17082975	17082975	__UNKNOWN__	RNA	SNP	A	A	G	rs1033403	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17082975A>G	ENST00000455405.2	-	0	1613							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						CAGAGGACAAATAATTTGTTT	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17082975A>G		NA	B7WPB1|Q13209	hg19		0.02	3.774453	CAAxTAA	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	0	2.739019	KEEP	16	1	34	21	569	AA	0.99986	0.999837	0		-	11	48	355	0	0	25.607044	91	60	2725	190	ENST00000455405.2	0.107843	0.999978
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17083577	17083577	__UNKNOWN__	RNA	SNP	C	C	T	rs2610655		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17083577C>T	ENST00000455405.2	-	0	1011							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						tgtttacttgcagggggaaaa	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17083577C>T		NA	B7WPB1|Q13209	hg19		0.02	2.938594	TTGxAGG	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	5	3.342894	KEEP	9	1	25	20	618	CC	0.99986	0.999858	0		-	20	47	544	0	0	40.797947	96	60	3329	213	ENST00000455405.2	0.172414	0.999998
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17083597	17083597	__UNKNOWN__	RNA	SNP	G	G	A	rs186155999		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17083597G>A	ENST00000455405.2	-	0	991							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)				NA						aaccattttcgtttaagaaag	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17083597G>A		NA	B7WPB1|Q13209	hg19		0.02	2.923485	TTCxTTT	COVERED																																																																																			NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	1	3.340914	KEEP	9	1	31	22	630	GG	0.999869	0.999869	0		-	35	60	1039	0	0	87.713793	95	60	3139	232	ENST00000455405.2	0.269231	1
MST1L	11223	__UNKNOWN__	__UNKNOWN__	1	17084021	17084021	__UNKNOWN__	RNA	SNP	C	C	G	rs2446543	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17084021C>G	ENST00000455405.2	-	0	691							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.A634P(1)			NA						ACCTCACAGGCCCCCACAGGG	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	kidney(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715	11223			7390	other	unknown		NA	macrophage stimulating, pseudogene 7, macrophage stimulating, pseudogene 9, macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9	MSTP7, MSTP9, MST1P9	NA	10728827	Standard	NM_001271733	NM_001271733	NA	Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578	ENST00000455405.2:	chr1.hg19:g.17084021C>G		NA	B7WPB1|Q13209	hg19		0.02	1.8184	AGGxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	.	9.021	0.984781	0.18889	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41938	D	0.000787	T	0.57431	0.2053	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.61426	-0.7065	6	0.15499	T	0.54	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	rs2446543	634;660	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	P	634;660	.	ENSP00000439273:A634P	A	-	1	0	MST1P9	16956608	0.997000	0.39634	0.867000	0.34043	0.000000	0.00434	4.380000	0.59581	0.502000	0.28037	0.000000	0.15137	GCC	NOVEL	MST1L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000400328.1	3	3.609145	KEEP	12	0	0	12	340	CC	0.993072	0.986819	0		-	12	27	400	0	0	32.314496	52	50	1728	96	ENST00000455405.2	0.1875	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17087593	17087593	__UNKNOWN__	IGR	SNP	C	C	T	rs12145944	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17087593C>T			NA	NA				MST1L (2226 upstream) : RP11-108M9.1 (90222 downstream)						NA		NA									NA						ATGGCGAGCGCTGCCCTGCAG	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17087593C>T		NA		hg19		0.02	4.709332	GCGxTGC	COVERED																																																																																			NOVEL					0			5	3.628088	KEEP	4	1	25	21	630	CC	0.99986	0.99986	0			33	49	978	0	0	76.580425	144	60	4926	282		0.186441	1
CROCC	9696	__UNKNOWN__	__UNKNOWN__	1	17267163	17267163	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17267163A>G	ENST00000375541.5	+	13	1877				CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin	NA		NA								breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		gattacaggcatgagccaccg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453	9696			21299	protein-coding gene	gene with protein product	rootletin, ciliary rootlet protein	615776			NA	12427867, 17971504	Standard	NM_014675	XM_006711056	NA	Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1808+575A>G	chr1.hg19:g.17267163A>G		NA		hg19	CCDS30616.1	0.02	-0.271873	GGCxTGA	COVERED																																																																																			NOVEL	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006249.2	6	5.412635	KEEP	0	0	0	18	487	AA	0.999859	0.717214	0		+	3	60	96	0	0	6.893052	25	60	740	74	ENST00000375541.5	0.107143	0.717315
ATP13A2	23400	__UNKNOWN__	__UNKNOWN__	1	17327043	17327043	__UNKNOWN__	Intron	SNP	G	G	A	rs371532404	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17327043G>A	ENST00000326735.8	-	9	739				ATP13A2_ENST00000452699.1_Intron|RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Intron			Q9NQ11	AT132_HUMAN	ATPase type 13A2	NA		NA			cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		GGGGAGGGGCGGGAGGCAGCG	0.672		NA											G|||	3	0.000599042	0.0023	0.0	5008	,	,	NA	12625	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0								G	,,	19,4383	26.2+/-53.5	0,19,2182	35	35	35		,,	-4.8	0	1		35	0,8594		0,0,4297	no	intron,intron,intron	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	0,19,6479	AA,AG,GG	NA	0.0,0.4316,0.1462	,,	,,	17327043	19,12977	2201	4297	6498	SO:0001627	intron_variant			AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363	23400		ATPases / P-type, Parkinson disease	30213	protein-coding gene	gene with protein product		610513	Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)	PARK9	NA	15381061, 16964263	Standard	NM_022089	XM_005245809	NA	Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.706-14C>T	chr1.hg19:g.17327043G>A		NA	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	hg19	CCDS175.1	0.02	-0.368397	GGCxGGA	COVERED																																																																																			NOVEL	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000006617.1	2	2.406653	KEEP	0	0	0	8	232	GG	0.99257	0.892632	0		-	4	60	110	0	0	7.186864	38	60	1268	62	ENST00000326735.8	0.095238	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	17483409	17483409	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:17483409T>C			NA	NA				PADI2 (37461 upstream) : Y_RNA (1282 downstream)						NA		NA									NA						tggctgggcatggtggctcac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.17483409T>C		NA		hg19		0.02	-0.131512	GCAxGGT	COVERED																																																																																			NOVEL					0			1	2.707235	KEEP	0	0	0	9	254	TT	0.99254	0.227464	0			3	60	95	0	1	7.882811	10	60	292	37		0.230769	0.229173
PAX7	5081	__UNKNOWN__	__UNKNOWN__	1	19071194	19071194	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:19071194G>A	ENST00000420770.2	+	9	1485					NM_001135254.1	NP_001128726.1	P23759	PAX7_HUMAN	paired box 7	NA		NA			anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		atggatggatggatggatgga	0.438		NA	T	FOXO1A	alveolar rhabdomyosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709	5081		Paired boxes, Homeoboxes / PRD class	8621	protein-coding gene	gene with protein product		167410	paired box gene 7		NA	7981748, 8431641	Standard	NM_002584	NM_001135254	NA	Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000420770.2:c.1403-114G>A	chr1.hg19:g.19071194G>A		NA	E9PFV9|Q0VA99|Q2PJS5	hg19	CCDS44074.1	0.02	-0.149107	GATxGAT	COVERED																																																																																			NOVEL	PAX7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372482.1	4	2.706874	KEEP	0	0	0	9	251	GG	0.99254	0.289823	0		+	5	60	136	0	1	12.021636	9	60	297	28	ENST00000420770.2	0.357143	0.292001
PAX7	5081	__UNKNOWN__	__UNKNOWN__	1	19071195	19071195	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:19071195G>A	ENST00000420770.2	+	9	1485					NM_001135254.1	NP_001128726.1	P23759	PAX7_HUMAN	paired box 7	NA		NA			anatomical structure morphogenesis (GO:0009653)|cartilage development (GO:0051216)|chromatin remodeling (GO:0006338)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic skeletal system development (GO:0048706)|muscle tissue morphogenesis (GO:0060415)|negative regulation of apoptotic process (GO:0043066)|neuron fate commitment (GO:0048663)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell fate commitment (GO:0010453)|regulation of protein binding (GO:0043393)|skeletal muscle satellite cell commitment (GO:0014813)|skeletal muscle tissue regeneration (GO:0043403)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)		PAX7/FOXO1(197)	breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)	31		Colorectal(325;3.46e-05)|all_lung(284;0.000439)|Renal(390;0.000518)|Lung NSC(340;0.000543)|Breast(348;0.00093)|Ovarian(437;0.00768)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00609)|BRCA - Breast invasive adenocarcinoma(304;4.71e-05)|Kidney(64;0.000279)|KIRC - Kidney renal clear cell carcinoma(64;0.00371)|STAD - Stomach adenocarcinoma(196;0.00658)|READ - Rectum adenocarcinoma(331;0.0576)		tggatggatggatggatggat	0.433		NA	T	FOXO1A	alveolar rhabdomyosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X96743	CCDS186.1, CCDS44074.1, CCDS44075.1	1p36.13	2011-06-20	2007-07-12		ENSG00000009709	ENSG00000009709	5081		Paired boxes, Homeoboxes / PRD class	8621	protein-coding gene	gene with protein product		167410	paired box gene 7		NA	7981748, 8431641	Standard	NM_002584	NM_001135254	NA	Approved	Hup1	uc001bay.3	P23759	OTTHUMG00000002433	ENST00000420770.2:c.1403-113G>A	chr1.hg19:g.19071195G>A		NA	E9PFV9|Q0VA99|Q2PJS5	hg19	CCDS44074.1	0.02	-0.14912	ATGxATG	COVERED																																																																																			NOVEL	PAX7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372482.1	4	2.705751	KEEP	0	0	0	9	240	GG	0.99254	0.289823	0		+	5	60	156	0	1	14.022705	9	60	295	28	ENST00000420770.2	0.357143	0.292001
IFFO2	126917	__UNKNOWN__	__UNKNOWN__	1	19262387	19262387	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:19262387G>C	ENST00000455833.2	-	2	1019					NM_001136265.1	NP_001129737.1	Q5TF58	IFFO2_HUMAN	intermediate filament family orphan 2	NA		NA				intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)	2						tttttgtagagacaaggtctc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024480, AL080251	CCDS44076.1	1p36.13	2013-10-11			ENSG00000169991	ENSG00000169991	126917		Intermediate filament family orphans	27006	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_001136265	NM_001136265	NA	Approved		uc001bbd.2	Q5TF58	OTTHUMG00000002499	ENST00000455833.2:c.666-14772C>G	chr1.hg19:g.19262387G>C		NA	Q9H7K0	hg19	CCDS44076.1	0.02	-0.035092	AGAxACA	UNCOVERED																																																																																			NOVEL	IFFO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007099.2	7	2.407306	KEEP	5	0	0	8	250	GG	0	0	0		-	2	60	72	2	0	7.324848	1	60	35	17	ENST00000455833.2	0.666667	0.019982
CAPZB	832	__UNKNOWN__	__UNKNOWN__	1	19720535	19720535	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:19720535C>T	ENST00000264203.3	-	4	665				CAPZB_ENST00000401084.2_Intron|CAPZB_ENST00000264202.6_Intron|CAPZB_ENST00000375142.1_Intron|CAPZB_ENST00000482808.1_Intron|CAPZB_ENST00000433834.1_Intron|CAPZB_ENST00000375144.1_Intron	NM_001206541.2	NP_001193470.1	P47756	CAPZB_HUMAN	capping protein (actin filament) muscle Z-line, beta	NA		NA			actin cytoskeleton organization (GO:0030036)|barbed-end actin filament capping (GO:0051016)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|muscle fiber development (GO:0048747)|negative regulation of microtubule polymerization (GO:0031115)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)|regulation of protein kinase C signaling (GO:0090036)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|membrane (GO:0016020)|WASH complex (GO:0071203)|Z disc (GO:0030018)	actin binding (GO:0003779)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	7		Colorectal(325;3.93e-05)|Renal(390;0.000147)|all_lung(284;0.000169)|Lung NSC(340;0.000202)|Breast(348;0.000496)|Ovarian(437;0.00428)|Myeloproliferative disorder(586;0.0262)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Kidney(64;8.63e-06)|BRCA - Breast invasive adenocarcinoma(304;4.06e-05)|KIRC - Kidney renal clear cell carcinoma(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000525)|STAD - Stomach adenocarcinoma(196;0.00779)|READ - Rectum adenocarcinoma(331;0.103)|Lung(427;0.173)		cgctctgttgcccaggctgga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U03271	CCDS41277.1, CCDS55579.1, CCDS72717.1, CCDS72718.1	1p36.1	2014-05-09			ENSG00000077549	ENSG00000077549	832			1491	protein-coding gene	gene with protein product		601572			NA		Standard		NM_004930	NA	Approved		uc021ohr.1	P47756	OTTHUMG00000002556	ENST00000264203.3:c.172-8415G>A	chr1.hg19:g.19720535C>T		NA	Q32Q68|Q5U0L4|Q8TB49|Q9NUC4	hg19		0.02	-0.122804	TTGxCCA	UNCOVERED																																																																																			NOVEL	CAPZB-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000007259.1	7	3.009134	KEEP	6	0	0	10	313	CC	0	0	0		-	3	60	84	0	0	6.673002	11	60	373	30	ENST00000264203.3	0.214286	0.196312
RP5-1056L3.1	0	__UNKNOWN__	__UNKNOWN__	1	19919998	19919998	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:19919998T>C	ENST00000416470.1	-	0	123										NA		NA									NA						agtgatcctcttgcctcggcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000416470.1:	chr1.hg19:g.19919998T>C		NA		hg19		0.02	-0.20175	CTCxTGC	COVERED																																																																																			NOVEL	RP5-1056L3.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000007696.1	4	3.007861	KEEP	0	0	0	10	284	TT	0.992708	0.486967	0		-	3	60	103	0	0	8.060556	17	60	528	47	ENST00000416470.1	0.15	0.490544
DDOST	1650	__UNKNOWN__	__UNKNOWN__	1	20978956	20978956	__UNKNOWN__	Silent	SNP	G	G	A	rs376894317		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:20978956G>A	ENST00000602624.2	-	11	1276	c.1236C>T	c.(1234-1236)taC>taT	p.Y412Y	DDOST_ENST00000375048.3_Silent_p.Y429Y|DDOST_ENST00000415136.2_Silent_p.Y392Y			P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	429		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AGGCGCTGGCGTAGTAGGGGT	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								G		1,4405	2.1+/-5.4	0,1,2202	60	60	60		1287	-3.9	0.9	1		60	0,8600		0,0,4300	no	coding-synonymous	DDOST	NM_005216.4		0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077		429/457	20978956	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	1650	2.4.1.119		2728	protein-coding gene	gene with protein product	oligosaccharyltransferase subunit 48	602202	dolichyl-diphosphooligosaccharide-protein glycosyltransferase, dolichyl-diphosphooligosaccharide--protein glycosyltransferase		NA	9367678	Standard	NM_005216	NM_005216	NA	Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000602624.2:c.1236C>T	chr1.hg19:g.20978956G>A		NA	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	hg19		0.02	1.330799	GGCxTAG	COVERED																																																																																			NOVEL	DDOST-006	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000467856.2	1	4.211726	KEEP	0	0	0	14	415	GG	0.995343	0.988302	0		-	5	60	146	0	0	9.37358	59	60	1907	116	ENST00000602624.2	0.078125	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	21123476	21123476	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:21123476C>T			NA	NA				HP1BP3 (10295 upstream) : EIF4G3 (9486 downstream)						NA		NA									NA						gtcaggagttcgagaccagcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.21123476C>T		NA		hg19		0.02	-0.139785	GTTxGAG	COVERED																																																																																			NOVEL					0			9	3.307497	KEEP	7	0	0	11	299	CC	0.99254	0.259018	0			3	47	89	0	0	7.17298	11	60	342	44		0.214286	0.260965
EIF4G3	8672	__UNKNOWN__	__UNKNOWN__	1	21137479	21137479	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:21137479A>G	ENST00000602326.1	-	34	5031				EIF4G3_ENST00000400422.1_Intron|EIF4G3_ENST00000374937.3_Intron|EIF4G3_ENST00000264211.8_Intron|EIF4G3_ENST00000374935.3_Intron|EIF4G3_ENST00000537738.1_Intron|EIF4G3_ENST00000536266.1_Intron	NM_001198802.1	NP_001185731.1	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		gcctcactctattgcccaggc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151	8672			3298	protein-coding gene	gene with protein product		603929			NA	9418880	Standard	NM_003760	NM_001198801	NA	Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000602326.1:c.4448-102T>C	chr1.hg19:g.21137479A>G		NA	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	hg19	CCDS55580.1	0.02	-0.043852	TCTxTTG	UNCOVERED																																																																																			NOVEL	EIF4G3-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467634.1	5	2.706425	KEEP	0	0	0	9	242	AA	0.99254	0.023894	0		-	2	60	67	0	0	6.450292	2	60	56	20	ENST00000602326.1	0.5	0.024074
EIF4G3	8672	__UNKNOWN__	__UNKNOWN__	1	21407731	21407731	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:21407731A>C	ENST00000602326.1	-	3	389				EIF4G3_ENST00000356916.3_Intron|EIF4G3_ENST00000400422.1_Intron|EIF4G3_ENST00000374927.4_Intron	NM_001198802.1	NP_001185731.1	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		caagaccatcatggccaacat	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151	8672			3298	protein-coding gene	gene with protein product		603929			NA	9418880	Standard	NM_003760	NM_001198801	NA	Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000602326.1:c.194+7899T>G	chr1.hg19:g.21407731A>C		NA	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	hg19	CCDS55580.1	0.02	-0.070163	ATCxTGG	UNCOVERED																																																																																			NOVEL	EIF4G3-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467634.1	4	2.706394	KEEP	1	0	0	9	244	AA	0.99254	0.053733	0		-	3	60	93	0	0	8.654769	4	60	118	26	ENST00000602326.1	0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	21693613	21693613	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:21693613C>T			NA	NA				ECE1 (21616 upstream) : RP11-293F5.1 (48777 downstream)						NA		NA									NA						cccatctctacaaaaataaag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.21693613C>T		NA		hg19		0.02	-0.16667	CTAxAAA	COVERED																																																																																			NOVEL					0			7	3.309919	KEEP	0	0	0	11	339	CC	0.993072	0.351495	0			3	60	84	0	1	6.310844	15	60	512	43		0.166667	0.353947
RAP1GAP	5909	__UNKNOWN__	__UNKNOWN__	1	21930444	21930444	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:21930444C>G	ENST00000374765.4	-	19	1629				RAP1GAP_ENST00000374763.2_Intron|RAP1GAP_ENST00000374761.2_Intron|RAP1GAP_ENST00000542643.2_Intron|RAP1GAP_ENST00000290101.4_Intron	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	NA		NA			GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		gagagagagacagagagagag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													11	11	11			NA	NA	1		NA											NA				21930444		1443	3362	4805	SO:0001627	intron_variant			BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864	5909			9858	protein-coding gene	gene with protein product		600278	RAP1, GTPase activating protein 1	RAP1GA1	NA	1904317	Standard	NM_002885	NM_001145657	NA	Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1429-1038G>C	chr1.hg19:g.21930444C>G		NA	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	hg19	CCDS218.1	0.02	1.909256	AGAxAGA	COVERED																																																																																			NOVEL	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019759.2	11	8.72556	KEEP	0	0	0	29	883	CC	0.999997	0.994419	0		-	4	60	143	1	0	9.712447	60	60	2053	142	ENST00000374765.4	0.0625	0.994422
HSPG2	3339	__UNKNOWN__	__UNKNOWN__	1	22243892	22243892	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:22243892T>C	ENST00000374695.3	-	1	143					NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	NA		NA			angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	tgccactgcattccagcctgg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798	3339		Proteoglycans / Extracellular Matrix : Other, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	5273	protein-coding gene	gene with protein product	perlecan proteoglycan	142461	Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)	SJS1	NA	1685141, 11941538	Standard	NM_005529	XM_005245863	NA	Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.63+19755A>G	chr1.hg19:g.22243892T>C		NA	Q16287|Q5SZI3|Q9H3V5	hg19	CCDS30625.1	0.02	-0.070177	GCAxTCC	UNCOVERED																																																																																			NOVEL	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000007598.1	1	2.406362	KEEP	0	0	0	8	224	TT	0.99257	0.053735	0		-	3	60	105	0	0	9.63302	5	60	156	28	ENST00000374695.3	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	22875715	22875715	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:22875715A>G			NA	NA				ZBTB40 (18065 upstream) : EPHA8 (14341 downstream)						NA		NA									NA						cgaactcctgacctcaagtga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.22875715A>G		NA		hg19		0.02	-0.122796	CTGxCCT	COVERED																																																																																			NOVEL					0			11	2.706592	KEEP	8	0	0	9	246	AC	0.99257	0.194853	0			3	60	96	0	0	8.232341	8	60	252	42		0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	23527071	23527071	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:23527071C>T			NA	NA				HTR1D (5849 upstream) : RP5-1057J7.6 (80730 downstream)						NA		NA									NA						ctccctgtgtcgcccaggctg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.23527071C>T		NA		hg19		0.02	-0.166643	TGTxGCC	COVERED																																																																																			NOVEL					0			12	2.707503	KEEP	0	0	0	9	264	CC	0.99254	0.351306	0			3	60	90	0	0	6.992176	14	60	438	39		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	23865346	23865346	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:23865346C>T			NA	NA				E2F2 (7634 upstream) : RP1-150O5.3 (10283 downstream)						NA		NA									NA						ggctggagtgcagtggcatga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.23865346C>T		NA		hg19		0.02	-0.087709	GTGxAGT	UNCOVERED																																																																																			NOVEL					0			12	2.40134	KEEP	4	0	0	8	227	CC	0	0	0			3	41	80	0	0	6.942743	6	60	198	23		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	23982843	23982843	__UNKNOWN__	IGR	SNP	C	C	G	rs7539756	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:23982843C>G			NA	NA				MDS2 (15785 upstream) : RPL11 (35425 downstream)						NA		NA									NA						gccactgcacccggccTTTTA	0.478		NA											C|||	1769	0.353235	0.0847	0.3458	5008	,	,	NA	15920	0.5099	NA	0.492	False	NA	,,,	NA	NA	NA	2504	0.4172	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.23982843C>G		NA		hg19		0.02	-0.201745	CACxCGG	COVERED																																																																																			NOVEL					0			4	2.407214	KEEP	0	0	0	8	246	CC	0.99257	0.4869	0			13	60	400	0	0	39.360151	10	60	347	40		0.565217	0.490544
CNR2	1269	__UNKNOWN__	__UNKNOWN__	1	24280355	24280355	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:24280355G>A	ENST00000536471.1	-	2	137							P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	NA		NA			G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of action potential (GO:0045759)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|response to amphetamine (GO:0001975)|response to lipopolysaccharide (GO:0032496)|sensory perception of pain (GO:0019233)	dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(9)|pancreas(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(2)	26		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.32e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;2.9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.0131)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.146)	Dronabinol(DB00470)|Nabilone(DB00486)	ggccaacatggtgaaacccca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X74328	CCDS245.1	1p	2012-08-08			ENSG00000188822	ENSG00000188822	1269		GPCR / Class A : Cannabinoid receptors	2160	protein-coding gene	gene with protein product		605051			NA		Standard	NM_001841	NM_001841	NA	Approved	CB2	uc001bif.3	P34972	OTTHUMG00000013892	ENST00000536471.1:c.122-4363C>T	chr1.hg19:g.24280355G>A		NA	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	hg19	CCDS245.1	0.02	-0.149124	ATGxTGA	COVERED																																																																																			NOVEL	CNR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		7	4.512916	KEEP	3	0	0	15	447	GG	0.994391	0.290363	0		-	3	57	91	0	0	7.481855	10	60	332	45	ENST00000536471.1	0.230769	0.292001
CLIC4	25932	__UNKNOWN__	__UNKNOWN__	1	25084970	25084970	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:25084970G>A	ENST00000374379.4	+	1	269				CLIC4_ENST00000497755.1_Intron	NM_013943.2	NP_039234.1	Q9Y696	CLIC4_HUMAN	chloride intracellular channel 4	NA		NA			angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|endothelial cell morphogenesis (GO:0001886)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|fertilization (GO:0009566)|keratinocyte differentiation (GO:0030216)|multicellular organism growth (GO:0035264)|negative regulation of cell migration (GO:0030336)|regulation of cytoskeleton organization (GO:0051493)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|vacuolar acidification (GO:0007035)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|microvillus (GO:0005902)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			large_intestine(3)|lung(2)|skin(1)	6		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000778)|all_lung(284;0.00106)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0479)|OV - Ovarian serous cystadenocarcinoma(117;1.06e-24)|Colorectal(126;1.03e-07)|COAD - Colon adenocarcinoma(152;4.93e-06)|STAD - Stomach adenocarcinoma(196;0.000418)|GBM - Glioblastoma multiforme(114;0.000451)|BRCA - Breast invasive adenocarcinoma(304;0.00215)|KIRC - Kidney renal clear cell carcinoma(1967;0.00216)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.18)		tttttttgaggcagagtctca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF097330	CCDS256.1	1p	2012-09-26			ENSG00000169504	ENSG00000169504	25932		Ion channels / Chloride channels : Intracellular	13518	protein-coding gene	gene with protein product		606536			NA	9139710, 10070163	Standard	NM_013943	NM_013943	NA	Approved	DKFZP566G223, CLIC4L, P64H1, H1, huH1, p64H1	uc001bjo.2	Q9Y696	OTTHUMG00000003327	ENST00000374379.4:c.72+12854G>A	chr1.hg19:g.25084970G>A		NA	Q9UFW9|Q9UQJ6	hg19	CCDS256.1	0.02	-0.131581	GAGxCAG	COVERED																																																																																			NOVEL	CLIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009332.1	7	2.407101	KEEP	1	0	0	8	243	GG	0.99257	0.22747	0		+	3	60	85	0	0	6.77287	11	60	376	36	ENST00000374379.4	0.214286	0.229173
C1orf63	0	__UNKNOWN__	__UNKNOWN__	1	25586246	25586246	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:25586246C>T	ENST00000450820.2	-	2	146							Q9BUV0	RSRP1_HUMAN		NA		NA								breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		cagcctgcctcggcctcccaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000450820.2:c.825-5818G>A	chr1.hg19:g.25586246C>T		NA	A8K917|Q49AA4|Q5TH71|Q9GZP6	hg19		0.02	2.764871	CCTxGGC	COVERED																																																																																			NOVEL	C1orf63-021	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000420930.1	25	10.091974	KEEP	28	2	49	51	1488	CC	1	0.999987	0		-	6	49	170	0	0	10.161539	89	60	2834	251	ENST00000450820.2	0.063158	0.999987
MAN1C1	57134	__UNKNOWN__	__UNKNOWN__	1	26023404	26023404	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26023404T>C	ENST00000374332.4	+	2	967				MAN1C1_ENST00000263979.3_Intron|MAN1C1_ENST00000473891.1_Intron	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		tcccacagtgttgggattaca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643	57134			19080	protein-coding gene	gene with protein product		NA			NA	10915796	Standard	NM_020379	XM_005245945	NA	Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.637+10377T>C	chr1.hg19:g.26023404T>C		NA	A6NNE2|B2RNP2|Q9Y545	hg19	CCDS265.1	0.02	-0.16656	GTGxTGG	COVERED																																																																																			NOVEL	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012828.3	9	3.307619	KEEP	0	0	0	11	299	TT	0.993072	0.351495	0		+	3	60	102	0	0	8.279846	13	60	379	42	ENST00000374332.4	0.1875	0.353947
RP1-125I3.2	0	__UNKNOWN__	__UNKNOWN__	1	26186936	26186936	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26186936C>T	ENST00000455431.1	+	0	263										NA		NA									NA						catgagccaccgcgcccggcc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000455431.1:	chr1.hg19:g.26186936C>T		NA		hg19		0.02	-0.271885	CACxGCG	COVERED																																																																																			NOVEL	RP1-125I3.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000019313.1	6	5.113947	KEEP	2	0	0	17	497	CC	0.999366	0.739203	0		+	3	60	92	0	0	6.398687	27	60	856	71	ENST00000455431.1	0.1	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	26412780	26412780	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26412780A>G			NA	NA				AL391650.1 (14612 upstream) : PDIK1L (25547 downstream)						NA		NA									NA						ttgctctgtcacccaggctgg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.26412780A>G		NA		hg19		0.02	-0.192949	GTCxCCC	COVERED																																																																																			NOVEL					0			5	3.307448	KEEP	0	0	0	11	293	AA	0.993072	0.454585	0			3	60	95	0	1	7.261374	17	60	501	53		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	26456802	26456802	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26456802A>G			NA	NA				PDIK1L (4768 upstream) : FAM110D (28708 downstream)						NA		NA									NA						gggcaacataatgagacctca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.26456802A>G		NA		hg19		0.02	-0.201685	ATAxTGA	COVERED																																																																																			NOVEL					0			11	2.704973	KEEP	0	0	0	9	229	AA	0.99254	0.486885	0			3	60	97	0	0	7.392674	18	60	527	44		0.142857	0.490544
UBXN11	91544	__UNKNOWN__	__UNKNOWN__	1	26608885	26608885	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201454352	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26608885C>T	ENST00000374222.1	-	16	1932	c.1468G>A	c.(1468-1470)Ggt>Agt	p.G490S	UBXN11_ENST00000374223.1_Missense_Mutation_p.G247S|UBXN11_ENST00000314675.7_Missense_Mutation_p.G370S|UBXN11_ENST00000357089.4_Missense_Mutation_p.G457S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G490S|UBXN11_ENST00000374217.2_Missense_Mutation_p.G457S			Q5T124	UBX11_HUMAN	UBX domain protein 11	490	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.	NA	Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggccgggaccgggaccggga	0.711		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Deletion - In frame(1)	ovary(1)											40	50	47			NA	NA	1		NA											NA				26608885		1828	4053	5881	SO:0001583	missense			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062	91544		UBX domain containing	30600	protein-coding gene	gene with protein product	socius	609151	UBX domain containing 5	UBXD5	NA	11940653	Standard	NM_145345	NM_183008	NA	Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1468G>A	chr1.hg19:g.26608885C>T	ENSP00000363339:p.Gly490Ser	NA	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	hg19	CCDS41288.1	0.02	2.78455	GACxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	-	2.886	-0.230636	0.05983	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.22945	1.93;2.02;2.37;2.3;2.3;2.37	2.5	-2.32	0.06745	.	2.616560	0.01918	N	0.040283	T	0.06096	0.0158	N	0.00926	-1.1	0.09310	N	0.999997	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.28004	-1.0057	10	0.02654	T	1	.	0.4862	0.00556	0.1926:0.2649:0.1644:0.378	.	457;452;370;490	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	370;247;457;490;490;457	ENSP00000324721:G370S;ENSP00000363340:G247S;ENSP00000349601:G457S;ENSP00000363338:G490S;ENSP00000363339:G490S;ENSP00000363334:G457S	ENSP00000324721:G370S	G	-	1	0	UBXN11	26481472	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-1.097000	0.03349	-0.363000	0.08101	0.472000	0.43445	GGT	NOVEL	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009500.1	0	2.406943	KEEP	1	0	0	8	240	CC	0.99257	0.992566	0		-	8	60	226	0	0	14.121749	98	70	3255	164	ENST00000374222.1	0.075472	0.999996
AIM1L	55057	__UNKNOWN__	__UNKNOWN__	1	26648745	26648745	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	A	rs374694318		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26648745C>A	ENST00000527815.1	-	18	2234	c.2185G>T	c.(2185-2187)Gag>Tag	p.E729*	AIM1L_ENST00000308182.5_Nonsense_Mutation_p.E558*	NM_001039775.3	NP_001034864.2	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	558		NA					carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		AGGCGGCTCTCGGCCCACAGC	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													74	74	74			NA	NA	1		NA											NA				26648745		2203	4300	6503	SO:0001587	stop_gained					1p35	2010-07-14			ENSG00000176092	ENSG00000176092	55057			17295	protein-coding gene	gene with protein product	beta-gamma crystallin domain containing 2	NA			NA		Standard	NM_001039775.2	NM_001039775	NA	Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000527815.1:c.2185G>T	chr1.hg19:g.26648745C>A	ENSP00000433931:p.Glu729*	NA	B2RNG3|Q5T137|Q5T150	hg19		0.02	4.526127	TCTxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	42	9.611122	0.99219	.	.	ENSG00000176092	ENST00000527815;ENST00000308182	.	.	.	5.18	5.18	0.71444	.	0.045149	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	18.6964	0.91603	0.0:1.0:0.0:0.0	.	.	.	.	X	729;558	.	ENSP00000310435:E558X	E	-	1	0	AIM1L	26521332	0.997000	0.39634	0.991000	0.47740	0.974000	0.67602	3.542000	0.53625	2.425000	0.82216	0.561000	0.74099	GAG	NOVEL	AIM1L-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000009703.5	0	8.719568	KEEP	0	0	0	29	767	CC	0.999997	0.999997	0		-	43	60	1246	0	0	104.273822	120	60	3748	285	ENST00000527815.1	0.263804	1
AIM1L	55057	__UNKNOWN__	__UNKNOWN__	1	26662049	26662049	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26662049A>G	ENST00000527815.1	-	13	1612				AIM1L_ENST00000308182.5_Intron	NM_001039775.3	NP_001034864.2	Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	NA		NA					carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		agcactttggaaggccgaggt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					1p35	2010-07-14			ENSG00000176092	ENSG00000176092	55057			17295	protein-coding gene	gene with protein product	beta-gamma crystallin domain containing 2	NA			NA		Standard	NM_001039775.2	NM_001039775	NA	Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000527815.1:c.1562+536T>C	chr1.hg19:g.26662049A>G		NA	B2RNG3|Q5T137|Q5T150	hg19		0.02	-0.245559	TGGxAGG	COVERED																																																																																			NOVEL	AIM1L-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000009703.5	9	2.404882	KEEP	0	0	0	8	218	AA	0.99257	0.636582	0		-	4	60	133	0	0	10.436364	21	60	607	54	ENST00000527815.1	0.16	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	26714799	26714799	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26714799G>A			NA	NA				ZNF683 (15533 upstream) : LIN28A (22469 downstream)						NA		NA									NA						cccaggaggcggaggctgcag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.26714799G>A		NA		hg19		0.02	-0.122804	GGCxGAG	COVERED																																																																																			NOVEL					0			6	2.405925	KEEP	2	0	0	8	226	GG	0.99257	0.194853	0			3	60	91	0	0	7.481876	10	60	333	32		0.230769	0.196312
DHDDS	79947	__UNKNOWN__	__UNKNOWN__	1	26788142	26788142	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26788142A>C	ENST00000360009.2	+	8	842				DHDDS_ENST00000525682.2_Intron|DHDDS_ENST00000526219.1_Intron|DHDDS_ENST00000236342.7_Intron	NM_024887.3|NM_205861.2	NP_079163.2|NP_995583.1	Q86SQ9	DHDDS_HUMAN	dehydrodolichyl diphosphate synthase	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	transferase activity, transferring alkyl or aryl (other than methyl) groups (GO:0016765)			breast(5)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	15		all_cancers(24;2.04e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.0161)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.166)|LUSC - Lung squamous cell carcinoma(448;0.239)		tcccaaagtgatgggattaca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023164	CCDS281.1, CCDS282.1, CCDS57984.1, CCDS57983.1	1p35.3	2014-01-28			ENSG00000117682	ENSG00000117682	79947			20603	protein-coding gene	gene with protein product		608172			NA	12591616	Standard	NM_024887	NM_024887	NA	Approved	HDS, FLJ13102, DS, RP59	uc001bmk.3	Q86SQ9	OTTHUMG00000003554	ENST00000360009.2:c.765+1507A>C	chr1.hg19:g.26788142A>C		NA	B7Z4B9|B7ZB20|D3DPK7|D3DPK8|D3DPK9|E9KL43|Q5T0A4|Q8NE90|Q9BTG5|Q9BTK3|Q9H905	hg19	CCDS281.1	0.02	-0.166641	GTGxTGG	COVERED																																																																																			NOVEL	DHDDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009895.3	10	2.40565	KEEP	0	0	0	8	214	AA	0.99257	0.384528	0		+	3	58	106	0	0	8.591674	14	60	416	41	ENST00000360009.2	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	26808636	26808636	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:26808636T>C			NA	NA				HMGN2 (6173 upstream) : RPS6KA1 (47621 downstream)						NA		NA									NA						ttagtagagatggggtttcgc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.26808636T>C		NA		hg19		0.02	-0.122722	AGAxGGG	COVERED																																																																																			NOVEL					0			4	2.405578	KEEP	0	0	0	8	213	TT	0.99257	0.194853	0			3	60	89	0	0	7.283083	10	60	262	27		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	27199298	27199298	__UNKNOWN__	IGR	SNP	C	C	T	rs6688781	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27199298C>T			NA	NA				SFN (8351 upstream) : RP1-50O24.6 (3325 downstream)						NA		NA									NA						atggtgaaaccctgtctctac	0.552		NA											C|||	613	0.122404	0.0182	0.1138	5008	,	,	NA	14622	0.0288	NA	0.2435	False	NA	,,,	NA	NA	NA	2504	0.2413	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.27199298C>T		NA		hg19		0.02	-0.078927	AACxCTG	UNCOVERED																																																																																			NOVEL					0			6	2.407014	KEEP	3	0	0	8	244	CC	0	0	0			4	60	120	0	0	11.832415	3	60	93	24		0.571429	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	27228098	27228098	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27228098A>G			NA	NA				GPATCH3 (1141 upstream) : NR0B2 (9881 downstream)						NA		NA									NA						gtttcaccatattggtcaggc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.27228098A>G		NA		hg19		0.02	-0.140297	CATxTTG	COVERED																																																																																			NOVEL					0			10	3.908427	KEEP	6	0	0	13	339	AA	0.99254	0.259018	0			3	41	96	0	0	7.87346	11	60	305	40		0.214286	0.260965
NUDC	10726	__UNKNOWN__	__UNKNOWN__	1	27261432	27261432	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27261432A>G	ENST00000321265.5	+	3	282					NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	NA		NA			cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)				cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;6.1e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.87e-29)|Colorectal(126;5.74e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000281)|STAD - Stomach adenocarcinoma(196;0.000604)|KIRC - Kidney renal clear cell carcinoma(1967;0.000739)|READ - Rectum adenocarcinoma(331;0.0421)		acaggcgtgaaccaccgcgcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS292.1	1p35-p34	2013-08-06	2013-08-06		ENSG00000090273	ENSG00000090273	10726			8045	protein-coding gene	gene with protein product		610325	nuclear distribution gene C homolog (A. nidulans), nuclear distribution C homolog (A. nidulans)		NA		Standard		NM_006600	NA	Approved	NudC	uc001bng.2	Q9Y266	OTTHUMG00000004226	ENST00000321265.5:c.160-6516A>G	chr1.hg19:g.27261432A>G		NA	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	hg19	CCDS292.1	0.02	-0.333251	TGAxCCA	COVERED																																																																																			NOVEL	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012172.2	10	5.412854	KEEP	0	0	0	18	487	AA	0.999859	0.851864	0		+	4	49	136	0	0	10.108731	31	60	900	81	ENST00000321265.5	0.114286	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	27359321	27359321	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27359321G>A			NA	NA				FAM46B (19994 upstream) : SLC9A1 (65984 downstream)						NA		NA									NA						ggccaggctggtcttgaactc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.27359321G>A		NA		hg19		0.02	-0.166664	CTGxTCT	UNCOVERED																																																																																			NOVEL					0			7	2.707693	KEEP	4	0	0	9	263	GG	0	0	0			3	39	89	0	0	6.979016	13	60	418	47		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	27359438	27359438	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27359438G>A			NA	NA				FAM46B (20111 upstream) : SLC9A1 (65867 downstream)						NA		NA									NA						acagggtttcgccatgttagc	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.27359438G>A		NA		hg19		0.02	-0.254369	TTCxCCA	COVERED																																																																																			NOVEL					0			8	3.910006	KEEP	0	0	0	13	371	GG	0.994391	0.664773	0			4	60	120	0	0	9.213775	20	60	662	65		0.166667	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	27513427	27513427	__UNKNOWN__	IGR	SNP	T	T	C	rs12725378	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27513427T>C			NA	NA				SLC9A1 (32026 upstream) : RP11-40H20.4 (42169 downstream)						NA		NA									NA						gaggccgaggtgggtggatca	0.552		NA											c|||	1340	0.267572	0.3336	0.2032	5008	,	,	NA	14362	0.1151	NA	0.3141	False	NA	,,,	NA	NA	NA	2504	0.3333	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.27513427T>C		NA		hg19		0.02	-0.184202	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			3	2.406377	KEEP	10	0	0	8	224	TT	0	0	0			9	60	302	0	0	29.07547	9	60	274	60		0.5	0.457757
WDTC1	23038	__UNKNOWN__	__UNKNOWN__	1	27578120	27578120	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27578120A>G	ENST00000361771.3	+	2	284				WDTC1_ENST00000319394.3_Intron			Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	NA		NA			cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		gtcaagaccaacctgggcaac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784	23038		DDB1 and CUL4 associated factors, WD repeat domain containing, Tetratricopeptide (TTC) repeat domain containing	29175	protein-coding gene	gene with protein product	adipose homolog (Drosophila), DDB1 and CUL4 associated factor 9	NA			NA	12717455, 19238144	Standard	NM_015023	NM_015023	NA	Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000361771.3:c.-99-9327A>G	chr1.hg19:g.27578120A>G		NA	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	hg19	CCDS296.1	0.02	-0.201698	CCAxCCT	COVERED																																																																																			NOVEL	WDTC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012341.1	9	2.70643	KEEP	0	0	0	9	242	AA	0.99254	0.486885	0		+	3	60	94	0	0	7.02832	19	60	565	44	ENST00000361771.3	0.136364	0.490544
WDTC1	23038	__UNKNOWN__	__UNKNOWN__	1	27613174	27613174	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27613174G>C	ENST00000361771.3	+	6	674				WDTC1_ENST00000319394.3_Intron			Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	NA		NA			cellular chemical homeostasis (GO:0055082)|cellular response to insulin stimulus (GO:0032869)|glucose metabolic process (GO:0006006)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell size (GO:0008361)	cytosol (GO:0005829)|nucleus (GO:0005634)	enzyme inhibitor activity (GO:0004857)			central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	21		all_cancers(24;3.12e-19)|all_epithelial(13;4.18e-18)|Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.00257)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0443)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;1.02e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000544)|KIRC - Kidney renal clear cell carcinoma(1967;0.00201)|STAD - Stomach adenocarcinoma(196;0.00321)|READ - Rectum adenocarcinoma(331;0.0476)		aggatggtctggatctcctga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023778	CCDS296.1, CCDS60044.1	1p35.3	2013-01-11			ENSG00000142784	ENSG00000142784	23038		DDB1 and CUL4 associated factors, WD repeat domain containing, Tetratricopeptide (TTC) repeat domain containing	29175	protein-coding gene	gene with protein product	adipose homolog (Drosophila), DDB1 and CUL4 associated factor 9	NA			NA	12717455, 19238144	Standard	NM_015023	NM_015023	NA	Approved	KIAA1037, ADP, DCAF9	uc009vst.3	Q8N5D0	OTTHUMG00000004273	ENST00000361771.3:c.292-991G>C	chr1.hg19:g.27613174G>C		NA	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	hg19	CCDS296.1	0.02	-0.140361	TCTxGAT	COVERED																																																																																			NOVEL	WDTC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012341.1	7	3.006065	KEEP	1	0	0	10	290	GG	0.992708	0.259062	0		+	3	60	91	0	0	7.17883	13	60	459	36	ENST00000361771.3	0.1875	0.260965
WASF2	10163	__UNKNOWN__	__UNKNOWN__	1	27756900	27756900	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27756900C>T	ENST00000430629.2	-	2	173				WASF2_ENST00000536657.1_Intron	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	NA		NA			actin cytoskeleton organization (GO:0030036)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of lamellipodium assembly (GO:0010592)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	actin binding (GO:0003779)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		gacagggtctcgctctgtcac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB026542	CCDS304.1, CCDS55582.1	1p36.11	2011-05-10			ENSG00000158195	ENSG00000158195	10163			12733	protein-coding gene	gene with protein product		605875			NA	10381382	Standard	NM_006990	NM_006990	NA	Approved	WAVE2, SCAR2	uc001bof.2	Q9Y6W5	OTTHUMG00000003393	ENST00000430629.2:c.43-1457G>A	chr1.hg19:g.27756900C>T		NA	B4DZN0|O60794|Q9UDY7	hg19	CCDS304.1	0.02	-0.192977	TCTxGCT	COVERED																																																																																			NOVEL	WASF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009516.1	7	3.309546	KEEP	3	0	0	11	330	CC	0.992708	0.454419	0		-	3	60	90	0	0	6.761233	17	60	551	49	ENST00000430629.2	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	27838954	27838954	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:27838954C>T			NA	NA				WASF2 (22285 upstream) : RP1-159A19.4 (13361 downstream)						NA		NA									NA						cacctcggccccccagagtgc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.27838954C>T		NA		hg19		0.02	-0.175438	GCCxCCC	COVERED																																																																																			NOVEL					0			6	2.708423	KEEP	0	0	0	9	288	CC	0.99254	0.384517	0			3	44	88	0	0	6.633936	16	60	535	46		0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	28004395	28004395	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28004395T>G			NA	NA				RNU6-949P (2175 upstream) : RNU6-424P (15846 downstream)						NA		NA									NA						ccagctactttggaggctgaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.28004395T>G		NA		hg19		0.02	-0.149096	CTTxGGA	COVERED																																																																																			NOVEL					0			10	2.705953	KEEP	1	0	0	9	242	TT	0.99257	0.289832	0			3	60	103	1	0	8.291786	14	60	418	36		0.176471	0.292001
STX12	23673	__UNKNOWN__	__UNKNOWN__	1	28124898	28124898	__UNKNOWN__	Intron	SNP	A	A	G	rs141263006	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28124898A>G	ENST00000373943.4	+	4	413				STX12_ENST00000468761.1_Intron	NM_177424.2	NP_803173.1	Q86Y82	STX12_HUMAN	syntaxin 12	NA		NA			cholesterol efflux (GO:0033344)|intracellular protein transport (GO:0006886)|protein stabilization (GO:0050821)|synaptic vesicle exocytosis (GO:0016079)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|central_nervous_system(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|all_lung(284;9.43e-05)|Lung NSC(340;0.000185)|Renal(390;0.00121)|Breast(348;0.0021)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;3.96e-24)|Colorectal(126;3.46e-08)|COAD - Colon adenocarcinoma(152;1.83e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00258)|KIRC - Kidney renal clear cell carcinoma(1967;0.00302)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0649)		gctcatgcctataatcccagc	0.542		NA											A|||	10	0.00199681	0.0076	0.0	5008	,	,	NA	13916	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Ovarian(5;5 342 2097 9488 34083)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC046999	CCDS310.1	1p35.3	2008-05-14			ENSG00000117758	ENSG00000117758	23673			11430	protein-coding gene	gene with protein product		606892			NA	9507000	Standard	NM_177424	NM_177424	NA	Approved	STX13, STX14	uc001bou.4	Q86Y82	OTTHUMG00000003730	ENST00000373943.4:c.289-3291A>G	chr1.hg19:g.28124898A>G		NA	B1AJQ7|O95564	hg19	CCDS310.1	0.02	-0.157839	CCTxTAA	COVERED																																																																																			NOVEL	STX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010519.1	9	3.906607	KEEP	3	0	0	13	340	AA	0.993634	0.320751	0		+	4	60	133	0	0	11.431979	11	60	306	40	ENST00000373943.4	0.266667	0.322807
SMPDL3B	27293	__UNKNOWN__	__UNKNOWN__	1	28277541	28277541	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28277541A>T	ENST00000373894.3	+	3	564				SMPDL3B_ENST00000373888.4_Intron|RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Intron	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	NA		NA			sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		cccaaagtgtagggattacag	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768	27293			21416	protein-coding gene	gene with protein product		NA			NA		Standard	NM_014474	NM_014474	NA	Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.373+1868A>T	chr1.hg19:g.28277541A>T		NA	B7ZB35|Q5T0Z0|Q96CB7	hg19	CCDS30655.1	0.02	-0.245556	TGTxGGG	COVERED																																																																																			NOVEL	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011170.1	8	3.307408	KEEP	0	0	0	11	288	AA	0.993072	0.636904	0		+	3	60	93	0	0	6.643334	24	60	709	51	ENST00000373894.3	0.111111	0.641347
RP11-460I13.2	0	__UNKNOWN__	__UNKNOWN__	1	28285867	28285867	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28285867G>A	ENST00000448015.1	-	0	34										NA		NA									NA						acggggtttcgccatgtttgc	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000448015.1:	chr1.hg19:g.28285867G>A		NA		hg19		0.02	-0.130992	TTCxCCA	COVERED																																																																																			NOVEL	RP11-460I13.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000011174.1	1	2.40557	KEEP	0	0	0	8	217	GT	0.992708	0.227502	0		-	3	60	89	0	0	7.180566	11	60	297	26	ENST00000448015.1	0.214286	0.229173
EYA3	2140	__UNKNOWN__	__UNKNOWN__	1	28327323	28327323	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28327323T>C	ENST00000373871.3	-	12	1234				EYA3_ENST00000471498.1_Intron|EYA3_ENST00000436342.2_Intron|EYA3_ENST00000540618.1_Intron|EYA3_ENST00000545175.1_Intron|EYA3_ENST00000373863.3_Intron|EYA3_ENST00000373864.1_Intron	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	NA		NA			anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		cctgtaatcctagcactttgg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161	2140		Protein tyrosine phosphatases / Asp-based PTPs	3521	protein-coding gene	gene with protein product		601655	eyes absent (Drosophila) homolog 3, eyes absent homolog 3 (Drosophila)		NA	9020840	Standard	NM_001990	NM_001990	NA	Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.994-763A>G	chr1.hg19:g.28327323T>C		NA	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	hg19	CCDS316.1	0.02	-0.219275	TCCxAGC	COVERED																																																																																			NOVEL	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011184.1	11	4.206448	KEEP	0	0	0	14	356	TT	0.995343	0.550313	0		-	3	60	104	0	0	8.026748	19	60	571	52	ENST00000373871.3	0.136364	0.552887
EYA3	2140	__UNKNOWN__	__UNKNOWN__	1	28368236	28368236	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28368236A>G	ENST00000373871.3	-	4	398				EYA3_ENST00000471498.1_Intron|EYA3_ENST00000436342.2_Intron|EYA3_ENST00000540618.1_Intron|EYA3_ENST00000545175.1_Intron|EYA3_ENST00000373863.3_Intron|EYA3_ENST00000373864.1_Intron	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	NA		NA			anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		gcccaggctgatctcaaactc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161	2140		Protein tyrosine phosphatases / Asp-based PTPs	3521	protein-coding gene	gene with protein product		601655	eyes absent (Drosophila) homolog 3, eyes absent homolog 3 (Drosophila)		NA	9020840	Standard	NM_001990	NM_001990	NA	Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.157+845T>C	chr1.hg19:g.28368236A>G		NA	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	hg19	CCDS316.1	0.02	-0.105256	CTGxTCT	UNCOVERED																																																																																			NOVEL	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011184.1	8	3.575145	KEEP	0	0	0	12	319	AA	0.993634	0.138942	0		-	3	60	102	0	0	8.978734	7	60	212	33	ENST00000373871.3	0.3	0.139832
EYA3	2140	__UNKNOWN__	__UNKNOWN__	1	28400215	28400215	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28400215A>G	ENST00000373871.3	-	1	173				EYA3_ENST00000471498.1_Intron|EYA3_ENST00000436342.2_Intron|EYA3_ENST00000540618.1_Intron|EYA3_ENST00000545175.1_Intron|EYA3_ENST00000373863.3_Intron	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	NA		NA			anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		ccagagtgctaggattacaga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161	2140		Protein tyrosine phosphatases / Asp-based PTPs	3521	protein-coding gene	gene with protein product		601655	eyes absent (Drosophila) homolog 3, eyes absent homolog 3 (Drosophila)		NA	9020840	Standard	NM_001990	NM_001990	NA	Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.67+14819T>C	chr1.hg19:g.28400215A>G		NA	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	hg19	CCDS316.1	0.02	-0.192958	GCTxGGA	COVERED																																																																																			NOVEL	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011184.1	5	3.007293	KEEP	0	0	0	10	275	AA	0.992708	0.454419	0		-	3	60	91	0	0	7.010884	15	60	452	47	ENST00000373871.3	0.166667	0.457757
PTAFR	5724	__UNKNOWN__	__UNKNOWN__	1	28475133	28475133	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28475133A>C	ENST00000373857.3	-	0	3034				PTAFR_ENST00000539896.1_3'UTR	NM_000952.4|NM_001164722.2|NM_001164723.2	NP_000943.1|NP_001158194.1|NP_001158195.1	P25105	PTAFR_HUMAN	platelet-activating factor receptor	NA		NA			chemotaxis (GO:0006935)|cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|inositol trisphosphate biosynthetic process (GO:0032959)|interferon-gamma-mediated signaling pathway (GO:0060333)|phosphatidylinositol-mediated signaling (GO:0048015)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|phospholipid binding (GO:0005543)|platelet activating factor receptor activity (GO:0004992)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|stomach(1)	15		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		ccaccacgccaggctaatttt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC063000	CCDS318.1	1p35-p34.3	2012-08-20			ENSG00000169403	ENSG00000169403	5724		GPCR / Class A : Platelet-activating factor receptors	9582	protein-coding gene	gene with protein product		173393			NA	1322356	Standard	NM_000952	NM_001164721	NA	Approved		uc001bpl.3	P25105	OTTHUMG00000003953	ENST00000373857.3:c.*1371T>G	chr1.hg19:g.28475133A>C		NA	A3KMC8|A8K2H5	hg19	CCDS318.1	0.02	3.663344	GCCxGGC	COVERED																																																																																			NOVEL	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011258.1	29	8.284326	KEEP	2	2	58	48	1323	AA	1	1	0		-	8	60	280	1	0	19.088115	111	60	3302	258	ENST00000373857.3	0.067227	1
PTAFR	5724	__UNKNOWN__	__UNKNOWN__	1	28481846	28481846	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28481846T>C	ENST00000373857.3	-	2	597				PTAFR_ENST00000539896.1_Intron|PTAFR_ENST00000305392.3_Intron	NM_000952.4|NM_001164722.2|NM_001164723.2	NP_000943.1|NP_001158194.1|NP_001158195.1	P25105	PTAFR_HUMAN	platelet-activating factor receptor	NA		NA			chemotaxis (GO:0006935)|cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|inositol trisphosphate biosynthetic process (GO:0032959)|interferon-gamma-mediated signaling pathway (GO:0060333)|phosphatidylinositol-mediated signaling (GO:0048015)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|phospholipid binding (GO:0005543)|platelet activating factor receptor activity (GO:0004992)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|stomach(1)	15		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		ctcagcctcctgagtagctgg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063000	CCDS318.1	1p35-p34.3	2012-08-20			ENSG00000169403	ENSG00000169403	5724		GPCR / Class A : Platelet-activating factor receptors	9582	protein-coding gene	gene with protein product		173393			NA	1322356	Standard	NM_000952	NM_001164721	NA	Approved		uc001bpl.3	P25105	OTTHUMG00000003953	ENST00000373857.3:c.38-4276A>G	chr1.hg19:g.28481846T>C		NA	A3KMC8|A8K2H5	hg19	CCDS318.1	0.02	-0.114021	TCCxGAG	UNCOVERED																																																																																			NOVEL	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011258.1	9	3.30889	KEEP	4	0	0	11	313	TT	0.99254	0.161255	0		-	3	40	83	0	0	6.801127	9	60	277	35	ENST00000373857.3	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	28686921	28686921	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28686921A>C			NA	NA				MED18 (24445 upstream) : PHACTR4 (9192 downstream)						NA		NA									NA						ccaaggcgggaggatcacgag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.28686921A>C		NA		hg19		0.02	-0.166639	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			8	2.404843	KEEP	6	0	0	8	211	AA	0	0	0			3	60	87	0	0	6.692406	14	60	417	40		0.176471	0.353947
PHACTR4	65979	__UNKNOWN__	__UNKNOWN__	1	28715091	28715091	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28715091G>A	ENST00000373839.3	+	1	223				PHACTR4_ENST00000493669.1_Intron	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	NA		NA			actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ggctgggcacggtggctcacg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138	65979		Phosphatase and actin regulators	25793	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 124	608726			NA	11483580, 15107502	Standard	NM_023923	NM_023923	NA	Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.-39+18755G>A	chr1.hg19:g.28715091G>A		NA	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	hg19	CCDS41293.1	0.02	-0.210468	CACxGTG	COVERED																																																																																			NOVEL	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009868.4	9	3.607825	KEEP	1	0	0	12	324	GG	0.993072	0.518544	0		+	3	60	93	0	0	7.210699	15	60	486	51	ENST00000373839.3	0.166667	0.522161
PHACTR4	65979	__UNKNOWN__	__UNKNOWN__	1	28720802	28720802	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28720802A>G	ENST00000373839.3	+	2	223				PHACTR4_ENST00000493669.1_Intron	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	NA		NA			actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		agggaaggaaaggagggaggg	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138	65979		Phosphatase and actin regulators	25793	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 124	608726			NA	11483580, 15107502	Standard	NM_023923	NM_023923	NA	Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.-38-13119A>G	chr1.hg19:g.28720802A>G		NA	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	hg19	CCDS41293.1	0.02	-0.184171	GAAxGGA	COVERED																																																																																			NOVEL	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000009868.4	3	2.405076	KEEP	0	0	0	8	210	AA	0.99257	0.420331	0		+	3	60	97	0	1	7.392532	18	60	531	34	ENST00000373839.3	0.142857	0.423478
PHACTR4	65979	__UNKNOWN__	__UNKNOWN__	1	28773058	28773058	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28773058G>A	ENST00000373836.3	+	1	260				PHACTR4_ENST00000493669.1_Intron|PHACTR4_ENST00000373839.3_Intron	NM_023923.3	NP_076412.3	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	NA		NA			actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ttgggaggccgaggcaggtgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138	65979		Phosphatase and actin regulators	25793	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 124	608726			NA	11483580, 15107502	Standard	NM_023923	NM_023923	NA	Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373836.3:c.46+8117G>A	chr1.hg19:g.28773058G>A		NA	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	hg19	CCDS41294.1	0.02	-0.25439	GCCxAGG	UNCOVERED																																																																																			NOVEL	PHACTR4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000158544.1	8	2.406724	KEEP	4	0	0	8	239	GG	0	0	0		+	3	60	92	0	0	6.445012	26	60	854	62	ENST00000373836.3	0.103448	0.668523
PHACTR4	65979	__UNKNOWN__	__UNKNOWN__	1	28807279	28807279	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28807279T>C	ENST00000373836.3	+	8	2004				PHACTR4_ENST00000493669.1_Intron|PHACTR4_ENST00000373839.3_Intron	NM_023923.3	NP_076412.3	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	NA		NA			actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		cggctcactgtaacctccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138	65979		Phosphatase and actin regulators	25793	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 124	608726			NA	11483580, 15107502	Standard	NM_023923	NM_023923	NA	Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373836.3:c.1790+163T>C	chr1.hg19:g.28807279T>C		NA	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	hg19	CCDS41294.1	0.02	-0.30686	CTGxAAC	COVERED																																																																																			NOVEL	PHACTR4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000158544.1	7	2.404433	KEEP	0	0	0	8	203	TT	0.99257	0.7943	0		+	5	60	164	0	0	12.841174	26	60	726	54	ENST00000373836.3	0.16129	0.800245
PHACTR4	65979	__UNKNOWN__	__UNKNOWN__	1	28825567	28825567	__UNKNOWN__	3'UTR	SNP	G	G	A	rs534907338	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28825567G>A	ENST00000373836.3	+	0	4859				PHACTR4_ENST00000373839.3_3'UTR	NM_023923.3	NP_076412.3	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	NA		NA			actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		gcaacagagcgagactccatc	0.458		NA											G|||	8	0.00159744	0.0061	0.0	5008	,	,	NA	10474	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138	65979		Phosphatase and actin regulators	25793	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 124	608726			NA	11483580, 15107502	Standard	NM_023923	NM_023923	NA	Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373836.3:c.*2506G>A	chr1.hg19:g.28825567G>A		NA	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	hg19	CCDS41294.1	0.02	4.324542	AGCxAGA	COVERED																																																																																			NOVEL	PHACTR4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000158544.1	38	24.512281	KEEP	7	2	55	101	2759	GG	1	1	0		+	7	60	208	0	0	11.775592	148	60	4585	421	ENST00000373836.3	0.045161	1
TRNAU1AP	54952	__UNKNOWN__	__UNKNOWN__	1	28889841	28889841	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28889841C>T	ENST00000373830.3	+	5	304				TRNAU1AP_ENST00000495995.1_Intron	NM_017846.4	NP_060316.1	Q9NX07	TSAP1_HUMAN	tRNA selenocysteine 1 associated protein 1	NA		NA			selenocysteine incorporation (GO:0001514)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	8						acgggcagatcacaaggtcag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS324.1	1p35.3	2013-02-12	2008-09-05	2008-09-05	ENSG00000180098	ENSG00000180098	54952		RNA binding motif (RRM) containing	30813	protein-coding gene	gene with protein product		NA	tRNA selenocysteine associated protein 1	TRSPAP1	NA	10606267, 16230358	Standard	NM_017846	NM_017846	NA	Approved	SECP43, FLJ20503	uc001bqi.3	Q9NX07	OTTHUMG00000003653	ENST00000373830.3:c.279-1374C>T	chr1.hg19:g.28889841C>T		NA	Q86SU7	hg19	CCDS324.1	0.02	-0.166665	GATxACA	COVERED																																																																																			NOVEL	TRNAU1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010346.1	3	3.610782	KEEP	0	0	0	12	373	CC	0.993634	0.351693	0		+	3	30	87	0	0	6.779094	13	60	428	51	ENST00000373830.3	0.1875	0.353947
RAB42	115273	__UNKNOWN__	__UNKNOWN__	1	28920880	28920880	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28920880G>A	ENST00000373826.3	+	0	875				TAF12_ENST00000471683.1_Intron	NM_152304.1	NP_689517.1	Q8N4Z0	RAB42_HUMAN	RAB42, member RAS oncogene family	NA		NA			small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00618)|all_lung(284;0.00909)|Breast(348;0.0249)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0577)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00298)|KIRC - Kidney renal clear cell carcinoma(1967;0.00948)|BRCA - Breast invasive adenocarcinoma(304;0.0213)|READ - Rectum adenocarcinoma(331;0.0649)		tgaggtcaggggttcgagacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC033175	CCDS325.1	1p35.3	2014-02-12	2006-04-28		ENSG00000188060	ENSG00000188060	115273		RAB, member RAS oncogene	28702	protein-coding gene	gene with protein product		NA	RAB42, member RAS homolog family		NA		Standard	NM_152304	NM_152304	NA	Approved	MGC45806	uc001bqv.3	Q8N4Z0	OTTHUMG00000003656	ENST00000373826.3:c.*251G>A	chr1.hg19:g.28920880G>A		NA	B2R5G2	hg19	CCDS325.1	0.02	1.400968	AGGxGTT	COVERED																																																																																			NOVEL	RAB42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010371.1	2	3.542831	KEEP	0	1	26	21	629	GG	0.999879	0.979408	0		+	5	60	144	0	0	9.779473	44	60	1430	84	ENST00000373826.3	0.102041	0.979526
TAF12	6883	__UNKNOWN__	__UNKNOWN__	1	28940938	28940938	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28940938A>G	ENST00000263974.4	-	4	681				TAF12_ENST00000373824.4_Intron|TAF12_ENST00000471683.1_Intron	NM_001135218.1	NP_001128690.1	Q16514	TAF12_HUMAN	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa	NA		NA			chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			ovary(1)|upper_aerodigestive_tract(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		gctcatgcctataatcccagc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011986	CCDS326.1	1p35	2008-02-05	2002-08-29	2001-12-07	ENSG00000120656	ENSG00000120656	6883			11545	protein-coding gene	gene with protein product		600773	TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD	TAF2J	NA	7729427	Standard	NM_005644	NM_005644	NA	Approved	TAFII20	uc001bqy.3	Q16514	OTTHUMG00000003655	ENST00000263974.4:c.247-1065T>C	chr1.hg19:g.28940938A>G		NA	D3DPM5|Q15775|Q5T077	hg19	CCDS326.1	0.02	-0.227987	CCTxTAA	COVERED																																																																																			NOVEL	TAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010367.1	10	3.006824	KEEP	1	0	0	10	265	AA	0.992708	0.578679	0		-	4	60	138	0	0	11.094883	19	60	534	52	ENST00000263974.4	0.173913	0.58293
TAF12	6883	__UNKNOWN__	__UNKNOWN__	1	28961429	28961429	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28961429A>G	ENST00000263974.4	-	1	351				TAF12_ENST00000373824.4_Intron	NM_001135218.1	NP_001128690.1	Q16514	TAF12_HUMAN	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa	NA		NA			chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			ovary(1)|upper_aerodigestive_tract(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		caacaagagcaaaactccatc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011986	CCDS326.1	1p35	2008-02-05	2002-08-29	2001-12-07	ENSG00000120656	ENSG00000120656	6883			11545	protein-coding gene	gene with protein product		600773	TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD	TAF2J	NA	7729427	Standard	NM_005644	NM_005644	NA	Approved	TAFII20	uc001bqy.3	Q16514	OTTHUMG00000003655	ENST00000263974.4:c.83+7737T>C	chr1.hg19:g.28961429A>G		NA	D3DPM5|Q15775|Q5T077	hg19	CCDS326.1	0.02	-0.324499	AGCxAAA	UNCOVERED																																																																																			NOVEL	TAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010367.1	6	2.406093	KEEP	1	0	0	8	220	AA	0	0	0		-	5	60	154	2	0	11.622693	29	60	856	66	ENST00000263974.4	0.147059	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	28986999	28986999	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:28986999A>G			NA	NA				RNU11 (11754 upstream) : GMEB1 (8244 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.28986999A>G		NA		hg19		0.02	-0.140315	CACxCCT	COVERED																																																																																			NOVEL					0			7	3.907599	KEEP	0	0	0	13	336	AA	0.994391	0.259501	0			3	60	106	0	0	8.678993	13	60	375	43		0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	29050814	29050814	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29050814A>G			NA	NA				GMEB1 (4949 upstream) : YTHDF2 (12318 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.29050814A>G		NA		hg19		0.02	-0.219227	GGCxTGA	COVERED																																																																																			NOVEL					0			4	2.70064	KEEP	0	0	0	9	232	AA	0.99254	0.548763	0			3	60	97	0	0	7.206131	21	60	615	47		0.125	0.552887
YTHDF2	51441	__UNKNOWN__	__UNKNOWN__	1	29079096	29079096	__UNKNOWN__	Intron	SNP	A	A	G	rs71642246		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29079096A>G	ENST00000373812.3	+	4	2078				YTHDF2_ENST00000478283.1_Intron|YTHDF2_ENST00000542507.1_Intron|YTHDF2_ENST00000541996.1_Intron	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	NA		NA			humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		gtgagccaccatgcctggccc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492	51441			31675	protein-coding gene	gene with protein product		610640	YTH domain family 2		NA	10508479	Standard	NM_016258	NM_016258	NA	Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.1716+8598A>G	chr1.hg19:g.29079096A>G		NA	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	hg19	CCDS41296.1	0.02	-0.289441	ACCxTGC	COVERED																																																																																			NOVEL	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010335.1	10	3.608474	KEEP	0	0	0	12	322	AA	0.993634	0.756043	0		+	3	60	98	0	0	6.909612	29	60	873	65	ENST00000373812.3	0.09375	0.760887
YTHDF2	51441	__UNKNOWN__	__UNKNOWN__	1	29092139	29092139	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29092139G>A	ENST00000373812.3	+	5	2078				YTHDF2_ENST00000478283.1_Intron|YTHDF2_ENST00000542507.1_Intron|YTHDF2_ENST00000541996.1_Intron	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	NA		NA			humoral immune response (GO:0006959)|regulation of mRNA stability (GO:0043488)	cytoplasmic mRNA processing body (GO:0000932)	N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		tgttgttgttgttgttgtaga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155095	CCDS41296.1, CCDS53287.1	1p35	2008-02-05	2004-11-16		ENSG00000198492	ENSG00000198492	51441			31675	protein-coding gene	gene with protein product		610640	YTH domain family 2		NA	10508479	Standard	NM_016258	NM_016258	NA	Approved	HGRG8, NY-REN-2	uc021okf.1	Q9Y5A9	OTTHUMG00000003648	ENST00000373812.3:c.1717-3302G>A	chr1.hg19:g.29092139G>A		NA	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	hg19	CCDS41296.1	0.02	-0.175447	GTTxTTG	COVERED																																																																																			NOVEL	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010335.1	12	3.008916	KEEP	0	0	0	10	305	GG	0.992708	0.384582	0		+	3	60	87	0	0	6.691987	14	60	481	45	ENST00000373812.3	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	29207400	29207400	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29207400A>G			NA	NA				RP1-212P9.3 (3552 upstream) : Y_RNA (837 downstream)						NA		NA									NA						acaggcgtgaaccaccacact	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.29207400A>G		NA		hg19		0.02	-0.18416	TGAxCCA	COVERED																																																																																			NOVEL					0			15	2.70637	KEEP	0	0	0	9	243	AA	0.99254	0.420319	0			3	60	88	0	0	6.635412	16	60	478	35		0.157895	0.423478
EPB41	2035	__UNKNOWN__	__UNKNOWN__	1	29257067	29257067	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29257067A>G	ENST00000343067.4	+	1	120				EPB41_ENST00000398863.2_Intron|EPB41_ENST00000347529.3_Intron|EPB41_ENST00000373797.1_Intron|EPB41_ENST00000349460.4_Intron|EPB41_ENST00000373800.3_Intron|EPB41_ENST00000356093.2_Intron|EPB41_ENST00000373798.1_Intron	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	NA		NA			actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		cacgatcttgactcactgcaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023	2035			3377	protein-coding gene	gene with protein product		130500	elliptocytosis 1, RH-linked	EL1	NA		Standard	NM_203342	NM_001166005	NA	Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.-8+43345A>G	chr1.hg19:g.29257067A>G		NA	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	hg19	CCDS53288.1	0.02	-0.166628	TTGxCTC	COVERED																																																																																			NOVEL	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010312.1	6	2.404807	KEEP	0	0	0	8	206	AA	0.99257	0.351317	0		+	4	60	134	0	0	11.168729	14	60	410	36	ENST00000343067.4	0.222222	0.353947
EPB41	2035	__UNKNOWN__	__UNKNOWN__	1	29269914	29269914	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29269914T>C	ENST00000343067.4	+	2	120				EPB41_ENST00000398863.2_Intron|EPB41_ENST00000347529.3_Intron|EPB41_ENST00000373797.1_Intron|EPB41_ENST00000349460.4_Intron|EPB41_ENST00000373800.3_Intron|EPB41_ENST00000356093.2_Intron|EPB41_ENST00000373798.1_Intron	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	NA		NA			actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		cctgtaatcctagcactttgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023	2035			3377	protein-coding gene	gene with protein product		130500	elliptocytosis 1, RH-linked	EL1	NA		Standard	NM_203342	NM_001166005	NA	Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.-7-44029T>C	chr1.hg19:g.29269914T>C		NA	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	hg19	CCDS53288.1	0.02	-0.228012	TCCxAGC	COVERED																																																																																			NOVEL	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010312.1	6	4.51117	KEEP	0	0	0	15	409	TT	0.99649	0.580884	0		+	3	60	103	1	0	7.992259	18	60	534	66	ENST00000343067.4	0.142857	0.58293
EPB41	2035	__UNKNOWN__	__UNKNOWN__	1	29297630	29297630	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29297630A>G	ENST00000343067.4	+	2	120				EPB41_ENST00000398863.2_Intron|EPB41_ENST00000347529.3_Intron|EPB41_ENST00000373797.1_Intron|EPB41_ENST00000349460.4_Intron|EPB41_ENST00000373800.3_Intron|EPB41_ENST00000356093.2_Intron|EPB41_ENST00000373798.1_Intron	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	NA		NA			actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		aaagtgctggaattacaggca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023	2035			3377	protein-coding gene	gene with protein product		130500	elliptocytosis 1, RH-linked	EL1	NA		Standard	NM_203342	NM_001166005	NA	Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.-7-16313A>G	chr1.hg19:g.29297630A>G		NA	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	hg19	CCDS53288.1	0.02	-0.245578	TGGxATT	COVERED																																																																																			NOVEL	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010312.1	16	5.113072	KEEP	1	0	0	17	471	AA	0.999366	0.640941	0		+	4	60	127	0	0	10.169183	17	60	510	65	ENST00000343067.4	0.190476	0.641347
EPB41	2035	__UNKNOWN__	__UNKNOWN__	1	29330544	29330544	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29330544A>G	ENST00000343067.4	+	4	913				EPB41_ENST00000398863.2_Intron|EPB41_ENST00000347529.3_Intron|EPB41_ENST00000373797.1_Intron|EPB41_ENST00000349460.4_Intron|EPB41_ENST00000373800.3_Intron|EPB41_ENST00000356093.2_Intron|EPB41_ENST00000373798.1_Intron	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	NA		NA			actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		aaagtgctggaattacaggca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023	2035			3377	protein-coding gene	gene with protein product		130500	elliptocytosis 1, RH-linked	EL1	NA		Standard	NM_203342	NM_001166005	NA	Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.786+6713A>G	chr1.hg19:g.29330544A>G		NA	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	hg19	CCDS53288.1	0.02	-0.166647	TGGxATT	COVERED																																																																																			NOVEL	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010312.1	4	3.006899	KEEP	0	0	0	10	273	AA	0.992708	0.351366	0		+	3	60	94	0	0	7.572352	12	60	359	41	ENST00000343067.4	0.2	0.353947
EPB41	2035	__UNKNOWN__	__UNKNOWN__	1	29393456	29393456	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29393456A>G	ENST00000343067.4	+	16	2311				EPB41_ENST00000398863.2_Intron|EPB41_ENST00000347529.3_Intron|EPB41_ENST00000349460.4_Intron|EPB41_ENST00000373800.3_Intron|EPB41_ENST00000356093.2_Intron|EPB41_ENST00000373798.1_Intron	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	NA		NA			actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		caaagtgctgagattacaggc	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023	2035			3377	protein-coding gene	gene with protein product		130500	elliptocytosis 1, RH-linked	EL1	NA		Standard	NM_203342	NM_001166005	NA	Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.2184+1786A>G	chr1.hg19:g.29393456A>G		NA	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	hg19	CCDS53288.1	0.02	-0.131563	CTGxGAT	COVERED																																																																																			NOVEL	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010312.1	8	2.406306	KEEP	2	0	0	8	224	AA	0.99257	0.22747	0		+	3	60	102	0	0	8.582047	10	60	299	39	ENST00000343067.4	0.230769	0.229173
EPB41	2035	__UNKNOWN__	__UNKNOWN__	1	29413675	29413675	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29413675C>G	ENST00000343067.4	+	17	2311				EPB41_ENST00000398863.2_Intron|EPB41_ENST00000347529.3_Intron|EPB41_ENST00000349460.4_Intron|EPB41_ENST00000373800.3_Intron|EPB41_ENST00000356093.2_Intron|EPB41_ENST00000373798.1_Intron	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	NA		NA			actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		ggatggtctccatctcctgac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023	2035			3377	protein-coding gene	gene with protein product		130500	elliptocytosis 1, RH-linked	EL1	NA		Standard	NM_203342	NM_001166005	NA	Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.2185-10644C>G	chr1.hg19:g.29413675C>G		NA	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	hg19	CCDS53288.1	0.02	-0.131578	CTCxATC	COVERED																																																																																			NOVEL	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010312.1	6	3.610573	KEEP	2	0	0	12	364	CC	0.993072	0.259157	0		+	3	40	88	0	1	7.072907	11	60	371	43	ENST00000343067.4	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	29470243	29470243	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29470243A>G			NA	NA				TMEM200B (19796 upstream) : RP11-242O24.3 (762 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.29470243A>G		NA		hg19		0.02	-0.297214	CTGxGAT	COVERED																																																																																			NOVEL					0			14	5.113658	KEEP	2	0	0	17	483	AA	0.999366	0.780565	0			4	60	105	0	0	7.386833	26	60	763	74		0.133333	0.78106
MECR	51102	__UNKNOWN__	__UNKNOWN__	1	29543986	29543986	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29543986T>C	ENST00000263702.6	-	2	202				MECR_ENST00000489248.1_Intron|MECR_ENST00000373791.3_Intron			Q9BV79	MECR_HUMAN	mitochondrial trans-2-enoyl-CoA reductase	NA		NA			fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)	11		Colorectal(325;0.000389)|Breast(348;0.00765)|Lung NSC(340;0.0081)|all_lung(284;0.00914)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.39e-07)|COAD - Colon adenocarcinoma(152;2.04e-05)|STAD - Stomach adenocarcinoma(196;0.0195)|BRCA - Breast invasive adenocarcinoma(304;0.053)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.137)		ctcggcctcctaaagtgctgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS30659.1, CCDS30660.1	1p35.3	2012-09-20			ENSG00000116353	ENSG00000116353	51102	1.3.1.38		19691	protein-coding gene	gene with protein product	nuclear receptor binding factor 1, mitochondrial 2-enoyl thioester reductase	608205			NA	9795230, 12654921	Standard	NM_016011	XM_005245885	NA	Approved	CGI-63, NRBF1, FASN2B	uc001brq.1	Q9BV79	OTTHUMG00000059082	ENST00000263702.6:c.177-789A>G	chr1.hg19:g.29543986T>C		NA	B3KT72|Q5SYU0|Q5SYU1|Q5SYU2|Q6IBU9|Q9Y373	hg19	CCDS30659.1	0.02	-0.175387	TCCxAAA	UNCOVERED																																																																																			NOVEL	MECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130740.1	13	3.007665	KEEP	4	0	0	10	275	TT	0	0	0		-	3	60	89	0	0	6.662054	17	60	496	40	ENST00000263702.6	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	29819035	29819035	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:29819035A>G			NA	NA				AL139151.1 (59961 upstream) : AC092265.1 (298356 downstream)						NA		NA									NA						tcatgccactacactccagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.29819035A>G		NA		hg19		0.02	-0.166638	ACTxCAC	COVERED																																																																																			NOVEL					0			5	2.705982	KEEP	0	0	0	9	235	AA	0.99254	0.351306	0			3	52	105	0	0	8.491742	14	60	405	35		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	30083787	30083787	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:30083787A>G			NA	NA				AL139151.1 (324713 upstream) : AC092265.1 (33604 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.30083787A>G		NA		hg19		0.02	-0.28066	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.70673	KEEP	2	0	0	9	247	AC	0.992708	0.734278	0			3	60	102	0	0	7.492319	25	60	739	67		0.107143	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	30184388	30184388	__UNKNOWN__	IGR	SNP	C	C	T	rs144003208	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:30184388C>T			NA	NA				RP4-656G21.1 (1994 upstream) : AL645944.1 (173360 downstream)						NA		NA									NA						aggtgtgagccaccgcgcccg	0.542		NA											-|||	46	0.0091853	0.003	0.0058	5008	,	,	NA	15088	0.002	NA	0.0348	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.30184388C>T		NA		hg19		0.02	-0.105205	AGCxACC	UNCOVERED																																																																																			NOVEL					0			3	2.707073	KEEP	17	0	0	9	253	CC	0	0	0			5	60	139	0	0	12.988255	6	60	201	39		0.454545	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	31075727	31075727	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31075727T>C			NA	NA				RP4-591L5.2 (181772 upstream) : MATN1 (108396 downstream)						NA		NA									NA						gagcaagacttcatctcaaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.31075727T>C		NA		hg19		0.02	-0.08769	ACTxCAT	UNCOVERED																																																																																			NOVEL					0			2	2.404846	KEEP	2	0	0	8	204	TT	0.99257	0.09898	0			3	60	89	0	0	7.67869	7	60	196	35		0.3	0.099721
PUM1	9698	__UNKNOWN__	__UNKNOWN__	1	31445009	31445009	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31445009C>G	ENST00000257075.5	-	10	1600				PUM1_ENST00000423018.2_Intron|PUM1_ENST00000424085.2_Intron|PUM1_ENST00000373742.2_Intron|PUM1_ENST00000426105.2_Intron|PUM1_ENST00000373747.3_Intron|PUM1_ENST00000490546.1_Intron|PUM1_ENST00000440538.2_Intron|PUM1_ENST00000373741.4_Intron	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	NA		NA			membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		ggctgaggcacgagaattgct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644	9698			14957	protein-coding gene	gene with protein product		607204	pumilio (Drosophila) homolog 1, pumilio homolog 1 (Drosophila)		NA		Standard		NM_001020658	NA	Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1506+2488G>C	chr1.hg19:g.31445009C>G		NA	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	hg19	CCDS338.1	0.02	-0.131576	GCAxGAG	COVERED																																																																																			NOVEL	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010671.1	6	2.406919	KEEP	0	0	0	8	237	CC	0.99257	0.289832	0		-	3	60	90	0	0	7.381908	10	60	325	33	ENST00000257075.5	0.230769	0.292001
PUM1	9698	__UNKNOWN__	__UNKNOWN__	1	31530347	31530347	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31530347G>A	ENST00000257075.5	-	2	457				PUM1_ENST00000423018.2_Intron|PUM1_ENST00000424085.2_Intron|PUM1_ENST00000373742.2_Intron|PUM1_ENST00000426105.2_Intron|PUM1_ENST00000373747.3_Intron|PUM1_ENST00000440538.2_Intron|PUM1_ENST00000373741.4_Intron	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	NA		NA			membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		tgaggcaggtggatcacatga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644	9698			14957	protein-coding gene	gene with protein product		607204	pumilio (Drosophila) homolog 1, pumilio homolog 1 (Drosophila)		NA		Standard		NM_001020658	NA	Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.363+1703C>T	chr1.hg19:g.31530347G>A		NA	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	hg19	CCDS338.1	0.02	-0.1579	GGTxGAT	COVERED																																																																																			NOVEL	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010671.1	11	3.008417	KEEP	3	0	0	10	294	GG	0.99254	0.320398	0		-	3	42	92	0	0	7.372117	12	60	401	41	ENST00000257075.5	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	31570781	31570781	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31570781C>T			NA	NA				PUM1 (31943 upstream) : NKAIN1 (81810 downstream)						NA		NA									NA						ctcaaagtgccgggattacag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.31570781C>T		NA		hg19		0.02	-0.228042	TGCxGGG	COVERED																																																																																			NOVEL					0			8	3.308647	KEEP	0	0	0	11	315	CC	0.993072	0.578892	0			4	60	117	0	0	8.995109	19	60	603	52		0.173913	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	31597585	31597585	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31597585A>G			NA	NA				PUM1 (58747 upstream) : NKAIN1 (55006 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.31597585A>G		NA		hg19		0.02	-0.236772	GCTxGGA	COVERED																																																																																			NOVEL					0			13	3.909366	KEEP	1	0	0	13	356	AA	0.994391	0.608972	0			3	60	98	0	0	7.143151	24	60	699	56		0.111111	0.612407
SNRNP40	9410	__UNKNOWN__	__UNKNOWN__	1	31766637	31766637	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31766637T>C	ENST00000263694.4	-	2	160				SNRNP40_ENST00000446633.2_Intron	NM_004814.2	NP_004805.2	Q96DI7	SNR40_HUMAN	small nuclear ribonucleoprotein 40kDa (U5)	NA		NA			gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	7						ctacgttgcctaggctggtct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF090988	CCDS340.1	1p35.2	2013-01-09	2008-10-29	2008-10-29	ENSG00000060688	ENSG00000060688	9410		WD repeat domain containing	30857	protein-coding gene	gene with protein product		607797	WD repeat domain 57 (U5 snRNP specific)	WDR57	NA	9774689, 9731529, 10788320	Standard	NM_004814	NM_004814	NA	Approved	PRP8BP, SPF38, PRPF8BP, HPRP8BP	uc009vtt.3	Q96DI7	OTTHUMG00000003790	ENST00000263694.4:c.142-442A>G	chr1.hg19:g.31766637T>C		NA	B4DQJ1|O75938|O95320	hg19	CCDS340.1	0.02	-0.219267	GCCxAGG	COVERED																																																																																			NOVEL	SNRNP40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010657.1	5	3.609175	KEEP	0	0	0	12	330	TT	0.993634	0.549368	0		-	3	60	105	0	0	8.064633	20	60	597	57	ENST00000263694.4	0.130435	0.552887
ZCCHC17	51538	__UNKNOWN__	__UNKNOWN__	1	31813445	31813445	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31813445C>T	ENST00000373714.1	+	5	578				ZCCHC17_ENST00000344147.5_Intron|RP11-266K22.2_ENST00000430143.1_RNA|ZCCHC17_ENST00000479629.1_Intron|ZCCHC17_ENST00000422613.2_Intron|ZCCHC17_ENST00000546109.1_Intron	NM_001282568.1|NM_001282570.1	NP_001269497.1|NP_001269499.1	Q9NP64	NO40_HUMAN	zinc finger, CCHC domain containing 17	NA		NA				cytosolic large ribosomal subunit (GO:0022625)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)|all_neural(195;0.146)|Medulloblastoma(700;0.151)|Breast(348;0.222)		STAD - Stomach adenocarcinoma(196;0.0215)|READ - Rectum adenocarcinoma(331;0.168)		attacaggcgcgagccaccgc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151085	CCDS341.1, CCDS60061.1, CCDS72741.1, CCDS72742.1, CCDS72743.1, CCDS72744.1	1p35.2	2008-05-02			ENSG00000121766	ENSG00000121766	51538		Zinc fingers, CCHC domain containing	30246	protein-coding gene	gene with protein product		NA			NA	12202495, 12893261	Standard	NM_016505	NM_001282572	NA	Approved	PS1D, HSPC251, pNO40	uc001bsp.1	Q9NP64	OTTHUMG00000003791	ENST00000373714.1:c.317+1550C>T	chr1.hg19:g.31813445C>T		NA	B4DY38|D3DPN4|Q6PKH4|Q9NYG4|Q9P0M8	hg19	CCDS341.1	0.02	-0.307001	GCGxGAG	COVERED																																																																																			NOVEL	ZCCHC17-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000010665.1	3	2.707101	KEEP	0	0	0	9	262	CC	0.99254	0.794276	0		+	4	60	120	0	0	8.858155	25	60	806	72	ENST00000373714.1	0.137931	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	31861788	31861788	__UNKNOWN__	IGR	SNP	G	G	A	rs565018965		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:31861788G>A			NA	NA				FABP3 (15865 upstream) : SERINC2 (20623 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.592		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18626	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.31861788G>A		NA		hg19		0.02	-0.131577	CACxCCT	COVERED																																																																																			NOVEL					0			4	3.308986	KEEP	1	0	0	11	327	GG	0.993072	0.227586	0			3	60	92	0	0	7.472812	11	60	357	41		0.214286	0.229173
TINAGL1	64129	__UNKNOWN__	__UNKNOWN__	1	32047895	32047895	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32047895T>C	ENST00000271064.7	+	4	450				TINAGL1_ENST00000537531.1_Intron|TINAGL1_ENST00000457433.2_Intron|TINAGL1_ENST00000481165.1_Intron	NM_001204415.1|NM_022164.2	NP_001191344.1|NP_071447.1	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	NA		NA			endosomal transport (GO:0016197)|immune response (GO:0006955)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type peptidase activity (GO:0008234)|extracellular matrix structural constituent (GO:0005201)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			breast(2)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		caccactgcattccagcctgg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB050716	CCDS343.1, CCDS55586.1, CCDS72745.1	1p34.3	2014-04-22	2005-08-18	2005-08-18	ENSG00000142910	ENSG00000142910	64129			19168	protein-coding gene	gene with protein product		NA	lipocalin 7, TINAG-like 1	LCN7	NA	11170462	Standard	NM_022164	NM_022164	NA	Approved	P3ECSL, LIECG3, ARG1, TINAGRP	uc001bta.3	Q9GZM7	OTTHUMG00000003884	ENST00000271064.7:c.375-855T>C	chr1.hg19:g.32047895T>C		NA	A8K9Q5|B4DPK6|D3DPN8|Q8TEJ9|Q8WZ23|Q96GZ4|Q96JW3	hg19	CCDS343.1	0.02	-0.201726	GCAxTCC	COVERED																																																																																			NOVEL	TINAGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011072.1	10	2.406138	KEEP	0	0	0	8	225	TT	0.99257	0.4869	0		+	4	60	133	1	0	10.863097	16	60	469	42	ENST00000271064.7	0.2	0.490544
TINAGL1	64129	__UNKNOWN__	__UNKNOWN__	1	32053075	32053075	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32053075A>G	ENST00000271064.7	+	0	1975				TINAGL1_ENST00000457433.2_3'UTR|TINAGL1_ENST00000481165.1_3'UTR	NM_001204415.1|NM_022164.2	NP_001191344.1|NP_071447.1	Q9GZM7	TINAL_HUMAN	tubulointerstitial nephritis antigen-like 1	NA		NA			endosomal transport (GO:0016197)|immune response (GO:0006955)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type peptidase activity (GO:0008234)|extracellular matrix structural constituent (GO:0005201)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			breast(2)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(4)|prostate(1)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		STAD - Stomach adenocarcinoma(196;0.0526)|READ - Rectum adenocarcinoma(331;0.145)		gcaccaccacacctggctaat	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB050716	CCDS343.1, CCDS55586.1, CCDS72745.1	1p34.3	2014-04-22	2005-08-18	2005-08-18	ENSG00000142910	ENSG00000142910	64129			19168	protein-coding gene	gene with protein product		NA	lipocalin 7, TINAG-like 1	LCN7	NA	11170462	Standard	NM_022164	NM_022164	NA	Approved	P3ECSL, LIECG3, ARG1, TINAGRP	uc001bta.3	Q9GZM7	OTTHUMG00000003884	ENST00000271064.7:c.*495A>G	chr1.hg19:g.32053075A>G		NA	A8K9Q5|B4DPK6|D3DPN8|Q8TEJ9|Q8WZ23|Q96GZ4|Q96JW3	hg19	CCDS343.1	0.02	-0.412214	CACxCCT	COVERED																																																																																			NOVEL	TINAGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011072.1	13	4.812595	KEEP	0	0	0	16	449	AA	0.997832	0.939699	0		+	4	60	130	0	0	9.175111	38	60	1126	85	ENST00000271064.7	0.095238	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	32182025	32182025	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32182025G>A			NA	NA				COL16A1 (12105 upstream) : BAI2 (10692 downstream)						NA		NA									NA						cacccgcctcggcctcccaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.32182025G>A		NA		hg19		0.02	-0.175429	CTCxGCC	COVERED																																																																																			NOVEL					0			9	2.406982	KEEP	2	0	0	8	243	GG	0.99257	0.420331	0			3	60	85	0	0	6.334388	16	60	542	44		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	32443890	32443890	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32443890A>G			NA	NA				PTP4A2 (33433 upstream) : KHDRBS1 (35539 downstream)						NA		NA									NA						tctgcctcccaggttcaagtg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.32443890A>G		NA		hg19		0.02	-0.149104	CCCxGGT	UNCOVERED																																																																																			NOVEL					0			8	2.405907	KEEP	3	0	0	8	218	AA	0	0	0			3	60	90	0	0	7.079112	13	60	395	32		0.1875	0.292001
RP11-277A4.4	0	__UNKNOWN__	__UNKNOWN__	1	32527652	32527652	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32527652G>A	ENST00000366152.3	-	0	138										NA		NA									NA						tgtaatcctagcactttggga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000366152.3:	chr1.hg19:g.32527652G>A		NA		hg19		0.02	-0.149132	CTAxCAC	COVERED																																																																																			NOVEL	RP11-277A4.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000020555.2	5	3.610856	KEEP	1	0	0	12	371	GG	0.993072	0.289978	0		-	3	30	86	0	0	6.772265	12	60	426	40	ENST00000366152.3	0.2	0.292001
KPNA6	23633	__UNKNOWN__	__UNKNOWN__	1	32607607	32607607	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32607607T>C	ENST00000373625.3	+	2	97				KPNA6_ENST00000537234.1_Intron	NM_012316.4	NP_036448.1	O60684	IMA7_HUMAN	karyopherin alpha 6 (importin alpha 7)	NA		NA			maternal process involved in female pregnancy (GO:0060135)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			large_intestine(2)	2		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				cagtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF060543	CCDS352.1	1p35.1	2013-02-14			ENSG00000025800	ENSG00000025800	23633		Importins, Armadillo repeat containing	6399	protein-coding gene	gene with protein product		610563			NA	10523667	Standard	NM_012316	NM_012316	NA	Approved	IPOA7, KPNA7, MGC17918, FLJ11249	uc001bug.3	O60684	OTTHUMG00000004333	ENST00000373625.3:c.5-12582T>C	chr1.hg19:g.32607607T>C		NA	B2RDC7|D3DPP5|Q5VVU3	hg19	CCDS352.1	0.02	-0.263058	TCAxGCC	COVERED																																																																																			NOVEL	KPNA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012527.4	5	2.705961	KEEP	1	0	0	9	240	TT	0.99254	0.688494	0		+	3	60	99	0	0	7.144604	26	60	738	54	ENST00000373625.3	0.103448	0.693668
HDAC1	3065	__UNKNOWN__	__UNKNOWN__	1	32758720	32758720	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32758720G>A	ENST00000373548.3	+	1	133				HDAC1_ENST00000373541.2_Intron	NM_004964.2	NP_004955.2	Q13547	HDAC1_HUMAN	histone deacetylase 1	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|mitotic cell cycle (GO:0000278)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deacetylation (GO:0006476)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	tcaggagttcgagaccagcct	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D50405	CCDS360.1	1p34	2008-02-05			ENSG00000116478	ENSG00000116478	3065			4852	protein-coding gene	gene with protein product		601241		RPD3L1	NA	8602529	Standard	NM_004964	NM_004964	NA	Approved	HD1, GON-10	uc001bvb.1	Q13547	OTTHUMG00000007529	ENST00000373548.3:c.49+901G>A	chr1.hg19:g.32758720G>A		NA	Q92534	hg19	CCDS360.1	0.02	-0.210512	TTCxAGA	COVERED																																																																																			NOVEL	HDAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019815.3	8	6.000724	KEEP	14	0	0	20	557	GG	0.995343	0.550313	0		+	3	34	90	0	0	6.627659	19	60	606	86	ENST00000373548.3	0.136364	0.552887
HDAC1	3065	__UNKNOWN__	__UNKNOWN__	1	32766785	32766785	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32766785T>C	ENST00000373548.3	+	2	133				HDAC1_ENST00000373541.2_Intron	NM_004964.2	NP_004955.2	Q13547	HDAC1_HUMAN	histone deacetylase 1	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|circadian regulation of gene expression (GO:0032922)|embryonic digit morphogenesis (GO:0042733)|epidermal cell differentiation (GO:0009913)|eyelid development in camera-type eye (GO:0061029)|fungiform papilla formation (GO:0061198)|gene expression (GO:0010467)|hair follicle placode formation (GO:0060789)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|mitotic cell cycle (GO:0000278)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell proliferation (GO:0008284)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein deacetylation (GO:0006476)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	cggtggctcatgcctgtaatc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D50405	CCDS360.1	1p34	2008-02-05			ENSG00000116478	ENSG00000116478	3065			4852	protein-coding gene	gene with protein product		601241		RPD3L1	NA	8602529	Standard	NM_004964	NM_004964	NA	Approved	HD1, GON-10	uc001bvb.1	Q13547	OTTHUMG00000007529	ENST00000373548.3:c.50-1437T>C	chr1.hg19:g.32766785T>C		NA	Q92534	hg19	CCDS360.1	0.02	-0.289426	TCAxGCC	COVERED																																																																																			NOVEL	HDAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019815.3	7	3.007275	KEEP	1	0	0	10	270	TT	0.992708	0.755338	0		+	3	60	103	0	0	7.543977	26	60	766	67	ENST00000373548.3	0.103448	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	32906482	32906482	__UNKNOWN__	IGR	SNP	G	G	A	rs112978343	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32906482G>A			NA	NA				BSDC1 (46433 upstream) : RN7SL122P (16953 downstream)						NA		NA									NA						gaggtgggtggatcacctgaa	0.468		NA											G|||	410	0.081869	0.1233	0.0908	5008	,	,	NA	16020	0.0	NA	0.1352	False	NA	,,,	NA	NA	NA	2504	0.0491	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.32906482G>A		NA		hg19		0.02	-0.14035	GTGxATC	COVERED																																																																																			NOVEL					0			4	2.407226	KEEP	2	0	0	8	248	GG	0.99257	0.259026	0			3	60	87	0	0	6.972878	11	60	373	41		0.214286	0.260965
RP1-27O5.3	0	__UNKNOWN__	__UNKNOWN__	1	32989992	32989992	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:32989992A>G	ENST00000480336.1	+	5	1492										NA		NA									NA						tctgcctcccaggttcaagcg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000480336.1:c.1403-11722A>G	chr1.hg19:g.32989992A>G		NA		hg19		0.02	-0.114017	CCCxGGT	UNCOVERED																																																																																			NOVEL	RP1-27O5.3-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000392985.1	4	2.405787	KEEP	4	0	0	8	216	AA	0	0	0		+	3	35	87	0	0	7.201099	9	60	280	29	ENST00000480336.1	0.25	0.162467
ZBTB8A	653121	__UNKNOWN__	__UNKNOWN__	1	33033123	33033123	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:33033123T>C	ENST00000373510.4	+	2	228				ZBTB8A_ENST00000316459.4_Intron|RP1-27O5.3_ENST00000480336.1_Intron	NM_001040441.1	NP_001035531.1	Q96BR9	ZBT8A_HUMAN	zinc finger and BTB domain containing 8A	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(2)|large_intestine(2)|lung(2)|prostate(1)	7						Aggctgggcatggtggctcac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF548353	CCDS30664.1	1p34.3	2013-01-08	2009-03-25	2009-03-25	ENSG00000160062	ENSG00000160062	653121		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	24172	protein-coding gene	gene with protein product		NA	zinc finger and BTB domain containing 8	ZBTB8	NA	12477932	Standard	NM_144621	NM_001040441	NA	Approved	BOZF1, FLJ90065, ZNF916A	uc001bvn.3	Q96BR9	OTTHUMG00000007855	ENST00000373510.4:c.-2+13982T>C	chr1.hg19:g.33033123T>C		NA	Q8IUL5|Q8IWR9|Q8N2Y5|Q96BX0	hg19	CCDS30664.1	0.02	-0.25433	GCAxGGT	UNCOVERED																																																																																			NOVEL	ZBTB8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021665.2	11	2.705023	KEEP	8	0	0	9	234	TT	0	0	0		+	3	60	94	0	0	6.744893	24	60	702	62	ENST00000373510.4	0.111111	0.668523
RP11-114B7.6	0	__UNKNOWN__	__UNKNOWN__	1	33189014	33189014	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:33189014C>G	ENST00000421619.1	-	0	160										NA		NA									NA						cgcaccactgcactccagcct	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000421619.1:	chr1.hg19:g.33189014C>G		NA		hg19		0.02	-0.149134	CTGxACT	UNCOVERED																																																																																			NOVEL	RP11-114B7.6-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000099440.1	8	2.406946	KEEP	2	0	0	8	238	CC	0	0	0		-	3	58	104	0	0	8.672548	11	60	371	29	ENST00000421619.1	0.214286	0.292001
KIAA1522	57648	__UNKNOWN__	__UNKNOWN__	1	33233437	33233437	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:33233437G>T	ENST00000294521.3	+	2	244	c.108G>T	c.(106-108)caG>caT	p.Q36H	KIAA1522_ENST00000373480.1_Missense_Mutation_p.Q36H|KIAA1522_ENST00000401073.2_Missense_Mutation_p.Q95H|KIAA1522_ENST00000373481.3_Missense_Mutation_p.Q47H	NM_001198973.1	NP_001185902.1	Q9P206	K1522_HUMAN	KIAA1522	36		NA								breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				GGCCTGGCCAGGGGCCAGGGT	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													88	92	91			NA	NA	1		NA											NA				33233437		1922	4114	6036	SO:0001583	missense			AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522	57648			29301	protein-coding gene	gene with protein product		NA			NA	10819331	Standard		NM_020888	NA	Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000294521.3:c.108G>T	chr1.hg19:g.33233437G>T	ENSP00000294521:p.Gln36His	NA	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	hg19	CCDS55589.1	0.02	4.229358	CCAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.15	2.448259	0.43429	.	.	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000294521;ENST00000373480	T;T;T;T	0.34072	2.64;2.59;1.38;2.61	4.5	2.49	0.30216	.	0.253337	0.27134	N	0.020777	T	0.38558	0.1045	L	0.44542	1.39	0.28274	N	0.924269	B;D;B;B	0.64830	0.001;0.994;0.001;0.006	B;P;B;B	0.56163	0.002;0.793;0.007;0.01	T	0.16660	-1.0395	10	0.66056	D	0.02	-7.614	5.3821	0.16197	0.2273:0.167:0.6057:0.0	.	36;47;36;95	B4DQU8;Q9P206-3;Q9P206;Q9P206-2	.;.;K1522_HUMAN;.	H	95;47;36;36	ENSP00000383851:Q95H;ENSP00000362580:Q47H;ENSP00000294521:Q36H;ENSP00000362579:Q36H	ENSP00000294521:Q36H	Q	+	3	2	KIAA1522	33006024	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	1.292000	0.33342	1.268000	0.44264	0.462000	0.41574	CAG	NOVEL	KIAA1522-005	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382044.1	2	5.115238	KEEP	0	0	0	17	525	GG	0.999366	0.999366	0		+	7	60	208	0	0	11.618517	156	60	5329	257	ENST00000294521.3	0.042945	1
YARS	8565	__UNKNOWN__	__UNKNOWN__	1	33260596	33260596	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:33260596T>C	ENST00000373477.4	-	5	1500					NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	NA		NA			apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	agagcaagactctgtctcaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	8565	6.1.1.1	Aminoacyl tRNA synthetases / Class I	12840	protein-coding gene	gene with protein product	tyrosine tRNA ligase 1, cytoplasmic	603623			NA	8552597, 9162081	Standard	NM_003680	NM_003680	NA	Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.591+2767A>G	chr1.hg19:g.33260596T>C		NA	B3KWK4|D3DPQ4|O43276|Q53EN1	hg19	CCDS368.1	0.02	-0.11397	GACxCTG	UNCOVERED																																																																																			NOVEL	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011225.1	9	2.70639	KEEP	4	0	0	9	242	TT	0	0	0		-	3	42	93	0	0	8.655063	4	47	122	26	ENST00000373477.4	0.428571	0.162467
S100PBP	64766	__UNKNOWN__	__UNKNOWN__	1	33306237	33306237	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:33306237T>C	ENST00000373475.5	+	5	1278				S100PBP_ENST00000373476.1_Intron	NM_022753.3	NP_073590.2			S100P binding protein	NA		NA								endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497	64766			25768	protein-coding gene	gene with protein product	S100P binding protein 1	611889			NA	12477932	Standard	NM_022753	NM_022753	NA	Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.1024+10569T>C	chr1.hg19:g.33306237T>C		NA		hg19	CCDS30666.1	0.02	-0.22803	AGGxGTG	UNCOVERED																																																																																			NOVEL	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011266.1	11	2.406519	KEEP	3	0	0	8	227	TT	0	0	0		+	3	60	94	0	0	6.849527	22	60	648	52	ENST00000373475.5	0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	33506537	33506537	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:33506537T>A			NA	NA				AK2 (3944 upstream) : ADC (40176 downstream)						NA		NA									NA						gtggtggctctcacctgtaat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.33506537T>A		NA		hg19		0.02	-0.175411	CTCxCAC	COVERED																																																																																			NOVEL					0			10	3.00742	KEEP	0	0	0	10	272	TT	0.992708	0.384582	0			3	60	89	0	0	6.733964	16	60	478	40		0.157895	0.387407
DLGAP3	58512	__UNKNOWN__	__UNKNOWN__	1	35385274	35385274	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35385274A>G	ENST00000373347.1	-	1	135				DLGAP3_ENST00000495979.1_Intron			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	NA		NA			cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				ccagctactcaggaggctgag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544	58512			30368	protein-coding gene	gene with protein product		611413			NA	8619474, 9110174	Standard	NM_021234	NM_001080418	NA	Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.133+9777T>C	chr1.hg19:g.35385274A>G		NA	Q5TDD5|Q9H3X7	hg19	CCDS30670.1	0.02	-0.166637	CTCxGGA	COVERED																																																																																			NOVEL	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011554.1	4	2.406215	KEEP	0	0	0	8	222	AA	0.99257	0.351317	0		-	4	60	130	0	0	10.768601	14	60	411	33	ENST00000373347.1	0.222222	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	35417721	35417721	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35417721C>T			NA	NA				SNORD112 (8296 upstream) : RP11-244H3.1 (22235 downstream)						NA		NA									NA						catgagccaccgcacccagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.35417721C>T		NA		hg19		0.02	-0.157877	CACxGCA	COVERED																																																																																			NOVEL					0			7	2.406665	KEEP	1	0	0	8	236	CG	0.99254	0.320398	0			4	60	115	0	0	9.381028	13	60	410	39		0.235294	0.322807
ZMYM6	9204	__UNKNOWN__	__UNKNOWN__	1	35466118	35466118	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35466118A>G	ENST00000357182.4	-	14	2220				ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000493328.1_Intron|ZMYM6_ENST00000373340.2_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	NA		NA			cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				gggattacagacgtgagccac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867	9204		Zinc fingers, MYM type, Zinc fingers, BED-type	13050	protein-coding gene	gene with protein product	zinc finger, BED-type containing 7	613567	zinc finger protein 258, zinc finger, MYM-type containing 6	ZNF258	NA	10486218, 23533661	Standard	NM_007167	NM_007167	NA	Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.1992+3450T>C	chr1.hg19:g.35466118A>G		NA	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	hg19	CCDS387.2	0.02	-0.210483	CAGxCGT	COVERED																																																																																			NOVEL	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011999.1	5	2.405555	KEEP	0	0	0	8	214	AA	0.99257	0.518282	0		-	3	60	95	0	0	7.26125	17	60	496	47	ENST00000357182.4	0.15	0.522161
ZMYM6	9204	__UNKNOWN__	__UNKNOWN__	1	35483861	35483861	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35483861T>C	ENST00000357182.4	-	4	656				ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000317538.5_3'UTR|ZMYM6_ENST00000493328.1_Intron|ZMYM6_ENST00000373340.2_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	NA		NA			cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				gggaggatcatctgagcccgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867	9204		Zinc fingers, MYM type, Zinc fingers, BED-type	13050	protein-coding gene	gene with protein product	zinc finger, BED-type containing 7	613567	zinc finger protein 258, zinc finger, MYM-type containing 6	ZNF258	NA	10486218, 23533661	Standard	NM_007167	NM_007167	NA	Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.428+1092A>G	chr1.hg19:g.35483861T>C		NA	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	hg19	CCDS387.2	0.02	1.789217	TCAxCTG	COVERED																																																																																			NOVEL	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000011999.1	10	6.014789	KEEP	0	0	0	20	544	TT	0.999863	0.981821	0		-	4	60	127	1	0	8.490953	48	60	1366	107	ENST00000357182.4	0.076923	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	35586891	35586891	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35586891A>G			NA	NA				ZMYM1 (5431 upstream) : SFPQ (55087 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.35586891A>G		NA		hg19		0.02	-0.403377	CACxCCT	COVERED																																																																																			NOVEL					0			13	4.508896	KEEP	4	0	0	15	393	AA	0.993634	0.928543	0			5	60	158	0	0	12.023278	29	60	833	87		0.147059	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	35594328	35594328	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35594328A>G			NA	NA				ZMYM1 (12868 upstream) : SFPQ (47650 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.35594328A>G		NA		hg19		0.02	-0.236809	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.405832	KEEP	0	0	0	8	216	AA	0.99257	0.607857	0			3	60	105	0	1	8.126842	19	60	564	52		0.136364	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	35631784	35631784	__UNKNOWN__	IGR	SNP	T	T	C	rs562849539	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35631784T>C			NA	NA				ZMYM1 (50324 upstream) : SFPQ (10194 downstream)						NA		NA									NA						agtgaaaccctgtttctacta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.35631784T>C		NA		hg19		0.02	-0.192912	CCCxGTT	COVERED																																																																																			NOVEL					0			11	2.707377	KEEP	1	0	0	9	257	TT	0.99257	0.454356	0			3	60	86	0	0	6.362384	17	60	493	40		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	35631787	35631787	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35631787T>C			NA	NA				ZMYM1 (50327 upstream) : SFPQ (10191 downstream)						NA		NA									NA						gaaaccctgtttctactaaaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.35631787T>C		NA		hg19		0.02	-0.184148	TGTxTCT	COVERED																																																																																			NOVEL					0			11	2.706691	KEEP	2	0	0	9	245	TT	0.99257	0.420331	0			5	60	148	0	0	12.302408	15	60	437	40		0.25	0.423478
ZMYM4	9202	__UNKNOWN__	__UNKNOWN__	1	35739977	35739977	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35739977A>G	ENST00000314607.6	+	1	119				ZMYM4_ENST00000373297.2_Intron	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	NA		NA			cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				aggccgaggcaggaggatggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463	9202		Zinc fingers, MYM type	13055	protein-coding gene	gene with protein product		613568	zinc finger protein 262	ZNF262	NA	10449923	Standard	NM_005095	NM_005095	NA	Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.39+5291A>G	chr1.hg19:g.35739977A>G		NA	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	hg19	CCDS389.1	0.02	-0.306998	GGCxGGA	COVERED																																																																																			NOVEL	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012207.3	13	3.609542	KEEP	1	0	0	12	336	AA	0.993072	0.794702	0		+	3	60	103	0	0	7.497285	27	60	825	65	ENST00000314607.6	0.1	0.800245
ZMYM4	9202	__UNKNOWN__	__UNKNOWN__	1	35745767	35745767	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35745767T>C	ENST00000314607.6	+	1	119				ZMYM4_ENST00000373297.2_Intron	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	NA		NA			cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				cttcctcccttcctcccttcc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463	9202		Zinc fingers, MYM type	13055	protein-coding gene	gene with protein product		613568	zinc finger protein 262	ZNF262	NA	10449923	Standard	NM_005095	NM_005095	NA	Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.39+11081T>C	chr1.hg19:g.35745767T>C		NA	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	hg19	CCDS389.1	0.02	-0.25385	CCTxCCT	COVERED																																																																																			NOVEL	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012207.3	11	2.404993	KEEP	0	0	0	8	206	TT	0.99257	0.663556	0		+	3	60	102	0	2	7.495207	25	60	668	49	ENST00000314607.6	0.107143	0.668523
ZMYM4	9202	__UNKNOWN__	__UNKNOWN__	1	35755611	35755611	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35755611T>C	ENST00000314607.6	+	1	119				ZMYM4_ENST00000373297.2_Intron	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	NA		NA			cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ctctgtcacctaggctggagt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463	9202		Zinc fingers, MYM type	13055	protein-coding gene	gene with protein product		613568	zinc finger protein 262	ZNF262	NA	10449923	Standard	NM_005095	NM_005095	NA	Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.39+20925T>C	chr1.hg19:g.35755611T>C		NA	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	hg19	CCDS389.1	0.02	-0.219273	ACCxAGG	COVERED																																																																																			NOVEL	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012207.3	10	3.308422	KEEP	0	0	0	11	303	TT	0.993072	0.549057	0		+	4	60	132	0	0	10.580128	18	60	546	55	ENST00000314607.6	0.181818	0.552887
ZMYM4	9202	__UNKNOWN__	__UNKNOWN__	1	35770731	35770731	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35770731G>C	ENST00000314607.6	+	2	119				ZMYM4_ENST00000373297.2_Intron	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	NA		NA			cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				aggcgtgagcgactgcgccca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463	9202		Zinc fingers, MYM type	13055	protein-coding gene	gene with protein product		613568	zinc finger protein 262	ZNF262	NA	10449923	Standard	NM_005095	NM_005095	NA	Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.40-20230G>C	chr1.hg19:g.35770731G>C		NA	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	hg19	CCDS389.1	0.02	-0.131576	AGCxACT	COVERED																																																																																			NOVEL	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012207.3	2	2.707412	KEEP	0	0	0	9	261	GG	0.99254	0.227464	0		+	3	60	95	0	0	7.672207	12	60	385	35	ENST00000314607.6	0.2	0.229173
KIAA0319L	79932	__UNKNOWN__	__UNKNOWN__	1	35976439	35976439	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:35976439G>C	ENST00000325722.3	-	3	377					NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	NA		NA				cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				gaactcctgggttcaagcaat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687	79932			30071	protein-coding gene	gene with protein product		613535			NA	11347906	Standard	NM_024874	NM_024874	NA	Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.143-3703C>G	chr1.hg19:g.35976439G>C		NA	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	hg19	CCDS390.1	0.02	-0.219321	TGGxTTC	COVERED																																																																																			NOVEL	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012684.2	7	3.911044	KEEP	0	0	0	13	403	GG	0.994391	0.57966	0		-	3	60	103	0	0	7.864388	20	60	691	57	ENST00000325722.3	0.130435	0.58293
PSMB2	5690	__UNKNOWN__	__UNKNOWN__	1	36067671	36067671	__UNKNOWN__	3'UTR	SNP	C	C	T	rs553326215		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36067671C>T	ENST00000373237.3	-	0	2214					NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	cggtggctcacgcctgtaatc	0.428		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	19085	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067	5690		Proteasome (prosome, macropain) subunits	9539	protein-coding gene	gene with protein product		602175			NA	7918633	Standard	NM_002794	NM_002794	NA	Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.*1197G>A	chr1.hg19:g.36067671C>T		NA	D3DPS0|P31145|Q9BWZ9	hg19	CCDS394.1	0.02	1.166617	TCAxGCC	COVERED																																																																																			NOVEL	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012016.1	21	5.714926	KEEP	0	0	0	19	543	CC	0.99986	0.99979	0		-	5	60	139	0	0	8.045558	80	60	2587	135	ENST00000373237.3	0.058824	0.99993
PSMB2	5690	__UNKNOWN__	__UNKNOWN__	1	36093006	36093006	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36093006T>C	ENST00000373237.3	-	3	697					NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	cctgtaatcctagcactttgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067	5690		Proteasome (prosome, macropain) subunits	9539	protein-coding gene	gene with protein product		602175			NA	7918633	Standard	NM_002794	NM_002794	NA	Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.285+3868A>G	chr1.hg19:g.36093006T>C		NA	D3DPS0|P31145|Q9BWZ9	hg19	CCDS394.1	0.02	-0.315745	TCCxAGC	UNCOVERED																																																																																			NOVEL	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012016.1	11	2.40644	KEEP	1	0	0	8	226	TT	0	0	0		-	5	60	161	0	0	12.392169	28	60	825	63	ENST00000373237.3	0.151515	0.818465
PSMB2	5690	__UNKNOWN__	__UNKNOWN__	1	36093076	36093076	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36093076A>T	ENST00000373237.3	-	3	697					NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	ggcaacatggagaaaccccat	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067	5690		Proteasome (prosome, macropain) subunits	9539	protein-coding gene	gene with protein product		602175			NA	7918633	Standard	NM_002794	NM_002794	NA	Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.285+3798T>A	chr1.hg19:g.36093076A>T		NA	D3DPS0|P31145|Q9BWZ9	hg19	CCDS394.1	0.02	-0.271837	TGGxGAA	COVERED																																																																																			NOVEL	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012016.1	14	2.707442	KEEP	0	0	0	9	258	AA	0.99254	0.711964	0		-	4	60	103	0	0	7.229516	24	60	725	51	ENST00000373237.3	0.142857	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	36131555	36131555	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36131555T>C			NA	NA				PSMB2 (24110 upstream) : RN7SL281P (40070 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.36131555T>C		NA		hg19		0.02	-0.271858	AGGxGTG	COVERED																																																																																			NOVEL					0			9	2.404326	KEEP	1	0	0	8	208	TT	0.99257	0.711986	0			4	60	127	0	0	9.69191	23	60	659	56		0.148148	0.717315
CLSPN	63967	__UNKNOWN__	__UNKNOWN__	1	36193966	36193966	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36193966T>A	ENST00000251195.5	-	25	4006							Q9HAW4	CLSPN_HUMAN	claspin	NA		NA			activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				tacaggcatgtgccaccatgc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853	63967			19715	protein-coding gene	gene with protein product		605434	claspin homolog (Xenopus laevis)		NA	11090622, 12766152	Standard	NM_022111	NM_022111	NA	Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000251195.5:c.3910-7385A>T	chr1.hg19:g.36193966T>A		NA	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	hg19		0.02	-0.315739	ATGxGCC	COVERED																																																																																			NOVEL	CLSPN-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000012014.4	12	2.70673	KEEP	0	0	0	9	245	TT	0.99254	0.812359	0		-	4	60	123	0	0	9.033887	27	60	807	56	ENST00000251195.5	0.129032	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	36259674	36259674	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36259674C>T			NA	NA				CLSPN (24106 upstream) : AGO4 (14098 downstream)						NA		NA									NA						tgtgagctaccgcgcccggcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.36259674C>T		NA		hg19		0.02	-0.263099	TACxGCG	COVERED																																																																																			NOVEL					0			11	3.610196	KEEP	0	0	0	12	355	CC	0.993634	0.689252	0			3	60	95	0	0	6.895195	23	60	734	58		0.115385	0.693668
AGO4	192670	__UNKNOWN__	__UNKNOWN__	1	36306020	36306020	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36306020T>C	ENST00000373210.3	+	14	1969					NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)				NA						gcctcagccttccaaagtgct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698	192670		Argonaute/PIWI family	18424	protein-coding gene	gene with protein product	argonaute 4	607356	eukaryotic translation initiation factor 2C, 4	EIF2C4	NA	12906857	Standard	NM_017629	NM_017629	NA	Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1725-746T>C	chr1.hg19:g.36306020T>C		NA	A7MD27	hg19	CCDS397.1	0.02	-0.175401	CCTxCCA	COVERED																																																																																			NOVEL	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012213.3	13	2.40507	KEEP	1	0	0	8	214	AT	0.99254	0.384517	0		+	3	60	96	0	0	7.434193	16	60	469	39	ENST00000373210.3	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	36324619	36324619	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36324619G>A			NA	NA				AGO4 (1128 upstream) : AGO1 (10789 downstream)						NA		NA									NA						gagctcaagcgatcctcccgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.36324619G>A		NA		hg19		0.02	-0.298213	AGCxATC	COVERED																																																																																			NOVEL					0			14	4.511884	KEEP	2	0	0	15	444	GG	0.994391	0.776679	0			4	60	116	0	0	8.524189	24	60	771	74		0.142857	0.78106
THRAP3	9967	__UNKNOWN__	__UNKNOWN__	1	36725627	36725627	__UNKNOWN__	Intron	SNP	G	G	T	rs11578811	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:36725627G>T	ENST00000354618.5	+	2	193				THRAP3_ENST00000469141.2_Intron	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	NA		NA			androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				gtgatcacttgaggtcaagag	0.483		NA	T	USP6	aneurysmal bone cysts								G|||	549	0.109625	0.0144	0.1037	5008	,	,	NA	16161	0.1151	NA	0.2068	False	NA	,,,	NA	NA	NA	2504	0.137	NA	NA	NA	Pancreas(129;785 1795 20938 23278 32581)		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118	9967			22964	protein-coding gene	gene with protein product		603809			NA		Standard	NM_005119	NM_005119	NA	Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.-32+542G>T	chr1.hg19:g.36725627G>T		NA	D3DPS5|Q5VTK6	hg19	CCDS405.1	0.02	-0.131568	CTTxAGG	UNCOVERED																																																																																			NOVEL	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021688.2	9	2.407223	KEEP	1	0	0	8	246	GG	0	0	0		+	5	60	148	0	0	13.222382	9	60	296	33	ENST00000354618.5	0.357143	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	37257570	37257570	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:37257570T>G			NA	NA				RP4-614N24.1 (16201 upstream) : GRIK3 (3557 downstream)						NA		NA									NA						tacttgggagtctgaggtggg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.37257570T>G		NA		hg19		0.02	-0.149084	GAGxCTG	COVERED																																																																																			NOVEL					0			10	2.706453	KEEP	0	0	0	9	247	TT	0.99254	0.289823	0			3	60	93	0	0	7.379497	13	60	373	35		0.1875	0.292001
RP11-422J8.1	0	__UNKNOWN__	__UNKNOWN__	1	37928964	37928964	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:37928964C>G	ENST00000424989.1	-	0	268					NR_038842.1					NA		NA									NA						tgcagtggcacgatctcagct	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424989.1:	chr1.hg19:g.37928964C>G		NA		hg19		0.02	-0.228076	GCAxGAT	COVERED																																																																																			NOVEL	RP11-422J8.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000012168.1	29	5.10117	KEEP	25	0	0	17	463	AC	0.99257	0.578599	0		-	3	22	98	0	0	7.42682	19	54	632	77	ENST00000424989.1	0.136364	0.58293
RP11-422J8.1	0	__UNKNOWN__	__UNKNOWN__	1	37928965	37928965	__UNKNOWN__	RNA	SNP	G	G	A	rs2660560	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:37928965G>A	ENST00000424989.1	-	0	268					NR_038842.1					NA		NA									NA						gcagtggcacgatctcagctc	0.443		NA											G|||	1815	0.36242	0.5756	0.2291	5008	,	,	NA	839	0.0585	NA	0.33	False	NA	,,,	NA	NA	NA	2504	0.5153	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424989.1:	chr1.hg19:g.37928965G>A		NA		hg19		0.02	-0.228042	CACxATC	COVERED																																																																																			NOVEL	RP11-422J8.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000012168.1	29	5.681797	KEEP	25	0	0	19	537	GG	0.99257	0.578599	0		-	7	40	208	0	0	18.163663	15	54	466	78	ENST00000424989.1	0.318182	0.58293
MEAF6	64769	__UNKNOWN__	__UNKNOWN__	1	37960741	37960741	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:37960741A>C	ENST00000296214.5	-	6	595				MEAF6_ENST00000475828.1_Intron|MEAF6_ENST00000373075.2_Intron|MEAF6_ENST00000373073.4_Intron|MEAF6_ENST00000373074.1_Intron	NM_001270875.1	NP_001257804.1	Q9HAF1	EAF6_HUMAN	MYST/Esa1-associated factor 6	NA		NA			chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)	7						tgagaccagcatgaccaacat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016328	CCDS418.1, CCDS59195.1, CCDS59196.1	1p35.3-p33	2011-08-12	2009-07-13	2009-07-13	ENSG00000163875	ENSG00000163875	64769			25674	protein-coding gene	gene with protein product	Esa1p-associated factor 6 homolog (S. cerevisiae), centromere protein 28	611001	chromosome 1 open reading frame 149	C1orf149	NA	8619474, 9110174, 12963728, 14966270, 16387653	Standard	NM_022756	NM_022756	NA	Approved	NY-SAR-91, FLJ11730, Eaf6, CENP-28	uc001cbe.2	Q9HAF1	OTTHUMG00000004223	ENST00000296214.5:c.567+744T>G	chr1.hg19:g.37960741A>C		NA	B1AK64|Q4F967|Q7Z311|Q86WE3	hg19	CCDS59196.1	0.02	-0.219213	AGCxTGA	COVERED																																																																																			NOVEL	MEAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012161.1	3	3.307315	KEEP	2	0	0	11	292	AA	0.99254	0.548763	0		-	3	60	103	0	0	7.865111	20	60	551	50	ENST00000296214.5	0.130435	0.552887
SNIP1	79753	__UNKNOWN__	__UNKNOWN__	1	38003879	38003879	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38003879A>G	ENST00000296215.6	-	4	999					NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	NA		NA			I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				ggaggccgagacgggcggatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877	79753			30587	protein-coding gene	gene with protein product		608241			NA	10887155, 15378006	Standard	NM_024700	NM_024700	NA	Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.927-266T>C	chr1.hg19:g.38003879A>G		NA	Q96SP9|Q9H9T7	hg19	CCDS419.1	0.02	-0.245547	GAGxCGG	COVERED																																																																																			NOVEL	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012169.2	9	3.30711	KEEP	3	0	0	11	296	AA	0.993072	0.636904	0		-	3	60	98	0	0	7.195049	23	60	665	66	ENST00000296215.6	0.115385	0.641347
SNIP1	79753	__UNKNOWN__	__UNKNOWN__	1	38014191	38014191	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38014191A>G	ENST00000296215.6	-	2	400				SNIP1_ENST00000468040.1_Intron	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	NA		NA			I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				gattacaggcatgagccactg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877	79753			30587	protein-coding gene	gene with protein product		608241			NA	10887155, 15378006	Standard	NM_024700	NM_024700	NA	Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.327+4054T>C	chr1.hg19:g.38014191A>G		NA	Q96SP9|Q9H9T7	hg19	CCDS419.1	0.02	-0.192941	GGCxTGA	UNCOVERED																																																																																			NOVEL	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012169.2	8	2.405919	KEEP	2	0	0	8	218	AA	0	0	0		-	3	60	96	0	0	7.51048	15	60	434	44	ENST00000296215.6	0.166667	0.457757
MTF1	4520	__UNKNOWN__	__UNKNOWN__	1	38284622	38284622	__UNKNOWN__	Intron	SNP	A	A	G	rs71642611		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38284622A>G	ENST00000373036.4	-	10	1908					NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ccgagatcgcaccactgcact	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786	4520			7428	protein-coding gene	gene with protein product		600172			NA	8065932	Standard	NM_005955	NM_005955	NA	Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1768-1468T>C	chr1.hg19:g.38284622A>G		NA	B2RAK6|Q96CB1	hg19	CCDS30676.1	0.02	-0.149028	CGCxCCA	COVERED																																																																																			NOVEL	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012984.2	3	2.706117	KEEP	2	0	0	9	241	AA	0.99257	0.289832	0		-	3	60	96	0	0	7.679869	13	60	371	43	ENST00000373036.4	0.1875	0.292001
MTF1	4520	__UNKNOWN__	__UNKNOWN__	1	38285400	38285400	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38285400A>G	ENST00000373036.4	-	10	1908					NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				gaggtgggcgaatcacctgag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786	4520			7428	protein-coding gene	gene with protein product		600172			NA	8065932	Standard	NM_005955	NM_005955	NA	Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1768-2246T>C	chr1.hg19:g.38285400A>G		NA	B2RAK6|Q96CB1	hg19	CCDS30676.1	0.02	-0.271852	GCGxATC	COVERED																																																																																			NOVEL	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012984.2	12	3.006637	KEEP	4	0	0	10	264	AA	0.99254	0.711964	0		-	3	60	91	0	0	6.307687	27	60	800	61	ENST00000373036.4	0.1	0.717315
INPP5B	3633	__UNKNOWN__	__UNKNOWN__	1	38335020	38335020	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38335020C>T	ENST00000373024.3	-	20	2275				INPP5B_ENST00000373026.1_Intron|INPP5B_ENST00000373023.2_Intron|INPP5B_ENST00000373027.1_Intron			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	NA		NA			in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				tctcgctatgctgcccaggct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3633	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	inositol polyphosphate-5-phosphatase, 75kD		NA	1718960	Standard	NM_005540	NM_005540	NA	Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373024.3:c.2188-734G>A	chr1.hg19:g.38335020C>T		NA	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	hg19	CCDS41306.1	0.02	-0.298255	ATGxTGC	COVERED																																																																																			NOVEL	INPP5B-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012966.1	11	4.814117	KEEP	0	0	0	16	489	CC	0.997832	0.779366	0		-	3	60	92	0	0	6.353558	28	60	936	68	ENST00000373024.3	0.096774	0.78106
INPP5B	3633	__UNKNOWN__	__UNKNOWN__	1	38337373	38337373	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38337373A>G	ENST00000373024.3	-	19	2275				INPP5B_ENST00000373026.1_Intron|INPP5B_ENST00000373023.2_Intron|INPP5B_ENST00000373027.1_Intron			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	NA		NA			in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				tcaggagttcaagaccagcct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3633	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	inositol polyphosphate-5-phosphatase, 75kD		NA	1718960	Standard	NM_005540	NM_005540	NA	Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373024.3:c.2187+1228T>C	chr1.hg19:g.38337373A>G		NA	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	hg19	CCDS41306.1	0.02	-0.254332	TTCxAGA	COVERED																																																																																			NOVEL	INPP5B-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012966.1	12	3.3058	KEEP	3	0	0	11	281	AA	0.99254	0.663536	0		-	3	60	97	0	0	7.043013	24	60	689	59	ENST00000373024.3	0.111111	0.668523
INPP5B	3633	__UNKNOWN__	__UNKNOWN__	1	38394455	38394455	__UNKNOWN__	Intron	SNP	C	C	T	rs550303510		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38394455C>T	ENST00000373024.3	-	7	620				INPP5B_ENST00000373026.1_Intron|INPP5B_ENST00000373021.1_3'UTR|INPP5B_ENST00000373023.2_Intron|INPP5B_ENST00000373027.1_Intron			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	NA		NA			in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				tgagccaccgcgcccagccAA	0.468		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	18695	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3633	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	inositol polyphosphate-5-phosphatase, 75kD		NA	1718960	Standard	NM_005540	NM_005540	NA	Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373024.3:c.532+3129G>A	chr1.hg19:g.38394455C>T		NA	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	hg19	CCDS41306.1	0.02	1.502566	CCGxGCC	COVERED																																																																																			NOVEL	INPP5B-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000012966.1	18	6.016403	KEEP	1	0	0	20	584	CC	0.999863	0.994947	0		-	5	60	156	1	0	10.479027	56	60	1850	125	ENST00000373024.3	0.081967	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	38478381	38478381	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38478381G>T			NA	NA				FHL3 (7204 upstream) : UTP11L (32 downstream)						NA		NA									NA						ACCGCCGGCGGCTAGGCCTAT	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.38478381G>T		NA		hg19		0.02	1.256944	GCGxCTA	COVERED																																																																																			NOVEL					0			4	6.920484	KEEP	0	0	0	23	713	GG	0.999892	0.999811	0			30	60	864	0	0	74.978974	65	60	2258	156		0.315789	0.999919
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	38498266	38498266	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38498266T>C			NA	NA				UTP11L (7770 upstream) : POU3F1 (11256 downstream)						NA		NA									NA						cacagtgagctgagatcgcgc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.38498266T>C		NA		hg19		0.02	-0.315753	AGCxGAG	COVERED																																																																																			NOVEL					0			12	2.707245	KEEP	0	0	0	9	254	TT	0.99254	0.812359	0			3	60	107	0	0	7.766721	30	60	899	65		0.090909	0.818465
RP5-884C9.2	0	__UNKNOWN__	__UNKNOWN__	1	38570104	38570104	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38570104T>C	ENST00000432922.1	+	0	490										NA		NA									NA						gtggctcacgtctgtaatccc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432922.1:	chr1.hg19:g.38570104T>C		NA		hg19		0.02	-0.219271	ACGxCTG	COVERED																																																																																			NOVEL	RP5-884C9.2-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000001201.1	13	3.308323	KEEP	5	0	0	11	304	TT	0.99257	0.54878	0		+	4	60	139	0	0	11.279341	18	60	541	52	ENST00000432922.1	0.181818	0.552887
RP5-884C9.2	0	__UNKNOWN__	__UNKNOWN__	1	38570139	38570139	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38570139T>C	ENST00000432922.1	+	0	490										NA		NA									NA						ctgaggtgggtggatcacctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432922.1:	chr1.hg19:g.38570139T>C		NA		hg19		0.02	-0.210474	GGGxGGA	COVERED																																																																																			NOVEL	RP5-884C9.2-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000001201.1	9	2.406447	KEEP	0	0	0	8	226	TT	0.99257	0.54878	0		+	4	60	124	1	0	9.869325	17	60	492	45	ENST00000432922.1	0.190476	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	38582241	38582241	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38582241G>A			NA	NA				RP5-884C9.2 (10835 upstream) : RP11-214L19.1 (92464 downstream)						NA		NA									NA						tcaggagtttgagaccagcct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.38582241G>A		NA		hg19		0.02	-0.14911	TTTxAGA	COVERED																																																																																			NOVEL					0			15	3.909005	KEEP	14	0	0	13	390	GG	0.99257	0.320408	0			3	51	84	0	0	6.673064	11	60	358	57		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	38992391	38992391	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:38992391G>A			NA	NA				RP11-329N22.1 (50235 upstream) : RRAGC (311478 downstream)						NA		NA									NA						cccgggaggcggaggttgcag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.38992391G>A		NA		hg19		0.02	-0.157842	GGCxGAG	COVERED																																																																																			NOVEL					0			7	3.007692	KEEP	1	0	0	10	286	GG	0.99254	0.320398	0			3	60	90	0	0	6.910854	15	60	473	37		0.166667	0.322807
RHBDL2	54933	__UNKNOWN__	__UNKNOWN__	1	39351906	39351906	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39351906C>T	ENST00000372990.1	-	0	1409				RP5-864K19.4_ENST00000433671.2_RNA	NM_017821.3	NP_060291.2	Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			ggattacaggcgtgagccact	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315	54933			16083	protein-coding gene	gene with protein product		608962	rhomboid (veinlet, Drosophila)-like 2		NA		Standard	NM_017821	NM_017821	NA	Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000372990.1:c.*270G>A	chr1.hg19:g.39351906C>T		NA	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	hg19	CCDS30680.1	0.02	2.366695	AGGxGTG	COVERED																																																																																			NOVEL	RHBDL2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001216.1	26	5.949358	KEEP	0	1	29	30	885	CC	0.999997	0.999997	0		-	6	60	161	1	0	8.765036	109	60	3551	225	ENST00000372990.1	0.052174	1
RHBDL2	54933	__UNKNOWN__	__UNKNOWN__	1	39368421	39368421	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39368421A>C	ENST00000289248.2	-	5	1517				RHBDL2_ENST00000538156.1_Intron|RHBDL2_ENST00000372985.3_Intron|RHBDL2_ENST00000372990.1_Intron|RP5-864K19.4_ENST00000433671.2_RNA			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			gatggggtttaaccatgttgc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315	54933			16083	protein-coding gene	gene with protein product		608962	rhomboid (veinlet, Drosophila)-like 2		NA		Standard	NM_017821	NM_017821	NA	Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.509-6680T>G	chr1.hg19:g.39368421A>C		NA	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	hg19	CCDS30680.1	0.02	-0.412151	TTTxACC	COVERED																																																																																			NOVEL	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001216.1	12	3.307219	KEEP	0	0	0	11	287	AA	0.993634	0.935746	0		-	3	60	100	0	0	6.773367	38	60	1075	78	ENST00000289248.2	0.073171	0.941741
RHBDL2	54933	__UNKNOWN__	__UNKNOWN__	1	39386530	39386530	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39386530G>A	ENST00000289248.2	-	2	884				RHBDL2_ENST00000538156.1_Intron|RHBDL2_ENST00000372985.3_Intron|RHBDL2_ENST00000372990.1_Intron|RHBDL2_ENST00000540558.1_Intron			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			ctcgtgatccgcccgcctcgg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315	54933			16083	protein-coding gene	gene with protein product		608962	rhomboid (veinlet, Drosophila)-like 2		NA		Standard	NM_017821	NM_017821	NA	Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.125-1521C>T	chr1.hg19:g.39386530G>A		NA	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	hg19	CCDS30680.1	0.02	-0.192533	TCCxCCC	UNCOVERED																																																																																			NOVEL	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001216.1	9	4.210843	KEEP	14	0	0	14	397	GG	0	0	0		-	3	60	91	0	0	6.796268	18	60	518	65	ENST00000289248.2	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	39420945	39420945	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39420945G>A			NA	NA				Y_RNA (4348 upstream) : AKIRIN1 (35949 downstream)						NA		NA									NA						ggatttcaccgtgttagccag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.39420945G>A		NA		hg19		0.02	-0.131415	ACCxTGT	COVERED																																																																																			NOVEL					0			9	2.405672	KEEP	2	0	0	8	220	GT	0.99254	0.227464	0			5	59	142	0	0	12.442096	10	60	292	33		0.333333	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	39476449	39476449	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39476449A>G			NA	NA				AKIRIN1 (4718 upstream) : NDUFS5 (15540 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.39476449A>G		NA		hg19		0.02	-0.298197	CCAxCAC	COVERED																																																																																			NOVEL					0			12	3.308287	KEEP	1	0	0	11	303	AA	0.992708	0.775364	0			5	60	165	0	0	13.45403	20	60	579	65		0.2	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	39507458	39507458	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39507458A>G			NA	NA				NDUFS5 (7150 upstream) : MACF1 (39529 downstream)						NA		NA									NA						aggctggagtacagtggcaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.39507458A>G		NA		hg19		0.02	-0.228034	AGTxCAG	COVERED																																																																																			NOVEL					0			8	2.405715	KEEP	1	0	0	8	215	AA	0.99257	0.578599	0			3	60	91	1	0	6.793383	18	60	529	53		0.142857	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	39524819	39524819	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39524819G>A			NA	NA				NDUFS5 (24511 upstream) : MACF1 (22168 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.39524819G>A		NA		hg19		0.02	-0.307005	CACxCCT	UNCOVERED																																																																																			NOVEL					0			6	2.4067	KEEP	3	0	0	8	235	GG	0	0	0			4	60	112	0	0	7.764761	30	60	994	66		0.117647	0.800245
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39579500	39579500	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39579500A>G	ENST00000372915.3	+	1	307				MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ctgaggtcagaagtttgagac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.220+29390A>G	chr1.hg19:g.39579500A>G		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.350805	CAGxAGT	UNCOVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	5	2.403654	KEEP	2	0	0	8	202	AA	0	0	0		+	3	39	96	0	0	6.477275	35	60	1030	73	ENST00000372915.3	0.078947	0.877708
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39589826	39589826	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39589826A>G	ENST00000372915.3	+	1	307				MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ccaaagtgctaggattacagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.220+39716A>G	chr1.hg19:g.39589826A>G		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.359577	GCTxGGA	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	9	2.403828	KEEP	0	0	0	8	203	AA	0.99257	0.882271	0		+	4	60	140	0	0	10.30963	35	60	1031	66	ENST00000372915.3	0.102564	0.888875
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39621799	39621799	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39621799G>A	ENST00000372915.3	+	1	307				MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			cgcctgcctcggcctcccaaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.220+71689G>A	chr1.hg19:g.39621799G>A		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.306973	CTCxGCC	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	18	5.086969	KEEP	7	0	0	17	466	GG	0.995343	0.796519	0		+	3	21	93	0	0	6.410244	29	60	916	69	ENST00000372915.3	0.09375	0.800245
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39621816	39621816	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39621816G>A	ENST00000372915.3	+	1	307				MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			caaagtgctgggattacaggc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.220+71706G>A	chr1.hg19:g.39621816G>A		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.359664	CTGxGAT	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	22	5.716735	KEEP	8	0	0	19	572	GG	0.997832	0.886948	0		+	3	21	96	0	0	6.475932	35	60	1174	82	ENST00000372915.3	0.078947	0.888875
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39707818	39707818	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39707818A>G	ENST00000372915.3	+	3	369				MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000536367.1_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ccaggagttcaagaccagcct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.283-7868A>G	chr1.hg19:g.39707818A>G		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.228022	TTCxAGA	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	10	2.406306	KEEP	0	0	0	8	223	AA	0.99257	0.578599	0		+	3	60	91	0	0	6.607243	21	60	615	46	ENST00000372915.3	0.125	0.58293
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39762238	39762238	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39762238T>C	ENST00000372915.3	+	19	2457				MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			cccttctctattaaaaataca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.2370+684T>C	chr1.hg19:g.39762238T>C		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.166647	CTAxTAA	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	7	2.704995	KEEP	0	0	0	9	237	TT	0.99254	0.351306	0		+	3	58	100	0	0	8.172272	12	60	359	38	ENST00000372915.3	0.2	0.353947
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39779823	39779823	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39779823A>G	ENST00000372915.3	+	26	3372				MACF1_ENST00000476350.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			gctcacgcctataatcccagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.3286-1362A>G	chr1.hg19:g.39779823A>G		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.306955	CCTxTAA	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	12	3.305208	KEEP	4	0	0	11	281	AA	0.99257	0.7943	0		+	4	60	126	0	0	9.276654	28	60	815	70	ENST00000372915.3	0.125	0.800245
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39842728	39842728	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39842728A>G	ENST00000372915.3	+	52	13315				MACF1_ENST00000289893.4_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			tgtcgcccagactggagtgcg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13229-1405A>G	chr1.hg19:g.39842728A>G		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.342015	CAGxCTG	COVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	11	2.406023	KEEP	0	0	0	8	220	AA	0.99257	0.871187	0		+	3	60	106	0	0	7.752492	28	60	828	65	ENST00000372915.3	0.096774	0.877708
MACF1	23499	__UNKNOWN__	__UNKNOWN__	1	39942008	39942008	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:39942008C>T	ENST00000372915.3	+	95	21655				MACF1_ENST00000289893.4_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000317713.7_Intron			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	NA		NA			ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			tttgggaggccgaggcgggca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603	23499		EF-hand domain containing	13664	protein-coding gene	gene with protein product	actin cross-linking factor, 620 kDa actin binding protein, macrophin 1, trabeculin-alpha, actin cross-linking family protein 7	608271			NA	7635207, 10529403	Standard	NM_033044	NM_012090	NA	Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.21569-3462C>T	chr1.hg19:g.39942008C>T		NA	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	hg19		0.02	-0.175434	GGCxGAG	UNCOVERED																																																																																			NOVEL	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392096.1	8	2.707618	KEEP	7	0	0	9	268	CC	0	0	0		+	3	60	89	0	0	6.810529	15	60	499	51	ENST00000372915.3	0.166667	0.387407
RP11-69E11.4	0	__UNKNOWN__	__UNKNOWN__	1	40009540	40009540	__UNKNOWN__	RNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40009540A>C	ENST00000440190.1	-	0	455				RP11-69E11.4_ENST00000417869.1_RNA						NA		NA									NA						tcaagaccagactggacaaca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000440190.1:	chr1.hg19:g.40009540A>C		NA		hg19		0.02	-0.245557	CAGxCTG	COVERED																																																																																			NOVEL	RP11-69E11.4-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000025214.1	13	3.909544	KEEP	0	0	0	13	354	AA	0.994391	0.63775	0		-	3	60	95	0	0	6.844339	24	60	710	53	ENST00000440190.1	0.111111	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40202449	40202449	__UNKNOWN__	IGR	SNP	G	G	A	rs74225684	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40202449G>A			NA	NA				RNU7-121P (13150 upstream) : PPIE (2104 downstream)						NA		NA									NA						ACCCTAggccgggtgtagtgg	0.502		NA											G|||	15	0.00299521	0.0	0.0	5008	,	,	NA	16034	0.0139	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40202449G>A		NA		hg19		0.02	-0.315704	GCCxGGT	COVERED																																																																																			NOVEL					0			6	2.704267	KEEP	0	0	0	9	238	GG	0.99254	0.812359	0			3	60	91	0	0	6.393781	25	60	768	62		0.107143	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40202467	40202467	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40202467T>C			NA	NA				RNU7-121P (13168 upstream) : PPIE (2086 downstream)						NA		NA									NA						tggctcacacttgtaatccca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40202467T>C		NA		hg19		0.02	-0.306988	CACxTGT	COVERED																																																																																			NOVEL					0			6	3.608189	KEEP	0	0	0	12	319	TT	0.993634	0.795151	0			4	60	132	0	0	10.123024	24	60	714	71		0.142857	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40259789	40259789	__UNKNOWN__	IGR	SNP	G	G	A	rs537158208		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40259789G>A			NA	NA				RP1-118J21.25 (3946 upstream) : TRIT1 (46933 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.537		NA											G|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16710	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40259789G>A		NA		hg19		0.02	-0.289455	CACxCCT	COVERED																																																																																			NOVEL					0			7	2.707629	KEEP	3	0	0	9	267	GG	0.99257	0.755234	0			4	60	111	0	0	7.720646	29	60	977	67		0.121212	0.760887
TRIT1	54802	__UNKNOWN__	__UNKNOWN__	1	40319374	40319374	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40319374A>G	ENST00000316891.5	-	3	429				TRIT1_ENST00000537440.1_Intron|TRIT1_ENST00000545233.1_Intron|TRIT1_ENST00000541099.1_Intron|TRIT1_ENST00000372818.1_Intron|TRIT1_ENST00000537223.1_Intron|TRIT1_ENST00000491865.1_Intron|TRIT1_ENST00000441669.2_Intron|TRIT1_ENST00000544981.1_Intron	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	NA		NA			tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			gtgagccaccacgcctggccT	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	54802	2.5.1.8		20286	protein-coding gene	gene with protein product		NA			NA	11111046, 15870694	Standard	NM_017646	NM_017646	NA	Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.414+267T>C	chr1.hg19:g.40319374A>G		NA	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	hg19	CCDS30681.1	0.02	-0.210464	ACCxCGC	COVERED																																																																																			NOVEL	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025627.2	10	2.706001	KEEP	0	0	0	9	239	AA	0.99254	0.518266	0		-	3	60	101	0	0	7.792584	18	60	507	41	ENST00000316891.5	0.142857	0.522161
TRIT1	54802	__UNKNOWN__	__UNKNOWN__	1	40337007	40337007	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40337007A>G	ENST00000316891.5	-	1	189				TRIT1_ENST00000537440.1_Intron|TRIT1_ENST00000545233.1_Intron|TRIT1_ENST00000541099.1_Intron|TRIT1_ENST00000372818.1_Intron|TRIT1_ENST00000537223.1_Intron|TRIT1_ENST00000491865.1_Intron|TRIT1_ENST00000441669.2_Intron|TRIT1_ENST00000544981.1_Intron	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	NA		NA			tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			gctcacgcctataatcggagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	54802	2.5.1.8		20286	protein-coding gene	gene with protein product		NA			NA	11111046, 15870694	Standard	NM_017646	NM_017646	NA	Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.174+11982T>C	chr1.hg19:g.40337007A>G		NA	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	hg19	CCDS30681.1	0.02	-0.341994	CCTxTAA	COVERED																																																																																			NOVEL	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025627.2	13	3.006025	KEEP	0	0	0	10	266	AA	0.992708	0.859432	0		-	3	60	94	0	0	6.391028	32	60	912	69	ENST00000316891.5	0.085714	0.865745
TRIT1	54802	__UNKNOWN__	__UNKNOWN__	1	40340367	40340367	__UNKNOWN__	Intron	SNP	C	C	T	rs188058618	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40340367C>T	ENST00000316891.5	-	1	189				TRIT1_ENST00000537440.1_Intron|TRIT1_ENST00000545233.1_Intron|TRIT1_ENST00000541099.1_Intron|TRIT1_ENST00000372818.1_Intron|TRIT1_ENST00000537223.1_Intron|TRIT1_ENST00000491865.1_Intron|TRIT1_ENST00000441669.2_Intron|TRIT1_ENST00000544981.1_Intron	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	NA		NA			tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			gatggagtttcgctcttgttg	0.413		NA											C|||	4	0.000798722	0.0023	0.0014	5008	,	,	NA	16310	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	54802	2.5.1.8		20286	protein-coding gene	gene with protein product		NA			NA	11111046, 15870694	Standard	NM_017646	NM_017646	NA	Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.174+8622G>A	chr1.hg19:g.40340367C>T		NA	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	hg19	CCDS30681.1	0.02	-0.219283	TTTxGCT	COVERED																																																																																			NOVEL	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025627.2	11	2.707351	KEEP	4	0	0	9	262	CC	0.99254	0.548763	0		-	3	60	88	0	0	6.306732	21	60	662	60	ENST00000316891.5	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40386830	40386830	__UNKNOWN__	IGR	SNP	T	T	C	rs542371540	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40386830T>C			NA	NA				MYCL (19143 upstream) : Y_RNA (23731 downstream)						NA		NA									NA						ggcgcgatcttggctcactgc	0.463		NA											T|||	10	0.00199681	0.0076	0.0	5008	,	,	NA	16164	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40386830T>C		NA		hg19		0.02	-0.280675	TCTxGGC	COVERED																																																																																			NOVEL					0			7	3.308182	KEEP	0	0	0	11	305	TT	0.993072	0.734547	0			3	60	99	0	0	7.052859	28	60	845	62		0.096774	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40397102	40397102	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40397102T>C			NA	NA				MYCL (29415 upstream) : Y_RNA (13459 downstream)						NA		NA									NA						ggattacaggtatgagccact	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40397102T>C		NA		hg19		0.02	-0.341485	AGGxATG	COVERED																																																																																			NOVEL					0			16	3.303984	KEEP	0	0	0	11	266	TT	0.993072	0.859748	0			3	60	105	0	0	7.655121	28	60	744	62		0.096774	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40397103	40397103	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40397103A>G			NA	NA				MYCL (29416 upstream) : Y_RNA (13458 downstream)						NA		NA									NA						gattacaggtatgagccactg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40397103A>G		NA		hg19		0.02	-0.33221	GGTxTGA	COVERED																																																																																			NOVEL					0			16	3.306147	KEEP	0	0	0	11	278	AA	0.993072	0.846082	0			4	60	132	0	0	9.994746	26	60	737	62		0.133333	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40412272	40412272	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40412272T>C			NA	NA				Y_RNA (1602 upstream) : MFSD2A (8529 downstream)						NA		NA									NA						gtagtcccagttactcgggag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40412272T>C		NA		hg19		0.02	-0.236811	CAGxTAC	UNCOVERED																																																																																			NOVEL					0			6	2.405408	KEEP	1	0	0	8	211	TT	0	0	0			4	60	124	0	0	9.537505	21	60	635	46		0.16	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40459938	40459938	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40459938T>C			NA	NA				MFSD2A (24300 upstream) : CAP1 (45966 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40459938T>C		NA		hg19		0.02	-0.166654	ATCxCAG	COVERED																																																																																			NOVEL					0			9	2.707221	KEEP	2	0	0	9	257	TT	0.99254	0.351306	0			4	60	130	0	0	10.881043	13	60	403	48		0.235294	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40488336	40488336	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40488336C>T			NA	NA				MFSD2A (52698 upstream) : CAP1 (17568 downstream)						NA		NA									NA						ccaccgcgcccggcctggaag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40488336C>T		NA		hg19		0.02	-0.245628	GCCxGGC	COVERED																																																																																			NOVEL					0			5	3.606905	KEEP	3	0	0	12	325	CC	0.99254	0.636563	0			3	60	99	0	0	7.242346	24	60	814	61		0.111111	0.641347
PPT1	5538	__UNKNOWN__	__UNKNOWN__	1	40559656	40559656	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40559656A>G	ENST00000433473.3	-	2	589				PPT1_ENST00000449045.2_Intron	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1	NA		NA			adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			cttgaggccaagagttcgaga	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	5538	3.1.2.22		9325	protein-coding gene	gene with protein product	ceroid-lipofuscinosis, neuronal 1, infantile	600722		PPT	NA	7637805, 8325646	Standard	NM_000310	NM_000310	NA	Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495	ENST00000433473.3:c.125-1477T>C	chr1.hg19:g.40559656A>G		NA	B4DY24|Q6FGQ4	hg19	CCDS447.1	0.02	3.815608	CCAxGAG	COVERED																																																																																			NOVEL	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000013126.2	23	4.773409	KEEP	1	5	136	64	1780	AA	1	0.999999	0		-	6	60	185	0	0	11.240246	105	60	3157	258	ENST00000433473.3	0.054054	0.999999
RLF	6018	__UNKNOWN__	__UNKNOWN__	1	40674381	40674381	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40674381C>T	ENST00000372771.4	+	5	837					NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	NA		NA			chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			cccagctactcgggaggctga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000	6018		Zinc fingers, C2H2-type	10025	protein-coding gene	gene with protein product		180610	rearranged L-myc fusion sequence		NA	1649386	Standard	NM_012421	NM_012421	NA	Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.810+6095C>T	chr1.hg19:g.40674381C>T		NA	Q14CQ1|Q9NU60	hg19	CCDS448.1	0.02	-0.27185	ACTxGGG	COVERED																																																																																			NOVEL	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000015767.1	7	3.008392	KEEP	0	0	0	10	295	CC	0.993072	0.712346	0		+	4	60	122	0	0	9.058368	25	60	790	58	ENST00000372771.4	0.137931	0.717315
RLF	6018	__UNKNOWN__	__UNKNOWN__	1	40697617	40697617	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40697617A>T	ENST00000372771.4	+	7	1116					NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	NA		NA			chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			cggtggctcaagcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000	6018		Zinc fingers, C2H2-type	10025	protein-coding gene	gene with protein product		180610	rearranged L-myc fusion sequence		NA	1649386	Standard	NM_012421	NM_012421	NA	Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.1089+287A>T	chr1.hg19:g.40697617A>T		NA	Q14CQ1|Q9NU60	hg19	CCDS448.1	0.02	-0.140323	TCAxGCC	COVERED																																																																																			NOVEL	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000015767.1	6	2.707429	KEEP	1	0	0	9	259	AA	0.99254	0.289823	0		+	3	60	82	0	0	6.582249	10	60	301	41	ENST00000372771.4	0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40841866	40841866	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40841866A>G			NA	NA				COL9A2 (58900 upstream) : SMAP2 (20640 downstream)						NA		NA									NA						caggtgatccacccgcctcag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40841866A>G		NA		hg19		0.02	-0.254265	TCCxCCC	COVERED																																																																																			NOVEL					0			19	4.204803	KEEP	10	0	0	14	352	AA	0.992708	0.68861	0			3	40	96	0	0	7.049777	22	60	637	67		0.12	0.693668
ZFP69	339559	__UNKNOWN__	__UNKNOWN__	1	40949716	40949716	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40949716T>C	ENST00000372706.1	+	3	1225				ZFP69_ENST00000372705.3_Intron			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						cattgcactctagcctgggca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815	339559		Zinc fingers, C2H2-type, -, -, -	24708	protein-coding gene	gene with protein product	ZFP69 zinc finger protein A	NA	zinc finger protein 642	ZNF642	NA		Standard	NM_198494	XM_005270808	NA	Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.219+2190T>C	chr1.hg19:g.40949716T>C		NA	Q5SWM5|Q6ZWK8	hg19	CCDS30686.1	0.02	-0.184185	CTCxAGC	COVERED																																																																																			NOVEL	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019082.1	5	3.007407	KEEP	1	0	0	10	274	TT	0.99254	0.420319	0		+	3	60	99	0	0	7.810269	15	60	450	50	ENST00000372706.1	0.166667	0.423478
RP11-656D10.3	0	__UNKNOWN__	__UNKNOWN__	1	40973613	40973613	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40973613C>T	ENST00000450713.1	-	0	73										NA		NA									NA						ccaccgtgcccggccttcata	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000450713.1:	chr1.hg19:g.40973613C>T		NA		hg19		0.02	-0.219252	GCCxGGC	UNCOVERED																																																																																			NOVEL	RP11-656D10.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000019085.1	4	2.406195	KEEP	5	0	0	8	223	CC	0	0	0		-	3	60	93	0	0	6.928026	19	60	601	51	ENST00000450713.1	0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	40996166	40996166	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:40996166T>C			NA	NA				RP11-656D10.6 (13320 upstream) : ZNF684 (1066 downstream)						NA		NA									NA						ccacctaagcttcccaaagtg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.40996166T>C		NA		hg19		0.02	-0.245575	AGCxTCC	COVERED																																																																																			NOVEL					0			6	2.406221	KEEP	0	0	0	8	226	TT	0.99257	0.636582	0			3	60	107	1	0	7.991975	25	60	744	53		0.107143	0.641347
ZNF684	127396	__UNKNOWN__	__UNKNOWN__	1	41010301	41010301	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41010301T>C	ENST00000372699.3	+	5	489				ZNF684_ENST00000372696.3_3'UTR|ZNF684_ENST00000493756.1_Intron|ZNF684_ENST00000372697.3_3'UTR	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			ggattacaggtgtgagccacc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010	127396		Zinc fingers, C2H2-type, -	28418	protein-coding gene	gene with protein product	hypothetical protein MGC27466	NA			NA	12477932	Standard	NM_152373	NM_152373	NA	Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.239-1933T>C	chr1.hg19:g.41010301T>C		NA	Q2NKY4	hg19	CCDS454.1	0.02	3.677938	AGGxGTG	COVERED																																																																																			NOVEL	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019260.3	19	9.318096	KEEP	1	0	0	31	818	TT	0.999997	0.999993	0		+	6	60	190	0	0	11.890518	99	60	2855	213	ENST00000372699.3	0.057143	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	41020216	41020216	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41020216C>T			NA	NA				ZNF684 (6375 upstream) : RIMS3 (66134 downstream)						NA		NA									NA						cccatgttggccaggctggtc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.41020216C>T		NA		hg19		0.02	-0.175385	TGGxCAG	UNCOVERED																																																																																			NOVEL					0			7	2.406514	KEEP	2	0	0	8	229	CC	0	0	0			4	60	101	0	0	7.869541	14	60	460	34		0.222222	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	41067196	41067196	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41067196A>C			NA	NA				ZNF684 (53355 upstream) : RIMS3 (19154 downstream)						NA		NA									NA						cttcggcctcacaaagtgctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.41067196A>C		NA		hg19		0.02	-0.201733	CTCxCAA	COVERED																																																																																			NOVEL					0			6	3.007155	KEEP	1	0	0	10	273	AA	0.992708	0.486967	0			4	60	135	0	0	10.879377	18	60	539	49		0.181818	0.490544
KCNQ4	9132	__UNKNOWN__	__UNKNOWN__	1	41275474	41275474	__UNKNOWN__	Intron	SNP	C	C	G	rs12736424	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41275474C>G	ENST00000347132.5	+	2	396				KCNQ4_ENST00000509682.2_Intron	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	NA		NA			inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	cggtggctcacgcctgtaatc	0.527		NA											C|||	1718	0.343051	0.2791	0.3588	5008	,	,	NA	18712	0.2708	NA	0.4165	False	NA	,,,	NA	NA	NA	2504	0.4172	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013	9132		Potassium channels, Voltage-gated ion channels / Potassium channels	6298	protein-coding gene	gene with protein product		603537		DFNA2	NA	10025409, 16382104	Standard	NM_004700	NM_004700	NA	Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.315-7463C>G	chr1.hg19:g.41275474C>G		NA	O96025	hg19	CCDS456.1	0.02	-0.219292	TCAxGCC	UNCOVERED																																																																																			NOVEL	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020812.1	13	2.406532	KEEP	15	0	0	8	231	CC	0	0	0		+	9	60	309	0	0	28.730764	13	60	397	67	ENST00000347132.5	0.409091	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	41401226	41401226	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41401226A>G			NA	NA				RP5-1066H13.4 (58884 upstream) : CTPS1 (43780 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.41401226A>G		NA		hg19		0.02	-0.385879	CACxCCT	COVERED																																																																																			NOVEL					0			8	4.208029	KEEP	2	0	0	14	369	AA	0.99649	0.914948	0			3	60	105	0	0	7.375218	35	60	1007	94		0.078947	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	41492682	41492682	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41492682C>G			NA	NA				SLFNL1 (3773 upstream) : SCMH1 (189 downstream)						NA		NA									NA						caccatgttgcccaggctggt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.41492682C>G		NA		hg19		0.02	-0.228048	TTGxCCA	COVERED																																																																																			NOVEL					0			7	2.407231	KEEP	0	0	0	8	249	AC	0.99254	0.578582	0			3	60	88	0	0	6.366553	20	60	646	50		0.130435	0.58293
SCMH1	22955	__UNKNOWN__	__UNKNOWN__	1	41532382	41532382	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41532382G>A	ENST00000326197.7	-	9	1375				SCMH1_ENST00000372596.1_Intron|SCMH1_ENST00000397174.2_Intron|SCMH1_ENST00000361191.5_Intron|SCMH1_ENST00000397171.2_Intron|SCMH1_ENST00000337495.5_Intron|SCMH1_ENST00000372595.1_Intron|SCMH1_ENST00000361705.3_Intron|SCMH1_ENST00000456518.2_Intron|SCMH1_ENST00000372597.1_Intron|SCMH1_ENST00000402904.2_Intron					sex comb on midleg homolog 1 (Drosophila)	NA		NA								breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(2)|pancreas(2)|upper_aerodigestive_tract(1)	15	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				agcctcccgagtagctgggac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF149045	CCDS461.1, CCDS30688.1, CCDS53301.1, CCDS53302.1, CCDS53303.1, CCDS53304.1	1p34	2013-01-10			ENSG00000010803	ENSG00000010803	22955		Sterile alpha motif (SAM) domain containing	19003	protein-coding gene	gene with protein product		NA			NA	10524249	Standard		NM_012236	NA	Approved	Scml3	uc001cgs.3	Q96GD3	OTTHUMG00000005720	ENST00000326197.7:c.1075+3884C>T	chr1.hg19:g.41532382G>A		NA		hg19	CCDS30688.1	0.02	-0.219049	CGAxTAG	COVERED																																																																																			NOVEL	SCMH1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000015656.1	4	3.911044	KEEP	1	0	0	13	396	GG	0.993634	0.549368	0		-	4	60	118	0	0	9.462562	15	60	512	56	ENST00000326197.7	0.210526	0.552887
RP11-399E6.1	0	__UNKNOWN__	__UNKNOWN__	1	41728973	41728973	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41728973G>A	ENST00000445073.1	+	0	132										NA		NA									NA						atggagtctcgctctgtcgcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000445073.1:	chr1.hg19:g.41728973G>A		NA		hg19		0.02	-0.28944	CTCxCTC	COVERED																																																																																			NOVEL	RP11-399E6.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000015626.1	11	2.70674	KEEP	3	0	0	9	257	GG	0.99257	0.755234	0		+	4	60	111	0	0	8.094153	23	60	751	65	ENST00000445073.1	0.148148	0.760887
RP11-399E6.1	0	__UNKNOWN__	__UNKNOWN__	1	41735747	41735747	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:41735747T>C	ENST00000445073.1	+	0	132										NA		NA									NA						tggctgggcgtggtggctcat	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000445073.1:	chr1.hg19:g.41735747T>C		NA		hg19		0.02	-0.219233	GCGxGGT	COVERED																																																																																			NOVEL	RP11-399E6.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000015626.1	9	3.007228	KEEP	2	0	0	10	272	TT	0.99254	0.548763	0		+	3	60	100	0	0	7.627276	19	60	542	51	ENST00000445073.1	0.136364	0.552887
HIVEP3	59269	__UNKNOWN__	__UNKNOWN__	1	42270756	42270756	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:42270756T>C	ENST00000372583.1	-	2	86				HIVEP3_ENST00000372584.1_Intron	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				acctgtaatctcagcactttg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124	59269		Zinc fingers, C2H2-type	13561	protein-coding gene	gene with protein product	kappabinding protein-1	606649	human immunodeficiency virus type I enhancer-binding protein 3		NA	11161801	Standard	NM_024503	NR_038260	NA	Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.800-104090A>G	chr1.hg19:g.42270756T>C		NA	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	hg19	CCDS463.1	0.02	-0.23683	ATCxCAG	COVERED																																																																																			NOVEL	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000016978.1	5	2.706871	KEEP	2	0	0	9	249	TT	0.99257	0.607857	0		-	3	60	99	0	0	7.348944	22	60	680	60	ENST00000372583.1	0.12	0.612407
HIVEP3	59269	__UNKNOWN__	__UNKNOWN__	1	42292121	42292121	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:42292121A>G	ENST00000372583.1	-	1	86				HIVEP3_ENST00000372584.1_Intron	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				ttttgctcttattgcccaggc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124	59269		Zinc fingers, C2H2-type	13561	protein-coding gene	gene with protein product	kappabinding protein-1	606649	human immunodeficiency virus type I enhancer-binding protein 3		NA	11161801	Standard	NM_024503	NR_038260	NA	Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.799+91962T>C	chr1.hg19:g.42292121A>G		NA	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	hg19	CCDS463.1	0.02	-0.140332	CTTxTTG	COVERED																																																																																			NOVEL	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000016978.1	9	2.706174	KEEP	1	0	0	9	240	AA	0.99254	0.259018	0		-	3	60	104	0	0	8.672938	11	60	319	37	ENST00000372583.1	0.214286	0.260965
CLDN19	149461	__UNKNOWN__	__UNKNOWN__	1	43199022	43199022	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43199022A>G	ENST00000296387.1	-	0	2600				CLDN19_ENST00000539749.1_3'UTR	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19	NA		NA			apical junction assembly (GO:0043297)|calcium-independent cell-cell adhesion (GO:0016338)|neuronal action potential propagation (GO:0019227)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	apical junction complex (GO:0043296)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(2)|large_intestine(1)|lung(2)|skin(1)	6	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				tgggattacaagcgtgagcca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096063	CCDS471.1, CCDS44125.1, CCDS53306.1	1p34.2	2008-05-14			ENSG00000164007	ENSG00000164007	149461		Claudins	2040	protein-coding gene	gene with protein product		610036			NA		Standard	NM_148960	NM_148960	NA	Approved		uc001cht.1	Q8N6F1	OTTHUMG00000007524	ENST00000296387.1:c.*1735T>C	chr1.hg19:g.43199022A>G		NA	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	hg19	CCDS471.1	0.02	-0.228051	ACAxGCG	COVERED																																																																																			NOVEL	CLDN19-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019788.1	4	2.406731	KEEP	1	0	0	8	232	AA	0.99257	0.578599	0		-	3	60	105	0	0	7.948591	22	60	676	48	ENST00000296387.1	0.12	0.58293
ERMAP	114625	__UNKNOWN__	__UNKNOWN__	1	43302265	43302265	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43302265G>A	ENST00000372517.2	+	7	827				ERMAP_ENST00000328249.3_Intron|RP11-342M1.3_ENST00000414798.1_RNA|ERMAP_ENST00000372514.3_Intron|ERMAP_ENST00000487556.1_Intron	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	NA		NA				cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				ggtggctcacgcctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010	114625		Blood group antigens, Immunoglobulin superfamily / V-set domain containing, Butyrophilins	15743	protein-coding gene	gene with protein product		609017	Radin blood group, Scianna blood group, erythroblast membrane-associated protein, erythroblast membrane-associated protein (RD and SC blood groups)	RD, SC	NA	11549310	Standard	NM_018538	XM_005270415	NA	Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.584-564G>A	chr1.hg19:g.43302265G>A		NA	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	hg19	CCDS475.1	0.02	-0.184196	CACxCCT	COVERED																																																																																			NOVEL	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020180.1	2	2.704524	KEEP	1	0	0	9	245	GG	0.99257	0.420331	0		+	3	60	88	0	1	6.792186	14	60	434	46	ENST00000372517.2	0.176471	0.423478
SLC2A1-AS1	440584	__UNKNOWN__	__UNKNOWN__	1	43438253	43438253	__UNKNOWN__	lincRNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43438253C>G	ENST00000431759.1	+	0	675					NR_033967.1				SLC2A1 antisense RNA 1	NA		NA									NA						ctcccaaagtcctaggattac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK056786		1p34.2	2012-10-12	2012-08-15		ENSG00000227533	ENSG00000227533	440584		Long non-coding RNAs	44187	non-coding RNA	RNA, long non-coding		NA	SLC2A1 antisense RNA 1 (non-protein coding)		NA		Standard	NR_033967	NR_033967	NA	Approved		uc001cil.3		OTTHUMG00000007699	ENST00000431759.1:	chr1.hg19:g.43438253C>G		NA		hg19		0.02	-0.228075	AGTxCTA	COVERED																																																																																			NOVEL	SLC2A1-AS1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000020688.1	8	3.007732	KEEP	1	0	0	10	284	CC	0.99254	0.578582	0		+	3	60	97	0	0	7.392148	18	60	581	51	ENST00000431759.1	0.142857	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	43466411	43466411	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43466411T>C			NA	NA				RNU6-880P (9196 upstream) : RNU6-870P (22808 downstream)						NA		NA									NA						ggtgcgatcttggctcaccac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.43466411T>C		NA		hg19		0.02	-0.192958	TCTxGGC	COVERED																																																																																			NOVEL					0			7	3.908951	KEEP	0	0	0	13	346	TT	0.995343	0.455625	0			4	60	128	0	0	10.268965	17	60	502	48		0.190476	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	43531812	43531812	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43531812T>C			NA	NA				RNU6-870P (42504 upstream) : FAM183A (79011 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.43531812T>C		NA		hg19		0.02	-0.228026	AGGxGTG	COVERED																																																																																			NOVEL					0			12	2.706287	KEEP	0	0	0	9	242	TT	0.99254	0.578582	0			3	60	100	0	0	7.505745	21	60	615	49		0.125	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	43545300	43545300	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43545300A>G			NA	NA				RNU6-870P (55992 upstream) : FAM183A (65523 downstream)						NA		NA									NA						cctgaggtcaagagtttgaga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.43545300A>G		NA		hg19		0.02	-0.131545	TCAxGAG	COVERED																																																																																			NOVEL					0			2	3.609254	KEEP	1	0	0	12	333	AA	0.993072	0.227586	0			3	60	98	0	0	8.182342	10	60	291	39		0.230769	0.229173
WDR65	0	__UNKNOWN__	__UNKNOWN__	1	43658345	43658345	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43658345T>C	ENST00000372492.4	+	7	1446				WDR65_ENST00000528956.1_Intron	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		NA		NA								NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				cctgtaatcctagcactttgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000372492.4:c.1123-4879T>C	chr1.hg19:g.43658345T>C		NA	A6NKQ3|Q17RI9|Q5TAI0	hg19		0.02	-0.192948	TCCxAGC	COVERED																																																																																			NOVEL	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384325.1	10	2.405317	KEEP	0	0	0	8	211	TT	0.99257	0.454356	0		+	3	60	96	0	0	7.361173	17	60	496	40	ENST00000372492.4	0.15	0.457757
MPL	4352	__UNKNOWN__	__UNKNOWN__	1	43807831	43807831	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43807831C>T	ENST00000372470.3	+	6	1022				MPL_ENST00000413998.2_Intron	NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	NA		NA			blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	cccaaagtgccgggattacag	0.433		NA	Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia														NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	myeloproliferative leukemia virus oncogene, thrombopoietin receptor	yes	L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400	4352		CD molecules, Fibronectin type III domain containing	7217	protein-coding gene	gene with protein product		159530	myeloproliferative leukemia virus oncogene		NA	1608974	Standard	NM_005373	NM_005373	NA	Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.980+1647C>T	chr1.hg19:g.43807831C>T		NA	Q5JUZ0	hg19	CCDS483.1	0.02	-0.157881	TGCxGGG	COVERED																																																																																			NOVEL	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019522.1	8	3.008484	KEEP	1	0	0	10	294	CC	0.992708	0.320453	0		+	3	60	86	0	0	6.679416	13	60	430	45	ENST00000372470.3	0.1875	0.322807
MPL	4352	__UNKNOWN__	__UNKNOWN__	1	43818069	43818069	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:43818069C>T	ENST00000372470.3	+	11	1695					NM_005373.2	NP_005364.1	P40238	TPOR_HUMAN	MPL proto-oncogene, thrombopoietin receptor	NA		NA			blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|platelet activation (GO:0030168)|regulation of chemokine production (GO:0032642)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(551)|large_intestine(3)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	567	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			Eltrombopag(DB06210)|Romiplostim(DB05332)	CCTTGCCCTACCAGTGTGCCA	0.597		NA	Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia														NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(52;534 1204 10016 41452 44427)	yes	Dom	yes	Familial essential thrombocythemia	1	p34	4352	myeloproliferative leukemia virus oncogene, thrombopoietin receptor	yes	L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M90102	CCDS483.1	1p34	2014-09-17	2014-06-26		ENSG00000117400	ENSG00000117400	4352		CD molecules, Fibronectin type III domain containing	7217	protein-coding gene	gene with protein product		159530	myeloproliferative leukemia virus oncogene		NA	1608974	Standard	NM_005373	NM_005373	NA	Approved	CD110, TPOR	uc001ciw.3	P40238	OTTHUMG00000007429	ENST00000372470.3:c.1653+95C>T	chr1.hg19:g.43818069C>T		NA	Q5JUZ0	hg19	CCDS483.1	0.02	1.438152	CTAxCAG	COVERED																																																																																			NOVEL	MPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019522.1	3	5.716814	KEEP	0	0	0	19	575	CC	0.99986	0.999799	0		+	30	60	911	0	0	79.846886	64	60	2147	160	ENST00000372470.3	0.319149	0.99994
KDM4A	9682	__UNKNOWN__	__UNKNOWN__	1	44118382	44118382	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:44118382C>T	ENST00000372396.3	+	2	95				KDM4A_ENST00000463151.1_Intron	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	NA		NA			cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						gacggagtttcgctcttgttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135	9682		Chromatin-modifying enzymes / K-demethylases, Tudor domain containing	22978	protein-coding gene	gene with protein product	jumonji C domain-containing histone demethylase 3A, tudor domain containing 14A	609764	jumonji domain containing 2, jumonji domain containing 2A	JMJD2, JMJD2A	NA	9734811, 15138608	Standard	NM_014663	XM_005271354	NA	Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.-39-426C>T	chr1.hg19:g.44118382C>T		NA	Q5VVB1	hg19	CCDS491.1	0.02	-0.149068	TTTxGCT	COVERED																																																																																			NOVEL	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000019960.1	4	3.60857	KEEP	1	0	0	12	326	CC	0.993072	0.289978	0		+	4	60	113	0	0	9.431433	11	60	330	38	ENST00000372396.3	0.266667	0.292001
SLC6A9	6536	__UNKNOWN__	__UNKNOWN__	1	44494166	44494166	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:44494166A>G	ENST00000372310.3	-	1	81				SLC6A9_ENST00000492434.2_Intron|SLC6A9_ENST00000537678.1_Intron|SLC6A9_ENST00000475075.2_Intron|SLC6A9_ENST00000372306.3_Intron	NM_001024845.2	NP_001020016.1	P48067	SC6A9_HUMAN	solute carrier family 6 (neurotransmitter transporter, glycine), member 9	NA		NA			transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(2)	22	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)	ggtggctcacacctgtaatcc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S70609	CCDS30695.1, CCDS41316.1, CCDS41317.1	1p33	2013-05-22			ENSG00000196517	ENSG00000196517	6536		Solute carriers	11056	protein-coding gene	gene with protein product		601019			NA	8183239, 7587377	Standard	NM_201649	NM_006934	NA	Approved	GLYT1	uc001cll.4	P48067	OTTHUMG00000008294	ENST00000372310.3:c.84+2811T>C	chr1.hg19:g.44494166A>G		NA	A6NDH1|A6NII2|A6NNZ8|Q5TAB8|Q5TAB9|Q5TAC0	hg19	CCDS30695.1	0.02	-0.175411	CACxCCT	COVERED																																																																																			NOVEL	SLC6A9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022827.1	5	2.706726	KEEP	3	0	0	9	249	AA	0.99257	0.384528	0		-	3	60	96	0	0	7.591937	14	60	419	50	ENST00000372310.3	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	44571623	44571623	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:44571623C>G			NA	NA				RP5-1198O20.4 (976 upstream) : RN7SL479P (11148 downstream)						NA		NA									NA						attgcttgagcccaggagttt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.44571623C>G		NA		hg19		0.02	-0.219298	GAGxCCA	COVERED																																																																																			NOVEL					0			12	3.308951	KEEP	0	0	0	11	318	CC	0.993634	0.579219	0			3	60	100	0	0	7.627071	19	60	627	53		0.136364	0.58293
ERI3	79033	__UNKNOWN__	__UNKNOWN__	1	44738278	44738278	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:44738278T>C	ENST00000372257.2	-	7	1013				ERI3_ENST00000372259.5_Intron|ERI3_ENST00000537474.1_Intron	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	NA		NA					exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						ctttgggaggttgaggcgggt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419	79033		Enhanced RNAi three prime mRNA exonucleases	17276	protein-coding gene	gene with protein product	enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans), exoribonuclease 3	609917	prion protein interacting protein	PRNPIP	NA		Standard	NM_024066	XM_005271184	NA	Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.831+12228A>G	chr1.hg19:g.44738278T>C		NA	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	hg19	CCDS30696.1	0.02	-0.192965	AGGxTGA	COVERED																																																																																			NOVEL	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020243.1	8	3.006147	KEEP	1	0	0	10	263	TT	0.992708	0.486967	0		-	3	60	99	0	0	7.592255	18	60	544	51	ENST00000372257.2	0.142857	0.490544
ERI3	79033	__UNKNOWN__	__UNKNOWN__	1	44800812	44800812	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:44800812A>G	ENST00000372257.2	-	3	671				ERI3_ENST00000495828.1_Intron|ERI3_ENST00000537474.1_Intron	NM_024066.1	NP_076971.1	O43414	ERI3_HUMAN	ERI1 exoribonuclease family member 3	NA		NA					exonuclease activity (GO:0004527)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						aggagtttgaaaccagcctgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007157	CCDS30696.1	1p34.1	2009-10-07	2009-10-07	2008-12-16	ENSG00000117419	ENSG00000117419	79033		Enhanced RNAi three prime mRNA exonucleases	17276	protein-coding gene	gene with protein product	enhanced RNAi three prime mRNA exonuclease homolog 3 (C.elegans), exoribonuclease 3	609917	prion protein interacting protein	PRNPIP	NA		Standard	NM_024066	XM_005271184	NA	Approved	FLJ22943, PINT1	uc001clt.3	O43414	OTTHUMG00000007637	ENST00000372257.2:c.489+3904T>C	chr1.hg19:g.44800812A>G		NA	B1AK98|Q5T2T7|Q5T2T9|Q5TG35|Q9BQA0|Q9UEB4	hg19	CCDS30696.1	0.02	-0.315735	TGAxACC	COVERED																																																																																			NOVEL	ERI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020243.1	12	3.307282	KEEP	0	0	0	11	288	AA	0.993072	0.812795	0		-	3	60	99	0	0	6.96752	30	60	884	71	ENST00000372257.2	0.090909	0.818465
RNF220	55182	__UNKNOWN__	__UNKNOWN__	1	45014432	45014432	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45014432A>G	ENST00000355387.2	+	3	1075				RNF220_ENST00000443020.2_Intron|RNF220_ENST00000361799.2_Intron|RNF220_ENST00000372247.2_Intron			Q5VTB9	RN220_HUMAN	ring finger protein 220	NA		NA			protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						ccaaagtgctaggattacagg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147	55182		RING-type (C3HC4) zinc fingers	25552	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 164	C1orf164	NA	11042152	Standard	NM_018150	NM_018150	NA	Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.626-65405A>G	chr1.hg19:g.45014432A>G		NA	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	hg19	CCDS510.1	0.02	-0.280659	GCTxGGA	COVERED																																																																																			NOVEL	RNF220-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020683.4	13	3.308434	KEEP	0	0	0	11	304	AA	0.993072	0.734547	0		+	3	60	98	0	0	7.04458	26	60	767	57	ENST00000355387.2	0.103448	0.739671
RNF220	55182	__UNKNOWN__	__UNKNOWN__	1	45105681	45105681	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45105681T>C	ENST00000355387.2	+	8	1576				RNF220_ENST00000443020.2_Intron|RNF220_ENST00000361799.2_Intron|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372242.3_Intron|RNF220_ENST00000372247.2_Intron|TMEM53_ENST00000372243.3_Intron			Q5VTB9	RN220_HUMAN	ring finger protein 220	NA		NA			protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						aggctggtcttgaactcctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147	55182		RING-type (C3HC4) zinc fingers	25552	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 164	C1orf164	NA	11042152	Standard	NM_018150	NM_018150	NA	Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.1126+3847T>C	chr1.hg19:g.45105681T>C		NA	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	hg19	CCDS510.1	0.02	-0.175387	TCTxGAA	COVERED																																																																																			NOVEL	RNF220-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020683.4	6	3.307856	KEEP	5	0	0	11	297	TT	0.992708	0.384582	0		+	3	60	86	0	0	6.435223	16	60	464	57	ENST00000355387.2	0.157895	0.387407
TMEM53	79639	__UNKNOWN__	__UNKNOWN__	1	45129950	45129950	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45129950T>C	ENST00000372237.3	-	2	225				TMEM53_ENST00000476724.1_Intron|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372235.3_Intron|TMEM53_ENST00000372242.3_Intron|TMEM53_ENST00000372243.3_Intron	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	NA		NA				integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					tggagaaacctcatctctact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106	79639			26186	protein-coding gene	gene with protein product		NA			NA	12958361	Standard	NM_024587	XR_425151	NA	Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.62-3983A>G	chr1.hg19:g.45129950T>C		NA	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	hg19	CCDS511.1	0.02	-0.140298	ACCxCAT	COVERED																																																																																			NOVEL	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021599.1	8	2.705801	KEEP	2	0	0	9	236	TT	0.99257	0.259026	0		-	4	60	115	0	0	9.63085	11	60	329	33	ENST00000372237.3	0.266667	0.260965
TMEM53	79639	__UNKNOWN__	__UNKNOWN__	1	45134438	45134438	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45134438T>C	ENST00000372237.3	-	1	225				TMEM53_ENST00000476724.1_Intron|TMEM53_ENST00000372244.3_Intron|TMEM53_ENST00000372235.3_Intron|TMEM53_ENST00000372242.3_Intron|TMEM53_ENST00000372243.3_Intron	NM_024587.2	NP_078863.2	Q6P2H8	TMM53_HUMAN	transmembrane protein 53	NA		NA				integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(3)|ovary(2)|urinary_tract(1)	10	Acute lymphoblastic leukemia(166;0.155)					tggtctcaaattcttgggctc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS511.1, CCDS72773.1	1p34.1	2008-02-26			ENSG00000126106	ENSG00000126106	79639			26186	protein-coding gene	gene with protein product		NA			NA	12958361	Standard	NM_024587	XR_425151	NA	Approved	FLJ22353, NET4	uc001cmc.3	Q6P2H8	OTTHUMG00000007833	ENST00000372237.3:c.61+5564A>G	chr1.hg19:g.45134438T>C		NA	B4DKG0|Q5JPH2|Q6IA07|Q9H6E2	hg19	CCDS511.1	0.02	-0.140312	AAAxTCT	UNCOVERED																																																																																			NOVEL	TMEM53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021599.1	7	2.405416	KEEP	1	0	0	8	212	TT	0	0	0		-	3	60	98	0	0	7.879449	13	60	373	33	ENST00000372237.3	0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	45193380	45193380	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45193380T>C			NA	NA				C1orf228 (2117 upstream) : RNU5D-1 (3346 downstream)						NA		NA									NA						gctgggattgtaggcatgagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.45193380T>C		NA		hg19		0.02	-0.254357	TTGxAGG	COVERED																																																																																			NOVEL					0			13	3.007044	KEEP	0	0	0	10	266	TT	0.992708	0.663648	0			3	60	105	0	0	8.005381	21	60	617	58		0.125	0.668523
PTCH2	8643	__UNKNOWN__	__UNKNOWN__	1	45289376	45289376	__UNKNOWN__	Intron	SNP	T	T	C	rs7514741	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45289376T>C	ENST00000372192.3	-	20	3245				PTCH2_ENST00000447098.2_Intron	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	NA		NA			epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					tttgggaggctgaggtgggtg	0.517		NA							Basal Cell Nevus syndrome				t|||	2232	0.445687	0.6021	0.4409	5008	,	,	NA	19776	0.4911	NA	0.3191	False	NA	,,,	NA	NA	NA	2504	0.3211	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425	8643			9586	protein-coding gene	gene with protein product		603673	patched (Drosophila) homolog 2, patched homolog 2 (Drosophila)		NA	9811851, 9931336	Standard	NM_003738	NM_003738	NA	Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.3115-319A>G	chr1.hg19:g.45289376T>C		NA	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	hg19	CCDS516.1	0.02	-0.157892	GGCxGAG	COVERED																																																																																			NOVEL	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023428.4	5	2.707412	KEEP	2	0	0	9	258	TT	0.99254	0.320398	0		-	10	60	329	1	0	34.032056	4	60	125	43	ENST00000372192.3	0.714286	0.322807
ZSWIM5	57643	__UNKNOWN__	__UNKNOWN__	1	45643890	45643890	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45643890C>G	ENST00000359600.5	-	1	801				ZSWIM5_ENST00000464588.1_Intron	NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	NA		NA				extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					ctgaggtcagcagttggagac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415	57643		Zinc fingers, SWIM-type	29299	protein-coding gene	gene with protein product		NA			NA	10819331	Standard	XM_046581	NM_020883	NA	Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.595+27537G>C	chr1.hg19:g.45643890C>G		NA	Q5SXQ9	hg19	CCDS41319.1	0.02	-0.324582	CAGxAGT	COVERED																																																																																			NOVEL	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024823.2	4	2.407172	KEEP	0	0	0	8	245	CC	0.99257	0.829507	0		-	4	60	122	0	0	8.658274	32	60	1096	52	ENST00000359600.5	0.111111	0.835716
TESK2	10420	__UNKNOWN__	__UNKNOWN__	1	45810923	45810923	__UNKNOWN__	Silent	SNP	G	G	A	rs3893383	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45810923G>A	ENST00000372086.3	-	11	1705	c.1305C>T	c.(1303-1305)ccC>ccT	p.P435P	TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000341771.6_Silent_p.P406P|TESK2_ENST00000538496.1_Silent_p.P352P|TESK2_ENST00000372084.1_Silent_p.P406P	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	435		NA			actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					GCATAGTTCCGGGCCCTGGTG	0.582		NA											G|||	872	0.174121	0.2852	0.1095	5008	,	,	NA	18447	0.1935	NA	0.1044	False	NA	,,,	NA	NA	NA	2504	0.1217	NA	NA	NA								NA				0								G		940,2854		108,724,1065	41	44	43		1305	-0.8	1	1	dbSNP_108	43	849,7353		42,765,3294	no	coding-synonymous	TESK2	NM_007170.2		150,1489,4359	AA,AG,GG	NA	10.3511,24.776,14.9133		435/572	45810923	1789,10207	1897	4101	5998	SO:0001819	synonymous_variant			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	10420	2.7.12.1		11732	protein-coding gene	gene with protein product		604746			NA	10512679	Standard	NM_007170	NM_007170	NA	Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.1305C>T	chr1.hg19:g.45810923G>A		NA	Q5T422|Q5T423|Q8N520|Q9Y3Q6	hg19	CCDS41323.1	0.02	4.591448	TCCxGGC	COVERED																																																																																			NOVEL	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020523.1	2	6.317994	KEEP	0	0	0	21	631	GG	0.999869	0.999869	0		-	29	60	881	0	0	68.397707	139	60	4435	247	ENST00000372086.3	0.172619	1
TESK2	10420	__UNKNOWN__	__UNKNOWN__	1	45813195	45813195	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45813195T>C	ENST00000372086.3	-	7	1109				TESK2_ENST00000486676.1_Intron|TESK2_ENST00000341771.6_Intron|TESK2_ENST00000538496.1_Intron|TESK2_ENST00000372084.1_Intron	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	NA		NA			actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					tgccactgcattccagcctga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	10420	2.7.12.1		11732	protein-coding gene	gene with protein product		604746			NA	10512679	Standard	NM_007170	NM_007170	NA	Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.708+85A>G	chr1.hg19:g.45813195T>C		NA	Q5T422|Q5T423|Q8N520|Q9Y3Q6	hg19	CCDS41323.1	0.02	-0.324466	GCAxTCC	COVERED																																																																																			NOVEL	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020523.1	8	4.811474	KEEP	0	0	0	16	430	TT	0.997832	0.833904	0		-	4	60	128	0	0	9.596008	26	60	738	71	ENST00000372086.3	0.133333	0.835716
TESK2	10420	__UNKNOWN__	__UNKNOWN__	1	45833716	45833716	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45833716G>C	ENST00000372086.3	-	5	794				TESK2_ENST00000486676.1_Intron|TESK2_ENST00000341771.6_Intron|TESK2_ENST00000538496.1_Intron|TESK2_ENST00000372084.1_Intron	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	NA		NA			actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					gcccaggctggagtgcaatgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	10420	2.7.12.1		11732	protein-coding gene	gene with protein product		604746			NA	10512679	Standard	NM_007170	NM_007170	NA	Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.394-12595C>G	chr1.hg19:g.45833716G>C		NA	Q5T422|Q5T423|Q8N520|Q9Y3Q6	hg19	CCDS41323.1	0.02	-0.131589	CTGxAGT	COVERED																																																																																			NOVEL	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020523.1	8	3.910122	KEEP	8	0	0	13	377	GG	0.992708	0.227502	0		-	5	60	170	0	0	15.845824	7	60	235	48	ENST00000372086.3	0.416667	0.229173
TESK2	10420	__UNKNOWN__	__UNKNOWN__	1	45882665	45882665	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45882665A>G	ENST00000372086.3	-	3	745				TESK2_ENST00000451835.2_Intron|TESK2_ENST00000486676.1_Intron|TESK2_ENST00000341771.6_Intron|TESK2_ENST00000538496.1_Intron|TESK2_ENST00000372084.1_Intron	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	NA		NA			actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					tcaccgtgttagccaggatgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	10420	2.7.12.1		11732	protein-coding gene	gene with protein product		604746			NA	10512679	Standard	NM_007170	NM_007170	NA	Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.344+4731T>C	chr1.hg19:g.45882665A>G		NA	Q5T422|Q5T423|Q8N520|Q9Y3Q6	hg19	CCDS41323.1	0.02	-0.149042	GTTxGCC	COVERED																																																																																			NOVEL	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020523.1	9	4.809899	KEEP	4	0	0	16	420	AA	0.995343	0.290641	0		-	3	60	91	0	0	7.373929	11	60	301	47	ENST00000372086.3	0.214286	0.292001
TESK2	10420	__UNKNOWN__	__UNKNOWN__	1	45931938	45931938	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:45931938A>G	ENST00000372086.3	-	2	315				TESK2_ENST00000451835.2_Intron|TESK2_ENST00000486676.1_Intron|TESK2_ENST00000341771.6_Intron|TESK2_ENST00000538496.1_Intron	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	NA		NA			actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					cacaaggtcaagagatcgaga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	10420	2.7.12.1		11732	protein-coding gene	gene with protein product		604746			NA	10512679	Standard	NM_007170	NM_007170	NA	Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.86-8395T>C	chr1.hg19:g.45931938A>G		NA	Q5T422|Q5T423|Q8N520|Q9Y3Q6	hg19	CCDS41323.1	0.02	-0.210502	TCAxGAG	COVERED																																																																																			NOVEL	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020523.1	8	4.511553	KEEP	4	0	0	15	415	AA	0.994391	0.519232	0		-	3	60	90	0	0	6.628235	19	60	579	64	ENST00000372086.3	0.136364	0.522161
AKR1A1	10327	__UNKNOWN__	__UNKNOWN__	1	46026678	46026678	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46026678C>T	ENST00000372070.3	+	3	741				AKR1A1_ENST00000471651.1_Intron|AKR1A1_ENST00000351829.4_Intron	NM_001202413.1|NM_001202414.1|NM_006066.3	NP_001189342.1|NP_001189343.1|NP_006057.1	P14550	AK1A1_HUMAN	aldo-keto reductase family 1, member A1 (aldehyde reductase)	NA		NA			aldehyde catabolic process (GO:0046185)|cellular aldehyde metabolic process (GO:0006081)|D-glucuronate catabolic process (GO:0042840)|glucose metabolic process (GO:0006006)|L-ascorbic acid biosynthetic process (GO:0019853)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|L-glucuronate reductase activity (GO:0047939)			lung(3)|prostate(1)|urinary_tract(1)	5	Acute lymphoblastic leukemia(166;0.155)				Doxorubicin(DB00997)	ggattacaggcgtgagccacc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04794	CCDS523.1	1p33-p32	2010-04-08			ENSG00000117448	ENSG00000117448	10327	1.1.1.2	Aldo-keto reductases	380	protein-coding gene	gene with protein product	dihydrodiol dehydrogenase 3	103830			NA	2498333, 10393438	Standard	NM_006066	NM_001202414	NA	Approved	ALR, DD3	uc001coe.3	P14550	OTTHUMG00000007740	ENST00000372070.3:c.-6-783C>T	chr1.hg19:g.46026678C>T		NA	A8KAL8|D3DQ04|Q6IAZ4	hg19	CCDS523.1	0.02	-0.210518	AGGxGTG	COVERED																																																																																			NOVEL	AKR1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000020851.1	7	3.007624	KEEP	4	0	0	10	288	CC	0.99254	0.518266	0		+	3	60	89	0	0	6.592806	18	60	585	57	ENST00000372070.3	0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	46048817	46048817	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46048817A>C			NA	NA				AKR1A1 (13096 upstream) : NASP (899 downstream)						NA		NA									NA						gtgatccaccagcctaggcct	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.46048817A>C		NA		hg19		0.02	-0.210492	ACCxGCC	COVERED																																																																																			NOVEL					0			11	2.707329	KEEP	1	0	0	9	256	AA	0.99257	0.518282	0			3	57	98	0	0	7.427343	19	60	571	44		0.136364	0.522161
IPP	3652	__UNKNOWN__	__UNKNOWN__	1	46192617	46192617	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46192617T>C	ENST00000396478.3	-	5	1151					NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	NA		NA				actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					aggctggtcttgaactcctga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429	3652		Kelch-like, BTB/POZ domain containing	6108	protein-coding gene	gene with protein product	kelch-like family member 27	147485			NA	1905535, 8432546	Standard	NM_005897	NM_005897	NA	Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.1048+685A>G	chr1.hg19:g.46192617T>C		NA	A2A6V4|D3DQ11|Q8N5C3	hg19	CCDS30702.1	0.02	-0.122793	TCTxGAA	UNCOVERED																																																																																			NOVEL	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021974.3	7	2.406104	KEEP	2	0	0	8	221	TT	0	0	0		-	5	60	167	0	0	15.123379	9	60	265	30	ENST00000396478.3	0.357143	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	46236946	46236946	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46236946T>C			NA	NA				IPP (20625 upstream) : MAST2 (32338 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.46236946T>C		NA		hg19		0.02	-0.14871	TCAxGCC	COVERED																																																																																			NOVEL					0			5	2.705032	KEEP	1	0	0	9	236	TT	0.99254	0.289823	0			3	60	105	0	0	8.677	12	60	327	38		0.2	0.292001
MAST2	23139	__UNKNOWN__	__UNKNOWN__	1	46273429	46273429	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46273429A>G	ENST00000361297.2	+	1	460				MAST2_ENST00000372009.2_Intron	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2	NA		NA								breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					ggccaggctgatctcgaactc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015	23139			19035	protein-coding gene	gene with protein product		612257			NA		Standard	NM_015112	NM_015112	NA	Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.177+3685A>G	chr1.hg19:g.46273429A>G		NA		hg19	CCDS41326.1	0.02	-0.149105	CTGxTCT	COVERED																																																																																			NOVEL	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021977.1	5	3.609665	KEEP	9	0	0	12	341	AA	0.99254	0.289823	0		+	3	54	93	0	0	7.379007	13	60	392	49	ENST00000361297.2	0.1875	0.292001
MAST2	23139	__UNKNOWN__	__UNKNOWN__	1	46325052	46325052	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46325052A>G	ENST00000361297.2	+	4	751				MAST2_ENST00000372009.2_Intron	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2	NA		NA								breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					gattacaggcatgagccacca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015	23139			19035	protein-coding gene	gene with protein product		612257			NA		Standard	NM_015112	NM_015112	NA	Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.469-22984A>G	chr1.hg19:g.46325052A>G		NA		hg19	CCDS41326.1	0.02	-0.175418	GGCxTGA	COVERED																																																																																			NOVEL	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021977.1	3	3.007174	KEEP	1	0	0	10	272	AA	0.992708	0.384582	0		+	3	60	96	0	0	7.433613	16	60	479	49	ENST00000361297.2	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	46843002	46843002	__UNKNOWN__	IGR	SNP	G	G	A	rs146274460	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:46843002G>A			NA	NA				NSUN4 (15138 upstream) : FAAH (16934 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.443		NA											G|||	36	0.0071885	0.0272	0.0	5008	,	,	NA	18525	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.46843002G>A		NA		hg19		0.02	-0.280708	GGCxTGA	COVERED																																																																																			NOVEL					0			11	2.407084	KEEP	1	0	0	8	245	GG	0.99257	0.734176	0			3	60	88	0	0	6.306723	21	60	702	58		0.125	0.739671
MKNK1	8569	__UNKNOWN__	__UNKNOWN__	1	47046935	47046935	__UNKNOWN__	Intron	SNP	G	G	A	rs377635642		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:47046935G>A	ENST00000371946.4	-	4	300				MKNK1_ENST00000545730.1_Intron|MKNK1_ENST00000371944.4_Intron|MKNK1_ENST00000465783.1_Intron|MKNK1_ENST00000371945.4_Intron|MKNK1_ENST00000341183.5_Intron|MKNK1_ENST00000428112.2_Intron	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	NA		NA			extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					ctgtagtcccggcactttggg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277	8569			7110	protein-coding gene	gene with protein product		606724			NA	9155018	Standard	NM_003684	NM_003684	NA	Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.137-636C>T	chr1.hg19:g.47046935G>A		NA	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	hg19	CCDS538.1	0.02	-0.377167	CCCxGCA	COVERED																																																																																			NOVEL	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021897.2	7	3.008305	KEEP	0	0	0	10	293	GG	0.992708	0.90244	0		-	4	60	118	0	0	8.258665	32	60	1042	87	ENST00000371946.4	0.111111	0.909069
MKNK1	8569	__UNKNOWN__	__UNKNOWN__	1	47060630	47060630	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:47060630A>G	ENST00000371946.4	-	2	30				MKNK1_ENST00000545730.1_Intron|MKNK1_ENST00000371945.4_Intron|MKNK1_ENST00000525888.1_Intron|MKNK1_ENST00000341183.5_Intron|MKNK1_ENST00000428112.2_Intron	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	NA		NA			extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fibroblast growth factor receptor signaling pathway (GO:0008543)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|response to salt stress (GO:0009651)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	13	Acute lymphoblastic leukemia(166;0.155)					ctgcactccaacctgggtgac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000409	CCDS538.1, CCDS30705.1, CCDS44134.1	1p33	2008-02-05			ENSG00000079277	ENSG00000079277	8569			7110	protein-coding gene	gene with protein product		606724			NA	9155018	Standard	NM_003684	NM_003684	NA	Approved	MNK1	uc001cqb.4	Q9BUB5	OTTHUMG00000007983	ENST00000371946.4:c.134-678T>C	chr1.hg19:g.47060630A>G		NA	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	hg19	CCDS538.1	0.02	5.897217	CCAxCCT	COVERED																																																																																			NOVEL	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021897.2	24	3.535958	KEEP	0	4	117	53	1445	AA	1	1	0		-	11	60	382	0	0	26.718796	129	60	3829	312	ENST00000371946.4	0.078571	1
TAL1	6886	__UNKNOWN__	__UNKNOWN__	1	47682967	47682967	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:47682967A>G	ENST00000294339.3	-	0	3997				TAL1_ENST00000371883.3_3'UTR|TAL1_ENST00000371884.2_3'UTR	NM_003189.2	NP_003180.1	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	NA		NA			angiogenesis (GO:0001525)|astrocyte fate commitment (GO:0060018)|basophil differentiation (GO:0030221)|cell fate commitment (GO:0045165)|definitive hemopoiesis (GO:0060216)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|hemangioblast cell differentiation (GO:0060217)|hematopoietic stem cell differentiation (GO:0060218)|hemopoiesis (GO:0030097)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|platelet formation (GO:0030220)|positive regulation of cell division (GO:0051781)|positive regulation of chromatin assembly or disassembly (GO:0045799)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell proliferation (GO:0042127)|regulation of mast cell differentiation (GO:0060375)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord association neuron differentiation (GO:0021527)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|E-box binding (GO:0070888)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			haematopoietic_and_lymphoid_tissue(1)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	15						ggctgaggtgagaggattgct	0.493		NA	T	TRD@, SIL	lymphoblastic leukemia/biphasic																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p32	6886	T-cell acute lymphocytic leukemia 1 (SCL)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M29038	CCDS547.1	1p32	2013-05-21	2001-12-04		ENSG00000162367	ENSG00000162367	6886		Basic helix-loop-helix proteins	11556	protein-coding gene	gene with protein product		187040		TCL5	NA	2740341	Standard	NM_003189	NM_001287347	NA	Approved	SCL, bHLHa17	uc009vyq.2	P17542	OTTHUMG00000007847	ENST00000294339.3:c.*2425T>C	chr1.hg19:g.47682967A>G		NA	D3DQ24	hg19	CCDS547.1	0.02	-0.236729	GTGxGAG	COVERED																																																																																			NOVEL	TAL1-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021640.1	8	4.210735	KEEP	0	0	0	14	388	AA	0.995343	0.609555	0		-	3	60	92	0	0	6.706851	21	60	613	55	ENST00000294339.3	0.125	0.612407
STIL	6491	__UNKNOWN__	__UNKNOWN__	1	47725253	47725253	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:47725253G>A	ENST00000371877.3	-	16	3228				STIL_ENST00000396221.2_Intron|STIL_ENST00000243182.6_Intron|STIL_ENST00000337817.5_Intron|STIL_ENST00000360380.3_Intron			Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	NA		NA			cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				gagccaccgcgcccggccTAA	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473	6491			10879	protein-coding gene	gene with protein product		181590	TAL1 (SCL) interrupting locus	SIL	NA	2209547	Standard	NM_003035	NM_003035	NA	Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000371877.3:c.3080+707C>T	chr1.hg19:g.47725253G>A		NA	Q5T0C5|Q68CN9	hg19	CCDS41329.1	0.02	-0.210543	CGCxCCC	COVERED																																																																																			NOVEL	STIL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021652.2	8	2.708029	KEEP	1	0	0	9	274	GG	0.99254	0.548763	0		-	3	60	94	0	0	6.905765	21	60	721	52	ENST00000371877.3	0.125	0.552887
RP11-511I2.2	0	__UNKNOWN__	__UNKNOWN__	1	47866652	47866652	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:47866652C>T	ENST00000420876.1	-	0	158										NA		NA									NA						ggattacaggcgtgagccact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000420876.1:	chr1.hg19:g.47866652C>T		NA		hg19		0.02	-0.157877	AGGxGTG	UNCOVERED																																																																																			NOVEL	RP11-511I2.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000021847.2	9	2.406243	KEEP	1	0	0	8	226	CC	0	0	0		-	3	60	91	0	0	7.179094	13	60	413	38	ENST00000420876.1	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	48143787	48143787	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:48143787T>C			NA	NA				AL591415.1 (56938 upstream) : RP11-543D5.1 (10347 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.48143787T>C		NA		hg19		0.02	-0.175407	TCAxGCC	COVERED																																																																																			NOVEL					0			10	3.306856	KEEP	4	0	0	11	286	TT	0.99254	0.384517	0			3	60	103	0	0	8.378899	13	60	379	47		0.1875	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	48729537	48729537	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:48729537T>C			NA	NA				SLC5A9 (15221 upstream) : SPATA6 (31506 downstream)						NA		NA									NA						ctcactctgttgcccaggctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.48729537T>C		NA		hg19		0.02	-0.105236	TGTxGCC	UNCOVERED																																																																																			NOVEL					0			6	3.006509	KEEP	3	0	0	10	263	TT	0.99254	0.138789	0			3	60	107	0	0	9.20153	9	60	254	33		0.25	0.139832
SPATA6	54558	__UNKNOWN__	__UNKNOWN__	1	48762836	48762836	__UNKNOWN__	3'UTR	SNP	A	A	G	rs374605487		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:48762836A>G	ENST00000371847.3	-	0	3180					NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						gtgtgtgtgtatgtgtgtAGC	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122	54558			18309	protein-coding gene	gene with protein product	spermatogenesis-related factor-1	613947			NA		Standard	NM_019073	XM_005270948	NA	Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.*1549T>C	chr1.hg19:g.48762836A>G		NA	Q5T3N7|Q8WUE6	hg19	CCDS551.1	0.02	1.937062	TGTxTGT	COVERED																																																																																			NOVEL	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021347.1	18	3.371665	KEEP	0	2	44	27	722	AA	0.999997	0.992091	0		-	7	60	243	1	0	18.730784	45	60	1181	141	ENST00000371847.3	0.134615	0.992094
SPATA6	54558	__UNKNOWN__	__UNKNOWN__	1	48854611	48854611	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:48854611A>G	ENST00000371847.3	-	9	1033				SPATA6_ENST00000371843.3_Intron|SPATA6_ENST00000396199.3_Intron	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						aggctggagtacaatggtgtg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122	54558			18309	protein-coding gene	gene with protein product	spermatogenesis-related factor-1	613947			NA		Standard	NM_019073	XM_005270948	NA	Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.869-3590T>C	chr1.hg19:g.48854611A>G		NA	Q5T3N7|Q8WUE6	hg19	CCDS551.1	0.02	-0.096447	AGTxCAA	UNCOVERED																																																																																			NOVEL	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021347.1	4	2.401467	KEEP	1	0	0	8	191	AA	0	0	0		-	3	60	107	0	0	9.333255	8	60	226	26	ENST00000371847.3	0.272727	0.120436
SPATA6	54558	__UNKNOWN__	__UNKNOWN__	1	48911112	48911112	__UNKNOWN__	Intron	SNP	A	A	G	rs139479765	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:48911112A>G	ENST00000371847.3	-	3	403				SPATA6_ENST00000463938.1_Intron|SPATA6_ENST00000396199.3_Intron|SPATA6_ENST00000371843.3_Intron	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						aaggcgggtgaatcacgaggt	0.512		NA											A|||	71	0.0141773	0.0514	0.0029	5008	,	,	NA	15915	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122	54558			18309	protein-coding gene	gene with protein product	spermatogenesis-related factor-1	613947			NA		Standard	NM_019073	XM_005270948	NA	Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.238+6111T>C	chr1.hg19:g.48911112A>G		NA	Q5T3N7|Q8WUE6	hg19	CCDS551.1	0.02	-0.236772	GTGxATC	COVERED																																																																																			NOVEL	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021347.1	9	3.006714	KEEP	1	0	0	10	268	AA	0.992708	0.607941	0		-	5	60	156	0	0	12.554605	20	60	562	51	ENST00000371847.3	0.2	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	50763031	50763031	__UNKNOWN__	IGR	SNP	A	A	G	rs3012090	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:50763031A>G			NA	NA				RP11-567C20.3 (74232 upstream) : DMRTA2 (120190 downstream)						NA		NA									NA						gccgggcacgatggctcatgc	0.512		NA											G|||	4913	0.98103	0.9297	0.9971	5008	,	,	NA	12338	1.0	NA	1.0	False	NA	,,,	NA	NA	NA	2504	1.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.50763031A>G		NA		hg19		0.02	1.818464	ACGxTGG	COVERED																																																																																			NOVEL					0			84	7.515996	KEEP	23	3	85	55	1538	AA	1	0.993703	0			8	60	262	0	0	30.015055	0	0	0	177		1	0.993703
FAF1	11124	__UNKNOWN__	__UNKNOWN__	1	51194979	51194979	__UNKNOWN__	Intron	SNP	G	G	A	rs554557080		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:51194979G>A	ENST00000396153.2	-	6	1003				FAF1_ENST00000371778.4_Intron	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	NA		NA			apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(2)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		cacctgcctcggcctcccaaa	0.468		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	12169	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				2	Whole gene deletion(2)	thyroid(1)|haematopoietic_and_lymphoid_tissue(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104	11124		UBX domain containing	3578	protein-coding gene	gene with protein product	TNFRSF6-associated factor 1, UBX domain protein 3A	604460			NA	10462485	Standard	NM_007051	NM_007051	NA	Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.551+9555C>T	chr1.hg19:g.51194979G>A		NA	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	hg19	CCDS554.1	0.02	-0.140346	CTCxGCC	COVERED																																																																																			NOVEL	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000021807.1	8	3.310179	KEEP	0	0	0	11	349	GG	0.993072	0.289978	0		-	3	60	88	0	0	6.879108	13	60	437	41	ENST00000396153.2	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	51480663	51480663	__UNKNOWN__	IGR	SNP	C	C	G	rs12034792		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:51480663C>G			NA	NA				CDKN2C (40358 upstream) : MIR4421 (44845 downstream)						NA		NA						p.0?(4)|p.?(1)			NA						gagaaggaagcaaggggggag	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				5	Whole gene deletion(4)|Unknown(1)	central_nervous_system(3)|thyroid(1)|haematopoietic_and_lymphoid_tissue(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.51480663C>G		NA		hg19		0.02	-0.184194	AAGxAAG	COVERED																																																																																			NOVEL					0			6	2.708081	KEEP	1	0	0	9	275	CC	0.99257	0.420331	0			3	60	97	1	0	7.460892	17	60	562	44		0.15	0.423478
EPS15	2060	__UNKNOWN__	__UNKNOWN__	1	51829649	51829649	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs377372711		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:51829649C>T	ENST00000371733.3	-	23	2344	c.2248G>A	c.(2248-2250)Gta>Ata	p.V750I	EPS15_ENST00000371730.2_Missense_Mutation_p.V616I|EPS15_ENST00000396122.4_Missense_Mutation_p.V427I	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	750	15 X 3 AA repeats of D-P-F.	NA			cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GTAATCACTACGTTGCTGACA	0.423		NA	T	MLL	ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)						C	ILE/VAL,ILE/VAL	0,4406		0,0,2203	192	171	178		1306,2248	5	0	1		178	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPS15	NM_001159969.1,NM_001981.2	29,29	0,1,6502	TT,TC,CC	NA	0.0116,0.0,0.0077	benign,benign	436/583,750/897	51829649	1,13005	2203	4300	6503	SO:0001583	missense			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832	2060		EF-hand domain containing	3419	protein-coding gene	gene with protein product		600051			NA	8183552	Standard	NM_001981	NM_001159969	NA	Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2248G>A	chr1.hg19:g.51829649C>T	ENSP00000360798:p.Val750Ile	NA	B2R8J7|D3DPJ2|Q5SRH4	hg19	CCDS557.1	0.02	1.322016	CTAxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.851	0.944518	0.18356	0.0	1.16E-4	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000396122	T;T;T	0.47528	1.86;1.87;0.84	5.95	5.04	0.67666	.	.	.	.	.	T	0.45256	0.1333	L	0.57536	1.79	0.09310	N	1	P;P;P	0.47762	0.9;0.707;0.846	B;B;B	0.38921	0.106;0.07;0.285	T	0.38714	-0.9648	9	0.37606	T	0.19	.	15.3393	0.74284	0.0:0.933:0.0:0.067	.	616;750;436	B1AUU8;P42566;P42566-2	.;EPS15_HUMAN;.	I	616;750;427	ENSP00000360795:V616I;ENSP00000360798:V750I;ENSP00000379428:V427I	ENSP00000360795:V616I	V	-	1	0	EPS15	51602237	0.067000	0.21026	0.003000	0.11579	0.003000	0.03518	2.388000	0.44398	1.528000	0.49103	0.655000	0.94253	GTA	NOVEL	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022422.1	3	2.406089	KEEP	0	0	0	8	223	CC	0.99257	0.98632	0		-	5	60	150	0	0	9.772213	59	60	1918	110	ENST00000371733.3	0.078125	0.993703
EPS15	2060	__UNKNOWN__	__UNKNOWN__	1	51845471	51845471	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:51845471T>C	ENST00000371733.3	-	22	2216				EPS15_ENST00000371730.2_Intron|EPS15_ENST00000396122.4_Intron	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	NA		NA			cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						tggtggctcatgcctgtaatc	0.522		NA	T	MLL	ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832	2060		EF-hand domain containing	3419	protein-coding gene	gene with protein product		600051			NA	8183552	Standard	NM_001981	NM_001159969	NA	Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2120-13770A>G	chr1.hg19:g.51845471T>C		NA	B2R8J7|D3DPJ2|Q5SRH4	hg19	CCDS557.1	0.02	-0.306963	TCAxGCC	COVERED																																																																																			NOVEL	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022422.1	15	4.807971	KEEP	4	0	0	16	434	TT	0.995343	0.796519	0		-	3	60	99	0	0	7.009542	29	60	854	76	ENST00000371733.3	0.09375	0.800245
EPS15	2060	__UNKNOWN__	__UNKNOWN__	1	51948415	51948415	__UNKNOWN__	Intron	SNP	A	A	G	rs200759457		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:51948415A>G	ENST00000371733.3	-	2	130				EPS15_ENST00000371730.2_Intron	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	NA		NA			cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)			endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						tgggattacaagcatgagcca	0.483		NA	T	MLL	ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832	2060		EF-hand domain containing	3419	protein-coding gene	gene with protein product		600051			NA	8183552	Standard	NM_001981	NM_001159969	NA	Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.34-1429T>C	chr1.hg19:g.51948415A>G		NA	B2R8J7|D3DPJ2|Q5SRH4	hg19	CCDS557.1	0.02	-0.210516	ACAxGCA	COVERED																																																																																			NOVEL	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022422.1	5	3.007297	KEEP	0	0	0	10	270	AA	0.992708	0.518353	0		-	3	60	108	0	0	8.491758	18	60	551	52	ENST00000371733.3	0.142857	0.522161
RP11-191G24.1	0	__UNKNOWN__	__UNKNOWN__	1	51987684	51987684	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:51987684T>C	ENST00000426017.1	+	0	64				RP11-191G24.1_ENST00000415031.1_RNA						NA		NA									NA						ctgcctcggcttcccaaagtg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000426017.1:	chr1.hg19:g.51987684T>C		NA		hg19		0.02	-0.184186	GGCxTCC	COVERED																																																																																			NOVEL	RP11-191G24.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000022578.1	3	3.008255	KEEP	2	0	0	10	286	TT	0.99254	0.420319	0		+	4	60	124	0	0	9.963337	16	60	483	47	ENST00000426017.1	0.2	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	52042246	52042246	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52042246T>C			NA	NA				RP11-191G24.1 (14945 upstream) : OSBPL9 (604 downstream)						NA		NA									NA						gtcgcccaggttgcagtgcag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.52042246T>C		NA		hg19		0.02	-0.298157	AGGxTGC	COVERED																																																																																			NOVEL					0			7	2.406109	KEEP	1	0	0	8	222	TT	0.99257	0.775257	0			3	60	96	0	0	6.800534	27	60	772	56		0.1	0.78106
OSBPL9	114883	__UNKNOWN__	__UNKNOWN__	1	52199196	52199196	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52199196T>C	ENST00000428468.1	+	5	320				OSBPL9_ENST00000371710.3_Intron|OSBPL9_ENST00000473207.2_Intron|OSBPL9_ENST00000371714.1_Intron|OSBPL9_ENST00000531828.1_Intron|OSBPL9_ENST00000435686.2_Intron|OSBPL9_ENST00000530544.1_Intron|OSBPL9_ENST00000337809.4_Intron|OSBPL9_ENST00000462759.1_Intron|OSBPL9_ENST00000486942.1_Intron|OSBPL9_ENST00000447887.1_Intron|OSBPL9_ENST00000453295.1_Intron|OSBPL9_ENST00000361556.5_Intron			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	NA		NA			lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						gctgtaatcctagcactttgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859	114883		Oxysterol binding proteins, Pleckstrin homology (PH) domain containing	16386	protein-coding gene	gene with protein product		606737			NA		Standard		NM_148904	NA	Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.319-12012T>C	chr1.hg19:g.52199196T>C		NA	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	hg19	CCDS41332.3	0.02	-0.210524	TCCxAGC	COVERED																																																																																			NOVEL	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022584.4	7	3.007532	KEEP	1	0	0	10	275	TT	0.992708	0.518353	0		+	4	60	145	0	0	11.968403	17	60	527	54	ENST00000428468.1	0.190476	0.522161
OSBPL9	114883	__UNKNOWN__	__UNKNOWN__	1	52233855	52233855	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52233855A>C	ENST00000428468.1	+	12	940				OSBPL9_ENST00000371710.3_Intron|OSBPL9_ENST00000371714.1_Intron|OSBPL9_ENST00000531828.1_Intron|OSBPL9_ENST00000435686.2_Intron|OSBPL9_ENST00000530544.1_Intron|OSBPL9_ENST00000337809.4_Intron|OSBPL9_ENST00000462759.1_Intron|OSBPL9_ENST00000486942.1_Intron|OSBPL9_ENST00000447887.1_Intron|OSBPL9_ENST00000453295.1_Intron|OSBPL9_ENST00000361556.5_Intron			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	NA		NA			lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						cctcatgatcagcccgcctcg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859	114883		Oxysterol binding proteins, Pleckstrin homology (PH) domain containing	16386	protein-coding gene	gene with protein product		606737			NA		Standard		NM_148904	NA	Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.938+2202A>C	chr1.hg19:g.52233855A>C		NA	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	hg19	CCDS41332.3	0.02	-0.254367	ATCxGCC	COVERED																																																																																			NOVEL	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022584.4	6	2.637882	KEEP	7	1	29	19	525	AA	0.999366	0.6681	0		+	3	60	91	1	0	6.443375	24	60	741	75	ENST00000428468.1	0.111111	0.668523
OSBPL9	114883	__UNKNOWN__	__UNKNOWN__	1	52253864	52253864	__UNKNOWN__	3'UTR	SNP	G	G	A	rs1045785	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52253864G>A	ENST00000428468.1	+	0	2616				OSBPL9_ENST00000371710.3_3'UTR|OSBPL9_ENST00000371714.1_3'UTR|OSBPL9_ENST00000435686.2_3'UTR|OSBPL9_ENST00000337809.4_3'UTR|OSBPL9_ENST00000462759.1_3'UTR|OSBPL9_ENST00000486942.1_3'UTR|OSBPL9_ENST00000447887.1_3'UTR|OSBPL9_ENST00000453295.1_3'UTR|OSBPL9_ENST00000361556.5_3'UTR			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	NA		NA			lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						acacacatacgtatacacaca	0.338		NA											A|||	1185	0.236621	0.4781	0.1816	5008	,	,	NA	17172	0.119	NA	0.1928	False	NA	,,,	NA	NA	NA	2504	0.1155	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859	114883		Oxysterol binding proteins, Pleckstrin homology (PH) domain containing	16386	protein-coding gene	gene with protein product		606737			NA		Standard		NM_148904	NA	Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.*403G>A	chr1.hg19:g.52253864G>A		NA	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	hg19	CCDS41332.3	0.02	1.004203	TACxTAT	COVERED																																																																																			NOVEL	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022584.4	25	13.537442	KEEP	0	0	0	45	1337	GG	1	0.999835	0		+	5	60	142	0	0	8.315912	81	60	2572	188	ENST00000428468.1	0.05814	0.999835
NRD1	4898	__UNKNOWN__	__UNKNOWN__	1	52337832	52337832	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52337832G>C	ENST00000354831.7	-	1	531				NRD1_ENST00000352171.7_Intron|NRD1_ENST00000539524.1_Intron|NRD1_ENST00000544028.1_Intron	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	NA		NA			cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						cgtgagccacggcgcccagtc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618	4898			7995	protein-coding gene	gene with protein product		602651			NA	9581555, 9479496	Standard	NM_002525	NM_002525	NA	Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.341+6114C>G	chr1.hg19:g.52337832G>C		NA	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	hg19	CCDS559.1	0.02	-0.2105	CACxGCG	COVERED																																																																																			NOVEL	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023045.1	4	2.707278	KEEP	1	0	0	9	266	GG	0.99254	0.548763	0		-	3	60	100	0	0	7.62694	19	60	606	54	ENST00000354831.7	0.136364	0.552887
NRD1	4898	__UNKNOWN__	__UNKNOWN__	1	52341505	52341505	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52341505A>G	ENST00000354831.7	-	1	531				NRD1_ENST00000352171.7_Intron|NRD1_ENST00000539524.1_Intron|NRD1_ENST00000544028.1_Intron	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	NA		NA			cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						gattacaggcatgagccacca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618	4898			7995	protein-coding gene	gene with protein product		602651			NA	9581555, 9479496	Standard	NM_002525	NM_002525	NA	Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.341+2441T>C	chr1.hg19:g.52341505A>G		NA	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	hg19	CCDS559.1	0.02	-0.087455	GGCxTGA	UNCOVERED																																																																																			NOVEL	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023045.1	4	2.40117	KEEP	0	0	0	8	201	AA	0.99257	0.09898	0		-	3	60	85	0	0	7.446445	6	60	153	21	ENST00000354831.7	0.333333	0.099721
BTF3L4	91408	__UNKNOWN__	__UNKNOWN__	1	52541013	52541013	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52541013T>C	ENST00000313334.8	+	4	436				BTF3L4_ENST00000484036.1_Intron|BTF3L4_ENST00000472944.2_Intron|BTF3L4_ENST00000489308.2_Intron|BTF3L4_ENST00000533836.1_Intron	NM_152265.4	NP_689478.1	Q96K17	BT3L4_HUMAN	basic transcription factor 3-like 4	NA		NA								endometrium(2)|kidney(1)|large_intestine(2)	5						gccaacatggtgaaaccccat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021004	CCDS30713.1, CCDS44146.1, CCDS58001.1	1p32.3	2011-05-26			ENSG00000134717	ENSG00000134717	91408			30547	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152265	NM_001136497	NA	Approved	MGC23908	uc001ctk.3	Q96K17	OTTHUMG00000008960	ENST00000313334.8:c.169-7999T>C	chr1.hg19:g.52541013T>C		NA	B3KNJ1|D3DQ32|G3V1C6	hg19	CCDS30713.1	0.02	-0.201748	TGGxGAA	COVERED																																																																																			NOVEL	BTF3L4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024848.1	7	2.405832	KEEP	1	0	0	8	216	TT	0.99257	0.4869	0		+	3	60	105	0	0	8.126601	19	60	586	45	ENST00000313334.8	0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	52599865	52599865	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52599865T>G			NA	NA				BTF3L4 (43477 upstream) : ZFYVE9 (8180 downstream)						NA		NA									NA						ttcctgaccttgtgatccacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.52599865T>G		NA		hg19		0.02	-0.131504	CCTxGTG	COVERED																																																																																			NOVEL					0			10	3.6088	KEEP	3	0	0	12	332	TT	0.993072	0.227586	0			3	60	89	0	1	7.174494	11	60	314	42		0.214286	0.229173
ZCCHC11	23318	__UNKNOWN__	__UNKNOWN__	1	52893991	52893991	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52893991A>G	ENST00000257177.4	-	28	4856				ZCCHC11_ENST00000371544.3_Intron			Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	NA		NA			cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						atgaaaccccatctctactaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744	23318		Zinc fingers, CCHC domain containing	28981	protein-coding gene	gene with protein product	TUTase4	613692			NA	8724849, 12239557	Standard	XM_038288	NM_015269	NA	Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000257177.4:c.4711+2693T>C	chr1.hg19:g.52893991A>G		NA	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	hg19	CCDS30715.1	0.02	-0.342004	CCCxTCT	COVERED																																																																																			NOVEL	ZCCHC11-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022466.2	13	2.40568	KEEP	2	0	0	8	216	AA	0.99257	0.859313	0		-	3	60	99	0	0	6.7762	35	60	1022	67	ENST00000257177.4	0.078947	0.865745
ZCCHC11	23318	__UNKNOWN__	__UNKNOWN__	1	52909175	52909175	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52909175C>T	ENST00000257177.4	-	24	3967				ZCCHC11_ENST00000371544.3_Intron			Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	NA		NA			cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						gcaggagaatcgcttgaacct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744	23318		Zinc fingers, CCHC domain containing	28981	protein-coding gene	gene with protein product	TUTase4	613692			NA	8724849, 12239557	Standard	XM_038288	NM_015269	NA	Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000257177.4:c.3822+2283G>A	chr1.hg19:g.52909175C>T		NA	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	hg19	CCDS30715.1	0.02	-0.131574	AATxGCT	COVERED																																																																																			NOVEL	ZCCHC11-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022466.2	6	4.211697	KEEP	3	0	0	14	417	CC	0.993634	0.227714	0		-	3	60	88	0	0	7.181923	10	60	326	41	ENST00000257177.4	0.230769	0.229173
ZCCHC11	23318	__UNKNOWN__	__UNKNOWN__	1	52965217	52965217	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:52965217A>G	ENST00000257177.4	-	5	1144				ZCCHC11_ENST00000371544.3_Intron|ZCCHC11_ENST00000371541.1_Intron			Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	NA		NA			cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						agaccagcctaggcaacatgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744	23318		Zinc fingers, CCHC domain containing	28981	protein-coding gene	gene with protein product	TUTase4	613692			NA	8724849, 12239557	Standard	XM_038288	NM_015269	NA	Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000257177.4:c.1000-2362T>C	chr1.hg19:g.52965217A>G		NA	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	hg19	CCDS30715.1	0.02	-0.175418	CCTxGGC	COVERED																																																																																			NOVEL	ZCCHC11-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022466.2	8	2.405942	KEEP	0	0	0	8	217	AA	0.99257	0.384528	0		-	3	60	104	0	0	8.23325	16	60	475	37	ENST00000257177.4	0.157895	0.387407
ZYG11B	79699	__UNKNOWN__	__UNKNOWN__	1	53279973	53279973	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:53279973G>A	ENST00000294353.6	+	12	2091				ZYG11B_ENST00000443756.2_Intron|ZYG11B_ENST00000545132.1_Intron	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	NA		NA								breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						gattacaggcgtgagccacca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378	79699		ZYG11 cell cycle regulator family	25820	protein-coding gene	gene with protein product		NA	zyg-11 homolog (C. elegans), zyg-11 homolog B (C. elegans)	ZYG11	NA	11214970	Standard	NM_024646	NM_024646	NA	Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1946+389G>A	chr1.hg19:g.53279973G>A		NA	Q8N2X3|Q9H8L8	hg19	CCDS30717.1	0.02	-0.192977	GGCxTGA	COVERED																																																																																			NOVEL	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024749.1	7	3.007714	KEEP	1	0	0	10	284	GG	0.99254	0.454342	0		+	3	60	88	0	0	6.561551	17	60	566	45	ENST00000294353.6	0.15	0.457757
ECHDC2	55268	__UNKNOWN__	__UNKNOWN__	1	53372716	53372716	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:53372716C>G	ENST00000371522.4	-	5	458				ECHDC2_ENST00000358358.5_Intron|ECHDC2_ENST00000536120.1_Intron|ECHDC2_ENST00000541281.1_Intron	NM_001198961.1	NP_001185890.1	Q86YB7	ECHD2_HUMAN	enoyl CoA hydratase domain containing 2	NA		NA			fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	lyase activity (GO:0016829)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	12						gcctcccaaactgctgggatt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258590	CCDS571.1, CCDS55600.1, CCDS72794.1	1p32.3	2010-04-30	2010-04-30		ENSG00000121310	ENSG00000121310	55268			23408	protein-coding gene	gene with protein product		NA	enoyl Coenzyme A hydratase domain containing 2		NA		Standard	NM_018281	NM_018281	NA	Approved	FLJ10948	uc001cup.4	Q86YB7	OTTHUMG00000008927	ENST00000371522.4:c.365-433G>C	chr1.hg19:g.53372716C>G		NA	D3DQ36|Q9NV38	hg19	CCDS55600.1	0.02	-0.11403	AAAxTGC	UNCOVERED																																																																																			NOVEL	ECHDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024712.3	6	2.406712	KEEP	0	0	0	8	239	CC	0.99257	0.16126	0		-	3	57	92	0	0	7.700895	9	60	312	29	ENST00000371522.4	0.25	0.162467
SCP2	6342	__UNKNOWN__	__UNKNOWN__	1	53407401	53407401	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:53407401C>T	ENST00000528311.1	+	2	180				SCP2_ENST00000371514.3_Intron|SCP2_ENST00000371513.5_Intron|SCP2_ENST00000371509.4_Intron|SCP2_ENST00000407246.2_Intron	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	NA		NA			female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						agcaagactccgtctcaaaaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171	6342			10606	protein-coding gene	gene with protein product		184755			NA	1703300, 1718316	Standard	NM_002979	NM_001007098	NA	Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.-116-6280C>T	chr1.hg19:g.53407401C>T		NA	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	hg19	CCDS53319.1	0.02	-0.315751	CTCxGTC	COVERED																																																																																			NOVEL	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387558.1	10	4.210842	KEEP	2	0	0	14	407	CC	0.994391	0.813874	0		+	3	60	92	0	0	6.543379	24	60	750	63	ENST00000528311.1	0.111111	0.818465
LRP8	7804	__UNKNOWN__	__UNKNOWN__	1	53712586	53712586	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:53712586T>A	ENST00000465675.1	-	0	2323				LRP8_ENST00000371454.2_3'UTR|LRP8_ENST00000354412.3_3'UTR|LRP8_ENST00000306052.6_3'UTR			Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	NA		NA			ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						acacatacactcacacagacc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193	7804		Low density lipoprotein receptors	6700	protein-coding gene	gene with protein product		602600			NA	8626535, 9079678	Standard	NM_004631	NM_004631	NA	Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000465675.1:c.*104A>T	chr1.hg19:g.53712586T>A		NA	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	hg19		0.02	2.577044	CACxCAC	COVERED																																																																																			NOVEL	LRP8-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000024702.2	28	12.058922	KEEP	0	4	113	80	2222	TT	1	1	0		-	7	60	190	0	0	10.386251	130	60	3962	354	ENST00000465675.1	0.051095	1
LRP8	7804	__UNKNOWN__	__UNKNOWN__	1	53774718	53774718	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:53774718G>A	ENST00000465675.1	-	2	262				LRP8_ENST00000371454.2_Intron|LRP8_ENST00000347547.2_Intron|LRP8_ENST00000354412.3_Intron|LRP8_ENST00000306052.6_Intron			Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	NA		NA			ammon gyrus development (GO:0021541)|blood coagulation (GO:0007596)|cellular response to cholesterol (GO:0071397)|cellular response to growth factor stimulus (GO:0071363)|cytokine-mediated signaling pathway (GO:0019221)|endocytosis (GO:0006897)|layer formation in cerebral cortex (GO:0021819)|lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction, visible light (GO:0007603)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendrite development (GO:1900006)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|proteolysis (GO:0006508)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|regulation of synaptic transmission (GO:0050804)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)	caveola (GO:0005901)|dendrite (GO:0030425)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|high-density lipoprotein particle binding (GO:0008035)|reelin receptor activity (GO:0038025)|transmembrane signaling receptor activity (GO:0004888)|very-low-density lipoprotein particle receptor activity (GO:0030229)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(1)	21						aggctgagacgggcagatcac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D50678	CCDS578.1, CCDS579.1, CCDS580.1, CCDS30720.1	1p32.3	2013-05-29			ENSG00000157193	ENSG00000157193	7804		Low density lipoprotein receptors	6700	protein-coding gene	gene with protein product		602600			NA	8626535, 9079678	Standard	NM_004631	NM_004631	NA	Approved	APOER2, MCI1, LRP-8, HSZ75190	uc001cvi.2	Q14114	OTTHUMG00000008924	ENST00000465675.1:c.583+17826C>T	chr1.hg19:g.53774718G>A		NA	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	hg19		0.02	-0.192987	GACxGGC	UNCOVERED																																																																																			NOVEL	LRP8-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000024702.2	6	2.40715	KEEP	3	0	0	8	246	GG	0	0	0		-	3	60	93	0	0	7.133384	16	60	528	47	ENST00000465675.1	0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	53888513	53888513	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:53888513A>G			NA	NA				RP11-117D22.2 (54596 upstream) : SLC25A3P1 (14194 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.53888513A>G		NA		hg19		0.02	-0.280653	CACxCCT	COVERED																																																																																			NOVEL					0			7	3.60973	KEEP	1	0	0	12	342	AA	0.993634	0.734962	0			3	60	100	0	0	7.39486	23	60	681	68		0.115385	0.739671
GLIS1	148979	__UNKNOWN__	__UNKNOWN__	1	54169110	54169110	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54169110A>G	ENST00000312233.2	-	1	301					NM_147193.2	NP_671726.2			GLIS family zinc finger 1	NA		NA								endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						aggagtttgaaaccagcctgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332	148979		Zinc fingers, C2H2-type	29525	protein-coding gene	gene with protein product		610378			NA	12042312, 14500813	Standard	NM_147193	NM_147193	NA	Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.265+30466T>C	chr1.hg19:g.54169110A>G		NA		hg19	CCDS582.1	0.02	-0.40346	TGAxACC	COVERED																																																																																			NOVEL	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022109.1	17	3.607984	KEEP	0	0	0	12	315	AA	0.993634	0.928543	0		-	3	60	99	0	0	6.67312	38	60	1136	82	ENST00000312233.2	0.073171	0.934492
GLIS1	148979	__UNKNOWN__	__UNKNOWN__	1	54179113	54179113	__UNKNOWN__	Intron	SNP	C	C	A	rs112475304	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54179113C>A	ENST00000312233.2	-	1	301					NM_147193.2	NP_671726.2			GLIS family zinc finger 1	NA		NA								endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						tcttcaagaccagcctgggca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332	148979		Zinc fingers, C2H2-type	29525	protein-coding gene	gene with protein product		610378			NA	12042312, 14500813	Standard	NM_147193	NM_147193	NA	Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.265+20463G>T	chr1.hg19:g.54179113C>A		NA		hg19	CCDS582.1	0.02	-0.2456	GACxAGC	UNCOVERED																																																																																			NOVEL	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022109.1	16	2.772126	KEEP	66	2	53	28	818	CC	0	0	0		-	12	60	354	0	0	33.328819	14	60	470	135	ENST00000312233.2	0.461538	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	54211172	54211172	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54211172C>T			NA	NA				GLIS1 (11295 upstream) : NDC1 (19960 downstream)						NA		NA									NA						attgcttgaaccccggaggcg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.54211172C>T		NA		hg19		0.02	-0.113756	GAAxCCC	UNCOVERED																																																																																			NOVEL					0			6	2.707899	KEEP	1	0	0	9	272	CC	0.99254	0.161255	0			3	60	85	0	0	7.005453	9	60	260	28		0.25	0.162467
HSPB11	51668	__UNKNOWN__	__UNKNOWN__	1	54386612	54386612	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54386612A>G	ENST00000371378.2	-	5	351							Q9Y547	IFT25_HUMAN	heat shock protein family B (small), member 11	NA		NA			cell adhesion (GO:0007155)|heart development (GO:0007507)|left/right axis specification (GO:0070986)|lung development (GO:0030324)|protein transport (GO:0015031)|response to stress (GO:0006950)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle B (GO:0030992)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	9						ttgggaggccaaggtgggcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF100747	CCDS41341.1	1p32	2014-02-21	2008-06-24	2008-06-24	ENSG00000081870	ENSG00000081870	51668		Intraflagellar transport homologs, Heat shock proteins / HSPB	25019	protein-coding gene	gene with protein product	intraflagellar transport 25 homolog (Chlamydomonas)	NA	chromosome 1 open reading frame 41	C1orf41	NA	11042152, 19253336	Standard	NM_016126	NM_016126	NA	Approved	HSPCO34, PP25, IFT25	uc001cwh.3	Q9Y547	OTTHUMG00000008408	ENST00000371378.2:c.318+2964T>C	chr1.hg19:g.54386612A>G		NA	A6NG57|D3DQ45|Q9Y684	hg19		0.02	-0.219261	GCCxAGG	COVERED																																																																																			NOVEL	HSPB11-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000023215.2	9	2.377749	KEEP	0	0	0	8	186	AA	0.99257	0.54878	0		-	3	60	97	0	0	7.149289	22	60	648	42	ENST00000371378.2	0.12	0.552887
MRPL37	51253	__UNKNOWN__	__UNKNOWN__	1	54669346	54669346	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54669346A>G	ENST00000360840.5	+	2	423				MRPL37_ENST00000487096.1_Intron|MRPL37_ENST00000336230.6_Intron|MRPL37_ENST00000605337.1_Intron	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	NA		NA			translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						acggggttttaccatgttggc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221	51253		Mitochondrial ribosomal proteins / large subunits	14034	protein-coding gene	gene with protein product		611843			NA	10600119	Standard	NM_016491	NM_016491	NA	Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.347-1345A>G	chr1.hg19:g.54669346A>G		NA	Q96Q67|Q9BWR1|Q9P0P3	hg19	CCDS589.1	0.02	-0.131523	TTTxCCA	UNCOVERED																																																																																			NOVEL	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022224.1	9	3.30327	KEEP	7	0	0	11	280	AA	0	0	0		+	3	52	96	0	0	7.982592	10	60	270	32	ENST00000360840.5	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	54919958	54919958	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54919958T>C			NA	NA				RP4-705F19.1 (33425 upstream) : AC099796.1 (50382 downstream)						NA		NA									NA						tgagccactgtgcccggccac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.54919958T>C		NA		hg19		0.02	-0.245573	CTGxGCC	COVERED																																																																																			NOVEL					0			10	3.909923	KEEP	2	0	0	13	359	TT	0.993634	0.637264	0			4	60	128	0	0	10.013808	20	60	593	57		0.166667	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	54970499	54970499	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:54970499T>C			NA	NA				AC099796.1 (56 upstream) : RP5-866L20.1 (11585 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.54970499T>C		NA		hg19		0.02	-0.219269	AATxCCA	COVERED																																																																																			NOVEL					0			13	4.21021	KEEP	1	0	0	14	379	TT	0.994391	0.549786	0			3	42	101	0	0	7.665021	20	60	599	59		0.130435	0.552887
ACOT11	26027	__UNKNOWN__	__UNKNOWN__	1	55018528	55018528	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:55018528T>C	ENST00000343744.2	+	1	115				ACOT11_ENST00000481208.1_Intron|ACOT11_ENST00000371316.3_Intron	NM_147161.3	NP_671517.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	NA		NA			fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						gagacggagtttcgctcttgt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(148;1440 1861 22015 32453 51933)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	26027	3.1.2.-	Acyl CoA thioesterases, StAR-related lipid transfer (START) domain containing	18156	protein-coding gene	gene with protein product	StAR-related lipid transfer (START) domain containing 14	606803	thioesterase, adipose associated	THEA	NA	11696000, 16103133, 16940157	Standard	NM_015547	NM_015547	NA	Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000343744.2:c.33+4513T>C	chr1.hg19:g.55018528T>C		NA	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	hg19	CCDS593.1	0.02	-0.289351	AGTxTCG	COVERED																																																																																			NOVEL	ACOT11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027351.1	14	2.706143	KEEP	2	0	0	9	242	TT	0.99254	0.755211	0		+	3	60	95	1	1	6.79396	25	60	691	66	ENST00000343744.2	0.107143	0.760887
ACOT11	26027	__UNKNOWN__	__UNKNOWN__	1	55104473	55104473	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:55104473A>G	ENST00000371316.3	+	0	5977					NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	NA		NA			fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						acaggtgtgaaccactgtgct	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(148;1440 1861 22015 32453 51933)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	26027	3.1.2.-	Acyl CoA thioesterases, StAR-related lipid transfer (START) domain containing	18156	protein-coding gene	gene with protein product	StAR-related lipid transfer (START) domain containing 14	606803	thioesterase, adipose associated	THEA	NA	11696000, 16103133, 16940157	Standard	NM_015547	NM_015547	NA	Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.*4071A>G	chr1.hg19:g.55104473A>G		NA	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	hg19	CCDS592.1	0.02	1.628747	TGAxCCA	COVERED																																																																																			NOVEL	ACOT11-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027356.1	20	7.25086	KEEP	0	1	31	35	964	AA	0.999999	0.999955	0		+	5	60	178	0	0	11.729916	88	60	2627	197	ENST00000371316.3	0.053763	0.999956
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	55396687	55396687	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:55396687T>C			NA	NA				RP11-67L3.4 (42164 upstream) : TMEM61 (49777 downstream)						NA		NA									NA						tcccagcactttgggaggctg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.55396687T>C		NA		hg19		0.02	-0.236817	ACTxTGG	COVERED																																																																																			NOVEL					0			5	3.308584	KEEP	0	0	0	11	309	TT	0.993072	0.608164	0			3	60	101	0	0	7.605588	21	60	633	51		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	55483781	55483781	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:55483781T>C			NA	NA				BSND (7225 upstream) : PCSK9 (21439 downstream)						NA		NA									NA						cggggtttcatcatcttggcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.55483781T>C		NA		hg19		0.02	-0.210469	TCAxCAT	COVERED																																																																																			NOVEL					0			13	4.501222	KEEP	1	0	0	15	391	TT	0.99649	0.520328	0			4	60	121	0	0	9.480489	18	60	514	52		0.181818	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	55700914	55700914	__UNKNOWN__	IGR	SNP	G	G	A	rs373325667		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:55700914G>A			NA	NA				RP11-101C11.1 (1064 upstream) : RN7SKP291 (141284 downstream)						NA		NA									NA						tcaggagttcgagaccagcct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.55700914G>A		NA		hg19		0.02	-0.070172	TTCxAGA	UNCOVERED																																																																																			NOVEL					0			4	2.406516	KEEP	1	0	0	8	234	GG	0.99257	0.053735	0			3	47	89	0	0	8.254734	4	60	130	26		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	56273323	56273323	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:56273323T>C			NA	NA				RP11-466L17.1 (72648 upstream) : RP11-90C4.1 (16156 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.56273323T>C		NA		hg19		0.02	-0.26311	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			10	2.705612	KEEP	3	0	0	9	232	TT	0	0	0			3	60	104	0	0	7.643917	26	60	759	49		0.103448	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	56766069	56766069	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:56766069T>C			NA	NA				RP11-504A18.1 (41826 upstream) : AC119674.1 (76935 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.56766069T>C		NA		hg19		0.02	-0.201259	AGGxGTG	COVERED																																																																																			NOVEL					0			7	2.404785	KEEP	1	0	0	8	208	TT	0.99257	0.4869	0			3	60	88	0	0	6.434844	19	60	504	44		0.136364	0.490544
PPAP2B	8613	__UNKNOWN__	__UNKNOWN__	1	57039613	57039613	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:57039613A>G	ENST00000371250.3	-	1	691					NM_003713.4	NP_003704.3	O14495	LPP3_HUMAN	phosphatidic acid phosphatase type 2B	NA		NA			Bergmann glial cell differentiation (GO:0060020)|blood vessel development (GO:0001568)|canonical Wnt signaling pathway involved in positive regulation of cell-cell adhesion (GO:0044329)|canonical Wnt signaling pathway involved in positive regulation of endothelial cell migration (GO:0044328)|canonical Wnt signaling pathway involved in positive regulation of wound healing (GO:0044330)|dephosphorylation (GO:0016311)|gastrulation with mouth forming second (GO:0001702)|germ cell migration (GO:0008354)|homotypic cell-cell adhesion (GO:0034109)|lipid metabolic process (GO:0006629)|negative regulation of protein phosphorylation (GO:0001933)|phospholipid metabolic process (GO:0006644)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of sphingolipid mediated signaling pathway (GO:1902068)|regulation of Wnt signaling pathway (GO:0030111)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)|sphingosine-1-phosphate phosphatase activity (GO:0042392)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						ggtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000889	CCDS604.1	1p32.2	2009-05-27			ENSG00000162407	ENSG00000162407	8613	3.1.3.4		9229	protein-coding gene	gene with protein product		607125			NA	9305923	Standard	NM_003713	NM_003713	NA	Approved	PAP-2b, LPP3	uc001cyj.2	O14495	OTTHUMG00000008160	ENST00000371250.3:c.139+4937T>C	chr1.hg19:g.57039613A>G		NA	B2R651|D3DQ52|Q5U0F7|Q96GW0|Q99782	hg19	CCDS604.1	0.02	-0.175415	CACxCCT	COVERED																																																																																			NOVEL	PPAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022334.2	3	2.706718	KEEP	1	0	0	9	255	AA	0.99254	0.384517	0		-	3	60	104	0	0	8.233211	16	60	471	40	ENST00000371250.3	0.157895	0.387407
C8A	731	__UNKNOWN__	__UNKNOWN__	1	57351445	57351445	__UNKNOWN__	Intron	SNP	G	G	A	rs139789526	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:57351445G>A	ENST00000361249.3	+	7	951					NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	NA		NA			complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						ggatggtctcgatctcctgac	0.488		NA											G|||	349	0.0696885	0.0083	0.1383	5008	,	,	NA	15035	0.003	NA	0.1918	False	NA	,,,	NA	NA	NA	2504	0.047	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131	731		Complement system	1352	protein-coding gene	gene with protein product		120950			NA		Standard	NM_000562	NM_000562	NA	Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.856-155G>A	chr1.hg19:g.57351445G>A		NA	A2RUI4|A2RUI5|Q13668|Q9H130	hg19	CCDS606.1	0.02	-0.16666	CTCxATC	COVERED																																																																																			NOVEL	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000022890.1	14	3.60698	KEEP	6	0	0	12	323	GG	0.99254	0.351306	0		+	3	60	87	0	0	6.610745	15	60	485	50	ENST00000361249.3	0.166667	0.353947
DAB1	1600	__UNKNOWN__	__UNKNOWN__	1	57511120	57511120	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:57511120T>C	ENST00000371236.2	-	9	987				DAB1_ENST00000485760.1_Intron|DAB1_ENST00000420954.2_Intron|DAB1_ENST00000414851.2_Intron|DAB1_ENST00000371234.4_Intron|DAB1_ENST00000439789.2_Intron|DAB1_ENST00000371231.1_Intron			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	NA		NA			adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						cctgtaatcctagcactttgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406	1600			2661	protein-coding gene	gene with protein product		603448	disabled (Drosophila) homolog 1, disabled homolog 1 (Drosophila), Dab, reelin signal transducer, homolog 1 (Drosophila), Dab reelin signal transducer 1		NA	9790777	Standard	NM_021080	NM_021080	NA	Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000371236.2:c.723+17436A>G	chr1.hg19:g.57511120T>C		NA	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	hg19	CCDS607.1	0.02	-0.245572	TCCxAGC	UNCOVERED																																																																																			NOVEL	DAB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027814.2	11	2.706083	KEEP	2	0	0	9	242	TT	0	0	0		-	3	60	99	0	0	7.405789	21	60	630	51	ENST00000371236.2	0.125	0.641347
DAB1	1600	__UNKNOWN__	__UNKNOWN__	1	57905391	57905391	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:57905391A>G	ENST00000485760.1	-	8	625				DAB1_ENST00000371234.4_Intron			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	NA		NA			adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						gagccaccgcacccggccAGT	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406	1600			2661	protein-coding gene	gene with protein product		603448	disabled (Drosophila) homolog 1, disabled homolog 1 (Drosophila), Dab, reelin signal transducer, homolog 1 (Drosophila), Dab reelin signal transducer 1		NA	9790777	Standard	NM_021080	NM_021080	NA	Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000485760.1:c.2044-148553T>C	chr1.hg19:g.57905391A>G		NA	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	hg19		0.02	-0.140301	CGCxCCC	COVERED																																																																																			NOVEL	DAB1-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000023073.5	9	4.510997	KEEP	1	0	0	15	414	AA	0.997832	0.260399	0		-	3	60	101	0	0	8.373441	11	60	310	49	ENST00000485760.1	0.214286	0.260965
DAB1	1600	__UNKNOWN__	__UNKNOWN__	1	58080822	58080822	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:58080822A>G	ENST00000485760.1	-	7	625				DAB1_ENST00000371234.4_Intron			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	NA		NA			adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						gattacaggcatgagccactg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406	1600			2661	protein-coding gene	gene with protein product		603448	disabled (Drosophila) homolog 1, disabled homolog 1 (Drosophila), Dab, reelin signal transducer, homolog 1 (Drosophila), Dab reelin signal transducer 1		NA	9790777	Standard	NM_021080	NM_021080	NA	Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000485760.1:c.2043+34441T>C	chr1.hg19:g.58080822A>G		NA	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	hg19		0.02	-0.140306	GGCxTGA	COVERED																																																																																			NOVEL	DAB1-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000023073.5	9	4.511691	KEEP	4	0	0	15	419	AA	0.994391	0.259501	0		-	3	60	101	0	0	8.272442	12	60	341	42	ENST00000485760.1	0.2	0.260965
DAB1	1600	__UNKNOWN__	__UNKNOWN__	1	58213220	58213220	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:58213220G>A	ENST00000485760.1	-	7	551				DAB1_ENST00000371234.4_Intron			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	NA		NA			adult walking behavior (GO:0007628)|cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration (GO:0021813)|cerebellum structural organization (GO:0021589)|dendrite development (GO:0016358)|Golgi localization (GO:0051645)|lateral motor column neuron migration (GO:0097477)|midgut development (GO:0007494)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell adhesion (GO:0007162)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein kinase activity (GO:0045860)|radial glia guided migration of Purkinje cell (GO:0021942)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|ventral spinal cord development (GO:0021517)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(5)	64						ggtggctcacgcctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC067445	CCDS607.1	1p32-p31	2013-10-03	2013-10-03		ENSG00000173406	ENSG00000173406	1600			2661	protein-coding gene	gene with protein product		603448	disabled (Drosophila) homolog 1, disabled homolog 1 (Drosophila), Dab, reelin signal transducer, homolog 1 (Drosophila), Dab reelin signal transducer 1		NA	9790777	Standard	NM_021080	NM_021080	NA	Approved		uc001cys.1	O75553	OTTHUMG00000008391	ENST00000485760.1:c.2118-97883C>T	chr1.hg19:g.58213220G>A		NA	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	hg19		0.02	-0.166673	CACxCCT	COVERED																																																																																			NOVEL	DAB1-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000023073.5	8	5.112841	KEEP	8	0	0	17	487	GG	0.994391	0.351961	0		-	3	60	95	0	0	7.491634	14	60	467	62	ENST00000485760.1	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	59020669	59020669	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:59020669A>T			NA	NA				OMA1 (8197 upstream) : RN7SL713P (10631 downstream)						NA		NA									NA						aggtcaggagatcgagaccat	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.59020669A>T		NA		hg19		0.02	-0.096467	GAGxTCG	UNCOVERED																																																																																			NOVEL					0			7	2.405919	KEEP	12	0	0	8	217	AA	0	0	0			3	60	83	0	0	6.932374	8	60	235	44		0.272727	0.139832
TACSTD2	4070	__UNKNOWN__	__UNKNOWN__	1	59042367	59042367	__UNKNOWN__	Silent	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:59042367G>T	ENST00000371225.2	-	1	799	c.462C>A	c.(460-462)atC>atA	p.I154I		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	154		NA			cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)				NA	all_cancers(7;6.54e-05)					GGTCAATGAGGATGTGGTGGG	0.687		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													26	25	25			NA	NA	1		NA											NA				59042367		2198	4296	6494	SO:0001819	synonymous_variant			X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292	4070			11530	protein-coding gene	gene with protein product		137290		M1S1	NA	8382772, 11306819	Standard	NM_002353	NM_002353	NA	Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.462C>A	chr1.hg19:g.59042367G>T		NA	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	hg19	CCDS609.1	0.02	2.609074	GAGxATG	COVERED																																																																																			NOVEL	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027818.1	3	14.441973	KEEP	0	0	0	48	1453	GG	1	1	0		-	46	60	1284	0	0	112.907894	88	60	2953	252	ENST00000371225.2	0.343284	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	59105562	59105562	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:59105562G>A			NA	NA				TACSTD2 (62396 upstream) : MYSM1 (14848 downstream)						NA		NA									NA						ttgtatttttggtagacacag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.59105562G>A		NA		hg19		0.02	-0.070165	TTTxGTA	UNCOVERED																																																																																			NOVEL					0			1	2.399697	KEEP	0	0	0	8	226	GG	0.99257	0.053735	0			3	60	84	0	0	7.754323	4	60	135	18		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	59560241	59560241	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:59560241C>T			NA	NA				RP11-145M4.3 (6374 upstream) : RP11-470E16.1 (37366 downstream)						NA		NA									NA						tttgggaggccgaggcaggcg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.59560241C>T		NA		hg19		0.02	-0.219299	GGCxGAG	COVERED																																																																																			NOVEL					0			6	3.610455	KEEP	5	0	0	12	366	CC	0.993072	0.549057	0			3	60	92	0	0	6.827243	19	60	630	64		0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	59560247	59560247	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:59560247A>G			NA	NA				RP11-145M4.3 (6380 upstream) : RP11-470E16.1 (37360 downstream)						NA		NA									NA						aggccgaggcaggcggatcat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.59560247A>G		NA		hg19		0.02	-0.201735	GGCxGGC	COVERED																																																																																			NOVEL					0			6	3.309189	KEEP	5	0	0	11	318	AA	0.992708	0.486967	0			3	60	104	0	0	8.091955	18	60	544	62		0.142857	0.490544
FGGY	55277	__UNKNOWN__	__UNKNOWN__	1	60021409	60021409	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:60021409C>T	ENST00000371218.4	+	8	1087				FGGY_ENST00000303721.7_Intron|FGGY_ENST00000371210.1_Intron|FGGY_ENST00000371212.1_Intron|FGGY_ENST00000474476.1_Intron	NM_001113411.1	NP_001106882.1	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	NA		NA			carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					cagtggctcacgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456	55277			25610	protein-coding gene	gene with protein product		611370			NA	17671248	Standard	NM_001113411	NM_018291	NA	Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000371218.4:c.903+1510C>T	chr1.hg19:g.60021409C>T		NA	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	hg19	CCDS44155.1	0.02	-0.175431	TCAxGCC	COVERED																																																																																			NOVEL	FGGY-005	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023206.2	6	2.707534	KEEP	4	0	0	9	262	CC	0.99254	0.384517	0		+	4	60	115	0	0	9.063242	16	60	526	50	ENST00000371218.4	0.2	0.387407
HOOK1	51361	__UNKNOWN__	__UNKNOWN__	1	60326728	60326728	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:60326728G>A	ENST00000371208.3	+	15	1789				HOOK1_ENST00000395561.2_Intron|HOOK1_ENST00000465876.1_Intron	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	NA		NA			early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatid development (GO:0007286)	FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)			biliary_tract(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|urinary_tract(1)	29	all_cancers(7;0.000129)					gattacaggcgtgagccacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF044923	CCDS612.1	1p32.1	2013-08-21	2013-08-21		ENSG00000134709	ENSG00000134709	51361			19884	protein-coding gene	gene with protein product		607820	hook homolog 1 (Drosophila)		NA	9927460	Standard	NM_015888	XM_005270922	NA	Approved	HK1	uc001czo.3	Q9UJC3	OTTHUMG00000008990	ENST00000371208.3:c.1532+728G>A	chr1.hg19:g.60326728G>A		NA	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	hg19	CCDS612.1	0.02	-0.219299	GGCxTGA	COVERED																																																																																			NOVEL	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024934.1	13	3.309677	KEEP	2	0	0	11	329	GG	0.993072	0.549057	0		+	3	60	91	0	0	6.665441	20	60	654	52	ENST00000371208.3	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	60687396	60687396	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:60687396T>C			NA	NA				RP11-575B7.3 (72045 upstream) : RP11-776H12.1 (318524 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.60687396T>C		NA		hg19		0.02	-0.149108	TCCxAGC	COVERED																																																																																			NOVEL					0			12	4.511588	KEEP	0	0	0	15	415	TT	0.99649	0.290976	0			3	54	93	0	0	7.573012	11	60	332	44		0.214286	0.292001
NFIA	4774	__UNKNOWN__	__UNKNOWN__	1	61548379	61548379	__UNKNOWN__	5'UTR	SNP	C	C	T	rs543078710		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:61548379C>T	ENST00000403491.3	+	0	400				NFIA_ENST00000371191.1_Intron|NFIA_ENST00000371189.4_Intron|NFIA_ENST00000479364.1_Intron|NFIA_ENST00000371187.3_5'UTR|NFIA_ENST00000407417.3_Intron	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	NA		NA			DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						ttcctctctccctctttctcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													74	95	89			NA	NA	1		NA											NA				61548379		692	1591	2283	SO:0001623	5_prime_UTR_variant			U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599	4774			7784	protein-coding gene	gene with protein product		600727			NA	7590749	Standard	NM_005595	NM_001134673	NA	Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.-85C>T	chr1.hg19:g.61548379C>T		NA	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	hg19	CCDS44156.1	0.02	2.76693	CTCxCTC	COVERED																																																																																			NOVEL	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023799.3	35	2.990863	KEEP	0	9	246	97	2972	CC	1	0.999997	0		+	7	60	213	0	0	13.30831	104	60	3429	321	ENST00000403491.3	0.063063	0.999997
INADL	10207	__UNKNOWN__	__UNKNOWN__	1	62301139	62301139	__UNKNOWN__	Intron	SNP	G	G	A	rs549410823	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:62301139G>A	ENST00000371158.2	+	17	2226				INADL_ENST00000316485.6_Intron	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	NA		NA			cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						gcagtggtgcgatcttggctc	0.507		NA											G|||	2	0.000399361	0.0	0.0029	5008	,	,	NA	17549	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849	10207			28881	protein-coding gene	gene with protein product		603199			NA	9280290, 11374908	Standard	NM_170605	NM_176877	NA	Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.2112+1682G>A	chr1.hg19:g.62301139G>A		NA	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	hg19	CCDS617.2	0.02	-0.096289	TGCxATC	UNCOVERED																																																																																			NOVEL	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023639.2	10	2.40658	KEEP	2	0	0	8	234	GG	0	0	0		+	3	60	94	0	0	9.034301	3	60	80	23	ENST00000371158.2	0.5	0.120436
INADL	10207	__UNKNOWN__	__UNKNOWN__	1	62628571	62628571	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:62628571T>A	ENST00000371158.2	+	0	7484					NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	NA		NA			cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						gtgagccaagttcgtgccact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849	10207			28881	protein-coding gene	gene with protein product		603199			NA	9280290, 11374908	Standard	NM_170605	NM_176877	NA	Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.*1964T>A	chr1.hg19:g.62628571T>A		NA	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	hg19	CCDS617.2	0.02	1.356497	AAGxTCG	COVERED																																																																																			NOVEL	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000023639.2	9	7.00114	KEEP	0	3	75	50	1289	TT	1	0.999919	0		+	5	60	142	1	0	8.317432	81	60	2284	213	ENST00000371158.2	0.05814	0.999919
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	62632186	62632186	__UNKNOWN__	IGR	SNP	T	T	C	rs148159775	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:62632186T>C			NA	NA				INADL (2594 upstream) : L1TD1 (28316 downstream)						NA		NA									NA						tgagaccagcttggctaacat	0.527		NA											T|||	38	0.00758786	0.0015	0.0101	5008	,	,	NA	17209	0.0	NA	0.0278	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.62632186T>C		NA		hg19		0.02	-0.140328	AGCxTGG	COVERED																																																																																			NOVEL					0			6	3.007863	KEEP	0	0	0	10	279	TT	0.992708	0.259062	0			3	60	93	0	0	7.37918	13	60	389	33		0.1875	0.260965
KANK4	163782	__UNKNOWN__	__UNKNOWN__	1	62738013	62738013	__UNKNOWN__	Intron	SNP	C	C	T	rs2666502	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:62738013C>T	ENST00000371153.4	-	4	2279				KANK4_ENST00000354381.3_Intron|KANK4_ENST00000371150.1_De_novo_Start_OutOfFrame	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	NA		NA				cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						cgtacacacacacatgcacgc	0.458		NA											C|||	1588	0.317093	0.2315	0.3963	5008	,	,	NA	23737	0.5883	NA	0.2624	False	NA	,,,	NA	NA	NA	2504	0.1534	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854	163782		KN motif and ankyrin repeat domain containing, Ankyrin repeat domain containing	27263	protein-coding gene	gene with protein product		614612	ankyrin repeat domain 38	ANKRD38	NA	17996375, 19554261	Standard	NM_181712	NM_181712	NA	Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.1901-752G>A	chr1.hg19:g.62738013C>T		NA	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	hg19	CCDS620.1	0.02	1.517491	ACAxACA	COVERED																																																																																			NOVEL	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024877.1	5	2.339313	KEEP	0	1	29	18	533	CC	0.99986	0.973829	0		-	27	60	763	1	0	73.85535	24	60	819	93	ENST00000371153.4	0.529412	0.973965
KANK4	163782	__UNKNOWN__	__UNKNOWN__	1	62756702	62756702	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:62756702A>G	ENST00000371153.4	-	2	309				KANK4_ENST00000354381.3_Intron	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	NA		NA				cytoplasm (GO:0005737)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(49)|ovary(3)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	81						gattacaggcatgagccacca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096259	CCDS620.1	1p31.3	2013-10-11	2008-01-29	2008-01-29	ENSG00000132854	ENSG00000132854	163782		KN motif and ankyrin repeat domain containing, Ankyrin repeat domain containing	27263	protein-coding gene	gene with protein product		614612	ankyrin repeat domain 38	ANKRD38	NA	17996375, 19554261	Standard	NM_181712	NM_181712	NA	Approved	KIAA0172	uc001dah.4	Q5T7N3	OTTHUMG00000008971	ENST00000371153.4:c.70-9396T>C	chr1.hg19:g.62756702A>G		NA	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	hg19	CCDS620.1	0.02	-0.219266	GGCxTGA	COVERED																																																																																			NOVEL	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000024877.1	9	2.706893	KEEP	1	0	0	9	248	AA	0.99254	0.548763	0		-	3	60	91	0	0	6.606549	21	60	628	50	ENST00000371153.4	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	62882536	62882536	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:62882536T>A			NA	NA				KANK4 (97451 upstream) : USP1 (19438 downstream)						NA		NA									NA						atggtctggatctcctgacct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.62882536T>A		NA		hg19		0.02	-0.192941	GGAxCTC	COVERED																																																																																			NOVEL					0			10	3.006471	KEEP	5	0	0	10	268	TT	0.99254	0.454342	0			3	60	88	0	0	6.493465	18	60	525	53		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	63185339	63185339	__UNKNOWN__	IGR	SNP	C	C	T	rs565862458		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:63185339C>T			NA	NA				RP11-230B22.1 (8974 upstream) : ATG4C (64466 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.532		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16353	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.63185339C>T		NA		hg19		0.02	-0.149116	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.405665	KEEP	2	0	0	8	226	CC	0	0	0			3	47	87	1	0	6.692121	14	60	448	32		0.176471	0.292001
ATG4C	84938	__UNKNOWN__	__UNKNOWN__	1	63281625	63281625	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:63281625A>G	ENST00000317868.4	+	4	367				ATG4C_ENST00000371120.3_Intron	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	NA		NA			autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						caaagtgctgagattacaggc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703	84938			16040	protein-coding gene	gene with protein product		611339	AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae), APG4 autophagy 4 homolog C (S. cerevisiae), ATG4 autophagy related 4 homolog C (S. cerevisiae)	AUTL1, APG4C	NA	12446702	Standard	NM_032852	NM_032852	NA	Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.161-621A>G	chr1.hg19:g.63281625A>G		NA	A6NLR8|D3DQ58|Q96K04	hg19	CCDS623.1	0.02	-0.236824	CTGxGAT	COVERED																																																																																			NOVEL	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025332.2	7	2.706881	KEEP	1	0	0	9	250	AA	0.99254	0.607839	0		+	4	60	132	0	0	10.668727	17	60	523	53	ENST00000317868.4	0.190476	0.612407
ALG6	29929	__UNKNOWN__	__UNKNOWN__	1	63834264	63834264	__UNKNOWN__	Intron	SNP	C	C	T	rs570427072		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:63834264C>T	ENST00000371108.4	+	1	98					NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						ctctgcctcccgggttcgagc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	29929	2.4.1.267		23157	protein-coding gene	gene with protein product	dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase	604566	asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase), asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)		NA	10359825, 11875054	Standard	NM_013339	NM_013339	NA	Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.-208+906C>T	chr1.hg19:g.63834264C>T		NA	B3KMU2|Q5SXR9|Q9H3I0	hg19	CCDS30735.1	0.02	-0.122794	TCCxGGG	COVERED																																																																																			NOVEL	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025330.2	4	2.708306	KEEP	1	0	0	9	285	CC	0.99257	0.194853	0		+	3	60	89	0	0	7.172993	11	60	351	35	ENST00000371108.4	0.214286	0.196312
ALG6	29929	__UNKNOWN__	__UNKNOWN__	1	63883627	63883627	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:63883627A>T	ENST00000371108.4	+	12	1292				ALG6_ENST00000263440.4_Intron	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						accaacatggagaaaccctgt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	29929	2.4.1.267		23157	protein-coding gene	gene with protein product	dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase	604566	asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase), asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)		NA	10359825, 11875054	Standard	NM_013339	NM_013339	NA	Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.988-1414A>T	chr1.hg19:g.63883627A>T		NA	B3KMU2|Q5SXR9|Q9H3I0	hg19	CCDS30735.1	0.02	-0.122798	TGGxGAA	COVERED																																																																																			NOVEL	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025330.2	5	2.706042	KEEP	5	0	0	9	236	AA	0.99257	0.22747	0		+	3	40	95	1	0	7.772864	11	60	334	36	ENST00000371108.4	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	64873905	64873905	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:64873905A>G			NA	NA				RNU7-62P (23763 upstream) : CACHD1 (62522 downstream)						NA		NA									NA						cgcccgcctcagcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.64873905A>G		NA		hg19		0.02	-0.122801	CTCxGCC	COVERED																																																																																			NOVEL					0			6	3.609447	KEEP	1	0	0	12	334	AA	0.993634	0.195062	0			3	60	103	0	0	8.572779	11	60	336	40		0.214286	0.196312
CACHD1	57685	__UNKNOWN__	__UNKNOWN__	1	65028355	65028355	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:65028355T>C	ENST00000290039.5	+	2	214				CACHD1_ENST00000495994.1_Intron|CACHD1_ENST00000371073.2_Intron	NM_020925.2	NP_065976.2	Q5VU97	CAHD1_HUMAN	cache domain containing 1	NA		NA			calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						ctgcctgccttggcctcccaa	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966	57685			29314	protein-coding gene	gene with protein product		NA	von Willebrand factor type A and cache domain containing 1	VWCD1	NA	10997877	Standard	NM_020925	NM_020925	NA	Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000290039.5:c.108+12016T>C	chr1.hg19:g.65028355T>C		NA	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	hg19	CCDS628.2	0.02	-0.114017	CCTxGGC	UNCOVERED																																																																																			NOVEL	CACHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025238.1	7	2.707043	KEEP	1	0	0	9	252	TT	0.99254	0.161255	0		+	3	60	94	0	0	7.901283	9	60	264	35	ENST00000290039.5	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	65474585	65474585	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:65474585C>T			NA	NA				RP4-535B20.4 (4815 upstream) : RNU6-1176P (14065 downstream)						NA		NA									NA						ttgcccaggccggtctcaaac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.65474585C>T		NA		hg19		0.02	-0.175399	GGCxGGT	COVERED																																																																																			NOVEL					0			8	4.813644	KEEP	0	0	0	16	475	CC	0.997832	0.386567	0			3	60	93	0	0	7.37927	13	60	397	46		0.1875	0.387407
AK4	205	__UNKNOWN__	__UNKNOWN__	1	65681135	65681135	__UNKNOWN__	Intron	SNP	G	G	A	rs185998273	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:65681135G>A	ENST00000327299.7	+	3	470				AK4_ENST00000395334.2_Intron|AK4_ENST00000545314.1_Intron|AK4_ENST00000470888.2_Intron|AK4_ENST00000546702.1_Intron	NM_013410.3	NP_037542.1			adenylate kinase 4	NA		NA								breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						gattacaggcgtgagccacca	0.483		NA											G|||	3	0.000599042	0.0015	0.0	5008	,	,	NA	16495	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	205	2.7.4.3	Adenylate kinases	363	protein-coding gene	gene with protein product		103030	adenylate kinase 3, adenylate kinase 3-like 1	AK3, AK3L1	NA	11485571	Standard	NM_013410	NM_203464	NA	Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.266-3302G>A	chr1.hg19:g.65681135G>A		NA		hg19	CCDS629.1	0.02	-0.149118	GGCxTGA	COVERED																																																																																			NOVEL	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025040.2	5	2.707761	KEEP	0	0	0	9	267	GG	0.99254	0.289823	0		+	3	60	85	0	0	6.579172	13	60	431	30	ENST00000327299.7	0.1875	0.292001
PDE4B	5142	__UNKNOWN__	__UNKNOWN__	1	66262928	66262928	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:66262928C>T	ENST00000329654.4	+	1	117					NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	NA		NA			cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	tgagccactgcgcccggccaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588	5142		Phosphodiesterases	8781	protein-coding gene	gene with protein product	phosphodiesterase E4 dunce homolog (Drosophila)	600127	phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4), phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)	DPDE4	NA		Standard	NM_002600	XM_005270925	NA	Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.-71+4615C>T	chr1.hg19:g.66262928C>T		NA	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	hg19	CCDS632.1	0.02	-0.149121	CTGxGCC	COVERED																																																																																			NOVEL	PDE4B-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025188.3	6	2.405653	KEEP	1	0	0	8	217	CC	0.99257	0.289832	0		+	3	60	88	0	0	7.181867	10	60	333	33	ENST00000329654.4	0.230769	0.292001
PDE4B	5142	__UNKNOWN__	__UNKNOWN__	1	66740136	66740136	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:66740136A>G	ENST00000423207.2	+	5	1074				PDE4B_ENST00000329654.4_Intron|PDE4B_ENST00000371049.3_Intron	NM_001037340.1	NP_001032417.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific	NA		NA			cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	gattacaggcatgagccactg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588	5142		Phosphodiesterases	8781	protein-coding gene	gene with protein product	phosphodiesterase E4 dunce homolog (Drosophila)	600127	phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4), phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)	DPDE4	NA		Standard	NM_002600	XM_005270925	NA	Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000423207.2:c.589+8366A>G	chr1.hg19:g.66740136A>G		NA	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	hg19	CCDS30742.1	0.02	-0.192951	GGCxTGA	UNCOVERED																																																																																			NOVEL	PDE4B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025190.2	5	2.406108	KEEP	1	0	0	8	221	AA	0	0	0		+	3	60	100	0	0	7.760979	17	60	496	45	ENST00000423207.2	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	66914276	66914276	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:66914276T>C			NA	NA				PDE4B (74017 upstream) : SGIP1 (84789 downstream)						NA		NA									NA						tgtctgtaattccagcactct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.66914276T>C		NA		hg19		0.02	-0.289414	AATxCCA	COVERED																																																																																			NOVEL					0			10	4.209176	KEEP	0	0	0	14	367	TT	0.995343	0.777423	0			3	60	100	0	0	7.293662	25	60	725	68		0.107143	0.78106
WDR78	79819	__UNKNOWN__	__UNKNOWN__	1	67354140	67354140	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:67354140A>G	ENST00000371026.3	-	4	699				WDR78_ENST00000431318.1_Intron|WDR78_ENST00000371023.3_Intron|WDR78_ENST00000371022.3_Intron	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						cactttgggaagccgaggcag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763	79819		WD repeat domain containing	26252	protein-coding gene	gene with protein product		NA			NA	21953912	Standard	NM_024763	NM_207014	NA	Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.643+2696T>C	chr1.hg19:g.67354140A>G		NA	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	hg19	CCDS635.1	0.02	-0.131568	GGAxGCC	UNCOVERED																																																																																			NOVEL	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025404.1	8	2.406255	KEEP	1	0	0	8	224	AA	0	0	0		-	3	60	89	0	0	7.07258	12	60	377	31	ENST00000371026.3	0.2	0.229173
SLC35D1	23169	__UNKNOWN__	__UNKNOWN__	1	67465759	67465759	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:67465759T>C	ENST00000235345.5	-	0	5417					NM_015139.2	NP_055954.1	Q9NTN3	S35D1_HUMAN	solute carrier family 35 (UDP-GlcA/UDP-GalNAc transporter), member D1	NA		NA			carbohydrate transport (GO:0008643)|cellular glucuronidation (GO:0052695)|chondroitin sulfate biosynthetic process (GO:0030206)|embryonic skeletal system development (GO:0048706)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|UDP-glucuronate biosynthetic process (GO:0006065)|UDP-glucuronic acid transport (GO:0015787)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	UDP-glucuronic acid transmembrane transporter activity (GO:0005461)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)	10						ttgagaccagtctggcaacag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB044343	CCDS636.1	1p32-p31	2013-07-17	2013-07-17		ENSG00000116704	ENSG00000116704	23169		Solute carriers	20800	protein-coding gene	gene with protein product		610804	solute carrier family 35 (UDP-glucuronic acid/UDP-N-acetylgalactosamine dual transporter), member D1		NA	11322953	Standard	NM_015139	NM_015139	NA	Approved	UGTREL7, KIAA0260	uc001ddk.2	Q9NTN3	OTTHUMG00000009360	ENST00000235345.5:c.*4264A>G	chr1.hg19:g.67465759T>C		NA	A8K185|B7Z3X2|Q52LU5|Q92548	hg19	CCDS636.1	0.02	1.53835	CAGxCTG	COVERED																																																																																			NOVEL	SLC35D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025948.1	32	19.822335	KEEP	0	3	82	95	2392	TT	1	0.999948	0		-	6	60	196	0	1	13.115866	77	70	2066	310	ENST00000235345.5	0.072289	0.999948
C1orf141	400757	__UNKNOWN__	__UNKNOWN__	1	67619780	67619780	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:67619780A>G	ENST00000371007.2	-	2	7					NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	NA		NA								NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						ctgagttctaatttgattgca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963	400757			32044	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013674	NM_001276351	NA	Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.103-22870T>C	chr1.hg19:g.67619780A>G		NA	Q0P5P5|Q5JVX5	hg19	CCDS30745.1	0.02	-0.078925	CTAxTTT	UNCOVERED																																																																																			NOVEL	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026096.2	7	2.706659	KEEP	1	0	0	9	246	AA	0.99257	0.076761	0		-	3	40	101	0	0	9.044156	6	60	162	21	ENST00000371007.2	0.333333	0.077336
IL12RB2	3595	__UNKNOWN__	__UNKNOWN__	1	67840826	67840826	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:67840826A>C	ENST00000262345.1	+	12	2357				IL12RB2_ENST00000544434.1_Intron|IL12RB2_ENST00000541374.1_Intron|IL12RB2_ENST00000371000.1_Intron	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	NA		NA			cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						gcctgtaatcacagcactttg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985	3595		Interleukins and interleukin receptors, Fibronectin type III domain containing	5972	protein-coding gene	gene with protein product		601642			NA	9284929, 8943050	Standard	NM_001559	NM_001559	NA	Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1717+2360A>C	chr1.hg19:g.67840826A>C		NA	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	hg19	CCDS638.1	0.02	-0.166651	ATCxCAG	COVERED																																																																																			NOVEL	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025202.2	8	2.706969	KEEP	0	0	0	9	252	AA	0.99254	0.384517	0		+	3	60	101	0	0	8.178828	13	60	390	41	ENST00000262345.1	0.1875	0.387407
DEPDC1	55635	__UNKNOWN__	__UNKNOWN__	1	68960563	68960563	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:68960563T>C	ENST00000456315.2	-	2	163				DEPDC1_ENST00000370966.5_Intron	NM_001114120.1	NP_001107592.1	Q5TB30	DEP1A_HUMAN	DEP domain containing 1	NA		NA			intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(397;7.21e-36)		cggtggctcatgcctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000361	CCDS644.1, CCDS44159.1	1p31.2	2008-08-19			ENSG00000024526	ENSG00000024526	55635			22949	protein-coding gene	gene with protein product		612002			NA		Standard	NM_017779	NM_001114120	NA	Approved	DEP.8, FLJ20354, SDP35, DEPDC1A	uc001dem.4	Q5TB30	OTTHUMG00000009212	ENST00000456315.2:c.49-185A>G	chr1.hg19:g.68960563T>C		NA	A8QXE0|A8QXE1|Q05DU3|Q5TB28|Q9H9I3|Q9NX21|Q9NXZ0	hg19	CCDS44159.1	0.02	-0.078938	TCAxGCC	UNCOVERED																																																																																			NOVEL	DEPDC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025514.2	2	3.909984	KEEP	0	0	0	13	363	TT	0.994391	0.076902	0		-	2	60	72	0	0	6.335869	5	60	144	37	ENST00000456315.2	0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	69263690	69263690	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:69263690A>G			NA	NA				RP4-694A7.4 (259380 upstream) : RP11-424D14.1 (257890 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.69263690A>G		NA		hg19		0.02	-0.228015	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			11	2.403958	KEEP	5	0	0	8	210	AA	0	0	0			4	60	133	0	0	10.67963	18	60	522	55		0.181818	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	69802570	69802570	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:69802570C>T			NA	NA				RP11-74K19.1 (87464 upstream) : RP3-380B4.1 (96367 downstream)						NA		NA									NA						gacagagtctcgctctgtcgc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.69802570C>T		NA		hg19		0.02	-0.122806	TCTxGCT	COVERED																																																																																			NOVEL					0			9	3.309565	KEEP	1	0	0	11	335	CC	0.992708	0.19488	0			3	52	88	0	0	7.181885	10	60	333	37		0.230769	0.196312
ANKRD13C	81573	__UNKNOWN__	__UNKNOWN__	1	70768176	70768176	__UNKNOWN__	Intron	SNP	A	A	G	rs12140194	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:70768176A>G	ENST00000370944.4	-	7	1090				ANKRD13C_ENST00000262346.6_Intron	NM_030816.4	NP_110443.3	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	NA		NA			protein retention in ER lumen (GO:0006621)|regulation of anoikis (GO:2000209)|regulation of receptor biosynthetic process (GO:0010869)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	19						ttgggaggccaaggcgggcgg	0.507		NA											-|||	677	0.135184	0.1293	0.1009	5008	,	,	NA	11172	0.0774	NA	0.1054	False	NA	,,,	NA	NA	NA	2504	0.2577	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS648.2	1p32.3-p31.3	2013-01-10			ENSG00000118454	ENSG00000118454	81573		Ankyrin repeat domain containing	25374	protein-coding gene	gene with protein product		615125			NA	11230166	Standard	NM_030816	NM_030816	NA	Approved	DKFZP566D1346, dJ677H15.3	uc001dex.4	Q8N6S4	OTTHUMG00000009343	ENST00000370944.4:c.777-1585T>C	chr1.hg19:g.70768176A>G		NA	B3KQ97|Q5VYH4|Q5VYH5|Q6PJE4|Q9H0N9	hg19	CCDS648.2	0.02	-0.149067	GCCxAGG	UNCOVERED																																																																																			NOVEL	ANKRD13C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000025903.1	6	2.707464	KEEP	17	0	0	9	258	AA	0	0	0		-	3	60	102	0	0	8.279253	13	60	366	63	ENST00000370944.4	0.1875	0.292001
PTGER3	5733	__UNKNOWN__	__UNKNOWN__	1	71349742	71349742	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:71349742T>C	ENST00000370931.3	-	5	1407				PTGER3_ENST00000460330.1_Intron|PTGER3_ENST00000370932.2_Intron|PTGER3_ENST00000354608.5_Missense_Mutation_p.T394A|PTGER3_ENST00000351052.5_Intron	NM_198714.1	NP_942007.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	NA		NA			cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	tgcactccagtctgggtgaga	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628	5733		GPCR / Class A : Prostanoid receptors	9595	protein-coding gene	gene with protein product		176806			NA	7759114, 9073510	Standard	NM_000957	NM_001126044	NA	Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000370931.3:c.1171-31200A>G	chr1.hg19:g.71349742T>C		NA	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	hg19	CCDS656.1	0.02	-0.420993	CAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	1.871	-0.460242	0.04508	.	.	ENSG00000050628	ENST00000354608	T	0.36520	1.25	0.563	-1.13	0.09775	.	.	.	.	.	T	0.03871	0.0109	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39251	-0.9623	7	0.12103	T	0.63	.	.	.	.	.	377;394	Q147U0;Q147X8	.;.	A	394	ENSP00000346624:T394A	ENSP00000346624:T394A	T	-	1	0	PTGER3	71122330	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-1.089000	0.03376	-1.499000	0.01821	-0.765000	0.03448	ACT	NOVEL	PTGER3-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026077.1	10	8.720494	KEEP	0	0	0	29	787	TT	0.999997	0.948399	0		-	3	60	108	0	0	7.446344	42	60	1271	120	ENST00000370931.3	0.066667	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	73366368	73366368	__UNKNOWN__	IGR	SNP	G	G	A	rs10889997	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:73366368G>A			NA	NA				RP4-660H19.1 (1545 upstream) : RN7SKP19 (290918 downstream)						NA		NA									NA						gggtttcaccgttttagccgg	0.577		NA											N|||	2634	0.525958	0.4803	0.3862	5008	,	,	NA	9845	0.7302	NA	0.4304	False	NA	,,,	NA	NA	NA	2504	0.5746	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.73366368G>A		NA		hg19		0.02	-0.052624	ACCxTTT	UNCOVERED																																																																																			NOVEL					0			3	3.005544	KEEP	12	0	0	10	258	GG	0	0	0			3	40	88	0	0	9.253197	1	18	34	26		0.75	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	73518213	73518213	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:73518213T>C			NA	NA				RP4-660H19.1 (153390 upstream) : RN7SKP19 (139073 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.73518213T>C		NA		hg19		0.02	-0.149117	TCAxGCC	COVERED																																																																																			NOVEL					0			6	3.91001	KEEP	2	0	0	13	361	TT	0.993634	0.290142	0			3	60	104	0	0	8.672779	11	60	335	49		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	73649534	73649534	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:73649534G>C			NA	NA				RP4-660H19.1 (284711 upstream) : RN7SKP19 (7752 downstream)						NA		NA									NA						attctgattagctgctccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.73649534G>C		NA		hg19		0.02	-0.412312	TTAxCTG	COVERED																																																																																			NOVEL					0			13	6.920139	KEEP	0	0	0	23	699	GG	0.999892	0.94164	0			3	60	100	0	0	6.677528	41	60	1396	97		0.068182	0.941741
C1orf173	0	__UNKNOWN__	__UNKNOWN__	1	75037398	75037398	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:75037398C>T	ENST00000326665.5	-	14	4214	c.3996G>A	c.(3994-3996)atG>atA	p.M1332I	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1332	Glu-rich.	NA								NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TTCCTCCTCCCATGCCCTCAT	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													270	251	258			NA	NA	1		NA											NA				75037398		2203	4300	6503	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000326665.5:c.3996G>A	chr1.hg19:g.75037398C>T	ENSP00000322609:p.Met1332Ile	NA	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	hg19	CCDS30755.1	0.02	1.023757	TCCxATG	COVERED	.	.	.	.	.	.	.	.	.	.	C	9.595	1.127197	0.20959	.	.	ENSG00000178965	ENST00000326665	T	0.13307	2.6	4.73	-3.92	0.04155	.	.	.	.	.	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.47983	-0.9074	9	0.33141	T	0.24	.	7.8466	0.29428	0.0:0.214:0.5321:0.2539	.	1332	Q5RHP9	CA173_HUMAN	I	1332	ENSP00000322609:M1332I	ENSP00000322609:M1332I	M	-	3	0	C1orf173	74809986	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	0.089000	0.15002	-0.256000	0.09473	0.462000	0.41574	ATG	NOVEL	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026516.1	21	21.961173	KEEP	0	0	0	73	2198	CC	1	0.999956	0		-	5	60	150	0	0	8.961249	87	60	2938	238	ENST00000326665.5	0.054348	0.999956
ST6GALNAC5	81849	__UNKNOWN__	__UNKNOWN__	1	77460970	77460970	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:77460970A>C	ENST00000477717.1	+	3	496					NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	NA		NA			glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						gtagtcccagatacttgggag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069	81849		Sialyltransferases	19342	protein-coding gene	gene with protein product		610134	sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E	SIAT7E	NA	10521438, 10601645	Standard	NM_030965	NM_030965	NA	Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.262-48919A>C	chr1.hg19:g.77460970A>C		NA	B1AK82	hg19	CCDS673.1	0.02	-0.140332	CAGxTAC	COVERED																																																																																			NOVEL	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026692.2	5	2.405772	KEEP	0	0	0	8	216	AA	0.99257	0.259026	0		+	3	60	98	0	0	7.972365	12	60	356	32	ENST00000477717.1	0.2	0.260965
ZZZ3	26009	__UNKNOWN__	__UNKNOWN__	1	78053245	78053245	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:78053245A>G	ENST00000370801.3	-	6	1981				ZZZ3_ENST00000370798.1_Intron|ZZZ3_ENST00000476275.1_Intron	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	NA		NA			chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						caccgcgcccagccCTTTGAC	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549	26009		Zinc fingers, ZZ-type	24523	protein-coding gene	gene with protein product	ATAC component 1 homolog (Drosophila)	NA			NA	16428443, 21304275	Standard	NM_015534	NM_015534	NA	Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.1506-2905T>C	chr1.hg19:g.78053245A>G		NA	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	hg19	CCDS677.1	0.02	-0.175391	CCCxGCC	COVERED																																																																																			NOVEL	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000026615.1	4	3.007816	KEEP	2	0	0	10	278	AA	0.992708	0.384582	0		-	3	60	101	0	0	7.933514	16	60	475	44	ENST00000370801.3	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	80134825	80134825	__UNKNOWN__	IGR	SNP	C	C	T	rs142868869	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:80134825C>T			NA	NA				RP4-726F1.1 (344277 upstream) : RP11-339A11.2 (445802 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.542		NA											C|||	34	0.00678914	0.0	0.0	5008	,	,	NA	14218	0.0337	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.80134825C>T		NA		hg19		0.02	-0.192936	AGAxGGG	COVERED																																																																																			NOVEL					0			11	2.338063	KEEP	14	1	26	17	480	CC	0.992708	0.454419	0			7	40	180	0	0	15.532282	14	60	467	54		0.333333	0.457757
LPHN2	23266	__UNKNOWN__	__UNKNOWN__	1	82157912	82157912	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:82157912C>T	ENST00000370728.1	+	4	503				LPHN2_ENST00000370721.1_Intron|LPHN2_ENST00000370725.1_Intron|LPHN2_ENST00000370727.1_Intron|LPHN2_ENST00000370730.1_Intron|LPHN2_ENST00000370723.1_Intron|LPHN2_ENST00000469377.2_Intron			O95490	LPHN2_HUMAN	latrophilin 2	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(37)|ovary(3)|pancreas(1)|prostate(3)|skin(22)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	119				all cancers(265;0.00142)|Epithelial(280;0.00829)|OV - Ovarian serous cystadenocarcinoma(397;0.077)|STAD - Stomach adenocarcinoma(256;0.248)		gccaacatggcgaaaccccat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ131581	CCDS689.1, CCDS72811.1	1p31.1	2014-08-08	2003-03-17	2003-05-02	ENSG00000117114	ENSG00000117114	23266		-, GPCR / Class B : Orphans	18582	protein-coding gene	gene with protein product		607018	latrophilin 1	LPHH1	NA	10760572	Standard	NM_012302	XR_248786	NA	Approved	KIAA0786, LEC1	uc001diu.3	O95490	OTTHUMG00000009844	ENST00000370728.1:c.-142-69584C>T	chr1.hg19:g.82157912C>T		NA	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	hg19		0.02	-0.175392	TGGxGAA	COVERED																																																																																			NOVEL	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000027188.1	7	4.211217	KEEP	1	0	0	14	404	CC	0.995343	0.385603	0		+	3	60	86	0	0	6.511265	15	60	464	49	ENST00000370728.1	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	83711967	83711967	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:83711967C>T			NA	NA				RP4-601K24.1 (79469 upstream) : RP11-413G15.1 (199768 downstream)						NA		NA									NA						ccgcccgcctcggcctcccaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.83711967C>T		NA		hg19		0.02	-0.114012	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			8	2.707348	KEEP	5	0	0	9	262	CC	0	0	0			3	49	80	0	0	6.382216	10	60	316	39		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	84819165	84819165	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:84819165C>T			NA	NA				SAMD13 (2685 upstream) : UOX (14178 downstream)						NA		NA									NA						tgcagtggcacgatctcagct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.84819165C>T		NA		hg19		0.02	-0.157878	GCAxGAT	COVERED																																																																																			NOVEL					0			7	2.707326	KEEP	0	0	0	9	261	CC	0.99254	0.320398	0			3	60	89	0	0	6.892124	14	60	433	36		0.176471	0.322807
RPF1	80135	__UNKNOWN__	__UNKNOWN__	1	84948988	84948988	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:84948988C>T	ENST00000370654.5	+	3	381				RPF1_ENST00000370656.1_3'UTR	NM_025065.6	NP_079341.2	Q9H9Y2	RPF1_HUMAN	ribosome production factor 1 homolog (S. cerevisiae)	NA		NA			rRNA processing (GO:0006364)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						cttgctctgtcgcccatgctg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF322053	CCDS695.1	1p22.3	2009-09-25	2009-09-25	2009-09-25	ENSG00000117133	ENSG00000117133	80135			30350	protein-coding gene	gene with protein product	RNA processing factor 1, ribosome production factor 1	NA	brix domain containing 5	BXDC5	NA	11864606	Standard	NM_025065	NM_025065	NA	Approved		uc001djv.4	Q9H9Y2	OTTHUMG00000009857	ENST00000370654.5:c.366+310C>T	chr1.hg19:g.84948988C>T		NA	Q5VSK7|Q6AHX1|Q8WXZ8	hg19	CCDS695.1	0.02	-0.236765	TGTxGCC	COVERED																																																																																			NOVEL	RPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027238.1	5	4.511927	KEEP	0	0	0	15	426	CC	0.99649	0.666177	0		+	3	60	90	0	0	6.396049	23	60	689	54	ENST00000370654.5	0.115385	0.668523
LPAR3	23566	__UNKNOWN__	__UNKNOWN__	1	85278396	85278396	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:85278396A>G	ENST00000440886.1	-	0	2233							Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	NA		NA			activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						gattacaggcatgagccagcg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517	23566		GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid	14298	protein-coding gene	gene with protein product		605106	endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7	EDG7	NA	10488122	Standard	NM_012152	NM_012152	NA	Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.*1133T>C	chr1.hg19:g.85278396A>G		NA	A0AVA3	hg19	CCDS700.1	0.02	1.517227	GGCxTGA	COVERED																																																																																			NOVEL	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027467.1	14	9.35476	KEEP	0	1	25	40	1104	AA	1	0.999768	0		-	4	60	136	0	0	8.683908	73	60	2170	179	ENST00000440886.1	0.051948	0.999768
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	85377887	85377887	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:85377887T>G			NA	NA				LPAR3 (18991 upstream) : MCOLN2 (13380 downstream)						NA		NA									NA						ctcccaaagttctgggattac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.85377887T>G		NA		hg19		0.02	-0.140326	AGTxCTG	COVERED																																																																																			NOVEL					0			5	2.707083	KEEP	0	0	0	9	253	TT	0.99254	0.259018	0			4	60	137	1	0	11.831505	11	60	320	37		0.266667	0.260965
WDR63	126820	__UNKNOWN__	__UNKNOWN__	1	85478014	85478014	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:85478014C>T	ENST00000370596.1	+	1	192							Q8IWG1	WDR63_HUMAN	WD repeat domain 63	NA		NA								NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		Gggctgggcgcggtggctcat	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643	126820		WD repeat domain containing	30711	protein-coding gene	gene with protein product		NA			NA	21953912	Standard	NM_145172	XM_005270438	NA	Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000370596.1:c.-15+12993C>T	chr1.hg19:g.85478014C>T		NA	A8K988|Q96L72|Q96NU4	hg19		0.02	-0.157883	GCGxGGT	COVERED																																																																																			NOVEL	WDR63-004	KNOWN	alternative_5_UTR|basic	protein_coding	NA	protein_coding	OTTHUMT00000092673.1	6	2.707328	KEEP	2	0	0	9	259	CC	0.99254	0.320398	0		+	3	60	87	0	0	6.779322	13	60	415	45	ENST00000370596.1	0.1875	0.322807
MCOLN3	55283	__UNKNOWN__	__UNKNOWN__	1	85492211	85492211	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:85492211A>T	ENST00000370589.2	-	8	885				MCOLN3_ENST00000341115.4_Intron|WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000370587.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	NA		NA			auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		aggccgaggcaggcggatcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732	55283		Voltage-gated ion channels / Transient receptor potential cation channels	13358	protein-coding gene	gene with protein product		607400			NA	16382100	Standard	NM_018298	NM_018298	NA	Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.833-244T>A	chr1.hg19:g.85492211A>T		NA	Q5T4H5|Q5T4H6|Q9NV09	hg19	CCDS701.1	0.02	-0.113994	GGCxGGC	COVERED																																																																																			NOVEL	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027569.2	10	2.707472	KEEP	4	0	0	9	259	AA	0.99257	0.194853	0		-	3	44	93	0	0	7.801668	9	60	252	36	ENST00000370589.2	0.25	0.196312
MCOLN3	55283	__UNKNOWN__	__UNKNOWN__	1	85492212	85492212	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:85492212G>T	ENST00000370589.2	-	8	885				MCOLN3_ENST00000341115.4_Intron|WDR63_ENST00000370596.1_Intron|MCOLN3_ENST00000370587.1_Intron	NM_018298.10	NP_060768.8	Q8TDD5	MCLN3_HUMAN	mucolipin 3	NA		NA			auditory receptor cell differentiation (GO:0042491)|calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|locomotory behavior (GO:0007626)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(6)|kidney(3)|large_intestine(9)|lung(12)|prostate(3)|skin(1)	34				all cancers(265;0.00957)|Epithelial(280;0.0254)		ggccgaggcaggcggatcaca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF475085	CCDS701.1, CCDS58009.1	1p22.3	2011-12-16			ENSG00000055732	ENSG00000055732	55283		Voltage-gated ion channels / Transient receptor potential cation channels	13358	protein-coding gene	gene with protein product		607400			NA	16382100	Standard	NM_018298	NM_018298	NA	Approved	TRPML3, FLJ11006, TRP-ML3	uc001dkp.3	Q8TDD5	OTTHUMG00000009955	ENST00000370589.2:c.833-245C>A	chr1.hg19:g.85492212G>T		NA	Q5T4H5|Q5T4H6|Q9NV09	hg19	CCDS701.1	0.02	-0.114032	GCAxGCG	UNCOVERED																																																																																			NOVEL	MCOLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027569.2	10	2.708347	KEEP	4	0	0	9	287	GG	0.99257	0.16126	0		-	3	44	86	0	0	6.981908	10	60	337	35	ENST00000370589.2	0.230769	0.162467
WDR63	126820	__UNKNOWN__	__UNKNOWN__	1	85579975	85579975	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:85579975T>C	ENST00000294664.6	+	17	1966				WDR63_ENST00000326813.8_Intron|WDR63_ENST00000370596.1_Intron	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	NA		NA								NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		ggattacaggtatgagccacc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643	126820		WD repeat domain containing	30711	protein-coding gene	gene with protein product		NA			NA	21953912	Standard	NM_145172	XM_005270438	NA	Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.1787-3437T>C	chr1.hg19:g.85579975T>C		NA	A8K988|Q96L72|Q96NU4	hg19	CCDS702.1	0.02	-0.175394	AGGxATG	COVERED																																																																																			NOVEL	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027565.2	10	4.210062	KEEP	1	0	0	14	381	TT	0.995343	0.385603	0		+	3	51	98	0	0	7.710417	15	60	432	48	ENST00000294664.6	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	86187981	86187981	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:86187981A>G			NA	NA				ZNHIT6 (13865 upstream) : COL24A1 (6934 downstream)						NA		NA									NA						ttggccaggcatggtggctca	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.86187981A>G		NA		hg19		0.02	-0.149114	GGCxTGG	COVERED																																																																																			NOVEL					0			8	5.111442	KEEP	0	0	0	17	459	AA	0.999366	0.291816	0			3	60	103	0	0	8.572798	11	60	334	50		0.214286	0.292001
COL24A1	255631	__UNKNOWN__	__UNKNOWN__	1	86199866	86199866	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:86199866A>G	ENST00000370571.2	-	59	5365				COL24A1_ENST00000436319.1_Intron	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	NA		NA			extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		gattacaggcatgagccacca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502	255631		Collagens	20821	protein-coding gene	gene with protein product		610025			NA		Standard	NM_152890	NM_152890	NA	Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.4998+565T>C	chr1.hg19:g.86199866A>G		NA	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	hg19	CCDS41353.1	0.02	-0.149115	GGCxTGA	COVERED																																																																																			NOVEL	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029335.4	7	3.608003	KEEP	1	0	0	12	317	AA	0.993072	0.289978	0		-	3	60	106	0	0	8.7721	12	60	363	47	ENST00000370571.2	0.2	0.292001
ODF2L	57489	__UNKNOWN__	__UNKNOWN__	1	86816582	86816582	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:86816582C>T	ENST00000370566.3	-	15	2014				ODF2L_ENST00000359242.3_3'UTR|ODF2L_ENST00000294678.2_3'UTR|ODF2L_ENST00000317336.7_Intron|ODF2L_ENST00000394731.1_Intron|ODF2L_ENST00000370567.1_Intron	NM_001184766.1	NP_001171695.1	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	NA		NA				centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		aatgtcttctcttgagaagtg	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417	57489			29225	protein-coding gene	gene with protein product		NA			NA	10574462	Standard		NM_020729	NA	Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000370566.3:c.1647+1959G>A	chr1.hg19:g.86816582C>T		NA	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	hg19	CCDS53339.1	0.02	1.617535	TCTxTTG	COVERED																																																																																			NOVEL	ODF2L-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027877.3	8	3.610983	KEEP	0	0	0	12	377	CC	0.993634	0.967765	0		-	5	60	137	0	0	9.231514	41	60	1389	93	ENST00000370566.3	0.108696	0.973965
ODF2L	57489	__UNKNOWN__	__UNKNOWN__	1	86817494	86817494	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:86817494C>T	ENST00000370566.3	-	15	2014				ODF2L_ENST00000359242.3_3'UTR|ODF2L_ENST00000294678.2_3'UTR|ODF2L_ENST00000317336.7_Intron|ODF2L_ENST00000394731.1_Intron|ODF2L_ENST00000370567.1_Intron	NM_001184766.1	NP_001171695.1	Q9ULJ1	ODF2L_HUMAN	outer dense fiber of sperm tails 2-like	NA		NA				centrosome (GO:0005813)				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		ccttcacattccttgtaattt	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS30763.1, CCDS41354.1, CCDS30763.2, CCDS41354.2, CCDS53339.1	1p22.3	2008-02-05			ENSG00000122417	ENSG00000122417	57489			29225	protein-coding gene	gene with protein product		NA			NA	10574462	Standard		NM_020729	NA	Approved	KIAA1229	uc001dll.2	Q9ULJ1	OTTHUMG00000010080	ENST00000370566.3:c.1647+1047G>A	chr1.hg19:g.86817494C>T		NA	A8MU56|B4E037|Q05C40|Q5BJG5|Q5TBX3|Q5TBX4|Q86X31	hg19	CCDS53339.1	0.02	-0.254292	ATTxCTT	COVERED																																																																																			NOVEL	ODF2L-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027877.3	8	2.405716	KEEP	0	0	0	8	222	CC	0.99257	0.663556	0		-	7	60	169	0	0	13.402589	21	60	661	38	ENST00000370566.3	0.25	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	87319606	87319606	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:87319606G>A			NA	NA				SH3GLB1 (105739 upstream) : SEP15 (8525 downstream)						NA		NA									NA						tgatccgcccgcctcggcctc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.87319606G>A		NA		hg19		0.02	-0.13157	CCCxCCT	COVERED																																																																																			NOVEL					0			8	2.706841	KEEP	0	0	0	9	253	GG	0.99254	0.227464	0			3	60	82	0	0	6.582008	10	60	345	32		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	88047416	88047416	__UNKNOWN__	IGR	SNP	G	G	T	rs367737314		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:88047416G>T			NA	NA				RNA5SP52 (128360 upstream) : RP5-1027O11.1 (318175 downstream)						NA		NA									NA						gttttgttttgtttttgagat	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.88047416G>T		NA		hg19		0.02	-0.122806	TTTxTTT	COVERED																																																																																			NOVEL					0			6	2.707981	KEEP	1	0	0	9	274	GG	0.99257	0.194853	0			3	60	85	1	0	6.881902	10	60	340	32		0.230769	0.196312
PKN2	5586	__UNKNOWN__	__UNKNOWN__	1	89150088	89150088	__UNKNOWN__	De_novo_Start_OutOfFrame	SNP	G	G	A	rs571149431		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:89150088G>A	ENST00000370521.3	+	0	184				PKN2_ENST00000370505.3_De_novo_Start_InFrame|RP11-76N22.2_ENST00000458097.1_RNA|PKN2_ENST00000316005.7_De_novo_Start_OutOfFrame	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	NA		NA			apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		CGCCGCTCTCGATGAACCGGA	0.627		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	12770	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243	5586			9406	protein-coding gene	gene with protein product	cardiolipin-activated protein kinase Pak2	602549	protein kinase C-like 2	PRKCL2	NA	7988719, 7851406	Standard	NM_006256	NM_006256	NA	Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.-176G>A	chr1.hg19:g.89150088G>A		NA	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	hg19	CCDS714.1	0.02	-0.342038	CTCxATG	COVERED																																																																																			NOVEL	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027828.3	1	2.706893	KEEP	0	0	0	9	254	GG	0.99254	0.859287	0		+	14	60	397	0	0	35.319749	25	60	793	52	ENST00000370521.3	0.358974	0.865745
PKN2	5586	__UNKNOWN__	__UNKNOWN__	1	89221858	89221858	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:89221858T>C	ENST00000370521.3	+	3	708				PKN2_ENST00000370505.3_Intron|PKN2_ENST00000370513.5_Intron|PKN2_ENST00000316005.7_Intron	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	NA		NA			apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		ggattacaggtgtaagccacc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243	5586			9406	protein-coding gene	gene with protein product	cardiolipin-activated protein kinase Pak2	602549	protein kinase C-like 2	PRKCL2	NA	7988719, 7851406	Standard	NM_006256	NM_006256	NA	Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.350-4047T>C	chr1.hg19:g.89221858T>C		NA	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	hg19	CCDS714.1	0.02	-0.175415	AGGxGTA	COVERED																																																																																			NOVEL	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027828.3	8	2.704925	KEEP	1	0	0	9	234	TT	0.99257	0.384528	0		+	3	60	94	0	0	7.233623	16	60	477	39	ENST00000370521.3	0.157895	0.387407
PKN2	5586	__UNKNOWN__	__UNKNOWN__	1	89271900	89271900	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:89271900T>C	ENST00000370521.3	+	12	2162				PKN2_ENST00000370505.3_Intron|PKN2_ENST00000544045.1_Intron|PKN2_ENST00000370513.5_Intron|PKN2_ENST00000316005.7_3'UTR	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	NA		NA			apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		tgcaatggcatgatctcggct	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243	5586			9406	protein-coding gene	gene with protein product	cardiolipin-activated protein kinase Pak2	602549	protein kinase C-like 2	PRKCL2	NA	7988719, 7851406	Standard	NM_006256	NM_006256	NA	Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1803+200T>C	chr1.hg19:g.89271900T>C		NA	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	hg19	CCDS714.1	0.02	3.332871	GCAxGAT	COVERED																																																																																			NOVEL	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000027828.3	34	10.648602	KEEP	2	4	106	73	1959	TT	1	1	0		+	7	60	228	0	0	14.413486	119	60	3427	306	ENST00000370521.3	0.055556	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	89460313	89460313	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:89460313A>G			NA	NA				RBMXL1 (1670 upstream) : GBP3 (12035 downstream)						NA		NA									NA						ttgggaggccaaggtgggtgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.89460313A>G		NA		hg19		0.02	-0.280624	GCCxAGG	COVERED																																																																																			NOVEL					0			9	3.609541	KEEP	0	0	0	12	339	AA	0.993634	0.734962	0			3	60	95	0	0	6.653552	28	60	811	65		0.096774	0.739671
ZNF326	284695	__UNKNOWN__	__UNKNOWN__	1	90493065	90493065	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:90493065G>A	ENST00000370447.3	+	12	1408	c.1287G>A	c.(1285-1287)gtG>gtA	p.V429V	ZNF326_ENST00000340281.4_Silent_p.V518V|ZNF326_ENST00000455342.2_Silent_p.V312V			Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	518		NA			mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		tagaggaagtggaagaagtag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664	284695		Zinc fingers, C2H2-type	14104	protein-coding gene	gene with protein product	ZNF-protein interacting with nuclear mRNPs and DBC1	614601			NA	22446626	Standard	NM_181781	NM_182976	NA	Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000370447.3:c.1287G>A	chr1.hg19:g.90493065G>A		NA	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	hg19		0.02	-0.412278	AGTxGAA	COVERED																																																																																			NOVEL	ZNF326-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000029431.2	9	5.415788	KEEP	0	0	0	18	540	GG	0.999859	0.941609	0		+	5	60	151	0	0	10.723927	39	60	1275	80	ENST00000370447.3	0.113636	0.941741
ZNF326	284695	__UNKNOWN__	__UNKNOWN__	1	90493136	90493136	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:90493136G>A	ENST00000370447.3	+	12	1479	c.1358G>A	c.(1357-1359)gGg>gAg	p.G453E	ZNF326_ENST00000340281.4_Missense_Mutation_p.G542E|ZNF326_ENST00000455342.2_Missense_Mutation_p.G336E			Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	542		NA			mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ggggaaggaggggaagtaggg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													49	44	46			NA	NA	1		NA											NA				90493136		2201	4300	6501	SO:0001583	missense			BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664	284695		Zinc fingers, C2H2-type	14104	protein-coding gene	gene with protein product	ZNF-protein interacting with nuclear mRNPs and DBC1	614601			NA	22446626	Standard	NM_181781	NM_182976	NA	Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000370447.3:c.1358G>A	chr1.hg19:g.90493136G>A	ENSP00000359476:p.Gly453Glu	NA	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	hg19		0.02	0.974727	GAGxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.19	1.282412	0.23392	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.45668	0.91;0.89;0.89	4.02	-3.53	0.04667	.	1.173980	0.06543	N	0.743541	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23904	-1.0175	10	0.02654	T	1	-0.5927	5.4945	0.16795	0.3585:0.1548:0.4867:0.0	.	542;542	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	E	542;542;453;336	ENSP00000340796:G542E;ENSP00000359476:G453E;ENSP00000403470:G336E	ENSP00000340796:G542E	G	+	2	0	ZNF326	90265724	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.745000	0.04834	-0.672000	0.05266	-0.339000	0.08088	GGG	NOVEL	ZNF326-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000029431.2	11	9.327673	KEEP	0	0	0	31	956	GG	0.999997	0.99716	0		+	5	60	132	2	0	7.749593	66	60	2208	137	ENST00000370447.3	0.070423	0.997163
HFM1	164045	__UNKNOWN__	__UNKNOWN__	1	91797377	91797377	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:91797377C>T	ENST00000370425.3	-	21	2434				HFM1_ENST00000370424.3_Intron|HFM1_ENST00000294696.5_Intron|HFM1_ENST00000462405.1_Intron	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	NA		NA			resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		cacttgaacccgagaggcaga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669	164045			20193	protein-coding gene	gene with protein product		615684	SEC63 domain containing 1	SEC63D1	NA	14702039, 17286053	Standard	NM_001017975	XM_006710395	NA	Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2336-7054G>A	chr1.hg19:g.91797377C>T		NA	B1B0B6|Q8N9Q0	hg19	CCDS30769.2	0.02	-0.026307	ACCxGAG	UNCOVERED																																																																																			NOVEL	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316716.2	3	2.70716	KEEP	2	0	0	9	255	CC	0	0	0		-	2	49	55	0	0	6.452165	0	0	0	15	ENST00000370425.3	1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	91998815	91998815	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:91998815G>A			NA	NA				CDC7 (7494 upstream) : TGFBR3 (147086 downstream)						NA		NA									NA						acacacacaGGCACAGAGTAC	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.91998815G>A		NA		hg19		0.02	1.324897	CAGxCAC	COVERED																																																																																			NOVEL					0			16	8.424278	KEEP	0	0	0	28	850	GG	0.999997	0.998693	0			5	60	129	0	0	7.681687	63	60	2115	153		0.073529	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	92383222	92383222	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:92383222A>G			NA	NA				TGFBR3 (11330 upstream) : RN7SL235P (21603 downstream)						NA		NA									NA						tgcaagctccacctcccgggt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.92383222A>G		NA		hg19		0.02	-0.149053	TCCxCCT	COVERED																																																																																			NOVEL					0			8	2.703973	KEEP	4	0	0	9	222	AA	0.99257	0.289832	0			3	40	88	0	0	6.973134	12	60	327	38		0.2	0.292001
KIAA1107	23285	__UNKNOWN__	__UNKNOWN__	1	92641253	92641253	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:92641253T>C	ENST00000370378.4	+	5	419				KIAA1107_ENST00000409154.4_Intron	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	NA		NA								breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						ctcaggaggctgaggcaggag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712	23285			29192	protein-coding gene	gene with protein product		NA			NA	10470851	Standard	XM_034086	NM_015237	NA	Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.322-1133T>C	chr1.hg19:g.92641253T>C		NA	O14767|Q8N3X7	hg19	CCDS44172.1	0.02	-0.114028	GGCxGAG	UNCOVERED																																																																																			NOVEL	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000028375.3	6	4.210923	KEEP	1	0	0	14	389	TT	0.994391	0.161555	0		+	3	34	105	0	0	9.001183	9	60	272	36	ENST00000370378.4	0.25	0.162467
GLMN	11146	__UNKNOWN__	__UNKNOWN__	1	92712553	92712553	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:92712553T>C	ENST00000370360.3	-	18	1750				GLMN_ENST00000534881.1_Intron	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	NA		NA			muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		gcactccagcttgggcaagat	0.473		NA							Multiple Glomus Tumors (of the Skin), Familial												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842	11146			14373	protein-coding gene	gene with protein product		601749	venous malformation with glomus cells	VMGLOM	NA	8955134	Standard	NM_007070	XM_005270400	NA	Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.1668+65A>G	chr1.hg19:g.92712553T>C		NA	Q5VVC3|Q9BVE8	hg19	CCDS738.1	0.02	3.87381	AGCxTGG	COVERED																																																																																			NOVEL	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000028358.1	30	3.270738	KEEP	0	5	154	65	1832	TT	1	0.999978	0		-	5	60	175	1	0	11.313788	93	60	2860	253	ENST00000370360.3	0.05102	0.999978
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	92889048	92889048	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:92889048G>A			NA	NA				RN7SL824P (20806 upstream) : GFI1 (51270 downstream)						NA		NA									NA						tctgcctcccgggttcaagca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.92889048G>A		NA		hg19		0.02	-0.245621	CCCxGGT	COVERED																																																																																			NOVEL					0			21	2.540416	KEEP	13	1	27	18	545	GG	0.99649	0.639096	0			4	60	122	0	0	9.494559	19	60	626	75		0.173913	0.641347
FAM69A	388650	__UNKNOWN__	__UNKNOWN__	1	93393024	93393024	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:93393024C>A	ENST00000370310.4	-	1	125					NM_001006605.4|NM_001252269.1|NM_001252271.1	NP_001006606.2|NP_001239198.1|NP_001239200.1	Q5T7M9	FA69A_HUMAN	family with sequence similarity 69, member A	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4		all_lung(203;0.00265)|Lung NSC(277;0.00562)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000563)|all cancers(265;0.000751)|Epithelial(280;0.127)		tcagcctccccaagtgctggg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027146	CCDS44173.1, CCDS72822.1, CCDS72823.1, CCDS72824.1, CCDS72825.1	1p22	2014-06-25			ENSG00000154511	ENSG00000154511	388650			32213	protein-coding gene	gene with protein product		614542			NA	21334309	Standard	NM_001006605	NM_001006605	NA	Approved	FLJ23493	uc001dpg.3	Q5T7M9	OTTHUMG00000010894	ENST00000370310.4:c.54+33908G>T	chr1.hg19:g.93393024C>A		NA	Q6IRV2	hg19	CCDS44173.1	0.02	-0.236816	CCCxAAG	COVERED																																																																																			NOVEL	FAM69A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030046.2	7	3.008437	KEEP	1	0	0	10	302	CC	0.992708	0.607941	0		-	4	60	109	0	0	8.116406	20	60	674	51	ENST00000370310.4	0.166667	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	93472476	93472476	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:93472476C>T			NA	NA				AC093577.1 (24611 upstream) : RNU6-210P (3337 downstream)						NA		NA									NA						tttgggaggccgaggtgggtg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.93472476C>T		NA		hg19		0.02	-0.20177	GGCxGAG	COVERED																																																																																			NOVEL					0			6	4.21203	KEEP	7	0	0	14	420	CC	0.992708	0.486967	0			3	27	96	0	0	7.226857	19	60	658	69		0.136364	0.490544
CCDC18	343099	__UNKNOWN__	__UNKNOWN__	1	93692943	93692943	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:93692943A>T	ENST00000343253.7	+	17	2791				CCDC18_ENST00000421014.2_Intron|CCDC18_ENST00000401026.3_Intron|CCDC18_ENST00000557479.1_Intron|CCDC18_ENST00000338949.4_Intron|CCDC18_ENST00000334652.5_Intron			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	NA		NA								breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		caggctggtcacaaactcctg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483	343099			30370	protein-coding gene	gene with protein product		NA			NA	12601173	Standard	NM_206886	XM_006710609	NA	Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.2289+937A>T	chr1.hg19:g.93692943A>T		NA	Q6ZU17	hg19		0.02	-0.157858	GTCxCAA	COVERED																																																																																			NOVEL	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000382327.1	9	2.70388	KEEP	0	0	0	9	232	AA	0.99254	0.320398	0		+	3	32	94	0	0	7.392154	14	60	406	35	ENST00000343253.7	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	93842771	93842771	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:93842771C>T			NA	NA				DR1 (7716 upstream) : Y_RNA (8496 downstream)						NA		NA									NA						accccgtctccactaaaaata	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.93842771C>T		NA		hg19		0.02	-0.114025	CTCxACT	UNCOVERED																																																																																			NOVEL					0			11	2.707707	KEEP	2	0	0	9	266	CC	0.99257	0.16126	0			4	40	113	0	1	10.284052	6	60	203	28		0.4	0.162467
BCAR3	8412	__UNKNOWN__	__UNKNOWN__	1	94148388	94148388	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:94148388T>C	ENST00000370244.1	-	4	278					NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	NA		NA			lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		ggattacaggtgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936	8412		SH2 domain containing	973	protein-coding gene	gene with protein product		604704			NA	9582273	Standard		NM_001261408	NA	Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.11-7891A>G	chr1.hg19:g.94148388T>C		NA	D3DT43|Q5TEW3|Q6UW40|Q9BR50	hg19	CCDS745.1	0.02	-0.21927	AGGxGTG	COVERED																																																																																			NOVEL	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000028420.1	5	3.908419	KEEP	3	0	0	13	344	TT	0.993634	0.549368	0		-	3	60	91	0	0	6.934025	16	60	477	64	ENST00000370244.1	0.157895	0.552887
GCLM	2730	__UNKNOWN__	__UNKNOWN__	1	94353313	94353313	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:94353313T>C	ENST00000370238.3	-	0	2304					NM_002061.2	NP_002052.1	P48507	GSH0_HUMAN	glutamate-cysteine ligase, modifier subunit	NA		NA			apoptotic mitochondrial changes (GO:0008637)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of glutamate-cysteine ligase activity (GO:0035229)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to drug (GO:0042493)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	glutamate-cysteine ligase activity (GO:0004357)|glutamate-cysteine ligase catalytic subunit binding (GO:0035226)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10		all_lung(203;0.000815)|Lung NSC(277;0.00363)		all cancers(265;0.00566)|GBM - Glioblastoma multiforme(16;0.0203)|Epithelial(280;0.131)	L-Cysteine(DB00151)	tgtgagccactgcgcccggAT	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L35546	CCDS746.1	1p21	2008-02-05			ENSG00000023909	ENSG00000023909	2730	6.3.2.2		4312	protein-coding gene	gene with protein product	gamma-glutamylcysteine synthetase	601176		GLCLR	NA	7826375	Standard	NM_002061	NM_002061	NA	Approved		uc001dqg.1	P48507	OTTHUMG00000010562	ENST00000370238.3:c.*1233A>G	chr1.hg19:g.94353313T>C		NA	A8K334|D3DT45|M5A959|Q6FHC1|Q9NPX9|Q9NU74	hg19	CCDS746.1	0.02	1.581686	CACxGCG	COVERED																																																																																			NOVEL	GCLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029169.1	19	6.211541	KEEP	3	3	89	52	1446	TT	1	0.999895	0		-	6	60	196	0	0	13.213555	74	60	2221	212	ENST00000370238.3	0.075	0.999895
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	94438832	94438832	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:94438832A>G			NA	NA				GCLM (63866 upstream) : ABCA4 (19560 downstream)						NA		NA									NA						gagagagagaaagagacaaat	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.94438832A>G		NA		hg19		0.02	-0.105173	AGAxAGA	UNCOVERED																																																																																			NOVEL					0			5	2.704537	KEEP	0	0	0	9	229	AA	0.99254	0.138789	0			3	60	99	0	0	8.680374	7	60	191	33		0.3	0.139832
ABCA4	24	__UNKNOWN__	__UNKNOWN__	1	94496036	94496036	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:94496036G>A	ENST00000370225.3	-	29	4386	c.4300C>T	c.(4300-4302)Ctc>Ttc	p.L1434F		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1434		NA			phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TTATTCAGGAGGACGTCTGCA	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													137	119	125			NA	NA	1		NA											NA				94496036		2203	4300	6503	SO:0001583	missense			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691	24		ATP binding cassette transporters / subfamily A	34	protein-coding gene	gene with protein product	Stargardt disease	601691	ATP-binding cassette transporter, retinal-specific	STGD1, ABCR, RP19, STGD	NA	9490294	Standard	NM_000350	NM_000350	NA	Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.4300C>T	chr1.hg19:g.94496036G>A	ENSP00000359245:p.Leu1434Phe	NA	O15112|O60438|O60915|Q0QD48|Q4LE31	hg19	CCDS747.1	0.02	1.537602	GGAxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941427	0.34283	.	.	ENSG00000198691	ENST00000546054;ENST00000370225	D	0.97505	-4.41	4.65	4.65	0.58169	.	0.537044	0.19615	N	0.110055	D	0.91713	0.7380	M	0.66939	2.045	0.80722	D	1	B	0.23591	0.088	B	0.21708	0.036	D	0.87441	0.2395	10	0.21014	T	0.42	.	5.5005	0.16827	0.2419:0.0:0.7581:0.0	.	1434	P78363	ABCA4_HUMAN	F	226;1434	ENSP00000359245:L1434F	ENSP00000359245:L1434F	L	-	1	0	ABCA4	94268624	0.989000	0.36119	0.979000	0.43373	0.791000	0.44710	2.125000	0.42016	2.424000	0.82194	0.561000	0.74099	CTC	NOVEL	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029320.1	0	3.009135	KEEP	0	0	0	10	313	GG	0.992708	0.984859	0		-	22	60	676	0	0	60.774348	39	60	1331	109	ENST00000370225.3	0.360656	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	94723012	94723012	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:94723012T>C			NA	NA				RP11-148B18.1 (7964 upstream) : RP11-148B18.4 (61022 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.94723012T>C		NA		hg19		0.02	-0.306967	ATCxCAG	COVERED																																																																																			NOVEL					0			12	3.307999	KEEP	1	0	0	11	299	TT	0.992708	0.79441	0			3	60	105	1	0	7.697341	27	60	795	56		0.1	0.800245
SLC44A3	126969	__UNKNOWN__	__UNKNOWN__	1	95302350	95302350	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:95302350T>C	ENST00000529450.1	+	6	464				SLC44A3_ENST00000271227.6_Intron|SLC44A3_ENST00000532427.1_Intron|SLC44A3_ENST00000467909.1_Intron|SLC44A3_ENST00000530397.1_Intron|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000527077.1_Intron|SLC44A3_ENST00000446120.2_Intron			Q8N4M1	CTL3_HUMAN	solute carrier family 44, member 3	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|prostate(2)|stomach(1)|urinary_tract(1)	23		all_lung(203;0.000712)|Lung NSC(277;0.00316)		all cancers(265;0.039)|Epithelial(280;0.124)	Choline(DB00122)	gcctgtagtctcagctactca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC033858	CCDS751.1, CCDS44176.1, CCDS58011.1, CCDS58012.1, CCDS58013.1, CCDS72827.1	1p22.1	2013-05-22	2005-09-06		ENSG00000143036	ENSG00000143036	126969		Solute carriers	28689	protein-coding gene	gene with protein product		NA	solute carrier family, member 3		NA	15715662, 12975309	Standard	NM_152369	NM_001114106	NA	Approved	MGC45474, CTL3	uc001dqv.5	Q8N4M1	OTTHUMG00000010700	ENST00000529450.1:c.414-917T>C	chr1.hg19:g.95302350T>C		NA	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	hg19	CCDS58011.1	0.02	-0.070153	GTCxCAG	UNCOVERED																																																																																			NOVEL	SLC44A3-006	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382369.1	3	2.705908	KEEP	0	0	0	9	244	TT	0.99254	0.053733	0		+	3	60	98	0	0	9.42491	3	60	95	26	ENST00000529450.1	0.5	0.054137
ALG14	199857	__UNKNOWN__	__UNKNOWN__	1	95477213	95477213	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:95477213T>C	ENST00000370205.5	-	3	467					NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		ccttgtgatctgcccacctcg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339	199857			28287	protein-coding gene	gene with protein product		612866	asparagine-linked glycosylation 14 homolog (yeast), asparagine-linked glycosylation 14 homolog (S. cerevisiae)		NA	15615718	Standard	NM_144988	NM_144988	NA	Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.420+15471A>G	chr1.hg19:g.95477213T>C		NA	A8K030	hg19	CCDS752.1	0.02	-0.105257	ATCxGCC	UNCOVERED																																																																																			NOVEL	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029699.2	7	3.007263	KEEP	2	0	0	10	272	TT	0.99254	0.138789	0		-	3	60	99	0	0	8.843583	6	60	185	30	ENST00000370205.5	0.333333	0.139832
ALG14	199857	__UNKNOWN__	__UNKNOWN__	1	95494122	95494122	__UNKNOWN__	Intron	SNP	C	C	T	rs61488063	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:95494122C>T	ENST00000370205.5	-	3	335					NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		acctgtaatgcgagcactctg	0.468		NA											c|||	228	0.0455272	0.084	0.0187	5008	,	,	NA	18184	0.0	NA	0.0408	False	NA	,,,	NA	NA	NA	2504	0.0644	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339	199857			28287	protein-coding gene	gene with protein product		612866	asparagine-linked glycosylation 14 homolog (yeast), asparagine-linked glycosylation 14 homolog (S. cerevisiae)		NA	15615718	Standard	NM_144988	NM_144988	NA	Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.289-1306G>A	chr1.hg19:g.95494122C>T		NA	A8K030	hg19	CCDS752.1	0.02	-0.11404	ATGxGAG	UNCOVERED																																																																																			NOVEL	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029699.2	4	2.707858	KEEP	0	0	0	9	269	CC	0.99254	0.161255	0		-	5	60	157	0	0	14.545348	7	60	238	35	ENST00000370205.5	0.416667	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	95566690	95566690	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:95566690T>C			NA	NA				ALG14 (28189 upstream) : TMEM56 (16203 downstream)						NA		NA									NA						gtcttgaacttctgacctcgt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.95566690T>C		NA		hg19		0.02	-0.096468	ACTxCTG	UNCOVERED																																																																																			NOVEL					0			4	3.608996	KEEP	2	0	0	12	329	TT	0.992708	0.119558	0			3	60	87	0	0	7.332399	8	60	236	38		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	95986461	95986461	__UNKNOWN__	IGR	SNP	C	C	T	rs4950063	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:95986461C>T			NA	NA				RP11-286B14.1 (5441 upstream) : RP11-286B14.2 (222190 downstream)						NA		NA									NA						ccgaggcgggcggatcacgag	0.527		NA											-|||	486	0.0970447	0.0151	0.1427	5008	,	,	NA	13236	0.0228	NA	0.1909	False	NA	,,,	NA	NA	NA	2504	0.1554	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.95986461C>T		NA		hg19		0.02	-0.131528	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			8	3.309084	KEEP	19	0	0	11	319	CC	0	0	0			7	60	194	0	0	18.234644	8	60	245	57		0.466667	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	96251981	96251981	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:96251981C>T			NA	NA				RP11-286B14.2 (26955 upstream) : AC092812.1 (100114 downstream)						NA		NA									NA						tgagccaccgcgcccggccAT	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.96251981C>T		NA		hg19		0.02	-0.184185	CCGxGCC	COVERED																																																																																			NOVEL					0			8	4.211046	KEEP	0	0	0	14	401	CC	0.995343	0.421506	0			3	60	89	0	0	6.661524	17	60	550	51		0.15	0.423478
DPYD	1806	__UNKNOWN__	__UNKNOWN__	1	97867143	97867143	__UNKNOWN__	Intron	SNP	T	T	C	rs12045421	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:97867143T>C	ENST00000370192.3	-	15	2006				DPYD-IT1_ENST00000424982.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	NA		NA			beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	ttgctgggattacaggtgtga	0.428		NA											t|||	1123	0.224241	0.1604	0.1369	5008	,	,	NA	18025	0.2192	NA	0.1968	False	NA	,,,	NA	NA	NA	2504	0.4059	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1806	1.3.1.2		3012	protein-coding gene	gene with protein product		612779			NA	7713523	Standard	NM_000110	NM_000110	NA	Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1906-19126A>G	chr1.hg19:g.97867143T>C		NA	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	hg19	CCDS30777.1	0.02	-0.061401	GATxACA	UNCOVERED																																																																																			NOVEL	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095698.3	2	2.404379	KEEP	0	0	0	8	207	TT	0.99257	0.043461	0		-	3	60	107	0	0	10.325581	3	60	87	22	ENST00000370192.3	0.5	0.043787
DPYD	1806	__UNKNOWN__	__UNKNOWN__	1	98349274	98349274	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:98349274G>A	ENST00000370192.3	-	2	140				DPYD_ENST00000423006.2_Intron|DPYD_ENST00000306031.5_Intron	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	NA		NA			beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	aagtgctggggttacaggtgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1806	1.3.1.2		3012	protein-coding gene	gene with protein product		612779			NA	7713523	Standard	NM_000110	NM_000110	NA	Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.40-344C>T	chr1.hg19:g.98349274G>A		NA	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	hg19	CCDS30777.1	0.02	1.517399	GGGxTTA	COVERED																																																																																			NOVEL	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095698.3	9	3.443144	KEEP	1	1	27	21	644	GG	0.999869	0.973838	0		-	5	60	152	0	0	10.6725	42	60	1419	104	ENST00000370192.3	0.106383	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	99799143	99799143	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:99799143C>T			NA	NA				LPPR4 (23997 upstream) : RP11-413P11.1 (138827 downstream)						NA		NA									NA						ggcgacagagcgagactccat	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.99799143C>T		NA		hg19		0.02	-0.166666	GAGxGAG	UNCOVERED																																																																																			NOVEL					0			7	2.707117	KEEP	7	0	0	9	262	CC	0	0	0			3	60	90	0	0	6.910349	15	60	502	50		0.166667	0.353947
AGL	178	__UNKNOWN__	__UNKNOWN__	1	100365444	100365444	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:100365444A>G	ENST00000294724.4	+	26	3840				AGL_ENST00000361302.3_Intron|AGL_ENST00000361915.3_Intron|AGL_ENST00000361522.4_Intron|AGL_ENST00000370163.3_Intron|AGL_ENST00000370165.3_Intron|AGL_ENST00000370161.2_Intron	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	NA		NA			carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ccaaagtgctaggattacagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	178	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	glycogen debranching enzyme, glycogen storage disease type III	610860	amylo-1, 6-glucosidase, 4-alpha-glucanotransferase		NA	1505983	Standard	NM_000028	NM_000028	NA	Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3363-748A>G	chr1.hg19:g.100365444A>G		NA	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	hg19	CCDS759.1	0.02	-0.149102	GCTxGGA	COVERED																																																																																			NOVEL	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000029778.1	10	3.305913	KEEP	0	0	0	11	286	AA	0.993072	0.289978	0		+	4	52	129	0	0	10.901716	12	60	355	39	ENST00000294724.4	0.25	0.292001
DBT	1629	__UNKNOWN__	__UNKNOWN__	1	100661512	100661512	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:100661512T>C	ENST00000370132.4	-	0	1761					NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	NA		NA			branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		tgagccaccatgcccggccTA	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992	1629			2698	protein-coding gene	gene with protein product		248610	dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)		NA	1420314, 1429740	Standard	NM_001918	NM_001918	NA	Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.*299A>G	chr1.hg19:g.100661512T>C		NA	B2R811|Q5VVL8	hg19	CCDS767.1	0.02	-0.438499	CCAxGCC	COVERED																																																																																			NOVEL	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030101.2	3	7.517889	KEEP	1	0	0	25	677	TT	0.999909	0.959772	0		-	3	60	100	1	0	6.647887	42	60	1226	105	ENST00000370132.4	0.066667	0.959859
DBT	1629	__UNKNOWN__	__UNKNOWN__	1	100694991	100694991	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:100694991A>G	ENST00000370132.4	-	4	447				DBT_ENST00000370131.3_Intron	NM_001918.3	NP_001909.3	P11182	ODB2_HUMAN	dihydrolipoamide branched chain transacylase E2	NA		NA			branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity (GO:0043754)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(1)	19		all_epithelial(167;5.4e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0739)|all cancers(265;0.123)|COAD - Colon adenocarcinoma(174;0.154)|Lung(183;0.199)		caaagtgctgagattacaggc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016675	CCDS767.1	1p31	2008-02-05	2004-11-15		ENSG00000137992	ENSG00000137992	1629			2698	protein-coding gene	gene with protein product		248610	dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease)		NA	1420314, 1429740	Standard	NM_001918	NM_001918	NA	Approved		uc001dta.3	P11182	OTTHUMG00000010921	ENST00000370132.4:c.433+1297T>C	chr1.hg19:g.100694991A>G		NA	B2R811|Q5VVL8	hg19	CCDS767.1	0.02	-0.210501	CTGxGAT	COVERED																																																																																			NOVEL	DBT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030101.2	6	3.30908	KEEP	4	0	0	11	316	AA	0.99254	0.518266	0		-	3	29	90	0	0	6.628269	19	60	579	57	ENST00000370132.4	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	102047916	102047916	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:102047916G>A			NA	NA				RP11-157N3.1 (192057 upstream) : RP11-411H5.1 (141381 downstream)						NA		NA									NA						tgatctgcccgccttggcctc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.102047916G>A		NA		hg19		0.02	-0.175444	CCCxCCT	COVERED																																																																																			NOVEL					0			9	2.707244	KEEP	1	0	0	9	258	GG	0.99254	0.420319	0			3	60	92	0	0	7.278839	13	60	434	46		0.1875	0.423478
RNPC3	55599	__UNKNOWN__	__UNKNOWN__	1	104076495	104076495	__UNKNOWN__	Intron	SNP	A	A	G	rs6702220	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:104076495A>G	ENST00000533099.1	+	4	595				RNPC3_ENST00000423855.2_Intron|RNPC3_ENST00000524631.1_Intron			Q96LT9	RBM40_HUMAN	RNA-binding region (RNP1, RRM) containing 3	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Lung(183;0.111)|Epithelial(280;0.122)|all cancers(265;0.125)|Colorectal(144;0.163)		TAGATCAGTAAATCATACATT	0.323		NA											.|||	3226	0.644169	0.8986	0.5519	5008	,	,	NA	15843	0.3661	NA	0.6431	False	NA	,,,	NA	NA	NA	2504	0.6534	NA	NA	NA								NA				0													42	32	35			NA	NA	1		NA											NA				104076495		692	1589	2281	SO:0001627	intron_variant			AB058742, AY099329	CCDS781.1	1p21.1	2013-07-16			ENSG00000185946	ENSG00000185946	55599		RNA binding motif (RRM) containing	18666	protein-coding gene	gene with protein product	U11/U12 snRNP 65K	NA			NA	14974681, 15146077	Standard	NM_017619	NM_017619	NA	Approved	KIAA1839, FLJ20008, RBM40, SNRNP65	uc010oun.2	Q96LT9	OTTHUMG00000166613	ENST00000533099.1:c.359+16A>G	chr1.hg19:g.104076495A>G		NA	A8K1C9|D3DT74|Q5TZ87|Q96FK7|Q96JI8|Q9NSU7|Q9NXX2	hg19	CCDS781.1	0.02	1.815408	GTAxATC	COVERED																																																																																			NOVEL	RNPC3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390812.1	3	2.405677	KEEP	0	0	0	8	214	AA	0.99257	0.966729	0		+	23	60	763	1	0	72.029685	28	60	819	90	ENST00000533099.1	0.45098	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	105121177	105121177	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:105121177A>G			NA	NA				RP11-364B6.1 (501468 upstream) : None (None downstream)						NA		NA									NA						tgggattacaagcgtgagcca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.105121177A>G		NA		hg19		0.02	-0.114032	ACAxGCG	UNCOVERED																																																																																			NOVEL					0			3	3.007734	KEEP	0	0	0	10	277	AA	0.992708	0.161282	0			3	60	106	0	0	8.981896	10	60	306	36		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	107494119	107494119	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:107494119G>C			NA	NA				RP11-233E12.1 (113330 upstream) : PRMT6 (105147 downstream)						NA		NA									NA						gaacctaggaggcagaggttg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.107494119G>C		NA		hg19		0.02	-0.105265	GGAxGCA	UNCOVERED																																																																																			NOVEL					0			4	2.707792	KEEP	1	0	0	9	267	GG	0.99254	0.138789	0			4	60	139	0	0	12.885704	6	60	194	28		0.4	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	109073468	109073468	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109073468C>G			NA	NA				NBPF6 (59844 upstream) : FAM102B (29242 downstream)						NA		NA									NA						gagttcgagaccagcctgggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.109073468C>G		NA		hg19		0.02	-0.149117	AGAxCAG	COVERED																																																																																			NOVEL					0			5	2.707903	KEEP	2	0	0	9	272	CC	0.99254	0.289823	0			3	60	105	0	0	8.578652	13	60	415	39		0.1875	0.292001
STXBP3	6814	__UNKNOWN__	__UNKNOWN__	1	109332424	109332424	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109332424G>A	ENST00000370008.3	+	12	1013					NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	NA		NA			blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		atggtggctcgtgcctgtaat	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266	6814			11446	protein-coding gene	gene with protein product		608339			NA	10194441	Standard	NM_007269	NM_007269	NA	Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.964-3780G>A	chr1.hg19:g.109332424G>A		NA	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	hg19	CCDS790.1	0.02	-0.184172	CTCxTGC	COVERED																																																																																			NOVEL	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030591.1	9	3.008645	KEEP	0	0	0	10	297	GG	0.992708	0.42039	0		+	3	60	93	0	0	7.37936	13	60	414	46	ENST00000370008.3	0.1875	0.423478
WDR47	22911	__UNKNOWN__	__UNKNOWN__	1	109568095	109568095	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109568095C>T	ENST00000369965.4	-	2	252				WDR47_ENST00000357672.3_Intron|WDR47_ENST00000369962.3_Intron|WDR47_ENST00000361054.3_Intron|WDR47_ENST00000400794.3_Intron	NM_001142550.1|NM_001142551.1|NM_014969.5	NP_001136022.1|NP_001136023.1|NP_055784.3	O94967	WDR47_HUMAN	WD repeat domain 47	NA		NA			multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		cagtggctcacacctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433	22911		WD repeat domain containing	29141	protein-coding gene	gene with protein product		615734			NA	10048485	Standard	NM_014969	NM_014969	NA	Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369965.4:c.9-1952G>A	chr1.hg19:g.109568095C>T		NA	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	hg19	CCDS30787.1	0.02	-0.131571	TCAxACC	COVERED																																																																																			NOVEL	WDR47-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032413.2	9	3.608082	KEEP	1	0	0	12	345	CC	0.993072	0.227586	0		-	3	60	83	0	0	6.472581	12	60	392	36	ENST00000369965.4	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	109619199	109619199	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109619199T>G			NA	NA				TAF13 (575 upstream) : RP5-1065J22.8 (11393 downstream)						NA		NA									NA						tgattctccttcctcagcctc	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.109619199T>G		NA		hg19		0.02	-0.122776	CCTxCCT	COVERED																																																																																			NOVEL					0			7	3.006537	KEEP	0	0	0	10	263	TT	0.992708	0.19488	0			3	60	97	0	0	8.082333	10	60	288	31		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	109645714	109645714	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109645714A>G			NA	NA				SCARNA2 (2480 upstream) : C1orf194 (2858 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.109645714A>G		NA		hg19		0.02	-0.166634	GGCxTGA	COVERED																																																																																			NOVEL					0			7	3.007529	KEEP	0	0	0	10	278	AA	0.993072	0.351495	0			3	60	105	0	0	8.578926	13	60	373	42		0.1875	0.353947
KIAA1324	57535	__UNKNOWN__	__UNKNOWN__	1	109725476	109725476	__UNKNOWN__	Intron	SNP	A	A	G	rs620127	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109725476A>G	ENST00000369939.3	+	8	1135				KIAA1324_ENST00000529753.1_Intron	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	NA		NA			cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		gcaacagagcaagactccatc	0.473		NA											G|||	4219	0.842452	0.6861	0.8559	5008	,	,	NA	10669	0.997	NA	0.833	False	NA	,,,	NA	NA	NA	2504	0.8947	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299	57535			29618	protein-coding gene	gene with protein product	estrogen induced gene 121	611298			NA	10718198, 16322283	Standard	NM_020775	NM_020775	NA	Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.953-2191A>G	chr1.hg19:g.109725476A>G		NA	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	hg19	CCDS794.1	0.02	-0.061401	AGCxAGA	UNCOVERED																																																																																			NOVEL	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032389.2	6	2.406373	KEEP	9	0	0	8	225	AA	0	0	0		+	6	60	190	0	0	20.615243	1	5	29	28	ENST00000369939.3	0.857143	0.043787
CELSR2	1952	__UNKNOWN__	__UNKNOWN__	1	109816189	109816189	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs41279720	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109816189C>T	ENST00000271332.3	+	33	8702	c.8641C>T	c.(8641-8643)Cgc>Tgc	p.R2881C	CELSR2_ENST00000498157.1_3'UTR	NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2881		NA			cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		CCCCCCTCCCCGCCCACCGCC	0.697		NA											C|||	55	0.0109824	0.0023	0.0072	5008	,	,	NA	11521	0.0	NA	0.0229	False	NA	,,,	NA	NA	NA	2504	0.0245	NA	NA	NA	NSCLC(158;1285 2011 34800 34852 42084)							NA				0								C	CYS/ARG	12,4158		0,12,2073	9	12	11		8641	4.5	1	1	dbSNP_127	11	187,8167		2,183,3992	no	missense	CELSR2	NM_001408.2	180	2,195,6065	TT,TC,CC	NA	2.2384,0.2878,1.5889	possibly-damaging	2881/2924	109816189	199,12325	2085	4177	6262	SO:0001583	missense			D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126	1952		Cadherins / Major cadherins, -, GPCR / Class B : Orphans	3231	protein-coding gene	gene with protein product		604265	cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog	EGFL2	NA	9693030, 10907856	Standard	NM_001408	NM_001408	NA	Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.8641C>T	chr1.hg19:g.109816189C>T	ENSP00000271332:p.Arg2881Cys	NA	Q5T2Y7|Q92566	hg19	CCDS796.1	0.02	1.634188	CCCxGCC	COVERED	30	0.013736263736263736	8	0.016260162601626018	4	0.011049723756906077	1	0.0017482517482517483	17	0.022427440633245383	C	16.03	3.008214	0.54361	0.002878	0.022384	ENSG00000143126	ENST00000271332	T	0.70631	-0.5	4.54	4.54	0.55810	.	.	.	.	.	T	0.39682	0.1087	N	0.22421	0.69	0.47245	D	0.999363	D	0.63880	0.993	B	0.32928	0.155	T	0.56745	-0.7928	9	0.72032	D	0.01	.	14.8172	0.70045	0.0:1.0:0.0:0.0	rs41279720	2881	Q9HCU4	CELR2_HUMAN	C	2881	ENSP00000271332:R2881C	ENSP00000271332:R2881C	R	+	1	0	CELSR2	109617712	0.838000	0.29461	1.000000	0.80357	0.992000	0.81027	2.066000	0.41452	2.349000	0.79799	0.561000	0.74099	CGC	NOVEL	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033200.1	0	3.609384	KEEP	0	0	0	12	345	CC	0.993634	0.961266	0		+	25	60	730	0	0	69.572478	26	60	832	72	ENST00000271332.3	0.490196	0.967425
SORT1	6272	__UNKNOWN__	__UNKNOWN__	1	109864811	109864811	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:109864811C>T	ENST00000256637.6	-	15	2083				SORT1_ENST00000538502.1_Intron	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	NA		NA			endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		ccacccgcctcggcctcccaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243	6272			11186	protein-coding gene	gene with protein product		602458			NA		Standard	NM_002959	NM_002959	NA	Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.2024+742G>A	chr1.hg19:g.109864811C>T		NA	B4DWI3|C0JYZ0|Q8IZ49	hg19	CCDS798.1	0.02	-0.096483	CCTxGGC	UNCOVERED																																																																																			NOVEL	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033179.1	10	3.609865	KEEP	1	0	0	12	350	CC	0.993072	0.119602	0		-	3	60	88	0	0	7.578405	7	60	220	29	ENST00000256637.6	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	110347907	110347907	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:110347907T>C			NA	NA				RP4-735C1.4 (30033 upstream) : RP4-735C1.6 (23069 downstream)						NA		NA									NA						gctgggattataggtgtgagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.110347907T>C		NA		hg19		0.02	-0.201706	TTAxAGG	COVERED																																																																																			NOVEL					0			8	3.306731	KEEP	1	0	0	11	287	TT	0.993072	0.487146	0			3	60	96	0	0	7.292548	18	60	510	50		0.142857	0.490544
RP5-1074L1.1	0	__UNKNOWN__	__UNKNOWN__	1	110858601	110858601	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:110858601A>G	ENST00000449169.1	-	0	293					NR_036595.1					NA		NA									NA						gctcacgcctataatcccagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000449169.1:	chr1.hg19:g.110858601A>G		NA		hg19		0.02	-0.228033	CCTxTAA	COVERED																																																																																			NOVEL	RP5-1074L1.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000031113.1	9	3.607896	KEEP	1	0	0	12	316	AA	0.993072	0.578892	0		-	3	60	107	0	0	8.205315	21	60	616	53	ENST00000449169.1	0.125	0.58293
SLC16A4	9122	__UNKNOWN__	__UNKNOWN__	1	110906187	110906187	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:110906187A>G	ENST00000472422.2	-	0	1714				SLC16A4_ENST00000369781.4_3'UTR|SLC16A4_ENST00000369779.4_3'UTR	NM_001201546.1	NP_001188475.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	NA		NA			monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	ggcggagattacagtgagccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679	9122		Solute carriers	10925	protein-coding gene	gene with protein product		603878	solute carrier family 16 (monocarboxylic acid transporters), member 4, solute carrier family 16, member 4 (monocarboxylic acid transporter 5)		NA	9425115	Standard	NM_004696	NM_004696	NA	Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000472422.2:c.*201T>C	chr1.hg19:g.110906187A>G		NA	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	hg19	CCDS55623.1	0.02	1.742531	ATTxCAG	COVERED																																																																																			NOVEL	SLC16A4-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000031955.3	7	2.468035	KEEP	1	2	56	28	740	AA	0.999997	0.963771	0		-	4	58	129	0	0	9.032639	39	60	1091	87	ENST00000472422.2	0.093023	0.963774
FAM212B	55924	__UNKNOWN__	__UNKNOWN__	1	112269352	112269352	__UNKNOWN__	3'UTR	SNP	C	C	T	rs189860232|rs138918319	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:112269352C>T	ENST00000357260.5	-	0	1313				FAM212B_ENST00000444059.2_3'UTR|FAM212B_ENST00000534365.1_Intron	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	NA		NA								cervix(1)|endometrium(1)	2						cacacacacacgcacaGCTCA	0.562		NA											C|||	20	0.00399361	0.0151	0.0	5008	,	,	NA	17670	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852	55924			28045	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 183	C1orf183	NA		Standard	NM_019099	NM_019099	NA	Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.*238G>A	chr1.hg19:g.112269352C>T		NA	B3KP38|B4DF94|Q9NTI6	hg19	CCDS841.1	0.02	2.662286	ACAxGCA	COVERED																																																																																			NOVEL	FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033060.2	38	23.331782	KEEP	0	2	52	96	2861	CC	1	1	0		-	6	60	174	0	0	10.121197	106	60	3441	331	ENST00000357260.5	0.053571	1
CAPZA1	829	__UNKNOWN__	__UNKNOWN__	1	113170281	113170281	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:113170281A>C	ENST00000263168.3	+	1	711				CAPZA1_ENST00000476936.1_Intron	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	NA		NA			actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		aaaaaaaaaaaaaaaaaaGAA	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489	829			1488	protein-coding gene	gene with protein product		601580			NA	7665558, 9119363	Standard	NM_006135	NM_006135	NA	Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.39+7776A>C	chr1.hg19:g.113170281A>C		NA	Q53FQ6|Q6FHD5	hg19	CCDS30805.1	0.02	-0.122771	AAAxAAA	UNCOVERED																																																																																			NOVEL	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032567.2	11	2.405625	KEEP	6	0	0	8	212	AA	0	0	0		+	3	60	103	0	0	9.655523	4	60	116	42	ENST00000263168.3	0.428571	0.196312
MOV10	4343	__UNKNOWN__	__UNKNOWN__	1	113224805	113224805	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:113224805T>C	ENST00000413052.2	+	3	527				MOV10_ENST00000369644.1_Intron|MOV10_ENST00000357443.2_Intron|MOV10_ENST00000369645.1_Intron|MOV10_ENST00000544796.1_Intron|MOV10_ENST00000468624.1_Intron	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		gcgtgagccatcgcgcccggc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363	4343			7200	protein-coding gene	gene with protein product	functional spliceosome-associated protein 113	610742	Mov10 (Moloney leukemia virus 10, mouse) homolog, Mov10, Moloney leukemia virus 10, homolog (mouse)		NA	12226669	Standard	NM_020963	NM_001286072	NA	Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.138-6752T>C	chr1.hg19:g.113224805T>C		NA	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	hg19	CCDS853.1	0.02	-0.192935	CCAxCGC	COVERED																																																																																			NOVEL	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032906.1	11	2.404601	KEEP	2	0	0	8	210	TT	0.99257	0.454356	0		+	3	60	103	0	0	8.060924	17	60	499	43	ENST00000413052.2	0.15	0.457757
RP3-522D1.1	0	__UNKNOWN__	__UNKNOWN__	1	113393943	113393943	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:113393943C>T	ENST00000456651.1	+	0	400										NA		NA									NA						ggtgacagagcgagactctgt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000456651.1:	chr1.hg19:g.113393943C>T		NA		hg19		0.02	-0.149103	GAGxGAG	COVERED																																																																																			NOVEL	RP3-522D1.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000033261.1	8	2.707726	KEEP	2	0	0	9	273	CC	0.99254	0.289823	0		+	3	40	87	0	1	6.972951	11	60	365	43	ENST00000456651.1	0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	113431832	113431832	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:113431832T>C			NA	NA				RP3-522D1.1 (11339 upstream) : SLC16A1 (22636 downstream)						NA		NA									NA						cacctgtaattccagcccttt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.113431832T>C		NA		hg19		0.02	-0.122786	AATxCCA	COVERED																																																																																			NOVEL					0			4	3.007183	KEEP	1	0	0	10	272	TT	0.992708	0.19488	0			3	60	105	0	0	9.132743	8	60	230	35		0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	113551523	113551523	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:113551523A>G			NA	NA				RP11-31F15.1 (9405 upstream) : RP11-31F15.2 (2785 downstream)						NA		NA									NA						gcctcccaaaatgctgggatt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.113551523A>G		NA		hg19		0.02	-0.140342	AAAxTGC	COVERED																																																																																			NOVEL					0			6	3.003288	KEEP	1	0	0	10	266	AA	0.99254	0.259018	0			3	60	104	0	0	8.672838	11	60	330	36		0.214286	0.260965
LRIG2	9860	__UNKNOWN__	__UNKNOWN__	1	113667589	113667589	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:113667589G>C	ENST00000361127.5	+	0	4262				LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	NA		NA			innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		ttgagaccaggctgggcaaca	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799	9860		Immunoglobulin superfamily / I-set domain containing	20889	protein-coding gene	gene with protein product		608869			NA		Standard	NM_014813	XM_005271369	NA	Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.*866G>C	chr1.hg19:g.113667589G>C		NA	Q9NSN2	hg19	CCDS30808.1	0.02	5.780271	CAGxCTG	COVERED																																																																																			NOVEL	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033549.2	66	30.125778	KEEP	2	4	125	144	4454	GG	1	1	0		+	7	60	223	0	0	13.563348	134	60	4611	465	ENST00000361127.5	0.049645	1
PHTF1	10745	__UNKNOWN__	__UNKNOWN__	1	114268324	114268324	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:114268324G>A	ENST00000369604.1	-	6	972				PHTF1_ENST00000357783.2_Intron|PHTF1_ENST00000369598.1_Intron|PHTF1_ENST00000393357.2_Intron|PHTF1_ENST00000447664.2_Intron|PHTF1_ENST00000369596.2_Intron|PHTF1_ENST00000369600.1_Intron			Q9UMS5	PHTF1_HUMAN	putative homeodomain transcription factor 1	NA		NA			transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		agtggctcacgcctgtaatcc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ011863	CCDS861.1	1p13-p11	2008-07-18			ENSG00000116793	ENSG00000116793	10745			8939	protein-coding gene	gene with protein product		604950		PHTF	NA	10395808	Standard	NM_006608	NM_006608	NA	Approved		uc009wgp.1	Q9UMS5	OTTHUMG00000011800	ENST00000369604.1:c.488+715C>T	chr1.hg19:g.114268324G>A		NA	Q5VWP7|Q5VWP8|Q9BUP2|Q9H1X8	hg19	CCDS861.1	0.02	-0.105237	CACxCCT	UNCOVERED																																																																																			NOVEL	PHTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032666.1	4	3.007901	KEEP	0	0	0	10	286	GG	0.992708	0.138812	0		-	3	60	83	0	0	6.932172	8	60	247	26	ENST00000369604.1	0.272727	0.139832
RSBN1	54665	__UNKNOWN__	__UNKNOWN__	1	114349534	114349534	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:114349534T>C	ENST00000261441.5	-	1	767					NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	NA		NA				nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		actcaggaggttgaggtggga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019	54665			25642	protein-coding gene	gene with protein product		615858			NA	12477932	Standard	NM_018364	NM_018364	NA	Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.703+4797A>G	chr1.hg19:g.114349534T>C		NA	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	hg19	CCDS862.1	0.02	-0.22801	AGGxTGA	COVERED																																																																																			NOVEL	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033022.2	11	2.705258	KEEP	0	0	0	9	231	TT	0.99254	0.578582	0		-	3	60	92	0	0	6.650687	22	60	649	38	ENST00000261441.5	0.12	0.58293
PTPN22	26191	__UNKNOWN__	__UNKNOWN__	1	114383612	114383612	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:114383612T>C	ENST00000359785.5	-	12	1051				PTPN22_ENST00000528414.1_Intron|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000538253.1_Intron|PTPN22_ENST00000420377.2_Intron|PTPN22_ENST00000525799.1_Intron	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	NA		NA			negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		tttgggaggctgaggcgggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242	26191		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	9652	protein-coding gene	gene with protein product		600716	protein tyrosine phosphatase, non-receptor type 8	PTPN8	NA	10068674, 1373816	Standard	NM_015967	NM_015967	NA	Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.916-2370A>G	chr1.hg19:g.114383612T>C		NA	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	hg19	CCDS863.1	0.02	-0.219283	GGCxGAG	COVERED																																																																																			NOVEL	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033015.1	17	5.413039	KEEP	9	0	0	18	494	TT	0.995343	0.550313	0		-	3	60	94	0	0	6.905963	21	60	644	69	ENST00000359785.5	0.125	0.552887
AP4B1-AS1	100287722	__UNKNOWN__	__UNKNOWN__	1	114432100	114432100	__UNKNOWN__	RNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:114432100T>G	ENST00000419536.1	+	0	246					NR_037864.1				AP4B1 antisense RNA 1	NA		NA									NA						ggaggcggagtttgcagtgag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK123199		1p13.2	2012-10-12	2012-08-15		ENSG00000226167	ENSG00000226167	100287722		Long non-coding RNAs	44114	non-coding RNA	RNA, long non-coding		NA	AP4B1 antisense RNA 1 (non-protein coding)		NA		Standard	NR_037864	NR_037864	NA	Approved		uc001edv.2		OTTHUMG00000011941	ENST00000419536.1:	chr1.hg19:g.114432100T>G		NA		hg19		0.02	-0.228019	GAGxTTG	COVERED																																																																																			NOVEL	AP4B1-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000033027.1	8	2.706537	KEEP	0	0	0	9	244	TT	0.99254	0.578582	0		+	4	60	111	0	0	8.570487	17	60	505	43	ENST00000419536.1	0.190476	0.58293
HIPK1	204851	__UNKNOWN__	__UNKNOWN__	1	114482934	114482934	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:114482934T>G	ENST00000369558.1	+	2	230				HIPK1_ENST00000369555.2_Intron|HIPK1_ENST00000426820.2_Intron|HIPK1_ENST00000369559.4_Intron|HIPK1_ENST00000369561.4_Intron|HIPK1_ENST00000369554.2_Intron			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	NA		NA			anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTGTGTGTGTTTGTGTGTTTT	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349	204851			19006	protein-coding gene	gene with protein product		608003			NA		Standard	NM_198268	NM_198268	NA	Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.-2-70T>G	chr1.hg19:g.114482934T>G		NA	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	hg19	CCDS867.1	0.02	1.827365	TGTxTGT	COVERED																																																																																			NOVEL	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033127.1	9	4.769716	KEEP	0	2	57	36	930	TT	1	0.992926	0		+	5	60	172	0	0	12.004378	58	60	1642	130	ENST00000369558.1	0.079365	0.992926
TRIM33	51592	__UNKNOWN__	__UNKNOWN__	1	114939697	114939697	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:114939697T>C	ENST00000358465.2	-	0	4040					NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	NA		NA			gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTATATCAATTTAAAAACTA	0.318		NA	T	RET	papillary thyroid																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p13	51592	 tripartite motif-containing 33 (PTC7,TIF1G)		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323	51592		Tripartite motif containing / Tripartite motif containing, Zinc fingers, PHD-type, RING-type (C3HC4) zinc fingers	16290	protein-coding gene	gene with protein product	transcriptional intermediary factor 1 gamma, ret-fused gene 7	605769	tripartite motif-containing 33		NA	11331580, 10022127	Standard	NM_015906	XM_005270936	NA	Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.*573A>G	chr1.hg19:g.114939697T>C		NA	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	hg19	CCDS872.1	0.02	1.844811	CAAxTTA	COVERED																																																																																			NOVEL	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032854.1	2	4.210908	KEEP	0	0	0	14	390	TT	0.995343	0.986349	0		-	14	60	454	0	0	37.81183	47	60	1432	112	ENST00000358465.2	0.229508	0.990964
TRIM33	51592	__UNKNOWN__	__UNKNOWN__	1	115043632	115043632	__UNKNOWN__	Intron	SNP	A	A	G	rs10858045		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:115043632A>G	ENST00000358465.2	-	1	610				TRIM33_ENST00000369543.2_Intron	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	NA		NA			gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ctaacacggtaaaaccccgtc	0.602		NA	T	RET	papillary thyroid																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1p13	51592	 tripartite motif-containing 33 (PTC7,TIF1G)		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323	51592		Tripartite motif containing / Tripartite motif containing, Zinc fingers, PHD-type, RING-type (C3HC4) zinc fingers	16290	protein-coding gene	gene with protein product	transcriptional intermediary factor 1 gamma, ret-fused gene 7	605769	tripartite motif-containing 33		NA	11331580, 10022127	Standard	NM_015906	XM_005270936	NA	Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.526+9539T>C	chr1.hg19:g.115043632A>G		NA	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	hg19	CCDS872.1	0.02	-0.060406	GGTxAAA	UNCOVERED																																																																																			NOVEL	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032854.1	5	2.40532	KEEP	7	0	0	8	210	AA	0	0	0		-	4	40	128	0	0	13.136942	2	40	33	23	ENST00000358465.2	0.666667	0.043787
DENND2C	163259	__UNKNOWN__	__UNKNOWN__	1	115156652	115156652	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:115156652A>G	ENST00000393276.3	-	6	1486				DENND2C_ENST00000393277.1_Intron|DENND2C_ENST00000393274.1_Intron|DENND2C_ENST00000481894.1_Intron	NM_198459.3	NP_940861.3	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	NA		NA			positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ccaggaattcaagaccagcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984	163259		DENN/MADD domain containing	24748	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198459	NM_198459	NA	Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393276.3:c.1154-2914T>C	chr1.hg19:g.115156652A>G		NA	B1AL26|Q5TCX6|Q6P3R3	hg19	CCDS875.1	0.02	-0.114018	TTCxAGA	UNCOVERED																																																																																			NOVEL	DENND2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032863.2	4	2.405354	KEEP	0	0	0	8	212	AA	0.99257	0.16126	0		-	3	60	96	0	0	8.101306	9	60	262	27	ENST00000393276.3	0.25	0.162467
VANGL1	81839	__UNKNOWN__	__UNKNOWN__	1	116227048	116227048	__UNKNOWN__	Intron	SNP	A	A	T	rs10923186	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:116227048A>T	ENST00000355485.2	+	6	1350				VANGL1_ENST00000369510.4_Intron|VANGL1_ENST00000310260.3_Intron|VANGL1_ENST00000369509.1_Intron	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	NA		NA			multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|liver(2)|lung(13)|urinary_tract(1)	27	Lung SC(450;0.211)	all_cancers(81;1.24e-06)|all_epithelial(167;1.02e-06)|all_lung(203;7.95e-06)|Lung NSC(69;4.97e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		ggcatgagccaccatgcccgg	0.488		NA											A|||	2254	0.45008	0.5113	0.4957	5008	,	,	NA	14956	0.3244	NA	0.4473	False	NA	,,,	NA	NA	NA	2504	0.4673	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075805	CCDS883.1, CCDS53350.1	1p13.1	2013-03-05	2013-03-05		ENSG00000173218	ENSG00000173218	81839			15512	protein-coding gene	gene with protein product		610132	vang (van gogh, Drosophila)-like 1, vang, van gogh-like 1 (Drosophila), vang-like 1 (van gogh, Drosophila)		NA	11956595, 12011995	Standard		NM_001172411	NA	Approved	STB2	uc001efv.1	Q8TAA9	OTTHUMG00000011971	ENST00000355485.2:c.1079+351A>T	chr1.hg19:g.116227048A>T		NA	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	hg19	CCDS883.1	0.02	-0.087691	GCCxCCA	UNCOVERED																																																																																			NOVEL	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033096.1	2	3.006233	KEEP	0	0	0	10	265	AA	0.992708	0.098994	0		+	3	60	97	0	0	8.833283	5	60	144	26	ENST00000355485.2	0.375	0.099721
CASQ2	845	__UNKNOWN__	__UNKNOWN__	1	116278537	116278537	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:116278537T>C	ENST00000261448.5	-	4	772				CASQ2_ENST00000456138.2_Intron	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	NA		NA			cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		aatcccagcattttgggaggc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729	845		Protein disulfide isomerases	1513	protein-coding gene	gene with protein product		114251			NA	8406504	Standard	NM_001232	NM_001232	NA	Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.532+2307A>G	chr1.hg19:g.116278537T>C		NA	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	hg19	CCDS884.1	0.02	-0.061401	GCAxTTT	UNCOVERED																																																																																			NOVEL	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033091.1	6	2.405527	KEEP	3	0	0	8	214	TT	0	0	0		-	3	60	98	0	0	9.425183	3	60	89	21	ENST00000261448.5	0.5	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	116772246	116772246	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:116772246G>A			NA	NA				RP5-1185H19.2 (63384 upstream) : U3 (48981 downstream)						NA		NA									NA						aaaaaaaaaagaaaaagaaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.116772246G>A		NA		hg19		0.02	-0.122762	AAAxAAA	COVERED																																																																																			NOVEL					0			9	3.007652	KEEP	1	0	0	10	289	GG	0.992708	0.19488	0			3	60	79	0	0	6.678059	7	60	218	35		0.3	0.196312
TTF2	8458	__UNKNOWN__	__UNKNOWN__	1	117639027	117639027	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:117639027T>C	ENST00000369466.4	+	20	3230					NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	NA		NA			ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		gagacggagttttgctcttgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830	8458			12398	protein-coding gene	gene with protein product	zinc finger, GRF-type containing 6	604718			NA	9748214	Standard		NM_003594	NA	Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3186+106T>C	chr1.hg19:g.117639027T>C		NA	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	hg19	CCDS892.1	0.02	-0.245559	AGTxTTG	COVERED																																																																																			NOVEL	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033277.3	8	7.517431	KEEP	0	0	0	25	676	TT	0.999931	0.641303	0		+	3	60	104	0	0	7.905508	21	60	606	70	ENST00000369466.4	0.125	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120192034	120192034	__UNKNOWN__	IGR	SNP	G	G	A	rs587679201	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:120192034G>A			NA	NA				ZNF697 (1638 upstream) : PHGDH (62475 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.512		NA											G|||	14	0.00279553	0.0	0.0	5008	,	,	NA	16431	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0143	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120192034G>A		NA		hg19		0.02	-0.184187	CACxCCT	COVERED																																																																																			NOVEL					0			6	3.30955	KEEP	0	0	0	11	332	GG	0.993072	0.420544	0			3	60	89	0	0	6.592896	18	60	562	52		0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120625896	120625896	__UNKNOWN__	IGR	SNP	G	G	C	rs28516010		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:120625896G>C			NA	NA				RP11-114O18.1 (6198 upstream) : RNU6-465P (43665 downstream)						NA		NA									NA						ggtattacaggtgtgagccac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120625896G>C		NA		hg19		0.02	-0.342139	CAGxTGT	COVERED																																																																																			NOVEL					0			11	4.813984	KEEP	2	0	0	16	481	GG	0.99649	0.862707	0			5	60	177	0	0	14.138291	26	60	897	89		0.16129	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120752299	120752299	__UNKNOWN__	IGR	SNP	A	A	G	rs563035		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:120752299A>G			NA	NA				RP6-42F4.1 (55153 upstream) : RP11-439A17.7 (83510 downstream)						NA		NA									NA						caatgcaggcagaccacgagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120752299A>G		NA		hg19		0.02	-0.122784	GGCxGAC	COVERED																																																																																			NOVEL					0			9	2.405867	KEEP	0	0	0	8	219	AA	0.99257	0.194853	0			3	49	86	0	0	6.873217	11	60	328	27		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120758159	120758159	__UNKNOWN__	IGR	SNP	T	T	A	rs201241660	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:120758159T>A			NA	NA				RP6-42F4.1 (61013 upstream) : RP11-439A17.7 (77650 downstream)						NA		NA									NA						tctcacttggttgcccaggct	0.443		NA											.|||	2476	0.494409	0.5015	0.4856	5008	,	,	NA	17406	0.505	NA	0.4901	False	NA	,,,	NA	NA	NA	2504	0.4847	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120758159T>A		NA		hg19		0.02	-0.078923	TGGxTGC	UNCOVERED																																																																																			NOVEL					0			5	2.405757	KEEP	6	0	0	8	215	TT	0	0	0			3	59	81	0	0	7.23211	5	60	149	29		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	120767443	120767443	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:120767443T>C			NA	NA				RP6-42F4.1 (70297 upstream) : RP11-439A17.7 (68366 downstream)						NA		NA									NA						cctcctgccttggcctcccaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.120767443T>C		NA		hg19		0.02	1.888725	CCTxGGC	COVERED																																																																																			NOVEL					0			37	9.31901	KEEP	25	0	0	31	836	TT	0.999869	0.984032	0			4	60	126	0	0	8.323142	50	60	1454	144		0.074074	0.984161
RP11-343N15.1	0	__UNKNOWN__	__UNKNOWN__	1	121110033	121110033	__UNKNOWN__	lincRNA	SNP	G	G	A	rs10903167		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121110033G>A	ENST00000437515.1	-	0	329					NR_104189.1					NA		NA									NA						gggaggctgaggtgggcggat	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437515.1:	chr1.hg19:g.121110033G>A		NA		hg19		0.02	-0.289452	TGAxGTG	COVERED																																																																																			NOVEL	RP11-343N15.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000098477.2	9	4.513579	KEEP	1	0	0	15	466	GG	0.995343	0.757343	0		-	5	49	152	0	0	11.717371	25	60	805	66	ENST00000437515.1	0.166667	0.760887
RP11-343N15.1	0	__UNKNOWN__	__UNKNOWN__	1	121110039	121110039	__UNKNOWN__	lincRNA	SNP	C	C	T	rs10903166		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121110039C>T	ENST00000437515.1	-	0	329					NR_104189.1					NA		NA									NA						ctgaggtgggcggatcatgag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437515.1:	chr1.hg19:g.121110039C>T		NA		hg19		0.02	-0.26306	GGGxGGA	COVERED																																																																																			NOVEL	RP11-343N15.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000098477.2	8	4.211394	KEEP	1	0	0	14	410	CC	0.995343	0.690438	0		-	4	60	123	0	0	9.363202	22	60	669	60	ENST00000437515.1	0.153846	0.693668
RP11-343N15.1	0	__UNKNOWN__	__UNKNOWN__	1	121117469	121117469	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121117469A>G	ENST00000437515.1	-	0	329					NR_104189.1					NA		NA									NA						ccaaagtgctaggattacagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437515.1:	chr1.hg19:g.121117469A>G		NA		hg19		0.02	-0.254355	GCTxGGA	COVERED																																																																																			NOVEL	RP11-343N15.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000098477.2	9	3.909197	KEEP	0	0	0	13	354	AA	0.994391	0.664773	0		-	3	60	106	0	0	8.048579	22	60	660	59	ENST00000437515.1	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121484126	121484126	__UNKNOWN__	IGR	SNP	C	C	G	rs139896483|rs147283747		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121484126C>G			NA	NA				RP11-344P13.1 (161804 upstream) : None (None downstream)						NA		NA									NA						ttgaacgatcctttacacaga	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121484126C>G		NA		hg19		0.02	9.13824	ATCxTTT	COVERED																																																																																			NOVEL					0			182	37.380934	KEEP	119	5	156	179	5537	CC	1	1	0			8	51	266	0	0	15.968183	185	60	6369	873		0.041451	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121484133	121484133	__UNKNOWN__	IGR	SNP	C	C	G	rs149012018		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121484133C>G			NA	NA				RP11-344P13.1 (161811 upstream) : None (None downstream)						NA		NA									NA						atcctttacacagagcagact	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121484133C>G		NA		hg19		0.02	10.42442	ACAxAGA	COVERED																																																																																			NOVEL					0			172	3.685084	KEEP	104	14	423	161	5003	CC	1	1	0			12	49	427	0	0	28.692026	189	60	6578	832		0.059701	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121484945	121484945	__UNKNOWN__	IGR	SNP	T	T	C	rs71297459|rs59009300	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121484945T>C			NA	NA				RP11-344P13.1 (162623 upstream) : None (None downstream)						NA		NA									NA						tgcgttgtgatgtgtttgttc	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121484945T>C		NA		hg19		0.02	11.23891	TGAxGTG	COVERED																																																																																			NOVEL					0			52	17.498827	KEEP	8	8	229	139	3845	TT	1	1	0			14	60	451	0	0	28.759986	221	60	6552	690		0.059574	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121484957	121484957	__UNKNOWN__	IGR	SNP	A	A	T	rs56300744|rs71299595	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121484957A>T			NA	NA				RP11-344P13.1 (162635 upstream) : None (None downstream)						NA		NA									NA						tgtttgttcaactcacagagt	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121484957A>T		NA		hg19		0.02	9.511085	TCAxCTC	COVERED																																																																																			NOVEL					0			46	5.650751	KEEP	6	11	300	125	3339	AA	1	1	0			13	60	398	0	0	24.555436	208	60	6122	681		0.058824	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485140	121485140	__UNKNOWN__	IGR	SNP	C	C	T	rs36174284|rs74222711|rs67228163	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121485140C>T			NA	NA				RP11-344P13.1 (162818 upstream) : None (None downstream)						NA		NA									NA						cagagttgaacgatcctttac	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485140C>T		NA		hg19		0.02	24.255141	GAAxGAT	COVERED																																																																																			NOVEL					0			191	115.889118	KEEP	86	28	759	654	19137	CC	1	1	0			30	60	851	0	1	49.366139	504	60	16231	1997		0.05618	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485152	121485152	__UNKNOWN__	IGR	SNP	C	C	G	rs74189293|rs74222610|rs4092802|rs67605471	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121485152C>G			NA	NA				RP11-344P13.1 (162830 upstream) : None (None downstream)						NA		NA									NA						atcctttacacagagcagact	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485152C>G		NA		hg19		0.02	32.029978	ACAxAGA	COVERED																																																																																			NOVEL					0			193	28.311437	KEEP	72	55	1654	676	20510	CC	1	1	0			29	60	970	2	0	61.604732	519	60	17487	1998		0.05292	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485269	121485269	__UNKNOWN__	IGR	SNP	G	G	T	rs7414888|rs28973235		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121485269G>T			NA	NA				RP11-344P13.1 (162947 upstream) : None (None downstream)						NA		NA									NA						atgattctcagaaactccttt	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485269G>T		NA		hg19		0.02	23.042281	TCAxAAA	COVERED																																																																																			NOVEL					0			157	111.581376	KEEP	91	38	990	722	21634	GG	1	1	0			26	60	723	0	0	41.57055	429	60	14447	1992		0.057143	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485354	121485354	__UNKNOWN__	IGR	SNP	G	G	C	rs1138156		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121485354G>C			NA	NA				RP11-344P13.1 (163032 upstream) : None (None downstream)						NA		NA									NA						tgtttgtaaagtctgcaagtg	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485354G>C		NA		hg19		0.02	29.791364	AAAxTCT	COVERED																																																																																			NOVEL					0			231	53.326499	KEEP	81	38	1175	590	17960	GG	1	1	0			22	60	752	0	0	45.741093	521	60	17792	1921		0.040516	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	121485422	121485422	__UNKNOWN__	IGR	SNP	G	G	T	rs28971216|rs7414925		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:121485422G>T			NA	NA				RP11-344P13.1 (163100 upstream) : None (None downstream)						NA		NA									NA						tattctgctagacagaagAAT	0.234		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.121485422G>T		NA		hg19		0.02	7.141772	CTAxACA	COVERED																																																																																			NOVEL					0			107	21.186223	KEEP	29	10	273	167	4967	GG	1	1	0			9	60	257	0	0	14.40167	176	60	5745	625		0.048649	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142598484	142598484	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142598484G>C			NA	NA				RP11-417J8.2 (10251 upstream) : RP11-417J8.3 (20638 downstream)						NA		NA									NA						gggaggcttaggtgtgcggat	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142598484G>C		NA		hg19		0.02	-0.184224	TTAxGTG	COVERED																																																																																			NOVEL					0			21	3.142762	KEEP	8	1	27	20	630	GG	0.997832	0.422559	0			3	21	102	0	0	8.371958	12	60	410	58		0.2	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142599657	142599657	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142599657G>A			NA	NA				RP11-417J8.2 (11424 upstream) : RP11-417J8.3 (19465 downstream)						NA		NA									NA						taatttttgtggttttagtag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142599657G>A		NA		hg19		0.02	-0.149096	TGTxGTT	COVERED																																																																																			NOVEL					0			10	6.318282	KEEP	10	0	0	21	631	GG	0.999366	0.291816	0			4	42	102	0	0	8.201365	12	60	393	58		0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142603509	142603509	__UNKNOWN__	IGR	SNP	C	C	T	rs532447623	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142603509C>T			NA	NA				RP11-417J8.2 (15276 upstream) : RP11-417J8.3 (15613 downstream)						NA		NA									NA						ccaccatgcccggctaatttt	0.507		NA											.|||	5	0.000998403	0.003	0.0	5008	,	,	NA	26987	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142603509C>T		NA		hg19		0.02	-0.157886	GCCxGGC	COVERED																																																																																			NOVEL					0			7	3.910628	KEEP	5	0	0	13	377	CC	0.993634	0.320751	0			5	48	154	0	0	13.313184	12	60	378	43		0.294118	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142613916	142613916	__UNKNOWN__	IGR	SNP	G	G	T	rs2783281	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142613916G>T			NA	NA				RP11-417J8.2 (25683 upstream) : RP11-417J8.3 (5206 downstream)						NA		NA									NA						ttatttctgggttctctattc	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142613916G>T		NA		hg19		0.02	-0.192991	TGGxTTC	COVERED																																																																																			NOVEL					0			6	3.610623	KEEP	2	0	0	12	363	GG	0.993634	0.454842	0			7	60	220	0	0	19.534348	14	60	483	57		0.333333	0.457757
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142621035	142621035	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142621035G>A	ENST00000610091.1	-	0	6448				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						GTTTCCAAGAGCAACAGGAAA	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142621035G>A		NA		hg19		0.02	3.238694	AGAxCAA	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	11	2.425336	KEEP	16	1	28	18	551	GG	0.999366	0.999366	0		-	17	50	534	1	0	40.124631	105	60	3671	262	ENST00000610091.1	0.139344	1
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142626158	142626158	__UNKNOWN__	lincRNA	SNP	A	A	G	rs76039951		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142626158A>G	ENST00000610091.1	-	0	6271				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						gcagtgagccaagattgcacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142626158A>G		NA		hg19		0.02	-0.210481	GCCxAGA	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	12	3.54013	KEEP	4	1	23	20	548	AA	0.999859	0.522088	0		-	3	49	91	0	0	6.727803	19	60	548	60	ENST00000610091.1	0.136364	0.522161
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142634833	142634833	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142634833C>T	ENST00000610091.1	-	0	5701				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						ctttattgagcaacagtacag	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142634833C>T		NA		hg19		0.02	-0.377222	GAGxAAC	UNCOVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	5	2.407325	KEEP	7	0	0	8	252	CC	0	0	0		-	6	49	178	0	0	13.119594	37	50	1303	96	ENST00000610091.1	0.139535	0.909069
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142640909	142640909	__UNKNOWN__	lincRNA	SNP	G	G	T	rs112847378		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142640909G>T	ENST00000610091.1	-	0	3560				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						gggcatgttggcttatgctcg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142640909G>T		NA		hg19		0.02	-0.061368	TTGxCTT	UNCOVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	10	2.402668	KEEP	9	0	0	8	234	GG	0	0	0		-	3	46	77	0	0	7.322133	3	48	98	23	ENST00000610091.1	0.5	0.043787
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142640931	142640931	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142640931C>T	ENST00000610091.1	-	0	3560				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						aatctcagctctgtgggagtc	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142640931C>T		NA		hg19		0.02	-0.140341	GCTxTGT	UNCOVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	12	2.407092	KEEP	9	0	0	8	246	AC	0	0	0		-	5	60	149	0	0	13.138565	10	60	331	38	ENST00000610091.1	0.333333	0.260965
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142641014	142641014	__UNKNOWN__	lincRNA	SNP	A	A	G	rs111292117		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142641014A>G	ENST00000610091.1	-	0	3560				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						ctctctacaaaaaaaccaaac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142641014A>G		NA		hg19		0.02	-0.236819	CAAxAAA	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	18	4.542085	KEEP	2	1	31	26	701	AA	0.999931	0.612365	0		-	6	59	204	1	0	17.9574	14	60	426	81	ENST00000610091.1	0.3	0.612407
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142646233	142646233	__UNKNOWN__	lincRNA	SNP	G	G	A	rs76511256		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142646233G>A	ENST00000610091.1	-	0	3560				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						gatcatctgaggtcaggagtt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142646233G>A		NA		hg19		0.02	-0.412312	TGAxGTC	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	26	2.574197	KEEP	12	2	55	28	876	GG	0.999892	0.94164	0		-	4	27	126	0	0	8.863942	36	60	1237	122	ENST00000610091.1	0.1	0.941741
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142646904	142646904	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142646904A>G	ENST00000610091.1	-	0	3560				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						agtctgggtgacagagtgaga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142646904A>G		NA		hg19		0.02	-0.412225	GTGxCAG	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	23	3.572478	KEEP	8	2	60	33	908	AA	0.999998	0.941739	0		-	3	51	99	0	1	7.053221	28	60	842	128	ENST00000610091.1	0.096774	0.941741
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142649247	142649247	__UNKNOWN__	lincRNA	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142649247C>A	ENST00000610091.1	-	0	3560				RP11-417J8.3_ENST00000426408.1_lincRNA						NA		NA									NA						ctcactgcaacctccacctcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142649247C>A		NA		hg19		0.02	-0.219314	CAAxCTC	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	9	5.681871	KEEP	4	0	0	19	539	CC	0.999366	0.552537	0		-	3	60	92	0	0	6.892561	18	60	622	65	ENST00000610091.1	0.142857	0.552887
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142697188	142697188	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142697188G>T	ENST00000610091.1	-	0	3506										NA		NA									NA						cttgaacccgggaggtggagg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142697188G>T		NA		hg19		0.02	-0.26315	CCGxGAG	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	14	4.144661	KEEP	31	1	23	22	675	GG	0.993634	0.689252	0		-	5	42	132	1	1	10.060174	21	50	714	103	ENST00000610091.1	0.192308	0.693668
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142697259	142697259	__UNKNOWN__	lincRNA	SNP	C	C	A	rs201006413		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142697259C>A	ENST00000610091.1	-	0	3506										NA		NA									NA						gagacactgcctcaaaaaaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142697259C>A		NA		hg19		0.02	-0.350865	TGCxTCA	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	23	7.754837	KEEP	28	1	29	36	1106	CC	0.999892	0.877613	0		-	11	54	324	0	1	28.185761	24	50	797	118	ENST00000610091.1	0.314286	0.877708
RP11-417J8.6	0	__UNKNOWN__	__UNKNOWN__	1	142729619	142729619	__UNKNOWN__	lincRNA	SNP	G	G	A	rs146368879		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142729619G>A	ENST00000610091.1	-	0	82										NA		NA									NA						cacgatctccgctcactgcaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000610091.1:	chr1.hg19:g.142729619G>A		NA		hg19		0.02	-0.210459	TCCxCTC	COVERED																																																																																			NOVEL	RP11-417J8.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037265.2	12	2.739262	KEEP	12	1	25	18	515	GG	0.997832	0.521029	0		-	5	58	127	0	0	10.080913	16	60	544	72	ENST00000610091.1	0.238095	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142782395	142782395	__UNKNOWN__	IGR	SNP	T	T	C	rs71223779	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142782395T>C			NA	NA				RP11-417J8.6 (52428 upstream) : RP11-423O2.5 (20828 downstream)						NA		NA									NA						atagcttgaatctgggagaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142782395T>C		NA		hg19		0.02	-0.263111	GAAxCTG	COVERED																																																																																			NOVEL					0			18	3.740385	KEEP	1	1	30	23	617	TT	0.999909	0.693605	0			3	60	99	0	0	7.527176	19	60	566	74		0.136364	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142793332	142793332	__UNKNOWN__	IGR	SNP	C	C	A	rs151298119		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142793332C>A			NA	NA				RP11-417J8.6 (63365 upstream) : RP11-423O2.5 (9891 downstream)						NA		NA									NA						actacaggcgcccgccaccgc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142793332C>A		NA		hg19		0.02	-0.131585	GCGxCCG	COVERED																																																																																			NOVEL					0			3	3.008292	KEEP	4	0	0	10	295	CC	0.99257	0.22747	0			3	43	91	0	0	7.272154	12	60	412	38		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142793429	142793429	__UNKNOWN__	IGR	SNP	C	C	T	rs71256915		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142793429C>T			NA	NA				RP11-417J8.6 (63462 upstream) : RP11-423O2.5 (9794 downstream)						NA		NA									NA						tcgtgatctgcccgccttggc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142793429C>T		NA		hg19		0.02	-0.236858	CTGxCCG	COVERED																																																																																			NOVEL					0			7	5.115538	KEEP	2	0	0	17	536	CC	0.997832	0.611079	0			3	60	90	0	0	6.449591	22	60	766	67		0.12	0.612407
RP11-423O2.5	0	__UNKNOWN__	__UNKNOWN__	1	142807282	142807282	__UNKNOWN__	lincRNA	SNP	T	T	C	rs140943377		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142807282T>C	ENST00000423385.1	-	0	88										NA		NA									NA						ctcacacctgtaatcccagca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423385.1:	chr1.hg19:g.142807282T>C		NA		hg19		0.02	1.77794	CTGxAAT	COVERED																																																																																			NOVEL	RP11-423O2.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000193203.1	46	2.832808	KEEP	39	4	124	53	1423	TT	1	0.999317	0		-	7	47	247	0	1	18.448301	57	60	1643	236	ENST00000423385.1	0.109375	0.999317
RP11-423O2.5	0	__UNKNOWN__	__UNKNOWN__	1	142810409	142810409	__UNKNOWN__	lincRNA	SNP	C	C	T	rs71213748		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142810409C>T	ENST00000423385.1	-	0	88										NA		NA									NA						gtggctcacgcctgtaattcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423385.1:	chr1.hg19:g.142810409C>T		NA		hg19		0.02	-0.27194	ACGxCTG	COVERED																																																																																			NOVEL	RP11-423O2.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000193203.1	18	2.841055	KEEP	21	1	27	19	573	CC	0.994391	0.713292	0		-	5	47	151	0	0	11.958996	21	49	713	91	ENST00000423385.1	0.192308	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142816960	142816960	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142816960C>T			NA	NA				RP11-423O2.5 (956 upstream) : RP11-423O2.7 (134024 downstream)						NA		NA									NA						tggagaaacccatctctacta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142816960C>T		NA		hg19		0.02	-0.263142	ACCxATC	COVERED																																																																																			NOVEL					0			21	5.346899	KEEP	35	1	26	27	782	CC	0.995343	0.690438	0			4	39	123	1	2	9.157828	25	40	822	93		0.137931	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142816995	142816995	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142816995G>A			NA	NA				RP11-423O2.5 (991 upstream) : RP11-423O2.7 (133989 downstream)						NA		NA									NA						gctgttcatggtggcacatgc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142816995G>A		NA		hg19		0.02	-0.114037	ATGxTGG	UNCOVERED																																																																																			NOVEL					0			19	5.115442	KEEP	30	0	0	17	529	GG	0	0	0			3	27	86	0	0	7.100895	9	27	311	62		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142817640	142817640	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142817640G>A			NA	NA				RP11-423O2.5 (1636 upstream) : RP11-423O2.7 (133344 downstream)						NA		NA									NA						tcatgtctgtgatcccagcac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142817640G>A		NA		hg19		0.02	1.499938	TGTxATC	COVERED																																																																																			NOVEL					0			24	3.208764	KEEP	10	3	77	38	1183	GG	1	0.981955	0			4	52	122	0	1	8.024553	47	60	1588	149		0.078431	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142832034	142832034	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142832034A>T			NA	NA				RP11-423O2.5 (16030 upstream) : RP11-423O2.7 (118950 downstream)						NA		NA									NA						caggagaatcacttgaaccca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142832034A>T		NA		hg19		0.02	-0.201679	ATCxCTT	COVERED																																																																																			NOVEL					0			14	2.636123	KEEP	1	1	29	19	499	AG	0.999869	0.522093	0			4	60	119	0	0	9.463748	16	60	457	56		0.2	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142862024	142862024	__UNKNOWN__	IGR	SNP	C	C	G	rs61816133		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142862024C>G			NA	NA				RP11-423O2.5 (46020 upstream) : RP11-423O2.7 (88960 downstream)						NA		NA									NA						cccaggttcacaccattctcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142862024C>G		NA		hg19		0.02	-0.096495	TCAxACC	UNCOVERED																																																																																			NOVEL					0			4	3.008351	KEEP	7	0	0	10	292	CC	0	0	0			3	27	99	0	0	9.032805	5	27	166	31		0.375	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142917634	142917634	__UNKNOWN__	IGR	SNP	C	C	T	rs140450108		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142917634C>T			NA	NA				RP11-423O2.5 (101630 upstream) : RP11-423O2.7 (33350 downstream)						NA		NA									NA						ggccctgcctcagcttctctt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142917634C>T		NA		hg19		0.02	-0.429852	CCTxAGC	COVERED																																																																																			NOVEL					0			5	3.911108	KEEP	9	0	0	13	384	CC	0.993072	0.947879	0			6	27	182	0	0	13.212306	42	49	1427	82		0.125	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142923077	142923077	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142923077T>C			NA	NA				RP11-423O2.5 (107073 upstream) : RP11-423O2.7 (27907 downstream)						NA		NA									NA						ccgcccgccttggcctcccaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142923077T>C		NA		hg19		0.02	1.727741	CCTxGGC	COVERED																																																																																			NOVEL					0			33	14.737244	KEEP	12	0	0	49	1363	TT	1	0.992926	0			4	38	138	0	0	9.485679	51	50	1522	175		0.072727	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	142923119	142923119	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142923119A>C			NA	NA				RP11-423O2.5 (107115 upstream) : RP11-423O2.7 (27865 downstream)						NA		NA									NA						agccaccgtgAGTGACCTTGC	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.142923119A>C		NA		hg19		0.02	-0.350803	GTGxGTG	COVERED																																																																																			NOVEL					0			23	2.669321	KEEP	10	2	54	28	764	AA	0.999957	0.87767	0			7	44	209	0	0	16.542082	29	60	878	101		0.194444	0.877708
RP11-423O2.7	0	__UNKNOWN__	__UNKNOWN__	1	142953634	142953634	__UNKNOWN__	lincRNA	SNP	C	C	A	rs201763510		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142953634C>A	ENST00000424640.2	-	0	203										NA		NA									NA						AAAACAGAATCAggccaagca	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424640.2:	chr1.hg19:g.142953634C>A		NA		hg19		0.02	-0.368396	AATxAGG	COVERED																																																																																			NOVEL	RP11-423O2.7-001	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000193207.2	21	4.814	KEEP	3	0	0	16	480	CC	0.995343	0.895126	0		-	7	54	205	0	0	15.959244	31	60	1013	74	ENST00000424640.2	0.184211	0.899314
RP11-423O2.7	0	__UNKNOWN__	__UNKNOWN__	1	142953663	142953663	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142953663A>G	ENST00000424640.2	-	0	203										NA		NA									NA						tatgcctgtaatgccaacact	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424640.2:	chr1.hg19:g.142953663A>G		NA		hg19		0.02	1.844781	GTAxTGC	COVERED																																																																																			NOVEL	RP11-423O2.7-001	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000193207.2	38	3.07279	KEEP	2	2	65	33	907	AA	0.999998	0.990962	0		-	7	60	237	0	0	18.184195	44	60	1348	138	ENST00000424640.2	0.137255	0.990964
RP11-423O2.7	0	__UNKNOWN__	__UNKNOWN__	1	142953687	142953687	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142953687G>A	ENST00000424640.2	-	0	203										NA		NA									NA						ggaggccgaggcgggaggatc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424640.2:	chr1.hg19:g.142953687G>A		NA		hg19		0.02	1.511248	GAGxCGG	COVERED																																																																																			NOVEL	RP11-423O2.7-001	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000193207.2	44	2.905909	KEEP	2	3	77	37	1124	GG	1	0.994422	0		-	6	50	187	0	0	13.654336	43	60	1508	160	ENST00000424640.2	0.122449	0.994422
RP11-423O2.7	0	__UNKNOWN__	__UNKNOWN__	1	142953712	142953712	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:142953712G>A	ENST00000424640.2	-	0	203										NA		NA									NA						gaggtcaggagttcaagacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424640.2:	chr1.hg19:g.142953712G>A		NA		hg19		0.02	1.267201	GGAxTTC	COVERED																																																																																			NOVEL	RP11-423O2.7-001	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000193207.2	37	5.882211	KEEP	2	2	52	38	1163	GG	1	0.989542	0		-	4	49	116	1	0	7.612197	42	60	1420	140	ENST00000424640.2	0.086957	0.989542
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119056	143119056	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143119056C>T	ENST00000412204.2	-	0	5431										NA		NA									NA						TGCCTTCTATCCCAGCTATGT	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119056C>T		NA		hg19		0.02	4.007944	TATxCCA	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	24	10.396998	KEEP	126	2	55	54	1653	CC	0.999997	0.999997	0		-	9	28	259	0	0	15.353559	144	48	4820	487	ENST00000412204.2	0.058824	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119057	143119057	__UNKNOWN__	lincRNA	SNP	C	C	T	rs200917589		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143119057C>T	ENST00000412204.2	-	0	5430										NA		NA									NA						GCCTTCTATCCCAGCTATGTT	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119057C>T		NA		hg19		0.02	4.321947	ATCxCAG	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	24	3.843531	KEEP	134	4	111	52	1575	CC	0.999997	0.999997	0		-	16	46	467	0	0	32.187946	135	48	4542	498	ENST00000412204.2	0.10596	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119093	143119093	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143119093G>A	ENST00000412204.2	-	0	5394				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						GTGTTTCCAAGAGCAACAAGA	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119093G>A		NA		hg19		0.02	4.776381	CAAxAGC	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	28	9.428929	KEEP	163	3	78	59	1864	GG	0.999999	0.999999	0		-	10	28	320	1	0	20.319455	158	47	5482	629	ENST00000412204.2	0.059524	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119132	143119132	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143119132T>C	ENST00000412204.2	-	0	5355				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						GAGTTGTTTATTTGTTCTTCA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119132T>C		NA		hg19		0.02	5.669177	TTAxTTG	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	12	2.736223	KEEP	110	4	119	51	1410	TT	1	1	0		-	13	43	443	0	0	30.403392	162	47	4909	465	ENST00000412204.2	0.074286	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119143	143119143	__UNKNOWN__	lincRNA	SNP	C	C	T	rs6684812		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143119143C>T	ENST00000412204.2	-	0	5344				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						TTGTTCTTCACTTTGTTTTAC	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119143C>T		NA		hg19		0.02	2.719015	TCAxTTT	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	11	7.886849	KEEP	100	2	53	45	1328	CC	0.999998	0.999998	0		-	9	33	278	0	0	17.515273	134	47	4504	359	ENST00000412204.2	0.062937	1
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143119202	143119202	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143119202A>G	ENST00000412204.2	-	0	5308				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						AAGGaaaagtagaaataagta	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143119202A>G		NA		hg19		0.02	-0.377039	AGTxGAA	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	0	3.604984	KEEP	17	0	0	12	290	AA	0.993072	0.902771	0		-	4	40	126	0	0	8.733739	39	40	1099	78	ENST00000412204.2	0.093023	0.909069
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143139526	143139526	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143139526A>G	ENST00000412204.2	-	0	2503				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						agctcaagcaatctacccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143139526A>G		NA		hg19		0.02	-0.412169	GCAxTCT	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	31	6.448231	KEEP	20	1	33	33	902	AA	0.999988	0.94173	0		-	3	47	103	1	0	7.140256	36	53	1069	133	ENST00000412204.2	0.076923	0.941741
RP11-782C8.2	0	__UNKNOWN__	__UNKNOWN__	1	143143375	143143375	__UNKNOWN__	lincRNA	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143143375A>T	ENST00000412204.2	-	0	2503				RP11-782C8.1_ENST00000438000.1_lincRNA						NA		NA									NA						gctgactgcaacctccacctt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412204.2:	chr1.hg19:g.143143375A>T		NA		hg19		0.02	-0.140267	GCAxCCT	COVERED																																																																																			NOVEL	RP11-782C8.2-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037567.2	19	4.210252	KEEP	18	0	0	14	382	AA	0.992708	0.259062	0		-	3	46	91	0	0	7.273259	12	48	342	65	ENST00000412204.2	0.2	0.260965
RP11-782C8.1	0	__UNKNOWN__	__UNKNOWN__	1	143212812	143212812	__UNKNOWN__	lincRNA	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143212812A>T	ENST00000438000.1	+	0	59										NA		NA									NA						ggtgggcagaacacctgaggt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000438000.1:	chr1.hg19:g.143212812A>T		NA		hg19		0.02	-0.210481	AGAxCAC	COVERED																																																																																			NOVEL	RP11-782C8.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037560.1	10	5.714298	KEEP	23	0	0	19	520	AA	0.992708	0.518353	0		+	3	60	89	0	0	6.979311	13	60	376	91	ENST00000438000.1	0.1875	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143264776	143264776	__UNKNOWN__	IGR	SNP	C	C	T	rs371107423		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143264776C>T			NA	NA				RP11-782C8.1 (31359 upstream) : RP11-435B5.3 (83193 downstream)						NA		NA									NA						ttgagaccagcctgggcaaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143264776C>T		NA		hg19		0.02	1.047917	CAGxCTG	COVERED																																																																																			NOVEL					0			48	14.696662	KEEP	54	3	59	70	2121	CC	1	0.999622	0			5	25	132	0	0	7.516474	74	52	2527	261		0.063291	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143264827	143264827	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143264827C>G			NA	NA				RP11-782C8.1 (31410 upstream) : RP11-435B5.3 (83142 downstream)						NA		NA									NA						agaacatagccagatatgctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143264827C>G		NA		hg19		0.02	1.674956	AGCxAGA	COVERED																																																																																			NOVEL					0			45	4.079123	KEEP	55	5	134	61	1901	CC	1	0.996724	0			4	25	138	0	0	9.328764	56	50	1899	244		0.066667	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143281811	143281811	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143281811C>A			NA	NA				RP11-782C8.1 (48394 upstream) : RP11-435B5.3 (66158 downstream)						NA		NA									NA						gcatgctgggcttaataccta	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143281811C>A		NA		hg19		0.02	1.391262	GGGxTTA	COVERED																																																																																			NOVEL					0			43	12.236767	KEEP	134	3	80	69	2163	CC	0.999997	0.999878	0			5	36	158	0	0	9.987236	78	46	2704	364		0.060241	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143283226	143283226	__UNKNOWN__	IGR	SNP	G	G	C	rs147197560		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143283226G>C			NA	NA				RP11-782C8.1 (49809 upstream) : RP11-435B5.3 (64743 downstream)						NA		NA									NA						TCAGCGGCCGGAGCGTTTGGC	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143283226G>C		NA		hg19		0.02	1.800915	CCGxAGC	COVERED																																																																																			NOVEL					0			10	9.025404	KEEP	51	0	0	30	895	GG	0.999366	0.994453	0			4	40	137	0	0	9.031707	63	44	2064	179		0.059701	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143283399	143283399	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143283399G>A			NA	NA				RP11-782C8.1 (49982 upstream) : RP11-435B5.3 (64570 downstream)						NA		NA									NA						ACCTcacaccgcacacacaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143283399G>A		NA		hg19		0.02	1.470324	ACCxCAC	COVERED																																																																																			NOVEL					0			95	27.717964	KEEP	43	2	53	111	3295	GG	1	0.999487	0			4	59	126	0	2	8.389834	48	60	1528	299		0.076923	0.999487
RP11-435B5.5	0	__UNKNOWN__	__UNKNOWN__	1	143392585	143392585	__UNKNOWN__	lincRNA	SNP	G	G	A	rs10443587		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143392585G>A	ENST00000428624.1	+	0	2208				RP11-435B5.4_ENST00000423249.1_lincRNA						NA		NA									NA						TTACAACTGAGTTAGAAGAAT	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000428624.1:	chr1.hg19:g.143392585G>A		NA		hg19		0.02	-0.377232	TGAxTTA	UNCOVERED																																																																																			NOVEL	RP11-435B5.5-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037971.1	11	2.40714	KEEP	26	0	0	8	244	GG	0	0	0		+	4	22	124	0	0	8.532391	39	48	1370	107	ENST00000428624.1	0.093023	0.909069
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143444421	143444421	__UNKNOWN__	lincRNA	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143444421C>A	ENST00000423249.1	-	0	59										NA		NA									NA						gtagctgggactacaggtgcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143444421C>A		NA		hg19		0.02	-0.122796	GGAxTAC	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	11	4.814062	KEEP	7	0	0	16	485	CC	0.993634	0.227714	0		-	3	48	93	0	0	8.243451	6	60	198	44	ENST00000423249.1	0.333333	0.229173
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143444433	143444433	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143444433G>A	ENST00000423249.1	-	0	59										NA		NA									NA						acaggtgcccgccatcacgcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143444433G>A		NA		hg19		0.02	-0.114033	CCCxCCA	UNCOVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	11	4.209248	KEEP	6	0	0	14	389	GG	0.992708	0.161282	0		-	3	48	92	0	0	8.554875	4	49	133	41	ENST00000423249.1	0.428571	0.162467
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143444849	143444849	__UNKNOWN__	lincRNA	SNP	G	G	A	rs10443462		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143444849G>A	ENST00000423249.1	-	0	59										NA		NA									NA						gggcgtgggggcgcacgcctg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143444849G>A		NA		hg19		0.02	-0.131512	GGGxCGC	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	20	3.34286	KEEP	3	1	25	20	622	GG	0.999863	0.229142	0		-	3	60	88	0	0	7.301932	9	60	280	48	ENST00000423249.1	0.25	0.229173
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143445879	143445879	__UNKNOWN__	lincRNA	SNP	G	G	A	rs143081215		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143445879G>A	ENST00000423249.1	-	0	59										NA		NA									NA						gagtgcagtggtgcaatctca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143445879G>A		NA		hg19		0.02	-0.096489	GTGxTGC	UNCOVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	16	2.539444	KEEP	28	1	27	18	534	GG	0.99257	0.119541	0		-	4	60	119	0	0	10.884964	6	60	197	66	ENST00000423249.1	0.4	0.120436
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143448268	143448268	__UNKNOWN__	lincRNA	SNP	C	C	A	rs201038431		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143448268C>A	ENST00000423249.1	-	0	59										NA		NA									NA						taagcttaaccaaaagggcaa	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143448268C>A		NA		hg19		0.02	-0.131563	AACxAAA	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	6	4.206207	KEEP	7	0	0	14	399	CC	0.993634	0.227714	0		-	3	59	87	0	0	7.201041	9	60	299	42	ENST00000423249.1	0.25	0.229173
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143451250	143451250	__UNKNOWN__	lincRNA	SNP	C	C	T	rs7415362		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143451250C>T	ENST00000423249.1	-	0	59										NA		NA									NA						gcctcaacctcccaggctcaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143451250C>T		NA		hg19		0.02	-0.166626	CCTxCCA	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	15	5.115081	KEEP	18	0	0	17	517	CC	0.993634	0.351693	0		-	6	60	162	0	0	14.675228	9	60	286	64	ENST00000423249.1	0.4	0.353947
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143451349	143451349	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143451349G>A	ENST00000423249.1	-	0	59										NA		NA									NA						tttttttgtagagagggtttt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143451349G>A		NA		hg19		0.02	-0.333342	GTAxAGA	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	37	9.561393	KEEP	39	1	26	41	1262	GG	0.999879	0.851881	0		-	4	49	114	0	1	8.258723	25	60	842	123	ENST00000423249.1	0.137931	0.851984
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143462964	143462964	__UNKNOWN__	lincRNA	SNP	G	G	A	rs369987179		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143462964G>A	ENST00000423249.1	-	0	59										NA		NA									NA						tgcccacctcggcctcccaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143462964G>A		NA		hg19		0.02	1.499885	CTCxGCC	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	13	5.448888	KEEP	9	1	28	28	860	GG	0.999931	0.981888	0		-	6	60	179	0	0	12.85573	43	60	1424	149	ENST00000423249.1	0.122449	0.981955
RP11-435B5.4	0	__UNKNOWN__	__UNKNOWN__	1	143463002	143463002	__UNKNOWN__	lincRNA	SNP	G	G	T	rs9629280		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143463002G>T	ENST00000423249.1	-	0	59										NA		NA									NA						atgagccaccgtgcccagcca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423249.1:	chr1.hg19:g.143463002G>T		NA		hg19		0.02	1.842898	ACCxTGC	COVERED																																																																																			NOVEL	RP11-435B5.4-002	KNOWN	not_best_in_genome_evidence|basic	lincRNA	NA	lincRNA	OTTHUMT00000037552.1	13	6.318599	KEEP	10	0	0	21	634	CG	0.999869	0.973838	0		-	7	60	215	0	0	16.482603	37	60	1171	137	ENST00000423249.1	0.159091	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143468212	143468212	__UNKNOWN__	IGR	SNP	G	G	A	rs199925365		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143468212G>A			NA	NA				RP11-435B5.4 (2774 upstream) : RP11-435B5.6 (30131 downstream)						NA		NA									NA						ctcgtgatccgccctcctagg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143468212G>A		NA		hg19		0.02	1.599131	TCCxCCC	COVERED																																																																																			NOVEL					0			19	2.302547	KEEP	32	3	74	34	1004	GG	0.999988	0.981943	0			10	47	270	0	0	21.42289	35	51	1212	173		0.222222	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143468224	143468224	__UNKNOWN__	IGR	SNP	C	C	A	rs201020905		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143468224C>A			NA	NA				RP11-435B5.4 (2786 upstream) : RP11-435B5.6 (30119 downstream)						NA		NA									NA						cctcctaggcctcccaaagtg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143468224C>A		NA		hg19		0.02	1.403359	GGCxTCC	COVERED																																																																																			NOVEL					0			32	7.188545	KEEP	41	2	57	44	1374	CC	0.999999	0.995686	0			7	49	209	0	0	15.516303	42	51	1444	216		0.142857	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143468264	143468264	__UNKNOWN__	IGR	SNP	C	C	T	rs369086740		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143468264C>T			NA	NA				RP11-435B5.4 (2826 upstream) : RP11-435B5.6 (30079 downstream)						NA		NA									NA						ccaccgcgcccagccCTCAAG	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143468264C>T		NA		hg19		0.02	1.403412	GCCxAGC	COVERED																																																																																			NOVEL					0			36	4.613826	KEEP	38	3	84	45	1396	CC	1	0.995083	0			7	47	213	0	0	15.983907	41	51	1389	205		0.145833	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143470181	143470181	__UNKNOWN__	IGR	SNP	G	G	A	rs143943661		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143470181G>A			NA	NA				RP11-435B5.4 (4743 upstream) : RP11-435B5.6 (28162 downstream)						NA		NA									NA						aaactttaaagtcaaaccAAA	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143470181G>A		NA		hg19		0.02	1.742178	AAAxTCA	COVERED																																																																																			NOVEL					0			23	3.945044	KEEP	3	1	28	23	709	GG	0.999892	0.96367	0			4	27	125	0	0	8.764471	36	60	1246	106		0.1	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143484664	143484664	__UNKNOWN__	IGR	SNP	C	C	T	rs150117293		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143484664C>T			NA	NA				RP11-435B5.4 (19226 upstream) : RP11-435B5.6 (13679 downstream)						NA		NA									NA						gatggattttcgctcttgttg	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143484664C>T		NA		hg19		0.02	1.418528	TTTxGCT	COVERED																																																																																			NOVEL					0			31	3.609458	KEEP	15	3	85	42	1253	CC	1	0.973965	0			4	49	119	2	0	8.4101	31	60	999	149		0.114286	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143488324	143488324	__UNKNOWN__	IGR	SNP	G	G	A	rs9329601		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143488324G>A			NA	NA				RP11-435B5.4 (22886 upstream) : RP11-435B5.6 (10019 downstream)						NA		NA									NA						gggattacaggcgtgagccac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143488324G>A		NA		hg19		0.02	-0.219262	CAGxCGT	COVERED																																																																																			NOVEL					0			16	3.275788	KEEP	45	2	54	30	922	GG	0.993072	0.549057	0			4	60	104	0	0	7.782889	18	55	616	118		0.181818	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143488341	143488341	__UNKNOWN__	IGR	SNP	C	C	A	rs1712203		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143488341C>A			NA	NA				RP11-435B5.4 (22903 upstream) : RP11-435B5.6 (10002 downstream)						NA		NA									NA						ccaccgcgcccagccAGAAGC	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143488341C>A		NA		hg19		0.02	-0.175418	GCCxAGC	COVERED																																																																																			NOVEL					0			17	2.67406	KEEP	46	2	54	28	868	CC	0.99254	0.384517	0			6	27	165	0	0	14.05617	14	50	469	106		0.3	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	143536937	143536937	__UNKNOWN__	IGR	SNP	C	C	T	rs61824460		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143536937C>T			NA	NA				RP11-435B5.7 (3665 upstream) : RNVU1-1 (110076 downstream)						NA		NA									NA						gagactgtgccactgtactcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.143536937C>T		NA		hg19		0.02	-0.403519	TGCxACT	COVERED																																																																																			NOVEL					0			28	7.856804	KEEP	5	1	25	35	1094	CC	0.999998	0.93449	0			4	60	122	0	0	8.46463	36	60	1240	114		0.1	0.934492
SRGAP2B	647135	__UNKNOWN__	__UNKNOWN__	1	143977489	143977489	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:143977489T>C	ENST00000467933.1	+	0	915							P0DMP2	SRG2B_HUMAN	SLIT-ROBO Rho GTPase activating protein 2B	NA		NA			nervous system development (GO:0007399)						NA						gtgatccgcctgcctctgcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA						CCDS72854.1	1q21.1	2014-07-10	2013-02-13	2012-05-08	ENSG00000196369	ENSG00000196369	647135			35237	protein-coding gene	gene with protein product		614703	SLIT-ROBO Rho GTPase activating protein 2 pseudogene 2, SLIT-ROBO Rho GTPase activating protein 2B (pseudogene)	SRGAP2P2	NA	22559943, 22559944	Standard	NM_001271870	NM_001271870	NA	Approved		uc010oxm.1	P0DMP2	OTTHUMG00000041442	ENST00000467933.1:	chr1.hg19:g.143977489T>C		NA		hg19		0.02	-0.236803	GCCxGCC	COVERED																																																																																			NOVEL	SRGAP2B-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000352915.1	6	3.609621	KEEP	2	0	0	12	339	TT	0.993072	0.608164	0		+	3	60	92	0	0	6.64988	22	60	648	60	ENST00000467933.1	0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144306224	144306224	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144306224C>T			NA	NA				LINC00623 (21367 upstream) : RNVU1-4 (4988 downstream)						NA		NA									NA						ggaagctgagcggggcggggg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144306224C>T		NA		hg19		0.02	-0.157884	GAGxGGG	COVERED																																																																																			NOVEL					0			11	3.005966	KEEP	3	0	0	10	272	CC	0.992708	0.351366	0			3	25	94	0	0	7.391868	14	48	444	45		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144526724	144526724	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144526724T>G			NA	NA				RP11-640M9.1 (4754 upstream) : RNU1-59P (7313 downstream)						NA		NA									NA						gggaggctgatgcaggagaat	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144526724T>G		NA		hg19		0.02	-0.263097	TGAxGCA	COVERED																																																																																			NOVEL					0			13	4.511456	KEEP	0	0	0	15	416	TT	0.99649	0.691234	0			3	60	101	0	0	7.494778	23	60	671	63		0.115385	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144531020	144531020	__UNKNOWN__	IGR	SNP	A	A	C	rs74331499	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144531020A>C			NA	NA				RP11-640M9.1 (9050 upstream) : RNU1-59P (3017 downstream)						NA		NA									NA						aggctcaagcagtcctcctac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144531020A>C		NA		hg19		0.02	1.9062	AGCxGTC	COVERED																																																																																			NOVEL					0			24	3.940601	KEEP	1	1	28	23	632	AA	0.999909	0.976777	0			7	60	230	0	0	17.682984	41	60	1249	114		0.145833	0.976865
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144532489	144532489	__UNKNOWN__	IGR	SNP	C	C	T	rs55743442		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144532489C>T			NA	NA				RP11-640M9.1 (10519 upstream) : RNU1-59P (1548 downstream)						NA		NA									NA						tgataatatccctgtcccgaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144532489C>T		NA		hg19		0.02	-0.324216	ATCxCTG	COVERED																																																																																			NOVEL					0			5	2.706507	KEEP	0	0	0	9	261	CC	0.99254	0.829482	0			5	60	137	0	0	9.794858	31	60	1016	65		0.138889	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144536157	144536157	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144536157G>C			NA	NA				RNU1-59P (1958 upstream) : RP11-640M9.2 (57887 downstream)						NA		NA									NA						gaggctgagggaggagaatca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144536157G>C		NA		hg19		0.02	-0.368409	AGGxAGG	COVERED																																																																																			NOVEL					0			18	2.439442	KEEP	0	1	31	19	572	GG	0.999863	0.908944	0			3	60	103	0	0	7.175314	35	60	1153	85		0.078947	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144590946	144590946	__UNKNOWN__	IGR	SNP	C	C	T	rs6666718		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144590946C>T			NA	NA				RNU1-59P (56747 upstream) : RP11-640M9.2 (3098 downstream)						NA		NA									NA						ttttctggaacagattgtaca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144590946C>T		NA		hg19		0.02	-0.22806	GAAxAGA	UNCOVERED																																																																																			NOVEL					0			10	2.708289	KEEP	30	0	0	9	285	CG	0	0	0			6	45	171	0	0	14.22967	17	60	585	98		0.26087	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144686288	144686288	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144686288T>C			NA	NA				RP11-640M9.2 (80397 upstream) : NBPF9 (125455 downstream)						NA		NA									NA						aaaTAAGggctgggcacggtg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144686288T>C		NA		hg19		0.02	-0.394305	GGCxGGG	COVERED																																																																																			NOVEL					0			14	4.744533	KEEP	2	1	32	27	749	TT	0.999957	0.9266	0			4	60	119	0	0	8.043433	39	60	1181	101		0.093023	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144686304	144686304	__UNKNOWN__	IGR	SNP	C	C	T	rs75923987		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144686304C>T			NA	NA				RP11-640M9.2 (80413 upstream) : NBPF9 (125439 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144686304C>T		NA		hg19		0.02	-0.39471	TCAxGCC	COVERED																																																																																			NOVEL					0			15	4.542004	KEEP	2	1	31	26	738	CC	0.999957	0.9266	0			6	60	168	0	0	12.254935	35	60	1135	108		0.146341	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144686399	144686399	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144686399A>C			NA	NA				RP11-640M9.2 (80508 upstream) : NBPF9 (125344 downstream)						NA		NA									NA						ccccgtctctactaaaaatac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144686399A>C		NA		hg19		0.02	-0.166606	TCTxCTA	COVERED																																																																																			NOVEL					0			4	2.703636	KEEP	1	0	0	9	219	AA	0.99257	0.351317	0			5	60	164	0	0	14.471136	11	60	303	32		0.3125	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144702307	144702307	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144702307G>A			NA	NA				RP11-640M9.2 (96416 upstream) : NBPF9 (109436 downstream)						NA		NA									NA						gataggtttagtacaggcagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144702307G>A		NA		hg19		0.02	-0.377219	TTAxTAC	COVERED																																																																																			NOVEL					0			15	2.942049	KEEP	4	1	29	20	610	GG	0.99986	0.908941	0			4	49	123	0	0	8.565214	36	51	1239	96		0.1	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	144703351	144703351	__UNKNOWN__	IGR	SNP	A	A	G	rs200367749		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144703351A>G			NA	NA				RP11-640M9.2 (97460 upstream) : NBPF9 (108392 downstream)						NA		NA									NA						tcaggagatcaagaccattct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.144703351A>G		NA		hg19		0.02	-0.280594	ATCxAGA	COVERED																																																																																			NOVEL					0			10	3.307092	KEEP	7	0	0	11	290	AA	0.99254	0.734154	0			3	60	99	1	0	7.098024	27	60	757	66		0.1	0.739671
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144892041	144892041	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144892041T>C	ENST00000530740.1	-	25	3354				PDE4DIP_ENST00000369351.3_3'UTR|PDE4DIP_ENST00000369349.3_3'UTR|PDE4DIP_ENST00000524974.1_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313431.9_3'UTR|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369354.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGAGAAAGATTCTTGCTTTGG	0.483		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.3315+459A>G	chr1.hg19:g.144892041T>C		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	5.780213	GATxCTT	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	9	7.818752	KEEP	2	1	28	36	921	TT	1	1	0		-	8	33	267	0	0	16.824245	148	60	4306	280	ENST00000530740.1	0.051282	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144949383	144949383	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144949383G>A	ENST00000530740.1	-	8	968				PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369354.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		tcagcctcccgagtagctggg	0.537		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.930-2641C>T	chr1.hg19:g.144949383G>A		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.131563	CCCxAGT	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	10	2.436975	KEEP	14	1	25	17	488	GG	0.995343	0.228106	0		-	3	40	93	1	0	7.573005	11	60	332	55	ENST00000530740.1	0.214286	0.229173
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144951959	144951959	__UNKNOWN__	Intron	SNP	T	T	C	rs142985095		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144951959T>C	ENST00000530740.1	-	7	968				PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369348.3_3'UTR|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_3'UTR|PDE4DIP_ENST00000369354.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		aaatgtttgctgaataagtga	0.408		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.929+241A>G	chr1.hg19:g.144951959T>C		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	6.934264	TGCxGAA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	10	6.179024	KEEP	71	2	61	42	1161	TT	1	1	0		-	24	60	779	0	0	55.440359	217	60	6569	502	ENST00000530740.1	0.099585	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144952003	144952003	__UNKNOWN__	Intron	SNP	T	T	C	rs373048093		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144952003T>C	ENST00000530740.1	-	7	968				PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369348.3_3'UTR|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_3'UTR|PDE4DIP_ENST00000369354.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ATTTGCCCACTGAATCCATGA	0.423		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0								T	,,,,,,,	47,1705		0,47,829	140	142	142		,,,,,,,	2.3	0	1	dbSNP_134	142	6,3976		0,6,1985	no	utr-3,intron,utr-3,utr-3,intron,intron,intron,utr-3	PDE4DIP	NM_001002810.3,NM_001002812.1,NM_001195260.1,NM_001195261.1,NM_001198832.1,NM_001198834.2,NM_014644.4,NM_022359.5	,,,,,,,	0,53,2814	CC,CT,TT	NA	0.1507,2.6826,0.9243	,,,,,,,	,,,,,,,	144952003	53,5681	876	1991	2867	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.929+197A>G	chr1.hg19:g.144952003T>C		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	11.510503	CACxGAA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	15	4.170843	KEEP	56	5	142	64	1790	TT	1	1	0		-	44	60	1426	0	0	107.525044	283	60	8626	655	ENST00000530740.1	0.134557	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144954017	144954017	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144954017T>C	ENST00000530740.1	-	5	668				PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_Intron|PDE4DIP_ENST00000369354.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		tgcagtggcatgatctcggct	0.557		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.629+1198A>G	chr1.hg19:g.144954017T>C		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.157856	GCAxGAT	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	5	3.308414	KEEP	5	0	0	11	303	TT	0.99254	0.320398	0		-	3	60	92	0	0	7.279337	13	60	374	42	ENST00000530740.1	0.1875	0.322807
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144986972	144986972	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144986972C>T	ENST00000530740.1	-	4	591				PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_Intron|PDE4DIP_ENST00000369354.3_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		ggattactgacatgcgccaac	0.403		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.552+7618G>A	chr1.hg19:g.144986972C>T		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.24561	TGAxATG	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	5	3.008833	KEEP	0	0	0	10	302	CC	0.992708	0.63667	0		-	5	60	141	0	0	11.365671	17	60	573	55	ENST00000530740.1	0.227273	0.641347
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144991243	144991243	__UNKNOWN__	Intron	SNP	C	C	T	rs1664013	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144991243C>T	ENST00000530740.1	-	4	591				PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_Intron|PDE4DIP_ENST00000369354.3_Intron|AL590452.1_ENST00000596396.1_3'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGAACTGTggctgggtgtggt	0.478		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.552+3347G>A	chr1.hg19:g.144991243C>T		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	1.549182	TGGxTGG	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	17	3.878993	KEEP	0	2	60	34	1045	CC	0.999999	0.997897	0		-	14	60	427	0	0	34.674265	51	60	1763	158	ENST00000530740.1	0.215385	0.997898
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	144994902	144994902	__UNKNOWN__	Intron	SNP	G	G	A	rs4649499	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:144994902G>A	ENST00000530740.1	-	4	480				PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369356.4_5'UTR|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_5'UTR|PDE4DIP_ENST00000369354.3_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCCGGGACTCGGGACTGGGCT	0.617		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.442-201C>T	chr1.hg19:g.144994902G>A		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	14.202637	CTCxGGA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	6	2.566973	KEEP	0	5	140	58	1671	GG	1	1	0		-	49	60	1487	0	0	104.120371	416	60	13578	766	ENST00000530740.1	0.105376	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145005203	145005203	__UNKNOWN__	Intron	SNP	C	C	T	rs12061605	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145005203C>T	ENST00000530740.1	-	4	480				PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		gtggagatcacgccattgcac	0.463		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.442-10502G>A	chr1.hg19:g.145005203C>T		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	1.634117	TCAxGCC	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	11	5.447473	KEEP	0	1	28	28	812	CC	0.999997	0.967422	0		-	9	60	256	0	0	19.748715	40	60	1337	127	ENST00000530740.1	0.183673	0.967425
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145007525	145007525	__UNKNOWN__	Intron	SNP	C	C	G	rs1778724	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145007525C>G	ENST00000530740.1	-	3	480				PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		tctcggctcactgcaacctct	0.478		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.441+8334G>C	chr1.hg19:g.145007525C>G		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	-0.289492	TCAxTGC	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	20	2.23925	KEEP	3	1	30	18	534	CC	0.999366	0.760405	0		-	5	60	173	0	0	13.980571	23	60	783	65	ENST00000530740.1	0.178571	0.760887
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145038954	145038954	__UNKNOWN__	Intron	SNP	G	G	T	rs10797616|rs386635196	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145038954G>T	ENST00000530740.1	-	2	272				PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000478649.2_Intron|PDE4DIP_ENST00000493130.2_Intron|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAGTGTGTCTGGGGGAAGGAC	0.458		NA	T	PDGFRB	MPD								G|||	1086	0.216853	0.2617	0.2147	5008	,	,	NA	71704	0.3234	NA	0.1372	False	NA	,,,	NA	NA	NA	2504	0.1299	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.234-17787C>A	chr1.hg19:g.145038954G>T		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	10.840281	TCTxGGG	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	14	3.275932	KEEP	0	8	218	88	2713	GG	1	1	0		-	52	60	1531	1	0	112.326391	324	60	11183	733	ENST00000530740.1	0.138298	1
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145056851	145056851	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145056851A>G	ENST00000530740.1	-	1	272				PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369359.4_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		gctcacgcctataatcccagc	0.438		NA	T	PDGFRB	MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.233+18778T>C	chr1.hg19:g.145056851A>G		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	1.739609	CCTxTAA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	19	2.469599	KEEP	1	2	59	29	784	AA	0.999997	0.998198	0		-	4	60	129	0	0	8.463818	55	60	1615	166	ENST00000530740.1	0.067797	0.9982
PDE4DIP	9659	__UNKNOWN__	__UNKNOWN__	1	145073195	145073195	__UNKNOWN__	Intron	SNP	A	A	G	rs113917207	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145073195A>G	ENST00000530740.1	-	1	272				PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000369359.4_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	NA		NA			cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		gcttgaagccaggagtttgag	0.453		NA	T	PDGFRB	MPD								A|||	592	0.118211	0.0477	0.1225	5008	,	,	NA	59820	0.1349	NA	0.1113	False	NA	,,,	NA	NA	NA	2504	0.2004	NA	NA	NA			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104	9659			15580	protein-coding gene	gene with protein product	myomegalin	608117	cardiomyopathy associated 2	CMYA2	NA	9455484, 11134006	Standard	NM_022359	NM_022359	NA	Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.233+2434T>C	chr1.hg19:g.145073195A>G		NA	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	hg19		0.02	1.373949	GCCxGGA	COVERED																																																																																			NOVEL	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000384663.2	37	4.840519	KEEP	0	4	107	54	1506	AA	1	0.999895	0		-	6	60	189	0	0	12.352007	79	60	2372	221	ENST00000530740.1	0.070588	0.999895
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	145081390	145081390	__UNKNOWN__	IGR	SNP	C	C	T	rs609586	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145081390C>T			NA	NA				PDE4DIP (5204 upstream) : SEC22B (14829 downstream)						NA		NA									NA						gctgagatctcgccactgcac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.145081390C>T		NA		hg19		0.02	-0.149078	TCTxGCC	COVERED																																																																																			NOVEL					0			7	2.406323	KEEP	0	0	0	8	229	CC	0.99257	0.289832	0			6	60	181	0	0	16.578973	9	60	267	33		0.4	0.292001
SEC22B	9554	__UNKNOWN__	__UNKNOWN__	1	145111307	145111307	__UNKNOWN__	RNA	SNP	C	C	T	rs2655552	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145111307C>T	ENST00000453618.1	+	0	673							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)					NA						gtgcctcagcctcctgaatag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380		9554			10700	protein-coding gene	gene with protein product		604029	SEC22, vesicle trafficking protein (S. cerevisiae)-like 1, SEC22 vesicle trafficking protein-like 1 (S. cerevisiae), SEC22 vesicle trafficking protein homolog B (S. cerevisiae)	SEC22L1	NA	9094723, 16354670	Standard	NM_004892	NM_004892	NA	Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745	ENST00000453618.1:	chr1.hg19:g.145111307C>T		NA	A8K1G0	hg19		0.02	-0.210543	AGCxTCC	COVERED																																																																																			NOVEL	SEC22B-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000038523.5	12	5.413183	KEEP	0	0	0	18	527	CC	0.999859	0.522088	0		+	4	60	128	0	0	10.094181	19	60	658	53	ENST00000453618.1	0.173913	0.522161
SEC22B	9554	__UNKNOWN__	__UNKNOWN__	1	145112288	145112288	__UNKNOWN__	RNA	SNP	G	G	A	rs386635204|rs151321719	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145112288G>A	ENST00000453618.1	+	0	673							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)					NA						gagccaccgtgcctggccAAC	0.458		NA											G|||	2532	0.505591	0.5053	0.5029	5008	,	,	NA	76496	0.502	NA	0.507	False	NA	,,,	NA	NA	NA	2504	0.5102	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380		9554			10700	protein-coding gene	gene with protein product		604029	SEC22, vesicle trafficking protein (S. cerevisiae)-like 1, SEC22 vesicle trafficking protein-like 1 (S. cerevisiae), SEC22 vesicle trafficking protein homolog B (S. cerevisiae)	SEC22L1	NA	9094723, 16354670	Standard	NM_004892	NM_004892	NA	Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745	ENST00000453618.1:	chr1.hg19:g.145112288G>A		NA	A8K1G0	hg19		0.02	1.058882	CGTxCCT	COVERED																																																																																			NOVEL	SEC22B-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000038523.5	25	5.479125	KEEP	1	2	56	38	1082	GG	1	0.999919	0		+	5	60	141	0	0	8.276612	79	60	2600	171	ENST00000453618.1	0.059524	0.999919
SEC22B	9554	__UNKNOWN__	__UNKNOWN__	1	145112420	145112420	__UNKNOWN__	RNA	SNP	C	C	T	rs2794041	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145112420C>T	ENST00000453618.1	+	0	721							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)					NA						CAGTTGTGCTCGAAGAAACCT	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C	stop/ARG	1625,2509		6,1613,448	156	140	145		394	5.7	1	1	dbSNP_100	145	3389,5031		1,3387,822	no	stop-gained	SEC22B	NM_004892.4		7,5000,1270	TT,TC,CC	NA	40.2494,39.3082,39.9395		132/216	145112420	5014,7540	2067	4210	6277					AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380		9554			10700	protein-coding gene	gene with protein product		604029	SEC22, vesicle trafficking protein (S. cerevisiae)-like 1, SEC22 vesicle trafficking protein-like 1 (S. cerevisiae), SEC22 vesicle trafficking protein homolog B (S. cerevisiae)	SEC22L1	NA	9094723, 16354670	Standard	NM_004892	NM_004892	NA	Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745	ENST00000453618.1:	chr1.hg19:g.145112420C>T		NA	A8K1G0	hg19		0.02	11.210845	GCTxGAA	COVERED																																																																																			NOVEL	SEC22B-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000038523.5	15	8.884555	KEEP	0	5	134	77	2227	CC	1	1	0		+	55	60	1660	0	0	124.518387	318	60	10227	712	ENST00000453618.1	0.147453	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	145194126	145194126	__UNKNOWN__	IGR	SNP	G	G	A	rs61814492	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145194126G>A			NA	NA				RNU6-1071P (44286 upstream) : RP11-458D21.6 (6211 downstream)						NA		NA									NA						AGTGTTTTTCggccaggtgca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.145194126G>A		NA		hg19		0.02	-0.289477	TTCxGCC	COVERED																																																																																			NOVEL					0			13	4.199977	KEEP	2	0	0	14	402	GG	0.993634	0.756043	0			4	60	129	0	0	10.03603	21	60	686	72		0.16	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	145206282	145206282	__UNKNOWN__	IGR	SNP	C	C	A	rs200409996		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145206282C>A			NA	NA				RP11-458D21.6 (5391 upstream) : NOTCH2NL (2836 downstream)						NA		NA									NA						TGAGAAACTGCATACCTAttt	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.145206282C>A		NA		hg19		0.02	-0.210519	CTGxATA	COVERED																																																																																			NOVEL					0			17	4.813667	KEEP	2	0	0	16	470	CC	0.99649	0.550947	0			4	59	125	0	0	10.501396	12	60	398	52		0.25	0.552887
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145209666	145209666	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145209666C>T	ENST00000468030.1	+	1	292				NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000362074.6_Intron						NA		NA									NA						CGCCAACCGCCGGGGTTCCCC	0.731		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.-45+230C>T	chr1.hg19:g.145209666C>T		NA		hg19		0.02	2.749425	CGCxGGG	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	0	7.855113	KEEP	1	1	25	35	1064	CC	0.999999	0.999997	0		+	16	49	428	0	0	30.182011	101	70	3242	172	ENST00000468030.1	0.136752	0.999998
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145230356	145230356	__UNKNOWN__	Intron	SNP	A	A	C	rs200952185		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145230356A>C	ENST00000468030.1	+	2	292				NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000362074.6_Intron|NOTCH2NL_ENST00000369340.3_Intron						NA		NA									NA						aaaaaaaaaaaaaaaaaaaaa	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.-44-18457A>C	chr1.hg19:g.145230356A>C		NA		hg19		0.02	-0.140086	AAAxAAA	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	19	4.784078	KEEP	4	0	0	16	397	AA	0.995343	0.25975	0		+	3	60	80	0	0	6.942936	6	60	171	51	ENST00000468030.1	0.333333	0.260965
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145255611	145255611	__UNKNOWN__	Intron	SNP	G	G	A	rs2746788		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145255611G>A	ENST00000468030.1	+	2	374				NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000362074.6_Intron|NOTCH2NL_ENST00000369340.3_Intron						NA		NA									NA						ttacaggcgtgagccaccacg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.38+6717G>A	chr1.hg19:g.145255611G>A		NA		hg19		0.02	-0.342114	CGTxAGC	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	13	3.443131	KEEP	10	1	27	21	641	GG	0.999859	0.865624	0		+	10	49	294	0	0	25.225505	24	60	825	96	ENST00000468030.1	0.294118	0.865745
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145278460	145278460	__UNKNOWN__	Intron	SNP	C	C	T	rs10752815	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145278460C>T	ENST00000468030.1	+	4	634				NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000362074.6_Intron|NOTCH2NL_ENST00000369340.3_Intron						NA		NA									NA						ccacccgcctcggcctcccaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.299-2909C>T	chr1.hg19:g.145278460C>T		NA		hg19		0.02	1.236782	CCTxGGC	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	18	4.837058	KEEP	4	1	28	26	760	CC	0.999957	0.999634	0		+	12	60	342	0	0	25.689202	62	60	2038	177	ENST00000468030.1	0.162162	0.999678
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145281824	145281824	__UNKNOWN__	Intron	SNP	T	T	G	rs4089950	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145281824T>G	ENST00000468030.1	+	4	970				NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000362074.6_Intron|NOTCH2NL_ENST00000369340.3_Intron						NA		NA									NA						GAATTTTGTGTGGGGTGGGTT	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.634+120T>G	chr1.hg19:g.145281824T>G		NA		hg19		0.02	-0.254296	GTGxGGG	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	6	2.703713	KEEP	7	0	0	9	224	TT	0.99254	0.663536	0		+	6	60	185	0	0	15.046758	22	60	619	48	ENST00000468030.1	0.214286	0.668523
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145285308	145285308	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145285308T>G	ENST00000468030.1	+	4	970				NOTCH2NL_ENST00000344859.3_Intron|NOTCH2NL_ENST00000369340.3_3'UTR						NA		NA									NA						CAAAAATGACTCCTCTTGTAT	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.634+3604T>G	chr1.hg19:g.145285308T>G		NA		hg19		0.02	5.036984	GACxCCT	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	11	5.768206	KEEP	105	8	217	96	2664	TT	1	1	0		+	12	44	367	0	0	23.181677	172	60	5340	535	ENST00000468030.1	0.065217	1
RP11-458D21.5	0	__UNKNOWN__	__UNKNOWN__	1	145290535	145290535	__UNKNOWN__	Intron	SNP	C	C	T	rs76602996	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145290535C>T	ENST00000468030.1	+	5	970				NOTCH2NL_ENST00000479995.2_Intron|NBPF10_ENST00000369339.3_Intron|NOTCH2NL_ENST00000344859.3_Intron						NA		NA									NA						TCTTATAAACCTATTCTAGCC	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													123	129	127			NA	NA	1		NA											NA				145290535		876	1991	2867	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000468030.1:c.635-2579C>T	chr1.hg19:g.145290535C>T		NA		hg19		0.02	15.098045	AACxTAT	COVERED																																																																																			NOVEL	RP11-458D21.5-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000038553.9	17	10.998056	KEEP	8	8	225	116	3570	CC	1	1	0		+	17	60	532	0	0	30.318875	410	60	14059	922	ENST00000468030.1	0.039813	1
NBPF10	100132406	__UNKNOWN__	__UNKNOWN__	1	145323656	145323656	__UNKNOWN__	Intron	SNP	A	A	T	rs75252120	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145323656A>T	ENST00000369339.3	+	10	1293				NBPF10_ENST00000342960.5_Missense_Mutation_p.I1165F|NBPF10_ENST00000369338.1_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	NA		NA				cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.I1165F(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TATTGCAGGAATTAAAAAGGA	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				3	Substitution - Missense(3)	endometrium(2)|kidney(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425	100132406		neuroblastoma breakpoint family	31992	protein-coding gene	gene with protein product		614000			NA	16079250	Standard	NM_001039703	NM_001039703	NA	Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.1040+12502A>T	chr1.hg19:g.145323656A>T		NA	Q5RHC0|Q9NWN6	hg19		0.02	2.982444	GGAxTTA	COVERED	.	.	.	.	.	.	.	.	.	.	.	7.524	0.657305	0.14580	.	.	ENSG00000163386	ENST00000342960	T	0.03441	3.93	.	.	.	.	.	.	.	.	T	0.02342	0.0072	M	0.67953	2.075	0.09310	N	1	.	.	.	.	.	.	T	0.44065	-0.9352	5	0.28530	T	0.3	.	.	.	.	.	.	.	.	F	1165	ENSP00000345684:I1165F	ENSP00000345684:I1165F	I	+	1	0	NBPF10	144035013	0.353000	0.24904	0.005000	0.12908	0.123000	0.20343	1.122000	0.31295	0.386000	0.24997	0.128000	0.15822	ATT	NOVEL	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	NA	protein_coding	OTTHUMT00000038550.3	10	3.439416	KEEP	6	1	30	22	593	AA	0.999869	0.999865	0		+	12	60	337	0	0	22.882258	100	60	2990	204	ENST00000369339.3	0.107143	0.999996
POLR3GL	84265	__UNKNOWN__	__UNKNOWN__	1	145469237	145469237	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145469237A>G	ENST00000369314.1	-	1	66				POLR3GL_ENST00000369313.3_Intron	NM_032305.1	NP_115681.1	Q9BT43	RPC7L_HUMAN	polymerase (RNA) III (DNA directed) polypeptide G (32kD)-like	NA		NA			gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(1)|lung(1)	4	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					gattacaggcatgagccaccg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004355	CCDS72875.1	1q21.1	2008-02-05	2006-12-14		ENSG00000121851	ENSG00000121851	84265			28466	protein-coding gene	gene with protein product		NA	polymerase (RNA) III (DNA directed) polypeptide G (32kD) like		NA	12477932	Standard	NM_032305	NM_032305	NA	Approved	flj32422, MGC3200	uc001enp.1	Q9BT43	OTTHUMG00000013739	ENST00000369314.1:c.40+1084T>C	chr1.hg19:g.145469237A>G		NA	B1MVG5	hg19	CCDS914.1	0.02	-0.192899	GGCxTGA	COVERED																																																																																			NOVEL	POLR3GL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000038510.1	6	4.811238	KEEP	3	0	0	16	429	AA	0.99649	0.45615	0		-	3	60	92	0	0	7.111825	15	60	420	64	ENST00000369314.1	0.166667	0.457757
LIX1L	128077	__UNKNOWN__	__UNKNOWN__	1	145490966	145490966	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145490966A>G	ENST00000369308.3	+	3	530				RP11-315I20.1_ENST00000600340.1_RNA|RP11-315I20.1_ENST00000599469.1_RNA|RP11-315I20.1_ENST00000597144.1_RNA|RP11-315I20.1_ENST00000595518.1_RNA|RP11-315I20.1_ENST00000598354.1_RNA|RP11-315I20.1_ENST00000598103.1_RNA|RP11-315I20.1_ENST00000437207.1_RNA	NM_153713.1	NP_714924.1	Q8IVB5	LIX1L_HUMAN	Lix1 homolog (chicken) like	NA		NA								large_intestine(4)|lung(6)|ovary(2)|skin(1)	13	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ctcctgccttagcctcccaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128733	CCDS72873.1	1q21.1	2014-07-15	2014-07-15		ENSG00000152022	ENSG00000271601	128077			28715	protein-coding gene	gene with protein product		NA	Lix1 homolog (mouse) like, Lix1 homolog (chicken)-like		NA	12477932	Standard	NM_153713	NM_153713	NA	Approved	MGC46719	uc001enr.3	Q8IVB5	OTTHUMG00000013741	ENST00000369308.3:c.457-1269A>G	chr1.hg19:g.145490966A>G		NA	Q6AI36	hg19	CCDS915.1	0.02	-0.298189	CTTxGCC	COVERED																																																																																			NOVEL	LIX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000038513.1	13	3.908279	KEEP	3	0	0	13	349	AA	0.994391	0.776679	0		+	3	60	97	0	0	6.810045	29	60	854	67	ENST00000369308.3	0.09375	0.78106
CD160	11126	__UNKNOWN__	__UNKNOWN__	1	145698086	145698086	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145698086G>A	ENST00000369288.2	-	5	756				CD160_ENST00000401557.3_Intron|CD160_ENST00000369290.1_3'UTR|CD160_ENST00000235933.6_Intron	NM_007053.2	NP_008984.1	O95971	BY55_HUMAN	CD160 molecule	NA		NA			cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|defense response to Gram-negative bacterium (GO:0050829)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|plasma membrane (GO:0005886)	MHC class I receptor activity (GO:0032393)|receptor activity (GO:0004872)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(2)|lung(2)	7	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			gattacaggcgtgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(182;1122 1999 4065 44014 53024)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF060981	CCDS72861.1	1q21.2	2011-01-25	2006-03-28		ENSG00000117281	ENSG00000117281	11126		CD molecules	17013	protein-coding gene	gene with protein product		604463	CD160 antigen		NA	9743336, 9973372	Standard	NM_007053	NM_007053	NA	Approved	BY55, NK1, NK28	uc001eol.1	O95971	OTTHUMG00000013749	ENST00000369288.2:c.538+866C>T	chr1.hg19:g.145698086G>A		NA		hg19	CCDS923.1	0.02	2.863348	GGCxTGA	COVERED																																																																																			NOVEL	CD160-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000038532.2	26	5.346125	KEEP	1	1	26	27	779	GG	0.999997	0.999986	0		-	8	60	226	0	0	14.363431	91	60	2958	188	ENST00000369288.2	0.080808	0.999989
GPR89A	653519	__UNKNOWN__	__UNKNOWN__	1	145815306	145815306	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:145815306G>A	ENST00000313835.9	-	3	350				GPR89A_ENST00000534502.1_Intron|GPR89A_ENST00000454423.3_Intron|GPR89A_ENST00000462900.2_Intron			B7ZAQ6	GPHRA_HUMAN	G protein-coupled receptor 89A	NA		NA			intracellular pH reduction (GO:0051452)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|regulation of anion transport (GO:0044070)|signal transduction (GO:0007165)	Golgi cisterna membrane (GO:0032580)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)|voltage-gated anion channel activity (GO:0008308)			breast(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(18;0.00473)|Acute lymphoblastic leukemia(18;0.0786)		KIRC - Kidney renal clear cell carcinoma(6;0.0764)|Kidney(552;0.118)|Colorectal(543;0.229)			ttacaggcgtgagccaccgtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB097024	CCDS72857.1, CCDS72858.1	1q21.1	2008-12-17	2007-06-06	2007-06-06	ENSG00000117262	ENSG00000117262	653519			31984	protein-coding gene	gene with protein product		612821			NA		Standard	NM_001097612	NM_001097612	NA	Approved	UNQ192	uc001eot.2	B7ZAQ6	OTTHUMG00000013738	ENST00000313835.9:c.206+1330C>T	chr1.hg19:g.145815306G>A		NA	A6NN37|B2RUV3|B3KMN3|B4DLT3|B4DXE7|Q53FQ9|Q5T2V8|Q5T5P5|Q659E2|Q6NVY5|Q9P0S4|Q9Y302	hg19	CCDS41377.1	0.02	-0.342101	CGTxAGC	COVERED																																																																																			NOVEL	GPR89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000038507.2	12	4.814365	KEEP	8	0	0	16	490	GG	0.997832	0.863868	0		-	4	40	109	0	0	7.412103	31	60	1024	90	ENST00000313835.9	0.114286	0.865745
NBPF14	25832	__UNKNOWN__	__UNKNOWN__	1	148010972	148010972	__UNKNOWN__	Silent	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148010972A>G	ENST00000369219.1	-	14	1666	c.1650T>C	c.(1648-1650)tgT>tgC	p.C550C				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	550	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					TCAGTTCAAGACAACCTGAAG	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													2	2	2			NA	NA	1		NA											NA				148010972		557	1411	1968	SO:0001819	synonymous_variant			AK092351		1q21.1	2013-01-17			ENSG00000122497		25832		neuroblastoma breakpoint family	25232	protein-coding gene	gene with protein product		614003			NA	8619474, 9110174, 16079250	Standard	NM_015383	NM_015383	NA	Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1650T>C	chr1.hg19:g.148010972A>G		NA	Q5TI23|Q8IX76|Q9UJI9	hg19		0.02	1.634255	AAGxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	-	0.647	-0.811135	0.02798	.	.	ENSG00000122497	ENST00000310701	.	.	.	.	.	.	.	.	.	.	.	T	0.08714	0.0216	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.36480	-0.9746	2	.	.	.	.	.	.	.	.	.	.	.	A	556	.	.	V	-	2	0	NBPF14	146477596	0.960000	0.32886	0.003000	0.11579	0.003000	0.03518	-0.165000	0.09968	-0.568000	0.06038	-0.564000	0.04169	GTC	NOVEL	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		1	3.910077	KEEP	25	0	0	13	361	AA	0.993072	0.992752	0		-	5	40	176	0	0	11.704524	81	40	2507	205	ENST00000369219.1	0.05814	0.999678
NBPF14	25832	__UNKNOWN__	__UNKNOWN__	1	148010987	148010987	__UNKNOWN__	Silent	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148010987T>C	ENST00000369219.1	-	14	1651	c.1635A>G	c.(1633-1635)tcA>tcG	p.S545S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	545	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.	NA				cytoplasm (GO:0005737)		p.S545S(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(23)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	42	all_hematologic(923;0.032)					CTGAAGGAGTTGAATAACATC	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - coding silent(1)	kidney(1)											2	2	2			NA	NA	1		NA											NA				148010987		627	1514	2141	SO:0001819	synonymous_variant			AK092351		1q21.1	2013-01-17			ENSG00000122497		25832		neuroblastoma breakpoint family	25232	protein-coding gene	gene with protein product		614003			NA	8619474, 9110174, 16079250	Standard	NM_015383	NM_015383	NA	Approved	DJ328E19.C1.1	uc021owp.2	Q5TI25	OTTHUMG00000013900	ENST00000369219.1:c.1635A>G	chr1.hg19:g.148010987T>C		NA	Q5TI23|Q8IX76|Q9UJI9	hg19		0.02	1.13786	AGTxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	-	0.755	-0.771349	0.02951	.	.	ENSG00000122497	ENST00000310701	.	.	.	.	.	.	.	.	.	.	.	T	0.08714	0.0216	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.36480	-0.9746	2	.	.	.	.	.	.	.	.	.	.	.	R	551	.	.	Q	-	2	0	NBPF14	146477611	0.914000	0.31030	0.004000	0.12327	0.003000	0.03518	-0.265000	0.08644	-0.568000	0.06038	-0.564000	0.04169	CAA	NOVEL	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		1	3.909804	KEEP	22	0	0	13	359	TT	0.993072	0.992752	0		-	6	40	182	0	0	11.621379	80	40	2462	193	ENST00000369219.1	0.069767	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148184315	148184315	__UNKNOWN__	IGR	SNP	T	T	A	rs201442669		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148184315T>A			NA	NA				NBPF14 (158467 upstream) : PPIAL4D (17436 downstream)						NA		NA									NA						ATAGTAACATTTGTAggccgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148184315T>A		NA		hg19		0.02	-0.131553	CATxTGT	UNCOVERED																																																																																			NOVEL					0			7	3.307287	KEEP	9	0	0	11	293	TT	0	0	0			4	24	117	0	0	9.971358	10	60	290	46		0.285714	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148548966	148548966	__UNKNOWN__	IGR	SNP	C	C	T	rs192274810		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148548966C>T			NA	NA				NBPF20 (201915 upstream) : NBPF15 (7012 downstream)						NA		NA									NA						ATTGAAAGCTCAACACAACAC	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148548966C>T		NA		hg19		0.02	2.515175	GCTxAAC	COVERED																																																																																			NOVEL					0			2	3.610374	KEEP	3	0	0	12	362	CC	0.993072	0.993066	0			12	49	318	0	0	21.036704	99	60	3175	161		0.108108	0.999994
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148683373	148683373	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148683373G>A			NA	NA				RNVU1-15 (78301 upstream) : NBPF16 (56069 downstream)						NA		NA									NA						agaattgcttgaacgtggggg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148683373G>A		NA		hg19		0.02	-0.368436	CTTxAAC	COVERED																																																																																			NOVEL					0			22	2.941087	KEEP	10	1	26	19	565	GG	0.997832	0.897364	0			4	23	116	0	0	8.058941	32	60	1080	91		0.111111	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148683465	148683465	__UNKNOWN__	IGR	SNP	C	C	A	rs55748150	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148683465C>A			NA	NA				RNVU1-15 (78393 upstream) : NBPF16 (55977 downstream)						NA		NA									NA						gaaaaaaaaacccaaaaaaca	0.408		NA											.|||	204	0.0407348	0.1165	0.0144	5008	,	,	NA	34280	0.006	NA	0.0169	False	NA	,,,	NA	NA	NA	2504	0.0174	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148683465C>A		NA		hg19		0.02	-0.219296	AAAxCCA	COVERED																																																																																			NOVEL					0			18	4.346033	KEEP	6	1	27	24	739	CC	0.999879	0.55282	0			3	42	84	2	1	6.310764	15	60	519	72		0.166667	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148859529	148859529	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148859529G>A			NA	NA				RP11-763B22.6 (5812 upstream) : RNA5SP59 (53743 downstream)						NA		NA									NA						ctgcagtctcgaccttccagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148859529G>A		NA		hg19		0.02	-0.254371	CTCxACC	COVERED																																																																																			NOVEL					0			20	5.113576	KEEP	6	0	0	17	487	GG	0.999366	0.693229	0			4	48	120	1	0	9.062772	22	60	700	72		0.153846	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148863386	148863386	__UNKNOWN__	IGR	SNP	C	C	T	rs61812500		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148863386C>T			NA	NA				RP11-763B22.6 (9669 upstream) : RNA5SP59 (49886 downstream)						NA		NA									NA						TAAAGATCTCCCAGGTCCATC	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148863386C>T		NA		hg19		0.02	-0.096487	CTCxCAG	UNCOVERED																																																																																			NOVEL					0			8	2.707766	KEEP	5	0	0	9	266	CC	0	0	0			5	60	150	0	0	14.093188	6	60	195	28		0.454545	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148863387	148863387	__UNKNOWN__	IGR	SNP	C	C	T	rs200634446		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148863387C>T			NA	NA				RP11-763B22.6 (9670 upstream) : RNA5SP59 (49885 downstream)						NA		NA									NA						AAAGATCTCCCAGGTCCATCA	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148863387C>T		NA		hg19		0.02	-0.096484	TCCxAGG	UNCOVERED																																																																																			NOVEL					0			8	2.707843	KEEP	5	0	0	9	268	CC	0	0	0			4	60	114	0	0	10.17642	7	60	228	28		0.363636	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148874684	148874684	__UNKNOWN__	IGR	SNP	C	C	T	rs370260302		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148874684C>T			NA	NA				RP11-763B22.6 (20967 upstream) : RNA5SP59 (38588 downstream)						NA		NA									NA						tgcactccagcctgggcaaag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148874684C>T		NA		hg19		0.02	1.502486	CAGxCTG	COVERED																																																																																			NOVEL					0			31	6.954684	KEEP	12	1	28	33	1044	CC	0.999997	0.995081	0			4	27	121	0	0	8.410967	35	52	1210	157		0.102564	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148877963	148877963	__UNKNOWN__	IGR	SNP	G	G	A	rs71246031	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148877963G>A			NA	NA				RP11-763B22.6 (24246 upstream) : RNA5SP59 (35309 downstream)						NA		NA									NA						agccccctgggtagctgggat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148877963G>A		NA		hg19		0.02	-0.166654	TGGxTAG	COVERED																																																																																			NOVEL					0			9	3.309009	KEEP	11	0	0	11	318	GG	0.99257	0.351317	0			4	40	113	0	0	9.181002	13	50	421	45		0.235294	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	148915739	148915739	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148915739T>G			NA	NA				RNA5SP59 (2357 upstream) : RP11-14N7.2 (12605 downstream)						NA		NA									NA						tattttagtatagacggggtt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.148915739T>G		NA		hg19		0.02	-0.289253	GTAxAGA	COVERED																																																																																			NOVEL					0			14	5.410639	KEEP	9	0	0	18	464	TT	0.99649	0.758216	0			3	60	94	0	0	6.512617	29	60	795	70		0.09375	0.760887
RP11-14N7.2	0	__UNKNOWN__	__UNKNOWN__	1	148933504	148933504	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148933504C>T	ENST00000539543.1	+	0	254					NR_027355.2					NA		NA									NA						tttgggaggccgaggcgggtg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000539543.1:	chr1.hg19:g.148933504C>T		NA		hg19		0.02	-0.271826	GGCxGAG	COVERED																																																																																			NOVEL	RP11-14N7.2-201	KNOWN	basic	lincRNA	NA	lincRNA		15	3.040744	KEEP	24	1	28	20	585	CC	0.997832	0.71576	0		+	3	33	91	0	0	6.393567	25	60	785	93	ENST00000539543.1	0.107143	0.717315
RP11-14N7.2	0	__UNKNOWN__	__UNKNOWN__	1	148938571	148938571	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:148938571T>C	ENST00000539543.1	+	0	254					NR_027355.2					NA		NA									NA						gcactctagcttgggtgacag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000539543.1:	chr1.hg19:g.148938571T>C		NA		hg19		0.02	-0.096488	AGCxTGG	UNCOVERED																																																																																			NOVEL	RP11-14N7.2-201	KNOWN	basic	lincRNA	NA	lincRNA		7	4.509644	KEEP	14	0	0	15	404	TT	0	0	0		+	3	46	95	0	0	8.278526	7	48	218	41	ENST00000539543.1	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149029300	149029300	__UNKNOWN__	IGR	SNP	G	G	T	rs112498586		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149029300G>T			NA	NA				RP11-14N7.2 (77705 upstream) : AL732363.1 (7011 downstream)						NA		NA									NA						aaacaaagaaggaaagaagga	0.368		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	34225	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149029300G>T		NA		hg19		0.02	-0.122806	GAAxGAA	UNCOVERED																																																																																			NOVEL					0			10	3.008563	KEEP	3	0	0	10	298	GG	0	0	0			3	60	85	0	0	7.443	6	60	204	32		0.333333	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149267560	149267560	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149267560T>C			NA	NA				RP11-403I13.4 (2050 upstream) : RP11-403I13.7 (17084 downstream)						NA		NA									NA						aacggagtcttgctctgtcgc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149267560T>C		NA		hg19		0.02	-0.271709	TCTxGCT	COVERED																																																																																			NOVEL					0			9	2.405902	KEEP	0	0	0	8	220	TT	0.99257	0.711986	0			3	58	92	0	0	6.400426	27	60	779	60		0.1	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149283672	149283672	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149283672C>A			NA	NA				RP11-403I13.4 (18162 upstream) : RP11-403I13.7 (972 downstream)						NA		NA									NA						gcaccccagcctgggcgacag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149283672C>A		NA		hg19		0.02	-0.14034	AGCxTGG	COVERED																																																																																			NOVEL					0			11	3.008822	KEEP	6	0	0	10	302	CC	0.99257	0.259026	0			4	27	116	0	0	9.730924	11	60	344	33		0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149283960	149283960	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149283960G>A			NA	NA				RP11-403I13.4 (18450 upstream) : RP11-403I13.7 (684 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149283960G>A		NA		hg19		0.02	-0.350692	CACxCCT	COVERED																																																																																			NOVEL					0			21	3.340888	KEEP	10	1	28	21	598	GG	0.999859	0.877584	0			4	50	120	0	0	8.511103	31	50	1012	96		0.114286	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149284029	149284029	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149284029T>C			NA	NA				RP11-403I13.4 (18519 upstream) : RP11-403I13.7 (615 downstream)						NA		NA									NA						tgagaccagcttggccaatat	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149284029T>C		NA		hg19		0.02	-0.105185	AGCxTGG	UNCOVERED																																																																																			NOVEL					0			5	2.707031	KEEP	3	0	0	9	250	TT	0	0	0			3	48	83	0	0	7.076227	7	52	218	26		0.3	0.139832
RP11-403I13.8	0	__UNKNOWN__	__UNKNOWN__	1	149290881	149290881	__UNKNOWN__	lincRNA	SNP	C	C	T	rs61789500	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149290881C>T	ENST00000433084.1	+	0	1446										NA		NA									NA						AGCACCTGGGCCAATGAGGTA	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000433084.1:	chr1.hg19:g.149290881C>T		NA		hg19		0.02	1.306861	GGGxCAA	COVERED																																																																																			NOVEL	RP11-403I13.8-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000099633.1	5	4.814035	KEEP	38	0	0	16	482	CC	0.994391	0.993389	0		+	9	49	269	0	0	19.087118	69	60	2352	178	ENST00000433084.1	0.115385	0.998993
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	149366788	149366788	__UNKNOWN__	IGR	SNP	C	C	G	rs61805129		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149366788C>G			NA	NA				CR812485.1 (43366 upstream) : FCGR1C (2539 downstream)						NA		NA									NA						gcctgggtgacagagcgagac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.149366788C>G		NA		hg19		0.02	-0.070181	TGAxAGA	UNCOVERED																																																																																			NOVEL					0			11	3.008589	KEEP	17	0	0	10	294	CC	0	0	0			2	39	72	0	0	6.335562	5	60	168	52		0.285714	0.054137
FCGR1A	2209	__UNKNOWN__	__UNKNOWN__	1	149763115	149763115	__UNKNOWN__	3'UTR	SNP	C	C	T	rs15571		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:149763115C>T	ENST00000369168.4	+	0	1221				RP11-196G18.3_ENST00000428289.1_RNA|RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000545683.1_Intron	NM_000566.3	NP_000557.1	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor (CD64)	NA		NA			antibody-dependent cellular cytotoxicity (GO:0001788)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intracellular signal transduction (GO:0035556)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of phagocytosis (GO:0050766)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG receptor activity (GO:0019770)|receptor signaling protein activity (GO:0005057)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)	10	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCGTCCCCTGCCCACTTGCTC	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													27	28	27			NA	NA	1		NA											NA				149763115		2201	4296	6497	SO:0001624	3_prime_UTR_variant			BC032634	CCDS933.1	1q21.2-q21.3	2014-09-17	2005-02-02		ENSG00000150337	ENSG00000150337	2209		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	3613	protein-coding gene	gene with protein product		146760	Fc fragment of IgG, high affinity Ia, receptor for (CD64)		NA	8697799, 9763663	Standard	NM_000566	NM_000566	NA	Approved	CD64, CD64A	uc001esp.4	P12314	OTTHUMG00000012089	ENST00000369168.4:c.*42C>T	chr1.hg19:g.149763115C>T		NA	P12315|Q5QNW7|Q92495|Q92663	hg19	CCDS933.1	0.02	4.878733	CTGxCCA	COVERED																																																																																			NOVEL	FCGR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033446.1	6	7.989462	KEEP	47	2	55	46	1425	CC	1	1	0		+	30	43	909	1	0	70.81765	140	50	4925	388	ENST00000369168.4	0.176471	1
PLEKHO1	51177	__UNKNOWN__	__UNKNOWN__	1	150124773	150124773	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150124773G>A	ENST00000369124.4	+	2	455				PLEKHO1_ENST00000369126.1_Intron|PLEKHO1_ENST00000025469.6_Intron|PLEKHO1_ENST00000479194.1_Intron	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			gattacaggtgtgagccaccg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902	51177		Pleckstrin homology (PH) domain containing	24310	protein-coding gene	gene with protein product		608335			NA	10799509	Standard	NM_016274	NM_016274	NA	Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.177+1525G>A	chr1.hg19:g.150124773G>A		NA	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	hg19	CCDS945.1	0.02	-0.184214	GGTxTGA	COVERED																																																																																			NOVEL	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034962.1	7	3.610696	KEEP	2	0	0	12	367	GG	0.993072	0.420544	0		+	3	60	90	0	0	6.833597	16	60	525	45	ENST00000369124.4	0.157895	0.423478
PLEKHO1	51177	__UNKNOWN__	__UNKNOWN__	1	150130871	150130871	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150130871A>G	ENST00000369124.4	+	6	803				PLEKHO1_ENST00000369126.1_Intron|PLEKHO1_ENST00000025469.6_Intron|PLEKHO1_ENST00000479194.1_Intron	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			gtgacagagcaagactctgtc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902	51177		Pleckstrin homology (PH) domain containing	24310	protein-coding gene	gene with protein product		608335			NA	10799509	Standard	NM_016274	NM_016274	NA	Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.526-143A>G	chr1.hg19:g.150130871A>G		NA	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	hg19	CCDS945.1	0.02	1.508519	AGCxAGA	COVERED																																																																																			NOVEL	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034962.1	8	4.304874	KEEP	1	3	81	43	1174	AA	1	0.999804	0		+	4	60	128	1	0	7.818579	76	60	2219	168	ENST00000369124.4	0.05	0.999804
MRPS21	54460	__UNKNOWN__	__UNKNOWN__	1	150267668	150267668	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150267668T>G	ENST00000369084.5	+	1	530				MRPS21_ENST00000309092.7_Intron	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	NA		NA			translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			tgcctgcctctgcctcccaaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145		54460		Mitochondrial ribosomal proteins / small subunits	14046	protein-coding gene	gene with protein product		611984			NA		Standard	NM_018997	NM_031901	NA	Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.83+799T>G	chr1.hg19:g.150267668T>G		NA	Q5TB11|Q9BST6	hg19	CCDS950.1	0.02	-0.175403	CTCxGCC	COVERED																																																																																			NOVEL	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000035813.1	5	2.405954	KEEP	0	0	0	8	220	TT	0.99257	0.454356	0		+	3	43	97	0	0	7.610371	15	60	445	46	ENST00000369084.5	0.166667	0.457757
CTSS	1520	__UNKNOWN__	__UNKNOWN__	1	150713089	150713089	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150713089T>C	ENST00000368985.3	-	7	1157				CTSS_ENST00000448301.2_Intron	NM_001199739.1|NM_004079.4	NP_001186668.1|NP_004070.3	P25774	CATS_HUMAN	cathepsin S	NA		NA			adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|basement membrane disassembly (GO:0034769)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of inflammatory response (GO:0050729)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	15	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			aggatggtcttgatctcctga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M90696	CCDS968.1, CCDS55634.1	1q21	2008-02-05			ENSG00000163131	ENSG00000163131	1520	3.4.22.27	Cathepsins	2545	protein-coding gene	gene with protein product		116845			NA	1373132	Standard	NM_004079	NM_001199739	NA	Approved		uc001evn.3	P25774	OTTHUMG00000035010	ENST00000368985.3:c.896+7163A>G	chr1.hg19:g.150713089T>C		NA	B4DWC9|D3DV05|Q5T5I0|Q6FHS5|Q9BUG3	hg19	CCDS968.1	0.02	-0.114013	TCTxGAT	UNCOVERED																																																																																			NOVEL	CTSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084737.1	9	3.307018	KEEP	2	0	0	11	286	TT	0.993072	0.161341	0		-	4	60	116	0	0	10.376574	7	60	208	33	ENST00000368985.3	0.363636	0.162467
ARNT	405	__UNKNOWN__	__UNKNOWN__	1	150799358	150799358	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150799358A>G	ENST00000354396.2	-	13	1179				ARNT_ENST00000515192.1_Intron|ARNT_ENST00000358595.5_Intron|ARNT_ENST00000505755.1_Intron			P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	NA		NA			cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			cctgacctcaagtgatccacc	0.498		NA	T	ETV6	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437	405		Basic helix-loop-helix proteins	700	protein-coding gene	gene with protein product		126110			NA		Standard		NM_001668	NA	Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000354396.2:c.1168-265T>C	chr1.hg19:g.150799358A>G		NA	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	hg19		0.02	-0.166651	TCAxGTG	COVERED																																																																																			NOVEL	ARNT-010	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000360630.1	7	2.406342	KEEP	3	0	0	8	225	AA	0.99257	0.351317	0		-	3	60	94	1	0	7.234039	16	60	492	45	ENST00000354396.2	0.157895	0.353947
SETDB1	9869	__UNKNOWN__	__UNKNOWN__	1	150914442	150914442	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150914442T>C	ENST00000271640.5	+	5	737				SETDB1_ENST00000459773.1_Intron|SETDB1_ENST00000368963.1_Intron|SETDB1_ENST00000368969.4_Intron|SETDB1_ENST00000368962.2_Intron	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	NA		NA			bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			atggtgaaactctgtctctat	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379	9869		Chromatin-modifying enzymes / K-methyltransferases, Tudor domain containing	10761	protein-coding gene	gene with protein product	tudor domain containing 21	604396			NA	10343109	Standard		NM_001145415	NA	Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.547+538T>C	chr1.hg19:g.150914442T>C		NA	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	hg19	CCDS44217.1	0.02	-0.149119	AACxCTG	COVERED																																																																																			NOVEL	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084717.2	5	2.406227	KEEP	0	0	0	8	223	TT	0.99257	0.289832	0		+	3	54	96	0	0	7.678862	13	60	405	30	ENST00000271640.5	0.1875	0.292001
FAM63A	55793	__UNKNOWN__	__UNKNOWN__	1	150971121	150971121	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:150971121C>T	ENST00000361936.5	-	9	1936				FAM63A_ENST00000361738.6_Intron|FAM63A_ENST00000312210.5_Intron|FAM63A_ENST00000493834.2_Intron	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	NA		NA				extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			catgagccaccgcacccggAC	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409	55793			25648	protein-coding gene	gene with protein product		NA			NA	10718198	Standard	NM_018379	NM_001040217	NA	Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.982-372G>A	chr1.hg19:g.150971121C>T		NA	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	hg19	CCDS976.1	0.02	-0.228049	CACxGCA	COVERED																																																																																			NOVEL	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411753.1	9	3.609798	KEEP	4	0	0	12	359	CC	0.992708	0.578679	0		-	3	60	89	0	0	6.465762	20	60	630	57	ENST00000361936.5	0.130435	0.58293
GABPB2	126626	__UNKNOWN__	__UNKNOWN__	1	151083521	151083521	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151083521T>C	ENST00000368918.3	+	7	1253				GABPB2_ENST00000467551.1_Intron|GABPB2_ENST00000368916.1_Intron|GABPB2_ENST00000368917.1_Intron	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		tttgggaggctgaggcgggag	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458	126626		Ankyrin repeat domain containing	28441	protein-coding gene	gene with protein product		NA			NA	7958862	Standard	NM_144618	NM_144618	NA	Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.922+3823T>C	chr1.hg19:g.151083521T>C		NA	B1AVJ8|D3DV14|Q8NAR5	hg19	CCDS983.1	0.02	-0.210457	GGCxGAG	COVERED																																																																																			NOVEL	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033700.2	3	2.705221	KEEP	0	0	0	9	234	TT	0.99254	0.518266	0		+	3	60	93	0	0	6.927841	19	60	539	37	ENST00000368918.3	0.136364	0.522161
GABPB2	126626	__UNKNOWN__	__UNKNOWN__	1	151083586	151083586	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151083586G>C	ENST00000368918.3	+	7	1253				GABPB2_ENST00000467551.1_Intron|GABPB2_ENST00000368916.1_Intron|GABPB2_ENST00000368917.1_Intron	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		gaaaccccatgtctactgaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458	126626		Ankyrin repeat domain containing	28441	protein-coding gene	gene with protein product		NA			NA	7958862	Standard	NM_144618	NM_144618	NA	Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.922+3888G>C	chr1.hg19:g.151083586G>C		NA	B1AVJ8|D3DV14|Q8NAR5	hg19	CCDS983.1	0.02	1.607849	CATxTCT	COVERED																																																																																			NOVEL	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033700.2	20	2.36251	KEEP	0	2	63	30	890	GG	0.999998	0.999802	0		+	6	60	196	1	0	13.113426	77	60	2617	166	ENST00000368918.3	0.072289	0.999804
GABPB2	126626	__UNKNOWN__	__UNKNOWN__	1	151091332	151091332	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151091332A>G	ENST00000368918.3	+	0	2278				GABPB2_ENST00000368917.1_3'UTR	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		aggctagagtacagtggtgca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458	126626		Ankyrin repeat domain containing	28441	protein-coding gene	gene with protein product		NA			NA	7958862	Standard	NM_144618	NM_144618	NA	Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.*600A>G	chr1.hg19:g.151091332A>G		NA	B1AVJ8|D3DV14|Q8NAR5	hg19	CCDS983.1	0.02	-0.385718	AGTxCAG	COVERED																																																																																			NOVEL	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033700.2	4	2.934454	KEEP	1	1	23	18	459	AA	0.999859	0.918042	0		+	3	60	99	0	1	6.742153	36	60	966	72	ENST00000368918.3	0.076923	0.918171
GABPB2	126626	__UNKNOWN__	__UNKNOWN__	1	151091538	151091538	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151091538A>G	ENST00000368918.3	+	0	2484				GABPB2_ENST00000368917.1_3'UTR	NM_144618.2	NP_653219.1	Q8TAK5	GABP2_HUMAN	GA binding protein transcription factor, beta subunit 2	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(3)|liver(2)|lung(7)	15				all cancers(107;7.17e-05)|GBM - Glioblastoma multiforme(94;0.000662)		tgtaatcccaacactttggga	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS983.1	1q21.2	2013-01-10			ENSG00000143458	ENSG00000143458	126626		Ankyrin repeat domain containing	28441	protein-coding gene	gene with protein product		NA			NA	7958862	Standard	NM_144618	NM_144618	NA	Approved	MGC29891	uc001ewr.2	Q8TAK5	OTTHUMG00000012193	ENST00000368918.3:c.*806A>G	chr1.hg19:g.151091538A>G		NA	B1AVJ8|D3DV14|Q8NAR5	hg19	CCDS983.1	0.02	5.736272	CCAxCAC	COVERED																																																																																			NOVEL	GABPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000033700.2	35	15.795214	KEEP	0	5	140	102	2779	AA	1	1	0		+	7	60	242	1	0	15.221776	145	60	4391	379	ENST00000368918.3	0.046053	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	151098102	151098102	__UNKNOWN__	IGR	SNP	G	G	A	rs587665045		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151098102G>A			NA	NA				GABPB2 (84 upstream) : RP11-68I18.10 (4448 downstream)						NA		NA									NA						tttttgagacggagtctcgct	0.493		NA											-|||	1	0.000199681	0.0	0.0	5008	,	,	NA	8628	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.151098102G>A		NA		hg19		0.02	1.3683	GACxGAG	COVERED																																																																																			NOVEL					0			8	6.314755	KEEP	7	3	79	49	1428	GG	1	0.997163	0			4	60	123	0	2	7.862226	55	70	1804	152		0.067797	0.997163
TMOD4	29765	__UNKNOWN__	__UNKNOWN__	1	151146382	151146382	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151146382A>G	ENST00000416280.2	-	3	380							Q9NZQ9	TMOD4_HUMAN	tropomodulin 4 (muscle)	NA		NA			muscle contraction (GO:0006936)	striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			gtgaaaccccatctctactaa	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF177173	CCDS988.1	1q12	2008-05-23			ENSG00000163157	ENSG00000163157	29765			11874	protein-coding gene	gene with protein product	actin-capping protein	605834			NA	10662549, 10497209	Standard		NM_013353	NA	Approved	Sk-Tmod	uc001exc.4	Q9NZQ9	OTTHUMG00000012350	ENST00000416280.2:c.280+484T>C	chr1.hg19:g.151146382A>G		NA	B7Z6N9|Q5JR83|Q8WVL3|Q9UKH2	hg19		0.02	-0.20173	CCCxTCT	COVERED																																																																																			NOVEL	TMOD4-201	KNOWN	basic	protein_coding	NA	protein_coding		7	2.405857	KEEP	0	0	0	8	217	AA	0.99257	0.4869	0		-	3	60	91	1	0	6.792719	18	60	542	44	ENST00000416280.2	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	151242184	151242184	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151242184T>C			NA	NA				PSMD4 (2229 upstream) : RP11-126K1.2 (10315 downstream)						NA		NA									NA						tgcagtggcatgatcttggct	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.151242184T>C		NA		hg19		0.02	-0.166617	GCAxGAT	COVERED																																																																																			NOVEL					0			14	4.210976	KEEP	12	0	0	14	390	TT	0.99254	0.351306	0			5	40	146	0	0	12.512726	12	46	352	52		0.294118	0.353947
PI4KB	5298	__UNKNOWN__	__UNKNOWN__	1	151274199	151274199	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151274199A>G	ENST00000368874.4	-	7	2177				PI4KB_ENST00000368875.2_Intron|PI4KB_ENST00000529142.1_Intron|PI4KB_ENST00000368872.1_Intron|PI4KB_ENST00000271657.5_Intron|PI4KB_ENST00000368873.1_Intron	NM_001198774.1	NP_001185703.1	Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			tagtagagacagggtttcacc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(154;765 1838 9854 28443 37492)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393	5298			8984	protein-coding gene	gene with protein product		602758		PIK4CB	NA	9020160, 9405938	Standard	NM_002651	NM_002651	NA	Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348	ENST00000368874.4:c.1704+120T>C	chr1.hg19:g.151274199A>G		NA	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	hg19	CCDS55638.1	0.02	-0.280665	GACxGGG	COVERED																																																																																			NOVEL	PI4KB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034401.4	8	4.511189	KEEP	0	0	0	15	410	AA	0.99649	0.737075	0		-	4	60	122	0	0	8.995411	26	60	785	66	ENST00000368874.4	0.133333	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	151330467	151330467	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151330467T>C			NA	NA				RP11-126K1.6 (9964 upstream) : SELENBP1 (6310 downstream)						NA		NA									NA						ccttggcctctcaaagttctg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.151330467T>C		NA		hg19		0.02	-0.280639	CTCxCAA	COVERED																																																																																			NOVEL					0			12	2.335152	KEEP	0	1	26	17	447	TT	0.999859	0.739567	0			3	60	98	0	0	6.953294	28	60	825	68		0.096774	0.739671
TUFT1	7286	__UNKNOWN__	__UNKNOWN__	1	151527615	151527615	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151527615G>C	ENST00000368849.3	+	2	122				TUFT1_ENST00000368848.2_Intron|TUFT1_ENST00000353024.3_Intron|TUFT1_ENST00000538902.1_Intron|RP11-74C1.4_ENST00000434112.1_RNA|TUFT1_ENST00000392712.3_Intron	NM_020127.2	NP_064512.1	Q9NNX1	TUFT1_HUMAN	tuftelin 1	NA		NA			bone mineralization (GO:0030282)|odontogenesis (GO:0042476)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	structural constituent of tooth enamel (GO:0030345)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			accagcctgggcaacatggcg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF254260	CCDS1000.1, CCDS44223.1	1q21	2008-02-05			ENSG00000143367	ENSG00000143367	7286			12422	protein-coding gene	gene with protein product		600087			NA	7919663	Standard	NM_020127	NM_020127	NA	Approved		uc001eyl.3	Q9NNX1	OTTHUMG00000012536	ENST00000368849.3:c.61-6952G>C	chr1.hg19:g.151527615G>C		NA	B2RD57|D3DV21|D3DV22|Q5T384|Q5T385|Q9BU28|Q9H5L1	hg19	CCDS1000.1	0.02	-0.14912	TGGxCAA	COVERED																																																																																			NOVEL	TUFT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000035022.1	11	2.708048	KEEP	3	0	0	9	276	GG	0.99257	0.289832	0		+	3	60	85	0	0	6.772938	11	60	381	35	ENST00000368849.3	0.214286	0.292001
SNX27	81609	__UNKNOWN__	__UNKNOWN__	1	151592056	151592056	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151592056T>C	ENST00000368843.3	+	1	431				SNX27_ENST00000458013.2_Intron	NM_030918.5	NP_112180.4	Q96L92	SNX27_HUMAN	sorting nexin family member 27	NA		NA			endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			ggattacaggtgtgagccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(46;291 966 40145 41237 41888)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376	81609		Sorting nexins	20073	protein-coding gene	gene with protein product		611541			NA	12461558	Standard	NM_030918	XM_005245509	NA	Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000368843.3:c.311+7068T>C	chr1.hg19:g.151592056T>C		NA	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	hg19	CCDS1001.1	0.02	-0.271894	AGGxGTG	COVERED																																																																																			NOVEL	SNX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000104568.1	7	3.007784	KEEP	2	0	0	10	277	TT	0.99254	0.711964	0		+	3	60	100	0	0	7.19784	27	60	804	62	ENST00000368843.3	0.1	0.717315
SNX27	81609	__UNKNOWN__	__UNKNOWN__	1	151669006	151669006	__UNKNOWN__	3'UTR	SNP	T	T	G	rs1308138		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151669006T>G	ENST00000368843.3	+	0	4636				SNX27_ENST00000458013.2_3'UTR	NM_030918.5	NP_112180.4	Q96L92	SNX27_HUMAN	sorting nexin family member 27	NA		NA			endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			tcgttctttctttctttcttt	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(46;291 966 40145 41237 41888)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376	81609		Sorting nexins	20073	protein-coding gene	gene with protein product		611541			NA	12461558	Standard	NM_030918	XM_005245509	NA	Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000368843.3:c.*2929T>G	chr1.hg19:g.151669006T>G		NA	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	hg19	CCDS1001.1	0.02	2.891516	TTCxTTC	COVERED																																																																																			NOVEL	SNX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000104568.1	47	13.81008	KEEP	2	6	146	98	2539	TT	1	1	0		+	13	60	394	2	0	26.78432	128	60	3756	290	ENST00000368843.3	0.092199	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	151723868	151723868	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:151723868T>C			NA	NA				RNU6-662P (3692 upstream) : RP11-98D18.15 (4148 downstream)						NA		NA									NA						gtgatccacctgcctcggcct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.151723868T>C		NA		hg19		0.02	-0.306971	ACCxGCC	COVERED																																																																																			NOVEL					0			14	3.30855	KEEP	6	0	0	11	305	TT	0.992708	0.79441	0			3	60	99	0	0	7.097806	27	60	807	73		0.1	0.800245
HRNR	388697	__UNKNOWN__	__UNKNOWN__	1	152187166	152187166	__UNKNOWN__	Silent	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:152187166G>T	ENST00000368801.2	-	3	7014	c.6939C>A	c.(6937-6939)tcC>tcA	p.S2313S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2313		NA			establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCGTAGCTGGAAGAGTGCC	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													4	7	6			NA	NA	1		NA											NA				152187166		1105	2887	3992	SO:0001819	synonymous_variant			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915	388697		EF-hand domain containing	20846	protein-coding gene	gene with protein product	filaggrin family member 3	NA			NA		Standard	XM_373868	NM_001009931	NA	Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6939C>A	chr1.hg19:g.152187166G>T		NA	Q5DT20|Q5U1F4	hg19	CCDS30859.1	0.02	4.275438	GCTxGAA	COVERED																																																																																			NOVEL	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034016.1	29	5.248169	KEEP	394	4	106	55	1713	GG	0.999879	0.999879	0		-	11	27	333	0	0	20.839322	160	27	5309	839	ENST00000368801.2	0.064327	1
HRNR	388697	__UNKNOWN__	__UNKNOWN__	1	152187606	152187606	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs139799138		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:152187606G>A	ENST00000368801.2	-	3	6574	c.6499C>T	c.(6499-6501)Cgt>Tgt	p.R2167C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2167		NA			establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGACTGACGGGAGCCAGAC	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													191	230	217			NA	NA	1		NA											NA				152187606		2197	4277	6474	SO:0001583	missense			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915	388697		EF-hand domain containing	20846	protein-coding gene	gene with protein product	filaggrin family member 3	NA			NA		Standard	XM_373868	NM_001009931	NA	Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6499C>T	chr1.hg19:g.152187606G>A	ENSP00000357791:p.Arg2167Cys	NA	Q5DT20|Q5U1F4	hg19	CCDS30859.1	0.02	8.748987	GACxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	-	2.587	-0.296097	0.05532	.	.	ENSG00000197915	ENST00000368801	T	0.02216	4.39	2.68	-5.36	0.02689	.	.	.	.	.	T	0.00524	0.0017	L	0.39898	1.24	0.09310	N	1	B	0.19445	0.036	B	0.08055	0.003	T	0.42649	-0.9439	9	0.56958	D	0.05	.	2.6528	0.05003	0.1157:0.4324:0.2495:0.2024	.	2167	Q86YZ3	HORN_HUMAN	C	2167	ENSP00000357791:R2167C	ENSP00000357791:R2167C	R	-	1	0	HRNR	150454230	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-4.767000	0.00188	-2.797000	0.00353	-1.035000	0.02400	CGT	NOVEL	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034016.1	10	4.349483	KEEP	37	2	52	33	926	GG	0.999997	0.999997	0		-	33	47	968	0	0	65.81826	301	48	9849	608	ENST00000368801.2	0.098802	1
HRNR	388697	__UNKNOWN__	__UNKNOWN__	1	152188319	152188319	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201547528		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:152188319C>T	ENST00000368801.2	-	3	5861	c.5786G>A	c.(5785-5787)gGc>gAc	p.G1929D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1929		NA			establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGACGGGAGCCAGACCCATG	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													246	370	329			NA	NA	1		NA											NA				152188319		2123	4281	6404	SO:0001583	missense			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915	388697		EF-hand domain containing	20846	protein-coding gene	gene with protein product	filaggrin family member 3	NA			NA		Standard	XM_373868	NM_001009931	NA	Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5786G>A	chr1.hg19:g.152188319C>T	ENSP00000357791:p.Gly1929Asp	NA	Q5DT20|Q5U1F4	hg19	CCDS30859.1	0.02	5.930178	GAGxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	7.393	0.631191	0.14322	.	.	ENSG00000197915	ENST00000368801	T	0.04706	3.57	3.8	0.738	0.18319	.	.	.	.	.	T	0.02304	0.0071	L	0.59436	1.845	0.09310	N	1	D	0.59357	0.985	P	0.49477	0.612	T	0.36841	-0.9731	9	0.11182	T	0.66	.	7.319	0.26517	0.0:0.5813:0.3222:0.0965	.	1929	Q86YZ3	HORN_HUMAN	D	1929	ENSP00000357791:G1929D	ENSP00000357791:G1929D	G	-	2	0	HRNR	150454943	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.344000	0.19962	0.057000	0.16193	-0.265000	0.10407	GGC	NOVEL	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034016.1	23	8.591614	KEEP	75	2	55	48	1465	CC	1	1	0		-	13	47	387	0	0	23.209314	218	49	7267	486	ENST00000368801.2	0.056277	1
HRNR	388697	__UNKNOWN__	__UNKNOWN__	1	152188964	152188964	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs78582525	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:152188964C>T	ENST00000368801.2	-	3	5216	c.5141G>A	c.(5140-5142)aGc>aAc	p.S1714N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1714		NA			establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCGGCCGCGGCTAGGGGACTG	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													7	3	4			NA	NA	1		NA											NA				152188964		1115	2296	3411	SO:0001583	missense			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915	388697		EF-hand domain containing	20846	protein-coding gene	gene with protein product	filaggrin family member 3	NA			NA		Standard	XM_373868	NM_001009931	NA	Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.5141G>A	chr1.hg19:g.152188964C>T	ENSP00000357791:p.Ser1714Asn	NA	Q5DT20|Q5U1F4	hg19	CCDS30859.1	0.02	2.552339	CGGxTAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	5.643	0.303319	0.10678	.	.	ENSG00000197915	ENST00000368801	T	0.02085	4.46	2.47	1.44	0.22558	.	.	.	.	.	T	0.00695	0.0023	L	0.38175	1.15	0.09310	N	1	P	0.45531	0.86	B	0.43783	0.431	T	0.43278	-0.9401	9	0.16896	T	0.51	.	3.5335	0.07785	0.0:0.5652:0.2725:0.1623	.	1714	Q86YZ3	HORN_HUMAN	N	1714	ENSP00000357791:S1714N	ENSP00000357791:S1714N	S	-	2	0	HRNR	150455588	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.340000	0.19892	0.302000	0.22762	0.500000	0.49745	AGC	NOVEL	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000034016.1	8	4.077814	KEEP	155	2	49	31	959	CC	0.999366	0.999365	0		-	20	47	554	0	0	41.632768	98	45	3300	397	ENST00000368801.2	0.169492	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	153572704	153572704	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153572704C>G			NA	NA				S100A2 (32338 upstream) : S100A16 (6657 downstream)						NA		NA									NA						cagcactttgcgaggccgagg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.153572704C>G		NA		hg19		0.02	-0.140362	TTGxGAG	COVERED																																																																																			NOVEL					0			4	3.609797	KEEP	2	0	0	12	354	CC	0.993072	0.259157	0			3	60	106	0	0	8.678452	13	60	444	45		0.1875	0.260965
NPR1	4881	__UNKNOWN__	__UNKNOWN__	1	153658117	153658117	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153658117A>G	ENST00000368680.3	+	9	2077					NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	NA		NA			body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	tccagcctggatgacacaatg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(141;1349 1870 15144 15830 40702)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418	4881			7943	protein-coding gene	gene with protein product	guanylate cyclase A	108960	atrionatriuretic peptide receptor A, natriuretic peptide receptor A	ANPRA, NPRA	NA	1979052	Standard	NM_000906	NM_000906	NA	Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.1606-165A>G	chr1.hg19:g.153658117A>G		NA	B0ZBF0|Q5SR08|Q6P4Q3	hg19	CCDS1051.1	0.02	-0.219176	TGGxTGA	COVERED																																																																																			NOVEL	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090034.1	4	4.509353	KEEP	2	0	0	15	396	AA	0.994391	0.549786	0		+	4	60	129	0	0	10.280586	18	60	511	46	ENST00000368680.3	0.181818	0.552887
NPR1	4881	__UNKNOWN__	__UNKNOWN__	1	153662578	153662578	__UNKNOWN__	Intron	SNP	C	C	G	rs527673413		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153662578C>G	ENST00000368680.3	+	19	3404					NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	NA		NA			body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	ctctctctctctctctgtctc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(141;1349 1870 15144 15830 40702)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418	4881			7943	protein-coding gene	gene with protein product	guanylate cyclase A	108960	atrionatriuretic peptide receptor A, natriuretic peptide receptor A	ANPRA, NPRA	NA	1979052	Standard	NM_000906	NM_000906	NA	Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2932+122C>G	chr1.hg19:g.153662578C>G		NA	B0ZBF0|Q5SR08|Q6P4Q3	hg19	CCDS1051.1	0.02	-0.39474	TCTxTCT	COVERED																																																																																			NOVEL	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090034.1	8	3.911228	KEEP	6	0	0	13	388	CC	0.993634	0.920741	0		+	4	60	135	1	0	9.956389	32	60	1047	72	ENST00000368680.3	0.111111	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	153685846	153685846	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153685846T>C			NA	NA				RN7SL372P (8987 upstream) : Y_RNA (12881 downstream)						NA		NA									NA						tgcaatccagtctgggcaaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.153685846T>C		NA		hg19		0.02	-0.20172	CAGxCTG	COVERED																																																																																			NOVEL					0			10	2.705537	KEEP	0	0	0	9	233	TT	0.99254	0.486885	0			3	60	94	0	0	7.092565	18	60	526	47		0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	153756964	153756964	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153756964G>A			NA	NA				SLC27A3 (4331 upstream) : Y_RNA (1231 downstream)						NA		NA									NA						TTTtgtaaccgggcaccttaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.153756964G>A		NA		hg19		0.02	-0.263165	ACCxGGC	COVERED																																																																																			NOVEL					0			5	3.306276	KEEP	0	0	0	11	306	GG	0.993072	0.688863	0			7	60	217	0	0	18.462848	19	60	634	60		0.269231	0.693668
GATAD2B	57459	__UNKNOWN__	__UNKNOWN__	1	153886550	153886550	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153886550G>C	ENST00000368655.4	-	1	243					NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			gaaaccccatgtctactaaaa	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614	57459		GATA zinc finger domain containing	30778	protein-coding gene	gene with protein product	transcription repressor p66 beta component of the MeCP1 complex	614998			NA	10574461, 11756549	Standard	NM_020699	NM_020699	NA	Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.0+8658C>G	chr1.hg19:g.153886550G>C		NA	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	hg19	CCDS1054.1	0.02	-0.175436	CATxTCT	UNCOVERED																																																																																			NOVEL	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090305.1	7	2.406702	KEEP	2	0	0	8	234	GG	0	0	0		-	3	46	97	0	0	7.691934	14	60	454	36	ENST00000368655.4	0.176471	0.387407
DENND4B	9909	__UNKNOWN__	__UNKNOWN__	1	153909319	153909319	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153909319A>G	ENST00000361217.4	-	16	2651					NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	NA		NA			positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab protein signal transduction (GO:0032483)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	36	all_lung(78;2.89e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tcgctctgtcacccaggctgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007945	CCDS44228.1	1q21.3	2012-10-03	2006-01-27	2006-01-27	ENSG00000198837	ENSG00000198837	9909		DENN/MADD domain containing	29044	protein-coding gene	gene with protein product		NA	KIAA0476	KIAA0476	NA	9455484, 12906859	Standard	XM_375806	NM_014856	NA	Approved		uc001fdd.1	O75064	OTTHUMG00000037157	ENST00000361217.4:c.2233-95T>C	chr1.hg19:g.153909319A>G		NA	Q5T4K0	hg19	CCDS44228.1	0.02	1.605044	GTCxCCC	COVERED																																																																																			NOVEL	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090278.2	11	5.099492	KEEP	0	3	88	48	1255	AA	1	0.998993	0		-	4	60	131	1	0	8.208703	72	60	2056	182	ENST00000361217.4	0.052632	0.998993
CREB3L4	148327	__UNKNOWN__	__UNKNOWN__	1	153944588	153944588	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:153944588T>C	ENST00000368607.3	+	5	809				CREB3L4_ENST00000368601.1_Intron|CREB3L4_ENST00000368603.1_Intron|CREB3L4_ENST00000405694.3_Intron|CREB3L4_ENST00000368600.3_Intron|CREB3L4_ENST00000271889.4_Intron|CREB3L4_ENST00000468845.1_Intron	NM_001255978.1|NM_001255980.1|NM_130898.3	NP_001242907.1|NP_001242909.1|NP_570968.1	Q8TEY5	CR3L4_HUMAN	cAMP responsive element binding protein 3-like 4	NA		NA			response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(3)	13	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			tgtgagccactgtgcccggcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF394167	CCDS1056.1, CCDS58029.1	1q21.2	2013-01-10			ENSG00000143578	ENSG00000143578	148327		basic leucine zipper proteins	18854	protein-coding gene	gene with protein product		607138			NA		Standard	NM_130898	NM_130898	NA	Approved	AIbZIP, CREB4, CREB3, hJAL, ATCE1	uc001fdr.3	Q8TEY5	OTTHUMG00000037159	ENST00000368607.3:c.544-632T>C	chr1.hg19:g.153944588T>C		NA	D3DV62|Q5T4L0|Q86YW6	hg19	CCDS1056.1	0.02	-0.192928	CACxGTG	COVERED																																																																																			NOVEL	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090291.1	8	3.308156	KEEP	0	0	0	11	305	TT	0.993072	0.454585	0		+	3	60	89	0	0	6.593627	18	60	536	44	ENST00000368607.3	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	154271271	154271271	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:154271271T>C			NA	NA				RNU6-121P (1047 upstream) : AQP10 (22294 downstream)						NA		NA									NA						tgtggtggcttacgcctgtaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.154271271T>C		NA		hg19		0.02	-0.228003	GCTxACG	COVERED																																																																																			NOVEL					0			17	4.810265	KEEP	0	0	0	16	418	TT	0.997832	0.581666	0			3	60	98	0	0	7.195066	23	60	652	55		0.115385	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	154287188	154287188	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:154287188A>G			NA	NA				RNU6-121P (16964 upstream) : AQP10 (6377 downstream)						NA		NA									NA						tgcccaggctagagtgcaatg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.154287188A>G		NA		hg19		0.02	-0.184156	GCTxGAG	COVERED																																																																																			NOVEL					0			12	3.006942	KEEP	0	0	0	10	265	AA	0.992708	0.42039	0			3	60	90	0	0	7.382527	10	60	283	42		0.230769	0.423478
ADAR	103	__UNKNOWN__	__UNKNOWN__	1	154580287	154580287	__UNKNOWN__	Intron	SNP	C	C	A	rs113834550		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:154580287C>A	ENST00000368474.4	-	1	215				ADAR_ENST00000471068.1_Intron|ADAR_ENST00000368471.3_Intron|ADAR_ENST00000292205.5_Intron	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	NA		NA			adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		CGACACACACCCACACACACA	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	103	3.5.4.-		225	protein-coding gene	gene with protein product		146920	interferon-induced protein 4	IFI4, G1P1	NA	7972084	Standard	NM_001111	NM_001111	NA	Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.15+180G>T	chr1.hg19:g.154580287C>A		NA	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	hg19	CCDS1071.1	0.02	1.292123	CACxCAC	COVERED																																																																																			NOVEL	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090691.2	25	3.939046	KEEP	2	7	180	77	2247	CC	1	0.999862	0		-	5	60	136	0	0	7.833184	77	60	2518	217	ENST00000368474.4	0.060976	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	154605660	154605660	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:154605660A>G			NA	NA				ADAR (5185 upstream) : KCNN3 (64270 downstream)						NA		NA									NA						ggctgaggtgagcagatcacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.154605660A>G		NA		hg19		0.02	-0.166647	GTGxGCA	UNCOVERED																																																																																			NOVEL					0			9	2.707041	KEEP	3	0	0	9	251	AA	0	0	0			3	60	93	0	0	7.133642	16	60	482	38		0.157895	0.353947
KCNN3	3782	__UNKNOWN__	__UNKNOWN__	1	154823744	154823744	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:154823744T>C	ENST00000271915.4	-	1	1249				KCNN3_ENST00000361147.4_Intron|KCNN3_ENST00000358505.2_Intron	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	NA		NA			potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	tgagccaccgtgcccggccAA	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603	3782		Potassium channels, Voltage-gated ion channels / Potassium channels, calcium-activated	6292	protein-coding gene	gene with protein product		602983			NA	9491810, 16382103	Standard	NM_002249	NM_002249	NA	Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.933+17763A>G	chr1.hg19:g.154823744T>C		NA	B1ANX0|O43517|Q86VF9|Q8WXG7	hg19	CCDS30880.1	0.02	-0.17539	CCGxGCC	UNCOVERED																																																																																			NOVEL	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090688.3	7	2.706629	KEEP	2	0	0	9	247	TT	0	0	0		-	3	60	95	0	0	7.333877	16	60	457	36	ENST00000271915.4	0.157895	0.387407
TRIM46	80128	__UNKNOWN__	__UNKNOWN__	1	155155055	155155055	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155155055G>A	ENST00000334634.4	+	9	1886				TRIM46_ENST00000368383.3_3'UTR|TRIM46_ENST00000368382.1_Intron|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000545012.1_Intron|TRIM46_ENST00000468878.1_Intron|TRIM46_ENST00000392451.2_Intron	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	NA		NA				intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			ggtggctcacgcctgtaatcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462	80128		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	19019	protein-coding gene	gene with protein product		600986	tripartite motif-containing 46		NA		Standard	NM_025058	NM_025058	NA	Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.1886+430G>A	chr1.hg19:g.155155055G>A		NA	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	hg19	CCDS1097.1	0.02	2.302841	CACxCCT	COVERED																																																																																			NOVEL	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086728.1	16	3.039495	KEEP	0	4	92	43	1298	GG	1	0.999999	0		+	6	60	171	0	0	9.796894	107	60	3560	242	ENST00000334634.4	0.053097	0.999999
CLK2	1196	__UNKNOWN__	__UNKNOWN__	1	155244557	155244557	__UNKNOWN__	Intron	SNP	A	A	G	rs560859406	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155244557A>G	ENST00000536801.1	-	1	173							P49760	CLK2_HUMAN	CDC-like kinase 2	NA		NA			negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			ttgggaggccaaggcgggcgg	0.547		NA						Other conserved DNA damage response genes					C|||	109	0.0217652	0.0794	0.0058	5008	,	,	NA	13804	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444	1196		CDC-like kinases	2069	protein-coding gene	gene with protein product		602989			NA	7990150, 9856501	Standard	NM_003993	XM_005244876	NA	Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000536801.1:c.0+2771T>C	chr1.hg19:g.155244557A>G		NA	B1AVS9|B5MBX6|Q96CQ0	hg19		0.02	-0.184183	GCCxAGG	COVERED																																																																																			NOVEL	CLK2-201	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000087391.1	9	4.210828	KEEP	18	0	0	14	388	AA	0.99257	0.420331	0		-	3	60	102	0	0	8.033307	16	60	463	69	ENST00000536801.1	0.157895	0.423478
RUSC1	23623	__UNKNOWN__	__UNKNOWN__	1	155298640	155298640	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155298640T>C	ENST00000368352.5	+	9	2691				RUSC1_ENST00000292254.4_Intron|RUSC1_ENST00000368354.3_Intron|RUSC1_ENST00000462780.1_Intron|RUSC1_ENST00000368347.4_Intron|RUSC1_ENST00000368349.4_Intron	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	NA		NA			positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			ccgcccgccttggcctcccaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753	23623			17153	protein-coding gene	gene with protein product		NA			NA	10760598	Standard		NM_001105203	NA	Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.2540+574T>C	chr1.hg19:g.155298640T>C		NA	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	hg19	CCDS41410.1	0.02	-0.122779	CCTxGGC	COVERED																																																																																			NOVEL	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039071.1	10	2.343515	KEEP	0	0	0	8	191	TT	0.99257	0.194853	0		+	4	60	126	0	0	11.191545	8	60	232	26	ENST00000368352.5	0.333333	0.196312
ASH1L	55870	__UNKNOWN__	__UNKNOWN__	1	155364999	155364999	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155364999T>C	ENST00000392403.3	-	7	6582				ASH1L_ENST00000368346.3_Intron	NM_018489.2	NP_060959.2	Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	NA		NA			cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			gctaggattataggcatgagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539	55870		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	19088	protein-coding gene	gene with protein product		607999			NA	10860993, 16545939	Standard	NM_018489	NM_018489	NA	Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000392403.3:c.6103+250A>G	chr1.hg19:g.155364999T>C		NA	Q59GP1|Q5T714|Q5T715|Q9P2C7	hg19	CCDS1113.2	0.02	-0.157677	TTAxAGG	COVERED																																																																																			NOVEL	ASH1L-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039401.2	7	2.405446	KEEP	0	0	0	8	212	TT	0.99257	0.351317	0		-	3	60	105	0	0	8.493715	14	60	393	40	ENST00000392403.3	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	155547810	155547810	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155547810T>C			NA	NA				ASH1L-AS1 (14075 upstream) : RP11-29H23.4 (31756 downstream)						NA		NA									NA						gctgggattataggcatgagc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.155547810T>C		NA		hg19		0.02	-0.078929	TTAxAGG	UNCOVERED																																																																																			NOVEL					0			5	2.405633	KEEP	1	0	0	8	214	TT	0.99257	0.076761	0			3	60	102	0	0	9.144067	6	60	168	22		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	155579267	155579267	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155579267T>C			NA	NA				ASH1L-AS1 (45532 upstream) : RP11-29H23.4 (299 downstream)						NA		NA									NA						tctcgatctcttgacctcgtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.155579267T>C		NA		hg19		0.02	-0.140338	CTCxTGA	COVERED																																																																																			NOVEL					0			9	3.909068	KEEP	10	0	0	13	352	TT	0.99257	0.259026	0			3	48	102	0	0	8.372175	12	60	359	49		0.2	0.260965
MSTO1	55154	__UNKNOWN__	__UNKNOWN__	1	155584194	155584194	__UNKNOWN__	3'UTR	SNP	G	G	A	rs564968560	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155584194G>A	ENST00000245564.2	+	0	1867				MSTO1_ENST00000538143.1_Intron|MSTO1_ENST00000452804.2_Intron|MSTO1_ENST00000368341.4_3'UTR|MSTO1_ENST00000483734.1_3'UTR	NM_001256532.1|NM_001256533.1|NM_018116.3	NP_001243461.1|NP_001243462.1|NP_060586.2	Q9BUK6	MSTO1_HUMAN	misato 1, mitochondrial distribution and morphology regulator	NA		NA			mitochondrion distribution (GO:0048311)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)				breast(2)|endometrium(1)|lung(3)|skin(1)	7	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)					TTTACATTTAGAAACACTGTG	0.428		NA											G|||	14	0.00279553	0.0015	0.0	5008	,	,	NA	21919	0.0	NA	0.0119	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX537684	CCDS1114.1	1q22	2013-08-21	2013-08-21		ENSG00000125459	ENSG00000125459	55154			29678	protein-coding gene	gene with protein product		NA	misato homolog 1 (Drosophila)		NA	16545939, 17349998	Standard	NM_018116	NM_018116	NA	Approved	FLJ10504, LST005, MST, misato	uc001fky.4	Q9BUK6	OTTHUMG00000014014	ENST00000245564.2:c.*130G>A	chr1.hg19:g.155584194G>A		NA	Q53GR8|Q5CZ69|Q5T717|Q68CT6|Q7LBZ8|Q7Z3M7|Q7Z558|Q8TE05|Q9NQX2|Q9NVU4	hg19	CCDS1114.1	0.02	-0.324557	TTAxAAA	UNCOVERED																																																																																			NOVEL	MSTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039408.1	3	3.242655	KEEP	129	1	26	20	617	GG	0	0	0		+	14	33	424	0	0	38.420157	23	50	777	270	ENST00000245564.2	0.378378	0.835716
MSTO1	55154	__UNKNOWN__	__UNKNOWN__	1	155619074	155619074	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155619074T>C	ENST00000452804.2	+	6	621				MSTO1_ENST00000538143.1_Intron			Q9BUK6	MSTO1_HUMAN	misato 1, mitochondrial distribution and morphology regulator	NA		NA			mitochondrion distribution (GO:0048311)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)				breast(2)|endometrium(1)|lung(3)|skin(1)	7	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)					gatggagttttgctcttgttg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX537684	CCDS1114.1	1q22	2013-08-21	2013-08-21		ENSG00000125459	ENSG00000125459	55154			29678	protein-coding gene	gene with protein product		NA	misato homolog 1 (Drosophila)		NA	16545939, 17349998	Standard	NM_018116	NM_018116	NA	Approved	FLJ10504, LST005, MST, misato	uc001fky.4	Q9BUK6	OTTHUMG00000014014	ENST00000452804.2:c.560+37456T>C	chr1.hg19:g.155619074T>C		NA	Q53GR8|Q5CZ69|Q5T717|Q68CT6|Q7LBZ8|Q7Z3M7|Q7Z558|Q8TE05|Q9NQX2|Q9NVU4	hg19		0.02	-0.210467	TTTxGCT	UNCOVERED																																																																																			NOVEL	MSTO1-201	KNOWN	basic	protein_coding	NA	protein_coding		17	2.70649	KEEP	12	0	0	9	243	TT	0	0	0		+	3	40	90	0	1	6.506808	21	60	610	53	ENST00000452804.2	0.125	0.522161
MSTO1	55154	__UNKNOWN__	__UNKNOWN__	1	155619331	155619331	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155619331C>T	ENST00000452804.2	+	6	621				MSTO1_ENST00000538143.1_Intron			Q9BUK6	MSTO1_HUMAN	misato 1, mitochondrial distribution and morphology regulator	NA		NA			mitochondrion distribution (GO:0048311)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)				breast(2)|endometrium(1)|lung(3)|skin(1)	7	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)					catgagccaccgcacctggcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX537684	CCDS1114.1	1q22	2013-08-21	2013-08-21		ENSG00000125459	ENSG00000125459	55154			29678	protein-coding gene	gene with protein product		NA	misato homolog 1 (Drosophila)		NA	16545939, 17349998	Standard	NM_018116	NM_018116	NA	Approved	FLJ10504, LST005, MST, misato	uc001fky.4	Q9BUK6	OTTHUMG00000014014	ENST00000452804.2:c.560+37713C>T	chr1.hg19:g.155619331C>T		NA	Q53GR8|Q5CZ69|Q5T717|Q68CT6|Q7LBZ8|Q7Z3M7|Q7Z558|Q8TE05|Q9NQX2|Q9NVU4	hg19		0.02	1.493788	CACxGCA	COVERED																																																																																			NOVEL	MSTO1-201	KNOWN	basic	protein_coding	NA	protein_coding		11	9.627245	KEEP	0	0	0	32	947	CC	0.999997	0.995684	0		+	5	60	148	0	1	9.644772	57	60	1835	144	ENST00000452804.2	0.080645	0.995687
YY1AP1	55249	__UNKNOWN__	__UNKNOWN__	1	155643616	155643616	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155643616C>T	ENST00000359205.5	-	6	637				MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000355499.4_Intron|YY1AP1_ENST00000347088.5_Intron|YY1AP1_ENST00000368339.5_Intron|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000368330.2_Intron|YY1AP1_ENST00000404643.1_Intron|YY1AP1_ENST00000368340.5_Intron|YY1AP1_ENST00000535662.1_Intron|YY1AP1_ENST00000311573.5_Intron|YY1AP1_ENST00000361831.5_Intron|YY1AP1_ENST00000405763.3_Intron|YY1AP1_ENST00000295566.4_Intron|YY1AP1_ENST00000438245.2_Intron|YY1AP1_ENST00000407221.1_Intron|YY1AP1_ENST00000476093.1_Intron	NM_001198900.1	NP_001185829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	NA		NA			regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					agtgctgggactacaggcatg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374	55249			30935	protein-coding gene	gene with protein product		607860			NA	11710830	Standard	NM_139118	NM_139119	NA	Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000359205.5:c.379-1094G>A	chr1.hg19:g.155643616C>T		NA	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	hg19		0.02	-0.228079	GGAxTAC	COVERED																																																																																			NOVEL	YY1AP1-027	PUTATIVE	alternative_5_UTR|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000086021.2	16	4.513034	KEEP	0	0	0	15	451	CC	0.99649	0.580884	0		-	4	60	121	0	0	9.313725	20	60	682	50	ENST00000359205.5	0.166667	0.58293
YY1AP1	55249	__UNKNOWN__	__UNKNOWN__	1	155650613	155650613	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155650613T>C	ENST00000359205.5	-	3	247				MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000355499.4_Intron|YY1AP1_ENST00000347088.5_Intron|YY1AP1_ENST00000368339.5_Intron|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000368330.2_Intron|YY1AP1_ENST00000404643.1_Intron|YY1AP1_ENST00000368340.5_Intron|YY1AP1_ENST00000311573.5_Intron|YY1AP1_ENST00000361831.5_Intron|YY1AP1_ENST00000405763.3_Intron|YY1AP1_ENST00000295566.4_Intron|YY1AP1_ENST00000438245.2_Intron|YY1AP1_ENST00000407221.1_Intron|YY1AP1_ENST00000476093.1_Intron	NM_001198900.1	NP_001185829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	NA		NA			regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					ccaccttggcttcccaaagtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374	55249			30935	protein-coding gene	gene with protein product		607860			NA	11710830	Standard	NM_139118	NM_139119	NA	Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000359205.5:c.12-1310A>G	chr1.hg19:g.155650613T>C		NA	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	hg19		0.02	-0.175417	GGCxTCC	COVERED																																																																																			NOVEL	YY1AP1-027	PUTATIVE	alternative_5_UTR|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000086021.2	8	2.691653	KEEP	1	0	0	9	236	TT	0.99257	0.384528	0		-	3	60	92	0	0	7.110813	15	60	451	37	ENST00000359205.5	0.166667	0.387407
DAP3	7818	__UNKNOWN__	__UNKNOWN__	1	155701044	155701044	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155701044C>T	ENST00000368336.5	+	10	967				MSTO1_ENST00000538143.1_Intron|DAP3_ENST00000421487.2_Intron|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000471642.2_Intron|DAP3_ENST00000535183.1_Intron|DAP3_ENST00000343043.3_Intron	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	NA		NA			apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					ggcgacagagcgagactctgt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676	7818		Mitochondrial ribosomal proteins / small subunits	2673	protein-coding gene	gene with protein product	mitochondrial 28S ribosomal protein S29	602074			NA	7499268, 9284927	Standard	NM_004632	NM_004632	NA	Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.844-103C>T	chr1.hg19:g.155701044C>T		NA	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	hg19	CCDS1120.1	0.02	2.619446	GAGxGAG	COVERED																																																																																			NOVEL	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086042.1	23	9.252273	KEEP	1	4	99	66	1931	CC	1	1	0		+	7	60	188	0	2	10.744899	107	60	3515	328	ENST00000368336.5	0.061404	1
GON4L	54856	__UNKNOWN__	__UNKNOWN__	1	155729027	155729027	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155729027A>T	ENST00000437809.1	-	25	5232				GON4L_ENST00000271883.5_Intron|GON4L_ENST00000368331.1_Intron	NM_001282856.1	NP_001269785.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	NA		NA			regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					gtgctgggataacaggtgtga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580	54856			25973	protein-coding gene	gene with protein product		610393	gon-4 homolog (C.elegans)	GON4	NA	16545939, 21454521	Standard	NM_032292	XM_005245283	NA	Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000437809.1:c.5110-1202T>A	chr1.hg19:g.155729027A>T		NA	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	hg19	CCDS44242.1	0.02	-0.219244	GATxACA	COVERED																																																																																			NOVEL	GON4L-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340937.1	11	5.112204	KEEP	0	0	0	17	461	AA	0.999366	0.552537	0		-	3	60	88	0	0	6.366106	20	60	573	70	ENST00000437809.1	0.130435	0.552887
GON4L	54856	__UNKNOWN__	__UNKNOWN__	1	155798274	155798274	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155798274A>G	ENST00000437809.1	-	3	628				GON4L_ENST00000271883.5_Intron|GON4L_ENST00000361040.5_Intron|GON4L_ENST00000471341.1_Intron|GON4L_ENST00000368331.1_Intron	NM_001282856.1	NP_001269785.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	NA		NA			regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					aacagagcgaaactccatctc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580	54856			25973	protein-coding gene	gene with protein product		610393	gon-4 homolog (C.elegans)	GON4	NA	16545939, 21454521	Standard	NM_032292	XM_005245283	NA	Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000437809.1:c.506-1455T>C	chr1.hg19:g.155798274A>G		NA	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	hg19	CCDS44242.1	0.02	-0.210486	CGAxACT	COVERED																																																																																			NOVEL	GON4L-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340937.1	8	2.705758	KEEP	0	0	0	9	243	AA	0.99254	0.518266	0		-	3	60	89	0	0	6.734934	16	60	478	46	ENST00000437809.1	0.157895	0.522161
KIAA0907	22889	__UNKNOWN__	__UNKNOWN__	1	155885577	155885577	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155885577C>T	ENST00000368321.3	-	13	1669				KIAA0907_ENST00000368320.3_3'UTR	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	NA		NA					RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			ggattacaggcgtgagccact	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680	22889			29145	protein-coding gene	gene with protein product		NA			NA	10048485	Standard	NM_014949	NM_014949	NA	Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.1645+86G>A	chr1.hg19:g.155885577C>T		NA	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	hg19	CCDS30885.1	0.02	5.658883	AGGxGTG	COVERED																																																																																			NOVEL	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039583.1	80	26.700079	KEEP	2	4	108	127	3777	CC	1	1	0		-	8	60	236	0	0	13.00149	184	69	6105	546	ENST00000368321.3	0.041667	1
ARHGEF2	9181	__UNKNOWN__	__UNKNOWN__	1	155965332	155965332	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155965332A>G	ENST00000477754.2	-	2	657				RP11-336K24.5_ENST00000415726.1_RNA			Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	NA		NA			actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					tgatccgcccacctcggcctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(178;35 2768 6610 28839)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584	9181		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	682	protein-coding gene	gene with protein product		607560	rho/rac guanine nucleotide exchange factor (GEF) 2		NA	9857026, 9734811	Standard	NM_004723	NM_004723	NA	Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000477754.2:c.226+553T>C	chr1.hg19:g.155965332A>G		NA	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	hg19		0.02	-0.280652	CCCxCCT	COVERED																																																																																			NOVEL	ARHGEF2-014	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000046217.2	15	4.811695	KEEP	9	0	0	16	439	AA	0.994391	0.735522	0		-	3	60	92	0	0	6.446971	26	60	780	81	ENST00000477754.2	0.103448	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	155993018	155993018	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:155993018T>C			NA	NA				SSR2 (2268 upstream) : UBQLN4 (12073 downstream)						NA		NA									NA						aggatggtcttgatctcctga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.155993018T>C		NA		hg19		0.02	-0.184152	TCTxGAT	COVERED																																																																																			NOVEL					0			7	2.706575	KEEP	0	0	0	9	246	TT	0.99254	0.420319	0			3	60	87	0	0	6.779864	13	60	367	38		0.1875	0.423478
UBQLN4	56893	__UNKNOWN__	__UNKNOWN__	1	156016035	156016035	__UNKNOWN__	Intron	SNP	T	T	C	rs12136348	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156016035T>C	ENST00000368309.3	-	6	993					NM_020131.3	NP_064516.2	Q9NRR5	UBQL4_HUMAN	ubiquilin 4	NA		NA			regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|polyubiquitin binding (GO:0031593)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)	16	Hepatocellular(266;0.133)|all_neural(408;0.195)					tcccagcactttgggaggccg	0.433		NA											T|||	2041	0.407548	0.2678	0.5865	5008	,	,	NA	11843	0.1994	NA	0.5378	False	NA	,,,	NA	NA	NA	2504	0.5501	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC018403	CCDS1127.1	1q21	2013-02-12	2004-11-05	2004-11-06	ENSG00000160803	ENSG00000160803	56893		Ubiquilin family	1237	protein-coding gene	gene with protein product	ataxin-1 ubiquitin-like interacting protein	605440	chromosome 1 open reading frame 6	C1orf6	NA	10575211, 11001934	Standard	NM_020131	NM_020131	NA	Approved	A1U, UBIN	uc001fna.3	Q9NRR5	OTTHUMG00000017461	ENST00000368309.3:c.901-2021A>G	chr1.hg19:g.156016035T>C		NA	A6ND44|B2RAY7|Q5VYA0|Q5VYA1|Q9BR98|Q9UHX4	hg19	CCDS1127.1	0.02	-0.201743	ACTxTGG	UNCOVERED																																																																																			NOVEL	UBQLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046193.1	4	3.007906	KEEP	7	0	0	10	280	TT	0	0	0		-	3	60	103	0	0	7.991941	18	60	556	62	ENST00000368309.3	0.142857	0.490544
LMNA	4000	__UNKNOWN__	__UNKNOWN__	1	156090326	156090326	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156090326T>C	ENST00000368300.4	+	1	568				LMNA_ENST00000368301.2_Intron|LMNA_ENST00000361308.4_Intron|LMNA_ENST00000368299.3_Intron|LMNA_ENST00000347559.2_Intron	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					ttgagaccagtctgggcaaca	0.527		NA							Werner syndrome;Hutchinson-Gilford Progeria Syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789	4000		Intermediate filaments type V, lamins	6636	protein-coding gene	gene with protein product		150330	cardiomyopathy, dilated 1A (autosomal dominant), limb girdle muscular dystrophy 1B (autosomal dominant), progeria 1 (Hutchinson-Gilford type), lamin A/C-like 1	LMN1, CMD1A, LGMD1B, PRO1, LMNL1	NA	8511676, 8838815, 12702809	Standard	NM_170707	NM_005572	NA	Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.356+5261T>C	chr1.hg19:g.156090326T>C		NA	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	hg19	CCDS1129.1	0.02	-0.28067	CAGxCTG	COVERED																																																																																			NOVEL	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039200.2	13	4.812162	KEEP	2	0	0	16	439	TT	0.995343	0.736227	0		+	5	60	159	1	0	12.759484	21	60	631	70	ENST00000368300.4	0.192308	0.739671
RP11-284F21.8	0	__UNKNOWN__	__UNKNOWN__	1	156481237	156481237	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156481237A>G	ENST00000564032.1	+	0	1592										NA		NA									NA						cctgaggtcaagagtttgaga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000564032.1:	chr1.hg19:g.156481237A>G		NA		hg19		0.02	-0.105252	TCAxGAG	UNCOVERED																																																																																			NOVEL	RP11-284F21.8-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000431510.1	9	3.308524	KEEP	6	0	0	11	306	AA	0.993072	0.138863	0		+	3	60	107	0	0	9.201277	9	60	263	43	ENST00000564032.1	0.25	0.139832
IQGAP3	128239	__UNKNOWN__	__UNKNOWN__	1	156499467	156499467	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156499467T>C	ENST00000361170.2	-	34	4415					NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	NA		NA			activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					aatcccagcattttgggaggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856	128239			20669	protein-coding gene	gene with protein product		NA			NA		Standard	NM_178229	NM_178229	NA	Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.4404+429A>G	chr1.hg19:g.156499467T>C		NA	Q5T3H8	hg19	CCDS1144.1	0.02	-0.28052	GCAxTTT	COVERED																																																																																			NOVEL	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080657.1	14	3.007355	KEEP	0	0	0	10	274	TT	0.992708	0.734278	0		-	3	60	107	0	0	7.992714	25	60	714	56	ENST00000361170.2	0.107143	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	156600102	156600102	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156600102T>C			NA	NA				HAPLN2 (4585 upstream) : RP11-284F21.9 (7472 downstream)						NA		NA									NA						cttcccgccttggcctcccaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.156600102T>C		NA		hg19		0.02	-0.192956	CCTxGGC	COVERED																																																																																			NOVEL					0			7	3.910117	KEEP	2	0	0	13	361	TT	0.993634	0.454842	0			3	60	93	0	0	7.133703	16	60	473	48		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	156600117	156600117	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156600117T>C			NA	NA				HAPLN2 (4600 upstream) : RP11-284F21.9 (7457 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.156600117T>C		NA		hg19		0.02	-0.175428	GTGxTGG	COVERED																																																																																			NOVEL					0			6	3.909856	KEEP	2	0	0	13	359	TT	0.993634	0.38494	0			3	60	108	0	0	8.79154	14	60	424	47		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	156656004	156656004	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156656004T>C			NA	NA				NES (8815 upstream) : RP11-66D17.3 (1482 downstream)						NA		NA									NA						cgctctgtcatccaggctgga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.156656004T>C		NA		hg19		0.02	-0.236801	TCAxCCA	COVERED																																																																																			NOVEL					0			7	2.70654	KEEP	0	0	0	9	244	TT	0.99254	0.607839	0			3	60	102	0	0	7.542446	24	60	711	50		0.111111	0.612407
RP11-66D17.3	0	__UNKNOWN__	__UNKNOWN__	1	156657900	156657900	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156657900G>A	ENST00000441272.2	-	0	3708										NA		NA									NA						ctggagtgcagtggcgccatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000441272.2:	chr1.hg19:g.156657900G>A		NA		hg19		0.02	-0.175451	GCAxTGG	COVERED																																																																																			NOVEL	RP11-66D17.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000098960.2	5	4.212141	KEEP	0	0	0	14	422	GG	0.995343	0.385603	0		-	3	60	87	0	0	6.53377	16	60	562	49	ENST00000441272.2	0.157895	0.387407
MRPL24	79590	__UNKNOWN__	__UNKNOWN__	1	156709749	156709749	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156709749A>G	ENST00000361531.2	-	1	77				MRPL24_ENST00000368211.4_Intron			Q96A35	RM24_HUMAN	mitochondrial ribosomal protein L24	NA		NA			translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(1)|lung(4)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					gtgagccaccacgcccatcca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051341	CCDS1155.1	1q23.1	2012-11-14			ENSG00000143314	ENSG00000143314	79590		Mitochondrial ribosomal proteins / large subunits	14037	protein-coding gene	gene with protein product		611836			NA		Standard	NM_145729	NM_145729	NA	Approved	MRP-L18	uc001fpx.1	Q96A35	OTTHUMG00000041296	ENST00000361531.2:c.59+1054T>C	chr1.hg19:g.156709749A>G		NA	D3DVC8|Q53G65|Q53HT0|Q5SYZ9|Q5SZ00|Q5SZ02|Q96Q70|Q9H7G3	hg19	CCDS1155.1	0.02	-0.166617	ACCxCGC	COVERED																																																																																			NOVEL	MRPL24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098955.1	8	3.00627	KEEP	1	0	0	10	259	AA	0.992708	0.351366	0		-	3	60	102	0	0	8.279136	13	60	372	38	ENST00000361531.2	0.1875	0.353947
HDGF	3068	__UNKNOWN__	__UNKNOWN__	1	156721807	156721807	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:156721807C>T	ENST00000368209.5	-	1	196				HDGF_ENST00000368206.5_Intron|PRCC_ENST00000491853.1_Intron|HDGF_ENST00000465180.1_Intron	NM_001126051.1	NP_001119523.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		CCCGCCCTTCCCCCGACTCCG	0.721		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													56	54	55			NA	NA	1		NA											NA				156721807		692	1591	2283	SO:0001627	intron_variant			D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321	3068			4856	protein-coding gene	gene with protein product	high-mobility group protein 1-like	600339	hepatoma-derived growth factor (high-mobility group protein 1-like)		NA	8833162	Standard	NM_004494	NM_004494	NA	Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000368209.5:c.66+22G>A	chr1.hg19:g.156721807C>T		NA	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	hg19	CCDS44248.1	0.02	-0.350856	TTCxCCC	COVERED																																																																																			NOVEL	HDGF-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098947.1	0	4.814513	KEEP	0	0	0	16	500	CC	0.997832	0.875805	0		-	8	60	229	0	0	18.026562	32	60	1064	68	ENST00000368209.5	0.2	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	157528496	157528496	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:157528496T>C			NA	NA				FCRL5 (6186 upstream) : FCRL4 (15042 downstream)						NA		NA									NA						gtggctcacatctgtaatccc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.157528496T>C		NA		hg19		0.02	-0.219274	ACAxCTG	UNCOVERED																																																																																			NOVEL					0			7	2.405575	KEEP	1	0	0	8	213	TT	0	0	0			3	60	106	0	0	8.291933	18	60	537	50		0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	157924894	157924894	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:157924894T>C			NA	NA				RP11-451O13.1 (6033 upstream) : KIRREL (38168 downstream)						NA		NA									NA						ttgagaccagtctgggcaaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.157924894T>C		NA		hg19		0.02	-0.236751	CAGxCTG	COVERED																																																																																			NOVEL					0			14	2.704644	KEEP	0	0	0	9	230	TT	0.99254	0.607839	0			4	60	140	0	0	11.136531	21	60	605	45		0.16	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	158686869	158686869	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:158686869T>C			NA	NA				OR6K2 (16383 upstream) : OR6K3 (88 downstream)						NA		NA									NA						gatcatgccattgcactccag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.158686869T>C		NA		hg19		0.02	3.488073	CCAxTGC	COVERED																																																																																			NOVEL					0			19	3.281945	KEEP	3	9	264	104	2718	TT	1	1	0			6	60	208	2	0	13.236146	118	60	3358	347		0.048387	1
DCAF8	50717	__UNKNOWN__	__UNKNOWN__	1	160207569	160207569	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:160207569G>A	ENST00000556710.1	-	10	1577				DCAF8_ENST00000608310.1_Intron|DCAF8_ENST00000326837.2_Intron|DCAF8_ENST00000368073.3_Intron|DCAF8_ENST00000368074.1_Intron			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	NA		NA			protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(16)|skin(3)|upper_aerodigestive_tract(1)	33						gcctcaagcagtcctcccacc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093176	CCDS1200.1	1q22-q23	2013-01-09	2009-07-17	2009-07-17	ENSG00000132716	ENSG00000132716	50717		WD repeat domain containing, DDB1 and CUL4 associated factors	24891	protein-coding gene	gene with protein product		615820	WD repeat domain 42A	WDR42A	NA	11401431	Standard	NM_015726	NM_015726	NA	Approved	H326, FLJ35857	uc010pjb.1	Q5TAQ9	OTTHUMG00000031604	ENST00000556710.1:c.1327-550C>T	chr1.hg19:g.160207569G>A		NA	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	hg19		0.02	-0.324567	GCAxTCC	COVERED																																																																																			NOVEL	DCAF8-001	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000415203.1	8	3.610769	KEEP	0	0	0	12	366	GG	0.993634	0.830395	0		-	5	60	140	0	0	10.293545	28	60	957	74	ENST00000556710.1	0.151515	0.835716
COPA	1314	__UNKNOWN__	__UNKNOWN__	1	160267926	160267926	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:160267926A>G	ENST00000241704.7	-	20	2207				COPA_ENST00000368069.3_Intron	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	NA		NA			COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			agccgagatcatgccattgca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218	1314		WD repeat domain containing, Endogenous ligands	2230	protein-coding gene	gene with protein product	proxenin, xenin	601924			NA	8647451	Standard	NM_004371	NM_004371	NA	Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.1978-391T>C	chr1.hg19:g.160267926A>G		NA	Q5T201|Q8IXZ9	hg19	CCDS1202.1	0.02	-0.201708	ATCxTGC	COVERED																																																																																			NOVEL	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080638.1	5	3.007681	KEEP	1	0	0	10	276	AA	0.992708	0.486967	0		-	3	60	93	0	0	6.927539	19	60	548	50	ENST00000241704.7	0.136364	0.490544
CD84	8832	__UNKNOWN__	__UNKNOWN__	1	160515702	160515702	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:160515702G>A	ENST00000368054.3	-	0	3366				CD84_ENST00000534968.1_3'UTR|RP11-528G1.2_ENST00000446952.1_RNA	NM_003874.3	NP_003865.1	Q9UIB8	SLAF5_HUMAN	CD84 molecule	NA		NA			blood coagulation (GO:0007596)|defense response (GO:0006952)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(1)	24	all_cancers(52;3.62e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			gattacaggcgtgagccaccg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF054816	CCDS1206.1, CCDS53395.1, CCDS53396.1, CCDS53397.1	1q24	2013-01-11	2006-03-31		ENSG00000066294	ENSG00000066294	8832		CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	1704	protein-coding gene	gene with protein product		604513	CD84 antigen (leukocyte antigen), CD84 molecule 		NA	9310491	Standard	NM_003874	NM_003874	NA	Approved	SLAMF5, hCD84, mCD84	uc001fwh.4	Q9UIB8	OTTHUMG00000022788	ENST00000368054.3:c.*2344C>T	chr1.hg19:g.160515702G>A		NA	B2R8T1|B7Z3R8|O15430|O95266|O95660|Q5H9R1|Q6FHA8|Q8WLP1|Q8WWI8|Q9UF04|Q9UIB6|Q9UIB7|Q9UIT7	hg19	CCDS1206.1	0.02	7.135692	GGCxTGA	COVERED																																																																																			NOVEL	CD84-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059090.1	117	37.815713	KEEP	2	4	120	168	4794	GG	1	1	0		-	9	60	265	0	2	14.329756	221	60	7048	597	ENST00000368054.3	0.03913	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	160572655	160572655	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:160572655C>G			NA	NA				CD84 (23349 upstream) : SLAMF1 (5234 downstream)						NA		NA									NA						ctcccaaagtcctgggattac	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.160572655C>G		NA		hg19		0.02	-0.140358	AGTxCTG	COVERED																																																																																			NOVEL					0			7	2.708311	KEEP	1	0	0	9	284	CC	0.99254	0.289823	0			3	60	106	0	0	8.872617	11	60	364	41		0.214286	0.292001
USF1	7391	__UNKNOWN__	__UNKNOWN__	1	161014001	161014001	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:161014001T>G	ENST00000368021.3	-	2	120				USF1_ENST00000368020.1_Intron|USF1_ENST00000435396.1_Intron	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	NA		NA			carbon catabolite regulation of transcription (GO:0045990)|cellular response to insulin stimulus (GO:0032869)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|negative regulation of fibrinolysis (GO:0051918)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			ccaaagtgcttggattacagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035505	CCDS1214.1	1q22-q23	2013-05-21			ENSG00000158773	ENSG00000158773	7391		Basic helix-loop-helix proteins	12593	protein-coding gene	gene with protein product		191523			NA	8486371	Standard	NM_007122	NM_007122	NA	Approved	UEF, MLTFI, bHLHb11	uc031pqv.1	P22415	OTTHUMG00000031472	ENST00000368021.3:c.85-851A>C	chr1.hg19:g.161014001T>G		NA	B2RBZ4|Q5SY46|Q7Z5Y1	hg19	CCDS1214.1	0.02	-0.122462	GCTxGGA	COVERED																																																																																			NOVEL	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077050.1	2	2.706757	KEEP	1	0	0	9	251	AT	0.99254	0.227464	0		-	3	60	98	0	0	8.186877	10	60	282	40	ENST00000368021.3	0.230769	0.229173
ARHGAP30	257106	__UNKNOWN__	__UNKNOWN__	1	161030137	161030137	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:161030137A>G	ENST00000368013.3	-	2	418				ARHGAP30_ENST00000368016.3_Intron|ARHGAP30_ENST00000368015.1_Intron	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			tgtaatcccaacactttggga	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517	257106		Rho GTPase activating proteins	27414	protein-coding gene	gene with protein product		614264			NA		Standard	NM_181720	NM_001287602	NA	Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.98-631T>C	chr1.hg19:g.161030137A>G		NA	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	hg19	CCDS30918.1	0.02	-0.149105	CCAxCAC	COVERED																																																																																			NOVEL	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077090.2	6	4.209127	KEEP	0	0	0	14	376	AA	0.995343	0.290641	0		-	3	60	104	0	0	8.478818	13	60	392	39	ENST00000368013.3	0.1875	0.292001
DEDD	9191	__UNKNOWN__	__UNKNOWN__	1	161095544	161095544	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:161095544G>A	ENST00000368006.3	-	3	151				DEDD_ENST00000489249.1_Intron|DEDD_ENST00000545495.1_Intron|DEDD_ENST00000458050.2_Intron|DEDD_ENST00000392188.1_Intron|DEDD_ENST00000368005.1_Intron|DEDD_ENST00000490843.2_Intron	NM_032998.2	NP_127491.1	O75618	DEDD_HUMAN	death effector domain containing	NA		NA			decidualization (GO:0046697)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|regulation of apoptotic process (GO:0042981)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	DNA binding (GO:0003677)			cervix(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|skin(1)	10	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			cacccacctcggcctcccaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF043733	CCDS1219.1	1q23.1	2008-02-05	2002-01-14		ENSG00000158796	ENSG00000158796	9191			2755	protein-coding gene	gene with protein product		606841	death effector domain-containing		NA	9774341, 9832420	Standard	NM_004216	XM_005245597	NA	Approved	DEFT, FLDED1, CASP8IP1, KE05, DEDD1	uc001fxz.3	O75618	OTTHUMG00000033104	ENST00000368006.3:c.64-1228C>T	chr1.hg19:g.161095544G>A		NA	D3DVF5|O60737	hg19	CCDS1219.1	0.02	-0.131585	CTCxGCC	COVERED																																																																																			NOVEL	DEDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080582.1	6	3.297293	KEEP	3	0	0	11	314	GG	0.99254	0.227464	0		-	3	40	94	0	0	7.672684	11	60	369	42	ENST00000368006.3	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	161119902	161119902	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:161119902C>T			NA	NA				ACA64 (8776 upstream) : UFC1 (3639 downstream)						NA		NA									NA						gatggagtctcgctctgtcgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.161119902C>T		NA		hg19		0.02	-0.122782	TCTxGCT	UNCOVERED																																																																																			NOVEL					0			4	2.406083	KEEP	2	0	0	8	223	CC	0	0	0			3	60	83	0	0	6.573506	11	60	353	36		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	161414248	161414248	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:161414248C>T			NA	NA				RNU6-481P (43063 upstream) : FCGR2A (60971 downstream)						NA		NA									NA						CCACCCACCCCTTcactcaca	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.161414248C>T		NA		hg19		0.02	-0.16611	CCCxTTC	UNCOVERED																																																																																			NOVEL					0			13	2.407336	KEEP	6	0	0	8	251	CC	0	0	0			3	24	84	0	0	6.485468	13	60	404	38		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	161714573	161714573	__UNKNOWN__	IGR	SNP	C	C	T	rs4657097	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:161714573C>T			NA	NA				RN7SL466P (8684 upstream) : DUSP12 (4986 downstream)						NA		NA									NA						ccagcctgggcgacagagcaa	0.443		NA											C|||	2805	0.560104	0.8956	0.3242	5008	,	,	NA	15626	0.7034	NA	0.3439	False	NA	,,,	NA	NA	NA	2504	0.3487	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.161714573C>T		NA		hg19		0.02	-0.122775	GGGxGAC	UNCOVERED																																																																																			NOVEL					0			6	2.406684	KEEP	2	0	0	8	235	CC	0	0	0			5	60	137	0	0	12.120697	9	60	298	33		0.357143	0.196312
NOS1AP	9722	__UNKNOWN__	__UNKNOWN__	1	162150269	162150269	__UNKNOWN__	Intron	SNP	T	T	C	rs10918823	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:162150269T>C	ENST00000361897.5	+	2	579				NOS1AP_ENST00000530878.1_Intron	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	NA		NA			regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			ctcctgaccttgtgatccgcc	0.547		NA											C|||	3245	0.647963	0.8071	0.5202	5008	,	,	NA	13938	0.7718	NA	0.4095	False	NA	,,,	NA	NA	NA	2504	0.6411	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929	9722			16859	protein-coding gene	gene with protein product	C-terminal PDZ domain ligand of neuronal nitric oxide synthase	605551			NA	9455484, 9459447	Standard	NM_014697	NM_001126060	NA	Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.177+26003T>C	chr1.hg19:g.162150269T>C		NA	B7ZLF5|O43564|Q3T551|Q5VU95	hg19	CCDS1237.1	0.02	-0.131572	CCTxGTG	COVERED																																																																																			NOVEL	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060555.2	4	2.40629	KEEP	0	0	0	8	223	TT	0.99257	0.259026	0		+	9	60	291	0	1	29.009317	6	60	178	37	ENST00000361897.5	0.6	0.260965
NOS1AP	9722	__UNKNOWN__	__UNKNOWN__	1	162290383	162290383	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:162290383C>T	ENST00000361897.5	+	5	746				NOS1AP_ENST00000530878.1_Intron	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	NA		NA			regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			cggtggctcacgcctgtaatc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929	9722			16859	protein-coding gene	gene with protein product	C-terminal PDZ domain ligand of neuronal nitric oxide synthase	605551			NA	9455484, 9459447	Standard	NM_014697	NM_001126060	NA	Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.345-12424C>T	chr1.hg19:g.162290383C>T		NA	B7ZLF5|O43564|Q3T551|Q5VU95	hg19	CCDS1237.1	0.02	-0.192976	TCAxGCC	COVERED																																																																																			NOVEL	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060555.2	13	4.21186	KEEP	3	0	0	14	411	CC	0.994391	0.455189	0		+	3	60	87	0	0	6.461533	17	60	553	54	ENST00000361897.5	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	162397803	162397803	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:162397803T>C			NA	NA				SH2D1B (15875 upstream) : UHMK1 (69237 downstream)						NA		NA									NA						catggtggcttatgcctgtaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.162397803T>C		NA		hg19		0.02	-0.228026	GCTxATG	COVERED																																																																																			NOVEL					0			7	4.20814	KEEP	1	0	0	14	355	TT	0.995343	0.580216	0			3	60	100	0	0	7.692304	18	60	520	61		0.142857	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	162443130	162443130	__UNKNOWN__	IGR	SNP	C	C	G	rs12021870	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:162443130C>G			NA	NA				SH2D1B (61202 upstream) : UHMK1 (23910 downstream)						NA		NA									NA						gcgcgatctccgctcactgca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.162443130C>G		NA		hg19		0.02	-0.105251	CTCxGCT	UNCOVERED																																																																																			NOVEL					0			8	2.707317	KEEP	9	0	0	9	266	CC	0	0	0			3	60	94	0	0	7.901213	9	60	272	40		0.25	0.139832
UHMK1	127933	__UNKNOWN__	__UNKNOWN__	1	162488521	162488521	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:162488521A>G	ENST00000489294.1	+	7	1271				UHMK1_ENST00000538489.1_Intron|UHMK1_ENST00000282169.8_Intron|UHMK1_ENST00000545294.1_Intron	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	NA		NA			cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			gctcacgcctataatcccagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332	127933		RNA binding motif (RRM) containing	19683	protein-coding gene	gene with protein product		608849			NA	12093740, 12782393	Standard	NM_175866	NM_175866	NA	Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.1113+541A>G	chr1.hg19:g.162488521A>G		NA	A8K8K4|G3V1M1|Q96C22	hg19	CCDS1239.1	0.02	-0.263044	CCTxTAA	COVERED																																																																																			NOVEL	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076788.1	7	2.702037	KEEP	3	0	0	9	229	AA	0.99254	0.688494	0		+	3	60	103	0	0	7.694923	23	60	634	64	ENST00000489294.1	0.115385	0.693668
C1orf110	339512	__UNKNOWN__	__UNKNOWN__	1	162799669	162799669	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:162799669A>G	ENST00000524691.1	-	2	152							Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	NA		NA								endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						ccaaactgctaggattacagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC040018	CCDS44269.1	1q23.3	2012-06-26			ENSG00000185860	ENSG00000185860	339512			28736	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_178550	NM_178550	NA	Approved	MGC48998	uc001gck.2	Q86UF4	OTTHUMG00000034421	ENST00000524691.1:c.725-4698T>C	chr1.hg19:g.162799669A>G		NA	Q5JSG1|Q6ZW57	hg19		0.02	-0.149107	GCTxGGA	COVERED																																																																																			NOVEL	C1orf110-004	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000386391.1	7	3.308475	KEEP	0	0	0	11	304	AA	0.993072	0.289978	0		-	3	60	98	0	0	7.972276	12	60	357	39	ENST00000524691.1	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	164374608	164374608	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:164374608A>G			NA	NA				RNU5F-6P (53983 upstream) : PBX1 (153828 downstream)						NA		NA									NA						atgagccaccatgcccagccA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.164374608A>G		NA		hg19		0.02	-0.219253	ACCxTGC	COVERED																																																																																			NOVEL					0			7	2.706417	KEEP	1	0	0	9	245	AA	0.99254	0.548763	0			3	60	98	0	1	7.561021	17	60	494	53		0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	164427571	164427571	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:164427571A>G			NA	NA				RNU5F-6P (106946 upstream) : PBX1 (100865 downstream)						NA		NA									NA						gggcgcggtgactcacgcctg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.164427571A>G		NA		hg19		0.02	-0.27187	GTGxCTC	COVERED																																																																																			NOVEL					0			10	3.001638	KEEP	4	0	0	10	250	AA	0.99257	0.711986	0			3	60	108	0	0	7.952259	28	60	814	61		0.096774	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	164427613	164427613	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:164427613C>T			NA	NA				RNU5F-6P (106988 upstream) : PBX1 (100823 downstream)						NA		NA									NA						ccgaggcgggcggatcacgag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.164427613C>T		NA		hg19		0.02	-0.19292	GGGxGGA	COVERED																																																																																			NOVEL					0			10	3.303661	KEEP	6	0	0	11	281	CC	0.99257	0.454356	0			4	60	111	0	0	8.570088	17	60	493	46		0.190476	0.457757
PBX1	5087	__UNKNOWN__	__UNKNOWN__	1	164715653	164715653	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:164715653G>A	ENST00000559240.1	+	3	265				PBX1_ENST00000540236.1_Intron|PBX1_ENST00000367897.1_Intron|PBX1_ENST00000420696.2_Intron|PBX1_ENST00000560641.1_Intron|PBX1_ENST00000401534.1_Intron			P40424	PBX1_HUMAN	pre-B-cell leukemia homeobox 1	NA		NA			adrenal gland development (GO:0030325)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic hemopoiesis (GO:0035162)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system development (GO:0048706)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|proximal/distal pattern formation (GO:0009954)|regulation of ossification (GO:0030278)|sex differentiation (GO:0007548)|spleen development (GO:0048536)|steroid biosynthetic process (GO:0006694)|thymus development (GO:0048538)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)		EWSR1/PBX1(3)	large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	4						ttgctctgttgcccaggctgg	0.438		NA	T	TCF3, EWSR1	pre B-ALL, myoepithelioma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		L, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M86546	CCDS1246.1, CCDS55654.1	1q23.3	2011-06-20	2007-01-30		ENSG00000185630	ENSG00000185630	5087		Homeoboxes / TALE class	8632	protein-coding gene	gene with protein product		176310	pre-B-cell leukemia transcription factor 1		NA		Standard	NM_002585	NM_002585	NA	Approved		uc001gct.3	P40424	OTTHUMG00000034307	ENST00000559240.1:c.266-46078G>A	chr1.hg19:g.164715653G>A		NA	B4DSC1|F5H4U9|Q5T488	hg19	CCDS1246.1	0.02	-0.149116	GTTxCCC	COVERED																																																																																			NOVEL	PBX1-012	NOVEL	not_organism_supported|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417688.1	6	2.407348	KEEP	1	0	0	8	252	GG	0.99257	0.289832	0		+	4	60	109	0	0	8.780887	13	60	455	40	ENST00000559240.1	0.235294	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	166322377	166322377	__UNKNOWN__	IGR	SNP	C	C	A	rs199940285|rs142308128|rs77011580	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:166322377C>A			NA	NA				RP11-479J7.2 (17378 upstream) : RP11-479J7.1 (34586 downstream)						NA		NA									NA						aacaaacaaacaaacaaaaaa	0.478		NA											C|||	1633	0.326078	0.1203	0.3501	5008	,	,	NA	19050	0.6885	NA	0.2127	False	NA	,,,	NA	NA	NA	2504	0.3303	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.166322377C>A		NA		hg19		0.02	-0.105216	AAAxAAA	UNCOVERED																																																																																			NOVEL					0			7	2.708161	KEEP	1	0	0	9	278	CC	0.99257	0.138793	0			3	60	79	2	1	6.678633	7	60	223	35		0.3	0.139832
POU2F1	5451	__UNKNOWN__	__UNKNOWN__	1	167264109	167264109	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167264109A>G	ENST00000429375.2	+	2	68				POU2F1_ENST00000541643.3_Intron|POU2F1_ENST00000367865.1_Intron|POU2F1_ENST00000367866.2_Intron|POU2F1_ENST00000420254.3_Intron|POU2F1_ENST00000452019.1_Intron			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	NA		NA			gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						ggtggctcacacctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190	5451		Homeoboxes / POU class	9212	protein-coding gene	gene with protein product		164175	POU domain class 2, transcription factor 1	OTF1	NA	1887216	Standard	NM_002697	NM_002697	NA	Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000429375.2:c.62-37598A>G	chr1.hg19:g.167264109A>G		NA	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	hg19	CCDS55655.1	0.02	-0.166647	CACxCCT	COVERED																																																																																			NOVEL	POU2F1-010	KNOWN	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416073.1	6	3.005898	KEEP	0	0	0	10	259	AA	0.992708	0.384582	0		+	3	60	99	0	0	7.81016	15	60	449	43	ENST00000429375.2	0.166667	0.387407
MPZL1	9019	__UNKNOWN__	__UNKNOWN__	1	167758208	167758208	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167758208C>T	ENST00000392121.3	+	0	1573				MPZL1_ENST00000359523.2_3'UTR	NM_001146191.1	NP_001139663.1	O95297	MPZL1_HUMAN	myelin protein zero-like 1	NA		NA			cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					ctcagcctcccgagtagctgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965	9019		Immunoglobulin superfamily / V-set domain containing	7226	protein-coding gene	gene with protein product		604376			NA	9792637	Standard	NM_024569	NM_003953	NA	Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000392121.3:c.*1050C>T	chr1.hg19:g.167758208C>T		NA	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	hg19	CCDS53425.1	0.02	2.494921	TCCxGAG	COVERED																																																																																			NOVEL	MPZL1-006	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326411.1	46	32.017049	KEEP	0	1	27	116	3354	CC	1	1	0		+	7	60	215	1	1	12.851753	130	60	4181	369	ENST00000392121.3	0.051095	1
ADCY10	55811	__UNKNOWN__	__UNKNOWN__	1	167789082	167789082	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167789082T>C	ENST00000367851.4	-	31	4471				ADCY10_ENST00000367848.1_Intron|ADCY10_ENST00000545172.1_Intron	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	NA		NA			cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						ggattacaggtgtcagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	55811	4.6.1.1	Adenylate cyclases	21285	protein-coding gene	gene with protein product	soluble adenylyl cyclase, Hypercalciuria, absorptive, 2	605205			NA		Standard	NM_018417	XM_006711449	NA	Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.4287-1577A>G	chr1.hg19:g.167789082T>C		NA	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	hg19	CCDS1265.1	0.02	-0.254214	AGGxGTC	COVERED																																																																																			NOVEL	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083663.1	3	4.509828	KEEP	0	0	0	15	397	TT	0.997832	0.667074	0		-	3	60	95	0	0	7.007078	21	60	561	58	ENST00000367851.4	0.125	0.668523
ADCY10	55811	__UNKNOWN__	__UNKNOWN__	1	167816757	167816757	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167816757A>G	ENST00000367851.4	-	19	2622				ADCY10_ENST00000367848.1_Intron|ADCY10_ENST00000545172.1_Intron	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	NA		NA			cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						gggttcaagcaattctcctgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	55811	4.6.1.1	Adenylate cyclases	21285	protein-coding gene	gene with protein product	soluble adenylyl cyclase, Hypercalciuria, absorptive, 2	605205			NA		Standard	NM_018417	XM_006711449	NA	Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.2437+841T>C	chr1.hg19:g.167816757A>G		NA	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	hg19	CCDS1265.1	0.02	-0.298088	AGCxATT	COVERED																																																																																			NOVEL	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083663.1	9	5.407167	KEEP	0	0	0	18	443	AA	0.99986	0.800133	0		-	3	60	95	0	1	6.698928	27	60	741	57	ENST00000367851.4	0.1	0.800245
MPC2	25874	__UNKNOWN__	__UNKNOWN__	1	167889125	167889125	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167889125A>G	ENST00000367846.4	-	4	546				MPC2_ENST00000271373.4_Intron	NM_015415.3	NP_056230.1	O95563	MPC2_HUMAN	mitochondrial pyruvate carrier 2	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate transmembrane transporter activity (GO:0050833)				NA						cagcctgggcaacagagcgag	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1266.1	1q24	2012-07-30	2012-07-30	2012-07-30	ENSG00000143158	ENSG00000143158	25874			24515	protein-coding gene	gene with protein product		614737	brain protein 44	BRP44	NA	3022128, 22628558	Standard	NM_015415	NM_015415	NA	Approved	DKFZP564B167	uc001get.3	O95563	OTTHUMG00000034570	ENST00000367846.4:c.347+91T>C	chr1.hg19:g.167889125A>G		NA	A8K261|Q3SXR6|Q6FIF3	hg19	CCDS1266.1	0.02	3.350145	GGCxACA	COVERED																																																																																			NOVEL	MPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083652.1	27	4.112445	KEEP	0	7	181	78	2127	AA	1	0.999987	0		-	7	60	210	1	2	13.885732	77	70	2270	254	ENST00000367846.4	0.083333	0.999987
DCAF6	55827	__UNKNOWN__	__UNKNOWN__	1	167914768	167914768	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167914768C>T	ENST00000367840.3	+	2	191				DCAF6_ENST00000470919.1_Intron|DCAF6_ENST00000432587.2_Intron|DCAF6_ENST00000312263.6_Intron|DCAF6_ENST00000367843.3_Intron	NM_001198956.1	NP_001185885.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						ctcactctgtcacccaggctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164	55827		WD repeat domain containing, DDB1 and CUL4 associated factors	30002	protein-coding gene	gene with protein product		610494	IQ motif and WD repeats 1	IQWD1	NA	12032826	Standard	NM_018442	NM_018442	NA	Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000367840.3:c.98-6270C>T	chr1.hg19:g.167914768C>T		NA	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	hg19	CCDS55657.1	0.02	-0.11403	TGTxACC	UNCOVERED																																																																																			NOVEL	DCAF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083659.3	6	4.212593	KEEP	0	0	0	14	431	CC	0.995343	0.16171	0		+	3	60	85	0	0	6.881936	10	60	334	39	ENST00000367840.3	0.230769	0.162467
DCAF6	55827	__UNKNOWN__	__UNKNOWN__	1	167914769	167914769	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167914769A>G	ENST00000367840.3	+	2	191				DCAF6_ENST00000470919.1_Intron|DCAF6_ENST00000432587.2_Intron|DCAF6_ENST00000312263.6_Intron|DCAF6_ENST00000367843.3_Intron	NM_001198956.1	NP_001185885.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						tcactctgtcacccaggctgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164	55827		WD repeat domain containing, DDB1 and CUL4 associated factors	30002	protein-coding gene	gene with protein product		610494	IQ motif and WD repeats 1	IQWD1	NA	12032826	Standard	NM_018442	NM_018442	NA	Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000367840.3:c.98-6269A>G	chr1.hg19:g.167914769A>G		NA	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	hg19	CCDS55657.1	0.02	-0.12277	GTCxCCC	COVERED																																																																																			NOVEL	DCAF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083659.3	6	4.209738	KEEP	0	0	0	14	375	AA	0.995343	0.195397	0		+	3	60	88	0	0	7.073472	11	60	322	40	ENST00000367840.3	0.214286	0.196312
DCAF6	55827	__UNKNOWN__	__UNKNOWN__	1	167920551	167920551	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167920551A>G	ENST00000367840.3	+	2	191				DCAF6_ENST00000470919.1_Intron|DCAF6_ENST00000432587.2_Intron|DCAF6_ENST00000312263.6_Intron|DCAF6_ENST00000367843.3_Intron	NM_001198956.1	NP_001185885.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						ggtggctcacacctgtaatcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164	55827		WD repeat domain containing, DDB1 and CUL4 associated factors	30002	protein-coding gene	gene with protein product		610494	IQ motif and WD repeats 1	IQWD1	NA	12032826	Standard	NM_018442	NM_018442	NA	Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000367840.3:c.98-487A>G	chr1.hg19:g.167920551A>G		NA	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	hg19	CCDS55657.1	0.02	-0.201722	CACxCCT	COVERED																																																																																			NOVEL	DCAF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083659.3	7	3.00658	KEEP	0	0	0	10	275	AA	0.992708	0.486967	0		+	3	60	106	0	0	8.360702	17	60	493	52	ENST00000367840.3	0.15	0.490544
DCAF6	55827	__UNKNOWN__	__UNKNOWN__	1	167946235	167946235	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:167946235G>A	ENST00000367840.3	+	4	532				DCAF6_ENST00000470919.1_Intron|DCAF6_ENST00000432587.2_Intron|DCAF6_ENST00000312263.6_Intron|DCAF6_ENST00000367843.3_Intron	NM_001198956.1	NP_001185885.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						tctgcctcctgggttcaagta	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164	55827		WD repeat domain containing, DDB1 and CUL4 associated factors	30002	protein-coding gene	gene with protein product		610494	IQ motif and WD repeats 1	IQWD1	NA	12032826	Standard	NM_018442	NM_018442	NA	Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000367840.3:c.438+1982G>A	chr1.hg19:g.167946235G>A		NA	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	hg19	CCDS55657.1	0.02	-0.184212	CCTxGGT	COVERED																																																																																			NOVEL	DCAF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083659.3	6	3.610773	KEEP	1	0	0	12	373	GG	0.993072	0.420544	0		+	3	60	88	0	0	6.492827	18	60	596	47	ENST00000367840.3	0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	168146161	168146161	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:168146161C>T			NA	NA				GPR161 (39340 upstream) : TIPRL (2009 downstream)						NA		NA									NA						gtggctcacgcctgtaatccc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.168146161C>T		NA		hg19		0.02	-0.245624	ACGxCTG	COVERED																																																																																			NOVEL					0			10	3.610372	KEEP	6	0	0	12	356	CC	0.99254	0.636563	0			3	60	95	0	0	6.89481	23	60	775	60		0.115385	0.641347
TBX19	9095	__UNKNOWN__	__UNKNOWN__	1	168266830	168266830	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:168266830A>G	ENST00000367821.3	+	4	654					NM_005149.2	NP_005140.1	O60806	TBX19_HUMAN	T-box 19	NA		NA			anatomical structure morphogenesis (GO:0009653)|cell fate commitment (GO:0045165)|pituitary gland development (GO:0021983)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(11)|prostate(2)|skin(2)|urinary_tract(1)	34	all_hematologic(923;0.215)					gattacaggcataagccatcg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ010277	CCDS1272.1	1q23-q24	2008-02-05			ENSG00000143178	ENSG00000143178	9095		T-boxes	11596	protein-coding gene	gene with protein product	TBS 19	604614			NA	9888994	Standard	NM_005149	NM_005149	NA	Approved	dj747L4.1, TPIT	uc001gfl.3	O60806	OTTHUMG00000034648	ENST00000367821.3:c.604-132A>G	chr1.hg19:g.168266830A>G		NA	Q52M53	hg19	CCDS1272.1	0.02	1.862372	GGCxTAA	COVERED																																																																																			NOVEL	TBX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000083825.1	13	9.489309	KEEP	0	2	58	52	1447	AA	1	0.989542	0		+	4	60	132	0	0	8.854365	52	60	1545	168	ENST00000367821.3	0.071429	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	168393072	168393072	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:168393072T>C			NA	NA				RP5-968D22.1 (1178 upstream) : RP5-968D22.3 (40379 downstream)						NA		NA									NA						ttgagaccagtctgggcaaca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.168393072T>C		NA		hg19		0.02	-0.228036	CAGxCTG	COVERED																																																																																			NOVEL					0			9	4.510336	KEEP	2	0	0	15	401	TT	0.995343	0.580216	0			3	60	99	0	0	7.46515	20	60	590	60		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	168432061	168432061	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:168432061A>T			NA	NA				RP5-968D22.1 (40167 upstream) : RP5-968D22.3 (1390 downstream)						NA		NA									NA						acgcctgtaaacccagcactt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.168432061A>T		NA		hg19		0.02	-0.210489	TAAxCCC	COVERED																																																																																			NOVEL					0			7	2.405904	KEEP	0	0	0	8	219	AA	0.99257	0.518282	0			3	60	91	0	0	6.861417	17	60	505	47		0.15	0.522161
C1orf112	55732	__UNKNOWN__	__UNKNOWN__	1	169750370	169750370	__UNKNOWN__	Intron	SNP	A	A	G	rs575091175	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:169750370A>G	ENST00000498289.1	+	4	851							Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	NA		NA								breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					gattacaggcatgagccactg	0.413		NA											A|||	4	0.000798722	0.003	0.0	5008	,	,	NA	15272	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460	55732			25565	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018186	NM_018186	NA	Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000498289.1:c.852-2582A>G	chr1.hg19:g.169750370A>G		NA	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	hg19		0.02	-0.19293	GGCxTGA	COVERED																																																																																			NOVEL	C1orf112-004	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000087127.5	5	3.609259	KEEP	0	0	0	12	333	AA	0.993634	0.454842	0		+	3	60	102	0	0	8.033458	16	60	465	48	ENST00000498289.1	0.157895	0.457757
PRRX1	5396	__UNKNOWN__	__UNKNOWN__	1	170696025	170696025	__UNKNOWN__	Intron	SNP	A	A	G	rs71635676		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:170696025A>G	ENST00000239461.6	+	3	912				PRRX1_ENST00000367760.3_Intron|PRRX1_ENST00000476867.2_Intron|PRRX1_ENST00000497230.2_3'UTR	NM_022716.2	NP_073207.1	P54821	PRRX1_HUMAN	paired related homeobox 1	NA		NA			artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)	nucleolus (GO:0005730)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			large_intestine(2)|ovary(1)	3	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					aggaagaaagaaaggaaagaa	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M95929	CCDS1290.1, CCDS1291.1	1q24.3	2011-06-20	2003-11-12	2003-11-14	ENSG00000116132	ENSG00000116132	5396		Homeoboxes / PRD class	9142	protein-coding gene	gene with protein product		167420	paired mesoderm homeo box 1	PMX1	NA	1509260	Standard	NM_006902	NM_006902	NA	Approved	PHOX1	uc001ghf.3	P54821	OTTHUMG00000035231	ENST00000239461.6:c.599+483A>G	chr1.hg19:g.170696025A>G		NA	B5BUM7|O60807	hg19	CCDS1290.1	0.02	1.56407	AAGxAAG	COVERED																																																																																			NOVEL	PRRX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085236.3	9	5.31956	KEEP	0	3	74	44	1209	AA	1	0.987943	0		+	4	60	125	0	0	8.155869	52	70	1518	144	ENST00000239461.6	0.071429	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	171385312	171385312	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:171385312G>A			NA	NA				FMO4 (74089 upstream) : RNU6-290P (2470 downstream)						NA		NA									NA						gggtgacagagtgagactcca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.171385312G>A		NA		hg19		0.02	-0.105267	AGAxTGA	UNCOVERED																																																																																			NOVEL					0			6	2.406633	KEEP	2	0	0	8	235	GG	0.99257	0.138793	0			3	60	91	0	0	7.878257	7	60	250	33		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	171441095	171441095	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:171441095G>A			NA	NA				RNU6-290P (53206 upstream) : snoU13 (9950 downstream)						NA		NA									NA						caacaagagcgaaactctcaa	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.171441095G>A		NA		hg19		0.02	-0.157896	AGCxAAA	COVERED																																																																																			NOVEL					0			8	2.707379	KEEP	0	0	0	9	260	GG	0.99254	0.320398	0			3	60	88	0	1	6.792046	14	60	472	40		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	171562823	171562823	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:171562823G>C			NA	NA				PRRC2C (173 upstream) : MYOC (41733 downstream)						NA		NA									NA						accagcctgggcaacatggtg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.171562823G>C		NA		hg19		0.02	-0.307025	TGGxCAA	COVERED																																																																																			NOVEL					0			9	3.911528	KEEP	0	0	0	13	400	GT	0.99649	0.815592	0			5	60	159	0	0	12.33969	26	60	863	61		0.16129	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	172495482	172495482	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:172495482T>G			NA	NA				C1orf105 (57511 upstream) : SUCO (6006 downstream)						NA		NA									NA						cgcccgcctctgcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.172495482T>G		NA		hg19		0.02	-0.140341	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			10	2.406409	KEEP	10	0	0	8	225	AT	0	0	0			3	60	106	0	0	8.872801	11	60	331	52		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	172611236	172611236	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:172611236G>T			NA	NA				RNU6-693P (28562 upstream) : FASLG (16917 downstream)						NA		NA									NA						ctgagatcatgccactgcact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.172611236G>T		NA		hg19		0.02	-0.105264	CATxCCA	UNCOVERED																																																																																			NOVEL					0			9	2.407272	KEEP	2	0	0	8	247	GG	0.99257	0.16126	0			3	27	85	0	0	7.278166	7	60	241	34		0.3	0.162467
DARS2	55157	__UNKNOWN__	__UNKNOWN__	1	173814931	173814931	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:173814931A>G	ENST00000361951.4	+	12	1918				DARS2_ENST00000471476.1_Intron|DARS2_ENST00000239457.5_Intron	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	NA		NA			gene expression (GO:0010467)|mitochondrial asparaginyl-tRNA aminoacylation (GO:0070145)|tRNA aminoacylation (GO:0043039)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aspartate-tRNA ligase activity (GO:0004815)|aspartate-tRNA(Asn) ligase activity (GO:0050560)|ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(4)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	30					L-Aspartic Acid(DB00128)	aggccaaggcaggcggatcac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022754	CCDS1311.1	1q25.1	2011-07-01	2007-02-23		ENSG00000117593	ENSG00000117593	55157	6.1.1.12	Aminoacyl tRNA synthetases / Class II	25538	protein-coding gene	gene with protein product	aspartate tRNA ligase 2, mitochondrial	610956			NA	15779907	Standard	NM_018122	NM_018122	NA	Approved	FLJ10514	uc001gjh.2	Q6PI48	OTTHUMG00000034803	ENST00000361951.4:c.1191+502A>G	chr1.hg19:g.173814931A>G		NA		hg19	CCDS1311.1	0.02	-0.166636	GGCxGGC	COVERED																																																																																			NOVEL	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084220.1	6	3.609546	KEEP	1	0	0	12	337	AA	0.993634	0.38494	0		+	3	60	91	0	0	7.272596	12	60	360	48	ENST00000361951.4	0.2	0.387407
RC3H1	149041	__UNKNOWN__	__UNKNOWN__	1	173928646	173928646	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:173928646T>C	ENST00000367696.2	-	13	2722				RC3H1_ENST00000367694.2_Intron|RC3H1_ENST00000258349.4_Intron			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	NA		NA			B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						cggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870	149041		RING-type (C3HC4) zinc fingers, Zinc fingers, CCCH-type domain containing	29434	protein-coding gene	gene with protein product	KIAA2025 protein	609424	ring finger and CCCH-type zinc finger domains 1		NA	15917799	Standard	NM_172071	XM_005244918	NA	Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.2370+1568A>G	chr1.hg19:g.173928646T>C		NA	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	hg19	CCDS30940.1	0.02	-0.122779	TCAxGCC	COVERED																																																																																			NOVEL	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090733.2	9	3.308206	KEEP	2	0	0	11	303	TT	0.992708	0.19488	0		-	4	60	120	0	0	10.4236	9	60	270	35	ENST00000367696.2	0.307692	0.196312
RC3H1	149041	__UNKNOWN__	__UNKNOWN__	1	173961839	173961839	__UNKNOWN__	Intron	SNP	G	G	C	rs12754931	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:173961839G>C	ENST00000367696.2	-	2	583				RC3H1_ENST00000258349.4_Intron|RC3H1_ENST00000367694.2_Intron			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	NA		NA			B cell homeostasis (GO:0001782)|cytoplasmic mRNA processing body assembly (GO:0033962)|lymph node development (GO:0048535)|negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of germinal center formation (GO:0002635)|negative regulation of T-helper cell differentiation (GO:0045623)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|posttranscriptional regulation of gene expression (GO:0010608)|protein ubiquitination (GO:0016567)|regulation of germinal center formation (GO:0002634)|regulation of mRNA stability (GO:0043488)|regulation of T cell receptor signaling pathway (GO:0050856)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)	mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	50						cacacacacagagagagagag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093501	CCDS30940.1, CCDS72987.1	1q25.1	2013-01-18	2010-09-15		ENSG00000135870	ENSG00000135870	149041		RING-type (C3HC4) zinc fingers, Zinc fingers, CCCH-type domain containing	29434	protein-coding gene	gene with protein product	KIAA2025 protein	609424	ring finger and CCCH-type zinc finger domains 1		NA	15917799	Standard	NM_172071	XM_005244918	NA	Approved	KIAA2025, roquin, RP5-1198E17.5, RNF198	uc001gju.4	Q5TC82	OTTHUMG00000037275	ENST00000367696.2:c.231+53C>G	chr1.hg19:g.173961839G>C		NA	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	hg19	CCDS30940.1	0.02	1.73396	ACAxAGA	COVERED																																																																																			NOVEL	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090733.2	11	4.177739	KEEP	0	2	60	35	1055	GG	1	0.999677	0		-	4	60	132	0	0	8.358022	70	60	2333	164	ENST00000367696.2	0.054054	0.999678
RABGAP1L	9910	__UNKNOWN__	__UNKNOWN__	1	174710796	174710796	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:174710796G>A	ENST00000251507.4	+	18	2343				RABGAP1L_ENST00000347255.2_Intron|RABGAP1L_ENST00000325589.5_Intron|RABGAP1L_ENST00000367686.3_Intron|RABGAP1L_ENST00000367687.1_Intron	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	NA		NA								NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						cactgtacccggcccccagta	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061	9910			24663	protein-coding gene	gene with protein product		609238			NA	10585558	Standard	NM_001243765	NM_014857	NA	Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.2170-10655G>A	chr1.hg19:g.174710796G>A		NA	B7ZAA4	hg19	CCDS1314.1	0.02	-0.210521	CCCxGCC	COVERED																																																																																			NOVEL	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084497.1	4	3.610266	KEEP	0	0	0	12	354	GG	0.993634	0.518837	0		+	3	60	87	0	0	6.534208	16	60	521	49	ENST00000251507.4	0.157895	0.522161
RABGAP1L	9910	__UNKNOWN__	__UNKNOWN__	1	174822726	174822726	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:174822726A>G	ENST00000251507.4	+	19	2514				RABGAP1L_ENST00000347255.2_Intron|RABGAP1L_ENST00000325589.5_Intron|RABGAP1L_ENST00000489615.1_Intron|RABGAP1L_ENST00000367686.3_Intron|RABGAP1L_ENST00000367687.1_Intron	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	NA		NA								NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						aaaattagccaggcatggtgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061	9910			24663	protein-coding gene	gene with protein product		609238			NA	10585558	Standard	NM_001243765	NM_014857	NA	Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.2340+41628A>G	chr1.hg19:g.174822726A>G		NA	B7ZAA4	hg19	CCDS1314.1	0.02	-0.166644	GCCxGGC	COVERED																																																																																			NOVEL	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084497.1	15	3.908378	KEEP	5	0	0	13	347	AA	0.993634	0.351693	0		+	3	60	86	0	0	6.511211	15	60	459	45	ENST00000251507.4	0.166667	0.353947
RABGAP1L	9910	__UNKNOWN__	__UNKNOWN__	1	174840113	174840113	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:174840113G>A	ENST00000251507.4	+	19	2514				RABGAP1L_ENST00000347255.2_Intron|RABGAP1L_ENST00000325589.5_Intron|RABGAP1L_ENST00000489615.1_Intron|RABGAP1L_ENST00000367686.3_Intron|RABGAP1L_ENST00000367687.1_Intron	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	NA		NA								NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						tcctgacctcgtgatccaccc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061	9910			24663	protein-coding gene	gene with protein product		609238			NA	10585558	Standard	NM_001243765	NM_014857	NA	Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.2340+59015G>A	chr1.hg19:g.174840113G>A		NA	B7ZAA4	hg19	CCDS1314.1	0.02	-0.131577	CTCxTGA	UNCOVERED																																																																																			NOVEL	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084497.1	9	3.307103	KEEP	10	0	0	11	303	GG	0	0	0		+	3	60	94	0	0	7.672772	11	60	357	47	ENST00000251507.4	0.214286	0.229173
RABGAP1L	9910	__UNKNOWN__	__UNKNOWN__	1	174852241	174852241	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:174852241T>C	ENST00000251507.4	+	19	2514				RABGAP1L_ENST00000347255.2_Intron|RABGAP1L_ENST00000325589.5_Intron|RABGAP1L_ENST00000489615.1_Intron|RABGAP1L_ENST00000478442.1_Intron|RABGAP1L_ENST00000392064.2_Intron|RABGAP1L_ENST00000367686.3_Intron|RABGAP1L_ENST00000486220.1_Intron|RABGAP1L_ENST00000367687.1_Intron	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	NA		NA								NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						ggattacaggtgtgagccacc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061	9910			24663	protein-coding gene	gene with protein product		609238			NA	10585558	Standard	NM_001243765	NM_014857	NA	Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.2340+71143T>C	chr1.hg19:g.174852241T>C		NA	B7ZAA4	hg19	CCDS1314.1	0.02	-0.105237	AGGxGTG	UNCOVERED																																																																																			NOVEL	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084497.1	7	2.406356	KEEP	3	0	0	8	227	TT	0	0	0		+	4	60	124	0	0	10.991321	8	60	238	29	ENST00000251507.4	0.333333	0.139832
RABGAP1L	9910	__UNKNOWN__	__UNKNOWN__	1	174953611	174953611	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:174953611C>T	ENST00000489615.1	+	7	1163				RABGAP1L_ENST00000347255.2_Intron|RABGAP1L_ENST00000325589.5_Intron|RABGAP1L_ENST00000392064.2_Intron|RABGAP1L_ENST00000367686.3_Intron|RABGAP1L_ENST00000367688.3_Intron|RABGAP1L_ENST00000367687.1_Intron	NM_001243765.1	NP_001230694.1	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	NA		NA								NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						ggtgtggtggctcacgcctgt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061	9910			24663	protein-coding gene	gene with protein product		609238			NA	10585558	Standard	NM_001243765	NM_014857	NA	Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000489615.1:c.762+1569C>T	chr1.hg19:g.174953611C>T		NA	B7ZAA4	hg19	CCDS58046.1	0.02	-0.105227	TGGxTCA	UNCOVERED																																																																																			NOVEL	RABGAP1L-006	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084502.3	5	2.407016	KEEP	2	0	0	8	241	CC	0	0	0		+	3	39	82	0	0	7.141579	6	60	206	27	ENST00000489615.1	0.333333	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	175898580	175898580	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:175898580A>T			NA	NA				RP11-318C24.2 (8931 upstream) : RFWD2 (15386 downstream)						NA		NA									NA						gtgattctccagcctcagcct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.175898580A>T		NA		hg19		0.02	-0.157866	TCCxGCC	COVERED																																																																																			NOVEL					0			10	4.511556	KEEP	0	0	0	15	416	AA	0.99649	0.321674	0			3	60	90	0	0	7.079098	13	60	396	44		0.1875	0.322807
ASTN1	460	__UNKNOWN__	__UNKNOWN__	1	177117280	177117280	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:177117280T>C	ENST00000367657.3	-	1	474				ASTN1_ENST00000281881.3_Intron|ASTN1_ENST00000361833.2_Intron|ASTN1_ENST00000424564.2_Intron|ASTN1_ENST00000367654.3_Intron			O14525	ASTN1_HUMAN	astrotactin 1	NA		NA			locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TCAggccgggtgtggtggctc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092	460			773	protein-coding gene	gene with protein product		600904	astrotactin	ASTN	NA	9070947	Standard	NM_004319	NM_001286164	NA	Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367657.3:c.283+16249A>G	chr1.hg19:g.177117280T>C		NA	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	hg19		0.02	-0.263077	GGGxGTG	COVERED																																																																																			NOVEL	ASTN1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000084823.1	9	3.609452	KEEP	4	0	0	12	335	TT	0.992708	0.68861	0		-	3	60	91	0	0	6.443768	24	60	680	70	ENST00000367657.3	0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	177594354	177594354	__UNKNOWN__	IGR	SNP	C	C	T	rs12092589	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:177594354C>T			NA	NA				RP1-35C21.2 (48270 upstream) : RP11-63B19.1 (75304 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.177594354C>T		NA		hg19		0.02	-0.263151	TCAxGCC	COVERED																																																																																			NOVEL					0			10	4.812714	KEEP	1	0	0	16	460	CC	0.997832	0.692164	0			3	60	92	0	0	6.543208	24	60	787	68		0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	177867850	177867850	__UNKNOWN__	IGR	SNP	A	A	G	rs187594886	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:177867850A>G			NA	NA				RP11-63B19.1 (188385 upstream) : SEC16B (28850 downstream)						NA		NA									NA						ttgggaggccaaggtgggcgg	0.517		NA											A|||	18	0.00359425	0.0129	0.0014	5008	,	,	NA	20655	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.177867850A>G		NA		hg19		0.02	-0.078939	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			6	2.707285	KEEP	6	0	0	9	259	AA	0	0	0			3	60	97	0	0	8.832905	5	60	151	29		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	178050107	178050107	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:178050107A>G			NA	NA				RP11-568K15.1 (43022 upstream) : RASAL2-AS1 (10535 downstream)						NA		NA									NA						cagcactttgagaggccaagg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.178050107A>G		NA		hg19		0.02	-0.192982	TTGxGAG	COVERED																																																																																			NOVEL					0			6	2.70718	KEEP	0	0	0	9	259	AA	0.99254	0.454342	0			4	60	138	0	0	11.362735	16	60	497	45		0.2	0.457757
RASAL2	9462	__UNKNOWN__	__UNKNOWN__	1	178074974	178074974	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:178074974G>A	ENST00000367649.3	+	1	554				RASAL2_ENST00000448150.3_Intron			Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	NA		NA			negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						cgcccagctagttttttgttt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391	9462		Pleckstrin homology (PH) domain containing	9874	protein-coding gene	gene with protein product	Ras GTPase activating protein-like, Ras protein activator like 1	606136			NA	9877179	Standard	NM_170692	NM_004841	NA	Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000367649.3:c.202+11145G>A	chr1.hg19:g.178074974G>A		NA	F8W755|O95174|Q2TB22|Q5TFU9	hg19	CCDS1321.2	0.02	-0.087711	CTAxTTT	UNCOVERED																																																																																			NOVEL	RASAL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352415.1	11	3.008662	KEEP	0	0	0	10	299	GG	0.992708	0.098994	0		+	3	60	80	0	0	6.777901	7	60	242	22	ENST00000367649.3	0.3	0.099721
RALGPS2	55103	__UNKNOWN__	__UNKNOWN__	1	178843968	178843968	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:178843968A>G	ENST00000367635.3	+	9	945				RALGPS2_ENST00000367634.2_Intron	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	NA		NA			small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						tgttgcccagactggtctcaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191	55103		Pleckstrin homology (PH) domain containing	30279	protein-coding gene	gene with protein product		NA			NA	10747847, 12102558	Standard	NM_152663	NM_152663	NA	Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.608-2665A>G	chr1.hg19:g.178843968A>G		NA	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	hg19	CCDS1325.1	0.02	-0.114029	CAGxCTG	UNCOVERED																																																																																			NOVEL	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084926.2	7	3.281813	KEEP	1	0	0	11	279	AA	0.993072	0.161341	0		+	3	60	105	0	0	9.001147	9	60	275	37	ENST00000367635.3	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	178906543	178906543	__UNKNOWN__	IGR	SNP	C	C	T	rs373807420		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:178906543C>T			NA	NA				RALGPS2 (17305 upstream) : FAM20B (88487 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.178906543C>T		NA		hg19		0.02	-0.166629	AGGxGTG	COVERED																																																																																			NOVEL					0			10	4.512759	KEEP	17	0	0	15	447	CC	0.99254	0.351306	0			3	60	87	0	0	6.610889	15	60	466	66		0.166667	0.353947
FAM20B	9917	__UNKNOWN__	__UNKNOWN__	1	179037144	179037144	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:179037144T>C	ENST00000263733.4	+	7	1334					NM_014864.3	NP_055679.1	O75063	XYLK_HUMAN	family with sequence similarity 20, member B	NA		NA				Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)	14						gtgatccgcctgcctcagcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007944	CCDS1328.1	1q25.2	2013-04-29			ENSG00000116199	ENSG00000116199	9917			23017	protein-coding gene	gene with protein product	glycosaminoglycan xylosylkinase	611063			NA	9455484, 19473117	Standard	NM_014864	NM_014864	NA	Approved	KIAA0475, GXK1	uc001gmc.3	O75063	OTTHUMG00000035073	ENST00000263733.4:c.998+1150T>C	chr1.hg19:g.179037144T>C		NA	Q5W0C3|Q5W0C4	hg19	CCDS1328.1	0.02	-0.096481	GCCxGCC	UNCOVERED																																																																																			NOVEL	FAM20B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084922.1	4	2.707041	KEEP	1	0	0	9	251	TT	0.99254	0.119538	0		+	3	60	94	0	0	8.032418	8	60	241	31	ENST00000263733.4	0.272727	0.120436
FAM20B	9917	__UNKNOWN__	__UNKNOWN__	1	179044220	179044220	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:179044220G>A	ENST00000263733.4	+	0	4507					NM_014864.3	NP_055679.1	O75063	XYLK_HUMAN	family with sequence similarity 20, member B	NA		NA				Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(3)	14						ccagctactcgggaggctgag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB007944	CCDS1328.1	1q25.2	2013-04-29			ENSG00000116199	ENSG00000116199	9917			23017	protein-coding gene	gene with protein product	glycosaminoglycan xylosylkinase	611063			NA	9455484, 19473117	Standard	NM_014864	NM_014864	NA	Approved	KIAA0475, GXK1	uc001gmc.3	O75063	OTTHUMG00000035073	ENST00000263733.4:c.*2941G>A	chr1.hg19:g.179044220G>A		NA	Q5W0C3|Q5W0C4	hg19	CCDS1328.1	0.02	2.655224	CTCxGGA	COVERED																																																																																			NOVEL	FAM20B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084922.1	21	8.620733	KEEP	3	3	77	56	1630	GG	1	1	0		+	6	60	183	0	0	10.517713	129	60	4177	234	ENST00000263733.4	0.044444	1
ABL2	27	__UNKNOWN__	__UNKNOWN__	1	179181844	179181844	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:179181844A>G	ENST00000502732.1	-	1	361				ABL2_ENST00000507173.1_Intron|ABL2_ENST00000392043.3_Intron|ABL2_ENST00000511413.1_Intron|ABL2_ENST00000367623.4_Intron	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	NA		NA			actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)			breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	ctccagcctgagcaacaaggg	0.527		NA	T	ETV6	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322	27		SH2 domain containing	77	protein-coding gene	gene with protein product	Abelson-related gene	164690	v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene), v-abl Abelson murine leukemia viral oncogene homolog 2, c-abl oncogene 2, non-receptor tyrosine kinase	ABLL	NA	3787260	Standard	NM_005158	NM_001136001	NA	Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.157+16531T>C	chr1.hg19:g.179181844A>G		NA	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	hg19	CCDS30947.1	0.02	-0.184197	CTGxGCA	COVERED																																																																																			NOVEL	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085174.3	7	4.511603	KEEP	1	0	0	15	415	AA	0.99649	0.421991	0		-	4	60	143	0	0	11.96245	15	60	456	52	ENST00000502732.1	0.210526	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	179243365	179243365	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:179243365A>G			NA	NA				ABL2 (44546 upstream) : SOAT1 (19559 downstream)						NA		NA									NA						ccagcactttaggaggccgag	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.179243365A>G		NA		hg19		0.02	-0.140342	TTTxGGA	COVERED																																																																																			NOVEL					0			7	3.307947	KEEP	0	0	0	11	297	AA	0.993072	0.259157	0			4	60	127	0	0	10.971158	10	60	306	43		0.285714	0.260965
ACBD6	84320	__UNKNOWN__	__UNKNOWN__	1	180299349	180299349	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:180299349T>C	ENST00000367595.3	-	7	1351				ACBD6_ENST00000475338.2_Intron	NM_032360.3	NP_115736.1	Q9BR61	ACBD6_HUMAN	acyl-CoA binding domain containing 6	NA		NA				cytoplasm (GO:0005737)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)		ACBD6/RRP15(2)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)	7						gagtttgagatcagcctgggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006505	CCDS1339.1	1q25.1	2013-10-11	2010-04-30		ENSG00000135847		84320		Ankyrin repeat domain containing	23339	protein-coding gene	gene with protein product		NA	acyl-Coenzyme A binding domain containing 6		NA	18268358	Standard	NM_032360	NM_032360	NA	Approved	MGC2404	uc001gog.3	Q9BR61	OTTHUMG00000035117	ENST00000367595.3:c.664-15492A>G	chr1.hg19:g.180299349T>C		NA		hg19	CCDS1339.1	0.02	-0.192941	AGAxCAG	COVERED																																																																																			NOVEL	ACBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084998.1	6	3.909087	KEEP	0	0	0	13	350	TT	0.994391	0.455189	0		-	4	60	133	0	1	10.863151	16	60	461	49	ENST00000367595.3	0.2	0.457757
XPR1	9213	__UNKNOWN__	__UNKNOWN__	1	180714077	180714077	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:180714077A>G	ENST00000367590.4	+	3	319				XPR1_ENST00000367589.3_Intron	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						gtgagccaccatgcccggctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324	9213			12827	protein-coding gene	gene with protein product		605237	xenotropic and polytropic retrovirus receptor		NA	9990033	Standard	NM_004736	NM_004736	NA	Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.122-42812A>G	chr1.hg19:g.180714077A>G		NA	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	hg19	CCDS1340.1	0.02	-0.192944	ACCxTGC	COVERED																																																																																			NOVEL	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084996.2	5	3.308355	KEEP	0	0	0	11	302	AA	0.993072	0.454585	0		+	3	60	104	0	0	8.160808	17	60	496	51	ENST00000367590.4	0.15	0.457757
KIAA1614	57710	__UNKNOWN__	__UNKNOWN__	1	180903365	180903365	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:180903365A>G	ENST00000367588.4	+	5	1260				KIAA1614_ENST00000367587.1_Intron	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	NA		NA								NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						tccagcctggacaacaagagt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835	57710			29327	protein-coding gene	gene with protein product		NA			NA		Standard	XM_046531	NM_020950	NA	Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1206-886A>G	chr1.hg19:g.180903365A>G		NA	Q5VZ45|Q9HCF8	hg19	CCDS41442.1	0.02	-0.061397	TGGxCAA	UNCOVERED																																																																																			NOVEL	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085151.1	6	3.307991	KEEP	1	0	0	11	299	AA	0.992708	0.043467	0		+	2	50	69	1	0	6.392943	3	60	90	19	ENST00000367588.4	0.4	0.043787
MR1	3140	__UNKNOWN__	__UNKNOWN__	1	181012601	181012601	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:181012601C>G	ENST00000367580.5	+	2	72				MR1_ENST00000282990.6_Intron|MR1_ENST00000434571.2_Intron|MR1_ENST00000438435.2_Intron|MR1_ENST00000367579.3_Intron	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	NA		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	gctcacatctctaatcccagc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(174;1412 1962 45296 46549 47110)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029	3140		Immunoglobulin superfamily / C1-set domain containing	4975	protein-coding gene	gene with protein product		600764	major histocompatibility complex, class I-like sequence	HLALS	NA	7624800, 9784382	Standard	NM_001531	NM_001194999	NA	Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.68-5587C>G	chr1.hg19:g.181012601C>G		NA	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	hg19	CCDS1342.1	0.02	-0.210527	TCTxTAA	COVERED																																																																																			NOVEL	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085134.2	7	2.40745	KEEP	1	0	0	8	255	CC	0.99257	0.518282	0		+	3	60	94	0	0	7.027292	19	60	627	45	ENST00000367580.5	0.136364	0.522161
CACNA1E	777	__UNKNOWN__	__UNKNOWN__	1	181587655	181587655	__UNKNOWN__	Intron	SNP	C	C	T	rs376728415	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:181587655C>T	ENST00000367570.1	+	7	1116				CACNA1E_ENST00000358338.5_Intron|CACNA1E_ENST00000357570.5_Intron|CACNA1E_ENST00000360108.3_Intron|CACNA1E_ENST00000526775.1_Intron|CACNA1E_ENST00000367567.4_Intron|CACNA1E_ENST00000367573.2_Intron	NM_000721.3	NP_000712.2	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	NA		NA			calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						gagccaagatcgtgccactgc	0.522		NA											C|||	5	0.000998403	0.0	0.0	5008	,	,	NA	19653	0.005	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216	777		Calcium channel subunits, Voltage-gated ion channels / Calcium channels, EF-hand domain containing	1392	protein-coding gene	gene with protein product		601013		CACNL1A6	NA	8388125, 16382099	Standard	NM_000721	NM_001205293	NA	Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367570.1:c.952-32819C>T	chr1.hg19:g.181587655C>T		NA	B1AM12|B1AM13|B1AM14|Q14580|Q14581	hg19	CCDS53443.1	0.02	-0.149124	GATxGTG	COVERED																																																																																			NOVEL	CACNA1E-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090791.2	11	2.707863	KEEP	2	0	0	9	270	CC	0.99257	0.289832	0		+	3	60	87	0	0	6.692024	14	60	468	38	ENST00000367570.1	0.176471	0.292001
GS1-122H1.2	0	__UNKNOWN__	__UNKNOWN__	1	182197852	182197852	__UNKNOWN__	lincRNA	SNP	T	T	C	rs12034893	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:182197852T>C	ENST00000608183.1	-	0	118										NA		NA									NA						tctcagcactttgggaggccg	0.458		NA											t|||	470	0.0938498	0.0817	0.0403	5008	,	,	NA	15456	0.2143	NA	0.0388	False	NA	,,,	NA	NA	NA	2504	0.0808	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000608183.1:	chr1.hg19:g.182197852T>C		NA		hg19		0.02	-0.105265	ACTxTGG	UNCOVERED																																																																																			NOVEL	GS1-122H1.2-001	KNOWN	non_canonical_TEC|basic	lincRNA	NA	lincRNA	OTTHUMT00000091037.1	5	2.40559	KEEP	1	0	0	8	212	TT	0	0	0		-	7	60	237	0	0	23.908062	4	60	126	28	ENST00000608183.1	0.636364	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	183142538	183142538	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:183142538T>C			NA	NA				LAMC1 (27811 upstream) : LAMC2 (12834 downstream)						NA		NA									NA						tagcgaaacctcatctctaca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.183142538T>C		NA		hg19		0.02	-0.114004	ACCxCAT	UNCOVERED																																																																																			NOVEL					0			10	2.706522	KEEP	0	0	0	9	244	TT	0.99254	0.161255	0			3	60	81	1	0	6.482347	10	60	306	29		0.230769	0.162467
LAMC2	3918	__UNKNOWN__	__UNKNOWN__	1	183170796	183170796	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:183170796A>G	ENST00000264144.4	+	2	144				LAMC2_ENST00000493293.1_Intron	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	NA		NA			cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						tgtaatcccaacactttggga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085	3918		Laminins	6493	protein-coding gene	gene with protein product		150292	laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))	EBR2, LAMB2T, LAMNB2, EBR2A	NA	1383240	Standard	NM_005562	NM_005562	NA	Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.80-6220A>G	chr1.hg19:g.183170796A>G		NA	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	hg19	CCDS1352.1	0.02	-0.236822	CCAxCAC	COVERED																																																																																			NOVEL	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086258.1	6	3.302508	KEEP	0	0	0	11	290	AA	0.993072	0.608164	0		+	3	60	102	0	0	7.705594	21	60	635	59	ENST00000264144.4	0.125	0.612407
TSEN15	116461	__UNKNOWN__	__UNKNOWN__	1	184035791	184035791	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:184035791T>C	ENST00000361641.1	+	4	432				TSEN15_ENST00000423085.2_Intron|TSEN15_ENST00000533373.1_Intron	NM_052965.2	NP_443197.1	Q8WW01	SEN15_HUMAN	TSEN15 tRNA splicing endonuclease subunit	NA		NA			mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)	tRNA-intron endonuclease activity (GO:0000213)			breast(1)|kidney(3)|large_intestine(2)|lung(2)	8						ccgcctgccttagcctcttaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF288394	CCDS1361.1, CCDS44286.1, CCDS72993.1	1q25	2013-08-06	2013-08-06	2008-06-12	ENSG00000198860	ENSG00000198860	116461		tRNA splicing endonuclease subunits	16791	protein-coding gene	gene with protein product		608756	chromosome 1 open reading frame 19, tRNA splicing endonuclease 15 homolog (S. cerevisiae)	C1orf19	NA	11318611, 17166513	Standard		XM_006711148	NA	Approved		uc001gqt.4	Q8WW01	OTTHUMG00000035461	ENST00000361641.1:c.354-5500T>C	chr1.hg19:g.184035791T>C		NA	B4DKP0|Q9BZQ5	hg19	CCDS1361.1	0.02	-0.07892	CCTxAGC	UNCOVERED																																																																																			NOVEL	TSEN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086132.1	4	3.007417	KEEP	0	0	0	10	272	TT	0.992708	0.076772	0		+	2	60	73	0	0	6.301153	6	60	165	29	ENST00000361641.1	0.25	0.077336
SWT1	54823	__UNKNOWN__	__UNKNOWN__	1	185142904	185142904	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:185142904C>T	ENST00000367500.4	+	5	389				SWT1_ENST00000367501.3_Intron	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	NA		NA								breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						atcccagcaccttgggaggcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668	54823			16785	protein-coding gene	gene with protein product		NA	chromosome 1 open reading frame 26	C1orf26	NA	11318611, 19127978, 23768067	Standard	NM_017673	NM_017673	NA	Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.225-600C>T	chr1.hg19:g.185142904C>T		NA	Q8NEK9|Q9BZQ7|Q9NXQ0	hg19	CCDS1367.1	0.02	-0.175247	CACxTTG	COVERED																																																																																			NOVEL	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000085790.1	8	5.415657	KEEP	1	0	0	18	552	CC	0.999366	0.387161	0		+	4	60	122	0	0	10.204415	12	60	393	56	ENST00000367500.4	0.25	0.387407
HMCN1	83872	__UNKNOWN__	__UNKNOWN__	1	185833714	185833714	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:185833714G>A	ENST00000271588.4	+	3	681	c.452G>A	c.(451-453)cGg>cAg	p.R151Q	HMCN1_ENST00000367492.2_Missense_Mutation_p.R151Q	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	151	VWFA.	NA			response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AAAGATTACCGGCTCACCCAT	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													108	99	102			NA	NA	1		NA											NA				185833714		2203	4300	6503	SO:0001583	missense			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341	83872		Fibulins, Immunoglobulin superfamily / I-set domain containing	19194	protein-coding gene	gene with protein product	fibulin 6	608548	age-related macular degeneration 1 (senile macular degeneration)	ARMD1	NA	11222143	Standard	NM_031935	NM_031935	NA	Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.452G>A	chr1.hg19:g.185833714G>A	ENSP00000271588:p.Arg151Gln	NA	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	hg19	CCDS30956.1	0.02	-0.359653	ACCxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756588	0.49362	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.97575	-4.44;-4.44	5.43	4.51	0.55191	von Willebrand factor, type A (1);	0.253414	0.38381	N	0.001702	D	0.92698	0.7679	L	0.44542	1.39	0.35891	D	0.829682	P	0.35844	0.524	B	0.22601	0.04	D	0.93279	0.6658	10	0.38643	T	0.18	.	9.8867	0.41266	0.1513:0.0:0.8487:0.0	.	151	Q96RW7	HMCN1_HUMAN	Q	151	ENSP00000271588:R151Q;ENSP00000356462:R151Q	ENSP00000271588:R151Q	R	+	2	0	HMCN1	184100337	0.981000	0.34729	1.000000	0.80357	0.997000	0.91878	1.949000	0.40313	2.533000	0.85409	0.655000	0.94253	CGG	NOVEL	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131848.1	0	2.707782	KEEP	0	0	0	9	269	GG	0.99254	0.882244	0		+	3	60	96	0	0	6.373294	38	60	1248	80	ENST00000271588.4	0.073171	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	186247495	186247495	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:186247495A>G			NA	NA				HMCN1 (87410 upstream) : PRG4 (17909 downstream)						NA		NA									NA						tttttgagacagagtctcact	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.186247495A>G		NA		hg19		0.02	-0.078931	GACxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.406136	KEEP	3	0	0	8	220	AA	0	0	0			3	40	100	0	0	9.133215	5	60	142	26		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	186262751	186262751	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:186262751G>T			NA	NA				HMCN1 (102666 upstream) : PRG4 (2653 downstream)						NA		NA									NA						ctcacacctggaatcccagct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.186262751G>T		NA		hg19		0.02	-0.184182	CTGxAAT	COVERED																																																																																			NOVEL					0			7	2.407129	KEEP	0	0	0	8	247	AG	0.99254	0.420319	0			4	60	109	0	0	8.781021	13	60	443	46		0.235294	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	186402125	186402125	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:186402125T>C			NA	NA				C1orf27 (11615 upstream) : PDC (10572 downstream)						NA		NA									NA						accatgttggtcaggctggtc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.186402125T>C		NA		hg19		0.02	-0.087715	TGGxCAG	UNCOVERED																																																																																			NOVEL					0			5	3.007338	KEEP	3	0	0	10	271	TT	0	0	0			3	60	107	0	0	9.478786	7	60	210	31		0.3	0.099721
PTGS2	5743	__UNKNOWN__	__UNKNOWN__	1	186644033	186644033	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:186644033A>G	ENST00000367468.5	-	10	1542				PTGS2_ENST00000490885.2_Intron	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	NA		NA			anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	TTTAGGggccaggcgcggtgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	5743	1.14.99.1		9605	protein-coding gene	gene with protein product		600262			NA	1380156	Standard	NM_000963	NM_000963	NA	Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.1406-139T>C	chr1.hg19:g.186644033A>G		NA	A8K802|Q16876	hg19	CCDS1371.1	0.02	-0.175421	GCCxGGC	COVERED																																																																																			NOVEL	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000086157.2	7	3.308719	KEEP	0	0	0	11	310	AA	0.993072	0.384723	0		-	3	60	100	0	0	7.910076	15	60	456	40	ENST00000367468.5	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	189193855	189193855	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:189193855G>A			NA	NA				LINC01035 (187462 upstream) : RNA5SP73 (441423 downstream)						NA		NA									NA						ggccgaggcgggcggatcacg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.189193855G>A		NA		hg19		0.02	-0.131573	GCGxGCG	UNCOVERED																																																																																			NOVEL					0			7	2.708318	KEEP	7	0	0	9	285	GG	0	0	0			3	51	88	0	0	7.301037	9	60	299	44		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	189570205	189570205	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:189570205G>A			NA	NA				LINC01035 (563812 upstream) : RNA5SP73 (65073 downstream)						NA		NA									NA						cgcctgccttggcctcccaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.189570205G>A		NA		hg19		0.02	-0.149118	CTTxGCC	COVERED																																																																																			NOVEL					0			7	3.30959	KEEP	1	0	0	11	333	GG	0.992708	0.289872	0			3	46	96	0	0	7.981825	10	60	335	36		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	189666340	189666340	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:189666340A>G			NA	NA				RNA5SP73 (30954 upstream) : RP11-398M15.1 (78254 downstream)						NA		NA									NA						GGTgccgggcacggtggctcg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.189666340A>G		NA		hg19		0.02	1.853621	GGCxCGG	COVERED																																																																																			NOVEL					0			10	6.014827	KEEP	0	0	0	20	548	AA	0.999863	0.989407	0			4	60	137	0	0	9.229453	56	60	1640	123		0.066667	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	190803739	190803739	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:190803739C>T			NA	NA				RP11-463J7.2 (32951 upstream) : RP11-309H21.3 (316900 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.190803739C>T		NA		hg19		0.02	-0.201748	AGGxGTG	COVERED																																																																																			NOVEL					0			3	3.306064	KEEP	3	0	0	11	309	CC	0.99257	0.4869	0			3	60	86	0	0	6.434102	16	60	516	52		0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	192792311	192792311	__UNKNOWN__	IGR	SNP	G	G	A	rs377413693		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:192792311G>A			NA	NA				RGS2 (10908 upstream) : RN7SKP126 (52504 downstream)						NA		NA									NA						agaaaagaaaggagaaaagaa	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.192792311G>A		NA		hg19		0.02	-0.219305	AAAxGAG	COVERED																																																																																			NOVEL					0			12	6.018154	KEEP	0	0	0	20	621	GG	0.999863	0.552812	0			3	60	90	0	0	6.506229	21	60	699	62		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	192925810	192925810	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:192925810C>T			NA	NA				LINC01032 (8423 upstream) : UCHL5 (55569 downstream)						NA		NA									NA						ctcacacctgcaatcccagca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.192925810C>T		NA		hg19		0.02	-0.1491	CTGxAAT	COVERED																																																																																			NOVEL					0			7	2.407301	KEEP	0	0	0	8	249	CC	0.99257	0.289832	0			3	60	81	0	0	6.373065	11	60	377	38		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	195193110	195193110	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:195193110C>T			NA	NA				AL357932.1 (97204 upstream) : RP11-476B1.1 (821015 downstream)						NA		NA									NA						ttagtagagacggggtttctc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.195193110C>T		NA		hg19		0.02	-0.087697	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.706896	KEEP	2	0	0	9	257	CC	0.99257	0.09898	0			3	60	77	0	0	6.477847	7	60	225	22		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	197990653	197990653	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:197990653A>G			NA	NA				LHX9 (86045 upstream) : NEK7 (135439 downstream)						NA		NA									NA						tgggattacaagcgtgagcca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.197990653A>G		NA		hg19		0.02	-0.122806	ACAxGCG	COVERED																																																																																			NOVEL					0			7	3.908497	KEEP	8	0	0	13	351	AA	0.99254	0.194847	0			3	60	106	0	0	8.981846	10	60	312	50		0.230769	0.196312
RP11-382E9.1	0	__UNKNOWN__	__UNKNOWN__	1	199263454	199263454	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:199263454T>C	ENST00000452199.1	+	0	309										NA		NA									NA						ctcactctgttgcccagcctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000452199.1:	chr1.hg19:g.199263454T>C		NA		hg19		0.02	-0.175392	TGTxGCC	COVERED																																																																																			NOVEL	RP11-382E9.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000087440.1	9	2.706996	KEEP	0	0	0	9	250	TT	0.99254	0.420319	0		+	3	60	105	0	2	8.579048	13	60	375	44	ENST00000452199.1	0.1875	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	199763109	199763109	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:199763109T>C			NA	NA				AL450244.1 (178701 upstream) : RNU6-778P (94177 downstream)						NA		NA									NA						gtcacccaggttggagtgctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.199763109T>C		NA		hg19		0.02	-0.078944	AGGxTGG	UNCOVERED																																																																																			NOVEL					0			3	2.706201	KEEP	0	0	0	9	239	TT	0.99254	0.076759	0			2	60	72	0	0	6.335716	5	60	151	26		0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	199843552	199843552	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:199843552T>C			NA	NA				AL450244.1 (259144 upstream) : RNU6-778P (13734 downstream)						NA		NA									NA						tgcactccagtctgggcaaca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.199843552T>C		NA		hg19		0.02	-0.131406	CAGxCTG	COVERED																																																																																			NOVEL					0			8	3.910015	KEEP	0	0	0	13	359	TT	0.994391	0.227888	0			3	54	100	0	0	8.384325	10	60	277	41		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	199978996	199978996	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:199978996T>A			NA	NA				RNU6-716P (1261 upstream) : RNU6-609P (4820 downstream)						NA		NA									NA						acagggtttctccatgttggc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.199978996T>A		NA		hg19		0.02	-0.087702	TTCxCCA	UNCOVERED																																																																																			NOVEL					0			6	2.70655	KEEP	1	0	0	9	244	TT	0.99254	0.119538	0			3	51	86	0	0	7.732386	5	60	149	26		0.375	0.120436
NAV1	89796	__UNKNOWN__	__UNKNOWN__	1	201611653	201611653	__UNKNOWN__	Intron	SNP	T	T	C	rs71138344|rs145876654|rs12407966	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:201611653T>C	ENST00000367302.1	+	3	238							Q8NEY1	NAV1_HUMAN	neuron navigator 1	NA		NA			microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						ttctttctttttttctttctt	0.458		NA											t|||	3628	0.724441	0.8434	0.8473	5008	,	,	NA	19912	0.5764	NA	0.7724	False	NA	,,,	NA	NA	NA	2504	0.5798	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369	89796			15989	protein-coding gene	gene with protein product	neuron navigator-1, pore membrane and/or filament interacting like protein 3	611628			NA	12079279, 12062803	Standard	NM_020443	NM_020443	NA	Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367302.1:c.5-6109T>C	chr1.hg19:g.201611653T>C		NA	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	hg19		0.02	-0.096488	TTTxTTT	UNCOVERED																																																																																			NOVEL	NAV1-006	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000087018.1	12	3.909958	KEEP	1	0	0	13	361	TT	0.994391	0.119761	0		+	3	60	97	0	0	8.332376	8	60	250	37	ENST00000367302.1	0.272727	0.120436
IPO9	55705	__UNKNOWN__	__UNKNOWN__	1	201840583	201840583	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:201840583T>C	ENST00000361565.4	+	19	2645					NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	NA		NA			protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						ggcacaatcttggctcactgc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700	55705		Importins	19425	protein-coding gene	gene with protein product		NA			NA	11823430, 10574461	Standard	NM_018085	NM_018085	NA	Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.2576+128T>C	chr1.hg19:g.201840583T>C		NA	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	hg19	CCDS1415.1	0.02	-0.157853	TCTxGGC	UNCOVERED																																																																																			NOVEL	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087088.1	14	2.706971	KEEP	7	0	0	9	251	TT	0	0	0		+	4	52	110	0	0	9.001664	12	60	359	37	ENST00000361565.4	0.25	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	201992836	201992836	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:201992836T>C			NA	NA				ELF3 (6520 upstream) : GPR37L1 (99149 downstream)						NA		NA									NA						cgctggagtgtagtggtgcaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.201992836T>C		NA		hg19		0.02	-0.070172	GTGxAGT	UNCOVERED																																																																																			NOVEL					0			4	2.405575	KEEP	1	0	0	8	212	TT	0	0	0			3	60	100	0	0	9.625332	3	60	87	22		0.5	0.054137
PPP1R12B	4660	__UNKNOWN__	__UNKNOWN__	1	202407683	202407683	__UNKNOWN__	Intron	SNP	G	G	A	rs538185917	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:202407683G>A	ENST00000608999.1	+	10	1611				PPP1R12B_ENST00000336894.4_Intron	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GACAGCCCCCGGTGGAAGAGG	0.652		NA											G|||	4	0.000798722	0.0	0.0	5008	,	,	NA	16678	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157	4660		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Ankyrin repeat domain containing	7619	protein-coding gene	gene with protein product	myosin phosphatase regulatory subunit, myosin phosphatase, target subunit 2	603768	protein phosphatase 1, regulatory (inhibitor) subunit 12B	MYPT2	NA	9570949	Standard	NM_032105	NM_002481	NA	Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.1458+531G>A	chr1.hg19:g.202407683G>A		NA	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	hg19	CCDS1426.1	0.02	-0.263153	CCCxGTG	COVERED																																																																																			NOVEL	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000099166.3	0	2.704505	KEEP	0	0	0	9	247	GG	0.99254	0.688494	0		+	3	60	93	0	0	6.498413	27	60	884	55	ENST00000608999.1	0.1	0.693668
SYT2	127833	__UNKNOWN__	__UNKNOWN__	1	202565428	202565428	__UNKNOWN__	3'UTR	SNP	C	C	T	rs149900121		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:202565428C>T	ENST00000367267.1	-	0	1909				SYT2_ENST00000367268.4_3'UTR	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	NA		NA			neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	cacacacacacacacacatac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858	127833		Synaptotagmins	11510	protein-coding gene	gene with protein product		600104			NA	7749232	Standard	NM_177402	NM_177402	NA	Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.*457G>A	chr1.hg19:g.202565428C>T		NA	Q496K5|Q8NBE5	hg19	CCDS1427.1	0.02	0.887033	ACAxACA	COVERED																																																																																			NOVEL	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000099157.1	14	4.815638	KEEP	2	2	50	34	969	CC	0.999999	0.999406	0		-	6	60	158	2	1	10.443109	49	60	1573	147	ENST00000367267.1	0.109091	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	202940419	202940419	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:202940419A>G			NA	NA				CYB5R1 (4011 upstream) : RP11-38O14.5 (15985 downstream)						NA		NA									NA						atggagtctcactctgtcacc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.202940419A>G		NA		hg19		0.02	-0.096458	CTCxCTC	UNCOVERED																																																																																			NOVEL					0			12	3.236211	KEEP	11	1	23	19	489	AA	0.994391	0.119761	0			4	40	116	0	0	10.585171	6	60	174	42		0.4	0.120436
LAX1	54900	__UNKNOWN__	__UNKNOWN__	1	203744282	203744282	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:203744282T>C	ENST00000442561.2	+	0	2060				LAX1_ENST00000367215.1_3'UTR	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	NA		NA			antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			aatcccagcattttggtaggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188	54900			26005	protein-coding gene	gene with protein product	LAT-like membrane associated protein, linker for activation of x cells	NA			NA	12359715	Standard	NM_017773	NM_017773	NA	Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.*473T>C	chr1.hg19:g.203744282T>C		NA	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	hg19	CCDS1441.2	0.02	1.962024	GCAxTTT	COVERED																																																																																			NOVEL	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087468.3	11	6.647301	KEEP	1	1	31	33	897	TT	0.999998	0.989541	0		+	4	60	128	0	0	8.423717	53	60	1588	140	ENST00000442561.2	0.070175	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	203906790	203906790	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:203906790A>C			NA	NA				SNRPE (67112 upstream) : AC096645.1 (61582 downstream)						NA		NA									NA						aggggGaggaaggaaggaagg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.203906790A>C		NA		hg19		0.02	-0.087655	GGAxGGA	UNCOVERED																																																																																			NOVEL					0			9	3.306894	KEEP	0	0	0	11	285	AA	0.993072	0.09903	0			3	60	98	0	0	8.579895	7	60	187	28		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	204167255	204167255	__UNKNOWN__	IGR	SNP	C	C	T	rs114765023	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:204167255C>T			NA	NA				KISS1 (1641 upstream) : GOLT1A (32 downstream)						NA		NA									NA						tgtgagccaccgcgcccggcc	0.527		NA											C|||	28	0.00559105	0.0212	0.0	5008	,	,	NA	18659	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.204167255C>T		NA		hg19		0.02	1.24304	CACxGCG	COVERED																																																																																			NOVEL					0			25	5.912395	KEEP	1	3	77	47	1393	CC	1	0.998465	0			4	60	122	1	0	7.562023	62	60	2050	177		0.060606	0.998465
RP11-739N20.2	0	__UNKNOWN__	__UNKNOWN__	1	204387526	204387526	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:204387526T>C	ENST00000443515.1	+	0	146										NA		NA									NA						actcaggaggttgaggtggga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000443515.1:	chr1.hg19:g.204387526T>C		NA		hg19		0.02	-0.140302	AGGxTGA	COVERED																																																																																			NOVEL	RP11-739N20.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000087972.1	8	3.608053	KEEP	1	0	0	12	317	TT	0.993634	0.259304	0		+	3	60	103	0	0	8.472624	12	60	342	36	ENST00000443515.1	0.2	0.260965
MDM4	4194	__UNKNOWN__	__UNKNOWN__	1	204521262	204521262	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:204521262A>G	ENST00000367182.3	+	0	4087				MDM4_ENST00000507825.2_Intron|MDM4_ENST00000463049.1_3'UTR	NM_001204171.1|NM_001278516.1|NM_001278517.1|NM_001278518.1|NM_001278519.1|NM_002393.4	NP_001191100.1|NP_001265445.1|NP_001265446.1|NP_001265447.1|NP_001265448.1|NP_002384.2	O15151	MDM4_HUMAN	MDM4, p53 regulator	NA		NA			cell proliferation (GO:0008283)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|G0 to G1 transition (GO:0045023)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00146)|all_neural(3;0.0218)|Glioma(3;0.0382)|Breast(84;0.112)|all_epithelial(62;0.118)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;3.15e-47)|all cancers(3;3.56e-32)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|Epithelial(59;0.143)|BRCA - Breast invasive adenocarcinoma(75;0.143)			ttagctgggcatggtggtgca	0.517		NA	A		GBM, bladder, retinoblastoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q32	4194	Mdm4 p53 binding protein homolog		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF007111	CCDS1447.1, CCDS55674.1, CCDS55675.1, CCDS60396.1, CCDS73007.1, CCDS73008.1, CCDS73009.1	1q32	2014-03-03	2014-03-03		ENSG00000198625	ENSG00000198625	4194			6974	protein-coding gene	gene with protein product		602704	mouse double minute 4, human homolog of; p53-binding protein, Mdm4, transformed 3T3 cell double minute 4, p53 binding protein (mouse), Mdm4 p53 binding protein homolog (mouse)		NA	9226370, 14660608	Standard	NM_002393	NM_002393	NA	Approved	MDMX, HDMX	uc001hba.3	O15151	OTTHUMG00000035877	ENST00000367182.3:c.*2452A>G	chr1.hg19:g.204521262A>G		NA	Q2M2Y2|Q32SL2|Q6GS18|Q8IV83	hg19	CCDS1447.1	0.02	-0.254304	GGCxTGG	COVERED																																																																																			NOVEL	MDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000087415.2	9	6.244155	KEEP	4	1	26	30	791	AA	0.999997	0.668521	0		+	3	60	93	0	0	6.751242	22	60	617	68	ENST00000367182.3	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	204669261	204669261	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:204669261A>G			NA	NA				LRRN2 (14400 upstream) : RNA5SP75 (7186 downstream)						NA		NA									NA						aacagagtgaaacgtctcaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.204669261A>G		NA		hg19		0.02	-0.043855	TGAxACG	UNCOVERED																																																																																			NOVEL					0			3	2.405586	KEEP	0	0	0	8	213	AA	0.99257	0.023895	0			2	60	70	0	2	6.4931	3	60	90	16		0.4	0.024074
RBBP5	5929	__UNKNOWN__	__UNKNOWN__	1	205055644	205055644	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:205055644T>C	ENST00000264515.6	-	0	4029				RBBP5_ENST00000367164.1_3'UTR	NM_001193273.1|NM_005057.3	NP_001180202.1|NP_005048.2	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	methylated histone binding (GO:0035064)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	27	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			ggattacaggtgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC053856	CCDS30983.1, CCDS53463.1	1q32	2013-01-10	2001-11-28		ENSG00000117222	ENSG00000117222	5929		WD repeat domain containing	9888	protein-coding gene	gene with protein product	SWD1, Set1c WD40 repeat protein, homolog (S. cerevisiae)	600697	retinoblastoma-binding protein 5		NA	7558034	Standard	NM_005057	NM_005057	NA	Approved	RBQ3, SWD1	uc001hbu.2	Q15291	OTTHUMG00000037104	ENST00000264515.6:c.*2271A>G	chr1.hg19:g.205055644T>C		NA	A8K272|Q7Z6D8|Q8NDZ7	hg19	CCDS30983.1	0.02	-0.219215	AGGxGTG	COVERED																																																																																			NOVEL	RBBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090077.1	6	5.107681	KEEP	0	0	0	17	431	TT	0.999366	0.552537	0		-	3	60	101	1	0	7.792581	18	60	505	59	ENST00000264515.6	0.142857	0.552887
NUAK2	81788	__UNKNOWN__	__UNKNOWN__	1	205272066	205272066	__UNKNOWN__	3'UTR	SNP	G	G	A	rs563260815		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:205272066G>A	ENST00000367157.3	-	0	2525					NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2	NA		NA								breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ataaCGAAGCGTTACTCCAGA	0.443		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15783	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545	81788			29558	protein-coding gene	gene with protein product	SNF1/AMP activated protein kinase	608131			NA	11230166	Standard	NM_030952	NM_030952	NA	Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.*512C>T	chr1.hg19:g.205272066G>A		NA		hg19	CCDS1453.1	0.02	-0.122781	AGCxTTA	COVERED																																																																																			NOVEL	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090390.1	1	3.909769	KEEP	0	0	0	13	369	GG	0.994391	0.19521	0		-	3	60	90	0	0	7.27314	11	60	328	39	ENST00000367157.3	0.214286	0.196312
KLHDC8A	55220	__UNKNOWN__	__UNKNOWN__	1	205314847	205314847	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:205314847T>C	ENST00000367156.3	-	4	303				KLHDC8A_ENST00000367155.3_Intron|KLHDC8A_ENST00000460687.1_Intron|KLHDC8A_ENST00000606529.1_Intron|KLHDC8A_ENST00000537168.1_Intron	NM_001271863.1	NP_001258792.1	Q8IYD2	KLD8A_HUMAN	kelch domain containing 8A	NA		NA								breast(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(84;0.23)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ccagcctgggtgacagagcaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS30985.1	1q32.1	2008-02-05			ENSG00000162873	ENSG00000162873	55220			25573	protein-coding gene	gene with protein product		614503			NA		Standard	NM_018203	NM_018203	NA	Approved	FLJ10748	uc031prx.1	Q8IYD2	OTTHUMG00000037199	ENST00000367156.3:c.514-1261A>G	chr1.hg19:g.205314847T>C		NA	B3KU70|Q9NVG5	hg19	CCDS30985.1	0.02	-0.122717	GGGxGAC	COVERED																																																																																			NOVEL	KLHDC8A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090397.1	3	3.004877	KEEP	1	0	0	10	261	TT	0.992708	0.19488	0		-	3	60	102	0	0	8.473901	11	60	296	34	ENST00000367156.3	0.214286	0.196312
CDK18	5129	__UNKNOWN__	__UNKNOWN__	1	205476525	205476525	__UNKNOWN__	Intron	SNP	C	C	T	rs12126148	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:205476525C>T	ENST00000360066.2	+	1	280				CDK18_ENST00000429964.2_Intron|CDK18_ENST00000506784.1_Intron	NM_002596.3|NM_212502.2|NM_212503.2	NP_002587.2|NP_997667.1|NP_997668.1	Q07002	CDK18_HUMAN	cyclin-dependent kinase 18	NA		NA					ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|endometrium(2)|large_intestine(2)|lung(10)|stomach(2)|urinary_tract(1)	19						tttgggaggccgaggtggacg	0.473		NA											C|||	191	0.038139	0.0076	0.0519	5008	,	,	NA	17145	0.0079	NA	0.0924	False	NA	,,,	NA	NA	NA	2504	0.045	NA	NA	NA	Pancreas(180;489 2072 28461 40831 44265)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X66362	CCDS1454.1, CCDS44300.1	1q31-q32	2011-11-08	2009-12-16	2009-12-16	ENSG00000117266	ENSG00000117266	5129		Cyclin-dependent kinases	8751	protein-coding gene	gene with protein product		169190	PCTAIRE protein kinase 3	PCTK3	NA	1437147, 19884882	Standard	NM_002596	NM_002596	NA	Approved	PCTAIRE3	uc010pri.2	Q07002	OTTHUMG00000037203	ENST00000360066.2:c.-22+2519C>T	chr1.hg19:g.205476525C>T		NA	Q5VXQ2|Q6V3A2|Q6V3A3|Q96F90	hg19	CCDS44300.1	0.02	-0.333327	GGCxGAG	COVERED																																																																																			NOVEL	CDK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090407.2	48	6.017974	KEEP	79	3	85	50	1547	CC	0.999366	0.851444	0		+	7	60	218	0	0	18.1799	22	60	745	214	ENST00000360066.2	0.241379	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	205532629	205532629	__UNKNOWN__	IGR	SNP	T	T	C	rs10900514		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:205532629T>C			NA	NA				CDK18 (30708 upstream) : RNU2-19P (3214 downstream)						NA		NA									NA						ttctttctttttttttttttt	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.205532629T>C		NA		hg19		0.02	-0.078935	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			11	3.007325	KEEP	0	0	0	10	271	TT	0.992708	0.076772	0			4	60	137	1	0	13.532853	3	60	84	27		0.571429	0.077336
ELK4	2005	__UNKNOWN__	__UNKNOWN__	1	205591782	205591782	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:205591782C>G	ENST00000357992.4	-	2	547				ELK4_ENST00000468523.1_Intron|ELK4_ENST00000289703.4_Intron	NM_001973.3	NP_001964.2	P28324	ELK4_HUMAN	ELK4, ETS-domain protein (SRF accessory protein 1)	NA		NA			cell differentiation (GO:0030154)|histone H3 deacetylation (GO:0070932)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)		SLC45A3/ELK4(18)	breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|skin(1)	12	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			aaagtgctggcattacaggca	0.443		NA	T	SLC45A3	prostate																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		1	1q32	2005	ELK4, ETS-domain protein (SRF accessory protein 1)		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M85165	CCDS1456.1, CCDS1457.1	1q32	2008-02-05			ENSG00000158711	ENSG00000158711	2005			3326	protein-coding gene	gene with protein product		600246			NA	7851904, 8575773	Standard	NM_021795	NM_001973	NA	Approved	SAP1		P28324	OTTHUMG00000037221	ENST00000357992.4:c.207+1021G>C	chr1.hg19:g.205591782C>G		NA	P28323|Q6GSJ2	hg19	CCDS1456.1	0.02	-0.149101	TGGxATT	COVERED																																																																																			NOVEL	ELK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090615.1	9	3.309564	KEEP	1	0	0	11	328	CC	0.993072	0.289978	0		-	5	60	139	0	0	12.137748	10	60	333	33	ENST00000357992.4	0.333333	0.292001
SRGAP2	23380	__UNKNOWN__	__UNKNOWN__	1	206566195	206566195	__UNKNOWN__	Silent	SNP	C	C	T	rs12090039	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:206566195C>T	ENST00000414007.1	+	2	216	c.216C>T	c.(214-216)aaC>aaT	p.N72N	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	212	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.	NA			actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.N72N(1)		NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CCACGGCCAACGTTCGCATTG	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - coding silent(1)	prostate(1)											82	80	80			NA	NA	1		NA											NA				206566195		2170	4280	6450	SO:0001819	synonymous_variant			AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028	23380		Rho GTPase activating proteins	19751	protein-coding gene	gene with protein product		606524	formin binding protein 2	FNBP2	NA	15046868, 11672528	Standard	NM_015326	XM_005277510	NA	Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.216C>T	chr1.hg19:g.206566195C>T		NA		hg19		0.02	6.475231	CAAxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.707	0.911068	0.17833	.	.	ENSG00000163486	ENST00000295713	.	.	.	5.36	-10.7	0.00240	.	.	.	.	.	T	0.55847	0.1946	.	.	.	0.30974	N	0.7227589999999999	.	.	.	.	.	.	T	0.63642	-0.6591	3	.	.	.	.	19.6945	0.96019	0.0:0.164:0.0:0.836	.	.	.	.	C	126	.	.	R	+	1	0	SRGAP2	204632818	0.146000	0.22672	0.630000	0.29268	0.787000	0.44495	-0.403000	0.07214	-2.202000	0.00745	-0.384000	0.06662	CGT	NOVEL	SRGAP2-201	KNOWN	basic	protein_coding	NA	protein_coding		10	3.473734	KEEP	27	2	55	31	893	CC	0.999997	0.999997	0		+	24	49	743	0	0	53.151223	190	52	6071	384	ENST00000414007.1	0.11215	1
C1orf147	574431	__UNKNOWN__	__UNKNOWN__	1	206664655	206664655	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:206664655G>A	ENST00000367119.1	-	0	1889				IKBKE_ENST00000537984.1_Intron|IKBKE_ENST00000367120.3_Intron			Q96MC9	CA147_HUMAN	chromosome 1 open reading frame 147	NA		NA								central_nervous_system(1)	1						ACACACACACGCACTCACACA	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK057159		1q32.1	2012-04-19			ENSG00000162888	ENSG00000162888	574431			32061	protein-coding gene	gene with protein product		NA			NA		Standard			NA	Approved	FLJ32597		Q96MC9	OTTHUMG00000036338	ENST00000367119.1:c.*1066C>T	chr1.hg19:g.206664655G>A		NA	Q5JTS5	hg19		0.02	2.466503	CACxCAC	COVERED																																																																																			NOVEL	C1orf147-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000088457.1	59	13.998834	KEEP	0	8	213	122	3648	GG	1	1	0		-	11	60	307	0	0	19.96193	110	60	3643	396	ENST00000367119.1	0.090909	1
DYRK3	8444	__UNKNOWN__	__UNKNOWN__	1	206835283	206835283	__UNKNOWN__	Intron	SNP	T	T	C	rs34642437	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:206835283T>C	ENST00000489878.1	+	4	259							O43781	DYRK3_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	NA		NA			erythrocyte differentiation (GO:0030218)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(9)|lung(8)|skin(1)|stomach(2)	25	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			tttgggaggctgaggcgggtg	0.473		NA											C|||	1624	0.324281	0.2133	0.4078	5008	,	,	NA	14732	0.2927	NA	0.4105	False	NA	,,,	NA	NA	NA	2504	0.3589	NA	NA	NA	Melanoma(164;427 2622 26826 51707)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y12735	CCDS30999.1, CCDS31000.1	1q32	2008-07-18			ENSG00000143479	ENSG00000143479	8444	2.7.12.1		3094	protein-coding gene	gene with protein product	regulatory erythroid kinase, dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 5, protein kinase Dyrk3	603497			NA	9748265	Standard	NM_003582	NM_003582	NA	Approved	RED, REDK, hYAK3-2	uc001hej.3	O43781	OTTHUMG00000036339	ENST00000489878.1:c.260-20969T>C	chr1.hg19:g.206835283T>C		NA	D3DT79|Q7Z752|Q9HBY6|Q9HBY7	hg19		0.02	-0.324537	GGCxGAG	COVERED																																																																																			NOVEL	DYRK3-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000088460.1	17	3.826578	KEEP	8	1	26	22	605	TT	0.999863	0.835601	0		+	3	40	101	0	0	7.392241	25	60	770	98	ENST00000489878.1	0.107143	0.835716
IL19	29949	__UNKNOWN__	__UNKNOWN__	1	206992425	206992425	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:206992425G>C	ENST00000340758.2	+	2	137					NM_153758.2	NP_715639.1	Q9UHD0	IL19_HUMAN	interleukin 19	NA		NA			apoptotic process (GO:0006915)|immune response (GO:0006955)|interleukin-6 biosynthetic process (GO:0042226)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|reactive oxygen species metabolic process (GO:0072593)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			central_nervous_system(2)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7			BRCA - Breast invasive adenocarcinoma(75;0.211)			caaagtgctgggattacaggc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF192498	CCDS1468.1, CCDS1469.1	1q32.2	2008-07-18			ENSG00000142224	ENSG00000142224	29949		Interleukins and interleukin receptors	5990	protein-coding gene	gene with protein product	melanoma differentiation associated protein-like protein	605687			NA	11196675	Standard	NM_153758	NM_153758	NA	Approved	IL-19, MDA1, ZMDA1, IL-10C, NG.1	uc001heo.3	Q9UHD0	OTTHUMG00000036387	ENST00000340758.2:c.113-17581G>C	chr1.hg19:g.206992425G>C		NA	B6VEV9|Q5VUT3|Q96QR4|Q9NUA0	hg19	CCDS1468.1	0.02	-0.228092	CTGxGAT	COVERED																																																																																			NOVEL	IL19-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000088566.3	18	4.64789	KEEP	8	1	33	27	818	GG	0.999957	0.582905	0		+	4	43	144	0	0	11.693804	19	60	653	86	ENST00000340758.2	0.173913	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	208628657	208628657	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:208628657T>C			NA	NA				PLXNA2 (210992 upstream) : RP11-565N2.1 (151787 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.208628657T>C		NA		hg19		0.02	-0.201721	TCAxGCC	COVERED																																																																																			NOVEL					0			7	3.007756	KEEP	3	0	0	10	278	TT	0.992708	0.486967	0			3	60	94	0	0	7.310382	15	60	443	51		0.166667	0.490544
RD3	343035	__UNKNOWN__	__UNKNOWN__	1	211650855	211650855	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:211650855G>A	ENST00000367002.4	-	0	3274				RD3_ENST00000484910.1_5'UTR	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	NA		NA			response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)					central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		aataaaatacgtaagatgttt	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570	343035			19689	protein-coding gene	gene with protein product		180040	chromosome 1 open reading frame 36	C1orf36	NA	12914764	Standard	NM_183059	NM_183059	NA	Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.*1523C>T	chr1.hg19:g.211650855G>A		NA	A8K595	hg19	CCDS1498.1	0.02	1.409729	TACxTAA	COVERED																																																																																			NOVEL	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089837.1	13	10.228978	KEEP	0	0	0	34	1004	GG	0.999998	0.976863	0		-	4	60	123	0	0	8.054641	49	60	1615	122	ENST00000367002.4	0.075472	0.976865
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	212372864	212372864	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:212372864A>C			NA	NA				RP11-15I11.2 (9263 upstream) : RP11-15I11.3 (25757 downstream)						NA		NA									NA						cgcctgtaataccagcacttt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.212372864A>C		NA		hg19		0.02	-0.131522	AATxCCA	COVERED																																																																																			NOVEL					0			5	3.007071	KEEP	0	0	0	10	267	AA	0.992708	0.227502	0			3	60	103	0	0	8.6827	10	60	274	37		0.230769	0.229173
NSL1	25936	__UNKNOWN__	__UNKNOWN__	1	212904635	212904635	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:212904635T>C	ENST00000366978.1	-	5	317							Q96IY1	NSL1_HUMAN	NSL1, MIS12 kinetochore complex component	NA		NA			chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)		cagtggctcattcctgtaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF255793	CCDS1509.1, CCDS73025.1	1q41	2013-07-03	2013-07-03	2006-11-07	ENSG00000117697	ENSG00000117697	25936			24548	protein-coding gene	gene with protein product		609174	chromosome 1 open reading frame 48, NSL1, MIND kinetochore complex component, homolog (S. cerevisiae)	C1orf48	NA	20819937	Standard	NM_015471	NM_015471	NA	Approved	DC8, DKFZP566O1646, MIS14	uc001hjn.3	Q96IY1	OTTHUMG00000036806	ENST00000366978.1:c.191-4114A>G	chr1.hg19:g.212904635T>C		NA	E7ETD5|Q5SY75|Q9H2M5|Q9NRN8|Q9Y415	hg19		0.02	-0.12278	TCAxTCC	COVERED																																																																																			NOVEL	NSL1-005	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000089402.2	9	2.705939	KEEP	0	0	0	9	237	TT	0.99254	0.194847	0		-	3	60	91	0	0	7.601373	9	60	261	32	ENST00000366978.1	0.25	0.196312
C1orf227	0	__UNKNOWN__	__UNKNOWN__	1	213004564	213004564	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:213004564G>A	ENST00000332912.3	-	3	385					NM_001024601.2	NP_001019772.1	Q537H7	SPT45_HUMAN		NA		NA								kidney(1)|large_intestine(1)|lung(1)	3						taatcccagcgctttgggagg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000332912.3:c.278-961C>T	chr1.hg19:g.213004564G>A		NA		hg19	CCDS31020.1	0.02	-0.113972	AGCxCTT	UNCOVERED																																																																																			NOVEL	C1orf227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089672.2	10	3.007219	KEEP	0	0	0	10	277	GG	0.993072	0.161341	0		-	3	60	88	0	0	7.182791	10	60	310	31	ENST00000332912.3	0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	213087769	213087769	__UNKNOWN__	IGR	SNP	A	A	T	rs1770779	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:213087769A>T			NA	NA				FLVCR1 (15064 upstream) : VASH2 (36092 downstream)						NA		NA									NA						ctcaaaaagcacccccactga	0.517		NA											-|||	1829	0.365216	0.3245	0.2651	5008	,	,	NA	11933	0.374	NA	0.4215	False	NA	,,,	NA	NA	NA	2504	0.4243	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.213087769A>T		NA		hg19		0.02	-0.052586	AGCxCCC	UNCOVERED																																																																																			NOVEL					0			5	2.405885	KEEP	9	0	0	8	219	AA	0	0	0			4	31	116	0	0	11.851591	2	45	50	26		0.666667	0.036766
SMYD2	56950	__UNKNOWN__	__UNKNOWN__	1	214457810	214457810	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:214457810T>C	ENST00000366957.5	+	1	195				SMYD2_ENST00000491455.1_Intron|SMYD2_ENST00000415093.2_Intron	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	NA		NA			negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		tccatgttggtcaggctggtc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499	56950		Zinc fingers, MYND-type, Chromatin-modifying enzymes / K-methyltransferases	20982	protein-coding gene	gene with protein product		610663			NA		Standard	NM_020197	NM_020197	NA	Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.173+3040T>C	chr1.hg19:g.214457810T>C		NA	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	hg19	CCDS31022.1	0.02	-0.192938	TGGxCAG	COVERED																																																																																			NOVEL	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089998.1	7	3.308223	KEEP	2	0	0	11	301	TT	0.992708	0.486967	0		+	3	60	100	0	0	7.833733	16	60	459	51	ENST00000366957.5	0.157895	0.490544
PTPN14	5784	__UNKNOWN__	__UNKNOWN__	1	214697720	214697720	__UNKNOWN__	Intron	SNP	C	C	T	rs182721869	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:214697720C>T	ENST00000366956.5	-	1	41					NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	NA		NA			lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		GAGggctgggcgtggtggctc	0.478		NA											C|||	5	0.000998403	0.003	0.0	5008	,	,	NA	16008	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA	Colon(92;557 1424 24372 34121 40073)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104	5784		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	9647	protein-coding gene	gene with protein product		603155			NA	7733990	Standard	NM_005401	NM_005401	NA	Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.153+26805G>A	chr1.hg19:g.214697720C>T		NA	Q5VSI0	hg19	CCDS1514.1	0.02	-0.13158	GGGxGTG	COVERED																																																																																			NOVEL	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089918.2	10	3.309524	KEEP	1	0	0	11	327	CC	0.993072	0.227586	0		-	3	60	90	0	0	7.172242	12	60	397	35	ENST00000366956.5	0.2	0.229173
ESRRG	2104	__UNKNOWN__	__UNKNOWN__	1	216877741	216877741	__UNKNOWN__	Intron	SNP	C	C	G	rs73092176	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:216877741C>G	ENST00000366937.1	-	2	338				ESRRG_ENST00000487276.1_Intron|ESRRG_ENST00000493748.1_Intron|ESRRG_ENST00000359162.2_Intron|ESRRG_ENST00000360012.3_Intron|ESRRG_ENST00000361395.2_Intron|ESRRG_ENST00000408911.3_Intron|ESRRG_ENST00000391890.3_Intron|ESRRG_ENST00000463665.1_Intron|ESRRG_ENST00000366940.2_Intron|ESRRG_ENST00000366938.2_Intron|ESRRG_ENST00000361525.3_Intron|ESRRG_ENST00000493603.1_Intron	NM_001243518.1	NP_001230447.1	P62508	ERR3_HUMAN	estrogen-related receptor gamma	NA		NA			gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	cacctgtaatcccagctagtt	0.507		NA											C|||	827	0.165136	0.0802	0.1182	5008	,	,	NA	15275	0.2956	NA	0.1581	False	NA	,,,	NA	NA	NA	2504	0.1861	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482	2104		Nuclear hormone receptors	3474	protein-coding gene	gene with protein product		602969			NA	9676434, 10072763	Standard	NM_206595	NM_001243505	NA	Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000366937.1:c.71+2959G>C	chr1.hg19:g.216877741C>G		NA	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	hg19	CCDS58061.1	0.02	-0.070157	AATxCCA	UNCOVERED																																																																																			NOVEL	ESRRG-006	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000089881.4	1	2.406977	KEEP	1	0	0	8	240	CC	0.99257	0.053735	0		-	4	60	131	0	0	12.932404	3	60	87	24	ENST00000366937.1	0.571429	0.054137
ESRRG	2104	__UNKNOWN__	__UNKNOWN__	1	217027438	217027438	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:217027438T>C	ENST00000361525.3	-	3	338				ESRRG_ENST00000487276.1_Intron|ESRRG_ENST00000493748.1_Intron|ESRRG_ENST00000359162.2_Intron|ESRRG_ENST00000361395.2_Intron|ESRRG_ENST00000463665.1_Intron|ESRRG_ENST00000366940.2_Intron|ESRRG_ENST00000366938.2_Intron|ESRRG_ENST00000493603.1_Intron	NM_001243505.1|NM_206594.2	NP_001230434.1|NP_996317.1	P62508	ERR3_HUMAN	estrogen-related receptor gamma	NA		NA			gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	cggtggctcatgcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482	2104		Nuclear hormone receptors	3474	protein-coding gene	gene with protein product		602969			NA	9676434, 10072763	Standard	NM_206595	NM_001243505	NA	Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000361525.3:c.12+10964A>G	chr1.hg19:g.217027438T>C		NA	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	hg19	CCDS1517.1	0.02	-0.043855	TCAxGCC	UNCOVERED																																																																																			NOVEL	ESRRG-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357846.1	2	2.405094	KEEP	0	0	0	8	213	TT	0.99257	0.023895	0		-	2	52	66	0	0	6.350296	2	60	56	19	ENST00000361525.3	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	218661088	218661088	__UNKNOWN__	IGR	SNP	C	C	T	rs2964992		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:218661088C>T			NA	NA				TGFB2 (43127 upstream) : C1orf143 (22349 downstream)						NA		NA									NA						ttgcagtgagctgagatcgca	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.218661088C>T		NA		hg19		0.02	-0.122796	GAGxTGA	COVERED																																																																																			NOVEL					0			25	2.737936	KEEP	21	1	25	18	497	CC	0.993634	0.195062	0			6	60	176	0	0	16.563844	7	48	236	53		0.461538	0.196312
C1orf143	440714	__UNKNOWN__	__UNKNOWN__	1	218696775	218696775	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:218696775A>G	ENST00000443836.1	+	2	173	c.173A>G	c.(172-174)cAa>cGa	p.Q58R						chromosome 1 open reading frame 143	NA		NA									NA						tcagcctcccaagtagctggg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					1q41	2013-03-14			ENSG00000228208	ENSG00000228208	440714			32045	other	unknown		NA			NA		Standard			NA	Approved				OTTHUMG00000039569	ENST00000443836.1:c.173A>G	chr1.hg19:g.218696775A>G	ENSP00000415902:p.Gln58Arg	NA		hg19		0.02	1.622441	CCCxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	A	3.449	-0.112342	0.06881	.	.	ENSG00000228208	ENST00000443836	T	0.14766	2.48	0.294	0.294	0.15747	.	.	.	.	.	T	0.04861	0.0131	.	.	.	.	.	.	.	.	.	.	.	.	T	0.43393	-0.9394	4	0.06099	T	0.92	.	.	.	.	.	.	.	.	R	58	ENSP00000415902:Q58R	ENSP00000415902:Q58R	Q	+	2	0	C1orf143	216763398	0.045000	0.20229	0.639000	0.29394	0.797000	0.45037	-0.176000	0.09811	0.349000	0.23975	0.338000	0.21704	CAA	NOVEL	C1orf143-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000095456.2	16	6.578069	KEEP	0	2	54	41	1117	AA	1	0.998867	0		+	4	60	129	0	0	8.260417	62	60	1858	165	ENST00000443836.1	0.060606	0.998867
BPNT1	10380	__UNKNOWN__	__UNKNOWN__	1	220232162	220232162	__UNKNOWN__	3'UTR	SNP	C	C	T	rs376028003		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:220232162C>T	ENST00000469520.2	-	0	1400				BPNT1_ENST00000414869.2_3'UTR|BPNT1_ENST00000544404.1_3'UTR|BPNT1_ENST00000354807.3_Intron|BPNT1_ENST00000322067.7_3'UTR			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	NA		NA			3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		tgagccaccgcgcccggccAA	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C		0,3720		0,0,1860	67	65	66			-0.6	0	1		66	2,8194		0,2,4096	no	utr-3	BPNT1	NM_006085.4		0,2,5956	TT,TC,CC	NA	0.0244,0.0,0.0168			220232162	2,11914	1860	4098	5958	SO:0001624	3_prime_UTR_variant			AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	10380	3.1.3.7		1096	protein-coding gene	gene with protein product		604053			NA	10224133	Standard	NM_006085	XM_005272998	NA	Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.*24G>A	chr1.hg19:g.220232162C>T		NA	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	hg19	CCDS41469.1	0.02	3.043596	CCGxGCC	COVERED																																																																																			NOVEL	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091137.2	27	14.068907	KEEP	5	4	105	84	2525	CC	1	0.999992	0		-	6	60	181	1	0	11.144099	93	60	3083	299	ENST00000469520.2	0.060606	0.999992
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	223379238	223379238	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:223379238T>C			NA	NA				RP11-239E10.3 (17742 upstream) : SUSD4 (14922 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.223379238T>C		NA		hg19		0.02	-0.254321	TCAxGCC	COVERED																																																																																			NOVEL					0			11	5.713932	KEEP	3	0	0	19	517	TT	0.999859	0.668429	0			4	60	130	0	0	9.923283	24	60	701	68		0.142857	0.668523
CAPN2	824	__UNKNOWN__	__UNKNOWN__	1	223946659	223946659	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:223946659C>T	ENST00000295006.5	+	12	1626				CAPN2_ENST00000474026.1_3'UTR|CAPN2_ENST00000433674.2_Intron	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	NA		NA			blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		tcccaaagtgctggtattaca	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	824	3.4.22.52	EF-hand domain containing	1479	protein-coding gene	gene with protein product		114230			NA	2852952, 2539381	Standard	NM_001748	NM_001748	NA	Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1318-313C>T	chr1.hg19:g.223946659C>T		NA	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	hg19	CCDS31035.1	0.02	-0.19296	GTGxTGG	COVERED																																																																																			NOVEL	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090973.1	4	2.708046	KEEP	0	0	0	9	276	CC	0.99254	0.454342	0		+	4	60	106	0	0	8.070281	17	60	571	44	ENST00000295006.5	0.190476	0.457757
RP11-504P24.6	0	__UNKNOWN__	__UNKNOWN__	1	224197115	224197115	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:224197115A>G	ENST00000572124.1	+	0	687				RP11-504P24.4_ENST00000540997.1_lincRNA						NA		NA									NA						gggattacagatgtgaactac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000572124.1:	chr1.hg19:g.224197115A>G		NA		hg19		0.02	-0.298215	CAGxTGT	COVERED																																																																																			NOVEL	RP11-504P24.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000436999.1	32	10.924237	KEEP	100	3	87	67	1860	AA	0.999997	0.781058	0		+	4	27	139	0	0	10.632748	27	50	823	245	ENST00000572124.1	0.129032	0.78106
CNIH4	29097	__UNKNOWN__	__UNKNOWN__	1	224562384	224562384	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:224562384A>G	ENST00000465271.1	+	5	467				CNIH4_ENST00000366856.3_Intron|CNIH4_ENST00000366858.3_Intron|CNIH4_ENST00000366857.5_Intron|CNIH4_ENST00000468318.1_Intron	NM_014184.3	NP_054903.1	Q9P003	CNIH4_HUMAN	cornichon family AMPA receptor auxiliary protein 4	NA		NA			intracellular signal transduction (GO:0035556)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(3)|lung(2)|ovary(2)	7				GBM - Glioblastoma multiforme(131;0.00341)		gagccaccacacccggcctgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1543.1, CCDS60429.1, CCDS60430.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143771	ENSG00000143771	29097			25013	protein-coding gene	gene with protein product		NA	cornichon homolog 4 (Drosophila)		NA	11042152	Standard	NM_014184	NM_014184	NA	Approved	HSPC163	uc001hom.2	Q9P003	OTTHUMG00000037635	ENST00000465271.1:c.393-1113A>G	chr1.hg19:g.224562384A>G		NA	A8K1Q8|B2R553|Q9H0X8	hg19	CCDS1543.1	0.02	-0.201651	CACxCCC	COVERED																																																																																			NOVEL	CNIH4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091754.1	10	3.90526	KEEP	1	0	0	13	330	AA	0.994391	0.487793	0		+	3	60	97	0	0	7.46171	17	60	458	52	ENST00000465271.1	0.15	0.490544
WDR26	80232	__UNKNOWN__	__UNKNOWN__	1	224588527	224588527	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:224588527T>C	ENST00000414423.2	-	9	1613				WDR26_ENST00000366852.2_Intron|WDR26_ENST00000479727.1_Intron|WDR26_ENST00000295024.6_Intron	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		ggattacaggtgtgagccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923	80232		WD repeat domain containing	21208	protein-coding gene	gene with protein product	GID complex subunit 7 homolog (S. cerevisiae)	NA			NA		Standard	NM_025160	NM_001115113	NA	Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1419+124A>G	chr1.hg19:g.224588527T>C		NA	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	hg19	CCDS31037.2	0.02	-0.184107	AGGxGTG	COVERED																																																																																			NOVEL	WDR26-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091760.2	1	4.803479	KEEP	0	0	0	16	394	TT	0.997832	0.422559	0		-	3	40	85	0	0	6.335453	16	60	429	42	ENST00000414423.2	0.157895	0.423478
DNAH14	127602	__UNKNOWN__	__UNKNOWN__	1	225579055	225579055	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:225579055T>C	ENST00000445597.2	+	59	10000				DNAH14_ENST00000430092.1_Intron|DNAH14_ENST00000439375.2_Intron			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						acacctgtagtcccagctact	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842	127602		Axonemal dyneins	2945	protein-coding gene	gene with protein product		603341	dynein, axonemal, heavy polypeptide 14, chromosome 1 open reading frame 67	C1orf67	NA	8812413	Standard	XM_059166	NM_144989	NA	Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.10001-938T>C	chr1.hg19:g.225579055T>C		NA	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	hg19		0.02	-0.096483	TAGxCCC	UNCOVERED																																																																																			NOVEL	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331217.3	8	2.405978	KEEP	2	0	0	8	219	TT	0	0	0		+	2	60	72	0	0	6.335745	5	60	149	26	ENST00000445597.2	0.285714	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	225991198	225991198	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:225991198A>G			NA	NA				SRP9 (13030 upstream) : EPHX1 (6598 downstream)						NA		NA									NA						agtagagatgaggtttcacca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.225991198A>G		NA		hg19		0.02	-0.096437	ATGxGGT	UNCOVERED																																																																																			NOVEL					0			2	3.007332	KEEP	2	0	0	10	273	AA	0.99254	0.119538	0			3	60	99	0	0	8.679588	7	60	191	24		0.3	0.120436
LIN9	286826	__UNKNOWN__	__UNKNOWN__	1	226463171	226463171	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:226463171T>C	ENST00000328205.5	-	7	1276				LIN9_ENST00000481685.1_Intron|LIN9_ENST00000366801.1_Intron	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	NA		NA			DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		ccgaggcgggtggattatgag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(197;1696 2974 11248 14117)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814	286826			30830	protein-coding gene	gene with protein product	TUDOR gene similar, rb related pathway actor	609375	lin-9 homolog (C. elegans)		NA	15538385, 23667535	Standard	NM_173083	NM_173083	NA	Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.730+2304A>G	chr1.hg19:g.226463171T>C		NA	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	hg19	CCDS1553.1	0.02	-0.086347	GGGxGGA	UNCOVERED																																																																																			NOVEL	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091523.2	5	2.705911	KEEP	2	0	0	9	238	TT	0.99257	0.09898	0		-	2	28	73	0	0	6.461733	5	60	124	31	ENST00000328205.5	0.285714	0.099721
CDC42BPA	8476	__UNKNOWN__	__UNKNOWN__	1	227252565	227252565	__UNKNOWN__	Intron	SNP	G	G	A	rs577852889		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:227252565G>A	ENST00000366769.3	-	21	4196				CDC42BPA_ENST00000366764.2_Intron|CDC42BPA_ENST00000334218.5_Intron|CDC42BPA_ENST00000366766.2_Intron|CDC42BPA_ENST00000366767.3_Intron|CDC42BPA_ENST00000366765.3_Intron|CDC42BPA_ENST00000535525.1_Intron	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)	NA		NA								NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				ttgggaggccgaggtgggcag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776	8476			1737	protein-coding gene	gene with protein product	myotonic dystrophy kinase-related Cdc42-binding kinase	603412	CDC42-binding protein kinase alpha (DMPK-like)		NA		Standard	NM_014826	NM_003607	NA	Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.2904+4912C>T	chr1.hg19:g.227252565G>A		NA		hg19	CCDS1558.1	0.02	-0.122771	GCCxAGG	UNCOVERED																																																																																			NOVEL	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091696.1	6	2.707766	KEEP	5	0	0	9	268	GG	0	0	0		-	3	60	84	0	0	6.673388	11	60	342	41	ENST00000366769.3	0.214286	0.196312
CDC42BPA	8476	__UNKNOWN__	__UNKNOWN__	1	227323556	227323556	__UNKNOWN__	Intron	SNP	C	C	A	rs375192819|rs12724477|rs77435093		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:227323556C>A	ENST00000366769.3	-	10	2682				CDC42BPA_ENST00000366764.2_Intron|CDC42BPA_ENST00000334218.5_Intron|CDC42BPA_ENST00000366766.2_Intron|CDC42BPA_ENST00000366767.3_Intron|CDC42BPA_ENST00000366765.3_Intron|CDC42BPA_ENST00000535525.1_Intron	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)	NA		NA								NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				ctctgtctcccaaaaaaaaaa	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776	8476			1737	protein-coding gene	gene with protein product	myotonic dystrophy kinase-related Cdc42-binding kinase	603412	CDC42-binding protein kinase alpha (DMPK-like)		NA		Standard	NM_014826	NM_003607	NA	Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.1390+3720G>T	chr1.hg19:g.227323556C>A		NA		hg19	CCDS1558.1	0.02	-0.078574	TCCxAAA	UNCOVERED																																																																																			NOVEL	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091696.1	22	4.375494	KEEP	12	0	0	15	317	CC	0	0	0		-	4	60	108	1	1	10.629412	3	22	89	32	ENST00000366769.3	0.571429	0.077336
CDC42BPA	8476	__UNKNOWN__	__UNKNOWN__	1	227346967	227346967	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:227346967A>C	ENST00000366769.3	-	6	1985				CDC42BPA_ENST00000366764.2_Intron|CDC42BPA_ENST00000334218.5_Intron|CDC42BPA_ENST00000366766.2_Intron|CDC42BPA_ENST00000366767.3_Intron|CDC42BPA_ENST00000366765.3_Intron|CDC42BPA_ENST00000535525.1_Intron	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)	NA		NA								NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				gtgggcagataacctgaggtc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776	8476			1737	protein-coding gene	gene with protein product	myotonic dystrophy kinase-related Cdc42-binding kinase	603412	CDC42-binding protein kinase alpha (DMPK-like)		NA		Standard	NM_014826	NM_003607	NA	Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.693+1276T>G	chr1.hg19:g.227346967A>C		NA		hg19	CCDS1558.1	0.02	-0.113985	GATxACC	UNCOVERED																																																																																			NOVEL	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000091696.1	7	3.907945	KEEP	1	0	0	13	338	AA	0.994391	0.161555	0		-	3	60	84	0	0	6.782613	10	60	277	40	ENST00000366769.3	0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	228654245	228654245	__UNKNOWN__	IGR	SNP	C	C	T	rs564131159		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:228654245C>T			NA	NA				MIR4666A (4392 upstream) : RNF187 (20516 downstream)						NA		NA									NA						tcttcttcttcttcttcttct	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.228654245C>T		NA		hg19		0.02	-0.087715	CTTxTTC	UNCOVERED																																																																																			NOVEL					0			9	3.008774	KEEP	5	0	0	10	299	CC	0.99257	0.09898	0			3	49	83	0	0	7.078107	7	60	238	33		0.3	0.099721
NUP133	55746	__UNKNOWN__	__UNKNOWN__	1	229595011	229595011	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:229595011C>T	ENST00000261396.3	-	21	2936				NUP133_ENST00000537506.1_Intron	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	NA		NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				ggctcatgcccgtaatcccag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248	55746			18016	protein-coding gene	gene with protein product		607613	nucleoporin 133kD		NA	11684705	Standard	NM_018230	NM_018230	NA	Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.2845-968G>A	chr1.hg19:g.229595011C>T		NA	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	hg19	CCDS1579.1	0.02	-0.105246	GCCxGTA	UNCOVERED																																																																																			NOVEL	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095224.1	8	2.407216	KEEP	0	0	0	8	246	CC	0.99257	0.138793	0		-	3	60	85	0	0	7.13191	8	60	265	28	ENST00000261396.3	0.272727	0.139832
GALNT2	2590	__UNKNOWN__	__UNKNOWN__	1	230370865	230370865	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:230370865T>C	ENST00000366672.4	+	4	446				GALNT2_ENST00000541865.1_Intron|GALNT2_ENST00000543760.1_Intron	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	NA		NA			cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				gaggctgaggtaggagcatca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2590	2.4.1.41	Glycosyltransferase family 2 domain containing	4124	protein-coding gene	gene with protein product	polypeptide GalNAc transferase 2	602274	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)		NA	9592121, 7592619	Standard	NM_004481	NM_004481	NA	Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.375-895T>C	chr1.hg19:g.230370865T>C		NA	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	hg19	CCDS1582.1	0.02	-0.043826	AGGxAGG	UNCOVERED																																																																																			NOVEL	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092158.1	7	2.70398	KEEP	0	0	0	9	223	TT	0.99254	0.023894	0		+	2	60	70	0	0	6.750534	2	60	54	14	ENST00000366672.4	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	232259467	232259467	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:232259467C>A			NA	NA				DISC1 (82449 upstream) : RP5-865N13.2 (36369 downstream)						NA		NA									NA						gctcaaaaagcacccccactg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.232259467C>A		NA		hg19		0.02	-0.21929	AAGxACC	UNCOVERED																																																																																			NOVEL					0			9	5.047246	KEEP	59	1	23	25	754	CC	0	0	0			5	20	166	0	0	13.553573	20	40	636	147		0.2	0.552887
PCNXL2	80003	__UNKNOWN__	__UNKNOWN__	1	233167905	233167905	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:233167905A>G	ENST00000258229.9	-	26	4586				PCNXL2_ENST00000344698.2_Intron	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				ctggagtgcaatggcgcgatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749	80003			8736	protein-coding gene	gene with protein product		NA	pecanex (Drosophila)-like 2		NA	12477932	Standard	NM_014801	NM_014801	NA	Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4352-6760T>C	chr1.hg19:g.233167905A>G		NA	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	hg19	CCDS44335.1	0.02	-0.271876	GCAxTGG	COVERED																																																																																			NOVEL	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092480.3	16	3.171101	KEEP	1	2	58	31	838	AA	0.999998	0.717314	0		-	3	60	97	0	0	6.946042	26	60	768	93	ENST00000258229.9	0.103448	0.717315
PCNXL2	80003	__UNKNOWN__	__UNKNOWN__	1	233193442	233193442	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:233193442T>C	ENST00000258229.9	-	24	4311				PCNXL2_ENST00000344698.2_5'UTR	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				agtgtgaaactccatctctac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749	80003			8736	protein-coding gene	gene with protein product		NA	pecanex (Drosophila)-like 2		NA	12477932	Standard	NM_014801	NM_014801	NA	Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.4077-406A>G	chr1.hg19:g.233193442T>C		NA	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	hg19	CCDS44335.1	0.02	3.560704	AACxCCA	COVERED																																																																																			NOVEL	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000092480.3	53	34.083436	KEEP	0	1	30	124	3445	TT	1	0.999997	0		-	5	60	163	1	0	9.964113	100	60	3088	329	ENST00000258229.9	0.047619	0.999997
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	234469174	234469174	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:234469174T>C			NA	NA				SLC35F3 (8912 upstream) : RP5-827C21.2 (23577 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.234469174T>C		NA		hg19		0.02	-0.043858	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			4	3.909199	KEEP	1	0	0	13	350	TT	0.994391	0.023939	0			2	60	71	0	0	6.593013	3	60	89	27		0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	234632396	234632396	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:234632396T>C			NA	NA				TARBP1 (17547 upstream) : RP5-855F14.1 (31240 downstream)						NA		NA									NA						ccatgttgcctaggctggtct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.234632396T>C		NA		hg19		0.02	-0.105249	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			7	2.405804	KEEP	0	0	0	8	218	TT	0.99257	0.138793	0			3	60	104	0	0	9.178928	7	60	202	24		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	235243854	235243854	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235243854T>C			NA	NA				RP11-443B7.3 (127303 upstream) : RP4-597N16.4 (23640 downstream)						NA		NA									NA						tgcggtggcttatgcctgtaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.235243854T>C		NA		hg19		0.02	-0.263097	GCTxATG	COVERED																																																																																			NOVEL					0			14	6.614626	KEEP	2	0	0	22	579	TT	0.999879	0.693584	0			3	60	96	0	0	7.049509	22	60	630	83		0.12	0.693668
RBM34	23029	__UNKNOWN__	__UNKNOWN__	1	235294695	235294695	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235294695C>T	ENST00000408888.3	-	0	1856				RBM34_ENST00000366606.3_3'UTR			P42696	RBM34_HUMAN	RNA binding motif protein 34	NA		NA				nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			tggtggcaggcgcctgtaatc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739	23029		RNA binding motif (RRM) containing	28965	protein-coding gene	gene with protein product		NA			NA	7788527, 15134903	Standard	NM_015014	NM_015014	NA	Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.*333G>A	chr1.hg19:g.235294695C>T		NA	A8K8J7|Q8N2Z8|Q9H5A1	hg19	CCDS41477.2	0.02	-0.271868	AGGxGCC	COVERED																																																																																			NOVEL	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000100146.1	18	5.714705	KEEP	12	0	0	19	542	CC	0.99649	0.737075	0		-	4	60	104	0	0	7.395287	23	60	711	69	ENST00000408888.3	0.148148	0.739671
RBM34	23029	__UNKNOWN__	__UNKNOWN__	1	235323499	235323499	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235323499G>A	ENST00000408888.3	-	3	596				RBM34_ENST00000366606.3_Intron			P42696	RBM34_HUMAN	RNA binding motif protein 34	NA		NA				nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)			cctgggaagcggaggttgcag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41477.1, CCDS41477.2	1q42.3	2013-02-12			ENSG00000188739	ENSG00000188739	23029		RNA binding motif (RRM) containing	28965	protein-coding gene	gene with protein product		NA			NA	7788527, 15134903	Standard	NM_015014	NM_015014	NA	Approved	KIAA0117	uc001hwn.3	P42696	OTTHUMG00000039620	ENST00000408888.3:c.365+326C>T	chr1.hg19:g.235323499G>A		NA	A8K8J7|Q8N2Z8|Q9H5A1	hg19	CCDS41477.2	0.02	1.535005	AGCxGAG	COVERED																																																																																			NOVEL	RBM34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000100146.1	5	2.932939	KEEP	0	4	111	49	1366	GG	1	0.967425	0		-	4	60	120	0	0	7.861052	46	60	1452	133	ENST00000408888.3	0.08	0.967425
ARID4B	51742	__UNKNOWN__	__UNKNOWN__	1	235384432	235384432	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235384432T>C	ENST00000264183.3	-	14	1661				ARID4B_ENST00000349213.3_Intron|ARID4B_ENST00000366603.2_Intron	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	NA		NA			histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			aggctggtcttgaactcctga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267	51742		-	15550	protein-coding gene	gene with protein product		609696	retinoblastoma binding protein 1-like 1, AT rich interactive domain 4B (RBP1- like)	RBP1L1	NA	11481388	Standard	NM_016374	NM_016374	NA	Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1163+447A>G	chr1.hg19:g.235384432T>C		NA	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	hg19	CCDS31061.1	0.02	-0.070162	TCTxGAA	UNCOVERED																																																																																			NOVEL	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095566.3	10	3.607979	KEEP	1	0	0	12	315	TT	0.993072	0.053762	0		-	3	60	90	0	0	8.132463	5	60	149	24	ENST00000264183.3	0.375	0.054137
ARID4B	51742	__UNKNOWN__	__UNKNOWN__	1	235390074	235390074	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235390074G>A	ENST00000264183.3	-	12	1395				ARID4B_ENST00000349213.3_Intron|ARID4B_ENST00000366603.2_Intron	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	NA		NA			histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			cctgacctcaggtgatctgcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267	51742		-	15550	protein-coding gene	gene with protein product		609696	retinoblastoma binding protein 1-like 1, AT rich interactive domain 4B (RBP1- like)	RBP1L1	NA	11481388	Standard	NM_016374	NM_016374	NA	Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.898-1984C>T	chr1.hg19:g.235390074G>A		NA	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	hg19	CCDS31061.1	0.02	-0.263167	TCAxGTG	COVERED																																																																																			NOVEL	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095566.3	31	6.619997	KEEP	18	0	0	22	683	GG	0.99649	0.691234	0		-	4	60	120	0	0	9.294924	19	60	656	87	ENST00000264183.3	0.173913	0.693668
ARID4B	51742	__UNKNOWN__	__UNKNOWN__	1	235390081	235390081	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235390081T>C	ENST00000264183.3	-	12	1395				ARID4B_ENST00000349213.3_Intron|ARID4B_ENST00000366603.2_Intron	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	NA		NA			histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			tcaggtgatctgcctgccttg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267	51742		-	15550	protein-coding gene	gene with protein product		609696	retinoblastoma binding protein 1-like 1, AT rich interactive domain 4B (RBP1- like)	RBP1L1	NA	11481388	Standard	NM_016374	NM_016374	NA	Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.898-1991A>G	chr1.hg19:g.235390081T>C		NA	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	hg19	CCDS31061.1	0.02	-0.271905	ATCxGCC	COVERED																																																																																			NOVEL	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095566.3	32	6.61644	KEEP	18	0	0	22	606	TT	0.99649	0.714798	0		-	3	34	98	1	0	7.364939	20	60	605	88	ENST00000264183.3	0.130435	0.717315
ARID4B	51742	__UNKNOWN__	__UNKNOWN__	1	235458794	235458794	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235458794T>C	ENST00000264183.3	-	2	504				ARID4B_ENST00000349213.3_Intron|ARID4B_ENST00000366603.2_Intron	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	NA		NA			histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			cactgcactctagcctgcggg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267	51742		-	15550	protein-coding gene	gene with protein product		609696	retinoblastoma binding protein 1-like 1, AT rich interactive domain 4B (RBP1- like)	RBP1L1	NA	11481388	Standard	NM_016374	NM_016374	NA	Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.6+31434A>G	chr1.hg19:g.235458794T>C		NA	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	hg19	CCDS31061.1	0.02	-0.140327	CTCxAGC	COVERED																																																																																			NOVEL	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095566.3	12	6.613251	KEEP	1	0	0	22	567	TT	0.999879	0.260933	0		-	3	60	101	0	0	8.372965	11	60	319	52	ENST00000264183.3	0.214286	0.260965
TBCE	6905	__UNKNOWN__	__UNKNOWN__	1	235591588	235591588	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:235591588G>A	ENST00000366601.3	+	6	736				TBCE_ENST00000406207.1_Intron|TBCE_ENST00000543662.1_Intron|TBCE_ENST00000472011.1_Intron			Q15813	TBCE_HUMAN	tubulin folding cofactor E	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|developmental growth (GO:0048589)|microtubule cytoskeleton organization (GO:0000226)|muscle atrophy (GO:0014889)|peripheral nervous system neuron axonogenesis (GO:0048936)|post-chaperonin tubulin folding pathway (GO:0007023)|post-embryonic development (GO:0009791)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	chaperone binding (GO:0051087)			NS(1)|endometrium(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	14	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00192)|Prostate(94;0.0294)|all_epithelial(177;0.155)|Lung SC(1967;0.238)	OV - Ovarian serous cystadenocarcinoma(106;2.56e-05)			gcagtgagccgagattgtgcc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U61232	CCDS1605.1, CCDS73052.1	1q42.3	2014-02-04	2006-11-21		ENSG00000116957	ENSG00000116957	6905			11582	protein-coding gene	gene with protein product		604934	tubulin-specific chaperone e, Kenny-Caffey syndrome, hypoparathyroidism, growth and mental retardation, and dysmorphism	KCS, HRD	NA	8706133, 9806825, 12389028	Standard	NM_003193	NM_001079515	NA	Approved	KCS1, pac2	uc001hxa.1	Q15813	OTTHUMG00000039987	ENST00000366601.3:c.560+1034G>A	chr1.hg19:g.235591588G>A		NA	A8K8C2|B7Z3P1	hg19	CCDS1605.1	0.02	-0.131564	GCCxAGA	COVERED																																																																																			NOVEL	TBCE-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096458.3	7	4.211778	KEEP	6	0	0	14	418	GG	0.993634	0.227714	0		+	3	60	87	0	0	7.201071	9	60	293	47	ENST00000366601.3	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	236260555	236260555	__UNKNOWN__	IGR	SNP	C	C	T	rs12035152		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:236260555C>T			NA	NA				NID1 (32093 upstream) : GPR137B (45276 downstream)						NA		NA									NA						ATGgagcaggcggccaggggt	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.236260555C>T		NA		hg19		0.02	-0.070164	AGGxGGC	UNCOVERED																																																																																			NOVEL					0			12	4.51149	KEEP	12	0	0	15	426	CC	0	0	0			3	26	85	0	0	7.854541	4	22	124	32		0.428571	0.054137
ACTN2	88	__UNKNOWN__	__UNKNOWN__	1	236854702	236854702	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:236854702A>G	ENST00000366578.4	+	1	292				ACTN2_ENST00000542672.1_Intron|ACTN2_ENST00000492634.1_Intron	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	NA		NA			blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			cagcactttgagaggccaagg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522	88		EF-hand domain containing	164	protein-coding gene	gene with protein product		102573			NA	1339456	Standard	NM_001103	NM_001103	NA	Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.126+4603A>G	chr1.hg19:g.236854702A>G		NA	B1ANE4|B2RCS5|Q86TF4|Q86TI8	hg19	CCDS1613.1	0.02	-0.131573	TTGxGAG	COVERED																																																																																			NOVEL	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096628.1	6	3.008108	KEEP	0	0	0	10	284	AA	0.992708	0.227502	0		+	3	60	101	0	0	8.601145	9	60	275	36	ENST00000366578.4	0.25	0.229173
ACTN2	88	__UNKNOWN__	__UNKNOWN__	1	236913065	236913065	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:236913065G>C	ENST00000366578.4	+	14	1822				ACTN2_ENST00000542672.1_Intron|ACTN2_ENST00000546208.1_Intron	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	NA		NA			blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			cacgccattggactccatcct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522	88		EF-hand domain containing	164	protein-coding gene	gene with protein product		102573			NA	1339456	Standard	NM_001103	NM_001103	NA	Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1656+501G>C	chr1.hg19:g.236913065G>C		NA	B1ANE4|B2RCS5|Q86TF4|Q86TI8	hg19	CCDS1613.1	0.02	-0.043863	TTGxACT	UNCOVERED																																																																																			NOVEL	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096628.1	7	2.406777	KEEP	0	0	0	8	234	GG	0.99257	0.023895	0		+	2	25	71	0	0	6.850087	2	60	67	17	ENST00000366578.4	0.5	0.024074
RYR2	6262	__UNKNOWN__	__UNKNOWN__	1	237258172	237258172	__UNKNOWN__	Intron	SNP	T	T	A	rs9428375	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:237258172T>A	ENST00000366574.2	+	1	365					NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	NA		NA			BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			attacaggtgtgagccaccgc	0.507		NA											T|||	2206	0.440495	0.2549	0.3242	5008	,	,	NA	16121	0.5873	NA	0.4901	False	NA	,,,	NA	NA	NA	2504	0.5716	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626	6262		Ion channels / Ryanodine receptors, EF-hand domain containing	10484	protein-coding gene	gene with protein product		180902	arrhythmogenic right ventricular dysplasia 2	ARVD2	NA	2380170, 8406504, 11159936	Standard	NM_001035	NM_001035	NA	Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.48+52303T>A	chr1.hg19:g.237258172T>A		NA	Q15411|Q546N8|Q5T3P2	hg19	CCDS55691.1	0.02	-0.061391	GTGxGAG	UNCOVERED																																																																																			NOVEL	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095402.2	6	2.70726	KEEP	3	0	0	9	255	TT	0.99257	0.043461	0		+	3	60	90	0	0	8.355128	4	60	115	27	ENST00000366574.2	0.428571	0.043787
RYR2	6262	__UNKNOWN__	__UNKNOWN__	1	237320434	237320434	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:237320434G>A	ENST00000366574.2	+	2	365					NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	NA		NA			BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			catctctactgaaaatacaaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626	6262		Ion channels / Ryanodine receptors, EF-hand domain containing	10484	protein-coding gene	gene with protein product		180902	arrhythmogenic right ventricular dysplasia 2	ARVD2	NA	2380170, 8406504, 11159936	Standard	NM_001035	NM_001035	NA	Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.49-113363G>A	chr1.hg19:g.237320434G>A		NA	Q15411|Q546N8|Q5T3P2	hg19	CCDS55691.1	0.02	-0.157876	ACTxAAA	UNCOVERED																																																																																			NOVEL	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095402.2	5	2.406083	KEEP	3	0	0	8	227	GG	0	0	0		+	4	40	110	0	0	8.881076	13	60	415	30	ENST00000366574.2	0.235294	0.322807
RYR2	6262	__UNKNOWN__	__UNKNOWN__	1	237672261	237672261	__UNKNOWN__	Intron	SNP	T	T	C	rs6702646	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:237672261T>C	ENST00000366574.2	+	23	3035				RYR2_ENST00000360064.6_Intron|RYR2_ENST00000542537.1_Intron	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	NA		NA			BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ccaggatggtttcgatctcct	0.572		NA											-|||	3611	0.721046	0.8359	0.7248	5008	,	,	NA	11730	0.7292	NA	0.7147	False	NA	,,,	NA	NA	NA	2504	0.5613	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626	6262		Ion channels / Ryanodine receptors, EF-hand domain containing	10484	protein-coding gene	gene with protein product		180902	arrhythmogenic right ventricular dysplasia 2	ARVD2	NA	2380170, 8406504, 11159936	Standard	NM_001035	NM_001035	NA	Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2718+2147T>C	chr1.hg19:g.237672261T>C		NA	Q15411|Q546N8|Q5T3P2	hg19	CCDS55691.1	0.02	-0.122781	GGTxTCG	UNCOVERED																																																																																			NOVEL	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095402.2	3	2.706833	KEEP	14	0	0	9	247	TT	0	0	0		+	3	40	92	0	0	7.701394	9	60	258	43	ENST00000366574.2	0.25	0.196312
RYR2	6262	__UNKNOWN__	__UNKNOWN__	1	237808081	237808081	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:237808081T>C	ENST00000366574.2	+	48	7659				RYR2_ENST00000360064.6_Intron|RYR2_ENST00000542537.1_Intron	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	NA		NA			BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			cctgtaatcctagcactttgg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626	6262		Ion channels / Ryanodine receptors, EF-hand domain containing	10484	protein-coding gene	gene with protein product		180902	arrhythmogenic right ventricular dysplasia 2	ARVD2	NA	2380170, 8406504, 11159936	Standard	NM_001035	NM_001035	NA	Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7342+1334T>C	chr1.hg19:g.237808081T>C		NA	Q15411|Q546N8|Q5T3P2	hg19	CCDS55691.1	0.02	-0.096493	TCCxAGC	UNCOVERED																																																																																			NOVEL	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095402.2	6	3.308591	KEEP	2	0	0	11	307	TT	0.99254	0.119538	0		+	3	45	104	0	0	9.533035	5	60	154	33	ENST00000366574.2	0.375	0.120436
RYR2	6262	__UNKNOWN__	__UNKNOWN__	1	237955680	237955680	__UNKNOWN__	Intron	SNP	T	T	C	rs146659498	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:237955680T>C	ENST00000366574.2	+	94	14099				RYR2_ENST00000360064.6_Intron|RYR2_ENST00000542537.1_Intron	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	NA		NA			BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			tgtgtgtgtgtgcgtgtgtgt	0.473		NA											T|||	2645	0.528155	0.264	0.6254	5008	,	,	NA	14150	0.6746	NA	0.5696	False	NA	,,,	NA	NA	NA	2504	0.6227	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626	6262		Ion channels / Ryanodine receptors, EF-hand domain containing	10484	protein-coding gene	gene with protein product		180902	arrhythmogenic right ventricular dysplasia 2	ARVD2	NA	2380170, 8406504, 11159936	Standard	NM_001035	NM_001035	NA	Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13782+57T>C	chr1.hg19:g.237955680T>C		NA	Q15411|Q546N8|Q5T3P2	hg19	CCDS55691.1	0.02	-0.122765	GTGxGCG	UNCOVERED																																																																																			NOVEL	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095402.2	9	2.404605	KEEP	4	0	0	8	207	TT	0	0	0		+	3	60	80	2	0	6.382501	10	60	294	32	ENST00000366574.2	0.230769	0.196312
RYR2	6262	__UNKNOWN__	__UNKNOWN__	1	237955682	237955682	__UNKNOWN__	Intron	SNP	C	C	T	rs12739270	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:237955682C>T	ENST00000366574.2	+	94	14099				RYR2_ENST00000360064.6_Intron|RYR2_ENST00000542537.1_Intron	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	NA		NA			BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			tgtgtgtgtgcgtgtgtgtgt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626	6262		Ion channels / Ryanodine receptors, EF-hand domain containing	10484	protein-coding gene	gene with protein product		180902	arrhythmogenic right ventricular dysplasia 2	ARVD2	NA	2380170, 8406504, 11159936	Standard	NM_001035	NM_001035	NA	Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.13782+59C>T	chr1.hg19:g.237955682C>T		NA	Q15411|Q546N8|Q5T3P2	hg19	CCDS55691.1	0.02	-0.139262	GTGxGTG	UNCOVERED																																																																																			NOVEL	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095402.2	9	2.3757	KEEP	4	0	0	8	171	CC	0	0	0		+	5	60	147	2	0	13.122771	9	60	273	32	ENST00000366574.2	0.357143	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	239515054	239515054	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:239515054G>A			NA	NA				RP11-544D21.1 (75293 upstream) : CHRM3 (34810 downstream)						NA		NA									NA						tgcaacctccgcctcctgggt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.239515054G>A		NA		hg19		0.02	-0.087694	TCCxCCT	UNCOVERED																																																																																			NOVEL					0			7	2.406573	KEEP	6	0	0	8	238	GG	0	0	0			3	31	78	0	0	6.742084	6	60	199	28		0.333333	0.099721
FMN2	56776	__UNKNOWN__	__UNKNOWN__	1	240278146	240278146	__UNKNOWN__	Intron	SNP	T	T	C	rs6698220	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:240278146T>C	ENST00000319653.9	+	2	1845					NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			ttagtagagatggggtttcac	0.522		NA											C|||	2633	0.525759	0.5938	0.4726	5008	,	,	NA	16602	0.3462	NA	0.6163	False	NA	,,,	NA	NA	NA	2504	0.5634	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816	56776			14074	protein-coding gene	gene with protein product		606373			NA	10781961	Standard	XM_371352	NM_020066	NA	Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1616-8333T>C	chr1.hg19:g.240278146T>C		NA	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	hg19	CCDS31069.2	0.02	-0.131529	AGAxGGG	UNCOVERED																																																																																			NOVEL	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096217.2	11	2.402972	KEEP	10	0	0	8	202	TT	0	0	0		+	3	54	100	0	0	8.172669	12	60	336	36	ENST00000319653.9	0.2	0.229173
RGS7	6000	__UNKNOWN__	__UNKNOWN__	1	241170496	241170496	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:241170496T>C	ENST00000366565.1	-	4	557				RGS7_ENST00000407727.1_Intron|RGS7_ENST00000366563.1_Intron|RGS7_ENST00000366564.1_Intron|RGS7_ENST00000331110.7_Intron|RGS7_ENST00000401882.1_Intron|RGS7_ENST00000348120.2_Intron|RGS7_ENST00000366562.4_Intron|RGS7_ENST00000446183.2_Intron	NM_002924.4	NP_002915.3	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			ggattacaggtgtgagccact	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901	6000		Regulators of G-protein signaling	10003	protein-coding gene	gene with protein product		602517	regulator of G-protein signalling 7		NA	8548815	Standard	NM_002924	XM_005273218	NA	Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000366565.1:c.176-24067A>G	chr1.hg19:g.241170496T>C		NA	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	hg19	CCDS31071.1	0.02	-0.122784	AGGxGTG	COVERED																																																																																			NOVEL	RGS7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096719.3	4	2.405765	KEEP	0	0	0	8	216	TT	0.99257	0.194853	0		-	3	60	90	0	0	7.77849	7	60	207	30	ENST00000366565.1	0.3	0.196312
RGS7	6000	__UNKNOWN__	__UNKNOWN__	1	241283856	241283856	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:241283856A>G	ENST00000366565.1	-	3	460				RGS7_ENST00000407727.1_Intron|RGS7_ENST00000366563.1_Intron|RGS7_ENST00000366564.1_Intron|RGS7_ENST00000331110.7_Intron|RGS7_ENST00000401882.1_Intron|RGS7_ENST00000348120.2_Intron|RGS7_ENST00000366562.4_Intron|RGS7_ENST00000446183.2_Intron	NM_002924.4	NP_002915.3	P49802	RGS7_HUMAN	regulator of G-protein signaling 7	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			atgttgcccaagctggtctcg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901	6000		Regulators of G-protein signaling	10003	protein-coding gene	gene with protein product		602517	regulator of G-protein signalling 7		NA	8548815	Standard	NM_002924	XM_005273218	NA	Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000366565.1:c.79-21794T>C	chr1.hg19:g.241283856A>G		NA	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	hg19	CCDS31071.1	0.02	-0.157878	CCAxGCT	COVERED																																																																																			NOVEL	RGS7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096719.3	10	3.308386	KEEP	0	0	0	11	310	AA	0.993072	0.32057	0		-	3	60	89	0	0	6.892282	14	60	429	38	ENST00000366565.1	0.176471	0.322807
KMO	8564	__UNKNOWN__	__UNKNOWN__	1	241729279	241729279	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:241729279T>C	ENST00000366559.4	+	9	998				KMO_ENST00000366557.4_Intron|KMO_ENST00000366558.3_Intron	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	NA		NA								NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			ccgaggtgggtggatcacctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	8564	1.14.13.9		6381	protein-coding gene	gene with protein product		603538			NA	9237672	Standard	NM_003679	NM_003679	NA	Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.688-512T>C	chr1.hg19:g.241729279T>C		NA		hg19	CCDS1618.1	0.02	-0.11398	GGGxGGA	UNCOVERED																																																																																			NOVEL	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095612.1	4	2.405455	KEEP	4	0	0	8	215	TT	0	0	0		+	3	60	87	0	0	7.20173	9	60	264	32	ENST00000366559.4	0.25	0.196312
KMO	8564	__UNKNOWN__	__UNKNOWN__	1	241756217	241756217	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:241756217T>C	ENST00000366559.4	+	0	2534				KMO_ENST00000366557.4_3'UTR	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)	NA		NA								NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			atcctcccacttcagcctccc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	8564	1.14.13.9		6381	protein-coding gene	gene with protein product		603538			NA	9237672	Standard	NM_003679	NM_003679	NA	Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.*762T>C	chr1.hg19:g.241756217T>C		NA		hg19	CCDS1618.1	0.02	1.572928	CACxTCA	COVERED																																																																																			NOVEL	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095612.1	23	15.94088	KEEP	0	0	0	53	1489	TT	1	0.999895	0		+	5	60	162	0	0	10.335382	80	60	2413	219	ENST00000366559.4	0.058824	0.999895
WDR64	128025	__UNKNOWN__	__UNKNOWN__	1	241855037	241855037	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:241855037T>C	ENST00000366552.2	+	7	1151				WDR64_ENST00000437684.2_Intron	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	NA		NA								breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			aaacataggctgggcacagtg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843	128025		WD repeat domain containing	26570	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144625	NM_144625	NA	Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.944+4140T>C	chr1.hg19:g.241855037T>C		NA	B1ANT0|Q7Z573|Q96LY9	hg19		0.02	-0.061388	GGCxGGG	UNCOVERED																																																																																			NOVEL	WDR64-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		4	2.406684	KEEP	0	0	0	8	231	TT	0.99257	0.043461	0		+	2	60	70	0	0	6.750743	2	60	51	23	ENST00000366552.2	0.5	0.043787
SDCCAG8	10806	__UNKNOWN__	__UNKNOWN__	1	243655969	243655969	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:243655969G>A	ENST00000366541.3	+	17	2230				AKT3_ENST00000336199.5_Intron|SDCCAG8_ENST00000355875.4_Intron|SDCCAG8_ENST00000343783.6_Intron	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	NA		NA			establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		gagtacaatggcatggtcttg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282	10806			10671	protein-coding gene	gene with protein product		613524			NA	9610721, 20835237	Standard	NM_006642	NM_006642	NA	Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.2112+3527G>A	chr1.hg19:g.243655969G>A		NA	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	hg19	CCDS31075.1	0.02	-0.114035	ATGxCAT	UNCOVERED																																																																																			NOVEL	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096485.1	4	3.008692	KEEP	0	0	0	10	297	GG	0.992708	0.161282	0		+	3	60	84	0	0	7.032067	8	60	275	28	ENST00000366541.3	0.272727	0.162467
RP11-278H7.1	0	__UNKNOWN__	__UNKNOWN__	1	244095907	244095907	__UNKNOWN__	lincRNA	SNP	A	A	G	rs71574677		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:244095907A>G	ENST00000440494.1	+	0	125					NR_033883.1					NA		NA									NA						actccagcctaggcaacaaga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000440494.1:	chr1.hg19:g.244095907A>G		NA		hg19		0.02	-0.175405	CCTxGGC	COVERED																																																																																			NOVEL	RP11-278H7.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000096514.1	7	2.704928	KEEP	0	0	0	9	233	AA	0.99254	0.384517	0		+	3	60	105	0	0	8.260741	17	60	497	41	ENST00000440494.1	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	244331955	244331955	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:244331955A>G			NA	NA				RP11-278H7.3 (59642 upstream) : C1orf100 (183981 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.244331955A>G		NA		hg19		0.02	-0.175418	GGCxTGA	COVERED																																																																																			NOVEL					0			4	3.007499	KEEP	2	0	0	10	275	AA	0.99254	0.384517	0			4	60	137	0	0	11.362648	15	60	446	45		0.210526	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	244371094	244371094	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:244371094T>G			NA	NA				RP11-278H7.3 (98781 upstream) : C1orf100 (144842 downstream)						NA		NA									NA						gctcatgcctttaatcccagc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.244371094T>G		NA		hg19		0.02	-0.114028	CCTxTAA	UNCOVERED																																																																																			NOVEL					0			2	3.006854	KEEP	0	0	0	10	269	TT	0.992708	0.161282	0			4	60	136	0	0	12.377497	7	60	208	34		0.363636	0.162467
C1orf101	257044	__UNKNOWN__	__UNKNOWN__	1	244641276	244641276	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:244641276C>T	ENST00000366534.4	+	4	311	c.257C>T	c.(256-258)cCa>cTa	p.P86L	C1orf101_ENST00000366533.4_Splice_Site_p.P86L|C1orf101_ENST00000366531.3_5'UTR|C1orf101_ENST00000473875.1_3'UTR	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	86		NA				CatSper complex (GO:0036128)				NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	36	all_cancers(71;2.99e-05)|all_epithelial(71;0.00015)|all_neural(11;0.0269)|Breast(184;0.0654)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0874)|Lung NSC(105;0.121)		all cancers(7;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(106;0.001)|GBM - Glioblastoma multiforme(7;0.0154)			GTTACTGGCCCAGTAAGTTGT	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													109	102	104			NA	NA	1		NA											NA				244641276		2203	4300	6503	SO:0001630	splice_region_variant			BC032859	CCDS1625.1, CCDS44340.1, CCDS55693.1	1q44	2012-12-20			ENSG00000179397	ENSG00000179397	257044			28491	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173807	NM_173807	NA	Approved	MGC33370	uc001iam.3	Q5SY80	OTTHUMG00000040103	ENST00000366534.4:c.258+1C>T	chr1.hg19:g.244641276C>T		NA	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	hg19	CCDS44340.1	0.02	1.447209	GCCxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.93	1.785673	0.31593	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000428042	T;T;T	0.33654	1.44;1.44;1.4	4.33	3.39	0.38822	.	0.607435	0.14588	N	0.310437	T	0.48223	0.1488	L	0.47716	1.5	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.998	D;D;D	0.69479	0.964;0.964;0.964	T	0.32798	-0.9893	10	0.40728	T	0.16	.	9.3564	0.38168	0.2227:0.7773:0.0:0.0	.	76;86;86	B1AQM6;Q5SY80;Q5SY80-2	.;CA101_HUMAN;.	L	86;86;86;76	ENSP00000355492:P86L;ENSP00000355491:P86L;ENSP00000395796:P76L	ENSP00000355491:P86L	P	+	2	0	C1orf101	242707899	0.494000	0.26043	0.998000	0.56505	0.594000	0.36715	0.899000	0.28417	1.348000	0.45733	0.591000	0.81541	CCA	NOVEL	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096701.1	1	3.309642	KEEP	0	0	0	11	334	CC	0.993072	0.984099	0	Missense_Mutation	+	4	60	123	0	0	7.773218	58	60	1998	112	ENST00000366534.4	0.064516	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	244940249	244940249	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:244940249G>A			NA	NA				DESI2 (67914 upstream) : COX20 (58374 downstream)						NA		NA									NA						taatttttgtgtattttgtag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.244940249G>A		NA		hg19		0.02	-0.210539	TGTxTAT	COVERED																																																																																			NOVEL					0			12	3.308961	KEEP	0	0	0	11	320	GG	0.993072	0.518544	0			3	60	88	0	0	6.427666	19	60	656	43		0.136364	0.522161
EFCAB2	84288	__UNKNOWN__	__UNKNOWN__	1	245178740	245178740	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:245178740C>T	ENST00000366523.1	+	3	290				EFCAB2_ENST00000447569.2_Intron|EFCAB2_ENST00000366522.2_Intron|EFCAB2_ENST00000487845.1_Intron	NM_032328.3	NP_115704.1	Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2	NA		NA					calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			ctgccgggcgcggtggctcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666	84288		EF-hand domain containing	28166	protein-coding gene	gene with protein product	dynein regulatory complex subunit 8	NA			NA	23427265	Standard		NM_032328	NA	Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366523.1:c.26-1804C>T	chr1.hg19:g.245178740C>T		NA	B4DZE9|Q59G23|Q9BS36	hg19	CCDS31082.1	0.02	-0.210514	GCGxGGT	COVERED																																																																																			NOVEL	EFCAB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097409.1	9	4.211947	KEEP	5	0	0	14	415	CC	0.992708	0.518353	0		+	4	60	112	0	0	8.580349	18	60	591	58	ENST00000366523.1	0.181818	0.522161
EFCAB2	84288	__UNKNOWN__	__UNKNOWN__	1	245178998	245178998	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:245178998A>T	ENST00000366523.1	+	3	290				EFCAB2_ENST00000447569.2_Intron|EFCAB2_ENST00000366522.2_Intron|EFCAB2_ENST00000487845.1_Intron	NM_032328.3	NP_115704.1	Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2	NA		NA					calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			ggcaacagagagagactctgt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666	84288		EF-hand domain containing	28166	protein-coding gene	gene with protein product	dynein regulatory complex subunit 8	NA			NA	23427265	Standard		NM_032328	NA	Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366523.1:c.26-1546A>T	chr1.hg19:g.245178998A>T		NA	B4DZE9|Q59G23|Q9BS36	hg19	CCDS31082.1	0.02	0.993676	GAGxGAG	COVERED																																																																																			NOVEL	EFCAB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097409.1	16	12.398271	KEEP	1	3	66	65	1742	AA	1	0.999559	0		+	5	60	134	0	0	7.85639	69	60	2068	231	ENST00000366523.1	0.067568	0.999559
KIF26B	55083	__UNKNOWN__	__UNKNOWN__	1	245775407	245775407	__UNKNOWN__	Intron	SNP	T	T	A	rs28368385|rs111916263|rs3862180|rs3047661		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:245775407T>A	ENST00000407071.2	+	9	2538				KIF26B_ENST00000366518.4_Intron	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	NA		NA			establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			tgtgtgtgtgtgagagagaga	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849	55083		Kinesins	25484	protein-coding gene	gene with protein product		614026			NA		Standard	XM_371354	NM_018012	NA	Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2098+129T>A	chr1.hg19:g.245775407T>A		NA	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	hg19	CCDS44342.1	0.02	-0.201599	GTGxGAG	COVERED																																																																																			NOVEL	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381037.1	16	3.605628	KEEP	13	0	0	12	310	TT	0.99254	0.486885	0		+	5	60	153	1	0	13.068686	13	60	370	57	ENST00000407071.2	0.277778	0.490544
KIF26B	55083	__UNKNOWN__	__UNKNOWN__	1	245861331	245861331	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:245861331A>G	ENST00000407071.2	+	13	6264				KIF26B_ENST00000366518.4_Intron	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	NA		NA			establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			gcaacagagcaagaccctgtc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849	55083		Kinesins	25484	protein-coding gene	gene with protein product		614026			NA		Standard	XM_371354	NM_018012	NA	Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.5825-77A>G	chr1.hg19:g.245861331A>G		NA	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	hg19	CCDS44342.1	0.02	1.906205	AGCxAGA	COVERED																																																																																			NOVEL	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381037.1	9	6.315235	KEEP	1	0	0	21	571	AA	0.999869	0.976737	0		+	4	60	133	0	0	9.122824	47	60	1415	108	ENST00000407071.2	0.078431	0.976865
SMYD3	64754	__UNKNOWN__	__UNKNOWN__	1	246222453	246222453	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:246222453A>C	ENST00000490107.1	-	6	571				SMYD3_ENST00000541742.1_Intron|SMYD3_ENST00000388985.4_Intron	NM_001167740.1	NP_001161212.1	Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	NA		NA			cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		gctgggattaaaggcgtgagc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420	64754		Zinc fingers, MYND-type, Chromatin-modifying enzymes / K-methyltransferases	15513	protein-coding gene	gene with protein product		608783	zinc finger, MYND domain containing 1	ZNFN3A1, ZMYND1	NA		Standard	NM_022743	NM_022743	NA	Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000490107.1:c.355-129214T>G	chr1.hg19:g.246222453A>C		NA	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	hg19	CCDS31083.1	0.02	-0.184198	TTAxAGG	UNCOVERED																																																																																			NOVEL	SMYD3-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097487.3	4	2.405894	KEEP	1	0	0	8	216	AA	0	0	0		-	3	60	106	0	0	8.291842	18	60	549	51	ENST00000490107.1	0.142857	0.423478
CNST	163882	__UNKNOWN__	__UNKNOWN__	1	246755615	246755615	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:246755615G>C	ENST00000366513.4	+	2	648				CNST_ENST00000366512.3_Intron|CNST_ENST00000483271.1_Intron	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	NA		NA			negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						atggtgaaacgccatctctac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852	163882		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	26486	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 64	613439	chromosome 1 open reading frame 71	C1orf71	NA	19864490	Standard	NM_152609	NM_152609	NA	Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.379+372G>C	chr1.hg19:g.246755615G>C		NA	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	hg19	CCDS1628.1	0.02	-0.087722	AACxCCA	UNCOVERED																																																																																			NOVEL	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096780.1	2	2.405208	KEEP	0	0	0	8	226	GG	0.99257	0.119541	0		+	3	60	100	0	0	9.132767	5	60	168	20	ENST00000366513.4	0.375	0.120436
CNST	163882	__UNKNOWN__	__UNKNOWN__	1	246826574	246826574	__UNKNOWN__	Intron	SNP	G	G	A	rs12069242	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:246826574G>A	ENST00000366513.4	+	11	2241					NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	NA		NA			negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						tgggaggatcgcttgagccca	0.488		NA											G|||	83	0.0165735	0.062	0.0014	5008	,	,	NA	15210	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852	163882		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	26486	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 64	613439	chromosome 1 open reading frame 71	C1orf71	NA	19864490	Standard	NM_152609	NM_152609	NA	Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.1973-2428G>A	chr1.hg19:g.246826574G>A		NA	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	hg19	CCDS1628.1	0.02	-0.166648	ATCxCTT	COVERED																																																																																			NOVEL	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000096780.1	7	3.007411	KEEP	2	0	0	10	278	GG	0.992708	0.351366	0		+	3	60	82	0	0	6.373428	12	60	401	41	ENST00000366513.4	0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	247249978	247249978	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:247249978A>G			NA	NA				ZNF670 (7921 upstream) : ZNF669 (13285 downstream)						NA		NA									NA						gaccagcctgaccaacatggt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.247249978A>G		NA		hg19		0.02	-0.20171	CTGxCCA	COVERED																																																																																			NOVEL					0			6	2.404735	KEEP	1	0	0	8	205	AA	0.99257	0.4869	0			4	60	129	0	0	10.369112	17	60	486	43		0.190476	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	247258114	247258114	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:247258114G>A			NA	NA				ZNF670 (16057 upstream) : ZNF669 (5149 downstream)						NA		NA									NA						tagtagagacggggtttcacc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.247258114G>A		NA		hg19		0.02	-0.122788	GACxGGG	UNCOVERED																																																																																			NOVEL					0			9	3.00672	KEEP	5	0	0	10	273	GG	0	0	0			4	60	107	1	0	8.970475	10	60	334	35		0.285714	0.196312
ZNF124	7678	__UNKNOWN__	__UNKNOWN__	1	247318890	247318890	__UNKNOWN__	Intron	SNP	G	G	A	rs569923636		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:247318890G>A	ENST00000472531.1	-	3	346				ZNF124_ENST00000491356.1_Intron	NM_001243740.1	NP_001230669.1	Q15973	ZN124_HUMAN	zinc finger protein 124	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			TCAgctgggcgtggtggctca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418	7678		Zinc fingers, C2H2-type, -	12907	protein-coding gene	gene with protein product		194631	zinc finger protein 124 (HZF-16)		NA	7916577	Standard	NM_003431	XM_005273256	NA	Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000472531.1:c.218+3417C>T	chr1.hg19:g.247318890G>A		NA	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	hg19	CCDS58067.1	0.02	-0.175431	GGCxTGG	COVERED																																																																																			NOVEL	ZNF124-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098570.2	6	3.308434	KEEP	2	0	0	11	309	GG	0.992708	0.384582	0		-	3	60	90	0	0	6.833724	16	60	512	44	ENST00000472531.1	0.157895	0.387407
ZNF124	7678	__UNKNOWN__	__UNKNOWN__	1	247318901	247318901	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:247318901C>T	ENST00000472531.1	-	3	346				ZNF124_ENST00000491356.1_Intron	NM_001243740.1	NP_001230669.1	Q15973	ZN124_HUMAN	zinc finger protein 124	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(2)	14	all_cancers(71;5.07e-05)|all_epithelial(71;8.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00739)			tggtggctcacgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S54641	CCDS31089.1, CCDS58067.1, CCDS73057.1	1q44	2013-01-08	2006-06-13		ENSG00000196418	ENSG00000196418	7678		Zinc fingers, C2H2-type, -	12907	protein-coding gene	gene with protein product		194631	zinc finger protein 124 (HZF-16)		NA	7916577	Standard	NM_003431	XM_005273256	NA	Approved	HZF16, HZF-16	uc001icj.1	Q15973	OTTHUMG00000041112	ENST00000472531.1:c.218+3406G>A	chr1.hg19:g.247318901C>T		NA	B3KNP3|J3KSE1|Q15974|Q4VAJ7|Q5T2V4	hg19	CCDS58067.1	0.02	-0.17544	TCAxGCC	COVERED																																																																																			NOVEL	ZNF124-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000098570.2	6	3.911426	KEEP	2	0	0	13	391	CC	0.993634	0.38494	0		-	3	60	93	0	0	7.133454	16	60	522	52	ENST00000472531.1	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	1	248070689	248070689	__UNKNOWN__	IGR	SNP	C	C	T	rs61857471	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:248070689C>T			NA	NA				OR2W3 (10240 upstream) : OR2T8 (13630 downstream)						NA		NA									NA						ctctctctctctctctctctc	0.358		NA											N|||	2931	0.585264	0.3646	0.6499	5008	,	,	NA	13304	0.6845	NA	0.7068	False	NA	,,,	NA	NA	NA	2504	0.6104	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr1.hg19:g.248070689C>T		NA		hg19		0.02	-0.105246	TCTxTCT	UNCOVERED																																																																																			NOVEL					0			13	2.406096	KEEP	4	0	0	8	233	CG	0	0	0			5	60	144	0	0	13.773792	5	60	155	26		0.5	0.139832
OR2T3	343173	__UNKNOWN__	__UNKNOWN__	1	248637291	248637291	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs1770109	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr1:248637291G>A	ENST00000359594.2	+	1	665	c.640G>A	c.(640-642)Gcc>Acc	p.A214T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	214		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A214T(1)		breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATGCTTCTCGCCCCCATCAT	0.557		NA											.|||	954	0.190495	0.1263	0.1916	5008	,	,	NA	17132	0.2867	NA	0.1064	False	NA	,,,	NA	NA	NA	2504	0.2638	NA	NA	NA								NA				1	Substitution - Missense(1)	skin(1)											211	168	182			NA	NA	1		NA											NA				248637291		2136	4233	6369	SO:0001583	missense				CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539	343173		GPCR / Class A : Olfactory receptors	14727	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001005495	NM_001005495	NA	Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.640G>A	chr1.hg19:g.248637291G>A	ENSP00000352604:p.Ala214Thr	NA	B2RNJ1	hg19	CCDS31117.1	0.02	1.243089	CTCxCCC	COVERED	537	0.24587912087912087	86	0.17479674796747968	71	0.19613259668508287	238	0.4160839160839161	142	0.18733509234828497	g	13.03	2.115628	0.37339	.	.	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	-2.22	0.06952	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10629	0.01	0.09310	N	1	P	0.39535	0.677	B	0.33568	0.166	T	0.42275	-0.9461	9	0.56958	D	0.05	.	0.5423	0.00647	0.2646:0.2059:0.3262:0.2032	rs1770109	214	Q8NH03	OR2T3_HUMAN	T	214	ENSP00000352604:A214T	ENSP00000352604:A214T	A	+	1	0	OR2T3	246703914	0.000000	0.05858	0.163000	0.22734	0.269000	0.26545	-1.638000	0.02013	0.011000	0.14865	0.186000	0.17326	GCC	NOVEL	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000097348.1	5	8.724659	KEEP	3	0	0	29	864	GG	0.999997	0.998198	0		+	6	47	166	0	0	10.435012	68	60	2218	144	ENST00000359594.2	0.081081	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	37349	37349	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:37349T>G			NA	NA				None (None upstream) : FAM110C (1464 downstream)						NA		NA									NA						agaatggctttaacctgggag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.37349T>G		NA		hg19		0.02	-0.210436	CTTxAAC	COVERED																																																																																			NOVEL					0			8	2.404338	KEEP	0	0	0	8	202	TT	0.99257	0.518282	0			3	60	89	0	0	6.407115	21	60	576	41		0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	136056	136056	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136056C>T			NA	NA				FAM110C (89671 upstream) : AC079779.7 (61512 downstream)						NA		NA									NA						acagactgggcgtggtggctc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.136056C>T		NA		hg19		0.02	-0.236846	GGGxGTG	COVERED																																																																																			NOVEL					0			8	2.707551	KEEP	2	0	0	9	260	CC	0.99257	0.607857	0			3	60	97	0	0	7.042548	24	60	786	52		0.111111	0.612407
SNTG2	54221	__UNKNOWN__	__UNKNOWN__	2	1306010	1306010	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:1306010T>C	ENST00000308624.5	+	15	1413				SNTG2_ENST00000407292.1_Intron	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	NA		NA			central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		ggattacaggtgtgagccacc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554	54221			13741	protein-coding gene	gene with protein product		608715			NA	10747910	Standard	NM_018968	NM_018968	NA	Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.1285-6256T>C	chr2.hg19:g.1306010T>C		NA	Q05AH5	hg19	CCDS46220.1	0.02	-0.184199	AGGxGTG	COVERED																																																																																			NOVEL	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322454.1	10	3.609059	KEEP	2	0	0	12	332	TT	0.993634	0.420782	0		+	3	60	99	0	0	7.810102	15	60	455	57	ENST00000308624.5	0.166667	0.423478
COLEC11	78989	__UNKNOWN__	__UNKNOWN__	2	3651118	3651118	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:3651118A>G	ENST00000349077.4	+	2	77				COLEC11_ENST00000382062.2_Intron|COLEC11_ENST00000487365.1_Intron|AC010907.2_ENST00000456450.1_RNA|COLEC11_ENST00000418971.2_Intron|COLEC11_ENST00000236693.7_Intron	NM_024027.4	NP_076932.1	Q9BWP8	COL11_HUMAN	collectin sub-family member 11	NA		NA			developmental process (GO:0032502)|multicellular organismal development (GO:0007275)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)	mannose binding (GO:0005537)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|soft_tissue(1)	22	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.127)		tgttgtccagactggtctcga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC000078	CCDS1649.1, CCDS1650.1, CCDS58689.1, CCDS58690.1, CCDS58691.1, CCDS58692.1, CCDS58693.1, CCDS58694.1	2p25.3	2014-09-17			ENSG00000118004	ENSG00000118004	78989		Collectins	17213	protein-coding gene	gene with protein product	Collectin K1	612502			NA		Standard	NM_024027	NM_024027	NA	Approved	MGC3279, CL-K1	uc031rnn.1	Q9BWP8	OTTHUMG00000090304	ENST00000349077.4:c.-26-787A>G	chr2.hg19:g.3651118A>G		NA	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	hg19	CCDS1649.1	0.02	1.584468	CAGxCTG	COVERED																																																																																			NOVEL	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206666.1	5	3.841932	KEEP	1	1	29	23	639	AA	0.999892	0.996125	0		+	5	60	146	0	0	9.307211	61	60	1820	99	ENST00000349077.4	0.075758	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	4429844	4429844	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:4429844A>G			NA	NA				AC068292.1 (153736 upstream) : AC022311.1 (245967 downstream)						NA		NA									NA						ggtggctcatacctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.4429844A>G		NA		hg19		0.02	-0.192955	CATxCCT	COVERED																																																																																			NOVEL					0			5	2.706635	KEEP	1	0	0	9	243	AA	0.99257	0.4869	0			5	60	164	0	0	14.470638	11	60	321	50		0.3125	0.490544
AC022311.1	0	__UNKNOWN__	__UNKNOWN__	2	4680350	4680350	__UNKNOWN__	lincRNA	SNP	G	G	C	rs201348888		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:4680350G>C	ENST00000412134.1	-	0	494					NR_034134.1					NA		NA									NA						ctggagtgcagtggcacaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412134.1:	chr2.hg19:g.4680350G>C		NA		hg19		0.02	-0.149136	GCAxTGG	COVERED																																																																																			NOVEL	AC022311.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000323189.1	4	3.610463	KEEP	4	0	0	12	358	GG	0.992708	0.289872	0		-	4	40	137	0	0	11.701229	12	60	409	39	ENST00000412134.1	0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	4766356	4766356	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:4766356G>C			NA	NA				AC022311.1 (62551 upstream) : SNORA31 (108234 downstream)						NA		NA									NA						cccatctctagtaaaaataca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.4766356G>C		NA		hg19		0.02	-0.166666	CTAxTAA	COVERED																																																																																			NOVEL					0			2	2.708246	KEEP	0	0	0	9	282	GG	0.99254	0.351306	0			3	45	84	0	0	6.311066	15	60	506	38		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	5701801	5701801	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:5701801T>C			NA	NA				AC107057.1 (5638 upstream) : AC107057.2 (40835 downstream)						NA		NA									NA						caggttcaagtgattctcctg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.5701801T>C		NA		hg19		0.02	-0.096481	AAGxGAT	UNCOVERED																																																																																			NOVEL					0			7	2.706889	KEEP	3	0	0	9	248	TT	0	0	0			3	60	100	0	0	8.778769	7	60	206	30		0.3	0.120436
AC108025.2	0	__UNKNOWN__	__UNKNOWN__	2	5775995	5775995	__UNKNOWN__	RNA	SNP	C	C	T	rs190172883	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:5775995C>T	ENST00000453678.1	-	0	331				AC107057.2_ENST00000458264.1_RNA						NA		NA									NA						cagtggctcacgcctgtaatc	0.552		NA											C|||	18	0.00359425	0.0015	0.0086	5008	,	,	NA	18887	0.0	NA	0.0089	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000453678.1:	chr2.hg19:g.5775995C>T		NA		hg19		0.02	-0.122802	TCAxGCC	UNCOVERED																																																																																			NOVEL	AC108025.2-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000322564.1	6	3.008691	KEEP	7	0	0	10	298	CC	0	0	0		-	3	60	86	0	0	7.232206	8	60	261	42	ENST00000453678.1	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	6417990	6417990	__UNKNOWN__	IGR	SNP	G	G	C	rs545853280	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:6417990G>C			NA	NA				AC073479.1 (292965 upstream) : AC017053.1 (35095 downstream)						NA		NA									NA						cctgtaatccgagcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.6417990G>C		NA		hg19		0.02	1.812838	TCCxAGC	COVERED																																																																																			NOVEL					0			11	2.26766	KEEP	0	2	49	25	737	GG	0.999997	0.99899	0			6	60	214	0	0	15.412085	63	60	1995	141		0.086957	0.998993
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	7386198	7386198	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:7386198C>T			NA	NA				RN7SKP112 (104523 upstream) : RP11-557L19.1 (14803 downstream)						NA		NA									NA						tgtgtgtgtgcgtgtgtgtat	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.7386198C>T		NA		hg19		0.02	2.216822	GTGxGTG	COVERED																																																																																			NOVEL					0			32	6.752309	KEEP	1	10	240	108	3248	CC	1	1	0			16	60	447	0	1	31.291568	114	60	3808	383		0.123077	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	7610790	7610790	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:7610790T>C			NA	NA				AC013460.1 (20405 upstream) : RNU6ATAC37P (106181 downstream)						NA		NA									NA						tttgggaggctaaggcgggtg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.7610790T>C		NA		hg19		0.02	-0.175428	GGCxAAG	COVERED																																																																																			NOVEL					0			7	2.707147	KEEP	0	0	0	9	253	TT	0.99254	0.384517	0			3	60	97	0	0	7.691917	14	60	429	45		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	8059622	8059622	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:8059622T>C			NA	NA				AC007463.2 (19836 upstream) : AC007464.1 (2933 downstream)						NA		NA									NA						gtgatctgcctgccttggcct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.8059622T>C		NA		hg19		0.02	-0.280623	GCCxGCC	COVERED																																																																																			NOVEL					0			9	3.006314	KEEP	1	0	0	10	271	TT	0.99254	0.734154	0			4	60	122	0	0	9.058323	25	60	723	59		0.137931	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	8583775	8583775	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:8583775T>C			NA	NA				LINC00299 (115226 upstream) : AC011747.3 (99946 downstream)						NA		NA									NA						cgcctgtaattccagcacttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.8583775T>C		NA		hg19		0.02	-0.245597	AATxCCA	COVERED																																																																																			NOVEL					0			12	2.40618	KEEP	1	0	0	8	221	TT	0.99257	0.636582	0			3	60	105	0	0	7.948568	22	60	674	53		0.12	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9145899	9145899	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9145899T>A			NA	NA				MBOAT2 (1957 upstream) : RP11-734K21.2 (97669 downstream)						NA		NA									NA						cagtgagctgtgatcgcacca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9145899T>A		NA		hg19		0.02	-0.324372	CTGxGAT	COVERED																																																																																			NOVEL					0			11	2.706026	KEEP	0	0	0	9	239	TT	0.99254	0.829482	0			4	60	119	0	0	8.635277	27	60	743	63		0.129032	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9169714	9169714	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9169714A>G			NA	NA				MBOAT2 (25772 upstream) : RP11-734K21.2 (73854 downstream)						NA		NA									NA						agctacttagaaggctgaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9169714A>G		NA		hg19		0.02	-0.21919	TAGxAGG	COVERED																																																																																			NOVEL					0			9	2.406065	KEEP	0	0	0	8	221	AA	0.99257	0.54878	0			3	60	91	0	0	6.607463	21	60	602	41		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9258072	9258072	__UNKNOWN__	IGR	SNP	G	G	A	rs3929501	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9258072G>A			NA	NA				RP11-734K21.3 (1059 upstream) : RP11-734K21.4 (25222 downstream)						NA		NA									NA						ccaaagtgctgggattacagg	0.418		NA											G|||	1719	0.343251	0.4387	0.4078	5008	,	,	NA	17313	0.1498	NA	0.3976	False	NA	,,,	NA	NA	NA	2504	0.3119	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9258072G>A		NA		hg19		0.02	-0.298236	GCTxGGA	COVERED																																																																																			NOVEL					0			13	3.009342	KEEP	2	0	0	10	319	GG	0.99257	0.775257	0			18	60	540	0	0	53.426506	13	60	449	63		0.580645	0.78106
ASAP2	8853	__UNKNOWN__	__UNKNOWN__	2	9349959	9349959	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9349959C>A	ENST00000281419.3	+	1	466				ASAP2_ENST00000315273.4_Intron	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	NA		NA			positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						cagcctcccacagtgctggga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693	8853		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	2721	protein-coding gene	gene with protein product	centaurin, beta 3	603817	development and differentiation enhancing factor 2	DDEF2	NA	10022920, 9455477	Standard	NM_003887	NM_003887	NA	Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.126+2600C>A	chr2.hg19:g.9349959C>A		NA	D6W4Y8	hg19	CCDS1661.1	0.02	-0.324576	CCAxAGT	COVERED																																																																																			NOVEL	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000237522.1	9	3.610702	KEEP	4	0	0	12	366	CC	0.992708	0.829622	0		+	5	60	146	0	0	10.822513	29	60	995	77	ENST00000281419.3	0.147059	0.835716
ASAP2	8853	__UNKNOWN__	__UNKNOWN__	2	9535775	9535775	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9535775C>T	ENST00000281419.3	+	24	3024				ASAP2_ENST00000315273.4_Intron|ASAP2_ENST00000491413.1_Intron	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	NA		NA			positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						cttgctctgtcgcccaggctg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693	8853		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	2721	protein-coding gene	gene with protein product	centaurin, beta 3	603817	development and differentiation enhancing factor 2	DDEF2	NA	10022920, 9455477	Standard	NM_003887	NM_003887	NA	Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2684+1999C>T	chr2.hg19:g.9535775C>T		NA	D6W4Y8	hg19	CCDS1661.1	0.02	-0.070151	TGTxGCC	UNCOVERED																																																																																			NOVEL	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000237522.1	14	2.40318	KEEP	7	0	0	8	209	CC	0	0	0		+	3	43	91	0	0	8.233244	5	60	151	25	ENST00000281419.3	0.375	0.054137
ASAP2	8853	__UNKNOWN__	__UNKNOWN__	2	9538678	9538678	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9538678C>T	ENST00000281419.3	+	25	3024				ASAP2_ENST00000315273.4_Intron|ASAP2_ENST00000491413.1_Intron	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	NA		NA			positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ggctcacacccgtaatcctag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693	8853		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	2721	protein-coding gene	gene with protein product	centaurin, beta 3	603817	development and differentiation enhancing factor 2	DDEF2	NA	10022920, 9455477	Standard	NM_003887	NM_003887	NA	Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.2685-1474C>T	chr2.hg19:g.9538678C>T		NA	D6W4Y8	hg19	CCDS1661.1	0.02	-0.166643	ACCxGTA	COVERED																																																																																			NOVEL	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000237522.1	3	2.707244	KEEP	0	0	0	9	259	CC	0.99254	0.351306	0		+	4	60	105	0	0	8.268878	14	60	467	39	ENST00000281419.3	0.222222	0.353947
ADAM17	6868	__UNKNOWN__	__UNKNOWN__	2	9650649	9650649	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9650649T>C	ENST00000310823.3	-	11	1374				RP11-400L8.2_ENST00000480764.1_RNA|RP11-400L8.2_ENST00000472619.1_RNA	NM_003183.4	NP_003174.3	P78536	ADA17_HUMAN	ADAM metallopeptidase domain 17	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell motility (GO:0048870)|collagen catabolic process (GO:0030574)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|germinal center formation (GO:0002467)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil mediated immunity (GO:0002446)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of chemokine production (GO:0032722)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|proteolysis (GO:0006508)|regulation of mast cell apoptotic process (GO:0033025)|response to drug (GO:0042493)|response to high density lipoprotein particle (GO:0055099)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|wound healing, spreading of epidermal cells (GO:0035313)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|interleukin-6 receptor binding (GO:0005138)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|Notch binding (GO:0005112)|PDZ domain binding (GO:0030165)|zinc ion binding (GO:0008270)			breast(1)|cervix(4)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	28	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.225)		aaaaattagctgggcatggag	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69611	CCDS1665.1	2p25	2010-08-05	2008-07-31		ENSG00000151694	ENSG00000151694	6868		ADAM metallopeptidase domain containing, CD molecules	195	protein-coding gene	gene with protein product		603639	tumor necrosis factor, alpha, converting enzyme	TACE	NA	9034190, 9574564	Standard		NM_003183	NA	Approved	cSVP, CD156B	uc002qzu.3	P78536	OTTHUMG00000090425	ENST00000310823.3:c.1192-389A>G	chr2.hg19:g.9650649T>C		NA	O60226	hg19	CCDS1665.1	0.02	-0.184185	AGCxGGG	COVERED																																																																																			NOVEL	ADAM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206857.1	8	3.007153	KEEP	4	0	0	10	271	TT	0.99257	0.420331	0		-	3	60	89	0	0	6.59291	18	60	538	43	ENST00000310823.3	0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9711550	9711550	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9711550A>G			NA	NA				RP11-214N9.1 (14646 upstream) : YWHAQ (12550 downstream)						NA		NA									NA						tgcccaggctagagtgcagtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9711550A>G		NA		hg19		0.02	-0.280616	GCTxGAG	COVERED																																																																																			NOVEL					0			8	3.307239	KEEP	0	0	0	11	294	AA	0.993072	0.734547	0			3	60	98	0	0	6.909954	29	60	864	66		0.09375	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9716715	9716715	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9716715T>C			NA	NA				RP11-214N9.1 (19811 upstream) : YWHAQ (7385 downstream)						NA		NA									NA						atctgcccacttcggcctccc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9716715T>C		NA		hg19		0.02	-0.24559	CACxTCG	COVERED																																																																																			NOVEL					0			19	4.811975	KEEP	2	0	0	16	441	TT	0.997832	0.639957	0			4	60	130	0	0	10.213593	20	60	601	59		0.166667	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9716745	9716745	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9716745T>C			NA	NA				RP11-214N9.1 (19841 upstream) : YWHAQ (7355 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9716745T>C		NA		hg19		0.02	-0.376915	AGGxGTG	COVERED																																																																																			NOVEL					0			33	3.198656	KEEP	2	2	40	25	630	TT	0.999997	0.909066	0			3	60	100	0	0	6.988143	32	60	863	95		0.085714	0.909069
RP11-521D12.1	0	__UNKNOWN__	__UNKNOWN__	2	9782459	9782459	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9782459A>G	ENST00000478468.1	+	0	244										NA		NA									NA						gggattacagacgtgagccac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000478468.1:	chr2.hg19:g.9782459A>G		NA		hg19		0.02	-0.149085	CAGxCGT	COVERED																																																																																			NOVEL	RP11-521D12.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000353402.1	5	3.308105	KEEP	1	0	0	11	301	AA	0.992708	0.289872	0		+	3	60	104	0	0	8.572452	12	60	342	41	ENST00000478468.1	0.2	0.292001
RP11-521D12.2	0	__UNKNOWN__	__UNKNOWN__	2	9830106	9830106	__UNKNOWN__	lincRNA	SNP	T	T	C	rs539764285		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9830106T>C	ENST00000483023.1	+	0	444										NA		NA									NA						gcaggagaattgcttgaaccc	0.537		NA											T|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	16954	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000483023.1:	chr2.hg19:g.9830106T>C		NA		hg19		0.02	-0.166613	AATxGCT	COVERED																																																																																			NOVEL	RP11-521D12.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000353415.1	7	2.40399	KEEP	1	0	0	8	205	TT	0.99257	0.384528	0		+	3	60	93	0	0	7.133926	16	60	445	35	ENST00000483023.1	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	9922101	9922101	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9922101G>A			NA	NA				RP11-521D12.5 (11631 upstream) : TAF1B (61381 downstream)						NA		NA									NA						tgctgggattgcaggcgtgag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.9922101G>A		NA		hg19		0.02	-0.315814	ATTxCAG	COVERED																																																																																			NOVEL					0			5	2.708029	KEEP	0	0	0	9	277	GG	0.99254	0.829482	0			5	60	147	0	1	10.922387	29	60	1023	75		0.147059	0.835716
TAF1B	9014	__UNKNOWN__	__UNKNOWN__	2	9995145	9995145	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:9995145C>T	ENST00000263663.5	+	5	587				TAF1B_ENST00000396242.3_Intron|TAF1B_ENST00000402170.1_Intron	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	NA		NA			gene expression (GO:0010467)|RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript (GO:0001189)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I core factor complex (GO:0070860)	metal ion binding (GO:0046872)|RNA polymerase I CORE element sequence-specific DNA binding (GO:0001164)|RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001187)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TBP-class protein binding (GO:0017025)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ttttttgagacggagtttcac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L39061	CCDS33143.1	2p25	2008-06-02	2002-08-29		ENSG00000115750	ENSG00000115750	9014			11533	protein-coding gene	gene with protein product		604904	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kD		NA	7801123	Standard	NM_005680	NM_005680	NA	Approved	TAFI63, SL1, RAF1B, RAFI63	uc002qzz.3	Q53T94	OTTHUMG00000151673	ENST00000263663.5:c.399+595C>T	chr2.hg19:g.9995145C>T		NA	B4DI42|F8WD72|Q15574|Q8WVC3	hg19	CCDS33143.1	0.02	-0.175444	AGAxGGA	COVERED																																																																																			NOVEL	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323426.2	6	3.300315	KEEP	2	0	0	11	315	CC	0.992708	0.384582	0		+	3	60	91	0	0	7.178852	13	60	437	47	ENST00000263663.5	0.1875	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	10365399	10365399	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10365399G>A			NA	NA				C2orf48 (13548 upstream) : RN7SL66P (55357 downstream)						NA		NA									NA						tgcccgcctcggcctcccaaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.10365399G>A		NA		hg19		0.02	-0.24561	CTCxGCC	COVERED																																																																																			NOVEL					0			5	2.708343	KEEP	0	0	0	9	286	GG	0.99254	0.636563	0			3	60	97	1	0	7.094669	23	60	756	60		0.115385	0.641347
NOL10	79954	__UNKNOWN__	__UNKNOWN__	2	10809771	10809771	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10809771A>G	ENST00000381685.5	-	7	570				NOL10_ENST00000538384.1_Intron|NOL10_ENST00000345985.3_Intron|NOL10_ENST00000542668.1_Intron	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	NA		NA				nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)				NA	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		tgtaatcccaacactttggga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761	79954			25862	protein-coding gene	gene with protein product		NA	polyglutamine binding protein 5	PQBP5	NA	12477932	Standard	NM_024894	NM_024894	NA	Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.465-922T>C	chr2.hg19:g.10809771A>G		NA	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	hg19	CCDS1673.2	0.02	-0.263106	CCAxCAC	COVERED																																																																																			NOVEL	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239227.1	7	2.706627	KEEP	0	0	0	9	250	AA	0.99254	0.688494	0		-	4	60	135	0	0	10.491372	23	60	670	57	ENST00000381685.5	0.148148	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	10834230	10834230	__UNKNOWN__	IGR	SNP	T	T	C	rs186228123	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10834230T>C			NA	NA				RN7SL832P (2005 upstream) : AC092687.3 (23668 downstream)						NA		NA									NA						tcaagcgattttcctgcctca	0.507		NA											t|||	40	0.00798722	0.0287	0.0029	5008	,	,	NA	17343	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.10834230T>C		NA		hg19		0.02	-0.140329	ATTxTCC	UNCOVERED																																																																																			NOVEL					0			7	2.40536	KEEP	4	0	0	8	217	TT	0	0	0			3	60	93	0	0	7.472488	12	60	351	35		0.2	0.260965
PDIA6	10130	__UNKNOWN__	__UNKNOWN__	2	10934826	10934826	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10934826A>G	ENST00000404371.2	-	7	840				PDIA6_ENST00000381611.4_Intron|PDIA6_ENST00000272227.3_Intron|PDIA6_ENST00000404824.2_Intron|PDIA6_ENST00000540494.1_Intron	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		aggccgaggcaggcggatcat	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(73;509 1219 34219 41343 41551)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	10130	5.3.4.1	Protein disulfide isomerases	30168	protein-coding gene	gene with protein product	protein disulfide isomerase-related protein	611099	thioredoxin domain containing 7 (protein disulfide isomerase), protein disulfide isomerase-associated 6	TXNDC7	NA	7590364, 12204115	Standard	NM_005742	XM_005246145	NA	Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.503-1498T>C	chr2.hg19:g.10934826A>G		NA	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	hg19		0.02	-0.34202	GGCxGGC	COVERED																																																																																			NOVEL	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323575.2	4	3.30888	KEEP	2	0	0	11	311	AA	0.993072	0.859748	0		-	4	60	130	0	0	9.358338	34	60	992	78	ENST00000404371.2	0.105263	0.865745
PDIA6	10130	__UNKNOWN__	__UNKNOWN__	2	10936564	10936564	__UNKNOWN__	Intron	SNP	G	G	A	rs10174167	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10936564G>A	ENST00000404371.2	-	6	840				PDIA6_ENST00000381611.4_Intron|PDIA6_ENST00000272227.3_Intron|PDIA6_ENST00000404824.2_Intron|PDIA6_ENST00000540494.1_Intron	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		gctgaagtaggaggactgcct	0.413		NA											G|||	2417	0.482628	0.2148	0.536	5008	,	,	NA	16822	0.4573	NA	0.6252	False	NA	,,,	NA	NA	NA	2504	0.6861	NA	NA	NA	GBM(73;509 1219 34219 41343 41551)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	10130	5.3.4.1	Protein disulfide isomerases	30168	protein-coding gene	gene with protein product	protein disulfide isomerase-related protein	611099	thioredoxin domain containing 7 (protein disulfide isomerase), protein disulfide isomerase-associated 6	TXNDC7	NA	7590364, 12204115	Standard	NM_005742	XM_005246145	NA	Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.502+642C>T	chr2.hg19:g.10936564G>A		NA	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	hg19		0.02	-0.140351	TAGxAGG	COVERED																																																																																			NOVEL	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323575.2	8	2.707883	KEEP	0	0	0	9	270	GG	0.99254	0.259018	0		-	5	60	155	0	0	14.123436	8	60	265	33	ENST00000404371.2	0.384615	0.260965
PDIA6	10130	__UNKNOWN__	__UNKNOWN__	2	10936569	10936569	__UNKNOWN__	Intron	SNP	C	C	T	rs7572982	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10936569C>T	ENST00000404371.2	-	6	840				PDIA6_ENST00000381611.4_Intron|PDIA6_ENST00000272227.3_Intron|PDIA6_ENST00000404824.2_Intron|PDIA6_ENST00000540494.1_Intron	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		agtaggaggactgcctgagcc	0.418		NA											T|||	2484	0.496006	0.2224	0.5418	5008	,	,	NA	16566	0.4583	NA	0.6392	False	NA	,,,	NA	NA	NA	2504	0.7249	NA	NA	NA	GBM(73;509 1219 34219 41343 41551)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	10130	5.3.4.1	Protein disulfide isomerases	30168	protein-coding gene	gene with protein product	protein disulfide isomerase-related protein	611099	thioredoxin domain containing 7 (protein disulfide isomerase), protein disulfide isomerase-associated 6	TXNDC7	NA	7590364, 12204115	Standard	NM_005742	XM_005246145	NA	Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.502+637G>A	chr2.hg19:g.10936569C>T		NA	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	hg19		0.02	-0.140343	GGAxTGC	COVERED																																																																																			NOVEL	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323575.2	8	2.708023	KEEP	0	0	0	9	274	CC	0.99254	0.259018	0		-	5	60	152	0	0	13.823372	8	60	270	34	ENST00000404371.2	0.384615	0.260965
PDIA6	10130	__UNKNOWN__	__UNKNOWN__	2	10944314	10944314	__UNKNOWN__	Intron	SNP	G	G	A	rs548539389	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10944314G>A	ENST00000404371.2	-	4	513				PDIA6_ENST00000381611.4_Intron|PDIA6_ENST00000272227.3_Intron|PDIA6_ENST00000404824.2_Intron|PDIA6_ENST00000540494.1_Intron|PDIA6_ENST00000489662.1_Intron	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		gattacaggcgtgagccaccg	0.468		NA											G|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	15602	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA	GBM(73;509 1219 34219 41343 41551)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	10130	5.3.4.1	Protein disulfide isomerases	30168	protein-coding gene	gene with protein product	protein disulfide isomerase-related protein	611099	thioredoxin domain containing 7 (protein disulfide isomerase), protein disulfide isomerase-associated 6	TXNDC7	NA	7590364, 12204115	Standard	NM_005742	XM_005246145	NA	Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.176-1548C>T	chr2.hg19:g.10944314G>A		NA	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	hg19		0.02	-0.403474	GGCxTGA	UNCOVERED																																																																																			NOVEL	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323575.2	16	3.610355	KEEP	12	0	0	12	356	GG	0	0	0		-	4	60	114	0	0	7.578858	38	60	1238	87	ENST00000404371.2	0.095238	0.934492
PDIA6	10130	__UNKNOWN__	__UNKNOWN__	2	10958915	10958915	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:10958915C>T	ENST00000404371.2	-	3	513				PDIA6_ENST00000381611.4_Intron|PDIA6_ENST00000404824.2_Intron	NM_001282704.1	NP_001269633.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		tcccaaagtgctgggattata	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(73;509 1219 34219 41343 41551)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	10130	5.3.4.1	Protein disulfide isomerases	30168	protein-coding gene	gene with protein product	protein disulfide isomerase-related protein	611099	thioredoxin domain containing 7 (protein disulfide isomerase), protein disulfide isomerase-associated 6	TXNDC7	NA	7590364, 12204115	Standard	NM_005742	XM_005246145	NA	Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000404371.2:c.175+484G>A	chr2.hg19:g.10958915C>T		NA	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	hg19		0.02	-0.140351	GTGxTGG	UNCOVERED																																																																																			NOVEL	PDIA6-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323575.2	10	3.009201	KEEP	5	0	0	10	314	CC	0	0	0		-	3	60	83	0	0	6.472527	12	60	413	36	ENST00000404371.2	0.2	0.260965
ROCK2	9475	__UNKNOWN__	__UNKNOWN__	2	11378753	11378753	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:11378753G>C	ENST00000315872.6	-	5	911				ROCK2_ENST00000462366.1_Intron	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	NA		NA			actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		gtgggaggatgacttgaggcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	9475	2.7.11.1	Pleckstrin homology (PH) domain containing	10252	protein-coding gene	gene with protein product		604002			NA	9933571	Standard		NM_004850	NA	Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.463-2665C>G	chr2.hg19:g.11378753G>C		NA	Q53QZ0|Q53SJ7|Q9UQN5	hg19	CCDS42654.1	0.02	-0.236806	GATxACT	COVERED																																																																																			NOVEL	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313886.3	14	4.512704	KEEP	1	0	0	15	452	GG	0.99649	0.639096	0		-	4	60	131	0	0	10.394705	19	60	622	62	ENST00000315872.6	0.173913	0.641347
GREB1	9687	__UNKNOWN__	__UNKNOWN__	2	11747121	11747121	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:11747121A>C	ENST00000381486.2	+	18	2966				GREB1_ENST00000234142.5_Intron	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	NA		NA				integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		gttagccaggatggtctcgat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(39;850 945 2785 23371 33093)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208	9687			24885	protein-coding gene	gene with protein product	gene regulated by estrogen in breast cancer	611736			NA	11103799	Standard	NM_014668	NM_014668	NA	Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2667-3693A>C	chr2.hg19:g.11747121A>C		NA	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	hg19	CCDS42655.1	0.02	-0.157873	AGGxTGG	UNCOVERED																																																																																			NOVEL	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280490.1	8	2.40574	KEEP	5	0	0	8	214	AA	0	0	0		+	3	60	101	0	0	8.178854	13	60	386	43	ENST00000381486.2	0.1875	0.322807
LPIN1	23175	__UNKNOWN__	__UNKNOWN__	2	11924236	11924236	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:11924236C>G	ENST00000396097.1	+	4	843				LPIN1_ENST00000256720.2_Intron|LPIN1_ENST00000449576.2_Intron|LPIN1_ENST00000396099.1_Intron|LPIN1_ENST00000425416.2_Intron			Q14693	LPIN1_HUMAN	lipin 1	NA		NA			cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ttcaagaccaccctggccaac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324	23175			13345	protein-coding gene	gene with protein product		605518			NA	11138012, 8724849, 16950137	Standard	NM_145693	NM_145693	NA	Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000396097.1:c.440+188C>G	chr2.hg19:g.11924236C>G		NA	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	hg19		0.02	-0.254397	CCAxCCT	COVERED																																																																																			NOVEL	LPIN1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000277151.1	7	2.407008	KEEP	2	0	0	8	242	AC	0.99257	0.663556	0		+	3	60	98	0	0	7.194552	23	60	760	48	ENST00000396097.1	0.115385	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	12033191	12033191	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:12033191T>C			NA	NA				MIR4262 (56079 upstream) : AC096559.1 (114062 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.12033191T>C		NA		hg19		0.02	-0.368342	TCAxGCC	COVERED																																																																																			NOVEL					0			10	3.307656	KEEP	0	0	0	11	298	TT	0.993072	0.893084	0			3	60	100	0	0	6.875998	35	60	1014	80		0.078947	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	12063841	12063841	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:12063841C>G			NA	NA				MIR4262 (86729 upstream) : AC096559.1 (83412 downstream)						NA		NA									NA						ggaggcggagcttgcagtgag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.12063841C>G		NA		hg19		0.02	-0.114038	GAGxTTG	UNCOVERED																																																																																			NOVEL					0			8	3.310034	KEEP	11	0	0	11	343	CC	0	0	0			4	35	120	0	0	10.590835	8	46	279	41		0.333333	0.162467
AC096559.1	0	__UNKNOWN__	__UNKNOWN__	2	12256121	12256121	__UNKNOWN__	lincRNA	SNP	C	C	T	rs369483313	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:12256121C>T	ENST00000412294.1	+	0	197										NA		NA									NA						cctcgtgatccgcccaccttg	0.522		NA											c|||	11	0.00219649	0.0083	0.0	5008	,	,	NA	18025	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412294.1:	chr2.hg19:g.12256121C>T		NA		hg19		0.02	-0.201763	ATCxGCC	COVERED																																																																																			NOVEL	AC096559.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000323583.2	7	3.008856	KEEP	7	0	0	10	303	CC	0.99257	0.4869	0		+	3	60	88	0	0	6.492806	18	60	607	58	ENST00000412294.1	0.142857	0.490544
AC096559.1	0	__UNKNOWN__	__UNKNOWN__	2	12606850	12606850	__UNKNOWN__	lincRNA	SNP	A	A	G	rs66485772|rs56321609	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:12606850A>G	ENST00000412294.1	+	0	412										NA		NA									NA						tgatccacccacctcggcctc	0.542		NA											A|||	2200	0.439297	0.5053	0.4193	5008	,	,	NA	7925	0.3294	NA	0.5527	False	NA	,,,	NA	NA	NA	2504	0.3609	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000412294.1:	chr2.hg19:g.12606850A>G		NA		hg19		0.02	-0.228037	CCCxCCT	COVERED																																																																																			NOVEL	AC096559.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000323583.2	5	2.406539	KEEP	2	0	0	8	228	AA	0.99257	0.578599	0		+	4	60	128	0	0	10.363285	16	60	472	55	ENST00000412294.1	0.2	0.58293
NBAS	51594	__UNKNOWN__	__UNKNOWN__	2	15476595	15476595	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:15476595C>T	ENST00000281513.5	-	36	4205				NBAS_ENST00000441750.1_Intron	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	NA		NA			negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						cggtggctcacgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779	51594			15625	protein-coding gene	gene with protein product		608025			NA	9926938, 12706883	Standard	NM_015909	NM_015909	NA	Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.4180-5706G>A	chr2.hg19:g.15476595C>T		NA	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	hg19	CCDS1685.1	0.02	-0.175444	TCAxGCC	COVERED																																																																																			NOVEL	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000241638.1	5	3.309218	KEEP	2	0	0	11	323	CC	0.992708	0.384582	0		-	3	42	88	1	0	6.633839	16	60	540	50	ENST00000281513.5	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	15995807	15995807	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:15995807A>G			NA	NA				AC113608.1 (44806 upstream) : RNU5E-7P (9251 downstream)						NA		NA									NA						ctccagcctgagcaacagagc	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.15995807A>G		NA		hg19		0.02	-0.210454	CTGxGCA	COVERED																																																																																			NOVEL					0			8	3.910441	KEEP	0	0	0	13	367	AA	0.994391	0.519232	0			3	60	90	0	0	6.628645	19	60	551	53		0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	16092931	16092931	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:16092931C>T			NA	NA				RN7SL104P (1828 upstream) : AC010145.4 (44239 downstream)						NA		NA									NA						aggctggtctcgaactcctga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.16092931C>T		NA		hg19		0.02	-0.140337	TCTxGAA	COVERED																																																																																			NOVEL					0			12	2.406719	KEEP	0	0	0	8	239	CC	0.99257	0.259026	0			3	60	89	0	0	7.072393	12	60	376	34		0.2	0.260965
AC010145.4	0	__UNKNOWN__	__UNKNOWN__	2	16179646	16179646	__UNKNOWN__	lincRNA	SNP	T	T	C	rs183999906	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:16179646T>C	ENST00000422415.2	-	0	152										NA		NA									NA						cccttccctttcctttccttt	0.448		NA											t|||	4513	0.901158	0.795	0.902	5008	,	,	NA	18112	0.9603	NA	0.9433	False	NA	,,,	NA	NA	NA	2504	0.9397	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000422415.2:	chr2.hg19:g.16179646T>C		NA		hg19		0.02	-0.166642	CTTxCCT	COVERED																																																																																			NOVEL	AC010145.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000323749.2	10	2.40629	KEEP	0	0	0	8	223	TT	0.99257	0.351317	0		-	3	60	92	0	0	7.110474	15	60	450	35	ENST00000422415.2	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	16365064	16365064	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:16365064G>A			NA	NA				AC142119.1 (119280 upstream) : SNORA40 (15406 downstream)						NA		NA									NA						cacgcctgtagtcccagcact	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.16365064G>A		NA		hg19		0.02	-0.149118	GTAxTCC	COVERED																																																																																			NOVEL					0			9	2.707952	KEEP	1	0	0	9	279	GG	0.99254	0.289823	0			3	60	83	0	0	6.472754	12	60	411	36		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	16851702	16851702	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:16851702T>C			NA	NA				FAM49A (4600 upstream) : AC008069.1 (57688 downstream)						NA		NA									NA						ctcactgcaatctctgcctcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.16851702T>C		NA		hg19		0.02	-0.096455	CAAxCTC	UNCOVERED																																																																																			NOVEL					0			8	2.405472	KEEP	1	0	0	8	219	TT	0	0	0			3	60	91	0	0	7.732604	8	60	229	25		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	16983852	16983852	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:16983852C>T			NA	NA				AC008069.1 (35030 upstream) : AC080094.1 (167448 downstream)						NA		NA									NA						cagtggctcacgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.16983852C>T		NA		hg19		0.02	-0.201752	TCAxGCC	COVERED																																																																																			NOVEL					0			11	3.309242	KEEP	1	0	0	11	324	CC	0.992708	0.518353	0			3	60	87	0	0	6.327829	19	60	632	47		0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	17691065	17691065	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:17691065A>G			NA	NA				RN7SKP168 (386658 upstream) : RAD51AP2 (785 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.17691065A>G		NA		hg19		0.02	-0.236792	CACxCCT	COVERED																																																																																			NOVEL					0			3	2.406155	KEEP	0	0	0	8	221	AA	0.99257	0.607857	0			3	60	95	0	0	6.949513	22	60	637	56		0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	18671395	18671395	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:18671395A>G			NA	NA				KCNS3 (128513 upstream) : RP11-111J6.2 (57256 downstream)						NA		NA									NA						cacctgcctcagcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.18671395A>G		NA		hg19		0.02	-0.254372	CTCxGCC	COVERED																																																																																			NOVEL					0			13	4.812438	KEEP	6	0	0	16	450	AA	0.993634	0.664267	0			4	60	128	0	0	9.862304	22	60	674	65		0.153846	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	19068702	19068702	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:19068702G>A			NA	NA				AC106053.1 (99684 upstream) : AC092594.1 (99026 downstream)						NA		NA									NA						tccgcctcccgggttcacgcc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.19068702G>A		NA		hg19		0.02	-0.219014	CCCxGGT	COVERED																																																																																			NOVEL					0			12	5.113196	KEEP	14	0	0	17	488	GG	0.99254	0.548763	0			3	60	94	0	0	6.907832	21	60	646	64		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	20352369	20352369	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:20352369G>T			NA	NA				AC098828.2 (45779 upstream) : RN7SL140P (22737 downstream)						NA		NA									NA						ttttgtttttgtttttgagac	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.20352369G>T		NA		hg19		0.02	-0.096493	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			9	3.009011	KEEP	0	0	0	10	307	GG	0.992708	0.119558	0			3	60	86	1	0	7.232068	8	60	281	29		0.272727	0.120436
C2orf43	60526	__UNKNOWN__	__UNKNOWN__	2	21014411	21014411	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:21014411G>A	ENST00000419825.2	-	1	74				C2orf43_ENST00000381090.3_Intron|C2orf43_ENST00000541941.1_Intron|C2orf43_ENST00000403006.2_Intron|C2orf43_ENST00000237822.3_Intron|C2orf43_ENST00000440866.2_Intron|C2orf43_ENST00000435420.2_Intron			Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	NA		NA								endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tggtagagaaggggtttcacc	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961	60526			26145	protein-coding gene	gene with protein product		613570			NA	17135363, 24357060	Standard	NM_021925	NM_001282723	NA	Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000419825.2:c.1+8385C>T	chr2.hg19:g.21014411G>A		NA	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	hg19		0.02	-0.096462	GAAxGGG	UNCOVERED																																																																																			NOVEL	C2orf43-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323909.1	5	2.407152	KEEP	0	0	0	8	244	GG	0.99257	0.119541	0		-	3	60	81	0	0	6.877865	7	60	222	26	ENST00000419825.2	0.3	0.120436
AC068490.2	0	__UNKNOWN__	__UNKNOWN__	2	22538960	22538960	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:22538960T>C	ENST00000450551.1	-	0	70										NA		NA									NA						aggctggtcttgaactcctga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000450551.1:	chr2.hg19:g.22538960T>C		NA		hg19		0.02	-0.201676	TCTxGAA	COVERED																																																																																			NOVEL	AC068490.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000324016.2	7	2.4052	KEEP	0	0	0	8	214	TT	0.99257	0.4869	0		-	3	60	97	0	0	7.461365	17	60	468	43	ENST00000450551.1	0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	23160151	23160151	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:23160151C>T			NA	NA				RN7SKP27 (75395 upstream) : AC016768.1 (80845 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.23160151C>T		NA		hg19		0.02	-0.175405	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			8	2.405926	KEEP	4	0	0	8	223	CC	0	0	0			3	60	88	0	0	6.879397	13	60	404	44		0.1875	0.387407
UBXN2A	165324	__UNKNOWN__	__UNKNOWN__	2	24172067	24172067	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24172067G>A	ENST00000309033.4	+	1	230				UBXN2A_ENST00000404924.1_Intron|UBXN2A_ENST00000535786.1_Intron|UBXN2A_ENST00000446425.2_Intron	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	NA		NA			regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						cctaacctcaggtgatccgcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960	165324		UBX domain containing	27265	protein-coding gene	gene with protein product		NA	UBX domain containing 4	UBXD4	NA	12477932	Standard	NM_181713	NM_181713	NA	Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.-15+8549G>A	chr2.hg19:g.24172067G>A		NA	A8K577|B7ZKP8|Q569G8	hg19	CCDS1704.1	0.02	-0.175448	TCAxGTG	COVERED																																																																																			NOVEL	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246824.2	10	2.708163	KEEP	1	0	0	9	282	GG	0.99257	0.384528	0		+	3	60	88	0	0	6.561331	17	60	587	38	ENST00000309033.4	0.15	0.387407
UBXN2A	165324	__UNKNOWN__	__UNKNOWN__	2	24172099	24172099	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24172099C>T	ENST00000309033.4	+	1	230				UBXN2A_ENST00000404924.1_Intron|UBXN2A_ENST00000535786.1_Intron|UBXN2A_ENST00000446425.2_Intron	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	NA		NA			regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						cccaaagtgccgggattacag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960	165324		UBX domain containing	27265	protein-coding gene	gene with protein product		NA	UBX domain containing 4	UBXD4	NA	12477932	Standard	NM_181713	NM_181713	NA	Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.-15+8581C>T	chr2.hg19:g.24172099C>T		NA	A8K577|B7ZKP8|Q569G8	hg19	CCDS1704.1	0.02	-0.25439	TGCxGGG	COVERED																																																																																			NOVEL	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246824.2	13	2.706649	KEEP	0	0	0	9	248	CC	0.99254	0.663536	0		+	3	60	91	0	0	6.495315	23	60	770	58	ENST00000309033.4	0.115385	0.668523
UBXN2A	165324	__UNKNOWN__	__UNKNOWN__	2	24195431	24195431	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24195431T>C	ENST00000309033.4	+	3	424				UBXN2A_ENST00000404924.1_Intron|UBXN2A_ENST00000535786.1_Intron|UBXN2A_ENST00000446425.2_Intron	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	NA		NA			regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						cggtggctcatgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960	165324		UBX domain containing	27265	protein-coding gene	gene with protein product		NA	UBX domain containing 4	UBXD4	NA	12477932	Standard	NM_181713	NM_181713	NA	Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.180+1147T>C	chr2.hg19:g.24195431T>C		NA	A8K577|B7ZKP8|Q569G8	hg19	CCDS1704.1	0.02	-0.254324	TCAxGCC	COVERED																																																																																			NOVEL	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246824.2	10	3.00672	KEEP	0	0	0	10	272	TT	0.992708	0.663648	0		+	4	60	136	0	0	10.662201	22	60	642	59	ENST00000309033.4	0.153846	0.668523
UBXN2A	165324	__UNKNOWN__	__UNKNOWN__	2	24196780	24196780	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24196780A>G	ENST00000309033.4	+	3	424				UBXN2A_ENST00000404924.1_Intron|UBXN2A_ENST00000535786.1_Intron|UBXN2A_ENST00000446425.2_Intron	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	NA		NA			regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						gattacaggcatgagccaccg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960	165324		UBX domain containing	27265	protein-coding gene	gene with protein product		NA	UBX domain containing 4	UBXD4	NA	12477932	Standard	NM_181713	NM_181713	NA	Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.180+2496A>G	chr2.hg19:g.24196780A>G		NA	A8K577|B7ZKP8|Q569G8	hg19	CCDS1704.1	0.02	-0.23673	GGCxTGA	COVERED																																																																																			NOVEL	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246824.2	6	2.405373	KEEP	0	0	0	8	212	AA	0.99257	0.607857	0		+	3	60	99	0	0	7.406095	21	60	618	46	ENST00000309033.4	0.125	0.612407
UBXN2A	165324	__UNKNOWN__	__UNKNOWN__	2	24223248	24223248	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24223248G>C	ENST00000309033.4	+	0	1535				UBXN2A_ENST00000446425.2_3'UTR	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	NA		NA			regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						cccatctctagtaaaaataca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960	165324		UBX domain containing	27265	protein-coding gene	gene with protein product		NA	UBX domain containing 4	UBXD4	NA	12477932	Standard	NM_181713	NM_181713	NA	Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.*511G>C	chr2.hg19:g.24223248G>C		NA	A8K577|B7ZKP8|Q569G8	hg19	CCDS1704.1	0.02	-0.201759	CTAxTAA	COVERED																																																																																			NOVEL	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246824.2	6	3.911174	KEEP	1	0	0	13	387	GG	0.995343	0.48826	0		+	3	60	98	0	0	7.365726	20	60	670	40	ENST00000309033.4	0.130435	0.490544
UBXN2A	165324	__UNKNOWN__	__UNKNOWN__	2	24225349	24225349	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24225349T>C	ENST00000309033.4	+	0	3636					NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	NA		NA			regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)				endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						ggcgcgatcttggctcactgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960	165324		UBX domain containing	27265	protein-coding gene	gene with protein product		NA	UBX domain containing 4	UBXD4	NA	12477932	Standard	NM_181713	NM_181713	NA	Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.*2612T>C	chr2.hg19:g.24225349T>C		NA	A8K577|B7ZKP8|Q569G8	hg19	CCDS1704.1	0.02	3.023661	TCTxGGC	COVERED																																																																																			NOVEL	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246824.2	36	18.346346	KEEP	1	0	0	61	1680	TT	1	1	0		+	6	60	186	0	0	10.979811	121	60	3442	280	ENST00000309033.4	0.047244	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24231600	24231600	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24231600G>A			NA	NA				UBXN2A (3821 upstream) : MFSD2B (1350 downstream)						NA		NA									NA						gggttcaagcgattctcctgc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24231600G>A		NA		hg19		0.02	-0.15789	AGCxATT	COVERED																																																																																			NOVEL					0			7	3.60976	KEEP	2	0	0	12	351	GG	0.992708	0.320453	0			3	60	92	0	0	7.110289	15	60	483	42		0.166667	0.322807
FKBP1B	2281	__UNKNOWN__	__UNKNOWN__	2	24285318	24285318	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24285318A>G	ENST00000380986.4	+	4	334				FKBP1B_ENST00000380991.4_Intron|FKBP1B_ENST00000452109.1_Intron	NM_004116.3|NM_054033.2	NP_004107.1|NP_473374.1	P68106	FKB1B_HUMAN	FK506 binding protein 1B, 12.6 kDa	NA		NA			'de novo' protein folding (GO:0006458)|calcium ion transmembrane transport (GO:0070588)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|chaperone-mediated protein folding (GO:0061077)|cytosolic calcium ion homeostasis (GO:0051480)|insulin secretion (GO:0030073)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neuronal action potential propagation (GO:0019227)|positive regulation of axon regeneration (GO:0048680)|positive regulation of sequestering of calcium ion (GO:0051284)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to redox state (GO:0051775)|response to vitamin E (GO:0033197)|smooth muscle contraction (GO:0006939)|T cell proliferation (GO:0042098)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium channel inhibitor activity (GO:0019855)|cyclic nucleotide binding (GO:0030551)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|receptor binding (GO:0005102)			lung(2)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					caaagtgctgagattacaggt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D38037	CCDS1706.1, CCDS33153.1	2p23.3	2013-03-20	2002-08-29		ENSG00000119782	ENSG00000119782	2281			3712	protein-coding gene	gene with protein product	calstabin 2	600620	FK506-binding protein 1B (12.6 kD)	FKBP1L	NA	7513996	Standard	NM_004116	NM_004116	NA	Approved	OTK4, FKBP12.6, PPIase, FKBP9	uc002rer.3	P68106	OTTHUMG00000151889	ENST00000380986.4:c.199-616A>G	chr2.hg19:g.24285318A>G		NA	Q13664|Q16645|Q53TM2|Q9BQ40	hg19	CCDS1706.1	0.02	-0.342083	CTGxGAT	COVERED																																																																																			NOVEL	FKBP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207622.1	13	2.405974	KEEP	0	0	0	8	218	AA	0.99257	0.859313	0		+	4	60	133	0	0	9.808564	31	60	950	68	ENST00000380986.4	0.114286	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24331498	24331498	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24331498A>G			NA	NA				FAM228B (11176 upstream) : PFN4 (6742 downstream)						NA		NA									NA						TTggccgggcacagtggctca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24331498A>G		NA		hg19		0.02	-0.403443	GGCxCAG	COVERED																																																																																			NOVEL					0			14	2.406866	KEEP	0	0	0	8	235	AA	0.99257	0.927549	0			3	60	99	0	0	6.706495	37	60	1097	79		0.075	0.934492
ITSN2	50618	__UNKNOWN__	__UNKNOWN__	2	24427965	24427965	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24427965A>G	ENST00000355123.4	-	38	5206				ITSN2_ENST00000361999.3_Intron	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	NA		NA			endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					gcagtgagccaagatcgtgcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399	50618		Rho guanine nucleotide exchange factors, EF-hand domain containing	6184	protein-coding gene	gene with protein product	SH3 domain protein 1B, SH3P18-like WASP associated protein	604464	SH3 domain protein 1B	SH3D1B	NA	10922467, 11748279	Standard	NM_006277	NM_006277	NA	Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.4762+117T>C	chr2.hg19:g.24427965A>G		NA	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	hg19	CCDS1710.2	0.02	1.923757	GCCxAGA	COVERED																																																																																			NOVEL	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207620.2	7	3.005221	KEEP	0	0	0	10	271	AA	0.992708	0.966863	0		-	6	60	188	0	0	13.872215	41	60	1232	83	ENST00000355123.4	0.12766	0.973965
ITSN2	50618	__UNKNOWN__	__UNKNOWN__	2	24524564	24524564	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24524564A>T	ENST00000355123.4	-	10	1439				ITSN2_ENST00000406921.3_Intron|ITSN2_ENST00000361999.3_Intron	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	NA		NA			endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ctggctaattatttttatttt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399	50618		Rho guanine nucleotide exchange factors, EF-hand domain containing	6184	protein-coding gene	gene with protein product	SH3 domain protein 1B, SH3P18-like WASP associated protein	604464	SH3 domain protein 1B	SH3D1B	NA	10922467, 11748279	Standard	NM_006277	NM_006277	NA	Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.995+269T>A	chr2.hg19:g.24524564A>T		NA	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	hg19	CCDS1710.2	0.02	-0.306893	ATTxTTT	COVERED																																																																																			NOVEL	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207620.2	14	3.604076	KEEP	0	0	0	12	305	AA	0.993634	0.795151	0		-	4	60	109	0	1	7.69753	26	60	736	63	ENST00000355123.4	0.133333	0.800245
ITSN2	50618	__UNKNOWN__	__UNKNOWN__	2	24548250	24548250	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24548250A>G	ENST00000355123.4	-	2	475				ITSN2_ENST00000407704.1_Intron|ITSN2_ENST00000406921.3_Intron|ITSN2_ENST00000361999.3_Intron	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	NA		NA			endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ctacactccaacctgggcaac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399	50618		Rho guanine nucleotide exchange factors, EF-hand domain containing	6184	protein-coding gene	gene with protein product	SH3 domain protein 1B, SH3P18-like WASP associated protein	604464	SH3 domain protein 1B	SH3D1B	NA	10922467, 11748279	Standard	NM_006277	NM_006277	NA	Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.31+2670T>C	chr2.hg19:g.24548250A>G		NA	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	hg19	CCDS1710.2	0.02	-0.175397	CCAxCCT	COVERED																																																																																			NOVEL	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207620.2	3	2.707051	KEEP	0	0	0	9	251	AA	0.99254	0.384517	0		-	3	60	97	0	0	7.461147	17	60	494	41	ENST00000355123.4	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24618828	24618828	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24618828G>C			NA	NA				ITSN2 (35245 upstream) : NCOA1 (95972 downstream)						NA		NA									NA						tttgggaggcggaggcaggtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24618828G>C		NA		hg19		0.02	-0.140365	GGCxGAG	COVERED																																																																																			NOVEL					0			9	3.61065	KEEP	4	0	0	12	370	GG	0.994391	0.290363	0			4	60	138	0	0	12.071062	10	60	341	51		0.285714	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24636689	24636689	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24636689T>C			NA	NA				ITSN2 (53106 upstream) : NCOA1 (78111 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24636689T>C		NA		hg19		0.02	-0.324097	ATCxCAG	COVERED																																																																																			NOVEL					0			12	2.405824	KEEP	1	0	0	8	216	TT	0.99257	0.829507	0			6	60	183	0	0	14.154817	30	60	910	66		0.166667	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24660702	24660702	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24660702T>C			NA	NA				ITSN2 (77119 upstream) : NCOA1 (54098 downstream)						NA		NA									NA						gtctcgaacttctgacctcgt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24660702T>C		NA		hg19		0.02	-0.175414	ACTxCTG	COVERED																																																																																			NOVEL					0			11	3.307831	KEEP	2	0	0	11	296	TT	0.992708	0.384582	0			3	60	94	0	0	7.572423	12	60	350	47		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24708977	24708977	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24708977C>T			NA	NA				ITSN2 (125394 upstream) : NCOA1 (5823 downstream)						NA		NA									NA						AAAAATCAggctgggtgcggt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24708977C>T		NA		hg19		0.02	-0.271946	AGGxTGG	COVERED																																																																																			NOVEL					0			15	2.708091	KEEP	0	0	0	9	278	CC	0.99254	0.711964	0			4	60	118	0	0	8.7236	24	60	829	57		0.142857	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	24711960	24711960	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24711960C>T			NA	NA				ITSN2 (128377 upstream) : NCOA1 (2840 downstream)						NA		NA									NA						gaggcagaggctgcagtgagc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.24711960C>T		NA		hg19		0.02	-0.219265	AGGxTGC	UNCOVERED																																																																																			NOVEL					0			12	2.407277	KEEP	6	0	0	8	248	CC	0	0	0			4	60	103	0	0	7.681778	18	60	595	46		0.181818	0.552887
NCOA1	8648	__UNKNOWN__	__UNKNOWN__	2	24968310	24968310	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:24968310C>T	ENST00000406961.1	+	19	4358				NCOA1_ENST00000348332.3_Intron|NCOA1_ENST00000405141.1_Intron|NCOA1_ENST00000288599.5_Intron|NCOA1_ENST00000538539.1_Intron|NCOA1_ENST00000395856.3_Intron|NCOA1_ENST00000407230.1_Intron			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	NA		NA			androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ggattacaggcgtgagccacc	0.468		NA	T	PAX3	alveolar rhadomyosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676	8648		Chromatin-modifying enzymes / K-acetyltransferases, Basic helix-loop-helix proteins	7668	protein-coding gene	gene with protein product		602691			NA	7481822, 9575154	Standard	NM_147223	XM_005264625	NA	Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3706+3255C>T	chr2.hg19:g.24968310C>T		NA	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	hg19	CCDS1712.1	0.02	-0.245592	AGGxGTG	COVERED																																																																																			NOVEL	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246852.3	14	3.009015	KEEP	10	0	0	10	309	CC	0.99257	0.636582	0		+	3	60	92	0	0	6.706173	21	60	673	68	ENST00000406961.1	0.125	0.641347
CENPO	79172	__UNKNOWN__	__UNKNOWN__	2	25034619	25034619	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25034619T>C	ENST00000380834.2	+	4	641				CENPO_ENST00000473706.1_Intron|CENPO_ENST00000260662.1_Intron			Q9BU64	CENPO_HUMAN	centromere protein O	NA		NA			CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					cgtgagccactgcgcccggcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092	79172			28152	protein-coding gene	gene with protein product		611504			NA	16622420, 16622419	Standard	NM_024322	NM_024322	NA	Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.217-2626T>C	chr2.hg19:g.25034619T>C		NA	B2RDC0|D6W536|Q53T55|Q96JV3	hg19	CCDS1714.1	0.02	-0.420998	CACxGCG	COVERED																																																																																			NOVEL	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246856.2	18	3.007957	KEEP	2	0	0	10	281	TT	0.992708	0.941486	0		+	3	60	103	0	0	7.140039	36	60	1072	88	ENST00000380834.2	0.076923	0.948402
CENPO	79172	__UNKNOWN__	__UNKNOWN__	2	25034678	25034678	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25034678T>G	ENST00000380834.2	+	4	641				CENPO_ENST00000473706.1_Intron|CENPO_ENST00000260662.1_Intron			Q9BU64	CENPO_HUMAN	centromere protein O	NA		NA			CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					tgttggccagtctggtcttga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092	79172			28152	protein-coding gene	gene with protein product		611504			NA	16622420, 16622419	Standard	NM_024322	NM_024322	NA	Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.217-2567T>G	chr2.hg19:g.25034678T>G		NA	B2RDC0|D6W536|Q53T55|Q96JV3	hg19	CCDS1714.1	0.02	-0.306979	CAGxCTG	COVERED																																																																																			NOVEL	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246856.2	13	2.706418	KEEP	0	0	0	9	241	AT	0.992708	0.79441	0		+	3	60	104	0	0	7.466983	30	60	900	60	ENST00000380834.2	0.090909	0.800245
DNAJC27	51277	__UNKNOWN__	__UNKNOWN__	2	25188283	25188283	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25188283T>C	ENST00000264711.2	-	2	360				DNAJC27_ENST00000534855.1_Intron|DNAJC27_ENST00000468467.1_Intron	NM_001198559.1|NM_016544.2	NP_001185488.1|NP_057628.1	Q9NZQ0	DJC27_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 27	NA		NA			small GTPase mediated signal transduction (GO:0007264)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						tgccaccacgtccggctaatt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1716.1, CCDS74493.1	2p23.3	2011-09-02	2008-08-20	2008-08-20	ENSG00000115137	ENSG00000115137	51277		Heat shock proteins / DNAJ (HSP40)	30290	protein-coding gene	gene with protein product		613527	rab and DnaJ domain containing	RBJ	NA	14980719	Standard	NM_016544	NM_016544	NA	Approved	RabJS	uc002rft.2	Q9NZQ0	OTTHUMG00000125524	ENST00000264711.2:c.170+1796A>G	chr2.hg19:g.25188283T>C		NA	Q5JV88|Q86Y24	hg19	CCDS1716.1	0.02	-0.175395	ACGxCCG	COVERED																																																																																			NOVEL	DNAJC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246855.3	7	3.005451	KEEP	2	0	0	10	266	TT	0.99254	0.384517	0		-	3	60	102	0	0	8.033473	16	60	455	39	ENST00000264711.2	0.157895	0.387407
EFR3B	22979	__UNKNOWN__	__UNKNOWN__	2	25339400	25339400	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25339400T>G	ENST00000403714.3	+	5	546				EFR3B_ENST00000405108.1_Intron|EFR3B_ENST00000402191.1_Intron|EFR3B_ENST00000401432.3_Intron	NM_014971.1	NP_055786.1	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B (S. cerevisiae)	NA		NA								endometrium(1)	1						ggctgaggcatgagaattgct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023170	CCDS46231.1	2p24.1	2008-02-05	2007-11-14	2007-11-14	ENSG00000084710	ENSG00000084710	22979			29155	protein-coding gene	gene with protein product		NA	KIAA0953	KIAA0953	NA	10231032	Standard	NM_014971	NM_014971	NA	Approved	FLJ37871	uc010eyh.3	Q9Y2G0	OTTHUMG00000151988	ENST00000403714.3:c.364-5142T>G	chr2.hg19:g.25339400T>G		NA	B7WPL8|Q86XU6	hg19	CCDS46231.1	0.02	-0.052632	GCAxGAG	UNCOVERED																																																																																			NOVEL	EFR3B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324808.1	6	2.405899	KEEP	0	0	0	8	220	TT	0.99257	0.043461	0		+	2	60	69	0	0	6.392887	3	60	93	19	ENST00000403714.3	0.4	0.043787
EFR3B	22979	__UNKNOWN__	__UNKNOWN__	2	25351593	25351593	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25351593T>C	ENST00000403714.3	+	6	818				EFR3B_ENST00000405108.1_Intron|EFR3B_ENST00000402191.1_Intron|EFR3B_ENST00000401432.3_Intron	NM_014971.1	NP_055786.1	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B (S. cerevisiae)	NA		NA								endometrium(1)	1						tttgggaggctgaggcgggca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023170	CCDS46231.1	2p24.1	2008-02-05	2007-11-14	2007-11-14	ENSG00000084710	ENSG00000084710	22979			29155	protein-coding gene	gene with protein product		NA	KIAA0953	KIAA0953	NA	10231032	Standard	NM_014971	NM_014971	NA	Approved	FLJ37871	uc010eyh.3	Q9Y2G0	OTTHUMG00000151988	ENST00000403714.3:c.635+392T>C	chr2.hg19:g.25351593T>C		NA	B7WPL8|Q86XU6	hg19	CCDS46231.1	0.02	-0.192969	GGCxGAG	COVERED																																																																																			NOVEL	EFR3B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324808.1	5	3.007866	KEEP	3	0	0	10	281	TT	0.99254	0.454342	0		+	3	60	92	0	0	6.892639	18	60	555	48	ENST00000403714.3	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	25574478	25574478	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25574478T>C			NA	NA				DNMT3A (9019 upstream) : AC012074.2 (17563 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.25574478T>C		NA		hg19		0.02	-0.263116	TCAxGCC	COVERED																																																																																			NOVEL					0			10	3.007681	KEEP	4	0	0	10	278	TT	0.99257	0.688515	0			3	60	104	0	0	7.742288	24	60	704	62		0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	25579917	25579917	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25579917G>A			NA	NA				DNMT3A (14458 upstream) : AC012074.2 (12124 downstream)						NA		NA									NA						atgcctggctgatttttgtat	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.25579917G>A		NA		hg19		0.02	-0.087705	GCTxATT	UNCOVERED																																																																																			NOVEL					0			3	3.009282	KEEP	0	0	0	10	318	GG	0.992708	0.098994	0			3	60	90	0	1	8.132531	5	60	161	26		0.375	0.099721
DTNB	1838	__UNKNOWN__	__UNKNOWN__	2	25766199	25766199	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25766199C>G	ENST00000406818.3	-	9	1126				DTNB_ENST00000545439.1_Intron|DTNB_ENST00000407661.3_Intron|DTNB_ENST00000496972.2_Intron|DTNB_ENST00000288642.8_Intron|DTNB_ENST00000404103.3_Intron|DTNB_ENST00000407186.1_Intron|DTNB_ENST00000407038.3_Intron|DTNB_ENST00000405222.1_Intron	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	NA		NA				cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttttgagacacagtcttgctc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101	1838			3058	protein-coding gene	gene with protein product		602415			NA	9419360	Standard	NM_033147	NM_021907	NA	Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.877-11733G>C	chr2.hg19:g.25766199C>G		NA	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	hg19	CCDS46237.1	0.02	-0.148851	ACAxAGT	COVERED																																																																																			NOVEL	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325361.1	12	2.705975	KEEP	0	0	0	9	267	CC	0.992708	0.289872	0		-	3	60	96	0	0	7.77544	12	60	373	36	ENST00000406818.3	0.2	0.292001
DTNB	1838	__UNKNOWN__	__UNKNOWN__	2	25776447	25776447	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25776447A>T	ENST00000406818.3	-	9	1126				DTNB_ENST00000545439.1_Intron|DTNB_ENST00000407661.3_Intron|DTNB_ENST00000496972.2_Intron|DTNB_ENST00000288642.8_Intron|DTNB_ENST00000404103.3_Intron|DTNB_ENST00000407186.1_Intron|DTNB_ENST00000407038.3_Intron|DTNB_ENST00000405222.1_Intron	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	NA		NA				cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tctctactaaaaatacaaaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101	1838			3058	protein-coding gene	gene with protein product		602415			NA	9419360	Standard	NM_033147	NM_021907	NA	Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.877-21981T>A	chr2.hg19:g.25776447A>T		NA	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	hg19	CCDS46237.1	0.02	-0.140318	TAAxAAT	COVERED																																																																																			NOVEL	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325361.1	7	3.006515	KEEP	5	0	0	10	262	AA	0.99257	0.259026	0		-	3	46	83	1	0	6.682313	10	60	293	38	ENST00000406818.3	0.230769	0.260965
DTNB	1838	__UNKNOWN__	__UNKNOWN__	2	25875571	25875571	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:25875571G>A	ENST00000406818.3	-	2	249				DTNB_ENST00000545439.1_Intron|DTNB_ENST00000407661.3_Intron|DTNB_ENST00000288642.8_Intron|DTNB_ENST00000404103.3_Intron|DTNB_ENST00000407186.1_Intron|DTNB_ENST00000407038.3_Intron|DTNB_ENST00000405222.1_Intron	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	NA		NA				cytoplasm (GO:0005737)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGTATAATTCGACAATTCAAT	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													95	89	91			NA	NA	2		NA											NA				25875571		1885	4100	5985	SO:0001627	intron_variant			AF022728	CCDS46233.1, CCDS46234.1, CCDS46235.1, CCDS46236.1, CCDS46237.1, CCDS58702.1, CCDS74496.1	2p23.2	2008-05-15			ENSG00000138101	ENSG00000138101	1838			3058	protein-coding gene	gene with protein product		602415			NA	9419360	Standard	NM_033147	NM_021907	NA	Approved		uc002rgh.4	O60941	OTTHUMG00000152129	ENST00000406818.3:c.1-41C>T	chr2.hg19:g.25875571G>A		NA	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	hg19	CCDS46237.1	0.02	2.510942	TTCxACA	COVERED																																																																																			NOVEL	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325361.1	4	9.62615	KEEP	0	0	0	32	922	GG	0.999997	0.999997	0		-	7	60	206	0	0	12.071872	125	60	3990	228	ENST00000406818.3	0.05303	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	26129227	26129227	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26129227C>G			NA	NA				ASXL2 (27842 upstream) : KIF3C (20243 downstream)						NA		NA									NA						gattacaggtctgagccacca	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.26129227C>G		NA		hg19		0.02	-0.184222	GGTxTGA	COVERED																																																																																			NOVEL					0			7	3.008614	KEEP	1	0	0	10	300	CC	0.99254	0.454342	0			4	60	131	0	0	10.980696	13	60	442	48		0.235294	0.457757
KIF3C	3797	__UNKNOWN__	__UNKNOWN__	2	26165528	26165528	__UNKNOWN__	Intron	SNP	C	C	T	rs7578393	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26165528C>T	ENST00000496378.1	-	1	131				KIF3C_ENST00000405914.1_Intron|KIF3C_ENST00000264712.3_Intron			O14782	KIF3C_HUMAN	kinesin family member 3C	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					atctgcccgccttggcctccc	0.478		NA											C|||	2566	0.51238	0.5113	0.5216	5008	,	,	NA	14232	0.0992	NA	0.7903	False	NA	,,,	NA	NA	NA	2504	0.6472	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731	3797		Kinesins	6321	protein-coding gene	gene with protein product		602845			NA	9480755	Standard		NM_002254	NA	Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000496378.1:c.165+9129G>A	chr2.hg19:g.26165528C>T		NA	O43544|Q4ZG18|Q53SX5|Q562F7	hg19		0.02	-0.175449	CGCxTTG	UNCOVERED																																																																																			NOVEL	KIF3C-007	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000325601.1	6	3.611081	KEEP	11	0	0	12	381	CC	0	0	0		-	4	60	125	0	0	10.268069	14	60	485	58	ENST00000496378.1	0.222222	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	26222054	26222054	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26222054T>C			NA	NA				KIF3C (16436 upstream) : AC013449.1 (29019 downstream)						NA		NA									NA						tctttctttctttccttcctt	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.26222054T>C		NA		hg19		0.02	-0.070147	TTCxTTC	UNCOVERED																																																																																			NOVEL					0			3	2.405849	KEEP	0	0	0	8	220	TT	0.99257	0.053735	0			3	60	83	0	0	7.653337	4	60	124	18		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	26231276	26231276	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26231276A>G			NA	NA				KIF3C (25658 upstream) : AC013449.1 (19797 downstream)						NA		NA									NA						ccagcactttaagaggccgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.26231276A>G		NA		hg19		0.02	-0.271872	TTTxAGA	COVERED																																																																																			NOVEL					0			9	2.706478	KEEP	0	0	0	9	244	AA	0.99254	0.711964	0			3	60	101	0	1	7.344235	26	60	752	60		0.103448	0.717315
RAB10	10890	__UNKNOWN__	__UNKNOWN__	2	26289926	26289926	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26289926T>C	ENST00000264710.4	+	2	626					NM_016131.4	NP_057215.3	P61026	RAB10_HUMAN	RAB10, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|axonogenesis (GO:0007409)|basolateral protein localization (GO:0061467)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum tubular network organization (GO:0071786)|endosomal transport (GO:0016197)|establishment of neuroblast polarity (GO:0045200)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|establishment of protein localization to membrane (GO:0090150)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi to plasma membrane transport (GO:0006893)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|polarized epithelial cell differentiation (GO:0030859)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum tubular network (GO:0071782)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|insulin-responsive compartment (GO:0032593)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					gctgggattataggtgtgagc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF106681	CCDS1720.1	2p23.3	2008-05-21			ENSG00000084733	ENSG00000084733	10890		RAB, member RAS oncogene	9759	protein-coding gene	gene with protein product	ras-related GTP-binding protein	612672			NA	7688123	Standard	NM_016131	NM_016131	NA	Approved		uc002rgv.3	P61026	OTTHUMG00000094796	ENST00000264710.4:c.128-31605T>C	chr2.hg19:g.26289926T>C		NA	D6W538|O88386|Q6IA52|Q9D7X6|Q9H0T3	hg19	CCDS1720.1	0.02	-0.245543	TTAxAGG	COVERED																																																																																			NOVEL	RAB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211610.1	15	4.810382	KEEP	1	0	0	16	414	TT	0.997832	0.639957	0		+	4	60	140	0	0	11.136211	21	60	591	60	ENST00000264710.4	0.16	0.641347
RAB10	10890	__UNKNOWN__	__UNKNOWN__	2	26345264	26345264	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26345264A>G	ENST00000264710.4	+	4	826				RAB10_ENST00000462003.1_Intron	NM_016131.4	NP_057215.3	P61026	RAB10_HUMAN	RAB10, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|axonogenesis (GO:0007409)|basolateral protein localization (GO:0061467)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum tubular network organization (GO:0071786)|endosomal transport (GO:0016197)|establishment of neuroblast polarity (GO:0045200)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|establishment of protein localization to membrane (GO:0090150)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi to plasma membrane transport (GO:0006893)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|polarized epithelial cell differentiation (GO:0030859)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum tubular network (GO:0071782)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|insulin-responsive compartment (GO:0032593)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ttgggaggccaaggcgggcag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF106681	CCDS1720.1	2p23.3	2008-05-21			ENSG00000084733	ENSG00000084733	10890		RAB, member RAS oncogene	9759	protein-coding gene	gene with protein product	ras-related GTP-binding protein	612672			NA	7688123	Standard	NM_016131	NM_016131	NA	Approved		uc002rgv.3	P61026	OTTHUMG00000094796	ENST00000264710.4:c.328-4749A>G	chr2.hg19:g.26345264A>G		NA	D6W538|O88386|Q6IA52|Q9D7X6|Q9H0T3	hg19	CCDS1720.1	0.02	-0.166628	GCCxAGG	COVERED																																																																																			NOVEL	RAB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211610.1	7	4.209563	KEEP	5	0	0	14	380	AA	0.993634	0.351693	0		+	3	60	92	0	0	7.110515	15	60	442	55	ENST00000264710.4	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	26361137	26361137	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26361137C>T			NA	NA				RAB10 (814 upstream) : GAREML (34822 downstream)						NA		NA									NA						gatgaaaccccgtctctacta	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.26361137C>T		NA		hg19		0.02	-0.166643	CCCxGTC	COVERED																																																																																			NOVEL					0			3	2.405874	KEEP	3	0	0	8	220	CC	0.99257	0.351317	0			3	60	84	0	0	6.311108	15	60	463	37		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	26394935	26394935	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26394935C>T			NA	NA				RAB10 (34612 upstream) : GAREML (1024 downstream)						NA		NA									NA						tgcagtgagccgagatcgcgc	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.26394935C>T		NA		hg19		0.02	-0.280707	AGCxGAG	COVERED																																																																																			NOVEL					0			4	3.610081	KEEP	0	0	0	12	349	CC	0.993634	0.734962	0			4	60	124	0	0	9.194379	26	60	850	53		0.133333	0.739671
GAREML	150946	__UNKNOWN__	__UNKNOWN__	2	26404838	26404838	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26404838C>T	ENST00000407684.1	+	0	1254				GAREML_ENST00000401533.2_Intron	NM_001191033.1	NP_001177962.1	Q75VX8	GAREL_HUMAN	GRB2 associated, regulator of MAPK1-like	NA		NA				extracellular vesicular exosome (GO:0070062)					NA						acagcaagaccctgtctcaaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK090454, AB015349, AB124552	CCDS54336.1, CCDS54337.1	2p23.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000157833	ENSG00000157833	150946			27172	protein-coding gene	gene with protein product		NA	family with sequence similarity 59, member B	FAM59B	NA		Standard	NM_001168241	NM_001168241	NA	Approved	KIAA2038, FLJ00375	uc002rgw.2	Q75VX8	OTTHUMG00000151935	ENST00000407684.1:c.-503C>T	chr2.hg19:g.26404838C>T		NA	B5MC97|B7WNK9|Q8NF27|Q9UIK8	hg19	CCDS54337.1	0.02	1.19038	GACxCTG	COVERED																																																																																			NOVEL	GAREML-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324499.1	23	6.686712	KEEP	0	2	56	42	1305	CC	1	0.999218	0		+	6	60	180	0	0	11.79083	69	60	2369	180	ENST00000407684.1	0.08	0.999218
CIB4	130106	__UNKNOWN__	__UNKNOWN__	2	26811940	26811940	__UNKNOWN__	Intron	SNP	C	C	T	rs375837668|rs66688159|rs12470658	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26811940C>T	ENST00000288861.4	-	5	382				CIB4_ENST00000405346.3_Intron	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	NA		NA					calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cttcctcttcctcttcttctt	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884	130106		EF-hand domain containing	33703	protein-coding gene	gene with protein product		610646			NA	15574431	Standard		NM_001029881	NA	Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.329-5174G>A	chr2.hg19:g.26811940C>T		NA	B2RU18	hg19	CCDS33160.1	0.02	-0.140352	TTCxTCT	UNCOVERED																																																																																			NOVEL	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324709.1	11	3.610713	KEEP	13	0	0	12	366	CC	0	0	0		-	3	40	90	1	0	7.381861	10	48	332	50	ENST00000288861.4	0.230769	0.260965
CIB4	130106	__UNKNOWN__	__UNKNOWN__	2	26811985	26811985	__UNKNOWN__	Intron	SNP	T	T	C	rs190700295		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26811985T>C	ENST00000288861.4	-	5	382				CIB4_ENST00000405346.3_Intron	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	NA		NA					calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cctcttcttcttcttcttctt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884	130106		EF-hand domain containing	33703	protein-coding gene	gene with protein product		610646			NA	15574431	Standard		NM_001029881	NA	Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.329-5219A>G	chr2.hg19:g.26811985T>C		NA	B2RU18	hg19	CCDS33160.1	0.02	-0.157871	TTCxTCT	UNCOVERED																																																																																			NOVEL	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324709.1	6	2.405851	KEEP	3	0	0	8	216	TT	0	0	0		-	3	60	99	1	0	7.978926	13	60	383	34	ENST00000288861.4	0.1875	0.322807
KCNK3	3777	__UNKNOWN__	__UNKNOWN__	2	26952682	26952682	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:26952682T>C	ENST00000302909.3	+	0	2556					NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	NA		NA			brain development (GO:0007420)|cellular response to hypoxia (GO:0071456)|cellular response to zinc ion (GO:0071294)|cochlea development (GO:0090102)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)|open rectifier potassium channel activity (GO:0005252)|potassium channel activity (GO:0005267)|potassium ion leak channel activity (GO:0022841)|S100 protein binding (GO:0044548)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Doxapram(DB00561)|Halothane(DB01159)	ccagcctgggtgacagggcaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(80;1457 1631 27100 45946)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF006823	CCDS1727.1	2p23	2012-03-07			ENSG00000171303	ENSG00000171303	3777		Potassium channels, Voltage-gated ion channels / Potassium channels, Two-P	6278	protein-coding gene	gene with protein product		603220			NA	9312005, 9721223, 16382106	Standard	NM_002246	NM_002246	NA	Approved	K2p3.1, TASK, TASK-1	uc002rhn.2	O14649	OTTHUMG00000125530	ENST00000302909.3:c.*1246T>C	chr2.hg19:g.26952682T>C		NA	Q53SU2	hg19	CCDS1727.1	0.02	-0.280424	GGGxGAC	COVERED																																																																																			NOVEL	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246861.2	2	2.40354	KEEP	0	0	0	8	194	AT	0.99254	0.734154	0		+	3	60	92	0	0	6.893732	18	60	473	51	ENST00000302909.3	0.142857	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	27052589	27052589	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27052589A>G			NA	NA				CENPA (35128 upstream) : DPYSL5 (18379 downstream)						NA		NA									NA						tgcaacctctacctcccaggt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.27052589A>G		NA		hg19		0.02	-0.122702	TCTxCCT	COVERED																																																																																			NOVEL					0			9	3.899891	KEEP	1	0	0	13	319	AA	0.994391	0.19521	0			3	60	103	0	0	8.68331	10	60	270	37		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	27251888	27251888	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27251888T>C			NA	NA				MAPRE3 (1824 upstream) : TMEM214 (3933 downstream)						NA		NA									NA						agttggagactagcctggaca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.27251888T>C		NA		hg19		0.02	-0.184189	GACxAGC	COVERED																																																																																			NOVEL					0			14	2.706956	KEEP	0	0	0	9	249	TT	0.99254	0.420319	0			3	60	98	0	0	7.633453	16	60	480	38		0.157895	0.423478
AGBL5	60509	__UNKNOWN__	__UNKNOWN__	2	27280686	27280686	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27280686A>G	ENST00000360131.4	+	9	1830				AGBL5_ENST00000323064.8_Intron	NM_021831.5	NP_068603.4	Q8NDL9	CBPC5_HUMAN	ATP/GTP binding protein-like 5	NA		NA			protein branching point deglutamylation (GO:0035611)|protein deglutamylation (GO:0035608)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|pancreas(1)|prostate(2)|skin(1)	28	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					gctcatgcctataatcccagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007415	CCDS1732.3, CCDS42665.1	2p23.3	2014-06-23			ENSG00000084693	ENSG00000084693	60509			26147	protein-coding gene	gene with protein product	cytosolic carboxypeptidase 5	615900			NA	24022482	Standard	NM_021831	NM_001035507	NA	Approved	FLJ21839, CCP5	uc002rie.3	Q8NDL9	OTTHUMG00000128406	ENST00000360131.4:c.1671+380A>G	chr2.hg19:g.27280686A>G		NA	A2VDI7|B7WPG9|B7Z7I7|D6W548|Q53SW0|Q53SZ0|Q96IK8|Q9H6V0|Q9H8P8	hg19	CCDS1732.3	0.02	-0.166627	CCTxTAA	COVERED																																																																																			NOVEL	AGBL5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309033.1	6	2.707096	KEEP	3	0	0	9	251	AA	0.99257	0.351317	0		+	3	60	96	0	0	7.592443	14	60	406	43	ENST00000360131.4	0.176471	0.353947
CGREF1	10669	__UNKNOWN__	__UNKNOWN__	2	27326469	27326469	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27326469T>C	ENST00000402394.1	-	2	349				CGREF1_ENST00000312734.4_Intron|CGREF1_ENST00000260595.5_Intron|CGREF1_ENST00000402550.1_Intron|CGREF1_ENST00000452318.2_Intron|CGREF1_ENST00000404694.3_Intron|CGREF1_ENST00000405600.1_Intron	NM_006569.5	NP_006560.3	Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	NA		NA			cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ctcgaactcctgacctcaggt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028	10669		EF-hand domain containing	16962	protein-coding gene	gene with protein product		606137			NA	8968090	Standard	NM_006569	NM_006569	NA	Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000402394.1:c.80+685A>G	chr2.hg19:g.27326469T>C		NA	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	hg19	CCDS33162.2	0.02	-0.192886	TCCxGAC	COVERED																																																																																			NOVEL	CGREF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324823.1	5	3.007856	KEEP	3	0	0	10	279	AT	0.99254	0.454342	0		-	3	46	99	0	0	7.592778	18	60	516	48	ENST00000402394.1	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	27413266	27413266	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27413266A>G			NA	NA				TCF23 (36888 upstream) : SLC5A6 (9188 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.27413266A>G		NA		hg19		0.02	-0.184196	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			4	2.406433	KEEP	2	0	0	8	227	AA	0	0	0			4	60	139	0	0	11.462848	16	60	486	48		0.2	0.423478
TRIM54	57159	__UNKNOWN__	__UNKNOWN__	2	27506754	27506754	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27506754A>G	ENST00000380075.2	+	1	508				TRIM54_ENST00000296098.4_Intron	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	NA		NA			cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|negative regulation of microtubule depolymerization (GO:0007026)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tgtaatcccaacactttggga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ291714	CCDS1745.2, CCDS1746.2	2p23.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000138100	ENSG00000138100	57159		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	16008	protein-coding gene	gene with protein product		606474	ring finger protein 30, tripartite motif-containing 54	RNF30	NA	11243782	Standard	NM_187841	NM_032546	NA	Approved	MURF, MURF-3	uc002rjn.3	Q9BYV2	OTTHUMG00000097078	ENST00000380075.2:c.168+987A>G	chr2.hg19:g.27506754A>G		NA	A5D8T7|Q53SY4|Q9BYV3	hg19	CCDS1746.2	0.02	-0.245502	CCAxCAC	COVERED																																																																																			NOVEL	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214199.2	8	2.404227	KEEP	0	0	0	8	210	AA	0.99257	0.636582	0		+	3	60	103	0	0	7.805882	21	60	600	49	ENST00000380075.2	0.125	0.641347
GTF3C2	2976	__UNKNOWN__	__UNKNOWN__	2	27570863	27570863	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27570863T>C	ENST00000359541.2	-	2	406				GTF3C2_ENST00000264720.3_Intron			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	NA		NA			5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					cagggccaggtgcagtggctc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207	2976		General transcription factors, WD repeat domain containing	4665	protein-coding gene	gene with protein product		604883	general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)		NA	7729686	Standard		NM_001521	NA	Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.24-4418A>G	chr2.hg19:g.27570863T>C		NA	D6W557|Q16632|Q9BWI7	hg19	CCDS1749.1	0.02	-0.315678	AGGxGCA	COVERED																																																																																			NOVEL	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215028.2	10	4.210282	KEEP	0	0	0	14	381	TT	0.99649	0.815592	0		-	4	60	138	0	1	10.362215	30	60	847	72	ENST00000359541.2	0.117647	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	27647390	27647390	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27647390T>C			NA	NA				PPM1G (14836 upstream) : NRBP1 (3266 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.27647390T>C		NA		hg19		0.02	-0.342035	AGGxGTG	COVERED																																																																																			NOVEL					0			17	3.437392	KEEP	4	1	33	23	610	TT	0.999892	0.865652	0			3	60	95	0	0	6.488776	32	60	942	98		0.085714	0.865745
NRBP1	29959	__UNKNOWN__	__UNKNOWN__	2	27658131	27658131	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27658131G>A	ENST00000233557.3	+	8	1493				NRBP1_ENST00000379852.3_Intron|NRBP1_ENST00000379863.3_Intron			Q9UHY1	NRBP_HUMAN	nuclear receptor binding protein 1	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|gene expression (GO:0010467)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell projection (GO:0042995)|endomembrane system (GO:0012505)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Acute lymphoblastic leukemia(172;0.155)					GGGGAGCCTCGGGAATTTGGG	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													40	35	36			NA	NA	2		NA											NA				27658131		2203	4300	6503	SO:0001627	intron_variant			AF113249	CCDS1753.1	2p23	2008-02-05	2005-12-22	2005-12-22	ENSG00000115216	ENSG00000115216	29959			7993	protein-coding gene	gene with protein product		606010	nuclear receptor binding protein	NRBP	NA	10843813, 11956649	Standard	NM_013392	NM_013392	NA	Approved	BCON3, MUDPNP, MADM	uc002rkp.3	Q9UHY1	OTTHUMG00000097789	ENST00000233557.3:c.661+37G>A	chr2.hg19:g.27658131G>A		NA	B3KV40|D6W558|Q53FZ5|Q96SU3	hg19	CCDS1753.1	0.02	1.236717	CTCxGGA	COVERED																																																																																			NOVEL	NRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215033.1	7	6.017094	KEEP	0	0	0	20	599	GG	0.999863	0.99954	0		+	6	60	182	0	0	11.621097	80	60	2619	154	ENST00000233557.3	0.069767	0.999678
IFT172	26160	__UNKNOWN__	__UNKNOWN__	2	27667758	27667758	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27667758C>T	ENST00000260570.3	-	47	5264				KRTCAP3_ENST00000543753.1_Intron	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	NA		NA			bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					tcaggtgatccgcccaccttg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002	26160		Intraflagellar transport homologs, WD repeat domain containing	30391	protein-coding gene	gene with protein product	wimple homolog	607386	intraflagellar transport 172 homolog (Chlamydomonas)		NA	10788441, 10574461, 24140113	Standard	NM_015662	XM_005264254	NA	Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.5160+122G>A	chr2.hg19:g.27667758C>T		NA	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	hg19	CCDS1755.1	0.02	1.429723	ATCxGCC	COVERED																																																																																			NOVEL	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250213.2	5	5.648228	KEEP	3	1	23	27	792	CC	0.999997	0.9937	0		-	13	60	383	0	0	31.326434	43	60	1400	110	ENST00000260570.3	0.232143	0.993703
IFT172	26160	__UNKNOWN__	__UNKNOWN__	2	27698765	27698765	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27698765G>C	ENST00000260570.3	-	14	1515				IFT172_ENST00000416524.2_Intron|IFT172_ENST00000359466.6_Intron	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	NA		NA			bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					tcccaaagtggtgggattaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002	26160		Intraflagellar transport homologs, WD repeat domain containing	30391	protein-coding gene	gene with protein product	wimple homolog	607386	intraflagellar transport 172 homolog (Chlamydomonas)		NA	10788441, 10574461, 24140113	Standard	NM_015662	XM_005264254	NA	Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.1411+742C>G	chr2.hg19:g.27698765G>C		NA	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	hg19	CCDS1755.1	0.02	-0.307043	GTGxTGG	COVERED																																																																																			NOVEL	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250213.2	10	2.406549	KEEP	2	0	0	8	233	GG	0.99257	0.829507	0		-	5	60	166	0	0	12.964087	27	60	937	70	ENST00000260570.3	0.15625	0.835716
IFT172	26160	__UNKNOWN__	__UNKNOWN__	2	27707196	27707196	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27707196T>C	ENST00000260570.3	-	4	400				IFT172_ENST00000416524.2_Intron|IFT172_ENST00000359466.6_Intron	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	NA		NA			bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					tggtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													47	41	42			NA	NA	2		NA											NA				27707196		692	1591	2283	SO:0001627	intron_variant			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002	26160		Intraflagellar transport homologs, WD repeat domain containing	30391	protein-coding gene	gene with protein product	wimple homolog	607386	intraflagellar transport 172 homolog (Chlamydomonas)		NA	10788441, 10574461, 24140113	Standard	NM_015662	XM_005264254	NA	Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.297-63A>G	chr2.hg19:g.27707196T>C		NA	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	hg19	CCDS1755.1	0.02	1.648803	TCAxGCC	COVERED																																																																																			NOVEL	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250213.2	7	2.43686	KEEP	1	1	25	17	458	TT	0.99986	0.997758	0		-	5	60	165	0	0	11.166273	62	60	1820	114	ENST00000260570.3	0.074627	0.997898
SUPT7L	9913	__UNKNOWN__	__UNKNOWN__	2	27874742	27874742	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27874742A>G	ENST00000337768.5	-	0	3424					NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	NA		NA			chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					ggccaggtgcagtggctcacg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760	9913			30632	protein-coding gene	gene with protein product		612762			NA	9872452, 11564863	Standard	NM_014860	NM_001282732	NA	Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.*1610T>C	chr2.hg19:g.27874742A>G		NA	B4E3W3|Q6IB21|Q9H2T6	hg19	CCDS42667.1	0.02	-0.359598	TGCxGTG	COVERED																																																																																			NOVEL	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324568.1	8	2.53815	KEEP	0	1	30	19	518	AA	0.999869	0.888759	0		-	3	60	100	0	0	6.80619	37	60	1100	80	ENST00000337768.5	0.075	0.888875
AC074091.13	0	__UNKNOWN__	__UNKNOWN__	2	27936714	27936714	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27936714C>T	ENST00000379677.2	-	1	149										NA		NA									NA						gtgatccacccgccttggcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000379677.2:c.330+1736G>A	chr2.hg19:g.27936714C>T		NA		hg19		0.02	-0.201748	ACCxGCC	UNCOVERED																																																																																			NOVEL	AC074091.13-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000324558.1	7	2.70694	KEEP	4	0	0	9	262	CC	0	0	0		-	3	60	87	0	0	6.461871	17	60	564	54	ENST00000379677.2	0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	27966580	27966580	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:27966580T>C			NA	NA				AC074091.13 (27981 upstream) : MRPL33 (28003 downstream)						NA		NA									NA						tggctcatgcttgtaatccca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.27966580T>C		NA		hg19		0.02	-0.166619	TGCxTGT	COVERED																																																																																			NOVEL					0			7	2.406549	KEEP	0	0	0	8	229	TT	0.99257	0.351317	0			3	60	86	0	0	6.681615	13	60	410	37		0.1875	0.353947
BRE	9577	__UNKNOWN__	__UNKNOWN__	2	28116588	28116588	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:28116588T>C	ENST00000342045.2	+	3	117				BRE_ENST00000361704.2_Intron|BRE_ENST00000603461.1_Intron|BRE_ENST00000379624.1_Intron|BRE_ENST00000344773.2_Intron|BRE_ENST00000379632.2_Intron	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)	NA		NA								NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					GTAggccgggtgcggtggctc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019	9577			1106	protein-coding gene	gene with protein product	BRCA1/BRCA2-containing complex, subunit 4	610497			NA	9737713, 7826398	Standard		NM_004899	NA	Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.-24-812T>C	chr2.hg19:g.28116588T>C		NA		hg19	CCDS1763.1	0.02	-0.245506	GGGxGCG	COVERED																																																																																			NOVEL	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215114.1	4	3.907623	KEEP	1	0	0	13	343	TT	0.994391	0.63775	0		+	3	60	100	0	0	7.449321	22	60	638	63	ENST00000342045.2	0.12	0.641347
BRE	9577	__UNKNOWN__	__UNKNOWN__	2	28160215	28160215	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:28160215A>G	ENST00000342045.2	+	4	346				BRE_ENST00000361704.2_Intron|BRE_ENST00000603461.1_Intron|BRE_ENST00000379624.1_Intron|BRE_ENST00000344773.2_Intron|BRE_ENST00000379632.2_Intron	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)	NA		NA								NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					ggctggtctcaaactcctgac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019	9577			1106	protein-coding gene	gene with protein product	BRCA1/BRCA2-containing complex, subunit 4	610497			NA	9737713, 7826398	Standard		NM_004899	NA	Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.205+7440A>G	chr2.hg19:g.28160215A>G		NA		hg19	CCDS1763.1	0.02	-0.271913	CTCxAAC	COVERED																																																																																			NOVEL	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215114.1	13	3.607496	KEEP	1	0	0	12	320	AA	0.993634	0.734962	0		+	4	60	135	0	0	10.422757	24	60	733	67	ENST00000342045.2	0.142857	0.739671
BRE	9577	__UNKNOWN__	__UNKNOWN__	2	28171408	28171408	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:28171408T>C	ENST00000342045.2	+	4	346				BRE_ENST00000361704.2_Intron|BRE_ENST00000603461.1_Intron|BRE_ENST00000379624.1_Intron|BRE_ENST00000344773.2_Intron|BRE_ENST00000379632.2_Intron	NM_199194.2	NP_954664.1			brain and reproductive organ-expressed (TNFRSF1A modulator)	NA		NA								NS(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(2)	23	Acute lymphoblastic leukemia(172;0.155)					gaggccgaggtgggtggatca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF015767	CCDS1763.1, CCDS1764.1, CCDS1765.1	2p23	2008-02-05			ENSG00000158019	ENSG00000158019	9577			1106	protein-coding gene	gene with protein product	BRCA1/BRCA2-containing complex, subunit 4	610497			NA	9737713, 7826398	Standard		NM_004899	NA	Approved	BRCC45, BRCC4	uc002rls.3	Q9NXR7	OTTHUMG00000097831	ENST00000342045.2:c.205+18633T>C	chr2.hg19:g.28171408T>C		NA		hg19	CCDS1763.1	0.02	-0.166606	AGGxGGG	COVERED																																																																																			NOVEL	BRE-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215114.1	8	3.60889	KEEP	3	0	0	12	336	TT	0.993072	0.351495	0		+	3	35	93	0	0	7.135853	16	60	465	50	ENST00000342045.2	0.157895	0.353947
AC074011.2	0	__UNKNOWN__	__UNKNOWN__	2	28876588	28876588	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:28876588C>T	ENST00000431376.1	-	0	459										NA		NA									NA						agtgctgggactacaggcgtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000431376.1:	chr2.hg19:g.28876588C>T		NA		hg19		0.02	-0.210524	GGAxTAC	COVERED																																																																																			NOVEL	AC074011.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000324853.1	7	3.00896	KEEP	1	0	0	10	311	CC	0.99254	0.518266	0		-	4	60	109	0	0	8.562976	15	60	523	48	ENST00000431376.1	0.210526	0.522161
AC074011.2	0	__UNKNOWN__	__UNKNOWN__	2	28883184	28883184	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:28883184A>G	ENST00000431376.1	-	0	459										NA		NA									NA						ccagcactttaggaggccgag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000431376.1:	chr2.hg19:g.28883184A>G		NA		hg19		0.02	-0.149099	TTTxGGA	COVERED																																																																																			NOVEL	AC074011.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000324853.1	9	3.909743	KEEP	2	0	0	13	370	AA	0.993634	0.290142	0		-	3	60	100	0	0	8.382152	10	60	290	45	ENST00000431376.1	0.230769	0.292001
ALK	238	__UNKNOWN__	__UNKNOWN__	2	29449121	29449121	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:29449121A>G	ENST00000389048.3	-	18	3974				ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	NA		NA			activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	gaggcgggtgaatcacctgag	0.532		NA	T, Mis, A	NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22	ALCL, NSCLC, Neuroblastoma	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		L, E, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094	238		CD molecules	427	protein-coding gene	gene with protein product		105590	anaplastic lymphoma kinase (Ki-1)		NA	8122112	Standard	NM_004304	NM_004304	NA	Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.3067+666T>C	chr2.hg19:g.29449121A>G		NA	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	hg19	CCDS33172.1	0.02	-0.236803	GTGxATC	UNCOVERED																																																																																			NOVEL	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324994.1	11	2.405637	KEEP	4	0	0	8	215	AA	0	0	0		-	3	50	107	0	0	8.392007	18	60	516	55	ENST00000389048.3	0.142857	0.612407
ALK	238	__UNKNOWN__	__UNKNOWN__	2	30007300	30007300	__UNKNOWN__	Intron	SNP	G	G	A	rs556217578		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:30007300G>A	ENST00000389048.3	-	2	1574				ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	NA		NA			activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	agtggctcacgcctgtaatcc	0.517		NA	T, Mis, A	NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22	ALCL, NSCLC, Neuroblastoma	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		L, E, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094	238		CD molecules	427	protein-coding gene	gene with protein product		105590	anaplastic lymphoma kinase (Ki-1)		NA	8122112	Standard	NM_004304	NM_004304	NA	Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.668-66737C>T	chr2.hg19:g.30007300G>A		NA	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	hg19	CCDS33172.1	0.02	-0.12279	CACxCCT	COVERED																																																																																			NOVEL	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324994.1	10	3.007956	KEEP	4	0	0	10	294	GG	0.99254	0.194847	0		-	3	60	87	0	0	6.973069	11	60	357	39	ENST00000389048.3	0.214286	0.196312
AC016907.3	0	__UNKNOWN__	__UNKNOWN__	2	30311984	30311984	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:30311984A>G	ENST00000453606.1	-	0	109										NA		NA									NA						gcagtgagccaagatcgtgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000453606.1:	chr2.hg19:g.30311984A>G		NA		hg19		0.02	-0.298201	GCCxAGA	COVERED																																																																																			NOVEL	AC016907.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000324761.1	12	3.909799	KEEP	10	0	0	13	357	AA	0.99254	0.775233	0		-	4	60	128	0	0	9.595576	26	60	783	81	ENST00000453606.1	0.133333	0.78106
LCLAT1	253558	__UNKNOWN__	__UNKNOWN__	2	30779889	30779889	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:30779889C>T	ENST00000379509.3	+	4	516				LCLAT1_ENST00000491680.2_Intron|LCLAT1_ENST00000540623.1_Intron|LCLAT1_ENST00000359433.1_Intron|LCLAT1_ENST00000309052.4_Intron|LCLAT1_ENST00000319406.4_Intron	NM_001002257.1	NP_001002257.1	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	NA		NA			cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						ggattacaggcatgagccacc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954	253558			26756	protein-coding gene	gene with protein product		614241	lysocardiolipin acyltransferase	LYCAT	NA	18931347, 15152008, 16620771, 17675553	Standard	NM_182551	NM_001002257	NA	Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000379509.3:c.365-5123C>T	chr2.hg19:g.30779889C>T		NA	A6H8Z7|Q8N1Q7	hg19	CCDS42670.1	0.02	-0.184223	AGGxATG	COVERED																																																																																			NOVEL	LCLAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353432.1	4	4.51354	KEEP	1	0	0	15	462	CC	0.99649	0.421991	0		+	3	60	88	0	0	6.633849	16	60	564	56	ENST00000379509.3	0.157895	0.423478
LCLAT1	253558	__UNKNOWN__	__UNKNOWN__	2	30830109	30830109	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:30830109A>G	ENST00000379509.3	+	6	780				LCLAT1_ENST00000491680.2_Intron|LCLAT1_ENST00000540623.1_Intron|LCLAT1_ENST00000309052.4_Intron|LCLAT1_ENST00000319406.4_3'UTR	NM_001002257.1	NP_001002257.1	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	NA		NA			cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						tcaccatgttagccaggatgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954	253558			26756	protein-coding gene	gene with protein product		614241	lysocardiolipin acyltransferase	LYCAT	NA	18931347, 15152008, 16620771, 17675553	Standard	NM_182551	NM_001002257	NA	Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000379509.3:c.629-32874A>G	chr2.hg19:g.30830109A>G		NA	A6H8Z7|Q8N1Q7	hg19	CCDS42670.1	0.02	-0.394636	GTTxGCC	COVERED																																																																																			NOVEL	LCLAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353432.1	2	5.407126	KEEP	2	0	0	18	449	AA	0.997832	0.932466	0		+	4	60	126	0	0	9.057784	32	60	912	71	ENST00000379509.3	0.111111	0.934492
LCLAT1	253558	__UNKNOWN__	__UNKNOWN__	2	30830148	30830148	__UNKNOWN__	Intron	SNP	C	C	T	rs1975559	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:30830148C>T	ENST00000379509.3	+	6	780				LCLAT1_ENST00000491680.2_Intron|LCLAT1_ENST00000540623.1_Intron|LCLAT1_ENST00000309052.4_Intron|LCLAT1_ENST00000319406.4_3'UTR	NM_001002257.1	NP_001002257.1	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	NA		NA			cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						atgatccacccgcctcagctt	0.478		NA											C|||	1568	0.313099	0.0703	0.4078	5008	,	,	NA	19132	0.5694	NA	0.3111	False	NA	,,,	NA	NA	NA	2504	0.3119	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954	253558			26756	protein-coding gene	gene with protein product		614241	lysocardiolipin acyltransferase	LYCAT	NA	18931347, 15152008, 16620771, 17675553	Standard	NM_182551	NM_001002257	NA	Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000379509.3:c.629-32835C>T	chr2.hg19:g.30830148C>T		NA	A6H8Z7|Q8N1Q7	hg19	CCDS42670.1	0.02	-0.23682	ACCxGCC	UNCOVERED																																																																																			NOVEL	LCLAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353432.1	8	2.707677	KEEP	3	0	0	9	268	CC	0	0	0		+	7	60	204	0	0	17.4481	17	60	540	48	ENST00000379509.3	0.291667	0.612407
MEMO1	51072	__UNKNOWN__	__UNKNOWN__	2	32110468	32110468	__UNKNOWN__	Intron	SNP	C	C	T	rs547095203	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32110468C>T	ENST00000295065.5	-	7	890				MEMO1_ENST00000490459.1_Intron|MEMO1_ENST00000379383.3_Intron|DPY30_ENST00000446765.1_Intron|MEMO1_ENST00000426310.2_Intron|MEMO1_ENST00000404530.1_Intron	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	NA		NA			regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					ggattacaggcgtgagccacc	0.488		NA											C|||	2	0.000399361	0.0	0.0014	5008	,	,	NA	16562	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959	51072			14014	protein-coding gene	gene with protein product		611786	chromosome 2 open reading frame 4	C2orf4	NA	15156151	Standard	NM_015955	NM_015955	NA	Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.581-1937G>A	chr2.hg19:g.32110468C>T		NA	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	hg19	CCDS1776.1	0.02	-0.236835	AGGxGTG	COVERED																																																																																			NOVEL	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250251.2	12	3.008429	KEEP	6	0	0	10	299	CC	0.99257	0.607857	0		-	3	60	88	0	0	6.428022	19	60	616	62	ENST00000295065.5	0.136364	0.612407
MEMO1	51072	__UNKNOWN__	__UNKNOWN__	2	32144873	32144873	__UNKNOWN__	Intron	SNP	C	C	T	rs114449407	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32144873C>T	ENST00000295065.5	-	4	635				MEMO1_ENST00000490459.1_Intron|MEMO1_ENST00000379383.3_Intron|DPY30_ENST00000446765.1_Intron|MEMO1_ENST00000426310.2_Intron|MEMO1_ENST00000404530.1_Intron	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	NA		NA			regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					gcctgggcaacggagtgagac	0.473		NA											C|||	281	0.0561102	0.059	0.0778	5008	,	,	NA	15841	0.0	NA	0.1074	False	NA	,,,	NA	NA	NA	2504	0.0419	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959	51072			14014	protein-coding gene	gene with protein product		611786	chromosome 2 open reading frame 4	C2orf4	NA	15156151	Standard	NM_015955	NM_015955	NA	Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.325+993G>A	chr2.hg19:g.32144873C>T		NA	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	hg19	CCDS1776.1	0.02	-0.192968	CAAxGGA	COVERED																																																																																			NOVEL	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250251.2	7	3.61033	KEEP	0	0	0	12	361	CC	0.993634	0.454842	0		-	3	60	86	1	0	6.51083	15	60	477	45	ENST00000295065.5	0.166667	0.457757
MEMO1	51072	__UNKNOWN__	__UNKNOWN__	2	32144874	32144874	__UNKNOWN__	Intron	SNP	G	G	A	rs367549361		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32144874G>A	ENST00000295065.5	-	4	635				MEMO1_ENST00000490459.1_Intron|MEMO1_ENST00000379383.3_Intron|DPY30_ENST00000446765.1_Intron|MEMO1_ENST00000426310.2_Intron|MEMO1_ENST00000404530.1_Intron	NM_015955.2	NP_057039.1	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1	NA		NA			regulation of microtubule-based process (GO:0032886)	cytosol (GO:0005829)|nucleus (GO:0005634)				NS(1)|breast(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|skin(2)	17	Acute lymphoblastic leukemia(172;0.155)					cctgggcaacggagtgagacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF132961	CCDS1776.1, CCDS46255.1	2p22-p21	2010-05-24	2007-02-12	2007-02-12	ENSG00000162959	ENSG00000162959	51072			14014	protein-coding gene	gene with protein product		611786	chromosome 2 open reading frame 4	C2orf4	NA	15156151	Standard	NM_015955	NM_015955	NA	Approved	CGI-27, MEMO	uc002rnx.3	Q9Y316	OTTHUMG00000128453	ENST00000295065.5:c.325+992C>T	chr2.hg19:g.32144874G>A		NA	B4DLS0|D6W575|Q5R2V8|Q5R2V9|Q6NSL5	hg19	CCDS1776.1	0.02	-0.175424	AACxGAG	COVERED																																																																																			NOVEL	MEMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250251.2	7	3.309543	KEEP	0	0	0	11	330	GG	0.993072	0.384723	0		-	4	60	118	1	0	9.568318	14	60	466	43	ENST00000295065.5	0.222222	0.387407
SLC30A6	55676	__UNKNOWN__	__UNKNOWN__	2	32433176	32433176	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32433176T>C	ENST00000282587.5	+	12	853				SLC30A6_ENST00000406369.1_Intron|SLC30A6_ENST00000379343.2_Intron|SLC30A6_ENST00000357055.3_Intron|SLC30A6_ENST00000435660.1_Intron|SLC30A6_ENST00000538303.1_Intron	NM_017964.3	NP_060434.2	Q6NXT4	ZNT6_HUMAN	solute carrier family 30 (zinc transporter), member 6	NA		NA			cellular protein metabolic process (GO:0044267)|Golgi to endosome transport (GO:0006895)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(4)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					gctgggattataggtgtgagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055663	CCDS1780.1, CCDS54341.1, CCDS54342.1, CCDS54343.1	2p22.3	2013-05-22			ENSG00000152683	ENSG00000152683	55676		Solute carriers	19305	protein-coding gene	gene with protein product		611148			NA		Standard		NM_017964	NA	Approved	FLJ31101, ZNT6	uc002rof.2	Q6NXT4	OTTHUMG00000128456	ENST00000282587.5:c.816+1174T>C	chr2.hg19:g.32433176T>C		NA	A5YM45|B7Z901|Q8N5C9|Q96NC3	hg19	CCDS1780.1	0.02	-0.31563	TTAxAGG	COVERED																																																																																			NOVEL	SLC30A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250254.2	9	5.076135	KEEP	2	0	0	17	422	TT	0.997832	0.81669	0		+	3	60	95	0	0	6.569133	30	60	841	80	ENST00000282587.5	0.090909	0.818465
NLRC4	58484	__UNKNOWN__	__UNKNOWN__	2	32486901	32486901	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32486901T>C	ENST00000404025.2	-	2	371				NLRC4_ENST00000402280.1_Intron|NLRC4_ENST00000360906.5_Intron|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					cctgtaatcctagcactttgg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106	58484		Nucleotide-binding domain and leucine rich repeat containing	16412	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4, NOD-like receptor C4	606831	caspase recruitment domain family, member 12	CARD12	NA	11374873	Standard	NM_021209	NM_021209	NA	Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.117+2905A>G	chr2.hg19:g.32486901T>C		NA	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	hg19	CCDS33174.1	0.02	-0.184201	TCCxAGC	COVERED																																																																																			NOVEL	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325222.2	8	2.405706	KEEP	2	0	0	8	217	TT	0.99257	0.420331	0		-	4	60	140	0	0	11.88093	13	60	398	49	ENST00000404025.2	0.235294	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	32566315	32566315	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32566315A>G			NA	NA				AL133245.2 (18244 upstream) : BIRC6 (15780 downstream)						NA		NA									NA						gtttcaccatattggccaggc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.32566315A>G		NA		hg19		0.02	-0.254329	CATxTTG	COVERED																																																																																			NOVEL					0			7	3.305502	KEEP	1	0	0	11	275	AA	0.993072	0.663892	0			5	60	171	1	0	13.8685	22	60	624	53		0.185185	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	32575516	32575516	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32575516T>A			NA	NA				AL133245.2 (27445 upstream) : BIRC6 (6579 downstream)						NA		NA									NA						acctgaggtctggagttcgag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.32575516T>A		NA		hg19		0.02	-0.14029	GTCxGGA	COVERED																																																																																			NOVEL					0			7	3.608288	KEEP	0	0	0	12	322	TT	0.993634	0.259304	0			3	60	82	0	0	6.37342	12	60	343	36		0.2	0.260965
BIRC6	57448	__UNKNOWN__	__UNKNOWN__	2	32599829	32599829	__UNKNOWN__	Intron	SNP	C	C	T	rs569539646		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32599829C>T	ENST00000421745.2	+	2	459					NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	NA		NA			apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					cgtgagccaccgcgcccggca	0.527		NA											c|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14096	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA	Pancreas(94;175 1509 16028 18060 45422)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760	57448		Baculoviral IAP repeat containing, Ubiquitin-conjugating enzymes E2	13516	protein-coding gene	gene with protein product	apollon	605638	baculoviral IAP repeat-containing 6		NA	10544019	Standard	NM_016252	NM_016252	NA	Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.326-2827C>T	chr2.hg19:g.32599829C>T		NA	Q9ULD1	hg19	CCDS33175.2	0.02	-0.210531	CACxGCG	COVERED																																																																																			NOVEL	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318769.3	9	5.714994	KEEP	4	0	0	19	545	CC	0.997832	0.521029	0		+	3	60	93	0	0	7.210127	15	60	499	65	ENST00000421745.2	0.166667	0.522161
BIRC6	57448	__UNKNOWN__	__UNKNOWN__	2	32675273	32675273	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32675273A>G	ENST00000421745.2	+	22	4752					NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	NA		NA			apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TCggccgggcacggtggctca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(94;175 1509 16028 18060 45422)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760	57448		Baculoviral IAP repeat containing, Ubiquitin-conjugating enzymes E2	13516	protein-coding gene	gene with protein product	apollon	605638	baculoviral IAP repeat-containing 6		NA	10544019	Standard	NM_016252	NM_016252	NA	Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4618+1277A>G	chr2.hg19:g.32675273A>G		NA	Q9ULD1	hg19	CCDS33175.2	0.02	-0.219277	GGCxCGG	COVERED																																																																																			NOVEL	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318769.3	9	3.609783	KEEP	7	0	0	12	341	AA	0.993072	0.549057	0		+	3	60	101	0	0	7.792104	18	60	542	61	ENST00000421745.2	0.142857	0.552887
TTC27	55622	__UNKNOWN__	__UNKNOWN__	2	32859547	32859547	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32859547A>G	ENST00000317907.4	+	3	627					NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	NA		NA								breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						gtagagatggagttttgccat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699	55622		Tetratricopeptide (TTC) repeat domain containing	25986	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017735	NM_001193509	NA	Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.396+475A>G	chr2.hg19:g.32859547A>G		NA	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	hg19	CCDS33176.1	0.02	-0.175416	TGGxGTT	COVERED																																																																																			NOVEL	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325395.1	8	2.706592	KEEP	0	0	0	9	246	AA	0.99254	0.384517	0		+	3	60	93	0	0	7.210645	15	60	457	39	ENST00000317907.4	0.166667	0.387407
TTC27	55622	__UNKNOWN__	__UNKNOWN__	2	32908221	32908221	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:32908221C>T	ENST00000317907.4	+	9	1350					NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	NA		NA								breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						tgcaccaggccaatttttgta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699	55622		Tetratricopeptide (TTC) repeat domain containing	25986	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017735	NM_001193509	NA	Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1119+4232C>T	chr2.hg19:g.32908221C>T		NA	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	hg19	CCDS33176.1	0.02	-0.33335	GGCxAAT	COVERED																																																																																			NOVEL	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325395.1	10	3.611024	KEEP	0	0	0	12	376	CC	0.993634	0.84656	0		+	4	60	119	0	2	8.575167	28	60	946	80	ENST00000317907.4	0.125	0.851984
TTC27	55622	__UNKNOWN__	__UNKNOWN__	2	33004042	33004042	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:33004042A>G	ENST00000317907.4	+	14	2010					NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	NA		NA								breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38						tgtaatcccaacactttggga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC063791, AK000279	CCDS33176.1	2p22.3	2013-01-10			ENSG00000018699	ENSG00000018699	55622		Tetratricopeptide (TTC) repeat domain containing	25986	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017735	NM_001193509	NA	Approved	FLJ20272	uc002rom.3	Q6P3X3	OTTHUMG00000152134	ENST00000317907.4:c.1779+995A>G	chr2.hg19:g.33004042A>G		NA	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	hg19	CCDS33176.1	0.02	-0.271869	CCAxCAC	COVERED																																																																																			NOVEL	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325395.1	8	3.608636	KEEP	1	0	0	12	328	AA	0.993072	0.734547	0		+	3	60	103	0	0	7.642585	24	60	710	64	ENST00000317907.4	0.111111	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	33166183	33166183	__UNKNOWN__	IGR	SNP	C	C	T	rs112555914	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:33166183C>T			NA	NA				AL121656.5 (12711 upstream) : Y_RNA (4222 downstream)						NA		NA									NA						ccgcccacctcggcctcccaa	0.517		NA											C|||	368	0.0734824	0.0658	0.0865	5008	,	,	NA	17657	0.002	NA	0.1511	False	NA	,,,	NA	NA	NA	2504	0.0685	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.33166183C>T		NA		hg19		0.02	-0.140335	CCTxGGC	COVERED																																																																																			NOVEL					0			6	3.0088	KEEP	3	0	0	10	304	CC	0.99257	0.259026	0			8	60	243	0	0	24.354145	5	60	154	40		0.615385	0.260965
LTBP1	4052	__UNKNOWN__	__UNKNOWN__	2	33500741	33500741	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:33500741A>G	ENST00000402934.1	+	14	1845				LTBP1_ENST00000354476.3_Intron|LTBP1_ENST00000404525.1_Intron|LTBP1_ENST00000390003.4_Intron|LTBP1_ENST00000404816.2_Intron|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000407925.1_Intron			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	NA		NA			extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				acaagagcgaaactccatctc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323	4052		Latent transforming growth factor, beta binding proteins	6714	protein-coding gene	gene with protein product	TGF-beta1-BP-1	150390			NA	2350783, 11104663	Standard	NM_206943	NM_206943	NA	Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000402934.1:c.1733-127A>G	chr2.hg19:g.33500741A>G		NA	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	hg19		0.02	1.935752	CGAxACT	COVERED																																																																																			NOVEL	LTBP1-008	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325421.3	11	4.642119	KEEP	3	1	30	26	699	AA	0.999957	0.992051	0		+	7	60	215	1	0	15.863723	46	60	1370	112	ENST00000402934.1	0.132075	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	33867487	33867487	__UNKNOWN__	IGR	SNP	T	T	C	rs534062570		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:33867487T>C			NA	NA				FAM98A (43058 upstream) : AC009499.1 (64465 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.33867487T>C		NA		hg19		0.02	-0.219206	AGGxGTG	COVERED																																																																																			NOVEL					0			8	2.406429	KEEP	0	0	0	8	227	TT	0.99257	0.54878	0			3	60	98	0	0	7.365733	20	60	597	46		0.130435	0.552887
AC009499.1	0	__UNKNOWN__	__UNKNOWN__	2	33961284	33961284	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:33961284T>C	ENST00000366209.2	+	0	68										NA		NA									NA						ggtcacgccattgcactccag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000366209.2:	chr2.hg19:g.33961284T>C		NA		hg19		0.02	-0.219253	CCAxTGC	COVERED																																																																																			NOVEL	AC009499.1-002	KNOWN	non_canonical_polymorphism|basic	lincRNA	NA	lincRNA	OTTHUMT00000325406.1	7	3.307753	KEEP	0	0	0	11	300	TT	0.993072	0.549057	0		+	3	60	99	0	0	7.465109	20	60	582	55	ENST00000366209.2	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	34929943	34929943	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:34929943G>A			NA	NA				RP11-529E15.1 (1496 upstream) : AC073218.2 (8713 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.34929943G>A		NA		hg19		0.02	-0.17544	GGCxTGA	COVERED																																																																																			NOVEL					0			11	3.00888	KEEP	4	0	0	10	303	GG	0.99257	0.384528	0			3	60	89	0	0	6.73375	16	60	525	45		0.157895	0.387407
AC012593.1	0	__UNKNOWN__	__UNKNOWN__	2	35328355	35328355	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:35328355A>G	ENST00000588944.1	+	0	115										NA		NA									NA						ttgggaggccaaggcaggcag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000588944.1:	chr2.hg19:g.35328355A>G		NA		hg19		0.02	-0.175413	GCCxAGG	COVERED																																																																																			NOVEL	AC012593.1-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000459976.1	9	3.007506	KEEP	6	0	0	10	277	AA	0.99257	0.384528	0		+	4	60	124	0	0	10.168541	14	60	417	54	ENST00000588944.1	0.222222	0.387407
FEZ2	9637	__UNKNOWN__	__UNKNOWN__	2	36813534	36813534	__UNKNOWN__	Intron	SNP	T	T	G	rs848614|rs374879991	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:36813534T>G	ENST00000379245.4	-	3	424				FEZ2_ENST00000405912.3_Intron|FEZ2_ENST00000305852.7_Intron	NM_001042548.1	NP_001036013.1	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	NA		NA			axon guidance (GO:0007411)|nervous system development (GO:0007399)|signal transduction (GO:0007165)					breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	7		all_hematologic(82;0.21)				tcccagcactttgggaggctg	0.438		NA											T|||	2856	0.570288	0.584	0.585	5008	,	,	NA	16895	0.8661	NA	0.3946	False	NA	,,,	NA	NA	NA	2504	0.4172	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U60061	CCDS46257.1, CCDS46258.1	2p21	2008-05-15			ENSG00000171055	ENSG00000171055	9637			3660	protein-coding gene	gene with protein product		604826			NA	9096408	Standard		NM_005102	NA	Approved		uc002rpg.2	Q9UHY8	OTTHUMG00000152148	ENST00000379245.4:c.376-2922A>C	chr2.hg19:g.36813534T>G		NA	Q5EBN3|Q76LN0|Q99690	hg19	CCDS46258.1	0.02	-0.114008	ACTxTGG	UNCOVERED																																																																																			NOVEL	FEZ2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325431.2	7	2.706155	KEEP	3	0	0	9	238	TT	0	0	0		-	3	60	105	0	0	9.001528	9	60	255	31	ENST00000379245.4	0.25	0.162467
HEATR5B	54497	__UNKNOWN__	__UNKNOWN__	2	37266337	37266337	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:37266337T>C	ENST00000233099.5	-	20	3142				HEATR5B_ENST00000354531.2_Intron	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	NA		NA				extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				Aggccgggtgtggtggctcac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869	54497			29273	protein-coding gene	gene with protein product		NA			NA	10718198	Standard	NM_019024	XM_005264379	NA	Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.3046+1134A>G	chr2.hg19:g.37266337T>C		NA	B5MDU8|Q7Z3B2|Q9NVL7	hg19	CCDS33181.1	0.02	-0.184053	GTGxGGT	COVERED																																																																																			NOVEL	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325492.1	13	4.508652	KEEP	7	0	0	15	401	TT	0.999366	0.423209	0		-	3	60	98	0	0	7.493408	18	60	494	68	ENST00000233099.5	0.142857	0.423478
GPATCH11	253635	__UNKNOWN__	__UNKNOWN__	2	37318499	37318499	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:37318499T>C	ENST00000409774.1	+	5	461				GPATCH11_ENST00000608836.1_Intron|GPATCH11_ENST00000281932.5_Intron			Q8N954	GPT11_HUMAN	G patch domain containing 11	NA		NA					nucleic acid binding (GO:0003676)				NA						gccaggaatttgagaccagcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095667	CCDS1785.2, CCDS62891.1, CCDS1785.3	2p22.2	2013-11-05	2013-01-28	2013-01-28	ENSG00000152133	ENSG00000152133	253635		G patch domain containing	26768	protein-coding gene	gene with protein product	centromere protein Y	NA	coiled-coil domain containing 75	CCDC75	NA		Standard	NM_174931	NM_001278505	NA	Approved	FLJ38348, CENPY, CENP-Y	uc010ezz.3	Q8N954	OTTHUMG00000128469	ENST00000409774.1:c.395-560T>C	chr2.hg19:g.37318499T>C		NA	A8K0D9|B7Z2G4|B8ZZ44	hg19		0.02	-0.25433	ATTxGAG	COVERED																																																																																			NOVEL	GPATCH11-002	KNOWN	downstream_ATG|basic	protein_coding	NA	protein_coding	OTTHUMT00000250269.3	13	6.313354	KEEP	0	0	0	21	574	TT	0.999869	0.668436	0		+	3	60	99	0	0	7.661106	17	60	493	69	ENST00000409774.1	0.15	0.668523
SULT6B1	391365	__UNKNOWN__	__UNKNOWN__	2	37423245	37423245	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:37423245T>C	ENST00000407963.1	-	1	83							Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	NA		NA				cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				gctgggattataggcgtgagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068	391365		Sulfotransferases, cytosolic	33433	protein-coding gene	gene with protein product		NA			NA	14676822	Standard	NM_001032377	XM_005264307	NA	Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000407963.1:c.20+413A>G	chr2.hg19:g.37423245T>C		NA	B2RTS7	hg19	CCDS33182.1	0.02	-0.21925	TTAxAGG	COVERED																																																																																			NOVEL	SULT6B1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325505.1	4	2.404472	KEEP	0	0	0	8	206	TT	0.99257	0.54878	0		-	4	60	137	0	0	11.07962	18	60	507	52	ENST00000407963.1	0.181818	0.552887
CEBPZ	10153	__UNKNOWN__	__UNKNOWN__	2	37449153	37449153	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:37449153A>G	ENST00000234170.5	-	4	2211					NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				TGggccaggtacagtggctca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816	10153			24218	protein-coding gene	gene with protein product		612828			NA	2247079, 12534345	Standard	NM_005760	NM_005760	NA	Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.2065+369T>C	chr2.hg19:g.37449153A>G		NA	Q8NE75	hg19	CCDS1787.1	0.02	-0.078938	GGTxCAG	UNCOVERED																																																																																			NOVEL	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000218569.2	4	3.001172	KEEP	1	0	0	10	240	AA	0.992708	0.076772	0		-	3	60	100	0	0	9.133166	5	60	144	27	ENST00000234170.5	0.375	0.077336
NDUFAF7	55471	__UNKNOWN__	__UNKNOWN__	2	37475795	37475795	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:37475795T>C	ENST00000002125.4	+	0	1668				NDUFAF7_ENST00000336237.6_3'UTR	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	NA		NA			methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)				NA						tggtggctcatgcctgtaatc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509	55471		Mitochondrial respiratory chain complex assembly factors	28816	protein-coding gene	gene with protein product	mitochondrial dysfunction protein A homolog	615898	chromosome 2 open reading frame 56	C2orf56	NA		Standard	NM_144736	NM_144736	NA	Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.*302T>C	chr2.hg19:g.37475795T>C		NA	Q7Z399|Q9P1G3	hg19	CCDS1788.1	0.02	-0.420977	TCAxGCC	COVERED																																																																																			NOVEL	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250267.1	8	3.240312	KEEP	1	1	32	22	604	TT	0.999879	0.948287	0		+	3	60	101	0	0	6.777706	41	60	1224	90	ENST00000002125.4	0.068182	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	38417048	38417048	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38417048C>T			NA	NA				CYP1B1-AS1 (8051 upstream) : RP11-314C9.2 (3441 downstream)						NA		NA									NA						ctgcaagctccgcctcctggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.38417048C>T		NA		hg19		0.02	-0.175427	CTCxGCC	COVERED																																																																																			NOVEL					0			7	3.609638	KEEP	3	0	0	12	352	CC	0.993072	0.384723	0			3	60	90	0	0	6.761352	17	60	551	44		0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	38501492	38501492	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38501492A>C			NA	NA				AC009229.5 (34760 upstream) : ATL2 (20529 downstream)						NA		NA									NA						agttcaagacaagcctggcca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.38501492A>C		NA		hg19		0.02	-0.140328	GACxAGC	COVERED																																																																																			NOVEL					0			8	2.706014	KEEP	0	0	0	9	236	AA	0.99254	0.259018	0			3	53	99	0	0	8.072334	12	60	351	32		0.2	0.260965
ATL2	64225	__UNKNOWN__	__UNKNOWN__	2	38539578	38539578	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38539578T>C	ENST00000378954.4	-	7	806				ATL2_ENST00000419554.2_Intron|ATL2_ENST00000406122.1_Intron|ATL2_ENST00000332337.4_Intron|ATL2_ENST00000546051.1_Intron|ATL2_ENST00000402054.1_Intron|ATL2_ENST00000539122.1_Intron|ATL2_ENST00000452935.2_Intron	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	NA		NA			endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						gctggctgggtgcggtggctc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787	64225			24047	protein-coding gene	gene with protein product		609368	ADP-ribosylation factor-like 6 interacting protein 2	ARL6IP2	NA	10508919, 18270207	Standard	NM_022374	NM_022374	NA	Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.804+714A>G	chr2.hg19:g.38539578T>C		NA	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	hg19	CCDS46260.1	0.02	-0.306916	GGGxGCG	COVERED																																																																																			NOVEL	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219886.2	13	3.608178	KEEP	1	0	0	12	322	TT	0.993634	0.795151	0		-	4	60	140	0	0	10.857363	25	60	706	66	ENST00000378954.4	0.137931	0.800245
ATL2	64225	__UNKNOWN__	__UNKNOWN__	2	38591258	38591258	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38591258C>G	ENST00000378954.4	-	1	120				ATL2_ENST00000419554.2_Intron|ATL2_ENST00000406122.1_Intron|ATL2_ENST00000332337.4_Intron|ATL2_ENST00000546051.1_Intron|ATL2_ENST00000402054.1_Intron|ATL2_ENST00000539122.1_Intron|ATL2_ENST00000452935.2_Intron	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	NA		NA			endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						acaaaaattacccgggcgtgg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787	64225			24047	protein-coding gene	gene with protein product		609368	ADP-ribosylation factor-like 6 interacting protein 2	ARL6IP2	NA	10508919, 18270207	Standard	NM_022374	NM_022374	NA	Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.118+13026G>C	chr2.hg19:g.38591258C>G		NA	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	hg19	CCDS46260.1	0.02	-0.078945	TTAxCCG	UNCOVERED																																																																																			NOVEL	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219886.2	4	2.707888	KEEP	0	0	0	9	271	CC	0.99254	0.076759	0		-	3	60	92	0	0	8.82474	3	60	96	22	ENST00000378954.4	0.5	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	38623787	38623787	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38623787A>G			NA	NA				ATL2 (19360 upstream) : AC016995.3 (10082 downstream)						NA		NA									NA						gctcactgcaacctccacctc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.38623787A>G		NA		hg19		0.02	-0.149077	GCAxCCT	COVERED																																																																																			NOVEL					0			11	3.306439	KEEP	5	0	0	11	286	AA	0.992708	0.289872	0			3	60	97	0	0	7.692098	14	60	393	39		0.176471	0.292001
AC016995.3	0	__UNKNOWN__	__UNKNOWN__	2	38693424	38693424	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38693424A>G	ENST00000417039.1	-	0	894										NA		NA									NA						gtgcgatctcagctcactgca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417039.1:	chr2.hg19:g.38693424A>G		NA		hg19		0.02	-0.096459	CTCxGCT	UNCOVERED																																																																																			NOVEL	AC016995.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000331173.1	5	2.706861	KEEP	2	0	0	9	248	AA	0.99257	0.119541	0		-	3	60	93	0	0	7.932844	8	60	233	28	ENST00000417039.1	0.272727	0.120436
AC016995.3	0	__UNKNOWN__	__UNKNOWN__	2	38741327	38741327	__UNKNOWN__	lincRNA	SNP	C	C	T	rs189633851		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38741327C>T	ENST00000417039.1	-	0	294										NA		NA									NA						gtcaggagttcgagaccagcc	0.517		NA											C|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16828	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417039.1:	chr2.hg19:g.38741327C>T		NA		hg19		0.02	-0.192973	GTTxGAG	COVERED																																																																																			NOVEL	AC016995.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000331173.1	10	4.210154	KEEP	6	0	0	14	390	CC	0.993072	0.454585	0		-	3	38	91	0	1	6.933659	16	60	507	59	ENST00000417039.1	0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	38889226	38889226	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38889226A>G			NA	NA				HNRNPLL (58498 upstream) : GALM (3825 downstream)						NA		NA									NA						gcttacaggcatgagccaccg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.38889226A>G		NA		hg19		0.02	-0.254336	GGCxTGA	COVERED																																																																																			NOVEL					0			14	3.007602	KEEP	0	0	0	10	275	AA	0.992708	0.663648	0			4	60	119	0	0	8.892592	23	60	678	50		0.148148	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	38967847	38967847	__UNKNOWN__	IGR	SNP	G	G	A	rs112011213	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38967847G>A			NA	NA				GALM (5937 upstream) : SRSF7 (2893 downstream)						NA		NA									NA						aaaaTTAgccgggcgtggtgg	0.547		NA											g|||	100	0.0199681	0.0053	0.0245	5008	,	,	NA	14605	0.0	NA	0.0656	False	NA	,,,	NA	NA	NA	2504	0.0102	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.38967847G>A		NA		hg19		0.02	-0.403506	GCCxGGC	COVERED																																																																																			NOVEL					0			36	3.976835	KEEP	19	2	59	34	1005	GG	0.999957	0.934452	0			11	60	328	1	0	27.972558	28	60	931	125		0.282051	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	38967863	38967863	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:38967863A>G			NA	NA				GALM (5953 upstream) : SRSF7 (2877 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.38967863A>G		NA		hg19		0.02	-0.412184	CACxCCT	COVERED																																																																																			NOVEL					0			34	6.747301	KEEP	16	1	27	32	863	AA	0.999957	0.941701	0			3	60	96	0	0	6.40716	37	60	1071	129		0.075	0.941741
DHX57	90957	__UNKNOWN__	__UNKNOWN__	2	39081931	39081931	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:39081931C>T	ENST00000295373.6	-	8	2032					NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	NA		NA					ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				ctcgaactcccgacctcaggt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(191;1090 2095 4375 23729 47341)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214	90957		DEAH-boxes	20086	protein-coding gene	gene with protein product		NA			NA		Standard	NM_145646	NM_198963	NA	Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.1905+267G>A	chr2.hg19:g.39081931C>T		NA	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	hg19	CCDS1800.1	0.02	-0.15786	TCCxGAC	COVERED																																																																																			NOVEL	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219940.2	9	2.707573	KEEP	3	0	0	9	268	CC	0.99257	0.320408	0		-	3	54	88	0	0	6.792338	14	60	455	41	ENST00000295373.6	0.176471	0.322807
AC007246.3	0	__UNKNOWN__	__UNKNOWN__	2	39690114	39690114	__UNKNOWN__	RNA	SNP	C	C	A	rs10208288	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:39690114C>A	ENST00000449569.1	+	0	282				AC007246.3_ENST00000443038.1_RNA|AC007246.3_ENST00000445520.1_RNA|AC007246.3_ENST00000426083.1_RNA|AC007246.3_ENST00000446698.1_RNA|AC007246.3_ENST00000422128.1_RNA	NR_037875.1					NA		NA									NA						tcaagaccagcctggccaaca	0.542		NA											C|||	1415	0.282548	0.1097	0.4222	5008	,	,	NA	14967	0.1339	NA	0.4433	False	NA	,,,	NA	NA	NA	2504	0.4049	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000449569.1:	chr2.hg19:g.39690114C>A		NA		hg19		0.02	-0.219212	CAGxCTG	UNCOVERED																																																																																			NOVEL	AC007246.3-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000325723.1	10	2.70815	KEEP	7	0	0	9	279	CC	0	0	0		+	9	60	249	0	0	22.506969	14	60	449	49	ENST00000449569.1	0.391304	0.552887
THUMPD2	80745	__UNKNOWN__	__UNKNOWN__	2	39965454	39965454	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:39965454A>G	ENST00000505747.1	-	10	1215				THUMPD2_ENST00000260619.6_Intron	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2	NA		NA					methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				tgtaatcccaacattttggga	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050	80745			14890	protein-coding gene	gene with protein product		611751	chromosome 2 open reading frame 8	C2orf8	NA	12063391	Standard	NM_025264	NM_025264	NA	Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.1188-1255T>C	chr2.hg19:g.39965454A>G		NA	A8K7I7|Q53TT8|Q53TV0	hg19	CCDS1805.2	0.02	-0.157864	CCAxCAT	COVERED																																																																																			NOVEL	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219991.2	8	2.406166	KEEP	0	0	0	8	224	AA	0.99257	0.320408	0		-	3	60	85	0	0	6.579668	13	60	387	35	ENST00000505747.1	0.1875	0.322807
SLC8A1-AS1	100128590	__UNKNOWN__	__UNKNOWN__	2	40099577	40099577	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:40099577C>G	ENST00000599740.1	+	0	73									SLC8A1 antisense RNA 1	NA		NA									NA						gctcaggctgcagtgcaatgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							2p22.1	2012-10-12	2012-08-15		ENSG00000227028	ENSG00000227028	100128590		Long non-coding RNAs	44102	non-coding RNA	RNA, long non-coding		NA	SLC8A1 antisense RNA 1 (non-protein coding)		NA		Standard		NR_038441	NA	Approved		uc002rrw.3		OTTHUMG00000152308	ENST00000599740.1:	chr2.hg19:g.40099577C>G		NA		hg19		0.02	-0.31582	CTGxAGT	COVERED																																																																																			NOVEL	SLC8A1-AS1-017	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000461544.1	14	6.920582	KEEP	0	0	0	23	708	CC	0.999892	0.818376	0		+	3	60	104	0	0	7.643575	26	60	912	94	ENST00000599740.1	0.103448	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	41243211	41243211	__UNKNOWN__	IGR	SNP	G	G	T	rs13021241	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:41243211G>T			NA	NA				AC007317.1 (248619 upstream) : HNRNPA1P57 (127708 downstream)						NA		NA									NA						caccgtgttagccaggatggt	0.577		NA											G|||	2479	0.495008	0.3116	0.4107	5008	,	,	NA	14216	0.8135	NA	0.5606	False	NA	,,,	NA	NA	NA	2504	0.407	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.41243211G>T		NA		hg19		0.02	-0.157841	TTAxCCA	UNCOVERED																																																																																			NOVEL					0			4	3.008966	KEEP	16	0	0	10	306	GG	0	0	0			14	60	393	0	0	41.828688	4	40	134	59		0.777778	0.322807
C2orf91	400950	__UNKNOWN__	__UNKNOWN__	2	42165909	42165909	__UNKNOWN__	Intron	SNP	C	C	T	rs142875646		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:42165909C>T	ENST00000378711.2	-	4	475					NM_001242815.1	NP_001229744.1	Q6ZV80	CB091_HUMAN	chromosome 2 open reading frame 91	NA		NA									NA						CACACCtgtgcgtgtgtgtgt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56116.1	2p21	2012-02-17			ENSG00000205086	ENSG00000205086	400950			42966	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001242815	NM_001242815	NA	Approved		uc002rsf.1	Q6ZV80	OTTHUMG00000152307	ENST00000378711.2:c.386-156G>A	chr2.hg19:g.42165909C>T		NA		hg19	CCDS56116.1	0.02	-0.201715	GTGxGTG	COVERED																																																																																			NOVEL	C2orf91-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325755.1	2	5.099724	KEEP	0	0	0	17	439	CC	0.999366	0.490234	0		-	3	60	94	0	0	6.965342	20	60	599	46	ENST00000378711.2	0.130435	0.490544
MTA3	57504	__UNKNOWN__	__UNKNOWN__	2	42890676	42890676	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:42890676T>G	ENST00000407270.3	+	8	931				MTA3_ENST00000405094.1_Intron|MTA3_ENST00000406911.1_Intron|MTA3_ENST00000405592.1_Intron|MTA3_ENST00000406652.1_Intron	NM_020744.2	NP_065795.1	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	NA		NA				intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						tgaggcaggatgatcacttga	0.433		NA									OREG0014571	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)									NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935	57504		GATA zinc finger domain containing	23784	protein-coding gene	gene with protein product		609050	metastasis associated gene family, member 3		NA	12705869, 14613024	Standard	NM_020744	NM_001282755	NA	Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000407270.3:c.702+3674T>G	chr2.hg19:g.42890676T>G		912	Q9NSP2|Q9ULF4	hg19	CCDS46267.1	0.02	-0.411208	GGAxGAT	COVERED																																																																																			NOVEL	MTA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318144.2	14	5.44239	KEEP	0	1	31	29	771	TT	0.999997	0.941739	0		+	4	60	131	0	0	9.280221	38	60	1094	106	ENST00000407270.3	0.095238	0.941741
MTA3	57504	__UNKNOWN__	__UNKNOWN__	2	42929139	42929139	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:42929139C>T	ENST00000407270.3	+	12	1254				MTA3_ENST00000405094.1_Intron|MTA3_ENST00000406911.1_Intron|MTA3_ENST00000405592.1_Intron|MTA3_ENST00000406652.1_Intron|MTA3_ENST00000472767.1_Intron	NM_020744.2	NP_065795.1	Q9BTC8	MTA3_HUMAN	metastasis associated 1 family, member 3	NA		NA				intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(9)|ovary(2)|stomach(1)	15						tcacctgaggccaggagtttg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033092	CCDS46267.1, CCDS62900.1	2p22.1	2013-01-25	2004-12-15		ENSG00000057935	ENSG00000057935	57504		GATA zinc finger domain containing	23784	protein-coding gene	gene with protein product		609050	metastasis associated gene family, member 3		NA	12705869, 14613024	Standard	NM_020744	NM_001282755	NA	Approved	KIAA1266	uc002rsq.3	Q9BTC8	OTTHUMG00000150452	ENST00000407270.3:c.1026-2195C>T	chr2.hg19:g.42929139C>T		NA	Q9NSP2|Q9ULF4	hg19	CCDS46267.1	0.02	-0.228085	AGGxCAG	COVERED																																																																																			NOVEL	MTA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318144.2	13	3.309998	KEEP	8	0	0	11	343	CC	0.992708	0.578679	0		+	3	40	90	0	1	6.44961	22	60	761	67	ENST00000407270.3	0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	43063752	43063752	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43063752C>T			NA	NA				HAAO (44020 upstream) : AC016735.1 (164742 downstream)						NA		NA									NA						tcccagcactctgggaggccg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.43063752C>T		NA		hg19		0.02	-0.122812	ACTxTGG	UNCOVERED																																																																																			NOVEL					0			1	2.406944	KEEP	2	0	0	8	242	CC	0	0	0			3	60	91	0	0	7.372725	11	60	374	36		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	43113976	43113976	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43113976C>T			NA	NA				HAAO (94244 upstream) : AC016735.1 (114518 downstream)						NA		NA									NA						ccgaggtgggcggatcacctg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.43113976C>T		NA		hg19		0.02	-0.2017	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			9	2.707618	KEEP	3	0	0	9	267	CC	0	0	0			3	40	92	0	0	6.961593	17	60	531	47		0.15	0.490544
THADA	63892	__UNKNOWN__	__UNKNOWN__	2	43443583	43443583	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43443583G>T	ENST00000330266.7	-	20	3188							Q6YHU6	THADA_HUMAN	thyroid adenoma associated	NA		NA								breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				cggtggctcaggcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970	63892			19217	protein-coding gene	gene with protein product		611800			NA	12063398, 11214970	Standard	NM_022065	NM_022065	NA	Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000330266.7:c.3189-49678C>A	chr2.hg19:g.43443583G>T		NA	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	hg19		0.02	-0.184218	TCAxGCC	COVERED																																																																																			NOVEL	THADA-201	KNOWN	basic	protein_coding	NA	protein_coding		5	2.407221	KEEP	0	0	0	8	246	CG	0.992708	0.486967	0		-	3	60	93	0	0	7.061084	17	60	588	51	ENST00000330266.7	0.15	0.490544
THADA	63892	__UNKNOWN__	__UNKNOWN__	2	43611883	43611883	__UNKNOWN__	Intron	SNP	T	T	C	rs76675804	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43611883T>C	ENST00000405006.4	-	29	4579				THADA_ENST00000485353.1_Intron|THADA_ENST00000405975.2_Intron|THADA_ENST00000330266.7_Intron|THADA_ENST00000415080.2_Intron	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	NA		NA								breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ggcgggagaattgcttcagcc	0.383		NA											T|||	183	0.0365415	0.0386	0.0576	5008	,	,	NA	15847	0.0	NA	0.0795	False	NA	,,,	NA	NA	NA	2504	0.0123	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970	63892			19217	protein-coding gene	gene with protein product		611800			NA	12063398, 11214970	Standard	NM_022065	NM_022065	NA	Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.4227+13226A>G	chr2.hg19:g.43611883T>C		NA	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	hg19	CCDS46268.1	0.02	-0.052623	GAAxTGC	UNCOVERED																																																																																			NOVEL	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326070.3	2	2.405156	KEEP	2	0	0	8	210	TT	0	0	0		-	3	60	104	0	0	10.025733	3	60	85	22	ENST00000405006.4	0.5	0.036766
THADA	63892	__UNKNOWN__	__UNKNOWN__	2	43637007	43637007	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43637007A>T	ENST00000405006.4	-	29	4410				THADA_ENST00000485353.1_Intron|THADA_ENST00000405975.2_Intron|THADA_ENST00000330266.7_Intron|THADA_ENST00000415080.2_Intron	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	NA		NA								breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				aataaaaaaaatagccaggca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970	63892			19217	protein-coding gene	gene with protein product		611800			NA	12063398, 11214970	Standard	NM_022065	NM_022065	NA	Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.4059-11729T>A	chr2.hg19:g.43637007A>T		NA	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	hg19	CCDS46268.1	0.02	-0.13154	AAAxTAG	COVERED																																																																																			NOVEL	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326070.3	8	4.811822	KEEP	0	0	0	16	437	AA	0.997832	0.228676	0		-	3	60	83	0	0	6.682418	10	60	287	47	ENST00000405006.4	0.230769	0.229173
THADA	63892	__UNKNOWN__	__UNKNOWN__	2	43792558	43792558	__UNKNOWN__	Intron	SNP	G	G	A	rs207461682		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43792558G>A	ENST00000405006.4	-	15	2663				THADA_ENST00000405975.2_Intron|THADA_ENST00000330266.7_Intron|THADA_ENST00000404790.1_Intron|THADA_ENST00000415080.2_Intron|THADA_ENST00000403856.1_3'UTR|THADA_ENST00000402360.2_Intron	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	NA		NA								breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				gcaacagagcgagactccgtc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970	63892			19217	protein-coding gene	gene with protein product		611800			NA	12063398, 11214970	Standard	NM_022065	NM_022065	NA	Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.2311+1278C>T	chr2.hg19:g.43792558G>A		NA	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	hg19	CCDS46268.1	0.02	1.645817	AGCxAGA	COVERED																																																																																			NOVEL	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326070.3	8	6.440919	KEEP	0	1	27	31	793	GG	0.999997	0.990962	0		-	4	60	123	0	0	8.519936	37	60	1099	112	ENST00000405006.4	0.097561	0.990964
PLEKHH2	130271	__UNKNOWN__	__UNKNOWN__	2	43927853	43927853	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:43927853G>A	ENST00000282406.4	+	8	1760					NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	NA		NA			negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				gtgcagtggcgcgatcttggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527	130271		Pleckstrin homology (PH) domain containing	30506	protein-coding gene	gene with protein product		612723			NA		Standard	NM_172069	NM_172069	NA	Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.1650+106G>A	chr2.hg19:g.43927853G>A		NA	Q5JPJ6|Q6P4Q1|Q8N3Q3	hg19	CCDS1812.1	0.02	-0.333337	GGCxCGA	COVERED																																																																																			NOVEL	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250537.1	4	2.6397	KEEP	0	1	23	17	501	GG	0.999859	0.851864	0		+	4	60	112	0	0	7.711769	31	60	1045	64	ENST00000282406.4	0.114286	0.851984
DYNC2LI1	51626	__UNKNOWN__	__UNKNOWN__	2	44020809	44020809	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:44020809G>A	ENST00000398823.2	+	0	1390				DYNC2LI1_ENST00000443170.3_Intron|DYNC2LI1_ENST00000260605.8_Intron|DYNC2LI1_ENST00000489222.2_Intron|DYNC2LI1_ENST00000605786.1_Intron|DYNC2LI1_ENST00000406852.3_Intron			Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				tgaactcctggcctcaagtga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036	51626		Cytoplasmic dyneins	24595	protein-coding gene	gene with protein product		NA			NA	10810093, 11907264	Standard	NM_016008	NM_016008	NA	Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000398823.2:c.*880G>A	chr2.hg19:g.44020809G>A		NA	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	hg19		0.02	1.145175	CTGxCCT	COVERED																																																																																			NOVEL	DYNC2LI1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000326194.1	12	4.577704	KEEP	2	2	47	32	938	GG	0.999998	0.998694	0		+	6	60	154	1	0	9.638785	58	60	1900	128	ENST00000398823.2	0.09375	0.998696
LRPPRC	10128	__UNKNOWN__	__UNKNOWN__	2	44202932	44202932	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:44202932A>G	ENST00000409946.1	-	6	768				LRPPRC_ENST00000260665.7_Intron|LRPPRC_ENST00000409659.1_Intron			P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	NA		NA			mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				atgttggccaagctggtcttg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095	10128			15714	protein-coding gene	gene with protein product		607544	Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)	LSFC	NA	8012652, 8619474, 22045337	Standard	NM_133259	NM_133259	NA	Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000409946.1:c.737+349T>C	chr2.hg19:g.44202932A>G		NA	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	hg19		0.02	-0.061404	CCAxGCT	UNCOVERED																																																																																			NOVEL	LRPPRC-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000327824.1	8	2.705982	KEEP	4	0	0	9	237	AA	0	0	0		-	2	60	72	0	0	6.495799	4	60	124	24	ENST00000409946.1	0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	44259264	44259264	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:44259264A>G			NA	NA				LRPPRC (36120 upstream) : RNU6-566P (122663 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.44259264A>G		NA		hg19		0.02	-0.166652	GCTxGGA	COVERED																																																																																			NOVEL					0			9	3.308108	KEEP	1	0	0	11	300	AA	0.993072	0.351495	0			3	60	106	0	0	8.772146	12	60	358	46		0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	44392918	44392918	__UNKNOWN__	IGR	SNP	G	G	A	rs565054527	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:44392918G>A			NA	NA				RNU6-566P (10884 upstream) : RP11-559M23.1 (1845 downstream)						NA		NA									NA						aggctgaggcgggaggatcac	0.527		NA											G|||	2	0.000399361	0.0	0.0	5008	,	,	NA	16327	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.44392918G>A		NA		hg19		0.02	-0.131581	GGCxGGA	COVERED																																																																																			NOVEL					0			5	3.008524	KEEP	1	0	0	10	299	GG	0.992708	0.227502	0			4	60	118	0	0	10.22339	9	60	307	40		0.307692	0.229173
SLC3A1	6519	__UNKNOWN__	__UNKNOWN__	2	44542348	44542348	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:44542348T>C	ENST00000409387.1	+	9	1689				SLC3A1_ENST00000409380.1_Intron|SLC3A1_ENST00000260649.6_Intron|SLC3A1_ENST00000409740.3_Intron|SLC3A1_ENST00000409229.3_3'UTR			Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	NA		NA			amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	tcccaaagtgttgggattaca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079	6519		Solute carriers	11025	protein-coding gene	gene with protein product		104614	solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1		NA	8486766, 9186880	Standard	NM_000341	NM_000341	NA	Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000409387.1:c.1617+1258T>C	chr2.hg19:g.44542348T>C		NA	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	hg19		0.02	3.830009	GTGxTGG	COVERED																																																																																			NOVEL	SLC3A1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000327835.1	13	3.553442	KEEP	1	2	60	33	899	TT	0.999999	0.999989	0		+	5	60	171	0	0	10.847967	96	60	2839	226	ENST00000409387.1	0.049505	0.999991
PREPL	9581	__UNKNOWN__	__UNKNOWN__	2	44583654	44583654	__UNKNOWN__	Intron	SNP	G	G	A	rs149213259	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:44583654G>A	ENST00000409411.1	-	1	167				PREPL_ENST00000410081.1_Intron|PREPL_ENST00000260648.6_Intron|PREPL_ENST00000378520.3_Intron|PREPL_ENST00000409272.1_Intron|PREPL_ENST00000409957.1_Intron|PREPL_ENST00000541738.1_Intron|PREPL_ENST00000378511.3_Intron|PREPL_ENST00000409936.1_Intron|PREPL_ENST00000540817.1_Intron	NM_001171613.1	NP_001165084.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	NA		NA				cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				attgcactccggcctgggcaa	0.493		NA											G|||	45	0.00898562	0.0333	0.0014	5008	,	,	NA	17689	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078	9581			30228	protein-coding gene	gene with protein product		609557			NA	11524703	Standard	NM_006036	NM_006036	NA	Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409411.1:c.47+4864C>T	chr2.hg19:g.44583654G>A		NA	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	hg19	CCDS54353.1	0.02	-0.105263	TCCxGCC	UNCOVERED																																																																																			NOVEL	PREPL-007	NOVEL	alternative_5_UTR|not_organism_supported|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327899.6	10	3.30949	KEEP	1	0	0	11	327	GG	0.992708	0.161282	0		-	3	60	91	0	0	8.043265	6	60	198	32	ENST00000409411.1	0.333333	0.162467
PRKCE	5581	__UNKNOWN__	__UNKNOWN__	2	46084803	46084803	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:46084803T>C	ENST00000306156.3	+	2	739					NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	NA		NA			activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	ctgcctgccttggcctcccaa	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	5581	2.7.11.1		9401	protein-coding gene	gene with protein product		176975			NA	1382605, 7877991	Standard		NM_005400	NA	Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.412+14601T>C	chr2.hg19:g.46084803T>C		NA	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	hg19	CCDS1824.1	0.02	-0.17541	CCTxGGC	COVERED																																																																																			NOVEL	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250751.2	13	3.910135	KEEP	5	0	0	13	363	TT	0.993634	0.38494	0		+	3	49	101	0	0	8.178933	13	60	376	53	ENST00000306156.3	0.1875	0.387407
PRKCE	5581	__UNKNOWN__	__UNKNOWN__	2	46247246	46247246	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:46247246T>C	ENST00000306156.3	+	10	1764					NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	NA		NA			activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	gcctcggccttccacaatgct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	5581	2.7.11.1		9401	protein-coding gene	gene with protein product		176975			NA	1382605, 7877991	Standard		NM_005400	NA	Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.1437+9590T>C	chr2.hg19:g.46247246T>C		NA	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	hg19	CCDS1824.1	0.02	-0.096436	CCTxCCA	UNCOVERED																																																																																			NOVEL	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250751.2	6	2.705336	KEEP	1	0	0	9	242	TT	0.99254	0.119538	0		+	3	60	88	0	0	7.432423	8	60	220	27	ENST00000306156.3	0.272727	0.120436
SOCS5	9655	__UNKNOWN__	__UNKNOWN__	2	46984819	46984819	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:46984819A>G	ENST00000306503.5	+	2	160				SOCS5_ENST00000394861.2_Intron	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	NA		NA			cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			caacctgaccaacatggtgaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150	9655		Suppressors of cytokine signaling, SH2 domain containing	16852	protein-coding gene	gene with protein product		607094			NA	9734811, 11230166	Standard		NM_014011	NA	Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.-12-839A>G	chr2.hg19:g.46984819A>G		NA	Q53SD4|Q8IYZ4	hg19	CCDS1830.1	0.02	-0.114005	ACCxACA	UNCOVERED																																																																																			NOVEL	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250791.2	5	2.403061	KEEP	3	0	0	8	194	AA	0.99257	0.16126	0		+	7	60	240	0	0	23.802179	5	60	130	29	ENST00000306503.5	0.583333	0.162467
AC073283.4	0	__UNKNOWN__	__UNKNOWN__	2	47472812	47472812	__UNKNOWN__	lincRNA	SNP	G	G	A	rs7587311	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:47472812G>A	ENST00000419035.1	-	0	66										NA		NA						p.0?(2)|p.?(1)			NA						caaacatggcgaaatcttgtc	0.522		NA											g|||	970	0.19369	0.2602	0.2522	5008	,	,	NA	13821	0.1438	NA	0.163	False	NA	,,,	NA	NA	NA	2504	0.1452	NA	NA	NA								NA				3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000419035.1:	chr2.hg19:g.47472812G>A		NA		hg19		0.02	-0.078935	GGCxAAA	UNCOVERED																																																																																			NOVEL	AC073283.4-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000323519.1	3	2.407053	KEEP	0	0	0	8	242	GG	0.99257	0.076761	0		-	3	60	82	0	0	7.332098	5	60	159	22	ENST00000419035.1	0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	47628632	47628632	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:47628632T>C			NA	NA				EPCAM (14459 upstream) : MSH2 (1475 downstream)						NA		NA						p.0?(2)|p.?(1)			NA						tcaggtgatctgcccgcctcg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.47628632T>C		NA		hg19		0.02	-0.157853	ATCxGCC	UNCOVERED																																																																																			NOVEL					0			13	3.007878	KEEP	14	0	0	10	279	TT	0	0	0			4	60	133	0	0	11.068774	14	60	405	51		0.222222	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	47888224	47888224	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:47888224C>T			NA	NA				AC138655.1 (86226 upstream) : MSH6 (34444 downstream)						NA		NA						p.0?(2)|p.?(1)			NA						tagctgggaccacagactcat	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(2)|prostate(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.47888224C>T		NA		hg19		0.02	-0.377222	GACxACA	COVERED																																																																																			NOVEL					0			16	4.81418	KEEP	0	0	0	16	488	CC	0.997832	0.907098	0			3	60	95	0	0	6.340962	36	60	1236	82		0.076923	0.909069
MSH6	2956	__UNKNOWN__	__UNKNOWN__	2	48012646	48012646	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:48012646C>T	ENST00000234420.5	+	1	412				MSH6_ENST00000538136.1_Intron|MSH6_ENST00000540021.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	NA		NA			ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			tgtgagccaccgtgcccggcc	0.463		NA	Mis, N, F, S		colorectal	colorectal, endometrial, ovarian		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062	2956			7329	protein-coding gene	gene with protein product		600678	mutS (E. coli) homolog 6, mutS homolog 6 (E. coli)	GTBP	NA	7604266	Standard	NM_000179	NM_000179	NA	Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.260+2014C>T	chr2.hg19:g.48012646C>T		NA	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	hg19	CCDS1836.1	0.02	-0.157895	CACxGTG	UNCOVERED																																																																																			NOVEL	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251180.4	4	2.405867	KEEP	1	0	0	8	221	CC	0	0	0		+	3	60	93	0	0	7.29176	14	60	453	32	ENST00000234420.5	0.176471	0.322807
AC079807.4	0	__UNKNOWN__	__UNKNOWN__	2	48230098	48230098	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:48230098T>C	ENST00000447571.1	-	0	366										NA		NA						p.0?(2)			NA						TTTTCAGggctgggcacggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000447571.1:	chr2.hg19:g.48230098T>C		NA		hg19		0.02	-0.157864	GGCxGGG	COVERED																																																																																			NOVEL	AC079807.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000323780.4	6	2.705805	KEEP	0	0	0	9	251	AT	0.992708	0.351366	0		-	3	60	93	1	0	7.210901	15	60	449	42	ENST00000447571.1	0.166667	0.353947
STON1	11037	__UNKNOWN__	__UNKNOWN__	2	48799138	48799138	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:48799138C>T	ENST00000406226.1	+	3	148				STON1-GTF2A1L_ENST00000394754.1_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron|STON1-GTF2A1L_ENST00000405008.1_Intron|STON1_ENST00000404752.1_Intron	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	NA		NA			endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			cctgtctctactaaaaataca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244	11037			17003	protein-coding gene	gene with protein product	stoned B homolog 1 (Drosophila)	605357			NA	14504226, 10364255	Standard	NM_006873	NM_001198595	NA	Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.-47-8588C>T	chr2.hg19:g.48799138C>T		NA	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	hg19	CCDS1841.1	0.02	-0.105266	CTAxTAA	UNCOVERED																																																																																			NOVEL	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323848.2	7	2.407259	KEEP	1	0	0	8	250	CC	0	0	0		+	3	33	91	0	0	7.600928	9	60	305	26	ENST00000406226.1	0.25	0.139832
STON1-GTF2A1L	286749	__UNKNOWN__	__UNKNOWN__	2	48874011	48874011	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:48874011A>G	ENST00000394754.1	+	8	3034	c.2920A>G	c.(2920-2922)Atg>Gtg	p.M974V	GTF2A1L_ENST00000430487.2_Missense_Mutation_p.M236V|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.M974V|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.M974V|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.M927V|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.M974V|GTF2A1L_ENST00000403751.3_Missense_Mutation_p.M270V|LHCGR_ENST00000420913.3_Intron	NM_172311.2	NP_758515.1			STON1-GTF2A1L readthrough	NA		NA								NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(22)|liver(2)|lung(49)|ovary(3)|pancreas(1)|prostate(4)|skin(4)	91		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TTCAGCTAGCATGGCTCAAAA	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													91	89	90			NA	NA	2		NA											NA				48874011		2203	4300	6503	SO:0001583	missense			AF026169	CCDS1840.1, CCDS56118.1, CCDS56119.1	2p16.3	2009-09-17			ENSG00000068781	ENSG00000068781	286749			30651	other	readthrough	stoned B/TFIIA alpha/beta like factor	NA			NA	10364255, 11159353	Standard		NM_172311	NA	Approved	SALF	uc010yol.2		OTTHUMG00000152037	ENST00000394754.1:c.2920A>G	chr2.hg19:g.48874011A>G	ENSP00000378236:p.Met974Val	NA		hg19	CCDS1840.1	0.02	1.853587	AGCxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.360	-0.940087	0.02322	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T;T;T	0.37752	1.18;1.18;1.18;1.18;1.18;1.18;1.18;1.18	4.69	-4.49	0.03504	.	1.083190	0.07015	N	0.825733	T	0.18593	0.0446	N	0.17082	0.46	0.29540	N	0.852114	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.001	T	0.36648	-0.9739	10	0.15499	T	0.54	.	8.7198	0.34434	0.3246:0.1389:0.5366:0.0	.	236;927;974;270;974	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	V	974;974;974;974;927;269;279;236;270	ENSP00000385499:M974V;ENSP00000385701:M974V;ENSP00000378236:M974V;ENSP00000311493:M974V;ENSP00000378234:M927V;ENSP00000396702:M279V;ENSP00000387896:M236V;ENSP00000384597:M270V	ENSP00000384597:M270V	M	+	1	0	STON1-GTF2A1L;GTF2A1L	48727515	0.000000	0.05858	0.005000	0.12908	0.892000	0.51952	-1.283000	0.02796	-0.693000	0.05121	0.482000	0.46254	ATG	NOVEL	STON1-GTF2A1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251241.1	2	3.007452	KEEP	0	0	0	10	273	AA	0.992708	0.982326	0		+	20	60	654	0	0	58.358589	40	60	1193	104	ENST00000394754.1	0.333333	0.989542
NRXN1	9378	__UNKNOWN__	__UNKNOWN__	2	50249400	50249400	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:50249400A>G	ENST00000404971.1	-	22	5588				NRXN1_ENST00000406316.2_Intron|NRXN1_ENST00000342183.5_Intron|NRXN1_ENST00000402717.3_Intron|NRXN1_ENST00000401710.1_Intron|NRXN1_ENST00000406859.3_Intron|NRXN1_ENST00000405472.3_Intron|NRXN1_ENST00000401669.2_Intron	NM_001135659.1	NP_001129131.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	NA		NA			adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			gattacaggcatgagccactg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915	9378			8008	protein-coding gene	gene with protein product		600565			NA		Standard		NM_001135659	NA	Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000404971.1:c.4248+31008T>C	chr2.hg19:g.50249400A>G		NA	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	hg19	CCDS46282.1	0.02	-0.131566	GGCxTGA	COVERED																																																																																			NOVEL	NRXN1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323894.3	8	2.405483	KEEP	0	0	0	8	213	AA	0.99257	0.22747	0		-	3	60	96	0	0	7.98203	10	60	299	33	ENST00000404971.1	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	53830572	53830572	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:53830572T>C			NA	NA				RNU6-997P (32955 upstream) : AC008064.1 (47965 downstream)						NA		NA									NA						cctataatcctggcactttgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.53830572T>C		NA		hg19		0.02	-0.157894	TCCxGGC	COVERED																																																																																			NOVEL					0			8	3.308948	KEEP	0	0	0	11	314	TT	0.993072	0.32057	0			3	60	102	0	0	8.472738	11	60	341	44		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	53830573	53830573	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:53830573G>A			NA	NA				RNU6-997P (32956 upstream) : AC008064.1 (47964 downstream)						NA		NA									NA						ctataatcctggcactttggg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.53830573G>A		NA		hg19		0.02	-0.157895	CCTxGCA	COVERED																																																																																			NOVEL					0			8	3.0091	KEEP	0	0	0	10	311	GG	0.992708	0.320453	0			3	60	88	1	0	7.072809	11	60	371	44		0.214286	0.322807
ACYP2	98	__UNKNOWN__	__UNKNOWN__	2	54229750	54229750	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:54229750A>G	ENST00000422521.2	+	2	312				ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000458030.3_Intron			P14621	ACYP2_HUMAN	acylphosphatase 2, muscle type	NA		NA			phosphate-containing compound metabolic process (GO:0006796)	mitochondrion (GO:0005739)	acylphosphatase activity (GO:0003998)			lung(1)	1						ccaaagtgctaggattatagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X84195	CCDS1850.1	2p16.2	2008-02-05			ENSG00000170634	ENSG00000170634	98	3.6.1.7		180	protein-coding gene	gene with protein product		102595			NA	8268218	Standard		NM_138448	NA	Approved		uc002rxq.4	P14621	OTTHUMG00000129287	ENST00000422521.2:c.62+28803A>G	chr2.hg19:g.54229750A>G		NA		hg19		0.02	-0.131553	GCTxGGA	COVERED																																																																																			NOVEL	ACYP2-007	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000470826.1	4	2.706629	KEEP	0	0	0	9	244	AA	0.99254	0.227464	0		+	3	60	96	0	0	7.772428	12	60	350	35	ENST00000422521.2	0.2	0.229173
ACYP2	98	__UNKNOWN__	__UNKNOWN__	2	54369625	54369625	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:54369625T>C	ENST00000394666.3	+	3	380				ACYP2_ENST00000406041.1_3'UTR|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron	NM_138448.3	NP_612457.1	P14621	ACYP2_HUMAN	acylphosphatase 2, muscle type	NA		NA			phosphate-containing compound metabolic process (GO:0006796)	mitochondrion (GO:0005739)	acylphosphatase activity (GO:0003998)			lung(1)	1						ttcgggaggctgaggcgggcg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X84195	CCDS1850.1	2p16.2	2008-02-05			ENSG00000170634	ENSG00000170634	98	3.6.1.7		180	protein-coding gene	gene with protein product		102595			NA	8268218	Standard		NM_138448	NA	Approved		uc002rxq.4	P14621	OTTHUMG00000129287	ENST00000394666.3:c.185+3740T>C	chr2.hg19:g.54369625T>C		NA		hg19	CCDS1850.1	0.02	3.38843	GGCxGAG	COVERED																																																																																			NOVEL	ACYP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251415.3	37	5.759293	KEEP	1	7	180	83	2258	TT	1	1	0		+	7	60	217	0	0	13.263475	121	60	3544	336	ENST00000394666.3	0.054687	1
RTN4	57142	__UNKNOWN__	__UNKNOWN__	2	55209306	55209306	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:55209306A>G	ENST00000394609.2	-	3	710				RTN4_ENST00000394611.2_Intron|RTN4_ENST00000337526.6_Intron|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Intron|RTN4_ENST00000354474.6_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Intron|RTN4_ENST00000486085.1_Intron|RTN4_ENST00000404909.1_Intron	NM_007008.2	NP_008939.1	Q9NQC3	RTN4_HUMAN	reticulon 4	NA		NA			angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						tggccaggctagtctcaaact	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310	57142			14085	protein-coding gene	gene with protein product		604475			NA	10667797, 10773680	Standard		NM_020532	NA	Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000394609.2:c.381+344T>C	chr2.hg19:g.55209306A>G		NA	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	hg19	CCDS42685.1	0.02	-0.140323	GCTxGTC	COVERED																																																																																			NOVEL	RTN4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326317.1	7	3.608565	KEEP	1	0	0	12	323	AA	0.993634	0.259304	0		-	3	40	106	0	0	8.982264	10	60	293	40	ENST00000394609.2	0.230769	0.260965
CCDC88A	55704	__UNKNOWN__	__UNKNOWN__	2	55533328	55533328	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:55533328A>G	ENST00000263630.8	-	25	5164				CCDC88A_ENST00000422883.2_Intron|CCDC88A_ENST00000336838.6_Intron|CCDC88A_ENST00000436346.1_Intron|CCDC88A_ENST00000413716.2_Intron	NM_018084.4	NP_060554.3	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	NA		NA			activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						tggaattacaagtgtgagcca	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355	55704			25523	protein-coding gene	gene with protein product	Galpha-interacting vesicle-associated protein, Akt-phosphorylation enhancer, girdin, girders of actin filaments	609736	KIAA1212	KIAA1212	NA	15749703, 15753085	Standard	NM_017571	NM_001135597	NA	Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000263630.8:c.4387+2616T>C	chr2.hg19:g.55533328A>G		NA	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	hg19	CCDS33203.1	0.02	-0.184208	ACAxGTG	COVERED																																																																																			NOVEL	CCDC88A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324406.3	10	3.309074	KEEP	0	0	0	11	314	AA	0.993072	0.420544	0		-	3	60	109	0	0	8.732912	16	60	501	49	ENST00000263630.8	0.157895	0.423478
CCDC104	0	__UNKNOWN__	__UNKNOWN__	2	55752852	55752852	__UNKNOWN__	Intron	SNP	C	C	T	rs573721744	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:55752852C>T	ENST00000349456.4	+	3	430				CCDC104_ENST00000406691.3_Intron|CCDC104_ENST00000407816.3_Intron|CCDC104_ENST00000403007.3_Intron|CCDC104_ENST00000339012.3_Intron			Q96G28	CFA36_HUMAN		NA		NA								breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(2)|lung(1)|ovary(2)	14			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ctgcaacctccgtctcctagg	0.483		NA											C|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	19146	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000349456.4:c.282+1894C>T	chr2.hg19:g.55752852C>T		NA	Q53SF0|Q53ST9|Q6UY34	hg19	CCDS1854.2	0.02	-0.114021	CTCxGTC	UNCOVERED																																																																																			NOVEL	CCDC104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319610.2	8	3.007612	KEEP	1	0	0	10	279	CC	0.992708	0.161282	0		+	4	30	116	0	0	10.023646	9	60	282	29	ENST00000349456.4	0.307692	0.162467
SMEK2	57223	__UNKNOWN__	__UNKNOWN__	2	55775033	55775033	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:55775033A>G	ENST00000272313.5	-	0	4636					NM_020463.2	NP_065196.1	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	NA		NA			positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			cagcctgggcaacagagcgag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041		57223			29267	protein-coding gene	gene with protein product		610352			NA	16085932, 18614045	Standard	NM_020463	NM_001122964	NA	Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000272313.5:c.*2014T>C	chr2.hg19:g.55775033A>G		NA	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	hg19	CCDS1855.1	0.02	3.358996	GGCxACA	COVERED																																																																																			NOVEL	SMEK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251482.1	49	11.514265	KEEP	1	9	248	126	3465	AA	1	1	0		-	6	60	194	0	0	11.714437	124	60	3656	381	ENST00000272313.5	0.046154	1
SMEK2	57223	__UNKNOWN__	__UNKNOWN__	2	55823827	55823827	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:55823827A>G	ENST00000272313.5	-	4	1249				SMEK2_ENST00000345102.5_Intron|SMEK2_ENST00000407823.3_Intron	NM_020463.2	NP_065196.1	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	NA		NA			positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ggccaggtgcagtggctcacg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041		57223			29267	protein-coding gene	gene with protein product		610352			NA	16085932, 18614045	Standard	NM_020463	NM_001122964	NA	Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000272313.5:c.921+1724T>C	chr2.hg19:g.55823827A>G		NA	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	hg19	CCDS1855.1	0.02	-0.219287	TGCxGTG	COVERED																																																																																			NOVEL	SMEK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251482.1	8	2.707357	KEEP	6	0	0	9	256	AA	0.99257	0.54878	0		-	3	60	103	0	0	7.864567	20	60	615	58	ENST00000272313.5	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	55943918	55943918	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:55943918C>G			NA	NA				PNPT1 (22873 upstream) : EFEMP1 (149183 downstream)						NA		NA									NA						CATGCCAAGTCTGAGGTACTT	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.55943918C>G		NA		hg19		0.02	-0.087725	AGTxTGA	UNCOVERED																																																																																			NOVEL					0			6	2.406795	KEEP	0	0	0	8	240	CC	0.99257	0.09898	0			3	60	96	0	0	8.543369	6	60	206	26		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	57175532	57175532	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:57175532A>G			NA	NA				CCDC85A (562224 upstream) : snoU13 (67663 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.57175532A>G		NA		hg19		0.02	-0.157874	GGCxTGA	COVERED																																																																																			NOVEL					0			8	3.308181	KEEP	0	0	0	11	300	AA	0.993072	0.32057	0			3	60	101	0	0	8.010155	15	60	445	41		0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	57466163	57466163	__UNKNOWN__	IGR	SNP	T	T	C	rs556189562		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:57466163T>C			NA	NA				snoU13 (222864 upstream) : SNORD78 (305506 downstream)						NA		NA									NA						acctcggccttccaaagtgct	0.448		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14653	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.57466163T>C		NA		hg19		0.02	-0.140333	CCTxCCA	COVERED																																																																																			NOVEL					0			4	2.4054	KEEP	1	0	0	8	215	TT	0.99257	0.259026	0			3	60	97	0	0	8.332463	8	60	243	37		0.272727	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	57597880	57597880	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:57597880T>C			NA	NA				snoU13 (354581 upstream) : SNORD78 (173789 downstream)						NA		NA									NA						atcctcctgcttcagcctgcc	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.57597880T>C		NA		hg19		0.02	-0.087689	TGCxTCA	UNCOVERED																																																																																			NOVEL					0			7	2.40632	KEEP	0	0	0	8	225	TT	0.99257	0.09898	0			3	60	101	0	0	9.044157	6	60	170	24		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	57704292	57704292	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:57704292T>C			NA	NA				snoU13 (460993 upstream) : SNORD78 (67377 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.57704292T>C		NA		hg19		0.02	-0.017538	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			8	2.705203	KEEP	5	0	0	9	228	TT	0	0	0			2	31	62	0	1	7.15278	0	0	0	14		1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	58560367	58560367	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:58560367T>C			NA	NA				AC007250.4 (36684 upstream) : AC007092.1 (95105 downstream)						NA		NA									NA						aatcccagcattttggaaagc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.58560367T>C		NA		hg19		0.02	-0.157843	GCAxTTT	COVERED																																																																																			NOVEL					0			4	3.909636	KEEP	1	0	0	13	357	TT	0.993634	0.320751	0			3	60	103	0	0	8.573291	11	60	304	43		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	60925733	60925733	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:60925733C>T			NA	NA				RN7SL361P (57598 upstream) : RNU6-612P (21041 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.60925733C>T		NA		hg19		0.02	-0.140351	AGGxGTG	COVERED																																																																																			NOVEL					0			12	3.008561	KEEP	10	0	0	10	299	AC	0.99257	0.259026	0			3	60	87	0	0	6.872328	12	60	403	50		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61027394	61027394	__UNKNOWN__	IGR	SNP	C	C	G	rs6704900	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61027394C>G			NA	NA				PAPOLG (1296 upstream) : RN7SL632P (31405 downstream)						NA		NA									NA						gatctcacctcactgcaacct	0.443		NA											C|||	391	0.0780751	0.056	0.1138	5008	,	,	NA	17388	0.0	NA	0.1968	False	NA	,,,	NA	NA	NA	2504	0.0409	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61027394C>G		NA		hg19		0.02	-0.096492	CCTxACT	UNCOVERED																																																																																			NOVEL					0			4	2.402429	KEEP	0	0	0	8	224	CC	0.99257	0.119541	0			7	60	219	0	0	22.58522	3	60	104	23		0.7	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61283802	61283802	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61283802G>A			NA	NA				PEX13 (4677 upstream) : KIAA1841 (9203 downstream)						NA		NA									NA						gacgagtctcgcactgtcgcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61283802G>A		NA		hg19		0.02	-0.105225	CTCxCAC	UNCOVERED																																																																																			NOVEL					0			7	3.007583	KEEP	0	0	0	10	286	GG	0.992708	0.138812	0			3	44	82	0	0	6.832653	8	60	234	28		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61283804	61283804	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61283804A>T			NA	NA				PEX13 (4679 upstream) : KIAA1841 (9201 downstream)						NA		NA									NA						cgagtctcgcactgtcgccca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61283804A>T		NA		hg19		0.02	-0.105216	CGCxCTG	UNCOVERED																																																																																			NOVEL					0			7	3.006276	KEEP	0	0	0	10	261	AA	0.992708	0.138812	0			3	44	91	0	0	7.733098	8	60	218	28		0.272727	0.139832
KIAA1841	84542	__UNKNOWN__	__UNKNOWN__	2	61307632	61307632	__UNKNOWN__	Intron	SNP	C	C	T	rs530278510	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61307632C>T	ENST00000402291.1	+	7	911				KIAA1841_ENST00000453873.1_Intron|KIAA1841_ENST00000295031.5_Intron|KIAA1841_ENST00000482513.1_Intron|KIAA1841_ENST00000356719.2_Intron	NM_001129993.1	NP_001123465.1	Q6NSI8	K1841_HUMAN	KIAA1841	NA		NA								breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			ccaaggcgggcggatcacgag	0.527		NA											C|||	4	0.000798722	0.0023	0.0014	5008	,	,	NA	15826	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929	84542			29387	protein-coding gene	gene with protein product		NA			NA	11347906	Standard	NM_032506	NM_032506	NA	Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000402291.1:c.671-955C>T	chr2.hg19:g.61307632C>T		NA	Q49AF0|Q6ZND0|Q96JI6	hg19	CCDS46296.1	0.02	-0.140334	GGGxGGA	COVERED																																																																																			NOVEL	KIAA1841-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325477.1	4	3.008717	KEEP	1	0	0	10	305	CC	0.99254	0.259018	0		+	3	60	95	0	0	7.672354	12	60	366	37	ENST00000402291.1	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61366099	61366099	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61366099C>T			NA	NA				KIAA1841 (930 upstream) : AC016747.3 (2632 downstream)						NA		NA									NA						tccttctttccttccttcctt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61366099C>T		NA		hg19		0.02	-0.114035	TTCxTTC	UNCOVERED																																																																																			NOVEL					0			6	2.407292	KEEP	0	0	0	8	249	CC	0.99257	0.16126	0			3	50	85	0	0	6.881869	10	60	341	30		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61366103	61366103	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61366103C>T			NA	NA				KIAA1841 (934 upstream) : AC016747.3 (2628 downstream)						NA		NA									NA						tctttccttccttcctttttc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61366103C>T		NA		hg19		0.02	-0.131581	TTCxTTC	COVERED																																																																																			NOVEL					0			8	2.708182	KEEP	0	0	0	9	279	CC	0.99254	0.227464	0			3	50	89	0	0	7.072239	12	60	401	33		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61394483	61394483	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61394483T>C			NA	NA				C2orf74 (2519 upstream) : AHSA2 (10069 downstream)						NA		NA									NA						agccttggcctcccaaagtgc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61394483T>C		NA		hg19		0.02	-0.166662	GCCxCCC	COVERED																																																																																			NOVEL					0			8	5.113266	KEEP	3	0	0	17	476	TT	0.99649	0.352705	0			3	36	104	0	0	8.57208	12	60	370	62		0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61394487	61394487	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61394487A>T			NA	NA				C2orf74 (2523 upstream) : AHSA2 (10065 downstream)						NA		NA									NA						ttggcctcccaaagtgctggg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61394487A>T		NA		hg19		0.02	-0.175407	CCCxAAG	COVERED																																																																																			NOVEL					0			9	5.113441	KEEP	3	0	0	17	476	AA	0.99649	0.386047	0			3	36	94	0	0	7.572434	12	60	350	62		0.2	0.387407
USP34	9736	__UNKNOWN__	__UNKNOWN__	2	61464828	61464828	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61464828T>C	ENST00000398571.2	-	54	6854					NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	NA		NA			positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ctcaacctcctgagcagctgg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464	9736		Ubiquitin-specific peptidases	20066	protein-coding gene	gene with protein product		615295	ubiquitin specific protease 34		NA	12838346	Standard		NM_014709	NA	Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.6778-1304A>G	chr2.hg19:g.61464828T>C		NA	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	hg19	CCDS42686.1	0.02	-0.140338	TCCxGAG	COVERED																																																																																			NOVEL	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325650.4	10	2.706908	KEEP	0	0	0	9	250	TT	0.99254	0.259018	0		-	3	42	89	0	0	6.979268	13	60	403	33	ENST00000398571.2	0.1875	0.260965
USP34	9736	__UNKNOWN__	__UNKNOWN__	2	61499548	61499548	__UNKNOWN__	Intron	SNP	A	A	G	rs72811494	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61499548A>G	ENST00000398571.2	-	41	5510					NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	NA		NA			positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			cccatctcaaaaaaaaaaaaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464	9736		Ubiquitin-specific peptidases	20066	protein-coding gene	gene with protein product		615295	ubiquitin specific protease 34		NA	12838346	Standard		NM_014709	NA	Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5433+5751T>C	chr2.hg19:g.61499548A>G		NA	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	hg19	CCDS42686.1	0.02	-0.070167	CAAxAAA	UNCOVERED																																																																																			NOVEL	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325650.4	25	3.306843	KEEP	17	0	0	11	289	AA	0	0	0		-	2	60	69	1	0	6.39291	3	60	93	44	ENST00000398571.2	0.4	0.054137
USP34	9736	__UNKNOWN__	__UNKNOWN__	2	61538621	61538621	__UNKNOWN__	Intron	SNP	G	G	A	rs73936115|rs373837162	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61538621G>A	ENST00000398571.2	-	27	3894					NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	NA		NA			positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			aagagaaagagaaaaagaaag	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464	9736		Ubiquitin-specific peptidases	20066	protein-coding gene	gene with protein product		615295	ubiquitin specific protease 34		NA	12838346	Standard		NM_014709	NA	Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3817+53C>T	chr2.hg19:g.61538621G>A		NA	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	hg19	CCDS42686.1	0.02	-0.201763	AGAxAAA	COVERED																																																																																			NOVEL	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325650.4	2	2.6404	KEEP	1	1	23	17	516	GG	0.999366	0.490234	0		-	3	60	89	0	2	6.527626	19	60	639	43	ENST00000398571.2	0.136364	0.490544
RP11-355B11.2	0	__UNKNOWN__	__UNKNOWN__	2	61704478	61704478	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61704478G>A	ENST00000603652.1	+	0	192				RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000603199.1_RNA|RP11-355B11.2_ENST00000603028.1_RNA						NA		NA									NA						agattctcctggctcagcctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603652.1:	chr2.hg19:g.61704478G>A		NA		hg19		0.02	-0.105262	CCTxGCT	UNCOVERED																																																																																			NOVEL	RP11-355B11.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000469979.1	6	2.707871	KEEP	0	0	0	9	271	GG	0.99254	0.138789	0		+	3	60	90	0	0	7.778286	7	60	242	25	ENST00000603652.1	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61857922	61857922	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61857922A>G			NA	NA				RNU6-1145P (25065 upstream) : FAM161A (194068 downstream)						NA		NA									NA						tgatccacccacctcagcctc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61857922A>G		NA		hg19		0.02	-0.175416	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			13	2.405298	KEEP	11	0	0	8	214	AA	0	0	0			3	51	95	0	1	7.261305	17	60	513	51		0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	61882054	61882054	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:61882054A>G			NA	NA				RNU6-1145P (49197 upstream) : FAM161A (169936 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.61882054A>G		NA		hg19		0.02	-0.236796	CACxCCT	COVERED																																																																																			NOVEL					0			9	2.406268	KEEP	0	0	0	8	223	AA	0.99257	0.607857	0			3	60	103	0	0	7.748834	22	60	649	51		0.12	0.612407
COMMD1	150684	__UNKNOWN__	__UNKNOWN__	2	62141044	62141044	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62141044C>T	ENST00000311832.5	+	1	212				COMMD1_ENST00000538736.1_Intron|COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	NA		NA			copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			cggtggctcacgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163	150684			23024	protein-coding gene	gene with protein product	copper metabolism gene MURR1	607238	chromosome 2 open reading frame 5 (MURR1)	C2orf5	NA	9001233, 11809725	Standard	NM_152516	NM_152516	NA	Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.180+8051C>T	chr2.hg19:g.62141044C>T		NA	B4DFQ4|Q96GS0	hg19	CCDS1869.1	0.02	-0.157341	TCAxGCC	COVERED																																																																																			NOVEL	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251607.2	3	2.407149	KEEP	2	0	0	8	244	CC	0.99257	0.320408	0		+	3	60	86	0	0	6.516257	15	60	481	43	ENST00000311832.5	0.166667	0.322807
COMMD1	150684	__UNKNOWN__	__UNKNOWN__	2	62181092	62181092	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62181092T>C	ENST00000311832.5	+	2	212				COMMD1_ENST00000538736.1_Intron|COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	NA		NA			copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			cggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163	150684			23024	protein-coding gene	gene with protein product	copper metabolism gene MURR1	607238	chromosome 2 open reading frame 5 (MURR1)	C2orf5	NA	9001233, 11809725	Standard	NM_152516	NM_152516	NA	Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.181-46744T>C	chr2.hg19:g.62181092T>C		NA	B4DFQ4|Q96GS0	hg19	CCDS1869.1	0.02	-0.210473	TCAxGCC	UNCOVERED																																																																																			NOVEL	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251607.2	5	2.405277	KEEP	1	0	0	8	213	TT	0	0	0		+	3	60	104	0	0	7.964826	20	60	578	44	ENST00000311832.5	0.130435	0.522161
COMMD1	150684	__UNKNOWN__	__UNKNOWN__	2	62289400	62289400	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62289400T>C	ENST00000311832.5	+	2	494				COMMD1_ENST00000472729.1_Intron	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	NA		NA			copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			tcgctcttgttgcccaggctg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163	150684			23024	protein-coding gene	gene with protein product	copper metabolism gene MURR1	607238	chromosome 2 open reading frame 5 (MURR1)	C2orf5	NA	9001233, 11809725	Standard	NM_152516	NM_152516	NA	Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.462+61283T>C	chr2.hg19:g.62289400T>C		NA	B4DFQ4|Q96GS0	hg19	CCDS1869.1	0.02	-0.183696	TGTxGCC	COVERED																																																																																			NOVEL	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251607.2	11	4.508573	KEEP	3	0	0	15	395	TT	0.995343	0.421506	0		+	3	60	90	2	0	6.765961	17	60	451	57	ENST00000311832.5	0.15	0.423478
COMMD1	150684	__UNKNOWN__	__UNKNOWN__	2	62350379	62350379	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62350379A>G	ENST00000311832.5	+	3	494				AC018462.2_ENST00000425966.2_RNA|COMMD1_ENST00000472729.1_Intron|AC018462.2_ENST00000421323.1_RNA	NM_152516.2	NP_689729.1	Q8N668	COMD1_HUMAN	copper metabolism (Murr1) domain containing 1	NA		NA			copper ion homeostasis (GO:0055070)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of protein ubiquitination (GO:0031398)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)	Cul2-RING ubiquitin ligase complex (GO:0031462)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			large_intestine(1)|liver(2)|lung(5)|ovary(1)	9	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;4.73e-07)|Epithelial(17;0.0216)|all cancers(80;0.0934)			ggtggctcacacctgtaatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022046	CCDS1869.1	2p15	2004-03-02	2004-02-13	2004-02-18	ENSG00000173163	ENSG00000173163	150684			23024	protein-coding gene	gene with protein product	copper metabolism gene MURR1	607238	chromosome 2 open reading frame 5 (MURR1)	C2orf5	NA	9001233, 11809725	Standard	NM_152516	NM_152516	NA	Approved	MURR1, MGC27155	uc002sbp.3	Q8N668	OTTHUMG00000129445	ENST00000311832.5:c.463-12587A>G	chr2.hg19:g.62350379A>G		NA	B4DFQ4|Q96GS0	hg19	CCDS1869.1	0.02	-0.280653	CACxCCT	COVERED																																																																																			NOVEL	COMMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251607.2	11	4.207317	KEEP	3	0	0	14	369	AA	0.99649	0.737075	0		+	3	60	99	1	0	7.144471	26	60	768	74	ENST00000311832.5	0.103448	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	62419456	62419456	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62419456C>T			NA	NA				AC018462.2 (45440 upstream) : B3GNT2 (3791 downstream)						NA		NA									NA						ggattacaggcgtgagccact	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.62419456C>T		NA		hg19		0.02	-0.19297	AGGxGTG	COVERED																																																																																			NOVEL					0			9	4.211385	KEEP	7	0	0	14	409	CC	0.992708	0.454419	0			3	60	88	1	0	6.634221	16	60	509	57		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	62484235	62484235	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62484235T>C			NA	NA				B3GNT2 (32369 upstream) : RN7SL51P (5288 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.62484235T>C		NA		hg19		0.02	-0.271884	TCAxGCC	COVERED																																																																																			NOVEL					0			16	3.007592	KEEP	5	0	0	10	276	TT	0.99254	0.711964	0			5	60	169	0	0	13.581293	23	60	675	59		0.178571	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	62572559	62572559	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:62572559T>C			NA	NA				snoU13 (80326 upstream) : AC093159.1 (117702 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.62572559T>C		NA		hg19		0.02	-0.140304	TCAxGCC	COVERED																																																																																			NOVEL					0			4	3.008023	KEEP	0	0	0	10	288	TT	0.992708	0.259062	0			3	60	102	0	0	8.279153	13	60	374	40		0.1875	0.260965
MDH1	4190	__UNKNOWN__	__UNKNOWN__	2	63830127	63830127	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:63830127C>T	ENST00000409476.1	+	3	197				MDH1_ENST00000233114.8_Intron|MDH1_ENST00000539945.1_Intron|MDH1_ENST00000394423.1_Intron|MDH1_ENST00000409908.1_Intron|MDH1_ENST00000544381.1_Intron			P40925	MDHC_HUMAN	malate dehydrogenase 1, NAD (soluble)	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	diiodophenylpyruvate reductase activity (GO:0047860)|L-malate dehydrogenase activity (GO:0030060)|malic enzyme activity (GO:0004470)|NAD binding (GO:0051287)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(4)	13						agagtctcgccctgtcgccta	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1874.1, CCDS56121.1, CCDS56122.1	2p23	2012-10-02			ENSG00000014641	ENSG00000014641	4190	1.1.1.37		6970	protein-coding gene	gene with protein product		154200			NA		Standard		NM_005917	NA	Approved		uc010ypv.2	P40925	OTTHUMG00000129512	ENST00000409476.1:c.127-1703C>T	chr2.hg19:g.63830127C>T		NA	B2R5V5|B4DUN2|B7Z3I7|F5H098|Q6I9V0	hg19		0.02	-0.105265	CGCxCTG	UNCOVERED																																																																																			NOVEL	MDH1-011	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000326992.1	12	3.008978	KEEP	3	0	0	10	307	CC	0.992708	0.138812	0		+	3	36	90	0	0	7.943216	6	60	199	30	ENST00000409476.1	0.333333	0.139832
PELI1	57162	__UNKNOWN__	__UNKNOWN__	2	64354425	64354425	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:64354425A>C	ENST00000358912.4	-	1	374				PELI1_ENST00000466177.2_Intron	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	NA		NA			innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						gtaatcccagaactttgggag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329	57162		Pellino homologs	8827	protein-coding gene	gene with protein product		614797	pellino (Drosophila) homolog 1, pellino homolog 1 (Drosophila)		NA	11306823, 16951688	Standard	NM_020651	NM_020651	NA	Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.68+16789T>G	chr2.hg19:g.64354425A>C		NA	Q96SM0|Q9GZY5|Q9HCX0	hg19	CCDS1876.1	0.02	-0.114029	CAGxACT	UNCOVERED																																																																																			NOVEL	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251686.1	5	2.405859	KEEP	1	0	0	8	218	AA	0	0	0		-	3	60	96	0	0	8.232347	8	60	248	31	ENST00000358912.4	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	64603206	64603206	__UNKNOWN__	IGR	SNP	T	T	C	rs140818980		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:64603206T>C			NA	NA				AC114752.3 (34425 upstream) : AC008074.3 (19147 downstream)						NA		NA									NA						accaccaccatcaccaccatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.64603206T>C		NA		hg19		0.02	-0.095881	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			7	2.403246	KEEP	6	0	0	8	200	AT	0	0	0			3	28	90	1	0	7.790697	7	57	167	31		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	64622340	64622340	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:64622340A>G			NA	NA				AC114752.3 (53559 upstream) : AC008074.3 (13 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.64622340A>G		NA		hg19		0.02	-0.140332	CACxCCT	COVERED																																																																																			NOVEL					0			3	2.406609	KEEP	2	0	0	8	230	AA	0.99257	0.259026	0			3	60	94	0	0	7.572389	12	60	362	40		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	65265613	65265613	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:65265613T>C			NA	NA				AC007386.4 (982 upstream) : CEP68 (17892 downstream)						NA		NA									NA						gtaatcccagtactttgggag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.65265613T>C		NA		hg19		0.02	-0.254328	CAGxACT	COVERED																																																																																			NOVEL					0			10	3.305759	KEEP	0	0	0	11	283	TT	0.993072	0.688863	0			4	60	134	0	0	10.61392	20	60	582	56		0.166667	0.693668
RAB1A	5861	__UNKNOWN__	__UNKNOWN__	2	65353528	65353528	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:65353528A>G	ENST00000409784.3	-	1	214				RAB1A_ENST00000409892.1_Intron|RAB1A_ENST00000494188.1_Intron|RAB1A_ENST00000398529.3_Intron|RAB1A_ENST00000356214.7_Intron|RAB1A_ENST00000409751.1_Intron	NM_004161.4	NP_004152.1	P62820	RAB1A_HUMAN	RAB1A, member RAS oncogene family	NA		NA			autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cargo loading into COPII-coated vesicle (GO:0090110)|cell migration (GO:0016477)|defense response to bacterium (GO:0042742)|endocytosis (GO:0006897)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|growth hormone secretion (GO:0030252)|GTP catabolic process (GO:0006184)|interleukin-8 secretion (GO:0072606)|melanosome transport (GO:0032402)|mitotic cell cycle (GO:0000278)|positive regulation of glycoprotein metabolic process (GO:1903020)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle transport along microtubule (GO:0047496)|vesicle-mediated transport (GO:0016192)|virion assembly (GO:0019068)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|melanosome (GO:0042470)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|kidney(1)|lung(3)|prostate(1)	6						tgtaatcccaacactttggga	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M28209	CCDS46305.1, CCDS46306.1	2p14	2008-02-05		2002-03-17	ENSG00000138069	ENSG00000138069	5861		RAB, member RAS oncogene	9758	protein-coding gene	gene with protein product	Rab GTPase YPT1 homolog (yeast)	179508		RAB1	NA	2501306	Standard	NM_004161	NM_004161	NA	Approved	YPT1	uc002sdm.3	P62820	OTTHUMG00000152725	ENST00000409784.3:c.23+3498T>C	chr2.hg19:g.65353528A>G		NA	P11476|Q6FIE7|Q96N61|Q9Y3T2	hg19	CCDS46306.1	0.02	-0.280571	CCAxCAC	COVERED																																																																																			NOVEL	RAB1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327572.1	7	5.412232	KEEP	0	0	0	18	479	AA	0.999859	0.739567	0		-	4	60	139	0	0	10.891754	23	60	638	72	ENST00000409784.3	0.148148	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	65418412	65418412	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:65418412T>C			NA	NA				SNORA74 (32418 upstream) : ACTR2 (36474 downstream)						NA		NA									NA						cctgtagtcctagctactctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.65418412T>C		NA		hg19		0.02	-0.140319	TCCxAGC	COVERED																																																																																			NOVEL					0			4	3.007617	KEEP	0	0	0	10	276	TT	0.992708	0.259062	0			3	60	97	0	0	7.779166	13	60	375	32		0.1875	0.260965
AC074391.1	0	__UNKNOWN__	__UNKNOWN__	2	65713102	65713102	__UNKNOWN__	lincRNA	SNP	A	A	G	rs840941	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:65713102A>G	ENST00000377977.3	+	0	343										NA		NA									NA						gtgcaccaccatgcttggcta	0.512		NA											G|||	1733	0.346046	0.441	0.3963	5008	,	,	NA	21245	0.1538	NA	0.4155	False	NA	,,,	NA	NA	NA	2504	0.3088	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000377977.3:	chr2.hg19:g.65713102A>G		NA		hg19		0.02	-0.114023	ACCxTGC	UNCOVERED																																																																																			NOVEL	AC074391.1-010	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000470883.1	7	2.706588	KEEP	0	0	0	9	245	AA	0.99254	0.161255	0		+	4	60	129	0	0	11.885565	6	60	183	26	ENST00000377977.3	0.4	0.162467
AC074391.1	0	__UNKNOWN__	__UNKNOWN__	2	65800036	65800036	__UNKNOWN__	lincRNA	SNP	T	T	C	rs13024276	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:65800036T>C	ENST00000377977.3	+	0	862										NA		NA									NA						tggcgcgatcttggctcactg	0.552		NA											T|||	3332	0.665335	0.5703	0.7363	5008	,	,	NA	10366	0.6022	NA	0.6322	False	NA	,,,	NA	NA	NA	2504	0.8425	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000377977.3:	chr2.hg19:g.65800036T>C		NA		hg19		0.02	-0.078944	ATCxTGG	UNCOVERED																																																																																			NOVEL	AC074391.1-010	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000470883.1	6	2.706433	KEEP	8	0	0	9	243	TT	0	0	0		+	3	42	99	0	0	9.255352	4	48	120	37	ENST00000377977.3	0.428571	0.077336
MEIS1	4211	__UNKNOWN__	__UNKNOWN__	2	66757573	66757573	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:66757573A>G	ENST00000272369.9	+	9	1345				MEIS1_ENST00000444274.2_Intron|MEIS1_ENST00000560281.2_Intron|MEIS1_ENST00000495021.2_Intron|MEIS1_ENST00000488550.1_Intron|MEIS1_ENST00000398506.2_Intron|MEIS1_ENST00000409517.1_Intron|MEIS1_ENST00000407092.2_Intron	NM_002398.2	NP_002389.1	O00470	MEIS1_HUMAN	Meis homeobox 1	NA		NA			angiogenesis (GO:0001525)|definitive hemopoiesis (GO:0060216)|lens morphogenesis in camera-type eye (GO:0002089)|megakaryocyte development (GO:0035855)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron differentiation (GO:0045665)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	24						GGggccgggtacggtggctca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46309.1	2p14	2011-06-20	2007-02-15		ENSG00000143995	ENSG00000143995	4211		Homeoboxes / TALE class	7000	protein-coding gene	gene with protein product		601739	Meis1 (mouse) homolog, Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)		NA	7565694	Standard	NM_002398	NM_002398	NA	Approved		uc002sdu.3	O00470	OTTHUMG00000150714	ENST00000272369.9:c.889-17502A>G	chr2.hg19:g.66757573A>G		NA	A8MV50	hg19	CCDS46309.1	0.02	-0.184164	GGTxCGG	COVERED																																																																																			NOVEL	MEIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319725.4	3	2.705443	KEEP	1	0	0	9	233	AA	0.99254	0.420319	0		+	3	60	97	0	1	7.393253	18	60	514	48	ENST00000272369.9	0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	68497128	68497128	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:68497128G>T			NA	NA				RP11-474G23.1 (8766 upstream) : AC017083.3 (3107 downstream)						NA		NA									NA						cactgcgcccggccGGATATA	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.68497128G>T		NA		hg19		0.02	-0.184194	CCCxGCC	COVERED																																																																																			NOVEL					0			2	2.707949	KEEP	1	0	0	9	272	GG	0.99257	0.420331	0			3	60	88	1	0	6.63426	16	60	516	48		0.157895	0.423478
APLF	200558	__UNKNOWN__	__UNKNOWN__	2	68723533	68723533	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:68723533A>G	ENST00000303795.4	+	2	339					NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						caccgtgcccagcctgacttt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621	200558			28724	protein-coding gene	gene with protein product	XRCC1-interacting protein 1, zinc finger, CX5CX6HX5H motif containing 1	611035	chromosome 2 open reading frame 13	C2orf13	NA	18474613, 18077224, 17353262	Standard	NM_173545	NM_173545	NA	Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.168+6140A>G	chr2.hg19:g.68723533A>G		NA	A8K476|Q53P47|Q53PB9|Q53QU0	hg19	CCDS1888.1	0.02	-0.315742	CCCxGCC	COVERED																																																																																			NOVEL	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251759.1	12	4.210503	KEEP	1	0	0	14	389	AA	0.994391	0.813874	0		+	3	60	108	0	0	8.043672	26	60	771	72	ENST00000303795.4	0.103448	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	68903350	68903350	__UNKNOWN__	IGR	SNP	A	A	C	rs4353684	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:68903350A>C			NA	NA				PROKR1 (20642 upstream) : ARHGAP25 (34283 downstream)						NA		NA									NA						aactcttgggatcaaagtatc	0.448		NA											C|||	3331	0.665136	0.8888	0.4741	5008	,	,	NA	13183	0.6429	NA	0.4911	False	NA	,,,	NA	NA	NA	2504	0.7004	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.68903350A>C		NA		hg19		0.02	-0.087714	GGGxTCA	UNCOVERED																																																																																			NOVEL					0			6	2.403578	KEEP	0	0	0	8	208	AA	0.99257	0.09898	0			5	60	170	0	0	16.375567	5	60	146	22		0.5	0.099721
GKN1	56287	__UNKNOWN__	__UNKNOWN__	2	69201798	69201798	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs141746794		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:69201798C>T	ENST00000377938.2	+	1	94	c.31C>T	c.(31-33)Cgt>Tgt	p.R11C		NM_019617.3	NP_062563.3	Q9NS71	GKN1_HUMAN	gastrokine 1	11		NA			digestion (GO:0007586)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|secretory granule (GO:0030141)		p.R11C(1)		breast(2)|large_intestine(4)|lung(5)	11						CCACTGCTTTCGTGAAGACAA	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	large_intestine(1)						C	CYS/ARG	0,4406		0,0,2203	173	154	161		31	-1.6	0.1	2	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense	GKN1	NM_019617.3	180	0,1,6502	TT,TC,CC	NA	0.0116,0.0,0.0077	benign	11/200	69201798	1,13005	2203	4300	6503	SO:0001583	missense			AY139182	CCDS1891.2	2p13.3	2012-10-10			ENSG00000169605	ENSG00000169605	56287		BRICHOS domain containing	23217	protein-coding gene	gene with protein product	BRICHOS domain containing 1	606402			NA	12851218, 11562744	Standard	NM_019617	NM_019617	NA	Approved	AMP18, CA11, BRICD1	uc002sfc.3	Q9NS71	OTTHUMG00000129574	ENST00000377938.2:c.31C>T	chr2.hg19:g.69201798C>T	ENSP00000367172:p.Arg11Cys	NA	Q8IUA9	hg19	CCDS1891.2	0.02	1.210446	TTTxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.210	0.800099	0.16397	0.0	1.16E-4	ENSG00000169605	ENST00000377938	T	0.48522	0.81	5.35	-1.6	0.08426	.	1.119980	0.06955	N	0.815227	T	0.24122	0.0584	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.23655	-1.0182	10	0.48119	T	0.1	0.0244	9.0111	0.36142	0.0:0.3346:0.4654:0.2001	.	11	Q9NS71	GKN1_HUMAN	C	11	ENSP00000367172:R11C	ENSP00000367172:R11C	R	+	1	0	GKN1	69055302	0.000000	0.05858	0.114000	0.21550	0.559000	0.35586	-0.230000	0.09083	-0.154000	0.11118	-0.982000	0.02568	CGT	NOVEL	GKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251769.2	2	5.11358	KEEP	0	0	0	17	488	CC	0.999366	0.999171	0		+	5	60	149	0	0	9.013796	81	60	2587	165	ENST00000377938.2	0.05814	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	69541134	69541134	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:69541134A>G			NA	NA				ANTXR1 (64675 upstream) : GFPT1 (5770 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.69541134A>G		NA		hg19		0.02	-0.236766	GGCxTGA	COVERED																																																																																			NOVEL					0			7	4.511654	KEEP	0	0	0	15	416	AA	0.99649	0.610258	0			3	60	94	0	0	6.965706	20	60	579	70		0.130435	0.612407
AAK1	22848	__UNKNOWN__	__UNKNOWN__	2	69789970	69789970	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:69789970T>C	ENST00000409085.4	-	3	540				AAK1_ENST00000409068.1_Intron|AAK1_ENST00000406297.3_Intron	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	NA		NA			endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						tgcagtgagctgagatcgcac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977	22848			19679	protein-coding gene	gene with protein product		NA			NA	11877461, 12471243	Standard	NM_014911	NM_014911	NA	Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.164-5860A>G	chr2.hg19:g.69789970T>C		NA	Q4ZFZ3|Q53RX6|Q9UPV4	hg19	CCDS1893.2	0.02	-0.149109	AGCxGAG	UNCOVERED																																																																																			NOVEL	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251847.4	8	2.706378	KEEP	9	0	0	9	243	TT	0	0	0		-	3	60	102	0	0	8.191678	14	60	419	42	ENST00000409085.4	0.176471	0.292001
ANXA4	307	__UNKNOWN__	__UNKNOWN__	2	69929595	69929595	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:69929595T>C	ENST00000418066.2	+	3	766				AC092431.3_ENST00000415342.1_lincRNA			P09525	ANXA4_HUMAN	annexin A4	NA		NA			epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						tggctcacacttgtaatccca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975	307		Annexins	542	protein-coding gene	gene with protein product		106491		ANX4	NA	1346776	Standard	NM_001153	NM_001153	NA	Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000418066.2:c.767-18311T>C	chr2.hg19:g.69929595T>C		NA	B4DDF9|Q96F33|Q9BWK1	hg19		0.02	-0.13157	CACxTGT	COVERED																																																																																			NOVEL	ANXA4-013	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000470748.1	4	2.706438	KEEP	0	0	0	9	241	TT	0.99254	0.227464	0		+	3	60	95	0	0	7.882031	10	60	303	30	ENST00000418066.2	0.230769	0.229173
ANXA4	307	__UNKNOWN__	__UNKNOWN__	2	69950075	69950075	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:69950075T>C	ENST00000418066.2	+	3	864							P09525	ANXA4_HUMAN	annexin A4	NA		NA			epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						gaggccgaggtgggcggatca	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975	307		Annexins	542	protein-coding gene	gene with protein product		106491		ANX4	NA	1346776	Standard	NM_001153	NM_001153	NA	Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000418066.2:c.864+2072T>C	chr2.hg19:g.69950075T>C		NA	B4DDF9|Q96F33|Q9BWK1	hg19		0.02	-0.166638	AGGxGGG	COVERED																																																																																			NOVEL	ANXA4-013	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000470748.1	6	3.909355	KEEP	4	0	0	13	354	TT	0.993634	0.351693	0		+	3	60	97	0	0	7.533533	16	60	481	59	ENST00000418066.2	0.157895	0.353947
PCBP1-AS1	400960	__UNKNOWN__	__UNKNOWN__	2	70301697	70301697	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:70301697C>T	ENST00000416395.1	-	0	291				PCBP1-AS1_ENST00000439670.2_RNA|PCBP1-AS1_ENST00000421255.1_RNA|PCBP1-AS1_ENST00000423402.1_RNA|PCBP1-AS1_ENST00000418308.1_RNA|PCBP1-AS1_ENST00000596665.1_RNA|PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000437456.1_RNA|PCBP1-AS1_ENST00000415742.1_RNA|PCBP1-AS1_ENST00000422515.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000596573.1_RNA|PCBP1-AS1_ENST00000444320.1_RNA|PCBP1-AS1_ENST00000411429.1_RNA|PCBP1-AS1_ENST00000439892.1_RNA|PCBP1-AS1_ENST00000413791.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000420309.1_RNA|PCBP1-AS1_ENST00000416068.1_RNA|PCBP1-AS1_ENST00000595459.1_RNA|PCBP1-AS1_ENST00000442040.1_RNA|PCBP1-AS1_ENST00000594548.1_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000425333.1_RNA|PCBP1-AS1_ENST00000452431.1_RNA|PCBP1-AS1_ENST00000449178.1_RNA|PCBP1-AS1_ENST00000457770.1_RNA|PCBP1-AS1_ENST00000458686.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000432604.1_RNA|PCBP1-AS1_ENST00000425601.1_RNA|PCBP1-AS1_ENST00000429599.2_RNA|PCBP1-AS1_ENST00000456161.1_RNA|PCBP1-AS1_ENST00000366234.3_RNA|PCBP1-AS1_ENST00000458698.2_RNA|PCBP1-AS1_ENST00000419963.1_RNA|PCBP1-AS1_ENST00000413069.1_RNA|PCBP1-AS1_ENST00000415060.2_RNA|PCBP1-AS1_ENST00000444410.1_RNA|PCBP1-AS1_ENST00000434781.1_RNA|PCBP1-AS1_ENST00000599673.1_RNA|PCBP1-AS1_ENST00000421843.1_RNA|PCBP1-AS1_ENST00000601396.1_RNA|PCBP1-AS1_ENST00000596028.1_RNA					PCBP1 antisense RNA 1	NA		NA									NA						catgagccaccgcgcctggcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							2p13.3	2012-10-12	2012-08-15		ENSG00000179818	ENSG00000179818	400960		Long non-coding RNAs	42948	non-coding RNA	RNA, long non-coding		NA	PCBP1 antisense RNA 1 (non-protein coding)		NA		Standard	NR_033872	NR_033872	NA	Approved		uc002sga.3		OTTHUMG00000153728	ENST00000416395.1:	chr2.hg19:g.70301697C>T		NA		hg19		0.02	-0.23611	CACxGCG	COVERED																																																																																			NOVEL	PCBP1-AS1-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000329416.1	7	3.008395	KEEP	0	0	0	10	299	CC	0.992708	0.607941	0		-	3	60	92	0	1	6.599913	23	60	729	54	ENST00000416395.1	0.115385	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	70374998	70374998	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:70374998A>G			NA	NA				AC016700.5 (22549 upstream) : C2orf42 (2013 downstream)						NA		NA									NA						tcacgccactacactccagcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.70374998A>G		NA		hg19		0.02	-0.149044	ACTxCAC	COVERED																																																																																			NOVEL					0			8	3.306046	KEEP	1	0	0	11	279	AA	0.993072	0.289978	0			3	60	104	0	0	8.673639	11	60	299	41		0.214286	0.292001
C2orf42	54980	__UNKNOWN__	__UNKNOWN__	2	70416896	70416896	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:70416896C>T	ENST00000264434.2	-	1	99				C2orf42_ENST00000470096.1_Intron	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	NA		NA								endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						tggtggctcacgcctgtaatc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998	54980			26056	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_017880	XM_005264389	NA	Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.280+1208G>A	chr2.hg19:g.70416896C>T		NA	D6W5G3|Q9H629	hg19	CCDS1899.1	0.02	-0.184203	TCAxGCC	COVERED																																																																																			NOVEL	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251840.1	7	2.405866	KEEP	1	0	0	8	219	CC	0.99257	0.420331	0		-	3	60	89	0	0	6.733752	16	60	510	39	ENST00000264434.2	0.157895	0.423478
C2orf42	54980	__UNKNOWN__	__UNKNOWN__	2	70427868	70427868	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:70427868A>G	ENST00000470096.1	-	2	211							Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	NA		NA								endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						aaaaaaaaaaaaaagaaaTCA	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998	54980			26056	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_017880	XM_005264389	NA	Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000470096.1:c.369-18739T>C	chr2.hg19:g.70427868A>G		NA	D6W5G3|Q9H629	hg19		0.02	-0.105241	AAAxAAA	UNCOVERED																																																																																			NOVEL	C2orf42-015	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000333758.1	8	2.404934	KEEP	10	0	0	8	206	AA	0	0	0		-	4	60	129	0	0	13.149835	2	60	57	30	ENST00000470096.1	0.666667	0.139832
TIA1	7072	__UNKNOWN__	__UNKNOWN__	2	70459327	70459327	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:70459327C>T	ENST00000415783.2	-	3	353				TIA1_ENST00000282574.4_Intron|TIA1_ENST00000416149.2_Intron|TIA1_ENST00000433529.2_Intron|C2orf42_ENST00000470096.1_Intron|TIA1_ENST00000445587.1_Intron	NM_022037.2	NP_071320.2	P31483	TIA1_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein	NA		NA			apoptotic process (GO:0006915)|negative regulation of cytokine biosynthetic process (GO:0042036)|negative regulation of translation (GO:0017148)|regulation of mRNA splicing, via spliceosome (GO:0048024)	cytoplasmic stress granule (GO:0010494)|nuclear stress granule (GO:0097165)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|urinary_tract(1)	17						ggcgacagagcgagactctgt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1900.1, CCDS1901.1	2p13	2013-02-12	2001-11-28		ENSG00000116001	ENSG00000116001	7072		RNA binding motif (RRM) containing	11802	protein-coding gene	gene with protein product	T-cell-restricted intracellular antigen-1, nucleolysin TIA-1 isoform p40	603518	TIA1 cytotoxic granule-associated RNA-binding protein		NA	8176212, 12486009	Standard	NM_022037	NM_022173	NA	Approved		uc002sgj.4	P31483	OTTHUMG00000129644	ENST00000415783.2:c.124-1341G>A	chr2.hg19:g.70459327C>T		NA	Q53SS9	hg19	CCDS1900.1	0.02	-0.114032	GAGxGAG	COVERED																																																																																			NOVEL	TIA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251843.1	8	3.888515	KEEP	6	0	0	13	339	CC	0.992708	0.19488	0		-	3	60	86	0	0	6.981906	10	60	336	35	ENST00000415783.2	0.230769	0.196312
FAM136A	84908	__UNKNOWN__	__UNKNOWN__	2	70524576	70524576	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs75086964	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:70524576C>G	ENST00000430566.1	-	3	616	c.583G>C	c.(583-585)Gac>Cac	p.D195H	FAM136A_ENST00000037869.3_Missense_Mutation_p.D88H|FAM136A_ENST00000450256.1_3'UTR			Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	88		NA				cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						TTGGCTTTGTCGTTGCAATGC	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													100	93	95			NA	NA	2		NA											NA				70524576		2203	4300	6503	SO:0001583	missense			BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141	84908			25911	protein-coding gene	gene with protein product	hypothetical protein FLJ14668	NA			NA	12477932	Standard	NM_032822	NM_032822	NA	Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000430566.1:c.583G>C	chr2.hg19:g.70524576C>G	ENSP00000397269:p.Asp195His	NA	Q96SS3	hg19		0.02	1.520147	TGTxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.6	4.936290	0.92458	.	.	ENSG00000035141	ENST00000037869;ENST00000430566;ENST00000438759	.	.	.	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.85008	0.5599	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.88214	0.2892	9	0.72032	D	0.01	.	17.2342	0.86994	0.0:1.0:0.0:0.0	.	88	Q96C01	F136A_HUMAN	H	88;195;158	.	ENSP00000037869:D88H	D	-	1	0	FAM136A	70378080	1.000000	0.71417	0.964000	0.40570	0.995000	0.86356	6.951000	0.75983	2.470000	0.83445	0.561000	0.74099	GAC	NOVEL	FAM136A-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331506.1	8	2.239581	KEEP	1	1	30	18	535	CC	0.999869	0.999825	0		-	4	60	131	0	0	7.850742	89	60	2990	178	ENST00000430566.1	0.043011	0.999956
PAIP2B	400961	__UNKNOWN__	__UNKNOWN__	2	71444534	71444534	__UNKNOWN__	Intron	SNP	C	C	A	rs11683955	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:71444534C>A	ENST00000244221.8	-	1	156					NM_020459.1	NP_065192.1	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B	NA		NA			negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)	translation repressor activity, nucleic acid binding (GO:0000900)			large_intestine(1)|lung(1)	2						gggcctcccacagtgctgggg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46322.1	2p13.3	2007-07-16			ENSG00000124374	ENSG00000124374	400961			29200	protein-coding gene	gene with protein product		611018			NA	16804161	Standard	XM_376062	NM_020459	NA	Approved	KIAA1155	uc002shu.2	Q9ULR5	OTTHUMG00000153284	ENST00000244221.8:c.10+9523G>T	chr2.hg19:g.71444534C>A		NA		hg19	CCDS46322.1	0.02	-0.263173	CCAxAGT	COVERED																																																																																			NOVEL	PAIP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330547.2	9	2.708036	KEEP	1	0	0	9	276	CC	0.99254	0.688494	0		-	4	60	115	0	0	8.492314	23	60	803	61	ENST00000244221.8	0.148148	0.693668
ZNF638	27332	__UNKNOWN__	__UNKNOWN__	2	71521599	71521599	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:71521599G>A	ENST00000410075.1	+	1	162							Q14966	ZN638_HUMAN	zinc finger protein 638	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						gggtttcaccgtgttagccag	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292	27332		RNA binding motif (RRM) containing	17894	protein-coding gene	gene with protein product		614349	zinc finger, matrin-like	ZFML	NA	8647861	Standard	NM_014497	NM_014497	NA	Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000410075.1:c.162+17715G>A	chr2.hg19:g.71521599G>A		NA	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	hg19		0.02	-0.122788	ACCxTGT	UNCOVERED																																																																																			NOVEL	ZNF638-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000327432.2	7	3.007095	KEEP	10	0	0	10	274	GG	0	0	0		+	3	22	90	1	0	7.273052	11	40	332	37	ENST00000410075.1	0.214286	0.196312
ZNF638	27332	__UNKNOWN__	__UNKNOWN__	2	71561791	71561791	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:71561791T>C	ENST00000409544.1	+	1	102				ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000410075.1_Intron|ZNF638_ENST00000377802.2_Intron|ZNF638_ENST00000264447.4_Intron	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						cggtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292	27332		RNA binding motif (RRM) containing	17894	protein-coding gene	gene with protein product		614349	zinc finger, matrin-like	ZFML	NA	8647861	Standard	NM_014497	NM_014497	NA	Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.-529+2796T>C	chr2.hg19:g.71561791T>C		NA	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	hg19	CCDS1917.1	0.02	-0.210492	TCAxGCC	COVERED																																																																																			NOVEL	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327431.1	10	3.307646	KEEP	0	0	0	11	295	TT	0.993072	0.518544	0		+	3	60	102	0	0	7.826929	19	60	556	51	ENST00000409544.1	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	71987011	71987011	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:71987011A>G			NA	NA				DYSF (73113 upstream) : CYP26B1 (369355 downstream)						NA		NA									NA						tttttgagacagagtctcgct	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.71987011A>G		NA		hg19		0.02	-0.070174	GACxGAG	UNCOVERED																																																																																			NOVEL					0			4	2.706877	KEEP	5	0	0	9	247	AA	0	0	0			3	46	104	0	0	9.755409	4	60	121	27		0.428571	0.054137
EXOC6B	23233	__UNKNOWN__	__UNKNOWN__	2	72812481	72812481	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:72812481T>C	ENST00000272427.6	-	7	800				EXOC6B_ENST00000410104.1_Intron	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	NA		NA			protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						aatcccagcattttgggaggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036	23233			17085	protein-coding gene	gene with protein product		607880	SEC15-like 2 (S. cerevisiae), SEC15 homolog B (S. cerevisiae)	SEC15L2, SEC15B	NA	10231032, 11406615	Standard	XM_039570	NM_015189	NA	Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.670-9684A>G	chr2.hg19:g.72812481T>C		NA	B8ZZY3	hg19	CCDS46333.1	0.02	-0.236806	GCAxTTT	COVERED																																																																																			NOVEL	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327558.1	10	3.908637	KEEP	2	0	0	13	345	TT	0.993634	0.608508	0		-	3	60	103	0	0	7.805439	21	60	618	59	ENST00000272427.6	0.125	0.612407
EXOC6B	23233	__UNKNOWN__	__UNKNOWN__	2	72812493	72812493	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:72812493A>G	ENST00000272427.6	-	7	800				EXOC6B_ENST00000410104.1_Intron	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	NA		NA			protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						ttgggaggccaaggcaggtgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036	23233			17085	protein-coding gene	gene with protein product		607880	SEC15-like 2 (S. cerevisiae), SEC15 homolog B (S. cerevisiae)	SEC15L2, SEC15B	NA	10231032, 11406615	Standard	XM_039570	NM_015189	NA	Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.670-9696T>C	chr2.hg19:g.72812493A>G		NA	B8ZZY3	hg19	CCDS46333.1	0.02	-0.23677	GCCxAGG	COVERED																																																																																			NOVEL	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327558.1	11	4.511244	KEEP	3	0	0	15	413	AA	0.993634	0.608508	0		-	3	60	98	0	0	7.306034	21	60	619	60	ENST00000272427.6	0.125	0.612407
EXOC6B	23233	__UNKNOWN__	__UNKNOWN__	2	73050651	73050651	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:73050651G>A	ENST00000272427.6	-	1	244				EXOC6B_ENST00000410104.1_Intron	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	NA		NA			protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						agtggctcaagcctgtaatcc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036	23233			17085	protein-coding gene	gene with protein product		607880	SEC15-like 2 (S. cerevisiae), SEC15 homolog B (S. cerevisiae)	SEC15L2, SEC15B	NA	10231032, 11406615	Standard	XM_039570	NM_015189	NA	Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.113+2275C>T	chr2.hg19:g.73050651G>A		NA	B8ZZY3	hg19	CCDS46333.1	0.02	-0.131585	CAAxCCT	COVERED																																																																																			NOVEL	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327558.1	9	3.610288	KEEP	0	0	0	12	357	GG	0.993634	0.227714	0		-	3	60	90	0	0	7.272734	11	60	373	35	ENST00000272427.6	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	73427520	73427520	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:73427520T>C			NA	NA				RP11-44N22.3 (86762 upstream) : NOTO (1865 downstream)						NA		NA									NA						cttggcctcctaaagtgctgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.73427520T>C		NA		hg19		0.02	-0.201741	TCCxAAA	COVERED																																																																																			NOVEL					0			7	2.40541	KEEP	0	0	0	8	214	TT	0.99257	0.4869	0			3	60	107	0	0	8.326562	19	60	578	45		0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	73441305	73441305	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:73441305G>C			NA	NA				NOTO (1664 upstream) : SMYD5 (44 downstream)						NA		NA									NA						GCAGCCTCAGGGGCACTCTCG	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.73441305G>C		NA		hg19		0.02	4.072933	CAGxGGC	COVERED																																																																																			NOVEL					0			0	7.495024	KEEP	0	0	0	25	716	GG	0.999957	0.999934	0			28	60	952	0	0	82.388573	75	60	2549	169		0.271845	0.999978
FBXO41	150726	__UNKNOWN__	__UNKNOWN__	2	73509140	73509140	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:73509140G>T	ENST00000521871.1	-	1	278				FBXO41_ENST00000520530.2_Intron|FBXO41_ENST00000520186.1_Intron			Q8TF61	FBX41_HUMAN	F-box protein 41	NA		NA								breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						tcttttttttgagatggagtt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075820	CCDS46337.1, CCDS46337.2	2p13.2	2004-08-24				ENSG00000163013	150726		F-boxes /  other	29409	protein-coding gene	gene with protein product		609108			NA	11853319	Standard		NM_001080410	NA	Approved	KIAA1940, Fbx41	uc021vjh.1	Q8TF61		ENST00000521871.1:c.137+2141C>A	chr2.hg19:g.73509140G>T		NA	G3V0Z7|Q2M1V8	hg19	CCDS46337.2	0.02	-0.131575	TTTxAGA	COVERED																																																																																			NOVEL	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377381.1	11	2.406808	KEEP	1	0	0	8	240	GG	0.99257	0.22747	0		-	3	57	81	0	0	6.600941	9	60	303	29	ENST00000521871.1	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	73923565	73923565	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:73923565T>C			NA	NA				ALMS1P (10862 upstream) : TPRKB (33391 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.73923565T>C		NA		hg19		0.02	-0.175419	AATxCCA	COVERED																																																																																			NOVEL					0			7	2.405385	KEEP	1	0	0	8	214	TT	0.99257	0.384528	0			3	60	95	0	0	7.579006	13	60	384	39		0.1875	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	74109501	74109501	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74109501A>G			NA	NA				STAMBP (8741 upstream) : ACTG2 (10592 downstream)						NA		NA									NA						tgtggtggtgactcatgcctg	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.74109501A>G		NA		hg19		0.02	-0.149092	GTGxCTC	COVERED																																																																																			NOVEL					0			7	2.40651	KEEP	0	0	0	8	229	AA	0.99257	0.289832	0			3	60	92	1	0	7.279209	13	60	382	31		0.1875	0.292001
ACTG2	72	__UNKNOWN__	__UNKNOWN__	2	74130806	74130806	__UNKNOWN__	Intron	SNP	T	T	C	rs1721245	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74130806T>C	ENST00000409731.3	+	2	247				ACTG2_ENST00000345517.3_Intron|ACTG2_ENST00000409624.1_Intron	NM_001199893.1	NP_001186822.1	P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	NA		NA			muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			large_intestine(3)|lung(14)|skin(1)	18						tggtggcttatgcctgtaatc	0.438		NA											C|||	3645	0.727835	0.7602	0.8372	5008	,	,	NA	16575	0.5873	NA	0.7982	False	NA	,,,	NA	NA	NA	2504	0.6789	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017	72			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3	NA	1710027, 1673027	Standard	NM_001615	NM_001199893	NA	Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409731.3:c.126+2242T>C	chr2.hg19:g.74130806T>C		NA	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	hg19	CCDS56124.1	0.02	-0.201746	TTAxGCC	COVERED																																																																																			NOVEL	ACTG2-008	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328090.2	6	3.006913	KEEP	1	0	0	10	268	TT	0.99254	0.486885	0		+	13	60	428	0	0	42.538134	9	60	271	51	ENST00000409731.3	0.590909	0.490544
DGUOK	1716	__UNKNOWN__	__UNKNOWN__	2	74172921	74172921	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74172921T>C	ENST00000264093.4	+	3	340				DGUOK_ENST00000348222.1_Intron|DGUOK_ENST00000462685.1_Intron|DGUOK_ENST00000356837.6_Intron	NM_080916.2	NP_550438.1	Q16854	DGUOK_HUMAN	deoxyguanosine kinase	NA		NA			deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|dGTP metabolic process (GO:0046070)|guanosine metabolic process (GO:0008617)|negative regulation of neuron projection development (GO:0010977)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein phosphorylation (GO:0006468)|purine deoxyribonucleoside metabolic process (GO:0046122)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxyguanosine kinase activity (GO:0004138)|nucleoside kinase activity (GO:0019206)			endometrium(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	8					Nelarabine(DB01280)	cgcctgtaattccagcacttt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41668	CCDS1931.1, CCDS1932.1	2p13	2008-02-05			ENSG00000114956	ENSG00000114956	1716	2.7.1.113		2858	protein-coding gene	gene with protein product		601465			NA		Standard		NM_080916	NA	Approved	dGK	uc002sjx.3	Q16854	OTTHUMG00000129819	ENST00000264093.4:c.256-925T>C	chr2.hg19:g.74172921T>C		NA	P78532|Q16759|Q4ZG09|Q7L1W9|Q96BC1	hg19	CCDS1931.1	0.02	-0.131569	AATxCCA	COVERED																																																																																			NOVEL	DGUOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252050.1	6	2.406069	KEEP	1	0	0	8	220	TT	0.99257	0.22747	0		+	3	60	102	0	0	8.7012	9	60	272	37	ENST00000264093.4	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	74414029	74414029	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74414029G>A			NA	NA				MOB1A (8034 upstream) : CATX-2 (4487 downstream)						NA		NA									NA						ctgcccactcggcctcccaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.74414029G>A		NA		hg19		0.02	-0.096484	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			5	3.609977	KEEP	1	0	0	12	350	GG	0.993072	0.119602	0			3	60	88	0	1	7.578443	7	60	218	30		0.3	0.120436
RP11-287D1.3	0	__UNKNOWN__	__UNKNOWN__	2	74447743	74447743	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74447743A>T	ENST00000451608.2	-	36	4627				SLC4A5_ENST00000346834.4_Intron|SLC4A5_ENST00000423644.1_Intron|SLC4A5_ENST00000359484.4_Intron|SLC4A5_ENST00000483195.1_Intron|SLC4A5_ENST00000394019.2_Intron						NA		NA									NA						tcccaggttcacgccattctc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000451608.2:c.573+817T>A	chr2.hg19:g.74447743A>T		NA		hg19		0.02	-0.174912	TTCxCGC	COVERED																																																																																			NOVEL	RP11-287D1.3-002	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000445907.1	5	3.004955	KEEP	8	0	0	10	256	AA	0.99257	0.384528	0		-	7	60	183	0	0	16.185756	12	60	331	50	ENST00000451608.2	0.368421	0.387407
RP11-287D1.3	0	__UNKNOWN__	__UNKNOWN__	2	74522077	74522077	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74522077T>C	ENST00000451608.2	-	13	1435				SLC4A5_ENST00000377632.1_Intron|SLC4A5_ENST00000377634.4_Intron|SLC4A5_ENST00000346834.4_Intron|SLC4A5_ENST00000357822.5_Intron|SLC4A5_ENST00000423644.1_Intron|SLC4A5_ENST00000359484.4_Intron|SLC4A5_ENST00000358683.4_Intron|SLC4A5_ENST00000483195.1_Intron|SLC4A5_ENST00000394019.2_Intron						NA		NA									NA						ggattacaggtgtgagccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000451608.2:c.574-9048A>G	chr2.hg19:g.74522077T>C		NA		hg19		0.02	-0.289406	AGGxGTG	COVERED																																																																																			NOVEL	RP11-287D1.3-002	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000445907.1	10	2.707509	KEEP	0	0	0	9	260	TT	0.99254	0.755211	0		-	3	60	105	0	0	7.743989	26	60	753	61	ENST00000451608.2	0.103448	0.760887
M1AP	130951	__UNKNOWN__	__UNKNOWN__	2	74855463	74855463	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74855463G>A	ENST00000409585.1	-	1	292				M1AP_ENST00000536235.1_Intron|M1AP_ENST00000290536.5_Intron|M1AP_ENST00000358434.2_Intron			Q8TC57	M1AP_HUMAN	meiosis 1 associated protein	NA		NA			cell differentiation (GO:0030154)|chromatin assembly (GO:0031497)|female gamete generation (GO:0007292)|male meiosis chromosome separation (GO:0051308)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)					NA						AAGCTTCTCCGATCATCTCCA	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33229.1, CCDS62941.1	2p13.1	2013-02-05	2013-02-05	2013-01-16	ENSG00000159374	ENSG00000159374	130951			25183	protein-coding gene	gene with protein product	meiosis 1 arresting protein, spermatogenesis associated 37	NA	chromosome 2 open reading frame 65	C2orf65	NA	16881047, 23269666	Standard	NM_138804	NM_138804	NA	Approved	D6Mm5e, SPATA37	uc002smy.3	Q8TC57	OTTHUMG00000152918	ENST00000409585.1:c.240+11699C>T	chr2.hg19:g.74855463G>A		NA	B7Z6E7|E9PGG8|Q6ZP30|Q96L07	hg19		0.02	1.403374	TCCxATC	COVERED																																																																																			NOVEL	M1AP-002	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000328570.1	0	4.811457	KEEP	0	0	0	16	450	GG	0.997832	0.992926	0		-	4	60	124	0	0	7.734625	63	60	2051	126	ENST00000409585.1	0.059701	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	74913468	74913468	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74913468T>C			NA	NA				SEMA4F (4282 upstream) : RP11-259N19.1 (146313 downstream)						NA		NA									NA						cctcgtgatctgcccgcctcg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.74913468T>C		NA		hg19		0.02	-0.149077	ATCxGCC	UNCOVERED																																																																																			NOVEL					0			8	3.909824	KEEP	11	0	0	13	357	TT	0	0	0			3	60	95	0	0	7.579305	13	60	375	55		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	74939018	74939018	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:74939018A>G			NA	NA				SEMA4F (29832 upstream) : RP11-259N19.1 (120763 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.74939018A>G		NA		hg19		0.02	-0.19294	GCTxGGA	COVERED																																																																																			NOVEL					0			8	2.40591	KEEP	0	0	0	8	218	AA	0.99257	0.454356	0			3	60	109	0	0	8.891821	14	60	406	42		0.176471	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	75004190	75004190	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:75004190T>C			NA	NA				SEMA4F (95004 upstream) : RP11-259N19.1 (55591 downstream)						NA		NA									NA						tgcagtgagctgagatcgcgc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.75004190T>C		NA		hg19		0.02	-0.17541	AGCxGAG	COVERED																																																																																			NOVEL					0			5	2.705689	KEEP	3	0	0	9	235	TT	0.99257	0.384528	0			3	60	92	0	0	7.110541	15	60	440	44		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	75034471	75034471	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:75034471G>A			NA	NA				SEMA4F (125285 upstream) : RP11-259N19.1 (25310 downstream)						NA		NA									NA						ggtggatcacgaggtcaggag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.75034471G>A		NA		hg19		0.02	-0.175442	CACxAGG	COVERED																																																																																			NOVEL					0			4	3.610575	KEEP	7	0	0	12	367	GG	0.993072	0.384723	0			3	50	88	0	0	6.561389	17	60	567	62		0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	75130724	75130724	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:75130724C>T			NA	NA				HK2 (10238 upstream) : AC104135.2 (15957 downstream)						NA		NA									NA						tgagccaccgcgcccagtctt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.75130724C>T		NA		hg19		0.02	-0.149116	CCGxGCC	UNCOVERED																																																																																			NOVEL					0			8	2.405929	KEEP	4	0	0	8	222	CC	0	0	0			3	60	91	0	0	7.372926	11	60	342	38		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	75470230	75470230	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:75470230C>A			NA	NA				TACR1 (43404 upstream) : snoU13 (175741 downstream)						NA		NA									NA						tcatgcctgtcatcccagcac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.75470230C>A		NA		hg19		0.02	-0.184209	TGTxATC	COVERED																																																																																			NOVEL					0			9	3.008779	KEEP	1	0	0	10	300	CC	0.992708	0.42039	0			3	60	86	0	0	6.434026	16	60	539	50		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	76704993	76704993	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:76704993A>G			NA	NA				RN7SKP203 (32457 upstream) : RN7SKP164 (117545 downstream)						NA		NA									NA						ggtcccagctactcaggagac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.76704993A>G		NA		hg19		0.02	-0.061386	GCTxCTC	UNCOVERED																																																																																			NOVEL					0			7	3.607146	KEEP	0	0	0	12	305	AA	0.993634	0.043508	0			2	60	72	0	0	6.496183	4	60	109	26		0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	78299648	78299648	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:78299648A>G			NA	NA				AC073628.1 (154513 upstream) : AC012494.1 (16207 downstream)						NA		NA									NA						gcgacagagcaagactccgtc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.78299648A>G		NA		hg19		0.02	-0.140327	AGCxAGA	COVERED																																																																																			NOVEL					0			7	2.405218	KEEP	0	0	0	8	213	AA	0.99257	0.259026	0			3	60	95	0	0	7.88214	10	60	296	33		0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	83613757	83613757	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:83613757A>G			NA	NA				AC010105.1 (847922 upstream) : AC010744.1 (136180 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.83613757A>G		NA		hg19		0.02	-0.122795	CTGxGAT	COVERED																																																																																			NOVEL					0			6	4.510631	KEEP	0	0	0	15	402	AA	0.99649	0.195623	0			4	60	130	0	0	11.591572	8	60	236	39		0.333333	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	84242571	84242571	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:84242571T>C			NA	NA				SNORD112 (156548 upstream) : FUNDC2P2 (275235 downstream)						NA		NA									NA						gacggagtcttgctctgtcgc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.84242571T>C		NA		hg19		0.02	-0.140318	TCTxGCT	UNCOVERED																																																																																			NOVEL					0			13	2.405499	KEEP	9	0	0	8	214	TT	0	0	0			4	60	119	0	0	10.171405	10	60	286	42		0.285714	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	84628012	84628012	__UNKNOWN__	IGR	SNP	G	G	A	rs558729699	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:84628012G>A			NA	NA				AC106874.1 (50114 upstream) : SUCLG1 (22634 downstream)						NA		NA									NA						cgaggcgggcggatcacgagg	0.527		NA											G|||	2	0.000399361	0.0008	0.0014	5008	,	,	NA	14310	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.84628012G>A		NA		hg19		0.02	-0.096445	GGCxGAT	UNCOVERED																																																																																			NOVEL					0			8	3.003838	KEEP	3	0	0	10	275	GG	0.99257	0.119541	0			3	60	79	0	0	6.678144	7	60	207	30		0.3	0.120436
KCMF1	56888	__UNKNOWN__	__UNKNOWN__	2	85232659	85232659	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85232659T>C	ENST00000409785.4	+	2	375					NM_020122.4	NP_064507.3	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	NA		NA					ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						atgatccacctgcctcggcct	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155652	CCDS46350.1	2p11.2	2010-11-23			ENSG00000176407	ENSG00000176407	56888		Zinc fingers, ZZ-type	20589	protein-coding gene	gene with protein product		614719			NA		Standard	NM_020122	NM_020122	NA	Approved	DEBT91, PCMF, DKFZP434L1021, ZZZ1	uc002sox.4	Q9P0J7	OTTHUMG00000153004	ENST00000409785.4:c.17-22353T>C	chr2.hg19:g.85232659T>C		NA	Q4ZG04|Q53SC7|Q9BWK2|Q9H8P5|Q9UFE8	hg19	CCDS46350.1	0.02	-0.219281	ACCxGCC	COVERED																																																																																			NOVEL	KCMF1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328942.4	13	3.308242	KEEP	6	0	0	11	304	TT	0.992708	0.578679	0		+	3	60	108	0	0	8.491787	18	60	546	63	ENST00000409785.4	0.142857	0.58293
KCMF1	56888	__UNKNOWN__	__UNKNOWN__	2	85232693	85232693	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85232693A>G	ENST00000409785.4	+	2	375					NM_020122.4	NP_064507.3	Q9P0J7	KCMF1_HUMAN	potassium channel modulatory factor 1	NA		NA					ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						gattacaggcatgagccactg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155652	CCDS46350.1	2p11.2	2010-11-23			ENSG00000176407	ENSG00000176407	56888		Zinc fingers, ZZ-type	20589	protein-coding gene	gene with protein product		614719			NA		Standard	NM_020122	NM_020122	NA	Approved	DEBT91, PCMF, DKFZP434L1021, ZZZ1	uc002sox.4	Q9P0J7	OTTHUMG00000153004	ENST00000409785.4:c.17-22319A>G	chr2.hg19:g.85232693A>G		NA	Q4ZG04|Q53SC7|Q9BWK2|Q9H8P5|Q9UFE8	hg19	CCDS46350.1	0.02	-0.2105	GGCxTGA	COVERED																																																																																			NOVEL	KCMF1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328942.4	5	2.704776	KEEP	0	0	0	9	225	AA	0.99254	0.518266	0		+	3	60	101	0	0	8.010159	15	60	447	52	ENST00000409785.4	0.166667	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	85288290	85288290	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85288290A>G			NA	NA				KCMF1 (1695 upstream) : RP11-60H5.1 (2940 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.85288290A>G		NA		hg19		0.02	-0.245569	GGCxTGA	COVERED																																																																																			NOVEL					0			13	5.714697	KEEP	1	0	0	19	527	AA	0.99986	0.641257	0			3	60	101	1	0	7.494605	23	60	678	70		0.115385	0.641347
TCF7L1	83439	__UNKNOWN__	__UNKNOWN__	2	85472711	85472711	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85472711A>G	ENST00000282111.3	+	4	716					NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	NA		NA			anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						cgaggcgggcagatcacgagg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284	83439			11640	protein-coding gene	gene with protein product		604652		TCF3	NA	1741298, 11085512	Standard	NM_031283	NM_031283	NA	Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.442-37907A>G	chr2.hg19:g.85472711A>G		NA	Q53R97|Q6PD70|Q9NP00	hg19	CCDS1971.1	0.02	-0.157768	GGCxGAT	UNCOVERED																																																																																			NOVEL	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252301.2	6	3.008183	KEEP	7	0	0	10	285	AA	0	0	0		+	3	60	88	0	0	6.79353	14	60	396	50	ENST00000282111.3	0.176471	0.322807
TCF7L1	83439	__UNKNOWN__	__UNKNOWN__	2	85512094	85512094	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85512094C>T	ENST00000282111.3	+	4	800					NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	NA		NA			anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						cagtggctcacgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284	83439			11640	protein-coding gene	gene with protein product		604652		TCF3	NA	1741298, 11085512	Standard	NM_031283	NM_031283	NA	Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.525+1393C>T	chr2.hg19:g.85512094C>T		NA	Q53R97|Q6PD70|Q9NP00	hg19	CCDS1971.1	0.02	-0.157892	TCAxGCC	UNCOVERED																																																																																			NOVEL	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252301.2	5	2.406563	KEEP	5	0	0	8	231	CC	0	0	0		+	3	60	86	0	0	6.772362	12	60	396	42	ENST00000282111.3	0.2	0.322807
TCF7L1	83439	__UNKNOWN__	__UNKNOWN__	2	85519973	85519973	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85519973A>T	ENST00000282111.3	+	4	800					NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	NA		NA			anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						agtgctgggaatacaggcatg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284	83439			11640	protein-coding gene	gene with protein product		604652		TCF3	NA	1741298, 11085512	Standard	NM_031283	NM_031283	NA	Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.525+9272A>T	chr2.hg19:g.85519973A>T		NA	Q53R97|Q6PD70|Q9NP00	hg19	CCDS1971.1	0.02	-0.280656	GGAxTAC	COVERED																																																																																			NOVEL	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252301.2	7	4.511154	KEEP	0	0	0	15	410	AA	0.99649	0.737075	0		+	4	60	114	0	0	8.196284	26	60	791	72	ENST00000282111.3	0.133333	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	85692106	85692106	__UNKNOWN__	IGR	SNP	A	A	T	rs557096005		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85692106A>T			NA	NA				Y_RNA (4731 upstream) : RN7SL830P (67360 downstream)						NA		NA									NA						atggggtttcaccatgttggt	0.562		NA											A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14735	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.85692106A>T		NA		hg19		0.02	-0.131566	TTCxCCA	COVERED																																																																																			NOVEL					0			8	2.405637	KEEP	1	0	0	8	213	AA	0.99257	0.22747	0			3	40	89	1	0	7.072423	12	60	369	33		0.2	0.229173
USP39	10713	__UNKNOWN__	__UNKNOWN__	2	85840359	85840359	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85840359T>C	ENST00000459775.1	+	2	226				USP39_ENST00000450066.2_Intron	NR_046347.1		Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						GAgccgggcgtggtggctcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883	10713		Ubiquitin-specific peptidases	20071	protein-coding gene	gene with protein product	snRNP assembly defective 1 homolog (S.cerevisiae), small nuclear ribonucleoprotein 65kDa (U4/U6.U5)	611594	ubiquitin specific protease 39		NA	12838346	Standard	NM_006590	NM_006590	NA	Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000459775.1:c.227-5984T>C	chr2.hg19:g.85840359T>C		NA	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	hg19		0.02	-0.271869	GCGxGGT	COVERED																																																																																			NOVEL	USP39-012	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000329895.1	6	2.236508	KEEP	0	1	24	16	432	TT	0.999366	0.716861	0		+	3	60	102	0	0	7.542527	24	60	695	70	ENST00000459775.1	0.111111	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	85966852	85966852	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:85966852T>C			NA	NA				RNU1-38P (11392 upstream) : ATOH8 (14164 downstream)						NA		NA									NA						gcctgggcaatatagcaagac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.85966852T>C		NA		hg19		0.02	-0.350795	CAAxATA	COVERED																																																																																			NOVEL					0			10	10.223376	KEEP	0	0	0	34	900	TT	0.999998	0.877706	0			3	60	100	0	0	6.949858	33	60	947	104		0.083333	0.877708
IMMT	10989	__UNKNOWN__	__UNKNOWN__	2	86373909	86373909	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:86373909A>G	ENST00000410111.3	-	14	1921				IMMT_ENST00000409051.2_Intron|IMMT_ENST00000442664.2_Intron|IMMT_ENST00000254636.5_Intron|IMMT_ENST00000449247.2_Intron	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	NA		NA			mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						tttgagacagaatcttgctct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305	10989			6047	protein-coding gene	gene with protein product	mitofilin, mitochondrial inner membrane organizing system 2	600378	inner membrane protein, mitochondrial (mitofilin)		NA	9168817, 8039717	Standard	NM_006839	NM_001100169	NA	Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1534-589T>C	chr2.hg19:g.86373909A>G		NA	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	hg19	CCDS46355.1	0.02	-0.096473	CAGxATC	UNCOVERED																																																																																			NOVEL	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329909.2	10	2.406522	KEEP	0	0	0	8	227	AA	0.99257	0.119541	0		-	3	60	108	0	0	9.579079	7	60	214	24	ENST00000410111.3	0.3	0.120436
IMMT	10989	__UNKNOWN__	__UNKNOWN__	2	86386465	86386465	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:86386465G>C	ENST00000410111.3	-	9	1420				IMMT_ENST00000449247.2_Intron|IMMT_ENST00000442664.2_Intron|IMMT_ENST00000490238.1_Intron|IMMT_ENST00000254636.5_Intron|IMMT_ENST00000409051.2_Intron	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	NA		NA			mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						acctcggcctgccaaagtgct	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305	10989			6047	protein-coding gene	gene with protein product	mitofilin, mitochondrial inner membrane organizing system 2	600378	inner membrane protein, mitochondrial (mitofilin)		NA	9168817, 8039717	Standard	NM_006839	NM_001100169	NA	Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1032+193C>G	chr2.hg19:g.86386465G>C		NA	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	hg19	CCDS46355.1	0.02	1.731656	CCTxCCA	COVERED																																																																																			NOVEL	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329909.2	17	4.880246	KEEP	0	2	59	37	1125	GG	1	0.998867	0		-	4	60	134	0	0	8.631831	67	60	2234	151	ENST00000410111.3	0.056338	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87623804	87623804	__UNKNOWN__	IGR	SNP	A	A	G	rs62653904		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:87623804A>G			NA	NA				IGKV3OR2-268 (57646 upstream) : LINC00152 (131082 downstream)						NA		NA									NA						agccagccaaaccagccaagc	0.692		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87623804A>G		NA		hg19		0.02	-0.254221	CAAxCCA	COVERED																																																																																			NOVEL					0			26	3.833812	KEEP	7	1	29	23	603	AA	0.999892	0.668451	0			3	49	99	0	0	7.592646	18	60	534	69		0.142857	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87623895	87623895	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:87623895C>T			NA	NA				IGKV3OR2-268 (57737 upstream) : LINC00152 (130991 downstream)						NA		NA									NA						gccagccaagccagccagcct	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87623895C>T		NA		hg19		0.02	-0.236771	AAGxCAG	COVERED																																																																																			NOVEL					0			29	3.443095	KEEP	9	1	18	18	529	CC	0.995343	0.609555	0			4	60	118	0	0	9.931015	11	60	353	65		0.266667	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	87748729	87748729	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:87748729A>G			NA	NA				IGKV3OR2-268 (182571 upstream) : LINC00152 (6157 downstream)						NA		NA									NA						ttacaggcgtaagccaccatg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.87748729A>G		NA		hg19		0.02	-0.227465	CGTxAGC	COVERED																																																																																			NOVEL					0			8	3.607175	KEEP	10	0	0	12	309	AA	0.99254	0.607839	0			3	27	100	0	0	7.564994	20	60	572	61		0.130435	0.612407
RGPD2	729857	__UNKNOWN__	__UNKNOWN__	2	88177167	88177167	__UNKNOWN__	Intron	SNP	G	G	A	rs34095118		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:88177167G>A	ENST00000420840.2	-	2	64							P0DJD1	RGPD2_HUMAN	RANBP2-like and GRIP domain containing 2	NA		NA			protein targeting to Golgi (GO:0000042)					breast(1)|pancreas(1)	2						ctaaaaacatgcaaaaaatta	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42710.1, CCDS42710.2	2p11.2	2013-01-10			ENSG00000185304	ENSG00000185304	729857		Tetratricopeptide (TTC) repeat domain containing	32415	protein-coding gene	gene with protein product		612705			NA	15710750, 15815621	Standard	NM_001078170	NM_001078170	NA	Approved	RGP2, RANBP2L2		P0DJD1	OTTHUMG00000153276	ENST00000420840.2:c.49-59025C>T	chr2.hg19:g.88177167G>A		NA	P0C839|Q68DN6|Q6V1X0	hg19		0.02	-0.122782	CATxCAA	COVERED																																																																																			NOVEL	RGPD2-202	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding		10	3.308304	KEEP	0	0	0	11	320	GG	0.993072	0.194952	0		-	4	60	112	0	0	9.62351	9	60	294	30	ENST00000420840.2	0.307692	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	89305387	89305387	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:89305387T>C			NA	NA				IGKV1-8 (12937 upstream) : IGKV1-9 (4091 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.89305387T>C		NA		hg19		0.02	-0.114022	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			8	3.608664	KEEP	10	0	0	12	327	TT	0	0	0			3	40	99	1	0	8.401286	9	60	262	46		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	89878485	89878485	__UNKNOWN__	IGR	SNP	A	A	C	rs374873207		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:89878485A>C			NA	NA				IGKV2-40 (248299 upstream) : IGKV2D-40 (12510 downstream)						NA		NA									NA						tggaatgaaaaggaatggaat	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.89878485A>C		NA		hg19		0.02	-0.394683	AAAxGGA	COVERED																																																																																			NOVEL					0			43	8.355014	KEEP	30	1	29	38	1078	AT	0.999997	0.934489	0			2	60	67	0	1	6.824903	1	60	30	160		0.666667	0.934492
CH17-132F21.1	0	__UNKNOWN__	__UNKNOWN__	2	90458606	90458606	__UNKNOWN__	Silent	SNP	C	C	T	rs368855200		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90458606C>T	ENST00000603238.1	+	2	282	c.282C>T	c.(280-282)acC>acT	p.T94T							NA		NA									NA						ACACTCTCACCATCCGCAGCC	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000603238.1:c.282C>T	chr2.hg19:g.90458606C>T		NA		hg19		0.02	4.091184	CACxATC	COVERED																																																																																			NOVEL	CH17-132F21.1-001	PUTATIVE	not_best_in_genome_evidence|mRNA_end_NF|cds_end_NF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000468882.1	3	11.132936	KEEP	18	0	0	37	1137	CC	0.999999	0.999999	0		+	12	49	358	0	0	22.0542	180	51	6094	355	ENST00000603238.1	0.0625	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90463687	90463687	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90463687T>C			NA	NA				CH17-132F21.1 (5016 upstream) : RP11-685N3.1 (74151 downstream)						NA		NA									NA						GTCTATAggctgggcgcggtg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90463687T>C		NA		hg19		0.02	1.854032	GGCxGGG	COVERED																																																																																			NOVEL					0			18	3.542659	KEEP	2	1	32	23	651	TT	0.999879	0.989422	0			4	57	125	0	0	8.157923	52	60	1534	130		0.071429	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90473685	90473685	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90473685C>T			NA	NA				CH17-132F21.1 (15014 upstream) : RP11-685N3.1 (64153 downstream)						NA		NA									NA						gcgcctgATCCGAACGTTGAC	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90473685C>T		NA		hg19		0.02	-0.333259	ATCxGAA	COVERED																																																																																			NOVEL					0			14	7.212199	KEEP	3	0	0	24	682	CC	0.999909	0.851907	0			4	49	124	0	0	8.909521	31	60	983	97		0.114286	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90478516	90478516	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90478516C>A			NA	NA				CH17-132F21.1 (19845 upstream) : RP11-685N3.1 (59322 downstream)						NA		NA									NA						ggattacaggcgtgtgccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90478516C>A		NA		hg19		0.02	-0.289115	AGGxGTG	COVERED																																																																																			NOVEL					0			16	5.112788	KEEP	6	0	0	17	486	CC	0.999366	0.760405	0			5	60	155	0	0	12.458107	20	60	632	77		0.2	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90478985	90478985	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90478985G>C			NA	NA				CH17-132F21.1 (20314 upstream) : RP11-685N3.1 (58853 downstream)						NA		NA									NA						gagtgcagtggtgcaatcttg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90478985G>C		NA		hg19		0.02	-0.412298	GTGxTGC	COVERED																																																																																			NOVEL					0			24	9.927589	KEEP	3	0	0	33	971	GG	0.999998	0.941739	0			4	60	118	0	0	8.208483	33	60	1127	106		0.108108	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90479055	90479055	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90479055A>G			NA	NA				CH17-132F21.1 (20384 upstream) : RP11-685N3.1 (58783 downstream)						NA		NA									NA						cctcctgggtagctgggatta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90479055A>G		NA		hg19		0.02	1.815483	GGTxGCT	COVERED																																																																																			NOVEL					0			35	8.116302	KEEP	3	0	0	27	696	AA	0.999988	0.973953	0			6	60	195	0	0	14.512077	42	60	1211	96		0.125	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	90479130	90479130	__UNKNOWN__	IGR	SNP	G	G	A	rs375562085		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:90479130G>A			NA	NA				CH17-132F21.1 (20459 upstream) : RP11-685N3.1 (58708 downstream)						NA		NA									NA						gtttcaccatgttggccaggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.90479130G>A		NA		hg19		0.02	1.419588	CATxTTG	COVERED																																																																																			NOVEL					0			43	9.929366	KEEP	5	0	0	33	1003	GG	0.999997	0.979523	0			4	60	118	1	0	7.938289	39	60	1259	122		0.093023	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91719891	91719891	__UNKNOWN__	IGR	SNP	A	A	G	rs191038121		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91719891A>G			NA	NA				None (None upstream) : RP11-575H3.1 (48501 downstream)						NA		NA									NA						GCTGTTTAGAATCATCAACAT	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91719891A>G		NA		hg19		0.02	-0.39468	AGAxTCA	UNCOVERED																																																																																			NOVEL					0			8	2.405458	KEEP	8	0	0	8	214	AA	0	0	0			6	60	201	0	0	15.41836	37	47	1107	81		0.139535	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91719933	91719933	__UNKNOWN__	IGR	SNP	T	T	G	rs370007209		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91719933T>G			NA	NA				None (None upstream) : RP11-575H3.1 (48459 downstream)						NA		NA									NA						gcctgtcatctcagcactttg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91719933T>G		NA		hg19		0.02	1.780293	ATCxCAG	COVERED																																																																																			NOVEL					0			11	6.61759	KEEP	12	0	0	22	620	CT	0.999869	0.991964	0			4	60	128	0	0	8.553771	49	48	1495	145		0.075472	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91760789	91760789	__UNKNOWN__	IGR	SNP	C	C	T	rs2558024	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91760789C>T			NA	NA				None (None upstream) : RP11-575H3.1 (7603 downstream)						NA		NA									NA						cacatgcatgctcacatgcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91760789C>T		NA		hg19		0.02	-0.210519	ATGxTCA	COVERED																																																																																			NOVEL					0			7	2.406999	KEEP	0	0	0	8	243	CC	0.99257	0.518282	0			6	60	183	0	0	15.564451	16	60	536	44		0.272727	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91765467	91765467	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91765467C>T			NA	NA				None (None upstream) : RP11-575H3.1 (2925 downstream)						NA		NA									NA						tcacccaggccggagtgcagt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91765467C>T		NA		hg19		0.02	-0.219279	GGCxGGA	COVERED																																																																																			NOVEL					0			17	4.511947	KEEP	0	0	0	15	428	CC	0.99649	0.550947	0			3	60	87	0	0	6.393195	18	60	565	48		0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91766609	91766609	__UNKNOWN__	IGR	SNP	G	G	A	rs2433883		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91766609G>A			NA	NA				None (None upstream) : RP11-575H3.1 (1783 downstream)						NA		NA									NA						TATGGGGGTTGTAATGTTTAT	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91766609G>A		NA		hg19		0.02	10.191128	GTTxTAA	COVERED																																																																																			NOVEL					0			15	8.053564	KEEP	3	4	102	63	1861	GG	1	1	0			47	60	1329	0	0	93.910785	328	60	11136	657		0.125333	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91774646	91774646	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91774646T>C			NA	NA				RP11-575H3.1 (5726 upstream) : AC027612.6 (30539 downstream)						NA		NA									NA						Aggccaggtgtggtggctcat	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91774646T>C		NA		hg19		0.02	1.687009	GTGxGGT	COVERED																																																																																			NOVEL					0			29	4.673304	KEEP	0	2	61	37	993	TT	1	0.999407	0			5	60	166	0	0	11.104627	67	60	1949	168		0.069444	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91780300	91780300	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91780300T>C			NA	NA				RP11-575H3.1 (11380 upstream) : AC027612.6 (24885 downstream)						NA		NA									NA						cctcgtgatctgcctgcctca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91780300T>C		NA		hg19		0.02	1.672094	ATCxGCC	COVERED																																																																																			NOVEL					0			19	6.616857	KEEP	3	0	0	22	617	TT	0.999869	0.987814	0			4	60	123	0	0	8.02212	50	60	1510	116		0.074074	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91780310	91780310	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91780310A>G			NA	NA				RP11-575H3.1 (11390 upstream) : AC027612.6 (24875 downstream)						NA		NA									NA						tgcctgcctcagcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91780310A>G		NA		hg19		0.02	1.818468	CTCxGCC	COVERED																																																																																			NOVEL					0			27	6.046405	KEEP	2	1	25	29	812	AA	0.999997	0.9937	0			5	60	164	0	0	11.392408	53	60	1625	132		0.086207	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91787900	91787900	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91787900G>A			NA	NA				RP11-575H3.1 (18980 upstream) : AC027612.6 (17285 downstream)						NA		NA									NA						tgagacaggcggagcacttga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91787900G>A		NA		hg19		0.02	-0.342094	GGCxGAG	COVERED																																																																																			NOVEL					0			17	5.412923	KEEP	1	0	0	18	507	GG	0.999859	0.865624	0			4	60	125	0	0	9.009033	31	60	1014	84		0.114286	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91796867	91796867	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91796867T>G			NA	NA				RP11-575H3.1 (27947 upstream) : AC027612.6 (8318 downstream)						NA		NA									NA						ctgcctcccatgttcaagtga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91796867T>G		NA		hg19		0.02	-0.236801	CCAxGTT	COVERED																																																																																			NOVEL					0			18	3.037766	KEEP	0	1	31	21	558	TT	0.999879	0.612333	0			4	60	134	0	0	10.694532	19	60	559	66		0.173913	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91797063	91797063	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91797063G>A			NA	NA				RP11-575H3.1 (28143 upstream) : AC027612.6 (8122 downstream)						NA		NA									NA						gagccactgcgcctggcctca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91797063G>A		NA		hg19		0.02	-0.376621	TGCxCCT	COVERED																																																																																			NOVEL					0			14	5.71646	KEEP	1	0	0	19	566	GG	0.99986	0.908941	0			4	60	114	0	0	7.968103	30	60	957	86		0.117647	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91797553	91797553	__UNKNOWN__	IGR	SNP	G	G	A	rs13426227	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91797553G>A			NA	NA				RP11-575H3.1 (28633 upstream) : AC027612.6 (7632 downstream)						NA		NA									NA						gactgatgcaggaggatcact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91797553G>A		NA		hg19		0.02	-0.35088	GCAxGAG	COVERED																																																																																			NOVEL					0			15	3.073637	KEEP	4	2	53	29	871	GG	0.999988	0.877697	0			5	60	150	0	0	10.963388	33	60	1104	91		0.131579	0.877708
AC027612.6	0	__UNKNOWN__	__UNKNOWN__	2	91811923	91811923	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91811923G>A	ENST00000609777.1	-	0	199										NA		NA									NA						tacagacgtgggccaccgcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000609777.1:	chr2.hg19:g.91811923G>A		NA		hg19		0.02	1.131432	GTGxGCC	COVERED																																																																																			NOVEL	AC027612.6-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000471986.1	27	2.30515	KEEP	1	3	83	37	1125	GG	1	0.999948	0		-	5	60	152	0	0	9.835357	63	60	2118	193	ENST00000609777.1	0.073529	0.999948
AC027612.6	0	__UNKNOWN__	__UNKNOWN__	2	91833149	91833149	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91833149T>C	ENST00000609777.1	-	0	199										NA		NA									NA						ctgcacagccTAGACTTCAAG	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000609777.1:	chr2.hg19:g.91833149T>C		NA		hg19		0.02	-0.113997	GCCxAGA	UNCOVERED																																																																																			NOVEL	AC027612.6-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000471986.1	9	3.303368	KEEP	3	0	0	11	282	TT	0.99254	0.161255	0		-	3	21	92	0	0	7.582416	10	54	284	33	ENST00000609777.1	0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91872023	91872023	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91872023C>T			NA	NA				RNA5SP100 (9031 upstream) : AC027612.3 (2104 downstream)						NA		NA									NA						CACAAAGCCACGGGAATCCAG	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91872023C>T		NA		hg19		0.02	8.886208	CCAxGGG	COVERED																																																																																			NOVEL					0			87	8.446121	KEEP	81	19	529	215	6376	CC	1	1	0			28	49	810	0	0	52.256757	316	50	10386	905		0.081395	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91872069	91872069	__UNKNOWN__	IGR	SNP	C	C	T	rs2537164	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91872069C>T			NA	NA				RNA5SP100 (9077 upstream) : AC027612.3 (2058 downstream)						NA		NA									NA						CATCACTGCACACACACAAAA	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91872069C>T		NA		hg19		0.02	12.361252	GCAxACA	COVERED																																																																																			NOVEL					0			97	8.385217	KEEP	87	23	592	238	7227	CC	1	1	0			72	49	2133	0	0	165.447356	332	51	11351	1005		0.178218	1
AC027612.3	0	__UNKNOWN__	__UNKNOWN__	2	91896136	91896136	__UNKNOWN__	RNA	SNP	G	G	A	rs200309536		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91896136G>A	ENST00000436174.1	-	0	168										NA		NA									NA						AGTTTTAATGGATAGTACTAA	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000436174.1:	chr2.hg19:g.91896136G>A		NA		hg19		0.02	-0.24562	ATGxATA	COVERED																																																																																			NOVEL	AC027612.3-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000338339.1	11	2.941718	KEEP	25	1	29	20	599	GG	0.993072	0.636904	0		-	3	40	92	0	0	6.493117	25	47	823	92	ENST00000436174.1	0.107143	0.641347
AC027612.3	0	__UNKNOWN__	__UNKNOWN__	2	91898566	91898566	__UNKNOWN__	RNA	SNP	C	C	G	rs112777555		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91898566C>G	ENST00000436174.1	-	0	168										NA		NA									NA						agactacaggcTGgggcatgg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000436174.1:	chr2.hg19:g.91898566C>G		NA		hg19		0.02	-0.193	AGGxTGG	COVERED																																																																																			NOVEL	AC027612.3-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000338339.1	17	4.212201	KEEP	13	0	0	14	419	CC	0.993634	0.454842	0		-	3	57	98	1	0	7.633019	16	60	562	66	ENST00000436174.1	0.157895	0.457757
AC027612.3	0	__UNKNOWN__	__UNKNOWN__	2	91898585	91898585	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91898585G>A	ENST00000436174.1	-	0	168										NA		NA									NA						ggtgactcacgcctgtaatcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000436174.1:	chr2.hg19:g.91898585G>A		NA		hg19		0.02	-0.192986	CACxCCT	COVERED																																																																																			NOVEL	AC027612.3-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000338339.1	17	5.114258	KEEP	19	0	0	17	502	GG	0.994391	0.455189	0		-	3	57	91	0	0	6.861241	17	60	573	77	ENST00000436174.1	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91916012	91916012	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91916012T>C			NA	NA				AC027612.3 (15876 upstream) : AC027612.2 (35938 downstream)						NA		NA									NA						aagacgtgattttgccttgtt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91916012T>C		NA		hg19		0.02	-0.342071	GATxTTG	COVERED																																																																																			NOVEL					0			42	9.555541	KEEP	71	1	29	42	1148	TT	0.999869	0.865632	0			3	25	109	0	0	7.774669	35	49	1062	179		0.078947	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	91987242	91987242	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:91987242G>T			NA	NA				AC027612.2 (35198 upstream) : SLC9B1P2 (93255 downstream)						NA		NA									NA						aaggaaggaaggagaaaaaaa	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.91987242G>T		NA		hg19		0.02	-0.166662	GAAxGAG	COVERED																																																																																			NOVEL					0			22	2.841574	KEEP	20	1	27	19	588	GG	0.995343	0.352299	0			4	52	112	0	1	9.470759	10	60	333	64		0.285714	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92104498	92104498	__UNKNOWN__	IGR	SNP	T	T	C	rs76196824		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92104498T>C			NA	NA				SLC9B1P2 (2260 upstream) : None (None downstream)						NA		NA									NA						gaggctgaggtggacagatca	0.483		NA											t|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17795	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92104498T>C		NA		hg19		0.02	-0.236769	AGGxGGA	COVERED																																																																																			NOVEL					0			11	2.735941	KEEP	3	1	28	19	500	TT	0.999859	0.612321	0			4	32	122	0	0	9.339444	21	60	618	66		0.16	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92107274	92107274	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92107274T>C			NA	NA				SLC9B1P2 (5036 upstream) : None (None downstream)						NA		NA									NA						cctcggcctctcaaagtgctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92107274T>C		NA		hg19		0.02	-0.140349	CTCxCAA	UNCOVERED																																																																																			NOVEL					0			4	2.707015	KEEP	4	0	0	9	254	TT	0	0	0			3	60	106	0	0	9.378632	7	60	221	44		0.3	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92186799	92186799	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92186799G>A			NA	NA				SLC9B1P2 (84561 upstream) : None (None downstream)						NA		NA									NA						AGGTCATGAAGGGGGCTGATG	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92186799G>A		NA		hg19		0.02	-0.377229	GAAxGGG	COVERED																																																																																			NOVEL					0			2	3.310016	KEEP	12	0	0	11	342	GG	0.99254	0.902287	0			4	28	125	0	0	8.675223	38	60	1332	100		0.095238	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92186801	92186801	__UNKNOWN__	IGR	SNP	G	G	T	rs74328916	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92186801G>T			NA	NA				SLC9B1P2 (84563 upstream) : None (None downstream)						NA		NA									NA						GTCATGAAGGGGGCTGATGAC	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92186801G>T		NA		hg19		0.02	-0.377204	AGGxGGC	COVERED																																																																																			NOVEL					0			2	3.610243	KEEP	12	0	0	12	359	GG	0.992708	0.90244	0			4	28	111	0	0	7.278895	38	60	1291	102		0.095238	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92307391	92307391	__UNKNOWN__	IGR	SNP	T	T	G	rs4120029		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92307391T>G			NA	NA				SLC9B1P2 (205153 upstream) : None (None downstream)						NA		NA									NA						tgaaacactctttttgtggaa	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92307391T>G		NA		hg19		0.02	1.689609	CTCxTTT	COVERED																																																																																			NOVEL					0			41	22.390288	KEEP	217	1	30	85	2374	TT	0.999863	0.981821	0			5	22	163	0	0	12.142788	35	40	1088	442		0.125	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92308508	92308508	__UNKNOWN__	IGR	SNP	A	A	G	rs2172570		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92308508A>G			NA	NA				SLC9B1P2 (206270 upstream) : None (None downstream)						NA		NA									NA						attctcagaaacttcattggg	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92308508A>G		NA		hg19		0.02	-0.140349	GAAxCTT	COVERED																																																																																			NOVEL					0			19	3.040566	KEEP	54	1	31	21	589	AA	0.993072	0.259157	0			4	27	139	0	0	15.807832	0	0	0	125		1	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92315359	92315359	__UNKNOWN__	IGR	SNP	G	G	A	rs62147234		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92315359G>A			NA	NA				SLC9B1P2 (213121 upstream) : None (None downstream)						NA		NA									NA						catagagcaggtttgaaacac	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92315359G>A		NA		hg19		0.02	4.864203	CAGxTTT	COVERED																																																																																			NOVEL					0			100	17.075345	KEEP	117	7	181	121	3563	GG	1	1	0			12	49	345	0	0	32.164152	15	47	496	501		0.444444	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92315977	92315977	__UNKNOWN__	IGR	SNP	C	C	G	rs201404726	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92315977C>G			NA	NA				SLC9B1P2 (213739 upstream) : None (None downstream)						NA		NA									NA						ttcccagaaacttctttgtga	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92315977C>G		NA		hg19		0.02	-0.4386	AAAxTTC	COVERED																																																																																			NOVEL					0			16	5.247628	KEEP	33	1	33	29	855	CC	0.999869	0.959733	0			3	25	106	0	0	10.225061	3	45	106	133		0.5	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92321632	92321632	__UNKNOWN__	IGR	SNP	T	T	C	rs28799133	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92321632T>C			NA	NA				SLC9B1P2 (219394 upstream) : None (None downstream)						NA		NA									NA						tgaacctttcttttcagagag	0.348		NA											.|||	218	0.0435304	0.118	0.0187	5008	,	,	NA	89776	0.0248	NA	0.0139	False	NA	,,,	NA	NA	NA	2504	0.0102	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92321632T>C		NA		hg19		0.02	-0.078844	TTCxTTT	UNCOVERED																																																																																			NOVEL					0			3	3.007058	KEEP	11	0	0	10	271	TT	0	0	0			3	46	76	2	0	7.55862	2	34	61	36		0.6	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325055	92325055	__UNKNOWN__	IGR	SNP	T	T	C	rs4309040		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92325055T>C			NA	NA				SLC9B1P2 (222817 upstream) : None (None downstream)						NA		NA									NA						acactctttttgtaaaatctg	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325055T>C		NA		hg19		0.02	-0.333241	TTTxGTA	COVERED																																																																																			NOVEL					0			16	4.367328	KEEP	64	2	61	36	953	TT	0.995343	0.848017	0			3	20	99	1	0	7.405932	21	44	584	158		0.125	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325060	92325060	__UNKNOWN__	IGR	SNP	A	A	T	rs2210343	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92325060A>T			NA	NA				SLC9B1P2 (222822 upstream) : None (None downstream)						NA		NA									NA						ctttttgtaaaatctgcaaga	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325060A>T		NA		hg19		0.02	-0.359586	TAAxATC	COVERED																																																																																			NOVEL					0			17	4.575136	KEEP	66	2	56	35	964	AA	0.995343	0.884736	0			5	44	132	1	0	10.155657	20	39	611	170		0.2	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325079	92325079	__UNKNOWN__	IGR	SNP	G	G	T	rs4120206	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92325079G>T			NA	NA				SLC9B1P2 (222841 upstream) : None (None downstream)						NA		NA									NA						gaggatatttggatagctttg	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325079G>T		NA		hg19		0.02	1.642851	TTTxGAT	COVERED																																																																																			NOVEL					0			20	8.022158	KEEP	82	2	37	40	1238	GG	0.997832	0.961684	0			4	20	116	0	0	8.16405	30	44	1027	223		0.117647	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325136	92325136	__UNKNOWN__	IGR	SNP	A	A	T	rs59167504		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92325136A>T			NA	NA				SLC9B1P2 (222898 upstream) : None (None downstream)						NA		NA									NA						ctctagacagaagcattctca	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325136A>T		NA		hg19		0.02	1.421043	CAGxAGC	COVERED																																																																																			NOVEL					0			10	5.607761	KEEP	85	3	71	44	1192	AA	0.999879	0.993582	0			5	27	140	0	0	9.293028	46	39	1397	234		0.098039	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	92325205	92325205	__UNKNOWN__	IGR	SNP	G	G	A	rs6739144		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:92325205G>A			NA	NA				SLC9B1P2 (222967 upstream) : None (None downstream)						NA		NA									NA						ctttcatagagcaggtttgaa	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.92325205G>A		NA		hg19		0.02	-0.350885	AGAxCAG	COVERED																																																																																			NOVEL					0			6	4.512841	KEEP	94	3	85	45	1378	GG	0.995343	0.87362	0			6	37	173	0	0	13.458578	26	39	892	214		0.1875	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	96687684	96687684	__UNKNOWN__	IGR	SNP	A	A	G	rs2918924		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:96687684A>G			NA	NA				FAHD2CP (102 upstream) : GPAT2 (9 downstream)						NA		NA									NA						ACACACATACACCAAAAAGAT	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.96687684A>G		NA		hg19		0.02	1.620179	TACxCCA	COVERED																																																																																			NOVEL					0			5	7.275483	KEEP	2	2	56	44	1176	AA	1	0.999956	0			7	33	242	0	0	16.594232	91	60	2645	207		0.071429	0.999956
SNRNP200	23020	__UNKNOWN__	__UNKNOWN__	2	96942349	96942349	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:96942349G>A	ENST00000323853.5	-	43	6252				SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	NA		NA			ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						tagtagagacggggtttcact	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028	23020			30859	protein-coding gene	gene with protein product	U5 snRNP specific protein, 200 KD	601664	activating signal cointegrator 1 complex subunit 3-like 1, retinitis pigmentosa 33 (autosomal dominant)	ASCC3L1, RP33	NA	9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014	NM_014014	NA	Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.6174+292C>T	chr2.hg19:g.96942349G>A		NA	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	hg19	CCDS2020.1	0.02	-0.27159	GACxGGG	COVERED																																																																																			NOVEL	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252846.2	6	3.528139	KEEP	8	1	26	21	524	GG	0.999863	0.717217	0		-	4	44	114	0	1	8.198229	26	60	743	65	ENST00000323853.5	0.133333	0.717315
ANKRD36	375248	__UNKNOWN__	__UNKNOWN__	2	97830108	97830108	__UNKNOWN__	Intron	SNP	A	A	G	rs74323232		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:97830108A>G	ENST00000461153.2	+	20	1702				ANKRD36_ENST00000420699.2_Intron			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	NA		NA								endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						TGATATGTTAATCATTATGTT	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													50	38	42			NA	NA	2		NA											NA				97830108		692	1590	2282	SO:0001627	intron_variant			BC046186	CCDS54379.1	2q11.2	2013-09-24			ENSG00000135976	ENSG00000135976	375248		Ankyrin repeat domain containing	24079	protein-coding gene	gene with protein product		NA			NA	12975309	Standard		NM_001164315	NA	Approved	UNQ2430	uc010yva.2	A6QL64	OTTHUMG00000155256	ENST00000461153.2:c.1459-26A>G	chr2.hg19:g.97830108A>G		NA	B4E3I8|Q6UX02|Q86X62|Q9HCD1	hg19	CCDS54379.1	0.02	1.909361	TTAxTCA	COVERED																																																																																			NOVEL	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339154.5	1	4.210573	KEEP	9	0	0	14	386	AA	0.993072	0.987533	0		+	6	49	209	0	0	15.160915	57	60	1731	125	ENST00000461153.2	0.095238	0.994422
VWA3B	200403	__UNKNOWN__	__UNKNOWN__	2	98712978	98712978	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:98712978T>C	ENST00000477737.1	+	2	400				VWA3B_ENST00000435344.1_Intron|VWA3B_ENST00000451075.2_Intron	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	NA		NA								NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						ctgatccacctgcctcggcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658	200403			28385	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_144992	NM_144992	NA	Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.196+3227T>C	chr2.hg19:g.98712978T>C		NA	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	hg19	CCDS42718.1	0.02	-0.210491	ACCxGCC	COVERED																																																																																			NOVEL	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353469.2	7	3.608902	KEEP	1	0	0	12	330	TT	0.993634	0.518837	0		+	3	48	91	0	0	6.728273	19	60	566	54	ENST00000477737.1	0.136364	0.522161
MGAT4A	11320	__UNKNOWN__	__UNKNOWN__	2	99295817	99295817	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:99295817T>C	ENST00000264968.3	-	2	458				MGAT4A_ENST00000393487.1_Intron|MGAT4A_ENST00000409391.1_Intron			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	NA		NA			cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						tgcagtgagctgagatcgcgc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	11320	2.4.1.145	Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases	7047	protein-coding gene	gene with protein product		604623	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A		NA	10024668	Standard	NM_012214	NM_001160154	NA	Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.95-883A>G	chr2.hg19:g.99295817T>C		NA	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	hg19	CCDS2036.1	0.02	-0.263093	AGCxGAG	COVERED																																																																																			NOVEL	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252988.2	11	4.135763	KEEP	22	1	29	24	632	TT	0.99986	0.693571	0		-	3	32	92	0	0	6.445401	26	46	752	79	ENST00000264968.3	0.103448	0.693668
MGAT4A	11320	__UNKNOWN__	__UNKNOWN__	2	99295951	99295951	__UNKNOWN__	Intron	SNP	T	T	C	rs72825758	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:99295951T>C	ENST00000264968.3	-	2	458				MGAT4A_ENST00000393487.1_Intron|MGAT4A_ENST00000409391.1_Intron			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	NA		NA			cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						aaaaattagctaggcatggtg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	11320	2.4.1.145	Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases	7047	protein-coding gene	gene with protein product		604623	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A		NA	10024668	Standard	NM_012214	NM_001160154	NA	Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.95-1017A>G	chr2.hg19:g.99295951T>C		NA	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	hg19	CCDS2036.1	0.02	-0.359543	AGCxAGG	COVERED																																																																																			NOVEL	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252988.2	29	8.717807	KEEP	0	0	0	29	750	TT	0.999997	0.888873	0		-	3	60	100	0	0	6.840955	36	60	1040	83	ENST00000264968.3	0.076923	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	99363718	99363718	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:99363718T>C			NA	NA				MGAT4A (16129 upstream) : AC109826.1 (14682 downstream)						NA		NA									NA						gagccgagattgtgccactgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.99363718T>C		NA		hg19		0.02	-0.174822	GATxGTG	UNCOVERED																																																																																			NOVEL					0			8	2.706406	KEEP	2	0	0	9	242	TT	0	0	0			3	60	96	0	0	7.598305	14	60	374	41		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	99407727	99407727	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:99407727A>G			NA	NA				RNU4-84P (8716 upstream) : KIAA1211L (2581 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.99407727A>G		NA		hg19		0.02	-0.21049	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			5	2.691823	KEEP	3	0	0	9	240	AA	0	0	0			3	60	100	0	0	7.760928	17	60	500	56		0.15	0.552887
TSGA10	80705	__UNKNOWN__	__UNKNOWN__	2	99741327	99741327	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:99741327T>C	ENST00000393483.3	-	2	354				TSGA10_ENST00000539964.1_Intron|TSGA10_ENST00000542655.1_Intron|TSGA10_ENST00000478090.1_Intron|TSGA10_ENST00000355053.4_Intron	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	NA		NA			cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						ggattacaggtgtgagccact	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951	80705			14927	protein-coding gene	gene with protein product	cancer/testis antigen 79	607166			NA	11179690	Standard	NM_182911	NM_025244	NA	Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.490+2183A>G	chr2.hg19:g.99741327T>C		NA	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	hg19	CCDS2037.1	0.02	-0.096482	AGGxGTG	UNCOVERED																																																																																			NOVEL	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253125.1	6	2.706894	KEEP	6	0	0	9	251	TT	0	0	0		-	3	60	102	0	0	8.832587	8	60	240	35	ENST00000393483.3	0.272727	0.120436
C2orf15	150590	__UNKNOWN__	__UNKNOWN__	2	99931808	99931808	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:99931808A>G	ENST00000465095.1	+	2	38									chromosome 2 open reading frame 15	NA		NA								autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(1)	6						aattacaggcatgagccaccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021264	CCDS2038.1	2q11.2	2008-02-05			ENSG00000241962	ENSG00000241962	150590			28436	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144706	NM_144706	NA	Approved	MGC29762	uc002szk.3	Q8WU43	OTTHUMG00000130635	ENST00000465095.1:c.39-5808A>G	chr2.hg19:g.99931808A>G		NA		hg19		0.02	-0.192886	GGCxTGA	COVERED																																																																																			NOVEL	C2orf15-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000472130.1	7	3.608177	KEEP	5	0	0	12	323	AA	0.992708	0.454419	0		+	3	60	95	0	0	7.261343	17	60	492	51	ENST00000465095.1	0.15	0.457757
REV1	51455	__UNKNOWN__	__UNKNOWN__	2	100060561	100060561	__UNKNOWN__	Intron	SNP	T	T	C	rs1901283	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:100060561T>C	ENST00000258428.3	-	5	579				REV1_ENST00000465835.1_Intron|REV1_ENST00000393445.3_Intron	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ggattacaggtgtgagccacc	0.478		NA						Direct reversal of damage					.|||	2907	0.580471	0.7315	0.7003	5008	,	,	NA	15309	0.3621	NA	0.5666	False	NA	,,,	NA	NA	NA	2504	0.5307	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945	51455		DNA polymerases	14060	protein-coding gene	gene with protein product		606134	REV1 (yeast homolog)- like, REV1-like (yeast), REV1 homolog (S. cerevisiae)	REV1L	NA	10536157	Standard	NM_016316	XM_005263968	NA	Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.351-1630A>G	chr2.hg19:g.100060561T>C		NA	O95941|Q53SI7|Q9C0J4|Q9NUP2	hg19	CCDS2045.1	0.02	-0.070172	AGGxGTG	UNCOVERED																																																																																			NOVEL	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253123.2	5	2.405938	KEEP	2	0	0	8	218	GT	0	0	0		-	4	60	128	0	0	12.631922	3	60	91	24	ENST00000258428.3	0.571429	0.054137
REV1	51455	__UNKNOWN__	__UNKNOWN__	2	100063912	100063912	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:100063912G>A	ENST00000258428.3	-	4	579				REV1_ENST00000465835.1_Intron|REV1_ENST00000393445.3_Intron	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						gattacaggcgtgagccaccg	0.433		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945	51455		DNA polymerases	14060	protein-coding gene	gene with protein product		606134	REV1 (yeast homolog)- like, REV1-like (yeast), REV1 homolog (S. cerevisiae)	REV1L	NA	10536157	Standard	NM_016316	XM_005263968	NA	Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.350+1885C>T	chr2.hg19:g.100063912G>A		NA	O95941|Q53SI7|Q9C0J4|Q9NUP2	hg19	CCDS2045.1	0.02	-0.201735	GGCxTGA	COVERED																																																																																			NOVEL	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253123.2	5	2.407301	KEEP	0	0	0	8	250	GG	0.99257	0.4869	0		-	3	60	89	0	0	6.733883	16	60	508	44	ENST00000258428.3	0.157895	0.490544
REV1	51455	__UNKNOWN__	__UNKNOWN__	2	100082693	100082693	__UNKNOWN__	Intron	SNP	G	G	A	rs557308087		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:100082693G>A	ENST00000258428.3	-	2	219				REV1_ENST00000393445.3_Intron	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						gattacaggcgtaagccaccg	0.577		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945	51455		DNA polymerases	14060	protein-coding gene	gene with protein product		606134	REV1 (yeast homolog)- like, REV1-like (yeast), REV1 homolog (S. cerevisiae)	REV1L	NA	10536157	Standard	NM_016316	XM_005263968	NA	Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.10-1246C>T	chr2.hg19:g.100082693G>A		NA	O95941|Q53SI7|Q9C0J4|Q9NUP2	hg19	CCDS2045.1	0.02	-0.201751	GGCxTAA	COVERED																																																																																			NOVEL	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253123.2	6	2.406233	KEEP	0	0	0	8	227	GG	0.99257	0.4869	0		-	3	60	88	0	0	6.427896	19	60	619	45	ENST00000258428.3	0.136364	0.490544
REV1	51455	__UNKNOWN__	__UNKNOWN__	2	100082695	100082695	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:100082695A>G	ENST00000258428.3	-	2	219				REV1_ENST00000393445.3_Intron	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ttacaggcgtaagccaccgtg	0.582		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945	51455		DNA polymerases	14060	protein-coding gene	gene with protein product		606134	REV1 (yeast homolog)- like, REV1-like (yeast), REV1 homolog (S. cerevisiae)	REV1L	NA	10536157	Standard	NM_016316	XM_005263968	NA	Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.10-1248T>C	chr2.hg19:g.100082695A>G		NA	O95941|Q53SI7|Q9C0J4|Q9NUP2	hg19	CCDS2045.1	0.02	-0.201703	CGTxAGC	COVERED																																																																																			NOVEL	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253123.2	6	2.405131	KEEP	0	0	0	8	207	AA	0.99257	0.4869	0		-	3	60	105	0	0	8.126947	19	60	538	45	ENST00000258428.3	0.136364	0.490544
AFF3	3899	__UNKNOWN__	__UNKNOWN__	2	100597534	100597534	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:100597534A>G	ENST00000409236.2	-	5	986				AFF3_ENST00000409579.1_Intron|AFF3_ENST00000317233.4_Intron|AFF3_ENST00000356421.2_Intron			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	NA		NA			embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ctggagtgcaatggcgtgatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218	3899			6473	protein-coding gene	gene with protein product		601464	lymphoid nuclear protein related to AF4	LAF4	NA	8662235, 8555498	Standard	NM_002285	XM_005263945	NA	Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.873+25559T>C	chr2.hg19:g.100597534A>G		NA	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	hg19	CCDS42723.1	0.02	-0.149103	GCAxTGG	COVERED																																																																																			NOVEL	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328982.3	9	3.307153	KEEP	2	0	0	11	287	AA	0.992708	0.320453	0		-	3	60	100	0	0	8.172281	12	60	360	41	ENST00000409236.2	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	101207262	101207262	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:101207262G>A			NA	NA				snoU13 (13243 upstream) : RN7SL360P (10065 downstream)						NA		NA									NA						cgaggcgggcggatcacgagg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.101207262G>A		NA		hg19		0.02	-0.280655	GGCxGAT	COVERED																																																																																			NOVEL					0			4	3.610397	KEEP	8	0	0	12	357	GG	0.99254	0.734154	0			4	60	102	0	0	6.939568	27	60	864	61		0.129032	0.739671
NPAS2	4862	__UNKNOWN__	__UNKNOWN__	2	101575562	101575562	__UNKNOWN__	Intron	SNP	A	A	C	rs2309939	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:101575562A>C	ENST00000335681.5	+	8	883				NPAS2_ENST00000542504.1_Intron|NPAS2_ENST00000486017.1_Intron	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	NA		NA			cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						aaaaaaaaaaaaaaaaaaaac	0.458		NA											a|||	1165	0.232628	0.1982	0.2622	5008	,	,	NA	15270	0.0655	NA	0.3787	False	NA	,,,	NA	NA	NA	2504	0.2802	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485	4862		Basic helix-loop-helix proteins	7895	protein-coding gene	gene with protein product		603347			NA	9012850, 9079689	Standard		NM_002518	NA	Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.599-4958A>C	chr2.hg19:g.101575562A>C		NA	Q4ZFV9|Q53SQ3|Q86V96|Q99629	hg19	CCDS2048.1	0.02	-0.105255	AAAxAAA	UNCOVERED																																																																																			NOVEL	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253168.3	12	4.812296	KEEP	1	0	0	16	441	AA	0.997832	0.139529	0		+	2	60	66	2	1	6.350213	2	60	57	40	ENST00000335681.5	0.5	0.139832
TBC1D8	11138	__UNKNOWN__	__UNKNOWN__	2	101627085	101627085	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:101627085A>G	ENST00000376840.4	-	19	2970				RPL31_ENST00000409028.4_Intron|RPL31_ENST00000409650.1_Intron|RPL31_ENST00000409038.1_Intron|TBC1D8_ENST00000409318.1_Intron			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	NA		NA			blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						ggtggctcaaacctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634	11138			17791	protein-coding gene	gene with protein product	BUB2-like protein 1, vascular Rab-GAP/TBC-containing protein	NA			NA	10373574	Standard	NM_007063	NM_001102426	NA	Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.2970+305T>C	chr2.hg19:g.101627085A>G		NA	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	hg19	CCDS46375.1	0.02	-0.157878	CAAxCCT	COVERED																																																																																			NOVEL	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376092.1	8	3.308129	KEEP	0	0	0	11	299	AA	0.993072	0.32057	0		-	3	60	97	0	0	7.692196	14	60	425	43	ENST00000376840.4	0.176471	0.322807
RNF149	284996	__UNKNOWN__	__UNKNOWN__	2	101913491	101913491	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:101913491C>T	ENST00000295317.3	-	2	568					NM_173647.3	NP_775918.2	Q8NC42	RN149_HUMAN	ring finger protein 149	NA		NA			cellular response to drug (GO:0035690)|negative regulation of MAPK cascade (GO:0043409)|regulation of protein stability (GO:0031647)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12						gccaaaatggcgaaaccccgt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(25;331 612 6521 7355 31028)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074985	CCDS2051.1	2q12.1	2013-01-09			ENSG00000163162	ENSG00000163162	284996		RING-type (C3HC4) zinc fingers	23137	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173647	NM_173647	NA	Approved	FLJ90504	uc002taz.2	Q8NC42	OTTHUMG00000130685	ENST00000295317.3:c.461-1848G>A	chr2.hg19:g.101913491C>T		NA	Q53S14|Q8N5I8|Q8NBY5|Q8WUU3	hg19	CCDS2051.1	0.02	-0.087714	TGGxGAA	UNCOVERED																																																																																			NOVEL	RNF149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253180.2	4	2.405535	KEEP	3	0	0	8	215	CC	0	0	0		-	3	52	89	0	0	7.678365	7	60	225	26	ENST00000295317.3	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	102309671	102309671	__UNKNOWN__	IGR	SNP	T	T	C	rs375295937|rs74802907	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:102309671T>C			NA	NA				AC092570.2 (206387 upstream) : MAP4K4 (4534 downstream)						NA		NA									NA						tctctctctctctccctccct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.102309671T>C		NA		hg19		0.02	-0.105237	CTCxCTC	UNCOVERED																																																																																			NOVEL					0			6	3.307708	KEEP	0	0	0	11	294	TT	0.993072	0.138863	0			3	60	98	0	0	8.301467	9	60	266	34		0.25	0.139832
AC073987.1	0	__UNKNOWN__	__UNKNOWN__	2	103734047	103734047	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:103734047G>A	ENST00000422683.1	-	0	213										NA		NA									NA						cgcccgcctcggcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000422683.1:	chr2.hg19:g.103734047G>A		NA		hg19		0.02	-0.166676	CTCxGCC	COVERED																																																																																			NOVEL	AC073987.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000329587.1	1	3.609464	KEEP	7	0	0	12	348	GG	0.99257	0.351317	0		-	3	60	93	0	0	7.133328	16	60	549	55	ENST00000422683.1	0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	104015669	104015669	__UNKNOWN__	IGR	SNP	T	T	C	rs367878175		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:104015669T>C			NA	NA				AC073987.1 (222951 upstream) : AC013727.1 (457758 downstream)						NA		NA									NA						aggatggtcttgatctcctga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.104015669T>C		NA		hg19		0.02	-0.149079	TCTxGAT	COVERED																																																																																			NOVEL					0			6	3.006076	KEEP	5	0	0	10	260	TT	0.99257	0.289832	0			4	40	119	0	0	9.781494	13	60	371	40		0.235294	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	104015724	104015724	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:104015724A>T			NA	NA				AC073987.1 (223006 upstream) : AC013727.1 (457703 downstream)						NA		NA									NA						ctgggattacaggcgtgagcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.104015724A>T		NA		hg19		0.02	-0.166636	TACxGGC	COVERED																																																																																			NOVEL					0			7	3.308718	KEEP	6	0	0	11	309	AA	0.993072	0.351495	0			3	26	92	0	0	7.03376	16	60	486	53		0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	105165559	105165559	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:105165559A>G			NA	NA				U3 (16117 upstream) : AC013402.1 (19715 downstream)						NA		NA									NA						ttgagctcagaagttcaagac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.105165559A>G		NA		hg19		0.02	-0.131535	CAGxAGT	COVERED																																																																																			NOVEL					0			4	2.405847	KEEP	0	0	0	8	217	AA	0.99257	0.22747	0			3	60	90	0	0	7.382531	10	60	295	34		0.230769	0.229173
FHL2	2274	__UNKNOWN__	__UNKNOWN__	2	105976854	105976854	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:105976854T>C	ENST00000409177.1	-	0	2195							Q14192	FHL2_HUMAN	four and a half LIM domains 2	NA		NA			androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						ctctttgtcttccaggctgga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641	2274			3703	protein-coding gene	gene with protein product		602633			NA	8753811	Standard		NM_201557	NA	Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409177.1:c.*886A>G	chr2.hg19:g.105976854T>C		NA	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	hg19		0.02	1.821662	TCTxCCA	COVERED																																																																																			NOVEL	FHL2-006	PUTATIVE	alternative_5_UTR|downstream_ATG|basic	protein_coding	NA	protein_coding	OTTHUMT00000329659.2	34	8.114368	KEEP	0	3	88	58	1589	TT	1	0.998696	0		-	5	60	156	0	0	10.17007	65	70	1973	180	ENST00000409177.1	0.071429	0.998696
UXS1	80146	__UNKNOWN__	__UNKNOWN__	2	106759851	106759851	__UNKNOWN__	Intron	SNP	A	A	C	rs549798207	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:106759851A>C	ENST00000283148.7	-	6	570				UXS1_ENST00000428048.2_Intron|UXS1_ENST00000540130.1_Intron|UXS1_ENST00000409501.3_Intron	NM_001253875.1|NM_025076.4	NP_001240804.1|NP_079352.2	Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	NA		NA			protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						ggcaacagagagagactccgt	0.483		NA											A|||	8	0.00159744	0.0	0.0	5008	,	,	NA	9968	0.0	NA	0.008	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	80146	4.1.1.35	Short chain dehydrogenase/reductase superfamily / Extended SDR fold	17729	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 6E, member 12	609749			NA	19027726	Standard	NM_025076.3	NM_001253875	NA	Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000283148.7:c.472+1794T>G	chr2.hg19:g.106759851A>C		NA	Q8NBX3|Q9H5C2	hg19	CCDS58721.1	0.02	-0.070174	GAGxGAG	UNCOVERED																																																																																			NOVEL	UXS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329776.1	9	2.706729	KEEP	6	0	0	9	246	AA	0	0	0		-	4	45	144	0	0	13.900673	4	60	122	21	ENST00000283148.7	0.5	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	107099714	107099714	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:107099714C>G			NA	NA				RGPD3 (14882 upstream) : AC108868.1 (13 downstream)						NA		NA									NA						TATTCTACATCGTTCAAAATG	0.289		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.107099714C>G		NA		hg19		0.02	1.420617	CATxGTT	COVERED																																																																																			NOVEL					0			30	2.436579	KEEP	7	4	116	49	1398	CC	1	0.999956	0			5	29	162	0	0	9.996503	94	60	3035	202		0.050505	0.999956
AC108868.1	0	__UNKNOWN__	__UNKNOWN__	2	107099860	107099860	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:107099860T>C	ENST00000596204.1	-	2	23										NA		NA									NA						ggcgcaatcttggctcactgc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000596204.1:c.24-111A>G	chr2.hg19:g.107099860T>C		NA		hg19		0.02	-0.192923	TCTxGGC	COVERED																																																																																			NOVEL	AC108868.1-201	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding		4	7.518297	KEEP	5	0	0	25	684	TT	0.999879	0.457701	0		-	4	40	124	0	1	9.963849	16	60	469	52	ENST00000596204.1	0.2	0.457757
CD8BP	927	__UNKNOWN__	__UNKNOWN__	2	107112546	107112546	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:107112546A>G	ENST00000416057.1	+	0	401							A6NJW9	CD8BL_HUMAN	CD8b molecule pseudogene	NA		NA			immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)					NA						gagccaccgcacccggccATA	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							2q12.2	2012-10-03	2006-03-28	2006-03-09	ENSG00000254126	ENSG00000254126	927			1708	pseudogene	pseudogene		NA	CD8 antigen, beta polypeptide 2, pseudogene (p37)	CD8B2	NA	1541829	Standard	XM_166000	NG_002423	NA	Approved			A6NJW9	OTTHUMG00000153183	ENST00000416057.1:	chr2.hg19:g.107112546A>G		NA		hg19		0.02	-0.403404	CGCxCCC	COVERED																																																																																			NOVEL	CD8BP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000331218.1	7	3.007016	KEEP	0	0	0	10	267	AA	0.992708	0.934874	0		+	3	59	100	0	0	6.678835	41	60	1189	75	ENST00000416057.1	0.068182	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	107721068	107721068	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:107721068A>G			NA	NA				ST6GAL2 (217504 upstream) : AC006227.1 (150078 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.107721068A>G		NA		hg19		0.02	-0.19293	CACxCCT	COVERED																																																																																			NOVEL					0			9	2.406288	KEEP	1	0	0	8	226	AT	0.99257	0.454356	0			4	60	124	0	0	9.870131	17	60	503	45		0.190476	0.457757
AC096669.2	0	__UNKNOWN__	__UNKNOWN__	2	108063550	108063550	__UNKNOWN__	lincRNA	SNP	G	G	A	rs575868826	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:108063550G>A	ENST00000414300.1	-	0	295										NA		NA									NA						ggctgggtgcggtggctcatg	0.458		NA											g|||	8	0.00159744	0.0008	0.0029	5008	,	,	NA	14423	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000414300.1:	chr2.hg19:g.108063550G>A		NA		hg19		0.02	-0.166639	TGCxGTG	COVERED																																																																																			NOVEL	AC096669.2-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000330061.1	13	3.007986	KEEP	3	0	0	10	290	GG	0.992708	0.351366	0		-	3	60	92	0	0	7.110482	15	60	469	44	ENST00000414300.1	0.166667	0.353947
AC096669.2	0	__UNKNOWN__	__UNKNOWN__	2	108063559	108063559	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:108063559T>C	ENST00000414300.1	-	0	295										NA		NA									NA						cggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000414300.1:	chr2.hg19:g.108063559T>C		NA		hg19		0.02	-0.175391	TCAxGCC	COVERED																																																																																			NOVEL	AC096669.2-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000330061.1	14	3.308529	KEEP	5	0	0	11	308	TT	0.992708	0.384582	0		-	3	60	97	0	0	7.533682	16	60	463	45	ENST00000414300.1	0.157895	0.387407
SEPT10	151011	__UNKNOWN__	__UNKNOWN__	2	110345490	110345490	__UNKNOWN__	Intron	SNP	C	C	A	rs59990177		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:110345490C>A	ENST00000356688.4	-	3	415				SEPT10_ENST00000415095.1_Intron|SEPT10_ENST00000545389.1_Intron|SEPT10_ENST00000397712.2_Intron|SEPT10_ENST00000437928.1_Intron|SEPT10_ENST00000334001.6_Intron|SEPT10_ENST00000397714.2_Intron			Q9P0V9	SEP10_HUMAN	septin 10	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(3)|large_intestine(4)|lung(8)|prostate(1)	18						actccatctccaaaaaaaaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF146760	CCDS42726.1, CCDS46383.1	2q13	2013-01-21			ENSG00000186522	ENSG00000186522	151011		Septins	14349	protein-coding gene	gene with protein product	sept1-like	611737			NA	12711328	Standard	NM_144710	NM_144710	NA	Approved	FLJ11619	uc002tew.4	Q9P0V9	OTTHUMG00000154957	ENST00000356688.4:c.100-2075G>T	chr2.hg19:g.110345490C>A		NA	B3KRQ9|Q86VP5|Q9HAH6	hg19		0.02	-0.157838	CTCxAAA	COVERED																																																																																			NOVEL	SEPT10-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000337805.1	11	3.30917	KEEP	1	0	0	11	320	CC	0.993072	0.32057	0		-	3	60	89	0	1	6.810963	15	60	449	40	ENST00000356688.4	0.166667	0.322807
ACOXL	55289	__UNKNOWN__	__UNKNOWN__	2	111550277	111550277	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:111550277A>G	ENST00000389811.4	+	4	383				ACOXL_ENST00000439055.1_Intron|ACOXL_ENST00000340561.4_Intron			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	NA		NA			fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						tcaggaggctaaggcaggagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093	55289			25621	protein-coding gene	gene with protein product		NA	acyl-Coenzyme A oxidase-like		NA		Standard	NM_018308	NM_001142807	NA	Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.160-950A>G	chr2.hg19:g.111550277A>G		NA	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	hg19		0.02	-0.157863	GCTxAGG	COVERED																																																																																			NOVEL	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000254024.2	7	2.405273	KEEP	0	0	0	8	210	AA	0.99257	0.320408	0		+	3	60	101	0	0	8.091868	14	60	400	32	ENST00000389811.4	0.176471	0.322807
ACOXL	55289	__UNKNOWN__	__UNKNOWN__	2	111851348	111851348	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:111851348C>G	ENST00000389811.4	+	0	2141				ACOXL_ENST00000439055.1_Intron			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	NA		NA			fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						ggctgaggcacgagaatcgct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093	55289			25621	protein-coding gene	gene with protein product		NA	acyl-Coenzyme A oxidase-like		NA		Standard	NM_018308	NM_001142807	NA	Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.*273C>G	chr2.hg19:g.111851348C>G		NA	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	hg19		0.02	-0.219296	GCAxGAG	COVERED																																																																																			NOVEL	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000254024.2	5	3.610039	KEEP	0	0	0	12	350	CC	0.993634	0.579219	0		+	4	60	118	1	0	8.937015	21	60	693	42	ENST00000389811.4	0.16	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	112649313	112649313	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:112649313A>G			NA	NA				ANAPC1 (7046 upstream) : MERTK (6742 downstream)						NA		NA									NA						gtagagacggagtttcaccat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.112649313A>G		NA		hg19		0.02	-0.219283	CGGxGTT	COVERED																																																																																			NOVEL					0			7	2.706746	KEEP	1	0	0	9	246	AA	0.99254	0.548763	0			4	60	131	1	0	10.394383	19	60	585	47		0.173913	0.552887
MERTK	10461	__UNKNOWN__	__UNKNOWN__	2	112752292	112752292	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:112752292A>G	ENST00000295408.4	+	9	1707				MERTK_ENST00000409780.1_Intron|MERTK_ENST00000421804.2_Intron			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	NA		NA			apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						ggaggcagagattgcagtgag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208	10461		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	7027	protein-coding gene	gene with protein product		604705	c-mer proto-oncogene tyrosine kinase		NA	8086340, 10343112	Standard		XM_005263565	NA	Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1450+311A>G	chr2.hg19:g.112752292A>G		NA	Q9HBB4	hg19	CCDS2094.1	0.02	-0.271904	GAGxTTG	COVERED																																																																																			NOVEL	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254046.2	7	2.517922	KEEP	0	1	21	16	417	AA	0.999366	0.739203	0		+	3	60	100	0	0	7.34252	24	60	727	73	ENST00000295408.4	0.111111	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	113123314	113123314	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:113123314T>C			NA	NA				ZC3H6 (25674 upstream) : RGPD8 (4354 downstream)						NA		NA									NA						gaccttgtgatacgcccacct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.113123314T>C		NA		hg19		0.02	-0.184177	TGAxACG	UNCOVERED																																																																																			NOVEL					0			6	2.405388	KEEP	8	0	0	8	213	TT	0	0	0			6	60	214	0	0	18.958089	14	60	395	52		0.3	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	113657648	113657648	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:113657648T>G			NA	NA				AC079753.1 (55660 upstream) : IL37 (12899 downstream)						NA		NA									NA						tgtaatctcatcactttggga	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.113657648T>G		NA		hg19		0.02	-0.043861	TCAxCAC	UNCOVERED																																																																																			NOVEL					0			4	2.705939	KEEP	0	0	0	9	237	TT	0.99254	0.023894	0			2	60	66	0	0	6.349981	2	60	66	17		0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	114541557	114541557	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:114541557C>T			NA	NA				SLC35F5 (27157 upstream) : AC024704.2 (45409 downstream)						NA		NA									NA						tggtggctcacgcctgtaatc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.114541557C>T		NA		hg19		0.02	-0.096488	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			3	3.91125	KEEP	0	0	0	13	390	CC	0.994391	0.119761	0			3	60	87	0	0	7.64316	6	60	200	37		0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	115100087	115100087	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:115100087T>C			NA	NA				snoU13 (61335 upstream) : RNU2-41P (77614 downstream)						NA		NA									NA						agtgctgggattacaggcgtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.115100087T>C		NA		hg19		0.02	-0.210499	GGAxTAC	UNCOVERED																																																																																			NOVEL					0			10	2.707093	KEEP	6	0	0	9	251	TT	0	0	0			4	23	138	0	0	11.0944	19	60	563	55		0.173913	0.522161
DPP10	57628	__UNKNOWN__	__UNKNOWN__	2	115615605	115615605	__UNKNOWN__	Intron	SNP	C	C	T	rs139737231	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:115615605C>T	ENST00000410059.1	+	1	540				DPP10_ENST00000409163.1_Intron	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	NA		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						tttgctctgtcgcccaggctg	0.498		NA											C|||	41	0.0081869	0.0287	0.0029	5008	,	,	NA	18729	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497	57628			20823	protein-coding gene	gene with protein product		608209	dipeptidylpeptidase 10, dipeptidyl-peptidase 10		NA	10819331, 12662155	Standard	NM_020868	NM_020868	NA	Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.60+415190C>T	chr2.hg19:g.115615605C>T		NA	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	hg19	CCDS46400.1	0.02	-0.16668	TGTxGCC	COVERED																																																																																			NOVEL	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330580.4	4	2.708186	KEEP	0	0	0	9	282	CC	0.99254	0.351306	0		+	3	60	96	0	1	7.771974	12	60	413	46	ENST00000410059.1	0.2	0.353947
CCDC93	54520	__UNKNOWN__	__UNKNOWN__	2	118751529	118751529	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:118751529T>C	ENST00000376300.2	-	6	657				CCDC93_ENST00000460781.1_Intron|CCDC93_ENST00000319432.5_Intron	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	NA		NA								breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						aggctggtcttgaactcctga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633	54520			25611	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_019044	NM_019044	NA	Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.519+1492A>G	chr2.hg19:g.118751529T>C		NA	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	hg19	CCDS2121.2	0.02	-0.035085	TCTxGAA	UNCOVERED																																																																																			NOVEL	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000129615.1	5	2.707101	KEEP	0	0	0	9	254	TT	0.99254	0.019833	0		-	2	60	72	0	0	6.950449	2	60	56	19	ENST00000376300.2	0.5	0.019982
SCTR	6344	__UNKNOWN__	__UNKNOWN__	2	120258813	120258813	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:120258813T>C	ENST00000019103.5	-	2	340					NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	NA		NA			digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	ggtgaaaccctgtctctacta	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293	6344		GPCR / Class B : Glucagon receptors	10608	protein-coding gene	gene with protein product		182098			NA	1646711	Standard		NM_002980	NA	Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.73-6689A>G	chr2.hg19:g.120258813T>C		NA	Q12961|Q13213|Q53T00	hg19	CCDS2127.1	0.02	-0.070122	CCCxGTC	UNCOVERED																																																																																			NOVEL	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254198.2	5	2.706425	KEEP	8	0	0	9	245	TT	0	0	0		-	3	40	88	1	0	7.933897	5	60	139	28	ENST00000019103.5	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	121921442	121921442	__UNKNOWN__	IGR	SNP	T	T	C	rs547442117	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:121921442T>C			NA	NA				AC067960.1 (75140 upstream) : AC079988.3 (14460 downstream)						NA		NA									NA						gatccgcccgtctcggcctcc	0.517		NA											-|||	38	0.00758786	0.0	0.0432	5008	,	,	NA	15669	0.0	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.121921442T>C		NA		hg19		0.02	-0.061394	CCGxCTC	UNCOVERED																																																																																			NOVEL					0			10	2.706161	KEEP	17	0	0	9	239	TT	0	0	0			2	60	72	0	0	6.335867	5	60	144	41		0.285714	0.043787
CLASP1	23332	__UNKNOWN__	__UNKNOWN__	2	122336101	122336101	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:122336101C>T	ENST00000409078.3	-	2	696				CLASP1_ENST00000397587.3_Intron|CLASP1_ENST00000455322.2_Intron|CLASP1_ENST00000541377.1_Intron|CLASP1_ENST00000263710.4_Intron			Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	NA		NA			axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					gtcaggagatcgagaccatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054	23332			17088	protein-coding gene	gene with protein product	multiple asters 1	605852			NA	9734811, 10899121, 16914514	Standard	NM_015282	NM_015282	NA	Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000409078.3:c.195+27175G>A	chr2.hg19:g.122336101C>T		NA	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	hg19		0.02	-0.131562	GATxGAG	COVERED																																																																																			NOVEL	CLASP1-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000330853.4	6	3.007297	KEEP	2	0	0	10	281	CC	0.992708	0.227502	0		-	3	60	93	0	0	7.472385	12	60	360	36	ENST00000409078.3	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	122605482	122605482	__UNKNOWN__	IGR	SNP	T	T	C	rs367764499		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:122605482T>C			NA	NA				AC018737.3 (51204 upstream) : None (None downstream)						NA		NA									NA						tgagccactgtgcccggccgg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.122605482T>C		NA		hg19		0.02	-0.096486	CTGxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.706457	KEEP	2	0	0	9	243	TT	0.99257	0.119541	0			3	60	99	0	0	8.843668	6	60	181	30		0.333333	0.120436
CNTNAP5	129684	__UNKNOWN__	__UNKNOWN__	2	124963099	124963099	__UNKNOWN__	Intron	SNP	G	G	A	rs1807922	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:124963099G>A	ENST00000431078.1	+	2	446					NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	NA		NA			cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		gggttcaagcgattctcctgc	0.502		NA											G|||	1891	0.377596	0.3389	0.3112	5008	,	,	NA	16310	0.3958	NA	0.2922	False	NA	,,,	NA	NA	NA	2504	0.546	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052	129684			18748	protein-coding gene	gene with protein product		610519			NA		Standard		NM_130773	NA	Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.83-16183G>A	chr2.hg19:g.124963099G>A		NA	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	hg19	CCDS46401.1	0.02	-0.122787	AGCxATT	COVERED																																																																																			NOVEL	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330864.3	14	3.008122	KEEP	4	0	0	10	285	GG	0.99257	0.194853	0		+	3	60	86	0	0	6.873142	11	60	348	31	ENST00000431078.1	0.214286	0.196312
CNTNAP5	129684	__UNKNOWN__	__UNKNOWN__	2	125672815	125672815	__UNKNOWN__	3'UTR	SNP	G	G	A	rs556769219	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:125672815G>A	ENST00000431078.1	+	0	5235					NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	NA		NA			cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		atacacacacgcacacatata	0.303		NA											G|||	20	0.00399361	0.0076	0.0029	5008	,	,	NA	15496	0.003	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052	129684			18748	protein-coding gene	gene with protein product		610519			NA		Standard		NM_130773	NA	Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.*950G>A	chr2.hg19:g.125672815G>A		NA	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	hg19	CCDS46401.1	0.02	1.438537	CACxCAC	COVERED																																																																																			NOVEL	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330864.3	10	5.972622	KEEP	0	2	51	38	1049	GG	1	0.992094	0		+	6	60	180	0	0	12.353059	55	60	1760	153	ENST00000431078.1	0.098361	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	125873861	125873861	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:125873861A>G			NA	NA				RNU6-259P (126959 upstream) : snosnR60_Z15 (12547 downstream)						NA		NA									NA						caggaggatcacttgaaccca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.125873861A>G		NA		hg19		0.02	-0.070146	ATCxCTT	UNCOVERED																																																																																			NOVEL					0			9	3.303763	KEEP	0	0	0	11	276	AA	0.993072	0.0768	0			3	60	97	0	0	9.056185	4	60	107	23		0.428571	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	126413316	126413316	__UNKNOWN__	IGR	SNP	G	G	A	rs182089474	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:126413316G>A			NA	NA				snosnR60_Z15 (526826 upstream) : AC097499.1 (55229 downstream)						NA		NA									NA						AGCAATggccgggtgcggtgt	0.408		NA											G|||	32	0.00638978	0.0038	0.0058	5008	,	,	NA	10079	0.0	NA	0.0219	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.126413316G>A		NA		hg19		0.02	-0.052629	GCCxGGT	UNCOVERED																																																																																			NOVEL					0			5	3.308036	KEEP	3	0	0	11	300	GG	0.992708	0.036498	0			3	60	92	0	0	8.824768	3	60	96	25		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	126678258	126678258	__UNKNOWN__	IGR	SNP	G	G	A	rs12478686	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:126678258G>A			NA	NA				AC097499.1 (154839 upstream) : AC114813.1 (189417 downstream)						NA		NA									NA						cactttgggaggccaaggcgg	0.537		NA											G|||	985	0.196685	0.1082	0.196	5008	,	,	NA	15902	0.1627	NA	0.2525	False	NA	,,,	NA	NA	NA	2504	0.2945	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.126678258G>A		NA		hg19		0.02	-0.105267	GGAxGCC	UNCOVERED																																																																																			NOVEL					0			5	3.009129	KEEP	11	0	0	10	311	GG	0	0	0			4	60	121	0	0	10.876563	7	60	249	49		0.363636	0.139832
CYP27C1	339761	__UNKNOWN__	__UNKNOWN__	2	127944023	127944023	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:127944023A>G	ENST00000335247.7	-	0	2073				CYP27C1_ENST00000409327.1_3'UTR	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	NA		NA				membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		acccaggctgaagtgcagtgg	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684	339761		Cytochrome P450s	33480	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001001665	NM_001001665	NA	Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.*824T>C	chr2.hg19:g.127944023A>G		NA	Q6ZNI7	hg19	CCDS33285.1	0.02	-0.438514	CTGxAGT	COVERED																																																																																			NOVEL	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331046.1	27	9.055639	KEEP	0	1	31	41	1139	AA	1	0.959859	0		-	3	60	99	0	0	6.578096	41	60	1218	136	ENST00000335247.7	0.068182	0.959859
POLR2D	5433	__UNKNOWN__	__UNKNOWN__	2	128604942	128604942	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:128604942T>G	ENST00000409955.1	-	0	1088				POLR2D_ENST00000272645.4_3'UTR|POLR2D_ENST00000487079.1_5'UTR			O15514	RPB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide D	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus in response to heat stress (GO:0031990)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleotide-excision repair (GO:0006289)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|nucleotide binding (GO:0000166)|translation initiation factor binding (GO:0031369)			large_intestine(1)|lung(4)|urinary_tract(1)	6	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		TTCAggccagttgtggtggct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U85510	CCDS2151.1	2q21	2013-01-21			ENSG00000144231	ENSG00000144231	5433		RNA polymerase subunits	9191	protein-coding gene	gene with protein product	RNA polymerase II subunit hsRBP4	606017			NA	9528765	Standard	NM_004805	NM_004805	NA	Approved	RBP4	uc002tpj.3	O15514	OTTHUMG00000131531	ENST00000409955.1:c.*739A>C	chr2.hg19:g.128604942T>G		NA	Q52LT4	hg19		0.02	1.722018	CAGxTGT	COVERED																																																																																			NOVEL	POLR2D-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331149.1	11	9.022232	KEEP	0	0	0	30	831	TT	0.999997	0.998693	0		-	4	60	135	0	0	8.859015	62	60	1873	145	ENST00000409955.1	0.060606	0.998696
UGGT1	56886	__UNKNOWN__	__UNKNOWN__	2	128950868	128950868	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:128950868C>G	ENST00000259253.6	+	0	8267				UGGT1_ENST00000375990.3_3'UTR	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						ttctgtcacccaggctggagt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731	56886			15663	protein-coding gene	gene with protein product		605897	UDP-glucose ceramide glucosyltransferase-like 1	UGCGL1	NA	10694380	Standard	NM_020120	NM_020120	NA	Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.*3552C>G	chr2.hg19:g.128950868C>G		NA	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	hg19	CCDS2154.1	0.02	1.140146	ACCxAGG	COVERED																																																																																			NOVEL	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254435.2	22	22.867469	KEEP	2	0	0	76	2326	CC	1	0.99994	0		+	5	60	159	0	0	9.981714	82	60	2867	240	ENST00000259253.6	0.057471	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	130988203	130988203	__UNKNOWN__	IGR	SNP	C	C	T	rs79048658		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:130988203C>T			NA	NA				TUBA3E (32169 upstream) : AC018804.7 (724 downstream)						NA		NA									NA						GTCCTGAGCACTGTGGGCCCC	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.130988203C>T		NA		hg19		0.02	1.435154	GCAxTGT	COVERED																																																																																			NOVEL					0			0	2.440389	KEEP	3	1	28	18	562	CC	0.99986	0.999537	0			17	60	507	0	0	40.24648	69	60	2369	153		0.197674	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	131083132	131083132	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:131083132T>C			NA	NA				AC018804.7 (93453 upstream) : CCDC115 (12681 downstream)						NA		NA									NA						tttgggaggctgaggtgggcg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.131083132T>C		NA		hg19		0.02	-0.149124	GGCxGAG	COVERED																																																																																			NOVEL					0			7	2.707094	KEEP	0	0	0	9	254	TT	0.99254	0.320398	0			3	60	105	0	0	8.672009	12	60	377	41		0.2	0.322807
ARHGEF4	50649	__UNKNOWN__	__UNKNOWN__	2	131719584	131719584	__UNKNOWN__	Intron	SNP	C	C	T	rs547930951		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:131719584C>T	ENST00000326016.5	+	4	946				ARHGEF4_ENST00000392953.3_Intron|ARHGEF4_ENST00000409303.1_Intron|ARHGEF4_ENST00000525839.1_Intron|ARHGEF4_ENST00000428230.2_Intron	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	NA		NA			apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		gaggccgaggcgggcggatca	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002	50649		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	684	protein-coding gene	gene with protein product	APC-stimulated guanine nucleotide exchange factor	605216			NA	10873612	Standard		NM_015320	NA	Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.427+15376C>T	chr2.hg19:g.131719584C>T		NA	Q9HDC6|Q9UPP0	hg19	CCDS2165.1	0.02	-0.201747	AGGxGGG	COVERED																																																																																			NOVEL	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254554.4	12	3.609717	KEEP	7	0	0	12	351	CC	0.99254	0.486885	0		+	3	31	89	0	0	6.52767	19	60	624	56	ENST00000326016.5	0.136364	0.490544
PLEKHB2	55041	__UNKNOWN__	__UNKNOWN__	2	131886725	131886725	__UNKNOWN__	Intron	SNP	T	T	C	rs201023595		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:131886725T>C	ENST00000409158.1	+	5	853				PLEKHB2_ENST00000439822.2_Intron|PLEKHB2_ENST00000403716.1_Intron|PLEKHB2_ENST00000538982.1_Intron|PLEKHB2_ENST00000404460.1_Intron|PLEKHB2_ENST00000409612.1_Intron|PLEKHB2_ENST00000409279.1_Intron|PLEKHB2_ENST00000438882.2_Intron|PLEKHB2_ENST00000234115.6_Intron|PLEKHB2_ENST00000303908.3_Intron			Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	NA		NA				endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		tggtgaaacctcgtctctact	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762	55041		Pleckstrin homology (PH) domain containing	19236	protein-coding gene	gene with protein product		NA			NA	10200314	Standard	NM_017958	NM_017958	NA	Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000409158.1:c.294-1569T>C	chr2.hg19:g.131886725T>C		NA	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	hg19	CCDS58730.1	0.02	-0.087562	ACCxCGT	UNCOVERED																																																																																			NOVEL	PLEKHB2-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331302.1	5	2.406365	KEEP	6	0	0	8	224	TT	0	0	0		+	3	40	80	0	1	6.936338	6	60	186	29	ENST00000409158.1	0.333333	0.099721
PLEKHB2	55041	__UNKNOWN__	__UNKNOWN__	2	131951999	131951999	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:131951999A>G	ENST00000404460.1	+	6	477				PLEKHB2_ENST00000303908.3_Intron			Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	NA		NA				endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		TAAACtgtgtatgcgtgtgtg	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762	55041		Pleckstrin homology (PH) domain containing	19236	protein-coding gene	gene with protein product		NA			NA	10200314	Standard	NM_017958	NM_017958	NA	Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000404460.1:c.423+61435A>G	chr2.hg19:g.131951999A>G		NA	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	hg19		0.02	-0.175368	TGTxTGC	COVERED																																																																																			NOVEL	PLEKHB2-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000318943.2	2	3.891977	KEEP	0	0	0	13	311	AA	0.994391	0.385234	0		+	3	60	101	0	0	7.861179	17	60	461	35	ENST00000404460.1	0.15	0.387407
PLEKHB2	55041	__UNKNOWN__	__UNKNOWN__	2	132021815	132021815	__UNKNOWN__	Intron	SNP	G	G	A	rs369764537	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:132021815G>A	ENST00000404460.1	+	7	477				POTEE_ENST00000358087.5_3'UTR|POTEE_ENST00000356920.5_Silent_p.T929T|PLEKHB2_ENST00000303908.3_Intron			Q96CS7	PKHB2_HUMAN	pleckstrin homology domain containing, family B (evectins) member 2	NA		NA				endosome (GO:0005768)|membrane (GO:0016020)				large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(221;0.0828)		AGATGGCCACGGCGGCCTCCA	0.617		NA											.|||	283	0.0565096	0.0893	0.0447	5008	,	,	NA	43636	0.0069	NA	0.0795	False	NA	,,,	NA	NA	NA	2504	0.0481	NA	NA	NA								NA				0													141	156	151			NA	NA	2		NA											NA				132021815		2201	4297	6498	SO:0001627	intron_variant				CCDS2166.1, CCDS46413.1, CCDS58729.1, CCDS58730.1, CCDS74576.1, CCDS74577.1	2q22.1	2013-01-10			ENSG00000115762	ENSG00000115762	55041		Pleckstrin homology (PH) domain containing	19236	protein-coding gene	gene with protein product		NA			NA	10200314	Standard	NM_017958	NM_017958	NA	Approved	EVT2, FLJ20783	uc031rpd.1	Q96CS7	OTTHUMG00000131656	ENST00000404460.1:c.424-88778G>A	chr2.hg19:g.132021815G>A		NA	B4DF08|B4DZ66|B8ZZN1|Q53FF1|Q53TH7|Q86W37|Q9BV75|Q9NWK1	hg19		0.02	1.368366	CACxGCG	COVERED																																																																																			NOVEL	PLEKHB2-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000318943.2	3	2.70793	KEEP	3	0	0	9	272	GG	0.99254	0.989724	0		+	11	44	339	0	0	25.858814	60	50	1918	119	ENST00000404460.1	0.15493	0.997163
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	132217606	132217606	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:132217606T>C			NA	NA				AC073869.19 (50984 upstream) : RP11-109E12.1 (1787 downstream)						NA		NA									NA						actcttgttgtccaggctgga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.132217606T>C		NA		hg19		0.02	-0.166653	TTGxCCA	UNCOVERED																																																																																			NOVEL					0			9	2.405875	KEEP	5	0	0	8	216	TT	0	0	0			3	49	103	0	0	8.291602	14	60	424	48		0.176471	0.353947
ANKRD30BL	554226	__UNKNOWN__	__UNKNOWN__	2	133014579	133014579	__UNKNOWN__	Intron	SNP	A	A	G	rs62165009		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133014579A>G	ENST00000470729.1	-	1	441				MIR663B_ENST00000408361.1_RNA	NR_027020.2		A7E2S9	A30BL_HUMAN	ankyrin repeat domain 30B-like	NA		NA								endometrium(1)|kidney(3)	4						AAACACGGCCACGGGATCCCA	0.721		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													22	38	33			NA	NA	2		NA											NA				133014579		1549	3575	5124	SO:0001627	intron_variant					2q21.2	2013-01-22	2010-06-14	2010-06-14	ENSG00000163046	ENSG00000163046	554226		Ankyrin repeat domain containing	35167	protein-coding gene	gene with protein product		NA	non-protein coding RNA 164, ankyrin repeat domain 30B pseudogene 3	NCRNA00164, ANKRD30BP3	NA	17114284	Standard	NR_027019	NR_027019	NA	Approved		uc002tti.3	A7E2S9	OTTHUMG00000153491	ENST00000470729.1:c.984+522T>C	chr2.hg19:g.133014579A>G		NA	B8ZZL7	hg19		0.02	8.884228	GCCxCGG	COVERED																																																																																			NOVEL	ANKRD30BL-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000331354.1	23	7.816493	KEEP	8	0	0	26	680	AA	0.999931	0.999931	0		-	12	43	397	0	0	26.351303	166	60	4811	434	ENST00000470729.1	0.067416	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133016627	133016627	__UNKNOWN__	IGR	SNP	G	G	T	rs62165017		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133016627G>T			NA	NA				ANKRD30BL (1085 upstream) : AC097532.2 (26740 downstream)						NA		NA									NA						aTTAAGCACTGTATTCTGTTA	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133016627G>T		NA		hg19		0.02	1.438277	ACTxTAT	COVERED																																																																																			NOVEL					0			28	3.338562	KEEP	11	4	104	48	1392	GG	1	0.99994	0			8	60	235	0	0	22.207499	9	60	288	175		0.470588	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133019226	133019226	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133019226T>C			NA	NA				ANKRD30BL (3684 upstream) : AC097532.2 (24141 downstream)						NA		NA									NA						CGAATCATTATGTGAAATAGG	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133019226T>C		NA		hg19		0.02	5.063228	TTAxGTG	COVERED																																																																																			NOVEL					0			4	8.421852	KEEP	0	0	0	28	781	TT	0.999997	0.999997	0			6	60	192	0	0	14.098794	44	60	1320	283		0.12	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133019261	133019261	__UNKNOWN__	IGR	SNP	A	A	G	rs142731717		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133019261A>G			NA	NA				ANKRD30BL (3719 upstream) : AC097532.2 (24106 downstream)						NA		NA									NA						CTGACCAAACATTTAAATTCA	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133019261A>G		NA		hg19		0.02	3.727905	AACxTTT	COVERED																																																																																			NOVEL					0			3	2.235976	KEEP	0	1	33	19	498	AA	0.999863	0.999861	0			6	60	199	0	0	15.566918	32	60	941	181		0.157895	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133019578	133019578	__UNKNOWN__	IGR	SNP	C	C	G	rs112681737		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133019578C>G			NA	NA				ANKRD30BL (4036 upstream) : AC097532.2 (23789 downstream)						NA		NA									NA						GGAGGACCAGCAGCTCTTAGT	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133019578C>G		NA		hg19		0.02	18.232579	CAGxAGC	COVERED																																																																																			NOVEL					0			24	16.284076	KEEP	10	4	125	98	3012	CC	1	1	0			17	60	569	0	0	52.48161	26	60	870	1021		0.395349	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020059	133020059	__UNKNOWN__	IGR	SNP	C	C	T	rs113975411	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133020059C>T			NA	NA				ANKRD30BL (4517 upstream) : AC097532.2 (23308 downstream)						NA		NA									NA						TTGGACTCTTCCATCATTTCA	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020059C>T		NA		hg19		0.02	4.280337	CTTxCAT	COVERED																																																																																			NOVEL					0			3	2.972871	KEEP	5	2	51	28	818	CC	0.999997	0.999997	0			13	60	356	0	0	31.018727	26	60	878	322		0.333333	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020137	133020137	__UNKNOWN__	IGR	SNP	G	G	A	rs143018704		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133020137G>A			NA	NA				ANKRD30BL (4595 upstream) : AC097532.2 (23230 downstream)						NA		NA									NA						GCAGCAGAAGGCTTGATGAGC	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020137G>A		NA		hg19		0.02	13.534809	AAGxCTT	COVERED																																																																																			NOVEL					0			14	18.303143	KEEP	0	2	48	78	2388	GG	1	1	0			13	60	379	0	0	28.038686	76	60	2596	831		0.146067	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020226	133020226	__UNKNOWN__	IGR	SNP	C	C	T	rs113400576		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133020226C>T			NA	NA				ANKRD30BL (4684 upstream) : AC097532.2 (23141 downstream)						NA		NA									NA						TTTGAGCCATCTACCTTCTCA	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020226C>T		NA		hg19		0.02	3.665257	CATxTAC	COVERED																																																																																			NOVEL					0			2	7.820631	KEEP	0	0	0	26	764	CC	0.999957	0.999957	0			4	60	114	0	0	9.99203	8	60	229	223		0.333333	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133020763	133020763	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133020763T>C			NA	NA				ANKRD30BL (5221 upstream) : AC097532.2 (22604 downstream)						NA		NA									NA						ATGAATTTGGTTACTAATACT	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133020763T>C		NA		hg19		0.02	3.897754	TGGxTAC	COVERED																																																																																			NOVEL					0			2	3.007681	KEEP	1	0	0	10	279	TT	0.992708	0.992707	0			8	60	279	0	0	20.426457	72	60	2200	206		0.1	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133024196	133024196	__UNKNOWN__	IGR	SNP	G	G	A	rs139690703		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133024196G>A			NA	NA				ANKRD30BL (8654 upstream) : AC097532.2 (19171 downstream)						NA		NA									NA						gagagacagagagaaagaaag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133024196G>A		NA		hg19		0.02	-0.29824	AGAxAGA	COVERED																																																																																			NOVEL					0			18	3.242893	KEEP	6	1	29	21	642	GG	0.999863	0.780953	0			3	60	89	2	0	6.979035	13	60	421	69		0.1875	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133024652	133024652	__UNKNOWN__	IGR	SNP	G	G	C	rs375835638		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133024652G>C			NA	NA				ANKRD30BL (9110 upstream) : AC097532.2 (18715 downstream)						NA		NA									NA						gacggacagagagaaacaaag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133024652G>C		NA		hg19		0.02	-0.210379	AGAxAGA	COVERED																																																																																			NOVEL					0			32	8.124223	KEEP	6	0	0	27	831	GG	0.999931	0.522125	0			3	51	106	1	0	9.955281	4	60	132	65		0.428571	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133024668	133024668	__UNKNOWN__	IGR	SNP	G	G	C	rs62647085		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133024668G>C			NA	NA				ANKRD30BL (9126 upstream) : AC097532.2 (18699 downstream)						NA		NA									NA						caaagagagagagacagagag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133024668G>C		NA		hg19		0.02	-0.122815	AGAxAGA	COVERED																																																																																			NOVEL					0			11	3.610621	KEEP	2	0	0	12	364	GG	0.993072	0.194952	0			3	51	106	0	1	9.543626	6	60	193	33		0.333333	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133027191	133027191	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133027191A>G			NA	NA				ANKRD30BL (11649 upstream) : AC097532.2 (16176 downstream)						NA		NA									NA						agagagagaaacagaaaggga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133027191A>G		NA		hg19		0.02	16.355111	GAAxCAG	COVERED																																																																																			NOVEL					0			1075	80.036404	KEEP	613	48	1449	776	21088	AA	1	1	0			10	57	318	0	1	23.210069	75	60	2196	1990		0.117647	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133027808	133027808	__UNKNOWN__	IGR	SNP	G	G	A	rs76316991		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133027808G>A			NA	NA				ANKRD30BL (12266 upstream) : AC097532.2 (15559 downstream)						NA		NA									NA						tcgtgccacagaaaaagaaag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133027808G>A		NA		hg19		0.02	1.192916	ACAxAAA	COVERED																																																																																			NOVEL					0			262	39.675676	KEEP	155	2	54	151	4445	GG	1	0.999862	0			3	60	91	0	0	7.878678	7	60	213	354		0.3	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133028073	133028073	__UNKNOWN__	IGR	SNP	G	G	C	rs374041575		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133028073G>C			NA	NA				ANKRD30BL (12531 upstream) : AC097532.2 (15294 downstream)						NA		NA									NA						gacggacagagagagacaaag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133028073G>C		NA		hg19		0.02	-0.087723	AGAxAGA	UNCOVERED																																																																																			NOVEL					0			5	3.008811	KEEP	5	0	0	10	302	GG	0	0	0			2	60	69	2	0	7.024863	1	60	32	31		0.666667	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133029040	133029040	__UNKNOWN__	IGR	SNP	G	G	C	rs201865616		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133029040G>C			NA	NA				ANKRD30BL (13498 upstream) : AC097532.2 (14327 downstream)						NA		NA									NA						cagagagagagagacagacag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133029040G>C		NA		hg19		0.02	1.853731	AGAxAGA	COVERED																																																																																			NOVEL					0			43	6.743328	KEEP	37	4	121	65	1886	GG	1	0.989542	0			4	31	140	0	0	11.213312	20	60	623	154		0.166667	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133074781	133074781	__UNKNOWN__	IGR	SNP	G	G	A	rs111509913	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133074781G>A			NA	NA				AC097532.2 (22831 upstream) : RP11-725P16.2 (28407 downstream)						NA		NA									NA						CAAAGGATCCGGGATTTAAGT	0.403		NA											.|||	61	0.0121805	0.0015	0.0245	5008	,	,	NA	18961	0.0	NA	0.0398	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133074781G>A		NA		hg19		0.02	1.540471	TCCxGGA	COVERED																																																																																			NOVEL					0			1	2.707518	KEEP	3	0	0	9	261	GG	0.99257	0.990784	0			16	60	492	0	0	41.859386	43	60	1424	118		0.271186	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133101771	133101771	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133101771G>A			NA	NA				AC097532.2 (49821 upstream) : RP11-725P16.2 (1417 downstream)						NA		NA									NA						gcagtggcacgatctcagctc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133101771G>A		NA		hg19		0.02	-0.306999	CACxATC	COVERED																																																																																			NOVEL					0			8	4.813144	KEEP	2	0	0	16	463	GG	0.995343	0.814653	0			4	60	111	0	0	7.777243	28	60	894	75		0.125	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	133102465	133102465	__UNKNOWN__	IGR	SNP	C	C	A	rs2598771	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:133102465C>A			NA	NA				AC097532.2 (50515 upstream) : RP11-725P16.2 (723 downstream)						NA		NA									NA						ccagcctggccaacatggtga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.133102465C>A		NA		hg19		0.02	-0.192961	GGCxAAC	UNCOVERED																																																																																			NOVEL					0			11	2.707204	KEEP	7	0	0	9	261	CC	0	0	0			7	59	203	0	0	18.207816	12	60	398	47		0.368421	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	134559165	134559165	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:134559165T>C			NA	NA				RN7SKP93 (205195 upstream) : MGAT5 (318388 downstream)						NA		NA									NA						ggcatggtggttcacgcctgt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.134559165T>C		NA		hg19		0.02	-0.131554	TGGxTCA	COVERED																																																																																			NOVEL					0			8	2.706669	KEEP	0	0	0	9	249	TT	0.99254	0.227464	0			3	60	105	0	1	9.001359	9	60	263	35		0.25	0.229173
RAB3GAP1	22930	__UNKNOWN__	__UNKNOWN__	2	135855066	135855066	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:135855066T>C	ENST00000264158.8	+	5	405				RAB3GAP1_ENST00000539493.1_Intron|RAB3GAP1_ENST00000442034.1_Intron|RAB3GAP1_ENST00000487003.1_Intron	NM_012233.2	NP_036365.1	Q15042	RB3GP_HUMAN	RAB3 GTPase activating protein subunit 1 (catalytic)	NA		NA			brain development (GO:0007420)|camera-type eye development (GO:0043010)|establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|face morphogenesis (GO:0060325)|hypothalamus development (GO:0021854)|lipid particle organization (GO:0034389)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of calcium ion-dependent exocytosis of neurotransmitter (GO:1903233)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of GTPase activity (GO:0043087)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cytoplasm (GO:0005737)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(10)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32				BRCA - Breast invasive adenocarcinoma(221;0.117)		actgggattataggtgtgagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D31886	CCDS33294.1, CCDS54402.1	2q21.3	2013-07-09			ENSG00000115839	ENSG00000115839	22930			17063	protein-coding gene	gene with protein product		602536			NA	9030515, 15696165	Standard	NM_012233	NM_012233	NA	Approved	RAB3GAP, KIAA0066, RAB3GAP130, WARBM1	uc010fnf.3	Q15042	OTTHUMG00000154889	ENST00000264158.8:c.362+3803T>C	chr2.hg19:g.135855066T>C		NA	A6H8Z3|C9J837|Q659F5|Q8TBB4	hg19	CCDS33294.1	0.02	-0.140326	TTAxAGG	COVERED																																																																																			NOVEL	RAB3GAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337514.2	4	3.00757	KEEP	1	0	0	10	273	TT	0.99254	0.259018	0		+	3	60	90	0	0	7.273221	11	60	322	33	ENST00000264158.8	0.214286	0.260965
ZRANB3	84083	__UNKNOWN__	__UNKNOWN__	2	136122403	136122403	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136122403G>A	ENST00000264159.6	-	4	297				ZRANB3_ENST00000401392.1_Intron|ZRANB3_ENST00000536680.1_Intron	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		ggcagatcacgaggtcaggag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988	84083		Zinc fingers, RAN-binding domain containing	25249	protein-coding gene	gene with protein product		NA			NA	11230166	Standard	NM_032143	XM_005263809	NA	Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.181-11205C>T	chr2.hg19:g.136122403G>A		NA	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	hg19	CCDS46419.1	0.02	-0.113983	CACxAGG	UNCOVERED																																																																																			NOVEL	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318254.1	7	2.406457	KEEP	4	0	0	8	234	GG	0	0	0		-	3	60	83	0	0	6.801688	9	60	260	33	ENST00000264159.6	0.25	0.162467
R3HDM1	23518	__UNKNOWN__	__UNKNOWN__	2	136449898	136449898	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136449898A>G	ENST00000410054.1	+	17	2520				R3HDM1_ENST00000329971.3_Intron|R3HDM1_ENST00000409478.1_Intron|R3HDM1_ENST00000409606.1_Intron|R3HDM1_ENST00000264160.4_Intron	NM_001282800.1	NP_001269729.1	Q15032	R3HD1_HUMAN	R3H domain containing 1	NA		NA					poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		ggccgggcacagtggctcacg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991	23518			9757	protein-coding gene	gene with protein product		NA	R3H domain (binds single-stranded nucleic acids) containing	R3HDM	NA	7584026	Standard	NM_015361	NM_001282798	NA	Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000410054.1:c.2189+12004A>G	chr2.hg19:g.136449898A>G		NA	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	hg19		0.02	-0.157874	CACxGTG	COVERED																																																																																			NOVEL	R3HDM1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331546.2	2	2.706707	KEEP	1	0	0	9	246	AA	0.99257	0.320408	0		+	3	60	97	0	0	7.691869	14	60	415	42	ENST00000410054.1	0.176471	0.322807
R3HDM1	23518	__UNKNOWN__	__UNKNOWN__	2	136479396	136479396	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136479396A>G	ENST00000410054.1	+	21	2942				R3HDM1_ENST00000329971.3_Intron|R3HDM1_ENST00000409478.1_Intron|R3HDM1_ENST00000409606.1_Intron|R3HDM1_ENST00000264160.4_Intron	NM_001282800.1	NP_001269729.1	Q15032	R3HD1_HUMAN	R3H domain containing 1	NA		NA					poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		ggccttaagtaatccgcctgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991	23518			9757	protein-coding gene	gene with protein product		NA	R3H domain (binds single-stranded nucleic acids) containing	R3HDM	NA	7584026	Standard	NM_015361	NM_001282798	NA	Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000410054.1:c.2612-98A>G	chr2.hg19:g.136479396A>G		NA	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	hg19		0.02	-0.201631	AGTxATC	COVERED																																																																																			NOVEL	R3HDM1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331546.2	4	3.006074	KEEP	0	0	0	10	257	AA	0.992708	0.486967	0		+	3	60	91	1	0	6.728538	19	60	525	41	ENST00000410054.1	0.136364	0.490544
LCT	3938	__UNKNOWN__	__UNKNOWN__	2	136568334	136568334	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136568334C>T	ENST00000264162.2	-	8	2364					NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	NA		NA			carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	tggtggctcacgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3938	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202			NA		Standard	NM_002299	NM_002299	NA	Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.2354-771G>A	chr2.hg19:g.136568334C>T		NA	Q4ZG58	hg19	CCDS2178.1	0.02	-0.245496	TCAxGCC	COVERED																																																																																			NOVEL	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254657.1	9	3.007578	KEEP	1	0	0	10	280	CC	0.99254	0.636563	0		-	3	60	96	0	0	7.106429	21	60	611	55	ENST00000264162.2	0.125	0.641347
DARS	1615	__UNKNOWN__	__UNKNOWN__	2	136686133	136686133	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136686133G>A	ENST00000264161.4	-	8	780				DARS_ENST00000537273.1_Intron	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	NA		NA			aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	ggccaggctggtcttgaactc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	1615	6.1.1.12	Aminoacyl tRNA synthetases / Class II	2678	protein-coding gene	gene with protein product	aspartate tRNA ligase 1, cytoplasmic	603084			NA	2674137	Standard	NM_001349	NM_001349	NA	Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.565-4065C>T	chr2.hg19:g.136686133G>A		NA	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	hg19	CCDS2180.1	0.02	-0.184215	CTGxTCT	COVERED																																																																																			NOVEL	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254660.5	10	3.610049	KEEP	3	0	0	12	350	GG	0.994391	0.421102	0		-	3	60	87	0	0	6.533838	16	60	536	49	ENST00000264161.4	0.157895	0.423478
DARS	1615	__UNKNOWN__	__UNKNOWN__	2	136721194	136721194	__UNKNOWN__	Intron	SNP	A	A	G	rs568364024		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136721194A>G	ENST00000264161.4	-	4	433				DARS_ENST00000463008.1_Intron|DARS_ENST00000537273.1_Intron	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	NA		NA			aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	cacccacctcagcctcccaaa	0.498		NA											A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18177	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	1615	6.1.1.12	Aminoacyl tRNA synthetases / Class II	2678	protein-coding gene	gene with protein product	aspartate tRNA ligase 1, cytoplasmic	603084			NA	2674137	Standard	NM_001349	NM_001349	NA	Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.218-2126T>C	chr2.hg19:g.136721194A>G		NA	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	hg19	CCDS2180.1	0.02	-0.140326	CTCxGCC	COVERED																																																																																			NOVEL	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254660.5	10	5.715363	KEEP	9	0	0	19	542	AA	0.99649	0.260049	0		-	3	60	93	0	0	7.472565	12	60	364	54	ENST00000264161.4	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	136890806	136890806	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136890806A>G			NA	NA				CXCR4 (15071 upstream) : RN7SKP141 (257095 downstream)						NA		NA									NA						gtctcactctattgcccaggc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.136890806A>G		NA		hg19		0.02	-0.263111	TCTxTTG	COVERED																																																																																			NOVEL					0			10	4.210365	KEEP	0	0	0	14	382	AA	0.995343	0.690438	0			3	53	105	0	0	7.842253	24	60	703	60		0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	136916501	136916501	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:136916501T>C			NA	NA				CXCR4 (40766 upstream) : RN7SKP141 (231400 downstream)						NA		NA									NA						gatcatgccattgcactccag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.136916501T>C		NA		hg19		0.02	-0.228043	CCAxTGC	COVERED																																																																																			NOVEL					0			6	3.608851	KEEP	1	0	0	12	325	TT	0.993634	0.579219	0			3	60	103	0	0	7.864715	20	60	601	55		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	138994930	138994930	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:138994930A>G			NA	NA				AC069394.1 (131455 upstream) : AC097721.2 (180923 downstream)						NA		NA									NA						agcactttggaaggctgaggt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.138994930A>G		NA		hg19		0.02	-0.1228	TGGxAGG	COVERED																																																																																			NOVEL					0			3	2.406093	KEEP	0	0	0	8	221	AA	0.99257	0.194853	0			3	60	98	0	0	8.181947	10	60	306	36		0.230769	0.196312
TEX41	401014	__UNKNOWN__	__UNKNOWN__	2	145666032	145666032	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:145666032C>T	ENST00000445791.1	+	0	307					NR_033870.2				testis expressed 41 (non-protein coding)	NA		NA									NA						gtggctcatgcctgtaattcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC043549		2q22.3	2014-02-12	2013-06-04		ENSG00000226674	ENSG00000226674	401014		Long non-coding RNAs	48667	non-coding RNA	RNA, long non-coding	long intergenic non-protein coding RNA 953	NA			NA		Standard	NR_033870	NR_033870	NA	Approved	DKFZp686O1327, LINC00953			OTTHUMG00000153701	ENST00000445791.1:	chr2.hg19:g.145666032C>T		NA		hg19		0.02	-0.122808	ATGxCTG	COVERED																																																																																			NOVEL	TEX41-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000332156.1	10	2.407215	KEEP	0	0	0	8	246	CC	0.99257	0.194853	0		+	3	60	85	0	0	6.772873	11	60	376	27	ENST00000445791.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	148360863	148360863	__UNKNOWN__	IGR	SNP	G	G	A	rs4534992	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:148360863G>A			NA	NA				RNU6-715P (107755 upstream) : RNA5SP106 (110160 downstream)						NA		NA									NA						acaggcgtgagccaccgcgcc	0.517		NA											-|||	1731	0.345647	0.1679	0.4467	5008	,	,	NA	15943	0.4792	NA	0.3221	False	NA	,,,	NA	NA	NA	2504	0.4008	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.148360863G>A		NA		hg19		0.02	-0.078867	TGAxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.708123	KEEP	8	0	0	9	280	GG	0	0	0			4	60	100	0	0	9.215873	5	60	170	31		0.444444	0.077336
KIF5C	3800	__UNKNOWN__	__UNKNOWN__	2	149852430	149852430	__UNKNOWN__	Intron	SNP	C	C	G	rs146469929	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:149852430C>G	ENST00000435030.1	+	18	2391				KIF5C_ENST00000414838.2_Intron|KIF5C_ENST00000397413.1_Intron|KIF5C_ENST00000464066.1_Intron			O60282	KIF5C_HUMAN	kinesin family member 5C	NA		NA			ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		cagcactttgcgaggctgagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280	3800		Kinesins	6325	protein-coding gene	gene with protein product		604593			NA	7514426	Standard	NM_004522	NM_004522	NA	Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2024-1348C>G	chr2.hg19:g.149852430C>G		NA	O95079|Q2YDC5	hg19		0.02	-0.254386	TTGxGAG	COVERED																																																																																			NOVEL	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000332562.3	10	3.009244	KEEP	2	0	0	10	316	AC	0.993072	0.663892	0		+	3	60	103	0	0	7.864528	20	60	647	65	ENST00000435030.1	0.130435	0.668523
LYPD6B	130576	__UNKNOWN__	__UNKNOWN__	2	150069455	150069455	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:150069455T>C	ENST00000409642.3	+	6	729				LYPD6B_ENST00000498249.1_Intron|LYPD6B_ENST00000409876.1_Intron|LYPD6B_ENST00000409029.1_Intron|LYPD6B_ENST00000280115.7_Intron	NM_177964.3	NP_808879.2	Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	NA		NA				anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11						GTAATATGGATATTGAAATTA	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													33	32	32			NA	NA	2		NA											NA				150069455		1005	2122	3127	SO:0001627	intron_variant				CCDS46423.1	2q23.2	2012-07-20			ENSG00000150556	ENSG00000150556	130576			27018	protein-coding gene	gene with protein product	cancer/testis antigen 116	NA			NA	18360792	Standard	NM_177964	NM_177964	NA	Approved	CT116, LYPD7	uc002twv.1	Q8NI32	OTTHUMG00000153743	ENST00000409642.3:c.329-51T>C	chr2.hg19:g.150069455T>C		NA	D3DP90|Q53TK0|Q7Z747|Q8IXK7	hg19	CCDS46423.1	0.02	-0.377089	GGAxATT	COVERED																																																																																			NOVEL	LYPD6B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000332297.1	3	3.301757	KEEP	0	0	0	11	260	TT	0.993072	0.902771	0		+	12	60	405	0	0	35.171658	31	60	881	69	ENST00000409642.3	0.27907	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	151956341	151956341	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:151956341C>G			NA	NA				AC023469.1 (51053 upstream) : AC018731.3 (18127 downstream)						NA		NA									NA						ccagcgctttcggaggccgag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.151956341C>G		NA		hg19		0.02	-0.122804	TTTxGGA	COVERED																																																																																			NOVEL					0			4	2.70758	KEEP	0	0	0	9	265	CC	0.99254	0.227464	0			3	60	94	0	0	7.781917	10	60	320	36		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	151956365	151956365	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:151956365A>G			NA	NA				AC023469.1 (51077 upstream) : AC018731.3 (18103 downstream)						NA		NA									NA						ggcggatcacaaggtcaggag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.151956365A>G		NA		hg19		0.02	-0.122754	CACxAGG	COVERED																																																																																			NOVEL					0			5	2.404448	KEEP	0	0	0	8	205	AA	0.99257	0.194853	0			3	60	83	0	0	6.573991	11	60	316	31		0.214286	0.196312
AC018731.3	0	__UNKNOWN__	__UNKNOWN__	2	151989952	151989952	__UNKNOWN__	lincRNA	SNP	A	A	G	rs367804936|rs61180914|rs563389053|rs376754881|rs57670463		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:151989952A>G	ENST00000447078.1	-	0	156										NA		NA									NA						gacagacagaaagagagagag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000447078.1:	chr2.hg19:g.151989952A>G		NA		hg19		0.02	4.242224	AGAxAGA	COVERED																																																																																			NOVEL	AC018731.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000332398.1	255	24.38671	KEEP	107	4	122	124	3388	AA	1	1	0		-	5	60	144	1	0	15.609385	1	27	27	471	ENST00000447078.1	0.833333	1
RIF1	55183	__UNKNOWN__	__UNKNOWN__	2	152278573	152278573	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:152278573T>C	ENST00000243326.5	+	7	1176				RIF1_ENST00000428287.2_Intron|RIF1_ENST00000453091.2_Intron|RIF1_ENST00000433166.2_Intron|RIF1_ENST00000444746.2_Intron|RIF1_ENST00000430328.2_Intron			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	NA		NA			fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ctcgaactcctgaccttgtga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345	55183			23207	protein-coding gene	gene with protein product		608952	RAP1 interacting factor homolog (yeast)		NA	15342490, 15042697, 22850674	Standard		NM_018151	NA	Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.694-891T>C	chr2.hg19:g.152278573T>C		NA	A0AVS0|Q9NS16	hg19	CCDS2194.1	0.02	-0.140279	TCCxGAC	COVERED																																																																																			NOVEL	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254836.3	4	2.706222	KEEP	1	0	0	9	245	TT	0.99254	0.259018	0		+	5	60	146	0	0	12.839455	10	60	292	38	ENST00000243326.5	0.333333	0.260965
RIF1	55183	__UNKNOWN__	__UNKNOWN__	2	152303551	152303551	__UNKNOWN__	Intron	SNP	G	G	A	rs55982073	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:152303551G>A	ENST00000243326.5	+	19	2727				RIF1_ENST00000428287.2_Intron|RIF1_ENST00000453091.2_Intron|RIF1_ENST00000444746.2_Intron|RIF1_ENST00000430328.2_Intron			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	NA		NA			fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		tccgcctcccgggttcacgcc	0.567		NA											-|||	1242	0.248003	0.0923	0.3631	5008	,	,	NA	15041	0.3185	NA	0.3221	False	NA	,,,	NA	NA	NA	2504	0.228	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345	55183			23207	protein-coding gene	gene with protein product		608952	RAP1 interacting factor homolog (yeast)		NA	15342490, 15042697, 22850674	Standard		NM_018151	NA	Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.2244+462G>A	chr2.hg19:g.152303551G>A		NA	A0AVS0|Q9NS16	hg19	CCDS2194.1	0.02	-0.017543	CCCxGGT	UNCOVERED																																																																																			NOVEL	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254836.3	3	2.707894	KEEP	12	0	0	9	272	GG	0	0	0		+	2	40	61	0	0	7.053463	0	0	0	26	ENST00000243326.5	1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	152599472	152599472	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:152599472T>C			NA	NA				NEB (8471 upstream) : ARL5A (55843 downstream)						NA		NA									NA						ccttgtgatctgcccgcctcg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.152599472T>C		NA		hg19		0.02	-0.228046	ATCxGCC	COVERED																																																																																			NOVEL					0			10	4.512035	KEEP	9	0	0	15	424	TT	0.992708	0.578679	0			3	60	101	0	0	7.548832	22	60	664	72		0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	152647441	152647441	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:152647441G>C			NA	NA				NEB (56440 upstream) : ARL5A (7874 downstream)						NA		NA									NA						aaactcttgggctcaggttct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.152647441G>C		NA		hg19		0.02	-0.307042	TGGxCTC	COVERED																																																																																			NOVEL					0			5	2.407292	KEEP	0	0	0	8	249	GG	0.99257	0.7943	0			6	60	204	0	0	16.382816	28	60	958	68		0.176471	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	153808629	153808629	__UNKNOWN__	IGR	SNP	G	G	A	rs6706889	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:153808629G>A			NA	NA				ARL6IP6 (190862 upstream) : AC011901.2 (219871 downstream)						NA		NA									NA						aattttttgtgtttttagtag	0.522		NA											A|||	2158	0.430911	0.1997	0.6009	5008	,	,	NA	16981	0.6181	NA	0.4374	False	NA	,,,	NA	NA	NA	2504	0.4233	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.153808629G>A		NA		hg19		0.02	-0.061403	TGTxTTT	UNCOVERED																																																																																			NOVEL					0			5	2.407016	KEEP	2	0	0	8	243	GG	0	0	0			3	60	87	0	0	8.05448	4	60	142	22		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	155415213	155415213	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:155415213T>C			NA	NA				AC009227.3 (97881 upstream) : RNA5SP107 (31705 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.155415213T>C		NA		hg19		0.02	-0.078938	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			3	2.405245	KEEP	0	0	0	8	214	TT	0.99257	0.076761	0			2	60	72	0	0	6.335837	5	60	143	25		0.285714	0.077336
PKP4	8502	__UNKNOWN__	__UNKNOWN__	2	159337028	159337028	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:159337028T>C	ENST00000389759.3	+	1	107				PKP4_ENST00000389757.3_Intron	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	NA		NA			cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						ggattacaggtgtgagccacc	0.428		NA								HNSCC(62;0.18)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283	8502		Armadillo repeat containing	9026	protein-coding gene	gene with protein product		604276			NA	9342840, 8937994	Standard		NM_003628	NA	Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.-6+23298T>C	chr2.hg19:g.159337028T>C		NA	Q86W91	hg19	CCDS33305.1	0.02	-0.13149	AGGxGTG	COVERED																																																																																			NOVEL	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333250.1	6	3.006231	KEEP	0	0	0	10	269	TT	0.992708	0.227502	0		+	3	60	104	0	0	8.783116	10	60	273	38	ENST00000389759.3	0.230769	0.229173
BAZ2B	29994	__UNKNOWN__	__UNKNOWN__	2	160279575	160279575	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:160279575T>C	ENST00000392783.2	-	13	2962				BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000355831.2_Intron|BAZ2B_ENST00000392782.1_Intron	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						acctgtaatctcagcactttg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636	29994		Zinc fingers, PHD-type	963	protein-coding gene	gene with protein product		605683			NA	10662543	Standard		XM_005246488	NA	Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2466+4876A>G	chr2.hg19:g.160279575T>C		NA	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	hg19	CCDS2209.2	0.02	-0.298225	ATCxCAG	COVERED																																																																																			NOVEL	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255037.2	7	3.308594	KEEP	0	0	0	11	311	TT	0.993072	0.775649	0		-	3	60	95	0	0	6.84534	24	60	742	68	ENST00000392783.2	0.111111	0.78106
BAZ2B	29994	__UNKNOWN__	__UNKNOWN__	2	160446807	160446807	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:160446807G>A	ENST00000392783.2	-	1	451				BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000483316.1_Intron|BAZ2B_ENST00000355831.2_Intron|BAZ2B_ENST00000392782.1_Intron	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						AAGTAAAAATGCCTCAAAAAT	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636	29994		Zinc fingers, PHD-type	963	protein-coding gene	gene with protein product		605683			NA	10662543	Standard		XM_005246488	NA	Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.44+25945C>T	chr2.hg19:g.160446807G>A		NA	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	hg19	CCDS2209.2	0.02	-0.061388	AATxCCT	UNCOVERED																																																																																			NOVEL	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255037.2	5	2.708293	KEEP	0	0	0	9	283	GG	0.99254	0.04346	0		-	3	60	86	0	0	7.954891	4	60	124	19	ENST00000392783.2	0.428571	0.043787
LY75-CD302	100526664	__UNKNOWN__	__UNKNOWN__	2	160666464	160666464	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:160666464T>C	ENST00000504764.1	-	32	4727				LY75_ENST00000553424.1_Intron|LY75_ENST00000263636.4_Intron|LY75_ENST00000554112.1_Intron|LY75-CD302_ENST00000505052.1_Intron	NM_001198759.1	NP_001185688.1			LY75-CD302 readthrough	NA		NA									NA						gctgggattataggcgtgagc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56140.1, CCDS56141.1	2q24.2	2011-04-19			ENSG00000248672	ENSG00000248672	100526664			38828	other	readthrough		NA			NA		Standard		NM_001198759	NA	Approved		uc002ubb.4		OTTHUMG00000161661	ENST00000504764.1:c.4699+572A>G	chr2.hg19:g.160666464T>C		NA		hg19	CCDS56141.1	0.02	-0.280632	TTAxAGG	COVERED																																																																																			NOVEL	LY75-CD302-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365654.1	10	4.507422	KEEP	1	0	0	15	390	TT	0.995343	0.736227	0		-	3	60	101	0	0	7.297828	27	60	795	72	ENST00000504764.1	0.1	0.739671
RBMS1	5937	__UNKNOWN__	__UNKNOWN__	2	161297983	161297983	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:161297983T>C	ENST00000348849.3	-	1	506				RBMS1_ENST00000474820.1_Intron|RBMS1_ENST00000392753.3_Intron	NM_002897.4|NM_016836.3	NP_002888.1|NP_058520.1	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting protein 1	NA		NA			DNA replication (GO:0006260)|RNA processing (GO:0006396)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)		PLA2R1/RBMS1(2)		NA						acctgtaatctcagcactttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D28482	CCDS2213.1	2q24.2	2013-02-12			ENSG00000153250	ENSG00000153250	5937		RNA binding motif (RRM) containing	9907	protein-coding gene	gene with protein product	suppressor of cdc 2 (cdc13) with RNA binding motif 2, c-myc gene single strand binding protein 2	602310	chromosome 2 open reading frame 12	C2orf12	NA	8041632, 8134115, 7838710	Standard	NM_016836	NM_016836	NA	Approved	SCR2, MSSP-1, MSSP-2, MSSP-3, YC1, HCC-4, DKFZp564H0764	uc002ubo.3	P29558	OTTHUMG00000132031	ENST00000348849.3:c.75+51816A>G	chr2.hg19:g.161297983T>C		NA	Q14869|Q15433|Q53P46|Q53QX8|Q53RG6|Q8WV20	hg19	CCDS2213.1	0.02	-0.069444	ATCxCAG	UNCOVERED																																																																																			NOVEL	RBMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255043.4	9	3.609083	KEEP	0	0	0	12	330	TT	0.993634	0.053793	0		-	2	60	72	0	0	6.513449	4	60	98	26	ENST00000348849.3	0.333333	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	161455815	161455815	__UNKNOWN__	IGR	SNP	C	C	A	rs6707018	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:161455815C>A			NA	NA				RBMS1 (105510 upstream) : RN7SL423P (278242 downstream)						NA		NA									NA						tcaagaccagcctgaccaaca	0.517		NA											C|||	4285	0.855631	0.8865	0.9424	5008	,	,	NA	18859	0.6577	NA	0.9354	False	NA	,,,	NA	NA	NA	2504	0.8742	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.161455815C>A		NA		hg19		0.02	-0.087703	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			7	3.008803	KEEP	0	0	0	10	302	CC	0.992708	0.098994	0			6	60	168	0	0	17.705441	2	60	71	27		0.75	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	161476908	161476908	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:161476908A>G			NA	NA				RBMS1 (126603 upstream) : RN7SL423P (257149 downstream)						NA		NA									NA						aaaatgctggaattacaggtg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.161476908A>G		NA		hg19		0.02	-0.228045	TGGxATT	COVERED																																																																																			NOVEL					0			7	2.405954	KEEP	0	0	0	8	219	AA	0.99257	0.578599	0			3	60	104	0	0	7.964681	20	60	596	55		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	162136457	162136457	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:162136457C>T			NA	NA				AC009299.2 (25278 upstream) : PSMD14 (28091 downstream)						NA		NA									NA						cacatataccccagaacttag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.162136457C>T		NA		hg19		0.02	1.312293	ACCxCAG	COVERED																																																																																			NOVEL					0			76	24.005273	KEEP	68	1	29	90	2812	CC	1	0.999962	0			4	53	126	0	0	7.83043	67	60	2326	374		0.056338	0.999962
SLC4A10	57282	__UNKNOWN__	__UNKNOWN__	2	162517449	162517449	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:162517449T>C	ENST00000446997.1	+	1	141				SLC4A10_ENST00000535165.1_Intron|SLC4A10_ENST00000272716.5_Intron|SLC4A10_ENST00000375514.5_Intron|SLC4A10_ENST00000421911.1_Intron|SLC4A10_ENST00000493021.1_Intron|SLC4A10_ENST00000415876.2_Intron	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	NA		NA			bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	ggattacaggtgtgagccacc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290	57282		Solute carriers	13811	protein-coding gene	gene with protein product		605556	solute carrier family 4, sodium bicarbonate transporter-like, member 10		NA	10964153, 18319254	Standard	NM_022058	NM_022058	NA	Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.48+36373T>C	chr2.hg19:g.162517449T>C		NA	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	hg19	CCDS54411.1	0.02	-0.210507	AGGxGTG	COVERED																																																																																			NOVEL	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333090.1	7	2.406482	KEEP	0	0	0	8	230	TT	0.99257	0.518282	0		+	3	60	104	0	0	7.964574	20	60	610	51	ENST00000446997.1	0.130435	0.522161
STK39	27347	__UNKNOWN__	__UNKNOWN__	2	169075676	169075676	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:169075676A>G	ENST00000355999.4	-	1	914					NM_013233.2	NP_037365.2	Q9UEW8	STK39_HUMAN	serine threonine kinase 39	NA		NA			cellular hypotonic response (GO:0071476)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of potassium ion transport (GO:0043268)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|response to stress (GO:0006950)|signal transduction by phosphorylation (GO:0023014)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	13						catgcctgtaatcccagctac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099989	CCDS42770.1	2q24.3	2010-06-25	2010-06-25		ENSG00000198648	ENSG00000198648	27347			17717	protein-coding gene	gene with protein product	STE20/SPS1 homolog (yeast)	607648			NA	10980603	Standard	NM_013233	NM_013233	NA	Approved	DCHT, SPAK	uc002uea.3	Q9UEW8	OTTHUMG00000133745	ENST00000355999.4:c.208+28061T>C	chr2.hg19:g.169075676A>G		NA	O14774|Q53S90|Q53SL7|Q53SS1|Q9UER4|X5D9C8	hg19	CCDS42770.1	0.02	-0.148957	GTAxTCC	COVERED																																																																																			NOVEL	STK39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258112.2	12	3.910165	KEEP	6	0	0	13	364	AA	0.993072	0.289978	0		-	3	60	94	0	0	7.67496	11	60	300	48	ENST00000355999.4	0.214286	0.292001
RP11-724O16.1	0	__UNKNOWN__	__UNKNOWN__	2	170358018	170358018	__UNKNOWN__	Intron	SNP	C	C	T	rs191059397	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:170358018C>T	ENST00000513963.1	+	10	890				BBS5_ENST00000392663.2_Intron|BBS5_ENST00000295240.3_Intron|BBS5_ENST00000554017.1_Intron						NA		NA									NA						gggagaatcacgtgaggccag	0.423		NA											c|||	3	0.000599042	0.0	0.0	5008	,	,	NA	18278	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000513963.1:c.817-1587C>T	chr2.hg19:g.170358018C>T		NA		hg19		0.02	-0.140345	TCAxGTG	COVERED																																																																																			NOVEL	RP11-724O16.1-001	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000368400.1	7	2.707502	KEEP	0	0	0	9	262	CC	0.99254	0.259018	0		+	3	60	91	0	0	7.372875	11	60	360	37	ENST00000513963.1	0.214286	0.260965
KLHL23	151230	__UNKNOWN__	__UNKNOWN__	2	170560069	170560069	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:170560069T>G	ENST00000272797.4	+	3	336				KLHL23_ENST00000602521.1_Intron	NM_001199290.1	NP_001186219.1	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	NA		NA								breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						gctcacacctttaatcccagc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160	151230		Kelch-like, BTB/POZ domain containing	27506	protein-coding gene	gene with protein product		NA	kelch-like 23 (Drosophila)		NA		Standard	NM_144711	NM_144711	NA	Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000272797.4:c.-3+6028T>G	chr2.hg19:g.170560069T>G		NA	Q8N9B9|Q96FT8	hg19	CCDS2236.1	0.02	-0.184195	CCTxTAA	COVERED																																																																																			NOVEL	KLHL23-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333330.1	6	4.209615	KEEP	0	0	0	14	378	TT	0.99649	0.421991	0		+	3	60	103	0	0	8.060639	17	60	514	51	ENST00000272797.4	0.15	0.423478
MYO3B	140469	__UNKNOWN__	__UNKNOWN__	2	171260820	171260820	__UNKNOWN__	Silent	SNP	T	T	C	rs6751520	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:171260820T>C	ENST00000408978.4	+	20	2484	c.2341T>C	c.(2341-2343)Ttg>Ctg	p.L781L	MYO3B_ENST00000334231.6_Silent_p.L790L|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.L781L	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	781	Myosin motor.	NA			peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						CCGCCCGCTCTTGGACATGTT	0.502		NA											T|||	3911	0.78095	0.6846	0.889	5008	,	,	NA	18753	0.7321	NA	0.8966	False	NA	,,,	NA	NA	NA	2504	0.7658	NA	NA	NA								NA				0								T	,,	2771,1043		1010,751,146	121	116	117		2341,2341,2341	-2.8	1	2	dbSNP_116	117	7408,826		3332,744,41	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	4342,1495,187	CC,CT,TT	NA	10.0316,27.3466,15.5129	,,	781/1315,781/1276,781/1342	171260820	10179,1869	1907	4117	6024	SO:0001819	synonymous_variant				CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909	140469		Myosins / Myosin superfamily : Class III	15576	protein-coding gene	gene with protein product		610040			NA		Standard		NM_001083615	NA	Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.2341T>C	chr2.hg19:g.171260820T>C		NA	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	hg19	CCDS42773.1	0.02	1.918056	CTCxTGG	COVERED																																																																																			NOVEL	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333410.1	4	2.406018	KEEP	0	0	0	8	221	TT	0.99257	0.98632	0		+	33	60	1150	0	0	112.137675	29	60	901	108	ENST00000408978.4	0.532258	0.993703
ERICH2	285141	__UNKNOWN__	__UNKNOWN__	2	171654119	171654119	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:171654119G>C	ENST00000409885.1	+	4	327							A1L162	ERIC2_HUMAN	glutamate-rich 2	NA		NA									NA						actagcctgggcaacatggtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC127676, BC150546		2q31.1	2012-09-25			ENSG00000204334	ENSG00000204334	285141			44395	protein-coding gene	gene with protein product		NA			NA		Standard		XM_001714892	NA	Approved		uc002ugg.3	A1L162	OTTHUMG00000154074	ENST00000409885.1:c.275-432G>C	chr2.hg19:g.171654119G>C		NA	A7E2T7	hg19		0.02	-0.087718	TGGxCAA	UNCOVERED																																																																																			NOVEL	ERICH2-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000333723.1	9	3.008958	KEEP	4	0	0	10	314	GG	0.99257	0.09898	0		+	3	60	102	0	0	9.143561	6	60	191	32	ENST00000409885.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	172088316	172088316	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:172088316A>G			NA	NA				TLK1 (492 upstream) : METTL8 (85602 downstream)						NA		NA									NA						ccagcactttaggaggccaag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.172088316A>G		NA		hg19		0.02	-0.122796	TTTxGGA	COVERED																																																																																			NOVEL					0			4	3.007514	KEEP	1	0	0	10	273	AA	0.992708	0.19488	0			3	60	105	0	0	8.882002	10	60	299	40		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	172132239	172132239	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:172132239T>C			NA	NA				TLK1 (44415 upstream) : METTL8 (41679 downstream)						NA		NA									NA						tcctgagtagttgggaccaca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.172132239T>C		NA		hg19		0.02	-0.122802	TAGxTGG	COVERED																																																																																			NOVEL					0			7	3.007597	KEEP	0	0	0	10	277	TT	0.992708	0.19488	0			3	60	108	0	0	9.432464	8	60	250	33		0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	172170004	172170004	__UNKNOWN__	IGR	SNP	G	G	A	rs189264759	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:172170004G>A			NA	NA				TLK1 (82180 upstream) : METTL8 (3914 downstream)						NA		NA									NA						ttgggaggccgaggtgggcgg	0.473		NA											A|||	25	0.00499201	0.0015	0.0086	5008	,	,	NA	18499	0.0	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0112	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.172170004G>A		NA		hg19		0.02	-0.298256	GCCxAGG	COVERED																																																																																			NOVEL					0			9	3.909542	KEEP	3	0	0	13	367	GG	0.993634	0.776087	0			3	40	93	0	0	6.453405	28	60	922	72		0.096774	0.78106
SLC25A12	8604	__UNKNOWN__	__UNKNOWN__	2	172687282	172687282	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:172687282T>C	ENST00000422440.2	-	8	883				SLC25A12_ENST00000392592.4_Intron	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	NA		NA			aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	cttggcctcctaaagtgctgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840	8604		Solute carriers, EF-hand domain containing	10982	protein-coding gene	gene with protein product		603667	solute carrier family 25 (mitochondrial carrier, Aralar), member 12		NA	9722566, 10702666, 11566871	Standard	NM_003705	NM_003705	NA	Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.845+3190A>G	chr2.hg19:g.172687282T>C		NA	B3KR64|Q96AM8	hg19	CCDS33327.1	0.02	-0.175406	TCCxAAA	COVERED																																																																																			NOVEL	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259010.2	6	3.007687	KEEP	1	0	0	10	277	TT	0.99254	0.384517	0		-	3	60	102	0	0	7.960925	17	60	503	46	ENST00000422440.2	0.15	0.387407
SLC25A12	8604	__UNKNOWN__	__UNKNOWN__	2	172732172	172732172	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:172732172T>C	ENST00000422440.2	-	3	104				SLC25A12_ENST00000472748.1_Intron|SLC25A12_ENST00000392592.4_Intron	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	NA		NA			aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	acctgtaatctcagcactttg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840	8604		Solute carriers, EF-hand domain containing	10982	protein-coding gene	gene with protein product		603667	solute carrier family 25 (mitochondrial carrier, Aralar), member 12		NA	9722566, 10702666, 11566871	Standard	NM_003705	NM_003705	NA	Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.67-6839A>G	chr2.hg19:g.172732172T>C		NA	B3KR64|Q96AM8	hg19	CCDS33327.1	0.02	-0.228055	ATCxCAG	COVERED																																																																																			NOVEL	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259010.2	2	2.406221	KEEP	0	0	0	8	222	TT	0.99257	0.578599	0		-	3	60	104	1	0	7.848648	22	60	675	57	ENST00000422440.2	0.12	0.58293
ITGA6	3655	__UNKNOWN__	__UNKNOWN__	2	173292335	173292335	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:173292335C>T	ENST00000264107.7	+	0	53				ITGA6_ENST00000375221.2_5'UTR|ITGA6_ENST00000264106.6_5'UTR|ITGA6_ENST00000409532.1_Intron|ITGA6_ENST00000343713.4_5'UTR	NM_000210.2	NP_000201.2	P23229	ITA6_HUMAN	integrin, alpha 6	NA		NA			amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TCAGCGGTCGCGAGCTGCCCG	0.726		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409	3655		CD molecules, Integrins	6142	protein-coding gene	gene with protein product		147556			NA		Standard		NM_001079818	NA	Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264107.7:c.-182C>T	chr2.hg19:g.173292335C>T		NA	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	hg19	CCDS2249.1	0.02	1.482367	TCGxGAG	COVERED																																																																																			NOVEL	ITGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255369.2	0	6.018191	KEEP	0	0	0	20	624	CC	0.999863	0.984026	0		+	20	60	585	0	0	51.813832	38	60	1310	140	ENST00000264107.7	0.344828	0.984161
PDK1	5163	__UNKNOWN__	__UNKNOWN__	2	173423953	173423953	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:173423953A>G	ENST00000282077.3	+	2	520				PDK1_ENST00000543905.1_Intron|PDK1_ENST00000392571.2_Intron|PDK1_ENST00000410055.1_Intron|PDK1_ENST00000544863.1_Intron			Q15118	PDK1_HUMAN	pyruvate dehydrogenase kinase, isozyme 1	NA		NA			cell proliferation (GO:0008283)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|hypoxia-inducible factor-1alpha signaling pathway (GO:0097411)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of glucose metabolic process (GO:0010906)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)	16			OV - Ovarian serous cystadenocarcinoma(117;0.12)			gggattacagacgtgagccac	0.527		NA							Autosomal Dominant Polycystic Kidney Disease												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	ADPKD	L42450	CCDS2250.1, CCDS63059.1	2q31.1	2008-05-23	2005-11-16		ENSG00000152256	ENSG00000152256	5163			8809	protein-coding gene	gene with protein product		602524	pyruvate dehydrogenase kinase, isoenzyme 1		NA	7499431	Standard	NM_002610	NR_103731	NA	Approved		uc002uhs.3	Q15118	OTTHUMG00000132285	ENST00000282077.3:c.338+376A>G	chr2.hg19:g.173423953A>G		NA	B2R6T1|B7Z937|D3DPD8|E9PD65|Q308M4	hg19	CCDS2250.1	0.02	-0.324529	CAGxCGT	COVERED																																																																																			NOVEL	PDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255380.3	10	3.007275	KEEP	1	0	0	10	271	AA	0.99254	0.829482	0		+	5	60	167	1	0	12.921501	29	60	872	68	ENST00000282077.3	0.147059	0.835716
CDCA7	83879	__UNKNOWN__	__UNKNOWN__	2	174222693	174222693	__UNKNOWN__	Intron	SNP	C	C	T	rs12987125		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:174222693C>T	ENST00000347703.3	+	2	165				CDCA7_ENST00000410101.3_Intron|CDCA7_ENST00000410019.3_Intron|CDCA7_ENST00000392567.2_Intron|CDCA7_ENST00000306721.3_Intron	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7	NA		NA			apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			ctttgggaggccgaggcaggc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354	83879			14628	protein-coding gene	gene with protein product		609937			NA	11598121, 12188893	Standard	NM_031942	NM_145810	NA	Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.22-747C>T	chr2.hg19:g.174222693C>T		NA	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	hg19	CCDS2253.1	0.02	-0.245629	AGGxCGA	UNCOVERED																																																																																			NOVEL	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255400.1	13	2.708165	KEEP	9	0	0	9	281	CC	0	0	0		+	5	48	155	0	0	12.181103	23	60	794	68	ENST00000347703.3	0.178571	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	174483772	174483772	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:174483772A>G			NA	NA				CDCA7 (250047 upstream) : RP11-796E10.1 (192031 downstream)						NA		NA									NA						gtgcgatctcagctcacctca	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.174483772A>G		NA		hg19		0.02	-0.114007	CTCxGCT	UNCOVERED																																																																																			NOVEL					0			5	2.406021	KEEP	0	0	0	8	220	AA	0.99257	0.16126	0			3	60	101	0	2	8.482265	10	60	286	26		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	174852533	174852533	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:174852533A>G			NA	NA				RP11-394I13.2 (18387 upstream) : RP11-394I13.3 (24050 downstream)						NA		NA									NA						ggccaggctgatctcaaactc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.174852533A>G		NA		hg19		0.02	-0.228045	CTGxTCT	COVERED																																																																																			NOVEL					0			7	2.539233	KEEP	2	1	30	19	537	AA	0.99986	0.582848	0			3	60	96	0	0	7.227153	19	60	569	60		0.136364	0.58293
OLA1	29789	__UNKNOWN__	__UNKNOWN__	2	175008569	175008569	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175008569C>T	ENST00000409546.1	-	5	1064				OLA1_ENST00000284719.3_Intron|OLA1_ENST00000344357.5_Intron|OLA1_ENST00000428402.2_Intron					Obg-like ATPase 1	NA		NA								breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						tggtggctcacacctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430	29789			28833	protein-coding gene	gene with protein product		611175	GTP-binding protein 9 (putative)	GTPBP9	NA	17430889, 24486488	Standard	NM_013341	NM_013341	NA	Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.434-1841G>A	chr2.hg19:g.175008569C>T		NA		hg19		0.02	-0.280709	TCAxACC	COVERED																																																																																			NOVEL	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000333877.1	7	2.406646	KEEP	0	0	0	8	233	CC	0.99257	0.734176	0		-	4	60	112	0	0	7.935349	27	60	920	58	ENST00000409546.1	0.129032	0.739671
OLA1	29789	__UNKNOWN__	__UNKNOWN__	2	175111821	175111821	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175111821G>C	ENST00000409546.1	-	2	691				OLA1_ENST00000284719.3_Intron|OLA1_ENST00000344357.5_Intron|OLA1_ENST00000428402.2_Intron					Obg-like ATPase 1	NA		NA								breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						cggtggctcaggcctgtaatc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430	29789			28833	protein-coding gene	gene with protein product		611175	GTP-binding protein 9 (putative)	GTPBP9	NA	17430889, 24486488	Standard	NM_013341	NM_013341	NA	Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.61-278C>G	chr2.hg19:g.175111821G>C		NA		hg19		0.02	-0.140352	TCAxGCC	COVERED																																																																																			NOVEL	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000333877.1	4	2.707845	KEEP	0	0	0	9	277	GG	0.99254	0.259018	0		-	3	60	105	0	0	8.672002	12	60	404	36	ENST00000409546.1	0.2	0.260965
GPR155	151556	__UNKNOWN__	__UNKNOWN__	2	175298984	175298984	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175298984T>C	ENST00000392552.2	-	0	4711				GPR155_ENST00000392551.2_3'UTR	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	NA		NA			cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						caggtatgagtcaccatgccc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328	151556			22951	protein-coding gene	gene with protein product		NA			NA	12679517	Standard	NM_152529	NM_001033045	NA	Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.*1860A>G	chr2.hg19:g.175298984T>C		NA	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	hg19	CCDS2259.1	0.02	-0.42966	GAGxCAC	COVERED																																																																																			NOVEL	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255455.1	10	2.537908	KEEP	0	1	30	19	515	TT	0.999863	0.95436	0		-	4	60	119	2	0	7.998287	40	60	1143	102	ENST00000392552.2	0.090909	0.954491
GPR155	151556	__UNKNOWN__	__UNKNOWN__	2	175348593	175348593	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175348593G>A	ENST00000392552.2	-	2	208				GPR155_ENST00000295500.4_Intron|GPR155_ENST00000392551.2_Intron	NM_001267051.1|NM_152529.6	NP_001253980.1|NP_689742.4	Q7Z3F1	GP155_HUMAN	G protein-coupled receptor 155	NA		NA			cognition (GO:0050890)|intracellular signal transduction (GO:0035556)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	26						gattataggtgtgagccacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY255528	CCDS2259.1, CCDS74605.1	2q31.1	2012-04-10			ENSG00000163328	ENSG00000163328	151556			22951	protein-coding gene	gene with protein product		NA			NA	12679517	Standard	NM_152529	NM_001033045	NA	Approved	DEPDC3, DEP.7, FLJ31819, PGR22	uc002uiu.4	Q7Z3F1	OTTHUMG00000132336	ENST00000392552.2:c.31-1878C>T	chr2.hg19:g.175348593G>A		NA	B2RCI2|D3DPE2|Q4G0Y6|Q53SJ3|Q53TA8|Q69YG8|Q86SP9|Q8N261|Q8N639|Q8N8K3|Q96MV6	hg19	CCDS2259.1	0.02	-0.175416	GGTxTGA	COVERED																																																																																			NOVEL	GPR155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255455.1	5	2.407197	KEEP	0	0	0	8	246	GG	0.99257	0.420331	0		-	3	60	88	0	0	6.879311	13	60	415	41	ENST00000392552.2	0.1875	0.423478
WIPF1	7456	__UNKNOWN__	__UNKNOWN__	2	175428046	175428046	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175428046C>T	ENST00000392547.2	-	8	1556				WIPF1_ENST00000359761.3_Intron|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000272746.5_Intron|WIPF1_ENST00000392546.2_Intron|AC018890.6_ENST00000412835.1_RNA	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	NA		NA			actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						acgcctgtaaccccagcactt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935	7456			12736	protein-coding gene	gene with protein product		602357	Wiskott-Aldrich syndrome protein interacting protein	WASPIP	NA	9405671	Standard	NM_003387	NM_001077269	NA	Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1457-716G>A	chr2.hg19:g.175428046C>T		NA	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	hg19	CCDS2260.1	0.02	-0.114041	TAAxCCC	UNCOVERED																																																																																			NOVEL	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255453.1	6	2.708069	KEEP	0	0	0	9	275	CC	0.99254	0.161255	0		-	3	60	90	0	0	7.381774	10	60	356	28	ENST00000392547.2	0.230769	0.162467
WIPF1	7456	__UNKNOWN__	__UNKNOWN__	2	175430898	175430898	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175430898G>A	ENST00000392547.2	-	7	1556				WIPF1_ENST00000359761.3_Intron|AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000272746.5_Intron|WIPF1_ENST00000409891.1_3'UTR|WIPF1_ENST00000392546.2_Intron|AC018890.6_ENST00000412835.1_RNA	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	NA		NA			actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						gattacaggcgtgagccacca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935	7456			12736	protein-coding gene	gene with protein product		602357	Wiskott-Aldrich syndrome protein interacting protein	WASPIP	NA	9405671	Standard	NM_003387	NM_001077269	NA	Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.1456+899C>T	chr2.hg19:g.175430898G>A		NA	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	hg19	CCDS2260.1	0.02	-0.228069	GGCxTGA	UNCOVERED																																																																																			NOVEL	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255453.1	10	3.609972	KEEP	9	0	0	12	350	GG	0	0	0		-	3	60	90	0	0	6.692669	18	60	589	57	ENST00000392547.2	0.142857	0.58293
WIPF1	7456	__UNKNOWN__	__UNKNOWN__	2	175530758	175530758	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175530758T>C	ENST00000359761.3	-	1	110				AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000272746.5_Intron|WIPF1_ENST00000409415.3_Intron			O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	NA		NA			actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)			NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						cctgtaatcctagcactttgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935	7456			12736	protein-coding gene	gene with protein product		602357	Wiskott-Aldrich syndrome protein interacting protein	WASPIP	NA	9405671	Standard	NM_003387	NM_001077269	NA	Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000359761.3:c.37+16743A>G	chr2.hg19:g.175530758T>C		NA	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	hg19	CCDS2260.1	0.02	-0.175421	TCCxAGC	COVERED																																																																																			NOVEL	WIPF1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334133.1	7	2.70607	KEEP	0	0	0	9	247	TT	0.99254	0.384517	0		-	3	60	90	0	0	6.992156	14	60	427	43	ENST00000359761.3	0.176471	0.387407
CHN1	1123	__UNKNOWN__	__UNKNOWN__	2	175705113	175705113	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175705113T>C	ENST00000409900.3	-	7	941				CHN1_ENST00000488080.1_Intron|CHN1_ENST00000409156.3_Intron|CHN1_ENST00000295497.7_Intron|CHN1_ENST00000409597.1_Intron	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	NA		NA			ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			aggctggtcttaaactcctgg	0.478		NA	T	TAF15	extraskeletal myxoid chondrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656	1123		Rho GTPase activating proteins, SH2 domain containing	1943	protein-coding gene	gene with protein product	Chimerin 1 (GTPase-activating protein, rho, 2), chimaerin 1	118423	Duane retraction syndrome 2, chimerin (chimaerin) 1	CHN, DURS2	NA	2299665, 15013773, 18653847	Standard	NM_001822	NM_001822	NA	Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.627+6494A>G	chr2.hg19:g.175705113T>C		NA	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	hg19	CCDS46455.1	0.02	-0.210472	TCTxAAA	COVERED																																																																																			NOVEL	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334453.1	6	2.405096	KEEP	0	0	0	8	211	TT	0.99257	0.518282	0		-	3	60	102	0	0	8.033507	16	60	448	49	ENST00000409900.3	0.157895	0.522161
CHN1	1123	__UNKNOWN__	__UNKNOWN__	2	175755842	175755842	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175755842T>C	ENST00000409900.3	-	6	574				CHN1_ENST00000488080.1_Intron|CHN1_ENST00000409156.3_Intron	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	NA		NA			ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			gcactccagcttgggcgacag	0.428		NA	T	TAF15	extraskeletal myxoid chondrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656	1123		Rho GTPase activating proteins, SH2 domain containing	1943	protein-coding gene	gene with protein product	Chimerin 1 (GTPase-activating protein, rho, 2), chimaerin 1	118423	Duane retraction syndrome 2, chimerin (chimaerin) 1	CHN, DURS2	NA	2299665, 15013773, 18653847	Standard	NM_001822	NM_001822	NA	Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.261-12986A>G	chr2.hg19:g.175755842T>C		NA	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	hg19	CCDS46455.1	0.02	-0.09649	AGCxTGG	UNCOVERED																																																																																			NOVEL	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334453.1	9	3.308125	KEEP	3	0	0	11	298	TT	0.99254	0.119538	0		-	3	40	105	0	0	9.278704	7	60	214	26	ENST00000409900.3	0.3	0.120436
CHN1	1123	__UNKNOWN__	__UNKNOWN__	2	175853871	175853871	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175853871T>C	ENST00000409900.3	-	1	333				CHN1_ENST00000488080.1_Intron|CHN1_ENST00000409156.3_Intron	NM_001822.5	NP_001813.1	P15882	CHIN_HUMAN	chimerin 1	NA		NA			ephrin receptor signaling pathway (GO:0048013)|motor neuron axon guidance (GO:0008045)|positive regulation of signal transduction (GO:0009967)|regulation of axonogenesis (GO:0050770)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.226)			ttagggaggctgaggtgggca	0.448		NA	T	TAF15	extraskeletal myxoid chondrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		2	2q31-q32.1	1123	chimerin (chimaerin) 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46454.1, CCDS46455.1, CCDS56147.1	2q31-q32.1	2013-02-14	2012-10-17		ENSG00000128656	ENSG00000128656	1123		Rho GTPase activating proteins, SH2 domain containing	1943	protein-coding gene	gene with protein product	Chimerin 1 (GTPase-activating protein, rho, 2), chimaerin 1	118423	Duane retraction syndrome 2, chimerin (chimaerin) 1	CHN, DURS2	NA	2299665, 15013773, 18653847	Standard	NM_001822	NM_001822	NA	Approved	RhoGAP2, ARHGAP2, n-chimerin	uc002uji.3	P15882	OTTHUMG00000154225	ENST00000409900.3:c.19+15750A>G	chr2.hg19:g.175853871T>C		NA	A8K1M6|B3KNU6|B4DV19|Q53SD6|Q53SH5|Q96FB0	hg19	CCDS46455.1	0.02	-0.131542	GGCxGAG	UNCOVERED																																																																																			NOVEL	CHN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334453.1	9	2.405938	KEEP	1	0	0	8	218	TT	0	0	0		-	4	60	123	0	0	10.722616	9	60	280	31	ENST00000409900.3	0.307692	0.229173
ATF2	1386	__UNKNOWN__	__UNKNOWN__	2	175974979	175974979	__UNKNOWN__	Intron	SNP	C	C	T	rs183020392	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:175974979C>T	ENST00000264110.2	-	10	1127				ATF2_ENST00000409437.1_Intron|ATF2_ENST00000392543.2_Intron|ATF2_ENST00000345739.5_Intron|ATF2_ENST00000392544.1_Intron|ATF2_ENST00000538946.1_Intron|ATF2_ENST00000426833.3_Intron|ATF2_ENST00000409499.1_Intron|ATF2_ENST00000409635.1_Intron|ATF2_ENST00000487334.2_Intron	NM_001256090.1|NM_001256091.1|NM_001880.3	NP_001243019.1|NP_001243020.1|NP_001871.2	P15336	ATF2_HUMAN	activating transcription factor 2	NA		NA			adipose tissue development (GO:0060612)|cellular response to DNA damage stimulus (GO:0006974)|chromatin organization (GO:0006325)|fat cell differentiation (GO:0045444)|histone acetylation (GO:0016573)|innate immune response (GO:0045087)|intra-S DNA damage checkpoint (GO:0031573)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|outflow tract morphogenesis (GO:0003151)|positive regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902110)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta2 production (GO:0032915)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	cAMP response element binding (GO:0035497)|cAMP response element binding protein binding (GO:0008140)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.125)		Pseudoephedrine(DB00852)	aggagaattgcttgaacccag	0.478		NA											C|||	90	0.0179712	0.0023	0.0821	5008	,	,	NA	15501	0.0	NA	0.0119	False	NA	,,,	NA	NA	NA	2504	0.0184	NA	NA	NA	Pancreas(17;87 705 4534 15538 30988)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X15875	CCDS2262.1, CCDS58737.1, CCDS58738.1, CCDS58739.1	2q32	2013-01-10			ENSG00000115966	ENSG00000115966	1386		basic leucine zipper proteins	784	protein-coding gene	gene with protein product		123811	cAMP responsive element binding protein 2	CREB2	NA	1833307, 1838349	Standard	NM_001880	NM_001880	NA	Approved	TREB7, CRE-BP1, HB16	uc002ujl.4	P15336	OTTHUMG00000132424	ENST00000264110.2:c.828+1316G>A	chr2.hg19:g.175974979C>T		NA	A1L3Z2|A4D7U4|A4D7U5|A4D7V1|D3DPE9|G8JLM5|Q13000|Q3B7B7|Q4ZFU9|Q53RY2|Q8TAR1|Q96JT8	hg19	CCDS2262.1	0.02	-0.096494	TTGxTTG	UNCOVERED																																																																																			NOVEL	ATF2-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255562.1	10	3.008657	KEEP	6	0	0	10	297	CC	0.99257	0.119541	0		-	3	42	89	0	0	8.032303	5	60	179	32	ENST00000264110.2	0.375	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	176879855	176879855	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:176879855A>G			NA	NA				KIAA1715 (12341 upstream) : EVX2 (62344 downstream)						NA		NA									NA						taatcccagcactttgggaag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.176879855A>G		NA		hg19		0.02	-0.1754	AGCxCTT	COVERED																																																																																			NOVEL					0			10	3.909303	KEEP	1	0	0	13	353	AA	0.993634	0.38494	0			6	60	198	0	0	18.066464	10	60	290	52		0.375	0.387407
HOXD9	3235	__UNKNOWN__	__UNKNOWN__	2	176988602	176988602	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:176988602G>A	ENST00000249499.6	+	2	1226				HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	NA		NA			adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		cccaccctgtggtctctccct	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(47;924 952 7959 9248 12176)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709	3235		Homeoboxes / ANTP class : HOXL subclass	5140	protein-coding gene	gene with protein product		142982	homeo box D9	HOX4C, HOX4	NA	1973146, 1358459	Standard		NM_014213	NA	Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.818-60G>A	chr2.hg19:g.176988602G>A		NA	Q86ST1	hg19	CCDS2267.2	0.02	-0.157852	TGTxGTC	COVERED																																																																																			NOVEL	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255698.4	3	2.407059	KEEP	0	0	0	8	242	GG	0.99257	0.320408	0		+	6	60	165	0	0	14.385862	12	60	385	30	ENST00000249499.6	0.333333	0.322807
NFE2L2	4780	__UNKNOWN__	__UNKNOWN__	2	178111588	178111588	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:178111588G>A	ENST00000446151.2	-	2	170				NFE2L2_ENST00000397063.4_Intron|NFE2L2_ENST00000423513.1_Intron|NFE2L2_ENST00000464747.1_Intron|NFE2L2_ENST00000397062.3_Intron			Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	NA		NA			cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			agcctcccaaggtgctgggat	0.423		NA	Mis		NSCLC, HNSCC					HNSCC(56;0.16)											NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044	4780		basic leucine zipper proteins	7782	protein-coding gene	gene with protein product	NF-E2-related factor 2	600492	nuclear factor (erythroid-derived 2)-like 2		NA	7937919	Standard	NM_006164	NM_006164	NA	Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000446151.2:c.3-12589C>T	chr2.hg19:g.178111588G>A		NA	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	hg19	CCDS46458.1	0.02	-0.219295	CAAxGTG	COVERED																																																																																			NOVEL	NFE2L2-008	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334263.1	7	4.51247	KEEP	0	0	0	15	439	GG	0.99649	0.550947	0		-	3	60	87	0	0	6.328288	19	60	634	50	ENST00000446151.2	0.136364	0.552887
AGPS	8540	__UNKNOWN__	__UNKNOWN__	2	178290090	178290090	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:178290090C>T	ENST00000264167.4	+	2	496				AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	NA		NA			cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			ggctcacacccgtaatcccag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	8540	2.5.1.26		327	protein-coding gene	gene with protein product		603051			NA	9187299, 9553082	Standard		NM_003659	NA	Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.350+5004C>T	chr2.hg19:g.178290090C>T		NA	A5D8U9|Q2TU35	hg19	CCDS2275.1	0.02	-0.20176	ACCxGTA	COVERED																																																																																			NOVEL	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255730.2	7	2.708096	KEEP	3	0	0	9	277	CC	0.99254	0.486885	0		+	3	60	89	0	0	6.733705	16	60	544	52	ENST00000264167.4	0.157895	0.490544
PDE11A	50940	__UNKNOWN__	__UNKNOWN__	2	178520401	178520401	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:178520401A>G	ENST00000286063.6	-	19	2964				PDE11A_ENST00000450799.2_Intron|PDE11A_ENST00000409504.1_Intron|PDE11A_ENST00000358450.4_Intron|PDE11A_ENST00000389683.3_Intron|PDE11A_ENST00000449286.2_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	NA		NA			blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	caagtagctgagactacaggt	0.473		NA							Primary Pigmented Nodular Adrenocortical Disease, Familial												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	50940	3.1.4.17	Phosphodiesterases	8773	protein-coding gene	gene with protein product		604961			NA	10725373	Standard		NM_001077196	NA	Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2646+8192T>C	chr2.hg19:g.178520401A>G		NA	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	hg19	CCDS33334.1	0.02	-0.122799	CTGxGAC	COVERED																																																																																			NOVEL	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334313.2	11	2.405879	KEEP	0	0	0	8	217	AA	0.99257	0.194853	0		-	3	60	100	0	0	8.632512	8	60	241	27	ENST00000286063.6	0.272727	0.196312
OSBPL6	114880	__UNKNOWN__	__UNKNOWN__	2	179071594	179071594	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:179071594A>G	ENST00000392505.2	+	1	194				OSBPL6_ENST00000357080.4_Intron|OSBPL6_ENST00000409045.3_Intron|OSBPL6_ENST00000359685.3_Intron|OSBPL6_ENST00000190611.4_Intron	NM_001201480.1	NP_001188409.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	NA		NA			lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			cgcccacctcagcctcccaaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156	114880		Oxysterol binding proteins	16388	protein-coding gene	gene with protein product	OSBP-related protein 6	606734			NA	11483621	Standard	NM_032523	NM_001201480	NA	Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000392505.2:c.-351+12193A>G	chr2.hg19:g.179071594A>G		NA	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	hg19	CCDS56150.1	0.02	-0.298202	CTCxGCC	COVERED																																																																																			NOVEL	OSBPL6-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334394.1	17	6.016502	KEEP	3	0	0	20	573	AA	0.999859	0.78095	0		+	3	60	100	0	0	7.067587	30	60	900	73	ENST00000392505.2	0.090909	0.78106
DFNB59	494513	__UNKNOWN__	__UNKNOWN__	2	179321950	179321950	__UNKNOWN__	Intron	SNP	C	C	T	rs151299514	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:179321950C>T	ENST00000409117.3	+	4	905				DFNB59_ENST00000605419.1_Intron|DFNB59_ENST00000375129.4_Intron	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	NA		NA			sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			tgagccaccgcgcctggccTG	0.428		NA											C|||	20	0.00399361	0.0	0.0014	5008	,	,	NA	17114	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0184	NA	NA	NA								NA				0													16	14	14			NA	NA	2		NA											NA				179321950		690	1589	2279	SO:0001627	intron_variant			BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311	494513			29502	protein-coding gene	gene with protein product		610219			NA	16804542	Standard		NM_001042702	NA	Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.549+1072C>T	chr2.hg19:g.179321950C>T		NA	A0PK14|B9EJE2	hg19	CCDS42787.1	0.02	-0.174874	CCGxGCC	COVERED																																																																																			NOVEL	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335160.1	5	3.007516	KEEP	0	0	0	10	279	CC	0.992708	0.384582	0		+	4	60	127	0	0	10.369806	15	60	456	44	ENST00000409117.3	0.210526	0.387407
TTN	7273	__UNKNOWN__	__UNKNOWN__	2	179398050	179398050	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs192001910		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:179398050G>A	ENST00000589042.1	-	358	103516	c.103292C>T	c.(103291-103293)aCg>aTg	p.T34431M	TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.T32790M|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T25558M|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T25366M|TTN_ENST00000359218.5_Missense_Mutation_p.T25491M|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T31863M|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585451.1_RNA	NM_001267550.1	NP_001254479.1	Q8WZ42	TITIN_HUMAN	titin	32790		NA			adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATAATAACCCGTGTCTTCAGG	0.488		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	21287	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0								G	MET/THR,MET/THR,MET/THR,MET/THR	0,3992		0,0,1996	75	74	74		76097,95588,76472,76673	5.7	1	2		74	10,8336		0,10,4163	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	81,81,81,81	0,10,6159	AA,AG,GG	NA	0.1198,0.0,0.0811	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25366/26927,31863/33424,25491/27052,25558/27119	179398050	10,12328	1996	4173	6169	SO:0001583	missense			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657	7273		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	12403	protein-coding gene	gene with protein product		188840	cardiomyopathy, dilated 1G (autosomal dominant)	CMD1G	NA	2129545, 10051295	Standard	NM_133378	NM_003319	NA	Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000589042.1:c.103292C>T	chr2.hg19:g.179398050G>A	ENSP00000467141:p.Thr34431Met	NA	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	hg19	CCDS59435.1	0.02	1.091825	CCCxTGT	COVERED	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	16.18	3.049212	0.55110	0.0	0.001198	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.69305	0.3096	L	0.41961	1.31	0.36384	D	0.862113	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	P;P;P;P	0.58577	0.841;0.841;0.841;0.841	T	0.76397	-0.2974	9	0.87932	D	0	.	15.3087	0.74014	0.0:0.1806:0.8194:0.0	.	25366;25491;25558;32790	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	31863;25366;25558;25491;25363	ENSP00000343764:T31863M;ENSP00000434586:T25366M;ENSP00000340554:T25558M;ENSP00000352154:T25491M	ENSP00000340554:T25558M	T	-	2	0	TTN	179106296	1.000000	0.71417	0.978000	0.43139	0.982000	0.71751	5.301000	0.65727	2.688000	0.91661	0.555000	0.69702	ACG	NOVEL	TTN-018	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450680.2	2	3.008278	KEEP	0	0	0	10	291	GG	0.992708	0.991932	0		-	5	60	141	0	0	8.3772	75	60	2394	121	ENST00000589042.1	0.0625	0.999218
TTN	7273	__UNKNOWN__	__UNKNOWN__	2	179458093	179458093	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:179458093G>C	ENST00000589042.1	-	299	59066	c.58842C>G	c.(58840-58842)atC>atG	p.I19614M	TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000591111.1_Missense_Mutation_p.I17973M|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I10741M|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I10549M|TTN_ENST00000359218.5_Missense_Mutation_p.I10674M|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I17046M|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA	NM_001267550.1	NP_001254479.1	Q8WZ42	TITIN_HUMAN	titin	17973	Ig-like 109.	NA			adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTTTTCCAGGATGTAGTTTG	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													119	120	119			NA	NA	2		NA											NA				179458093		1871	4097	5968	SO:0001583	missense			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657	7273		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	12403	protein-coding gene	gene with protein product		188840	cardiomyopathy, dilated 1G (autosomal dominant)	CMD1G	NA	2129545, 10051295	Standard	NM_133378	NM_003319	NA	Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000589042.1:c.58842C>G	chr2.hg19:g.179458093G>C	ENSP00000467141:p.Ile19614Met	NA	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	hg19	CCDS59435.1	0.02	1.882977	CAGxATG	COVERED	.	.	.	.	.	.	.	.	.	.	G	2.527	-0.309375	0.05458	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	6.16	3.07	0.35406	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.63803	0.2542	M	0.80982	2.52	0.44555	D	0.997518	D;P;D;P	0.54601	0.967;0.942;0.967;0.942	P;P;P;P	0.60012	0.867;0.867;0.867;0.867	T	0.64580	-0.6374	9	0.87932	D	0	.	2.7479	0.05272	0.4157:0.0:0.3824:0.2019	.	10549;10674;10741;17973	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	17046;10549;10741;10674;10547	ENSP00000343764:I17046M;ENSP00000434586:I10549M;ENSP00000340554:I10741M;ENSP00000352154:I10674M	ENSP00000340554:I10741M	I	-	3	3	TTN	179166339	0.994000	0.37717	1.000000	0.80357	0.502000	0.33828	1.079000	0.30766	0.939000	0.37446	-0.145000	0.13849	ATC	NOVEL	TTN-018	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450680.2	1	4.211893	KEEP	0	0	0	14	416	GG	0.995343	0.991593	0		-	20	60	681	0	0	59.905826	47	60	1541	126	ENST00000589042.1	0.298507	0.996233
SSFA2	6744	__UNKNOWN__	__UNKNOWN__	2	182780275	182780275	__UNKNOWN__	Silent	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:182780275A>C	ENST00000409136.1	+	3	547	c.435A>C	c.(433-435)ctA>ctC	p.L145L	SSFA2_ENST00000428267.2_Silent_p.L483L|SSFA2_ENST00000431877.2_Silent_p.L636L|SSFA2_ENST00000320370.7_Silent_p.L636L|SSFA2_ENST00000409001.1_Silent_p.L636L			P28290	SSFA2_HUMAN	sperm specific antigen 2	636		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			CAGTAGAGCTACTGAGGGAAG	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													90	82	85			NA	NA	2		NA											NA				182780275		2203	4300	6503	SO:0001819	synonymous_variant			M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434	6744			11319	protein-coding gene	gene with protein product	cleavage signal-1 protein, KRAS-induced actin-interacting protein, sperm associated antigen 13	118990			NA	1555770	Standard	NM_006751	XM_005246812	NA	Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000409136.1:c.435A>C	chr2.hg19:g.182780275A>C		NA	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	hg19		0.02	1.836074	GCTxCTG	COVERED																																																																																			NOVEL	SSFA2-009	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000334804.1	0	3.007865	KEEP	0	0	0	10	280	AA	0.992708	0.984859	0		+	15	60	483	0	0	40.806868	45	60	1301	114	ENST00000409136.1	0.25	0.992094
PPP1R1C	151242	__UNKNOWN__	__UNKNOWN__	2	182964989	182964989	__UNKNOWN__	Intron	SNP	G	G	A	rs1962724	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:182964989G>A	ENST00000280295.3	+	5	496				PPP1R1C_ENST00000475249.1_Intron|PPP1R1C_ENST00000409137.3_Intron|PPP1R1C_ENST00000452904.1_Intron|PPP1R1C_ENST00000409702.1_Intron			Q8WVI7	PPR1C_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1C	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|negative regulation of catalytic activity (GO:0043086)|positive regulation of cell growth (GO:0030307)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0628)			ctgtagtcccggcactttggg	0.478		NA											A|||	1424	0.284345	0.4024	0.1988	5008	,	,	NA	17107	0.2708	NA	0.2147	False	NA	,,,	NA	NA	NA	2504	0.271	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF494535, BC017943	CCDS46468.1, CCDS58740.1	2q31.3	2012-04-17			ENSG00000150722	ENSG00000150722	151242		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	14940	protein-coding gene	gene with protein product		613240			NA	11948623	Standard	NM_001080545	NM_001261424	NA	Approved	Inhibitor-1-like	uc010frm.2	Q8WVI7	OTTHUMG00000154326	ENST00000280295.3:c.263-16945G>A	chr2.hg19:g.182964989G>A		NA	Q5HYJ5|Q8TD54	hg19	CCDS58740.1	0.02	-0.192973	CCCxGCA	COVERED																																																																																			NOVEL	PPP1R1C-004	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334875.1	7	2.406181	KEEP	0	0	0	8	226	GG	0.99257	0.454356	0		+	3	60	88	0	0	6.633929	16	60	508	42	ENST00000280295.3	0.157895	0.457757
PDE1A	5136	__UNKNOWN__	__UNKNOWN__	2	183102753	183102753	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:183102753C>T	ENST00000435564.1	-	3	599				PDE1A_ENST00000351439.5_Intron|PDE1A_ENST00000456212.1_Intron|PDE1A_ENST00000409365.1_Intron|PDE1A_ENST00000482538.1_Intron|PDE1A_ENST00000346717.4_Intron|PDE1A_ENST00000331935.6_Intron|PDE1A_ENST00000358139.2_Intron|PDE1A_ENST00000536095.1_Intron|PDE1A_ENST00000410103.1_Intron	NM_001258312.1|NM_005019.4	NP_001245241.1|NP_005010.2	P54750	PDE1A_HUMAN	phosphodiesterase 1A, calmodulin-dependent	NA		NA			activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of smooth muscle cell apoptotic process (GO:0034391)|regulation of smooth muscle cell proliferation (GO:0048660)|signal transduction (GO:0007165)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity (GO:0048101)|calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			endometrium(5)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(2)	35			OV - Ovarian serous cystadenocarcinoma(117;0.061)		Bepridil(DB01244)|Caffeine(DB00201)|Felodipine(DB01023)|Nicardipine(DB00622)	cccagcacttcgggaggccta	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2285.1, CCDS33344.1, CCDS58741.1, CCDS74612.1	2q32.1	2008-03-18			ENSG00000115252	ENSG00000115252	5136	3.1.4.17	Phosphodiesterases	8774	protein-coding gene	gene with protein product		171890			NA	8557689, 11342109	Standard		NM_005019	NA	Approved		uc010zfq.2	P54750	OTTHUMG00000132596	ENST00000435564.1:c.398+2083G>A	chr2.hg19:g.183102753C>T		NA	D3DPG5|Q86VZ0|Q9C0K8|Q9C0K9|Q9C0L0|Q9C0L1|Q9C0L2|Q9C0L3|Q9C0L4|Q9UFX3	hg19	CCDS2285.1	0.02	-0.10526	CTTxGGG	UNCOVERED																																																																																			NOVEL	PDE1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255807.1	3	2.707811	KEEP	0	0	0	9	273	CC	0.99254	0.138789	0		-	3	60	89	0	0	7.401009	9	60	293	34	ENST00000435564.1	0.25	0.139832
NUP35	129401	__UNKNOWN__	__UNKNOWN__	2	183987084	183987084	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:183987084A>G	ENST00000409798.1	+	2	222							Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	NA		NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8						gattacaggcatgagccacca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF514993	CCDS2290.1, CCDS74614.1	2q32	2008-02-05			ENSG00000163002	ENSG00000163002	129401			29797	protein-coding gene	gene with protein product		608140			NA		Standard	NM_138285	XM_005246284	NA	Approved	MP44	uc002upf.3	Q8NFH5	OTTHUMG00000132621	ENST00000409798.1:c.-12+2242A>G	chr2.hg19:g.183987084A>G		NA	B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1	hg19		0.02	-0.184164	GGCxTGA	COVERED																																																																																			NOVEL	NUP35-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000334518.1	10	3.60892	KEEP	7	0	0	12	332	AA	0.99257	0.420331	0		+	3	60	99	0	0	7.733578	16	60	451	50	ENST00000409798.1	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	184569875	184569875	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:184569875A>G			NA	NA				RP11-438L19.1 (489747 upstream) : AC093639.1 (199380 downstream)						NA		NA									NA						gcaagactccatctcaaaaca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.184569875A>G		NA		hg19		0.02	-0.376775	TCCxTCT	COVERED																																																																																			NOVEL					0			8	4.812017	KEEP	1	0	0	16	440	AA	0.99649	0.905878	0			4	60	131	0	1	9.412093	35	60	985	89		0.102564	0.909069
AC093639.1	0	__UNKNOWN__	__UNKNOWN__	2	184805649	184805649	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:184805649A>G	ENST00000441026.1	+	0	232										NA		NA									NA						tgggccgggcacggtggctca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000441026.1:	chr2.hg19:g.184805649A>G		NA		hg19		0.02	-0.192956	GGCxCGG	COVERED																																																																																			NOVEL	AC093639.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000332356.1	2	2.406442	KEEP	0	0	0	8	227	AA	0.99257	0.454356	0		+	3	60	98	0	0	7.427067	19	60	570	47	ENST00000441026.1	0.136364	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	185426734	185426734	__UNKNOWN__	IGR	SNP	C	C	T	rs368666138		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:185426734C>T			NA	NA				MIR548AE1 (182963 upstream) : ZNF804A (36358 downstream)						NA		NA									NA						tgtgagccaccgtgcctggcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.185426734C>T		NA		hg19		0.02	-0.149115	CACxGTG	COVERED																																																																																			NOVEL					0			6	2.406497	KEEP	1	0	0	8	231	CC	0.99257	0.289832	0			3	60	89	0	0	7.072376	12	60	379	39		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	186327023	186327023	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:186327023A>C			NA	NA				ZNF804A (522804 upstream) : U8 (199477 downstream)						NA		NA									NA						gtaatcccagaactttgggag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.186327023A>C		NA		hg19		0.02	-0.096476	CAGxACT	UNCOVERED																																																																																			NOVEL					0			9	3.308857	KEEP	0	0	0	11	311	AA	0.993072	0.119602	0			4	60	131	0	0	12.323739	5	60	139	28		0.444444	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	187135387	187135387	__UNKNOWN__	IGR	SNP	T	T	C	rs184362773	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:187135387T>C			NA	NA				AC097500.2 (187427 upstream) : RP11-410E4.1 (83911 downstream)						NA		NA									NA						cgcaccattgtactccagcct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.187135387T>C		NA		hg19		0.02	-0.227561	TTGxACT	COVERED																																																																																			NOVEL					0			4	2.405138	KEEP	0	0	0	8	209	TT	0.99257	0.578599	0			4	60	109	0	0	8.075661	21	60	589	51		0.16	0.58293
GULP1	51454	__UNKNOWN__	__UNKNOWN__	2	189406766	189406766	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:189406766A>G	ENST00000409580.1	+	8	1113				GULP1_ENST00000359135.3_Intron|GULP1_ENST00000409609.1_Intron|GULP1_ENST00000410051.1_3'UTR|GULP1_ENST00000409830.1_Intron|GULP1_ENST00000409805.1_Intron|GULP1_ENST00000409843.1_Intron			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	NA		NA			apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			cctgggaggcagaggttgcag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(178;563 2065 20199 42378 52815)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366	51454			18649	protein-coding gene	gene with protein product		608165			NA	11729193	Standard	NM_016315	NM_001252668	NA	Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.399+721A>G	chr2.hg19:g.189406766A>G		NA	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	hg19	CCDS2295.1	0.02	3.07011	GGCxGAG	COVERED																																																																																			NOVEL	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335722.1	22	12.858098	KEEP	2	4	96	77	2112	AA	1	0.999981	0		+	6	60	168	0	0	9.920085	91	70	2707	234	ENST00000409580.1	0.061856	0.999981
COL5A2	1290	__UNKNOWN__	__UNKNOWN__	2	190002952	190002952	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:190002952G>A	ENST00000374866.3	-	2	372					NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	NA		NA			axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			caccctcctcggcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262	1290		Collagens	2210	protein-coding gene	gene with protein product	AB collagen	120190			NA	1572660	Standard	NM_000393	NM_000393	NA	Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.98-27777C>T	chr2.hg19:g.190002952G>A		NA	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	hg19	CCDS33350.1	0.02	-0.271914	CTCxGCC	COVERED																																																																																			NOVEL	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313523.1	10	4.209387	KEEP	0	0	0	14	390	GG	0.995343	0.713975	0		-	3	60	92	0	0	6.543235	24	60	778	62	ENST00000374866.3	0.111111	0.717315
PMS1	5378	__UNKNOWN__	__UNKNOWN__	2	190728591	190728591	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:190728591G>A	ENST00000441310.2	+	10	2212	c.1979G>A	c.(1978-1980)tGg>tAg	p.W660*	PMS1_ENST00000447232.2_Intron|PMS1_ENST00000409823.3_Nonsense_Mutation_p.W621*|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000418224.3_Nonsense_Mutation_p.W484*|PMS1_ENST00000432292.3_Nonsense_Mutation_p.W484*	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	660		NA			ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)	MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|mismatched DNA binding (GO:0030983)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			OV - Ovarian serous cystadenocarcinoma(117;0.0013)|Epithelial(96;0.0263)|all cancers(119;0.0751)			ACCAGCGCATGGAATTTGGCC	0.378		NA	Mis, N			colorectal, endometrial, ovarian		Direct reversal of damage;Mismatch excision repair (MMR)													NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Hereditary non-polyposis colorectal cancer	2	2q31-q33	5378	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)		E	0													109	118	115			NA	NA	2		NA											NA				190728591		2203	4300	6503	SO:0001587	stop_gained				CCDS2302.1, CCDS46473.1, CCDS46474.1, CCDS74615.1	2q31-q33	2014-09-17	2001-11-28		ENSG00000064933	ENSG00000064933	5378			9121	protein-coding gene	gene with protein product		600258	postmeiotic segregation increased (S. cerevisiae) 1	PMSL1	NA	8072530	Standard		NM_000534	NA	Approved		uc002urh.4	P54277	OTTHUMG00000132664	ENST00000441310.2:c.1979G>A	chr2.hg19:g.190728591G>A	ENSP00000406490:p.Trp660*	NA	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	hg19	CCDS2302.1	0.02	1.271823	CATxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.67	3.871534	0.72065	.	.	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000432292;ENST00000424307;ENST00000452382	.	.	.	5.36	4.41	0.53225	.	0.789446	0.11913	N	0.517457	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-4.5091	6.1193	0.20144	0.1013:0.1926:0.7061:0.0	.	.	.	.	X	484;660;484;621;484;599;48	.	ENSP00000376149:W484X	W	+	2	0	PMS1	190436836	0.874000	0.30092	0.996000	0.52242	0.624000	0.37722	0.721000	0.25911	2.806000	0.96561	0.644000	0.83932	TGG	NOVEL	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255918.2	2	7.813955	KEEP	0	0	0	26	787	GG	0.999957	0.999364	0		+	24	60	701	0	0	60.639584	54	60	1859	165	ENST00000441310.2	0.307692	0.999407
C2orf88	84281	__UNKNOWN__	__UNKNOWN__	2	190795334	190795334	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:190795334A>G	ENST00000478197.1	+	1	219							Q9BSF0	SMAKA_HUMAN	chromosome 2 open reading frame 88	NA		NA				plasma membrane (GO:0005886)				kidney(1)|large_intestine(1)|lung(1)	3						cctgggaggcagaggttgcag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005083	CCDS42792.1	2q32.2	2014-02-12	2009-04-08		ENSG00000187699	ENSG00000187699	84281			28191	protein-coding gene	gene with protein product	small membrane AKAP	615117			NA	23996002	Standard	NM_032321	NM_032321	NA	Approved	MGC13057, smAKAP	uc002urt.3	Q9BSF0	OTTHUMG00000154361	ENST00000478197.1:c.219+50781A>G	chr2.hg19:g.190795334A>G		NA	D3DPI3|P0C876|Q53TC7	hg19		0.02	-0.438462	GGCxGAG	COVERED																																																																																			NOVEL	C2orf88-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000334952.1	3	3.17023	KEEP	1	2	52	29	791	AA	0.999997	0.959856	0		+	5	60	147	0	0	10.436702	37	60	1071	85	ENST00000478197.1	0.119048	0.959859
MFSD6	54842	__UNKNOWN__	__UNKNOWN__	2	191299437	191299437	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:191299437T>C	ENST00000392328.1	+	3	271					NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(3)|stomach(1)	23						ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2306.1	2q32.2	2008-10-29			ENSG00000151690	ENSG00000151690	54842			24711	protein-coding gene	gene with protein product		613476			NA		Standard		NM_017694	NA	Approved	FLJ20160	uc002urz.2	Q6ZSS7	OTTHUMG00000132671	ENST00000392328.1:c.-53-1266T>C	chr2.hg19:g.191299437T>C		NA	D3KSZ4|Q86TH2|Q9NXM3	hg19	CCDS2306.1	0.02	-0.175404	AGGxGTG	COVERED																																																																																			NOVEL	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255931.1	0	2.707332	KEEP	0	0	0	9	255	TT	0.99254	0.384517	0		+	3	60	106	0	0	8.591787	14	60	401	45	ENST00000392328.1	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	191615692	191615692	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:191615692T>C			NA	NA				AC006460.2 (42250 upstream) : AC005540.3 (129830 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.191615692T>C		NA		hg19		0.02	-0.210507	GCAxTTT	COVERED																																																																																			NOVEL					0			11	3.609743	KEEP	2	0	0	12	342	TT	0.993072	0.518544	0			3	60	99	0	0	7.46502	20	60	610	54		0.130435	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	192307468	192307468	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:192307468A>G			NA	NA				MYO1B (17353 upstream) : NABP1 (235393 downstream)						NA		NA									NA						ggatggtctcaatctcctgac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.192307468A>G		NA		hg19		0.02	-0.149087	CTCxATC	UNCOVERED																																																																																			NOVEL					0			10	2.404953	KEEP	3	0	0	8	213	AA	0	0	0			3	60	100	0	0	7.991917	14	60	400	35		0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	192457953	192457953	__UNKNOWN__	IGR	SNP	T	T	C	rs537542051		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:192457953T>C			NA	NA				MYO1B (167838 upstream) : NABP1 (84908 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.527		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14070	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.192457953T>C		NA		hg19		0.02	-0.166642	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.4065	KEEP	2	0	0	8	228	TT	0	0	0			3	60	98	0	0	7.791904	14	60	408	39		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	194157192	194157192	__UNKNOWN__	IGR	SNP	C	C	T	rs1813820	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:194157192C>T			NA	NA				PCGEM1 (515567 upstream) : RP11-764E7.1 (605898 downstream)						NA		NA									NA						gccaagatggcgccactgcac	0.478		NA											c|||	2494	0.498003	0.2625	0.6628	5008	,	,	NA	12320	0.621	NA	0.5457	False	NA	,,,	NA	NA	NA	2504	0.5235	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.194157192C>T		NA		hg19		0.02	-0.175427	TGGxGCC	UNCOVERED																																																																																			NOVEL					0			8	3.008286	KEEP	8	0	0	10	293	CC	0	0	0			7	60	203	1	0	18.414633	11	60	360	52		0.388889	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	195074559	195074559	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:195074559A>G			NA	NA				RP11-764E7.1 (310441 upstream) : AC018799.1 (134446 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.195074559A>G		NA		hg19		0.02	-0.078929	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			9	2.707347	KEEP	2	0	0	9	256	AA	0.99254	0.076759	0			2	60	72	0	0	6.33604	5	60	149	27		0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	196483771	196483771	__UNKNOWN__	IGR	SNP	C	C	T	rs138702345	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:196483771C>T			NA	NA				AC064834.3 (46077 upstream) : SLC39A10 (37699 downstream)						NA		NA									NA						gagctgagatcgcaccattgc	0.498		NA											C|||	423	0.0844649	0.0386	0.17	5008	,	,	NA	13478	0.0516	NA	0.0974	False	NA	,,,	NA	NA	NA	2504	0.1063	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.196483771C>T		NA		hg19		0.02	-0.087706	GATxGCA	UNCOVERED																																																																																			NOVEL					0			10	2.70737	KEEP	9	0	0	9	259	CC	0	0	0			3	60	87	0	0	7.832474	5	60	157	28		0.375	0.099721
CCDC150	284992	__UNKNOWN__	__UNKNOWN__	2	197505958	197505958	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:197505958T>C	ENST00000389175.4	+	1	147				CCDC150_ENST00000472405.2_Intron|CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000423093.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	NA		NA								breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						gcctcggccttccaaagtgct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395	284992			26834	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080539	NM_001080539	NA	Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.12+1456T>C	chr2.hg19:g.197505958T>C		NA	Q6P5U6|Q6P663|Q8N8V5	hg19	CCDS46478.1	0.02	-0.149103	CCTxCCA	COVERED																																																																																			NOVEL	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335377.2	3	4.211202	KEEP	2	0	0	14	396	TT	0.994391	0.290363	0		+	3	60	101	0	0	8.178879	13	60	384	49	ENST00000389175.4	0.1875	0.292001
CCDC150	284992	__UNKNOWN__	__UNKNOWN__	2	197592547	197592547	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:197592547T>C	ENST00000389175.4	+	23	2691				CCDC150_ENST00000409270.1_Intron|CCDC150_ENST00000487663.1_Intron|CCDC150_ENST00000272831.7_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	NA		NA								breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ccatcctggctaacatggtga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395	284992			26834	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080539	NM_001080539	NA	Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.2557-1370T>C	chr2.hg19:g.197592547T>C		NA	Q6P5U6|Q6P663|Q8N8V5	hg19	CCDS46478.1	0.02	-0.07017	GGCxAAC	UNCOVERED																																																																																			NOVEL	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335377.2	6	2.706145	KEEP	1	0	0	9	238	TT	0.99254	0.053733	0		+	3	53	99	0	0	9.255405	4	60	118	25	ENST00000389175.4	0.428571	0.054137
RFTN2	130132	__UNKNOWN__	__UNKNOWN__	2	198520288	198520288	__UNKNOWN__	Intron	SNP	G	G	A	rs536849922		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:198520288G>A	ENST00000295049.4	-	2	676					NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	NA		NA			dsRNA transport (GO:0033227)|response to exogenous dsRNA (GO:0043330)	plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(13)|urinary_tract(3)	30						ggtggctcacgcctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055136	CCDS2323.1	2q33.1	2008-02-05	2006-09-28	2006-09-28	ENSG00000162944	ENSG00000162944	130132			26402	protein-coding gene	gene with protein product		NA	chromosome 2 open reading frame 11	C2orf11	NA		Standard	NM_144629	NM_144629	NA	Approved	FLJ30574, Raftlin-2	uc002uuo.4	Q52LD8	OTTHUMG00000132746	ENST00000295049.4:c.140-8898C>T	chr2.hg19:g.198520288G>A		NA	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	hg19	CCDS2323.1	0.02	-0.192985	CACxCCT	UNCOVERED																																																																																			NOVEL	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256106.2	7	2.406029	KEEP	7	0	0	8	224	GG	0	0	0		-	3	60	88	0	0	6.633826	16	60	546	50	ENST00000295049.4	0.157895	0.457757
SATB2	23314	__UNKNOWN__	__UNKNOWN__	2	200244530	200244530	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:200244530T>C	ENST00000417098.1	-	5	1414				SATB2_ENST00000428695.1_Intron|SATB2_ENST00000443023.1_Intron|SATB2_ENST00000260926.5_Intron|SATB2_ENST00000484124.1_Intron|SATB2_ENST00000457245.1_Intron	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	NA		NA			cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(30;262 767 11040 24421 36230)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042	23314		Homeoboxes / CUT class	21637	protein-coding gene	gene with protein product		608148	SATB family member 2		NA		Standard	NM_015265	NM_015265	NA	Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.597+556A>G	chr2.hg19:g.200244530T>C		NA	A8K5Z8|Q3ZB87|Q4V763	hg19	CCDS2327.1	0.02	-0.201657	AGGxGTG	COVERED																																																																																			NOVEL	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256140.1	12	3.607784	KEEP	1	0	0	12	326	TT	0.993634	0.487421	0		-	3	60	88	0	0	6.634953	16	60	457	48	ENST00000417098.1	0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	200723316	200723316	__UNKNOWN__	IGR	SNP	G	G	A	rs2918044	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:200723316G>A			NA	NA				FTCDNL1 (7420 upstream) : AC073043.1 (35975 downstream)						NA		NA									NA						cattacaggcgtgagccaccg	0.502		NA											G|||	3823	0.763379	0.7315	0.7896	5008	,	,	NA	12642	0.8155	NA	0.6471	False	NA	,,,	NA	NA	NA	2504	0.8538	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.200723316G>A		NA		hg19		0.02	-0.114008	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			7	2.70764	KEEP	1	0	0	9	268	GG	0.99257	0.16126	0			7	60	194	0	0	19.19712	5	60	161	31		0.583333	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	201128805	201128805	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:201128805C>T			NA	NA				C2orf47 (299957 upstream) : SPATS2L (41810 downstream)						NA		NA									NA						tcacttgaggccaggagtttg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.201128805C>T		NA		hg19		0.02	-0.149124	AGGxCAG	COVERED																																																																																			NOVEL					0			11	2.406886	KEEP	2	0	0	8	237	CC	0.99257	0.289832	0			3	60	94	0	0	7.478849	13	60	430	36		0.1875	0.292001
KCTD18	130535	__UNKNOWN__	__UNKNOWN__	2	201373064	201373064	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:201373064C>T	ENST00000359878.3	-	2	436				KCTD18_ENST00000468413.1_Intron|KCTD18_ENST00000409157.1_Intron	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	NA		NA			protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						ccacccacctcggcctcccaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729	130535			26446	protein-coding gene	gene with protein product		NA	potassium channel tetramerisation domain containing 18		NA		Standard	NM_152387	NM_152387	NA	Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.75-1250G>A	chr2.hg19:g.201373064C>T		NA	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	hg19	CCDS2330.1	0.02	-0.157896	CCTxGGC	COVERED																																																																																			NOVEL	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256188.1	9	4.513086	KEEP	3	0	0	15	451	CC	0.995343	0.321303	0		-	3	60	86	0	0	6.5921	14	60	467	48	ENST00000359878.3	0.176471	0.322807
FAM126B	285172	__UNKNOWN__	__UNKNOWN__	2	201927110	201927110	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:201927110A>G	ENST00000418596.3	-	1	60					NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	NA		NA				intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						ggtggctcacacctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744	285172			28593	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173822	NM_173822	NA	Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.127+9222T>C	chr2.hg19:g.201927110A>G		NA	B2RCG7|Q4ZG87|Q53TX6	hg19	CCDS2335.1	0.02	-0.245574	CACxCCT	COVERED																																																																																			NOVEL	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256285.3	14	2.235759	KEEP	2	1	27	17	453	AA	0.999859	0.641257	0		-	4	60	136	0	0	10.736085	21	60	622	66	ENST00000418596.3	0.16	0.641347
CFLAR	8837	__UNKNOWN__	__UNKNOWN__	2	202000630	202000630	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202000630A>G	ENST00000342795.5	+	4	767				CFLAR_ENST00000494258.1_Intron|CFLAR_ENST00000341222.6_Intron|CFLAR_ENST00000440180.1_Intron|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000479953.2_Intron|CFLAR_ENST00000457277.1_Intron|CFLAR_ENST00000340870.5_Intron|CFLAR_ENST00000341582.6_Intron|CFLAR_ENST00000423241.2_Intron|CFLAR_ENST00000309955.3_Intron|CFLAR_ENST00000395148.2_Intron			O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						gattacaggtatgaacttctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(16;548 657 22190 32864 42338)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402	8837		Endogenous ligands	1876	protein-coding gene	gene with protein product		603599		CASP8AP1	NA	9208847, 9217161	Standard	NM_003879	NM_003879	NA	Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000342795.5:c.388-65A>G	chr2.hg19:g.202000630A>G		NA	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	hg19		0.02	1.4824	GGTxTGA	COVERED																																																																																			NOVEL	CFLAR-007	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336701.1	10	3.247875	KEEP	0	2	63	33	848	AA	0.999999	0.999879	0		+	5	60	168	0	0	10.986213	78	60	2261	178	ENST00000342795.5	0.060241	0.999881
CFLAR	8837	__UNKNOWN__	__UNKNOWN__	2	202022115	202022115	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202022115T>C	ENST00000309955.3	+	9	1308				CFLAR-AS1_ENST00000415011.2_RNA|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000355558.4_Intron|CFLAR_ENST00000479953.2_Intron|CFLAR_ENST00000457277.1_Intron|CFLAR_ENST00000340870.5_Intron|CFLAR_ENST00000341582.6_Intron|CFLAR_ENST00000423241.2_Intron	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						ccacccgccttggcctcccaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(16;548 657 22190 32864 42338)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402	8837		Endogenous ligands	1876	protein-coding gene	gene with protein product		603599		CASP8AP1	NA	9208847, 9217161	Standard	NM_003879	NM_003879	NA	Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.794-3040T>C	chr2.hg19:g.202022115T>C		NA	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	hg19	CCDS2337.1	0.02	-0.140324	CCTxGGC	COVERED																																																																																			NOVEL	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256276.3	2	2.404502	KEEP	0	0	0	8	207	TT	0.99257	0.259026	0		+	3	60	93	0	0	7.573096	11	60	318	32	ENST00000309955.3	0.214286	0.260965
CASP10	843	__UNKNOWN__	__UNKNOWN__	2	202060504	202060504	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202060504A>G	ENST00000286186.6	+	5	1012				CASP10_ENST00000346817.5_Intron|CASP10_ENST00000492363.1_Intron|CASP10_ENST00000313728.7_Intron|CASP10_ENST00000448480.1_Intron|CASP10_ENST00000360132.3_Intron|CASP10_ENST00000272879.5_Intron|CASP10_ENST00000374650.3_Intron	NM_032977.3	NP_116759.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						gggttcaagcaattctcctgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	843	3.4.22.63	Caspases	1500	protein-coding gene	gene with protein product		601762	caspase 10, apoptosis-related cysteine protease		NA	8755496	Standard	NM_032977	NM_032974	NA	Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000286186.6:c.578-61A>G	chr2.hg19:g.202060504A>G		NA	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	hg19	CCDS2340.1	0.02	-0.271895	AGCxATT	COVERED																																																																																			NOVEL	CASP10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256272.2	2	3.909579	KEEP	0	0	0	13	354	AA	0.994391	0.713292	0		+	3	60	96	0	0	6.943026	24	60	719	53	ENST00000286186.6	0.111111	0.717315
CASP10	843	__UNKNOWN__	__UNKNOWN__	2	202082925	202082925	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202082925C>T	ENST00000286186.6	+	0	2465				CASP10_ENST00000346817.5_3'UTR|CASP10_ENST00000448480.1_Intron|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000272879.5_Intron	NM_032977.3	NP_116759.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						attataggcacgagccaccac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	843	3.4.22.63	Caspases	1500	protein-coding gene	gene with protein product		601762	caspase 10, apoptosis-related cysteine protease		NA	8755496	Standard	NM_032977	NM_032974	NA	Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000286186.6:c.*461C>T	chr2.hg19:g.202082925C>T		NA	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	hg19	CCDS2340.1	0.02	1.436078	GCAxGAG	COVERED																																																																																			NOVEL	CASP10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256272.2	5	2.237731	KEEP	0	1	24	16	466	CC	0.999366	0.966812	0		+	4	60	121	0	0	7.996947	45	60	1449	101	ENST00000286186.6	0.081633	0.967425
STRADB	55437	__UNKNOWN__	__UNKNOWN__	2	202344915	202344915	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202344915T>C	ENST00000194530.3	+	0	1639				STRADB_ENST00000392249.2_3'UTR	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	NA		NA			activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						CAAATCATTTTATGTCCTATA	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													109	112	111			NA	NA	2		NA											NA				202344915		2203	4300	6503	SO:0001624	3_prime_UTR_variant			AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146	55437			13205	protein-coding gene	gene with protein product		607333	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2	ALS2CR2	NA	11161814, 14511394	Standard	NM_018571	NM_018571	NA	Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.*17T>C	chr2.hg19:g.202344915T>C		NA	Q5BKY7|Q9P1L0	hg19	CCDS2348.1	0.02	1.470406	TTTxATG	COVERED																																																																																			NOVEL	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256297.1	3	2.538105	KEEP	4	1	24	17	470	TT	0.999859	0.999266	0		+	5	27	161	0	0	10.397398	74	60	2195	156	ENST00000194530.3	0.063291	0.999407
ALS2	57679	__UNKNOWN__	__UNKNOWN__	2	202624929	202624929	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202624929A>G	ENST00000264276.6	-	4	1486				ALS2_ENST00000467448.1_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	NA		NA			behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						agctacttggaaggctgaaat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393	57679		Rho guanine nucleotide exchange factors	443	protein-coding gene	gene with protein product	alsin	606352	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6	ALS2CR6	NA	11586298	Standard	NM_020919	NM_020919	NA	Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.1113+674T>C	chr2.hg19:g.202624929A>G		NA	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	hg19	CCDS42800.1	0.02	1.61135	TGGxAGG	COVERED																																																																																			NOVEL	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335562.3	22	11.953102	KEEP	0	1	23	48	1265	AA	1	0.999962	0		-	6	60	191	0	0	12.312221	87	60	2518	195	ENST00000264276.6	0.064516	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	202815675	202815675	__UNKNOWN__	IGR	SNP	T	T	C	rs556526319		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202815675T>C			NA	NA				RNU6-440P (23409 upstream) : AC007358.1 (2304 downstream)						NA		NA									NA						tggctcacgcttgtaatccca	0.488		NA											t|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18004	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.202815675T>C		NA		hg19		0.02	-0.157879	CGCxTGT	COVERED																																																																																			NOVEL					0			9	3.308562	KEEP	0	0	0	11	305	TT	0.993072	0.32057	0			3	60	107	0	0	8.691581	14	60	418	40		0.176471	0.322807
AC079354.1	0	__UNKNOWN__	__UNKNOWN__	2	202987516	202987516	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:202987516A>C	ENST00000409515.3	+	12	2098				AC079354.1_ENST00000541917.1_Intron|AC079354.1_ENST00000295844.3_Intron						NA		NA									NA						cgtgagccacagcgcccagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409515.3:c.2099-2421A>C	chr2.hg19:g.202987516A>C		NA		hg19		0.02	-0.228038	CACxGCG	COVERED																																																																																			NOVEL	AC079354.1-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000336161.2	8	3.007194	KEEP	0	0	0	10	274	AA	0.993072	0.578892	0		+	3	60	94	0	0	6.849836	22	60	658	49	ENST00000409515.3	0.12	0.58293
AC079354.1	0	__UNKNOWN__	__UNKNOWN__	2	203011014	203011014	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203011014T>C	ENST00000409515.3	+	14	2321				AC079354.1_ENST00000541917.1_Intron|AC079354.1_ENST00000295844.3_Intron						NA		NA									NA						ttacttgagctcaggagtttg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409515.3:c.2321+7783T>C	chr2.hg19:g.203011014T>C		NA		hg19		0.02	-0.192968	AGCxCAG	COVERED																																																																																			NOVEL	AC079354.1-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000336161.2	8	2.406302	KEEP	1	0	0	8	223	TT	0.99257	0.454356	0		+	3	60	104	0	0	8.160615	17	60	519	48	ENST00000409515.3	0.15	0.457757
NOP58	51602	__UNKNOWN__	__UNKNOWN__	2	203141336	203141336	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203141336G>A	ENST00000264279.5	+	3	348				NOP58_ENST00000467734.1_Intron	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	NA		NA			cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						gccaaggcaggcggatcagtt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044	51602			29926	protein-coding gene	gene with protein product		NA	NOP58 ribonucleoprotein homolog (yeast)		NA	10606270, 10925205	Standard	NM_015934	NM_015934	NA	Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.123-1337G>A	chr2.hg19:g.203141336G>A		NA	Q53SA4|Q6PK08|Q9P036|Q9UFN3	hg19	CCDS2353.1	0.02	-0.131575	CAGxCGG	COVERED																																																																																			NOVEL	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256313.2	8	2.707834	KEEP	0	0	0	9	274	GG	0.99254	0.227464	0		+	3	60	83	0	0	7.078043	7	60	239	30	ENST00000264279.5	0.3	0.229173
BMPR2	659	__UNKNOWN__	__UNKNOWN__	2	203253768	203253768	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203253768T>C	ENST00000374574.2	+	1	117				BMPR2_ENST00000374580.4_Intron			Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	NA		NA			activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						gcctgggcaatataatgagaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217	659			1078	protein-coding gene	gene with protein product		600799	primary pulmonary hypertension 1	PPH1	NA	7791754	Standard	NM_001204	NM_001204	NA	Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374574.2:c.76+11495T>C	chr2.hg19:g.203253768T>C		NA	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	hg19		0.02	-0.22802	CAAxATA	COVERED																																																																																			NOVEL	BMPR2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000257744.1	8	4.810792	KEEP	0	0	0	16	426	TT	0.997832	0.581666	0		+	3	60	105	1	0	8.005604	21	60	609	54	ENST00000374574.2	0.125	0.58293
BMPR2	659	__UNKNOWN__	__UNKNOWN__	2	203411647	203411647	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203411647T>A	ENST00000374574.2	+	10	1454				BMPR2_ENST00000374580.4_Intron			Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	NA		NA			activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						tgttttgttttgttttgtttt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217	659			1078	protein-coding gene	gene with protein product		600799	primary pulmonary hypertension 1	PPH1	NA	7791754	Standard	NM_001204	NM_001204	NA	Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374574.2:c.1413+4477T>A	chr2.hg19:g.203411647T>A		NA	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	hg19		0.02	-0.149099	TTTxGTT	COVERED																																																																																			NOVEL	BMPR2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000257744.1	6	2.406098	KEEP	0	0	0	8	221	TT	0.99257	0.289832	0		+	3	60	89	1	0	6.979226	13	60	386	35	ENST00000374574.2	0.1875	0.292001
FAM117B	150864	__UNKNOWN__	__UNKNOWN__	2	203604643	203604643	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203604643T>C	ENST00000392238.2	+	4	960				FAM117B_ENST00000303116.6_Intron			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	NA		NA								breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						acctgtaatctcagcactttg	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439	150864			14440	protein-coding gene	gene with protein product		NA	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13	ALS2CR13	NA	11586298	Standard	NM_173511	NM_173511	NA	Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.960+13557T>C	chr2.hg19:g.203604643T>C		NA	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	hg19	CCDS33362.2	0.02	-0.184205	ATCxCAG	COVERED																																																																																			NOVEL	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335888.3	12	2.70745	KEEP	0	0	0	9	259	TT	0.99254	0.420319	0		+	3	60	99	0	0	7.978765	13	60	404	40	ENST00000392238.2	0.1875	0.423478
ICA1L	130026	__UNKNOWN__	__UNKNOWN__	2	203642056	203642056	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203642056G>A	ENST00000392237.2	-	0	3806					NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	NA		NA								breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						gattacaggcgtgagccacca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596	130026			14442	protein-coding gene	gene with protein product		NA	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15, amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14	ALS2CR15, ALS2CR14	NA	11586298	Standard	NM_138468	NM_138468	NA	Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.*2200C>T	chr2.hg19:g.203642056G>A		NA	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	hg19	CCDS2354.1	0.02	1.500101	GGCxTGA	COVERED																																																																																			NOVEL	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256330.1	10	4.813159	KEEP	1	0	0	16	470	GG	0.997832	0.977402	0		-	4	60	123	0	0	8.160916	46	60	1395	98	ENST00000392237.2	0.08	0.979526
WDR12	55759	__UNKNOWN__	__UNKNOWN__	2	203872279	203872279	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203872279T>C	ENST00000477723.1	-	1	242									WD repeat domain 12	NA		NA								endometrium(3)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)	13						ggggtttcactatgttggcca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF242546	CCDS2356.1	2q33.1	2013-01-09			ENSG00000138442	ENSG00000138442	55759		WD repeat domain containing	14098	protein-coding gene	gene with protein product		NA			NA	16043514, 17353269	Standard	NM_018256	NM_018256	NA	Approved	YTM1, FLJ10881	uc002uzl.3	Q9GZL7	OTTHUMG00000132855	ENST00000477723.1:c.464+7000A>G	chr2.hg19:g.203872279T>C		NA		hg19		0.02	-0.122787	CACxATG	COVERED																																																																																			NOVEL	WDR12-009	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340348.1	3	2.705998	KEEP	1	0	0	9	238	TT	0.99257	0.194853	0		-	3	60	86	0	0	6.982161	10	60	295	24	ENST00000477723.1	0.230769	0.196312
NBEAL1	65065	__UNKNOWN__	__UNKNOWN__	2	203963819	203963819	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:203963819A>T	ENST00000449802.1	+	11	1431					NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	NA		NA								NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						accaacatggagaaaccctgt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426	65065		WD repeat domain containing	20681	protein-coding gene	gene with protein product		609816	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17, amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16	ALS2CR17, ALS2CR16	NA	15193433	Standard		NM_001114132	NA	Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.1099-533A>T	chr2.hg19:g.203963819A>T		NA	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	hg19	CCDS46495.1	0.02	-0.105242	TGGxGAA	UNCOVERED																																																																																			NOVEL	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333982.4	6	2.40548	KEEP	5	0	0	8	211	AA	0	0	0		+	3	60	82	0	0	6.70114	9	60	273	29	ENST00000449802.1	0.25	0.139832
CYP20A1	57404	__UNKNOWN__	__UNKNOWN__	2	204131994	204131994	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:204131994A>G	ENST00000429815.2	+	5	681				CYP20A1_ENST00000461371.1_Intron|CYP20A1_ENST00000356079.4_Intron			Q6UW02	CP20A_HUMAN	cytochrome P450, family 20, subfamily A, polypeptide 1	NA		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			cervix(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	11						ggtggctcacacctgtaatcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK021770	CCDS2357.1	2q33	2008-02-05			ENSG00000119004	ENSG00000119004	57404		Cytochrome P450s	20576	protein-coding gene	gene with protein product		NA			NA		Standard	NM_020674	NM_177538	NA	Approved	CYP-M	uc002uzv.4	Q6UW02	OTTHUMG00000132854	ENST00000429815.2:c.600+590A>G	chr2.hg19:g.204131994A>G		NA	Q4ZG61|Q8N4Q8|Q8WWA9|Q9HC04	hg19		0.02	-0.219201	CACxCCT	COVERED																																																																																			NOVEL	CYP20A1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336102.1	11	2.705487	KEEP	1	0	0	9	234	AA	0.99254	0.548763	0		+	3	60	97	0	0	7.327693	19	60	550	46	ENST00000429815.2	0.136364	0.552887
ABI2	10152	__UNKNOWN__	__UNKNOWN__	2	204268675	204268675	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:204268675T>C	ENST00000422511.2	+	9	1124				ABI2_ENST00000261016.6_Intron|ABI2_ENST00000430574.1_Intron|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Intron|ABI2_ENST00000295851.5_Intron|ABI2_ENST00000261017.5_Intron|ABI2_ENST00000430418.1_Intron|ABI2_ENST00000261018.7_Intron			Q9NYB9	ABI2_HUMAN	abl-interactor 2	NA		NA			actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						agggtttcactatgttggcca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443	10152			24011	protein-coding gene	gene with protein product		606442			NA	7590236, 10964520	Standard	NM_005759	XM_005246217	NA	Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1093+1218T>C	chr2.hg19:g.204268675T>C		NA	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	hg19		0.02	-0.175405	CACxATG	COVERED																																																																																			NOVEL	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336179.2	4	2.405348	KEEP	0	0	0	8	210	TT	0.99257	0.384528	0		+	3	51	91	0	0	7.010591	15	60	434	33	ENST00000422511.2	0.166667	0.387407
ABI2	10152	__UNKNOWN__	__UNKNOWN__	2	204285338	204285338	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:204285338A>G	ENST00000422511.2	+	10	1298				ABI2_ENST00000261016.6_Intron|RAPH1_ENST00000457812.1_Intron|ABI2_ENST00000424558.1_Intron|ABI2_ENST00000295851.5_Intron|ABI2_ENST00000261017.5_Intron|ABI2_ENST00000430418.1_Intron|ABI2_ENST00000261018.7_Intron			Q9NYB9	ABI2_HUMAN	abl-interactor 2	NA		NA			actin polymerization or depolymerization (GO:0008154)|cell migration (GO:0016477)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|Rac protein signal transduction (GO:0016601)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|SCAR complex (GO:0031209)	cytoskeletal adaptor activity (GO:0008093)|DNA binding (GO:0003677)|kinase binding (GO:0019900)|proline-rich region binding (GO:0070064)|protein complex binding (GO:0032403)|SH3 domain binding (GO:0017124)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(3)|large_intestine(1)|liver(2)|lung(4)|prostate(2)|skin(1)|urinary_tract(1)	15						ggatggtctcaatctcctgac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF260261	CCDS2358.1, CCDS63093.1, CCDS63094.1, CCDS74634.1	2q33	2010-09-20	2009-07-23		ENSG00000138443	ENSG00000138443	10152			24011	protein-coding gene	gene with protein product		606442			NA	7590236, 10964520	Standard	NM_005759	XM_005246217	NA	Approved	ABI-2, AIP-1, ABI2B, AblBP3, argBPIA, SSH3BP2	uc002uzz.3	Q9NYB9	OTTHUMG00000132879	ENST00000422511.2:c.1267+3534A>G	chr2.hg19:g.204285338A>G		NA	B4DSN1|Q13147|Q13249|Q13801|Q9BV70	hg19		0.02	-0.254273	CTCxATC	COVERED																																																																																			NOVEL	ABI2-007	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336179.2	11	3.910374	KEEP	8	0	0	13	365	AA	0.993072	0.663892	0		+	4	30	124	0	0	9.258769	25	60	731	74	ENST00000422511.2	0.137931	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	204445156	204445156	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:204445156A>G			NA	NA				RAPH1 (45023 upstream) : CD28 (126041 downstream)						NA		NA									NA						aggctgaggcaggtggatcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.204445156A>G		NA		hg19		0.02	-0.175411	GGCxGGT	COVERED																																																																																			NOVEL					0			9	4.812658	KEEP	1	0	0	16	451	AA	0.99649	0.386047	0			3	60	91	1	0	7.17947	13	60	395	55		0.1875	0.387407
PARD3B	117583	__UNKNOWN__	__UNKNOWN__	2	206107837	206107837	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206107837A>C	ENST00000351153.1	+	16	2140				PARD3B_ENST00000406610.2_Intron|PARD3B_ENST00000358768.2_Intron|PARD3B_ENST00000349953.3_Intron|PARD3B_ENST00000462231.1_Intron			Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		ttgcagtgagacgagatcgtg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117	117583			14446	protein-coding gene	gene with protein product		NA	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19, par-3 partitioning defective 3 homolog B (C. elegans)	ALS2CR19	NA	11586298, 12459187	Standard	NM_057177	NM_057177	NA	Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000351153.1:c.2141-2665A>C	chr2.hg19:g.206107837A>C		NA	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	hg19	CCDS42805.1	0.02	-0.114017	GAGxCGA	UNCOVERED																																																																																			NOVEL	PARD3B-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335994.1	6	2.405635	KEEP	1	0	0	8	216	AA	0.99257	0.16126	0		+	3	55	101	0	0	8.878812	7	60	204	32	ENST00000351153.1	0.3	0.162467
PARD3B	117583	__UNKNOWN__	__UNKNOWN__	2	206233154	206233154	__UNKNOWN__	Intron	SNP	T	T	C	rs529985306		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206233154T>C	ENST00000351153.1	+	18	2423				PARD3B_ENST00000406610.2_Intron|PARD3B_ENST00000358768.2_Intron|PARD3B_ENST00000349953.3_Intron			Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		gccaggagtttaagaccagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117	117583			14446	protein-coding gene	gene with protein product		NA	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19, par-3 partitioning defective 3 homolog B (C. elegans)	ALS2CR19	NA	11586298, 12459187	Standard	NM_057177	NM_057177	NA	Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000351153.1:c.2424-32583T>C	chr2.hg19:g.206233154T>C		NA	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	hg19	CCDS42805.1	0.02	-0.114017	GTTxAAG	UNCOVERED																																																																																			NOVEL	PARD3B-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335994.1	7	3.30763	KEEP	1	0	0	11	292	TT	0.992708	0.161282	0		+	3	60	101	0	0	8.732732	8	60	229	33	ENST00000351153.1	0.272727	0.162467
INO80D	54891	__UNKNOWN__	__UNKNOWN__	2	206925564	206925564	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206925564G>A	ENST00000403263.1	-	3	623					NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	NA		NA			DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						gattacaggcgtgagccaccg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933	54891		INO80 complex subunits	25997	protein-coding gene	gene with protein product		NA			NA	16230350	Standard	NM_017759	NM_017759	NA	Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.218+1958C>T	chr2.hg19:g.206925564G>A		NA	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	hg19	CCDS46500.1	0.02	-0.184184	GGCxTGA	COVERED																																																																																			NOVEL	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336459.1	8	2.707623	KEEP	2	0	0	9	264	GG	0.99254	0.420319	0		-	3	60	84	0	0	6.311205	15	60	487	44	ENST00000403263.1	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	206972109	206972109	__UNKNOWN__	IGR	SNP	C	C	T	rs571529534	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206972109C>T			NA	NA				AC007383.3 (20821 upstream) : NDUFS1 (7431 downstream)						NA		NA									NA						ccaccacacccggctaatttt	0.547		NA											C|||	2	0.000399361	0.0	0.0014	5008	,	,	NA	13671	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.206972109C>T		NA		hg19		0.02	-0.096489	ACCxGGC	UNCOVERED																																																																																			NOVEL					0			11	3.910768	KEEP	6	0	0	13	379	CC	0.99254	0.119538	0			3	60	92	0	0	7.978489	7	60	225	34		0.3	0.120436
NDUFS1	4719	__UNKNOWN__	__UNKNOWN__	2	206981536	206981536	__UNKNOWN__	3'UTR	SNP	G	G	A	rs34133956	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206981536G>A	ENST00000233190.6	-	0	9823				AC007383.4_ENST00000453039.1_RNA	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	NA		NA			apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						atgaggtcaggagtttgagac	0.478		NA											G|||	2304	0.460064	0.6483	0.5778	5008	,	,	NA	14681	0.2609	NA	0.4771	False	NA	,,,	NA	NA	NA	2504	0.3098	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	4719	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7707	protein-coding gene	gene with protein product	complex I 75kDa subunit, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	157655	NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)		NA	1935949	Standard	NM_005006	NM_005006	NA	Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.*7373C>T	chr2.hg19:g.206981536G>A		NA	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	hg19	CCDS2366.1	0.02	-0.105265	CAGxAGT	UNCOVERED																																																																																			NOVEL	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256391.4	4	2.40561	KEEP	4	0	0	8	239	GG	0	0	0		-	3	60	89	0	0	7.843097	6	60	211	30	ENST00000233190.6	0.333333	0.139832
NDUFS1	4719	__UNKNOWN__	__UNKNOWN__	2	206987319	206987319	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206987319T>C	ENST00000233190.6	-	0	4040					NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	NA		NA			apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						tgccactgcattccagccttg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	4719	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7707	protein-coding gene	gene with protein product	complex I 75kDa subunit, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	157655	NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)		NA	1935949	Standard	NM_005006	NM_005006	NA	Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.*1590A>G	chr2.hg19:g.206987319T>C		NA	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	hg19	CCDS2366.1	0.02	1.321529	GCAxTCC	COVERED																																																																																			NOVEL	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256391.4	16	17.656665	KEEP	11	4	117	100	2568	TT	1	0.999962	0		-	6	60	195	0	0	12.982611	78	60	2124	245	ENST00000233190.6	0.071429	0.999962
NDUFS1	4719	__UNKNOWN__	__UNKNOWN__	2	206987340	206987340	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:206987340T>C	ENST00000233190.6	-	0	4019					NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	NA		NA			apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ggtgacagagtaagactccat	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	4719	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7707	protein-coding gene	gene with protein product	complex I 75kDa subunit, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	157655	NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)		NA	1935949	Standard	NM_005006	NM_005006	NA	Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.*1569A>G	chr2.hg19:g.206987340T>C		NA	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	hg19	CCDS2366.1	0.02	3.59312	GAGxAAG	COVERED																																																																																			NOVEL	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256391.4	15	14.229429	KEEP	12	7	200	118	2932	TT	1	0.999968	0		-	5	60	162	0	1	10.361305	79	60	2125	302	ENST00000233190.6	0.059524	0.999968
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	207115676	207115676	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:207115676T>C			NA	NA				RN7SKP200 (29318 upstream) : RN7SKP260 (9113 downstream)						NA		NA									NA						gtagctgggattacaggcacg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.207115676T>C		NA		hg19		0.02	-0.061385	GGAxTAC	UNCOVERED																																																																																			NOVEL					0			3	2.705826	KEEP	1	0	0	9	238	TT	0.99257	0.043461	0			2	60	69	0	0	6.393139	3	60	84	22		0.4	0.043787
CPO	130749	__UNKNOWN__	__UNKNOWN__	2	207823081	207823081	__UNKNOWN__	Silent	SNP	C	C	T	rs375384008		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:207823081C>T	ENST00000272852.3	+	4	370	c.324C>T	c.(322-324)caC>caT	p.H108H		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	108		NA				extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		GTGGAATTCACGCCAGAGAAT	0.408		NA											C|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	20791	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0								C		0,4406		0,0,2203	215	203	207		324	-2	1	2		207	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CPO	NM_173077.2		0,1,6502	TT,TC,CC	NA	0.0116,0.0,0.0077		108/375	207823081	1,13005	2203	4300	6503	SO:0001819	synonymous_variant				CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410	130749			21011	protein-coding gene	gene with protein product	metallocarboxypeptidase O, metallocarboxypeptidase C	609563			NA	11836249	Standard	NM_173077	NM_173077	NA	Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.324C>T	chr2.hg19:g.207823081C>T		NA	Q2M277|Q7RTW7	hg19	CCDS2372.1	0.02	1.18163	TCAxGCC	COVERED																																																																																			NOVEL	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000202040.2	4	12.03163	KEEP	0	0	0	40	1158	CC	1	0.999317	0		+	5	60	145	0	0	8.832094	73	60	2442	185	ENST00000272852.3	0.064103	0.999317
METTL21A	151194	__UNKNOWN__	__UNKNOWN__	2	208477090	208477090	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:208477090G>C	ENST00000432416.1	-	3	348				METTL21A_ENST00000448007.2_3'UTR|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000411432.1_3'UTR|METTL21A_ENST00000477919.1_5'UTR			Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	NA		NA			peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						tcccaaagtggtgggattaca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401	151194			30476	protein-coding gene	gene with protein product	Hepatocellular carcinoma-associated antigen 557b, heat shock protein 70kDa lysine (K) methyltransferase	615257	family with sequence similarity 119, member A	FAM119A	NA	23921388	Standard	NM_145280	NM_145280	NA	Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000432416.1:c.259+9439C>G	chr2.hg19:g.208477090G>C		NA	Q53RV0|Q8N1Z9|Q96GH6	hg19		0.02	-0.210548	GTGxTGG	COVERED																																																																																			NOVEL	METTL21A-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000337043.1	10	3.911616	KEEP	6	0	0	13	399	GG	0.99257	0.54878	0		-	3	60	106	0	0	8.4328	16	60	553	54	ENST00000432416.1	0.157895	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	208507158	208507158	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:208507158G>A			NA	NA				METTL21A (16507 upstream) : AC079767.4 (19940 downstream)						NA		NA									NA						ttgggaggccgaggcgggtgg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.208507158G>A		NA		hg19		0.02	-0.105256	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			6	3.910952	KEEP	4	0	0	13	380	GG	0.993072	0.138863	0			3	60	86	0	0	7.232205	8	60	256	38		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	208568050	208568050	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:208568050A>G			NA	NA				Y_RNA (15267 upstream) : CCNYL1 (8213 downstream)						NA		NA									NA						agtgactcacacctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.208568050A>G		NA		hg19		0.02	-0.192905	CACxCCT	COVERED																																																																																			NOVEL					0			8	2.704152	KEEP	1	0	0	9	252	AA	0.99254	0.454342	0			3	60	102	0	0	8.279122	13	60	372	44		0.1875	0.457757
PLEKHM3	389072	__UNKNOWN__	__UNKNOWN__	2	208705944	208705944	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:208705944C>A	ENST00000427836.2	-	8	2598					NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	NA		NA			intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						taatcccagccctttgggagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385	389072		Pleckstrin homology (PH) domain containing	34006	protein-coding gene	gene with protein product	differentiation associated protein	NA	pleckstrin homology domain containing, family M, member 1-like	PLEKHM1L	NA	19028694	Standard	NM_001080475	NM_001080475	NA	Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.2109-12724G>T	chr2.hg19:g.208705944C>A		NA	B9EKV2|Q8WW68	hg19	CCDS42808.1	0.02	-0.131579	AGCxCTT	COVERED																																																																																			NOVEL	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337036.1	4	2.407127	KEEP	0	0	0	8	245	CC	0.99257	0.22747	0		-	3	60	86	0	0	7.232069	8	60	276	31	ENST00000427836.2	0.272727	0.229173
PLEKHM3	389072	__UNKNOWN__	__UNKNOWN__	2	208724546	208724546	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:208724546C>T	ENST00000427836.2	-	7	2598				PLEKHM3_ENST00000389247.4_Intron	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	NA		NA			intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ggtcttgaacccctgacctca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385	389072		Pleckstrin homology (PH) domain containing	34006	protein-coding gene	gene with protein product	differentiation associated protein	NA	pleckstrin homology domain containing, family M, member 1-like	PLEKHM1L	NA	19028694	Standard	NM_001080475	NM_001080475	NA	Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.2108+1282G>A	chr2.hg19:g.208724546C>T		NA	B9EKV2|Q8WW68	hg19	CCDS42808.1	0.02	-0.131577	AACxCCT	COVERED																																																																																			NOVEL	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337036.1	8	3.911666	KEEP	0	0	0	13	400	CC	0.994391	0.227888	0		-	3	40	85	0	0	6.672488	12	60	408	44	ENST00000427836.2	0.2	0.229173
PLEKHM3	389072	__UNKNOWN__	__UNKNOWN__	2	208748788	208748788	__UNKNOWN__	Intron	SNP	C	C	T	rs148188667	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:208748788C>T	ENST00000427836.2	-	7	2440				PLEKHM3_ENST00000389247.4_Intron	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	NA		NA			intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						tttgggaggccgaggtgggag	0.527		NA											C|||	113	0.0225639	0.0802	0.0101	5008	,	,	NA	12208	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385	389072		Pleckstrin homology (PH) domain containing	34006	protein-coding gene	gene with protein product	differentiation associated protein	NA	pleckstrin homology domain containing, family M, member 1-like	PLEKHM1L	NA	19028694	Standard	NM_001080475	NM_001080475	NA	Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1951-22802G>A	chr2.hg19:g.208748788C>T		NA	B9EKV2|Q8WW68	hg19	CCDS42808.1	0.02	-0.140347	GGCxGAG	COVERED																																																																																			NOVEL	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337036.1	10	3.006529	KEEP	0	0	0	10	272	CC	0.992708	0.259062	0		-	3	60	86	0	0	6.872977	11	60	368	33	ENST00000427836.2	0.214286	0.260965
ERBB4	2066	__UNKNOWN__	__UNKNOWN__	2	212419932	212419932	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:212419932C>T	ENST00000342788.4	-	20	2798				ERBB4_ENST00000402597.1_Intron|ERBB4_ENST00000436443.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	NA		NA			cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ttttttgagacggagtttcgc	0.488		NA								TSP Lung(8;0.080)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568	2066			3432	protein-coding gene	gene with protein product		600543	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4		NA	7700649, 17018285	Standard	NM_001042599	NM_001042599	NA	Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.2487+6695G>A	chr2.hg19:g.212419932C>T		NA	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	hg19	CCDS2394.1	0.02	-0.175179	AGAxGGA	UNCOVERED																																																																																			NOVEL	ERBB4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256597.1	7	2.405942	KEEP	2	0	0	8	225	CC	0	0	0		-	4	60	121	0	0	9.765952	15	60	468	44	ENST00000342788.4	0.210526	0.387407
ERBB4	2066	__UNKNOWN__	__UNKNOWN__	2	212934608	212934608	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:212934608T>C	ENST00000342788.4	-	2	545				ERBB4_ENST00000402597.1_Intron|ERBB4_ENST00000436443.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	NA		NA			cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	tttgggaggctgaggtgagag	0.398		NA								TSP Lung(8;0.080)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568	2066			3432	protein-coding gene	gene with protein product		600543	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4		NA	7700649, 17018285	Standard	NM_001042599	NM_001042599	NA	Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.234+54868A>G	chr2.hg19:g.212934608T>C		NA	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	hg19	CCDS2394.1	0.02	-0.175425	GGCxGAG	COVERED																																																																																			NOVEL	ERBB4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256597.1	4	2.406138	KEEP	0	0	0	8	221	TT	0.99257	0.384528	0		-	3	60	94	0	0	7.478934	13	60	398	39	ENST00000342788.4	0.1875	0.387407
ERBB4	2066	__UNKNOWN__	__UNKNOWN__	2	213071560	213071560	__UNKNOWN__	Intron	SNP	A	A	G	rs62182598	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:213071560A>G	ENST00000342788.4	-	2	393				ERBB4_ENST00000402597.1_Intron|ERBB4_ENST00000436443.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	NA		NA			cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	tgatccgcccacctcggcctc	0.493		NA								TSP Lung(8;0.080)			A|||	505	0.100839	0.0885	0.1066	5008	,	,	NA	13425	0.005	NA	0.2336	False	NA	,,,	NA	NA	NA	2504	0.0757	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568	2066			3432	protein-coding gene	gene with protein product		600543	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4		NA	7700649, 17018285	Standard	NM_001042599	NM_001042599	NA	Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.83-81932T>C	chr2.hg19:g.213071560A>G		NA	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	hg19	CCDS2394.1	0.02	-0.140333	CCCxCCT	UNCOVERED																																																																																			NOVEL	ERBB4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256597.1	2	2.405855	KEEP	6	0	0	8	221	AA	0	0	0		-	5	60	175	0	0	15.7397	10	60	297	45	ENST00000342788.4	0.333333	0.260965
ERBB4	2066	__UNKNOWN__	__UNKNOWN__	2	213071570	213071570	__UNKNOWN__	Intron	SNP	C	C	T	rs62182599	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:213071570C>T	ENST00000342788.4	-	2	393				ERBB4_ENST00000402597.1_Intron|ERBB4_ENST00000436443.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	NA		NA			cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	acctcggcctcccaaagtgct	0.473		NA								TSP Lung(8;0.080)			C|||	506	0.101038	0.0893	0.1066	5008	,	,	NA	13590	0.005	NA	0.2336	False	NA	,,,	NA	NA	NA	2504	0.0757	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568	2066			3432	protein-coding gene	gene with protein product		600543	v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4		NA	7700649, 17018285	Standard	NM_001042599	NM_001042599	NA	Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.83-81942G>A	chr2.hg19:g.213071570C>T		NA	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	hg19	CCDS2394.1	0.02	-0.149125	CCTxCCA	UNCOVERED																																																																																			NOVEL	ERBB4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256597.1	2	2.708162	KEEP	6	0	0	9	281	CC	0	0	0		-	6	60	183	0	0	16.564799	10	60	351	49	ENST00000342788.4	0.375	0.292001
RP11-105N14.2	0	__UNKNOWN__	__UNKNOWN__	2	214132233	214132233	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:214132233T>C	ENST00000606960.1	-	0	81										NA		NA									NA						ggattacaggtgtgagccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000606960.1:	chr2.hg19:g.214132233T>C		NA		hg19		0.02	-0.210473	AGGxGTG	COVERED																																																																																			NOVEL	RP11-105N14.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000470662.1	3	2.406609	KEEP	0	0	0	8	230	TT	0.99257	0.518282	0		-	3	60	102	0	0	7.76492	20	60	596	53	ENST00000606960.1	0.130435	0.522161
FN1	2335	__UNKNOWN__	__UNKNOWN__	2	216250012	216250012	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:216250012T>C	ENST00000354785.4	-	29	4982				FN1_ENST00000443816.1_Intron|FN1_ENST00000323926.6_Intron|FN1_ENST00000432072.2_Intron|FN1_ENST00000356005.4_Intron|FN1_ENST00000421182.1_Intron|FN1_ENST00000346544.3_Intron|FN1_ENST00000336916.4_Intron|FN1_ENST00000446046.1_Intron|FN1_ENST00000357867.4_Intron|FN1_ENST00000359671.1_Intron|FN1_ENST00000357009.2_Intron|FN1_ENST00000345488.5_Intron			P02751	FINC_HUMAN	fibronectin 1	NA		NA			acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	Aggccgggcgtggtggctcac	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414	2335		Fibronectin type III domain containing, Endogenous ligands	3778	protein-coding gene	gene with protein product	migration-stimulating factor, cold-insoluble globulin	135600			NA	2992939, 3003095	Standard	NM_212476	NM_054034	NA	Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000354785.4:c.4613-313A>G	chr2.hg19:g.216250012T>C		NA	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	hg19	CCDS42814.1	0.02	-0.184114	GCGxGGT	COVERED																																																																																			NOVEL	FN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256667.2	8	3.605374	KEEP	2	0	0	12	305	TT	0.993072	0.420544	0		-	3	60	98	0	0	7.561593	17	60	472	49	ENST00000354785.4	0.15	0.423478
LINC00607	646324	__UNKNOWN__	__UNKNOWN__	2	216511548	216511548	__UNKNOWN__	lincRNA	SNP	G	G	A	rs60922357	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:216511548G>A	ENST00000445174.1	-	0	723				AC012668.2_ENST00000417485.2_lincRNA	NR_037195.1				long intergenic non-protein coding RNA 607	NA		NA									NA						tgtaatcccagcactttggga	0.493		NA											G|||	1323	0.264177	0.3124	0.2334	5008	,	,	NA	17215	0.1925	NA	0.2256	False	NA	,,,	NA	NA	NA	2504	0.3344	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK091865		2q35	2012-10-12			ENSG00000235770	ENSG00000235770	646324		Long non-coding RNAs	43944	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_037195	NR_037195	NA	Approved		uc002vfm.1		OTTHUMG00000154834	ENST00000445174.1:	chr2.hg19:g.216511548G>A		NA		hg19		0.02	-0.114035	CCAxCAC	UNCOVERED																																																																																			NOVEL	LINC00607-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000337314.1	11	2.7079	KEEP	4	0	0	9	270	GG	0	0	0		-	4	60	121	0	0	10.876493	7	60	240	28	ENST00000445174.1	0.363636	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	216787240	216787240	__UNKNOWN__	IGR	SNP	C	C	A	rs4527195	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:216787240C>A			NA	NA				AC122136.1 (43598 upstream) : AC093382.1 (16790 downstream)						NA		NA									NA						cctggctcatcctggctcaaa	0.473		NA											-|||	1434	0.286342	0.3533	0.2882	5008	,	,	NA	19157	0.0694	NA	0.4443	False	NA	,,,	NA	NA	NA	2504	0.2556	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.216787240C>A		NA		hg19		0.02	-0.122802	CATxCTG	UNCOVERED																																																																																			NOVEL					0			10	3.309855	KEEP	28	0	0	11	344	CC	0	0	0			9	56	271	0	0	27.906189	4	42	140	69		0.692308	0.196312
MREG	55686	__UNKNOWN__	__UNKNOWN__	2	216833733	216833733	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:216833733T>C	ENST00000263268.6	-	3	551					NM_018000.2	NP_060470.2	Q8N565	MREG_HUMAN	melanoregulin	NA		NA				plasma membrane (GO:0005886)				large_intestine(1)|lung(2)	3		Renal(323;0.0328)		Epithelial(149;4.64e-07)|all cancers(144;5.56e-05)|LUSC - Lung squamous cell carcinoma(224;0.00832)|Lung(261;0.0111)		cctcctgccttagcctcccaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000978	CCDS46513.1	2q35	2013-09-27			ENSG00000118242	ENSG00000118242	55686			25478	protein-coding gene	gene with protein product		609207			NA	19240024, 22275436	Standard	NM_018000	NM_018000	NA	Approved	FLJ10116, DSU, WDT2	uc002vfo.3	Q8N565	OTTHUMG00000154828	ENST00000263268.6:c.256-21897A>G	chr2.hg19:g.216833733T>C		NA	Q53R89|Q53TC1|Q5XKB6|Q9NWC9|Q9P1S1	hg19	CCDS46513.1	0.02	-0.043858	CCTxAGC	UNCOVERED																																																																																			NOVEL	MREG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337297.1	3	3.006992	KEEP	0	0	0	10	270	TT	0.992708	0.023898	0		-	2	32	67	0	0	6.450085	2	60	62	23	ENST00000263268.6	0.5	0.024074
PECR	55825	__UNKNOWN__	__UNKNOWN__	2	216913067	216913067	__UNKNOWN__	Intron	SNP	G	G	C	rs182591763	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:216913067G>C	ENST00000265322.7	-	6	789					NM_018441.5	NP_060911.2	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	NA		NA			fatty acid biosynthetic process (GO:0006633)|oxidation-reduction process (GO:0055114)|phytol metabolic process (GO:0033306)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			endometrium(2)|kidney(1)|liver(1)|lung(9)|stomach(1)	14		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	caaagtgctgggattacaggc	0.463		NA											g|||	103	0.0205671	0.0045	0.0562	5008	,	,	NA	10379	0.001	NA	0.0368	False	NA	,,,	NA	NA	NA	2504	0.0204	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF119841	CCDS33375.1	2q35	2011-09-14			ENSG00000115425	ENSG00000115425	55825	1.3.1.38	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1	18281	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 29C, member 1	605843			NA	10811639, 11669066, 19027726	Standard	NM_018441	NM_018441	NA	Approved	HSA250303, TERP, SDR29C1	uc002vft.3	Q9BY49	OTTHUMG00000154825	ENST00000265322.7:c.714+918C>G	chr2.hg19:g.216913067G>C		NA	B2RE42|Q53TC4|Q6IAK9|Q9NRD4|Q9NY60|Q9P1A4	hg19	CCDS33375.1	0.02	-0.149114	CTGxGAT	COVERED																																																																																			NOVEL	PECR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337277.1	2	2.707803	KEEP	2	0	0	9	269	GG	0.99257	0.289832	0		-	5	60	168	0	0	15.03955	10	60	317	43	ENST00000265322.7	0.333333	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	217121648	217121648	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:217121648C>T			NA	NA				RP11-566E18.3 (36733 upstream) : MARCH4 (939 downstream)						NA		NA									NA						cccaggctggcctcaaactcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.217121648C>T		NA		hg19		0.02	-0.210537	TGGxCTC	COVERED																																																																																			NOVEL					0			9	4.212154	KEEP	1	0	0	14	419	CC	0.994391	0.519232	0			3	60	89	0	0	6.592637	18	60	611	52		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	217873374	217873374	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:217873374A>G			NA	NA				RP11-574O16.1 (12161 upstream) : AC010887.1 (167846 downstream)						NA		NA									NA						gggattacagatgtgagccac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.217873374A>G		NA		hg19		0.02	-0.122765	CAGxTGT	COVERED																																																																																			NOVEL					0			3	3.608953	KEEP	0	0	0	12	328	AA	0.993634	0.195062	0			3	60	98	0	0	8.073299	11	60	316	38		0.214286	0.196312
DIRC3	729582	__UNKNOWN__	__UNKNOWN__	2	218186727	218186727	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:218186727T>C	ENST00000474063.1	-	10	1739				AC009492.1_ENST00000452813.1_lincRNA					disrupted in renal carcinoma 3	NA		NA									NA						ggattacaggtgtgagccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024261		2q35	2013-01-16			ENSG00000231672	ENSG00000231672	729582			17805	other	unknown		608262			NA	12939738	Standard	NR_026597	NR_026597	NA	Approved	FLJ14199	uc002vgo.3		OTTHUMG00000155287	ENST00000474063.1:c.1340-2827A>G	chr2.hg19:g.218186727T>C		NA		hg19		0.02	-0.245581	AGGxGTG	COVERED																																																																																			NOVEL	DIRC3-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000339331.1	10	3.308569	KEEP	2	0	0	11	306	TT	0.992708	0.63667	0		-	4	60	139	0	0	10.890897	23	60	678	58	ENST00000474063.1	0.148148	0.641347
TNS1	7145	__UNKNOWN__	__UNKNOWN__	2	218694057	218694057	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:218694057G>A	ENST00000419504.1	-	20	3184				TNS1_ENST00000171887.4_Intron|TNS1_ENST00000430930.1_Intron			Q9HBL0	TENS1_HUMAN	tensin 1	NA		NA			cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		gcagtgagccgagatcgtgcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308	7145		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs, SH2 domain containing	11973	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 155	600076	tensin, matrix-remodelling associated 6	TNS, MXRA6	NA		Standard	NM_022648	NM_022648	NA	Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000419504.1:c.3022+1032C>T	chr2.hg19:g.218694057G>A		NA	Q4ZG71|Q6IPI5	hg19		0.02	-0.2368	GCCxAGA	COVERED																																																																																			NOVEL	TNS1-004	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000339207.1	10	3.910616	KEEP	5	0	0	13	381	GG	0.993072	0.608164	0		-	3	60	95	0	0	7.065055	20	60	621	60	ENST00000419504.1	0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	219239546	219239546	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:219239546T>C			NA	NA				C2orf62 (6724 upstream) : SLC11A1 (7205 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.219239546T>C		NA		hg19		0.02	-0.324416	AGGxGTG	COVERED																																																																																			NOVEL					0			14	5.111286	KEEP	1	0	0	17	457	TT	0.997832	0.833904	0			4	60	134	0	0	10.258037	25	60	696	78		0.137931	0.835716
USP37	57695	__UNKNOWN__	__UNKNOWN__	2	219362377	219362377	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:219362377A>T	ENST00000415516.1	-	12	1494				USP37_ENST00000454775.1_Intron|USP37_ENST00000418019.1_Intron|USP37_ENST00000258399.3_Intron			Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	NA		NA			G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		ctgcccacctaggcctcccaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913	57695		Ubiquitin-specific peptidases	20063	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 37		NA	12838346	Standard	NM_020935	NM_020935	NA	Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000415516.1:c.1065+79T>A	chr2.hg19:g.219362377A>T		NA	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	hg19		0.02	-0.403381	CCTxGGC	COVERED																																																																																			NOVEL	USP37-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000338136.2	12	6.915887	KEEP	1	0	0	23	618	AA	0.999909	0.941656	0		-	5	60	130	0	0	8.68423	38	60	1103	90	ENST00000415516.1	0.116279	0.941741
USP37	57695	__UNKNOWN__	__UNKNOWN__	2	219362404	219362404	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:219362404A>G	ENST00000415516.1	-	12	1494				USP37_ENST00000454775.1_Intron|USP37_ENST00000418019.1_Intron|USP37_ENST00000258399.3_Intron			Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	NA		NA			G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		ggaattacagacgtgagccac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913	57695		Ubiquitin-specific peptidases	20063	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 37		NA	12838346	Standard	NM_020935	NM_020935	NA	Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000415516.1:c.1065+52T>C	chr2.hg19:g.219362404A>G		NA	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	hg19		0.02	1.853578	CAGxCGT	COVERED																																																																																			NOVEL	USP37-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000338136.2	17	2.370593	KEEP	1	2	60	29	803	AA	0.999997	0.98954	0		-	4	60	135	0	0	9.186159	51	60	1522	125	ENST00000415516.1	0.072727	0.989542
USP37	57695	__UNKNOWN__	__UNKNOWN__	2	219404474	219404474	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:219404474G>C	ENST00000415516.1	-	8	893				USP37_ENST00000454775.1_Intron|USP37_ENST00000418019.1_Intron|USP37_ENST00000258399.3_Intron|USP37_ENST00000338465.5_Intron			Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	NA		NA			G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)			NS(2)|breast(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(5)|stomach(1)	35		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)		gtggctcatggctgtaatccc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046814	CCDS2418.1	2q35	2008-02-05	2005-08-08		ENSG00000135913	ENSG00000135913	57695		Ubiquitin-specific peptidases	20063	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 37		NA	12838346	Standard	NM_020935	NM_020935	NA	Approved	KIAA1594	uc010fvs.1	Q86T82	OTTHUMG00000133113	ENST00000415516.1:c.465-5045C>G	chr2.hg19:g.219404474G>C		NA	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	hg19		0.02	-0.078954	ATGxCTG	UNCOVERED																																																																																			NOVEL	USP37-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000338136.2	5	2.707109	KEEP	0	0	0	9	259	GG	0.99254	0.076759	0		-	3	60	99	0	0	8.843398	6	60	208	25	ENST00000415516.1	0.333333	0.077336
PLCD4	84812	__UNKNOWN__	__UNKNOWN__	2	219489605	219489605	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:219489605A>G	ENST00000432688.1	+	6	1014				PLCD4_ENST00000417849.1_Intron|PLCD4_ENST00000450993.2_Intron			Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	NA		NA			acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		aggccgaggcaggaggatcac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	84812	3.1.4.11	EF-hand domain containing	9062	protein-coding gene	gene with protein product		605939			NA	10702683, 9056492	Standard		NM_032726	NA	Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000432688.1:c.772+2004A>G	chr2.hg19:g.219489605A>G		NA	Q53FS8	hg19		0.02	-0.149114	GGCxGGA	COVERED																																																																																			NOVEL	PLCD4-007	NOVEL	non_canonical_conserved|not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336882.1	6	2.406532	KEEP	0	0	0	8	227	AA	0.99257	0.289832	0		+	4	60	130	0	0	11.131099	11	60	336	39	ENST00000432688.1	0.266667	0.292001
NHEJ1	79840	__UNKNOWN__	__UNKNOWN__	2	220004670	220004670	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:220004670C>G	ENST00000356853.5	-	5	722				NHEJ1_ENST00000409720.1_Intron	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	NA		NA			B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		caaagtgctgcgattacaggc	0.423		NA						Non-homologous end-joining													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736	79840			25737	protein-coding gene	gene with protein product		611290			NA	16439204, 16439205	Standard	NM_024782	NM_024782	NA	Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.588+6731G>C	chr2.hg19:g.220004670C>G		NA	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	hg19	CCDS2432.1	0.02	-0.140356	CTGxGAT	COVERED																																																																																			NOVEL	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256817.2	5	2.406953	KEEP	0	0	0	8	241	CC	0.99257	0.289832	0		-	4	60	137	0	0	11.971224	10	60	318	35	ENST00000356853.5	0.285714	0.292001
NHEJ1	79840	__UNKNOWN__	__UNKNOWN__	2	220004683	220004683	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:220004683A>G	ENST00000356853.5	-	5	722				NHEJ1_ENST00000409720.1_Intron	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	NA		NA			B cell differentiation (GO:0030183)|central nervous system development (GO:0007417)|DNA recombination (GO:0006310)|double-strand break repair via nonhomologous end joining (GO:0006303)|positive regulation of ligase activity (GO:0051351)|response to ionizing radiation (GO:0010212)|T cell differentiation (GO:0030217)	nonhomologous end joining complex (GO:0070419)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		ttacaggcgtaagccaccgca	0.448		NA						Non-homologous end-joining													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ972687	CCDS2432.1	2q35	2014-09-17			ENSG00000187736	ENSG00000187736	79840			25737	protein-coding gene	gene with protein product		611290			NA	16439204, 16439205	Standard	NM_024782	NM_024782	NA	Approved	Cernunnos, XLF, FLJ12610	uc002vjp.4	Q9H9Q4	OTTHUMG00000133127	ENST00000356853.5:c.588+6718T>C	chr2.hg19:g.220004683A>G		NA	B8ZZA4|Q4ZFW7|Q6IA64|Q96JS9	hg19	CCDS2432.1	0.02	-0.140321	CGTxAGC	COVERED																																																																																			NOVEL	NHEJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256817.2	6	3.006867	KEEP	0	0	0	10	264	AA	0.992708	0.259062	0		-	3	60	104	0	0	8.673095	11	60	313	35	ENST00000356853.5	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	220207054	220207054	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:220207054T>C			NA	NA				RESP18 (9155 upstream) : DNPEP (31213 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.220207054T>C		NA		hg19		0.02	-0.14033	TCAxGCC	COVERED																																																																																			NOVEL					0			5	3.007372	KEEP	3	0	0	10	272	TT	0.99254	0.259018	0			3	60	90	0	0	7.172638	12	60	359	42		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	220521203	220521203	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:220521203T>C			NA	NA				RP11-256I23.3 (10850 upstream) : AC009502.4 (28899 downstream)						NA		NA									NA						tgttcaatcttattagctatt	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.220521203T>C		NA		hg19		0.02	-0.324401	TCTxATT	COVERED																																																																																			NOVEL					0			4	5.412601	KEEP	0	0	0	18	483	TT	0.999859	0.835598	0			11	60	339	0	0	29.52797	25	60	685	69		0.305556	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	220639017	220639017	__UNKNOWN__	IGR	SNP	C	C	T	rs377535770		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:220639017C>T			NA	NA				AC009502.4 (86950 upstream) : AC008281.1 (129754 downstream)						NA		NA									NA						gtcaggagttcgagaccagcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.220639017C>T		NA		hg19		0.02	-0.096421	GTTxGAG	UNCOVERED																																																																																			NOVEL					0			7	2.406474	KEEP	2	0	0	8	229	CC	0	0	0			3	60	77	0	0	6.332662	8	60	240	26		0.272727	0.120436
AC067956.1	0	__UNKNOWN__	__UNKNOWN__	2	221422737	221422737	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:221422737A>G	ENST00000414512.1	+	0	368										NA		NA									NA						gctcatgcctataatcccagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000414512.1:	chr2.hg19:g.221422737A>G		NA		hg19		0.02	-0.192939	CCTxTAA	COVERED																																																																																			NOVEL	AC067956.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000332710.1	7	3.007716	KEEP	2	0	0	10	277	AA	0.99257	0.454356	0		+	3	60	104	0	1	8.092127	18	60	519	47	ENST00000414512.1	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	222599964	222599964	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:222599964G>A			NA	NA				AC068489.1 (93431 upstream) : PAX3 (464642 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.222599964G>A		NA		hg19		0.02	-0.149122	GGCxTGA	COVERED																																																																																			NOVEL					0			6	3.609714	KEEP	2	0	0	12	342	GG	0.992708	0.289872	0			3	52	85	0	0	6.881919	10	60	329	45		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	223680382	223680382	__UNKNOWN__	IGR	SNP	G	G	C	rs13395673		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:223680382G>C			NA	NA				MOGAT1 (105733 upstream) : ACSL3 (45269 downstream)						NA		NA									NA						ctctccctctgcctctgcctc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.223680382G>C		NA		hg19		0.02	-0.078943	TCTxCCT	UNCOVERED																																																																																			NOVEL					0			12	3.008636	KEEP	13	0	0	10	300	GG	0	0	0			3	60	99	0	0	11.330415	0	0	0	33		1	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	223680388	223680388	__UNKNOWN__	IGR	SNP	G	G	C	rs13395752	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:223680388G>C			NA	NA				MOGAT1 (105739 upstream) : ACSL3 (45263 downstream)						NA		NA									NA						ctctgcctctgcctctgcctc	0.577		NA											-|||	2442	0.48762	0.7216	0.2896	5008	,	,	NA	11407	0.494	NA	0.3569	False	NA	,,,	NA	NA	NA	2504	0.4397	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.223680388G>C		NA		hg19		0.02	-0.078946	TCTxCCT	UNCOVERED																																																																																			NOVEL					0			12	3.309804	KEEP	13	0	0	11	334	GG	0	0	0			3	60	99	0	0	11.330699	0	0	0	35		1	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	224537581	224537581	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:224537581G>T			NA	NA				SCG2 (70360 upstream) : AP1S3 (78821 downstream)						NA		NA									NA						gctcaagcgagcctcctgcct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.224537581G>T		NA		hg19		0.02	-0.183484	CGAxCCT	COVERED																																																																																			NOVEL					0			7	3.008995	KEEP	0	0	0	10	307	CG	0.993072	0.420544	0			3	60	90	0	0	6.767419	17	60	564	44		0.15	0.423478
AP1S3	130340	__UNKNOWN__	__UNKNOWN__	2	224679533	224679533	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:224679533A>G	ENST00000446015.2	-	1	37				AP1S3_ENST00000423110.1_Intron|AP1S3_ENST00000396653.2_Intron|AP1S3_ENST00000409375.1_Intron|AP1S3_ENST00000396654.2_Intron|AP1S3_ENST00000443700.1_Intron			Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3 subunit	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane coat (GO:0030117)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			NS(1)|breast(1)|lung(2)	4		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		ttactctgtcacccaggctgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF393369	CCDS42827.1	2q36.3	2008-02-05			ENSG00000152056	ENSG00000152056	130340			18971	protein-coding gene	gene with protein product		615781			NA		Standard		NR_110905	NA	Approved		uc002vnn.3	Q96PC3	OTTHUMG00000133165	ENST00000446015.2:c.3+22631T>C	chr2.hg19:g.224679533A>G		NA	B4DQZ1|Q8WTY1|Q96DD1	hg19		0.02	-0.24556	GTCxCCC	COVERED																																																																																			NOVEL	AP1S3-008	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000383293.1	12	2.706709	KEEP	1	0	0	9	252	AA	0.99254	0.636563	0		-	3	60	103	0	0	7.748933	22	60	644	51	ENST00000446015.2	0.12	0.641347
AP1S3	130340	__UNKNOWN__	__UNKNOWN__	2	224693840	224693840	__UNKNOWN__	Intron	SNP	T	T	C	rs386655624		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:224693840T>C	ENST00000446015.2	-	1	37				AP1S3_ENST00000423110.1_Intron|AP1S3_ENST00000396653.2_Intron|AP1S3_ENST00000409375.1_Intron|AP1S3_ENST00000396654.2_Intron|AP1S3_ENST00000443700.1_Intron			Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3 subunit	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane coat (GO:0030117)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			NS(1)|breast(1)|lung(2)	4		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		catgagccactgcacccagcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF393369	CCDS42827.1	2q36.3	2008-02-05			ENSG00000152056	ENSG00000152056	130340			18971	protein-coding gene	gene with protein product		615781			NA		Standard		NR_110905	NA	Approved		uc002vnn.3	Q96PC3	OTTHUMG00000133165	ENST00000446015.2:c.3+8324A>G	chr2.hg19:g.224693840T>C		NA	B4DQZ1|Q8WTY1|Q96DD1	hg19		0.02	-0.157884	CACxGCA	COVERED																																																																																			NOVEL	AP1S3-008	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000383293.1	5	2.406011	KEEP	3	0	0	8	222	TT	0.99257	0.320408	0		-	3	60	106	0	0	8.591551	14	60	423	46	ENST00000446015.2	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	224928849	224928849	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:224928849A>G			NA	NA				SERPINE2 (24813 upstream) : AC104802.1 (175329 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.224928849A>G		NA		hg19		0.02	-0.236799	GGCxTGA	COVERED																																																																																			NOVEL					0			12	5.112934	KEEP	1	0	0	17	472	AA	0.997832	0.611079	0			3	60	103	0	0	7.80549	21	60	620	67		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	227537053	227537053	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:227537053T>C			NA	NA				MIR5702 (13544 upstream) : IRS1 (58979 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.227537053T>C		NA		hg19		0.02	-0.254337	TCAxGCC	COVERED																																																																																			NOVEL					0			11	5.413387	KEEP	3	0	0	18	493	TT	0.997832	0.667074	0			3	60	104	0	0	7.905457	21	60	611	74		0.125	0.668523
COL4A4	1286	__UNKNOWN__	__UNKNOWN__	2	228003088	228003088	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228003088G>A	ENST00000396625.3	-	4	400				COL4A4_ENST00000329662.7_Intron	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	NA		NA			axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		agtggctcacgcctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052	1286		Collagens	2206	protein-coding gene	gene with protein product	collagen of basement membrane, alpha-4 chain	120131			NA	1639407	Standard	NM_000092	NM_000092	NA	Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.192+1788C>T	chr2.hg19:g.228003088G>A		NA	A8MTZ1|Q53RW9|Q53S42|Q53WR1	hg19	CCDS42828.1	0.02	-0.219271	CACxCCT	COVERED																																																																																			NOVEL	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313770.1	9	3.609873	KEEP	0	0	0	12	352	GG	0.993634	0.549368	0		-	3	60	90	0	0	6.627861	19	60	603	47	ENST00000396625.3	0.136364	0.552887
COL4A4	1286	__UNKNOWN__	__UNKNOWN__	2	228003102	228003102	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228003102A>C	ENST00000396625.3	-	4	400				COL4A4_ENST00000329662.7_Intron	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	NA		NA			axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		gtaatcccagaactttgggag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052	1286		Collagens	2206	protein-coding gene	gene with protein product	collagen of basement membrane, alpha-4 chain	120131			NA	1639407	Standard	NM_000092	NM_000092	NA	Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.192+1774T>G	chr2.hg19:g.228003102A>C		NA	A8MTZ1|Q53RW9|Q53S42|Q53WR1	hg19	CCDS42828.1	0.02	-0.192956	CAGxACT	COVERED																																																																																			NOVEL	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313770.1	8	3.007122	KEEP	0	0	0	10	277	AA	0.992708	0.486967	0		-	3	60	107	0	0	8.533154	16	60	474	46	ENST00000396625.3	0.157895	0.490544
COL4A3	1285	__UNKNOWN__	__UNKNOWN__	2	228094493	228094493	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228094493G>A	ENST00000396578.3	+	2	249				AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		ggccgggcgcggtggctcacg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031	1285		Collagens	2204	protein-coding gene	gene with protein product	tumstatin	120070			NA	1737849	Standard	NM_000091	NM_000091	NA	Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.88-8191G>A	chr2.hg19:g.228094493G>A		NA	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	hg19	CCDS42829.1	0.02	-0.236826	CGCxGTG	COVERED																																																																																			NOVEL	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331409.2	16	3.910445	KEEP	7	0	0	13	377	GG	0.993634	0.637264	0		+	4	60	115	0	0	8.795125	19	60	613	62	ENST00000396578.3	0.173913	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	228322225	228322225	__UNKNOWN__	IGR	SNP	C	C	T	rs12616340	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228322225C>T			NA	NA				TM4SF20 (78203 upstream) : MIR5703 (14622 downstream)						NA		NA									NA						actgctaagactactggcgtg	0.473		NA											T|||	3315	0.661941	0.6853	0.6398	5008	,	,	NA	15004	0.6647	NA	0.6292	False	NA	,,,	NA	NA	NA	2504	0.6769	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.228322225C>T		NA		hg19		0.02	-0.201734	AGAxTAC	COVERED																																																																																			NOVEL					0			8	2.407123	KEEP	0	0	0	8	243	CC	0.99257	0.4869	0			11	60	319	0	0	31.528635	8	60	255	43		0.578947	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	228534018	228534018	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228534018A>G			NA	NA				C2orf83 (35982 upstream) : SLC19A3 (16552 downstream)						NA		NA									NA						agtggctcatacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.228534018A>G		NA		hg19		0.02	-0.228024	CATxCCT	COVERED																																																																																			NOVEL					0			8	3.005829	KEEP	0	0	0	10	257	AA	0.992708	0.578679	0			5	60	172	0	0	14.580976	16	60	456	52		0.238095	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	228545215	228545215	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228545215T>C			NA	NA				C2orf83 (47179 upstream) : SLC19A3 (5355 downstream)						NA		NA									NA						gtttttgagatggagtctcac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.228545215T>C		NA		hg19		0.02	-0.166619	AGAxGGA	UNCOVERED																																																																																			NOVEL					0			7	2.406302	KEEP	2	0	0	8	224	TT	0	0	0			4	60	120	0	0	9.769207	14	60	422	35		0.222222	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	228659001	228659001	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:228659001T>C			NA	NA				RNA5SP121 (31133 upstream) : CCL20 (19556 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.228659001T>C		NA		hg19		0.02	-0.105249	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			7	3.609431	KEEP	9	0	0	12	337	TT	0	0	0			3	60	97	0	0	8.20127	9	60	266	44		0.25	0.139832
AC009410.1	0	__UNKNOWN__	__UNKNOWN__	2	229430619	229430619	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:229430619A>G	ENST00000432481.2	-	0	144										NA		NA									NA						aaaaaaaaaaaaaaaaaagaa	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432481.2:	chr2.hg19:g.229430619A>G		NA		hg19		0.02	-0.070164	AAAxAAA	UNCOVERED																																																																																			NOVEL	AC009410.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000331758.2	9	2.406168	KEEP	3	0	0	8	221	AA	0	0	0		-	3	60	99	0	0	9.525359	3	60	85	19	ENST00000432481.2	0.5	0.054137
TRIP12	9320	__UNKNOWN__	__UNKNOWN__	2	230745412	230745412	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:230745412T>C	ENST00000389045.3	-	2	24				TRIP12_ENST00000389044.4_Intron|TRIP12_ENST00000283943.5_Intron|TRIP12_ENST00000409677.1_Intron|TRIP12_ENST00000543084.1_Intron			Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|embryo development (GO:0009790)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligase activity (GO:0016874)|thyroid hormone receptor binding (GO:0046966)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(19)|lung(32)|ovary(5)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		gtaatcccagtattttgggag	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L40383	CCDS33391.1, CCDS63145.1, CCDS63146.1	2q36.3	2008-05-27			ENSG00000153827	ENSG00000153827	9320			12306	protein-coding gene	gene with protein product		604506			NA	7776974	Standard	NM_004238	XM_005246961	NA	Approved	KIAA0045	uc002vpw.1	Q14669	OTTHUMG00000153623	ENST00000389045.3:c.49-568A>G	chr2.hg19:g.230745412T>C		NA	D4HL82|Q14CA3|Q14CF1|Q15644|Q53R87|Q53TE7	hg19		0.02	-0.131516	CAGxATT	COVERED																																																																																			NOVEL	TRIP12-005	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331865.1	4	2.40521	KEEP	0	0	0	8	209	TT	0.99254	0.227464	0		-	3	39	96	0	0	7.772885	12	60	339	36	ENST00000389045.3	0.2	0.229173
FBXO36	130888	__UNKNOWN__	__UNKNOWN__	2	230788706	230788706	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:230788706T>C	ENST00000373652.3	+	1	308				FBXO36_ENST00000283946.3_Intron|FBXO36_ENST00000409992.1_Intron			Q8NEA4	FBX36_HUMAN	F-box protein 36	NA		NA								endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		gtgatccgcctgcctcggcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832	130888		F-boxes /  other	27020	protein-coding gene	gene with protein product		609105	F-box only protein 36		NA	12477932	Standard	NM_174899	NM_174899	NA	Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000373652.3:c.-114+1381T>C	chr2.hg19:g.230788706T>C		NA	B3KVQ6|Q53TE6|Q8WWD4	hg19		0.02	-0.236807	GCCxGCC	COVERED																																																																																			NOVEL	FBXO36-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331831.1	5	4.20917	KEEP	2	0	0	14	379	TT	0.994391	0.608972	0		+	3	60	97	0	0	7.206117	21	60	625	64	ENST00000373652.3	0.125	0.612407
FBXO36	130888	__UNKNOWN__	__UNKNOWN__	2	230800845	230800845	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:230800845A>G	ENST00000373652.3	+	2	424				FBXO36_ENST00000283946.3_Intron|FBXO36_ENST00000409992.1_Intron			Q8NEA4	FBX36_HUMAN	F-box protein 36	NA		NA								endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	7		Renal(207;0.0112)|all_lung(227;0.0179)|Lung NSC(271;0.0804)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;7.56e-14)|all cancers(144;7.74e-11)|Lung(119;0.00488)|LUSC - Lung squamous cell carcinoma(224;0.008)		gttgcagtgaaccgaggtcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC033935	CCDS2472.1	2q37.1	2008-02-05	2004-06-15		ENSG00000153832	ENSG00000153832	130888		F-boxes /  other	27020	protein-coding gene	gene with protein product		609105	F-box only protein 36		NA	12477932	Standard	NM_174899	NM_174899	NA	Approved	Fbx36, FLJ37592	uc002vqa.3	Q8NEA4	OTTHUMG00000133206	ENST00000373652.3:c.3+3243A>G	chr2.hg19:g.230800845A>G		NA	B3KVQ6|Q53TE6|Q8WWD4	hg19		0.02	-0.306978	TGAxCCG	COVERED																																																																																			NOVEL	FBXO36-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331831.1	6	3.308387	KEEP	1	0	0	11	303	AA	0.993072	0.794702	0		+	3	60	96	0	0	6.627423	31	60	930	65	ENST00000373652.3	0.088235	0.800245
SLC16A14	151473	__UNKNOWN__	__UNKNOWN__	2	230929713	230929713	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:230929713T>C	ENST00000295190.4	-	1	445					NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		gcaacaagagtgaaactccat	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053	151473		Solute carriers	26417	protein-coding gene	gene with protein product	monocarboxylic acid transporter 14	NA	solute carrier family 16 (monocarboxylic acid transporters), member 14		NA		Standard	NM_152527	NM_152527	NA	Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.13+3557A>G	chr2.hg19:g.230929713T>C		NA	A8KA08|Q53R92|Q96NI7	hg19	CCDS2473.1	0.02	-0.175423	GAGxGAA	COVERED																																																																																			NOVEL	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256918.2	3	3.007916	KEEP	1	0	0	10	280	TT	0.99254	0.384517	0		-	3	60	98	0	0	7.561325	17	60	523	49	ENST00000295190.4	0.15	0.387407
CAB39	51719	__UNKNOWN__	__UNKNOWN__	2	231650608	231650608	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:231650608G>A	ENST00000258418.5	+	3	543				CAB39_ENST00000484398.1_Intron|CAB39_ENST00000409788.3_Intron|CAB39_ENST00000410084.3_Intron	NM_016289.3	NP_057373.1	Q9Y376	CAB39_HUMAN	calcium binding protein 39	NA		NA			activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cellular hypotonic response (GO:0071476)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of rubidium ion transmembrane transporter activity (GO:2000687)|negative regulation of rubidium ion transport (GO:2000681)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein heterooligomerization (GO:0051291)|signal transduction by phosphorylation (GO:0023014)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activator activity (GO:0043539)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_lung(227;4.63e-07)|all_hematologic(139;1.83e-06)|Lung NSC(271;2.11e-05)|Acute lymphoblastic leukemia(138;5.51e-05)|Hepatocellular(293;0.0207)|Lung SC(224;0.187)		all cancers(144;1.64e-12)|Epithelial(121;5.29e-11)|LUSC - Lung squamous cell carcinoma(224;0.0154)|Lung(119;0.0177)|COAD - Colon adenocarcinoma(134;0.226)		ggccgggcgcggtggctcaca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF113536	CCDS2478.1	2q37.1	2008-02-05			ENSG00000135932	ENSG00000135932	51719			20292	protein-coding gene	gene with protein product		612174			NA		Standard	NM_016289	NM_016289	NA	Approved	CGI-66, MO25	uc002vqx.3	Q9Y376	OTTHUMG00000133220	ENST00000258418.5:c.115-4979G>A	chr2.hg19:g.231650608G>A		NA	A8K8L7	hg19	CCDS2478.1	0.02	-0.263137	CGCxGTG	COVERED																																																																																			NOVEL	CAB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256955.2	10	2.338499	KEEP	4	1	26	17	498	GG	0.997832	0.692164	0		+	3	60	91	0	0	6.393375	25	60	790	70	ENST00000258418.5	0.107143	0.693668
ARMC9	80210	__UNKNOWN__	__UNKNOWN__	2	232098425	232098425	__UNKNOWN__	Intron	SNP	G	G	T	rs148377938	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232098425G>T	ENST00000349938.4	+	8	816				ARMC9_ENST00000483477.1_Intron	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	NA		NA				extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		ggaggcggaggttgcagtgag	0.478		NA											g|||	176	0.0351438	0.003	0.0562	5008	,	,	NA	15058	0.0	NA	0.1054	False	NA	,,,	NA	NA	NA	2504	0.0276	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931	80210		Armadillo repeat containing	20730	protein-coding gene	gene with protein product		NA			NA	11347906	Standard	NM_025139	NM_025139	NA	Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.623-1512G>T	chr2.hg19:g.232098425G>T		NA	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	hg19	CCDS2484.1	0.02	-0.131553	GAGxTTG	UNCOVERED																																																																																			NOVEL	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256966.3	7	2.407143	KEEP	7	0	0	8	243	GG	0	0	0		+	7	60	200	0	0	19.1222	7	60	230	36	ENST00000349938.4	0.5	0.229173
ARMC9	80210	__UNKNOWN__	__UNKNOWN__	2	232203194	232203194	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232203194C>T	ENST00000349938.4	+	21	2072				ARMC9_ENST00000483477.1_Intron	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	NA		NA				extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		ctgcctcagcctctcaaagtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931	80210		Armadillo repeat containing	20730	protein-coding gene	gene with protein product		NA			NA	11347906	Standard	NM_025139	NM_025139	NA	Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.1879-6493C>T	chr2.hg19:g.232203194C>T		NA	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	hg19	CCDS2484.1	0.02	-0.166666	AGCxTCT	COVERED																																																																																			NOVEL	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256966.3	9	2.707368	KEEP	1	0	0	9	259	CC	0.99257	0.351317	0		+	3	60	90	0	0	6.991896	14	60	462	34	ENST00000349938.4	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	232363655	232363655	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232363655G>A			NA	NA				AC017104.1 (8655 upstream) : RNU2-22P (3045 downstream)						NA		NA									NA						gagccaccacgcccggcccag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.232363655G>A		NA		hg19		0.02	-0.254397	CACxCCC	COVERED																																																																																			NOVEL					0			8	4.212695	KEEP	3	0	0	14	433	GG	0.993634	0.664267	0			3	60	91	0	0	6.443377	24	60	810	69		0.111111	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	232471394	232471394	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232471394T>C			NA	NA				C2orf57 (12400 upstream) : RN7SL499P (39316 downstream)						NA		NA									NA						catggtggcttatgcctgtaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.232471394T>C		NA		hg19		0.02	-0.236793	GCTxATG	COVERED																																																																																			NOVEL					0			6	6.312484	KEEP	1	0	0	21	554	TT	0.999863	0.612323	0			4	60	133	0	0	10.362328	22	60	633	75		0.153846	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	232511139	232511139	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232511139T>C			NA	NA				RN7SL499P (155 upstream) : MGC4771 (60377 downstream)						NA		NA									NA						tgcagtggcatgatcacggct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.232511139T>C		NA		hg19		0.02	-0.149095	GCAxGAT	COVERED																																																																																			NOVEL					0			9	3.308408	KEEP	0	0	0	11	306	TT	0.993072	0.289978	0			3	60	84	0	0	6.393202	14	60	429	44		0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	232556935	232556935	__UNKNOWN__	IGR	SNP	C	C	A	rs567427140		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232556935C>A			NA	NA				RN7SL499P (45951 upstream) : MGC4771 (14581 downstream)						NA		NA									NA						ctgggattaccggcatgagcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.232556935C>A		NA		hg19		0.02	-0.289464	TACxGGC	COVERED																																																																																			NOVEL					0			9	2.407179	KEEP	1	0	0	8	245	CC	0.99257	0.755234	0			3	60	96	0	0	6.753116	28	60	896	55		0.096774	0.760887
COPS7B	64708	__UNKNOWN__	__UNKNOWN__	2	232655727	232655727	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232655727C>T	ENST00000409295.1	+	2	206				COPS7B_ENST00000373608.3_Intron|COPS7B_ENST00000410024.1_Intron|COPS7B_ENST00000350033.3_Intron|COPS7B_ENST00000409091.1_Intron|COPS7B_ENST00000410017.1_Intron			Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	NA		NA			cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		ggattacaggcgtgagccacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524	64708			16760	protein-coding gene	gene with protein product		NA	COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B, COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)		NA	9707402	Standard	NM_022730	NM_001282950	NA	Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000409295.1:c.61-716C>T	chr2.hg19:g.232655727C>T		NA	Q53S22|Q5BJG3|Q9H7V6	hg19		0.02	4.658036	AGGxGTG	COVERED																																																																																			NOVEL	COPS7B-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331907.1	46	30.56647	KEEP	6	9	229	183	5439	CC	1	1	0		+	8	60	228	0	0	11.699711	214	60	7187	610	ENST00000409295.1	0.036036	1
COPS7B	64708	__UNKNOWN__	__UNKNOWN__	2	232655728	232655728	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232655728G>A	ENST00000409295.1	+	2	206				COPS7B_ENST00000373608.3_Intron|COPS7B_ENST00000410024.1_Intron|COPS7B_ENST00000350033.3_Intron|COPS7B_ENST00000409091.1_Intron|COPS7B_ENST00000410017.1_Intron			Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	NA		NA			cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		gattacaggcgtgagccaccg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524	64708			16760	protein-coding gene	gene with protein product		NA	COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B, COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)		NA	9707402	Standard	NM_022730	NM_001282950	NA	Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000409295.1:c.61-715G>A	chr2.hg19:g.232655728G>A		NA	Q53S22|Q5BJG3|Q9H7V6	hg19		0.02	5.95052	GGCxTGA	COVERED																																																																																			NOVEL	COPS7B-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000331907.1	46	35.610145	KEEP	6	7	203	190	5379	GG	1	1	0		+	9	60	274	0	0	15.400494	211	60	6903	624	ENST00000409295.1	0.040909	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	232802778	232802778	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232802778T>C			NA	NA				NPPC (11665 upstream) : DIS3L2 (23176 downstream)						NA		NA									NA						cctcgtgatctgcctgacttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.232802778T>C		NA		hg19		0.02	-0.19292	ATCxGCC	COVERED																																																																																			NOVEL					0			9	2.705199	KEEP	0	0	0	9	242	TT	0.99254	0.454342	0			3	60	92	0	0	6.893091	18	60	537	43		0.142857	0.457757
DIS3L2	129563	__UNKNOWN__	__UNKNOWN__	2	232953027	232953027	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:232953027T>C	ENST00000409307.1	+	5	601				DIS3L2_ENST00000360410.4_Intron|DIS3L2_ENST00000409401.3_Intron|DIS3L2_ENST00000273009.6_Intron|DIS3L2_ENST00000325385.7_Intron|DIS3L2_ENST00000470087.1_Intron					DIS3 like 3'-5' exoribonuclease 2	NA		NA								breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		gaggccgaggtgggcggatca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535	129563			28648	protein-coding gene	gene with protein product		614184	family with sequence similarity 6, member A, DIS3 mitotic control homolog (S. cerevisiae)-like 2	FAM6A	NA	22306653, 23503588	Standard	NM_152383	NM_152383	NA	Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.601+596T>C	chr2.hg19:g.232953027T>C		NA		hg19	CCDS42834.1	0.02	-0.21924	AGGxGGG	COVERED																																																																																			NOVEL	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330988.1	12	3.607317	KEEP	6	0	0	12	318	TT	0.99257	0.54878	0		+	4	60	115	1	0	8.716127	20	60	590	52	ENST00000409307.1	0.166667	0.552887
GIGYF2	26058	__UNKNOWN__	__UNKNOWN__	2	233613254	233613254	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:233613254A>C	ENST00000409196.3	+	4	269				GIGYF2_ENST00000409547.1_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000409480.1_Intron	NM_001103148.1	NP_001096618.1	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	NA		NA			adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		cttggcctccaaaagtgctgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120	26058		Trinucleotide (CAG) repeat containing	11960	protein-coding gene	gene with protein product	GYF domain containing 2	612003	PERQ amino acid rich, with GYF domain 2, PERQ amino acid rich, with GYF domain 3, trinucleotide repeat containing 15, Parkinson disease (autosomal recessive, early onset) 11	PERQ2, PERQ3, TNRC15, PARK11	NA	9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_001103146	NM_015575	NA	Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409196.3:c.172-443A>C	chr2.hg19:g.233613254A>C		NA	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	hg19	CCDS46543.1	0.02	-0.105263	TCCxAAA	UNCOVERED																																																																																			NOVEL	GIGYF2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330318.1	3	2.406013	KEEP	0	0	0	8	221	AA	0.99257	0.138793	0		+	3	60	102	0	0	9.555474	4	60	119	32	ENST00000409196.3	0.428571	0.139832
NEU2	4759	__UNKNOWN__	__UNKNOWN__	2	233899429	233899429	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:233899429C>T	ENST00000233840.3	+	2	805	c.805C>T	c.(805-807)Ccc>Tcc	p.P269S		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	269		NA			ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	GGAGCCGCCGCCCCAGGGCTG	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													16	19	18			NA	NA	2		NA											NA				233899429		2200	4296	6496	SO:0001583	missense			Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488	4759			7759	protein-coding gene	gene with protein product	N-acetyl-alpha-neuraminidase 2	605528			NA	10191093, 14613940	Standard	NM_005383	NM_005383	NA	Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.805C>T	chr2.hg19:g.233899429C>T	ENSP00000233840:p.Pro269Ser	NA	Q3KNW4|Q6NTB4	hg19	CCDS2501.1	0.02	3.189511	CCGxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	4.593	0.110197	0.08780	.	.	ENSG00000115488	ENST00000233840	T	0.81163	-1.46	4.91	4.91	0.64330	Neuraminidase (2);	.	.	.	.	D	0.82273	0.5001	M	0.85299	2.745	0.23120	N	0.998267	B	0.25105	0.118	B	0.28232	0.087	T	0.71258	-0.4646	9	0.09338	T	0.73	-36.7657	17.1106	0.86673	0.0:1.0:0.0:0.0	.	269	Q9Y3R4	NEUR2_HUMAN	S	269	ENSP00000233840:P269S	ENSP00000233840:P269S	P	+	1	0	NEU2	233607673	0.024000	0.19004	0.047000	0.18901	0.004000	0.04260	1.392000	0.34486	2.255000	0.74692	0.655000	0.94253	CCC	NOVEL	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257053.2	1	4.212216	KEEP	0	0	0	14	426	CC	0.995343	0.995339	0		+	37	60	1040	0	0	90.607706	76	60	2572	175	ENST00000233840.3	0.327434	0.999995
USP40	55230	__UNKNOWN__	__UNKNOWN__	2	234392783	234392783	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:234392783A>G	ENST00000427112.2	-	29	3537				USP40_ENST00000251722.6_Intron|USP40_ENST00000450966.1_Intron			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	NA		NA			ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		cagcctgggcaacagagcgag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982	55230		Ubiquitin-specific peptidases	20069	protein-coding gene	gene with protein product		610570	ubiquitin specific protease 40		NA	12838346	Standard	XM_114294	NM_018218	NA	Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3501+1393T>C	chr2.hg19:g.234392783A>G		NA	Q6NX38|Q70EL0	hg19	CCDS46547.1	0.02	-0.096483	GGCxACA	UNCOVERED																																																																																			NOVEL	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397235.1	8	2.406828	KEEP	0	0	0	8	235	AA	0.99257	0.119541	0		-	3	60	102	0	0	8.832559	8	60	238	28	ENST00000427112.2	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	235313234	235313234	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:235313234C>T			NA	NA				RP11-309M7.1 (180076 upstream) : AC097713.3 (33737 downstream)						NA		NA									NA						cgtgagccaccgtgcccggcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.235313234C>T		NA		hg19		0.02	-0.182787	CACxGTG	COVERED																																																																																			NOVEL					0			6	2.70679	KEEP	4	0	0	9	258	CC	0.99257	0.420331	0			3	60	90	0	0	6.773353	17	60	518	48		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	235609767	235609767	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:235609767T>C			NA	NA				ARL4C (204070 upstream) : AC010148.1 (181155 downstream)						NA		NA									NA						tttgggaggctgaggcaggtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.235609767T>C		NA		hg19		0.02	-0.131564	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			10	2.406025	KEEP	7	0	0	8	223	TT	0	0	0			3	60	99	0	0	8.1729	11	60	331	38		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	235728646	235728646	__UNKNOWN__	IGR	SNP	A	A	G	rs557419697		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:235728646A>G			NA	NA				ARL4C (322949 upstream) : AC010148.1 (62276 downstream)						NA		NA									NA						atcacctgagatcaggagttc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.235728646A>G		NA		hg19		0.02	-0.192938	GAGxTCA	COVERED																																																																																			NOVEL					0			4	2.406093	KEEP	0	0	0	8	221	AA	0.99257	0.454356	0			3	60	93	1	0	6.992752	18	60	522	40		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	236039238	236039238	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236039238A>G			NA	NA				AC114814.4 (42008 upstream) : AC114814.3 (47301 downstream)						NA		NA									NA						gggtagctggaactacaggtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.236039238A>G		NA		hg19		0.02	-0.114023	TGGxACT	UNCOVERED																																																																																			NOVEL					0			4	2.705938	KEEP	0	0	0	9	241	AA	0.99254	0.161255	0			3	60	101	0	0	8.732509	8	60	242	31		0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	236159054	236159054	__UNKNOWN__	IGR	SNP	G	G	A	rs2099264	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236159054G>A			NA	NA				AC114814.3 (71505 upstream) : AC092576.1 (75947 downstream)						NA		NA									NA						tggatcatgaggtcaggagat	0.527		NA											-|||	2974	0.59385	0.1543	0.6859	5008	,	,	NA	11509	0.8125	NA	0.7107	False	NA	,,,	NA	NA	NA	2504	0.7771	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.236159054G>A		NA		hg19		0.02	-0.061394	TGAxGTC	UNCOVERED																																																																																			NOVEL					0			2	2.407163	KEEP	12	0	0	8	246	GG	0	0	0			3	60	86	0	0	8.223789	3	60	100	31		0.5	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	236211464	236211464	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236211464G>A			NA	NA				AC114814.3 (123915 upstream) : AC092576.1 (23537 downstream)						NA		NA									NA						tcaggagatcgagaccatcct	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.236211464G>A		NA		hg19		0.02	1.552807	ATCxAGA	COVERED																																																																																			NOVEL					0			77	3.626417	KEEP	23	4	98	47	1345	GG	1	0.963774	0			5	55	142	2	0	10.226359	32	60	998	161		0.135135	0.963774
AGAP1	116987	__UNKNOWN__	__UNKNOWN__	2	236602818	236602818	__UNKNOWN__	Intron	SNP	C	C	T	rs190886394	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236602818C>T	ENST00000336665.5	+	2	743				AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000409457.1_Intron|AGAP1_ENST00000304032.8_Intron	NM_014914.4	NP_055729.2	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	NA		NA			protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						tgaaaccccgcctctactaaa	0.527		NA											C|||	83	0.0165735	0.0598	0.0043	5008	,	,	NA	15688	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985	116987		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16922	protein-coding gene	gene with protein product		608651	centaurin, gamma 2	CENTG2	NA		Standard	NM_014914	NM_001037131	NA	Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000336665.5:c.164-15005C>T	chr2.hg19:g.236602818C>T		NA	B2RTX7|Q541S5|Q6P9D7|Q9NV93	hg19	CCDS2514.1	0.02	-0.210508	CCGxCTC	COVERED																																																																																			NOVEL	AGAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257077.1	12	2.406376	KEEP	1	0	0	8	230	CC	0.99257	0.518282	0		+	3	60	91	0	0	6.665482	20	60	661	45	ENST00000336665.5	0.130435	0.522161
AGAP1	116987	__UNKNOWN__	__UNKNOWN__	2	236746565	236746565	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236746565A>G	ENST00000336665.5	+	9	1630				AGAP1_ENST00000428334.2_Intron|AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000409457.1_Intron|AGAP1_ENST00000304032.8_Intron	NM_014914.4	NP_055729.2	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	NA		NA			protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ggtggctcacacctgtagtcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985	116987		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16922	protein-coding gene	gene with protein product		608651	centaurin, gamma 2	CENTG2	NA		Standard	NM_014914	NM_001037131	NA	Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000336665.5:c.1050+30590A>G	chr2.hg19:g.236746565A>G		NA	B2RTX7|Q541S5|Q6P9D7|Q9NV93	hg19	CCDS2514.1	0.02	-0.140314	CACxCCT	COVERED																																																																																			NOVEL	AGAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257077.1	4	2.406484	KEEP	0	0	0	8	226	AA	0.99257	0.259026	0		+	4	60	135	0	0	11.771608	10	60	291	38	ENST00000336665.5	0.285714	0.260965
AGAP1	116987	__UNKNOWN__	__UNKNOWN__	2	236791410	236791410	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236791410T>C	ENST00000336665.5	+	10	1630				AGAP1_ENST00000428334.2_Intron|AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000304032.8_Intron	NM_014914.4	NP_055729.2	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	NA		NA			protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						tgagccaccgtgcccggccTG	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985	116987		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16922	protein-coding gene	gene with protein product		608651	centaurin, gamma 2	CENTG2	NA		Standard	NM_014914	NM_001037131	NA	Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000336665.5:c.1051-579T>C	chr2.hg19:g.236791410T>C		NA	B2RTX7|Q541S5|Q6P9D7|Q9NV93	hg19	CCDS2514.1	0.02	-0.210441	CCGxGCC	COVERED																																																																																			NOVEL	AGAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257077.1	7	2.404634	KEEP	1	0	0	8	209	TT	0.99257	0.518282	0		+	3	60	92	0	0	6.893182	18	60	512	47	ENST00000336665.5	0.142857	0.522161
AGAP1	116987	__UNKNOWN__	__UNKNOWN__	2	236880661	236880661	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:236880661A>G	ENST00000336665.5	+	12	2066				AGAP1_ENST00000428334.2_Intron|AGAP1_ENST00000409538.1_Intron|AGAP1_ENST00000304032.8_Intron	NM_014914.4	NP_055729.2	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	NA		NA			protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						gggctcaagcaatcctcccac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985	116987		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16922	protein-coding gene	gene with protein product		608651	centaurin, gamma 2	CENTG2	NA		Standard	NM_014914	NM_001037131	NA	Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000336665.5:c.1486+3394A>G	chr2.hg19:g.236880661A>G		NA	B2RTX7|Q541S5|Q6P9D7|Q9NV93	hg19	CCDS2514.1	0.02	-0.201724	AGCxATC	COVERED																																																																																			NOVEL	AGAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257077.1	12	3.909746	KEEP	1	0	0	13	362	AA	0.994391	0.487793	0		+	3	60	97	0	0	7.265139	20	60	594	55	ENST00000336665.5	0.130435	0.490544
ASB18	401036	__UNKNOWN__	__UNKNOWN__	2	237152765	237152765	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:237152765G>A	ENST00000409749.3	-	2	205				AC079135.1_ENST00000415226.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	NA		NA			intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		caccgtgcccggccTGTTTTT	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177	401036		Ankyrin repeat domain containing	19770	protein-coding gene	gene with protein product		NA	ankyrin repeat and SOCS box-containing 18		NA	12076535	Standard	NM_212556	NM_212556	NA	Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.206-2720C>T	chr2.hg19:g.237152765G>A		NA	B6ZDL7	hg19	CCDS46548.1	0.02	-0.17544	CCCxGCC	COVERED																																																																																			NOVEL	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329436.1	10	4.211792	KEEP	0	0	0	14	417	GG	0.995343	0.385603	0		-	3	60	93	0	1	7.291734	14	60	455	46	ENST00000409749.3	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	2	237231158	237231158	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:237231158G>A			NA	NA				AC079135.1 (27588 upstream) : IQCA1 (1635 downstream)						NA		NA									NA						caaagtgctgggattacaggt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr2.hg19:g.237231158G>A		NA		hg19		0.02	-0.21053	CTGxGAT	COVERED																																																																																			NOVEL					0			10	3.310169	KEEP	5	0	0	11	348	GG	0.992708	0.518353	0			3	60	95	0	0	7.19217	18	60	617	60		0.142857	0.522161
RAB17	64284	__UNKNOWN__	__UNKNOWN__	2	238483331	238483331	__UNKNOWN__	3'UTR	SNP	G	G	C	rs8184	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:238483331G>C	ENST00000264601.3	-	0	1599				RAB17_ENST00000409576.1_Intron|RAB17_ENST00000538644.1_3'UTR	NM_022449.3	NP_071894.1	Q9H0T7	RAB17_HUMAN	RAB17, member RAS oncogene family	NA		NA			cilium assembly (GO:0042384)|endocytic recycling (GO:0032456)|establishment of melanosome localization (GO:0032401)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor (GO:0002415)|melanosome transport (GO:0032402)|protein transport (GO:0015031)|regulation of dendrite development (GO:0050773)|regulation of filopodium assembly (GO:0051489)|regulation of synapse assembly (GO:0051963)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|dendrite (GO:0030425)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|melanosome (GO:0042470)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(1)	4		Renal(207;0.00272)|Breast(86;0.00297)|all_hematologic(139;0.182)|Ovarian(221;0.221)		Epithelial(121;9.36e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.26e-10)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000354)|Lung(119;0.011)|LUSC - Lung squamous cell carcinoma(224;0.026)		TCGCTGTGCTGCGGGGACTTT	0.632		NA											C|||	2357	0.470647	0.8495	0.3285	5008	,	,	NA	18661	0.4167	NA	0.2217	False	NA	,,,	NA	NA	NA	2504	0.3712	NA	NA	NA	Colon(56;987 1029 6466 13943 27336)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK022600	CCDS2520.1	2q37.3	2008-05-23			ENSG00000124839	ENSG00000124839	64284		RAB, member RAS oncogene	16523	protein-coding gene	gene with protein product		602206			NA	9624171	Standard		NM_022449	NA	Approved		uc002vwz.2	Q9H0T7	OTTHUMG00000133299	ENST00000264601.3:c.*331C>G	chr2.hg19:g.238483331G>C		NA	Q53QV6|Q6IA73|Q6PJZ0|Q9BVU1|Q9H9U9	hg19	CCDS2520.1	0.02	1.897338	GCTxCGG	COVERED																																																																																			NOVEL	RAB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257084.2	1	2.707812	KEEP	0	0	0	9	269	GG	0.99254	0.972219	0		-	22	60	736	0	0	67.800974	34	60	1160	88	ENST00000264601.3	0.392857	0.979526
RBM44	375316	__UNKNOWN__	__UNKNOWN__	2	238745251	238745251	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:238745251C>T	ENST00000316997.4	+	15	3313					NM_001080504.2	NP_001073973.2	Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	NA		NA				cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		ggtgaaaccccgtctctacta	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483	375316		RNA binding motif (RRM) containing	24756	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080504	NM_001080504	NA	Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000316997.4:c.3156+2185C>T	chr2.hg19:g.238745251C>T		NA	A0AUW3	hg19	CCDS46554.1	0.02	-0.122794	CCCxGTC	COVERED																																																																																			NOVEL	RBM44-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		8	3.907483	KEEP	11	0	0	13	336	CC	0.992708	0.19488	0		+	3	40	90	0	0	7.272977	11	60	340	42	ENST00000316997.4	0.214286	0.196312
RAMP1	10267	__UNKNOWN__	__UNKNOWN__	2	238808840	238808840	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:238808840C>T	ENST00000404910.2	+	3	374				RAMP1_ENST00000254661.4_Intron|RAMP1_ENST00000409726.1_Intron|RAMP1_ENST00000403885.1_Intron			O60894	RAMP1_HUMAN	receptor (G protein-coupled) activity modifying protein 1	NA		NA			angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|intracellular protein transport (GO:0006886)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein glycosylation (GO:0060050)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcitonin receptor activity (GO:0004948)|calcitonin receptor binding (GO:0031716)|coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			kidney(1)|large_intestine(1)|lung(2)	4		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)	ctggctctgtcgcccaggctg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(177;211 2889 43936 50767)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ001014	CCDS2522.1	2q36-q37.1	2008-02-05	2006-11-21		ENSG00000132329	ENSG00000132329	10267		Receptor (G protein-coupled) activity modifying proteins	9843	protein-coding gene	gene with protein product		605153	receptor activity modifying protein 1, receptor (calcitonin) activity modifying protein 1		NA		Standard	NM_005855	NM_005855	NA	Approved		uc002vxj.3	O60894	OTTHUMG00000133337	ENST00000404910.2:c.126-11330C>T	chr2.hg19:g.238808840C>T		NA	Q6FGS5	hg19		0.02	-0.122795	TGTxGCC	COVERED																																																																																			NOVEL	RAMP1-003	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000317766.2	5	4.210536	KEEP	0	0	0	14	402	CC	0.995343	0.195397	0		+	3	60	81	1	0	6.482074	10	60	330	40	ENST00000404910.2	0.230769	0.196312
RAMP1	10267	__UNKNOWN__	__UNKNOWN__	2	238817099	238817099	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:238817099T>C	ENST00000404910.2	+	3	374				RAMP1_ENST00000254661.4_Intron|RAMP1_ENST00000409726.1_Intron|RAMP1_ENST00000403885.1_Intron			O60894	RAMP1_HUMAN	receptor (G protein-coupled) activity modifying protein 1	NA		NA			angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|intracellular protein transport (GO:0006886)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein glycosylation (GO:0060050)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcitonin receptor activity (GO:0004948)|calcitonin receptor binding (GO:0031716)|coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			kidney(1)|large_intestine(1)|lung(2)	4		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)	gacagagtcttgctctgtcac	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(177;211 2889 43936 50767)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ001014	CCDS2522.1	2q36-q37.1	2008-02-05	2006-11-21		ENSG00000132329	ENSG00000132329	10267		Receptor (G protein-coupled) activity modifying proteins	9843	protein-coding gene	gene with protein product		605153	receptor activity modifying protein 1, receptor (calcitonin) activity modifying protein 1		NA		Standard	NM_005855	NM_005855	NA	Approved		uc002vxj.3	O60894	OTTHUMG00000133337	ENST00000404910.2:c.126-3071T>C	chr2.hg19:g.238817099T>C		NA	Q6FGS5	hg19		0.02	-0.31573	TCTxGCT	COVERED																																																																																			NOVEL	RAMP1-003	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000317766.2	11	2.93905	KEEP	1	1	26	19	524	TT	0.99986	0.81835	0		+	3	60	104	0	0	7.643768	26	60	786	87	ENST00000404910.2	0.103448	0.818465
UBE2F-SCLY	100533179	__UNKNOWN__	__UNKNOWN__	2	238957888	238957888	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:238957888C>T	ENST00000449191.1	+	8	639									UBE2F-SCLY readthrough (NMD candidate)	NA		NA									NA						ccctggccaacacggtgaaac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					2q37.3	2013-05-09			ENSG00000258984	ENSG00000258984	100533179			48339	other	readthrough		NA			NA		Standard		NR_037904	NA	Approved				OTTHUMG00000170602	ENST00000449191.1:c.393+3463C>T	chr2.hg19:g.238957888C>T		NA		hg19		0.02	-0.114022	CAAxACG	UNCOVERED																																																																																			NOVEL	UBE2F-SCLY-002	KNOWN	basic|appris_candidate_longest|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000409780.1	10	3.008847	KEEP	1	0	0	10	302	CC	0.992708	0.161282	0		+	3	39	81	0	0	6.482071	10	60	323	27	ENST00000449191.1	0.230769	0.162467
UBE2F-SCLY	100533179	__UNKNOWN__	__UNKNOWN__	2	238957890	238957890	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:238957890C>T	ENST00000449191.1	+	8	639									UBE2F-SCLY readthrough (NMD candidate)	NA		NA									NA						ctggccaacacggtgaaaccc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					2q37.3	2013-05-09			ENSG00000258984	ENSG00000258984	100533179			48339	other	readthrough		NA			NA		Standard		NR_037904	NA	Approved				OTTHUMG00000170602	ENST00000449191.1:c.393+3465C>T	chr2.hg19:g.238957890C>T		NA		hg19		0.02	-0.10521	ACAxGGT	UNCOVERED																																																																																			NOVEL	UBE2F-SCLY-002	KNOWN	basic|appris_candidate_longest|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000409780.1	10	2.706728	KEEP	1	0	0	9	250	CC	0.99254	0.138789	0		+	3	39	87	0	0	7.201807	9	60	257	25	ENST00000449191.1	0.25	0.139832
PER2	8864	__UNKNOWN__	__UNKNOWN__	2	239162134	239162134	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs138292908	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:239162134C>T	ENST00000254657.3	-	19	2809	c.2530G>A	c.(2530-2532)Gtg>Atg	p.V844M	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	844	Pro-rich.	NA			circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		GGAAAGGGCACGGCTGGGCAG	0.701		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													20	20	20			NA	NA	2		NA											NA				239162134		2202	4298	6500	SO:0001583	missense			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326	8864			8846	protein-coding gene	gene with protein product		603426	period (Drosophila) homolog 2, period homolog 2 (Drosophila)		NA	9427249, 17218255	Standard	NM_022817	NM_022817	NA	Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2530G>A	chr2.hg19:g.239162134C>T	ENSP00000254657:p.Val844Met	NA	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	hg19	CCDS2528.1	0.02	1.109483	GCAxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.461350	0.01062	.	.	ENSG00000132326	ENST00000254657	T	0.11169	2.8	3.6	-0.765	0.11023	.	8.220530	0.01889	N	0.038429	T	0.03608	0.0103	N	0.01438	-0.865	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.04013	0.001;0.001	T	0.33675	-0.9859	10	0.12430	T	0.62	-10.8035	4.0524	0.09801	0.0:0.2298:0.3628:0.4074	.	844;844	B4DH14;O15055	.;PER2_HUMAN	M	844	ENSP00000254657:V844M	ENSP00000254657:V844M	V	-	1	0	PER2	238826873	0.000000	0.05858	0.039000	0.18376	0.017000	0.09413	-2.378000	0.01068	-0.063000	0.13065	-0.424000	0.05967	GTG	NOVEL	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257167.1	2	3.908309	KEEP	0	0	0	13	350	CC	0.994391	0.993389	0		-	5	60	138	0	0	8.137028	73	60	2306	117	ENST00000254657.3	0.064103	0.998993
PER2	8864	__UNKNOWN__	__UNKNOWN__	2	239186727	239186727	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:239186727G>C	ENST00000254657.3	-	2	261				PER2_ENST00000440245.1_Intron|PER2_ENST00000254658.3_Intron	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	NA		NA			circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TCTTCTCTCTGTCTCTCtctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326	8864			8846	protein-coding gene	gene with protein product		603426	period (Drosophila) homolog 2, period homolog 2 (Drosophila)		NA	9427249, 17218255	Standard	NM_022817	NM_022817	NA	Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.19-131C>G	chr2.hg19:g.239186727G>C		NA	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	hg19	CCDS2528.1	0.02	-0.341853	TCTxTCT	COVERED																																																																																			NOVEL	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257167.1	3	6.017634	KEEP	0	0	0	20	605	GG	0.999863	0.865627	0		-	3	60	106	0	0	7.586458	32	70	1048	70	ENST00000254657.3	0.085714	0.865745
THAP4	51078	__UNKNOWN__	__UNKNOWN__	2	242525398	242525398	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:242525398C>T	ENST00000402545.1	-	5	534				THAP4_ENST00000407315.1_Intron|THAP4_ENST00000402136.1_Intron			Q8WY91	THAP4_HUMAN	THAP domain containing 4	NA		NA					DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		Aggttgggcacggtggttcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946	51078		THAP (C2CH-type zinc finger) domain containing	23187	protein-coding gene	gene with protein product		612533			NA	12575992, 10810093	Standard	NM_015963	NM_015963	NA	Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000402545.1:c.460-1258G>A	chr2.hg19:g.242525398C>T		NA	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	hg19		0.02	-0.149115	GCAxGGT	COVERED																																																																																			NOVEL	THAP4-006	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323048.1	13	4.208683	KEEP	1	0	0	14	367	CC	0.995343	0.290641	0		-	3	60	91	0	0	7.179025	13	60	416	40	ENST00000402545.1	0.1875	0.292001
THAP4	51078	__UNKNOWN__	__UNKNOWN__	2	242525404	242525404	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr2:242525404T>C	ENST00000402545.1	-	5	534				THAP4_ENST00000407315.1_Intron|THAP4_ENST00000402136.1_Intron			Q8WY91	THAP4_HUMAN	THAP domain containing 4	NA		NA					DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		ggcacggtggttcacgcctgt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946	51078		THAP (C2CH-type zinc finger) domain containing	23187	protein-coding gene	gene with protein product		612533			NA	12575992, 10810093	Standard	NM_015963	NM_015963	NA	Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000402545.1:c.460-1264A>G	chr2.hg19:g.242525404T>C		NA	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	hg19		0.02	-0.149097	TGGxTCA	COVERED																																																																																			NOVEL	THAP4-006	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323048.1	13	4.210571	KEEP	1	0	0	14	383	TT	0.995343	0.290641	0		-	4	60	135	0	0	11.501801	12	60	348	40	ENST00000402545.1	0.25	0.292001
CNTN4	152330	__UNKNOWN__	__UNKNOWN__	3	2272650	2272650	__UNKNOWN__	Intron	SNP	C	C	T	rs538721549		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:2272650C>T	ENST00000418658.1	+	3	135					NM_175607.2	NP_783200.1	Q8IWV2	CNTN4_HUMAN	contactin 4	NA		NA			axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		ccagcctgggcgacaaagcga	0.413		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17631	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619	152330		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	2174	protein-coding gene	gene with protein product		607280			NA	8586965, 12202991	Standard		NM_175607	NA	Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000418658.1:c.-144-108212C>T	chr3.hg19:g.2272650C>T		NA	B2RAX3|Q8IX14|Q8TC35	hg19	CCDS43041.1	0.02	-0.087711	GGGxGAC	UNCOVERED																																																																																			NOVEL	CNTN4-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337405.2	4	2.406992	KEEP	1	0	0	8	244	CC	0.99257	0.09898	0		+	5	60	148	0	0	14.173932	5	60	166	30	ENST00000418658.1	0.5	0.099721
CNTN4	152330	__UNKNOWN__	__UNKNOWN__	3	2937467	2937467	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:2937467C>A	ENST00000397461.1	+	10	1324				CNTN4_ENST00000358480.3_Intron|CNTN4_ENST00000397459.2_Intron|CNTN4_ENST00000427331.1_Intron|CNTN4_ENST00000418658.1_Intron	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	NA		NA			axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		gcctgtcatcccagcactttg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619	152330		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	2174	protein-coding gene	gene with protein product		607280			NA	8586965, 12202991	Standard		NM_175607	NA	Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.941-4902C>A	chr3.hg19:g.2937467C>A		NA	B2RAX3|Q8IX14|Q8TC35	hg19	CCDS43041.1	0.02	-0.157899	ATCxCAG	COVERED																																																																																			NOVEL	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239236.2	6	3.911548	KEEP	7	0	0	13	394	CC	0.993072	0.32057	0		+	3	40	86	0	0	6.59216	14	60	483	55	ENST00000397461.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	3163573	3163573	__UNKNOWN__	IGR	SNP	T	T	G	rs531528314		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:3163573T>G			NA	NA				IL5RA (11515 upstream) : TRNT1 (5026 downstream)						NA		NA									NA						gattacaggcttgagccaccg	0.478		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14977	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.3163573T>G		NA		hg19		0.02	-0.201742	GGCxTGA	COVERED																																																																																			NOVEL					0			5	3.008085	KEEP	3	0	0	10	284	TT	0.99254	0.518266	0			4	60	130	0	0	10.468748	17	60	518	53		0.190476	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	3247243	3247243	__UNKNOWN__	IGR	SNP	C	C	T	rs112993977	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:3247243C>T			NA	NA				CRBN (25849 upstream) : AC026188.1 (109746 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.527		NA											C|||	35	0.00698882	0.0106	0.0072	5008	,	,	NA	15952	0.001	NA	0.0149	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.3247243C>T		NA		hg19		0.02	-0.122781	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			9	3.910637	KEEP	10	0	0	13	378	CC	0	0	0			3	53	86	0	0	6.982062	10	60	318	43		0.230769	0.196312
SUMF1	285362	__UNKNOWN__	__UNKNOWN__	3	4092224	4092224	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:4092224A>G	ENST00000534863.1	-	9	1191							Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	NA		NA			cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		ccaggagttcaagaccagcct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455	285362			20376	protein-coding gene	gene with protein product		607939			NA	12757705, 12757706	Standard	NM_182760	NM_182760	NA	Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000534863.1:c.1191+18028T>C	chr3.hg19:g.4092224A>G		NA	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	hg19		0.02	-0.192963	TTCxAGA	COVERED																																																																																			NOVEL	SUMF1-201	KNOWN	basic	protein_coding	NA	protein_coding		9	3.007194	KEEP	1	0	0	10	272	AA	0.992708	0.454419	0		-	3	60	98	0	0	7.427036	19	60	570	49	ENST00000534863.1	0.136364	0.457757
AC018816.3	0	__UNKNOWN__	__UNKNOWN__	3	4899564	4899564	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:4899564A>G	ENST00000449914.1	-	2	66				AC018816.3_ENST00000441894.1_Intron						NA		NA									NA						gattacaggtatgagccacca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000449914.1:c.45-26862T>C	chr3.hg19:g.4899564A>G		NA		hg19		0.02	-0.333265	GGTxTGA	COVERED																																																																																			NOVEL	AC018816.3-001	PUTATIVE	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000338948.1	7	3.587561	KEEP	0	0	0	12	300	AA	0.993634	0.84656	0		-	3	60	104	0	0	7.311439	34	60	983	78	ENST00000449914.1	0.081081	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	5030193	5030193	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:5030193G>T			NA	NA				BHLHE40 (3185 upstream) : Y_RNA (97669 downstream)						NA		NA									NA						aggatcacttgaggctgggag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.5030193G>T		NA		hg19		0.02	-0.122807	CTTxAGG	COVERED																																																																																			NOVEL					0			9	6.920707	KEEP	1	0	0	23	705	GG	0.999892	0.19629	0			3	60	85	0	0	6.772903	11	60	374	56		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	5109207	5109207	__UNKNOWN__	IGR	SNP	C	C	G	rs71623015	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:5109207C>G			NA	NA				BHLHE40 (82199 upstream) : Y_RNA (18655 downstream)						NA		NA									NA						tggagtctcgctctgttgccc	0.418		NA											C|||	192	0.0383387	0.025	0.0432	5008	,	,	NA	10019	0.002	NA	0.0895	False	NA	,,,	NA	NA	NA	2504	0.0378	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.5109207C>G		NA		hg19		0.02	-0.026319	TCGxTCT	UNCOVERED																																																																																			NOVEL					0			2	2.406899	KEEP	3	0	0	8	238	CT	0	0	0			2	60	71	0	0	8.053996	0	0	0	15		1	0
LMCD1-AS1	100288428	__UNKNOWN__	__UNKNOWN__	3	8074068	8074068	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:8074068G>A	ENST00000446281.1	-	0	514									LMCD1 antisense RNA 1 (head to head)	NA		NA									NA						agggccgggcgctgtggctca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							3p26.1	2012-11-05			ENSG00000227110	ENSG00000227110	100288428		Long non-coding RNAs	44477	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_033378	NR_033378	NA	Approved		uc021wso.1		OTTHUMG00000154968	ENST00000446281.1:	chr3.hg19:g.8074068G>A		NA		hg19		0.02	-0.149127	GGCxCTG	COVERED																																																																																			NOVEL	LMCD1-AS1-006	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000337850.1	6	3.007864	KEEP	0	0	0	10	294	GG	0.992708	0.289872	0		-	3	60	86	0	0	6.872855	11	60	376	39	ENST00000446281.1	0.214286	0.292001
SSUH2	51066	__UNKNOWN__	__UNKNOWN__	3	8665360	8665360	__UNKNOWN__	Intron	SNP	A	A	G	rs9809581	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:8665360A>G	ENST00000317371.4	-	18	2033				SSUH2_ENST00000415132.1_Intron|SSUH2_ENST00000544814.1_Intron|SSUH2_ENST00000341795.3_Intron			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	NA		NA				cytoplasm (GO:0005737)					NA						AAAGAGAGAGAGACACAGACC	0.617		NA											A|||	1260	0.251597	0.466	0.2118	5008	,	,	NA	18172	0.1587	NA	0.162	False	NA	,,,	NA	NA	NA	2504	0.1779	NA	NA	NA								NA				0								A		1663,2431		358,947,742	28	25	26			-2.2	0	3	dbSNP_119	26	1342,6614		135,1072,2771	no	intron	C3orf32	NM_015931.1		493,2019,3513	GG,GA,AA	NA	16.8678,40.6204,24.9378			8665360	3005,9045	2047	3978	6025	SO:0001627	intron_variant			AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046	51066			24809	protein-coding gene	gene with protein product		NA	chromosome 3 open reading frame 32	C3orf32	NA	20205943	Standard	NM_015931	NM_001256748	NA	Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.808-18T>C	chr3.hg19:g.8665360A>G		NA	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	hg19	CCDS2568.1	0.02	1.865506	GAGxGAC	COVERED																																																																																			NOVEL	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337900.1	4	2.687015	KEEP	0	0	0	9	233	AA	0.99254	0.989724	0		-	32	60	1088	0	0	102.846803	39	60	1148	105	ENST00000317371.4	0.450704	0.997163
RAD18	56852	__UNKNOWN__	__UNKNOWN__	3	8987356	8987356	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:8987356A>G	ENST00000264926.2	-	4	383				RAD18_ENST00000495087.1_Intron	NM_020165.3	NP_064550.3	Q9NS91	RAD18_HUMAN	RAD18 E3 ubiquitin protein ligase	NA		NA			DNA repair (GO:0006281)|negative regulation of DNA recombination (GO:0045910)|protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|spermatogenesis (GO:0007283)	chromatin (GO:0000785)|nucleus (GO:0005634)|replication fork (GO:0005657)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|ligase activity (GO:0016874)|polyubiquitin binding (GO:0031593)|ubiquitin protein ligase binding (GO:0031625)|Y-form DNA binding (GO:0000403)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(3)	15				OV - Ovarian serous cystadenocarcinoma(96;0.0552)		gggtttcaccatgttggccag	0.557		NA						Rad6 pathway													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2571.1	3p25-p24	2014-08-04	2014-08-04		ENSG00000070950	ENSG00000070950	56852		RING-type (C3HC4) zinc fingers	18278	protein-coding gene	gene with protein product		605256	RAD18 homolog (S. cerevisiae)		NA	10884424, 10908344	Standard	NM_020165	NM_020165	NA	Approved	RNF73	uc003brd.3	Q9NS91	OTTHUMG00000090545	ENST00000264926.2:c.266+1547T>C	chr3.hg19:g.8987356A>G		NA	Q58F55|Q9NRT6	hg19	CCDS2571.1	0.02	-0.122782	ACCxTGT	UNCOVERED																																																																																			NOVEL	RAD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207071.2	9	3.006368	KEEP	8	0	0	10	261	AA	0	0	0		-	3	60	86	0	0	7.101278	9	60	264	34	ENST00000264926.2	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	9328132	9328132	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:9328132A>C			NA	NA				SRGAP3-AS4 (28941 upstream) : RP11-380O24.1 (6139 downstream)						NA		NA									NA						atcacttgagaccaggagttc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.9328132A>C		NA		hg19		0.02	-0.254338	GAGxCCA	COVERED																																																																																			NOVEL					0			13	3.608207	KEEP	2	0	0	12	319	AA	0.993634	0.664267	0			3	60	101	0	0	7.549076	22	60	630	56		0.12	0.668523
THUMPD3	25917	__UNKNOWN__	__UNKNOWN__	3	9410734	9410734	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:9410734A>G	ENST00000345094.3	+	4	664				SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000515662.2_Intron|THUMPD3_ENST00000452837.2_Intron	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	NA		NA				cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		ggtggctcacacctgtaatcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077	25917			24493	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_015453	NM_015453	NA	Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.331-2010A>G	chr3.hg19:g.9410734A>G		NA	Q9H8V6|Q9NVC1|Q9UFS3	hg19	CCDS2573.1	0.02	-0.245566	CACxCCT	COVERED																																																																																			NOVEL	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214127.1	9	3.607925	KEEP	1	0	0	12	323	AA	0.994391	0.63775	0		+	3	60	102	0	0	7.594675	23	60	673	64	ENST00000345094.3	0.115385	0.641347
SETD5	55209	__UNKNOWN__	__UNKNOWN__	3	9483874	9483874	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:9483874G>A	ENST00000406341.1	+	9	1212	c.1022G>A	c.(1021-1023)cGt>cAt	p.R341H	SETD5_ENST00000407969.1_Missense_Mutation_p.R360H|SETD5_ENST00000402198.1_Missense_Mutation_p.R341H|SETD5_ENST00000302463.6_Missense_Mutation_p.R243H|SETD5_ENST00000402466.1_Missense_Mutation_p.R243H			Q9C0A6	SETD5_HUMAN	SET domain containing 5	341	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.	NA								NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		GTGGATGCCCGTACTTTCGGT	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													143	131	135			NA	NA	3		NA											NA				9483874		1923	4143	6066	SO:0001583	missense			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137	55209			25566	protein-coding gene	gene with protein product		615743			NA	11214970	Standard	XM_371614	XM_005265299	NA	Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.1022G>A	chr3.hg19:g.9483874G>A	ENSP00000383939:p.Arg341His	NA	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	hg19	CCDS46741.1	0.02	1.487789	CCCxTAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	34	5.377628	0.95945	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59	5.49	5.49	0.81192	SET domain (3);	0.120638	0.56097	D	0.000029	D	0.91576	0.7339	M	0.79475	2.455	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.92217	0.5781	10	0.87932	D	0	-2.8383	19.3711	0.94488	0.0:0.0:1.0:0.0	.	243;341;360	Q9C0A6-3;Q9C0A6;E7EWN3	.;SETD5_HUMAN;.	H	341;243;341;360;243	ENSP00000385852:R341H;ENSP00000384429:R243H;ENSP00000383939:R341H;ENSP00000384114:R360H;ENSP00000302028:R243H	ENSP00000302028:R243H	R	+	2	0	SETD5	9458874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.585000	0.87301	0.655000	0.94253	CGT	NOVEL	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318425.1	1	6.917816	KEEP	0	0	0	23	659	GG	0.999892	0.999111	0		+	4	60	130	0	0	8.039327	75	60	2477	162	ENST00000406341.1	0.050633	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	9638528	9638528	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:9638528A>G			NA	NA				LHFPL4 (43042 upstream) : MTMR14 (52588 downstream)						NA		NA									NA						cggcctcccaaaatgctggga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.9638528A>G		NA		hg19		0.02	-0.183437	CCAxAAT	COVERED																																																																																			NOVEL					0			7	4.21155	KEEP	1	0	0	14	403	AA	0.994391	0.421102	0			3	60	104	0	0	8.31731	15	60	411	45		0.166667	0.423478
CAMK1	8536	__UNKNOWN__	__UNKNOWN__	3	9806254	9806254	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:9806254T>C	ENST00000256460.3	-	3	393				OGG1_ENST00000349503.5_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000302008.8_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	NA		NA			cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		cttcagcctctcaaagtgctg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072	8536			1459	protein-coding gene	gene with protein product		604998			NA	7641687	Standard	NM_003656	NM_003656	NA	Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.215+1188A>G	chr3.hg19:g.9806254T>C		NA	Q3KPF6	hg19	CCDS2582.1	0.02	-0.149101	CTCxCAA	COVERED																																																																																			NOVEL	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250206.1	6	2.705273	KEEP	1	0	0	9	235	TT	0.99254	0.289823	0		-	3	60	95	0	0	7.67246	12	60	353	39	ENST00000256460.3	0.2	0.292001
FANCD2	2177	__UNKNOWN__	__UNKNOWN__	3	10143359	10143359	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:10143359T>G	ENST00000419585.1	+	0	4930				FANCD2OS_ENST00000524279.1_Intron|FANCD2_ENST00000383807.1_3'UTR|FANCD2_ENST00000383806.1_3'UTR			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	NA		NA			DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		gagccaccgctcccagccATA	0.488		NA	D, Mis, N, F			AML, leukemia		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Fanconi anaemia D2	3	3p26	2177	Fanconi anemia, complementation group D2		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554	2177		Fanconi anemia, complementation groups	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD	NA	7581463, 11239453, 18475298	Standard		XM_005264946	NA	Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.*413T>G	chr3.hg19:g.10143359T>G		NA	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	hg19	CCDS33696.1	0.02	-0.342037	CGCxCCC	COVERED																																																																																			NOVEL	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339873.1	7	3.308289	KEEP	1	0	0	11	302	CT	0.993634	0.883216	0		+	3	60	103	0	0	7.211583	34	60	1000	77	ENST00000419585.1	0.081081	0.888875
IRAK2	3656	__UNKNOWN__	__UNKNOWN__	3	10255893	10255893	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:10255893G>A	ENST00000256458.4	+	6	878					NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	NA		NA			activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						gattacaggcgtgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070	3656			6113	protein-coding gene	gene with protein product		603304			NA	9374458	Standard		XR_245126	NA	Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.788+661G>A	chr3.hg19:g.10255893G>A		NA	B4DQZ6|Q08AG6|Q5K546	hg19	CCDS33697.1	0.02	-0.192987	GGCxTGA	COVERED																																																																																			NOVEL	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339623.1	5	2.961971	KEEP	1	0	0	10	257	GG	0.99254	0.454342	0		+	3	60	87	0	0	6.461516	17	60	576	45	ENST00000256458.4	0.15	0.457757
TATDN2	9797	__UNKNOWN__	__UNKNOWN__	3	10306639	10306639	__UNKNOWN__	Intron	SNP	C	C	T	rs183726988	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:10306639C>T	ENST00000287652.4	+	3	1999				RP11-438J1.1_ENST00000450534.1_Intron|TATDN2_ENST00000448281.2_Intron	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						ggattacaggcgtgagccacc	0.448		NA											C|||	85	0.0169728	0.0605	0.0072	5008	,	,	NA	13263	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014	9797			28988	protein-coding gene	gene with protein product		NA			NA	9039502	Standard	XM_376203	NM_014760	NA	Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.948+4285C>T	chr3.hg19:g.10306639C>T		NA	Q3MIL9|Q5BKU0	hg19	CCDS33698.1	0.02	-0.157885	AGGxGTG	COVERED																																																																																			NOVEL	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339641.1	8	5.415038	KEEP	0	0	0	18	527	CC	0.999859	0.322761	0		+	3	60	87	0	0	6.872569	12	60	384	57	ENST00000287652.4	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	11021512	11021512	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:11021512T>C			NA	NA				SLC6A11 (39093 upstream) : SLC6A1 (12897 downstream)						NA		NA									NA						ctcgctctgttgcccaggctg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.11021512T>C		NA		hg19		0.02	-0.271866	TGTxGCC	COVERED																																																																																			NOVEL					0			13	2.536995	KEEP	0	1	24	17	459	TT	0.999859	0.717214	0			3	60	95	1	1	6.895313	23	60	680	71		0.115385	0.717315
HRH1	3269	__UNKNOWN__	__UNKNOWN__	3	11258883	11258883	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:11258883A>C	ENST00000431010.2	+	2	27				HRH1_ENST00000438284.2_Intron	NM_001098212.1|NM_001098213.1	NP_001091682.1|NP_001091683.1	P35367	HRH1_HUMAN	histamine receptor H1	NA		NA			cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	aaaaacaaacacacaaacaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639	3269		GPCR / Class A : Histamine receptors	5182	protein-coding gene	gene with protein product		600167			NA	8003029	Standard		NM_001098211	NA	Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000431010.2:c.-35-41806A>C	chr3.hg19:g.11258883A>C		NA	A8K047|Q6P9E5	hg19	CCDS2604.1	0.02	-0.175376	AACxCAC	COVERED																																																																																			NOVEL	HRH1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339090.1	6	3.910528	KEEP	0	0	0	13	368	AA	0.994391	0.385234	0		+	5	60	169	0	0	14.668364	13	60	369	52	ENST00000431010.2	0.277778	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	11827967	11827967	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:11827967T>C			NA	NA				AC090939.1 (61514 upstream) : TAMM41 (3948 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.11827967T>C		NA		hg19		0.02	-0.131547	AGAxGGG	COVERED																																																																																			NOVEL					0			21	6.013902	KEEP	22	0	0	20	535	TT	0.993072	0.227586	0			3	40	99	0	0	8.173149	11	60	315	63		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	12012696	12012696	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:12012696T>G			NA	NA				RN7SL147P (18137 upstream) : SYN2 (33183 downstream)						NA		NA									NA						gggaggctgatgcaggaggat	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.12012696T>G		NA		hg19		0.02	-0.131574	TGAxGCA	COVERED																																																																																			NOVEL					0			4	2.406464	KEEP	0	0	0	8	227	TT	0.99257	0.22747	0			5	60	175	0	0	16.346321	7	60	212	37		0.416667	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	12488111	12488111	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:12488111A>G			NA	NA				PPARG (12256 upstream) : TSEN2 (37819 downstream)						NA		NA									NA						tgggagtcagaagttcgagac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.12488111A>G		NA		hg19		0.02	-0.105217	CAGxAGT	UNCOVERED																																																																																			NOVEL					0			5	2.405595	KEEP	0	0	0	8	217	AA	0.99257	0.138793	0			3	60	100	0	0	8.633219	8	60	223	30		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	12728270	12728270	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:12728270C>T			NA	NA				RAF1 (22545 upstream) : TMEM40 (46753 downstream)						NA		NA									NA						tgagccaccgcgcccggccTA	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.12728270C>T		NA		hg19		0.02	-0.210503	CCGxGCC	COVERED																																																																																			NOVEL					0			9	3.640836	KEEP	4	1	22	20	562	CC	0.999366	0.52183	0			3	60	89	0	0	6.661613	17	60	553	67		0.15	0.522161
TMEM40	55287	__UNKNOWN__	__UNKNOWN__	3	12795794	12795794	__UNKNOWN__	Intron	SNP	G	G	C	rs9310409	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:12795794G>C	ENST00000314124.7	-	2	349				TMEM40_ENST00000435218.2_Intron|TMEM40_ENST00000431022.2_Intron|TMEM40_ENST00000435575.1_Intron|TMEM40_ENST00000264728.8_Intron	NM_001284406.1|NM_018306.2	NP_001271335.1|NP_060776.2	Q8WWA1	TMM40_HUMAN	transmembrane protein 40	NA		NA				integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(5)|urinary_tract(1)	10						ctgggcgacagagcacgattc	0.537		NA											C|||	1940	0.38738	0.416	0.3588	5008	,	,	NA	17189	0.3343	NA	0.5288	False	NA	,,,	NA	NA	NA	2504	0.2781	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC020658	CCDS2613.1, CCDS68347.1, CCDS68348.1	3p25.2	2005-01-10			ENSG00000088726	ENSG00000088726	55287			25620	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018306	NM_018306	NA	Approved	FLJ11036	uc003bxg.1	Q8WWA1	OTTHUMG00000129801	ENST00000314124.7:c.8-4455C>G	chr3.hg19:g.12795794G>C		NA	C9JID5|Q8NAL4|Q9NUZ4	hg19	CCDS2613.1	0.02	-0.140364	ACAxAGC	COVERED																																																																																			NOVEL	TMEM40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252029.2	3	2.406903	KEEP	0	0	0	8	239	GG	0.99257	0.259026	0		-	7	60	244	0	0	26.430144	1	60	35	34	ENST00000314124.7	0.875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	12832604	12832604	__UNKNOWN__	IGR	SNP	G	G	C	rs13086170	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:12832604G>C			NA	NA				TMEM40 (21648 upstream) : CAND2 (5366 downstream)						NA		NA									NA						ttgagctcaggagtttgagac	0.507		NA											.|||	2467	0.492612	0.5673	0.4467	5008	,	,	NA	14245	0.4325	NA	0.6282	False	NA	,,,	NA	NA	NA	2504	0.3466	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.12832604G>C		NA		hg19		0.02	-0.078956	CAGxAGT	UNCOVERED																																																																																			NOVEL					0			8	2.707252	KEEP	6	0	0	9	271	GT	0	0	0			5	60	175	0	0	17.586767	3	60	104	33		0.625	0.077336
CAND2	23066	__UNKNOWN__	__UNKNOWN__	3	12853687	12853687	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:12853687T>C	ENST00000456430.2	+	6	798				CAND2_ENST00000295989.5_Intron	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ggattacaggtgtgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(43;676 868 1633 6395 37496)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712	23066			30689	protein-coding gene	gene with protein product	TBP interacting protein	610403			NA	9734811, 10441524	Standard	XM_371617	NM_012298	NA	Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.758-802T>C	chr3.hg19:g.12853687T>C		NA	B9EGM9|E9KL24	hg19	CCDS54554.1	0.02	-0.087709	AGGxGTG	UNCOVERED																																																																																			NOVEL	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339856.4	7	2.704857	KEEP	0	0	0	9	228	TT	0.99254	0.098977	0		+	3	48	101	0	0	9.043782	6	60	175	26	ENST00000456430.2	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	14369722	14369722	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:14369722A>G			NA	NA				RP11-536I6.2 (24377 upstream) : RP11-536I6.1 (20228 downstream)						NA		NA									NA						ctcttgcctcagcctcccaaa	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.14369722A>G		NA		hg19		0.02	-0.298224	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			15	2.406743	KEEP	5	0	0	8	232	AC	0	0	0			3	60	101	0	1	7.252624	28	60	856	68		0.096774	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	14671656	14671656	__UNKNOWN__	IGR	SNP	G	G	A	rs58807199	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:14671656G>A			NA	NA				GRIP2 (89775 upstream) : AC090952.5 (18044 downstream)						NA		NA									NA						cagatcacttgaggccaggag	0.517		NA											G|||	1588	0.317093	0.4213	0.3242	5008	,	,	NA	18958	0.121	NA	0.4066	False	NA	,,,	NA	NA	NA	2504	0.2812	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.14671656G>A		NA		hg19		0.02	-0.15788	CTTxAGG	COVERED																																																																																			NOVEL					0			2	2.707985	KEEP	1	0	0	9	275	GG	0.99254	0.320398	0			5	60	138	0	0	11.868767	11	60	378	40		0.3125	0.322807
FGD5	152273	__UNKNOWN__	__UNKNOWN__	3	14943526	14943526	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:14943526C>T	ENST00000285046.5	+	9	3374				FGD5_ENST00000476851.1_Intron|FGD5_ENST00000543601.1_Intron	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	NA		NA			actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						tggtggctcacgcctgtaatc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783	152273		Zinc fingers, FYVE domain containing, Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	19117	protein-coding gene	gene with protein product		614788			NA		Standard	NM_152536	NM_152536	NA	Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.3264+958C>T	chr3.hg19:g.14943526C>T		NA	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	hg19	CCDS46767.1	0.02	-0.140344	TCAxGCC	COVERED																																																																																			NOVEL	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340628.1	8	3.911214	KEEP	7	0	0	13	387	CC	0.993634	0.259304	0		+	3	60	84	0	0	6.572579	12	60	393	51	ENST00000285046.5	0.2	0.260965
ZFYVE20	64145	__UNKNOWN__	__UNKNOWN__	3	15130166	15130166	__UNKNOWN__	Intron	SNP	C	C	T	rs139763697	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15130166C>T	ENST00000253699.3	-	5	903				ZFYVE20_ENST00000476527.2_Intron|ZFYVE20_ENST00000449964.2_Intron|ZFYVE20_ENST00000435849.3_Intron	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	NA		NA			blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						ggattacaggcgtgagccact	0.458		NA											C|||	14	0.00279553	0.0	0.0	5008	,	,	NA	15035	0.0139	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381	64145		Zinc fingers, FYVE domain containing	20759	protein-coding gene	gene with protein product		609511			NA	11062261	Standard	NM_022340	XR_427283	NA	Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.289+1739G>A	chr3.hg19:g.15130166C>T		NA	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	hg19	CCDS2623.1	0.02	-0.157896	AGGxGTG	COVERED																																																																																			NOVEL	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252102.2	10	3.900601	KEEP	0	0	0	13	340	CC	0.994391	0.320996	0		-	3	60	88	1	0	6.791968	14	60	472	44	ENST00000253699.3	0.176471	0.322807
ZFYVE20	64145	__UNKNOWN__	__UNKNOWN__	3	15136641	15136641	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15136641T>C	ENST00000253699.3	-	4	762				ZFYVE20_ENST00000476527.2_Intron|ZFYVE20_ENST00000449964.2_Intron|ZFYVE20_ENST00000435849.3_Intron	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	NA		NA			blood coagulation (GO:0007596)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	endosome (GO:0005768)|endosome membrane (GO:0010008)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|skin(3)|stomach(1)|urinary_tract(2)	26						cctacctcagtctcctgagta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY009133	CCDS2623.1	3p25.1	2014-01-15			ENSG00000131381	ENSG00000131381	64145		Zinc fingers, FYVE domain containing	20759	protein-coding gene	gene with protein product		609511			NA	11062261	Standard	NM_022340	XR_427283	NA	Approved	Rabenosyn-5	uc003bzm.1	Q9H1K0	OTTHUMG00000129860	ENST00000253699.3:c.148+838A>G	chr3.hg19:g.15136641T>C		NA	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	hg19	CCDS2623.1	0.02	-0.228017	CAGxCTC	COVERED																																																																																			NOVEL	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252102.2	10	3.608163	KEEP	0	0	0	12	320	TT	0.993634	0.579219	0		-	3	60	97	0	0	7.206168	21	60	606	45	ENST00000253699.3	0.125	0.58293
CAPN7	23473	__UNKNOWN__	__UNKNOWN__	3	15252272	15252272	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15252272C>G	ENST00000253693.2	+	2	355					NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	NA		NA			positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						caccatgttgcccaggctgAA	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375	23473			1484	protein-coding gene	gene with protein product	calpain like protease, homolog of Aspergillus Nidulans PALB	606400			NA	8163008, 10051333	Standard	NM_014296	NM_014296	NA	Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.103-1339C>G	chr3.hg19:g.15252272C>G		NA		hg19	CCDS2624.1	0.02	1.660501	TTGxCCA	COVERED																																																																																			NOVEL	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252105.2	11	4.546307	KEEP	0	4	116	56	1698	CC	1	0.999559	0		+	7	60	234	0	0	16.395722	74	60	2497	198	ENST00000253693.2	0.08642	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	15413429	15413429	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15413429A>G			NA	NA				SH3BP5 (30554 upstream) : METTL6 (9352 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.15413429A>G		NA		hg19		0.02	-0.131554	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			7	2.390344	KEEP	3	0	0	8	201	AA	0	0	0			3	60	94	0	0	8.032588	8	60	238	40		0.272727	0.229173
HACL1	26061	__UNKNOWN__	__UNKNOWN__	3	15611633	15611633	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15611633A>G	ENST00000451445.2	-	10	973				HACL1_ENST00000456194.2_Intron|HACL1_ENST00000457447.2_Intron|HACL1_ENST00000321169.5_Intron|HACL1_ENST00000435217.2_Intron	NM_001284416.1	NP_001271345.1	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	NA		NA			cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)			NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						cacgaggtcaagagatcaaga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	26061	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	2-hydroxyphytanoyl-CoA lyase	HPCL	NA	10468558, 15644336	Standard	NM_012260	NM_001284416	NA	Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000451445.2:c.850-1540T>C	chr3.hg19:g.15611633A>G		NA	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	hg19		0.02	-0.157856	TCAxGAG	COVERED																																																																																			NOVEL	HACL1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000342872.1	6	3.609105	KEEP	4	0	0	12	330	AA	0.99254	0.320398	0		-	3	60	90	0	0	6.992295	14	60	410	48	ENST00000451445.2	0.176471	0.322807
ANKRD28	23243	__UNKNOWN__	__UNKNOWN__	3	15757769	15757769	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15757769A>G	ENST00000399451.2	-	9	1274				ANKRD28_ENST00000497037.1_Intron|ANKRD28_ENST00000383777.1_Intron	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	NA		NA				nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						gattacaggcatgagccaccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560	23243		Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits, Ankyrin repeat domain containing	29024	protein-coding gene	gene with protein product	phosphatase interactor targeting K protein, protein phosphatase 6 ankyrin repeat subunit A, protein phosphatase 1, regulatory subunit 65	611122			NA	9205841	Standard	NM_015199	NM_015199	NA	Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.907-1606T>C	chr3.hg19:g.15757769A>G		NA	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	hg19	CCDS46769.1	0.02	-0.263086	GGCxTGA	COVERED																																																																																			NOVEL	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339758.1	8	5.713268	KEEP	1	0	0	19	515	AA	0.99986	0.693571	0		-	3	60	94	0	0	6.795289	23	60	677	65	ENST00000399451.2	0.115385	0.693668
ANKRD28	23243	__UNKNOWN__	__UNKNOWN__	3	15768816	15768816	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:15768816C>G	ENST00000399451.2	-	7	918				ANKRD28_ENST00000497037.1_Intron|ANKRD28_ENST00000383777.1_Intron	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	NA		NA				nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						aggtgcggtgcctcacgcctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560	23243		Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits, Ankyrin repeat domain containing	29024	protein-coding gene	gene with protein product	phosphatase interactor targeting K protein, protein phosphatase 6 ankyrin repeat subunit A, protein phosphatase 1, regulatory subunit 65	611122			NA	9205841	Standard	NM_015199	NM_015199	NA	Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.551-2785G>C	chr3.hg19:g.15768816C>G		NA	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	hg19	CCDS46769.1	0.02	-0.13159	GTGxCTC	COVERED																																																																																			NOVEL	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339758.1	7	3.008802	KEEP	1	0	0	10	308	CC	0.992708	0.227502	0		-	3	60	97	0	0	8.20089	9	60	312	40	ENST00000399451.2	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	16288108	16288108	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:16288108C>T			NA	NA				GALNT15 (14609 upstream) : DPH3 (11376 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.16288108C>T		NA		hg19		0.02	-0.18419	AGGxGTG	COVERED																																																																																			NOVEL					0			7	2.706842	KEEP	0	0	0	9	254	CC	0.99254	0.420319	0			3	60	89	0	0	6.733934	16	60	503	43		0.157895	0.423478
TBC1D5	9779	__UNKNOWN__	__UNKNOWN__	3	17754980	17754980	__UNKNOWN__	Intron	SNP	C	C	T	rs141974484	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:17754980C>T	ENST00000253692.7	-	1	1565				TBC1D5_ENST00000429383.4_Intron|TBC1D5_ENST00000414318.2_Intron	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	NA		NA				retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						atgatccgcccgccttggcct	0.468		NA											C|||	46	0.0091853	0.0318	0.0058	5008	,	,	NA	16080	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374	9779			19166	protein-coding gene	gene with protein product		615740			NA	19531583	Standard	NM_014744	NM_014744	NA	Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.99+25854G>A	chr3.hg19:g.17754980C>T		NA	A6NP25|C9JP52	hg19	CCDS33714.1	0.02	-0.122806	GCCxGCC	COVERED																																																																																			NOVEL	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340301.3	3	3.911398	KEEP	1	0	0	13	389	CC	0.993634	0.195062	0		-	3	60	90	0	0	7.381896	10	60	327	42	ENST00000253692.7	0.230769	0.196312
TBC1D5	9779	__UNKNOWN__	__UNKNOWN__	3	17763222	17763222	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:17763222T>C	ENST00000253692.7	-	1	1565				TBC1D5_ENST00000429383.4_Intron|TBC1D5_ENST00000414318.2_Intron	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	NA		NA				retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						cctgtaatcctagcactttgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374	9779			19166	protein-coding gene	gene with protein product		615740			NA	19531583	Standard	NM_014744	NM_014744	NA	Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.99+17612A>G	chr3.hg19:g.17763222T>C		NA	A6NP25|C9JP52	hg19	CCDS33714.1	0.02	-0.122794	TCCxAGC	COVERED																																																																																			NOVEL	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340301.3	7	3.608703	KEEP	0	0	0	12	326	TT	0.993634	0.195062	0		-	3	60	103	0	0	8.572864	11	60	326	37	ENST00000253692.7	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	20061093	20061093	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:20061093T>C			NA	NA				PP2D1 (7271 upstream) : KAT2B (20421 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.20061093T>C		NA		hg19		0.02	-0.157875	TCAxGCC	COVERED																																																																																			NOVEL					0			7	2.405722	KEEP	0	0	0	8	216	TT	0.99257	0.320408	0			3	60	101	1	0	8.010108	15	60	444	36		0.166667	0.322807
SGOL1	151648	__UNKNOWN__	__UNKNOWN__	3	20225153	20225153	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:20225153G>A	ENST00000412997.1	-	3	637	c.286C>T	c.(286-288)Cta>Tta	p.L96L	SGOL1_ENST00000412868.1_Silent_p.L96L|SGOL1_ENST00000442720.1_Silent_p.L96L|SGOL1_ENST00000417364.1_Silent_p.L96L|SGOL1_ENST00000425061.1_Silent_p.L96L|SGOL1_ENST00000429446.3_Silent_p.L96L|SGOL1_ENST00000306698.2_Silent_p.L96L|SGOL1_ENST00000263753.4_Silent_p.L96L|SGOL1_ENST00000443724.1_Silent_p.L96L|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000421451.1_Silent_p.L96L|SGOL1_ENST00000452020.1_Silent_p.L96L|SGOL1_ENST00000383774.1_Silent_p.L96L|SGOL1_ENST00000437051.1_Silent_p.L96L|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000419233.2_Silent_p.L96L	NM_001199251.1	NP_001186180.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	96	Necessary for interaction with PPP2CA and PPP2R1A.	NA			attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						AATGCATATAGCTGACATGTG	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													198	185	189			NA	NA	3		NA											NA				20225153		2203	4300	6503	SO:0001819	synonymous_variant			BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810	151648			25088	protein-coding gene	gene with protein product		609168			NA	12747765	Standard	NM_138484	NM_001199251	NA	Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000412997.1:c.286C>T	chr3.hg19:g.20225153G>A		NA	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	hg19	CCDS46773.1	0.02	-0.438607	ATAxCTG	COVERED																																																																																			NOVEL	SGOL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340012.2	0	2.707573	KEEP	0	0	0	9	271	GG	0.99254	0.952699	0		-	19	60	586	0	0	53.242071	31	60	1099	91	ENST00000412997.1	0.38	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	20555981	20555981	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:20555981A>C			NA	NA				RNU6-815P (6733 upstream) : AC104441.1 (623773 downstream)						NA		NA									NA						gttggccaggatggtctcgat	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.20555981A>C		NA		hg19		0.02	-0.061397	AGGxTGG	UNCOVERED																																																																																			NOVEL					0			4	2.405385	KEEP	0	0	0	8	213	AA	0.99257	0.043461	0			2	60	72	0	0	6.335801	5	60	147	22		0.285714	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	22967791	22967791	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:22967791G>A			NA	NA				HMGB1P5 (543371 upstream) : UBE2E2-AS1 (268769 downstream)						NA		NA									NA						gctcatgcctgtaatcccagc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.22967791G>A		NA		hg19		0.02	-0.096493	CCTxTAA	UNCOVERED																																																																																			NOVEL					0			2	2.406956	KEEP	1	0	0	8	238	GG	0	0	0			3	60	88	0	0	7.932375	5	60	168	29		0.375	0.120436
UBE2E2	7325	__UNKNOWN__	__UNKNOWN__	3	23620978	23620978	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:23620978T>C	ENST00000396703.1	+	6	688				UBE2E2_ENST00000425792.1_Intron	NM_152653.3	NP_689866.1	Q96LR5	UB2E2_HUMAN	ubiquitin-conjugating enzyme E2E 2	NA		NA			ISG15-protein conjugation (GO:0032020)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)		ATP binding (GO:0005524)|ISG15 ligase activity (GO:0042296)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(2)	10						gccaggagtttgagaccagcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(85;1941 2083 9456)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057886	CCDS2637.1	3p24.2	2011-05-19	2011-05-19		ENSG00000182247	ENSG00000182247	7325		Ubiquitin-conjugating enzymes E2	12478	protein-coding gene	gene with protein product		602163	ubiquitin-conjugating enzyme E2E 2 (homologous to yeast UBC4/5), ubiquitin-conjugating enzyme E2E 2 (UBC4/5 homolog, yeast)		NA	9371400	Standard	NM_152653	NM_152653	NA	Approved	UbcH8, FLJ25157	uc003ccg.2	Q96LR5	OTTHUMG00000130482	ENST00000396703.1:c.509-10247T>C	chr3.hg19:g.23620978T>C		NA		hg19	CCDS2637.1	0.02	-0.35084	GTTxGAG	COVERED																																																																																			NOVEL	UBE2E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252881.2	19	3.608201	KEEP	0	0	0	12	321	TT	0.994391	0.872784	0		+	3	56	100	0	0	6.87573	35	60	1069	72	ENST00000396703.1	0.078947	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	23828270	23828270	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:23828270A>G			NA	NA				AC020626.1 (19075 upstream) : UBE2E1-AS1 (17244 downstream)						NA		NA									NA						tgcctgcctcagcctcccaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.23828270A>G		NA		hg19		0.02	-0.157468	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.406337	KEEP	3	0	0	8	224	AA	0	0	0			6	60	197	0	0	17.965774	10	60	310	40		0.375	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	23828307	23828307	__UNKNOWN__	IGR	SNP	C	C	T	rs34466550	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:23828307C>T			NA	NA				AC020626.1 (19112 upstream) : UBE2E1-AS1 (17207 downstream)						NA		NA									NA						catgagccaccgcacccggcc	0.517		NA											C|||	724	0.144569	0.1551	0.1686	5008	,	,	NA	17735	0.0417	NA	0.0487	False	NA	,,,	NA	NA	NA	2504	0.318	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.23828307C>T		NA		hg19		0.02	-0.166655	CACxGCA	COVERED																																																																																			NOVEL					0			5	3.600199	KEEP	1	0	0	12	328	CC	0.993072	0.351495	0			5	60	146	0	0	12.838531	10	60	341	45		0.333333	0.353947
THRB	7068	__UNKNOWN__	__UNKNOWN__	3	24321164	24321164	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:24321164G>A	ENST00000356447.4	-	3	243				THRB_ENST00000396671.2_Intron|THRB_ENST00000416420.1_Intron	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	NA		NA			female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	gggattacaggcgtgagccac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(21;896 1043 15021 37958)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090	7068		Nuclear hormone receptors	11799	protein-coding gene	gene with protein product	avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, oncogene ERBA2, generalized resistance to thyroid hormone, thyroid hormone receptor beta 1	190160	thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2), pituitary resistance to thyroid hormone, thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)	ERBA2, PRTH	NA	1973914, 8040303	Standard	NM_000461	NM_000461	NA	Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.42-50672C>T	chr3.hg19:g.24321164G>A		NA	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	hg19	CCDS2641.1	0.02	-0.201765	CAGxCGT	COVERED																																																																																			NOVEL	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252877.3	7	2.708148	KEEP	3	0	0	9	280	GG	0.99254	0.486885	0		-	3	60	90	0	0	6.692541	18	60	618	58	ENST00000356447.4	0.142857	0.490544
THRB	7068	__UNKNOWN__	__UNKNOWN__	3	24374363	24374363	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:24374363T>C	ENST00000356447.4	-	2	243				THRB_ENST00000396671.2_Intron|THRB_ENST00000416420.1_Intron	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	NA		NA			female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	ctggctaacatggtgaaaccc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(21;896 1043 15021 37958)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090	7068		Nuclear hormone receptors	11799	protein-coding gene	gene with protein product	avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, oncogene ERBA2, generalized resistance to thyroid hormone, thyroid hormone receptor beta 1	190160	thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2), pituitary resistance to thyroid hormone, thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)	ERBA2, PRTH	NA	1973914, 8040303	Standard	NM_000461	NM_000461	NA	Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.41+4427A>G	chr3.hg19:g.24374363T>C		NA	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	hg19	CCDS2641.1	0.02	-0.114018	ACAxGGT	UNCOVERED																																																																																			NOVEL	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252877.3	6	3.306964	KEEP	5	0	0	11	292	TT	0	0	0		-	3	40	86	0	0	6.982111	10	60	304	35	ENST00000356447.4	0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	24597999	24597999	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:24597999T>C			NA	NA				MIR4792 (35073 upstream) : AC133680.1 (131410 downstream)						NA		NA									NA						tttgggaggctgaggcgggtg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.24597999T>C		NA		hg19		0.02	-0.4122	GGCxGAG	COVERED																																																																																			NOVEL					0			9	3.54093	KEEP	2	1	26	21	587	TT	0.999863	0.941612	0			6	60	180	0	0	13.256456	38	60	1126	86		0.136364	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	24598005	24598005	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:24598005G>A			NA	NA				MIR4792 (35079 upstream) : AC133680.1 (131404 downstream)						NA		NA									NA						aggctgaggcgggtggatcac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.24598005G>A		NA		hg19		0.02	-0.324537	GGCxGGT	COVERED																																																																																			NOVEL					0			6	2.540242	KEEP	2	1	30	19	557	GG	0.999859	0.835598	0			4	60	110	0	0	7.514682	31	60	1000	72		0.114286	0.835716
RARB	5915	__UNKNOWN__	__UNKNOWN__	3	25495014	25495014	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:25495014A>G	ENST00000330688.4	+	2	578				RARB_ENST00000437042.2_Intron|RARB_ENST00000404969.1_Intron|RARB_ENST00000462272.1_Intron	NM_000965.3	NP_000956.2	P10826	RARB_HUMAN	retinoic acid receptor, beta	NA		NA			embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	gattacaggcatgagccactg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092	5915		Nuclear hormone receptors	9865	protein-coding gene	gene with protein product		180220			NA		Standard	NM_000965, NM_016152	NM_016152	NA	Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000330688.4:c.158-7670A>G	chr3.hg19:g.25495014A>G		NA	P12891|Q00989|Q15298|Q9UN48	hg19	CCDS2642.1	0.02	-0.15787	GGCxTGA	COVERED																																																																																			NOVEL	RARB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340847.1	5	2.40592	KEEP	0	0	0	8	224	AA	0.99257	0.320408	0		+	3	60	89	0	0	7.072745	12	60	360	39	ENST00000330688.4	0.2	0.322807
RARB	5915	__UNKNOWN__	__UNKNOWN__	3	25586485	25586485	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:25586485T>C	ENST00000330688.4	+	4	869				RARB_ENST00000437042.2_Intron|RARB_ENST00000404969.1_Intron|RARB_ENST00000458646.1_Intron|RARB_ENST00000462272.1_Intron	NM_000965.3	NP_000956.2	P10826	RARB_HUMAN	retinoic acid receptor, beta	NA		NA			embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	cggagtctcgttctgtcgccc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092	5915		Nuclear hormone receptors	9865	protein-coding gene	gene with protein product		180220			NA		Standard	NM_000965, NM_016152	NM_016152	NA	Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000330688.4:c.449-24764T>C	chr3.hg19:g.25586485T>C		NA	P12891|Q00989|Q15298|Q9UN48	hg19	CCDS2642.1	0.02	-0.131526	TCGxTCT	COVERED																																																																																			NOVEL	RARB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340847.1	4	3.307057	KEEP	0	0	0	11	290	TT	0.993072	0.227586	0		+	3	60	89	0	0	7.532109	8	60	231	39	ENST00000330688.4	0.272727	0.229173
NGLY1	55768	__UNKNOWN__	__UNKNOWN__	3	25810313	25810313	__UNKNOWN__	Intron	SNP	G	G	A	rs9828806	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:25810313G>A	ENST00000417874.2	-	3	294				NGLY1_ENST00000422724.2_Intron|NGLY1_ENST00000428257.1_Intron|NGLY1_ENST00000280700.5_Intron|NGLY1_ENST00000396649.3_Intron	NM_001145294.1	NP_001138766.1	Q96IV0	NGLY1_HUMAN	N-glycanase 1	NA		NA			glycoprotein catabolic process (GO:0006516)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity (GO:0000224)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)	18						gattacaggcgtgagccacgg	0.458		NA											G|||	2	0.000399361	0.0008	0.0014	5008	,	,	NA	13011	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF250924	CCDS33719.1, CCDS46777.1, CCDS46778.1, CCDS46779.1	3p23	2006-08-30			ENSG00000151092	ENSG00000151092	55768			17646	protein-coding gene	gene with protein product		610661			NA		Standard		NM_018297	NA	Approved	FLJ11005, PNG1	uc003cdl.3	Q96IV0	OTTHUMG00000155600	ENST00000417874.2:c.121-4511C>T	chr3.hg19:g.25810313G>A		NA	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	hg19	CCDS46777.1	0.02	-0.219295	GGCxTGA	COVERED																																																																																			NOVEL	NGLY1-008	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340839.2	9	3.008663	KEEP	1	0	0	10	300	GG	0.992708	0.578679	0		-	3	60	88	0	0	6.561446	17	60	564	54	ENST00000417874.2	0.15	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	27533231	27533231	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:27533231A>C			NA	NA				SLC4A7 (7344 upstream) : RNU1-96P (22130 downstream)						NA		NA									NA						gattctcctgactcagcctcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.27533231A>C		NA		hg19		0.02	-0.113992	CTGxCTC	COVERED																																																																																			NOVEL					0			7	2.404854	KEEP	0	0	0	8	209	AA	0.99257	0.194853	0			3	60	101	0	0	8.601716	9	60	265	29		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	27564121	27564121	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:27564121C>T			NA	NA				RNU1-96P (8598 upstream) : Y_RNA (25126 downstream)						NA		NA									NA						gagccgagatcgtgccattgc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.27564121C>T		NA		hg19		0.02	-0.175425	GATxGTG	COVERED																																																																																			NOVEL					0			6	3.609875	KEEP	4	0	0	12	358	CC	0.992708	0.384582	0			3	60	84	0	0	6.479329	13	60	426	50		0.1875	0.387407
RBMS3	27303	__UNKNOWN__	__UNKNOWN__	3	30020461	30020461	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:30020461A>C	ENST00000452462.1	+	12	1180				RBMS3_ENST00000473799.1_Intron|RBMS3_ENST00000396583.3_Intron|RBMS3_ENST00000456853.1_Intron|RBMS3_ENST00000273139.9_Intron|RBMS3_ENST00000383766.2_Intron|RBMS3_ENST00000383767.2_Intron|RBMS3_ENST00000434693.2_Intron			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	NA		NA			positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				tacaaaaataaaagtaaaaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642	27303		RNA binding motif (RRM) containing	13427	protein-coding gene	gene with protein product	RNA-binding protein	605786	RNA binding motif, single stranded interacting protein		NA	10675610	Standard	NM_001003792	NM_001003793	NA	Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000452462.1:c.1051-9173A>C	chr3.hg19:g.30020461A>C		NA	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	hg19	CCDS54558.1	0.02	-0.052627	ATAxAAG	UNCOVERED																																																																																			NOVEL	RBMS3-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341303.1	6	2.404687	KEEP	0	0	0	8	208	AA	0.99257	0.036492	0		+	2	60	72	0	0	6.495922	4	60	122	19	ENST00000452462.1	0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	30076080	30076080	__UNKNOWN__	IGR	SNP	A	A	G	rs182050367		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:30076080A>G			NA	NA				RBMS3 (24194 upstream) : AC137674.1 (103658 downstream)						NA		NA									NA						gaaagaaaagaaaggaaggaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.30076080A>G		NA		hg19		0.02	-0.131538	AAGxAAG	COVERED																																																																																			NOVEL					0			14	2.99952	KEEP	3	0	0	10	242	AA	0.99254	0.227464	0			4	60	127	1	0	11.124281	9	60	257	41		0.307692	0.229173
TGFBR2	7048	__UNKNOWN__	__UNKNOWN__	3	30677741	30677741	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:30677741G>A	ENST00000295754.5	+	2	476				TGFBR2_ENST00000359013.4_Intron	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	NA		NA			activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						ccCGTACTAGGTATTTTACTA	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513	7048			11773	protein-coding gene	gene with protein product		190182	transforming growth factor, beta receptor II (70-80kD)	MFS2	NA	1319842, 15235604	Standard		NM_001024847	NA	Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.95-8498G>A	chr3.hg19:g.30677741G>A		NA	B4DTV5|Q15580|Q6DKT6|Q99474	hg19	CCDS2648.1	0.02	-0.175446	TAGxTAT	COVERED																																																																																			NOVEL	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252994.2	5	4.813755	KEEP	1	0	0	16	477	GG	0.997832	0.386567	0		+	3	60	95	0	0	7.33327	16	60	531	53	ENST00000295754.5	0.157895	0.387407
GADL1	339896	__UNKNOWN__	__UNKNOWN__	3	30840160	30840160	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:30840160T>C	ENST00000282538.5	-	12	1401				GADL1_ENST00000454381.3_3'UTR	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	NA		NA			carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						aacagtcccctaaagtcttaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644	339896			27949	protein-coding gene	gene with protein product		615601			NA		Standard	NM_207359	NM_207359	NA	Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1250+2220A>G	chr3.hg19:g.30840160T>C		NA		hg19	CCDS2649.2	0.02	-0.315717	CCCxAAA	COVERED																																																																																			NOVEL	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253106.2	2	2.404486	KEEP	0	0	0	8	213	TT	0.99257	0.812384	0		-	5	60	150	0	0	11.089191	31	60	910	56	ENST00000282538.5	0.138889	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	31553822	31553822	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:31553822G>A			NA	NA				AC099540.1 (116299 upstream) : STT3B (20307 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.31553822G>A		NA		hg19		0.02	-0.131562	GGCxTGA	COVERED																																																																																			NOVEL					0			4	4.211584	KEEP	5	0	0	14	408	GG	0.993634	0.227714	0			3	60	84	0	0	6.782144	10	60	324	49		0.230769	0.229173
GPD1L	23171	__UNKNOWN__	__UNKNOWN__	3	32153869	32153869	__UNKNOWN__	Intron	SNP	G	G	A	rs13099475	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:32153869G>A	ENST00000282541.5	+	1	248					NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						gctcatgcctgtaatcccaac	0.438		NA											G|||	2470	0.493211	0.6362	0.2478	5008	,	,	NA	9951	0.6131	NA	0.2843	False	NA	,,,	NA	NA	NA	2504	0.5654	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642	23171			28956	protein-coding gene	gene with protein product		611778			NA	7788527	Standard	NM_015141	NM_015141	NA	Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.47+5619G>A	chr3.hg19:g.32153869G>A		NA	A8K9U3|Q14702|Q9BRM5	hg19	CCDS33729.1	0.02	-0.149123	CCTxTAA	UNCOVERED																																																																																			NOVEL	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341975.2	7	2.407191	KEEP	1	0	0	8	246	GG	0	0	0		+	3	60	88	0	0	7.181865	10	60	332	37	ENST00000282541.5	0.230769	0.292001
GPD1L	23171	__UNKNOWN__	__UNKNOWN__	3	32153875	32153875	__UNKNOWN__	Intron	SNP	C	C	T	rs13099166	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:32153875C>T	ENST00000282541.5	+	1	248					NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						gcctgtaatcccaacactttg	0.423		NA											C|||	2466	0.492412	0.6331	0.2478	5008	,	,	NA	10429	0.6131	NA	0.2843	False	NA	,,,	NA	NA	NA	2504	0.5654	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642	23171			28956	protein-coding gene	gene with protein product		611778			NA	7788527	Standard	NM_015141	NM_015141	NA	Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.47+5625C>T	chr3.hg19:g.32153875C>T		NA	A8K9U3|Q14702|Q9BRM5	hg19	CCDS33729.1	0.02	-0.157891	ATCxCAA	UNCOVERED																																																																																			NOVEL	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341975.2	8	2.407096	KEEP	1	0	0	8	246	CC	0	0	0		+	3	60	92	0	0	7.581946	10	60	322	39	ENST00000282541.5	0.230769	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	32679084	32679084	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:32679084G>A			NA	NA				DYNC1LI1 (66718 upstream) : CNOT10 (47552 downstream)						NA		NA									NA						ccaaagtgctgggattatagg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.32679084G>A		NA		hg19		0.02	-0.201766	GCTxGGA	COVERED																																																																																			NOVEL					0			11	2.708065	KEEP	0	0	0	9	274	GG	0.99254	0.486885	0			3	60	91	0	0	6.727312	19	60	644	47		0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	32679091	32679091	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:32679091T>C			NA	NA				DYNC1LI1 (66725 upstream) : CNOT10 (47545 downstream)						NA		NA									NA						gctgggattataggggtgagc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.32679091T>C		NA		hg19		0.02	-0.201676	TTAxAGG	COVERED																																																																																			NOVEL					0			11	2.705947	KEEP	0	0	0	9	235	TT	0.99254	0.486885	0			4	57	122	0	0	9.580949	18	60	523	46		0.181818	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	33317834	33317834	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:33317834G>A			NA	NA				SUSD5 (57127 upstream) : FBXL2 (1079 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.33317834G>A		NA		hg19		0.02	-0.412272	GGCxTGA	COVERED																																																																																			NOVEL					0			12	4.812189	KEEP	0	0	0	16	453	GG	0.997832	0.939699	0			4	60	120	0	1	8.092012	40	60	1301	93		0.090909	0.941741
CLASP2	23122	__UNKNOWN__	__UNKNOWN__	3	33672925	33672925	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:33672925C>T	ENST00000468888.2	-	9	992				CLASP2_ENST00000313350.6_Intron|CLASP2_ENST00000307312.7_Intron|CLASP2_ENST00000482896.1_Intron|CLASP2_ENST00000399362.4_Intron|CLASP2_ENST00000539981.1_Intron|CLASP2_ENST00000461133.3_Intron|CLASP2_ENST00000333778.6_Intron|CLASP2_ENST00000487200.1_Intron|CLASP2_ENST00000480013.1_Intron|CLASP2_ENST00000359576.5_Intron			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	NA		NA			axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						tggtggctcacgcctgtaacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539	23122			17078	protein-coding gene	gene with protein product		605853			NA	9734811, 10899121	Standard	NM_001207044	NM_015097	NA	Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.945+858G>A	chr3.hg19:g.33672925C>T		NA	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	hg19		0.02	-0.096463	TCAxGCC	UNCOVERED																																																																																			NOVEL	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000344320.4	4	2.40672	KEEP	0	0	0	8	235	CC	0.99257	0.119541	0		-	3	60	89	0	0	7.532687	8	60	254	29	ENST00000468888.2	0.272727	0.120436
AC018359.1	0	__UNKNOWN__	__UNKNOWN__	3	34375493	34375493	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:34375493G>A	ENST00000424786.1	+	0	226										NA		NA									NA						ggatggtctcgatctcctgac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000424786.1:	chr3.hg19:g.34375493G>A		NA		hg19		0.02	-0.114026	CTCxATC	UNCOVERED																																																																																			NOVEL	AC018359.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341538.1	8	3.008505	KEEP	8	0	0	10	300	GG	0	0	0		+	3	44	87	0	0	7.081997	10	60	318	37	ENST00000424786.1	0.230769	0.162467
LRRFIP2	9209	__UNKNOWN__	__UNKNOWN__	3	37144270	37144270	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:37144270A>G	ENST00000396428.2	-	8	542				LRRFIP2_ENST00000421307.1_Intron|LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000336686.4_Intron|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421276.2_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	NA		NA			Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						tgggattacaagtgtgagcca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Whole gene deletion(1)	ovary(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167	9209			6703	protein-coding gene	gene with protein product		614043			NA	10366446	Standard	NM_006309	NM_017724	NA	Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000396428.2:c.393+5857T>C	chr3.hg19:g.37144270A>G		NA	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	hg19		0.02	-0.236791	ACAxGTG	COVERED																																																																																			NOVEL	LRRFIP2-006	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000342195.1	10	3.308736	KEEP	0	0	0	11	309	AA	0.993072	0.608164	0		-	3	60	106	0	0	8.164743	20	60	590	50	ENST00000396428.2	0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	37264183	37264183	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:37264183A>G			NA	NA				RP11-259K5.1 (4704 upstream) : RP11-259K5.2 (19096 downstream)						NA		NA									NA						tttttgagacagggtcttgct	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.37264183A>G		NA		hg19		0.02	-0.122802	GACxGGG	COVERED																																																																																			NOVEL					0			8	2.406114	KEEP	1	0	0	8	222	AA	0.99257	0.194853	0			3	60	94	0	0	7.901085	9	60	280	32		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	39401925	39401925	__UNKNOWN__	IGR	SNP	G	G	A	rs13090528	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:39401925G>A			NA	NA				CCR8 (26754 upstream) : SLC25A38 (22913 downstream)						NA		NA									NA						gaggtcaggagtttgagacca	0.488		NA											G|||	1882	0.375799	0.0129	0.451	5008	,	,	NA	14426	0.7024	NA	0.2982	False	NA	,,,	NA	NA	NA	2504	0.5562	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.39401925G>A		NA		hg19		0.02	-0.122789	GGAxTTT	COVERED																																																																																			NOVEL					0			7	3.306186	KEEP	5	0	0	11	320	GG	0.99257	0.194853	0			4	60	111	0	0	9.690443	8	60	258	37		0.333333	0.196312
MOBP	4336	__UNKNOWN__	__UNKNOWN__	3	39514174	39514174	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:39514174T>C	ENST00000383754.3	+	1	136				MOBP_ENST00000420739.1_Intron|MOBP_ENST00000428261.1_Intron|MOBP_ENST00000311042.6_Intron|MOBP_ENST00000415443.1_Intron|MOBP_ENST00000441980.2_Intron|MOBP_ENST00000447324.1_Intron|MOBP_ENST00000354668.4_Intron	NM_182935.2	NP_891980.1	Q13875	MOBP_HUMAN	myelin-associated oligodendrocyte basic protein	NA		NA			intracellular protein transport (GO:0006886)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6				KIRC - Kidney renal clear cell carcinoma(284;0.082)|Kidney(284;0.0998)		cctagcactttgggaggctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D28113	CCDS2687.1, CCDS63598.1, CCDS2688.1	3p21.33	2004-03-02			ENSG00000168314	ENSG00000168314	4336			7189	protein-coding gene	gene with protein product		600948			NA	7989345	Standard	NM_006501, NM_182934, NM_182935	NM_001278322	NA	Approved		uc031ryw.1	Q13875	OTTHUMG00000131347	ENST00000383754.3:c.-89+4943T>C	chr3.hg19:g.39514174T>C		NA	A8K2C2|G5E945|Q13874|Q6DHZ6|Q8TBJ1	hg19	CCDS2687.1	0.02	-0.140337	CTTxGGG	COVERED																																																																																			NOVEL	MOBP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254134.2	6	4.210097	KEEP	2	0	0	14	380	TT	0.993634	0.259304	0		+	3	27	99	0	0	8.401257	9	60	267	44	ENST00000383754.3	0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	41062700	41062700	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:41062700T>C			NA	NA				RP11-520A21.1 (49631 upstream) : RP11-372H2.1 (141077 downstream)						NA		NA									NA						ctgcaacctctgcctcctggg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.41062700T>C		NA		hg19		0.02	-0.166644	CTCxGCC	COVERED																																																																																			NOVEL					0			6	3.908656	KEEP	4	0	0	13	351	TT	0.993072	0.351495	0			3	60	88	0	0	6.710735	15	60	455	47		0.166667	0.353947
ULK4	54986	__UNKNOWN__	__UNKNOWN__	3	41716481	41716481	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:41716481T>C	ENST00000301831.4	-	29	3441					NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	NA		NA			cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		gcctgtaatctcagcactttg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038	54986			15784	protein-coding gene	gene with protein product		NA	unc-51-like kinase 4 (C. elegans)		NA	12477932	Standard	XM_929989	NM_017886	NA	Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2978+6517A>G	chr3.hg19:g.41716481T>C		NA	A6NF15|Q8IW79|Q9NWV6|Q9UF96	hg19	CCDS43071.1	0.02	-0.175406	ATCxCAG	COVERED																																																																																			NOVEL	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343490.1	4	2.706936	KEEP	0	0	0	9	250	TT	0.99254	0.384517	0		-	3	60	99	0	0	7.661197	17	60	515	39	ENST00000301831.4	0.15	0.387407
ULK4	54986	__UNKNOWN__	__UNKNOWN__	3	41817090	41817090	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:41817090T>C	ENST00000301831.4	-	21	2656					NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	NA		NA			cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		ggggtttcactatgttggcca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038	54986			15784	protein-coding gene	gene with protein product		NA	unc-51-like kinase 4 (C. elegans)		NA	12477932	Standard	XM_929989	NM_017886	NA	Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2193+14062A>G	chr3.hg19:g.41817090T>C		NA	A6NF15|Q8IW79|Q9NWV6|Q9UF96	hg19	CCDS43071.1	0.02	-0.131559	CACxATG	UNCOVERED																																																																																			NOVEL	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343490.1	5	2.706425	KEEP	6	0	0	9	243	TT	0	0	0		-	3	40	95	0	0	7.672365	12	60	353	34	ENST00000301831.4	0.2	0.229173
NKTR	4820	__UNKNOWN__	__UNKNOWN__	3	42656822	42656822	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:42656822T>C	ENST00000232978.8	+	3	246				RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|NKTR_ENST00000442970.1_Intron	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	NA		NA			protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		ctgcctgccttggcctcccaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857	4820			7833	protein-coding gene	gene with protein product	NK-tumor recognition protein, natural-killer cells cyclophilin-related protein, NK-TR protein	161565	natural killer-tumor recognition sequence		NA	8314596, 8144875	Standard	NM_005385	XM_005265173	NA	Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.59-2240T>C	chr3.hg19:g.42656822T>C		NA		hg19	CCDS2702.1	0.02	-0.201733	CCTxGGC	COVERED																																																																																			NOVEL	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256642.2	13	4.810633	KEEP	6	0	0	16	438	TT	0.995343	0.48826	0		+	3	60	101	0	0	7.86078	17	60	510	65	ENST00000232978.8	0.15	0.490544
NKTR	4820	__UNKNOWN__	__UNKNOWN__	3	42656851	42656851	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:42656851G>A	ENST00000232978.8	+	3	246				RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|NKTR_ENST00000442970.1_Intron	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	NA		NA			protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		gattacaggcgtgagccacca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857	4820			7833	protein-coding gene	gene with protein product	NK-tumor recognition protein, natural-killer cells cyclophilin-related protein, NK-TR protein	161565	natural killer-tumor recognition sequence		NA	8314596, 8144875	Standard	NM_005385	XM_005265173	NA	Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.59-2211G>A	chr3.hg19:g.42656851G>A		NA		hg19	CCDS2702.1	0.02	-0.22801	GGCxTGA	COVERED																																																																																			NOVEL	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256642.2	13	4.211891	KEEP	6	0	0	14	409	GG	0.993072	0.608164	0		+	3	60	92	0	0	6.706599	21	60	658	66	ENST00000232978.8	0.125	0.612407
NKTR	4820	__UNKNOWN__	__UNKNOWN__	3	42656861	42656861	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:42656861A>G	ENST00000232978.8	+	3	246				RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|NKTR_ENST00000442970.1_Intron	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	NA		NA			protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		gtgagccaccatgcctggccG	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857	4820			7833	protein-coding gene	gene with protein product	NK-tumor recognition protein, natural-killer cells cyclophilin-related protein, NK-TR protein	161565	natural killer-tumor recognition sequence		NA	8314596, 8144875	Standard	NM_005385	XM_005265173	NA	Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.59-2201A>G	chr3.hg19:g.42656861A>G		NA		hg19	CCDS2702.1	0.02	-0.227034	ACCxTGC	COVERED																																																																																			NOVEL	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256642.2	12	3.306451	KEEP	6	0	0	11	284	AA	0.99257	0.578599	0		+	3	60	90	0	0	6.56601	20	60	589	57	ENST00000232978.8	0.130435	0.58293
KRBOX1	100506243	__UNKNOWN__	__UNKNOWN__	3	42959559	42959559	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:42959559T>C	ENST00000426937.1	+	3	248				ZNF662_ENST00000541208.1_3'UTR			C9JBD0	KRBX1_HUMAN	KRAB box domain containing 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			lung(2)	2						gattgtgccattgcactccag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS54572.1	3p22.1	2014-02-12	2010-07-29		ENSG00000240747	ENSG00000240747	100506243		-	38708	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001205272	NM_001205272	NA	Approved		uc003cmm.4	C9JBD0	OTTHUMG00000156448	ENST00000426937.1:c.-47+9158T>C	chr3.hg19:g.42959559T>C		NA	B4DJE8	hg19	CCDS54572.1	0.02	3.759922	CCAxTGC	COVERED																																																																																			NOVEL	KRBOX1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344162.1	28	2.585632	KEEP	3	7	205	81	2130	TT	1	0.999997	0		+	5	60	175	0	0	11.182025	99	60	2850	281	ENST00000426937.1	0.048077	0.999997
ANO10	55129	__UNKNOWN__	__UNKNOWN__	3	43440516	43440516	__UNKNOWN__	Intron	SNP	C	C	G	rs552373988	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:43440516C>G	ENST00000414522.2	-	12	1911				ANO10_ENST00000292246.3_Intron|ANO10_ENST00000451430.2_Intron|ANO10_ENST00000350459.4_Intron|ANO10_ENST00000396091.3_Intron	NM_001204831.1	NP_001191760.1	Q9NW15	ANO10_HUMAN	anoctamin 10	NA		NA			cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						gatggggtttcgccatgttgc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746	55129		Ion channels / Chloride channels : Calcium activated : Anoctamins	25519	protein-coding gene	gene with protein product		613726	transmembrane protein 16K	TMEM16K	NA	12477932, 24692353	Standard	NM_018075	NM_001204831	NA	Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000414522.2:c.1798-26177G>C	chr3.hg19:g.43440516C>G		NA	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	hg19	CCDS56250.1	0.02	-0.096484	TTTxGCC	UNCOVERED																																																																																			NOVEL	ANO10-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344332.2	9	2.406243	KEEP	0	0	0	8	224	CC	0.99254	0.119538	0		-	3	36	98	0	0	8.57873	7	60	211	21	ENST00000414522.2	0.3	0.120436
ANO10	55129	__UNKNOWN__	__UNKNOWN__	3	43440517	43440517	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:43440517G>T	ENST00000414522.2	-	12	1911				ANO10_ENST00000292246.3_Intron|ANO10_ENST00000451430.2_Intron|ANO10_ENST00000350459.4_Intron|ANO10_ENST00000396091.3_Intron	NM_001204831.1	NP_001191760.1	Q9NW15	ANO10_HUMAN	anoctamin 10	NA		NA			cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell death (GO:0008219)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(3)|skin(3)	29						atggggtttcgccatgttgcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832508	CCDS2710.2, CCDS56247.1, CCDS56248.1, CCDS56249.1, CCDS56250.1	3p22.1-p21.33	2014-04-09	2008-08-28	2008-08-28	ENSG00000160746	ENSG00000160746	55129		Ion channels / Chloride channels : Calcium activated : Anoctamins	25519	protein-coding gene	gene with protein product		613726	transmembrane protein 16K	TMEM16K	NA	12477932, 24692353	Standard	NM_018075	NM_001204831	NA	Approved	FLJ10375, MGC47890, SCAR10	uc003cmv.3	Q9NW15	OTTHUMG00000133044	ENST00000414522.2:c.1798-26178C>A	chr3.hg19:g.43440517G>T		NA	A8K8K3|A8MV74|B3KTZ1|B3KY93|B4DJ83|B4DNK2|B7WP12|C9JHS1|Q8IXX9	hg19	CCDS56250.1	0.02	-0.087702	TTCxCCA	UNCOVERED																																																																																			NOVEL	ANO10-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344332.2	9	2.706687	KEEP	0	0	0	9	249	GG	0.99254	0.119538	0		-	3	36	93	0	0	8.078811	7	60	206	21	ENST00000414522.2	0.3	0.120436
ZNF445	353274	__UNKNOWN__	__UNKNOWN__	3	44485396	44485396	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:44485396A>C	ENST00000396077.2	-	0	6114				ZNF445_ENST00000425708.2_3'UTR	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	NA		NA			transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		tttgggaggcagaggtgggtg	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219	353274		Zinc fingers, C2H2-type, -, -, -	21018	protein-coding gene	gene with protein product		NA	zinc finger protein 168	ZNF168	NA	7814019	Standard	NM_181489	NM_181489	NA	Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.*2671T>G	chr3.hg19:g.44485396A>C		NA	Q3MJD1	hg19	CCDS2713.1	0.02	5.563609	GGCxGAG	COVERED																																																																																			NOVEL	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256647.2	36	3.630929	KEEP	3	7	204	84	2316	AA	1	1	0		-	9	60	274	0	0	16.896362	143	60	4295	380	ENST00000396077.2	0.059211	1
ZNF445	353274	__UNKNOWN__	__UNKNOWN__	3	44499610	44499610	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:44499610T>C	ENST00000396077.2	-	2	201				ZNF445_ENST00000425708.2_Intron	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	NA		NA			transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		cacctgtaattccagcacttt	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219	353274		Zinc fingers, C2H2-type, -, -, -	21018	protein-coding gene	gene with protein product		NA	zinc finger protein 168	ZNF168	NA	7814019	Standard	NM_181489	NM_181489	NA	Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.146+125A>G	chr3.hg19:g.44499610T>C		NA	Q3MJD1	hg19	CCDS2713.1	0.02	-0.228044	AATxCCA	COVERED																																																																																			NOVEL	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256647.2	7	2.390354	KEEP	1	0	0	8	205	TT	0.99257	0.578599	0		-	3	60	90	0	0	6.69333	18	60	551	49	ENST00000396077.2	0.142857	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	44529621	44529621	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:44529621A>G			NA	NA				ZNF445 (10459 upstream) : ZNF852 (10840 downstream)						NA		NA									NA						acaagagcaaaactctgtctc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.44529621A>G		NA		hg19		0.02	-0.201734	CAAxACT	COVERED																																																																																			NOVEL					0			8	3.30705	KEEP	2	0	0	11	293	AA	0.99254	0.486885	0			3	60	98	0	0	7.492246	18	60	544	50		0.142857	0.490544
ZDHHC3	51304	__UNKNOWN__	__UNKNOWN__	3	44967610	44967610	__UNKNOWN__	3'UTR	SNP	C	C	T	rs191480973	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:44967610C>T	ENST00000424952.2	-	0	1739				ZDHHC3_ENST00000296127.3_3'UTR	NM_001135179.1	NP_001128651.1	Q9NYG2	ZDHC3_HUMAN	zinc finger, DHHC-type containing 3	NA		NA			protein palmitoylation (GO:0018345)|protein targeting (GO:0006605)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00943)|KIRC - Kidney renal clear cell carcinoma(197;0.053)|Kidney(197;0.0665)		AATTGCTTTGCGAGTTAGCAG	0.517		NA											C|||	4	0.000798722	0.0	0.0029	5008	,	,	NA	19872	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF247703	CCDS2724.1, CCDS46811.1	3p21.31	2010-02-09			ENSG00000163812	ENSG00000163812	51304		Zinc fingers, DHHC-type	18470	protein-coding gene	gene with protein product	golgi-specific DHHC Zinc Finger Protein	NA			NA	19955568	Standard	NM_016598	NM_016598	NA	Approved	ZNF373, GODZ	uc003cod.3	Q9NYG2	OTTHUMG00000133093	ENST00000424952.2:c.*571G>A	chr3.hg19:g.44967610C>T		NA	Q53A17|Q96BL0	hg19	CCDS46811.1	0.02	1.157779	TTGxGAG	COVERED																																																																																			NOVEL	ZDHHC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347004.1	3	6.016563	KEEP	0	0	0	20	580	CC	0.999869	0.999788	0		-	5	60	142	0	0	8.143936	88	60	2915	164	ENST00000424952.2	0.053763	0.999919
LIMD1	8994	__UNKNOWN__	__UNKNOWN__	3	45628323	45628323	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:45628323G>A	ENST00000465039.1	+	2	101							Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	NA		NA			cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		gattacaggcgtgagccaccg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791	8994			6612	protein-coding gene	gene with protein product		604543			NA	10647888	Standard	NM_014240	NM_014240	NA	Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000465039.1:c.102-26061G>A	chr3.hg19:g.45628323G>A		NA	Q17RQ1|Q9BQQ9|Q9NQ47	hg19		0.02	-0.166655	GGCxTGA	COVERED																																																																																			NOVEL	LIMD1-004	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000345081.1	12	3.008511	KEEP	4	0	0	10	295	GG	0.99254	0.351306	0		+	3	60	91	0	0	7.179017	13	60	425	42	ENST00000465039.1	0.1875	0.353947
LIMD1	8994	__UNKNOWN__	__UNKNOWN__	3	45630377	45630377	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:45630377C>T	ENST00000465039.1	+	2	101							Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	NA		NA			cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		tgagctgagaccatgccattg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791	8994			6612	protein-coding gene	gene with protein product		604543			NA	10647888	Standard	NM_014240	NM_014240	NA	Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000465039.1:c.102-24007C>T	chr3.hg19:g.45630377C>T		NA	Q17RQ1|Q9BQQ9|Q9NQ47	hg19		0.02	-0.149119	AGAxCAT	COVERED																																																																																			NOVEL	LIMD1-004	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000345081.1	6	2.406762	KEEP	0	0	0	8	241	CC	0.99257	0.289832	0		+	4	60	115	0	0	9.380875	13	60	431	33	ENST00000465039.1	0.235294	0.292001
LIMD1	8994	__UNKNOWN__	__UNKNOWN__	3	45722020	45722020	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:45722020A>C	ENST00000273317.4	+	0	5521				LIMD1-AS1_ENST00000427644.1_RNA|LIMD1-AS1_ENST00000429798.1_RNA	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	NA		NA			cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		gttgcccaggatggtctggaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791	8994			6612	protein-coding gene	gene with protein product		604543			NA	10647888	Standard	NM_014240	NM_014240	NA	Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.*3469A>C	chr3.hg19:g.45722020A>C		NA	Q17RQ1|Q9BQQ9|Q9NQ47	hg19	CCDS2729.1	0.02	1.845053	AGGxTGG	COVERED																																																																																			NOVEL	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257327.1	11	5.017268	KEEP	0	1	6	19	518	AA	0.999863	0.990828	0		+	5	60	170	0	0	11.915725	55	60	1593	106	ENST00000273317.4	0.083333	0.990964
LIMD1-AS1	644714	__UNKNOWN__	__UNKNOWN__	3	45728970	45728970	__UNKNOWN__	RNA	SNP	A	A	T	rs149999871	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:45728970A>T	ENST00000427644.1	-	0	507				LIMD1-AS1_ENST00000429798.1_RNA	NR_033947.1				LIMD1 antisense RNA 1	NA		NA									NA						aaaaatacaaaaaattagtcg	0.522		NA											A|||	78	0.0155751	0.0008	0.013	5008	,	,	NA	17094	0.002	NA	0.0447	False	NA	,,,	NA	NA	NA	2504	0.0215	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK026206		3p21.31	2012-10-12	2012-08-15		ENSG00000230530	ENSG00000230530	644714		Long non-coding RNAs	44107	non-coding RNA	RNA, long non-coding		NA	LIMD1 antisense RNA 1 (non-protein coding)		NA		Standard	NR_033947	NR_033947	NA	Approved		uc003cor.3		OTTHUMG00000156652	ENST00000427644.1:	chr3.hg19:g.45728970A>T		NA		hg19		0.02	-0.122768	CAAxAAA	COVERED																																																																																			NOVEL	LIMD1-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000345062.1	9	3.004892	KEEP	1	0	0	10	250	AA	0.99254	0.194847	0		-	6	60	169	0	0	15.609231	8	60	229	33	ENST00000427644.1	0.428571	0.196312
TDGF1	6997	__UNKNOWN__	__UNKNOWN__	3	46623214	46623214	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:46623214T>G	ENST00000296145.5	+	0	1774				TDGF1_ENST00000542931.1_3'UTR	NM_003212.3	NP_003203.1	P13385	TDGF1_HUMAN	teratocarcinoma-derived growth factor 1	NA		NA			activation of MAPK activity (GO:0000187)|anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle cell differentiation (GO:0055007)|cell differentiation (GO:0030154)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-6 (GO:0071354)|cellular response to tumor necrosis factor (GO:0071356)|embryo development (GO:0009790)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of signal transduction (GO:0009966)|vasculogenesis (GO:0001570)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	growth factor activity (GO:0008083)|receptor binding (GO:0005102)			cervix(2)|endometrium(1)|kidney(1)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0173)|Kidney(197;0.0204)		tattggccagtctggtctcga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M96955	CCDS2742.1, CCDS54575.1	3p21.31	2012-10-03			ENSG00000241186	ENSG00000241186	6997			11701	protein-coding gene	gene with protein product		187395			NA	1882841, 10393436	Standard	NM_003212	NM_003212	NA	Approved	CRIPTO, CR, Cripto-1	uc021wxd.1	P13385	OTTHUMG00000133482	ENST00000296145.5:c.*474T>G	chr3.hg19:g.46623214T>G		NA	Q8TCC1	hg19	CCDS2742.1	0.02	1.467729	CAGxCTG	COVERED																																																																																			NOVEL	TDGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257378.2	3	3.437845	KEEP	0	1	30	22	572	TT	0.999909	0.997073	0		+	4	60	129	0	0	8.233917	63	60	1719	117	ENST00000296145.5	0.059701	0.997163
KIF9-AS1	285352	__UNKNOWN__	__UNKNOWN__	3	47212028	47212028	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47212028G>A	ENST00000429315.3	+	0	329					NR_033373.1				KIF9 antisense RNA 1	NA		NA									NA						ggtggctcacgcctgtaatcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							3p21.31	2012-11-19			ENSG00000227398	ENSG00000227398	285352		Long non-coding RNAs	26822	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_033373	NA	Approved	FLJ39534	uc003cqw.2		OTTHUMG00000156533	ENST00000429315.3:	chr3.hg19:g.47212028G>A		NA		hg19		0.02	-0.140338	CACxCCT	UNCOVERED																																																																																			NOVEL	KIF9-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000344527.3	7	2.406252	KEEP	2	0	0	8	229	GG	0	0	0		+	3	60	88	0	0	7.072986	11	60	357	38	ENST00000429315.3	0.214286	0.260965
KIF9-AS1	285352	__UNKNOWN__	__UNKNOWN__	3	47228284	47228284	__UNKNOWN__	RNA	SNP	G	G	C	rs295438		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47228284G>C	ENST00000429315.3	+	0	329					NR_033373.1				KIF9 antisense RNA 1	NA		NA									NA						gccaggagttggagaccagcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							3p21.31	2012-11-19			ENSG00000227398	ENSG00000227398	285352		Long non-coding RNAs	26822	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_033373	NA	Approved	FLJ39534	uc003cqw.2		OTTHUMG00000156533	ENST00000429315.3:	chr3.hg19:g.47228284G>C		NA		hg19		0.02	-0.114031	GTTxGAG	COVERED																																																																																			NOVEL	KIF9-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000344527.3	6	3.610611	KEEP	1	0	0	12	361	GG	0.993072	0.194952	0		+	3	60	88	0	0	7.432163	8	60	265	32	ENST00000429315.3	0.272727	0.196312
KLHL18	23276	__UNKNOWN__	__UNKNOWN__	3	47373203	47373203	__UNKNOWN__	Intron	SNP	G	G	A	rs548024354		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47373203G>A	ENST00000232766.5	+	5	620				KLHL18_ENST00000455924.2_Intron	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	NA		NA								endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		gattacaggcgtgagccactg	0.493		NA											g|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	12618	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648	23276		Kelch-like, BTB/POZ domain containing	29120	protein-coding gene	gene with protein product		NA	kelch-like 18 (Drosophila)		NA	9872452	Standard	NM_025010	NM_025010	NA	Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.601-1444G>A	chr3.hg19:g.47373203G>A		NA	A8K612|Q7Z3E8|Q8N125	hg19	CCDS33749.1	0.02	-0.236759	GGCxTGA	COVERED																																																																																			NOVEL	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344493.1	9	3.602837	KEEP	2	0	0	12	312	GG	0.993634	0.608508	0		+	3	60	88	0	0	6.36661	20	60	625	55	ENST00000232766.5	0.130435	0.612407
KLHL18	23276	__UNKNOWN__	__UNKNOWN__	3	47380751	47380751	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47380751A>G	ENST00000232766.5	+	8	1141				KLHL18_ENST00000455924.2_Intron	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	NA		NA								endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	21		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00645)|Kidney(197;0.00741)		ttgggaggctaaggcgggagg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018338	CCDS33749.1	3p21	2013-01-30	2013-01-30		ENSG00000114648	ENSG00000114648	23276		Kelch-like, BTB/POZ domain containing	29120	protein-coding gene	gene with protein product		NA	kelch-like 18 (Drosophila)		NA	9872452	Standard	NM_025010	NM_025010	NA	Approved	KIAA0795, FLJ13703	uc003crd.3	O94889	OTTHUMG00000156522	ENST00000232766.5:c.1122-1311A>G	chr3.hg19:g.47380751A>G		NA	A8K612|Q7Z3E8|Q8N125	hg19	CCDS33749.1	0.02	-0.140312	GCTxAGG	COVERED																																																																																			NOVEL	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344493.1	6	2.405495	KEEP	1	0	0	8	211	AT	0.99257	0.259026	0		+	3	60	97	0	0	7.872646	12	60	343	30	ENST00000232766.5	0.2	0.260965
PTPN23	25930	__UNKNOWN__	__UNKNOWN__	3	47432498	47432498	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47432498T>G	ENST00000265562.4	+	2	161				PTPN23_ENST00000431726.1_Intron	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	NA		NA			cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		actttgggagtctgaggcaga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201	25930		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	14406	protein-coding gene	gene with protein product		606584			NA	11095967	Standard	NM_015466	NM_015466	NA	Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.85-5135T>G	chr3.hg19:g.47432498T>G		NA	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	hg19	CCDS2754.1	0.02	-0.149003	GAGxCTG	COVERED																																																																																			NOVEL	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257492.2	7	2.406265	KEEP	0	0	0	8	225	TT	0.99257	0.289832	0		+	4	60	135	0	0	11.632916	11	60	310	34	ENST00000265562.4	0.266667	0.292001
SCAP	22937	__UNKNOWN__	__UNKNOWN__	3	47465090	47465090	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47465090C>G	ENST00000265565.5	-	9	1563				SCAP_ENST00000441517.2_Intron|SCAP_ENST00000545718.1_Intron	NM_012235.2	NP_036367.2	Q12770	SCAP_HUMAN	SREBF chaperone	NA		NA			aging (GO:0007568)|cholesterol metabolic process (GO:0008203)|negative regulation of cholesterol biosynthetic process (GO:0045541)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|regulation of fatty acid biosynthetic process (GO:0042304)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|SREBP signaling pathway (GO:0032933)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	26				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.00592)|Kidney(197;0.00679)		caccatgttgcccaggctggt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(149;978 1908 29304 37806 46700)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC020987	CCDS2755.2	3p21.31	2013-01-10			ENSG00000114650	ENSG00000114650	22937		WD repeat domain containing	30634	protein-coding gene	gene with protein product	SREBP cleavage activating protein	601510			NA	8898195, 8724849, 10570913	Standard	NM_012235	XM_005264967	NA	Approved	KIAA0199	uc003crh.1	Q12770	OTTHUMG00000125539	ENST00000265565.5:c.1150+332G>C	chr3.hg19:g.47465090C>G		NA	Q8N2E0|Q8WUA1	hg19	CCDS2755.2	0.02	-0.122818	TTGxCCA	COVERED																																																																																			NOVEL	SCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246872.2	11	3.610674	KEEP	5	0	0	12	365	CC	0.99254	0.194847	0		-	3	51	100	0	0	8.381696	10	60	350	42	ENST00000265565.5	0.230769	0.196312
ELP6	54859	__UNKNOWN__	__UNKNOWN__	3	47551530	47551530	__UNKNOWN__	Intron	SNP	G	G	A	rs138165741	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47551530G>A	ENST00000446787.1	-	2	174				ELP6_ENST00000439305.1_Intron|ELP6_ENST00000296149.4_Intron			Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	NA		NA			chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)					NA						gattacaggcgtgagccacca	0.502		NA											G|||	4	0.000798722	0.0	0.0	5008	,	,	NA	18335	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832	54859		Elongator acetyltransferase complex subunits	25976	protein-coding gene	gene with protein product		615020	transmembrane protein 103, chromosome 3 open reading frame 75	TMEM103, C3orf75	NA	22854966	Standard	NM_017713	XM_005265241	NA	Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000446787.1:c.14+108C>T	chr3.hg19:g.47551530G>A		NA	Q9BW57|Q9NXJ3	hg19		0.02	1.280701	GGCxTGA	COVERED																																																																																			NOVEL	ELP6-016	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000345349.2	18	12.631467	KEEP	3	0	0	42	1166	GG	1	0.999317	0		-	5	60	151	0	0	9.546661	69	60	2166	163	ENST00000446787.1	0.067568	0.999317
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	47572469	47572469	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47572469T>C			NA	NA				ELP6 (17218 upstream) : AC099778.1 (9034 downstream)						NA		NA									NA						cttgctctgttacccaggctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.47572469T>C		NA		hg19		0.02	-0.070171	TGTxACC	UNCOVERED																																																																																			NOVEL					0			6	2.404124	KEEP	1	0	0	8	210	TT	0.99257	0.053735	0			3	60	99	0	0	9.033023	5	60	149	20		0.375	0.054137
SMARCC1	6599	__UNKNOWN__	__UNKNOWN__	3	47805321	47805321	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47805321A>G	ENST00000254480.5	-	2	435				SMARCC1_ENST00000425518.1_Intron	NM_003074.3	NP_003065.3	Q92922	SMRC1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(15)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33				BRCA - Breast invasive adenocarcinoma(193;7.47e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)		agatcctcctacctcagcctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U66615	CCDS2758.1	3p21.31	2008-05-15			ENSG00000173473	ENSG00000173473	6599			11104	protein-coding gene	gene with protein product		601732			NA	8804307	Standard		NM_003074	NA	Approved	BAF155, SRG3, Rsc8, CRACC1	uc003crq.2	Q92922	OTTHUMG00000133519	ENST00000254480.5:c.315+8985T>C	chr3.hg19:g.47805321A>G		NA	Q17RS0|Q6P172|Q8IWH2	hg19	CCDS2758.1	0.02	-0.254341	CCTxCCT	COVERED																																																																																			NOVEL	SMARCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257491.1	14	2.706106	KEEP	1	0	0	9	243	AA	0.99257	0.663556	0		-	3	60	100	0	0	7.449059	22	60	642	52	ENST00000254480.5	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	47832592	47832592	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47832592T>G			NA	NA				SMARCC1 (8996 upstream) : DHX30 (11806 downstream)						NA		NA									NA						tgcccgcctctgcctcccaaa	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.47832592T>G		NA		hg19		0.02	-0.166644	CTCxGCC	COVERED																																																																																			NOVEL					0			7	2.707284	KEEP	1	0	0	9	258	TT	0.99257	0.351317	0			3	60	84	0	1	6.479394	13	60	398	38		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	47843716	47843716	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:47843716G>A			NA	NA				SMARCC1 (20120 upstream) : DHX30 (682 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.47843716G>A		NA		hg19		0.02	-0.175423	GGCxTGA	COVERED																																																																																			NOVEL					0			11	3.608674	KEEP	1	0	0	12	347	GG	0.993634	0.38494	0			3	60	90	0	0	6.910512	15	60	488	49		0.166667	0.387407
MAP4	4134	__UNKNOWN__	__UNKNOWN__	3	48026071	48026071	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48026071T>C	ENST00000426837.2	-	3	362				MAP4_ENST00000395734.3_Intron|MAP4_ENST00000439356.1_Intron|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000434267.1_Intron|MAP4_ENST00000360240.6_Intron			P27816	MAP4_HUMAN	microtubule-associated protein 4	NA		NA			cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	cctgtaatcctagcactttgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849	4134			6862	protein-coding gene	gene with protein product		157132			NA	1905296	Standard	NM_002375	NM_002375	NA	Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000426837.2:c.274+2801A>G	chr3.hg19:g.48026071T>C		NA	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	hg19		0.02	-0.105259	TCCxAGC	UNCOVERED																																																																																			NOVEL	MAP4-005	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000346089.2	7	3.609303	KEEP	0	0	0	12	332	TT	0.994391	0.139048	0		-	3	60	99	0	0	8.678689	7	60	210	32	ENST00000426837.2	0.3	0.139832
MAP4	4134	__UNKNOWN__	__UNKNOWN__	3	48029411	48029411	__UNKNOWN__	Intron	SNP	A	A	G	rs561831137		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48029411A>G	ENST00000426837.2	-	3	311				MAP4_ENST00000395734.3_Intron|MAP4_ENST00000439356.1_Intron|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000434267.1_Intron|MAP4_ENST00000360240.6_Intron			P27816	MAP4_HUMAN	microtubule-associated protein 4	NA		NA			cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	caggccgggcacggtggctca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849	4134			6862	protein-coding gene	gene with protein product		157132			NA	1905296	Standard	NM_002375	NM_002375	NA	Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000426837.2:c.224-488T>C	chr3.hg19:g.48029411A>G		NA	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	hg19		0.02	-0.192919	GGCxCGG	COVERED																																																																																			NOVEL	MAP4-005	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000346089.2	6	3.309005	KEEP	0	0	0	11	315	AA	0.993072	0.454585	0		-	3	60	87	0	0	6.462497	17	60	499	48	ENST00000426837.2	0.15	0.457757
MAP4	4134	__UNKNOWN__	__UNKNOWN__	3	48095844	48095844	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48095844G>A	ENST00000426837.2	-	1	69				MAP4_ENST00000395734.3_Intron|MAP4_ENST00000439356.1_Intron|MAP4_ENST00000383737.4_Intron|MAP4_ENST00000360240.6_Intron			P27816	MAP4_HUMAN	microtubule-associated protein 4	NA		NA			cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	ggccaggcacggtggctcacg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849	4134			6862	protein-coding gene	gene with protein product		157132			NA	1905296	Standard	NM_002375	NM_002375	NA	Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000426837.2:c.18+34418C>T	chr3.hg19:g.48095844G>A		NA	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	hg19		0.02	-0.263162	CACxGTG	COVERED																																																																																			NOVEL	MAP4-005	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000346089.2	14	8.121581	KEEP	0	0	0	27	770	GG	0.999988	0.69366	0		-	3	60	93	0	0	6.642956	24	60	786	76	ENST00000426837.2	0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	48147322	48147322	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48147322T>C			NA	NA				RN7SL664P (10727 upstream) : CDC25A (51313 downstream)						NA		NA									NA						tggctcacgcttgtaatccca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.48147322T>C		NA		hg19		0.02	-0.11403	CGCxTGT	UNCOVERED																																																																																			NOVEL					0			4	3.007156	KEEP	2	0	0	10	268	TT	0.99254	0.161255	0			3	60	105	0	0	9.001176	9	60	271	31		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	48190472	48190472	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48190472A>G			NA	NA				RN7SL664P (53877 upstream) : CDC25A (8163 downstream)						NA		NA									NA						tttttttgagatggagtttca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.48190472A>G		NA		hg19		0.02	-0.0877	GAGxTGG	UNCOVERED																																																																																			NOVEL					0			6	2.706212	KEEP	1	0	0	9	238	AA	0.99254	0.098977	0			2	41	72	2	0	6.693263	3	60	83	25		0.4	0.099721
SPINK8	646424	__UNKNOWN__	__UNKNOWN__	3	48352072	48352072	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48352072C>T	ENST00000434006.1	-	4	239					NM_001080525.1	NP_001073994.1	P0C7L1	ISK8_HUMAN	serine peptidase inhibitor, Kazal type 8 (putative)	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		actgcaacctctgcctcctgg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46822.1	3p21.31	2011-08-31			ENSG00000229453	ENSG00000229453	646424		Serine peptidase inhibitors, Kazal type	33160	protein-coding gene	gene with protein product		NA			NA	16930550	Standard	NM_001080525	NM_001080525	NA	Approved		uc003csq.1	P0C7L1	OTTHUMG00000156832	ENST00000434006.1:c.240-636G>A	chr3.hg19:g.48352072C>T		NA		hg19	CCDS46822.1	0.02	-0.149129	CCTxTGC	UNCOVERED																																																																																			NOVEL	SPINK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346123.1	12	2.707897	KEEP	4	0	0	9	274	CC	0	0	0		-	3	60	91	0	1	7.272143	12	60	404	35	ENST00000434006.1	0.2	0.292001
SHISA5	51246	__UNKNOWN__	__UNKNOWN__	3	48526001	48526001	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48526001T>C	ENST00000443308.2	-	3	247				SHISA5_ENST00000444115.1_Intron|SHISA5_ENST00000442747.1_Intron|SHISA5_ENST00000296444.2_Intron			Q8N114	SHSA5_HUMAN	shisa family member 5	NA		NA			intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			large_intestine(1)|lung(1)	2						cagtggctcatgcctgtaatc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF520698	CCDS2770.1, CCDS63621.1, CCDS63622.1, CCDS63623.1	3p21.31	2013-07-31	2013-07-31		ENSG00000164054	ENSG00000164054	51246		Shisa homologs	30376	protein-coding gene	gene with protein product		607290	shisa homolog 5 (Xenopus laevis)		NA	11042152, 12135983	Standard	NM_016479	NM_016479	NA	Approved	SCOTIN, hShisa5	uc011bbk.1	Q8N114	OTTHUMG00000133529	ENST00000443308.2:c.213-5335A>G	chr3.hg19:g.48526001T>C		NA	B3KW99|F8W9N8|Q69YY9|Q7Z433|Q8NHL9|Q96MW8|Q9BV58	hg19		0.02	-0.184193	TCAxGCC	COVERED																																																																																			NOVEL	SHISA5-009	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344713.2	6	3.308422	KEEP	0	0	0	11	306	TT	0.993072	0.420544	0		-	3	60	101	0	0	7.933313	16	60	480	51	ENST00000443308.2	0.157895	0.423478
NCKIPSD	51517	__UNKNOWN__	__UNKNOWN__	3	48709718	48709718	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48709718T>C	ENST00000341520.4	-	12	2059							Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	NA		NA			cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		caccattgcattccagcctgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672	51517			15486	protein-coding gene	gene with protein product	dia interacting protein, diaphanous protein interacting protein, SH3 protein interacting with Nck, 90 kDa	606671			NA	10648423, 10619843	Standard	NM_016453	NM_016453	NA	Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000341520.4:c.1965+6278A>G	chr3.hg19:g.48709718T>C		NA	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	hg19		0.02	-0.16662	GCAxTCC	COVERED																																																																																			NOVEL	NCKIPSD-201	KNOWN	basic	protein_coding	NA	protein_coding		5	3.90551	KEEP	1	0	0	13	329	TT	0.993634	0.351693	0		-	3	60	90	0	0	6.992636	14	60	395	34	ENST00000341520.4	0.176471	0.353947
PRKAR2A	5576	__UNKNOWN__	__UNKNOWN__	3	48787536	48787536	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48787536T>C	ENST00000296446.8	-	0	2862				PRKAR2A_ENST00000265563.8_3'UTR|PRKAR2A_ENST00000454963.1_Intron			P13861	KAP2_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, alpha	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)		SLC26A6/PRKAR2A(2)	breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)		gtggctcacatctgtaatccc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS2778.1	3p21.3-p21.2	2009-07-10			ENSG00000114302	ENSG00000114302	5576	2.7.11.1		9391	protein-coding gene	gene with protein product		176910		PRKAR2	NA	9676433	Standard		NM_004157	NA	Approved		uc003cux.1	P13861	OTTHUMG00000133540	ENST00000296446.8:c.*1482A>G	chr3.hg19:g.48787536T>C		NA	Q16823|Q9BUB1	hg19		0.02	1.660614	ACAxCTG	COVERED																																																																																			NOVEL	PRKAR2A-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344962.1	19	5.239981	KEEP	0	4	118	59	1609	TT	1	0.999487	0		-	4	60	129	0	0	8.114249	68	60	2060	213	ENST00000296446.8	0.055556	0.999487
PRKAR2A	5576	__UNKNOWN__	__UNKNOWN__	3	48791674	48791674	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48791674C>T	ENST00000296446.8	-	9	1105				PRKAR2A_ENST00000265563.8_Intron|PRKAR2A_ENST00000454963.1_Intron			P13861	KAP2_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, alpha	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)		SLC26A6/PRKAR2A(2)	breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)		CTACttttttctttttttttt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2778.1	3p21.3-p21.2	2009-07-10			ENSG00000114302	ENSG00000114302	5576	2.7.11.1		9391	protein-coding gene	gene with protein product		176910		PRKAR2	NA	9676433	Standard		NM_004157	NA	Approved		uc003cux.1	P13861	OTTHUMG00000133540	ENST00000296446.8:c.874-1924G>A	chr3.hg19:g.48791674C>T		NA	Q16823|Q9BUB1	hg19		0.02	-0.192948	TTTxTTT	COVERED																																																																																			NOVEL	PRKAR2A-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344962.1	10	3.609536	KEEP	0	0	0	12	350	CC	0.993634	0.454842	0		-	3	60	87	1	0	6.610828	15	60	479	48	ENST00000296446.8	0.166667	0.457757
PRKAR2A	5576	__UNKNOWN__	__UNKNOWN__	3	48802351	48802351	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48802351T>C	ENST00000296446.8	-	8	1105				PRKAR2A_ENST00000265563.8_Intron|PRKAR2A_ENST00000454963.1_Intron			P13861	KAP2_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, alpha	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)		SLC26A6/PRKAR2A(2)	breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|ovary(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000176)|Kidney(197;0.00246)|KIRC - Kidney renal clear cell carcinoma(197;0.00261)		agccactgcgtccggcAAGAA	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2778.1	3p21.3-p21.2	2009-07-10			ENSG00000114302	ENSG00000114302	5576	2.7.11.1		9391	protein-coding gene	gene with protein product		176910		PRKAR2	NA	9676433	Standard		NM_004157	NA	Approved		uc003cux.1	P13861	OTTHUMG00000133540	ENST00000296446.8:c.873+85A>G	chr3.hg19:g.48802351T>C		NA	Q16823|Q9BUB1	hg19		0.02	1.687061	GCGxCCG	COVERED																																																																																			NOVEL	PRKAR2A-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344962.1	8	2.56819	KEEP	0	2	61	30	806	TT	0.999997	0.999216	0		-	4	60	135	0	0	8.631455	71	60	2015	152	ENST00000296446.8	0.053333	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	48944228	48944228	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48944228T>C			NA	NA				SLC25A20 (7802 upstream) : ARIH2OS (10992 downstream)						NA		NA									NA						gctgggattataggcgtgagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.48944228T>C		NA		hg19		0.02	-0.184175	TTAxAGG	COVERED																																																																																			NOVEL					0			4	2.404928	KEEP	0	0	0	8	213	TT	0.99257	0.420331	0			4	60	135	0	0	10.968902	17	60	494	42		0.190476	0.423478
ARIH2	10425	__UNKNOWN__	__UNKNOWN__	3	48964032	48964032	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48964032A>G	ENST00000356401.4	+	3	242				ARIH2_ENST00000449376.1_Intron|ARIH2_ENST00000490095.1_Intron	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	NA		NA			developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		catccaggctagagtgcagtg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479	10425			690	protein-coding gene	gene with protein product	all-trans retinoic acid inducible RING finger	605615	ariadne (Drosophila) homolog 2, ariadne homolog 2 (Drosophila)		NA	10422847, 24058416	Standard	NM_006321	XM_005264798	NA	Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.-97-863A>G	chr3.hg19:g.48964032A>G		NA	Q9HBZ6|Q9UEM9	hg19	CCDS2780.1	0.02	-0.12279	GCTxGAG	COVERED																																																																																			NOVEL	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257525.1	6	3.307558	KEEP	0	0	0	11	292	AA	0.993072	0.194952	0		+	3	60	101	0	0	8.372938	11	60	323	35	ENST00000356401.4	0.214286	0.196312
ARIH2	10425	__UNKNOWN__	__UNKNOWN__	3	48964262	48964262	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:48964262C>T	ENST00000356401.4	+	3	242				ARIH2_ENST00000449376.1_Intron|ARIH2_ENST00000490095.1_Intron	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	NA		NA			developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		ggattacaggcatgagtcacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479	10425			690	protein-coding gene	gene with protein product	all-trans retinoic acid inducible RING finger	605615	ariadne (Drosophila) homolog 2, ariadne homolog 2 (Drosophila)		NA	10422847, 24058416	Standard	NM_006321	XM_005264798	NA	Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.-97-633C>T	chr3.hg19:g.48964262C>T		NA	Q9HBZ6|Q9UEM9	hg19	CCDS2780.1	0.02	-0.166667	AGGxATG	COVERED																																																																																			NOVEL	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257525.1	8	2.407359	KEEP	2	0	0	8	251	CC	0.99257	0.351317	0		+	3	60	86	0	0	6.772361	12	60	408	43	ENST00000356401.4	0.2	0.353947
P4HTM	54681	__UNKNOWN__	__UNKNOWN__	3	49029761	49029761	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49029761G>T	ENST00000383729.4	+	2	807				P4HTM_ENST00000343546.4_Intron	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	AGACAGggccgggcgtggtgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467	54681			28858	protein-coding gene	gene with protein product	Prolyl hydroxlase domain-containing 4, hypoxia inducible factor prolyl 4 hydroxylase	614584			NA	12163023, 17726031	Standard	NM_177938	XR_245139	NA	Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.436+1414G>T	chr3.hg19:g.49029761G>T		NA	Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	hg19	CCDS43089.1	0.02	-0.210527	GCCxGGC	COVERED																																																																																			NOVEL	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157211.1	11	2.405973	KEEP	0	0	0	8	228	GG	0.99257	0.518282	0		+	3	60	93	0	0	6.865109	20	60	654	43	ENST00000383729.4	0.130435	0.522161
LAMB2	3913	__UNKNOWN__	__UNKNOWN__	3	49165220	49165220	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49165220A>G	ENST00000418109.1	-	16	2183				LAMB2_ENST00000305544.4_Intron	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	NA		NA			astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ttgggaggccaaggcgggcag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037	3913		Laminins	6487	protein-coding gene	gene with protein product	laminin S	150325		LAMS	NA	2922051, 10393422	Standard	NM_002292	NM_002292	NA	Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2018+670T>C	chr3.hg19:g.49165220A>G		NA	Q16321	hg19	CCDS2789.1	0.02	-0.254251	GCCxAGG	COVERED																																																																																			NOVEL	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345939.1	11	2.706698	KEEP	0	0	0	9	244	AA	0.99254	0.663536	0		-	3	49	90	0	1	6.396903	23	60	642	53	ENST00000418109.1	0.115385	0.668523
CCDC36	339834	__UNKNOWN__	__UNKNOWN__	3	49283996	49283996	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49283996G>A	ENST00000438782.1	+	6	768				CCDC36_ENST00000296449.5_Intron|CCDC36_ENST00000452691.2_Intron			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	NA		NA								endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		caggagaatcgcttgaaccca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421	339834			27945	protein-coding gene	gene with protein product	cancer/testis antigen 74	NA			NA		Standard	NM_178173	NM_178173	NA	Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.532+1830G>A	chr3.hg19:g.49283996G>A		NA	C9JJL0|Q05DG9|Q96LP7	hg19	CCDS33755.2	0.02	-0.157874	ATCxCTT	UNCOVERED																																																																																			NOVEL	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342332.1	9	2.707046	KEEP	3	0	0	9	258	GG	0	0	0		+	3	60	92	0	0	7.58182	10	60	334	38	ENST00000438782.1	0.230769	0.322807
NICN1	84276	__UNKNOWN__	__UNKNOWN__	3	49461321	49461321	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49461321C>G	ENST00000273598.3	-	0	1673				NICN1-AS1_ENST00000424915.1_RNA	NM_032316.3	NP_115692.1	Q9BSH3	NICN1_HUMAN	nicolin 1	NA		NA				microtubule (GO:0005874)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(193;4.52e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		tttcgctcttcttgcccaggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ299740	CCDS2798.1	3p21.31	2008-07-18			ENSG00000145029	ENSG00000145029	84276			18317	protein-coding gene	gene with protein product		611516			NA	12392556	Standard	NM_032316	NM_032316	NA	Approved	MGC12936	uc003cwz.1	Q9BSH3	OTTHUMG00000156848	ENST00000273598.3:c.*945G>C	chr3.hg19:g.49461321C>G		NA	Q8IZQ2	hg19	CCDS2798.1	0.02	3.431869	CTTxTTG	COVERED																																																																																			NOVEL	NICN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346224.3	25	4.070289	KEEP	0	5	149	66	1995	CC	1	0.999991	0		-	9	60	286	2	1	19.683057	93	60	3069	252	ENST00000273598.3	0.088235	0.999991
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	49477174	49477174	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49477174T>C			NA	NA				NICN1 (10415 upstream) : RNA5SP130 (27373 downstream)						NA		NA									NA						cgtgagccactgcacctggcA	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.49477174T>C		NA		hg19		0.02	-0.096481	CACxGCA	UNCOVERED																																																																																			NOVEL					0			8	2.995871	KEEP	1	0	0	10	263	TT	0.992708	0.119558	0			3	60	93	0	0	7.932467	8	60	240	29		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	49477184	49477184	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49477184A>C			NA	NA				NICN1 (10425 upstream) : RNA5SP130 (27363 downstream)						NA		NA									NA						tgcacctggcATGGGCCTAtt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.49477184A>C		NA		hg19		0.02	-0.078932	GGCxTGG	UNCOVERED																																																																																			NOVEL					0			8	2.702906	KEEP	1	0	0	9	230	AA	0.99254	0.076759	0			3	60	103	0	0	9.244034	6	60	168	24		0.333333	0.077336
DAG1	1605	__UNKNOWN__	__UNKNOWN__	3	49564669	49564669	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49564669G>A	ENST00000539901.1	+	3	843				DAG1_ENST00000479935.1_Intron|DAG1_ENST00000308775.2_Intron|DAG1_ENST00000545947.1_Intron|DAG1_ENST00000515359.2_Intron|DAG1_ENST00000541308.1_Intron|DAG1_ENST00000538711.1_Intron	NM_001177644.2	NP_001171115	Q14118	DAG1_HUMAN	dystroglycan 1 (dystrophin-associated glycoprotein 1)	NA		NA			basement membrane organization (GO:0071711)|branching involved in salivary gland morphogenesis (GO:0060445)|calcium-dependent cell-matrix adhesion (GO:0016340)|commissural neuron axon guidance (GO:0071679)|cytoskeletal anchoring at plasma membrane (GO:0007016)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|microtubule anchoring (GO:0034453)|modulation by virus of host morphology or physiology (GO:0019048)|morphogenesis of an epithelial sheet (GO:0002011)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell migration (GO:0030336)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase B signaling (GO:0051898)|nerve maturation (GO:0021682)|NLS-bearing protein import into nucleus (GO:0006607)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell outer membrane (GO:0009279)|cell-cell adherens junction (GO:0005913)|contractile ring (GO:0070938)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystroglycan complex (GO:0016011)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|node of Ranvier (GO:0033268)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|alpha-actinin binding (GO:0051393)|calcium ion binding (GO:0005509)|laminin-1 binding (GO:0043237)|SH2 domain binding (GO:0042169)|structural constituent of muscle (GO:0008307)|tubulin binding (GO:0015631)|vinculin binding (GO:0017166)|virus receptor activity (GO:0001618)			NS(1)|autonomic_ganglia(2)|breast(2)|endometrium(1)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	23				BRCA - Breast invasive adenocarcinoma(193;5.13e-05)|Kidney(197;0.00241)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		ctaaaaatacgaaaaattgcc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L19711	CCDS2799.1	3p21	2014-09-17			ENSG00000173402	ENSG00000173402	1605			2666	protein-coding gene	gene with protein product	alpha-dystroglycan, dystrophin-associated glycoprotein-1, beta-dystroglycan	128239			NA	7774920, 1741056	Standard		NM_001177643	NA	Approved	A3a, 156DAG, AGRNR, DAG	uc021wyd.1	Q14118	OTTHUMG00000156869	ENST00000539901.1:c.286-3561G>A	chr3.hg19:g.49564669G>A		NA	A8K6M7|Q969J9	hg19	CCDS2799.1	0.02	-0.263084	TACxAAA	COVERED																																																																																			NOVEL	DAG1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346326.1	12	2.406812	KEEP	1	0	0	8	239	GG	0.99257	0.688515	0		+	4	60	109	1	2	7.893639	23	60	751	56	ENST00000539901.1	0.148148	0.693668
MST1	4485	__UNKNOWN__	__UNKNOWN__	3	49722356	49722356	__UNKNOWN__	Intron	SNP	G	G	A	rs9837520	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49722356G>A	ENST00000449682.2	-	15	1984				AC099668.5_ENST00000563780.1_RNA	NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth factor-like)	NA		NA			embryo implantation (GO:0007566)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GTGACTCTCAGTCCATTGCCC	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(110;181 1524 8005 22865 46297)							NA				0													39	40	40			NA	NA	3		NA											NA				49722356		2203	4300	6503	SO:0001627	intron_variant			M74178	CCDS33757.2	3p21	2008-09-05			ENSG00000173531	ENSG00000173531	4485			7380	protein-coding gene	gene with protein product	hepatocyte growth factor-like protein homolog	142408		D3F15S2, HGFL, DNF15S2	NA	2902784, 8393443	Standard	NM_020998	NM_020998	NA	Approved	MSP, NF15S2	uc003cxg.3	P26927	OTTHUMG00000155918	ENST00000449682.2:c.1623-39C>T	chr3.hg19:g.49722356G>A		NA	A6NLA3|A8MSX3|Q13350|Q14870|Q6GTN4	hg19	CCDS33757.2	0.02	1.44114	TCAxTCC	UNCOVERED																																																																																			NOVEL	MST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342315.3	2	3.006172	KEEP	15	0	0	10	292	GG	0	0	0		-	24	60	712	0	0	62.92112	47	60	1634	146	ENST00000449682.2	0.338028	0.9982
MST1	4485	__UNKNOWN__	__UNKNOWN__	3	49723687	49723687	__UNKNOWN__	Intron	SNP	T	T	C	rs2087731		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49723687T>C	ENST00000449682.2	-	8	1378				MST1_ENST00000383728.3_3'UTR	NM_020998.3	NP_066278.3	P26927	HGFL_HUMAN	macrophage stimulating 1 (hepatocyte growth factor-like)	NA		NA			embryo implantation (GO:0007566)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			NS(4)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|skin(9)|stomach(1)|urinary_tract(2)	41				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CGTGACTACCTTCCTCCCGTC	0.657		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(110;181 1524 8005 22865 46297)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74178	CCDS33757.2	3p21	2008-09-05			ENSG00000173531	ENSG00000173531	4485			7380	protein-coding gene	gene with protein product	hepatocyte growth factor-like protein homolog	142408		D3F15S2, HGFL, DNF15S2	NA	2902784, 8393443	Standard	NM_020998	NM_020998	NA	Approved	MSP, NF15S2	uc003cxg.3	P26927	OTTHUMG00000155918	ENST00000449682.2:c.1016+58A>G	chr3.hg19:g.49723687T>C		NA	A6NLA3|A8MSX3|Q13350|Q14870|Q6GTN4	hg19	CCDS33757.2	0.02	1.792279	ACCxTCC	COVERED																																																																																			NOVEL	MST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342315.3	9	5.413663	KEEP	0	0	0	18	494	TT	0.999859	0.995546	0		-	4	33	128	0	0	8.273323	58	60	1724	118	ENST00000449682.2	0.064516	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	49975218	49975218	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:49975218C>T			NA	NA				MON1A (7612 upstream) : RBM6 (2221 downstream)						NA		NA									NA						ttcaggagttcgagaccagcc	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.49975218C>T		NA		hg19		0.02	-0.096462	GTTxGAG	UNCOVERED																																																																																			NOVEL					0			2	2.406899	KEEP	0	0	0	8	239	CC	0.99257	0.119541	0			3	60	81	0	0	6.877576	7	60	224	30		0.3	0.120436
RBM6	10180	__UNKNOWN__	__UNKNOWN__	3	50020334	50020334	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:50020334A>G	ENST00000266022.4	+	5	1742				RBM6_ENST00000539992.1_Intron|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000443081.1_Intron|RBM6_ENST00000442092.1_Intron|RBM6_ENST00000441115.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	NA		NA			RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		tagtagagacagggtttcacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534	10180		RNA binding motif (RRM) containing, G patch domain containing	9903	protein-coding gene	gene with protein product		606886			NA	10352938	Standard	NM_005777	NM_001167582	NA	Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.1483+7509A>G	chr3.hg19:g.50020334A>G		NA	O60549|O75524|Q86SS3	hg19	CCDS2809.1	0.02	-0.114017	GACxGGG	UNCOVERED																																																																																			NOVEL	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345528.4	2	2.40389	KEEP	2	0	0	8	208	AA	0	0	0		+	3	60	93	0	0	7.682121	10	60	298	25	ENST00000266022.4	0.230769	0.162467
HYAL1	3373	__UNKNOWN__	__UNKNOWN__	3	50346423	50346423	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:50346423A>G	ENST00000320295.8	-	2	237					NM_153281.1	NP_695013.1	Q12794	HYAL1_HUMAN	hyaluronoglucosaminidase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to interleukin-1 (GO:0071347)|cellular response to pH (GO:0071467)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV-B (GO:0071493)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal joint morphogenesis (GO:0060272)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|negative regulation of cell growth (GO:0030308)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of growth (GO:0045927)|positive regulation of hyaluranon cable assembly (GO:1900106)|response to antibiotic (GO:0046677)|response to reactive oxygen species (GO:0000302)|response to virus (GO:0009615)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|hyaluranon cable (GO:0036117)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	hyaluronan synthase activity (GO:0050501)|hyalurononglucosaminidase activity (GO:0004415)|transcription factor binding (GO:0008134)			cervix(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		gcctcccaaaatgctgggatt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U90094	CCDS2816.1, CCDS2817.1, CCDS46832.1, CCDS46833.1	3p21.31	2014-07-17			ENSG00000114378	ENSG00000114378	3373	3.2.1.35		5320	protein-coding gene	gene with protein product		607071			NA	9223416, 9409739	Standard		NM_153281	NA	Approved	LUCA1, HYAL-1, FUS2, NAT6	uc003czp.4	Q12794	OTTHUMG00000156941	ENST00000320295.8:c.189+666T>C	chr3.hg19:g.50346423A>G		NA	Q6FH23|Q6PIZ6|Q7KYU2|Q7LE34|Q8NFK5|Q8NFK6|Q8NFK7|Q8NFK8|Q8NFK9|Q93013|Q9UKD5|Q9UNI8	hg19	CCDS2816.1	0.02	-0.149108	AAAxTGC	UNCOVERED																																																																																			NOVEL	HYAL1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346704.1	3	2.706839	KEEP	3	0	0	9	249	AA	0	0	0		-	3	60	103	0	0	8.472168	12	60	360	42	ENST00000320295.8	0.2	0.292001
CACNA2D2	9254	__UNKNOWN__	__UNKNOWN__	3	50451084	50451084	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:50451084A>C	ENST00000479441.1	-	4	405				CACNA2D2_ENST00000360963.3_Intron|CACNA2D2_ENST00000424201.2_Intron|CACNA2D2_ENST00000435965.1_Intron|CACNA2D2_ENST00000266039.3_Intron|CACNA2D2_ENST00000429770.1_Intron|CACNA2D2_ENST00000395083.1_Intron|CACNA2D2_ENST00000423994.2_Intron			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	NA		NA			energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	tcgagaccagactggccaaca	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402	9254		Calcium channel subunits	1400	protein-coding gene	gene with protein product	gene 26	607082			NA		Standard	NM_006030	XM_005265581	NA	Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.406-19485T>G	chr3.hg19:g.50451084A>C		NA	A7MD15|Q9NY48|Q9UEW0|Q9Y268	hg19	CCDS54588.1	0.02	-0.061397	CAGxCTG	UNCOVERED																																																																																			NOVEL	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346457.1	4	2.404818	KEEP	0	0	0	8	205	AT	0.99254	0.04346	0		-	2	60	71	0	0	6.395971	4	60	115	25	ENST00000479441.1	0.333333	0.043787
DOCK3	1795	__UNKNOWN__	__UNKNOWN__	3	50851956	50851956	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:50851956T>C	ENST00000266037.9	+	3	144					NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	NA		NA			small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		cttggcctcctaaagtgttgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538	1795			2989	protein-coding gene	gene with protein product		603123	dedicator of cyto-kinesis 3		NA	9205841	Standard	NM_004947	NM_004947	NA	Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.122-27150T>C	chr3.hg19:g.50851956T>C		NA	O15017	hg19	CCDS46835.1	0.02	-0.192969	TCCxAAA	COVERED																																																																																			NOVEL	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346478.5	4	2.70661	KEEP	0	0	0	9	245	TT	0.99254	0.454342	0		+	3	60	100	0	0	7.833299	16	60	487	46	ENST00000266037.9	0.157895	0.457757
DOCK3	1795	__UNKNOWN__	__UNKNOWN__	3	51162379	51162379	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:51162379G>A	ENST00000266037.9	+	10	769					NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	NA		NA			small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		tggccaacatggtgaaaccct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538	1795			2989	protein-coding gene	gene with protein product		603123	dedicator of cyto-kinesis 3		NA	9205841	Standard	NM_004947	NM_004947	NA	Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.747-21601G>A	chr3.hg19:g.51162379G>A		NA	O15017	hg19	CCDS46835.1	0.02	-0.078931	CATxGTG	UNCOVERED																																																																																			NOVEL	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346478.5	10	2.707907	KEEP	4	0	0	9	271	GG	0.99257	0.076761	0		+	3	52	80	0	0	7.13193	5	60	160	27	ENST00000266037.9	0.375	0.077336
DOCK3	1795	__UNKNOWN__	__UNKNOWN__	3	51211624	51211624	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:51211624C>G	ENST00000266037.9	+	12	1060					NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	NA		NA			small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		ggtggctcacccctgtaatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538	1795			2989	protein-coding gene	gene with protein product		603123	dedicator of cyto-kinesis 3		NA	9205841	Standard	NM_004947	NM_004947	NA	Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1037+13491C>G	chr3.hg19:g.51211624C>G		NA	O15017	hg19	CCDS46835.1	0.02	-0.122816	CACxCCT	UNCOVERED																																																																																			NOVEL	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346478.5	8	3.610435	KEEP	7	0	0	12	367	CC	0	0	0		+	3	60	101	0	1	8.372587	11	60	369	40	ENST00000266037.9	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	51524679	51524679	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:51524679G>A			NA	NA				VPRBP (6825 upstream) : RAD54L2 (50916 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.51524679G>A		NA		hg19		0.02	-0.114031	CACxCCT	UNCOVERED																																																																																			NOVEL					0			7	2.40609	KEEP	0	0	0	8	228	GG	0.99257	0.16126	0			3	60	93	0	0	7.801085	9	60	283	28		0.25	0.162467
RAD54L2	23132	__UNKNOWN__	__UNKNOWN__	3	51617049	51617049	__UNKNOWN__	Intron	SNP	A	A	G	rs376529198		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:51617049A>G	ENST00000409535.2	+	2	71					NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	NA		NA				nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		ccaaagtgctaggattacagg	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080	23132			29123	protein-coding gene	gene with protein product		NA			NA	9872452	Standard	NM_015106	NM_015106	NA	Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.-54-7334A>G	chr3.hg19:g.51617049A>G		NA	Q8TB57|Q9BV54	hg19	CCDS33765.2	0.02	-0.166653	GCTxGGA	COVERED																																																																																			NOVEL	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328700.2	3	2.33703	KEEP	5	1	23	16	440	AA	0.995343	0.352299	0		+	3	60	100	0	0	7.833271	16	60	490	62	ENST00000409535.2	0.157895	0.353947
RAD54L2	23132	__UNKNOWN__	__UNKNOWN__	3	51637360	51637360	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:51637360A>G	ENST00000409535.2	+	2	264					NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	NA		NA				nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		agtggctcacacctgtaatcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080	23132			29123	protein-coding gene	gene with protein product		NA			NA	9872452	Standard	NM_015106	NM_015106	NA	Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.139+12785A>G	chr3.hg19:g.51637360A>G		NA	Q8TB57|Q9BV54	hg19	CCDS33765.2	0.02	-0.157867	CACxCCT	COVERED																																																																																			NOVEL	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328700.2	7	2.403698	KEEP	1	0	0	8	208	AA	0.99257	0.320408	0		+	3	60	99	0	0	7.891916	14	60	415	38	ENST00000409535.2	0.176471	0.322807
RAD54L2	23132	__UNKNOWN__	__UNKNOWN__	3	51694548	51694548	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:51694548T>C	ENST00000409535.2	+	21	3534				RAD54L2_ENST00000296477.3_Intron	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	NA		NA				nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		aggatggtcttgatctcctga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080	23132			29123	protein-coding gene	gene with protein product		NA			NA	9872452	Standard	NM_015106	NM_015106	NA	Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.3409+414T>C	chr3.hg19:g.51694548T>C		NA	Q8TB57|Q9BV54	hg19	CCDS33765.2	0.02	-0.157749	TCTxGAT	UNCOVERED																																																																																			NOVEL	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328700.2	7	2.404336	KEEP	3	0	0	8	202	TT	0	0	0		+	3	60	84	0	0	6.393896	14	60	367	38	ENST00000409535.2	0.176471	0.322807
NEK4	6787	__UNKNOWN__	__UNKNOWN__	3	52783794	52783794	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:52783794T>A	ENST00000383721.4	-	7	1561				NEK4_ENST00000233027.5_Missense_Mutation_p.S474C|NEK4_ENST00000535191.1_Missense_Mutation_p.S385C			P51957	NEK4_HUMAN	NIMA-related kinase 4	NA		NA			mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		cggaggttgctgtgagccaag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	6787	2.7.11.1		11399	protein-coding gene	gene with protein product	serine/threonine protein kinase-2	601959	serine/threonine kinase 2, NIMA (never in mitosis gene a)-related kinase 4	STK2	NA	8208544	Standard	NM_003157	NM_001193533	NA	Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000383721.4:c.1368+2153A>T	chr3.hg19:g.52783794T>A		NA	A5YM70|B2R633|B7Z200|Q6P576	hg19		0.02	1.482436	TGCxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	1.626	-0.520346	0.04171	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000461689	T;T;T	0.08193	3.12;3.12;3.12	0.352	-0.703	0.11261	.	1.893660	0.03901	N	0.280273	T	0.03915	0.0110	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39418	-0.9615	9	0.51188	T	0.08	.	.	.	.	.	385;474	B7Z200;P51957	.;NEK4_HUMAN	C	474;385;385	ENSP00000233027:S474C;ENSP00000437703:S385C;ENSP00000419666:S385C	ENSP00000233027:S474C	S	-	1	0	NEK4	52758834	0.397000	0.25270	0.042000	0.18584	0.040000	0.13550	0.201000	0.17276	-0.505000	0.06568	-0.508000	0.04489	AGC	NOVEL	NEK4-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352387.1	11	2.801395	KEEP	2	3	81	38	1036	TT	1	0.984161	0		-	6	60	171	0	0	11.842283	47	60	1385	132	ENST00000383721.4	0.113208	0.984161
NEK4	6787	__UNKNOWN__	__UNKNOWN__	3	52785267	52785267	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:52785267C>T	ENST00000383721.4	-	7	1561				NEK4_ENST00000233027.5_Intron|NEK4_ENST00000535191.1_Intron			P51957	NEK4_HUMAN	NIMA-related kinase 4	NA		NA			mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		gtcaggagatcgagaccatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	6787	2.7.11.1		11399	protein-coding gene	gene with protein product	serine/threonine protein kinase-2	601959	serine/threonine kinase 2, NIMA (never in mitosis gene a)-related kinase 4	STK2	NA	8208544	Standard	NM_003157	NM_001193533	NA	Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000383721.4:c.1368+680G>A	chr3.hg19:g.52785267C>T		NA	A5YM70|B2R633|B7Z200|Q6P576	hg19		0.02	-0.166663	GATxGAG	COVERED																																																																																			NOVEL	NEK4-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352387.1	7	2.707687	KEEP	2	0	0	9	273	CG	0.99254	0.351306	0		-	3	33	89	0	0	6.810421	15	60	486	47	ENST00000383721.4	0.166667	0.353947
RP11-894J14.5	0	__UNKNOWN__	__UNKNOWN__	3	53103076	53103076	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:53103076T>C	ENST00000607203.1	-	3	317										NA		NA									NA						ctgcctcagcttcctgagtag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000607203.1:c.74+8627A>G	chr3.hg19:g.53103076T>C		NA		hg19		0.02	-0.087711	AGCxTCC	UNCOVERED																																																																																			NOVEL	RP11-894J14.5-003	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000470877.1	2	2.405879	KEEP	0	0	0	8	217	TT	0.99257	0.09898	0		-	3	60	102	0	0	8.978783	7	60	207	22	ENST00000607203.1	0.3	0.099721
DCP1A	55802	__UNKNOWN__	__UNKNOWN__	3	53366629	53366629	__UNKNOWN__	Intron	SNP	T	T	C	rs181705004	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:53366629T>C	ENST00000480258.1	-	3	397				DCP1A_ENST00000607628.1_Intron|DCP1A_ENST00000294241.6_Intron|DCP1A_ENST00000606822.1_Intron			Q9NPI6	DCP1A_HUMAN	decapping mRNA 1A	NA		NA			exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.000164)|KIRC - Kidney renal clear cell carcinoma(197;0.00525)|Kidney(197;0.00579)|OV - Ovarian serous cystadenocarcinoma(275;0.0647)		cggtggctcatgcctgtaatc	0.473		NA											t|||	7	0.00139776	0.0053	0.0	5008	,	,	NA	14805	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ275986	CCDS74946.1	3p21.1	2013-05-02	2013-05-02		ENSG00000162290	ENSG00000272886	55802			18714	protein-coding gene	gene with protein product		607010	DCP1 decapping enzyme homolog A (S. cerevisiae)		NA		Standard	NM_018403	XM_005278360	NA	Approved	HSA275986, SMIF, SMAD4IP1	uc021wzi.1	Q9NPI6	OTTHUMG00000158193	ENST00000480258.1:c.5601+9541A>G	chr3.hg19:g.53366629T>C		NA	B4DHN9|U3KQM8	hg19		0.02	-0.149106	TCAxGCC	COVERED																																																																																			NOVEL	DCP1A-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000350374.2	10	4.51177	KEEP	11	0	0	15	418	TT	0.994391	0.290363	0		-	3	60	98	0	0	8.072972	11	60	321	61	ENST00000480258.1	0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	53433669	53433669	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:53433669A>G			NA	NA				SNORA26 (11806 upstream) : CACNA1D (95013 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.53433669A>G		NA		hg19		0.02	-0.149104	GCTxGGA	UNCOVERED																																																																																			NOVEL					0			11	2.405954	KEEP	2	0	0	8	217	AA	0	0	0			4	60	132	0	0	11.624165	9	60	263	33		0.307692	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	53442176	53442176	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:53442176T>C			NA	NA				SNORA26 (20313 upstream) : CACNA1D (86506 downstream)						NA		NA									NA						caacctctgcttcccggggtc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.53442176T>C		NA		hg19		0.02	-0.070173	TGCxTCC	UNCOVERED																																																																																			NOVEL					0			2	2.406136	KEEP	0	0	0	8	222	TT	0.99257	0.053735	0			2	60	74	0	0	6.400778	6	60	181	24		0.25	0.054137
CACNA1D	776	__UNKNOWN__	__UNKNOWN__	3	53813077	53813077	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:53813077A>G	ENST00000422281.2	+	37	4542				CACNA1D_ENST00000288139.4_Intron|CACNA1D_ENST00000540742.1_Intron|CACNA1D_ENST00000350061.5_Intron	NM_001128839.1	NP_001122311.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	NA		NA			adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	tgtaatcccaacattttggga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388	776		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2	NA	1664412	Standard	NM_000720	NM_000720	NA	Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000422281.2:c.4543-976A>G	chr3.hg19:g.53813077A>G		NA	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	hg19	CCDS46849.1	0.02	-0.21048	CCAxCAT	COVERED																																																																																			NOVEL	CACNA1D-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350556.1	7	3.609275	KEEP	0	0	0	12	334	AA	0.993634	0.518837	0		+	3	60	93	0	0	7.061924	17	60	496	49	ENST00000422281.2	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	53937267	53937267	__UNKNOWN__	IGR	SNP	A	A	G	rs6804715|rs386661019	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:53937267A>G			NA	NA				SELK (11252 upstream) : CACNA2D3 (219306 downstream)						NA		NA									NA						gcagtggcacaatctcagctc	0.493		NA											G|||	3313	0.661542	0.6687	0.6052	5008	,	,	NA	10309	0.9435	NA	0.4225	False	NA	,,,	NA	NA	NA	2504	0.6472	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.53937267A>G		NA		hg19		0.02	-0.131562	CACxATC	UNCOVERED																																																																																			NOVEL					0			6	2.384752	KEEP	6	0	0	8	186	AA	0	0	0			8	60	247	0	0	24.36388	6	60	176	33		0.571429	0.229173
CACNA2D3	55799	__UNKNOWN__	__UNKNOWN__	3	54632099	54632099	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:54632099T>C	ENST00000474759.1	+	9	1011				CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000490478.1_Intron	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	NA		NA				integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	ggtggatcacttgaggtcagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445	55799		Calcium channel subunits	15460	protein-coding gene	gene with protein product		606399			NA	11245980	Standard		XM_005265318	NA	Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.963+16195T>C	chr3.hg19:g.54632099T>C		NA	B2RPL6|Q9NY16|Q9NY18	hg19	CCDS54598.1	0.02	-0.192904	CACxTGA	COVERED																																																																																			NOVEL	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351402.1	5	3.007246	KEEP	0	0	0	10	272	TT	0.992708	0.454419	0		+	3	60	101	2	0	7.727499	19	60	538	41	ENST00000474759.1	0.136364	0.457757
CACNA2D3	55799	__UNKNOWN__	__UNKNOWN__	3	54636520	54636520	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:54636520A>G	ENST00000474759.1	+	9	1011				CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000490478.1_Intron	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	NA		NA				integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	gcgagattccatctcaaaaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445	55799		Calcium channel subunits	15460	protein-coding gene	gene with protein product		606399			NA	11245980	Standard		XM_005265318	NA	Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.963+20616A>G	chr3.hg19:g.54636520A>G		NA	B2RPL6|Q9NY16|Q9NY18	hg19	CCDS54598.1	0.02	-0.09629	TCCxTCT	UNCOVERED																																																																																			NOVEL	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351402.1	15	2.705347	KEEP	12	0	0	9	248	AC	0	0	0		+	3	25	106	0	0	9.236114	8	60	224	34	ENST00000474759.1	0.272727	0.139832
ERC2	26059	__UNKNOWN__	__UNKNOWN__	3	55569988	55569988	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:55569988C>T	ENST00000288221.6	-	18	3169				ERC2_ENST00000486496.1_Intron	NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	NA		NA				cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		gatcacaccactgcactccag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672	26059			31922	protein-coding gene	gene with protein product		NA			NA		Standard	NM_015576	NM_015576	NA	Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2872-24684G>A	chr3.hg19:g.55569988C>T		NA	Q2T9F6|Q86TK4	hg19	CCDS46851.1	0.02	-0.070178	CCAxTGC	UNCOVERED																																																																																			NOVEL	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350884.2	5	3.009058	KEEP	0	0	0	10	310	CC	0.992708	0.053742	0		-	3	60	94	0	0	8.53262	5	60	169	28	ENST00000288221.6	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	56724359	56724359	__UNKNOWN__	IGR	SNP	C	C	G	rs66529035	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:56724359C>G			NA	NA				FAM208A (7094 upstream) : ARHGEF3 (37086 downstream)						NA		NA									NA						gctgggattacaggtgtgagt	0.463		NA											C|||	2001	0.399561	0.4766	0.4928	5008	,	,	NA	14088	0.4633	NA	0.2962	False	NA	,,,	NA	NA	NA	2504	0.2699	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.56724359C>G		NA		hg19		0.02	-0.175455	TTAxAGG	COVERED																																																																																			NOVEL					0			7	3.009078	KEEP	4	0	0	10	311	CC	0.99257	0.384528	0			11	60	378	0	0	37.070494	9	60	310	47		0.55	0.387407
IL17RD	54756	__UNKNOWN__	__UNKNOWN__	3	57175181	57175181	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57175181A>C	ENST00000296318.7	-	2	215				IL17RD_ENST00000320057.5_Intron|IL17RD_ENST00000463523.1_Intron|IL17RD_ENST00000427856.2_Intron|IL17RD_ENST00000479825.1_Intron	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	NA		NA			signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		cctcctgcctaagcctcccaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730	54756		Interleukins and interleukin receptors	17616	protein-coding gene	gene with protein product		606807			NA	11802164, 12604616	Standard	NM_017563	NM_017563	NA	Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.127-20840T>G	chr3.hg19:g.57175181A>C		NA	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	hg19	CCDS2880.2	0.02	-0.18417	CCTxAGC	COVERED																																																																																			NOVEL	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316680.1	4	3.007062	KEEP	0	0	0	10	267	AA	0.992708	0.42039	0		-	3	60	100	0	0	7.910291	15	60	429	47	ENST00000296318.7	0.166667	0.423478
DNAH12	201625	__UNKNOWN__	__UNKNOWN__	3	57385046	57385046	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57385046A>C	ENST00000351747.2	-	45	7251				DNAH12_ENST00000344804.4_Intron	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						cacctgtaataccagcacttt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844	201625		Axonemal dyneins	2943	protein-coding gene	gene with protein product		603340	dynein, axonemal, heavy polypeptide 12, dynein heavy chain domain 2, dynein heavy domain 2, dynein, axonemal, heavy chain 12-like, dynein, axonemal, heavy chain 7-like	DNHD2, DNAH12L, DNAH7L	NA	8812413, 8666668	Standard	NM_178504	NM_198564	NA	Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.7070+1066T>G	chr3.hg19:g.57385046A>C		NA	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	hg19		0.02	-0.254343	AATxCCA	COVERED																																																																																			NOVEL	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		8	3.307717	KEEP	2	0	0	11	293	AA	0.993072	0.663892	0		-	3	60	97	0	0	7.095099	23	60	677	64	ENST00000351747.2	0.115385	0.668523
DNAH12	201625	__UNKNOWN__	__UNKNOWN__	3	57484373	57484373	__UNKNOWN__	Intron	SNP	A	A	T	rs73078594	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57484373A>T	ENST00000389536.4	-	11	1516				DNAH12_ENST00000351747.2_Intron|DNAH12_ENST00000311202.6_Intron			Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						aatatccatcaaaacgtgaat	0.348		NA											A|||	145	0.0289537	0.0038	0.0346	5008	,	,	NA	20265	0.0	NA	0.0676	False	NA	,,,	NA	NA	NA	2504	0.0491	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844	201625		Axonemal dyneins	2943	protein-coding gene	gene with protein product		603340	dynein, axonemal, heavy polypeptide 12, dynein heavy chain domain 2, dynein heavy domain 2, dynein, axonemal, heavy chain 12-like, dynein, axonemal, heavy chain 7-like	DNHD2, DNAH12L, DNAH7L	NA	8812413, 8666668	Standard	NM_178504	NM_198564	NA	Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000389536.4:c.1335+2674T>A	chr3.hg19:g.57484373A>T		NA	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	hg19		0.02	-0.245504	ATCxAAA	COVERED																																																																																			NOVEL	DNAH12-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000351433.1	4	3.005088	KEEP	0	0	0	10	255	AA	0.992708	0.63667	0		-	10	60	290	0	0	26.04236	17	60	463	39	ENST00000389536.4	0.37037	0.641347
RP11-755B10.4	0	__UNKNOWN__	__UNKNOWN__	3	57586235	57586235	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57586235C>T	ENST00000607782.1	+	0	367				RP11-755B10.4_ENST00000606192.1_RNA|RP11-755B10.4_ENST00000607297.1_RNA						NA		NA									NA						ccttTTtcctcctgcctcagc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000607782.1:	chr3.hg19:g.57586235C>T		NA		hg19		0.02	-0.210504	CCTxCTG	COVERED																																																																																			NOVEL	RP11-755B10.4-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000470905.1	10	4.513227	KEEP	0	0	0	15	453	CC	0.99649	0.520328	0		+	3	60	89	0	0	6.527912	19	60	621	54	ENST00000607782.1	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	57588679	57588679	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57588679A>G			NA	NA				RP11-755B10.4 (2025 upstream) : RNU6ATAC26P (16494 downstream)						NA		NA									NA						ttgggaggccaaggtgggagt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.57588679A>G		NA		hg19		0.02	-0.166648	GCCxAGG	COVERED																																																																																			NOVEL					0			11	4.811538	KEEP	1	0	0	16	436	AA	0.99649	0.352705	0			3	60	86	0	0	6.510957	15	60	462	49		0.166667	0.353947
DENND6A	201627	__UNKNOWN__	__UNKNOWN__	3	57612380	57612380	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57612380C>G	ENST00000311128.5	-	0	3458					NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	NA		NA			positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)				NA						aggttgcagtcagccgagatt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839	201627		DENN/MADD domain containing	26635	protein-coding gene	gene with protein product		NA	family with sequence similarity 116, member A	FAM116A	NA	21330364	Standard	NM_152678	NM_152678	NA	Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.*1561G>C	chr3.hg19:g.57612380C>G		NA	Q7Z5T4|Q8N235|Q8TEG8	hg19	CCDS33773.1	0.02	-0.175444	AGTxAGC	COVERED																																																																																			NOVEL	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351594.1	6	3.911109	KEEP	2	0	0	13	383	CC	0.994391	0.385234	0		-	3	40	99	0	0	7.660601	17	60	560	48	ENST00000311128.5	0.15	0.387407
DENND6A	201627	__UNKNOWN__	__UNKNOWN__	3	57653165	57653165	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57653165A>T	ENST00000311128.5	-	4	390					NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	NA		NA			positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)				NA						attacaggcgagagccaccac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839	201627		DENN/MADD domain containing	26635	protein-coding gene	gene with protein product		NA	family with sequence similarity 116, member A	FAM116A	NA	21330364	Standard	NM_152678	NM_152678	NA	Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.320-1203T>A	chr3.hg19:g.57653165A>T		NA	Q7Z5T4|Q8N235|Q8TEG8	hg19	CCDS33773.1	0.02	-0.228012	GCGxGAG	COVERED																																																																																			NOVEL	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351594.1	2	2.405016	KEEP	0	0	0	8	212	AA	0.99257	0.578599	0		-	3	58	89	0	0	6.465993	20	60	578	46	ENST00000311128.5	0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	57976721	57976721	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:57976721T>C			NA	NA				SLMAP (61826 upstream) : FLNB (17405 downstream)						NA		NA									NA						ccacctcagcttccctagtag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.57976721T>C		NA		hg19		0.02	-0.096477	AGCxTCC	UNCOVERED																																																																																			NOVEL					0			6	2.706979	KEEP	0	0	0	9	253	TT	0.99254	0.119538	0			4	60	132	0	0	11.97754	7	60	206	26		0.363636	0.120436
FLNB	2317	__UNKNOWN__	__UNKNOWN__	3	58047606	58047606	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:58047606A>G	ENST00000490882.1	+	2	457				FLNB_ENST00000357272.4_Intron|FLNB_ENST00000295956.4_Intron|FLNB_ENST00000348383.5_Intron|FLNB_ENST00000429972.2_Intron|FLNB_ENST00000358537.3_Intron	NM_001164317.1	NP_001157789.1	O75369	FLNB_HUMAN	filamin B, beta	NA		NA			actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		atcacctgagatcaggagttc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068	2317			3755	protein-coding gene	gene with protein product	actin binding protein 278	603381	filamin B, beta (actin binding protein 278), Larsen syndrome 1 (autosomal dominant)	FLN1L, LRS1	NA	8327473, 10449914, 14991055, 16801345	Standard	NM_001457	NM_001457	NA	Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000490882.1:c.293-15167A>G	chr3.hg19:g.58047606A>G		NA	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	hg19	CCDS54599.1	0.02	-0.21926	GAGxTCA	COVERED																																																																																			NOVEL	FLNB-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353570.1	11	3.910165	KEEP	7	0	0	13	362	AA	0.993072	0.549057	0		+	4	60	125	0	0	9.880175	18	60	538	70	ENST00000490882.1	0.181818	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	58175896	58175896	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:58175896A>C			NA	NA				FLNB (17914 upstream) : DNASE1L3 (2087 downstream)						NA		NA									NA						accaccatgcacagctaattt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.58175896A>C		NA		hg19		0.02	-0.166652	TGCxCAG	COVERED																																																																																			NOVEL					0			7	3.609209	KEEP	0	0	0	12	332	AA	0.993634	0.351693	0			3	60	104	0	0	8.572195	12	60	365	43		0.2	0.353947
PXK	54899	__UNKNOWN__	__UNKNOWN__	3	58366713	58366713	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:58366713C>T	ENST00000356151.2	+	4	310				PXK_ENST00000383716.3_Intron|PXK_ENST00000484288.1_Intron|PXK_ENST00000479241.1_Intron|PXK_ENST00000302779.5_Intron|PXK_ENST00000463280.1_Intron|PXK_ENST00000383715.4_Intron|PXK_ENST00000536660.1_Intron	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase	NA		NA								cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		cggtggctcacgcctgtaatc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297	54899			23326	protein-coding gene	gene with protein product		611450			NA		Standard	NM_017771	XM_005265255	NA	Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.202-1528C>T	chr3.hg19:g.58366713C>T		NA		hg19	CCDS2889.1	0.02	-0.210525	TCAxGCC	UNCOVERED																																																																																			NOVEL	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353499.1	6	2.70788	KEEP	8	0	0	9	270	CC	0	0	0		+	3	60	87	0	0	6.327966	19	60	627	62	ENST00000356151.2	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	58723031	58723031	__UNKNOWN__	IGR	SNP	T	T	A	rs72290352		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:58723031T>A			NA	NA				FAM3D (70456 upstream) : C3orf67 (4701 downstream)						NA		NA									NA						CAAATCTCTCTcacacacaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.58723031T>A		NA		hg19		0.02	-0.350231	CTCxCAC	COVERED																																																																																			NOVEL					0			5	3.00758	KEEP	1	0	0	10	276	TT	0.992708	0.882393	0			4	60	104	1	0	6.867473	32	60	923	55		0.111111	0.888875
C3orf67	200844	__UNKNOWN__	__UNKNOWN__	3	58908894	58908894	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:58908894T>A	ENST00000472469.1	-	5	774				C3orf67_ENST00000491845.1_Intron|C3orf67_ENST00000295966.7_Intron|RP11-147N17.1_ENST00000492031.1_RNA|RP11-147N17.1_ENST00000482372.1_RNA|C3orf67_ENST00000482387.1_Intron|RP11-147N17.1_ENST00000493123.1_RNA|RP11-147N17.1_ENST00000463703.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	NA		NA								endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		cagcctcccatagtgctggga	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689	200844			24763	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198463	NM_198463	NA	Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000472469.1:c.64+14479A>T	chr3.hg19:g.58908894T>A		NA	B9EKV6|Q6ZV69	hg19		0.02	-0.192934	CCAxAGT	COVERED																																																																																			NOVEL	C3orf67-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000353804.1	8	2.70644	KEEP	0	0	0	9	242	TT	0.99254	0.454342	0		-	4	60	121	0	0	9.663536	16	60	473	44	ENST00000472469.1	0.2	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	61339959	61339959	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:61339959T>C			NA	NA				FHIT (102826 upstream) : PTPRG (207283 downstream)						NA		NA									NA						tctcaatctcttgacctcatg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.61339959T>C		NA		hg19		0.02	-0.131558	CTCxTGA	COVERED																																																																																			NOVEL					0			3	2.406193	KEEP	0	0	0	8	222	TT	0.99257	0.22747	0			3	60	84	0	0	6.572714	12	60	361	29		0.2	0.229173
PTPRG	5793	__UNKNOWN__	__UNKNOWN__	3	61786386	61786386	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:61786386C>T	ENST00000474889.1	+	2	567				PTPRG_ENST00000295874.10_Intron	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	NA		NA			brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		ggcatgatctcggcttactgc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724	5793		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Fibronectin type III domain containing	9671	protein-coding gene	gene with protein product		176886		PTPG	NA	1711217	Standard	NM_002841	NM_002841	NA	Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.190+51730C>T	chr3.hg19:g.61786386C>T		NA	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	hg19	CCDS2895.1	0.02	-0.11402	TCTxGGC	UNCOVERED																																																																																			NOVEL	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351674.1	15	4.511117	KEEP	6	0	0	15	418	CC	0.993634	0.161432	0		+	3	60	89	0	0	7.532467	8	60	245	43	ENST00000474889.1	0.272727	0.162467
PTPRG	5793	__UNKNOWN__	__UNKNOWN__	3	62045856	62045856	__UNKNOWN__	Intron	SNP	A	A	T	rs12492078	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:62045856A>T	ENST00000474889.1	+	5	896				PTPRG_ENST00000295874.10_Intron	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	NA		NA			brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		accgcactctagcctgagcaa	0.493		NA											A|||	558	0.111422	0.0408	0.196	5008	,	,	NA	13269	0.1954	NA	0.1163	False	NA	,,,	NA	NA	NA	2504	0.0552	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724	5793		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Fibronectin type III domain containing	9671	protein-coding gene	gene with protein product		176886		PTPG	NA	1711217	Standard	NM_002841	NM_002841	NA	Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.520-17981A>T	chr3.hg19:g.62045856A>T		NA	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	hg19	CCDS2895.1	0.02	-0.087701	TCTxGCC	UNCOVERED																																																																																			NOVEL	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351674.1	4	2.405393	KEEP	0	0	0	8	210	AA	0.99257	0.09898	0		+	3	60	88	0	0	7.743558	6	60	174	25	ENST00000474889.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	64036486	64036486	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:64036486T>A			NA	NA				PSMD6 (26828 upstream) : RP11-129B22.1 (17153 downstream)						NA		NA									NA						ggagtttgagtccagcctggg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.64036486T>A		NA		hg19		0.02	-0.131561	GAGxCCA	COVERED																																																																																			NOVEL					0			14	3.607586	KEEP	0	0	0	12	316	TT	0.993634	0.227714	0			3	60	95	1	0	8.001339	9	60	265	33		0.25	0.229173
PRICKLE2	166336	__UNKNOWN__	__UNKNOWN__	3	64296768	64296768	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:64296768C>A	ENST00000564377.1	-	3	138							Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	NA		NA			establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		ccttggcctcccaaagtgctg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637	166336			20340	protein-coding gene	gene with protein product		608501	prickle-like 2 (Drosophila)		NA	12525887	Standard	NM_198859	NM_198859	NA	Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000564377.1:c.129-112125G>T	chr3.hg19:g.64296768C>A		NA	Q0VF44	hg19		0.02	-0.157891	CTCxCAA	COVERED																																																																																			NOVEL	PRICKLE2-003	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000431928.1	4	2.708233	KEEP	0	0	0	9	281	CT	0.992708	0.351366	0		-	4	49	117	0	0	9.830617	11	60	385	45	ENST00000564377.1	0.266667	0.353947
PRICKLE2	166336	__UNKNOWN__	__UNKNOWN__	3	64321697	64321697	__UNKNOWN__	Intron	SNP	G	G	A	rs537625521	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:64321697G>A	ENST00000564377.1	-	2	138							Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	NA		NA			establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|neuron projection development (GO:0031175)	apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(9)|liver(1)|lung(10)|ovary(4)|prostate(2)|skin(2)|stomach(1)	32		Lung NSC(201;0.136)		BRCA - Breast invasive adenocarcinoma(55;0.000971)|KIRC - Kidney renal clear cell carcinoma(15;0.00443)|Kidney(15;0.00497)		tgtaatcccagctactcagga	0.527		NA											G|||	2	0.000399361	0.0	0.0	5008	,	,	NA	15663	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK127839	CCDS2902.1	3p14.3	2006-09-12	2006-09-12		ENSG00000163637	ENSG00000163637	166336			20340	protein-coding gene	gene with protein product		608501	prickle-like 2 (Drosophila)		NA	12525887	Standard	NM_198859	NM_198859	NA	Approved	DKFZp686D143	uc003dmf.3	Q7Z3G6	OTTHUMG00000158789	ENST00000564377.1:c.128+108461C>T	chr3.hg19:g.64321697G>A		NA	Q0VF44	hg19		0.02	-0.052624	CCAxCTA	UNCOVERED																																																																																			NOVEL	PRICKLE2-003	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000431928.1	10	2.708071	KEEP	6	0	0	9	276	GG	0	0	0		-	3	60	88	1	0	9.252722	1	48	32	22	ENST00000564377.1	0.75	0.036766
MAGI1	9223	__UNKNOWN__	__UNKNOWN__	3	65783725	65783725	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:65783725C>A	ENST00000497477.2	-	2	313				MAGI1_ENST00000330909.8_Intron|MAGI1_ENST00000470990.1_Intron|MAGI1_ENST00000402939.2_Intron|MAGI1_ENST00000483466.1_Intron			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	NA		NA			cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		tcacacctgtcatcccagcac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276	9223			946	protein-coding gene	gene with protein product		602625	BAI1-associated protein 1	BAIAP1	NA	9647739, 9225980	Standard	NM_004742	XM_005265563	NA	Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.314-175962G>T	chr3.hg19:g.65783725C>A		NA	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	hg19		0.02	-0.23686	TGTxATC	COVERED																																																																																			NOVEL	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000349132.2	4	3.310132	KEEP	1	0	0	11	348	CC	0.993072	0.608164	0		-	3	60	90	0	0	6.449587	22	60	767	66	ENST00000497477.2	0.12	0.612407
EOGT	285203	__UNKNOWN__	__UNKNOWN__	3	69026259	69026259	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:69026259T>C	ENST00000383701.3	-	0	2836				EOGT_ENST00000295571.5_3'UTR	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	NA		NA			protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)				NA						tgcagtgagctgagatcatgc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	285203	2.4.1.255		28526	protein-coding gene	gene with protein product	AER61 glycosyltransferase	614789	chromosome 3 open reading frame 64	C3orf64	NA	22310717	Standard	NM_173654	NM_001278689	NA	Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.*510A>G	chr3.hg19:g.69026259T>C		NA	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	hg19		0.02	3.493872	AGCxGAG	COVERED																																																																																			NOVEL	EOGT-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000343722.1	46	7.975235	KEEP	1	5	146	78	2096	TT	1	1	0		-	6	60	183	0	1	10.703191	120	60	3541	287	ENST00000383701.3	0.047619	1
EOGT	285203	__UNKNOWN__	__UNKNOWN__	3	69058945	69058945	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:69058945C>T	ENST00000383701.3	-	4	795	c.53G>A	c.(52-54)gGt>gAt	p.G18D	EOGT_ENST00000540955.1_5'UTR|EOGT_ENST00000295571.5_Missense_Mutation_p.G18D	NM_001278689.1	NP_001265618.1	Q5NDL2	EOGT_HUMAN	EGF domain-specific O-linked N-acetylglucosamine (GlcNAc) transferase	18		NA			protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)	protein N-acetylglucosaminyltransferase activity (GO:0016262)				NA						TTCATTCTGACCACTCAGTGA	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													117	105	109			NA	NA	3		NA											NA				69058945		2203	4300	6503	SO:0001583	missense			AK091089	CCDS2908.1, CCDS63684.1	3p14.1	2013-10-11	2012-05-21	2012-05-21	ENSG00000163378	ENSG00000163378	285203	2.4.1.255		28526	protein-coding gene	gene with protein product	AER61 glycosyltransferase	614789	chromosome 3 open reading frame 64	C3orf64	NA	22310717	Standard	NM_173654	NM_001278689	NA	Approved	AER61, FLJ33770	uc003dnk.3	Q5NDL2	OTTHUMG00000156279	ENST00000383701.3:c.53G>A	chr3.hg19:g.69058945C>T	ENSP00000373206:p.Gly18Asp	NA	A8K2U1|B4DFH5|L7X1M5|Q6MZY0|Q6P985|Q6ZTV0	hg19		0.02	2.214948	TGAxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.211	-1.036201	0.02029	.	.	ENSG00000163378	ENST00000383701;ENST00000295571;ENST00000424374;ENST00000456376	.	.	.	5.83	3.71	0.42584	.	0.761741	0.12724	N	0.444442	T	0.31071	0.0785	L	0.36672	1.1	0.21064	N	0.999799	B;B	0.22983	0.0;0.078	B;B	0.27380	0.001;0.079	T	0.25950	-1.0117	9	0.37606	T	0.19	-9.8406	4.4446	0.11591	0.1106:0.563:0.1195:0.2069	.	18;18	Q5NDL2;Q5NDL2-3	AER61_HUMAN;.	D	18	.	ENSP00000295571:G18D	G	-	2	0	C3orf64	69141635	0.290000	0.24343	0.404000	0.26397	0.087000	0.18053	0.521000	0.22893	0.825000	0.34637	-1.128000	0.01989	GGT	NOVEL	EOGT-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000343722.1	36	17.450262	KEEP	0	0	0	58	1743	CC	1	1	0		-	6	60	173	0	0	9.603526	125	60	4210	267	ENST00000383701.3	0.045802	1
FRMD4B	23150	__UNKNOWN__	__UNKNOWN__	3	69248170	69248170	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:69248170A>C	ENST00000398540.3	-	12	960				FRMD4B_ENST00000478263.1_Intron|FRMD4B_ENST00000542259.1_Intron	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	NA		NA			establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		gcctgtaatcacagcactttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541	23150			24886	protein-coding gene	gene with protein product		NA			NA	10231032, 11445584	Standard		XM_005264720	NA	Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.877-245T>G	chr3.hg19:g.69248170A>C		NA	Q8TAI3	hg19	CCDS46863.1	0.02	-0.192949	ATCxCAG	COVERED																																																																																			NOVEL	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352111.1	12	3.007467	KEEP	5	0	0	10	277	AA	0.99257	0.454356	0		-	3	60	107	0	0	8.391972	18	60	526	47	ENST00000398540.3	0.142857	0.457757
FRMD4B	23150	__UNKNOWN__	__UNKNOWN__	3	69359700	69359700	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:69359700G>C	ENST00000398540.3	-	3	407				FRMD4B_ENST00000542259.1_Intron	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	NA		NA			establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		gatacacacagacaaacacac	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541	23150			24886	protein-coding gene	gene with protein product		NA			NA	10231032, 11445584	Standard		XM_005264720	NA	Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.323+713C>G	chr3.hg19:g.69359700G>C		NA	Q8TAI3	hg19	CCDS46863.1	0.02	1.60093	ACAxACA	COVERED																																																																																			NOVEL	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352111.1	26	3.529616	KEEP	1	6	141	62	1873	GG	1	0.999835	0		-	8	60	255	0	0	18.162478	70	60	2162	225	ENST00000398540.3	0.102564	0.999835
MITF	4286	__UNKNOWN__	__UNKNOWN__	3	69863727	69863727	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:69863727A>G	ENST00000352241.4	+	2	267				MITF_ENST00000472437.1_Intron|MITF_ENST00000328528.6_Intron|MITF_ENST00000448226.2_Intron	NM_198159.2	NP_937802.1	O75030	MITF_HUMAN	microphthalmia-associated transcription factor	NA		NA			bone remodeling (GO:0046849)|camera-type eye development (GO:0043010)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|melanocyte differentiation (GO:0030318)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(6)|stomach(1)|urinary_tract(2)	30		Lung NSC(201;0.0384)|Prostate(884;0.0526)		BRCA - Breast invasive adenocarcinoma(55;3.07e-05)|Epithelial(33;0.000138)|LUSC - Lung squamous cell carcinoma(21;0.008)|Lung(16;0.0107)|KIRC - Kidney renal clear cell carcinoma(39;0.204)|Kidney(39;0.239)		caatcctcctacctcggcctc	0.488		NA	A		melanoma		Waardenburg syndrome type 2, Tietz syndrome														NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(29;269 969 31479 41502 42961)		Dom	yes		3	3p14.1	4286	microphthalmia-associated transcription factor	yes	E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2913.1, CCDS43106.1, CCDS43107.1, CCDS46865.1, CCDS46866.1, CCDS46866.2, CCDS54607.1, CCDS74962.1	3p14.1-p12.3	2014-09-17			ENSG00000187098	ENSG00000187098	4286		Basic helix-loop-helix proteins	7105	protein-coding gene	gene with protein product	homolog of mouse microphthalmia	156845	Waardenburg syndrome, type 2A	WS2A, WS2	NA	8069297, 7874167, 7951321	Standard	NM_198159	NM_198159	NA	Approved	MI, bHLHe32	uc003dnz.3	O75030	OTTHUMG00000149921	ENST00000352241.4:c.105-64558A>G	chr3.hg19:g.69863727A>G		NA	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	hg19	CCDS43106.1	0.02	-0.306871	CCTxCCT	COVERED																																																																																			NOVEL	MITF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313920.2	10	5.409423	KEEP	1	0	0	18	454	AA	0.999859	0.800133	0		+	3	60	99	0	0	6.968093	30	60	812	75	ENST00000352241.4	0.090909	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	71715886	71715886	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:71715886A>G			NA	NA				RP11-154H23.3 (79326 upstream) : EIF4E3 (8680 downstream)						NA		NA									NA						tcaggagttcaacaccagcct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.71715886A>G		NA		hg19		0.02	-0.078931	TTCxACA	UNCOVERED																																																																																			NOVEL					0			3	2.405819	KEEP	0	0	0	8	216	AA	0.99257	0.076761	0			3	60	91	1	0	8.455277	4	60	114	23		0.428571	0.077336
EIF4E3	317649	__UNKNOWN__	__UNKNOWN__	3	71799818	71799818	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:71799818C>T	ENST00000448225.1	-	1	167				EIF4E3_ENST00000421769.2_Intron|EIF4E3_ENST00000295612.3_Intron	NM_001134649.1|NM_001282886.1	NP_001128121.1|NP_001269815.1	Q8N5X7	IF4E3_HUMAN	eukaryotic translation initiation factor 4E family member 3	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|regulation of translation (GO:0006417)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	translation initiation factor activity (GO:0003743)			large_intestine(1)|lung(3)	4		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)		cgcctgtaatcccagcacttt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126999	CCDS33786.1, CCDS46867.1	3p14	2008-02-05	2006-11-13		ENSG00000163412	ENSG00000163412	317649			31837	protein-coding gene	gene with protein product		609896	eukaryotic translation initiation factor 4E member 3		NA	15153109	Standard	NM_173359	NM_173359	NA	Approved	MGC39820	uc003dov.4	Q8N5X7	OTTHUMG00000158797	ENST00000448225.1:c.289+3547G>A	chr3.hg19:g.71799818C>T		NA	B2R963|Q6NUT1	hg19	CCDS33786.1	0.02	-0.166665	AATxCCA	COVERED																																																																																			NOVEL	EIF4E3-202	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352243.2	14	5.414797	KEEP	7	0	0	18	533	CC	0.99649	0.352705	0		-	3	60	84	0	0	6.310795	15	60	501	56	ENST00000448225.1	0.166667	0.353947
EIF4E3	317649	__UNKNOWN__	__UNKNOWN__	3	71799826	71799826	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:71799826T>C	ENST00000448225.1	-	1	167				EIF4E3_ENST00000421769.2_Intron|EIF4E3_ENST00000295612.3_Intron	NM_001134649.1|NM_001282886.1	NP_001128121.1|NP_001269815.1	Q8N5X7	IF4E3_HUMAN	eukaryotic translation initiation factor 4E family member 3	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|regulation of translation (GO:0006417)	cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)	translation initiation factor activity (GO:0003743)			large_intestine(1)|lung(3)	4		Prostate(10;0.0166)		BRCA - Breast invasive adenocarcinoma(55;2.56e-05)|Epithelial(33;2.9e-05)|Lung(16;9.28e-05)|LUSC - Lung squamous cell carcinoma(21;0.00227)		atcccagcactttgggaggct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126999	CCDS33786.1, CCDS46867.1	3p14	2008-02-05	2006-11-13		ENSG00000163412	ENSG00000163412	317649			31837	protein-coding gene	gene with protein product		609896	eukaryotic translation initiation factor 4E member 3		NA	15153109	Standard	NM_173359	NM_173359	NA	Approved	MGC39820	uc003dov.4	Q8N5X7	OTTHUMG00000158797	ENST00000448225.1:c.289+3539A>G	chr3.hg19:g.71799826T>C		NA	B2R963|Q6NUT1	hg19	CCDS33786.1	0.02	-0.184192	CACxTTG	COVERED																																																																																			NOVEL	EIF4E3-202	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352243.2	15	6.615772	KEEP	6	0	0	22	603	TT	0.999863	0.42342	0		-	4	60	130	0	0	10.562989	16	60	485	65	ENST00000448225.1	0.2	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	72026248	72026248	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:72026248T>A			NA	NA				RN7SL271P (149634 upstream) : LINC00877 (58202 downstream)						NA		NA									NA						gtggtggctcttgcctgtaat	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.72026248T>A		NA		hg19		0.02	-0.175416	CTCxTGC	COVERED																																																																																			NOVEL					0			4	3.308283	KEEP	0	0	0	11	303	TT	0.993072	0.384723	0			3	60	90	0	0	6.910548	15	60	453	40		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	72771576	72771576	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:72771576T>C			NA	NA				RNA5SP136 (30614 upstream) : SHQ1 (26851 downstream)						NA		NA									NA						tggccgggcgtggtggctcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.72771576T>C		NA		hg19		0.02	-0.289392	GCGxGGT	COVERED																																																																																			NOVEL					0			10	4.50978	KEEP	1	0	0	15	396	TT	0.99649	0.758216	0			3	60	99	0	0	7.09829	27	60	776	69		0.1	0.760887
SHQ1	55164	__UNKNOWN__	__UNKNOWN__	3	72895466	72895466	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:72895466T>G	ENST00000325599.8	-	1	283				SHQ1_ENST00000463369.1_5'UTR	NM_018130.2	NP_060600.2	Q6PI26	SHQ1_HUMAN	SHQ1, H/ACA ribonucleoprotein assembly factor	NA		NA			negative regulation of rRNA processing (GO:2000233)|positive regulation of apoptotic process (GO:0043065)|ribonucleoprotein complex assembly (GO:0022618)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	27		Prostate(10;0.00482)|Lung NSC(201;0.0339)|Myeloproliferative disorder(1037;0.204)		BRCA - Breast invasive adenocarcinoma(55;9.68e-05)|Epithelial(33;0.000563)|LUSC - Lung squamous cell carcinoma(21;0.00229)|Lung(16;0.00688)|KIRC - Kidney renal clear cell carcinoma(39;0.018)|Kidney(39;0.0213)		tttttttttttagacagtctc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC025270	CCDS33788.1	3p13	2013-01-08	2013-01-08		ENSG00000144736	ENSG00000144736	55164			25543	protein-coding gene	gene with protein product		613663	SHQ1 homolog (S. cerevisiae)		NA	12477932	Standard	NM_018130	NM_018130	NA	Approved	FLJ10539, Shq1p	uc003dpf.3	Q6PI26	OTTHUMG00000158814	ENST00000325599.8:c.143+1882A>C	chr3.hg19:g.72895466T>G		NA	B4DL05|Q6MZJ4|Q7Z748|Q9H7E5|Q9NVS8	hg19	CCDS33788.1	0.02	1.80985	TTTxAGA	COVERED																																																																																			NOVEL	SHQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352310.1	11	9.546858	KEEP	0	0	0	32	785	TT	0.999997	0.99442	0		-	5	60	170	1	1	11.991846	53	70	1499	137	ENST00000325599.8	0.086207	0.994422
GXYLT2	727936	__UNKNOWN__	__UNKNOWN__	3	72993114	72993114	__UNKNOWN__	Intron	SNP	C	C	T	rs570728979	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:72993114C>T	ENST00000389617.4	+	4	761					NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	NA		NA			O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						ggattacaggcgtgagccacc	0.438		NA											C|||	14	0.00279553	0.0	0.0	5008	,	,	NA	17504	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0143	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986	727936		Glycosyltransferase family 8 domain containing	33383	protein-coding gene	gene with protein product		613322	glycosyltransferase 8 domain containing 4	GLT8D4	NA	19940119	Standard	NM_001080393	NM_001080393	NA	Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.601-11135C>T	chr3.hg19:g.72993114C>T		NA		hg19	CCDS46870.1	0.02	-0.122797	AGGxGTG	COVERED																																																																																			NOVEL	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352318.1	5	2.706414	KEEP	0	0	0	9	250	CC	0.99254	0.194847	0		+	3	60	93	1	0	7.932357	8	60	254	31	ENST00000389617.4	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	73330816	73330816	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:73330816A>T			NA	NA				RNU6-1270P (39769 upstream) : PDZRN3 (100767 downstream)						NA		NA									NA						gaggttgcagagagctgagat	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.73330816A>T		NA		hg19		0.02	-0.131518	CAGxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.406148	KEEP	4	0	0	8	221	AA	0	0	0			4	40	93	0	0	7.72198	9	60	275	34		0.307692	0.229173
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75679944	75679944	__UNKNOWN__	RNA	SNP	C	C	T	rs7614638	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75679944C>T	ENST00000408868.1	+	0	31					NR_031714.1				microRNA 1324	NA		NA									NA						CTGGTCCTGCCCTCACTGGGA	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													48	51	50			NA	NA	3		NA											NA				75679944		1568	3576	5144							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75679944C>T		NA		hg19		0.02	4.435871	TGCxCTC	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		4	5.715609	KEEP	10	0	0	19	548	CC	0.99986	0.99986	0		+	15	50	430	0	0	34.7978	51	50	1606	226	ENST00000408868.1	0.227273	1
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75679945	75679945	__UNKNOWN__	RNA	SNP	C	C	G	rs201625997	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75679945C>G	ENST00000408868.1	+	0	32					NR_031714.1				microRNA 1324	NA		NA									NA						TGGTCCTGCCCTCACTGGGAA	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													50	53	52			NA	NA	3		NA											NA				75679945		1568	3578	5146							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75679945C>G		NA		hg19		0.02	5.166129	GCCxTCA	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		5	5.113567	KEEP	10	0	0	17	489	CT	0.999869	0.999869	0		+	15	49	441	0	0	35.786601	52	50	1667	236	ENST00000408868.1	0.223881	1
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75679963	75679963	__UNKNOWN__	RNA	SNP	C	C	T	rs201125883	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75679963C>T	ENST00000408868.1	+	0	50					NR_031714.1				microRNA 1324	NA		NA									NA						GAACCCCCTTCCCTCTGGGTA	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													66	67	67			NA	NA	3		NA											NA				75679963		1568	3578	5146							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75679963C>T		NA		hg19		0.02	5.042617	CTTxCCT	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		5	10.530424	KEEP	6	0	0	35	1050	CC	0.999999	0.999999	0		+	18	51	492	0	0	36.907857	87	52	2845	374	ENST00000408868.1	0.171429	1
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75679993	75679993	__UNKNOWN__	RNA	SNP	C	C	T	rs202177109	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75679993C>T	ENST00000408868.1	+	0	80					NR_031714.1				microRNA 1324	NA		NA									NA						ATTCTATGCACTTTCCTGGAG	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													60	61	61			NA	NA	3		NA											NA				75679993		1568	3575	5143							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75679993C>T		NA		hg19		0.02	11.669657	GCAxTTT	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		19	4.377169	KEEP	23	5	134	62	1888	CC	1	1	0		+	25	60	742	0	1	54.204356	162	60	5541	690	ENST00000408868.1	0.13369	1
MIR1324	100302212	__UNKNOWN__	__UNKNOWN__	3	75680006	75680006	__UNKNOWN__	RNA	SNP	T	T	C	rs58827088	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75680006T>C	ENST00000408868.1	+	0	93					NR_031714.1				microRNA 1324	NA		NA									NA						TCCTGGAGGCTCCATGCTGGT	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													52	50	51			NA	NA	3		NA											NA				75680006		1568	3573	5141							3	2011-09-12		2008-12-18	ENSG00000221795	ENSG00000221795	100302212		ncRNAs / Micro RNAs	35377	non-coding RNA	RNA, micro		NA		MIRN1324	NA		Standard	NR_031714	NR_031714	NA	Approved	hsa-mir-1324	uc021xar.1			ENST00000408868.1:	chr3.hg19:g.75680006T>C		NA		hg19		0.02	15.629965	GGCxCCA	COVERED																																																																																			NOVEL	MIR1324-201	KNOWN	basic	miRNA	NA	miRNA		21	18.379812	KEEP	27	1	28	71	2000	TT	1	1	0		+	25	60	859	1	0	64.43855	187	60	5722	787	ENST00000408868.1	0.117925	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75691718	75691718	__UNKNOWN__	IGR	SNP	T	T	C	rs151337419		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75691718T>C			NA	NA				MIR1324 (11709 upstream) : FRG2C (21762 downstream)						NA		NA									NA						agtcagaacatgcttactata	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75691718T>C		NA		hg19		0.02	3.707442	ACAxGCT	COVERED																																																																																			NOVEL					0			4	3.040449	KEEP	0	1	25	19	543	TT	0.999863	0.999862	0			4	60	135	0	0	10.118715	29	60	884	208		0.121212	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75695626	75695626	__UNKNOWN__	IGR	SNP	C	C	A	rs200882557		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75695626C>A			NA	NA				MIR1324 (15617 upstream) : FRG2C (17854 downstream)						NA		NA									NA						caccccccagctgggcacggt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75695626C>A		NA		hg19		0.02	1.286887	CAGxTGG	COVERED																																																																																			NOVEL					0			23	9.026253	KEEP	0	0	0	30	906	CC	0.999997	0.99623	0			4	60	118	0	0	7.772842	43	60	1482	139		0.085106	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75695634	75695634	__UNKNOWN__	IGR	SNP	G	G	A	rs200385971		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75695634G>A			NA	NA				MIR1324 (15625 upstream) : FRG2C (17846 downstream)						NA		NA									NA						agctgggcacggtggctcaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75695634G>A		NA		hg19		0.02	1.289475	CACxGTG	COVERED																																																																																			NOVEL					0			25	10.228559	KEEP	0	0	0	34	1003	GG	0.999998	0.999216	0			5	60	145	0	0	9.65829	49	60	1588	156		0.092593	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75695799	75695799	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75695799A>G			NA	NA				MIR1324 (15790 upstream) : FRG2C (17681 downstream)						NA		NA									NA						ccagctactcaggaggctgag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75695799A>G		NA		hg19		0.02	-0.298195	CTCxGGA	COVERED																																																																																			NOVEL					0			16	4.64437	KEEP	3	1	30	26	727	AA	0.999957	0.781026	0			3	60	94	0	0	6.849506	22	60	668	83		0.12	0.78106
FRG2C	100288801	__UNKNOWN__	__UNKNOWN__	3	75714895	75714895	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75714895G>A	ENST00000464571.1	+	4	599	c.549G>A	c.(547-549)tcG>tcA	p.S183S	FRG2C_ENST00000308062.3_Silent_p.S184S			A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C	184		NA				nucleus (GO:0005634)				breast(2)|ovary(1)	3						GAGCTATGTCGGAGGCTGTTT	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969	100288801			33626	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001124759.1	NM_001124759	NA	Approved			A6NGY1	OTTHUMG00000158963	ENST00000464571.1:c.549G>A	chr3.hg19:g.75714895G>A		NA		hg19		0.02	6.274057	GTCxGAG	COVERED																																																																																			NOVEL	FRG2C-002	NOVEL	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352695.1	1	6.919538	KEEP	2	0	0	23	683	GG	0.999892	0.999892	0		+	8	40	251	0	0	15.768172	126	60	4127	319	ENST00000464571.1	0.059701	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75718474	75718474	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75718474G>A			NA	NA				FRG2C (2103 upstream) : LINC00960 (5089 downstream)						NA		NA									NA						CCAGAGAGACGGGCCTCCCGG	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75718474G>A		NA		hg19		0.02	1.219194	GACxGGC	COVERED																																																																																			NOVEL					0			4	2.706692	KEEP	10	0	0	9	256	GG	0.99257	0.992452	0			5	60	148	0	1	11.754112	20	60	640	161		0.2	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75749235	75749235	__UNKNOWN__	IGR	SNP	A	A	C	rs143339980		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75749235A>C			NA	NA				LINC00960 (23459 upstream) : ZNF717 (9558 downstream)						NA		NA									NA						caatctatacatttcatgcca	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75749235A>C		NA		hg19		0.02	-0.421022	TACxTTT	COVERED																																																																																			NOVEL					0			27	3.040401	KEEP	11	1	31	21	586	AA	0.99986	0.948269	0			6	49	192	0	0	15.449515	25	60	769	111		0.193548	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	75749271	75749271	__UNKNOWN__	IGR	SNP	G	G	A	rs112345033		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75749271G>A			NA	NA				LINC00960 (23495 upstream) : ZNF717 (9522 downstream)						NA		NA									NA						caggccaggggcagtggctca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.75749271G>A		NA		hg19		0.02	1.552487	GGGxCAG	COVERED																																																																																			NOVEL					0			34	5.148425	KEEP	20	1	28	27	830	GG	0.999892	0.967321	0			4	60	119	0	0	8.575166	28	60	962	137		0.125	0.967425
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75771941	75771941	__UNKNOWN__	Intron	SNP	T	T	A	rs2918484	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75771941T>A	ENST00000491507.1	-	5	544							Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						ggtgacagagtgaaactccat	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000491507.1:c.1798-6249A>T	chr3.hg19:g.75771941T>A		NA		hg19		0.02	-0.192935	GAGxGAA	COVERED																																																																																			NOVEL	ZNF717-004	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000352766.1	9	2.991529	KEEP	1	0	0	10	254	TT	0.992708	0.486967	0		-	5	60	143	0	0	12.369858	11	60	321	47	ENST00000491507.1	0.3125	0.490544
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75779827	75779827	__UNKNOWN__	Intron	SNP	C	C	T	rs376655351		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75779827C>T	ENST00000477374.1	-	6	511				ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						atccatcagaccaaatgaacc	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000477374.1:c.340-58G>A	chr3.hg19:g.75779827C>T		NA		hg19		0.02	1.511284	AGAxCAA	COVERED																																																																																			NOVEL	ZNF717-005	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000352767.1	2	3.910946	KEEP	0	0	0	13	383	CC	0.994391	0.988844	0		-	6	60	177	0	0	12.238783	51	70	1693	90	ENST00000477374.1	0.105263	0.994422
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75780821	75780821	__UNKNOWN__	Intron	SNP	T	T	C	rs145358341		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75780821T>C	ENST00000477374.1	-	5	511				ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						cccagcactttgggaggccaa	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000477374.1:c.339+389A>G	chr3.hg19:g.75780821T>C		NA		hg19		0.02	1.444136	CTTxGGG	COVERED																																																																																			NOVEL	ZNF717-005	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000352767.1	56	10.989777	KEEP	6	2	55	56	1545	TT	1	0.999622	0		-	7	60	219	0	0	17.836095	26	60	751	200	ENST00000477374.1	0.212121	0.999622
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75784056	75784056	__UNKNOWN__	Intron	SNP	C	C	T	rs112196493	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75784056C>T	ENST00000477374.1	-	5	449				ZNF717_ENST00000491507.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						tcactgcaacctccacctcct	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000477374.1:c.278-2784G>A	chr3.hg19:g.75784056C>T		NA		hg19		0.02	-0.21918	AACxTCC	COVERED																																																																																			NOVEL	ZNF717-005	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000352767.1	14	3.309554	KEEP	1	0	0	11	339	CC	0.993072	0.549057	0		-	8	60	232	0	0	22.20206	8	54	234	54	ENST00000477374.1	0.5	0.552887
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75785664	75785664	__UNKNOWN__	3'UTR	SNP	C	C	G	rs74770635	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75785664C>G	ENST00000478296.1	-	0	3236				ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						tctgagtggtccacatagaag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.*365G>C	chr3.hg19:g.75785664C>G		NA		hg19		0.02	12.344861	GGTxCAC	COVERED																																																																																			NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	22	11.869312	KEEP	0	4	121	82	2516	CC	1	1	0		-	39	60	1369	0	0	119.970957	98	60	3316	574	ENST00000478296.1	0.284672	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75786888	75786888	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs1615736		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75786888C>T	ENST00000478296.1	-	4	2012	c.1736G>A	c.(1735-1737)cGt>cAt	p.R579H	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.R622H|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.R629H			Q9BY31	ZN717_HUMAN	zinc finger protein 717	622		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGACTTCTGACGAAAGGTTTT	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													20	24	23			NA	NA	3		NA											NA				75786888		631	1552	2183	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1736G>A	chr3.hg19:g.75786888C>T	ENSP00000419377:p.Arg579His	NA		hg19		0.02	2.958673	TGAxGAA	COVERED	834	0.38186813186813184	149	0.30284552845528456	158	0.43646408839779005	217	0.3793706293706294	310	0.40897097625329815	.	5.928	0.355334	0.11239	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.08102	3.13;3.13;3.13	1.9	-3.81	0.04294	.	.	.	.	.	T	0.00012	0.0000	L	0.42744	1.35	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46512	-0.9186	8	0.23891	T	0.37	.	5.2238	0.15383	0.0:0.1993:0.3294:0.4713	rs1615736	629	C9JSV9	.	H	579;629;622	ENSP00000419377:R579H;ENSP00000409514:R629H;ENSP00000383643:R622H	ENSP00000383643:R622H	R	-	2	0	ZNF717	75869578	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.218000	0.00553	-1.710000	0.01397	-1.132000	0.01976	CGT	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	10	2.371165	KEEP	0	2	60	29	827	CC	0.999997	0.999997	0		-	22	60	634	0	0	54.037292	54	60	1713	198	ENST00000478296.1	0.289474	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75786993	75786993	__UNKNOWN__	Missense_Mutation	SNP	T	T	A	rs149887072		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75786993T>A	ENST00000478296.1	-	4	1907	c.1631A>T	c.(1630-1632)aAt>aTt	p.N544I	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.N587I|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.N594I			Q9BY31	ZN717_HUMAN	zinc finger protein 717	587		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CTCACATTCATTACATTCATA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													4	5	4			NA	NA	3		NA											NA				75786993		562	1458	2020	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1631A>T	chr3.hg19:g.75786993T>A	ENSP00000419377:p.Asn544Ile	NA		hg19		0.02	4.544107	TCAxTAC	COVERED	.	.	.	.	.	.	.	.	.	.	.	12.22	1.873449	0.33069	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.07567	3.18;3.18;3.18	1.9	-2.88	0.05682	.	.	.	.	.	T	0.10380	0.0254	L	0.52823	1.66	0.09310	N	1	P	0.50369	0.934	P	0.49421	0.61	T	0.12811	-1.0533	9	0.41790	T	0.15	.	3.9431	0.09336	0.0:0.3016:0.4104:0.288	.	594	C9JSV9	.	I	544;594;587	ENSP00000419377:N544I;ENSP00000409514:N594I;ENSP00000383643:N587I	ENSP00000383643:N587I	N	-	2	0	ZNF717	75869683	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.944000	0.01538	-0.642000	0.05480	0.450000	0.29827	AAT	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	11	3.069499	KEEP	0	2	56	30	812	TT	0.999997	0.999997	0		-	11	60	323	0	0	21.27713	117	60	3495	281	ENST00000478296.1	0.085937	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75787199	75787199	__UNKNOWN__	Missense_Mutation	SNP	A	A	C	rs138214171		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75787199A>C	ENST00000478296.1	-	4	1701	c.1425T>G	c.(1423-1425)caT>caG	p.H475Q	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.H518Q|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.H525Q			Q9BY31	ZN717_HUMAN	zinc finger protein 717	518		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GAGTTCTCTGATGGACAGTGA	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1	1	1			NA	NA	3		NA											NA				75787199		55	127	182	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1425T>G	chr3.hg19:g.75787199A>C	ENSP00000419377:p.His475Gln	NA		hg19		0.02	8.519043	CTGxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	.	13.98	2.398634	0.42512	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	D;D;D	0.86865	-2.18;-2.18;-2.18	1.79	1.79	0.24919	.	.	.	.	.	D	0.94377	0.8192	H	0.96398	3.815	0.40279	P	0.021626000000000034	D	0.89917	1.0	D	0.76071	0.987	D	0.94314	0.7548	8	0.87932	D	0	.	7.6713	0.28460	1.0:0.0:0.0:0.0	.	525	C9JSV9	.	Q	475;525;518	ENSP00000419377:H475Q;ENSP00000409514:H525Q;ENSP00000383643:H518Q	ENSP00000383643:H518Q	H	-	3	2	ZNF717	75869889	0.820000	0.29190	0.706000	0.30403	0.007000	0.05969	0.991000	0.29654	1.130000	0.42092	0.367000	0.22151	CAT	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	13	6.204111	KEEP	1	3	86	51	1349	AA	1	1	0		-	14	60	491	0	0	39.038606	74	70	2217	358	ENST00000478296.1	0.159091	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75787840	75787840	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs138029418		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75787840C>A	ENST00000478296.1	-	4	1060	c.784G>T	c.(784-786)Gcc>Tcc	p.A262S	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.A305S|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.A312S			Q9BY31	ZN717_HUMAN	zinc finger protein 717	305		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CAGTTACAGGCATAAGGTTTT	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													6	5	5			NA	NA	3		NA											NA				75787840		328	685	1013	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.784G>T	chr3.hg19:g.75787840C>A	ENSP00000419377:p.Ala262Ser	NA		hg19		0.02	9.903725	AGGxATA	COVERED	.	.	.	.	.	.	.	.	.	.	.	7.840	0.721687	0.15372	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.15017	2.46;2.46;2.46	1.26	-0.885	0.10593	.	.	.	.	.	T	0.09247	0.0228	N	0.25201	0.72	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32348	-0.9910	9	0.46703	T	0.11	.	2.6948	0.05132	0.4788:0.3441:0.0:0.1771	.	312	C9JSV9	.	S	262;312;305	ENSP00000419377:A262S;ENSP00000409514:A312S;ENSP00000383643:A305S	ENSP00000383643:A305S	A	-	1	0	ZNF717	75870530	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.529000	0.00440	-0.260000	0.09418	-0.430000	0.05897	GCC	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	16	8.390176	KEEP	0	5	136	76	2325	CC	1	1	0		-	18	60	538	0	0	39.134329	121	60	4190	621	ENST00000478296.1	0.129496	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75787926	75787926	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs200828229		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75787926T>C	ENST00000478296.1	-	4	974	c.698A>G	c.(697-699)tAt>tGt	p.Y233C	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.Y276C|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.Y283C			Q9BY31	ZN717_HUMAN	zinc finger protein 717	276		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						AACACATTCATAGGGTTTCTC	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1	1	1			NA	NA	3		NA											NA				75787926		183	384	567	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.698A>G	chr3.hg19:g.75787926T>C	ENSP00000419377:p.Tyr233Cys	NA		hg19		0.02	7.847478	TCAxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	.	8.705	0.910654	0.17833	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.25414	1.8;1.8;1.8	1.6	-3.2	0.05156	.	.	.	.	.	T	0.19446	0.0467	L	0.56124	1.755	0.09310	N	1	B	0.29432	0.244	B	0.32762	0.152	T	0.36359	-0.9751	9	0.66056	D	0.02	.	0.2488	0.00202	0.385:0.1495:0.1943:0.2712	.	283	C9JSV9	.	C	233;283;276	ENSP00000419377:Y233C;ENSP00000409514:Y283C;ENSP00000383643:Y276C	ENSP00000383643:Y276C	Y	-	2	0	ZNF717	75870616	0.000000	0.05858	0.002000	0.10522	0.414000	0.31173	-0.533000	0.06157	-1.084000	0.03092	0.240000	0.17902	TAT	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	7	3.201752	KEEP	0	3	86	41	1116	TT	1	1	0		-	9	60	305	0	0	23.926393	49	60	1408	325	ENST00000478296.1	0.155172	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788158	75788158	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs143605267		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75788158G>C	ENST00000478296.1	-	4	742	c.466C>G	c.(466-468)Ctg>Gtg	p.L156V	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.L199V|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.L206V			Q9BY31	ZN717_HUMAN	zinc finger protein 717	199		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L206V(1)		autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						AAAGTCTGCAGCAGAGTTTGA	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	stomach(1)											46	38	41			NA	NA	3		NA											NA				75788158		567	1399	1966	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.466C>G	chr3.hg19:g.75788158G>C	ENSP00000419377:p.Leu156Val	NA		hg19		0.02	12.181327	GCAxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	.	8.902	0.956517	0.18507	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.60299	0.2;0.2;0.2	2.07	1.13	0.20643	.	.	.	.	.	T	0.25494	0.0620	N	0.02202	-0.64	0.80722	P	0.0	P	0.37864	0.61	B	0.28305	0.088	T	0.24083	-1.0170	8	0.59425	D	0.04	.	7.9234	0.29859	0.0:0.5081:0.4918:0.0	rs3009004;rs52807189;rs3009004	206	C9JSV9	.	V	156;206;199	ENSP00000419377:L156V;ENSP00000409514:L206V;ENSP00000383643:L199V	ENSP00000383643:L199V	L	-	1	2	ZNF717	75870848	.	.	0.003000	0.11579	0.012000	0.07955	.	.	0.447000	0.26695	0.545000	0.68477	CTG	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	8	14.076208	KEEP	0	1	29	57	1772	GG	1	1	0		-	31	60	1064	0	0	86.756727	132	60	4542	599	ENST00000478296.1	0.190184	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788411	75788411	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs149968740		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75788411G>C	ENST00000478296.1	-	4	489	c.213C>G	c.(211-213)aaC>aaG	p.N71K	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.N114K|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.N121K			Q9BY31	ZN717_HUMAN	zinc finger protein 717	114	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						GAGTTGATGTGTTGCTGTTGG	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1	1	1			NA	NA	3		NA											NA				75788411		277	683	960	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.213C>G	chr3.hg19:g.75788411G>C	ENSP00000419377:p.Asn71Lys	NA		hg19		0.02	4.009197	TGTxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.398198	0.00198	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.42131	0.98;0.98;0.98	2.13	-4.26	0.03755	.	.	.	.	.	T	0.17280	0.0415	N	0.14661	0.345	0.09310	N	1	B	0.17852	0.024	B	0.12837	0.008	T	0.32348	-0.9910	9	0.06099	T	0.92	.	5.869	0.18793	0.1271:0.0:0.6195:0.2533	rs4011156	121	C9JSV9	.	K	71;121;114	ENSP00000419377:N71K;ENSP00000409514:N121K;ENSP00000383643:N114K	ENSP00000383643:N114K	N	-	3	2	ZNF717	75871101	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.826000	0.04429	-1.403000	0.02053	-1.851000	0.00568	AAC	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	2	2.240994	KEEP	0	1	33	19	580	GG	0.999863	0.999863	0		-	14	60	463	0	0	34.321794	104	60	3587	207	ENST00000478296.1	0.118644	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788414	75788414	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75788414G>A	ENST00000478296.1	-	4	486	c.210C>T	c.(208-210)agC>agT	p.S70S	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Silent_p.S113S|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Silent_p.S120S			Q9BY31	ZN717_HUMAN	zinc finger protein 717	113	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TTGATGTGTTGCTGTTGGTGA	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1	1	1			NA	NA	3		NA											NA				75788414		279	698	977	SO:0001819	synonymous_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.210C>T	chr3.hg19:g.75788414G>A		NA		hg19		0.02	2.888333	GTTxCTG	COVERED																																																																																			NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	2	2.641317	KEEP	0	1	29	19	582	GG	0.999863	0.999863	0		-	7	60	196	0	0	11.363226	114	60	3943	215	ENST00000478296.1	0.057851	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75788432	75788432	__UNKNOWN__	Missense_Mutation	SNP	T	T	A	rs143693332		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75788432T>A	ENST00000478296.1	-	4	468	c.192A>T	c.(190-192)caA>caT	p.Q64H	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Missense_Mutation_p.Q107H|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.Q114H			Q9BY31	ZN717_HUMAN	zinc finger protein 717	107	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.	NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q114H(1)		autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGATTACAATTTGCCAGAAAA	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	stomach(1)											1	1	1			NA	NA	3		NA											NA				75788432		366	869	1235	SO:0001583	missense			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.192A>T	chr3.hg19:g.75788432T>A	ENSP00000419377:p.Gln64His	NA		hg19		0.02	2.943945	AATxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	.	10.54	1.378407	0.24944	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.46819	0.86;0.86;0.86	2.13	0.901	0.19284	.	.	.	.	.	T	0.43322	0.1242	N	0.21373	0.66	0.09310	N	1	D	0.54964	0.969	P	0.56042	0.79	T	0.25433	-1.0132	9	0.51188	T	0.08	.	6.8345	0.23929	0.0:0.0:0.2348:0.7651	rs11122680	114	C9JSV9	.	H	64;114;107	ENSP00000419377:Q64H;ENSP00000409514:Q114H;ENSP00000383643:Q107H	ENSP00000383643:Q107H	Q	-	3	2	ZNF717	75871122	0.001000	0.12720	0.006000	0.13384	0.005000	0.04900	0.097000	0.15168	0.264000	0.21851	-0.462000	0.05337	CAA	NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	0	3.039922	KEEP	0	1	25	19	541	TT	0.999863	0.999863	0		-	9	60	270	0	0	17.103738	121	60	3638	231	ENST00000478296.1	0.069231	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75790536	75790536	__UNKNOWN__	Intron	SNP	A	A	T	rs148282009		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75790536A>T	ENST00000478296.1	-	3	311				ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Intron|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						ATGAGAAACAATGGAAGACTT	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													41	27	31			NA	NA	3		NA											NA				75790536		260	647	907	SO:0001627	intron_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.35-17T>A	chr3.hg19:g.75790536A>T		NA		hg19		0.02	8.875429	ACAxTGG	COVERED																																																																																			NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	10	6.008753	KEEP	0	3	82	49	1336	AA	1	1	0		-	21	60	643	0	0	49.916627	102	60	3060	520	ENST00000478296.1	0.170732	1
ZNF717	100131827	__UNKNOWN__	__UNKNOWN__	3	75815225	75815225	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:75815225T>C	ENST00000478296.1	-	1	184				ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000400845.3_Intron|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						accattgcactacagtctggg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124	100131827		Zinc fingers, C2H2-type, -	29448	protein-coding gene	gene with protein product		NA	zinc finger protein 838	ZNF838	NA		Standard	NM_001128223	NM_001128223	NA	Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.92+19309A>G	chr3.hg19:g.75815225T>C		NA		hg19		0.02	-0.228047	CACxACA	COVERED																																																																																			NOVEL	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000352764.2	22	3.842798	KEEP	10	1	32	24	667	TT	0.999879	0.58286	0		-	3	48	101	0	0	7.860708	17	60	510	83	ENST00000478296.1	0.15	0.58293
ROBO2	6092	__UNKNOWN__	__UNKNOWN__	3	76883149	76883149	__UNKNOWN__	Intron	SNP	C	C	T	rs371083028		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:76883149C>T	ENST00000487694.3	+	3	388					NM_001128929.2	NP_001122401.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	NA		NA			apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		tctttctttccttctttcttt	0.294		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008	6092		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	10250	protein-coding gene	gene with protein product		602431	roundabout (axon guidance receptor, Drosophila) homolog 2		NA	9458045	Standard	XM_031246	NM_002942	NA	Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000487694.3:c.110-264016C>T	chr3.hg19:g.76883149C>T		NA	O43608|Q19AB4|Q19AB5	hg19	CCDS54609.1	0.02	-0.254381	TTCxTTC	COVERED																																																																																			NOVEL	ROBO2-013	NOVEL	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467720.1	5	4.881041	KEEP	0	2	41	31	932	CC	0.999998	0.668522	0		+	4	60	117	0	2	8.69218	23	60	767	87	ENST00000487694.3	0.148148	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	78370899	78370899	__UNKNOWN__	IGR	SNP	T	T	G	rs376619018|rs111667843	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:78370899T>G			NA	NA				RP11-314M24.1 (30558 upstream) : ROBO1 (275490 downstream)						NA		NA									NA						agtttttttgtttttttttgt	0.433		NA											T|||	294	0.0587061	0.0666	0.0663	5008	,	,	NA	16481	0.002	NA	0.1342	False	NA	,,,	NA	NA	NA	2504	0.0235	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.78370899T>G		NA		hg19		0.02	-0.061398	TTGxTTT	UNCOVERED																																																																																			NOVEL					0			12	3.608048	KEEP	7	0	0	12	316	TT	0.99257	0.043461	0			3	60	104	0	0	10.025497	3	60	86	28		0.5	0.043787
ROBO1	6091	__UNKNOWN__	__UNKNOWN__	3	78653428	78653428	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:78653428C>T	ENST00000464233.1	-	29	4858				ROBO1_ENST00000436010.2_Intron|ROBO1_ENST00000466906.1_Intron|ROBO1_ENST00000495273.1_Intron|ROBO1_ENST00000467549.1_Intron	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		accatgttggccaggctggtc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855	6091		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	10249	protein-coding gene	gene with protein product		602430	roundabout (axon guidance receptor, Drosophila) homolog 1		NA	9458045, 9608531	Standard	NM_002941	NM_002941	NA	Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.4744+2454G>A	chr3.hg19:g.78653428C>T		NA	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	hg19	CCDS54611.1	0.02	-0.131554	TGGxCAG	COVERED																																																																																			NOVEL	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352610.1	11	6.015946	KEEP	7	0	0	20	597	CC	0.999366	0.229028	0		-	3	47	82	0	0	6.977747	7	60	230	53	ENST00000464233.1	0.3	0.229173
ROBO1	6091	__UNKNOWN__	__UNKNOWN__	3	78965149	78965149	__UNKNOWN__	Intron	SNP	C	C	T	rs331183	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:78965149C>T	ENST00000464233.1	-	4	613				ROBO1_ENST00000436010.2_Intron|ROBO1_ENST00000495273.1_Intron|ROBO1_ENST00000467549.1_Intron	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		cgcctgtaatcccagcacttt	0.547		NA											c|||	1647	0.328874	0.4834	0.2781	5008	,	,	NA	12442	0.1915	NA	0.3469	False	NA	,,,	NA	NA	NA	2504	0.2791	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855	6091		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	10249	protein-coding gene	gene with protein product		602430	roundabout (axon guidance receptor, Drosophila) homolog 1		NA	9458045, 9608531	Standard	NM_002941	NM_002941	NA	Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.499+22601G>A	chr3.hg19:g.78965149C>T		NA	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	hg19	CCDS54611.1	0.02	-0.166678	AATxCCA	COVERED																																																																																			NOVEL	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352610.1	3	3.00694	KEEP	4	0	0	10	285	CC	0.99257	0.351317	0		-	5	60	156	0	0	13.230087	14	60	485	44	ENST00000464233.1	0.263158	0.353947
ROBO1	6091	__UNKNOWN__	__UNKNOWN__	3	79381030	79381030	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:79381030T>C	ENST00000464233.1	-	3	202					NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		cggtggctcatgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855	6091		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	10249	protein-coding gene	gene with protein product		602430	roundabout (axon guidance receptor, Drosophila) homolog 1		NA	9458045, 9608531	Standard	NM_002941	NM_002941	NA	Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.89-206341A>G	chr3.hg19:g.79381030T>C		NA	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	hg19	CCDS54611.1	0.02	-0.192806	TCAxGCC	COVERED																																																																																			NOVEL	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352610.1	5	3.308835	KEEP	1	0	0	11	313	TT	0.993072	0.454585	0		-	4	60	131	0	0	10.764693	15	60	429	56	ENST00000464233.1	0.210526	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	80422735	80422735	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:80422735G>T			NA	NA				ROBO1 (605770 upstream) : RP11-47P18.1 (387457 downstream)						NA		NA									NA						ttttctgagagggagtcttgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.80422735G>T		NA		hg19		0.02	-0.122807	AGAxGGA	COVERED																																																																																			NOVEL					0			7	3.009224	KEEP	1	0	0	10	316	GG	0.992708	0.227502	0			3	60	82	0	0	6.581885	10	60	354	40		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	80719134	80719134	__UNKNOWN__	IGR	SNP	A	A	G	rs641949	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:80719134A>G			NA	NA				ROBO1 (902169 upstream) : RP11-47P18.1 (91058 downstream)						NA		NA									NA						atggtggctcacatctgtaat	0.478		NA											a|||	3993	0.797324	0.9395	0.7536	5008	,	,	NA	14569	0.872	NA	0.7247	False	NA	,,,	NA	NA	NA	2504	0.6339	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.80719134A>G		NA		hg19		0.02	-0.19296	CTCxCAT	UNCOVERED																																																																																			NOVEL					0			38	6.917972	KEEP	52	0	0	23	644	AA	0	0	0			9	60	285	0	0	28.030892	7	60	213	117		0.5625	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	82854815	82854815	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:82854815C>T			NA	NA				RP11-260O18.1 (341989 upstream) : None (None downstream)						NA		NA									NA						ccagcctgggcgacagagcga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.82854815C>T		NA		hg19		0.02	-0.394332	GGGxGAC	COVERED																																																																																			NOVEL					0			11	5.54767	KEEP	6	1	24	27	796	CC	0.999957	0.934452	0			4	40	106	0	0	7.278307	28	60	912	79		0.125	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	84144509	84144509	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:84144509T>C			NA	NA				None (None upstream) : AC108696.1 (194753 downstream)						NA		NA									NA						gtgatccgcctgcctcggcct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.84144509T>C		NA		hg19		0.02	-0.087681	GCCxGCC	UNCOVERED																																																																																			NOVEL					0			3	2.40649	KEEP	0	0	0	8	228	TT	0.99257	0.09898	0			3	60	90	0	0	7.942492	6	60	177	27		0.333333	0.099721
LINC00971	440970	__UNKNOWN__	__UNKNOWN__	3	84873409	84873409	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:84873409A>G	ENST00000484892.1	-	0	1294					NR_033860.1				long intergenic non-protein coding RNA 971	NA		NA									NA						ccaaagtgctaggattacagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							3p12.1	2013-06-07			ENSG00000242641	ENSG00000242641	440970		Long non-coding RNAs	48737	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_033860	NA	Approved				OTTHUMG00000158981	ENST00000484892.1:	chr3.hg19:g.84873409A>G		NA		hg19		0.02	-0.219285	GCTxGGA	COVERED																																																																																			NOVEL	LINC00971-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000352776.2	5	6.616952	KEEP	0	0	0	22	610	AA	0.999879	0.55282	0		-	3	60	103	0	0	8.060626	17	60	515	78	ENST00000484892.1	0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	84989627	84989627	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:84989627G>A			NA	NA				AC132660.1 (34731 upstream) : CADM2 (18504 downstream)						NA		NA									NA						cacccgcctcggcctcccaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.84989627G>A		NA		hg19		0.02	-0.175425	CTCxGCC	COVERED																																																																																			NOVEL					0			13	4.513261	KEEP	12	0	0	15	460	GG	0.993634	0.38494	0			3	60	90	0	0	6.833795	16	60	529	64		0.157895	0.387407
CADM2	253559	__UNKNOWN__	__UNKNOWN__	3	85468344	85468344	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:85468344G>A	ENST00000407528.2	+	2	123				CADM2_ENST00000383699.3_Intron	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	NA		NA			adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|synapse (GO:0045202)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(1)|prostate(1)|skin(4)	38		Lung NSC(201;0.0148)		LUSC - Lung squamous cell carcinoma(29;0.000815)|Lung(72;0.00304)|BRCA - Breast invasive adenocarcinoma(55;0.156)|Epithelial(33;0.157)		ggtggctcacgcctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF538973	CCDS33792.1, CCDS54613.1, CCDS54614.1	3p12.2	2013-01-11	2007-02-07	2007-02-07	ENSG00000175161	ENSG00000175161	253559		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / C2-set domain containing	29849	protein-coding gene	gene with protein product	nectin-like 3	609938	immunoglobulin superfamily, member 4D	IGSF4D	NA		Standard	NM_153184	NM_153184	NA	Approved	NECL3, Necl-3, SynCAM2	uc003dqj.3	Q8N3J6	OTTHUMG00000158990	ENST00000407528.2:c.62-382853G>A	chr3.hg19:g.85468344G>A		NA	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	hg19	CCDS54614.1	0.02	-0.122813	CACxCCT	COVERED																																																																																			NOVEL	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352822.1	4	3.901187	KEEP	3	0	0	13	336	GG	0.993072	0.194952	0		+	3	60	90	0	0	7.500917	9	60	310	46	ENST00000407528.2	0.25	0.196312
VGLL3	389136	__UNKNOWN__	__UNKNOWN__	3	86992181	86992181	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:86992181A>G	ENST00000398399.2	-	0	5337					NM_016206.2	NP_057290.2			vestigial-like family member 3	NA		NA								NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		gtgtgtgtgtatgtgATTTCC	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538	389136			24327	protein-coding gene	gene with protein product		609980	vestigial like 3 (Drosophila)		NA	12376544	Standard	NM_016206	NM_016206	NA	Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.*3993T>C	chr3.hg19:g.86992181A>G		NA		hg19	CCDS43110.1	0.02	1.701527	TGTxTGT	COVERED																																																																																			NOVEL	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352805.1	18	3.739093	KEEP	0	1	30	23	609	AA	0.999931	0.995015	0		-	4	60	138	2	0	9.390476	54	60	1528	133	ENST00000398399.2	0.068966	0.995084
VGLL3	389136	__UNKNOWN__	__UNKNOWN__	3	87011963	87011963	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:87011963T>C	ENST00000398399.2	-	3	1301				VGLL3_ENST00000383698.3_3'UTR	NM_016206.2	NP_057290.2			vestigial-like family member 3	NA		NA								NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		gtcaggagtttgagaccagcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538	389136			24327	protein-coding gene	gene with protein product		609980	vestigial like 3 (Drosophila)		NA	12376544	Standard	NM_016206	NM_016206	NA	Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.937+5776A>G	chr3.hg19:g.87011963T>C		NA		hg19	CCDS43110.1	0.02	3.24534	GTTxGAG	COVERED																																																																																			NOVEL	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352805.1	21	9.641193	KEEP	0	4	110	71	1894	TT	1	0.999998	0		-	8	60	245	0	0	15.751539	106	60	3100	275	ENST00000398399.2	0.070175	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	88944355	88944355	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:88944355A>G			NA	NA				Y_RNA (463896 upstream) : EPHA3 (212318 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.88944355A>G		NA		hg19		0.02	-0.201695	GGCxTGA	COVERED																																																																																			NOVEL					0			5	3.007661	KEEP	2	0	0	10	278	AA	0.99254	0.486885	0			3	60	98	0	0	7.710517	15	60	433	50		0.166667	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	89568372	89568372	__UNKNOWN__	IGR	SNP	T	T	C	rs146365873		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:89568372T>C			NA	NA				EPHA3 (37088 upstream) : U3 (511061 downstream)						NA		NA									NA						cttccttccttcctccctccc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.89568372T>C		NA		hg19		0.02	-0.096375	CCTxCCT	UNCOVERED																																																																																			NOVEL					0			7	2.40524	KEEP	1	0	0	8	214	TT	0.99257	0.119541	0			3	60	96	0	0	8.234409	8	60	195	26		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	89586463	89586463	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:89586463G>A			NA	NA				EPHA3 (55179 upstream) : U3 (492970 downstream)						NA		NA									NA						ttggactcccgaagtgctggg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.89586463G>A		NA		hg19		0.02	-0.13157	CCCxAAG	COVERED																																																																																			NOVEL					0			5	2.707365	KEEP	0	0	0	9	261	GG	0.99254	0.227464	0			3	60	81	0	0	6.373192	11	60	369	38		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	89825439	89825439	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:89825439C>T			NA	NA				EPHA3 (294155 upstream) : U3 (253994 downstream)						NA		NA									NA						ttcttcttctccttctccttc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.89825439C>T		NA		hg19		0.02	-0.131514	TCTxCTT	UNCOVERED																																																																																			NOVEL					0			8	2.407408	KEEP	4	0	0	8	254	CC	0	0	0			3	60	81	1	0	6.373932	11	60	345	38		0.214286	0.229173
PROS1	5627	__UNKNOWN__	__UNKNOWN__	3	93602551	93602551	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:93602551C>T	ENST00000394236.3	-	12	1809				PROS1_ENST00000407433.1_Intron	NM_000313.3	NP_000304.2	P07225	PROS_HUMAN	protein S (alpha)	NA		NA			blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|negative regulation of endopeptidase activity (GO:0010951)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|endopeptidase inhibitor activity (GO:0004866)			endometrium(3)|kidney(5)|large_intestine(8)|lung(26)|ovary(1)|skin(2)|urinary_tract(1)	46					Drotrecogin alfa(DB00055)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	cggtggctcacacctgtaatc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS2923.1	3q11.1	2013-06-03			ENSG00000184500	ENSG00000184500	5627			9456	protein-coding gene	gene with protein product		176880		PROS	NA	214811, 1833851	Standard	NM_000313	NM_000313	NA	Approved		uc003drb.4	P07225	OTTHUMG00000150354	ENST00000394236.3:c.1492+1020G>A	chr3.hg19:g.93602551C>T		NA	A8KAC9|D3DN28|Q15518|Q7Z715|Q9UCZ8	hg19	CCDS2923.1	0.02	-0.201766	TCAxACC	COVERED																																																																																			NOVEL	PROS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317762.1	10	2.706903	KEEP	1	0	0	9	251	CG	0.992708	0.486967	0		-	3	60	93	0	0	7.133356	16	60	543	50	ENST00000394236.3	0.157895	0.490544
DHFRL1	200895	__UNKNOWN__	__UNKNOWN__	3	93777752	93777752	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:93777752A>G	ENST00000394221.2	-	0	3053				DHFRL1_ENST00000481631.1_Intron|DHFRL1_ENST00000314636.2_3'UTR	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	NA		NA			glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)			kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						tgggactacaagcatgggcca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700	200895			27309	protein-coding gene	gene with protein product		NA	dihydrofolate reductase pseudogene 4	DHFRP4	NA	12477932	Standard	NM_176815	NM_001195643	NA	Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.*2040T>C	chr3.hg19:g.93777752A>G		NA	D3DN30|Q6P4I9	hg19	CCDS2926.1	0.02	1.800957	ACAxGCA	COVERED																																																																																			NOVEL	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352910.1	13	3.668845	KEEP	0	2	59	33	873	AA	0.999999	0.995082	0		-	5	60	170	0	0	11.804464	58	60	1775	126	ENST00000394221.2	0.079365	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	94828407	94828407	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:94828407A>G			NA	NA				LINC00879 (118235 upstream) : MTHFD2P1 (544859 downstream)						NA		NA									NA						atgagccaccacgcccagcca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.94828407A>G		NA		hg19		0.02	-0.157867	ACCxCGC	COVERED																																																																																			NOVEL					0			4	3.007781	KEEP	0	0	0	10	280	AA	0.992708	0.320453	0			3	60	102	0	0	8.278915	13	60	381	41		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	96099957	96099957	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:96099957C>T			NA	NA				AC108739.1 (214211 upstream) : AC108697.1 (52201 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.96099957C>T		NA		hg19		0.02	-0.1751	AGGxGTG	COVERED																																																																																			NOVEL					0			6	2.707844	KEEP	1	0	0	9	273	CC	0.99257	0.384528	0			3	60	88	0	0	6.795523	14	60	438	48		0.176471	0.387407
RP11-325B23.2	0	__UNKNOWN__	__UNKNOWN__	3	98092370	98092370	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:98092370G>A	ENST00000508616.1	+	0	188										NA		NA									NA						cgcccgcctcggcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000508616.1:	chr3.hg19:g.98092370G>A		NA		hg19		0.02	-0.149127	CTCxGCC	UNCOVERED																																																																																			NOVEL	RP11-325B23.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000359282.1	2	2.406808	KEEP	3	0	0	8	243	GG	0	0	0		+	3	60	94	0	0	7.672706	11	60	368	43	ENST00000508616.1	0.214286	0.292001
RP11-325B23.2	0	__UNKNOWN__	__UNKNOWN__	3	98115819	98115819	__UNKNOWN__	lincRNA	SNP	C	C	A	rs145947649	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:98115819C>A	ENST00000508616.1	+	0	188										NA		NA									NA						gctcaaaaagcacccccactg	0.483		NA											C|||	31	0.0061901	0.0	0.0058	5008	,	,	NA	19916	0.0	NA	0.0229	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000508616.1:	chr3.hg19:g.98115819C>A		NA		hg19		0.02	-0.105249	AAGxACC	UNCOVERED																																																																																			NOVEL	RP11-325B23.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000359282.1	3	2.707888	KEEP	39	0	0	9	270	CC	0	0	0		+	3	20	85	0	0	7.001068	9	40	293	81	ENST00000508616.1	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	98324733	98324733	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:98324733C>A			NA	NA				CPOX (12166 upstream) : AC021660.1 (18059 downstream)						NA		NA									NA						aatcttggctcactgcaacct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.98324733C>A		NA		hg19		0.02	-0.166659	GCTxACT	UNCOVERED																																																																																			NOVEL					0			9	2.708258	KEEP	5	0	0	9	282	CC	0	0	0			4	60	108	0	0	8.568482	14	60	478	44		0.222222	0.353947
ST3GAL6	10402	__UNKNOWN__	__UNKNOWN__	3	98467529	98467529	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:98467529C>T	ENST00000483910.1	+	1	278				ST3GAL6_ENST00000394162.1_Intron|ST3GAL6_ENST00000265261.6_Intron|ST3GAL6_ENST00000462152.1_Intron	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						aggctggtctcgaactcctga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225	10402		Sialyltransferases	18080	protein-coding gene	gene with protein product		607156	sialyltransferase 10 (alpha-2,3-sialyltransferase VI)	SIAT10	NA	10206952	Standard	NM_006100	NM_006100	NA	Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.-12+16153C>T	chr3.hg19:g.98467529C>T		NA	B2RCH2|B3KMI1|D3DN39|F8W6U0	hg19	CCDS2933.1	0.02	-0.201718	TCTxGAA	COVERED																																																																																			NOVEL	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353013.2	13	3.911279	KEEP	10	0	0	13	388	CC	0.992708	0.486967	0		+	4	60	106	0	0	7.981823	18	60	580	55	ENST00000483910.1	0.181818	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	99213259	99213259	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:99213259A>G			NA	NA				AC078828.1 (127526 upstream) : RP11-779P15.1 (5931 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.99213259A>G		NA		hg19		0.02	-0.17542	CCAxCAC	COVERED																																																																																			NOVEL					0			3	3.307856	KEEP	1	0	0	11	297	AA	0.992708	0.384582	0			3	60	106	0	0	8.509905	15	60	453	46		0.166667	0.387407
FILIP1L	11259	__UNKNOWN__	__UNKNOWN__	3	99622346	99622346	__UNKNOWN__	Intron	SNP	G	G	A	rs181682802		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:99622346G>A	ENST00000331335.5	-	4	1076				FILIP1L_ENST00000398326.2_Intron|CMSS1_ENST00000421999.2_Intron|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000354552.3_Intron	NM_001042459.1	NP_001035924.1	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	NA		NA				cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						cacctgcctcggcctcccaaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386	11259			24589	protein-coding gene	gene with protein product	downregulated in ovarian cancer 1, GPBP-interacting protein of 130 kDa	612993			NA	8314147, 15935955, 21832087	Standard	NM_014890	NM_001282793	NA	Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000331335.5:c.605+20727C>T	chr3.hg19:g.99622346G>A		NA	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	hg19	CCDS43118.1	0.02	-0.184211	CTCxGCC	COVERED																																																																																			NOVEL	FILIP1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353070.1	6	2.437236	KEEP	6	1	28	18	530	GG	0.99649	0.421991	0		-	3	21	95	0	0	7.260861	17	60	565	64	ENST00000331335.5	0.15	0.423478
FILIP1L	11259	__UNKNOWN__	__UNKNOWN__	3	99735127	99735127	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:99735127C>T	ENST00000331335.5	-	2	461				FILIP1L_ENST00000398326.2_Intron|CMSS1_ENST00000421999.2_Intron|CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000354552.3_Intron	NM_001042459.1	NP_001035924.1	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	NA		NA				cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						acctccgcctcctgggttcaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386	11259			24589	protein-coding gene	gene with protein product	downregulated in ovarian cancer 1, GPBP-interacting protein of 130 kDa	612993			NA	8314147, 15935955, 21832087	Standard	NM_014890	NM_001282793	NA	Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000331335.5:c.10-85253G>A	chr3.hg19:g.99735127C>T		NA	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	hg19	CCDS43118.1	0.02	-0.201757	CCTxCTG	COVERED																																																																																			NOVEL	FILIP1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353070.1	5	3.008371	KEEP	2	0	0	10	295	CC	0.992708	0.486967	0		-	3	37	95	0	0	7.333276	16	60	525	45	ENST00000331335.5	0.157895	0.490544
IMPG2	50939	__UNKNOWN__	__UNKNOWN__	3	100945634	100945634	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:100945634T>A	ENST00000193391.7	-	0	4092					NM_016247.3	NP_057331.2	Q9BZV3	IMPG2_HUMAN	interphotoreceptor matrix proteoglycan 2	NA		NA			visual perception (GO:0007601)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)|receptor complex (GO:0043235)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(14)|lung(32)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64					Hyaluronan(DB08818)	AATGGTAACATCTCTTACTAC	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF173155	CCDS2940.1	3q12.2-q12.3	2014-01-28			ENSG00000081148	ENSG00000081148	50939			18362	protein-coding gene	gene with protein product		607056			NA	10542133	Standard		NM_016247	NA	Approved	IPM200, RP56	uc003duq.2	Q9BZV3	OTTHUMG00000159091	ENST00000193391.7:c.*179A>T	chr3.hg19:g.100945634T>A		NA	A8MWT5|Q9UKD4|Q9UKK5	hg19	CCDS2940.1	0.02	-0.429724	ACAxCTC	COVERED																																																																																			NOVEL	IMPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353256.3	1	3.607251	KEEP	0	0	0	12	317	TT	0.993634	0.948414	0		-	16	60	492	0	0	43.391849	33	60	982	94	ENST00000193391.7	0.326531	0.954491
ZBTB11	27107	__UNKNOWN__	__UNKNOWN__	3	101383509	101383509	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:101383509C>G	ENST00000312938.4	-	5	2253	c.1673G>C	c.(1672-1674)aGa>aCa	p.R558T		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	558		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TTTAGCATCTCTTTTTGGCTG	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													189	174	179			NA	NA	3		NA											NA				101383509		2202	4300	6502	SO:0001583	missense			U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422	27107		-, BTB/POZ domain containing, Zinc fingers, C2H2-type	16740	protein-coding gene	gene with protein product		NA			NA		Standard	NM_014415	NM_014415	NA	Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.1673G>C	chr3.hg19:g.101383509C>G	ENSP00000326200:p.Arg558Thr	NA	Q2NKP9	hg19	CCDS2943.1	0.02	1.572756	TCTxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.28	3.590119	0.66105	.	.	ENSG00000066422	ENST00000312938	T	0.12147	2.71	5.69	5.69	0.88448	.	0.355931	0.35235	N	0.003356	T	0.14657	0.0354	L	0.27053	0.805	0.80722	D	1	P	0.52463	0.953	P	0.47744	0.556	T	0.00722	-1.1594	10	0.52906	T	0.07	-17.305	13.0671	0.59041	0.0:0.9268:0.0:0.0732	.	558	O95625	ZBT11_HUMAN	T	558	ENSP00000326200:R558T	ENSP00000326200:R558T	R	-	2	0	ZBTB11	102866199	0.996000	0.38824	0.999000	0.59377	0.983000	0.72400	3.125000	0.50469	2.683000	0.91414	0.655000	0.94253	AGA	NOVEL	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353441.2	9	8.725754	KEEP	0	0	0	29	884	CC	0.999997	0.999892	0		-	25	60	857	0	0	74.394823	66	60	2247	180	ENST00000312938.4	0.274725	0.999895
CEP97	79598	__UNKNOWN__	__UNKNOWN__	3	101442867	101442867	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:101442867A>G	ENST00000341893.3	+	0	99							Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	NA		NA			cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						gggattacagacgtgaaccac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504	79598			26244	protein-coding gene	gene with protein product		615864	leucine-rich repeats and IQ motif containing 2	LRRIQ2	NA	17719545, 18068367	Standard	NM_024548	NM_024548	NA	Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.-654A>G	chr3.hg19:g.101442867A>G		NA	B5MDY8|Q8NA71|Q9H5T9	hg19	CCDS2944.1	0.02	-0.410868	CAGxCGT	COVERED																																																																																			NOVEL	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353597.2	7	3.638582	KEEP	0	1	28	22	587	AA	0.999892	0.9483	0		+	4	60	109	0	0	7.300373	38	60	1147	98	ENST00000341893.3	0.095238	0.948402
NXPE3	91775	__UNKNOWN__	__UNKNOWN__	3	101531410	101531410	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:101531410G>C	ENST00000491511.2	+	7	1878				NXPE3_ENST00000422132.1_Intron|NXPE3_ENST00000477909.1_Intron|NXPE3_ENST00000273347.5_Intron	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	NA		NA				extracellular region (GO:0005576)					NA						gtaatcccaggactttgggag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815	91775			28238	protein-coding gene	gene with protein product		NA	family with sequence similarity 55, member C	FAM55C	NA	12975309	Standard	NM_145037	NM_001134456	NA	Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.923-4229G>C	chr3.hg19:g.101531410G>C		NA	A8K0X4|D3DN53|Q7Z2S8	hg19	CCDS2945.1	0.02	-0.14914	CAGxACT	COVERED																																																																																			NOVEL	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353711.2	4	2.707363	KEEP	0	0	0	9	272	GG	0.99254	0.289823	0		+	3	60	105	0	0	8.578416	13	60	459	42	ENST00000491511.2	0.1875	0.292001
NXPE3	91775	__UNKNOWN__	__UNKNOWN__	3	101536849	101536849	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:101536849C>T	ENST00000491511.2	+	7	2085				NXPE3_ENST00000422132.1_Intron|NXPE3_ENST00000477909.1_Intron|NXPE3_ENST00000273347.5_Intron	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	NA		NA				extracellular region (GO:0005576)					NA						atcctcccacctcagcctccc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815	91775			28238	protein-coding gene	gene with protein product		NA	family with sequence similarity 55, member C	FAM55C	NA	12975309	Standard	NM_145037	NM_001134456	NA	Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.1129+1004C>T	chr3.hg19:g.101536849C>T		NA	A8K0X4|D3DN53|Q7Z2S8	hg19	CCDS2945.1	0.02	-0.271953	CACxTCA	COVERED																																																																																			NOVEL	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353711.2	11	4.813614	KEEP	1	0	0	16	487	CC	0.997832	0.71576	0		+	3	51	93	0	0	6.498149	27	60	934	71	ENST00000491511.2	0.1	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	101646382	101646382	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:101646382G>A			NA	NA				NFKBIZ (66516 upstream) : RP11-221J22.1 (13320 downstream)						NA		NA									NA						gaccagcctggccaacatggt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.101646382G>A		NA		hg19		0.02	-0.149124	CTGxCCA	COVERED																																																																																			NOVEL					0			4	2.406946	KEEP	1	0	0	8	238	GG	0.99254	0.289823	0			3	60	85	0	0	7.000887	9	60	313	33		0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	103744624	103744624	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:103744624C>T			NA	NA				MIR548AB (501664 upstream) : AC016970.1 (28927 downstream)						NA		NA									NA						gactcggtGGCGGGGGCGCGG	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.103744624C>T		NA		hg19		0.02	-0.122783	TGGxGGG	COVERED																																																																																			NOVEL					0			7	2.708113	KEEP	1	0	0	9	279	CC	0.99254	0.227464	0			3	60	85	1	0	7.001333	9	60	281	35		0.25	0.229173
TRAT1	50852	__UNKNOWN__	__UNKNOWN__	3	108570965	108570965	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:108570965C>T	ENST00000295756.6	+	6	533				TRAT1_ENST00000426646.1_Intron	NM_016388.2	NP_057472.2	Q6PIZ9	TRAT1_HUMAN	T cell receptor associated transmembrane adaptor 1	NA		NA			cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of receptor recycling (GO:0001920)|negative regulation of transport (GO:0051051)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of T cell receptor signaling pathway (GO:0050862)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(3)	28						tggtggctcacgcctataatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ240084	CCDS33813.1	3q13	2005-05-04	2005-05-04	2005-05-04	ENSG00000163519	ENSG00000163519	50852			30698	protein-coding gene	gene with protein product		604962	T cell receptor interacting molecule	TCRIM	NA	10663578, 9687533	Standard	NM_016388	NM_016388	NA	Approved	HSPC062, TRIM	uc003dxi.1	Q6PIZ9	OTTHUMG00000159198	ENST00000295756.6:c.304-1502C>T	chr3.hg19:g.108570965C>T		NA	Q9NZX5	hg19	CCDS33813.1	0.02	-0.228065	TCAxGCC	COVERED																																																																																			NOVEL	TRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353794.1	15	5.112171	KEEP	1	0	0	17	503	CC	0.997832	0.611079	0		+	4	60	118	0	0	8.862811	22	60	719	65	ENST00000295756.6	0.153846	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	108870397	108870397	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:108870397A>G			NA	NA				RP11-59E19.1 (1427 upstream) : RP11-59E19.4 (24887 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.108870397A>G		NA		hg19		0.02	-0.157815	CACxCCT	COVERED																																																																																			NOVEL					0			10	3.005455	KEEP	3	0	0	10	250	AA	0.99254	0.320398	0			3	60	94	0	0	7.392696	14	60	392	39		0.176471	0.322807
PLCXD2	257068	__UNKNOWN__	__UNKNOWN__	3	111519108	111519108	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:111519108T>C	ENST00000477665.1	+	5	1275				PHLDB2_ENST00000393923.3_Intron|PLCXD2_ENST00000393934.3_Intron	NM_001185106.1	NP_001172035.1	Q0VAA5	PLCX2_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 2	NA		NA			lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)	17						ctgcctcggcttcccaaagtg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056141	CCDS2961.1, CCDS54619.1	3q13.2	2004-09-09			ENSG00000240891	ENSG00000240891	257068			26462	protein-coding gene	gene with protein product		NA			NA		Standard	NM_153268	NM_001185106	NA	Approved	FLJ31579	uc003dxz.3	Q0VAA5	OTTHUMG00000159279	ENST00000477665.1:c.916-45560T>C	chr3.hg19:g.111519108T>C		NA	Q96N12	hg19	CCDS54619.1	0.02	-0.114035	GGCxTCC	UNCOVERED																																																																																			NOVEL	PLCXD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354322.1	10	5.411357	KEEP	1	0	0	18	480	TT	0.999366	0.162364	0		+	3	49	106	0	0	9.101063	9	60	282	38	ENST00000477665.1	0.25	0.162467
SLC9C1	285335	__UNKNOWN__	__UNKNOWN__	3	111986115	111986115	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:111986115A>G	ENST00000305815.5	-	8	1028				SLC9C1_ENST00000487372.1_Intron	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	NA		NA			cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)				NA						gcaacagagcaagactctgtt	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139	285335		Solute carriers	31401	protein-coding gene	gene with protein product	sperm-NHE	612738	solute carrier family 9, isoform 10, solute carrier family 9, member 10	SLC9A10	NA	12783626	Standard	NM_183061	NM_183061	NA	Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.776-928T>C	chr3.hg19:g.111986115A>G		NA	Q6ZRP4|Q7RTP2	hg19	CCDS33817.1	0.02	-0.184171	AGCxAGA	COVERED																																																																																			NOVEL	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354066.1	7	6.015286	KEEP	1	0	0	20	552	AA	0.99986	0.423418	0		-	3	60	102	0	0	8.191906	14	60	404	57	ENST00000305815.5	0.176471	0.423478
C3orf17	25871	__UNKNOWN__	__UNKNOWN__	3	112721998	112721998	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:112721998A>G	ENST00000314400.5	-	0	4280				C3orf17_ENST00000383675.2_3'UTR	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	NA		NA			negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						agaccagcctaagcaacatgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608	25871			24496	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_015412	NR_027794	NA	Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.*2385T>C	chr3.hg19:g.112721998A>G		NA	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	hg19	CCDS33824.1	0.02	1.529087	CCTxAGC	COVERED																																																																																			NOVEL	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354405.3	22	6.509368	KEEP	0	3	92	54	1431	AA	1	0.999948	0		-	4	60	134	0	0	8.287977	82	70	2414	231	ENST00000314400.5	0.046512	0.999948
RP11-572M11.4	0	__UNKNOWN__	__UNKNOWN__	3	112741907	112741907	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:112741907T>C	ENST00000460707.1	+	0	166				RP11-572M11.4_ENST00000470313.1_RNA|RP11-572M11.4_ENST00000467342.1_RNA|RP11-572M11.4_ENST00000496389.1_RNA						NA		NA									NA						ctcactctgttgcccaggctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000460707.1:	chr3.hg19:g.112741907T>C		NA		hg19		0.02	-0.13154	TGTxGCC	UNCOVERED																																																																																			NOVEL	RP11-572M11.4-006	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000354897.1	11	2.405586	KEEP	4	0	0	8	213	TT	0	0	0		+	3	60	91	0	0	7.482405	10	60	283	31	ENST00000460707.1	0.230769	0.229173
KIAA2018	205717	__UNKNOWN__	__UNKNOWN__	3	113372429	113372429	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:113372429A>G	ENST00000491165.1	-	7	667				KIAA2018_ENST00000478658.1_3'UTR|KIAA2018_ENST00000316407.4_3'UTR			Q68DE3	K2018_HUMAN	KIAA2018	NA		NA				membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						cagcctgggcaacagagccag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542	205717			30494	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001009899	XM_005247208	NA	Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000491165.1:c.257-3732T>C	chr3.hg19:g.113372429A>G		NA	Q7Z3L9|Q8IVF3|Q9H8T4	hg19		0.02	-0.236796	GGCxACA	COVERED																																																																																			NOVEL	KIAA2018-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000354588.2	5	7.517761	KEEP	3	0	0	25	678	AA	0.999879	0.612333	0		-	3	58	95	1	0	7.192608	18	60	525	60	ENST00000491165.1	0.142857	0.612407
KIAA2018	205717	__UNKNOWN__	__UNKNOWN__	3	113390740	113390740	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:113390740A>T	ENST00000491165.1	-	4	487				KIAA2018_ENST00000478658.1_Intron|KIAA2018_ENST00000316407.4_Intron			Q68DE3	K2018_HUMAN	KIAA2018	NA		NA				membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						ctcagcctccagagtagctgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542	205717			30494	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001009899	XM_005247208	NA	Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000491165.1:c.76+1454T>A	chr3.hg19:g.113390740A>T		NA	Q7Z3L9|Q8IVF3|Q9H8T4	hg19		0.02	-0.140308	TCCxGAG	COVERED																																																																																			NOVEL	KIAA2018-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000354588.2	5	2.406108	KEEP	0	0	0	8	220	AC	0.99254	0.259018	0		-	3	60	83	0	0	6.682503	10	60	299	29	ENST00000491165.1	0.230769	0.260965
ATP6V1A	523	__UNKNOWN__	__UNKNOWN__	3	113516364	113516364	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:113516364G>A	ENST00000273398.3	+	12	1398				ATP6V1A_ENST00000538620.1_Intron	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	cagcctcccagagtgctagga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	523	3.6.3.14	ATPases / V-type	851	protein-coding gene	gene with protein product		607027	ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1	VPP2, ATP6A1, ATP6V1A1	NA	8463241	Standard	NM_001690	NM_001690	NA	Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1291-726G>A	chr3.hg19:g.113516364G>A		NA	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	hg19	CCDS2976.1	0.02	-0.166671	CCAxAGT	UNCOVERED																																																																																			NOVEL	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354457.1	8	2.407417	KEEP	2	0	0	8	253	GG	0	0	0		+	3	60	85	0	0	6.772863	11	60	390	42	ENST00000273398.3	0.214286	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	113546025	113546025	__UNKNOWN__	IGR	SNP	C	C	T	rs35494857	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:113546025C>T			NA	NA				ATP6V1A (15122 upstream) : GRAMD1C (1003 downstream)						NA		NA									NA						tgagctcaggcaatctgcctg	0.522		NA											C|||	1278	0.255192	0.236	0.3012	5008	,	,	NA	11109	0.3016	NA	0.2326	False	NA	,,,	NA	NA	NA	2504	0.2239	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.113546025C>T		NA		hg19		0.02	-0.122798	AGGxAAT	UNCOVERED																																																																																			NOVEL					0			6	2.407191	KEEP	1	0	0	8	247	CC	0	0	0			6	60	167	0	0	15.408379	8	60	283	31		0.428571	0.196312
ZBTB20	26137	__UNKNOWN__	__UNKNOWN__	3	114656671	114656671	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:114656671A>G	ENST00000462705.1	-	2	208				ZBTB20_ENST00000488663.1_Intron|ZBTB20_ENST00000357258.3_Intron	NM_001164343.1	NP_001157815.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	NA		NA				nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		ctggccgggcacggtggctca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(69;748 1344 9802 11203 30933)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722	26137		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	13503	protein-coding gene	gene with protein product		606025	zinc finger protein 288	ZNF288	NA	10965110, 11352661	Standard	NM_015642	XM_005247339	NA	Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000462705.1:c.613+36541T>C	chr3.hg19:g.114656671A>G		NA	Q63HP6|Q8N6R5|Q9Y410	hg19	CCDS2981.1	0.02	-0.183738	GGCxCGG	COVERED																																																																																			NOVEL	ZBTB20-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354954.1	6	4.209744	KEEP	1	0	0	14	379	AA	0.995343	0.421506	0		-	3	60	90	0	0	6.697636	18	60	511	51	ENST00000462705.1	0.142857	0.423478
LSAMP	4045	__UNKNOWN__	__UNKNOWN__	3	116217779	116217779	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:116217779A>G	ENST00000539563.1	-	2	67							Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	NA		NA			cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		gttcatgcctataatcccagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565	4045		Immunoglobulin superfamily / I-set domain containing	6705	protein-coding gene	gene with protein product	IgLON family member 3	603241			NA	9615236	Standard	NM_002338	NM_002338	NA	Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000539563.1:c.68-53977T>C	chr3.hg19:g.116217779A>G		NA	Q8IV49	hg19		0.02	-0.27185	CCTxTAA	COVERED																																																																																			NOVEL	LSAMP-201	KNOWN	basic	protein_coding	NA	protein_coding		12	2.837207	KEEP	0	1	30	20	524	AA	0.999869	0.717222	0		-	3	60	93	0	0	6.545431	26	60	735	72	ENST00000539563.1	0.103448	0.717315
LSAMP	4045	__UNKNOWN__	__UNKNOWN__	3	116355582	116355582	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:116355582A>C	ENST00000539563.1	-	2	67							Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	NA		NA			cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		gagattgtgcaactgcactcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565	4045		Immunoglobulin superfamily / I-set domain containing	6705	protein-coding gene	gene with protein product	IgLON family member 3	603241			NA	9615236	Standard	NM_002338	NM_002338	NA	Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000539563.1:c.68-191780T>G	chr3.hg19:g.116355582A>C		NA	Q8IV49	hg19		0.02	-0.08772	TGCxACT	UNCOVERED																																																																																			NOVEL	LSAMP-201	KNOWN	basic	protein_coding	NA	protein_coding		8	2.40647	KEEP	0	0	0	8	227	AA	0.99257	0.09898	0		-	3	60	108	0	0	9.578689	7	60	218	21	ENST00000539563.1	0.3	0.099721
LSAMP	4045	__UNKNOWN__	__UNKNOWN__	3	117061531	117061531	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:117061531A>G	ENST00000539563.1	-	1	67							Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	NA		NA			cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		ggctggtctcaaactcctgac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565	4045		Immunoglobulin superfamily / I-set domain containing	6705	protein-coding gene	gene with protein product	IgLON family member 3	603241			NA	9615236	Standard	NM_002338	NM_002338	NA	Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000539563.1:c.67+654497T>C	chr3.hg19:g.117061531A>G		NA	Q8IV49	hg19		0.02	-0.12279	CTCxAAC	UNCOVERED																																																																																			NOVEL	LSAMP-201	KNOWN	basic	protein_coding	NA	protein_coding		7	2.406203	KEEP	3	0	0	8	224	AA	0	0	0		-	3	60	96	0	0	8.101127	9	60	276	29	ENST00000539563.1	0.25	0.196312
GSK3B	2932	__UNKNOWN__	__UNKNOWN__	3	119795401	119795401	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:119795401G>A	ENST00000264235.8	-	1	1071				GSK3B_ENST00000316626.5_Intron	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	NA		NA			axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ggtggctcacgcctgtaatcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701	2932			4617	protein-coding gene	gene with protein product		605004			NA	10486203	Standard		NM_002093	NA	Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.88+16792C>T	chr3.hg19:g.119795401G>A		NA	D3DN89|Q9BWH3|Q9UL47	hg19	CCDS54628.1	0.02	-0.192973	CACxCCT	COVERED																																																																																			NOVEL	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258240.2	6	3.610868	KEEP	11	0	0	12	372	GG	0.99254	0.454342	0		-	3	60	89	0	0	6.527683	19	60	619	67	ENST00000264235.8	0.136364	0.457757
GSK3B	2932	__UNKNOWN__	__UNKNOWN__	3	119801495	119801495	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:119801495T>C	ENST00000264235.8	-	1	1071				GSK3B_ENST00000316626.5_Intron	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	NA		NA			axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	cccgcctcggtctcccaatgt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701	2932			4617	protein-coding gene	gene with protein product		605004			NA	10486203	Standard		NM_002093	NA	Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.88+10698A>G	chr3.hg19:g.119801495T>C		NA	D3DN89|Q9BWH3|Q9UL47	hg19	CCDS54628.1	0.02	-0.166637	CGGxCTC	COVERED																																																																																			NOVEL	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258240.2	11	3.006515	KEEP	1	0	0	10	263	TT	0.992708	0.351366	0		-	4	60	134	0	0	11.281306	13	60	371	44	ENST00000264235.8	0.235294	0.353947
GSK3B	2932	__UNKNOWN__	__UNKNOWN__	3	119801503	119801503	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:119801503T>A	ENST00000264235.8	-	1	1071				GSK3B_ENST00000316626.5_Intron	NM_001146156.1|NM_002093.3	NP_001139628.1|NP_002084.2	P49841	GSK3B_HUMAN	glycogen synthase kinase 3 beta	NA		NA			axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell migration (GO:0016477)|cellular response to interleukin-3 (GO:0036016)|cellular response to mechanical stimulus (GO:0071260)|circadian rhythm (GO:0007623)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|ER overload response (GO:0006983)|establishment of cell polarity (GO:0030010)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fat cell differentiation (GO:0045444)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glycogen metabolic process (GO:0005977)|hippocampus development (GO:0021766)|hypermethylation of CpG island (GO:0044027)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|myoblast fusion (GO:0007520)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of type B pancreatic cell development (GO:2000077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein binding (GO:0032092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|protein localization to microtubule (GO:0035372)|protein phosphorylation (GO:0006468)|re-entry into mitotic cell cycle (GO:0000320)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of microtubule-based process (GO:0032886)|regulation of neuronal synaptic plasticity (GO:0048168)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|superior temporal gyrus development (GO:0071109)	beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|kinase activity (GO:0016301)|NF-kappaB binding (GO:0051059)|p53 binding (GO:0002039)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II transcription factor binding (GO:0001085)|tau-protein kinase activity (GO:0050321)|ubiquitin protein ligase binding (GO:0031625)			endometrium(1)|large_intestine(8)|lung(7)|prostate(2)	18				GBM - Glioblastoma multiforme(114;0.24)	Lithium(DB01356)	ggtctcccaatgtgctgggat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012760	CCDS2996.1, CCDS54628.1	3q13.3	2008-02-15			ENSG00000082701	ENSG00000082701	2932			4617	protein-coding gene	gene with protein product		605004			NA	10486203	Standard		NM_002093	NA	Approved		uc003edm.3	P49841	OTTHUMG00000133765	ENST00000264235.8:c.88+10690A>T	chr3.hg19:g.119801503T>A		NA	D3DN89|Q9BWH3|Q9UL47	hg19	CCDS54628.1	0.02	-0.201707	CAAxGTG	COVERED																																																																																			NOVEL	GSK3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258240.2	9	3.007768	KEEP	0	0	0	10	278	TT	0.992708	0.486967	0		-	5	60	144	0	0	12.03065	14	60	405	49	ENST00000264235.8	0.263158	0.490544
POLQ	10721	__UNKNOWN__	__UNKNOWN__	3	121161969	121161969	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:121161969T>C	ENST00000264233.5	-	27	7393					NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	NA		NA			ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		tcccagagtgttgggattaca	0.458		NA						DNA polymerases (catalytic subunits)													NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(152;907 1925 26081 31236 36904)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	10721	2.7.7.7	DNA polymerases	9186	protein-coding gene	gene with protein product		604419			NA	10395804	Standard	NM_199420	NM_199420	NA	Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.7265-3006A>G	chr3.hg19:g.121161969T>C		NA	O95160|Q6VMB5	hg19	CCDS33833.1	0.02	-0.175423	GTGxTGG	COVERED																																																																																			NOVEL	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355097.1	7	3.006929	KEEP	2	0	0	10	267	TT	0.992708	0.384582	0		-	3	40	102	0	0	8.191664	14	60	425	50	ENST00000264233.5	0.176471	0.387407
HCLS1	3059	__UNKNOWN__	__UNKNOWN__	3	121363709	121363709	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:121363709C>G	ENST00000314583.3	-	5	446	c.355G>C	c.(355-357)Ggc>Cgc	p.G119R	HCLS1_ENST00000428394.2_Missense_Mutation_p.G119R	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	119		NA			actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		CCCCCAAAGCCTTTGGCAGCA	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													188	156	167			NA	NA	3		NA											NA				121363709		2203	4300	6503	SO:0001583	missense				CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353	3059			4844	protein-coding gene	gene with protein product	cortactin-like	601306			NA	8978766, 15710041	Standard	NM_005335	NM_001292041	NA	Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.355G>C	chr3.hg19:g.121363709C>G	ENSP00000320176:p.Gly119Arg	NA	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	hg19	CCDS3003.1	0.02	1.76575	AGCxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.4	4.919037	0.92249	.	.	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.59906	0.25;0.23	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.79046	0.4380	M	0.87971	2.92	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.82717	-0.0319	10	0.72032	D	0.01	-15.645	15.7504	0.77980	0.0:1.0:0.0:0.0	.	119;119;119	B4DTP2;E7EVW7;P14317	.;.;HCLS1_HUMAN	R	119	ENSP00000320176:G119R;ENSP00000387645:G119R	ENSP00000320176:G119R	G	-	1	0	HCLS1	122846399	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.006000	0.76329	2.582000	0.87167	0.650000	0.86243	GGC	NOVEL	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355144.1	6	7.221038	KEEP	0	0	0	24	732	CC	0.999909	0.997073	0		-	14	60	458	0	0	37.269514	56	60	1923	141	ENST00000314583.3	0.2	0.997163
PARP14	54625	__UNKNOWN__	__UNKNOWN__	3	122431346	122431346	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:122431346C>T	ENST00000474629.2	+	10	3885					NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		ccacctgcctcggcctcccaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193	54625		Poly (ADP-ribose) polymerases	29232	protein-coding gene	gene with protein product		610028			NA	15273990	Standard	NM_017554	NM_017554	NA	Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.3620-925C>T	chr3.hg19:g.122431346C>T		NA	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	hg19	CCDS46894.1	0.02	-0.131567	CCTxGGC	COVERED																																																																																			NOVEL	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356173.2	4	3.308974	KEEP	1	0	0	11	321	CC	0.993072	0.227586	0		+	3	60	86	0	0	7.101087	9	60	284	34	ENST00000474629.2	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	123185031	123185031	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:123185031G>C			NA	NA				ADCY5 (16426 upstream) : PTPLB (24635 downstream)						NA		NA									NA						aatcccagcagtttgggaggc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.123185031G>C		NA		hg19		0.02	-0.078951	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			3	2.407245	KEEP	1	0	0	8	248	GG	0.99257	0.076761	0			3	60	97	0	0	8.643305	6	60	206	29		0.333333	0.077336
KALRN	8997	__UNKNOWN__	__UNKNOWN__	3	124439100	124439100	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:124439100C>T	ENST00000291478.5	+	0	4816				KALRN_ENST00000360013.3_3'UTR|KALRN_ENST00000428018.2_3'UTR	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	NA		NA			apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AAACGCTCCCCGCAAATTCAC	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145	8997		Rho guanine nucleotide exchange factors, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	4814	protein-coding gene	gene with protein product	serine/threonine kinase with Dbl and pleckstrin homology domains	604605	huntingtin-associated protein interacting protein (duo)	HAPIP	NA	9285789, 10023074	Standard	NM_003947	NM_001024660	NA	Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.*783C>T	chr3.hg19:g.124439100C>T		NA	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	hg19	CCDS3028.1	0.02	-0.403512	CCCxGCA	COVERED																																																																																			NOVEL	KALRN-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246891.5	1	3.008448	KEEP	0	0	0	10	294	CC	0.992708	0.927678	0		+	10	60	304	0	0	24.712933	36	60	1209	87	ENST00000291478.5	0.217391	0.934492
UMPS	7372	__UNKNOWN__	__UNKNOWN__	3	124463545	124463545	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:124463545T>C	ENST00000232607.2	+	0	2163				UMPS_ENST00000413078.2_3'UTR|UMPS_ENST00000538242.1_3'UTR|UMPS_ENST00000536109.1_3'UTR	NM_000373.3	NP_000364.1	P11172	UMPS_HUMAN	uridine monophosphate synthetase	NA		NA			'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|cellular response to drug (GO:0035690)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|small molecule metabolic process (GO:0044281)|UMP biosynthetic process (GO:0006222)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	orotate phosphoribosyltransferase activity (GO:0004588)|orotidine-5'-phosphate decarboxylase activity (GO:0004590)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(114;0.146)	Fluorouracil(DB00544)	tgtgagccactgtgcccagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3029.1	3q13	2008-02-04	2008-02-04		ENSG00000114491	ENSG00000114491	7372	2.4.2.10, 4.1.1.23		12563	protein-coding gene	gene with protein product	orotate phosphoribosyl transferase and orotidine-5'-decarboxylase	613891			NA	2767686	Standard	NM_000373	NM_000373	NA	Approved		uc003ehl.4	P11172	OTTHUMG00000159431	ENST00000232607.2:c.*614T>C	chr3.hg19:g.124463545T>C		NA	B5LY68|B5LY72|O00758|O00759|O00760|Q16862|Q9H3Q2|Q9UG49	hg19	CCDS3029.1	0.02	-0.429687	CACxGTG	COVERED																																																																																			NOVEL	UMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355271.1	11	6.314579	KEEP	1	0	0	21	570	TT	0.999863	0.95436	0		+	4	60	130	0	0	9.050109	41	60	1194	93	ENST00000232607.2	0.088889	0.954491
HEG1	57493	__UNKNOWN__	__UNKNOWN__	3	124703590	124703590	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:124703590T>C	ENST00000311127.4	-	14	3801					NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	NA		NA			cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						gcaacaagagtgaaactccgt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706	57493			29227	protein-coding gene	gene with protein product	heart of glass	614182	HEG homolog 1 (zebrafish)		NA	10574462, 19151727, 23007647	Standard	XM_087386	NM_020733	NA	Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.3733+6040A>G	chr3.hg19:g.124703590T>C		NA	Q6NX66|Q8NC40|Q9BSV0	hg19	CCDS46898.1	0.02	-0.166649	GAGxGAA	COVERED																																																																																			NOVEL	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355732.2	7	3.60898	KEEP	0	0	0	12	327	TT	0.993634	0.351693	0		-	4	60	126	2	0	10.601606	12	60	360	44	ENST00000311127.4	0.25	0.353947
SLC12A8	84561	__UNKNOWN__	__UNKNOWN__	3	124825439	124825439	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:124825439A>G	ENST00000393469.4	-	9	1755				SLC12A8_ENST00000469902.1_Intron|SLC12A8_ENST00000430155.2_Intron|SLC12A8_ENST00000314584.7_Intron|SLC12A8_ENST00000423114.2_Intron|SLC12A8_ENST00000465475.1_Intron	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	NA		NA			potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						agtagagacaaggtttcacca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955	84561		Solute carriers	15595	protein-coding gene	gene with protein product	solute carrier family 12 (sodium/potassium/chloride transporters), member 8, cation-chloride cotransporter 9	611316			NA	11863360	Standard	NM_024628	NM_024628	NA	Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1705+885T>C	chr3.hg19:g.124825439A>G		NA	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	hg19	CCDS43143.1	0.02	-0.149103	ACAxGGT	COVERED																																																																																			NOVEL	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355711.4	7	2.706873	KEEP	0	0	0	9	253	AA	0.99254	0.320398	0		-	3	60	101	2	0	8.272299	12	60	362	40	ENST00000393469.4	0.2	0.322807
ZNF148	7707	__UNKNOWN__	__UNKNOWN__	3	125049203	125049203	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:125049203A>G	ENST00000360647.4	-	2	334				ZNF148_ENST00000492394.1_Intron|ZNF148_ENST00000468369.1_Intron|ZNF148_ENST00000484491.1_Intron|ZNF148_ENST00000544464.1_Intron|ZNF148_ENST00000485866.1_Intron	NM_021964.2	NP_068799.2	Q9UQR1	ZN148_HUMAN	zinc finger protein 148	NA		NA			cellular defense response (GO:0006968)|gamete generation (GO:0007276)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein complex assembly (GO:0006461)|substantia nigra development (GO:0021762)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)	28						cagctacttgagaggcctgag	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U09851	CCDS3031.1	3q21.2	2013-01-08	2006-06-13		ENSG00000163848	ENSG00000163848	7707		Zinc fingers, C2H2-type	12933	protein-coding gene	gene with protein product		601897	zinc finger protein 148 (pHZ-52)		NA	7557990, 9925940	Standard	NM_021964	NM_021964	NA	Approved	BERF-1, ZBP-89, BFCOL1, HT-BETA, ZFP148, pHZ-52	uc003ehx.4	Q9UQR1	OTTHUMG00000159448	ENST00000360647.4:c.151+798T>C	chr3.hg19:g.125049203A>G		NA	D3DN27|O00389|O43591|Q58EY5|Q6PJ98	hg19	CCDS3031.1	0.02	-0.105253	TTGxGAG	UNCOVERED																																																																																			NOVEL	ZNF148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355452.4	8	3.308469	KEEP	0	0	0	11	305	AA	0.993072	0.138863	0		-	3	60	101	2	0	8.732365	8	60	253	31	ENST00000360647.4	0.272727	0.139832
SNX4	8723	__UNKNOWN__	__UNKNOWN__	3	125168009	125168009	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:125168009C>T	ENST00000251775.4	-	14	1330				SNX4_ENST00000536067.1_Intron	NM_003794.2	NP_003785.1	O95219	SNX4_HUMAN	sorting nexin 4	NA		NA			endocytic recycling (GO:0032456)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|early endosome membrane (GO:0031901)|membrane (GO:0016020)|protein complex (GO:0043234)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(2)|central_nervous_system(1)|lung(6)|ovary(1)|skin(1)	11						ggctcacacccgtaatcccag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF065485	CCDS3032.1	3q21.2	2014-02-12			ENSG00000114520	ENSG00000114520	8723		Sorting nexins	11175	protein-coding gene	gene with protein product		605931			NA	9819414	Standard	NM_003794	NM_003794	NA	Approved	ATG24B	uc003eib.4	O95219	OTTHUMG00000159575	ENST00000251775.4:c.1306-1339G>A	chr3.hg19:g.125168009C>T		NA	B3KMH0|B4DQV4|D3DNA3	hg19	CCDS3032.1	0.02	-0.148121	ACCxGTA	COVERED																																																																																			NOVEL	SNX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356299.1	4	2.707602	KEEP	0	0	0	9	270	CC	0.99254	0.289823	0		-	4	60	92	0	0	7.452492	10	60	318	36	ENST00000251775.4	0.285714	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	125396548	125396548	__UNKNOWN__	IGR	SNP	T	T	C	rs370306513	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:125396548T>C			NA	NA				OSBPL11 (82614 upstream) : AF186996.2 (12551 downstream)						NA		NA									NA						gtcaggagtttgagaccagcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.125396548T>C		NA		hg19		0.02	-0.140327	GTTxGAG	COVERED																																																																																			NOVEL					0			4	3.007479	KEEP	2	0	0	10	275	TT	0.99257	0.259026	0			3	60	93	0	0	7.573083	11	60	330	39		0.214286	0.260965
RP11-379B18.5	0	__UNKNOWN__	__UNKNOWN__	3	125582146	125582146	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:125582146C>T	ENST00000468859.1	-	0	1456										NA		NA									NA						tcacctgaggccaggaattca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000468859.1:	chr3.hg19:g.125582146C>T		NA		hg19		0.02	-0.228073	AGGxCAG	COVERED																																																																																			NOVEL	RP11-379B18.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000356335.2	10	2.402714	KEEP	1	0	0	8	233	CC	0.99257	0.578599	0		-	4	60	123	1	0	9.594573	19	60	623	44	ENST00000468859.1	0.173913	0.58293
EEFSEC	60678	__UNKNOWN__	__UNKNOWN__	3	127941154	127941154	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:127941154A>G	ENST00000254730.6	+	2	370				EEFSEC_ENST00000483457.1_Intron	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	NA		NA			selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						gggattacagatgtgagccac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394	60678			24614	protein-coding gene	gene with protein product	elongation factor for selenoprotein translation	607695			NA	10970870, 15229221	Standard	NM_021937	XM_005247696	NA	Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.317-24525A>G	chr3.hg19:g.127941154A>G		NA	Q96HZ6	hg19	CCDS33849.1	0.02	-0.070175	CAGxTGT	UNCOVERED																																																																																			NOVEL	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356738.2	4	2.699544	KEEP	0	0	0	9	233	AA	0.99254	0.053733	0		+	2	60	72	0	0	6.335641	5	60	157	28	ENST00000254730.6	0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	128315252	128315252	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128315252A>G			NA	NA				C3orf27 (20323 upstream) : RPN1 (23564 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.128315252A>G		NA		hg19		0.02	-0.14034	CCAxCAC	COVERED																																																																																			NOVEL					0			5	2.404486	KEEP	0	0	0	8	211	AA	0.99257	0.259026	0			4	60	135	1	0	12.091697	8	60	236	35		0.333333	0.260965
ISY1-RAB43	100534599	__UNKNOWN__	__UNKNOWN__	3	128824285	128824285	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128824285A>G	ENST00000418265.1	-	12	912				RAB43_ENST00000393305.1_Intron|RAB43_ENST00000393308.1_Intron|RAB43_ENST00000393307.1_Intron|RAB43_ENST00000393304.1_Intron|RAB43_ENST00000315150.5_Intron|RAB43_ENST00000476465.1_Intron	NM_001204890.1	NP_001191819.1			ISY1-RAB43 readthrough	NA		NA									NA						aacagagtgaaacttcatctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56276.1	3q21.3	2013-01-23	2011-09-27		ENSG00000261796	ENSG00000261796	100534599			42969	other	readthrough		NA			NA		Standard		NM_001204890	NA	Approved		uc003elo.2		OTTHUMG00000177122	ENST00000418265.1:c.852-10273T>C	chr3.hg19:g.128824285A>G		NA		hg19	CCDS56276.1	0.02	-0.314376	TGAxACT	COVERED																																																																																			NOVEL	ISY1-RAB43-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435461.1	7	3.007916	KEEP	0	0	0	10	280	AA	0.992708	0.812496	0		-	3	60	101	0	0	7.173936	30	60	866	65	ENST00000418265.1	0.090909	0.818465
ISY1-RAB43	100534599	__UNKNOWN__	__UNKNOWN__	3	128824361	128824361	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128824361T>C	ENST00000418265.1	-	12	912				RAB43_ENST00000393305.1_Intron|RAB43_ENST00000393308.1_Intron|RAB43_ENST00000393307.1_Intron|RAB43_ENST00000393304.1_Intron|RAB43_ENST00000315150.5_Intron|RAB43_ENST00000476465.1_Intron	NM_001204890.1	NP_001191819.1			ISY1-RAB43 readthrough	NA		NA									NA						cagtggctcatgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56276.1	3q21.3	2013-01-23	2011-09-27		ENSG00000261796	ENSG00000261796	100534599			42969	other	readthrough		NA			NA		Standard		NM_001204890	NA	Approved		uc003elo.2		OTTHUMG00000177122	ENST00000418265.1:c.852-10349A>G	chr3.hg19:g.128824361T>C		NA		hg19	CCDS56276.1	0.02	-0.34206	TCAxGCC	COVERED																																																																																			NOVEL	ISY1-RAB43-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435461.1	15	6.315824	KEEP	2	0	0	21	578	TT	0.999863	0.865627	0		-	3	60	101	0	0	6.975478	35	60	1042	88	ENST00000418265.1	0.078947	0.865745
ISY1	57461	__UNKNOWN__	__UNKNOWN__	3	128877282	128877282	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128877282A>G	ENST00000393292.3	-	3	140				ISY1_ENST00000393295.3_Intron|ISY1_ENST00000273541.8_Intron|ISY1-RAB43_ENST00000418265.1_Intron			Q9ULR0	ISY1_HUMAN	ISY1 splicing factor homolog (S. cerevisiae)	NA		NA			mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|skin(1)	15						gattacaggcatgagccactg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													64	50	54			NA	NA	3		NA											NA				128877282		692	1591	2283	SO:0001627	intron_variant				CCDS43149.1, CCDS56277.1	3q21.3	2008-11-25			ENSG00000240682	ENSG00000240682	57461			29201	protein-coding gene	gene with protein product	functional spliceosome-associated protein 33	612764			NA	16103217	Standard	NM_020701	NM_020701	NA	Approved	KIAA1160, fSAP33		Q9ULR0	OTTHUMG00000137365	ENST00000393292.3:c.78+68T>C	chr3.hg19:g.128877282A>G		NA	Q96IL2|Q9BT05	hg19		0.02	-0.368347	GGCxTGA	COVERED																																																																																			NOVEL	ISY1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000267857.3	14	8.721766	KEEP	0	0	0	29	803	AA	0.999997	0.899311	0		-	5	60	165	0	0	12.401682	34	60	998	87	ENST00000393292.3	0.128205	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	128919262	128919262	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128919262G>A			NA	NA				CNBP (16497 upstream) : COPG1 (49186 downstream)						NA		NA									NA						gagccaccacgcctggctaat	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.128919262G>A		NA		hg19		0.02	-0.140288	CACxCCT	COVERED																																																																																			NOVEL					0			9	3.307644	KEEP	3	0	0	11	309	GG	0.992708	0.259062	0			4	31	100	0	0	8.270165	10	60	310	38		0.285714	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	128958270	128958270	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128958270G>T			NA	NA				CNBP (55505 upstream) : COPG1 (10178 downstream)						NA		NA									NA						ggctggggtgggagggtcgct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.128958270G>T		NA		hg19		0.02	-0.122805	GTGxGAG	COVERED																																																																																			NOVEL					0			5	3.00868	KEEP	0	0	0	10	306	GG	0.992708	0.19488	0			5	60	150	0	0	13.623232	8	60	269	29		0.384615	0.196312
HMCES	56941	__UNKNOWN__	__UNKNOWN__	3	128999957	128999957	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:128999957T>C	ENST00000383463.4	+	2	272				HMCES_ENST00000389735.3_Intron|HMCES_ENST00000417226.2_Intron|HMCES_ENST00000502878.2_Intron	NM_020187.2	NP_064572.2	Q96FZ2	HMCES_HUMAN	5-hydroxymethylcytosine (hmC) binding, ES cell-specific	NA		NA					DNA binding (GO:0003677)|peptidase activity (GO:0008233)				NA						cccagttacttgggaggctga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF201934	CCDS33852.1	3q21.3	2013-08-30	2013-08-30	2013-08-30	ENSG00000183624	ENSG00000183624	56941			24446	protein-coding gene	gene with protein product	SOS response associated peptidase domain containing 1	NA	chromosome 3 open reading frame 37	C3orf37	NA	23434322, 23945014	Standard	NM_020187	XM_005247636	NA	Approved	DC12, SRAPD1	uc003elt.3	Q96FZ2	OTTHUMG00000159452	ENST00000383463.4:c.183+1199T>C	chr3.hg19:g.128999957T>C		NA	A6NJR9|Q96G34|Q9NRP3	hg19	CCDS33852.1	0.02	-0.149094	ACTxGGG	UNCOVERED																																																																																			NOVEL	HMCES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355470.2	10	2.40631	KEEP	3	0	0	8	225	TT	0	0	0		+	3	40	94	0	0	7.479118	13	60	382	34	ENST00000383463.4	0.1875	0.292001
H1FX	8971	__UNKNOWN__	__UNKNOWN__	3	129035092	129035092	__UNKNOWN__	5'UTR	SNP	G	G	A	rs553326631	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:129035092G>A	ENST00000333762.4	-	0	28				H1FX-AS1_ENST00000511998.1_RNA|H1FX-AS1_ENST00000433902.2_RNA	NM_006026.3	NP_006017.1	Q92522	H1X_HUMAN	H1 histone family, member X	NA		NA			nucleosome assembly (GO:0006334)	nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			kidney(1)|ovary(1)|urinary_tract(2)	4						GCTTCCACTGGCGCCTCTGGA	0.662		NA											G|||	7	0.00139776	0.0045	0.0014	5008	,	,	NA	9115	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			D64142	CCDS3057.1	3q21.3	2011-08-16			ENSG00000184897	ENSG00000184897	8971		Histones / Replication-independent	4722	protein-coding gene	gene with protein product		602785			NA	8964515, 9439656	Standard	NM_006026	NM_006026	NA	Approved	MGC15959, MGC8350, H1X	uc003elx.3	Q92522	OTTHUMG00000159450	ENST00000333762.4:c.-347C>T	chr3.hg19:g.129035092G>A		NA		hg19	CCDS3057.1	0.02	3.017585	CTGxCGC	COVERED																																																																																			NOVEL	H1FX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355455.2	1	16.487066	KEEP	0	0	0	55	1675	GG	1	0.999993	0		-	32	60	905	0	0	77.109284	77	60	2657	238	ENST00000333762.4	0.293578	0.999993
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	129344751	129344751	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:129344751C>T			NA	NA				PLXND1 (19090 upstream) : TMCC1 (21883 downstream)						NA		NA									NA						gaggccgaggcgggcggatca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.129344751C>T		NA		hg19		0.02	-0.16665	AGGxGGG	COVERED																																																																																			NOVEL					0			9	3.608922	KEEP	2	0	0	12	339	CC	0.992708	0.351366	0			3	45	85	0	0	6.410935	15	60	485	46		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	129359561	129359561	__UNKNOWN__	IGR	SNP	C	C	T	rs372285904		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:129359561C>T			NA	NA				PLXND1 (33900 upstream) : TMCC1 (7073 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.512		NA											N|||	1	0.000199681	0.0	0.0	5008	,	,	NA	10861	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.129359561C>T		NA		hg19		0.02	-0.21929	AGGxGTG	COVERED																																																																																			NOVEL					0			6	3.008368	KEEP	1	0	0	10	298	CC	0.99254	0.548763	0			4	60	112	0	0	8.580153	18	60	592	54		0.181818	0.552887
TMCC1	23023	__UNKNOWN__	__UNKNOWN__	3	129457078	129457078	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:129457078T>C	ENST00000393238.3	-	4	917				TMCC1_ENST00000426664.2_Intron|TMCC1_ENST00000329333.5_Intron	NM_001017395.3	NP_001017395.2	O94876	TMCC1_HUMAN	transmembrane and coiled-coil domain family 1	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)			PLXND1/TMCC1(4)	breast(1)|endometrium(3)|large_intestine(8)|lung(12)|skin(1)	25						tgtgccattgtactccggcct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018322	CCDS33855.1	3q21.3	2010-04-19	2005-07-13		ENSG00000172765	ENSG00000172765	23023		Transmembrane and coiled-coil domain containing	29116	protein-coding gene	gene with protein product		NA	transmembrane and coiled-coil domains 1		NA	9872452	Standard	NM_015008	NR_033361	NA	Approved	KIAA0779	uc021xdy.1	O94876	OTTHUMG00000159579	ENST00000393238.3:c.577-66971A>G	chr3.hg19:g.129457078T>C		NA	A8K5Y3|B4DE04|Q68E06|Q8IXM8	hg19	CCDS33855.1	0.02	-0.140298	TTGxACT	UNCOVERED																																																																																			NOVEL	TMCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356418.2	7	2.404113	KEEP	1	0	0	8	205	TT	0	0	0		-	3	60	93	0	0	7.682447	10	60	283	26	ENST00000393238.3	0.230769	0.260965
ATP2C1	27032	__UNKNOWN__	__UNKNOWN__	3	130655472	130655472	__UNKNOWN__	Intron	SNP	T	T	C	rs852227	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:130655472T>C	ENST00000510168.1	+	6	874				ATP2C1_ENST00000533801.2_Intron|ATP2C1_ENST00000359644.3_Intron|ATP2C1_ENST00000504948.1_Intron|ATP2C1_ENST00000328560.8_Intron|ATP2C1_ENST00000507488.2_Intron|ATP2C1_ENST00000422190.2_Intron|ATP2C1_ENST00000508532.1_Intron|ATP2C1_ENST00000504381.1_Intron|ATP2C1_ENST00000513801.1_Intron|ATP2C1_ENST00000393221.4_Intron|ATP2C1_ENST00000428331.2_Intron|ATP2C1_ENST00000505330.1_Intron			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	NA		NA			actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	ctggctaacatggtgaaaccc	0.537		NA							Hailey-Hailey disease				C|||	3695	0.737819	0.7731	0.7075	5008	,	,	NA	13984	0.626	NA	0.8121	False	NA	,,,	NA	NA	NA	2504	0.7505	NA	NA	NA	Esophageal Squamous(99;456 1443 27647 34099 42636)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	27032	3.6.3.8	ATPases / P-type	13211	protein-coding gene	gene with protein product	secretory pathway Ca2+/Mn2+ ATPase 1, calcium-transporting ATPase type 2C member 1	604384	benign chronic pemphigus (Hailey-Hailey disease)	BCPM	NA	10615129, 10767338	Standard	NM_001001486	NM_001001485	NA	Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.325-800T>C	chr3.hg19:g.130655472T>C		NA	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	hg19	CCDS46914.1	0.02	-0.087606	ACAxGGT	UNCOVERED																																																																																			NOVEL	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356648.2	9	2.405872	KEEP	11	0	0	8	217	TT	0	0	0		+	4	60	101	0	0	9.078455	6	60	174	29	ENST00000510168.1	0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	132035350	132035350	__UNKNOWN__	IGR	SNP	G	G	A	rs539248187	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:132035350G>A			NA	NA				CPNE4 (31096 upstream) : ACPP (860 downstream)						NA		NA									NA						tgcccacctcggcctcccaaa	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.132035350G>A		NA		hg19		0.02	-0.140265	CTCxGCC	COVERED																																																																																			NOVEL					0			4	3.608376	KEEP	1	0	0	12	352	GG	0.993072	0.259157	0			3	60	89	0	0	7.283179	10	60	303	45		0.230769	0.260965
ACPP	55	__UNKNOWN__	__UNKNOWN__	3	132076632	132076632	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:132076632T>C	ENST00000351273.7	+	10	1188				ACPP_ENST00000336375.5_3'UTR	NM_001134194.1	NP_001127666.1	P15309	PPAP_HUMAN	acid phosphatase, prostate	NA		NA			adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						aatcccagcattttgggagtc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	55	3.1.3.2		125	protein-coding gene	gene with protein product		171790			NA		Standard	NM_001099	NM_001099	NA	Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000351273.7:c.1138+933T>C	chr3.hg19:g.132076632T>C		NA	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	hg19	CCDS46916.1	0.02	-0.341969	GCAxTTT	COVERED																																																																																			NOVEL	ACPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356701.1	4	3.908763	KEEP	0	0	0	13	351	TT	0.994391	0.860889	0		+	4	60	125	0	0	9.119391	29	60	801	60	ENST00000351273.7	0.121212	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	132110808	132110808	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:132110808G>A			NA	NA				ACPP (23666 upstream) : DNAJC13 (25561 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.132110808G>A		NA		hg19		0.02	-0.254391	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			10	2.386685	KEEP	2	0	0	8	216	GG	0	0	0			3	60	90	0	0	6.627598	19	60	629	59		0.136364	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	133221141	133221141	__UNKNOWN__	IGR	SNP	A	A	G	rs62280374	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:133221141A>G			NA	NA				BFSP2 (27104 upstream) : RP11-91K8.5 (40766 downstream)						NA		NA									NA						aggaaggaagaaagaaagAgg	0.557		NA											-|||	2755	0.55012	0.4841	0.4438	5008	,	,	NA	6332	0.6567	NA	0.4344	False	NA	,,,	NA	NA	NA	2504	0.7239	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.133221141A>G		NA		hg19		0.02	-0.201731	AAGxAAG	COVERED																																																																																			NOVEL					0			6	2.706555	KEEP	0	0	0	9	247	AA	0.99254	0.486885	0			4	60	129	0	0	11.031208	11	60	329	50		0.266667	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	133221145	133221145	__UNKNOWN__	IGR	SNP	A	A	G	rs62280375	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:133221145A>G			NA	NA				BFSP2 (27108 upstream) : RP11-91K8.5 (40762 downstream)						NA		NA									NA						aggaagaaagaaagAggccgg	0.552		NA											A|||	2755	0.55012	0.4841	0.4438	5008	,	,	NA	6649	0.6567	NA	0.4344	False	NA	,,,	NA	NA	NA	2504	0.7239	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.133221145A>G		NA		hg19		0.02	-0.201707	AAGxAAG	COVERED																																																																																			NOVEL					0			6	3.00626	KEEP	0	0	0	10	270	AA	0.992708	0.486967	0			4	60	127	0	0	10.971389	10	60	299	50		0.285714	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	134048390	134048390	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:134048390C>G			NA	NA				RP11-200A1.1 (8377 upstream) : RP11-375I20.6 (17739 downstream)						NA		NA									NA						ttgtagagaccgggtttcacc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.134048390C>G		NA		hg19		0.02	-0.140354	GACxGGG	COVERED																																																																																			NOVEL					0			3	2.406937	KEEP	1	0	0	8	241	AC	0.99254	0.259018	0			3	60	98	0	0	7.878713	13	60	435	43		0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	134061535	134061535	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:134061535T>C			NA	NA				RP11-200A1.1 (21522 upstream) : RP11-375I20.6 (4594 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.134061535T>C		NA		hg19		0.02	-0.192918	TCAxGCC	COVERED																																																																																			NOVEL					0			9	2.707237	KEEP	3	0	0	9	256	TT	0.99257	0.4869	0			3	60	94	0	0	7.092936	18	60	526	51		0.142857	0.490544
CEP63	80254	__UNKNOWN__	__UNKNOWN__	3	134293720	134293720	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:134293720A>G	ENST00000354446.3	+	12	1702	c.1415A>G	c.(1414-1416)gAa>gGa	p.E472G		NM_001042384.1	NP_001035843.1	Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	0		NA			centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)				kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						aaagtgctggaattacaagtg	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1	1	1			NA	NA	3		NA											NA				134293720		122	111	233	SO:0001583	missense			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923	80254			25815	protein-coding gene	gene with protein product		614724			NA	14654843, 24240477	Standard	NM_025180	NM_001042383	NA	Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000354446.3:c.1415A>G	chr3.hg19:g.134293720A>G	ENSP00000346432:p.Glu472Gly	NA	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	hg19	CCDS43152.1	0.02	3.429082	TGGxATT	COVERED	.	.	.	.	.	.	.	.	.	.	a	0.292	-0.979393	0.02197	.	.	ENSG00000182923	ENST00000354446;ENST00000514678	T;T	0.21543	2.0;2.0	0.445	-0.629	0.11533	.	.	.	.	.	T	0.07683	0.0193	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35968	-0.9767	8	0.18710	T	0.47	.	.	.	.	.	472	Q96MT8-4	.	G	472;191	ENSP00000346432:E472G;ENSP00000427526:E191G	ENSP00000346432:E472G	E	+	2	0	CEP63	135776410	0.001000	0.12720	0.024000	0.17045	0.031000	0.12232	-0.945000	0.03909	-1.217000	0.02604	-0.764000	0.03450	GAA	NOVEL	CEP63-004	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357047.1	27	5.37701	KEEP	1	5	157	73	2027	AA	1	1	0		+	5	60	166	0	0	9.859115	121	60	3621	316	ENST00000354446.3	0.039683	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	134300768	134300768	__UNKNOWN__	IGR	SNP	C	C	T	rs4245902	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:134300768C>T			NA	NA				CEP63 (6915 upstream) : KY (21211 downstream)						NA		NA									NA						ccgcccgcctcggcctcccaa	0.502		NA											-|||	3375	0.673922	0.4887	0.7651	5008	,	,	NA	11005	0.8224	NA	0.6879	False	NA	,,,	NA	NA	NA	2504	0.6922	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.134300768C>T		NA		hg19		0.02	-0.131557	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			2	2.406842	KEEP	4	0	0	8	240	CC	0	0	0			5	60	140	1	0	12.622876	8	60	256	41		0.384615	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	134507235	134507235	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:134507235T>G			NA	NA				RNA5SP141 (4838 upstream) : EPHB1 (6868 downstream)						NA		NA									NA						gcctcccagattgctgggatt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.134507235T>G		NA		hg19		0.02	-0.131562	AGAxTGC	COVERED																																																																																			NOVEL					0			6	2.707106	KEEP	0	0	0	9	254	TT	0.99254	0.227464	0			3	60	94	0	0	7.673019	11	60	334	35		0.214286	0.229173
EPHB1	2047	__UNKNOWN__	__UNKNOWN__	3	134514141	134514141	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:134514141C>T	ENST00000398015.3	+	0	38					NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	NA		NA			angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						TCCGCTGTAGCTAGCAATGTG	0.657		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928	2047		EPH receptors, Sterile alpha motif (SAM) domain containing, Fibronectin type III domain containing	3392	protein-coding gene	gene with protein product		600600	EphB1	EPHT2	NA	8666391	Standard	NM_004441	NM_004441	NA	Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.-333C>T	chr3.hg19:g.134514141C>T		NA	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	hg19	CCDS46921.1	0.02	2.178546	TAGxTAG	COVERED																																																																																			NOVEL	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357671.1	27	19.252375	KEEP	0	0	0	64	1883	CC	1	1	0		+	7	60	178	0	0	9.521489	116	60	3963	270	ENST00000398015.3	0.056911	1
PPP2R3A	5523	__UNKNOWN__	__UNKNOWN__	3	135866184	135866184	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:135866184C>T	ENST00000264977.3	+	0	6246					NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	NA		NA			eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ccagcctaggcgacagagcaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	5523	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits, EF-hand domain containing	9307	protein-coding gene	gene with protein product		604944	protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform, protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha	PPP2R3	NA	8392071	Standard	NM_002718	NM_002718	NA	Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.*2176C>T	chr3.hg19:g.135866184C>T		NA	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	hg19	CCDS3087.1	0.02	-0.254126	AGGxGAC	COVERED																																																																																			NOVEL	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357232.1	7	3.94134	KEEP	0	1	22	21	587	CC	0.999879	0.668442	0		+	4	60	124	0	0	9.538688	21	60	664	71	ENST00000264977.3	0.16	0.668523
STAG1	10274	__UNKNOWN__	__UNKNOWN__	3	136076059	136076059	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:136076059A>G	ENST00000236698.5	-	28	3332				STAG1_ENST00000383202.2_Intron|STAG1_ENST00000434713.2_Intron|STAG1_ENST00000536929.1_Intron			Q8WVM7	STAG1_HUMAN	stromal antigen 1	NA		NA			chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						caaagtgctgagattacaggt	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007	10274			11354	protein-coding gene	gene with protein product		604358			NA	9305759	Standard	NM_005862	XM_006713471	NA	Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000236698.5:c.3065+502T>C	chr3.hg19:g.136076059A>G		NA	O00539|Q6P275	hg19		0.02	-0.201744	CTGxGAT	COVERED																																																																																			NOVEL	STAG1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357403.1	8	3.007967	KEEP	2	0	0	10	282	AA	0.992708	0.486967	0		-	3	60	107	0	0	8.460475	17	60	522	54	ENST00000236698.5	0.15	0.490544
STAG1	10274	__UNKNOWN__	__UNKNOWN__	3	136385409	136385409	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:136385409T>C	ENST00000236698.5	-	2	184				STAG1_ENST00000480733.1_Intron|STAG1_ENST00000383202.2_Intron|STAG1_ENST00000434713.2_Intron			Q8WVM7	STAG1_HUMAN	stromal antigen 1	NA		NA			chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						cctgtaatcctagcactttgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007	10274			11354	protein-coding gene	gene with protein product		604358			NA	9305759	Standard	NM_005862	XM_006713471	NA	Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000236698.5:c.83-35586A>G	chr3.hg19:g.136385409T>C		NA	O00539|Q6P275	hg19		0.02	-0.149101	TCCxAGC	UNCOVERED																																																																																			NOVEL	STAG1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357403.1	8	2.707049	KEEP	2	0	0	9	250	TT	0	0	0		-	3	60	103	0	0	8.291717	14	60	411	36	ENST00000236698.5	0.176471	0.292001
STAG1	10274	__UNKNOWN__	__UNKNOWN__	3	136456196	136456196	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:136456196A>G	ENST00000236698.5	-	1	184				STAG1_ENST00000480733.1_Intron|STAG1_ENST00000383202.2_Intron|STAG1_ENST00000434713.2_Intron			Q8WVM7	STAG1_HUMAN	stromal antigen 1	NA		NA			chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						cacccacctcagcctcccaaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007	10274			11354	protein-coding gene	gene with protein product		604358			NA	9305759	Standard	NM_005862	XM_006713471	NA	Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000236698.5:c.82+14840T>C	chr3.hg19:g.136456196A>G		NA	O00539|Q6P275	hg19		0.02	-0.236763	CTCxGCC	UNCOVERED																																																																																			NOVEL	STAG1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357403.1	10	2.706225	KEEP	4	0	0	9	244	AA	0	0	0		-	4	60	101	0	0	7.241524	21	60	629	49	ENST00000236698.5	0.16	0.641347
NCK1	4690	__UNKNOWN__	__UNKNOWN__	3	136607054	136607054	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:136607054A>G	ENST00000481752.1	+	1	146				NCK1_ENST00000288986.2_Intron			P16333	NCK1_HUMAN	NCK adaptor protein 1	NA		NA			actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)			cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						caaagtgctgagattacaggt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092	4690		SH2 domain containing	7664	protein-coding gene	gene with protein product		600508		NCK	NA	7806213, 9737977	Standard	NM_006153	XM_005247498	NA	Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.-19+25859A>G	chr3.hg19:g.136607054A>G		NA	B7Z751|D3DNE3	hg19	CCDS3092.1	0.02	-0.26313	CTGxGAT	COVERED																																																																																			NOVEL	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357307.1	12	4.210516	KEEP	8	0	0	14	385	AA	0.993072	0.688863	0		+	3	60	100	0	0	7.342949	24	60	725	73	ENST00000481752.1	0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	136746441	136746441	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:136746441T>C			NA	NA				IL20RB (16514 upstream) : RNA5SP142 (490534 downstream)						NA		NA									NA						gacagggtcttactctgttgc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.136746441T>C		NA		hg19		0.02	-0.061385	TCTxACT	UNCOVERED																																																																																			NOVEL					0			4	2.404233	KEEP	0	0	0	8	200	TT	0.99257	0.043461	0			2	60	72	0	0	6.336041	5	60	135	18		0.285714	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	136753031	136753031	__UNKNOWN__	IGR	SNP	T	T	A	rs4678278	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:136753031T>A			NA	NA				IL20RB (23104 upstream) : RNA5SP142 (483944 downstream)						NA		NA									NA						taatcccagctctttgggagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.136753031T>A		NA		hg19		0.02	-0.149096	AGCxCTT	COVERED																																																																																			NOVEL					0			7	3.00692	KEEP	1	0	0	10	277	TT	0.99254	0.289823	0			3	60	87	0	0	6.872716	12	60	362	36		0.2	0.292001
PIK3CB	5291	__UNKNOWN__	__UNKNOWN__	3	138407433	138407433	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:138407433G>A	ENST00000477593.1	-	15	2210				PIK3CB_ENST00000544716.1_Intron|PIK3CB_ENST00000289153.2_Intron			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	NA		NA			activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	GAATATATTAGGAATGCCGAG	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	5291	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	phosphoinositide-3-kinase, catalytic, beta polypeptide	PIK3C1	NA	8246984	Standard		NM_006219	NA	Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2136+283C>T	chr3.hg19:g.138407433G>A		NA	D3DNF0|Q24JU2	hg19	CCDS3104.1	0.02	-0.438274	TTAxGAA	COVERED																																																																																			NOVEL	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358019.1	27	7.512223	KEEP	0	0	0	25	730	GG	0.999931	0.959793	0		-	4	60	110	0	0	6.902046	45	60	1431	88	ENST00000477593.1	0.081633	0.959859
PIK3CB	5291	__UNKNOWN__	__UNKNOWN__	3	138529487	138529487	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:138529487A>G	ENST00000477593.1	-	1	58							P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	NA		NA			activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	tgggccgggcatggtggctca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	5291	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	phosphoinositide-3-kinase, catalytic, beta polypeptide	PIK3C1	NA	8246984	Standard		NM_006219	NA	Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.15+24049T>C	chr3.hg19:g.138529487A>G		NA	D3DNF0|Q24JU2	hg19	CCDS3104.1	0.02	-0.271892	GGCxTGG	UNCOVERED																																																																																			NOVEL	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358019.1	7	2.405629	KEEP	5	0	0	8	217	AA	0	0	0		-	3	60	94	0	0	6.644858	26	60	778	60	ENST00000477593.1	0.103448	0.717315
PIK3CB	5291	__UNKNOWN__	__UNKNOWN__	3	138529488	138529488	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:138529488T>C	ENST00000477593.1	-	1	58							P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	NA		NA			activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	gggccgggcatggtggctcac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	5291	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	phosphoinositide-3-kinase, catalytic, beta polypeptide	PIK3C1	NA	8246984	Standard		NM_006219	NA	Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.15+24048A>G	chr3.hg19:g.138529488T>C		NA	D3DNF0|Q24JU2	hg19	CCDS3104.1	0.02	-0.271896	GCAxGGT	UNCOVERED																																																																																			NOVEL	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358019.1	7	2.405366	KEEP	5	0	0	8	211	TT	0	0	0		-	3	60	95	0	0	6.74472	26	60	778	60	ENST00000477593.1	0.103448	0.717315
PIK3CB	5291	__UNKNOWN__	__UNKNOWN__	3	138531559	138531559	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:138531559T>C	ENST00000477593.1	-	1	58							P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	NA		NA			activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	ttagaagagatggggtttcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	5291	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	phosphoinositide-3-kinase, catalytic, beta polypeptide	PIK3C1	NA	8246984	Standard		NM_006219	NA	Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.15+21977A>G	chr3.hg19:g.138531559T>C		NA	D3DNF0|Q24JU2	hg19	CCDS3104.1	0.02	-0.087707	AGAxGGG	UNCOVERED																																																																																			NOVEL	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358019.1	3	2.404375	KEEP	0	0	0	8	207	TT	0.99257	0.09898	0		-	3	44	95	0	0	8.278736	7	60	206	21	ENST00000477593.1	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	140739986	140739986	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:140739986T>C			NA	NA				SLC25A36 (41211 upstream) : SPSB4 (30257 downstream)						NA		NA									NA						ggctggagtgtagtggtgcaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.140739986T>C		NA		hg19		0.02	-0.087705	GTGxAGT	UNCOVERED																																																																																			NOVEL					0			7	2.405242	KEEP	0	0	0	8	208	TT	0.99257	0.09898	0			3	60	107	0	0	10.325611	3	60	85	22		0.5	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	140739995	140739995	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:140739995A>G			NA	NA				SLC25A36 (41220 upstream) : SPSB4 (30248 downstream)						NA		NA									NA						gtagtggtgcaatctcggctc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.140739995A>G		NA		hg19		0.02	-0.052622	TGCxATC	UNCOVERED																																																																																			NOVEL					0			4	2.405762	KEEP	0	0	0	8	217	AA	0.99257	0.036492	0			2	21	70	0	0	6.750581	2	60	54	20		0.5	0.036766
SPSB4	92369	__UNKNOWN__	__UNKNOWN__	3	140851130	140851130	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:140851130T>C	ENST00000310546.2	+	3	1438				SPSB4_ENST00000507895.1_Intron	NM_080862.1	NP_543138.1	Q96A44	SPSB4_HUMAN	splA/ryanodine receptor domain and SOCS box containing 4	NA		NA			intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	4						ctgcctcagcttcccgagtag	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3115.1	3q23	2008-02-05			ENSG00000175093	ENSG00000175093	92369			30630	protein-coding gene	gene with protein product		611660			NA	12076535	Standard	NM_080862	NM_080862	NA	Approved	SSB-4	uc003ett.3	Q96A44	OTTHUMG00000160223	ENST00000310546.2:c.695-14854T>C	chr3.hg19:g.140851130T>C		NA		hg19	CCDS3115.1	0.02	-0.298137	AGCxTCC	COVERED																																																																																			NOVEL	SPSB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359727.1	3	2.706956	KEEP	1	0	0	9	249	TT	0.99254	0.775233	0		+	3	60	94	0	0	6.468642	30	60	859	48	ENST00000310546.2	0.090909	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	140910154	140910154	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:140910154G>A			NA	NA				SPSB4 (42701 upstream) : ACPL2 (40515 downstream)						NA		NA									NA						tggatggatggatggatggat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.140910154G>A		NA		hg19		0.02	-0.175434	ATGxATG	COVERED																																																																																			NOVEL					0			9	3.610128	KEEP	7	0	0	12	352	GG	0.992708	0.384582	0			3	60	83	1	0	6.472754	12	58	407	50		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	140910168	140910168	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:140910168T>C			NA	NA				SPSB4 (42715 upstream) : ACPL2 (40501 downstream)						NA		NA									NA						gatggatggatggatggatgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.140910168T>C		NA		hg19		0.02	-0.236639	GGAxGGA	COVERED																																																																																			NOVEL					0			13	4.509982	KEEP	11	0	0	15	399	TT	0.993634	0.608508	0			4	60	130	1	1	10.215278	20	60	552	80		0.166667	0.612407
ZBTB38	253461	__UNKNOWN__	__UNKNOWN__	3	141113138	141113138	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141113138G>A	ENST00000514251.1	+	1	76									zinc finger and BTB domain containing 38	NA		NA								breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						gattacaggcgtgagccaccg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311	253461		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	26636	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 171	612218			NA	12477932	Standard		NM_001080412	NA	Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.-204+6409G>A	chr3.hg19:g.141113138G>A		NA		hg19	CCDS43157.1	0.02	-0.219302	GGCxTGA	COVERED																																																																																			NOVEL	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359329.2	6	3.911124	KEEP	1	0	0	13	386	GG	0.994391	0.549786	0		+	3	60	93	0	0	6.805985	21	60	688	58	ENST00000514251.1	0.125	0.552887
RP11-340E6.1	0	__UNKNOWN__	__UNKNOWN__	3	141407571	141407571	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141407571A>G	ENST00000474979.3	+	0	662										NA		NA									NA						cctgggaggcagaggttgtgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000474979.3:	chr3.hg19:g.141407571A>G		NA		hg19		0.02	-0.245419	GGCxGAG	UNCOVERED																																																																																			NOVEL	RP11-340E6.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000354923.2	17	3.006678	KEEP	12	0	0	10	264	AA	0	0	0		+	5	46	131	0	0	9.786192	23	60	663	60	ENST00000474979.3	0.178571	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	141574903	141574903	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141574903A>G			NA	NA				GRK7 (37571 upstream) : ATP1B3 (20552 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.141574903A>G		NA		hg19		0.02	-0.192881	CTGxGAT	COVERED																																																																																			NOVEL					0			7	3.59958	KEEP	1	0	0	12	315	AA	0.993072	0.454585	0			3	60	93	0	0	6.928021	19	60	582	41		0.136364	0.457757
ATP1B3	483	__UNKNOWN__	__UNKNOWN__	3	141619905	141619905	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141619905G>A	ENST00000286371.3	+	2	297				ATP1B3_ENST00000462082.1_Intron|ATP1B3_ENST00000539728.1_Intron	NM_001679.2	NP_001670.1	P54709	AT1B3_HUMAN	ATPase, Na+/K+ transporting, beta 3 polypeptide	NA		NA			blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	caveola (GO:0005901)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)			cervix(1)|endometrium(1)|lung(2)	4						gattacaggcgtgagccactg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011835	CCDS3121.1	3q23	2012-10-22			ENSG00000069849	ENSG00000069849	483		CD molecules, ATPases / P-type	806	protein-coding gene	gene with protein product	sodium/potassium-transporting ATPase subunit beta-3, sodium pump subunit beta-3, sodium-potassium ATPase subunit beta 3 (non-catalytic)	601867			NA	8798450, 9457675	Standard	NM_001679	NM_001679	NA	Approved	FLJ29027, CD298	uc003eug.1	P54709	OTTHUMG00000159081	ENST00000286371.3:c.110-2557G>A	chr3.hg19:g.141619905G>A		NA	B7Z1N7	hg19	CCDS3121.1	0.02	-0.19298	GGCxTGA	COVERED																																																																																			NOVEL	ATP1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353218.1	5	2.40617	KEEP	1	0	0	8	232	GG	0.99257	0.454356	0		+	3	60	88	0	0	6.633893	16	60	521	44	ENST00000286371.3	0.157895	0.457757
ATP1B3	483	__UNKNOWN__	__UNKNOWN__	3	141629060	141629060	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141629060T>C	ENST00000286371.3	+	3	534				ATP1B3_ENST00000462082.1_Intron|ATP1B3_ENST00000539728.1_Intron	NM_001679.2	NP_001670.1	P54709	AT1B3_HUMAN	ATPase, Na+/K+ transporting, beta 3 polypeptide	NA		NA			blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	caveola (GO:0005901)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)			cervix(1)|endometrium(1)|lung(2)	4						gtgatccacctgcctccgcct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011835	CCDS3121.1	3q23	2012-10-22			ENSG00000069849	ENSG00000069849	483		CD molecules, ATPases / P-type	806	protein-coding gene	gene with protein product	sodium/potassium-transporting ATPase subunit beta-3, sodium pump subunit beta-3, sodium-potassium ATPase subunit beta 3 (non-catalytic)	601867			NA	8798450, 9457675	Standard	NM_001679	NM_001679	NA	Approved	FLJ29027, CD298	uc003eug.1	P54709	OTTHUMG00000159081	ENST00000286371.3:c.346+2944T>C	chr3.hg19:g.141629060T>C		NA	B7Z1N7	hg19	CCDS3121.1	0.02	-0.175427	ACCxGCC	COVERED																																																																																			NOVEL	ATP1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353218.1	7	3.609997	KEEP	0	0	0	12	345	TT	0.993634	0.38494	0		+	3	47	98	0	0	7.878831	13	60	396	49	ENST00000286371.3	0.1875	0.387407
ATP1B3	483	__UNKNOWN__	__UNKNOWN__	3	141629066	141629066	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141629066C>A	ENST00000286371.3	+	3	534				ATP1B3_ENST00000462082.1_Intron|ATP1B3_ENST00000539728.1_Intron	NM_001679.2	NP_001670.1	P54709	AT1B3_HUMAN	ATPase, Na+/K+ transporting, beta 3 polypeptide	NA		NA			blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|leukocyte migration (GO:0050900)|membrane repolarization (GO:0086009)|positive regulation of ATP catabolic process (GO:1903291)|positive regulation of ATPase activity (GO:0032781)|positive regulation of potassium ion import (GO:1903288)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of sodium ion export from cell (GO:1903278)|potassium ion import (GO:0010107)|protein localization to plasma membrane (GO:0072659)|protein stabilization (GO:0050821)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)|transport (GO:0006810)	caveola (GO:0005901)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|sodium:potassium-exchanging ATPase activity (GO:0005391)			cervix(1)|endometrium(1)|lung(2)	4						cacctgcctccgcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011835	CCDS3121.1	3q23	2012-10-22			ENSG00000069849	ENSG00000069849	483		CD molecules, ATPases / P-type	806	protein-coding gene	gene with protein product	sodium/potassium-transporting ATPase subunit beta-3, sodium pump subunit beta-3, sodium-potassium ATPase subunit beta 3 (non-catalytic)	601867			NA	8798450, 9457675	Standard	NM_001679	NM_001679	NA	Approved	FLJ29027, CD298	uc003eug.1	P54709	OTTHUMG00000159081	ENST00000286371.3:c.346+2950C>A	chr3.hg19:g.141629066C>A		NA	B7Z1N7	hg19	CCDS3121.1	0.02	-0.149119	CTCxGCC	COVERED																																																																																			NOVEL	ATP1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353218.1	6	3.308931	KEEP	0	0	0	11	324	CC	0.993072	0.420544	0		+	4	47	119	0	0	10.030924	11	60	358	46	ENST00000286371.3	0.266667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	141869394	141869394	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141869394G>C			NA	NA				TFDP2 (1008 upstream) : RP11-485G4.2 (6974 downstream)						NA		NA									NA						tcccaaagtggtgggattaca	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.141869394G>C		NA		hg19		0.02	-0.105274	GTGxTGG	UNCOVERED																																																																																			NOVEL					0			6	2.407185	KEEP	1	0	0	8	245	GG	0	0	0			3	60	102	0	0	8.97845	7	60	242	28		0.3	0.139832
GK5	256356	__UNKNOWN__	__UNKNOWN__	3	141899269	141899269	__UNKNOWN__	Intron	SNP	A	A	C	rs553016593		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:141899269A>C	ENST00000392993.2	-	11	1200					NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	NA		NA			glycerol catabolic process (GO:0019563)		ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			kidney(1)|large_intestine(1)|lung(7)|urinary_tract(1)	10						ctcagcctccagagtagctgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648681	CCDS33871.1	3q23	2014-02-12	2006-09-21		ENSG00000175066	ENSG00000175066	256356		Glycerol kinases	28635	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_001039547	NM_001039547	NA	Approved	MGC40579	uc003euq.2	Q6ZS86	OTTHUMG00000133572	ENST00000392993.2:c.1048+1033T>G	chr3.hg19:g.141899269A>C		NA	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	hg19	CCDS33871.1	0.02	-0.096488	TCCxGAG	UNCOVERED																																																																																			NOVEL	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353999.1	5	2.405752	KEEP	1	0	0	8	215	AT	0.99257	0.119541	0		-	3	48	101	0	0	8.73245	8	60	246	25	ENST00000392993.2	0.272727	0.120436
TRPC1	7220	__UNKNOWN__	__UNKNOWN__	3	142523689	142523689	__UNKNOWN__	Intron	SNP	T	T	C	rs113744430		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:142523689T>C	ENST00000476941.1	+	12	2640				TRPC1_ENST00000273482.6_Intron	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	NA		NA			axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						tggctcacgcttgtaatccca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935	7220		Voltage-gated ion channels / Transient receptor potential cation channels	12333	protein-coding gene	gene with protein product		602343			NA	7568191, 16382100	Standard	NM_003304	NM_001251845	NA	Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2154+217T>C	chr3.hg19:g.142523689T>C		NA	Q14CE4	hg19	CCDS58856.1	0.02	-0.149121	CGCxTGT	COVERED																																																																																			NOVEL	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354520.1	3	2.707454	KEEP	0	0	0	9	258	TT	0.99254	0.289823	0		+	3	60	108	0	0	8.878575	13	60	405	43	ENST00000476941.1	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	142618779	142618779	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:142618779G>C			NA	NA				PCOLCE2 (10734 upstream) : RP11-372E1.4 (26737 downstream)						NA		NA									NA						gttgcccagggtggtctcaaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.142618779G>C		NA		hg19		0.02	-0.131585	AGGxTGG	COVERED																																																																																			NOVEL					0			10	2.708009	KEEP	0	0	0	9	273	GG	0.99254	0.259018	0			3	60	101	0	0	8.732227	8	60	269	30		0.272727	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	142634233	142634233	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:142634233G>C			NA	NA				PCOLCE2 (26188 upstream) : RP11-372E1.4 (11283 downstream)						NA		NA									NA						aaactcctgggctcaaatgat	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.142634233G>C		NA		hg19		0.02	-0.184226	TGGxCTC	COVERED																																																																																			NOVEL					0			9	3.008888	KEEP	0	0	0	10	304	GG	0.993072	0.420544	0			3	60	100	0	0	7.760492	17	60	584	45		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	144583053	144583053	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:144583053T>C			NA	NA				RNA5SP144 (677191 upstream) : None (None downstream)						NA		NA									NA						gctgggattataggcgtgggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.144583053T>C		NA		hg19		0.02	-0.052605	TTAxAGG	UNCOVERED																																																																																			NOVEL					0			4	2.403748	KEEP	1	0	0	8	202	TT	0.99257	0.036492	0			3	60	82	0	0	7.823375	3	60	85	20		0.5	0.036766
PLSCR1	5359	__UNKNOWN__	__UNKNOWN__	3	146252588	146252588	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:146252588G>A	ENST00000342435.4	-	3	424				PLSCR1_ENST00000487389.1_Intron|PLSCR1_ENST00000448205.1_Intron|PLSCR1_ENST00000448787.2_Intron	NM_021105.2	NP_066928.1	O15162	PLS1_HUMAN	phospholipid scramblase 1	NA		NA			acute-phase response (GO:0006953)|apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|negative regulation of viral genome replication (GO:0045071)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid scrambling (GO:0017121)|platelet activation (GO:0030168)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of gene expression (GO:0010628)|positive regulation of innate immune response (GO:0045089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|regulation of mast cell activation (GO:0033003)|response to interferon-beta (GO:0035456)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|CD4 receptor binding (GO:0042609)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|epidermal growth factor receptor binding (GO:0005154)|phospholipid scramblase activity (GO:0017128)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15						acttaaacccgggaggcggag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF098642	CCDS3135.1	3q23	2004-02-27			ENSG00000188313	ENSG00000188313	5359			9092	protein-coding gene	gene with protein product		604170			NA	9218461	Standard	NM_021105	NM_021105	NA	Approved	MMTRA1B	uc003evx.4	O15162	OTTHUMG00000159427	ENST00000342435.4:c.14-1251C>T	chr3.hg19:g.146252588G>A		NA	B2R8H8|B4DTE8	hg19	CCDS3135.1	0.02	-0.166661	CCCxGGA	COVERED																																																																																			NOVEL	PLSCR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355257.2	8	3.609833	KEEP	2	0	0	12	353	GG	0.992708	0.351366	0		-	3	60	86	0	0	6.510932	15	60	493	43	ENST00000342435.4	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	146508225	146508225	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:146508225C>T			NA	NA				PLSCR5 (184222 upstream) : RP11-649A16.1 (119246 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.146508225C>T		NA		hg19		0.02	-0.175432	TCAxGCC	COVERED																																																																																			NOVEL					0			3	3.007878	KEEP	0	0	0	10	286	CC	0.992708	0.384582	0			3	60	89	0	0	6.810447	15	60	492	44		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	147452683	147452683	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:147452683A>G			NA	NA				ZIC1 (224603 upstream) : RP11-78O22.1 (109226 downstream)						NA		NA									NA						cacgatctcgactcactgcaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.147452683A>G		NA		hg19		0.02	-0.20172	TCGxCTC	COVERED																																																																																			NOVEL					0			8	2.706537	KEEP	0	0	0	9	243	AA	0.99254	0.486885	0			3	60	94	0	0	7.02775	19	60	566	40		0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	147497469	147497469	__UNKNOWN__	IGR	SNP	G	G	A	rs535756409		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:147497469G>A			NA	NA				ZIC1 (269389 upstream) : RP11-78O22.1 (64440 downstream)						NA		NA									NA						gagccaccgcgcccagccatg	0.453		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15009	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.147497469G>A		NA		hg19		0.02	-0.149113	CGCxCCC	COVERED																																																																																			NOVEL					0			8	3.309405	KEEP	0	0	0	11	323	GG	0.993072	0.289978	0			3	60	84	0	0	6.673069	11	60	360	37		0.214286	0.292001
GYG1	2992	__UNKNOWN__	__UNKNOWN__	3	148730929	148730929	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:148730929T>C	ENST00000479119.1	+	2	224				GYG1_ENST00000345003.4_Intron|GYG1_ENST00000483267.1_Intron|GYG1_ENST00000484197.1_Intron|GYG1_ENST00000296048.6_Intron			P46976	GLYG_HUMAN	glycogenin 1	NA		NA			carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogenin glucosyltransferase activity (GO:0008466)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			cgtgagccactgtgcccagcc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF087942	CCDS3139.1, CCDS54654.1, CCDS54655.1	3q24-q25.1	2013-02-22	2005-11-04	2005-11-04	ENSG00000163754	ENSG00000163754	2992	2.4.1.186	Glycosyltransferase family 8 domain containing	4699	protein-coding gene	gene with protein product	glycogenin glucosyltransferase	603942	glycogenin	GYG	NA	8602861	Standard	NM_004130	NM_004130	NA	Approved		uc003ewn.3	P46976	OTTHUMG00000159533	ENST00000479119.1:c.224+3740T>C	chr3.hg19:g.148730929T>C		NA	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	hg19		0.02	-0.131534	CACxGTG	COVERED																																																																																			NOVEL	GYG1-013	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000356058.1	5	2.706877	KEEP	1	0	0	9	247	TT	0.99257	0.22747	0		+	3	60	104	0	0	8.673293	11	60	316	32	ENST00000479119.1	0.214286	0.229173
HLTF	6596	__UNKNOWN__	__UNKNOWN__	3	148797642	148797642	__UNKNOWN__	Intron	SNP	C	C	T	rs537023745		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:148797642C>T	ENST00000310053.5	-	3	422				HLTF_ENST00000465259.1_Intron|HLTF_ENST00000494055.1_Intron|HLTF_ENST00000392912.2_Intron	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	NA		NA			chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			cctcccaaagcgctgggatta	0.448		NA											C|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	14586	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794	6596		RING-type (C3HC4) zinc fingers	11099	protein-coding gene	gene with protein product		603257	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3	SNF2L3, SMARCA3	NA	7558014	Standard		NM_139048	NA	Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.229-3808G>A	chr3.hg19:g.148797642C>T		NA	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	hg19	CCDS33875.1	0.02	-0.149126	AAGxGCT	COVERED																																																																																			NOVEL	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356064.1	5	2.40707	KEEP	0	0	0	8	244	CC	0.99257	0.289832	0		-	4	60	118	0	0	9.801219	12	60	408	42	ENST00000310053.5	0.25	0.292001
WWTR1	25937	__UNKNOWN__	__UNKNOWN__	3	149240652	149240652	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:149240652T>C	ENST00000465804.1	-	8	1275				WWTR1_ENST00000360632.3_Intron|WWTR1_ENST00000467467.1_Intron	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	NA		NA			cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			ggtgaaaccctgtctctacta	0.507		NA	T	CAMTA1	epitheliod hemangioendothelioma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408	25937			24042	protein-coding gene	gene with protein product		607392			NA	11118213, 15096513	Standard	NM_015472	NM_015472	NA	Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.1019-1876A>G	chr3.hg19:g.149240652T>C		NA	D3DNH7|Q8N3P2|Q9Y3W6	hg19	CCDS3144.1	0.02	-0.122737	CCCxGTC	COVERED																																																																																			NOVEL	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356498.1	7	3.60896	KEEP	0	0	0	12	332	TT	0.993634	0.195062	0		-	3	60	91	0	0	7.48287	10	60	289	34	ENST00000465804.1	0.230769	0.196312
WWTR1	25937	__UNKNOWN__	__UNKNOWN__	3	149343414	149343414	__UNKNOWN__	Intron	SNP	C	C	T	rs182396954	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:149343414C>T	ENST00000465804.1	-	3	688				WWTR1_ENST00000360632.3_Intron|WWTR1_ENST00000467467.1_Intron	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	NA		NA			cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			cccatctctactaaaaataca	0.502		NA	T	CAMTA1	epitheliod hemangioendothelioma								C|||	7	0.00139776	0.0	0.0014	5008	,	,	NA	15621	0.0	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA			Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408	25937			24042	protein-coding gene	gene with protein product		607392			NA	11118213, 15096513	Standard	NM_015472	NM_015472	NA	Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.431+31248G>A	chr3.hg19:g.149343414C>T		NA	D3DNH7|Q8N3P2|Q9Y3W6	hg19	CCDS3144.1	0.02	-0.052634	CTAxTAA	UNCOVERED																																																																																			NOVEL	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356498.1	4	2.406996	KEEP	3	0	0	8	243	CC	0	0	0		-	4	60	131	0	0	13.349289	2	60	67	19	ENST00000465804.1	0.666667	0.036766
WWTR1	25937	__UNKNOWN__	__UNKNOWN__	3	149367057	149367057	__UNKNOWN__	Intron	SNP	G	G	T	rs12487158	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:149367057G>T	ENST00000465804.1	-	3	688				WWTR1_ENST00000360632.3_Intron|WWTR1_ENST00000467467.1_Intron|WWTR1-IT1_ENST00000463167.1_RNA	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	NA		NA			cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			gggattacaggcgtgagccac	0.498		NA	T	CAMTA1	epitheliod hemangioendothelioma								G|||	592	0.118211	0.031	0.2176	5008	,	,	NA	15248	0.2222	NA	0.0199	False	NA	,,,	NA	NA	NA	2504	0.1595	NA	NA	NA			Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408	25937			24042	protein-coding gene	gene with protein product		607392			NA	11118213, 15096513	Standard	NM_015472	NM_015472	NA	Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.431+7605C>A	chr3.hg19:g.149367057G>T		NA	D3DNH7|Q8N3P2|Q9Y3W6	hg19	CCDS3144.1	0.02	-0.122806	CAGxCGT	UNCOVERED																																																																																			NOVEL	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356498.1	7	3.608364	KEEP	7	0	0	12	350	GG	0	0	0		-	9	60	278	0	0	29.161012	3	60	104	43	ENST00000465804.1	0.75	0.196312
WWTR1	25937	__UNKNOWN__	__UNKNOWN__	3	149381080	149381080	__UNKNOWN__	Intron	SNP	C	C	T	rs73155031	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:149381080C>T	ENST00000465804.1	-	3	254					NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	NA		NA			cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			gctgggattacagatgtgagc	0.478		NA	T	CAMTA1	epitheliod hemangioendothelioma								C|||	1758	0.351038	0.3116	0.3228	5008	,	,	NA	16084	0.2937	NA	0.4095	False	NA	,,,	NA	NA	NA	2504	0.4233	NA	NA	NA			Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408	25937			24042	protein-coding gene	gene with protein product		607392			NA	11118213, 15096513	Standard	NM_015472	NM_015472	NA	Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.3-5984G>A	chr3.hg19:g.149381080C>T		NA	D3DNH7|Q8N3P2|Q9Y3W6	hg19	CCDS3144.1	0.02	-0.105172	TTAxAGA	UNCOVERED																																																																																			NOVEL	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356498.1	8	2.407028	KEEP	2	0	0	8	241	CC	0	0	0		-	4	60	107	0	0	10.190432	4	60	140	28	ENST00000465804.1	0.5	0.139832
RNF13	11342	__UNKNOWN__	__UNKNOWN__	3	149666629	149666629	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:149666629A>C	ENST00000344229.3	+	10	1402				RNF13_ENST00000361785.6_Intron|RNF13_ENST00000392894.3_Intron	NM_007282.4	NP_009213.1	O43567	RNF13_HUMAN	ring finger protein 13	NA		NA			protein autoubiquitination (GO:0051865)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(2)	11		all_neural(597;0.0138)|Myeloproliferative disorder(1037;0.0255)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			gcctgggcaaaatggtgaaac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF037204	CCDS3146.1	3q25.1	2013-01-09			ENSG00000082996	ENSG00000082996	11342		RING-type (C3HC4) zinc fingers	10057	protein-coding gene	gene with protein product		609247			NA		Standard	NM_183384	NM_183381	NA	Approved	RZF	uc003exp.4	O43567	OTTHUMG00000150338	ENST00000344229.3:c.701-11214A>C	chr3.hg19:g.149666629A>C		NA	A6NC87|B3KR12|Q05D66|Q6IBJ9	hg19	CCDS3146.1	0.02	-0.114027	CAAxATG	UNCOVERED																																																																																			NOVEL	RNF13-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356876.1	4	3.0071	KEEP	0	0	0	10	268	AA	0.992708	0.161282	0		+	3	60	94	1	0	8.343576	6	60	179	32	ENST00000344229.3	0.333333	0.162467
RP11-167H9.4	0	__UNKNOWN__	__UNKNOWN__	3	149769320	149769320	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:149769320C>T	ENST00000487840.1	+	0	46										NA		NA									NA						ttttttgagacggagtctcgc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000487840.1:	chr3.hg19:g.149769320C>T		NA		hg19		0.02	3.017653	AGAxGGA	COVERED																																																																																			NOVEL	RP11-167H9.4-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000357120.1	20	5.760907	KEEP	8	5	138	68	1871	CC	1	0.999993	0		+	6	60	175	2	0	10.864312	82	60	2562	238	ENST00000487840.1	0.068182	0.999993
RP11-103G8.2	0	__UNKNOWN__	__UNKNOWN__	3	150427145	150427145	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:150427145T>C	ENST00000475393.1	+	0	343				RP11-103G8.2_ENST00000463755.1_RNA|RP11-103G8.2_ENST00000471093.1_RNA						NA		NA									NA						cctgtaatcctagcactttgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000475393.1:	chr3.hg19:g.150427145T>C		NA		hg19		0.02	-0.219286	TCCxAGC	COVERED																																																																																			NOVEL	RP11-103G8.2-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000357693.1	11	2.406124	KEEP	0	0	0	8	223	TT	0.99257	0.54878	0		+	4	60	138	0	0	11.179206	18	60	548	49	ENST00000475393.1	0.181818	0.552887
MED12L	116931	__UNKNOWN__	__UNKNOWN__	3	151052553	151052553	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:151052553A>G	ENST00000474524.1	+	15	2183				MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	NA		NA				mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ctcccaaagtactgggattac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893	116931			16050	protein-coding gene	gene with protein product		611318	mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like		NA	11524702	Standard	NM_053002	XM_006713487	NA	Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.2146-15294A>G	chr3.hg19:g.151052553A>G		NA	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	hg19	CCDS33876.1	0.02	-0.254306	AGTxCTG	COVERED																																																																																			NOVEL	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357707.2	7	3.909288	KEEP	1	0	0	13	348	AA	0.994391	0.664773	0		+	3	60	108	0	0	8.248867	22	60	623	70	ENST00000474524.1	0.12	0.668523
MED12L	116931	__UNKNOWN__	__UNKNOWN__	3	151143374	151143374	__UNKNOWN__	Intron	SNP	C	C	G	rs201186601		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:151143374C>G	ENST00000474524.1	+	42	6341				MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	NA		NA				mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			gtgtgtgtgtctgtgtTTAAT	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893	116931			16050	protein-coding gene	gene with protein product		611318	mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like		NA	11524702	Standard	NM_053002	XM_006713487	NA	Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6304-4713C>G	chr3.hg19:g.151143374C>G		NA	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	hg19	CCDS33876.1	0.02	3.765593	TGTxTGT	COVERED																																																																																			NOVEL	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357707.2	35	11.134114	KEEP	0	0	0	37	1173	CC	1	0.999987	0		+	6	60	203	0	0	13.392393	91	60	3107	212	ENST00000474524.1	0.061856	0.999987
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	151718858	151718858	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:151718858G>A			NA	NA				RP11-454C18.2 (72895 upstream) : RP11-246A10.1 (117103 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.151718858G>A		NA		hg19		0.02	-0.149105	CACxCCT	COVERED																																																																																			NOVEL					0			7	3.307209	KEEP	5	0	0	11	308	GG	0.99254	0.289823	0			3	40	87	0	0	6.692223	14	60	465	43		0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	151741752	151741752	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:151741752T>C			NA	NA				RP11-454C18.2 (95789 upstream) : RP11-246A10.1 (94209 downstream)						NA		NA									NA						atggtgaaactccgtctctac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.151741752T>C		NA		hg19		0.02	-0.113931	AACxCCG	UNCOVERED																																																																																			NOVEL					0			5	3.007068	KEEP	1	0	0	10	267	TT	0.99254	0.161255	0			3	40	85	0	0	7.002451	9	60	251	32		0.25	0.162467
MBNL1	4154	__UNKNOWN__	__UNKNOWN__	3	152004746	152004746	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:152004746T>C	ENST00000461436.1	+	2	187				MBNL1_ENST00000493459.1_Intron|MBNL1_ENST00000282488.7_Intron|MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000324210.5_Intron|MBNL1_ENST00000282486.6_Intron			Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	NA		NA			alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			tggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601	4154		Zinc fingers, CCCH-type domain containing	6923	protein-coding gene	gene with protein product		606516	muscleblind (Drosophila)-like, muscleblind-like (Drosophila)	MBNL	NA		Standard	NM_021038	NM_021038	NA	Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000461436.1:c.188-12448T>C	chr3.hg19:g.152004746T>C		NA	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	hg19		0.02	-0.210422	TCAxGCC	UNCOVERED																																																																																			NOVEL	MBNL1-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000353600.1	6	2.405326	KEEP	1	0	0	8	210	TT	0	0	0		+	3	60	99	0	0	7.527629	19	60	524	47	ENST00000461436.1	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	152674388	152674388	__UNKNOWN__	IGR	SNP	A	A	G	rs9289881	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:152674388A>G			NA	NA				RP11-38P22.2 (115160 upstream) : RP11-529G21.2 (199911 downstream)						NA		NA									NA						tgatccgcccacctcggcctc	0.532		NA											-|||	2895	0.578075	0.5197	0.572	5008	,	,	NA	14807	0.6458	NA	0.6103	False	NA	,,,	NA	NA	NA	2504	0.5583	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.152674388A>G		NA		hg19		0.02	-0.184174	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			3	2.644252	KEEP	10	0	0	9	219	AA	0	0	0			4	60	122	0	0	9.763517	16	60	471	51		0.2	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	152748732	152748732	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:152748732A>G			NA	NA				RP11-38P22.2 (189504 upstream) : RP11-529G21.2 (125567 downstream)						NA		NA									NA						ggccaacatgatgaaacccca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.152748732A>G		NA		hg19		0.02	-0.184175	ATGxTGA	COVERED																																																																																			NOVEL					0			6	3.907633	KEEP	0	0	0	13	339	AA	0.994391	0.421102	0			3	60	94	0	0	7.234435	16	60	469	49		0.157895	0.423478
ARHGEF26	26084	__UNKNOWN__	__UNKNOWN__	3	153904275	153904275	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:153904275T>C	ENST00000356448.4	+	7	1771				ARHGEF26_ENST00000465093.1_Intron|ARHGEF26_ENST00000465817.1_Intron	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	NA		NA			endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						CCTggccgggtgcagtggctc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790	26084		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	24490	protein-coding gene	gene with protein product	Src homology 3 domain-containing guanine nucleotide exchange factor	NA			NA	15133129, 12697679	Standard	NM_015595	NM_015595	NA	Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.1488-1199T>C	chr3.hg19:g.153904275T>C		NA	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	hg19	CCDS46938.1	0.02	-0.210426	GGGxGCA	COVERED																																																																																			NOVEL	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353287.3	5	3.006961	KEEP	1	0	0	10	269	TT	0.992708	0.518353	0		+	3	60	96	0	0	7.29298	18	60	492	52	ENST00000356448.4	0.142857	0.522161
DHX36	170506	__UNKNOWN__	__UNKNOWN__	3	153992054	153992054	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:153992054A>G	ENST00000496811.1	-	0	5013					NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	NA		NA			ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ccaagatcacaccactgcact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953	170506		DEAH-boxes	14410	protein-coding gene	gene with protein product		612767	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36	DDX36	NA		Standard	NM_020865	NM_020865	NA	Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.*1906T>C	chr3.hg19:g.153992054A>G		NA	B2RB00|Q70JU3|Q8IYE5|Q9P240	hg19	CCDS3171.1	0.02	-0.192939	CACxCCA	COVERED																																																																																			NOVEL	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353349.1	1	5.714224	KEEP	0	0	0	19	520	AA	0.99986	0.457692	0		-	3	60	101	0	0	8.010442	15	60	433	49	ENST00000496811.1	0.166667	0.457757
DHX36	170506	__UNKNOWN__	__UNKNOWN__	3	153992111	153992111	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:153992111C>G	ENST00000496811.1	-	0	4956					NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	NA		NA			ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			aaacaaaaaacaaaacaaaac	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953	170506		DEAH-boxes	14410	protein-coding gene	gene with protein product		612767	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36	DDX36	NA		Standard	NM_020865	NM_020865	NA	Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.*1849G>C	chr3.hg19:g.153992111C>G		NA	B2RB00|Q70JU3|Q8IYE5|Q9P240	hg19	CCDS3171.1	0.02	1.552193	AAAxAAA	COVERED																																																																																			NOVEL	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353349.1	36	13.538693	KEEP	0	0	0	45	1345	CC	1	0.999678	0		-	4	60	140	2	1	9.014725	76	60	2587	175	ENST00000496811.1	0.05	0.999678
PLCH1	23007	__UNKNOWN__	__UNKNOWN__	3	155147583	155147583	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:155147583A>C	ENST00000494598.1	-	22	3315							Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	NA		NA			inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			gcatgtccagactgggtgaca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	23007	3.1.4.11	EF-hand domain containing	29185	protein-coding gene	gene with protein product		612835	phospholipase C-like 3	PLCL3	NA	15702972	Standard	NM_014996	NM_014996	NA	Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000494598.1:c.2939-54005T>G	chr3.hg19:g.155147583A>C		NA	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	hg19		0.02	-0.096488	CAGxCTG	UNCOVERED																																																																																			NOVEL	PLCH1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000351122.2	10	2.70711	KEEP	0	0	0	9	253	AA	0.99254	0.119538	0		-	3	60	102	0	0	9.333032	5	60	151	26	ENST00000494598.1	0.375	0.120436
PLCH1	23007	__UNKNOWN__	__UNKNOWN__	3	155285091	155285091	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:155285091G>A	ENST00000340059.7	-	6	829				PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000460012.1_Intron|PLCH1_ENST00000414191.1_Intron|PLCH1_ENST00000447496.2_Intron|PLCH1_ENST00000334686.6_Intron	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	NA		NA			inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			caaactcctggcctcaagtga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	23007	3.1.4.11	EF-hand domain containing	29185	protein-coding gene	gene with protein product		612835	phospholipase C-like 3	PLCL3	NA	15702972	Standard	NM_014996	NM_014996	NA	Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.829+928C>T	chr3.hg19:g.155285091G>A		NA	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	hg19	CCDS46939.1	0.02	-0.149124	CTGxCCT	COVERED																																																																																			NOVEL	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351125.1	7	2.687499	KEEP	2	0	0	9	251	GG	0.99257	0.289832	0		-	3	59	83	1	0	6.379336	13	60	452	38	ENST00000340059.7	0.1875	0.292001
GMPS	8833	__UNKNOWN__	__UNKNOWN__	3	155616922	155616922	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:155616922C>T	ENST00000496455.2	+	3	659				GMPS_ENST00000295920.7_Intron|GMPS_ENST00000476145.1_Intron	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	NA		NA			glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase biosynthetic process (GO:0009113)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|GMP synthase (glutamine-hydrolyzing) activity (GO:0003922)|GMP synthase activity (GO:0003921)|pyrophosphatase activity (GO:0016462)			breast(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)		L-Glutamine(DB00130)	tttgggaggccgaggcgggtg	0.537		NA	T	MLL	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(153;896 1876 4149 15499 28134)		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U10860	CCDS46941.1	3q25.31	2013-06-18	2013-06-18		ENSG00000163655	ENSG00000163655	8833	6.3.5.2		4378	protein-coding gene	gene with protein product	GMP synthase	600358	guanine monphosphate synthetase		NA	8089153, 9195163	Standard		NM_003875	NA	Approved		uc003faq.3	P49915	OTTHUMG00000158551	ENST00000496455.2:c.324+1092C>T	chr3.hg19:g.155616922C>T		NA	A8K639|B4DXV7|F8W720	hg19	CCDS46941.1	0.02	-0.192981	GGCxGAG	COVERED																																																																																			NOVEL	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351260.2	2	2.706489	KEEP	1	0	0	9	253	CC	0.99257	0.4869	0		+	3	60	90	0	0	6.62754	19	60	618	51	ENST00000496455.2	0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	155800520	155800520	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:155800520A>G			NA	NA				GMPS (138705 upstream) : KCNAB1 (37816 downstream)						NA		NA									NA						gcctcccaaaatgctgggatt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.155800520A>G		NA		hg19		0.02	-0.210506	AAAxTGC	COVERED																																																																																			NOVEL					0			9	2.706829	KEEP	1	0	0	9	246	AA	0.99254	0.518266	0			3	60	104	0	0	8.026699	19	60	573	53		0.136364	0.522161
SSR3	6747	__UNKNOWN__	__UNKNOWN__	3	156259391	156259391	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:156259391C>T	ENST00000265044.2	-	0	2253					NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			ttagtagagacggggtttcac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850	6747			11325	protein-coding gene	gene with protein product		606213			NA		Standard	NM_007107	NM_007107	NA	Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.*1601G>A	chr3.hg19:g.156259391C>T		NA	B2R7D0|B4E2P2|D3DNK5|Q549M4	hg19	CCDS3176.1	0.02	-0.333044	AGAxGGG	COVERED																																																																																			NOVEL	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351521.1	4	3.307869	KEEP	0	0	0	11	300	CC	0.993072	0.846082	0		-	4	60	114	0	0	7.810712	33	60	1013	53	ENST00000265044.2	0.108108	0.851984
TIPARP	25976	__UNKNOWN__	__UNKNOWN__	3	156421320	156421320	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:156421320C>T	ENST00000461166.1	+	5	1943	c.1355C>T	c.(1354-1356)aCt>aTt	p.T452I	TIPARP_ENST00000542783.1_Missense_Mutation_p.T452I|TIPARP_ENST00000295924.7_Missense_Mutation_p.T452I|TIPARP_ENST00000486483.1_Missense_Mutation_p.T452I	NM_001184717.1	NP_001171646.1	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	452	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.	NA			androgen metabolic process (GO:0008209)|cellular response to organic cyclic compound (GO:0071407)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|multicellular organismal metabolic process (GO:0044236)|negative regulation of gene expression (GO:0010629)|nitrogen compound metabolic process (GO:0006807)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of protein catabolic process (GO:0045732)|post-embryonic development (GO:0009791)|protein ADP-ribosylation (GO:0006471)|skeletal system morphogenesis (GO:0048705)|smooth muscle tissue development (GO:0048745)|vasculogenesis (GO:0001570)	nucleus (GO:0005634)	enhancer binding (GO:0035326)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TACCCTGAAACTTGGGTTTAT	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(171;276 1987 3319 6837 11197)							NA				0													97	97	97			NA	NA	3		NA											NA				156421320		2203	4300	6503	SO:0001583	missense			BX537965	CCDS3177.1	3q25.31	2011-06-22			ENSG00000163659	ENSG00000163659	25976		Poly (ADP-ribose) polymerases	23696	protein-coding gene	gene with protein product		612480			NA	12851707	Standard	NM_015508	NM_001184717	NA	Approved	DKFZP434J214, DKFZp686N0351, DDF1, PARP7, PARP-7, PARP-1, pART14, RM1	uc021xgg.1	Q7Z3E1	OTTHUMG00000158646	ENST00000461166.1:c.1355C>T	chr3.hg19:g.156421320C>T	ENSP00000420612:p.Thr452Ile	NA	D3DNK6|Q68CY9|Q86VP4|Q9Y4P7	hg19	CCDS3177.1	0.02	3.493266	AAAxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.59	3.164816	0.57476	.	.	ENSG00000163659	ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000542783	T;T;T;T;T;T	0.26223	2.77;2.77;2.77;1.75;2.77;2.77	5.44	5.44	0.79542	Poly(ADP-ribose) polymerase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.34250	0.0891	M	0.74881	2.28	0.80722	D	1	P	0.35272	0.493	B	0.35931	0.214	T	0.10474	-1.0628	10	0.29301	T	0.29	.	18.8777	0.92345	0.0:1.0:0.0:0.0	.	452	Q7Z3E1	PARPT_HUMAN	I	452	ENSP00000418757:T452I;ENSP00000295924:T452I;ENSP00000420612:T452I;ENSP00000419982:T452I;ENSP00000418829:T452I;ENSP00000438345:T452I	ENSP00000295924:T452I	T	+	2	0	TIPARP	157904014	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.551000	0.86045	0.650000	0.86243	ACT	NOVEL	TIPARP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351618.1	1	4.814289	KEEP	0	0	0	16	488	CC	0.997832	0.9978	0		+	15	60	450	0	0	33.736886	86	60	2956	172	ENST00000461166.1	0.148515	0.999968
RP11-550I24.2	0	__UNKNOWN__	__UNKNOWN__	3	156921446	156921446	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:156921446T>C	ENST00000488040.1	+	0	43				RP11-550I24.2_ENST00000487238.1_RNA						NA		NA									NA						ccatgttgcctaggctggtct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000488040.1:	chr3.hg19:g.156921446T>C		NA		hg19		0.02	-0.236787	GCCxAGG	COVERED																																																																																			NOVEL	RP11-550I24.2-003	KNOWN	basic	antisense	NA	processed_transcript	OTTHUMT00000352025.1	8	4.210616	KEEP	0	0	0	14	384	TT	0.995343	0.609555	0		+	3	60	91	0	0	6.550892	22	60	645	60	ENST00000488040.1	0.12	0.612407
VEPH1	79674	__UNKNOWN__	__UNKNOWN__	3	157149895	157149895	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:157149895T>C	ENST00000362010.2	-	5	837				VEPH1_ENST00000543418.1_Intron|VEPH1_ENST00000392832.2_Intron|VEPH1_ENST00000392833.2_Intron	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	NA		NA				plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			cctcagcctctcaaagtgctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415	79674		Pleckstrin homology (PH) domain containing	25735	protein-coding gene	gene with protein product		609594	ventricular zone expressed PH domain homolog 1 (zebrafish)		NA	11214970, 15388229	Standard	NM_024621	NM_024621	NA	Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.530-3618A>G	chr3.hg19:g.157149895T>C		NA	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	hg19	CCDS3179.1	0.02	-0.175425	CTCxCAA	COVERED																																																																																			NOVEL	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351845.3	11	2.406522	KEEP	2	0	0	8	230	TT	0.99257	0.384528	0		-	3	60	107	0	0	8.53306	16	60	483	46	ENST00000362010.2	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	157556613	157556613	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:157556613A>G			NA	NA				C3orf55 (161075 upstream) : RN7SKP46 (91667 downstream)						NA		NA									NA						agccaggcacagtggctcacg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.157556613A>G		NA		hg19		0.02	-0.22804	CACxGTG	COVERED																																																																																			NOVEL					0			6	2.406114	KEEP	0	0	0	8	222	AA	0.99257	0.578599	0			3	60	88	0	0	6.429123	19	60	582	51		0.136364	0.58293
IQCJ-SCHIP1	100505385	__UNKNOWN__	__UNKNOWN__	3	159423534	159423534	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:159423534C>T	ENST00000485419.1	+	5	460				IQCJ-SCHIP1_ENST00000467442.1_Intron|IQCJ-SCHIP1_ENST00000527095.1_Intron|IQCJ-SCHIP1_ENST00000476809.1_Intron|IQCJ-SCHIP1_ENST00000337808.6_Intron|IQCJ-SCHIP1_ENST00000412423.2_Intron	NM_001197113.1	NP_001184042.1			IQCJ-SCHIP1 readthrough	NA		NA								central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(7)	12						ctcgctctgtcgcccaggctg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56289.1, CCDS56291.1	3q25.33	2011-03-24			ENSG00000250588	ENSG00000250588	100505385			38842	other	readthrough		NA			NA		Standard	NM_001197113	NM_001197113	NA	Approved		uc003fcq.2		OTTHUMG00000162426	ENST00000485419.1:c.292-58698C>T	chr3.hg19:g.159423534C>T		NA		hg19	CCDS56289.1	0.02	-0.377108	TGTxGCC	COVERED																																																																																			NOVEL	IQCJ-SCHIP1-001	KNOWN	basic|appris_candidate_longest|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368858.1	29	8.4235	KEEP	25	0	0	28	817	CC	0.999859	0.908941	0		+	4	60	105	1	0	6.916111	33	60	1054	110	ENST00000485419.1	0.108108	0.909069
IL12A-AS1	101928376	__UNKNOWN__	__UNKNOWN__	3	159632530	159632530	__UNKNOWN__	RNA	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:159632530A>T	ENST00000497452.1	-	0	1350									IL12A antisense RNA 1	NA		NA									NA						cggtggctcaagcttgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK097161		3q25.33	2013-09-02			ENSG00000244040	ENSG00000244040	101928376		Long non-coding RNAs	49094	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_108088	NA	Approved				OTTHUMG00000158951	ENST00000497452.1:	chr3.hg19:g.159632530A>T		NA		hg19		0.02	-0.149109	TCAxGCT	COVERED																																																																																			NOVEL	IL12A-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000352647.1	4	2.406781	KEEP	0	0	0	8	233	AA	0.99257	0.320408	0		-	3	60	91	0	0	7.179047	13	60	395	39	ENST00000497452.1	0.1875	0.322807
IL12A-AS1	101928376	__UNKNOWN__	__UNKNOWN__	3	159632533	159632533	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:159632533T>C	ENST00000497452.1	-	0	1350									IL12A antisense RNA 1	NA		NA									NA						tggctcaagcttgtaatccca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK097161		3q25.33	2013-09-02			ENSG00000244040	ENSG00000244040	101928376		Long non-coding RNAs	49094	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_108088	NA	Approved				OTTHUMG00000158951	ENST00000497452.1:	chr3.hg19:g.159632533T>C		NA		hg19		0.02	-0.157886	AGCxTGT	COVERED																																																																																			NOVEL	IL12A-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000352647.1	4	2.406205	KEEP	0	0	0	8	223	TT	0.99257	0.320408	0		-	4	60	141	0	0	11.980994	13	60	391	39	ENST00000497452.1	0.235294	0.322807
IL12A-AS1	101928376	__UNKNOWN__	__UNKNOWN__	3	159703899	159703899	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:159703899A>G	ENST00000497452.1	-	0	1350									IL12A antisense RNA 1	NA		NA									NA						agaccagcctaggcaacaaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK097161		3q25.33	2013-09-02			ENSG00000244040	ENSG00000244040	101928376		Long non-coding RNAs	49094	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_108088	NA	Approved				OTTHUMG00000158951	ENST00000497452.1:	chr3.hg19:g.159703899A>G		NA		hg19		0.02	-0.271859	CCTxGGC	COVERED																																																																																			NOVEL	IL12A-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000352647.1	12	3.609514	KEEP	0	0	0	12	337	AA	0.993634	0.712749	0		-	4	60	130	0	0	10.294957	19	60	560	64	ENST00000497452.1	0.173913	0.717315
CTD-2049J23.3	0	__UNKNOWN__	__UNKNOWN__	3	159736421	159736421	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:159736421A>G	ENST00000473137.1	+	2	57				IL12A-AS1_ENST00000497452.1_RNA						NA		NA									NA						tgggattacaagtgtgagcca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000473137.1:c.16-503A>G	chr3.hg19:g.159736421A>G		NA		hg19		0.02	-0.228065	ACAxGTG	COVERED																																																																																			NOVEL	CTD-2049J23.3-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000352656.1	7	2.706916	KEEP	3	0	0	9	253	AA	0.99257	0.578599	0		+	3	46	97	0	0	7.327028	19	60	593	55	ENST00000473137.1	0.136364	0.58293
KPNA4	3840	__UNKNOWN__	__UNKNOWN__	3	160214469	160214469	__UNKNOWN__	3'UTR	SNP	G	G	A	rs3732706	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:160214469G>A	ENST00000334256.4	-	0	7294					NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			GAAGTAATCTGGAGTAGGCAG	0.368		NA											G|||	1373	0.274161	0.1498	0.3501	5008	,	,	NA	20316	0.1815	NA	0.4314	False	NA	,,,	NA	NA	NA	2504	0.3221	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432	3840		Importins, Armadillo repeat containing	6397	protein-coding gene	gene with protein product		602970			NA	9168958, 9395085	Standard	NM_002268	NM_002268	NA	Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.*5423C>T	chr3.hg19:g.160214469G>A		NA	A8K4S6|D3DNM2|O00190	hg19	CCDS3191.1	0.02	1.441139	TCTxGAG	COVERED																																																																																			NOVEL	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352960.1	3	2.407149	KEEP	0	0	0	8	243	GG	0.99257	0.990784	0		-	33	60	999	0	0	94.340773	38	60	1299	120	ENST00000334256.4	0.464789	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	160328042	160328042	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:160328042G>A			NA	NA				KRT8P12 (42055 upstream) : ARL14 (66905 downstream)						NA		NA									NA						acagagtctcgctctgtcgcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.160328042G>A		NA		hg19		0.02	-0.219296	CTCxCTC	COVERED																																																																																			NOVEL					0			5	3.911281	KEEP	0	0	0	13	389	GG	0.995343	0.550313	0			3	60	88	0	0	6.792062	14	60	470	62		0.176471	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	160344911	160344911	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:160344911T>A			NA	NA				KRT8P12 (58924 upstream) : ARL14 (50036 downstream)						NA		NA									NA						catgttgtcctggctggtctc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.160344911T>A		NA		hg19		0.02	-0.149109	TCCxGGC	COVERED																																																																																			NOVEL					0			8	3.308283	KEEP	1	0	0	11	300	TT	0.993072	0.289978	0			3	60	91	0	0	7.179017	13	60	398	34		0.1875	0.292001
PPM1L	151742	__UNKNOWN__	__UNKNOWN__	3	160675657	160675657	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:160675657G>C	ENST00000498165.1	+	2	500				PPM1L_ENST00000497343.1_Intron|PPM1L_ENST00000464260.1_Intron|PPM1L_ENST00000295839.9_Intron|PPM1L_ENST00000480117.1_Intron	NM_139245.2	NP_640338.2	Q5SGD2	PPM1L_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1L	NA		NA			MAPK cascade (GO:0000165)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(1)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			agccactgcggccggcctctc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(86;250 1994 13715 43211)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055115	CCDS33886.1	3q26.1	2012-04-17	2010-03-05		ENSG00000163590	ENSG00000163590	151742	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	16381	protein-coding gene	gene with protein product	PP2Cepsilon, Protein phosphatase 2C epsilon isoform	611931	protein phosphatase 1 (formerly 2C)-like		NA	12556533	Standard	NM_139245	XM_006713507	NA	Approved	PP2CE	uc003fdr.3	Q5SGD2	OTTHUMG00000159048	ENST00000498165.1:c.400-3867G>C	chr3.hg19:g.160675657G>C		NA	Q2M3J2|Q96NM7	hg19	CCDS33886.1	0.02	-0.236832	GCGxCCG	COVERED																																																																																			NOVEL	PPM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353019.1	1	2.708031	KEEP	0	0	0	9	276	GG	0.99254	0.607839	0		+	3	60	102	1	0	7.594402	23	60	793	55	ENST00000498165.1	0.115385	0.612407
PPM1L	151742	__UNKNOWN__	__UNKNOWN__	3	160742472	160742472	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:160742472G>A	ENST00000498165.1	+	3	675				PPM1L_ENST00000464260.1_Intron|PPM1L_ENST00000295839.9_Intron|PPM1L_ENST00000480117.1_Intron	NM_139245.2	NP_640338.2	Q5SGD2	PPM1L_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1L	NA		NA			MAPK cascade (GO:0000165)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(1)|large_intestine(4)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			ggcaacaagagtgaaactcca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(86;250 1994 13715 43211)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055115	CCDS33886.1	3q26.1	2012-04-17	2010-03-05		ENSG00000163590	ENSG00000163590	151742	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	16381	protein-coding gene	gene with protein product	PP2Cepsilon, Protein phosphatase 2C epsilon isoform	611931	protein phosphatase 1 (formerly 2C)-like		NA	12556533	Standard	NM_139245	XM_006713507	NA	Approved	PP2CE	uc003fdr.3	Q5SGD2	OTTHUMG00000159048	ENST00000498165.1:c.575-40719G>A	chr3.hg19:g.160742472G>A		NA	Q2M3J2|Q96NM7	hg19	CCDS33886.1	0.02	-0.105263	AGAxTGA	UNCOVERED																																																																																			NOVEL	PPM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353019.1	6	2.406966	KEEP	2	0	0	8	242	GG	0.99257	0.138793	0		+	3	60	89	0	0	7.678313	7	60	237	32	ENST00000498165.1	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	160928935	160928935	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:160928935T>C			NA	NA				B3GALNT1 (105775 upstream) : NMD3 (10142 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.160928935T>C		NA		hg19		0.02	-0.245579	TCAxGCC	COVERED																																																																																			NOVEL					0			12	4.209335	KEEP	0	0	0	14	374	TT	0.995343	0.638361	0			3	60	89	0	0	6.466001	20	60	590	59		0.130435	0.641347
RP11-10O22.1	0	__UNKNOWN__	__UNKNOWN__	3	162795459	162795459	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:162795459C>T	ENST00000490357.1	+	0	103										NA		NA									NA						ttagtagagacggggtttcac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000490357.1:	chr3.hg19:g.162795459C>T		NA		hg19		0.02	-0.122738	AGAxGGG	COVERED																																																																																			NOVEL	RP11-10O22.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000350008.1	3	2.707749	KEEP	1	0	0	9	266	CC	0.99257	0.194853	0		+	4	60	96	0	0	7.869498	10	60	321	28	ENST00000490357.1	0.285714	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	163175409	163175409	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:163175409C>T			NA	NA				CT64 (154320 upstream) : RP11-418B12.1 (17445 downstream)						NA		NA									NA						tggtggctcacgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.163175409C>T		NA		hg19		0.02	-0.201718	TCAxGCC	COVERED																																																																																			NOVEL					0			8	4.513158	KEEP	0	0	0	15	454	CC	0.99649	0.488823	0			3	60	96	0	0	7.433551	16	60	519	56		0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	164258820	164258820	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:164258820A>G			NA	NA				MIR720 (199582 upstream) : RP11-71H9.2 (129845 downstream)						NA		NA									NA						tgtaatcccaacactttgggt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.164258820A>G		NA		hg19		0.02	-0.149102	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			5	2.405746	KEEP	1	0	0	8	220	AA	0	0	0			3	60	92	0	0	7.279243	13	60	392	36		0.1875	0.292001
GOLIM4	27333	__UNKNOWN__	__UNKNOWN__	3	167773308	167773308	__UNKNOWN__	Intron	SNP	C	C	T	rs577631462		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:167773308C>T	ENST00000309027.4	-	2	246				GOLIM4_ENST00000470487.1_Intron			O00461	GOLI4_HUMAN	golgi integral membrane protein 4	NA		NA			transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						gactcagggccgggcgcggtg	0.507		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17734	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905	27333			15448	protein-coding gene	gene with protein product		606805	golgi phosphoprotein 4	GOLPH4	NA	9201717, 15004235	Standard		NM_014498	NA	Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000309027.4:c.188-7155G>A	chr3.hg19:g.167773308C>T		NA		hg19		0.02	-0.236854	GGCxGGG	COVERED																																																																																			NOVEL	GOLIM4-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351279.1	8	2.708034	KEEP	0	0	0	9	274	CC	0.99254	0.607839	0		-	3	60	93	0	0	6.749318	22	60	742	54	ENST00000309027.4	0.12	0.612407
GOLIM4	27333	__UNKNOWN__	__UNKNOWN__	3	167788135	167788135	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:167788135T>C	ENST00000309027.4	-	2	246				GOLIM4_ENST00000470487.1_Intron			O00461	GOLI4_HUMAN	golgi integral membrane protein 4	NA		NA			transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						aagccgagattgcaccactgc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905	27333			15448	protein-coding gene	gene with protein product		606805	golgi phosphoprotein 4	GOLPH4	NA	9201717, 15004235	Standard		NM_014498	NA	Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000309027.4:c.188-21982A>G	chr3.hg19:g.167788135T>C		NA		hg19		0.02	-0.175418	GATxGCA	COVERED																																																																																			NOVEL	GOLIM4-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351279.1	10	3.90859	KEEP	2	0	0	13	341	TT	0.993072	0.384723	0		-	3	60	93	0	0	7.133685	16	60	480	44	ENST00000309027.4	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	168286375	168286375	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:168286375A>C			NA	NA				MIR551B (16638 upstream) : EGFEM1P (238965 downstream)						NA		NA									NA						tcccaagtagataggactaca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.168286375A>C		NA		hg19		0.02	-0.298163	TAGxTAG	COVERED																																																																																			NOVEL					0			15	2.403675	KEEP	0	0	0	8	208	AA	0.99257	0.775257	0			3	60	96	0	0	6.893095	25	60	746	55		0.107143	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	168523813	168523813	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:168523813C>T			NA	NA				MIR551B (254076 upstream) : EGFEM1P (1527 downstream)						NA		NA									NA						agggtctcgccctgtcaccca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.168523813C>T		NA		hg19		0.02	-0.11404	CGCxCTG	UNCOVERED																																																																																			NOVEL					0			7	2.40744	KEEP	0	0	0	8	255	CC	0.99257	0.16126	0			3	60	95	0	0	8.000934	9	60	304	32		0.25	0.162467
ACTRT3	84517	__UNKNOWN__	__UNKNOWN__	3	169486584	169486584	__UNKNOWN__	Intron	SNP	A	A	G	rs200854017		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169486584A>G	ENST00000330368.2	-	2	575					NM_032487.4	NP_115876.3	Q9BYD9	ACTT3_HUMAN	actin-related protein T3	NA		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)					NA						ccaaagtgctaggattacagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055346	CCDS3206.1	3q26.2	2012-04-10			ENSG00000184378	ENSG00000184378	84517			24022	protein-coding gene	gene with protein product	actin related protein M1	608534			NA	11750065, 18692047	Standard	NM_032487	NM_032487	NA	Approved	ARPM1	uc003ffs.2	Q9BYD9		ENST00000330368.2:c.201-446T>C	chr3.hg19:g.169486584A>G		NA	Q96IS0|Q96NJ0	hg19	CCDS3206.1	0.02	-0.254334	GCTxGGA	COVERED																																																																																			NOVEL	ACTRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467797.1	6	2.405352	KEEP	0	0	0	8	211	AA	0.99257	0.663556	0		-	3	60	102	0	0	7.492368	25	60	734	51	ENST00000330368.2	0.107143	0.668523
LRRC31	79782	__UNKNOWN__	__UNKNOWN__	3	169585380	169585380	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169585380T>C	ENST00000316428.5	-	1	233				LRRC31_ENST00000523069.1_Intron|LRRC31_ENST00000264676.5_Intron|LRRC31_ENST00000397805.2_Intron	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	NA		NA								cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			aggctggtcttaaactactgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248	79782			26261	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_024727	NM_001277127	NA	Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.175+2040A>G	chr3.hg19:g.169585380T>C		NA	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	hg19	CCDS43167.1	0.02	-0.33328	TCTxAAA	COVERED																																																																																			NOVEL	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378699.1	16	4.510979	KEEP	0	0	0	15	405	TT	0.99649	0.848994	0		-	3	60	96	0	0	6.798531	27	60	805	83	ENST00000316428.5	0.1	0.851984
LRRC31	79782	__UNKNOWN__	__UNKNOWN__	3	169585416	169585416	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169585416T>C	ENST00000316428.5	-	1	233				LRRC31_ENST00000523069.1_Intron|LRRC31_ENST00000264676.5_Intron|LRRC31_ENST00000397805.2_Intron	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	NA		NA								cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			ctgcctcagcttgccaaagtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248	79782			26261	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_024727	NM_001277127	NA	Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.175+2004A>G	chr3.hg19:g.169585416T>C		NA	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	hg19	CCDS43167.1	0.02	-0.210456	AGCxTGC	COVERED																																																																																			NOVEL	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378699.1	7	2.707227	KEEP	0	0	0	9	255	TT	0.99254	0.518266	0		-	3	60	104	0	0	8.09242	18	60	536	44	ENST00000316428.5	0.142857	0.522161
LRRC31	79782	__UNKNOWN__	__UNKNOWN__	3	169585418	169585418	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169585418G>C	ENST00000316428.5	-	1	233				LRRC31_ENST00000523069.1_Intron|LRRC31_ENST00000264676.5_Intron|LRRC31_ENST00000397805.2_Intron	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	NA		NA								cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			gcctcagcttgccaaagtgct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248	79782			26261	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_024727	NM_001277127	NA	Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.175+2002C>G	chr3.hg19:g.169585418G>C		NA	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	hg19	CCDS43167.1	0.02	-0.184222	CTTxCCA	COVERED																																																																																			NOVEL	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378699.1	6	2.707904	KEEP	0	0	0	9	273	GG	0.99254	0.420319	0		-	3	60	102	0	0	8.109771	15	60	502	41	ENST00000316428.5	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	169719205	169719205	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169719205A>G			NA	NA				SEC62 (3044 upstream) : GPR160 (36511 downstream)						NA		NA									NA						aggccgaggcaggtggatcat	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.169719205A>G		NA		hg19		0.02	-0.201723	GGCxGGT	COVERED																																																																																			NOVEL					0			8	3.008217	KEEP	6	0	0	10	285	AA	0.99254	0.486885	0			3	60	91	0	0	6.793138	18	60	537	56		0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	169723606	169723606	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169723606C>G			NA	NA				SEC62 (7445 upstream) : GPR160 (32110 downstream)						NA		NA									NA						gagcccaggacttcaagacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.169723606C>G		NA		hg19		0.02	-0.315811	GGAxTTC	COVERED																																																																																			NOVEL					0			11	2.708189	KEEP	0	0	0	9	282	CC	0.99254	0.812359	0			3	60	93	0	0	6.41146	29	60	1009	69		0.09375	0.818465
PHC3	80012	__UNKNOWN__	__UNKNOWN__	3	169842208	169842208	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169842208C>T	ENST00000495893.2	-	9	1820				PHC3_ENST00000494943.1_Intron|PHC3_ENST00000467570.1_Intron	NM_024947.3	NP_079223.3	Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	NA		NA			multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			tctcactctgctgcccaggct	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889	80012		Sterile alpha motif (SAM) domain containing	15682	protein-coding gene	gene with protein product	early development regulator 3, polyhomeotic like 3	NA	polyhomeotic like 3 (Drosophila)		NA	12167701, 12384788	Standard	NM_024947	NM_024947	NA	Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000495893.2:c.1789-1676G>A	chr3.hg19:g.169842208C>T		NA	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	hg19	CCDS46952.1	0.02	-0.140355	CTGxTGC	COVERED																																																																																			NOVEL	PHC3-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352186.3	9	2.407059	KEEP	0	0	0	8	242	CC	0.99257	0.259026	0		-	4	60	116	0	0	9.730671	11	60	386	32	ENST00000495893.2	0.266667	0.260965
PHC3	80012	__UNKNOWN__	__UNKNOWN__	3	169867524	169867524	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169867524A>G	ENST00000495893.2	-	5	446				PHC3_ENST00000494943.1_Intron|PHC3_ENST00000467570.1_Intron|PHC3_ENST00000474275.1_Intron	NM_024947.3	NP_079223.3	Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	NA		NA			multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			gattacaggcatgagccactg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889	80012		Sterile alpha motif (SAM) domain containing	15682	protein-coding gene	gene with protein product	early development regulator 3, polyhomeotic like 3	NA	polyhomeotic like 3 (Drosophila)		NA	12167701, 12384788	Standard	NM_024947	NM_024947	NA	Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000495893.2:c.415-492T>C	chr3.hg19:g.169867524A>G		NA	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	hg19	CCDS46952.1	0.02	-0.280643	GGCxTGA	COVERED																																																																																			NOVEL	PHC3-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352186.3	12	4.812355	KEEP	2	0	0	16	448	AA	0.99649	0.737075	0		-	3	60	99	0	0	7.294926	23	60	660	73	ENST00000495893.2	0.115385	0.739671
PHC3	80012	__UNKNOWN__	__UNKNOWN__	3	169886291	169886291	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169886291C>T	ENST00000495893.2	-	4	446				PHC3_ENST00000494943.1_Intron|PHC3_ENST00000467570.1_Intron|PHC3_ENST00000474275.1_Intron	NM_024947.3	NP_079223.3	Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	NA		NA			multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			cggtggctcacgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889	80012		Sterile alpha motif (SAM) domain containing	15682	protein-coding gene	gene with protein product	early development regulator 3, polyhomeotic like 3	NA	polyhomeotic like 3 (Drosophila)		NA	12167701, 12384788	Standard	NM_024947	NM_024947	NA	Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000495893.2:c.414+2869G>A	chr3.hg19:g.169886291C>T		NA	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	hg19	CCDS46952.1	0.02	-0.324551	TCAxGCC	COVERED																																																																																			NOVEL	PHC3-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352186.3	9	4.812802	KEEP	4	0	0	16	466	CC	0.995343	0.831824	0		-	3	60	93	0	0	6.410147	29	60	962	90	ENST00000495893.2	0.09375	0.835716
PHC3	80012	__UNKNOWN__	__UNKNOWN__	3	169890777	169890777	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169890777A>G	ENST00000495893.2	-	3	212				PHC3_ENST00000481639.1_Intron|PHC3_ENST00000494943.1_Intron|PHC3_ENST00000467570.1_Intron|PHC3_ENST00000497658.1_Intron|PHC3_ENST00000474275.1_Intron	NM_024947.3	NP_079223.3	Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	NA		NA			multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			tcaggagatcaagaccatcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889	80012		Sterile alpha motif (SAM) domain containing	15682	protein-coding gene	gene with protein product	early development regulator 3, polyhomeotic like 3	NA	polyhomeotic like 3 (Drosophila)		NA	12167701, 12384788	Standard	NM_024947	NM_024947	NA	Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000495893.2:c.181-277T>C	chr3.hg19:g.169890777A>G		NA	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	hg19	CCDS46952.1	0.02	-0.21922	ATCxAGA	UNCOVERED																																																																																			NOVEL	PHC3-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352186.3	10	2.40452	KEEP	2	0	0	8	207	AA	0	0	0		-	3	60	95	0	0	7.006737	21	60	593	43	ENST00000495893.2	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	169908592	169908592	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169908592A>G			NA	NA				PHC3 (9055 upstream) : PRKCI (31560 downstream)						NA		NA									NA						ggatcacgagatcaggagttc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.169908592A>G		NA		hg19		0.02	-0.219132	GAGxTCA	COVERED																																																																																			NOVEL					0			10	2.706097	KEEP	0	0	0	9	237	AA	0.99254	0.548763	0			3	60	101	0	0	7.861959	17	60	471	49		0.15	0.552887
PRKCI	5584	__UNKNOWN__	__UNKNOWN__	3	169965043	169965043	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:169965043T>C	ENST00000295797.4	+	2	528					NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	NA		NA			actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	gggatcttgctatgttgccca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	5584	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E	NA	7607695, 11978974	Standard	NM_002740	NM_002740	NA	Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.223+11904T>C	chr3.hg19:g.169965043T>C		NA	D3DNQ4|Q8WW06	hg19	CCDS3212.2	0.02	-0.228033	TGCxATG	COVERED																																																																																			NOVEL	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316866.3	13	2.705796	KEEP	0	0	0	9	237	TT	0.99254	0.578582	0		+	3	60	91	0	0	6.666144	20	60	590	45	ENST00000295797.4	0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	170031285	170031285	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:170031285T>C			NA	NA				PRKCI (7516 upstream) : RP11-543D10.2 (32180 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.170031285T>C		NA		hg19		0.02	-0.333319	ATCxCAG	COVERED																																																																																			NOVEL					0			13	3.007507	KEEP	1	0	0	10	273	TT	0.992708	0.845771	0			5	60	162	0	0	12.63922	26	60	805	69		0.16129	0.851984
SKIL	6498	__UNKNOWN__	__UNKNOWN__	3	170085153	170085153	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:170085153A>G	ENST00000426052.2	+	3	1270				SKIL_ENST00000259119.4_Intron|SKIL_ENST00000458537.3_Intron|SKIL_ENST00000413427.2_Intron	NM_001145098.2	NP_001138570.1	P12757	SKIL_HUMAN	SKI-like proto-oncogene	NA		NA			blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ccaaagtgctaggattacagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603	6498		SKI transcriptional corepressors	10897	protein-coding gene	gene with protein product		165340	SKI-like oncogene		NA	2762147	Standard	NM_005414	NM_005414	NA	Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000426052.2:c.1038+5936A>G	chr3.hg19:g.170085153A>G		NA	A6NGT1|B4DT50|O00464|P12756|Q07501	hg19	CCDS46954.1	0.02	-0.306975	GCTxGGA	COVERED																																																																																			NOVEL	SKIL-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352405.2	6	2.40575	KEEP	0	0	0	8	217	AA	0.99257	0.7943	0		+	3	60	104	0	0	7.742201	24	60	719	61	ENST00000426052.2	0.111111	0.800245
SKIL	6498	__UNKNOWN__	__UNKNOWN__	3	170085337	170085337	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:170085337T>C	ENST00000426052.2	+	3	1270				SKIL_ENST00000259119.4_Intron|SKIL_ENST00000458537.3_Intron|SKIL_ENST00000413427.2_Intron	NM_001145098.2	NP_001138570.1	P12757	SKIL_HUMAN	SKI-like proto-oncogene	NA		NA			blastocyst formation (GO:0001825)|cell cycle arrest (GO:0007050)|gene expression (GO:0010467)|lens fiber cell differentiation (GO:0070306)|lymphocyte homeostasis (GO:0002260)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of axonogenesis (GO:0050772)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|protein heterotrimerization (GO:0070208)|protein homotrimerization (GO:0070207)|regulation of apoptotic process (GO:0042981)|response to antibiotic (GO:0046677)|response to cytokine (GO:0034097)|response to growth factor (GO:0070848)|skeletal muscle tissue development (GO:0007519)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	25	all_cancers(22;7.13e-23)|all_epithelial(15;9.95e-28)|all_lung(20;1.23e-16)|Lung NSC(18;5.15e-16)|Ovarian(172;0.000337)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			tcactgcaacttccgcctccc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X15217	CCDS33890.1, CCDS46953.1, CCDS46954.1	3q26	2014-06-25	2014-06-25		ENSG00000136603	ENSG00000136603	6498		SKI transcriptional corepressors	10897	protein-coding gene	gene with protein product		165340	SKI-like oncogene		NA	2762147	Standard	NM_005414	NM_005414	NA	Approved	SNO, SnoN, SnoA	uc003fgw.3	P12757	OTTHUMG00000158831	ENST00000426052.2:c.1038+6120T>C	chr3.hg19:g.170085337T>C		NA	A6NGT1|B4DT50|O00464|P12756|Q07501	hg19	CCDS46954.1	0.02	-0.298006	AACxTCC	COVERED																																																																																			NOVEL	SKIL-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352405.2	7	2.406114	KEEP	0	0	0	8	220	TT	0.99257	0.775257	0		+	4	60	121	0	0	8.897093	26	60	759	62	ENST00000426052.2	0.133333	0.78106
CLDN11	5010	__UNKNOWN__	__UNKNOWN__	3	170151149	170151149	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:170151149G>A	ENST00000064724.3	+	0	1431				CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000489485.1_3'UTR	NM_005602.5	NP_005593.2	O75508	CLD11_HUMAN	claudin 11	NA		NA			axon ensheathment (GO:0008366)|calcium-independent cell-cell adhesion (GO:0016338)|spermatogenesis (GO:0007283)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|liver(2)|lung(3)|ovary(2)	12	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			ggttggtctcgaactcctgga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF068863	CCDS3213.1	3q26.2-q26.3	2008-08-01	2008-08-01		ENSG00000013297	ENSG00000013297	5010		Claudins	8514	protein-coding gene	gene with protein product		601326	oligodendrocyte transmembrane protein	OTM	NA	8661061, 8797478	Standard	NM_005602	NM_005602	NA	Approved	OSP	uc003fgx.3	O75508	OTTHUMG00000158940	ENST00000064724.3:c.*605G>A	chr3.hg19:g.170151149G>A		NA	B2R7C1|D3DNQ5|Q5U0P3	hg19	CCDS3213.1	0.02	2.877053	CTCxAAC	COVERED																																																																																			NOVEL	CLDN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352403.1	40	18.049527	KEEP	0	0	0	60	1753	GG	1	1	0		+	7	60	208	0	0	12.674912	109	60	3452	268	ENST00000064724.3	0.060345	1
TNIK	23043	__UNKNOWN__	__UNKNOWN__	3	170838401	170838401	__UNKNOWN__	Intron	SNP	C	C	G	rs13085904	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:170838401C>G	ENST00000436636.2	-	18	2465				TNIK_ENST00000341852.6_Intron|TNIK_ENST00000460047.1_Intron|TNIK_ENST00000475336.1_Intron|TNIK_ENST00000488470.1_Intron|TNIK_ENST00000284483.8_Intron|TNIK_ENST00000357327.5_Intron|TNIK_ENST00000369326.5_Intron|TNIK_ENST00000470834.1_Intron|TNIK_ENST00000538048.1_Intron	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	NA		NA			actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			agccaccgcgcccggccTCTT	0.483		NA											C|||	1946	0.388578	0.0877	0.4539	5008	,	,	NA	15386	0.5417	NA	0.5487	False	NA	,,,	NA	NA	NA	2504	0.4264	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310	23043			30765	protein-coding gene	gene with protein product		610005			NA	9628581, 10521462	Standard	XM_039796	NR_027767	NA	Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.2120+2983G>C	chr3.hg19:g.170838401C>G		NA	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	hg19	CCDS46956.1	0.02	-0.184211	GCGxCCG	UNCOVERED																																																																																			NOVEL	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352973.2	3	2.707885	KEEP	4	0	0	9	271	CC	0	0	0		-	10	60	351	0	0	34.162517	9	60	311	50	ENST00000436636.2	0.526316	0.423478
TNIK	23043	__UNKNOWN__	__UNKNOWN__	3	171042683	171042683	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:171042683C>T	ENST00000436636.2	-	2	468				TNIK_ENST00000341852.6_Intron|TNIK_ENST00000460047.1_Intron|TNIK_ENST00000475336.1_Intron|TNIK_ENST00000488470.1_Intron|TNIK_ENST00000284483.8_Intron|TNIK_ENST00000357327.5_Intron|TNIK_ENST00000369326.5_Intron|TNIK_ENST00000538048.1_Intron|TNIK_ENST00000470834.1_Intron	NM_015028.2	NP_055843.1	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase	NA		NA			actin cytoskeleton reorganization (GO:0031532)|activation of JNKK activity (GO:0007256)|cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite morphogenesis (GO:0048814)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			gtcaggagatcgagaccatcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF172264	CCDS46956.1, CCDS54673.1, CCDS54674.1, CCDS54675.1, CCDS54676.1, CCDS54677.1, CCDS54678.1, CCDS54679.1	3q26.31	2008-01-23			ENSG00000154310	ENSG00000154310	23043			30765	protein-coding gene	gene with protein product		610005			NA	9628581, 10521462	Standard	XM_039796	NR_027767	NA	Approved	KIAA0551	uc003fhh.2	Q9UKE5	OTTHUMG00000159036	ENST00000436636.2:c.123+44725G>A	chr3.hg19:g.171042683C>T		NA	A7E2A3|A8K4U1|D3DNQ6|O60298|Q8WUY7|Q9UKD8|Q9UKD9|Q9UKE0|Q9UKE1|Q9UKE2|Q9UKE3|Q9UKE4	hg19	CCDS46956.1	0.02	-0.219287	GATxGAG	UNCOVERED																																																																																			NOVEL	TNIK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352973.2	13	2.706886	KEEP	8	0	0	9	251	CC	0	0	0		-	3	50	90	0	0	6.50643	21	60	663	51	ENST00000436636.2	0.125	0.552887
TMEM212	389177	__UNKNOWN__	__UNKNOWN__	3	171573232	171573232	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:171573232A>G	ENST00000334567.5	+	4	578					NM_001164436.1	NP_001157908.1	A6NML5	TM212_HUMAN	transmembrane protein 212	NA		NA				integral component of membrane (GO:0016021)				endometrium(1)	1						gtgaaaccccatctctactaa	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46958.1	3q26.31	2010-06-22			ENSG00000186329	ENSG00000186329	389177			34295	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001164436	NA	Approved	FLJ23172	uc003fhw.2	A6NML5	OTTHUMG00000156839	ENST00000334567.5:c.544-1221A>G	chr3.hg19:g.171573232A>G		NA		hg19	CCDS46958.1	0.02	-0.131516	CCCxTCT	COVERED																																																																																			NOVEL	TMEM212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346158.1	5	2.404561	KEEP	0	0	0	8	206	AA	0.99257	0.22747	0		+	3	60	92	0	0	7.832621	8	60	230	27	ENST00000334567.5	0.272727	0.229173
FNDC3B	64778	__UNKNOWN__	__UNKNOWN__	3	171981807	171981807	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:171981807T>C	ENST00000336824.4	+	6	889				FNDC3B_ENST00000416957.1_Intron|FNDC3B_ENST00000415807.2_Intron	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	NA		NA			cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		gacagggtcttgctctgttac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420	64778		Fibronectin type III domain containing	24670	protein-coding gene	gene with protein product		611909			NA	15527760	Standard	NM_022763	NM_022763	NA	Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.790+12476T>C	chr3.hg19:g.171981807T>C		NA	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	hg19	CCDS3217.1	0.02	-0.184145	TCTxGCT	COVERED																																																																																			NOVEL	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345618.2	10	2.406046	KEEP	0	0	0	8	221	TT	0.99257	0.420331	0		+	3	60	91	1	1	7.011181	15	60	419	36	ENST00000336824.4	0.166667	0.423478
FNDC3B	64778	__UNKNOWN__	__UNKNOWN__	3	172032916	172032916	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172032916T>C	ENST00000336824.4	+	11	1353				FNDC3B_ENST00000416957.1_Intron|FNDC3B_ENST00000415807.2_Intron	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	NA		NA			cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		cctgtaatcctagcactttgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420	64778		Fibronectin type III domain containing	24670	protein-coding gene	gene with protein product		611909			NA	15527760	Standard	NM_022763	NM_022763	NA	Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1254+4245T>C	chr3.hg19:g.172032916T>C		NA	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	hg19	CCDS3217.1	0.02	-0.289402	TCCxAGC	COVERED																																																																																			NOVEL	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345618.2	11	3.60936	KEEP	0	0	0	12	333	TT	0.993634	0.756043	0		+	4	60	113	0	0	8.097722	26	60	770	66	ENST00000336824.4	0.133333	0.760887
FNDC3B	64778	__UNKNOWN__	__UNKNOWN__	3	172035013	172035013	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172035013G>A	ENST00000336824.4	+	11	1353				AC092964.1_ENST00000366261.2_Missense_Mutation_p.A20T|FNDC3B_ENST00000416957.1_Intron|FNDC3B_ENST00000415807.2_Intron	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	NA		NA			cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		ttgctctgtcgcccaggctgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420	64778		Fibronectin type III domain containing	24670	protein-coding gene	gene with protein product		611909			NA	15527760	Standard	NM_022763	NM_022763	NA	Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1254+6342G>A	chr3.hg19:g.172035013G>A		NA	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	hg19	CCDS3217.1	0.02	2.112285	GTCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.631055	0.00813	.	.	ENSG00000203443	ENST00000366261	T	0.48522	0.81	0.113	-0.226	0.13106	.	.	.	.	.	T	0.21509	0.0518	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.19289	-1.0310	5	0.14252	T	0.57	.	.	.	.	.	.	.	.	T	20	ENSP00000388733:A20T	ENSP00000388733:A20T	A	+	1	0	AC092964.1	173517707	0.006000	0.16342	0.009000	0.14445	0.009000	0.06853	-0.888000	0.04148	-1.482000	0.01860	-1.497000	0.00963	GCC	NOVEL	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345618.2	29	10.546884	KEEP	2	7	167	95	2713	GG	1	1	0		+	7	60	174	2	0	9.051172	120	60	3737	336	ENST00000336824.4	0.055118	1
FNDC3B	64778	__UNKNOWN__	__UNKNOWN__	3	172035034	172035034	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172035034T>C	ENST00000336824.4	+	11	1353				AC092964.1_ENST00000366261.2_Splice_Site|FNDC3B_ENST00000416957.1_Intron|FNDC3B_ENST00000415807.2_Intron	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	NA		NA			cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		agtgcagtggtgcgatctcag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420	64778		Fibronectin type III domain containing	24670	protein-coding gene	gene with protein product		611909			NA	15527760	Standard	NM_022763	NM_022763	NA	Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1254+6363T>C	chr3.hg19:g.172035034T>C		NA	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	hg19	CCDS3217.1	0.02	1.391537	TGGxGCG	COVERED																																																																																			NOVEL	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345618.2	5	2.4961	KEEP	2	6	151	62	1726	TT	1	0.999881	0		+	5	60	140	0	0	8.372736	72	60	2100	176	ENST00000336824.4	0.064935	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	172149319	172149319	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172149319T>C			NA	NA				FNDC3B (29864 upstream) : GHSR (13603 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.172149319T>C		NA		hg19		0.02	-0.236777	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			8	2.405363	KEEP	1	0	0	8	219	TT	0	0	0			3	60	103	0	0	7.805624	21	60	615	49		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	172216100	172216100	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172216100T>C			NA	NA				GHSR (49854 upstream) : TNFSF10 (7197 downstream)						NA		NA									NA						aggatggtcttgatctcctga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.172216100T>C		NA		hg19		0.02	-0.192931	TCTxGAT	COVERED																																																																																			NOVEL					0			10	3.00701	KEEP	6	0	0	10	271	TT	0.99257	0.454356	0			3	60	91	1	0	6.861899	17	60	483	51		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	172321114	172321114	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172321114A>G			NA	NA				RP11-408H1.3 (8654 upstream) : NCEH1 (26924 downstream)						NA		NA									NA						gtgtgtgtgtacgtgCACAAA	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.172321114A>G		NA		hg19		0.02	1.711075	TGTxCGT	COVERED																																																																																			NOVEL					0			15	10.496496	KEEP	8	0	0	35	897	AA	0.999997	0.99899	0			4	60	138	0	0	8.924669	72	60	1674	148		0.052632	0.998993
NCEH1	57552	__UNKNOWN__	__UNKNOWN__	3	172358320	172358320	__UNKNOWN__	Intron	SNP	C	C	T	rs234005	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172358320C>T	ENST00000475381.1	-	4	671				NCEH1_ENST00000273512.3_Intron|NCEH1_ENST00000543711.1_Intron|NCEH1_ENST00000538775.1_Intron			Q6PIU2	NCEH1_HUMAN	neutral cholesterol ester hydrolase 1	NA		NA			lipid catabolic process (GO:0016042)|protein dephosphorylation (GO:0006470)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carboxylic ester hydrolase activity (GO:0052689)|phosphate ion binding (GO:0042301)|serine hydrolase activity (GO:0017171)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15						tattttgagacggagtctcgc	0.468		NA											C|||	1262	0.251997	0.1876	0.2579	5008	,	,	NA	12755	0.3026	NA	0.3131	False	NA	,,,	NA	NA	NA	2504	0.2198	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037784	CCDS54681.1, CCDS54682.1	3q26.31	2009-07-23	2009-07-23	2009-07-23	ENSG00000144959	ENSG00000144959	57552			29260	protein-coding gene	gene with protein product		613234	arylacetamide deacetylase-like 1	AADACL1	NA	10718198	Standard	NM_020792	NM_001146276	NA	Approved	KIAA1363, NCEH	uc011bpx.2	Q6PIU2	OTTHUMG00000156872	ENST00000475381.1:c.438-4443G>A	chr3.hg19:g.172358320C>T		NA	B7Z2K4|B7Z3A1|B7Z5U2|B7Z906|B7ZAW6|F5H7K4|Q86WZ1|Q9P2I4	hg19		0.02	-0.052623	AGAxGGA	UNCOVERED																																																																																			NOVEL	NCEH1-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000346367.3	4	2.407311	KEEP	5	0	0	8	249	CC	0	0	0		-	3	60	84	0	0	8.023835	3	48	99	25	ENST00000475381.1	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	172432142	172432142	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172432142C>T			NA	NA				NCEH1 (3134 upstream) : ECT2 (36329 downstream)						NA		NA									NA						tgcttgaacccgggaggtgga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.172432142C>T		NA		hg19		0.02	-0.192985	ACCxGGG	UNCOVERED																																																																																			NOVEL					0			14	2.406168	KEEP	4	0	0	8	227	CC	0	0	0			3	37	92	0	0	6.961061	17	60	559	39		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	172433920	172433920	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:172433920A>G			NA	NA				NCEH1 (4912 upstream) : ECT2 (34551 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.172433920A>G		NA		hg19		0.02	-0.245604	GCTxGGA	COVERED																																																																																			NOVEL					0			6	2.706792	KEEP	2	0	0	9	247	AA	0.99254	0.636563	0			5	60	175	0	0	14.65645	18	60	549	56		0.217391	0.641347
NLGN1	22871	__UNKNOWN__	__UNKNOWN__	3	173137486	173137486	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:173137486C>T	ENST00000457714.1	+	2	40					NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	NA		NA			alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			cctggttgggcgtggtggctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760	22871			14291	protein-coding gene	gene with protein product		600568			NA	10767552, 10819331	Standard	NM_014932	NM_014932	NA	Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.-389-15314C>T	chr3.hg19:g.173137486C>T		NA	Q9UPT2	hg19	CCDS3222.1	0.02	-0.21033	GGGxGTG	COVERED																																																																																			NOVEL	NLGN1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347054.3	8	3.608498	KEEP	1	0	0	12	343	CC	0.993072	0.518544	0		+	3	60	89	0	0	6.592882	18	60	595	53	ENST00000457714.1	0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	176072314	176072314	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:176072314G>T			NA	NA				RP11-809F4.3 (413489 upstream) : RP11-71G7.1 (249616 downstream)						NA		NA									NA						ggattacaggggtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.176072314G>T		NA		hg19		0.02	-0.175448	AGGxGTG	COVERED																																																																																			NOVEL					0			9	2.40746	KEEP	1	0	0	8	256	CG	0.99257	0.454356	0			3	60	88	0	0	6.561426	17	60	584	46		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	176719632	176719632	__UNKNOWN__	IGR	SNP	G	G	A	rs150400733	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:176719632G>A			NA	NA				RP11-644C3.1 (134006 upstream) : TBL1XR1 (17510 downstream)						NA		NA									NA						cccaggaagcggaggctgcag	0.498		NA											G|||	7	0.00139776	0.0045	0.0014	5008	,	,	NA	17361	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.176719632G>A		NA		hg19		0.02	-0.096486	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.406539	KEEP	0	0	0	8	229	GG	0.99257	0.119541	0			3	60	91	0	0	7.878494	7	60	220	24		0.3	0.120436
KCNMB2	10242	__UNKNOWN__	__UNKNOWN__	3	178479953	178479953	__UNKNOWN__	Intron	SNP	C	C	T	rs142732716	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:178479953C>T	ENST00000432997.1	+	2	285				RP11-385J1.2_ENST00000451742.1_RNA|RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000421498.1_RNA|RP11-385J1.2_ENST00000432385.1_RNA|KCNMB2_ENST00000452583.1_Intron|KCNMB2_ENST00000420517.2_Intron|KCNMB2_ENST00000470361.2_Intron|RP11-385J1.2_ENST00000437488.1_RNA	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	NA		NA			action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	agcgagactccgtctcaaaaa	0.517		NA											C|||	5	0.000998403	0.0	0.0029	5008	,	,	NA	17699	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584	10242		Potassium channels	6286	protein-coding gene	gene with protein product		605214			NA	10097176	Standard	NM_181361	NM_181361	NA	Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.-67-45178C>T	chr3.hg19:g.178479953C>T		NA	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	hg19	CCDS3223.1	0.02	-0.140352	CTCxGTC	COVERED																																																																																			NOVEL	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348251.1	7	2.705407	KEEP	2	0	0	9	242	CC	0.99257	0.259026	0		+	4	60	123	0	1	10.430887	11	60	363	37	ENST00000432997.1	0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	179034742	179034742	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:179034742G>A			NA	NA				KCNMB3 (49952 upstream) : ZNF639 (6036 downstream)						NA		NA									NA						gcagtggtgtgatctcggctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.179034742G>A		NA		hg19		0.02	-0.140352	TGTxATC	COVERED																																																																																			NOVEL					0			3	2.407331	KEEP	0	0	0	8	251	GG	0.99257	0.259026	0			3	60	87	1	0	7.081877	10	60	341	42		0.230769	0.260965
MFN1	55669	__UNKNOWN__	__UNKNOWN__	3	179076985	179076985	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:179076985C>T	ENST00000471841.1	+	4	537				MFN1_ENST00000280653.7_Intron|MFN1_ENST00000263969.5_Intron	NM_033540.2	NP_284941	Q8IWA4	MFN1_HUMAN	mitofusin 1	NA		NA			mitochondrial fusion (GO:0008053)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(3)|prostate(1)|urinary_tract(1)	31	all_cancers(143;1.67e-16)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.00225)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			ctcggctcaccgcaacctctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF054986	CCDS3228.1	3q26.32	2006-12-13			ENSG00000171109	ENSG00000171109	55669			18262	protein-coding gene	gene with protein product		608506			NA	8358434, 11181170	Standard	NM_017927	NM_033540	NA	Approved	FLJ20693	uc003fjs.3	Q8IWA4	OTTHUMG00000157385	ENST00000471841.1:c.411+195C>T	chr3.hg19:g.179076985C>T		NA	B2RAR1|D3DNR6|O15323|O60639|Q9BZB5|Q9NWQ2	hg19	CCDS3228.1	0.02	-0.122785	CACxGCA	COVERED																																																																																			NOVEL	MFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348654.2	2	2.707522	KEEP	2	0	0	9	265	CC	0.99257	0.194853	0		+	4	60	111	0	0	9.69047	8	60	259	31	ENST00000471841.1	0.333333	0.196312
USP13	8975	__UNKNOWN__	__UNKNOWN__	3	179375298	179375298	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:179375298T>C	ENST00000263966.3	+	1	639				USP13_ENST00000482333.1_Intron|USP13_ENST00000496897.1_Intron	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	NA		NA			autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			cacctgtaattccagcacttt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056	8975		Ubiquitin-specific peptidases	12611	protein-coding gene	gene with protein product		603591	ubiquitin specific protease 13 (isopeptidase T-3)		NA	12838346	Standard		NM_003940	NA	Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.168+4117T>C	chr3.hg19:g.179375298T>C		NA	A8K2S3|B4DYF3|D3DNS2|Q96B25	hg19	CCDS3235.1	0.02	-0.307	AATxCCA	COVERED																																																																																			NOVEL	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349617.1	12	6.01533	KEEP	1	0	0	20	553	TT	0.999863	0.800136	0		+	3	60	95	0	0	6.609837	29	60	897	88	ENST00000263966.3	0.09375	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	181392764	181392764	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:181392764T>G			NA	NA				RP11-4B14.3 (139102 upstream) : SOX2-OT (24728 downstream)						NA		NA									NA						gtcttgctattttgcccaggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.181392764T>G		NA		hg19		0.02	-0.192958	TATxTTG	COVERED																																																																																			NOVEL					0			15	2.706481	KEEP	0	0	0	9	243	TT	0.99254	0.486885	0			3	60	107	0	0	8.460566	17	60	503	45		0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	181927689	181927689	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:181927689A>G			NA	NA				RP11-416O18.2 (67764 upstream) : RP11-338L18.1 (155245 downstream)						NA		NA									NA						tgcccaggctagagtgcaatg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.181927689A>G		NA		hg19		0.02	-0.11403	GCTxGAG	UNCOVERED																																																																																			NOVEL					0			10	3.909618	KEEP	0	0	0	13	353	AA	0.994391	0.161555	0			4	60	141	0	0	12.87747	7	60	211	38		0.363636	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	182048371	182048371	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:182048371T>C			NA	NA				RP11-416O18.2 (188446 upstream) : RP11-338L18.1 (34563 downstream)						NA		NA									NA						tgccactgcattccagcctgg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.182048371T>C		NA		hg19		0.02	-0.043862	GCAxTCC	UNCOVERED																																																																																			NOVEL					0			3	3.007527	KEEP	0	0	0	10	274	TT	0.992708	0.023898	0			2	60	73	0	0	7.050168	2	60	64	22		0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	182648498	182648498	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:182648498T>C			NA	NA				RP11-531F16.4 (8772 upstream) : DCUN1D1 (7363 downstream)						NA		NA									NA						cggtggctcatacctgtaatc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.182648498T>C		NA		hg19		0.02	-0.201705	TCAxACC	COVERED																																																																																			NOVEL					0			6	4.209323	KEEP	0	0	0	14	370	TT	0.995343	0.48826	0			3	60	90	0	0	6.911313	15	60	428	52		0.166667	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	182894966	182894966	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:182894966T>C			NA	NA				LAMP3 (13340 upstream) : MCF2L2 (864 downstream)						NA		NA									NA						GAGggccgggtgtggtggctc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.182894966T>C		NA		hg19		0.02	-0.192943	GGGxGTG	COVERED																																																																																			NOVEL					0			4	3.005556	KEEP	1	0	0	10	261	TT	0.99254	0.486885	0			4	60	132	0	0	10.862961	15	60	435	50		0.210526	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	183293627	183293627	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183293627A>G			NA	NA				KLHL6 (20150 upstream) : KLHL24 (59728 downstream)						NA		NA									NA						cactttgggaagccaaggcgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.183293627A>G		NA		hg19		0.02	-0.149101	GGAxGCC	UNCOVERED																																																																																			NOVEL					0			8	2.405699	KEEP	9	0	0	8	219	AA	0	0	0			3	60	109	0	0	8.891619	14	60	412	47		0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	183341161	183341161	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183341161G>C			NA	NA				KLHL6 (67684 upstream) : KLHL24 (12194 downstream)						NA		NA									NA						gcctggccaagatggtgaaac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.183341161G>C		NA		hg19		0.02	-0.175446	CAAxATG	UNCOVERED																																																																																			NOVEL					0			9	3.008409	KEEP	10	0	0	10	297	GG	0	0	0			4	49	137	0	0	11.262626	16	60	528	42		0.2	0.387407
PARL	55486	__UNKNOWN__	__UNKNOWN__	3	183598406	183598406	__UNKNOWN__	Intron	SNP	T	T	C	rs57299858	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183598406T>C	ENST00000317096.4	-	1	186				PARL_ENST00000311101.5_Intron|PARL_ENST00000435888.1_Intron	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	NA		NA			membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			gccagggtggtctcgaactcc	0.542		NA											T|||	1989	0.397165	0.2844	0.4813	5008	,	,	NA	15214	0.4097	NA	0.4761	False	NA	,,,	NA	NA	NA	2504	0.3957	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193	55486			18253	protein-coding gene	gene with protein product	rhomboid 7 homolog 1 (Drosophila)	607858		PSARL	NA		Standard	NM_018622	XM_005247587	NA	Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.125+4103A>G	chr3.hg19:g.183598406T>C		NA	Q96CQ4|Q9BTJ6|Q9P1E3	hg19	CCDS3248.1	0.02	-0.114026	TGGxCTC	UNCOVERED																																																																																			NOVEL	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346465.1	7	2.404777	KEEP	3	0	0	8	207	TT	0	0	0		-	5	60	174	0	0	16.246448	7	60	205	32	ENST00000317096.4	0.416667	0.162467
ABCC5	10057	__UNKNOWN__	__UNKNOWN__	3	183706890	183706890	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183706890C>T	ENST00000382494.2	-	3	402				ABCC5_ENST00000392579.2_Intron|ABCC5_ENST00000265586.6_Intron|ABCC5_ENST00000427120.2_Intron|ABCC5_ENST00000334444.6_Intron	NM_001023587.1	NP_001018881.1	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	acccaggaggcggaggttgca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770	10057		ATP binding cassette transporters / subfamily C	56	protein-coding gene	gene with protein product		605251			NA	8894702, 9827529	Standard	NM_005688	XM_005247058	NA	Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000382494.2:c.287+123G>A	chr3.hg19:g.183706890C>T		NA	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	hg19	CCDS33898.1	0.02	-0.263109	AGGxGGA	COVERED																																																																																			NOVEL	ABCC5-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346354.1	2	5.447147	KEEP	1	1	22	26	745	CC	0.999957	0.693638	0		-	4	60	103	0	0	7.228735	24	60	770	58	ENST00000382494.2	0.142857	0.693668
ABCC5	10057	__UNKNOWN__	__UNKNOWN__	3	183707871	183707871	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183707871A>G	ENST00000382494.2	-	3	244				ABCC5_ENST00000392579.2_Intron|ABCC5_ENST00000265586.6_Intron|ABCC5_ENST00000427120.2_Intron|ABCC5_ENST00000334444.6_Intron	NM_001023587.1	NP_001018881.1	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	gattacaggcatgagccaccg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770	10057		ATP binding cassette transporters / subfamily C	56	protein-coding gene	gene with protein product		605251			NA	8894702, 9827529	Standard	NM_005688	XM_005247058	NA	Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000382494.2:c.130-700T>C	chr3.hg19:g.183707871A>G		NA	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	hg19	CCDS33898.1	0.02	-0.280667	GGCxTGA	COVERED																																																																																			NOVEL	ABCC5-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346354.1	6	6.614618	KEEP	0	0	0	22	597	AA	0.999879	0.739582	0		-	5	60	170	0	0	13.597407	24	60	715	80	ENST00000382494.2	0.172414	0.739671
HTR3C	170572	__UNKNOWN__	__UNKNOWN__	3	183776505	183776505	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183776505T>C	ENST00000318351.1	+	6	754					NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	NA		NA			ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	gtaatcccagtactttgggag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084	170572		5-HT (serotonin) receptors, Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic	24003	protein-coding gene	gene with protein product		610121	5-hydroxytryptamine (serotonin) receptor 3, family member C		NA	12801637, 15157181	Standard	NM_130770	NM_130770	NA	Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.720+130T>C	chr3.hg19:g.183776505T>C		NA	A2RRR5	hg19	CCDS3250.1	0.02	-0.27957	CAGxACT	COVERED																																																																																			NOVEL	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346296.1	3	3.003905	KEEP	0	0	0	10	251	TT	0.992708	0.734278	0		+	3	60	96	0	0	6.850715	26	60	691	58	ENST00000318351.1	0.103448	0.739671
DVL3	1857	__UNKNOWN__	__UNKNOWN__	3	183880179	183880179	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:183880179A>C	ENST00000313143.3	+	2	409				DVL3_ENST00000462665.1_Intron|EIF2B5_ENST00000444495.1_Intron|DVL3_ENST00000431765.1_Intron	NM_004423.3	NP_004414.3	Q92997	DVL3_HUMAN	dishevelled segment polarity protein 3	NA		NA			canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|intracellular signal transduction (GO:0035556)|non-canonical Wnt signaling pathway (GO:0035567)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|outflow tract septum morphogenesis (GO:0003148)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	cell cortex (GO:0005938)	beta-catenin binding (GO:0008013)|frizzled binding (GO:0005109)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(6)|liver(1)|lung(13)|ovary(1)|prostate(1)	35	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.08e-34)|OV - Ovarian serous cystadenocarcinoma(80;1.31e-22)			cgctatgttgaccaggcaggt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D86963	CCDS3253.1	3q27	2013-05-22	2013-05-22		ENSG00000161202	ENSG00000161202	1857		Dishevelled homologs	3087	protein-coding gene	gene with protein product		601368	dishevelled 3 (homologous to Drosophila dsh), dishevelled, dsh homolog 3 (Drosophila)		NA	8817329	Standard	NM_004423	NM_004423	NA	Approved	KIAA0208	uc003fms.3	Q92997	OTTHUMG00000156841	ENST00000313143.3:c.162-1266A>C	chr3.hg19:g.183880179A>C		NA	B4E3E5|D3DNT0|O14642|Q13531|Q8N5E9|Q92607	hg19	CCDS3253.1	0.02	-0.131538	TTGxCCA	COVERED																																																																																			NOVEL	DVL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346184.1	6	2.405689	KEEP	0	0	0	8	217	AT	0.99254	0.259018	0		+	3	60	104	0	0	8.673235	11	60	307	35	ENST00000313143.3	0.214286	0.260965
EIF4G1	1981	__UNKNOWN__	__UNKNOWN__	3	184033114	184033114	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:184033114G>T	ENST00000392537.2	+	1	133				EIF4G1_ENST00000414031.1_Intron|EIF4G1_ENST00000427845.1_5'UTR|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000350481.5_Intron|EIF4G1_ENST00000352767.3_Intron|EIF4G1_ENST00000382330.3_Intron|EIF4G1_ENST00000342981.4_5'UTR|EIF4G1_ENST00000319274.6_5'UTR|EIF4G1_ENST00000346169.2_Intron	NM_198244.2	NP_937887	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	NA		NA			cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CCTGGGCCAGGCCCGAACCCG	0.716		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													7	8	8			NA	NA	3		NA											NA				184033114		861	1973	2834	SO:0001627	intron_variant			D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867	1981		Parkinson disease	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F	NA	1429670, 9372926, 21907011	Standard	NM_182917	NM_182917	NA	Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000392537.2:c.-115+652G>T	chr3.hg19:g.184033114G>T		NA	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	hg19	CCDS3260.1	0.02	1.328852	CAGxCCC	COVERED																																																																																			NOVEL	EIF4G1-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345729.2	0	3.008123	KEEP	0	0	0	10	297	GG	0.992708	0.963741	0		+	8	60	219	0	0	15.958189	45	60	1433	76	ENST00000392537.2	0.150943	0.97082
EIF2B5	8893	__UNKNOWN__	__UNKNOWN__	3	184246462	184246462	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:184246462T>C	ENST00000444495.1	+	16	2116							Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	NA		NA			astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			tggtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191	8893			3261	protein-coding gene	gene with protein product		603945	eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)		NA	8688466	Standard		NM_003907	NA	Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000444495.1:c.2107-155812T>C	chr3.hg19:g.184246462T>C		NA	Q541Z1|Q96D04	hg19		0.02	-0.333281	TCAxGCC	COVERED																																																																																			NOVEL	EIF2B5-017	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000346333.1	7	3.3071	KEEP	1	0	0	11	286	TT	0.992708	0.845771	0		+	3	60	95	0	0	6.489848	32	60	949	70	ENST00000444495.1	0.085714	0.851984
EIF2B5	8893	__UNKNOWN__	__UNKNOWN__	3	184362682	184362682	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:184362682G>A	ENST00000444495.1	+	16	2116							Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	NA		NA			astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			catgcctgtagtcccagcact	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191	8893			3261	protein-coding gene	gene with protein product		603945	eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)		NA	8688466	Standard		NM_003907	NA	Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000444495.1:c.2107-39592G>A	chr3.hg19:g.184362682G>A		NA	Q541Z1|Q96D04	hg19		0.02	-0.236862	GTAxTCC	COVERED																																																																																			NOVEL	EIF2B5-017	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000346333.1	4	3.611223	KEEP	1	0	0	12	384	GG	0.993072	0.608164	0		+	3	60	94	0	0	6.905712	21	60	733	62	ENST00000444495.1	0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	184447163	184447163	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:184447163T>C			NA	NA				MAGEF1 (17327 upstream) : RP11-329B9.4 (4699 downstream)						NA		NA									NA						cgtgagccactgcgcccggcc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.184447163T>C		NA		hg19		0.02	-0.105246	CACxGCG	UNCOVERED																																																																																			NOVEL					0			2	2.406365	KEEP	0	0	0	8	224	TT	0.99257	0.138793	0			3	60	101	0	0	8.732519	8	60	242	33		0.272727	0.139832
VPS8	23355	__UNKNOWN__	__UNKNOWN__	3	184603962	184603962	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:184603962G>T	ENST00000436792.2	+	21	1918				VPS8_ENST00000437079.3_Intron|VPS8_ENST00000446204.2_Intron|VPS8_ENST00000287546.4_Intron			Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	NA		NA					zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TGCGTTGCCTGTCACATTCAA	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													156	148	151			NA	NA	3		NA											NA				184603962		1926	4137	6063	SO:0001627	intron_variant			AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931	23355			29122	protein-coding gene	gene with protein product		NA	KIAA0804	KIAA0804	NA	9872452	Standard	NM_015303	NM_001009921	NA	Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000436792.2:c.1775+18G>T	chr3.hg19:g.184603962G>T		NA	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	hg19	CCDS46972.1	0.02	-0.394749	CCTxTCA	COVERED																																																																																			NOVEL	VPS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345396.2	6	3.309692	KEEP	0	0	0	11	334	GG	0.993072	0.920221	0		+	8	60	247	0	0	19.373051	37	60	1261	85	ENST00000436792.2	0.177778	0.92664
VPS8	23355	__UNKNOWN__	__UNKNOWN__	3	184758981	184758981	__UNKNOWN__	Intron	SNP	G	G	A	rs559934854		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:184758981G>A	ENST00000436792.2	+	46	4193				VPS8_ENST00000437079.3_Intron|VPS8_ENST00000446204.2_Intron|VPS8_ENST00000287546.4_Intron			Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	NA		NA					zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			caacaagagcgaaactccatc	0.473		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18097	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931	23355			29122	protein-coding gene	gene with protein product		NA	KIAA0804	KIAA0804	NA	9872452	Standard	NM_015303	NM_001009921	NA	Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000436792.2:c.4051-7286G>A	chr3.hg19:g.184758981G>A		NA	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	hg19	CCDS46972.1	0.02	-0.157882	AGCxAAA	COVERED																																																																																			NOVEL	VPS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345396.2	10	2.70766	KEEP	1	0	0	9	268	GG	0.99257	0.320408	0		+	3	60	86	0	0	6.510734	15	60	471	46	ENST00000436792.2	0.166667	0.322807
MAP3K13	9175	__UNKNOWN__	__UNKNOWN__	3	185144029	185144029	__UNKNOWN__	Intron	SNP	C	C	T	rs572125222		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:185144029C>T	ENST00000265026.3	+	2	249				MAP3K13_ENST00000443863.1_Intron|MAP3K13_ENST00000424227.1_Intron|MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000535426.1_Intron	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13	NA		NA								NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			ccaccatgcccggctaatttt	0.542		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17993	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803	9175		Mitogen-activated protein kinase cascade / Kinase kinase kinases	6852	protein-coding gene	gene with protein product	leucine zipper-bearing kinase	604915			NA	9353328	Standard	NM_004721	NM_004721	NA	Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.-85-2256C>T	chr3.hg19:g.185144029C>T		NA		hg19	CCDS3270.1	0.02	-0.078933	GCCxGGC	UNCOVERED																																																																																			NOVEL	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345268.1	5	2.407166	KEEP	2	0	0	8	247	CC	0.99257	0.076761	0		+	3	60	82	0	0	7.554118	4	60	125	24	ENST00000265026.3	0.428571	0.077336
IGF2BP2	10644	__UNKNOWN__	__UNKNOWN__	3	185397432	185397432	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:185397432T>C	ENST00000382199.2	-	8	908				IGF2BP2_ENST00000494906.1_Intron|IGF2BP2_ENST00000457616.2_Intron|IGF2BP2_ENST00000421047.2_Intron|IGF2BP2_ENST00000346192.3_Intron	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	NA		NA			anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			gagatggagtttcactctttt	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792	10644		RNA binding motif (RRM) containing	28867	protein-coding gene	gene with protein product	IGF II mRNA binding protein 2	608289			NA	10190901, 9891060	Standard	NM_006548	NM_001007225	NA	Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.813-3731A>G	chr3.hg19:g.185397432T>C		NA	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	hg19	CCDS3273.2	0.02	-0.140326	AGTxTCA	COVERED																																																																																			NOVEL	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157087.2	8	2.706799	KEEP	2	0	0	9	251	TT	0.99254	0.259018	0		-	3	48	106	0	0	8.872926	11	60	324	42	ENST00000382199.2	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	185667019	185667019	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:185667019T>C			NA	NA				TRA2B (11095 upstream) : RP11-443P15.2 (10712 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.185667019T>C		NA		hg19		0.02	-0.219228	TCAxGCC	COVERED																																																																																			NOVEL					0			12	4.210664	KEEP	0	0	0	14	386	TT	0.995343	0.550313	0			3	60	91	0	0	6.793531	18	60	525	53		0.142857	0.552887
HRG	3273	__UNKNOWN__	__UNKNOWN__	3	186393122	186393122	__UNKNOWN__	Intron	SNP	C	C	G	rs377220063|rs13093283		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:186393122C>G	ENST00000232003.4	+	6	821					NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		gagagagagacagagacagag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905	3273			5181	protein-coding gene	gene with protein product	histidine-proline rich glycoprotein, thrombophilia due to elevated HRG	142640			NA	1678514	Standard	NM_000412	NM_000412	NA	Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.741+143C>G	chr3.hg19:g.186393122C>G		NA	B9EK35|D3DNU7	hg19	CCDS3280.1	0.02	-0.140155	AGAxAGA	COVERED																																																																																			NOVEL	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344655.1	11	3.309357	KEEP	5	0	0	11	326	CC	0.99254	0.259018	0		+	4	60	108	0	0	9.066564	10	60	336	35	ENST00000232003.4	0.285714	0.260965
KNG1	3827	__UNKNOWN__	__UNKNOWN__	3	186435401	186435401	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs145533184		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:186435401G>A	ENST00000265023.4	+	1	282	c.70G>A	c.(70-72)Gag>Aag	p.E24K	RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000287611.2_Missense_Mutation_p.E24K|KNG1_ENST00000447445.1_Missense_Mutation_p.E24K	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	24		NA			blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|inflammatory response (GO:0006954)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|smooth muscle contraction (GO:0006939)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			endometrium(1)|lung(15)|prostate(1)|skin(2)|stomach(2)	21	all_cancers(143;8.96e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.12e-20)	GBM - Glioblastoma multiforme(93;0.0798)		ATCACAGTCCGAGGAAATTGA	0.403		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16130	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0								G	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	120	122	121		70,70,70	-10	0	3	dbSNP_134	121	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	KNG1	NM_001166451.1,NM_001102416.2,NM_000893.3	56,56,56	0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077	benign,benign,benign	24/392,24/645,24/428	186435401	1,13005	2203	4300	6503	SO:0001583	missense				CCDS3281.1, CCDS43183.1, CCDS54695.1	3q27.3	2014-05-15	2004-05-21	2004-05-26	ENSG00000113889	ENSG00000113889	3827		Endogenous ligands	6383	protein-coding gene	gene with protein product	alpha-2-thiol proteinase inhibitor, bradykinin	612358	kininogen	KNG, BDK	NA	1733668	Standard	NM_001102416	NM_000893	NA	Approved	BK	uc011bsa.2	P01042	OTTHUMG00000150348	ENST00000265023.4:c.70G>A	chr3.hg19:g.186435401G>A	ENSP00000265023:p.Glu24Lys	NA	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	hg19	CCDS43183.1	0.02	1.166579	TCCxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434853	0.62955	0.0	1.16E-4	ENSG00000113889	ENST00000287611;ENST00000265023;ENST00000447445;ENST00000432028	T;T;T	0.26373	1.74;1.74;1.74	4.98	-9.97	0.00440	Proteinase inhibitor I25, cystatin (2);	1.201450	0.06139	N	0.671962	T	0.16981	0.0408	L	0.43152	1.355	0.09310	N	1	B;B	0.20988	0.05;0.04	B;B	0.13407	0.009;0.003	T	0.26430	-1.0103	10	0.16420	T	0.52	-0.0041	12.5121	0.56011	0.2073:0.6857:0.1069:0.0	.	24;24	P01042;P01042-2	KNG1_HUMAN;.	K	24;24;24;12	ENSP00000287611:E24K;ENSP00000265023:E24K;ENSP00000396025:E24K	ENSP00000265023:E24K	E	+	1	0	KNG1	187918095	0.000000	0.05858	0.000000	0.03702	0.957000	0.61999	-1.388000	0.02533	-1.281000	0.02399	0.455000	0.32223	GAG	NOVEL	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317738.1	2	2.707762	KEEP	0	0	0	9	268	GG	0.99254	0.992448	0		+	5	60	146	0	0	8.516922	89	60	2868	156	ENST00000265023.4	0.053191	0.999907
RP11-573D15.8	0	__UNKNOWN__	__UNKNOWN__	3	186467601	186467601	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:186467601T>C	ENST00000596329.1	-	0	514				RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA						NA		NA									NA						gcctgtaatctcagcactttg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000596329.1:	chr3.hg19:g.186467601T>C		NA		hg19		0.02	-0.174884	ATCxCAG	COVERED																																																																																			NOVEL	RP11-573D15.8-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000461601.1	6	3.007178	KEEP	2	0	0	10	270	TT	0.99254	0.384517	0		-	4	60	141	0	0	11.875869	14	60	412	44	ENST00000596329.1	0.222222	0.387407
RP11-573D15.8	0	__UNKNOWN__	__UNKNOWN__	3	186470283	186470283	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:186470283C>T	ENST00000596329.1	-	0	514				RP11-573D15.8_ENST00000599314.1_RNA|RP11-573D15.8_ENST00000596632.1_RNA|RP11-573D15.8_ENST00000609652.1_RNA						NA		NA									NA						cccagcacttcgggaggctga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000596329.1:	chr3.hg19:g.186470283C>T		NA		hg19		0.02	-0.219268	CTTxGGG	COVERED																																																																																			NOVEL	RP11-573D15.8-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000461601.1	13	3.307478	KEEP	1	0	0	11	303	CC	0.992708	0.548856	0		-	4	60	115	0	0	8.714828	20	60	622	48	ENST00000596329.1	0.166667	0.552887
ADIPOQ	9370	__UNKNOWN__	__UNKNOWN__	3	186575705	186575705	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:186575705T>C	ENST00000412955.2	+	0	4088				ADIPOQ_ENST00000320741.2_3'UTR|ADIPOQ_ENST00000444204.2_3'UTR			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	NA		NA			adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		ttcctttctttcttccttcct	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092	9370		Endogenous ligands	13633	protein-coding gene	gene with protein product	adipose most abundant gene transcript 1, adiponectin precursor	605441	adipocyte, C1Q and collagen domain containing	ACDC	NA	7592907, 8631877	Standard	NM_004797	NM_001177800	NA	Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.*3212T>C	chr3.hg19:g.186575705T>C		NA	Q58EX9	hg19	CCDS3284.1	0.02	-0.313606	CTTxCTT	COVERED																																																																																			NOVEL	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344490.2	4	5.41236	KEEP	0	0	0	18	483	TT	0.999859	0.818349	0		+	4	60	104	0	1	7.045005	32	60	912	67	ENST00000412955.2	0.111111	0.818465
ST6GAL1	6480	__UNKNOWN__	__UNKNOWN__	3	186766027	186766027	__UNKNOWN__	Intron	SNP	A	A	G	rs148539356	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:186766027A>G	ENST00000169298.3	+	5	1281				ST6GAL1_ENST00000448044.1_Intron|ST6GAL1_ENST00000457772.2_Intron	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	NA		NA			cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		caccgtgcccagccTGATTGG	0.522		NA											A|||	17	0.00339457	0.0053	0.0029	5008	,	,	NA	19688	0.0079	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	6480	2.4.99.1		10860	protein-coding gene	gene with protein product	ST6Gal I	109675	sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)	SIAT1	NA	2408023	Standard	NM_173216	NM_003032	NA	Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.608-3010A>G	chr3.hg19:g.186766027A>G		NA	A8KA14|B2R513|D3DNV3	hg19	CCDS3285.1	0.02	-0.166627	CCCxGCC	COVERED																																																																																			NOVEL	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344399.1	5	2.707103	KEEP	4	0	0	9	254	AA	0.99257	0.351317	0		+	3	60	106	0	0	8.510155	15	60	434	44	ENST00000169298.3	0.166667	0.353947
RP11-430L16.1	0	__UNKNOWN__	__UNKNOWN__	3	187855942	187855942	__UNKNOWN__	lincRNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:187855942T>A	ENST00000449845.1	+	0	241										NA		NA									NA						tggcctcaggtgatccgccca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000449845.1:	chr3.hg19:g.187855942T>A		NA		hg19		0.02	-0.15783	AGGxGAT	COVERED																																																																																			NOVEL	RP11-430L16.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000344060.1	12	3.907904	KEEP	9	0	0	13	343	TT	0.992708	0.351366	0		+	6	60	177	0	0	15.77013	11	60	305	59	ENST00000449845.1	0.352941	0.353947
LPP	4026	__UNKNOWN__	__UNKNOWN__	3	188300249	188300249	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:188300249A>G	ENST00000312675.4	+	6	675				LPP_ENST00000543006.1_Intron|LPP_ENST00000448637.1_Intron|LPP_ENST00000471917.1_Intron	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	NA		NA			cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		gattacaggcatgagccaccg	0.547		NA	T	HMGA2, MLL, C12orf9	lipoma, leukemia																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		L, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012	4026			6679	protein-coding gene	gene with protein product		600700	LIM domain-containing preferred translocation partner in lipoma		NA	8812423	Standard	NM_005578	XM_005247453	NA	Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.430-26700A>G	chr3.hg19:g.188300249A>G		NA	A1L4L6|D3DNV6|Q8NFX5	hg19	CCDS3291.1	0.02	-0.166639	GGCxTGA	COVERED																																																																																			NOVEL	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344030.1	4	2.405587	KEEP	0	0	0	8	216	AA	0.99257	0.351317	0		+	3	60	100	0	0	7.910247	15	60	438	41	ENST00000312675.4	0.166667	0.353947
TPRG1	285386	__UNKNOWN__	__UNKNOWN__	3	188668493	188668493	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:188668493T>C	ENST00000433971.1	+	1	212							Q6ZUI0	TPRG1_HUMAN	tumor protein p63 regulated 1	NA		NA				cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|skin(2)|urinary_tract(1)	16	all_cancers(143;6.12e-12)|all_hematologic(3;0.0359)|Ovarian(172;0.0925)	all_lung(153;8.23e-09)|Lung NSC(153;3.55e-06)|all_neural(597;0.0019)|Myeloproliferative disorder(1037;0.0255)	Lung(62;6.93e-06)	GBM - Glioblastoma multiforme(93;4.77e-14)		gctgggattataggcatgagc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK125682	CCDS3292.1	3q28	2008-02-04	2008-01-16	2008-01-16	ENSG00000188001	ENSG00000188001	285386			24759	protein-coding gene	gene with protein product		NA	family with sequence similarity 79, member B	FAM79B	NA		Standard	NM_198485	NM_198485	NA	Approved	FLJ41238, FLJ43694	uc003frw.2	Q6ZUI0	OTTHUMG00000156321	ENST00000433971.1:c.-1016+3279T>C	chr3.hg19:g.188668493T>C		NA		hg19	CCDS3292.1	0.02	-0.201732	TTAxAGG	COVERED																																																																																			NOVEL	TPRG1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343932.1	10	5.413138	KEEP	4	0	0	18	488	TT	0.997832	0.489481	0		+	3	60	102	0	0	7.960702	17	60	508	65	ENST00000433971.1	0.15	0.490544
TP63	8626	__UNKNOWN__	__UNKNOWN__	3	189605702	189605702	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:189605702A>G	ENST00000354600.5	+	9	1366				TP63_ENST00000449992.1_Intron|TP63_ENST00000440651.2_Intron|TP63_ENST00000264731.3_Intron|TP63_ENST00000392461.3_Intron|TP63_ENST00000456148.1_Intron|TP63_ENST00000392463.2_Intron|TP63_ENST00000320472.5_Intron|TP63_ENST00000382063.4_Intron|TP63_ENST00000392460.3_Intron	NM_001114980.1|NM_001114981.1	NP_001108452.1|NP_001108453.1	Q9H3D4	P63_HUMAN	tumor protein p63	NA		NA			apoptotic process (GO:0006915)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|cloacal septation (GO:0060197)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|ectoderm and mesoderm interaction (GO:0007499)|embryonic limb morphogenesis (GO:0030326)|epidermal cell division (GO:0010481)|epithelial cell development (GO:0002064)|establishment of planar polarity (GO:0001736)|establishment of skin barrier (GO:0061436)|female genitalia morphogenesis (GO:0048807)|hair follicle morphogenesis (GO:0031069)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organismal aging (GO:0010259)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mesoderm development (GO:2000381)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|polarized epithelial cell differentiation (GO:0030859)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|prostatic bud formation (GO:0060513)|protein homotetramerization (GO:0051289)|proximal/distal pattern formation (GO:0009954)|regulation of epidermal cell division (GO:0010482)|regulation of neuron apoptotic process (GO:0043523)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|sympathetic nervous system development (GO:0048485)|urinary bladder development (GO:0060157)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region DNA binding (GO:0044212)|WW domain binding (GO:0050699)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(5)|large_intestine(12)|lung(15)|ovary(2)|skin(9)|upper_aerodigestive_tract(6)	61	all_cancers(143;3.35e-10)|Ovarian(172;0.0925)		Lung(62;3.33e-05)	GBM - Glioblastoma multiforme(93;0.0227)		ctggagtgcaatggcgcaatc	0.468		NA								HNSCC(45;0.13)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB010153	CCDS3293.1, CCDS46976.1, CCDS46977.1, CCDS46978.1, CCDS46979.1, CCDS46980.1	3q27-q29	2014-09-17			ENSG00000073282	ENSG00000073282	8626			15979	protein-coding gene	gene with protein product		603273	tumor protein p73-like, tumor protein p53-like, tumor protein p53-competing protein	TP73L, TP53L, TP53CP	NA	9774969, 9662378, 11181441, 11181451	Standard	NM_003722	NM_003722	NA	Approved	p51, SHFM4, EEC3, p63, p73L, OFC8, KET, p73H, NBP, p53CP	uc003fry.2	Q9H3D4	OTTHUMG00000156313	ENST00000354600.5:c.1225+1362A>G	chr3.hg19:g.189605702A>G		NA	O75080|O75195|O75922|O76078|Q6VEG2|Q6VEG3|Q6VEG4|Q6VFJ1|Q6VFJ2|Q6VFJ3|Q6VH20|Q7LDI3|Q7LDI4|Q7LDI5|Q96KR0|Q9H3D2|Q9H3D3|Q9H3P8|Q9NPH7|Q9P1B4|Q9P1B5|Q9P1B6|Q9P1B7|Q9UBV9|Q9UE10|Q9UP26|Q9UP27|Q9UP28|Q9UP74	hg19	CCDS46978.1	0.02	-0.166618	GCAxTGG	COVERED																																																																																			NOVEL	TP63-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343868.1	4	2.405832	KEEP	1	0	0	8	216	AA	0.99257	0.351317	0		+	3	25	100	0	0	8.079219	13	60	366	43	ENST00000354600.5	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	189873355	189873355	__UNKNOWN__	IGR	SNP	G	G	A	rs861423	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:189873355G>A			NA	NA				LEPREL1-AS1 (10720 upstream) : RNU6-1109P (9850 downstream)						NA		NA									NA						tgcctgcctcggcctcccaaa	0.522		NA											A|||	2648	0.528754	0.6324	0.5461	5008	,	,	NA	18534	0.2907	NA	0.6342	False	NA	,,,	NA	NA	NA	2504	0.5133	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.189873355G>A		NA		hg19		0.02	-0.14035	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.406819	KEEP	5	0	0	8	238	GG	0	0	0			4	60	119	0	0	10.170914	10	60	331	41		0.285714	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	189873364	189873364	__UNKNOWN__	IGR	SNP	A	A	G	rs858180	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:189873364A>G			NA	NA				LEPREL1-AS1 (10729 upstream) : RNU6-1109P (9841 downstream)						NA		NA									NA						cggcctcccaaagtgctggga	0.517		NA											A|||	2648	0.528754	0.6324	0.5461	5008	,	,	NA	18994	0.2907	NA	0.6342	False	NA	,,,	NA	NA	NA	2504	0.5133	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.189873364A>G		NA		hg19		0.02	-0.157864	CCAxAGT	UNCOVERED																																																																																			NOVEL					0			5	2.405883	KEEP	5	0	0	8	220	AA	0	0	0			4	60	134	0	0	11.281227	13	60	381	41		0.235294	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	190014590	190014590	__UNKNOWN__	IGR	SNP	T	T	C	rs9822827|rs201669833	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:190014590T>C			NA	NA				RNU6-1109P (131278 upstream) : CLDN1 (8899 downstream)						NA		NA									NA						ccgcccgtcttggcctcccaa	0.522		NA											C|||	2888	0.576677	0.7368	0.5231	5008	,	,	NA	16154	0.6726	NA	0.5398	False	NA	,,,	NA	NA	NA	2504	0.3374	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.190014590T>C		NA		hg19		0.02	-0.122785	TCTxGGC	UNCOVERED																																																																																			NOVEL					0			3	3.308497	KEEP	5	0	0	11	305	TT	0	0	0			4	60	135	0	0	12.091644	8	60	236	46		0.333333	0.196312
ATP13A4	84239	__UNKNOWN__	__UNKNOWN__	3	193135557	193135557	__UNKNOWN__	Intron	SNP	G	G	A	rs113123567		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:193135557G>A	ENST00000342695.4	-	26	3165				ATP13A4_ENST00000392443.3_Intron|ATP13A4_ENST00000400270.2_Intron	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	NA		NA				integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ggtggatcacgaggtcaggag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249	84239		ATPases / P-type	25422	protein-coding gene	gene with protein product		609556			NA	14702039, 12975309	Standard	NM_032279	XM_005247829	NA	Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.2843-3018C>T	chr3.hg19:g.193135557G>A		NA	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	hg19	CCDS3304.2	0.02	-0.149113	CACxAGG	COVERED																																																																																			NOVEL	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157244.4	4	2.707651	KEEP	2	0	0	9	267	GG	0.99257	0.289832	0		-	3	60	92	0	0	7.191891	14	60	441	37	ENST00000342695.4	0.176471	0.292001
ATP13A4	84239	__UNKNOWN__	__UNKNOWN__	3	193173066	193173066	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:193173066C>G	ENST00000342695.4	-	17	2238				ATP13A4_ENST00000392443.3_Intron	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	NA		NA				integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ggaggcggagcttgcagtgag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249	84239		ATPases / P-type	25422	protein-coding gene	gene with protein product		609556			NA	14702039, 12975309	Standard	NM_032279	XM_005247829	NA	Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.1916-1065G>C	chr3.hg19:g.193173066C>G		NA	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	hg19	CCDS3304.2	0.02	-0.04385	GAGxTTG	UNCOVERED																																																																																			NOVEL	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157244.4	6	2.707781	KEEP	9	0	0	9	267	CC	0	0	0		-	3	40	90	0	0	8.969608	2	60	61	25	ENST00000342695.4	0.6	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	194010869	194010869	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194010869T>C			NA	NA				RP11-513G11.2 (5712 upstream) : LINC00887 (8118 downstream)						NA		NA									NA						aagcaatccttccaccttggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.194010869T>C		NA		hg19		0.02	-0.184202	CCTxCCA	COVERED																																																																																			NOVEL					0			4	3.008104	KEEP	0	0	0	10	283	TT	0.993072	0.420544	0			3	60	93	0	0	7.061061	17	60	527	47		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	194115074	194115074	__UNKNOWN__	IGR	SNP	G	G	A	rs370504832	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194115074G>A			NA	NA				LRRC15 (24602 upstream) : GP5 (475 downstream)						NA		NA									NA						tccgcctcccgggttcaagtg	0.507		NA											G|||	28	0.00559105	0.0204	0.0014	5008	,	,	NA	13241	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.194115074G>A		NA		hg19		0.02	-0.157899	CCCxGGT	COVERED																																																																																			NOVEL					0			10	2.405667	KEEP	2	0	0	8	223	GG	0.99257	0.320408	0			3	37	94	0	0	7.310081	15	60	497	36		0.166667	0.322807
GP5	2814	__UNKNOWN__	__UNKNOWN__	3	194116708	194116708	__UNKNOWN__	3'UTR	SNP	C	C	T	rs183855669	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194116708C>T	ENST00000401815.1	-	0	2375				GP5_ENST00000323007.3_3'UTR			P40197	GPV_HUMAN	glycoprotein V (platelet)	NA		NA			blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		gaggcggaggctgcagtgaac	0.502		NA											C|||	9	0.00179712	0.0	0.0	5008	,	,	NA	18025	0.0079	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732	2814		CD molecules	4443	protein-coding gene	gene with protein product		173511			NA	7690959	Standard	NM_004488	NM_004488	NA	Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.*621G>A	chr3.hg19:g.194116708C>T		NA	D1MER9	hg19	CCDS3307.1	0.02	0.844361	AGGxTGC	COVERED																																																																																			NOVEL	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317710.1	9	5.915824	KEEP	0	3	71	45	1391	CC	1	0.99994	0		-	8	60	209	1	0	13.020612	82	60	2806	208	ENST00000401815.1	0.088889	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	194663467	194663467	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194663467A>G			NA	NA				AC090505.1 (110146 upstream) : XXYLT1 (125540 downstream)						NA		NA									NA						ggccgggcgcagtggctcacg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.194663467A>G		NA		hg19		0.02	-0.114029	CGCxGTG	COVERED																																																																																			NOVEL					0			5	2.707427	KEEP	1	0	0	9	258	AA	0.99257	0.194853	0			3	60	100	0	0	8.381943	10	60	307	35		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	194779040	194779040	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194779040A>G			NA	NA				AC090505.1 (225719 upstream) : XXYLT1 (9967 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.194779040A>G		NA		hg19		0.02	-0.236568	GGCxTGA	COVERED																																																																																			NOVEL					0			2	4.211015	KEEP	1	0	0	14	392	AA	0.995343	0.609555	0			4	60	128	0	0	9.793472	23	60	681	68		0.148148	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	194779052	194779052	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194779052A>G			NA	NA				AC090505.1 (225731 upstream) : XXYLT1 (9955 downstream)						NA		NA									NA						gagccaccgcacccggccAGA	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.194779052A>G		NA		hg19		0.02	-0.245482	CGCxCCC	COVERED																																																																																			NOVEL					0			2	4.208915	KEEP	1	0	0	14	374	AA	0.995343	0.638361	0			3	60	93	0	0	6.643875	24	60	704	69		0.111111	0.641347
XXYLT1	152002	__UNKNOWN__	__UNKNOWN__	3	194872027	194872027	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:194872027C>T	ENST00000310380.6	-	3	894				XXYLT1_ENST00000429994.1_Intron|XXYLT1_ENST00000437101.1_Intron|XXYLT1-AS2_ENST00000426468.1_RNA|XXYLT1-AS2_ENST00000447975.1_RNA|XXYLT1_ENST00000355729.4_Intron	NM_152531.4	NP_689744.3	Q8NBI6	XXLT1_HUMAN	xyloside xylosyltransferase 1	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring pentosyl groups (GO:0016763)				NA						catcccagtactttgggaggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK075551	CCDS43188.1	3q29	2013-02-22	2011-10-19	2011-10-19	ENSG00000173950	ENSG00000173950	152002		Glycosyltransferase family 8 domain containing	26639	protein-coding gene	gene with protein product		614552	chromosome 3 open reading frame 21	C3orf21	NA	22117070	Standard	NM_152531	NM_152531	NA	Approved	FLJ35155	uc003fum.4	Q8NBI6	OTTHUMG00000155915	ENST00000310380.6:c.785+5150G>A	chr3.hg19:g.194872027C>T		NA	D3DNW5|Q8NAL3|Q8WV03|Q96ME0	hg19	CCDS43188.1	0.02	-0.17545	GTAxTTT	COVERED																																																																																			NOVEL	XXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342290.1	4	3.611047	KEEP	2	0	0	12	377	CC	0.992708	0.384582	0		-	3	60	86	0	0	6.433853	16	60	562	58	ENST00000310380.6	0.157895	0.387407
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195410192	195410192	__UNKNOWN__	lincRNA	SNP	C	C	A	rs9867004		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195410192C>A	ENST00000445430.1	+	0	1819									long intergenic non-protein coding RNA 969	NA		NA									NA						ttgattgagcccgggaagtca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195410192C>A		NA		hg19		0.02	-0.131583	AGCxCGG	UNCOVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	6	2.40694	KEEP	14	0	0	8	240	CC	0	0	0		+	3	27	85	0	0	6.672337	12	60	416	44	ENST00000445430.1	0.2	0.229173
LINC00969	440993	__UNKNOWN__	__UNKNOWN__	3	195412920	195412920	__UNKNOWN__	lincRNA	SNP	C	C	T	rs111576530		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195412920C>T	ENST00000445430.1	+	0	4117									long intergenic non-protein coding RNA 969	NA		NA									NA						ACCCAGTGGCCGGGGAGCGTG	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086	440993		Long non-coding RNAs	48729	non-coding RNA	RNA, long non-coding		NA			NA		Standard		XR_427455	NA	Approved				OTTHUMG00000155834	ENST00000445430.1:	chr3.hg19:g.195412920C>T		NA		hg19		0.02	3.055111	GGCxGGG	COVERED																																																																																			NOVEL	LINC00969-038	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000341951.1	5	4.211729	KEEP	14	0	0	14	421	CC	0.993634	0.993631	0		+	27	60	839	0	0	70.92064	77	60	2517	218	ENST00000445430.1	0.259615	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195433795	195433795	__UNKNOWN__	IGR	SNP	C	C	T	rs547035212	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195433795C>T			NA	NA				MIR570 (7427 upstream) : MUC20 (13957 downstream)						NA		NA									NA						tttgcaattccaccagcagtg	0.373		NA											c|||	14	0.00279553	0.0106	0.0	5008	,	,	NA	32027	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195433795C>T		NA		hg19		0.02	1.015202	TTCxACC	COVERED																																																																																			NOVEL					0			42	8.35598	KEEP	0	1	26	37	1085	CC	1	0.999962	0			5	60	141	0	0	7.975559	91	60	2845	164		0.052083	0.999962
MUC20	200958	__UNKNOWN__	__UNKNOWN__	3	195448607	195448607	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195448607C>G	ENST00000436408.1	+	1	200				MUC20_ENST00000320736.6_Intron|MUC20_ENST00000485430.1_Intron|MUC20_ENST00000447234.2_Intron			Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	NA		NA			activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTCTAAACCTCGAGTGGAGAg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945	200958		Mucins	23282	protein-coding gene	gene with protein product		610360			NA	14565953	Standard	NM_152673	NM_001282506	NA	Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000436408.1:c.76+653C>G	chr3.hg19:g.195448607C>G		NA	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	hg19		0.02	-0.254385	CCTxGAG	COVERED																																																																																			NOVEL	MUC20-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341836.1	6	3.911619	KEEP	0	0	0	13	398	CC	0.994391	0.664773	0		+	5	60	162	0	0	13.252474	19	60	628	63	ENST00000436408.1	0.208333	0.668523
MUC20	200958	__UNKNOWN__	__UNKNOWN__	3	195448608	195448608	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195448608G>A	ENST00000436408.1	+	1	200				MUC20_ENST00000320736.6_Intron|MUC20_ENST00000485430.1_Intron|MUC20_ENST00000447234.2_Intron			Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	NA		NA			activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		TCTAAACCTCGAGTGGAGAgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945	200958		Mucins	23282	protein-coding gene	gene with protein product		610360			NA	14565953	Standard	NM_152673	NM_001282506	NA	Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000436408.1:c.76+654G>A	chr3.hg19:g.195448608G>A		NA	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	hg19		0.02	-0.245599	CTCxAGT	COVERED																																																																																			NOVEL	MUC20-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341836.1	6	3.911154	KEEP	0	0	0	13	392	GG	0.994391	0.63775	0		+	5	60	151	0	0	12.053871	20	60	636	62	ENST00000436408.1	0.2	0.641347
MUC20	200958	__UNKNOWN__	__UNKNOWN__	3	195461618	195461618	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195461618C>T	ENST00000436408.1	+	4	2185				MUC20_ENST00000320736.6_3'UTR			Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	NA		NA			activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ttttttttttctttttgagat	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945	200958		Mucins	23282	protein-coding gene	gene with protein product		610360			NA	14565953	Standard	NM_152673	NM_001282506	NA	Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000436408.1:c.2062-9C>T	chr3.hg19:g.195461618C>T		NA	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	hg19		0.02	1.272401	TTTxTTT	COVERED																																																																																			NOVEL	MUC20-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341836.1	21	6.263446	KEEP	0	4	58	42	1270	CC	1	0.999407	0		+	6	60	150	0	0	8.866754	68	60	2132	203	ENST00000436408.1	0.081081	0.999407
MUC20	200958	__UNKNOWN__	__UNKNOWN__	3	195461862	195461862	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195461862C>T	ENST00000436408.1	+	0	2421				MUC20_ENST00000320736.6_3'UTR			Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	NA		NA			activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		ccacccacctcggcctcccaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945	200958		Mucins	23282	protein-coding gene	gene with protein product		610360			NA	14565953	Standard	NM_152673	NM_001282506	NA	Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000436408.1:c.*125C>T	chr3.hg19:g.195461862C>T		NA	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	hg19		0.02	3.13411	CCTxGGC	COVERED																																																																																			NOVEL	MUC20-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341836.1	26	11.189625	KEEP	1	2	47	54	1547	CC	1	0.999992	0		+	7	60	207	0	0	13.231795	87	60	2788	228	ENST00000436408.1	0.074468	0.999992
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195513491	195513491	__UNKNOWN__	Intron	SNP	G	G	T	rs79338930		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195513491G>T	ENST00000346145.4	-	2	122				MUC4_ENST00000463781.3_Missense_Mutation_p.P1654T|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1654T	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGGGCTGGTGACA	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													26	30	29			NA	NA	3		NA											NA				195513491		690	1576	2266	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-8165C>A	chr3.hg19:g.195513491G>T		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.289456	AAGxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	-	0.095	-1.161025	0.01673	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.55;1.54	0.595	-1.19	0.09585	.	.	.	.	.	T	0.11410	0.0278	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.19289	-1.0310	8	.	.	.	.	0.8499	0.01170	0.2662:0.3695:0.1785:0.1858	.	1654	E7ESK3	.	T	1654	ENSP00000417498:P1654T;ENSP00000420243:P1654T	.	P	-	1	0	MUC4	196997886	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.346000	0.07760	-4.700000	0.00035	-4.108000	0.00011	CCT	NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	13	2.77436	KEEP	8	2	41	24	726	GG	0.999869	0.780958	0		-	5	49	150	0	0	11.769052	22	60	721	93	ENST00000346145.4	0.185185	0.78106
MUC4	4585	__UNKNOWN__	__UNKNOWN__	3	195513519	195513519	__UNKNOWN__	Intron	SNP	A	A	T	rs201585392	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195513519A>T	ENST00000346145.4	-	2	122				MUC4_ENST00000463781.3_Silent_p.G1644G|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.G1644G	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	NA		NA			cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.N1637_T1652delNASSLSTGHATPLHVT(2)|p.G1644G(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGTGGCGTGACCTGTGGATA	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				3	Deletion - In frame(2)|Substitution - coding silent(1)	stomach(2)|endometrium(1)											30	37	35			NA	NA	3		NA											NA				195513519		690	1580	2270	SO:0001627	intron_variant			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113	4585		Mucins	7514	protein-coding gene	gene with protein product		158372	mucin 4, tracheobronchial		NA	1673336	Standard	NM_018406	NM_004532	NA	Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.83-8193T>A	chr3.hg19:g.195513519A>T		NA	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	hg19	CCDS3310.1	0.02	-0.263027	GTGxCCT	COVERED																																																																																			NOVEL	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341862.1	10	2.233121	KEEP	7	1	30	18	459	AA	0.997832	0.692164	0		-	5	60	137	0	0	10.561285	21	60	578	72	ENST00000346145.4	0.192308	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195570614	195570614	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195570614C>T			NA	NA				AC124944.5 (6698 upstream) : TNK2 (19620 downstream)						NA		NA									NA						tcccagcactctggaaggccg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195570614C>T		NA		hg19		0.02	-0.105208	ACTxTGG	UNCOVERED																																																																																			NOVEL					0			3	3.310047	KEEP	1	0	0	11	343	CC	0.992708	0.138812	0			3	42	90	0	0	7.633219	8	60	259	34		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195664977	195664977	__UNKNOWN__	IGR	SNP	T	T	C	rs201431379	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195664977T>C			NA	NA				RNU2-11P (9331 upstream) : RP11-480A16.1 (11081 downstream)						NA		NA									NA						CAAAGAAAGCTGTGGTACCCG	0.453		NA											C|||	307	0.0613019	0.0045	0.1138	5008	,	,	NA	19154	0.0942	NA	0.0457	False	NA	,,,	NA	NA	NA	2504	0.0828	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195664977T>C		NA		hg19		0.02	1.730799	AGCxGTG	COVERED																																																																																			NOVEL					0			4	2.404975	KEEP	2	0	0	8	212	TT	0.99257	0.991047	0			9	40	280	0	0	20.349627	66	60	2003	124		0.12	0.998465
SDHAP1	255812	__UNKNOWN__	__UNKNOWN__	3	195706246	195706246	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195706246C>T	ENST00000427841.1	-	0	1022					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1	NA		NA									NA						caccatgttgcgcaggctggt	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(67;1158 1227 12109 20189 43170)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485	255812			32455	pseudogene	pseudogene		NA	succinate dehydrogenase complex, subunit A, flavoprotein-like 1	SDHAL1, SDHALP1	NA		Standard		NR_003264	NA	Approved		uc003fvy.3		OTTHUMG00000155716	ENST00000427841.1:	chr3.hg19:g.195706246C>T		NA		hg19		0.02	-0.122793	TTGxGCA	COVERED																																																																																			NOVEL	SDHAP1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000341367.1	9	2.707463	KEEP	4	0	0	9	263	CG	0.99254	0.227464	0		-	4	39	107	0	0	9.122935	9	60	301	32	ENST00000427841.1	0.307692	0.229173
SDHAP1	255812	__UNKNOWN__	__UNKNOWN__	3	195706297	195706297	__UNKNOWN__	RNA	SNP	C	C	T	rs199826544		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195706297C>T	ENST00000427841.1	-	0	1022					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1	NA		NA									NA						gccttggcctcccaaagtgct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(67;1158 1227 12109 20189 43170)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485	255812			32455	pseudogene	pseudogene		NA	succinate dehydrogenase complex, subunit A, flavoprotein-like 1	SDHAL1, SDHALP1	NA		Standard		NR_003264	NA	Approved		uc003fvy.3		OTTHUMG00000155716	ENST00000427841.1:	chr3.hg19:g.195706297C>T		NA		hg19		0.02	-0.280711	CCTxCCA	COVERED																																																																																			NOVEL	SDHAP1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000341367.1	12	4.211774	KEEP	5	0	0	14	428	CC	0.993634	0.734962	0		-	5	48	147	0	0	11.559216	21	60	729	73	ENST00000427841.1	0.192308	0.739671
TFRC	7037	__UNKNOWN__	__UNKNOWN__	3	195778845	195778845	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195778845C>A	ENST00000360110.4	-	19	2420	c.2251G>T	c.(2251-2253)Ggt>Tgt	p.G751C	TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000535031.1_Missense_Mutation_p.G469C|TFRC_ENST00000392396.3_Missense_Mutation_p.G751C|TFRC_ENST00000420415.1_Missense_Mutation_p.G670C	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	751	Ligand-binding.	NA			cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	CAAACGTCACCAGAGAGGGCA	0.443		NA	T	BCL6	NHL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		3	3q29	7037	transferrin receptor (p90, CD71)		L	0													99	91	94			NA	NA	3		NA											NA				195778845		2203	4300	6503	SO:0001583	missense			X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274	7037		CD molecules	11763	protein-coding gene	gene with protein product		190010	transferrin receptor (p90, CD71)		NA		Standard		NM_003234	NA	Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.2251G>T	chr3.hg19:g.195778845C>A	ENSP00000353224:p.Gly751Cys	NA	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	hg19	CCDS3312.1	0.02	1.441832	CACxAGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.49	3.636290	0.67130	.	.	ENSG00000072274	ENST00000360110;ENST00000420415;ENST00000392396;ENST00000535031	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	6.06	5.19	0.71726	Transferrin receptor-like, dimerisation domain (3);	0.138535	0.64402	D	0.000003	T	0.77498	0.4139	M	0.83603	2.65	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81402	-0.0949	10	0.87932	D	0	-15.2722	14.2046	0.65725	0.0:0.9292:0.0:0.0708	.	751	P02786	TFR1_HUMAN	C	751;670;751;469	ENSP00000353224:G751C;ENSP00000390133:G670C;ENSP00000376197:G751C;ENSP00000437753:G469C	ENSP00000353224:G751C	G	-	1	0	TFRC	197263242	0.996000	0.38824	0.983000	0.44433	0.990000	0.78478	5.515000	0.67049	1.579000	0.49836	0.655000	0.94253	GGT	NOVEL	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341346.1	4	3.610329	KEEP	0	0	0	12	357	CC	0.993634	0.991846	0		-	19	60	564	0	0	47.284617	54	60	1829	127	ENST00000360110.4	0.260274	0.9982
TFRC	7037	__UNKNOWN__	__UNKNOWN__	3	195778846	195778846	__UNKNOWN__	Silent	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195778846A>G	ENST00000360110.4	-	19	2419	c.2250T>C	c.(2248-2250)tcT>tcC	p.S750S	TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000535031.1_Silent_p.S468S|TFRC_ENST00000392396.3_Silent_p.S750S|TFRC_ENST00000420415.1_Silent_p.S669S	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	750	Ligand-binding.	NA			cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	AAACGTCACCAGAGAGGGCAT	0.443		NA	T	BCL6	NHL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		3	3q29	7037	transferrin receptor (p90, CD71)		L	0													100	91	94			NA	NA	3		NA											NA				195778846		2203	4300	6503	SO:0001819	synonymous_variant			X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274	7037		CD molecules	11763	protein-coding gene	gene with protein product		190010	transferrin receptor (p90, CD71)		NA		Standard		NM_003234	NA	Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.2250T>C	chr3.hg19:g.195778846A>G		NA	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	hg19	CCDS3312.1	0.02	1.921334	ACCxGAG	COVERED																																																																																			NOVEL	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341346.1	4	3.609219	KEEP	0	0	0	12	332	AA	0.993634	0.992337	0		-	21	60	711	0	0	61.807639	54	60	1672	128	ENST00000360110.4	0.28	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195840261	195840261	__UNKNOWN__	IGR	SNP	G	G	A	rs61047863	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195840261G>A			NA	NA				TFRC (31201 upstream) : LINC00885 (29245 downstream)						NA		NA									NA						gcctcccaaagtggtgggatt	0.498		NA											G|||	512	0.102236	0.0136	0.1787	5008	,	,	NA	12902	0.0526	NA	0.2028	False	NA	,,,	NA	NA	NA	2504	0.1155	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195840261G>A		NA		hg19		0.02	-0.201754	AAAxTGG	UNCOVERED																																																																																			NOVEL					0			8	2.406711	KEEP	1	0	0	8	238	GG	0	0	0			8	60	238	0	0	21.555048	13	60	454	42		0.380952	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	195858397	195858397	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195858397G>T			NA	NA				TFRC (49337 upstream) : LINC00885 (11109 downstream)						NA		NA									NA						tgtggtggtgggcacctgtaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.195858397G>T		NA		hg19		0.02	-0.09649	GTGxGCA	UNCOVERED																																																																																			NOVEL					0			10	2.707086	KEEP	6	0	0	9	262	GG	0	0	0			3	40	87	0	1	7.643112	6	60	199	32		0.333333	0.120436
ZDHHC19	131540	__UNKNOWN__	__UNKNOWN__	3	195927417	195927417	__UNKNOWN__	Intron	SNP	G	G	A	rs71323705	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195927417G>A	ENST00000296326.3	-	6	767					NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		agtagagacggggtttcaccg	0.557		NA											G|||	380	0.0758786	0.0219	0.1484	5008	,	,	NA	10502	0.003	NA	0.1581	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958	131540		Zinc fingers, DHHC-type	20713	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144637	XR_246038	NA	Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.688-1672C>T	chr3.hg19:g.195927417G>A		NA	A8MSY6|B3KVI1	hg19	CCDS43190.1	0.02	-0.087701	ACGxGGT	UNCOVERED																																																																																			NOVEL	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341533.1	5	2.707509	KEEP	7	0	0	9	263	GG	0	0	0		-	3	37	78	0	0	7.153432	4	60	133	27	ENST00000296326.3	0.428571	0.099721
ZDHHC19	131540	__UNKNOWN__	__UNKNOWN__	3	195927427	195927427	__UNKNOWN__	Intron	SNP	G	G	A	rs67751943	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195927427G>A	ENST00000296326.3	-	6	767					NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		gggtttcaccgtgttagccag	0.557		NA											A|||	2270	0.453275	0.3253	0.5389	5008	,	,	NA	11835	0.4177	NA	0.5716	False	NA	,,,	NA	NA	NA	2504	0.4806	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958	131540		Zinc fingers, DHHC-type	20713	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144637	XR_246038	NA	Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.688-1682C>T	chr3.hg19:g.195927427G>A		NA	A8MSY6|B3KVI1	hg19	CCDS43190.1	0.02	-0.105235	ACCxTGT	UNCOVERED																																																																																			NOVEL	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341533.1	7	2.707384	KEEP	8	0	0	9	264	GG	0	0	0		-	8	60	229	0	0	25.348654	1	11	35	32	ENST00000296326.3	0.888889	0.139832
ZDHHC19	131540	__UNKNOWN__	__UNKNOWN__	3	195927449	195927449	__UNKNOWN__	Intron	SNP	T	T	A	rs545265920	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195927449T>A	ENST00000296326.3	-	6	767					NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		atggtctcgatctcctgacct	0.507		NA											T|||	3	0.000599042	0.0	0.0	5008	,	,	NA	11934	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958	131540		Zinc fingers, DHHC-type	20713	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144637	XR_246038	NA	Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.688-1704A>T	chr3.hg19:g.195927449T>A		NA	A8MSY6|B3KVI1	hg19	CCDS43190.1	0.02	-0.131527	CGAxCTC	UNCOVERED																																																																																			NOVEL	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341533.1	8	3.006592	KEEP	8	0	0	10	266	TT	0	0	0		-	3	60	83	0	0	6.473413	12	60	341	41	ENST00000296326.3	0.2	0.229173
SLC51A	200931	__UNKNOWN__	__UNKNOWN__	3	195954019	195954019	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195954019G>A	ENST00000296327.5	+	3	497					NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	NA		NA			bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)				NA					Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	CCCTGTGGGGGGAACTGAAAA	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													35	35	35			NA	NA	3		NA											NA				195954019		2203	4300	6503	SO:0001627	intron_variant				CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959	200931		Solute carriers	29955	protein-coding gene	gene with protein product	organic solute transporter, alpha subunit	612084			NA	12719432, 20538072	Standard	NM_152672	NM_152672	NA	Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.288+29G>A	chr3.hg19:g.195954019G>A		NA	Q6ZMC7	hg19	CCDS3314.1	0.02	2.762867	GGGxGAA	COVERED																																																																																			NOVEL	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341253.1	1	6.619912	KEEP	0	0	0	22	686	GG	0.999879	0.999879	0		+	20	70	606	0	0	45.351283	118	70	3995	231	ENST00000296327.5	0.144928	1
PCYT1A	5130	__UNKNOWN__	__UNKNOWN__	3	195993696	195993696	__UNKNOWN__	Intron	SNP	C	C	T	rs12634304	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:195993696C>T	ENST00000292823.2	-	3	290				PCYT1A_ENST00000491544.1_Intron|RP11-447L10.1_ENST00000431391.1_Intron|PCYT1A_ENST00000431016.1_Intron|PCYT1A_ENST00000419333.1_Intron	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	NA		NA			CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	cctgggaggccgagatcacac	0.522		NA											C|||	2301	0.459465	0.3389	0.4409	5008	,	,	NA	14586	0.7966	NA	0.3618	False	NA	,,,	NA	NA	NA	2504	0.3885	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	5130	2.7.7.15		8754	protein-coding gene	gene with protein product	phosphate cytidylyltransferase 1, choline, alpha isoform	123695	phosphate cytidylyltransferase 1, choline, alpha isoform	PCYT1	NA	7918629	Standard	NM_005017	NM_005017	NA	Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.117+3589G>A	chr3.hg19:g.195993696C>T		NA	A9LYK9|D3DXB1|Q86Y88	hg19	CCDS3315.1	0.02	-0.131553	GGCxGAG	COVERED																																																																																			NOVEL	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341147.1	8	3.309363	KEEP	0	0	0	11	328	CC	0.994391	0.227888	0		-	8	60	236	0	0	23.653778	5	60	150	36	ENST00000292823.2	0.615385	0.229173
RNF168	165918	__UNKNOWN__	__UNKNOWN__	3	196206131	196206131	__UNKNOWN__	Intron	SNP	G	G	A	rs112276010	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196206131G>A	ENST00000318037.3	-	5	1275					NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00348)		tgatccacccgcctcggcctc	0.532		NA											A|||	510	0.101837	0.267	0.0764	5008	,	,	NA	17789	0.003	NA	0.0855	False	NA	,,,	NA	NA	NA	2504	0.0153	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961	165918		RING-type (C3HC4) zinc fingers	26661	protein-coding gene	gene with protein product		612688	ring finger protein 168		NA	12477932	Standard	NM_152617	NM_152617	NA	Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.681-3948C>T	chr3.hg19:g.196206131G>A		NA	Q8NA67|Q96NS4	hg19	CCDS3317.1	0.02	-0.228029	CCCxCCT	UNCOVERED																																																																																			NOVEL	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340778.1	10	2.406734	KEEP	4	0	0	8	237	GG	0	0	0		-	5	60	145	0	0	11.657112	18	60	586	50	ENST00000318037.3	0.217391	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	196230926	196230926	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196230926G>A			NA	NA				RNF168 (287 upstream) : SMCO1 (2821 downstream)						NA		NA									NA						ggccgggtgcggtggctcacg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.196230926G>A		NA		hg19		0.02	-0.245617	TGCxGTG	COVERED																																																																																			NOVEL					0			11	5.113521	KEEP	2	0	0	17	488	GG	0.997832	0.667074	0			3	60	89	0	0	6.349821	22	60	724	69		0.12	0.668523
SMCO1	255798	__UNKNOWN__	__UNKNOWN__	3	196236178	196236178	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196236178G>A	ENST00000397537.2	-	2	357					NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	NA		NA				integral component of membrane (GO:0016021)					NA						ctcgtgatccgcccgcctcgg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097	255798			27407	protein-coding gene	gene with protein product		NA	chromosome 3 open reading frame 43	C3orf43	NA		Standard	NM_001006109	NM_001077657	NA	Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.200+212C>T	chr3.hg19:g.196236178G>A		NA	B3KW20	hg19	CCDS43192.1	0.02	-0.184169	TCCxCCC	COVERED																																																																																			NOVEL	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340776.1	5	2.706481	KEEP	1	0	0	9	246	GG	0.99254	0.420319	0		-	3	60	87	0	0	6.53453	16	60	477	41	ENST00000397537.2	0.157895	0.423478
WDR53	348793	__UNKNOWN__	__UNKNOWN__	3	196293171	196293171	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196293171A>G	ENST00000433160.1	-	2	273				WDR53_ENST00000332629.5_Intron|WDR53_ENST00000429115.1_Intron			Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	NA		NA								breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		atgttgcccaagctggtctaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798	348793		WD repeat domain containing	28786	protein-coding gene	gene with protein product		615110			NA	12477932	Standard	NM_182627	NM_182627	NA	Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000433160.1:c.3+890T>C	chr3.hg19:g.196293171A>G		NA	A0MNP1	hg19		0.02	-0.149105	CCAxGCT	COVERED																																																																																			NOVEL	WDR53-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000340690.1	7	3.007337	KEEP	0	0	0	10	273	AA	0.992708	0.289872	0		-	3	40	103	0	0	8.572882	11	60	334	43	ENST00000433160.1	0.214286	0.292001
FBXO45	200933	__UNKNOWN__	__UNKNOWN__	3	196305185	196305185	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196305185C>T	ENST00000311630.6	+	2	972				FBXO45_ENST00000440469.1_Intron	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	NA		NA			anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ggattacaggcgtgagccacc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013	200933		F-boxes /  other	29148	protein-coding gene	gene with protein product		609112			NA		Standard		NM_001105573	NA	Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.675+505C>T	chr3.hg19:g.196305185C>T		NA	A6NF90|D3DXB5	hg19	CCDS46985.1	0.02	-0.18421	AGGxGTG	UNCOVERED																																																																																			NOVEL	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340687.2	11	2.407004	KEEP	3	0	0	8	242	CC	0	0	0		+	4	60	113	0	0	8.962769	15	60	509	47	ENST00000311630.6	0.210526	0.457757
SENP5	205564	__UNKNOWN__	__UNKNOWN__	3	196607778	196607778	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196607778T>C	ENST00000323460.5	+	2	218				SENP5_ENST00000445299.2_Intron|SENP5_ENST00000419026.1_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		tcccaaagtgttgggattaca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(47;891 1095 11174 13858 51271)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231	205564			28407	protein-coding gene	gene with protein product		612845	SUMO1/sentrin specific protease 5		NA	12477932	Standard	NM_152699	NM_152699	NA	Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.-31-4244T>C	chr3.hg19:g.196607778T>C		NA	B4DY82|Q96SA5	hg19	CCDS3322.1	0.02	-0.175393	GTGxTGG	COVERED																																																																																			NOVEL	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340524.1	5	2.405587	KEEP	0	0	0	8	213	TT	0.99257	0.384528	0		+	3	60	106	1	0	8.873279	11	60	308	39	ENST00000323460.5	0.214286	0.387407
SENP5	205564	__UNKNOWN__	__UNKNOWN__	3	196625718	196625718	__UNKNOWN__	Intron	SNP	G	G	C	rs564306832	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196625718G>C	ENST00000323460.5	+	3	1762				SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		attcgatgacgattccattca	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(47;891 1095 11174 13858 51271)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231	205564			28407	protein-coding gene	gene with protein product		612845	SUMO1/sentrin specific protease 5		NA	12477932	Standard	NM_152699	NM_152699	NA	Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1514-819G>C	chr3.hg19:g.196625718G>C		NA	B4DY82|Q96SA5	hg19	CCDS3322.1	0.02	1.438172	GACxATT	COVERED																																																																																			NOVEL	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340524.1	70	20.589204	KEEP	74	1	30	79	2290	GG	1	0.999956	0		+	4	49	133	2	0	8.554415	66	60	2109	370	ENST00000323460.5	0.057143	0.999956
SENP5	205564	__UNKNOWN__	__UNKNOWN__	3	196625739	196625739	__UNKNOWN__	Intron	SNP	A	A	G	rs13070752	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196625739A>G	ENST00000323460.5	+	3	1762				SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Intron	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		attccgttcaatgattccatt	0.408		NA											-|||	539	0.107628	0.0825	0.2349	5008	,	,	NA	97272	0.001	NA	0.2177	False	NA	,,,	NA	NA	NA	2504	0.0481	NA	NA	NA	Ovarian(47;891 1095 11174 13858 51271)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231	205564			28407	protein-coding gene	gene with protein product		612845	SUMO1/sentrin specific protease 5		NA	12477932	Standard	NM_152699	NM_152699	NA	Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1514-798A>G	chr3.hg19:g.196625739A>G		NA	B4DY82|Q96SA5	hg19	CCDS3322.1	0.02	1.628693	TCAxTGA	COVERED																																																																																			NOVEL	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340524.1	58	18.680065	KEEP	59	1	31	73	2035	AA	1	0.999948	0		+	5	60	167	0	0	11.336049	63	60	1942	320	ENST00000323460.5	0.073529	0.999948
NCBP2	22916	__UNKNOWN__	__UNKNOWN__	3	196663424	196663424	__UNKNOWN__	3'UTR	SNP	C	C	G	rs570317673		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196663424C>G	ENST00000447325.1	-	0	1068				NCBP2_ENST00000427641.2_3'UTR|NCBP2_ENST00000467803.1_Intron|NCBP2_ENST00000321256.5_3'UTR			P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of RNA export from nucleus (GO:0046833)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|RNA cap binding (GO:0000339)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)		tgggattacacgtgtgagcca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D59253	CCDS3323.1, CCDS46986.1	3q29	2013-02-12	2002-08-29		ENSG00000114503	ENSG00000114503	22916		RNA binding motif (RRM) containing	7659	protein-coding gene	gene with protein product		605133	nuclear cap binding protein subunit 2, 20kD		NA	7478990, 7651522, 8682299	Standard	NM_007362	NM_001042540	NA	Approved	NIP1, CBP20, Cbc2	uc003fxd.1	P52298	OTTHUMG00000155520	ENST00000447325.1:c.*458G>C	chr3.hg19:g.196663424C>G		NA	B2RE91|B4DMK7|E9PAR5|Q14924|Q2TS50	hg19		0.02	-0.298226	ACAxGTG	COVERED																																																																																			NOVEL	NCBP2-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000340476.1	2	3.308988	KEEP	0	0	0	11	318	CC	0.993072	0.794702	0		-	3	60	103	0	0	7.452553	28	60	888	61	ENST00000447325.1	0.096774	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	196725020	196725020	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:196725020C>T			NA	NA				AC011322.1 (11207 upstream) : MFI2-AS1 (1310 downstream)						NA		NA									NA						ctcaagcaatcctcctgcctc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.196725020C>T		NA		hg19		0.02	-0.175409	AATxCTC	COVERED																																																																																			NOVEL					0			4	2.406849	KEEP	0	0	0	8	240	CC	0.99257	0.384528	0			3	60	87	0	0	6.534299	16	60	534	36		0.157895	0.387407
AC024560.3	0	__UNKNOWN__	__UNKNOWN__	3	197348634	197348634	__UNKNOWN__	RNA	SNP	G	G	C	rs370500896	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:197348634G>C	ENST00000418868.1	-	0	625					NR_003266.2					NA		NA									NA						CAGCAGCACCGATGGGCCTGC	0.542		NA											G|||	18	0.00359425	0.0	0.0	5008	,	,	NA	22692	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0174	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000418868.1:	chr3.hg19:g.197348634G>C		NA		hg19		0.02	3.856145	ACCxATG	COVERED																																																																																			NOVEL	AC024560.3-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000340283.1	2	4.813085	KEEP	7	0	0	16	461	GG	0.997832	0.997816	0		-	6	60	205	0	0	13.483914	95	60	3085	183	ENST00000418868.1	0.059406	0.999984
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	197376835	197376835	__UNKNOWN__	IGR	SNP	T	T	C	rs6786162		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:197376835T>C			NA	NA				RP11-496H1.2 (3947 upstream) : AC024560.2 (10600 downstream)						NA		NA									NA						AATAAAGAACTTCAGAGAGGA	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.197376835T>C		NA		hg19		0.02	1.883173	AACxTCA	COVERED																																																																																			NOVEL					0			12	7.51916	KEEP	8	0	0	25	693	TT	0.999909	0.996142	0			6	40	191	1	0	13.155157	62	60	1816	146		0.088235	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	3	197376981	197376981	__UNKNOWN__	IGR	SNP	A	A	G	rs1058626		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr3:197376981A>G			NA	NA				RP11-496H1.2 (4093 upstream) : AC024560.2 (10454 downstream)						NA		NA									NA						AGCCCCCACGATGAGGAAAAA	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr3.hg19:g.197376981A>G		NA		hg19		0.02	1.514272	ACGxTGA	COVERED																																																																																			NOVEL					0			6	3.308596	KEEP	3	0	0	11	308	AA	0.992708	0.991583	0			4	40	132	0	0	8.331599	71	60	2089	137		0.053333	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	50199	50199	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:50199G>A			NA	NA				Z95704.4 (349 upstream) : ZNF595 (2979 downstream)						NA		NA									NA						ATAGCCggccgggcgcggtgg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.50199G>A		NA		hg19		0.02	1.508846	GCCxGGC	COVERED																																																																																			NOVEL					0			22	7.553112	KEEP	9	1	28	35	1042	GG	0.999997	0.976863	0			4	60	121	0	0	8.034623	44	60	1396	140		0.083333	0.976865
ZNF595	152687	__UNKNOWN__	__UNKNOWN__	4	53310	53310	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:53310C>T	ENST00000509152.2	+	0	113				ZNF595_ENST00000339368.6_3'UTR|ZNF595_ENST00000526473.2_5'UTR			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		CAGCCTCTGCCTCCCGTTGCT	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													130	107	114			NA	NA	4		NA											NA				53310		692	1591	2283	SO:0001623	5_prime_UTR_variant			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602	152687		Zinc fingers, C2H2-type, -	27196	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182524	NM_182524	NA	Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.-73C>T	chr4.hg19:g.53310C>T		NA		hg19		0.02	11.222367	TGCxTCC	COVERED																																																																																			NOVEL	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357817.2	13	6.681134	KEEP	0	8	220	100	3011	CC	1	1	0		+	67	60	2042	0	0	157.929338	330	60	11188	709	ENST00000509152.2	0.168766	1
ZNF595	152687	__UNKNOWN__	__UNKNOWN__	4	68079	68079	__UNKNOWN__	3'UTR	SNP	C	C	A	rs6599365		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:68079C>A	ENST00000509152.2	+	0	759				ZNF595_ENST00000339368.6_Intron			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TATGTTAATGCGAAATATGCA	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602	152687		Zinc fingers, C2H2-type, -	27196	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182524	NM_182524	NA	Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.*316C>A	chr4.hg19:g.68079C>A		NA		hg19		0.02	7.499434	ATGxGAA	COVERED																																																																																			NOVEL	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357817.2	54	3.463577	KEEP	0	11	310	121	3473	CC	1	1	0		+	19	60	566	0	0	36.173498	241	60	7864	582	ENST00000509152.2	0.073077	1
ZNF595	152687	__UNKNOWN__	__UNKNOWN__	4	68144	68144	__UNKNOWN__	3'UTR	SNP	G	G	A	rs61792212		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:68144G>A	ENST00000509152.2	+	0	824				ZNF595_ENST00000339368.6_Intron			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		GTCAGAGGAGGCACGTCAGGG	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602	152687		Zinc fingers, C2H2-type, -	27196	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182524	NM_182524	NA	Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.*381G>A	chr4.hg19:g.68144G>A		NA		hg19		0.02	6.248355	GAGxCAC	COVERED																																																																																			NOVEL	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357817.2	16	2.269511	KEEP	0	5	134	55	1639	GG	1	1	0		+	14	60	401	0	0	24.767283	187	60	6379	383	ENST00000509152.2	0.069652	1
ZNF876P	642280	__UNKNOWN__	__UNKNOWN__	4	212394	212394	__UNKNOWN__	RNA	SNP	T	T	C	rs75698580		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:212394T>C	ENST00000356347.3	+	0	172					NR_027481.1		Q49A33	Z876P_HUMAN	zinc finger protein 876, pseudogene	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						agcaagactctgtctcaaaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC028359		4p16.3	2011-04-20	2010-08-03	2009-07-22	ENSG00000198155	ENSG00000198155	642280			32472	pseudogene	pseudogene		NA			NA		Standard	NR_027481	NR_027481	NA	Approved		uc010iba.4	Q49A33	OTTHUMG00000159874	ENST00000356347.3:	chr4.hg19:g.212394T>C		NA		hg19		0.02	1.534701	CTCxGTC	COVERED																																																																																			NOVEL	ZNF876P-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000357870.2	24	6.344706	KEEP	1	4	122	64	1769	TT	1	0.999678	0		+	5	60	166	1	1	11.135646	66	60	2010	217	ENST00000356347.3	0.070423	0.999678
ZNF721	170960	__UNKNOWN__	__UNKNOWN__	4	471307	471307	__UNKNOWN__	Intron	SNP	A	A	G	rs188228608	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:471307A>G	ENST00000511833.2	-	2	101				ZNF721_ENST00000338977.5_Intron	NM_133474.3	NP_597731.2	Q8TF20	ZN721_HUMAN	zinc finger protein 721	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						gattacaggcatgagccaccg	0.532		NA											A|||	5	0.000998403	0.0008	0.0043	5008	,	,	NA	14849	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903	170960		Zinc fingers, C2H2-type, -	29425	protein-coding gene	gene with protein product		NA			NA	11853319	Standard	NM_133474	NM_133474	NA	Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000511833.2:c.93-4817T>C	chr4.hg19:g.471307A>G		NA	Q69YG7	hg19	CCDS46991.1	0.02	-0.271882	GGCxTGA	COVERED																																																																																			NOVEL	ZNF721-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357942.2	7	8.420093	KEEP	0	0	0	28	767	AA	0.999997	0.717313	0		-	3	60	100	0	0	7.152873	28	60	824	80	ENST00000511833.2	0.096774	0.717315
SLC26A1	10861	__UNKNOWN__	__UNKNOWN__	4	980493	980493	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:980493T>C	ENST00000398520.2	-	2	679					NM_134425.1	NP_602297.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	NA		NA			3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			tgcagtgagctgagatcgcgc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217	10861		Solute carriers	10993	protein-coding gene	gene with protein product		610130	solute carrier family 26 (sulfate transporter), member 1		NA		Standard	NM_022042, NM_134425	NM_213613	NA	Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000398520.2:c.576+4422A>G	chr4.hg19:g.980493T>C		NA	A8K9N2|Q7Z5R3|Q96BK0	hg19	CCDS33933.1	0.02	-0.412185	AGCxGAG	COVERED																																																																																			NOVEL	SLC26A1-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358785.1	7	4.69616	KEEP	0	3	86	46	1194	TT	1	0.954491	0		-	4	60	118	0	0	8.159761	34	60	981	112	ENST00000398520.2	0.105263	0.954491
CTBP1	1487	__UNKNOWN__	__UNKNOWN__	4	1231470	1231470	__UNKNOWN__	Intron	SNP	C	C	T	rs376112446		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:1231470C>T	ENST00000382952.3	-	3	547				CTBP1_ENST00000290921.6_Intron|CTBP1_ENST00000510568.1_3'UTR|CTBP1_ENST00000515690.1_Intron	NM_001012614.1	NP_001012632.1	Q13363	CTBP1_HUMAN	C-terminal binding protein 1	NA		NA			Golgi organization (GO:0007030)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone H4 acetylation (GO:0090241)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone deacetylation (GO:0031065)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of transcription by chromatin organization (GO:0034401)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|urinary_tract(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.00818)	Colorectal(103;0.2)		ACCCCGTGTCCACCTCCTGAT	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U37408	CCDS3348.1, CCDS43203.1	4p16	2008-02-05			ENSG00000159692	ENSG00000159692	1487			2494	protein-coding gene	gene with protein product	brefeldin A-ribosylated substrate	602618			NA	9479502	Standard	NM_001328	XM_005272261	NA	Approved	BARS	uc003gcv.1	Q13363	OTTHUMG00000089259	ENST00000382952.3:c.162+500G>A	chr4.hg19:g.1231470C>T		NA	Q4W5N3|Q7Z2Q5	hg19	CCDS43203.1	0.02	-0.324545	GTCxACC	UNCOVERED																																																																																			NOVEL	CTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359459.1	2	2.40653	KEEP	3	0	0	8	228	CC	0	0	0		-	8	60	232	0	0	18.847416	27	60	898	77	ENST00000382952.3	0.228571	0.835716
WHSC1	7468	__UNKNOWN__	__UNKNOWN__	4	1883232	1883232	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:1883232C>A	ENST00000508803.1	+	1	119				WHSC1_ENST00000514045.1_Intron	NM_001042424.2	NP_001035889.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	NA		NA			anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		cctcatgatccacccgcctcg	0.532		NA	T	IGH@	MM																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685	7468		Zinc fingers, PHD-type	12766	protein-coding gene	gene with protein product		602952			NA	9618163, 9787135	Standard	NM_133330	NM_133334	NA	Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000508803.1:c.-30+9963C>A	chr4.hg19:g.1883232C>A		NA	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	hg19	CCDS33940.1	0.02	-0.070174	ATCxACC	UNCOVERED																																																																																			NOVEL	WHSC1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366357.2	7	3.610022	KEEP	13	0	0	12	354	CC	0	0	0		+	3	60	88	0	0	8.15468	4	60	132	42	ENST00000508803.1	0.428571	0.054137
NELFA	7469	__UNKNOWN__	__UNKNOWN__	4	1996048	1996048	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:1996048C>T	ENST00000411638.2	-	2	226				NELFA_ENST00000542778.1_Intron|NELFA_ENST00000382882.3_Intron	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	NA		NA			gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)				NA						tcccagcactctgggaggcta	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049	7469			12768	protein-coding gene	gene with protein product		606026	Wolf-Hirschhorn syndrome candidate 2	WHSC2	NA	10409432	Standard	NM_005663	NM_005663	NA	Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.211-2606G>A	chr4.hg19:g.1996048C>T		NA	A2A2T1|O95392	hg19		0.02	-0.105262	ACTxTGG	UNCOVERED																																																																																			NOVEL	NELFA-015	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000473007.1	10	2.407044	KEEP	0	0	0	8	247	CC	0.99257	0.138793	0		-	3	60	85	1	0	7.132034	8	60	278	28	ENST00000411638.2	0.272727	0.139832
POLN	353497	__UNKNOWN__	__UNKNOWN__	4	2190094	2190094	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:2190094G>A	ENST00000511885.2	-	7	1375				POLN_ENST00000382865.1_Intron|POLN_ENST00000515357.1_Intron			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	NA		NA			double-strand break repair via homologous recombination (GO:0000724)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	nucleus (GO:0005634)	cyclin binding (GO:0030332)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(2)|skin(4)|urinary_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(23;0.0955)			ttgggaggccgaggtgggcag	0.493		NA						DNA polymerases (catalytic subunits)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF044578	CCDS3360.1	4p16.3	2012-05-18			ENSG00000130997	ENSG00000130997	353497		DNA polymerases	18870	protein-coding gene	gene with protein product		610887			NA	12794064	Standard	NM_181808	NM_181808	NA	Approved		uc003ger.2	Q7Z5Q5	OTTHUMG00000090081	ENST00000511885.2:c.1021+4836C>T	chr4.hg19:g.2190094G>A		NA	A2A336|B4E158|Q4TTW4|Q6ZNF4	hg19	CCDS3360.1	0.02	-0.210531	GCCxAGG	UNCOVERED																																																																																			NOVEL	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000205684.2	8	3.008667	KEEP	8	0	0	10	300	GG	0	0	0		-	3	60	89	0	0	6.465596	20	60	667	55	ENST00000511885.2	0.130435	0.522161
SH3BP2	6452	__UNKNOWN__	__UNKNOWN__	4	2841544	2841544	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:2841544A>G	ENST00000356331.5	+	0	7930				SH3BP2_ENST00000503393.2_3'UTR|SH3BP2_ENST00000442312.2_3'UTR	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	NA		NA			positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		tcccatcttgacctcccaaag	0.408		NA							Cherubism												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266	6452		Pleckstrin homology (PH) domain containing, SH2 domain containing	10825	protein-coding gene	gene with protein product		602104	Cherubism		NA	9299232, 11381256	Standard	NM_003023	NM_003023	NA	Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.*5983A>G	chr4.hg19:g.2841544A>G		NA	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	hg19	CCDS33944.1	0.02	-0.29805	TTGxCCT	COVERED																																																																																			NOVEL	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362406.2	6	5.410456	KEEP	0	0	0	18	464	AA	0.99986	0.78095	0		+	3	60	92	0	0	6.313282	29	70	794	66	ENST00000356331.5	0.09375	0.78106
ADD1	118	__UNKNOWN__	__UNKNOWN__	4	2872978	2872978	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:2872978G>A	ENST00000355842.3	+	2	843				ADD1_ENST00000398125.1_Intron|ADD1_ENST00000446856.1_Intron|ADD1_ENST00000503455.2_Intron|ADD1_ENST00000264758.7_Intron|ADD1_ENST00000513328.2_Intron			P35611	ADDA_HUMAN	adducin 1 (alpha)	NA		NA			actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		gattacaggcgtgagccaccg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(71;505 1201 20414 34538 37449)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274	118			243	protein-coding gene	gene with protein product		102680			NA	1840603	Standard	NM_014189	NM_001119	NA	Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000355842.3:c.-21+3122G>A	chr4.hg19:g.2872978G>A		NA	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	hg19		0.02	-0.420966	GGCxTGA	COVERED																																																																																			NOVEL	ADD1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000242839.1	6	9.626301	KEEP	0	0	0	32	937	GG	0.999997	0.954489	0		+	4	60	111	0	0	7.169791	41	60	1288	108	ENST00000355842.3	0.088889	0.954491
NOP14	8602	__UNKNOWN__	__UNKNOWN__	4	2940455	2940455	__UNKNOWN__	Intron	SNP	G	G	A	rs377608894		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:2940455G>A	ENST00000314262.6	-	18	2642				NOP14-AS1_ENST00000515194.1_RNA|NOP14_ENST00000502735.1_Intron|NOP14-AS1_ENST00000512802.1_RNA|NOP14_ENST00000398071.4_Intron|NOP14_ENST00000416614.2_3'UTR|NOP14-AS1_ENST00000512712.2_RNA|NOP14-AS1_ENST00000507999.1_RNA|NOP14-AS1_ENST00000507702.1_RNA|NOP14-AS1_ENST00000503709.1_RNA|NOP14-AS1_ENST00000505731.1_RNA|NOP14_ENST00000507120.1_Intron	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	NA		NA			endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						ggctggtctcgaactcctggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269	8602			16821	protein-coding gene	gene with protein product	NOP14 homolog (S. cerevisiae)	611526	chromosome 4 open reading frame 9, nucleolar protein 14, nucleolar protein 14 homolog (yeast), NOP14 nucleolar protein homolog (yeast)	C4orf9, NOL14	NA	9734812, 11694595	Standard	NM_003703	XR_241655	NA	Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.2571+83C>T	chr4.hg19:g.2940455G>A		NA	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	hg19	CCDS33945.1	0.02	2.900887	CTCxAAC	COVERED																																																																																			NOVEL	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358135.2	44	21.488805	KEEP	0	4	100	107	3181	GG	1	0.999995	0		-	8	60	230	0	0	14.620497	95	60	3056	323	ENST00000314262.6	0.07767	0.999995
DOK7	285489	__UNKNOWN__	__UNKNOWN__	4	3502468	3502468	__UNKNOWN__	3'UTR	SNP	G	G	A	rs546206365		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:3502468G>A	ENST00000512714.1	+	0	935				DOK7_ENST00000389653.2_Silent_p.T581T			Q18PE1	DOK7_HUMAN	docking protein 7	NA		NA			neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CCACCGAGACGGCGCACAGAG	0.692		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15775	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920	285489			26594	protein-coding gene	gene with protein product		610285	chromosome 4 open reading frame 25	C4orf25	NA	16794080	Standard	NM_173660	NM_173660	NA	Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000512714.1:c.*932G>A	chr4.hg19:g.3502468G>A		NA	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	hg19		0.02	-0.34206	GACxGCG	COVERED																																																																																			NOVEL	DOK7-007	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000357910.1	1	2.707581	KEEP	0	0	0	9	267	GG	0.99254	0.859287	0		+	3	60	94	0	0	6.349913	33	60	1063	70	ENST00000512714.1	0.083333	0.865745
LINC00955	285492	__UNKNOWN__	__UNKNOWN__	4	3589503	3589503	__UNKNOWN__	Intron	SNP	T	T	C	rs28551488	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:3589503T>C	ENST00000514422.1	+	2	255									long intergenic non-protein coding RNA 955	NA		NA									NA						CACCTGCACTTCCAGATGAGA	0.552		NA											N|||	999	0.199481	0.4244	0.1988	5008	,	,	NA	21491	0.0069	NA	0.2097	False	NA	,,,	NA	NA	NA	2504	0.0838	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092743		4p16.3	2014-04-09			ENSG00000216560	ENSG00000216560	285492			26644	other	unknown		NA			NA		Standard		NR_040045	NA	Approved	FLJ35424			OTTHUMG00000159817	ENST00000514422.1:c.-31-99T>C	chr4.hg19:g.3589503T>C		NA		hg19		0.02	-0.438581	ACTxCCA	COVERED																																																																																			NOVEL	LINC00955-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000357538.6	1	2.406175	KEEP	0	0	0	8	224	TT	0.99257	0.952727	0		+	8	60	265	0	0	23.682934	16	60	493	93	ENST00000514422.1	0.333333	0.959859
LINC00955	285492	__UNKNOWN__	__UNKNOWN__	4	3589508	3589508	__UNKNOWN__	Intron	SNP	A	A	G	rs28676579	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:3589508A>G	ENST00000514422.1	+	2	255									long intergenic non-protein coding RNA 955	NA		NA									NA						GCACTTCCAGATGAGACTTCC	0.557		NA											N|||	998	0.199281	0.4236	0.1988	5008	,	,	NA	21374	0.0069	NA	0.2097	False	NA	,,,	NA	NA	NA	2504	0.0838	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092743		4p16.3	2014-04-09			ENSG00000216560	ENSG00000216560	285492			26644	other	unknown		NA			NA		Standard		NR_040045	NA	Approved	FLJ35424			OTTHUMG00000159817	ENST00000514422.1:c.-31-94A>G	chr4.hg19:g.3589508A>G		NA		hg19		0.02	-0.429813	CAGxTGA	COVERED																																																																																			NOVEL	LINC00955-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000357538.6	1	2.406437	KEEP	0	0	0	8	228	AA	0.99257	0.9474	0		+	8	60	264	0	0	23.763567	15	60	467	94	ENST00000514422.1	0.347826	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	4057205	4057205	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:4057205C>T			NA	NA				AC116562.2 (18291 upstream) : AC116562.1 (28855 downstream)						NA		NA									NA						ttagtagaaacgaggtctcgt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.4057205C>T		NA		hg19		0.02	-0.236843	AAAxGAG	COVERED																																																																																			NOVEL					0			16	6.016169	KEEP	5	0	0	20	580	CC	0.997832	0.611079	0			3	49	88	0	0	6.306627	21	52	699	65		0.125	0.612407
STX18-AS1	100507266	__UNKNOWN__	__UNKNOWN__	4	4628013	4628013	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:4628013A>G	ENST00000610009.1	+	0	442				STX18-AS1_ENST00000502693.1_RNA	NR_037888.1				STX18 antisense RNA 1 (head to head)	NA		NA									NA						gtcttgctctattgcccaggc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							4p16.2	2013-06-21			ENSG00000247708	ENSG00000247708	100507266		Long non-coding RNAs	48877	non-coding RNA	RNA, long non-coding		NA			NA	23708191	Standard		NR_037888	NA	Approved	LOC100507266			OTTHUMG00000159923	ENST00000610009.1:	chr4.hg19:g.4628013A>G		NA		hg19		0.02	-0.052626	TCTxTTG	UNCOVERED																																																																																			NOVEL	STX18-AS1-006	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000472458.1	2	2.405218	KEEP	2	0	0	8	209	AA	0	0	0		+	2	60	69	0	0	6.393013	3	60	88	26	ENST00000610009.1	0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	4859399	4859399	__UNKNOWN__	IGR	SNP	G	G	A	rs201368770		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:4859399G>A			NA	NA				RP11-326I19.3 (6845 upstream) : MSX1 (1993 downstream)						NA		NA									NA						gaagaagaaggaggaggagga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.4859399G>A		NA		hg19		0.02	-0.192934	AAGxAGG	COVERED																																																																																			NOVEL					0			11	2.706855	KEEP	0	0	0	9	261	GG	0.99254	0.454342	0			4	60	107	0	0	8.581245	13	60	414	37		0.235294	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	5711577	5711577	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:5711577C>A			NA	NA				EVC2 (302 upstream) : EVC (1346 downstream)						NA		NA									NA						caggcgtgagcaaccacacct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.5711577C>A		NA		hg19		0.02	-0.07017	GAGxAAC	UNCOVERED																																																																																			NOVEL					0			4	3.009059	KEEP	0	0	0	10	309	CC	0.992708	0.053742	0			3	60	83	0	0	7.432054	5	60	169	25		0.375	0.054137
PPP2R2C	5522	__UNKNOWN__	__UNKNOWN__	4	6384272	6384272	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:6384272C>T	ENST00000382599.4	-	2	287				PPP2R2C_ENST00000314348.8_Intron|PPP2R2C_ENST00000506140.1_Intron|PPP2R2C_ENST00000515571.1_Intron|PPP2R2C_ENST00000507294.1_Intron			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	NA		NA			regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	28						tcagcctcatcctctgcagct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF086924	CCDS3388.1, CCDS56304.1, CCDS56305.1, CCDS3387.1	4p16.1	2013-01-10	2010-04-14		ENSG00000074211	ENSG00000074211	5522	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits, WD repeat domain containing	9306	protein-coding gene	gene with protein product	PP2A subunit B isoform gamma	605997	protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), gamma isoform, protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform		NA	10574460, 10945473	Standard	NM_181876	NM_020416	NA	Approved	PR52, IMYPNO, MGC33570, PR55G	uc003gja.3	Q9Y2T4	OTTHUMG00000090445	ENST00000382599.4:c.71-1451G>A	chr4.hg19:g.6384272C>T		NA	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	hg19		0.02	0.98333	CATxCTC	COVERED																																																																																			NOVEL	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000206889.2	12	14.741997	KEEP	0	0	0	49	1448	CC	1	0.996724	0		-	6	60	162	0	0	10.223366	63	60	2088	157	ENST00000382599.4	0.086957	0.996724
KIAA0232	9778	__UNKNOWN__	__UNKNOWN__	4	6813235	6813235	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:6813235T>A	ENST00000307659.5	+	2	186				KIAA0232_ENST00000503278.1_Intron|KIAA0232_ENST00000425103.1_Intron	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	NA		NA					ATP binding (GO:0005524)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						tttggcatgatcttggctcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871	9778			28992	protein-coding gene	gene with protein product		NA			NA	9039502	Standard	NM_014743	NM_014743	NA	Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.-270+6902T>A	chr4.hg19:g.6813235T>A		NA	A7E2D2	hg19	CCDS43209.1	0.02	-0.114016	TGAxCTT	UNCOVERED																																																																																			NOVEL	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359102.2	3	2.70654	KEEP	0	0	0	9	244	TT	0.99254	0.161255	0		+	3	60	86	0	0	6.982151	10	60	300	31	ENST00000307659.5	0.230769	0.162467
TBC1D14	57533	__UNKNOWN__	__UNKNOWN__	4	6914973	6914973	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:6914973G>T	ENST00000409757.4	+	1	107				TBC1D14_ENST00000448507.1_Intron	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	NA		NA			negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						ccacctgcctgggcctcccaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405	57533			29246	protein-coding gene	gene with protein product		614855			NA	10718198	Standard	NM_020773	NM_020773	NA	Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.-18+3295G>T	chr4.hg19:g.6914973G>T		NA	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	hg19	CCDS3394.2	0.02	-0.087721	CCTxGGC	UNCOVERED																																																																																			NOVEL	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206981.3	5	3.009082	KEEP	1	0	0	10	311	CG	0.992708	0.138812	0		+	3	60	87	0	0	7.643011	6	60	211	34	ENST00000409757.4	0.333333	0.139832
TBC1D14	57533	__UNKNOWN__	__UNKNOWN__	4	6937623	6937623	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:6937623G>A	ENST00000409757.4	+	2	846				TBC1D14_ENST00000448507.1_Intron	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	NA		NA			negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						cacccacctcggcctcccaaa	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405	57533			29246	protein-coding gene	gene with protein product		614855			NA	10718198	Standard	NM_020773	NM_020773	NA	Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.722+11785G>A	chr4.hg19:g.6937623G>A		NA	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	hg19	CCDS3394.2	0.02	-0.131569	CTCxGCC	COVERED																																																																																			NOVEL	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206981.3	7	3.008538	KEEP	4	0	0	10	298	GG	0.99257	0.22747	0		+	3	60	85	0	0	6.773051	11	60	366	42	ENST00000409757.4	0.214286	0.229173
TADA2B	93624	__UNKNOWN__	__UNKNOWN__	4	7059393	7059393	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:7059393A>G	ENST00000310074.7	+	0	4064					NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	NA		NA			chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	SAGA-type complex (GO:0070461)|STAGA complex (GO:0030914)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						gcatgcctgtagtcccagcta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK026299	CCDS47007.1	4p16.1	2009-10-02			ENSG00000173011	ENSG00000173011	93624			30781	protein-coding gene	gene with protein product		608790			NA	12972612, 18936164	Standard	NM_152293	NM_152293	NA	Approved	MGC21874	uc003gjw.4	Q86TJ2	OTTHUMG00000159983	ENST00000310074.7:c.*2612A>G	chr4.hg19:g.7059393A>G		NA	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	hg19	CCDS47007.1	0.02	-0.026317	TGTxGTC	UNCOVERED																																																																																			NOVEL	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358687.2	5	2.404687	KEEP	7	0	0	8	207	AA	0	0	0		+	2	51	69	0	0	7.024896	1	10	31	22	ENST00000310074.7	0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	9487318	9487318	__UNKNOWN__	IGR	SNP	C	C	G	rs111725470		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:9487318C>G			NA	NA				AC116655.1 (14534 upstream) : MIR548I2 (70470 downstream)						NA		NA									NA						ttcaatgtcacggtctcggct	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.9487318C>G		NA		hg19		0.02	-0.052632	TCAxGGT	UNCOVERED																																																																																			NOVEL					0			7	2.705329	KEEP	6	0	0	9	237	CC	0	0	0			2	25	74	0	0	6.695833	4	49	126	27		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	9740222	9740222	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:9740222A>G			NA	NA				AC097493.1 (138171 upstream) : DRD5 (43035 downstream)						NA		NA									NA						cacctgcctcagcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.9740222A>G		NA		hg19		0.02	-0.105261	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			10	3.910307	KEEP	3	0	0	13	365	AA	0.993634	0.138942	0			3	60	103	0	0	8.932423	8	60	249	37		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	12430310	12430310	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:12430310A>G			NA	NA				RNU6-578P (115996 upstream) : RP11-22A3.2 (430414 downstream)						NA		NA									NA						tcctgacctcatgatccgccc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.12430310A>G		NA		hg19		0.02	-0.105258	CTCxTGA	UNCOVERED																																																																																			NOVEL					0			3	2.406729	KEEP	2	0	0	8	233	AA	0	0	0			3	60	96	0	0	8.101117	9	60	279	31		0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	13201132	13201132	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:13201132T>C			NA	NA				RNU6-962P (148097 upstream) : HSP90AB2P (133905 downstream)						NA		NA									NA						Gggctgggcgtggtggctcac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.13201132T>C		NA		hg19		0.02	-0.157875	GCGxGGT	COVERED																																																																																			NOVEL					0			9	3.608093	KEEP	1	0	0	12	321	TT	0.993072	0.32057	0			3	59	100	0	0	8.078864	13	60	386	47		0.1875	0.322807
BST1	683	__UNKNOWN__	__UNKNOWN__	4	15734220	15734220	__UNKNOWN__	3'UTR	SNP	C	C	T	rs111400048	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:15734220C>T	ENST00000382346.3	+	0	1803							Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	NA		NA			humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)			central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						ggattacaggcgtgagccacc	0.438		NA											C|||	432	0.086262	0.031	0.0447	5008	,	,	NA	15765	0.2639	NA	0.0089	False	NA	,,,	NA	NA	NA	2504	0.0869	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	683	3.2.2.5	CD molecules	1118	protein-coding gene	gene with protein product	NAD(+) nucleosidase, ADP-ribosyl cyclase 2	600387			NA	8202488	Standard	NM_004334	NM_004334	NA	Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000382346.3:c.*752C>T	chr4.hg19:g.15734220C>T		NA	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	hg19		0.02	1.122784	AGGxGTG	COVERED																																																																																			NOVEL	BST1-002	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000214969.1	32	11.922157	KEEP	0	3	71	65	1869	CC	1	0.999956	0		+	5	60	151	0	0	9.111059	85	60	2693	238	ENST00000382346.3	0.055556	0.999956
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	15749566	15749566	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:15749566T>C			NA	NA				BST1 (15156 upstream) : CD38 (30334 downstream)						NA		NA									NA						tcctaaagtgttgggattaca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.15749566T>C		NA		hg19		0.02	-0.078941	GTGxTGG	UNCOVERED																																																																																			NOVEL					0			3	2.405819	KEEP	0	0	0	8	218	TT	0.99257	0.076761	0			3	60	99	0	0	9.255488	4	60	120	26		0.428571	0.077336
AC006160.5	0	__UNKNOWN__	__UNKNOWN__	4	17610957	17610957	__UNKNOWN__	RNA	SNP	G	G	A	rs28630006	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:17610957G>A	ENST00000511010.1	-	0	537										NA		NA									NA						gaggcaggtggatcacctgag	0.502		NA											G|||	3094	0.617812	0.4319	0.7032	5008	,	,	NA	14119	0.8542	NA	0.6461	False	NA	,,,	NA	NA	NA	2504	0.5358	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000511010.1:	chr4.hg19:g.17610957G>A		NA		hg19		0.02	-0.289463	GTGxATC	COVERED																																																																																			NOVEL	AC006160.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000360040.1	29	4.277729	KEEP	18	2	47	31	936	GG	0.999879	0.780965	0		-	6	60	169	1	0	13.446156	22	60	754	103	ENST00000511010.1	0.214286	0.78106
MED28	80306	__UNKNOWN__	__UNKNOWN__	4	17620243	17620243	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:17620243A>G	ENST00000237380.7	+	2	183					NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	NA		NA			negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						aggttcaagcaattctcctgc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579	80306			24628	protein-coding gene	gene with protein product		610311	mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)		NA	11779215, 15467741	Standard	NM_025205	NM_025205	NA	Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.160-1281A>G	chr4.hg19:g.17620243A>G		NA	Q9BZJ5	hg19	CCDS33963.1	0.02	-0.096482	AGCxATT	UNCOVERED																																																																																			NOVEL	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360055.3	7	3.003609	KEEP	3	0	0	10	262	AA	0.99257	0.119541	0		+	3	42	94	0	0	8.178639	7	60	213	31	ENST00000237380.7	0.3	0.120436
LCORL	254251	__UNKNOWN__	__UNKNOWN__	4	17898184	17898184	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:17898184T>C	ENST00000326877.4	-	6	807				LCORL_ENST00000382226.5_Intron|LCORL_ENST00000382224.1_Intron|LCORL_ENST00000539056.1_Intron	NM_153686.7	NP_710153.2	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	NA		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						ggattacaggtgtgagccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177	254251			30776	protein-coding gene	gene with protein product		611799			NA	12560079	Standard	NM_153686	NM_153686	NA	Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000326877.4:c.683-10400A>G	chr4.hg19:g.17898184T>C		NA	Q96NK1	hg19	CCDS3425.1	0.02	-0.122785	AGGxGTG	COVERED																																																																																			NOVEL	LCORL-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250373.2	8	3.910089	KEEP	0	0	0	13	366	TT	0.994391	0.19521	0		-	3	60	95	0	0	8.001178	9	60	274	42	ENST00000326877.4	0.25	0.196312
KCNIP4	80333	__UNKNOWN__	__UNKNOWN__	4	21305686	21305686	__UNKNOWN__	Intron	SNP	G	G	C	rs59118185		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:21305686G>C	ENST00000382148.3	-	1	425				KCNIP4_ENST00000382152.2_Intron|KCNIP4_ENST00000509207.1_Intron|KCNIP4_ENST00000447367.2_Intron	NM_001035003.1	NP_001030175.1	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	NA		NA				dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				gagagagagagagagacagag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774	80333		EF-hand domain containing	30083	protein-coding gene	gene with protein product		608182			NA	11805342, 11847232	Standard	NM_025221	XM_005248190	NA	Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382148.3:c.88+393286C>G	chr4.hg19:g.21305686G>C		NA	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	hg19	CCDS43217.1	0.02	-0.175265	AGAxAGA	COVERED																																																																																			NOVEL	KCNIP4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360410.3	15	2.407038	KEEP	8	0	0	8	241	GG	0.99257	0.384528	0		-	3	60	94	0	1	7.675028	11	60	319	43	ENST00000382148.3	0.214286	0.387407
PPARGC1A	10891	__UNKNOWN__	__UNKNOWN__	4	23797127	23797127	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:23797127T>C	ENST00000264867.2	-	0	2834				PPARGC1A_ENST00000509702.1_Intron	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	NA		NA			androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				cacacatacatacacacacac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(29;694 744 13796 34866 44181)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819	10891		RNA binding motif (RRM) containing	9237	protein-coding gene	gene with protein product		604517	peroxisome proliferative activated receptor, gamma, coactivator 1, peroxisome proliferative activated receptor, gamma, coactivator 1, alpha	PPARGC1	NA	10585775	Standard	NM_013261	NM_013261	NA	Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.*318A>G	chr4.hg19:g.23797127T>C		NA	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	hg19	CCDS3429.1	0.02	1.66343	ACAxACA	COVERED																																																																																			NOVEL	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214976.1	13	5.674288	KEEP	0	3	85	49	1225	TT	1	0.987943	0		-	4	70	125	0	0	8.12455	53	70	1496	146	ENST00000264867.2	0.070175	0.987943
CCDC149	91050	__UNKNOWN__	__UNKNOWN__	4	24827850	24827850	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:24827850A>G	ENST00000389609.4	-	11	1109				CCDC149_ENST00000504487.1_Intron|CCDC149_ENST00000428116.2_Intron|CCDC149_ENST00000502801.1_Intron	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	NA		NA								cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				ccaaagtgctaggattacagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982	91050			25405	protein-coding gene	gene with protein product		NA			NA	17457313	Standard	NM_173463	NM_173463	NA	Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.966-3655T>C	chr4.hg19:g.24827850A>G		NA	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	hg19	CCDS33967.2	0.02	-0.157868	GCTxGGA	COVERED																																																																																			NOVEL	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360157.1	10	2.706247	KEEP	0	0	0	9	246	AA	0.99254	0.320398	0		-	4	60	133	0	0	11.181216	13	60	382	38	ENST00000389609.4	0.235294	0.322807
SEPSECS	51091	__UNKNOWN__	__UNKNOWN__	4	25161303	25161303	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:25161303C>A	ENST00000382103.2	-	1	187				SEPSECS_ENST00000302922.3_Intron	NM_016955.3	NP_058651.3	Q9HD40	SPCS_HUMAN	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase	NA		NA			selenocysteine incorporation (GO:0001514)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	pyridoxal phosphate binding (GO:0030170)|transferase activity, transferring selenium-containing groups (GO:0016785)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(2)|stomach(1)	8		Breast(46;0.173)				ctgaggcaggcgaatggcgtg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ238617	CCDS3432.1, CCDS3432.2	4p15.2	2008-10-27			ENSG00000109618	ENSG00000109618	51091			30605	protein-coding gene	gene with protein product	soluble liver antigen/liver pancreas antigen	613009			NA	16230358, 10931155, 17142313, 17194211	Standard	NM_016955	NM_016955	NA	Approved	SLA/LP, SLA	uc003grg.3	Q9HD40	OTTHUMG00000128563	ENST00000382103.2:c.114+574G>T	chr4.hg19:g.25161303C>A		NA	A8K8W1|Q0D2P3|Q17RT1|Q9NXZ5|Q9UGM9|Q9Y353	hg19	CCDS3432.2	0.02	-0.244934	AGGxGAA	COVERED																																																																																			NOVEL	SEPSECS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250414.2	2	2.335365	KEEP	0	1	26	17	460	CC	0.999859	0.641257	0		-	4	60	118	0	0	8.729913	24	60	671	50	ENST00000382103.2	0.142857	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	25636916	25636916	__UNKNOWN__	IGR	SNP	C	C	A	rs13117563		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:25636916C>A			NA	NA				RP11-302F12.3 (15829 upstream) : SLC34A2 (20527 downstream)						NA		NA									NA						aaataaaaaacaaaaaaaccc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.25636916C>A		NA		hg19		0.02	-0.078948	AAAxAAA	UNCOVERED																																																																																			NOVEL					0			7	3.610878	KEEP	0	0	0	12	371	CC	0.993634	0.076843	0			3	60	87	0	0	7.643059	6	60	209	30		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	26211331	26211331	__UNKNOWN__	IGR	SNP	C	C	T	rs62409703		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:26211331C>T			NA	NA				SMIM20 (279896 upstream) : RBPJ (110000 downstream)						NA		NA									NA						ctctctccctcccttcctcct	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.26211331C>T		NA		hg19		0.02	-0.078136	CCTxCCT	UNCOVERED																																																																																			NOVEL					0			8	3.309836	KEEP	9	0	0	11	336	CC	0	0	0			5	40	102	0	0	12.476462	0	0	0	39		1	0.077336
RBPJ	3516	__UNKNOWN__	__UNKNOWN__	4	26337525	26337525	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:26337525A>G	ENST00000348160.4	+	1	249				RBPJ_ENST00000507561.1_Intron|RBPJ_ENST00000345843.3_Intron|RBPJ_ENST00000342295.1_Intron|RBPJ_ENST00000511401.1_Intron|RBPJ_ENST00000361572.6_Intron|RBPJ_ENST00000355476.3_Intron	NM_015874.4	NP_056958.3	Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	NA		NA			angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				gattacaggcatgagccacca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214	3516			5724	protein-coding gene	gene with protein product	suppressor of hairless homolog (Drosophila)	147183	recombining binding protein suppressor of hairless (Drosophila)	IGKJRB1, RBPSUH	NA	8406481, 9290259	Standard	NM_015874	NM_005349	NA	Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000348160.4:c.20+14855A>G	chr4.hg19:g.26337525A>G		NA	B4DY22|Q5XKH9|Q6P1N3	hg19	CCDS43219.1	0.02	-0.131557	GGCxTGA	COVERED																																																																																			NOVEL	RBPJ-030	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361631.1	3	3.607863	KEEP	1	0	0	12	319	AA	0.993072	0.227586	0		+	3	60	104	0	0	8.672986	11	60	315	46	ENST00000348160.4	0.214286	0.229173
RP11-180C1.1	0	__UNKNOWN__	__UNKNOWN__	4	28394884	28394884	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:28394884C>T	ENST00000507759.1	-	3	243	c.43G>A	c.(43-45)Gat>Aat	p.D15N	RP11-180C1.1_ENST00000515720.1_Missense_Mutation_p.D15N						NA		NA									NA						acaggagaatcgcttgagccc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000507759.1:c.43G>A	chr4.hg19:g.28394884C>T	ENSP00000426781:p.Asp15Asn	NA		hg19		0.02	1.240933	AATxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.498	-0.552834	0.03996	.	.	ENSG00000250038	ENST00000507759;ENST00000515720	T;T	0.21734	1.99;1.99	0.418	-0.59	0.11679	.	.	.	.	.	T	0.15522	0.0374	.	.	.	.	.	.	.	.	.	.	.	.	T	0.33675	-0.9859	3	.	.	.	.	.	.	.	.	.	.	.	N	15	ENSP00000426781:D15N;ENSP00000424420:D15N	.	D	-	1	0	RP11-180C1.1	28003982	0.002000	0.14202	0.002000	0.10522	0.002000	0.02628	-0.689000	0.05144	-0.365000	0.08076	-0.361000	0.07541	GAT	NOVEL	RP11-180C1.1-001	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000365731.1	8	14.20081	KEEP	0	2	47	64	1838	CC	1	0.993703	0		-	5	60	135	0	0	8.3521	57	60	1839	156	ENST00000507759.1	0.080645	0.993703
RP11-180C1.1	0	__UNKNOWN__	__UNKNOWN__	4	28394891	28394891	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:28394891G>A	ENST00000507759.1	-	3	236	c.36C>T	c.(34-36)ggC>ggT	p.G12G	RP11-180C1.1_ENST00000515720.1_Silent_p.G12G						NA		NA									NA						aatcgcttgagcccaggaggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000507759.1:c.36C>T	chr4.hg19:g.28394891G>A		NA		hg19		0.02	1.441077	TGAxCCC	COVERED																																																																																			NOVEL	RP11-180C1.1-001	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000365731.1	11	14.508843	KEEP	0	2	56	68	2067	GG	1	0.9982	0		-	5	60	148	0	0	9.309833	67	60	2314	178	ENST00000507759.1	0.069444	0.9982
PCDH7	5099	__UNKNOWN__	__UNKNOWN__	4	30738450	30738450	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:30738450G>A	ENST00000543491.1	+	1	3174							O60245	PCDH7_HUMAN	protocadherin 7	NA		NA			homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						gagccaccgcgcccggccACA	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851	5099		Cadherins / Protocadherins : Non-clustered	8659	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 120	602988	BH-protocadherin (brain-heart)		NA	9615233	Standard	NM_032457, NM_002589	NM_002589	NA	Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000543491.1:c.3174+12232G>A	chr4.hg19:g.30738450G>A		NA	O60246|O60247|Q4W5C4	hg19	CCDS54753.1	0.02	-0.140353	CGCxCCC	UNCOVERED																																																																																			NOVEL	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding		4	2.407023	KEEP	3	0	0	8	242	GG	0	0	0		+	3	60	89	0	0	7.072245	12	60	399	44	ENST00000543491.1	0.2	0.260965
RP11-734I18.1	0	__UNKNOWN__	__UNKNOWN__	4	32035442	32035442	__UNKNOWN__	lincRNA	SNP	C	C	T	rs11725736	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:32035442C>T	ENST00000513211.1	+	0	426										NA		NA									NA						cgtgagccaccgcgcccggcc	0.468		NA											C|||	1764	0.352236	0.2209	0.2867	5008	,	,	NA	10252	0.37	NA	0.4583	False	NA	,,,	NA	NA	NA	2504	0.4489	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000513211.1:	chr4.hg19:g.32035442C>T		NA		hg19		0.02	-0.078941	CACxGCG	UNCOVERED																																																																																			NOVEL	RP11-734I18.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000360587.1	5	2.406539	KEEP	2	0	0	8	231	CC	0	0	0		+	6	60	184	0	0	18.773785	3	60	99	26	ENST00000513211.1	0.666667	0.077336
RP11-548L20.1	0	__UNKNOWN__	__UNKNOWN__	4	34222965	34222965	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:34222965G>A	ENST00000514877.1	-	0	265										NA		NA									NA						ggtggctcacgcctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000514877.1:	chr4.hg19:g.34222965G>A		NA		hg19		0.02	-0.105197	CACxCCT	UNCOVERED																																																																																			NOVEL	RP11-548L20.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000360364.1	7	2.407039	KEEP	12	0	0	8	243	GG	0	0	0		-	3	60	85	0	0	7.133228	8	60	248	40	ENST00000514877.1	0.272727	0.139832
ARAP2	116984	__UNKNOWN__	__UNKNOWN__	4	36163610	36163610	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:36163610G>A	ENST00000303965.4	-	12	2663					NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	NA		NA			regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						ggcacctgtagtcccagctac	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365	116984		ADP-ribosylation factor GTPase activating proteins, Sterile alpha motif (SAM) domain containing, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	16924	protein-coding gene	gene with protein product		606645	centaurin, delta 1	CENTD1	NA		Standard	NM_015230	NM_015230	NA	Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.2174-438C>T	chr4.hg19:g.36163610G>A		NA	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	hg19	CCDS3441.1	0.02	-0.035077	GTAxTCC	UNCOVERED																																																																																			NOVEL	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215074.2	6	3.007887	KEEP	3	0	0	10	285	GG	0.992708	0.019836	0		-	3	60	82	0	0	8.652269	1	25	36	20	ENST00000303965.4	0.75	0.019982
RP11-722M1.1	0	__UNKNOWN__	__UNKNOWN__	4	36546643	36546643	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:36546643T>C	ENST00000505298.1	-	0	366										NA		NA									NA						gagatggagtttcgctcttgt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000505298.1:	chr4.hg19:g.36546643T>C		NA		hg19		0.02	-0.035087	AGTxTCG	UNCOVERED																																																																																			NOVEL	RP11-722M1.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000365821.1	4	2.404544	KEEP	4	0	0	8	209	TT	0	0	0		-	2	25	73	0	0	7.050357	2	60	58	15	ENST00000505298.1	0.5	0.019982
C4orf19	55286	__UNKNOWN__	__UNKNOWN__	4	37462249	37462249	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:37462249C>G	ENST00000381980.4	+	1	100				C4orf19_ENST00000508175.1_Intron	NM_001104629.1	NP_001098099.1	Q8IY42	CD019_HUMAN	chromosome 4 open reading frame 19	NA		NA								large_intestine(1)|lung(3)|skin(3)|stomach(1)|urinary_tract(1)	9						tcacataaatctcctcttttg	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037906	CCDS3442.1	4p14	2008-02-05			ENSG00000154274	ENSG00000154274	55286			25618	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018302	NM_001104629	NA	Approved	FLJ11017	uc003gsw.4	Q8IY42	OTTHUMG00000128580	ENST00000381980.4:c.-73+6587C>G	chr4.hg19:g.37462249C>G		NA	Q9NV03	hg19	CCDS3442.1	0.02	-0.236856	AATxTCC	COVERED																																																																																			NOVEL	C4orf19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250433.1	2	3.910893	KEEP	0	0	0	13	389	CC	0.994391	0.608972	0		+	4	60	133	0	0	10.513141	20	60	671	47	ENST00000381980.4	0.166667	0.612407
C4orf19	55286	__UNKNOWN__	__UNKNOWN__	4	37462252	37462252	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:37462252C>T	ENST00000381980.4	+	1	100				C4orf19_ENST00000508175.1_Intron	NM_001104629.1	NP_001098099.1	Q8IY42	CD019_HUMAN	chromosome 4 open reading frame 19	NA		NA								large_intestine(1)|lung(3)|skin(3)|stomach(1)|urinary_tract(1)	9						cataaatctcctcttttgaga	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037906	CCDS3442.1	4p14	2008-02-05			ENSG00000154274	ENSG00000154274	55286			25618	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018302	NM_001104629	NA	Approved	FLJ11017	uc003gsw.4	Q8IY42	OTTHUMG00000128580	ENST00000381980.4:c.-73+6590C>T	chr4.hg19:g.37462252C>T		NA	Q9NV03	hg19	CCDS3442.1	0.02	-0.219302	CTCxTCT	COVERED																																																																																			NOVEL	C4orf19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250433.1	1	3.60961	KEEP	0	0	0	12	353	CC	0.993634	0.549368	0		+	4	60	116	0	0	8.979739	18	60	610	42	ENST00000381980.4	0.181818	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	38216835	38216835	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:38216835T>C			NA	NA				TBC1D1 (76039 upstream) : AC098680.1 (23398 downstream)						NA		NA									NA						gtcacccaggttggagtgcag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.38216835T>C		NA		hg19		0.02	-0.070175	AGGxTGG	UNCOVERED																																																																																			NOVEL					0			9	3.003102	KEEP	1	0	0	10	259	TT	0.992708	0.053742	0			2	53	69	0	0	6.392936	3	60	91	26		0.4	0.054137
TMEM156	80008	__UNKNOWN__	__UNKNOWN__	4	39020602	39020602	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:39020602C>T	ENST00000381938.3	-	1	196				TMEM156_ENST00000372489.2_Intron	NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	NA		NA				integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						gatcacgccactgcactccag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895	80008			26260	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024943	NM_024943	NA	Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.88+13243G>A	chr4.hg19:g.39020602C>T		NA	Q9H5N9	hg19	CCDS3448.1	0.02	-0.087716	CCAxTGC	UNCOVERED																																																																																			NOVEL	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250435.3	9	3.610374	KEEP	5	0	0	12	357	CC	0.99257	0.09898	0		-	3	60	87	0	0	7.643156	6	60	197	30	ENST00000381938.3	0.333333	0.099721
TMEM156	80008	__UNKNOWN__	__UNKNOWN__	4	39020604	39020604	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:39020604G>A	ENST00000381938.3	-	1	196				TMEM156_ENST00000372489.2_Intron	NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	NA		NA				integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						tcacgccactgcactccagcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895	80008			26260	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024943	NM_024943	NA	Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.88+13241C>T	chr4.hg19:g.39020604G>A		NA	Q9H5N9	hg19	CCDS3448.1	0.02	-0.087713	ACTxCAC	UNCOVERED																																																																																			NOVEL	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250435.3	9	3.609273	KEEP	5	0	0	12	350	GG	0.99257	0.09898	0		-	3	60	93	0	0	8.243552	6	60	194	31	ENST00000381938.3	0.333333	0.099721
LIAS	11019	__UNKNOWN__	__UNKNOWN__	4	39478887	39478887	__UNKNOWN__	3'UTR	SNP	G	G	A	rs568569828		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:39478887G>A	ENST00000261434.3	+	0	1389				LIAS_ENST00000340169.2_3'UTR|LIAS_ENST00000381846.1_3'UTR	NM_006859.2	NP_006850.2			lipoic acid synthetase	NA		NA								breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)|ovary(2)	12						agtggctcacgcctgtaatcc	0.512		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16233	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ224162	CCDS3453.1, CCDS3454.1, CCDS63950.1	4p14	2008-02-05			ENSG00000121897	ENSG00000121897	11019			16429	protein-coding gene	gene with protein product		607031			NA	11124703	Standard	NM_194451	NM_006859	NA	Approved	LAS	uc003guf.3	O43766	OTTHUMG00000099369	ENST00000261434.3:c.*152G>A	chr4.hg19:g.39478887G>A		NA		hg19	CCDS3453.1	0.02	-0.298235	CACxCCT	COVERED																																																																																			NOVEL	LIAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216815.1	13	2.367526	KEEP	3	2	48	25	738	GG	0.999988	0.800236	0		+	3	60	94	0	0	6.692821	25	60	830	96	ENST00000261434.3	0.107143	0.800245
UGDH	7358	__UNKNOWN__	__UNKNOWN__	4	39527103	39527103	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:39527103T>C	ENST00000316423.6	-	1	336				UGDH_ENST00000501493.2_Intron|UGDH_ENST00000515398.1_Intron|UGDH_ENST00000507089.1_Intron|UGDH_ENST00000506179.1_Intron	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	NA		NA			cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						cgtgagccactgcgcccagcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	7358	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	UDP-glucose dehydrogenase		NA	9737970, 10575217	Standard	NM_003359	NM_003359	NA	Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.6+1799A>G	chr4.hg19:g.39527103T>C		NA	B3KUU2|B4DN25|O60589	hg19	CCDS3455.1	0.02	-0.166629	CACxGCG	COVERED																																																																																			NOVEL	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216818.3	9	4.510935	KEEP	1	0	0	15	407	TT	0.99649	0.352705	0		-	3	48	92	0	0	7.1114	15	60	442	47	ENST00000316423.6	0.166667	0.353947
SMIM14	201895	__UNKNOWN__	__UNKNOWN__	4	39557680	39557680	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:39557680A>G	ENST00000295958.5	-	4	654				SMIM14_ENST00000511809.1_Intron|UGDH-AS1_ENST00000504032.1_RNA|SMIM14_ENST00000510628.1_Intron	NM_174921.1	NP_777581.1	Q96QK8	SIM14_HUMAN	small integral membrane protein 14	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)					NA						tgtggtcccaactacttggga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008502	CCDS3456.1	4p14	2014-02-10	2012-12-03	2012-12-03	ENSG00000163683	ENSG00000163683	201895			27321	protein-coding gene	gene with protein product		NA	chromosome 4 open reading frame 34	C4orf34	NA	15231747, 24499674, 23759569	Standard	NM_174921	NM_174921	NA	Approved	FLJ13289	uc003guo.3	Q96QK8	OTTHUMG00000128581	ENST00000295958.5:c.267+367T>C	chr4.hg19:g.39557680A>G		NA		hg19	CCDS3456.1	0.02	-0.12278	CCAxCTA	COVERED																																																																																			NOVEL	SMIM14-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250434.4	3	2.406186	KEEP	0	0	0	8	222	AA	0.99257	0.194853	0		-	3	60	98	0	0	8.30137	9	60	263	34	ENST00000295958.5	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	39658891	39658891	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:39658891A>G			NA	NA				RP11-539G18.2 (5199 upstream) : UBE2K (40772 downstream)						NA		NA									NA						ttacaggcgtaagccaccgca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.39658891A>G		NA		hg19		0.02	-0.149094	CGTxAGC	COVERED																																																																																			NOVEL					0			11	4.2097	KEEP	1	0	0	14	373	AA	0.995343	0.290641	0			3	60	96	0	0	7.772511	12	60	346	48		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	40027503	40027503	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:40027503A>G			NA	NA				PDS5A (47927 upstream) : RP11-333E13.4 (17033 downstream)						NA		NA									NA						gtaacagagcaagactttgtc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.40027503A>G		NA		hg19		0.02	-0.157875	AGCxAGA	COVERED																																																																																			NOVEL					0			8	2.705906	KEEP	0	0	0	9	243	AA	0.99254	0.320398	0			3	60	91	1	0	7.272517	12	60	366	38		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	40301458	40301458	__UNKNOWN__	IGR	SNP	G	G	A	rs4406053	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:40301458G>A			NA	NA				RP11-395I6.2 (33381 upstream) : AC195454.1 (17043 downstream)						NA		NA									NA						tagagatggggttctctctat	0.498		NA											G|||	1715	0.342452	0.2247	0.4597	5008	,	,	NA	14707	0.2272	NA	0.4145	False	NA	,,,	NA	NA	NA	2504	0.4632	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.40301458G>A		NA		hg19		0.02	-0.087706	GGGxTTC	UNCOVERED																																																																																			NOVEL					0			1	2.707495	KEEP	0	0	0	9	277	GG	0.99254	0.098977	0			3	60	89	0	0	7.843428	6	60	199	28		0.333333	0.099721
RBM47	54502	__UNKNOWN__	__UNKNOWN__	4	40432911	40432911	__UNKNOWN__	Intron	SNP	T	T	C	rs371865641		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:40432911T>C	ENST00000381793.2	-	5	1939				RBM47_ENST00000295971.7_Intron|RBM47_ENST00000381795.6_Intron|RBM47_ENST00000319592.4_Intron|RBM47_ENST00000514014.1_Intron			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						caataccagcttgggcaacat	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694	54502		RNA binding motif (RRM) containing	30358	protein-coding gene	gene with protein product		NA			NA		Standard	NM_019027	NM_019027	NA	Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.1542+1756A>G	chr4.hg19:g.40432911T>C		NA	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	hg19	CCDS43223.1	0.02	-0.184164	AGCxTGG	COVERED																																																																																			NOVEL	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250456.2	12	3.909826	KEEP	0	0	0	13	356	TT	0.994391	0.421102	0		-	3	60	101	0	0	7.7923	18	60	526	42	ENST00000381793.2	0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	40649352	40649352	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:40649352T>C			NA	NA				RBM47 (16712 upstream) : NSUN7 (102561 downstream)						NA		NA									NA						tgcagtggcatgatctcagct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.40649352T>C		NA		hg19		0.02	-0.14034	GCAxGAT	COVERED																																																																																			NOVEL					0			4	3.308454	KEEP	1	0	0	11	304	TT	0.993072	0.259157	0			3	60	92	1	0	7.372344	12	60	369	42		0.2	0.260965
APBB2	323	__UNKNOWN__	__UNKNOWN__	4	41154578	41154578	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:41154578C>T	ENST00000508593.1	-	2	128				APBB2_ENST00000511572.1_Intron|APBB2_ENST00000295974.8_Intron|APBB2_ENST00000513140.1_Intron|APBB2_ENST00000506352.1_Intron			Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	NA		NA			axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						atctcctgacctcgtgatcta	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(3;20 75 16686 49997)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697	323			582	protein-coding gene	gene with protein product	Fe65-like	602710			NA	8955346, 9585438	Standard	NM_173075	NM_173075	NA	Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000508593.1:c.416-9419G>A	chr4.hg19:g.41154578C>T		NA	B4DSL4|E9PG87|Q8IUI6	hg19	CCDS54762.1	0.02	-0.184214	GACxTCG	COVERED																																																																																			NOVEL	APBB2-003	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360524.1	9	6.319538	KEEP	8	0	0	21	671	CC	0.999366	0.423209	0		-	3	21	86	0	1	6.510635	15	60	513	73	ENST00000508593.1	0.166667	0.423478
LIMCH1	22998	__UNKNOWN__	__UNKNOWN__	4	41461397	41461397	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:41461397A>C	ENST00000313860.7	+	2	150				LIMCH1_ENST00000513024.1_Intron|LIMCH1_ENST00000508501.1_Intron|LIMCH1_ENST00000509638.1_Intron|LIMCH1_ENST00000512632.1_Intron|LIMCH1_ENST00000512946.1_Intron|LIMCH1_ENST00000512820.1_Intron	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	NA		NA			actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						ggctcattgcagcctcgacct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042	22998			29191	protein-coding gene	gene with protein product		NA			NA	10470851	Standard	NM_014988	XM_005248057	NA	Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.97-35156A>C	chr4.hg19:g.41461397A>C		NA	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	hg19	CCDS33977.1	0.02	-0.131578	TGCxGCC	COVERED																																																																																			NOVEL	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361249.2	9	3.006771	KEEP	0	0	0	10	271	AA	0.992708	0.227502	0		+	5	60	163	0	0	14.722922	9	60	279	32	ENST00000313860.7	0.357143	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	43411096	43411096	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:43411096T>C			NA	NA				RP11-1E6.1 (63479 upstream) : RP11-324J13.2 (48447 downstream)						NA		NA									NA						gtggctcacgtctgtaatccc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.43411096T>C		NA		hg19		0.02	-0.052632	ACGxCTG	UNCOVERED																																																																																			NOVEL					0			3	2.404706	KEEP	0	0	0	8	214	TT	0.99257	0.036492	0			2	60	71	0	0	6.85032	2	60	60	21		0.5	0.036766
COX7B2	170712	__UNKNOWN__	__UNKNOWN__	4	46866722	46866722	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:46866722C>T	ENST00000396533.1	-	2	147				COX7B2_ENST00000355591.3_Intron|COX7B2_ENST00000543208.1_Intron|COX7B2_ENST00000302930.5_Intron			Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2	NA		NA				integral component of membrane (GO:0016021)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			large_intestine(1)|lung(4)	5						agtgcagtggcgcgatctagg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF125109	CCDS3472.2	4p12	2011-07-04			ENSG00000170516	ENSG00000170516	170712		Mitochondrial respiratory chain complex / Complex IV	24381	protein-coding gene	gene with protein product		609811			NA	15623157	Standard	NM_130902	NM_130902	NA	Approved		uc003gxf.3	Q8TF08	OTTHUMG00000099423	ENST00000396533.1:c.103+11933G>A	chr4.hg19:g.46866722C>T		NA	Q32Q40	hg19	CCDS3472.2	0.02	-0.30701	TGGxGCG	COVERED																																																																																			NOVEL	COX7B2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313899.1	13	8.723535	KEEP	1	0	0	29	855	CC	0.999997	0.800243	0		-	4	60	118	0	0	8.36409	30	60	1002	98	ENST00000396533.1	0.117647	0.800245
CORIN	10699	__UNKNOWN__	__UNKNOWN__	4	47784437	47784437	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:47784437A>G	ENST00000273857.4	-	3	409				CORIN_ENST00000504584.1_Intron|CORIN_ENST00000508498.1_Intron|CORIN_ENST00000505909.1_Intron|CORIN_ENST00000502252.1_Intron	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	NA		NA			female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						agaaaaaaagacaagaaacag	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244	10699		Serine peptidases / Transmembrane	19012	protein-coding gene	gene with protein product		605236	corin, serine protease		NA	10329693	Standard		NM_006587	NA	Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.409+4304T>C	chr4.hg19:g.47784437A>G		NA	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	hg19	CCDS3477.1	0.02	-0.070157	AAGxCAA	UNCOVERED																																																																																			NOVEL	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216906.2	8	3.304972	KEEP	1	0	0	11	273	AA	0.993072	0.053762	0		-	3	60	101	0	0	9.725403	3	60	86	26	ENST00000273857.4	0.5	0.054137
FRYL	285527	__UNKNOWN__	__UNKNOWN__	4	48575834	48575834	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:48575834T>C	ENST00000503238.1	-	23	2846				FRYL_ENST00000507711.1_Intron|FRYL_ENST00000264319.7_Intron|FRYL_ENST00000358350.4_Intron|FRYL_ENST00000537810.1_Intron			O94915	FRYL_HUMAN	FRY-like	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						tcccaaagtgttgggattaca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539	285527			29127	protein-coding gene	gene with protein product		NA	KIAA0826, furry homolog-like (Drosophila)	KIAA0826	NA	10048485	Standard		NM_015030	NA	Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.2847-574A>G	chr4.hg19:g.48575834T>C		NA	O95640|Q8WTZ5|Q9NT40	hg19	CCDS43227.1	0.02	-0.087718	GTGxTGG	UNCOVERED																																																																																			NOVEL	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369265.2	7	3.307838	KEEP	2	0	0	11	300	TT	0.993072	0.09903	0		-	3	25	108	0	0	9.578734	7	60	214	33	ENST00000503238.1	0.3	0.099721
FRYL	285527	__UNKNOWN__	__UNKNOWN__	4	48770885	48770885	__UNKNOWN__	Intron	SNP	T	T	C	rs187593677	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:48770885T>C	ENST00000507711.1	-	1	171				FRYL_ENST00000514783.1_Intron|FRYL_ENST00000264319.7_Intron|FRYL_ENST00000358350.4_Intron|FRYL_ENST00000537810.1_Intron			O94915	FRYL_HUMAN	FRY-like	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						cagtggctcatgcctgtaatc	0.458		NA											C|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	18765	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539	285527			29127	protein-coding gene	gene with protein product		NA	KIAA0826, furry homolog-like (Drosophila)	KIAA0826	NA	10048485	Standard		NM_015030	NA	Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000507711.1:c.382+11209A>G	chr4.hg19:g.48770885T>C		NA	O95640|Q8WTZ5|Q9NT40	hg19		0.02	-0.070165	TCAxGCC	UNCOVERED																																																																																			NOVEL	FRYL-007	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000361412.5	3	2.406043	KEEP	0	0	0	8	221	TT	0.99257	0.053735	0		-	3	60	96	0	0	9.224913	3	60	95	22	ENST00000507711.1	0.5	0.054137
OCIAD2	132299	__UNKNOWN__	__UNKNOWN__	4	48887286	48887286	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:48887286A>G	ENST00000508632.1	-	0	912					NM_001014446.1	NP_001014446.1	Q56VL3	OCAD2_HUMAN	OCIA domain containing 2	NA		NA				endosome (GO:0005768)|mitochondrial inner membrane (GO:0005743)				kidney(1)|lung(3)|skin(1)|urinary_tract(1)	6						gattacaggcatgagccactg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC032808	CCDS3485.1, CCDS33981.1	4p12	2013-10-11			ENSG00000145247	ENSG00000145247	132299			28685	protein-coding gene	gene with protein product		NA			NA	17054434	Standard	NM_152398	NM_001286774	NA	Approved	MGC45416	uc003gyt.3	Q56VL3	OTTHUMG00000128626	ENST00000508632.1:c.*215T>C	chr4.hg19:g.48887286A>G		NA	B4DPE7|Q8N544	hg19	CCDS33981.1	0.02	1.692613	GGCxTGA	COVERED																																																																																			NOVEL	OCIAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361984.5	22	3.705597	KEEP	2	3	81	41	1147	AA	1	0.995687	0		-	5	60	173	0	0	12.068292	59	60	1770	165	ENST00000508632.1	0.078125	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49094795	49094795	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49094795C>G			NA	NA				CWH43 (30699 upstream) : AC118282.3 (104424 downstream)						NA		NA									NA						ttccattccactcgggttgat	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49094795C>G		NA		hg19		0.02	5.563026	CCAxTCG	COVERED																																																																																			NOVEL					0			54	15.014609	KEEP	142	5	154	104	3224	CC	1	1	0			6	40	208	1	1	15.104254	56	60	1906	677		0.096774	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49104598	49104598	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49104598G>C			NA	NA				CWH43 (40502 upstream) : AC118282.3 (94621 downstream)						NA		NA									NA						attccactcgggttgattcca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49104598G>C		NA		hg19		0.02	1.715876	TCGxGTT	COVERED																																																																																			NOVEL					0			22	9.25479	KEEP	73	1	26	40	1175	GG	0.999366	0.981333	0			4	44	115	0	0	9.162696	15	60	493	204		0.210526	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49133719	49133719	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49133719C>T			NA	NA				CWH43 (69623 upstream) : AC118282.3 (65500 downstream)						NA		NA									NA						cattccattcctttccattcc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49133719C>T		NA		hg19		0.02	-0.087717	TTCxTTT	UNCOVERED																																																																																			NOVEL					0			5	2.707826	KEEP	7	0	0	9	274	CC	0	0	0			2	49	62	0	0	7.153552	0	0	0	35		1	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49159687	49159687	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49159687T>C			NA	NA				CWH43 (95591 upstream) : AC118282.3 (39532 downstream)						NA		NA									NA						ttttctttgctaggagatgtt	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49159687T>C		NA		hg19		0.02	-0.096467	TGCxAGG	UNCOVERED																																																																																			NOVEL					0			17	4.508573	KEEP	12	0	0	15	384	TT	0.992708	0.119558	0			3	27	91	0	0	8.043792	6	47	169	37		0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49160676	49160676	__UNKNOWN__	IGR	SNP	A	A	T	rs9986052		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49160676A>T			NA	NA				CWH43 (96580 upstream) : AC118282.3 (38543 downstream)						NA		NA									NA						ggatggactcaatctcctgac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49160676A>T		NA		hg19		0.02	1.581601	CTCxATC	COVERED																																																																																			NOVEL					0			19	4.373608	KEEP	9	2	52	33	902	AA	0.999988	0.987931	0			9	60	261	0	0	20.429486	38	60	1130	141		0.191489	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49165479	49165479	__UNKNOWN__	IGR	SNP	T	T	C	rs4695482		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49165479T>C			NA	NA				CWH43 (101383 upstream) : AC118282.3 (33740 downstream)						NA		NA									NA						CTCTCCTTAATCCACGTCATT	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49165479T>C		NA		hg19		0.02	1.915079	TAAxCCA	COVERED																																																																																			NOVEL					0			14	7.215088	KEEP	69	0	0	24	634	TT	0.999366	0.973348	0			5	23	180	0	0	13.283784	46	60	1300	204		0.098039	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49181848	49181848	__UNKNOWN__	IGR	SNP	C	C	T	rs201537013		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49181848C>T			NA	NA				CWH43 (117752 upstream) : AC118282.3 (17371 downstream)						NA		NA									NA						ccacatgtttcgtcctcccaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49181848C>T		NA		hg19		0.02	-0.105262	TTTxGTC	UNCOVERED																																																																																			NOVEL					0			4	3.008624	KEEP	1	0	0	10	300	CC	0.99254	0.138789	0			3	60	91	0	0	8.454779	4	60	134	35		0.428571	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49195850	49195850	__UNKNOWN__	IGR	SNP	C	C	T	rs200319202		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49195850C>T			NA	NA				CWH43 (131754 upstream) : AC118282.3 (3369 downstream)						NA		NA									NA						gaggccgaggcgggcagatca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49195850C>T		NA		hg19		0.02	-0.263134	AGGxGGG	COVERED																																																																																			NOVEL					0			24	7.219408	KEEP	21	0	0	24	694	CC	0.999366	0.716861	0			4	24	101	0	0	7.23933	21	60	684	87		0.16	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49268227	49268227	__UNKNOWN__	IGR	SNP	C	C	T	rs12152676		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49268227C>T			NA	NA				AC118282.4 (56762 upstream) : AC119751.5 (316814 downstream)						NA		NA									NA						GGTggacgggcgcagtgtctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49268227C>T		NA		hg19		0.02	-0.228068	GGGxGCA	COVERED																																																																																			NOVEL					0			11	3.242338	KEEP	18	1	23	19	582	CC	0.993634	0.579219	0			3	40	88	0	0	6.366011	20	51	656	79		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49268263	49268263	__UNKNOWN__	IGR	SNP	A	A	G	rs4118706		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49268263A>G			NA	NA				AC118282.4 (56798 upstream) : AC119751.5 (316778 downstream)						NA		NA									NA						gcactttgggaggccaaggtg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49268263A>G		NA		hg19		0.02	-0.377146	GGGxGGC	COVERED																																																																																			NOVEL					0			19	2.971778	KEEP	23	2	60	31	858	AA	0.999892	0.908971	0			3	54	99	0	0	6.812225	34	54	1029	123		0.081081	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49268305	49268305	__UNKNOWN__	IGR	SNP	C	C	A	rs9282976		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49268305C>A			NA	NA				AC118282.4 (56840 upstream) : AC119751.5 (316736 downstream)						NA		NA									NA						agttcaagaccagcctggcca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49268305C>A		NA		hg19		0.02	-0.412253	GACxAGC	COVERED																																																																																			NOVEL					0			28	3.978597	KEEP	18	2	59	34	1041	CC	0.999997	0.941739	0			5	49	147	0	0	10.432057	37	60	1227	127		0.119048	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49268313	49268313	__UNKNOWN__	IGR	SNP	C	C	A	rs6837764		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49268313C>A			NA	NA				AC118282.4 (56848 upstream) : AC119751.5 (316728 downstream)						NA		NA									NA						accagcctggccaacatggtg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49268313C>A		NA		hg19		0.02	-0.421051	TGGxCAA	COVERED																																																																																			NOVEL					0			27	6.932679	KEEP	16	1	28	33	970	CC	0.999997	0.948399	0			4	49	119	1	0	8.034349	39	60	1296	124		0.093023	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49530621	49530621	__UNKNOWN__	IGR	SNP	G	G	A	rs370184116		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49530621G>A			NA	NA				AC118282.4 (319156 upstream) : AC119751.5 (54420 downstream)						NA		NA									NA						ttgagacagagtctcactctg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49530621G>A		NA		hg19		0.02	-0.210532	AGAxTCT	UNCOVERED																																																																																			NOVEL					0			9	2.68789	KEEP	5	0	0	9	256	GG	0	0	0			3	30	90	0	0	6.833574	16	50	538	48		0.157895	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49531964	49531964	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49531964A>C			NA	NA				AC118282.4 (320499 upstream) : AC119751.5 (53077 downstream)						NA		NA									NA						ttctgggctcacatgatcctc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49531964A>C		NA		hg19		0.02	-0.306852	CTCxCAT	COVERED																																																																																			NOVEL					0			20	9.924597	KEEP	27	0	0	33	925	AA	0.999879	0.800148	0			4	47	127	0	0	9.376056	28	60	824	130		0.125	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49534810	49534810	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49534810A>T			NA	NA				AC118282.4 (323345 upstream) : AC119751.5 (50231 downstream)						NA		NA									NA						ataaaaaTTAATAAAATATAA	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49534810A>T		NA		hg19		0.02	-0.184181	TTAxTAA	COVERED																																																																																			NOVEL					0			16	6.614263	KEEP	8	0	0	22	580	AA	0.999859	0.423418	0			6	42	187	0	0	16.107188	15	53	443	64		0.285714	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49536200	49536200	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49536200T>C			NA	NA				AC118282.4 (324735 upstream) : AC119751.5 (48841 downstream)						NA		NA									NA						tttttttttctttctagagac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49536200T>C		NA		hg19		0.02	-0.175413	TTCxTTC	COVERED																																																																																			NOVEL					0			8	3.307527	KEEP	4	0	0	11	294	TT	0.993072	0.384723	0			3	45	100	0	0	8.501356	9	45	261	47		0.25	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49536213	49536213	__UNKNOWN__	IGR	SNP	G	G	A	rs76163054	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49536213G>A			NA	NA				AC118282.4 (324748 upstream) : AC119751.5 (48828 downstream)						NA		NA									NA						ctagagacagggttttgttct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49536213G>A		NA		hg19		0.02	-0.166678	CAGxGTT	COVERED																																																																																			NOVEL					0			10	3.911506	KEEP	12	0	0	13	398	GG	0.993072	0.351495	0			3	45	94	0	1	7.900882	9	58	316	57		0.25	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49539230	49539230	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49539230C>T			NA	NA				AC118282.4 (327765 upstream) : AC119751.5 (45811 downstream)						NA		NA									NA						gctggaattacaggcatgagc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49539230C>T		NA		hg19		0.02	-0.201772	TTAxAGG	COVERED																																																																																			NOVEL					0			17	5.114764	KEEP	29	0	0	17	510	CC	0.99257	0.4869	0			5	46	157	0	0	13.612901	12	49	420	80		0.294118	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49539235	49539235	__UNKNOWN__	IGR	SNP	A	A	T	rs377574547		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49539235A>T			NA	NA				AC118282.4 (327770 upstream) : AC119751.5 (45806 downstream)						NA		NA									NA						aattacaggcatgagccactc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49539235A>T		NA		hg19		0.02	-0.175428	GGCxTGA	COVERED																																																																																			NOVEL					0			17	4.510609	KEEP	29	0	0	15	401	AG	0.99257	0.4869	0			3	27	97	0	0	7.778819	13	49	398	80		0.1875	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49608409	49608409	__UNKNOWN__	IGR	SNP	T	T	A	rs9631983	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49608409T>A			NA	NA				AC119751.4 (6883 upstream) : None (None downstream)						NA		NA									NA						tggagtgcagtggcactatct	0.522		NA											T|||	1624	0.324281	0.1589	0.4539	5008	,	,	NA	20431	0.3403	NA	0.5427	False	NA	,,,	NA	NA	NA	2504	0.2147	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49608409T>A		NA		hg19		0.02	-0.228016	CAGxGGC	COVERED																																																																																			NOVEL					0			25	3.037927	KEEP	26	1	31	21	556	TT	0.993072	0.578892	0			7	60	214	0	0	18.449212	17	48	499	83		0.291667	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49611119	49611119	__UNKNOWN__	IGR	SNP	G	G	A	rs371040584		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49611119G>A			NA	NA				AC119751.4 (9593 upstream) : None (None downstream)						NA		NA									NA						atgacatttggccgggtgcgg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49611119G>A		NA		hg19		0.02	-0.289481	TTGxCCG	COVERED																																																																																			NOVEL					0			17	7.956748	KEEP	12	1	27	36	1109	GG	0.999997	0.760885	0			6	46	182	0	0	14.745504	22	50	742	105		0.214286	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49611153	49611153	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49611153A>T			NA	NA				AC119751.4 (9627 upstream) : None (None downstream)						NA		NA									NA						caatcccagcagtttgggagg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49611153A>T		NA		hg19		0.02	-0.245576	AGCxGTT	COVERED																																																																																			NOVEL					0			18	6.648421	KEEP	17	1	28	32	880	AA	0.999931	0.641303	0			5	46	149	0	0	11.9532	19	50	566	103		0.208333	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49631926	49631926	__UNKNOWN__	IGR	SNP	C	C	T	rs181712453		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49631926C>T			NA	NA				AC119751.4 (30400 upstream) : None (None downstream)						NA		NA									NA						attgaaaaacctggaagaaat	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49631926C>T		NA		hg19		0.02	-0.105269	AACxTGG	UNCOVERED																																																																																			NOVEL					0			13	2.440483	KEEP	25	1	28	18	553	CC	0	0	0			3	54	93	0	0	7.932179	8	60	276	60		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49637212	49637212	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49637212G>T			NA	NA				AC119751.4 (35686 upstream) : None (None downstream)						NA		NA									NA						gaatggaatggaatggaatgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49637212G>T		NA		hg19		0.02	1.484971	ATGxAAT	COVERED																																																																																			NOVEL					0			53	8.522559	KEEP	111	3	78	56	1680	GG	0.999998	0.996722	0			4	26	117	1	1	8.37652	28	60	933	345		0.125	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	49637253	49637253	__UNKNOWN__	IGR	SNP	A	A	C	rs202182628		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:49637253A>C			NA	NA				AC119751.4 (35727 upstream) : None (None downstream)						NA		NA									NA						agtggaatggaatggaatgga	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.49637253A>C		NA		hg19		0.02	1.874275	TGGxATG	COVERED																																																																																			NOVEL					0			59	8.317225	KEEP	118	3	92	60	1660	AA	0.999997	0.99716	0			4	28	141	0	0	10.556096	32	45	976	372		0.111111	0.997163
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	53627664	53627664	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:53627664T>C			NA	NA				ERVMER34-1 (9857 upstream) : Y_RNA (25039 downstream)						NA		NA									NA						ttttttttttttttttagatg	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.53627664T>C		NA		hg19		0.02	-0.078944	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			9	3.005988	KEEP	0	0	0	10	264	TT	0.992708	0.076772	0			2	29	74	1	0	6.400787	6	60	180	29		0.25	0.077336
FIP1L1	81608	__UNKNOWN__	__UNKNOWN__	4	54996911	54996911	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:54996911T>C	ENST00000507166.1	+	13	1017							Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	NA		NA			mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			aggctggtcttgaactcctag	0.438		NA	T	PDGFRA	idiopathic hypereosinophilic syndrome																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216	81608			19124	protein-coding gene	gene with protein product		607686	FIP1 like 1 (S. cerevisiae), FIP1L1 cleavage and polyadenylation specific factor subunit		NA	11230166, 14749727	Standard	NM_030917	NM_030917	NA	Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000507166.1:c.1018-144181T>C	chr4.hg19:g.54996911T>C		NA	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	hg19		0.02	-0.149113	TCTxGAA	COVERED																																																																																			NOVEL	FIP1L1-005	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000361317.2	9	2.706388	KEEP	1	0	0	9	242	TT	0.99257	0.289832	0		+	4	60	136	0	0	11.871403	10	60	302	37	ENST00000507166.1	0.285714	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	55266170	55266170	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:55266170C>G			NA	NA				RP11-231C18.2 (23251 upstream) : RP11-545H22.1 (40498 downstream)						NA		NA									NA						aggattgcttcaggccaggag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.55266170C>G		NA		hg19		0.02	-0.043861	CTTxAGG	UNCOVERED																																																																																			NOVEL					0			5	2.407392	KEEP	0	0	0	8	252	CC	0.99257	0.023895	0			2	60	69	0	0	6.392857	3	60	96	20		0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	55447767	55447767	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:55447767C>T			NA	NA				RP11-545H22.1 (134877 upstream) : AC006552.1 (21610 downstream)						NA		NA									NA						gtggctcatgcctgtaatccc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.55447767C>T		NA		hg19		0.02	-0.114026	ATGxCTG	UNCOVERED																																																																																			NOVEL					0			4	2.708293	KEEP	0	0	0	9	285	CC	0.99254	0.161255	0			3	60	87	0	0	7.478319	7	60	227	30		0.3	0.162467
RP11-530I17.1	0	__UNKNOWN__	__UNKNOWN__	4	55933361	55933361	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:55933361C>T	ENST00000511222.1	+	0	38										NA		NA									NA						tcactcttgtcgcccaggctg	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000511222.1:	chr4.hg19:g.55933361C>T		NA		hg19		0.02	-0.114006	TGTxGCC	UNCOVERED																																																																																			NOVEL	RP11-530I17.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000361577.2	42	8.719528	KEEP	24	0	0	29	772	CC	0.997832	0.162114	0		+	3	60	87	0	1	7.201212	9	60	269	55	ENST00000511222.1	0.25	0.162467
CEP135	9662	__UNKNOWN__	__UNKNOWN__	4	56826856	56826856	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:56826856C>T	ENST00000257287.4	+	6	823				CEP135_ENST00000422247.2_3'UTR	NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	NA		NA			centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					tttgggaggccgaggcgggtg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799	9662			29086	protein-coding gene	gene with protein product		611423	KIAA0635, centrosomal protein 4	KIAA0635, CEP4	NA	9734811, 14654843	Standard	NM_025009	NM_025009	NA	Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.699+924C>T	chr4.hg19:g.56826856C>T		NA	B2RMY0|O75130|Q58F25|Q9H8H7	hg19	CCDS33986.1	0.02	-0.201731	GGCxGAG	COVERED																																																																																			NOVEL	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362092.2	6	3.007713	KEEP	0	0	0	10	284	CC	0.993072	0.487146	0		+	3	60	88	1	0	6.493439	18	60	562	44	ENST00000257287.4	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	56950101	56950101	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:56950101C>T			NA	NA				CEP135 (50572 upstream) : RNA5SP161 (13454 downstream)						NA		NA									NA						tgtgattgtgccactgcactc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.56950101C>T		NA		hg19		0.02	-0.08772	GTGxCAC	UNCOVERED																																																																																			NOVEL					0			7	2.406792	KEEP	0	0	0	8	237	CC	0.99257	0.09898	0			3	60	88	0	0	7.743139	6	60	202	24		0.333333	0.099721
SRP72	6731	__UNKNOWN__	__UNKNOWN__	4	57359290	57359290	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:57359290G>A	ENST00000342756.5	+	16	2361				SRP72_ENST00000510663.1_Intron	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					tgcaacctccgcctcctgggt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780	6731		Tetratricopeptide (TTC) repeat domain containing	11303	protein-coding gene	gene with protein product		602122	signal recognition particle 72kD		NA	9224693, 9857079	Standard		NM_006947	NA	Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.1640+1556G>A	chr4.hg19:g.57359290G>A		NA	G5E9Z8|Q7Z3C0	hg19	CCDS3506.1	0.02	-0.140315	TCCxCCT	COVERED																																																																																			NOVEL	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250782.7	6	2.706823	KEEP	2	0	0	9	252	GG	0.99254	0.259018	0		+	4	60	99	0	0	7.901411	12	60	380	32	ENST00000342756.5	0.25	0.260965
ARL9	132946	__UNKNOWN__	__UNKNOWN__	4	57380095	57380095	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:57380095A>G	ENST00000360096.2	+	2	330					NM_206919.1	NP_996802.1	Q6T311	ARL9_HUMAN	ADP-ribosylation factor-like 9	NA		NA			small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			lung(2)	2	Glioma(25;0.08)|all_neural(26;0.101)					cagcactttgagaggccgggg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY439003	CCDS59474.1	4q12	2014-05-09				ENSG00000196503	132946		ADP-ribosylation factors-like, ADP-ribosylation factors	23592	protein-coding gene	gene with protein product		612405			NA		Standard	NM_206919	NM_206919	NA	Approved		uc003hby.1	Q6T311		ENST00000360096.2:c.16+2582A>G	chr4.hg19:g.57380095A>G		NA		hg19	CCDS59474.1	0.02	-0.192248	TTGxGAG	COVERED																																																																																			NOVEL	ARL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467724.1	7	2.706566	KEEP	0	0	0	9	249	AA	0.99254	0.454342	0		+	3	60	105	0	0	8.586828	13	60	383	49	ENST00000360096.2	0.1875	0.457757
THEGL	100506564	__UNKNOWN__	__UNKNOWN__	4	57428116	57428116	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:57428116T>C	ENST00000512175.2	+	4	790				THEGL_ENST00000510716.1_Intron	NM_001256475.1	NP_001243404.1	P0DJG4	THEGL_HUMAN	theg spermatid protein-like	NA		NA									NA						tcttgaactcttgacctcagg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			DB450279	CCDS58899.1	4q12	2013-04-04	2012-02-24	2012-02-24	ENSG00000249693	ENSG00000249693	100506564			43771	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001256475	NM_001256475	NA	Approved		uc031seh.1	P0DJG4	OTTHUMG00000160770	ENST00000512175.2:c.722+2430T>C	chr4.hg19:g.57428116T>C		NA		hg19	CCDS58899.1	0.02	-0.166653	CTCxTGA	UNCOVERED																																																																																			NOVEL	THEGL-001	KNOWN	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362201.2	7	3.007721	KEEP	4	0	0	10	276	TT	0	0	0		+	3	38	101	0	0	8.178778	13	60	391	48	ENST00000512175.2	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	57612352	57612352	__UNKNOWN__	IGR	SNP	G	G	A	rs1809376	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:57612352G>A			NA	NA				HOPX (64287 upstream) : RN7SL492P (48163 downstream)						NA		NA									NA						cctggccaacgtggtgaaacc	0.522		NA											A|||	608	0.121406	0.0643	0.1023	5008	,	,	NA	10890	0.1181	NA	0.0915	False	NA	,,,	NA	NA	NA	2504	0.2464	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.57612352G>A		NA		hg19		0.02	-0.043818	AACxTGG	UNCOVERED																																																																																			NOVEL					0			3	2.707635	KEEP	0	0	0	9	266	GG	0.99254	0.023894	0			4	60	104	0	0	11.215451	1	60	33	19		0.8	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	57716664	57716664	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:57716664A>G			NA	NA				SPINK2 (28756 upstream) : REST (57410 downstream)						NA		NA									NA						aggccgaggcaggcggatcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.57716664A>G		NA		hg19		0.02	-0.131508	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			11	3.910065	KEEP	21	0	0	13	360	AA	0	0	0			3	60	102	0	0	8.582761	10	60	292	62		0.230769	0.229173
REST	5978	__UNKNOWN__	__UNKNOWN__	4	57790290	57790290	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:57790290T>C	ENST00000309042.7	+	3	1296				REST_ENST00000514063.1_Intron	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	NA		NA			cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					tcccaaagtgttgggattaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093	5978			9966	protein-coding gene	gene with protein product		600571			NA	7871435, 7697725	Standard	NM_005612	NM_005612	NA	Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.982+4254T>C	chr4.hg19:g.57790290T>C		NA	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	hg19	CCDS3509.1	0.02	-0.210454	GTGxTGG	COVERED																																																																																			NOVEL	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250691.2	15	2.706889	KEEP	0	0	0	9	247	TT	0.99254	0.518266	0		+	3	60	108	0	0	8.633578	16	60	471	41	ENST00000309042.7	0.157895	0.522161
RP11-4O3.1	0	__UNKNOWN__	__UNKNOWN__	4	58493249	58493249	__UNKNOWN__	lincRNA	SNP	C	C	T	rs534922399		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:58493249C>T	ENST00000507808.1	-	0	55										NA		NA									NA						attagtcaggcgtggtggcag	0.532		NA											C|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16763	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000507808.1:	chr4.hg19:g.58493249C>T		NA		hg19		0.02	-0.087691	AGGxGTG	UNCOVERED																																																																																			NOVEL	RP11-4O3.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000365846.1	4	2.406666	KEEP	0	0	0	8	231	CC	0.99257	0.09898	0		-	3	60	82	0	0	6.977885	7	60	219	23	ENST00000507808.1	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	59942774	59942774	__UNKNOWN__	IGR	SNP	C	C	T	rs11942467	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:59942774C>T			NA	NA				RP11-340A13.3 (1800 upstream) : RP11-622J8.1 (75777 downstream)						NA		NA									NA						cagagccagactctgtctcca	0.393		NA											C|||	1961	0.391573	0.4592	0.3977	5008	,	,	NA	9053	0.1984	NA	0.5189	False	NA	,,,	NA	NA	NA	2504	0.364	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.59942774C>T		NA		hg19		0.02	-0.052623	AGAxTCT	UNCOVERED																																																																																			NOVEL					0			11	2.707555	KEEP	9	0	0	9	262	CC	0	0	0			3	60	88	0	0	8.768567	2	40	65	22		0.6	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	61261364	61261364	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:61261364G>A			NA	NA				RNU6-1325P (561479 upstream) : AC095061.1 (268302 downstream)						NA		NA									NA						agtggctcacgcctgtaatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.61261364G>A		NA		hg19		0.02	-0.114036	CACxCCT	COVERED																																																																																			NOVEL					0			4	2.708024	KEEP	0	0	0	9	280	GG	0.99254	0.194847	0			3	60	88	0	0	7.432191	8	60	269	38		0.272727	0.196312
RP11-84A1.3	0	__UNKNOWN__	__UNKNOWN__	4	62966112	62966112	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:62966112G>A	ENST00000506704.1	-	0	456				RP11-84A1.3_ENST00000509461.1_RNA|RP11-84A1.3_ENST00000504135.1_RNA						NA		NA									NA						gattacaggcgtgagccactg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000506704.1:	chr4.hg19:g.62966112G>A		NA		hg19		0.02	-0.114005	GGCxTGA	UNCOVERED																																																																																			NOVEL	RP11-84A1.3-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000361784.1	8	2.707015	KEEP	0	0	0	9	257	GG	0.99254	0.161255	0		-	3	60	80	0	0	6.942013	6	60	191	31	ENST00000506704.1	0.333333	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	63987083	63987083	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:63987083A>C			NA	NA				AC110810.1 (525903 upstream) : RP11-257A22.1 (6945 downstream)						NA		NA									NA						gcagtggtgcaatcttggctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.63987083A>C		NA		hg19		0.02	-0.061392	TGCxATC	UNCOVERED																																																																																			NOVEL					0			4	3.608993	KEEP	2	0	0	12	328	AA	0.993634	0.043508	0			2	42	71	0	0	6.396045	4	60	114	32		0.333333	0.043787
TECRL	253017	__UNKNOWN__	__UNKNOWN__	4	65179627	65179627	__UNKNOWN__	Intron	SNP	G	G	A	rs576261130	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:65179627G>A	ENST00000381210.3	-	5	662				TECRL_ENST00000507440.1_Intron|TECRL_ENST00000513125.1_Intron	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	NA		NA			lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)			endometrium(2)|kidney(5)|large_intestine(7)|lung(30)|prostate(1)|skin(1)|stomach(1)	47						cgaggcgggcggatcacgagg	0.433		NA											g|||	4	0.000798722	0.003	0.0	5008	,	,	NA	5066	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833108	CCDS33990.1	4q13.1	2009-07-21			ENSG00000205678	ENSG00000205678	253017			27365	protein-coding gene	gene with protein product	glycoprotein, synaptic 2-like	NA			NA	12477932	Standard	NM_001010874	NM_001010874	NA	Approved	GPSN2L, SRD5A2L2, DKFZp313D0829, DKFZp313B2333, TERL	uc003hcv.3	Q5HYJ1	OTTHUMG00000160680	ENST00000381210.3:c.551+738C>T	chr4.hg19:g.65179627G>A		NA		hg19	CCDS33990.1	0.02	-0.122759	GGCxGAT	UNCOVERED																																																																																			NOVEL	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361705.4	6	3.007198	KEEP	3	0	0	10	281	GG	0	0	0		-	3	60	85	0	0	7.001657	9	60	272	35	ENST00000381210.3	0.25	0.196312
RP11-584P21.2	0	__UNKNOWN__	__UNKNOWN__	4	68292226	68292226	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:68292226T>C	ENST00000502400.1	-	0	34										NA		NA									NA						acctgtaatctcagcactttg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502400.1:	chr4.hg19:g.68292226T>C		NA		hg19		0.02	-0.201739	ATCxCAG	COVERED																																																																																			NOVEL	RP11-584P21.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000361926.2	7	2.707188	KEEP	4	0	0	9	253	TT	0.99257	0.4869	0		-	4	60	131	0	0	10.479459	18	60	550	50	ENST00000502400.1	0.181818	0.490544
RP11-584P21.2	0	__UNKNOWN__	__UNKNOWN__	4	68294369	68294369	__UNKNOWN__	lincRNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:68294369C>G	ENST00000502400.1	-	0	34										NA		NA									NA						accagcctggccaacatggtg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502400.1:	chr4.hg19:g.68294369C>G		NA		hg19		0.02	-0.166668	TGGxCAA	UNCOVERED																																																																																			NOVEL	RP11-584P21.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000361926.2	11	3.008908	KEEP	7	0	0	10	307	CC	0	0	0		-	3	40	105	0	0	8.409796	15	60	504	45	ENST00000502400.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	71429942	71429942	__UNKNOWN__	IGR	SNP	A	A	G	rs556130249	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71429942A>G			NA	NA				AMTN (31483 upstream) : AMBN (28030 downstream)						NA		NA									NA						gccgggcgcgacggctcacgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.71429942A>G		NA		hg19		0.02	-0.043861	GCGxCGG	UNCOVERED																																																																																			NOVEL					0			6	2.405856	KEEP	2	0	0	8	217	AA	0	0	0			2	60	69	0	0	6.650092	2	60	64	16		0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	71559473	71559473	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71559473C>T			NA	NA				UTP3 (3206 upstream) : RNU6-520P (7998 downstream)						NA		NA									NA						ggcaacagagcaagactgtct	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.71559473C>T		NA		hg19		0.02	-0.122797	GAGxAAG	COVERED																																																																																			NOVEL					0			6	2.708163	KEEP	0	0	0	9	280	CC	0.99254	0.194847	0			3	60	83	1	0	6.573125	11	60	373	34		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	71566943	71566943	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71566943C>T			NA	NA				UTP3 (10676 upstream) : RNU6-520P (528 downstream)						NA		NA									NA						caggttcaagcgattctgctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.71566943C>T		NA		hg19		0.02	-0.219276	AAGxGAT	COVERED																																																																																			NOVEL					0			6	3.304878	KEEP	0	0	0	11	298	CC	0.993072	0.549057	0			4	60	108	0	0	8.096364	19	60	631	52		0.173913	0.552887
RUFY3	22902	__UNKNOWN__	__UNKNOWN__	4	71579006	71579006	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71579006T>C	ENST00000417478.2	+	1	494					NM_001130709.1	NP_001124181.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	NA		NA			negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			tcccaaagtgttgggattaca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189	22902		Zinc fingers, FYVE domain containing	30285	protein-coding gene	gene with protein product	single axon-related 1	611194			NA	17439943	Standard	NM_014961	NM_001130709	NA	Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000417478.2:c.358+7995T>C	chr4.hg19:g.71579006T>C		NA	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	hg19	CCDS47068.1	0.02	-0.192968	GTGxTGG	COVERED																																																																																			NOVEL	RUFY3-005	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362591.1	11	2.706691	KEEP	0	0	0	9	249	TT	0.99254	0.454342	0		+	3	60	110	0	0	8.832956	16	60	491	46	ENST00000417478.2	0.157895	0.457757
RUFY3	22902	__UNKNOWN__	__UNKNOWN__	4	71588258	71588258	__UNKNOWN__	5'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71588258C>G	ENST00000381006.3	+	0	547				RUFY3_ENST00000417478.2_Intron|RUFY3_ENST00000226328.4_5'UTR	NM_001037442.2	NP_001032519.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	NA		NA			negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			gtgtgtgtgtctgtgtgtgtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													97	84	88			NA	NA	4		NA											NA				71588258		2203	4300	6503	SO:0001623	5_prime_UTR_variant			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189	22902		Zinc fingers, FYVE domain containing	30285	protein-coding gene	gene with protein product	single axon-related 1	611194			NA	17439943	Standard	NM_014961	NM_001130709	NA	Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000381006.3:c.-33C>G	chr4.hg19:g.71588258C>G		NA	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	hg19	CCDS34001.1	0.02	3.630657	TGTxTGT	COVERED																																																																																			NOVEL	RUFY3-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252162.1	25	6.753065	KEEP	0	10	291	125	3797	CC	1	0.999991	0		+	6	60	204	0	0	13.229882	101	60	3351	325	ENST00000381006.3	0.056075	0.999991
RUFY3	22902	__UNKNOWN__	__UNKNOWN__	4	71595892	71595892	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71595892G>A	ENST00000381006.3	+	1	757				RUFY3_ENST00000417478.2_Intron|RUFY3_ENST00000226328.4_Intron|RUFY3_ENST00000536664.1_Intron	NM_001037442.2	NP_001032519.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	NA		NA			negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			aacctgcctcggcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189	22902		Zinc fingers, FYVE domain containing	30285	protein-coding gene	gene with protein product	single axon-related 1	611194			NA	17439943	Standard	NM_014961	NM_001130709	NA	Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000381006.3:c.178+7424G>A	chr4.hg19:g.71595892G>A		NA	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	hg19	CCDS34001.1	0.02	-0.201756	CTCxGCC	COVERED																																																																																			NOVEL	RUFY3-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252162.1	5	2.406013	KEEP	0	0	0	8	230	GG	0.99257	0.518282	0		+	3	60	93	0	0	6.992372	18	60	589	47	ENST00000381006.3	0.142857	0.522161
MOB1B	92597	__UNKNOWN__	__UNKNOWN__	4	71801847	71801847	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:71801847T>C	ENST00000309395.2	+	2	215				MOB1B_ENST00000511449.1_Intron|MOB1B_ENST00000396051.2_Intron	NM_001244766.1|NM_173468.3	NP_001231695.1|NP_775739.1	Q7L9L4	MOB1B_HUMAN	MOB kinase activator 1B	NA		NA			hippo signaling (GO:0035329)|positive regulation of phosphorylation (GO:0042327)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	kinase activator activity (GO:0019209)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)				NA						ggattacaggtgtgagccacc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC038112	CCDS34002.1, CCDS58903.1	4q13.3	2011-09-28	2011-09-28	2011-09-27	ENSG00000173542	ENSG00000173542	92597		MOB kinase activators	29801	protein-coding gene	gene with protein product	Mob4A protein	609282	MOB1, Mps One Binder kinase activator-like 1A (yeast), MOB1 Mps One Binder homolog B (yeast)	MOBKL1A	NA	15067004	Standard	NM_173468	NM_173468	NA	Approved	MOB4A	uc003hfw.3	Q7L9L4	OTTHUMG00000160844	ENST00000309395.2:c.15-22744T>C	chr4.hg19:g.71801847T>C		NA	B2R8U6|B4DRY3|Q8IY23	hg19	CCDS34002.1	0.02	-0.280588	AGGxGTG	COVERED																																																																																			NOVEL	MOB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362634.1	13	2.537416	KEEP	11	1	30	19	517	TT	0.995343	0.736227	0		+	3	60	94	1	0	6.555371	28	60	795	80	ENST00000309395.2	0.096774	0.739671
RP11-692D12.1	0	__UNKNOWN__	__UNKNOWN__	4	74146044	74146044	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:74146044T>A	ENST00000502790.1	+	0	330										NA		NA									NA						ctgtctcctgtgtagctggga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502790.1:	chr4.hg19:g.74146044T>A		NA		hg19		0.02	-0.122767	CTGxGTA	COVERED																																																																																			NOVEL	RP11-692D12.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000362542.1	2	2.404989	KEEP	0	0	0	8	212	TT	0.99257	0.194853	0		+	3	60	83	0	0	6.573703	11	60	328	32	ENST00000502790.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	74216977	74216977	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:74216977T>C			NA	NA				RP11-692D12.1 (33307 upstream) : ALB (52978 downstream)						NA		NA									NA						acctgtaatctcagcacttcg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.74216977T>C		NA		hg19		0.02	-0.175424	ATCxCAG	COVERED																																																																																			NOVEL					0			8	3.308507	KEEP	1	0	0	11	308	TT	0.992708	0.384582	0			3	60	108	0	0	8.633053	16	60	484	44		0.157895	0.387407
SCARB2	950	__UNKNOWN__	__UNKNOWN__	4	77126237	77126237	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:77126237A>G	ENST00000452464.2	-	1	177				SCARB2_ENST00000264896.2_Intron	NM_001204255.1	NP_001191184.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	NA		NA			cell adhesion (GO:0007155)|protein targeting to lysosome (GO:0006622)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(3)|prostate(2)|skin(1)	22			Lung(101;0.196)			ccagcactttaggaggcaaag	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D12676	CCDS3577.1, CCDS56335.1	4q21.1	2014-07-11	2002-09-06	2002-09-06	ENSG00000138760	ENSG00000138760	950			1665	protein-coding gene	gene with protein product		602257	CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)	CD36L2	NA	1374238	Standard	NM_005506	NM_005506	NA	Approved	HLGP85, LIMPII, SR-BII, LIMP-2	uc003hju.2	Q14108	OTTHUMG00000130099	ENST00000452464.2:c.117+8342T>C	chr4.hg19:g.77126237A>G		NA	B4DKD8|E7EM68|Q53Y63	hg19	CCDS56335.1	0.02	-0.306915	TTTxGGA	COVERED																																																																																			NOVEL	SCARB2-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362702.1	10	3.909559	KEEP	0	0	0	13	361	AA	0.994391	0.795757	0		-	3	60	99	0	0	7.053328	28	60	838	70	ENST00000452464.2	0.096774	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	78595481	78595481	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:78595481A>G			NA	NA				CXCL13 (62493 upstream) : SNORD75 (28418 downstream)						NA		NA									NA						cacccgcctcagcctcccaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.78595481A>G		NA		hg19		0.02	-0.13149	CTCxGCC	COVERED																																																																																			NOVEL					0			13	4.211316	KEEP	11	0	0	14	397	AA	0.99254	0.227464	0			3	60	92	0	0	7.374118	12	60	357	49		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	78930157	78930157	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:78930157A>G			NA	NA				MRPL1 (56213 upstream) : FRAS1 (48566 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.78930157A>G		NA		hg19		0.02	-0.166634	CACxCCT	COVERED																																																																																			NOVEL					0			10	4.812859	KEEP	5	0	0	16	455	AA	0.995343	0.352299	0			3	58	100	0	0	7.833459	16	60	473	55		0.157895	0.353947
FRAS1	80144	__UNKNOWN__	__UNKNOWN__	4	79374742	79374742	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:79374742T>C	ENST00000264895.6	+	47	7203					NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	NA		NA			cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						ctcccttgagtccaggagttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759	80144			19185	protein-coding gene	gene with protein product		607830	Fraser syndrome 1		NA	12766769, 3118036	Standard		NM_025074	NA	Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.6763+1234T>C	chr4.hg19:g.79374742T>C		NA	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	hg19	CCDS54771.1	0.02	-0.254332	GAGxCCA	COVERED																																																																																			NOVEL	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		6	3.30687	KEEP	0	0	0	11	298	TT	0.993072	0.663892	0		+	3	20	103	0	0	7.694595	23	60	666	59	ENST00000264895.6	0.115385	0.668523
FGF5	2250	__UNKNOWN__	__UNKNOWN__	4	81210336	81210336	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:81210336G>A	ENST00000312465.7	+	0	3543				FGF5_ENST00000456523.3_3'UTR	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	NA		NA			cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell differentiation (GO:0010001)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction involved in regulation of gene expression (GO:0023019)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	fibroblast growth factor receptor binding (GO:0005104)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	22						tagtagagacggggtttcacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M23534	CCDS3586.1, CCDS34021.1	4q21	2014-01-30			ENSG00000138675	ENSG00000138675	2250		Endogenous ligands	3683	protein-coding gene	gene with protein product		165190			NA	3211147, 2577873	Standard		NM_001291812	NA	Approved		uc003hmd.3	P12034	OTTHUMG00000130288	ENST00000312465.7:c.*2510G>A	chr4.hg19:g.81210336G>A		NA	B2R554|O75846|Q3Y8M3|Q8NF90	hg19	CCDS34021.1	0.02	-0.385963	GACxGGG	COVERED																																																																																			NOVEL	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252627.2	14	6.34758	KEEP	0	1	31	32	908	GG	0.999998	0.926638	0		+	5	60	157	0	0	11.376033	38	60	1247	119	ENST00000312465.7	0.116279	0.92664
PRKG2	5593	__UNKNOWN__	__UNKNOWN__	4	82101274	82101274	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:82101274T>G	ENST00000395578.1	-	3	578				PRKG2_ENST00000264399.1_Intron|RP11-100N20.1_ENST00000505175.1_RNA|RP11-100N20.1_ENST00000512502.1_RNA|PRKG2_ENST00000418486.2_Intron			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	NA		NA			blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						gcaacaagagtgaaactccat	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	5593	2.7.11.1		9416	protein-coding gene	gene with protein product		601591			NA	7498513	Standard	NM_006259	XM_005263126	NA	Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.462-5161A>C	chr4.hg19:g.82101274T>G		NA	B4DMX3|E7EPE6|O00125|O60916	hg19	CCDS3589.1	0.02	-0.09649	GAGxGAA	UNCOVERED																																																																																			NOVEL	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252639.1	11	3.308592	KEEP	3	0	0	11	308	TT	0.992708	0.119558	0		-	3	23	103	0	0	8.932422	8	60	248	32	ENST00000395578.1	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	83185191	83185191	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83185191T>C			NA	NA				RNU6-499P (89385 upstream) : RP11-127B20.2 (80837 downstream)						NA		NA									NA						tgcagtggcttatgcctgtaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.83185191T>C		NA		hg19		0.02	-0.149101	GCTxATG	COVERED																																																																																			NOVEL					0			6	3.007304	KEEP	0	0	0	10	274	TT	0.992708	0.289872	0			3	60	103	0	0	8.47231	12	60	348	37		0.2	0.292001
TMEM150C	441027	__UNKNOWN__	__UNKNOWN__	4	83466898	83466898	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83466898C>T	ENST00000508701.1	-	1	50				TMEM150C_ENST00000515780.2_Intron|TMEM150C_ENST00000449862.2_Intron			B9EJG8	T150C_HUMAN	transmembrane protein 150C	NA		NA				integral component of membrane (GO:0016021)				ovary(1)	1						gcctggccaacatggcaaaac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC147027	CCDS47087.1	4q21.22	2010-06-25			ENSG00000249242	ENSG00000249242	441027			37263	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080506	NM_001080506	NA	Approved	FLJ12993	uc003hmy.1	B9EJG8	OTTHUMG00000161083	ENST00000508701.1:c.9+16160G>A	chr4.hg19:g.83466898C>T		NA	B7Z4J5|B7Z4L3|B7Z692|B7Z6X6	hg19		0.02	-0.122807	CAAxATG	COVERED																																																																																			NOVEL	TMEM150C-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363689.1	10	2.707099	KEEP	0	0	0	9	261	CC	0.99254	0.194847	0		-	3	60	86	0	0	7.232092	8	60	279	26	ENST00000508701.1	0.272727	0.196312
TMEM150C	441027	__UNKNOWN__	__UNKNOWN__	4	83467721	83467721	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83467721T>C	ENST00000508701.1	-	1	50				TMEM150C_ENST00000515780.2_Intron|TMEM150C_ENST00000449862.2_Intron			B9EJG8	T150C_HUMAN	transmembrane protein 150C	NA		NA				integral component of membrane (GO:0016021)				ovary(1)	1						gtggctcacgtctgtaatccc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC147027	CCDS47087.1	4q21.22	2010-06-25			ENSG00000249242	ENSG00000249242	441027			37263	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080506	NM_001080506	NA	Approved	FLJ12993	uc003hmy.1	B9EJG8	OTTHUMG00000161083	ENST00000508701.1:c.9+15337A>G	chr4.hg19:g.83467721T>C		NA	B7Z4J5|B7Z4L3|B7Z692|B7Z6X6	hg19		0.02	-0.131567	ACGxCTG	COVERED																																																																																			NOVEL	TMEM150C-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363689.1	4	2.706406	KEEP	0	0	0	9	241	TT	0.99254	0.227464	0		-	3	60	103	0	0	8.572868	11	60	326	40	ENST00000508701.1	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	83722222	83722222	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83722222G>A			NA	NA				SCD5 (2212 upstream) : SEC31A (17591 downstream)						NA		NA									NA						cttgtgatccgccagccttgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.83722222G>A		NA		hg19		0.02	-0.157899	TCCxCCA	COVERED																																																																																			NOVEL					0			5	2.405862	KEEP	0	0	0	8	225	GG	0.99257	0.320408	0			3	60	89	0	0	6.978931	13	60	440	39		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	83727992	83727992	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83727992T>C			NA	NA				SCD5 (7982 upstream) : SEC31A (11821 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.83727992T>C		NA		hg19		0.02	-0.192965	TCAxGCC	COVERED																																																																																			NOVEL					0			9	2.405398	KEEP	5	0	0	8	212	TT	0.99257	0.454356	0			3	60	99	0	0	7.660845	17	60	510	51		0.15	0.457757
SEC31A	22872	__UNKNOWN__	__UNKNOWN__	4	83792941	83792941	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83792941A>G	ENST00000395310.2	-	7	965				SEC31A_ENST00000264405.5_5'UTR|SEC31A_ENST00000436790.2_Intron|SEC31A_ENST00000326950.5_Intron|SEC31A_ENST00000508502.1_Intron|SEC31A_ENST00000513858.1_Intron|SEC31A_ENST00000509142.1_Intron|SEC31A_ENST00000505984.1_Intron|SEC31A_ENST00000508479.1_Intron|SEC31A_ENST00000355196.2_Intron|SEC31A_ENST00000505472.1_Intron|SEC31A_ENST00000311785.7_Intron|SEC31A_ENST00000348405.4_Intron|SEC31A_ENST00000500777.2_Intron|SEC31A_ENST00000443462.2_Intron|SEC31A_ENST00000432794.1_Intron|SEC31A_ENST00000448323.1_Intron	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				gcagtgagccaagatcttgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674	22872		WD repeat domain containing	17052	protein-coding gene	gene with protein product		610257	SEC31-like 1 (S. cerevisiae), Sec31 homolog A (S. cerevisiae)	SEC31L1	NA	10048485, 10788476	Standard	NM_016211	NM_001077206	NA	Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.782+155T>C	chr4.hg19:g.83792941A>G		NA	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	hg19	CCDS3596.1	0.02	3.616382	GCCxAGA	COVERED																																																																																			NOVEL	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252640.1	17	3.700646	KEEP	1	6	163	70	1932	AA	1	0.999999	0		-	5	60	167	2	0	10.279878	104	60	3088	271	ENST00000395310.2	0.045872	0.999999
COPS4	51138	__UNKNOWN__	__UNKNOWN__	4	83960085	83960085	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:83960085C>T	ENST00000509093.1	+	1	852				COPS4_ENST00000511708.1_Intron|COPS4_ENST00000503682.1_Intron|COPS4_ENST00000511653.1_Intron|COPS4_ENST00000264389.2_Intron	NM_001258006.1	NP_001244935.1	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	NA		NA			cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				cgtgagccaccgcgcctggcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663	51138			16702	protein-coding gene	gene with protein product		NA	COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4, COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)		NA	9707402	Standard		NM_016129	NA	Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000509093.1:c.74+3634C>T	chr4.hg19:g.83960085C>T		NA	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	hg19	CCDS58909.1	0.02	-0.184191	CACxGCG	COVERED																																																																																			NOVEL	COPS4-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363091.1	11	3.909675	KEEP	2	0	0	13	359	CC	0.993634	0.420782	0		+	3	60	91	0	0	6.933804	16	60	514	50	ENST00000509093.1	0.157895	0.423478
PLAC8	51316	__UNKNOWN__	__UNKNOWN__	4	84011675	84011675	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:84011675T>C	ENST00000311507.4	-	0	972					NM_016619.2	NP_057703.1	Q9UHV8	PP13_HUMAN	placenta-specific 8	NA		NA			apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			large_intestine(2)|lung(3)|ovary(1)	6		Hepatocellular(203;0.114)				agcgagactctatctcaaaaa	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF208846	CCDS3601.1	4q21.22	2006-05-20			ENSG00000145287	ENSG00000145287	51316			19254	protein-coding gene	gene with protein product		607515			NA	12758124, 12384430	Standard	NM_016619	NM_016619	NA	Approved	onzin, C15	uc003hoe.3	Q9NZF1	OTTHUMG00000130294	ENST00000311507.4:c.*459A>G	chr4.hg19:g.84011675T>C		NA	C5HZ15	hg19	CCDS3601.1	0.02	-0.052628	CTCxATC	UNCOVERED																																																																																			NOVEL	PLAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252637.2	5	2.40576	KEEP	4	0	0	8	214	TT	0	0	0		-	2	55	72	1	0	6.693073	3	60	88	22	ENST00000311507.4	0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	84082523	84082523	__UNKNOWN__	IGR	SNP	C	C	T	rs534854641		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:84082523C>T			NA	NA				PLAC8 (24295 upstream) : RP11-576N17.5 (72141 downstream)						NA		NA									NA						ggcatgatctcggctcactgc	0.512		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	20069	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.84082523C>T		NA		hg19		0.02	-0.210496	TCTxGGC	COVERED																																																																																			NOVEL					0			10	4.492469	KEEP	3	0	0	15	424	CC	0.993634	0.518837	0			3	55	87	0	0	6.534046	16	60	497	48		0.157895	0.522161
RP11-576N17.5	0	__UNKNOWN__	__UNKNOWN__	4	84160716	84160716	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:84160716A>G	ENST00000515670.1	-	0	154										NA		NA									NA						tgggattacaagcgtgagcca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000515670.1:	chr4.hg19:g.84160716A>G		NA		hg19		0.02	-0.166656	ACAxGCG	COVERED																																																																																			NOVEL	RP11-576N17.5-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000363974.3	7	4.510808	KEEP	1	0	0	15	411	AA	0.99649	0.352705	0		-	3	60	101	0	0	8.091634	14	60	434	49	ENST00000515670.1	0.176471	0.353947
HPSE	10855	__UNKNOWN__	__UNKNOWN__	4	84244044	84244044	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:84244044T>C	ENST00000513463.1	-	2	227				HPSE_ENST00000512196.1_Intron|HPSE_ENST00000311412.5_Intron|HPSE_ENST00000405413.2_Intron	NM_001199830.1	NP_001186759.1	Q9Y251	HPSE_HUMAN	heparanase	NA		NA			carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	gtctcaaacttctggcttcaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083	10855			5164	protein-coding gene	gene with protein product		604724			NA	10395325, 10395326	Standard	NM_006665	NM_006665	NA	Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000513463.1:c.228-527A>G	chr4.hg19:g.84244044T>C		NA	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	hg19	CCDS56337.1	0.02	-0.184167	ACTxCTG	COVERED																																																																																			NOVEL	HPSE-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363967.1	10	3.608716	KEEP	0	0	0	12	327	TT	0.993634	0.420782	0		-	3	60	98	0	0	7.879136	13	60	381	39	ENST00000513463.1	0.1875	0.423478
HELQ	113510	__UNKNOWN__	__UNKNOWN__	4	84340487	84340487	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:84340487C>T	ENST00000510985.1	-	15	2878				HELQ_ENST00000295488.3_Intron			Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	NA		NA			double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						tcccagcactctgggaggcca	0.502		NA						Other identified genes with known or suspected DNA repair function													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312	113510			18536	protein-coding gene	gene with protein product		606769			NA	11751861	Standard	NM_133636	XM_005262711	NA	Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000510985.1:c.2749-1128G>A	chr4.hg19:g.84340487C>T		NA	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	hg19		0.02	-0.175448	ACTxTGG	COVERED																																																																																			NOVEL	HELQ-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363955.1	6	3.610865	KEEP	1	0	0	12	373	CC	0.993634	0.38494	0		-	3	60	94	0	0	7.23329	16	60	535	47	ENST00000510985.1	0.157895	0.387407
MRPS18C	51023	__UNKNOWN__	__UNKNOWN__	4	84381531	84381531	__UNKNOWN__	Intron	SNP	T	T	C	rs376982685		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:84381531T>C	ENST00000295491.4	+	4	405				MRPS18C_ENST00000507019.1_Intron|MRPS18C_ENST00000507349.1_Intron	NM_016067.2	NP_057151.1	Q9Y3D5	RT18C_HUMAN	mitochondrial ribosomal protein S18C	NA		NA			translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5		Hepatocellular(203;0.114)				tggtcttgaattcctgacctc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3604.1, CCDS75159.1	4q21.21-q21.23	2012-09-13			ENSG00000163319	ENSG00000163319	51023		Mitochondrial ribosomal proteins / small subunits	16633	protein-coding gene	gene with protein product		611983			NA	11279123, 10810093	Standard		XM_005263043	NA	Approved	MRPS18-1, CGI-134, FLJ11146, FLJ22967	uc003hor.4	Q9Y3D5	OTTHUMG00000130430	ENST00000295491.4:c.292+581T>C	chr4.hg19:g.84381531T>C		NA		hg19	CCDS3604.1	0.02	-0.14032	GAAxTCC	UNCOVERED																																																																																			NOVEL	MRPS18C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252820.2	5	2.405979	KEEP	1	0	0	8	218	TT	0	0	0		+	3	60	87	0	0	6.872821	12	60	349	36	ENST00000295491.4	0.2	0.260965
ARHGAP24	83478	__UNKNOWN__	__UNKNOWN__	4	86599439	86599439	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:86599439T>C	ENST00000395184.1	+	3	646				ARHGAP24_ENST00000506421.1_Intron|ARHGAP24_ENST00000503995.1_Intron	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	NA		NA			activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		aggaggatcgtttgagcccag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639	83478		Rho GTPase activating proteins, Pleckstrin homology (PH) domain containing	25361	protein-coding gene	gene with protein product		610586			NA	11230166, 15254788	Standard	NM_031305	NM_001042669	NA	Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.181-43599T>C	chr4.hg19:g.86599439T>C		NA	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	hg19	CCDS34025.1	0.02	-0.043847	TCGxTTG	UNCOVERED																																																																																			NOVEL	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252815.2	5	3.007107	KEEP	0	0	0	10	273	TT	0.992708	0.023898	0		+	2	60	69	0	0	6.393305	3	60	80	21	ENST00000395184.1	0.4	0.024074
ARHGAP24	83478	__UNKNOWN__	__UNKNOWN__	4	86746232	86746232	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:86746232G>A	ENST00000395184.1	+	4	734				ARHGAP24_ENST00000503995.1_Intron|ARHGAP24_ENST00000395183.2_Intron	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	NA		NA			activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		aacagagcaagacttcatctc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639	83478		Rho GTPase activating proteins, Pleckstrin homology (PH) domain containing	25361	protein-coding gene	gene with protein product		610586			NA	11230166, 15254788	Standard	NM_031305	NM_001042669	NA	Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.269-98569G>A	chr4.hg19:g.86746232G>A		NA	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	hg19	CCDS34025.1	0.02	-0.105272	CAAxACT	UNCOVERED																																																																																			NOVEL	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252815.2	7	3.610163	KEEP	1	0	0	12	362	GG	0.993634	0.138942	0		+	3	60	95	0	0	8.000874	9	60	315	38	ENST00000395184.1	0.25	0.139832
ARHGAP24	83478	__UNKNOWN__	__UNKNOWN__	4	86761271	86761271	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:86761271C>G	ENST00000395184.1	+	4	734				ARHGAP24_ENST00000503995.1_Intron|ARHGAP24_ENST00000395183.2_Intron	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	NA		NA			activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		acccacctcaccctcccaaag	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639	83478		Rho GTPase activating proteins, Pleckstrin homology (PH) domain containing	25361	protein-coding gene	gene with protein product		610586			NA	11230166, 15254788	Standard	NM_031305	NM_001042669	NA	Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.269-83530C>G	chr4.hg19:g.86761271C>G		NA	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	hg19	CCDS34025.1	0.02	-0.166673	TCAxCCT	UNCOVERED																																																																																			NOVEL	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252815.2	4	2.407011	KEEP	1	0	0	8	244	CC	0	0	0		+	3	60	98	0	0	7.791576	14	60	475	40	ENST00000395184.1	0.176471	0.353947
MAPK10	5602	__UNKNOWN__	__UNKNOWN__	4	86938317	86938317	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:86938317C>T	ENST00000395169.3	-	0	2065				MAPK10_ENST00000395157.3_3'UTR|MAPK10_ENST00000395166.1_3'UTR|MAPK10_ENST00000395160.3_3'UTR|MAPK10_ENST00000449047.2_3'UTR|MAPK10_ENST00000361569.2_3'UTR|MAPK10_ENST00000359221.3_3'UTR	NM_138980.2|NM_138982.2	NP_620446.1|NP_620448.1	P53779	MK10_HUMAN	mitogen-activated protein kinase 10	NA		NA			activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		tgtgtgtctgcgtgtgtgtgt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	5602	2.7.11.1	Mitogen-activated protein kinase cascade / Kinases	6872	protein-coding gene	gene with protein product		602897		PRKM10	NA	8654373, 12436199	Standard		NM_002753	NA	Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000395169.3:c.*64G>A	chr4.hg19:g.86938317C>T		NA	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	hg19	CCDS3612.1	0.02	1.226608	CTGxGTG	COVERED																																																																																			NOVEL	MAPK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253054.3	9	7.954514	KEEP	0	1	24	35	1026	CC	0.999999	0.998866	0		-	9	60	255	2	1	18.087264	62	60	1994	161	ENST00000395169.3	0.126761	0.998867
KLHL8	57563	__UNKNOWN__	__UNKNOWN__	4	88145382	88145382	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:88145382A>G	ENST00000506274.1	-	2	57							Q9P2G9	KLHL8_HUMAN	kelch-like family member 8	NA		NA			protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)				breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000603)		gattacaagcatgagccaccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037799	CCDS3617.1, CCDS75163.1	4q21.3	2013-01-30	2013-01-30		ENSG00000145332	ENSG00000145332	57563		Kelch-like, BTB/POZ domain containing	18644	protein-coding gene	gene with protein product		611967	kelch-like 8 (Drosophila)		NA		Standard		XM_005263153	NA	Approved	KIAA1378	uc003hql.1	Q9P2G9	OTTHUMG00000130593	ENST00000506274.1:c.1868-2840T>C	chr4.hg19:g.88145382A>G		NA	Q53XA3|Q6N018	hg19		0.02	-0.175428	AGCxTGA	COVERED																																																																																			NOVEL	KLHL8-008	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000363209.1	5	3.007734	KEEP	0	0	0	10	281	AA	0.992708	0.384582	0		-	3	60	101	0	0	8.010039	15	60	461	47	ENST00000506274.1	0.166667	0.387407
SPARCL1	8404	__UNKNOWN__	__UNKNOWN__	4	88426976	88426976	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:88426976A>G	ENST00000503414.1	-	2	48				SPARCL1_ENST00000282470.6_Intron|SPARCL1_ENST00000418378.1_Intron			Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	NA		NA			signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ctcctaaagtactgggattac	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583	8404		EF-hand domain containing	11220	protein-coding gene	gene with protein product		606041	SPARC-like 1 (mast9, hevin)		NA	8488563, 7600298, 16844696	Standard		NM_001128310	NA	Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000503414.1:c.495-6239T>C	chr4.hg19:g.88426976A>G		NA	B4E2Z0|E7ESU2|Q14800	hg19		0.02	-0.192907	AGTxCTG	COVERED																																																																																			NOVEL	SPARCL1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363611.2	8	3.00505	KEEP	1	0	0	10	251	AA	0.992708	0.454419	0		-	3	60	98	1	0	7.427451	19	60	530	43	ENST00000503414.1	0.136364	0.457757
DSPP	1834	__UNKNOWN__	__UNKNOWN__	4	88536917	88536917	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs199901845		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:88536917G>A	ENST00000282478.7	+	4	3136	c.3103G>A	c.(3103-3105)Gat>Aat	p.D1035N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1035N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.	NA			biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035N(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgacagcagcgatagcagtga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	kidney(1)											62	68	66			NA	NA	4		NA											NA				88536917		1560	2750	4310	SO:0001583	missense			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591	1834			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1	NA	8995371, 9533027	Standard	NM_014208	NM_014208	NA	Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3103G>A	chr4.hg19:g.88536917G>A	ENSP00000282478:p.Asp1035Asn	NA	A8MUI0|O95815	hg19	CCDS43248.1	0.02	-0.263123	AGCxATA	COVERED	.	.	.	.	.	.	.	.	.	.	g	5.819	0.335399	0.11013	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88664	-2.41;-2.41	1.43	0.544	0.17185	.	.	.	.	.	T	0.73999	0.3659	L	0.29908	0.895	0.18873	N	0.999989	B	0.30542	0.284	B	0.13407	0.009	T	0.59783	-0.7389	9	0.06494	T	0.89	-6.585	4.0989	0.10004	0.2347:0.0:0.7653:0.0	.	1035	Q9NZW4	DSPP_HUMAN	N	1035	ENSP00000382213:D1035N;ENSP00000282478:D1035N	ENSP00000282478:D1035N	D	+	1	0	DSPP	88755941	0.238000	0.23825	0.544000	0.28141	0.014000	0.08584	1.337000	0.33862	0.180000	0.19960	-0.791000	0.03333	GAT	NOVEL	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363616.3	4	3.007364	KEEP	1	0	0	10	278	GG	0.992708	0.68861	0		+	6	60	179	0	0	14.552872	21	60	638	60	ENST00000282478.7	0.222222	0.693668
DSPP	1834	__UNKNOWN__	__UNKNOWN__	4	88536919	88536919	__UNKNOWN__	Silent	SNP	T	T	C	rs369387818		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:88536919T>C	ENST00000282478.7	+	4	3138	c.3105T>C	c.(3103-3105)gaT>gaC	p.D1035D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1035D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	Asp/Ser-rich.	NA			biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1035D(2)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcgatagcagtgaca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - coding silent(2)	kidney(2)											63	70	67			NA	NA	4		NA											NA				88536919		1560	2747	4307	SO:0001819	synonymous_variant			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591	1834			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1	NA	8995371, 9533027	Standard	NM_014208	NM_014208	NA	Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3105T>C	chr4.hg19:g.88536919T>C		NA	A8MUI0|O95815	hg19	CCDS43248.1	0.02	-0.254257	CGAxAGC	COVERED																																																																																			NOVEL	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363616.3	4	2.704922	KEEP	2	0	0	9	227	TT	0.99254	0.663536	0		+	5	58	160	0	0	12.860299	21	60	565	53	ENST00000282478.7	0.192308	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	88831117	88831117	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:88831117T>A			NA	NA				MEPE (63148 upstream) : SPP1 (65701 downstream)						NA		NA									NA						ggccaggcgctgtggctcatg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.88831117T>A		NA		hg19		0.02	-0.184197	CGCxGTG	COVERED																																																																																			NOVEL					0			8	3.609093	KEEP	1	0	0	12	329	TT	0.993634	0.454842	0			3	60	94	0	0	7.310233	15	60	459	47		0.166667	0.457757
PPM1K	152926	__UNKNOWN__	__UNKNOWN__	4	89199426	89199426	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs549825065		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:89199426G>A	ENST00000608933.1	-	2	699	c.310C>T	c.(310-312)Cgg>Tgg	p.R104W	PPM1K_ENST00000295908.7_Missense_Mutation_p.R104W|PPM1K_ENST00000514204.1_Missense_Mutation_p.R104W|PPM1K_ENST00000508256.1_Intron|PPM1K_ENST00000315194.4_Missense_Mutation_p.R104W|PPM1K_ENST00000506423.1_5'UTR	NM_152542.4	NP_689755.3	Q8N3J5	PPM1K_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1K	104	PP2C-like.	NA			protein dephosphorylation (GO:0006470)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000192)		TTCTCTTTCCGTTTGCCAATC	0.488		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	22928	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													109	96	100			NA	NA	4		NA											NA				89199426		2203	4300	6503	SO:0001583	missense			BC037552	CCDS3629.1	4q22.1	2012-04-17	2010-03-05		ENSG00000163644	ENSG00000163644	152926	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	25415	protein-coding gene	gene with protein product	PP2C-type mitochondrial phosphoprotein phosphatase, protein phosphatase 2C kappa, branched-chain &#945;-ketoacid dehydrogenase phosphatase	611065	protein phosphatase 1K (PP2C domain containing)		NA	22291014	Standard	NM_152542	NM_152542	NA	Approved	DKFZp761G058, PP2Ckappa, hPTMP, PP2Cm, BDP	uc003hrm.5	Q8N3J5	OTTHUMG00000130952	ENST00000608933.1:c.310C>T	chr4.hg19:g.89199426G>A	ENSP00000477341:p.Arg104Trp	NA	B2RAZ1|Q05CT5|Q49AB5|Q4W5E6|Q56AN8|Q8IUZ7|Q8IXG7|Q8ND70|Q96NT4	hg19	CCDS3629.1	0.02	1.271809	TCCxTTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.93	3.510091	0.64522	.	.	ENSG00000163644	ENST00000295908;ENST00000506423;ENST00000315194	T;T;T	0.17691	2.26;2.26;2.26	4.39	2.57	0.30868	Protein phosphatase 2C-like (4);	0.000000	0.85682	D	0.000000	T	0.51787	0.1695	H	0.97365	3.99	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.57412	-0.7816	10	0.87932	D	0	-6.6345	7.6349	0.28261	0.0:0.1501:0.4001:0.4498	.	104;104;104	Q8N3J5-2;Q8N3J5-3;Q8N3J5	.;.;PPM1K_HUMAN	W	104	ENSP00000295908:R104W;ENSP00000424155:R104W;ENSP00000324761:R104W	ENSP00000295908:R104W	R	-	1	2	PPM1K	89418450	1.000000	0.71417	0.992000	0.48379	0.882000	0.50991	6.302000	0.72788	0.553000	0.29044	0.313000	0.20887	CGG	NOVEL	PPM1K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253553.4	0	5.716155	KEEP	0	0	0	19	564	GG	0.99986	0.999267	0		-	5	60	151	0	0	9.400252	74	60	2426	156	ENST00000608933.1	0.063291	0.999407
HERC6	55008	__UNKNOWN__	__UNKNOWN__	4	89325615	89325615	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:89325615G>A	ENST00000264346.7	+	9	1151				HERC6_ENST00000380265.5_Intron	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		tgctgggattgcaggcatgag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642	55008			26072	protein-coding gene	gene with protein product		609249	hect domain and RLD 6		NA		Standard		NM_001165136	NA	Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1093-413G>A	chr4.hg19:g.89325615G>A		NA	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	hg19	CCDS47098.1	0.02	-0.087702	ATTxCAG	UNCOVERED																																																																																			NOVEL	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363259.2	4	2.407113	KEEP	0	0	0	8	243	GG	0.99257	0.09898	0		+	3	60	79	0	0	6.842283	6	60	207	22	ENST00000264346.7	0.333333	0.099721
HERC5	51191	__UNKNOWN__	__UNKNOWN__	4	89423155	89423155	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:89423155T>C	ENST00000264350.3	+	20	2735				HERC5_ENST00000508159.1_Intron	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		ttcaccgtgttagccaggatg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(39;887 1012 34045 50514)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646	51191			24368	protein-coding gene	gene with protein product		608242	hect domain and RLD 5		NA	10581175	Standard	NM_016323	NM_016323	NA	Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.2582+1019T>C	chr4.hg19:g.89423155T>C		NA	B2RTQ1|Q69G20	hg19	CCDS3630.1	0.02	-0.131517	TGTxAGC	UNCOVERED																																																																																			NOVEL	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253554.2	6	2.405072	KEEP	5	0	0	8	206	TT	0	0	0		+	3	58	91	0	0	7.482591	10	60	268	34	ENST00000264350.3	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	89450720	89450720	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:89450720G>C			NA	NA				HERC3 (5756 upstream) : RN7SKP244 (54096 downstream)						NA		NA									NA						gcctggccaagatggtgaaac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.89450720G>C		NA		hg19		0.02	-0.105264	CAAxATG	UNCOVERED																																																																																			NOVEL					0			6	2.406973	KEEP	0	0	0	8	239	GG	0.99257	0.138793	0			3	60	94	0	0	8.032276	8	60	259	21		0.272727	0.139832
FAM13A	10144	__UNKNOWN__	__UNKNOWN__	4	90001869	90001869	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:90001869A>G	ENST00000502459.1	-	1	357							O94988	FA13A_HUMAN	family with sequence similarity 13, member A	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						ggccgggtgcagtggctcaca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640	10144		Rho GTPase activating proteins	19367	protein-coding gene	gene with protein product		613299	family with sequence similarity 13, member A1	FAM13A1	NA		Standard		NM_014883	NA	Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000502459.1:c.1636+30323T>C	chr4.hg19:g.90001869A>G		NA	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	hg19		0.02	-0.149116	TGCxGTG	COVERED																																																																																			NOVEL	FAM13A-011	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000363360.1	6	2.405139	KEEP	0	0	0	8	214	AA	0.99257	0.289832	0		-	3	60	102	0	0	8.191583	14	60	430	37	ENST00000502459.1	0.176471	0.292001
MMRN1	22915	__UNKNOWN__	__UNKNOWN__	4	90818549	90818549	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:90818549T>C	ENST00000394980.1	+	2	942				MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000264790.2_Intron			Q13201	MMRN1_HUMAN	multimerin 1	NA		NA			blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		ttagtagagatggggtttcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722	22915		EMI domain containing	7178	protein-coding gene	gene with protein product	glycoprotein Ia*	601456	multimerin	MMRN	NA	7629143, 10828608	Standard	NM_007351	NM_007351	NA	Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.623+1804T>C	chr4.hg19:g.90818549T>C		NA	Q4W5L1|Q6P3T8|Q6ZUL9	hg19	CCDS3635.1	0.02	-0.149042	AGAxGGG	COVERED																																																																																			NOVEL	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253546.2	5	2.404602	KEEP	1	0	0	8	207	TT	0.99257	0.289832	0		+	3	49	101	0	0	8.179547	13	60	354	29	ENST00000394980.1	0.1875	0.292001
CCSER1	401145	__UNKNOWN__	__UNKNOWN__	4	91381244	91381244	__UNKNOWN__	Intron	SNP	A	A	G	rs113565540	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:91381244A>G	ENST00000509176.1	+	5	1891				CCSER1_ENST00000333691.8_Intron|CCSER1_ENST00000432775.2_Intron	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	NA		NA									NA						ttgggaggccaagacgggcgg	0.498		NA											-|||	492	0.0982428	0.2292	0.0418	5008	,	,	NA	13661	0.0169	NA	0.0716	False	NA	,,,	NA	NA	NA	2504	0.0726	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305	401145			29349	protein-coding gene	gene with protein product		NA	family with sequence similarity 190, member A	FAM190A	NA	11214970	Standard	NM_001145065	NM_001145065	NA	Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1604-8141A>G	chr4.hg19:g.91381244A>G		NA	Q4W5M0|Q86V57	hg19	CCDS47099.1	0.02	-0.087712	GCCxAGA	UNCOVERED																																																																																			NOVEL	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363109.3	6	3.308038	KEEP	17	0	0	11	299	AA	0	0	0		+	5	60	160	0	0	16.086715	3	40	89	45	ENST00000509176.1	0.625	0.099721
CCSER1	401145	__UNKNOWN__	__UNKNOWN__	4	91620413	91620413	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:91620413A>G	ENST00000509176.1	+	7	2220				CCSER1_ENST00000504150.1_Intron|CCSER1_ENST00000333691.8_Intron|CCSER1_ENST00000432775.2_Intron	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	NA		NA									NA						ccaggagttcaagaccaggct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305	401145			29349	protein-coding gene	gene with protein product		NA	family with sequence similarity 190, member A	FAM190A	NA	11214970	Standard	NM_001145065	NM_001145065	NA	Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.1933-24652A>G	chr4.hg19:g.91620413A>G		NA	Q4W5M0|Q86V57	hg19	CCDS47099.1	0.02	-0.026312	TTCxAGA	UNCOVERED																																																																																			NOVEL	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363109.3	6	3.007966	KEEP	0	0	0	10	280	AA	0.992708	0	0		+	2	60	63	0	0	7.253623	0	0	0	17	ENST00000509176.1	1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	95332314	95332314	__UNKNOWN__	IGR	SNP	G	G	A	rs147406425		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:95332314G>A			NA	NA				HPGDS (68287 upstream) : PDLIM5 (40722 downstream)						NA		NA									NA						aaagaaagaaggaaagaaagg	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.95332314G>A		NA		hg19		0.02	-0.087721	GAAxGAA	UNCOVERED																																																																																			NOVEL					0			7	3.911531	KEEP	1	0	0	13	402	GG	0.994391	0.099162	0			3	39	94	0	0	8.343388	6	60	197	35		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	95332966	95332966	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:95332966A>G			NA	NA				HPGDS (68939 upstream) : PDLIM5 (40070 downstream)						NA		NA									NA						tagtagagacagggtttcacc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.95332966A>G		NA		hg19		0.02	-0.131547	GACxGGG	COVERED																																																																																			NOVEL					0			9	3.308594	KEEP	8	0	0	11	307	AA	0.99254	0.227464	0			3	47	93	0	0	7.573243	11	60	320	41		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	95333047	95333047	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:95333047A>G			NA	NA				HPGDS (69020 upstream) : PDLIM5 (39989 downstream)						NA		NA									NA						aaagtgctggaattacaggcg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.95333047A>G		NA		hg19		0.02	-0.149103	TGGxATT	COVERED																																																																																			NOVEL					0			4	3.308541	KEEP	6	0	0	11	306	AA	0.992708	0.289872	0			3	60	103	0	0	8.378871	13	60	383	54		0.1875	0.292001
PDLIM5	10611	__UNKNOWN__	__UNKNOWN__	4	95482158	95482158	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:95482158T>G	ENST00000514743.1	+	3	292				PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000542407.1_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000317968.4_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000450793.1_Intron	NM_001256426.1	NP_001243355	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	NA		NA			regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		gattacaggcttgagccaccg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110	10611			17468	protein-coding gene	gene with protein product		605904			NA	15346770	Standard		NM_006457	NA	Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000514743.1:c.249-12344T>G	chr4.hg19:g.95482158T>G		NA	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	hg19	CCDS58916.1	0.02	-0.096475	GGCxTGA	UNCOVERED																																																																																			NOVEL	PDLIM5-010	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362993.1	5	2.406328	KEEP	1	0	0	8	224	AT	0.99254	0.119538	0		+	4	60	129	0	0	11.677375	7	60	210	32	ENST00000514743.1	0.363636	0.120436
BMPR1B	658	__UNKNOWN__	__UNKNOWN__	4	95720705	95720705	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:95720705A>G	ENST00000515059.1	+	1	101					NM_001203.2	NP_001194.1	O00238	BMR1B_HUMAN	bone morphogenetic protein receptor, type IB	NA		NA			BMP signaling pathway (GO:0030509)|cartilage condensation (GO:0001502)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|eye development (GO:0001654)|inflammatory response (GO:0006954)|limb morphogenesis (GO:0035108)|ovarian cumulus expansion (GO:0001550)|ovulation cycle (GO:0042698)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell differentiation (GO:0045597)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of osteoblast differentiation (GO:0045669)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|skeletal system development (GO:0001501)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.51e-07)		tgcccatctcagcctcccaaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D89675	CCDS3642.1, CCDS58919.1	4q23-q24	2008-02-05			ENSG00000138696	ENSG00000138696	658		CD molecules	1077	protein-coding gene	gene with protein product		603248			NA	8140412, 9730621	Standard	NM_001203	NM_001203	NA	Approved	ALK6, CDw293	uc031sgn.1	O00238	OTTHUMG00000130991	ENST00000515059.1:c.-183+41486A>G	chr4.hg19:g.95720705A>G		NA	B2R953|B4DSV1|P78366	hg19	CCDS3642.1	0.02	-0.149095	CTCxGCC	COVERED																																																																																			NOVEL	BMPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253609.3	13	3.609394	KEEP	3	0	0	12	335	AA	0.992708	0.289872	0		+	3	60	84	1	0	6.479827	13	60	400	38	ENST00000515059.1	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	96577523	96577523	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:96577523T>G			NA	NA				RP11-710C12.1 (103915 upstream) : PDHA2 (183715 downstream)						NA		NA									NA						ctcccaaagttctgggattac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.96577523T>G		NA		hg19		0.02	-0.15789	AGTxCTG	COVERED																																																																																			NOVEL					0			8	3.007758	KEEP	0	0	0	10	284	TT	0.992708	0.351366	0			3	60	103	1	0	8.37867	13	60	404	41		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	99137123	99137123	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:99137123T>A			NA	NA				Y_RNA (42093 upstream) : RP11-323J4.1 (35715 downstream)						NA		NA									NA						aaaaaaaaactaaaaaCAACA	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.99137123T>A		NA		hg19		0.02	-0.149094	AACxAAA	COVERED																																																																																			NOVEL					0			15	3.905582	KEEP	1	0	0	13	336	TT	0.994391	0.290363	0			3	52	84	0	0	6.479511	13	60	383	42		0.1875	0.292001
EIF4E	1977	__UNKNOWN__	__UNKNOWN__	4	99801975	99801975	__UNKNOWN__	3'UTR	SNP	G	G	T	rs3926191	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:99801975G>T	ENST00000450253.2	-	0	2382				EIF4E_ENST00000280892.6_3'UTR	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	NA		NA			cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		TGGGATAGTGGAAACTCTAGC	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247	1977			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F	NA	9330633, 1916814	Standard	NM_001968	NM_001968	NA	Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.*204C>A	chr4.hg19:g.99801975G>T		NA	B7Z6V1|D6RCQ6|Q96E95	hg19	CCDS34031.1	0.02	1.26723	GTGxAAA	COVERED																																																																																			NOVEL	EIF4E-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363739.1	18	8.383623	KEEP	2	2	42	43	1270	GG	1	0.987943	0		-	5	47	131	0	0	8.350693	47	60	1581	176	ENST00000450253.2	0.096154	0.987943
DAPP1	27071	__UNKNOWN__	__UNKNOWN__	4	100784142	100784142	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:100784142T>G	ENST00000512369.1	+	6	605				DAPP1_ENST00000296414.7_Intron	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	NA		NA			protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		gtctgtgtgtttgtgtgtgtg	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													46	45	46			NA	NA	4		NA											NA				100784142		1836	4089	5925	SO:0001627	intron_variant			AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190	27071		Pleckstrin homology (PH) domain containing, SH2 domain containing	16500	protein-coding gene	gene with protein product		605768			NA	10432293	Standard		NM_014395	NA	Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.538-25T>G	chr4.hg19:g.100784142T>G		NA	Q8TCK5|Q9UHF2	hg19	CCDS47112.1	0.02	1.581739	TGTxTGT	COVERED																																																																																			NOVEL	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363215.1	26	10.71494	KEEP	0	3	89	67	1762	TT	1	0.999895	0		+	10	60	334	2	0	24.542084	80	60	2358	239	ENST00000512369.1	0.111111	0.999895
LAMTOR3	8649	__UNKNOWN__	__UNKNOWN__	4	100802162	100802162	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:100802162G>A	ENST00000499666.2	-	0	1556					NM_001243736.1|NM_021970.3	NP_001230665.1|NP_068805.1	Q9UHA4	LTOR3_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 3	NA		NA			cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Ragulator complex (GO:0071986)				endometrium(1)|large_intestine(1)|lung(1)	3						cccaggctggggtgcagtggc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF201947	CCDS3652.1, CCDS58920.1	4q24-q26	2012-02-28	2011-02-15	2011-02-15	ENSG00000109270	ENSG00000109270	8649			15606	protein-coding gene	gene with protein product	MEK partner 1	603296	mitogen-activated protein kinase kinase 1 interacting protein 1, MAPK scaffold protein 1	MAP2K1IP1, MAPKSP1	NA	9733512, 15016825	Standard	NM_021970	NM_021970	NA	Approved	MP1, MAPBP, Ragulator3	uc003hvg.2	Q9UHA4	OTTHUMG00000131050	ENST00000499666.2:c.*989C>T	chr4.hg19:g.100802162G>A		NA	B2R4A1|J3KMX4|Q9H364	hg19	CCDS3652.1	0.02	-0.210532	TGGxGTG	COVERED																																																																																			NOVEL	LAMTOR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253698.2	4	3.342952	KEEP	2	1	28	21	638	GG	0.999863	0.522089	0		-	3	60	94	0	0	6.965125	20	60	679	60	ENST00000499666.2	0.130435	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	103420878	103420878	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:103420878A>C			NA	NA				RP11-499E18.1 (68472 upstream) : AF213884.2 (1119 downstream)						NA		NA									NA						TTCTcagagtatcgctctgtc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.103420878A>C		NA		hg19		0.02	-0.122755	AGTxTCG	COVERED																																																																																			NOVEL					0			9	3.905909	KEEP	0	0	0	13	334	AA	0.995343	0.228106	0			3	60	97	1	0	7.973477	11	60	317	39		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	104166213	104166213	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:104166213T>C			NA	NA				CENPE (46647 upstream) : RP11-328K4.1 (131946 downstream)						NA		NA									NA						acctcagccttccaaagtgct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.104166213T>C		NA		hg19		0.02	-0.114027	CCTxCCA	UNCOVERED																																																																																			NOVEL					0			6	2.405934	KEEP	6	0	0	8	220	TT	0	0	0			3	60	98	0	0	8.432448	8	60	244	37		0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	109348733	109348733	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:109348733G>A			NA	NA				LEF1-AS1 (170741 upstream) : RPL34-AS1 (110612 downstream)						NA		NA									NA						gtttcaccatgttagccagga	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.109348733G>A		NA		hg19		0.02	-0.061404	CATxTTA	UNCOVERED																																																																																			NOVEL					0			8	2.707924	KEEP	9	0	0	9	271	GG	0	0	0			3	27	92	0	0	9.16933	2	42	64	23		0.6	0.043787
COL25A1	84570	__UNKNOWN__	__UNKNOWN__	4	109791196	109791196	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:109791196T>G	ENST00000399132.1	-	20	1551				COL25A1_ENST00000399127.1_Intron|COL25A1_ENST00000399126.1_Intron	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1	NA		NA								NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		atcacttgagtccaggagttt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517	84570		Collagens	18603	protein-coding gene	gene with protein product		610004			NA	11927537	Standard	NM_032518	NM_001256074	NA	Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.1021-890A>C	chr4.hg19:g.109791196T>G		NA		hg19	CCDS43258.1	0.02	-0.228036	GAGxCCA	COVERED																																																																																			NOVEL	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315938.2	11	2.338384	KEEP	2	1	32	19	524	TT	0.999863	0.641259	0		-	3	60	93	0	0	6.750545	22	60	661	74	ENST00000399132.1	0.12	0.641347
SEC24B-AS1	100533182	__UNKNOWN__	__UNKNOWN__	4	110336881	110336881	__UNKNOWN__	RNA	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:110336881G>C	ENST00000505895.1	-	0	105				SEC24B-AS1_ENST00000510971.1_RNA					SEC24B antisense RNA 1	NA		NA									NA						gacccagctagcttttttttt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC009800		4q25	2012-10-12	2012-08-15		ENSG00000247950	ENSG00000247950	100533182		Long non-coding RNAs	44003	non-coding RNA	RNA, long non-coding		NA	SEC24B antisense RNA 1 (non-protein coding)		NA	21307942	Standard	NR_039978	NR_039978	NA	Approved	1/2-SBSRNA4	uc003hzj.4		OTTHUMG00000161048	ENST00000505895.1:	chr4.hg19:g.110336881G>C		NA		hg19		0.02	-0.052635	CTAxCTT	UNCOVERED																																																																																			NOVEL	SEC24B-AS1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000363575.1	9	3.309875	KEEP	1	0	0	11	339	GG	0.993072	0.036511	0		-	2	28	66	2	0	6.34996	2	60	68	20	ENST00000505895.1	0.5	0.036766
C4orf21	0	__UNKNOWN__	__UNKNOWN__	4	113530489	113530489	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:113530489A>G	ENST00000505019.1	-	8	2844				C4orf21_ENST00000309071.5_Intron	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		NA		NA				integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		gattacaggcatgagccacca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													23	26	25			NA	NA	4		NA											NA				113530489		2197	4297	6494	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000505019.1:c.2718+45T>C	chr4.hg19:g.113530489A>G		NA	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	hg19		0.02	-0.359621	GGCxTGA	COVERED																																																																																			NOVEL	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000256413.1	11	5.179314	KEEP	2	2	59	38	1083	AA	1	0.888875	0		-	4	60	141	0	0	10.505749	33	60	994	136	ENST00000505019.1	0.108108	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	113695432	113695432	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:113695432T>C			NA	NA				Y_RNA (18359 upstream) : ANK2 (43832 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													67	63	64			NA	NA	4		NA											NA				113695432		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.113695432T>C		NA		hg19		0.02	-0.175424	TCCxAGC	COVERED																																																																																			NOVEL					0			5	2.705975	KEEP	0	0	0	9	237	TT	0.99254	0.384517	0			3	60	104	0	0	8.309985	15	60	450	46		0.166667	0.387407
UGT8	7368	__UNKNOWN__	__UNKNOWN__	4	115543870	115543870	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:115543870T>C	ENST00000394511.3	+	0	348				UGT8_ENST00000310836.6_Intron	NM_003360.3	NP_003351	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	NA		NA			axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		tttcatgtgttttttggctgc	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	7368	2.4.1.45	UDP glucuronosyltransferases	12555	protein-coding gene	gene with protein product	2-hydroxyacylsphingosine 1-beta-galactosyltransferase	601291	UDP-galactose ceramide galactosyltransferase	CGT	NA	8661025	Standard	NM_003360	NM_003360	NA	Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000394511.3:c.-167T>C	chr4.hg19:g.115543870T>C		NA	B3KXU7|O00196	hg19	CCDS3705.1	0.02	-0.315703	TGTxTTT	COVERED																																																																																			NOVEL	UGT8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363751.1	4	4.232433	KEEP	1	1	28	24	582	TT	0.999957	0.818429	0		+	3	60	95	0	0	6.488117	32	60	903	71	ENST00000394511.3	0.085714	0.818465
RP11-659O3.1	0	__UNKNOWN__	__UNKNOWN__	4	117116188	117116188	__UNKNOWN__	lincRNA	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:117116188G>C	ENST00000509983.1	-	0	333										NA		NA									NA						cggtggctcaggcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000509983.1:	chr4.hg19:g.117116188G>C		NA		hg19		0.02	-0.026319	TCAxGCC	UNCOVERED																																																																																			NOVEL	RP11-659O3.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000363908.1	9	2.407238	KEEP	1	0	0	8	248	GT	0.992708	0.019836	0		-	2	60	70	0	0	7.953968	0	0	0	19	ENST00000509983.1	1	0.019982
NDST3	9348	__UNKNOWN__	__UNKNOWN__	4	119027971	119027971	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:119027971T>C	ENST00000296499.5	+	3	1472				NDST3_ENST00000433996.2_Intron	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	NA		NA			heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						ATTggctgggtgtggtggctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100	9348		Sulfotransferases, membrane-bound	7682	protein-coding gene	gene with protein product		603950			NA	9915799	Standard	NM_004784	NM_004784	NA	Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.1069+1711T>C	chr4.hg19:g.119027971T>C		NA	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	hg19	CCDS3708.1	0.02	-0.157783	GGGxGTG	COVERED																																																																																			NOVEL	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256517.4	12	4.210454	KEEP	3	0	0	14	384	TT	0.993634	0.320751	0		+	3	60	89	0	0	7.17436	11	60	294	44	ENST00000296499.5	0.214286	0.322807
SEC24D	9871	__UNKNOWN__	__UNKNOWN__	4	119650385	119650385	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:119650385T>C	ENST00000511481.1	-	15	1904				SEC24D_ENST00000429811.2_Intron|SEC24D_ENST00000379735.5_Intron|SEC24D_ENST00000280551.6_Intron|SEC24D_ENST00000505134.1_Intron			O94855	SC24D_HUMAN	SEC24 family member D	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						ggattataggtgtgagccacc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961	9871			10706	protein-coding gene	gene with protein product		607186	SEC24 (S. cerevisiae) related gene family, member D, SEC24 family, member D (S. cerevisiae)		NA	9872452, 10075675	Standard		NM_014822	NA	Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000511481.1:c.1762-580A>G	chr4.hg19:g.119650385T>C		NA	Q8IYI7	hg19		0.02	-0.078942	AGGxGTG	UNCOVERED																																																																																			NOVEL	SEC24D-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000256515.4	4	2.70712	KEEP	0	0	0	9	253	TT	0.99254	0.076759	0		-	3	60	99	0	0	9.033042	5	60	148	27	ENST00000511481.1	0.375	0.077336
MYOZ2	51778	__UNKNOWN__	__UNKNOWN__	4	120086402	120086402	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:120086402T>C	ENST00000307128.5	+	5	773					NM_016599.4	NP_057683.1			myozenin 2	NA		NA								endometrium(1)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						tggtggctcatgcctgtcatc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF249873	CCDS3711.1	4q26-q27	2014-09-17	2002-01-07	2002-01-11	ENSG00000172399	ENSG00000172399	51778			1330	protein-coding gene	gene with protein product		605602	chromosome 4 open reading frame 5	C4orf5	NA	8619474, 9110174	Standard		NM_016599	NA	Approved	CS-1	uc003icp.4	Q9NPC6	OTTHUMG00000132968	ENST00000307128.5:c.560+853T>C	chr4.hg19:g.120086402T>C		NA		hg19	CCDS3711.1	0.02	-0.043859	TCAxGCC	UNCOVERED																																																																																			NOVEL	MYOZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256526.2	8	2.405216	KEEP	2	0	0	8	208	TT	0.99257	0.023895	0		+	2	60	68	0	0	6.550183	2	60	60	18	ENST00000307128.5	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	122979427	122979427	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:122979427C>T			NA	NA				TRPC3 (106518 upstream) : RN7SL335P (29233 downstream)						NA		NA									NA						cgtgagccaccgcgcccggcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.122979427C>T		NA		hg19		0.02	-0.149125	CACxGCG	UNCOVERED																																																																																			NOVEL					0			3	2.403795	KEEP	1	0	0	8	213	CC	0	0	0			3	60	93	0	0	7.572728	11	60	366	38		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	123478932	123478932	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:123478932G>C			NA	NA				IL2 (101052 upstream) : IL21 (54850 downstream)						NA		NA									NA						gccggacgcagtggctcacgc	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.123478932G>C		NA		hg19		0.02	-0.06141	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			2	2.406753	KEEP	0	0	0	8	235	GG	0.99257	0.043461	0			2	60	70	0	0	6.750107	2	60	65	21		0.5	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	125509351	125509351	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:125509351C>T			NA	NA				RP11-93I21.3 (29762 upstream) : ANKRD50 (75855 downstream)						NA		NA									NA						gcactccagcctgggcaacaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.125509351C>T		NA		hg19		0.02	-0.175449	AGCxTGG	COVERED																																																																																			NOVEL					0			11	4.212499	KEEP	0	0	0	14	430	CC	0.995343	0.385603	0			3	60	90	0	0	6.761099	17	60	582	47		0.15	0.387407
ANKRD50	57182	__UNKNOWN__	__UNKNOWN__	4	125626227	125626227	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:125626227T>C	ENST00000504087.1	-	2	1550				ANKRD50_ENST00000515641.1_Intron	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	NA		NA								NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						ccagcctgggtaacagagcaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458	57182		Ankyrin repeat domain containing	29223	protein-coding gene	gene with protein product		NA			NA		Standard	NM_020337	NM_020337	NA	Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.512+4927A>G	chr4.hg19:g.125626227T>C		NA	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	hg19	CCDS34060.1	0.02	-0.096443	GGGxAAC	UNCOVERED																																																																																			NOVEL	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364775.1	6	3.307505	KEEP	1	0	0	11	290	TT	0.993072	0.138863	0		-	3	60	102	0	0	9.334323	5	60	128	35	ENST00000504087.1	0.375	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	128491226	128491226	__UNKNOWN__	IGR	SNP	T	T	A	rs28645236	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:128491226T>A			NA	NA				RP11-125O18.1 (99519 upstream) : INTU (62860 downstream)						NA		NA									NA						gagaatggcgtgaacccggga	0.532		NA											T|||	1866	0.372604	0.3139	0.4409	5008	,	,	NA	13080	0.3175	NA	0.3121	False	NA	,,,	NA	NA	NA	2504	0.5225	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.128491226T>A		NA		hg19		0.02	-0.043852	GCGxGAA	UNCOVERED																																																																																			NOVEL					0			7	2.705809	KEEP	8	0	0	9	236	TT	0	0	0			3	40	91	0	0	9.069683	2	40	56	21		0.6	0.024074
LARP1B	55132	__UNKNOWN__	__UNKNOWN__	4	129062190	129062190	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:129062190T>C	ENST00000326639.6	+	11	1735				LARP1B_ENST00000264584.5_Intron|LARP1B_ENST00000354456.3_Intron|LARP1B_ENST00000441387.1_Intron	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	NA		NA				nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						aggctggtcttgaactcctga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709	55132		La ribonucleoprotein domain containing	24704	protein-coding gene	gene with protein product		NA	La ribonucleoprotein domain family, member 2	LARP2	NA	12045101	Standard	NM_018078	NM_018078	NA	Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.1524+18847T>C	chr4.hg19:g.129062190T>C		NA	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	hg19	CCDS3738.1	0.02	-0.087699	TCTxGAA	UNCOVERED																																																																																			NOVEL	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257173.2	6	2.705651	KEEP	3	0	0	9	235	TT	0.99257	0.09898	0		+	3	60	92	0	0	7.978793	7	60	200	26	ENST00000326639.6	0.3	0.099721
SCLT1	132320	__UNKNOWN__	__UNKNOWN__	4	129959053	129959053	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:129959053T>C	ENST00000281142.5	-	5	794				SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000439369.2_Intron|SCLT1_ENST00000506368.1_3'UTR|SCLT1_ENST00000434680.1_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	NA		NA			cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						aatgggaggctgaggcgggca	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466	132320			26406	protein-coding gene	gene with protein product		611399			NA	15797711	Standard	NM_144643	XM_005262732	NA	Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.290+1142A>G	chr4.hg19:g.129959053T>C		NA	A4QN04|Q0VAH2|Q6P2M4	hg19	CCDS3740.1	0.02	-0.368371	GGCxGAG	COVERED																																																																																			NOVEL	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257176.2	4	4.142548	KEEP	0	1	23	22	616	TT	0.999892	0.899217	0		-	3	60	99	0	0	6.812643	34	60	1020	88	ENST00000281142.5	0.081081	0.899314
SCLT1	132320	__UNKNOWN__	__UNKNOWN__	4	130003463	130003463	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:130003463G>C	ENST00000503401.1	-	2	486	c.31C>G	c.(31-33)Cag>Gag	p.Q11E	SCLT1_ENST00000281142.5_Missense_Mutation_p.Q34E|SCLT1_ENST00000511426.1_Missense_Mutation_p.Q34E|SCLT1_ENST00000503215.1_Missense_Mutation_p.Q11E|SCLT1_ENST00000439369.2_Missense_Mutation_p.Q34E|SCLT1_ENST00000506368.1_Missense_Mutation_p.Q34E|SCLT1_ENST00000434680.1_Missense_Mutation_p.Q34E			Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	34		NA			cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TTACATACCTGTACAGATGAA	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													68	68	68			NA	NA	4		NA											NA				130003463		2202	4297	6499	SO:0001583	missense			AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466	132320			26406	protein-coding gene	gene with protein product		611399			NA	15797711	Standard	NM_144643	XM_005262732	NA	Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000503401.1:c.31C>G	chr4.hg19:g.130003463G>C	ENSP00000425315:p.Gln11Glu	NA	A4QN04|Q0VAH2|Q6P2M4	hg19		0.02	-0.412292	CCTxTAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400325	0.62177	.	.	ENSG00000151466	ENST00000281142;ENST00000434680;ENST00000439369;ENST00000503215;ENST00000506368;ENST00000511426;ENST00000503401	T	0.41758	0.99	5.09	4.23	0.50019	.	0.078347	0.52532	D	0.000068	T	0.35595	0.0937	L	0.32530	0.975	0.34314	D	0.685831	B;D;P;B;B	0.56035	0.356;0.974;0.865;0.356;0.229	B;P;P;B;B	0.46940	0.143;0.51;0.532;0.143;0.143	T	0.49021	-0.8982	9	.	.	.	-8.7698	10.6182	0.45462	0.0:0.0:0.8086:0.1914	.	34;34;34;34;34	Q96NL6-3;Q96NL6-4;D6RBA6;Q96NL6-2;Q96NL6	.;.;.;.;SCLT1_HUMAN	E	34;34;34;11;34;34;11	ENSP00000281142:Q34E	.	Q	-	1	0	SCLT1	130222913	0.952000	0.32445	0.862000	0.33874	0.889000	0.51656	1.548000	0.36201	1.335000	0.45486	0.650000	0.86243	CAG	NOVEL	SCLT1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000364276.1	1	6.618418	KEEP	0	0	0	22	657	GG	0.999879	0.941627	0		-	14	60	473	0	0	41.548508	33	60	1095	97	ENST00000503401.1	0.297872	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	130606945	130606945	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:130606945T>C			NA	NA				RP11-419L4.1 (380768 upstream) : RP11-519M16.1 (38380 downstream)						NA		NA									NA						gtggctcacatctgtaatcct	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.130606945T>C		NA		hg19		0.02	-0.131537	ACAxCTG	COVERED																																																																																			NOVEL					0			5	2.705753	KEEP	0	0	0	9	237	TT	0.99254	0.227464	0			3	60	97	0	0	8.479236	7	60	201	31		0.3	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	132664207	132664207	__UNKNOWN__	IGR	SNP	C	C	T	rs75779011		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:132664207C>T			NA	NA				RN7SL205P (22509 upstream) : SNORA70 (25087 downstream)						NA		NA									NA						ctccccgcccccgctctttcc	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.132664207C>T		NA		hg19		0.02	-0.131576	CCCxCGC	COVERED																																																																																			NOVEL					0			14	4.512382	KEEP	6	0	0	15	442	CC	0.993072	0.227586	0			4	60	114	0	0	9.53073	11	60	374	37		0.266667	0.229173
CTD-2012I17.1	0	__UNKNOWN__	__UNKNOWN__	4	135731962	135731962	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:135731962T>C	ENST00000504882.1	+	0	344										NA		NA									NA						ctgaggcaggtggatcatgag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000504882.1:	chr4.hg19:g.135731962T>C		NA		hg19		0.02	-0.078932	AGGxGGA	UNCOVERED																																																																																			NOVEL	CTD-2012I17.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000364193.1	3	2.405747	KEEP	4	0	0	8	218	TT	0.99257	0.076761	0		+	3	60	90	0	1	7.943523	6	60	176	31	ENST00000504882.1	0.333333	0.077336
RP11-138I17.1	0	__UNKNOWN__	__UNKNOWN__	4	138079565	138079565	__UNKNOWN__	lincRNA	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:138079565A>T	ENST00000505736.1	-	0	63										NA		NA									NA						cctcctgagtagctgggacta	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000505736.1:	chr4.hg19:g.138079565A>T		NA		hg19		0.02	-0.096474	AGTxGCT	UNCOVERED																																																																																			NOVEL	RP11-138I17.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000364263.2	7	2.406482	KEEP	0	0	0	8	227	AA	0.99257	0.119541	0		-	6	60	183	0	0	17.870448	5	60	146	27	ENST00000505736.1	0.545455	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	138674668	138674668	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:138674668G>A			NA	NA				RP13-884E18.4 (18537 upstream) : RP11-793B23.1 (54191 downstream)						NA		NA									NA						taatcccagcgctttgggagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.138674668G>A		NA		hg19		0.02	-0.122796	AGCxCTT	COVERED																																																																																			NOVEL					0			6	2.706834	KEEP	1	0	0	9	253	GT	0.992708	0.19488	0			3	60	87	0	0	7.082039	10	60	316	36		0.230769	0.196312
SLC7A11-AS1	641364	__UNKNOWN__	__UNKNOWN__	4	139031316	139031316	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:139031316A>G	ENST00000510767.1	+	0	1725				LINC00616_ENST00000514600.1_lincRNA|SLC7A11-AS1_ENST00000512786.1_RNA	NR_038380.1				SLC7A11 antisense RNA 1	NA		NA									NA						ccaaagtgctaggattacagg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							4q28.3	2012-10-12	2012-08-15		ENSG00000250033	ENSG00000250033	641364		Long non-coding RNAs	44064	non-coding RNA	RNA, long non-coding		NA	SLC7A11 antisense RNA 1 (non-protein coding)		NA		Standard	NR_038380	NR_038380	NA	Approved		uc003ihi.2		OTTHUMG00000161284	ENST00000510767.1:	chr4.hg19:g.139031316A>G		NA		hg19		0.02	-0.105257	GCTxGGA	UNCOVERED																																																																																			NOVEL	SLC7A11-AS1-001	KNOWN	basic	antisense	NA	processed_transcript	OTTHUMT00000364382.1	7	3.308028	KEEP	0	0	0	11	299	AA	0.993072	0.138863	0		+	3	60	104	0	0	9.178778	7	60	211	30	ENST00000510767.1	0.3	0.139832
ELF2	1998	__UNKNOWN__	__UNKNOWN__	4	140019902	140019902	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:140019902A>G	ENST00000394235.2	-	5	741				ELF2_ENST00000379550.1_Intron|ELF2_ENST00000265495.4_Intron	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)	NA		NA								endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					gattacaggcatgagccaccg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381	1998			3317	protein-coding gene	gene with protein product		NA			NA	8756667	Standard	NM_006874	NM_201999	NA	Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.239-25181T>C	chr4.hg19:g.140019902A>G		NA		hg19	CCDS3744.1	0.02	-0.263091	GGCxTGA	COVERED																																																																																			NOVEL	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257233.2	11	3.910196	KEEP	3	0	0	13	362	AA	0.993072	0.688863	0		-	4	60	133	0	0	10.291445	23	60	651	63	ENST00000394235.2	0.148148	0.693668
ELF2	1998	__UNKNOWN__	__UNKNOWN__	4	140069017	140069017	__UNKNOWN__	Intron	SNP	C	C	T	rs534603437		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:140069017C>T	ENST00000394235.2	-	2	252					NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)	NA		NA								endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					ctcggctcaccgcaacctccg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381	1998			3317	protein-coding gene	gene with protein product		NA			NA	8756667	Standard	NM_006874	NM_201999	NA	Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.251-8366G>A	chr4.hg19:g.140069017C>T		NA		hg19	CCDS3744.1	0.02	-0.21047	CACxGCA	COVERED																																																																																			NOVEL	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257233.2	8	3.008769	KEEP	8	0	0	10	307	CC	0.99254	0.518266	0		-	3	52	89	0	0	6.528126	19	60	589	58	ENST00000394235.2	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	140147161	140147161	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:140147161A>G			NA	NA				Y_RNA (25494 upstream) : RNU6-506P (5018 downstream)						NA		NA									NA						ggtggatcacaaggtcaggag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.140147161A>G		NA		hg19		0.02	-0.166635	CACxAGG	COVERED																																																																																			NOVEL					0			7	4.510379	KEEP	1	0	0	15	401	AA	0.99649	0.386047	0			3	30	97	0	1	7.77912	13	60	384	53		0.1875	0.387407
NAA15	80155	__UNKNOWN__	__UNKNOWN__	4	140312722	140312722	__UNKNOWN__	Intron	SNP	C	C	T	rs560628654		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:140312722C>T	ENST00000515576.1	+	2	63							Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	NA		NA			angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						ctcggctcaccgcaacctcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134	80155		N(alpha)-acetyltransferase subunits	30782	protein-coding gene	gene with protein product		608000	NMDA receptor regulated 1	NARG1	NA	12140756, 11478804, 19660095	Standard	NM_057175	XM_005263236	NA	Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000515576.1:c.-12-2023C>T	chr4.hg19:g.140312722C>T		NA	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	hg19		0.02	-0.210534	CACxGCA	COVERED																																																																																			NOVEL	NAA15-003	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000364343.2	6	3.309306	KEEP	0	0	0	11	330	CC	0.993072	0.518544	0		+	3	60	90	0	0	6.627483	19	60	640	54	ENST00000515576.1	0.136364	0.522161
SETD7	80854	__UNKNOWN__	__UNKNOWN__	4	140472937	140472937	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:140472937A>G	ENST00000406354.1	-	2	111				SETD7_ENST00000274031.3_Intron|SETD7_ENST00000506866.2_Intron|SETD7_ENST00000404104.3_Intron			Q8WTS6	SETD7_HUMAN	SET domain containing (lysine methyltransferase) 7	NA		NA			chromatin modification (GO:0016568)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	8	all_hematologic(180;0.156)					cactttgggaagccaaggtgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051504	CCDS3748.1	4q31.1	2011-07-01			ENSG00000145391	ENSG00000145391	80854		Chromatin-modifying enzymes / K-methyltransferases	30412	protein-coding gene	gene with protein product		606594			NA	11850410, 11779497	Standard	NM_030648	NM_030648	NA	Approved	KIAA1717, SET7, SET7/9, Set9, KMT7	uc003ihw.3	Q8WTS6	OTTHUMG00000133385	ENST00000406354.1:c.113-3664T>C	chr4.hg19:g.140472937A>G		NA	B5WWL3|Q0VAH3|Q4W5A9|Q9C0E6	hg19		0.02	-0.157896	GGAxGCC	COVERED																																																																																			NOVEL	SETD7-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000318414.1	6	3.609609	KEEP	0	0	0	12	341	AA	0.993634	0.320751	0		-	3	60	99	0	1	7.978715	13	60	411	47	ENST00000406354.1	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	141162253	141162253	__UNKNOWN__	IGR	SNP	C	C	T	rs547415007		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:141162253C>T			NA	NA				MAML3 (86915 upstream) : SCOC (16186 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.141162253C>T		NA		hg19		0.02	-0.122785	AGGxGTG	COVERED																																																																																			NOVEL					0			2	2.707277	KEEP	0	0	0	9	262	CC	0.99254	0.194847	0			3	60	81	0	0	6.48221	10	60	327	33		0.230769	0.196312
RNF150	57484	__UNKNOWN__	__UNKNOWN__	4	142098124	142098124	__UNKNOWN__	Intron	SNP	T	T	C	rs557356537	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:142098124T>C	ENST00000420921.2	-	1	84							Q9ULK6	RN150_HUMAN	ring finger protein 150	NA		NA				integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					aatcccagcattttgggaggc	0.433		NA											C|||	10	0.00199681	0.0076	0.0	5008	,	,	NA	15761	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153	57484		RING-type (C3HC4) zinc fingers	23138	protein-coding gene	gene with protein product		NA			NA	10574462	Standard	XM_291090	XM_005263150	NA	Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000420921.2:c.4+35823A>G	chr4.hg19:g.142098124T>C		NA	Q3T1D0|Q6ZNW6	hg19		0.02	-0.149052	GCAxTTT	COVERED																																																																																			NOVEL	RNF150-004	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000364742.1	3	2.705607	KEEP	1	0	0	9	235	TT	0.99254	0.289823	0		-	3	60	94	0	0	7.392805	14	60	399	38	ENST00000420921.2	0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	142684183	142684183	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:142684183T>C			NA	NA				IL15 (29043 upstream) : INPP4B (260129 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.142684183T>C		NA		hg19		0.02	-0.228058	TCCxAGC	COVERED																																																																																			NOVEL					0			11	3.308191	KEEP	1	0	0	11	303	TT	0.993072	0.578892	0			3	60	103	0	0	7.805355	21	60	641	48		0.125	0.58293
GAB1	2549	__UNKNOWN__	__UNKNOWN__	4	144344592	144344592	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:144344592A>T	ENST00000262995.4	+	2	794				GAB1_ENST00000262994.4_Intron|GAB1_ENST00000505913.1_Intron	NM_207123.2	NP_997006.1	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	NA		NA			activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					ggctcacgccagtaatcccag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458	2549		Pleckstrin homology (PH) domain containing	4066	protein-coding gene	gene with protein product		604439			NA	8596638	Standard	NM_002039	NM_207123	NA	Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262995.4:c.367+7668A>T	chr4.hg19:g.144344592A>T		NA	A8K152|Q4W5G2|Q6P1W2	hg19	CCDS3760.1	0.02	-0.078943	GCCxGTA	UNCOVERED																																																																																			NOVEL	GAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364898.3	3	3.007851	KEEP	1	0	0	10	279	AA	0.99254	0.076759	0		+	3	60	97	0	0	8.832939	5	60	151	27	ENST00000262995.4	0.375	0.077336
GAB1	2549	__UNKNOWN__	__UNKNOWN__	4	144394361	144394361	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:144394361T>C	ENST00000262995.4	+	0	6621					NM_207123.2	NP_997006.1	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	NA		NA			activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					CAAAATCATATGTATAAATTT	0.299		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458	2549		Pleckstrin homology (PH) domain containing	4066	protein-coding gene	gene with protein product		604439			NA	8596638	Standard	NM_002039	NM_207123	NA	Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262995.4:c.*4019T>C	chr4.hg19:g.144394361T>C		NA	A8K152|Q4W5G2|Q6P1W2	hg19	CCDS3760.1	0.02	2.040939	ATAxGTA	COVERED																																																																																			NOVEL	GAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364898.3	1	3.909502	KEEP	0	0	0	13	357	TT	0.994391	0.958368	0		+	27	60	868	0	0	84.367528	24	60	720	90	ENST00000262995.4	0.529412	0.963774
SMARCA5	8467	__UNKNOWN__	__UNKNOWN__	4	144442633	144442633	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:144442633T>C	ENST00000283131.3	+	3	766	c.304T>C	c.(304-306)Ttt>Ctt	p.F102L		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	102		NA			ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA-templated transcription, initiation (GO:0006352)|double-strand break repair (GO:0006302)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromatin silencing complex (GO:0005677)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NURF complex (GO:0016589)|RSF complex (GO:0031213)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)		EWSR1/SMARCA5(2)	endometrium(2)|kidney(2)|large_intestine(9)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(180;0.158)					GACAGAACTTTTTGCACATTT	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													59	63	62			NA	NA	4		NA											NA				144442633		2203	4300	6503	SO:0001583	missense			AB010882	CCDS3761.1	4q31.1-q31.2	2011-04-20			ENSG00000153147	ENSG00000153147	8467			11101	protein-coding gene	gene with protein product		603375			NA	9730600	Standard		NM_003601	NA	Approved	hSNF2H, hISWI, ISWI	uc003ijg.3	O60264	OTTHUMG00000161474	ENST00000283131.3:c.304T>C	chr4.hg19:g.144442633T>C	ENSP00000283131:p.Phe102Leu	NA		hg19	CCDS3761.1	0.02	3.973742	CTTxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	35	5.481248	0.96307	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.93906	-3.31	5.37	5.37	0.77165	.	0.117400	0.64402	D	0.000018	D	0.96605	0.8892	M	0.84082	2.675	0.80722	D	1	D	0.76494	0.999	D	0.68192	0.956	D	0.97247	0.9895	10	0.87932	D	0	0.0789	15.6766	0.77332	0.0:0.0:0.0:1.0	.	102	O60264	SMCA5_HUMAN	L	102;45;45	ENSP00000283131:F102L	ENSP00000283131:F102L	F	+	1	0	SMARCA5	144662083	1.000000	0.71417	0.972000	0.41901	0.926000	0.56050	7.917000	0.87498	2.165000	0.68154	0.533000	0.62120	TTT	NOVEL	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365077.3	4	8.41985	KEEP	0	0	0	28	758	TT	0.999997	0.999975	0		+	23	60	753	0	0	62.749409	78	60	2257	192	ENST00000283131.3	0.227723	0.999978
GYPB	2994	__UNKNOWN__	__UNKNOWN__	4	144979487	144979487	__UNKNOWN__	Intron	SNP	C	C	T	rs70953771|rs201017533|rs143485779		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:144979487C>T	ENST00000283126.7	-	2	93				RP11-673E1.4_ENST00000506982.1_RNA			P06028	GLPB_HUMAN	glycophorin B (MNS blood group)	NA		NA				integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					ttccttccttccttcctttct	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361	2994		CD molecules, Blood group antigens	4703	protein-coding gene	gene with protein product		111740	glycophorin B (includes Ss blood group), glycophorin B (Ss blood group)	MNS	NA		Standard	NM_002100	NM_002100	NA	Approved	GPB, SS, CD235b		P06028		ENST00000283126.7:c.38-57051G>A	chr4.hg19:g.144979487C>T		NA	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	hg19		0.02	-0.035086	CTTxCTT	UNCOVERED																																																																																			NOVEL	GYPB-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		5	3.009068	KEEP	2	0	0	10	310	CC	0.99257	0.019833	0		-	2	60	60	0	0	6.953373	0	0	0	22	ENST00000283126.7	1	0.019982
SMAD1	4086	__UNKNOWN__	__UNKNOWN__	4	146416896	146416896	__UNKNOWN__	Intron	SNP	C	C	T	rs558029014	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:146416896C>T	ENST00000515385.1	+	1	366				SMAD1_ENST00000515527.1_Intron|SMAD1_ENST00000394092.2_Intron|SMAD1_ENST00000302085.4_Intron			Q15797	SMAD1_HUMAN	SMAD family member 1	NA		NA			BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cardiac muscle cell proliferation (GO:0060038)|cartilage development (GO:0051216)|cellular response to BMP stimulus (GO:0071773)|embryonic pattern specification (GO:0009880)|gamete generation (GO:0007276)|hindbrain development (GO:0030902)|homeostatic process (GO:0042592)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|mesodermal cell fate commitment (GO:0001710)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|osteoblast fate commitment (GO:0002051)|positive regulation of cartilage development (GO:0061036)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of gene expression (GO:0010628)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|primary miRNA processing (GO:0031053)|protein phosphorylation (GO:0006468)|response to drug (GO:0042493)|response to organonitrogen compound (GO:0010243)|signal transduction (GO:0007165)|SMAD protein complex assembly (GO:0007183)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrion (GO:0005739)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	17	all_hematologic(180;0.151)					gcctcccaagcagctgggact	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(182;1287 2092 10326 35158 50562)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U59423	CCDS3765.1	4q31.21	2013-10-22	2006-11-06	2004-05-26	ENSG00000170365	ENSG00000170365	4086		SMADs	6767	protein-coding gene	gene with protein product		601595	MAD, mothers against decapentaplegic homolog 1 (Drosophila), SMAD, mothers against DPP homolog 1 (Drosophila)	MADH1	NA	8653785, 8673135	Standard	NM_005900	NM_005900	NA	Approved	MADR1, JV4-1	uc003ikc.3	Q15797	OTTHUMG00000161592	ENST00000515385.1:c.-177+12568C>T	chr4.hg19:g.146416896C>T		NA	A8KAJ0|D3DNZ9|Q16636|Q9UFT8	hg19	CCDS3765.1	0.02	-0.131517	AAGxAGC	COVERED																																																																																			NOVEL	SMAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365467.1	2	2.406271	KEEP	0	0	0	8	228	CC	0.99257	0.22747	0		+	3	60	87	0	0	6.873071	12	60	379	32	ENST00000515385.1	0.2	0.229173
NR3C2	4306	__UNKNOWN__	__UNKNOWN__	4	149007613	149007613	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:149007613C>T	ENST00000358102.3	-	9	3162				NR3C2_ENST00000512865.1_Intron|NR3C2_ENST00000511528.1_Intron|NR3C2_ENST00000344721.4_Intron|NR3C2_ENST00000355292.3_Intron	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	NA		NA			gene expression (GO:0010467)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|receptor complex (GO:0043235)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.0614)	Drospirenone(DB01395)|Eplerenone(DB00700)|Felodipine(DB01023)|Fludrocortisone(DB00687)|Fluticasone Propionate(DB00588)|Nimodipine(DB00393)|Progesterone(DB00396)|Spironolactone(DB00421)	tagctgggcgcggtggctcac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(27;428 957 40335 51025 51111)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M16801	CCDS3772.1, CCDS54811.1	4q31	2013-01-16			ENSG00000151623	ENSG00000151623	4306		Nuclear hormone receptors	7979	protein-coding gene	gene with protein product		600983		MLR	NA	2558856	Standard		NM_000901	NA	Approved	MR	uc003ilj.4	P08235	OTTHUMG00000161455	ENST00000358102.3:c.2800-4963G>A	chr4.hg19:g.149007613C>T		NA	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	hg19	CCDS3772.1	0.02	-0.157895	GCGxGGT	COVERED																																																																																			NOVEL	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364986.1	9	2.707172	KEEP	1	0	0	9	256	CC	0.99257	0.320408	0		-	3	60	87	0	0	6.692168	14	60	468	37	ENST00000358102.3	0.176471	0.322807
DCLK2	166614	__UNKNOWN__	__UNKNOWN__	4	151092404	151092404	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:151092404G>A	ENST00000302176.8	+	3	756				DCLK2_ENST00000506325.1_Intron|DCLK2_ENST00000296550.7_Intron	NM_001040261.4	NP_001035351.4	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	NA		NA			intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					aggccgaggcgggtgaatcat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(195;186 2215 13375 16801 37459)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390	166614			19002	protein-coding gene	gene with protein product		613166	doublecortin and CaM kinase-like 2	DCAMKL2	NA	12477932	Standard	NM_001040260	NM_001040260	NA	Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000302176.8:c.757-21886G>A	chr4.hg19:g.151092404G>A		NA	C9J5Q9|Q59GC8|Q8N399	hg19	CCDS47142.2	0.02	-0.192986	GGCxGGT	COVERED																																																																																			NOVEL	DCLK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364954.1	12	2.708158	KEEP	4	0	0	9	279	GG	0.99257	0.454356	0		+	3	60	89	0	0	6.733702	16	60	527	51	ENST00000302176.8	0.157895	0.457757
LRBA	987	__UNKNOWN__	__UNKNOWN__	4	151798144	151798144	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:151798144G>A	ENST00000510413.1	-	18	2450				LRBA_ENST00000535741.1_Intron|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000357115.3_Intron	NM_001199282.2	NP_001186211.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	NA		NA				cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					agtggctcacgcctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589	987		WD repeat domain containing	1742	protein-coding gene	gene with protein product		606453		CDC4L	NA	1505956, 11254716	Standard		NM_006726	NA	Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000510413.1:c.2166-4237C>T	chr4.hg19:g.151798144G>A		NA	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	hg19	CCDS58928.1	0.02	-0.122802	CACxCCT	COVERED																																																																																			NOVEL	LRBA-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364938.1	6	4.512092	KEEP	4	0	0	15	433	GG	0.994391	0.19521	0		-	3	60	89	0	0	7.172896	11	60	361	47	ENST00000510413.1	0.214286	0.196312
LRBA	987	__UNKNOWN__	__UNKNOWN__	4	151798180	151798180	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:151798180A>T	ENST00000510413.1	-	18	2450				LRBA_ENST00000535741.1_Intron|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000357115.3_Intron	NM_001199282.2	NP_001186211.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	NA		NA				cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(20)|lung(32)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	91	all_hematologic(180;0.151)					ccgaggcaggaggatcacgag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF216648	CCDS3773.1, CCDS58928.1	4q13	2013-01-10		2001-10-05	ENSG00000198589	ENSG00000198589	987		WD repeat domain containing	1742	protein-coding gene	gene with protein product		606453		CDC4L	NA	1505956, 11254716	Standard		NM_006726	NA	Approved	BGL, LAB300, LBA	uc010ipj.3	P50851	OTTHUMG00000161443	ENST00000510413.1:c.2166-4273T>A	chr4.hg19:g.151798180A>T		NA	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	hg19	CCDS58928.1	0.02	-0.122767	AGGxGGA	COVERED																																																																																			NOVEL	LRBA-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364938.1	4	2.405959	KEEP	4	0	0	8	220	AC	0.99257	0.194853	0		-	3	60	97	0	0	7.973269	11	60	312	38	ENST00000510413.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	151992186	151992186	__UNKNOWN__	IGR	SNP	G	G	A	rs552360591	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:151992186G>A			NA	NA				LRBA (55307 upstream) : RPS3A (28538 downstream)						NA		NA									NA						tagtagagacggggtttctcc	0.517		NA											G|||	7	0.00139776	0.0	0.0	5008	,	,	NA	14522	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0061	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.151992186G>A		NA		hg19		0.02	-0.096463	GACxGGG	UNCOVERED																																																																																			NOVEL					0			7	2.70721	KEEP	5	0	0	9	261	GG	0	0	0			3	60	79	0	0	6.678009	7	60	212	28		0.3	0.120436
SH3D19	152503	__UNKNOWN__	__UNKNOWN__	4	152132383	152132383	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:152132383T>C	ENST00000409252.2	-	1	20				SH3D19_ENST00000409598.4_Intron|SH3D19_ENST00000304527.4_Intron|SH3D19_ENST00000514152.1_Intron|SH3D19_ENST00000455740.1_Intron|SH3D19_ENST00000424281.1_Intron|SH3D19_ENST00000604030.1_Intron			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	NA		NA			cytoskeleton organization (GO:0007010)|membrane organization (GO:0061024)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of cell morphogenesis (GO:0022604)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(1)|skin(3)|urinary_tract(1)	20	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.138)				gattgtgccattgcactccag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX647422	CCDS34077.2, CCDS47143.1, CCDS47144.1	4q31.3	2009-03-05	2009-03-05	2009-03-05	ENSG00000109686	ENSG00000109686	152503			30418	protein-coding gene	gene with protein product	EEN binding protein	608674			NA	12477932	Standard	NM_001009555	NM_001009555	NA	Approved	DKFZp434D0215, EVE1, EBP, Kryn, SH3P19	uc010ipl.1	Q5HYK7	OTTHUMG00000154051	ENST00000409252.2:c.687+14815A>G	chr4.hg19:g.152132383T>C		NA	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	hg19	CCDS34077.2	0.02	-0.219256	CCAxTGC	UNCOVERED																																																																																			NOVEL	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335132.3	16	3.306659	KEEP	7	0	0	11	281	TT	0	0	0		-	4	52	141	0	0	11.479287	18	60	533	51	ENST00000409252.2	0.181818	0.552887
RP11-73G16.3	0	__UNKNOWN__	__UNKNOWN__	4	152843378	152843378	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:152843378A>G	ENST00000510416.1	-	0	107				RP11-73G16.2_ENST00000507949.1_lincRNA						NA		NA									NA						tccagcctggaccacagagca	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000510416.1:	chr4.hg19:g.152843378A>G		NA		hg19		0.02	-0.105256	TGGxCCA	UNCOVERED																																																																																			NOVEL	RP11-73G16.3-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000365888.1	6	2.405986	KEEP	0	0	0	8	222	AA	0.99257	0.138793	0		-	3	60	100	0	0	8.943718	6	60	180	28	ENST00000510416.1	0.333333	0.139832
FHDC1	85462	__UNKNOWN__	__UNKNOWN__	4	153870325	153870325	__UNKNOWN__	Intron	SNP	C	C	A	rs200900852		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:153870325C>A	ENST00000511601.1	+	3	686				FHDC1_ENST00000260008.3_Intron			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	NA		NA							ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					gaagaagaagcagaagaagaa	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460	85462			29363	protein-coding gene	gene with protein product		NA			NA	15138637	Standard	NM_033393	NM_033393	NA	Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.499-4326C>A	chr4.hg19:g.153870325C>A		NA		hg19	CCDS34081.1	0.02	3.014519	AAGxAGA	COVERED																																																																																			NOVEL	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364981.2	45	18.474563	KEEP	2	6	151	115	3435	CC	1	1	0		+	5	60	161	0	0	9.414076	118	60	3973	382	ENST00000511601.1	0.04065	1
FHDC1	85462	__UNKNOWN__	__UNKNOWN__	4	153884135	153884135	__UNKNOWN__	Intron	SNP	A	A	G	rs74812681|rs58275172	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:153884135A>G	ENST00000511601.1	+	8	1109				FHDC1_ENST00000260008.3_Intron			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	NA		NA							ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					gtgtgtgtgtatgtATACATA	0.363		NA											A|||	1047	0.209065	0.2912	0.2017	5008	,	,	NA	16718	0.2004	NA	0.1889	False	NA	,,,	NA	NA	NA	2504	0.1329	NA	NA	NA								NA				0													50	53	52			NA	NA	4		NA											NA				153884135		2203	4300	6503	SO:0001627	intron_variant			AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460	85462			29363	protein-coding gene	gene with protein product		NA			NA	15138637	Standard	NM_033393	NM_033393	NA	Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.922-40A>G	chr4.hg19:g.153884135A>G		NA		hg19	CCDS34081.1	0.02	3.761627	TGTxTGT	COVERED																																																																																			NOVEL	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364981.2	34	6.076665	KEEP	0	3	90	52	1366	AA	1	0.999997	0		+	6	60	211	2	0	13.835688	105	60	2913	250	ENST00000511601.1	0.054054	0.999997
KIAA0922	23240	__UNKNOWN__	__UNKNOWN__	4	154483293	154483293	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:154483293A>G	ENST00000409959.3	+	7	709				KIAA0922_ENST00000409663.3_Intron|KIAA0922_ENST00000440693.1_Intron	NM_001131007.1	NP_001124479.1	A2VDJ0	T131L_HUMAN	KIAA0922	NA		NA				integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				gggttcaagcaattctgctgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210	23240			29146	protein-coding gene	gene with protein product		NA			NA	10231032, 11230166	Standard	NM_015196	NM_015196	NA	Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409959.3:c.660+3773A>G	chr4.hg19:g.154483293A>G		NA	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	hg19	CCDS47148.1	0.02	-0.087712	AGCxATT	UNCOVERED																																																																																			NOVEL	KIAA0922-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000330369.1	5	2.7063	KEEP	1	0	0	9	240	AA	0.99257	0.09898	0		+	3	23	99	0	0	8.843736	6	60	178	23	ENST00000409959.3	0.333333	0.099721
CTSO	1519	__UNKNOWN__	__UNKNOWN__	4	156858998	156858998	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:156858998A>G	ENST00000433477.3	-	5	622					NM_001334.2	NP_001325.1	P43235	CATK_HUMAN	cathepsin O	NA		NA			bone resorption (GO:0045453)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|intramembranous ossification (GO:0001957)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|proteoglycan binding (GO:0043394)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|prostate(1)	16	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.05)|Kidney(143;0.0627)|COAD - Colon adenocarcinoma(41;0.148)		aaactcctggactcaagaaat	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(148;2303 2598 8989 35298)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X77383	CCDS3794.1	4q32.1	2012-10-03			ENSG00000256043	ENSG00000256043	1519		Cathepsins	2542	protein-coding gene	gene with protein product		600550		CTSO1	NA	9790772	Standard	NM_001334	NM_001334	NA	Approved		uc003ipg.3	P43234	OTTHUMG00000161942	ENST00000433477.3:c.553-363T>C	chr4.hg19:g.156858998A>G		NA	Q6FHS6	hg19	CCDS3794.1	0.02	-0.227961	TGGxCTC	COVERED																																																																																			NOVEL	CTSO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366469.1	7	2.405477	KEEP	0	0	0	8	219	AA	0.99257	0.607857	0		-	3	57	88	0	0	6.711349	15	60	425	53	ENST00000433477.3	0.166667	0.612407
PDGFC	56034	__UNKNOWN__	__UNKNOWN__	4	157849089	157849089	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:157849089A>G	ENST00000502773.1	-	1	609				PDGFC_ENST00000541126.1_Intron|PDGFC_ENST00000422544.2_Intron	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		aggtttaatcagacttacagt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431	56034			8801	protein-coding gene	gene with protein product		608452			NA	10858496, 10858548	Standard		NM_016205	NA	Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.118+42848T>C	chr4.hg19:g.157849089A>G		NA	B4DU34|B9EGR8|Q4W5M9|Q9UL22	hg19	CCDS3795.1	0.02	-0.140334	ATCxGAC	COVERED																																																																																			NOVEL	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366123.1	2	4.211107	KEEP	0	0	0	14	393	AA	0.995343	0.25975	0		-	3	60	89	0	0	7.072627	12	60	373	40	ENST00000502773.1	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	158741856	158741856	__UNKNOWN__	IGR	SNP	C	C	T	rs540297879	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:158741856C>T			NA	NA				Y_RNA (52591 upstream) : FAM198B (303769 downstream)						NA		NA									NA						cacaaacaaacggaaaaacat	0.363		NA											C|||	5	0.000998403	0.003	0.0	5008	,	,	NA	18372	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.158741856C>T		NA		hg19		0.02	-0.175432	AAAxGGA	COVERED																																																																																			NOVEL					0			5	3.308157	KEEP	0	0	0	11	304	CC	0.993072	0.384723	0			3	60	91	0	0	6.933625	16	60	513	45		0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	160052552	160052552	__UNKNOWN__	IGR	SNP	G	G	A	rs549096673		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:160052552G>A			NA	NA				MIR3688-2 (2506 upstream) : RAPGEF2 (96853 downstream)						NA		NA									NA						atgagccaccgcgcccagccT	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.160052552G>A		NA		hg19		0.02	-0.210463	ACCxCGC	COVERED																																																																																			NOVEL					0			5	3.008904	KEEP	0	0	0	10	305	GG	0.992708	0.518353	0			5	60	138	0	0	11.066522	17	60	549	48		0.227273	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	160124013	160124013	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:160124013T>C			NA	NA				MIR3688-2 (73967 upstream) : RAPGEF2 (25392 downstream)						NA		NA									NA						ctctgcctcctaaagtgctgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.160124013T>C		NA		hg19		0.02	-0.114016	TCCxAAA	UNCOVERED																																																																																			NOVEL					0			7	2.406108	KEEP	2	0	0	8	222	TT	0.99257	0.16126	0			3	60	103	0	0	9.079003	7	60	207	34		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	164281812	164281812	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:164281812A>G			NA	NA				NPY5R (8726 upstream) : TKTL2 (110444 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.164281812A>G		NA		hg19		0.02	-0.175423	CTGxGAT	COVERED																																																																																			NOVEL					0			5	3.308317	KEEP	0	0	0	11	303	AA	0.993072	0.384723	0			5	60	178	0	0	15.430727	14	60	425	50		0.263158	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	165780146	165780146	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:165780146T>C			NA	NA				RP11-294O2.2 (55199 upstream) : RP11-366M4.3 (18009 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.165780146T>C		NA		hg19		0.02	-0.192972	TCAxGCC	COVERED																																																																																			NOVEL					0			12	3.609531	KEEP	2	0	0	12	338	TT	0.993072	0.454585	0			3	60	97	0	0	7.392243	18	60	553	50		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	166495675	166495675	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:166495675A>G			NA	NA				CPE (76203 upstream) : RP11-340B18.1 (110115 downstream)						NA		NA									NA						aggccgaggcaggcggatcac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.166495675A>G		NA		hg19		0.02	-0.11402	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			4	3.307653	KEEP	0	0	0	11	294	AA	0.993072	0.161341	0			3	60	94	0	0	8.533009	5	60	146	33		0.375	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	166581465	166581465	__UNKNOWN__	IGR	SNP	C	C	T	rs564622000		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:166581465C>T			NA	NA				CPE (161993 upstream) : RP11-340B18.1 (24325 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.468		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15918	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.166581465C>T		NA		hg19		0.02	-0.16662	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			13	3.280654	KEEP	8	0	0	11	303	CC	0	0	0			3	40	89	0	0	6.979458	13	60	398	46		0.1875	0.387407
DDX60L	91351	__UNKNOWN__	__UNKNOWN__	4	169380925	169380925	__UNKNOWN__	Intron	SNP	G	G	A	rs13353681|rs58331415|rs70961524|rs571949779		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:169380925G>A	ENST00000511577.1	-	6	854				DDX60L_ENST00000505890.1_Intron|DDX60L_ENST00000260184.7_Intron			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	NA		NA					ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		gaaggaaggagggaaggaagg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381	91351			26429	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001012967	XM_005263341	NA	Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.607-1766C>T	chr4.hg19:g.169380925G>A		NA	Q96ND6	hg19		0.02	-0.114011	GGAxGGA	UNCOVERED																																																																																			NOVEL	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000364839.1	8	2.400848	KEEP	2	0	0	8	219	GG	0.99257	0.16126	0		-	4	60	116	0	2	10.37701	7	60	221	25	ENST00000511577.1	0.363636	0.162467
PALLD	23022	__UNKNOWN__	__UNKNOWN__	4	169547828	169547828	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:169547828T>C	ENST00000505667.1	+	3	1081				PALLD_ENST00000333488.4_Intron|PALLD_ENST00000335742.7_Intron|PALLD_ENST00000261509.6_Intron			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	NA		NA			cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		tgccactgcattccagcctgg	0.463		NA							Pancreatic Cancer, Familial Clustering of												NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(109;1482 1532 18347 40239 51172)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116	23022		Immunoglobulin superfamily / I-set domain containing	17068	protein-coding gene	gene with protein product		608092			NA	10231032, 10931874	Standard	NM_016081	NM_001166108	NA	Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.909-41513T>C	chr4.hg19:g.169547828T>C		NA	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	hg19	CCDS54818.1	0.02	-0.052477	GCAxTCC	UNCOVERED																																																																																			NOVEL	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363762.1	5	2.704218	KEEP	0	0	0	9	223	TT	0.99254	0.036491	0		+	2	60	68	0	0	6.557573	2	60	44	19	ENST00000505667.1	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	169975347	169975347	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:169975347A>G			NA	NA				RP11-483A20.3 (43257 upstream) : SH3RF1 (40059 downstream)						NA		NA									NA						ggctggtctcaaactcctgac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.169975347A>G		NA		hg19		0.02	-0.122779	CTCxAAC	UNCOVERED																																																																																			NOVEL					0			7	2.706814	KEEP	12	0	0	9	247	AA	0	0	0			3	40	89	2	0	7.282282	10	60	297	51		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	170013026	170013026	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:170013026A>G			NA	NA				RP11-483A20.3 (80936 upstream) : SH3RF1 (2380 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.170013026A>G		NA		hg19		0.02	-0.192941	GGCxTGA	COVERED																																																																																			NOVEL					0			8	2.406085	KEEP	1	0	0	8	220	AT	0.99254	0.454342	0			3	60	96	0	0	7.361181	17	60	492	43		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	170219203	170219203	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:170219203T>C			NA	NA				SH3RF1 (26947 upstream) : NEK1 (95222 downstream)						NA		NA									NA						tgcagtgagctgagatcgcgc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.170219203T>C		NA		hg19		0.02	-0.122799	AGCxGAG	COVERED																																																																																			NOVEL					0			11	3.91003	KEEP	9	0	0	13	361	TT	0.99257	0.194853	0			3	33	97	0	0	8.081939	10	60	307	41		0.230769	0.196312
NEK1	4750	__UNKNOWN__	__UNKNOWN__	4	170416645	170416645	__UNKNOWN__	Intron	SNP	G	G	A	rs7435147	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:170416645G>A	ENST00000507142.1	-	23	2587				NEK1_ENST00000510533.1_Intron|NEK1_ENST00000439128.2_Intron|NEK1_ENST00000512193.1_Intron|NEK1_ENST00000511633.1_Intron	NM_001199397.1	NP_001186326.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		cgcccgtctcggcctcccaaa	0.478		NA											-|||	672	0.134185	0.1823	0.098	5008	,	,	NA	16425	0.1825	NA	0.0994	False	NA	,,,	NA	NA	NA	2504	0.0808	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601	4750			7744	protein-coding gene	gene with protein product		604588	NIMA (never in mitosis gene a)-related kinase 1		NA	1382974, 8274451	Standard		NM_012224	NA	Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000507142.1:c.2007+11542C>T	chr4.hg19:g.170416645G>A		NA	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	hg19	CCDS56351.1	0.02	-0.149108	CTCxGCC	UNCOVERED																																																																																			NOVEL	NEK1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363174.1	6	3.30955	KEEP	8	0	0	11	338	GG	0	0	0		-	7	60	211	0	0	19.676826	9	60	286	46	ENST00000507142.1	0.4375	0.292001
NEK1	4750	__UNKNOWN__	__UNKNOWN__	4	170489831	170489831	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:170489831T>C	ENST00000507142.1	-	13	1600				NEK1_ENST00000510533.1_Intron|NEK1_ENST00000439128.2_Intron|NEK1_ENST00000512193.1_Intron|NEK1_ENST00000511633.1_Intron	NM_001199397.1	NP_001186326.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		tggctcacgcttgtaatccta	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601	4750			7744	protein-coding gene	gene with protein product		604588	NIMA (never in mitosis gene a)-related kinase 1		NA	1382974, 8274451	Standard		NM_012224	NA	Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000507142.1:c.1021-6484A>G	chr4.hg19:g.170489831T>C		NA	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	hg19	CCDS56351.1	0.02	-0.061403	CGCxTGT	UNCOVERED																																																																																			NOVEL	NEK1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000363174.1	4	2.405325	KEEP	0	0	0	8	213	TT	0.99257	0.043461	0		-	3	60	108	0	0	10.155553	4	60	120	23	ENST00000507142.1	0.428571	0.043787
GALNTL6	442117	__UNKNOWN__	__UNKNOWN__	4	173103160	173103160	__UNKNOWN__	Intron	SNP	G	G	A	rs11722427	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:173103160G>A	ENST00000506823.1	+	3	795				GALNTL6_ENST00000508122.1_Intron	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	NA		NA			protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						gagccaccgcgcccggccttc	0.493		NA											G|||	2467	0.492612	0.1059	0.4654	5008	,	,	NA	15809	0.8165	NA	0.5318	False	NA	,,,	NA	NA	NA	2504	0.6605	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473	442117		Glycosyltransferase family 2 domain containing	33844	protein-coding gene	gene with protein product	polypeptide GalNAc transferase-like 6	615138	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6		NA		Standard	NM_001034845	NM_001034845	NA	Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.139-47647G>A	chr4.hg19:g.173103160G>A		NA	Q2L4S6	hg19	CCDS34104.1	0.02	-0.122806	CGCxCCC	COVERED																																																																																			NOVEL	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000362395.1	4	2.406359	KEEP	0	0	0	8	231	GG	0.99257	0.194853	0		+	7	60	217	0	0	20.823974	7	60	239	33	ENST00000506823.1	0.5	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	174406951	174406951	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:174406951C>T			NA	NA				RP11-489G11.3 (15759 upstream) : HAND2 (40290 downstream)						NA		NA									NA						tgaaaccccgcctctactaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.174406951C>T		NA		hg19		0.02	-0.122795	CCGxCTC	COVERED																																																																																			NOVEL					0			4	3.008452	KEEP	0	0	0	10	294	CC	0.992708	0.19488	0			3	60	81	1	0	6.482068	10	60	328	28		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	176251364	176251364	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:176251364G>A			NA	NA				RP13-577H12.2 (350832 upstream) : RP11-287F9.2 (16144 downstream)						NA		NA									NA						aaacacaaaagttagctgggc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.176251364G>A		NA		hg19		0.02	-0.13115	AAAxTTA	UNCOVERED																																																																																			NOVEL					0			8	2.407517	KEEP	1	0	0	8	259	GG	0	0	0			3	52	84	1	0	6.577652	12	60	380	33		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	179965074	179965074	__UNKNOWN__	IGR	SNP	G	G	C	rs13139113	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:179965074G>C			NA	NA				SNORD65 (357964 upstream) : RP11-404J23.1 (345213 downstream)						NA		NA									NA						gggtttcactgtgttagccag	0.577		NA											G|||	2817	0.5625	0.7292	0.4251	5008	,	,	NA	11348	0.4722	NA	0.5865	False	NA	,,,	NA	NA	NA	2504	0.5031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.179965074G>C		NA		hg19		0.02	-0.078956	ACTxTGT	UNCOVERED																																																																																			NOVEL					0			7	2.706062	KEEP	13	0	0	9	249	GG	0	0	0			3	40	100	0	0	9.13272	5	60	176	29		0.375	0.077336
LINC00290	728081	__UNKNOWN__	__UNKNOWN__	4	182012659	182012659	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:182012659T>C	ENST00000512487.1	-	0	201					NR_033918.1				long intergenic non-protein coding RNA 290	NA		NA									NA						aatcccagcattttgggaggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF088005		4q34.3	2012-10-12	2011-08-11	2011-08-11	ENSG00000248197	ENSG00000248197	728081		Long non-coding RNAs	38515	non-coding RNA	RNA, long non-coding		NA	non-protein coding RNA 290	NCRNA00290	NA		Standard	NR_033918	NR_033918	NA	Approved		uc003iuz.3		OTTHUMG00000160706	ENST00000512487.1:	chr4.hg19:g.182012659T>C		NA		hg19		0.02	-0.149102	GCAxTTT	COVERED																																																																																			NOVEL	LINC00290-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000361848.1	8	3.608719	KEEP	4	0	0	12	325	TT	0.993072	0.289978	0		-	3	60	94	0	0	7.392278	14	60	428	50	ENST00000512487.1	0.176471	0.292001
AC108142.1	0	__UNKNOWN__	__UNKNOWN__	4	183022345	183022345	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:183022345G>A	ENST00000509012.1	-	0	149										NA		NA									NA						agaagggagggaggaaggaaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000509012.1:	chr4.hg19:g.183022345G>A		NA		hg19		0.02	-0.105249	AGGxAGG	UNCOVERED																																																																																			NOVEL	AC108142.1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000361744.1	9	2.407124	KEEP	5	0	0	8	248	GG	0	0	0		-	4	55	110	2	1	9.776187	7	60	223	28	ENST00000509012.1	0.363636	0.139832
AC108142.1	0	__UNKNOWN__	__UNKNOWN__	4	183022441	183022441	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:183022441G>A	ENST00000509012.1	-	0	149										NA		NA									NA						agaagggagggaggaaggaag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000509012.1:	chr4.hg19:g.183022441G>A		NA		hg19		0.02	-0.149098	AGGxAGG	COVERED																																																																																			NOVEL	AC108142.1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000361744.1	12	4.513064	KEEP	4	0	0	15	451	GG	0.994391	0.290363	0		-	5	60	134	0	0	11.638044	10	60	317	43	ENST00000509012.1	0.333333	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	183974098	183974098	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:183974098C>T			NA	NA				FAM92A1P2 (12826 upstream) : RP11-335L23.4 (22534 downstream)						NA		NA									NA						tcacctgaggccaggagttca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.183974098C>T		NA		hg19		0.02	-0.157892	AGGxCAG	UNCOVERED																																																																																			NOVEL					0			8	2.406825	KEEP	3	0	0	8	238	CC	0	0	0			3	46	85	1	0	6.579245	13	60	453	39		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	184263403	184263403	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:184263403G>A			NA	NA				snoU13 (12849 upstream) : AC093844.1 (42302 downstream)						NA		NA									NA						gagccaccgcgcccgaccCGC	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.184263403G>A		NA		hg19		0.02	-0.254375	CGCxCCC	UNCOVERED																																																																																			NOVEL					0			10	2.406341	KEEP	1	0	0	8	235	GG	0	0	0			3	60	92	0	0	6.64957	22	60	741	58		0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	184432291	184432291	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:184432291C>T			NA	NA				ING2 (42 upstream) : RP11-367N14.3 (5755 downstream)						NA		NA									NA						CAAATATTTCCAACCAGGTAG	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.184432291C>T		NA		hg19		0.02	1.581465	TTCxAAC	COVERED																																																																																			NOVEL					0			2	2.708283	KEEP	0	0	0	9	282	CC	0.99254	0.97682	0			16	60	489	0	0	41.697742	42	60	1423	101		0.275862	0.984161
STOX2	56977	__UNKNOWN__	__UNKNOWN__	4	184930649	184930649	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:184930649A>G	ENST00000308497.4	+	3	2093	c.658A>G	c.(658-660)Aag>Gag	p.K220E	STOX2_ENST00000438269.1_Missense_Mutation_p.K220E	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	220		NA			embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		GAAGTCTGCCAAGGACTGCAA	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													53	57	56			NA	NA	4		NA											NA				184930649		2055	4203	6258	SO:0001583	missense			AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320	56977			25450	protein-coding gene	gene with protein product		NA			NA		Standard	NM_020225	XM_005263142	NA	Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.658A>G	chr4.hg19:g.184930649A>G	ENSP00000311257:p.Lys220Glu	NA	A6H8U4|Q9NPS8	hg19	CCDS47167.1	0.02	5.44693	GCCxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	17.82	3.483758	0.63962	.	.	ENSG00000173320	ENST00000308497;ENST00000438269	T;T	0.79247	-0.25;-1.25	6.08	4.88	0.63580	.	0.094165	0.64402	D	0.000001	T	0.75354	0.3838	L	0.33245	0.995	0.58432	D	0.999999	D	0.59357	0.985	P	0.50314	0.637	T	0.77117	-0.2706	10	0.62326	D	0.03	-25.3231	13.5997	0.62011	0.8705:0.1295:0.0:0.0	.	220	Q9P2F5	STOX2_HUMAN	E	220	ENSP00000311257:K220E;ENSP00000390127:K220E	ENSP00000311257:K220E	K	+	1	0	STOX2	185167643	1.000000	0.71417	0.998000	0.56505	0.569000	0.35902	7.500000	0.81588	1.096000	0.41439	0.533000	0.62120	AAG	NOVEL	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361433.3	6	9.62036	KEEP	0	0	0	32	854	AA	0.999997	0.999997	0		+	52	60	1671	1	0	143.07759	141	60	4091	331	ENST00000308497.4	0.26943	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	184951903	184951903	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:184951903T>C			NA	NA				STOX2 (7224 upstream) : ENPP6 (57955 downstream)						NA		NA									NA						tgtgagccactgcgcccagcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.184951903T>C		NA		hg19		0.02	-0.228028	CACxGCG	COVERED																																																																																			NOVEL					0			8	3.308952	KEEP	3	0	0	11	315	TT	0.992708	0.578679	0			3	60	90	1	0	6.694128	18	60	531	56		0.142857	0.58293
ACSL1	2180	__UNKNOWN__	__UNKNOWN__	4	185730685	185730685	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:185730685A>G	ENST00000515030.1	-	2	294				ACSL1_ENST00000281455.2_Intron|ACSL1_ENST00000504342.1_Intron|ACSL1_ENST00000454703.2_Intron|ACSL1_ENST00000504900.1_Intron|ACSL1_ENST00000507295.1_Intron			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	NA		NA			adiponectin-activated signaling pathway (GO:0033211)|alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|linoleic acid metabolic process (GO:0043651)|lipid biosynthetic process (GO:0008610)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid metabolic process (GO:0033559)|xenobiotic catabolic process (GO:0042178)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|liver(1)|lung(17)|ovary(2)|prostate(1)|skin(2)	38		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Colorectal(36;0.00172)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0315)|all_neural(102;0.107)|Medulloblastoma(177;0.146)		all cancers(43;1.33e-28)|Epithelial(43;5.3e-25)|OV - Ovarian serous cystadenocarcinoma(60;4.88e-11)|Colorectal(24;3.59e-06)|STAD - Stomach adenocarcinoma(60;2.72e-05)|GBM - Glioblastoma multiforme(59;2.83e-05)|BRCA - Breast invasive adenocarcinoma(30;7.66e-05)|COAD - Colon adenocarcinoma(29;0.000538)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.0419)	Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ggtggctcacacctgtaatcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026290	CCDS3839.1, CCDS68825.1, CCDS68826.1, CCDS75213.1	4q35.1	2014-08-08	2004-02-19	2004-02-20	ENSG00000151726	ENSG00000151726	2180	6.2.1.3	Acyl-CoA synthetase family	3569	protein-coding gene	gene with protein product	lignoceroyl-CoA synthase, long-chain fatty-acid-coenzyme A ligase 1	152425	fatty-acid-Coenzyme A ligase, long-chain 2	FACL2	NA	2341402, 1531127	Standard	NM_001995	XM_005262828	NA	Approved	LACS2, LACS, ACS1, LACS1, FACL1	uc003iwu.1	P33121	OTTHUMG00000160547	ENST00000515030.1:c.32-5985T>C	chr4.hg19:g.185730685A>G		NA	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	hg19	CCDS3839.1	0.02	-0.236824	CACxCCT	UNCOVERED																																																																																			NOVEL	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361112.2	6	2.706718	KEEP	6	0	0	9	247	AA	0	0	0		-	5	60	160	0	0	12.953755	20	60	608	58	ENST00000515030.1	0.2	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	185885322	185885322	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:185885322T>C			NA	NA				MIR4455 (25728 upstream) : RP11-386B13.4 (24828 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.185885322T>C		NA		hg19		0.02	-0.236793	GCAxTTT	COVERED																																																																																			NOVEL					0			6	2.406484	KEEP	0	0	0	8	228	TT	0.99257	0.636582	0			3	60	97	0	0	7.150063	22	60	647	59		0.12	0.641347
KIAA1430	0	__UNKNOWN__	__UNKNOWN__	4	186112723	186112723	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:186112723T>C	ENST00000458385.2	-	2	104				KIAA1430_ENST00000514798.1_Intron|KIAA1430_ENST00000296775.6_Intron	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		NA		NA								endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		cggtggctcatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000458385.2:c.16-357A>G	chr4.hg19:g.186112723T>C		NA	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	hg19	CCDS47168.1	0.02	-0.280627	TCAxGCC	COVERED																																																																																			NOVEL	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360717.2	8	4.210902	KEEP	0	0	0	14	390	TT	0.995343	0.736227	0		-	3	49	102	0	0	7.542581	24	60	679	68	ENST00000458385.2	0.111111	0.739671
SORBS2	8470	__UNKNOWN__	__UNKNOWN__	4	186616137	186616137	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:186616137A>G	ENST00000437304.2	-	3	351				SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000431808.1_Intron|SORBS2_ENST00000355634.5_Intron|SORBS2_ENST00000284776.7_Intron|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron	NM_001145673.1	NP_001139145.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	NA		NA			actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		gggattacagatgtgagccac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(153;41 2433 9491 36028)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556	8470			24098	protein-coding gene	gene with protein product	Arg/Abl interacting protein	NA			NA	9211900, 9872452	Standard	NM_003603	NM_021069	NA	Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000437304.2:c.233-16161T>C	chr4.hg19:g.186616137A>G		NA	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	hg19	CCDS47175.1	0.02	-0.201729	CAGxTGT	COVERED																																																																																			NOVEL	SORBS2-009	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347952.2	10	3.008057	KEEP	0	0	0	10	284	AA	0.992708	0.518353	0		-	3	60	99	0	0	7.810197	15	60	444	48	ENST00000437304.2	0.166667	0.522161
FAM149A	25854	__UNKNOWN__	__UNKNOWN__	4	187041884	187041884	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:187041884C>G	ENST00000503432.1	+	1	102				FAM149A_ENST00000356371.5_Intron			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	NA		NA								breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		ggaggtggagcttgcagtgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794	25854			24527	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001006655	NM_015398	NA	Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000503432.1:c.-308+16210C>G	chr4.hg19:g.187041884C>G		NA	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	hg19	CCDS34117.1	0.02	-0.105259	GAGxTTG	UNCOVERED																																																																																			NOVEL	FAM149A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361158.1	6	2.707707	KEEP	3	0	0	9	268	CC	0.99257	0.138793	0		+	3	40	90	0	0	8.132618	5	60	159	33	ENST00000503432.1	0.375	0.139832
FAM149A	25854	__UNKNOWN__	__UNKNOWN__	4	187071853	187071853	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:187071853G>A	ENST00000502970.1	+	3	361				FAM149A_ENST00000227065.4_Intron|FAM149A_ENST00000514829.1_Intron|FAM149A_ENST00000389354.5_Intron|FAM149A_ENST00000514153.1_Intron|FAM149A_ENST00000356371.5_Intron|FAM149A_ENST00000503432.1_Intron			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	NA		NA								breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		gattacaggcgtgagccaccg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794	25854			24527	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001006655	NM_015398	NA	Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000502970.1:c.-57-1204G>A	chr4.hg19:g.187071853G>A		NA	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	hg19	CCDS34117.1	0.02	-0.307013	GGCxTGA	COVERED																																																																																			NOVEL	FAM149A-006	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361206.1	9	3.609491	KEEP	2	0	0	12	343	GG	0.993072	0.794702	0		+	4	60	120	0	0	8.675502	28	60	903	75	ENST00000502970.1	0.125	0.800245
FAM149A	25854	__UNKNOWN__	__UNKNOWN__	4	187087621	187087621	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:187087621A>G	ENST00000502970.1	+	11	1582				FAM149A_ENST00000227065.4_Intron|FAM149A_ENST00000389354.5_Intron|FAM149A_ENST00000514153.1_Intron|FAM149A_ENST00000356371.5_Intron|FAM149A_ENST00000503432.1_Intron			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	NA		NA								breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		tggccaacatagtgaaacctc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794	25854			24527	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001006655	NM_015398	NA	Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000502970.1:c.1165-501A>G	chr4.hg19:g.187087621A>G		NA	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	hg19	CCDS34117.1	0.02	-0.131534	CATxGTG	COVERED																																																																																			NOVEL	FAM149A-006	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361206.1	7	2.40553	KEEP	0	0	0	8	212	AA	0.99257	0.22747	0		+	3	60	93	0	0	7.573436	11	60	315	29	ENST00000502970.1	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	188910681	188910681	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:188910681A>G			NA	NA				RP11-565A3.1 (329158 upstream) : ZFP42 (6243 downstream)						NA		NA									NA						agcactttggaaggccaaggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.188910681A>G		NA		hg19		0.02	-0.175417	TGGxAGG	COVERED																																																																																			NOVEL					0			7	3.547722	KEEP	3	0	0	12	320	AA	0.993072	0.384723	0			3	60	105	0	0	8.491659	14	60	418	51		0.176471	0.387407
ZFP42	132625	__UNKNOWN__	__UNKNOWN__	4	188925721	188925721	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:188925721A>G	ENST00000326866.4	+	0	2168				ZFP42_ENST00000509524.1_3'UTR	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	NA		NA			female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		tgatctgcccacctcggcctc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059	132625		Zinc fingers, C2H2-type	30949	protein-coding gene	gene with protein product		614572	zinc finger protein 42 homolog (mouse), zinc finger protein 42		NA	12110702	Standard	NM_174900	NM_174900	NA	Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.*827A>G	chr4.hg19:g.188925721A>G		NA	D3DP65|Q8WXE2	hg19	CCDS3849.1	0.02	1.651934	CCCxCCT	COVERED																																																																																			NOVEL	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359794.1	19	6.847197	KEEP	1	1	29	33	894	AA	0.999998	0.999557	0		+	4	60	129	0	0	8.009558	72	60	2125	162	ENST00000326866.4	0.052632	0.999559
ZFP42	132625	__UNKNOWN__	__UNKNOWN__	4	188925753	188925753	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:188925753T>C	ENST00000326866.4	+	0	2200				ZFP42_ENST00000509524.1_3'UTR	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	NA		NA			female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		ggattacaggtgtgagccact	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059	132625		Zinc fingers, C2H2-type	30949	protein-coding gene	gene with protein product		614572	zinc finger protein 42 homolog (mouse), zinc finger protein 42		NA	12110702	Standard	NM_174900	NM_174900	NA	Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.*859T>C	chr4.hg19:g.188925753T>C		NA	D3DP65|Q8WXE2	hg19	CCDS3849.1	0.02	3.579266	AGGxGTG	COVERED																																																																																			NOVEL	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359794.1	46	7.338878	KEEP	2	4	127	69	1813	TT	1	1	0		+	5	60	173	0	0	10.472141	126	60	3506	320	ENST00000326866.4	0.038168	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	188974014	188974014	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:188974014T>C			NA	NA				ZFP42 (47810 upstream) : TRIML2 (38412 downstream)						NA		NA									NA						agttcaagactagcctggcca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.188974014T>C		NA		hg19		0.02	-0.105247	GACxAGC	UNCOVERED																																																																																			NOVEL					0			3	3.908823	KEEP	0	0	0	13	349	TT	0.994391	0.139048	0			3	60	110	0	0	9.944122	6	60	169	35		0.333333	0.139832
TRIML2	205860	__UNKNOWN__	__UNKNOWN__	4	189013610	189013610	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189013610A>G	ENST00000512729.1	-	7	970				TRIML2_ENST00000326754.3_Intron	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	NA		NA			protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)			central_nervous_system(2)|kidney(1)|large_intestine(7)|lung(25)|prostate(3)|urinary_tract(1)	39		all_cancers(14;3.11e-44)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|all_hematologic(60;0.0202)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)		OV - Ovarian serous cystadenocarcinoma(60;1.79e-11)|BRCA - Breast invasive adenocarcinoma(30;4.52e-06)|GBM - Glioblastoma multiforme(59;1.62e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.0091)|READ - Rectum adenocarcinoma(43;0.163)		gcaagactccatctcaaaaca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098667	CCDS3850.1	4q35.2	2014-02-12	2007-12-14		ENSG00000179046	ENSG00000179046	205860			26378	protein-coding gene	gene with protein product	SPRY domain containing 6	NA			NA		Standard	NM_173553	NM_173553	NA	Approved	FLJ25801, SPRYD6	uc003izl.2	Q8N7C3	OTTHUMG00000160225	ENST00000512729.1:c.596-515T>C	chr4.hg19:g.189013610A>G		NA	B7Z6J6	hg19	CCDS3850.1	0.02	-0.157607	TCCxTCT	UNCOVERED																																																																																			NOVEL	TRIML2-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359733.1	9	2.707055	KEEP	6	0	0	9	253	AA	0	0	0		-	3	60	97	0	0	7.875566	12	60	329	50	ENST00000512729.1	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	189143348	189143348	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189143348T>C			NA	NA				RP11-366H4.1 (61055 upstream) : LINC01060 (233383 downstream)						NA		NA									NA						gctgagattatagacatgagc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.189143348T>C		NA		hg19		0.02	-0.236813	TTAxAGA	COVERED																																																																																			NOVEL					0			8	3.006973	KEEP	1	0	0	10	269	TT	0.992708	0.607941	0			3	60	98	0	0	7.710263	15	60	446	56		0.166667	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	189292663	189292663	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189292663G>A			NA	NA				RP11-366H4.1 (210370 upstream) : LINC01060 (84068 downstream)						NA		NA									NA						ggctggtctcgaactcctgac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.189292663G>A		NA		hg19		0.02	-0.087719	CTCxAAC	UNCOVERED																																																																																			NOVEL					0			2	2.406313	KEEP	3	0	0	8	230	GG	0	0	0			3	39	91	0	0	8.043267	6	60	197	31		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	189330818	189330818	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189330818G>A			NA	NA				RP11-366H4.1 (248525 upstream) : LINC01060 (45913 downstream)						NA		NA									NA						ttgggaggccgaggcgggtgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.189330818G>A		NA		hg19		0.02	-0.17543	GCCxAGG	COVERED																																																																																			NOVEL					0			8	3.008806	KEEP	0	0	0	10	304	GG	0.992708	0.384582	0			3	60	86	0	0	6.51069	15	60	493	42		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	189334630	189334630	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189334630T>C			NA	NA				RP11-366H4.1 (252337 upstream) : LINC01060 (42101 downstream)						NA		NA									NA						ctcagcctcctaaagtgctgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.189334630T>C		NA		hg19		0.02	-0.201725	TCCxAAA	COVERED																																																																																			NOVEL					0			8	4.209633	KEEP	0	0	0	14	376	TT	0.995343	0.48826	0			3	60	91	0	0	7.092336	14	60	412	58		0.176471	0.490544
LINC01060	401164	__UNKNOWN__	__UNKNOWN__	4	189418113	189418113	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189418113G>A	ENST00000510832.1	+	0	617									long intergenic non-protein coding RNA 1060	NA		NA									NA						gattacaggtgtgagccacca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							4q35.2	2013-08-23			ENSG00000249378	ENSG00000249378	401164		Long non-coding RNAs	49081	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_033869	NA	Approved				OTTHUMG00000160242	ENST00000510832.1:	chr4.hg19:g.189418113G>A		NA		hg19		0.02	-0.298246	GGTxTGA	COVERED																																																																																			NOVEL	LINC01060-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000359857.1	9	3.008575	KEEP	2	0	0	10	295	GG	0.99254	0.775233	0		+	3	60	93	0	0	6.453458	28	60	937	64	ENST00000510832.1	0.096774	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	189462541	189462541	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:189462541T>C			NA	NA				LINC01060 (2835 upstream) : RNU7-192P (175277 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.189462541T>C		NA		hg19		0.02	-0.20172	AGGxGTG	COVERED																																																																																			NOVEL					0			10	3.006277	KEEP	1	0	0	10	273	TT	0.99254	0.486885	0			4	60	129	0	0	10.368995	17	60	499	44		0.190476	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	190155148	190155148	__UNKNOWN__	IGR	SNP	C	C	T	rs112153489		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:190155148C>T			NA	NA				RP11-706F1.1 (29117 upstream) : RP11-706F1.2 (54682 downstream)						NA		NA									NA						ggtgtagttgcagtagtgctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.190155148C>T		NA		hg19		0.02	-0.166639	TTGxAGT	COVERED																																																																																			NOVEL					0			66	8.020945	KEEP	49	3	74	53	1590	CC	0.999997	0.353946	0			5	24	137	0	1	11.612509	12	60	406	131		0.294118	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	190563302	190563302	__UNKNOWN__	IGR	SNP	T	T	C	rs148379728	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:190563302T>C			NA	NA				HSP90AA4P (166958 upstream) : RP11-462G22.1 (17456 downstream)						NA		NA									NA						gggcggatcatgaggtcagga	0.542		NA											T|||	1828	0.365016	0.3298	0.4092	5008	,	,	NA	9250	0.1925	NA	0.5537	False	NA	,,,	NA	NA	NA	2504	0.365	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.190563302T>C		NA		hg19		0.02	-0.096483	TCAxGAG	UNCOVERED																																																																																			NOVEL					0			2	3.007856	KEEP	2	0	0	10	282	TT	0.99254	0.119538	0			3	53	92	0	0	8.143353	6	60	187	33		0.333333	0.120436
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878508	190878508	__UNKNOWN__	Intron	SNP	C	C	T	rs12643924		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:190878508C>T	ENST00000226798.4	+	6	654				FRG1_ENST00000514482.1_Intron	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ATGTTTCTCCCACAAGAAGTA	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													11	13	12			NA	NA	4		NA											NA				190878508		1968	4206	6174	SO:0001627	intron_variant			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.433-45C>T	chr4.hg19:g.190878508C>T		NA	A8K775	hg19	CCDS34121.1	0.02	1.201611	TCCxACA	COVERED																																																																																			NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	5	3.61126	KEEP	5	0	0	12	386	CC	0.993072	0.992909	0		+	5	40	151	0	0	9.26309	79	60	2653	149	ENST00000226798.4	0.059524	0.999835
FRG1	2483	__UNKNOWN__	__UNKNOWN__	4	190878577	190878577	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs200267221		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:190878577A>G	ENST00000226798.4	+	6	679	c.457A>G	c.(457-459)Aat>Gat	p.N153D	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	153		NA			mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GTTGGCCTCAAATAGCTGCTT	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													14	18	17			NA	NA	4		NA											NA				190878577		2154	4261	6415	SO:0001583	missense			L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536	2483			3954	protein-coding gene	gene with protein product		601278			NA	8733123	Standard	NM_004477	XM_005262880	NA	Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.457A>G	chr4.hg19:g.190878577A>G	ENSP00000226798:p.Asn153Asp	NA	A8K775	hg19	CCDS34121.1	0.02	8.711735	TCAxATA	COVERED	.	.	.	.	.	.	.	.	.	.	.	16.34	3.096595	0.56075	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.50548	1.75;0.74	4.19	2.99	0.34606	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.62950	0.2470	M	0.88105	2.93	0.58432	D	0.999994	P	0.35033	0.481	P	0.49085	0.6	T	0.60182	-0.7313	10	0.38643	T	0.18	-7.9248	8.2154	0.31507	0.9006:0.0:0.0994:0.0	.	153	Q14331	FRG1_HUMAN	D	153;25;90	ENSP00000226798:N153D;ENSP00000435943:N90D	ENSP00000226798:N153D	N	+	1	0	FRG1	191115571	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	9.035000	0.93752	0.593000	0.29745	-0.580000	0.04137	AAT	NOVEL	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359622.4	12	8.283749	KEEP	56	2	55	47	1283	AA	1	1	0		+	11	49	353	0	0	21.558679	211	60	6340	449	ENST00000226798.4	0.04955	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	4	190974217	190974217	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr4:190974217A>G			NA	NA				FRG2 (25805 upstream) : U85056.4 (7317 downstream)						NA		NA									NA						ctttgagacgaagtcttgctc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr4.hg19:g.190974217A>G		NA		hg19		0.02	1.792211	ACGxAGT	COVERED																																																																																			NOVEL					0			19	4.674645	KEEP	0	2	61	37	1026	AA	1	0.995687	0			4	60	139	0	0	9.429133	56	60	1670	164		0.066667	0.995687
PDCD6	10016	__UNKNOWN__	__UNKNOWN__	5	292615	292615	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:292615T>C	ENST00000264933.4	+	3	263				PDCD6_ENST00000507528.1_Intron|PDCD6_ENST00000505221.1_Intron	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			ctcaggtgattctcccacctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915	10016		EF-hand domain containing	8765	protein-coding gene	gene with protein product	apoptosis-linked gene-2	601057			NA	8560270	Standard	NM_013232	NM_013232	NA	Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.164-11677T>C	chr5.hg19:g.292615T>C		NA	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	hg19	CCDS3854.1	0.02	-0.280676	GATxCTC	COVERED																																																																																			NOVEL	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206609.2	6	2.406626	KEEP	2	0	0	8	229	TT	0.99257	0.734176	0		+	3	60	101	0	0	7.252648	28	60	845	68	ENST00000264933.4	0.096774	0.739671
AHRR	57491	__UNKNOWN__	__UNKNOWN__	5	339485	339485	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:339485C>G	ENST00000515206.1	+	2	23				AHRR_ENST00000505113.1_Intron|AHRR_ENST00000512529.1_Intron|AHRR_ENST00000316418.5_Intron			A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			attctcccaccttggcctccc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438	57491		Basic helix-loop-helix proteins	346	protein-coding gene	gene with protein product		606517	aryl hydrocarbon receptor regulator	AHH, AHHR	NA	1070014, 11423533	Standard	NM_020731	NM_020731	NA	Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000515206.1:c.-10-4523C>G	chr5.hg19:g.339485C>G		NA	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	hg19		0.02	-0.271952	CACxTTG	COVERED																																																																																			NOVEL	AHRR-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367812.2	14	3.309304	KEEP	6	0	0	11	331	CC	0.993072	0.712346	0		+	3	22	104	0	0	7.691828	25	60	855	64	ENST00000515206.1	0.107143	0.717315
AHRR	57491	__UNKNOWN__	__UNKNOWN__	5	410609	410609	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:410609A>G	ENST00000316418.5	+	5	407				AHRR_ENST00000505113.1_Intron|AHRR_ENST00000512529.1_Intron	NM_020731.4	NP_065782.2	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			ttacaagcataagccaccatg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438	57491		Basic helix-loop-helix proteins	346	protein-coding gene	gene with protein product		606517	aryl hydrocarbon receptor regulator	AHH, AHHR	NA	1070014, 11423533	Standard	NM_020731	NM_020731	NA	Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000316418.5:c.364-2850A>G	chr5.hg19:g.410609A>G		NA	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	hg19	CCDS43297.1	0.02	-0.219249	CATxAGC	COVERED																																																																																			NOVEL	AHRR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367719.2	7	2.705426	KEEP	0	0	0	9	231	AA	0.99254	0.548763	0		+	3	60	95	0	0	7.127577	19	60	546	49	ENST00000316418.5	0.136364	0.552887
BRD9	65980	__UNKNOWN__	__UNKNOWN__	5	876391	876391	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:876391C>G	ENST00000467963.1	-	12	1438				BRD9_ENST00000388890.4_Intron|BRD9_ENST00000323510.4_Intron|BRD9_ENST00000435709.2_Intron|BRD9_ENST00000483173.1_Intron	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	NA		NA			chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			TCGCGGCAGCCCTGATCACAG	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310	65980			25818	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_023924	NM_023924	NA	Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1272-64G>C	chr5.hg19:g.876391C>G		NA	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	hg19	CCDS34127.2	0.02	1.865518	AGCxCTG	COVERED																																																																																			NOVEL	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354113.1	0	2.407055	KEEP	0	0	0	8	248	CC	0.99257	0.989754	0		-	11	60	373	0	0	29.2569	60	60	1950	98	ENST00000467963.1	0.15493	0.997163
BRD9	65980	__UNKNOWN__	__UNKNOWN__	5	878461	878461	__UNKNOWN__	Intron	SNP	G	G	A	rs76072224	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:878461G>A	ENST00000467963.1	-	11	1438				BRD9_ENST00000388890.4_Intron|BRD9_ENST00000323510.4_Intron|BRD9_ENST00000435709.2_Intron|BRD9_ENST00000483173.1_Intron	NM_023924.4	NP_076413.3	Q9H8M2	BRD9_HUMAN	bromodomain containing 9	NA		NA			chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		lysine-acetylated histone binding (GO:0070577)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(3)	29			Epithelial(17;0.00202)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00815)|Lung(60;0.185)			CCCCGGGGCCGACACTTGCCT	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													104	87	93			NA	NA	5		NA											NA				878461		2203	4300	6503	SO:0001627	intron_variant			AK023503	CCDS34127.1, CCDS34128.1, CCDS34127.2, CCDS34128.2	5p15.33	2008-02-05			ENSG00000028310	ENSG00000028310	65980			25818	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_023924	NM_023924	NA	Approved	FLJ13441	uc003jbq.3	Q9H8M2	OTTHUMG00000159258	ENST00000467963.1:c.1271+8C>T	chr5.hg19:g.878461G>A		NA	A6NFY8|B4DMQ2|B4DR93|Q2XUS1|Q6UWU9|Q8IUS4|Q9H5Q5|Q9H7R9	hg19	CCDS34127.2	0.02	6.96316	GCCxACA	COVERED																																																																																			NOVEL	BRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354113.1	8	4.173681	KEEP	4	2	54	33	954	GG	0.999998	0.999998	0		-	12	59	352	0	0	20.181421	232	60	7733	450	ENST00000467963.1	0.04918	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	1126493	1126493	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1126493T>C			NA	NA				SLC12A7 (14343 upstream) : CTD-3080P12.3 (46762 downstream)						NA		NA									NA						cgtgagccactgcacccagcc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.1126493T>C		NA		hg19		0.02	-0.254332	CACxGCA	COVERED																																																																																			NOVEL					0			14	2.406383	KEEP	1	0	0	8	228	TT	0.99257	0.663556	0			4	60	115	0	0	8.492865	23	60	690	52		0.148148	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	1182524	1182524	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1182524G>C			NA	NA				CTD-3080P12.3 (3804 upstream) : SLC6A19 (19185 downstream)						NA		NA									NA						ctcagcccccgaaagtgctgg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.1182524G>C		NA		hg19		0.02	-0.122815	CCCxAAA	UNCOVERED																																																																																			NOVEL					0			3	2.407186	KEEP	1	0	0	8	245	GG	0	0	0			3	60	110	0	0	9.632359	8	60	263	35		0.272727	0.196312
CTD-2245E15.3	0	__UNKNOWN__	__UNKNOWN__	5	1548392	1548392	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1548392A>G	ENST00000503113.1	-	0	375										NA		NA									NA						gattacaggcatgagccaccg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000503113.1:	chr5.hg19:g.1548392A>G		NA		hg19		0.02	-0.385916	GGCxTGA	COVERED																																																																																			NOVEL	CTD-2245E15.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000369485.1	14	3.239322	KEEP	0	1	23	19	516	AA	0.999863	0.918045	0		-	4	60	141	0	0	10.409281	35	60	1037	96	ENST00000503113.1	0.102564	0.918171
CTD-2245E15.3	0	__UNKNOWN__	__UNKNOWN__	5	1548404	1548404	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1548404A>G	ENST00000503113.1	-	0	375										NA		NA									NA						gagccaccgcacccggccAGC	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000503113.1:	chr5.hg19:g.1548404A>G		NA		hg19		0.02	-0.377069	CGCxCCC	COVERED																																																																																			NOVEL	CTD-2245E15.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000369485.1	13	2.736104	KEEP	0	1	28	19	494	AA	0.999863	0.908944	0		-	3	60	108	0	0	7.639889	36	60	1024	91	ENST00000503113.1	0.076923	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	1572294	1572294	__UNKNOWN__	IGR	SNP	T	T	C	rs191974795		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1572294T>C			NA	NA				CTD-2245E15.3 (20469 upstream) : SDHAP3 (16848 downstream)						NA		NA									NA						TATACATAATTACAAAAGCTG	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.1572294T>C		NA		hg19		0.02	5.815417	AATxACA	COVERED																																																																																			NOVEL					0			5	4.507328	KEEP	1	0	0	15	380	TT	0.99649	0.99649	0			7	51	236	0	0	14.969239	129	60	3595	217		0.051471	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	1572318	1572318	__UNKNOWN__	IGR	SNP	C	C	T	rs112275926	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1572318C>T			NA	NA				CTD-2245E15.3 (20493 upstream) : SDHAP3 (16824 downstream)						NA		NA									NA						CTGTCATCACCGCATCTTGTC	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.1572318C>T		NA		hg19		0.02	4.376899	CACxGCA	COVERED																																																																																			NOVEL					0			7	2.639916	KEEP	1	1	26	18	537	CC	0.99986	0.99986	0			11	60	334	0	0	20.939362	160	60	5213	291		0.064327	1
CTD-2012J19.3	0	__UNKNOWN__	__UNKNOWN__	5	1597054	1597054	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:1597054T>C	ENST00000605200.1	+	0	622										NA		NA									NA						cttgcttttctccacaCCACA	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000605200.1:	chr5.hg19:g.1597054T>C		NA		hg19		0.02	-0.38594	TTCxCCA	COVERED																																																																																			NOVEL	CTD-2012J19.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469651.1	6	2.404014	KEEP	6	0	0	8	221	TT	0.99257	0.911349	0		+	4	60	138	0	0	9.8894	40	60	1245	86	ENST00000605200.1	0.090909	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	3647565	3647565	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:3647565A>G			NA	NA				IRX1 (46048 upstream) : CTD-2287N17.1 (365256 downstream)						NA		NA									NA						gattacaggtatgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.3647565A>G		NA		hg19		0.02	-0.236776	GGTxTGA	COVERED																																																																																			NOVEL					0			10	2.706158	KEEP	0	0	0	9	240	AA	0.99254	0.607839	0			4	60	135	0	0	10.879859	18	60	510	52		0.181818	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	3866118	3866118	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:3866118T>G			NA	NA				IRX1 (264601 upstream) : CTD-2287N17.1 (146703 downstream)						NA		NA									NA						gattacaggcttgagccacca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.3866118T>G		NA		hg19		0.02	-0.262687	GGCxTGA	COVERED																																																																																			NOVEL					0			9	2.706336	KEEP	0	0	0	9	241	TT	0.99254	0.734154	0			4	60	101	0	0	7.074795	24	60	706	54		0.142857	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	4087346	4087346	__UNKNOWN__	IGR	SNP	C	C	G	rs199702769|rs141424757|rs202221970	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:4087346C>G			NA	NA				CTD-2383I20.1 (45469 upstream) : CTD-2008N3.1 (48448 downstream)						NA		NA									NA						TTTCgtgtgtctgtgtgtgtg	0.502		NA											C|||	41	0.0081869	0.0227	0.0029	5008	,	,	NA	20700	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.4087346C>G		NA		hg19		0.02	-0.271951	TGTxTGT	COVERED																																																																																			NOVEL					0			9	3.309773	KEEP	0	0	0	11	334	CC	0.993072	0.734547	0			5	60	176	1	1	14.038384	26	60	877	59		0.16129	0.739671
RP11-445O3.2	0	__UNKNOWN__	__UNKNOWN__	5	4601927	4601927	__UNKNOWN__	lincRNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:4601927C>G	ENST00000507435.1	-	0	429										NA		NA									NA						caccatgttgctcaggctggt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000507435.1:	chr5.hg19:g.4601927C>G		NA		hg19		0.02	-0.139937	TTGxTCA	COVERED																																																																																			NOVEL	RP11-445O3.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000365582.1	7	2.407019	KEEP	0	0	0	8	243	CC	0.99257	0.259026	0		-	3	60	102	0	0	8.707769	9	60	288	30	ENST00000507435.1	0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	4925083	4925083	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:4925083A>G			NA	NA				CTD-2046I8.1 (50211 upstream) : CTD-2247C11.2 (42793 downstream)						NA		NA									NA						ctgtgtctgtatagaaagaag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.4925083A>G		NA		hg19		0.02	-0.412215	TGTxTAG	COVERED																																																																																			NOVEL					0			4	3.307766	KEEP	7	0	0	11	294	AA	0.99254	0.934716	0			4	60	133	0	0	9.349181	41	60	1215	100		0.088889	0.941741
CTD-2247C11.1	0	__UNKNOWN__	__UNKNOWN__	5	5000017	5000017	__UNKNOWN__	lincRNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:5000017C>G	ENST00000509057.1	-	0	228										NA		NA									NA						agaacatgcgctgtttggttt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000509057.1:	chr5.hg19:g.5000017C>G		NA		hg19		0.02	-0.210551	GCGxTGT	COVERED																																																																																			NOVEL	CTD-2247C11.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000365583.2	3	2.708287	KEEP	0	0	0	9	283	CC	0.992708	0.548856	0		-	3	60	102	0	0	7.764448	20	60	705	54	ENST00000509057.1	0.130435	0.552887
ADAMTS16	170690	__UNKNOWN__	__UNKNOWN__	5	5317709	5317709	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:5317709T>C	ENST00000274181.7	+	22	3549					NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	NA		NA			branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						cggggtttcatcatgttgccc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ315734	CCDS43299.1	5p15	2008-07-18	2005-08-19		ENSG00000145536	ENSG00000145536	170690		ADAM metallopeptidases with thrombospondin type 1 motif	17108	protein-coding gene	gene with protein product		607510	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 16		NA	11867212	Standard	NM_139056	NM_139056	NA	Approved	ADAMTS16s	uc003jdl.3	Q8TE57	OTTHUMG00000161663	ENST00000274181.7:c.3412-538T>C	chr5.hg19:g.5317709T>C		NA	C6G490|Q8IVE2	hg19	CCDS43299.1	0.02	-0.131553	TCAxCAT	COVERED																																																																																			NOVEL	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365657.1	5	3.307909	KEEP	0	0	0	11	296	TT	0.993072	0.227586	0		+	3	60	87	0	0	7.082215	10	60	297	36	ENST00000274181.7	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	5525178	5525178	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:5525178C>T			NA	NA				KIAA0947 (34831 upstream) : CTC-471C19.1 (493963 downstream)						NA		NA									NA						ctcagcctcccgagtagctgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.5525178C>T		NA		hg19		0.02	-0.166648	TCCxGAG	COVERED																																																																																			NOVEL					0			12	5.113372	KEEP	8	0	0	17	485	CC	0.993072	0.351495	0			4	40	120	0	0	9.662816	15	60	475	48		0.210526	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	5839348	5839348	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:5839348A>G			NA	NA				KIAA0947 (349001 upstream) : CTC-471C19.1 (179793 downstream)						NA		NA									NA						atggacacagagagggggaca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.5839348A>G		NA		hg19		0.02	-0.11402	CAGxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.406293	KEEP	0	0	0	8	223	AA	0.99257	0.16126	0			3	60	103	0	0	8.801327	9	60	264	28		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	5855282	5855282	__UNKNOWN__	IGR	SNP	G	G	A	rs4702299	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:5855282G>A			NA	NA				KIAA0947 (364935 upstream) : CTC-471C19.1 (163859 downstream)						NA		NA									NA						tgcattttcagtagagacggg	0.557		NA											G|||	1038	0.207268	0.1747	0.1556	5008	,	,	NA	15071	0.2669	NA	0.1978	False	NA	,,,	NA	NA	NA	2504	0.2362	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.5855282G>A		NA		hg19		0.02	-0.23684	TCAxTAG	UNCOVERED																																																																																			NOVEL					0			6	2.406199	KEEP	1	0	0	8	231	GG	0	0	0			6	60	185	0	0	15.629806	17	60	583	46		0.26087	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	5950216	5950216	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:5950216G>T			NA	NA				KIAA0947 (459869 upstream) : CTC-471C19.1 (68925 downstream)						NA		NA									NA						gtgctgggatgacaggcgtga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.5950216G>T		NA		hg19		0.02	-0.140338	GATxACA	COVERED																																																																																			NOVEL					0			8	2.406707	KEEP	0	0	0	8	233	AG	0.99254	0.259018	0			3	60	87	0	0	7.332198	8	60	265	39		0.272727	0.260965
UBE2QL1	134111	__UNKNOWN__	__UNKNOWN__	5	6454218	6454218	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:6454218T>C	ENST00000399816.3	+	1	625					NM_001145161.2	NP_001138633.1	A1L167	U2QL1_HUMAN	ubiquitin-conjugating enzyme E2Q family-like 1	NA		NA			protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			breast(1)|endometrium(1)	2						tggtctcaaattcctgggctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057805	CCDS47189.1	5p15.31	2010-02-17			ENSG00000215218	ENSG00000215218	134111			37269	protein-coding gene	gene with protein product		615832			NA		Standard	NM_001145161	NM_001145161	NA	Approved	FLJ25076	uc003jdp.4	A1L167	OTTHUMG00000161683	ENST00000399816.3:c.354+4858T>C	chr5.hg19:g.6454218T>C		NA		hg19	CCDS47189.1	0.02	-0.263089	AAAxTCC	COVERED																																																																																			NOVEL	UBE2QL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365717.1	10	3.307694	KEEP	0	0	0	11	298	TT	0.993072	0.688863	0		+	3	60	104	0	0	7.644064	26	60	757	58	ENST00000399816.3	0.103448	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	6511918	6511918	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:6511918A>G			NA	NA				UBE2QL1 (16896 upstream) : LINC01018 (70332 downstream)						NA		NA									NA						tggctaacacagtgaaacccc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.6511918A>G		NA		hg19		0.02	-0.166629	CACxGTG	COVERED																																																																																			NOVEL					0			6	3.006679	KEEP	2	0	0	10	264	AA	0.99254	0.351306	0			3	60	91	0	0	7.010647	15	60	437	32		0.166667	0.353947
ADCY2	108	__UNKNOWN__	__UNKNOWN__	5	7504769	7504769	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:7504769G>A	ENST00000338316.4	+	3	497					NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						tctgttgcctgggctggagtg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	108	4.6.1.1	Adenylate cyclases	233	protein-coding gene	gene with protein product		103071			NA	1427768	Standard	NM_020546	NM_020546	NA	Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.409-16082G>A	chr5.hg19:g.7504769G>A		NA	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	hg19	CCDS3872.2	0.02	-0.122811	CCTxGGC	COVERED																																																																																			NOVEL	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206930.2	12	2.407155	KEEP	1	0	0	8	243	GG	0.99257	0.194853	0		+	3	60	93	0	0	8.078401	7	60	233	30	ENST00000338316.4	0.3	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	9581501	9581501	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:9581501C>T			NA	NA				SNHG18 (30780 upstream) : CTD-2001E22.1 (39987 downstream)						NA		NA									NA						tagccaggtgcggtggtgggt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.9581501C>T		NA		hg19		0.02	-0.175301	GTGxGGT	COVERED																																																																																			NOVEL					0			7	2.707153	KEEP	3	0	0	9	258	CC	0.99257	0.384528	0			4	31	121	0	0	9.982614	13	60	389	40		0.235294	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	9616992	9616992	__UNKNOWN__	IGR	SNP	C	C	A	rs160498	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:9616992C>A			NA	NA				SNHG18 (66271 upstream) : CTD-2001E22.1 (4496 downstream)						NA		NA									NA						gcgtgagccaccatgcccggc	0.443		NA											C|||	3659	0.730631	0.7912	0.6196	5008	,	,	NA	15226	0.7867	NA	0.668	False	NA	,,,	NA	NA	NA	2504	0.7342	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.9616992C>A		NA		hg19		0.02	-0.184187	CCAxCAT	COVERED																																																																																			NOVEL					0			9	2.406836	KEEP	0	0	0	8	238	CC	0.99257	0.420331	0			12	60	346	0	0	36.411896	4	60	139	41		0.75	0.423478
FAM173B	134145	__UNKNOWN__	__UNKNOWN__	5	10245280	10245280	__UNKNOWN__	Intron	SNP	T	T	C	rs143632580	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10245280T>C	ENST00000511437.1	-	1	29				FAM173B_ENST00000510052.1_Intron|FAM173B_ENST00000280330.8_Intron|FAM173B_ENST00000510047.1_Intron	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	NA		NA				integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						cgcctgtaattccagcacttt	0.423		NA											T|||	38	0.00758786	0.0	0.0187	5008	,	,	NA	16292	0.001	NA	0.0179	False	NA	,,,	NA	NA	NA	2504	0.0061	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756	134145			27029	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_199133	NM_199133	NA	Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.16+4689A>G	chr5.hg19:g.10245280T>C		NA	B4DT41|B4DXK2|E9PBZ4	hg19	CCDS43301.1	0.02	-0.149104	AATxCCA	COVERED																																																																																			NOVEL	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366048.2	7	2.406488	KEEP	0	0	0	8	228	TT	0.99257	0.289832	0		-	3	60	97	0	0	8.082073	10	60	293	34	ENST00000511437.1	0.230769	0.292001
CMBL	134147	__UNKNOWN__	__UNKNOWN__	5	10279944	10279944	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10279944A>G	ENST00000296658.3	-	0	1779					NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	NA		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						gagccaccgcacccggccTGT	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	134147	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	carboxymethylenebutenolidase-like (Pseudomonas)		NA	3804974, 20177059	Standard	NM_138809	NM_138809	NA	Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.*621T>C	chr5.hg19:g.10279944A>G		NA	D3DTC7|Q8TED6	hg19	CCDS3878.1	0.02	1.591918	CGCxCCC	COVERED																																																																																			NOVEL	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253689.1	24	3.165443	KEEP	10	2	55	30	781	AA	0.999997	0.999859	0		-	6	60	176	0	0	11.601303	71	60	2035	189	ENST00000296658.3	0.077922	0.999862
CMBL	134147	__UNKNOWN__	__UNKNOWN__	5	10285974	10285974	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10285974C>G	ENST00000296658.3	-	4	887				CMBL_ENST00000510532.1_Intron	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	NA		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						ccacgcccagctaatttttgt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	134147	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	carboxymethylenebutenolidase-like (Pseudomonas)		NA	3804974, 20177059	Standard	NM_138809	NM_138809	NA	Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.466+491G>C	chr5.hg19:g.10285974C>G		NA	D3DTC7|Q8TED6	hg19	CCDS3878.1	0.02	-0.192994	CAGxTAA	COVERED																																																																																			NOVEL	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253689.1	9	3.009102	KEEP	0	0	0	10	311	CC	0.992708	0.454419	0		-	3	60	96	0	0	7.226868	19	60	643	44	ENST00000296658.3	0.136364	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	10325797	10325797	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10325797A>G			NA	NA				CMBL (17659 upstream) : Y_RNA (11591 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.10325797A>G		NA		hg19		0.02	-0.184193	GCTxGGA	COVERED																																																																																			NOVEL					0			12	2.404771	KEEP	0	0	0	8	213	AA	0.99257	0.420331	0			3	60	104	0	0	8.391631	14	60	418	36		0.176471	0.423478
MARCH6	10299	__UNKNOWN__	__UNKNOWN__	5	10368951	10368951	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10368951T>C	ENST00000274140.5	+	2	151				MARCH6_ENST00000503788.1_Intron|MARCH6_ENST00000449913.2_Intron	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	NA		NA			protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						tcccaaagtgttgggattaca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495	10299		MARCH membrane-associated ring fingers, RING-type (C3HC4) zinc fingers	30550	protein-coding gene	gene with protein product		613297	membrane-associated ring finger (C3HC4) 6		NA	14722266	Standard	NM_005885	NM_001270660	NA	Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.20-8959T>C	chr5.hg19:g.10368951T>C		NA	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	hg19	CCDS34135.1	0.02	-0.342036	GTGxTGG	COVERED																																																																																			NOVEL	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366919.2	10	2.405088	KEEP	1	0	0	8	210	TT	0.99257	0.859313	0		+	5	60	180	0	0	14.02352	32	60	939	76	ENST00000274140.5	0.135135	0.865745
ROPN1L	83853	__UNKNOWN__	__UNKNOWN__	5	10452421	10452421	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10452421G>C	ENST00000503804.1	+	4	938				ROPN1L_ENST00000510520.1_Intron|ROPN1L_ENST00000274134.4_Intron			Q96C74	ROP1L_HUMAN	rhophilin associated tail protein 1-like	NA		NA			epithelial cilium movement (GO:0003351)|regulation of protein phosphorylation (GO:0001932)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)	14						gtgtgtgtgtgtgtgtctgtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF239723	CCDS3879.1	5p15	2011-01-20	2011-01-20		ENSG00000145491	ENSG00000145491	83853			24060	protein-coding gene	gene with protein product	radial spoke head 11 homolog (Chlamydomonas)	611756	ropporin 1-like		NA	11278869	Standard	NM_031916	NM_031916	NA	Approved	ASP, FLJ25776, RSPH11	uc021xwo.1	Q96C74	OTTHUMG00000090507	ENST00000503804.1:c.417+2196G>C	chr5.hg19:g.10452421G>C		NA	D3DTC9|Q9BZX0	hg19	CCDS3879.1	0.02	-0.298007	TGTxTGT	COVERED																																																																																			NOVEL	ROPN1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367033.1	8	2.707759	KEEP	0	0	0	9	273	GG	0.99254	0.794276	0		+	4	60	112	2	0	8.031929	26	60	865	60	ENST00000503804.1	0.133333	0.800245
RP11-1C1.4	0	__UNKNOWN__	__UNKNOWN__	5	10498089	10498089	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10498089T>C	ENST00000515243.1	-	0	1524										NA		NA									NA						gccaacatggtaaaaccccat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000515243.1:	chr5.hg19:g.10498089T>C		NA		hg19		0.02	-0.131529	TGGxAAA	UNCOVERED																																																																																			NOVEL	RP11-1C1.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000367039.1	3	3.006079	KEEP	3	0	0	10	259	TT	0	0	0		-	3	60	104	0	0	9.033141	8	60	216	37	ENST00000515243.1	0.272727	0.229173
ANKRD33B	651746	__UNKNOWN__	__UNKNOWN__	5	10570285	10570285	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10570285A>G	ENST00000296657.5	+	1	366					NM_001164440.1	NP_001157912.1	A6NCL7	AN33B_HUMAN	ankyrin repeat domain 33B	NA		NA									NA						cactgcacccagccCCCATGT	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47191.1	5p15.2	2013-01-10			ENSG00000164236	ENSG00000164236	651746		Ankyrin repeat domain containing	35240	protein-coding gene	gene with protein product		NA			NA		Standard	XM_001130634	NM_001164440	NA	Approved		uc021xwp.1	A6NCL7	OTTHUMG00000162050	ENST00000296657.5:c.366+5340A>G	chr5.hg19:g.10570285A>G		NA		hg19	CCDS47191.1	0.02	-0.210507	CCCxGCC	COVERED																																																																																			NOVEL	ANKRD33B-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367037.3	6	3.307794	KEEP	4	0	0	11	298	AA	0.99254	0.518266	0		+	3	60	101	1	0	7.860801	17	60	518	56	ENST00000296657.5	0.15	0.522161
DAP	1611	__UNKNOWN__	__UNKNOWN__	5	10684216	10684216	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10684216A>G	ENST00000230895.6	-	3	356				DAP_ENST00000432074.2_Intron	NM_004394.2	NP_004385.1	P51397	DAP1_HUMAN	death-associated protein	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cellular response to amino acid starvation (GO:0034198)|negative regulation of autophagy (GO:0010507)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)		death domain binding (GO:0070513)			endometrium(1)|large_intestine(1)|lung(1)	3		Ovarian(839;1.34e-05)|Breast(839;0.0634)|Lung NSC(810;0.0804)				gattacagggatgagccactg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X76105	CCDS3880.1	5p15.2	2008-07-18			ENSG00000112977	ENSG00000112977	1611			2672	protein-coding gene	gene with protein product		600954			NA	8530096, 7828849	Standard	NM_004394	NM_004394	NA	Approved		uc003jez.4	P51397	OTTHUMG00000131041	ENST00000230895.6:c.153-533T>C	chr5.hg19:g.10684216A>G		NA	Q6FGC3|Q9BUC9	hg19	CCDS3880.1	0.02	-0.324434	GGGxTGA	COVERED																																																																																			NOVEL	DAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253687.1	12	2.379313	KEEP	0	0	0	8	194	AA	0.99257	0.829507	0		-	3	60	102	0	0	7.149066	33	60	924	57	ENST00000230895.6	0.083333	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	10800788	10800788	__UNKNOWN__	IGR	SNP	C	C	T	rs185186644	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10800788C>T			NA	NA				CTD-2154B17.1 (23614 upstream) : CTNND2 (171163 downstream)						NA		NA									NA						gagctgagatcgcgccactgc	0.463		NA											C|||	2	0.000399361	0.0	0.0	5008	,	,	NA	15240	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.10800788C>T		NA		hg19		0.02	-0.149116	GATxGCG	COVERED																																																																																			NOVEL					0			7	2.707514	KEEP	1	0	0	9	261	CC	0.99254	0.320398	0			4	60	114	0	0	9.823395	9	60	292	40		0.307692	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	10922397	10922397	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10922397T>C			NA	NA				CTD-2154B17.1 (145223 upstream) : CTNND2 (49554 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.10922397T>C		NA		hg19		0.02	-0.21049	TCAxGCC	COVERED																																																																																			NOVEL					0			13	2.405593	KEEP	1	0	0	8	215	TT	0.99257	0.518282	0			3	60	100	1	0	7.76097	17	60	504	47		0.15	0.522161
CTNND2	1501	__UNKNOWN__	__UNKNOWN__	5	10992132	10992132	__UNKNOWN__	Intron	SNP	T	T	C	rs146898867	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:10992132T>C	ENST00000304623.8	-	19	3401				CTNND2_ENST00000359640.2_Intron|CTNND2_ENST00000503622.1_Intron|CTNND2_ENST00000511377.1_Intron|CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000495388.2_Intron	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	NA		NA			cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						cgggttcaagtgattctcctg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862	1501		Armadillo repeat containing	2516	protein-coding gene	gene with protein product	neural plakophilin-related arm-repeat protein	604275	catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)		NA	9342840, 9223106	Standard	NM_001332	XM_005248251	NA	Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.3211+530A>G	chr5.hg19:g.10992132T>C		NA	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	hg19	CCDS3881.1	0.02	-0.087704	AAGxGAT	UNCOVERED																																																																																			NOVEL	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206999.1	6	2.706751	KEEP	1	0	0	9	247	TT	0.99257	0.09898	0		-	3	60	95	0	0	8.44385	6	60	173	25	ENST00000304623.8	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	14091389	14091389	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:14091389A>G			NA	NA				DNAH5 (146737 upstream) : TRIO (52421 downstream)						NA		NA									NA						ggtggaggttacagtgagcca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.14091389A>G		NA		hg19		0.02	-0.175372	GTTxCAG	COVERED																																																																																			NOVEL					0			7	2.405191	KEEP	1	0	0	8	209	AA	0.99257	0.384528	0			4	60	111	0	0	8.981686	13	60	370	34		0.235294	0.387407
TRIO	7204	__UNKNOWN__	__UNKNOWN__	5	14152519	14152519	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:14152519A>G	ENST00000344204.4	+	1	181				TRIO_ENST00000537187.1_Intron	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	NA		NA			apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					tcgctctgtcacccaggctgg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382	7204		Rho guanine nucleotide exchange factors, Immunoglobulin superfamily / I-set domain containing	12303	protein-coding gene	gene with protein product		601893	triple functional domain (PTPRF interacting)		NA	8643598	Standard	NM_007118	NM_007118	NA	Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.157+8528A>G	chr5.hg19:g.14152519A>G		NA	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	hg19	CCDS3883.1	0.02	-0.166649	GTCxCCC	COVERED																																																																																			NOVEL	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253711.2	9	4.21054	KEEP	4	0	0	14	386	AA	0.995343	0.421506	0		+	4	60	138	0	0	11.568414	14	60	417	58	ENST00000344204.4	0.222222	0.423478
TRIO	7204	__UNKNOWN__	__UNKNOWN__	5	14294185	14294185	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:14294185T>C	ENST00000344204.4	+	6	1200				TRIO_ENST00000509967.2_Intron|TRIO_ENST00000537187.1_Intron	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	NA		NA			apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					gtcccagctatttgggaggct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382	7204		Rho guanine nucleotide exchange factors, Immunoglobulin superfamily / I-set domain containing	12303	protein-coding gene	gene with protein product		601893	triple functional domain (PTPRF interacting)		NA	8643598	Standard	NM_007118	NM_007118	NA	Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.1176+942T>C	chr5.hg19:g.14294185T>C		NA	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	hg19	CCDS3883.1	0.02	-0.263107	CTAxTTG	COVERED																																																																																			NOVEL	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253711.2	9	3.007829	KEEP	2	0	0	10	279	TT	0.992708	0.68861	0		+	3	60	97	0	0	7.042906	24	60	697	57	ENST00000344204.4	0.111111	0.693668
ANKH	56172	__UNKNOWN__	__UNKNOWN__	5	14813220	14813220	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:14813220C>T	ENST00000284268.6	-	2	427					NM_054027.4	NP_473368.1	Q9HCJ1	ANKH_HUMAN	ANKH inorganic pyrophosphate transport regulator	NA		NA			locomotory behavior (GO:0007626)|regulation of bone mineralization (GO:0030500)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	inorganic diphosphate transmembrane transporter activity (GO:0030504)|inorganic phosphate transmembrane transporter activity (GO:0005315)|phosphate ion transmembrane transporter activity (GO:0015114)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						catggtggcacatacctgtag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF274753	CCDS3885.1	5p15.2	2013-06-19	2013-06-19		ENSG00000154122	ENSG00000154122	56172			15492	protein-coding gene	gene with protein product		605145	ankylosis, progressive (mouse) homolog, craniometaphyseal dysplasia, Jackson type (dominant), ankylosis, progressive homolog (mouse)	CCAL2, CMDJ	NA	10894769, 12297989, 11326338	Standard	NM_054027	NM_054027	NA	Approved	HANK, ANK, CPPDD	uc003jfm.4	Q9HCJ1	OTTHUMG00000090539	ENST00000284268.6:c.97-43920G>A	chr5.hg19:g.14813220C>T		NA	B2RCA7|B3KMG4|D3DTD4|Q9NQW2	hg19	CCDS3885.1	0.02	-0.201767	GCAxATA	COVERED																																																																																			NOVEL	ANKH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207063.1	12	3.911468	KEEP	0	0	0	13	393	CC	0.994391	0.487793	0		-	3	42	87	0	0	6.327722	19	60	660	50	ENST00000284268.6	0.136364	0.490544
FBXL7	23194	__UNKNOWN__	__UNKNOWN__	5	15529687	15529687	__UNKNOWN__	Intron	SNP	C	C	T	rs189973568	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:15529687C>T	ENST00000504595.1	+	1	518				FBXL7_ENST00000510662.1_Intron	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	NA		NA			cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						gtagtagagacggggtttcac	0.572		NA											-|||	24	0.00479233	0.0	0.0029	5008	,	,	NA	15377	0.0	NA	0.0179	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580	23194		F-boxes / Leucine-rich repeats	13604	protein-coding gene	gene with protein product		605656			NA	10048485, 10531035	Standard	NM_012304	NM_012304	NA	Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.37+28865C>T	chr5.hg19:g.15529687C>T		NA	B9EGF1|D6RDY7|O94926	hg19	CCDS54833.1	0.02	-0.070138	AGAxGGG	UNCOVERED																																																																																			NOVEL	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366117.1	0	2.404658	KEEP	2	0	0	8	220	CC	0.99257	0.053735	0		+	3	40	72	0	0	6.33022	5	60	163	24	ENST00000504595.1	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	16352125	16352125	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:16352125A>G			NA	NA				RP11-19O2.2 (166431 upstream) : RP1-167G20.1 (21344 downstream)						NA		NA									NA						ccaggccaacatggcgaaact	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.16352125A>G		NA		hg19		0.02	-0.149093	AACxTGG	COVERED																																																																																			NOVEL					0			6	3.908232	KEEP	0	0	0	13	344	AA	0.994391	0.290363	0			3	56	103	0	0	8.378924	13	60	372	33		0.1875	0.292001
FAM134B	54463	__UNKNOWN__	__UNKNOWN__	5	16522906	16522906	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:16522906A>G	ENST00000306320.9	-	4	545					NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	NA		NA			sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						ttgagcccagaagttcaagac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153	54463			25964	protein-coding gene	gene with protein product		613114			NA	19838196, 24327336	Standard	NM_001034850	NM_001034850	NA	Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.459-39325T>C	chr5.hg19:g.16522906A>G		NA	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	hg19	CCDS43304.1	0.02	-0.166638	CAGxAGT	COVERED																																																																																			NOVEL	FAM134B-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366090.1	3	3.307662	KEEP	0	0	0	11	292	AA	0.993072	0.351495	0		-	3	60	101	1	0	7.933387	16	60	464	42	ENST00000306320.9	0.157895	0.353947
FAM134B	54463	__UNKNOWN__	__UNKNOWN__	5	16603058	16603058	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:16603058G>A	ENST00000306320.9	-	1	407					NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	NA		NA			sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						aggaggttgcggtgagccgag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153	54463			25964	protein-coding gene	gene with protein product		613114			NA	19838196, 24327336	Standard	NM_001034850	NM_001034850	NA	Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.320+13702C>T	chr5.hg19:g.16603058G>A		NA	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	hg19	CCDS43304.1	0.02	-0.17541	TGCxGTG	COVERED																																																																																			NOVEL	FAM134B-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366090.1	7	2.40625	KEEP	0	0	0	8	235	GG	0.99257	0.384528	0		-	3	60	88	0	0	6.710775	15	60	473	38	ENST00000306320.9	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	17049679	17049679	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:17049679T>C			NA	NA				RNU6-660P (107619 upstream) : CTD-2228A4.1 (57789 downstream)						NA		NA									NA						acctgtaatctcagcactttg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.17049679T>C		NA		hg19		0.02	-0.184172	ATCxCAG	COVERED																																																																																			NOVEL					0			4	3.006548	KEEP	0	0	0	10	270	TT	0.992708	0.42039	0			3	60	92	0	0	7.033892	16	60	473	39		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	17121349	17121349	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:17121349T>C			NA	NA				Y_RNA (3554 upstream) : AC091878.1 (8787 downstream)						NA		NA									NA						ggtgaaaccctgtctctacta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.17121349T>C		NA		hg19		0.02	-0.254371	CCCxGTC	COVERED																																																																																			NOVEL					0			23	3.910763	KEEP	9	0	0	13	374	TT	0.993634	0.664267	0			3	21	100	0	0	7.448855	22	60	679	72		0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	17777524	17777524	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:17777524A>G			NA	NA				RP11-321E2.4 (293469 upstream) : RP11-454P21.1 (72843 downstream)						NA		NA									NA						cccgacctcaagtgatccgcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.17777524A>G		NA		hg19		0.02	-0.16665	TCAxGTG	COVERED																																																																																			NOVEL					0			4	2.406482	KEEP	1	0	0	8	227	AA	0.99257	0.351317	0			3	60	96	0	0	7.591904	14	60	433	44		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	17792579	17792579	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:17792579T>C			NA	NA				RP11-321E2.4 (308524 upstream) : RP11-454P21.1 (57788 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.17792579T>C		NA		hg19		0.02	-0.157883	TCAxGCC	COVERED																																																																																			NOVEL					0			2	4.21078	KEEP	11	0	0	14	389	TT	0.99257	0.351317	0			3	60	102	0	0	8.191587	14	60	429	56		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	18467987	18467987	__UNKNOWN__	IGR	SNP	C	C	T	rs62347628	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:18467987C>T			NA	NA				SNORD81 (231682 upstream) : RN7SL58P (79433 downstream)						NA		NA									NA						gctgggattacaggcgtgagc	0.512		NA											C|||	523	0.104433	0.0893	0.1138	5008	,	,	NA	17035	0.0754	NA	0.1581	False	NA	,,,	NA	NA	NA	2504	0.093	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.18467987C>T		NA		hg19		0.02	-0.140345	TTAxAGG	COVERED																																																																																			NOVEL					0			6	2.407113	KEEP	1	0	0	8	244	CC	0.99257	0.259026	0			4	60	111	1	0	9.370708	10	60	336	36		0.285714	0.260965
CDH18	1016	__UNKNOWN__	__UNKNOWN__	5	20253024	20253024	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:20253024A>G	ENST00000507958.1	-	2	474							Q13634	CAD18_HUMAN	cadherin 18, type 2	NA		NA			adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					cagcctgggcaacagagcgag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526	1016		Cadherins / Major cadherins	1757	protein-coding gene	gene with protein product		603019			NA	9030594, 10191097	Standard	NM_004934	NM_004934	NA	Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.516+2528T>C	chr5.hg19:g.20253024A>G		NA	A8K0I2|B4DHG6|Q8N5Z2	hg19	CCDS3889.1	0.02	-0.114007	GGCxACA	UNCOVERED																																																																																			NOVEL	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366747.1	2	2.406255	KEEP	0	0	0	8	223	AA	0.99257	0.16126	0		-	3	60	92	0	0	7.701436	9	60	254	32	ENST00000507958.1	0.25	0.162467
GUSBP1	728411	__UNKNOWN__	__UNKNOWN__	5	21475250	21475250	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:21475250C>G	ENST00000607545.1	+	0	179					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1	NA		NA			carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)				NA						agctccgcctcccaggttcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666	728411			13670	pseudogene	pseudogene		NA			NA	8565635	Standard	NG_008324	NR_027026	NA	Approved		uc010iub.3	Q15486	OTTHUMG00000162474	ENST00000607545.1:	chr5.hg19:g.21475250C>G		NA	A6NLY8|A8K1B7|Q969T8|Q9BUH2	hg19		0.02	-0.061408	CCTxCCA	UNCOVERED																																																																																			NOVEL	GUSBP1-006	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000470546.1	11	3.610123	KEEP	16	0	0	12	358	CC	0	0	0		+	5	25	171	0	0	17.666152	2	40	70	35	ENST00000607545.1	0.714286	0.043787
GUSBP1	728411	__UNKNOWN__	__UNKNOWN__	5	21496874	21496874	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:21496874T>A	ENST00000607545.1	+	0	179					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1	NA		NA			carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)				NA						ggcctcccaatgtgctgggat	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666	728411			13670	pseudogene	pseudogene		NA			NA	8565635	Standard	NG_008324	NR_027026	NA	Approved		uc010iub.3	Q15486	OTTHUMG00000162474	ENST00000607545.1:	chr5.hg19:g.21496874T>A		NA	A6NLY8|A8K1B7|Q969T8|Q9BUH2	hg19		0.02	2.958984	CAAxGTG	COVERED																																																																																			NOVEL	GUSBP1-006	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000470546.1	58	2.289347	KEEP	46	6	159	64	1708	TT	1	1	0		+	8	48	237	1	0	14.893588	108	44	3078	294	ENST00000607545.1	0.068966	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	23075937	23075937	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:23075937C>T			NA	NA				CTD-2234B20.1 (61301 upstream) : RN7SL572P (125616 downstream)						NA		NA									NA						tggctgggcacggtggctcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.23075937C>T		NA		hg19		0.02	-0.114024	GCAxGGT	UNCOVERED																																																																																			NOVEL					0			5	3.008632	KEEP	0	0	0	10	298	CC	0.992708	0.161282	0			3	60	84	0	0	6.900942	9	60	301	34		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	27658115	27658115	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:27658115T>C			NA	NA				LINC01021 (171862 upstream) : AC010455.1 (328166 downstream)						NA		NA									NA						tttgggaggctgaggtgggca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.27658115T>C		NA		hg19		0.02	-0.078943	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			7	3.00719	KEEP	3	0	0	10	273	TT	0.99257	0.076761	0			3	60	98	0	0	8.743591	6	60	183	25		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	30118569	30118569	__UNKNOWN__	IGR	SNP	G	G	A	rs113344592	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:30118569G>A			NA	NA				RN7SKP207 (169332 upstream) : RP11-152K4.2 (975514 downstream)						NA		NA									NA						acggagtttcgctcttgttgc	0.473		NA											G|||	615	0.122804	0.0182	0.1628	5008	,	,	NA	10105	0.003	NA	0.3072	False	NA	,,,	NA	NA	NA	2504	0.1697	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.30118569G>A		NA		hg19		0.02	-0.070104	TTCxCTC	UNCOVERED																																																																																			NOVEL					0			9	3.610379	KEEP	5	0	0	12	354	GG	0.99257	0.053735	0			5	60	139	0	0	15.108315	1	60	36	29		0.833333	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	30895545	30895545	__UNKNOWN__	IGR	SNP	T	T	C	rs12522935	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:30895545T>C			NA	NA				RN7SKP207 (946308 upstream) : RP11-152K4.2 (198538 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.562		NA											-|||	2920	0.583067	0.5756	0.6153	5008	,	,	NA	12040	0.4633	NA	0.6541	False	NA	,,,	NA	NA	NA	2504	0.6207	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.30895545T>C		NA		hg19		0.02	-0.078906	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			6	2.403504	KEEP	9	0	0	8	201	TT	0	0	0			4	40	131	0	0	12.324702	5	39	130	25		0.444444	0.077336
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	31652893	31652893	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:31652893G>A	ENST00000438447.1	+	1	28							O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						caaggcaggcggatcacttga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.-361+13349G>A	chr5.hg19:g.31652893G>A		NA	Q9BXD4	hg19	CCDS34137.1	0.02	-0.122762	GGCxGAT	UNCOVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	5	2.406591	KEEP	7	0	0	8	233	GG	0	0	0		+	3	43	91	0	0	7.733077	8	60	249	40	ENST00000438447.1	0.272727	0.196312
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	31698280	31698280	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:31698280A>G	ENST00000438447.1	+	1	28							O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						caaagtgctgagattacaggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.-361+58736A>G	chr5.hg19:g.31698280A>G		NA	Q9BXD4	hg19	CCDS34137.1	0.02	-0.192967	CTGxGAT	COVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	12	2.405847	KEEP	0	0	0	8	217	AA	0.99257	0.454356	0		+	3	40	97	0	0	7.392273	18	60	551	40	ENST00000438447.1	0.142857	0.457757
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	31841837	31841837	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:31841837A>G	ENST00000438447.1	+	2	864				PDZD2_ENST00000282493.3_Intron			O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						ccagcactttaggaggctgag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.476+42006A>G	chr5.hg19:g.31841837A>G		NA	Q9BXD4	hg19	CCDS34137.1	0.02	-0.166592	TTTxGGA	COVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	6	3.006053	KEEP	0	0	0	10	262	AA	0.992708	0.351366	0		+	3	56	98	0	0	7.710868	15	60	426	36	ENST00000438447.1	0.166667	0.353947
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	31848779	31848779	__UNKNOWN__	Intron	SNP	C	C	T	rs540031446	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:31848779C>T	ENST00000438447.1	+	2	864				PDZD2_ENST00000282493.3_Intron			O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						tgcttgaacccgggaggcaga	0.522		NA											C|||	6	0.00119808	0.0	0.0	5008	,	,	NA	18195	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0061	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.476+48948C>T	chr5.hg19:g.31848779C>T		NA	Q9BXD4	hg19	CCDS34137.1	0.02	-0.122802	ACCxGGG	COVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	4	3.006779	KEEP	2	0	0	10	274	CC	0.992708	0.19488	0		+	3	60	85	0	0	7.000956	9	60	300	31	ENST00000438447.1	0.25	0.196312
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	31885024	31885024	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:31885024T>C	ENST00000438447.1	+	2	864				PDZD2_ENST00000282493.3_Intron			O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						gctgggattataggtatgagc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.476+85193T>C	chr5.hg19:g.31885024T>C		NA	Q9BXD4	hg19	CCDS34137.1	0.02	-0.122793	TTAxAGG	COVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	4	3.007348	KEEP	0	0	0	10	270	TT	0.992708	0.227502	0		+	3	60	105	0	0	8.772864	11	60	324	39	ENST00000438447.1	0.214286	0.229173
PDZD2	23037	__UNKNOWN__	__UNKNOWN__	5	32078534	32078534	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:32078534A>G	ENST00000438447.1	+	19	4070				PDZD2_ENST00000282493.3_Intron			O15018	PDZD2_HUMAN	PDZ domain containing 2	NA		NA			cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						tcaggagtttaagaccagcct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401	23037			18486	protein-coding gene	gene with protein product		610697	PDZ domain containing 3	PDZK3	NA	9205841	Standard		XM_005248271	NA	Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3682+822A>G	chr5.hg19:g.32078534A>G		NA	Q9BXD4	hg19	CCDS34137.1	0.02	-0.131537	TTTxAGA	UNCOVERED																																																																																			NOVEL	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366608.1	10	2.404661	KEEP	1	0	0	8	209	AA	0	0	0		+	3	60	94	0	0	7.782373	10	60	279	26	ENST00000438447.1	0.230769	0.229173
SUB1	10923	__UNKNOWN__	__UNKNOWN__	5	32588815	32588815	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:32588815T>C	ENST00000265073.4	+	2	200				SUB1_ENST00000502897.1_Intron|SUB1_ENST00000512913.1_Intron|SUB1_ENST00000515355.1_Intron|SUB1_ENST00000504789.1_Intron	NM_006713.3	NP_006704.3	P53999	TCP4_HUMAN	SUB1 homolog (S. cerevisiae)	NA		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|single-stranded DNA binding (GO:0003697)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(1)|lung(1)|prostate(1)	4						cggtggctcatgcctgttatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X79805	CCDS3897.1	5p13.3	2008-02-05			ENSG00000113387	ENSG00000113387	10923			19985	protein-coding gene	gene with protein product		600503			NA	8062392, 8062391	Standard	NM_006713	NM_006713	NA	Approved	PC4, p15, p14	uc003jhs.2	P53999	OTTHUMG00000131071	ENST00000265073.4:c.72+125T>C	chr5.hg19:g.32588815T>C		NA	Q96L29	hg19	CCDS3897.1	0.02	1.604955	TCAxGCC	COVERED																																																																																			NOVEL	SUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253730.1	22	8.55341	KEEP	0	1	27	38	1049	TT	1	0.998993	0		+	4	60	131	0	0	8.304549	68	60	2058	161	ENST00000265073.4	0.055556	0.998993
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	33008251	33008251	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:33008251T>C			NA	NA				CTD-2218G20.2 (45678 upstream) : CTD-2066L21.1 (848 downstream)						NA		NA									NA						ctatattgcctaggctggtct	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.33008251T>C		NA		hg19		0.02	-0.140341	GCCxAGG	COVERED																																																																																			NOVEL					0			6	3.307417	KEEP	1	0	0	11	293	TT	0.992708	0.259062	0			3	60	105	0	0	8.772723	11	60	338	36		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	33472071	33472071	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:33472071C>T			NA	NA				TARS (2427 upstream) : CTD-2233C11.2 (47649 downstream)						NA		NA									NA						atcccagcaccttgggaggcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.33472071C>T		NA		hg19		0.02	-0.114006	CACxTTG	UNCOVERED																																																																																			NOVEL					0			3	2.708164	KEEP	0	0	0	9	280	CC	0.99254	0.161255	0			3	60	80	0	0	6.501118	9	60	300	29		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	33509669	33509669	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:33509669A>G			NA	NA				TARS (40025 upstream) : CTD-2233C11.2 (10051 downstream)						NA		NA									NA						gtgaaaccccatctctactaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.33509669A>G		NA		hg19		0.02	-0.061388	CCCxTCT	UNCOVERED																																																																																			NOVEL					0			7	3.306891	KEEP	4	0	0	11	286	AA	0.99257	0.043461	0			3	60	94	0	1	8.755444	4	60	112	24		0.428571	0.043787
ADAMTS12	81792	__UNKNOWN__	__UNKNOWN__	5	33590839	33590839	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:33590839G>C	ENST00000504830.1	-	18	2990				ADAMTS12_ENST00000352040.3_Intron|ADAMTS12_ENST00000504582.1_Intron	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	NA		NA			cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						ccgcggcctcgcaaagtgctg	0.428		NA								HNSCC(64;0.19)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388	81792		ADAM metallopeptidases with thrombospondin type 1 motif	14605	protein-coding gene	gene with protein product		606184	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12		NA	11279086	Standard	NM_030955	NM_030955	NA	Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.2655-1925C>G	chr5.hg19:g.33590839G>C		NA	A2RRN9|A5D6V6|Q6UWL3	hg19	CCDS34140.1	0.02	-0.140304	CTCxCAA	COVERED																																																																																			NOVEL	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367164.2	6	3.309432	KEEP	0	0	0	11	327	GG	0.993072	0.289978	0		-	3	60	102	0	0	8.473355	11	60	353	44	ENST00000504830.1	0.214286	0.292001
SLC45A2	51151	__UNKNOWN__	__UNKNOWN__	5	33969170	33969170	__UNKNOWN__	Intron	SNP	C	C	G	rs199542822|rs2652127|rs542818611|rs66961145		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:33969170C>G	ENST00000296589.4	-	3	709				SLC45A2_ENST00000345083.5_Intron|SLC45A2_ENST00000342059.3_Intron|SLC45A2_ENST00000509381.1_Intron|SLC45A2_ENST00000382102.3_Intron	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	NA		NA			developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						ctctctctctctgtgtgtgtg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(31;380 859 8490 22203 49048)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175	51151		Solute carriers	16472	protein-coding gene	gene with protein product		606202	membrane associated transporter	MATP	NA	11916009, 11574907	Standard	NM_016180	NM_001012509	NA	Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.563-5049G>C	chr5.hg19:g.33969170C>G		NA	Q6P2P0|Q9BTM3	hg19	CCDS3901.1	0.02	-0.315751	TCTxTGT	COVERED																																																																																			NOVEL	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207443.2	4	5.111707	KEEP	2	0	0	17	491	CC	0.999366	0.817946	0		-	3	60	95	0	2	6.698867	27	60	871	62	ENST00000296589.4	0.1	0.818465
RP11-1023L17.1	0	__UNKNOWN__	__UNKNOWN__	5	34184617	34184617	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:34184617C>G	ENST00000514048.1	-	0	43										NA		NA									NA						tcaggagttccagaccagcct	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000514048.1:	chr5.hg19:g.34184617C>G		NA		hg19		0.02	1.645681	TTCxAGA	COVERED																																																																																			NOVEL	RP11-1023L17.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000367775.1	19	4.346706	KEEP	8	1	30	25	768	CC	0.999879	0.992805	0		-	5	27	148	1	0	9.797615	53	60	1824	133	ENST00000514048.1	0.086207	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	34525221	34525221	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:34525221A>G			NA	NA				RP11-1023L17.1 (335602 upstream) : CTD-2024P10.2 (126340 downstream)						NA		NA									NA						tgcccgcctcagcctcccaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.34525221A>G		NA		hg19		0.02	-0.271796	CTCxGCC	COVERED																																																																																			NOVEL					0			4	3.609519	KEEP	0	0	0	12	339	AA	0.993634	0.712749	0			3	60	94	0	0	6.645735	26	60	762	63		0.103448	0.717315
RAI14	26064	__UNKNOWN__	__UNKNOWN__	5	34725808	34725808	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:34725808T>C	ENST00000265109.3	+	3	323				RAI14_ENST00000506376.1_Intron|RAI14_ENST00000515799.1_Intron|RAI14_ENST00000428746.2_Intron|RAI14_ENST00000503673.1_Intron|RAI14_ENST00000512629.1_Intron	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	NA		NA				actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					tggtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560	26064		Ankyrin repeat domain containing	14873	protein-coding gene	gene with protein product	novel retinal pigment epithelial	606586			NA	11042181	Standard	NM_015577	NM_015577	NA	Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.37-31765T>C	chr5.hg19:g.34725808T>C		NA	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	hg19	CCDS34142.1	0.02	-0.166633	TCAxGCC	COVERED																																																																																			NOVEL	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366786.1	9	3.307916	KEEP	2	0	0	11	297	TT	0.993072	0.351495	0		+	3	60	103	0	0	8.210174	15	60	435	45	ENST00000265109.3	0.166667	0.353947
RAI14	26064	__UNKNOWN__	__UNKNOWN__	5	34822983	34822983	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:34822983G>A	ENST00000265109.3	+	15	1400				RAI14_ENST00000397449.1_Intron|RAI14_ENST00000506376.1_Intron|RAI14_ENST00000515799.1_Intron|RAI14_ENST00000428746.2_Intron|RAI14_ENST00000503673.1_Intron|RAI14_ENST00000512629.1_Intron	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	NA		NA				actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					tagtagagacggggtttcacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560	26064		Ankyrin repeat domain containing	14873	protein-coding gene	gene with protein product	novel retinal pigment epithelial	606586			NA	11042181	Standard	NM_015577	NM_015577	NA	Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.1114-78G>A	chr5.hg19:g.34822983G>A		NA	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	hg19	CCDS34142.1	0.02	-0.412172	GACxGGG	COVERED																																																																																			NOVEL	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000366786.1	3	3.698272	KEEP	3	3	81	41	1098	GG	1	0.941741	0		+	4	60	123	1	0	8.350741	41	70	1220	103	ENST00000265109.3	0.088889	0.941741
C5orf42	65250	__UNKNOWN__	__UNKNOWN__	5	37225330	37225330	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:37225330G>A	ENST00000508244.1	-	12	2385				C5orf42_ENST00000274258.7_Intron|C5orf42_ENST00000425232.2_Intron			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	NA		NA				integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			cagcctcccaggtagctggga	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603	65250			25801	protein-coding gene	gene with protein product		614571			NA	22264561	Standard	NM_023073	NM_023073	NA	Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.2292-488C>T	chr5.hg19:g.37225330G>A		NA	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	hg19	CCDS34146.2	0.02	-0.175432	CCAxGTA	COVERED																																																																																			NOVEL	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000360806.1	8	2.707147	KEEP	1	0	0	9	269	GG	0.99254	0.384517	0		-	3	60	91	0	1	7.091939	14	60	457	39	ENST00000508244.1	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	37286276	37286276	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:37286276A>G			NA	NA				C5orf42 (36746 upstream) : NUP155 (1962 downstream)						NA		NA									NA						ctggagtgcaatggcacgatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.37286276A>G		NA		hg19		0.02	-0.175406	GCAxTGG	COVERED																																																																																			NOVEL					0			8	2.706509	KEEP	4	0	0	9	243	AA	0.99257	0.384528	0			3	60	106	0	0	8.360712	17	60	494	49		0.15	0.387407
WDR70	55100	__UNKNOWN__	__UNKNOWN__	5	37444725	37444725	__UNKNOWN__	Intron	SNP	A	A	G	rs527364805		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:37444725A>G	ENST00000504564.1	+	7	769				WDR70_ENST00000265107.4_Intron			Q9NW82	WDR70_HUMAN	WD repeat domain 70	NA		NA					enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			gattacaggcatgagccaccg	0.478		NA											A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18680	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068	55100		WD repeat domain containing	25495	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018034	NM_018034	NA	Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000504564.1:c.686+1251A>G	chr5.hg19:g.37444725A>G		NA	Q9H053	hg19		0.02	-0.087674	GGCxTGA	UNCOVERED																																																																																			NOVEL	WDR70-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000368295.1	5	3.30809	KEEP	2	0	0	11	300	AA	0.99254	0.098977	0		+	3	60	104	0	0	9.533568	5	60	138	29	ENST00000504564.1	0.375	0.099721
WDR70	55100	__UNKNOWN__	__UNKNOWN__	5	37583279	37583279	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:37583279G>A	ENST00000504564.1	+	10	1000				WDR70_ENST00000265107.4_Intron|WDR70_ENST00000510699.1_Intron			Q9NW82	WDR70_HUMAN	WD repeat domain 70	NA		NA					enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_lung(31;0.000285)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ctgtaatcccggcactttggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009648	CCDS34147.1	5p13.2	2013-01-09			ENSG00000082068	ENSG00000082068	55100		WD repeat domain containing	25495	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018034	NM_018034	NA	Approved	FLJ10233	uc003jkv.3	Q9NW82	OTTHUMG00000162263	ENST00000504564.1:c.918-21887G>A	chr5.hg19:g.37583279G>A		NA	Q9H053	hg19		0.02	-0.12281	CCCxGCA	COVERED																																																																																			NOVEL	WDR70-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000368295.1	5	3.609395	KEEP	0	0	0	12	345	GG	0.993634	0.195062	0		+	3	60	88	0	0	7.072803	11	60	377	40	ENST00000504564.1	0.214286	0.196312
C9	735	__UNKNOWN__	__UNKNOWN__	5	39331813	39331813	__UNKNOWN__	Silent	SNP	G	G	T	rs146217095		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:39331813G>T	ENST00000263408.4	-	5	675	c.580C>A	c.(580-582)Cga>Aga	p.R194R	C9_ENST00000509186.1_5'UTR	NM_001737.3	NP_001728.1	P02748	CO9_HUMAN	complement component 9	194	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.	NA			complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|hemolysis by symbiont of host erythrocytes (GO:0019836)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane attack complex (GO:0005579)|plasma membrane (GO:0005886)		p.R194R(1)		central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32	all_lung(31;0.000197)	all_neural(839;7.57e-10)|Lung NSC(810;2.62e-08)|Ovarian(839;0.00384)|Breast(839;0.0184)|Myeloproliferative disorder(839;0.0511)	Epithelial(62;0.158)			CAAGGTCTTCGGTAGTATGTC	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - coding silent(1)	lung(1)											167	161	163			NA	NA	5		NA											NA				39331813		2203	4300	6503	SO:0001819	synonymous_variant				CCDS3929.1	5p14-p12	2014-09-17			ENSG00000113600	ENSG00000113600	735		Complement system	1358	protein-coding gene	gene with protein product		120940			NA		Standard		NM_001737	NA	Approved		uc003jlv.4	P02748	OTTHUMG00000094767	ENST00000263408.4:c.580C>A	chr5.hg19:g.39331813G>T		NA		hg19	CCDS3929.1	0.02	-0.429788	TTCxGTA	COVERED																																																																																			NOVEL	C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211576.3	1	3.609624	KEEP	0	0	0	12	345	GG	0.993634	0.948414	0		-	13	60	391	0	0	33.127505	35	60	1115	83	ENST00000263408.4	0.270833	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	39802917	39802917	__UNKNOWN__	IGR	SNP	G	G	A	rs369735990	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:39802917G>A			NA	NA				CTD-2078B5.2 (278107 upstream) : LINC00603 (249475 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.463		NA											G|||	3	0.000599042	0.0023	0.0	5008	,	,	NA	16186	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.39802917G>A		NA		hg19		0.02	-0.157886	CACxCCT	COVERED																																																																																			NOVEL					0			6	3.309845	KEEP	2	0	0	11	337	GG	0.992708	0.320453	0			3	60	93	0	0	7.378957	13	60	416	44		0.1875	0.322807
PRKAA1	5562	__UNKNOWN__	__UNKNOWN__	5	40777792	40777792	__UNKNOWN__	Intron	SNP	T	T	C	rs62357560	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:40777792T>C	ENST00000296800.4	-	2	112				PRKAA1_ENST00000397128.2_Intron|PRKAA1_ENST00000354209.3_Intron			Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	NA		NA			activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[acetyl-CoA carboxylase] kinase activity (GO:0050405)|[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity (GO:0047322)|AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	tcccagcactttgggaggccg	0.383		NA											T|||	275	0.0549121	0.0174	0.062	5008	,	,	NA	16027	0.006	NA	0.167	False	NA	,,,	NA	NA	NA	2504	0.0358	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356	5562			9376	protein-coding gene	gene with protein product	AMPK, alpha, 1	602739			NA	8557660	Standard	NM_006251	XM_006714481	NA	Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000296800.4:c.101-104A>G	chr5.hg19:g.40777792T>C		NA	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	hg19		0.02	-0.140337	ACTxTGG	UNCOVERED																																																																																			NOVEL	PRKAA1-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367373.1	8	2.705963	KEEP	4	0	0	9	238	TT	0	0	0		-	4	60	132	0	0	11.791626	8	60	238	38	ENST00000296800.4	0.333333	0.260965
CARD6	84674	__UNKNOWN__	__UNKNOWN__	5	40860168	40860168	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:40860168C>T	ENST00000381677.3	+	3	985	c.910C>T	c.(910-912)Cgt>Tgt	p.R304C				Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	0		NA			apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						ggattacaggcgtgagccacc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357	84674			16394	protein-coding gene	gene with protein product		609986			NA	12775719	Standard		NM_032587	NA	Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000381677.3:c.910C>T	chr5.hg19:g.40860168C>T	ENSP00000371093:p.Arg304Cys	NA	Q52LR2	hg19		0.02	1.210728	AGGxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.623	-0.820290	0.02755	.	.	ENSG00000132357	ENST00000381677;ENST00000444789	T	0.29917	1.55	0.458	-0.616	0.11583	.	.	.	.	.	T	0.28400	0.0702	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32295	-0.9912	5	0.87932	D	0	.	.	.	.	.	.	.	.	C	304	ENSP00000371093:R304C	ENSP00000371093:R304C	R	+	1	0	CARD6	40895925	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.407000	0.07178	-0.437000	0.07243	-0.439000	0.05793	CGT	NOVEL	CARD6-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367557.1	29	10.695019	KEEP	0	2	49	53	1558	CC	1	0.999804	0		+	5	60	141	1	0	8.435783	73	60	2410	208	ENST00000381677.3	0.064103	0.999804
C7	730	__UNKNOWN__	__UNKNOWN__	5	40982526	40982526	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:40982526A>G	ENST00000313164.9	+	0	3742					NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	NA		NA			cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)					NA		Ovarian(839;0.0112)				gattacagacatgaaccacca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936	730		Complement system	1346	protein-coding gene	gene with protein product		217070			NA		Standard		NM_000587	NA	Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.*851A>G	chr5.hg19:g.40982526A>G		NA	Q6P3T5|Q92489	hg19	CCDS47201.1	0.02	-0.201729	GACxTGA	COVERED																																																																																			NOVEL	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317680.1	4	3.007071	KEEP	0	0	0	10	268	AA	0.992708	0.486967	0		+	3	60	103	0	0	7.926811	19	60	564	45	ENST00000313164.9	0.136364	0.490544
GHR	2690	__UNKNOWN__	__UNKNOWN__	5	42508706	42508706	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:42508706T>C	ENST00000230882.4	+	2	179				GHR_ENST00000357703.3_Intron	NM_000163.4|NM_001242399.2|NM_001242400.2|NM_001242401.3|NM_001242402.2|NM_001242403.2|NM_001242404.2|NM_001242405.2|NM_001242406.2	NP_000154.1|NP_001229328.1|NP_001229329.1|NP_001229330.1|NP_001229331.1|NP_001229332.1|NP_001229333.1|NP_001229334.1|NP_001229335.1	P10912	GHR_HUMAN	growth hormone receptor	NA		NA			2-oxoglutarate metabolic process (GO:0006103)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPK activity (GO:0000187)|allantoin metabolic process (GO:0000255)|cellular response to hormone stimulus (GO:0032870)|citrate metabolic process (GO:0006101)|creatine metabolic process (GO:0006600)|creatinine metabolic process (GO:0046449)|endocytosis (GO:0006897)|fatty acid metabolic process (GO:0006631)|growth hormone receptor signaling pathway (GO:0060396)|insulin-like growth factor receptor signaling pathway (GO:0048009)|isoleucine metabolic process (GO:0006549)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|multicellular organismal metabolic process (GO:0044236)|oxaloacetate metabolic process (GO:0006107)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|receptor internalization (GO:0031623)|regulation of multicellular organism growth (GO:0040014)|response to cycloheximide (GO:0046898)|response to estradiol (GO:0032355)|succinate metabolic process (GO:0006105)|taurine metabolic process (GO:0019530)|valine metabolic process (GO:0006573)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|growth hormone receptor complex (GO:0070195)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine receptor activity (GO:0004896)|growth factor binding (GO:0019838)|peptide hormone binding (GO:0017046)|proline-rich region binding (GO:0070064)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			NS(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	gacggagtcttgctctgtcgc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3940.1, CCDS56364.1, CCDS75239.1, CCDS75240.1	5p14-p12	2013-03-25			ENSG00000112964	ENSG00000112964	2690		Fibronectin type III domain containing	4263	protein-coding gene	gene with protein product	growth hormone binding protein	600946			NA		Standard	NM_000163	NM_001242460	NA	Approved	GHBP	uc003jmt.3	P10912	OTTHUMG00000094791	ENST00000230882.4:c.-11-57260T>C	chr5.hg19:g.42508706T>C		NA	Q9HCX2	hg19	CCDS3940.1	0.02	-0.096479	TCTxGCT	UNCOVERED																																																																																			NOVEL	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211605.2	5	2.406482	KEEP	1	0	0	8	227	TT	0	0	0		+	3	60	102	0	0	8.832633	8	60	233	29	ENST00000230882.4	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	42872243	42872243	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:42872243A>G			NA	NA				SEPP1 (46245 upstream) : CTD-2201E18.5 (134591 downstream)						NA		NA									NA						ggccaggcgcagtggctcacg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.42872243A>G		NA		hg19		0.02	-0.131547	CGCxGTG	COVERED																																																																																			NOVEL					0			5	2.401917	KEEP	0	0	0	8	213	AT	0.99254	0.227464	0			3	60	102	0	0	8.582299	10	60	290	35		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	43112353	43112353	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:43112353C>T			NA	NA				ZNF131 (18693 upstream) : ZNF131 (9256 downstream)						NA		NA									NA						tggtggctcacgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.43112353C>T		NA		hg19		0.02	-0.140334	TCAxGCC	COVERED																																																																																			NOVEL					0			3	3.008442	KEEP	1	0	0	10	295	CC	0.992708	0.259062	0			3	60	84	0	0	6.673338	11	60	361	40		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	43112442	43112442	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:43112442G>A			NA	NA				ZNF131 (18782 upstream) : ZNF131 (9167 downstream)						NA		NA									NA						gtgaaaccccgtctctactaa	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.43112442G>A		NA		hg19		0.02	-0.245615	CCCxTCT	COVERED																																																																																			NOVEL					0			3	3.006958	KEEP	0	0	0	10	269	GG	0.992708	0.63667	0			3	60	92	0	0	6.543191	24	60	789	51		0.111111	0.641347
CCL28	56477	__UNKNOWN__	__UNKNOWN__	5	43381722	43381722	__UNKNOWN__	3'UTR	SNP	G	G	A	rs561321733		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:43381722G>A	ENST00000513525.1	-	0	789				CCL28_ENST00000361115.4_3'UTR			Q9NRJ3	CCL28_HUMAN	chemokine (C-C motif) ligand 28	NA		NA			cell chemotaxis (GO:0060326)|chemotaxis (GO:0006935)|immune response (GO:0006955)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|response to nutrient (GO:0007584)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	chemokine activity (GO:0008009)			kidney(3)|lung(3)|ovary(1)	7						tcagcctcccgaagtgctggg	0.443		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16416	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Esophageal Squamous(178;1549 1997 2043 22794 27051)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF110384	CCDS3944.1	5p12	2013-02-25			ENSG00000151882	ENSG00000151882	56477		Chemokine ligands, Endogenous ligands	17700	protein-coding gene	gene with protein product	CC chemokine CCL28, mucosae-associated epithelial chemokine, small inducible cytokine subfamily A (Cys-Cys), member 28, small inducible cytokine A28	605240			NA	10781587, 11295038	Standard	NM_148672	XR_241707	NA	Approved	SCYA28, MEC, CCK1	uc003jnu.3	Q9NRJ3	OTTHUMG00000094811	ENST00000513525.1:c.*240C>T	chr5.hg19:g.43381722G>A		NA	D7RIE7	hg19		0.02	-0.315722	CCCxAAG	COVERED																																																																																			NOVEL	CCL28-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367999.1	7	4.212129	KEEP	1	0	0	14	418	GG	0.995343	0.814653	0		-	5	60	137	0	0	9.926826	29	60	908	64	ENST00000513525.1	0.147059	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	43938367	43938367	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:43938367T>C			NA	NA				RP11-8L21.1 (51637 upstream) : RNU6-381P (128358 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.43938367T>C		NA		hg19		0.02	-0.175418	TCAxGCC	COVERED																																																																																			NOVEL					0			4	3.007058	KEEP	1	0	0	10	272	TT	0.992708	0.384582	0			3	60	101	0	0	8.09172	14	60	417	49		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	44094632	44094632	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:44094632A>G			NA	NA				RNU6-381P (27799 upstream) : FGF10 (209013 downstream)						NA		NA									NA						cctgacctcaagtgatctgcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.44094632A>G		NA		hg19		0.02	-0.078945	TCAxGTG	UNCOVERED																																																																																			NOVEL					0			3	2.707056	KEEP	0	0	0	9	253	AA	0.99254	0.076759	0			2	60	72	0	0	6.33575	5	60	153	31		0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	50826507	50826507	__UNKNOWN__	IGR	SNP	C	C	T	rs6858981	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:50826507C>T			NA	NA				CTD-2335O3.3 (68584 upstream) : RNA5SP182 (356014 downstream)						NA		NA									NA						aagaacagaacaccaaatcct	0.418		NA											A|||	1074	0.214457	0.1225	0.2925	5008	,	,	NA	18687	0.1845	NA	0.2853	False	NA	,,,	NA	NA	NA	2504	0.2413	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.50826507C>T		NA		hg19		0.02	-0.131555	GAAxACC	COVERED																																																																																			NOVEL					0			2	2.707902	KEEP	0	0	0	9	271	CC	0.992708	0.227502	0			9	60	250	0	0	24.904841	6	60	209	37		0.6	0.229173
ARL15	54622	__UNKNOWN__	__UNKNOWN__	5	53208952	53208952	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:53208952G>A	ENST00000504924.1	-	5	556				ARL15_ENST00000510591.2_Intron|ARL15_ENST00000502271.1_Intron|ARL15_ENST00000507646.2_Intron	NM_019087.2	NP_061960.1	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	NA		NA			small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		Lung NSC(810;0.000779)				aacagagtgagaccccatctc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026093	CCDS54850.1	5p15.2	2014-05-09	2005-11-03	2005-11-03		ENSG00000185305	54622		ADP-ribosylation factors-like, ADP-ribosylation factors	25945	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor related protein 2	ARFRP2	NA	12477932	Standard	NM_019087	NM_019087	NA	Approved	FLJ20051	uc003jpg.1	Q9NXU5		ENST00000504924.1:c.463-26409C>T	chr5.hg19:g.53208952G>A		NA	Q6IAD0	hg19	CCDS54850.1	0.02	-0.096469	TGAxACC	UNCOVERED																																																																																			NOVEL	ARL15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368432.2	6	2.406811	KEEP	0	0	0	8	238	GG	0.99257	0.119541	0		-	3	60	81	0	0	6.732297	8	60	256	25	ENST00000504924.1	0.272727	0.120436
ARL15	54622	__UNKNOWN__	__UNKNOWN__	5	53290907	53290907	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:53290907G>A	ENST00000504924.1	-	5	556				ARL15_ENST00000510591.2_Intron|ARL15_ENST00000502271.1_Intron|ARL15_ENST00000507646.2_Intron	NM_019087.2	NP_061960.1	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	NA		NA			small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		Lung NSC(810;0.000779)				ttgggaggccgaggcaggcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026093	CCDS54850.1	5p15.2	2014-05-09	2005-11-03	2005-11-03		ENSG00000185305	54622		ADP-ribosylation factors-like, ADP-ribosylation factors	25945	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor related protein 2	ARFRP2	NA	12477932	Standard	NM_019087	NM_019087	NA	Approved	FLJ20051	uc003jpg.1	Q9NXU5		ENST00000504924.1:c.463-108364C>T	chr5.hg19:g.53290907G>A		NA	Q6IAD0	hg19	CCDS54850.1	0.02	-0.17542	GCCxAGG	COVERED																																																																																			NOVEL	ARL15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368432.2	7	3.61048	KEEP	4	0	0	12	362	GG	0.992708	0.384582	0		-	3	60	87	0	0	6.872648	12	60	376	49	ENST00000504924.1	0.2	0.387407
SLC38A9	153129	__UNKNOWN__	__UNKNOWN__	5	54938139	54938139	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:54938139T>C	ENST00000512595.1	-	10	1154				SLC38A9_ENST00000416547.2_Intron|SLC38A9_ENST00000318672.3_Intron|SLC38A9_ENST00000515629.1_Intron|SLC38A9_ENST00000539768.1_Intron|SLC38A9_ENST00000396865.2_Intron	NM_001258287.1	NP_001245216.1	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	NA		NA			amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				tcccaaagtgttgggattaca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058	153129		Solute carriers	26907	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173514	NM_173514	NA	Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000512595.1:c.978+3477A>G	chr5.hg19:g.54938139T>C		NA	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	hg19	CCDS58948.1	0.02	-0.140332	GTGxTGG	COVERED																																																																																			NOVEL	SLC38A9-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368275.1	5	3.008272	KEEP	3	0	0	10	288	TT	0.992708	0.259062	0		-	3	60	88	0	0	7.301101	9	60	285	41	ENST00000512595.1	0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	55316152	55316152	__UNKNOWN__	IGR	SNP	C	C	T	rs112269895	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:55316152C>T			NA	NA				CTD-2031P19.3 (16675 upstream) : CTD-2227I18.1 (38724 downstream)						NA		NA									NA						tgcagtgagccgagattgcca	0.517		NA											C|||	840	0.167732	0.0666	0.1643	5008	,	,	NA	13585	0.0665	NA	0.2803	False	NA	,,,	NA	NA	NA	2504	0.2955	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.55316152C>T		NA		hg19		0.02	-0.070175	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			3	2.707885	KEEP	0	0	0	9	272	CC	0.99254	0.053733	0			3	60	94	0	0	8.532702	5	60	161	22		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	55370781	55370781	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:55370781A>T			NA	NA				CTD-2227I18.1 (7582 upstream) : ANKRD55 (24725 downstream)						NA		NA									NA						ccagcctgggagacagagtga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.55370781A>T		NA		hg19		0.02	-0.140321	GGGxGAC	COVERED																																																																																			NOVEL					0			8	4.211159	KEEP	2	0	0	14	395	AA	0.99649	0.260049	0			4	60	113	1	0	9.431131	11	60	331	50		0.266667	0.260965
SETD9	133383	__UNKNOWN__	__UNKNOWN__	5	56209087	56209087	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56209087T>C	ENST00000285947.2	+	3	976				SETD9_ENST00000541720.1_Intron|SETD9_ENST00000475908.1_Intron	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	NA		NA					methyltransferase activity (GO:0008168)				NA						tgctatgttgtccaggctggt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542	133383			28508	protein-coding gene	gene with protein product		NA	chromosome 5 open reading frame 35	C5orf35	NA	20930037	Standard	NM_153706	NM_153706	NA	Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.590+126T>C	chr5.hg19:g.56209087T>C		NA	F5H713	hg19	CCDS3972.1	0.02	-0.350829	TTGxCCA	COVERED																																																																																			NOVEL	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132304.2	10	2.437051	KEEP	0	1	28	18	485	TT	0.99986	0.877585	0		+	4	60	128	0	0	9.206831	33	60	982	80	ENST00000285947.2	0.108108	0.877708
SETD9	133383	__UNKNOWN__	__UNKNOWN__	5	56211958	56211958	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56211958T>C	ENST00000285947.2	+	6	1198				SETD9_ENST00000541720.1_Intron|SETD9_ENST00000475908.1_Intron	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	NA		NA					methyltransferase activity (GO:0008168)				NA						cggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542	133383			28508	protein-coding gene	gene with protein product		NA	chromosome 5 open reading frame 35	C5orf35	NA	20930037	Standard	NM_153706	NM_153706	NA	Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.813-684T>C	chr5.hg19:g.56211958T>C		NA	F5H713	hg19	CCDS3972.1	0.02	-0.359358	TCAxGCC	COVERED																																																																																			NOVEL	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132304.2	5	2.406041	KEEP	4	0	0	8	219	TT	0.99257	0.882271	0		+	3	60	94	0	0	6.314046	34	60	1003	85	ENST00000285947.2	0.081081	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	56389488	56389488	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56389488A>G			NA	NA				MIER3 (121986 upstream) : Y_RNA (75446 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.56389488A>G		NA		hg19		0.02	-0.245431	CACxCCT	COVERED																																																																																			NOVEL					0			12	4.506263	KEEP	3	0	0	15	367	AA	0.995343	0.638361	0			3	60	93	0	0	6.928706	19	60	517	63		0.136364	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	56389504	56389504	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56389504A>C			NA	NA				MIER3 (122002 upstream) : Y_RNA (75430 downstream)						NA		NA									NA						aatcccagcaatttgggaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.56389504A>C		NA		hg19		0.02	-0.236785	GCAxTTT	COVERED																																																																																			NOVEL					0			11	3.307287	KEEP	3	0	0	11	290	AA	0.992708	0.607941	0			3	60	101	0	0	7.72713	19	60	542	54		0.136364	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	56438336	56438336	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56438336T>C			NA	NA				MIER3 (170834 upstream) : Y_RNA (26598 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.56438336T>C		NA		hg19		0.02	-0.236816	GTGxTGG	COVERED																																																																																			NOVEL					0			6	3.006913	KEEP	1	0	0	10	274	TT	0.99254	0.607839	0			4	60	129	0	0	9.96235	22	60	663	54		0.153846	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	56456505	56456505	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56456505C>T			NA	NA				MIER3 (189003 upstream) : Y_RNA (8429 downstream)						NA		NA									NA						tgcagtgagccgagatcgcgc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.56456505C>T		NA		hg19		0.02	-0.210529	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			5	3.008762	KEEP	5	0	0	10	304	CG	0	0	0			3	60	91	0	0	6.727359	19	60	624	56		0.136364	0.522161
GPBP1	65056	__UNKNOWN__	__UNKNOWN__	5	56513616	56513616	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56513616T>A	ENST00000264779.6	+	2	73				GPBP1_ENST00000511209.1_Intron|GPBP1_ENST00000514387.2_Intron|GPBP1_ENST00000506184.2_Intron|GPBP1_ENST00000538707.1_Intron|GPBP1_ENST00000424459.3_Intron|GPBP1_ENST00000454432.2_Intron	NM_001127236.2	NP_001120708.1	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		aggctgaggctggagaatctc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194	65056			29520	protein-coding gene	gene with protein product		608412			NA	12842993	Standard	NM_022913	NM_022913	NA	Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000264779.6:c.64-3587T>A	chr5.hg19:g.56513616T>A		NA	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	hg19	CCDS47211.1	0.02	-0.140339	GGCxGGA	COVERED																																																																																			NOVEL	GPBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368564.2	8	3.007589	KEEP	0	0	0	10	283	TT	0.992708	0.289872	0		+	3	60	94	0	0	7.478916	13	60	398	36	ENST00000264779.6	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	56586501	56586501	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:56586501T>C			NA	NA				GPBP1 (25995 upstream) : CTD-2023N9.1 (104385 downstream)						NA		NA									NA						gattgcgccattggactccag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.56586501T>C		NA		hg19		0.02	-0.324495	CCAxTGG	COVERED																																																																																			NOVEL					0			12	3.307388	KEEP	3	0	0	11	295	TT	0.99254	0.829482	0			3	60	101	0	0	7.167573	30	60	886	71		0.090909	0.835716
RAB3C	115827	__UNKNOWN__	__UNKNOWN__	5	58040962	58040962	__UNKNOWN__	Intron	SNP	C	C	T	rs183437524	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:58040962C>T	ENST00000282878.4	+	3	540				RP11-479O16.1_ENST00000504240.1_RNA|RAB3C_ENST00000507977.1_Intron|RP11-479O16.1_ENST00000509476.1_RNA	NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		cggtggctcacgcctgtaatc	0.542		NA											C|||	3	0.000599042	0.0	0.0043	5008	,	,	NA	14771	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932	115827		RAB, member RAS oncogene	30269	protein-coding gene	gene with protein product		612829			NA	12296628	Standard	NM_138453	NM_138453	NA	Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.371+19015C>T	chr5.hg19:g.58040962C>T		NA		hg19	CCDS3976.1	0.02	-0.166668	TCAxGCC	COVERED																																																																																			NOVEL	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214156.2	1	2.40578	KEEP	1	0	0	8	228	CC	0.99257	0.351317	0		+	3	60	86	0	0	6.679089	13	60	435	45	ENST00000282878.4	0.1875	0.353947
RAB3C	115827	__UNKNOWN__	__UNKNOWN__	5	58151166	58151166	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:58151166T>C	ENST00000282878.4	+	0	4841				CTD-2176I21.2_ENST00000510198.1_RNA	NM_138453.2	NP_612462.1	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|ovary(1)	21		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)		ATCTTCATAGTACTACTGGAA	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY026936	CCDS3976.1	5q13	2008-02-05			ENSG00000152932	ENSG00000152932	115827		RAB, member RAS oncogene	30269	protein-coding gene	gene with protein product		612829			NA	12296628	Standard	NM_138453	NM_138453	NA	Approved		uc003jrp.3	Q96E17	OTTHUMG00000097053	ENST00000282878.4:c.*3988T>C	chr5.hg19:g.58151166T>C		NA		hg19	CCDS3976.1	0.02	-0.411962	TAGxACT	COVERED																																																																																			NOVEL	RAB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214156.2	1	2.705545	KEEP	0	0	0	9	234	TT	0.99254	0.934716	0		+	10	60	320	0	0	26.214788	37	60	1033	74	ENST00000282878.4	0.212766	0.941741
PDE4D	5144	__UNKNOWN__	__UNKNOWN__	5	58459054	58459054	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:58459054T>C	ENST00000507116.1	-	5	752				PDE4D_ENST00000546160.1_Intron|PDE4D_ENST00000405755.2_Intron|PDE4D_ENST00000502575.1_Intron|PDE4D_ENST00000502484.2_Intron|PDE4D_ENST00000503258.1_Intron|PDE4D_ENST00000360047.5_Intron|PDE4D_ENST00000340635.6_Intron	NM_001197218.1	NP_001184147.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	NA		NA			adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	ggattacaggtgtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				5144	3.1.4.17	Phosphodiesterases	8783	protein-coding gene	gene with protein product	phosphodiesterase E3 dunce homolog (Drosophila)	600129	phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)	DPDE3	NA		Standard		NM_006203	NA	Approved		uc003jsa.2	Q08499		ENST00000507116.1:c.616+17366A>G	chr5.hg19:g.58459054T>C		NA	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	hg19	CCDS56373.1	0.02	-0.263086	AGGxGTG	COVERED																																																																																			NOVEL	PDE4D-012	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368103.2	14	4.809754	KEEP	0	0	0	16	426	TT	0.999366	0.716861	0		-	3	50	93	0	0	6.695682	23	60	668	67	ENST00000507116.1	0.115385	0.717315
PDE4D	5144	__UNKNOWN__	__UNKNOWN__	5	58630336	58630336	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:58630336A>G	ENST00000507116.1	-	2	399				PDE4D_ENST00000546160.1_Intron|PDE4D_ENST00000405755.2_Intron|PDE4D_ENST00000502575.1_Intron|PDE4D_ENST00000502484.2_Intron|PDE4D_ENST00000360047.5_Intron|PDE4D_ENST00000340635.6_Intron	NM_001197218.1	NP_001184147.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	NA		NA			adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	tgcccgcctcagcctcccaaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				5144	3.1.4.17	Phosphodiesterases	8783	protein-coding gene	gene with protein product	phosphodiesterase E3 dunce homolog (Drosophila)	600129	phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)	DPDE3	NA		Standard		NM_006203	NA	Approved		uc003jsa.2	Q08499		ENST00000507116.1:c.264-118542T>C	chr5.hg19:g.58630336A>G		NA	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	hg19	CCDS56373.1	0.02	-0.175435	CTCxGCC	UNCOVERED																																																																																			NOVEL	PDE4D-012	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368103.2	7	2.40632	KEEP	2	0	0	8	226	AA	0	0	0		-	3	60	106	0	0	8.432995	16	60	496	42	ENST00000507116.1	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	60005732	60005732	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:60005732A>G			NA	NA				DEPDC1B (9744 upstream) : ELOVL7 (41885 downstream)						NA		NA									NA						gggattacagacatgagccac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.60005732A>G		NA		hg19		0.02	-0.24557	CAGxCAT	COVERED																																																																																			NOVEL					0			11	2.705179	KEEP	0	0	0	9	230	AA	0.99254	0.636563	0			3	60	94	0	0	7.093357	18	60	528	54		0.142857	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	60606122	60606122	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:60606122A>G			NA	NA				CTC-436P18.3 (45366 upstream) : ZSWIM6 (21977 downstream)						NA		NA									NA						tgtaatcccaacattttggga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.60606122A>G		NA		hg19		0.02	-0.210467	CCAxCAT	COVERED																																																																																			NOVEL					0			7	2.40576	KEEP	0	0	0	8	217	AA	0.99257	0.518282	0			3	47	102	0	0	7.764969	20	60	599	43		0.130435	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	60606125	60606125	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:60606125T>C			NA	NA				CTC-436P18.3 (45369 upstream) : ZSWIM6 (21974 downstream)						NA		NA									NA						aatcccaacattttgggaggc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.60606125T>C		NA		hg19		0.02	-0.219265	ACAxTTT	COVERED																																																																																			NOVEL					0			8	2.406484	KEEP	0	0	0	8	226	TT	0.99257	0.54878	0			3	55	92	0	0	6.706792	21	60	631	45		0.125	0.552887
ZSWIM6	57688	__UNKNOWN__	__UNKNOWN__	5	60674646	60674646	__UNKNOWN__	Intron	SNP	C	C	G	rs201098755		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:60674646C>G	ENST00000252744.5	+	1	676					NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	NA		NA			neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						gcctcccaaactgctgggatt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449	57688		Zinc fingers, SWIM-type	29316	protein-coding gene	gene with protein product		615951			NA	10997877, 16427614	Standard	NM_020928	NM_020928	NA	Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.676+45871C>G	chr5.hg19:g.60674646C>G		NA		hg19	CCDS47215.1	0.02	-0.184193	AAAxTGC	UNCOVERED																																																																																			NOVEL	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368710.1	8	2.708125	KEEP	4	0	0	9	282	CC	0	0	0		+	5	60	154	0	0	13.030436	14	60	454	46	ENST00000252744.5	0.263158	0.457757
ZSWIM6	57688	__UNKNOWN__	__UNKNOWN__	5	60801826	60801826	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:60801826A>G	ENST00000252744.5	+	4	1333					NM_020928.1	NP_065979.1	Q9HCJ5	ZSWM6_HUMAN	zinc finger, SWIM-type containing 6	NA		NA			neuron projection morphogenesis (GO:0048812)|regulation of neuron migration (GO:2001222)		zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)	8						acccacctcgacctcccaaag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039438	CCDS47215.1	5q12.1	2011-03-17			ENSG00000130449	ENSG00000130449	57688		Zinc fingers, SWIM-type	29316	protein-coding gene	gene with protein product		615951			NA	10997877, 16427614	Standard	NM_020928	NM_020928	NA	Approved	KIAA1577	uc003jsr.3	Q9HCJ5	OTTHUMG00000162388	ENST00000252744.5:c.1333+11589A>G	chr5.hg19:g.60801826A>G		NA		hg19	CCDS47215.1	0.02	-0.333289	TCGxCCT	COVERED																																																																																			NOVEL	ZSWIM6-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368710.1	8	3.007954	KEEP	2	0	0	10	282	AA	0.99254	0.845628	0		+	3	60	105	1	0	7.48677	32	60	965	76	ENST00000252744.5	0.085714	0.851984
DIMT1	27292	__UNKNOWN__	__UNKNOWN__	5	61694986	61694986	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:61694986A>G	ENST00000199320.4	-	4	401				DIMT1_ENST00000506390.1_Intron|KIF2A_ENST00000509663.2_Intron	NM_014473.2	NP_055288.1	Q9UNQ2	DIM1_HUMAN	DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae)	NA		NA				cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)				NA						gtgaaaccccatctctactaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF102147	CCDS3981.1	5q12.1	2011-08-11	2011-08-11	2011-08-11	ENSG00000086189	ENSG00000086189	27292			30217	protein-coding gene	gene with protein product		612499	DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)	DIMT1L	NA	11124703	Standard	NM_014473	NM_014473	NA	Approved	HSA9761	uc003jta.3	Q9UNQ2	OTTHUMG00000131223	ENST00000199320.4:c.241-278T>C	chr5.hg19:g.61694986A>G		NA	O76025|Q9BU77|Q9UES1	hg19	CCDS3981.1	0.02	-0.350771	CCCxTCT	COVERED																																																																																			NOVEL	DIMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253967.1	10	3.307833	KEEP	2	0	0	11	295	AA	0.993072	0.871627	0		-	4	60	126	0	0	9.007635	33	60	958	69	ENST00000199320.4	0.108108	0.877708
IPO11	51194	__UNKNOWN__	__UNKNOWN__	5	61715867	61715867	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:61715867T>C	ENST00000325324.6	+	1	163				IPO11_ENST00000409296.3_Intron|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	NA		NA			ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		cctgtaatcttagcacttcgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200	51194		Importins	20628	protein-coding gene	gene with protein product		610889			NA		Standard	NM_016338	NM_016338	NA	Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.-7+7111T>C	chr5.hg19:g.61715867T>C		NA	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	hg19	CCDS34167.1	0.02	-0.263109	TCTxAGC	COVERED																																																																																			NOVEL	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335062.1	3	3.308305	KEEP	1	0	0	11	302	TT	0.993072	0.688863	0		+	3	60	103	0	0	7.642409	24	60	696	66	ENST00000325324.6	0.111111	0.693668
IPO11	51194	__UNKNOWN__	__UNKNOWN__	5	61726813	61726813	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:61726813A>T	ENST00000325324.6	+	2	163				IPO11_ENST00000409296.3_Intron|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	NA		NA			ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		gcctggccTTAttttattttt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200	51194		Importins	20628	protein-coding gene	gene with protein product		610889			NA		Standard	NM_016338	NM_016338	NA	Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.-6-6288A>T	chr5.hg19:g.61726813A>T		NA	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	hg19	CCDS34167.1	0.02	-0.23678	CTTxTTT	COVERED																																																																																			NOVEL	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335062.1	14	4.810796	KEEP	1	0	0	16	424	AA	0.99649	0.610258	0		+	4	60	114	0	1	8.695618	19	60	543	57	ENST00000325324.6	0.173913	0.612407
IPO11	51194	__UNKNOWN__	__UNKNOWN__	5	61726818	61726818	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:61726818A>T	ENST00000325324.6	+	2	163				IPO11_ENST00000409296.3_Intron|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	NA		NA			ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		gccTTAttttattttttgaga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200	51194		Importins	20628	protein-coding gene	gene with protein product		610889			NA		Standard	NM_016338	NM_016338	NA	Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.-6-6283A>T	chr5.hg19:g.61726818A>T		NA	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	hg19	CCDS34167.1	0.02	-0.236787	TTTxTTT	COVERED																																																																																			NOVEL	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335062.1	14	4.509356	KEEP	0	0	0	15	392	AA	0.99649	0.610258	0		+	4	60	116	0	0	8.814512	20	60	579	57	ENST00000325324.6	0.166667	0.612407
IPO11	51194	__UNKNOWN__	__UNKNOWN__	5	61743057	61743057	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:61743057T>C	ENST00000325324.6	+	4	408				IPO11_ENST00000409296.3_Intron|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	NA		NA			ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		ctcagcctcctgagtagctgt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200	51194		Importins	20628	protein-coding gene	gene with protein product		610889			NA		Standard	NM_016338	NM_016338	NA	Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.240-2697T>C	chr5.hg19:g.61743057T>C		NA	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	hg19	CCDS34167.1	0.02	-0.114027	TCCxGAG	UNCOVERED																																																																																			NOVEL	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335062.1	8	3.007225	KEEP	0	0	0	10	271	TT	0.992708	0.161282	0		+	3	60	99	0	0	8.401171	9	60	272	29	ENST00000325324.6	0.25	0.162467
IPO11	51194	__UNKNOWN__	__UNKNOWN__	5	61812389	61812389	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:61812389A>G	ENST00000325324.6	+	20	2065				IPO11_ENST00000409296.3_Intron|KIF2A_ENST00000509663.2_Intron	NM_016338.4	NP_057422.3	Q9UI26	IPO11_HUMAN	importin 11	NA		NA			ribosomal protein import into nucleus (GO:0006610)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			endometrium(2)|kidney(3)|large_intestine(5)|lung(14)|skin(4)|stomach(2)	30		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		ccaaagtgctaggattacagg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111109	CCDS34167.1, CCDS47217.1	5q12.1	2008-09-19			ENSG00000086200	ENSG00000086200	51194		Importins	20628	protein-coding gene	gene with protein product		610889			NA		Standard	NM_016338	NM_016338	NA	Approved	RanBP11	uc011cqr.2	Q9UI26	OTTHUMG00000154400	ENST00000325324.6:c.1896+1061A>G	chr5.hg19:g.61812389A>G		NA	A6NGJ5|B4DZ73|D3DW98|Q8N5R2|Q9NSJ6|Q9NVB1	hg19	CCDS34167.1	0.02	-0.184184	GCTxGGA	COVERED																																																																																			NOVEL	IPO11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335062.1	11	2.70715	KEEP	2	0	0	9	254	AA	0.99254	0.420319	0		+	3	60	98	0	0	7.710232	15	60	441	44	ENST00000325324.6	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	62122126	62122126	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:62122126A>C			NA	NA				IPO11 (197717 upstream) : None (None downstream)						NA		NA									NA						tgtcaccaggatggagtgcag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.62122126A>C		NA		hg19		0.02	-0.350816	AGGxTGG	COVERED																																																																																			NOVEL					0			7	4.209482	KEEP	0	0	0	14	369	AA	0.995343	0.87362	0			3	60	100	0	0	6.912317	34	60	1001	88		0.081081	0.877708
SREK1IP1	285672	__UNKNOWN__	__UNKNOWN__	5	64043493	64043493	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64043493C>T	ENST00000513458.4	-	3	229				SREK1IP1_ENST00000506252.1_Intron	NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						cggtggctcacgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006	285672			26716	protein-coding gene	gene with protein product	p18 splicing regulatory protein	NA	SFRS12-interacting protein 1	SFRS12IP1	NA	15456940	Standard	NM_173829	NM_173829	NA	Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.62-6466G>A	chr5.hg19:g.64043493C>T		NA	Q32NC8	hg19	CCDS34171.1	0.02	-0.219304	TCAxGCC	COVERED																																																																																			NOVEL	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368457.4	7	2.707623	KEEP	1	0	0	9	267	CC	0.99257	0.54878	0		-	3	60	90	0	0	7.078924	13	60	425	54	ENST00000513458.4	0.1875	0.552887
SREK1IP1	285672	__UNKNOWN__	__UNKNOWN__	5	64043738	64043738	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64043738T>C	ENST00000513458.4	-	2	229				SREK1IP1_ENST00000506252.1_Intron	NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						ccagcctgggtgacagagcga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006	285672			26716	protein-coding gene	gene with protein product	p18 splicing regulatory protein	NA	SFRS12-interacting protein 1	SFRS12IP1	NA	15456940	Standard	NM_173829	NM_173829	NA	Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.61+6403A>G	chr5.hg19:g.64043738T>C		NA	Q32NC8	hg19	CCDS34171.1	0.02	-0.263103	GGGxGAC	COVERED																																																																																			NOVEL	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368457.4	9	4.508598	KEEP	3	0	0	15	405	TT	0.995343	0.690438	0		-	3	60	102	1	0	7.492389	25	60	727	72	ENST00000513458.4	0.107143	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	64319330	64319330	__UNKNOWN__	IGR	SNP	C	C	G	rs553658464	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64319330C>G			NA	NA				RP11-307L14.2 (2514 upstream) : Y_RNA (99865 downstream)						NA		NA									NA						gtgaaaccctctctctactaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.64319330C>G		NA		hg19		0.02	-0.114044	CCTxTCT	COVERED																																																																																			NOVEL					0			5	3.009208	KEEP	0	0	0	10	316	CC	0.992708	0.19488	0			3	60	98	1	0	8.300912	9	60	313	33		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	64412645	64412645	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64412645A>G			NA	NA				RP11-307L14.2 (95829 upstream) : Y_RNA (6550 downstream)						NA		NA									NA						gtgagccaccacgcccagcct	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.64412645A>G		NA		hg19		0.02	-0.245486	ACCxCGC	COVERED																																																																																			NOVEL					0			10	3.305722	KEEP	2	0	0	11	295	AA	0.993072	0.636904	0			3	60	89	0	0	6.408037	21	60	586	57		0.125	0.641347
PPWD1	23398	__UNKNOWN__	__UNKNOWN__	5	64876611	64876611	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64876611A>G	ENST00000261308.5	+	7	1422				PPWD1_ENST00000535264.1_Intron|PPWD1_ENST00000538977.1_Intron	NM_015342.3	NP_056157.1	Q96BP3	PPWD1_HUMAN	peptidylprolyl isomerase domain and WD repeat containing 1	NA		NA			mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	19		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		Lung(70;0.00451)		aaagtgctggaattacaggcg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025679	CCDS3985.1, CCDS64161.1, CCDS64162.1	5q12.3	2013-01-09			ENSG00000113593	ENSG00000113593	23398		WD repeat domain containing	28954	protein-coding gene	gene with protein product		NA			NA	7584044	Standard	NM_015342	NM_015342	NA	Approved	KIAA0073	uc003jtv.5	Q96BP3	OTTHUMG00000131226	ENST00000261308.5:c.1350+1171A>G	chr5.hg19:g.64876611A>G		NA	B4DWR9|Q15002|Q7KZ89	hg19	CCDS3985.1	0.02	-0.228038	TGGxATT	COVERED																																																																																			NOVEL	PPWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253970.2	10	3.006935	KEEP	0	0	0	10	270	AA	0.992708	0.578679	0		+	3	60	91	0	0	6.550081	22	60	659	48	ENST00000261308.5	0.12	0.58293
TRAPPC13	80006	__UNKNOWN__	__UNKNOWN__	5	64933445	64933445	__UNKNOWN__	Intron	SNP	G	G	A	rs568946646		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64933445G>A	ENST00000399438.3	+	4	560				TRAPPC13_ENST00000545191.1_Intron|TRAPPC13_ENST00000505553.1_Intron|TRAPPC13_ENST00000231526.4_Intron|TRAPPC13_ENST00000438419.2_Intron	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	NA		NA									NA						gtgacagagcgagactctgtc	0.443		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	10917	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597	80006			25828	protein-coding gene	gene with protein product	Trs65-related	NA	chromosome 5 open reading frame 44	C5orf44	NA	12477932	Standard	NM_024941	NM_024941	NA	Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.216-78G>A	chr5.hg19:g.64933445G>A		NA	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	hg19	CCDS47222.1	0.02	1.447377	AGCxAGA	COVERED																																																																																			NOVEL	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370113.1	4	5.141608	KEEP	4	1	28	27	714	GG	0.999988	0.990952	0		+	5	60	140	2	0	9.12051	50	60	1501	106	ENST00000399438.3	0.090909	0.990964
TRAPPC13	80006	__UNKNOWN__	__UNKNOWN__	5	64940618	64940618	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64940618C>G	ENST00000399438.3	+	5	645				TRAPPC13_ENST00000545191.1_Intron|TRAPPC13_ENST00000505553.1_Intron|TRAPPC13_ENST00000231526.4_Intron|TRAPPC13_ENST00000438419.2_Intron	NM_001093755.1|NM_024941.3	NP_001087224.1|NP_079217.2	A5PLN9	TPC13_HUMAN	trafficking protein particle complex 13	NA		NA									NA						tgaggcaggacaatcacttga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47221.1, CCDS47222.1, CCDS47223.1, CCDS58950.1	5q12.3	2013-01-31	2013-01-24	2013-01-24	ENSG00000113597	ENSG00000113597	80006			25828	protein-coding gene	gene with protein product	Trs65-related	NA	chromosome 5 open reading frame 44	C5orf44	NA	12477932	Standard	NM_024941	NM_024941	NA	Approved	FLJ13611, FLJ26957, MGC48585	uc010iwu.1	A5PLN9	OTTHUMG00000163649	ENST00000399438.3:c.301-2264C>G	chr5.hg19:g.64940618C>G		NA	Q17RZ9|Q49A23|Q4JHG0|Q6MZG4|Q8TCM2|Q9H8I3	hg19	CCDS47222.1	0.02	-0.105264	GGAxAAT	UNCOVERED																																																																																			NOVEL	TRAPPC13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370113.1	4	2.407421	KEEP	1	0	0	8	254	CC	0	0	0		+	3	60	88	0	0	7.74303	6	60	207	30	ENST00000399438.3	0.333333	0.139832
SGTB	54557	__UNKNOWN__	__UNKNOWN__	5	64964069	64964069	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:64964069A>T	ENST00000381007.4	-	0	3154					NM_019072.2	NP_061945.1	Q96EQ0	SGTB_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, beta	NA		NA								large_intestine(3)|lung(3)|skin(3)	9		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Ovarian(174;0.0545)|Breast(144;0.174)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0657)|Lung(70;0.00487)		catgagccacagcgcccggcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096321	CCDS3988.1	5q12.3	2013-01-10			ENSG00000197860	ENSG00000197860	54557		Tetratricopeptide (TTC) repeat domain containing	23567	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_019072	XM_005248548	NA	Approved	Sgt2, FLJ39002	uc003jud.3	Q96EQ0	OTTHUMG00000097801	ENST00000381007.4:c.*2004T>A	chr5.hg19:g.64964069A>T		NA		hg19	CCDS3988.1	0.02	4.631646	CACxGCG	COVERED																																																																																			NOVEL	SGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215057.2	39	16.202053	KEEP	0	2	51	72	1975	AA	1	1	0		-	8	60	244	0	0	14.792669	137	60	4101	331	ENST00000381007.4	0.055172	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	65873785	65873785	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:65873785T>C			NA	NA				RP11-5P22.3 (66353 upstream) : MAST4 (18390 downstream)						NA		NA									NA						caagaccagattgggcaacat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.65873785T>C		NA		hg19		0.02	-0.157882	AGAxTGG	COVERED																																																																																			NOVEL					0			5	2.405889	KEEP	0	0	0	8	218	TT	0.99257	0.320408	0			3	60	94	0	0	7.901173	9	60	276	36		0.25	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	66476611	66476611	__UNKNOWN__	IGR	SNP	G	G	A	rs11740538	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:66476611G>A			NA	NA				CTD-2306M10.1 (196 upstream) : CD180 (1491 downstream)						NA		NA									NA						cagatcacttgaggtcaggag	0.507		NA											G|||	617	0.123203	0.0113	0.1729	5008	,	,	NA	15496	0.1141	NA	0.2475	False	NA	,,,	NA	NA	NA	2504	0.1207	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.66476611G>A		NA		hg19		0.02	-0.061394	CTTxAGG	UNCOVERED																																																																																			NOVEL					0			11	3.909213	KEEP	9	0	0	13	380	GG	0.992708	0.043467	0			4	60	112	0	0	11.447682	2	60	68	33		0.666667	0.043787
RP11-83M16.6	0	__UNKNOWN__	__UNKNOWN__	5	67071669	67071669	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:67071669G>A	ENST00000506819.1	-	0	152										NA		NA						p.0?(1)			NA						tgcctgccttggcctcccaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Whole gene deletion(1)	large_intestine(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000506819.1:	chr5.hg19:g.67071669G>A		NA		hg19		0.02	-0.201756	CTTxGCC	COVERED																																																																																			NOVEL	RP11-83M16.6-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000368613.1	9	2.707333	KEEP	0	0	0	9	268	GG	0.99254	0.486885	0		-	3	60	91	0	0	6.861101	17	60	582	45	ENST00000506819.1	0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	67470602	67470602	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:67470602A>G			NA	NA				RNU6-1232P (15628 upstream) : RP11-404L6.2 (15101 downstream)						NA		NA						p.0?(1)			NA						gaccagcctgaccaacatgga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Whole gene deletion(1)	large_intestine(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.67470602A>G		NA		hg19		0.02	-0.114008	CTGxCCA	UNCOVERED																																																																																			NOVEL					0			12	2.702692	KEEP	5	0	0	9	228	AA	0	0	0			3	41	99	0	0	8.678946	7	60	199	28		0.3	0.162467
CTC-340D7.1	0	__UNKNOWN__	__UNKNOWN__	5	68247569	68247569	__UNKNOWN__	lincRNA	SNP	A	A	G	rs6886511	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:68247569A>G	ENST00000503268.1	-	0	377										NA		NA						p.0?(1)			NA						ttgggaggccaaggcgggtgg	0.498		NA											G|||	3145	0.627995	0.8994	0.6254	5008	,	,	NA	16329	0.5655	NA	0.5199	False	NA	,,,	NA	NA	NA	2504	0.4387	NA	NA	NA								NA				1	Whole gene deletion(1)	large_intestine(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000503268.1:	chr5.hg19:g.68247569A>G		NA		hg19		0.02	-0.07892	GCCxAGG	UNCOVERED																																																																																			NOVEL	CTC-340D7.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000368581.1	4	3.609655	KEEP	2	0	0	12	339	AA	0.993072	0.0768	0		-	3	60	94	0	0	8.532952	5	60	145	36	ENST00000503268.1	0.375	0.077336
CDK7	1022	__UNKNOWN__	__UNKNOWN__	5	68542176	68542176	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:68542176A>C	ENST00000256443.3	+	3	229				CDK7_ENST00000502604.1_Intron|CDK7_ENST00000513629.1_Intron|CDK7_ENST00000514676.1_Intron	NM_001799.3	NP_001790.1	P50613	CDK7_HUMAN	cyclin-dependent kinase 7	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|androgen receptor signaling pathway (GO:0030521)|ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA-dependent ATPase activity (GO:0008094)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription coactivator activity (GO:0003713)			endometrium(1)|lung(2)	3		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)		gttggccaggatggtctcgat	0.547		NA						Nucleotide excision repair (NER)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS3999.1	5q12.1	2012-11-05	2007-11-21		ENSG00000134058	ENSG00000134058	1022		Cyclin-dependent kinases, General transcription factor IIH complex subunits	1778	protein-coding gene	gene with protein product		601955	cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk-activating kinase), cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)		NA	8069918	Standard	NM_001799	NM_001799	NA	Approved	CAK1, CDKN7, MO15, STK1, CAK	uc003jvs.4	P50613	OTTHUMG00000099358	ENST00000256443.3:c.127-6069A>C	chr5.hg19:g.68542176A>C		NA	Q9BS60|Q9UE19	hg19	CCDS3999.1	0.02	-0.087714	AGGxTGG	UNCOVERED																																																																																			NOVEL	CDK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216802.3	1	3.308362	KEEP	0	0	0	11	302	AA	0.993072	0.09903	0		+	3	60	102	0	0	8.978672	7	60	214	30	ENST00000256443.3	0.3	0.099721
MARVELD2	153562	__UNKNOWN__	__UNKNOWN__	5	68738941	68738941	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:68738941T>C	ENST00000413223.2	+	0	1541							Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	NA		NA			cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		caggcgtgagtcaccgcgccc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1	1	1			NA	NA	5		NA											NA				68738941		209	164	373	SO:0001624	3_prime_UTR_variant			AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939	153562			26401	protein-coding gene	gene with protein product	tricellulin	610572	MARVEL (membrane-associating) domain containing 2, deafness, autosomal recessive 49	MRVLDC2, DFNB49	NA	17186462	Standard	NM_144724	NM_001038603	NA	Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000413223.2:c.*194T>C	chr5.hg19:g.68738941T>C		NA	A1BQX0|A1BQX1|A8KA97|Q96NM9	hg19		0.02	1.690229	GAGxCAC	COVERED																																																																																			NOVEL	MARVELD2-201	KNOWN	basic	protein_coding	NA	protein_coding		22	3.765986	KEEP	0	5	155	67	1798	TT	1	0.999862	0		+	4	60	136	0	0	8.509527	81	60	2365	243	ENST00000413223.2	0.047059	0.999862
RP11-241G9.3	0	__UNKNOWN__	__UNKNOWN__	5	68783821	68783821	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:68783821T>C	ENST00000514270.1	-	0	93										NA		NA									NA						Gggccgggcgtggtggctcac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000514270.1:	chr5.hg19:g.68783821T>C		NA		hg19		0.02	-0.114022	GCGxGGT	UNCOVERED																																																																																			NOVEL	RP11-241G9.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000369580.1	4	2.706976	KEEP	0	0	0	9	255	TT	0.99254	0.161255	0		-	3	60	106	0	0	9.101277	9	60	269	35	ENST00000514270.1	0.25	0.162467
OCLN	100506658	__UNKNOWN__	__UNKNOWN__	5	68790295	68790295	__UNKNOWN__	Intron	SNP	A	A	G	rs190864783	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:68790295A>G	ENST00000355237.2	+	1	368				OCLN_ENST00000396442.2_Intron|RP11-241G9.3_ENST00000514270.1_RNA|OCLN_ENST00000380766.2_Intron	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	NA		NA			apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		ttacaggcgtaagccaccaca	0.483		NA											A|||	7	0.00139776	0.0053	0.0	5008	,	,	NA	19169	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822	100506658			8104	protein-coding gene	gene with protein product	tight junction protein occludin TM4 minus, phosphatase 1, regulatory subunit 115	602876			NA	8601611	Standard	NM_002538	NM_002538	NA	Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.-69+1809A>G	chr5.hg19:g.68790295A>G		NA	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	hg19	CCDS4006.1	0.02	-0.113973	CGTxAGC	UNCOVERED																																																																																			NOVEL	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216794.1	5	2.40554	KEEP	0	0	0	8	213	AA	0.99257	0.16126	0		+	3	60	101	0	0	8.602051	9	60	249	32	ENST00000355237.2	0.25	0.162467
OCLN	100506658	__UNKNOWN__	__UNKNOWN__	5	68851347	68851347	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:68851347C>T	ENST00000355237.2	+	0	3854					NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	NA		NA			apoptotic process (GO:0006915)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|protein complex assembly (GO:0006461)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethionine metabolic process (GO:0046500)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein domain specific binding (GO:0019904)|structural molecule activity (GO:0005198)|thiopurine S-methyltransferase activity (GO:0008119)			endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		ccatccacctcggcctcccaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822	100506658			8104	protein-coding gene	gene with protein product	tight junction protein occludin TM4 minus, phosphatase 1, regulatory subunit 115	602876			NA	8601611	Standard	NM_002538	NM_002538	NA	Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.*1849C>T	chr5.hg19:g.68851347C>T		NA	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	hg19	CCDS4006.1	0.02	-0.061392	CCTxGGC	UNCOVERED																																																																																			NOVEL	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216794.1	9	2.707451	KEEP	1	0	0	9	262	CC	0.99254	0.04346	0		+	3	49	87	0	0	8.669436	2	60	58	23	ENST00000355237.2	0.6	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	69515726	69515726	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:69515726A>G			NA	NA				SMN2 (142305 upstream) : GTF2H2B (195543 downstream)						NA		NA									NA						ACACAAGCAGAAAGTTCAACA	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.69515726A>G		NA		hg19		0.02	-0.368354	CAGxAAG	UNCOVERED																																																																																			NOVEL					0			4	4.210467	KEEP	50	0	0	14	383	AA	0	0	0			3	21	99	0	0	6.641157	39	24	1181	129		0.071429	0.899314
MRPS27	23107	__UNKNOWN__	__UNKNOWN__	5	71516249	71516249	__UNKNOWN__	3'UTR	SNP	C	C	T	rs111927288	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:71516249C>T	ENST00000261413.5	-	0	1771				MRPS27_ENST00000457646.4_3'UTR	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	NA		NA				mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		taaaggaggccgaggcaggag	0.507		NA											C|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	18709	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048	23107		Mitochondrial ribosomal proteins / small subunits	14512	protein-coding gene	gene with protein product		611989			NA		Standard	NM_015084	NM_015084	NA	Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.*487G>A	chr5.hg19:g.71516249C>T		NA	B4DRT2|Q6P1S1	hg19	CCDS4013.1	0.02	1.249825	GGCxGAG	COVERED																																																																																			NOVEL	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000218560.2	21	9.158659	KEEP	2	1	30	41	1211	CC	1	0.990964	0		-	5	60	126	0	0	7.574219	54	60	1686	148	ENST00000261413.5	0.084746	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	72235262	72235262	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:72235262T>C			NA	NA				TNPO1 (22702 upstream) : CTD-2376I4.1 (14199 downstream)						NA		NA									NA						aggccaggcgtggtggctcat	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.72235262T>C		NA		hg19		0.02	-0.149088	GCGxGGT	COVERED																																																																																			NOVEL					0			12	4.208213	KEEP	1	0	0	14	359	TT	0.994391	0.290363	0			3	60	100	0	0	8.079	13	60	380	39		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	72244746	72244746	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:72244746T>C			NA	NA				TNPO1 (32186 upstream) : CTD-2376I4.1 (4715 downstream)						NA		NA									NA						cggggtttcatcatgttgccc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.72244746T>C		NA		hg19		0.02	-0.184152	TCAxCAT	COVERED																																																																																			NOVEL					0			4	2.705457	KEEP	0	0	0	9	233	TT	0.99254	0.420319	0			3	60	94	0	0	7.310617	15	60	420	34		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	72839037	72839037	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:72839037A>C			NA	NA				BTF3 (37577 upstream) : ANKRA2 (9122 downstream)						NA		NA									NA						atgccattgcactccagcctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.72839037A>C		NA		hg19		0.02	-0.14034	TGCxCTC	COVERED																																																																																			NOVEL					0			5	3.910109	KEEP	1	0	0	13	361	AA	0.994391	0.259501	0			3	52	106	0	0	8.772121	12	60	363	49		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	74182236	74182236	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:74182236G>A			NA	NA				SNORA40 (3628 upstream) : CTD-2503O16.4 (31314 downstream)						NA		NA									NA						aggccgaggcgggcggatcac	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.74182236G>A		NA		hg19		0.02	-0.157875	GGCxGGC	COVERED																																																																																			NOVEL					0			7	3.340705	KEEP	19	1	25	20	586	GG	0.993634	0.320751	0			4	24	121	0	0	9.981132	13	60	409	71		0.235294	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	74613951	74613951	__UNKNOWN__	IGR	SNP	C	C	T	rs373619752		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:74613951C>T			NA	NA				ANKRD31 (81248 upstream) : CTD-2235C13.2 (2028 downstream)						NA		NA									NA						tccttccttccttccttcctt	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.74613951C>T		NA		hg19		0.02	-0.166649	TTCxTTC	UNCOVERED																																																																																			NOVEL					0			11	2.406753	KEEP	7	0	0	8	239	CC	0	0	0			4	40	109	0	1	8.901417	12	60	380	36		0.25	0.353947
SV2C	22987	__UNKNOWN__	__UNKNOWN__	5	75649000	75649000	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:75649000C>G	ENST00000322285.7	+	0	2246							Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	NA		NA			neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		gaactcctggcctcaagcaat	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012	22987			30670	protein-coding gene	gene with protein product		610291			NA	10470851, 9801366	Standard		XM_005248470	NA	Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000322285.7:c.*15C>G	chr5.hg19:g.75649000C>G		NA	Q496K1|Q9UPU8	hg19		0.02	-0.236847	TGGxCTC	COVERED																																																																																			NOVEL	SV2C-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000368701.1	5	4.144533	KEEP	0	1	29	24	706	CC	0.999931	0.612365	0		+	3	60	97	0	0	7.326945	19	70	626	55	ENST00000322285.7	0.136364	0.612407
IQGAP2	10788	__UNKNOWN__	__UNKNOWN__	5	75792911	75792911	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:75792911T>C	ENST00000274364.6	+	2	443				IQGAP2_ENST00000379730.3_Intron	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	NA		NA			negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		cctcagcctctcaaagtgctg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703	10788			6111	protein-coding gene	gene with protein product		605401			NA	8756646	Standard	NM_006633	XM_005248409	NA	Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.146+35417T>C	chr5.hg19:g.75792911T>C		NA	A8K4V1|B7Z8A4|J3KR91	hg19	CCDS34188.1	0.02	-0.157858	CTCxCAA	UNCOVERED																																																																																			NOVEL	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368877.1	6	3.007856	KEEP	5	0	0	10	279	TT	0	0	0		+	3	60	99	0	0	8.072173	12	60	370	47	ENST00000274364.6	0.2	0.322807
IQGAP2	10788	__UNKNOWN__	__UNKNOWN__	5	75816264	75816264	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:75816264A>G	ENST00000274364.6	+	3	443				IQGAP2_ENST00000379730.3_Intron	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	NA		NA			negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		tgggattacaagcgtgagcca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703	10788			6111	protein-coding gene	gene with protein product		605401			NA	8756646	Standard	NM_006633	XM_005248409	NA	Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.147-41957A>G	chr5.hg19:g.75816264A>G		NA	A8K4V1|B7Z8A4|J3KR91	hg19	CCDS34188.1	0.02	-0.122792	ACAxGCG	COVERED																																																																																			NOVEL	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368877.1	5	2.406141	KEEP	0	0	0	8	222	AA	0.99257	0.22747	0		+	3	60	98	0	0	8.18208	10	60	295	32	ENST00000274364.6	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	76091566	76091566	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:76091566T>C			NA	NA				snoU13 (11542 upstream) : F2RL1 (23235 downstream)						NA		NA									NA						tttgggaggctgaggtgggag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.76091566T>C		NA		hg19		0.02	-0.035086	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			4	2.406203	KEEP	0	0	0	8	223	TT	0.99257	0.019833	0			2	60	66	0	0	6.350169	2	60	59	17		0.5	0.019982
PDE8B	8622	__UNKNOWN__	__UNKNOWN__	5	76617223	76617223	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:76617223A>G	ENST00000264917.5	+	3	444				PDE8B_ENST00000342343.4_Intron|PDE8B_ENST00000333194.4_Intron|PDE8B_ENST00000340978.3_Intron|PDE8B_ENST00000346042.3_Intron	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	NA		NA			cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	tgatccacccaccttggcctc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	8622	3.1.4.17	Phosphodiesterases	8794	protein-coding gene	gene with protein product		603390			NA	9784418	Standard	NM_003719	NM_003719	NA	Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.400-4141A>G	chr5.hg19:g.76617223A>G		NA	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	hg19	CCDS4037.1	0.02	-0.043862	CCCxCCT	UNCOVERED																																																																																			NOVEL	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000220015.3	7	3.306923	KEEP	2	0	0	11	287	AA	0.992708	0.023898	0		+	2	60	67	0	0	6.450036	2	60	64	24	ENST00000264917.5	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	78023145	78023145	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:78023145A>G			NA	NA				LHFPL2 (78497 upstream) : ARSB (49886 downstream)						NA		NA									NA						gtgacagagcaagactccatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.78023145A>G		NA		hg19		0.02	-0.15783	AGCxAGA	COVERED																																																																																			NOVEL					0			15	4.811633	KEEP	7	0	0	16	436	AA	0.997832	0.322107	0			3	60	94	1	0	7.57287	12	60	347	55		0.2	0.322807
SERINC5	256987	__UNKNOWN__	__UNKNOWN__	5	79487220	79487220	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:79487220A>G	ENST00000512721.1	-	2	352				SERINC5_ENST00000512972.2_Intron|SERINC5_ENST00000507668.2_Intron|SERINC5_ENST00000513907.1_Intron|SERINC5_ENST00000509193.1_Intron	NM_001174072.1	NP_001167543.1	Q86VE9	SERC5_HUMAN	serine incorporator 5	NA		NA			myelination (GO:0042552)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(3)|kidney(1)|lung(3)|ovary(1)	8		Lung NSC(167;0.00328)|all_lung(232;0.00356)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;2.93e-46)|Epithelial(54;5.59e-40)|all cancers(79;1.89e-34)		agcactttggaaggctgaggc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF498273	CCDS54874.1	5q14.1	2014-01-28	2005-10-14	2005-10-14		ENSG00000164300	256987			18825	protein-coding gene	gene with protein product		614551	chromosome 5 open reading frame 12	C5orf12	NA	12688535	Standard	NM_178276	NM_178276	NA	Approved	TPO1	uc011ctj.2	Q86VE9		ENST00000512721.1:c.195+11484T>C	chr5.hg19:g.79487220A>G		NA	B4DMH7|Q495A4|Q495A6	hg19	CCDS54874.1	0.02	-0.140321	TGGxAGG	COVERED																																																																																			NOVEL	SERINC5-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369572.1	12	3.00794	KEEP	0	0	0	10	280	AA	0.992708	0.259062	0		-	3	43	94	0	0	7.572519	12	60	354	31	ENST00000512721.1	0.2	0.260965
ZCCHC9	84240	__UNKNOWN__	__UNKNOWN__	5	80604818	80604818	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:80604818A>G	ENST00000254037.2	+	3	3744	c.589A>G	c.(589-591)Aga>Gga	p.R197G	ZCCHC9_ENST00000438268.2_Missense_Mutation_p.R197G|ZCCHC9_ENST00000380199.5_Missense_Mutation_p.R197G|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000407610.3_Missense_Mutation_p.R197G			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	197		NA			negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		GCACCTGTCTAGATCTTGTCC	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													124	111	115			NA	NA	5		NA											NA				80604818		2203	4300	6503	SO:0001583	missense			BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732	84240		Zinc fingers, CCHC domain containing, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	25424	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 41	NA			NA	12477932	Standard	NM_032280	NM_032280	NA	Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.589A>G	chr5.hg19:g.80604818A>G	ENSP00000254037:p.Arg197Gly	NA	B2RAE7|Q9H027	hg19	CCDS4054.1	0.02	-0.412255	TCTxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	A	14.58	2.579147	0.46006	.	.	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	5.82	1.99	0.26369	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (3);	0.087968	0.64402	N	0.000001	T	0.61123	0.2322	M	0.92738	3.34	0.47511	D	0.999449	B	0.20988	0.05	B	0.28784	0.094	T	0.60120	-0.7325	10	0.72032	D	0.01	-20.3565	9.3317	0.38025	0.4394:0.4925:0.0681:0.0	.	197	Q8N567	ZCHC9_HUMAN	G	197	ENSP00000254037:R197G;ENSP00000385047:R197G;ENSP00000369546:R197G;ENSP00000412637:R197G	ENSP00000254037:R197G	R	+	1	2	ZCCHC9	80640574	0.982000	0.34865	0.991000	0.47740	0.975000	0.68041	2.244000	0.43124	0.102000	0.17638	0.533000	0.62120	AGA	NOVEL	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239213.1	1	3.007263	KEEP	0	0	0	10	272	AA	0.992708	0.934874	0		+	20	60	684	0	0	64.266736	26	60	779	81	ENST00000254037.2	0.434783	0.941741
SSBP2	23635	__UNKNOWN__	__UNKNOWN__	5	80977102	80977102	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:80977102A>G	ENST00000320672.4	-	2	273				SSBP2_ENST00000505980.1_Intron|SSBP2_ENST00000514493.1_Intron|SSBP2_ENST00000509053.1_Intron|SSBP2_ENST00000515395.1_Intron	NM_001256732.1|NM_001256733.1|NM_012446.3	NP_001243661.1|NP_001243662.1|NP_036578.2	P81877	SSBP2_HUMAN	single-stranded DNA binding protein 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)		SSBP2/JAK2(4)	central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10		Lung NSC(167;0.00154)|all_lung(232;0.00179)|Ovarian(174;0.0338)		OV - Ovarian serous cystadenocarcinoma(54;1.07e-41)|Epithelial(54;2.79e-35)|all cancers(79;1.18e-29)		actttgggagaccgaggaggg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF077048	CCDS4056.1, CCDS58960.1, CCDS58961.1, CCDS58962.1, CCDS58963.1, CCDS75268.1	5q14.1	2012-05-25	2001-11-28		ENSG00000145687	ENSG00000145687	23635			15831	protein-coding gene	gene with protein product		607389	single-stranded DNA-binding protein 2		NA	11230166, 11042152	Standard	NM_012446	NM_001256732	NA	Approved	HSPC116	uc003khp.4	P81877	OTTHUMG00000119039	ENST00000320672.4:c.63-30944T>C	chr5.hg19:g.80977102A>G		NA	B2R5W1|B7Z1J2|B7Z2L9|B7Z665|D6RH18|E9PB74|E9PDA8|Q8N2Q2|Q9BWW6|Q9Y4T7	hg19	CCDS4056.1	0.02	-0.122746	GAGxCCG	COVERED																																																																																			NOVEL	SSBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239249.1	3	3.007958	KEEP	2	0	0	10	281	AA	0.99254	0.194847	0		-	3	60	93	0	0	7.573581	11	60	317	41	ENST00000320672.4	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	81122951	81122951	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:81122951T>C			NA	NA				SSBP2 (75879 upstream) : CTD-2249K22.1 (24468 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.81122951T>C		NA		hg19		0.02	-0.078873	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			6	2.702613	KEEP	1	0	0	9	228	TT	0.99257	0.076761	0			3	60	87	0	0	8.051197	4	60	112	23		0.428571	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	82690692	82690692	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:82690692A>G			NA	NA				XRCC4 (41086 upstream) : VCAN (76591 downstream)						NA		NA									NA						tgggattacaagcgtgagcca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.82690692A>G		NA		hg19		0.02	-0.043856	ACAxGCG	UNCOVERED																																																																																			NOVEL					0			4	2.706956	KEEP	3	0	0	9	249	AA	0.99257	0.023895	0			3	60	105	0	0	10.470409	2	60	58	25		0.6	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	89056617	89056617	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:89056617C>T			NA	NA				RP11-116A1.1 (83099 upstream) : AC113167.1 (139863 downstream)						NA		NA									NA						tgccaccacgcccagctaatt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.89056617C>T		NA		hg19		0.02	-0.052635	ACGxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.707902	KEEP	5	0	0	9	272	CC	0.99257	0.036492	0			2	30	62	0	0	6.324479	1	20	34	28		0.666667	0.036766
GPR98	84059	__UNKNOWN__	__UNKNOWN__	5	89942880	89942880	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:89942880C>T	ENST00000405460.2	+	17	3118					NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	NA		NA			detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		tgagccactgcgcccagccTG	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199	84059		-, GPCR / Class B : Orphans	17416	protein-coding gene	gene with protein product		602851	monogenic, audiogenic seizure susceptibility 1 homolog (mouse)	USH2C, MASS1	NA	10976914, 14740321	Standard	NM_032119	NM_032119	NA	Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3023-435C>T	chr5.hg19:g.89942880C>T		NA	O75171|Q8TF58|Q9H0X5|Q9UL61	hg19	CCDS47246.1	0.02	-0.157897	CTGxGCC	COVERED																																																																																			NOVEL	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000369993.2	4	2.706923	KEEP	2	0	0	9	253	CC	0.99257	0.320408	0		+	3	60	93	0	0	7.291756	14	60	462	42	ENST00000405460.2	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	90565556	90565556	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:90565556A>G			NA	NA				RP11-414H23.3 (42668 upstream) : RNU4-90P (987 downstream)						NA		NA									NA						ccaaagtgctaggattatagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.90565556A>G		NA		hg19		0.02	-0.192948	GCTxGGA	COVERED																																																																																			NOVEL					0			2	3.604907	KEEP	0	0	0	12	301	AA	0.993634	0.454842	0			3	60	97	0	0	7.533549	16	60	466	43		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	90565563	90565563	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:90565563T>C			NA	NA				RP11-414H23.3 (42675 upstream) : RNU4-90P (980 downstream)						NA		NA									NA						gctaggattataggcgtgagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.90565563T>C		NA		hg19		0.02	-0.192772	TTAxAGG	COVERED																																																																																			NOVEL					0			2	3.907531	KEEP	0	0	0	13	330	TT	0.994391	0.455189	0			3	60	103	0	0	8.134934	16	60	430	42		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	90870415	90870415	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:90870415A>G			NA	NA				ARRDC3 (191239 upstream) : RP11-348J24.2 (624938 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.90870415A>G		NA		hg19		0.02	-0.236779	CACxCCT	UNCOVERED																																																																																			NOVEL					0			11	2.706101	KEEP	4	0	0	9	240	AA	0	0	0			3	60	103	0	0	7.927048	19	60	548	45		0.136364	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	91229824	91229824	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:91229824C>T			NA	NA				ARRDC3 (550648 upstream) : RP11-348J24.2 (265529 downstream)						NA		NA									NA						ccgaggcgggcggatcacgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.91229824C>T		NA		hg19		0.02	-0.122677	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			4	2.706089	KEEP	8	0	0	9	237	CC	0	0	0			3	42	92	0	0	7.583625	10	60	262	42		0.230769	0.196312
RP11-348J24.2	0	__UNKNOWN__	__UNKNOWN__	5	91629443	91629443	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:91629443A>G	ENST00000502934.1	+	0	328										NA		NA									NA						gattacaggcatgagcctcca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502934.1:	chr5.hg19:g.91629443A>G		NA		hg19		0.02	-0.131549	GGCxTGA	COVERED																																																																																			NOVEL	RP11-348J24.2-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000369755.1	7	2.406076	KEEP	0	0	0	8	222	AA	0.99257	0.22747	0		+	3	60	101	0	0	8.37313	11	60	317	36	ENST00000502934.1	0.214286	0.229173
CTD-2091N23.1	0	__UNKNOWN__	__UNKNOWN__	5	92397612	92397612	__UNKNOWN__	lincRNA	SNP	T	T	C	rs58430736	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:92397612T>C	ENST00000515153.1	-	0	44										NA		NA									NA						tggtggctcatgcctgtaatc	0.502		NA											C|||	1535	0.30651	0.3449	0.353	5008	,	,	NA	16811	0.371	NA	0.2604	False	NA	,,,	NA	NA	NA	2504	0.2025	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000515153.1:	chr5.hg19:g.92397612T>C		NA		hg19		0.02	-0.201721	TCAxGCC	COVERED																																																																																			NOVEL	CTD-2091N23.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000370024.1	5	3.007731	KEEP	2	0	0	10	278	TT	0.99254	0.486885	0		-	3	60	97	0	0	7.533512	16	60	461	50	ENST00000515153.1	0.157895	0.490544
FAM172A	83989	__UNKNOWN__	__UNKNOWN__	5	93053886	93053886	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:93053886A>G	ENST00000395965.3	-	10	1251				FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000509739.1_Intron|FAM172A_ENST00000505869.1_Intron	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	NA		NA				endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						ggtggctcacacctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391	83989			25365	protein-coding gene	gene with protein product		NA	chromosome 5 open reading frame 21	C5orf21	NA	11230166	Standard	NM_032042	NM_032042	NA	Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.1108+57978T>C	chr5.hg19:g.93053886A>G		NA	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	hg19	CCDS4069.1	0.02	-0.192897	CACxCCT	COVERED																																																																																			NOVEL	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254100.3	9	3.007639	KEEP	3	0	0	10	277	AA	0.99257	0.454356	0		-	3	60	89	0	0	6.528297	19	60	528	49	ENST00000395965.3	0.136364	0.457757
FAM172A	83989	__UNKNOWN__	__UNKNOWN__	5	93427795	93427795	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:93427795A>G	ENST00000395965.3	-	2	125				FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000505869.1_Intron	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	NA		NA				endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						agtggctcacacctgtaatcc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391	83989			25365	protein-coding gene	gene with protein product		NA	chromosome 5 open reading frame 21	C5orf21	NA	11230166	Standard	NM_032042	NM_032042	NA	Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.18-17321T>C	chr5.hg19:g.93427795A>G		NA	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	hg19	CCDS4069.1	0.02	-0.149093	CACxCCT	COVERED																																																																																			NOVEL	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254100.3	7	2.406597	KEEP	0	0	0	8	230	AT	0.99254	0.289823	0		-	4	60	127	0	0	10.83146	11	60	324	35	ENST00000395965.3	0.266667	0.292001
KIAA0825	285600	__UNKNOWN__	__UNKNOWN__	5	93720018	93720018	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:93720018G>A	ENST00000513200.3	-	19	3783				KIAA0825_ENST00000427991.2_Intron	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	NA		NA								breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						acacacacacgcacacacaca	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													123	100	107			NA	NA	5		NA											NA				93720018		692	1591	2283	SO:0001627	intron_variant			BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261	285600			28532	protein-coding gene	gene with protein product		NA	chromosome 5 open reading frame 36	C5orf36	NA	12477932	Standard	NM_173665	NM_173665	NA	Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3710+54C>T	chr5.hg19:g.93720018G>A		NA	O94914|Q6ZNN2	hg19		0.02	1.113911	CACxCAC	COVERED																																																																																			NOVEL	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000254102.5	22	6.142074	KEEP	0	4	112	60	1726	GG	1	0.999962	0		-	9	60	266	0	0	18.022687	85	60	2887	231	ENST00000513200.3	0.095745	0.999962
MCTP1	79772	__UNKNOWN__	__UNKNOWN__	5	94171874	94171874	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:94171874G>C	ENST00000515393.1	-	17	2436				MCTP1_ENST00000505078.1_Intron|MCTP1_ENST00000429576.2_Intron|MCTP1_ENST00000312216.8_Intron	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	NA		NA			calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		aacagagcaagactccgtctc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471	79772			26183	protein-coding gene	gene with protein product		NA			NA	15528213	Standard	NM_024717	XM_005272082	NA	Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2436+32163C>G	chr5.hg19:g.94171874G>C		NA	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	hg19	CCDS34203.1	0.02	-0.131586	CAAxACT	COVERED																																																																																			NOVEL	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370280.3	17	2.239959	KEEP	14	1	21	15	477	GG	0.992708	0.227502	0		-	3	33	96	0	0	8.232155	8	60	279	40	ENST00000515393.1	0.272727	0.229173
MCTP1	79772	__UNKNOWN__	__UNKNOWN__	5	94171880	94171880	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:94171880G>A	ENST00000515393.1	-	17	2436				MCTP1_ENST00000505078.1_Intron|MCTP1_ENST00000429576.2_Intron|MCTP1_ENST00000312216.8_Intron	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	NA		NA			calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		gcaagactccgtctcaaaaaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471	79772			26183	protein-coding gene	gene with protein product		NA			NA	15528213	Standard	NM_024717	XM_005272082	NA	Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2436+32157C>T	chr5.hg19:g.94171880G>A		NA	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	hg19	CCDS34203.1	0.02	-0.131569	TCCxTCT	COVERED																																																																																			NOVEL	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370280.3	17	5.11343	KEEP	14	0	0	17	486	GG	0.993072	0.227586	0		-	3	33	93	0	0	7.932447	8	60	250	42	ENST00000515393.1	0.272727	0.229173
MCTP1	79772	__UNKNOWN__	__UNKNOWN__	5	94181306	94181306	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:94181306A>G	ENST00000515393.1	-	17	2436				MCTP1_ENST00000505078.1_Intron|MCTP1_ENST00000429576.2_Intron|MCTP1_ENST00000312216.8_Intron	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	NA		NA			calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		ctggagtgcaatggcatgatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471	79772			26183	protein-coding gene	gene with protein product		NA			NA	15528213	Standard	NM_024717	XM_005272082	NA	Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2436+22731T>C	chr5.hg19:g.94181306A>G		NA	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	hg19	CCDS34203.1	0.02	-0.184199	GCAxTGG	COVERED																																																																																			NOVEL	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370280.3	3	2.706881	KEEP	0	0	0	9	248	AA	0.99254	0.420319	0		-	3	60	104	0	0	8.23311	16	60	485	47	ENST00000515393.1	0.157895	0.423478
RFESD	317671	__UNKNOWN__	__UNKNOWN__	5	94986558	94986558	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:94986558A>T	ENST00000311364.4	+	2	1221				RFESD_ENST00000380005.4_Intron|RFESD_ENST00000458310.1_Intron	NM_173362.3	NP_775498.1	Q8TAC1	RFESD_HUMAN	Rieske (Fe-S) domain containing	NA		NA					2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			autonomic_ganglia(2)|endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	6		all_cancers(142;0.000215)|all_epithelial(76;7.43e-07)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)|Colorectal(57;0.162)		all cancers(79;5.94e-17)		atcccagcacattgggaggcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035110	CCDS4075.1, CCDS47248.1	5q15	2010-12-07			ENSG00000175449	ENSG00000175449	317671			29587	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173362	NM_173362	NA	Approved		uc003klg.3	Q8TAC1	OTTHUMG00000121168	ENST00000311364.4:c.-196-1283A>T	chr5.hg19:g.94986558A>T		NA	J3KPH1	hg19	CCDS4075.1	0.02	-0.140338	CACxTTG	COVERED																																																																																			NOVEL	RFESD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000241654.1	8	3.007831	KEEP	0	0	0	10	279	AA	0.992708	0.259062	0		+	3	60	85	0	0	6.773074	11	60	341	38	ENST00000311364.4	0.214286	0.260965
RHOBTB3	22836	__UNKNOWN__	__UNKNOWN__	5	95128246	95128246	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:95128246T>C	ENST00000379982.3	+	12	2228				GLRX_ENST00000507605.1_Intron|RHOBTB3_ENST00000504179.1_Intron|GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	NA		NA			ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		cctgtaatcctagcactttgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292	22836		BTB/POZ domain containing	18757	protein-coding gene	gene with protein product		607353			NA	11222756, 17035353	Standard	NM_014899	NM_014899	NA	Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.1721-517T>C	chr5.hg19:g.95128246T>C		NA	A0PJA4|A8K1W9|Q8IW06	hg19	CCDS4077.1	0.02	-0.140343	TCCxAGC	COVERED																																																																																			NOVEL	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000241658.1	6	3.007448	KEEP	3	0	0	10	275	TT	0.99254	0.259018	0		+	3	58	96	0	0	7.872897	11	60	339	41	ENST00000379982.3	0.214286	0.260965
RHOBTB3	22836	__UNKNOWN__	__UNKNOWN__	5	95130763	95130763	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:95130763A>G	ENST00000379982.3	+	0	4229				GLRX_ENST00000507605.1_Intron|GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	NA		NA			ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		ccgagatcgcaccactgcact	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292	22836		BTB/POZ domain containing	18757	protein-coding gene	gene with protein product		607353			NA	11222756, 17035353	Standard	NM_014899	NM_014899	NA	Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.*1885A>G	chr5.hg19:g.95130763A>G		NA	A0PJA4|A8K1W9|Q8IW06	hg19	CCDS4077.1	0.02	-0.298187	CGCxCCA	UNCOVERED																																																																																			NOVEL	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000241658.1	7	2.706422	KEEP	2	0	0	9	243	AA	0	0	0		+	3	33	91	0	0	6.550269	22	60	642	52	ENST00000379982.3	0.12	0.800245
CTD-2337A12.1	0	__UNKNOWN__	__UNKNOWN__	5	95661404	95661404	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:95661404A>G	ENST00000502645.2	+	0	267										NA		NA									NA						ggctggtctcaaactcctaag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502645.2:	chr5.hg19:g.95661404A>G		NA		hg19		0.02	-0.122768	CTCxAAC	COVERED																																																																																			NOVEL	CTD-2337A12.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000370533.1	3	2.405515	KEEP	0	0	0	8	213	AA	0.99257	0.194853	0		+	3	60	93	0	0	7.573312	11	60	320	30	ENST00000502645.2	0.214286	0.196312
CAST	831	__UNKNOWN__	__UNKNOWN__	5	96058807	96058807	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:96058807C>T	ENST00000510756.1	+	4	270				CAST_ENST00000511782.1_Intron|CAST_ENST00000341926.3_Intron|CAST_ENST00000338252.3_Intron|CAST_ENST00000508830.1_Intron|CAST_ENST00000395813.1_Intron|CAST_ENST00000359176.4_Intron|CAST_ENST00000508608.1_Intron|CAST_ENST00000504465.1_Intron|CAST_ENST00000511049.1_Intron|CAST_ENST00000325674.7_Intron|CAST_ENST00000395812.2_Intron|CAST_ENST00000309190.5_Intron|CAST_ENST00000509903.1_Intron			P20810	ICAL_HUMAN	calpastatin	NA		NA			negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		ccaccatgcccggctaattgt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113	831			1515	protein-coding gene	gene with protein product		114090			NA	8340353, 14685690, 15820218	Standard	NM_173062	NM_173060	NA	Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000510756.1:c.270+405C>T	chr5.hg19:g.96058807C>T		NA	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	hg19	CCDS54882.1	0.02	-0.140342	GCCxGGC	COVERED																																																																																			NOVEL	CAST-010	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370546.1	9	5.113975	KEEP	2	0	0	17	495	CC	0.997832	0.260399	0		+	3	60	92	0	0	7.47289	11	60	345	45	ENST00000510756.1	0.214286	0.260965
CTD-2260A17.2	0	__UNKNOWN__	__UNKNOWN__	5	96208651	96208651	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:96208651G>A	ENST00000504056.1	-	2	191				CTD-2260A17.2_ENST00000501338.1_Intron						NA		NA									NA						ccagcactttgggaggccaag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000504056.1:c.137+337C>T	chr5.hg19:g.96208651G>A		NA		hg19		0.02	-0.184218	TTTxGGA	COVERED																																																																																			NOVEL	CTD-2260A17.2-003	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000370860.1	6	2.407216	KEEP	0	0	0	8	248	GG	0.99254	0.420319	0		-	3	60	90	0	0	6.761284	17	60	577	43	ENST00000504056.1	0.15	0.423478
CTD-2215E18.1	0	__UNKNOWN__	__UNKNOWN__	5	96439465	96439465	__UNKNOWN__	Intron	SNP	G	G	C	rs181747566	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:96439465G>C	ENST00000509481.1	+	3	573				LIX1_ENST00000274382.4_Intron						NA		NA								urinary_tract(1)	1						gtcaggagatggagaccatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000509481.1:c.32+667G>C	chr5.hg19:g.96439465G>C		NA		hg19		0.02	-0.148387	GATxGAG	COVERED																																																																																			NOVEL	CTD-2215E18.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370857.1	6	3.3099	KEEP	2	0	0	11	339	GG	0.992708	0.289872	0		+	4	41	123	0	1	10.313125	12	60	374	40	ENST00000509481.1	0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	98610726	98610726	__UNKNOWN__	IGR	SNP	G	G	A	rs377520249		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:98610726G>A			NA	NA				CTD-2007H13.3 (280009 upstream) : RP11-93O17.1 (214536 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.98610726G>A		NA		hg19		0.02	-0.13158	GGCxTGA	COVERED																																																																																			NOVEL					0			7	3.296093	KEEP	5	0	0	11	294	GG	0.99254	0.227464	0			3	60	86	0	0	6.872873	11	60	369	41		0.214286	0.229173
SLCO6A1	133482	__UNKNOWN__	__UNKNOWN__	5	101778653	101778653	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:101778653A>G	ENST00000506729.1	-	7	1303				SLCO6A1_ENST00000379810.1_Intron|SLCO6A1_ENST00000389019.3_Intron|SLCO6A1_ENST00000513675.1_Intron|SLCO6A1_ENST00000379807.3_Intron|SLCO6A1_ENST00000514551.1_Intron			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		tgtaatcccaacactttgaga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359	133482		Solute carriers	23613	protein-coding gene	gene with protein product	cancer/testis antigen 48	613365			NA		Standard	NM_173488	XM_005271874	NA	Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.1132-4188T>C	chr5.hg19:g.101778653A>G		NA	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	hg19	CCDS34206.1	0.02	-0.166608	CCAxCAC	COVERED																																																																																			NOVEL	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370335.1	8	2.405907	KEEP	0	0	0	8	221	AA	0.99257	0.351317	0		-	3	40	99	0	0	7.811019	15	60	431	36	ENST00000506729.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	102163846	102163846	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:102163846G>C			NA	NA				LINC00491 (156583 upstream) : PAM (37583 downstream)						NA		NA									NA						agttcaagacgagcctgggca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.102163846G>C		NA		hg19		0.02	-0.07018	GACxAGC	UNCOVERED																																																																																			NOVEL					0			5	2.707208	KEEP	0	0	0	9	264	GG	0.99254	0.076759	0			3	60	99	0	0	9.032594	5	60	173	27		0.375	0.077336
C5orf30	90355	__UNKNOWN__	__UNKNOWN__	5	102604882	102604882	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:102604882A>C	ENST00000319933.2	+	2	285				C5orf30_ENST00000515669.1_Intron|C5orf30_ENST00000510890.1_Intron	NM_033211.2	NP_149988.1	Q96GV9	CE030_HUMAN	chromosome 5 open reading frame 30	NA		NA			cilium morphogenesis (GO:0060271)|protein transport (GO:0015031)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9		all_cancers(142;2.22e-05)|all_epithelial(76;9.54e-08)|Prostate(80;0.0174)|Colorectal(57;0.0551)|Ovarian(225;0.11)|Lung NSC(167;0.136)|all_lung(232;0.18)		Epithelial(69;2.84e-14)|COAD - Colon adenocarcinoma(37;0.00762)		gcactccagcatgggtgacag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4095.1	5q21.1	2012-02-23			ENSG00000181751	ENSG00000181751	90355			25052	protein-coding gene	gene with protein product		NA			NA	22085962	Standard	NM_033211	NM_033211	NA	Approved	FLJ25291	uc003kog.1	Q96GV9	OTTHUMG00000128738	ENST00000319933.2:c.-24+3184A>C	chr5.hg19:g.102604882A>C		NA		hg19	CCDS4095.1	0.02	-0.035086	AGCxTGG	UNCOVERED																																																																																			NOVEL	C5orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250649.1	5	2.405326	KEEP	0	0	0	8	211	AA	0.99257	0.023895	0		+	2	60	72	0	0	6.950389	2	60	57	17	ENST00000319933.2	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	102657402	102657402	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:102657402A>G			NA	NA				C5orf30 (43041 upstream) : CTD-2154H6.1 (87239 downstream)						NA		NA									NA						gctcatgcctataatcccagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.102657402A>G		NA		hg19		0.02	-0.21926	CCTxTAA	COVERED																																																																																			NOVEL					0			14	2.405361	KEEP	6	0	0	8	211	AA	0.99257	0.54878	0			4	40	140	0	0	11.468882	17	60	485	55		0.190476	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	103061130	103061130	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:103061130T>C			NA	NA				NUDT12 (162636 upstream) : RP11-138J23.1 (354481 downstream)						NA		NA									NA						tgagccaccgtgcccagccTG	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.103061130T>C		NA		hg19		0.02	-0.122793	CCGxGCC	COVERED																																																																																			NOVEL					0			5	2.405096	KEEP	0	0	0	8	209	TT	0.99257	0.194853	0			3	57	102	0	0	8.701295	9	60	266	32		0.25	0.196312
RP11-6N13.1	0	__UNKNOWN__	__UNKNOWN__	5	104046545	104046545	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:104046545C>T	ENST00000503650.1	-	0	328										NA		NA									NA						gccgagattgcgccactgcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000503650.1:	chr5.hg19:g.104046545C>T		NA		hg19		0.02	-0.078939	TTGxGCC	UNCOVERED																																																																																			NOVEL	RP11-6N13.1-007	PUTATIVE	basic	lincRNA	NA	lincRNA	OTTHUMT00000371852.1	5	2.705818	KEEP	1	0	0	9	260	CC	0.99257	0.076761	0		-	3	60	83	0	0	7.431941	5	60	165	25	ENST00000503650.1	0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	105592187	105592187	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:105592187C>T			NA	NA				RNA5SP189 (333378 upstream) : SNORA31 (290178 downstream)						NA		NA									NA						acccaggaggcggagcttgca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.105592187C>T		NA		hg19		0.02	-0.017541	AGGxGGA	UNCOVERED																																																																																			NOVEL					0			2	2.406092	KEEP	1	0	0	8	234	CC	0	0	0			2	60	60	0	0	6.95328	0	0	0	13		1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	105913799	105913799	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:105913799A>G			NA	NA				SNORA31 (31295 upstream) : CTC-254B4.1 (237106 downstream)						NA		NA									NA						tgttgcccagactggagtgca	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.105913799A>G		NA		hg19		0.02	-0.078939	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			4	2.706746	KEEP	0	0	0	9	248	AA	0.99254	0.076759	0			2	60	73	0	0	6.300862	6	60	175	25		0.25	0.077336
FBXL17	64839	__UNKNOWN__	__UNKNOWN__	5	107411219	107411219	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:107411219C>A	ENST00000359660.5	-	7	1464				FBXL17_ENST00000496714.1_Intron|FBXL17_ENST00000542267.1_Intron			Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	NA		NA								endometrium(1)|large_intestine(4)|lung(1)	6		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		ctcttgttgcccaggctggag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL133602	CCDS54886.1	5q21.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000145743	ENSG00000145743	64839		F-boxes / Leucine-rich repeats	13615	protein-coding gene	gene with protein product		609083	F-box only protein 13	FBXO13	NA		Standard		NM_001163315	NA	Approved	DKFZP434C1715, Fbx13, Fbl17	uc011cvc.2	Q9UF56	OTTHUMG00000159785	ENST00000359660.5:c.552-54517G>T	chr5.hg19:g.107411219C>A		NA	A1A4E3	hg19		0.02	-0.096496	TGCxCAG	UNCOVERED																																																																																			NOVEL	FBXL17-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000357305.3	5	3.309779	KEEP	1	0	0	11	335	CC	0.992708	0.119558	0		-	3	60	96	0	0	8.378428	7	60	237	31	ENST00000359660.5	0.3	0.120436
NREP	9315	__UNKNOWN__	__UNKNOWN__	5	111163749	111163749	__UNKNOWN__	Intron	SNP	G	G	A	rs374810224	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:111163749G>A	ENST00000450761.2	-	2	141				NREP_ENST00000395634.3_Intron			Q16612	NREP_HUMAN	neuronal regeneration related protein	NA		NA			axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)					NA						tttttaagacggagtttcgct	0.408		NA											G|||	2	0.000399361	0.0	0.0	5008	,	,	NA	14163	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986	9315			16834	protein-coding gene	gene with protein product	neuronal protein 3.1	607332	chromosome 5 open reading frame 13, neuronal regeneration related protein homolog (rat)	C5orf13	NA	8261136, 10981724, 15485502	Standard	NM_004772	NM_004772	NA	Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000450761.2:c.58-72222C>T	chr5.hg19:g.111163749G>A		NA	B2RDN8|B7Z5D2|D3DSZ8	hg19	CCDS4105.1	0.02	-0.078913	GACxGAG	UNCOVERED																																																																																			NOVEL	NREP-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370888.1	4	4.211599	KEEP	0	0	0	14	412	GG	0.99649	0.077064	0		-	3	60	93	0	0	8.433661	5	60	155	36	ENST00000450761.2	0.375	0.077336
NREP	9315	__UNKNOWN__	__UNKNOWN__	5	111163784	111163784	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:111163784A>G	ENST00000450761.2	-	2	141				NREP_ENST00000395634.3_Intron			Q16612	NREP_HUMAN	neuronal regeneration related protein	NA		NA			axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)					NA						ctggagtgcaatggcacgatc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986	9315			16834	protein-coding gene	gene with protein product	neuronal protein 3.1	607332	chromosome 5 open reading frame 13, neuronal regeneration related protein homolog (rat)	C5orf13	NA	8261136, 10981724, 15485502	Standard	NM_004772	NM_004772	NA	Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000450761.2:c.58-72257T>C	chr5.hg19:g.111163784A>G		NA	B2RDN8|B7Z5D2|D3DSZ8	hg19	CCDS4105.1	0.02	-0.096475	GCAxTGG	UNCOVERED																																																																																			NOVEL	NREP-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370888.1	4	4.507317	KEEP	0	0	0	15	385	AA	0.99649	0.120013	0		-	3	60	98	0	0	8.578876	7	60	205	37	ENST00000450761.2	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	112039216	112039216	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:112039216T>A			NA	NA				RP11-159K7.2 (71419 upstream) : APC (4001 downstream)						NA		NA									NA						tcttcccatctcagcctccca	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.112039216T>A		NA		hg19		0.02	-0.096456	ATCxCAG	UNCOVERED																																																																																			NOVEL					0			2	2.70714	KEEP	0	0	0	9	253	TT	0.99254	0.119538	0			7	60	190	0	0	19.203724	4	60	123	28		0.636364	0.120436
MCC	4163	__UNKNOWN__	__UNKNOWN__	5	112651699	112651699	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:112651699T>C	ENST00000408903.3	-	3	1043					NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	NA		NA			negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ctcacacctgtaatccagcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444	4163		EF-hand domain containing	6935	protein-coding gene	gene with protein product		159350			NA	1848370	Standard	NM_001085377	NM_002387	NA	Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000408903.3:c.627+24516A>G	chr5.hg19:g.112651699T>C		NA	D3DT05|Q6ZR04	hg19	CCDS43351.1	0.02	-0.122782	CTGxAAT	COVERED																																																																																			NOVEL	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370839.1	6	3.006688	KEEP	2	0	0	10	262	TT	0.99257	0.194853	0		-	3	60	98	0	1	8.182188	10	60	286	35	ENST00000408903.3	0.230769	0.196312
PGGT1B	5229	__UNKNOWN__	__UNKNOWN__	5	114547185	114547185	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:114547185A>G	ENST00000419445.1	-	0	2068					NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	NA		NA			negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|protein geranylgeranylation (GO:0018344)|response to cytokine (GO:0034097)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)	CAAX-protein geranylgeranyltransferase activity (GO:0004662)|protein geranylgeranyltransferase activity (GO:0004661)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)		GTTTGAAATTAGAGCAGCTAA	0.264		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4116.1	5q23.1	2008-02-05			ENSG00000164219	ENSG00000164219	5229			8895	protein-coding gene	gene with protein product		602031			NA	8106351	Standard	NM_005023	NM_005023	NA	Approved	GGTI, BGGI	uc003kqw.4	P53609	OTTHUMG00000128893	ENST00000419445.1:c.*914T>C	chr5.hg19:g.114547185A>G		NA	Q5MJP9	hg19	CCDS4116.1	0.02	1.49132	ATTxGAG	COVERED																																																																																			NOVEL	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250855.2	18	9.019271	KEEP	0	0	0	30	787	AA	0.999997	0.981953	0		-	4	60	127	0	0	8.323651	53	60	1556	115	ENST00000419445.1	0.070175	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	114882432	114882432	__UNKNOWN__	IGR	SNP	G	G	A	rs117456018	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:114882432G>A			NA	NA				FEM1C (1841 upstream) : TMED7-TICAM2 (31906 downstream)						NA		NA									NA						ccacacacacgcacacacaca	0.542		NA											G|||	31	0.0061901	0.0	0.0	5008	,	,	NA	18775	0.0298	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.114882432G>A		NA		hg19		0.02	-0.122807	CACxCAC	COVERED																																																																																			NOVEL					0			6	3.541607	KEEP	0	1	23	20	585	GG	0.999869	0.196286	0			4	60	117	0	0	10.290869	8	60	265	52		0.333333	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	115140034	115140034	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:115140034G>T			NA	NA				RNU2-49P (29835 upstream) : CDO1 (395 downstream)						NA		NA									NA						tacaaaaaatggccgggcgcg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.115140034G>T		NA		hg19		0.02	-0.184217	AATxGCC	COVERED																																																																																			NOVEL					0			10	5.113989	KEEP	5	0	0	17	500	GG	0.995343	0.421506	0			3	21	89	0	0	6.733642	16	60	537	52		0.157895	0.423478
COMMD10	51397	__UNKNOWN__	__UNKNOWN__	5	115553680	115553680	__UNKNOWN__	Intron	SNP	C	C	T	rs6872730	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:115553680C>T	ENST00000274458.4	+	6	572				COMMD10_ENST00000515539.1_Intron	NM_016144.2	NP_057228.1	Q9Y6G5	COMDA_HUMAN	COMM domain containing 10	NA		NA								endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(2)	9		all_cancers(142;0.0834)|all_epithelial(76;0.00314)|Prostate(80;0.0102)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;4.3e-07)|Epithelial(69;8.06e-07)|all cancers(49;4.06e-05)		TCAAACTGTTCAGTCACCAGA	0.348		NA											C|||	2827	0.564497	0.1399	0.6916	5008	,	,	NA	20340	0.6528	NA	0.7614	False	NA	,,,	NA	NA	NA	2504	0.7546	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY542165	CCDS34215.1	5q23.1	2008-02-05				ENSG00000145781	51397			30201	protein-coding gene	gene with protein product		NA			NA	15799966	Standard	NM_016144	NM_016144	NA	Approved	PTD002	uc003krt.1	Q9Y6G5		ENST00000274458.4:c.511-73534C>T	chr5.hg19:g.115553680C>T		NA	D3DT07|Q9P077	hg19	CCDS34215.1	0.02	-0.201696	GTTxAGT	COVERED																																																																																			NOVEL	COMMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371033.1	0	2.407057	KEEP	0	0	0	8	244	CC	0.99257	0.4869	0		+	18	60	519	0	0	55.247729	5	60	163	46	ENST00000274458.4	0.782609	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	116028881	116028881	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:116028881A>G			NA	NA				CTB-118N6.2 (101787 upstream) : RP11-249M12.2 (49805 downstream)						NA		NA									NA						ggctgaggcaaaagaatcgct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.116028881A>G		NA		hg19		0.02	-0.061398	GCAxAAG	UNCOVERED																																																																																			NOVEL					0			7	2.405907	KEEP	1	0	0	8	217	AC	0.99254	0.04346	0			2	32	71	0	0	6.395963	4	60	116	22		0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	116128147	116128147	__UNKNOWN__	IGR	SNP	A	A	G	rs565686281	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:116128147A>G			NA	NA				RP11-249M12.2 (30242 upstream) : CTC-472C24.1 (28541 downstream)						NA		NA									NA						gagccaccgcacccggccAGA	0.453		NA											A|||	2	0.000399361	0.0	0.0	5008	,	,	NA	15234	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.116128147A>G		NA		hg19		0.02	-0.0614	CGCxCCC	UNCOVERED																																																																																			NOVEL					0			2	2.404845	KEEP	1	0	0	8	206	AA	0.99257	0.043461	0			2	60	72	0	0	6.495927	4	60	119	25		0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	116139361	116139361	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:116139361G>A			NA	NA				RP11-249M12.2 (41456 upstream) : CTC-472C24.1 (17327 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.116139361G>A		NA		hg19		0.02	-0.157803	GGCxTGA	COVERED																																																																																			NOVEL					0			7	3.610416	KEEP	2	0	0	12	357	GG	0.993634	0.320751	0			3	60	89	0	0	6.892913	14	60	453	47		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	120031712	120031712	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:120031712T>C			NA	NA				PRR16 (8685 upstream) : RNU4-69P (14680 downstream)						NA		NA									NA						ccaaggtgggtggatcacgag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.120031712T>C		NA		hg19		0.02	-0.052628	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			6	2.406014	KEEP	0	0	0	8	219	TT	0.99257	0.036492	0			2	36	68	0	0	6.550279	2	60	57	20		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	121078633	121078633	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:121078633A>G			NA	NA				CTC-546K23.1 (385540 upstream) : FTMT (109016 downstream)						NA		NA									NA						ccaggctggaatgcaatggcg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.121078633A>G		NA		hg19		0.02	-0.096461	GGAxTGC	UNCOVERED																																																																																			NOVEL					0			1	2.405749	KEEP	0	0	0	8	215	AA	0.99257	0.119541	0			3	60	83	0	0	7.242944	6	60	176	28		0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	122073813	122073813	__UNKNOWN__	IGR	SNP	T	T	A	rs201320014		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:122073813T>A			NA	NA				RP11-166A12.1 (7559 upstream) : SNX2 (36877 downstream)						NA		NA									NA						ccagcctgggtgacagagcaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.122073813T>A		NA		hg19		0.02	-0.096476	GGGxGAC	UNCOVERED																																																																																			NOVEL					0			8	3.308051	KEEP	2	0	0	11	299	TT	0.993072	0.119602	0			3	23	89	1	1	7.53248	8	60	236	36		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	122073819	122073819	__UNKNOWN__	IGR	SNP	A	A	G	rs199955524		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:122073819A>G			NA	NA				RP11-166A12.1 (7565 upstream) : SNX2 (36871 downstream)						NA		NA									NA						tgggtgacagagcaagactct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.122073819A>G		NA		hg19		0.02	-0.096487	CAGxGCA	UNCOVERED																																																																																			NOVEL					0			8	3.307557	KEEP	2	0	0	11	296	AA	0.993072	0.119602	0			3	23	102	0	1	8.832464	8	60	244	35		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	123087158	123087158	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:123087158T>C			NA	NA				CSNK1G3 (134419 upstream) : RP11-93O7.5 (562183 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.123087158T>C		NA		hg19		0.02	-0.087595	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			6	3.308759	KEEP	1	0	0	11	309	TT	0.993072	0.09903	0			4	60	129	0	0	12.739235	3	60	77	34		0.571429	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	124566773	124566773	__UNKNOWN__	IGR	SNP	C	C	T	rs555775291	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:124566773C>T			NA	NA				RP11-425E13.1 (28550 upstream) : RN7SKP117 (119787 downstream)						NA		NA									NA						gggctgggcgcggtggctcac	0.458		NA											C|||	2	0.000399361	0.0008	0.0014	5008	,	,	NA	18581	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.124566773C>T		NA		hg19		0.02	-0.236853	GCGxGGT	COVERED																																																																																			NOVEL					0			7	3.309	KEEP	2	0	0	11	320	CC	0.992708	0.607941	0			3	60	95	0	0	6.894771	23	60	772	57		0.115385	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	125973456	125973456	__UNKNOWN__	IGR	SNP	G	G	T	rs35966652	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:125973456G>T			NA	NA				C5orf48 (1477 upstream) : RP11-434D11.4 (114198 downstream)						NA		NA									NA						gcaggagaatggcttgaaccc	0.512		NA											T|||	895	0.178714	0.4924	0.0778	5008	,	,	NA	13819	0.005	NA	0.0736	False	NA	,,,	NA	NA	NA	2504	0.1135	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.125973456G>T		NA		hg19		0.02	-0.043852	AATxGCT	UNCOVERED																																																																																			NOVEL					0			6	2.407015	KEEP	3	0	0	8	240	CG	0.99257	0.023895	0			4	60	117	0	0	12.520105	1	60	32	21		0.8	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	126001543	126001543	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:126001543T>A			NA	NA				C5orf48 (29564 upstream) : RP11-434D11.4 (86111 downstream)						NA		NA									NA						tttttgagactgagtttcgct	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.126001543T>A		NA		hg19		0.02	-0.131557	GACxGAG	COVERED																																																																																			NOVEL					0			8	3.00689	KEEP	1	0	0	10	276	TT	0.992708	0.227502	0			3	60	84	0	0	6.901108	9	60	277	40		0.25	0.229173
PRRC1	133619	__UNKNOWN__	__UNKNOWN__	5	126888369	126888369	__UNKNOWN__	3'UTR	SNP	A	A	G	rs366515	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:126888369A>G	ENST00000296666.8	+	0	2287				PRRC1_ENST00000512635.2_Intron	NM_130809.3	NP_570721.1	Q96M27	PRRC1_HUMAN	proline-rich coiled-coil 1	NA		NA				Golgi apparatus (GO:0005794)				endometrium(1)|large_intestine(1)|lung(4)	6		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0851)|Epithelial(69;0.113)		AAGTATTCAAATTATTTTTGT	0.294		NA											G|||	1942	0.38778	0.3185	0.4524	5008	,	,	NA	16236	0.5506	NA	0.2893	False	NA	,,,	NA	NA	NA	2504	0.3691	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ515429	CCDS4143.1, CCDS68943.1	5q23.2	2008-02-05			ENSG00000164244	ENSG00000164244	133619			28164	protein-coding gene	gene with protein product		NA			NA	15541471	Standard	NM_130809	NM_130809	NA	Approved	FLJ32875	uc003kuk.3	Q96M27	OTTHUMG00000128982	ENST00000296666.8:c.*761A>G	chr5.hg19:g.126888369A>G		NA	Q69YM8|Q7L2U7|Q86Y42|Q8IVJ4|Q8IVL4|Q8NEZ7|Q96AJ3	hg19	CCDS4143.1	0.02	2.005829	CAAxTTA	COVERED																																																																																			NOVEL	PRRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250971.3	2	3.007364	KEEP	0	0	0	10	274	AA	0.992708	0.969742	0		+	17	60	586	0	0	52.104768	37	60	1138	92	ENST00000296666.8	0.314815	0.976865
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	128663589	128663589	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:128663589C>T			NA	NA				ISOC1 (213868 upstream) : MIR4460 (69165 downstream)						NA		NA									NA						ccagtgcactccagcctgggt	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.128663589C>T		NA		hg19		0.02	-0.052627	ACTxCAG	UNCOVERED																																																																																			NOVEL					0			10	3.610593	KEEP	0	0	0	12	365	CC	0.993634	0.036532	0			3	60	87	0	0	8.668879	2	60	64	20		0.6	0.036766
CHSY3	337876	__UNKNOWN__	__UNKNOWN__	5	129495064	129495064	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:129495064C>G	ENST00000305031.4	+	3	1444				CHSY3_ENST00000507545.1_Intron	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	NA		NA			carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		caccatgttgcccaggctggt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	337876	2.4.1.175, 2.4.1.226	Beta 3-glycosyltransferases, Beta 4-glycosyltransferases	24293	protein-coding gene	gene with protein product		609963			NA	12907687	Standard	NM_175856	XM_005271982	NA	Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.1087-24858C>G	chr5.hg19:g.129495064C>G		NA	B2RP97|Q76L22|Q86Y52	hg19	CCDS34223.1	0.02	-0.131581	TTGxCCA	COVERED																																																																																			NOVEL	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371453.1	8	2.391663	KEEP	0	0	0	8	229	CC	0.99257	0.22747	0		+	3	60	97	0	0	7.972727	11	60	357	31	ENST00000305031.4	0.214286	0.229173
RAPGEF6	51735	__UNKNOWN__	__UNKNOWN__	5	130794403	130794403	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:130794403G>A	ENST00000507093.1	-	20	3046				RAPGEF6_ENST00000307984.5_Intron|RAPGEF6_ENST00000308008.6_Intron|RAPGEF6_ENST00000512052.1_Intron|RAPGEF6_ENST00000509018.1_Intron|CTC-432M15.3_ENST00000514667.1_Intron|RAPGEF6_ENST00000296859.6_Intron	NM_001164388.1	NP_001157860.1	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	NA		NA			positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		ctggagtgcagtggcatgatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(168;435 1955 13113 13877 23213)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987	51735			20655	protein-coding gene	gene with protein product		610499	PDZ domain containing guanine nucleotide exchange factor (GEF) 2	PDZGEF2	NA	11524421, 12095257	Standard	NM_016340	NM_016340	NA	Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000507093.1:c.2865-2698C>T	chr5.hg19:g.130794403G>A		NA	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	hg19	CCDS54899.1	0.02	-0.087723	GCAxTGG	UNCOVERED																																																																																			NOVEL	RAPGEF6-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370061.1	6	3.310034	KEEP	1	0	0	11	342	GG	0.993634	0.099086	0		-	3	40	89	0	1	7.678246	7	60	245	36	ENST00000507093.1	0.3	0.099721
RAPGEF6	51735	__UNKNOWN__	__UNKNOWN__	5	130840354	130840354	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:130840354G>A	ENST00000507093.1	-	11	1400	c.1219C>T	c.(1219-1221)Cgg>Tgg	p.R407W	RAPGEF6_ENST00000307984.5_Missense_Mutation_p.R407W|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.R407W|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.R122W|RAPGEF6_ENST00000509018.1_Missense_Mutation_p.R407W|CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.R457W|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.R407W|RAPGEF6_ENST00000510071.1_Missense_Mutation_p.R407W	NM_001164388.1	NP_001157860.1	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	407		NA			positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GTTCCACTCCGGTCTAGTTCC	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(168;435 1955 13113 13877 23213)							NA				0													201	187	192			NA	NA	5		NA											NA				130840354		2203	4300	6503	SO:0001583	missense			AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987	51735			20655	protein-coding gene	gene with protein product		610499	PDZ domain containing guanine nucleotide exchange factor (GEF) 2	PDZGEF2	NA	11524421, 12095257	Standard	NM_016340	NM_016340	NA	Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000507093.1:c.1219C>T	chr5.hg19:g.130840354G>A	ENSP00000426081:p.Arg407Trp	NA	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	hg19	CCDS54899.1	0.02	1.227938	TCCxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	20.6	4.024550	0.75390	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000510071;ENST00000514667	T;T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53	4.43	3.53	0.40419	Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000001	T	0.48696	0.1514	L	0.51422	1.61	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.973;0.999;0.988;0.982;1.0;0.996;0.982	T	0.50600	-0.8809	10	0.87932	D	0	.	13.7491	0.62897	0.0:0.0:0.8449:0.1551	.	407;407;407;122;457;407;407	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	W	407;407;407;407;407;122;407;407;457	ENSP00000421684:R407W;ENSP00000309298:R407W;ENSP00000426081:R407W;ENSP00000296859:R407W;ENSP00000426910:R122W;ENSP00000311419:R407W;ENSP00000425389:R407W;ENSP00000426948:R457W	ENSP00000426948:R457W	R	-	1	2	RAPGEF6;FNIP1	130868253	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	9.813000	0.99286	0.938000	0.37419	0.313000	0.20887	CGG	NOVEL	RAPGEF6-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370061.1	5	9.326522	KEEP	0	0	0	31	925	GG	0.999997	0.999723	0		-	5	60	155	0	0	9.635219	80	60	2629	184	ENST00000507093.1	0.058824	0.999726
FNIP1	96459	__UNKNOWN__	__UNKNOWN__	5	131011579	131011579	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:131011579T>G	ENST00000307954.8	-	12	1413				FNIP1_ENST00000510461.1_Intron|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Intron			Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	NA		NA			cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		ttgagacagattctcgctctg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128	96459			29418	protein-coding gene	gene with protein product		610594			NA	11853319, 17028174	Standard	NM_133372	NM_001008738	NA	Approved	KIAA1961		Q8TF40		ENST00000307954.8:c.1384+1816A>C	chr5.hg19:g.131011579T>G		NA	D6RJH5|Q86T47|Q9BUT0	hg19		0.02	-0.052624	AGAxTCT	UNCOVERED																																																																																			NOVEL	FNIP1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370078.1	5	3.005858	KEEP	0	0	0	10	265	TT	0.992708	0.036498	0		-	2	60	71	0	0	6.395995	4	60	113	19	ENST00000307954.8	0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	131196411	131196411	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:131196411A>T			NA	NA				FNIP1 (63701 upstream) : AC034228.4 (83689 downstream)						NA		NA									NA						aagtgctgggattacaggcgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.131196411A>T		NA		hg19		0.02	-0.28063	GGGxTTA	COVERED																																																																																			NOVEL					0			13	3.004946	KEEP	0	0	0	10	266	AA	0.992708	0.734278	0			5	59	135	1	0	10.269994	22	60	645	55		0.185185	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	131196419	131196419	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:131196419C>T			NA	NA				FNIP1 (63709 upstream) : AC034228.4 (83681 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.131196419C>T		NA		hg19		0.02	-0.263127	AGGxGTG	COVERED																																																																																			NOVEL					0			14	4.505215	KEEP	0	0	0	15	423	CC	0.99649	0.691234	0			5	59	135	0	0	10.553387	19	60	612	60		0.208333	0.693668
AFF4	27125	__UNKNOWN__	__UNKNOWN__	5	132239912	132239912	__UNKNOWN__	Intron	SNP	A	A	G	rs145768432|rs72170789|rs76619832		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:132239912A>G	ENST00000265343.5	-	6	1467				AFF4_ENST00000491831.1_Intron|AFF4_ENST00000378595.3_Intron	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	NA		NA			spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ccacaccactacactccagAA	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(126;889 1733 2942 10745 11605)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364	27125			17869	protein-coding gene	gene with protein product	ALL1 fused gene from 5q31	604417			NA	10588740	Standard	NM_014423	XM_005271963	NA	Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.1087+147T>C	chr5.hg19:g.132239912A>G		NA	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	hg19	CCDS4164.1	0.02	3.659517	ACTxCAC	COVERED																																																																																			NOVEL	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133049.1	29	18.124843	KEEP	0	3	87	91	2329	AA	1	0.999984	0		-	5	60	165	0	0	10.413663	89	60	2436	320	ENST00000265343.5	0.053191	0.999984
ZCCHC10	54819	__UNKNOWN__	__UNKNOWN__	5	132334894	132334894	__UNKNOWN__	Intron	SNP	C	C	T	rs192340665	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:132334894C>T	ENST00000513848.1	-	3	237				ZCCHC10_ENST00000509437.1_Intron|ZCCHC10_ENST00000509008.1_Intron|ZCCHC10_ENST00000513541.1_Intron|ZCCHC10_ENST00000508080.1_Intron|ZCCHC10_ENST00000355372.2_Intron|ZCCHC10_ENST00000324170.3_Intron			Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	NA		NA					nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ggattacaggcgtgagccacc	0.473		NA											c|||	5	0.000998403	0.0038	0.0	5008	,	,	NA	19046	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005211	CCDS4165.1, CCDS75300.1, CCDS75301.1, CCDS75302.1	5q31.1	2008-05-02			ENSG00000155329	ENSG00000155329	54819		Zinc fingers, CCHC domain containing	25954	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_017665	XM_005272024	NA	Approved	FLJ20094	uc003kyg.3	Q8TBK6	OTTHUMG00000129013	ENST00000513848.1:c.204-352G>A	chr5.hg19:g.132334894C>T		NA	Q9NXR4	hg19		0.02	-0.1842	AGGxGTG	COVERED																																																																																			NOVEL	ZCCHC10-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370161.1	14	4.210019	KEEP	7	0	0	14	384	CC	0.993072	0.420544	0		-	3	60	89	0	0	6.81053	15	60	474	53	ENST00000513848.1	0.166667	0.423478
ZCCHC10	54819	__UNKNOWN__	__UNKNOWN__	5	132341047	132341047	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:132341047A>G	ENST00000513848.1	-	2	237				ZCCHC10_ENST00000509437.1_Intron|ZCCHC10_ENST00000509008.1_Intron|ZCCHC10_ENST00000513541.1_Intron|ZCCHC10_ENST00000508080.1_Intron|ZCCHC10_ENST00000355372.2_Intron|ZCCHC10_ENST00000324170.3_Intron			Q8TBK6	ZCH10_HUMAN	zinc finger, CCHC domain containing 10	NA		NA					nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			gctcatgcctataatcccagc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005211	CCDS4165.1, CCDS75300.1, CCDS75301.1, CCDS75302.1	5q31.1	2008-05-02			ENSG00000155329	ENSG00000155329	54819		Zinc fingers, CCHC domain containing	25954	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_017665	XM_005272024	NA	Approved	FLJ20094	uc003kyg.3	Q8TBK6	OTTHUMG00000129013	ENST00000513848.1:c.203+1403T>C	chr5.hg19:g.132341047A>G		NA	Q9NXR4	hg19		0.02	-0.184156	CCTxTAA	COVERED																																																																																			NOVEL	ZCCHC10-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000370161.1	2	2.704931	KEEP	0	0	0	9	231	AA	0.99254	0.420319	0		-	3	60	92	0	0	6.962632	17	60	488	43	ENST00000513848.1	0.15	0.423478
FSTL4	23105	__UNKNOWN__	__UNKNOWN__	5	132755073	132755073	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:132755073A>G	ENST00000265342.7	-	4	410					NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	NA		NA				extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			gcctcccaaaatgctgggact	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108	23105		EF-hand domain containing, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	21389	protein-coding gene	gene with protein product		NA			NA	10470851, 15527507	Standard	XM_048786	NM_015082	NA	Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.161-18395T>C	chr5.hg19:g.132755073A>G		NA	Q8TBU0|Q9UPU1	hg19	CCDS34238.1	0.02	-0.201725	AAAxTGC	COVERED																																																																																			NOVEL	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000370212.1	8	5.713607	KEEP	2	0	0	19	520	AA	0.999366	0.490234	0		-	3	60	95	0	0	7.192522	18	60	539	66	ENST00000265342.7	0.142857	0.490544
C5orf15	56951	__UNKNOWN__	__UNKNOWN__	5	133297002	133297002	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133297002C>T	ENST00000231512.3	-	2	342				C5orf15_ENST00000507191.1_Intron	NM_020199.2	NP_064584.1	Q8NC54	KCT2_HUMAN	chromosome 5 open reading frame 15	NA		NA				integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)			tttgggaggccgaggcaggct	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226055	CCDS4167.1	5q31.1	2012-02-22			ENSG00000113583	ENSG00000113583	56951			20656	protein-coding gene	gene with protein product	keratinocytes associated transmembrane protein 2	NA			NA		Standard	NM_020199	NM_020199	NA	Approved	KCT2, HTGN29	uc003kyo.3	Q8NC54	OTTHUMG00000129125	ENST00000231512.3:c.140-1291G>A	chr5.hg19:g.133297002C>T		NA	B2RD10|D3DQ92|Q9NRG2	hg19	CCDS4167.1	0.02	-0.070168	GGCxGAG	UNCOVERED																																																																																			NOVEL	C5orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251175.1	11	3.007415	KEEP	0	0	0	10	276	CC	0.992708	0.053742	0		-	3	60	83	0	0	7.65411	4	60	134	25	ENST00000231512.3	0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	133350297	133350297	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133350297A>G			NA	NA				CTB-113I20.2 (9044 upstream) : TCF7 (100104 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.133350297A>G		NA		hg19		0.02	-0.149097	CACxCCT	COVERED																																																																																			NOVEL					0			3	3.308892	KEEP	0	0	0	11	318	AA	0.993072	0.289978	0			3	60	100	0	0	8.273092	11	60	319	39		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	133356460	133356460	__UNKNOWN__	IGR	SNP	C	C	T	rs112504841	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133356460C>T			NA	NA				CTB-113I20.2 (15207 upstream) : TCF7 (93941 downstream)						NA		NA									NA						ctccgcctcccgggttcacgc	0.557		NA											C|||	997	0.199081	0.1679	0.1427	5008	,	,	NA	15175	0.3403	NA	0.1402	False	NA	,,,	NA	NA	NA	2504	0.1963	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.133356460C>T		NA		hg19		0.02	-0.122795	TCCxGGG	COVERED																																																																																			NOVEL					0			12	3.609229	KEEP	10	0	0	12	340	CC	0.99257	0.194853	0			5	60	146	0	0	13.693074	6	60	187	41		0.454545	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	133401973	133401973	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133401973A>G			NA	NA				CTB-113I20.2 (60720 upstream) : TCF7 (48428 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.133401973A>G		NA		hg19		0.02	-0.192925	GGCxTGA	COVERED																																																																																			NOVEL					0			8	2.405266	KEEP	2	0	0	8	210	AA	0.99257	0.454356	0			4	60	133	0	0	10.863447	16	60	450	44		0.2	0.457757
PPP2CA	5515	__UNKNOWN__	__UNKNOWN__	5	133531219	133531219	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133531219A>G	ENST00000481195.1	-	0	3454				CTD-2410N18.5_ENST00000519718.1_Intron	NM_002715.2	NP_002706.1	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha isozyme	NA		NA			apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|meiotic nuclear division (GO:0007126)|mesoderm development (GO:0007498)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein dephosphorylation (GO:0006470)|protein heterotrimerization (GO:0070208)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of protein autophosphorylation (GO:0031952)|regulation of protein catabolic process (GO:0042176)|regulation of receptor activity (GO:0010469)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase type 2A complex (GO:0000159)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|skin(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Vitamin E(DB00163)	gattacaggcatgagccactg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4173.1	5q31.1	2013-01-24	2010-03-05		ENSG00000113575	ENSG00000113575	5515	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase, catalytic subunits	9299	protein-coding gene	gene with protein product	protein phosphatase 2A catalytic subunit, alpha isoform	176915	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform		NA	8383590	Standard	NM_002715	NM_002715	NA	Approved	PP2Calpha		P67775	OTTHUMG00000129119	ENST00000481195.1:c.*2244T>C	chr5.hg19:g.133531219A>G		NA	P05323|P13197	hg19	CCDS4173.1	0.02	-0.306881	GGCxTGA	COVERED																																																																																			NOVEL	PPP2CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251165.1	5	2.405562	KEEP	0	0	0	8	214	AA	0.99257	0.7943	0		-	3	60	105	0	0	7.567389	30	60	884	56	ENST00000481195.1	0.090909	0.800245
CDKL3	51265	__UNKNOWN__	__UNKNOWN__	5	133608129	133608129	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133608129A>G	ENST00000609654.1	-	9	1226				CDKL3_ENST00000609383.1_Intron|CTD-2410N18.4_ENST00000518409.1_RNA			Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	NA		NA			cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ctcccaaagtactgggattac	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	51265	2.7.11.22	Cyclin-dependent kinases	15483	protein-coding gene	gene with protein product	serine-threonine protein kinase NKIAMRE	608459			NA	10463609	Standard	NM_001113575	NM_016508	NA	Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000609654.1:c.1152+30151T>C	chr5.hg19:g.133608129A>G		NA	D3DQA0|D3DQA1|Q9P114	hg19		0.02	-0.28065	AGTxCTG	COVERED																																																																																			NOVEL	CDKL3-205	KNOWN	basic	protein_coding	NA	protein_coding		8	5.709878	KEEP	1	0	0	19	487	AA	0.99986	0.739568	0		-	5	60	168	0	0	13.481621	23	60	667	81	ENST00000609654.1	0.178571	0.739671
CDKL3	51265	__UNKNOWN__	__UNKNOWN__	5	133647705	133647705	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133647705G>T	ENST00000265334.4	-	7	1000				CDKL3_ENST00000521118.1_Intron|CDKL3_ENST00000523832.1_Intron|CDKL3_ENST00000435211.1_Intron|CDKL3_ENST00000609654.1_Intron|CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000435240.2_Intron|CDKL3_ENST00000523054.1_Intron|CDKL3_ENST00000536186.1_Intron|CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000521755.1_Intron	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	NA		NA			cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			caggccggtcgtgaactccag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	51265	2.7.11.22	Cyclin-dependent kinases	15483	protein-coding gene	gene with protein product	serine-threonine protein kinase NKIAMRE	608459			NA	10463609	Standard	NM_001113575	NM_016508	NA	Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.881+277C>A	chr5.hg19:g.133647705G>T		NA	D3DQA0|D3DQA1|Q9P114	hg19	CCDS47264.1	0.02	-0.131552	GTCxTGA	COVERED																																																																																			NOVEL	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377697.1	5	3.008677	KEEP	0	0	0	10	300	GG	0.992708	0.227502	0		-	3	60	89	0	0	7.172844	11	60	367	36	ENST00000265334.4	0.214286	0.229173
UBE2B	7320	__UNKNOWN__	__UNKNOWN__	5	133717886	133717886	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133717886A>G	ENST00000265339.2	+	4	658				UBE2B_ENST00000511807.1_Intron	NM_003337.2	NP_003328.1	P63146	UBE2B_HUMAN	ubiquitin-conjugating enzyme E2B	NA		NA			canonical Wnt signaling pathway (GO:0060070)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to insulin stimulus (GO:0032869)|chiasma assembly (GO:0051026)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|histone lysine demethylation (GO:0070076)|in utero embryonic development (GO:0001701)|maintenance of chromatin silencing (GO:0006344)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of histone phosphorylation (GO:0033128)|positive regulation of reciprocal meiotic recombination (GO:0010845)|postreplication repair (GO:0006301)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|sperm axoneme assembly (GO:0007288)|spermatogenesis (GO:0007283)|synaptonemal complex organization (GO:0070193)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|replication fork (GO:0005657)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(2)|lung(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			gttcatacctataatcccagc	0.423		NA						Rad6 pathway													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74525	CCDS4174.1	5q31.1	2011-05-19	2011-05-19		ENSG00000119048	ENSG00000119048	7320		Ubiquitin-conjugating enzymes E2	12473	protein-coding gene	gene with protein product		179095	ubiquitin-conjugating enzyme E2B (RAD6 homolog)		NA	1559696	Standard	NM_003337	NM_003337	NA	Approved	UBC2, HHR6B, RAD6B	uc003kzh.3	P63146	OTTHUMG00000129120	ENST00000265339.2:c.241+1387A>G	chr5.hg19:g.133717886A>G		NA	B2R503|D3DQA2|P23567|Q4PJ15|Q9D0J6	hg19	CCDS4174.1	0.02	-0.175421	CCTxTAA	COVERED																																																																																			NOVEL	UBE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251166.2	6	2.705871	KEEP	0	0	0	9	238	AA	0.99254	0.384517	0		+	3	60	96	0	0	7.361246	17	60	516	33	ENST00000265339.2	0.15	0.387407
CDKN2AIPNL	91368	__UNKNOWN__	__UNKNOWN__	5	133743576	133743576	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133743576T>C	ENST00000458198.2	-	2	383					NM_080656.2	NP_542387.1	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like	NA		NA								central_nervous_system(1)|kidney(2)|prostate(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			cctgtaatcctagcactttgg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008293	CCDS4175.1	5q31.1	2008-02-05			ENSG00000237190	ENSG00000237190	91368			30545	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_080656	NM_080656	NA	Approved	MGC13017	uc011cxs.2	Q96HQ2	OTTHUMG00000129123	ENST00000458198.2:c.339+2017A>G	chr5.hg19:g.133743576T>C		NA	Q8WVE3	hg19	CCDS4175.1	0.02	-0.175236	TCCxAGC	COVERED																																																																																			NOVEL	CDKN2AIPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251171.2	10	2.70597	KEEP	1	0	0	9	238	TT	0.99254	0.384517	0		-	4	60	141	0	0	12.234654	11	60	296	44	ENST00000458198.2	0.266667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	133846421	133846421	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133846421C>G			NA	NA				AC005355.2 (1501 upstream) : RN7SL541P (7079 downstream)						NA		NA									NA						atgttgcccacgctggtctca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.133846421C>G		NA		hg19		0.02	-0.140366	CCAxGCT	COVERED																																																																																			NOVEL					0			10	3.308977	KEEP	1	0	0	11	315	CC	0.993072	0.259157	0			3	60	106	0	0	8.771829	12	60	414	42		0.2	0.260965
SAR1B	51128	__UNKNOWN__	__UNKNOWN__	5	133948387	133948387	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:133948387C>A	ENST00000402673.2	-	4	516	c.238G>T	c.(238-240)Gtt>Ttt	p.V80F	SAR1B_ENST00000507419.1_Missense_Mutation_p.V12F|SAR1B_ENST00000439578.1_Missense_Mutation_p.V80F|SAR1B_ENST00000509937.1_Missense_Mutation_p.V12F|SAR1B_ENST00000502539.1_Missense_Mutation_p.V12F	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	80		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|GTP catabolic process (GO:0006184)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			kidney(2)|lung(2)|urinary_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTACCTTGAACATGTCCACCC	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													57	62	61			NA	NA	5		NA											NA				133948387		2203	4300	6503	SO:0001583	missense			AF092130	CCDS4177.1	5q31.1	2014-03-07	2014-03-07	2005-10-21	ENSG00000152700	ENSG00000152700	51128			10535	protein-coding gene	gene with protein product		607690	SAR1a gene homolog (S. cerevisiae) 2, SAR1a gene homolog 2 (S. cerevisiae), SAR1 homolog B (S. cerevisiae)	SARA2	NA		Standard	NM_016103	NM_001033503	NA	Approved		uc003kzr.3	Q9Y6B6	OTTHUMG00000129114	ENST00000402673.2:c.238G>T	chr5.hg19:g.133948387C>A	ENSP00000385432:p.Val80Phe	NA	D3DQA4|Q567T4	hg19	CCDS4177.1	0.02	1.729222	GAAxATG	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.66	2.899331	0.52227	.	.	ENSG00000152700	ENST00000394992;ENST00000402673;ENST00000507419;ENST00000502539;ENST00000439578;ENST00000509937;ENST00000509730;ENST00000505758;ENST00000502286	D;D;D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	5.95	3.23	0.37069	Small GTP-binding protein domain (1);	0.682800	0.14791	N	0.298252	T	0.73900	0.3646	L	0.38838	1.175	0.30756	N	0.744644	B	0.15141	0.012	B	0.16722	0.016	T	0.68861	-0.5297	10	0.72032	D	0.01	-7.4382	6.4438	0.21865	0.1284:0.6747:0.0:0.1969	.	80	Q9Y6B6	SAR1B_HUMAN	F	12;80;12;12;80;12;12;80;80	ENSP00000385432:V80F;ENSP00000425339:V12F;ENSP00000426335:V12F;ENSP00000404997:V80F;ENSP00000424673:V12F;ENSP00000423197:V12F;ENSP00000425466:V80F;ENSP00000423005:V80F	ENSP00000378443:V12F	V	-	1	0	SAR1B	133976286	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	1.291000	0.33330	0.413000	0.25759	-0.150000	0.13652	GTT	NOVEL	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251158.2	67	66.989306	KEEP	0	1	6	225	6972	CC	1	1	0		-	8	60	181	0	0	9.178387	126	60	4305	430	ENST00000402673.2	0.059701	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	134180668	134180668	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:134180668T>C			NA	NA				DDX46 (13840 upstream) : C5orf24 (701 downstream)						NA		NA									NA						cctcgtgatctgcccgcctcg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.134180668T>C		NA		hg19		0.02	-0.254273	ATCxGCC	COVERED																																																																																			NOVEL					0			12	3.307647	KEEP	1	0	0	11	297	TT	0.993072	0.663892	0			4	60	132	0	0	10.262258	22	60	646	59		0.153846	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	136256159	136256159	__UNKNOWN__	IGR	SNP	C	C	T	rs558924849		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:136256159C>T			NA	NA				CTB-1I21.1 (165784 upstream) : RNA5SP193 (48729 downstream)						NA		NA									NA						gaggccgaggcgggcggatca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.136256159C>T		NA		hg19		0.02	-0.175426	AGGxGGG	COVERED																																																																																			NOVEL					0			10	4.513527	KEEP	4	0	0	15	469	CC	0.994391	0.385234	0			3	60	94	0	0	7.233505	16	60	523	57		0.157895	0.387407
KLHL3	26249	__UNKNOWN__	__UNKNOWN__	5	137027577	137027577	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:137027577G>A	ENST00000309755.4	-	5	970				KLHL3_ENST00000508657.1_Intron|KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000394937.3_Intron|KLHL3_ENST00000506491.1_Intron	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	NA		NA			distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		aaagtgctgggattacaggcg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021	26249		Kelch-like, BTB/POZ domain containing	6354	protein-coding gene	gene with protein product		605775	kelch (Drosophila)-like 3, kelch-like 3 (Drosophila)		NA	10843806	Standard		NM_017415	NA	Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.526+396C>T	chr5.hg19:g.137027577G>A		NA	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	hg19	CCDS4192.1	0.02	-0.157873	TGGxATT	COVERED																																																																																			NOVEL	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251220.2	4	2.706162	KEEP	2	0	0	9	251	GG	0.99257	0.320408	0		-	4	60	111	0	0	9.101474	12	60	390	39	ENST00000309755.4	0.25	0.322807
FAM13B	51306	__UNKNOWN__	__UNKNOWN__	5	137314969	137314969	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:137314969A>T	ENST00000033079.3	-	10	1631				FAM13B_ENST00000425075.2_Intron|FAM13B_ENST00000420893.2_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						cccaaagtgcaaggattacag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003	51306		Rho GTPase activating proteins	1335	protein-coding gene	gene with protein product		609371	chromosome 5 open reading frame 5, family with sequence similarity 13, member B1	C5orf5, FAM13B1	NA	11087669, 11161817	Standard		NM_016603	NA	Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.1179+5976T>A	chr5.hg19:g.137314969A>T		NA	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	hg19	CCDS4195.1	0.02	-0.192788	TGCxAGG	COVERED																																																																																			NOVEL	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251279.1	11	2.405887	KEEP	0	0	0	8	219	AA	0.99257	0.454356	0		-	3	60	84	0	0	6.574654	12	60	336	38	ENST00000033079.3	0.2	0.457757
CDC25C	995	__UNKNOWN__	__UNKNOWN__	5	137666749	137666749	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:137666749C>G	ENST00000323760.6	-	2	399	c.121G>C	c.(121-123)Gtc>Ctc	p.V41L	CDC25C_ENST00000348983.3_Missense_Mutation_p.V41L|CDC25C_ENST00000513970.1_Missense_Mutation_p.V41L|CDC25C_ENST00000356505.3_Missense_Mutation_p.V41L|CDC25C_ENST00000415130.2_Missense_Mutation_p.V41L|CDC25C_ENST00000514555.1_Missense_Mutation_p.V41L|CDC25C_ENST00000357274.3_Missense_Mutation_p.V41L	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	41		NA			cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TCTGGACAGACGGTAAAGGAA	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													109	109	109			NA	NA	5		NA											NA				137666749		2203	4300	6503	SO:0001583	missense			M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402	995		Protein tyrosine phosphatases / Class III Cys-based PTPs, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	1727	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 60	157680	cell division cycle 25C, cell division cycle 25 homolog C (S. cerevisiae), cell division cycle 25 homolog C (S. pombe)	CDC25	NA	1703321	Standard		XM_005272145	NA	Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.121G>C	chr5.hg19:g.137666749C>G	ENSP00000321656:p.Val41Leu	NA	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	hg19	CCDS4202.1	0.02	1.707588	AGAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	3.384	-0.125652	0.06795	.	.	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022;ENST00000510119	T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;2.05;1.57;1.57;1.57;1.57;1.57;1.57	4.49	-7.15	0.01521	.	1.562890	0.04046	N	0.303952	T	0.13415	0.0325	N	0.22421	0.69	0.09310	N	1	B;B;B;B;B;B	0.12013	0.005;0.005;0.003;0.005;0.001;0.003	B;B;B;B;B;B	0.08055	0.003;0.003;0.001;0.002;0.003;0.001	T	0.24548	-1.0157	10	0.06891	T	0.86	3.4214	3.3974	0.07311	0.1327:0.4461:0.1355:0.2857	.	58;41;58;41;41;41	G3V1P6;P30307-3;B4DX61;P30307-2;P30307-4;P30307	.;.;.;.;.;MPIP3_HUMAN	L	41;41;41;41;41;41;58;41;41;58	ENSP00000321656:V41L;ENSP00000348898:V41L;ENSP00000349821:V41L;ENSP00000345205:V41L;ENSP00000392631:V41L;ENSP00000424795:V41L;ENSP00000425470:V41L;ENSP00000427251:V41L;ENSP00000427105:V58L	ENSP00000321656:V41L	V	-	1	0	CDC25C	137694648	0.013000	0.17824	0.002000	0.10522	0.608000	0.37181	-0.168000	0.09925	-1.016000	0.03371	-0.768000	0.03414	GTC	NOVEL	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251280.1	1	4.511833	KEEP	0	0	0	15	436	CC	0.99649	0.996295	0		-	24	60	823	0	0	71.222538	65	60	2080	151	ENST00000323760.6	0.269663	0.999804
FAM53C	51307	__UNKNOWN__	__UNKNOWN__	5	137678464	137678464	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:137678464T>C	ENST00000239906.5	+	3	564				FAM53C_ENST00000513056.1_Intron|FAM53C_ENST00000507506.1_Intron|FAM53C_ENST00000434981.2_Intron	NM_016605.2	NP_057689.1	Q9NYF3	FA53C_HUMAN	family with sequence similarity 53, member C	NA		NA								breast(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			cctgtaatcctagcactttgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF251040	CCDS4204.1	5q31	2008-02-05	2004-11-24	2004-11-26	ENSG00000120709	ENSG00000120709	51307			1336	protein-coding gene	gene with protein product		609372	chromosome 5 open reading frame 6	C5orf6	NA	11087669, 11161817	Standard	NM_016605	NM_001135647	NA	Approved		uc003lcv.3	Q9NYF3	OTTHUMG00000129201	ENST00000239906.5:c.136+909T>C	chr5.hg19:g.137678464T>C		NA	B2RDJ5|D3DQB9	hg19	CCDS4204.1	0.02	-0.210402	TCCxAGC	COVERED																																																																																			NOVEL	FAM53C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251278.2	7	2.403182	KEEP	0	0	0	8	202	TT	0.99257	0.518282	0		+	3	60	98	0	0	7.711093	15	60	420	42	ENST00000239906.5	0.166667	0.522161
KDM3B	51780	__UNKNOWN__	__UNKNOWN__	5	137752017	137752017	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:137752017A>G	ENST00000314358.5	+	12	3507				KDM3B_ENST00000394866.1_Intron|KDM3B_ENST00000542866.1_Intron	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	NA		NA			chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						ggtggctcacacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733	51780		Chromatin-modifying enzymes / K-demethylases	1337	protein-coding gene	gene with protein product		609373	chromosome 5 open reading frame 7, jumonji domain containing 1B	C5orf7, JMJD1B	NA	15138608	Standard	NM_016604	NM_016604	NA	Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.3307+1089A>G	chr5.hg19:g.137752017A>G		NA	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	hg19	CCDS34242.1	0.02	-0.096473	CACxCCT	UNCOVERED																																																																																			NOVEL	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373597.1	5	3.0076	KEEP	3	0	0	10	278	AA	0	0	0		+	3	60	94	0	0	8.032612	8	60	239	31	ENST00000314358.5	0.272727	0.139832
KDM3B	51780	__UNKNOWN__	__UNKNOWN__	5	137753341	137753341	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:137753341T>G	ENST00000314358.5	+	13	3635				KDM3B_ENST00000394866.1_Intron|KDM3B_ENST00000542866.1_Intron	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	NA		NA			chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						AAGCCTAAATTTTTTTGTACC	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													80	74	76			NA	NA	5		NA											NA				137753341		2203	4300	6503	SO:0001627	intron_variant			AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733	51780		Chromatin-modifying enzymes / K-demethylases	1337	protein-coding gene	gene with protein product		609373	chromosome 5 open reading frame 7, jumonji domain containing 1B	C5orf7, JMJD1B	NA	15138608	Standard	NM_016604	NM_016604	NA	Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.3435+42T>G	chr5.hg19:g.137753341T>G		NA	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	hg19	CCDS34242.1	0.02	1.68135	AATxTTT	COVERED																																																																																			NOVEL	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373597.1	4	4.812451	KEEP	0	0	0	16	443	TT	0.997832	0.997713	0		+	22	60	770	1	0	65.642218	69	60	2044	163	ENST00000314358.5	0.241758	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	138035747	138035747	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:138035747G>A			NA	NA				snoU13 (76476 upstream) : AC034243.1 (44375 downstream)						NA		NA									NA						ggctgggtgcggtggctcatg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.138035747G>A		NA		hg19		0.02	-0.166665	TGCxGTG	COVERED																																																																																			NOVEL					0			3	2.405392	KEEP	0	0	0	8	214	GG	0.99257	0.384528	0			4	60	125	0	0	10.268226	14	60	459	40		0.222222	0.387407
CTNNA1	1495	__UNKNOWN__	__UNKNOWN__	5	138240691	138240691	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:138240691C>G	ENST00000518825.1	+	9	1391				CTNNA1_ENST00000540387.1_Intron|CTNNA1_ENST00000302763.7_Intron|CTNNA1_ENST00000355078.5_Intron|CTNNA1_ENST00000520400.1_Intron			P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	NA		NA			adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			gctgaggcagcagaatggcgt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115	1495			2509	protein-coding gene	gene with protein product		116805	catenin (cadherin-associated protein), alpha 1 (102kD)		NA	1924379	Standard	NM_001903	XM_005271898	NA	Approved	CAP102	uc003ldh.3	P35221		ENST00000518825.1:c.1389+561C>G	chr5.hg19:g.138240691C>G		NA	Q12795|Q8N1C0	hg19		0.02	-0.105274	CAGxAGA	UNCOVERED																																																																																			NOVEL	CTNNA1-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000373876.1	3	2.407173	KEEP	1	0	0	8	246	CC	0.99257	0.138793	0		+	3	60	104	0	0	8.90089	9	60	314	30	ENST00000518825.1	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	138275374	138275374	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:138275374T>C			NA	NA				CTNNA1 (4651 upstream) : SIL1 (7034 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.138275374T>C		NA		hg19		0.02	-0.280657	GTGxTGG	COVERED																																																																																			NOVEL					0			8	2.707136	KEEP	0	0	0	9	257	TT	0.99254	0.734154	0			3	60	101	0	0	7.442639	24	60	713	62		0.111111	0.739671
UBE2D2	7322	__UNKNOWN__	__UNKNOWN__	5	138936695	138936695	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:138936695G>A	ENST00000511725.1	+	1	182							P62837	UB2D2_HUMAN	ubiquitin-conjugating enzyme E2D 2	NA		NA			cellular protein modification process (GO:0006464)|cellular response to hypoxia (GO:0071456)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|protein complex (GO:0043234)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			tgggattacaggtatgagtca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L40146	CCDS43369.1, CCDS47275.1	5q31.2	2013-10-18	2011-05-19		ENSG00000131508	ENSG00000131508	7322		Ubiquitin-conjugating enzymes E2	12475	protein-coding gene	gene with protein product		602962	ubiquitin-conjugating enzyme E2D 2 (homologous to yeast UBC4/5), ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)		NA	8530467	Standard	NM_181838	NM_181838	NA	Approved	UbcH5B, UBC4	uc003ler.3	P62837	OTTHUMG00000163282	ENST00000511725.1:c.-64+30498G>A	chr5.hg19:g.138936695G>A		NA	D3DQC9|P51669|Q3MN78|Q96RP6	hg19	CCDS47275.1	0.02	-0.21054	ACAxGTA	COVERED																																																																																			NOVEL	UBE2D2-006	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372459.2	12	3.009011	KEEP	0	0	0	10	308	GG	0.992708	0.518353	0		+	3	60	90	0	0	6.627375	19	60	653	44	ENST00000511725.1	0.136364	0.522161
CTB-35F21.1	0	__UNKNOWN__	__UNKNOWN__	5	139095359	139095359	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:139095359T>C	ENST00000515296.1	+	0	181										NA		NA									NA						ccacccgccttggcctcccaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000515296.1:	chr5.hg19:g.139095359T>C		NA		hg19		0.02	-0.096486	CCTxGGC	UNCOVERED																																																																																			NOVEL	CTB-35F21.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000372775.1	7	3.005362	KEEP	1	0	0	10	258	TT	0.992708	0.119558	0		+	4	60	135	0	0	12.277412	7	60	210	30	ENST00000515296.1	0.363636	0.120436
CTB-35F21.1	0	__UNKNOWN__	__UNKNOWN__	5	139095388	139095388	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:139095388A>G	ENST00000515296.1	+	0	181										NA		NA									NA						gattacaggcatgagccactg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000515296.1:	chr5.hg19:g.139095388A>G		NA		hg19		0.02	-0.105249	GGCxTGA	UNCOVERED																																																																																			NOVEL	CTB-35F21.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000372775.1	7	2.706806	KEEP	0	0	0	9	252	AA	0.99254	0.161255	0		+	4	60	135	0	0	12.277601	7	60	204	30	ENST00000515296.1	0.363636	0.162467
NRG2	9542	__UNKNOWN__	__UNKNOWN__	5	139251478	139251478	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:139251478C>T	ENST00000358522.3	-	4	991				NRG2_ENST00000518130.1_Intron|NRG2_ENST00000289409.4_Intron|NRG2_ENST00000394770.1_Intron|NRG2_ENST00000545385.1_Intron|NRG2_ENST00000289422.7_Intron|NRG2_ENST00000340391.3_Intron|NRG2_ENST00000541337.1_Intron|NRG2_ENST00000361474.1_Intron	NM_013983.2	NP_053586.1	O14511	NRG2_HUMAN	neuregulin 2	NA		NA			embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCCTAGGCCCCAGGAATCA	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													68	58	62			NA	NA	5		NA											NA				139251478		1327	2309	3636	SO:0001627	intron_variant				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458	9542		Immunoglobulin superfamily / I-set domain containing	7998	protein-coding gene	gene with protein product	neural- and thymus-derived activator for ErbB kinases, divergent of neuregulin-1	603818			NA	9168114, 9168115	Standard	NM_013982	NM_004883	NA	Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000358522.3:c.992-52G>A	chr5.hg19:g.139251478C>T		NA		hg19	CCDS4217.1	0.02	3.513689	GGCxCCA	COVERED																																																																																			NOVEL	NRG2-007	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373995.1	4	3.309746	KEEP	0	0	0	11	333	CC	0.993072	0.993065	0		-	37	60	1121	0	0	99.602273	71	60	2414	163	ENST00000358522.3	0.342593	0.999993
PFDN1	5201	__UNKNOWN__	__UNKNOWN__	5	139643334	139643334	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:139643334T>C	ENST00000261813.4	-	4	333				PFDN1_ENST00000514611.1_Intron|PFDN1_ENST00000524074.1_Intron|CYSTM1_ENST00000509789.2_Intron|PFDN1_ENST00000510217.1_Intron	NM_002622.4	NP_002613.2	O60925	PFD1_HUMAN	prefoldin subunit 1	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|actin cytoskeleton organization (GO:0030036)|B cell activation (GO:0042113)|cell cycle (GO:0007049)|cellular protein metabolic process (GO:0044267)|cerebellum development (GO:0021549)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)|telencephalon development (GO:0021537)	prefoldin complex (GO:0016272)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(3)|prostate(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gagccgggcgtggtggctcat	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y17392	CCDS4222.1	5q31	2008-02-05	2006-02-24		ENSG00000113068	ENSG00000113068	5201			8866	protein-coding gene	gene with protein product		604897	prefoldin 1		NA	9630229	Standard	NM_002622	XM_005268465	NA	Approved	PFD1	uc003lff.1	O60925	OTTHUMG00000129249	ENST00000261813.4:c.286-17692A>G	chr5.hg19:g.139643334T>C		NA	B2RD02|Q53F95|Q96EX6	hg19	CCDS4222.1	0.02	-0.245569	GCGxGGT	COVERED																																																																																			NOVEL	PFDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251354.3	6	4.811554	KEEP	4	0	0	16	433	TT	0.995343	0.638361	0		-	3	60	104	0	0	7.794515	23	60	672	68	ENST00000261813.4	0.115385	0.641347
CTC-329D1.2	0	__UNKNOWN__	__UNKNOWN__	5	139754956	139754956	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:139754956A>G	ENST00000507521.1	-	0	257										NA		NA									NA						ctactcaggaagctgaggcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000507521.1:	chr5.hg19:g.139754956A>G		NA		hg19		0.02	-0.122774	GGAxGCT	COVERED																																																																																			NOVEL	CTC-329D1.2-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000372886.1	6	3.00594	KEEP	2	0	0	10	272	AA	0.99254	0.194847	0		-	3	60	91	0	0	7.373254	11	60	322	33	ENST00000507521.1	0.214286	0.196312
ANKHD1	54882	__UNKNOWN__	__UNKNOWN__	5	139863295	139863295	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:139863295G>A	ENST00000360839.2	+	11	2024				ANKHD1_ENST00000297183.6_Intron|ANKHD1-EIF4EBP3_ENST00000532219.1_Intron	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	NA		NA				cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tgcccgcctcggcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503	54882		Ankyrin repeat domain containing	24714	protein-coding gene	gene with protein product		610500			NA	10470851, 11230166, 16098192	Standard	NM_017747	NM_017747	NA	Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1870+1043G>A	chr5.hg19:g.139863295G>A		NA	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	hg19	CCDS4225.1	0.02	-0.184209	CTCxGCC	COVERED																																																																																			NOVEL	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251672.1	15	3.911284	KEEP	5	0	0	13	395	GG	0.992708	0.42039	0		+	4	60	126	1	0	10.26253	15	60	494	46	ENST00000360839.2	0.210526	0.423478
PCDHA6	56142	__UNKNOWN__	__UNKNOWN__	5	140208909	140208909	__UNKNOWN__	Silent	SNP	T	T	C	rs664837	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:140208909T>C	ENST00000529310.1	+	1	1347	c.1233T>C	c.(1231-1233)agT>agC	p.S411S	PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Silent_p.S411S|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	411	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGGACAGTGCCCTGGACC	0.622		NA											.|||	3	0.000599042	0.0	0.0043	5008	,	,	NA	20184	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													148	146	147			NA	NA	5		NA											NA				140208909		2203	4300	6503	SO:0001819	synonymous_variant			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842	56142		Cadherins / Protocadherins : Clustered	8672	other	complex locus constituent	KIAA0345-like 8	606312		CNRS2	NA	10380929, 10662547	Standard	NM_018909	NM_018909	NA	Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1233T>C	chr5.hg19:g.140208909T>C		NA	O75283|Q9NRT8	hg19	CCDS47281.1	0.02	1.534879	CAGxGCC	COVERED																																																																																			NOVEL	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372829.3	2	2.404715	KEEP	9	0	0	8	205	TT	0.99257	0.99225	0		+	9	33	299	0	0	21.681143	77	60	2203	132	ENST00000529310.1	0.104651	0.999678
PCDHA6	56142	__UNKNOWN__	__UNKNOWN__	5	140208938	140208938	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:140208938A>G	ENST00000529310.1	+	1	1376	c.1262A>G	c.(1261-1263)tAt>tGt	p.Y421C	PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Missense_Mutation_p.Y421C|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	421	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.	NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTCGGCCTATGAGTTGGTG	0.622		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													123	128	127			NA	NA	5		NA											NA				140208938		2203	4300	6503	SO:0001583	missense			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842	56142		Cadherins / Protocadherins : Clustered	8672	other	complex locus constituent	KIAA0345-like 8	606312		CNRS2	NA	10380929, 10662547	Standard	NM_018909	NM_018909	NA	Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1262A>G	chr5.hg19:g.140208938A>G	ENSP00000433378:p.Tyr421Cys	NA	O75283|Q9NRT8	hg19	CCDS47281.1	0.02	1.830735	CCTxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	10.99	1.508309	0.27036	.	.	ENSG00000081842	ENST00000529310;ENST00000527624	T;T	0.69561	-0.41;-0.41	3.55	3.55	0.40652	Cadherin (5);Cadherin-like (1);	0.000000	0.33610	U	0.004728	D	0.87819	0.6273	H	0.98370	4.215	0.41720	D	0.989507	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.91761	0.5420	10	0.87932	D	0	.	12.5335	0.56128	1.0:0.0:0.0:0.0	.	421;421;421	Q9UN73-3;Q9UN73;Q9UN73-2	.;PCDA6_HUMAN;.	C	421	ENSP00000433378:Y421C;ENSP00000434113:Y421C	ENSP00000434113:Y421C	Y	+	2	0	PCDHA6	140189122	1.000000	0.71417	0.009000	0.14445	0.023000	0.10783	6.836000	0.75349	1.607000	0.50170	0.260000	0.18958	TAT	NOVEL	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372829.3	3	2.404847	KEEP	8	0	0	8	206	AA	0.99257	0.991047	0		+	27	60	909	0	0	82.506579	48	60	1369	138	ENST00000529310.1	0.36	0.998465
PCDHA6	56142	__UNKNOWN__	__UNKNOWN__	5	140211155	140211155	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:140211155C>T	ENST00000529310.1	+	1	2508				PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	NA		NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tccatgttgcccaggctggtc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842	56142		Cadherins / Protocadherins : Clustered	8672	other	complex locus constituent	KIAA0345-like 8	606312		CNRS2	NA	10380929, 10662547	Standard	NM_018909	NM_018909	NA	Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.2394+1085C>T	chr5.hg19:g.140211155C>T		NA	O75283|Q9NRT8	hg19	CCDS47281.1	0.02	-0.096493	TGCxCAG	UNCOVERED																																																																																			NOVEL	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372829.3	9	3.911174	KEEP	1	0	0	13	386	CC	0.993634	0.119669	0		+	3	24	99	0	0	9.255281	4	60	126	32	ENST00000529310.1	0.428571	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	140470113	140470113	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:140470113A>C			NA	NA				PCDHB1 (36601 upstream) : PCDHB2 (4113 downstream)						NA		NA									NA						cccatcttggactcccaaagt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.140470113A>C		NA		hg19		0.02	-0.105252	TGGxCTC	UNCOVERED																																																																																			NOVEL					0			8	2.405495	KEEP	0	0	0	8	211	AA	0.99257	0.138793	0			3	60	101	0	0	8.732585	8	60	240	27		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	140583802	140583802	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:140583802A>G			NA	NA				PCDHB11 (1184 upstream) : PCDHB12 (4466 downstream)						NA		NA									NA						aaaaaaaaaaaaaaaaaaaga	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.140583802A>G		NA		hg19		0.02	-0.087683	AAAxAAA	UNCOVERED																																																																																			NOVEL					0			10	2.4054	KEEP	3	0	0	8	213	AA	0	0	0			2	60	66	0	0	6.350902	2	60	51	20		0.5	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	141417711	141417711	__UNKNOWN__	IGR	SNP	A	A	G	rs552655688		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:141417711A>G			NA	NA				GNPDA1 (25115 upstream) : NDFIP1 (70358 downstream)						NA		NA									NA						tgtggctcacacctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.141417711A>G		NA		hg19		0.02	-0.201702	CACxCCT	COVERED																																																																																			NOVEL					0			10	2.70709	KEEP	2	0	0	9	253	AA	0.99257	0.4869	0			3	60	87	0	0	6.393402	18	60	523	45		0.142857	0.490544
AC005592.2	0	__UNKNOWN__	__UNKNOWN__	5	141787200	141787200	__UNKNOWN__	RNA	SNP	G	G	A	rs539559658		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:141787200G>A	ENST00000510311.1	+	0	506				AC005592.2_ENST00000443800.1_RNA|AC005592.2_ENST00000425963.1_RNA						NA		NA									NA						ggccaggtgcggtggctcatg	0.567		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	12863	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000510311.1:	chr5.hg19:g.141787200G>A		NA		hg19		0.02	-0.210505	TGCxGTG	COVERED																																																																																			NOVEL	AC005592.2-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000370676.1	12	5.714537	KEEP	8	0	0	19	544	GG	0.994391	0.519232	0		+	3	40	90	0	0	6.506448	21	60	656	61	ENST00000510311.1	0.125	0.522161
AC005592.2	0	__UNKNOWN__	__UNKNOWN__	5	141913204	141913204	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:141913204T>C	ENST00000443800.1	+	0	243										NA		NA									NA						cattgcactctagcctgggca	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000443800.1:	chr5.hg19:g.141913204T>C		NA		hg19		0.02	-0.157879	CTCxAGC	UNCOVERED																																																																																			NOVEL	AC005592.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000257944.1	7	2.402125	KEEP	1	0	0	8	200	TT	0	0	0		+	3	60	100	0	0	8.078809	13	60	392	37	ENST00000443800.1	0.1875	0.322807
ARHGAP26	23092	__UNKNOWN__	__UNKNOWN__	5	142396045	142396045	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:142396045G>A	ENST00000274498.4	+	12	1522				ARHGAP26_ENST00000378004.3_Intron	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	NA		NA			actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			cgaggcgggcggatcacaagg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819	23092		Rho GTPase activating proteins	17073	protein-coding gene	gene with protein product	GTPase regulator associated with the focal adhesion kinase pp125	605370			NA	9858476, 8649427	Standard	NM_015071	NM_001135608	NA	Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.1144+2364G>A	chr5.hg19:g.142396045G>A		NA	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	hg19	CCDS4277.1	0.02	-0.14034	GGCxGAT	UNCOVERED																																																																																			NOVEL	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132744.3	6	2.405623	KEEP	4	0	0	8	221	GG	0	0	0		+	3	60	87	0	0	6.872556	12	60	379	45	ENST00000274498.4	0.2	0.260965
CTB-57H20.1	0	__UNKNOWN__	__UNKNOWN__	5	143072757	143072757	__UNKNOWN__	RNA	SNP	G	G	C	rs112532770	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:143072757G>C	ENST00000503323.1	+	0	379										NA		NA									NA						tgcactccaggctgggcaact	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000503323.1:	chr5.hg19:g.143072757G>C		NA		hg19		0.02	-0.149132	CAGxCTG	COVERED																																																																																			NOVEL	CTB-57H20.1-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000371896.1	6	2.708086	KEEP	0	0	0	9	283	GG	0.99254	0.289823	0		+	3	60	101	0	0	8.272	12	60	403	38	ENST00000503323.1	0.2	0.292001
SH3RF2	153769	__UNKNOWN__	__UNKNOWN__	5	145444343	145444343	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:145444343G>A	ENST00000511217.1	+	9	2275							Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	NA		NA			negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ggaaggaaaggaaggaaggaa	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463	153769		RING-type (C3HC4) zinc fingers, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	26299	protein-coding gene	gene with protein product	heart protein phosphatase 1-binding protein, POSH-eliminating RING protein	613377	protein phosphatase 1, regulatory subunit 39	PPP1R39	NA	22128169	Standard	NM_152550	NM_152550	NA	Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.2187+2046G>A	chr5.hg19:g.145444343G>A		NA	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	hg19	CCDS4280.1	0.02	-0.087714	AAGxAAG	UNCOVERED																																																																																			NOVEL	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372804.1	15	2.707822	KEEP	15	0	0	9	269	GG	0	0	0		+	3	60	85	1	0	7.442887	6	49	207	35	ENST00000511217.1	0.333333	0.099721
LARS	51520	__UNKNOWN__	__UNKNOWN__	5	145492835	145492835	__UNKNOWN__	3'UTR	SNP	T	T	C	rs138954063	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:145492835T>C	ENST00000394434.2	-	0	4531				RP11-118M9.3_ENST00000514002.1_RNA	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	NA		NA			gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|skin(2)|stomach(8)	34			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		L-Leucine(DB00149)	accatgttggtcaggctggtc	0.542		NA											T|||	66	0.0131789	0.0038	0.0159	5008	,	,	NA	16467	0.0	NA	0.0417	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF151026	CCDS34265.1	5q32	2012-10-02			ENSG00000133706	ENSG00000133706	51520	6.1.1.4	Aminoacyl tRNA synthetases / Class I	6512	protein-coding gene	gene with protein product	leucine tRNA ligase 1, cytoplasmic	151350			NA	6933703	Standard	NM_020117	NM_020117	NA	Approved	HSPC192, FLJ10595, FLJ21788, LARS1, LEUS, RNTLS	uc003lnx.1	Q9P2J5	OTTHUMG00000163429	ENST00000394434.2:c.*834A>G	chr5.hg19:g.145492835T>C		NA	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	hg19	CCDS34265.1	0.02	-0.227889	TGGxCAG	UNCOVERED																																																																																			NOVEL	LARS-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373367.1	4	2.404827	KEEP	2	0	0	8	203	TT	0	0	0		-	3	60	90	0	0	6.451653	22	60	598	41	ENST00000394434.2	0.12	0.58293
RBM27	54439	__UNKNOWN__	__UNKNOWN__	5	145600546	145600546	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:145600546C>T	ENST00000265271.5	+	2	344				RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	NA		NA			mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			tttgggaggccgaggcgggtg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009	54439		Zinc fingers, CCCH-type domain containing, RNA binding motif (RRM) containing	29243	protein-coding gene	gene with protein product	acidic rich RS domain containing 1	NA			NA	10718198, 15741184	Standard	XM_291128	NM_018989	NA	Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.178+1880C>T	chr5.hg19:g.145600546C>T		NA	Q8IYW9	hg19	CCDS43378.1	0.02	-0.175402	GGCxGAG	UNCOVERED																																																																																			NOVEL	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373420.1	8	2.407284	KEEP	4	0	0	8	249	CC	0	0	0		+	3	60	85	0	0	6.334635	16	60	527	45	ENST00000265271.5	0.157895	0.387407
RBM27	54439	__UNKNOWN__	__UNKNOWN__	5	145658741	145658741	__UNKNOWN__	Intron	SNP	G	G	A	rs376150562	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:145658741G>A	ENST00000265271.5	+	20	3154				RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	NA		NA			mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ggctgggtgcggtggctcaca	0.428		NA											G|||	40	0.00798722	0.0295	0.0014	5008	,	,	NA	13009	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009	54439		Zinc fingers, CCCH-type domain containing, RNA binding motif (RRM) containing	29243	protein-coding gene	gene with protein product	acidic rich RS domain containing 1	NA			NA	10718198, 15741184	Standard	XM_291128	NM_018989	NA	Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2989-5444G>A	chr5.hg19:g.145658741G>A		NA	Q8IYW9	hg19	CCDS43378.1	0.02	-0.184204	TGCxGTG	COVERED																																																																																			NOVEL	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373420.1	7	3.302432	KEEP	1	0	0	11	301	GG	0.992708	0.454419	0		+	3	60	95	0	0	7.491758	14	60	444	48	ENST00000265271.5	0.176471	0.457757
SH3TC2	79628	__UNKNOWN__	__UNKNOWN__	5	148425488	148425488	__UNKNOWN__	Intron	SNP	G	G	A	rs568452232		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:148425488G>A	ENST00000512049.1	-	4	346				SH3TC2_ENST00000515425.1_Intron|SH3TC2_ENST00000394358.2_De_novo_Start_InFrame			Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	NA		NA			cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			gattacaggcgtgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247	79628		Tetratricopeptide (TTC) repeat domain containing	29427	protein-coding gene	gene with protein product		608206			NA	14574644	Standard	NM_024577	NM_024577	NA	Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000512049.1:c.280-1287C>T	chr5.hg19:g.148425488G>A		NA	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	hg19		0.02	2.991066	GGCxTGA	COVERED																																																																																			NOVEL	SH3TC2-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000373360.1	30	12.330082	KEEP	10	3	85	71	2066	GG	1	0.999995	0		-	6	60	182	0	1	11.164621	96	60	3086	292	ENST00000512049.1	0.058824	0.999995
RPS14	6208	__UNKNOWN__	__UNKNOWN__	5	149823884	149823884	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:149823884G>T	ENST00000401695.3	-	5	467	c.421C>A	c.(421-423)Cgc>Agc	p.R141S	RPS14_ENST00000407193.1_Missense_Mutation_p.R141S|RPS14_ENST00000312037.5_Missense_Mutation_p.R141S			P62263	RS14_HUMAN	ribosomal protein S14	141		NA			cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|gene expression (GO:0010467)|maturation of SSU-rRNA (GO:0030490)|mRNA metabolic process (GO:0016071)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|ribosomal small subunit assembly (GO:0000028)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)|translation regulator activity (GO:0045182)			central_nervous_system(1)|lung(1)|skin(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCTTCCTGCGAGTGCTGTCA	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													67	80	76			NA	NA	5		NA											NA				149823884		2203	4299	6502	SO:0001583	missense				CCDS4307.1	5q31-q33	2012-10-02			ENSG00000164587	ENSG00000164587	6208		S ribosomal proteins	10387	protein-coding gene	gene with protein product	emetine resistance, 40S ribosomal protein S14	130620			NA	3785212, 1549121	Standard	NM_001025071	XM_006714790	NA	Approved	EMTB, S14	uc003lsj.3	P62263	OTTHUMG00000130080	ENST00000401695.3:c.421C>A	chr5.hg19:g.149823884G>T	ENSP00000385958:p.Arg141Ser	NA	B2R5G5|D3DQG5|P06366|Q5BJI0	hg19	CCDS4307.1	0.02	1.429789	TGCxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.48	3.633245	0.67015	.	.	ENSG00000164587	ENST00000401695;ENST00000407193;ENST00000521466;ENST00000312037	.	.	.	5.49	5.49	0.81192	.	0.050172	0.85682	D	0.000000	D	0.90089	0.6904	H	0.99026	4.405	0.80722	D	1	P	0.38565	0.637	P	0.53062	0.717	D	0.92597	0.6088	9	0.87932	D	0	.	19.7245	0.96157	0.0:0.0:1.0:0.0	.	141	P62263	RS14_HUMAN	S	141	.	ENSP00000311028:R141S	R	-	1	0	RPS14	149804077	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.831000	0.62752	2.735000	0.93741	0.561000	0.74099	CGC	NOVEL	RPS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252373.1	0	3.609006	KEEP	0	0	0	12	341	GG	0.993634	0.986604	0		-	18	60	512	0	0	43.274611	46	60	1495	104	ENST00000401695.3	0.28125	0.992926
NDST1	3340	__UNKNOWN__	__UNKNOWN__	5	149908183	149908183	__UNKNOWN__	Intron	SNP	T	T	G	rs147386079	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:149908183T>G	ENST00000523767.1	+	3	1597				NDST1_ENST00000261797.6_Intron			P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	NA		NA			carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			cgaaaccccatctctactaaa	0.522		NA											T|||	53	0.0105831	0.0008	0.0187	5008	,	,	NA	17103	0.0	NA	0.0298	False	NA	,,,	NA	NA	NA	2504	0.0092	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614	3340		Sulfotransferases, membrane-bound	7680	protein-coding gene	gene with protein product		600853		HSST	NA	7601448, 9230113	Standard	NM_001543	NM_001543	NA	Approved	NST1	uc003lsk.4	P52848		ENST00000523767.1:c.1008+323T>G	chr5.hg19:g.149908183T>G		NA	Q96E57	hg19		0.02	-0.114004	CCAxCTC	UNCOVERED																																																																																			NOVEL	NDST1-001	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000374313.1	10	2.40546	KEEP	1	0	0	8	214	TT	0	0	0		+	7	60	245	0	0	24.302641	5	60	132	24	ENST00000523767.1	0.583333	0.162467
CCDC69	26112	__UNKNOWN__	__UNKNOWN__	5	150595800	150595800	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:150595800G>A	ENST00000355417.2	-	1	223				CCDC69_ENST00000521308.1_Intron	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	NA		NA								haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			gattacaggcgtgagccacca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624	26112			24487	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_015621	NM_015621	NA	Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.48+7683C>T	chr5.hg19:g.150595800G>A		NA	A8K9X6	hg19	CCDS4312.1	0.02	-0.192977	GGCxTGA	COVERED																																																																																			NOVEL	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252435.1	5	3.610377	KEEP	0	0	0	12	360	GG	0.993634	0.454842	0		-	3	60	86	0	0	6.361981	17	60	560	54	ENST00000355417.2	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	150758963	150758963	__UNKNOWN__	IGR	SNP	T	T	C	rs530149353		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:150758963T>C			NA	NA				AC034205.1 (10887 upstream) : SLC36A1 (57644 downstream)						NA		NA									NA						ggcacgatcttggctcactgc	0.463		NA											t|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17348	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.150758963T>C		NA		hg19		0.02	-0.201733	TCTxGGC	COVERED																																																																																			NOVEL					0			12	4.508131	KEEP	3	0	0	15	399	TT	0.99649	0.488823	0			4	60	128	0	0	10.179579	18	60	541	60		0.181818	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	150759018	150759018	__UNKNOWN__	IGR	SNP	C	C	T	rs9324694	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:150759018C>T			NA	NA				AC034205.1 (10942 upstream) : SLC36A1 (57589 downstream)						NA		NA									NA						cctcagcctcccaagtagctg	0.527		NA											c|||	1220	0.24361	0.5439	0.183	5008	,	,	NA	15822	0.0109	NA	0.2247	False	NA	,,,	NA	NA	NA	2504	0.1401	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.150759018C>T		NA		hg19		0.02	-0.122802	CTCxCAA	UNCOVERED																																																																																			NOVEL					0			5	2.707314	KEEP	5	0	0	9	271	CC	0	0	0			5	60	148	0	0	13.644681	7	60	245	35		0.416667	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	150795484	150795484	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:150795484T>C			NA	NA				AC034205.1 (47408 upstream) : SLC36A1 (21123 downstream)						NA		NA									NA						ctggctaacatggtgaaaccc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.150795484T>C		NA		hg19		0.02	-0.122804	ACAxGGT	COVERED																																																																																			NOVEL					0			13	3.608989	KEEP	5	0	0	12	327	TT	0.99257	0.22747	0			4	48	141	0	0	12.524069	9	60	274	36		0.307692	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	152552961	152552961	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:152552961G>T			NA	NA				AC091969.1 (483872 upstream) : GRIA1 (317080 downstream)						NA		NA									NA						ggattacaggggtgagccacc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.152552961G>T		NA		hg19		0.02	-0.140322	AGGxGTG	COVERED																																																																																			NOVEL					0			8	2.407116	KEEP	1	0	0	8	246	CG	0.99257	0.259026	0			3	35	83	0	0	6.573456	11	60	352	33		0.214286	0.260965
GALNT10	55568	__UNKNOWN__	__UNKNOWN__	5	153769074	153769074	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:153769074A>G	ENST00000297107.6	+	7	1193				GALNT10_ENST00000519544.1_Intron|GALNT10_ENST00000425427.2_3'UTR|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000377661.2_Intron	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	NA		NA			cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			gctgggaggcagaggttgcag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	55568	2.4.1.41	Glycosyltransferase family 2 domain containing	19873	protein-coding gene	gene with protein product	polypeptide GalNAc transferase 10	608043	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)		NA	12417297	Standard	NM_198321	NM_198321	NA	Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1056+3084A>G	chr5.hg19:g.153769074A>G		NA	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	hg19	CCDS4325.1	0.02	2.706444	GGCxGAG	COVERED																																																																																			NOVEL	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252453.1	18	12.524156	KEEP	0	3	74	68	1845	AA	1	0.999999	0		+	8	60	216	0	0	12.887215	106	60	3091	259	ENST00000297107.6	0.070175	0.999999
LARP1	23367	__UNKNOWN__	__UNKNOWN__	5	154170375	154170375	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:154170375A>C	ENST00000336314.4	+	3	357					NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	NA		NA			cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CTCAGttttcattctttcttt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506	23367		La ribonucleoprotein domain containing	29531	protein-coding gene	gene with protein product		612059			NA	9872452, 10878606	Standard	NM_033551	NM_015315	NA	Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.333+105A>C	chr5.hg19:g.154170375A>C		NA	O94836|Q8N4M2|Q8NB73|Q9UFD7	hg19	CCDS4328.1	0.02	1.55816	TTCxTTC	COVERED																																																																																			NOVEL	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252509.1	17	9.624487	KEEP	0	0	0	32	886	AA	0.999997	0.99755	0		+	4	60	130	1	0	8.280794	65	60	1900	143	ENST00000336314.4	0.057971	0.997553
LARP1	23367	__UNKNOWN__	__UNKNOWN__	5	154170378	154170378	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:154170378C>T	ENST00000336314.4	+	3	357					NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	NA		NA			cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGttttcattctttctttttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506	23367		La ribonucleoprotein domain containing	29531	protein-coding gene	gene with protein product		612059			NA	9872452, 10878606	Standard	NM_033551	NM_015315	NA	Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.333+108C>T	chr5.hg19:g.154170378C>T		NA	O94836|Q8N4M2|Q8NB73|Q9UFD7	hg19	CCDS4328.1	0.02	0.983298	ATTxTTT	COVERED																																																																																			NOVEL	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252509.1	17	9.328375	KEEP	0	0	0	31	972	CC	0.999997	0.996721	0		+	5	60	140	1	0	8.706599	61	60	2077	138	ENST00000336314.4	0.075758	0.996724
MRPL22	29093	__UNKNOWN__	__UNKNOWN__	5	154323795	154323795	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:154323795G>A	ENST00000523037.1	+	2	118				MRPL22_ENST00000439747.3_Intron|MRPL22_ENST00000265229.8_Intron|MRPL22_ENST00000522038.1_Intron	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	NA		NA			translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			tgggattacaggcatgagcca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515	29093		Mitochondrial ribosomal proteins / large subunits	14480	protein-coding gene	gene with protein product		611835			NA		Standard		NM_014180	NA	Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.77+2970G>A	chr5.hg19:g.154323795G>A		NA	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	hg19	CCDS4331.1	0.02	-0.201771	ACAxGCA	COVERED																																																																																			NOVEL	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252508.2	8	4.212633	KEEP	2	0	0	14	432	GG	0.994391	0.487793	0		+	3	60	92	0	0	6.892355	18	60	626	57	ENST00000523037.1	0.142857	0.490544
SGCD	6444	__UNKNOWN__	__UNKNOWN__	5	155432703	155432703	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:155432703G>A	ENST00000517913.1	+	2	81							Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	NA		NA			muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ctcatgatccgcccgccttgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29				6444			10807	protein-coding gene	gene with protein product		601411	sarcoglycan, delta (35kD dystrophin-associated glycoprotein)		NA	8776597, 8841194, 10974018	Standard		NM_000337	NA	Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000517913.1:c.-281-112185G>A	chr5.hg19:g.155432703G>A		NA	A8K9S9|Q53XA5|Q99644	hg19	CCDS47326.1	0.02	-0.166667	TCCxCCC	COVERED																																																																																			NOVEL	SGCD-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373502.2	10	3.911573	KEEP	3	0	0	13	399	GG	0.993072	0.351495	0		+	3	60	94	0	0	7.310232	15	60	490	48	ENST00000517913.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	156275333	156275333	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:156275333C>T			NA	NA				RNU6-556P (34088 upstream) : TIMD4 (70959 downstream)						NA		NA									NA						cccgtaatccctgcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.156275333C>T		NA		hg19		0.02	-0.148796	TCCxTGC	COVERED																																																																																			NOVEL					0			10	4.21263	KEEP	1	0	0	14	432	CC	0.994391	0.290363	0			3	60	91	0	0	7.276229	12	60	382	42		0.2	0.292001
TIMD4	91937	__UNKNOWN__	__UNKNOWN__	5	156357245	156357245	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:156357245A>T	ENST00000274532.2	-	6	901				TIMD4_ENST00000407087.3_Intron|TIMD4_ENST00000406964.1_Intron	NM_138379.2	NP_612388.2	Q96H15	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain containing 4	NA		NA				integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(23)|ovary(2)|skin(2)	37	Renal(175;0.00488)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			gtgctgggataacaggcatga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008988	CCDS4332.1, CCDS54943.1	5q33.3	2013-01-11			ENSG00000145850	ENSG00000145850	91937		Immunoglobulin superfamily / V-set domain containing	25132	protein-coding gene	gene with protein product		610096			NA	12477932	Standard	NM_138379	NM_001146726	NA	Approved		uc003lwh.2	Q96H15	OTTHUMG00000130244	ENST00000274532.2:c.845-3922T>A	chr5.hg19:g.156357245A>T		NA	B5MCL9	hg19	CCDS4332.1	0.02	-0.131537	GATxACA	COVERED																																																																																			NOVEL	TIMD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252568.1	6	2.405241	KEEP	0	0	0	8	210	AA	0.99257	0.22747	0		-	3	60	89	0	0	7.17332	11	60	313	32	ENST00000274532.2	0.214286	0.229173
HAVCR2	84868	__UNKNOWN__	__UNKNOWN__	5	156522964	156522964	__UNKNOWN__	Intron	SNP	C	C	T	rs571939842		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:156522964C>T	ENST00000307851.4	-	5	1253				HAVCR2_ENST00000522593.1_Intron	NM_032782.4	NP_116171.3	Q8TDQ0	HAVR2_HUMAN	hepatitis A virus cellular receptor 2	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				cervix(1)|large_intestine(4)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			Aggccgggcgcggtggctaat	0.517		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16518	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027334	CCDS4333.1	5q34	2014-01-14			ENSG00000135077	ENSG00000135077	84868		Immunoglobulin superfamily / V-set domain containing	18437	protein-coding gene	gene with protein product	T-cell immunoglobulin mucin family member 3	606652			NA	11823861	Standard		NM_032782	NA	Approved	Tim-3, TIM3, FLJ14428, TIMD3	uc003lwk.2	Q8TDQ0	OTTHUMG00000130249	ENST00000307851.4:c.523-494G>A	chr5.hg19:g.156522964C>T		NA	B2RAY2|Q8WW60|Q96K94	hg19	CCDS4333.1	0.02	-0.131578	GCGxGGT	COVERED																																																																																			NOVEL	HAVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252574.2	3	3.309544	KEEP	1	0	0	11	331	CC	0.992708	0.227502	0		-	3	60	86	0	0	6.772401	12	60	408	36	ENST00000307851.4	0.2	0.229173
MED7	9443	__UNKNOWN__	__UNKNOWN__	5	156567838	156567838	__UNKNOWN__	Intron	SNP	C	C	T	rs246859	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:156567838C>T	ENST00000286317.5	-	2	365				MED7_ENST00000420343.1_Intron	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	NA		NA			gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			caggcgtgagccaccacaccc	0.413		NA											C|||	1657	0.330871	0.5749	0.2089	5008	,	,	NA	19410	0.1825	NA	0.3191	False	NA	,,,	NA	NA	NA	2504	0.2526	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868	9443			2378	protein-coding gene	gene with protein product		605045	cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa	CRSP9	NA	9989412	Standard	NM_004270	NM_004270	NA	Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.17-1379G>A	chr5.hg19:g.156567838C>T		NA		hg19	CCDS4334.1	0.02	-0.096488	GAGxCAC	UNCOVERED																																																																																			NOVEL	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252567.2	4	2.407023	KEEP	4	0	0	8	240	CC	0	0	0		-	4	60	118	0	0	11.02245	5	60	175	26	ENST00000286317.5	0.444444	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	157047072	157047072	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:157047072G>A			NA	NA				RNU6-390P (40465 upstream) : SOX30 (5614 downstream)						NA		NA									NA						AGAAggggaggggaggggagg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.157047072G>A		NA		hg19		0.02	-0.210532	GAGxGGA	COVERED																																																																																			NOVEL					0			24	7.220118	KEEP	1	0	0	24	713	GG	0.999909	0.522114	0			3	60	87	0	0	6.327876	19	60	640	62		0.136364	0.522161
CTB-11I22.1	0	__UNKNOWN__	__UNKNOWN__	5	158640754	158640754	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:158640754A>G	ENST00000521204.1	+	0	191										NA		NA									NA						gagccacagcacctggccTAG	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000521204.1:	chr5.hg19:g.158640754A>G		NA		hg19		0.02	-0.149055	AGCxCCT	COVERED																																																																																			NOVEL	CTB-11I22.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000373925.1	2	2.705334	KEEP	0	0	0	9	232	AA	0.99254	0.320398	0		+	3	60	89	0	0	6.893034	14	60	398	40	ENST00000521204.1	0.176471	0.322807
CTB-11I22.1	0	__UNKNOWN__	__UNKNOWN__	5	158672162	158672162	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:158672162T>C	ENST00000521204.1	+	0	191										NA		NA									NA						tctctgttgcttaggctggag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000521204.1:	chr5.hg19:g.158672162T>C		NA		hg19		0.02	-0.192957	TGCxTAG	COVERED																																																																																			NOVEL	CTB-11I22.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000373925.1	6	2.405769	KEEP	0	0	0	8	216	TT	0.99257	0.454356	0		+	4	60	126	1	0	10.06925	17	60	511	37	ENST00000521204.1	0.190476	0.457757
TTC1	7265	__UNKNOWN__	__UNKNOWN__	5	159456398	159456398	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:159456398C>T	ENST00000231238.5	+	3	440				TTC1_ENST00000522793.1_Intron	NM_001282500.1|NM_003314.1	NP_001269429.1|NP_003305.1	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1	NA		NA			protein folding (GO:0006457)	peroxisomal membrane (GO:0005778)	unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(1)|prostate(1)|skin(1)	12	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		cctgtaatctcagcaccttgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U46570	CCDS4348.1	5q32-q33.2	2013-01-10			ENSG00000113312	ENSG00000113312	7265		Tetratricopeptide (TTC) repeat domain containing	12391	protein-coding gene	gene with protein product		601963			NA	8836031	Standard	NM_003314	NM_003314	NA	Approved	TPR1	uc003lxu.3	Q99614	OTTHUMG00000130326	ENST00000231238.5:c.331-5749C>T	chr5.hg19:g.159456398C>T		NA	B2RCT2|D3DQJ8|Q9BVT3	hg19	CCDS4348.1	0.02	-0.184201	TCTxAGC	COVERED																																																																																			NOVEL	TTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252675.3	9	3.008132	KEEP	0	0	0	10	287	CC	0.992708	0.42039	0		+	3	60	84	0	0	6.310883	15	60	492	39	ENST00000231238.5	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	159549007	159549007	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:159549007C>T			NA	NA				PWWP2A (2577 upstream) : AC008706.1 (7209 downstream)						NA		NA									NA						TTAAAGGggccgggcgcggtg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.159549007C>T		NA		hg19		0.02	-0.157885	GGCxGGG	COVERED																																																																																			NOVEL					0			3	2.707781	KEEP	0	0	0	9	270	CC	0.99254	0.320398	0			3	60	92	0	0	7.372274	12	60	381	34		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	159559334	159559334	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:159559334A>C			NA	NA				AC008706.1 (3054 upstream) : FABP6 (55039 downstream)						NA		NA									NA						cagtggctcaagcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.159559334A>C		NA		hg19		0.02	-0.140337	TCAxGCC	COVERED																																																																																			NOVEL					0			10	2.405819	KEEP	0	0	0	8	215	AT	0.99254	0.384517	0			3	60	98	0	0	7.972326	12	60	359	37		0.2	0.387407
CCNJL	79616	__UNKNOWN__	__UNKNOWN__	5	159692382	159692382	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:159692382C>T	ENST00000257536.7	-	4	566				CCNJL_ENST00000377503.2_Intron|CCNJL_ENST00000541762.1_Intron|CCNJL_ENST00000519673.1_Intron|CCNJL_ENST00000393977.3_Intron			Q8IV13	CCNJL_HUMAN	cyclin J-like	NA		NA				nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tggtggctcacgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083	79616			25876	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024565	XM_005265982	NA	Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000257536.7:c.281-5604G>A	chr5.hg19:g.159692382C>T		NA	Q6ZN43|Q9H7W8	hg19		0.02	-0.15787	TCAxGCC	COVERED																																																																																			NOVEL	CCNJL-002	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000374062.1	8	2.406741	KEEP	0	0	0	8	235	CC	0.99257	0.320408	0		-	4	60	107	0	0	8.581146	13	60	425	36	ENST00000257536.7	0.235294	0.322807
ATP10B	23120	__UNKNOWN__	__UNKNOWN__	5	160001158	160001158	__UNKNOWN__	Intron	SNP	T	T	C	rs548996882	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:160001158T>C	ENST00000327245.5	-	25	4597					NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	NA		NA			phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tacatctggctgggtgcggtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322	23120		ATPases / P-type	13543	protein-coding gene	gene with protein product		NA	ATPase, Class V, type 10B		NA	9872452, 11015572	Standard	NM_025153	NM_025153	NA	Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.3751-4468A>G	chr5.hg19:g.160001158T>C		NA	Q9H725	hg19	CCDS43394.1	0.02	-0.14034	GGCxGGG	COVERED																																																																																			NOVEL	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374127.1	5	2.40558	KEEP	0	0	0	8	217	TT	0.99257	0.259026	0		-	3	60	94	0	0	7.672907	11	60	336	37	ENST00000327245.5	0.214286	0.260965
ATP10B	23120	__UNKNOWN__	__UNKNOWN__	5	160097970	160097970	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:160097970G>A	ENST00000327245.5	-	7	1317					NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	NA		NA			phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tcaggagttcgagaccagcct	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322	23120		ATPases / P-type	13543	protein-coding gene	gene with protein product		NA	ATPase, Class V, type 10B		NA	9872452, 11015572	Standard	NM_025153	NM_025153	NA	Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.471-296C>T	chr5.hg19:g.160097970G>A		NA	Q9H725	hg19	CCDS43394.1	0.02	-0.140343	TTCxAGA	COVERED																																																																																			NOVEL	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374127.1	9	5.415523	KEEP	2	0	0	18	535	GG	0.997832	0.260399	0		-	3	24	89	0	0	7.072363	12	60	392	46	ENST00000327245.5	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	161359273	161359273	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:161359273T>C			NA	NA				GABRA1 (32298 upstream) : GABRG2 (135272 downstream)						NA		NA									NA						gctgggattataggcgtgagc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.161359273T>C		NA		hg19		0.02	-0.087704	TTAxAGG	UNCOVERED																																																																																			NOVEL					0			8	2.706054	KEEP	0	0	0	9	239	TT	0.99254	0.098977	0			3	60	97	0	0	8.832594	5	60	151	23		0.375	0.099721
MAT2B	27430	__UNKNOWN__	__UNKNOWN__	5	162932535	162932535	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:162932535A>G	ENST00000280969.5	+	1	311					NM_182796.1	NP_877725.1	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|extracellular polysaccharide biosynthetic process (GO:0045226)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|regulation of catalytic activity (GO:0050790)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|methionine adenosyltransferase complex (GO:0048269)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dTDP-4-dehydrorhamnose reductase activity (GO:0008831)|enzyme binding (GO:0019899)|methionine adenosyltransferase regulator activity (GO:0048270)			endometrium(3)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	14	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)	AGCGTGGCCAATCAACGGGCG	0.701		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF182814	CCDS4364.1, CCDS4365.1	5q34-q35	2011-09-14			ENSG00000038274	ENSG00000038274	27430		Short chain dehydrogenase/reductase superfamily / Extended SDR fold	6905	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 23E, member 1	605527			NA	9055605, 10644686, 19027726	Standard	NM_013283	NM_182796	NA	Approved	MATIIbeta, SDR23E1	uc003lzk.4	Q9NZL9	OTTHUMG00000130379	ENST00000280969.5:c.30+2105A>G	chr5.hg19:g.162932535A>G		NA	B2R5Y6|Q1WAI7|Q27J92|Q3LIE8|Q567T7|Q6NYC7|Q9BS89|Q9H3E1|Q9UJ54	hg19	CCDS4364.1	0.02	-0.078937	CCAxTCA	UNCOVERED																																																																																			NOVEL	MAT2B-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252748.3	0	3.608731	KEEP	0	0	0	12	327	AA	0.993634	0.076843	0		+	3	60	105	0	0	9.443934	6	60	176	26	ENST00000280969.5	0.333333	0.077336
PANK3	79646	__UNKNOWN__	__UNKNOWN__	5	168001780	168001780	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:168001780T>C	ENST00000239231.6	-	1	345					NM_024594.3	NP_078870.1	Q9H999	PANK3_HUMAN	pantothenate kinase 3	NA		NA			coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			NS(1)|cervix(2)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	Renal(175;0.000159)|Lung NSC(126;0.0441)|all_lung(126;0.0909)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0989)|OV - Ovarian serous cystadenocarcinoma(192;0.147)|Epithelial(171;0.188)		gcaggagaattgcttgaaccc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022961	CCDS4368.1	5q35.1	2008-02-05			ENSG00000120137	ENSG00000120137	79646			19365	protein-coding gene	gene with protein product		606161			NA	11479594	Standard	NM_024594	NM_024594	NA	Approved	FLJ12899	uc003lzz.2	Q9H999	OTTHUMG00000130410	ENST00000239231.6:c.28+4480A>G	chr5.hg19:g.168001780T>C		NA	D3DQL1|Q53FJ9|Q7RTX4	hg19	CCDS4368.1	0.02	-0.035086	AATxGCT	UNCOVERED																																																																																			NOVEL	PANK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252793.2	6	2.697077	KEEP	1	0	0	9	236	TT	0.99254	0.019833	0		-	2	60	67	0	0	6.450189	2	60	59	20	ENST00000239231.6	0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	170760928	170760928	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:170760928C>G			NA	NA				TLX3 (21790 upstream) : RN7SL339P (25192 downstream)						NA		NA									NA						gccgggtgtgctggtgcacaa	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.170760928C>G		NA		hg19		0.02	-0.043863	GTGxTGG	UNCOVERED																																																																																			NOVEL					0			4	2.708197	KEEP	0	0	0	9	283	CC	0.99254	0.023894	0			2	51	70	0	0	6.492849	3	60	97	17		0.4	0.024074
UBTD2	92181	__UNKNOWN__	__UNKNOWN__	5	171678050	171678050	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:171678050A>G	ENST00000393792.2	-	2	476					NM_152277.2	NP_689490.2	Q8WUN7	UBTD2_HUMAN	ubiquitin domain containing 2	NA		NA				cytoplasm (GO:0005737)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|skin(1)	10	Renal(175;0.000159)|Lung NSC(126;0.00976)|all_lung(126;0.0156)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			cgggcacggtagctcacgcct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF251700	CCDS4379.2	5q35.1	2008-10-30			ENSG00000168246	ENSG00000168246	92181			24463	protein-coding gene	gene with protein product	dendritic cell derived ubiquitin like protein	610174			NA	12507522	Standard	NM_152277	NM_152277	NA	Approved	DC-UbP, MGC30022	uc003mbp.1	Q8WUN7	OTTHUMG00000130519	ENST00000393792.2:c.71-16688T>C	chr5.hg19:g.171678050A>G		NA	Q8TDQ3	hg19	CCDS4379.2	0.02	-0.157785	GGTxGCT	COVERED																																																																																			NOVEL	UBTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252936.1	10	3.308374	KEEP	0	0	0	11	302	AA	0.993072	0.32057	0		-	3	60	95	0	0	7.673522	12	60	342	41	ENST00000393792.2	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	171724583	171724583	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:171724583T>C			NA	NA				UBTD2 (13508 upstream) : SH3PXD2B (27601 downstream)						NA		NA									NA						aggctggtcttgaactcctga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.171724583T>C		NA		hg19		0.02	-0.0877	TCTxGAA	UNCOVERED																																																																																			NOVEL					0			9	3.607751	KEEP	1	0	0	12	313	TT	0.993072	0.09903	0			3	44	91	0	1	8.043628	6	60	171	32		0.333333	0.099721
SH3PXD2B	285590	__UNKNOWN__	__UNKNOWN__	5	171836970	171836970	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:171836970C>T	ENST00000519643.1	-	3	162				SH3PXD2B_ENST00000311601.5_Intron			A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	NA		NA			adipose tissue development (GO:0060612)|bone development (GO:0060348)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|eye development (GO:0001654)|heart development (GO:0007507)|podosome assembly (GO:0071800)|positive regulation of fat cell differentiation (GO:0045600)|protein localization to membrane (GO:0072657)|skeletal system development (GO:0001501)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|SH2 domain binding (GO:0042169)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0207)|all_neural(177;0.0625)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			tccacctgccccggcctccca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095834	CCDS34291.1	5q35.2	2008-02-05	2006-02-13	2006-02-13	ENSG00000174705	ENSG00000174705	285590			29242	protein-coding gene	gene with protein product		613293	KIAA1295	KIAA1295	NA	10718198	Standard	NM_017963	NM_001017995	NA	Approved	FLJ20831	uc003mbr.3	A1X283	OTTHUMG00000163280	ENST00000519643.1:c.157-3614G>A	chr5.hg19:g.171836970C>T		NA	B6F0V2|Q9P2Q1	hg19		0.02	-0.140354	GCCxCGG	COVERED																																																																																			NOVEL	SH3PXD2B-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000372450.1	3	2.380232	KEEP	1	0	0	8	212	CC	0.99257	0.259026	0		-	3	60	88	0	0	6.972236	12	60	413	35	ENST00000519643.1	0.2	0.260965
ERGIC1	57222	__UNKNOWN__	__UNKNOWN__	5	172337775	172337775	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:172337775A>G	ENST00000523291.1	+	4	253				ERGIC1_ENST00000326654.2_Intron|ERGIC1_ENST00000393784.3_Intron			Q969X5	ERGI1_HUMAN	endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)	9	Renal(175;0.000159)|Lung NSC(126;0.00344)|all_lung(126;0.00594)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			tgatccacccacctcagcctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF267855	CCDS34292.1	5q35.1	2009-11-06			ENSG00000113719	ENSG00000113719	57222			29205	protein-coding gene	gene with protein product		NA			NA	10574461, 15308636	Standard	NM_020462	NM_001031711	NA	Approved	ERGIC32, ERGIC-32, KIAA1181, NET24	uc003mbw.4	Q969X5	OTTHUMG00000130520	ENST00000523291.1:c.250+1011A>G	chr5.hg19:g.172337775A>G		NA	Q9H0L0|Q9H2J2|Q9ULN9	hg19		0.02	-0.184191	CCCxCCT	COVERED																																																																																			NOVEL	ERGIC1-013	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000329263.1	17	4.511889	KEEP	13	0	0	15	423	AA	0.993072	0.420544	0		+	4	60	125	0	0	10.162736	15	60	458	67	ENST00000523291.1	0.210526	0.423478
ATP6V0E1	8992	__UNKNOWN__	__UNKNOWN__	5	172454667	172454667	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:172454667A>G	ENST00000519374.1	+	4	386				ATP6V0E1_ENST00000519911.1_Intron|ATP6V0E1_ENST00000265093.4_Intron	NM_003945.3	NP_003936.1	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cell growth (GO:0016049)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|response to amino acid (GO:0043200)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)	ATPase activity, coupled to transmembrane movement of ions (GO:0042625)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			lung(2)	2	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ctgttacccaagctggtcttg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y15286	CCDS4383.1	5q35.2	2010-04-21	2006-10-12	2006-10-12	ENSG00000113732	ENSG00000113732	8992		ATPases / V-type	863	protein-coding gene	gene with protein product		603931	ATPase, H+ transporting, lysosomal (vacuolar proton pump) 9kD, ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e	ATP6H, ATP6V0E	NA	9556572, 14970230	Standard	NM_003945	NM_003945	NA	Approved	M9.2	uc003mcd.1	O15342	OTTHUMG00000130518	ENST00000519374.1:c.244-6735A>G	chr5.hg19:g.172454667A>G		NA	B2R557|D3DQM1|Q6IBE8	hg19	CCDS4383.1	0.02	-0.1929	CCAxGCT	COVERED																																																																																			NOVEL	ATP6V0E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252935.2	9	6.316278	KEEP	0	0	0	21	582	AA	0.999869	0.457697	0		+	3	60	104	0	0	8.233761	16	60	479	63	ENST00000519374.1	0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	172649024	172649024	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:172649024G>A			NA	NA				BNIP1 (57634 upstream) : NKX2-5 (10087 downstream)						NA		NA									NA						taaaaatacagaaattagccg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.172649024G>A		NA		hg19		0.02	-0.070173	ACAxAAA	UNCOVERED																																																																																			NOVEL					0			3	2.407076	KEEP	0	0	0	8	242	GG	0.99257	0.053735	0			3	60	87	0	0	8.05437	4	60	140	21		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	173235880	173235880	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:173235880G>C			NA	NA				CTB-43E15.4 (17935 upstream) : CPEB4 (79402 downstream)						NA		NA									NA						tgcctgtaatgccagcacttt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.173235880G>C		NA		hg19		0.02	-0.131591	AATxCCA	COVERED																																																																																			NOVEL					0			9	3.008752	KEEP	0	0	0	10	303	GG	0.992708	0.227502	0			4	60	137	0	0	11.97102	10	60	348	33		0.285714	0.229173
RP11-91H12.4	0	__UNKNOWN__	__UNKNOWN__	5	175347567	175347567	__UNKNOWN__	RNA	SNP	A	A	C	rs72823169		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175347567A>C	ENST00000502813.1	-	0	87										NA		NA									NA						tggcacaatcacagctcactg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502813.1:	chr5.hg19:g.175347567A>C		NA		hg19		0.02	-0.191945	ATCxCAG	COVERED																																																																																			NOVEL	RP11-91H12.4-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000470921.1	4	2.405709	KEEP	0	0	0	8	215	AT	0.992708	0.454419	0		-	4	60	133	0	0	10.875409	16	60	425	42	ENST00000502813.1	0.2	0.457757
RP11-91H12.4	0	__UNKNOWN__	__UNKNOWN__	5	175358247	175358247	__UNKNOWN__	RNA	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175358247A>T	ENST00000502813.1	-	0	87										NA		NA									NA						atcccagcacattgggaggcc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502813.1:	chr5.hg19:g.175358247A>T		NA		hg19		0.02	-0.254346	CACxTTG	COVERED																																																																																			NOVEL	RP11-91H12.4-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000470921.1	8	2.639177	KEEP	1	1	26	18	513	AA	0.999859	0.668429	0		-	3	50	93	0	0	6.69549	23	60	690	67	ENST00000502813.1	0.115385	0.668523
THOC3	84321	__UNKNOWN__	__UNKNOWN__	5	175392664	175392664	__UNKNOWN__	Intron	SNP	G	G	A	rs78058801		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175392664G>A	ENST00000265097.4	-	3	515				THOC3_ENST00000513482.1_Intron|THOC3_ENST00000510300.1_Intron|THOC3_ENST00000514861.1_Intron	NM_032361.2	NP_115737.1	Q96J01	THOC3_HUMAN	THO complex 3	NA		NA			mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)	4	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		tcctgacctcgtgatccgccc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006849	CCDS4397.1	5q35.3	2013-02-11			ENSG00000051596	ENSG00000051596	84321		WD repeat domain containing, THO complex subunits	19072	protein-coding gene	gene with protein product		606929			NA	11979277	Standard		NM_032361	NA	Approved	TEX1, MGC5469	uc003mdg.5	Q96J01	OTTHUMG00000130658	ENST00000265097.4:c.425-506C>T	chr5.hg19:g.175392664G>A		NA	Q6NZ53	hg19	CCDS4397.1	0.02	-0.201685	CTCxTGA	COVERED																																																																																			NOVEL	THOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253148.1	5	5.114188	KEEP	12	0	0	17	498	GG	0.993072	0.487146	0		-	5	60	134	0	0	10.781276	16	60	488	70	ENST00000265097.4	0.238095	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	175617669	175617669	__UNKNOWN__	IGR	SNP	G	G	A	rs376720461	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175617669G>A			NA	NA				RP11-844P9.2 (5511 upstream) : SIMC1 (47695 downstream)						NA		NA									NA						ttgggaggtcgaggcaggtgg	0.507		NA											.|||	6	0.00119808	0.0	0.0	5008	,	,	NA	15078	0.006	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.175617669G>A		NA		hg19		0.02	-0.11401	GTCxAGG	UNCOVERED																																																																																			NOVEL					0			4	2.706798	KEEP	0	0	0	9	263	GG	0.99254	0.161255	0			3	60	80	0	0	6.501189	9	60	285	34		0.25	0.162467
SIMC1	375484	__UNKNOWN__	__UNKNOWN__	5	175720187	175720187	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175720187C>T	ENST00000430704.2	+	2	271				SIMC1_ENST00000341199.6_Intron|SIMC1_ENST00000429602.2_Intron|SIMC1_ENST00000443967.1_Intron			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	NA		NA					SUMO polymer binding (GO:0032184)				NA						acgcctgtaaccccagcattt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085	375484			24779	protein-coding gene	gene with protein product	oocyte maturation associated 1, platform element for inhibition of autolytic degradation	NA	chromosome 5 open reading frame 25	C5orf25	NA	23086935, 23707407	Standard	NM_198567	NM_198567	NA	Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000430704.2:c.130-1846C>T	chr5.hg19:g.175720187C>T		NA	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	hg19	CCDS4398.2	0.02	-0.184218	TAAxCCC	COVERED																																																																																			NOVEL	SIMC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329099.2	5	2.406479	KEEP	0	0	0	8	239	CC	0.99257	0.420331	0		+	3	60	87	0	0	6.610635	15	60	521	43	ENST00000430704.2	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	175816975	175816975	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175816975A>G			NA	NA				HIGD2A (203 upstream) : CLTB (2480 downstream)						NA		NA									NA						cctgaggtcaagagttcaaga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.175816975A>G		NA		hg19		0.02	-0.140314	TCAxGAG	COVERED																																																																																			NOVEL					0			6	2.706695	KEEP	2	0	0	9	247	AA	0.99257	0.289832	0			3	60	93	0	0	7.472668	12	60	351	37		0.2	0.292001
FAF2	23197	__UNKNOWN__	__UNKNOWN__	5	175882549	175882549	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175882549G>A	ENST00000261942.6	+	1	116				FAF2_ENST00000510446.1_Intron	NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	NA		NA			lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						ccaggagtttgagaccagcct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194	23197		UBX domain containing	24666	protein-coding gene	gene with protein product	expressed in T cells and eosinophils in atopic dermatitis, UBX domain protein 3B	NA	UBX domain containing 8	UBXD8	NA	10048485, 12372427	Standard	NM_014613	NM_014613	NA	Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.63+7078G>A	chr5.hg19:g.175882549G>A		NA	O94963|Q8IUF2|Q9BRP2|Q9BVM7	hg19	CCDS34296.1	0.02	-0.166657	TTTxAGA	COVERED																																																																																			NOVEL	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372194.1	15	3.008408	KEEP	5	0	0	10	299	GG	0.99257	0.351317	0		+	3	33	90	1	0	6.910461	15	60	490	44	ENST00000261942.6	0.166667	0.353947
CDHR2	54825	__UNKNOWN__	__UNKNOWN__	5	175983389	175983389	__UNKNOWN__	Intron	SNP	C	C	T	rs180925428		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175983389C>T	ENST00000510636.1	+	2	259				CDHR2_ENST00000261944.5_Intron	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	NA		NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTAAACAggccgggcgcggtg	0.597		NA											c|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17872	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276	54825		Cadherins / Cadherin-related	18231	protein-coding gene	gene with protein product	protocadherin LKC	NA	protocadherin 24	PCDH24	NA	11082270, 12117771	Standard	NM_017675	NM_001171976	NA	Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.-15-8950C>T	chr5.hg19:g.175983389C>T		NA	A1L3U4|A6NC80|Q9NXP8	hg19	CCDS34297.1	0.02	-0.210531	GGCxGGG	COVERED																																																																																			NOVEL	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372201.1	9	3.308223	KEEP	8	0	0	11	314	CC	0.99257	0.518282	0		+	3	60	92	0	0	6.70606	21	60	696	58	ENST00000510636.1	0.125	0.522161
CDHR2	54825	__UNKNOWN__	__UNKNOWN__	5	175985743	175985743	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:175985743G>A	ENST00000510636.1	+	2	259				CDHR2_ENST00000261944.5_Intron	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	NA		NA			cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						ggatggtctcgatctcctgac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276	54825		Cadherins / Cadherin-related	18231	protein-coding gene	gene with protein product	protocadherin LKC	NA	protocadherin 24	PCDH24	NA	11082270, 12117771	Standard	NM_017675	NM_001171976	NA	Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.-15-6596G>A	chr5.hg19:g.175985743G>A		NA	A1L3U4|A6NC80|Q9NXP8	hg19	CCDS34297.1	0.02	-0.140327	CTCxATC	UNCOVERED																																																																																			NOVEL	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000372201.1	7	2.406329	KEEP	1	0	0	8	231	GG	0	0	0		+	3	60	87	0	0	6.779304	13	60	394	33	ENST00000510636.1	0.1875	0.260965
UIMC1	51720	__UNKNOWN__	__UNKNOWN__	5	176350615	176350615	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176350615T>A	ENST00000377227.4	-	11	1730				UIMC1_ENST00000506128.1_Intron|UIMC1_ENST00000511320.1_Intron|UIMC1_ENST00000503273.1_Intron|UIMC1_ENST00000377219.2_Intron			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	NA		NA			double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ctgtaatccctgcactttggg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206	51720			30298	protein-coding gene	gene with protein product	receptor associated protein 80	609433			NA	12080054	Standard	NM_016290	NM_001199297	NA	Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1598-12225A>T	chr5.hg19:g.176350615T>A		NA	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	hg19	CCDS4408.1	0.02	-0.245584	CCCxGCA	COVERED																																																																																			NOVEL	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253422.1	7	3.308166	KEEP	0	0	0	11	304	TT	0.993072	0.636904	0		-	3	60	90	0	0	6.450081	22	60	674	52	ENST00000377227.4	0.12	0.641347
UIMC1	51720	__UNKNOWN__	__UNKNOWN__	5	176405144	176405144	__UNKNOWN__	Intron	SNP	G	G	A	rs181457075	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176405144G>A	ENST00000377227.4	-	3	280				UIMC1_ENST00000506128.1_Intron|UIMC1_ENST00000511320.1_Intron|UIMC1_ENST00000377219.2_Intron			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	NA		NA			double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			aggccgaggcggacggatcac	0.502		NA											G|||	31	0.0061901	0.0015	0.0058	5008	,	,	NA	11352	0.001	NA	0.0179	False	NA	,,,	NA	NA	NA	2504	0.0061	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206	51720			30298	protein-coding gene	gene with protein product	receptor associated protein 80	609433			NA	12080054	Standard	NM_016290	NM_001199297	NA	Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.148-2663C>T	chr5.hg19:g.176405144G>A		NA	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	hg19	CCDS4408.1	0.02	-0.236624	GGCxGAC	COVERED																																																																																			NOVEL	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253422.1	27	3.529654	KEEP	51	2	57	32	927	GG	0.99649	0.639096	0		-	3	60	91	0	0	6.935105	16	60	518	151	ENST00000377227.4	0.157895	0.641347
ZNF346	23567	__UNKNOWN__	__UNKNOWN__	5	176472609	176472609	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176472609G>A	ENST00000503425.1	+	3	456				ZNF346_ENST00000512315.1_Intron|ZNF346_ENST00000511834.1_Intron|ZNF346_ENST00000358149.3_Intron|ZNF346_ENST00000503039.1_Intron|ZNF346_ENST00000506693.1_Intron|ZNF346_ENST00000261948.4_Intron			Q9UL40	ZN346_HUMAN	zinc finger protein 346	NA		NA			positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cacctgcctcggcctcccaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761	23567			16403	protein-coding gene	gene with protein product		605308			NA	10488071	Standard	NM_012279	NM_012279	NA	Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000503425.1:c.421+1075G>A	chr5.hg19:g.176472609G>A		NA	B7Z367|Q68CV9|Q6ZMW1	hg19		0.02	-0.14034	CTCxGCC	COVERED																																																																																			NOVEL	ZNF346-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000372584.1	4	2.406296	KEEP	2	0	0	8	228	GG	0.99257	0.259026	0		+	3	60	85	0	0	6.579382	13	60	422	34	ENST00000503425.1	0.1875	0.260965
ZNF346	23567	__UNKNOWN__	__UNKNOWN__	5	176478472	176478472	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176478472A>G	ENST00000503425.1	+	4	642				ZNF346_ENST00000512315.1_Intron|ZNF346_ENST00000511834.1_Intron|ZNF346_ENST00000358149.3_Intron|ZNF346_ENST00000503039.1_Intron|ZNF346_ENST00000506693.1_Intron|ZNF346_ENST00000261948.4_Intron			Q9UL40	ZN346_HUMAN	zinc finger protein 346	NA		NA			positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	14	all_cancers(89;6.3e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			caccgcgcccagccctctttc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF083340	CCDS4409.1	5q35.3	2012-10-05			ENSG00000113761	ENSG00000113761	23567			16403	protein-coding gene	gene with protein product		605308			NA	10488071	Standard	NM_012279	NM_012279	NA	Approved	JAZ, Zfp346	uc003mfi.3	Q9UL40	OTTHUMG00000130848	ENST00000503425.1:c.607+535A>G	chr5.hg19:g.176478472A>G		NA	B7Z367|Q68CV9|Q6ZMW1	hg19		0.02	-0.201715	CCCxGCC	COVERED																																																																																			NOVEL	ZNF346-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000372584.1	10	3.910097	KEEP	0	0	0	13	362	AA	0.994391	0.487793	0		+	3	60	108	0	0	8.560691	17	60	496	50	ENST00000503425.1	0.15	0.490544
NSD1	64324	__UNKNOWN__	__UNKNOWN__	5	176637576	176637576	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs28932178	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176637576T>C	ENST00000439151.2	+	5	2221	c.2176T>C	c.(2176-2178)Tct>Cct	p.S726P	NSD1_ENST00000354179.4_Missense_Mutation_p.S457P|NSD1_ENST00000347982.4_Missense_Mutation_p.S457P|NSD1_ENST00000361032.4_Missense_Mutation_p.S623P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	726		NA	S -> P (in dbSNP:rs28932178). {ECO:0000269|PubMed:12464997, ECO:0000269|PubMed:18987736}.		gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		AACCGAGACGTCTCAGGTTAA	0.423		NA	T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			T|||	1250	0.249601	0.1059	0.2233	5008	,	,	NA	19001	0.5119	NA	0.1441	False	NA	,,,	NA	NA	NA	2504	0.3006	NA	NA	NA			Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	0								T	PRO/SER,PRO/SER	452,3954	216.8+/-235.3	21,410,1772	74	75	75		2176,1369	1.3	0.3	5	dbSNP_125	75	1191,7409	241.8+/-272.0	88,1015,3197	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	74,74	109,1425,4969	CC,CT,TT	NA	13.8488,10.2587,12.6326	probably-damaging,probably-damaging	726/2697,457/2428	176637576	1643,11363	2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671	64324		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	14234	protein-coding gene	gene with protein product		606681	Sotos syndrome	STO	NA	9628876, 11896389	Standard	NM_172349	NM_022455	NA	Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.2176T>C	chr5.hg19:g.176637576T>C	ENSP00000395929:p.Ser726Pro	NA	Q96PD8|Q96RN7	hg19	CCDS4412.1	0.02	3.473091	ACGxCTC	COVERED	528	0.24175824175824176	49	0.09959349593495935	74	0.20441988950276244	292	0.5104895104895105	113	0.14907651715039577	T	8.852	0.944892	0.18356	0.102587	0.138488	ENSG00000165671	ENST00000354179;ENST00000355783;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93547	-3.14;-3.14;-3.14;-3.24	5.1	1.28	0.21552	.	0.528179	0.19032	N	0.124511	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	D;D;D	0.76494	0.999;0.994;0.998	D;P;P	0.64776	0.929;0.865;0.852	T	0.25779	-1.0122	8	.	.	.	.	4.1853	0.10395	0.0:0.3131:0.1764:0.5105	rs28932178;rs28932178	457;623;726	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	P	457;457;726;457;623	ENSP00000346111:S457P;ENSP00000395929:S726P;ENSP00000343209:S457P;ENSP00000354310:S623P	.	S	+	1	0	NSD1	176570182	0.350000	0.24878	0.254000	0.24359	0.004000	0.04260	0.397000	0.20883	0.130000	0.18549	0.533000	0.62120	TCT	NOVEL	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253412.2	0	4.742752	KEEP	0	1	29	26	710	TT	0.999988	0.999987	0		+	6	60	197	0	0	12.139163	118	60	3537	233	ENST00000439151.2	0.048387	1
NSD1	64324	__UNKNOWN__	__UNKNOWN__	5	176647974	176647974	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176647974T>C	ENST00000439151.2	+	5	3841				NSD1_ENST00000354179.4_Intron|NSD1_ENST00000347982.4_Intron|NSD1_ENST00000361032.4_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	NA		NA			gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		aagcgattcttgtgcctcagc	0.507		NA	T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)											NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671	64324		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	14234	protein-coding gene	gene with protein product		606681	Sotos syndrome	STO	NA	9628876, 11896389	Standard	NM_172349	NM_022455	NA	Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.3796+8778T>C	chr5.hg19:g.176647974T>C		NA	Q96PD8|Q96RN7	hg19	CCDS4412.1	0.02	1.690269	TCTxGTG	COVERED																																																																																			NOVEL	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253412.2	24	5.374475	KEEP	1	2	66	41	1087	TT	1	0.999862	0		+	5	60	165	0	0	10.743742	76	60	2144	184	ENST00000439151.2	0.061728	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	176784777	176784777	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176784777C>T			NA	NA				LMAN2 (5924 upstream) : RGS14 (60 downstream)						NA		NA									NA						tgtgtgtgtgcgcgtgtgtgt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.176784777C>T		NA		hg19		0.02	0.914504	GTGxGCG	COVERED																																																																																			NOVEL					0			11	6.250719	KEEP	0	1	23	29	873	CC	0.999997	0.999801	0			5	60	145	0	0	8.746508	76	60	2522	157		0.061728	0.999804
SLC34A1	6569	__UNKNOWN__	__UNKNOWN__	5	176814109	176814109	__UNKNOWN__	Intron	SNP	T	T	C	rs111689041	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:176814109T>C	ENST00000512593.1	+	5	633				SLC34A1_ENST00000324417.5_Intron	NM_001167579.1	NP_001161051.1	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	NA		NA			arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cagtggctcatgcctgtaatc	0.532		NA											C|||	107	0.0213658	0.0219	0.0865	5008	,	,	NA	18978	0.0069	NA	0.007	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183	6569		Solute carriers	11019	protein-coding gene	gene with protein product	sodium/phosphate co-transporter, solute carrier family 17 (sodium phosphate), member 2, Na+-phosphate cotransporter type II	182309	solute carrier family 34 (sodium phosphate), member 1	NPT2, SLC17A2	NA	8327470, 8693007	Standard	NM_003052	NM_003052	NA	Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000512593.1:c.532+542T>C	chr5.hg19:g.176814109T>C		NA	B4DPE3	hg19	CCDS54953.1	0.02	-0.236801	TCAxGCC	UNCOVERED																																																																																			NOVEL	SLC34A1-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373162.1	11	2.405986	KEEP	2	0	0	8	218	TT	0	0	0		+	3	60	94	0	0	6.907037	21	60	622	51	ENST00000512593.1	0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	177555319	177555319	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:177555319T>C			NA	NA				N4BP3 (2231 upstream) : RMND5B (2677 downstream)						NA		NA									NA						ctcagcctcctaaagtgctgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.177555319T>C		NA		hg19		0.02	-0.271882	TCCxAAA	COVERED																																																																																			NOVEL					0			9	2.707011	KEEP	1	0	0	9	253	TT	0.99254	0.711964	0			3	60	97	0	0	7.20588	21	60	632	54		0.125	0.717315
COL23A1	91522	__UNKNOWN__	__UNKNOWN__	5	177799842	177799842	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:177799842A>G	ENST00000390654.3	-	3	719				COL23A1_ENST00000407622.1_Intron	NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	NA		NA			collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		ctcccaaagtactgggattac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767	91522		Collagens	22990	protein-coding gene	gene with protein product		610043			NA	12644459	Standard	NM_173465	NM_173465	NA	Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.362-65922T>C	chr5.hg19:g.177799842A>G		NA	Q8IVR4|Q9NT93	hg19	CCDS4436.1	0.02	-0.210421	AGTxCTG	COVERED																																																																																			NOVEL	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253475.1	13	5.412323	KEEP	0	0	0	18	475	AA	0.999859	0.522088	0		-	4	60	134	0	0	10.869757	17	60	475	61	ENST00000390654.3	0.190476	0.522161
COL23A1	91522	__UNKNOWN__	__UNKNOWN__	5	177813194	177813194	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:177813194T>C	ENST00000390654.3	-	3	719				COL23A1_ENST00000407622.1_Intron	NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	NA		NA			collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		aatcctagcattttgggaggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767	91522		Collagens	22990	protein-coding gene	gene with protein product		610043			NA	12644459	Standard	NM_173465	NM_173465	NA	Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.362-79274A>G	chr5.hg19:g.177813194T>C		NA	Q8IVR4|Q9NT93	hg19	CCDS4436.1	0.02	-0.105239	GCAxTTT	UNCOVERED																																																																																			NOVEL	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253475.1	8	2.405966	KEEP	0	0	0	8	218	TT	0.99257	0.138793	0		-	3	60	101	0	0	8.878667	7	60	215	29	ENST00000390654.3	0.3	0.139832
COL23A1	91522	__UNKNOWN__	__UNKNOWN__	5	177976275	177976275	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:177976275A>G	ENST00000484750.1	-	3	359				COL23A1_ENST00000407622.1_Intron|COL23A1_ENST00000390654.3_Intron			Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	NA		NA			collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		gattacaggcatgagccacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767	91522		Collagens	22990	protein-coding gene	gene with protein product		610043			NA	12644459	Standard	NM_173465	NM_173465	NA	Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000484750.1:c.209+11407T>C	chr5.hg19:g.177976275A>G		NA	Q8IVR4|Q9NT93	hg19		0.02	-0.166614	GGCxTGA	COVERED																																																																																			NOVEL	COL23A1-002	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000315910.1	4	2.700806	KEEP	1	0	0	9	231	AA	0.99254	0.351306	0		-	4	60	122	0	0	10.202012	12	60	340	41	ENST00000484750.1	0.25	0.353947
ZNF354B	117608	__UNKNOWN__	__UNKNOWN__	5	178305165	178305165	__UNKNOWN__	Intron	SNP	A	A	T	rs56814168	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:178305165A>T	ENST00000322434.3	+	5	482					NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			cgggcggatcacgaggtcagg	0.552		NA											A|||	592	0.118211	0.2663	0.1066	5008	,	,	NA	13797	0.0	NA	0.1213	False	NA	,,,	NA	NA	NA	2504	0.045	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338	117608		Zinc fingers, C2H2-type, -	17197	protein-coding gene	gene with protein product		NA			NA		Standard	NM_058230	NM_058230	NA	Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.257-4545A>T	chr5.hg19:g.178305165A>T		NA	A8K0V2|Q5U5Z4	hg19	CCDS4439.1	0.02	-0.113964	ATCxCGA	UNCOVERED																																																																																			NOVEL	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253482.1	3	2.404732	KEEP	16	0	0	8	203	AA	0	0	0		+	5	60	154	0	1	14.025532	8	60	206	50	ENST00000322434.3	0.384615	0.162467
ZFP2	80108	__UNKNOWN__	__UNKNOWN__	5	178341146	178341146	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:178341146C>T	ENST00000361362.2	+	3	307				ZFP2_ENST00000503510.2_Intron|ZFP2_ENST00000520301.1_Intron|ZFP2_ENST00000523286.1_Intron	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		cgtgagccaccgtgcctggcc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939	80108		Zinc fingers, C2H2-type	26138	protein-coding gene	gene with protein product		NA	zinc finger protein 2 homolog (mouse)		NA		Standard	NM_030613	NM_030613	NA	Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.-224+1074C>T	chr5.hg19:g.178341146C>T		NA	A5PLN5|B7ZM23|Q9H6Z6	hg19	CCDS4440.1	0.02	-0.14912	CACxGTG	COVERED																																																																																			NOVEL	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253470.2	8	3.007572	KEEP	3	0	0	10	279	CC	0.99254	0.320398	0		+	3	60	91	0	0	7.091886	14	60	454	42	ENST00000361362.2	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	178861003	178861003	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:178861003C>G			NA	NA				RP11-443C10.2 (55137 upstream) : RP11-798K23.1 (21412 downstream)						NA		NA									NA						gtttcaccatcttggccaggc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.178861003C>G		NA		hg19		0.02	-0.078949	CATxTTG	UNCOVERED																																																																																			NOVEL					0			6	3.008905	KEEP	8	0	0	10	306	CC	0.99254	0.098977	0			3	60	104	0	0	9.343629	6	60	193	37		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	178910202	178910202	__UNKNOWN__	IGR	SNP	C	C	T	rs112338593	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:178910202C>T			NA	NA				RN7SL71P (16076 upstream) : RP11-798K23.4 (20120 downstream)						NA		NA									NA						ggctcacgcccgtaatcccag	0.473		NA											C|||	46	0.0091853	0.0038	0.0115	5008	,	,	NA	12406	0.003	NA	0.0249	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.178910202C>T		NA		hg19		0.02	-0.184177	GCCxGTA	COVERED																																																																																			NOVEL					0			7	3.608769	KEEP	2	0	0	12	326	CC	0.993634	0.420782	0			3	60	92	0	0	7.110606	15	60	442	48		0.166667	0.423478
RUFY1	80230	__UNKNOWN__	__UNKNOWN__	5	179016002	179016002	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:179016002A>G	ENST00000437570.2	+	8	1049				RUFY1_ENST00000319449.4_Intron|RUFY1_ENST00000377001.2_Intron|RUFY1_ENST00000393438.2_Intron	NM_001040451.2	NP_001035541.1	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	NA		NA			endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			aaagtgctggaattacaggtg	0.453		NA								HNSCC(44;0.11)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783	80230		Zinc fingers, FYVE domain containing	19760	protein-coding gene	gene with protein product		610327			NA	11877430	Standard	NM_001040451	NM_001040451	NA	Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000437570.2:c.703-545A>G	chr5.hg19:g.179016002A>G		NA	Q59FF3|Q71S93|Q9H6I3	hg19	CCDS34312.1	0.02	-0.209136	TGGxATT	COVERED																																																																																			NOVEL	RUFY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000371901.1	6	3.908922	KEEP	2	0	0	13	348	AA	0.994391	0.519232	0		+	3	60	95	0	0	7.203369	18	60	518	56	ENST00000437570.2	0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	179060258	179060258	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:179060258T>C			NA	NA				HNRNPH1 (8588 upstream) : C5orf60 (8286 downstream)						NA		NA									NA						tcccgaagtgttgggattaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.179060258T>C		NA		hg19		0.02	-0.175392	GTGxTGG	COVERED																																																																																			NOVEL					0			9	3.235825	KEEP	0	1	23	19	490	TT	0.999863	0.387354	0			3	60	101	0	0	8.092026	14	60	405	53		0.176471	0.387407
SQSTM1	8878	__UNKNOWN__	__UNKNOWN__	5	179253871	179253871	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:179253871G>A	ENST00000389805.4	+	5	932				SQSTM1_ENST00000360718.5_Intron|SQSTM1_ENST00000376929.3_Intron|SQSTM1_ENST00000402874.3_Intron|SQSTM1_ENST00000510187.1_Intron	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	NA		NA			apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			gtgagccaccgagcccggccA	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011	8878			11280	protein-coding gene	gene with protein product		601530	Paget disease of bone 3, oxidative stress induced like	PDB3, OSIL	NA	8650207, 8551575	Standard		NM_003900	NA	Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.754+1645G>A	chr5.hg19:g.179253871G>A		NA	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	hg19	CCDS34317.1	0.02	-0.219296	ACCxAGC	COVERED																																																																																			NOVEL	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319344.1	2	2.707075	KEEP	0	0	0	9	255	GG	0.99254	0.548763	0		+	3	60	89	0	0	6.465698	20	60	651	44	ENST00000389805.4	0.130435	0.552887
GFPT2	9945	__UNKNOWN__	__UNKNOWN__	5	179767553	179767553	__UNKNOWN__	Intron	SNP	C	C	T	rs538880624		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:179767553C>T	ENST00000253778.8	-	2	177					NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	NA		NA			carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	gctctgttgcccaggctggag	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459	9945			4242	protein-coding gene	gene with protein product	glutamine: fructose-6-phosphate aminotransferase 2	603865			NA	10198162	Standard	NM_005110	NM_005110	NA	Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.8-1953G>A	chr5.hg19:g.179767553C>T		NA	Q53XM2|Q9BWS4	hg19	CCDS43411.1	0.02	-0.087703	TGCxCAG	UNCOVERED																																																																																			NOVEL	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000373444.4	5	3.00884	KEEP	1	0	0	10	304	CC	0.992708	0.098994	0		-	3	60	77	0	0	6.477789	7	60	234	26	ENST00000253778.8	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	179862207	179862207	__UNKNOWN__	IGR	SNP	C	C	T	rs10073404	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:179862207C>T			NA	NA				GFPT2 (81820 upstream) : CTC-573N18.1 (6351 downstream)						NA		NA									NA						gcaatccatccgcctcggact	0.453		NA											C|||	1706	0.340655	0.1331	0.5043	5008	,	,	NA	15443	0.2282	NA	0.4891	False	NA	,,,	NA	NA	NA	2504	0.4683	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.179862207C>T		NA		hg19		0.02	-0.09649	ATCxGCC	UNCOVERED																																																																																			NOVEL					0			6	2.707905	KEEP	0	0	0	9	273	CC	0.99254	0.119538	0			5	60	153	0	0	14.674208	5	60	169	31		0.5	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	180291663	180291663	__UNKNOWN__	IGR	SNP	C	C	T	rs535788293		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180291663C>T			NA	NA				ZFP62 (3377 upstream) : BTNL8 (34413 downstream)						NA		NA									NA						ggattacaggcgtgagccact	0.522		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	16077	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.180291663C>T		NA		hg19		0.02	-0.122789	AGGxGTG	COVERED																																																																																			NOVEL					0			12	3.91136	KEEP	5	0	0	13	393	CC	0.993072	0.194952	0			3	60	91	0	0	7.482141	10	60	314	41		0.230769	0.196312
BTNL9	153579	__UNKNOWN__	__UNKNOWN__	5	180473031	180473031	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180473031C>A	ENST00000515271.1	+	2	167				BTNL9_ENST00000327705.9_Intron|BTNL9_ENST00000376841.2_Intron|BTNL9_ENST00000376842.3_Intron			Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	NA		NA				integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ccaccatctccccAGCCTGTA	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810	153579		Immunoglobulin superfamily / V-set domain containing, Butyrophilins	24176	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152547	NM_152547	NA	Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000515271.1:c.-98-1896C>A	chr5.hg19:g.180473031C>A		NA	A6NL42|Q6P660|Q96DM5	hg19		0.02	-0.096485	CTCxCCA	UNCOVERED																																																																																			NOVEL	BTNL9-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367224.1	20	2.540291	KEEP	9	1	27	18	546	CC	0.995343	0.119875	0		+	3	21	85	0	0	7.13204	8	54	272	42	ENST00000515271.1	0.272727	0.120436
BTNL9	153579	__UNKNOWN__	__UNKNOWN__	5	180486647	180486647	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180486647G>A	ENST00000327705.9	+	11	1624	c.1393G>A	c.(1393-1395)Gtg>Atg	p.V465M	BTNL9_ENST00000376842.3_Missense_Mutation_p.V466M	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	465	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA				integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTTCTTCAACGTGTCCGACGG	0.697		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													44	43	43			NA	NA	5		NA											NA				180486647		2203	4300	6503	SO:0001583	missense			AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810	153579		Immunoglobulin superfamily / V-set domain containing, Butyrophilins	24176	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152547	NM_152547	NA	Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.1393G>A	chr5.hg19:g.180486647G>A	ENSP00000330200:p.Val465Met	NA	A6NL42|Q6P660|Q96DM5	hg19	CCDS4460.2	0.02	3.891683	AACxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	g	8.178	0.793201	0.16327	.	.	ENSG00000165810	ENST00000327705;ENST00000376842	T;T	0.69175	-0.38;-0.38	4.66	2.81	0.32909	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.936787	0.08645	U	0.914971	T	0.59514	0.2199	N	0.25426	0.745	0.24507	N	0.994224	B	0.32350	0.366	P	0.45449	0.481	T	0.51505	-0.8697	10	0.09084	T	0.74	.	8.0943	0.30818	0.0916:0.1603:0.7481:0.0	.	465	Q6UXG8	BTNL9_HUMAN	M	465;466	ENSP00000330200:V465M;ENSP00000366038:V466M	ENSP00000330200:V465M	V	+	1	0	BTNL9	180419253	0.997000	0.39634	0.003000	0.11579	0.041000	0.13682	7.632000	0.83247	0.485000	0.27652	0.449000	0.29647	GTG	NOVEL	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157342.3	1	5.414612	KEEP	0	0	0	18	523	GG	0.999859	0.999859	0		+	7	60	205	0	0	10.998975	174	60	5528	268	ENST00000327705.9	0.038674	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	180561761	180561761	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180561761C>A			NA	NA				OR2V1 (9457 upstream) : OR2V2 (20181 downstream)						NA		NA									NA						aatagagagaccccatctcta	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.180561761C>A		NA		hg19		0.02	-0.114022	AGAxCCC	UNCOVERED																																																																																			NOVEL					0			5	2.406562	KEEP	0	0	0	8	238	CC	0.99257	0.16126	0			4	60	117	0	0	10.921775	5	60	168	31		0.444444	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	180605358	180605358	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180605358G>A			NA	NA				OR2V2 (22468 upstream) : CTC-338M12.2 (12687 downstream)						NA		NA									NA						tagtagagacggggtttcacc	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.180605358G>A		NA		hg19		0.02	-0.122806	GACxGGG	COVERED																																																																																			NOVEL					0			18	3.139993	KEEP	17	1	27	20	572	GG	0.99649	0.195623	0			3	40	87	0	0	7.200977	9	60	301	68		0.25	0.196312
GNB2L1	10399	__UNKNOWN__	__UNKNOWN__	5	180665626	180665626	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180665626A>G	ENST00000511900.1	-	5	572				GNB2L1_ENST00000514455.1_5'UTR|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000512805.1_Intron|GNB2L1_ENST00000376817.4_Intron|GNB2L1_ENST00000511566.1_Intron			P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		ccaacatggtaaaatcctctc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628	10399		WD repeat domain containing	4399	protein-coding gene	gene with protein product	Receptor for Activated C Kinase 1	176981			NA	8302854, 2499885	Standard	NM_006098	NM_006098	NA	Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000511900.1:c.493-387T>C	chr5.hg19:g.180665626A>G		NA	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	hg19		0.02	-0.298073	GGTxAAA	COVERED																																																																																			NOVEL	GNB2L1-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000373430.1	4	3.303507	KEEP	2	0	0	11	262	AA	0.992708	0.775364	0		-	3	60	96	0	0	6.710499	29	60	780	52	ENST00000511900.1	0.09375	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	5	180703302	180703302	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr5:180703302C>T			NA	NA				TRIM52-AS1 (3994 upstream) : CTC-338M12.9 (5073 downstream)						NA		NA									NA						gccaccacacctggcaaattt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr5.hg19:g.180703302C>T		NA		hg19		0.02	-0.298268	CACxTGG	COVERED																																																																																			NOVEL					0			26	5.749041	KEEP	10	1	22	27	811	CC	0.999892	0.780976	0			3	56	98	0	0	6.997504	27	60	928	90		0.1	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	289850	289850	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:289850G>A			NA	NA				RP3-416J7.5 (83458 upstream) : DUSP22 (2246 downstream)						NA		NA									NA						tcagcctcccgggtagctggg	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.289850G>A		NA		hg19		0.02	-0.114027	CCCxGGT	UNCOVERED																																																																																			NOVEL					0			8	2.707069	KEEP	1	0	0	9	258	GG	0.99257	0.16126	0			3	60	90	0	0	7.500977	9	60	301	30		0.25	0.162467
DUSP22	56940	__UNKNOWN__	__UNKNOWN__	6	329650	329650	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:329650T>C	ENST00000419235.2	+	4	216				DUSP22_ENST00000605863.1_Intron|DUSP22_ENST00000605315.1_Intron|DUSP22_ENST00000605035.1_Intron|DUSP22_ENST00000604971.1_Intron|DUSP22_ENST00000603290.1_Intron|DUSP22_ENST00000344450.5_Intron|DUSP22_ENST00000603453.1_Intron			Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		gacggggttttaccatgttgg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679	56940		Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases	16077	protein-coding gene	gene with protein product		NA			NA	9205128, 11717427	Standard	NM_020185	NM_001286555	NA	Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000419235.2:c.139-5464T>C	chr6.hg19:g.329650T>C		NA	B4DK56|Q59GW2|Q5VWR2|Q96AR1	hg19		0.02	-0.184157	TTTxACC	COVERED																																																																																			NOVEL	DUSP22-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039622.2	7	3.307073	KEEP	2	0	0	11	285	TT	0.99254	0.420319	0		+	4	60	114	0	0	9.063406	15	60	429	39	ENST00000419235.2	0.210526	0.423478
DUSP22	56940	__UNKNOWN__	__UNKNOWN__	6	335251	335251	__UNKNOWN__	Intron	SNP	T	T	C	rs71548131|rs3757305	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:335251T>C	ENST00000419235.2	+	4	266				DUSP22_ENST00000605863.1_Intron|DUSP22_ENST00000605315.1_Intron|DUSP22_ENST00000605035.1_Intron|DUSP22_ENST00000604971.1_Intron|DUSP22_ENST00000603290.1_Intron|DUSP22_ENST00000344450.5_Intron|DUSP22_ENST00000603453.1_Intron			Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		ACTGTGAAGTTGTCAGAGCTC	0.473		NA											C|||	2425	0.484225	0.4977	0.4755	5008	,	,	NA	31572	0.4663	NA	0.4831	False	NA	,,,	NA	NA	NA	2504	0.4918	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679	56940		Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases	16077	protein-coding gene	gene with protein product		NA			NA	9205128, 11717427	Standard	NM_020185	NM_001286555	NA	Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000419235.2:c.188+88T>C	chr6.hg19:g.335251T>C		NA	B4DK56|Q59GW2|Q5VWR2|Q96AR1	hg19		0.02	3.514451	AGTxGTC	COVERED																																																																																			NOVEL	DUSP22-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039622.2	1	3.237486	KEEP	0	1	26	20	529	TT	0.999869	0.999869	0		+	11	60	350	0	0	23.816425	121	60	3507	227	ENST00000419235.2	0.083333	1
DUSP22	56940	__UNKNOWN__	__UNKNOWN__	6	335253	335253	__UNKNOWN__	Intron	SNP	T	T	C	rs71548131|rs3757306	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:335253T>C	ENST00000419235.2	+	4	266				DUSP22_ENST00000605863.1_Intron|DUSP22_ENST00000605315.1_Intron|DUSP22_ENST00000605035.1_Intron|DUSP22_ENST00000604971.1_Intron|DUSP22_ENST00000603290.1_Intron|DUSP22_ENST00000344450.5_Intron|DUSP22_ENST00000603453.1_Intron			Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TGTGAAGTTGTCAGAGCTCAC	0.478		NA											T|||	2425	0.484225	0.4977	0.4755	5008	,	,	NA	30554	0.4663	NA	0.4831	False	NA	,,,	NA	NA	NA	2504	0.4918	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679	56940		Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases	16077	protein-coding gene	gene with protein product		NA			NA	9205128, 11717427	Standard	NM_020185	NM_001286555	NA	Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000419235.2:c.188+90T>C	chr6.hg19:g.335253T>C		NA	B4DK56|Q59GW2|Q5VWR2|Q96AR1	hg19		0.02	3.523033	TTGxCAG	COVERED																																																																																			NOVEL	DUSP22-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039622.2	1	2.838222	KEEP	0	1	30	20	537	TT	0.999869	0.999869	0		+	11	60	370	0	0	25.851211	120	60	3516	229	ENST00000419235.2	0.083969	1
DUSP22	56940	__UNKNOWN__	__UNKNOWN__	6	335268	335268	__UNKNOWN__	Intron	SNP	C	C	T	rs4959733	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:335268C>T	ENST00000419235.2	+	4	266				DUSP22_ENST00000605863.1_Intron|DUSP22_ENST00000605315.1_Intron|DUSP22_ENST00000605035.1_Intron|DUSP22_ENST00000604971.1_Intron|DUSP22_ENST00000603290.1_Intron|DUSP22_ENST00000344450.5_Intron|DUSP22_ENST00000603453.1_Intron			Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		GCTCACGGGACCCTTGCTGAC	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679	56940		Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases	16077	protein-coding gene	gene with protein product		NA			NA	9205128, 11717427	Standard	NM_020185	NM_001286555	NA	Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000419235.2:c.188+105C>T	chr6.hg19:g.335268C>T		NA	B4DK56|Q59GW2|Q5VWR2|Q96AR1	hg19		0.02	2.897192	GGAxCCT	COVERED																																																																																			NOVEL	DUSP22-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039622.2	1	5.416199	KEEP	0	0	0	18	558	CC	0.999859	0.999859	0		+	12	60	353	0	0	23.83066	114	60	3837	227	ENST00000419235.2	0.095238	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	1172559	1172559	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:1172559C>T			NA	NA				AL033381.1 (67378 upstream) : snoU13 (14193 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.1172559C>T		NA		hg19		0.02	-0.13157	AGAxGGG	COVERED																																																																																			NOVEL					0			9	3.910069	KEEP	5	0	0	13	362	CC	0.992708	0.227502	0			3	60	80	0	0	6.382041	10	60	330	35		0.230769	0.229173
RIPK1	8737	__UNKNOWN__	__UNKNOWN__	6	3113740	3113740	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3113740G>T	ENST00000259808.4	+	0	2481				RIPK1_ENST00000541791.1_3'UTR|RIPK1_ENST00000380409.2_3'UTR			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|amyloid fibril formation (GO:1990000)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to tumor necrosis factor (GO:0071356)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of ATP:ADP antiporter activity (GO:0070926)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to tumor necrosis factor (GO:0034612)|ripoptosome assembly (GO:0097343)|ripoptosome assembly involved in necroptotic process (GO:1901026)|T cell apoptotic process (GO:0070231)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|death domain binding (GO:0070513)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				AAAGAAAtctgcagcaaaggg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U25994	CCDS4482.1	6p25.2	2008-02-05			ENSG00000137275	ENSG00000137275	8737			10019	protein-coding gene	gene with protein product		603453			NA	7538908, 8612133	Standard	NM_003804	XM_005249458	NA	Approved	RIP	uc003mux.3	Q13546	OTTHUMG00000014134	ENST00000259808.4:c.*167G>T	chr6.hg19:g.3113740G>T		NA	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	hg19	CCDS4482.1	0.02	1.269337	TCTxCAG	COVERED																																																																																			NOVEL	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039659.2	17	6.920514	KEEP	0	0	0	23	709	GG	0.999892	0.997055	0		+	4	60	124	0	0	7.734308	63	60	2164	126	ENST00000259808.4	0.059701	0.997163
BPHL	670	__UNKNOWN__	__UNKNOWN__	6	3138334	3138334	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3138334T>C	ENST00000434640.1	+	6	974				BPHL_ENST00000380379.5_Intron|BPHL_ENST00000380368.2_3'UTR|BPHL_ENST00000380375.3_Intron			Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	NA		NA			cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				ctcactgcaatctctgtctcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274	670			1094	protein-coding gene	gene with protein product	breast epithelial mucin-associated antigen	603156		MCNAA	NA	7759552, 9721218, 15832508	Standard		NM_004332	NA	Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000434640.1:c.613+607T>C	chr6.hg19:g.3138334T>C		NA	Q00306|Q13855|Q3KP51	hg19		0.02	-0.254326	CAAxCTC	COVERED																																																																																			NOVEL	BPHL-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000346932.2	1	2.405966	KEEP	0	0	0	8	218	TT	0.99257	0.663556	0		+	4	60	113	0	0	8.293115	23	70	671	49	ENST00000434640.1	0.148148	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3205743	3205743	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3205743A>G			NA	NA				RP1-40E16.9 (9753 upstream) : TUBB2B (18751 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3205743A>G		NA		hg19		0.02	-0.245561	GGCxTGA	COVERED																																																																																			NOVEL					0			9	4.21091	KEEP	0	0	0	14	390	AA	0.995343	0.638361	0			3	60	98	0	0	7.194872	23	60	672	61		0.115385	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3215909	3215909	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3215909G>C			NA	NA				RP1-40E16.9 (19919 upstream) : TUBB2B (8585 downstream)						NA		NA									NA						gagtctcgctgtgtcacccag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3215909G>C		NA		hg19		0.02	-0.078949	GCTxTGT	UNCOVERED																																																																																			NOVEL					0			8	2.707706	KEEP	6	0	0	9	268	GG	0	0	0			3	60	100	0	0	9.132706	5	60	164	25		0.375	0.077336
PSMG4	389362	__UNKNOWN__	__UNKNOWN__	6	3244178	3244178	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3244178A>G	ENST00000380306.4	+	2	356							Q5JS54	PSMG4_HUMAN	proteasome (prosome, macropain) assembly chaperone 4	NA		NA								endometrium(1)	1						gattacaggcatgagccacca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47360.1, CCDS47361.1, CCDS47362.1	6p25.2	2010-06-23	2008-02-25	2008-02-25	ENSG00000180822	ENSG00000180822	389362			21108	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 86	C6orf86	NA	17707236	Standard		NM_001128591	NA	Approved	PAC4	uc010jnl.1	Q5JS54	OTTHUMG00000014142	ENST00000380306.4:c.75-11107A>G	chr6.hg19:g.3244178A>G		NA	C9J2F8|F8WBZ2|Q5JS53|Q5JS56	hg19		0.02	1.596179	GGCxTGA	COVERED																																																																																			NOVEL	PSMG4-001	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000039675.2	18	7.820291	KEEP	0	0	0	26	725	AA	0.999957	0.999067	0		+	4	60	134	0	0	8.579421	69	60	2037	157	ENST00000380306.4	0.054795	0.99911
SLC22A23	63027	__UNKNOWN__	__UNKNOWN__	6	3400355	3400355	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3400355A>G	ENST00000436008.2	-	3	1376				SLC22A23_ENST00000406686.3_Intron|SLC22A23_ENST00000490273.1_Intron|SLC22A23_ENST00000380298.2_Intron|SLC22A23_ENST00000380302.4_Intron			A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	NA		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				caagtgatccacccgcctcgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266	63027		Solute carriers	21106	protein-coding gene	gene with protein product		611697	chromosome 6 open reading frame 85	C6orf85	NA	17714910	Standard	NM_021945	NM_015482	NA	Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000436008.2:c.913+10066T>C	chr6.hg19:g.3400355A>G		NA	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	hg19		0.02	-0.096465	TCCxCCC	UNCOVERED																																																																																			NOVEL	SLC22A23-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039683.2	8	3.307135	KEEP	9	0	0	11	293	AA	0.99254	0.119538	0		-	3	60	100	0	0	8.632866	8	60	227	44	ENST00000436008.2	0.272727	0.120436
SLC22A23	63027	__UNKNOWN__	__UNKNOWN__	6	3437686	3437686	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3437686C>T	ENST00000436008.2	-	1	1117				SLC22A23_ENST00000406686.3_Intron|SLC22A23_ENST00000490273.1_Intron|SLC22A23_ENST00000380298.2_Intron|SLC22A23_ENST00000380302.4_Intron			A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	NA		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)	14	Ovarian(93;0.0493)	all_hematologic(90;0.0905)				ccgaggtgggcggatcatgag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ420525	CCDS34331.1, CCDS47363.1, CCDS75389.1	6p25.2	2013-05-22	2008-01-11	2008-01-11	ENSG00000137266	ENSG00000137266	63027		Solute carriers	21106	protein-coding gene	gene with protein product		611697	chromosome 6 open reading frame 85	C6orf85	NA	17714910	Standard	NM_021945	NM_015482	NA	Approved	FLJ22174	uc003mvm.3	A1A5C7	OTTHUMG00000014144	ENST00000436008.2:c.654+18453G>A	chr6.hg19:g.3437686C>T		NA	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	hg19		0.02	-0.201764	GGGxGGA	COVERED																																																																																			NOVEL	SLC22A23-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000039683.2	7	3.008463	KEEP	1	0	0	10	305	CC	0.99254	0.486885	0		-	3	60	92	1	0	6.765171	20	60	676	49	ENST00000436008.2	0.130435	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3691345	3691345	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3691345C>T			NA	NA				RP1-223B1.1 (66364 upstream) : PXDC1 (31502 downstream)						NA		NA									NA						ccgaggcgggcggatcacaag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3691345C>T		NA		hg19		0.02	-0.228038	GGGxGGA	COVERED																																																																																			NOVEL					0			10	3.609275	KEEP	6	0	0	12	336	CC	0.992708	0.607941	0			3	60	89	0	0	6.350447	22	60	672	71		0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3691386	3691386	__UNKNOWN__	IGR	SNP	T	T	C	rs538288212	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3691386T>C			NA	NA				RP1-223B1.1 (66405 upstream) : PXDC1 (31461 downstream)						NA		NA									NA						ctggctaacatggtgaaaccc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3691386T>C		NA		hg19		0.02	-0.175344	ACAxGGT	COVERED																																																																																			NOVEL					0			9	3.007288	KEEP	6	0	0	10	271	TT	0.99257	0.420331	0			3	60	87	0	0	6.535053	16	60	448	45		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3904046	3904046	__UNKNOWN__	IGR	SNP	G	G	A	rs9503791	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3904046G>A			NA	NA				RP1-140K8.1 (9522 upstream) : RP1-140K8.5 (1097 downstream)						NA		NA									NA						gaggtcaggagatcgagacca	0.572		NA											G|||	1328	0.265176	0.6135	0.2075	5008	,	,	NA	13822	0.0317	NA	0.1581	False	NA	,,,	NA	NA	NA	2504	0.1861	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3904046G>A		NA		hg19		0.02	-0.096466	GGAxATC	UNCOVERED																																																																																			NOVEL					0			4	2.406872	KEEP	10	0	0	8	237	GG	0	0	0			4	60	109	0	0	9.884349	6	60	186	44		0.4	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3904050	3904050	__UNKNOWN__	IGR	SNP	G	G	A	rs9503792	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3904050G>A			NA	NA				RP1-140K8.1 (9526 upstream) : RP1-140K8.5 (1093 downstream)						NA		NA									NA						tcaggagatcgagaccatcct	0.582		NA											g|||	969	0.19349	0.4251	0.1715	5008	,	,	NA	13939	0.004	NA	0.1252	False	NA	,,,	NA	NA	NA	2504	0.1616	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3904050G>A		NA		hg19		0.02	-0.087527	ATCxAGA	UNCOVERED																																																																																			NOVEL					0			3	2.406485	KEEP	9	0	0	8	231	GG	0	0	0			4	60	105	0	0	9.489085	6	60	164	39		0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	3969482	3969482	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:3969482T>C			NA	NA				RP1-140K8.5 (57269 upstream) : C6ORF50 (13426 downstream)						NA		NA									NA						gtggctcacgtctgtaatccc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.3969482T>C		NA		hg19		0.02	-0.306414	ACGxCTG	COVERED																																																																																			NOVEL					0			10	3.609265	KEEP	0	0	0	12	333	TT	0.993634	0.795151	0			3	60	108	0	0	8.000134	27	60	780	67		0.1	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	4006108	4006108	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:4006108T>G			NA	NA				C6ORF50 (21736 upstream) : RP3-406P24.4 (12838 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.4006108T>G		NA		hg19		0.02	-0.068796	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			11	3.007096	KEEP	6	0	0	10	267	TT	0	0	0			2	60	65	0	0	6.625309	1	60	25	28		0.666667	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	4370929	4370929	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:4370929C>G			NA	NA				RP3-527G5.1 (23658 upstream) : RNA5SP202 (57267 downstream)						NA		NA									NA						ggccaggctgctctcgaactc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.4370929C>G		NA		hg19		0.02	-0.219313	CTGxTCT	COVERED																																																																																			NOVEL					0			6	2.407185	KEEP	0	0	0	8	247	CC	0.99257	0.54878	0			4	60	137	0	0	10.913014	20	60	677	49		0.166667	0.552887
CDYL	9425	__UNKNOWN__	__UNKNOWN__	6	4726841	4726841	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:4726841G>A	ENST00000328908.5	+	3	234							Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		aggctgaggcgagaggattgc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046	9425			1811	protein-coding gene	gene with protein product	CDY-like, autosomal, testis-specific chromodomain Y-like protein	603778	chromodomain protein, Y chromosome-like		NA	10192397	Standard	NM_004824	NM_001143970	NA	Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.104-8155G>A	chr6.hg19:g.4726841G>A		NA	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	hg19		0.02	-0.21051	GGCxAGA	COVERED																																																																																			NOVEL	CDYL-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000039736.1	13	3.007537	KEEP	0	0	0	10	279	GG	0.992708	0.518353	0		+	4	60	111	0	0	8.480312	18	60	564	44	ENST00000328908.5	0.181818	0.522161
RPP40	10799	__UNKNOWN__	__UNKNOWN__	6	5003984	5003984	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:5003984G>C	ENST00000319533.5	-	1	157				RPP40_ENST00000380051.2_Intron			O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	NA		NA			RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				CTCCCAGCAAgccgggcgagg	0.692		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787	10799			20992	protein-coding gene	gene with protein product		606117	ribonuclease P1, ribonuclease P 40kDa subunit	RNASEP1	NA	9630247	Standard	NM_006638	NM_006638	NA	Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000319533.5:c.123+129C>G	chr6.hg19:g.5003984G>C		NA	Q5VX97|Q8WVK8	hg19		0.02	3.349895	CAAxCCG	COVERED																																																																																			NOVEL	RPP40-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000039734.2	0	11.130938	KEEP	0	0	0	37	1097	GG	1	1	0		-	20	60	653	0	0	49.91303	120	60	4067	203	ENST00000319533.5	0.142857	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	5009035	5009035	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:5009035G>C			NA	NA				RPP40 (4754 upstream) : RP11-428J1.5 (21170 downstream)						NA		NA									NA						cccaggagttggagaccagcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.5009035G>C		NA		hg19		0.02	-0.350894	GTTxGAG	COVERED																																																																																			NOVEL					0			16	3.008933	KEEP	3	0	0	10	305	GG	0.992708	0.90244	0			3	60	101	0	0	7.011663	34	60	1154	76		0.081081	0.909069
LYRM4	57128	__UNKNOWN__	__UNKNOWN__	6	5113638	5113638	__UNKNOWN__	Intron	SNP	C	C	T	rs185920797	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:5113638C>T	ENST00000330636.4	-	3	413				LYRM4_ENST00000468929.1_Intron|LYRM4_ENST00000464010.1_Intron	NM_020408.4	NP_065141.3	Q9HD34	LYRM4_HUMAN	LYR motif containing 4	NA		NA			small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)				endometrium(1)	1	Ovarian(93;0.11)	all_hematologic(90;0.0901)				ggtgacagagcgagattccgt	0.527		NA											C|||	9	0.00179712	0.0053	0.0029	5008	,	,	NA	18899	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	NSCLC(130;1006 2426 17608 36797)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258559	CCDS4493.1, CCDS54961.1	6p25.1	2008-02-05	2006-09-19	2006-09-19	ENSG00000214113	ENSG00000214113	57128		LYR motif containing	21365	protein-coding gene	gene with protein product		613311	chromosome 6 open reading frame 149	C6orf149	NA		Standard	NM_020408	XM_005249239	NA	Approved	CGI-203, ISD11	uc021ykw.1	Q9HD34	OTTHUMG00000014173	ENST00000330636.4:c.208-3913G>A	chr6.hg19:g.5113638C>T		NA	A8K543|Q5XKP1	hg19	CCDS4493.1	0.02	2.792522	GAGxGAG	COVERED																																																																																			NOVEL	LYRM4-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000353461.3	30	3.374972	KEEP	1	2	53	30	894	CC	0.999997	0.999997	0		-	6	60	173	0	0	9.567701	127	60	4220	265	ENST00000330636.4	0.045113	1
LYRM4	57128	__UNKNOWN__	__UNKNOWN__	6	5151531	5151531	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:5151531A>C	ENST00000480566.1	-	3	216				LYRM4_ENST00000468929.1_Intron|LYRM4_ENST00000464010.1_Intron|LYRM4_ENST00000330636.4_Intron			Q9HD34	LYRM4_HUMAN	LYR motif containing 4	NA		NA			small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)				endometrium(1)	1	Ovarian(93;0.11)	all_hematologic(90;0.0901)				gttggccaggatggtctctat	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(130;1006 2426 17608 36797)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258559	CCDS4493.1, CCDS54961.1	6p25.1	2008-02-05	2006-09-19	2006-09-19	ENSG00000214113	ENSG00000214113	57128		LYR motif containing	21365	protein-coding gene	gene with protein product		613311	chromosome 6 open reading frame 149	C6orf149	NA		Standard	NM_020408	XM_005249239	NA	Approved	CGI-203, ISD11	uc021ykw.1	Q9HD34	OTTHUMG00000014173	ENST00000480566.1:c.208-12558T>G	chr6.hg19:g.5151531A>C		NA	A8K543|Q5XKP1	hg19		0.02	-0.333233	AGGxTGG	COVERED																																																																																			NOVEL	LYRM4-005	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000353483.1	8	3.007736	KEEP	2	0	0	10	279	AA	0.99254	0.845628	0		-	3	60	103	0	0	7.287163	32	60	915	65	ENST00000480566.1	0.085714	0.851984
FARS2	10667	__UNKNOWN__	__UNKNOWN__	6	5456434	5456434	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:5456434A>G	ENST00000324331.6	+	4	1240				RP1-232P20.1_ENST00000602674.1_RNA|RP1-232P20.1_ENST00000602284.1_RNA|FARS2_ENST00000274680.4_Intron			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	NA		NA			gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	gtgacagagcaagaccctgtc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	10667	6.1.1.20	Aminoacyl tRNA synthetases / Class II	21062	protein-coding gene	gene with protein product	phenylalanine tRNA ligase 2, mitochondrial	611592	phenylalanine-tRNA synthetase 1 (mitochondrial)	FARS1	NA	10329163	Standard	NM_006567	NM_006567	NA	Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.904+25029A>G	chr6.hg19:g.5456434A>G		NA	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	hg19	CCDS4494.1	0.02	-0.271788	AGCxAGA	COVERED																																																																																			NOVEL	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467790.1	14	3.307263	KEEP	1	0	0	11	288	AA	0.993072	0.712346	0		+	3	60	101	0	0	7.549524	22	60	626	59	ENST00000324331.6	0.12	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	5820393	5820393	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:5820393G>A			NA	NA				FARS2 (48580 upstream) : RP3-380B8.4 (31345 downstream)						NA		NA									NA						cggcctcccagagtgctgaga	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.5820393G>A		NA		hg19		0.02	-0.412185	CCAxAGT	COVERED																																																																																			NOVEL					0			15	3.008586	KEEP	0	0	0	10	298	GG	0.992708	0.934874	0			7	60	169	0	0	12.112759	34	60	1135	75		0.170732	0.941741
LY86-AS1	285780	__UNKNOWN__	__UNKNOWN__	6	6377526	6377526	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:6377526G>A	ENST00000435641.1	-	0	639				LY86-AS1_ENST00000447858.1_RNA|LY86-AS1_ENST00000429345.1_RNA					LY86 antisense RNA 1	NA		NA									NA						cgccttggccgggcgcggtgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK091027		6p25.1	2012-10-12	2012-08-15	2010-11-25	ENSG00000216863	ENSG00000216863	285780		Long non-coding RNAs	26593	non-coding RNA	RNA, long non-coding		NA	LY86 antisense RNA (non-protein coding), LY86 antisense RNA 1 (non-protein coding)	LY86AS, LY86-AS	NA		Standard	NR_026970	NR_026970	NA	Approved	FLJ33708	uc003mwx.2		OTTHUMG00000014192	ENST00000435641.1:	chr6.hg19:g.6377526G>A		NA		hg19		0.02	-0.22807	GCCxGGC	COVERED																																																																																			NOVEL	LY86-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000280396.1	6	2.707352	KEEP	4	0	0	9	261	GG	0.99254	0.578582	0		-	3	60	94	0	0	6.849199	22	60	721	60	ENST00000435641.1	0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	6754792	6754792	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:6754792A>G			NA	NA				RP1-80N2.2 (43557 upstream) : RP3-470L22.1 (3716 downstream)						NA		NA									NA						ctcccaaagtactgggattac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.6754792A>G		NA		hg19		0.02	-0.385894	AGTxCTG	COVERED																																																																																			NOVEL					0			6	3.007191	KEEP	0	0	0	10	269	AA	0.992708	0.919883	0			4	60	136	0	0	9.818287	37	60	1074	89		0.097561	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	6813556	6813556	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:6813556G>T			NA	NA				RP3-470L22.1 (54032 upstream) : RP3-429O6.1 (87698 downstream)						NA		NA									NA						gtgagccactgcacctggcca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.6813556G>T		NA		hg19		0.02	1.473553	ACTxCAC	COVERED																																																																																			NOVEL					0			14	3.309492	KEEP	2	0	0	11	334	GG	0.993072	0.979322	0			7	60	215	0	0	15.984892	44	60	1477	106		0.137255	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	6855973	6855973	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:6855973G>C			NA	NA				RP3-470L22.1 (96449 upstream) : RP3-429O6.1 (45281 downstream)						NA		NA									NA						accagcctgggcaacatagtg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.6855973G>C		NA		hg19		0.02	-0.342139	TGGxCAA	COVERED																																																																																			NOVEL					0			15	3.30969	KEEP	0	0	0	11	334	GG	0.993072	0.871627	0			3	60	109	0	0	7.96628	30	60	1039	70		0.090909	0.877708
RP3-429O6.1	0	__UNKNOWN__	__UNKNOWN__	6	6914096	6914096	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:6914096T>C	ENST00000422310.2	-	0	206										NA		NA									NA						aactcctgggttcaagcaatc	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000422310.2:	chr6.hg19:g.6914096T>C		NA		hg19		0.02	-0.289392	GGGxTCA	COVERED																																																																																			NOVEL	RP3-429O6.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000039767.2	14	3.007163	KEEP	1	0	0	10	271	TT	0.992708	0.755338	0		-	3	60	108	0	0	8.092157	25	60	723	67	ENST00000422310.2	0.107143	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	6931329	6931329	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:6931329A>G			NA	NA				RP3-429O6.1 (12381 upstream) : RN7SL554P (7505 downstream)						NA		NA									NA						ccaaagtgctaggattactgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.6931329A>G		NA		hg19		0.02	-0.412228	GCTxGGA	COVERED																																																																																			NOVEL					0			14	3.609103	KEEP	0	0	0	12	329	AA	0.993634	0.935746	0			4	60	126	0	0	8.9589	34	60	1019	78		0.105263	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	7060260	7060260	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7060260A>G			NA	NA				snoU13 (19481 upstream) : RREB1 (47569 downstream)						NA		NA									NA						gtgacagagcaagactccgtc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.7060260A>G		NA		hg19		0.02	-0.298137	AGCxAGA	COVERED																																																																																			NOVEL					0			5	5.111756	KEEP	0	0	0	17	457	AA	0.999366	0.780565	0			3	60	94	0	0	6.598755	27	60	781	75		0.1	0.78106
RREB1	6239	__UNKNOWN__	__UNKNOWN__	6	7119148	7119148	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7119148A>C	ENST00000379938.2	+	1	253				RREB1_ENST00000349384.6_Intron|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Intron	NM_001003699.3|NM_001003700.1	NP_001003699.1|NP_001003700.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	NA		NA			multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				tcccaaagtgatgggattaca	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782	6239		Zinc fingers, C2H2-type	10449	protein-coding gene	gene with protein product	hindsight homolog (drosophila)	602209			NA	9367691, 18394891	Standard		NM_001003698	NA	Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000379938.2:c.-285+10855A>C	chr6.hg19:g.7119148A>C		NA	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	hg19	CCDS34335.1	0.02	-0.201716	GTGxTGG	COVERED																																																																																			NOVEL	RREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039774.3	7	3.007867	KEEP	0	0	0	10	281	AA	0.992708	0.486967	0		+	3	60	105	0	0	8.19206	18	60	529	52	ENST00000379938.2	0.142857	0.490544
RREB1	6239	__UNKNOWN__	__UNKNOWN__	6	7124163	7124163	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7124163G>A	ENST00000379938.2	+	1	253				RREB1_ENST00000349384.6_Intron|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Intron	NM_001003699.3|NM_001003700.1	NP_001003699.1|NP_001003700.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	NA		NA			multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GTGTCTTAAGGGTATCTGTGA	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782	6239		Zinc fingers, C2H2-type	10449	protein-coding gene	gene with protein product	hindsight homolog (drosophila)	602209			NA	9367691, 18394891	Standard		NM_001003698	NA	Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000379938.2:c.-285+15870G>A	chr6.hg19:g.7124163G>A		NA	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	hg19	CCDS34335.1	0.02	-0.289435	AAGxGTA	COVERED																																																																																			NOVEL	RREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039774.3	5	3.008803	KEEP	0	0	0	10	303	GG	0.992708	0.755338	0		+	3	60	94	0	0	6.598356	27	60	911	65	ENST00000379938.2	0.1	0.760887
SSR1	6745	__UNKNOWN__	__UNKNOWN__	6	7325859	7325859	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7325859C>T	ENST00000488834.1	-	2	144							P43307	SSRA_HUMAN	signal sequence receptor, alpha	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					ggattacaggcgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783	6745			11323	protein-coding gene	gene with protein product	translocon-associated protein alpha	600868			NA		Standard		NM_001292008	NA	Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000488834.1:c.441+8395G>A	chr6.hg19:g.7325859C>T		NA	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	hg19		0.02	-0.333328	AGGxGTG	COVERED																																																																																			NOVEL	SSR1-008	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000353167.1	7	2.70801	KEEP	0	0	0	9	273	CC	0.99254	0.845628	0		-	7	60	208	0	0	16.535391	28	60	925	72	ENST00000488834.1	0.2	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	7535581	7535581	__UNKNOWN__	IGR	SNP	C	C	A	rs370602142	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7535581C>A			NA	NA				RIOK1 (117311 upstream) : RP3-512B11.3 (5102 downstream)						NA		NA									NA						gttcaagacccgcttgggcaa	0.483		NA											C|||	10	0.00199681	0.003	0.0	5008	,	,	NA	15935	0.006	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.7535581C>A		NA		hg19		0.02	1.234298	ACCxGCT	COVERED																																																																																			NOVEL					0			11	3.911427	KEEP	0	0	0	13	394	CC	0.994391	0.992864	0			5	60	133	0	0	7.885522	65	60	2176	119		0.071429	0.998465
DSP	1832	__UNKNOWN__	__UNKNOWN__	6	7573577	7573577	__UNKNOWN__	Intron	SNP	C	C	T	rs538318076		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7573577C>T	ENST00000379802.3	+	16	2471				DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	NA		NA			adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		tttgggaggccgaggcgggtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696	1832			3052	protein-coding gene	gene with protein product		125647	desmoplakin (DPI, DPII)		NA	1889810	Standard	NM_004415	NM_004415	NA	Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2131-742C>T	chr6.hg19:g.7573577C>T		NA	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	hg19	CCDS4501.1	0.02	-0.385973	GGCxGAG	COVERED																																																																																			NOVEL	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039786.2	11	3.308859	KEEP	2	0	0	11	325	CC	0.993072	0.91181	0		+	4	60	125	0	0	8.906868	33	60	1090	84	ENST00000379802.3	0.108108	0.918171
BMP6	654	__UNKNOWN__	__UNKNOWN__	6	7857075	7857075	__UNKNOWN__	Intron	SNP	C	C	T	rs74461936	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7857075C>T	ENST00000283147.6	+	3	1016					NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	NA		NA			BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					gtgatccgcccgcctcggcct	0.527		NA											-|||	846	0.16893	0.0091	0.1787	5008	,	,	NA	16450	0.2391	NA	0.1998	False	NA	,,,	NA	NA	NA	2504	0.274	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162	654		Bone morphogenetic proteins, Endogenous ligands	1073	protein-coding gene	gene with protein product		112266	vegetal related growth factor (TGFB-related)	VGR	NA	1427904, 1453478	Standard	NM_001718	NM_001718	NA	Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.858-4609C>T	chr6.hg19:g.7857075C>T		NA	Q5TCP3	hg19	CCDS4503.1	0.02	-0.184206	GCCxGCC	UNCOVERED																																																																																			NOVEL	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039794.1	7	3.910564	KEEP	31	0	0	13	390	CC	0	0	0		+	6	51	177	1	0	15.106373	15	60	498	83	ENST00000283147.6	0.285714	0.423478
BLOC1S5-TXNDC5	100526836	__UNKNOWN__	__UNKNOWN__	6	7986306	7986306	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:7986306G>A	ENST00000439343.2	-	4	372				TXNDC5_ENST00000539054.1_Intron					BLOC1S5-TXNDC5 readthrough (NMD candidate)	NA		NA									NA						aaaaaaaaaagaaaaaaagaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					6p24.3	2013-05-09	2013-05-09	2012-08-01	ENSG00000259040	ENSG00000259040	100526836			42001	other	readthrough		NA	MUTED-TXNDC5 readthrough (non-protein coding)	MUTED-TXNDC5	NA		Standard	NR_037616.1	NR_037616	NA	Approved				OTTHUMG00000171453	ENST00000439343.2:c.372+40293C>T	chr6.hg19:g.7986306G>A		NA		hg19		0.02	1.248724	AAAxAAA	COVERED																																																																																			NOVEL	BLOC1S5-TXNDC5-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000413472.1	15	2.735425	KEEP	0	2	33	21	586	GG	0.999892	0.96367	0		-	6	60	169	0	0	12.039151	40	60	1142	102	ENST00000439343.2	0.130435	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	8117438	8117438	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:8117438T>C			NA	NA				EEF1E1 (14627 upstream) : RP11-203H2.1 (212449 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.8117438T>C		NA		hg19		0.02	-0.306983	AGGxGTG	COVERED																																																																																			NOVEL					0			9	2.40527	KEEP	0	0	0	8	213	TT	0.99257	0.7943	0			4	60	125	0	0	9.35802	25	60	762	62		0.137931	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	8206458	8206458	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:8206458T>C			NA	NA				EEF1E1 (103647 upstream) : RP11-203H2.1 (123429 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.8206458T>C		NA		hg19		0.02	-0.254314	AGGxGTG	COVERED																																																																																			NOVEL					0			6	3.308364	KEEP	0	0	0	11	307	TT	0.993072	0.663892	0			4	60	128	0	0	9.724477	24	60	704	60		0.142857	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	8754005	8754005	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:8754005A>G			NA	NA				HULC (99926 upstream) : RP11-314C16.1 (30405 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.8754005A>G		NA		hg19		0.02	-0.315427	GGCxTGA	COVERED																																																																																			NOVEL					0			12	3.308805	KEEP	0	0	0	11	310	AA	0.993072	0.812795	0			4	60	137	0	0	10.435172	27	60	788	73		0.129032	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	9270769	9270769	__UNKNOWN__	IGR	SNP	C	C	T	rs116202257	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:9270769C>T			NA	NA				RP11-354I10.1 (108759 upstream) : OFCC1 (626174 downstream)						NA		NA									NA						cagtggctcacgcctgtaatc	0.478		NA											C|||	72	0.014377	0.053	0.0029	5008	,	,	NA	17713	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.9270769C>T		NA		hg19		0.02	-0.184202	TCAxGCC	COVERED																																																																																			NOVEL					0			6	3.84912	KEEP	5	0	0	13	361	CC	0.992708	0.42039	0			3	60	93	0	0	7.133532	16	60	517	50		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	9817965	9817965	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:9817965A>G			NA	NA				RP11-354I10.1 (655955 upstream) : OFCC1 (78978 downstream)						NA		NA									NA						gtgagccaccacacccagccC	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.9817965A>G		NA		hg19		0.02	-0.3858	ACCxCAC	COVERED																																																																																			NOVEL					0			11	4.209639	KEEP	2	0	0	14	374	AA	0.994391	0.91302	0			3	60	105	0	0	7.340356	36	60	1024	90		0.076923	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	9817967	9817967	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:9817967A>G			NA	NA				RP11-354I10.1 (655957 upstream) : OFCC1 (78976 downstream)						NA		NA									NA						gagccaccacacccagccCAA	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.9817967A>G		NA		hg19		0.02	-0.377052	CACxCCC	COVERED																																																																																			NOVEL					0			10	3.908709	KEEP	1	0	0	13	345	AA	0.994391	0.90397	0			3	60	96	0	0	6.478853	35	60	998	85		0.078947	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10097184	10097184	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10097184A>G			NA	NA				OFCC1 (36186 upstream) : RNU6ATAC21P (125084 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10097184A>G		NA		hg19		0.02	-0.298198	CACxCCT	UNCOVERED																																																																																			NOVEL					0			10	2.406398	KEEP	1	0	0	8	225	AA	0	0	0			4	60	126	0	1	9.394876	26	60	782	63		0.133333	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10155815	10155815	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10155815G>A			NA	NA				OFCC1 (94817 upstream) : RNU6ATAC21P (66453 downstream)						NA		NA									NA						agtggctcacgcctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10155815G>A		NA		hg19		0.02	-0.324526	CACxCCT	COVERED																																																																																			NOVEL					0			7	2.406756	KEEP	0	0	0	8	238	GG	0.99257	0.829507	0			5	60	152	0	1	11.422468	29	60	933	67		0.147059	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10307034	10307034	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10307034C>A			NA	NA				RNU6ATAC21P (84640 upstream) : TFAP2A (89875 downstream)						NA		NA									NA						gcctgtaatcccagctctttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10307034C>A		NA		hg19		0.02	-0.254387	ATCxCAG	COVERED																																																																																			NOVEL					0			8	3.911756	KEEP	2	0	0	13	402	CC	0.993634	0.664267	0			3	60	92	0	0	6.827364	19	60	632	64		0.136364	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10308501	10308501	__UNKNOWN__	IGR	SNP	G	G	A	rs547501922		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10308501G>A			NA	NA				RNU6ATAC21P (86107 upstream) : TFAP2A (88408 downstream)						NA		NA									NA						cgcccacctcggcctcccaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10308501G>A		NA		hg19		0.02	1.563971	CTCxGCC	COVERED																																																																																			NOVEL					0			11	4.814704	KEEP	5	0	0	16	506	GG	0.994391	0.982401	0			4	60	124	0	0	8.121332	50	60	1654	124		0.074074	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10377565	10377565	__UNKNOWN__	IGR	SNP	G	G	A	rs686070	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10377565G>A			NA	NA				RNU6ATAC21P (155171 upstream) : TFAP2A (19344 downstream)						NA		NA									NA						aattacaggcgtgagccactg	0.522		NA											G|||	1432	0.285942	0.1278	0.2507	5008	,	,	NA	19245	0.4167	NA	0.3211	False	NA	,,,	NA	NA	NA	2504	0.3538	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10377565G>A		NA		hg19		0.02	-0.254365	GGCxTGA	COVERED																																																																																			NOVEL					0			6	2.407023	KEEP	0	0	0	8	242	GG	0.99257	0.663556	0			4	60	110	0	0	8.380489	18	60	598	56		0.181818	0.668523
C6orf52	347744	__UNKNOWN__	__UNKNOWN__	6	10693008	10693008	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10693008A>C	ENST00000503680.1	-	1	95				C6orf52_ENST00000379586.1_Intron|C6orf52_ENST00000460742.2_Intron|C6orf52_ENST00000259983.3_Intron|C6orf52_ENST00000467832.2_Intron			Q5T4I8	CF052_HUMAN	chromosome 6 open reading frame 52	NA		NA								endometrium(1)|prostate(1)	2						ccgcctgcctaggcctcgcaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016820	CCDS47371.1	6p24.2	2009-09-22	2007-06-07	2007-06-07	ENSG00000137434	ENSG00000137434	347744			20881	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_001145020	NM_001145020	NA	Approved		uc011dij.2	Q5T4I8	OTTHUMG00000014240	ENST00000503680.1:c.270+1927T>G	chr6.hg19:g.10693008A>C		NA	Q5T4I7|Q96AS6	hg19		0.02	-0.350804	CCTxGGC	COVERED																																																																																			NOVEL	C6orf52-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000367468.1	10	3.609279	KEEP	0	0	0	12	333	AA	0.993634	0.87212	0		-	3	60	99	0	0	6.887479	32	60	945	74	ENST00000503680.1	0.085714	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10716084	10716084	__UNKNOWN__	IGR	SNP	C	C	T	rs535144632	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10716084C>T			NA	NA				PAK1IP1 (6069 upstream) : TMEM14C (7063 downstream)						NA		NA									NA						gtgatccacccgcctcagcct	0.438		NA											C|||	2	0.000399361	0.0	0.0014	5008	,	,	NA	17038	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10716084C>T		NA		hg19		0.02	-0.219307	ACCxGCC	COVERED																																																																																			NOVEL					0			7	3.610805	KEEP	1	0	0	12	371	CC	0.993072	0.549057	0			3	60	92	0	0	6.827265	19	60	631	57		0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	10741054	10741054	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10741054A>G			NA	NA				TMEM14C (9692 upstream) : RP11-421M1.8 (2502 downstream)						NA		NA									NA						tcagcctcccaagtagctggg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.10741054A>G		NA		hg19		0.02	-0.149096	CCCxAGT	COVERED																																																																																			NOVEL					0			8	3.306144	KEEP	2	0	0	11	293	AA	0.992708	0.289872	0			4	60	128	0	0	10.801661	12	60	358	40		0.25	0.292001
RP11-637O19.3	0	__UNKNOWN__	__UNKNOWN__	6	10849396	10849396	__UNKNOWN__	Intron	SNP	T	T	G	rs4711105	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:10849396T>G	ENST00000480294.1	+	4	232				SYCP2L_ENST00000543878.1_Intron						NA		NA									NA						ccgaggtgggtggatcacctg	0.473		NA											T|||	1830	0.365415	0.1483	0.2536	5008	,	,	NA	18403	0.6835	NA	0.3648	False	NA	,,,	NA	NA	NA	2504	0.411	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000480294.1:c.101-42350T>G	chr6.hg19:g.10849396T>G		NA		hg19		0.02	-0.114034	GGGxGGA	UNCOVERED																																																																																			NOVEL	RP11-637O19.3-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000470399.1	9	2.40572	KEEP	2	0	0	8	216	TT	0	0	0		+	9	60	307	0	0	32.063628	3	60	87	29	ENST00000480294.1	0.75	0.196312
SMIM13	221710	__UNKNOWN__	__UNKNOWN__	6	11112770	11112770	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11112770A>G	ENST00000416247.2	+	1	357					NM_001135575.1	NP_001129047.1	P0DJ93	SIM13_HUMAN	small integral membrane protein 13	NA		NA				integral component of membrane (GO:0016021)					NA						acaggcatgaaccaccacacc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS56396.1	6p24.2	2012-12-03	2012-12-03	2012-12-03	ENSG00000224531	ENSG00000224531	221710			27356	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 228	C6orf228	NA		Standard	NM_001135575	NM_001135575	NA	Approved		uc011dio.2	P0DJ93	OTTHUMG00000014253	ENST00000416247.2:c.76+18148A>G	chr6.hg19:g.11112770A>G		NA	G3V581	hg19	CCDS56396.1	0.02	-0.315736	TGAxCCA	COVERED																																																																																			NOVEL	SMIM13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039851.3	12	3.608674	KEEP	1	0	0	12	325	AA	0.993634	0.813254	0		+	3	60	95	0	0	6.844298	24	60	714	72	ENST00000416247.2	0.111111	0.818465
NEDD9	4739	__UNKNOWN__	__UNKNOWN__	6	11200186	11200186	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11200186G>A	ENST00000379446.5	-	3	626				NEDD9_ENST00000379433.5_3'UTR|RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Intron	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	NA		NA			actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			gattacaggcgtgagccactg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859	4739		Cas scaffolding proteins	7733	protein-coding gene	gene with protein product	Cas scaffolding protein family member 2, Cas-like	602265			NA		Standard	NM_006403	NM_182966	NA	Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.460-6261C>T	chr6.hg19:g.11200186G>A		NA	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	hg19	CCDS4520.1	0.02	1.032603	GGCxTGA	COVERED																																																																																			NOVEL	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039853.2	8	4.51151	KEEP	0	0	0	15	424	GG	0.99649	0.996439	0		-	5	60	146	0	0	8.515961	89	60	2840	152	ENST00000379446.5	0.053191	0.999948
NEDD9	4739	__UNKNOWN__	__UNKNOWN__	6	11208153	11208153	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11208153A>G	ENST00000379446.5	-	2	626				NEDD9_ENST00000379433.5_Intron|RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Intron	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	NA		NA			actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			gctcatgcctattatcccagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859	4739		Cas scaffolding proteins	7733	protein-coding gene	gene with protein product	Cas scaffolding protein family member 2, Cas-like	602265			NA		Standard	NM_006403	NM_182966	NA	Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.459+5360T>C	chr6.hg19:g.11208153A>G		NA	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	hg19	CCDS4520.1	0.02	-0.298173	CCTxTTA	COVERED																																																																																			NOVEL	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039853.2	8	3.546928	KEEP	0	0	0	12	305	AA	0.993634	0.776087	0		-	3	60	106	0	0	7.708911	29	60	856	72	ENST00000379446.5	0.09375	0.78106
NEDD9	4739	__UNKNOWN__	__UNKNOWN__	6	11208155	11208155	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11208155T>A	ENST00000379446.5	-	2	626				NEDD9_ENST00000379433.5_Intron|RP3-510L9.1_ENST00000500636.2_RNA|NEDD9_ENST00000504387.1_Intron	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	NA		NA			actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			tcatgcctattatcccagcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859	4739		Cas scaffolding proteins	7733	protein-coding gene	gene with protein product	Cas scaffolding protein family member 2, Cas-like	602265			NA		Standard	NM_006403	NM_182966	NA	Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.459+5358A>T	chr6.hg19:g.11208155T>A		NA	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	hg19	CCDS4520.1	0.02	-0.289395	TATxATC	COVERED																																																																																			NOVEL	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039853.2	8	3.607634	KEEP	0	0	0	12	316	TT	0.993634	0.756043	0		-	4	60	119	0	0	8.575921	28	60	804	72	ENST00000379446.5	0.125	0.760887
NEDD9	4739	__UNKNOWN__	__UNKNOWN__	6	11239368	11239368	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11239368G>C	ENST00000504387.1	-	3	374				RP3-510L9.1_ENST00000500636.2_RNA	NM_001142393.1	NP_001135865.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	NA		NA			actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			ccactgcactgcagcctggga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859	4739		Cas scaffolding proteins	7733	protein-coding gene	gene with protein product	Cas scaffolding protein family member 2, Cas-like	602265			NA		Standard	NM_006403	NM_182966	NA	Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000504387.1:c.13-25408C>G	chr6.hg19:g.11239368G>C		NA	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	hg19	CCDS47373.1	0.02	-0.149006	ACTxCAG	COVERED																																																																																			NOVEL	NEDD9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039854.2	6	2.407207	KEEP	0	0	0	8	247	GG	0.99257	0.289832	0		-	3	60	98	0	0	7.973546	12	60	379	31	ENST00000504387.1	0.2	0.292001
RP11-716O23.2	0	__UNKNOWN__	__UNKNOWN__	6	11505841	11505841	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11505841T>C	ENST00000423149.1	+	0	570										NA		NA									NA						aggcatcaagttacctgactt	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423149.1:	chr6.hg19:g.11505841T>C		NA		hg19		0.02	-0.289396	AAGxTAC	COVERED																																																																																			NOVEL	RP11-716O23.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000039860.1	4	3.006534	KEEP	0	0	0	10	263	TT	0.992708	0.755338	0		+	4	60	132	0	0	10.057754	25	60	718	52	ENST00000423149.1	0.137931	0.760887
ADTRP	84830	__UNKNOWN__	__UNKNOWN__	6	11724239	11724239	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11724239T>G	ENST00000414691.3	-	5	917				ADTRP_ENST00000229583.5_Intron|ADTRP_ENST00000514824.1_Intron|ADTRP_ENST00000379413.2_Intron	NM_032744.3	NP_116133.1	Q96IZ2	ADTRP_HUMAN	androgen-dependent TFPI-regulating protein	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)					NA						gttgcagtgatccaagatcac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ420520	CCDS4521.1, CCDS47374.1	6p24.1	2012-01-30	2012-01-27	2012-01-27	ENSG00000111863	ENSG00000111863	84830			21214	protein-coding gene	gene with protein product	androgen-induced 1-like	614348	chromosome 6 open reading frame 105	C6orf105	NA	21868574	Standard	NM_032744	NM_032744	NA	Approved	dJ413H6.1, AIG1L	uc011dip.2	Q96IZ2	OTTHUMG00000014260	ENST00000414691.3:c.507-506A>C	chr6.hg19:g.11724239T>G		NA	B2R7T9|B4DV39|Q5THW1	hg19	CCDS4521.1	0.02	-0.315738	TGAxCCA	COVERED																																																																																			NOVEL	ADTRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039864.3	13	2.406255	KEEP	0	0	0	8	225	TT	0.99257	0.829507	0		-	3	60	99	2	0	7.053262	28	60	821	61	ENST00000414691.3	0.096774	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	11925097	11925097	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:11925097T>G			NA	NA				RP3-413H6.2 (113616 upstream) : RP11-456H18.1 (65478 downstream)						NA		NA									NA						attgagaccatcctggccaac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.11925097T>G		NA		hg19		0.02	-0.262397	CCAxCCT	COVERED																																																																																			NOVEL					0			7	2.706443	KEEP	0	0	0	9	244	TT	0.99254	0.688494	0			3	60	108	0	0	8.001009	27	60	789	53		0.1	0.693668
HIVEP1	3096	__UNKNOWN__	__UNKNOWN__	6	12038217	12038217	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:12038217A>G	ENST00000484210.1	+	0	341				HIVEP1_ENST00000379388.2_Intron			P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				caaagcactgagattacaggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951	3096		Zinc fingers, C2H2-type	4920	protein-coding gene	gene with protein product		194540	human immunodeficiency virus type I enhancer-binding protein 1, zinc finger protein 40	ZNF40	NA	2037300	Standard	NM_002114	XR_241895	NA	Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000484210.1:c.*155A>G	chr6.hg19:g.12038217A>G		NA	B2RTU3|Q14122|Q5MPB1|Q5VW60	hg19		0.02	1.634326	CTGxGAT	COVERED																																																																																			NOVEL	HIVEP1-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000353831.1	9	6.014877	KEEP	0	0	0	20	547	AA	0.999863	0.99954	0		+	5	60	158	0	0	10.042369	76	60	2267	129	ENST00000484210.1	0.061728	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	12548367	12548367	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:12548367T>G			NA	NA				RN7SKP293 (141354 upstream) : RP11-125M16.1 (34779 downstream)						NA		NA									NA						agcactttggtaggccaaggc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.12548367T>G		NA		hg19		0.02	1.923836	TGGxAGG	COVERED																																																																																			NOVEL					0			12	3.608358	KEEP	0	0	0	12	318	TT	0.994391	0.965375	0			5	60	170	0	0	12.520727	41	60	1166	106		0.108696	0.97082
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	12653223	12653223	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:12653223A>G			NA	NA				RP11-125M16.1 (67587 upstream) : PHACTR1 (64669 downstream)						NA		NA									NA						gcccaggctgatctcaaactc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.12653223A>G		NA		hg19		0.02	-0.394541	CTGxTCT	COVERED																																																																																			NOVEL					0			15	4.208547	KEEP	0	0	0	14	369	AA	0.995343	0.922325	0			3	60	105	0	0	7.340449	36	60	1053	81		0.076923	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	13518751	13518751	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:13518751T>C			NA	NA				GFOD1 (30857 upstream) : RN7SKP204 (29184 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.13518751T>C		NA		hg19		0.02	-0.438498	TCAxGCC	COVERED																																																																																			NOVEL					0			19	3.909409	KEEP	2	0	0	13	350	TT	0.994391	0.954475	0			4	60	132	0	0	9.209635	42	60	1225	93		0.086957	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	13561541	13561541	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:13561541T>C			NA	NA				RN7SKP204 (13296 upstream) : SIRT5 (13284 downstream)						NA		NA									NA						gtaatcccagtactttaggag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.13561541T>C		NA		hg19		0.02	-0.298184	CAGxACT	COVERED																																																																																			NOVEL					0			12	3.606244	KEEP	0	0	0	12	299	TT	0.993634	0.776087	0			3	60	104	0	0	7.597485	27	60	773	64		0.1	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	13720261	13720261	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:13720261T>C			NA	NA				RANBP9 (8465 upstream) : MCUR1 (66527 downstream)						NA		NA									NA						cctcagcctctcaaagtgctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.13720261T>C		NA		hg19		0.02	-0.271911	CTCxCAA	COVERED																																																																																			NOVEL					0			6	3.008063	KEEP	1	0	0	10	282	TT	0.99254	0.711964	0			3	60	96	0	0	6.844459	26	60	790	50		0.103448	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	13775283	13775283	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:13775283G>A			NA	NA				RANBP9 (63487 upstream) : MCUR1 (11505 downstream)						NA		NA									NA						cacctgcctcggcctcccaaa	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.13775283G>A		NA		hg19		0.02	-0.236845	CTCxGCC	COVERED																																																																																			NOVEL					0			9	3.910312	KEEP	1	0	0	13	376	GG	0.994391	0.608972	0			3	60	94	1	0	6.905996	21	60	712	64		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	13852504	13852504	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:13852504T>C			NA	NA				RP3-500L14.2 (25699 upstream) : RNF182 (72172 downstream)						NA		NA									NA						tttgtagagatggggtctccc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.13852504T>C		NA		hg19		0.02	-0.377024	AGAxGGG	COVERED																																																																																			NOVEL					0			10	3.60587	KEEP	0	0	0	12	308	TT	0.993634	0.903281	0			3	60	97	1	1	6.541698	36	60	1016	74		0.076923	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	14508029	14508029	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14508029A>G			NA	NA				RP3-448I9.1 (103509 upstream) : RP11-330A16.1 (89715 downstream)						NA		NA									NA						gtctgaggtgagaggattgct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.14508029A>G		NA		hg19		0.02	-0.306926	GTGxGAG	COVERED																																																																																			NOVEL					0			8	4.510313	KEEP	1	0	0	15	398	AA	0.99649	0.797437	0			3	60	99	0	0	6.92701	31	60	900	70		0.088235	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	14625294	14625294	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14625294A>G			NA	NA				RP11-330A16.1 (25373 upstream) : RNU6-793P (21471 downstream)						NA		NA									NA						caccatgttgaccaggctggt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.14625294A>G		NA		hg19		0.02	-0.280672	TTGxCCA	UNCOVERED																																																																																			NOVEL					0			12	2.405775	KEEP	2	0	0	8	214	AC	0	0	0			3	40	95	0	0	6.698155	27	60	816	56		0.1	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	14709167	14709167	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14709167A>G			NA	NA				RNU6-793P (62298 upstream) : RP11-146I2.1 (267851 downstream)						NA		NA									NA						tggccaacatagtgaaaccct	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.14709167A>G		NA		hg19		0.02	-0.219214	CATxGTG	COVERED																																																																																			NOVEL					0			7	2.706101	KEEP	4	0	0	9	237	AA	0.99257	0.54878	0			3	60	92	0	0	6.707097	21	60	591	49		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	14788813	14788813	__UNKNOWN__	IGR	SNP	T	T	C	rs569038130		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14788813T>C			NA	NA				RNU6-793P (141944 upstream) : RP11-146I2.1 (188205 downstream)						NA		NA									NA						agttcgagactagcctgggca	0.517		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15103	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.14788813T>C		NA		hg19		0.02	-0.403444	GACxAGC	COVERED																																																																																			NOVEL					0			14	3.3085	KEEP	0	0	0	11	305	TT	0.993072	0.928018	0			3	60	107	0	0	7.407737	40	60	1180	76		0.069767	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	14862957	14862957	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14862957A>G			NA	NA				RNU6-793P (216088 upstream) : RP11-146I2.1 (114061 downstream)						NA		NA									NA						aaagtgctggaattacaggca	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.14862957A>G		NA		hg19		0.02	-0.333254	TGGxATT	COVERED																																																																																			NOVEL					0			12	2.706066	KEEP	1	0	0	9	240	AA	0.99254	0.845628	0			7	60	207	0	2	16.963482	23	60	678	63		0.233333	0.851984
RP11-146I2.1	0	__UNKNOWN__	__UNKNOWN__	6	14983681	14983681	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14983681T>C	ENST00000437648.1	-	0	486										NA		NA									NA						gcctgtagtctcagttactca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437648.1:	chr6.hg19:g.14983681T>C		NA		hg19		0.02	-0.324439	GTCxCAG	COVERED																																																																																			NOVEL	RP11-146I2.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000039923.1	9	2.406175	KEEP	1	0	0	8	224	TT	0.99257	0.829507	0		-	3	60	95	0	0	6.450099	33	60	978	60	ENST00000437648.1	0.083333	0.835716
RP11-146I2.1	0	__UNKNOWN__	__UNKNOWN__	6	14983685	14983685	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:14983685T>C	ENST00000437648.1	-	0	486										NA		NA									NA						gtagtctcagttactcaggag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437648.1:	chr6.hg19:g.14983685T>C		NA		hg19		0.02	-0.315729	CAGxTAC	COVERED																																																																																			NOVEL	RP11-146I2.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000039923.1	10	2.40591	KEEP	1	0	0	8	221	TT	0.99257	0.812384	0		-	3	60	98	0	0	6.827165	31	60	910	57	ENST00000437648.1	0.088235	0.818465
RP11-146I2.1	0	__UNKNOWN__	__UNKNOWN__	6	15001068	15001068	__UNKNOWN__	lincRNA	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15001068G>C	ENST00000437648.1	-	0	426										NA		NA									NA						ctcactgcaagctccacctcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437648.1:	chr6.hg19:g.15001068G>C		NA		hg19		0.02	-0.21051	CAAxCTC	UNCOVERED																																																																																			NOVEL	RP11-146I2.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000039923.1	8	2.708069	KEEP	6	0	0	9	277	GG	0	0	0		-	3	60	97	0	0	7.327215	19	60	632	52	ENST00000437648.1	0.136364	0.522161
RP11-146I2.1	0	__UNKNOWN__	__UNKNOWN__	6	15001087	15001087	__UNKNOWN__	lincRNA	SNP	T	T	C	rs4715955	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15001087T>C	ENST00000437648.1	-	0	426										NA		NA									NA						cccaggttcatgccattctcc	0.512		NA											C|||	2599	0.51897	0.6513	0.3934	5008	,	,	NA	16107	0.3998	NA	0.3559	False	NA	,,,	NA	NA	NA	2504	0.7198	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437648.1:	chr6.hg19:g.15001087T>C		NA		hg19		0.02	-0.149069	TCAxGCC	UNCOVERED																																																																																			NOVEL	RP11-146I2.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000039923.1	9	2.706463	KEEP	4	0	0	9	244	TT	0	0	0		-	3	60	92	0	0	7.192438	14	60	405	37	ENST00000437648.1	0.176471	0.322807
RP11-146I2.1	0	__UNKNOWN__	__UNKNOWN__	6	15042411	15042411	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15042411A>G	ENST00000437648.1	-	0	426										NA		NA									NA						caggagaatcacttgaacgtg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000437648.1:	chr6.hg19:g.15042411A>G		NA		hg19		0.02	-0.087707	ATCxCTT	UNCOVERED																																																																																			NOVEL	RP11-146I2.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000039923.1	6	2.405864	KEEP	0	0	0	8	219	AA	0.99257	0.09898	0		-	3	60	97	0	0	8.478725	7	60	207	23	ENST00000437648.1	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15127917	15127917	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15127917T>C			NA	NA				RN7SL332P (14467 upstream) : AL050335.1 (22012 downstream)						NA		NA									NA						aaaggccgggtgcggtggctc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15127917T>C		NA		hg19		0.02	-0.35948	GGGxGCG	COVERED																																																																																			NOVEL					0			8	3.006267	KEEP	0	0	0	10	260	TT	0.992708	0.882393	0			4	60	125	0	0	8.965471	32	60	909	77		0.111111	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15127929	15127929	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15127929G>C			NA	NA				RN7SL332P (14479 upstream) : AL050335.1 (22000 downstream)						NA		NA									NA						cggtggctcaggcctgtaatc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15127929G>C		NA		hg19		0.02	-0.315672	TCAxGCC	COVERED																																																																																			NOVEL					0			7	3.008314	KEEP	0	0	0	10	299	GG	0.992708	0.859432	0			3	60	101	0	0	7.253105	28	60	906	75		0.096774	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15144629	15144629	__UNKNOWN__	IGR	SNP	G	G	A	rs1739088		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15144629G>A			NA	NA				RN7SL332P (31179 upstream) : AL050335.1 (5300 downstream)						NA		NA									NA						agaaagaaaggaaggaaggaa	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15144629G>A		NA		hg19		0.02	-0.078927	AAGxAAG	UNCOVERED																																																																																			NOVEL					0			11	2.407255	KEEP	9	0	0	8	249	GG	0	0	0			3	60	80	0	1	6.942874	6	60	184	31		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15147888	15147888	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15147888G>A			NA	NA				RN7SL332P (34438 upstream) : AL050335.1 (2041 downstream)						NA		NA									NA						gattacaggcgtgagccactg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15147888G>A		NA		hg19		0.02	-0.157896	GGCxTGA	COVERED																																																																																			NOVEL					0			3	2.406475	KEEP	1	0	0	8	229	GG	0.99257	0.320408	0			3	60	86	0	0	6.772381	12	60	395	40		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15169626	15169626	__UNKNOWN__	IGR	SNP	C	C	T	rs549157121		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15169626C>T			NA	NA				AL050335.1 (19596 upstream) : RP11-560J1.2 (74527 downstream)						NA		NA									NA						cccaggagttcgagaccagcc	0.468		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	18277	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15169626C>T		NA		hg19		0.02	-0.324568	GTTxGAG	COVERED																																																																																			NOVEL					0			3	3.911501	KEEP	1	0	0	13	394	CC	0.994391	0.831028	0			3	60	93	0	0	6.327583	31	60	1020	86		0.088235	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15213293	15213293	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15213293T>C			NA	NA				AL050335.1 (63263 upstream) : RP11-560J1.2 (30860 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15213293T>C		NA		hg19		0.02	-0.324494	TCAxGCC	COVERED																																																																																			NOVEL					0			11	2.706195	KEEP	2	0	0	9	243	TT	0.99254	0.829482	0			3	60	103	0	0	7.452616	28	60	813	72		0.096774	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15213305	15213305	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15213305T>C			NA	NA				AL050335.1 (63275 upstream) : RP11-560J1.2 (30848 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15213305T>C		NA		hg19		0.02	-0.324541	TCCxAGC	COVERED																																																																																			NOVEL					0			10	2.706968	KEEP	1	0	0	9	249	TT	0.99254	0.829482	0			5	60	166	0	0	12.964128	27	60	824	70		0.15625	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15216085	15216085	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15216085A>G			NA	NA				AL050335.1 (66055 upstream) : RP11-560J1.2 (28068 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15216085A>G		NA		hg19		0.02	-0.271904	CCAxCAC	COVERED																																																																																			NOVEL					0			11	2.405607	KEEP	0	0	0	8	217	AA	0.99257	0.711986	0			3	60	108	0	0	8.248412	22	60	676	55		0.12	0.717315
JARID2	3720	__UNKNOWN__	__UNKNOWN__	6	15251536	15251536	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15251536T>C	ENST00000341776.2	+	1	289				JARID2_ENST00000397311.3_Intron	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	NA		NA			central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				cgtgagccactgcacccagcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083	3720			6196	protein-coding gene	gene with protein product		601594	jumonji (mouse) homolog, Jumonji, AT rich interactive domain 2	JMJ	NA	8894700	Standard	NM_004973	NM_001267040	NA	Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.45+4721T>C	chr6.hg19:g.15251536T>C		NA	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	hg19	CCDS4533.1	0.02	-0.350849	CACxGCA	COVERED																																																																																			NOVEL	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039926.1	9	3.00828	KEEP	1	0	0	10	287	TT	0.99254	0.87116	0		+	3	60	95	0	0	6.527747	31	60	948	74	ENST00000341776.2	0.088235	0.877708
JARID2	3720	__UNKNOWN__	__UNKNOWN__	6	15251539	15251539	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15251539A>G	ENST00000341776.2	+	1	289				JARID2_ENST00000397311.3_Intron	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	NA		NA			central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				gagccactgcacccagccAGC	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083	3720			6196	protein-coding gene	gene with protein product		601594	jumonji (mouse) homolog, Jumonji, AT rich interactive domain 2	JMJ	NA	8894700	Standard	NM_004973	NM_001267040	NA	Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.45+4724A>G	chr6.hg19:g.15251539A>G		NA	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	hg19	CCDS4533.1	0.02	-0.350774	TGCxCCC	COVERED																																																																																			NOVEL	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039926.1	9	3.007851	KEEP	1	0	0	10	279	AA	0.99254	0.87116	0		+	3	60	103	0	0	7.287347	32	60	908	74	ENST00000341776.2	0.085714	0.877708
JARID2	3720	__UNKNOWN__	__UNKNOWN__	6	15284843	15284843	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15284843A>G	ENST00000341776.2	+	1	289				JARID2_ENST00000397311.3_Intron	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	NA		NA			central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				tcagcctcccaagtagctggg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083	3720			6196	protein-coding gene	gene with protein product		601594	jumonji (mouse) homolog, Jumonji, AT rich interactive domain 2	JMJ	NA	8894700	Standard	NM_004973	NM_001267040	NA	Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.45+38028A>G	chr6.hg19:g.15284843A>G		NA	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	hg19	CCDS4533.1	0.02	-0.192929	CCCxAGT	COVERED																																																																																			NOVEL	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039926.1	10	2.705406	KEEP	1	0	0	9	234	AA	0.99254	0.454342	0		+	3	60	103	0	0	8.061003	17	60	485	43	ENST00000341776.2	0.15	0.457757
JARID2	3720	__UNKNOWN__	__UNKNOWN__	6	15369031	15369031	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15369031C>T	ENST00000341776.2	+	2	289				JARID2_ENST00000397311.3_Intron	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	NA		NA			central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TTGAAGCATTCGTCTTGGAGG	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083	3720			6196	protein-coding gene	gene with protein product		601594	jumonji (mouse) homolog, Jumonji, AT rich interactive domain 2	JMJ	NA	8894700	Standard	NM_004973	NM_001267040	NA	Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.46-5317C>T	chr6.hg19:g.15369031C>T		NA	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	hg19	CCDS4533.1	0.02	4.798396	ATTxGTC	COVERED																																																																																			NOVEL	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039926.1	4	3.609199	KEEP	0	0	0	12	339	CC	0.993634	0.993634	0		+	24	60	719	0	0	53.523005	143	60	4476	264	ENST00000341776.2	0.143713	1
JARID2	3720	__UNKNOWN__	__UNKNOWN__	6	15420566	15420566	__UNKNOWN__	Intron	SNP	G	G	A	rs547919939		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15420566G>A	ENST00000341776.2	+	3	567				JARID2_ENST00000397311.3_Intron|JARID2_ENST00000541660.1_Intron	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	NA		NA			central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				cccaggaggcggaggttgcag	0.468		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15990	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083	3720			6196	protein-coding gene	gene with protein product		601594	jumonji (mouse) homolog, Jumonji, AT rich interactive domain 2	JMJ	NA	8894700	Standard	NM_004973	NM_001267040	NA	Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.323+9970G>A	chr6.hg19:g.15420566G>A		NA	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	hg19	CCDS4533.1	0.02	-0.245549	GGCxGAG	UNCOVERED																																																																																			NOVEL	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039926.1	8	2.406091	KEEP	1	0	0	8	231	GG	0	0	0		+	4	60	109	0	0	7.82554	24	60	733	47	ENST00000341776.2	0.142857	0.641347
DTNBP1	84062	__UNKNOWN__	__UNKNOWN__	6	15594421	15594421	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15594421T>C	ENST00000344537.5	-	7	661				DTNBP1_ENST00000355917.3_Intron|DTNBP1_ENST00000338950.5_Intron	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	NA		NA			actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			Tggctgggcgtggtggctcat	0.458		NA							Hermansky-Pudlak syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	HPS, HPS1-8	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579	84062		Biogenesis of lysosomal organelles complex-1 subunits	17328	protein-coding gene	gene with protein product	dysbindin-1, biogenesis of lysosomal organelles complex-1, subunit 8	607145			NA	11316798	Standard	NM_032122	NM_032122	NA	Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.489-1109A>G	chr6.hg19:g.15594421T>C		NA	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	hg19	CCDS4534.1	0.02	-0.394585	GCGxGGT	COVERED																																																																																			NOVEL	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039933.2	17	3.608546	KEEP	5	0	0	12	322	TT	0.993072	0.920221	0		-	3	60	99	1	0	6.673334	38	60	1062	91	ENST00000344537.5	0.073171	0.92664
DTNBP1	84062	__UNKNOWN__	__UNKNOWN__	6	15609822	15609822	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15609822G>T	ENST00000344537.5	-	6	661				DTNBP1_ENST00000355917.3_Intron|DTNBP1_ENST00000338950.5_Intron	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	NA		NA			actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			agtgctgggagtacaggcgtg	0.478		NA							Hermansky-Pudlak syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	HPS, HPS1-8	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579	84062		Biogenesis of lysosomal organelles complex-1 subunits	17328	protein-coding gene	gene with protein product	dysbindin-1, biogenesis of lysosomal organelles complex-1, subunit 8	607145			NA	11316798	Standard	NM_032122	NM_032122	NA	Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.488+5675C>A	chr6.hg19:g.15609822G>T		NA	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	hg19	CCDS4534.1	0.02	-0.394761	GGAxTAC	COVERED																																																																																			NOVEL	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039933.2	7	3.009371	KEEP	2	0	0	10	321	GG	0.992708	0.919883	0		-	4	60	120	0	0	8.26514	36	60	1256	90	ENST00000344537.5	0.1	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15681169	15681169	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15681169G>A			NA	NA				DTNBP1 (17896 upstream) : RP11-401E14.2 (314005 downstream)						NA		NA									NA						gcactttggggggctgaggtg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15681169G>A		NA		hg19		0.02	-0.333334	GGGxGGC	COVERED																																																																																			NOVEL					0			11	4.212674	KEEP	0	0	0	14	439	GG	0.995343	0.848017	0			4	60	122	2	0	8.994628	26	60	871	77		0.133333	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15850094	15850094	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15850094A>G			NA	NA				DTNBP1 (186821 upstream) : RP11-401E14.2 (145080 downstream)						NA		NA									NA						agtggctcatacctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15850094A>G		NA		hg19		0.02	-0.228011	CATxCCT	COVERED																																																																																			NOVEL					0			9	2.701868	KEEP	2	0	0	9	222	AA	0.99257	0.578599	0			3	60	95	0	0	7.12808	19	60	548	57		0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	15850122	15850122	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:15850122A>G			NA	NA				DTNBP1 (186849 upstream) : RP11-401E14.2 (145052 downstream)						NA		NA									NA						ttgggaggccaaggtgggcag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.15850122A>G		NA		hg19		0.02	-0.245586	GCCxAGG	COVERED																																																																																			NOVEL					0			7	2.705893	KEEP	2	0	0	9	245	AA	0.99257	0.636582	0			3	60	99	0	0	7.59225	18	60	536	60		0.142857	0.641347
GMPR	2766	__UNKNOWN__	__UNKNOWN__	6	16266816	16266816	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:16266816C>G	ENST00000259727.4	+	5	579					NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	NA		NA			nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				ggtggatcaccaggtcaggag	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	2766	1.7.1.7		4376	protein-coding gene	gene with protein product		139265			NA	2194676	Standard		NM_006877	NA	Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.466-7830C>G	chr6.hg19:g.16266816C>G		NA	Q96HQ6	hg19	CCDS4537.1	0.02	-0.201758	CACxAGG	COVERED																																																																																			NOVEL	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039942.2	6	2.70832	KEEP	0	0	0	9	284	CC	0.99254	0.486885	0		+	3	60	89	0	0	6.661936	17	60	582	46	ENST00000259727.4	0.15	0.490544
GMPR	2766	__UNKNOWN__	__UNKNOWN__	6	16286880	16286880	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:16286880A>G	ENST00000259727.4	+	7	811					NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	NA		NA			nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				ggtggctcacacctgtaatcc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	2766	1.7.1.7		4376	protein-coding gene	gene with protein product		139265			NA	2194676	Standard		NM_006877	NA	Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.697+814A>G	chr6.hg19:g.16286880A>G		NA	Q96HQ6	hg19	CCDS4537.1	0.02	1.599683	CACxCCT	COVERED																																																																																			NOVEL	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039942.2	34	3.269793	KEEP	1	2	54	30	809	AA	0.999997	0.999859	0		+	6	60	187	1	0	12.386764	72	60	2105	183	ENST00000259727.4	0.076923	0.999862
ATXN1	6310	__UNKNOWN__	__UNKNOWN__	6	16315101	16315101	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:16315101T>C	ENST00000244769.4	-	9	2854				ATXN1_ENST00000436367.1_Intron	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	NA		NA			adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				cttggcctcctaaagtgctgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788	6310		Ataxins	10548	protein-coding gene	gene with protein product		601556	spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)	SCA1	NA	1582256	Standard	NM_000332	NM_000332	NA	Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1918-8011A>G	chr6.hg19:g.16315101T>C		NA	Q17S02|Q9UJG2|Q9Y4J1	hg19	CCDS34342.1	0.02	-0.184182	TCCxAAA	UNCOVERED																																																																																			NOVEL	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039943.3	8	2.405932	KEEP	7	0	0	8	219	TT	0	0	0		-	3	60	96	0	0	7.293129	18	60	538	51	ENST00000244769.4	0.142857	0.423478
ATXN1	6310	__UNKNOWN__	__UNKNOWN__	6	16639621	16639621	__UNKNOWN__	Intron	SNP	C	C	T	rs565217875		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:16639621C>T	ENST00000244769.4	-	4	449				ATXN1_ENST00000436367.1_Intron	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	NA		NA			adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				acaggctcaccgcaacctcca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788	6310		Ataxins	10548	protein-coding gene	gene with protein product		601556	spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)	SCA1	NA	1582256	Standard	NM_000332	NM_000332	NA	Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.487+18385G>A	chr6.hg19:g.16639621C>T		NA	Q17S02|Q9UJG2|Q9Y4J1	hg19	CCDS34342.1	0.02	-0.280707	CACxGCA	COVERED																																																																																			NOVEL	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039943.3	4	2.406857	KEEP	1	0	0	8	240	CC	0.99257	0.734176	0		-	3	60	91	0	0	6.495284	23	60	783	63	ENST00000244769.4	0.115385	0.739671
STMND1	401236	__UNKNOWN__	__UNKNOWN__	6	17105613	17105613	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17105613C>A	ENST00000536551.1	+	1	81					NM_001190766.1	NP_001177695.1	H3BQB6	STMD1_HUMAN	stathmin domain containing 1	NA		NA			regulation of microtubule polymerization or depolymerization (GO:0031110)						NA						gtggtggctcctgcctgtaat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026805	CCDS58997.1	6p22.3	2012-12-11			ENSG00000230873	ENSG00000230873	401236			44668	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001190766	NM_001190766	NA	Approved	FLJ23152	uc021ymc.1	H3BQB6	OTTHUMG00000014304	ENST00000536551.1:c.81+3044C>A	chr6.hg19:g.17105613C>A		NA		hg19	CCDS58997.1	0.02	-0.263172	CTCxTGC	UNCOVERED																																																																																			NOVEL	STMND1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		3	2.40494	KEEP	1	0	0	8	231	CC	0	0	0		+	3	60	93	1	0	6.805848	21	60	711	60	ENST00000536551.1	0.125	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	17195374	17195374	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17195374G>A			NA	NA				STMND1 (63771 upstream) : RBM24 (86202 downstream)						NA		NA									NA						cacccacctcggcctcccaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.17195374G>A		NA		hg19		0.02	-0.315372	CTCxGCC	COVERED																																																																																			NOVEL					0			10	4.211523	KEEP	1	0	0	14	411	GG	0.994391	0.813874	0			3	60	95	0	0	6.48964	32	60	994	71		0.085714	0.818465
RBM24	221662	__UNKNOWN__	__UNKNOWN__	6	17288019	17288019	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17288019G>A	ENST00000379052.5	+	3	583				RBM24_ENST00000318204.5_Intron|RBM24_ENST00000425446.2_Intron	NM_001143942.1	NP_001137414.1	Q9BX46	RBM24_HUMAN	RNA binding motif protein 24	NA		NA			cell differentiation (GO:0030154)|regulation of mRNA stability (GO:0043488)|regulation of myotube differentiation (GO:0010830)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	13	Breast(50;0.0615)|Ovarian(93;0.0733)	all_hematologic(90;0.062)	all cancers(50;0.131)|Epithelial(50;0.15)			cagcctgggcgacagagcgag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC040928	CCDS4538.1, CCDS47378.1, CCDS47379.1	6p22.3	2013-02-12	2004-04-23	2004-04-23	ENSG00000112183	ENSG00000112183	221662		RNA binding motif (RRM) containing	21539	protein-coding gene	gene with protein product		NA	RNA-binding region (RNP1, RRM) containing 6	RNPC6	NA		Standard	NM_153020	NM_153020	NA	Approved	FLJ30829, dJ259A10.1	uc003nbz.4	Q9BX46	OTTHUMG00000014306	ENST00000379052.5:c.347+3077G>A	chr6.hg19:g.17288019G>A		NA	E9PAY4|Q6QDA4|Q8N9D3|Q96NI3	hg19	CCDS47378.1	0.02	-0.175387	GGCxACA	COVERED																																																																																			NOVEL	RBM24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039946.2	7	3.60944	KEEP	3	0	0	12	341	GG	0.992708	0.384582	0		+	3	60	91	1	0	7.010743	15	60	450	49	ENST00000379052.5	0.166667	0.387407
CAP2	10486	__UNKNOWN__	__UNKNOWN__	6	17540109	17540109	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17540109A>G	ENST00000229922.2	+	8	1358				CAP2_ENST00000378990.2_Intron|CAP2_ENST00000489374.1_Intron|CAP2_ENST00000465994.1_Intron|CAP2_ENST00000493172.1_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	NA		NA			activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			ccaggagttcaagaccagcct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186	10486			20039	protein-coding gene	gene with protein product		NA			NA	7962207, 8761950	Standard		NM_006366	NA	Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.826+420A>G	chr6.hg19:g.17540109A>G		NA	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	hg19	CCDS4539.1	0.02	-0.271899	TTCxAGA	COVERED																																																																																			NOVEL	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039952.2	4	2.706802	KEEP	1	0	0	9	247	AA	0.99257	0.734176	0		+	3	60	107	0	0	8.042032	24	60	724	62	ENST00000229922.2	0.111111	0.739671
FAM8A1	51439	__UNKNOWN__	__UNKNOWN__	6	17604053	17604053	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17604053A>G	ENST00000259963.3	+	3	888					NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	NA		NA				integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			ctgggctcaaatgatcctcct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414	51439			16372	protein-coding gene	gene with protein product		NA			NA	11707071	Standard		NM_016255	NA	Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.834-1084A>G	chr6.hg19:g.17604053A>G		NA	B2R725	hg19	CCDS4540.1	0.02	1.692885	CAAxTGA	COVERED																																																																																			NOVEL	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039950.1	19	3.308046	KEEP	1	0	0	11	304	AA	0.993072	0.988789	0		+	5	60	143	0	0	9.211831	57	60	1699	115	ENST00000259963.3	0.080645	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	17712412	17712412	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17712412T>C			NA	NA				RP11-500C11.3 (4837 upstream) : RNA5SP204 (9604 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.17712412T>C		NA		hg19		0.02	-0.280651	ATCxCAG	COVERED																																																																																			NOVEL					0			13	2.706557	KEEP	4	0	0	9	244	TT	0.99257	0.734176	0			3	60	95	0	0	6.795571	25	60	752	56		0.107143	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	17749314	17749314	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17749314A>G			NA	NA				Y_RNA (11524 upstream) : KIF13A (10099 downstream)						NA		NA									NA						ggctggtctcaaactcctgac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.17749314A>G		NA		hg19		0.02	-0.377143	CTCxAAC	UNCOVERED																																																																																			NOVEL					0			6	2.405161	KEEP	2	0	0	8	224	AA	0	0	0			3	60	95	0	0	6.341439	36	60	1092	78		0.076923	0.909069
KIF13A	63971	__UNKNOWN__	__UNKNOWN__	6	17796751	17796751	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17796751A>G	ENST00000259711.6	-	23	3048				KIF13A_ENST00000378843.2_Intron|KIF13A_ENST00000378814.5_Intron|KIF13A_ENST00000378826.2_Intron|KIF13A_ENST00000378816.5_Intron	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	NA		NA			ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			gattacaggcatgagccaccg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177	63971		Kinesins	14566	protein-coding gene	gene with protein product		605433			NA	11106728	Standard		NM_022113	NA	Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.2942+148T>C	chr6.hg19:g.17796751A>G		NA	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	hg19	CCDS47381.1	0.02	-0.2543	GGCxTGA	COVERED																																																																																			NOVEL	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039954.4	7	3.006158	KEEP	1	0	0	10	263	AA	0.992708	0.663648	0		-	3	60	93	0	0	7.061178	17	60	514	59	ENST00000259711.6	0.15	0.668523
KIF13A	63971	__UNKNOWN__	__UNKNOWN__	6	17983160	17983160	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:17983160G>C	ENST00000259711.6	-	2	252				KIF13A_ENST00000378843.2_Intron|KIF13A_ENST00000378814.5_Intron|KIF13A_ENST00000378826.2_Intron|KIF13A_ENST00000378816.5_Intron|KIF13A_ENST00000502704.1_Intron	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	NA		NA			ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			ccagcactttgggaggccgag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177	63971		Kinesins	14566	protein-coding gene	gene with protein product		605433			NA	11106728	Standard		NM_022113	NA	Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.146+4124C>G	chr6.hg19:g.17983160G>C		NA	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	hg19	CCDS47381.1	0.02	-0.42108	TTTxGGA	COVERED																																																																																			NOVEL	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039954.4	11	2.407416	KEEP	5	0	0	8	254	GG	0.99257	0.941356	0		-	3	60	101	0	0	6.777238	41	60	1417	97	ENST00000259711.6	0.068182	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	18074963	18074963	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18074963A>G			NA	NA				KIF13A (87109 upstream) : NHLRC1 (45754 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.18074963A>G		NA		hg19		0.02	-0.324495	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.405725	KEEP	2	0	0	8	215	AA	0.99257	0.829507	0			3	60	99	0	0	7.053054	28	60	817	72		0.096774	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	18080624	18080624	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18080624T>C			NA	NA				KIF13A (92770 upstream) : NHLRC1 (40093 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.18080624T>C		NA		hg19		0.02	-0.315765	TCCxAGC	COVERED																																																																																			NOVEL					0			8	3.007398	KEEP	1	0	0	10	272	TT	0.992708	0.812496	0			3	60	103	0	0	7.452423	28	60	846	68		0.096774	0.818465
KDM1B	221656	__UNKNOWN__	__UNKNOWN__	6	18174119	18174119	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18174119C>T	ENST00000297792.5	+	7	711				KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000397244.1_Intron|KDM1B_ENST00000388870.2_Intron			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	NA		NA			DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						cgggttcaagcgattctcctg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097	221656		Chromatin-modifying enzymes / K-demethylases	21577	protein-coding gene	gene with protein product		613081	amine oxidase, flavin containing 1, chromosome 6 open reading frame 193, amine oxidase (flavin containing) domain 1	C6orf193, AOF1	NA	19407342, 19727073	Standard	NM_153042	NM_153042	NA	Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.534+2409C>T	chr6.hg19:g.18174119C>T		NA	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	hg19	CCDS34343.1	0.02	-0.306901	AAGxGAT	COVERED																																																																																			NOVEL	KDM1B-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277080.1	10	3.30794	KEEP	4	0	0	11	298	CC	0.993072	0.794702	0		+	4	60	107	0	0	7.216318	31	60	968	68	ENST00000297792.5	0.114286	0.800245
KDM1B	221656	__UNKNOWN__	__UNKNOWN__	6	18218570	18218570	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18218570C>T	ENST00000297792.5	+	17	1866				KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000397244.1_Intron|KDM1B_ENST00000388870.2_Intron			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	NA		NA			DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						cccaggctggcctcaaacccg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097	221656		Chromatin-modifying enzymes / K-demethylases	21577	protein-coding gene	gene with protein product		613081	amine oxidase, flavin containing 1, chromosome 6 open reading frame 193, amine oxidase (flavin containing) domain 1	C6orf193, AOF1	NA	19407342, 19727073	Standard	NM_153042	NM_153042	NA	Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1689+454C>T	chr6.hg19:g.18218570C>T		NA	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	hg19	CCDS34343.1	0.02	1.150037	TGGxCTC	COVERED																																																																																			NOVEL	KDM1B-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277080.1	15	4.513469	KEEP	0	0	0	15	459	CC	0.99649	0.960391	0		+	5	60	133	0	0	8.730545	43	60	1438	89	ENST00000297792.5	0.104167	0.963774
KDM1B	221656	__UNKNOWN__	__UNKNOWN__	6	18219355	18219355	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18219355C>G	ENST00000297792.5	+	17	1866				KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000397244.1_Intron|KDM1B_ENST00000388870.2_Intron			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	NA		NA			DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						ggatggtctccatctcctgac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097	221656		Chromatin-modifying enzymes / K-demethylases	21577	protein-coding gene	gene with protein product		613081	amine oxidase, flavin containing 1, chromosome 6 open reading frame 193, amine oxidase (flavin containing) domain 1	C6orf193, AOF1	NA	19407342, 19727073	Standard	NM_153042	NM_153042	NA	Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1689+1239C>G	chr6.hg19:g.18219355C>G		NA	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	hg19	CCDS34343.1	0.02	-0.228071	CTCxATC	COVERED																																																																																			NOVEL	KDM1B-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277080.1	12	2.708103	KEEP	3	0	0	9	278	CC	0.99257	0.607857	0		+	4	30	124	0	0	9.537205	21	60	711	49	ENST00000297792.5	0.16	0.612407
DEK	7913	__UNKNOWN__	__UNKNOWN__	6	18238380	18238380	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18238380A>G	ENST00000397239.3	-	8	1210				DEK_ENST00000244776.7_Intron	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	NA		NA			chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			gattacaggcatgagccacca	0.468		NA	T	NUP214	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795	7913			2768	protein-coding gene	gene with protein product		125264	DEK oncogene (DNA binding), DEK oncogene		NA	1549122	Standard		NM_003472	NA	Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.763-633T>C	chr6.hg19:g.18238380A>G		NA	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	hg19	CCDS34344.1	0.02	-0.342037	GGCxTGA	UNCOVERED																																																																																			NOVEL	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039962.4	13	2.405615	KEEP	2	0	0	8	217	AA	0	0	0		-	3	60	97	0	0	6.76787	30	60	875	70	ENST00000397239.3	0.090909	0.865745
RNF144B	255488	__UNKNOWN__	__UNKNOWN__	6	18408493	18408493	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18408493G>A	ENST00000259939.3	+	2	482				RNF144B_ENST00000429054.2_Intron	NM_182757.3	NP_877434.2	Q7Z419	R144B_HUMAN	ring finger protein 144B	NA		NA			apoptotic process (GO:0006915)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)	11	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			tgggattacagatgtgagcca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096832	CCDS34345.1	6p22.3	2011-05-23	2009-01-05	2007-08-20	ENSG00000137393	ENSG00000137393	255488		RING-type (C3HC4) zinc fingers	21578	protein-coding gene	gene with protein product		NA	IBR domain containing 2	IBRDC2	NA		Standard	XM_172581	NM_182757	NA	Approved	bA528A10.3	uc003ncs.3	Q7Z419	OTTHUMG00000014322	ENST00000259939.3:c.165+8563G>A	chr6.hg19:g.18408493G>A		NA	B3KUA8|B4DZI2|Q5TB85|Q6P4Q0|Q8N3R7|Q9BX38	hg19	CCDS34345.1	0.02	-0.219282	ACAxATG	COVERED																																																																																			NOVEL	RNF144B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039965.2	13	2.407239	KEEP	0	0	0	8	247	GG	0.99257	0.54878	0		+	3	60	87	0	0	6.461701	17	60	531	42	ENST00000259939.3	0.15	0.552887
RNF144B	255488	__UNKNOWN__	__UNKNOWN__	6	18450568	18450568	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:18450568A>G	ENST00000259939.3	+	5	648				RNF144B_ENST00000429054.2_Intron	NM_182757.3	NP_877434.2	Q7Z419	R144B_HUMAN	ring finger protein 144B	NA		NA			apoptotic process (GO:0006915)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)	11	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			ttgctctgtcacccaggctgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096832	CCDS34345.1	6p22.3	2011-05-23	2009-01-05	2007-08-20	ENSG00000137393	ENSG00000137393	255488		RING-type (C3HC4) zinc fingers	21578	protein-coding gene	gene with protein product		NA	IBR domain containing 2	IBRDC2	NA		Standard	XM_172581	NM_182757	NA	Approved	bA528A10.3	uc003ncs.3	Q7Z419	OTTHUMG00000014322	ENST00000259939.3:c.332-6818A>G	chr6.hg19:g.18450568A>G		NA	B3KUA8|B4DZI2|Q5TB85|Q6P4Q0|Q8N3R7|Q9BX38	hg19	CCDS34345.1	0.02	-0.201682	GTCxCCC	COVERED																																																																																			NOVEL	RNF144B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039965.2	6	3.606707	KEEP	0	0	0	12	307	AA	0.993634	0.487421	0		+	3	60	99	0	0	7.527344	19	60	533	52	ENST00000259939.3	0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	19005022	19005022	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:19005022T>C			NA	NA				MIR548A1 (432911 upstream) : RP11-686D16.1 (285527 downstream)						NA		NA									NA						gcccaggaggttgaggttgca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.19005022T>C		NA		hg19		0.02	-0.333172	AGGxTGA	COVERED																																																																																			NOVEL					0			11	3.007495	KEEP	1	0	0	10	274	TT	0.992708	0.845771	0			3	60	101	0	1	7.049586	33	60	945	69		0.083333	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	19348030	19348030	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:19348030T>A			NA	NA				RP11-686D16.1 (26778 upstream) : RNA5SP205 (90483 downstream)						NA		NA									NA						ctgtaatccctgcactttggg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.19348030T>A		NA		hg19		0.02	-0.368381	CCCxGCA	COVERED																																																																																			NOVEL					0			8	3.609853	KEEP	1	0	0	12	344	TT	0.993634	0.893588	0			5	60	153	1	0	11.388576	31	60	942	85		0.138889	0.899314
RP1-167F1.2	0	__UNKNOWN__	__UNKNOWN__	6	19637262	19637262	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:19637262G>A	ENST00000432171.2	-	0	366										NA		NA									NA						aaggaaggaaggaaggaagga	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432171.2:	chr6.hg19:g.19637262G>A		NA		hg19		0.02	-0.140347	GAAxGAA	UNCOVERED																																																																																			NOVEL	RP1-167F1.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000039973.2	10	2.407017	KEEP	7	0	0	8	240	GG	0	0	0		-	3	21	85	0	0	6.881965	10	60	332	39	ENST00000432171.2	0.230769	0.260965
RP1-167F1.2	0	__UNKNOWN__	__UNKNOWN__	6	19637278	19637278	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:19637278A>G	ENST00000432171.2	-	0	366										NA		NA									NA						aaggaagggaaggagggaggg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432171.2:	chr6.hg19:g.19637278A>G		NA		hg19		0.02	-0.140314	GGAxGGA	UNCOVERED																																																																																			NOVEL	RP1-167F1.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000039973.2	12	2.643848	KEEP	6	0	0	9	215	AA	0	0	0		-	3	21	102	1	1	8.582298	10	60	285	41	ENST00000432171.2	0.230769	0.260965
RP1-167F1.2	0	__UNKNOWN__	__UNKNOWN__	6	19807944	19807944	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:19807944A>G	ENST00000432171.2	-	0	263										NA		NA									NA						gcaagactccatctcaaaaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432171.2:	chr6.hg19:g.19807944A>G		NA		hg19		0.02	-0.315668	TCCxTCT	UNCOVERED																																																																																			NOVEL	RP1-167F1.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000039973.2	6	2.405033	KEEP	1	0	0	8	212	AA	0	0	0		-	4	60	130	1	0	9.562686	30	60	846	65	ENST00000432171.2	0.117647	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	20020287	20020287	__UNKNOWN__	IGR	SNP	A	A	T	rs1202262	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20020287A>T			NA	NA				ID4 (179372 upstream) : MBOAT1 (80647 downstream)						NA		NA									NA						gccaacatggaaaaaccccat	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.20020287A>T		NA		hg19		0.02	-0.342019	TGGxAAA	COVERED																																																																																			NOVEL					0			13	3.3081	KEEP	0	0	0	11	299	AA	0.993072	0.871627	0			4	60	112	0	0	7.712536	31	60	921	73		0.114286	0.877708
MBOAT1	154141	__UNKNOWN__	__UNKNOWN__	6	20122320	20122320	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20122320A>T	ENST00000324607.7	-	8	1072				MBOAT1_ENST00000541730.1_Intron	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			cacttgaaccagggaggtgga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197	154141			21579	protein-coding gene	gene with protein product	lysophosphatidylethanolamine acyltransferase 1	611732	O-acyltransferase (membrane bound) domain containing 1	OACT1	NA	18287005	Standard		NM_001080480	NA	Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.907+2318T>A	chr6.hg19:g.20122320A>T		NA	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	hg19	CCDS34346.1	0.02	-0.210507	ACCxGGG	COVERED																																																																																			NOVEL	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039980.1	11	2.706954	KEEP	8	0	0	9	253	AC	0.99257	0.54878	0		-	3	24	93	0	0	6.927331	19	60	576	61	ENST00000324607.7	0.136364	0.552887
MBOAT1	154141	__UNKNOWN__	__UNKNOWN__	6	20130624	20130624	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20130624A>G	ENST00000324607.7	-	5	640				MBOAT1_ENST00000541730.1_Intron|MBOAT1_ENST00000536798.1_Intron	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			tcgctctgtcacccaggctgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197	154141			21579	protein-coding gene	gene with protein product	lysophosphatidylethanolamine acyltransferase 1	611732	O-acyltransferase (membrane bound) domain containing 1	OACT1	NA	18287005	Standard		NM_001080480	NA	Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.475+750T>C	chr6.hg19:g.20130624A>G		NA	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	hg19	CCDS34346.1	0.02	1.438239	GTCxCCC	COVERED																																																																																			NOVEL	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039980.1	23	4.443052	KEEP	4	1	29	25	692	AA	0.999988	0.999927	0		-	4	60	134	2	0	8.308608	81	60	2464	195	ENST00000324607.7	0.047059	0.99994
E2F3	1871	__UNKNOWN__	__UNKNOWN__	6	20490390	20490390	__UNKNOWN__	Intron	SNP	T	T	G	rs4134981	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20490390T>G	ENST00000346618.3	+	7	1201				E2F3_ENST00000535432.1_Intron	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	NA		NA			mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)	7	all_cancers(95;0.154)|all_epithelial(95;0.0585)|Breast(50;0.146)|Ovarian(93;0.148)		OV - Ovarian serous cystadenocarcinoma(7;0.0068)|all cancers(50;0.0148)|Epithelial(50;0.0562)			ATCAATGTTTTCTTTTCAGAC	0.388		NA											T|||	366	0.0730831	0.2224	0.0303	5008	,	,	NA	20526	0.001	NA	0.0149	False	NA	,,,	NA	NA	NA	2504	0.0358	NA	NA	NA								NA				0								T		741,3665	296.1+/-284.1	67,607,1529	60	61	61			-2.1	0	6	dbSNP_108	61	110,8490	55.6+/-116.7	0,110,4190	no	intron	E2F3	NM_001949.4		67,717,5719	GG,GT,TT	NA	1.2791,16.818,6.5431			20490390	851,12155	2203	4300	6503	SO:0001627	intron_variant			Y10479	CCDS4545.1, CCDS58999.1	6p22	2008-08-29			ENSG00000112242	ENSG00000112242	1871			3115	protein-coding gene	gene with protein product		600427			NA	8246996	Standard		NM_001949	NA	Approved		uc003nda.2	O00716	OTTHUMG00000016389	ENST00000346618.3:c.1136-9T>G	chr6.hg19:g.20490390T>G		NA	Q15000|Q68DT0|Q9BZ44	hg19	CCDS4545.1	0.02	4.111559	TTTxCTT	COVERED																																																																																			NOVEL	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043828.1	2	2.403674	KEEP	0	0	0	8	202	TT	0.99257	0.992563	0		+	19	60	640	0	0	51.338811	88	60	2538	164	ENST00000346618.3	0.17757	0.999993
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	20511231	20511231	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20511231C>T			NA	NA				Y_RNA (10724 upstream) : CDKAL1 (23456 downstream)						NA		NA									NA						tttgggaggccgaggtgggcg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.20511231C>T		NA		hg19		0.02	-0.359018	GGCxGAG	COVERED																																																																																			NOVEL					0			18	2.827354	KEEP	15	1	24	18	502	CC	0.993634	0.883216	0			4	60	116	0	0	7.916661	35	60	1111	99		0.102564	0.888875
CDKAL1	54901	__UNKNOWN__	__UNKNOWN__	6	20568714	20568714	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20568714C>A	ENST00000378610.1	+	2	296				CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Intron			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	NA		NA			maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			gcctgtaatcccagcactttg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996	54901			21050	protein-coding gene	gene with protein product		611259			NA		Standard	NM_017774	NM_017774	NA	Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.286+19778C>A	chr6.hg19:g.20568714C>A		NA	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	hg19	CCDS4546.1	0.02	-0.289489	ATCxCAG	COVERED																																																																																			NOVEL	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039986.1	8	3.610974	KEEP	4	0	0	12	376	CC	0.992708	0.755338	0		+	3	60	93	0	0	6.36815	30	60	1026	74	ENST00000378610.1	0.090909	0.760887
CDKAL1	54901	__UNKNOWN__	__UNKNOWN__	6	20613528	20613528	__UNKNOWN__	Intron	SNP	C	C	T	rs11752592	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20613528C>T	ENST00000378610.1	+	3	296				CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Intron			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	NA		NA			maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ttttttgagacggagtctcgc	0.373		NA											c|||	1553	0.310104	0.0825	0.3487	5008	,	,	NA	9856	0.5268	NA	0.2734	False	NA	,,,	NA	NA	NA	2504	0.4049	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996	54901			21050	protein-coding gene	gene with protein product		611259			NA		Standard	NM_017774	NM_017774	NA	Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.287-35996C>T	chr6.hg19:g.20613528C>T		NA	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	hg19	CCDS4546.1	0.02	-0.149107	AGAxGGA	COVERED																																																																																			NOVEL	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039986.1	33	4.341093	KEEP	27	1	30	25	664	CC	0.99257	0.320408	0		+	8	60	233	0	1	22.010099	9	60	290	57	ENST00000378610.1	0.470588	0.322807
CDKAL1	54901	__UNKNOWN__	__UNKNOWN__	6	20677346	20677346	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20677346A>G	ENST00000378610.1	+	3	381				CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Intron			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	NA		NA			maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ctgttgcccaagctggagtgc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996	54901			21050	protein-coding gene	gene with protein product		611259			NA		Standard	NM_017774	NM_017774	NA	Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.371+27738A>G	chr6.hg19:g.20677346A>G		NA	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	hg19	CCDS4546.1	0.02	-0.201747	CCAxGCT	COVERED																																																																																			NOVEL	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039986.1	9	3.60008	KEEP	1	0	0	12	319	AA	0.993634	0.487421	0		+	4	60	131	0	0	10.762527	15	60	462	50	ENST00000378610.1	0.210526	0.490544
CDKAL1	54901	__UNKNOWN__	__UNKNOWN__	6	20780249	20780249	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20780249A>G	ENST00000378610.1	+	6	527				CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Intron|RP3-348I23.2_ENST00000421167.1_RNA			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	NA		NA			maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ggaggctgagacaggaggact	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996	54901			21050	protein-coding gene	gene with protein product		611259			NA		Standard	NM_017774	NM_017774	NA	Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.518-1127A>G	chr6.hg19:g.20780249A>G		NA	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	hg19	CCDS4546.1	0.02	-0.271878	GAGxCAG	COVERED																																																																																			NOVEL	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039986.1	10	3.00662	KEEP	1	0	0	10	263	AA	0.99254	0.711964	0		+	3	60	97	0	0	6.944555	26	60	771	57	ENST00000378610.1	0.103448	0.717315
CDKAL1	54901	__UNKNOWN__	__UNKNOWN__	6	20935940	20935940	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:20935940T>C	ENST00000378610.1	+	8	752				CDKAL1_ENST00000378624.4_Intron|CDKAL1_ENST00000274695.4_Intron			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	NA		NA			maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)			breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			ggattacaggtatgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996	54901			21050	protein-coding gene	gene with protein product		611259			NA		Standard	NM_017774	NM_017774	NA	Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.743-19710T>C	chr6.hg19:g.20935940T>C		NA	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	hg19	CCDS4546.1	0.02	-0.403376	AGGxATG	COVERED																																																																																			NOVEL	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039986.1	18	3.00521	KEEP	1	0	0	10	252	TT	0.992708	0.927678	0		+	4	60	130	0	0	9.175829	38	60	1081	77	ENST00000378610.1	0.095238	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	21351681	21351681	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:21351681T>G			NA	NA				CDKAL1 (119046 upstream) : RP1-135L22.1 (2960 downstream)						NA		NA									NA						CAAACAAGATTTAAAAATGAT	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.21351681T>G		NA		hg19		0.02	-0.157878	GATxTAA	COVERED																																																																																			NOVEL					0			3	3.006949	KEEP	0	0	0	10	266	TT	0.992708	0.320453	0			6	60	205	0	0	18.766521	10	60	288	42		0.375	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	21608662	21608662	__UNKNOWN__	IGR	SNP	G	G	C	rs528954441	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:21608662G>C			NA	NA				SOX4 (9815 upstream) : RN7SKP240 (477110 downstream)						NA		NA									NA						tttgggaggcggaggcgggca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.21608662G>C		NA		hg19		0.02	-0.298237	GGCxGAG	COVERED																																																																																			NOVEL					0			11	3.610712	KEEP	2	0	0	12	371	GG	0.993072	0.794702	0			3	40	98	0	0	6.909543	29	60	954	72		0.09375	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	21629588	21629588	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:21629588A>G			NA	NA				SOX4 (30741 upstream) : RN7SKP240 (456184 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.21629588A>G		NA		hg19		0.02	-0.27185	GGCxTGA	COVERED																																																																																			NOVEL					0			6	3.908851	KEEP	1	0	0	13	346	AA	0.993634	0.712749	0			3	60	94	0	0	6.74409	24	60	700	67		0.111111	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	21804313	21804313	__UNKNOWN__	IGR	SNP	C	C	T	rs547848299		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:21804313C>T			NA	NA				SOX4 (205466 upstream) : RN7SKP240 (281459 downstream)						NA		NA									NA						cgtgagccaccgcgcccggcc	0.522		NA											c|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15215	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.21804313C>T		NA		hg19		0.02	-0.245603	CACxGCG	COVERED																																																																																			NOVEL					0			6	2.707971	KEEP	0	0	0	9	272	CC	0.99254	0.636563	0			3	60	92	0	0	6.765308	20	60	634	56		0.130435	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	21892461	21892461	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:21892461A>G			NA	NA				SOX4 (293614 upstream) : RN7SKP240 (193311 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.21892461A>G		NA		hg19		0.02	-0.350809	CACxCCT	UNCOVERED																																																																																			NOVEL					0			13	2.706902	KEEP	7	0	0	9	248	AA	0	0	0			3	60	97	0	0	6.541703	36	60	1060	84		0.076923	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	22014575	22014575	__UNKNOWN__	IGR	SNP	C	C	T	rs4712649	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:22014575C>T			NA	NA				SOX4 (415728 upstream) : RN7SKP240 (71197 downstream)						NA		NA									NA						gccaccgcgcccggccAGGGT	0.537		NA											C|||	1017	0.203075	0.2572	0.2752	5008	,	,	NA	18132	0.3274	NA	0.0636	False	NA	,,,	NA	NA	NA	2504	0.0941	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.22014575C>T		NA		hg19		0.02	-0.280681	CGCxCGG	COVERED																																																																																			NOVEL					0			12	2.407159	KEEP	5	0	0	8	244	CC	0.99257	0.734176	0			16	60	484	0	0	47.725184	12	60	391	57		0.571429	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	22124515	22124515	__UNKNOWN__	IGR	SNP	C	C	T	rs202091641		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:22124515C>T			NA	NA				RN7SKP240 (38368 upstream) : CASC14 (10670 downstream)						NA		NA									NA						caagaccagcctggccaacgt	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.22124515C>T		NA		hg19		0.02	-0.184226	AGCxTGG	COVERED																																																																																			NOVEL					0			10	4.21254	KEEP	9	0	0	14	439	CC	0.99254	0.420319	0			4	43	126	0	0	10.162687	16	60	558	52		0.2	0.423478
RP3-404K8.2	0	__UNKNOWN__	__UNKNOWN__	6	22266265	22266265	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:22266265C>G	ENST00000561912.1	+	0	75										NA		NA									NA						ggccgaggtgcgtggatcacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000561912.1:	chr6.hg19:g.22266265C>G		NA		hg19		0.02	-0.236848	GTGxGTG	COVERED																																																																																			NOVEL	RP3-404K8.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000422152.2	7	3.910926	KEEP	1	0	0	13	387	CC	0.993634	0.637264	0		+	3	60	103	0	0	7.805204	21	60	679	64	ENST00000561912.1	0.125	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	22496081	22496081	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:22496081A>C			NA	NA				RP3-404K8.2 (178054 upstream) : HDGFL1 (73596 downstream)						NA		NA									NA						gtaatcccagaactttgggag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.22496081A>C		NA		hg19		0.02	-0.219297	CAGxACT	COVERED																																																																																			NOVEL					0			7	3.007931	KEEP	1	0	0	10	281	AA	0.99254	0.548763	0			3	60	102	0	0	7.960598	17	60	530	51		0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	22517118	22517118	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:22517118A>G			NA	NA				RP3-404K8.2 (199091 upstream) : HDGFL1 (52559 downstream)						NA		NA									NA						gggattacagacatgagccac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.22517118A>G		NA		hg19		0.02	-0.254343	CAGxCAT	COVERED																																																																																			NOVEL					0			6	2.405439	KEEP	0	0	0	8	217	AA	0.99257	0.688515	0			3	46	93	0	0	6.806733	21	60	608	58		0.125	0.693668
RP1-209A6.1	0	__UNKNOWN__	__UNKNOWN__	6	22868035	22868035	__UNKNOWN__	lincRNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:22868035T>A	ENST00000420572.2	-	0	197										NA		NA									NA						aggtcaggagttcgagaccag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000420572.2:	chr6.hg19:g.22868035T>A		NA		hg19		0.02	-0.201685	GAGxTCG	UNCOVERED																																																																																			NOVEL	RP1-209A6.1-001	KNOWN	mRNA_end_NF|basic	lincRNA	NA	lincRNA	OTTHUMT00000039995.2	9	2.706663	KEEP	5	0	0	9	244	TT	0	0	0		-	4	60	97	0	0	7.265522	16	60	485	48	ENST00000420572.2	0.2	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	23733761	23733761	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:23733761A>G			NA	NA				RP11-439H9.1 (386973 upstream) : NRSN1 (392588 downstream)						NA		NA									NA						gcccaggctgatctcgaactc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.23733761A>G		NA		hg19		0.02	-0.28938	CTGxTCT	COVERED																																																																																			NOVEL					0			15	2.405515	KEEP	1	0	0	8	213	AA	0.99257	0.755234	0			5	60	150	0	0	11.683057	23	60	674	56		0.178571	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	24016638	24016638	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24016638A>T			NA	NA				RP11-439H9.1 (669850 upstream) : NRSN1 (109711 downstream)						NA		NA									NA						ggtctcaaacacctgggctca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.24016638A>T		NA		hg19		0.02	-0.157863	AACxCCT	COVERED																																																																																			NOVEL					0			14	3.608581	KEEP	0	0	0	12	330	AA	0.993634	0.320751	0			3	60	89	0	0	6.9793	13	60	386	41		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	24117170	24117170	__UNKNOWN__	IGR	SNP	C	C	T	rs55905647	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24117170C>T			NA	NA				RP11-439H9.1 (770382 upstream) : NRSN1 (9179 downstream)						NA		NA									NA						catgagccaccgcacccagcc	0.512		NA											C|||	794	0.158546	0.3835	0.1138	5008	,	,	NA	17367	0.0069	NA	0.1262	False	NA	,,,	NA	NA	NA	2504	0.0757	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.24117170C>T		NA		hg19		0.02	-0.219286	CACxGCA	COVERED																																																																																			NOVEL					0			8	2.405113	KEEP	4	0	0	8	213	CC	0.99257	0.54878	0			3	60	88	0	0	6.63397	16	60	509	54		0.157895	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	24358816	24358816	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24358816G>A			NA	NA				KAAG1 (304 upstream) : RNU6-391P (7062 downstream)						NA		NA									NA						aggctgaggcgggaggattgt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.24358816G>A		NA		hg19		0.02	-0.1579	GGCxGGA	COVERED																																																																																			NOVEL					0			4	2.406359	KEEP	0	0	0	8	228	GG	0.99257	0.320408	0			3	60	94	0	0	7.478754	13	60	430	35		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	24389345	24389345	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24389345T>C			NA	NA				RNU6-391P (23363 upstream) : MRS2 (13807 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.24389345T>C		NA		hg19		0.02	-0.280661	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			15	3.909533	KEEP	18	0	0	13	355	TT	0	0	0			4	60	131	0	0	9.957987	25	60	745	81		0.137931	0.739671
GPLD1	2822	__UNKNOWN__	__UNKNOWN__	6	24456143	24456143	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24456143T>C	ENST00000230036.1	-	13	1259					NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	NA		NA			cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						tggctcatgcttgtaatccca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293	2822			4459	protein-coding gene	gene with protein product		602515			NA	11072085	Standard	NM_001503	NM_001503	NA	Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.1148+582A>G	chr6.hg19:g.24456143T>C		NA	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	hg19	CCDS4553.1	0.02	1.932503	TGCxTGT	COVERED																																																																																			NOVEL	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043315.1	14	2.405507	KEEP	0	0	0	8	215	TT	0.99257	0.960237	0		-	6	60	200	0	0	15.254104	38	60	1147	80	ENST00000230036.1	0.136364	0.967425
GPLD1	2822	__UNKNOWN__	__UNKNOWN__	6	24465169	24465169	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24465169T>C	ENST00000230036.1	-	10	932					NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	NA		NA			cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to calcium ion (GO:0071277)|cellular response to cholesterol (GO:0071397)|cellular response to drug (GO:0035690)|cellular response to insulin stimulus (GO:0032869)|cellular response to pH (GO:0071467)|cellular response to triglyceride (GO:0071401)|chondrocyte differentiation (GO:0002062)|complement receptor mediated signaling pathway (GO:0002430)|GPI anchor release (GO:0006507)|hematopoietic stem cell migration (GO:0035701)|hematopoietic stem cell migration to bone marrow (GO:0097241)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cell proliferation (GO:0008285)|negative regulation of triglyceride catabolic process (GO:0010897)|ossification (GO:0001503)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of secretion (GO:0051047)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cellular response to insulin stimulus (GO:1900076)|response to glucose (GO:0009749)|transepithelial transport (GO:0070633)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|proteinaceous extracellular matrix (GO:0005578)	glycosylphosphatidylinositol phospholipase D activity (GO:0004621)|phospholipase D activity (GO:0004630)|sodium channel regulator activity (GO:0017080)			breast(3)|endometrium(5)|kidney(1)|large_intestine(11)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	32						gcctgtaatctcagcactttg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L11701	CCDS4553.1	6p22.1	2008-02-05			ENSG00000112293	ENSG00000112293	2822			4459	protein-coding gene	gene with protein product		602515			NA	11072085	Standard	NM_001503	NM_001503	NA	Approved		uc003ned.2	P80108	OTTHUMG00000016104	ENST00000230036.1:c.821+1738A>G	chr6.hg19:g.24465169T>C		NA	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	hg19	CCDS4553.1	0.02	-0.34209	ATCxCAG	COVERED																																																																																			NOVEL	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043315.1	7	2.40628	KEEP	0	0	0	8	225	TT	0.99257	0.859313	0		-	3	60	104	0	0	7.426238	31	60	958	71	ENST00000230036.1	0.088235	0.865745
FAM65B	9750	__UNKNOWN__	__UNKNOWN__	6	24854147	24854147	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24854147A>C	ENST00000259698.4	-	9	804				FAM65B_ENST00000540914.1_Intron|FAM65B_ENST00000378023.4_Intron|FAM65B_ENST00000538035.1_Intron|FAM65B_ENST00000510784.2_Intron	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	NA		NA			cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						agttcaagacaagcctgggca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913	9750			13872	protein-coding gene	gene with protein product	myogenesis-related and NCAM-associated protein homolog (chicken)	611410	chromosome 6 open reading frame 32	C6orf32	NA	9205841, 17150207, 17825087	Standard		NM_001286447	NA	Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.629-1301T>G	chr6.hg19:g.24854147A>C		NA	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	hg19	CCDS47383.1	0.02	-0.236809	GACxAGC	COVERED																																																																																			NOVEL	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040024.2	9	2.390641	KEEP	0	0	0	8	205	AA	0.99257	0.607857	0		-	3	60	108	0	0	8.248537	22	60	648	49	ENST00000259698.4	0.12	0.612407
FAM65B	9750	__UNKNOWN__	__UNKNOWN__	6	24895959	24895959	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24895959T>C	ENST00000259698.4	-	1	150				FAM65B_ENST00000538035.1_Intron|FAM65B_ENST00000510784.2_Intron	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	NA		NA			cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						tggctcacgcttgtaatccca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913	9750			13872	protein-coding gene	gene with protein product	myogenesis-related and NCAM-associated protein homolog (chicken)	611410	chromosome 6 open reading frame 32	C6orf32	NA	9205841, 17150207, 17825087	Standard		NM_001286447	NA	Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.25+15086A>G	chr6.hg19:g.24895959T>C		NA	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	hg19	CCDS47383.1	0.02	-0.333255	CGCxTGT	COVERED																																																																																			NOVEL	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040024.2	9	2.707197	KEEP	0	0	0	9	253	TT	0.99254	0.845628	0		-	3	60	103	0	0	7.287224	32	60	961	67	ENST00000259698.4	0.085714	0.851984
FAM65B	9750	__UNKNOWN__	__UNKNOWN__	6	24965595	24965595	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:24965595G>A	ENST00000510784.2	-	1	160							Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	NA		NA			cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						tgaactcctggcctcaaacaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913	9750			13872	protein-coding gene	gene with protein product	myogenesis-related and NCAM-associated protein homolog (chicken)	611410	chromosome 6 open reading frame 32	C6orf32	NA	9205841, 17150207, 17825087	Standard		NM_001286447	NA	Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000510784.2:c.76+76483C>T	chr6.hg19:g.24965595G>A		NA	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	hg19		0.02	-0.263165	CTGxCCT	COVERED																																																																																			NOVEL	FAM65B-201	KNOWN	basic	protein_coding	NA	protein_coding		16	4.212121	KEEP	3	0	0	14	417	GG	0.994391	0.689777	0		-	3	60	91	0	0	6.443452	24	60	796	60	ENST00000510784.2	0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	25059503	25059503	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:25059503A>G			NA	NA				RP3-425P12.1 (2202 upstream) : RP3-425P12.2 (2349 downstream)						NA		NA									NA						aggccagcctaggcaacatag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.25059503A>G		NA		hg19		0.02	1.906232	CCTxGGC	COVERED																																																																																			NOVEL					0			13	3.607947	KEEP	0	0	0	12	318	AA	0.993634	0.970646	0			4	60	143	0	0	10.121384	47	60	1382	96		0.078431	0.976865
CMAHP	8418	__UNKNOWN__	__UNKNOWN__	6	25081909	25081909	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:25081909A>G	ENST00000377989.4	-	0	2175							Q9Y471	CMAH_HUMAN	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene	NA		NA			CMP-N-acetylneuraminate metabolic process (GO:0046381)	cytoplasm (GO:0005737)	2 iron, 2 sulfur cluster binding (GO:0051537)|oxidoreductase activity (GO:0016491)			NS(1)	1						CAAGTAAAATATTTTTGAATC	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							6p23-p22	2011-04-28	2011-04-28	2011-04-28	ENSG00000168405	ENSG00000168405	8418			2098	pseudogene	pseudogene		603209	cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMP-N-acetylneuraminate monooxygenase)(pseudogene)	CMAH	NA	7608218, 9624188	Standard	NR_002174	NR_002174	NA	Approved		uc003ner.4	Q9Y471	OTTHUMG00000016099	ENST00000377989.4:	chr6.hg19:g.25081909A>G		NA	O95250|Q5TD41|Q5TD42|Q5TD43|Q5TD44|Q68DC3|Q9UEE7	hg19		0.02	5.696425	AATxTTT	COVERED																																																																																			NOVEL	CMAHP-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000043292.2	4	6.315048	KEEP	0	0	0	21	571	AA	0.999869	0.999869	0		-	28	60	933	0	0	73.262567	147	60	4275	284	ENST00000377989.4	0.16	1
LRRC16A	55604	__UNKNOWN__	__UNKNOWN__	6	25322242	25322242	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:25322242G>A	ENST00000329474.6	+	2	506				LRRC16A_ENST00000377969.3_Intron	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	NA		NA			actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						ggctgcgttagaactcctggg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691	55604			21581	protein-coding gene	gene with protein product	capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)	609593	leucine rich repeat containing 16	LRRC16	NA	19846667	Standard	NM_017640	NM_017640	NA	Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.138+37105G>A	chr6.hg19:g.25322242G>A		NA	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	hg19	CCDS54973.1	0.02	-0.184202	TTAxAAC	COVERED																																																																																			NOVEL	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040045.2	10	3.309755	KEEP	0	0	0	11	339	GG	0.993072	0.420544	0		+	4	60	107	1	0	8.263571	16	60	536	41	ENST00000329474.6	0.2	0.423478
LRRC16A	55604	__UNKNOWN__	__UNKNOWN__	6	25539801	25539801	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:25539801T>C	ENST00000329474.6	+	26	2564					NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	NA		NA			actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						tgcagtgagctgagatcgcgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691	55604			21581	protein-coding gene	gene with protein product	capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)	609593	leucine rich repeat containing 16	LRRC16	NA	19846667	Standard	NM_017640	NM_017640	NA	Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.2197-374T>C	chr6.hg19:g.25539801T>C		NA	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	hg19	CCDS54973.1	0.02	-0.184162	AGCxGAG	UNCOVERED																																																																																			NOVEL	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040045.2	16	4.208377	KEEP	12	0	0	14	360	TT	0	0	0		+	3	40	94	1	0	7.092693	18	60	518	47	ENST00000329474.6	0.142857	0.423478
LRRC16A	55604	__UNKNOWN__	__UNKNOWN__	6	25562755	25562755	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:25562755A>G	ENST00000329474.6	+	29	3110					NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	NA		NA			actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						gattacaggcatgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691	55604			21581	protein-coding gene	gene with protein product	capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)	609593	leucine rich repeat containing 16	LRRC16	NA	19846667	Standard	NM_017640	NM_017640	NA	Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.2742+5677A>G	chr6.hg19:g.25562755A>G		NA	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	hg19	CCDS54973.1	0.02	-0.201736	GGCxTGA	COVERED																																																																																			NOVEL	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040045.2	15	3.308414	KEEP	3	0	0	11	305	AA	0.99254	0.486885	0		+	4	60	134	0	0	10.779343	18	60	550	48	ENST00000329474.6	0.181818	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	26204293	26204293	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26204293A>C			NA	NA				HIST1H2BF (3351 upstream) : HIST1H4E (564 downstream)						NA		NA									NA						cgtgagccacaacgcccggcG	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.26204293A>C		NA		hg19		0.02	-0.14031	CACxACG	COVERED																																																																																			NOVEL					0			5	2.701871	KEEP	1	0	0	9	228	AA	0.99257	0.289832	0			3	60	104	0	0	8.47907	13	60	373	38		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	26204294	26204294	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26204294A>G			NA	NA				HIST1H2BF (3352 upstream) : HIST1H4E (563 downstream)						NA		NA									NA						gtgagccacaacgcccggcGG	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.26204294A>G		NA		hg19		0.02	-0.149093	ACAxCGC	COVERED																																																																																			NOVEL					0			5	2.402329	KEEP	0	0	0	8	198	AA	0.99257	0.289832	0			3	60	100	0	0	8.07902	13	60	381	37		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	26316394	26316394	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26316394G>A			NA	NA				HIST1H4H (30632 upstream) : RNU6-1259P (36804 downstream)						NA		NA									NA						tcgacctcccgaagtgcaggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.26316394G>A		NA		hg19		0.02	-0.175421	CCCxAAG	COVERED																																																																																			NOVEL					0			3	3.008447	KEEP	0	0	0	10	297	GG	0.992708	0.384582	0			3	60	86	0	0	6.592378	14	60	441	43		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	26335150	26335150	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26335150T>C			NA	NA				HIST1H4H (49388 upstream) : RNU6-1259P (18048 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.26335150T>C		NA		hg19		0.02	-0.385799	TCAxGCC	COVERED																																																																																			NOVEL					0			14	6.315969	KEEP	0	0	0	21	576	TT	0.999869	0.918051	0			3	60	101	0	0	6.940822	36	60	1055	93		0.076923	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	26480578	26480578	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26480578C>G			NA	NA				BTN2A1 (3729 upstream) : BTN1A1 (20870 downstream)						NA		NA									NA						gcctcccaaactgctgggatt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.26480578C>G		NA		hg19		0.02	-0.19275	AAAxTGC	COVERED																																																																																			NOVEL					0			5	2.407375	KEEP	1	0	0	8	251	CC	0.99257	0.454356	0			4	60	142	0	0	11.765523	16	60	538	49		0.2	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	26551672	26551672	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26551672A>G			NA	NA				HMGN4 (5190 upstream) : ABT1 (45507 downstream)						NA		NA									NA						aaagtgctggaattacaggca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.26551672A>G		NA		hg19		0.02	-0.228042	TGGxATT	COVERED																																																																																			NOVEL					0			7	2.406318	KEEP	0	0	0	8	223	AA	0.99257	0.578599	0			4	60	140	0	0	11.13596	21	60	621	54		0.16	0.58293
GUSBP2	387036	__UNKNOWN__	__UNKNOWN__	6	26871464	26871464	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:26871464A>G	ENST00000463434.1	-	0	94									glucuronidase, beta pseudogene 2	NA		NA									NA						tttttattttatcttatttaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							6p21	2011-06-09	2011-06-09	2011-06-09	ENSG00000241549	ENSG00000241549	387036			18792	pseudogene	pseudogene		NA	spinal muscular atrophy candidate gene 3-like 2, glucuronidase, beta-like 1	SMAC3L2, GUSBL1	NA		Standard		NR_003504	NA	Approved	bA239L20.5, bA239L20.1, SMA3-L, bGLU-Lp, SMAC3L	uc003nim.2		OTTHUMG00000014462	ENST00000463434.1:	chr6.hg19:g.26871464A>G		NA		hg19		0.02	-0.368339	TTTxTCT	COVERED																																																																																			NOVEL	GUSBP2-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000314060.1	12	4.810583	KEEP	10	0	0	16	421	AA	0.993634	0.893588	0		-	3	25	109	0	0	7.848282	33	60	954	103	ENST00000463434.1	0.083333	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	27550303	27550303	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:27550303C>T			NA	NA				ZNF184 (109406 upstream) : RNU6-471P (13887 downstream)						NA		NA									NA						tgagccaccgcgcccggccTG	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.27550303C>T		NA		hg19		0.02	-0.184168	CCGxGCC	COVERED																																																																																			NOVEL					0			4	2.406381	KEEP	2	0	0	8	229	CC	0.99257	0.420331	0			3	60	89	0	0	6.734111	16	60	518	49		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	27677432	27677432	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:27677432A>G			NA	NA				TRNAI6 (78121 upstream) : HIST1H2BL (97824 downstream)						NA		NA									NA						aggagtttgaaaccagcctgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.27677432A>G		NA		hg19		0.02	-0.184145	TGAxACC	COVERED																																																																																			NOVEL					0			5	2.705837	KEEP	1	0	0	9	240	AA	0.99257	0.420331	0			3	60	94	0	0	7.092966	18	60	507	39		0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	27786632	27786632	__UNKNOWN__	IGR	SNP	G	G	A	rs541493993		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:27786632G>A			NA	NA				HIST1H2BM (3365 upstream) : HIST1H4J (5251 downstream)						NA		NA									NA						gattacaggcgtgagccactg	0.478		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	16467	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.27786632G>A		NA		hg19		0.02	-0.157883	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.707106	KEEP	0	0	0	9	260	GG	0.99254	0.320398	0			3	60	92	0	0	7.372327	12	60	393	39		0.2	0.322807
HIST1H3J	8356	__UNKNOWN__	__UNKNOWN__	6	27860102	27860102	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:27860102T>C	ENST00000479986.1	-	1	346							P68431	H31_HUMAN	histone cluster 1, H3j	NA		NA			blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	8						gtgctgggattacaggcgtga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z83737	CCDS4638.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197153	ENSG00000197153	8356		Histones / Replication-dependent	4774	protein-coding gene	gene with protein product		602817	H3 histone family, member J, histone 1, H3j	H3FJ	NA	9439656, 12408966	Standard	NM_003535	NM_003535	NA	Approved	H3/j	uc003nka.3	P68431	OTTHUMG00000016185	ENST00000479986.1:c.176+436A>G	chr6.hg19:g.27860102T>C		NA	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	hg19		0.02	-0.175355	GATxACA	COVERED																																																																																			NOVEL	HIST1H3J-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000331293.1	2	2.705895	KEEP	0	0	0	9	235	TT	0.99254	0.384517	0		-	3	60	86	0	0	6.364769	17	60	476	48	ENST00000479986.1	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	28244160	28244160	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:28244160C>A			NA	NA				NKAPL (15424 upstream) : PGBD1 (5153 downstream)						NA		NA									NA						GAGATTCATCCAGCACTTGGA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													99	91	93			NA	NA	6		NA											NA				28244160		1916	4143	6059	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.28244160C>A		NA		hg19		0.02	1.408867	ATCxAGC	COVERED																																																																																			NOVEL					0			1	3.309943	KEEP	0	0	0	11	339	CC	0.993072	0.992878	0			16	60	478	0	0	37.318659	72	60	2400	146		0.181818	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	28608453	28608453	__UNKNOWN__	IGR	SNP	G	G	C	rs79124765	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:28608453G>C			NA	NA				SCAND3 (24464 upstream) : AL121932.1 (7520 downstream)						NA		NA									NA						ctaggtgacagagcaagactc	0.393		NA											G|||	711	0.141973	0.0726	0.1556	5008	,	,	NA	13084	0.1339	NA	0.1859	False	NA	,,,	NA	NA	NA	2504	0.1892	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.28608453G>C		NA		hg19		0.02	-0.149132	ACAxAGC	COVERED																																																																																			NOVEL					0			43	8.424675	KEEP	24	0	0	28	839	GG	0.995343	0.290641	0			5	60	164	0	0	14.639055	10	30	332	55		0.333333	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	28745544	28745544	__UNKNOWN__	IGR	SNP	C	C	T	rs559613200		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:28745544C>T			NA	NA				AL662890.1 (1744 upstream) : AL662890.3 (18204 downstream)						NA		NA									NA						cagtggctcacgcctgtaatc	0.438		NA											c|||	1	0.000199681	0.0	0.0	5008	,	,	NA	13398	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.28745544C>T		NA		hg19		0.02	-0.175415	TCAxGCC	COVERED																																																																																			NOVEL					0			9	3.309501	KEEP	0	0	0	11	333	CC	0.993072	0.384723	0			4	60	113	0	0	9.181131	13	60	423	45		0.235294	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	29616211	29616211	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:29616211T>C			NA	NA				GABBR1 (15249 upstream) : MOG (8546 downstream)						NA		NA									NA						agtgaaaccctgtctctacta	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.29616211T>C		NA		hg19		0.02	-0.254311	CCCxGTC	COVERED																																																																																			NOVEL					0			7	3.608087	KEEP	0	0	0	12	324	TT	0.993634	0.664267	0			3	60	104	0	0	7.742495	24	60	686	51		0.111111	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	29656097	29656097	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:29656097A>G			NA	NA				ZFP57 (7210 upstream) : HLA-F (34454 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.29656097A>G		NA		hg19		0.02	-0.17543	GCTxGGA	COVERED																																																																																			NOVEL					0			4	3.308249	KEEP	1	0	0	11	304	AA	0.992708	0.384582	0			3	60	99	0	0	7.73325	16	60	492	45		0.157895	0.387407
ZNRD1-AS1	80862	__UNKNOWN__	__UNKNOWN__	6	29977342	29977342	__UNKNOWN__	RNA	SNP	A	A	T	rs113017032	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:29977342A>T	ENST00000376797.3	-	0	731				ZNRD1-AS1_ENST00000425604.1_RNA|ZNRD1-AS1_ENST00000448093.1_RNA|HLA-J_ENST00000462773.1_RNA|ZNRD1-AS1_ENST00000420251.1_RNA			Q2KJ03	ZRAS1_HUMAN	ZNRD1 antisense RNA 1	NA		NA									NA						TGGGACTGAGAGGCAAGATTT	0.438		NA											A|||	16	0.00319489	0.003	0.0029	5008	,	,	NA	21762	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF032110		6p21.33	2014-08-14	2012-08-15	2010-11-25	ENSG00000204623	ENSG00000204623	80862		Long non-coding RNAs	13924	non-coding RNA	RNA, long non-coding		615714	chromosome 6 open reading frame 12, non-protein coding RNA 171, ZNRD1 antisense RNA (non-protein coding), ZNRD1 antisense RNA 1 (non-protein coding)	C6orf12, NCRNA00171, ZNRD1AS, ZNRD1-AS	NA	9553157, 11130983, 25110835	Standard	NR_026751	NR_026751	NA	Approved	HTEX4, Em:AB023056.3	uc003rto.3	Q2KJ03	OTTHUMG00000031109	ENST00000376797.3:	chr6.hg19:g.29977342A>T		NA		hg19		0.02	2.996469	GAGxGGC	COVERED																																																																																			NOVEL	ZNRD1-AS1-006	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000253083.1	18	4.976994	KEEP	4	2	55	36	1017	AA	1	1	0		-	13	60	373	0	0	26.272984	95	60	2927	282	ENST00000376797.3	0.12037	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	30088743	30088743	__UNKNOWN__	IGR	SNP	G	G	A	rs2844791	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30088743G>A			NA	NA				TRIM31-AS1 (6242 upstream) : SNORA48 (11838 downstream)						NA		NA									NA						ggctggtctcgaactcccgac	0.527		NA											G|||	388	0.077476	0.0174	0.1225	5008	,	,	NA	14997	0.0883	NA	0.1133	False	NA	,,,	NA	NA	NA	2504	0.0787	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.30088743G>A		NA		hg19		0.02	-0.219263	CTCxAAC	UNCOVERED																																																																																			NOVEL					0			8	2.406813	KEEP	2	0	0	8	239	GG	0	0	0			10	60	300	0	0	28.18612	12	60	383	47		0.454545	0.552887
PRR3	80742	__UNKNOWN__	__UNKNOWN__	6	30528373	30528373	__UNKNOWN__	Intron	SNP	A	A	G	rs2516642	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30528373A>G	ENST00000376560.3	+	3	628				PRR3_ENST00000376557.3_Intron|PRR3_ENST00000498336.1_Intron	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	NA		NA					metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						cagcctggccaatatggtaaa	0.522		NA											A|||	3482	0.695288	0.7693	0.5865	5008	,	,	NA	15576	0.622	NA	0.6759	False	NA	,,,	NA	NA	NA	2504	0.7679	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576	80742		Zinc fingers, CCCH-type domain containing	21149	protein-coding gene	gene with protein product		NA	proline-rich polpeptide 3		NA		Standard	NM_025263	NM_025263	NA	Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.170-1238A>G	chr6.hg19:g.30528373A>G		NA	A1A4H4|Q5RJB5|Q5STN6	hg19	CCDS43440.1	0.02	-0.175426	GCCxATA	COVERED																																																																																			NOVEL	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076033.2	5	2.402685	KEEP	1	0	0	8	201	AA	0.99257	0.384528	0		+	11	60	354	0	0	35.031647	8	60	235	41	ENST00000376560.3	0.578947	0.387407
ABCF1	23	__UNKNOWN__	__UNKNOWN__	6	30540516	30540516	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30540516A>G	ENST00000326195.8	+	1	185				ABCF1_ENST00000376545.3_Intron|ABCF1_ENST00000396515.4_Intron	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	NA		NA			inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						gggctcaagtaattctcctgc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574	23		ATP binding cassette transporters / subfamily F	70	protein-coding gene	gene with protein product		603429		ABC50	NA	9790762	Standard		NM_001025091	NA	Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.73+1179A>G	chr6.hg19:g.30540516A>G		NA	A2BF75|O14897|Q69YP6	hg19	CCDS34380.1	0.02	-0.210452	AGTxATT	COVERED																																																																																			NOVEL	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076137.3	8	4.207971	KEEP	0	0	0	14	359	AA	0.995343	0.550313	0		+	3	60	98	0	0	7.633811	16	60	455	53	ENST00000326195.8	0.157895	0.552887
PPP1R10	5514	__UNKNOWN__	__UNKNOWN__	6	30573623	30573623	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30573623T>C	ENST00000376511.2	-	10	1406					NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	NA		NA			protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						ggtgacagagtgagactctgt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569	5514		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	9284	protein-coding gene	gene with protein product	phosphatase 1 nuclear targeting subunit, HLA-C associated transcript 53	603771	protein phosphatase 1, regulatory (inhibitor) subunit 10		NA	9461602, 9784381	Standard	NM_002714	NM_002714	NA	Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.853+76A>G	chr6.hg19:g.30573623T>C		NA	O00405	hg19	CCDS4681.1	0.02	1.739908	GAGxGAG	COVERED																																																																																			NOVEL	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076556.2	12	5.333305	KEEP	4	1	26	27	644	TT	0.999931	0.998396	0		-	4	60	127	0	1	8.421853	50	60	1319	121	ENST00000376511.2	0.074074	0.998465
ATAT1	79969	__UNKNOWN__	__UNKNOWN__	6	30602701	30602701	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30602701C>G	ENST00000376485.4	+	7	567				ATAT1_ENST00000376483.4_Intron|ATAT1_ENST00000376478.2_Intron|ATAT1_ENST00000318999.7_Intron|ATAT1_ENST00000330083.5_Intron|ATAT1_ENST00000319027.5_Intron|ATAT1_ENST00000468713.1_Intron|ATAT1_ENST00000329992.8_Intron					alpha tubulin acetyltransferase 1	NA		NA								cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	9						ggaggcagagcttgcagtgag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023220	CCDS4683.2, CCDS54978.1, CCDS59002.1	6p21.32	2014-06-17	2010-10-11	2010-10-11	ENSG00000137343	ENSG00000137343	79969	2.3.1.108		21186	protein-coding gene	gene with protein product	alpha-tubulin N-acetyltransferase	615556	chromosome 6 open reading frame 134	C6orf134	NA	20829795	Standard	NM_024909	NM_024909	NA	Approved	FLJ13158, Em:AB023049.7, MEC17	uc003nqv.3	Q5SQI0	OTTHUMG00000031219	ENST00000376485.4:c.538-5453C>G	chr6.hg19:g.30602701C>G		NA		hg19		0.02	-0.166669	GAGxTTG	UNCOVERED																																																																																			NOVEL	ATAT1-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000076449.2	10	2.708328	KEEP	6	0	0	9	287	CC	0	0	0		+	3	60	88	0	0	6.710842	15	60	512	40	ENST00000376485.4	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	30663836	30663836	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30663836T>C			NA	NA				NRM (4639 upstream) : MDC1 (3747 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.30663836T>C		NA		hg19		0.02	-0.184116	GTGxTGG	COVERED																																																																																			NOVEL					0			5	2.705004	KEEP	1	0	0	9	230	TT	0.99257	0.420331	0			3	60	99	0	0	7.733597	16	60	460	45		0.157895	0.423478
FLOT1	10211	__UNKNOWN__	__UNKNOWN__	6	30708649	30708649	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30708649T>C	ENST00000376389.3	-	6	575				FLOT1_ENST00000470643.1_Intron|FLOT1_ENST00000456573.2_Intron	NM_005803.2	NP_005794.1	P41440	S19A1_HUMAN	flotillin 1	NA		NA			folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	13					Methotrexate(DB00563)|Pralatrexate(DB06813)	ctgcaacctctgcctcctggg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF089750	CCDS4688.1	6p21.3	2010-02-17			ENSG00000137312	ENSG00000137312	10211			3757	protein-coding gene	gene with protein product		606998			NA		Standard		XM_005248780	NA	Approved		uc003nrm.3	O75955	OTTHUMG00000031151	ENST00000376389.3:c.355-74A>G	chr6.hg19:g.30708649T>C		NA	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	hg19	CCDS4688.1	0.02	-0.306952	CTCxGCC	COVERED																																																																																			NOVEL	FLOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076276.2	3	2.638486	KEEP	0	1	26	18	500	TT	0.99986	0.81835	0		-	3	60	92	0	0	6.398717	27	60	805	60	ENST00000376389.3	0.1	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	30733836	30733836	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30733836A>G			NA	NA				RN7SL353P (14774 upstream) : HCG20 (765 downstream)						NA		NA									NA						aaagtgctggaattacaggca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.30733836A>G		NA		hg19		0.02	-0.263104	TGGxATT	COVERED																																																																																			NOVEL					0			11	4.510894	KEEP	1	0	0	15	407	AA	0.99649	0.691234	0			3	60	101	0	0	7.49476	23	60	679	60		0.115385	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	30828274	30828274	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:30828274A>G			NA	NA				XXbac-BPG27H4.8 (12338 upstream) : RN7SKP186 (3752 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.30828274A>G		NA		hg19		0.02	-0.201728	CCAxCAC	COVERED																																																																																			NOVEL					0			15	3.307879	KEEP	5	0	0	11	298	AA	0.993072	0.487146	0			3	60	105	0	0	8.333213	16	60	478	60		0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	31015377	31015377	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31015377T>C			NA	NA				MUC22 (12198 upstream) : HCG22 (6606 downstream)						NA		NA									NA						tggcaagacctcatctctaca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.31015377T>C		NA		hg19		0.02	-0.149112	ACCxCAT	COVERED																																																																																			NOVEL					0			6	2.707108	KEEP	0	0	0	9	253	TT	0.99254	0.289823	0			3	60	102	0	0	8.278765	13	60	403	35		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	31181161	31181161	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31181161T>C			NA	NA				HCG27 (9416 upstream) : HLA-C (55364 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.31181161T>C		NA		hg19		0.02	-0.201712	TCCxAGC	COVERED																																																																																			NOVEL					0			10	2.405835	KEEP	0	0	0	8	217	TT	0.99257	0.4869	0			3	60	106	0	0	8.292086	18	60	513	43		0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	31187463	31187463	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31187463A>G			NA	NA				HCG27 (15718 upstream) : HLA-C (49062 downstream)						NA		NA									NA						gaccagcctgaccaacatggt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.31187463A>G		NA		hg19		0.02	-0.228006	CTGxCCA	COVERED																																																																																			NOVEL					0			12	3.608882	KEEP	4	0	0	12	327	AA	0.993634	0.579219	0			4	60	136	0	0	10.894697	19	60	544	58		0.173913	0.58293
HLA-C	3107	__UNKNOWN__	__UNKNOWN__	6	31239544	31239544	__UNKNOWN__	Silent	SNP	G	G	T	rs281860356		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31239544G>T	ENST00000376228.5	-	2	189	c.175C>A	c.(175-177)Cgg>Agg	p.R59R	HLA-C_ENST00000383329.3_Silent_p.R59R	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	59	Alpha-1.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTGTCGAACCGCACGAACTGC	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													40	39	39			NA	NA	6		NA											NA				31239544		1511	2707	4218	SO:0001819	synonymous_variant			M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525	3107		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4933	protein-coding gene	gene with protein product		142840	psoriasis susceptibility 1	HLA-JY3, D6S204, PSORS1	NA	3863816, 16642438	Standard	NM_002117	NM_001243042	NA	Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.175C>A	chr6.hg19:g.31239544G>T		NA	O02864|O02958|Q29643|Q9MY30	hg19	CCDS34393.1	0.02	2.677118	ACCxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	-	7.431	0.638746	0.14386	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	2.81	0.32909	.	.	.	.	.	T	0.46347	0.1388	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43065	-0.9414	4	.	.	.	.	9.2778	0.37709	0.0:0.0:1.0:0.0	.	.	.	.	E	58	.	.	A	-	2	0	HLA-C	31347523	0.000000	0.05858	1.000000	0.80357	0.308000	0.27856	0.040000	0.13905	1.886000	0.54624	0.305000	0.20034	GCG	NOVEL	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076281.3	0	9.490477	KEEP	0	2	49	49	1440	GG	1	0.999997	0		-	11	51	302	0	0	19.720874	104	60	3419	216	ENST00000376228.5	0.095652	0.999997
HLA-B	3106	__UNKNOWN__	__UNKNOWN__	6	31323337	31323337	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs1050341	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31323337T>C	ENST00000412585.2	-	4	680	c.652A>G	c.(652-654)Atc>Gtc	p.I218V		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	218	Alpha-3.|Ig-like C1-type.	NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TGGTCAGAGATGGGGTGGTGG	0.582		NA							Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				T|||	1465	0.292532	0.3994	0.2853	5008	,	,	NA	18767	0.2034	NA	0.2097	False	NA	,,,	NA	NA	NA	2504	0.3303	NA	NA	NA								NA				0								T	VAL/ILE	1415,2991		224,967,1012	83	86	85	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	652	-6.4	0	6	dbSNP_86	85	1431,7169		122,1187,2991	no	missense	HLA-B	NM_005514.6	29	346,2154,4003	CC,CT,TT	NA	16.6395,32.1153,21.8822		218/363	31323337	2846,10160	2203	4300	6503	SO:0001583	missense	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745	3106		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4932	protein-coding gene	gene with protein product		142830	ankylosing spondylitis	AS	NA	3459708	Standard	NM_005514	NM_005514	NA	Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.652A>G	chr6.hg19:g.31323337T>C	ENSP00000399168:p.Ile218Val	NA	Q29764	hg19	CCDS34394.1	0.02	3.414928	AGAxGGG	COVERED	580	0.26556776556776557	177	0.3597560975609756	109	0.3011049723756906	143	0.25	151	0.19920844327176782	N	2.431	-0.330915	0.05314	0.321153	0.166395	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.13420	2.59;2.59	3.2	-6.41	0.01938	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.795450	0.02173	N	0.059893	T	0.02012	0.0063	L	0.39085	1.19	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28839	-1.0031	9	0.02654	T	1	.	8.9989	0.36069	0.1414:0.6582:0.0:0.2004	rs1050341;rs2308480;rs3177949;rs3916296;rs4563762;rs7451383	218	P01889	1B07_HUMAN	V	218;97;97;229	ENSP00000399168:I218V;ENSP00000405931:I229V	ENSP00000399168:I218V	I	-	1	0	HLA-B	31431316	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-3.036000	0.00635	-1.842000	0.01181	-1.924000	0.00514	ATC	NOVEL	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076280.4	3	5.338643	KEEP	1	1	32	29	759	TT	0.999997	0.999997	0		-	7	60	233	0	0	14.579879	133	60	3849	254	ENST00000412585.2	0.05	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	31492412	31492412	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31492412T>C			NA	NA				MICB (13511 upstream) : MCCD1 (4081 downstream)						NA		NA									NA						agattacaggtgtgagccact	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.31492412T>C		NA		hg19		0.02	-0.280655	AGGxGTG	COVERED																																																																																			NOVEL					0			7	3.609143	KEEP	2	0	0	12	333	TT	0.993072	0.734547	0			3	60	91	0	0	6.394008	25	60	753	65		0.107143	0.739671
PRRC2A	7916	__UNKNOWN__	__UNKNOWN__	6	31592871	31592871	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31592871A>G	ENST00000376033.2	+	6	697				PRRC2A_ENST00000376007.4_Intron|PRRC2A_ENST00000469577.1_Intron	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	NA		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						caccgcgcccagccAGAGTCT	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469	7916			13918	protein-coding gene	gene with protein product		142580	HLA-B associated transcript 2	BAT2	NA	2156268, 8499947	Standard	NM_080686	NM_080686	NA	Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.464-77A>G	chr6.hg19:g.31592871A>G		NA	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	hg19	CCDS4708.1	0.02	3.929585	CCCxGCC	COVERED																																																																																			NOVEL	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259319.1	10	5.845596	KEEP	0	1	30	30	827	AA	0.999997	0.999988	0		+	5	60	168	1	0	10.6619	91	60	2744	203	ENST00000376033.2	0.052083	0.999991
BAG6	7917	__UNKNOWN__	__UNKNOWN__	6	31614839	31614839	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31614839T>C	ENST00000211379.5	-	7	1083				BAG6_ENST00000375976.4_Intron|BAG6_ENST00000404765.2_Intron|BAG6_ENST00000375964.6_Intron|BAG6_ENST00000362049.6_Intron|BAG6_ENST00000439687.2_Intron	NM_080702.2	NP_542433.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	NA		NA			brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						cgtgagccactgtgcccggcc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463	7917			13919	protein-coding gene	gene with protein product		142590	HLA-B associated transcript 3	BAT3	NA	2156268	Standard	NM_080703	NM_004639	NA	Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000211379.5:c.788+528A>G	chr6.hg19:g.31614839T>C		NA	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	hg19	CCDS4709.1	0.02	-0.280678	CACxGTG	COVERED																																																																																			NOVEL	BAG6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076322.3	12	2.738365	KEEP	2	1	28	19	519	TT	0.999863	0.73957	0		-	3	46	105	0	0	7.652289	28	60	847	81	ENST00000211379.5	0.096774	0.739671
XXbac-BPG32J3.20	0	__UNKNOWN__	__UNKNOWN__	6	31674149	31674149	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31674149C>G	ENST00000461287.1	-	4	537										NA		NA									NA						ctcccgggttcaagcgattct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000461287.1:c.190-4242G>C	chr6.hg19:g.31674149C>G		NA		hg19		0.02	-0.105269	GTTxAAG	UNCOVERED																																																																																			NOVEL	XXbac-BPG32J3.20-001	PUTATIVE	basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000328320.4	8	2.707767	KEEP	1	0	0	9	266	CC	0.99257	0.138793	0		-	6	60	200	0	0	19.249886	6	60	202	28	ENST00000461287.1	0.5	0.139832
C6orf25	80739	__UNKNOWN__	__UNKNOWN__	6	31693136	31693136	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31693136C>T	ENST00000375809.3	+	0	1041					NM_025260.3|NM_138272.2|NM_138277.2	NP_079536.2|NP_612116.1|NP_612121.1			chromosome 6 open reading frame 25	NA		NA								endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	9						gacggagtctcgctctgttgc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4715.1, CCDS4716.1, CCDS4717.1, CCDS34405.1, CCDS34406.1, CCDS34407.1	6p21	2013-10-20			ENSG00000204420	ENSG00000204420	80739			13937	protein-coding gene	gene with protein product		606520			NA	10384126, 11544253	Standard	NM_138272	NM_025260	NA	Approved	G6b, NG31	uc011doc.2	O95866	OTTHUMG00000031130	ENST00000375809.3:c.*316C>T	chr6.hg19:g.31693136C>T		NA		hg19	CCDS34406.1	0.02	3.078829	TCTxGCT	COVERED																																																																																			NOVEL	C6orf25-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076227.5	13	6.474932	KEEP	1	2	58	42	1140	CC	1	0.999981	0		+	6	60	179	0	1	11.29195	81	70	2453	186	ENST00000375809.3	0.068966	0.999981
MSH5	4439	__UNKNOWN__	__UNKNOWN__	6	31709373	31709373	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31709373G>C	ENST00000375703.3	+	3	326				MSH5_ENST00000534153.4_Intron|MSH5-SAPCD1_ENST00000493662.2_Intron|MSH5_ENST00000375755.3_Intron|MSH5_ENST00000375750.3_Intron|MSH5_ENST00000482280.1_Intron|MSH5_ENST00000375742.3_Intron|MSH5_ENST00000375740.3_Intron			O43196	MSH5_HUMAN	mutS homolog 5	NA		NA			ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						gttggccagggtggtctcaaa	0.532		NA						Direct reversal of damage;Mismatch excision repair (MMR)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410	4439			7328	protein-coding gene	gene with protein product		603382	mutS (E. coli) homolog 5, mutS homolog 5 (E. coli)		NA	9740671, 9787078, 17977839	Standard		NM_002441	NA	Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375703.3:c.271+310G>C	chr6.hg19:g.31709373G>C		NA	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	hg19	CCDS34410.1	0.02	-0.18422	AGGxTGG	COVERED																																																																																			NOVEL	MSH5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268160.1	8	2.407418	KEEP	3	0	0	8	256	AG	0.99254	0.420319	0		+	4	60	137	0	0	11.468072	14	60	461	45	ENST00000375703.3	0.222222	0.423478
MSH5	4439	__UNKNOWN__	__UNKNOWN__	6	31724138	31724138	__UNKNOWN__	Intron	SNP	G	G	A	rs571076644	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31724138G>A	ENST00000375703.3	+	13	1069				MSH5_ENST00000431848.2_Intron|MSH5_ENST00000534153.4_Intron|MSH5-SAPCD1_ENST00000493662.2_Intron|MSH5_ENST00000375755.3_Intron|MSH5_ENST00000375750.3_Intron|MSH5_ENST00000375742.3_Intron|MSH5_ENST00000375740.3_Intron			O43196	MSH5_HUMAN	mutS homolog 5	NA		NA			ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						tagtagagacgggatttcacc	0.527		NA						Direct reversal of damage;Mismatch excision repair (MMR)					G|||	7	0.00139776	0.0	0.0	5008	,	,	NA	13899	0.006	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410	4439			7328	protein-coding gene	gene with protein product		603382	mutS (E. coli) homolog 5, mutS homolog 5 (E. coli)		NA	9740671, 9787078, 17977839	Standard		NM_002441	NA	Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375703.3:c.1015-1804G>A	chr6.hg19:g.31724138G>A		NA	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	hg19	CCDS34410.1	0.02	-0.192964	GACxGGA	COVERED																																																																																			NOVEL	MSH5-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268160.1	8	3.607437	KEEP	5	0	0	12	322	GG	0.99254	0.454342	0		+	3	47	90	0	0	6.761503	17	60	531	47	ENST00000375703.3	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	31801295	31801295	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:31801295C>T			NA	NA				HSPA1B (3264 upstream) : C6orf48 (1089 downstream)						NA		NA									NA						ggtaacagagcaagaccctat	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.31801295C>T		NA		hg19		0.02	-0.08768	GAGxAAG	UNCOVERED																																																																																			NOVEL					0			7	2.70796	KEEP	1	0	0	9	271	CC	0.99254	0.098977	0			3	53	80	0	0	7.132664	5	60	154	23		0.375	0.099721
TNXB	7148	__UNKNOWN__	__UNKNOWN__	6	32068592	32068592	__UNKNOWN__	Intron	SNP	T	T	C	rs568413310	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32068592T>C	ENST00000479795.1	-	2	133				TNXB_ENST00000375244.3_Intron|TNXB_ENST00000375247.2_Intron			P22105	TENX_HUMAN	tenascin XB	NA		NA			actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ggtgtggtggttcacacctga	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477	7148		Fibrinogen C domain containing, Fibronectin type III domain containing	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2	NA	8530023	Standard	NM_019105	NM_019105	NA	Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.8-2609A>G	chr6.hg19:g.32068592T>C		NA	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	hg19		0.02	-0.228028	TGGxTCA	COVERED																																																																																			NOVEL	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000357059.1	6	2.40628	KEEP	0	0	0	8	227	TT	0.99257	0.578599	0		-	3	60	104	0	0	8.092199	18	60	525	49	ENST00000479795.1	0.142857	0.58293
ATF6B	1388	__UNKNOWN__	__UNKNOWN__	6	32089185	32089185	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32089185G>T	ENST00000375203.3	-	6	511				ATF6B_ENST00000375201.4_Intron	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	NA		NA			response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						GGGTTAAGAGGGTTAAGATGG	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676	1388		basic leucine zipper proteins	2349	protein-coding gene	gene with protein product		600984	cAMP responsive element binding protein-like 1	CREBL1	NA	11256944, 14973138	Standard		NM_004381	NA	Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.479-60C>A	chr6.hg19:g.32089185G>T		NA	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	hg19	CCDS4737.1	0.02	-0.271905	GAGxGTT	COVERED																																																																																			NOVEL	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076638.2	4	4.812206	KEEP	0	0	0	16	468	GG	0.997832	0.71576	0		-	6	60	179	0	0	14.552738	21	60	680	59	ENST00000375203.3	0.222222	0.717315
ATF6B	1388	__UNKNOWN__	__UNKNOWN__	6	32094523	32094523	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32094523A>G	ENST00000375203.3	-	4	375				ATF6B_ENST00000375201.4_Intron|ATF6B_ENST00000468502.1_Intron	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	NA		NA			response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						tgtggtcccaactactcagga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676	1388		basic leucine zipper proteins	2349	protein-coding gene	gene with protein product		600984	cAMP responsive element binding protein-like 1	CREBL1	NA	11256944, 14973138	Standard		NM_004381	NA	Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.342+356T>C	chr6.hg19:g.32094523A>G		NA	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	hg19	CCDS4737.1	0.02	-0.166638	CCAxCTA	COVERED																																																																																			NOVEL	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076638.2	10	3.006027	KEEP	0	0	0	10	261	AA	0.992708	0.351366	0		-	3	60	98	0	0	7.633466	16	60	467	36	ENST00000375203.3	0.157895	0.353947
PPT2	9374	__UNKNOWN__	__UNKNOWN__	6	32130280	32130280	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32130280T>A	ENST00000324816.6	+	8	1278				PPT2_ENST00000361568.2_Intron|PPT2_ENST00000493548.1_Intron|PPT2-EGFL8_ENST00000422437.1_Intron|PPT2_ENST00000375137.2_Intron|PPT2_ENST00000437001.2_Intron|PPT2_ENST00000395523.1_Intron|PPT2-EGFL8_ENST00000453656.2_Intron|PPT2_ENST00000445576.2_Intron|PPT2_ENST00000375143.2_Intron			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	NA		NA			cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						tacaggcgtgtgccactgcgc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													23	25	24			NA	NA	6		NA											NA				32130280		692	1591	2283	SO:0001627	intron_variant			AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	9374	3.1.2.22		9326	protein-coding gene	gene with protein product		603298			NA	9341199, 10051407	Standard	NM_138717	NM_138717	NA	Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.711-65T>A	chr6.hg19:g.32130280T>A		NA	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	hg19	CCDS4742.1	0.02	1.140568	GTGxGCC	COVERED																																																																																			NOVEL	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076552.4	19	7.217368	KEEP	0	0	0	24	659	TT	0.999909	0.999849	0		+	6	60	170	0	0	10.401244	81	60	2268	182	ENST00000324816.6	0.068966	0.99994
PBX2	5089	__UNKNOWN__	__UNKNOWN__	6	32157597	32157597	__UNKNOWN__	Silent	SNP	G	G	A	rs201834744		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32157597G>A	ENST00000375050.4	-	1	366	c.96C>T	c.(94-96)ccC>ccT	p.P32P		NM_002586.4	NP_002577.2	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	32		NA			embryonic limb morphogenesis (GO:0030326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(9)|ovary(1)|prostate(2)	14						CTCCGCCACCGGGAGGCTCGC	0.716		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													13	18	16			NA	NA	6		NA											NA				32157597		1495	2693	4188	SO:0001819	synonymous_variant				CCDS4748.1	6p21.32	2011-06-20	2007-01-30		ENSG00000204304	ENSG00000204304	5089		Homeoboxes / TALE class	8633	protein-coding gene	gene with protein product		176311	pre-B-cell leukemia transcription factor 2		NA	7835890	Standard		NM_002586	NA	Approved	G17, HOX12, PBX2MHC	uc003oav.1	P40425	OTTHUMG00000031116	ENST00000375050.4:c.96C>T	chr6.hg19:g.32157597G>A		NA	A2BFJ2	hg19	CCDS4748.1	0.02	2.828225	ACCxGGA	COVERED																																																																																			NOVEL	PBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076194.4	1	2.503146	KEEP	9	3	78	36	1069	GG	1	0.999992	0		-	10	47	292	0	0	19.474103	99	60	3264	230	ENST00000375050.4	0.091743	0.999992
NOTCH4	4855	__UNKNOWN__	__UNKNOWN__	6	32165889	32165889	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32165889C>T	ENST00000375023.3	-	26	4895					NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	NA		NA			cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						tgagccaccacgcccggccTA	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301	4855		Ankyrin repeat domain containing	7884	protein-coding gene	gene with protein product		164951	Notch (Drosophila) homolog 4, Notch homolog 4 (Drosophila)	INT3	NA	7835890	Standard		NM_004557	NA	Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4756+308G>A	chr6.hg19:g.32165889C>T		NA	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	hg19	CCDS34420.1	0.02	-0.30685	CCAxGCC	COVERED																																																																																			NOVEL	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076045.2	6	2.705064	KEEP	3	0	0	9	238	CC	0.99257	0.7943	0		-	3	60	93	0	0	6.36957	30	60	945	63	ENST00000375023.3	0.090909	0.800245
C6orf10	10665	__UNKNOWN__	__UNKNOWN__	6	32256807	32256807	__UNKNOWN__	Intron	SNP	C	C	T	rs7757711	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32256807C>T	ENST00000442822.2	-	26	1552							Q5SRN2	CF010_HUMAN	chromosome 6 open reading frame 10	NA		NA				integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	25						tgcagtggcacgatctcggct	0.512		NA											C|||	1042	0.208067	0.2194	0.1009	5008	,	,	NA	16876	0.2163	NA	0.2227	False	NA	,,,	NA	NA	NA	2504	0.2454	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U60665	CCDS34422.1, CCDS69082.1, CCDS75430.1	6p21.32	2012-11-20			ENSG00000204296	ENSG00000204296	10665			13922	protein-coding gene	gene with protein product	testis specific basic protein	NA			NA	10803852	Standard	NM_006781	XM_005248810	NA	Approved	TSBP	uc021yvs.1	Q5SRN2	OTTHUMG00000031107	ENST00000442822.2:c.1360-361G>A	chr6.hg19:g.32256807C>T		NA	A2BET1|A2BET2|A6NME2|B0S7R2|B0S7R3|E9PMB1|Q5SPI9|Q5SPJ0|Q5SPK9|Q5SPL0|Q5SRN3|Q5TG25|Q5TG26|Q8N4B6	hg19		0.02	-0.149104	GCAxGAT	COVERED																																																																																			NOVEL	C6orf10-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000383393.1	3	2.406557	KEEP	3	0	0	8	230	CC	0.99257	0.289832	0		-	10	60	289	0	0	29.520576	5	60	162	36	ENST00000442822.2	0.666667	0.292001
HLA-DRB1	3123	__UNKNOWN__	__UNKNOWN__	6	32549452	32549452	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs77637983		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32549452C>G	ENST00000360004.5	-	3	639	c.534G>C	c.(532-534)caG>caC	p.Q178H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	178	Beta-2.|Ig-like C1-type.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGTCTCCATTCTGGATCAGGC	0.552		NA								Multiple Myeloma(14;0.17)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													141	159	152			NA	NA	6		NA											NA				32549452		1511	2709	4220	SO:0001583	missense			AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126	3123		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B	NA		Standard	NM_002124	NM_001243965	NA	Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.534G>C	chr6.hg19:g.32549452C>G	ENSP00000353099:p.Gln178His	NA	P01914|Q9MYF5	hg19	CCDS47409.1	0.02	3.742098	ATTxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	.	9.019	0.984432	0.18889	.	.	ENSG00000196126	ENST00000360004	T	0.03181	4.02	3.87	-6.02	0.02192	Immunoglobulin-like (3);Immunoglobulin C1-set (6);Immunoglobulin-like fold (3);	1.094850	0.06883	N	0.802821	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	B;B;B	0.17038	0.02;0.003;0.003	B;B;B	0.15870	0.014;0.014;0.007	T	0.47711	-0.9096	8	0.34782	T	0.22	.	8.422	0.32707	0.401:0.5079:0.0:0.0911	rs2308771;rs9269801	178;178;178	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	H	178	ENSP00000353099:Q178H	ENSP00000353099:Q178H	Q	-	3	2	HLA-DRB1	32657430	0.000000	0.05858	0.048000	0.18961	0.990000	0.78478	-3.650000	0.00403	-1.028000	0.03321	0.453000	0.30009	CAG	NOVEL	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076393.3	2	3.308526	KEEP	35	0	0	11	322	CC	0.992708	0.992706	0		-	22	49	735	0	0	66.676932	39	60	1294	244	ENST00000360004.5	0.360656	0.999998
HLA-DQA2	3118	__UNKNOWN__	__UNKNOWN__	6	32713674	32713674	__UNKNOWN__	Silent	SNP	C	C	A	rs34357612	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32713674C>A	ENST00000374940.3	+	3	540	c.438C>A	c.(436-438)acC>acA	p.T146T		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	146	Alpha-2.|Ig-like C1-type.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"Insulin(DB00071)	TCAACATCACCTGGCTGAGCA	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													271	240	251			NA	NA	6		NA											NA				32713674		1511	2709	4220	SO:0001819	synonymous_variant				CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541	3118		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4943	protein-coding gene	gene with protein product		613503		HLA-DXA	NA		Standard	NM_020056	NM_020056	NA	Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.438C>A	chr6.hg19:g.32713674C>A		NA	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	hg19	CCDS4753.1	0.02	1.274418	CACxTGG	COVERED																																																																																			NOVEL	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000076179.2	4	2.708413	KEEP	1	0	0	9	288	CC	0.99254	0.992435	0		+	6	49	185	0	0	11.798098	84	60	2884	154	ENST00000374940.3	0.066667	0.999895
HLA-DQB2	3120	__UNKNOWN__	__UNKNOWN__	6	32724899	32724899	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32724899T>C	ENST00000437316.2	-	5	845				HLA-DQB2_ENST00000435145.2_3'UTR|HLA-DQB2_ENST00000411527.1_Intron			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						tgggttcaagtgattctcttg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629	3120		Histocompatibility complex, Immunoglobulin superfamily / C1-set domain containing	4945	protein-coding gene	gene with protein product		615161		HLA-DXB	NA	2564844	Standard		NM_001198858	NA	Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.781+158A>G	chr6.hg19:g.32724899T>C		NA	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	hg19		0.02	-0.298046	AAGxGAT	COVERED																																																																																			NOVEL	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000076216.2	3	2.704382	KEEP	0	0	0	9	228	TT	0.99254	0.775233	0		-	4	60	120	1	0	8.993479	23	60	609	48	ENST00000437316.2	0.148148	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	32760219	32760219	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:32760219T>C			NA	NA				HLA-DQB2 (28908 upstream) : HLA-DOB (20320 downstream)						NA		NA									NA						ctgtgttgcctaggctggtct	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.32760219T>C		NA		hg19		0.02	-0.350843	GCCxAGG	COVERED																																																																																			NOVEL					0			13	4.51157	KEEP	0	0	0	15	415	TT	0.99649	0.874627	0			3	60	106	1	0	7.58658	32	60	974	87		0.085714	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	33206775	33206775	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:33206775A>G			NA	NA				RING1 (26276 upstream) : XXbac-BPG157A10.21 (7076 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.33206775A>G		NA		hg19		0.02	-0.333237	CACxCCT	UNCOVERED																																																																																			NOVEL					0			11	2.706308	KEEP	3	0	0	9	241	AA	0	0	0			3	60	96	0	0	6.668208	30	60	860	63		0.090909	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	33583432	33583432	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:33583432G>T			NA	NA				LINC00336 (22317 upstream) : ITPR3 (4709 downstream)						NA		NA									NA						ctcccaaagtgctgggattac	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.33583432G>T		NA		hg19		0.02	-0.105267	AGTxCTG	UNCOVERED																																																																																			NOVEL					0			9	3.309574	KEEP	6	0	0	11	334	GG	0.99257	0.138793	0			3	37	90	0	0	7.778304	7	60	240	40		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	33583447	33583447	__UNKNOWN__	IGR	SNP	G	G	A	rs182411527	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:33583447G>A			NA	NA				LINC00336 (22332 upstream) : ITPR3 (4694 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.463		NA											a|||	27	0.00539137	0.0	0.0043	5008	,	,	NA	9379	0.0119	NA	0.0099	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.33583447G>A		NA		hg19		0.02	-0.105235	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			9	3.610421	KEEP	5	0	0	12	361	GG	0.99254	0.138789	0			3	37	77	0	0	6.477379	7	60	234	37		0.3	0.139832
NUDT3	11165	__UNKNOWN__	__UNKNOWN__	6	34317643	34317643	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34317643G>A	ENST00000607016.1	-	2	411				RPS10-NUDT3_ENST00000605528.1_Intron	NM_006703.3	NP_006694.1	O95989	NUDT3_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 3	NA		NA			cell-cell signaling (GO:0007267)|diadenosine polyphosphate catabolic process (GO:0015961)|diphosphoinositol polyphosphate catabolic process (GO:0071544)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|magnesium ion binding (GO:0000287)			lung(2)	2						tgaggcgggcggatcacaagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(96;1206 1939 18658 39482)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF062530	CCDS4791.1	6p21.2	2014-07-16			ENSG00000272325	ENSG00000272325	11165		Nudix motif containing	8050	protein-coding gene	gene with protein product		609228			NA	9822604	Standard		NM_006703	NA	Approved	DIPP		O95989	OTTHUMG00000014545	ENST00000607016.1:c.100-7894C>T	chr6.hg19:g.34317643G>A		NA	B2R8N4	hg19	CCDS4791.1	0.02	-0.175421	GGCxGAT	COVERED																																																																																			NOVEL	NUDT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040224.2	10	3.306606	KEEP	3	0	0	11	303	GG	0.992708	0.384582	0		-	3	42	94	1	0	7.391877	14	60	448	48	ENST00000607016.1	0.176471	0.387407
NUDT3	11165	__UNKNOWN__	__UNKNOWN__	6	34322207	34322207	__UNKNOWN__	Intron	SNP	T	T	C	rs368836351|rs73403933	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34322207T>C	ENST00000607016.1	-	2	411				RPS10-NUDT3_ENST00000605528.1_Intron	NM_006703.3	NP_006694.1	O95989	NUDT3_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 3	NA		NA			cell-cell signaling (GO:0007267)|diadenosine polyphosphate catabolic process (GO:0015961)|diphosphoinositol polyphosphate catabolic process (GO:0071544)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|magnesium ion binding (GO:0000287)			lung(2)	2						cacacacacatacacacTCTT	0.517		NA											t|||	2297	0.458666	0.6082	0.513	5008	,	,	NA	9630	0.496	NA	0.2674	False	NA	,,,	NA	NA	NA	2504	0.3763	NA	NA	NA	GBM(96;1206 1939 18658 39482)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF062530	CCDS4791.1	6p21.2	2014-07-16			ENSG00000272325	ENSG00000272325	11165		Nudix motif containing	8050	protein-coding gene	gene with protein product		609228			NA	9822604	Standard		NM_006703	NA	Approved	DIPP		O95989	OTTHUMG00000014545	ENST00000607016.1:c.100-12458A>G	chr6.hg19:g.34322207T>C		NA	B2R8N4	hg19	CCDS4791.1	0.02	-0.289333	ACAxACA	COVERED																																																																																			NOVEL	NUDT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040224.2	12	2.689695	KEEP	0	0	0	9	211	TT	0.99254	0.755211	0		-	3	60	100	0	0	7.292919	25	60	685	67	ENST00000607016.1	0.107143	0.760887
NUDT3	11165	__UNKNOWN__	__UNKNOWN__	6	34332549	34332549	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34332549A>G	ENST00000607016.1	-	2	411				RPS10-NUDT3_ENST00000605528.1_Intron	NM_006703.3	NP_006694.1	O95989	NUDT3_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 3	NA		NA			cell-cell signaling (GO:0007267)|diadenosine polyphosphate catabolic process (GO:0015961)|diphosphoinositol polyphosphate catabolic process (GO:0071544)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|magnesium ion binding (GO:0000287)			lung(2)	2						ggtggctcacacctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(96;1206 1939 18658 39482)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF062530	CCDS4791.1	6p21.2	2014-07-16			ENSG00000272325	ENSG00000272325	11165		Nudix motif containing	8050	protein-coding gene	gene with protein product		609228			NA	9822604	Standard		NM_006703	NA	Approved	DIPP		O95989	OTTHUMG00000014545	ENST00000607016.1:c.100-22800T>C	chr6.hg19:g.34332549A>G		NA	B2R8N4	hg19	CCDS4791.1	0.02	-0.332292	CACxCCT	COVERED																																																																																			NOVEL	NUDT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040224.2	10	2.707557	KEEP	2	0	0	9	261	AA	0.99257	0.845654	0		-	4	60	99	0	0	6.467379	33	60	1004	77	ENST00000607016.1	0.108108	0.851984
RPS10-NUDT3	100529239	__UNKNOWN__	__UNKNOWN__	6	34367764	34367764	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34367764T>C	ENST00000605528.1	-	5	473					NM_001202470.2	NP_001189399.1			RPS10-NUDT3 readthrough	NA		NA									NA						cgggtccaagtgattctcctg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					6p21.31	2013-09-25			ENSG00000270800	ENSG00000270800	100529239			49181	other	readthrough		NA			NA		Standard		NM_001202470	NA	Approved				OTTHUMG00000185089	ENST00000605528.1:c.456+18381A>G	chr6.hg19:g.34367764T>C		NA		hg19		0.02	-0.140329	AAGxGAT	COVERED																																																																																			NOVEL	RPS10-NUDT3-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000469545.1	6	2.706574	KEEP	0	0	0	9	248	TT	0.99254	0.289823	0		-	4	60	128	0	0	10.93127	11	60	327	34	ENST00000605528.1	0.266667	0.292001
C6orf106	64771	__UNKNOWN__	__UNKNOWN__	6	34643041	34643041	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34643041A>G	ENST00000374023.3	-	2	402				C6orf106_ENST00000374026.3_Intron	NM_024294.2	NP_077270.1	Q9H6K1	CF106_HUMAN	chromosome 6 open reading frame 106	NA		NA								endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10						ctgggcgacaaagcaagactc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF052106	CCDS4795.1, CCDS4796.1	6p21.31	2012-01-27			ENSG00000196821	ENSG00000196821	64771			21215	protein-coding gene	gene with protein product		612217			NA		Standard	NM_022758	XM_005249298	NA	Approved	FLJ22195, dJ391O22.4	uc003ojr.2	Q9H6K1	OTTHUMG00000014553	ENST00000374023.3:c.159-20485T>C	chr6.hg19:g.34643041A>G		NA	B2R8K7|Q5VV77|Q96MG5|Q9BUR9	hg19	CCDS4796.1	0.02	-0.219259	ACAxAGC	COVERED																																																																																			NOVEL	C6orf106-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040251.1	11	4.210426	KEEP	0	0	0	14	383	AA	0.995343	0.550313	0		-	3	60	102	0	0	7.705716	21	60	618	57	ENST00000374023.3	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	34748040	34748040	__UNKNOWN__	IGR	SNP	G	G	A	rs111423246	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34748040G>A			NA	NA				SNRPC (6469 upstream) : UHRF1BP1 (11816 downstream)						NA		NA									NA						aggccgaggcgggcggatcac	0.527		NA											G|||	778	0.155351	0.2526	0.111	5008	,	,	NA	13714	0.1339	NA	0.1372	False	NA	,,,	NA	NA	NA	2504	0.0961	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.34748040G>A		NA		hg19		0.02	-0.149113	GGCxGGC	COVERED																																																																																			NOVEL					0			6	2.707938	KEEP	4	0	0	9	272	GG	0.99257	0.289832	0			3	60	90	0	0	7.172306	12	60	385	45		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	34753014	34753014	__UNKNOWN__	IGR	SNP	G	G	A	rs112935373	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34753014G>A			NA	NA				SNRPC (11443 upstream) : UHRF1BP1 (6842 downstream)						NA		NA									NA						caaggcgggcggatcacctga	0.527		NA											G|||	543	0.108427	0.0234	0.0793	5008	,	,	NA	13702	0.3006	NA	0.0606	False	NA	,,,	NA	NA	NA	2504	0.0951	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.34753014G>A		NA		hg19		0.02	-0.140345	GGCxGAT	UNCOVERED																																																																																			NOVEL					0			8	2.70816	KEEP	4	0	0	9	278	GG	0	0	0			3	60	88	0	0	6.972298	12	60	395	40		0.2	0.260965
ANKS1A	23294	__UNKNOWN__	__UNKNOWN__	6	34973612	34973612	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:34973612T>C	ENST00000360359.3	+	10	1561				ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	NA		NA			ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						ggtggatcacttgaggtcagg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999	23294		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	20961	protein-coding gene	gene with protein product		608994	ankyrin repeat and SAM domain containing 1, ankyrin repeat and sterile alpha motif domain containing 1	ANKS1	NA	9039502	Standard	XM_166478	NM_015245	NA	Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.1423+11413T>C	chr6.hg19:g.34973612T>C		NA	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	hg19	CCDS4798.1	0.02	-0.429752	CACxTGA	COVERED																																																																																			NOVEL	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040262.1	9	4.8109	KEEP	0	0	0	16	427	TT	0.997832	0.952421	0		+	3	60	104	0	0	7.046864	42	60	1263	79	ENST00000360359.3	0.066667	0.954491
PPARD	5467	__UNKNOWN__	__UNKNOWN__	6	35392975	35392975	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35392975C>T	ENST00000311565.4	+	8	1427				PPARD_ENST00000444397.1_3'UTR|PPARD_ENST00000337400.2_3'UTR|PPARD_ENST00000448077.2_Intron|PPARD_ENST00000540939.1_Intron|PPARD_ENST00000418635.2_Intron|PPARD_ENST00000360694.3_Intron	NM_001171818.1	NP_001165289.1	Q03181	PPARD_HUMAN	peroxisome proliferator-activated receptor delta	NA		NA			adipose tissue development (GO:0060612)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|axon ensheathment (GO:0008366)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular response to hypoxia (GO:0071456)|cholesterol metabolic process (GO:0008203)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|fatty acid beta-oxidation (GO:0006635)|fatty acid catabolic process (GO:0009062)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)|lipid metabolic process (GO:0006629)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of inflammatory response (GO:0050728)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid biosynthetic process (GO:0008654)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermis development (GO:0045684)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of insulin secretion (GO:0032024)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|proteoglycan metabolic process (GO:0006029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to vitamin A (GO:0033189)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin A metabolic process (GO:0006776)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|linoleic acid binding (GO:0070539)|lipid binding (GO:0008289)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(4)|liver(2)|lung(9)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23					Bezafibrate(DB01393)|Icosapent(DB00159)|Sulindac(DB00605)|Treprostinil(DB00374)	cgcttgaacccgagaggtgga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07592	CCDS4803.1, CCDS4804.1, CCDS54994.1, CCDS54995.1	6p21.2	2013-01-16	2006-10-17		ENSG00000112033	ENSG00000112033	5467		Nuclear hormone receptors	9235	protein-coding gene	gene with protein product		600409	peroxisome proliferative activated receptor, delta		NA	1333051	Standard	NM_006238	NM_177435	NA	Approved	NUC1, NUCII, FAAR, NR1C2	uc003okm.3	Q03181	OTTHUMG00000014567	ENST00000311565.4:c.1078+419C>T	chr6.hg19:g.35392975C>T		NA	A8K6J6|B4E3V3|B6ZGS1|B7Z3W1|E9PE18|Q5D1P0|Q7Z5K0|Q9BUD4	hg19	CCDS4803.1	0.02	-0.368394	ACCxGAG	COVERED																																																																																			NOVEL	PPARD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040288.1	3	5.414566	KEEP	1	0	0	18	528	CC	0.999859	0.908941	0		+	4	60	114	1	0	7.862485	32	60	1032	70	ENST00000311565.4	0.111111	0.909069
FANCE	2178	__UNKNOWN__	__UNKNOWN__	6	35432258	35432258	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35432258T>C	ENST00000229769.2	+	9	1694					NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	NA		NA			DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						ttgtgatctgtccgccttggc	0.557		NA	N, F, S			AML, leukemia		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	Fanconi anemia, complementation group E		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039	2178		Fanconi anemia, complementation groups	3586	protein-coding gene	gene with protein product		613976		FACE	NA	7662964, 11001585	Standard		XM_005248885	NA	Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1509+1567T>C	chr6.hg19:g.35432258T>C		NA	A8K907|Q4ZGH2	hg19	CCDS4805.1	0.02	-0.236786	CTGxCCG	COVERED																																																																																			NOVEL	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040282.1	7	2.705429	KEEP	0	0	0	9	233	TT	0.99254	0.607839	0		+	3	60	109	0	0	8.348637	22	60	639	50	ENST00000229769.2	0.12	0.612407
FANCE	2178	__UNKNOWN__	__UNKNOWN__	6	35432260	35432260	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35432260C>T	ENST00000229769.2	+	9	1694					NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	NA		NA			DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						gtgatctgtccgccttggcct	0.557		NA	N, F, S			AML, leukemia		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	Fanconi anemia, complementation group E		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039	2178		Fanconi anemia, complementation groups	3586	protein-coding gene	gene with protein product		613976		FACE	NA	7662964, 11001585	Standard		XM_005248885	NA	Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1509+1569C>T	chr6.hg19:g.35432260C>T		NA	A8K907|Q4ZGH2	hg19	CCDS4805.1	0.02	-0.236849	GTCxGCC	COVERED																																																																																			NOVEL	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040282.1	7	2.707576	KEEP	0	0	0	9	269	CC	0.99254	0.607839	0		+	3	60	92	0	0	6.649388	22	60	728	51	ENST00000229769.2	0.12	0.612407
TEAD3	7005	__UNKNOWN__	__UNKNOWN__	6	35446945	35446945	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35446945A>G	ENST00000402886.3	-	3	316				TEAD3_ENST00000338863.7_Intron			Q99594	TEAD3_HUMAN	TEA domain family member 3	NA		NA			female pregnancy (GO:0007565)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	10						gtgagccaccacgcccagccA	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X94439	CCDS47414.1	6p21.2	2008-07-28			ENSG00000007866	ENSG00000007866	7005			11716	protein-coding gene	gene with protein product		603170		TEAD5	NA	9889009, 9148898	Standard		NM_003214	NA	Approved	TEF-5, ETFR-1	uc003oku.4	Q99594	OTTHUMG00000014571	ENST00000402886.3:c.162+136T>C	chr6.hg19:g.35446945A>G		NA	O95910|Q5BJG7|Q8N6Y4	hg19		0.02	3.838794	ACCxCGC	COVERED																																																																																			NOVEL	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000316961.2	17	2.436591	KEEP	3	1	31	19	500	AA	0.99986	0.99985	0		-	5	60	169	0	0	10.715738	93	60	2721	184	ENST00000402886.3	0.05102	0.999991
FKBP5	2289	__UNKNOWN__	__UNKNOWN__	6	35586758	35586758	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35586758T>C	ENST00000539068.1	-	5	711				FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Intron|FKBP5_ENST00000536438.1_Intron|FKBP5_ENST00000357266.4_Intron	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	NA		NA			chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						caggcgtgagtcactgcgcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060	2289		Tetratricopeptide (TTC) repeat domain containing	3721	protein-coding gene	gene with protein product		602623	FK506-binding protein 5		NA	9001212	Standard		NM_004117	NA	Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.508+114A>G	chr6.hg19:g.35586758T>C		NA	F5H7R1|Q59EB8|Q5TGM6	hg19	CCDS4808.1	0.02	-0.333172	GAGxCAC	COVERED																																																																																			NOVEL	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040309.2	2	2.404169	KEEP	0	0	0	8	200	TT	0.99257	0.845654	0		-	5	60	169	0	0	12.862673	33	60	915	56	ENST00000539068.1	0.131579	0.851984
FKBP5	2289	__UNKNOWN__	__UNKNOWN__	6	35645095	35645095	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35645095C>A	ENST00000539068.1	-	1	184				FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Intron|FKBP5_ENST00000536438.1_Intron|FKBP5_ENST00000357266.4_Intron	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	NA		NA			chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						tgtgatccgcccgcctcggcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060	2289		Tetratricopeptide (TTC) repeat domain containing	3721	protein-coding gene	gene with protein product		602623	FK506-binding protein 5		NA	9001212	Standard		NM_004117	NA	Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.18+11413G>T	chr6.hg19:g.35645095C>A		NA	F5H7R1|Q59EB8|Q5TGM6	hg19	CCDS4808.1	0.02	-0.184213	CGCxCGC	COVERED																																																																																			NOVEL	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040309.2	11	5.114852	KEEP	2	0	0	17	513	CC	0.997832	0.422559	0		-	4	47	117	0	0	9.263049	16	60	544	54	ENST00000539068.1	0.2	0.423478
FKBP5	2289	__UNKNOWN__	__UNKNOWN__	6	35660460	35660460	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35660460T>C	ENST00000536438.1	-	2	297					NM_001145775.1	NP_001139247.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	NA		NA			chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						ccctgctacttgggaggctga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060	2289		Tetratricopeptide (TTC) repeat domain containing	3721	protein-coding gene	gene with protein product		602623	FK506-binding protein 5		NA	9001212	Standard		NM_004117	NA	Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000536438.1:c.18+27644A>G	chr6.hg19:g.35660460T>C		NA	F5H7R1|Q59EB8|Q5TGM6	hg19	CCDS4808.1	0.02	-0.263111	ACTxGGG	COVERED																																																																																			NOVEL	FKBP5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		7	3.006967	KEEP	0	0	0	10	269	TT	0.992708	0.68861	0		-	3	60	95	0	0	6.895485	23	60	689	55	ENST00000536438.1	0.115385	0.693668
FKBP5	2289	__UNKNOWN__	__UNKNOWN__	6	35675521	35675521	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35675521C>T	ENST00000536438.1	-	2	297					NM_001145775.1	NP_001139247.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	NA		NA			chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						atctgttgttcccctctttgt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060	2289		Tetratricopeptide (TTC) repeat domain containing	3721	protein-coding gene	gene with protein product		602623	FK506-binding protein 5		NA	9001212	Standard		NM_004117	NA	Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000536438.1:c.18+12583G>A	chr6.hg19:g.35675521C>T		NA	F5H7R1|Q59EB8|Q5TGM6	hg19	CCDS4808.1	0.02	-0.20176	GTTxCCC	COVERED																																																																																			NOVEL	FKBP5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		6	3.309297	KEEP	0	0	0	11	328	CC	0.993072	0.487146	0		-	3	60	88	0	0	6.365857	20	60	673	46	ENST00000536438.1	0.130435	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	35767731	35767731	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35767731T>C			NA	NA				CLPS (2643 upstream) : LHFPL5 (5338 downstream)						NA		NA									NA						aggcatgagctaccatgccca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.35767731T>C		NA		hg19		0.02	-0.157877	AGCxACC	COVERED																																																																																			NOVEL					0			8	2.405687	KEEP	0	0	0	8	216	TT	0.99257	0.320408	0			3	60	97	0	0	7.691908	14	60	420	40		0.176471	0.322807
SRPK1	6732	__UNKNOWN__	__UNKNOWN__	6	35872808	35872808	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35872808T>C	ENST00000373825.2	-	3	360				SRPK1_ENST00000423325.2_Intron|SRPK1_ENST00000373822.1_Intron					SRSF protein kinase 1	NA		NA								endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						ggtgtagtcctagctactcca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(31;67 978 16289 24856 26454)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063	6732			11305	protein-coding gene	gene with protein product	SR protein kinase 1, serine/arginine-rich splicing factor kinase 1	601939	SFRS protein kinase 1		NA	8208298, 10198174	Standard	NM_003137	NM_003137	NA	Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.75-14018A>G	chr6.hg19:g.35872808T>C		NA		hg19	CCDS47415.1	0.02	3.628391	TCCxAGC	COVERED																																																																																			NOVEL	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040319.3	44	24.389336	KEEP	0	4	122	124	3408	TT	1	1	0		-	6	60	204	0	0	12.816857	119	60	3570	347	ENST00000373825.2	0.048	1
SRPK1	6732	__UNKNOWN__	__UNKNOWN__	6	35877952	35877952	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35877952C>G	ENST00000373825.2	-	2	360				SRPK1_ENST00000423325.2_Intron|SRPK1_ENST00000373822.1_Intron					SRSF protein kinase 1	NA		NA								endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						tagagacgggctttcaccatg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(31;67 978 16289 24856 26454)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063	6732			11305	protein-coding gene	gene with protein product	SR protein kinase 1, serine/arginine-rich splicing factor kinase 1	601939	SFRS protein kinase 1		NA	8208298, 10198174	Standard	NM_003137	NM_003137	NA	Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.74+10292G>C	chr6.hg19:g.35877952C>G		NA		hg19	CCDS47415.1	0.02	-0.14032	GGGxTTT	COVERED																																																																																			NOVEL	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040319.3	6	3.008523	KEEP	1	0	0	10	298	CC	0.99254	0.259018	0		-	3	60	97	0	0	7.872463	12	60	396	34	ENST00000373825.2	0.2	0.260965
SLC26A8	116369	__UNKNOWN__	__UNKNOWN__	6	35927932	35927932	__UNKNOWN__	Intron	SNP	A	A	G	rs538548087		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:35927932A>G	ENST00000490799.1	-	15	1992				SLC26A8_ENST00000355574.2_Intron|SLC26A8_ENST00000394602.2_Intron	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						aaagtgctggaattacaggtg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053	116369		Solute carriers	14468	protein-coding gene	gene with protein product		608480	solute carrier family 26, member 8		NA	11834742, 11829495	Standard		NM_001193476	NA	Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.1639-349T>C	chr6.hg19:g.35927932A>G		NA		hg19	CCDS4813.1	0.02	-0.324531	TGGxATT	COVERED																																																																																			NOVEL	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040325.2	13	2.638983	KEEP	0	1	29	19	530	AA	0.999863	0.835601	0		-	4	60	135	0	0	10.061867	30	60	910	89	ENST00000490799.1	0.117647	0.835716
MAPK14	1432	__UNKNOWN__	__UNKNOWN__	6	36016031	36016031	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36016031A>G	ENST00000229795.3	+	2	563				MAPK14_ENST00000229794.4_Intron|MAPK14_ENST00000468133.1_Intron|MAPK14_ENST00000310795.4_Intron	NM_001315.2	NP_001306.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	NA		NA			3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						tgttggccagactggtattga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062	1432		Mitogen-activated protein kinase cascade / Kinases	6876	protein-coding gene	gene with protein product	p38 MAP kinase	600289		CSPB1, CSBP1, CSBP2	NA	7997261	Standard	NM_001315	NM_139012	NA	Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229795.3:c.117-4445A>G	chr6.hg19:g.36016031A>G		NA	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	hg19	CCDS4815.1	0.02	-0.184176	CAGxCTG	COVERED																																																																																			NOVEL	MAPK14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357449.1	8	3.609392	KEEP	1	0	0	12	334	AA	0.993072	0.420544	0		+	3	60	95	0	0	7.261251	17	60	504	43	ENST00000229795.3	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	36200877	36200877	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36200877C>T			NA	NA				BRPF3 (310 upstream) : PNPLA1 (10102 downstream)						NA		NA									NA						cccaggctggcctcaaactcc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.36200877C>T		NA		hg19		0.02	-0.27195	TGGxCTC	COVERED																																																																																			NOVEL					0			5	3.310158	KEEP	1	0	0	11	347	CC	0.992708	0.712085	0			3	60	94	0	0	6.74282	24	60	827	62		0.111111	0.717315
RP1-50J22.4	0	__UNKNOWN__	__UNKNOWN__	6	36356463	36356463	__UNKNOWN__	RNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36356463T>G	ENST00000411643.1	+	0	100										NA		NA									NA						cactttgggatgccaaggtgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000411643.1:	chr6.hg19:g.36356463T>G		NA		hg19		0.02	-0.122794	GGAxGCC	COVERED																																																																																			NOVEL	RP1-50J22.4-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000040339.1	6	3.005995	KEEP	1	0	0	10	274	TT	0.992708	0.19488	0		+	4	60	142	0	0	12.977606	7	60	205	40	ENST00000411643.1	0.363636	0.196312
STK38	11329	__UNKNOWN__	__UNKNOWN__	6	36507077	36507077	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36507077C>T	ENST00000229812.7	-	2	417					NM_007271.2	NP_009202.1			serine/threonine kinase 38	NA		NA								NS(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						gcacgagaaccgcttgaaccc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(180;997 3561 16158)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4822.1	6p21	2006-10-06			ENSG00000112079	ENSG00000112079	11329			17847	protein-coding gene	gene with protein product		606964			NA	7761441	Standard	NM_007271	NM_007271	NA	Approved	NDR	uc003omh.3	Q15208	OTTHUMG00000014598	ENST00000229812.7:c.131+771G>A	chr6.hg19:g.36507077C>T		NA		hg19	CCDS4822.1	0.02	-0.140344	AACxGCT	COVERED																																																																																			NOVEL	STK38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040346.1	6	3.007337	KEEP	0	0	0	10	277	CC	0.992708	0.259062	0		-	3	60	91	0	0	7.272339	12	60	384	33	ENST00000229812.7	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	36532616	36532616	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36532616T>C			NA	NA				STK38 (17369 upstream) : SRSF3 (29528 downstream)						NA		NA									NA						gtggctcatgtctgtaatccc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.36532616T>C		NA		hg19		0.02	-0.245579	ATGxCTG	COVERED																																																																																			NOVEL					0			7	2.706978	KEEP	0	0	0	9	250	TT	0.99254	0.663536	0			3	60	105	0	0	8.126697	19	60	570	62		0.136364	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	36664388	36664388	__UNKNOWN__	IGR	SNP	T	T	A	rs59257390	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36664388T>A			NA	NA				CDKN1A (9272 upstream) : RAB44 (18867 downstream)						NA		NA									NA						tttctttctttctttctttct	0.343		NA											t|||	1216	0.242812	0.2784	0.2205	5008	,	,	NA	11379	0.2183	NA	0.2565	False	NA	,,,	NA	NA	NA	2504	0.2219	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.36664388T>A		NA		hg19		0.02	-0.11401	CTTxCTT	UNCOVERED																																																																																			NOVEL					0			7	2.404332	KEEP	2	0	0	8	211	TT	0.99257	0.16126	0			4	60	117	0	0	10.291273	8	60	239	30		0.333333	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	36664389	36664389	__UNKNOWN__	IGR	SNP	C	C	G	rs58228337	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36664389C>G			NA	NA				CDKN1A (9273 upstream) : RAB44 (18866 downstream)						NA		NA									NA						ttctttctttctttctttctt	0.338		NA											c|||	1216	0.242812	0.2784	0.2205	5008	,	,	NA	11288	0.2183	NA	0.2565	False	NA	,,,	NA	NA	NA	2504	0.2219	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.36664389C>G		NA		hg19		0.02	-0.114036	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			7	2.406077	KEEP	2	0	0	8	234	CC	0.99257	0.16126	0			4	60	130	0	0	11.591309	8	60	268	30		0.333333	0.162467
CPNE5	57699	__UNKNOWN__	__UNKNOWN__	6	36750534	36750534	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36750534A>G	ENST00000244751.2	-	9	1153					NM_020939.1	NP_065990.1	Q9HCH3	CPNE5_HUMAN	copine V	NA		NA				extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(4)|liver(1)|lung(9)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25						ttgcgccactacactccagcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			H09181	CCDS4825.1	6p21.2	2010-05-28			ENSG00000124772	ENSG00000124772	57699			2318	protein-coding gene	gene with protein product		604209			NA	9430674	Standard	NM_020939	NM_020939	NA	Approved	CPN5, COPN5, KIAA1599	uc003omr.1	Q9HCH3	OTTHUMG00000014602	ENST00000244751.2:c.529-3800T>C	chr6.hg19:g.36750534A>G		NA	Q7Z6C8	hg19	CCDS4825.1	0.02	-0.157823	ACTxCAC	COVERED																																																																																			NOVEL	CPNE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040351.1	6	3.907627	KEEP	0	0	0	13	335	AA	0.994391	0.320996	0		-	3	60	104	0	0	8.479331	13	60	354	46	ENST00000244751.2	0.1875	0.322807
RP1-90K10.4	0	__UNKNOWN__	__UNKNOWN__	6	36911855	36911855	__UNKNOWN__	lincRNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:36911855T>G	ENST00000427609.2	-	0	204										NA		NA									NA						ggccgaggcgtgcggatcacg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000427609.2:	chr6.hg19:g.36911855T>G		NA		hg19		0.02	-0.140337	GCGxGCG	COVERED																																																																																			NOVEL	RP1-90K10.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000040379.2	3	2.406045	KEEP	0	0	0	8	219	TT	0.99257	0.259026	0		-	3	60	98	0	0	7.97228	12	60	361	34	ENST00000427609.2	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	37011155	37011155	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:37011155G>A			NA	NA				FGD2 (14309 upstream) : COX6A1P2 (1451 downstream)						NA		NA									NA						ttcttttttgggacagagtct	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.37011155G>A		NA		hg19		0.02	-0.350809	TTGxGAC	COVERED																																																																																			NOVEL					0			16	5.416014	KEEP	1	0	0	18	551	GG	0.999859	0.877584	0			4	60	122	1	0	8.763162	30	60	994	79		0.117647	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	37033365	37033365	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:37033365A>G			NA	NA				COX6A1P2 (20188 upstream) : PIM1 (104613 downstream)						NA		NA									NA						tcaccgtgttagccaggctgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.37033365A>G		NA		hg19		0.02	-0.113868	GTTxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.7065	KEEP	1	0	0	9	241	AA	0.99257	0.16126	0			4	60	101	0	0	8.68417	8	60	237	30		0.333333	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	37319993	37319993	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:37319993A>G			NA	NA				TBC1D22B (19247 upstream) : RNF8 (1754 downstream)						NA		NA									NA						ctggagtgcaatggcgagatc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.37319993A>G		NA		hg19		0.02	-0.27188	GCAxTGG	COVERED																																																																																			NOVEL					0			5	3.006645	KEEP	0	0	0	10	262	AA	0.992708	0.712085	0			4	60	139	0	0	10.962077	22	60	630	51		0.153846	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	37319999	37319999	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:37319999A>C			NA	NA				TBC1D22B (19253 upstream) : RNF8 (1748 downstream)						NA		NA									NA						tgcaatggcgagatctcggct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.37319999A>C		NA		hg19		0.02	-0.228015	GCGxGAT	COVERED																																																																																			NOVEL					0			5	2.704915	KEEP	0	0	0	9	235	AT	0.992708	0.63667	0			3	60	99	0	0	7.592517	18	60	516	47		0.142857	0.641347
CMTR1	23070	__UNKNOWN__	__UNKNOWN__	6	37434685	37434685	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:37434685A>G	ENST00000373451.4	+	13	1669					NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)				NA						ggtggctcacacctgtaatcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	23070	2.1.1.57	G patch domain containing	21077	protein-coding gene	gene with protein product		NA	KIAA0082, FtsJ methyltransferase domain containing 2	KIAA0082, FTSJD2	NA	20713356	Standard	NM_015050	NM_015050	NA	Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.1505+3901A>G	chr6.hg19:g.37434685A>G		NA	A8K949|Q14670|Q96FJ9	hg19	CCDS4835.1	0.02	-0.210475	CACxCCT	COVERED																																																																																			NOVEL	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040408.1	5	2.404581	KEEP	0	0	0	8	220	AA	0.99257	0.518282	0		+	3	60	100	0	0	7.692406	18	60	529	44	ENST00000373451.4	0.142857	0.522161
ZFAND3	60685	__UNKNOWN__	__UNKNOWN__	6	37975290	37975290	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:37975290C>T	ENST00000287218.4	+	3	559				ZFAND3_ENST00000373391.2_Intron	NM_021943.2	NP_068762.1	Q9H8U3	ZFAN3_HUMAN	zinc finger, AN1-type domain 3	NA		NA					DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(2)|ovary(1)	9						cactgcactccagtctgggtg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023284	CCDS4836.1	6p21.2	2013-09-19	2005-12-15	2005-12-15	ENSG00000156639	ENSG00000156639	60685		Zinc fingers, AN1-type domain containing	18019	protein-coding gene	gene with protein product		607455	testis expressed sequence 27	TEX27	NA		Standard	NM_021943	NM_021943	NA	Approved	FLJ13222	uc003onx.3	Q9H8U3	OTTHUMG00000014629	ENST00000287218.4:c.113-54079C>T	chr6.hg19:g.37975290C>T		NA	Q5SZZ0|Q5SZZ1	hg19	CCDS4836.1	0.02	-0.166679	CTCxAGT	COVERED																																																																																			NOVEL	ZFAND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040424.3	9	2.407235	KEEP	0	0	0	8	246	AC	0.99254	0.351306	0		+	3	56	93	0	0	7.378709	13	60	447	41	ENST00000287218.4	0.1875	0.353947
BTBD9	114781	__UNKNOWN__	__UNKNOWN__	6	38178978	38178978	__UNKNOWN__	Intron	SNP	G	G	A	rs186768187	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:38178978G>A	ENST00000419706.2	-	10	1731				BTBD9_ENST00000314100.6_Intron|BTBD9_ENST00000408958.1_Intron|BTBD9_ENST00000403056.1_Intron|BTBD9_ENST00000481247.1_Intron			Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9	NA		NA			adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|circadian sleep/wake cycle, non-REM sleep (GO:0042748)|long-term memory (GO:0007616)|multicellular organismal iron ion homeostasis (GO:0060586)|regulation of synaptic vesicle endocytosis (GO:1900242)|sensory perception of temperature stimulus (GO:0050951)|serotonin metabolic process (GO:0042428)					breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	12						ggccgaggcgggtggatcacg	0.522		NA											g|||	74	0.0147764	0.0023	0.0187	5008	,	,	NA	17381	0.001	NA	0.0328	False	NA	,,,	NA	NA	NA	2504	0.0245	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43458.1, CCDS47418.1, CCDS54998.1	6p21	2014-01-28			ENSG00000183826	ENSG00000183826	114781		BTB/POZ domain containing	21228	protein-coding gene	gene with protein product		611237			NA	11572484	Standard	NM_152733	NM_052893	NA	Approved	KIAA1880, dJ322I12.1	uc010jwx.3	Q96Q07	OTTHUMG00000014634	ENST00000419706.2:c.1473-18605C>T	chr6.hg19:g.38178978G>A		NA	Q494V9|Q494W1|Q96M00	hg19	CCDS54998.1	0.02	-0.140339	GCGxGTG	UNCOVERED																																																																																			NOVEL	BTBD9-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040436.3	4	2.407422	KEEP	5	0	0	8	256	GG	0	0	0		-	4	60	117	0	0	9.701451	12	60	382	37	ENST00000419706.2	0.25	0.260965
BTBD9	114781	__UNKNOWN__	__UNKNOWN__	6	38370632	38370632	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:38370632T>C	ENST00000419706.2	-	6	1283	c.1025A>G	c.(1024-1026)gAg>gGg	p.E342G	BTBD9_ENST00000314100.6_Intron|BTBD9_ENST00000408958.1_Intron|BTBD9_ENST00000403056.1_Intron|BTBD9_ENST00000481247.1_Intron			Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9	383		NA			adult locomotory behavior (GO:0008344)|cell adhesion (GO:0007155)|circadian sleep/wake cycle, non-REM sleep (GO:0042748)|long-term memory (GO:0007616)|multicellular organismal iron ion homeostasis (GO:0060586)|regulation of synaptic vesicle endocytosis (GO:1900242)|sensory perception of temperature stimulus (GO:0050951)|serotonin metabolic process (GO:0042428)					breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	12						ttgcttgagctcaggagttcg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS43458.1, CCDS47418.1, CCDS54998.1	6p21	2014-01-28			ENSG00000183826	ENSG00000183826	114781		BTB/POZ domain containing	21228	protein-coding gene	gene with protein product		611237			NA	11572484	Standard	NM_152733	NM_052893	NA	Approved	KIAA1880, dJ322I12.1	uc010jwx.3	Q96Q07	OTTHUMG00000014634	ENST00000419706.2:c.1025A>G	chr6.hg19:g.38370632T>C	ENSP00000415365:p.Glu342Gly	NA	Q494V9|Q494W1|Q96M00	hg19	CCDS54998.1	0.02	1.871146	AGCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	1.436	-0.568886	0.03910	.	.	ENSG00000183826	ENST00000419706	T	0.74632	-0.86	1.17	-2.34	0.06704	.	.	.	.	.	T	0.36552	0.0971	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23154	-1.0196	8	0.48119	T	0.1	.	5.4917	0.16779	0.0:0.5339:0.0:0.4661	.	342	Q494V9	.	G	342	ENSP00000415365:E342G	ENSP00000415365:E342G	E	-	2	0	BTBD9	38478610	0.002000	0.14202	0.000000	0.03702	0.005000	0.04900	-0.017000	0.12590	-1.034000	0.03295	-0.478000	0.04885	GAG	NOVEL	BTBD9-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040436.3	15	5.7445	KEEP	0	1	28	29	783	TT	0.999997	0.98794	0		-	4	60	129	0	0	8.655533	49	60	1448	127	ENST00000419706.2	0.075472	0.987943
DNAH8	1769	__UNKNOWN__	__UNKNOWN__	6	38923177	38923177	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:38923177T>C	ENST00000359357.3	+	80	12054				DNAH8_ENST00000441566.1_Intron|DNAH8_ENST00000449981.2_Intron			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	NA		NA			cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						gaggccgaggtgggtggatca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721	1769		Axonemal dyneins	2952	protein-coding gene	gene with protein product		603337	dynein, axonemal, heavy polypeptide 8		NA	9373155	Standard	NM_001206927	NM_001206927	NA	Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11800+3881T>C	chr6.hg19:g.38923177T>C		NA	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	hg19		0.02	-0.210469	AGGxGGG	COVERED																																																																																			NOVEL	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000043574.1	11	3.30693	KEEP	2	0	0	11	288	TT	0.992708	0.518353	0		+	5	60	151	0	0	12.480993	16	60	481	53	ENST00000359357.3	0.238095	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	39127180	39127180	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:39127180G>A			NA	NA				SAYSD1 (44215 upstream) : KCNK5 (29568 downstream)						NA		NA									NA						ggtggctcacgcctgtcatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.39127180G>A		NA		hg19		0.02	-0.254376	CACxCCT	COVERED																																																																																			NOVEL					0			14	4.814026	KEEP	13	0	0	16	484	GG	0.993072	0.663892	0			3	60	90	0	0	6.506382	21	60	676	78		0.125	0.668523
NFYA	4800	__UNKNOWN__	__UNKNOWN__	6	41062159	41062159	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:41062159C>T	ENST00000341376.6	+	9	1114	c.913C>T	c.(913-915)Cgt>Tgt	p.R305C	OARD1_ENST00000480585.1_Intron|NFYA_ENST00000353205.5_Missense_Mutation_p.R276C	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	305		NA			cellular lipid metabolic process (GO:0044255)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	9	Ovarian(28;0.0418)|Colorectal(47;0.196)					GTCTCGGCACCGTCATGCCAT	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													108	104	105			NA	NA	6		NA											NA				41062159		2203	4300	6503	SO:0001583	missense				CCDS4849.1, CCDS4850.1	6p21.3	2008-11-11			ENSG00000001167	ENSG00000001167	4800			7804	protein-coding gene	gene with protein product		189903			NA	1774067, 9612081	Standard		NM_002505	NA	Approved	HAP2, CBF-B, NF-YA	uc003opo.3	P23511	OTTHUMG00000014669	ENST00000341376.6:c.913C>T	chr6.hg19:g.41062159C>T	ENSP00000345702:p.Arg305Cys	NA	Q8IXU0	hg19	CCDS4849.1	0.02	1.175311	CACxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891709	0.91889	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.58	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.70202	0.3197	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.78314	0.982;0.991	T	0.75465	-0.3308	9	0.72032	D	0.01	-1.4701	15.0805	0.72110	0.1428:0.8572:0.0:0.0	.	276;305	P23511-2;P23511	.;NFYA_HUMAN	C	305;276	.	ENSP00000345702:R305C	R	+	1	0	NFYA	41170137	0.995000	0.38212	1.000000	0.80357	0.964000	0.63967	2.972000	0.49256	1.436000	0.47453	0.655000	0.94253	CGT	NOVEL	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040496.1	3	3.308748	KEEP	0	0	0	11	311	CC	0.993072	0.992968	0		+	5	60	152	0	0	9.210527	85	60	2782	160	ENST00000341376.6	0.055556	0.999895
RP11-328M4.2	0	__UNKNOWN__	__UNKNOWN__	6	41489985	41489985	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:41489985C>G	ENST00000440194.1	-	0	155										NA		NA									NA						aggtgatctgcctgccttggc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000440194.1:	chr6.hg19:g.41489985C>G		NA		hg19		0.02	-0.254409	CTGxCTG	COVERED																																																																																			NOVEL	RP11-328M4.2-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000040516.2	13	3.309493	KEEP	5	0	0	11	330	CC	0.992708	0.663648	0		-	3	60	106	0	0	7.94181	24	60	822	58	ENST00000440194.1	0.111111	0.668523
USP49	25862	__UNKNOWN__	__UNKNOWN__	6	41766282	41766282	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:41766282A>G	ENST00000394253.3	-	6	2206				USP49_ENST00000297229.2_3'UTR|USP49_ENST00000373006.1_3'UTR|USP49_ENST00000373010.1_Intron|USP49_ENST00000373009.3_Intron			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	NA		NA			histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ccaaagcgctaggattacagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663	25862		Ubiquitin-specific peptidases	20078	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 49		NA	14715245	Standard	NM_018561	NM_018561	NA	Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.1876+179T>C	chr6.hg19:g.41766282A>G		NA	Q5T3D9|Q5T3E0|Q96CK4	hg19		0.02	5.534571	GCTxGGA	COVERED																																																																																			NOVEL	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000316513.3	41	15.434672	KEEP	0	3	90	83	2273	AA	1	1	0		-	7	60	251	0	0	15.647633	170	60	4995	414	ENST00000394253.3	0.039548	1
C6orf132	647024	__UNKNOWN__	__UNKNOWN__	6	42069996	42069996	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42069996C>T	ENST00000341865.4	-	0	5069					NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	NA		NA								breast(1)	1						agacgagtctcgctctgtcgc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112	647024			21288	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001164446	NM_001164446	NA	Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.*1503G>A	chr6.hg19:g.42069996C>T		NA	A6NI05	hg19	CCDS47428.1	0.02	-0.289438	TCTxGCT	COVERED																																																																																			NOVEL	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040548.2	2	3.307361	KEEP	2	0	0	11	294	CC	0.993072	0.755616	0		-	3	60	90	0	0	6.833668	16	60	519	47	ENST00000341865.4	0.157895	0.760887
C6orf132	647024	__UNKNOWN__	__UNKNOWN__	6	42070335	42070335	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42070335T>C	ENST00000341865.4	-	0	4730					NM_001164446.1	NP_001157918.1	Q5T0Z8	CF132_HUMAN	chromosome 6 open reading frame 132	NA		NA								breast(1)	1						ttagtagagatggggtttcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS47428.1	6p21.1	2012-02-06			ENSG00000188112	ENSG00000188112	647024			21288	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001164446	NM_001164446	NA	Approved	bA7K24.2	uc003orw.2	Q5T0Z8	OTTHUMG00000014695	ENST00000341865.4:c.*1164A>G	chr6.hg19:g.42070335T>C		NA	A6NI05	hg19	CCDS47428.1	0.02	10.406803	AGAxGGG	COVERED																																																																																			NOVEL	C6orf132-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040548.2	93	15.388221	KEEP	2	16	416	199	5372	TT	1	1	0		-	13	60	363	0	2	19.563741	277	60	7884	810	ENST00000341865.4	0.044828	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	42116420	42116420	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42116420A>G			NA	NA				C6orf132 (6063 upstream) : GUCA1A (6723 downstream)						NA		NA									NA						ctggagtgcaatggcgcgatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.42116420A>G		NA		hg19		0.02	-0.24555	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			5	2.405361	KEEP	4	0	0	8	210	AA	0	0	0			3	60	95	0	0	6.896357	23	60	669	54		0.115385	0.641347
TRERF1	55809	__UNKNOWN__	__UNKNOWN__	6	42277975	42277975	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42277975A>G	ENST00000372922.4	-	4	193				TRERF1_ENST00000372917.4_Intron|TRERF1_ENST00000340840.2_Intron|TRERF1_ENST00000354325.2_Intron|TRERF1_ENST00000541110.1_Intron	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	NA		NA			cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ccaaagtgctaggagtatagg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496	55809			18273	protein-coding gene	gene with protein product		610322	breast cancer anti-estrogen resistance 2	BCAR2	NA	11349124	Standard	NM_033502	XM_005249223	NA	Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.370-9488T>C	chr6.hg19:g.42277975A>G		NA	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	hg19	CCDS4867.1	0.02	-0.263124	GCTxGGA	COVERED																																																																																			NOVEL	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040551.2	6	2.405602	KEEP	0	0	0	8	217	AA	0.99257	0.688515	0		-	3	60	102	0	0	7.49223	25	60	745	58	ENST00000372922.4	0.107143	0.693668
TRERF1	55809	__UNKNOWN__	__UNKNOWN__	6	42277979	42277979	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42277979G>T	ENST00000372922.4	-	4	193				TRERF1_ENST00000372917.4_Intron|TRERF1_ENST00000340840.2_Intron|TRERF1_ENST00000354325.2_Intron|TRERF1_ENST00000541110.1_Intron	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	NA		NA			cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			agtgctaggagtataggcatg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496	55809			18273	protein-coding gene	gene with protein product		610322	breast cancer anti-estrogen resistance 2	BCAR2	NA	11349124	Standard	NM_033502	XM_005249223	NA	Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.370-9492C>A	chr6.hg19:g.42277979G>T		NA	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	hg19	CCDS4867.1	0.02	-0.26317	GGAxTAT	COVERED																																																																																			NOVEL	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040551.2	8	3.008009	KEEP	0	0	0	10	300	GG	0.992708	0.68861	0		-	3	60	92	0	0	6.543087	24	60	827	59	ENST00000372922.4	0.111111	0.693668
TRERF1	55809	__UNKNOWN__	__UNKNOWN__	6	42355807	42355807	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42355807A>G	ENST00000372922.4	-	3	110				TRERF1_ENST00000372917.4_Intron|TRERF1_ENST00000340840.2_Intron|TRERF1_ENST00000354325.2_Intron|TRERF1_ENST00000541110.1_Intron	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	NA		NA			cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			ttacaggcataagccactgca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496	55809			18273	protein-coding gene	gene with protein product		610322	breast cancer anti-estrogen resistance 2	BCAR2	NA	11349124	Standard	NM_033502	XM_005249223	NA	Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.453-24990T>C	chr6.hg19:g.42355807A>G		NA	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	hg19	CCDS4867.1	0.02	-0.289399	CATxAGC	COVERED																																																																																			NOVEL	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040551.2	9	3.00613	KEEP	0	0	0	10	256	AA	0.992708	0.755338	0		-	5	60	170	0	0	13.597814	24	60	671	61	ENST00000372922.4	0.172414	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	42429796	42429796	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42429796A>G			NA	NA				TRERF1 (10007 upstream) : snoU13 (43441 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.42429796A>G		NA		hg19		0.02	-0.140342	CACxCCT	COVERED																																																																																			NOVEL					0			4	2.707407	KEEP	1	0	0	9	258	AA	0.99254	0.259018	0			3	60	105	0	0	8.672113	12	60	365	38		0.2	0.260965
UBR2	23304	__UNKNOWN__	__UNKNOWN__	6	42549760	42549760	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42549760A>G	ENST00000372899.1	+	2	596				UBR2_ENST00000372901.1_Intron|UBR2_ENST00000372903.2_Intron	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	NA		NA			cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			ggtggctcacacctgtaatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048	23304		Ubiquitin protein ligase E3 component n-recognins	21289	protein-coding gene	gene with protein product		609134	chromosome 6 open reading frame 133	C6orf133	NA		Standard	NM_015255	NM_015255	NA	Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.338+8029A>G	chr6.hg19:g.42549760A>G		NA	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	hg19	CCDS4870.1	0.02	-0.236829	CACxCCT	COVERED																																																																																			NOVEL	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040558.2	9	4.211149	KEEP	4	0	0	14	403	AA	0.995343	0.609555	0		+	3	60	100	0	0	7.448862	22	60	678	70	ENST00000372899.1	0.12	0.612407
UBR2	23304	__UNKNOWN__	__UNKNOWN__	6	42583435	42583435	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42583435A>G	ENST00000372899.1	+	10	1351				UBR2_ENST00000372901.1_Intron|UBR2_ENST00000372903.2_Intron	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	NA		NA			cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			ggctgaggcaagaggatcact	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048	23304		Ubiquitin protein ligase E3 component n-recognins	21289	protein-coding gene	gene with protein product		609134	chromosome 6 open reading frame 133	C6orf133	NA		Standard	NM_015255	NM_015255	NA	Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.1094-305A>G	chr6.hg19:g.42583435A>G		NA	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	hg19	CCDS4870.1	0.02	-0.228044	GCAxGAG	COVERED																																																																																			NOVEL	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040558.2	6	3.309023	KEEP	0	0	0	11	314	AA	0.993072	0.578892	0		+	3	60	98	0	0	7.364976	20	60	605	54	ENST00000372899.1	0.130435	0.58293
UBR2	23304	__UNKNOWN__	__UNKNOWN__	6	42638658	42638658	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42638658C>T	ENST00000372899.1	+	36	4344				UBR2_ENST00000372901.1_Intron|UBR2_ENST00000372883.3_Intron	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	NA		NA			cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			gcgcagtggcccacgcctgta	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048	23304		Ubiquitin protein ligase E3 component n-recognins	21289	protein-coding gene	gene with protein product		609134	chromosome 6 open reading frame 133	C6orf133	NA		Standard	NM_015255	NM_015255	NA	Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.4086+205C>T	chr6.hg19:g.42638658C>T		NA	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	hg19	CCDS4870.1	0.02	-0.184101	GGCxCAC	COVERED																																																																																			NOVEL	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040558.2	6	2.407215	KEEP	0	0	0	8	247	CC	0.99257	0.420331	0		+	4	60	110	0	0	8.666557	15	60	513	38	ENST00000372899.1	0.210526	0.423478
GLTSCR1L	23506	__UNKNOWN__	__UNKNOWN__	6	42770219	42770219	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42770219C>T	ENST00000314073.5	+	2	75							Q6AI39	GSC1L_HUMAN	GLTSCR1-like	NA		NA									NA						ggagtttcgcccttgttgccc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624	23506			21111	protein-coding gene	gene with protein product		NA	KIAA0240	KIAA0240	NA		Standard	NM_015349	XM_005248972	NA	Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.-101-7825C>T	chr6.hg19:g.42770219C>T		NA	A1L3W2|Q5TFZ3|Q92514	hg19	CCDS34451.1	0.02	-0.245615	CGCxCTT	COVERED																																																																																			NOVEL	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040562.3	10	3.009269	KEEP	2	0	0	10	318	CC	0.992708	0.63667	0		+	3	60	89	0	1	6.349905	22	60	727	60	ENST00000314073.5	0.12	0.641347
GLTSCR1L	23506	__UNKNOWN__	__UNKNOWN__	6	42771791	42771791	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42771791G>A	ENST00000314073.5	+	2	75							Q6AI39	GSC1L_HUMAN	GLTSCR1-like	NA		NA									NA						acggagtttcgctcttgttgc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624	23506			21111	protein-coding gene	gene with protein product		NA	KIAA0240	KIAA0240	NA		Standard	NM_015349	XM_005248972	NA	Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.-101-6253G>A	chr6.hg19:g.42771791G>A		NA	A1L3W2|Q5TFZ3|Q92514	hg19	CCDS34451.1	0.02	-0.219304	TTCxCTC	COVERED																																																																																			NOVEL	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040562.3	9	2.706965	KEEP	2	0	0	9	256	GG	0.99254	0.548763	0		+	3	60	88	1	0	6.427951	19	60	636	53	ENST00000314073.5	0.136364	0.552887
GLTSCR1L	23506	__UNKNOWN__	__UNKNOWN__	6	42780528	42780528	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42780528A>G	ENST00000314073.5	+	2	171							Q6AI39	GSC1L_HUMAN	GLTSCR1-like	NA		NA									NA						ccagcactttaggaggccaag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624	23506			21111	protein-coding gene	gene with protein product		NA	KIAA0240	KIAA0240	NA		Standard	NM_015349	XM_005248972	NA	Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.-6+2389A>G	chr6.hg19:g.42780528A>G		NA	A1L3W2|Q5TFZ3|Q92514	hg19	CCDS34451.1	0.02	-0.219272	TTTxGGA	COVERED																																																																																			NOVEL	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040562.3	14	3.308058	KEEP	0	0	0	11	297	AA	0.993072	0.549057	0		+	3	60	104	0	0	8.092021	18	60	535	51	ENST00000314073.5	0.142857	0.552887
GLTSCR1L	23506	__UNKNOWN__	__UNKNOWN__	6	42831029	42831029	__UNKNOWN__	Intron	SNP	G	G	A	rs400724	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42831029G>A	ENST00000314073.5	+	12	2628				GLTSCR1L_ENST00000394168.1_Intron			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	NA		NA									NA						ctcatgatccgcctgccttgg	0.552		NA											G|||	1654	0.330272	0.0219	0.4971	5008	,	,	NA	18499	0.5724	NA	0.3966	False	NA	,,,	NA	NA	NA	2504	0.3108	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624	23506			21111	protein-coding gene	gene with protein product		NA	KIAA0240	KIAA0240	NA		Standard	NM_015349	XM_005248972	NA	Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.2452+679G>A	chr6.hg19:g.42831029G>A		NA	A1L3W2|Q5TFZ3|Q92514	hg19	CCDS34451.1	0.02	-0.08771	TCCxCCT	UNCOVERED																																																																																			NOVEL	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040562.3	3	3.30991	KEEP	11	0	0	11	341	GG	0	0	0		+	5	60	145	0	0	13.873591	5	60	166	44	ENST00000314073.5	0.5	0.099721
RPL7L1	285855	__UNKNOWN__	__UNKNOWN__	6	42857353	42857353	__UNKNOWN__	3'UTR	SNP	A	A	G	rs1064123	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42857353A>G	ENST00000493763.1	+	0	4195				RPL7L1_ENST00000304734.5_3'UTR	NM_198486.2	NP_940888.2	Q6DKI1	RL7L_HUMAN	ribosomal protein L7-like 1	NA		NA				ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)	6	Colorectal(47;0.196)		Colorectal(64;0.00237)|all cancers(41;0.00288)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.088)			AGTTGTGACTATGGAAGCCCA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS4873.1	6p21.1	2011-01-14			ENSG00000146223	ENSG00000146223	285855		L ribosomal proteins	21370	protein-coding gene	gene with protein product		NA			NA		Standard	XM_209769	NM_198486	NA	Approved	dJ475N16.4	uc003osq.1	Q6DKI1	OTTHUMG00000014710	ENST00000493763.1:c.*3151A>G	chr6.hg19:g.42857353A>G		NA	A8K7D4|B7Z652|Q5TFZ5|Q6PEK3	hg19	CCDS4873.1	0.02	1.689653	ACTxTGG	COVERED																																																																																			NOVEL	RPL7L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000314417.1	0	3.605552	KEEP	7	0	0	12	309	AA	0.993634	0.975704	0		+	7	33	220	0	0	16.123929	50	60	1480	97	ENST00000493763.1	0.122807	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	42920810	42920810	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:42920810T>C			NA	NA				RP3-475N16.1 (4712 upstream) : GNMT (7685 downstream)						NA		NA									NA						gtggctcatgtctgtaatccc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.42920810T>C		NA		hg19		0.02	-0.175401	ATGxCTG	COVERED																																																																																			NOVEL					0			10	2.706335	KEEP	0	0	0	9	242	TT	0.99254	0.384517	0			3	60	106	0	0	8.7724	12	60	344	43		0.2	0.387407
PTK7	5754	__UNKNOWN__	__UNKNOWN__	6	43119235	43119235	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43119235G>C	ENST00000230419.4	+	17	2942				PTK7_ENST00000352931.2_Intron|PTK7_ENST00000349241.2_Intron|PTK7_ENST00000481273.1_Intron|PTK7_ENST00000345201.2_Intron	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	NA		NA			actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			caggcgtgaggcaccgcgccc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	5754	2.7.10.1	Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	9618	protein-coding gene	gene with protein product		601890	PTK7 protein tyrosine kinase 7		NA	7478540	Standard		NM_002821	NA	Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.2721+4799G>C	chr6.hg19:g.43119235G>C		NA	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	hg19	CCDS4884.1	0.02	-0.271931	GAGxCAC	UNCOVERED																																																																																			NOVEL	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040580.2	9	2.406248	KEEP	1	0	0	8	241	GG	0	0	0		+	3	49	102	0	0	7.542269	24	60	786	57	ENST00000230419.4	0.111111	0.717315
CUL9	23113	__UNKNOWN__	__UNKNOWN__	6	43151697	43151697	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43151697A>G	ENST00000372647.2	+	2	65				CUL9_ENST00000252050.4_Intron|CUL9_ENST00000354495.3_Intron			Q8IWT3	CUL9_HUMAN	cullin 9	NA		NA			microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						cactatgttgaccaggctgga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659	23113			15982	protein-coding gene	gene with protein product	parkin-like cytoplasmic p53 binding protein, p53-associated parkin-like cytoplasmic protein	607489			NA	17332328, 10521492, 12526791	Standard	NM_015089	NM_015089	NA	Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000372647.2:c.-9-343A>G	chr6.hg19:g.43151697A>G		NA	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	hg19		0.02	-0.122728	TTGxCCA	COVERED																																																																																			NOVEL	CUL9-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000358329.1	10	2.706669	KEEP	4	0	0	9	245	AA	0.99254	0.194847	0		+	3	60	82	0	0	6.583091	10	60	311	34	ENST00000372647.2	0.230769	0.196312
DNPH1	10591	__UNKNOWN__	__UNKNOWN__	6	43194824	43194824	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43194824A>G	ENST00000230431.6	-	2	224				DNPH1_ENST00000393987.2_Intron	NM_006443.2	NP_006434.1			2'-deoxynucleoside 5'-phosphate N-hydrolase 1	NA		NA									NA						cagcctgggcaacagagcaaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040105	CCDS4891.1, CCDS43465.1	6p21.1	2012-11-28	2012-11-28	2012-11-28	ENSG00000112667	ENSG00000112667	10591			21218	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 108	C6orf108	NA	9271375, 17234634	Standard	NM_006443	NM_006443	NA	Approved	rcl, dJ330M21.3	uc003ouo.3	O43598	OTTHUMG00000014724	ENST00000230431.6:c.197-691T>C	chr6.hg19:g.43194824A>G		NA		hg19	CCDS4891.1	0.02	-0.306944	GGCxACA	COVERED																																																																																			NOVEL	DNPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040583.2	14	3.909711	KEEP	1	0	0	13	358	AA	0.993634	0.795151	0		-	3	60	95	0	1	6.568446	30	60	872	61	ENST00000230431.6	0.090909	0.800245
ABCC10	89845	__UNKNOWN__	__UNKNOWN__	6	43407946	43407946	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43407946T>C	ENST00000372530.4	+	8	2342				ABCC10_ENST00000244533.3_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	ccgcccgccttggcctcccaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574	89845		ATP binding cassette transporters / subfamily C	52	protein-coding gene	gene with protein product		612509			NA	8894702	Standard	NM_033450	NM_033450	NA	Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2127+1413T>C	chr6.hg19:g.43407946T>C		NA	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	hg19	CCDS56430.1	0.02	-0.271892	CCTxGGC	COVERED																																																																																			NOVEL	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040603.2	8	3.308313	KEEP	3	0	0	11	305	TT	0.99254	0.711964	0		+	3	60	93	0	0	6.643919	24	60	723	71	ENST00000372530.4	0.111111	0.717315
TJAP1	93643	__UNKNOWN__	__UNKNOWN__	6	43472144	43472144	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43472144T>C	ENST00000259751.1	+	10	927				TJAP1_ENST00000372445.5_Intron|TJAP1_ENST00000372452.1_Intron|TJAP1_ENST00000372444.2_Intron|TJAP1_ENST00000438588.2_Intron|TJAP1_ENST00000372449.1_Intron|TJAP1_ENST00000483640.1_Intron|TJAP1_ENST00000436109.2_Intron	NM_080604.2	NP_542171.2	Q5JTD0	TJAP1_HUMAN	tight junction associated protein 1 (peripheral)	NA		NA			Golgi organization (GO:0007030)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)|trans-Golgi network (GO:0005802)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|urinary_tract(2)	21	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0122)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			tgagccactgtgcccggccCA	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024269	CCDS4898.1, CCDS55004.1	6p21.1	2008-02-05	2005-07-05	2005-07-05	ENSG00000137221	ENSG00000137221	93643			17949	protein-coding gene	gene with protein product		612658	tight junction protein 4 (peripheral)	TJP4	NA	11602598	Standard	NM_080604	NM_001146016	NA	Approved	PILT	uc011dvh.1	Q5JTD0	OTTHUMG00000014736	ENST00000259751.1:c.550-355T>C	chr6.hg19:g.43472144T>C		NA	Q05BH9|Q5JTD1|Q5JWW1|Q68DB2|Q6P2P3|Q9H7V7	hg19	CCDS4898.1	0.02	1.578617	CTGxGCC	COVERED																																																																																			NOVEL	TJAP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040626.1	24	7.819578	KEEP	7	0	0	26	723	TT	0.999892	0.99921	0		+	6	60	196	0	0	13.46206	67	60	1994	154	ENST00000259751.1	0.082192	0.999317
XPO5	57510	__UNKNOWN__	__UNKNOWN__	6	43497019	43497019	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43497019A>G	ENST00000265351.7	-	24	2888				POLR1C_ENST00000304004.3_Missense_Mutation_p.T319A	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	NA		NA			gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			ggtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													133	109	117			NA	NA	6		NA											NA				43497019		2203	4300	6503	SO:0001627	intron_variant			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571	57510		Exportins	17675	protein-coding gene	gene with protein product		607845			NA	11777942, 12426392	Standard	NM_020750	NM_020750	NA	Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2678-356T>C	chr6.hg19:g.43497019A>G		NA	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	hg19	CCDS47430.1	0.02	3.759906	CACxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.069	-1.206343	0.01568	.	.	ENSG00000171453	ENST00000304004	T	0.66280	-0.2	0.677	0.677	0.17964	.	.	.	.	.	T	0.13841	0.0335	.	.	.	0.09310	N	1	B	0.22541	0.071	B	0.14023	0.01	T	0.33163	-0.9879	7	0.08179	T	0.78	.	.	.	.	.	319	O15160-2	.	A	319	ENSP00000307212:T319A	ENSP00000307212:T319A	T	+	1	0	POLR1C	43604997	0.001000	0.12720	0.013000	0.15412	0.047000	0.14425	-0.303000	0.08210	0.531000	0.28639	0.172000	0.16884	ACC	NOVEL	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040657.2	34	2.902403	KEEP	2	3	92	42	1145	AA	1	0.999998	0		-	9	60	285	0	0	19.584739	93	60	2742	249	ENST00000265351.7	0.088235	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	43659979	43659979	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43659979T>C			NA	NA				MRPS18A (4451 upstream) : RP1-261G23.5 (30543 downstream)						NA		NA									NA						tctcgaactcttgacctctgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.43659979T>C		NA		hg19		0.02	-0.263088	CTCxTGA	COVERED																																																																																			NOVEL					0			10	2.405966	KEEP	0	0	0	8	218	TT	0.99257	0.688515	0			3	60	92	0	0	6.5447	24	60	701	49		0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	43664921	43664921	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43664921C>T			NA	NA				MRPS18A (9393 upstream) : RP1-261G23.5 (25601 downstream)						NA		NA									NA						gccaacatggcgaaaccccat	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.43664921C>T		NA		hg19		0.02	-0.166637	TGGxGAA	UNCOVERED																																																																																			NOVEL					0			6	2.40676	KEEP	5	0	0	8	237	CC	0	0	0			4	60	100	1	0	7.768906	14	60	461	44		0.222222	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	43892999	43892999	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:43892999G>A			NA	NA				RP11-344J7.2 (72929 upstream) : RP5-1120P11.1 (70460 downstream)						NA		NA									NA						ttgctctgtcgcccaggctgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.43892999G>A		NA		hg19		0.02	-0.184212	GTCxCCC	COVERED																																																																																			NOVEL					0			10	3.008067	KEEP	0	0	0	10	293	GG	0.992708	0.42039	0			3	60	89	0	0	6.733761	16	60	540	43		0.157895	0.423478
CAPN11	11131	__UNKNOWN__	__UNKNOWN__	6	44136677	44136677	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:44136677A>T	ENST00000398776.1	+	3	126				CAPN11_ENST00000542245.1_Intron	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	NA		NA			proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			atttttttttagagacaaggt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225	11131		EF-hand domain containing	1478	protein-coding gene	gene with protein product		604822			NA	10409436	Standard		NM_007058	NA	Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.89-341A>T	chr6.hg19:g.44136677A>T		NA	B2RA64|Q5T3G1|Q8N4R5	hg19	CCDS47436.1	0.02	3.026293	TTTxGAG	COVERED																																																																																			NOVEL	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040714.3	37	17.741605	KEEP	0	0	0	59	1599	AA	1	0.999992	0		+	5	60	157	0	0	9.45192	96	60	2864	240	ENST00000398776.1	0.049505	0.999992
CAPN11	11131	__UNKNOWN__	__UNKNOWN__	6	44147264	44147264	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:44147264G>C	ENST00000398776.1	+	13	1454				CAPN11_ENST00000542245.1_Intron	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	NA		NA			proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CACACACACAGACACACACTA	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													115	99	104			NA	NA	6		NA											NA				44147264		692	1591	2283	SO:0001627	intron_variant			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225	11131		EF-hand domain containing	1478	protein-coding gene	gene with protein product		604822			NA	10409436	Standard		NM_007058	NA	Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.1417-92G>C	chr6.hg19:g.44147264G>C		NA	B2RA64|Q5T3G1|Q8N4R5	hg19	CCDS47436.1	0.02	-0.350689	ACAxACA	COVERED																																																																																			NOVEL	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040714.3	8	6.90837	KEEP	0	0	0	23	683	GG	0.999909	0.877628	0		+	3	60	100	0	0	6.841181	36	60	1186	86	ENST00000398776.1	0.076923	0.877708
RP11-444E17.6	0	__UNKNOWN__	__UNKNOWN__	6	44302896	44302896	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:44302896T>G	ENST00000505802.1	+	4	855										NA		NA									NA						atcaagaccatcctggccaac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000505802.1:c.404-17567T>G	chr6.hg19:g.44302896T>G		NA		hg19		0.02	-0.07017	CCAxCCT	UNCOVERED																																																																																			NOVEL	RP11-444E17.6-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000470403.1	11	2.40618	KEEP	5	0	0	8	221	TT	0	0	0		+	2	50	72	0	0	6.495932	4	60	116	25	ENST00000505802.1	0.333333	0.054137
CDC5L	988	__UNKNOWN__	__UNKNOWN__	6	44417848	44417848	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:44417848A>G	ENST00000371477.3	+	0	6108					NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	NA		NA			cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			tgatccacctacctcggcctc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401	988			1743	protein-coding gene	gene with protein product		602868	CDC5 (cell division cycle 5, S. pombe, homolog)-like, CDC5 cell division cycle 5-like (S. pombe)		NA	9598309, 9038199	Standard		NM_001253	NA	Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.*3400A>G	chr6.hg19:g.44417848A>G		NA	Q76N46|Q99974	hg19	CCDS4912.1	0.02	-0.306938	CCTxCCT	COVERED																																																																																			NOVEL	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040743.1	12	3.607237	KEEP	1	0	0	12	314	AA	0.993634	0.813254	0		+	4	60	127	0	0	9.624584	24	60	700	68	ENST00000371477.3	0.142857	0.818465
SUPT3H	8464	__UNKNOWN__	__UNKNOWN__	6	44935809	44935809	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:44935809C>T	ENST00000371459.1	-	7	670				SUPT3H_ENST00000371461.2_Intron|SUPT3H_ENST00000306867.5_Intron|SUPT3H_ENST00000371460.1_Intron	NM_001261823.1|NM_003599.3	NP_001248752.1|NP_003590.1	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog (S. cerevisiae)	NA		NA			chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	transcription coactivator activity (GO:0003713)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	12						ggattacaggcatgagccact	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF069734	CCDS34465.1, CCDS34466.1, CCDS75464.1	6p21.1-p12.3	2008-05-15	2001-11-28		ENSG00000196284	ENSG00000196284	8464			11466	protein-coding gene	gene with protein product		602947	suppressor of Ty (S.cerevisiae) 3 homolog		NA	9674425, 9726987	Standard	NM_181356	NM_003599	NA	Approved	SPT3, SPT3L	uc003oxp.4	O75486	OTTHUMG00000014773	ENST00000371459.1:c.505-6244G>A	chr6.hg19:g.44935809C>T		NA	A6NKG9|B2R9Q5|O76066|Q5TAV9|Q86VN7	hg19	CCDS34465.1	0.02	-0.228084	AGGxATG	COVERED																																																																																			NOVEL	SUPT3H-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000106911.2	13	4.513511	KEEP	3	0	0	15	466	CC	0.99649	0.580884	0		-	3	60	89	0	0	6.406402	21	60	714	65	ENST00000371459.1	0.125	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	46179560	46179560	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:46179560A>G			NA	NA				ENPP5 (40852 upstream) : RCAN2 (8914 downstream)						NA		NA									NA						ggtggctcatacctgtaatcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.46179560A>G		NA		hg19		0.02	-0.254322	CATxCCT	COVERED																																																																																			NOVEL					0			6	3.307374	KEEP	0	0	0	11	295	AA	0.993072	0.663892	0			4	60	129	0	0	9.962429	22	60	638	56		0.153846	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	46751574	46751574	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:46751574A>C			NA	NA				RP11-268F1.3 (22679 upstream) : MEP1A (9552 downstream)						NA		NA									NA						gttggccaggatggtctcgat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.46751574A>C		NA		hg19		0.02	-0.140321	AGGxTGG	COVERED																																																																																			NOVEL					0			3	3.006799	KEEP	3	0	0	10	265	AA	0.99254	0.259018	0			3	60	102	0	0	8.372399	12	60	348	37		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	47046458	47046458	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:47046458T>C			NA	NA				GPR110 (36359 upstream) : TNFRSF21 (152809 downstream)						NA		NA									NA						tggtggctcatacctgtagtc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.47046458T>C		NA		hg19		0.02	-0.175384	TCAxACC	COVERED																																																																																			NOVEL					0			10	2.404696	KEEP	0	0	0	8	209	TT	0.99257	0.384528	0			3	60	95	0	0	7.579326	13	60	363	39		0.1875	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	48529236	48529236	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:48529236T>C			NA	NA				PTCHD4 (492811 upstream) : AL391538.1 (288323 downstream)						NA		NA									NA						aggctggtcttgaactcctga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.48529236T>C		NA		hg19		0.02	-0.140315	TCTxGAA	UNCOVERED																																																																																			NOVEL					0			3	2.406001	KEEP	3	0	0	8	218	TT	0	0	0			3	60	90	0	0	7.273445	11	60	329	40		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	48656245	48656245	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:48656245T>C			NA	NA				PTCHD4 (619820 upstream) : AL391538.1 (161314 downstream)						NA		NA									NA						tttgggaggctgaggcaggtg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.48656245T>C		NA		hg19		0.02	-0.114018	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.707233	KEEP	2	0	0	9	254	TT	0.99257	0.16126	0			3	60	93	0	0	8.07825	7	60	216	36		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	49218536	49218536	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:49218536A>G			NA	NA				AL391538.1 (400897 upstream) : RNU7-65P (93923 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.49218536A>G		NA		hg19		0.02	-0.105257	CACxCCT	UNCOVERED																																																																																			NOVEL					0			6	2.406874	KEEP	0	0	0	8	236	AA	0.99257	0.138793	0			3	60	103	0	0	8.932498	8	60	242	28		0.272727	0.139832
GLYATL3	389396	__UNKNOWN__	__UNKNOWN__	6	49476645	49476645	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:49476645A>G	ENST00000371197.4	+	2	85					NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	NA		NA				mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						agccaagatcatgccactgca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972	389396			21349	protein-coding gene	gene with protein product		614763	chromosome 6 open reading frame 140	C6orf140	NA		Standard	NM_001010904	NM_001010904	NA	Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.-28-3031A>G	chr6.hg19:g.49476645A>G		NA		hg19	CCDS47440.1	0.02	-0.359541	ATCxTGC	COVERED																																																																																			NOVEL	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040866.3	7	3.003996	KEEP	3	0	0	10	253	AA	0.992708	0.882393	0		+	3	47	95	0	0	6.488169	32	60	902	63	ENST00000371197.4	0.085714	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	49527764	49527764	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:49527764T>C			NA	NA				C6orf141 (7956 upstream) : RHAG (45106 downstream)						NA		NA									NA						cggtggctcatgcctttaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.49527764T>C		NA		hg19		0.02	-0.157872	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			8	2.405946	KEEP	1	0	0	8	219	TT	0	0	0			3	60	94	0	0	7.392001	14	60	414	39		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	50900960	50900960	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:50900960G>A			NA	NA				TFAP2B (85634 upstream) : SNORD66 (428527 downstream)						NA		NA									NA						tggaggttgcggtgagctgag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.50900960G>A		NA		hg19		0.02	-0.140338	TGCxGTG	COVERED																																																																																			NOVEL					0			6	3.309588	KEEP	3	0	0	11	332	GG	0.993072	0.259157	0			3	60	88	0	0	6.972486	12	60	380	45		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	52121584	52121584	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:52121584T>C			NA	NA				IL17F (12249 upstream) : MCM3 (7222 downstream)						NA		NA									NA						gctgggattataggcatgagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.52121584T>C		NA		hg19		0.02	-0.280647	TTAxAGG	COVERED																																																																																			NOVEL					0			5	2.4064	KEEP	0	0	0	8	225	TT	0.99257	0.734176	0			4	60	140	0	0	11.1361	21	60	608	63		0.16	0.739671
PAQR8	85315	__UNKNOWN__	__UNKNOWN__	6	52271627	52271627	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:52271627T>C	ENST00000442253.2	+	0	3790				PAQR8_ENST00000360726.3_3'UTR	NM_133367.4	NP_588608.1	Q8TEZ7	MPRB_HUMAN	progestin and adipoQ receptor family member VIII	NA		NA			multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)			endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|urinary_tract(2)	17	Lung NSC(77;0.0875)					tcccaaagtgttgggattaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF347029	CCDS4941.1	6p12	2012-08-10	2005-05-20	2005-05-20	ENSG00000170915	ENSG00000170915	85315			15708	protein-coding gene	gene with protein product		607780	chromosome 6 open reading frame 33	C6orf33	NA	11676489, 12574519	Standard	NM_133367	NM_133367	NA	Approved	LMPB1, MPRB	uc003pao.4	Q8TEZ7	OTTHUMG00000014846	ENST00000442253.2:c.*2551T>C	chr6.hg19:g.52271627T>C		NA	B2RCF6|Q86WL0|Q8N6D3|Q9HD02	hg19	CCDS4941.1	0.02	-0.31573	GTGxTGG	COVERED																																																																																			NOVEL	PAQR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040903.2	6	2.706746	KEEP	1	0	0	9	246	TT	0.99257	0.812384	0		+	4	60	136	0	0	10.333129	27	60	789	59	ENST00000442253.2	0.129032	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	52479825	52479825	__UNKNOWN__	IGR	SNP	C	C	T	rs76916450	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:52479825C>T			NA	NA				TRAM2-AS1 (31042 upstream) : RP1-152L7.5 (50120 downstream)						NA		NA									NA						ggtgaaaccccgtctctacta	0.527		NA											C|||	189	0.0377396	0.0	0.0014	5008	,	,	NA	14349	0.1726	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.52479825C>T		NA		hg19		0.02	-0.210517	CCCxGTC	COVERED																																																																																			NOVEL					0			6	3.607312	KEEP	11	0	0	12	317	CC	0.99257	0.518282	0			3	60	88	0	0	6.366162	20	60	642	51		0.130435	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	52800340	52800340	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:52800340G>A			NA	NA				GSTA3 (25857 upstream) : RP1-214M20.2 (4183 downstream)						NA		NA									NA						catgcctgtagtcctagcact	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.52800340G>A		NA		hg19		0.02	-0.228092	GTAxTCC	COVERED																																																																																			NOVEL					0			7	3.911677	KEEP	0	0	0	13	398	GG	0.994391	0.57966	0			3	60	94	0	0	6.964917	20	60	696	60		0.130435	0.58293
FBXO9	26268	__UNKNOWN__	__UNKNOWN__	6	52964093	52964093	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:52964093G>A	ENST00000323557.7	+	0	3110				FBXO9_ENST00000244426.6_3'UTR	NM_033480.2	NP_258441.1	Q9UK97	FBX9_HUMAN	F-box protein 9	NA		NA			fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|protein ubiquitination (GO:0016567)|regulation of TOR signaling (GO:0032006)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(4)|lung(1)|pancreas(2)|skin(1)	9	Lung NSC(77;0.103)					tgggaggctggggcaggagaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF155114	CCDS55022.1, CCDS55023.1, CCDS55024.1	6p12.3-p11.2	2004-06-15	2004-06-15		ENSG00000112146	ENSG00000112146	26268		F-boxes /  other	13588	protein-coding gene	gene with protein product		609091	F-box only protein 9		NA	10531035, 10531037	Standard		NM_012347	NA	Approved	FBX9, NY-REN-57	uc021zao.1	Q9UK97	OTTHUMG00000014869	ENST00000323557.7:c.*1465G>A	chr6.hg19:g.52964093G>A		NA	A6NFW3|B3KMM6|O75986|Q59EH8|Q6PKH7|Q9NT57|Q9Y593	hg19	CCDS55022.1	0.02	7.227848	CTGxGGC	COVERED																																																																																			NOVEL	FBXO9-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000040951.2	88	27.775564	KEEP	2	6	148	145	4327	GG	1	1	0		+	11	70	314	0	0	17.214376	234	70	7689	560	ENST00000323557.7	0.044898	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	53014217	53014217	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:53014217T>C			NA	NA				GCM1 (590 upstream) : RNU6-464P (4375 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.53014217T>C		NA		hg19		0.02	-0.245585	TCCxAGC	COVERED																																																																																			NOVEL					0			5	2.704354	KEEP	0	0	0	9	231	TT	0.99254	0.636563	0			3	60	97	0	0	7.206512	21	60	629	55		0.125	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	53032550	53032550	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:53032550G>A			NA	NA				RNU6-464P (13854 upstream) : RNU1-136P (51508 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.53032550G>A		NA		hg19		0.02	-0.175416	CACxCCT	COVERED																																																																																			NOVEL					0			7	4.512499	KEEP	1	0	0	15	442	GG	0.995343	0.385603	0			4	60	118	0	0	9.363302	16	60	511	51		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	53235816	53235816	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:53235816T>C			NA	NA				RP3-483K16.4 (20313 upstream) : RN7SKP256 (44275 downstream)						NA		NA									NA						cgcctgtaattccagcacttt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.53235816T>C		NA		hg19		0.02	-0.175426	AATxCCA	UNCOVERED																																																																																			NOVEL					0			6	2.406203	KEEP	1	0	0	8	222	TT	0	0	0			3	60	97	0	0	7.692004	14	60	437	40		0.176471	0.387407
MLIP	90523	__UNKNOWN__	__UNKNOWN__	6	53975061	53975061	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:53975061A>G	ENST00000514921.1	+	2	176				MLIP_ENST00000274897.5_Intron|MLIP_ENST00000370877.2_Intron|MLIP_ENST00000509997.1_Intron|MLIP_ENST00000370876.2_Intron	NM_001281746.1	NP_001268675.1	Q5VWP3	MLIP_HUMAN	muscular LMNA-interacting protein	NA		NA				nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|PML body (GO:0016605)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(16)|ovary(8)|skin(4)|stomach(1)|urinary_tract(1)	34						gattacaggcatgagccacgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055530	CCDS4954.1, CCDS64448.1, CCDS64449.1	6p12.2-p12.1	2011-04-29	2011-04-29	2011-04-29	ENSG00000146147	ENSG00000146147	90523			21355	protein-coding gene	gene with protein product	muscle-enriched A-type lamin interacting protein	614106	chromosome 6 open reading frame 142	C6orf142	NA	21498514	Standard	NM_138569	NM_138569	NA	Approved	MGC18257	uc011dxa.2	Q5VWP3	OTTHUMG00000014891	ENST00000514921.1:c.64-11184A>G	chr6.hg19:g.53975061A>G		NA	B7Z2N0|D6RE05|Q96H08|Q96NF7	hg19		0.02	-0.245544	GGCxTGA	COVERED																																																																																			NOVEL	MLIP-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000360019.1	7	3.607818	KEEP	0	0	0	12	315	AA	0.993634	0.637264	0		+	3	60	94	0	0	6.849694	22	60	643	64	ENST00000514921.1	0.12	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	55866462	55866462	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:55866462T>C			NA	NA				BMP5 (126100 upstream) : COL21A1 (54925 downstream)						NA		NA									NA						atctcctgacttcgtgatccg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.55866462T>C		NA		hg19		0.02	-0.14909	GACxTCG	UNCOVERED																																																																																			NOVEL					0			6	2.404981	KEEP	1	0	0	8	213	TT	0	0	0			3	60	100	0	0	8.382035	10	60	297	36		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	55866476	55866476	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:55866476A>G			NA	NA				BMP5 (126114 upstream) : COL21A1 (54911 downstream)						NA		NA									NA						tgatccgcccacctcggcctc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.55866476A>G		NA		hg19		0.02	-0.157875	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			5	2.40535	KEEP	2	0	0	8	215	AA	0	0	0			3	60	92	0	0	7.473085	11	60	320	41		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	56952297	56952297	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:56952297A>G			NA	NA				KIAA1586 (32274 upstream) : ZNF451 (2510 downstream)						NA		NA									NA						atgagccaccacgcccggccC	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.56952297A>G		NA		hg19		0.02	-0.385893	ACCxCGC	COVERED																																																																																			NOVEL					0			10	3.605523	KEEP	0	0	0	12	318	AA	0.994391	0.91302	0			3	60	107	0	0	7.648262	33	60	978	89		0.083333	0.918171
PRIM2	5558	__UNKNOWN__	__UNKNOWN__	6	57378647	57378647	__UNKNOWN__	Intron	SNP	G	G	A	rs79189912	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:57378647G>A	ENST00000389488.2	+	8	848				PRIM2_ENST00000607273.1_Intron			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	NA		NA			DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gcccactgtggtggtgcacac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143	5558			9370	protein-coding gene	gene with protein product		176636	primase, polypeptide 2A (58kD), primase, polypeptide 2A, 58kDa	PRIM2A	NA	8530050, 20675616	Standard	NM_000947	NM_001282487	NA	Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.848+6292G>A	chr6.hg19:g.57378647G>A		NA	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	hg19		0.02	-0.17543	GTGxTGG	COVERED																																																																																			NOVEL	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000043468.3	9	3.309819	KEEP	0	0	0	11	336	GG	0.993072	0.384723	0		+	5	60	148	0	0	12.869497	11	60	367	40	ENST00000389488.2	0.3125	0.387407
PRIM2	5558	__UNKNOWN__	__UNKNOWN__	6	57410192	57410192	__UNKNOWN__	Intron	SNP	G	G	A	rs62400972	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:57410192G>A	ENST00000389488.2	+	10	1107				PRIM2_ENST00000607273.1_Intron			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	NA		NA			DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		atgacctgaggtcgggagttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143	5558			9370	protein-coding gene	gene with protein product		176636	primase, polypeptide 2A (58kD), primase, polypeptide 2A, 58kDa	PRIM2A	NA	8530050, 20675616	Standard	NM_000947	NM_001282487	NA	Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.1107+11875G>A	chr6.hg19:g.57410192G>A		NA	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	hg19		0.02	-0.175435	GAGxTCG	COVERED																																																																																			NOVEL	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000043468.3	11	3.009361	KEEP	3	0	0	10	322	GG	0.99254	0.384517	0		+	4	60	121	0	0	9.762608	15	60	508	49	ENST00000389488.2	0.210526	0.387407
PRIM2	5558	__UNKNOWN__	__UNKNOWN__	6	57481323	57481323	__UNKNOWN__	Intron	SNP	C	C	A	rs79620288	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:57481323C>A	ENST00000389488.2	+	12	1317				PRIM2_ENST00000607273.1_Intron			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	NA		NA			DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		TTCTTATTGGCACCTCAGCTT	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143	5558			9370	protein-coding gene	gene with protein product		176636	primase, polypeptide 2A (58kD), primase, polypeptide 2A, 58kDa	PRIM2A	NA	8530050, 20675616	Standard	NM_000947	NM_001282487	NA	Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.1317+8882C>A	chr6.hg19:g.57481323C>A		NA	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	hg19		0.02	-0.245618	TGGxACC	COVERED																																																																																			NOVEL	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000043468.3	5	2.407034	KEEP	0	0	0	8	240	CC	0.99257	0.636582	0		+	8	60	247	0	0	21.242005	20	60	661	42	ENST00000389488.2	0.285714	0.641347
PRIM2	5558	__UNKNOWN__	__UNKNOWN__	6	57493774	57493774	__UNKNOWN__	Intron	SNP	C	C	T	rs62404097	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:57493774C>T	ENST00000389488.2	+	13	1317				PRIM2_ENST00000607273.1_Intron			P49643	PRI2_HUMAN	primase, DNA, polypeptide 2 (58kDa)	NA		NA			DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	nucleoplasm (GO:0005654)|primosome complex (GO:1990077)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA primase activity (GO:0003896)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(34)|prostate(6)|stomach(4)|upper_aerodigestive_tract(1)	59				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)		gccaccacacccagccTATTT	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS75476.1, CCDS75477.1	6p12-p11.1	2013-01-31	2007-06-19	2007-06-19	ENSG00000146143	ENSG00000146143	5558			9370	protein-coding gene	gene with protein product		176636	primase, polypeptide 2A (58kD), primase, polypeptide 2A, 58kDa	PRIM2A	NA	8530050, 20675616	Standard	NM_000947	NM_001282487	NA	Approved		uc003pdx.3	P49643	OTTHUMG00000016190	ENST00000389488.2:c.1318-5193C>T	chr6.hg19:g.57493774C>T		NA	Q53FJ8|Q6P1Q7|Q8WVL2|Q9H413	hg19		0.02	-0.438598	CACxCAG	COVERED																																																																																			NOVEL	PRIM2-001	KNOWN	sequence_error|basic	processed_transcript	NA	protein_coding	OTTHUMT00000043468.3	17	2.742008	KEEP	0	1	31	20	612	CC	0.999869	0.959733	0		+	6	60	179	0	0	13.35341	35	60	1175	100	ENST00000389488.2	0.146341	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58141000	58141000	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58141000A>G			NA	NA				RP11-343D24.2 (449355 upstream) : XXbac-BPGBPG55C20.1 (41168 downstream)						NA		NA									NA						aagaagaggaagaagaagaag	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58141000A>G		NA		hg19		0.02	-0.157867	GGAxGAA	UNCOVERED																																																																																			NOVEL					0			8	2.706999	KEEP	4	0	0	9	252	AA	0	0	0			3	60	96	2	0	7.982171	10	60	291	36		0.230769	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58251126	58251126	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58251126A>T			NA	NA				XXbac-BPGBPG55C20.2 (10937 upstream) : LINC00680 (21234 downstream)						NA		NA									NA						atcccagcacattgggaggcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58251126A>T		NA		hg19		0.02	-0.087707	CACxTTG	UNCOVERED																																																																																			NOVEL					0			8	3.908679	KEEP	8	0	0	13	349	AA	0.99254	0.098977	0			3	60	90	0	0	7.778585	7	60	209	32		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777156	58777156	__UNKNOWN__	IGR	SNP	C	C	G	rs4577825	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58777156C>G			NA	NA				RP11-143A22.1 (263296 upstream) : None (None downstream)						NA		NA									NA						agagtgaaacctcccttttca	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777156C>G		NA		hg19		0.02	-0.394764	AACxTCC	COVERED																																																																																			NOVEL					0			11	2.641521	KEEP	0	1	29	19	591	CC	0.999863	0.934364	0			3	60	101	0	0	6.975524	35	60	1191	97		0.078947	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777666	58777666	__UNKNOWN__	IGR	SNP	C	C	G	rs4374848	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58777666C>G			NA	NA				RP11-143A22.1 (263806 upstream) : None (None downstream)						NA		NA									NA						agagtggagtcttccgtttga	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777666C>G		NA		hg19		0.02	1.844706	AGTxTTC	COVERED																																																																																			NOVEL					0			19	6.051974	KEEP	0	1	31	31	951	CC	0.999997	0.990962	0			5	60	172	0	0	12.483281	46	60	1551	130		0.098039	0.990964
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777685	58777685	__UNKNOWN__	IGR	SNP	T	T	C	rs4388320	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58777685T>C			NA	NA				RP11-143A22.1 (263825 upstream) : None (None downstream)						NA		NA									NA						gatagagaagttttgaaaccc	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777685T>C		NA		hg19		0.02	2.040934	AAGxTTT	COVERED																																																																																			NOVEL					0			19	2.670529	KEEP	0	2	54	28	762	TT	0.999997	0.963771	0			4	60	134	0	0	9.531677	39	60	1200	108		0.093023	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58777790	58777790	__UNKNOWN__	IGR	SNP	C	C	G	rs4928379	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58777790C>G			NA	NA				RP11-143A22.1 (263930 upstream) : None (None downstream)						NA		NA									NA						tagaatcattctcagaaacaa	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58777790C>G		NA		hg19		0.02	-0.32458	ATTxTCA	COVERED																																																																																			NOVEL					0			10	4.078557	KEEP	6	2	58	34	1036	CC	0.999998	0.835714	0			3	60	104	0	0	7.426014	31	60	1049	108		0.088235	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58778452	58778452	__UNKNOWN__	IGR	SNP	A	A	C	rs4928629	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58778452A>C			NA	NA				RP11-143A22.1 (264592 upstream) : None (None downstream)						NA		NA									NA						atctttccataaaaggtagac	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58778452A>C		NA		hg19		0.02	1.871171	CATxAAA	COVERED																																																																																			NOVEL					0			22	13.230393	KEEP	1	0	0	44	1182	AA	1	0.986153	0			9	60	296	1	0	25.231479	26	60	753	148		0.257143	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58778637	58778637	__UNKNOWN__	IGR	SNP	A	A	C	rs60156593		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58778637A>C			NA	NA				RP11-143A22.1 (264777 upstream) : None (None downstream)						NA		NA									NA						cagacagaagaattctcagag	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58778637A>C		NA		hg19		0.02	1.874359	AAGxATT	COVERED																																																																																			NOVEL					0			24	5.907655	KEEP	2	3	95	53	1423	AA	1	0.996724	0			4	60	140	0	0	9.590118	54	60	1605	179		0.068966	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	58778888	58778888	__UNKNOWN__	IGR	SNP	C	C	T	rs28763394		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:58778888C>T			NA	NA				RP11-143A22.1 (265028 upstream) : None (None downstream)						NA		NA									NA						ttttgaaaccctctttctgaa	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.58778888C>T		NA		hg19		0.02	1.432312	ACCxTCT	COVERED																																																																																			NOVEL					0			15	11.432576	KEEP	1	0	0	38	1142	CC	1	0.998465	0			4	60	125	0	1	8.031528	56	60	1898	166		0.066667	0.998465
KHDRBS2	202559	__UNKNOWN__	__UNKNOWN__	6	62553549	62553549	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:62553549C>T	ENST00000281156.4	-	6	1089					NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		ggattacaggcgtgagccact	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232	202559			18114	protein-coding gene	gene with protein product	Sam68-like mammalian protein 1	610487			NA		Standard	NM_152688	NM_152688	NA	Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.810+50990G>A	chr6.hg19:g.62553549C>T		NA	A8K7M8|Q8N4I4|Q8TCZ4	hg19	CCDS4963.1	0.02	-0.131572	AGGxGTG	COVERED																																																																																			NOVEL	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041066.2	16	3.008194	KEEP	4	0	0	10	292	CC	0.99254	0.227464	0		-	3	60	95	0	0	8.001143	9	60	277	37	ENST00000281156.4	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	64310639	64310639	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:64310639G>A			NA	NA				PTP4A1 (17147 upstream) : PHF3 (35101 downstream)						NA		NA									NA						cgcctgcctcggcctcccaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.64310639G>A		NA		hg19		0.02	-0.122788	CTCxGCC	COVERED																																																																																			NOVEL					0			18	3.609202	KEEP	12	0	0	12	336	GG	0.992708	0.19488	0			3	60	87	0	0	7.33236	8	60	246	48		0.272727	0.196312
EYS	346007	__UNKNOWN__	__UNKNOWN__	6	65424709	65424709	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:65424709A>G	ENST00000503581.1	-	23	3981				EYS_ENST00000370616.2_Intron|EYS_ENST00000370621.3_Intron	NM_001142800.1	NP_001136272.1	Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	NA		NA			detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						gtgagccaccatgcccggccT	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107	346007			21555	protein-coding gene	gene with protein product		612424	chromosome 6 open reading frame 180, EGF-like-domain, multiple 11, retinitis pigmentosa 25 (autosomal recessive), EGF-like-domain, multiple 10, chromosome 6 open reading frame 178, chromosome 6 open reading frame 179	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179	NA	18836446, 18976725	Standard	XM_294050	NM_001142800	NA	Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000503581.1:c.3444-88571T>C	chr6.hg19:g.65424709A>G		NA	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	hg19	CCDS47445.1	0.02	-0.184156	ACCxTGC	COVERED																																																																																			NOVEL	EYS-012	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359944.1	6	2.706794	KEEP	4	0	0	9	248	AA	0.99257	0.420331	0		-	3	60	104	0	0	8.392	14	60	392	50	ENST00000503581.1	0.176471	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	67740200	67740200	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:67740200C>G			NA	NA				RNU7-66P (301403 upstream) : AL590874.1 (119201 downstream)						NA		NA									NA						ctcccaaagtcctgggattac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.67740200C>G		NA		hg19		0.02	-0.131584	AGTxCTG	COVERED																																																																																			NOVEL					0			4	2.40719	KEEP	0	0	0	8	247	AC	0.99254	0.227464	0			3	60	97	0	0	7.972752	11	60	371	38		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	70289740	70289740	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:70289740A>G			NA	NA				BAI3 (190337 upstream) : AL358133.1 (41524 downstream)						NA		NA									NA						aggctgaggcaggtggatcac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.70289740A>G		NA		hg19		0.02	-0.157866	GGCxGGT	COVERED																																																																																			NOVEL					0			13	4.210541	KEEP	12	0	0	14	394	AA	0.993072	0.32057	0			3	60	92	0	0	7.110526	15	60	443	55		0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	71015060	71015060	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:71015060G>A			NA	NA				COL9A1 (2274 upstream) : RP11-462G2.1 (89529 downstream)						NA		NA									NA						gaggtcaggagttcgagacca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.71015060G>A		NA		hg19		0.02	-0.096488	GGAxTTC	UNCOVERED																																																																																			NOVEL					0			6	2.407469	KEEP	4	0	0	8	255	GG	0	0	0			3	40	84	0	0	7.032093	8	60	274	33		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	73911565	73911565	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:73911565A>G			NA	NA				KCNQ5 (2991 upstream) : RP11-257K9.8 (7903 downstream)						NA		NA									NA						cgtccacctcagcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.73911565A>G		NA		hg19		0.02	-0.192962	CTCxGCC	COVERED																																																																																			NOVEL					0			6	4.211334	KEEP	2	0	0	14	402	AA	0.994391	0.455189	0			3	60	93	0	0	7.292074	14	60	428	58		0.176471	0.457757
MB21D1	115004	__UNKNOWN__	__UNKNOWN__	6	74134840	74134840	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74134840A>T	ENST00000370315.3	-	0	1773				MB21D1_ENST00000370318.1_Intron	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	NA		NA			activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						gcctccaaagagctgggatta	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430	115004			21367	protein-coding gene	gene with protein product		613973	chromosome 6 open reading frame 150	C6orf150	NA		Standard	NM_138441	NM_138441	NA	Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.*110T>A	chr6.hg19:g.74134840A>T		NA	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	hg19	CCDS4978.1	0.02	2.486288	AAGxGCT	COVERED																																																																																			NOVEL	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041221.5	41	10.724264	KEEP	1	3	74	62	1751	AA	1	1	0		-	12	70	337	0	1	21.782999	125	60	3835	305	ENST00000370315.3	0.087591	1
MB21D1	115004	__UNKNOWN__	__UNKNOWN__	6	74138862	74138862	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74138862G>A	ENST00000370315.3	-	4	1209				MB21D1_ENST00000370318.1_Intron	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	NA		NA			activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|lung(1)	6						gcagtgagccgagattgcacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430	115004			21367	protein-coding gene	gene with protein product		613973	chromosome 6 open reading frame 150	C6orf150	NA		Standard	NM_138441	NM_138441	NA	Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1115-328C>T	chr6.hg19:g.74138862G>A		NA	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	hg19	CCDS4978.1	0.02	-0.157702	GCCxAGA	COVERED																																																																																			NOVEL	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041221.5	11	4.210534	KEEP	0	0	0	14	389	GG	0.995343	0.321303	0		-	3	60	88	1	0	6.974615	12	60	332	40	ENST00000370315.3	0.2	0.322807
MTO1	25821	__UNKNOWN__	__UNKNOWN__	6	74212145	74212145	__UNKNOWN__	3'UTR	SNP	C	C	T	rs566492643		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74212145C>T	ENST00000498286.1	+	0	4043							Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	NA		NA			mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						ccagcctgggcgacagagtga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297	25821			19261	protein-coding gene	gene with protein product		614667	mitochondrial translation optimization 1 homolog (S. cerevisiae)		NA	12011058, 22608499	Standard	NM_012123	NM_012123	NA	Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000498286.1:c.*1687C>T	chr6.hg19:g.74212145C>T		NA	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	hg19	CCDS34485.1	0.02	2.782239	GGGxGAC	COVERED																																																																																			NOVEL	MTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041213.3	32	4.37643	KEEP	9	5	128	60	1823	CC	1	0.999978	0		+	8	60	228	0	0	14.635483	89	60	2956	253	ENST00000498286.1	0.082474	0.999978
MTO1	25821	__UNKNOWN__	__UNKNOWN__	6	74214885	74214885	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74214885C>T	ENST00000498286.1	+	0	6783							Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	NA		NA			mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						ccagcctgggcaacagagcaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297	25821			19261	protein-coding gene	gene with protein product		614667	mitochondrial translation optimization 1 homolog (S. cerevisiae)		NA	12011058, 22608499	Standard	NM_012123	NM_012123	NA	Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000498286.1:c.*4427C>T	chr6.hg19:g.74214885C>T		NA	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	hg19	CCDS34485.1	0.02	2.8459	GGGxAAC	COVERED																																																																																			NOVEL	MTO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041213.3	21	5.245008	KEEP	2	4	91	50	1480	CC	1	0.999989	0		+	6	60	170	1	1	10.218422	87	60	2845	221	ENST00000498286.1	0.064516	0.999989
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	74221316	74221316	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74221316T>C			NA	NA				MTO1 (2357 upstream) : EEF1A1 (4156 downstream)						NA		NA									NA						tcgagaccagtctggccaaca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.74221316T>C		NA		hg19		0.02	-0.149114	CAGxCTG	COVERED																																																																																			NOVEL					0			9	2.706491	KEEP	1	0	0	9	248	TT	0.99257	0.289832	0			4	60	143	0	0	12.431229	11	60	334	33		0.266667	0.292001
RP11-505P4.7	0	__UNKNOWN__	__UNKNOWN__	6	74234864	74234864	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74234864A>G	ENST00000429386.1	+	0	159				RP11-505P4.7_ENST00000431108.1_RNA						NA		NA									NA						gattacaggcatgagccacca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000429386.1:	chr6.hg19:g.74234864A>G		NA		hg19		0.02	-0.228052	GGCxTGA	COVERED																																																																																			NOVEL	RP11-505P4.7-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000316071.2	8	3.308501	KEEP	1	0	0	11	305	AA	0.993072	0.578892	0		+	3	60	99	0	0	7.349125	22	60	675	59	ENST00000429386.1	0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	74283001	74283001	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74283001A>G			NA	NA				RP11-505P4.7 (2682 upstream) : SLC17A5 (20100 downstream)						NA		NA									NA						gctcatgcctataatcccagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.74283001A>G		NA		hg19		0.02	-0.219267	CCTxTAA	COVERED																																																																																			NOVEL					0			8	2.706936	KEEP	1	0	0	9	250	AA	0.99254	0.548763	0			3	60	104	0	0	8.026811	19	60	562	51		0.136364	0.552887
SLC17A5	26503	__UNKNOWN__	__UNKNOWN__	6	74306940	74306940	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74306940T>C	ENST00000355773.5	-	11	1619					NM_012434.4	NP_036566.1	Q9NRA2	S17A5_HUMAN	solute carrier family 17 (acidic sugar transporter), member 5	NA		NA			amino acid transport (GO:0006865)|anion transport (GO:0006820)|ion transport (GO:0006811)|proton transport (GO:0015992)|sialic acid transport (GO:0015739)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	sialic acid transmembrane transporter activity (GO:0015136)|sugar:proton symporter activity (GO:0005351)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						cctgtaatcctagcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ387747	CCDS4981.1	6q13	2013-07-18	2013-07-18		ENSG00000119899	ENSG00000119899	26503		Solute carriers	10933	protein-coding gene	gene with protein product		604322	sialic acid storage disease, solute carrier family 17 (anion/sugar transporter), member 5	SIASD	NA	10581036, 8198127	Standard		NM_012434	NA	Approved	AST, SD, ISSD, NSD, SIALIN, SLD	uc003phn.4	Q9NRA2	OTTHUMG00000015039	ENST00000355773.5:c.1351-2003A>G	chr6.hg19:g.74306940T>C		NA	Q5SZ76|Q8NBR5|Q9UGH0	hg19	CCDS4981.1	0.02	-0.219269	TCCxAGC	COVERED																																																																																			NOVEL	SLC17A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041228.1	9	3.007273	KEEP	0	0	0	10	273	TT	0.992708	0.548856	0		-	4	60	133	0	1	10.594642	19	60	559	50	ENST00000355773.5	0.173913	0.552887
SLC17A5	26503	__UNKNOWN__	__UNKNOWN__	6	74321240	74321240	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74321240C>T	ENST00000355773.5	-	9	1380				SLC17A5_ENST00000393019.3_Intron	NM_012434.4	NP_036566.1	Q9NRA2	S17A5_HUMAN	solute carrier family 17 (acidic sugar transporter), member 5	NA		NA			amino acid transport (GO:0006865)|anion transport (GO:0006820)|ion transport (GO:0006811)|proton transport (GO:0015992)|sialic acid transport (GO:0015739)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	sialic acid transmembrane transporter activity (GO:0015136)|sugar:proton symporter activity (GO:0005351)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						tgacctcaagcgatccaccca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ387747	CCDS4981.1	6q13	2013-07-18	2013-07-18		ENSG00000119899	ENSG00000119899	26503		Solute carriers	10933	protein-coding gene	gene with protein product		604322	sialic acid storage disease, solute carrier family 17 (anion/sugar transporter), member 5	SIASD	NA	10581036, 8198127	Standard		NM_012434	NA	Approved	AST, SD, ISSD, NSD, SIALIN, SLD	uc003phn.4	Q9NRA2	OTTHUMG00000015039	ENST00000355773.5:c.1112-970G>A	chr6.hg19:g.74321240C>T		NA	Q5SZ76|Q8NBR5|Q9UGH0	hg19	CCDS4981.1	0.02	-0.236802	AAGxGAT	COVERED																																																																																			NOVEL	SLC17A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041228.1	6	2.407197	KEEP	0	0	0	8	246	CC	0.99257	0.607857	0		-	4	60	115	0	0	8.492818	23	60	771	49	ENST00000355773.5	0.148148	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	74585438	74585438	__UNKNOWN__	IGR	SNP	C	C	G	rs140040754	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:74585438C>G			NA	NA				CD109 (47398 upstream) : RP11-554D15.1 (193728 downstream)						NA		NA									NA						gtcaggagatcgagaccatcc	0.512		NA											C|||	145	0.0289537	0.1029	0.0086	5008	,	,	NA	14035	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.74585438C>G		NA		hg19		0.02	-0.078957	GATxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.405448	KEEP	0	0	0	8	222	CC	0.99257	0.076761	0			3	30	108	0	0	9.932857	5	60	174	27		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	76270641	76270641	__UNKNOWN__	IGR	SNP	A	A	G	rs374038922		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76270641A>G			NA	NA				FILIP1 (67187 upstream) : RNU6-1338P (32129 downstream)						NA		NA									NA						aagaagaagaagaagaagaag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.76270641A>G		NA		hg19		0.02	-0.27191	AGAxGAA	COVERED																																																																																			NOVEL					0			11	4.51145	KEEP	2	0	0	15	417	AA	0.99649	0.714798	0			3	37	104	0	0	7.848644	22	60	676	69		0.12	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	76291709	76291709	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76291709C>G			NA	NA				FILIP1 (88255 upstream) : RNU6-1338P (11061 downstream)						NA		NA									NA						aaagtgctggcattacaggca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.76291709C>G		NA		hg19		0.02	-0.140365	TGGxATT	COVERED																																																																																			NOVEL					0			5	2.407533	KEEP	0	0	0	8	258	CC	0.99257	0.289832	0			3	60	100	0	0	8.381687	10	60	347	38		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	76303427	76303427	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76303427A>G			NA	NA				RNU6-1338P (566 upstream) : SENP6 (7797 downstream)						NA		NA									NA						ttgggaggccaaggtgggctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.76303427A>G		NA		hg19		0.02	-0.210491	GCCxAGG	COVERED																																																																																			NOVEL					0			13	4.811273	KEEP	2	0	0	16	431	AA	0.99649	0.520328	0			3	60	99	0	0	7.592235	18	60	528	54		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	76304052	76304052	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76304052T>C			NA	NA				RNU6-1338P (1191 upstream) : SENP6 (7172 downstream)						NA		NA									NA						agcaagactctgtctcaaaaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.76304052T>C		NA		hg19		0.02	-0.18419	CTCxGTC	COVERED																																																																																			NOVEL					0			11	2.707186	KEEP	4	0	0	9	253	TT	0.99257	0.420331	0			3	55	101	1	0	7.933303	16	60	482	53		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	76306399	76306399	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76306399T>C			NA	NA				RNU6-1338P (3538 upstream) : SENP6 (4825 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.76306399T>C		NA		hg19		0.02	-0.236821	AATxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.405712	KEEP	1	0	0	8	215	TT	0	0	0			3	60	99	0	0	7.592156	18	60	543	53		0.142857	0.612407
SENP6	26054	__UNKNOWN__	__UNKNOWN__	6	76389099	76389099	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76389099T>G	ENST00000447266.2	+	16	2553				SENP6_ENST00000370014.3_Intron|SENP6_ENST00000370010.2_Intron|SENP6_ENST00000541192.1_Intron	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	NA		NA			protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				tccagcctggtcaacaaagca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701	26054			20944	protein-coding gene	gene with protein product		605003	SUMO1/sentrin specific protease 6		NA		Standard	NM_015571	NM_015571	NA	Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.2075+456T>G	chr6.hg19:g.76389099T>G		NA	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	hg19	CCDS47454.1	0.02	3.882665	TGGxCAA	COVERED																																																																																			NOVEL	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041272.2	25	6.810367	KEEP	0	3	89	54	1452	TT	1	0.999973	0		+	9	60	306	0	1	22.23927	80	60	2308	234	ENST00000447266.2	0.101124	0.999973
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	76456768	76456768	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76456768T>C			NA	NA				SENP6 (28771 upstream) : MYO6 (2140 downstream)						NA		NA									NA						gtggctcacgtctgtaatccc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.76456768T>C		NA		hg19		0.02	-0.254328	ACGxCTG	COVERED																																																																																			NOVEL					0			11	4.812107	KEEP	2	0	0	16	440	TT	0.995343	0.66541	0			3	60	103	0	0	8.060965	17	60	500	68		0.15	0.668523
MYO6	4646	__UNKNOWN__	__UNKNOWN__	6	76573492	76573492	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:76573492T>C	ENST00000369977.3	+	16	1813				MYO6_ENST00000369985.4_Intron|MYO6_ENST00000369975.1_Intron|MYO6_ENST00000369981.3_Intron	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	NA		NA			actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		tgagccaccgtgcccggcTCA	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586	4646		Myosins / Myosin superfamily : Class VI	7605	protein-coding gene	gene with protein product		600970	deafness, autosomal recessive 37	DFNA22, DFNB37	NA	9259267, 11468689	Standard	NM_004999	XM_005248719	NA	Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.1674+1052T>C	chr6.hg19:g.76573492T>C		NA	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	hg19	CCDS34487.1	0.02	-0.140329	CCGxGCC	COVERED																																																																																			NOVEL	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041279.2	6	2.406061	KEEP	0	0	0	8	220	TT	0.99257	0.259026	0		+	3	60	105	0	0	8.672264	12	60	349	31	ENST00000369977.3	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	77358299	77358299	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:77358299T>C			NA	NA				RP11-35J1.1 (54959 upstream) : RP11-354K4.2 (126400 downstream)						NA		NA									NA						gtcaggagattgagaccatcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.77358299T>C		NA		hg19		0.02	-0.131555	GATxGAG	UNCOVERED																																																																																			NOVEL					0			7	2.704457	KEEP	4	0	0	9	229	TT	0	0	0			3	40	92	0	0	7.582111	10	60	295	33		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	78061326	78061326	__UNKNOWN__	IGR	SNP	G	G	A	rs375951040		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:78061326G>A			NA	NA				RP11-354K4.2 (575749 upstream) : HTR1B (110621 downstream)						NA		NA									NA						ctgtaatcccggcactttggg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.78061326G>A		NA		hg19		0.02	-0.122798	CCCxGCA	COVERED																																																																																			NOVEL					0			6	3.609536	KEEP	0	0	0	12	343	GG	0.993634	0.195062	0			4	60	114	0	0	9.823142	9	60	306	39		0.307692	0.196312
IRAK1BP1	134728	__UNKNOWN__	__UNKNOWN__	6	79597210	79597210	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:79597210A>G	ENST00000369940.2	+	2	486				IRAK1BP1_ENST00000607739.1_Intron	NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	NA		NA			I-kappaB kinase/NF-kappaB signaling (GO:0007249)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(3)	12		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		gtgaaaccccatctctactaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AI478629	CCDS34488.1	6q14-q15	2006-04-12				ENSG00000146243	134728			17368	protein-coding gene	gene with protein product		615375			NA	11096118	Standard	XM_059729	XM_005248654	NA	Approved	AIP70, SIMPL	uc003pim.4	Q5VVH5		ENST00000369940.2:c.381+2050A>G	chr6.hg19:g.79597210A>G		NA		hg19	CCDS34488.1	0.02	-0.087706	CCCxTCT	UNCOVERED																																																																																			NOVEL	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041296.2	5	2.405191	KEEP	5	0	0	8	208	AA	0.99257	0.09898	0		+	3	60	97	0	0	8.643804	6	60	175	29	ENST00000369940.2	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	80707097	80707097	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:80707097A>G			NA	NA				ELOVL4 (49800 upstream) : TTK (6506 downstream)						NA		NA									NA						tgtaatcccaactacttgaga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.80707097A>G		NA		hg19		0.02	-0.114011	CCAxCTA	UNCOVERED																																																																																			NOVEL					0			4	2.405577	KEEP	0	0	0	8	216	AA	0.99257	0.16126	0			3	60	86	0	0	7.101202	9	60	270	28		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	83146437	83146437	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:83146437G>A			NA	NA				TPBG (65892 upstream) : UBE3D (455679 downstream)						NA		NA									NA						tcaagagttcgagaccagcct	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.83146437G>A		NA		hg19		0.02	-0.078947	TTCxAGA	UNCOVERED																																																																																			NOVEL					0			8	3.008448	KEEP	2	0	0	10	293	GG	0.992708	0.098994	0			3	60	94	0	0	8.343409	6	60	195	29		0.333333	0.099721
UBE3D	90025	__UNKNOWN__	__UNKNOWN__	6	83607081	83607081	__UNKNOWN__	Intron	SNP	G	G	C	rs550480453	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:83607081G>C	ENST00000369747.3	-	10	1272					NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	NA		NA			protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)				NA						aggctgaggtgggtggatcac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420	90025			21381	protein-coding gene	gene with protein product	UBCH10 binding protein with a hect-like domain	612495	chromosome 6 open reading frame 157, ubiquitin-conjugating enzyme E2C binding protein	C6orf157, UBE2CBP	NA	15749827	Standard	NM_198920	NM_198920	NA	Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1150-4320C>G	chr6.hg19:g.83607081G>C		NA	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	hg19	CCDS34491.1	0.02	-0.122813	GGTxGGT	COVERED																																																																																			NOVEL	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041347.7	11	3.309966	KEEP	4	0	0	11	340	GG	0.99254	0.194847	0		-	3	40	98	0	0	8.181776	10	60	332	39	ENST00000369747.3	0.230769	0.196312
UBE3D	90025	__UNKNOWN__	__UNKNOWN__	6	83607092	83607092	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:83607092C>T	ENST00000369747.3	-	10	1272					NM_198920.1	NP_944602.1	Q7Z6J8	UBE3D_HUMAN	ubiquitin protein ligase E3D	NA		NA			protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)				NA						ggtggatcacctgaggtcagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137544	CCDS34491.1	6q15	2012-02-24	2012-02-24	2012-02-24	ENSG00000118420	ENSG00000118420	90025			21381	protein-coding gene	gene with protein product	UBCH10 binding protein with a hect-like domain	612495	chromosome 6 open reading frame 157, ubiquitin-conjugating enzyme E2C binding protein	C6orf157, UBE2CBP	NA	15749827	Standard	NM_198920	NM_198920	NA	Approved	DKFZp434A1520, H10BH, YJR141W	uc003pjp.2	Q7Z6J8	OTTHUMG00000015108	ENST00000369747.3:c.1150-4331G>A	chr6.hg19:g.83607092C>T		NA	B4DP63|Q5T4W2|Q6IPR4|Q75UG0|Q9NT42	hg19	CCDS34491.1	0.02	-0.09649	CACxTGA	UNCOVERED																																																																																			NOVEL	UBE3D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041347.7	10	3.309346	KEEP	4	0	0	11	333	CC	0.99257	0.119541	0		-	3	40	92	0	0	7.978401	7	60	231	30	ENST00000369747.3	0.3	0.120436
DOPEY1	23033	__UNKNOWN__	__UNKNOWN__	6	83858128	83858128	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:83858128A>G	ENST00000349129.2	+	27	5992				DOPEY1_ENST00000369739.3_Intron|DOPEY1_ENST00000237163.5_Intron|DOPEY1_ENST00000484282.1_Intron	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	NA		NA			protein transport (GO:0015031)					breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		gtgagactccatctcaaaaaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097	23033			21194	protein-coding gene	gene with protein product		NA	KIAA1117	KIAA1117	NA	16301316, 16303751, 10931277	Standard	NM_015018	NM_015018	NA	Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.5733-350A>G	chr6.hg19:g.83858128A>G		NA	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	hg19	CCDS4996.1	0.02	-0.104523	TCCxTCT	UNCOVERED																																																																																			NOVEL	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043785.2	5	2.405027	KEEP	0	0	0	8	208	AA	0.99257	0.138793	0		+	3	60	77	0	0	6.322775	8	60	243	24	ENST00000349129.2	0.272727	0.139832
SNX14	57231	__UNKNOWN__	__UNKNOWN__	6	86298916	86298916	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:86298916C>T	ENST00000314673.3	-	1	317				RP11-321N4.5_ENST00000503906.1_Intron|SNX14_ENST00000346348.3_Intron|SNX14_ENST00000369627.2_Intron|SNX14_ENST00000505648.1_Intron|SNX14_ENST00000513865.1_Intron	NM_153816.3	NP_722523.1	Q9Y5W7	SNX14_HUMAN	sorting nexin 14	NA		NA			protein transport (GO:0015031)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)	phosphatidylinositol binding (GO:0035091)			NS(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(11)|skin(1)	22		all_cancers(76;4.83e-07)|Acute lymphoblastic leukemia(125;3.3e-08)|Prostate(29;2.55e-07)|all_hematologic(105;3.66e-05)|all_epithelial(107;0.000695)|Lung NSC(302;0.197)|all_lung(197;0.24)		BRCA - Breast invasive adenocarcinoma(108;0.0423)		gccatattgtctactgtcaat	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121863	CCDS5003.1, CCDS5004.1, CCDS75490.1	6q15	2008-10-22			ENSG00000135317	ENSG00000135317	57231		Sorting nexins	14977	protein-coding gene	gene with protein product		NA			NA	11485546, 11736640	Standard	NM_153816	XM_005248738	NA	Approved	RGS-PX2	uc003pkr.3	Q9Y5W7	OTTHUMG00000015140	ENST00000314673.3:c.140+4380G>A	chr6.hg19:g.86298916C>T		NA	B4DI55|Q4VBR3|Q5TCF9|Q5TCG0|Q6NUI7|Q6PI37|Q9BSD1	hg19	CCDS5004.1	0.02	4.658179	TGTxTAC	COVERED																																																																																			NOVEL	SNX14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041393.2	170	70.996823	KEEP	0	0	0	236	6993	CC	1	1	0		-	8	60	225	1	0	11.312291	220	60	7155	655	ENST00000314673.3	0.035088	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	86380661	86380661	__UNKNOWN__	IGR	SNP	G	G	C	rs542594324		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:86380661G>C			NA	NA				SYNCRIP (27658 upstream) : SNHG5 (6350 downstream)						NA		NA									NA						ctcagcctccggagtagctgg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.86380661G>C		NA		hg19		0.02	-0.280702	TCCxGAG	COVERED																																																																																			NOVEL					0			9	2.639033	KEEP	0	1	26	18	520	GG	0.999863	0.73957	0			3	60	102	0	0	7.397519	27	60	870	67		0.1	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	87116658	87116658	__UNKNOWN__	IGR	SNP	A	A	G	rs573044781	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:87116658A>G			NA	NA				RNU4-12P (413781 upstream) : RN7SL643P (28911 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.428		NA											A|||	2	0.000399361	0.0	0.0	5008	,	,	NA	16102	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.87116658A>G		NA		hg19		0.02	-0.15787	GGCxTGA	COVERED																																																																																			NOVEL					0			8	3.306678	KEEP	6	0	0	11	294	AA	0.99254	0.320398	0			3	60	103	0	0	8.378882	13	60	377	45		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	87116667	87116667	__UNKNOWN__	IGR	SNP	C	C	T	rs540177486		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:87116667C>T			NA	NA				RNU4-12P (413790 upstream) : RN7SL643P (28902 downstream)						NA		NA									NA						catgagccaccgcgcctggcc	0.438		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16274	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.87116667C>T		NA		hg19		0.02	-0.131571	CACxGCG	UNCOVERED																																																																																			NOVEL					0			7	2.707508	KEEP	5	0	0	9	267	CC	0	0	0			3	60	90	0	0	7.501118	9	60	283	39		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	87614923	87614923	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:87614923C>T			NA	NA				AL391417.1 (431610 upstream) : HTR1E (32100 downstream)						NA		NA									NA						gaggctgaggcgggcagatca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.87614923C>T		NA		hg19		0.02	-0.087713	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			7	2.707825	KEEP	2	0	0	9	271	CC	0.99254	0.098977	0			3	60	83	0	0	7.242838	6	60	206	30		0.333333	0.099721
HTR1E	3354	__UNKNOWN__	__UNKNOWN__	6	87717343	87717343	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:87717343T>A	ENST00000305344.5	+	2	518					NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	NA		NA			adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	ccacaaaaaatttaaaaTTTT	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830	3354		5-HT (serotonin) receptors, GPCR / Class A : 5-HT (serotonin) receptors, GPCR only	5291	protein-coding gene	gene with protein product		182132	5-hydroxytryptamine (serotonin) receptor 1E		NA	1608964	Standard	NM_000865	NM_000865	NA	Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.-185-7525T>A	chr6.hg19:g.87717343T>A		NA	E1P503|Q9P1Y1	hg19	CCDS5006.1	0.02	-0.061401	AAAxTTA	UNCOVERED																																																																																			NOVEL	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000472488.2	2	2.404877	KEEP	0	0	0	8	210	TT	0.99257	0.043461	0		+	6	60	188	0	0	21.660691	0	0	0	20	ENST00000305344.5	1	0.043787
C6orf165	154313	__UNKNOWN__	__UNKNOWN__	6	88144486	88144486	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:88144486A>G	ENST00000507897.1	+	11	1383				C6ORF165_ENST00000369562.4_Intron			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	NA		NA								NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		aaagtgctggaattacaggcg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204	154313			21405	protein-coding gene	gene with protein product		NA			NA		Standard	NM_178823	NM_001031743	NA	Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1301-92A>G	chr6.hg19:g.88144486A>G		NA	A8K969|E1P507|Q8N9U4	hg19	CCDS34498.1	0.02	-0.157858	TGGxATT	COVERED																																																																																			NOVEL	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000470406.1	8	2.707447	KEEP	2	0	0	9	258	AA	0.99257	0.320408	0		+	3	60	88	0	0	6.8795	13	60	380	41	ENST00000507897.1	0.1875	0.322807
ORC3	23595	__UNKNOWN__	__UNKNOWN__	6	88372107	88372107	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:88372107A>G	ENST00000257789.4	+	17	1728				ORC3_ENST00000417380.2_Intron|ORC3_ENST00000392844.3_Intron|ORC3_ENST00000546266.1_Intron			Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	NA		NA			DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						ccgagattgcaccactgcact	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336	23595			8489	protein-coding gene	gene with protein product		604972	origin recognition complex, subunit 3 (yeast homolog)-like, origin recognition complex, subunit 3-like (yeast), origin recognition complex, subunit 3 honolog (yeast)	ORC3L	NA	9829972, 10402192	Standard		NM_181837	NA	Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000257789.4:c.1695-614A>G	chr6.hg19:g.88372107A>G		NA	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	hg19	CCDS5012.1	0.02	-0.131473	TGCxCCA	COVERED																																																																																			NOVEL	ORC3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286374.1	5	3.308154	KEEP	1	0	0	11	300	AA	0.992708	0.227502	0		+	3	60	99	0	0	8.174126	11	60	317	34	ENST00000257789.4	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	88383309	88383309	__UNKNOWN__	IGR	SNP	A	A	C	rs1186179		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:88383309A>C			NA	NA				ORC3 (6140 upstream) : AKIRIN2 (1480 downstream)						NA		NA									NA						gcctgtaatcacagcactttg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.88383309A>C		NA		hg19		0.02	-0.131553	ATCxCAG	UNCOVERED																																																																																			NOVEL					0			3	2.706529	KEEP	3	0	0	9	245	AA	0	0	0			3	60	92	0	0	7.582221	10	60	294	36		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	89795623	89795623	__UNKNOWN__	IGR	SNP	G	G	A	rs543149212		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:89795623G>A			NA	NA				PNRC1 (744 upstream) : RN7SL336P (5041 downstream)						NA		NA									NA						gatggatcacgaggtcaggag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.89795623G>A		NA		hg19		0.02	-0.157844	CACxAGG	COVERED																																																																																			NOVEL					0			8	2.406846	KEEP	0	0	0	8	238	GG	0.99257	0.320408	0			3	60	85	0	0	6.579729	13	60	412	40		0.1875	0.322807
SRSF12	135295	__UNKNOWN__	__UNKNOWN__	6	89825297	89825297	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:89825297A>G	ENST00000452027.2	-	1	259					NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	NA		NA			cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						caccgcgcccagccTTATATT	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548	135295		Serine/arginine-rich splicing factors, RNA binding motif (RRM) containing	21220	protein-coding gene	gene with protein product	splicing factor, arginine/serine-rich 19, SR splicing factor 12	NA	splicing factor, arginine/serine-rich 13B	SFRS13B	NA	11684676, 20516191	Standard	NM_080743	NM_080743	NA	Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.65+2244T>C	chr6.hg19:g.89825297A>G		NA	B2RA22|Q5T7K0|Q8WW25	hg19	CCDS47459.1	0.02	-0.192939	CCCxGCC	COVERED																																																																																			NOVEL	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041474.2	5	2.705162	KEEP	0	0	0	9	237	AA	0.99254	0.454342	0		-	4	60	131	0	0	10.569009	17	60	496	42	ENST00000452027.2	0.190476	0.457757
LYRM2	57226	__UNKNOWN__	__UNKNOWN__	6	90346590	90346590	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:90346590A>G	ENST00000520441.1	-	2	221				LYRM2_ENST00000523377.1_3'UTR|LYRM2_ENST00000517396.1_5'UTR			Q9NU23	LYRM2_HUMAN	LYR motif containing 2	NA		NA				mitochondrion (GO:0005739)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(76;2.76e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;3.72e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0131)		agtagagatgaggtttcacca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009782	CCDS5023.1	6q15	2006-09-19			ENSG00000083099	ENSG00000083099	57226		LYR motif containing	25229	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_020466	NM_020466	NA	Approved	DJ122O8.2	uc003pnm.3	Q9NU23	OTTHUMG00000015203	ENST00000520441.1:c.203+853T>C	chr6.hg19:g.90346590A>G		NA	B2R4U2|E1P517	hg19		0.02	-0.403469	ATGxGGT	COVERED																																																																																			NOVEL	LYRM2-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000375696.1	1	2.839359	KEEP	2	1	27	19	533	AA	0.99986	0.934361	0		-	4	60	121	1	0	8.234184	39	60	1200	79	ENST00000520441.1	0.093023	0.934492
MDN1	23195	__UNKNOWN__	__UNKNOWN__	6	90506049	90506049	__UNKNOWN__	Intron	SNP	A	A	C	rs55721734|rs56001734		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:90506049A>C	ENST00000369393.3	-	3	445				MDN1_ENST00000428876.1_Intron			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	NA		NA			ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		gtctcaaaaaaaaaaaaaaaa	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159	23195			18302	protein-coding gene	gene with protein product		NA			NA	9205841, 12102729	Standard		XM_005248699	NA	Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.330-1529T>G	chr6.hg19:g.90506049A>C		NA	O15019|Q5T794	hg19	CCDS5024.1	0.02	-0.052621	AAAxAAA	UNCOVERED																																																																																			NOVEL	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041514.2	12	2.706388	KEEP	7	0	0	9	242	AA	0	0	0		-	2	49	70	1	1	6.493161	3	60	84	24	ENST00000369393.3	0.4	0.036766
MDN1	23195	__UNKNOWN__	__UNKNOWN__	6	90521983	90521983	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:90521983G>A	ENST00000369393.3	-	1	218				MDN1_ENST00000428876.1_Intron			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	NA		NA			ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		gattacaggcgtgagccaccg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159	23195			18302	protein-coding gene	gene with protein product		NA			NA	9205841, 12102729	Standard		XM_005248699	NA	Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.102+7241C>T	chr6.hg19:g.90521983G>A		NA	O15019|Q5T794	hg19	CCDS5024.1	0.02	-0.192964	GGCxTGA	COVERED																																																																																			NOVEL	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041514.2	6	3.308804	KEEP	0	0	0	11	317	GG	0.993072	0.454585	0		-	3	51	87	0	0	6.393079	18	60	566	47	ENST00000369393.3	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	91026854	91026854	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:91026854T>C			NA	NA				MIR4464 (4302 upstream) : RP1-45N11.1 (28083 downstream)						NA		NA									NA						gctgggattataggtgtgagc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.91026854T>C		NA		hg19		0.02	-0.131545	TTAxAGG	COVERED																																																																																			NOVEL					0			8	2.706873	KEEP	1	0	0	9	248	TT	0.99254	0.227464	0			3	60	100	0	0	8.273145	11	60	310	33		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	94646623	94646623	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:94646623G>A			NA	NA				RP11-524K14.1 (47495 upstream) : RP3-463P15.1 (227014 downstream)						NA		NA									NA						taatcccagcgctttgggagg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.94646623G>A		NA		hg19		0.02	-0.228084	AGCxCTT	COVERED																																																																																			NOVEL					0			6	3.007039	KEEP	3	0	0	10	282	GG	0.99257	0.578599	0			3	60	90	0	0	6.506253	21	60	723	61		0.125	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	96670680	96670680	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:96670680T>G			NA	NA				FUT9 (7192 upstream) : RN7SL797P (59762 downstream)						NA		NA									NA						gtagagacggtgtttcaccgt	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.96670680T>G		NA		hg19		0.02	-0.105234	CGGxGTT	UNCOVERED																																																																																			NOVEL					0			6	2.404632	KEEP	1	0	0	8	205	AT	0.99257	0.16126	0			3	51	89	0	0	7.53261	8	60	230	27		0.272727	0.162467
GPR63	81491	__UNKNOWN__	__UNKNOWN__	6	97245090	97245090	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:97245090A>G	ENST00000229955.3	-	0	2863					NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		ctgggtggcaaagcgagactc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218	81491		GPCR / Class A : Orphans	13302	protein-coding gene	gene with protein product		606915			NA		Standard		NM_030784	NA	Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.*1258T>C	chr6.hg19:g.97245090A>G		NA	Q9UJH3	hg19	CCDS5036.1	0.02	-0.061393	GCAxAGC	UNCOVERED																																																																																			NOVEL	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041566.2	4	2.404498	KEEP	0	0	0	8	208	AA	0.99257	0.043461	0		-	2	60	69	0	0	6.650328	2	60	57	20	ENST00000229955.3	0.5	0.043787
MMS22L	253714	__UNKNOWN__	__UNKNOWN__	6	97723132	97723132	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:97723132T>C	ENST00000275053.4	-	5	606				MMS22L_ENST00000369251.2_Intron	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	NA		NA			double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						Tggccgggcatggtggctcac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263	253714			21475	protein-coding gene	gene with protein product		615614	chromosome 6 open reading frame 167	C6orf167	NA	21055983, 21055984	Standard	NM_198468	NM_198468	NA	Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.341-2194A>G	chr6.hg19:g.97723132T>C		NA	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	hg19	CCDS5039.1	0.02	-0.114003	GCAxGGT	UNCOVERED																																																																																			NOVEL	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041573.3	4	2.405242	KEEP	0	0	0	8	219	TT	0.99257	0.16126	0		-	3	60	88	0	0	7.432524	8	60	227	30	ENST00000275053.4	0.272727	0.162467
USP45	85015	__UNKNOWN__	__UNKNOWN__	6	99931488	99931488	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:99931488G>A	ENST00000327681.6	-	8	1247				USP45_ENST00000500704.2_Intron|USP45_ENST00000472914.2_Intron|USP45_ENST00000369233.2_Intron|USP45_ENST00000329966.6_Intron|USP45_ENST00000392738.2_Intron	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	NA		NA			protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		gccgaggcgggtggatcatga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552	85015		Ubiquitin-specific peptidases	20080	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 45		NA	12838346	Standard	NM_032929	NM_001080481	NA	Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.715-729C>T	chr6.hg19:g.99931488G>A		NA	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	hg19	CCDS34501.1	0.02	-0.149112	CGGxTGG	UNCOVERED																																																																																			NOVEL	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041609.2	9	3.007024	KEEP	11	0	0	10	290	GG	0	0	0		-	3	44	90	0	0	6.991992	14	60	467	48	ENST00000327681.6	0.176471	0.292001
USP45	85015	__UNKNOWN__	__UNKNOWN__	6	99954455	99954455	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:99954455A>G	ENST00000327681.6	-	4	910				USP45_ENST00000369232.2_Intron|USP45_ENST00000500704.2_Intron|USP45_ENST00000369231.3_Intron|USP45_ENST00000472914.2_Intron|USP45_ENST00000369233.2_Intron|USP45_ENST00000329966.6_Intron|USP45_ENST00000392738.2_Intron	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	NA		NA			protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		taagtgctggaattacaggtg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552	85015		Ubiquitin-specific peptidases	20080	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 45		NA	12838346	Standard	NM_032929	NM_001080481	NA	Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.377+848T>C	chr6.hg19:g.99954455A>G		NA	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	hg19	CCDS34501.1	0.02	-0.0614	TGGxATT	UNCOVERED																																																																																			NOVEL	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041609.2	10	2.405929	KEEP	0	0	0	8	218	AA	0.99257	0.043461	0		-	3	60	102	0	0	9.555442	4	60	120	19	ENST00000327681.6	0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	100279697	100279697	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:100279697A>G			NA	NA				Y_RNA (189474 upstream) : MCHR2 (88088 downstream)						NA		NA									NA						tagccaggatagtctcgatct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.100279697A>G		NA		hg19		0.02	-0.175418	GATxGTC	COVERED																																																																																			NOVEL					0			7	2.705954	KEEP	4	0	0	9	237	AA	0.99257	0.384528	0			3	60	91	1	0	6.93383	16	60	480	47		0.157895	0.387407
MCHR2	84539	__UNKNOWN__	__UNKNOWN__	6	100367882	100367882	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:100367882A>G	ENST00000281806.2	-	0	2271					NM_001040179.1	NP_001035269.1	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	39		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		gattacaggcatgagccactg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF347063	CCDS5044.1	6q16	2012-08-08	2006-02-15	2006-02-15	ENSG00000152034	ENSG00000152034	84539		GPCR / Class A : MCH receptors	20867	protein-coding gene	gene with protein product		606111	G protein-coupled receptor 145	GPR145	NA	11355873, 11274220	Standard	NM_032503	NM_032503	NA	Approved	SLT, MCH2, MCH2R	uc003pqi.1	Q969V1	OTTHUMG00000015270	ENST00000281806.2:c.*934T>C	chr6.hg19:g.100367882A>G		NA	B3KVW4|E1P5D7|Q5VTV7|Q6Q377|Q9BXA8	hg19	CCDS5044.1	0.02	-0.359568	GGCxTGA	COVERED																																																																																			NOVEL	MCHR2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041620.2	7	2.538166	KEEP	0	1	30	19	521	AA	0.999863	0.888753	0		-	3	60	101	0	0	7.011968	34	60	992	81	ENST00000281806.2	0.081081	0.888875
MCHR2-AS1	728012	__UNKNOWN__	__UNKNOWN__	6	100505589	100505589	__UNKNOWN__	RNA	SNP	C	C	A	rs9496338	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:100505589C>A	ENST00000430122.2	+	0	352				MCHR2-AS1_ENST00000451220.2_RNA|MCHR2-AS1_ENST00000443234.2_RNA	NR_038384.1				MCHR2 antisense RNA 1	NA		NA									NA						tccctccctgccttcctccct	0.532		NA											C|||	1330	0.265575	0.2201	0.3746	5008	,	,	NA	17479	0.2351	NA	0.3459	False	NA	,,,	NA	NA	NA	2504	0.1984	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							6q16.2	2013-07-24			ENSG00000229315	ENSG00000229315	728012		Long non-coding RNAs	48980	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_038384	NA	Approved				OTTHUMG00000015271	ENST00000430122.2:	chr6.hg19:g.100505589C>A		NA		hg19		0.02	-0.157868	CTGxCTT	COVERED																																																																																			NOVEL	MCHR2-AS1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000041622.2	9	2.708059	KEEP	0	0	0	9	277	CC	0.99254	0.320398	0		+	4	60	120	0	0	9.88125	13	60	413	37	ENST00000430122.2	0.235294	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	101593858	101593858	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:101593858T>C			NA	NA				snoU13 (188719 upstream) : GRIK2 (252805 downstream)						NA		NA									NA						gcaacaagagtgaaactccat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.101593858T>C		NA		hg19		0.02	-0.228032	GAGxGAA	COVERED																																																																																			NOVEL					0			6	4.809823	KEEP	3	0	0	16	429	TT	0.99649	0.580884	0			3	60	104	0	0	8.026873	19	60	569	69		0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	103445718	103445718	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:103445718C>T			NA	NA				GRIK2 (927760 upstream) : SNORA33 (585291 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.103445718C>T		NA		hg19		0.02	-0.15786	AGGxGTG	COVERED																																																																																			NOVEL					0			8	4.211127	KEEP	0	0	0	14	400	CC	0.99649	0.321674	0			3	60	96	0	0	7.679127	13	60	392	45		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	104609659	104609659	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:104609659A>G			NA	NA				SNORA33 (578516 upstream) : HACE1 (566308 downstream)						NA		NA									NA						gcgtgaacccaggaggcggag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.104609659A>G		NA		hg19		0.02	-0.061399	CCCxGGA	UNCOVERED																																																																																			NOVEL					0			8	2.406397	KEEP	2	0	0	8	225	AA	0	0	0			3	23	100	0	0	9.355457	4	60	118	21		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	106775313	106775313	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:106775313T>C			NA	NA				ATG5 (1647 upstream) : RP11-404H14.1 (31127 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.106775313T>C		NA		hg19		0.02	-0.114013	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.405976	KEEP	0	0	0	8	219	TT	0.99257	0.16126	0			3	60	98	0	0	8.432686	8	60	238	28		0.272727	0.162467
QRSL1	55278	__UNKNOWN__	__UNKNOWN__	6	107086283	107086283	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107086283G>A	ENST00000369046.4	+	2	128				QRSL1_ENST00000369044.1_Intron|QRSL1_ENST00000467262.1_Intron	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1	NA		NA								endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		gggttcaagcgattcttctgc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(192;2127 2142 11668 26277 49545)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348	55278			21020	protein-coding gene	gene with protein product	glutamyl-tRNA(Gln) amidotransferase, subunit A	NA			NA	11230166, 19805282	Standard	NM_018292	NM_018292	NA	Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.25-1941G>A	chr6.hg19:g.107086283G>A		NA		hg19	CCDS5057.1	0.02	-0.087705	AGCxATT	UNCOVERED																																																																																			NOVEL	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041667.1	3	3.610531	KEEP	0	0	0	12	361	GG	0.993634	0.099086	0		+	4	60	113	0	0	10.284842	6	60	188	30	ENST00000369046.4	0.4	0.099721
QRSL1	55278	__UNKNOWN__	__UNKNOWN__	6	107094613	107094613	__UNKNOWN__	Intron	SNP	G	G	T	rs182684950	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107094613G>T	ENST00000369046.4	+	5	484				QRSL1_ENST00000369044.1_Intron	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1	NA		NA								endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		ttaaaaaattgatagacttgg	0.433		NA											G|||	11	0.00219649	0.0083	0.0	5008	,	,	NA	16388	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	NSCLC(192;2127 2142 11668 26277 49545)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348	55278			21020	protein-coding gene	gene with protein product	glutamyl-tRNA(Gln) amidotransferase, subunit A	NA			NA	11230166, 19805282	Standard	NM_018292	NM_018292	NA	Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.381-2287G>T	chr6.hg19:g.107094613G>T		NA		hg19	CCDS5057.1	0.02	-0.184216	ATTxATA	COVERED																																																																																			NOVEL	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041667.1	4	3.310005	KEEP	0	0	0	11	340	GG	0.993072	0.420544	0		+	3	60	87	0	2	6.392874	18	60	607	46	ENST00000369046.4	0.142857	0.423478
QRSL1	55278	__UNKNOWN__	__UNKNOWN__	6	107094630	107094630	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107094630A>G	ENST00000369046.4	+	5	484				QRSL1_ENST00000369044.1_Intron	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1	NA		NA								endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		ttggccgggcacggtggctca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(192;2127 2142 11668 26277 49545)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348	55278			21020	protein-coding gene	gene with protein product	glutamyl-tRNA(Gln) amidotransferase, subunit A	NA			NA	11230166, 19805282	Standard	NM_018292	NM_018292	NA	Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.381-2270A>G	chr6.hg19:g.107094630A>G		NA		hg19	CCDS5057.1	0.02	-0.192928	GGCxCGG	COVERED																																																																																			NOVEL	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041667.1	5	4.210704	KEEP	2	0	0	14	389	AA	0.995343	0.455625	0		+	4	60	126	0	0	9.980222	18	60	517	57	ENST00000369046.4	0.181818	0.457757
QRSL1	55278	__UNKNOWN__	__UNKNOWN__	6	107094642	107094642	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107094642A>G	ENST00000369046.4	+	5	484				QRSL1_ENST00000369044.1_Intron	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1	NA		NA								endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		ggtggctcacacctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(192;2127 2142 11668 26277 49545)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348	55278			21020	protein-coding gene	gene with protein product	glutamyl-tRNA(Gln) amidotransferase, subunit A	NA			NA	11230166, 19805282	Standard	NM_018292	NM_018292	NA	Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.381-2258A>G	chr6.hg19:g.107094642A>G		NA		hg19	CCDS5057.1	0.02	-0.17538	CACxCCT	COVERED																																																																																			NOVEL	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041667.1	7	5.112902	KEEP	5	0	0	17	471	AA	0.997832	0.386567	0		+	3	60	100	0	0	7.833583	16	60	459	61	ENST00000369046.4	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	107183529	107183529	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107183529A>G			NA	NA				RP1-60O19.2 (35660 upstream) : RNU6-117P (3293 downstream)						NA		NA									NA						ttgcagggccaggcatggtgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.107183529A>G		NA		hg19		0.02	-0.175406	GCCxGGC	COVERED																																																																																			NOVEL					0			6	3.308757	KEEP	0	0	0	11	310	AA	0.993072	0.384723	0			3	60	97	0	0	7.461124	17	60	502	44		0.15	0.387407
BEND3	57673	__UNKNOWN__	__UNKNOWN__	6	107393927	107393927	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107393927G>A	ENST00000369042.1	-	4	431				BEND3_ENST00000429433.2_Intron			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	NA		NA								central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						ggtggctcacgcctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409	57673		BEN domain containing	23040	protein-coding gene	gene with protein product		NA	KIAA1553	KIAA1553	NA		Standard	NM_020913	NM_001080450	NA	Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.241-1773C>T	chr6.hg19:g.107393927G>A		NA	A2RRH2|Q9HCL9	hg19	CCDS34507.1	0.02	-0.254366	CACxCCT	COVERED																																																																																			NOVEL	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041686.1	6	2.707298	KEEP	0	0	0	9	262	GG	0.99254	0.663536	0		-	4	60	116	0	0	8.592191	23	60	735	57	ENST00000369042.1	0.148148	0.668523
BEND3	57673	__UNKNOWN__	__UNKNOWN__	6	107434144	107434144	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107434144T>C	ENST00000369042.1	-	1	180				BEND3_ENST00000429433.2_Intron			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	NA		NA								central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						gagcggatcatgaggtcagga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409	57673		BEN domain containing	23040	protein-coding gene	gene with protein product		NA	KIAA1553	KIAA1553	NA		Standard	NM_020913	NM_001080450	NA	Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.10+2149A>G	chr6.hg19:g.107434144T>C		NA	A2RRH2|Q9HCL9	hg19	CCDS34507.1	0.02	-0.21923	TCAxGAG	COVERED																																																																																			NOVEL	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041686.1	3	2.403721	KEEP	0	0	0	8	203	TT	0.99257	0.54878	0		-	4	60	116	0	0	8.98049	18	60	526	42	ENST00000369042.1	0.181818	0.552887
SOBP	55084	__UNKNOWN__	__UNKNOWN__	6	107873183	107873183	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:107873183C>T	ENST00000317357.5	+	4	1232					NM_018013.3	NP_060483.3			sine oculis binding protein homolog (Drosophila)	NA		NA								endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	26		all_cancers(87;5.26e-06)|Acute lymphoblastic leukemia(125;2.87e-08)|all_hematologic(75;1.14e-06)|all_epithelial(87;0.00193)|Colorectal(196;0.156)		BRCA - Breast invasive adenocarcinoma(108;0.026)|all cancers(137;0.087)|Epithelial(106;0.104)|OV - Ovarian serous cystadenocarcinoma(136;0.154)		tgagatcgcaccactgcactc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001021	CCDS43488.1	6q21	2007-03-15			ENSG00000112320	ENSG00000112320	55084			29256	protein-coding gene	gene with protein product		613667			NA		Standard	NM_018013	NM_018013	NA	Approved	FLJ10159	uc003prx.3	A7XYQ1	OTTHUMG00000015312	ENST00000317357.5:c.573+18369C>T	chr6.hg19:g.107873183C>T		NA		hg19	CCDS43488.1	0.02	-0.122807	GCAxCAC	COVERED																																																																																			NOVEL	SOBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041693.2	10	3.009202	KEEP	1	0	0	10	315	CC	0.992708	0.19488	0		+	3	47	87	0	0	7.643036	6	60	208	33	ENST00000317357.5	0.333333	0.196312
RP1-191J18.66	0	__UNKNOWN__	__UNKNOWN__	6	108280128	108280128	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:108280128T>C	ENST00000606070.1	+	0	1512										NA		NA									NA						cagtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000606070.1:	chr6.hg19:g.108280128T>C		NA		hg19		0.02	-0.228021	TCAxGCC	COVERED																																																																																			NOVEL	RP1-191J18.66-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000471328.1	6	3.305805	KEEP	0	0	0	11	282	TT	0.993072	0.578892	0		+	3	60	91	0	0	6.550037	22	60	647	44	ENST00000606070.1	0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	108356560	108356560	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:108356560A>G			NA	NA				RP1-111B22.3 (4638 upstream) : OSTM1 (6052 downstream)						NA		NA									NA						gattataggcatgagccacca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.108356560A>G		NA		hg19		0.02	-0.149085	GGCxTGA	COVERED																																																																																			NOVEL					0			12	2.706582	KEEP	4	0	0	9	247	AA	0.99257	0.289832	0			3	60	98	0	0	8.182014	10	60	304	39		0.230769	0.292001
SNX3	8724	__UNKNOWN__	__UNKNOWN__	6	108540547	108540547	__UNKNOWN__	Intron	SNP	T	T	C	rs534137979		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:108540547T>C	ENST00000230085.8	-	2	597				SNX3_ENST00000349379.5_Intron|SNX3_ENST00000426155.2_Intron	NM_003795.4	NP_003786.1	O60493	SNX3_HUMAN	sorting nexin 3	NA		NA			hemoglobin biosynthetic process (GO:0042541)|intracellular protein transport (GO:0006886)|intralumenal vesicle formation (GO:0070676)|membrane invagination (GO:0010324)|negative regulation of early endosome to late endosome transport (GO:2000642)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein transport (GO:0051224)|negative regulation of viral entry into host cell (GO:0046597)|regulation of cellular protein metabolic process (GO:0032268)|regulation of intracellular protein transport (GO:0033157)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol-3-phosphate binding (GO:0032266)|protein phosphatase binding (GO:0019903)			large_intestine(1)	1		all_cancers(87;3.82e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000195)|Colorectal(196;0.0293)|all_lung(197;0.0938)		BRCA - Breast invasive adenocarcinoma(108;0.0136)|Epithelial(106;0.0564)|OV - Ovarian serous cystadenocarcinoma(136;0.0717)|all cancers(137;0.0743)		tggtggctcatgcctgtaatc	0.483		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16559	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF034546	CCDS5064.1, CCDS5065.1, CCDS75501.1	6q21	2010-08-05			ENSG00000112335	ENSG00000112335	8724		Sorting nexins	11174	protein-coding gene	gene with protein product		605930			NA	9819414	Standard		XM_005267192	NA	Approved	Grd19	uc003psh.3	O60493	OTTHUMG00000015323	ENST00000230085.8:c.258+3606A>G	chr6.hg19:g.108540547T>C		NA	A8K0B1|E1P5E4|E1P5E5|O60718|Q4TT29|Q4TT31|Q5JXJ7|Q5JXJ8|Q96AP9|Q9C0J5|Q9NU45	hg19	CCDS5064.1	0.02	-0.140328	TCAxGCC	COVERED																																																																																			NOVEL	SNX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041717.1	5	2.405966	KEEP	0	0	0	8	218	TT	0.99257	0.259026	0		-	3	60	101	0	0	8.37296	11	60	322	34	ENST00000230085.8	0.214286	0.260965
ARMC2	84071	__UNKNOWN__	__UNKNOWN__	6	109225408	109225408	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:109225408T>G	ENST00000392644.4	+	8	1015				ARMC2_ENST00000368972.3_Intron	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	NA		NA								endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		TAGTAAGTGTTGCTTTACTCT	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													116	124	122			NA	NA	6		NA											NA				109225408		2203	4300	6503	SO:0001627	intron_variant			BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690	84071		Armadillo repeat containing	23045	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032131	XM_005267154	NA	Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.848-25T>G	chr6.hg19:g.109225408T>G		NA	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	hg19	CCDS5069.2	0.02	-0.403426	TGTxGCT	COVERED																																																																																			NOVEL	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041732.2	1	3.002874	KEEP	0	0	0	10	243	TT	0.992708	0.927678	0		+	26	60	869	0	0	85.631836	20	60	567	74	ENST00000392644.4	0.565217	0.934492
CEP57L1	285753	__UNKNOWN__	__UNKNOWN__	6	109449109	109449109	__UNKNOWN__	Intron	SNP	A	A	G	rs9486996	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:109449109A>G	ENST00000368968.2	+	2	56				CEP57L1_ENST00000368970.2_Intron|CEP57L1_ENST00000520883.1_Intron|CEP57L1_ENST00000521522.1_Intron|CEP57L1_ENST00000519095.1_Intron|CEP57L1_ENST00000517392.1_Intron|CEP57L1_ENST00000407272.1_Intron|CEP57L1_ENST00000523787.1_Intron|CEP57L1_ENST00000521277.1_Intron|CEP57L1_ENST00000521737.1_Intron|CEP57L1_ENST00000336977.4_Intron			Q8IYX8	CE57L_HUMAN	centrosomal protein 57kDa-like 1	NA		NA			microtubule anchoring (GO:0034453)	cytoplasm (GO:0005737)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)	11						gggattacagacatgagccac	0.488		NA											G|||	2268	0.452875	0.8691	0.3213	5008	,	,	NA	15618	0.126	NA	0.3668	False	NA	,,,	NA	NA	NA	2504	0.409	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092723	CCDS5071.1, CCDS64491.1	6q21	2014-01-28	2010-09-30	2010-09-30	ENSG00000183137	ENSG00000183137	285753			21561	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 182	C6orf182	NA		Standard	NM_173830	NM_001083535	NA	Approved	bA487F23.2, MGC21731	uc003psy.4	Q8IYX8	OTTHUMG00000015336	ENST00000368968.2:c.-3-17313A>G	chr6.hg19:g.109449109A>G		NA	G5E992	hg19		0.02	-0.23682	CAGxCAT	COVERED																																																																																			NOVEL	CEP57L1-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000377078.1	5	2.405408	KEEP	0	0	0	8	212	AA	0.99257	0.607857	0		+	3	60	104	0	0	7.905355	21	60	625	53	ENST00000368968.2	0.125	0.612407
CCDC162P	221262	__UNKNOWN__	__UNKNOWN__	6	109624824	109624824	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:109624824A>G	ENST00000422819.1	+	0	461							A2VCL2	CC162_HUMAN	coiled-coil domain containing 162, pseudogene	NA		NA									NA						tggccaggctagtctcgaact	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							6q21	2011-04-28	2011-04-28	2011-04-28	ENSG00000203799	ENSG00000203799	221262			21565	pseudogene	pseudogene		NA	chromosome 6 open reading frame 184, chromosome 6 open reading frame 185	C6orf184, C6orf185, CCDC162	NA		Standard	NR_028595	NR_028595	NA	Approved	bA425D10.7, bA425D10.3	uc003ptb.1	A2VCL2	OTTHUMG00000015342	ENST00000422819.1:	chr6.hg19:g.109624824A>G		NA	A1A4V1|A4QMU0|Q5JSU0|Q5JSU7	hg19		0.02	-0.192973	GCTxGTC	COVERED																																																																																			NOVEL	CCDC162P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000365631.1	7	3.007091	KEEP	1	0	0	10	269	AA	0.99254	0.454342	0		+	3	60	103	0	0	8.378788	13	60	387	43	ENST00000422819.1	0.1875	0.457757
RP5-919F19.5	0	__UNKNOWN__	__UNKNOWN__	6	109810693	109810693	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:109810693T>C	ENST00000423747.2	+	0	154										NA		NA									NA						cctgccaccatgcccggctaa	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423747.2:	chr6.hg19:g.109810693T>C		NA		hg19		0.02	-0.070143	CCAxGCC	UNCOVERED																																																																																			NOVEL	RP5-919F19.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000041754.1	5	2.402058	KEEP	4	0	0	8	202	TT	0	0	0		+	3	60	84	0	0	7.532552	5	60	137	19	ENST00000423747.2	0.375	0.054137
CDC40	51362	__UNKNOWN__	__UNKNOWN__	6	110562259	110562259	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:110562259A>G	ENST00000368930.1	+	14	1586							O60508	PRP17_HUMAN	cell division cycle 40	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;6.23e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00159)|Colorectal(196;0.0488)		Epithelial(106;0.0221)|all cancers(137;0.0314)|OV - Ovarian serous cystadenocarcinoma(136;0.034)		tgatccgcccacctcggcctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF015044	CCDS5081.1	6q22.1	2013-01-17	2013-01-17		ENSG00000168438	ENSG00000168438	51362		WD repeat domain containing	17350	protein-coding gene	gene with protein product		605585	cell division cycle 40 homolog (yeast), cell division cycle 40 homolog (S. cerevisiae)		NA	9769104, 9830021	Standard	NM_015891	NM_015891	NA	Approved	PRP17, EHB3, PRPF17, FLJ10564	uc003pua.3	O60508	OTTHUMG00000015358	ENST00000368930.1:c.1562+12080A>G	chr6.hg19:g.110562259A>G		NA	B2RBC5|O75471|Q5SRN0|Q9UPG1	hg19		0.02	-0.122772	CCCxCCT	COVERED																																																																																			NOVEL	CDC40-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000041790.1	6	2.705577	KEEP	2	0	0	9	237	AA	0.99254	0.194847	0		+	3	60	95	0	0	7.773411	11	60	320	35	ENST00000368930.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	110840191	110840191	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:110840191A>G			NA	NA				CTA-331P3.1 (39552 upstream) : CDK19 (90989 downstream)						NA		NA									NA						gggattacagacgtgagccac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.110840191A>G		NA		hg19		0.02	-0.122794	CAGxCGT	COVERED																																																																																			NOVEL					0			6	2.405303	KEEP	0	0	0	8	210	AA	0.99257	0.194853	0			3	60	103	0	0	8.932634	8	60	236	33		0.272727	0.196312
CDK19	23097	__UNKNOWN__	__UNKNOWN__	6	110976302	110976302	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:110976302A>G	ENST00000368911.3	-	4	636				CDK19_ENST00000323817.3_Intron	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	NA		NA					ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						cgggcacggtagctcacgcct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL122055	CCDS5085.1, CCDS75503.1	6q21	2011-10-25	2009-12-16	2009-12-16	ENSG00000155111	ENSG00000155111	23097		Cyclin-dependent kinases	19338	protein-coding gene	gene with protein product		614720	cyclin-dependent kinase (CDC2-like) 11, cell division cycle 2-like 6 (CDK8-like)	CDK11, CDC2L6	NA	10470851, 19884882	Standard	NM_015076	XM_005266871	NA	Approved	KIAA1028, bA346C16.3	uc003puh.1	Q9BWU1	OTTHUMG00000015365	ENST00000368911.3:c.456+12334T>C	chr6.hg19:g.110976302A>G		NA	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	hg19	CCDS5085.1	0.02	-0.166623	GGTxGCT	COVERED																																																																																			NOVEL	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041804.1	4	2.405291	KEEP	0	0	0	8	212	AA	0.99257	0.351317	0		-	3	60	102	0	0	8.191966	14	60	404	35	ENST00000368911.3	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	111184865	111184865	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111184865G>A			NA	NA				RNU6-1115P (7140 upstream) : AMD1 (11107 downstream)						NA		NA									NA						gagccaccgcgcccggccTGA	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.111184865G>A		NA		hg19		0.02	-0.18421	CGCxCCC	COVERED																																																																																			NOVEL					0			8	2.707828	KEEP	1	0	0	9	269	GG	0.99254	0.420319	0			3	60	88	0	0	6.561608	17	60	569	45		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	111256753	111256753	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111256753G>A			NA	NA				AMD1 (39837 upstream) : GTF3C6 (23009 downstream)						NA		NA									NA						gcaatggcacgatctcggctc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.111256753G>A		NA		hg19		0.02	-0.201749	CACxATC	UNCOVERED																																																																																			NOVEL					0			7	2.405686	KEEP	9	0	0	8	232	GG	0	0	0			3	60	86	0	0	6.36166	17	60	551	58		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	111260155	111260155	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111260155C>T			NA	NA				AMD1 (43239 upstream) : GTF3C6 (19607 downstream)						NA		NA									NA						TGGACtttctctttttttttt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.111260155C>T		NA		hg19		0.02	-0.192969	TCTxTTT	COVERED																																																																																			NOVEL					0			14	3.006813	KEEP	0	0	0	10	284	CC	0.992708	0.454419	0			4	60	112	0	0	9.330738	11	60	368	43		0.266667	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	111350800	111350800	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111350800T>C			NA	NA				RPF2 (3497 upstream) : SLC16A10 (57980 downstream)						NA		NA									NA						tttgggaggctgaggcgggcg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.111350800T>C		NA		hg19		0.02	-0.210503	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			3	3.007993	KEEP	7	0	0	10	282	TT	0	0	0			3	60	91	0	0	6.665563	20	60	603	62		0.130435	0.552887
SLC16A10	117247	__UNKNOWN__	__UNKNOWN__	6	111499721	111499721	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111499721G>C	ENST00000368851.5	+	3	1117				SLC16A10_ENST00000368850.3_Intron	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	NA		NA			amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	caagaccagcgtgggcaacat	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394	117247		Solute carriers	17027	protein-coding gene	gene with protein product		607550	solute carrier family 16 (monocarboxylic acid transporters), member 10		NA	11278508, 11827462	Standard		NM_018593	NA	Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.942+853G>C	chr6.hg19:g.111499721G>C		NA	B3KWY0|Q6ZMG0|Q8WVI5	hg19	CCDS5089.1	0.02	-0.210514	AGCxTGG	COVERED																																																																																			NOVEL	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041822.2	0	3.306392	KEEP	0	0	0	11	312	GG	0.993072	0.518544	0		+	5	60	165	0	0	13.552683	19	60	595	48	ENST00000368851.5	0.208333	0.522161
RP11-428F8.2	0	__UNKNOWN__	__UNKNOWN__	6	111554427	111554427	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111554427T>C	ENST00000425364.1	-	0	190										NA		NA									NA						ggattacaggtgtgagccacc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000425364.1:	chr6.hg19:g.111554427T>C		NA		hg19		0.02	-0.219194	AGGxGTG	COVERED																																																																																			NOVEL	RP11-428F8.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000041830.1	7	5.711796	KEEP	3	0	0	19	500	TT	0.999366	0.552537	0		-	3	60	99	0	0	7.527575	19	60	542	66	ENST00000425364.1	0.136364	0.552887
TRAF3IP2-AS1	643749	__UNKNOWN__	__UNKNOWN__	6	111836460	111836460	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:111836460A>G	ENST00000438298.2	+	0	125				TRAF3IP2-AS1_ENST00000532353.1_RNA|TRAF3IP2-AS1_ENST00000440395.1_RNA|TRAF3IP2-AS1_ENST00000442928.2_RNA|TRAF3IP2-AS1_ENST00000449449.2_RNA|TRAF3IP2-AS1_ENST00000456352.2_RNA	NR_034110.1				TRAF3IP2 antisense RNA 1	NA		NA									NA						gcgagactccatctcaaaaaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							6q21	2012-10-12	2012-08-15		ENSG00000231889	ENSG00000231889	643749		Long non-coding RNAs	40005	non-coding RNA	RNA, long non-coding		NA	TRAF3IP2 antisense RNA 2 (non-protein coding), chromosome 6 open reading frame 3, non-protein coding RNA 248, TRAF3IP2 antisense RNA 1 (non-protein coding)	TRAF3IP2-AS2, C6orf3, NCRNA00248	NA		Standard	NR_034108	NR_034108	NA	Approved	C6UAS	uc021zdt.1		OTTHUMG00000015378	ENST00000438298.2:	chr6.hg19:g.111836460A>G		NA		hg19		0.02	-0.122795	TCCxTCT	UNCOVERED																																																																																			NOVEL	TRAF3IP2-AS1-006	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000041838.2	14	2.707225	KEEP	10	0	0	9	253	AA	0	0	0		+	3	40	99	1	1	8.172882	11	60	327	35	ENST00000438298.2	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	112286122	112286122	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:112286122A>G			NA	NA				RP1-97J1.2 (63068 upstream) : WISP3 (89152 downstream)						NA		NA									NA						ttagccaggcatggtggtgca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.112286122A>G		NA		hg19		0.02	-0.315632	GGCxTGG	COVERED																																																																																			NOVEL					0			16	4.811119	KEEP	1	0	0	16	430	AA	0.997832	0.81669	0			3	60	101	0	0	7.253319	28	60	796	70		0.096774	0.818465
LAMA4	3910	__UNKNOWN__	__UNKNOWN__	6	112545738	112545738	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:112545738T>C	ENST00000431543.2	-	3	450				LAMA4_ENST00000389463.4_Intron|LAMA4_ENST00000230538.7_Intron|LAMA4_ENST00000522006.1_Intron|LAMA4_ENST00000424408.2_Intron			Q16363	LAMA4_HUMAN	laminin, alpha 4	NA		NA			blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		TGTTGATggctgggtgcggtg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769	3910		Laminins	6484	protein-coding gene	gene with protein product		600133			NA	7959779	Standard	NM_001105206	NM_001105206	NA	Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000431543.2:c.196-8068A>G	chr6.hg19:g.112545738T>C		NA	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	hg19		0.02	-0.201731	GGCxGGG	COVERED																																																																																			NOVEL	LAMA4-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000041877.3	7	3.910032	KEEP	2	0	0	13	362	TT	0.994391	0.487793	0		-	3	60	102	0	0	7.764733	20	60	599	55	ENST00000431543.2	0.130435	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	113909528	113909528	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:113909528T>C			NA	NA				RP11-346D19.1 (44533 upstream) : AL357519.2 (14588 downstream)						NA		NA									NA						acctcagccttccaaagtgct	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.113909528T>C		NA		hg19		0.02	-0.131559	CCTxCCA	COVERED																																																																																			NOVEL					0			6	3.91075	KEEP	0	0	0	13	373	TT	0.994391	0.227888	0			3	60	88	0	0	6.972609	12	60	362	40		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	114009063	114009063	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:114009063A>G			NA	NA				RP11-367G18.1 (55347 upstream) : AL357519.1 (16971 downstream)						NA		NA									NA						actccagcctaggcaacaaga	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.114009063A>G		NA		hg19		0.02	-0.245586	CCTxGGC	COVERED																																																																																			NOVEL					0			9	3.007542	KEEP	0	0	0	10	275	AA	0.992708	0.63667	0			3	60	96	0	0	7.04932	22	60	659	57		0.12	0.641347
FAM26E	254228	__UNKNOWN__	__UNKNOWN__	6	116840866	116840866	__UNKNOWN__	3'UTR	SNP	A	A	G	rs1051172	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:116840866A>G	ENST00000368599.3	+	0	4695				TRAPPC3L_ENST00000368602.3_Intron	NM_153711.2	NP_714922.1	Q8N5C1	FA26E_HUMAN	family with sequence similarity 26, member E	NA		NA			ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7		all_cancers(87;0.0608)|all_epithelial(87;0.05)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0242)|all cancers(137;0.0419)|OV - Ovarian serous cystadenocarcinoma(136;0.0671)|Epithelial(106;0.212)		TACATAAGAGAAAAGGATTGG	0.408		NA											G|||	1994	0.398163	0.1452	0.585	5008	,	,	NA	18616	0.5536	NA	0.4712	False	NA	,,,	NA	NA	NA	2504	0.3722	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC032556	CCDS5108.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000178033	ENSG00000178033	254228			21568	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 188	C6orf188	NA		Standard	NM_153711	NM_153711	NA	Approved	dJ493F7.3, MGC45451	uc003pwy.3	Q8N5C1	OTTHUMG00000015442	ENST00000368599.3:c.*3714A>G	chr6.hg19:g.116840866A>G		NA	B2RDJ9|B3KSR3	hg19	CCDS5108.1	0.02	-0.333302	GAGxAAA	COVERED																																																																																			NOVEL	FAM26E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000041956.1	3	2.406241	KEEP	0	0	0	8	225	AA	0.99257	0.845654	0		+	24	60	797	0	0	80.734871	13	60	388	65	ENST00000368599.3	0.648649	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	117093171	117093171	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:117093171C>G			NA	NA				FAM162B (6285 upstream) : GPRC6A (20076 downstream)						NA		NA									NA						acctccacctcccaggttcaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.117093171C>G		NA		hg19		0.02	-0.149108	CCTxCCA	COVERED																																																																																			NOVEL					0			11	4.511955	KEEP	6	0	0	15	436	CC	0.994391	0.290363	0			3	22	108	0	0	8.972186	12	60	396	48		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	117093175	117093175	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:117093175G>A			NA	NA				FAM162B (6289 upstream) : GPRC6A (20072 downstream)						NA		NA									NA						ccacctcccaggttcaagcga	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.117093175G>A		NA		hg19		0.02	-0.149127	CCAxGTT	COVERED																																																																																			NOVEL					0			11	3.309518	KEEP	5	0	0	11	332	GG	0.992708	0.289872	0			3	22	93	0	0	7.472127	12	60	402	43		0.2	0.292001
GOPC	57120	__UNKNOWN__	__UNKNOWN__	6	117792773	117792773	__UNKNOWN__	Intron	SNP	G	G	A	rs10081022	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:117792773G>A	ENST00000467125.1	-	4	547							Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	NA		NA			apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		ctcccaaagtgctgggattac	0.458		NA	O	ROS1	glioblastoma								G|||	494	0.0986422	0.1657	0.0793	5008	,	,	NA	16230	0.0288	NA	0.0875	False	NA	,,,	NA	NA	NA	2504	0.1053	NA	NA	NA			Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932	57120			17643	protein-coding gene	gene with protein product		606845			NA	11162552, 11520064	Standard	NM_020399	NM_020399	NA	Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000467125.1:c.383+95243C>T	chr6.hg19:g.117792773G>A		NA	A6NM30|Q59FS4|Q969U8	hg19		0.02	-0.105265	AGTxCTG	UNCOVERED																																																																																			NOVEL	GOPC-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000041978.1	5	3.610647	KEEP	5	0	0	12	365	GG	0.99254	0.138789	0		-	4	60	117	0	0	10.684701	6	60	216	42	ENST00000467125.1	0.4	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	118111180	118111180	__UNKNOWN__	IGR	SNP	C	C	T	rs11153699	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:118111180C>T			NA	NA				NUS1 (79377 upstream) : SLC35F1 (117508 downstream)						NA		NA									NA						ccgcccgcctcggcctcccaa	0.512		NA											-|||	1752	0.34984	0.143	0.3631	5008	,	,	NA	14315	0.2212	NA	0.4712	False	NA	,,,	NA	NA	NA	2504	0.6278	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.118111180C>T		NA		hg19		0.02	-0.149098	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			13	3.008783	KEEP	19	0	0	10	304	CG	0	0	0			4	60	109	0	0	9.170756	10	60	326	58		0.285714	0.292001
FAM184A	79632	__UNKNOWN__	__UNKNOWN__	6	119344014	119344014	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:119344014T>C	ENST00000522284.1	-	3	1166				FAM184A_ENST00000368475.4_Intron|FAM184A_ENST00000352896.5_Intron|FAM184A_ENST00000521531.1_Intron|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000338891.7_Intron			Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	NA		NA				extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						tgcactcccgtctgggcgaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879	79632			20991	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 60	C6orf60	NA	11230166	Standard	NM_024581	NM_024581	NA	Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000522284.1:c.790+95A>G	chr6.hg19:g.119344014T>C		NA	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	hg19		0.02	-0.26287	CCGxCTG	COVERED																																																																																			NOVEL	FAM184A-010	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380869.2	1	2.403394	KEEP	0	0	0	8	193	TT	0.99257	0.688515	0		-	3	60	98	0	0	7.144209	24	60	644	39	ENST00000522284.1	0.111111	0.693668
MAN1A1	4121	__UNKNOWN__	__UNKNOWN__	6	119619081	119619081	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:119619081T>C	ENST00000368468.3	-	4	1258				MAN1A1_ENST00000368466.2_Intron	NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|mannosidase activity (GO:0015923)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|skin(3)	24		all_epithelial(87;0.173)		OV - Ovarian serous cystadenocarcinoma(136;0.0612)|GBM - Glioblastoma multiforme(226;0.0702)|all cancers(137;0.115)		tcccaaagtgttgggattaca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(136;8 1825 12608 33541 47587)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025599	CCDS5122.1	6q22	2008-08-29			ENSG00000111885	ENSG00000111885	4121	3.2.1.113		6821	protein-coding gene	gene with protein product		604344			NA	8223597	Standard	NM_005907	NM_005907	NA	Approved		uc003pym.2	P33908	OTTHUMG00000015472	ENST00000368468.3:c.816+4071A>G	chr6.hg19:g.119619081T>C		NA	E7EU32|Q6P052|Q9NU44|Q9UJI3	hg19	CCDS5122.1	0.02	-0.175412	GTGxTGG	COVERED																																																																																			NOVEL	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042015.1	8	3.604972	KEEP	0	0	0	12	316	TT	0.993634	0.38494	0		-	3	60	109	0	0	8.891665	14	60	407	46	ENST00000368468.3	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	120126398	120126398	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:120126398A>G			NA	NA				MAN1A1 (455472 upstream) : MIR3144 (209926 downstream)						NA		NA									NA						ccaaagtgttaggattacagg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.120126398A>G		NA		hg19		0.02	-0.166643	GTTxGGA	COVERED																																																																																			NOVEL					0			6	4.811641	KEEP	0	0	0	16	434	AA	0.997832	0.353179	0			3	60	92	0	0	7.192203	14	60	419	54		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	121127193	121127193	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:121127193T>C			NA	NA				RNA5SP215 (119305 upstream) : TBC1D32 (273446 downstream)						NA		NA									NA						gaggccgaggtgggcggatca	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.121127193T>C		NA		hg19		0.02	-0.166656	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			9	2.702604	KEEP	7	0	0	9	229	TT	0	0	0			3	43	100	0	0	7.833344	16	60	492	45		0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	121904746	121904746	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:121904746C>A			NA	NA				RNU2-8P (3079 upstream) : RNU1-18P (628047 downstream)						NA		NA									NA						ataactgagactacagacaat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.121904746C>A		NA		hg19		0.02	-0.070164	AGAxTAC	UNCOVERED																																																																																			NOVEL					0			6	2.707217	KEEP	0	0	0	9	264	CC	0.99254	0.053733	0			5	60	147	0	0	14.784688	3	60	102	22		0.625	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	122535573	122535573	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:122535573A>G			NA	NA				RNU1-18P (2616 upstream) : HSF2 (185117 downstream)						NA		NA									NA						gagccaccgcacccggcctaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.122535573A>G		NA		hg19		0.02	-0.201638	CGCxCCC	COVERED																																																																																			NOVEL					0			5	2.236661	KEEP	12	1	18	14	364	AA	0.993072	0.487146	0			4	60	136	0	0	10.980388	18	60	486	64		0.181818	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	122594485	122594485	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:122594485G>A			NA	NA				RNU1-18P (61528 upstream) : HSF2 (126205 downstream)						NA		NA									NA						ggccgggtgcggtggctcacg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.122594485G>A		NA		hg19		0.02	-0.114028	TGCxGTG	UNCOVERED																																																																																			NOVEL					0			6	2.406727	KEEP	0	0	0	8	238	GG	0.99257	0.16126	0			5	60	149	0	0	13.993286	6	60	185	33		0.454545	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	122594495	122594495	__UNKNOWN__	IGR	SNP	G	G	A	rs9398666	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:122594495G>A			NA	NA				RNU1-18P (61538 upstream) : HSF2 (126195 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.122594495G>A		NA		hg19		0.02	-0.12281	CACxCCT	COVERED																																																																																			NOVEL					0			7	2.406882	KEEP	1	0	0	8	244	GG	0.99257	0.194853	0			3	60	94	0	0	7.900952	9	60	301	36		0.25	0.196312
RNF217	154214	__UNKNOWN__	__UNKNOWN__	6	125329174	125329174	__UNKNOWN__	Intron	SNP	G	G	A	rs550428630		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:125329174G>A	ENST00000521654.2	+	2	882				RNF217_ENST00000454842.2_Intron|RNF217_ENST00000359704.2_Intron|RNF217_ENST00000368414.2_Intron|RNF217_ENST00000560949.1_Intron			Q8TC41	RN217_HUMAN	ring finger protein 217	NA		NA			protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	11			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0162)		aggccgaggcgggtggatcac	0.463		NA											g|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14097	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026087	CCDS5129.1, CCDS69191.1	6q22.33	2014-07-15	2007-08-20	2007-08-20	ENSG00000146373	ENSG00000146373	154214		RING-type (C3HC4) zinc fingers	21487	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 172, IBR domain containing 1	C6orf172, IBRDC1	NA		Standard	NM_152553	NM_001286398	NA	Approved	MGC26996, dJ84N20.1	uc003pzs.3	Q8TC41	OTTHUMG00000015504	ENST00000521654.2:c.883-37183G>A	chr6.hg19:g.125329174G>A		NA	H7C5V4|Q5TCA4|Q9BX48	hg19		0.02	-0.175305	GGCxGGT	COVERED																																																																																			NOVEL	RNF217-002	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000042063.3	5	2.406648	KEEP	1	0	0	8	236	GG	0.99257	0.384528	0		+	3	60	91	0	0	6.862299	17	60	536	42	ENST00000521654.2	0.15	0.387407
TPD52L1	7164	__UNKNOWN__	__UNKNOWN__	6	125488231	125488231	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:125488231C>T	ENST00000528193.1	+	1	71				TPD52L1_ENST00000534000.1_Intron|TPD52L1_ENST00000532429.1_Intron|TPD52L1_ENST00000527711.1_Intron|TPD52L1_ENST00000368402.5_Intron|TPD52L1_ENST00000304877.13_Intron|TPD52L1_ENST00000534199.1_Intron|TPD52L1_ENST00000368388.2_Intron			Q16890	TPD53_HUMAN	tumor protein D52-like 1	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|prostate(1)	5			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0265)		agcaagacctcgtctctacta	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U44427	CCDS5130.1, CCDS34527.1, CCDS34528.1, CCDS43502.1, CCDS75513.1, CCDS75514.1	6q22-q23	2008-07-29			ENSG00000111907	ENSG00000111907	7164			12006	protein-coding gene	gene with protein product		604069			NA	8812487, 16112108	Standard		NM_003287	NA	Approved	D53, hD53	uc003pzu.1	Q16890	OTTHUMG00000015505	ENST00000528193.1:c.19+13115C>T	chr6.hg19:g.125488231C>T		NA	A8K757|A8K772|A8MUD2|A8MUJ7|A8MW70|F6V707|O43397|Q5TC99|Q5TDQ0|Q9BUQ6|Q9C054	hg19		0.02	-0.219274	CCTxGTC	COVERED																																																																																			NOVEL	TPD52L1-013	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000382750.1	13	4.510934	KEEP	0	0	0	15	424	CC	0.99649	0.550947	0		+	3	60	88	0	0	6.791941	14	60	471	57	ENST00000528193.1	0.176471	0.552887
TRMT11	60487	__UNKNOWN__	__UNKNOWN__	6	126348244	126348244	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:126348244G>A	ENST00000368332.3	+	12	1317				TRMT11_ENST00000334379.5_Intron			Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	NA		NA			tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		gagccaccgcgcccggccGTT	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651	60487			21080	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 75	C6orf75	NA		Standard	NM_021820	XM_006715546	NA	Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000368332.3:c.1245+5833G>A	chr6.hg19:g.126348244G>A		NA	E1P570|Q5JY11|Q6PGQ5|Q9HC13	hg19		0.02	-0.166605	CGCxCCC	COVERED																																																																																			NOVEL	TRMT11-006	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000042096.3	7	4.212035	KEEP	3	0	0	14	422	GG	0.993634	0.351693	0		+	3	60	84	0	0	6.392968	14	60	452	51	ENST00000368332.3	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	126371711	126371711	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:126371711G>C			NA	NA				TRMT11 (11289 upstream) : RP11-527F13.1 (126627 downstream)						NA		NA									NA						caggtgtagtggcacatgcct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.126371711G>C		NA		hg19		0.02	-0.061408	AGTxGCA	UNCOVERED																																																																																			NOVEL					0			5	2.708216	KEEP	0	0	0	9	280	GG	0.99254	0.04346	0			3	60	101	0	0	9.455114	4	60	137	24		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	127666872	127666872	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:127666872A>G			NA	NA				ECHDC1 (2118 upstream) : SOGA3 (92678 downstream)						NA		NA									NA						aggcacagtgactcacacctg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.127666872A>G		NA		hg19		0.02	-0.157813	GTGxCTC	COVERED																																																																																			NOVEL					0			4	3.307761	KEEP	0	0	0	11	297	AA	0.993072	0.32057	0			3	60	93	0	0	7.211396	15	60	441	44		0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	127743644	127743644	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:127743644T>C			NA	NA				ECHDC1 (78890 upstream) : SOGA3 (15906 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.127743644T>C		NA		hg19		0.02	-0.2105	AGAxGGG	COVERED																																																																																			NOVEL					0			9	2.433573	KEEP	3	1	25	17	446	TT	0.999366	0.52183	0			5	60	165	0	0	13.656805	18	60	537	64		0.217391	0.522161
SOGA3	387104	__UNKNOWN__	__UNKNOWN__	6	127837461	127837461	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:127837461C>T	ENST00000525778.1	-	2	1044	c.299G>A	c.(298-300)gGt>gAt	p.G100D	SOGA3_ENST00000465909.2_Missense_Mutation_p.G100D|SOGA3_ENST00000481848.2_Missense_Mutation_p.G100D|SOGA3_ENST00000368268.2_Missense_Mutation_p.G100D|SOGA3_ENST00000556132.1_Missense_Mutation_p.G100D			Q5TF21	SOGA3_HUMAN	SOGA family member 3	100	Gly-rich.	NA			regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)					NA						CTCGGCCCCACCTCCGCCTCC	0.721		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													6	7	7			NA	NA	6		NA											NA				127837461		1527	3558	5085	SO:0001583	missense			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338	387104			21494	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 174	C6orf174	NA		Standard	NM_001012279	NM_001012279	NA	Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.299G>A	chr6.hg19:g.127837461C>T	ENSP00000434570:p.Gly100Asp	NA		hg19	CCDS43505.1	0.02	1.223442	CCAxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.22	1.575523	0.28092	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	5.25	4.39	0.52855	.	0.262507	0.27056	N	0.021150	T	0.15132	0.0365	N	0.14661	0.345	0.32430	N	0.548149	B	0.12013	0.005	B	0.10450	0.005	T	0.06807	-1.0806	10	0.48119	T	0.1	-15.589	11.2762	0.49168	0.0:0.913:0.0:0.087	.	100	Q5TF21	CF174_HUMAN	D	100	ENSP00000451768:G100D;ENSP00000357251:G100D;ENSP00000434570:G100D;ENSP00000435559:G100D	ENSP00000435559:G100D	G	-	2	0	C6orf174	127879154	1.000000	0.71417	0.998000	0.56505	0.277000	0.26821	3.071000	0.50041	1.220000	0.43490	0.313000	0.20887	GGT	NOVEL	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388246.1	2	3.609689	KEEP	0	0	0	12	356	CC	0.993634	0.987376	0		-	21	60	581	0	0	50.525313	43	60	1448	104	ENST00000525778.1	0.328125	0.993703
THEMIS	387357	__UNKNOWN__	__UNKNOWN__	6	128077151	128077151	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:128077151C>A	ENST00000368250.1	-	6	2020				THEMIS_ENST00000543064.1_Intron|THEMIS_ENST00000368248.2_Intron|THEMIS_ENST00000537166.1_Intron			Q8N1K5	THMS1_HUMAN	thymocyte selection associated	NA		NA			negative T cell selection (GO:0043383)|positive T cell selection (GO:0043368)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(3)	60						cagcctgggccacagagtgag	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094863	CCDS34534.1, CCDS55055.1	6q22.33	2012-02-08	2009-06-25	2009-06-25	ENSG00000172673	ENSG00000172673	387357			21569	protein-coding gene	gene with protein product	thymocyte expressed molecule involved in selection	613607	chromosome 6 open reading frame 207, chromosome 6 open reading frame 190, thymocyte selection pathway associated	C6orf207, C6orf190, TSEPA	NA	19597499, 19597498, 19597497	Standard	NM_001010923	NM_001010923	NA	Approved	bA325O24.4, FLJ40584, bA325O24.3	uc011ebt.2	Q8N1K5	OTTHUMG00000015534	ENST00000368250.1:c.1522-36183G>T	chr6.hg19:g.128077151C>A		NA	A1L4F0|A8K7N1|B3KT31|B3KW32|B3KY07|F5H1J9|Q5T3C4|Q5T3C5|Q6MZT7	hg19		0.02	-0.105253	GGCxACA	UNCOVERED																																																																																			NOVEL	THEMIS-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000042156.1	4	2.707284	KEEP	0	0	0	9	267	CC	0.99254	0.138789	0		-	3	60	83	0	0	7.077907	7	60	240	32	ENST00000368250.1	0.3	0.139832
PTPRK	5796	__UNKNOWN__	__UNKNOWN__	6	128426388	128426388	__UNKNOWN__	Intron	SNP	G	G	C	rs181179014	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:128426388G>C	ENST00000368213.5	-	8	1387				PTPRK_ENST00000524481.1_Intron|PTPRK_ENST00000368210.3_Intron|PTPRK_ENST00000368207.3_Intron|PTPRK_ENST00000368227.3_Intron|PTPRK_ENST00000368226.4_Intron|PTPRK_ENST00000532331.1_Intron|PTPRK_ENST00000368215.3_Intron	NM_001135648.1	NP_001129120.1	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	NA		NA			cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		gcgccattctgctgcctcagc	0.587		NA											G|||	46	0.0091853	0.0348	0.0	5008	,	,	NA	13501	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894	5796		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	9674	protein-coding gene	gene with protein product		602545			NA	9047348, 8663237	Standard		NM_002844	NA	Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368213.5:c.1163-15251C>G	chr6.hg19:g.128426388G>C		NA	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	hg19	CCDS47473.1	0.02	-0.096493	TCTxCTG	UNCOVERED																																																																																			NOVEL	PTPRK-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390044.2	2	2.406814	KEEP	0	0	0	8	237	GG	0.99257	0.119541	0		-	3	60	86	0	0	7.232025	8	60	287	25	ENST00000368213.5	0.272727	0.120436
PTPRK	5796	__UNKNOWN__	__UNKNOWN__	6	128445378	128445378	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:128445378A>G	ENST00000368213.5	-	8	1387				PTPRK_ENST00000524481.1_Intron|PTPRK_ENST00000368210.3_Intron|PTPRK_ENST00000368207.3_Intron|PTPRK_ENST00000368227.3_Intron|PTPRK_ENST00000368226.4_Intron|PTPRK_ENST00000532331.1_Intron|PTPRK_ENST00000368215.3_Intron	NM_001135648.1	NP_001129120.1	Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	NA		NA			cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		tagtagagacagggtttcgcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894	5796		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	9674	protein-coding gene	gene with protein product		602545			NA	9047348, 8663237	Standard		NM_002844	NA	Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368213.5:c.1163-34241T>C	chr6.hg19:g.128445378A>G		NA	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	hg19	CCDS47473.1	0.02	-0.078945	GACxGGG	UNCOVERED																																																																																			NOVEL	PTPRK-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390044.2	5	3.006807	KEEP	1	0	0	10	266	AA	0.99254	0.076759	0		-	3	60	95	0	0	8.443377	6	60	190	23	ENST00000368213.5	0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	131825712	131825712	__UNKNOWN__	IGR	SNP	T	T	C	rs9483299	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:131825712T>C			NA	NA				AKAP7 (221037 upstream) : ARG1 (68571 downstream)						NA		NA									NA						caggatgagctaggaaaagga	0.493		NA											T|||	1656	0.330671	0.4569	0.3617	5008	,	,	NA	7267	0.3006	NA	0.2435	False	NA	,,,	NA	NA	NA	2504	0.2587	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.131825712T>C		NA		hg19		0.02	-0.096488	AGCxAGG	UNCOVERED																																																																																			NOVEL					0			3	2.707094	KEEP	2	0	0	9	252	TT	0.99254	0.119538	0			2	49	74	0	0	6.535752	5	60	149	35		0.285714	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	133331655	133331655	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:133331655A>G			NA	NA				RPS12 (192952 upstream) : LINC00326 (77563 downstream)						NA		NA									NA						ggccaggctgatctcaaactc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.133331655A>G		NA		hg19		0.02	-0.157813	CTGxTCT	COVERED																																																																																			NOVEL					0			6	3.609117	KEEP	0	0	0	12	330	AA	0.993634	0.320751	0			3	60	103	0	0	8.210658	15	60	447	40		0.166667	0.322807
HBS1L	10767	__UNKNOWN__	__UNKNOWN__	6	135356654	135356654	__UNKNOWN__	Intron	SNP	G	G	A	rs570460183		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:135356654G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000415177.2_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	NA		NA			signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		caaggcgggcggatcatgagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339	10767			4834	protein-coding gene	gene with protein product	eRF3 family member	612450	HBS1 (S. cerevisiae)-like, HBS1-like (S. cerevisiae)		NA	9872408, 23667253	Standard		NM_006620	NA	Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.430+4056C>T	chr6.hg19:g.135356654G>A		NA	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	hg19	CCDS5173.1	0.02	-0.175437	GGCxGAT	COVERED																																																																																			NOVEL	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042339.2	10	4.513224	KEEP	0	0	0	15	454	GG	0.99649	0.386047	0		-	3	60	91	0	0	6.933583	16	60	522	51	ENST00000367837.5	0.157895	0.387407
HBS1L	10767	__UNKNOWN__	__UNKNOWN__	6	135360344	135360344	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:135360344T>C	ENST00000367820.2	-	4	539				HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367837.5_Intron|HBS1L_ENST00000525067.1_Intron|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Intron			Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	NA		NA			signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		gtaatcccagttacttgggag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339	10767			4834	protein-coding gene	gene with protein product	eRF3 family member	612450	HBS1 (S. cerevisiae)-like, HBS1-like (S. cerevisiae)		NA	9872408, 23667253	Standard		NM_006620	NA	Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367820.2:c.430+366A>G	chr6.hg19:g.135360344T>C		NA	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	hg19		0.02	-0.131519	CAGxTAC	UNCOVERED																																																																																			NOVEL	HBS1L-014	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000391471.1	10	2.405159	KEEP	1	0	0	8	211	TT	0	0	0		-	3	60	100	1	0	8.633135	8	60	230	28	ENST00000367820.2	0.272727	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	135586190	135586190	__UNKNOWN__	IGR	SNP	A	A	G	rs9483817	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:135586190A>G			NA	NA				RP1-32B1.4 (4119 upstream) : AHI1 (18479 downstream)						NA		NA									NA						aggccgaggcaggcggatcac	0.552		NA											-|||	1889	0.377196	0.7708	0.1945	5008	,	,	NA	16902	0.1101	NA	0.2624	False	NA	,,,	NA	NA	NA	2504	0.3681	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.135586190A>G		NA		hg19		0.02	-0.122804	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			5	3.006414	KEEP	10	0	0	10	267	AA	0	0	0			6	60	204	0	0	19.650643	6	60	177	41		0.5	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	135586225	135586225	__UNKNOWN__	IGR	SNP	T	T	C	rs9494199	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:135586225T>C			NA	NA				RP1-32B1.4 (4154 upstream) : AHI1 (18444 downstream)						NA		NA									NA						gagaccatcctggctaaaacg	0.597		NA											-|||	1605	0.320487	0.5779	0.1599	5008	,	,	NA	15764	0.1101	NA	0.2565	False	NA	,,,	NA	NA	NA	2504	0.3691	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.135586225T>C		NA		hg19		0.02	-0.096478	TCCxGGC	UNCOVERED																																																																																			NOVEL					0			4	3.003874	KEEP	12	0	0	10	258	TT	0	0	0			4	40	116	0	0	10.822637	5	48	151	40		0.444444	0.120436
LINC00271	100131814	__UNKNOWN__	__UNKNOWN__	6	135930446	135930446	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:135930446A>G	ENST00000421378.2	+	0	147					NR_026805.1		P0C7V0	CF217_HUMAN	long intergenic non-protein coding RNA 271	NA		NA									NA						ggtcaggctgatctcgagctc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							6q23.3	2012-10-12	2011-08-11	2011-08-11	ENSG00000231028	ENSG00000231028	100131814		Long non-coding RNAs	32526	non-coding RNA	RNA, long non-coding		NA	chromosome 6 open reading frame 217, non-protein coding RNA 271	C6orf217, NCRNA00271	NA		Standard	NR_026805	NR_026805	NA	Approved		uc010kgm.2	P0C7V0	OTTHUMG00000015632	ENST00000421378.2:	chr6.hg19:g.135930446A>G		NA		hg19		0.02	-0.166655	CTGxTCT	COVERED																																																																																			NOVEL	LINC00271-003	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000443467.1	3	2.706615	KEEP	1	0	0	9	246	AA	0.99257	0.351317	0		+	3	60	96	0	0	7.982059	10	60	307	36	ENST00000421378.2	0.230769	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	136146901	136146901	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:136146901T>C			NA	NA				RP11-394G3.2 (17297 upstream) : PDE7B (25932 downstream)						NA		NA									NA						cctcgtgatctgcccgcctcg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.136146901T>C		NA		hg19		0.02	-0.157864	ATCxGCC	COVERED																																																																																			NOVEL					0			5	2.707048	KEEP	0	0	0	9	252	TT	0.99254	0.320398	0			4	60	124	0	0	10.168706	14	60	420	38		0.222222	0.322807
MTFR2	113115	__UNKNOWN__	__UNKNOWN__	6	136559958	136559958	__UNKNOWN__	Intron	SNP	G	G	A	rs554225972		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:136559958G>A	ENST00000420702.1	-	6	1259				MTFR2_ENST00000451457.2_Intron	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	NA		NA			aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)					NA						taatcccagcgctttgggagg	0.423		NA											G|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	17898	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410	113115			21115	protein-coding gene	gene with protein product		NA	DUF729 domain containing 1, family with sequence similarity 54, member A	DUFD1, FAM54A	NA		Standard	NM_138419	NM_138419	NA	Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.869+645C>T	chr6.hg19:g.136559958G>A		NA	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	hg19	CCDS5176.1	0.02	-0.219284	AGCxCTT	COVERED																																																																																			NOVEL	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042378.2	9	2.406721	KEEP	0	0	0	8	232	GG	0.99257	0.54878	0		-	3	60	89	0	0	6.527914	19	60	624	45	ENST00000420702.1	0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	137135771	137135771	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:137135771A>G			NA	NA				MAP3K5 (22115 upstream) : PEX7 (7945 downstream)						NA		NA									NA						tgtaatcctaacactttggga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.137135771A>G		NA		hg19		0.02	-0.254277	CTAxCAC	COVERED																																																																																			NOVEL					0			7	3.006502	KEEP	0	0	0	10	264	AA	0.992708	0.663648	0			3	60	92	0	0	6.651145	22	60	617	50		0.12	0.668523
OLIG3	167826	__UNKNOWN__	__UNKNOWN__	6	137815459	137815459	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:137815459G>T	ENST00000367734.2	-	0	72					NM_175747.2	NP_786923.1	Q7RTU3	OLIG3_HUMAN	oligodendrocyte transcription factor 3	NA		NA			spinal cord motor neuron cell fate specification (GO:0021520)|spinal cord motor neuron migration (GO:0097476)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II transcription corepressor activity (GO:0001106)			endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	11	Breast(32;0.165)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00161)|OV - Ovarian serous cystadenocarcinoma(155;0.00447)		GCTTTTCCCCGCCTCTCTCCC	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AK096362	CCDS5186.1	6q23.3	2013-05-21			ENSG00000177468	ENSG00000177468	167826		Basic helix-loop-helix proteins	18003	protein-coding gene	gene with protein product		609323			NA		Standard	NM_175747	NM_175747	NA	Approved	Bhlhb7, bHLHe20	uc003qhp.1	Q7RTU3	OTTHUMG00000015657	ENST00000367734.2:c.-152C>A	chr6.hg19:g.137815459G>T		NA	Q8N8Q0	hg19	CCDS5186.1	0.02	-0.298237	CCCxCCT	COVERED																																																																																			NOVEL	OLIG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042405.1	2	2.407031	KEEP	0	0	0	8	241	CG	0.99254	0.775233	0		-	11	60	330	0	0	29.125202	22	60	722	67	ENST00000367734.2	0.333333	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	138252011	138252011	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:138252011G>C			NA	NA				TNFAIP3 (47562 upstream) : RP11-10J5.1 (12204 downstream)						NA		NA									NA						ctccgaaagtgctgggattac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.138252011G>C		NA		hg19		0.02	-0.149112	AGTxCTG	COVERED																																																																																			NOVEL					0			3	3.008441	KEEP	0	0	0	10	301	GG	0.992708	0.289872	0			7	60	225	0	0	21.336575	8	60	268	40		0.466667	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	138350459	138350459	__UNKNOWN__	IGR	SNP	C	C	T	rs570804435|rs56081342|rs200222953|rs560155606|rs201902542		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:138350459C>T			NA	NA				RP11-240M16.1 (77748 upstream) : PERP (59182 downstream)						NA		NA									NA						tccttccttccttccttcctt	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.138350459C>T		NA		hg19		0.02	-0.096486	TTCxTTC	UNCOVERED																																																																																			NOVEL					0			14	3.911615	KEEP	12	0	0	13	395	CC	0.99257	0.119541	0			5	60	145	0	0	14.198305	4	60	146	45		0.555556	0.120436
KIAA1244	57221	__UNKNOWN__	__UNKNOWN__	6	138508075	138508075	__UNKNOWN__	Intron	SNP	A	A	G	rs535499517	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:138508075A>G	ENST00000251691.4	+	2	303					NM_020340.4	NP_065073.3			KIAA1244	NA		NA								NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		tttttgagacagagtttcact	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379	57221		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	21213	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 33	NA	chromosome 6 open reading frame 92	C6orf92	NA		Standard	NM_020340	NM_020340	NA	Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.137+16225A>G	chr6.hg19:g.138508075A>G		NA		hg19	CCDS5189.2	0.02	-0.078935	GACxGAG	UNCOVERED																																																																																			NOVEL	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042425.4	8	2.406161	KEEP	3	0	0	8	221	AA	0	0	0		+	2	20	71	1	0	6.396	4	60	116	21	ENST00000251691.4	0.333333	0.077336
KIAA1244	57221	__UNKNOWN__	__UNKNOWN__	6	138508080	138508080	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:138508080T>C	ENST00000251691.4	+	2	303					NM_020340.4	NP_065073.3			KIAA1244	NA		NA								NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		gagacagagtttcactcttgt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379	57221		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	21213	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 33	NA	chromosome 6 open reading frame 92	C6orf92	NA		Standard	NM_020340	NM_020340	NA	Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.137+16230T>C	chr6.hg19:g.138508080T>C		NA		hg19	CCDS5189.2	0.02	-0.078937	AGTxTCA	UNCOVERED																																																																																			NOVEL	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042425.4	8	2.405337	KEEP	3	0	0	8	219	TT	0	0	0		+	2	20	72	0	0	6.496026	4	60	114	21	ENST00000251691.4	0.333333	0.077336
KIAA1244	57221	__UNKNOWN__	__UNKNOWN__	6	138554761	138554761	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:138554761G>A	ENST00000251691.4	+	5	586					NM_020340.4	NP_065073.3			KIAA1244	NA		NA								NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		tgatccacccgcctcggcctc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379	57221		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	21213	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 33	NA	chromosome 6 open reading frame 92	C6orf92	NA		Standard	NM_020340	NM_020340	NA	Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.420+3772G>A	chr6.hg19:g.138554761G>A		NA		hg19	CCDS5189.2	0.02	-0.149077	CCCxCCT	COVERED																																																																																			NOVEL	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042425.4	4	3.911446	KEEP	3	0	0	13	393	GG	0.993072	0.289978	0		+	3	60	85	0	0	6.672918	12	60	390	52	ENST00000251691.4	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	138981921	138981921	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:138981921T>C			NA	NA				NHSL1 (88244 upstream) : RP11-390P2.4 (31763 downstream)						NA		NA									NA						ggtgaaaccctgtctctacaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.138981921T>C		NA		hg19		0.02	-0.184163	CCCxGTC	COVERED																																																																																			NOVEL					0			12	3.308418	KEEP	4	0	0	11	303	TT	0.99257	0.420331	0			3	60	86	0	0	6.362915	17	60	501	47		0.15	0.423478
ECT2L	345930	__UNKNOWN__	__UNKNOWN__	6	139185196	139185196	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:139185196A>G	ENST00000423192.1	+	11	1452				ECT2L_ENST00000541398.1_Intron|ECT2L_ENST00000495970.1_Intron|ECT2L_ENST00000367682.2_Intron			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	NA		NA					Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						agtggctcacacctgtaatcc	0.468		NA	N, Splice, Mis		ETP ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734	345930		Rho guanine nucleotide exchange factors, F-boxes /  other	21118	protein-coding gene	gene with protein product	lung specific F-box and DH domain containing protein, F-box protein 49	NA	chromosome 6 open reading frame 91, epithelial cell transforming sequence 2 oncogene-like	C6orf91	NA		Standard	NM_001077706	NM_001077706	NA	Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.1292-937A>G	chr6.hg19:g.139185196A>G		NA	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	hg19	CCDS43508.1	0.02	-0.149087	CACxCCT	COVERED																																																																																			NOVEL	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042441.3	8	4.209236	KEEP	2	0	0	14	368	AA	0.995343	0.290641	0		+	3	60	105	0	0	8.672299	12	60	344	43	ENST00000423192.1	0.2	0.292001
ECT2L	345930	__UNKNOWN__	__UNKNOWN__	6	139187515	139187515	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:139187515G>A	ENST00000423192.1	+	11	1635				ECT2L_ENST00000541398.1_Intron|ECT2L_ENST00000495970.1_Intron|ECT2L_ENST00000367682.2_Intron			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	NA		NA					Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						ggcctcccaagtagctgggat	0.473		NA	N, Splice, Mis		ETP ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734	345930		Rho guanine nucleotide exchange factors, F-boxes /  other	21118	protein-coding gene	gene with protein product	lung specific F-box and DH domain containing protein, F-box protein 49	NA	chromosome 6 open reading frame 91, epithelial cell transforming sequence 2 oncogene-like	C6orf91	NA		Standard	NM_001077706	NM_001077706	NA	Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.1474+1200G>A	chr6.hg19:g.139187515G>A		NA	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	hg19	CCDS43508.1	0.02	-0.184207	CAAxTAG	COVERED																																																																																			NOVEL	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042441.3	12	4.212111	KEEP	0	0	0	14	420	GG	0.995343	0.421506	0		+	3	60	88	0	0	6.710512	15	60	501	48	ENST00000423192.1	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	139331633	139331633	__UNKNOWN__	IGR	SNP	C	C	T	rs190449934	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:139331633C>T			NA	NA				REPS1 (22235 upstream) : ABRACL (18185 downstream)						NA		NA									NA						ctcagcctcccgagtagctgg	0.532		NA											c|||	2	0.000399361	0.0	0.0029	5008	,	,	NA	16285	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.139331633C>T		NA		hg19		0.02	-0.131574	TCCxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.406535	KEEP	4	0	0	8	229	CC	0	0	0			3	60	93	0	0	7.472224	12	60	383	33		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	139856490	139856490	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:139856490C>G			NA	NA				RP11-12A2.3 (62298 upstream) : RP5-899B16.1 (319565 downstream)						NA		NA									NA						gtaatcccagcactttgggag	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.139856490C>G		NA		hg19		0.02	-0.078883	CAGxACT	UNCOVERED																																																																																			NOVEL					0			3	2.407259	KEEP	0	0	0	8	247	CC	0.99257	0.076761	0			3	60	90	0	0	7.939859	6	60	216	27		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	139934560	139934560	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:139934560A>G			NA	NA				RP11-12A2.3 (140368 upstream) : RP5-899B16.1 (241495 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.139934560A>G		NA		hg19		0.02	-0.19295	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.706465	KEEP	2	0	0	9	243	AA	0.99257	0.454356	0			3	60	93	0	0	7.061247	17	60	496	53		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	141128375	141128375	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:141128375A>G			NA	NA				MIR4465 (123355 upstream) : RP3-460G2.2 (38719 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.141128375A>G		NA		hg19		0.02	-0.140347	GCTxGGA	UNCOVERED																																																																																			NOVEL					0			6	4.207719	KEEP	15	0	0	14	371	AA	0	0	0			3	60	107	0	0	8.972735	11	60	337	66		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	141350766	141350766	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:141350766A>G			NA	NA				RP3-460G2.2 (176705 upstream) : RP11-63E9.1 (417381 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.141350766A>G		NA		hg19		0.02	-0.166646	CACxCCT	COVERED																																																																																			NOVEL					0			8	3.608938	KEEP	1	0	0	12	333	AA	0.993634	0.351693	0			3	60	96	0	0	7.87299	11	60	333	47		0.214286	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	141368596	141368596	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:141368596A>G			NA	NA				RP3-460G2.2 (194535 upstream) : RP11-63E9.1 (399551 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.141368596A>G		NA		hg19		0.02	-0.210466	CACxCCT	COVERED																																																																																			NOVEL					0			9	3.007337	KEEP	1	0	0	10	278	AA	0.992708	0.518353	0			3	60	107	0	0	8.326895	19	60	541	52		0.136364	0.522161
GPR126	57211	__UNKNOWN__	__UNKNOWN__	6	142680130	142680130	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:142680130T>C	ENST00000367609.3	+	3	504				GPR126_ENST00000367608.2_Intron|GPR126_ENST00000230173.6_Intron|GPR126_ENST00000296932.8_Intron|GPR126_ENST00000545477.1_Intron	NM_198569.2	NP_940971	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		atcacttgagtccaggagttt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414	57211		-, GPCR / Class B : Orphans	13841	protein-coding gene	gene with protein product		612243			NA	12565841	Standard		NM_001032395	NA	Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000367609.3:c.104-8576T>C	chr6.hg19:g.142680130T>C		NA	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	hg19	CCDS47489.1	0.02	-0.149105	GAGxCCA	COVERED																																																																																			NOVEL	GPR126-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396706.1	5	3.30822	KEEP	0	0	0	11	302	TT	0.993072	0.289978	0		+	3	60	97	0	0	7.872309	12	60	357	37	ENST00000367609.3	0.2	0.292001
HIVEP2	3097	__UNKNOWN__	__UNKNOWN__	6	143100494	143100494	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:143100494T>C	ENST00000367604.1	-	3	208				HIVEP2_ENST00000367603.2_Intron|HIVEP2_ENST00000012134.2_Intron			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		tggtggctcatgcctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(107;843 1510 13293 16805 42198)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818	3097		Zinc fingers, C2H2-type	4921	protein-coding gene	gene with protein product	c-myc intron binding protein 1	143054	human immunodeficiency virus type I enhancer-binding protein 2		NA	1733857, 2022670	Standard		NM_006734	NA	Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.432-3166A>G	chr6.hg19:g.143100494T>C		NA	Q02646|Q5THT5|Q9NS05	hg19	CCDS43510.1	0.02	-0.149073	TCAxGCC	COVERED																																																																																			NOVEL	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042495.1	3	2.706679	KEEP	1	0	0	9	245	TT	0.99257	0.289832	0		-	3	60	92	0	0	7.37311	12	60	343	37	ENST00000367604.1	0.2	0.292001
PLAGL1	5325	__UNKNOWN__	__UNKNOWN__	6	144314186	144314186	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:144314186T>C	ENST00000444202.1	-	2	148				PLAGL1_ENST00000392307.1_Intron|PLAGL1_ENST00000429150.1_Intron|PLAGL1_ENST00000437412.1_Intron|PLAGL1_ENST00000416623.1_Intron|PLAGL1_ENST00000392309.1_Intron|PLAGL1_ENST00000493898.1_Intron	NM_001080951.1	NP_001074420.1	Q9UM63	PLAL1_HUMAN	pleiomorphic adenoma gene-like 1	NA		NA			apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(1)|large_intestine(4)|lung(2)|prostate(1)|skin(3)|stomach(2)	13				OV - Ovarian serous cystadenocarcinoma(155;5.74e-07)|GBM - Glioblastoma multiforme(68;0.0885)		tggctcacgcttgtaatccca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U81992	CCDS5202.1, CCDS5203.1	6q24-q25	2013-01-08			ENSG00000118495	ENSG00000118495	5325		Zinc fingers, C2H2-type	9046	protein-coding gene	gene with protein product		603044			NA	9722527, 9671765	Standard		NM_006718	NA	Approved	ZAC, LOT1	uc003qkf.3	Q9UM63	OTTHUMG00000015738	ENST00000444202.1:c.615-7875A>G	chr6.hg19:g.144314186T>C		NA	B2RBA4|B2RCM8|E1P595|E1P597|O76019|Q7Z3V8|Q92981|Q96JR9|Q9UIZ0	hg19	CCDS5202.1	0.02	-0.30698	CGCxTGT	COVERED																																																																																			NOVEL	PLAGL1-206	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042540.1	9	2.537355	KEEP	0	1	30	19	517	TT	0.999863	0.800136	0		-	3	60	104	0	0	7.742192	24	60	737	79	ENST00000444202.1	0.111111	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	144597360	144597360	__UNKNOWN__	IGR	SNP	A	A	G	rs646837	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:144597360A>G			NA	NA				STX11 (87853 upstream) : UTRN (15604 downstream)						NA		NA									NA						tgcccaggctagagtgcaatg	0.527		NA											G|||	2346	0.46845	0.528	0.4683	5008	,	,	NA	17437	0.4028	NA	0.3688	False	NA	,,,	NA	NA	NA	2504	0.5583	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.144597360A>G		NA		hg19		0.02	-0.166638	GCTxGAG	UNCOVERED																																																																																			NOVEL					0			10	2.396455	KEEP	2	0	0	8	200	AA	0	0	0			3	60	100	0	0	8.273041	11	60	320	42		0.214286	0.353947
SAMD5	389432	__UNKNOWN__	__UNKNOWN__	6	147886618	147886618	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:147886618A>G	ENST00000367474.1	+	0	1550					NM_001030060.2	NP_001025231.1	Q5TGI4	SAMD5_HUMAN	sterile alpha motif domain containing 5	NA		NA									NA		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;9.55e-10)|GBM - Glioblastoma multiforme(68;0.112)		ttttttagacagagtctcgct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL354880	CCDS34548.1	6q24.3	2013-01-10			ENSG00000203727	ENSG00000203727	389432		Sterile alpha motif (SAM) domain containing	21180	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001030060	NM_001030060	NA	Approved	dJ875H10.1	uc003qmc.2	Q5TGI4	OTTHUMG00000015767	ENST00000367474.1:c.*1026A>G	chr6.hg19:g.147886618A>G		NA		hg19	CCDS34548.1	0.02	-0.377125	GACxGAG	COVERED																																																																																			NOVEL	SAMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042610.1	23	5.645077	KEEP	0	1	29	29	792	AA	0.999997	0.909066	0		+	3	47	102	0	2	7.075497	35	60	1036	103	ENST00000367474.1	0.078947	0.909069
RP11-307P5.1	0	__UNKNOWN__	__UNKNOWN__	6	148226311	148226311	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:148226311A>G	ENST00000427015.1	+	0	117										NA		NA									NA						ggcgtgagccactgcgcccgg	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000427015.1:	chr6.hg19:g.148226311A>G		NA		hg19		0.02	-0.166625	GCCxCTG	COVERED																																																																																			NOVEL	RP11-307P5.1-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000042615.1	8	3.00649	KEEP	4	0	0	10	264	AA	0.992708	0.351366	0		+	3	37	87	0	0	6.534286	16	60	471	47	ENST00000427015.1	0.157895	0.353947
RP11-307P5.1	0	__UNKNOWN__	__UNKNOWN__	6	148226313	148226313	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:148226313T>C	ENST00000427015.1	+	0	117										NA		NA									NA						cgtgagccactgcgcccggcc	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000427015.1:	chr6.hg19:g.148226313T>C		NA		hg19		0.02	-0.166644	CACxGCG	COVERED																																																																																			NOVEL	RP11-307P5.1-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000042615.1	8	2.707063	KEEP	4	0	0	9	251	TT	0.99254	0.351306	0		+	3	37	101	0	0	7.933287	16	60	474	48	ENST00000427015.1	0.157895	0.353947
SASH1	23328	__UNKNOWN__	__UNKNOWN__	6	148660879	148660879	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:148660879T>C	ENST00000367469.1	+	2	74							O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	NA		NA			positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		tggggttttgtcatgttggcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961	23328		SAM and SH3 domain containing, Sterile alpha motif (SAM) domain containing	19182	protein-coding gene	gene with protein product		607955			NA	9872452, 12771949	Standard	NM_015278	NM_015278	NA	Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367469.1:c.22-50391T>C	chr6.hg19:g.148660879T>C		NA	Q5TGN5|Q8TAI0|Q9H7R7	hg19		0.02	-0.166636	TTGxCAT	COVERED																																																																																			NOVEL	SASH1-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000042620.1	6	3.909617	KEEP	1	0	0	13	354	TT	0.993634	0.351693	0		+	3	60	87	0	0	6.611131	15	60	445	43	ENST00000367469.1	0.166667	0.353947
ZC3H12D	340152	__UNKNOWN__	__UNKNOWN__	6	149801848	149801848	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:149801848A>G	ENST00000409948.1	-	1	83				ZC3H12D_ENST00000409806.3_Intron|ZC3H12D_ENST00000416573.2_Intron|ZC3H12D_ENST00000389942.5_Intron|ZC3H12D_ENST00000542614.1_Intron			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	NA		NA			negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		ctccagcctgagcaacaagag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199	340152		Zinc fingers, CCCH-type domain containing	21175	protein-coding gene	gene with protein product	MCP induced protein 4	611106	chromosome 6 open reading frame 95	C6orf95	NA	18178554	Standard	NM_207360	NM_207360	NA	Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409948.1:c.69+2338T>C	chr6.hg19:g.149801848A>G		NA	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	hg19		0.02	-0.140338	CTGxGCA	COVERED																																																																																			NOVEL	ZC3H12D-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000042640.2	8	2.405689	KEEP	0	0	0	8	222	AA	0.99257	0.259026	0		-	3	60	103	0	0	8.682042	10	60	298	37	ENST00000409948.1	0.230769	0.260965
GINM1	116254	__UNKNOWN__	__UNKNOWN__	6	149912253	149912253	__UNKNOWN__	3'UTR	SNP	T	T	C	rs71720057|rs113946399	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:149912253T>C	ENST00000367419.5	+	0	1393					NM_138785.3	NP_620140.1	Q9NU53	GINM1_HUMAN	glycoprotein integral membrane 1	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)					NA						ggtgaaaccctgtctctacta	0.532		NA											.|||	54	0.0107827	0.0378	0.0014	5008	,	,	NA	15443	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC014320	CCDS5216.1	6q24.3	2012-07-20	2012-07-20	2012-07-20	ENSG00000055211	ENSG00000055211	116254			21074	protein-coding gene	gene with protein product		NA	chromosome 6 open reading frame 72	C6orf72	NA		Standard	NM_138785	NM_138785	NA	Approved	dJ12G14.2	uc003qmq.1	Q9NU53	OTTHUMG00000015789	ENST00000367419.5:c.*279T>C	chr6.hg19:g.149912253T>C		NA	B2RDY7|E1P5A2	hg19	CCDS5216.1	0.02	-0.271863	CCCxGTC	COVERED																																																																																			NOVEL	GINM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042644.1	7	4.810969	KEEP	0	0	0	16	430	TT	0.997832	0.738068	0		+	4	60	107	0	0	7.626072	24	60	708	53	ENST00000367419.5	0.142857	0.739671
KATNA1	11104	__UNKNOWN__	__UNKNOWN__	6	149931056	149931056	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:149931056A>T	ENST00000335647.5	-	4	546				KATNA1_ENST00000335643.8_Intron|KATNA1_ENST00000367411.2_Intron|KATNA1_ENST00000494504.1_Intron					katanin p60 (ATPase containing) subunit A 1	NA		NA								endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		accaacatggagaaaccctgt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625	11104		ATPases / AAA-type	6216	protein-coding gene	gene with protein product		606696	katanin p60 (ATPase-containing) subunit A 1		NA	9658175	Standard	NM_007044	NM_007044	NA	Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.502-5138T>A	chr6.hg19:g.149931056A>T		NA		hg19	CCDS5217.1	0.02	-0.113998	TGGxGAA	UNCOVERED																																																																																			NOVEL	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042641.2	7	3.908821	KEEP	0	0	0	13	349	AA	0.994391	0.161555	0		-	3	60	84	0	0	6.782415	10	60	291	32	ENST00000335647.5	0.230769	0.162467
LATS1	9113	__UNKNOWN__	__UNKNOWN__	6	149995042	149995042	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:149995042T>C	ENST00000543571.1	-	7	3431				LATS1_ENST00000253339.5_Intron	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1	NA		NA								central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		aactcccgacttcaggtgatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023	9113			6514	protein-coding gene	gene with protein product		603473	LATS (large tumor suppressor, Drosophila) homolog 1, LATS, large tumor suppressor, homolog 1 (Drosophila)		NA	9988268, 15122335	Standard	NM_004690	NM_004690	NA	Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.2883+2353A>G	chr6.hg19:g.149995042T>C		NA		hg19	CCDS34551.1	0.02	-0.149103	GACxTCA	COVERED																																																																																			NOVEL	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043923.4	10	2.405907	KEEP	1	0	0	8	217	TT	0.99257	0.289832	0		-	4	49	129	0	0	10.901707	12	60	354	37	ENST00000543571.1	0.25	0.292001
RP11-244K5.8	0	__UNKNOWN__	__UNKNOWN__	6	150196581	150196581	__UNKNOWN__	RNA	SNP	A	A	G	rs7452592	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:150196581A>G	ENST00000606915.1	+	0	889					NR_045126.1					NA		NA									NA						taggtgtacaatggcataatc	0.398		NA											a|||	615	0.122804	0.0325	0.2608	5008	,	,	NA	18048	0.0258	NA	0.2475	False	NA	,,,	NA	NA	NA	2504	0.1186	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000606915.1:	chr6.hg19:g.150196581A>G		NA		hg19		0.02	-0.026318	ACAxTGG	UNCOVERED																																																																																			NOVEL	RP11-244K5.8-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000470302.1	3	2.405287	KEEP	0	0	0	8	219	AA	0.99257	0	0		+	2	60	70	0	0	7.95396	0	0	0	18	ENST00000606915.1	1	0
RAET1L	154064	__UNKNOWN__	__UNKNOWN__	6	150343008	150343008	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:150343008G>A	ENST00000367341.1	-	2	349				RAET1L_ENST00000286380.2_Intron			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	NA		NA			antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5		Ovarian(120;0.028)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.4e-12)		gactacaggcgtgagccaccg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY039682	CCDS5224.1	6q24.1-25.1	2008-02-05			ENSG00000155918	ENSG00000155918	154064			16798	protein-coding gene	gene with protein product		611047			NA	11827464	Standard	NM_130900	NM_130900	NA	Approved		uc011eei.2	Q5VY80	OTTHUMG00000015809	ENST00000367341.1:c.349+107C>T	chr6.hg19:g.150343008G>A		NA	A3KME4|Q8TE74	hg19	CCDS5224.1	0.02	-0.298231	GGCxTGA	COVERED																																																																																			NOVEL	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042676.1	8	3.437031	KEEP	8	1	27	21	561	GG	0.999366	0.780565	0		-	3	49	93	0	0	6.453494	28	60	881	67	ENST00000367341.1	0.096774	0.78106
PLEKHG1	57480	__UNKNOWN__	__UNKNOWN__	6	150946787	150946787	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:150946787C>T	ENST00000367328.1	+	2	155				RP11-136K14.2_ENST00000456018.1_RNA	NM_001029884.1	NP_001025055.1	Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	NA		NA					Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		caccaccatgcctggctaatt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278	57480		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	20884	protein-coding gene	gene with protein product		NA			NA	10574462	Standard		XM_005267064	NA	Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000367328.1:c.-157-25077C>T	chr6.hg19:g.150946787C>T		NA	Q5T1F2	hg19	CCDS34552.1	0.02	-0.166627	ATGxCTG	UNCOVERED																																																																																			NOVEL	PLEKHG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		14	3.307532	KEEP	10	0	0	11	299	CC	0	0	0		+	4	40	110	1	0	8.769246	14	60	466	41	ENST00000367328.1	0.222222	0.353947
AKAP12	9590	__UNKNOWN__	__UNKNOWN__	6	151669406	151669406	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:151669406A>G	ENST00000253332.1	+	3	508				AKAP12_ENST00000490177.1_Intron|AKAP12_ENST00000402676.2_Intron|AKAP12_ENST00000359755.5_Intron|AKAP12_ENST00000354675.6_Intron			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		gttgcagtgaaccgagatcgt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(141;1616 1805 10049 24534 51979)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016	9590		A-kinase anchor proteins	370	protein-coding gene	gene with protein product	gravin, Src-Suppressed C Kinase Substrate	604698	A kinase (PRKA) anchor protein (gravin) 12		NA	9000000	Standard		NM_144497	NA	Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.320-440A>G	chr6.hg19:g.151669406A>G		NA	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	hg19	CCDS5229.1	0.02	-0.289432	TGAxCCG	COVERED																																																																																			NOVEL	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042712.1	9	9.022778	KEEP	0	0	0	30	831	AA	0.999997	0.760885	0		+	4	60	124	0	0	9.258057	25	60	748	72	ENST00000253332.1	0.137931	0.760887
AKAP12	9590	__UNKNOWN__	__UNKNOWN__	6	151669446	151669446	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:151669446T>C	ENST00000253332.1	+	3	508				AKAP12_ENST00000490177.1_Intron|AKAP12_ENST00000402676.2_Intron|AKAP12_ENST00000359755.5_Intron|AKAP12_ENST00000354675.6_Intron			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		ggcgacagagtgagactctgt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(141;1616 1805 10049 24534 51979)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016	9590		A-kinase anchor proteins	370	protein-coding gene	gene with protein product	gravin, Src-Suppressed C Kinase Substrate	604698	A kinase (PRKA) anchor protein (gravin) 12		NA	9000000	Standard		NM_144497	NA	Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.320-400T>C	chr6.hg19:g.151669446T>C		NA	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	hg19	CCDS5229.1	0.02	1.443137	GAGxGAG	COVERED																																																																																			NOVEL	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042712.1	27	8.371526	KEEP	1	2	57	48	1212	TT	1	0.998465	0		+	5	60	162	1	0	10.874067	62	60	1562	184	ENST00000253332.1	0.074627	0.998465
ESR1	2099	__UNKNOWN__	__UNKNOWN__	6	152032583	152032583	__UNKNOWN__	Intron	SNP	T	T	C	rs113618976		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:152032583T>C	ENST00000440973.1	+	2	300					NM_001122742.1	NP_001116214.1	P03372	ESR1_HUMAN	estrogen receptor 1	NA		NA			androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	gtctcgatcttctgacctcgt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831	2099		Nuclear hormone receptors	3467	protein-coding gene	gene with protein product		133430		ESR	NA	3754034	Standard		NM_000125	NA	Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000440973.1:c.-71+9443T>C	chr6.hg19:g.152032583T>C		NA	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	hg19	CCDS5234.1	0.02	-0.131439	TCTxCTG	COVERED																																																																																			NOVEL	ESR1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		8	3.005334	KEEP	1	0	0	10	258	TT	0.992708	0.227502	0		+	4	58	133	0	0	11.433485	11	60	305	35	ENST00000440973.1	0.266667	0.229173
SYNE1	23345	__UNKNOWN__	__UNKNOWN__	6	152644552	152644552	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:152644552C>T	ENST00000367255.5	-	82	16519				SYNE1_ENST00000423061.1_Intron|SYNE1_ENST00000448038.1_Intron|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Intron	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	NA		NA			cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		ccagcctgggcgacagagcga	0.522		NA								HNSCC(10;0.0054)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018	23345			17089	protein-coding gene	gene with protein product	myocyte nuclear envelope protein 1, nuclear envelope spectrin repeat-1	608441	chromosome 6 open reading frame 98	C6orf98	NA	9872452, 10878022	Standard	NM_182961	NM_182961	NA	Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.15917+60G>A	chr6.hg19:g.152644552C>T		NA	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	hg19	CCDS5236.2	0.02	1.420944	GGGxGAC	COVERED																																																																																			NOVEL	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334755.2	14	6.145844	KEEP	1	1	27	30	871	CC	0.999997	0.99442	0		-	5	60	129	2	0	8.196076	46	60	1545	140	ENST00000367255.5	0.098039	0.994422
MYCT1	80177	__UNKNOWN__	__UNKNOWN__	6	153044147	153044147	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:153044147A>G	ENST00000367245.5	+	0	1475				MYCT1_ENST00000529453.1_3'UTR	NM_025107.2	NP_079383.2	Q8N699	MYCT1_HUMAN	myc target 1	NA		NA				nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	20		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;1.33e-10)|BRCA - Breast invasive adenocarcinoma(81;0.143)		aaagtgctggaattaGCCTGG	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF527367	CCDS5239.1	6q25.1	2008-02-05			ENSG00000120279	ENSG00000120279	80177			23172	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_025107	NM_025107	NA	Approved	MTLC, FLJ21269	uc003qpc.4	Q8N699	OTTHUMG00000015850	ENST00000367245.5:c.*759A>G	chr6.hg19:g.153044147A>G		NA	Q8N396|Q8TBE8|Q9H763	hg19	CCDS5239.1	0.02	-0.306964	TGGxATT	COVERED																																																																																			NOVEL	MYCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042750.2	14	6.616684	KEEP	0	0	0	22	606	AA	0.999879	0.800148	0		+	4	60	137	0	0	10.317106	29	60	851	76	ENST00000367245.5	0.121212	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	153257282	153257282	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:153257282T>C			NA	NA				AL133269.1 (79403 upstream) : FBXO5 (34381 downstream)						NA		NA									NA						tgagccaccatgcccagccGA	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.153257282T>C		NA		hg19		0.02	-0.114029	CCAxGCC	UNCOVERED																																																																																			NOVEL					0			7	3.30821	KEEP	1	0	0	11	301	TT	0.992708	0.161282	0			3	60	98	0	0	8.301099	9	60	279	32		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	153772873	153772873	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:153772873C>T			NA	NA				RNA5SP225 (31166 upstream) : RNU6-896P (229708 downstream)						NA		NA									NA						ccgaggtgggcggatcacgag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.153772873C>T		NA		hg19		0.02	-0.105259	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			3	2.406938	KEEP	4	0	0	8	240	CC	0	0	0			3	60	87	0	0	7.478278	7	60	234	34		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	153800066	153800066	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:153800066A>T			NA	NA				RNA5SP225 (58359 upstream) : RNU6-896P (202515 downstream)						NA		NA									NA						cactccagccagggcaacaag	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.153800066A>T		NA		hg19		0.02	-0.114021	GCCxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.406544	KEEP	0	0	0	8	230	AA	0.99257	0.16126	0			3	60	90	0	0	7.632437	8	60	239	31		0.272727	0.162467
IPCEF1	26034	__UNKNOWN__	__UNKNOWN__	6	154478723	154478723	__UNKNOWN__	3'UTR	SNP	C	C	T	rs139988979	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:154478723C>T	ENST00000265198.4	-	0	3709				OPRM1_ENST00000337049.4_Intron	NM_001130700.1|NM_015553.2	NP_001124172.1|NP_056368.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	NA		NA			oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						TATGTCTTCACGAAAAGCCAA	0.398		NA											G|||	18	0.00359425	0.0	0.0058	5008	,	,	NA	18328	0.0	NA	0.0109	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706	26034		Pleckstrin homology (PH) domain containing	21204	protein-coding gene	gene with protein product	phosphoinositide binding protein PIP3-E	NA			NA	11804589, 19756519	Standard	NM_001130699	NM_001130699	NA	Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000265198.4:c.*2240G>A	chr6.hg19:g.154478723C>T		NA	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	hg19	CCDS5245.1	0.02	-0.280654	TCAxGAA	COVERED																																																																																			NOVEL	IPCEF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042789.2	0	2.406783	KEEP	0	0	0	8	234	CC	0.99257	0.734176	0		-	23	60	673	0	0	70.575646	8	60	260	59	ENST00000265198.4	0.741935	0.739671
IPCEF1	26034	__UNKNOWN__	__UNKNOWN__	6	154618426	154618426	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:154618426A>G	ENST00000422970.2	-	3	135				IPCEF1_ENST00000367220.4_Intron|IPCEF1_ENST00000265198.4_Intron	NM_001130699.1	NP_001124171.1	Q8WWN9	ICEF1_HUMAN	interaction protein for cytohesin exchange factors 1	NA		NA			oxidation-reduction process (GO:0055114)|oxygen transport (GO:0015671)|positive regulation of GTP catabolic process (GO:0033126)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	oxygen transporter activity (GO:0005344)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	12						cacccacctcagcctcccaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007863	CCDS5245.1, CCDS47509.1	6q25.2	2013-01-10			ENSG00000074706	ENSG00000074706	26034		Pleckstrin homology (PH) domain containing	21204	protein-coding gene	gene with protein product	phosphoinositide binding protein PIP3-E	NA			NA	11804589, 19756519	Standard	NM_001130699	NM_001130699	NA	Approved	PIP3-E, KIAA0403	uc021zhc.1	Q8WWN9	OTTHUMG00000015872	ENST00000422970.2:c.61-7536T>C	chr6.hg19:g.154618426A>G		NA	A8K1K2|B7ZL78|B7ZL80|O43153|Q5HYL8	hg19	CCDS47509.1	0.02	-0.122774	CTCxGCC	COVERED																																																																																			NOVEL	IPCEF1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375787.1	5	3.909662	KEEP	0	0	0	13	358	AA	0.994391	0.19521	0		-	3	60	89	0	0	7.282389	10	60	301	39	ENST00000422970.2	0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	154703405	154703405	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:154703405C>T			NA	NA				IPCEF1 (25505 upstream) : CNKSR3 (5232 downstream)						NA		NA									NA						cccagcacttcgggaggctga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.154703405C>T		NA		hg19		0.02	-0.131574	CTTxGGG	COVERED																																																																																			NOVEL					0			7	2.406888	KEEP	0	0	0	8	240	CC	0.99257	0.22747	0			4	60	115	0	0	9.770823	10	60	333	34		0.285714	0.229173
TIAM2	26230	__UNKNOWN__	__UNKNOWN__	6	155325803	155325803	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:155325803T>C	ENST00000461783.3	+	3	1065							Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	NA		NA			apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		gctgggattataggcatgagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426	26230		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11806	protein-coding gene	gene with protein product		604709			NA	10512681	Standard	NM_012454	NM_012454	NA	Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.-209+60463T>C	chr6.hg19:g.155325803T>C		NA	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	hg19	CCDS34558.1	0.02	-0.114003	TTAxAGG	UNCOVERED																																																																																			NOVEL	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387980.2	5	3.007053	KEEP	0	0	0	10	267	TT	0.992708	0.161282	0		+	3	60	102	0	0	8.832974	8	60	222	30	ENST00000461783.3	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	158621213	158621213	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:158621213C>T			NA	NA				GTF2H5 (837 upstream) : RP11-732M18.3 (82081 downstream)						NA		NA									NA						cccgggttcacgccattctcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.158621213C>T		NA		hg19		0.02	-0.078914	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.707237	KEEP	5	0	0	9	257	AC	0.99257	0.076761	0			3	40	84	0	0	7.532829	5	60	156	33		0.375	0.077336
SYTL3	94120	__UNKNOWN__	__UNKNOWN__	6	159142511	159142511	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:159142511A>G	ENST00000297239.9	+	9	914				SYTL3_ENST00000360448.3_Intron|SYTL3_ENST00000367081.3_Intron			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	NA		NA			exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)			endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		ccaaagtgctaggattacagg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674	94120			15587	protein-coding gene	gene with protein product		NA			NA	11773082	Standard		NM_001242384	NA	Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.720+3268A>G	chr6.hg19:g.159142511A>G		NA	Q496J4|Q496J6|Q5U3B9	hg19	CCDS56458.1	0.02	-0.149071	GCTxGGA	COVERED																																																																																			NOVEL	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042876.1	2	2.705628	KEEP	1	0	0	9	242	AA	0.99254	0.289823	0		+	3	60	91	0	0	7.273159	12	60	349	43	ENST00000297239.9	0.2	0.292001
RP1-111C20.4	0	__UNKNOWN__	__UNKNOWN__	6	159442134	159442134	__UNKNOWN__	RNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:159442134A>C	ENST00000607391.1	+	0	236				RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA						NA		NA									NA						gctgggattaaaggcgtgagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000607391.1:	chr6.hg19:g.159442134A>C		NA		hg19		0.02	-0.070175	TTAxAGG	UNCOVERED																																																																																			NOVEL	RP1-111C20.4-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000471437.1	4	2.706841	KEEP	1	0	0	9	250	AT	0.99254	0.076759	0		+	2	60	72	0	0	6.335709	5	60	152	31	ENST00000607391.1	0.285714	0.077336
SOD2	6648	__UNKNOWN__	__UNKNOWN__	6	160132836	160132836	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:160132836A>C	ENST00000546087.1	-	4	1713							P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	NA		NA			age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		tctgatcaccataaccacctc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	6648	1.15.1.1		11180	protein-coding gene	gene with protein product		147460			NA		Standard	NM_000636	NM_000636	NA	Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.115-18941T>G	chr6.hg19:g.160132836A>C		NA	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	hg19		0.02	-0.175388	ACCxTAA	COVERED																																																																																			NOVEL	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399943.1	20	3.103168	KEEP	24	3	87	41	1119	AA	0.999957	0.38739	0		-	3	40	91	0	0	6.862083	17	60	504	91	ENST00000546087.1	0.15	0.387407
SOD2	6648	__UNKNOWN__	__UNKNOWN__	6	160133337	160133337	__UNKNOWN__	Intron	SNP	T	T	C	rs375395728		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:160133337T>C	ENST00000546087.1	-	3	1713							P04179	SODM_HUMAN	superoxide dismutase 2, mitochondrial	NA		NA			age-dependent response to reactive oxygen species (GO:0001315)|cellular response to ethanol (GO:0071361)|detection of oxygen (GO:0003032)|erythrophore differentiation (GO:0048773)|glutathione metabolic process (GO:0006749)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|hydrogen peroxide biosynthetic process (GO:0050665)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|iron ion homeostasis (GO:0055072)|liver development (GO:0001889)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|oxygen homeostasis (GO:0032364)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to gamma radiation (GO:0010332)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to lipopolysaccharide (GO:0032496)|response to manganese ion (GO:0010042)|response to selenium ion (GO:0010269)|response to silicon dioxide (GO:0034021)|response to superoxide (GO:0000303)|response to zinc ion (GO:0010043)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)|vasodilation by acetylcholine involved in regulation of systemic arterial blood pressure (GO:0003069)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|manganese ion binding (GO:0030145)|oxygen binding (GO:0019825)|superoxide dismutase activity (GO:0004784)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(3)|skin(1)	14		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.103)		OV - Ovarian serous cystadenocarcinoma(65;1.4e-18)|BRCA - Breast invasive adenocarcinoma(81;5.77e-06)		accacctccataaccaccacT	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M36693	CCDS5265.1, CCDS34564.1	6q25	2008-02-05			ENSG00000112096	ENSG00000112096	6648	1.15.1.1		11180	protein-coding gene	gene with protein product		147460			NA		Standard	NM_000636	NM_000636	NA	Approved		uc003qsg.3	P04179	OTTHUMG00000015940	ENST00000546087.1:c.114+18579A>G	chr6.hg19:g.160133337T>C		NA	B2R7R1|B3KUK2|B4DL20|B4E3K9|E1P5A9|P78434|Q16792|Q5TCM1|Q96EE6|Q9P2Z3	hg19		0.02	1.681451	CCAxAAC	COVERED																																																																																			NOVEL	SOD2-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399943.1	65	3.257171	KEEP	21	8	236	94	2485	TT	1	0.999881	0		-	14	53	461	0	0	36.270626	71	60	2011	281	ENST00000546087.1	0.164706	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	160280342	160280342	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:160280342T>C			NA	NA				PNLDC1 (38607 upstream) : RP1-249F5.3 (39875 downstream)						NA		NA									NA						gtaatcccagtactttgggag	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.160280342T>C		NA		hg19		0.02	-0.122776	CAGxACT	COVERED																																																																																			NOVEL					0			4	3.607331	KEEP	1	0	0	12	308	TT	0.993072	0.194952	0			3	60	100	0	0	8.273127	11	60	315	36		0.214286	0.196312
IGF2R	3482	__UNKNOWN__	__UNKNOWN__	6	160529992	160529992	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:160529992C>T	ENST00000475584.1	+	4	402				RP11-288H12.4_ENST00000604521.1_lincRNA			P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	NA		NA			insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ggattacaggcgtgagccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081	3482		CD molecules	5467	protein-coding gene	gene with protein product	cation-independent mannose-6 phosphate receptor	147280			NA		Standard	NM_000876	NM_000876	NA	Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000475584.1:c.403-3605C>T	chr6.hg19:g.160529992C>T		NA	Q7Z7G9|Q96PT5	hg19		0.02	-0.140327	AGGxGTG	UNCOVERED																																																																																			NOVEL	IGF2R-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000042936.1	6	2.40735	KEEP	1	0	0	8	250	CC	0	0	0		+	3	60	92	0	0	7.372413	12	60	384	36	ENST00000475584.1	0.2	0.260965
SLC22A3	6581	__UNKNOWN__	__UNKNOWN__	6	160857953	160857953	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:160857953A>G	ENST00000275300.2	+	6	1225				SLC22A3_ENST00000392145.1_Intron	NM_021977.3	NP_068812.1	O75751	S22A3_HUMAN	solute carrier family 22 (organic cation transporter), member 3	NA		NA			dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|histamine uptake (GO:0051615)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|regulation of appetite (GO:0032098)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dopamine transmembrane transporter activity (GO:0005329)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|toxin transporter activity (GO:0019534)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		Breast(66;0.00028)|Ovarian(120;0.0308)|Prostate(117;0.218)		OV - Ovarian serous cystadenocarcinoma(65;9.47e-17)|BRCA - Breast invasive adenocarcinoma(81;9.75e-06)	Adefovir Dipivoxil(DB00718)|Amphetamine(DB00182)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Colchicine(DB01394)|Desipramine(DB01151)|Dopamine(DB00988)|Estradiol(DB00783)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imipramine(DB00458)|Irinotecan(DB00762)|Lamivudine(DB00709)|Melphalan(DB01042)|Metformin(DB00331)|Methamphetamine(DB01577)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Phenoxybenzamine(DB00925)|Prazosin(DB00457)|Procainamide(DB01035)|Progesterone(DB00396)|Testosterone(DB00624)|Vincristine(DB00541)	CGTTAAATTTACAATACATCC	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													90	86	88			NA	NA	6		NA											NA				160857953		2203	4300	6503	SO:0001627	intron_variant			AF078749	CCDS5277.1	6q25.3	2013-07-18	2013-07-18		ENSG00000146477	ENSG00000146477	6581		Solute carriers	10967	protein-coding gene	gene with protein product		604842	solute carrier family 22 (extraneuronal monoamine transporter), member 3		NA	9632645, 9933568	Standard	NM_021977	NM_021977	NA	Approved	OCT3, EMT	uc003qti.4	O75751	OTTHUMG00000015953	ENST00000275300.2:c.1073+44A>G	chr6.hg19:g.160857953A>G		NA	Q5SYN6|Q9UP02	hg19	CCDS5277.1	0.02	2.03217	TTTxCAA	COVERED																																																																																			NOVEL	SLC22A3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042953.1	1	4.510985	KEEP	0	0	0	15	407	AA	0.99649	0.96403	0		+	19	60	655	0	0	59.942718	32	60	946	92	ENST00000275300.2	0.372549	0.967425
RP3-428L16.1	0	__UNKNOWN__	__UNKNOWN__	6	161367849	161367849	__UNKNOWN__	RNA	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:161367849G>C	ENST00000417479.1	+	0	293										NA		NA									NA						gggtctcgctgtgttgcccag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417479.1:	chr6.hg19:g.161367849G>C		NA		hg19		0.02	-0.087727	GCTxTGT	UNCOVERED																																																																																			NOVEL	RP3-428L16.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000042974.1	4	3.00918	KEEP	0	0	0	10	313	GG	0.993072	0.09903	0		+	3	60	100	0	0	8.778433	7	60	242	30	ENST00000417479.1	0.3	0.099721
PARK2	5071	__UNKNOWN__	__UNKNOWN__	6	161851932	161851932	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:161851932T>C	ENST00000366898.1	-	10	1186				PARK2_ENST00000366894.1_Intron|PARK2_ENST00000338468.3_Intron|PARK2_ENST00000366896.1_Intron|PARK2_ENST00000366897.1_Intron	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	NA		NA			adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		ctttgggaggtcaaggcaggc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345	5071		Parkinson disease	8607	protein-coding gene	gene with protein product	E3 ubiquitin ligase	602544	Parkinson disease (autosomal recessive, juvenile) 2, parkin, parkinson protein 2, E3 ubiquitin protein ligase (parkin)		NA	9560156, 9570960	Standard		NM_004562	NA	Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.1084-44023A>G	chr6.hg19:g.161851932T>C		NA	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	hg19	CCDS5281.1	0.02	-0.131559	AGGxCAA	COVERED																																																																																			NOVEL	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042995.1	3	2.406121	KEEP	1	0	0	8	223	TT	0.99257	0.22747	0		-	3	60	95	0	0	7.773116	11	60	328	34	ENST00000366898.1	0.214286	0.229173
PARK2	5071	__UNKNOWN__	__UNKNOWN__	6	162521754	162521754	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:162521754A>G	ENST00000366898.1	-	5	637				PARK2_ENST00000366892.1_Intron|PARK2_ENST00000366894.1_Intron|PARK2_ENST00000338468.3_Intron|PARK2_ENST00000366896.1_Intron|PARK2_ENST00000366897.1_Intron	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	NA		NA			adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		gattacaggcatgagccaccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345	5071		Parkinson disease	8607	protein-coding gene	gene with protein product	E3 ubiquitin ligase	602544	Parkinson disease (autosomal recessive, juvenile) 2, parkin, parkinson protein 2, E3 ubiquitin protein ligase (parkin)		NA	9560156, 9570960	Standard		NM_004562	NA	Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.535-46548T>C	chr6.hg19:g.162521754A>G		NA	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	hg19	CCDS5281.1	0.02	-0.166651	GGCxTGA	COVERED																																																																																			NOVEL	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042995.1	7	3.607282	KEEP	1	0	0	12	314	AA	0.993072	0.351495	0		-	3	60	99	0	0	7.978853	13	60	386	43	ENST00000366898.1	0.1875	0.353947
PARK2	5071	__UNKNOWN__	__UNKNOWN__	6	162992306	162992306	__UNKNOWN__	Intron	SNP	G	G	A	rs532051934	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:162992306G>A	ENST00000366898.1	-	2	110				PARK2_ENST00000366892.1_Intron|PARK2_ENST00000366894.1_Intron|PARK2_ENST00000338468.3_Intron|PARK2_ENST00000366896.1_Intron|PARK2_ENST00000366897.1_Intron	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	NA		NA			adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		gcagtgagccgagatcgtgcc	0.443		NA											a|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	13966	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345	5071		Parkinson disease	8607	protein-coding gene	gene with protein product	E3 ubiquitin ligase	602544	Parkinson disease (autosomal recessive, juvenile) 2, parkin, parkinson protein 2, E3 ubiquitin protein ligase (parkin)		NA	9560156, 9570960	Standard		NM_004562	NA	Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.8-127801C>T	chr6.hg19:g.162992306G>A		NA	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	hg19	CCDS5281.1	0.02	-0.210492	GCCxAGA	COVERED																																																																																			NOVEL	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000042995.1	12	9.350212	KEEP	2	1	28	41	1070	GG	1	0.522161	0		-	4	60	118	0	0	9.269454	17	60	509	100	ENST00000366898.1	0.190476	0.522161
QKI	9444	__UNKNOWN__	__UNKNOWN__	6	163900044	163900044	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:163900044G>A	ENST00000361752.3	+	3	953				QKI_ENST00000424802.3_Intron|QKI_ENST00000361195.2_Intron|QKI_ENST00000453779.2_Intron|QKI_ENST00000392127.2_Intron|QKI_ENST00000275262.7_Intron	NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	NA		NA			long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		CAggccgggcgcggtggctca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531	9444			21100	protein-coding gene	gene with protein product		609590	quaking homolog, KH domain RNA binding (mouse)		NA	10535969	Standard	NM_006775	NM_006775	NA	Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.402+116G>A	chr6.hg19:g.163900044G>A		NA	Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	hg19	CCDS5285.1	0.02	-0.157882	GGCxCGG	COVERED																																																																																			NOVEL	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043016.2	4	3.609529	KEEP	0	0	0	12	346	GG	0.993634	0.320751	0		+	3	60	88	0	0	6.792203	14	60	460	39	ENST00000361752.3	0.176471	0.322807
RP1-230L10.1	0	__UNKNOWN__	__UNKNOWN__	6	164175354	164175354	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:164175354C>T	ENST00000452944.1	+	0	102										NA		NA									NA						ccacctaactcgcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000452944.1:	chr6.hg19:g.164175354C>T		NA		hg19		0.02	-0.1228	ACTxGCC	COVERED																																																																																			NOVEL	RP1-230L10.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000043020.1	4	2.707846	KEEP	0	0	0	9	269	CC	0.99254	0.194847	0		+	3	60	88	0	0	7.072936	11	60	355	36	ENST00000452944.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	6	164333140	164333140	__UNKNOWN__	IGR	SNP	C	C	G	rs12201375	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:164333140C>G			NA	NA				RN7SL366P (71258 upstream) : RP1-155D22.2 (171914 downstream)						NA		NA									NA						cacggtgaaaccctgtctcta	0.567		NA											C|||	97	0.019369	0.0068	0.0259	5008	,	,	NA	14760	0.004	NA	0.0646	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr6.hg19:g.164333140C>G		NA		hg19		0.02	-0.052635	AAAxCCT	UNCOVERED																																																																																			NOVEL					0			9	2.406654	KEEP	10	0	0	8	236	CC	0	0	0			4	40	135	0	0	13.749561	2	40	65	26		0.666667	0.054137
RPS6KA2	6196	__UNKNOWN__	__UNKNOWN__	6	166847517	166847517	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:166847517A>G	ENST00000405189.3	-	15	1398				RPS6KA2_ENST00000265678.4_Intron|RPS6KA2_ENST00000510118.1_Intron|RPS6KA2_ENST00000503859.1_Intron|RPS6KA2_ENST00000481261.2_Intron			Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	NA		NA			axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		caaagtgctgagattacaggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242	6196			10431	protein-coding gene	gene with protein product		601685	ribosomal protein S6 kinase, 90kD, polypeptide 2		NA	8141249	Standard	NM_021135	NM_001006932	NA	Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000405189.3:c.1066-1539T>C	chr6.hg19:g.166847517A>G		NA	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	hg19		0.02	-0.131562	CTGxGAT	COVERED																																																																																			NOVEL	RPS6KA2-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000362838.2	2	2.405999	KEEP	0	0	0	8	220	AT	0.992708	0.227502	0		-	3	60	91	0	0	7.482117	10	60	305	34	ENST00000405189.3	0.230769	0.229173
RP3-470B24.5	0	__UNKNOWN__	__UNKNOWN__	6	168376847	168376847	__UNKNOWN__	lincRNA	SNP	C	C	G	rs77867907		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:168376847C>G	ENST00000538528.1	-	0	772										NA		NA									NA						GTGTGGGGAGCAGGAGGCAGT	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													32	30	30			NA	NA	6		NA											NA				168376847		692	1591	2283													NA			NA				NA			NA					NA						ENST00000538528.1:	chr6.hg19:g.168376847C>G		NA		hg19		0.02	-0.149125	GAGxAGG	COVERED																																																																																			NOVEL	RP3-470B24.5-201	KNOWN	basic	lincRNA	NA	lincRNA		3	2.406585	KEEP	0	0	0	8	232	CC	0.99257	0.289832	0		-	7	60	225	0	0	22.70676	4	60	143	34	ENST00000538528.1	0.636364	0.292001
WDR27	253769	__UNKNOWN__	__UNKNOWN__	6	170035201	170035201	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:170035201T>C	ENST00000448612.1	-	20	2113				WDR27_ENST00000423258.1_Intron|WDR27_ENST00000333572.6_Intron|WDR27_ENST00000546525.1_Intron	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	NA		NA				nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		tggtggctcatgcctgtaatc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465	253769		WD repeat domain containing	21248	protein-coding gene	gene with protein product		NA			NA		Standard	NM_182552	NM_182552	NA	Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.2004-580A>G	chr6.hg19:g.170035201T>C		NA	A5PLM8|C9JGV0|Q5T066	hg19	CCDS47520.2	0.02	-0.122796	TCAxGCC	COVERED																																																																																			NOVEL	WDR27-010	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407334.1	4	4.811109	KEEP	3	0	0	16	432	TT	0.99649	0.195623	0		-	3	60	99	0	0	8.17288	11	60	330	51	ENST00000448612.1	0.214286	0.196312
RP5-1086L22.1	0	__UNKNOWN__	__UNKNOWN__	6	170569554	170569554	__UNKNOWN__	RNA	SNP	C	C	T	rs186372536	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr6:170569554C>T	ENST00000452071.1	-	0	154					NR_002787.1					NA		NA									NA						gaggccgaggcgggcggatca	0.522		NA											T|||	13	0.00259585	0.0008	0.0029	5008	,	,	NA	14767	0.0069	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000452071.1:	chr6.hg19:g.170569554C>T		NA		hg19		0.02	-0.105257	AGGxGGG	UNCOVERED																																																																																			NOVEL	RP5-1086L22.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000043250.1	6	2.406439	KEEP	3	0	0	8	235	CC	0	0	0		-	6	60	179	0	0	17.149036	6	60	198	34	ENST00000452071.1	0.5	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	385432	385432	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:385432C>T			NA	NA				WI2-2373I1.2 (51044 upstream) : AC226118.1 (33892 downstream)						NA		NA									NA						cggtgaaaccccgtctctact	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.385432C>T		NA		hg19		0.02	1.467463	ACCxCGT	COVERED																																																																																			NOVEL					0			104	19.422739	KEEP	27	2	58	85	2566	CC	1	0.997163	0			5	23	136	0	1	9.077128	42	60	1393	223		0.106383	0.997163
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	404026	404026	__UNKNOWN__	IGR	SNP	G	G	A	rs191914893		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:404026G>A			NA	NA				WI2-2373I1.2 (69638 upstream) : AC226118.1 (15298 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.552		NA											-|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	16948	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.404026G>A		NA		hg19		0.02	-0.192977	CACxCCT	UNCOVERED																																																																																			NOVEL					0			4	2.40333	KEEP	6	0	0	8	222	GG	0	0	0			4	60	117	0	0	9.701392	12	60	387	53		0.25	0.457757
PRKAR1B	5575	__UNKNOWN__	__UNKNOWN__	7	697833	697833	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:697833T>G	ENST00000406797.1	-	4	615				PRKAR1B_ENST00000544935.1_Intron|PRKAR1B_ENST00000537384.1_Intron|PRKAR1B_ENST00000360274.4_Intron|PRKAR1B_ENST00000403562.1_Intron	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		cactttgagatgccaaggagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	5575	2.7.11.1		9390	protein-coding gene	gene with protein product		176911			NA	1358799, 3479018	Standard		NM_002735	NA	Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.440+19032A>C	chr7.hg19:g.697833T>G		NA	Q8N422	hg19	CCDS34579.1	0.02	-0.22803	AGAxGCC	COVERED																																																																																			NOVEL	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322525.1	4	3.006839	KEEP	0	0	0	10	265	TT	0.992708	0.578679	0		-	3	60	100	0	0	7.565278	20	60	581	60	ENST00000406797.1	0.130435	0.58293
PRKAR1B	5575	__UNKNOWN__	__UNKNOWN__	7	717312	717312	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:717312T>C	ENST00000406797.1	-	4	523				PRKAR1B_ENST00000544935.1_Intron|PRKAR1B_ENST00000537384.1_Intron|PRKAR1B_ENST00000360274.4_Intron|PRKAR1B_ENST00000403562.1_Intron	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		aatcctcccatctcagcctcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	5575	2.7.11.1		9390	protein-coding gene	gene with protein product		176911			NA	1358799, 3479018	Standard		NM_002735	NA	Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.349-355A>G	chr7.hg19:g.717312T>C		NA	Q8N422	hg19	CCDS34579.1	0.02	-0.289433	CCAxCTC	COVERED																																																																																			NOVEL	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322525.1	6	3.138833	KEEP	2	1	24	19	520	TT	0.999859	0.76078	0		-	4	60	125	0	0	9.295391	26	60	781	78	ENST00000406797.1	0.133333	0.760887
PRKAR1B	5575	__UNKNOWN__	__UNKNOWN__	7	734465	734465	__UNKNOWN__	Intron	SNP	A	A	G	rs185337465	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:734465A>G	ENST00000406797.1	-	3	352				PRKAR1B_ENST00000544935.1_Intron|PRKAR1B_ENST00000537384.1_Intron|PRKAR1B_ENST00000360274.4_Intron|PRKAR1B_ENST00000403562.1_Intron	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		ctgaggtcagaagttcgagac	0.542		NA											G|||	178	0.0355431	0.1278	0.013	5008	,	,	NA	16410	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	5575	2.7.11.1		9390	protein-coding gene	gene with protein product		176911			NA	1358799, 3479018	Standard		NM_002735	NA	Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.178-14102T>C	chr7.hg19:g.734465A>G		NA	Q8N422	hg19	CCDS34579.1	0.02	-0.096473	CAGxAGT	UNCOVERED																																																																																			NOVEL	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322525.1	7	3.308406	KEEP	6	0	0	11	303	AA	0	0	0		-	3	60	87	0	0	7.332424	8	60	237	33	ENST00000406797.1	0.272727	0.139832
GET4	51608	__UNKNOWN__	__UNKNOWN__	7	935119	935119	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:935119C>T	ENST00000265857.3	+	0	1138				GET4_ENST00000407192.1_3'UTR	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	NA		NA			tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GTTTCAGAGGCGAGTCCTGGG	0.701		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857	51608			21690	protein-coding gene	gene with protein product	CGI-20 protein, conserved edge protein, transmembrane domain recognition complex, 35kDa	612056	chromosome 7 open reading frame 20	C7orf20	NA	10810093, 20106980, 20676083	Standard	NM_015949	NM_015949	NA	Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.*60C>T	chr7.hg19:g.935119C>T		NA	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	hg19	CCDS5317.1	0.02	1.111618	AGGxGAG	COVERED																																																																																			NOVEL	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000231930.1	1	3.908888	KEEP	0	0	0	13	363	CC	0.994391	0.994196	0		+	5	60	142	0	0	8.242758	84	60	2606	110	ENST00000265857.3	0.05618	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	1217271	1217271	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:1217271G>C			NA	NA				AC091729.9 (12368 upstream) : UNCX (55271 downstream)						NA		NA									NA						gaactcctgggctcaaatgat	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.1217271G>C		NA		hg19		0.02	-0.377224	TGGxCTC	COVERED																																																																																			NOVEL					0			16	6.92046	KEEP	4	0	0	23	709	GG	0.999869	0.90895	0			3	60	104	1	0	7.311233	34	60	1159	102		0.081081	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	1228727	1228727	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:1228727A>G			NA	NA				AC091729.9 (23824 upstream) : UNCX (43815 downstream)						NA		NA									NA						aggaggaggaagaggaggagg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.1228727A>G		NA		hg19		0.02	-0.306938	GGAxGAG	COVERED																																																																																			NOVEL					0			12	5.413417	KEEP	0	0	0	18	495	AA	0.999859	0.800133	0			3	60	98	1	1	6.95352	28	60	811	77		0.096774	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	1240487	1240487	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:1240487A>G			NA	NA				AC091729.9 (35584 upstream) : UNCX (32055 downstream)						NA		NA									NA						ggccaggcacagtggctcatg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.1240487A>G		NA		hg19		0.02	-0.166655	CACxGTG	COVERED																																																																																			NOVEL					0			14	4.21103	KEEP	4	0	0	14	391	AA	0.993634	0.351693	0			3	60	104	1	0	8.233113	16	60	485	47		0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	1845563	1845563	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:1845563C>T			NA	NA				AC074389.1 (25136 upstream) : MAD1L1 (9866 downstream)						NA		NA									NA						ctgcccgcctcggcctcccaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.1845563C>T		NA		hg19		0.02	-0.201741	CCTxGGC	COVERED																																																																																			NOVEL					0			12	5.11382	KEEP	15	0	0	17	492	CC	0.99257	0.4869	0			3	45	85	0	0	6.411191	15	60	485	66		0.166667	0.490544
SNX8	29886	__UNKNOWN__	__UNKNOWN__	7	2304718	2304718	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2304718A>G	ENST00000222990.3	-	6	664					NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	NA		NA			early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		Tgccgggcgcagtggctcacg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266	29886		Sorting nexins	14972	protein-coding gene	gene with protein product		614905			NA		Standard		NM_013321	NA	Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512	ENST00000222990.3:c.622-625T>C	chr7.hg19:g.2304718A>G		NA	A4D207|Q96I67	hg19	CCDS5331.1	0.02	-0.438402	CGCxGTG	COVERED																																																																																			NOVEL	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322949.2	13	2.406243	KEEP	0	0	0	8	223	AA	0.99257	0.952727	0		-	3	60	99	0	0	6.518045	43	60	1305	83	ENST00000222990.3	0.065217	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	2391335	2391335	__UNKNOWN__	IGR	SNP	A	A	G	rs13310848	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2391335A>G			NA	NA				SNX8 (37236 upstream) : EIF3B (3165 downstream)						NA		NA									NA						gtgtggtggcaggcgcctgta	0.557		NA											G|||	3869	0.772564	0.7632	0.7378	5008	,	,	NA	8915	0.7976	NA	0.7664	False	NA	,,,	NA	NA	NA	2504	0.7904	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.2391335A>G		NA		hg19		0.02	-0.070173	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			6	2.386088	KEEP	4	0	0	8	202	AA	0	0	0			3	60	99	0	0	9.525005	3	47	93	25		0.5	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	2438946	2438946	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2438946C>T			NA	NA				AC004840.8 (10714 upstream) : CHST12 (4276 downstream)						NA		NA									NA						cttttcttttctttttttgag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.2438946C>T		NA		hg19		0.02	-0.140351	TTTxTTT	COVERED																																																																																			NOVEL					0			5	3.009188	KEEP	0	0	0	10	317	CC	0.992708	0.259062	0			3	60	89	0	0	7.172829	11	60	369	40		0.214286	0.260965
CHST12	55501	__UNKNOWN__	__UNKNOWN__	7	2454771	2454771	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2454771G>A	ENST00000258711.6	+	1	58					NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	NA		NA			carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		aggccaaggcgggtggatcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	55501	2.8.2.5	Sulfotransferases, membrane-bound	17423	protein-coding gene	gene with protein product		610129			NA	10781601	Standard	NM_018641	NM_018641	NA	Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.-78+11491G>A	chr7.hg19:g.2454771G>A		NA	A4D1Z9|Q502W3|Q9NXY7	hg19	CCDS5333.1	0.02	-0.19293	GGCxGGT	COVERED																																																																																			NOVEL	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060170.3	8	3.30827	KEEP	3	0	0	11	304	GG	0.992708	0.454419	0		+	3	60	88	0	0	6.493397	18	60	591	52	ENST00000258711.6	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	2512400	2512400	__UNKNOWN__	IGR	SNP	A	A	G	rs11525049	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2512400A>G			NA	NA				AC004840.9 (24915 upstream) : GRIFIN (2664 downstream)						NA		NA									NA						ccgagatcacaccactgcact	0.567		NA											A|||	306	0.0611022	0.0045	0.0893	5008	,	,	NA	11750	0.0139	NA	0.1491	False	NA	,,,	NA	NA	NA	2504	0.0757	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.2512400A>G		NA		hg19		0.02	-0.122755	CACxCCA	COVERED																																																																																			NOVEL					0			12	3.004605	KEEP	8	0	0	10	256	AA	0.99257	0.194853	0			3	40	90	0	0	7.633018	8	60	217	42		0.272727	0.196312
IQCE	23288	__UNKNOWN__	__UNKNOWN__	7	2645013	2645013	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2645013T>G	ENST00000402050.2	+	19	1927				IQCE_ENST00000438376.2_Intron|IQCE_ENST00000325979.7_Intron|IQCE_ENST00000404984.1_Intron	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	NA		NA				mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		ccagcacttttggaggccgag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012	23288			29171	protein-coding gene	gene with protein product		NA			NA	10470851	Standard	NM_152558	XR_242067	NA	Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.1743+388T>G	chr7.hg19:g.2645013T>G		NA	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	hg19	CCDS43542.1	0.02	-0.05263	TTTxGGA	UNCOVERED																																																																																			NOVEL	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325063.2	5	2.406103	KEEP	2	0	0	8	223	AT	0.99257	0.043461	0		+	2	30	69	0	0	6.392948	3	60	90	23	ENST00000402050.2	0.4	0.043787
AMZ1	155185	__UNKNOWN__	__UNKNOWN__	7	2725226	2725226	__UNKNOWN__	Intron	SNP	T	T	C	rs373174046	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2725226T>C	ENST00000312371.4	+	1	150					NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	NA		NA					metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		cggtggctcatgcctgtaatc	0.552		NA											T|||	25	0.00499201	0.0	0.0	5008	,	,	NA	12734	0.0248	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945	155185			22231	protein-coding gene	gene with protein product	archaemetzincin-1	615168			NA	15972818	Standard	NM_133463	NM_133463	NA	Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.-219+5921T>C	chr7.hg19:g.2725226T>C		NA	B3KRS0|Q8TF51	hg19	CCDS34589.1	0.02	-0.184156	TCAxGCC	COVERED																																																																																			NOVEL	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325244.1	10	3.909808	KEEP	2	0	0	13	356	TT	0.993634	0.420782	0		+	3	60	97	0	0	7.461255	17	60	481	48	ENST00000312371.4	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	2894631	2894631	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2894631T>C			NA	NA				GNA12 (10673 upstream) : CARD11 (51143 downstream)						NA		NA									NA						ccatcctggctaacatggtga	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.2894631T>C		NA		hg19		0.02	-0.236751	GGCxAAC	UNCOVERED																																																																																			NOVEL					0			6	2.705403	KEEP	4	0	0	9	232	TT	0	0	0			3	49	96	0	0	6.943199	24	60	689	49		0.111111	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	2914407	2914407	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:2914407A>G			NA	NA				GNA12 (30449 upstream) : CARD11 (31367 downstream)						NA		NA									NA						agctggtctcaaactcctggc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.2914407A>G		NA		hg19		0.02	-0.324232	CTCxAAC	COVERED																																																																																			NOVEL					0			12	4.21083	KEEP	2	0	0	14	393	AA	0.995343	0.831824	0			4	60	104	0	0	7.011427	30	60	886	76		0.117647	0.835716
CARD11	84433	__UNKNOWN__	__UNKNOWN__	7	3017013	3017013	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:3017013A>G	ENST00000396946.4	-	2	279					NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	NA		NA			Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		caggaggattacttgagccca	0.483		NA	Mis		DLBCL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7p22	84433	caspase recruitment domain family, member 11		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286	84433			16393	protein-coding gene	gene with protein product	card-maguk protein 1, bcl10-interacting maguk protein 3	607210			NA	11278692, 11356195	Standard	NM_032415	NM_032415	NA	Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.125-18748T>C	chr7.hg19:g.3017013A>G		NA	A4D1Z7|Q2NKN7|Q548H3	hg19	CCDS5336.2	0.02	-0.359543	ATTxCTT	COVERED																																																																																			NOVEL	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059344.4	8	3.003818	KEEP	0	0	0	10	252	AA	0.992708	0.882393	0		-	4	60	134	0	0	9.909772	31	60	886	79	ENST00000396946.4	0.114286	0.888875
AC091801.1	0	__UNKNOWN__	__UNKNOWN__	7	3183174	3183174	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:3183174C>T	ENST00000402115.1	-	4	287				AC091801.1_ENST00000403226.1_Intron						NA		NA									NA						tctacaaaaacacaaacaaaa	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000402115.1:c.181-2340G>A	chr7.hg19:g.3183174C>T		NA		hg19		0.02	-0.394727	AAAxACA	COVERED																																																																																			NOVEL	AC091801.1-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325284.1	10	11.431129	KEEP	0	0	0	38	1111	CC	1	0.92664	0		-	4	60	105	0	0	6.639435	39	60	1299	112	ENST00000402115.1	0.093023	0.92664
AC091801.1	0	__UNKNOWN__	__UNKNOWN__	7	3205685	3205685	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:3205685T>A	ENST00000404626.3	-	2	137	c.44A>T	c.(43-45)aAc>aTc	p.N15I							NA		NA									NA						aggcaggaggtttgcttgaac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000404626.3:c.44A>T	chr7.hg19:g.3205685T>A	ENSP00000384254:p.Asn15Ile	NA		hg19		0.02	2.583269	AGGxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	T	6.093	0.385464	0.11524	.	.	ENSG00000217455	ENST00000404626	.	.	.	0.225	0.225	0.15325	.	.	.	.	.	T	0.53481	0.1799	.	.	.	.	.	.	.	.	.	.	.	.	T	0.63065	-0.6720	3	0.87932	D	0	.	.	.	.	.	.	.	.	I	15	.	ENSP00000384254:N15I	N	-	2	0	AC091801.1	3172211	0.151000	0.22747	0.039000	0.18376	0.039000	0.13416	0.279000	0.18771	0.257000	0.21650	0.254000	0.18369	AAC	NOVEL	AC091801.1-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325283.1	28	7.634039	KEEP	1	4	103	62	1588	TT	1	1	0		-	6	60	173	0	0	9.687203	121	60	3292	245	ENST00000404626.3	0.047244	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	3274134	3274134	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:3274134C>T			NA	NA				AC073316.2 (36246 upstream) : AC073316.1 (29529 downstream)						NA		NA									NA						gtcaggagatcaagaccatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.3274134C>T		NA		hg19		0.02	-0.210529	GATxAAG	COVERED																																																																																			NOVEL					0			7	2.707897	KEEP	2	0	0	9	272	CC	0.99257	0.54878	0			3	40	92	0	0	6.827273	19	60	638	51		0.136364	0.552887
SDK1	221935	__UNKNOWN__	__UNKNOWN__	7	3462195	3462195	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:3462195G>C	ENST00000389531.3	+	1	298				SDK1_ENST00000404826.2_Intron			Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	NA		NA			cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		gaggctgagggaggaggattg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555	221935		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	19307	protein-coding gene	gene with protein product		607216	sidekick homolog 1 (chicken), sidekick homolog 1, cell adhesion molecule (chicken)		NA	12230981, 17307840, 15213259	Standard	NM_152744	NM_001079653	NA	Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000389531.3:c.298+120679G>C	chr7.hg19:g.3462195G>C		NA	Q8TEN9|Q8TEP5|Q96N44	hg19		0.02	-0.236857	AGGxAGG	COVERED																																																																																			NOVEL	SDK1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323705.2	5	3.911379	KEEP	0	0	0	13	392	GG	0.994391	0.608972	0		+	3	60	100	0	0	7.39432	23	60	779	58	ENST00000389531.3	0.115385	0.612407
SDK1	221935	__UNKNOWN__	__UNKNOWN__	7	4093597	4093597	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4093597A>G	ENST00000389531.3	+	19	2911				SDK1_ENST00000404826.2_Intron			Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	NA		NA			cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ttgagacagaatcttgctctg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555	221935		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	19307	protein-coding gene	gene with protein product		607216	sidekick homolog 1 (chicken), sidekick homolog 1, cell adhesion molecule (chicken)		NA	12230981, 17307840, 15213259	Standard	NM_152744	NM_001079653	NA	Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000389531.3:c.2911+2135A>G	chr7.hg19:g.4093597A>G		NA	Q8TEN9|Q8TEP5|Q96N44	hg19		0.02	-0.149085	AGAxTCT	COVERED																																																																																			NOVEL	SDK1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323705.2	7	3.608471	KEEP	1	0	0	12	323	AA	0.993072	0.289978	0		+	3	60	108	0	0	8.972442	12	60	337	39	ENST00000389531.3	0.2	0.292001
SDK1	221935	__UNKNOWN__	__UNKNOWN__	7	4218135	4218135	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs373316963		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4218135G>A	ENST00000389531.3	+	34	4955	c.4955G>A	c.(4954-4956)cGc>cAc	p.R1652H	SDK1_ENST00000404826.2_Missense_Mutation_p.R1672H			Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1672	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AAGTACCGGCGCTATGAAGTA	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	100	110	106		5015	4.2	1	7		106	0,8600		0,0,4300	no	missense	SDK1	NM_152744.3	29	0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077	benign	1672/2214	4218135	1,13005	2203	4300	6503	SO:0001583	missense			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555	221935		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	19307	protein-coding gene	gene with protein product		607216	sidekick homolog 1 (chicken), sidekick homolog 1, cell adhesion molecule (chicken)		NA	12230981, 17307840, 15213259	Standard	NM_152744	NM_001079653	NA	Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000389531.3:c.4955G>A	chr7.hg19:g.4218135G>A	ENSP00000374182:p.Arg1652His	NA	Q8TEN9|Q8TEP5|Q96N44	hg19		0.02	1.221898	GGCxCTA	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.55	2.568435	0.45798	2.27E-4	0.0	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.57436	0.4;0.4	5.09	4.19	0.49359	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000002	T	0.52853	0.1760	M	0.74881	2.28	0.42644	D	0.993429	P;P;P	0.42649	0.746;0.786;0.611	B;B;B	0.40444	0.262;0.329;0.185	T	0.61584	-0.7033	10	0.59425	D	0.04	.	11.6065	0.51035	0.083:0.0:0.917:0.0	.	1652;159;1672	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	H	1672;1652	ENSP00000385899:R1672H;ENSP00000374182:R1652H	ENSP00000374182:R1652H	R	+	2	0	SDK1	4184661	1.000000	0.71417	1.000000	0.80357	0.564000	0.35744	5.808000	0.69165	2.525000	0.85131	0.655000	0.94253	CGC	NOVEL	SDK1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000323705.2	1	4.211932	KEEP	0	0	0	14	416	GG	0.995343	0.995299	0		+	45	60	1330	0	0	125.641312	51	60	1706	167	ENST00000389531.3	0.46875	0.999956
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	4344062	4344062	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4344062A>G			NA	NA				SDK1 (35430 upstream) : FOXK1 (339325 downstream)						NA		NA									NA						ttttgctcttattgcccaggc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.4344062A>G		NA		hg19		0.02	-0.31573	CTTxTTG	COVERED																																																																																			NOVEL					0			10	2.336557	KEEP	1	1	26	17	460	AA	0.999859	0.818349	0			3	60	97	1	0	6.768255	30	60	891	83		0.090909	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	4679416	4679416	__UNKNOWN__	IGR	SNP	T	T	C	rs59828597	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4679416T>C			NA	NA				SDK1 (370784 upstream) : FOXK1 (3971 downstream)						NA		NA									NA						ccaccctccttggcctcccaa	0.527		NA											C|||	3860	0.770767	0.9713	0.7493	5008	,	,	NA	16752	0.7837	NA	0.5765	False	NA	,,,	NA	NA	NA	2504	0.7014	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.4679416T>C		NA		hg19		0.02	-0.26304	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			7	2.406176	KEEP	4	0	0	8	223	TT	0	0	0			12	60	407	0	0	37.887842	17	60	480	58		0.413793	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	4679417	4679417	__UNKNOWN__	IGR	SNP	G	G	A	rs561344858		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4679417G>A			NA	NA				SDK1 (370785 upstream) : FOXK1 (3970 downstream)						NA		NA									NA						caccctccttggcctcccaaa	0.522		NA											G|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16581	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.4679417G>A		NA		hg19		0.02	-0.26317	CTTxGCC	COVERED																																																																																			NOVEL					0			7	3.009251	KEEP	4	0	0	10	316	GG	0.99257	0.711986	0			3	60	93	0	0	6.544699	26	60	892	63		0.103448	0.717315
FOXK1	221937	__UNKNOWN__	__UNKNOWN__	7	4702349	4702349	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4702349A>G	ENST00000446823.1	+	4	216									forkhead box K1	NA		NA								breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		caaagtgctgagattacaggt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916	221937		Forkhead boxes	23480	protein-coding gene	gene with protein product		NA			NA	15202027	Standard		NM_001037165	NA	Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000446823.1:c.-27-12510A>G	chr7.hg19:g.4702349A>G		NA		hg19		0.02	-0.149118	CTGxGAT	COVERED																																																																																			NOVEL	FOXK1-201	KNOWN	basic	protein_coding	NA	protein_coding		8	3.3085	KEEP	0	0	0	11	308	AA	0.993072	0.289978	0		+	3	60	105	0	0	8.578644	13	60	401	41	ENST00000446823.1	0.1875	0.292001
FOXK1	221937	__UNKNOWN__	__UNKNOWN__	7	4736464	4736464	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4736464T>C	ENST00000328914.4	+	1	560				FOXK1_ENST00000446823.1_Intron	NM_001037165.1	NP_001032242.1			forkhead box K1	NA		NA								breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		tttgggaggctgaggtgggtg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916	221937		Forkhead boxes	23480	protein-coding gene	gene with protein product		NA			NA	15202027	Standard		NM_001037165	NA	Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.560+13965T>C	chr7.hg19:g.4736464T>C		NA		hg19	CCDS34591.1	0.02	-0.175419	GGCxGAG	COVERED																																																																																			NOVEL	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323729.2	10	3.609357	KEEP	4	0	0	12	337	TT	0.99254	0.384517	0		+	3	60	86	0	0	6.592996	14	60	434	45	ENST00000328914.4	0.176471	0.387407
AP5Z1	9907	__UNKNOWN__	__UNKNOWN__	7	4825514	4825514	__UNKNOWN__	Intron	SNP	G	G	A	rs184442543	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4825514G>A	ENST00000348624.4	+	9	1226				AP5Z1_ENST00000401897.1_Intron	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	NA		NA			cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)					NA						ctgggattacgggcatgagcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802	9907			22197	protein-coding gene	gene with protein product		613653	KIAA0415	KIAA0415	NA	20613862, 22022230	Standard		NM_014855	NA	Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1132+199G>A	chr7.hg19:g.4825514G>A		NA	Q8N3X2|Q96H80	hg19	CCDS47528.1	0.02	-0.210521	TACxGGC	COVERED																																																																																			NOVEL	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323771.1	8	2.707605	KEEP	0	0	0	9	262	GG	0.99254	0.518266	0		+	3	50	86	0	0	6.361638	17	60	563	45	ENST00000348624.4	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	4836394	4836394	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4836394C>A			NA	NA				AP5Z1 (4995 upstream) : RADIL (2341 downstream)						NA		NA									NA						tcacgcctgtcatcccagcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.4836394C>A		NA		hg19		0.02	-0.280715	TGTxATC	COVERED																																																																																			NOVEL					0			13	6.318401	KEEP	18	0	0	21	633	CC	0.995343	0.736227	0			3	60	87	0	0	6.327728	19	60	658	84		0.136364	0.739671
RADIL	55698	__UNKNOWN__	__UNKNOWN__	7	4853669	4853669	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4853669T>C	ENST00000399583.3	-	9	2327				RADIL_ENST00000536091.1_Intron|RADIL_ENST00000538469.1_Intron	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	NA		NA			multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		cctcagcctctcaaagcactg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927	55698			22226	protein-coding gene	gene with protein product		611491			NA	16051602, 17704304	Standard	NM_018059	NM_018059	NA	Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2139+1239A>G	chr7.hg19:g.4853669T>C		NA	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	hg19	CCDS43544.1	0.02	-0.219264	CTCxCAA	COVERED																																																																																			NOVEL	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323769.2	11	2.404364	KEEP	0	0	0	8	207	TT	0.99257	0.54878	0		-	3	60	109	0	0	8.348516	22	60	662	43	ENST00000399583.3	0.12	0.552887
RADIL	55698	__UNKNOWN__	__UNKNOWN__	7	4880338	4880338	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4880338G>A	ENST00000399583.3	-	3	723				RADIL_ENST00000536091.1_Intron	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	NA		NA			multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		ggtggctcacgcctgtaatcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927	55698			22226	protein-coding gene	gene with protein product		611491			NA	16051602, 17704304	Standard	NM_018059	NM_018059	NA	Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.536-4102C>T	chr7.hg19:g.4880338G>A		NA	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	hg19	CCDS43544.1	0.02	-0.219296	CACxCCT	COVERED																																																																																			NOVEL	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323769.2	9	3.609843	KEEP	4	0	0	12	348	GG	0.993072	0.549057	0		-	4	60	116	0	0	9.163181	16	60	529	59	ENST00000399583.3	0.2	0.552887
RADIL	55698	__UNKNOWN__	__UNKNOWN__	7	4884821	4884821	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4884821C>T	ENST00000399583.3	-	3	723				RADIL_ENST00000536091.1_Intron	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	NA		NA			multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		gaggctgaggcgggaggatca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927	55698			22226	protein-coding gene	gene with protein product		611491			NA	16051602, 17704304	Standard	NM_018059	NM_018059	NA	Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.536-8585G>A	chr7.hg19:g.4884821C>T		NA	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	hg19	CCDS43544.1	0.02	-0.438482	AGGxGGG	COVERED																																																																																			NOVEL	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000323769.2	9	2.738945	KEEP	2	1	25	18	516	CC	0.999859	0.959724	0		-	4	60	108	0	0	6.901537	40	60	1287	100	ENST00000399583.3	0.090909	0.959859
MMD2	221938	__UNKNOWN__	__UNKNOWN__	7	4976637	4976637	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:4976637A>G	ENST00000401401.3	-	2	243				MMD2_ENST00000404774.3_Intron|MMD2_ENST00000406755.1_Intron	NM_198403.3	NP_940685.3	Q8IY49	PAQRA_HUMAN	monocyte to macrophage differentiation-associated 2	NA		NA				Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(11)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		aaagtgttggaattacaggcg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037881	CCDS47529.1, CCDS47530.1, CCDS59047.1	7p22	2004-06-23			ENSG00000136297	ENSG00000136297	221938			30133	protein-coding gene	gene with protein product		614581			NA	12477932	Standard	NM_198403	NM_198403	NA	Approved	PAQR10	uc003sno.4	Q8IY49	OTTHUMG00000151844	ENST00000401401.3:c.48-11474T>C	chr7.hg19:g.4976637A>G		NA	B5MBW4|Q6NVU5|Q6TCH0	hg19	CCDS47530.1	0.02	-0.175413	TGGxATT	COVERED																																																																																			NOVEL	MMD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324141.1	7	2.405338	KEEP	0	0	0	8	210	AA	0.99257	0.384528	0		-	3	60	89	1	0	6.810807	15	60	453	39	ENST00000401401.3	0.166667	0.387407
ZNF890P	645700	__UNKNOWN__	__UNKNOWN__	7	5167129	5167129	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:5167129C>T	ENST00000422060.2	-	0	604					NR_034163.1				zinc finger protein 890, pseudogene	NA		NA									NA						gtgctgggatcacaggcatga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7p22.1	2011-05-24			ENSG00000159904	ENSG00000159904	645700			38691	pseudogene	pseudogene		NA			NA		Standard	NR_034163	NR_034163	NA	Approved		uc003snu.1		OTTHUMG00000166790	ENST00000422060.2:	chr7.hg19:g.5167129C>T		NA		hg19		0.02	-0.149132	GATxACA	COVERED																																																																																			NOVEL	ZNF890P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000391474.1	5	3.310117	KEEP	1	0	0	11	346	CC	0.992708	0.289872	0		-	3	60	93	0	0	7.472046	12	60	413	42	ENST00000422060.2	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	5184940	5184940	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:5184940A>G			NA	NA				ZNF890P (763 upstream) : RNU6-215P (34751 downstream)						NA		NA									NA						tggctctgtcacccaggctgg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.5184940A>G		NA		hg19		0.02	-0.201734	GTCxCCC	COVERED																																																																																			NOVEL					0			8	3.007515	KEEP	0	0	0	10	275	AA	0.992708	0.486967	0			3	60	95	0	0	7.333568	16	60	488	51		0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	5226309	5226309	__UNKNOWN__	IGR	SNP	G	G	A	rs13223283	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:5226309G>A			NA	NA				RNU6-215P (6516 upstream) : WIPI2 (3509 downstream)						NA		NA									NA						gcaagactccgtctcaaaaaa	0.338		NA											G|||	1675	0.334465	0.2648	0.4611	5008	,	,	NA	6182	0.3194	NA	0.3121	False	NA	,,,	NA	NA	NA	2504	0.3773	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.5226309G>A		NA		hg19		0.02	-0.078909	TCCxTCT	UNCOVERED																																																																																			NOVEL					0			22	3.308669	KEEP	16	0	0	11	312	GG	0	0	0			4	60	102	0	0	9.419687	5	60	163	33		0.444444	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	5277745	5277745	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:5277745C>T			NA	NA				WIPI2 (4288 upstream) : AC093376.1 (38221 downstream)						NA		NA									NA						ggtgaaaccccgtctctacta	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.5277745C>T		NA		hg19		0.02	-0.175427	CCCxGTC	UNCOVERED																																																																																			NOVEL					0			7	2.406786	KEEP	1	0	0	8	240	CC	0	0	0			3	46	89	0	0	6.810514	15	60	485	39		0.166667	0.387407
TNRC18	84629	__UNKNOWN__	__UNKNOWN__	7	5437853	5437853	__UNKNOWN__	Intron	SNP	G	G	C	rs111778858	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:5437853G>C	ENST00000399537.4	-	3	536				TNRC18_ENST00000430969.1_Intron|TNRC18_ENST00000399434.2_Intron			O15417	TNC18_HUMAN	trinucleotide repeat containing 18	NA		NA					chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		ccagggtggagtgcaatggcg	0.532		NA											G|||	708	0.141374	0.3903	0.1311	5008	,	,	NA	13809	0.0228	NA	0.0437	False	NA	,,,	NA	NA	NA	2504	0.0348	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095	84629		Trinucleotide (CAG) repeat containing	11962	protein-coding gene	gene with protein product		NA			NA	9225980	Standard		NM_001080495	NA	Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000399537.4:c.188-3627C>G	chr7.hg19:g.5437853G>C		NA	A8MX41|Q96JH1|Q96K91	hg19		0.02	-0.078946	GGAxTGC	UNCOVERED																																																																																			NOVEL	TNRC18-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000324088.6	8	2.407143	KEEP	10	0	0	8	243	GG	0	0	0		-	4	60	138	0	0	13.30048	4	60	126	29	ENST00000399537.4	0.5	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	5493466	5493466	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:5493466A>G			NA	NA				RP11-1275H24.3 (24163 upstream) : AC092171.4 (21968 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.5493466A>G		NA		hg19		0.02	-0.244568	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.706648	KEEP	0	0	0	9	246	AA	0.99254	0.636563	0			3	60	97	0	0	7.212921	21	60	586	50		0.125	0.641347
AIMP2	7965	__UNKNOWN__	__UNKNOWN__	7	6055103	6055103	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6055103T>C	ENST00000400479.2	+	3	482				AIMP2_ENST00000395236.2_Intron|AIMP2_ENST00000223029.3_Intron			Q13155	AIMP2_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 2	NA		NA			apoptotic process (GO:0006915)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|tRNA aminoacylation for protein translation (GO:0006418)|Type II pneumocyte differentiation (GO:0060510)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						cgcctgtaattccagcacttt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U24169	CCDS5344.1	7p22.1	2009-05-29			ENSG00000106305	ENSG00000106305	7965			20609	protein-coding gene	gene with protein product		600859			NA	8666379, 18695251	Standard	NM_006303	NM_006303	NA	Approved	p38, PRO0992, JTV-1, JTV1	uc003spo.3	Q13155	OTTHUMG00000122077	ENST00000400479.2:c.108+120T>C	chr7.hg19:g.6055103T>C		NA	Q75MR1|Q96CZ5|Q9P1L2	hg19		0.02	-0.184185	AATxCCA	COVERED																																																																																			NOVEL	AIMP2-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000325473.2	6	2.706465	KEEP	0	0	0	9	242	TT	0.99254	0.420319	0		+	3	60	92	0	0	7.111307	15	60	450	43	ENST00000400479.2	0.166667	0.423478
KDELR2	11014	__UNKNOWN__	__UNKNOWN__	7	6503782	6503782	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6503782T>G	ENST00000258739.4	-	5	789				DAGLB_ENST00000436575.1_Intron|KDELR2_ENST00000463747.1_Intron|KDELR2_ENST00000490996.1_Intron	NM_006854.3	NP_006845.1	P33947	ERD22_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	NA		NA			intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	KDEL sequence binding (GO:0005046)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		gagccaagattgtaccattgc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X63745	CCDS5351.1, CCDS43550.1	7p	2008-05-02			ENSG00000136240	ENSG00000136240	11014			6305	protein-coding gene	gene with protein product		609024			NA	1316805, 1325562	Standard		NM_006854	NA	Approved	ELP-1, ERD2.2	uc003sqe.4	P33947	OTTHUMG00000023103	ENST00000258739.4:c.605-976A>C	chr7.hg19:g.6503782T>G		NA	A4D2P4|Q6IPC5|Q96E30	hg19	CCDS5351.1	0.02	-0.192874	GATxGTA	COVERED																																																																																			NOVEL	KDELR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059424.2	30	4.534107	KEEP	18	1	31	26	638	TT	0.999859	0.457692	0		-	3	59	100	0	0	7.910928	15	60	392	65	ENST00000258739.4	0.166667	0.457757
GRID2IP	392862	__UNKNOWN__	__UNKNOWN__	7	6539859	6539859	__UNKNOWN__	Intron	SNP	C	C	T	rs149502418	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6539859C>T	ENST00000457091.2	-	20	3399				GRID2IP_ENST00000435185.1_Intron|GRID2IP_ENST00000452113.1_Intron	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	NA		NA			long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						ctttgggaggccgaggcaggt	0.493		NA											C|||	537	0.107228	0.0386	0.0418	5008	,	,	NA	15254	0.2312	NA	0.0517	False	NA	,,,	NA	NA	NA	2504	0.1759	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045	392862			18464	protein-coding gene	gene with protein product		610639	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1		NA	14612983	Standard	XM_294249	NM_001145118	NA	Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.3399+1552G>A	chr7.hg19:g.6539859C>T		NA		hg19	CCDS47537.1	0.02	-0.157899	AGGxCGA	UNCOVERED																																																																																			NOVEL	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340534.1	7	3.008883	KEEP	4	0	0	10	304	CC	0	0	0		-	6	60	188	0	0	16.868945	11	60	373	41	ENST00000457091.2	0.352941	0.322807
GRID2IP	392862	__UNKNOWN__	__UNKNOWN__	7	6569941	6569941	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6569941A>C	ENST00000457091.2	-	3	584				GRID2IP_ENST00000435185.1_Intron|GRID2IP_ENST00000452113.1_Intron	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	NA		NA			long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						gtcgcccaggatggagtgcag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045	392862			18464	protein-coding gene	gene with protein product		610639	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1		NA	14612983	Standard	XM_294249	NM_001145118	NA	Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.585-3541T>G	chr7.hg19:g.6569941A>C		NA		hg19	CCDS47537.1	0.02	-0.324498	AGGxTGG	COVERED																																																																																			NOVEL	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340534.1	11	3.006049	KEEP	0	0	0	10	261	AA	0.992708	0.829622	0		-	4	60	142	1	0	10.656265	32	60	931	64	ENST00000457091.2	0.111111	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	6665809	6665809	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6665809C>T			NA	NA				ZNF853 (1888 upstream) : RP11-611L7.1 (28685 downstream)						NA		NA									NA						gttgcccaggctagagtacaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.6665809C>T		NA		hg19		0.02	-0.087701	AGGxTAG	UNCOVERED																																																																																			NOVEL					0			6	2.40724	KEEP	1	0	0	8	248	CC	0.99257	0.09898	0			3	60	75	0	0	6.442281	6	60	202	22		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	6672597	6672597	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6672597T>C			NA	NA				ZNF853 (8676 upstream) : RP11-611L7.1 (21897 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.6672597T>C		NA		hg19		0.02	-0.236803	AGGxGTG	COVERED																																																																																			NOVEL					0			6	2.705813	KEEP	3	0	0	9	243	TT	0.99257	0.607857	0			3	60	104	0	0	7.964761	20	60	584	60		0.130435	0.612407
CCZ1B	221960	__UNKNOWN__	__UNKNOWN__	7	6851847	6851847	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:6851847T>C	ENST00000316731.8	-	10	1415				CCZ1B_ENST00000538180.1_Intron	NM_198097.3	NP_932765.1	P86790	CCZ1B_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog B (S. cerevisiae)	NA		NA				lysosome (GO:0005764)|membrane (GO:0016020)					NA						Cggctgggcgtggtggctcat	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC010130	CCDS5354.1	7p22.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000146574	ENSG00000146574	221960			21717	protein-coding gene	gene with protein product	similar to CGI-43 protein	NA	chromosome 7 open reading frame 28B	C7orf28B	NA	12477932	Standard	NM_198097	NM_198097	NA	Approved	DKFZP586I1023, H_NH0577018.2, MGC19819	uc003sqx.2	P86790	OTTHUMG00000152441	ENST00000316731.8:c.843-153A>G	chr7.hg19:g.6851847T>C		NA	A2RU45|O95766|Q9UG65|Q9Y359	hg19	CCDS5354.1	0.02	-0.271834	GCGxGGT	UNCOVERED																																																																																			NOVEL	CCZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000246858.1	8	2.405119	KEEP	2	0	0	8	209	TT	0	0	0		-	3	45	92	0	0	6.596149	23	60	656	58	ENST00000316731.8	0.115385	0.717315
RPA3	6119	__UNKNOWN__	__UNKNOWN__	7	7732309	7732309	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:7732309C>T	ENST00000223129.4	-	3	145				RPA3-AS1_ENST00000469183.1_Intron	NM_002947.3	NP_002938.1	P35244	RFA3_HUMAN	replication protein A3, 14kDa	NA		NA			base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of cell proliferation (GO:0042127)|regulation of mitotic cell cycle (GO:0007346)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.202)		agcgtgatctcagctcactgc	0.488		NA						Direct reversal of damage;Nucleotide excision repair (NER)													NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(148;376 1816 25359 26011 31717)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5356.1	7p21.3	2013-09-23	2002-08-29		ENSG00000106399	ENSG00000106399	6119			10291	protein-coding gene	gene with protein product		179837	replication protein A3 (14kD)		NA	8454588	Standard	NM_002947	NM_002947	NA	Approved	REPA3	uc003sri.3	P35244	OTTHUMG00000023748	ENST00000223129.4:c.1027-5350G>A	chr7.hg19:g.7732309C>T		NA	Q549U6	hg19	CCDS5356.1	0.02	-0.122799	TCTxAGC	COVERED																																																																																			NOVEL	RPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324778.2	3	2.407282	KEEP	1	0	0	8	249	CC	0.99257	0.194853	0		-	3	60	83	0	0	6.80096	9	60	300	31	ENST00000223129.4	0.25	0.196312
GLCCI1	113263	__UNKNOWN__	__UNKNOWN__	7	8052167	8052167	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:8052167T>C	ENST00000223145.5	+	2	1166				GLCCI1_ENST00000474269.1_Intron	NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	NA		NA				cytoplasm (GO:0005737)				endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		ctccacctcctgggttcatgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415	113263			18713	protein-coding gene	gene with protein product		614283			NA		Standard	NM_138426	NM_138426	NA	Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.609+8478T>C	chr7.hg19:g.8052167T>C		NA	A4D103|Q96FD0	hg19	CCDS34601.1	0.02	-0.105253	TCCxGGG	UNCOVERED																																																																																			NOVEL	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324672.1	7	3.308684	KEEP	5	0	0	11	307	TT	0.992708	0.138812	0		+	3	41	96	0	0	8.101178	9	50	270	35	ENST00000223145.5	0.25	0.139832
NXPH1	30010	__UNKNOWN__	__UNKNOWN__	7	8619229	8619229	__UNKNOWN__	Intron	SNP	T	T	C	rs6954156	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:8619229T>C	ENST00000405863.1	+	2	965				NXPH1_ENST00000602349.1_Intron	NM_152745.2	NP_689958.1	P58417	NXPH1_HUMAN	neurexophilin 1	NA		NA				extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|ovary(1)	17		Ovarian(82;0.0628)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		ctcaaactcctgacctcagat	0.502		NA											C|||	2083	0.415935	0.7761	0.2925	5008	,	,	NA	18012	0.2708	NA	0.2555	False	NA	,,,	NA	NA	NA	2504	0.3313	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047362	CCDS47540.1	7p22	2003-03-20			ENSG00000122584	ENSG00000122584	30010			20693	protein-coding gene	gene with protein product		604639			NA	9570794	Standard	NM_152745	NM_152745	NA	Approved		uc003srv.3	P58417	OTTHUMG00000151941	ENST00000405863.1:c.54+143832T>C	chr7.hg19:g.8619229T>C		NA	Q8NB31	hg19	CCDS47540.1	0.02	-0.105259	TCCxGAC	UNCOVERED																																																																																			NOVEL	NXPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000324591.1	2	2.406033	KEEP	0	0	0	8	220	TT	0.99257	0.138793	0		+	4	60	132	0	0	11.977235	7	60	214	28	ENST00000405863.1	0.363636	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	9151115	9151115	__UNKNOWN__	IGR	SNP	G	G	A	rs549904313	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:9151115G>A			NA	NA				NXPH1 (358522 upstream) : AC079756.1 (483131 downstream)						NA		NA									NA						gcaagactccgtctcaaaaaa	0.448		NA											G|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	19634	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.9151115G>A		NA		hg19		0.02	-0.210531	TCCxTCT	COVERED																																																																																			NOVEL					0			13	3.309525	KEEP	4	0	0	11	329	GG	0.99254	0.518266	0			3	60	92	0	0	6.960996	17	60	575	55		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	9196093	9196093	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:9196093A>G			NA	NA				NXPH1 (403500 upstream) : AC079756.1 (438153 downstream)						NA		NA									NA						tcttttttcaaatggagtctt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.9196093A>G		NA		hg19		0.02	-0.087711	TCAxATG	UNCOVERED																																																																																			NOVEL					0			4	2.405966	KEEP	0	0	0	8	218	AA	0.99257	0.09898	0			3	60	91	0	1	8.232367	5	60	156	25		0.375	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	12195225	12195225	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:12195225A>G			NA	NA				THSD7A (323401 upstream) : TMEM106B (55641 downstream)						NA		NA									NA						aggccgaggcaggcggatcac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.12195225A>G		NA		hg19		0.02	-0.131557	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			7	2.70598	KEEP	6	0	0	9	245	AA	0	0	0			3	60	94	0	0	7.572475	12	60	354	41		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	12717737	12717737	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:12717737A>G			NA	NA				AC011891.5 (23127 upstream) : ARL4A (8743 downstream)						NA		NA									NA						cgaggcgggcagatcacgagg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.12717737A>G		NA		hg19		0.02	-0.228038	GGCxGAT	UNCOVERED																																																																																			NOVEL					0			5	2.40624	KEEP	1	0	0	8	225	AA	0	0	0			4	60	119	0	0	9.037156	21	60	627	51		0.16	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	12995357	12995357	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:12995357G>A			NA	NA				RN7SKP228 (78786 upstream) : AC011288.2 (145658 downstream)						NA		NA									NA						ggccgggcgcggtggctcatg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.12995357G>A		NA		hg19		0.02	-0.14912	CGCxGTG	COVERED																																																																																			NOVEL					0			5	3.910639	KEEP	1	0	0	13	381	GG	0.994391	0.290363	0			3	59	89	0	0	6.979043	13	60	426	45		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	13194244	13194244	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:13194244A>C			NA	NA				AC011288.2 (52230 upstream) : AC006000.5 (184581 downstream)						NA		NA									NA						tggctcacgcatgtaatccca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.13194244A>C		NA		hg19		0.02	-0.254352	CGCxTGT	COVERED																																																																																			NOVEL					0			10	4.211004	KEEP	1	0	0	14	393	AA	0.995343	0.690438	0			6	60	212	0	0	17.745818	22	60	640	64		0.214286	0.693668
ETV1	2115	__UNKNOWN__	__UNKNOWN__	7	13934688	13934688	__UNKNOWN__	3'UTR	SNP	A	A	G	rs3735344	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:13934688A>G	ENST00000405192.2	-	0	2368				ETV1_ENST00000403527.1_3'UTR|ETV1_ENST00000405218.2_3'UTR|ETV1_ENST00000242066.5_3'UTR|ETV1_ENST00000430479.1_3'UTR|ETV1_ENST00000399357.3_3'UTR|ETV1_ENST00000420159.2_3'UTR|ETV1_ENST00000405358.4_3'UTR|ETV1_ENST00000343495.5_3'UTR	NM_001163147.1	NP_001156619.1	P50549	ETV1_HUMAN	ets variant 1	NA		NA			axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						GGACCATGACATGTCATTATT	0.333		NA	T	EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3	Ewing sarcoma, prostate								A|||	1768	0.353035	0.3691	0.3703	5008	,	,	NA	17776	0.247	NA	0.3976	False	NA	,,,	NA	NA	NA	2504	0.3824	NA	NA	NA			Dom	yes		7	7p22	2115	ets variant gene 1		M, E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468	2115			3490	protein-coding gene	gene with protein product		600541	ets variant gene 1		NA	1340465	Standard	NM_004956	NM_004956	NA	Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000405192.2:c.*803T>C	chr7.hg19:g.13934688A>G		NA	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	hg19	CCDS55087.1	0.02	1.926928	GACxTGT	COVERED																																																																																			NOVEL	ETV1-005	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326115.2	3	2.70715	KEEP	0	0	0	9	254	AA	0.99254	0.985519	0		-	32	60	1051	0	0	102.365451	28	60	822	116	ENST00000405192.2	0.533333	0.992926
ETV1	2115	__UNKNOWN__	__UNKNOWN__	7	13967982	13967982	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:13967982T>C	ENST00000405192.2	-	8	1003				ETV1_ENST00000403685.1_Intron|ETV1_ENST00000476720.2_Intron|ETV1_ENST00000403527.1_Intron|ETV1_ENST00000405218.2_Intron|ETV1_ENST00000242066.5_Intron|ETV1_ENST00000430479.1_Intron|ETV1_ENST00000399357.3_Intron|ETV1_ENST00000420159.2_Intron|ETV1_ENST00000405358.4_Intron|ETV1_ENST00000343495.5_Intron	NM_001163147.1	NP_001156619.1	P50549	ETV1_HUMAN	ets variant 1	NA		NA			axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						tggctcacgcttgtaatccca	0.443		NA	T	EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3	Ewing sarcoma, prostate																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7p22	2115	ets variant gene 1		M, E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468	2115			3490	protein-coding gene	gene with protein product		600541	ets variant gene 1		NA	1340465	Standard	NM_004956	NM_004956	NA	Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000405192.2:c.802+3144A>G	chr7.hg19:g.13967982T>C		NA	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	hg19	CCDS55087.1	0.02	-0.17542	CGCxTGT	COVERED																																																																																			NOVEL	ETV1-005	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326115.2	4	3.262213	KEEP	3	0	0	11	277	TT	0.99257	0.384528	0		-	3	60	107	0	0	8.872196	12	60	366	51	ENST00000405192.2	0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	14979530	14979530	__UNKNOWN__	IGR	SNP	A	A	G	rs386710636|rs386710635|rs150659512	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:14979530A>G			NA	NA				DGKB (36544 upstream) : AC006458.3 (126301 downstream)						NA		NA									NA						gagccaccacacccagccAAT	0.423		NA											a|||	751	0.14996	0.1626	0.1902	5008	,	,	NA	12874	0.0992	NA	0.1262	False	NA	,,,	NA	NA	NA	2504	0.181	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.14979530A>G		NA		hg19		0.02	-0.10519	CACxCCC	UNCOVERED																																																																																			NOVEL					0			3	2.704026	KEEP	2	0	0	9	220	AA	0.99254	0.138789	0			3	60	97	0	0	8.480136	7	60	176	31		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	14979534	14979534	__UNKNOWN__	IGR	SNP	A	A	G	rs386710636|rs113069844	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:14979534A>G			NA	NA				DGKB (36548 upstream) : AC006458.3 (126297 downstream)						NA		NA									NA						caccacacccagccAATTCat	0.423		NA											A|||	751	0.14996	0.1626	0.1902	5008	,	,	NA	12983	0.0992	NA	0.1262	False	NA	,,,	NA	NA	NA	2504	0.181	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.14979534A>G		NA		hg19		0.02	-0.105258	CCCxGCC	UNCOVERED																																																																																			NOVEL					0			3	2.7062	KEEP	2	0	0	9	237	AA	0.99254	0.138789	0			3	60	102	0	0	8.978761	7	60	209	30		0.3	0.139832
ANKMY2	57037	__UNKNOWN__	__UNKNOWN__	7	16671525	16671525	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:16671525G>C	ENST00000306999.2	-	2	376				ANKMY2_ENST00000421746.1_Intron	NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	NA		NA				cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		caggcgtgaggcactgtgccc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524	57037		Zinc fingers, MYND-type, Ankyrin repeat domain containing	25370	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_020319	NM_020319	NA	Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.132+4490C>G	chr7.hg19:g.16671525G>C		NA	A4D124|Q659G1|Q96BL3	hg19	CCDS5361.1	0.02	-0.140362	GAGxCAC	COVERED																																																																																			NOVEL	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207600.2	7	2.40718	KEEP	0	0	0	8	247	GG	0.99257	0.259026	0		-	3	60	105	0	0	8.671879	12	60	405	29	ENST00000306999.2	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	16787579	16787579	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:16787579T>G			NA	NA				AC073333.8 (28056 upstream) : TSPAN13 (5580 downstream)						NA		NA									NA						caaagtgctgtgattacaggc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.16787579T>G		NA		hg19		0.02	-0.192951	CTGxGAT	COVERED																																																																																			NOVEL					0			4	2.40527	KEEP	0	0	0	8	211	TT	0.99257	0.454356	0			4	60	130	0	0	10.881372	13	60	383	41		0.235294	0.457757
AGR3	155465	__UNKNOWN__	__UNKNOWN__	7	16901262	16901262	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:16901262T>C	ENST00000310398.2	-	6	374				AGR3_ENST00000402239.3_Intron	NM_176813.3	NP_789783.1	Q8TD06	AGR3_HUMAN	anterior gradient 3	NA		NA				extracellular region (GO:0005576)	dystroglycan binding (GO:0002162)			central_nervous_system(1)|kidney(8)|lung(2)|skin(1)|stomach(1)	13	Lung NSC(10;0.0376)|all_lung(11;0.0721)|all_epithelial(12;0.202)			UCEC - Uterine corpus endometrioid carcinoma (126;0.184)		tggtggctcatgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY069977	CCDS5365.1	7p21.1	2013-07-31	2013-07-31		ENSG00000173467	ENSG00000173467	155465		Protein disulfide isomerases	24167	protein-coding gene	gene with protein product	breast cancer membrane protein 11, protein disulfide isomerase family A, member 18	609482	anterior gradient 3 homolog (Xenopus laevis)		NA	12592373, 12477722	Standard	NM_176813	NM_176813	NA	Approved	HAG3, hAG-3, BCMP11, PDIA18	uc003sts.3	Q8TD06	OTTHUMG00000128411	ENST00000310398.2:c.304-191A>G	chr7.hg19:g.16901262T>C		NA	A4D120	hg19	CCDS5365.1	0.02	-0.149093	TCAxGCC	COVERED																																																																																			NOVEL	AGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250191.2	4	2.707015	KEEP	1	0	0	9	250	TT	0.99254	0.289823	0		-	3	60	99	0	0	8.072384	12	60	347	42	ENST00000310398.2	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	17792314	17792314	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:17792314T>C			NA	NA				AC006482.1 (72031 upstream) : SNX13 (38070 downstream)						NA		NA									NA						cggtggctcatgcctataatc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.17792314T>C		NA		hg19		0.02	-0.201731	TCAxGCC	COVERED																																																																																			NOVEL					0			13	3.908723	KEEP	4	0	0	13	346	TT	0.993072	0.487146	0			3	60	93	0	0	6.993884	18	60	549	57		0.142857	0.490544
SNX13	23161	__UNKNOWN__	__UNKNOWN__	7	17920962	17920962	__UNKNOWN__	3'UTR	SNP	A	A	C	rs558460566|rs149379873	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:17920962A>C	ENST00000409604.1	-	0	2233				SNX13_ENST00000409389.1_Intron|SNX13_ENST00000428135.3_Intron			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	NA		NA			intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					cacatacacaaacacacacac	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189	23161		Sorting nexins	21335	protein-coding gene	gene with protein product		606589			NA	11485546, 11729322	Standard	NM_015132	NM_015132	NA	Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409604.1:c.*1475T>G	chr7.hg19:g.17920962A>C		NA	B2RCI9|O94821|Q8WVZ2|Q8WXH8	hg19		0.02	-0.306859	ACAxACA	COVERED																																																																																			NOVEL	SNX13-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000327609.1	12	3.035519	KEEP	0	1	28	20	522	AA	0.999869	0.800141	0		-	4	60	136	1	0	10.109133	31	60	848	69	ENST00000409604.1	0.114286	0.800245
HDAC9	9734	__UNKNOWN__	__UNKNOWN__	7	18688057	18688057	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:18688057A>G	ENST00000524023.1	+	9	1214				HDAC9_ENST00000406451.4_Intron|HDAC9_ENST00000432645.2_Intron|HDAC9_ENST00000417496.2_Intron|HDAC9_ENST00000401921.1_Intron|HDAC9_ENST00000405010.3_Intron|HDAC9_ENST00000428307.2_Intron|HDAC9_ENST00000406072.1_Intron|HDAC9_ENST00000456174.2_Intron|HDAC9_ENST00000441542.2_Intron	NM_001204147.1	NP_001191076.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	NA		NA			B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	gtgtgtgtgtATACACACATA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													31	30	30			NA	NA	7		NA											NA				18688057		1875	4115	5990	SO:0001627	intron_variant			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052	9734			14065	protein-coding gene	gene with protein product		606543			NA	10523670, 10487760	Standard		NM_178425	NA	Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000524023.1:c.1010-32A>G	chr7.hg19:g.18688057A>G		NA	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	hg19	CCDS56468.1	0.02	1.809905	TGTxTAC	COVERED																																																																																			NOVEL	HDAC9-022	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376089.1	12	3.906318	KEEP	0	0	0	13	325	AA	0.994391	0.988844	0		+	4	60	132	1	1	8.617351	60	60	1727	107	ENST00000524023.1	0.0625	0.994422
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	19312157	19312157	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:19312157C>A			NA	NA				AC003986.5 (126281 upstream) : AC007091.1 (80999 downstream)						NA		NA									NA						taatcccagccctttgggagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.19312157C>A		NA		hg19		0.02	-0.148079	AGCxCTT	COVERED																																																																																			NOVEL					0			4	3.309736	KEEP	1	0	0	11	336	CC	0.992708	0.289872	0			4	60	104	0	0	8.688841	10	60	298	36		0.285714	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	20057696	20057696	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:20057696C>T			NA	NA				AC005062.2 (15151 upstream) : RP11-486P11.1 (78063 downstream)						NA		NA									NA						catgagccaccgcgcccagcc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.20057696C>T		NA		hg19		0.02	-0.315753	CACxGCG	COVERED																																																																																			NOVEL					0			15	6.916259	KEEP	7	0	0	23	662	CC	0.999863	0.818352	0			3	56	93	0	0	6.544933	26	60	821	86		0.103448	0.818465
DNAH11	8701	__UNKNOWN__	__UNKNOWN__	7	21649631	21649631	__UNKNOWN__	Intron	SNP	G	G	C	rs1976885	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:21649631G>C	ENST00000409508.3	+	20	3883				DNAH11_ENST00000328843.6_Intron	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ccagcactttgggaggctgag	0.517		NA							Kartagener syndrome				G|||	2789	0.556909	0.6362	0.3991	5008	,	,	NA	16985	0.7817	NA	0.4125	False	NA	,,,	NA	NA	NA	2504	0.4785	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04				8701		Axonemal dyneins	2942	protein-coding gene	gene with protein product	dynein, ciliary, heavy chain 11, dynein, heavy chain beta-like	603339	dynein, axonemal, heavy polypeptide 11		NA	9256245	Standard	NM_003777	NM_001277115	NA	Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.3852+3280G>C	chr7.hg19:g.21649631G>C		NA	Q9UJ82	hg19		0.02	-0.201766	TTTxGGA	COVERED																																																																																			NOVEL	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000326582.6	8	3.008545	KEEP	8	0	0	10	295	GG	0.99257	0.4869	0		+	10	60	337	0	0	33.099979	8	60	281	61	ENST00000409508.3	0.555556	0.490544
DNAH11	8701	__UNKNOWN__	__UNKNOWN__	7	21849212	21849212	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:21849212C>A	ENST00000409508.3	+	63	10363				DNAH11_ENST00000328843.6_Intron	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						acggagtttccctcttgttgc	0.413		NA							Kartagener syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04				8701		Axonemal dyneins	2942	protein-coding gene	gene with protein product	dynein, ciliary, heavy chain 11, dynein, heavy chain beta-like	603339	dynein, axonemal, heavy polypeptide 11		NA	9256245	Standard	NM_003777	NM_001277115	NA	Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.10332+1545C>A	chr7.hg19:g.21849212C>A		NA	Q9UJ82	hg19		0.02	-0.24562	TTCxCTC	COVERED																																																																																			NOVEL	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000326582.6	9	3.611027	KEEP	0	0	0	12	377	CC	0.994391	0.664773	0		+	4	60	114	1	0	8.463401	22	60	762	62	ENST00000409508.3	0.153846	0.668523
FAM126A	84668	__UNKNOWN__	__UNKNOWN__	7	23046133	23046133	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:23046133A>G	ENST00000432176.2	-	1	205				FAM126A_ENST00000409763.1_Intron|FAM126A_ENST00000409923.1_Intron	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	NA		NA			signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						tgatccacccacctcggcctc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591	84668			24587	protein-coding gene	gene with protein product	down regulated by Ctnnb1, a	610531			NA	10910037, 16951682	Standard	NM_032581	NM_032581	NA	Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.27+7410T>C	chr7.hg19:g.23046133A>G		NA	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	hg19	CCDS5377.1	0.02	-0.279299	CCCxCCT	COVERED																																																																																			NOVEL	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250230.1	11	4.210822	KEEP	5	0	0	14	388	AA	0.993634	0.756043	0		-	3	59	110	0	0	8.251178	26	60	752	80	ENST00000432176.2	0.103448	0.760887
KLHL7	55975	__UNKNOWN__	__UNKNOWN__	7	23180001	23180001	__UNKNOWN__	Intron	SNP	G	G	A	rs544784150		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:23180001G>A	ENST00000339077.5	+	5	685				KLHL7_ENST00000545443.1_Intron|KLHL7_ENST00000409689.1_Intron|KLHL7_ENST00000539124.1_Intron|KLHL7_ENST00000322231.7_Intron|KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000479288.1_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	NA		NA			protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						gtgaaaccccgtctctactaa	0.552		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	15340	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550	55975		Kelch-like, BTB/POZ domain containing	15646	protein-coding gene	gene with protein product	retinitis pigmentosa 42	611119	kelch-like 7 (Drosophila)		NA	19520207	Standard	NM_018846	NM_001031710	NA	Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.443-387G>A	chr7.hg19:g.23180001G>A		NA	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	hg19	CCDS34609.1	0.02	-0.105245	CCCxTCT	UNCOVERED																																																																																			NOVEL	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326860.3	3	2.406881	KEEP	1	0	0	8	236	GG	0	0	0		+	3	60	81	0	0	6.731958	8	60	269	25	ENST00000339077.5	0.272727	0.139832
KLHL7	55975	__UNKNOWN__	__UNKNOWN__	7	23210775	23210775	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:23210775T>C	ENST00000339077.5	+	10	1622				KLHL7_ENST00000545443.1_Intron|KLHL7_ENST00000409689.1_Intron|KLHL7_ENST00000539124.1_Intron|AC005082.1_ENST00000366347.4_Missense_Mutation_p.W6R|KLHL7_ENST00000322231.7_Intron|KLHL7_ENST00000542558.1_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	NA		NA			protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ctgcccaccttggcctcccaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550	55975		Kelch-like, BTB/POZ domain containing	15646	protein-coding gene	gene with protein product	retinitis pigmentosa 42	611119	kelch-like 7 (Drosophila)		NA	19520207	Standard	NM_018846	NM_001031710	NA	Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.1380-1792T>C	chr7.hg19:g.23210775T>C		NA	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	hg19	CCDS34609.1	0.02	3.291788	CCTxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.447915	0.00012	.	.	ENSG00000214871	ENST00000366347	T	0.52754	0.65	0.149	-0.298	0.12814	.	.	.	.	.	T	0.20659	0.0497	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.18713	-1.0328	5	0.12430	T	0.62	.	.	.	.	.	.	.	.	R	6	ENSP00000382107:W6R	ENSP00000382107:W6R	W	+	1	0	AC005082.1	23177300	0.011000	0.17503	0.003000	0.11579	0.004000	0.04260	-0.955000	0.03869	-1.221000	0.02591	-1.232000	0.01568	TGG	NOVEL	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000326860.3	23	2.800418	KEEP	0	3	90	41	1097	TT	1	0.999999	0		+	6	60	198	0	0	12.5097	106	60	2986	233	ENST00000339077.5	0.053571	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	23536869	23536869	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:23536869A>G			NA	NA				Y_RNA (5357 upstream) : TRA2A (7529 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.23536869A>G		NA		hg19		0.02	-0.192939	GGCxTGA	COVERED																																																																																			NOVEL					0			2	2.405722	KEEP	1	0	0	8	215	AA	0.99257	0.454356	0			3	60	87	0	0	6.534658	16	60	467	45		0.157895	0.457757
TRA2A	29896	__UNKNOWN__	__UNKNOWN__	7	23553186	23553186	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:23553186A>G	ENST00000297071.4	-	4	553				TRA2A_ENST00000474586.1_Intron|TRA2A_ENST00000538367.1_Intron|TRA2A_ENST00000392502.4_Intron	NM_013293.3	NP_037425.1	Q13595	TRA2A_HUMAN	transformer 2 alpha homolog (Drosophila)	NA		NA			mRNA splicing, via spliceosome (GO:0000398)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	10						gcagtgagccaagatcgagcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(121;2137 2973 46590)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U53209	CCDS5383.1, CCDS64609.1, CCDS75569.1	7p15.3	2014-02-12			ENSG00000164548	ENSG00000164548	29896		RNA binding motif (RRM) containing	16645	protein-coding gene	gene with protein product		602718			NA	8799144, 9546399	Standard	NM_013293	XM_005249725	NA	Approved	htra-2-alpha, tra2a, AWMS1	uc003swi.3	Q13595	OTTHUMG00000128459	ENST00000297071.4:c.337-485T>C	chr7.hg19:g.23553186A>G		NA	B4DUA9	hg19	CCDS5383.1	0.02	-0.298207	GCCxAGA	COVERED																																																																																			NOVEL	TRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250257.1	2	3.008043	KEEP	0	0	0	10	283	AA	0.992708	0.775364	0		-	3	60	94	0	0	6.510173	29	60	871	52	ENST00000297071.4	0.09375	0.78106
CCDC126	90693	__UNKNOWN__	__UNKNOWN__	7	23663190	23663190	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:23663190A>G	ENST00000307471.3	+	3	695				CCDC126_ENST00000410069.1_Intron|CCDC126_ENST00000409765.1_Intron	NM_138771.3	NP_620126.2	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126	NA		NA			protein N-linked glycosylation (GO:0006487)	extracellular region (GO:0005576)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)			endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7						attccagcctaggtgacagag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012427	CCDS5384.1	7p15.3	2006-08-15			ENSG00000169193	ENSG00000169193	90693			22398	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_138771	NM_138771	NA	Approved	FLJ23031	uc003swl.3	Q96EE4	OTTHUMG00000128461	ENST00000307471.3:c.238+12018A>G	chr7.hg19:g.23663190A>G		NA	A8K1J6|Q6UWP1|Q75MQ6	hg19	CCDS5384.1	0.02	3.759895	CCTxGGT	COVERED																																																																																			NOVEL	CCDC126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250259.1	18	5.565984	KEEP	2	5	128	64	1678	AA	1	0.999997	0		+	8	60	258	1	0	17.667938	88	60	2562	265	ENST00000307471.3	0.083333	0.999997
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	24471286	24471286	__UNKNOWN__	IGR	SNP	C	C	T	rs11973625	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:24471286C>T			NA	NA				NPY (139802 upstream) : RNU6-1103P (105664 downstream)						NA		NA									NA						Gggccggacgcggtggctcac	0.498		NA											C|||	1101	0.219848	0.2534	0.2003	5008	,	,	NA	15954	0.0615	NA	0.3618	False	NA	,,,	NA	NA	NA	2504	0.2055	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.24471286C>T		NA		hg19		0.02	-0.184177	ACGxGGT	COVERED																																																																																			NOVEL					0			3	2.406547	KEEP	0	0	0	8	232	CC	0.99257	0.420331	0			9	60	249	0	0	23.482074	10	60	327	41		0.473684	0.423478
DFNA5	1687	__UNKNOWN__	__UNKNOWN__	7	24787405	24787405	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:24787405A>G	ENST00000342947.3	-	2	637				DFNA5_ENST00000409970.1_Intron|DFNA5_ENST00000419307.1_Intron|DFNA5_ENST00000545231.1_Intron|DFNA5_ENST00000409775.3_Intron	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	NA		NA			apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						tcccacctcaacctcttgagt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(78;184 1250 20134 20900 23600)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928	1687			2810	protein-coding gene	gene with protein product		608798			NA	8589696, 9450185	Standard	NM_004403	NM_004403	NA	Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.211+1777T>C	chr7.hg19:g.24787405A>G		NA	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	hg19	CCDS5389.1	0.02	-0.184131	TCAxCCT	COVERED																																																																																			NOVEL	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214060.2	9	2.405885	KEEP	0	0	0	8	221	AA	0.99257	0.420331	0		-	3	60	92	0	1	6.962507	17	60	481	37	ENST00000342947.3	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	25949942	25949942	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:25949942A>G			NA	NA				AC003090.1 (247269 upstream) : CTD-2227E11.1 (38334 downstream)						NA		NA									NA						gccgaggtggatggatcacct	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.25949942A>G		NA		hg19		0.02	-0.289441	TGGxTGG	COVERED																																																																																			NOVEL					0			4	2.406258	KEEP	2	0	0	8	222	AA	0.99257	0.755234	0			4	60	142	0	0	10.873663	28	60	841	68		0.125	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	26294327	26294327	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:26294327A>G			NA	NA				CBX3 (41351 upstream) : SNX10 (37215 downstream)						NA		NA									NA						gcctcccaaaatgctgggatt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.26294327A>G		NA		hg19		0.02	-0.271897	AAAxTGC	COVERED																																																																																			NOVEL					0			13	3.00744	KEEP	0	0	0	10	274	AA	0.993072	0.712346	0			3	60	99	0	0	7.052886	28	60	846	56		0.096774	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	26294339	26294339	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:26294339T>C			NA	NA				CBX3 (41363 upstream) : SNX10 (37203 downstream)						NA		NA									NA						gctgggattataggcataagc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.26294339T>C		NA		hg19		0.02	-0.263099	TTAxAGG	COVERED																																																																																			NOVEL					0			12	3.007111	KEEP	0	0	0	10	268	TT	0.992708	0.68861	0			3	60	95	0	0	6.699337	27	60	778	54		0.1	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	26295778	26295778	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:26295778G>A			NA	NA				CBX3 (42802 upstream) : SNX10 (35764 downstream)						NA		NA									NA						ccgcctcccgggttcaagcaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.26295778G>A		NA		hg19		0.02	-0.122798	CCGxGTT	COVERED																																																																																			NOVEL					0			5	2.406972	KEEP	0	0	0	8	239	GG	0.99257	0.194853	0			3	51	80	0	0	6.382003	10	60	339	26		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	26325492	26325492	__UNKNOWN__	IGR	SNP	G	G	T	rs28413943	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:26325492G>T			NA	NA				CBX3 (72516 upstream) : SNX10 (6050 downstream)						NA		NA									NA						gacctcaagtgatctgcccgc	0.488		NA											G|||	1498	0.299121	0.1551	0.2118	5008	,	,	NA	17872	0.3323	NA	0.3757	False	NA	,,,	NA	NA	NA	2504	0.4427	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.26325492G>T		NA		hg19		0.02	-0.184208	AGTxATC	UNCOVERED																																																																																			NOVEL					0			11	3.009183	KEEP	8	0	0	10	314	GG	0	0	0			5	60	146	0	0	12.101593	15	60	515	48		0.25	0.423478
SNX10	29887	__UNKNOWN__	__UNKNOWN__	7	26350582	26350582	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:26350582C>T	ENST00000338523.4	+	1	164				SNX10_ENST00000396376.1_Intron|SNX10_ENST00000446848.2_Intron	NM_001199835.1|NM_013322.2	NP_001186764.1|NP_037454.2	Q9Y5X0	SNX10_HUMAN	sorting nexin 10	NA		NA			cilium assembly (GO:0042384)|endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|osteoclast differentiation (GO:0030316)|protein localization to centrosome (GO:0071539)|protein localization to cilium (GO:0061512)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extrinsic component of endosome membrane (GO:0031313)|nucleus (GO:0005634)	1-phosphatidylinositol binding (GO:0005545)|ATPase binding (GO:0051117)			endometrium(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	6						ggattacaggcgtgagccacc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121860	CCDS5399.1, CCDS56470.1	7p15.2	2008-05-22			ENSG00000086300	ENSG00000086300	29887		Sorting nexins	14974	protein-coding gene	gene with protein product		614780			NA	17012226	Standard		NM_013322	NA	Approved		uc010kuu.3	Q9Y5X0	OTTHUMG00000023650	ENST00000338523.4:c.-24+18876C>T	chr7.hg19:g.26350582C>T		NA	E9PFH5|Q8IYT5	hg19	CCDS5399.1	0.02	-0.16666	AGGxGTG	COVERED																																																																																			NOVEL	SNX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214120.1	5	2.406897	KEEP	2	0	0	8	241	CC	0.99257	0.384528	0		+	3	60	91	0	0	7.178949	13	60	439	46	ENST00000338523.4	0.1875	0.387407
SKAP2	8935	__UNKNOWN__	__UNKNOWN__	7	26757137	26757137	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:26757137A>G	ENST00000345317.2	-	9	1110				SKAP2_ENST00000539623.1_Intron|SKAP2_ENST00000489977.1_Intron	NM_003930.3	NP_003921.2	O75563	SKAP2_HUMAN	src kinase associated phosphoprotein 2	NA		NA			B cell activation (GO:0042113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(3)	17						tcaaaaaaaaaaaaaaaaaaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5400.1	7p15.2	2013-01-10	2006-09-28	2006-09-28	ENSG00000005020	ENSG00000005020	8935		Pleckstrin homology (PH) domain containing	15687	protein-coding gene	gene with protein product		605215	src family associated phosphoprotein 2	SCAP2	NA	9837776, 9755858	Standard		NM_003930	NA	Approved	RA70, SKAP-HOM, SKAP55R, SAPS	uc003syc.3	O75563	OTTHUMG00000023495	ENST00000345317.2:c.796+7909T>C	chr7.hg19:g.26757137A>G		NA	A4D173|Q53GP6|Q75MK6|Q75MZ4|Q9UBZ3|Q9UED8	hg19	CCDS5400.1	0.02	-0.05261	AAAxAAA	UNCOVERED																																																																																			NOVEL	SKAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214128.1	10	4.210357	KEEP	2	0	0	14	382	AA	0.995343	0.036594	0		-	2	60	74	0	0	7.525084	1	57	30	31	ENST00000345317.2	0.666667	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	27104894	27104894	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:27104894A>G			NA	NA				AC004079.1 (42599 upstream) : HOXA1 (27717 downstream)						NA		NA									NA						cagcctgggcaacagagcaag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.27104894A>G		NA		hg19		0.02	-0.131567	GGCxACA	COVERED																																																																																			NOVEL					0			7	3.005636	KEEP	5	0	0	10	258	AA	0.99257	0.22747	0			3	60	98	0	2	8.301193	9	60	270	40		0.25	0.229173
HOXA3	3200	__UNKNOWN__	__UNKNOWN__	7	27147070	27147070	__UNKNOWN__	3'UTR	SNP	C	C	T	rs140825617	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:27147070C>T	ENST00000396352.4	-	0	1995				HOXA3_ENST00000317201.2_3'UTR	NM_030661.4	NP_109377.1	O43365	HXA3_HUMAN	homeobox A3	NA		NA			angiogenesis (GO:0001525)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(18)|skin(1)	29						GCACAGAGAGCCCCTGTTTCA	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(136;1368 1743 5685 7935 50360)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5404.1	7p15.2	2011-06-20	2005-12-22		ENSG00000105997	ENSG00000105997	3200		Homeoboxes / ANTP class : HOXL subclass	5104	protein-coding gene	gene with protein product		142954	homeo box A3	HOX1E, HOX1	NA	1973146, 1358459	Standard		XM_005249730	NA	Approved		uc011jzl.2	O43365	OTTHUMG00000023209	ENST00000396352.4:c.*464G>A	chr7.hg19:g.27147070C>T		NA	A4D181	hg19	CCDS5404.1	0.02	1.464476	GAGxCCC	COVERED																																																																																			NOVEL	HOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358708.2	2	10.229664	KEEP	0	0	0	34	1032	CC	0.999998	0.999905	0		-	45	70	1365	0	0	129.699661	49	70	1699	200	ENST00000396352.4	0.478723	0.999907
HIBADH	11112	__UNKNOWN__	__UNKNOWN__	7	27630896	27630896	__UNKNOWN__	Intron	SNP	C	C	T	rs192503678		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:27630896C>T	ENST00000265395.2	-	4	691					NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	NA		NA			branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|pentose-phosphate shunt (GO:0006098)|small molecule metabolic process (GO:0044281)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	3-hydroxyisobutyrate dehydrogenase activity (GO:0008442)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(4)|kidney(2)|lung(3)|ovary(2)|prostate(1)	12			GBM - Glioblastoma multiforme(3;0.0368)			TGTggccgggcgtggtggctc	0.532		NA											c|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15917	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF529362	CCDS5414.1	7p15	2009-06-12			ENSG00000106049	ENSG00000106049	11112	1.1.1.31		4907	protein-coding gene	gene with protein product		608475			NA		Standard	NM_152740	NM_152740	NA	Approved	NS5ATP1	uc003szf.3	P31937	OTTHUMG00000097035	ENST00000265395.2:c.484+38093G>A	chr7.hg19:g.27630896C>T		NA	Q546Z2|Q9UDN3	hg19	CCDS5414.1	0.02	-0.122804	GGGxGTG	COVERED																																																																																			NOVEL	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214132.1	11	5.416461	KEEP	11	0	0	18	562	CC	0.99649	0.228369	0		-	3	60	88	0	0	7.18191	10	60	326	62	ENST00000265395.2	0.230769	0.229173
TAX1BP1	8887	__UNKNOWN__	__UNKNOWN__	7	27782277	27782277	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:27782277A>G	ENST00000396319.2	+	1	81				TAX1BP1_ENST00000265393.6_Intron|TAX1BP1_ENST00000543117.1_Intron|TAX1BP1_ENST00000433216.2_Intron|TAX1BP1_ENST00000409980.1_Intron	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	NA		NA			apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			agtagagacgaggtttctcca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052	8887			11575	protein-coding gene	gene with protein product		605326			NA	10435631	Standard	NM_006024	NM_006024	NA	Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.-8+2389A>G	chr7.hg19:g.27782277A>G		NA	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	hg19	CCDS5415.1	0.02	1.704526	ACGxGGT	COVERED																																																																																			NOVEL	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214142.1	5	3.838897	KEEP	0	1	32	24	626	AA	0.999931	0.999149	0		+	5	60	161	1	1	10.637222	66	60	1937	130	ENST00000396319.2	0.070423	0.999218
TAX1BP1	8887	__UNKNOWN__	__UNKNOWN__	7	27805790	27805790	__UNKNOWN__	Intron	SNP	G	G	A	rs374018230	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:27805790G>A	ENST00000396319.2	+	4	541				TAX1BP1_ENST00000265393.6_Intron|TAX1BP1_ENST00000543117.1_Intron|TAX1BP1_ENST00000433216.2_Intron|TAX1BP1_ENST00000409980.1_Intron	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	NA		NA			apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			ctgtaatcccggcactctggg	0.478		NA											A|||	9	0.00179712	0.0061	0.0	5008	,	,	NA	17186	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052	8887			11575	protein-coding gene	gene with protein product		605326			NA	10435631	Standard	NM_006024	NM_006024	NA	Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.453+150G>A	chr7.hg19:g.27805790G>A		NA	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	hg19	CCDS5415.1	0.02	-0.263118	CCCxGCA	COVERED																																																																																			NOVEL	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214142.1	4	3.008561	KEEP	0	0	0	10	297	GG	0.992708	0.68861	0		+	4	60	111	0	0	8.238894	21	60	669	56	ENST00000396319.2	0.16	0.693668
JAZF1	221895	__UNKNOWN__	__UNKNOWN__	7	28037401	28037401	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:28037401T>C	ENST00000283928.5	-	2	281					NM_175061.3	NP_778231.2	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		JAZF1/SUZ12(133)	endometrium(1)|large_intestine(1)|lung(4)	6						ctatgttgcctaggctggtct	0.498		NA	T	SUZ12	endometrial stromal tumours																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7p15.2-p15.1	221895	juxtaposed with another zinc finger gene 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047229	CCDS5416.1	7p15.2-p15.1	2010-04-14			ENSG00000153814	ENSG00000153814	221895		Zinc fingers, C2H2-type	28917	protein-coding gene	gene with protein product		606246			NA	8401585	Standard	NM_175061	XM_006715656	NA	Approved	TIP27, DKFZp761K2222, ZNF802	uc003szn.3	Q86VZ6	OTTHUMG00000128545	ENST00000283928.5:c.116-5801A>G	chr7.hg19:g.28037401T>C		NA	A4D195|Q8N3L7	hg19	CCDS5416.1	0.02	-0.324452	GCCxAGG	COVERED																																																																																			NOVEL	JAZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250382.2	20	6.61475	KEEP	1	0	0	22	580	TT	0.999869	0.835607	0		-	3	60	96	0	0	6.895053	25	60	703	93	ENST00000283928.5	0.107143	0.835716
JAZF1	221895	__UNKNOWN__	__UNKNOWN__	7	28204554	28204554	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:28204554T>G	ENST00000283928.5	-	1	281					NM_175061.3	NP_778231.2	Q86VZ6	JAZF1_HUMAN	JAZF zinc finger 1	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transcription corepressor activity (GO:0003714)		JAZF1/SUZ12(133)	endometrium(1)|large_intestine(1)|lung(4)	6						ttgggaggcctaggcggaagg	0.463		NA	T	SUZ12	endometrial stromal tumours																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7p15.2-p15.1	221895	juxtaposed with another zinc finger gene 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047229	CCDS5416.1	7p15.2-p15.1	2010-04-14			ENSG00000153814	ENSG00000153814	221895		Zinc fingers, C2H2-type	28917	protein-coding gene	gene with protein product		606246			NA	8401585	Standard	NM_175061	XM_006715656	NA	Approved	TIP27, DKFZp761K2222, ZNF802	uc003szn.3	Q86VZ6	OTTHUMG00000128545	ENST00000283928.5:c.115+15527A>C	chr7.hg19:g.28204554T>G		NA	A4D195|Q8N3L7	hg19	CCDS5416.1	0.02	-0.236687	GCCxAGG	COVERED																																																																																			NOVEL	JAZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250382.2	7	3.60914	KEEP	0	0	0	12	331	TT	0.993634	0.637264	0		-	3	60	102	0	0	7.649652	22	60	630	55	ENST00000283928.5	0.12	0.641347
JAZF1-AS1	100128081	__UNKNOWN__	__UNKNOWN__	7	28268602	28268602	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:28268602T>C	ENST00000455963.1	+	0	301				JAZF1-AS1_ENST00000436758.1_RNA					JAZF1 antisense RNA 1	NA		NA									NA						tggtggctcatgcctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7p15.1	2012-10-12	2012-08-15		ENSG00000234336	ENSG00000234336	100128081		Long non-coding RNAs	41218	non-coding RNA	RNA, long non-coding		NA	JAZF1 antisense RNA 1 (non-protein coding)		NA		Standard	NR_034097	NR_034097	NA	Approved		uc011jzq.2		OTTHUMG00000152771	ENST00000455963.1:	chr7.hg19:g.28268602T>C		NA		hg19		0.02	-0.201725	TCAxGCC	UNCOVERED																																																																																			NOVEL	JAZF1-AS1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000327759.1	9	2.405942	KEEP	4	0	0	8	217	TT	0	0	0		+	3	60	100	0	0	7.69236	18	60	531	53	ENST00000455963.1	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	28305562	28305562	__UNKNOWN__	IGR	SNP	T	T	C	rs138857548	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:28305562T>C			NA	NA				JAZF1-AS1 (22026 upstream) : CREB5 (33377 downstream)						NA		NA									NA						gtggaggttgtagtgagccaa	0.483		NA											T|||	93	0.0185703	0.0643	0.0115	5008	,	,	NA	17026	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.28305562T>C		NA		hg19		0.02	-0.245485	TTGxAGT	COVERED																																																																																			NOVEL					0			8	2.405801	KEEP	0	0	0	8	216	TT	0.99257	0.636582	0			3	60	95	0	0	6.896439	23	60	616	51		0.115385	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	28307236	28307236	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:28307236G>A			NA	NA				JAZF1-AS1 (23700 upstream) : CREB5 (31703 downstream)						NA		NA									NA						caggtgatccgcccacctcgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.28307236G>A		NA		hg19		0.02	-0.131551	TCCxCCC	COVERED																																																																																			NOVEL					0			5	3.309376	KEEP	2	0	0	11	336	GG	0.993072	0.227586	0			3	60	82	1	0	6.3735	12	60	387	41		0.2	0.229173
CHN2	1124	__UNKNOWN__	__UNKNOWN__	7	29270236	29270236	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:29270236C>T	ENST00000222792.6	+	1	579				CHN2_ENST00000539406.1_Intron|CHN2_ENST00000435288.2_Intron|CHN2_ENST00000546235.1_Intron|CHN2_ENST00000539389.1_Intron|CHN2_ENST00000495789.2_Intron	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	NA		NA			positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						ggattacaggcgtgagccacc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(1;44 48 13232 18918 31480)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069	1124		Rho GTPase activating proteins, SH2 domain containing	1944	protein-coding gene	gene with protein product	beta chimerin, chimaerin 2	602857	chimerin (chimaerin) 2		NA	8175705	Standard	NM_004067	XM_005249602	NA	Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.49+35630C>T	chr7.hg19:g.29270236C>T		NA	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	hg19	CCDS5420.1	0.02	-0.13149	AGGxGTG	COVERED																																																																																			NOVEL	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214228.2	8	3.008004	KEEP	0	0	0	10	288	CC	0.992708	0.227502	0		+	3	60	83	0	0	6.932205	8	60	255	32	ENST00000222792.6	0.272727	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	29674131	29674131	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:29674131A>G			NA	NA				PRR15 (67220 upstream) : ZNRF2P2 (16527 downstream)						NA		NA									NA						tcaggagttcaagaccagcct	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.29674131A>G		NA		hg19		0.02	-0.157844	TTCxAGA	UNCOVERED																																																																																			NOVEL					0			9	3.608609	KEEP	16	0	0	12	325	AA	0	0	0			3	40	93	1	0	7.292232	14	60	390	55		0.176471	0.322807
ZNRF2P2	100271874	__UNKNOWN__	__UNKNOWN__	7	29696569	29696569	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:29696569C>T	ENST00000426767.1	-	0	366					NR_024278.1				zinc and ring finger 2 pseudogene 2	NA		NA									NA						aagcaattctcctgcctcaac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7p14.3	2011-08-22			ENSG00000239968	ENSG00000225264	100271874			42793	pseudogene	pseudogene		NA			NA		Standard	NR_027347	NR_027347	NA	Approved				OTTHUMG00000152750	ENST00000426767.1:	chr7.hg19:g.29696569C>T		NA		hg19		0.02	-0.149123	TCTxCTG	COVERED																																																																																			NOVEL	ZNRF2P2-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000327679.1	11	2.407274	KEEP	0	0	0	8	250	CC	0.99257	0.289832	0		-	4	39	120	0	0	10.270769	10	60	345	36	ENST00000426767.1	0.285714	0.292001
ZNRF2P2	100271874	__UNKNOWN__	__UNKNOWN__	7	29696578	29696578	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:29696578A>G	ENST00000426767.1	-	0	366					NR_024278.1				zinc and ring finger 2 pseudogene 2	NA		NA									NA						tcctgcctcaacctccctagc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7p14.3	2011-08-22			ENSG00000239968	ENSG00000225264	100271874			42793	pseudogene	pseudogene		NA			NA		Standard	NR_027347	NR_027347	NA	Approved				OTTHUMG00000152750	ENST00000426767.1:	chr7.hg19:g.29696578A>G		NA		hg19		0.02	-0.122787	TCAxCCT	COVERED																																																																																			NOVEL	ZNRF2P2-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000327679.1	10	2.404906	KEEP	0	0	0	8	210	AA	0.99257	0.194853	0		-	3	42	106	0	0	9.232728	8	60	229	31	ENST00000426767.1	0.272727	0.196312
SCRN1	9805	__UNKNOWN__	__UNKNOWN__	7	30018779	30018779	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30018779G>A	ENST00000426154.1	-	2	176				SCRN1_ENST00000242059.5_Intron|SCRN1_ENST00000434476.2_Intron|SCRN1_ENST00000409570.1_Intron|SCRN1_ENST00000494620.1_Intron|SCRN1_ENST00000425819.2_Intron	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	NA		NA			exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						aggagttcgagaccagcctga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193	9805			22192	protein-coding gene	gene with protein product		614965			NA	12221138	Standard	NM_014766	NM_014766	NA	Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.1-10095C>T	chr7.hg19:g.30018779G>A		NA	A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	hg19	CCDS5422.1	0.02	-0.14911	CGAxACC	COVERED																																																																																			NOVEL	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214231.2	6	2.707477	KEEP	2	0	0	9	275	GG	0.99257	0.289832	0		-	3	21	83	0	0	6.379405	13	60	440	45	ENST00000426154.1	0.1875	0.292001
FKBP14	55033	__UNKNOWN__	__UNKNOWN__	7	30050918	30050918	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30050918T>A	ENST00000222803.5	-	0	4244				AC007285.6_ENST00000419103.1_RNA|AC007285.6_ENST00000422239.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						tggcctcccataatgctggga	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080	55033		EF-hand domain containing	18625	protein-coding gene	gene with protein product		614505	FK506 binding protein 14 (22 kDa)		NA	12036304	Standard	NM_017946	NM_017946	NA	Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.*3433A>T	chr7.hg19:g.30050918T>A		NA		hg19	CCDS5423.1	0.02	2.720338	CCAxAAT	COVERED																																																																																			NOVEL	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214229.1	32	5.872315	KEEP	1	5	128	65	1792	TT	1	1	0		-	8	60	240	0	0	14.924741	117	60	3411	316	ENST00000222803.5	0.064	1
FKBP14	55033	__UNKNOWN__	__UNKNOWN__	7	30050920	30050920	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30050920A>G	ENST00000222803.5	-	0	4242				AC007285.6_ENST00000419103.1_RNA|AC007285.6_ENST00000422239.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						gcctcccataatgctgggatt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080	55033		EF-hand domain containing	18625	protein-coding gene	gene with protein product		614505	FK506 binding protein 14 (22 kDa)		NA	12036304	Standard	NM_017946	NM_017946	NA	Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.*3431T>C	chr7.hg19:g.30050920A>G		NA		hg19	CCDS5423.1	0.02	3.578734	ATAxTGC	COVERED																																																																																			NOVEL	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214229.1	34	7.348796	KEEP	1	4	121	67	1865	AA	1	1	0		-	5	60	174	0	0	10.604711	124	60	3752	321	ENST00000222803.5	0.03876	1
PLEKHA8	84725	__UNKNOWN__	__UNKNOWN__	7	30073877	30073877	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30073877G>A	ENST00000396259.1	+	1	362				PLEKHA8_ENST00000483799.1_Intron|PLEKHA8_ENST00000258679.7_Intron|PLEKHA8_ENST00000449726.1_Intron|PLEKHA8_ENST00000396257.2_Intron			Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	NA		NA			ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						cgcctgcctcggcctcccaaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086	84725		Pleckstrin homology (PH) domain containing	30037	protein-coding gene	gene with protein product		608639			NA	11001876	Standard	NM_032639	NM_001197027	NA	Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000396259.1:c.40+5459G>A	chr7.hg19:g.30073877G>A		NA	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	hg19		0.02	-0.210519	CTCxGCC	COVERED																																																																																			NOVEL	PLEKHA8-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000214984.1	9	3.008885	KEEP	1	0	0	10	308	GG	0.99254	0.518266	0		+	3	60	91	0	0	6.792756	18	60	597	49	ENST00000396259.1	0.142857	0.522161
PLEKHA8	84725	__UNKNOWN__	__UNKNOWN__	7	30103914	30103914	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30103914T>C	ENST00000396259.1	+	12	1622				PLEKHA8_ENST00000258679.7_Intron|PLEKHA8_ENST00000449726.1_Intron|PLEKHA8_ENST00000396257.2_Intron			Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	NA		NA			ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						tggtggctcatgcctgtactt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086	84725		Pleckstrin homology (PH) domain containing	30037	protein-coding gene	gene with protein product		608639			NA	11001876	Standard	NM_032639	NM_001197027	NA	Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000396259.1:c.1300+1556T>C	chr7.hg19:g.30103914T>C		NA	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	hg19		0.02	-0.175407	TCAxGCC	COVERED																																																																																			NOVEL	PLEKHA8-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000214984.1	16	6.014325	KEEP	1	0	0	20	548	TT	0.99986	0.387352	0		+	3	60	100	0	0	8.273013	11	60	317	52	ENST00000396259.1	0.214286	0.387407
ZNRF2	223082	__UNKNOWN__	__UNKNOWN__	7	30340037	30340037	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30340037G>A	ENST00000323037.4	+	1	1520					NM_147128.3	NP_667339.1	Q8NHG8	ZNRF2_HUMAN	zinc and ring finger 2	NA		NA				cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|prostate(1)	5						tgctgggattgcaggcatgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF513707	CCDS5426.1	7p15.1	2013-01-09			ENSG00000180233	ENSG00000180233	223082		RING-type (C3HC4) zinc fingers	22316	protein-coding gene	gene with protein product		612061			NA		Standard	NM_147128	NM_147128	NA	Approved	RNF202	uc003tat.3	Q8NHG8	OTTHUMG00000097759	ENST00000323037.4:c.469+14595G>A	chr7.hg19:g.30340037G>A		NA		hg19	CCDS5426.1	0.02	-0.271935	ATTxCAG	COVERED																																																																																			NOVEL	ZNRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214992.1	7	2.708224	KEEP	1	0	0	9	281	GG	0.99254	0.711964	0		+	4	60	118	0	0	8.791783	23	60	780	61	ENST00000323037.4	0.148148	0.717315
NOD1	10392	__UNKNOWN__	__UNKNOWN__	7	30475543	30475543	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:30475543A>C	ENST00000222823.4	-	11	3147					NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						caatgcactcaagcctggacg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100	10392		Nucleotide-binding domain and leucine rich repeat containing	16390	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1, NLR family, CARD domain containing 1	605980	caspase recruitment domain family, member 4	CARD4	NA	10224040, 10329646	Standard		NM_006092	NA	Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.2621+70T>G	chr7.hg19:g.30475543A>C		NA	B4DTU3|Q549U4|Q8IWF5	hg19	CCDS5427.1	0.02	1.643073	CTCxAGC	COVERED																																																																																			NOVEL	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250443.2	16	6.414925	KEEP	2	3	90	53	1493	AA	1	0.999622	0		-	4	60	136	0	0	8.754664	70	60	2095	205	ENST00000222823.4	0.054054	0.999622
CCDC129	223075	__UNKNOWN__	__UNKNOWN__	7	31678652	31678652	__UNKNOWN__	Intron	SNP	A	A	G	rs38387	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:31678652A>G	ENST00000409210.1	+	8	1136				CCDC129_ENST00000319386.3_Intron|CCDC129_ENST00000407970.3_Intron|CCDC129_ENST00000451887.2_Intron			Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	NA		NA								cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						cggcctcccaaagtgctggga	0.488		NA											A|||	679	0.135583	0.0182	0.1556	5008	,	,	NA	16461	0.1776	NA	0.2177	False	NA	,,,	NA	NA	NA	2504	0.1524	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347	223075			27363	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_194300	NM_001257967	NA	Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000409210.1:c.953-3138A>G	chr7.hg19:g.31678652A>G		NA	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	hg19		0.02	-0.096455	CCAxAGT	UNCOVERED																																																																																			NOVEL	CCDC129-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000328240.2	7	2.707128	KEEP	9	0	0	9	252	AA	0	0	0		+	5	60	167	0	0	16.076902	5	60	142	33	ENST00000409210.1	0.5	0.120436
CCDC129	223075	__UNKNOWN__	__UNKNOWN__	7	31692391	31692391	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs142016406		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:31692391C>A	ENST00000409210.1	+	12	2991	c.2807C>A	c.(2806-2808)aCc>aAc	p.T936N	CCDC129_ENST00000319386.3_Missense_Mutation_p.T880N|CCDC129_ENST00000407970.3_Missense_Mutation_p.T1028N|CCDC129_ENST00000451887.2_Intron			Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	1028		NA								cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TTAGGTCCAACCCCTTTGTCA	0.478		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	20389	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0								C	ASN/THR	1,4405	2.1+/-5.4	0,1,2202	113	103	106		3083	-0.1	0	7	dbSNP_134	106	0,8600		0,0,4300	no	missense	CCDC129	NM_194300.2	65	0,1,6502	AA,AC,CC	NA	0.0,0.0227,0.0077	benign	1028/1045	31692391	1,13005	2203	4300	6503	SO:0001583	missense			AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347	223075			27363	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_194300	NM_001257967	NA	Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000409210.1:c.2807C>A	chr7.hg19:g.31692391C>A	ENSP00000387214:p.Thr936Asn	NA	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	hg19		0.02	1.397348	CAAxCCC	COVERED	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.773	1.173310	0.21704	2.27E-4	0.0	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000538406;ENST00000409210	T;T;T	0.18810	2.19;2.46;2.2	4.07	-0.107	0.13592	.	1.084680	0.07245	N	0.864901	T	0.14874	0.0359	L	0.36672	1.1	0.09310	N	1	B;B;B	0.29508	0.246;0.246;0.246	B;B;B	0.23574	0.047;0.047;0.047	T	0.29549	-1.0008	10	0.49607	T	0.09	.	5.0683	0.14592	0.0:0.4533:0.3423:0.2045	.	1038;1028;880	F5H2J8;Q6ZRS4;Q6ZRS4-2	.;CC129_HUMAN;.	N	880;1028;1038;936	ENSP00000313062:T880N;ENSP00000384416:T1028N;ENSP00000387214:T936N	ENSP00000313062:T880N	T	+	2	0	CCDC129	31658916	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-0.090000	0.11163	-0.136000	0.11475	-0.140000	0.14226	ACC	NOVEL	CCDC129-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000328240.2	6	4.512922	KEEP	0	0	0	15	454	CC	0.99649	0.995603	0		+	16	60	450	0	0	36.075084	56	60	1875	133	ENST00000409210.1	0.222222	0.99911
AVL9	23080	__UNKNOWN__	__UNKNOWN__	7	32833720	32833720	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:32833720T>C	ENST00000404479.1	+	10	1215							Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	NA		NA			cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ccttgtgatctgcccacctcg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778	23080			28994	protein-coding gene	gene with protein product		612927	KIAA0241	KIAA0241	NA	17229886, 22595670	Standard	NM_015060	XM_005249668	NA	Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000404479.1:c.1215+234644T>C	chr7.hg19:g.32833720T>C		NA	Q92573	hg19		0.02	-0.157878	ATCxGCC	UNCOVERED																																																																																			NOVEL	AVL9-201	KNOWN	basic	protein_coding	NA	protein_coding		8	2.706147	KEEP	7	0	0	9	245	TT	0	0	0		+	3	60	99	0	0	7.89187	14	60	418	44	ENST00000404479.1	0.176471	0.322807
AVL9	23080	__UNKNOWN__	__UNKNOWN__	7	32833725	32833725	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:32833725A>G	ENST00000404479.1	+	10	1215							Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	NA		NA			cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						tgatctgcccacctcggcctc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778	23080			28994	protein-coding gene	gene with protein product		612927	KIAA0241	KIAA0241	NA	17229886, 22595670	Standard	NM_015060	XM_005249668	NA	Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000404479.1:c.1215+234649A>G	chr7.hg19:g.32833725A>G		NA	Q92573	hg19		0.02	-0.166647	CCCxCCT	UNCOVERED																																																																																			NOVEL	AVL9-201	KNOWN	basic	protein_coding	NA	protein_coding		8	2.707015	KEEP	7	0	0	9	250	AA	0	0	0		+	3	60	95	0	0	7.410318	15	60	451	46	ENST00000404479.1	0.166667	0.353947
AVL9	23080	__UNKNOWN__	__UNKNOWN__	7	32978266	32978266	__UNKNOWN__	Intron	SNP	T	T	A	rs34556400	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:32978266T>A	ENST00000404479.1	+	11	1215				RP9P_ENST00000381639.3_RNA			Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	NA		NA			cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						gccaaaatcatgccactgcac	0.483		NA											T|||	2710	0.541134	0.7927	0.3876	5008	,	,	NA	10480	0.5367	NA	0.3091	False	NA	,,,	NA	NA	NA	2504	0.5532	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778	23080			28994	protein-coding gene	gene with protein product		612927	KIAA0241	KIAA0241	NA	17229886, 22595670	Standard	NM_015060	XM_005249668	NA	Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000404479.1:c.1216-90956T>A	chr7.hg19:g.32978266T>A		NA	Q92573	hg19		0.02	-0.096475	TCAxGCC	UNCOVERED																																																																																			NOVEL	AVL9-201	KNOWN	basic	protein_coding	NA	protein_coding		12	2.706058	KEEP	9	0	0	9	236	CT	0	0	0		+	5	60	156	0	0	14.694085	6	60	176	36	ENST00000404479.1	0.454545	0.120436
FKBP9	11328	__UNKNOWN__	__UNKNOWN__	7	33007656	33007656	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:33007656C>T	ENST00000242209.4	+	2	390				FKBP9_ENST00000538336.1_Intron|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538443.1_Intron	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	NA		NA			chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			cgtgagccaccgcgcccagcT	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642	11328		EF-hand domain containing	3725	protein-coding gene	gene with protein product		NA	FK506-binding protein 9 (63 kD)		NA	12036304	Standard	NM_007270	NM_007270	NA	Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.222-6573C>T	chr7.hg19:g.33007656C>T		NA	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	hg19	CCDS5439.1	0.02	-0.114039	CACxGCG	UNCOVERED																																																																																			NOVEL	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215137.1	7	4.5126	KEEP	0	0	0	15	443	CC	0.99649	0.161897	0		+	3	54	92	0	0	7.581805	10	60	339	43	ENST00000242209.4	0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	33123451	33123451	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:33123451A>G			NA	NA				NT5C3A (21042 upstream) : RP9 (10957 downstream)						NA		NA									NA						ccagcactttaggaggccgag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.33123451A>G		NA		hg19		0.02	-0.149115	TTTxGGA	COVERED																																																																																			NOVEL					0			3	2.405907	KEEP	0	0	0	8	217	AA	0.99257	0.289832	0			3	60	106	0	0	8.772105	12	60	362	37		0.2	0.292001
BBS9	27241	__UNKNOWN__	__UNKNOWN__	7	33179916	33179916	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:33179916A>G	ENST00000242067.6	+	2	510				BBS9_ENST00000425508.2_Intron|BBS9_ENST00000355070.2_Intron|BBS9_ENST00000396127.2_Intron|BBS9_ENST00000354265.4_Intron|BBS9_ENST00000482941.1_Intron|BBS9_ENST00000350941.3_Intron	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	NA		NA			cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			gattacaggcatgagccaccg	0.522		NA							Bardet-Biedl syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507	27241			30000	protein-coding gene	gene with protein product	parathyroid hormone responsive B1 gene	607968			NA	16380913, 10221542	Standard		XM_005249701	NA	Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.-11-5938A>G	chr7.hg19:g.33179916A>G		NA	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	hg19	CCDS43566.1	0.02	-0.192963	GGCxTGA	COVERED																																																																																			NOVEL	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329064.1	9	4.81132	KEEP	12	0	0	16	427	AA	0.993072	0.454585	0		+	3	60	105	0	0	8.260611	17	60	509	68	ENST00000242067.6	0.15	0.457757
BBS9	27241	__UNKNOWN__	__UNKNOWN__	7	33390585	33390585	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:33390585C>T	ENST00000242067.6	+	14	1953				BBS9_ENST00000355070.2_Intron|BBS9_ENST00000396127.2_Intron|BBS9_ENST00000354265.4_Intron|BBS9_ENST00000350941.3_Intron	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	NA		NA			cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			ggattacaggcgtgagccact	0.458		NA							Bardet-Biedl syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507	27241			30000	protein-coding gene	gene with protein product	parathyroid hormone responsive B1 gene	607968			NA	16380913, 10221542	Standard		XM_005249701	NA	Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1433-246C>T	chr7.hg19:g.33390585C>T		NA	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	hg19	CCDS43566.1	0.02	2.311532	AGGxGTG	COVERED																																																																																			NOVEL	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329064.1	21	11.498936	KEEP	2	2	53	57	1711	CC	1	0.999999	0		+	6	60	167	0	0	9.447605	105	60	3521	272	ENST00000242067.6	0.054054	0.999999
BBS9	27241	__UNKNOWN__	__UNKNOWN__	7	33392474	33392474	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:33392474G>A	ENST00000242067.6	+	15	2062	c.1541G>A	c.(1540-1542)cGa>cAa	p.R514Q	BBS9_ENST00000355070.2_Intron|BBS9_ENST00000396127.2_Missense_Mutation_p.R479Q|BBS9_ENST00000354265.4_Intron|BBS9_ENST00000350941.3_Intron	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	514		NA			cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			TGGACAGATCGAAATCCTGAT	0.323		NA							Bardet-Biedl syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													107	97	100			NA	NA	7		NA											NA				33392474		1818	4086	5904	SO:0001583	missense	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507	27241			30000	protein-coding gene	gene with protein product	parathyroid hormone responsive B1 gene	607968			NA	16380913, 10221542	Standard		XM_005249701	NA	Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1541G>A	chr7.hg19:g.33392474G>A	ENSP00000242067:p.Arg514Gln	NA	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	hg19	CCDS43566.1	0.02	1.278129	ATCxAAA	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.481|8.481	0.859796|0.859796	0.17178|0.17178	.|.	.|.	ENSG00000122507|ENSG00000122507	ENST00000537775|ENST00000242067;ENST00000396127	.|T;T	.|0.57595	.|1.72;0.39	3.77|3.77	2.8|2.8	0.32819|0.32819	.|.	.|.	.|.	.|.	.|.	T|T	0.25082|0.25082	0.0609|0.0609	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.32653	.|0.379;0.379;0.144	.|B;B;B	.|0.24269	.|0.052;0.05;0.052	T|T	0.07829|0.07829	-1.0752|-1.0752	6|9	0.05959|0.22109	T|T	0.93|0.4	1.0665|1.0665	7.9503|7.9503	0.30010|0.30010	0.0:0.0:0.7555:0.2445|0.0:0.0:0.7555:0.2445	.|.	.|514;479;514	.|Q3SYG4-3;Q3SYG4-4;Q3SYG4	.|.;.;PTHB1_HUMAN	K|Q	392|514;479	.|ENSP00000242067:R514Q;ENSP00000379433:R479Q	ENSP00000441763:E392K|ENSP00000242067:R514Q	E|R	+|+	1|2	0|0	BBS9|BBS9	33358999|33358999	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.944000|0.944000	0.59088|0.59088	2.128000|2.128000	0.42045|0.42045	2.120000|2.120000	0.65058|0.65058	0.655000|0.655000	0.94253|0.94253	GAA|CGA	NOVEL	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329064.1	1	4.512405	KEEP	0	0	0	15	443	GG	0.99649	0.993226	0		+	5	60	151	0	0	9.702828	64	60	2105	131	ENST00000242067.6	0.072464	0.996724
BBS9	27241	__UNKNOWN__	__UNKNOWN__	7	33581899	33581899	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:33581899A>G	ENST00000242067.6	+	21	3042				BBS9_ENST00000355070.2_Intron|BBS9_ENST00000396127.2_Intron|BBS9_ENST00000354265.4_Intron|BBS9_ENST00000350941.3_Intron	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	NA		NA			cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			gtttcaccatattggtcaggc	0.562		NA							Bardet-Biedl syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507	27241			30000	protein-coding gene	gene with protein product	parathyroid hormone responsive B1 gene	607968			NA	16380913, 10221542	Standard		XM_005249701	NA	Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.2521+8111A>G	chr7.hg19:g.33581899A>G		NA	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	hg19	CCDS43566.1	0.02	-0.236775	CATxTTG	UNCOVERED																																																																																			NOVEL	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329064.1	12	2.405405	KEEP	5	0	0	8	210	AA	0	0	0		+	3	55	93	0	0	6.696502	23	60	660	46	ENST00000242067.6	0.115385	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	35355837	35355837	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:35355837A>G			NA	NA				AC009531.2 (56497 upstream) : AC007652.1 (179793 downstream)						NA		NA									NA						ggttacaggcatgagccactg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.35355837A>G		NA		hg19		0.02	-0.280565	GGCxTGA	COVERED																																																																																			NOVEL					0			12	2.235993	KEEP	0	1	24	16	427	AA	0.999366	0.739203	0			3	60	101	0	0	7.344625	26	60	727	67		0.103448	0.739671
SEPT7	989	__UNKNOWN__	__UNKNOWN__	7	35916338	35916338	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:35916338A>G	ENST00000435235.1	+	5	785				SEPT7_ENST00000475109.1_Intron|SEPT7_ENST00000350320.6_Intron|SEPT7_ENST00000494488.2_Intron|SEPT7_ENST00000399035.3_Intron|SEPT7_ENST00000469679.2_Intron|SEPT7_ENST00000399034.2_Intron			Q16181	SEPT7_HUMAN	septin 7	NA		NA			cilium morphogenesis (GO:0060271)|cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein heterooligomerization (GO:0051291)|regulation of embryonic cell shape (GO:0016476)	actin cytoskeleton (GO:0015629)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|septin complex (GO:0031105)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)	14						tagcactttgagaggctgagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S72008	CCDS75582.1	7p14.2	2013-01-21	2005-01-11	2005-01-12	ENSG00000122545	ENSG00000122545	989		Septins	1717	protein-coding gene	gene with protein product		603151	CDC10 cell division cycle 10 homolog (S. cerevisiae)	CDC10	NA	8037772	Standard	NM_001788	NM_001788	NA	Approved	CDC3, SEPT7A	uc011kau.2	Q16181	OTTHUMG00000155063	ENST00000435235.1:c.353+2953A>G	chr7.hg19:g.35916338A>G		NA	Q52M76|Q6NX50	hg19		0.02	-0.184197	TTGxGAG	COVERED																																																																																			NOVEL	SEPT7-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000338285.1	4	3.007821	KEEP	0	0	0	10	280	AA	0.992708	0.42039	0		+	3	60	98	1	0	7.492254	18	60	551	50	ENST00000435235.1	0.142857	0.423478
KIAA0895	23366	__UNKNOWN__	__UNKNOWN__	7	36396017	36396017	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:36396017G>A	ENST00000436884.1	-	2	848				KIAA0895_ENST00000440378.1_Intron|KIAA0895_ENST00000317020.6_Intron|KIAA0895_ENST00000415803.2_3'UTR|KIAA0895_ENST00000297063.6_Intron|KIAA0895_ENST00000338533.5_Intron|KIAA0895_ENST00000480192.1_Intron|KIAA0895_ENST00000453212.1_Intron	NM_001199708.1	NP_001186637.1	Q8NCT3	K0895_HUMAN	KIAA0895	NA		NA								breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						ccagctactcgggaggctgag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542	23366			22206	protein-coding gene	gene with protein product		NA			NA		Standard	NM_015314	NM_015314	NA	Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000436884.1:c.414+493C>T	chr7.hg19:g.36396017G>A		NA	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	hg19	CCDS56482.1	0.02	-0.096482	CTCxGGA	UNCOVERED																																																																																			NOVEL	KIAA0895-006	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337722.1	5	2.405248	KEEP	2	0	0	8	211	GG	0	0	0		-	3	60	93	0	0	8.078658	7	60	212	23	ENST00000436884.1	0.3	0.120436
ANLN	54443	__UNKNOWN__	__UNKNOWN__	7	36474406	36474406	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:36474406C>T	ENST00000265748.2	+	21	3104				ANLN_ENST00000396068.2_Intron	NM_018685.2	NP_061155.2	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|regulation of exit from mitosis (GO:0007096)|septin ring assembly (GO:0000921)	actin cytoskeleton (GO:0015629)|actomyosin contractile ring (GO:0005826)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	actin binding (GO:0003779)			breast(2)|endometrium(5)|kidney(5)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(2)	45						acctgggaggcggaggttgca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF273437	CCDS5447.1, CCDS64628.1	7p15-p14	2013-01-10	2006-08-22		ENSG00000011426	ENSG00000011426	54443		Pleckstrin homology (PH) domain containing	14082	protein-coding gene	gene with protein product		NA	anillin (Drosophila Scraps homolog), actin binding protein, anillin, actin binding protein (scraps homolog, Drosophila)		NA	10931866	Standard	NM_018685	NM_001284301	NA	Approved	ANILLIN, Scraps, scra	uc003tff.3	Q9NQW6	OTTHUMG00000023143	ENST00000265748.2:c.2884-4407C>T	chr7.hg19:g.36474406C>T		NA	Q5CZ78|Q6NSK5|Q9H8Y4|Q9NVN9|Q9NVP0	hg19	CCDS5447.1	0.02	-0.105255	AGGxGGA	UNCOVERED																																																																																			NOVEL	ANLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000218582.3	3	2.40605	KEEP	0	0	0	8	239	CC	0.99257	0.138793	0		+	3	60	86	0	0	7.101057	9	60	303	31	ENST00000265748.2	0.25	0.139832
ELMO1	9844	__UNKNOWN__	__UNKNOWN__	7	37414414	37414414	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:37414414T>C	ENST00000310758.4	-	2	575				ELMO1_ENST00000448602.1_Intron	NM_001206480.1|NM_014800.10	NP_001193409.1|NP_055615.8	Q92556	ELMO1_HUMAN	engulfment and cell motility 1	NA		NA			actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phagocytosis, engulfment (GO:0006911)|Rac protein signal transduction (GO:0016601)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(28)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	58						gcctgtaatctcagcactttg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF398885	CCDS5449.1, CCDS5450.1	7p14.1	2012-07-10	2006-01-20		ENSG00000155849	ENSG00000155849	9844		Engulfment and cell motility proteins	16286	protein-coding gene	gene with protein product		606420	engulfment and cell motility 1 (ced-12 homolog, C. elegans)		NA	11595183	Standard	NM_130442	NM_001039459	NA	Approved	KIAA0281, CED12, ELMO-1, CED-12	uc003tfk.2	Q92556	OTTHUMG00000023701	ENST00000310758.4:c.73-32047A>G	chr7.hg19:g.37414414T>C		NA	A4D1X6|Q29R79|Q6ZTJ0|Q96PB0|Q9H0I1	hg19	CCDS5449.1	0.02	-0.13156	ATCxCAG	COVERED																																																																																			NOVEL	ELMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219830.4	4	3.30839	KEEP	1	0	0	11	303	TT	0.993072	0.227586	0		-	3	60	96	0	0	7.982148	10	60	299	37	ENST00000310758.4	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	38152979	38152979	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:38152979C>T			NA	NA				EPDR1 (161436 upstream) : STARD3NL (64844 downstream)						NA		NA									NA						caaaaattaccgaggcatggt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.38152979C>T		NA		hg19		0.02	-0.087713	TACxGAG	UNCOVERED																																																																																			NOVEL					0			2	2.406617	KEEP	0	0	0	8	231	CC	0.99257	0.09898	0			3	60	91	0	0	7.878515	7	60	220	22		0.3	0.099721
POU6F2	11281	__UNKNOWN__	__UNKNOWN__	7	39507318	39507318	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:39507318T>C	ENST00000518318.2	+	0	5043							P78424	PO6F2_HUMAN	POU class 6 homeobox 2	NA		NA			central nervous system development (GO:0007417)|ganglion mother cell fate determination (GO:0007402)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	42						CACACACACATACACATACAA	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U91934	CCDS34620.2, CCDS55103.1	7p14.1	2011-06-20	2007-07-13		ENSG00000106536	ENSG00000106536	11281		Homeoboxes / POU class	21694	protein-coding gene	gene with protein product	Retina-derived POU-domain factor-1	609062	POU domain, class 6, transcription factor 2		NA	8601806	Standard	NM_007252	NM_007252	NA	Approved	RPF-1	uc003thb.2	P78424	OTTHUMG00000150803	ENST00000518318.2:c.*3033T>C	chr7.hg19:g.39507318T>C		NA	A4D1W2|C4AMB9|P78425|Q75ME8|Q86UM6|Q9UDS7	hg19	CCDS55103.1	0.02	3.2742	ACAxACA	COVERED																																																																																			NOVEL	POU6F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320145.5	29	18.763779	KEEP	0	4	121	105	2745	TT	1	1	0		+	6	60	200	0	0	12.547253	113	60	3246	329	ENST00000518318.2	0.05042	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	39517653	39517653	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:39517653A>G			NA	NA				POU6F2 (9453 upstream) : AC011290.4 (67591 downstream)						NA		NA									NA						tgggtgtggtagctcacgcct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.39517653A>G		NA		hg19		0.02	-0.140328	GGTxGCT	COVERED																																																																																			NOVEL					0			6	2.706764	KEEP	1	0	0	9	247	AA	0.99257	0.259026	0			3	60	98	0	0	8.073048	11	60	322	37		0.214286	0.260965
RALA	5898	__UNKNOWN__	__UNKNOWN__	7	39696602	39696602	__UNKNOWN__	Intron	SNP	G	G	T	rs144904297	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:39696602G>T	ENST00000005257.2	+	2	343				RALA_ENST00000468201.1_Intron	NM_005402.3	NP_005393.2	P11233	RALA_HUMAN	v-ral simian leukemia viral oncogene homolog A (ras related)	NA		NA			actin cytoskeleton reorganization (GO:0031532)|chemotaxis (GO:0006935)|cytokinesis (GO:0000910)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|membrane raft localization (GO:0051665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of filopodium assembly (GO:0051491)|Ras protein signal transduction (GO:0007265)|regulation of exocytosis (GO:0017157)|signal transduction (GO:0007165)|viral process (GO:0016032)	cell surface (GO:0009986)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(9)|skin(3)	16						agtcttgctcggtcacccagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5460.1	7p22-p15	2014-05-09			ENSG00000006451	ENSG00000006451	5898			9839	protein-coding gene	gene with protein product	RAS-like protein A, Ras-related protein Ral-A, Ras family small GTP binding protein RALA, ras related GTP binding protein A	179550		RAL	NA	3292391	Standard	NM_005402	NM_005402	NA	Approved		uc003thd.3	P11233	OTTHUMG00000128775	ENST00000005257.2:c.-37-29628G>T	chr7.hg19:g.39696602G>T		NA	A4D1W3	hg19	CCDS5460.1	0.02	-0.157871	CTCxGTC	COVERED																																																																																			NOVEL	RALA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250696.2	10	2.407113	KEEP	0	0	0	8	248	GG	0.99257	0.320408	0		+	3	60	90	1	0	6.992206	14	60	454	35	ENST00000005257.2	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	39897183	39897183	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:39897183C>T			NA	NA				LINC00265 (64492 upstream) : RN7SL496P (30788 downstream)						NA		NA									NA						ggattacaggcgtgagccact	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.39897183C>T		NA		hg19		0.02	-0.140346	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			2	2.406791	KEEP	2	0	0	8	237	CC	0	0	0			4	60	120	0	0	10.130881	11	60	363	42		0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	39930883	39930883	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:39930883A>G			NA	NA				RN7SL496P (2622 upstream) : RP11-467D6.1 (56237 downstream)						NA		NA									NA						gaggtcaggaattcgagacca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.39930883A>G		NA		hg19		0.02	-0.166598	GGAxTTC	COVERED																																																																																			NOVEL					0			3	2.40536	KEEP	0	0	0	8	213	AA	0.99257	0.351317	0			3	60	99	0	0	7.810762	15	60	419	42		0.166667	0.353947
CDK13	8621	__UNKNOWN__	__UNKNOWN__	7	40124695	40124695	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:40124695C>T	ENST00000181839.4	+	12	3634				CDK13_ENST00000340829.5_Intron	NM_003718.4|NM_031267.3	NP_003709.3|NP_112557.2	Q14004	CDK13_HUMAN	cyclin-dependent kinase 13	NA		NA			alternative mRNA splicing, via spliceosome (GO:0000380)|hemopoiesis (GO:0030097)|multicellular organismal development (GO:0007275)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|positive regulation of cell proliferation (GO:0008284)|regulation of mitosis (GO:0007088)|viral process (GO:0016032)	cyclin K-CDK13 complex (GO:0002945)|extracellular space (GO:0005615)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(2)|prostate(2)|skin(5)|stomach(2)|urinary_tract(1)	49						tacggtagctcatgcctgtaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M80629	CCDS5461.1, CCDS5462.1	7p14.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000065883	ENSG00000065883	8621		Cyclin-dependent kinases	1733	protein-coding gene	gene with protein product	cholinesterase-related cell division controller	603309	cell division cycle 2-like 5 (cholinesterase-related cell division controller)	CDC2L5	NA	1731328, 19884882	Standard	NM_003718	NM_003718	NA	Approved	CHED, CDC2L, KIAA1791	uc003thh.4	Q14004	OTTHUMG00000023726	ENST00000181839.4:c.3030-3030C>T	chr7.hg19:g.40124695C>T		NA	Q53G78|Q6DKQ9|Q75MH4|Q75MH5|Q96JN4|Q9H4A0|Q9H4A1|Q9UDR4	hg19	CCDS5461.1	0.02	-0.078917	GCTxATG	UNCOVERED																																																																																			NOVEL	CDK13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250726.2	9	2.407386	KEEP	0	0	0	8	252	CC	0.99257	0.076761	0		+	3	60	77	0	0	7.05305	4	60	130	22	ENST00000181839.4	0.428571	0.077336
C7orf10	0	__UNKNOWN__	__UNKNOWN__	7	40257091	40257091	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:40257091A>G	ENST00000335693.4	+	7	528				C7orf10_ENST00000401647.2_Intron|C7orf10_ENST00000309930.5_Intron|C7orf10_ENST00000540834.1_Missense_Mutation_p.M194V	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		NA		NA			metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						gattacaggaatgagccaccg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000335693.4:c.506-20143A>G	chr7.hg19:g.40257091A>G		NA	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	hg19	CCDS55105.1	0.02	3.622031	GGAxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.705359	0.00719	.	.	ENSG00000175600	ENST00000540834	T	0.00745	5.75	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.46775	-0.9167	5	0.87932	D	0	.	.	.	.	.	.	.	.	V	194	ENSP00000445521:M194V	ENSP00000445521:M194V	M	+	1	0	C7orf10	40223616	0.000000	0.05858	0.023000	0.16930	0.011000	0.07611	-0.920000	0.04013	-0.759000	0.04684	-0.756000	0.03474	ATG	NOVEL	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338388.1	21	4.639824	KEEP	0	4	115	56	1544	AA	1	0.999993	0		+	5	60	170	1	0	10.814715	93	60	2795	237	ENST00000335693.4	0.05102	0.999993
C7orf10	0	__UNKNOWN__	__UNKNOWN__	7	40472022	40472022	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:40472022T>C	ENST00000335693.4	+	10	860				C7orf10_ENST00000401647.2_Intron|C7orf10_ENST00000309930.5_Intron	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		NA		NA			metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						tgcggtggcttacgcctgtaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000335693.4:c.838-16864T>C	chr7.hg19:g.40472022T>C		NA	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	hg19	CCDS55105.1	0.02	-0.166635	GCTxACG	COVERED																																																																																			NOVEL	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338388.1	10	2.405737	KEEP	1	0	0	8	215	TT	0.99257	0.351317	0		+	3	60	98	0	0	7.878978	13	60	382	43	ENST00000335693.4	0.1875	0.353947
C7orf10	0	__UNKNOWN__	__UNKNOWN__	7	40753666	40753666	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:40753666T>C	ENST00000335693.4	+	13	1133				C7orf10_ENST00000401647.2_Intron|C7orf10_ENST00000309930.5_Intron	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		NA		NA			metabolic process (GO:0008152)	mitochondrion (GO:0005739)	succinate-hydroxymethylglutarate CoA-transferase activity (GO:0047369)			endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)	18						cagtggctcatgcctgtaatc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000335693.4:c.1111-35367T>C	chr7.hg19:g.40753666T>C		NA	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	hg19	CCDS55105.1	0.02	-0.140336	TCAxGCC	COVERED																																																																																			NOVEL	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338388.1	5	2.405797	KEEP	1	0	0	8	217	TT	0.99257	0.259026	0		+	3	60	102	0	0	8.372215	12	60	357	35	ENST00000335693.4	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	41402830	41402830	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:41402830T>C			NA	NA				AC005022.1 (229725 upstream) : AC005027.3 (303935 downstream)						NA		NA									NA						ccacccaccttggccttccaa	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.41402830T>C		NA		hg19		0.02	-0.175425	CCTxGGC	COVERED																																																																																			NOVEL					0			10	3.007342	KEEP	1	0	0	10	274	TT	0.992708	0.384582	0			3	60	97	0	0	7.691754	14	60	427	42		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	42548834	42548834	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:42548834A>G			NA	NA				GLI3 (272176 upstream) : AC027269.2 (152490 downstream)						NA		NA									NA						caacactttgagaggccaagg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.42548834A>G		NA		hg19		0.02	-0.166667	TTGxGAG	COVERED																																																																																			NOVEL					0			7	2.406343	KEEP	0	0	0	8	228	AA	0.99257	0.351317	0			3	60	96	0	0	7.591667	14	60	443	41		0.176471	0.353947
HECW1	23072	__UNKNOWN__	__UNKNOWN__	7	43408807	43408807	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:43408807T>C	ENST00000453890.1	+	5	879				HECW1_ENST00000395891.2_Intron			Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	NA		NA			protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						cttgtaatcctagcactttgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746	23072			22195	protein-coding gene	gene with protein product		610384			NA	12690205, 14684739	Standard	NM_015052	XM_005249665	NA	Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000453890.1:c.555+8228T>C	chr7.hg19:g.43408807T>C		NA	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	hg19		0.02	-0.131565	TCCxAGC	COVERED																																																																																			NOVEL	HECW1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000338775.1	6	3.609419	KEEP	0	0	0	12	334	TT	0.993634	0.227714	0		+	3	60	98	0	0	8.072955	11	60	329	36	ENST00000453890.1	0.214286	0.229173
HECW1	23072	__UNKNOWN__	__UNKNOWN__	7	43546656	43546656	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:43546656G>A	ENST00000453890.1	+	20	3853				HECW1_ENST00000395891.2_Intron			Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	NA		NA			protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						gcaacagagcgagactccttc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746	23072			22195	protein-coding gene	gene with protein product		610384			NA	12690205, 14684739	Standard	NM_015052	XM_005249665	NA	Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000453890.1:c.3530-80G>A	chr7.hg19:g.43546656G>A		NA	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	hg19		0.02	1.420972	AGCxAGA	COVERED																																																																																			NOVEL	HECW1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000338775.1	23	3.86376	KEEP	0	2	54	32	887	GG	0.999998	0.993701	0		+	5	60	151	0	0	10.214964	50	60	1604	122	ENST00000453890.1	0.090909	0.993703
COA1	55744	__UNKNOWN__	__UNKNOWN__	7	43722680	43722680	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:43722680T>C	ENST00000310564.6	-	2	61				COA1_ENST00000223336.6_Intron|COA1_ENST00000395880.3_Intron			Q9GZY4	COA1_HUMAN	cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae)	NA		NA			mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)	cytoplasm (GO:0005737)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrion (GO:0005739)					NA						tggtctcaaattcctgacctc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001665	CCDS5471.1	7p13	2012-12-05	2012-10-15	2012-06-25	ENSG00000106603	ENSG00000106603	55744		Mitochondrial respiratory chain complex assembly factors	21868	protein-coding gene	gene with protein product		614769	chromosome 7 open reading frame 44	C7orf44	NA	22356826	Standard	NM_018224	NM_018224	NA	Approved	FLJ10803, MITRAC15	uc003tin.2	Q9GZY4	OTTHUMG00000128949	ENST00000310564.6:c.258-32369A>G	chr7.hg19:g.43722680T>C		NA	A6NJU8|A8KAH8|Q9HAB7|Q9NVD2	hg19	CCDS5471.1	0.02	-0.201697	AAAxTCC	COVERED																																																																																			NOVEL	COA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313663.1	6	2.405894	KEEP	0	0	0	8	216	TT	0.99257	0.4869	0		-	4	60	130	0	0	10.469475	17	60	481	41	ENST00000310564.6	0.190476	0.490544
COA1	55744	__UNKNOWN__	__UNKNOWN__	7	43746078	43746078	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:43746078G>A	ENST00000310564.6	-	1	61				COA1_ENST00000223336.6_Intron|COA1_ENST00000395880.3_Intron			Q9GZY4	COA1_HUMAN	cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae)	NA		NA			mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex IV assembly (GO:0033617)	cytoplasm (GO:0005737)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrion (GO:0005739)					NA						gccaggaggcggaggctgcag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001665	CCDS5471.1	7p13	2012-12-05	2012-10-15	2012-06-25	ENSG00000106603	ENSG00000106603	55744		Mitochondrial respiratory chain complex assembly factors	21868	protein-coding gene	gene with protein product		614769	chromosome 7 open reading frame 44	C7orf44	NA	22356826	Standard	NM_018224	NM_018224	NA	Approved	FLJ10803, MITRAC15	uc003tin.2	Q9GZY4	OTTHUMG00000128949	ENST00000310564.6:c.257+22949C>T	chr7.hg19:g.43746078G>A		NA	A6NJU8|A8KAH8|Q9HAB7|Q9NVD2	hg19	CCDS5471.1	0.02	-0.096488	GGCxGAG	UNCOVERED																																																																																			NOVEL	COA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313663.1	5	2.405028	KEEP	0	0	0	8	224	GG	0.99257	0.119541	0		-	3	60	88	0	0	7.578325	7	60	229	26	ENST00000310564.6	0.3	0.120436
POLR2J4	84820	__UNKNOWN__	__UNKNOWN__	7	44024186	44024186	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44024186T>C	ENST00000427076.1	-	0	894				RP5-1165K10.2_ENST00000454572.1_RNA	NR_003655.2				polymerase (RNA) II (DNA directed) polypeptide J4, pseudogene	NA		NA									NA						AGAAACAATCTCTCTCgccag	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7p13	2008-08-21			ENSG00000214783	ENSG00000214783	84820			28195	pseudogene	pseudogene		NA			NA	15586814	Standard	NR_003655	NR_003655	NA	Approved	MGC13098	uc010kxw.2		OTTHUMG00000155253	ENST00000427076.1:	chr7.hg19:g.44024186T>C		NA		hg19		0.02	2.040924	ATCxCTC	COVERED																																																																																			NOVEL	POLR2J4-002	KNOWN	basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000473169.1	8	5.712238	KEEP	7	0	0	19	524	TT	0.999366	0.963163	0		-	9	55	301	0	0	24.1603	41	60	1238	95	ENST00000427076.1	0.18	0.963774
TMED4	222068	__UNKNOWN__	__UNKNOWN__	7	44620479	44620479	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44620479G>A	ENST00000289577.5	-	3	468				TMED4_ENST00000481238.1_3'UTR|TMED4_ENST00000457408.2_Intron			Q7Z7H5	TMED4_HUMAN	transmembrane emp24 protein transport domain containing 4	NA		NA			positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein transport (GO:0015031)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6						ctggggaggcggaggttgcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035467	CCDS5493.1	7p13	2004-12-21			ENSG00000158604	ENSG00000158604	222068			22301	protein-coding gene	gene with protein product		612038			NA	12761501	Standard	NM_182547	NM_182547	NA	Approved	HNLF	uc003tli.3	Q7Z7H5	OTTHUMG00000129210	ENST00000289577.5:c.387+568C>T	chr7.hg19:g.44620479G>A		NA	A4D2K8|B4DFJ4|Q56VW3|Q7Z432|Q8N2P6	hg19		0.02	2.850857	GGCxGAG	COVERED																																																																																			NOVEL	TMED4-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000339388.1	12	2.483619	KEEP	2	9	242	94	2558	GG	1	1	0		-	11	60	313	0	0	20.729514	106	70	3284	281	ENST00000289577.5	0.094017	1
OGDH	4967	__UNKNOWN__	__UNKNOWN__	7	44648047	44648047	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44648047T>C	ENST00000449767.1	+	1	63				OGDH_ENST00000447398.1_Intron|OGDH_ENST00000222673.5_Intron|OGDH_ENST00000444676.1_Intron|OGDH_ENST00000443864.2_Intron|OGDH_ENST00000439616.2_Intron	NM_001165036.1	NP_001158508.1	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	NA		NA			2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	cctgtaatcctagcactttgg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	4967	1.2.4.2		8124	protein-coding gene	gene with protein product		613022			NA	8020988, 1542694	Standard		NM_002541	NA	Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000449767.1:c.-28+1795T>C	chr7.hg19:g.44648047T>C		NA	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	hg19	CCDS55107.1	0.02	-0.2105	TCCxAGC	COVERED																																																																																			NOVEL	OGDH-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339392.1	7	5.712217	KEEP	1	0	0	19	500	TT	0.999859	0.522088	0		+	3	60	102	0	0	7.892081	18	60	534	63	ENST00000449767.1	0.142857	0.522161
AC013436.6	0	__UNKNOWN__	__UNKNOWN__	7	44826354	44826354	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44826354T>A	ENST00000425077.1	-	0	217										NA		NA									NA						ggatcacctgtggtcaggagt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000425077.1:	chr7.hg19:g.44826354T>A		NA		hg19		0.02	-0.166634	CTGxGGT	COVERED																																																																																			NOVEL	AC013436.6-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000341782.1	9	3.307654	KEEP	1	0	0	11	297	TT	0.992708	0.351366	0		-	3	60	87	1	0	6.610811	15	60	452	46	ENST00000425077.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	44828747	44828747	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44828747A>G			NA	NA				AC013436.6 (1808 upstream) : PPIA (7531 downstream)						NA		NA									NA						ttgaacccggaaggcggaggt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.44828747A>G		NA		hg19		0.02	-0.149105	CGGxAGG	COVERED																																																																																			NOVEL					0			5	2.405132	KEEP	0	0	0	8	218	AA	0.99257	0.289832	0			3	60	102	0	0	8.278849	13	60	385	35		0.1875	0.292001
H2AFV	94239	__UNKNOWN__	__UNKNOWN__	7	44870407	44870407	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44870407G>A	ENST00000222690.6	-	5	431				H2AFV_ENST00000437072.1_Intron	NM_138635.3	NP_619541.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	NA		NA				extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						gaccagcctggccaacatggt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968	94239		Histones / Replication-independent	20664	protein-coding gene	gene with protein product		NA		H2AV	NA		Standard	NM_012412	NM_012412	NA	Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000222690.6:c.326-645C>T	chr7.hg19:g.44870407G>A		NA	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	hg19	CCDS5495.1	0.02	-0.13155	CTGxCCA	COVERED																																																																																			NOVEL	H2AFV-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251304.1	11	3.910985	KEEP	6	0	0	13	391	GG	0.993072	0.227586	0		-	3	60	77	0	0	6.477155	7	60	238	40	ENST00000222690.6	0.3	0.229173
PURB	5814	__UNKNOWN__	__UNKNOWN__	7	44917402	44917402	__UNKNOWN__	3'UTR	SNP	C	C	T	rs547284155		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44917402C>T	ENST00000395699.2	-	0	7558					NM_033224.3	NP_150093.1	Q96QR8	PURB_HUMAN	purine-rich element binding protein B	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of myeloid cell differentiation (GO:0045637)|transcription, DNA-templated (GO:0006351)	DNA replication factor A complex (GO:0005662)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(3)|prostate(1)|skin(1)	7						agcgaaactccgtctcaaaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5499.1	7p13	2008-07-18			ENSG00000146676	ENSG00000146676	5814			9702	protein-coding gene	gene with protein product		608887			NA	1448097	Standard	NM_033224	NM_033224	NA	Approved	PURBETA	uc003tme.3	Q96QR8	OTTHUMG00000023578	ENST00000395699.2:c.*6607G>A	chr7.hg19:g.44917402C>T		NA	A4D2L7	hg19	CCDS5499.1	0.02	-0.324459	CTCxGTC	COVERED																																																																																			NOVEL	PURB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251332.2	16	3.474309	KEEP	0	2	49	29	847	CC	0.999997	0.835714	0		-	4	60	96	0	0	6.4665	25	60	778	98	ENST00000395699.2	0.137931	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	44944009	44944009	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44944009G>C			NA	NA				RP4-673M15.1 (18017 upstream) : RP4-647J21.1 (54588 downstream)						NA		NA									NA						accagcctgggcaacatggca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.44944009G>C		NA		hg19		0.02	-0.149067	TGGxCAA	COVERED																																																																																			NOVEL					0			5	2.707882	KEEP	1	0	0	9	271	GG	0.99254	0.289823	0			3	60	86	0	0	6.68235	13	60	422	37		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	44973705	44973705	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:44973705T>C			NA	NA				RP4-673M15.1 (47713 upstream) : RP4-647J21.1 (24892 downstream)						NA		NA									NA						gttgcccaggttggagtgcgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.44973705T>C		NA		hg19		0.02	-0.236799	AGGxTGG	COVERED																																																																																			NOVEL					0			9	4.210715	KEEP	0	0	0	14	388	TT	0.995343	0.609555	0			3	60	106	0	0	8.105384	21	60	621	57		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	45021639	45021639	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:45021639A>G			NA	NA				MYO1G (2942 upstream) : SNHG15 (3337 downstream)						NA		NA									NA						gaccagcctgaccaacatggt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.45021639A>G		NA		hg19		0.02	-0.175388	CTGxCCA	COVERED																																																																																			NOVEL					0			8	2.704841	KEEP	0	0	0	9	229	AA	0.99254	0.384517	0			4	60	127	0	0	10.46886	14	60	398	37		0.222222	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	45284476	45284476	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:45284476T>C			NA	NA				RAMP3 (58575 upstream) : AC073325.1 (215834 downstream)						NA		NA									NA						gctgggattataggcgtgagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.45284476T>C		NA		hg19		0.02	-0.175414	TTAxAGG	UNCOVERED																																																																																			NOVEL					0			6	2.705767	KEEP	5	0	0	9	237	TT	0	0	0			3	60	107	0	0	8.691683	14	60	404	49		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	45435382	45435382	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:45435382T>C			NA	NA				RAMP3 (209481 upstream) : AC073325.1 (64928 downstream)						NA		NA									NA						accatgttgctcaggctggtc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.45435382T>C		NA		hg19		0.02	-0.114018	TGCxCAG	UNCOVERED																																																																																			NOVEL					0			7	2.40628	KEEP	0	0	0	8	224	TT	0.99257	0.16126	0			3	60	100	0	0	8.778844	7	60	204	25		0.3	0.162467
ADCY1	107	__UNKNOWN__	__UNKNOWN__	7	45677127	45677127	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:45677127A>C	ENST00000432715.1	+	6	724				ADCY1_ENST00000297323.7_Intron	NM_001281768.1	NP_001268697.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	ttgagaccagactggacaaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	107	4.6.1.1	Adenylate cyclases	232	protein-coding gene	gene with protein product		103072			NA	8314585	Standard	NM_021116	NM_021116	NA	Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000432715.1:c.346-11142A>C	chr7.hg19:g.45677127A>C		NA	A4D2L8|Q75MI1	hg19		0.02	-0.342042	CAGxCTG	COVERED																																																																																			NOVEL	ADCY1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000340056.1	8	3.908791	KEEP	1	0	0	13	345	AA	0.994391	0.860889	0		+	4	60	143	0	0	10.808091	31	60	906	79	ENST00000432715.1	0.114286	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	45862019	45862019	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:45862019A>G			NA	NA				RP11-638I8.1 (7157 upstream) : RNU6-326P (21213 downstream)						NA		NA									NA						CTTTTTATACATGTTGTTAAA	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.45862019A>G		NA		hg19		0.02	-0.324428	TACxTGT	COVERED																																																																																			NOVEL					0			4	3.003726	KEEP	0	0	0	10	245	AA	0.992708	0.829622	0			6	54	194	0	0	15.469746	27	60	773	57		0.181818	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	48171951	48171951	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:48171951A>G			NA	NA				UPP1 (23621 upstream) : ABCA13 (39105 downstream)						NA		NA									NA						tgcctcccggattcaagcaat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.48171951A>G		NA		hg19		0.02	-0.07016	CGGxTTC	UNCOVERED																																																																																			NOVEL					0			5	3.306683	KEEP	0	0	0	11	287	AA	0.993072	0.053762	0			3	60	89	0	0	8.254804	4	60	116	24		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	49067966	49067966	__UNKNOWN__	IGR	SNP	T	T	C	rs6963978	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:49067966T>C			NA	NA				AC004899.1 (176745 upstream) : AC010971.1 (201766 downstream)						NA		NA									NA						gtcaggagattgagaccatcc	0.557		NA											-|||	2827	0.564497	0.7965	0.5245	5008	,	,	NA	10961	0.3343	NA	0.5408	False	NA	,,,	NA	NA	NA	2504	0.5409	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.49067966T>C		NA		hg19		0.02	-0.061385	GATxGAG	UNCOVERED																																																																																			NOVEL					0			4	2.405654	KEEP	14	0	0	8	221	TT	0	0	0			3	40	93	0	0	8.924775	3	40	94	38		0.5	0.043787
COBL	23242	__UNKNOWN__	__UNKNOWN__	7	51340768	51340768	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:51340768A>G	ENST00000265136.7	-	1	207				COBL_ENST00000441453.1_Intron|COBL_ENST00000395542.2_Intron|COBL_ENST00000395540.2_Intron	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	NA		NA			actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					gctcatgcctataatcccagc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(189;2119 2138 12223 30818 34679)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078	23242			22199	protein-coding gene	gene with protein product		610317	cordon-bleu homolog (mouse)		NA		Standard	NM_015198	NM_015198	NA	Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.41+43521T>C	chr7.hg19:g.51340768A>G		NA	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	hg19	CCDS34637.1	0.02	-0.122788	CCTxTAA	COVERED																																																																																			NOVEL	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342682.1	4	2.706632	KEEP	0	0	0	9	245	AA	0.99254	0.194847	0		-	3	60	101	0	0	8.60138	9	60	264	38	ENST00000265136.7	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	52175671	52175671	__UNKNOWN__	IGR	SNP	G	G	A	rs62465899	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:52175671G>A			NA	NA				RN7SL292P (391056 upstream) : RP11-153N17.1 (57259 downstream)						NA		NA									NA						acaggcacacgccaccatgcc	0.527		NA											G|||	1181	0.235823	0.053	0.3761	5008	,	,	NA	12286	0.25	NA	0.3449	False	NA	,,,	NA	NA	NA	2504	0.2566	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.52175671G>A		NA		hg19		0.02	-0.096482	CACxCCA	UNCOVERED																																																																																			NOVEL					0			12	2.406666	KEEP	5	0	0	8	233	GG	0	0	0			3	60	83	0	0	7.078169	7	60	227	26		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	53907977	53907977	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:53907977A>G			NA	NA				GS1-179L18.1 (28353 upstream) : RP11-806J6.1 (86391 downstream)						NA		NA									NA						agaaagaaagaaagaaagaaa	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.53907977A>G		NA		hg19		0.02	-0.122785	AAGxAAG	UNCOVERED																																																																																			NOVEL					0			6	3.306824	KEEP	4	0	0	11	281	AA	0	0	0			3	40	95	0	1	7.882122	10	60	293	32		0.230769	0.196312
LANCL2	55915	__UNKNOWN__	__UNKNOWN__	7	55460170	55460170	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:55460170T>A	ENST00000254770.2	+	2	900					NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			cagcctcctgtgtagctggga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434	55915			6509	protein-coding gene	gene with protein product	testis-specific adriamycin sensitivity protein, G protein-coupled receptor 69B	612919	LanC (bacterial lantibiotic synthetase component C)-like 2	GPR69B	NA	11762191	Standard	NM_018697	NM_018697	NA	Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.322+567T>A	chr7.hg19:g.55460170T>A		NA	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	hg19	CCDS5517.1	0.02	-0.122779	CTGxGTA	COVERED																																																																																			NOVEL	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251459.1	2	2.706646	KEEP	0	0	0	9	254	TT	0.99254	0.194847	0		+	3	60	82	0	0	6.473561	11	60	340	37	ENST00000254770.2	0.214286	0.196312
FKBP9L	0	__UNKNOWN__	__UNKNOWN__	7	55749334	55749334	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:55749334T>C	ENST00000455909.1	-	0	1883					NR_027340.1|NR_027342.1		Q75LS8	FKB9L_HUMAN		NA		NA			protein folding (GO:0006457)		calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5						gaggccgaggtgggcggatca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000455909.1:	chr7.hg19:g.55749334T>C		NA	B2R7H1	hg19		0.02	-0.412094	AGGxGGG	COVERED																																																																																			NOVEL	FKBP9L-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000251473.2	7	3.84079	KEEP	1	1	26	22	602	TT	0.999892	0.94164	0		-	3	60	96	0	0	6.407399	37	60	1068	89	ENST00000455909.1	0.075	0.941741
SEPT14	346288	__UNKNOWN__	__UNKNOWN__	7	55862383	55862383	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:55862383A>G	ENST00000388975.3	-	0	2638					NM_207366.2	NP_997249.2	Q6ZU15	SEP14_HUMAN	septin 14	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|skin(2)	23	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			Gcgctctgtcacccaggctgg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK126048	CCDS5519.2	7p11.2	2013-01-21			ENSG00000154997	ENSG00000154997	346288		Septins	33280	protein-coding gene	gene with protein product		612140			NA		Standard	NM_207366	NM_207366	NA	Approved	FLJ44060	uc003tqz.2	Q6ZU15	OTTHUMG00000129341	ENST00000388975.3:c.*1223T>C	chr7.hg19:g.55862383A>G		NA	A6NCC2|B4DXD6	hg19	CCDS5519.2	0.02	1.655132	GTCxCCC	COVERED																																																																																			NOVEL	SEPT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251489.2	21	5.506802	KEEP	0	3	81	47	1277	AA	1	0.999919	0		-	4	60	134	2	0	8.188697	87	60	2554	221	ENST00000388975.3	0.043956	0.999919
MRPS17	51373	__UNKNOWN__	__UNKNOWN__	7	55966780	55966780	__UNKNOWN__	Intron	SNP	T	T	C	rs201876262		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:55966780T>C	ENST00000426595.1	+	2	404							Q9Y2R5	RT17_HUMAN	mitochondrial ribosomal protein S17	NA		NA			translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ggcacggtggttcatgcctgt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051352	CCDS5520.1	7p11-q11.21	2012-09-13			ENSG00000239789	ENSG00000239789	51373		Mitochondrial ribosomal proteins / small subunits	14047	protein-coding gene	gene with protein product	28S ribosomal protein S17, mitochondrial	611980			NA	11279123	Standard	NM_015969	NM_015969	NA	Approved	HSPC011, RPMS17, MRP-S17	uc003trd.3	Q9Y2R5	OTTHUMG00000023153	ENST00000426595.1:c.-589-7166T>C	chr7.hg19:g.55966780T>C		NA	Q86X15	hg19		0.02	-0.16664	TGGxTCA	COVERED																																																																																			NOVEL	MRPS17-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000363286.1	4	2.405659	KEEP	1	0	0	8	216	TT	0.99257	0.351317	0		+	3	60	102	0	0	8.278958	13	60	382	39	ENST00000426595.1	0.1875	0.353947
MRPS17	51373	__UNKNOWN__	__UNKNOWN__	7	56023732	56023732	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56023732C>G	ENST00000285298.4	+	0	1383					NM_015969.2	NP_057053.1	Q9Y2R5	RT17_HUMAN	mitochondrial ribosomal protein S17	NA		NA			translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	8	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			gattacaggcctgagccactg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB051352	CCDS5520.1	7p11-q11.21	2012-09-13			ENSG00000239789	ENSG00000239789	51373		Mitochondrial ribosomal proteins / small subunits	14047	protein-coding gene	gene with protein product	28S ribosomal protein S17, mitochondrial	611980			NA	11279123	Standard	NM_015969	NM_015969	NA	Approved	HSPC011, RPMS17, MRP-S17	uc003trd.3	Q9Y2R5	OTTHUMG00000023153	ENST00000285298.4:c.*861C>G	chr7.hg19:g.56023732C>G		NA	Q86X15	hg19	CCDS5520.1	0.02	1.607936	GGCxTGA	COVERED																																																																																			NOVEL	MRPS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251527.2	20	5.849788	KEEP	0	1	27	29	868	CC	0.999997	0.999892	0		+	4	60	134	1	0	8.329754	80	60	2647	161	ENST00000285298.4	0.047619	0.999895
PSPH	5723	__UNKNOWN__	__UNKNOWN__	7	56079175	56079175	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56079175C>T	ENST00000395471.3	-	0	1763				PSPH_ENST00000275605.3_3'UTR			P78330	SERB_HUMAN	phosphoserine phosphatase	NA		NA			cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			tgagccgagaccgcgccactg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	5723	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP	NA	6297854, 9188776	Standard	NM_004577	NM_004577	NA	Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.*280G>A	chr7.hg19:g.56079175C>T		NA	B2RCR5|Q7Z3S5	hg19	CCDS5522.1	0.02	-0.342105	AGAxCGC	COVERED																																																																																			NOVEL	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343304.1	5	6.016422	KEEP	2	0	0	20	587	CC	0.999859	0.865624	0		-	4	60	110	0	0	7.410443	33	60	1097	67	ENST00000395471.3	0.108108	0.865745
SUMF2	25870	__UNKNOWN__	__UNKNOWN__	7	56137629	56137629	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56137629T>C	ENST00000413756.1	+	2	247				SUMF2_ENST00000395436.2_Intron|SUMF2_ENST00000275607.9_Intron|SUMF2_ENST00000342190.6_Intron|SUMF2_ENST00000437307.2_Intron|SUMF2_ENST00000395435.2_Intron|SUMF2_ENST00000434526.2_Intron			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	NA		NA			cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			gagacacagttttcctcttgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103	25870			20415	protein-coding gene	gene with protein product		607940			NA	12757706	Standard	NM_015411	NM_015411	NA	Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.224+1298T>C	chr7.hg19:g.56137629T>C		NA	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	hg19		0.02	-0.061391	AGTxTTC	UNCOVERED																																																																																			NOVEL	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000341457.2	2	2.70739	KEEP	0	0	0	9	257	TT	0.99254	0.04346	0		+	2	60	74	0	0	6.535941	5	60	140	25	ENST00000413756.1	0.285714	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56166849	56166849	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56166849C>T			NA	NA				PHKG1 (6160 upstream) : snoU13 (1502 downstream)						NA		NA									NA						tgagacagtcctgctctgttg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56166849C>T		NA		hg19		0.02	-0.078944	GTCxTGC	UNCOVERED																																																																																			NOVEL					0			10	2.406779	KEEP	1	0	0	8	238	CC	0.99257	0.076761	0			3	49	84	0	0	7.532016	5	60	178	29		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56179419	56179419	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56179419T>C			NA	NA				CHCHD2 (5150 upstream) : NUPR1L (2954 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56179419T>C		NA		hg19		0.02	-0.210497	TCAxGCC	COVERED																																																																																			NOVEL					0			9	3.00687	KEEP	1	0	0	10	265	AT	0.993634	0.549368	0			3	60	96	0	0	7.292464	18	60	534	55		0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56262387	56262387	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56262387T>C			NA	NA				NUPR1L (78294 upstream) : AC073136.1 (75088 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56262387T>C		NA		hg19		0.02	-0.140316	TCAxGCC	COVERED																																																																																			NOVEL					0			6	2.706086	KEEP	0	0	0	9	238	TT	0.99254	0.259018	0			4	60	134	0	0	11.8243	9	60	258	39		0.307692	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56408641	56408641	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56408641G>A			NA	NA				RNU6-1335P (611 upstream) : RNU6-1052P (61121 downstream)						NA		NA									NA						tgtaatcccagcactttggga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56408641G>A		NA		hg19		0.02	-0.157894	CCAxCAC	COVERED																																																																																			NOVEL					0			11	2.639293	KEEP	1	1	23	17	488	GG	0.999366	0.322602	0			4	60	113	0	0	9.180843	13	60	437	50		0.235294	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56441286	56441286	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56441286C>G			NA	NA				RNU6-1335P (33256 upstream) : RNU6-1052P (28476 downstream)						NA		NA									NA						CCAGGAGGCCCAAGCTGGGCG	0.672		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56441286C>G		NA		hg19		0.02	-0.298274	GCCxAAG	COVERED																																																																																			NOVEL					0			6	3.309687	KEEP	12	0	0	11	338	CC	0.99257	0.775257	0			3	47	96	0	0	6.627154	31	49	1079	86		0.088235	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56672389	56672389	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56672389C>T			NA	NA				RP11-760D2.5 (66566 upstream) : RP13-580B18.1 (270688 downstream)						NA		NA									NA						ccagcctgggcgacagagcgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56672389C>T		NA		hg19		0.02	-0.105264	GGGxGAC	UNCOVERED																																																																																			NOVEL					0			5	4.212166	KEEP	0	0	0	14	426	CC	0.995343	0.139181	0			3	42	90	1	0	7.632209	8	60	269	41		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56914252	56914252	__UNKNOWN__	IGR	SNP	G	G	A	rs2178680		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56914252G>A			NA	NA				RP11-760D2.5 (308429 upstream) : RP13-580B18.1 (28825 downstream)						NA		NA									NA						ggccagatacggtggctcaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56914252G>A		NA		hg19		0.02	-0.070139	TACxGTG	UNCOVERED																																																																																			NOVEL					0			5	2.406362	KEEP	2	0	0	8	229	GG	0.99257	0.053735	0			4	27	126	0	0	12.432334	3	60	85	23		0.571429	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	56964348	56964348	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:56964348C>A			NA	NA				RP13-580B18.1 (14509 upstream) : MIR4283-1 (59143 downstream)						NA		NA									NA						agttctggaccagcctgggca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.56964348C>A		NA		hg19		0.02	-0.087717	GACxAGC	UNCOVERED																																																																																			NOVEL					0			3	2.707654	KEEP	0	0	0	9	267	CC	0.99254	0.098977	0			3	40	88	0	0	7.743189	6	60	200	28		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	57624667	57624667	__UNKNOWN__	IGR	SNP	C	C	T	rs201814359		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:57624667C>T			NA	NA				ZNF716 (91415 upstream) : RP11-368M16.3 (65119 downstream)						NA		NA									NA						gagttcaagactagcctgacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.57624667C>T		NA		hg19		0.02	-0.18422	AGAxTAG	COVERED																																																																																			NOVEL					0			14	4.814626	KEEP	0	0	0	16	501	CC	0.997832	0.422559	0			3	49	97	0	0	7.691511	14	55	484	51		0.176471	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	57637531	57637531	__UNKNOWN__	IGR	SNP	C	C	A	rs374716782|rs143143970|rs201454748		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:57637531C>A			NA	NA				ZNF716 (104279 upstream) : RP11-368M16.3 (52255 downstream)						NA		NA									NA						aaacaaaaaacaaaaaaaaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.57637531C>A		NA		hg19		0.02	-0.122074	AAAxAAA	COVERED																																																																																			NOVEL					0			4	2.40662	KEEP	0	0	0	8	238	CC	0.99257	0.194853	0			3	21	86	2	0	7.112773	9	60	278	31		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	57735544	57735544	__UNKNOWN__	IGR	SNP	T	T	A	rs141423222	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:57735544T>A			NA	NA				RP11-368M16.3 (30649 upstream) : None (None downstream)						NA		NA									NA						atcccagcactttgggaggcc	0.478		NA											t|||	200	0.0399361	0.0023	0.085	5008	,	,	NA	18011	0.0	NA	0.0746	False	NA	,,,	NA	NA	NA	2504	0.0644	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.57735544T>A		NA		hg19		0.02	-0.324526	CACxTTG	COVERED																																																																																			NOVEL					0			15	2.638222	KEEP	4	1	29	19	526	TT	0.99986	0.835599	0			5	60	153	0	0	13.213376	12	60	361	86		0.294118	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61845556	61845556	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61845556A>G			NA	NA				None (None upstream) : RNU6-417P (626284 downstream)						NA		NA									NA						gaaataaggaaagaaagaaga	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61845556A>G		NA		hg19		0.02	-0.184206	GGAxAGA	UNCOVERED																																																																																			NOVEL					0			13	3.609143	KEEP	9	0	0	12	331	AA	0	0	0			7	59	242	2	1	22.538323	10	60	305	58		0.411765	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61968868	61968868	__UNKNOWN__	IGR	SNP	A	A	C	rs2167864		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61968868A>C			NA	NA				None (None upstream) : RNU6-417P (502972 downstream)						NA		NA									NA						tcattctcagaaaattctttg	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61968868A>C		NA		hg19		0.02	7.575615	CAGxAAA	COVERED																																																																																			NOVEL					0			55	19.668682	KEEP	66	7	215	141	3835	AA	1	1	0			19	60	631	2	0	44.284545	196	60	5903	575		0.088372	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61968977	61968977	__UNKNOWN__	IGR	SNP	A	A	T	rs74187916|rs66812331|rs36170818	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61968977A>T			NA	NA				None (None upstream) : RNU6-417P (502863 downstream)						NA		NA									NA						tatggaccgcattgaggcctt	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61968977A>T		NA		hg19		0.02	12.643589	CGCxTTG	COVERED																																																																																			NOVEL					0			58	16.55219	KEEP	5	13	356	181	5012	AA	1	1	0			15	60	445	0	0	24.553863	350	60	10518	919		0.041096	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969232	61969232	__UNKNOWN__	IGR	SNP	C	C	T	rs4365974		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61969232C>T			NA	NA				None (None upstream) : RNU6-417P (502608 downstream)						NA		NA									NA						tgtgtgccttcaactcacaga	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969232C>T		NA		hg19		0.02	8.814035	CTTxAAC	COVERED																																																																																			NOVEL					0			64	35.197018	KEEP	21	3	76	144	4349	CC	1	1	0			10	60	297	2	0	16.107021	250	60	8336	684		0.038462	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61969291	61969291	__UNKNOWN__	IGR	SNP	T	T	C	rs9654817|rs74213713		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61969291T>C			NA	NA				None (None upstream) : RNU6-417P (502549 downstream)						NA		NA									NA						ctgcttgttatgtctgcaagt	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61969291T>C		NA		hg19		0.02	11.918046	TTAxGTC	COVERED																																																																																			NOVEL					0			55	7.704486	KEEP	13	12	347	148	4138	TT	1	1	0			22	60	741	1	0	50.725625	270	60	8047	747		0.075342	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970291	61970291	__UNKNOWN__	IGR	SNP	T	T	C	rs4717990		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61970291T>C			NA	NA				None (None upstream) : RNU6-417P (501549 downstream)						NA		NA									NA						catagaggagtttggaaacac	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970291T>C		NA		hg19		0.02	1.781245	GAGxTTG	COVERED																																																																																			NOVEL					0			26	15.45796	KEEP	61	1	33	63	1624	TT	1	0.999881	0			6	60	208	0	0	14.660472	67	60	1897	258		0.082192	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970349	61970349	__UNKNOWN__	IGR	SNP	T	T	C	rs4320428		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61970349T>C			NA	NA				None (None upstream) : RNU6-417P (501491 downstream)						NA		NA									NA						tttgaggccttcgttggaaac	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970349T>C		NA		hg19		0.02	7.570284	CCTxCGT	COVERED																																																																																			NOVEL					0			60	13.879977	KEEP	50	8	232	128	3431	TT	1	1	0			17	60	563	0	0	38.645856	197	60	5696	582		0.079439	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970423	61970423	__UNKNOWN__	IGR	SNP	C	C	G	rs4302715		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61970423C>G			NA	NA				None (None upstream) : RNU6-417P (501417 downstream)						NA		NA									NA						tgtgtgcattcaactcacaga	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970423C>G		NA		hg19		0.02	9.931636	ATTxAAC	COVERED																																																																																			NOVEL					0			55	21.564764	KEEP	51	6	189	138	4184	CC	1	1	0			11	60	367	0	0	22.802331	218	60	7373	636		0.048035	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	61970454	61970454	__UNKNOWN__	IGR	SNP	G	G	C	rs4316045		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:61970454G>C			NA	NA				None (None upstream) : RNU6-417P (501386 downstream)						NA		NA									NA						cctttagacagagcagatttg	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.61970454G>C		NA		hg19		0.02	5.961586	ACAxAGC	COVERED																																																																																			NOVEL					0			29	21.43095	KEEP	71	2	62	93	2846	GG	1	1	0			9	60	313	2	0	20.815304	141	60	4680	411		0.06	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	62983625	62983625	__UNKNOWN__	IGR	SNP	C	C	T	rs12540616	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:62983625C>T			NA	NA				RP11-340I6.3 (101201 upstream) : RN7SL855P (88197 downstream)						NA		NA									NA						gtctcaaactcctgacctcag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.62983625C>T		NA		hg19		0.02	-0.131577	ACTxCTG	COVERED																																																																																			NOVEL					0			3	2.406136	KEEP	1	0	0	8	223	CC	0.99257	0.22747	0			3	60	86	0	0	6.981913	10	60	331	30		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63036668	63036668	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:63036668C>T			NA	NA				RP11-340I6.3 (154244 upstream) : RN7SL855P (35154 downstream)						NA		NA									NA						ggattacaggcgtgagccact	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63036668C>T		NA		hg19		0.02	-0.078744	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			5	2.406612	KEEP	6	0	0	8	232	CC	0	0	0			3	49	87	0	0	7.647959	6	55	176	26		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63270969	63270969	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:63270969G>C			NA	NA				MIR4283-2 (189422 upstream) : RP11-340I6.7 (77608 downstream)						NA		NA									NA						gccaggagttggagaccagcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63270969G>C		NA		hg19		0.02	-0.035092	GTTxGAG	UNCOVERED																																																																																			NOVEL					0			7	2.708076	KEEP	9	0	0	9	275	GG	0	0	0			2	52	67	0	0	6.824686	1	14	36	27		0.666667	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63305467	63305467	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:63305467C>G			NA	NA				MIR4283-2 (223920 upstream) : RP11-340I6.7 (43110 downstream)						NA		NA									NA						attctcctgcctcagcctcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63305467C>G		NA		hg19		0.02	-0.096491	TGCxTCA	UNCOVERED																																																																																			NOVEL					0			3	3.609719	KEEP	0	0	0	12	359	CC	0.993634	0.138942	0			3	60	92	0	0	7.97842	7	57	234	32		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63393941	63393941	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:63393941T>C			NA	NA				AC092634.2 (6662 upstream) : LINC01005 (94288 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63393941T>C		NA		hg19		0.02	-0.184181	TCAxGCC	COVERED																																																																																			NOVEL					0			1	3.29913	KEEP	0	0	0	11	291	TT	0.993072	0.420544	0			3	60	99	0	0	7.733437	16	60	468	49		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	63680358	63680358	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:63680358C>A			NA	NA				GUSBP6 (69259 upstream) : ZNF679 (8493 downstream)						NA		NA									NA						AGCGTATCCTCAGCCCTCATT	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													20	21	21			NA	NA	7		NA											NA				63680358		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.63680358C>A		NA		hg19		0.02	1.401119	CCTxAGC	COVERED																																																																																			NOVEL					0			9	6.619656	KEEP	0	0	0	22	673	CC	0.999879	0.979408	0			4	60	121	0	0	7.756861	52	60	1743	120		0.071429	0.979526
ZNF680	340252	__UNKNOWN__	__UNKNOWN__	7	64022048	64022048	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:64022048G>C	ENST00000447137.2	-	1	117				ZNF680_ENST00000476563.1_Intron|ZNF680_ENST00000309683.6_Intron	NM_001130022.1	NP_001123494.1	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				cgcggtggctgacgcctgtaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041	340252		Zinc fingers, C2H2-type, -	26897	protein-coding gene	gene with protein product	hypothetical protein FLJ90430	NA			NA	12477932	Standard	NM_178558	NM_178558	NA	Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000447137.2:c.30+1254C>G	chr7.hg19:g.64022048G>C		NA	B3KVJ4|Q6ZNF3|Q8NC79	hg19	CCDS47594.1	0.02	-0.166682	GCTxACG	COVERED																																																																																			NOVEL	ZNF680-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344571.2	4	2.707877	KEEP	1	0	0	9	274	GG	0.99254	0.351306	0		-	3	44	99	0	0	7.978555	13	60	451	45	ENST00000447137.2	0.1875	0.353947
ZNF273	10793	__UNKNOWN__	__UNKNOWN__	7	64389279	64389279	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:64389279C>T	ENST00000476120.1	+	4	1644	c.1573C>T	c.(1573-1575)Cgg>Tgg	p.R525W	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.R460W	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	525		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Lung NSC(55;0.0295)|all_lung(88;0.0691)				AGCTTTTAACCGGTCCTCAAA	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)							NA				0													60	66	64			NA	NA	7		NA											NA				64389279		2203	4300	6503	SO:0001583	missense			X78932	CCDS5528.2	7q11.21	2013-01-08				ENSG00000198039	10793		Zinc fingers, C2H2-type, -	13067	protein-coding gene	gene with protein product		604756			NA	7865130	Standard		NR_003099	NA	Approved	HZF9	uc003tto.3	Q14593		ENST00000476120.1:c.1573C>T	chr7.hg19:g.64389279C>T	ENSP00000418719:p.Arg525Trp	NA	B3KQZ5|Q6P3V4	hg19	CCDS5528.2	0.02	1.344671	AACxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	.	8.866	0.948193	0.18356	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.36520	1.25;1.25	1.16	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25082	0.0609	L	0.48642	1.525	0.09310	N	1	B	0.27316	0.175	B	0.20384	0.029	T	0.19745	-1.0296	9	0.26408	T	0.33	.	4.1332	0.10159	0.401:0.599:0.0:0.0	.	525	Q14593	ZN273_HUMAN	W	525;460	ENSP00000418719:R525W;ENSP00000324518:R460W	ENSP00000324518:R460W	R	+	1	2	ZNF273	64026714	0.000000	0.05858	0.771000	0.31576	0.771000	0.43674	-0.164000	0.09983	0.202000	0.20498	0.205000	0.17691	CGG	NOVEL	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313502.1	10	9.326197	KEEP	1	0	0	31	910	CC	0.999997	0.999619	0		+	4	60	127	0	0	7.74045	75	60	2393	162	ENST00000476120.1	0.050633	0.999622
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	64476252	64476252	__UNKNOWN__	IGR	SNP	C	C	T	rs79152256		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:64476252C>T			NA	NA				ERV3-1 (9131 upstream) : RNU6-1229P (7329 downstream)						NA		NA									NA						ccagcctgggcaacagagcaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.64476252C>T		NA		hg19		0.02	-0.21054	GGGxAAC	COVERED																																																																																			NOVEL					0			7	3.009105	KEEP	3	0	0	10	311	CC	0.992708	0.518353	0			3	39	88	0	0	6.561667	17	60	600	53		0.15	0.522161
CCT6P3	643180	__UNKNOWN__	__UNKNOWN__	7	64525582	64525582	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:64525582A>G	ENST00000426828.1	+	0	341					NR_033416.1				chaperonin containing TCP1, subunit 6 (zeta) pseudogene 3	NA		NA									NA						gctggagtgcaatggcatctc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7q11.21	2010-06-29			ENSG00000234585	ENSG00000234585	643180			35137	pseudogene	pseudogene		NA			NA		Standard		NR_033416	NA	Approved		uc010kzt.1		OTTHUMG00000156630	ENST00000426828.1:	chr7.hg19:g.64525582A>G		NA		hg19		0.02	-0.263087	TGCxATG	COVERED																																																																																			NOVEL	CCT6P3-004	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000344862.1	8	4.508705	KEEP	1	0	0	15	388	AA	0.995343	0.690438	0		+	5	60	159	0	0	12.759543	21	60	597	52	ENST00000426828.1	0.192308	0.693668
CCT6P1	643253	__UNKNOWN__	__UNKNOWN__	7	65228263	65228263	__UNKNOWN__	RNA	SNP	T	T	C	rs368094433		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:65228263T>C	ENST00000442266.1	+	0	1241									chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1	NA		NA									NA						TTATCCCCCTTTCAGCACTGG	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409	643253			33094	pseudogene	pseudogene		NA	chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1	CCT6AP1	NA		Standard	NR_003110	NR_003110	NA	Approved		uc003tug.3		OTTHUMG00000156733	ENST00000442266.1:	chr7.hg19:g.65228263T>C		NA		hg19		0.02	1.730859	CCTxTCA	COVERED																																																																																			NOVEL	CCT6P1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000345507.1	0	2.405844	KEEP	1	0	0	8	221	TT	0.99257	0.991275	0		+	14	44	435	0	0	34.597164	60	60	1748	122	ENST00000442266.1	0.189189	0.998696
CCT6P1	643253	__UNKNOWN__	__UNKNOWN__	7	65228273	65228273	__UNKNOWN__	RNA	SNP	G	G	A	rs372024277		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:65228273G>A	ENST00000442266.1	+	0	1247									chaperonin containing TCP1, subunit 6 (zeta) pseudogene 1	NA		NA									NA						TTCAGCACTGGTTGCCACCAA	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC052238, BC073761		7q11.21	2010-06-29	2008-09-22	2008-09-22	ENSG00000228409	ENSG00000228409	643253			33094	pseudogene	pseudogene		NA	chaperonin containing TCP1, subunit 6A (zeta 1) pseudogene 1	CCT6AP1	NA		Standard	NR_003110	NR_003110	NA	Approved		uc003tug.3		OTTHUMG00000156733	ENST00000442266.1:	chr7.hg19:g.65228273G>A		NA		hg19		0.02	1.289379	CTGxTTG	COVERED																																																																																			NOVEL	CCT6P1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000345507.1	0	2.707057	KEEP	0	0	0	9	266	GG	0.99254	0.991764	0		+	15	44	444	0	0	34.886325	64	60	2144	127	ENST00000442266.1	0.189873	0.999218
VKORC1L1	154807	__UNKNOWN__	__UNKNOWN__	7	65424073	65424073	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:65424073T>C	ENST00000360768.3	+	0	5422					NM_001284342.1|NM_173517.4	NP_001271271.1|NP_775788.2	Q8N0U8	VKORL_HUMAN	vitamin K epoxide reductase complex, subunit 1-like 1	NA		NA			cellular response to oxidative stress (GO:0034599)|peptidyl-glutamic acid carboxylation (GO:0017187)|vitamin K metabolic process (GO:0042373)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	quinone binding (GO:0048038)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			large_intestine(1)|prostate(1)	2		Lung NSC(55;0.197)			Menadione(DB00170)	ggtggatcacttgaggtcagg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5529.1, CCDS64663.1	7q11.21	2013-10-07			ENSG00000196715	ENSG00000196715	154807			21492	protein-coding gene	gene with protein product		608838			NA	23928358	Standard	NM_173517	NM_001284342	NA	Approved		uc003tul.3	Q8N0U8	OTTHUMG00000129449	ENST00000360768.3:c.*4786T>C	chr7.hg19:g.65424073T>C		NA	B4E222|E7ETM5|Q6AHW9|Q6TEK6	hg19	CCDS5529.1	0.02	1.751639	CACxTGA	COVERED																																																																																			NOVEL	VKORC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251612.3	28	6.005003	KEEP	1	3	91	52	1395	TT	1	0.999559	0		+	4	60	132	2	0	8.285788	73	60	2119	217	ENST00000360768.3	0.051948	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	65523864	65523864	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:65523864A>G			NA	NA				AC068533.1 (2559 upstream) : ASL (16920 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.65523864A>G		NA		hg19		0.02	-0.140332	CCAxCAC	COVERED																																																																																			NOVEL					0			7	3.006244	KEEP	3	0	0	10	268	AA	0.99257	0.259026	0			3	51	98	0	0	7.972503	12	60	366	39		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	65524158	65524158	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:65524158G>A			NA	NA				AC068533.1 (2853 upstream) : ASL (16626 downstream)						NA		NA									NA						ttatgcctgtggtcccagcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.65524158G>A		NA		hg19		0.02	-0.210472	TGTxGTC	COVERED																																																																																			NOVEL					0			16	2.841229	KEEP	0	1	27	19	572	GG	0.999863	0.522089	0			3	60	87	0	0	6.327801	19	60	632	60		0.136364	0.522161
TPST1	8460	__UNKNOWN__	__UNKNOWN__	7	65785476	65785476	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:65785476T>C	ENST00000304842.5	+	4	1469				TPST1_ENST00000480281.1_Intron	NM_003596.3	NP_003587.1	O60507	TPST1_HUMAN	tyrosylprotein sulfotransferase 1	NA		NA			inflammatory response (GO:0006954)|peptidyl-tyrosine sulfation (GO:0006478)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			NS(1)|biliary_tract(1)|breast(1)|kidney(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11						ccttgtgatctgcccgcctcg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF038009	CCDS5533.1	7q11.21	2012-12-13			ENSG00000169902	ENSG00000169902	8460	2.8.2.20	Sulfotransferases, membrane-bound	12020	protein-coding gene	gene with protein product	transport and golgi organization 13 homolog A (Drosophila)	603125			NA	9501187	Standard	NM_003596	NM_003596	NA	Approved	TANGO13A	uc003tuw.3	O60507	OTTHUMG00000023871	ENST00000304842.5:c.1045-32016T>C	chr7.hg19:g.65785476T>C		NA	A4D2M0|Q6FGM7	hg19	CCDS5533.1	0.02	-0.24556	ATCxGCC	UNCOVERED																																																																																			NOVEL	TPST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251705.2	10	2.406337	KEEP	9	0	0	8	224	TT	0	0	0		+	3	60	92	0	0	6.493945	25	60	737	62	ENST00000304842.5	0.107143	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	66070636	66070636	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:66070636G>A			NA	NA				GS1-124K5.11 (63100 upstream) : KCTD7 (23231 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.66070636G>A		NA		hg19		0.02	-0.175413	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.636483	KEEP	0	1	26	18	481	GG	0.99986	0.387352	0			3	60	88	0	0	6.879318	13	60	395	55		0.1875	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	66337868	66337868	__UNKNOWN__	IGR	SNP	C	C	T	rs531553322	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:66337868C>T			NA	NA				GTF2IRD1P1 (28055 upstream) : RNU6-1254P (18306 downstream)						NA		NA									NA						gtgatccgcccgcctcagcct	0.512		NA											c|||	7	0.00139776	0.0015	0.0	5008	,	,	NA	14965	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.66337868C>T		NA		hg19		0.02	-0.140341	GCCxGCC	COVERED																																																																																			NOVEL					0			8	2.407174	KEEP	0	0	0	8	245	CC	0.99257	0.259026	0			3	60	85	0	0	6.773038	11	60	362	35		0.214286	0.260965
TMEM248	55069	__UNKNOWN__	__UNKNOWN__	7	66410770	66410770	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:66410770A>T	ENST00000341567.4	+	3	700					NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	NA		NA				integral component of membrane (GO:0016021)					NA						aaaccccatcactactaaaat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609	55069			25476	protein-coding gene	gene with protein product		NA	chromosome 7 open reading frame 42	C7orf42	NA	12477932	Standard	NM_017994	XM_005250482	NA	Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.445+522A>T	chr7.hg19:g.66410770A>T		NA	Q53H07|Q96FR2	hg19	CCDS5536.1	0.02	-0.149087	ATCxCTA	COVERED																																																																																			NOVEL	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251745.2	8	3.308881	KEEP	1	0	0	11	311	AA	0.993072	0.289978	0		+	3	60	86	0	0	6.679486	13	60	382	44	ENST00000341567.4	0.1875	0.292001
STAG3L4	64940	__UNKNOWN__	__UNKNOWN__	7	66780727	66780727	__UNKNOWN__	RNA	SNP	A	A	G	rs7783942	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:66780727A>G	ENST00000416602.2	+	0	719					NR_040586.1		Q8TBR4	ST3L4_HUMAN	stromal antigen 3-like 4 (pseudogene)	NA		NA								endometrium(2)|lung(5)	7		Lung NSC(55;0.0839)|all_lung(88;0.181)				ggatggtctcaatctgacctt	0.537		NA											a|||	915	0.182708	0.2292	0.1599	5008	,	,	NA	16573	0.1062	NA	0.1879	False	NA	,,,	NA	NA	NA	2504	0.2096	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7q11.21	2013-06-26	2013-06-26		ENSG00000106610	ENSG00000106610	64940			33887	pseudogene	pseudogene		NA	stromal antigen 3-like 4		NA		Standard	NM_022906	NR_040585	NA	Approved	FLJ13195, STAG3L4P	uc010laj.3	Q8TBR4	OTTHUMG00000156920	ENST00000416602.2:	chr7.hg19:g.66780727A>G		NA	Q9H8W0	hg19		0.02	-0.131554	CTCxATC	UNCOVERED																																																																																			NOVEL	STAG3L4-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000346611.1	6	2.40485	KEEP	1	0	0	8	217	AA	0	0	0		+	5	60	163	0	0	14.539809	10	60	292	28	ENST00000416602.2	0.333333	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	66818457	66818457	__UNKNOWN__	IGR	SNP	T	T	C	rs10273547	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:66818457T>C			NA	NA				RP11-166O4.5 (13446 upstream) : AC006480.1 (3209 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.527		NA											C|||	3256	0.65016	0.7345	0.6354	5008	,	,	NA	18244	0.6587	NA	0.6113	False	NA	,,,	NA	NA	NA	2504	0.5777	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.66818457T>C		NA		hg19		0.02	-0.149102	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.405992	KEEP	4	0	0	8	219	TT	0	0	0			4	60	133	0	0	11.301707	12	60	354	48		0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	66906659	66906659	__UNKNOWN__	IGR	SNP	A	A	G	rs7788771	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:66906659A>G			NA	NA				AC006480.1 (84893 upstream) : RP4-736H5.3 (249385 downstream)						NA		NA									NA						tgccatgttgaccaggctggt	0.488		NA											G|||	3321	0.663139	0.652	0.6513	5008	,	,	NA	17815	0.7976	NA	0.4851	False	NA	,,,	NA	NA	NA	2504	0.7311	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.66906659A>G		NA		hg19		0.02	-0.061395	TTGxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.404925	KEEP	0	0	0	8	207	AA	0.99257	0.043461	0			3	60	95	0	0	8.855294	4	60	118	21		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	67280748	67280748	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:67280748A>C			NA	NA				RP4-736H5.3 (118732 upstream) : RP11-358M3.1 (204491 downstream)						NA		NA									NA						gggctgggcaaggtggctcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.67280748A>C		NA		hg19		0.02	-0.122687	GCAxGGT	COVERED																																																																																			NOVEL					0			7	2.406475	KEEP	0	0	0	8	226	AA	0.99257	0.194853	0			3	60	101	0	0	8.881093	7	60	203	32		0.3	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	68314447	68314447	__UNKNOWN__	IGR	SNP	T	T	C	rs374186786		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:68314447T>C			NA	NA				RNA5SP231 (125412 upstream) : RP11-123O1.1 (190691 downstream)						NA		NA									NA						agcaagactctgtctcaaaaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.68314447T>C		NA		hg19		0.02	-0.087721	CTCxGTC	UNCOVERED																																																																																			NOVEL					0			9	2.406816	KEEP	0	0	0	8	234	TT	0.99257	0.09898	0			4	47	140	0	0	12.985828	6	60	186	24		0.4	0.099721
RP11-3P22.2	0	__UNKNOWN__	__UNKNOWN__	7	68852829	68852829	__UNKNOWN__	lincRNA	SNP	A	A	G	rs386714402|rs11769100	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:68852829A>G	ENST00000435148.1	-	0	156										NA		NA									NA						acggagtctcactctgttgcc	0.433		NA											G|||	3801	0.758986	0.6702	0.8473	5008	,	,	NA	19013	0.7054	NA	0.8449	False	NA	,,,	NA	NA	NA	2504	0.7832	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000435148.1:	chr7.hg19:g.68852829A>G		NA		hg19		0.02	-0.078938	CTCxCTC	UNCOVERED																																																																																			NOVEL	RP11-3P22.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000344765.1	5	2.405669	KEEP	1	0	0	8	216	AA	0	0	0		-	7	60	221	0	0	24.128535	1	60	32	25	ENST00000435148.1	0.875	0.077336
AUTS2	26053	__UNKNOWN__	__UNKNOWN__	7	69653795	69653795	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:69653795T>C	ENST00000342771.4	+	4	981				AUTS2_ENST00000406775.2_Intron|AUTS2_ENST00000403018.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	NA		NA								breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		gagacggagttgcgctctgtc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321	26053			14262	protein-coding gene	gene with protein product		607270			NA	12160723	Standard		XM_005250257	NA	Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.660+54238T>C	chr7.hg19:g.69653795T>C		NA	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	hg19	CCDS5539.1	0.02	-0.11401	AGTxGCG	UNCOVERED																																																																																			NOVEL	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251971.2	8	3.608312	KEEP	0	0	0	12	327	TT	0.993634	0.161432	0		+	3	60	101	0	0	8.732828	8	60	228	38	ENST00000342771.4	0.272727	0.162467
AUTS2	26053	__UNKNOWN__	__UNKNOWN__	7	69653796	69653796	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:69653796G>T	ENST00000342771.4	+	4	981				AUTS2_ENST00000406775.2_Intron|AUTS2_ENST00000403018.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	NA		NA								breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		agacggagttgcgctctgtcg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321	26053			14262	protein-coding gene	gene with protein product		607270			NA	12160723	Standard		XM_005250257	NA	Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.660+54239G>T	chr7.hg19:g.69653796G>T		NA	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	hg19	CCDS5539.1	0.02	-0.114039	GTTxCGC	UNCOVERED																																																																																			NOVEL	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251971.2	9	3.610977	KEEP	0	0	0	12	377	GG	0.993634	0.161432	0		+	3	60	92	0	0	7.832232	8	60	273	39	ENST00000342771.4	0.272727	0.162467
AUTS2	26053	__UNKNOWN__	__UNKNOWN__	7	69676721	69676721	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:69676721T>C	ENST00000342771.4	+	4	981				AUTS2_ENST00000406775.2_Intron|AUTS2_ENST00000403018.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	NA		NA								breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		gcctgtaatctcagcactttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321	26053			14262	protein-coding gene	gene with protein product		607270			NA	12160723	Standard		XM_005250257	NA	Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.660+77164T>C	chr7.hg19:g.69676721T>C		NA	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	hg19	CCDS5539.1	0.02	-0.236816	ATCxCAG	UNCOVERED																																																																																			NOVEL	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251971.2	11	2.706849	KEEP	5	0	0	9	249	TT	0	0	0		+	3	60	93	0	0	6.807434	21	60	646	55	ENST00000342771.4	0.125	0.612407
AUTS2	26053	__UNKNOWN__	__UNKNOWN__	7	70019344	70019344	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:70019344T>C	ENST00000342771.4	+	5	1011				AUTS2_ENST00000406775.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	NA		NA								breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		cgtgagccactgtgcccggcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321	26053			14262	protein-coding gene	gene with protein product		607270			NA	12160723	Standard		XM_005250257	NA	Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.690+118577T>C	chr7.hg19:g.70019344T>C		NA	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	hg19	CCDS5539.1	0.02	-0.105258	CACxGTG	UNCOVERED																																																																																			NOVEL	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251971.2	5	3.007408	KEEP	2	0	0	10	272	TT	0.99254	0.138789	0		+	3	40	103	0	0	8.801136	9	60	275	31	ENST00000342771.4	0.25	0.139832
WBSCR17	64409	__UNKNOWN__	__UNKNOWN__	7	71143520	71143520	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:71143520C>T	ENST00000333538.5	+	9	2134				WBSCR17_ENST00000498380.2_Intron	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	NA		NA			protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				cggtggctcacgcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274	64409		Glycosyltransferase family 2 domain containing	16347	protein-coding gene	gene with protein product	polypeptide N-acetylgalactosaminyltransferase-like 3, polypeptide GalNAc transferase 3	615137			NA	12073013, 15744064, 22787146	Standard	NM_022479	NM_022479	NA	Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1500+1229C>T	chr7.hg19:g.71143520C>T		NA	Q8NFV9|Q9NTA8	hg19	CCDS5540.1	0.02	-0.166651	TCAxGCC	COVERED																																																																																			NOVEL	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252006.1	13	4.201565	KEEP	0	0	0	14	384	CC	0.995343	0.352299	0		+	3	60	84	0	0	6.572821	12	60	392	49	ENST00000333538.5	0.2	0.353947
CALN1	83698	__UNKNOWN__	__UNKNOWN__	7	71266727	71266727	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:71266727T>C	ENST00000329008.5	-	5	831				CALN1_ENST00000405452.2_Intron|CALN1_ENST00000412588.1_Intron|CALN1_ENST00000395276.2_Intron|CALN1_ENST00000395275.2_Intron|CALN1_ENST00000431984.1_Intron	NM_001017440.2	NP_001017440.1	Q9BXU9	CABP8_HUMAN	calneuron 1	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(6)|lung(19)|skin(2)	32		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				tttgggaggctgaggtgggtg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF282250	CCDS5541.1, CCDS47603.1	7q11	2013-01-10			ENSG00000183166	ENSG00000183166	83698		EF-hand domain containing	13248	protein-coding gene	gene with protein product	calcium-binding protein CABP8	607176			NA	11286509	Standard	NM_031468	NM_031468	NA	Approved		uc003twb.4	Q9BXU9	OTTHUMG00000023787	ENST00000329008.5:c.532+8593A>G	chr7.hg19:g.71266727T>C		NA	J3KQA7	hg19	CCDS5541.1	0.02	-0.105249	GGCxGAG	UNCOVERED																																																																																			NOVEL	CALN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320044.2	11	3.60921	KEEP	14	0	0	12	332	TT	0	0	0		-	3	60	93	0	0	7.932364	8	60	242	46	ENST00000329008.5	0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	71977004	71977004	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:71977004T>C			NA	NA				CALN1 (64868 upstream) : TYW1B (46724 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.71977004T>C		NA		hg19		0.02	-0.201728	TCAxGCC	COVERED																																																																																			NOVEL					0			5	2.706537	KEEP	0	0	0	9	243	TT	0.99254	0.486885	0			3	60	100	0	0	7.692194	18	60	533	47		0.142857	0.490544
TYW1B	441250	__UNKNOWN__	__UNKNOWN__	7	72093065	72093065	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:72093065C>T	ENST00000435769.2	-	0	1741				TYW1B_ENST00000343721.5_RNA|TYW1B_ENST00000438125.1_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)	NA		NA			tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)				NA						tcgcttgaggccaggagtttg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149	441250			33908	protein-coding gene	gene with protein product	radical S-adenosyl methionine and flavodoxin domains 1, non-protein coding RNA 69, long intergenic non-protein coding RNA 69	NA	tRNA-yW synthesizing protein 1 homolog B (non-protein coding)		NA		Standard	NM_001145440	NM_001145440	NA	Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067	ENST00000435769.2:	chr7.hg19:g.72093065C>T		NA	A6NG09|B4DFY2|Q3KQX2	hg19		0.02	-0.219311	AGGxCAG	COVERED																																																																																			NOVEL	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	NA	polymorphic_pseudogene	OTTHUMT00000347346.2	16	3.609958	KEEP	7	0	0	12	368	CC	0.993072	0.549057	0		-	3	49	89	0	0	6.465474	20	60	694	61	ENST00000435769.2	0.130435	0.552887
TYW1B	441250	__UNKNOWN__	__UNKNOWN__	7	72178039	72178039	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:72178039T>C	ENST00000435769.2	-	0	1494				TYW1B_ENST00000343721.5_RNA|TYW1B_ENST00000438125.1_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)	NA		NA			tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)				NA						ggaggatcacttgaggtcagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149	441250			33908	protein-coding gene	gene with protein product	radical S-adenosyl methionine and flavodoxin domains 1, non-protein coding RNA 69, long intergenic non-protein coding RNA 69	NA	tRNA-yW synthesizing protein 1 homolog B (non-protein coding)		NA		Standard	NM_001145440	NM_001145440	NA	Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067	ENST00000435769.2:	chr7.hg19:g.72178039T>C		NA	A6NG09|B4DFY2|Q3KQX2	hg19		0.02	-0.061206	CACxTGA	UNCOVERED																																																																																			NOVEL	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	NA	polymorphic_pseudogene	OTTHUMT00000347346.2	5	3.608714	KEEP	0	0	0	12	328	TT	0.993634	0.043508	0		-	3	59	107	0	0	10.325427	3	60	89	27	ENST00000435769.2	0.5	0.043787
TYW1B	441250	__UNKNOWN__	__UNKNOWN__	7	72257319	72257319	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:72257319A>G	ENST00000435769.2	-	0	969				TYW1B_ENST00000438904.2_RNA|TYW1B_ENST00000438125.1_RNA			Q6NUM6	TYW1B_HUMAN	tRNA-yW synthesizing protein 1 homolog B (S. cerevisiae)	NA		NA			tRNA processing (GO:0008033)		4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)				NA						cagcctgggcaacagagcaag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC068520	CCDS69309.1	7q11.23	2011-08-11	2009-07-28		ENSG00000254184	ENSG00000277149	441250			33908	protein-coding gene	gene with protein product	radical S-adenosyl methionine and flavodoxin domains 1, non-protein coding RNA 69, long intergenic non-protein coding RNA 69	NA	tRNA-yW synthesizing protein 1 homolog B (non-protein coding)		NA		Standard	NM_001145440	NM_001145440	NA	Approved	RSAFD2, MGC87315, NCRNA00069, LINC00069	uc011kej.2	Q6NUM6	OTTHUMG00000157067	ENST00000435769.2:	chr7.hg19:g.72257319A>G		NA	A6NG09|B4DFY2|Q3KQX2	hg19		0.02	-0.114	GGCxACA	UNCOVERED																																																																																			NOVEL	TYW1B-001	KNOWN	basic	polymorphic_pseudogene	NA	polymorphic_pseudogene	OTTHUMT00000347346.2	7	2.707018	KEEP	0	0	0	9	252	AA	0.99254	0.161255	0		-	3	60	91	0	0	7.482371	10	60	289	30	ENST00000435769.2	0.230769	0.162467
GTF2IRD2P1	401375	__UNKNOWN__	__UNKNOWN__	7	72656918	72656918	__UNKNOWN__	RNA	SNP	C	C	T	rs200447577		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:72656918C>T	ENST00000425256.1	-	0	2993									GTF2I repeat domain containing 2 pseudogene 1	NA		NA									NA						gaactcatttcgtcagctggg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AY312852		7q11.23	2010-03-19	2010-02-09	2010-02-09	ENSG00000214544	ENSG00000214544	401375			33127	pseudogene	pseudogene		NA	GTF2I repeat domain containing 2 pseudogene	GTF2IRD2P	NA	15100712	Standard	NR_002164	NG_033736	NA	Approved		uc003txs.1		OTTHUMG00000156803	ENST00000425256.1:	chr7.hg19:g.72656918C>T		NA		hg19		0.02	1.610725	TTTxGTC	COVERED																																																																																			NOVEL	GTF2IRD2P1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000345921.1	9	3.568387	KEEP	0	2	57	32	929	CC	0.999998	0.99442	0		-	6	40	192	0	0	13.689513	52	60	1605	149	ENST00000425256.1	0.103448	0.994422
BAZ1B	9031	__UNKNOWN__	__UNKNOWN__	7	72908972	72908972	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:72908972A>G	ENST00000339594.4	-	5	910				BAZ1B_ENST00000404251.1_Intron	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				ccagctactcaggaggctgag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(112;1167 1561 21085 43672 48228)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954	9031		Zinc fingers, PHD-type	961	protein-coding gene	gene with protein product	Williams-Beuren syndrome chromosome region 9, Williams-Beuren syndrome chromosome region 10, transcription factor WSTF	605681		WBSCR9, WBSCR10	NA	9858827, 9828126	Standard	NM_032408	NM_032408	NA	Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.572-1721T>C	chr7.hg19:g.72908972A>G		NA	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	hg19	CCDS5549.1	0.02	-0.131569	CTCxGGA	COVERED																																																																																			NOVEL	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252123.4	11	3.007766	KEEP	1	0	0	10	278	AA	0.99254	0.227464	0		-	3	60	101	0	0	8.272197	12	60	363	31	ENST00000339594.4	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	72995292	72995292	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:72995292T>C			NA	NA				TBL2 (2171 upstream) : MLXIPL (12231 downstream)						NA		NA									NA						tcaagaccagtctgggcaaca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.72995292T>C		NA		hg19		0.02	-0.131565	CAGxCTG	COVERED																																																																																			NOVEL					0			4	3.006994	KEEP	0	0	0	10	268	TT	0.992708	0.227502	0			3	60	100	0	0	8.272888	11	60	335	39		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	73177747	73177747	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73177747T>C			NA	NA				ABHD11 (24550 upstream) : CLDN3 (5580 downstream)						NA		NA									NA						gctgggattataggtgtgagc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.73177747T>C		NA		hg19		0.02	-0.2978	TTAxAGG	COVERED																																																																																			NOVEL					0			14	4.207458	KEEP	1	0	0	14	356	TT	0.994391	0.776679	0			5	60	136	0	0	10.06151	26	60	705	68		0.16129	0.78106
CLDN4	1364	__UNKNOWN__	__UNKNOWN__	7	73232344	73232344	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73232344G>A	ENST00000466411.1	+	2	288							O14493	CLD4_HUMAN	claudin 4	NA		NA			calcium-independent cell-cell adhesion (GO:0016338)|establishment of skin barrier (GO:0061436)|female pregnancy (GO:0007565)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basal plasma membrane (GO:0009925)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)|transmembrane signaling receptor activity (GO:0004888)			kidney(2)|lung(4)|urinary_tract(1)	7		Lung NSC(55;0.159)				gtagtgagccgagatcacacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB000712	CCDS5560.1	7q11.23	2008-07-18			ENSG00000189143	ENSG00000189143	1364		Claudins	2046	protein-coding gene	gene with protein product	Clostridium perfringens enterotoxin receptor 1, Williams-Beuren syndrome chromosomal region 8 protein	602909		CPETR, CPETR1	NA	9334247, 9892664	Standard	NM_001305	NM_001305	NA	Approved	CPE-R, WBSCR8, hCPE-R	uc003tzi.4	O14493	OTTHUMG00000023425	ENST00000466411.1:c.289-9599G>A	chr7.hg19:g.73232344G>A		NA		hg19		0.02	-0.105255	GCCxAGA	UNCOVERED																																																																																			NOVEL	CLDN4-003	KNOWN	mRNA_end_NF|basic	processed_transcript	NA	protein_coding	OTTHUMT00000348031.1	4	3.609317	KEEP	4	0	0	12	340	GG	0.992708	0.138812	0		+	3	47	90	0	0	7.632367	8	60	248	40	ENST00000466411.1	0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	73287617	73287617	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73287617A>G			NA	NA				WBSCR28 (7394 upstream) : RP11-731K22.1 (112704 downstream)						NA		NA									NA						ggccaggctgatctcaaactc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.73287617A>G		NA		hg19		0.02	-0.140333	CTGxTCT	COVERED																																																																																			NOVEL					0			5	3.007812	KEEP	2	0	0	10	277	AA	0.99254	0.259018	0			3	40	101	0	0	8.482083	10	60	292	38		0.230769	0.260965
ELN	2006	__UNKNOWN__	__UNKNOWN__	7	73479369	73479369	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73479369A>G	ENST00000252034.7	+	30	2392				ELN_ENST00000429192.1_Intron|ELN_ENST00000320399.6_Intron|ELN_ENST00000320492.7_Intron|ELN_ENST00000357036.5_Intron|ELN_ENST00000380562.4_Intron|ELN_ENST00000380584.4_Intron|ELN_ENST00000445912.1_Intron|ELN_ENST00000380575.4_Intron|ELN_ENST00000414324.1_Intron|ELN_ENST00000380553.4_Intron|ELN_ENST00000380576.5_Intron|ELN_ENST00000358929.4_Intron|ELN_ENST00000458204.1_Intron	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	NA		NA			blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				ccaggagttcaagaccagcct	0.507		NA	T	PAX5	B-ALL		Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome														NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7q11.23	2006	elastin	yes	L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540	2006			3327	protein-coding gene	gene with protein product	tropoelastin, supravalvular aortic stenosis, Williams-Beuren syndrome	130160			NA	8096434	Standard	NM_000501	NM_001278939	NA	Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1994-655A>G	chr7.hg19:g.73479369A>G		NA	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	hg19	CCDS5562.2	0.02	-0.192966	TTCxAGA	COVERED																																																																																			NOVEL	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316913.1	10	6.31598	KEEP	0	0	0	21	581	AA	0.999869	0.457697	0		+	3	60	97	1	0	7.778906	13	60	388	60	ENST00000252034.7	0.1875	0.457757
LAT2	7462	__UNKNOWN__	__UNKNOWN__	7	73627744	73627744	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73627744C>T	ENST00000460943.1	+	2	671				LAT2_ENST00000398475.1_Intron|LAT2_ENST00000344995.5_Intron|LAT2_ENST00000275635.7_Intron	NM_032464.2	NP_115853.2	Q9UHI5	LAT2_HUMAN	linker for activation of T cells family, member 2	NA		NA			amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6					L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	agccactgtgcccggccAttt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF257135	CCDS5566.2	7q11.23	2011-11-01	2005-04-26	2005-04-26	ENSG00000086730	ENSG00000086730	7462			12749	protein-coding gene	gene with protein product	linker for activation of B cells, non-T cell activation linker, linker for activation of T cells, transmembrane adaptor 2	605719	Williams-Beuren syndrome chromosome region 5	WBSCR15, WBSCR5	NA	8812460, 12514734	Standard		NM_032464	NA	Approved	WSCR5, HSPC046, LAB, NTAL	uc003uai.3	Q9GZY6	OTTHUMG00000130151	ENST00000460943.1:c.-218-1408C>T	chr7.hg19:g.73627744C>T		NA	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	hg19	CCDS5566.2	0.02	-0.219226	GTGxCCG	COVERED																																																																																			NOVEL	LAT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277062.1	18	4.512119	KEEP	4	0	0	15	451	CC	0.99649	0.550947	0		+	3	49	87	0	0	6.972855	11	60	367	64	ENST00000460943.1	0.214286	0.552887
CLIP2	7461	__UNKNOWN__	__UNKNOWN__	7	73745485	73745485	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73745485G>A	ENST00000395060.1	+	2	121				CLIP2_ENST00000223398.6_Intron|CLIP2_ENST00000361545.5_Intron			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	NA		NA				cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						gcagtgagccgagatcatgcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665	7461			2586	protein-coding gene	gene with protein product		603432	cytoplasmic linker 2, Williams-Beuren syndrome chromosome region 3	WBSCR4, CYLN2, WBSCR3	NA	8812460, 9799601	Standard	NM_003388	NM_003388	NA	Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.122-7293G>A	chr7.hg19:g.73745485G>A		NA	O14527|O43611	hg19	CCDS5569.1	0.02	-0.087704	GCCxAGA	UNCOVERED																																																																																			NOVEL	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252556.1	16	2.534606	KEEP	5	1	27	18	490	GG	0.997832	0.099505	0		+	3	60	88	0	0	8.42495	3	60	87	38	ENST00000395060.1	0.5	0.099721
GTF2IRD1	9569	__UNKNOWN__	__UNKNOWN__	7	73887886	73887886	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73887886T>C	ENST00000455841.2	+	1	207				GTF2IRD1_ENST00000265755.3_Intron|GTF2IRD1_ENST00000424337.2_Intron	NM_001199207.1	NP_001186136.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						tcccaaaatgttgggattaca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704	9569			4661	protein-coding gene	gene with protein product	binding factor for early enhancer	604318	GTF2I repeat domain-containing 1	WBSCR11	NA	9774679, 10198167	Standard	NM_016328	NM_016328	NA	Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000455841.2:c.-7+19380T>C	chr7.hg19:g.73887886T>C		NA	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	hg19	CCDS56492.1	0.02	-0.070167	ATGxTGG	UNCOVERED																																																																																			NOVEL	GTF2IRD1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000351530.1	7	2.40656	KEEP	0	0	0	8	229	TT	0.99257	0.053735	0		+	3	60	106	0	0	9.733318	5	60	150	19	ENST00000455841.2	0.375	0.054137
GTF2IRD1	9569	__UNKNOWN__	__UNKNOWN__	7	73931334	73931334	__UNKNOWN__	Intron	SNP	G	G	T	rs72613370|rs201242540|rs367995242		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73931334G>T	ENST00000476977.1	+	5	2112				GTF2IRD1_ENST00000489094.1_Intron|GTF2IRD1_ENST00000455841.2_Intron|GTF2IRD1_ENST00000265755.3_Intron|GTF2IRD1_ENST00000424337.2_Intron			Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						tcctgtctttgttgttgttgt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704	9569			4661	protein-coding gene	gene with protein product	binding factor for early enhancer	604318	GTF2I repeat domain-containing 1	WBSCR11	NA	9774679, 10198167	Standard	NM_016328	NM_016328	NA	Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000476977.1:c.422-1135G>T	chr7.hg19:g.73931334G>T		NA	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	hg19		0.02	-0.105258	TTTxTTG	UNCOVERED																																																																																			NOVEL	GTF2IRD1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351531.1	9	2.407199	KEEP	0	0	0	8	245	GG	0.99257	0.138793	0		+	3	60	88	0	0	7.932323	5	60	173	27	ENST00000476977.1	0.375	0.139832
GTF2IRD1	9569	__UNKNOWN__	__UNKNOWN__	7	73942808	73942808	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73942808G>T	ENST00000476977.1	+	9	2781				GTF2IRD1_ENST00000489094.1_Intron|GTF2IRD1_ENST00000455841.2_Intron|GTF2IRD1_ENST00000265755.3_Intron|GTF2IRD1_ENST00000424337.2_Intron			Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						gtgctgggatgacaggcatga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704	9569			4661	protein-coding gene	gene with protein product	binding factor for early enhancer	604318	GTF2I repeat domain-containing 1	WBSCR11	NA	9774679, 10198167	Standard	NM_016328	NM_016328	NA	Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000476977.1:c.1091-1256G>T	chr7.hg19:g.73942808G>T		NA	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	hg19		0.02	-0.122813	GATxACA	COVERED																																																																																			NOVEL	GTF2IRD1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351531.1	2	3.008624	KEEP	0	0	0	10	297	GG	0.992708	0.19488	0		+	3	60	89	0	0	7.17273	11	60	381	34	ENST00000476977.1	0.214286	0.196312
GTF2IRD1	9569	__UNKNOWN__	__UNKNOWN__	7	73999498	73999498	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:73999498G>A	ENST00000476977.1	+	23	4011				GTF2IRD1_ENST00000455841.2_Intron|GTF2IRD1_ENST00000265755.3_Intron|GTF2IRD1_ENST00000424337.2_Intron			Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ctggagtgcagtggcgcaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704	9569			4661	protein-coding gene	gene with protein product	binding factor for early enhancer	604318	GTF2I repeat domain-containing 1	WBSCR11	NA	9774679, 10198167	Standard	NM_016328	NM_016328	NA	Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000476977.1:c.2321-4682G>A	chr7.hg19:g.73999498G>A		NA	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	hg19		0.02	-0.105256	GCAxTGG	UNCOVERED																																																																																			NOVEL	GTF2IRD1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351531.1	11	3.1417	KEEP	3	1	21	18	534	GG	0.999366	0.139743	0		+	3	60	82	0	0	6.978098	7	60	231	35	ENST00000476977.1	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	74027938	74027938	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:74027938T>C			NA	NA				RP5-1186P10.2 (6313 upstream) : GTF2I (44072 downstream)						NA		NA									NA						ctgcctcagcttcccaaagtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.74027938T>C		NA		hg19		0.02	-0.28065	AGCxTCC	COVERED																																																																																			NOVEL					0			6	2.406557	KEEP	0	0	0	8	229	TT	0.99257	0.734176	0			4	60	137	0	0	10.622888	24	60	712	61		0.142857	0.739671
GTF2I	2969	__UNKNOWN__	__UNKNOWN__	7	74172500	74172500	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:74172500C>T	ENST00000324896.4	+	33	3327				GTF2I_ENST00000346152.4_Intron|GTF2I_ENST00000416070.1_Intron|GTF2I_ENST00000353920.4_Intron	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	NA		NA			negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						ctcagcctcccgagtagctgg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001	2969		General transcription factors	4659	protein-coding gene	gene with protein product		601679	general transcription factor II, i	WBSCR6	NA	9334314, 9012831	Standard	NM_032999	NM_032999	NA	Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.2938+167C>T	chr7.hg19:g.74172500C>T		NA	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	hg19	CCDS5573.1	0.02	-0.219236	TCCxGAG	COVERED																																																																																			NOVEL	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252708.1	4	6.314582	KEEP	14	0	0	21	568	CC	0.99649	0.550947	0		+	3	40	91	0	0	6.606715	21	40	602	59	ENST00000324896.4	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	74330972	74330972	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:74330972T>C			NA	NA				Y_RNA (18935 upstream) : GATSL1 (48110 downstream)						NA		NA									NA						ggtcgcaccattgcactccag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.74330972T>C		NA		hg19		0.02	-0.078939	CCAxTGC	UNCOVERED																																																																																			NOVEL					0			4	3.007115	KEEP	5	0	0	10	269	TT	0	0	0			3	60	99	0	0	9.033144	5	46	146	29		0.375	0.077336
GTF2IRD2B	389524	__UNKNOWN__	__UNKNOWN__	7	74527759	74527759	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:74527759C>T	ENST00000312575.7	+	3	274				GTF2IRD2B_ENST00000430511.2_Intron|GTF2IRD2B_ENST00000356115.5_Intron	NM_001003795.2	NP_001003795.1	Q6EKJ0	GTD2B_HUMAN	GTF2I repeat domain containing 2B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|ovary(2)|prostate(1)	4						cctggccgggcgcagtggctc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY312850	CCDS34659.1	7q11.23	2014-05-06			ENSG00000174428	ENSG00000174428	389524			33125	protein-coding gene	gene with protein product		608900			NA	15100712	Standard	NM_001003795	XM_005277580	NA	Approved		uc003ubt.3	Q6EKJ0	OTTHUMG00000181534	ENST00000312575.7:c.100-432C>T	chr7.hg19:g.74527759C>T		NA	B2RNE9|Q69GU6|Q8N979|Q9H739	hg19	CCDS34659.1	0.02	-0.131584	GGGxGCA	UNCOVERED																																																																																			NOVEL	GTF2IRD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342728.1	7	4.81383	KEEP	18	0	0	16	481	CC	0	0	0		+	3	49	91	0	0	7.27217	12	50	405	58	ENST00000312575.7	0.2	0.229173
GTF2IRD2B	389524	__UNKNOWN__	__UNKNOWN__	7	74558775	74558775	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:74558775C>T	ENST00000312575.7	+	14	1392				GTF2IRD2B_ENST00000430511.2_Intron|GTF2IRD2B_ENST00000418185.2_Intron|GTF2IRD2B_ENST00000356115.5_Intron	NM_001003795.2	NP_001003795.1	Q6EKJ0	GTD2B_HUMAN	GTF2I repeat domain containing 2B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|ovary(2)|prostate(1)	4						cggtggctcacgcctgtaatc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY312850	CCDS34659.1	7q11.23	2014-05-06			ENSG00000174428	ENSG00000174428	389524			33125	protein-coding gene	gene with protein product		608900			NA	15100712	Standard	NM_001003795	XM_005277580	NA	Approved		uc003ubt.3	Q6EKJ0	OTTHUMG00000181534	ENST00000312575.7:c.1217+303C>T	chr7.hg19:g.74558775C>T		NA	B2RNE9|Q69GU6|Q8N979|Q9H739	hg19	CCDS34659.1	0.02	-0.131582	TCAxGCC	UNCOVERED																																																																																			NOVEL	GTF2IRD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342728.1	7	2.406822	KEEP	18	0	0	8	235	CC	0	0	0		+	3	49	91	0	0	7.272187	12	50	402	54	ENST00000312575.7	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	74608770	74608770	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:74608770A>T			NA	NA				GTF2IRD2B (43147 upstream) : Y_RNA (104076 downstream)						NA		NA									NA						aagagatggtatctcacgatg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.74608770A>T		NA		hg19		0.02	2.90141	GGTxTCT	COVERED																																																																																			NOVEL					0			32	6.21164	KEEP	21	7	184	86	2265	AA	1	1	0			9	37	269	0	0	16.738912	130	50	3536	370		0.064748	1
TRIM73	375593	__UNKNOWN__	__UNKNOWN__	7	75028240	75028240	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs73702636		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75028240T>C	ENST00000437796.1	+	1	42	c.23T>C	c.(22-24)cTg>cCg	p.L8P	TRIM73_ENST00000463766.1_3'UTR|TRIM73_ENST00000323819.3_Missense_Mutation_p.L8P|TRIM73_ENST00000450434.1_Intron|TRIM73_ENST00000430211.1_Missense_Mutation_p.L8P|TRIM73_ENST00000447409.2_Missense_Mutation_p.L8P			Q86UV7	TRI73_HUMAN	tripartite motif containing 73	8		NA				intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)	4						GTGAGCCTGCTGGAGCTGGAG	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													134	135	135			NA	NA	7		NA											NA				75028240		2203	4300	6503	SO:0001583	missense			AF498998	CCDS34665.1	7q11.23	2013-01-09	2011-01-25	2006-03-31		ENSG00000178809	375593		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	18162	protein-coding gene	gene with protein product		612549	tripartite motif-containing 50B, tripartite motif-containing 73	TRIM50B	NA		Standard		NM_198924	NA	Approved		uc003udc.1	Q86UV7		ENST00000437796.1:c.23T>C	chr7.hg19:g.75028240T>C	ENSP00000417040:p.Leu8Pro	NA	Q8N0S3	hg19	CCDS34665.1	0.02	3.687152	TGCxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.453889	0.00175	.	.	ENSG00000178809	ENST00000323819;ENST00000430211;ENST00000447409;ENST00000437796	D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84	2.31	2.31	0.28768	Zinc finger, RING/FYVE/PHD-type (2);	0.716055	0.13135	N	0.411154	T	0.65037	0.2653	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.56282	-0.8005	9	0.20046	T	0.44	.	3.1123	0.06363	0.2601:0.5871:0.0:0.1528	.	8;8	Q86UV6;Q86UV7	TRI74_HUMAN;TRI73_HUMAN	P	8	ENSP00000318615:L8P;ENSP00000410121:L8P;ENSP00000407135:L8P;ENSP00000417040:L8P	ENSP00000318615:L8P	L	+	2	0	TRIM73	74866176	0.000000	0.05858	0.274000	0.24659	0.362000	0.29581	-0.984000	0.03755	0.549000	0.28973	-0.511000	0.04467	CTG	NOVEL	TRIM73-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342950.1	9	6.751174	KEEP	4	1	33	34	960	TT	0.999998	0.999998	0		+	9	47	320	0	0	21.792586	131	51	3977	293	ENST00000437796.1	0.064286	1
TRIM73	375593	__UNKNOWN__	__UNKNOWN__	7	75028241	75028241	__UNKNOWN__	Silent	SNP	G	G	A	rs73702637		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75028241G>A	ENST00000437796.1	+	1	43	c.24G>A	c.(22-24)ctG>ctA	p.L8L	TRIM73_ENST00000463766.1_3'UTR|TRIM73_ENST00000323819.3_Silent_p.L8L|TRIM73_ENST00000450434.1_Intron|TRIM73_ENST00000430211.1_Silent_p.L8L|TRIM73_ENST00000447409.2_Silent_p.L8L			Q86UV7	TRI73_HUMAN	tripartite motif containing 73	8		NA				intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)|pancreas(1)	4						TGAGCCTGCTGGAGCTGGAGG	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													137	139	138			NA	NA	7		NA											NA				75028241		2203	4300	6503	SO:0001819	synonymous_variant			AF498998	CCDS34665.1	7q11.23	2013-01-09	2011-01-25	2006-03-31		ENSG00000178809	375593		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	18162	protein-coding gene	gene with protein product		612549	tripartite motif-containing 50B, tripartite motif-containing 73	TRIM50B	NA		Standard		NM_198924	NA	Approved		uc003udc.1	Q86UV7		ENST00000437796.1:c.24G>A	chr7.hg19:g.75028241G>A		NA	Q8N0S3	hg19	CCDS34665.1	0.02	4.639882	GCTxGAG	COVERED																																																																																			NOVEL	TRIM73-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342950.1	9	7.255355	KEEP	3	1	28	34	1063	GG	0.999998	0.999998	0		+	10	47	309	0	0	19.881167	135	51	4628	295	ENST00000437796.1	0.068966	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	75135012	75135012	__UNKNOWN__	IGR	SNP	G	G	A	rs587625325	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75135012G>A			NA	NA				POM121C (19464 upstream) : PMS2P3 (2062 downstream)						NA		NA									NA						ggatggtctcgatctcctgac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.75135012G>A		NA		hg19		0.02	-0.026314	CTCxATC	UNCOVERED																																																																																			NOVEL					0			8	2.706974	KEEP	13	0	0	9	254	GG	0	0	0			2	25	63	0	0	6.424685	1	4	30	27		0.666667	0
HIP1	3092	__UNKNOWN__	__UNKNOWN__	7	75272708	75272708	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75272708A>G	ENST00000434438.2	-	2	141				HIP1_ENST00000336926.6_Intron	NM_001243198.1	NP_001230127.1	O00291	HIP1_HUMAN	huntingtin interacting protein 1	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						ccagcactttaggaggccaag	0.438		NA	T	PDGFRB	CMML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946	3092			4913	protein-coding gene	gene with protein product		601767			NA	9140394, 9147654	Standard	NM_005338	NM_005338	NA	Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000434438.2:c.121-44143T>C	chr7.hg19:g.75272708A>G		NA	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	hg19	CCDS59060.1	0.02	-0.210513	TTTxGGA	COVERED																																																																																			NOVEL	HIP1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342864.2	4	3.609048	KEEP	1	0	0	12	332	AA	0.993634	0.518837	0		-	4	60	130	0	1	10.562957	16	60	490	61	ENST00000434438.2	0.2	0.522161
HIP1	3092	__UNKNOWN__	__UNKNOWN__	7	75345820	75345820	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75345820A>G	ENST00000434438.2	-	1	141				HIP1_ENST00000336926.6_Intron	NM_001243198.1	NP_001230127.1	O00291	HIP1_HUMAN	huntingtin interacting protein 1	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						gattacaggcatgagccaccg	0.522		NA	T	PDGFRB	CMML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946	3092			4913	protein-coding gene	gene with protein product		601767			NA	9140394, 9147654	Standard	NM_005338	NM_005338	NA	Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000434438.2:c.120+22298T>C	chr7.hg19:g.75345820A>G		NA	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	hg19	CCDS59060.1	0.02	-0.210483	GGCxTGA	COVERED																																																																																			NOVEL	HIP1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342864.2	12	2.707055	KEEP	2	0	0	9	251	AA	0.99257	0.518282	0		-	3	54	91	0	0	7.011424	15	60	444	47	ENST00000434438.2	0.166667	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	75529622	75529622	__UNKNOWN__	IGR	SNP	G	G	A	rs35298022	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75529622G>A			NA	NA				RHBDD2 (11378 upstream) : POR (14774 downstream)						NA		NA									NA						ctatgatcgcgccactgcact	0.547		NA											G|||	4	0.000798722	0.0	0.0014	5008	,	,	NA	16445	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.75529622G>A		NA		hg19		0.02	-0.149119	CGCxCCA	COVERED																																																																																			NOVEL					0			8	3.308577	KEEP	0	0	0	11	320	GG	0.993072	0.289978	0			3	60	86	0	0	6.592206	14	60	462	37		0.176471	0.292001
POR	5447	__UNKNOWN__	__UNKNOWN__	7	75607888	75607888	__UNKNOWN__	Intron	SNP	C	C	G	rs13231817	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75607888C>G	ENST00000461988.1	+	4	342				POR_ENST00000394893.1_Intron|POR_ENST00000475509.1_Intron|POR_ENST00000419840.1_Intron	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	NA		NA			carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	gtagcccaggctggagtgcaa	0.493		NA											C|||	831	0.165935	0.0159	0.2075	5008	,	,	NA	18144	0.0377	NA	0.339	False	NA	,,,	NA	NA	NA	2504	0.2935	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948	5447			9208	protein-coding gene	gene with protein product		124015			NA	2516426	Standard	NM_000941	NM_000941	NA	Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.238-881C>G	chr7.hg19:g.75607888C>G		NA	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	hg19	CCDS5579.1	0.02	-0.096501	AGGxTGG	UNCOVERED																																																																																			NOVEL	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252796.7	6	2.407411	KEEP	2	0	0	8	256	CC	0	0	0		+	3	60	105	0	0	9.278452	7	60	248	28	ENST00000461988.1	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	75920295	75920295	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75920295A>G			NA	NA				RN7SL212P (1924 upstream) : HSPB1 (11565 downstream)						NA		NA									NA						gagccactgcacccggccatt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.75920295A>G		NA		hg19		0.02	-0.36833	TGCxCCC	COVERED																																																																																			NOVEL					0			10	7.21817	KEEP	0	0	0	24	663	AA	0.999909	0.899232	0			3	60	103	0	0	7.106191	37	60	1104	97		0.075	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	75930541	75930541	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75930541A>C			NA	NA				RN7SL212P (12170 upstream) : HSPB1 (1319 downstream)						NA		NA									NA						atcctcccacatcagcctccc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.75930541A>C		NA		hg19		0.02	-0.122789	CACxTCA	COVERED																																																																																			NOVEL					0			7	5.111722	KEEP	0	0	0	17	462	AA	0.999366	0.196187	0			4	60	135	0	0	11.924259	9	60	266	45		0.307692	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	75990375	75990375	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:75990375A>C			NA	NA				YWHAG (2027 upstream) : SRCRB4D (28275 downstream)						NA		NA									NA						gaaactccatatcaaaaaaca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.75990375A>C		NA		hg19		0.02	-0.175398	CATxTCA	COVERED																																																																																			NOVEL					0			9	4.209861	KEEP	0	0	0	14	373	AA	0.995343	0.421506	0			3	60	99	0	1	7.733539	16	60	453	47		0.157895	0.423478
ZP3	7784	__UNKNOWN__	__UNKNOWN__	7	76063333	76063333	__UNKNOWN__	Intron	SNP	T	T	C	rs3972768	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76063333T>C	ENST00000394857.3	+	5	771				ZP3_ENST00000416245.1_Intron|ZP3_ENST00000336517.4_Intron	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	NA		NA			binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						CTGGCTTTAATACCGTTCTGT	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													62	71	68			NA	NA	7		NA											NA				76063333		2017	4131	6148	SO:0001627	intron_variant			M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372	7784		Zona pellucida glycoproteins	13189	protein-coding gene	gene with protein product		182889	zona pellucida glycoprotein 3A (sperm receptor)	ZP3A, ZP3B	NA	1478648	Standard		NM_007155	NA	Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.714-22T>C	chr7.hg19:g.76063333T>C		NA	Q06633|Q29RW0	hg19	CCDS47618.1	0.02	1.470522	TAAxACC	COVERED																																																																																			NOVEL	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253004.1	13	11.723732	KEEP	0	0	0	39	1010	TT	1	0.999407	0		+	4	40	133	0	0	8.33915	75	52	2114	178	ENST00000394857.3	0.050633	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	76080615	76080615	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76080615C>T			NA	NA				ZP3 (9227 upstream) : DTX2 (10402 downstream)						NA		NA									NA						ttttttgagacggagtctcgc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.76080615C>T		NA		hg19		0.02	-0.105219	AGAxGGA	UNCOVERED																																																																																			NOVEL					0			6	2.405538	KEEP	5	0	0	8	215	CC	0	0	0			3	60	93	1	0	7.933029	8	60	228	28		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	76081317	76081317	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76081317G>C			NA	NA				ZP3 (9929 upstream) : DTX2 (9700 downstream)						NA		NA									NA						cagtggctcaggcctgtaatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.76081317G>C		NA		hg19		0.02	-0.149112	TCAxGCC	COVERED																																																																																			NOVEL					0			7	2.993081	KEEP	2	0	0	10	277	GG	0.992708	0.384582	0			3	50	89	0	0	7.072371	12	60	419	41		0.2	0.387407
DTX2	113878	__UNKNOWN__	__UNKNOWN__	7	76131695	76131695	__UNKNOWN__	Silent	SNP	A	A	G	rs4728775	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76131695A>G	ENST00000324432.5	+	9	1821	c.1311A>G	c.(1309-1311)ctA>ctG	p.L437L	DTX2_ENST00000430490.2_Silent_p.L437L|DTX2_ENST00000413936.2_Silent_p.L437L|DTX2_ENST00000446820.2_Silent_p.L390L|DTX2_ENST00000307569.8_Silent_p.L390L|DTX2_ENST00000446600.1_Silent_p.L346L	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	437		NA			Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TCGGGTCCCTAGCTGTGGGCC	0.597		NA											.|||	3436	0.686102	0.5749	0.7219	5008	,	,	NA	17797	0.8095	NA	0.6581	False	NA	,,,	NA	NA	NA	2504	0.7127	NA	NA	NA								NA				0								G	,,,	2531,1871		723,1085,393	93	63	73		1311,1311,1170,1311	2.6	0.1	7	dbSNP_111	73	5426,3168		1733,1960,604	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	2456,3045,997	GG,GA,AA	NA	36.8629,42.5034,38.7735	,,,	437/623,437/623,390/576,437/623	76131695	7957,5039	2201	4297	6498	SO:0001819	synonymous_variant				CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073	113878		RING-type (C3HC4) zinc fingers	15973	protein-coding gene	gene with protein product		613141	deltex (Drosophila) homolog 2, deltex homolog 2 (Drosophila)		NA	12670957	Standard		NM_020892	NA	Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1311A>G	chr7.hg19:g.76131695A>G		NA	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	hg19	CCDS5587.1	0.02	1.862415	CCTxGCT	COVERED																																																																																			NOVEL	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253104.2	1	3.607212	KEEP	0	0	0	12	317	AA	0.993634	0.981653	0		+	5	60	170	0	0	11.952943	54	60	1563	113	ENST00000324432.5	0.084746	0.987943
UPK3B	80761	__UNKNOWN__	__UNKNOWN__	7	76584244	76584244	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76584244G>A	ENST00000443097.2	+	8	1323				UPK3B_ENST00000419923.2_Intron			Q9BT76	UPK3B_HUMAN	uroplakin 3B	NA		NA			negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				cttgtgatccgcccgcctcgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566	80761			21444	protein-coding gene	gene with protein product	uroplakin IIIb	611887			NA	12446744	Standard	NM_030570	XM_005250612	NA	Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000443097.2:c.829-63897G>A	chr7.hg19:g.76584244G>A		NA	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	hg19	CCDS5589.1	0.02	-0.17404	TCCxCCC	UNCOVERED																																																																																			NOVEL	UPK3B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		7	3.909852	KEEP	17	0	0	13	363	GG	0	0	0		+	3	55	86	0	0	6.446883	16	55	452	60	ENST00000443097.2	0.157895	0.387407
UPK3B	80761	__UNKNOWN__	__UNKNOWN__	7	76628233	76628233	__UNKNOWN__	Intron	SNP	T	T	C	rs370394259|rs144163556		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76628233T>C	ENST00000443097.2	+	8	1323				UPK3B_ENST00000419923.2_Intron|DTX2P1-UPK3BP1-PMS2P11_ENST00000584900.1_RNA			Q9BT76	UPK3B_HUMAN	uroplakin 3B	NA		NA			negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				tggattggggtgtgtggtgtg	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566	80761			21444	protein-coding gene	gene with protein product	uroplakin IIIb	611887			NA	12446744	Standard	NM_030570	XM_005250612	NA	Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000443097.2:c.829-19908T>C	chr7.hg19:g.76628233T>C		NA	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	hg19	CCDS5589.1	0.02	-0.052623	GGGxGTG	UNCOVERED																																																																																			NOVEL	UPK3B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		8	2.341159	KEEP	0	0	0	8	174	TT	0.99257	0.036492	0		+	2	60	69	1	0	6.393202	3	60	83	19	ENST00000443097.2	0.4	0.036766
UPK3B	80761	__UNKNOWN__	__UNKNOWN__	7	76637265	76637265	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:76637265T>A	ENST00000443097.2	+	8	1323				UPK3B_ENST00000419923.2_Intron|DTX2P1-UPK3BP1-PMS2P11_ENST00000584900.1_RNA			Q9BT76	UPK3B_HUMAN	uroplakin 3B	NA		NA			negative regulation of gene expression (GO:0010629)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(1)|lung(1)|skin(2)	8		Myeloproliferative disorder(862;0.204)				gctggagtgctgtggcgcgat	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004304	CCDS5588.1, CCDS5589.1, CCDS64693.1	7q11.2	2003-07-29			ENSG00000243566	ENSG00000243566	80761			21444	protein-coding gene	gene with protein product	uroplakin IIIb	611887			NA	12446744	Standard	NM_030570	XM_005250612	NA	Approved	MGC10902, p35, UPIIIb, FLJ32198	uc003ufq.3	Q9BT76	OTTHUMG00000149929	ENST00000443097.2:c.829-10876T>A	chr7.hg19:g.76637265T>A		NA	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	hg19	CCDS5589.1	0.02	-0.078924	TGCxGTG	UNCOVERED																																																																																			NOVEL	UPK3B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		3	3.005401	KEEP	0	0	0	10	261	TT	0.992708	0.076772	0		+	3	60	84	0	0	7.531381	5	60	156	31	ENST00000443097.2	0.375	0.077336
PTPN12	5782	__UNKNOWN__	__UNKNOWN__	7	77193287	77193287	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:77193287T>C	ENST00000248594.6	+	2	371				PTPN12_ENST00000435495.2_Intron|PTPN12_ENST00000415482.2_Intron	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	NA		NA			protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						agtgcagtggtgtgatctcgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947	5782		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	9645	protein-coding gene	gene with protein product		600079			NA	7509295	Standard		NM_002835	NA	Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.100-7108T>C	chr7.hg19:g.77193287T>C		NA	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	hg19	CCDS5592.1	0.02	-0.307002	TGGxGTG	COVERED																																																																																			NOVEL	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253183.3	7	2.736662	KEEP	2	1	25	18	493	TT	0.99986	0.800133	0		+	4	60	133	0	0	10.157227	25	60	769	67	ENST00000248594.6	0.137931	0.800245
PTPN12	5782	__UNKNOWN__	__UNKNOWN__	7	77255138	77255138	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:77255138T>C	ENST00000248594.6	+	13	1297				PTPN12_ENST00000435495.2_Intron|PTPN12_ENST00000415482.2_Intron	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	NA		NA			protein dephosphorylation (GO:0006470)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|podosome (GO:0002102)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|SH3 domain binding (GO:0017124)			breast(2)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(12)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	39						ccacccaccttggcctcccaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5592.1, CCDS47619.1, CCDS47620.1	7q11.23	2011-06-09			ENSG00000127947	ENSG00000127947	5782		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	9645	protein-coding gene	gene with protein product		600079			NA	7509295	Standard		NM_002835	NA	Approved	PTPG1, PTP-PEST	uc003ugh.2	Q05209	OTTHUMG00000023501	ENST00000248594.6:c.1026-884T>C	chr7.hg19:g.77255138T>C		NA	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	hg19	CCDS5592.1	0.02	-0.166622	CCTxGGC	COVERED																																																																																			NOVEL	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253183.3	8	3.608853	KEEP	1	0	0	12	328	TT	0.993634	0.38494	0		+	3	60	95	0	0	7.410627	15	60	429	48	ENST00000248594.6	0.166667	0.387407
MAGI2	9863	__UNKNOWN__	__UNKNOWN__	7	77729941	77729941	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:77729941C>T	ENST00000354212.4	-	21	3821				MAGI2_ENST00000419488.1_Intron|MAGI2_ENST00000522391.1_Intron	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	NA		NA			cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				agtgctgggactaaaggtgtg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391	9863			18957	protein-coding gene	gene with protein product		606382			NA	10681527, 9734811	Standard	NM_012301	XM_005250725	NA	Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.3568-21539G>A	chr7.hg19:g.77729941C>T		NA	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	hg19	CCDS5594.1	0.02	-0.228081	GGAxTAA	COVERED																																																																																			NOVEL	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253197.3	8	2.708141	KEEP	0	0	0	9	277	CC	0.99254	0.578582	0		-	3	60	89	0	0	6.406448	21	60	722	47	ENST00000354212.4	0.125	0.58293
MAGI2	9863	__UNKNOWN__	__UNKNOWN__	7	78164194	78164194	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:78164194A>G	ENST00000354212.4	-	4	792				MAGI2_ENST00000419488.1_Intron|MAGI2_ENST00000536571.1_Intron|MAGI2_ENST00000535697.1_Intron|MAGI2_ENST00000522391.1_Intron	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	NA		NA			cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				gctcacgcctataatcccagc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391	9863			18957	protein-coding gene	gene with protein product		606382			NA	10681527, 9734811	Standard	NM_012301	XM_005250725	NA	Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.539-13232T>C	chr7.hg19:g.78164194A>G		NA	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	hg19	CCDS5594.1	0.02	-0.140327	CCTxTAA	UNCOVERED																																																																																			NOVEL	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253197.3	6	2.405468	KEEP	1	0	0	8	212	AA	0	0	0		-	3	60	100	0	0	8.272994	11	60	318	34	ENST00000354212.4	0.214286	0.260965
MAGI2	9863	__UNKNOWN__	__UNKNOWN__	7	78231752	78231752	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:78231752C>T	ENST00000354212.4	-	3	792				MAGI2_ENST00000419488.1_Intron|MAGI2_ENST00000536571.1_Intron|MAGI2_ENST00000535697.1_Intron|MAGI2_ENST00000522391.1_Intron	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	NA		NA			cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				gctgggattacaggcatgagc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391	9863			18957	protein-coding gene	gene with protein product		606382			NA	10681527, 9734811	Standard	NM_012301	XM_005250725	NA	Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.538+24683G>A	chr7.hg19:g.78231752C>T		NA	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	hg19	CCDS5594.1	0.02	-0.184225	TTAxAGG	COVERED																																																																																			NOVEL	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253197.3	12	4.793894	KEEP	2	0	0	16	464	CC	0.999366	0.423209	0		-	3	51	89	0	0	6.810299	15	60	531	55	ENST00000354212.4	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	79271785	79271785	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:79271785G>T			NA	NA				MAGI2-AS3 (171261 upstream) : RNA5SP234 (11639 downstream)						NA		NA									NA						AATGggccaggtgcagtggct	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.79271785G>T		NA		hg19		0.02	-0.184203	CAGxTGC	COVERED																																																																																			NOVEL					0			8	2.707762	KEEP	3	0	0	9	266	GG	0.99254	0.420319	0			4	60	114	0	0	9.062675	15	60	512	45		0.210526	0.423478
SEMA3C	10512	__UNKNOWN__	__UNKNOWN__	7	80456717	80456717	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:80456717T>G	ENST00000265361.3	-	4	889				SEMA3C_ENST00000419255.2_Intron|SEMA3C_ENST00000544525.1_Intron|SEMA3C_ENST00000536800.1_Intron	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	NA		NA			axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TGttttttttttttttttttt	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													10	12	11			NA	NA	7		NA											NA				80456717		2139	4263	6402	SO:0001627	intron_variant			AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223	10512		Semaphorins, Immunoglobulin superfamily / I-set domain containing	10725	protein-coding gene	gene with protein product		602645		SEMAE	NA	7748561, 9168980	Standard	NM_006379	NM_006379	NA	Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.327+23A>C	chr7.hg19:g.80456717T>G		NA	B4DRL8	hg19	CCDS5596.1	0.02	-0.324332	TTTxTTT	COVERED																																																																																			NOVEL	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253279.1	3	5.712803	KEEP	0	0	0	19	500	TT	0.99986	0.835599	0		-	3	60	98	0	0	7.249273	22	60	618	68	ENST00000265361.3	0.12	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	80647860	80647860	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:80647860C>T			NA	NA				SEMA3C (96185 upstream) : AC005008.2 (156963 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.80647860C>T		NA		hg19		0.02	-0.210529	AGGxGTG	COVERED																																																																																			NOVEL					0			10	2.707073	KEEP	3	0	0	9	259	CC	0.99254	0.518266	0			3	60	89	0	0	6.527578	19	60	632	52		0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	80897538	80897538	__UNKNOWN__	IGR	SNP	T	T	C	rs373410881		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:80897538T>C			NA	NA				AC005008.2 (77832 upstream) : AC008163.4 (260180 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.80897538T>C		NA		hg19		0.02	-0.149121	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			5	2.406221	KEEP	2	0	0	8	224	TT	0	0	0			4	60	135	0	0	11.501451	12	60	372	39		0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	82111967	82111967	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:82111967A>G			NA	NA				CACNA2D1 (38853 upstream) : PCLO (271361 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.82111967A>G		NA		hg19		0.02	-0.052509	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			4	3.007816	KEEP	2	0	0	10	279	AA	0.99254	0.036491	0			2	60	71	0	0	6.398794	4	60	106	27		0.333333	0.036766
PCLO	27445	__UNKNOWN__	__UNKNOWN__	7	82595795	82595795	__UNKNOWN__	Silent	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:82595795T>C	ENST00000333891.9	-	4	3646	c.3309A>G	c.(3307-3309)gaA>gaG	p.E1103E	PCLO_ENST00000423517.2_Silent_p.E1103E	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein	NA		NA								breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						AACAAAGCCATTCTTGAATCT	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													79	76	77			NA	NA	7		NA											NA				82595795		1912	4138	6050	SO:0001819	synonymous_variant			AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472	27445			13406	protein-coding gene	gene with protein product	aczonin	604918	piccolo (presynaptic cytomatrix protein)		NA	8900486, 9628581	Standard	NM_014510	NM_014510	NA	Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.3309A>G	chr7.hg19:g.82595795T>C		NA		hg19	CCDS47630.1	0.02	1.991556	CCAxTCT	COVERED																																																																																			NOVEL	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337368.5	1	3.609766	KEEP	0	0	0	12	341	TT	0.993634	0.989348	0		-	19	60	657	0	0	57.273688	49	60	1478	117	ENST00000333891.9	0.279412	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	84320374	84320374	__UNKNOWN__	IGR	SNP	G	G	A	rs200816334		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:84320374G>A			NA	NA				AC092022.1 (25050 upstream) : AC074183.4 (248290 downstream)						NA		NA									NA						aagaagaagaggaggaggagg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.84320374G>A		NA		hg19		0.02	-0.148945	AGAxGAG	COVERED																																																																																			NOVEL					0			32	3.235799	KEEP	29	1	26	20	570	GG	0.994391	0.290363	0			3	60	88	2	1	7.075236	11	60	309	92		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	84559224	84559224	__UNKNOWN__	IGR	SNP	T	T	A	rs542733424	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:84559224T>A			NA	NA				AC092022.1 (263900 upstream) : AC074183.4 (9440 downstream)						NA		NA									NA						gctaacacggtgaaaccccgt	0.597		NA											-|||	2	0.000399361	0.0	0.0	5008	,	,	NA	14306	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.84559224T>A		NA		hg19		0.02	-0.105245	CGGxGAA	UNCOVERED																																																																																			NOVEL					0			14	4.51176	KEEP	18	0	0	15	417	TT	0	0	0			5	43	149	0	0	13.993504	6	46	179	42		0.454545	0.139832
ABCB1	5243	__UNKNOWN__	__UNKNOWN__	7	87164059	87164059	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:87164059T>A	ENST00000265724.3	-	21	2899				ABCB1_ENST00000543898.1_Intron	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	NA		NA			drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	agggagaccctgtctctacaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563	5243		CD molecules, ATP binding cassette transporters / subfamily B	40	protein-coding gene	gene with protein product	multidrug resistance protein 1	171050	colchicin sensitivity	PGY1, MDR1, CLCS	NA	3027054	Standard	NM_000927	NM_000927	NA	Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.2481+1714A>T	chr7.hg19:g.87164059T>A		NA	A8K294|B5AK60|Q12755|Q14812	hg19	CCDS5608.1	0.02	-0.166646	CCCxGTC	COVERED																																																																																			NOVEL	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335444.2	8	3.609425	KEEP	0	0	0	12	334	TT	0.993634	0.351693	0		-	6	60	173	0	0	15.016156	13	60	403	42	ENST00000265724.3	0.315789	0.353947
ABCB1	5243	__UNKNOWN__	__UNKNOWN__	7	87177070	87177070	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:87177070T>C	ENST00000265724.3	-	15	2143				ABCB1_ENST00000543898.1_Intron	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	NA		NA			drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	cctgtaatcctagctactcag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563	5243		CD molecules, ATP binding cassette transporters / subfamily B	40	protein-coding gene	gene with protein product	multidrug resistance protein 1	171050	colchicin sensitivity	PGY1, MDR1, CLCS	NA	3027054	Standard	NM_000927	NM_000927	NA	Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1725+1593A>G	chr7.hg19:g.87177070T>C		NA	A8K294|B5AK60|Q12755|Q14812	hg19	CCDS5608.1	0.02	-0.105239	TCCxAGC	UNCOVERED																																																																																			NOVEL	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335444.2	11	3.006291	KEEP	1	0	0	10	261	TT	0.99254	0.138789	0		-	3	60	94	0	0	7.901367	9	60	260	27	ENST00000265724.3	0.25	0.139832
ABCB1	5243	__UNKNOWN__	__UNKNOWN__	7	87268296	87268296	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:87268296G>A	ENST00000265724.3	-	2	88				RUNDC3B_ENST00000394654.3_Intron|RUNDC3B_ENST00000338056.3_Intron|RUNDC3B_ENST00000493037.1_Intron	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	NA		NA			drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	gtgaaaccccgtctctactaa	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563	5243		CD molecules, ATP binding cassette transporters / subfamily B	40	protein-coding gene	gene with protein product	multidrug resistance protein 1	171050	colchicin sensitivity	PGY1, MDR1, CLCS	NA	3027054	Standard	NM_000927	NM_000927	NA	Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.330-37902C>T	chr7.hg19:g.87268296G>A		NA	A8K294|B5AK60|Q12755|Q14812	hg19	CCDS5608.1	0.02	-0.175416	CCCxTCT	COVERED																																																																																			NOVEL	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335444.2	4	3.008333	KEEP	3	0	0	10	289	CG	0.99254	0.384517	0		-	5	40	137	0	0	11.201711	15	60	488	39	ENST00000265724.3	0.25	0.387407
ZNF804B	219578	__UNKNOWN__	__UNKNOWN__	7	88807105	88807105	__UNKNOWN__	Intron	SNP	G	G	A	rs570979496		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:88807105G>A	ENST00000333190.4	+	2	717					NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	NA		NA					metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			cgttgctcacgcctgtaatcc	0.493		NA								HNSCC(36;0.09)			G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	15653	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348	219578			21958	protein-coding gene	gene with protein product		NA	zinc finger 804B		NA		Standard	NM_181646	NM_181646	NA	Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.109-40364G>A	chr7.hg19:g.88807105G>A		NA	B2RTV2|Q7Z714|Q96MN7	hg19	CCDS5613.1	0.02	-0.087716	CACxCCT	UNCOVERED																																																																																			NOVEL	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253683.2	10	3.91092	KEEP	0	0	0	13	382	GG	0.994391	0.099162	0		+	3	60	87	0	0	7.642872	6	60	212	32	ENST00000333190.4	0.333333	0.099721
STEAP2-AS1	100874100	__UNKNOWN__	__UNKNOWN__	7	89774042	89774042	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:89774042T>C	ENST00000478318.2	-	0	424									STEAP2 antisense RNA 1	NA		NA									NA						cgcctgtaattccagcacttt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							7q21.13	2012-10-12	2012-08-15		ENSG00000227646	ENSG00000227646	100874100		Long non-coding RNAs	40820	non-coding RNA	RNA, long non-coding		NA	STEAP2 antisense RNA 1 (non-protein coding)		NA		Standard		NR_110029	NA	Approved				OTTHUMG00000065036	ENST00000478318.2:	chr7.hg19:g.89774042T>C		NA		hg19		0.02	-0.114026	AATxCCA	UNCOVERED																																																																																			NOVEL	STEAP2-AS1-002	KNOWN	basic	antisense	NA	processed_transcript	OTTHUMT00000350909.2	10	3.007095	KEEP	13	0	0	10	270	TT	0.99257	0.16126	0		-	3	49	102	1	0	8.581984	10	60	299	49	ENST00000478318.2	0.230769	0.162467
C7orf63	0	__UNKNOWN__	__UNKNOWN__	7	89905191	89905191	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:89905191C>T	ENST00000389297.4	+	10	1235				C7orf63_ENST00000497910.1_Intron|C7orf63_ENST00000316089.8_Intron	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		NA		NA								breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						gctgggattacaggcgtgagc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000389297.4:c.985-1196C>T	chr7.hg19:g.89905191C>T		NA	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	hg19	CCDS43613.2	0.02	-0.175442	TTAxAGG	COVERED																																																																																			NOVEL	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139891.4	4	2.708172	KEEP	1	0	0	9	278	CC	0.99257	0.384528	0		+	3	60	87	0	0	6.533843	16	60	545	42	ENST00000389297.4	0.157895	0.387407
RP11-142A5.1	0	__UNKNOWN__	__UNKNOWN__	7	91029412	91029412	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:91029412C>T	ENST00000456952.1	-	0	112										NA		NA									NA						tgcactccagcctgggtgaca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000456952.1:	chr7.hg19:g.91029412C>T		NA		hg19		0.02	-0.070172	CAGxCTG	UNCOVERED																																																																																			NOVEL	RP11-142A5.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000342905.1	4	2.406823	KEEP	0	0	0	8	239	CC	0.99257	0.053735	0		-	3	60	89	0	0	8.032505	5	60	162	20	ENST00000456952.1	0.375	0.054137
LRRD1	401387	__UNKNOWN__	__UNKNOWN__	7	91804938	91804938	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:91804938G>A	ENST00000458448.1	-	1	127				LRRD1_ENST00000343318.5_Intron|LRRD1_ENST00000422722.1_Intron|CTB-161K23.1_ENST00000453068.1_RNA			A4D1F6	LRRD1_HUMAN	leucine-rich repeats and death domain containing 1	NA		NA			signal transduction (GO:0007165)					breast(4)|endometrium(1)	5						actccagcctgggcaacaaga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC026112	CCDS55124.1	7q21.2	2011-05-23			ENSG00000240720	ENSG00000240720	401387			34300	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001045475	NM_001161528	NA	Approved	IMAGE:4798971	uc011khp.1	A4D1F6	OTTHUMG00000155861	ENST00000458448.1:c.73+3382C>T	chr7.hg19:g.91804938G>A		NA	B7ZMM9|Q49AT9	hg19	CCDS55124.1	0.02	-0.105252	CCTxGGC	UNCOVERED																																																																																			NOVEL	LRRD1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342027.2	8	3.604968	KEEP	1	0	0	12	353	GG	0.993634	0.138942	0		-	3	60	78	0	0	6.577897	7	60	235	34	ENST00000458448.1	0.3	0.139832
ANKIB1	54467	__UNKNOWN__	__UNKNOWN__	7	92003724	92003724	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:92003724G>A	ENST00000265742.3	+	11	1993					NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	NA		NA					zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			cctgggaggcggaggttgcag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629	54467		Ankyrin repeat domain containing	22215	protein-coding gene	gene with protein product		NA			NA		Standard		NM_019004	NA	Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1617+2803G>A	chr7.hg19:g.92003724G>A		NA	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	hg19	CCDS47639.1	0.02	-0.157876	GGCxGAG	COVERED																																																																																			NOVEL	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342018.1	5	3.306292	KEEP	0	0	0	11	302	GG	0.993072	0.32057	0		+	3	60	92	0	0	7.191997	14	60	437	39	ENST00000265742.3	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	92172959	92172959	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:92172959G>A			NA	NA				RBM48 (5640 upstream) : FAM133B (17147 downstream)						NA		NA									NA						ctggaaggcagaggttgcagt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.92172959G>A		NA		hg19		0.02	-0.149102	GCAxAGG	UNCOVERED																																																																																			NOVEL					0			6	2.406812	KEEP	3	0	0	8	235	GG	0	0	0			4	26	120	0	0	10.130925	11	60	363	39		0.266667	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	93996792	93996792	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:93996792A>G			NA	NA				AC003092.2 (290323 upstream) : COL1A2 (27080 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.93996792A>G		NA		hg19		0.02	-0.14032	CACxCCT	COVERED																																																																																			NOVEL					0			10	4.811606	KEEP	3	0	0	16	439	AA	0.995343	0.290641	0			3	60	92	0	0	7.473247	11	60	326	47		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	94117185	94117185	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:94117185A>G			NA	NA				COL1A2 (56641 upstream) : RNU6-1328P (7425 downstream)						NA		NA									NA						acaggcatgaaccaccacgcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.94117185A>G		NA		hg19		0.02	-0.236808	TGAxCCA	COVERED																																																																																			NOVEL					0			4	2.40558	KEEP	0	0	0	8	216	AA	0.99257	0.607857	0			3	60	100	0	0	7.449076	22	60	658	51		0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	94494258	94494258	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:94494258G>A			NA	NA				RN7SKP129 (63134 upstream) : PPP1R9A (42690 downstream)						NA		NA									NA						AGggccaggcgtggtggctca	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.94494258G>A		NA		hg19		0.02	-0.280701	GGCxTGG	COVERED																																																																																			NOVEL					0			8	3.004359	KEEP	4	0	0	10	266	GG	0.992708	0.734278	0			4	60	118	0	0	8.534178	27	60	890	67		0.129032	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	94517033	94517033	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:94517033C>T			NA	NA				RN7SKP129 (85909 upstream) : PPP1R9A (19915 downstream)						NA		NA									NA						cagtggctcacgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.94517033C>T		NA		hg19		0.02	-0.18421	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			7	3.008445	KEEP	6	0	0	10	295	CC	0	0	0			3	60	86	0	0	6.361716	17	60	575	52		0.15	0.423478
PPP1R9A	55607	__UNKNOWN__	__UNKNOWN__	7	94667156	94667156	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:94667156C>T	ENST00000433360.1	+	3	1677				PPP1R9A_ENST00000424654.1_Intron|PPP1R9A_ENST00000433881.1_Intron|PPP1R9A_ENST00000289495.5_Intron|PPP1R9A_ENST00000340694.4_Intron|PPP1R9A_ENST00000456331.2_Intron	NM_001166160.1	NP_001159632.1	Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	NA		NA			actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			gtggctcacacctgtaatccc	0.428		NA								HNSCC(28;0.073)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528	55607		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Sterile alpha motif (SAM) domain containing	14946	protein-coding gene	gene with protein product		602468	protein phosphatase 1, regulatory (inhibitor) subunit 9A		NA	10574462	Standard	NM_001166160	NM_001166160	NA	Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433360.1:c.1396-73415C>T	chr7.hg19:g.94667156C>T		NA	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	hg19	CCDS55127.1	0.02	-0.08772	ACAxCTG	UNCOVERED																																																																																			NOVEL	PPP1R9A-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340664.1	9	4.513146	KEEP	2	0	0	15	452	CC	0.995343	0.099257	0		+	3	60	89	0	0	7.678289	7	60	241	34	ENST00000433360.1	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	95257602	95257602	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:95257602T>C			NA	NA				AC002451.3 (14571 upstream) : DYNC1I1 (144263 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.95257602T>C		NA		hg19		0.02	-0.236759	AGGxGTG	COVERED																																																																																			NOVEL					0			5	2.70392	KEEP	1	0	0	9	226	TT	0.99254	0.607839	0			4	60	140	0	0	11.136485	21	60	587	56		0.16	0.612407
DYNC1I1	1780	__UNKNOWN__	__UNKNOWN__	7	95409812	95409812	__UNKNOWN__	Intron	SNP	G	G	A	rs7783416	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:95409812G>A	ENST00000413338.1	+	1	170				DYNC1I1_ENST00000324972.6_Intron|DYNC1I1_ENST00000437599.1_Intron|DYNC1I1_ENST00000447467.2_Intron|DYNC1I1_ENST00000359388.4_Intron|DYNC1I1_ENST00000537881.1_Intron			O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|metabolic process (GO:0008152)|vesicle transport along microtubule (GO:0047496)	cytoplasmic dynein complex (GO:0005868)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)|spectrin binding (GO:0030507)			NS(2)|autonomic_ganglia(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(27)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	54	all_cancers(62;9.39e-10)|all_epithelial(64;2.28e-09)|Lung NSC(181;0.165)|all_lung(186;0.191)		STAD - Stomach adenocarcinoma(171;0.0957)			ggatggtctcgatctcctgac	0.507		NA											G|||	2372	0.473642	0.2398	0.402	5008	,	,	NA	11646	0.629	NA	0.5308	False	NA	,,,	NA	NA	NA	2504	0.6217	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF063228	CCDS5644.1, CCDS47645.1, CCDS47646.1, CCDS64718.1	7q21.3-q22.1	2013-01-18	2005-11-24	2005-11-24	ENSG00000158560	ENSG00000158560	1780		Cytoplasmic dyneins, WD repeat domain containing	2963	protein-coding gene	gene with protein product		603772	dynein, cytoplasmic, intermediate polypeptide 1	DNCI1	NA	10049579, 16260502	Standard	NM_004411	NM_004411	NA	Approved	DNCIC1	uc003uoc.4	O14576	OTTHUMG00000153983	ENST00000413338.1:c.-10+7727G>A	chr7.hg19:g.95409812G>A		NA	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	hg19		0.02	-0.078914	CTCxATC	UNCOVERED																																																																																			NOVEL	DYNC1I1-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000333431.1	12	3.910745	KEEP	17	0	0	13	380	GG	0	0	0		+	3	40	81	1	1	7.042067	6	60	186	44	ENST00000413338.1	0.333333	0.077336
SHFM1	7979	__UNKNOWN__	__UNKNOWN__	7	96280007	96280007	__UNKNOWN__	Intron	SNP	C	C	T	rs386715937|rs76715800	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:96280007C>T	ENST00000444799.1	-	3	265				RP11-682N22.1_ENST00000606019.1_lincRNA|SHFM1_ENST00000417009.1_Intron			P60896	DSS1_HUMAN	split hand/foot malformation (ectrodactyly) type 1	NA		NA			double-strand break repair via homologous recombination (GO:0000724)	proteasome complex (GO:0000502)				breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_cancers(62;4.24e-09)|all_epithelial(64;5.59e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0353)|Lung NSC(181;0.0987)					cacacacacacacacacTCAG	0.368		NA						Homologous recombination					C|||	278	0.0555112	0.0166	0.0576	5008	,	,	NA	16852	0.0407	NA	0.0656	False	NA	,,,	NA	NA	NA	2504	0.1115	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41515	CCDS5646.1	7q21.3	2010-04-22			ENSG00000127922	ENSG00000127922	7979			10845	protein-coding gene	gene with protein product	deleted in split-hand/foot 1	601285		SHFD1	NA	1895319, 8733122	Standard	NM_006304	NM_006304	NA	Approved	DSS1, Shfdg1, ECD, SEM1, SHSF1	uc003uoi.3	P60896	OTTHUMG00000150680	ENST00000444799.1:c.171-176G>A	chr7.hg19:g.96280007C>T		NA	Q13437|Q61067	hg19		0.02	-0.131511	ACAxACA	COVERED																																																																																			NOVEL	SHFM1-007	PUTATIVE	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000319599.1	4	2.40607	KEEP	0	0	0	8	234	CC	0.99257	0.22747	0		-	4	60	107	0	0	8.971406	10	60	310	28	ENST00000444799.1	0.285714	0.229173
SHFM1	7979	__UNKNOWN__	__UNKNOWN__	7	96320329	96320329	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:96320329G>C	ENST00000248566.2	-	3	298				SHFM1_ENST00000444799.1_Intron|SHFM1_ENST00000413065.1_Intron|SHFM1_ENST00000417009.1_Intron	NM_006304.1	NP_006295.1	P60896	DSS1_HUMAN	split hand/foot malformation (ectrodactyly) type 1	NA		NA			double-strand break repair via homologous recombination (GO:0000724)	proteasome complex (GO:0000502)				breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	all_cancers(62;4.24e-09)|all_epithelial(64;5.59e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0353)|Lung NSC(181;0.0987)					gtgatccaccggcctcggcct	0.512		NA						Homologous recombination													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41515	CCDS5646.1	7q21.3	2010-04-22			ENSG00000127922	ENSG00000127922	7979			10845	protein-coding gene	gene with protein product	deleted in split-hand/foot 1	601285		SHFD1	NA	1895319, 8733122	Standard	NM_006304	NM_006304	NA	Approved	DSS1, Shfdg1, ECD, SEM1, SHSF1	uc003uoi.3	P60896	OTTHUMG00000150680	ENST00000248566.2:c.171-2051C>G	chr7.hg19:g.96320329G>C		NA	Q13437|Q61067	hg19	CCDS5646.1	0.02	-0.131577	ACCxGCC	COVERED																																																																																			NOVEL	SHFM1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319595.1	6	2.40636	KEEP	0	0	0	8	233	GG	0.99257	0.259026	0		-	3	60	96	0	0	8.378635	7	60	220	36	ENST00000248566.2	0.3	0.260965
ACN9	57001	__UNKNOWN__	__UNKNOWN__	7	96780163	96780163	__UNKNOWN__	Intron	SNP	C	C	T	rs545613912	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:96780163C>T	ENST00000360382.4	+	2	255				ACN9_ENST00000432641.2_Intron|ACN9_ENST00000479853.1_Intron					ACN9 homolog (S. cerevisiae)	NA		NA								large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(3)	10	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)					tgtgagccaccgcacccggcc	0.537		NA											C|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	14558	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC028409	CCDS5648.1	7q22.1	2006-02-09			ENSG00000196636	ENSG00000196636	57001			21752	protein-coding gene	gene with protein product		615773			NA		Standard	NM_020186	NM_020186	NA	Approved	DC11	uc003uoo.4	Q9NRP4	OTTHUMG00000154064	ENST00000360382.4:c.204+14384C>T	chr7.hg19:g.96780163C>T		NA		hg19		0.02	-0.201597	CACxGCA	COVERED																																																																																			NOVEL	ACN9-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000333686.3	6	2.707328	KEEP	0	0	0	9	261	CC	0.99254	0.518266	0		+	3	60	95	0	0	7.193516	18	60	555	46	ENST00000360382.4	0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	96867360	96867360	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:96867360A>G			NA	NA				ACN9 (56285 upstream) : AC004745.1 (53465 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.96867360A>G		NA		hg19		0.02	-0.324481	CACxCCT	COVERED																																																																																			NOVEL					0			7	4.509167	KEEP	2	0	0	15	393	AA	0.995343	0.831824	0			3	60	94	1	0	6.468702	30	60	874	82		0.090909	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	97596149	97596149	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:97596149G>A			NA	NA				MIR5692C2 (2356 upstream) : OCM2 (17846 downstream)						NA		NA									NA						AGGTTGGAGAGGAAGAAGTAC	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.97596149G>A		NA		hg19		0.02	-0.210519	AGAxGAA	UNCOVERED																																																																																			NOVEL					0			3	2.708363	KEEP	19	0	0	9	287	GG	0	0	0			3	22	89	1	0	6.406468	21	47	691	66		0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	97596155	97596155	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:97596155A>C			NA	NA				MIR5692C2 (2362 upstream) : OCM2 (17840 downstream)						NA		NA									NA						GAGAGGAAGAAGTACATGGGG	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.97596155A>C		NA		hg19		0.02	-0.210488	AGAxGTA	UNCOVERED																																																																																			NOVEL					0			3	2.70713	KEEP	17	0	0	9	251	AA	0	0	0			3	22	91	0	0	6.60648	21	47	624	63		0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	97601976	97601976	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:97601976A>G			NA	NA				MIR5692C2 (8183 upstream) : OCM2 (12019 downstream)						NA		NA									NA						ccaagtagctaggattacagg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.97601976A>G		NA		hg19		0.02	-0.403464	GCTxGGA	COVERED																																																																																			NOVEL					0			14	2.870399	KEEP	0	2	61	31	840	AA	0.999998	0.93449	0			3	60	103	0	0	6.977184	41	60	1230	107		0.068182	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	97719113	97719113	__UNKNOWN__	IGR	SNP	T	T	G	rs148036852		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:97719113T>G			NA	NA				RN7SL13P (65825 upstream) : LMTK2 (17083 downstream)						NA		NA									NA						GGttttttttttttttttttt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.97719113T>G		NA		hg19		0.02	-0.05263	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			27	3.007056	KEEP	10	0	0	10	266	TT	0	0	0			4	60	136	0	0	14.421962	1	60	29	35		0.8	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	97719119	97719119	__UNKNOWN__	IGR	SNP	T	T	G	rs28382312	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:97719119T>G			NA	NA				RN7SL13P (65831 upstream) : LMTK2 (17077 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.443		NA											T|||	1504	0.300319	0.2148	0.3689	5008	,	,	NA	24798	0.3462	NA	0.3897	False	NA	,,,	NA	NA	NA	2504	0.228	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.97719119T>G		NA		hg19		0.02	-0.052628	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			24	3.007295	KEEP	11	0	0	10	270	TT	0	0	0			4	60	138	0	0	14.622035	1	60	29	32		0.8	0.036766
BAIAP2L1	55971	__UNKNOWN__	__UNKNOWN__	7	98023289	98023289	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98023289C>T	ENST00000005260.8	-	1	267				BAIAP2L1_ENST00000462558.1_Intron	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	NA		NA			filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			cggtggctcacgcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453	55971			21649	protein-coding gene	gene with protein product		611877			NA		Standard	NM_018842	NM_018842	NA	Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.51+6824G>A	chr7.hg19:g.98023289C>T		NA	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	hg19	CCDS34687.1	0.02	-0.16665	TCAxGCC	COVERED																																																																																			NOVEL	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334681.1	6	4.512026	KEEP	2	0	0	15	441	CC	0.994391	0.351961	0		-	3	60	92	0	0	7.372344	12	60	380	51	ENST00000005260.8	0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	98075736	98075736	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98075736T>C			NA	NA				BAIAP2L1 (45356 upstream) : NPTX2 (170872 downstream)						NA		NA									NA						ctggctaacatggtgaaaccc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.98075736T>C		NA		hg19		0.02	-0.070164	ACAxGGT	UNCOVERED																																																																																			NOVEL					0			6	3.00817	KEEP	4	0	0	10	284	TT	0	0	0			3	60	90	0	0	8.132472	5	60	150	21		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	98260696	98260696	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98260696C>T			NA	NA				NPTX2 (1516 upstream) : RNU6-393P (131644 downstream)						NA		NA									NA						ggtgcgatctcggctcactgc	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.98260696C>T		NA		hg19		0.02	-0.157888	TCTxGGC	COVERED																																																																																			NOVEL					0			7	2.707673	KEEP	4	0	0	9	269	AC	0.99257	0.320408	0			3	23	84	1	0	6.672883	11	60	378	47		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	98260705	98260705	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98260705G>A			NA	NA				NPTX2 (1525 upstream) : RNU6-393P (131635 downstream)						NA		NA									NA						tcggctcactgcaacctccac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.98260705G>A		NA		hg19		0.02	-0.149131	ACTxCAA	UNCOVERED																																																																																			NOVEL					0			7	2.707877	KEEP	4	0	0	9	275	GG	0	0	0			3	23	90	0	0	7.272703	11	60	381	45		0.214286	0.292001
TRRAP	8295	__UNKNOWN__	__UNKNOWN__	7	98575050	98575050	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98575050A>G	ENST00000446306.3	+	53	8371				TRRAP_ENST00000355540.3_Intron|TRRAP_ENST00000359863.4_Intron			Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	NA		NA			chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ccaaagtgctaggattacagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367	8295			12347	protein-coding gene	gene with protein product		603015			NA	9708738, 9885574	Standard	NM_003496	NM_003496	NA	Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000446306.3:c.8310+351A>G	chr7.hg19:g.98575050A>G		NA	A4D265|O75218|Q9Y631|Q9Y6H4	hg19		0.02	-0.096481	GCTxGGA	UNCOVERED																																																																																			NOVEL	TRRAP-004	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000317981.3	5	2.406102	KEEP	0	0	0	8	220	AA	0.99257	0.119541	0		+	4	60	129	0	0	11.677201	7	60	208	27	ENST00000446306.3	0.363636	0.120436
ARPC1A	10552	__UNKNOWN__	__UNKNOWN__	7	98934482	98934482	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98934482T>C	ENST00000262942.5	+	3	188				ARPC1A_ENST00000432884.2_Intron	NM_001190996.1|NM_006409.3	NP_001177925.1|NP_006400.2	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex, subunit 1A, 41kDa	NA		NA			actin cytoskeleton organization (GO:0030036)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of actin filament polymerization (GO:0030833)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|liver(2)|lung(7)|ovary(1)|prostate(1)	19	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			tcgtggctcatgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y08999	CCDS5660.1	7q22.1	2013-03-14	2002-08-29		ENSG00000241685	ENSG00000241685	10552		Actin related protein 2/3 complex subunits, WD repeat domain containing	703	protein-coding gene	gene with protein product	actin binding protein (Schizosaccharomyces pombe sop2-like), SOP2-like protein	604220	actin related protein 2/3 complex, subunit 1A (41 kD)		NA	8978670, 9230079	Standard	NM_006409	NM_006409	NA	Approved	SOP2Hs, SOP2L, Arc40	uc003upx.2	Q92747	OTTHUMG00000154553	ENST00000262942.5:c.65-1322T>C	chr7.hg19:g.98934482T>C		NA	A4D276|B4DLQ7|D6W5S1|Q7Z5U8|Q86WU5|Q8IXQ0	hg19	CCDS5660.1	0.02	-0.271863	TCAxGCC	COVERED																																																																																			NOVEL	ARPC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335908.1	8	2.405827	KEEP	1	0	0	8	218	TT	0.99257	0.711986	0		+	4	60	130	0	0	9.733801	27	60	782	53	ENST00000262942.5	0.129032	0.717315
PDAP1	11333	__UNKNOWN__	__UNKNOWN__	7	98999191	98999191	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:98999191G>A	ENST00000350498.3	-	4	494					NM_014891.6	NP_055706.1	Q13442	HAP28_HUMAN	PDGFA associated protein 1	NA		NA			cell proliferation (GO:0008283)|signal transduction (GO:0007165)		poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)|prostate(1)|skin(1)	9	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			caggtgatccgcccgccttgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41745	CCDS5662.1	7q	2008-07-18			ENSG00000106244	ENSG00000106244	11333			14634	protein-coding gene	gene with protein product	PDGF associated protein	607075			NA	8780057	Standard	NM_014891	NM_014891	NA	Approved	PAP1, PAP, HASPP28	uc003uqe.3	Q13442	OTTHUMG00000154629	ENST00000350498.3:c.214-1144C>T	chr7.hg19:g.98999191G>A		NA	D6W5S5|Q92906	hg19	CCDS5662.1	0.02	-0.166577	TCCxCCC	COVERED																																																																																			NOVEL	PDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000336388.2	8	3.909685	KEEP	1	0	0	13	380	GG	0.995343	0.352299	0		-	3	60	84	0	0	6.393322	14	60	438	51	ENST00000350498.3	0.176471	0.353947
ZNF789	285989	__UNKNOWN__	__UNKNOWN__	7	99078105	99078105	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99078105C>T	ENST00000448667.1	+	4	455				ZNF789_ENST00000493485.1_Intron|ZNF789_ENST00000331410.5_Intron|ZNF789_ENST00000379724.3_Intron|ZNF789_ENST00000483089.1_3'UTR			Q5FWF6	ZN789_HUMAN	zinc finger protein 789	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)	11	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					ctaagggtttcacataaggga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093141	CCDS34693.1, CCDS34694.1	7q22.1	2013-01-08			ENSG00000198556	ENSG00000198556	285989		Zinc fingers, C2H2-type, -	27801	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_213603	XM_005250281	NA	Approved		uc003uqq.1	Q5FWF6	OTTHUMG00000154601	ENST00000448667.1:c.130+695C>T	chr7.hg19:g.99078105C>T		NA	A4D282|A6NH61|Q6ZMZ9	hg19		0.02	1.292038	TTTxACA	COVERED																																																																																			NOVEL	ZNF789-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000336251.1	2	4.813859	KEEP	0	0	0	16	482	CC	0.997832	0.997694	0		+	25	60	733	0	0	62.276248	64	60	2159	159	ENST00000448667.1	0.280899	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	99233436	99233436	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99233436T>C			NA	NA				ZSCAN25 (3406 upstream) : CYP3A5 (12380 downstream)						NA		NA									NA						tttgggaggctgaggcgggcg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.99233436T>C		NA		hg19		0.02	-0.192955	GGCxGAG	COVERED																																																																																			NOVEL					0			10	3.008167	KEEP	4	0	0	10	284	TT	0.99257	0.454356	0			5	60	173	0	0	14.565841	17	60	514	49		0.227273	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	99299987	99299987	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99299987C>T			NA	NA				CYP3A5 (22366 upstream) : CYP3A7 (2679 downstream)						NA		NA									NA						gtgctgggatcacaggcatga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.99299987C>T		NA		hg19		0.02	-0.105239	GATxACA	UNCOVERED																																																																																			NOVEL					0			2	2.407028	KEEP	1	0	0	8	240	CC	0	0	0			3	60	87	0	0	7.478687	7	60	210	26		0.3	0.139832
TRIM4	89122	__UNKNOWN__	__UNKNOWN__	7	99509900	99509900	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99509900C>T	ENST00000355947.2	-	3	601				TRIM4_ENST00000354241.5_Intron|TRIM4_ENST00000349062.2_Intron	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	NA		NA			protein trimerization (GO:0070206)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				acgcctgtaaccccagcattt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF220023	CCDS5678.1, CCDS5679.1	7q22-q31.1	2013-01-09	2011-01-25		ENSG00000146833	ENSG00000146833	89122		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	16275	protein-coding gene	gene with protein product	tripartite motif protein TRIM4, tripartite motif protein 4	NA	tripartite motif-containing 4		NA	11331580	Standard	NM_033017	NM_033017	NA	Approved	RNF87	uc003use.3	Q9C037	OTTHUMG00000156648	ENST00000355947.2:c.472-2617G>A	chr7.hg19:g.99509900C>T		NA	A4D298|Q75MK1|Q96F06|Q9C036	hg19	CCDS5679.1	0.02	-0.210507	TAAxCCC	COVERED																																																																																			NOVEL	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345050.1	7	2.707954	KEEP	0	0	0	9	273	CC	0.99254	0.518266	0		-	3	60	100	0	0	7.760792	17	60	570	49	ENST00000355947.2	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	99745048	99745048	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99745048G>A			NA	NA				AC073842.19 (6986 upstream) : LAMTOR4 (1481 downstream)						NA		NA									NA						cagcctcccgggtagctggga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.99745048G>A		NA		hg19		0.02	-0.149123	CCGxGTA	UNCOVERED																																																																																			NOVEL					0			7	2.40724	KEEP	2	0	0	8	247	GG	0	0	0			3	60	87	0	0	6.872345	12	60	401	37		0.2	0.292001
GAL3ST4	79690	__UNKNOWN__	__UNKNOWN__	7	99759908	99759908	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99759908A>G	ENST00000360039.4	-	4	822				GAL3ST4_ENST00000413800.1_Intron|GAL3ST4_ENST00000411994.1_Intron|GAL3ST4_ENST00000423751.1_Intron|GAL3ST4_ENST00000426974.2_Intron	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	NA		NA			cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					agtgactcacacctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093	79690		Sulfotransferases, membrane-bound	24145	protein-coding gene	gene with protein product		608235			NA	11333265	Standard	NM_024637	NM_024637	NA	Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.430-1326T>C	chr7.hg19:g.99759908A>G		NA	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	hg19	CCDS5688.1	0.02	-0.280617	CACxCCT	COVERED																																																																																			NOVEL	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337495.2	8	3.606265	KEEP	1	0	0	12	310	AA	0.993072	0.734547	0		-	3	60	92	0	0	6.40014	27	60	773	66	ENST00000360039.4	0.1	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	99878431	99878431	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99878431T>C			NA	NA				GATS (8576 upstream) : SPDYE3 (26893 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.99878431T>C		NA		hg19		0.02	-0.131554	ATCxCAG	COVERED																																																																																			NOVEL					0			4	3.606697	KEEP	0	0	0	12	323	TT	0.993634	0.227714	0			3	60	107	0	0	9.20147	9	60	265	41		0.25	0.229173
PILRB	29990	__UNKNOWN__	__UNKNOWN__	7	99935592	99935592	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:99935592T>C	ENST00000610247.1	+	2	224				STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)				endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ggattacaggtgtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716	29990		Immunoglobulin superfamily / V-set domain containing	18297	protein-coding gene	gene with protein product		605342			NA	10660620	Standard	NM_178238	NM_178238	NA	Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000610247.1:c.-2272-210T>C	chr7.hg19:g.99935592T>C		NA	Q69YF9|Q9HBS0	hg19	CCDS43622.1	0.02	-0.236802	AGGxGTG	COVERED																																																																																			NOVEL	PILRB-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		8	3.007659	KEEP	1	0	0	10	279	TT	0.992708	0.607941	0		+	4	37	129	0	0	10.368935	17	60	512	56	ENST00000610247.1	0.190476	0.612407
TSC22D4	81628	__UNKNOWN__	__UNKNOWN__	7	100075975	100075975	__UNKNOWN__	Intron	SNP	T	T	A	rs563266932|rs10250551|rs35439211		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100075975T>A	ENST00000393991.1	-	1	439				TSC22D4_ENST00000300181.2_Intron			Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					agagagagagtgtgtgtgtgt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925	81628			21696	protein-coding gene	gene with protein product		611914			NA		Standard	NM_030935	NM_030935	NA	Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000393991.1:c.137+441A>T	chr7.hg19:g.100075975T>A		NA	A4D2C3|A8MWR6|D6W5V9	hg19		0.02	-0.070028	GAGxGTG	UNCOVERED																																																																																			NOVEL	TSC22D4-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000316971.1	7	2.691174	KEEP	6	0	0	9	228	TT	0	0	0		-	3	60	67	0	0	6.655361	2	60	56	28	ENST00000393991.1	0.6	0.054137
FBXO24	26261	__UNKNOWN__	__UNKNOWN__	7	100184961	100184961	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100184961A>T	ENST00000241071.6	+	1	361				FBXO24_ENST00000360609.2_Intron|FBXO24_ENST00000465843.1_Intron|FBXO24_ENST00000498195.1_Intron	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	NA		NA			protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					agtctcgctcagtcgcccagg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336	26261		F-boxes /  other	13595	protein-coding gene	gene with protein product		609097	F-box only protein 24		NA	10531035, 10531037	Standard		NM_012172	NA	Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.39+674A>T	chr7.hg19:g.100184961A>T		NA	A4D2D4|B4DX91|B4DY42|Q9H0G1	hg19	CCDS5698.1	0.02	-0.184169	CTCxGTC	COVERED																																																																																			NOVEL	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356104.1	3	2.705169	KEEP	0	0	0	9	238	AA	0.99254	0.420319	0		+	3	60	87	0	0	6.610991	15	60	437	45	ENST00000241071.6	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	100396797	100396797	__UNKNOWN__	IGR	SNP	C	C	T	rs73170790|rs374457348|rs150636326	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100396797C>T			NA	NA				ZAN (1378 upstream) : EPHB4 (3389 downstream)						NA		NA									NA						ccttccttccctccttccttc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.100396797C>T		NA		hg19		0.02	-0.131584	TCCxTCC	COVERED																																																																																			NOVEL					0			3	2.708084	KEEP	0	0	0	9	276	CC	0.99254	0.227464	0			3	60	91	0	1	7.372729	11	60	377	29		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	100550850	100550850	__UNKNOWN__	IGR	SNP	C	C	G	rs62483691		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100550850C>G			NA	NA				MUC3A (426 upstream) : MUC3A (399 downstream)						NA		NA									NA						TCACCACCACCGAGACCACCT	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C		126,1626		0,126,750	291	272	278		1431	-3.7	0	7	dbSNP_129	278	554,3428		0,554,1437	no	coding-synonymous	MUC3A	XM_001725354.4		0,680,2187	GG,GC,CC	NA	13.9126,7.1918,11.8591		477/1487	100550850	680,5054	876	1991	2867	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.100550850C>G		NA		hg19		0.02	27.21471	CACxGAG	COVERED																																																																																			NOVEL					0			199	42.36616	KEEP	284	42	1190	561	16375	CT	1	1	0			17	60	566	2	0	53.363117	21	60	662	1877		0.447368	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	100711266	100711266	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100711266G>A			NA	NA				MUC17 (9246 upstream) : TRIM56 (17453 downstream)						NA		NA									NA						gtgcaatctcggctcactgca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.100711266G>A		NA		hg19		0.02	-0.21924	CTCxGCT	COVERED																																																																																			NOVEL					0			36	3.266147	KEEP	19	2	51	29	791	GG	0.999863	0.58285	0			3	60	86	0	0	6.592417	14	60	430	72		0.176471	0.58293
TRIM56	81844	__UNKNOWN__	__UNKNOWN__	7	100729584	100729584	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100729584A>G	ENST00000306085.6	+	2	133					NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	NA		NA			defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					gctcacgcctataatcccagc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(89;1092 1379 22756 38989 39611)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871	81844		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	19028	protein-coding gene	gene with protein product		NA	tripartite motif-containing 56		NA		Standard	NM_030961	NM_030961	NA	Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.-164-703A>G	chr7.hg19:g.100729584A>G		NA	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	hg19	CCDS43625.1	0.02	-0.149083	CCTxTAA	COVERED																																																																																			NOVEL	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347185.1	5	2.705094	KEEP	0	0	0	9	229	AA	0.99254	0.289823	0		+	3	60	94	0	1	7.479378	13	60	368	36	ENST00000306085.6	0.1875	0.292001
TRIM56	81844	__UNKNOWN__	__UNKNOWN__	7	100733656	100733656	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:100733656G>A	ENST00000306085.6	+	0	3360				TRIM56_ENST00000487252.1_3'UTR	NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	NA		NA			defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					ctataatcccggcactttggg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(89;1092 1379 22756 38989 39611)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871	81844		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	19028	protein-coding gene	gene with protein product		NA	tripartite motif-containing 56		NA		Standard	NM_030961	NM_030961	NA	Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.*795G>A	chr7.hg19:g.100733656G>A		NA	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	hg19	CCDS43625.1	0.02	1.429782	CCCxGCA	COVERED																																																																																			NOVEL	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347185.1	8	6.614453	KEEP	0	0	0	22	594	GG	0.999879	0.992805	0		+	6	60	169	0	0	11.642572	47	60	1450	101	ENST00000306085.6	0.113208	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	101375621	101375621	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:101375621G>A			NA	NA				MYL10 (103045 upstream) : CUX1 (83337 downstream)						NA		NA									NA						gtgaatccccgtctctactaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.101375621G>A		NA		hg19		0.02	-0.114009	CCCxTCT	UNCOVERED																																																																																			NOVEL					0			7	2.406406	KEEP	0	0	0	8	227	GG	0.99257	0.16126	0			3	60	90	0	0	7.77863	7	60	215	24		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	101445748	101445748	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:101445748A>G			NA	NA				MYL10 (173172 upstream) : CUX1 (13210 downstream)						NA		NA									NA						cctgacctcaagtgatccacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.101445748A>G		NA		hg19		0.02	-0.149114	TCAxGTG	UNCOVERED																																																																																			NOVEL					0			7	2.40546	KEEP	5	0	0	8	215	AA	0	0	0			3	60	102	0	0	8.472815	11	60	337	46		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	101449876	101449876	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:101449876T>A			NA	NA				MYL10 (177300 upstream) : CUX1 (9082 downstream)						NA		NA									NA						ggtggctcactcctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.101449876T>A		NA		hg19		0.02	-0.157863	CACxCCT	COVERED																																																																																			NOVEL					0			7	3.609957	KEEP	1	0	0	12	345	TT	0.994391	0.385234	0			3	60	90	0	0	7.079253	13	60	386	51		0.1875	0.387407
CUX1	1523	__UNKNOWN__	__UNKNOWN__	7	101681083	101681083	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:101681083T>C	ENST00000560541.1	+	3	810				CUX1_ENST00000292538.4_Intron|CUX1_ENST00000550008.2_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000549414.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000546411.2_Intron|CUX1_ENST00000360264.3_Intron|CUX1_ENST00000292535.7_Intron|CUX1_ENST00000556210.1_Intron			P39880	CUX1_HUMAN	cut-like homeobox 1	NA		NA			auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						gcctgtaatctcagcactttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923	1523		Homeoboxes / CUT class	2557	protein-coding gene	gene with protein product	golgi integral membrane protein 6	116896	cut (Drosophila)-like 1 (CCAAT displacement protein), cut-like 1, CCAAT displacement protein (Drosophila)	CUTL1	NA	8468066, 9799793, 15004235	Standard	NM_001913	NM_001202543	NA	Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000560541.1:c.810+9658T>C	chr7.hg19:g.101681083T>C		NA	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	hg19		0.02	-0.166651	ATCxCAG	COVERED																																																																																			NOVEL	CUX1-019	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000418419.1	6	3.307608	KEEP	3	0	0	11	302	TT	0.993072	0.351495	0		+	3	60	99	0	0	7.978889	13	60	394	48	ENST00000560541.1	0.1875	0.353947
RASA4B	100271927	__UNKNOWN__	__UNKNOWN__	7	102146730	102146730	__UNKNOWN__	Intron	SNP	G	G	A	rs79703831		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:102146730G>A	ENST00000465829.1	-	5	499				RASA4B_ENST00000306682.6_Intron|RASA4B_ENST00000541662.1_Intron|RP11-514P8.8_ENST00000481893.1_RNA			C9J798	RAS4B_HUMAN	RAS p21 protein activator 4B	NA		NA			intracellular signal transduction (GO:0035556)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			skin(1)	1						atacagtctcgcttgtcaccc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS59506.1	7q22.1	2013-01-10			ENSG00000170667	ENSG00000170667	100271927		Pleckstrin homology (PH) domain containing	35202	protein-coding gene	gene with protein product		NA			NA		Standard	XM_003118600	NM_001277335	NA	Approved		uc003uzu.2	C9J798	OTTHUMG00000022944	ENST00000465829.1:c.428+411C>T	chr7.hg19:g.102146730G>A		NA		hg19		0.02	-0.21053	CTCxCTT	COVERED																																																																																			NOVEL	RASA4B-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000059600.6	9	3.308596	KEEP	4	0	0	11	317	GG	0.992708	0.518353	0		-	5	49	146	0	0	13.022072	9	50	308	61	ENST00000465829.1	0.357143	0.522161
ARMC10	83787	__UNKNOWN__	__UNKNOWN__	7	102739179	102739179	__UNKNOWN__	3'UTR	SNP	A	A	G	rs34745227		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:102739179A>G	ENST00000441711.2	+	0	1498				ARMC10_ENST00000541300.1_3'UTR|ARMC10_ENST00000323716.3_3'UTR|ARMC10_ENST00000425331.1_3'UTR|ARMC10_ENST00000454559.1_3'UTR|ARMC10_ENST00000428183.2_3'UTR	NM_001161009.2	NP_001154481.1	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	NA		NA			regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						TGCCAAGTGAATATAAGAGCT	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632	83787		Armadillo repeat containing	21706	protein-coding gene	gene with protein product	specific Splicing Variant involved in Hepatocarcinogenesis	611864			NA	12839973	Standard	NM_031905	NM_031905	NA	Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000441711.2:c.*179A>G	chr7.hg19:g.102739179A>G		NA	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	hg19	CCDS55146.1	0.02	1.798647	TGAxTAT	COVERED																																																																																			NOVEL	ARMC10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347884.1	2	2.707186	KEEP	5	0	0	9	256	AA	0.99254	0.992377	0		+	10	44	342	0	0	25.344939	80	60	2405	139	ENST00000441711.2	0.111111	0.999835
ARMC10	83787	__UNKNOWN__	__UNKNOWN__	7	102739945	102739945	__UNKNOWN__	3'UTR	SNP	C	C	T	rs200460623		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:102739945C>T	ENST00000441711.2	+	0	2264				ARMC10_ENST00000541300.1_3'UTR|ARMC10_ENST00000323716.3_3'UTR|ARMC10_ENST00000425331.1_3'UTR|ARMC10_ENST00000454559.1_3'UTR|ARMC10_ENST00000428183.2_3'UTR	NM_001161009.2	NP_001154481.1	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	NA		NA			regulation of growth (GO:0040008)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	11						GATGGAGCTCCGAATGTGCTT	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY150853	CCDS5728.1, CCDS55145.1, CCDS55146.1, CCDS55147.1, CCDS55148.1, CCDS55149.1	7q22.1	2013-02-14			ENSG00000170632	ENSG00000170632	83787		Armadillo repeat containing	21706	protein-coding gene	gene with protein product	specific Splicing Variant involved in Hepatocarcinogenesis	611864			NA	12839973	Standard	NM_031905	NM_031905	NA	Approved	MGC3195, SVH	uc003vaw.2	Q8N2F6	OTTHUMG00000157201	ENST00000441711.2:c.*945C>T	chr7.hg19:g.102739945C>T		NA	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	hg19	CCDS55146.1	0.02	10.16845	CTCxGAA	COVERED																																																																																			NOVEL	ARMC10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347884.1	227	40.043441	KEEP	25	12	318	246	6796	CC	1	1	0		+	14	33	404	0	0	22.344422	297	60	9120	860	ENST00000441711.2	0.045016	1
SLC26A5	375611	__UNKNOWN__	__UNKNOWN__	7	103024802	103024802	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:103024802C>G	ENST00000306312.3	-	15	1776				SLC26A5_ENST00000354356.4_Intron|SLC26A5_ENST00000393723.1_Intron|SLC26A5_ENST00000393730.1_Intron|SLC26A5_ENST00000393729.1_Intron|SLC26A5_ENST00000432958.2_Intron|SLC26A5_ENST00000339444.6_Intron|SLC26A5_ENST00000393735.2_Intron|SLC26A5_ENST00000393727.1_Intron|SLC26A5_ENST00000356767.4_Intron	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	NA		NA			regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)			endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						gctcatgcctctaatcccagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615	375611		Solute carriers	9359	protein-coding gene	gene with protein product	deafness, neurosensory, autosomal recessive, 61	604943	prestin (motor protein)	PRES	NA	10821263	Standard	NM_198999	NM_206883	NA	Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.1515-3806G>C	chr7.hg19:g.103024802C>G		NA	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	hg19	CCDS5733.1	0.02	-0.157904	CCTxTAA	COVERED																																																																																			NOVEL	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313860.1	6	3.00914	KEEP	1	0	0	10	315	CC	0.992708	0.320453	0		-	3	60	104	1	0	8.30973	15	60	516	44	ENST00000306312.3	0.166667	0.322807
LHFPL3	375612	__UNKNOWN__	__UNKNOWN__	7	104243613	104243613	__UNKNOWN__	Intron	SNP	T	T	C	rs145743691|rs9640679		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:104243613T>C	ENST00000401970.2	+	2	525				LHFPL3_ENST00000424859.1_Intron|LHFPL3_ENST00000535008.1_Intron|LHFPL3_ENST00000543266.1_Intron			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	NA		NA				integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)	9						ttccttcctttctttctttct	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416	375612			6589	protein-coding gene	gene with protein product		609719	lipoma HMGIC fusion partner-like 4	LHFPL4	NA	10329012	Standard	NM_199000	NM_199000	NA	Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000401970.2:c.404-133509T>C	chr7.hg19:g.104243613T>C		NA	A1L383|A4D0Q5	hg19		0.02	-0.070175	CTTxCTT	UNCOVERED																																																																																			NOVEL	LHFPL3-002	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000348284.1	8	2.405685	KEEP	0	0	0	8	216	TT	0.99257	0.053735	0		+	3	60	102	2	0	9.332914	5	60	156	22	ENST00000401970.2	0.375	0.054137
LHFPL3	375612	__UNKNOWN__	__UNKNOWN__	7	104249452	104249452	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:104249452G>A	ENST00000401970.2	+	2	525				LHFPL3_ENST00000424859.1_Intron|LHFPL3_ENST00000535008.1_Intron|LHFPL3_ENST00000543266.1_Intron			Q86UP9	LHPL3_HUMAN	lipoma HMGIC fusion partner-like 3	NA		NA				integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(6)	9						ggtggctcacgcctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY260763		7q22.2	2006-06-13			ENSG00000187416	ENSG00000187416	375612			6589	protein-coding gene	gene with protein product		609719	lipoma HMGIC fusion partner-like 4	LHFPL4	NA	10329012	Standard	NM_199000	NM_199000	NA	Approved		uc003vce.3	Q86UP9	OTTHUMG00000157273	ENST00000401970.2:c.404-127670G>A	chr7.hg19:g.104249452G>A		NA	A1L383|A4D0Q5	hg19		0.02	-0.210529	CACxCCT	COVERED																																																																																			NOVEL	LHFPL3-002	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000348284.1	12	3.609574	KEEP	1	0	0	12	351	GG	0.993072	0.518544	0		+	3	60	92	0	0	6.827315	19	60	620	53	ENST00000401970.2	0.136364	0.522161
SRPK2	6733	__UNKNOWN__	__UNKNOWN__	7	104795477	104795477	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:104795477G>C	ENST00000393651.3	-	7	709				SRPK2_ENST00000489828.1_Intron|SRPK2_ENST00000357311.3_Intron	NM_182692.1	NP_872634.1			SRSF protein kinase 2	NA		NA								NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						acccaggctggagtgcaatgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250	6733			11306	protein-coding gene	gene with protein product	SR protein kinase 2, serine/arginine-rich splicing factor kinase 2	602980	SFRS protein kinase 2		NA	8208298, 9472028	Standard	NM_182691	NM_182692	NA	Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.621+5476C>G	chr7.hg19:g.104795477G>C		NA		hg19	CCDS34724.1	0.02	-0.096484	CTGxAGT	UNCOVERED																																																																																			NOVEL	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348723.1	5	3.309863	KEEP	0	0	0	11	338	GG	0.993072	0.119602	0		-	5	60	166	0	0	16.300189	4	60	127	27	ENST00000393651.3	0.555556	0.120436
SRPK2	6733	__UNKNOWN__	__UNKNOWN__	7	104941657	104941657	__UNKNOWN__	Intron	SNP	G	G	A	rs572923897	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:104941657G>A	ENST00000393651.3	-	2	159					NM_182692.1	NP_872634.1			SRSF protein kinase 2	NA		NA								NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						ttgggaggccgaggcaggcgg	0.488		NA											G|||	6	0.00119808	0.0008	0.0	5008	,	,	NA	14696	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250	6733			11306	protein-coding gene	gene with protein product	SR protein kinase 2, serine/arginine-rich splicing factor kinase 2	602980	SFRS protein kinase 2		NA	8208298, 9472028	Standard	NM_182691	NM_182692	NA	Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.71+87437C>T	chr7.hg19:g.104941657G>A		NA		hg19	CCDS34724.1	0.02	-0.131569	GCCxAGG	COVERED																																																																																			NOVEL	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348723.1	3	3.308857	KEEP	1	0	0	11	313	GG	0.993072	0.227586	0		-	3	60	80	0	0	6.382043	10	60	329	38	ENST00000393651.3	0.230769	0.229173
SRPK2	6733	__UNKNOWN__	__UNKNOWN__	7	104971747	104971747	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:104971747C>T	ENST00000393651.3	-	2	159					NM_182692.1	NP_872634.1			SRSF protein kinase 2	NA		NA								NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						cagagcgagactccgtctcaa	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250	6733			11306	protein-coding gene	gene with protein product	SR protein kinase 2, serine/arginine-rich splicing factor kinase 2	602980	SFRS protein kinase 2		NA	8208298, 9472028	Standard	NM_182691	NM_182692	NA	Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.71+57347G>A	chr7.hg19:g.104971747C>T		NA		hg19	CCDS34724.1	0.02	-0.1228	AGAxTCC	UNCOVERED																																																																																			NOVEL	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348723.1	19	4.812227	KEEP	16	0	0	16	468	CC	0	0	0		-	3	25	83	0	0	6.801008	9	60	306	41	ENST00000393651.3	0.25	0.196312
SRPK2	6733	__UNKNOWN__	__UNKNOWN__	7	104974379	104974379	__UNKNOWN__	Intron	SNP	G	G	T	rs369713051		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:104974379G>T	ENST00000393651.3	-	2	159					NM_182692.1	NP_872634.1			SRSF protein kinase 2	NA		NA								NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(11)|large_intestine(6)|lung(4)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	35						gttttgttttgtttttttgag	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U88666	CCDS5735.1, CCDS34724.1	7q22-q31.1	2010-06-23	2010-06-23		ENSG00000135250	ENSG00000135250	6733			11306	protein-coding gene	gene with protein product	SR protein kinase 2, serine/arginine-rich splicing factor kinase 2	602980	SFRS protein kinase 2		NA	8208298, 9472028	Standard	NM_182691	NM_182692	NA	Approved	SFRSK2	uc003vcv.4	P78362	OTTHUMG00000157405	ENST00000393651.3:c.71+54715C>A	chr7.hg19:g.104974379G>T		NA		hg19	CCDS34724.1	0.02	-0.210544	TTTxTTT	COVERED																																																																																			NOVEL	SRPK2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348723.1	13	3.611158	KEEP	0	0	0	12	380	GG	0.993634	0.518837	0		-	3	60	88	1	0	6.306439	21	60	737	53	ENST00000393651.3	0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	105069490	105069490	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:105069490C>T			NA	NA				SRPK2 (40149 upstream) : PUS7 (27467 downstream)						NA		NA									NA						tcccaaagtgctggtattaca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.105069490C>T		NA		hg19		0.02	-0.17544	GTGxTGG	COVERED																																																																																			NOVEL					0			12	3.911446	KEEP	0	0	0	13	392	CC	0.994391	0.385234	0			3	60	84	0	0	6.311114	15	60	512	42		0.166667	0.387407
RINT1	60561	__UNKNOWN__	__UNKNOWN__	7	105207013	105207013	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:105207013A>G	ENST00000257700.2	+	15	2417				EFCAB10_ENST00000480514.1_Intron|EFCAB10_ENST00000485614.1_Intron|EFCAB10_ENST00000486180.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	NA		NA			G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						tagctacttgagaggctgagg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249	60561			21876	protein-coding gene	gene with protein product		610089			NA	11096100, 15029241	Standard	NM_021930	NM_021930	NA	Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.2187-553A>G	chr7.hg19:g.105207013A>G		NA	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	hg19	CCDS34726.1	0.02	3.845207	TTGxGAG	COVERED																																																																																			NOVEL	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348686.1	65	14.755857	KEEP	0	7	210	123	3297	AA	1	1	0		+	5	60	171	0	0	10.485164	114	60	3344	354	ENST00000257700.2	0.042017	1
CDHR3	222256	__UNKNOWN__	__UNKNOWN__	7	105674079	105674079	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:105674079G>A	ENST00000317716.9	+	0	3674				CDHR3_ENST00000542731.1_3'UTR|CDHR3_ENST00000343407.5_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	NA		NA			homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ccagctacttgggaggctgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536	222256		Cadherins / Cadherin-related	26308	protein-coding gene	gene with protein product		615610			NA		Standard	NM_152750	NM_152750	NA	Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.*936G>A	chr7.hg19:g.105674079G>A		NA	Q8TCI7	hg19	CCDS47684.1	0.02	-0.201761	CTTxGGA	COVERED																																																																																			NOVEL	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349025.2	2	2.339575	KEEP	0	1	26	17	516	GG	0.999859	0.490475	0		+	3	60	90	1	0	6.565616	20	60	667	45	ENST00000317716.9	0.130435	0.490544
CDHR3	222256	__UNKNOWN__	__UNKNOWN__	7	105674156	105674156	__UNKNOWN__	3'UTR	SNP	T	T	C	rs190132223	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:105674156T>C	ENST00000317716.9	+	0	3751				CDHR3_ENST00000542731.1_3'UTR|CDHR3_ENST00000343407.5_3'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	NA		NA			homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						cactgcactctagcctgggtg	0.428		NA											t|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	19391	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536	222256		Cadherins / Cadherin-related	26308	protein-coding gene	gene with protein product		615610			NA		Standard	NM_152750	NM_152750	NA	Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.*1013T>C	chr7.hg19:g.105674156T>C		NA	Q8TCI7	hg19	CCDS47684.1	0.02	3.707207	CTCxAGC	COVERED																																																																																			NOVEL	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349025.2	27	5.101755	KEEP	0	6	179	80	2140	TT	1	0.999999	0		+	6	60	190	0	0	11.738897	105	60	3081	310	ENST00000317716.9	0.054054	0.999999
PIK3CG	5294	__UNKNOWN__	__UNKNOWN__	7	106547578	106547578	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:106547578T>A	ENST00000359195.3	+	0	5365					NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	NA		NA			adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						aaaaataaaataaaaaataaa	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	5294	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	phosphoinositide-3-kinase, catalytic, gamma polypeptide		NA		Standard		XM_005250443	NA	Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.*1746T>A	chr7.hg19:g.106547578T>A		NA	A4D0Q6|Q8IV23|Q9BZC8	hg19	CCDS5739.1	0.02	1.067832	AAAxAAA	COVERED																																																																																			NOVEL	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349294.1	28	10.61665	KEEP	0	3	78	63	1676	TT	1	0.999907	0		+	5	60	147	0	0	8.736889	84	60	2449	231	ENST00000359195.3	0.05618	0.999907
BCAP29	55973	__UNKNOWN__	__UNKNOWN__	7	107255822	107255822	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:107255822C>T	ENST00000445771.2	+	8	820				BCAP29_ENST00000005259.4_Intron|BCAP29_ENST00000465919.1_Intron|BCAP29_ENST00000494086.1_Intron|BCAP29_ENST00000379117.2_Intron|BCAP29_ENST00000379121.2_3'UTR|BCAP29_ENST00000379119.2_Intron			Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	NA		NA			apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						ctgaggcgggcggatcatggg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790	55973			24131	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_018844	NM_018844	NA	Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000445771.2:c.769+1645C>T	chr7.hg19:g.107255822C>T		NA	G5E9L4|O95003	hg19	CCDS34730.1	0.02	1.241184	GGGxGGA	COVERED																																																																																			NOVEL	BCAP29-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337022.2	18	10.513571	KEEP	0	3	82	64	1680	CC	1	0.99994	0		+	6	60	151	0	0	8.737562	84	60	2454	227	ENST00000445771.2	0.066667	0.99994
CBLL1	79872	__UNKNOWN__	__UNKNOWN__	7	107392917	107392917	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:107392917C>G	ENST00000415884.2	+	3	190				CBLL1_ENST00000440859.3_Intron|CBLL1_ENST00000222597.2_Intron			Q75N03	HAKAI_HUMAN	Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase	NA		NA			negative regulation of cell adhesion (GO:0007162)|positive regulation of cell migration (GO:0030335)|positive regulation of endocytosis (GO:0045807)|protein ubiquitination (GO:0016567)|single organismal cell-cell adhesion (GO:0016337)	ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(3)	21						gtgtctgtgtctgtgtATAGG	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026762	CCDS5747.1, CCDS64754.1	7q22.3	2013-07-09	2013-07-09		ENSG00000105879	ENSG00000105879	79872		RING-type (C3HC4) zinc fingers	21225	protein-coding gene	gene with protein product	Casitas B-lineage lymphoma-like	606872	Cas-Br-M (murine) ecotropic retroviral transforming sequence-like 1		NA	11836526, 11944035	Standard	NM_024814	NM_001284291	NA	Approved	HAKAI, FLJ23109, RNF188	uc003veq.3	Q75N03	OTTHUMG00000154809	ENST00000415884.2:c.182-939C>G	chr7.hg19:g.107392917C>G		NA	B7ZM03|Q8TAJ4|Q9H5S6	hg19		0.02	1.54661	TGTxTGT	COVERED																																																																																			NOVEL	CBLL1-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000337160.2	15	3.736531	KEEP	0	4	112	52	1564	CC	1	0.99993	0		+	4	60	141	2	0	8.986382	82	60	2734	207	ENST00000415884.2	0.046512	0.99993
NRCAM	4897	__UNKNOWN__	__UNKNOWN__	7	107939309	107939309	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:107939309T>G	ENST00000379024.4	-	3	304				NRCAM_ENST00000379022.4_Intron|NRCAM_ENST00000413765.2_Intron|NRCAM_ENST00000379028.3_Intron|NRCAM_ENST00000351718.4_Intron	NM_001193582.1|NM_001193583.1|NM_001193584.1	NP_001180511.1|NP_001180512.1|NP_001180513.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	NA		NA			angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						cagcactttgtgaagccgagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129	4897		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	7994	protein-coding gene	gene with protein product	NgCAM-related cell adhesion molecule	601581			NA	8812479	Standard	NM_001037132	NM_001037132	NA	Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000379024.4:c.105+13799A>C	chr7.hg19:g.107939309T>G		NA	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	hg19	CCDS55153.1	0.02	-0.184163	TTGxGAA	COVERED																																																																																			NOVEL	NRCAM-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337863.2	7	2.707255	KEEP	0	0	0	9	255	TT	0.99254	0.420319	0		-	3	60	86	0	0	6.362317	17	60	491	42	ENST00000379024.4	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	108402249	108402249	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:108402249T>C			NA	NA				AC005487.2 (147538 upstream) : C7orf66 (121782 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.108402249T>C		NA		hg19		0.02	-0.131554	TCAxGCC	COVERED																																																																																			NOVEL					0			9	3.006874	KEEP	0	0	0	10	272	TT	0.992708	0.227502	0			3	60	105	0	0	9.132869	8	60	223	36		0.272727	0.229173
DOCK4	9732	__UNKNOWN__	__UNKNOWN__	7	111403094	111403094	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:111403094A>G	ENST00000437633.1	-	38	4250				DOCK4_ENST00000494651.2_Intron|DOCK4_ENST00000428084.1_Intron	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	NA		NA			cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				aaagtgctgcaattacaggca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512	9732			19192	protein-coding gene	gene with protein product		607679			NA	12432077, 12628187	Standard	NM_014705	XM_006716188	NA	Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.3993+2079T>C	chr7.hg19:g.111403094A>G		NA	O14584|O94824|Q8NB45	hg19	CCDS47688.1	0.02	-0.096454	TGCxATT	UNCOVERED																																																																																			NOVEL	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338369.4	6	2.706794	KEEP	0	0	0	9	248	AA	0.99254	0.119538	0		-	3	60	98	0	0	8.744161	6	60	165	26	ENST00000437633.1	0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	112144204	112144204	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:112144204G>A			NA	NA				LSMEM1 (13087 upstream) : AC002463.3 (118228 downstream)						NA		NA									NA						caacatGAggggatgtcagtg	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.112144204G>A		NA		hg19		0.02	-0.210509	AGGxGAT	COVERED																																																																																			NOVEL					0			1	3.610929	KEEP	0	0	0	12	376	GG	0.993634	0.518837	0			3	60	92	1	0	6.765673	20	60	655	51		0.130435	0.522161
C7orf60	154743	__UNKNOWN__	__UNKNOWN__	7	112497397	112497397	__UNKNOWN__	Intron	SNP	C	C	T	rs540001696	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:112497397C>T	ENST00000297145.4	-	4	639				C7orf60_ENST00000485446.1_Intron	NM_152556.2	NP_689769.2	Q1RMZ1	BMT2_HUMAN	chromosome 7 open reading frame 60	NA		NA					rRNA (adenine) methyltransferase activity (GO:0016433)			breast(1)|endometrium(2)|lung(7)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	17						ccacccgcctcggcctcccaa	0.498		NA											-|||	21	0.00419329	0.0151	0.0	5008	,	,	NA	12704	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43634.1	7q31.1	2011-01-11	2008-06-19		ENSG00000164603	ENSG00000164603	154743			26475	protein-coding gene	gene with protein product	hypothetical protein FLJ31818	NA			NA		Standard	NM_152556	NM_152556	NA	Approved	DKFZp762M126, FLJ31818	uc003vgo.1	Q1RMZ1	OTTHUMG00000155233	ENST00000297145.4:c.474-24667G>A	chr7.hg19:g.112497397C>T		NA	Q8N3D0|Q96MV7	hg19	CCDS43634.1	0.02	-0.131579	CCTxGGC	UNCOVERED																																																																																			NOVEL	C7orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338923.1	4	3.909416	KEEP	19	0	0	13	370	CC	0	0	0		-	3	60	88	0	0	7.300952	9	60	301	60	ENST00000297145.4	0.25	0.229173
C7orf60	154743	__UNKNOWN__	__UNKNOWN__	7	112546900	112546900	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:112546900T>C	ENST00000297145.4	-	2	468				C7orf60_ENST00000485446.1_Intron	NM_152556.2	NP_689769.2	Q1RMZ1	BMT2_HUMAN	chromosome 7 open reading frame 60	NA		NA					rRNA (adenine) methyltransferase activity (GO:0016433)			breast(1)|endometrium(2)|lung(7)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	17						gctgggattataggcatgagc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS43634.1	7q31.1	2011-01-11	2008-06-19		ENSG00000164603	ENSG00000164603	154743			26475	protein-coding gene	gene with protein product	hypothetical protein FLJ31818	NA			NA		Standard	NM_152556	NM_152556	NA	Approved	DKFZp762M126, FLJ31818	uc003vgo.1	Q1RMZ1	OTTHUMG00000155233	ENST00000297145.4:c.302+8460A>G	chr7.hg19:g.112546900T>C		NA	Q8N3D0|Q96MV7	hg19	CCDS43634.1	0.02	-0.175364	TTAxAGG	COVERED																																																																																			NOVEL	C7orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338923.1	5	2.405433	KEEP	0	0	0	8	211	TT	0.99257	0.384528	0		-	3	60	103	0	1	8.061177	17	60	479	42	ENST00000297145.4	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	112982488	112982488	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:112982488T>C			NA	NA				RP11-736E3.1 (196103 upstream) : TSRM (108638 downstream)						NA		NA									NA						tacttctttctacacagacac	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.112982488T>C		NA		hg19		0.02	-0.263117	TTCxACA	UNCOVERED																																																																																			NOVEL					0			12	3.309115	KEEP	11	0	0	11	316	TT	0	0	0			3	60	108	0	0	8.043652	26	60	773	74		0.103448	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	113178945	113178945	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:113178945A>G			NA	NA				TSRM (87488 upstream) : PPP1R3A (337886 downstream)						NA		NA									NA						aaaaaaaaaaaaaaagaagac	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.113178945A>G		NA		hg19		0.02	-0.052603	AAAxAAA	UNCOVERED																																																																																			NOVEL					0			12	2.705904	KEEP	9	0	0	9	236	AA	0	0	0			2	54	62	0	0	6.324728	1	60	29	23		0.666667	0.036766
FOXP2	93986	__UNKNOWN__	__UNKNOWN__	7	114319304	114319304	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:114319304A>G	ENST00000393494.2	+	17	2282				FOXP2_ENST00000350908.4_Intron|FOXP2_ENST00000393491.3_Intron|FOXP2_ENST00000393489.3_Intron|FOXP2_ENST00000403559.4_Intron|FOXP2_ENST00000408937.3_Intron|FOXP2_ENST00000393498.2_Intron			O15409	FOXP2_HUMAN	forkhead box P2	NA		NA			camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						acaggcgtgaaccaccatgcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573	93986		Forkhead boxes	13875	protein-coding gene	gene with protein product	trinucleotide repeat containing 10, forkhead/winged-helix transcription factor, speech and language disorder 1, CAG repeat protein 44	605317		TNRC10, SPCH1	NA	11586359, 9225980	Standard	NM_014491	NM_014491	NA	Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.2004-10533A>G	chr7.hg19:g.114319304A>G		NA	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	hg19	CCDS5760.1	0.02	-0.157877	TGAxCCA	COVERED																																																																																			NOVEL	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317366.1	5	3.006016	KEEP	0	0	0	10	258	AA	0.992708	0.320453	0		+	3	60	107	0	0	8.691619	14	60	412	39	ENST00000393494.2	0.176471	0.322807
TFEC	22797	__UNKNOWN__	__UNKNOWN__	7	115791544	115791544	__UNKNOWN__	Intron	SNP	A	A	G	rs574572752		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:115791544A>G	ENST00000484212.1	-	1	107				TFEC_ENST00000474337.1_Intron			O14948	TFEC_HUMAN	transcription factor EC	NA		NA			cellular response to heat (GO:0034605)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|kidney(1)|large_intestine(5)|lung(13)|prostate(2)|skin(1)|urinary_tract(2)	25			STAD - Stomach adenocarcinoma(10;0.00878)			tgatccgcccacctcggcctc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D43945	CCDS5762.1, CCDS34738.1, CCDS59076.1	7q31.2	2013-05-21			ENSG00000105967	ENSG00000105967	22797		Basic helix-loop-helix proteins	11754	protein-coding gene	gene with protein product		604732			NA	9256061	Standard	NM_012252	NM_012252	NA	Approved	TCFEC, TFECL, bHLHe34	uc003vhj.2	O14948	OTTHUMG00000023518	ENST00000484212.1:c.67+8299T>C	chr7.hg19:g.115791544A>G		NA	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	hg19		0.02	-0.157874	CCCxCCT	COVERED																																																																																			NOVEL	TFEC-008	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000351050.2	7	2.702854	KEEP	1	0	0	9	227	AA	0.99257	0.320408	0		-	3	60	92	0	0	7.110442	15	60	450	36	ENST00000484212.1	0.166667	0.322807
CAPZA2	830	__UNKNOWN__	__UNKNOWN__	7	116561198	116561198	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:116561198A>G	ENST00000361183.3	+	0	4277					NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	NA		NA			actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)				endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			ccagcactttaggaggctgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898	830			1490	protein-coding gene	gene with protein product	F-actin capping protein alpha-2 subunit	601571			NA		Standard	NM_006136	NM_006136	NA	Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.*3277A>G	chr7.hg19:g.116561198A>G		NA	B4DG50	hg19	CCDS5768.1	0.02	-0.201736	TTTxGGA	COVERED																																																																																			NOVEL	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059506.4	9	2.706204	KEEP	0	0	0	9	243	AA	0.99254	0.486885	0		+	5	60	170	0	0	14.380656	16	60	476	42	ENST00000361183.3	0.238095	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	117729108	117729108	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:117729108C>A			NA	NA				AC003084.2 (85009 upstream) : NAA38 (94977 downstream)						NA		NA									NA						ggcaacagagcgaggctctgt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.117729108C>A		NA		hg19		0.02	-0.219307	GAGxGAG	COVERED																																																																																			NOVEL					0			12	2.708389	KEEP	0	0	0	9	286	CT	0.992708	0.548856	0			3	60	94	0	0	6.905804	21	60	707	53		0.125	0.552887
NAA38	84316	__UNKNOWN__	__UNKNOWN__	7	117829560	117829560	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:117829560G>C	ENST00000249299.2	+	3	392				NAA38_ENST00000422760.1_Intron|NAA38_ENST00000424702.1_3'UTR	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	NA		NA			negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						cgagatcgcagcactgcattc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11122.1	17p13.1	2014-01-21	2014-01-21	2014-01-21		ENSG00000183011	84316		N(alpha)-acetyltransferase subunits	28212	protein-coding gene	gene with protein product		NA	LSM domain containing 1	LSMD1	NA	16484612, 19398576	Standard	NM_032356	NM_032356	NA	Approved	MGC14151, PFAAP2	uc002gja.3	Q9BRA0		ENST00000249299.2:c.200+1101G>C	chr7.hg19:g.117829560G>C		NA	Q8N4M0	hg19	CCDS5775.1	0.02	5.475695	GCAxCAC	COVERED																																																																																			NOVEL	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346774.2	35	18.190667	KEEP	1	10	291	163	5101	GG	1	1	0		+	7	60	231	0	0	14.004663	151	60	5238	482	ENST00000249299.2	0.044304	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	117853426	117853426	__UNKNOWN__	IGR	SNP	C	C	T	rs538392477	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:117853426C>T			NA	NA				NAA38 (20548 upstream) : ANKRD7 (1300 downstream)						NA		NA									NA						gaggccgaggcgggcggatca	0.473		NA											c|||	3	0.000599042	0.0023	0.0	5008	,	,	NA	15734	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.117853426C>T		NA		hg19		0.02	-0.15789	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			11	2.707469	KEEP	8	0	0	9	269	CC	0	0	0			3	60	89	0	1	6.810451	15	60	487	45		0.166667	0.322807
RP5-1006K12.1	0	__UNKNOWN__	__UNKNOWN__	7	119816784	119816784	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:119816784A>G	ENST00000421825.1	+	0	50										NA		NA									NA						ctgcactccaacctgggcaac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000421825.1:	chr7.hg19:g.119816784A>G		NA		hg19		0.02	-0.131563	CCAxCCT	COVERED																																																																																			NOVEL	RP5-1006K12.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000346762.1	5	2.406449	KEEP	0	0	0	8	225	AA	0.99257	0.22747	0		+	3	60	104	0	0	8.572221	12	60	356	35	ENST00000421825.1	0.2	0.229173
CPED1	79974	__UNKNOWN__	__UNKNOWN__	7	120794845	120794845	__UNKNOWN__	Intron	SNP	A	A	G	rs10240772	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:120794845A>G	ENST00000310396.5	+	16	2522				CPED1_ENST00000423795.1_Intron|CPED1_ENST00000450913.2_Intron	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	NA		NA				endoplasmic reticulum (GO:0005783)					NA						tgatccgcccacctcggcctc	0.502		NA											G|||	2998	0.598642	0.5219	0.6671	5008	,	,	NA	12005	0.8532	NA	0.5398	False	NA	,,,	NA	NA	NA	2504	0.4519	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034	79974			26159	protein-coding gene	gene with protein product		NA	chromosome 7 open reading frame 58	C7orf58	NA	20056006	Standard	NM_024913	NM_024913	NA	Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2055+12650A>G	chr7.hg19:g.120794845A>G		NA	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	hg19	CCDS34739.1	0.02	-0.236774	CCCxCCT	COVERED																																																																																			NOVEL	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346959.1	13	6.015295	KEEP	14	0	0	20	554	AA	0.99649	0.610258	0		+	10	60	323	0	0	29.763195	15	60	437	92	ENST00000310396.5	0.4	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	121504753	121504753	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:121504753C>T			NA	NA				RN7SKP277 (127974 upstream) : PTPRZ1 (8389 downstream)						NA		NA									NA						tggtggctcacgcctgtaatc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.121504753C>T		NA		hg19		0.02	-0.219271	TCAxGCC	COVERED																																																																																			NOVEL					0			6	3.609223	KEEP	2	0	0	12	343	CC	0.993634	0.549368	0			4	60	117	0	0	9.080038	18	60	590	63		0.181818	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	121835610	121835610	__UNKNOWN__	IGR	SNP	G	G	A	rs62474305	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:121835610G>A			NA	NA				AASS (51276 upstream) : RP11-560I19.1 (20790 downstream)						NA		NA									NA						cctgggaggcggaggttgtag	0.483		NA											G|||	1500	0.299521	0.0371	0.4107	5008	,	,	NA	15058	0.38	NA	0.4245	False	NA	,,,	NA	NA	NA	2504	0.364	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.121835610G>A		NA		hg19		0.02	-0.105265	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.406161	KEEP	1	0	0	8	226	GG	0	0	0			4	60	126	0	0	11.376886	7	60	232	27		0.363636	0.139832
CADPS2	93664	__UNKNOWN__	__UNKNOWN__	7	122440781	122440781	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:122440781G>A	ENST00000412584.2	-	2	460				CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000313070.7_Intron	NM_001009571.3	NP_001009571.2	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	NA		NA			cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						ggtggctcacgtctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803	93664		Pleckstrin homology (PH) domain containing	16018	protein-coding gene	gene with protein product		609978	Ca++-dependent activator protein for secretion 2		NA		Standard	NM_017954	NM_017954	NA	Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000412584.2:c.340-63659C>T	chr7.hg19:g.122440781G>A		NA	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	hg19	CCDS47691.1	0.02	-0.149123	CACxTCT	COVERED																																																																																			NOVEL	CADPS2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347415.2	3	2.706439	KEEP	0	0	0	9	247	GG	0.99254	0.289823	0		-	3	60	83	0	0	6.681923	10	60	337	37	ENST00000412584.2	0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	125038649	125038649	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:125038649G>A			NA	NA				RP11-3B12.2 (19274 upstream) : RP11-807H17.1 (32751 downstream)						NA		NA									NA						ggccaggtgcggtggctcacg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.125038649G>A		NA		hg19		0.02	-0.22806	TGCxGTG	COVERED																																																																																			NOVEL					0			6	3.30848	KEEP	0	0	0	11	308	GG	0.993072	0.608164	0			3	60	90	0	0	6.565577	20	60	657	56		0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	125418692	125418692	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:125418692A>G			NA	NA				RP11-807H17.1 (317027 upstream) : AC005276.1 (139232 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.125418692A>G		NA		hg19		0.02	-0.16666	CACxCCT	COVERED																																																																																			NOVEL					0			10	3.007614	KEEP	3	0	0	10	277	AA	0.99254	0.351306	0			3	60	97	0	0	7.69175	14	60	436	43		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	125823762	125823762	__UNKNOWN__	IGR	SNP	T	T	C	rs59893366	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:125823762T>C			NA	NA				AC003968.1 (143408 upstream) : AC000370.2 (195261 downstream)						NA		NA									NA						tttgggaggctgaggcgggcg	0.488		NA											-|||	1277	0.254992	0.3684	0.1427	5008	,	,	NA	12994	0.3075	NA	0.1461	False	NA	,,,	NA	NA	NA	2504	0.2393	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.125823762T>C		NA		hg19		0.02	-0.105253	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			13	4.512051	KEEP	15	0	0	15	424	TT	0	0	0			4	60	136	0	0	12.377371	7	60	206	50		0.363636	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	126011433	126011433	__UNKNOWN__	IGR	SNP	G	G	A	rs189057480		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:126011433G>A			NA	NA				AC003968.1 (331079 upstream) : AC000370.2 (7590 downstream)						NA		NA									NA						aaagaaagaaggaaggaagga	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.126011433G>A		NA		hg19		0.02	-0.105245	GAAxGAA	UNCOVERED																																																																																			NOVEL					0			12	3.610086	KEEP	14	0	0	12	354	GG	0	0	0			3	60	88	1	0	7.43252	8	40	256	39		0.272727	0.139832
ZNF800	168850	__UNKNOWN__	__UNKNOWN__	7	127024566	127024566	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:127024566A>G	ENST00000393313.1	-	3	749				ZNF800_ENST00000265827.3_Intron|ZNF800_ENST00000393312.1_Intron			Q2TB10	ZN800_HUMAN	zinc finger protein 800	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						gggattacagacgtgagccac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405	168850		Zinc fingers, C2H2-type	27267	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_176814	NM_176814	NA	Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.157+1547T>C	chr7.hg19:g.127024566A>G		NA	Q9HBN0	hg19	CCDS5795.1	0.02	-0.227996	CAGxCGT	COVERED																																																																																			NOVEL	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000141823.1	9	4.210054	KEEP	3	0	0	14	378	AA	0.994391	0.57966	0		-	3	60	103	0	0	7.992416	18	60	530	65	ENST00000393313.1	0.142857	0.58293
METTL2B	55798	__UNKNOWN__	__UNKNOWN__	7	128138976	128138976	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128138976A>G	ENST00000262432.8	+	7	953				METTL2B_ENST00000480046.1_Intron	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	NA		NA			tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						gcttgaacccaggaggcggag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055	55798			18272	protein-coding gene	gene with protein product		607846	methyltransferase like 2	METTL2	NA	11738826	Standard	NM_018396	NM_018396	NA	Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.916+780A>G	chr7.hg19:g.128138976A>G		NA	B4DZ68|Q0IJ54|Q3B7J1	hg19	CCDS5803.2	0.02	-0.105237	CCCxGGA	UNCOVERED																																																																																			NOVEL	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000289817.1	6	4.210932	KEEP	5	0	0	14	392	AA	0.994391	0.139048	0		+	3	48	95	0	0	8.00134	9	60	267	48	ENST00000262432.8	0.25	0.139832
RP11-274B21.1	0	__UNKNOWN__	__UNKNOWN__	7	128198520	128198520	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128198520T>A	ENST00000605862.1	+	0	189										NA		NA									NA						ctataatctctgcactttggg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000605862.1:	chr7.hg19:g.128198520T>A		NA		hg19		0.02	-0.149105	CTCxGCA	COVERED																																																																																			NOVEL	RP11-274B21.1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000468355.1	8	2.406409	KEEP	0	0	0	8	227	TT	0.99257	0.289832	0		+	3	49	89	0	0	7.173035	11	60	335	36	ENST00000605862.1	0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	128305971	128305971	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128305971C>T			NA	NA				RP11-274B21.1 (36459 upstream) : RP11-274B21.10 (1125 downstream)						NA		NA									NA						gcctcccaggctcaagtgatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.128305971C>T		NA		hg19		0.02	-0.14036	AGGxTCA	COVERED																																																																																			NOVEL					0			9	3.008924	KEEP	3	0	0	10	304	CC	0.99254	0.259018	0			3	60	91	0	0	7.372686	11	60	388	37		0.214286	0.260965
FAM71F2	346653	__UNKNOWN__	__UNKNOWN__	7	128316296	128316296	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128316296T>C	ENST00000480462.1	+	2	471				FAM71F2_ENST00000477515.1_Intron|FAM71F2_ENST00000378704.3_Intron|FAM71F2_ENST00000460349.1_Intron			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	NA		NA								NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						gatctcctgatctcgtgatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085	346653			27998	protein-coding gene	gene with protein product		NA	family with sequence similarity 137, member B	FAM137B	NA	12477932	Standard		XM_006715964	NA	Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.365+383T>C	chr7.hg19:g.128316296T>C		NA	Q0VGF6|Q0VGF7|Q86X39	hg19	CCDS47701.1	0.02	-0.043856	TGAxCTC	UNCOVERED																																																																																			NOVEL	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350537.1	5	2.404587	KEEP	3	0	0	8	206	TT	0	0	0		+	2	60	72	0	0	6.693104	3	60	86	20	ENST00000480462.1	0.4	0.024074
FAM71F2	346653	__UNKNOWN__	__UNKNOWN__	7	128323924	128323924	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128323924A>T	ENST00000480462.1	+	0	1747							Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	NA		NA								NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						cttacaatcaaggcagaaggc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085	346653			27998	protein-coding gene	gene with protein product		NA	family with sequence similarity 137, member B	FAM137B	NA	12477932	Standard		XM_006715964	NA	Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.*711A>T	chr7.hg19:g.128323924A>T		NA	Q0VGF6|Q0VGF7|Q86X39	hg19	CCDS47701.1	0.02	3.052751	TCAxGGC	COVERED																																																																																			NOVEL	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350537.1	17	5.711415	KEEP	0	3	82	48	1355	AA	1	0.999987	0		+	7	60	185	0	0	10.776371	96	60	2957	236	ENST00000480462.1	0.067961	0.999987
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	128343598	128343598	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128343598G>A			NA	NA				RNA5SP243 (5800 upstream) : FAM71F1 (5516 downstream)						NA		NA									NA						taatcccagcgctttgggagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.128343598G>A		NA		hg19		0.02	-0.096487	AGCxCTT	UNCOVERED																																																																																			NOVEL					0			4	2.707836	KEEP	0	0	0	9	276	GG	0.99254	0.119538	0			3	60	91	0	0	8.454818	4	60	129	32		0.428571	0.120436
TNPO3	23534	__UNKNOWN__	__UNKNOWN__	7	128601095	128601095	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128601095A>G	ENST00000482320.1	-	23	3195				TNPO3_ENST00000471234.1_Intron|TNPO3_ENST00000393245.1_Intron|TNPO3_ENST00000471166.1_Intron|TNPO3_ENST00000265388.5_Intron			Q9Y5L0	TNPO3_HUMAN	transportin 3	NA		NA			splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						gattacaggcatgagccaccg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(147;583 2585 39696 52331)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419	23534		Importins	17103	protein-coding gene	gene with protein product	importin 12	610032	limb girdle muscular dystrophy 1F (autosomal dominant)	LGMD1F	NA	10366588, 10713112, 23543484, 23667635	Standard	NM_012470	NM_012470	NA	Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000482320.1:c.2514-3726T>C	chr7.hg19:g.128601095A>G		NA	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	hg19		0.02	-0.175408	GGCxTGA	COVERED																																																																																			NOVEL	TNPO3-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000350930.2	16	4.510416	KEEP	10	0	0	15	401	AA	0.993634	0.38494	0		-	4	60	134	0	0	11.168508	14	60	409	61	ENST00000482320.1	0.222222	0.387407
TNPO3	23534	__UNKNOWN__	__UNKNOWN__	7	128613769	128613769	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128613769G>T	ENST00000482320.1	-	20	2757				TNPO3_ENST00000471234.1_Intron|TNPO3_ENST00000393245.1_Intron|TNPO3_ENST00000471166.1_Intron|TNPO3_ENST00000265388.5_Intron			Q9Y5L0	TNPO3_HUMAN	transportin 3	NA		NA			splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						cagcctgggcgacagagcgag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(147;583 2585 39696 52331)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419	23534		Importins	17103	protein-coding gene	gene with protein product	importin 12	610032	limb girdle muscular dystrophy 1F (autosomal dominant)	LGMD1F	NA	10366588, 10713112, 23543484, 23667635	Standard	NM_012470	NM_012470	NA	Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000482320.1:c.2076-1133C>A	chr7.hg19:g.128613769G>T		NA	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	hg19		0.02	-0.061394	GGCxACA	UNCOVERED																																																																																			NOVEL	TNPO3-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000350930.2	10	4.812567	KEEP	17	0	0	16	449	GG	0.992708	0.043467	0		-	3	40	90	0	0	8.355106	4	16	117	40	ENST00000482320.1	0.428571	0.043787
TNPO3	23534	__UNKNOWN__	__UNKNOWN__	7	128613781	128613781	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:128613781C>T	ENST00000482320.1	-	19	2757				TNPO3_ENST00000471234.1_Intron|TNPO3_ENST00000393245.1_Intron|TNPO3_ENST00000471166.1_Intron|TNPO3_ENST00000265388.5_Intron			Q9Y5L0	TNPO3_HUMAN	transportin 3	NA		NA			splicing factor protein import into nucleus (GO:0035048)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(3)	22						cagagcgagactccgtctcaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(147;583 2585 39696 52331)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145029	CCDS5809.1, CCDS55162.1	7q32.2	2014-02-03			ENSG00000064419	ENSG00000064419	23534		Importins	17103	protein-coding gene	gene with protein product	importin 12	610032	limb girdle muscular dystrophy 1F (autosomal dominant)	LGMD1F	NA	10366588, 10713112, 23543484, 23667635	Standard	NM_012470	NM_012470	NA	Approved	TRN-SR, MTR10A, TRN-SR2, IPO12	uc003vol.2	Q9Y5L0	OTTHUMG00000158409	ENST00000482320.1:c.2075+1140G>A	chr7.hg19:g.128613781C>T		NA	A4D1K9|C9IZM0|Q6NUM1|Q96G71|Q96GU9|Q9Y3R2	hg19		0.02	-0.05263	AGAxTCC	UNCOVERED																																																																																			NOVEL	TNPO3-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000350930.2	9	4.813467	KEEP	14	0	0	16	484	CC	0.992708	0.036498	0		-	3	40	87	0	0	8.324227	3	16	105	34	ENST00000482320.1	0.5	0.036766
AHCYL2	23382	__UNKNOWN__	__UNKNOWN__	7	129033980	129033980	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129033980A>G	ENST00000325006.3	+	5	774				AHCYL2_ENST00000490911.1_Intron|AHCYL2_ENST00000446212.1_Intron|AHCYL2_ENST00000531335.2_Intron|AHCYL2_ENST00000474594.1_Intron|AHCYL2_ENST00000472554.1_Intron|AHCYL2_ENST00000446544.2_Intron	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	NA		NA			one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						ctcccaagtaactgggactac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(160;1736 1964 29875 40941 45605)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467	23382			22204	protein-coding gene	gene with protein product		NA	S-adenosylhomocysteine hydrolase-like 2		NA		Standard		NM_001130720	NA	Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.721-3083A>G	chr7.hg19:g.129033980A>G		NA	B4DIZ5|D9N155|O94917	hg19	CCDS5812.1	0.02	-0.149091	GTAxCTG	COVERED																																																																																			NOVEL	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354065.1	9	2.706243	KEEP	1	0	0	9	240	AA	0.99254	0.289823	0		+	3	60	100	0	0	8.07904	13	60	374	33	ENST00000325006.3	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	129177166	129177166	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129177166T>C			NA	NA				SMKR1 (24393 upstream) : RP11-448A19.1 (67222 downstream)						NA		NA									NA						tcctggccaatatggcgaaac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.129177166T>C		NA		hg19		0.02	-0.061393	CAAxATG	UNCOVERED																																																																																			NOVEL					0			3	2.705972	KEEP	0	0	0	9	236	TT	0.99254	0.04346	0			2	60	71	0	0	6.593121	3	60	85	22		0.4	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	129229602	129229602	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129229602A>G			NA	NA				SMKR1 (76829 upstream) : RP11-448A19.1 (14786 downstream)						NA		NA									NA						gattacaggcatgagtcaccg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.129229602A>G		NA		hg19		0.02	-0.236807	GGCxTGA	COVERED																																																																																			NOVEL					0			10	3.307956	KEEP	2	0	0	11	298	AA	0.993072	0.608164	0			4	60	137	0	0	10.994414	19	60	560	56		0.173913	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	129229607	129229607	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129229607T>C			NA	NA				SMKR1 (76834 upstream) : RP11-448A19.1 (14781 downstream)						NA		NA									NA						caggcatgagtcaccgcgccc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.129229607T>C		NA		hg19		0.02	-0.245557	GAGxCAC	COVERED																																																																																			NOVEL					0			11	3.908716	KEEP	2	0	0	13	343	TT	0.993634	0.637264	0			5	60	168	0	0	13.85321	19	60	554	57		0.208333	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	129454118	129454118	__UNKNOWN__	IGR	SNP	G	G	A	rs141895963	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129454118G>A			NA	NA				RP11-738B7.1 (29093 upstream) : UBE2H (16453 downstream)						NA		NA									NA						gtgagatctcggctcactgca	0.438		NA											G|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	14181	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.129454118G>A		NA		hg19		0.02	-0.1491	CTCxGCT	UNCOVERED																																																																																			NOVEL					0			15	3.308648	KEEP	9	0	0	11	316	GG	0	0	0			3	60	82	0	0	6.473473	11	60	357	38		0.214286	0.292001
UBE2H	7328	__UNKNOWN__	__UNKNOWN__	7	129535489	129535489	__UNKNOWN__	Intron	SNP	G	G	C	rs540578917	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129535489G>C	ENST00000355621.3	-	2	447				UBE2H_ENST00000473814.2_Intron	NM_001202498.1|NM_003344.3	NP_001189427.1|NP_003335.1	P62256	UBE2H_HUMAN	ubiquitin-conjugating enzyme E2H	NA		NA			protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|skin(1)	10	Melanoma(18;0.0435)					acctgtaatcgcagcactttg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006277	CCDS5814.1, CCDS47710.1	7q32	2012-07-20	2011-05-19		ENSG00000186591	ENSG00000186591	7328	6.3.2.19	Ubiquitin-conjugating enzymes E2	12484	protein-coding gene	gene with protein product	GID complex subunit 3, UBC8 homolog (S. cerevisiae)	601082	ubiquitin-conjugating enzyme E2H (homologous to yeast UBC8), ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast)		NA	8132613	Standard	NM_003344	NM_003344	NA	Approved	UBCH, UBC8, GID3	uc003vpf.2	P62256	OTTHUMG00000157650	ENST00000355621.3:c.54-14678C>G	chr7.hg19:g.129535489G>C		NA	A4D1L6|C9JY93|P37286|Q7Z6F4	hg19	CCDS5814.1	0.02	-0.184223	ATCxCAG	COVERED																																																																																			NOVEL	UBE2H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349327.2	8	3.008787	KEEP	1	0	0	10	303	GG	0.99254	0.420319	0		-	3	60	104	0	0	8.309735	15	60	508	47	ENST00000355621.3	0.166667	0.423478
RP11-306G20.1	0	__UNKNOWN__	__UNKNOWN__	7	129615853	129615853	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129615853A>G	ENST00000587038.1	+	0	247										NA		NA									NA						ctgggcgacaaagtgagactc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000587038.1:	chr7.hg19:g.129615853A>G		NA		hg19		0.02	-0.122796	ACAxAGT	COVERED																																																																																			NOVEL	RP11-306G20.1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000447888.1	6	3.008018	KEEP	2	0	0	10	282	AA	0.99254	0.194847	0		+	3	60	99	0	0	8.282016	10	60	299	40	ENST00000587038.1	0.230769	0.196312
ZC3HC1	51530	__UNKNOWN__	__UNKNOWN__	7	129677145	129677145	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129677145G>A	ENST00000481503.1	-	4	516				ZC3HC1_ENST00000360708.5_Intron|ZC3HC1_ENST00000358303.4_Intron|ZC3HC1_ENST00000311873.5_Intron			Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	NA		NA			mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					ttagctgggtgtggtggcacg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(115;540 1606 16325 28853 48167)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732	51530		Zinc fingers, C3HC-type	29913	protein-coding gene	gene with protein product	nuclear interaction partner of ALK	NA			NA	11042152	Standard	NM_016478	XM_005250403	NA	Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000481503.1:c.493+2158C>T	chr7.hg19:g.129677145G>A		NA	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	hg19		0.02	-0.122793	GGTxTGG	COVERED																																																																																			NOVEL	ZC3HC1-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000349319.1	6	3.008486	KEEP	2	0	0	10	293	GG	0.99257	0.194853	0		-	3	60	84	0	0	6.67312	11	60	356	33	ENST00000481503.1	0.214286	0.196312
KLHDC10	23008	__UNKNOWN__	__UNKNOWN__	7	129720047	129720047	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129720047A>G	ENST00000335420.5	+	1	300					NM_014997.3	NP_055812.1	Q6PID8	KLD10_HUMAN	kelch domain containing 10	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|liver(2)|lung(10)|prostate(1)	17						ctcccaaagtactaggattac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5815.1	7q32.2	2008-08-20			ENSG00000128607	ENSG00000128607	23008			22194	protein-coding gene	gene with protein product	scruin like at the midline homolog (Drosophila)	615152			NA		Standard		NM_014997	NA	Approved	KIAA0265, slim	uc003vpj.2	Q6PID8	OTTHUMG00000157654	ENST00000335420.5:c.166+9398A>G	chr7.hg19:g.129720047A>G		NA	Q86Y99|Q92554	hg19	CCDS5815.1	0.02	-0.192892	AGTxCTA	COVERED																																																																																			NOVEL	KLHDC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349347.2	9	3.305457	KEEP	0	0	0	11	276	AA	0.993634	0.454842	0		+	3	60	98	0	0	7.634594	16	60	443	47	ENST00000335420.5	0.157895	0.457757
KLHDC10	23008	__UNKNOWN__	__UNKNOWN__	7	129746571	129746571	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129746571G>A	ENST00000335420.5	+	3	387					NM_014997.3	NP_055812.1	Q6PID8	KLD10_HUMAN	kelch domain containing 10	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|liver(2)|lung(10)|prostate(1)	17						taatcccagcgctttgggagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS5815.1	7q32.2	2008-08-20			ENSG00000128607	ENSG00000128607	23008			22194	protein-coding gene	gene with protein product	scruin like at the midline homolog (Drosophila)	615152			NA		Standard		NM_014997	NA	Approved	KIAA0265, slim	uc003vpj.2	Q6PID8	OTTHUMG00000157654	ENST00000335420.5:c.254-9714G>A	chr7.hg19:g.129746571G>A		NA	Q86Y99|Q92554	hg19	CCDS5815.1	0.02	-0.21051	AGCxCTT	COVERED																																																																																			NOVEL	KLHDC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349347.2	10	3.911103	KEEP	0	0	0	13	387	GG	0.994391	0.519232	0		+	5	60	141	0	0	11.480495	16	60	528	51	ENST00000335420.5	0.238095	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	129964886	129964886	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:129964886A>G			NA	NA				CPA4 (866 upstream) : snoU13 (19368 downstream)						NA		NA									NA						gagccaccacacccggccAAG	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.129964886A>G		NA		hg19		0.02	-0.201623	CACxCCC	COVERED																																																																																			NOVEL					0			10	3.306262	KEEP	1	0	0	11	283	AA	0.993072	0.487146	0			3	60	106	0	0	8.511012	15	60	409	49		0.166667	0.490544
CEP41	95681	__UNKNOWN__	__UNKNOWN__	7	130080059	130080059	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:130080059G>A	ENST00000223208.5	-	1	304				CEP41_ENST00000343969.5_Intron|CEP41_ENST00000495702.1_Intron|CEP41_ENST00000489512.1_Intron|CEP41_ENST00000541543.1_Intron	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	NA		NA			cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)					NA						acggggtttcgccatgttggc	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477	95681			12370	protein-coding gene	gene with protein product		610523	testis specific, 14	TSGA14	NA	14654843, 22246503	Standard	NM_018718	NM_018718	NA	Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.33+715C>T	chr7.hg19:g.130080059G>A		NA	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	hg19	CCDS5821.1	0.02	-0.070141	TTCxCCA	UNCOVERED																																																																																			NOVEL	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349702.2	2	3.308383	KEEP	1	0	0	11	307	GG	0.992708	0.053742	0		-	3	60	75	0	0	6.630521	5	60	163	27	ENST00000223208.5	0.375	0.054137
MKLN1	4289	__UNKNOWN__	__UNKNOWN__	7	131177416	131177416	__UNKNOWN__	3'UTR	SNP	A	A	G	rs1138264		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:131177416A>G	ENST00000352689.6	+	0	7177					NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	NA		NA			signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					gatcacttgaacccaggagtt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585	4289			7109	protein-coding gene	gene with protein product		605623			NA	10640805	Standard	NM_013255	NM_001145354	NA	Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.*4929A>G	chr7.hg19:g.131177416A>G		NA	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	hg19	CCDS34754.1	0.02	1.643072	TGAxCCC	COVERED																																																																																			NOVEL	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337473.4	8	3.338629	KEEP	0	1	31	22	583	AA	0.999892	0.96367	0		+	4	60	122	0	0	8.097422	45	60	1249	83	ENST00000352689.6	0.081633	0.963774
AC009365.3	0	__UNKNOWN__	__UNKNOWN__	7	132388175	132388175	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:132388175A>G	ENST00000332558.4	+	4	407										NA		NA									NA						ttacaggcgtaagccaccatg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000332558.4:c.-211-21361A>G	chr7.hg19:g.132388175A>G		NA		hg19		0.02	-0.254324	CGTxAGC	COVERED																																																																																			NOVEL	AC009365.3-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000318676.5	10	4.509882	KEEP	0	0	0	15	393	AA	0.99649	0.666177	0		+	3	60	102	0	0	7.649026	22	60	624	65	ENST00000332558.4	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	132413805	132413805	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:132413805A>G			NA	NA				AC009365.3 (277 upstream) : SNORD46 (23977 downstream)						NA		NA									NA						gctcacacctataatcccagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.132413805A>G		NA		hg19		0.02	-0.184147	CCTxTAA	COVERED																																																																																			NOVEL					0			6	3.006039	KEEP	1	0	0	10	256	AA	0.99254	0.420319	0			3	60	105	0	0	8.410343	15	60	411	44		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	132457463	132457463	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:132457463T>C			NA	NA				AC009365.4 (12071 upstream) : CHCHD3 (12165 downstream)						NA		NA									NA						tttgtatttttagtagagaca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.132457463T>C		NA		hg19		0.02	-0.42096	TTTxAGT	COVERED																																																																																			NOVEL					0			64	5.125861	KEEP	30	4	125	61	1613	TT	1	0.948402	0			4	56	144	1	0	11.016854	29	60	827	188		0.121212	0.948402
CHCHD3	54927	__UNKNOWN__	__UNKNOWN__	7	132588828	132588828	__UNKNOWN__	Intron	SNP	C	C	T	rs558538144		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:132588828C>T	ENST00000262570.5	-	5	514				CHCHD3_ENST00000476546.1_Intron|CHCHD3_ENST00000448878.1_Intron	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	NA		NA			inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						aagaccagcccgggcaacatg	0.522		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17470	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554	54927		Coiled-coil-helix-coiled-coil-helix domain containing, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	21906	protein-coding gene	gene with protein product	mitochondrial inner membrane organizing system 3, protein phosphatase 1, regulatory subunit 22	613748			NA	22252321, 23019327, 21081504, 17624330	Standard	NM_017812	NM_017812	NA	Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.370-18323G>A	chr7.hg19:g.132588828C>T		NA		hg19	CCDS5828.1	0.02	-0.149128	GCCxGGG	COVERED																																																																																			NOVEL	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000338899.1	3	2.707682	KEEP	0	0	0	9	268	CC	0.99254	0.289823	0		-	3	60	90	0	0	7.078872	13	60	436	39	ENST00000262570.5	0.1875	0.292001
EXOC4	60412	__UNKNOWN__	__UNKNOWN__	7	133607337	133607337	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:133607337T>C	ENST00000253861.4	+	13	2056				EXOC4_ENST00000545148.1_Intron|EXOC4_ENST00000539845.1_Intron	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	NA		NA			cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				cggtggctcatgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558	60412			30389	protein-coding gene	gene with protein product		608185	SEC8-like 1 (S. cerevisiae)	SEC8L1	NA	11214970, 12687004	Standard	NM_021807	XM_005250523	NA	Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2027+4846T>C	chr7.hg19:g.133607337T>C		NA	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	hg19	CCDS5829.1	0.02	-0.131557	TCAxGCC	COVERED																																																																																			NOVEL	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000339182.1	4	2.406196	KEEP	0	0	0	8	225	TT	0.99257	0.22747	0		+	3	60	99	0	0	8.282183	10	60	292	33	ENST00000253861.4	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	135219136	135219136	__UNKNOWN__	IGR	SNP	G	G	T	rs542921798		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:135219136G>T			NA	NA				CNOT4 (24261 upstream) : NUP205 (23530 downstream)						NA		NA									NA						aggccaaggcgggtggatcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.135219136G>T		NA		hg19		0.02	-0.219298	GGCxGGT	COVERED																																																																																			NOVEL					0			21	3.944102	KEEP	18	1	28	23	687	GG	0.999366	0.552537	0			5	40	153	0	0	12.80172	15	60	490	95		0.25	0.552887
MTPN	136319	__UNKNOWN__	__UNKNOWN__	7	135613054	135613054	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:135613054C>A	ENST00000393085.3	-	0	2192				AC015987.1_ENST00000419211.1_RNA|AC015987.2_ENST00000416501.1_3'UTR	NM_001128619.2|NM_145808.3	NP_001122091.2|NP_665807.1	P58546	MTPN_HUMAN	myotrophin	NA		NA			catecholamine metabolic process (GO:0006584)|cell growth (GO:0016049)|cerebellar granule cell differentiation (GO:0021707)|neuron differentiation (GO:0030182)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell growth (GO:0030307)|positive regulation of macromolecule biosynthetic process (GO:0010557)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein metabolic process (GO:0051247)|regulation of barbed-end actin filament capping (GO:2000812)|regulation of striated muscle tissue development (GO:0016202)|regulation of translation (GO:0006417)|skeletal muscle tissue regeneration (GO:0043403)|striated muscle cell differentiation (GO:0051146)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|nucleus (GO:0005634)				endometrium(1)|lung(4)|prostate(1)	6						acacacacacccacacacacc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AC015987	CCDS5842.1	7q33-q35	2013-01-10			ENSG00000105887	ENSG00000105887	136319		Ankyrin repeat domain containing	15667	protein-coding gene	gene with protein product	granule cell differentiation protein	606484			NA	11474205	Standard	NM_145808	NM_145808	NA	Approved	MYOTROPHIN, GCDP, V-1		P58546	OTTHUMG00000155627	ENST00000393085.3:c.*1620G>T	chr7.hg19:g.135613054C>A		NA		hg19	CCDS5842.1	0.02	1.499866	CACxCAC	COVERED																																																																																			NOVEL	MTPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000340921.1	17	4.010413	KEEP	1	3	78	41	1258	CC	1	0.979526	0		-	4	60	120	0	1	7.860942	46	60	1552	143	ENST00000393085.3	0.08	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	136275065	136275065	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:136275065A>G			NA	NA				AC009784.3 (153154 upstream) : hsa-mir-490 (95240 downstream)						NA		NA									NA						gaccagcctgaccaacatggt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.136275065A>G		NA		hg19		0.02	-0.070162	CTGxCCA	UNCOVERED																																																																																			NOVEL					0			3	2.705991	KEEP	1	0	0	9	235	AA	0.99254	0.053733	0			3	60	89	0	0	8.255031	4	60	117	22		0.428571	0.054137
CREB3L2	64764	__UNKNOWN__	__UNKNOWN__	7	137673642	137673642	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:137673642T>C	ENST00000330387.6	-	1	454				CREB3L2_ENST00000456390.1_Intron|CREB3L2_ENST00000452463.1_Intron	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	NA		NA			cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						gagttcaagatcagcctgggc	0.532		NA	T	FUS	fibromyxoid sarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158	64764		basic leucine zipper proteins	23720	protein-coding gene	gene with protein product		608834			NA		Standard	NM_194071	NM_194071	NA	Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.102+12707A>G	chr7.hg19:g.137673642T>C		NA	Q6P454|Q6ZMR6	hg19	CCDS34760.1	0.02	-0.078924	AGAxCAG	UNCOVERED																																																																																			NOVEL	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341462.1	6	3.307489	KEEP	0	0	0	11	292	TT	0.993072	0.0768	0		-	3	60	101	0	0	9.23335	5	60	142	24	ENST00000330387.6	0.375	0.077336
AKR1D1	6718	__UNKNOWN__	__UNKNOWN__	7	137779098	137779098	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:137779098A>T	ENST00000432161.1	+	3	465				AKR1D1_ENST00000242375.3_Intron|AKR1D1_ENST00000411726.2_Intron|AKR1D1_ENST00000468877.2_Intron	NM_001190907.1	NP_001177836.1	P51857	AK1D1_HUMAN	aldo-keto reductase family 1, member D1	NA		NA			androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|C21-steroid hormone metabolic process (GO:0008207)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|steroid binding (GO:0005496)			endometrium(1)|kidney(2)|large_intestine(1)|lung(14)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	23					Azelaic Acid(DB00548)|Finasteride(DB01216)	ccatctctacaaaaaatacaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z28339	CCDS5846.1, CCDS55169.1, CCDS55170.1	7q32-q33	2012-12-04	2012-12-04		ENSG00000122787	ENSG00000122787	6718	1.3.99.6	Aldo-keto reductases	388	protein-coding gene	gene with protein product	delta 4-3-ketosteroid-5-beta-reductase	604741	aldo-keto reductase family 1, member D1 (delta 4-3-ketosteroid-5-beta-reductase)	SRD5B1	NA	7508385, 10343119	Standard	NM_005989	NM_005989	NA	Approved		uc003vtz.3	P51857	OTTHUMG00000155787	ENST00000432161.1:c.378+2468A>T	chr7.hg19:g.137779098A>T		NA	A1L4P6|A8K060|B4DPN3|B4DPN8	hg19	CCDS55169.1	0.02	-0.087694	TACxAAA	UNCOVERED																																																																																			NOVEL	AKR1D1-006	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341643.1	5	2.706877	KEEP	2	0	0	9	249	AA	0.99257	0.09898	0		+	3	60	78	0	0	6.931792	5	60	152	27	ENST00000432161.1	0.375	0.099721
TRIM24	8805	__UNKNOWN__	__UNKNOWN__	7	138159149	138159149	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:138159149T>C	ENST00000343526.4	+	1	579				TRIM24_ENST00000497516.1_Intron|TRIM24_ENST00000415680.2_Intron			O15164	TIF1A_HUMAN	tripartite motif containing 24	NA		NA			calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						ggattacaggtgtgagccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779	8805		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers, Zinc fingers, PHD-type	11812	protein-coding gene	gene with protein product		603406	transcriptional intermediary factor 1, tripartite motif-containing 24	TIF1	NA	9115274, 9191165	Standard	NM_015905	NM_003852	NA	Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.364+13492T>C	chr7.hg19:g.138159149T>C		NA	A4D1R7|A4D1R8|O95854	hg19	CCDS5847.1	0.02	-0.149077	AGGxGTG	COVERED																																																																																			NOVEL	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341814.1	5	2.706426	KEEP	4	0	0	9	245	TT	0.99254	0.289823	0		+	4	60	127	0	0	11.124484	9	60	254	44	ENST00000343526.4	0.307692	0.292001
TRIM24	8805	__UNKNOWN__	__UNKNOWN__	7	138178783	138178783	__UNKNOWN__	Intron	SNP	A	A	G	rs531155296	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:138178783A>G	ENST00000343526.4	+	2	579				TRIM24_ENST00000497516.1_Intron|TRIM24_ENST00000415680.2_Intron			O15164	TIF1A_HUMAN	tripartite motif containing 24	NA		NA			calcium ion homeostasis (GO:0055074)|cellular response to estrogen stimulus (GO:0071391)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of protein stability (GO:0031647)|regulation of signal transduction by p53 class mediator (GO:1901796)|regulation of vitamin D receptor signaling pathway (GO:0070562)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nuclear euchromatin (GO:0005719)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|ligase activity (GO:0016874)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	40						ctggagtgcaatggcgcgatc	0.453		NA											A|||	3	0.000599042	0.0023	0.0	5008	,	,	NA	16831	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Pancreas(179;936 2074 16128 47811 50326)|Colon(136;168 1735 9344 12243 52014)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF009353	CCDS5847.1, CCDS47720.1	7q32-q34	2013-01-28	2011-01-25	2005-06-02	ENSG00000122779	ENSG00000122779	8805		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers, Zinc fingers, PHD-type	11812	protein-coding gene	gene with protein product		603406	transcriptional intermediary factor 1, tripartite motif-containing 24	TIF1	NA	9115274, 9191165	Standard	NM_015905	NM_003852	NA	Approved	hTIF1, Tif1a, RNF82, TIF1A	uc003vuc.3	O15164	OTTHUMG00000155820	ENST00000343526.4:c.365-10252A>G	chr7.hg19:g.138178783A>G		NA	A4D1R7|A4D1R8|O95854	hg19	CCDS5847.1	0.02	-0.052629	GCAxTGG	UNCOVERED																																																																																			NOVEL	TRIM24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000341814.1	2	2.706509	KEEP	0	0	0	9	247	AA	0.99254	0.036491	0		+	2	60	69	0	0	6.65026	2	60	59	23	ENST00000343526.4	0.5	0.036766
ATP6V0A4	50617	__UNKNOWN__	__UNKNOWN__	7	138466354	138466354	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:138466354T>C	ENST00000310018.2	-	2	266				ATP6V0A4_ENST00000353492.4_Intron	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ggattacaggtgtgagccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929	50617		ATPases / V-type	866	protein-coding gene	gene with protein product		605239	ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B, ATPase, H+ transporting, lysosomal V0 subunit a isoform 4, ATPase, H+ transporting, lysosomal V0 subunit A4	ATP6N1B, ATP6N2, RTA1C	NA	10577919, 10973252	Standard	NM_020632	XM_005250393	NA	Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.16+4548A>G	chr7.hg19:g.138466354T>C		NA	A4D1R4|A8KA80|Q32M47	hg19	CCDS5849.1	0.02	-0.122746	AGGxGTG	COVERED																																																																																			NOVEL	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347514.1	7	3.007415	KEEP	1	0	0	10	275	TT	0.99254	0.194847	0		-	3	60	88	0	0	7.301333	9	60	260	35	ENST00000310018.2	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	138691410	138691410	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:138691410G>A			NA	NA				KIAA1549 (25346 upstream) : ZC3HAV1L (19041 downstream)						NA		NA									NA						ttacaggcgtgagccaccgcg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.138691410G>A		NA		hg19		0.02	-0.149123	CGTxAGC	COVERED																																																																																			NOVEL					0			9	3.009257	KEEP	6	0	0	10	317	GG	0.99254	0.289823	0			3	60	87	0	0	6.872332	12	60	399	49		0.2	0.292001
ZC3HAV1	56829	__UNKNOWN__	__UNKNOWN__	7	138733091	138733091	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:138733091T>C	ENST00000242351.5	-	13	2766				ZC3HAV1_ENST00000464606.1_Intron	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	NA		NA			defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						gtggctcatgtctgtaatccc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939	56829		Zinc fingers, CCCH-type domain containing, Poly (ADP-ribose) polymerases	23721	protein-coding gene	gene with protein product	zinc finger antiviral protein,  CCCH-type zinc finger antiviral protein	607312			NA	12215647, 12851707	Standard	NM_020119	NM_024625	NA	Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2450-492A>G	chr7.hg19:g.138733091T>C		NA	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	hg19	CCDS5851.1	0.02	-0.149107	ATGxCTG	COVERED																																																																																			NOVEL	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348915.1	6	2.405242	KEEP	0	0	0	8	208	TT	0.99257	0.289832	0		-	3	60	101	0	0	8.272161	12	60	367	34	ENST00000242351.5	0.2	0.292001
TBXAS1	6916	__UNKNOWN__	__UNKNOWN__	7	139547860	139547860	__UNKNOWN__	Intron	SNP	C	C	T	rs538843780		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:139547860C>T	ENST00000455353.1	+	1	226				TBXAS1_ENST00000263552.6_Intron|TBXAS1_ENST00000416849.2_Intron|TBXAS1_ENST00000336425.5_Intron|TBXAS1_ENST00000458722.1_Intron|TBXAS1_ENST00000411653.1_Intron|TBXAS1_ENST00000448866.1_Intron|TBXAS1_ENST00000462275.1_Intron|TBXAS1_ENST00000436047.2_Intron|TBXAS1_ENST00000539806.1_Intron|TBXAS1_ENST00000414508.2_Intron|TBXAS1_ENST00000425687.1_Intron			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	NA		NA			arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	cctcaagtgaccctcctacct	0.393		NA											c|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17357	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	6916	5.3.99.5	Cytochrome P450s	11609	protein-coding gene	gene with protein product	cytochrome P450, family 5, subfamily A, polypeptide 1	274180	thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)		NA	1714723, 8964509	Standard		NM_001061	NA	Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000455353.1:c.89+18582C>T	chr7.hg19:g.139547860C>T		NA	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	hg19		0.02	-0.043854	TGAxCCT	UNCOVERED																																																																																			NOVEL	TBXAS1-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000348380.1	2	2.406852	KEEP	0	0	0	8	239	CC	0.99257	0.023895	0		+	3	60	87	0	0	9.153042	1	60	33	19	ENST00000455353.1	0.75	0.024074
SLC37A3	84255	__UNKNOWN__	__UNKNOWN__	7	140069429	140069429	__UNKNOWN__	Silent	SNP	G	G	A	rs150737745	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140069429G>A	ENST00000326232.9	-	4	455	c.252C>T	c.(250-252)ctC>ctT	p.L84L	SLC37A3_ENST00000340308.3_Silent_p.L84L|SLC37A3_ENST00000447932.2_Silent_p.L84L|SLC37A3_ENST00000461089.1_5'UTR|SLC37A3_ENST00000429996.2_Silent_p.L84L	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	84		NA			carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CCAGTGTGCCGAGGAAAAGAG	0.448		NA											G|||	2	0.000399361	0.0	0.0	5008	,	,	NA	17313	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Esophageal Squamous(133;211 1716 4665 11387 37873)							NA				0								G	,	1,4405	2.1+/-5.4	0,1,2202	107	96	100		252,252	-10.4	0.1	7	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC37A3	NM_032295.2,NM_207113.1	,	0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077	,	84/444,84/495	140069429	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800	84255		Solute carriers	20651	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032295	NM_001287498	NA	Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.252C>T	chr7.hg19:g.140069429G>A		NA	Q6PIU7|Q86SS4|Q9BQG7	hg19	CCDS5859.1	0.02	1.563935	GCCxAGG	COVERED	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	4.331	0.060750	0.08339	2.27E-4	0.0	ENSG00000157800	ENST00000485861	.	.	.	5.2	-10.4	0.00318	.	.	.	.	.	T	0.33644	0.0870	.	.	.	0.47037	D	0.999293	.	.	.	.	.	.	T	0.40365	-0.9567	4	.	.	.	-22.3588	2.614	0.04899	0.3589:0.349:0.1041:0.1879	.	.	.	.	L	9	.	.	S	-	2	0	SLC37A3	139715898	0.092000	0.21681	0.053000	0.19242	0.451000	0.32288	-1.160000	0.03147	-2.098000	0.00850	-0.218000	0.12543	TCG	NOVEL	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348492.1	2	5.715583	KEEP	0	0	0	19	555	GG	0.99986	0.987804	0		-	4	60	127	0	0	8.231174	56	60	1821	122	ENST00000326232.9	0.066667	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	140137906	140137906	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140137906A>G			NA	NA				RAB19 (11856 upstream) : MKRN1 (14933 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.140137906A>G		NA		hg19		0.02	-0.192908	CACxCCT	COVERED																																																																																			NOVEL					0			10	2.707055	KEEP	2	0	0	9	251	AA	0.99257	0.454356	0			3	60	94	0	0	7.234065	16	60	450	42		0.157895	0.457757
MKRN1	23608	__UNKNOWN__	__UNKNOWN__	7	140175116	140175116	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140175116T>C	ENST00000255977.2	-	2	410				MKRN1_ENST00000443720.2_Intron|MKRN1_ENST00000437223.2_Intron|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000474576.1_Intron|MKRN1_ENST00000481705.1_Intron	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	NA		NA			protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					gcactccagcttgggcgacac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606	23608		RING-type (C3HC4) zinc fingers	7112	protein-coding gene	gene with protein product		607754			NA	10843807	Standard	NM_013446	NM_013446	NA	Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.186-3305A>G	chr7.hg19:g.140175116T>C		NA	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	hg19	CCDS5860.1	0.02	3.487804	AGCxTGG	COVERED																																																																																			NOVEL	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348752.1	48	36.48918	KEEP	0	3	93	154	4276	TT	1	1	0		-	5	60	176	0	0	10.720545	129	60	3956	472	ENST00000255977.2	0.037313	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	140194221	140194221	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140194221A>G			NA	NA				MKRN1 (14852 upstream) : DENND2A (23998 downstream)						NA		NA									NA						ttgggaggccaaggcaggcgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.140194221A>G		NA		hg19		0.02	-0.114019	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			4	2.405706	KEEP	2	0	0	8	218	AA	0	0	0			3	60	95	0	0	8.278628	7	60	208	31		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	140210971	140210971	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140210971A>G			NA	NA				MKRN1 (31602 upstream) : DENND2A (7248 downstream)						NA		NA									NA						cacgatctcgactcactgcaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.140210971A>G		NA		hg19		0.02	-0.052595	TCGxCTC	UNCOVERED																																																																																			NOVEL					0			6	2.40564	KEEP	2	0	0	8	218	AA	0.99257	0.036492	0			2	60	68	0	0	6.550521	2	60	53	21		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	140211781	140211781	__UNKNOWN__	IGR	SNP	C	C	T	rs188296889	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140211781C>T			NA	NA				MKRN1 (32412 upstream) : DENND2A (6438 downstream)						NA		NA									NA						ggattacaggcgtgagccact	0.493		NA											C|||	8	0.00159744	0.0	0.0072	5008	,	,	NA	16974	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.140211781C>T		NA		hg19		0.02	-0.096481	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			8	3.610334	KEEP	0	0	0	12	359	CC	0.993634	0.119669	0			4	60	109	0	0	9.884146	6	60	202	28		0.4	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	140345597	140345597	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:140345597T>C			NA	NA				DENND2A (5021 upstream) : RN7SL771P (46 downstream)						NA		NA									NA						ttgctcttgttgcccaggctg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.140345597T>C		NA		hg19		0.02	-0.035086	TGTxGCC	UNCOVERED																																																																																			NOVEL					0			1	2.405592	KEEP	0	0	0	8	218	TT	0.99257	0.019833	0			2	60	66	1	0	6.350098	2	60	60	21		0.5	0.019982
TMEM178B	100507421	__UNKNOWN__	__UNKNOWN__	7	141114127	141114127	__UNKNOWN__	Intron	SNP	G	G	A	rs577576302		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:141114127G>A	ENST00000565468.1	+	3	575					NM_001195278.1	NP_001182207.1	H3BS89	T178B_HUMAN	transmembrane protein 178B	NA		NA				integral component of membrane (GO:0016021)					NA						cttgtgatccgcccgcctcgg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS59086.1	7q34	2012-06-29			ENSG00000261115	ENSG00000261115	100507421			44112	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001195278	NA	Approved	DKFZp547G036	uc003vwg.2	H3BS89	OTTHUMG00000172737	ENST00000565468.1:c.497-23281G>A	chr7.hg19:g.141114127G>A		NA		hg19	CCDS59086.1	0.02	-0.070169	TCCxCCC	UNCOVERED																																																																																			NOVEL	TMEM178B-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000420337.4	7	3.007453	KEEP	12	0	0	10	280	GG	0	0	0		+	3	32	87	0	0	7.832472	5	60	160	35	ENST00000565468.1	0.375	0.054137
TMEM178B	100507421	__UNKNOWN__	__UNKNOWN__	7	141114131	141114131	__UNKNOWN__	Intron	SNP	G	G	A	rs187184341		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:141114131G>A	ENST00000565468.1	+	3	575					NM_001195278.1	NP_001182207.1	H3BS89	T178B_HUMAN	transmembrane protein 178B	NA		NA				integral component of membrane (GO:0016021)					NA						tgatccgcccgcctcggcctc	0.522		NA											-|||	1	0.000199681	0.0	0.0	5008	,	,	NA	6401	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS59086.1	7q34	2012-06-29			ENSG00000261115	ENSG00000261115	100507421			44112	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001195278	NA	Approved	DKFZp547G036	uc003vwg.2	H3BS89	OTTHUMG00000172737	ENST00000565468.1:c.497-23277G>A	chr7.hg19:g.141114131G>A		NA		hg19	CCDS59086.1	0.02	-0.078938	CCCxCCT	UNCOVERED																																																																																			NOVEL	TMEM178B-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000420337.4	7	3.005481	KEEP	12	0	0	10	285	GG	0	0	0		+	3	32	81	0	0	7.042765	6	60	203	38	ENST00000565468.1	0.333333	0.077336
RP11-744I24.2	0	__UNKNOWN__	__UNKNOWN__	7	141242580	141242580	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:141242580T>C	ENST00000567503.1	-	0	230				RP11-744I24.2_ENST00000566357.1_RNA						NA		NA									NA						TGAgaccaggtgcagtggctc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000567503.1:	chr7.hg19:g.141242580T>C		NA		hg19		0.02	-0.114017	AGGxGCA	UNCOVERED																																																																																			NOVEL	RP11-744I24.2-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000420381.1	7	3.306788	KEEP	0	0	0	11	285	TT	0.993072	0.161341	0		-	3	60	104	0	0	8.901336	9	60	264	36	ENST00000567503.1	0.25	0.162467
RP11-1220K2.2	0	__UNKNOWN__	__UNKNOWN__	7	141829393	141829393	__UNKNOWN__	Intron	SNP	G	G	A	rs12155416	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:141829393G>A	ENST00000477922.3	+	4	240				RP11-1220K2.2_ENST00000550469.2_Intron						NA		NA								endometrium(1)|lung(5)	6						gggaggctgaggtgggtggat	0.458		NA											G|||	499	0.0996406	0.0386	0.1787	5008	,	,	NA	15085	0.0377	NA	0.1014	False	NA	,,,	NA	NA	NA	2504	0.1881	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000477922.3:c.187-1355G>A	chr7.hg19:g.141829393G>A		NA		hg19		0.02	-0.052631	TGAxGTG	UNCOVERED																																																																																			NOVEL	RP11-1220K2.2-003	PUTATIVE	not_best_in_genome_evidence|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000351325.3	7	2.407174	KEEP	11	0	0	8	247	GG	0	0	0		+	3	60	89	0	0	8.868904	2	60	70	29	ENST00000477922.3	0.6	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	142157743	142157743	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:142157743C>G			NA	NA				TRBV5-5 (8344 upstream) : TRBV6-6 (4187 downstream)						NA		NA									NA						cacacacaaacacacacacac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.142157743C>G		NA		hg19		0.02	-0.394733	AAAxACA	COVERED																																																																																			NOVEL					0			13	7.221242	KEEP	0	0	0	24	728	CC	0.999909	0.934407	0			3	60	100	0	1	6.806016	37	60	1211	95		0.075	0.934492
TRBV6-5	28602	__UNKNOWN__	__UNKNOWN__	7	142180849	142180849	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:142180849T>C	ENST00000390368.2	-	0	115									T cell receptor beta variable 6-5	NA		NA									NA						GCAGCCCCAATGGGAAGGCGC	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													72	74	73			NA	NA	7		NA											NA				142180849		1946	4137	6083					L36092		7q34	2012-02-07			ENSG00000211721	ENSG00000211721	28602		T cell receptors / TRB locus	12230	other	T cell receptor gene		NA			NA	8650574	Standard	NG_001333	NG_001333	NA	Approved	TRBV65, TCRBV13S1, TCRBV6S5			OTTHUMG00000158519	ENST00000390368.2:	chr7.hg19:g.142180849T>C		NA		hg19		0.02	1.806686	CAAxGGG	COVERED																																																																																			NOVEL	TRBV6-5-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	NA	TR_V_gene	OTTHUMT00000351225.1	0	2.405879	KEEP	0	0	0	8	218	TT	0.99257	0.969607	0		-	6	40	193	0	0	14.19923	44	60	1276	89	ENST00000390368.2	0.12	0.976865
TPK1	27010	__UNKNOWN__	__UNKNOWN__	7	144487118	144487118	__UNKNOWN__	Intron	SNP	T	T	C	rs1635361	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:144487118T>C	ENST00000360057.3	-	3	146				TPK1_ENST00000378099.3_Intron	NM_022445.3	NP_071890.2	Q9H3S4	TPK1_HUMAN	thiamin pyrophosphokinase 1	NA		NA			small molecule metabolic process (GO:0044281)|thiamine diphosphate biosynthetic process (GO:0009229)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|thiamine binding (GO:0030975)|thiamine diphosphokinase activity (GO:0004788)			large_intestine(3)|lung(12)|ovary(2)|urinary_tract(2)	19					Thiamine(DB00152)	tggagtgcaatggcacgatct	0.512		NA											T|||	2185	0.436302	0.736	0.4164	5008	,	,	NA	15244	0.1954	NA	0.497	False	NA	,,,	NA	NA	NA	2504	0.2311	NA	NA	NA	Ovarian(45;88 1034 2073 5829 28455)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028138	CCDS5888.1, CCDS55178.1	7q34-q35	2008-07-18			ENSG00000196511	ENSG00000196511	27010			17358	protein-coding gene	gene with protein product	placental protein 20, thiamine pyrophosphokinase 1, thiamine kinase, thiamine diphosphokinase	606370			NA	11342111	Standard	NM_022445	NM_022445	NA	Approved	HTPK1, PP20	uc003weq.3	Q9H3S4	OTTHUMG00000152774	ENST00000360057.3:c.44-24074A>G	chr7.hg19:g.144487118T>C		NA	A8K0T7|D3DWG0|I6L9B8|Q6NUR5|Q9H602	hg19	CCDS5888.1	0.02	-0.035078	CAAxGGC	UNCOVERED																																																																																			NOVEL	TPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327777.1	7	3.00763	KEEP	1	0	0	10	275	TT	0.99254	0.019833	0		-	3	30	94	0	0	9.853251	1	60	29	17	ENST00000360057.3	0.75	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	144960350	144960350	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:144960350A>G			NA	NA				RN7SKP174 (413173 upstream) : AC006007.1 (412624 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.144960350A>G		NA		hg19		0.02	-0.140329	CACxCCT	COVERED																																																																																			NOVEL					0			7	2.981391	KEEP	1	0	0	10	256	AA	0.992708	0.259062	0			3	60	95	0	0	7.882146	10	60	297	44		0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	144999468	144999468	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:144999468T>C			NA	NA				RN7SKP174 (452291 upstream) : AC006007.1 (373506 downstream)						NA		NA									NA						gctgggattatagatgtgagc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.144999468T>C		NA		hg19		0.02	-0.157736	TTAxAGA	COVERED																																																																																			NOVEL					0			8	2.98049	KEEP	1	0	0	10	245	TT	0.99254	0.320398	0			3	60	102	0	0	8.280435	13	60	350	39		0.1875	0.322807
CNTNAP2	26047	__UNKNOWN__	__UNKNOWN__	7	146896349	146896349	__UNKNOWN__	Intron	SNP	C	C	T	rs117412983|rs35558023	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:146896349C>T	ENST00000361727.3	+	8	1864					NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	NA		NA			adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ccaccgcgcccggccCTAATC	0.483		NA								HNSCC(39;0.1)			c|||	290	0.0579073	0.056	0.0576	5008	,	,	NA	14581	0.0139	NA	0.1064	False	NA	,,,	NA	NA	NA	2504	0.0562	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469	26047			13830	protein-coding gene	gene with protein product		604569			NA	10624965, 10048485	Standard		NM_014141	NA	Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1348+66748C>T	chr7.hg19:g.146896349C>T		NA	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	hg19	CCDS5889.1	0.02	-0.12278	GCCxGGC	UNCOVERED																																																																																			NOVEL	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327668.1	7	2.406808	KEEP	4	0	0	8	238	CC	0	0	0		+	4	60	124	0	0	10.823991	9	60	289	32	ENST00000361727.3	0.307692	0.196312
PDIA4	9601	__UNKNOWN__	__UNKNOWN__	7	148716572	148716572	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:148716572C>G	ENST00000286091.4	-	3	502					NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	NA		NA			cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			agcactttggcaggctgaggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	9601	5.3.4.1	Protein disulfide isomerases	30167	protein-coding gene	gene with protein product		NA	protein disulfide isomerase-associated 4		NA	2549034, 2002068	Standard	NM_004911	NM_004911	NA	Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.270-283G>C	chr7.hg19:g.148716572C>G		NA	A8K4K6|Q549T6	hg19	CCDS5893.1	0.02	-0.105274	TGGxAGG	UNCOVERED																																																																																			NOVEL	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317077.1	2	2.406862	KEEP	0	0	0	8	241	CC	0.99257	0.138793	0		-	3	60	101	0	0	9.043407	6	60	210	30	ENST00000286091.4	0.333333	0.139832
ZNF425	155054	__UNKNOWN__	__UNKNOWN__	7	148809506	148809506	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:148809506T>A	ENST00000378061.2	-	3	278				ZNF425_ENST00000484196.1_Intron	NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			caggcagatctcttgaggtca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947	155054		Zinc fingers, C2H2-type, -	20690	protein-coding gene	gene with protein product		NA			NA		Standard	XM_088140	NM_001001661	NA	Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.146-119A>T	chr7.hg19:g.148809506T>A		NA	B3KPM1|Q08AG3	hg19	CCDS34773.1	0.02	-0.22801	ATCxCTT	COVERED																																																																																			NOVEL	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352726.1	3	5.112614	KEEP	1	0	0	17	468	TT	0.997832	0.581666	0		-	4	60	114	1	0	8.695809	19	60	567	54	ENST00000378061.2	0.173913	0.58293
ZNF398	57541	__UNKNOWN__	__UNKNOWN__	7	148851842	148851842	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:148851842G>A	ENST00000475153.1	+	2	687				ZNF398_ENST00000420008.2_Intron|ZNF398_ENST00000483892.1_Intron|ZNF398_ENST00000540950.1_Intron|ZNF398_ENST00000485111.1_Intron|ZNF398_ENST00000491174.1_Intron|ZNF398_ENST00000426851.2_Intron|ZNF398_ENST00000335901.4_Intron			Q8TD17	ZN398_HUMAN	zinc finger protein 398	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			agcactttgggaggctgagat	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024	57541		Zinc fingers, C2H2-type, -	18373	protein-coding gene	gene with protein product		NA			NA	11779858	Standard		NM_170686	NA	Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.420+410G>A	chr7.hg19:g.148851842G>A		NA	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	hg19	CCDS5894.1	0.02	-0.026308	TGGxAGG	UNCOVERED																																																																																			NOVEL	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352722.2	2	2.407174	KEEP	0	0	0	8	245	GG	0.99257	0	0		+	2	60	54	0	0	6.352461	0	0	0	15	ENST00000475153.1	1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	149588712	149588712	__UNKNOWN__	IGR	SNP	G	G	A	rs2626755		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:149588712G>A			NA	NA				RP11-728K20.3 (207 upstream) : RP11-728K20.2 (109128 downstream)						NA		NA									NA						ccaggagttcgagaccagcct	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.149588712G>A		NA		hg19		0.02	-0.166662	TTCxAGA	COVERED																																																																																			NOVEL					0			6	3.609386	KEEP	1	0	0	12	343	GG	0.994391	0.351961	0			3	60	87	0	0	6.692132	14	60	449	48		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	149863525	149863525	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:149863525T>C			NA	NA				RP11-545G3.1 (92060 upstream) : ACTR3C (80776 downstream)						NA		NA									NA						ctgtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.149863525T>C		NA		hg19		0.02	-0.114004	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			3	2.405487	KEEP	3	0	0	8	213	TT	0	0	0			3	49	106	0	0	9.10154	9	60	256	32		0.25	0.162467
TMEM176A	55365	__UNKNOWN__	__UNKNOWN__	7	150499202	150499202	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:150499202C>T	ENST00000484928.1	+	3	755				TMEM176A_ENST00000461345.1_Intron|TMEM176A_ENST00000004103.3_Intron			Q96HP8	T176A_HUMAN	transmembrane protein 176A	NA		NA			negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ctttctttctctctctctCTA	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933	55365			24930	protein-coding gene	gene with protein product		610334			NA	12097419, 8889548	Standard	NM_018487	NM_018487	NA	Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.175-101C>T	chr7.hg19:g.150499202C>T		NA	D3DX00|Q9NYC7	hg19	CCDS5909.1	0.02	-0.412275	TCTxTCT	COVERED																																																																																			NOVEL	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350222.1	14	7.354393	KEEP	0	1	21	32	989	CC	0.999998	0.941739	0		+	4	60	116	0	0	7.612174	42	60	1410	107	ENST00000484928.1	0.086957	0.941741
TMEM176A	55365	__UNKNOWN__	__UNKNOWN__	7	150499206	150499206	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:150499206C>T	ENST00000484928.1	+	3	755				TMEM176A_ENST00000461345.1_Intron|TMEM176A_ENST00000004103.3_Intron			Q96HP8	T176A_HUMAN	transmembrane protein 176A	NA		NA			negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ctttctctctctctCTACCTC	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933	55365			24930	protein-coding gene	gene with protein product		610334			NA	12097419, 8889548	Standard	NM_018487	NM_018487	NA	Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.175-97C>T	chr7.hg19:g.150499206C>T		NA	D3DX00|Q9NYC7	hg19	CCDS5909.1	0.02	-0.438585	TCTxTCT	COVERED																																																																																			NOVEL	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350222.1	14	9.929664	KEEP	0	0	0	33	1028	CC	0.999998	0.959857	0		+	4	60	120	0	0	7.934234	44	60	1451	112	ENST00000484928.1	0.083333	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	151219016	151219016	__UNKNOWN__	IGR	SNP	C	C	T	rs190154131	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151219016C>T			NA	NA				RHEB (1810 upstream) : PRKAG2 (34180 downstream)						NA		NA									NA						Aggctgggcgcggtggttcac	0.512		NA											C|||	3	0.000599042	0.0008	0.0014	5008	,	,	NA	13942	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.151219016C>T		NA		hg19		0.02	-0.175432	GCGxGGT	COVERED																																																																																			NOVEL					0			3	2.706887	KEEP	0	0	0	9	256	CC	0.99254	0.384517	0			3	60	89	0	0	6.89205	14	60	452	42		0.176471	0.387407
PRKAG2	51422	__UNKNOWN__	__UNKNOWN__	7	151424055	151424055	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151424055G>A	ENST00000287878.4	-	4	971				PRKAG2_ENST00000433631.2_Intron|PRKAG2_ENST00000492843.1_Intron|PRKAG2_ENST00000392801.2_Intron|PRKAG2_ENST00000461529.1_Intron	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	NA		NA			ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	taatcccagcgctttgggagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617	51422			9386	protein-coding gene	gene with protein product	AMPK gamma2	602743			NA	8557660, 8621499	Standard	NM_016203	NM_024429	NA	Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.467-51332C>T	chr7.hg19:g.151424055G>A		NA	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	hg19	CCDS5928.1	0.02	-0.10525	AGCxCTT	UNCOVERED																																																																																			NOVEL	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348440.2	4	2.691324	KEEP	0	0	0	9	240	GG	0.99254	0.138789	0		-	3	60	86	0	0	7.101024	9	60	290	30	ENST00000287878.4	0.25	0.139832
GALNT11	63917	__UNKNOWN__	__UNKNOWN__	7	151755496	151755496	__UNKNOWN__	Intron	SNP	C	C	T	rs182179762	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151755496C>T	ENST00000430044.2	+	1	192				GALNT11_ENST00000482812.1_Intron|GALNT11_ENST00000452146.2_Intron	NM_022087.2	NP_071370.2	Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	NA		NA			cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		ctcggctcaccgcaacctctg	0.498		NA											C|||	3	0.000599042	0.0015	0.0	5008	,	,	NA	17177	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	63917	2.4.1.41	Glycosyltransferase family 2 domain containing	19875	protein-coding gene	gene with protein product	polypeptide GalNAc transferase 11	615130	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)		NA	11925450	Standard	NM_022087	NM_022087	NA	Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000430044.2:c.-39+32527C>T	chr7.hg19:g.151755496C>T		NA	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	hg19	CCDS5930.1	0.02	-0.114022	CACxGCA	UNCOVERED																																																																																			NOVEL	GALNT11-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348189.1	4	3.008054	KEEP	0	0	0	10	291	CC	0.992708	0.161282	0		+	5	60	143	0	0	12.922804	8	60	260	30	ENST00000430044.2	0.384615	0.162467
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151908889	151908889	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151908889C>T	ENST00000262189.6	-	24	3931				KMT2C_ENST00000355193.2_Intron	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	NA		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						atcccagcaccttgggaggct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.3713-4376G>A	chr7.hg19:g.151908889C>T		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	-0.077584	CACxTTG	UNCOVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	1	2.707929	KEEP	2	0	0	9	274	CC	0.99254	0.076759	0		-	3	60	89	0	0	8.070743	5	60	139	29	ENST00000262189.6	0.375	0.077336
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962134	151962134	__UNKNOWN__	Nonsense_Mutation	SNP	G	G	T	rs146238849		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151962134G>T	ENST00000262189.6	-	8	1391	c.1173C>A	c.(1171-1173)tgC>tgA	p.C391*	KMT2C_ENST00000355193.2_Nonsense_Mutation_p.C391*	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	391		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.C391*(2)			NA						TGCAGTTCTGGCACACTTTGC	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Nonsense(2)	NS(2)											230	213	219			NA	NA	7		NA											NA				151962134		2203	4297	6500	SO:0001587	stop_gained			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1173C>A	chr7.hg19:g.151962134G>T	ENSP00000262189:p.Cys391*	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	3.94444	CTGxCAC	COVERED	.	.	.	.	.	.	.	.	.	.	G	39	7.887843	0.98545	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	.	.	.	4.53	3.62	0.41486	.	0.000000	0.45867	U	0.000330	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2395	0.54534	0.0835:0.0:0.9165:0.0	.	.	.	.	X	391	.	ENSP00000262189:C391X	C	-	3	2	MLL3	151593067	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.718000	0.74713	2.206000	0.71126	0.460000	0.39030	TGC	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	8	3.30781	KEEP	21	3	76	38	1152	GG	1	1	0		-	7	49	198	0	0	10.434646	167	60	5633	337	ENST00000262189.6	0.04023	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962168	151962168	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs138908625	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151962168C>A	ENST00000262189.6	-	8	1357	c.1139G>T	c.(1138-1140)cGt>cTt	p.R380L	KMT2C_ENST00000355193.2_Missense_Mutation_p.R380L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	380		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R380L(4)			NA						CCAACCTGCACGTTTTAATGG	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				4	Substitution - Missense(4)	skin(4)						C	LEU/ARG	29,4377	25.3+/-52.1	0,29,2174	410	369	383		1139	4.7	1	7	dbSNP_134	383	15,8585	3.7+/-12.6	0,15,4285	no	missense	MLL3	NM_170606.2	102	0,44,6459	AA,AC,CC	NA	0.1744,0.6582,0.3383	probably-damaging	380/4912	151962168	44,12962	2203	4300	6503	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1139G>T	chr7.hg19:g.151962168C>A	ENSP00000262189:p.Arg380Leu	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	8.016078	GCAxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.95	2.688003	0.48097	0.006582	0.001744	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98876	-5.2;-5.2	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.38548	U	0.001645	D	0.98560	0.9519	M	0.74881	2.28	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	D	0.96263	0.9192	10	0.52906	T	0.07	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	380	Q8NEZ4	MLL3_HUMAN	L	380	ENSP00000262189:R380L;ENSP00000347325:R380L	ENSP00000262189:R380L	R	-	2	0	MLL3	151593101	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	6.039000	0.70972	2.271000	0.75665	0.557000	0.71058	CGT	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	10	3.17348	KEEP	15	5	143	61	1795	CC	1	1	0		-	9	50	284	0	0	15.824689	245	51	8116	507	ENST00000262189.6	0.035433	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962257	151962257	__UNKNOWN__	Silent	SNP	C	C	T	rs62478357		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151962257C>T	ENST00000262189.6	-	8	1268	c.1050G>A	c.(1048-1050)ccG>ccA	p.P350P	KMT2C_ENST00000355193.2_Silent_p.P350P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	350		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						AGAGGTCTCCCGGGCTGTCGC	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													146	134	138			NA	NA	7		NA											NA				151962257		2203	4296	6499	SO:0001819	synonymous_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1050G>A	chr7.hg19:g.151962257C>T		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	4.333052	TCCxGGG	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	12	4.071405	KEEP	48	5	137	62	1768	CC	1	1	0		-	10	50	303	0	0	18.151155	177	51	5722	421	ENST00000262189.6	0.053476	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151962265	151962265	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201834857		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151962265C>T	ENST00000262189.6	-	8	1260	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	KMT2C_ENST00000355193.2_Missense_Mutation_p.D348N	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	348		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D348N(2)			NA						CCCGGGCTGTCGCACACTGCA	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	skin(2)											112	101	104			NA	NA	7		NA											NA				151962265		2203	4296	6499	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1042G>A	chr7.hg19:g.151962265C>T	ENSP00000262189:p.Asp348Asn	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	4.508744	TGTxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.09	2.730606	0.48939	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98807	-5.15;-5.15	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.43919	U	0.000512	D	0.98516	0.9505	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.98479	1.0604	10	0.23302	T	0.38	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	348	Q8NEZ4	MLL3_HUMAN	N	348	ENSP00000262189:D348N;ENSP00000347325:D348N	ENSP00000262189:D348N	D	-	1	0	MLL3	151593198	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAC	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	12	6.143304	KEEP	48	4	109	59	1662	CC	1	1	0		-	9	49	270	0	0	16.098336	158	60	4982	373	ENST00000262189.6	0.053892	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	151970859	151970859	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs149992209	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:151970859C>T	ENST00000262189.6	-	7	1161	c.943G>A	c.(943-945)Ggc>Agc	p.G315S	KMT2C_ENST00000355193.2_Missense_Mutation_p.G315S	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	315		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						TGAAAGGTGCCGGCTCCTGCA	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													263	245	251			NA	NA	7		NA											NA				151970859		2203	4300	6503	SO:0001583	missense			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.943G>A	chr7.hg19:g.151970859C>T	ENSP00000262189:p.Gly315Ser	NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	9.041572	TGCxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265939	0.80358	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.72615	-0.67;-0.67	4.87	4.87	0.63330	Zinc finger, PHD-type (1);	0.000000	0.45606	D	0.000359	D	0.85999	0.5828	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87947	0.2721	10	0.59425	D	0.04	.	18.3752	0.90433	0.0:1.0:0.0:0.0	.	315	Q8NEZ4	MLL3_HUMAN	S	315	ENSP00000262189:G315S;ENSP00000347325:G315S	ENSP00000262189:G315S	G	-	1	0	MLL3	151601792	1.000000	0.71417	0.992000	0.48379	0.975000	0.68041	7.752000	0.85141	2.423000	0.82170	0.650000	0.86243	GGC	NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	7	20.889594	KEEP	6	1	27	79	2311	CC	1	1	0		-	11	59	332	0	0	17.821922	301	60	9839	633	ENST00000262189.6	0.035256	1
KMT2C	58508	__UNKNOWN__	__UNKNOWN__	7	152103041	152103041	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152103041C>G	ENST00000262189.6	-	1	380				KMT2C_ENST00000355193.2_Intron	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	NA		NA			histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)				NA						ccattgcactccaacctgggc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609	58508		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	13726	protein-coding gene	gene with protein product		606833	myeloid/lymphoid or mixed-lineage leukemia 3	MLL3	NA	10819331	Standard		XM_005250026	NA	Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.161+29669G>C	chr7.hg19:g.152103041C>G		NA	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	hg19	CCDS5931.1	0.02	-0.412292	ACTxCAA	COVERED																																																																																			NOVEL	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318887.3	21	7.857689	KEEP	6	1	31	37	1156	CC	0.999998	0.9484	0		-	3	60	108	0	0	8.426415	19	60	615	131	ENST00000262189.6	0.136364	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	152175026	152175026	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152175026T>C			NA	NA				LINC01003 (12392 upstream) : RNA5SP250 (115031 downstream)						NA		NA									NA						aaggcagagctgagatcgtgc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.152175026T>C		NA		hg19		0.02	-0.061399	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			7	3.007422	KEEP	0	0	0	10	277	TT	0.992708	0.043467	0			3	60	102	0	0	9.555427	4	60	119	22		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	152209729	152209729	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152209729T>C			NA	NA				LINC01003 (47095 upstream) : RNA5SP250 (80328 downstream)						NA		NA									NA						gtcaggagtttgagaccagcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.152209729T>C		NA		hg19		0.02	-0.105251	GTTxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.406343	KEEP	1	0	0	8	224	TT	0	0	0			3	40	99	0	0	8.401256	9	60	269	28		0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	152387537	152387537	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152387537C>A			NA	NA				XRCC2 (14287 upstream) : RN7SL811P (47989 downstream)						NA		NA									NA						gcagtccggcctgggcgacag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.152387537C>A		NA		hg19		0.02	-0.070155	GGCxTGG	UNCOVERED																																																																																			NOVEL					0			17	4.212516	KEEP	15	0	0	14	429	CC	0	0	0			3	60	79	0	0	7.866493	2	43	73	33		0.6	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	152413021	152413021	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152413021C>T			NA	NA				XRCC2 (39771 upstream) : RN7SL811P (22505 downstream)						NA		NA									NA						tcgctcttgtcgcccaggctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.152413021C>T		NA		hg19		0.02	-0.131548	TGTxGCC	COVERED																																																																																			NOVEL					0			4	3.007467	KEEP	0	0	0	10	279	CC	0.992708	0.227502	0			3	60	89	0	0	7.282307	10	60	297	37		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	152558572	152558572	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152558572T>C			NA	NA				ACTR3B (6109 upstream) : AF104455.1 (195249 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.152558572T>C		NA		hg19		0.02	-0.166651	GTGxTGG	COVERED																																																																																			NOVEL					0			3	3.008397	KEEP	0	0	0	10	290	TT	0.992708	0.351366	0			3	60	99	0	0	7.81014	15	60	456	42		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	7	152898100	152898100	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:152898100C>T			NA	NA				AF104455.1 (144196 upstream) : AC073236.3 (210218 downstream)						NA		NA									NA						tgcagtgagccgagatcatgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr7.hg19:g.152898100C>T		NA		hg19		0.02	-0.219295	AGCxGAG	COVERED																																																																																			NOVEL					0			27	4.786397	KEEP	16	0	0	16	430	CC	0.992708	0.548856	0			3	46	89	0	0	6.592793	18	60	584	63		0.142857	0.552887
DPP6	1804	__UNKNOWN__	__UNKNOWN__	7	154180866	154180866	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:154180866A>G	ENST00000377770.3	+	3	598				DPP6_ENST00000332007.3_Intron|DPP6_ENST00000404039.1_Intron|DPP6_ENST00000406326.1_Intron|DPP6_ENST00000496611.1_Intron|DPP6_ENST00000427557.1_Intron			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	NA		NA			cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			tgcaacctccacctcccgggt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(125;1384 1783 2490 7422 34254)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226	1804			3010	protein-coding gene	gene with protein product		126141	dipeptidylpeptidase VI, dipeptidylpeptidase 6		NA	1729689	Standard	NM_130797	XM_006715871	NA	Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.457+8744A>G	chr7.hg19:g.154180866A>G		NA		hg19		0.02	-0.157863	TCCxCCT	UNCOVERED																																																																																			NOVEL	DPP6-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000322932.1	11	2.404595	KEEP	3	0	0	8	205	AA	0	0	0		+	3	60	94	0	0	7.310493	15	60	440	37	ENST00000377770.3	0.166667	0.322807
AC009403.2	0	__UNKNOWN__	__UNKNOWN__	7	155410483	155410483	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:155410483T>C	ENST00000401694.1	-	3	325										NA		NA									NA						Tggctgggcgtggtggctcac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000401694.1:c.102-6372A>G	chr7.hg19:g.155410483T>C		NA		hg19		0.02	-0.157819	GCGxGGT	COVERED																																																																																			NOVEL	AC009403.2-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000322338.1	3	3.909726	KEEP	3	0	0	13	360	TT	0.993072	0.32057	0		-	3	60	103	0	0	8.472958	12	60	333	52	ENST00000401694.1	0.2	0.322807
LMBR1	64327	__UNKNOWN__	__UNKNOWN__	7	156659585	156659585	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:156659585T>C	ENST00000353442.5	-	1	303				LMBR1_ENST00000354505.4_Intron|LMBR1_ENST00000540390.1_Intron	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	NA		NA			embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		catgagccactgcgcccagcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983	64327			13243	protein-coding gene	gene with protein product		605522	chromosome 7 open reading frame 2, limb region 1 homolog (mouse)	C7orf2	NA	10329000, 11090342	Standard	NM_022458	NM_022458	NA	Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.66+26036A>G	chr7.hg19:g.156659585T>C		NA	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	hg19	CCDS5945.1	0.02	-0.114026	CACxGCG	UNCOVERED																																																																																			NOVEL	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347939.3	4	2.40642	KEEP	1	0	0	8	226	TT	0.99257	0.16126	0		-	3	45	95	0	0	8.132488	8	60	241	30	ENST00000353442.5	0.272727	0.162467
DNAJB6	10049	__UNKNOWN__	__UNKNOWN__	7	157147111	157147111	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:157147111G>A	ENST00000429029.2	+	2	179				DNAJB6_ENST00000262177.4_Intron|DNAJB6_ENST00000443280.1_Intron|DNAJB6_ENST00000452797.2_Intron	NM_005494.2	NP_005485.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	NA		NA			intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		aaagtgctgggattacaggtg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(46;195 967 1350 20350 43814)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993	10049		Heat shock proteins / DNAJ (HSP40)	14888	protein-coding gene	gene with protein product		611332	limb girdle muscular dystrophy 1D (autosomal dominant)	LGMD1D	NA	10319584, 9915854, 22366786	Standard		NM_005494	NA	Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000429029.2:c.-26-4130G>A	chr7.hg19:g.157147111G>A		NA	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	hg19	CCDS47755.1	0.02	-0.026314	TGGxATT	UNCOVERED																																																																																			NOVEL	DNAJB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348120.1	4	2.407038	KEEP	0	0	0	8	241	GG	0.99257	0	0		+	2	60	60	0	0	6.953373	0	0	0	15	ENST00000429029.2	1	0
ESYT2	57488	__UNKNOWN__	__UNKNOWN__	7	158537324	158537324	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr7:158537324A>G	ENST00000251527.5	-	16	1791					NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	NA		NA			endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						caaagtactgagattacaggt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868	57488		Synaptotagmins	22211	protein-coding gene	gene with protein product		NA	family with sequence similarity 62 (C2 domain containing), member B	FAM62B	NA	17672888	Standard	NM_020728	NM_020728	NA	Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1726-955T>C	chr7.hg19:g.158537324A>G		NA	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	hg19	CCDS34791.1	0.02	-0.192979	CTGxGAT	COVERED																																																																																			NOVEL	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322647.1	9	4.511397	KEEP	1	0	0	15	414	AA	0.99649	0.45615	0		-	3	60	106	0	0	8.36047	17	60	536	58	ENST00000251527.5	0.15	0.457757
FBXO25	26260	__UNKNOWN__	__UNKNOWN__	8	389830	389830	__UNKNOWN__	Intron	SNP	G	G	A	rs561338661	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:389830G>A	ENST00000350302.3	+	5	647				FBXO25_ENST00000352684.2_Intron|FBXO25_ENST00000382824.1_Intron|FBXO25_ENST00000276326.5_Intron	NM_183420.1	NP_904356.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	NA		NA			protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		cactttgggaggctgaggcag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364	26260		F-boxes /  other	13596	protein-coding gene	gene with protein product		609098	F-box only protein 25		NA	10531035, 10531037	Standard	NM_012173	NM_012173	NA	Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000350302.3:c.381+4123G>A	chr8.hg19:g.389830G>A		NA	Q6PJ83|Q7Z4V4|Q9UKB8	hg19	CCDS5952.1	0.02	-0.149136	GGAxGCT	COVERED																																																																																			NOVEL	FBXO25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206711.1	5	3.610887	KEEP	2	0	0	12	373	GG	0.993634	0.290142	0		+	3	31	94	0	0	7.478667	13	60	460	49	ENST00000350302.3	0.1875	0.292001
DLGAP2	9228	__UNKNOWN__	__UNKNOWN__	8	1581004	1581004	__UNKNOWN__	Silent	SNP	G	G	A	rs527705861		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:1581004G>A	ENST00000421627.2	+	5	1496	c.1362G>A	c.(1360-1362)gcG>gcA	p.A454A		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	533		NA			neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.A476A(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		TGAGCGAGGCGGAGATCAATG	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - coding silent(1)	pancreas(1)											109	115	113			NA	NA	8		NA											NA				1581004		2183	4272	6455	SO:0001819	synonymous_variant			AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010	9228			2906	protein-coding gene	gene with protein product		605438	discs, large (Drosophila) homolog-associated protein 2		NA	9286858, 10854099	Standard	NM_004745	NM_004745	NA	Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1362G>A	chr8.hg19:g.1581004G>A		NA	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	hg19	CCDS47760.1	0.02	-0.192952	GGCxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.371	-0.933905	0.02340	.	.	ENSG00000198010	ENST00000520901	.	.	.	5.06	-10.1	0.00402	.	.	.	.	.	T	0.34250	0.0891	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50550	-0.8815	4	.	.	.	-15.8913	2.5798	0.04816	0.4052:0.2479:0.0658:0.281	.	.	.	.	Q	471	.	.	R	+	2	0	DLGAP2	1568411	0.000000	0.05858	0.001000	0.08648	0.122000	0.20287	-5.046000	0.00156	-3.988000	0.00084	-0.378000	0.06908	CGG	NOVEL	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374478.1	1	2.706056	KEEP	0	0	0	9	239	GG	0.99254	0.454342	0		+	8	60	248	0	0	22.354492	14	60	436	36	ENST00000421627.2	0.363636	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	2125717	2125717	__UNKNOWN__	IGR	SNP	A	A	G	rs552012839		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:2125717A>G			NA	NA				MYOM2 (32337 upstream) : AC133633.2 (225274 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.2125717A>G		NA		hg19		0.02	-0.070153	CACxCCT	UNCOVERED																																																																																			NOVEL					0			3	3.3072	KEEP	1	0	0	11	291	AA	0.992708	0.053742	0			3	60	90	0	0	8.624641	3	60	86	29		0.5	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	2148999	2148999	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:2148999A>G			NA	NA				MYOM2 (55619 upstream) : AC133633.2 (201992 downstream)						NA		NA									NA						ttgtgtgtgtatgtatgtgtA	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.2148999A>G		NA		hg19		0.02	1.464759	TGTxTGT	COVERED																																																																																			NOVEL					0			55	31.607674	KEEP	0	1	16	111	2998	AA	1	0.999919	0			4	60	129	0	0	7.919245	76	60	2233	302		0.05	0.999919
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	2223458	2223458	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:2223458G>A			NA	NA				MYOM2 (130078 upstream) : AC133633.2 (127533 downstream)						NA		NA									NA						gcaacagagcgagaccctgtc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.2223458G>A		NA		hg19		0.02	-0.140335	AGCxAGA	COVERED																																																																																			NOVEL					0			11	3.911305	KEEP	0	0	0	13	391	GG	0.994391	0.259501	0			3	60	82	0	0	6.473167	11	60	350	39		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	8141655	8141655	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:8141655C>T			NA	NA				FAM86B3P (39270 upstream) : SGK223 (33602 downstream)						NA		NA									NA						aaaaattagccgggcgtggtg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.8141655C>T		NA		hg19		0.02	-0.078212	AGCxGGG	UNCOVERED																																																																																			NOVEL					0			13	2.404622	KEEP	7	0	0	8	203	CC	0	0	0			3	60	92	0	0	8.859243	3	60	68	23		0.5	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	8753833	8753833	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:8753833T>G			NA	NA				RNU6-682P (405 upstream) : RP11-62H7.2 (64876 downstream)						NA		NA									NA						ttgttgcccatgctggactcg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.8753833T>G		NA		hg19		0.02	-0.166651	CCAxGCT	COVERED																																																																																			NOVEL					0			5	3.007001	KEEP	0	0	0	10	270	TT	0.992708	0.351366	0			3	60	88	0	0	6.792392	14	60	430	44		0.176471	0.353947
TNKS	8658	__UNKNOWN__	__UNKNOWN__	8	9617280	9617280	__UNKNOWN__	Intron	SNP	C	C	G	rs551412406		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:9617280C>G	ENST00000518281.1	+	21	2873				TNKS_ENST00000310430.6_Intron			O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	NA		NA			mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		gtcaggagatcgagaccatcc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273	8658		Poly (ADP-ribose) polymerases, Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	11941	protein-coding gene	gene with protein product		603303			NA	9822378, 10198177	Standard	NM_003747	XM_006716263	NA	Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000518281.1:c.2443-1746C>G	chr8.hg19:g.9617280C>G		NA	O95272|Q4G0F2	hg19		0.02	-0.131581	GATxGAG	COVERED																																																																																			NOVEL	TNKS-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000375036.1	6	3.609761	KEEP	7	0	0	12	352	CC	0.99257	0.22747	0		+	3	41	108	1	0	9.072646	11	60	356	47	ENST00000518281.1	0.214286	0.229173
TNKS	8658	__UNKNOWN__	__UNKNOWN__	8	9620179	9620179	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:9620179G>A	ENST00000518281.1	+	22	2994				TNKS_ENST00000310430.6_Intron			O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	NA		NA			mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		ttgggaggccgaggcaggcag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273	8658		Poly (ADP-ribose) polymerases, Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	11941	protein-coding gene	gene with protein product		603303			NA	9822378, 10198177	Standard	NM_003747	XM_006716263	NA	Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000518281.1:c.2564-478G>A	chr8.hg19:g.9620179G>A		NA	O95272|Q4G0F2	hg19		0.02	-0.105256	GCCxAGG	UNCOVERED																																																																																			NOVEL	TNKS-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000375036.1	7	2.40651	KEEP	0	0	0	8	232	GG	0.99257	0.138793	0		+	3	60	86	0	0	7.232147	8	60	268	26	ENST00000518281.1	0.272727	0.139832
SOX7	83595	__UNKNOWN__	__UNKNOWN__	8	10582477	10582477	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:10582477A>C	ENST00000304501.1	-	0	2016					NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	NA		NA			endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		ggtgatccacatgcctcggcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056	83595		SRY (sex determining region Y)-boxes	18196	protein-coding gene	gene with protein product		612202			NA	11691915	Standard		NM_031439	NA	Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.*771T>G	chr8.hg19:g.10582477A>C		NA	B4DKV0|Q53YD0	hg19	CCDS5977.1	0.02	-0.166623	CACxTGC	COVERED																																																																																			NOVEL	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207131.1	4	2.406218	KEEP	0	0	0	8	225	AA	0.99257	0.351317	0		-	3	60	81	0	0	6.482422	10	60	307	35	ENST00000304501.1	0.230769	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	11814532	11814532	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:11814532T>A			NA	NA				CTSB (88794 upstream) : DEFB136 (16913 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.11814532T>A		NA		hg19		0.02	-0.219212	AGGxGTG	COVERED																																																																																			NOVEL					0			9	5.110259	KEEP	2	0	0	17	444	TT	0.99649	0.610258	0			3	60	94	0	0	7.234142	16	60	446	66		0.157895	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12054174	12054174	__UNKNOWN__	IGR	SNP	A	A	G	rs147584280		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12054174A>G			NA	NA				FAM85A (385 upstream) : DEFB130 (114296 downstream)						NA		NA									NA						atttttagtaaagacagggtt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12054174A>G		NA		hg19		0.02	-0.157859	GTAxAGA	COVERED																																																																																			NOVEL					0			9	3.608848	KEEP	1	0	0	12	327	AA	0.993634	0.320751	0			3	47	93	0	0	7.292408	14	60	413	39		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12404534	12404534	__UNKNOWN__	IGR	SNP	G	G	A	rs530669078		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12404534G>A			NA	NA				AC130352.1 (20184 upstream) : AC068587.2 (30979 downstream)						NA		NA									NA						TCggccgggcgcggtggctca	0.562		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	51600	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12404534G>A		NA		hg19		0.02	-0.412275	GGCxCGG	COVERED																																																																																			NOVEL					0			14	3.24048	KEEP	0	1	29	21	603	GG	0.999879	0.941627	0			4	60	116	0	0	7.652192	41	60	1355	95		0.088889	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12413871	12413871	__UNKNOWN__	IGR	SNP	G	G	A	rs201105179		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12413871G>A			NA	NA				AC130352.1 (29521 upstream) : AC068587.2 (21642 downstream)						NA		NA									NA						caaaatcattgcggaagtcaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12413871G>A		NA		hg19		0.02	-0.078954	ATTxCGG	UNCOVERED																																																																																			NOVEL					0			4	2.708135	KEEP	10	0	0	9	278	GG	0	0	0			3	27	93	0	0	8.243209	6	27	217	39		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12420584	12420584	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12420584T>A			NA	NA				AC130352.1 (36234 upstream) : AC068587.2 (14929 downstream)						NA		NA									NA						ttttttgagatggagtctcgc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12420584T>A		NA		hg19		0.02	-0.157836	AGAxGGA	COVERED																																																																																			NOVEL					0			15	8.712131	KEEP	1	0	0	29	767	TT	0.999997	0.322806	0			5	60	152	0	0	13.440033	10	60	279	67		0.333333	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12439144	12439144	__UNKNOWN__	IGR	SNP	C	C	T	rs3988625	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12439144C>T			NA	NA				AC068587.2 (3483 upstream) : AC068587.1 (54468 downstream)						NA		NA									NA						atgcccagccCCCTCACTTAC	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12439144C>T		NA		hg19		0.02	-0.157892	GCCxCCT	COVERED																																																																																			NOVEL					0			4	3.309254	KEEP	3	0	0	11	321	CC	0.99257	0.320408	0			6	49	179	0	0	15.96848	11	49	375	38		0.352941	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12514654	12514654	__UNKNOWN__	IGR	SNP	T	T	C	rs200647569		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12514654T>C			NA	NA				AC068587.1 (20893 upstream) : MIR5692A2 (61981 downstream)						NA		NA									NA						agtggcatgatcacagctcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12514654T>C		NA		hg19		0.02	-0.087722	TGAxCAC	UNCOVERED																																																																																			NOVEL					0			3	2.403689	KEEP	2	0	0	8	196	TT	0	0	0			4	47	139	0	0	12.88574	6	60	188	29		0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	12514683	12514683	__UNKNOWN__	IGR	SNP	G	G	A	rs201954868		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:12514683G>A			NA	NA				AC068587.1 (20922 upstream) : MIR5692A2 (61952 downstream)						NA		NA									NA						gaccttccaggctctagcaat	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.12514683G>A		NA		hg19		0.02	-0.087723	CAGxCTC	UNCOVERED																																																																																			NOVEL					0			7	3.309252	KEEP	6	0	0	11	322	GG	0.992708	0.098994	0			4	51	127	0	0	11.685321	6	60	200	37		0.4	0.099721
DLC1	10395	__UNKNOWN__	__UNKNOWN__	8	13043087	13043087	__UNKNOWN__	Intron	SNP	G	G	A	rs550292581		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:13043087G>A	ENST00000276297.4	-	6	1758				DLC1_ENST00000512044.2_Intron	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						aagtgctggggttacaggtgt	0.463		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17154	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741	10395		Rho GTPase activating proteins, StAR-related lipid transfer (START) domain containing	2897	protein-coding gene	gene with protein product	StAR-related lipid transfer (START) domain containing 12	604258	deleted in liver cancer 1		NA	9605766, 11214970	Standard	NM_182643, NM_006094	NM_182643	NA	Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1349-69921C>T	chr8.hg19:g.13043087G>A		NA	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	hg19	CCDS5989.1	0.02	-0.043857	GGGxTTA	UNCOVERED																																																																																			NOVEL	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207632.2	6	2.407245	KEEP	1	0	0	8	247	GG	0.99257	0.023895	0		-	4	60	120	0	0	12.820376	1	60	37	19	ENST00000276297.4	0.8	0.024074
DLC1	10395	__UNKNOWN__	__UNKNOWN__	8	13288929	13288929	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:13288929T>C	ENST00000276297.4	-	3	1433				DLC1_ENST00000511869.1_Intron|DLC1_ENST00000316609.5_Intron	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						gaggcggagcttgcagtgagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741	10395		Rho GTPase activating proteins, StAR-related lipid transfer (START) domain containing	2897	protein-coding gene	gene with protein product	StAR-related lipid transfer (START) domain containing 12	604258	deleted in liver cancer 1		NA	9605766, 11214970	Standard	NM_182643, NM_006094	NM_182643	NA	Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1024-29801A>G	chr8.hg19:g.13288929T>C		NA	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	hg19	CCDS5989.1	0.02	-0.017545	AGCxTGC	UNCOVERED																																																																																			NOVEL	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207632.2	8	3.004371	KEEP	7	0	0	10	268	TT	0	0	0		-	2	31	68	0	0	7.753897	0	0	0	19	ENST00000276297.4	1	0
DLC1	10395	__UNKNOWN__	__UNKNOWN__	8	13288949	13288949	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:13288949G>A	ENST00000276297.4	-	3	1433				DLC1_ENST00000511869.1_Intron|DLC1_ENST00000316609.5_Intron	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	NA		NA			actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						ccaagatcacgccactgcact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741	10395		Rho GTPase activating proteins, StAR-related lipid transfer (START) domain containing	2897	protein-coding gene	gene with protein product	StAR-related lipid transfer (START) domain containing 12	604258	deleted in liver cancer 1		NA	9605766, 11214970	Standard	NM_182643, NM_006094	NM_182643	NA	Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.1024-29821C>T	chr8.hg19:g.13288949G>A		NA	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	hg19	CCDS5989.1	0.02	-0.017542	CACxCCA	UNCOVERED																																																																																			NOVEL	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207632.2	9	3.30832	KEEP	9	0	0	11	307	GG	0	0	0		-	2	31	60	0	0	6.953373	0	0	0	19	ENST00000276297.4	1	0
SGCZ	137868	__UNKNOWN__	__UNKNOWN__	8	14095142	14095142	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:14095142G>A	ENST00000382080.1	-	4	1098	c.383C>T	c.(382-384)gCa>gTa	p.A128V	SGCZ_ENST00000421524.2_Missense_Mutation_p.A81V	NM_139167.2	NP_631906.2	Q96LD1	SGCZ_HUMAN	sarcoglycan, zeta	115		NA			membrane organization (GO:0061024)|muscle cell cellular homeostasis (GO:0046716)|muscle cell development (GO:0055001)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|sarcoglycan complex (GO:0016012)				NS(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(14)|lung(15)|ovary(2)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	47				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		GTGATTTCTTGCATTCACTGT	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													349	334	339			NA	NA	8		NA											NA				14095142		2203	4300	6503	SO:0001583	missense			AY028700	CCDS5992.2	8p22	2014-09-17	2010-04-21		ENSG00000185053	ENSG00000185053	137868			14075	protein-coding gene	gene with protein product		608113			NA	12189167	Standard	NM_139167	XM_006716287	NA	Approved	ZSG1	uc003wwq.3	Q96LD1	OTTHUMG00000090827	ENST00000382080.1:c.383C>T	chr8.hg19:g.14095142G>A	ENSP00000371512:p.Ala128Val	NA	Q6REU0	hg19	CCDS5992.2	0.02	0.68421	CTTxCAT	COVERED	.	.	.	.	.	.	.	.	.	.	g	19.55	3.847800	0.71603	.	.	ENSG00000185053	ENST00000382080;ENST00000421524	D;D	0.94723	-3.5;-3.5	5.39	5.39	0.77823	.	0.106321	0.64402	D	0.000006	D	0.93759	0.8005	M	0.71581	2.175	0.53688	D	0.999979	B;B	0.21225	0.053;0.043	B;B	0.23716	0.048;0.019	D	0.90639	0.4573	10	0.27785	T	0.31	.	18.5837	0.91181	0.0:0.0:1.0:0.0	.	81;128	Q08AT0;Q96LD1-2	.;.	V	128;81	ENSP00000371512:A128V;ENSP00000405224:A81V	ENSP00000371512:A128V	A	-	2	0	SGCZ	14139513	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.746000	0.91604	2.708000	0.92522	0.585000	0.79938	GCA	NOVEL	SGCZ-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207636.2	24	38.201084	KEEP	0	0	0	127	3644	GG	1	0.999895	0		-	5	60	131	0	0	7.123907	85	60	2853	276	ENST00000382080.1	0.055556	0.999895
PDGFRL	5157	__UNKNOWN__	__UNKNOWN__	8	17466464	17466464	__UNKNOWN__	Intron	SNP	A	A	G	rs11786690	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:17466464A>G	ENST00000541323.1	+	4	798				PDGFRL_ENST00000398074.3_Intron|PDGFRL_ENST00000251630.6_Intron	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		aaggcagctcatgcctgtaat	0.512		NA											A|||	1834	0.366214	0.3714	0.2781	5008	,	,	NA	18660	0.2937	NA	0.3161	False	NA	,,,	NA	NA	NA	2504	0.5481	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213	5157		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	8805	protein-coding gene	gene with protein product		604584			NA		Standard	NM_006207	NM_006207	NA	Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.354-12096A>G	chr8.hg19:g.17466464A>G		NA	A8K085|Q6FH04	hg19	CCDS6003.1	0.02	-0.114008	CTCxTGC	UNCOVERED																																																																																			NOVEL	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253366.3	3	2.406221	KEEP	0	0	0	8	222	AA	0.99257	0.16126	0		+	6	60	199	0	0	20.274474	3	60	91	32	ENST00000541323.1	0.666667	0.162467
PCM1	5108	__UNKNOWN__	__UNKNOWN__	8	17800276	17800276	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:17800276A>G	ENST00000519253.1	+	6	1034				PCM1_ENST00000518537.1_Intron|PCM1_ENST00000325083.8_Intron|PCM1_ENST00000524226.1_Intron			Q15154	PCM1_HUMAN	pericentriolar material 1	NA		NA			centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		aggccgaggcaggcggatcac	0.478		NA	T	RET, JAK2	papillary thyroid, CML, MPD																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		E, L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674	5108			8727	protein-coding gene	gene with protein product		600299			NA	8120099, 15659651	Standard	NM_006197	NM_006197	NA	Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.783+2906A>G	chr8.hg19:g.17800276A>G		NA	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	hg19		0.02	-0.140338	GGCxGGC	COVERED																																																																																			NOVEL	PCM1-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000374800.1	6	4.811475	KEEP	6	0	0	16	444	AA	0.993072	0.259157	0		+	3	29	102	0	0	8.472885	11	60	326	58	ENST00000519253.1	0.214286	0.260965
CSGALNACT1	55790	__UNKNOWN__	__UNKNOWN__	8	19390814	19390814	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:19390814A>G	ENST00000454498.2	-	4	718				CSGALNACT1_ENST00000311540.4_Intron|CSGALNACT1_ENST00000544602.1_Intron|CSGALNACT1_ENST00000522854.1_Intron|CSGALNACT1_ENST00000332246.6_Intron	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	NA		NA			anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		ttttatttttatagagatggg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408	55790		Beta 4-glycosyltransferases	24290	protein-coding gene	gene with protein product	chondroitin beta1,4 N-acetylgalactosaminyltransferase	NA			NA	17145758, 12446672	Standard	NM_018371	NM_018371	NA	Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.296-27173T>C	chr8.hg19:g.19390814A>G		NA	B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	hg19	CCDS6010.1	0.02	-0.114017	TTTxTAG	UNCOVERED																																																																																			NOVEL	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375204.1	6	2.938048	KEEP	0	1	23	18	484	AA	0.99986	0.162444	0		-	3	60	96	0	0	8.232509	8	60	236	47	ENST00000454498.2	0.272727	0.162467
LZTS1	11178	__UNKNOWN__	__UNKNOWN__	8	20138809	20138809	__UNKNOWN__	Intron	SNP	G	G	A	rs544924496		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:20138809G>A	ENST00000381569.1	-	1	224							Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	NA		NA			cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ggtggctcacgcctgtaatcc	0.567		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	15118	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337	11178			13861	protein-coding gene	gene with protein product		606551	F37/Esophageal cancer-related gene-coding leucine-zipper motif		NA	10097140, 17349584	Standard	NM_021020	NM_021020	NA	Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.133+22441C>T	chr8.hg19:g.20138809G>A		NA	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	hg19	CCDS6015.1	0.02	-0.13158	CACxCCT	COVERED																																																																																			NOVEL	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214122.1	7	3.008187	KEEP	0	0	0	10	290	GG	0.992708	0.227502	0		-	3	60	91	0	0	7.372766	11	60	366	36	ENST00000381569.1	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	20791581	20791581	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:20791581G>A			NA	NA				RP11-108E14.1 (234126 upstream) : RP11-369E15.1 (7357 downstream)						NA		NA									NA						ggttgcagtgggccgagatca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.20791581G>A		NA		hg19		0.02	-0.236842	GTGxGCC	COVERED																																																																																			NOVEL					0			1	4.513263	KEEP	0	0	0	15	457	GG	0.99649	0.610258	0			4	60	122	0	0	9.262429	22	60	710	43		0.153846	0.612407
XPO7	23039	__UNKNOWN__	__UNKNOWN__	8	21824903	21824903	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:21824903G>A	ENST00000252512.9	+	2	265				XPO7_ENST00000434536.1_Intron|XPO7_ENST00000433566.4_Intron|XPO7_ENST00000518017.1_Intron	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	NA		NA			mRNA transport (GO:0051028)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	nuclear export signal receptor activity (GO:0005049)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		gtgcaatggcgtgatcttggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF064729	CCDS47818.1	8p21	2011-04-13	2003-03-11	2003-03-14	ENSG00000130227	ENSG00000130227	23039		Exportins	14108	protein-coding gene	gene with protein product		606140	RAN binding protein 16	RANBP16	NA	11024021, 9872452	Standard	NM_015024	NM_015024	NA	Approved	KIAA0745	uc003xaa.4	Q9UIA9	OTTHUMG00000163789	ENST00000252512.9:c.165+389G>A	chr8.hg19:g.21824903G>A		NA	O94846|Q6PJK9|Q8NEK7	hg19	CCDS47818.1	0.02	-0.166652	GGCxTGA	COVERED																																																																																			NOVEL	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375494.1	10	2.84092	KEEP	9	1	27	19	567	GG	0.997832	0.386567	0		+	4	60	107	0	0	8.468645	14	60	466	69	ENST00000252512.9	0.222222	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	22097835	22097835	__UNKNOWN__	IGR	SNP	C	C	T	rs71513872	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22097835C>T			NA	NA				PHYHIP (7981 upstream) : MIR320A (4639 downstream)						NA		NA									NA						cggtggctcgcgcctgtaatc	0.478		NA											-|||	1549	0.309305	0.0514	0.3559	5008	,	,	NA	15337	0.5486	NA	0.335	False	NA	,,,	NA	NA	NA	2504	0.3517	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.22097835C>T		NA		hg19		0.02	-0.096463	TCGxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.407314	KEEP	2	0	0	8	250	CC	0.99257	0.119541	0			11	60	314	0	0	36.640978	0	0	0	29		1	0.120436
SLC39A14	23516	__UNKNOWN__	__UNKNOWN__	8	22229020	22229020	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22229020C>T	ENST00000359741.5	+	1	160				SLC39A14_ENST00000289952.5_Intron|SLC39A14_ENST00000381237.1_Intron|SLC39A14_ENST00000240095.6_Intron	NM_015359.4	NP_056174.2	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	NA		NA			cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		gatctcggctcactgcaacct	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635	23516		Solute carriers	20858	protein-coding gene	gene with protein product		608736	solute carrier family 39 (metal ion transporter), member 14		NA	12659941	Standard	XM_046677	NM_015359	NA	Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000359741.5:c.-16+4099C>T	chr8.hg19:g.22229020C>T		NA	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	hg19	CCDS6030.1	0.02	-0.096495	GCTxACT	UNCOVERED																																																																																			NOVEL	SLC39A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215038.2	15	5.415166	KEEP	20	0	0	18	525	CC	0.99257	0.119541	0		+	3	28	90	0	0	7.778308	7	60	238	48	ENST00000359741.5	0.3	0.120436
SLC39A14	23516	__UNKNOWN__	__UNKNOWN__	8	22229022	22229022	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22229022C>T	ENST00000359741.5	+	1	160				SLC39A14_ENST00000289952.5_Intron|SLC39A14_ENST00000381237.1_Intron|SLC39A14_ENST00000240095.6_Intron	NM_015359.4	NP_056174.2	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	NA		NA			cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		tctcggctcactgcaacctct	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635	23516		Solute carriers	20858	protein-coding gene	gene with protein product		608736	solute carrier family 39 (metal ion transporter), member 14		NA	12659941	Standard	XM_046677	NM_015359	NA	Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000359741.5:c.-16+4101C>T	chr8.hg19:g.22229022C>T		NA	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	hg19	CCDS6030.1	0.02	-0.096492	TCAxTGC	UNCOVERED																																																																																			NOVEL	SLC39A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215038.2	15	5.394592	KEEP	20	0	0	18	503	CC	0.99257	0.119541	0		+	3	28	93	0	0	8.078458	7	60	233	49	ENST00000359741.5	0.3	0.120436
SLC39A14	23516	__UNKNOWN__	__UNKNOWN__	8	22254110	22254110	__UNKNOWN__	Intron	SNP	A	A	G	rs34491052|rs201865129|rs138188932		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22254110A>G	ENST00000359741.5	+	2	160				SLC39A14_ENST00000289952.5_Intron|SLC39A14_ENST00000381237.1_Intron|SLC39A14_ENST00000240095.6_Intron	NM_015359.4	NP_056174.2	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	NA		NA			cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		agagagagagagaAGACTAAG	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635	23516		Solute carriers	20858	protein-coding gene	gene with protein product		608736	solute carrier family 39 (metal ion transporter), member 14		NA	12659941	Standard	XM_046677	NM_015359	NA	Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000359741.5:c.-15-8099A>G	chr8.hg19:g.22254110A>G		NA	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	hg19	CCDS6030.1	0.02	-0.03508	GAGxGAA	UNCOVERED																																																																																			NOVEL	SLC39A14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215038.2	17	2.704761	KEEP	9	0	0	9	227	AA	0	0	0		+	2	60	64	0	0	6.525399	1	7	25	21	ENST00000359741.5	0.666667	0.019982
PEBP4	157310	__UNKNOWN__	__UNKNOWN__	8	22783888	22783888	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22783888G>T	ENST00000256404.6	-	2	223				PEBP4_ENST00000521284.1_Intron	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	NA		NA				extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		ggcagggtctggctctgttgc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020	157310			28319	protein-coding gene	gene with protein product	cousin-of-RKIP 1 protein	612473			NA	15302887, 16865237	Standard	NM_144962	NM_144962	NA	Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.131+1208C>A	chr8.hg19:g.22783888G>T		NA	Q5EVA1|Q8WW74	hg19	CCDS43724.1	0.02	-0.09649	TCTxGCT	UNCOVERED																																																																																			NOVEL	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375141.2	1	3.008509	KEEP	0	0	0	10	298	GG	0.992708	0.119558	0		-	3	60	92	0	0	7.832278	8	60	263	33	ENST00000256404.6	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	22841459	22841459	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22841459A>G			NA	NA				RN7SL303P (5821 upstream) : RP11-875O11.1 (649 downstream)						NA		NA									NA						atgttggccaagatggtctcg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.22841459A>G		NA		hg19		0.02	-0.140332	CCAxGAT	UNCOVERED																																																																																			NOVEL					0			4	2.406111	KEEP	4	0	0	8	221	AA	0	0	0			3	60	91	0	0	7.179253	13	60	393	35		0.1875	0.260965
TNFRSF10B	8795	__UNKNOWN__	__UNKNOWN__	8	22902477	22902477	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:22902477C>T	ENST00000276431.4	-	2	429				TNFRSF10B_ENST00000347739.3_Intron|TNFRSF10B_ENST00000542226.1_Intron|TNFRSF10B_ENST00000519910.1_Intron	NM_003842.4|NM_147187.2	NP_003833.4|NP_671716.2	O14763	TR10B_HUMAN	tumor necrosis factor receptor superfamily, member 10b	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to endoplasmic reticulum stress (GO:0034976)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|TRAIL binding (GO:0045569)			NS(1)|endometrium(2)|large_intestine(7)|liver(1)|lung(3)|skin(1)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0179)|COAD - Colon adenocarcinoma(73;0.0703)		gcctataatcccagcattttg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(94;1064 1342 1839 21060 42553)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF012628	CCDS6035.1, CCDS6036.1	8p22-p21	2006-02-22			ENSG00000120889	ENSG00000120889	8795		Tumor necrosis factor receptor superfamily, CD molecules	11905	protein-coding gene	gene with protein product		603612			NA	9285725, 9311998	Standard	NM_147187	NM_003842	NA	Approved	DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262	uc003xcu.2	O14763	OTTHUMG00000097826	ENST00000276431.4:c.145-1721G>A	chr8.hg19:g.22902477C>T		NA	O14720|O15508|O15517|O15531|Q6UXM8|Q7Z360|Q9BVE0	hg19	CCDS6035.1	0.02	-0.131581	ATCxCAG	COVERED																																																																																			NOVEL	TNFRSF10B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215099.2	8	2.681656	KEEP	0	0	0	9	250	CC	0.99254	0.227464	0		-	3	60	93	0	0	7.681859	10	60	331	36	ENST00000276431.4	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	23724759	23724759	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:23724759T>C			NA	NA				STC1 (12439 upstream) : RNU1-148P (209750 downstream)						NA		NA									NA						cgtgagccactgcacccggcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.23724759T>C		NA		hg19		0.02	-0.184201	CACxGCA	COVERED																																																																																			NOVEL					0			6	2.704609	KEEP	0	0	0	9	238	TT	0.99254	0.420319	0			3	60	104	0	0	8.233092	16	60	485	40		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	24795639	24795639	__UNKNOWN__	IGR	SNP	G	G	A	rs201375739|rs369580566|rs201951324		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:24795639G>A			NA	NA				NEFM (19032 upstream) : NEFL (12828 downstream)						NA		NA									NA						gaaagagaaggaaagaaagaa	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.24795639G>A		NA		hg19		0.02	-0.11404	AAGxAAA	UNCOVERED																																																																																			NOVEL					0			7	3.309881	KEEP	1	0	0	11	338	GG	0.992708	0.161282	0			3	60	99	2	0	8.281779	10	60	328	30		0.230769	0.162467
DOCK5	80005	__UNKNOWN__	__UNKNOWN__	8	25145615	25145615	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:25145615T>C	ENST00000276440.7	+	6	365				DOCK5_ENST00000481100.1_Intron	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	NA		NA			positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ttggtcaggctggtctcgaac	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(145;34 1887 3271 10937 30165)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459	80005			23476	protein-coding gene	gene with protein product		NA			NA	12432077	Standard	NM_024940	NM_024940	NA	Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.322-3925T>C	chr8.hg19:g.25145615T>C		NA	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	hg19	CCDS6047.1	0.02	-0.236817	GGCxGGT	UNCOVERED																																																																																			NOVEL	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254955.2	15	4.210502	KEEP	13	0	0	14	386	TT	0	0	0		+	4	45	127	0	0	9.913706	20	60	602	67	ENST00000276440.7	0.166667	0.612407
DOCK5	80005	__UNKNOWN__	__UNKNOWN__	8	25145622	25145622	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:25145622G>A	ENST00000276440.7	+	6	365				DOCK5_ENST00000481100.1_Intron	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	NA		NA			positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ggctggtctcgaactcctgac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(145;34 1887 3271 10937 30165)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459	80005			23476	protein-coding gene	gene with protein product		NA			NA	12432077	Standard	NM_024940	NM_024940	NA	Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.322-3918G>A	chr8.hg19:g.25145622G>A		NA	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	hg19	CCDS6047.1	0.02	-0.245599	CTCxAAC	UNCOVERED																																																																																			NOVEL	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254955.2	17	4.211781	KEEP	13	0	0	14	410	GG	0	0	0		+	5	45	144	0	1	11.259527	21	60	677	70	ENST00000276440.7	0.192308	0.668523
CDCA2	157313	__UNKNOWN__	__UNKNOWN__	8	25355786	25355786	__UNKNOWN__	Intron	SNP	C	C	T	rs371228054		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:25355786C>T	ENST00000330560.3	+	14	2148				CDCA2_ENST00000521098.2_Intron|CDCA2_ENST00000380665.3_Intron	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	NA		NA			mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		ttcagtggcacgatctcggct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661	157313			14623	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 81	NA			NA	12188893, 16492807	Standard	NM_152562	NM_152562	NA	Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.1672-5103C>T	chr8.hg19:g.25355786C>T		NA	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	hg19	CCDS6049.1	0.02	-0.105259	GCAxGAT	UNCOVERED																																																																																			NOVEL	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216891.3	6	3.003073	KEEP	0	0	0	10	265	CC	0.992708	0.138812	0		+	3	60	85	0	0	7.443049	6	60	197	29	ENST00000330560.3	0.333333	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	25379456	25379456	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:25379456G>A			NA	NA				CDCA2 (14020 upstream) : RP11-219J21.1 (163857 downstream)						NA		NA									NA						ATAAATCAATggccgggcacg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.25379456G>A		NA		hg19		0.02	-0.184217	AATxGCC	COVERED																																																																																			NOVEL					0			10	2.407061	KEEP	0	0	0	8	241	GG	0.99257	0.420331	0			3	60	87	0	0	6.610489	15	60	504	41		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	26100084	26100084	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:26100084G>A			NA	NA				RNA5SP258 (105570 upstream) : PPP2R2A (48922 downstream)						NA		NA									NA						AGAACACCCAGGCACCTAGCT	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.26100084G>A		NA		hg19		0.02	-0.043856	CCAxGCA	UNCOVERED																																																																																			NOVEL					0			3	3.309825	KEEP	0	0	0	11	335	GG	0.993072	0.023907	0			3	60	91	0	0	9.553561	1	60	34	22		0.75	0.024074
DPYSL2	1808	__UNKNOWN__	__UNKNOWN__	8	26430864	26430864	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:26430864C>T	ENST00000521913.1	+	2	405					NM_001197293.2	NP_001184222.1	Q16555	DPYL2_HUMAN	dihydropyrimidinase-like 2	NA		NA			axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|olfactory bulb development (GO:0021772)|positive regulation of glutamate secretion (GO:0014049)|pyrimidine nucleobase catabolic process (GO:0006208)|regulation of neuron differentiation (GO:0045664)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|synaptic vesicle transport (GO:0048489)	axon (GO:0030424)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	dihydropyrimidinase activity (GO:0004157)			breast(1)|endometrium(5)|large_intestine(8)|lung(3)|prostate(1)|skin(1)|stomach(1)	20		all_cancers(63;0.121)|Ovarian(32;2.68e-05)|all_epithelial(46;0.116)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;3.33e-10)|Colorectal(74;0.183)		tatggtgaaacccccatctct	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D78013	CCDS6051.1, CCDS59096.1	8p22-p21	2011-09-28			ENSG00000092964	ENSG00000092964	1808			3014	protein-coding gene	gene with protein product		602463			NA	8973361	Standard	NM_001386	NM_001197293	NA	Approved	DRP-2, DHPRP2, CRMP2, DRP2	uc003xfa.3	Q16555	OTTHUMG00000099439	ENST00000521913.1:c.-69-8621C>T	chr8.hg19:g.26430864C>T		NA	A8K5H2|B4DR31|D3DSS7|O00424	hg19	CCDS59096.1	0.02	-0.157903	AAAxCCC	COVERED																																																																																			NOVEL	DPYSL2-005	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376101.1	10	3.609929	KEEP	0	0	0	12	349	CC	0.993634	0.320751	0		+	3	60	86	1	0	6.510533	15	60	523	40	ENST00000521913.1	0.166667	0.322807
SCARA3	51435	__UNKNOWN__	__UNKNOWN__	8	27505866	27505866	__UNKNOWN__	Intron	SNP	G	G	A	rs538179	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:27505866G>A	ENST00000301904.3	+	2	27				SCARA3_ENST00000337221.4_Intron	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	NA		NA			receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		gctcacgcctgtaatcccagc	0.463		NA											G|||	917	0.183107	0.0242	0.2565	5008	,	,	NA	18752	0.1716	NA	0.2545	False	NA	,,,	NA	NA	NA	2504	0.2843	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077	51435			19000	protein-coding gene	gene with protein product	macrophage scavenger receptor-like 1	602728			NA	9747040, 9580669	Standard	NM_016240	NM_182826	NA	Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.8-1353G>A	chr8.hg19:g.27505866G>A		NA	Q9UM15|Q9UM16	hg19	CCDS34871.1	0.02	-0.052605	CCTxTAA	UNCOVERED																																																																																			NOVEL	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376258.2	3	2.707927	KEEP	0	0	0	9	273	GG	0.99254	0.036491	0		+	4	60	109	0	0	12.804	0	0	0	24	ENST00000301904.3	1	0.036766
NUGGC	389643	__UNKNOWN__	__UNKNOWN__	8	27887004	27887004	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:27887004A>G	ENST00000413272.2	-	17	2160				NUGGC_ENST00000341513.6_Intron	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)				NA						ggtggctcacacctgtaatcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233	389643			33550	protein-coding gene	gene with protein product	speckled-like pattern in the germinal center	NA	chromosome 8 open reading frame 80	C8orf80	NA	19734146	Standard	NM_001010906	NM_001010906	NA	Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.2018-85T>C	chr8.hg19:g.27887004A>G		NA	Q6ZP73	hg19	CCDS47833.1	0.02	-0.306733	CACxCCT	COVERED																																																																																			NOVEL	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342494.1	8	3.936078	KEEP	2	1	28	23	594	AA	0.999892	0.818376	0		-	4	60	134	0	0	10.134956	27	60	723	83	ENST00000413272.2	0.129032	0.818465
NUGGC	389643	__UNKNOWN__	__UNKNOWN__	8	27889972	27889972	__UNKNOWN__	Intron	SNP	T	T	C	rs12682588	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:27889972T>C	ENST00000413272.2	-	15	1912				NUGGC_ENST00000341513.6_Intron	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)				NA						cggtggctcatgcctgtaatc	0.542		NA											C|||	3063	0.611621	0.6838	0.6686	5008	,	,	NA	16612	0.7093	NA	0.4443	False	NA	,,,	NA	NA	NA	2504	0.545	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233	389643			33550	protein-coding gene	gene with protein product	speckled-like pattern in the germinal center	NA	chromosome 8 open reading frame 80	C8orf80	NA	19734146	Standard	NM_001010906	NM_001010906	NA	Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1770-1074A>G	chr8.hg19:g.27889972T>C		NA	Q6ZP73	hg19	CCDS47833.1	0.02	-0.096491	TCAxGCC	UNCOVERED																																																																																			NOVEL	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000342494.1	4	2.706824	KEEP	2	0	0	9	249	TT	0	0	0		-	7	60	234	0	0	24.086442	3	60	92	32	ENST00000413272.2	0.7	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	28253110	28253110	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:28253110T>C			NA	NA				ZNF395 (9127 upstream) : RP11-181B11.1 (19930 downstream)						NA		NA									NA						ccagcctgagtaacataaggg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.28253110T>C		NA		hg19		0.02	-0.184163	GAGxAAC	COVERED																																																																																			NOVEL					0			7	3.30588	KEEP	0	0	0	11	282	TT	0.993072	0.420544	0			3	60	91	0	0	6.934195	16	60	458	39		0.157895	0.423478
FBXO16	157574	__UNKNOWN__	__UNKNOWN__	8	28323025	28323025	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:28323025A>G	ENST00000346498.2	-	3	208				FBXO16_ENST00000380254.2_Intron|FBXO16_ENST00000518734.1_Intron|FBXO16_ENST00000517436.1_Intron|FBXO16_ENST00000519471.2_Intron			Q8IX29	FBX16_HUMAN	F-box protein 16	NA		NA								large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		ccagctactcaggaggctgag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050	157574		F-boxes /  other	13618	protein-coding gene	gene with protein product		608519	F-box only protein 16		NA	12243353	Standard	NM_172366	NM_172366	NA	Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000346498.2:c.100-1690T>C	chr8.hg19:g.28323025A>G		NA	Q3T1B2|Q3T1B3|Q3T1B4	hg19		0.02	1.593191	CTCxGGA	COVERED																																																																																			NOVEL	FBXO16-007	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000376323.1	17	3.500369	KEEP	0	3	89	43	1132	AA	1	0.996724	0		-	4	60	126	0	0	7.988517	61	60	1784	143	ENST00000346498.2	0.061538	0.996724
FZD3	7976	__UNKNOWN__	__UNKNOWN__	8	28424751	28424751	__UNKNOWN__	3'UTR	SNP	A	A	G	rs548415288		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:28424751A>G	ENST00000240093.3	+	0	6702					NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	NA		NA			canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		gctcactgcaacctccacctc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290	7976		GPCR / Class F : Frizzled receptors	4041	protein-coding gene	gene with protein product		606143	frizzled (Drosophila) homolog 3, frizzled homolog 3 (Drosophila), frizzled 3, seven transmembrane spanning receptor, frizzled family receptor 3		NA	10777673, 10873558	Standard	NM_145866	NM_145866	NA	Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.*4223A>G	chr8.hg19:g.28424751A>G		NA	A8K615	hg19	CCDS6069.1	0.02	-0.324337	GCAxCCT	COVERED																																																																																			NOVEL	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219986.2	5	5.10521	KEEP	2	0	0	17	414	AA	0.997832	0.833904	0		+	3	60	91	0	0	6.300429	27	60	712	63	ENST00000240093.3	0.1	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	29864347	29864347	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:29864347A>G			NA	NA				MIR3148 (49483 upstream) : RNU6-1218P (36969 downstream)						NA		NA									NA						aaagaaagaaagaaagaaaga	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.29864347A>G		NA		hg19		0.02	-0.052628	GAAxGAA	UNCOVERED																																																																																			NOVEL					0			8	2.97335	KEEP	6	0	0	10	257	AA	0	0	0			3	33	92	0	0	8.824795	3	39	92	22		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	29864351	29864351	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:29864351A>G			NA	NA				MIR3148 (49487 upstream) : RNU6-1218P (36965 downstream)						NA		NA									NA						aaagaaagaaagaaagaaaga	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.29864351A>G		NA		hg19		0.02	-0.052633	GAAxGAA	UNCOVERED																																																																																			NOVEL					0			9	3.004397	KEEP	7	0	0	10	267	AA	0	0	0			3	33	100	1	1	9.625076	3	39	95	23		0.5	0.036766
RBPMS	11030	__UNKNOWN__	__UNKNOWN__	8	30285468	30285468	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:30285468A>G	ENST00000339877.4	+	1	648				RBPMS_ENST00000320203.4_Intron|RBPMS_ENST00000519647.1_Intron|RBPMS_ENST00000397323.4_Intron|RBPMS_ENST00000287771.5_Intron|RBPMS_ENST00000517860.1_Intron|RBPMS_ENST00000538486.1_Intron|RBPMS_ENST00000520161.1_Intron	NM_001008712.1	NP_001008712.1	Q93062	RBPMS_HUMAN	RNA binding protein with multiple splicing	NA		NA			positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13				KIRC - Kidney renal clear cell carcinoma(542;0.144)|Kidney(114;0.172)		agtttgggagactgaggtggg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D84110	CCDS6077.1, CCDS34875.1, CCDS34876.1	8p12	2013-06-07			ENSG00000157110	ENSG00000157110	11030		RNA binding motif (RRM) containing	19097	protein-coding gene	gene with protein product		601558			NA	8855282	Standard		NM_001008710	NA	Approved	HERMES	uc003xib.3	Q93062	OTTHUMG00000163845	ENST00000339877.4:c.66+42794A>G	chr8.hg19:g.30285468A>G		NA	D3DSU9|Q92516|Q92517|Q92518|Q96J26	hg19	CCDS34876.1	0.02	-0.131348	GAGxCTG	COVERED																																																																																			NOVEL	RBPMS-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376356.1	7	3.005107	KEEP	0	0	0	10	259	AA	0.992708	0.227502	0		+	3	60	90	0	0	7.275897	11	60	314	36	ENST00000339877.4	0.214286	0.229173
NRG1	3084	__UNKNOWN__	__UNKNOWN__	8	32124312	32124312	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:32124312A>G	ENST00000520407.1	+	2	975				NRG1_ENST00000519301.1_Intron|NRG1-IT2_ENST00000523320.1_RNA	NM_013962.2	NP_039256.2	Q02297	NRG1_HUMAN	neuregulin 1	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		agcactttggaaggctgaggt	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168	3084		Immunoglobulin superfamily / I-set domain containing	7997	protein-coding gene	gene with protein product		142445	NRG1 intronic transcript 2 (non-protein coding)	HGL, NRG1-IT2	NA	1350381, 8095334	Standard		NM_013962	NA	Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000520407.1:c.746-329034A>G	chr8.hg19:g.32124312A>G		NA	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	hg19	CCDS47836.1	0.02	-0.166648	TGGxAGG	COVERED																																																																																			NOVEL	NRG1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376412.2	6	2.406183	KEEP	0	0	0	8	225	AA	0.99257	0.351317	0		+	3	60	104	0	0	8.310019	15	60	446	37	ENST00000520407.1	0.166667	0.353947
NRG1	3084	__UNKNOWN__	__UNKNOWN__	8	32186734	32186734	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:32186734T>C	ENST00000520407.1	+	2	975				NRG1_ENST00000519301.1_Intron	NM_013962.2	NP_039256.2	Q02297	NRG1_HUMAN	neuregulin 1	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		atcctcccacttcagcctccc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168	3084		Immunoglobulin superfamily / I-set domain containing	7997	protein-coding gene	gene with protein product		142445	NRG1 intronic transcript 2 (non-protein coding)	HGL, NRG1-IT2	NA	1350381, 8095334	Standard		NM_013962	NA	Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000520407.1:c.746-266612T>C	chr8.hg19:g.32186734T>C		NA	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	hg19	CCDS47836.1	0.02	-0.22803	CACxTCA	COVERED																																																																																			NOVEL	NRG1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376412.2	14	3.007614	KEEP	0	0	0	10	275	TT	0.992708	0.578679	0		+	3	60	95	0	0	6.950109	22	60	665	51	ENST00000520407.1	0.12	0.58293
NRG1	3084	__UNKNOWN__	__UNKNOWN__	8	32535069	32535069	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:32535069G>A	ENST00000287842.3	+	6	962				NRG1_ENST00000287845.5_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000520407.1_Intron|NRG1_ENST00000405005.3_Intron|NRG1_ENST00000520502.2_Intron|NRG1_ENST00000341377.5_Intron	NM_001160004.1|NM_013957.3	NP_001153476.1|NP_039251.2	Q02297	NRG1_HUMAN	neuregulin 1	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		ccagctacttgggaggctgag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168	3084		Immunoglobulin superfamily / I-set domain containing	7997	protein-coding gene	gene with protein product		142445	NRG1 intronic transcript 2 (non-protein coding)	HGL, NRG1-IT2	NA	1350381, 8095334	Standard		NM_013962	NA	Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000287842.3:c.503-50398G>A	chr8.hg19:g.32535069G>A		NA	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	hg19	CCDS6084.1	0.02	-0.122788	CTTxGGA	COVERED																																																																																			NOVEL	NRG1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376467.1	7	2.708178	KEEP	1	0	0	9	278	GG	0.99257	0.194853	0		+	3	60	81	0	0	6.600975	9	60	297	28	ENST00000287842.3	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	33388979	33388979	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:33388979A>G			NA	NA				TTI2 (17860 upstream) : SNORA70 (8578 downstream)						NA		NA									NA						gggattacagatgtgagccac	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.33388979A>G		NA		hg19		0.02	-0.228045	CAGxTGT	COVERED																																																																																			NOVEL					0			9	3.007586	KEEP	1	0	0	10	277	AA	0.992708	0.578679	0			3	60	106	0	0	8.164575	20	60	597	57		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	33398332	33398332	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:33398332T>C			NA	NA				SNORA70 (677 upstream) : RNF122 (6940 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.33398332T>C		NA		hg19		0.02	-0.306501	AGGxGTG	COVERED																																																																																			NOVEL					0			13	4.210527	KEEP	0	0	0	14	384	TT	0.995343	0.796519	0			3	60	94	0	0	6.602958	27	60	758	66		0.1	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	33400083	33400083	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:33400083A>G			NA	NA				SNORA70 (2428 upstream) : RNF122 (5189 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.33400083A>G		NA		hg19		0.02	-0.271781	CACxCCT	COVERED																																																																																			NOVEL					0			9	3.306246	KEEP	2	0	0	11	283	AA	0.993072	0.712346	0			3	60	102	0	0	7.542719	24	60	686	65		0.111111	0.717315
RNF122	79845	__UNKNOWN__	__UNKNOWN__	8	33412790	33412790	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:33412790A>G	ENST00000256257.1	-	2	584					NM_024787.2	NP_079063.2	Q9H9V4	RN122_HUMAN	ring finger protein 122	NA		NA				endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(67;0.0966)|Kidney(114;0.116)		gcatgatcttagctcactgca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022588	CCDS6091.1	8p12	2013-01-09			ENSG00000133874	ENSG00000133874	79845		RING-type (C3HC4) zinc fingers	21147	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024787	NM_024787	NA	Approved	FLJ12526	uc003xjo.1	Q9H9V4	OTTHUMG00000163960	ENST00000256257.1:c.182+3342T>C	chr8.hg19:g.33412790A>G		NA	Q52LK3	hg19	CCDS6091.1	0.02	-0.228033	CTTxGCT	UNCOVERED																																																																																			NOVEL	RNF122-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376562.1	6	2.405204	KEEP	1	0	0	8	211	AA	0	0	0		-	3	60	97	1	1	7.265221	20	60	591	49	ENST00000256257.1	0.130435	0.58293
UNC5D	137970	__UNKNOWN__	__UNKNOWN__	8	35157961	35157961	__UNKNOWN__	Intron	SNP	T	T	A	rs12676634	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:35157961T>A	ENST00000287272.2	+	1	123				UNC5D_ENST00000420357.1_Intron|UNC5D_ENST00000416672.1_Intron|UNC5D_ENST00000404895.2_Intron			Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	NA		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		agagactccctctcaaaaaaa	0.348		NA											T|||	4113	0.821286	0.6581	0.8775	5008	,	,	NA	13196	0.9821	NA	0.7952	False	NA	,,,	NA	NA	NA	2504	0.863	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687	137970		Immunoglobulin superfamily / I-set domain containing	18634	protein-coding gene	gene with protein product		NA			NA	18402767	Standard		NM_080872	NA	Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000287272.2:c.103+64556T>A	chr8.hg19:g.35157961T>A		NA	Q8WYP7	hg19		0.02	-0.017538	CCCxCTC	UNCOVERED																																																																																			NOVEL	UNC5D-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000347597.1	20	4.203389	KEEP	14	0	0	14	370	TT	0	0	0		+	2	60	56	0	0	6.552828	0	0	0	29	ENST00000287272.2	1	0
UNC5D	137970	__UNKNOWN__	__UNKNOWN__	8	35250898	35250898	__UNKNOWN__	Intron	SNP	G	G	A	rs185108102	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:35250898G>A	ENST00000287272.2	+	2	123				UNC5D_ENST00000420357.1_Intron|UNC5D_ENST00000416672.1_Intron|UNC5D_ENST00000404895.2_Intron			Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	NA		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		tgatccgcccgcctcggcctc	0.542		NA											-|||	209	0.0417332	0.0053	0.049	5008	,	,	NA	13239	0.0635	NA	0.0388	False	NA	,,,	NA	NA	NA	2504	0.0665	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687	137970		Immunoglobulin superfamily / I-set domain containing	18634	protein-coding gene	gene with protein product		NA			NA	18402767	Standard		NM_080872	NA	Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000287272.2:c.104-155912G>A	chr8.hg19:g.35250898G>A		NA	Q8WYP7	hg19		0.02	-0.078849	CCCxCCT	UNCOVERED																																																																																			NOVEL	UNC5D-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000347597.1	3	2.406584	KEEP	14	0	0	8	239	GG	0	0	0		+	5	60	130	0	0	13.552924	2	30	72	39	ENST00000287272.2	0.714286	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	37436658	37436658	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37436658C>G			NA	NA				RP11-150O12.5 (13774 upstream) : RP11-150O12.3 (18339 downstream)						NA		NA									NA						gctcatgcctctaatcccagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.37436658C>G		NA		hg19		0.02	-0.149136	CCTxTAA	COVERED																																																																																			NOVEL					0			6	2.407483	KEEP	1	0	0	8	257	CC	0.99257	0.320408	0			3	60	107	0	0	8.871845	12	60	407	44		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	37545195	37545195	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37545195G>A			NA	NA				RP11-346L1.2 (13290 upstream) : ZNF703 (8073 downstream)						NA		NA									NA						cagaggttgcggtaaaccgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.37545195G>A		NA		hg19		0.02	-0.192969	TGCxGTA	COVERED																																																																																			NOVEL					0			9	3.007859	KEEP	0	0	0	10	285	GG	0.992708	0.454419	0			3	60	92	0	0	6.961163	17	60	534	43		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	37573001	37573001	__UNKNOWN__	IGR	SNP	G	G	A	rs200831293		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37573001G>A			NA	NA				ZNF703 (15464 upstream) : RP11-863K10.2 (2095 downstream)						NA		NA									NA						agaaaggaaggaaggaaggaa	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.37573001G>A		NA		hg19		0.02	-0.078931	AAGxAAG	UNCOVERED																																																																																			NOVEL					0			3	2.707908	KEEP	3	0	0	9	270	GG	0	0	0			4	60	115	0	0	10.998871	4	55	125	30		0.5	0.077336
RP11-863K10.7	0	__UNKNOWN__	__UNKNOWN__	8	37593545	37593545	__UNKNOWN__	Silent	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37593545C>T	ENST00000330539.1	-	2	819	c.471G>A	c.(469-471)tcG>tcA	p.S157S							NA		NA									NA						tttgggaggccgaggcaggag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000330539.1:c.471G>A	chr8.hg19:g.37593545C>T		NA		hg19		0.02	6.069143	GGCxGAG	COVERED																																																																																			NOVEL	RP11-863K10.7-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000376897.1	93	27.232058	KEEP	2	12	326	206	5977	CC	1	1	0		-	8	60	250	0	0	13.851504	216	60	6913	658	ENST00000330539.1	0.035714	1
RP11-863K10.7	0	__UNKNOWN__	__UNKNOWN__	8	37593646	37593646	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37593646G>A	ENST00000330539.1	-	2	718	c.370C>T	c.(370-372)Cac>Tac	p.H124Y							NA		NA									NA						gtgcgcctgtggtcccagcta	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense											NA			NA				NA			NA					NA						ENST00000330539.1:c.370C>T	chr8.hg19:g.37593646G>A	ENSP00000328874:p.His124Tyr	NA		hg19		0.02	4.407053	TGTxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.522450	0.00010	.	.	ENSG00000183154	ENST00000330539	T	0.26067	1.76	0.534	-0.689	0.11313	.	.	.	.	.	T	0.07458	0.0188	.	.	.	.	.	.	B	0.17268	0.021	B	0.16289	0.015	T	0.34030	-0.9845	6	0.02654	T	1	.	.	.	.	.	124	B7WP66	.	Y	124	ENSP00000328874:H124Y	ENSP00000328874:H124Y	H	-	1	0	RP11-863K10.7	37712804	0.006000	0.16342	0.008000	0.14137	0.020000	0.10135	0.415000	0.21181	-2.025000	0.00935	-2.281000	0.00270	CAC	NOVEL	RP11-863K10.7-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000376897.1	35	10.326481	KEEP	0	6	154	89	2677	GG	1	1	0		-	7	60	197	0	0	10.919044	137	60	4554	312	ENST00000330539.1	0.048611	1
GPR124	25960	__UNKNOWN__	__UNKNOWN__	8	37663366	37663366	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37663366G>A	ENST00000412232.2	+	1	279				GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	NA		NA			central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			tagcctgggcgacagagtgag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181	25960		-, GPCR / Class B : Orphans, Immunoglobulin superfamily / Immunoglobulin-like domain containing	17849	protein-coding gene	gene with protein product	tumor endothelial marker 5	606823			NA	11559528, 12565841	Standard		NM_032777	NA	Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.266+8314G>A	chr8.hg19:g.37663366G>A		NA	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	hg19	CCDS6097.2	0.02	-0.175424	GGCxACA	COVERED																																																																																			NOVEL	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343331.2	6	3.911132	KEEP	0	0	0	13	391	GG	0.994391	0.385234	0		+	3	60	88	0	0	6.710669	15	60	474	45	ENST00000412232.2	0.166667	0.387407
RAB11FIP1	80223	__UNKNOWN__	__UNKNOWN__	8	37741938	37741938	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37741938G>A	ENST00000287263.4	-	2	397				RAB11FIP1_ENST00000330843.4_Intron|RAB11FIP1_ENST00000522727.1_Intron	NM_025151.4	NP_079427.4	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	NA		NA			protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			atggggtcttgctctgttgtc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675	80223			30265	protein-coding gene	gene with protein product		608737			NA	11786538, 11495908	Standard	NM_025151	NM_001002814	NA	Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000287263.4:c.372-6869C>T	chr8.hg19:g.37741938G>A		NA	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	hg19	CCDS34881.1	0.02	-0.280718	CTTxCTC	COVERED																																																																																			NOVEL	RAB11FIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376815.1	11	3.008982	KEEP	0	0	0	10	309	GG	0.992708	0.734278	0		-	4	43	124	0	0	9.25744	25	60	855	60	ENST00000287263.4	0.137931	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	37764862	37764862	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37764862T>C			NA	NA				RAB11FIP1 (7877 upstream) : RN7SL709P (1396 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.37764862T>C		NA		hg19		0.02	-0.271897	AGGxGTG	COVERED																																																																																			NOVEL					0			7	3.309203	KEEP	1	0	0	11	319	TT	0.992708	0.712085	0			3	60	97	0	0	7.14946	22	60	663	65		0.12	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	37765883	37765883	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:37765883T>C			NA	NA				RAB11FIP1 (8898 upstream) : RN7SL709P (375 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.37765883T>C		NA		hg19		0.02	-0.157865	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			7	2.705432	KEEP	6	0	0	9	231	TT	0	0	0			3	40	89	0	0	6.979289	13	60	380	35		0.1875	0.322807
RP11-90P5.2	0	__UNKNOWN__	__UNKNOWN__	8	38016755	38016755	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38016755A>G	ENST00000520598.1	+	0	99										NA		NA									NA						ggctggtctcaaactcctgac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000520598.1:	chr8.hg19:g.38016755A>G		NA		hg19		0.02	-0.140332	CTCxAAC	UNCOVERED																																																																																			NOVEL	RP11-90P5.2-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000376745.1	6	2.405994	KEEP	3	0	0	8	220	AA	0	0	0		+	3	60	92	0	0	7.473004	11	60	330	37	ENST00000520598.1	0.214286	0.260965
BAG4	9530	__UNKNOWN__	__UNKNOWN__	8	38037768	38037768	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38037768T>C	ENST00000287322.4	+	1	541				BAG4_ENST00000521282.1_Intron|BAG4_ENST00000432471.2_Intron	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	NA		NA			cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				Tggccgggcgtggtggctcac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735	9530			940	protein-coding gene	gene with protein product	silencer of death domains	603884			NA	9873016, 9915703	Standard	NM_004874	NM_004874	NA	Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.270+3111T>C	chr8.hg19:g.38037768T>C		NA	B4E217|O95818	hg19	CCDS6104.1	0.02	-0.236792	GCGxGGT	COVERED																																																																																			NOVEL	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377038.2	6	3.00615	KEEP	0	0	0	10	262	TT	0.992708	0.607941	0		+	3	60	91	0	0	6.607322	21	60	617	56	ENST00000287322.4	0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38074431	38074431	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38074431C>G			NA	NA				BAG4 (3612 upstream) : DDHD2 (14429 downstream)						NA		NA									NA						aatcccagcactttgggaggc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38074431C>G		NA		hg19		0.02	-0.228077	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			14	3.308938	KEEP	9	0	0	11	318	CC	0	0	0			3	60	105	0	0	8.260405	17	60	558	61		0.15	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38074466	38074466	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38074466G>A			NA	NA				BAG4 (3647 upstream) : DDHD2 (14394 downstream)						NA		NA									NA						cacaaggtcaggagatcgaga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38074466G>A		NA		hg19		0.02	-0.157862	TCAxGAG	UNCOVERED																																																																																			NOVEL					0			9	2.706857	KEEP	9	0	0	9	271	GG	0	0	0			3	60	88	0	0	6.792342	14	60	462	51		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38074473	38074473	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38074473G>A			NA	NA				BAG4 (3654 upstream) : DDHD2 (14387 downstream)						NA		NA									NA						tcaggagatcgagaccatcct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38074473G>A		NA		hg19		0.02	-0.157874	ATCxAGA	UNCOVERED																																																																																			NOVEL					0			9	2.707894	KEEP	9	0	0	9	274	GG	0	0	0			4	60	109	0	0	8.781111	13	60	425	53		0.235294	0.322807
DDHD2	23259	__UNKNOWN__	__UNKNOWN__	8	38104354	38104354	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38104354G>A	ENST00000397166.2	+	9	1650				DDHD2_ENST00000520272.2_Intron|DDHD2_ENST00000517385.1_5'UTR|DDHD2_ENST00000528888.1_Intron	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	NA		NA			cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			gtgagactccgtctcaaaaaT	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07			23259		Sterile alpha motif (SAM) domain containing	29106	protein-coding gene	gene with protein product		615003	SAM, WWE and DDHD domain containing 1	SAMWD1	NA	9872452, 11788596, 19632984, 20932832	Standard	XM_291291	NM_015214	NA	Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.1125+536G>A	chr8.hg19:g.38104354G>A		NA	B3KWV2|B3KXB5|Q9H8X7	hg19	CCDS34883.1	0.02	1.113938	TCCxTCT	COVERED																																																																																			NOVEL	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377251.2	14	5.347438	KEEP	2	1	26	27	793	GG	0.999988	0.99995	0		+	5	60	153	1	1	9.284151	86	60	2817	185	ENST00000397166.2	0.054945	0.999962
DDHD2	23259	__UNKNOWN__	__UNKNOWN__	8	38104916	38104916	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38104916A>G	ENST00000397166.2	+	10	1650				DDHD2_ENST00000520272.2_Intron|DDHD2_ENST00000517385.1_5'UTR|DDHD2_ENST00000528888.1_Intron	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	NA		NA			cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			gggattacagatgtgagccac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07			23259		Sterile alpha motif (SAM) domain containing	29106	protein-coding gene	gene with protein product		615003	SAM, WWE and DDHD domain containing 1	SAMWD1	NA	9872452, 11788596, 19632984, 20932832	Standard	XM_291291	NM_015214	NA	Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.1126-315A>G	chr8.hg19:g.38104916A>G		NA	B3KWV2|B3KXB5|Q9H8X7	hg19	CCDS34883.1	0.02	1.690099	CAGxTGT	COVERED																																																																																			NOVEL	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377251.2	17	5.143316	KEEP	4	1	31	28	758	AA	0.999988	0.999849	0		+	7	60	238	0	0	16.956892	70	60	2088	159	ENST00000397166.2	0.090909	0.999862
PPAPDC1B	84513	__UNKNOWN__	__UNKNOWN__	8	38121903	38121903	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38121903A>G	ENST00000424479.2	-	0	874				PPAPDC1B_ENST00000529359.1_3'UTR	NM_001102559.1	NP_001096029.1	Q8NEB5	PPC1B_HUMAN	phosphatidic acid phosphatase type 2 domain containing 1B	NA		NA			phospholipid dephosphorylation (GO:0046839)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			kidney(1)|lung(1)	2	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)	BRCA - Breast invasive adenocarcinoma(5;3.04e-26)|COAD - Colon adenocarcinoma(9;0.188)			caccctcctcagcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF212238	CCDS47841.1, CCDS47842.1, CCDS47843.1	8p12	2005-08-09			ENSG00000147535	ENSG00000147535	84513			25026	protein-coding gene	gene with protein product		610626			NA		Standard	NM_032483	NM_032483	NA	Approved	HTPAP	uc003xlf.4	Q8NEB5	OTTHUMG00000165104	ENST00000424479.2:c.*59T>C	chr8.hg19:g.38121903A>G		NA	C9JKF5|Q3KQX6|Q9BY45	hg19	CCDS47841.1	0.02	-0.385909	CTCxGCC	COVERED																																																																																			NOVEL	PPAPDC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381832.2	16	5.113283	KEEP	1	0	0	17	478	AA	0.997832	0.91618	0		-	3	60	100	0	0	6.806338	37	60	1126	75	ENST00000424479.2	0.075	0.918171
WHSC1L1	54904	__UNKNOWN__	__UNKNOWN__	8	38195813	38195813	__UNKNOWN__	Intron	SNP	G	G	A	rs200849797		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38195813G>A	ENST00000317025.8	-	3	1265				WHSC1L1_ENST00000433384.2_Intron|WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000316985.3_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	NA		NA			histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			gtgagactccgtctcaaaaag	0.423		NA	T	NUP98	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548	54904			12767	protein-coding gene	gene with protein product		607083			NA	10802047, 23269674	Standard	NM_023034	NM_023034	NA	Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.747+240C>T	chr8.hg19:g.38195813G>A		NA	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	hg19	CCDS43729.1	0.02	-0.13155	TCCxTCT	COVERED																																																																																			NOVEL	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381924.3	6	2.707354	KEEP	1	0	0	9	261	GG	0.99254	0.227464	0		-	3	60	82	0	0	6.372903	12	60	368	38	ENST00000317025.8	0.2	0.229173
WHSC1L1	54904	__UNKNOWN__	__UNKNOWN__	8	38225583	38225583	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38225583T>C	ENST00000317025.8	-	1	474				WHSC1L1_ENST00000433384.2_Intron|WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000316985.3_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	NA		NA			histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			ctgcaacctctgcctccaggg	0.473		NA	T	NUP98	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548	54904			12767	protein-coding gene	gene with protein product		607083			NA	10802047, 23269674	Standard	NM_023034	NM_023034	NA	Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.43+13733A>G	chr8.hg19:g.38225583T>C		NA	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	hg19	CCDS43729.1	0.02	-0.131567	CTCxGCC	COVERED																																																																																			NOVEL	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381924.3	6	2.707382	KEEP	2	0	0	9	256	TT	0.99254	0.227464	0		-	3	51	99	0	0	8.401197	9	60	271	34	ENST00000317025.8	0.25	0.229173
FGFR1	2260	__UNKNOWN__	__UNKNOWN__	8	38306024	38306024	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38306024A>C	ENST00000397103.1	-	1	148				FGFR1_ENST00000425967.3_Intron|FGFR1_ENST00000397091.5_Intron|FGFR1_ENST00000397113.2_Intron|FGFR1_ENST00000532791.1_Intron|FGFR1_ENST00000447712.2_Intron|FGFR1_ENST00000326324.6_Intron|FGFR1_ENST00000335922.5_Intron|FGFR1_ENST00000341462.5_Intron|FGFR1_ENST00000356207.5_Intron|FGFR1_ENST00000397108.4_Intron			P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	NA		NA			angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)		FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	gGATTACAGGAGTGAGCCACC	0.453		1	T	BCR, FOP, ZNF198, CEP1	MPD, NHL		Pfeiffer syndrome, Kallman syndrome														NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2260	2.7.10.1	CD molecules, Immunoglobulin superfamily / I-set domain containing	3688	protein-coding gene	gene with protein product	Pfeiffer syndrome	136350	fms-related tyrosine kinase 2	FLT2, KAL2	NA	2162671	Standard		NM_015850	NA	Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000397103.1:c.91+8849T>G	chr8.hg19:g.38306024A>C		NA	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	hg19		0.02	-0.201744	AGGxGTG	COVERED																																																																																			NOVEL	FGFR1-011	NOVEL	non_canonical_conserved|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000304020.1	6	2.70727	KEEP	1	0	0	9	255	AA	0.99254	0.486885	0		-	3	60	104	1	0	8.026649	19	60	582	55	ENST00000397103.1	0.136364	0.490544
RP11-675F6.3	0	__UNKNOWN__	__UNKNOWN__	8	38405104	38405104	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38405104C>T	ENST00000521623.1	-	0	184										NA		NA									NA						ggtttcaccacgttggccagg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000521623.1:	chr8.hg19:g.38405104C>T		NA		hg19		0.02	-0.140338	CCAxGTT	COVERED																																																																																			NOVEL	RP11-675F6.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000376670.1	1	3.309476	KEEP	1	0	0	11	327	CC	0.993072	0.259157	0		-	4	49	111	0	0	9.230767	11	60	357	39	ENST00000521623.1	0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38537064	38537064	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38537064C>T			NA	NA				RP11-675F6.4 (120526 upstream) : RP11-495O10.1 (21079 downstream)						NA		NA									NA						gagaccagcccaggcaacata	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38537064C>T		NA		hg19		0.02	-0.271944	GCCxAGG	COVERED																																																																																			NOVEL					0			13	2.541008	KEEP	0	1	27	18	566	CC	0.99986	0.717215	0			3	60	91	0	0	6.393194	25	60	856	74		0.107143	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38539318	38539318	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38539318C>T			NA	NA				RP11-675F6.4 (122780 upstream) : RP11-495O10.1 (18825 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38539318C>T		NA		hg19		0.02	-0.184179	TCAxGCC	COVERED																																																																																			NOVEL					0			3	3.007871	KEEP	1	0	0	10	291	CC	0.992708	0.42039	0			5	60	136	0	0	11.101623	15	60	494	48		0.25	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38569091	38569091	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38569091A>G			NA	NA				RP11-495O10.1 (6718 upstream) : TACC1 (16612 downstream)						NA		NA									NA						cctgaggtcaagagttcgaga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38569091A>G		NA		hg19		0.02	-0.25435	TCAxGAG	COVERED																																																																																			NOVEL					0			9	2.707028	KEEP	0	0	0	9	250	AA	0.99254	0.663536	0			4	48	136	0	0	10.522867	24	60	716	53		0.142857	0.668523
TACC1	6867	__UNKNOWN__	__UNKNOWN__	8	38650383	38650383	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38650383C>G	ENST00000317827.4	+	2	656				TACC1_ENST00000518415.1_Intron|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000443286.2_Intron|TACC1_ENST00000519416.1_Intron|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000520615.1_Intron|TACC1_ENST00000520973.1_Intron|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000379931.3_Intron|TACC1_ENST00000520340.1_Intron	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			ctcccaaagtcctgggattac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526	6867			11522	protein-coding gene	gene with protein product		605301			NA		Standard	NM_006283	NM_006283	NA	Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.277+4046C>G	chr8.hg19:g.38650383C>G		NA	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	hg19	CCDS6109.1	0.02	-0.201749	AGTxCTG	COVERED																																																																																			NOVEL	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376768.1	6	3.008995	KEEP	0	0	0	10	308	CC	0.992708	0.486967	0		+	3	60	91	0	0	6.861264	17	60	553	43	ENST00000317827.4	0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	38719313	38719313	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:38719313G>C			NA	NA				TACC1 (8767 upstream) : PLEKHA2 (39439 downstream)						NA		NA									NA						accagcctgggcaacataggg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.38719313G>C		NA		hg19		0.02	-0.228087	TGGxCAA	COVERED																																																																																			NOVEL					0			9	3.849618	KEEP	1	0	0	13	380	GG	0.993634	0.579219	0			3	60	96	0	0	7.227034	19	60	655	54		0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	39719741	39719741	__UNKNOWN__	IGR	SNP	C	C	T	rs535677492	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:39719741C>T			NA	NA				ADAM2 (23933 upstream) : IDO1 (40152 downstream)						NA		NA									NA						ggcaaaaccccgtctctacta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.39719741C>T		NA		hg19		0.02	-0.298256	CCCxGTC	COVERED																																																																																			NOVEL					0			13	3.00775	KEEP	0	0	0	10	286	CC	0.992708	0.775364	0			3	60	95	0	0	6.697959	27	60	898	66		0.1	0.78106
ZMAT4	79698	__UNKNOWN__	__UNKNOWN__	8	40392965	40392965	__UNKNOWN__	Intron	SNP	G	G	A	rs143485370	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:40392965G>A	ENST00000297737.6	-	7	821				ZMAT4_ENST00000315769.7_Intron	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	NA		NA				nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			tgaggcaggcggatcatgagg	0.498		NA											G|||	379	0.0756789	0.0991	0.0821	5008	,	,	NA	18311	0.0	NA	0.1342	False	NA	,,,	NA	NA	NA	2504	0.0573	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061	79698		Zinc fingers, matrin-type	25844	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024645	NM_024645	NA	Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.675-3208C>T	chr8.hg19:g.40392965G>A		NA	Q8WUT8	hg19	CCDS34885.1	0.02	-0.192932	GGCxGAT	UNCOVERED																																																																																			NOVEL	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376950.1	11	3.007641	KEEP	10	0	0	10	280	GG	0	0	0		-	5	60	157	0	0	13.08112	16	60	504	55	ENST00000297737.6	0.238095	0.457757
ZMAT4	79698	__UNKNOWN__	__UNKNOWN__	8	40434488	40434488	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:40434488A>G	ENST00000297737.6	-	6	821				ZMAT4_ENST00000315769.7_Intron	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	NA		NA				nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			tgaggcgggcagatcacctga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061	79698		Zinc fingers, matrin-type	25844	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024645	NM_024645	NA	Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.674+4195T>C	chr8.hg19:g.40434488A>G		NA	Q8WUT8	hg19	CCDS34885.1	0.02	-0.210503	GGCxGAT	COVERED																																																																																			NOVEL	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376950.1	18	5.413203	KEEP	14	0	0	18	494	AA	0.993634	0.518837	0		-	3	40	96	0	0	7.360977	17	60	508	74	ENST00000297737.6	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	40916362	40916362	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:40916362T>C			NA	NA				RNU6-356P (25845 upstream) : SFRP1 (203118 downstream)						NA		NA									NA						tggtggttcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.40916362T>C		NA		hg19		0.02	-0.289405	TCAxGCC	COVERED																																																																																			NOVEL					0			7	2.706719	KEEP	2	0	0	9	247	TT	0.99254	0.755211	0			3	60	91	0	0	6.35007	26	60	762	63		0.103448	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	40959365	40959365	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:40959365T>C			NA	NA				RNU6-356P (68848 upstream) : SFRP1 (160115 downstream)						NA		NA									NA						gtgatccacctgcctcggcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.40959365T>C		NA		hg19		0.02	-0.157829	ACCxGCC	UNCOVERED																																																																																			NOVEL					0			6	2.406387	KEEP	4	0	0	8	225	TT	0	0	0			3	60	89	0	0	6.979727	13	60	367	43		0.1875	0.322807
GOLGA7	51125	__UNKNOWN__	__UNKNOWN__	8	41354581	41354581	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41354581A>G	ENST00000357743.4	+	2	312				GOLGA7_ENST00000405786.2_Intron|GOLGA7_ENST00000518270.1_Intron|GOLGA7_ENST00000520817.1_Intron	NM_001002296.1	NP_001002296.1	Q7Z5G4	GOGA7_HUMAN	golgin A7	NA		NA			Golgi to plasma membrane protein transport (GO:0043001)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)				breast(1)|large_intestine(1)	2	Ovarian(28;0.014)|Colorectal(14;0.0234)|Lung SC(25;0.211)	all_lung(54;0.000771)|Lung NSC(58;0.0031)|Hepatocellular(245;0.014)|Esophageal squamous(32;0.0559)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00596)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)			cgcccacctcagcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF125102	CCDS34887.1, CCDS55226.1	8p11.21	2011-10-25	2010-02-12		ENSG00000147533	ENSG00000147533	51125			24876	protein-coding gene	gene with protein product		609453	golgi autoantigen, golgin subfamily a, 7		NA	11042152	Standard	NM_016099	NM_001174124	NA	Approved	GCP16, HSPC041, GOLGA3AP1, GOLGA7A	uc003xnu.3	Q7Z5G4	OTTHUMG00000164077	ENST00000357743.4:c.112-447A>G	chr8.hg19:g.41354581A>G		NA	D3DSX9|J3KQ24|Q96EQ4|Q9P1S0|Q9Y5U7	hg19	CCDS34887.1	0.02	-0.219283	CTCxGCC	UNCOVERED																																																																																			NOVEL	GOLGA7-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377142.1	12	3.007947	KEEP	9	0	0	10	285	AA	0	0	0		+	4	60	127	0	0	10.263021	16	60	485	60	ENST00000357743.4	0.2	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	41370426	41370426	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41370426A>G			NA	NA				GOLGA7 (1927 upstream) : GINS4 (16298 downstream)						NA		NA									NA						gtgagccaccacacccagccT	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.41370426A>G		NA		hg19		0.02	-0.36835	ACCxCAC	UNCOVERED																																																																																			NOVEL					0			13	2.706414	KEEP	7	0	0	9	245	AA	0	0	0			3	60	100	1	0	6.840632	36	60	1054	83		0.076923	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	41377713	41377713	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41377713A>G			NA	NA				GOLGA7 (9214 upstream) : GINS4 (9011 downstream)						NA		NA									NA						tgcctgcctcagcctcccaaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.41377713A>G		NA		hg19		0.02	-0.175431	CTCxGCC	COVERED																																																																																			NOVEL					0			3	3.008369	KEEP	2	0	0	10	289	AA	0.99254	0.384517	0			4	60	129	0	0	10.780905	13	60	413	54		0.235294	0.387407
GINS4	84296	__UNKNOWN__	__UNKNOWN__	8	41399864	41399864	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41399864T>C	ENST00000276533.3	+	0	1140				GINS4_ENST00000523277.2_3'UTR|RP11-360L9.7_ENST00000578500.1_RNA|RP11-360L9.7_ENST00000524133.1_RNA|GINS4_ENST00000518671.1_3'UTR|RP11-360L9.4_ENST00000523081.1_RNA	NM_032336.2	NP_115712.1	Q9BRT9	SLD5_HUMAN	GINS complex subunit 4 (Sld5 homolog)	NA		NA			DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)				breast(1)|lung(2)|skin(1)	4	Ovarian(28;0.014)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.00732)|Lung NSC(58;0.0207)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00329)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)			ggtcgtgccattgcactccag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC005995	CCDS6116.1	8p11.21	2006-05-04			ENSG00000147536	ENSG00000147536	84296			28226	protein-coding gene	gene with protein product		610611			NA	12477932	Standard	NM_032336	NM_032336	NA	Approved	MGC14799, SLD5	uc003xnx.3	Q9BRT9	OTTHUMG00000164079	ENST00000276533.3:c.*258T>C	chr8.hg19:g.41399864T>C		NA	B2R8H5|D3DSY0|Q8N648	hg19	CCDS6116.1	0.02	3.341751	CCAxTGC	COVERED																																																																																			NOVEL	GINS4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377150.1	21	13.212636	KEEP	0	6	173	105	2714	TT	1	1	0		+	5	60	166	0	0	9.931132	117	60	3272	289	ENST00000276533.3	0.040984	1
AGPAT6	137964	__UNKNOWN__	__UNKNOWN__	8	41481652	41481652	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41481652A>G	ENST00000396987.3	+	0	5430					NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	NA		NA			acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			cactgcgcccagccAAGAGGG	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	137964	2.3.1.15	1-acylglycerol-3-phosphate O-acyltransferases	20880	protein-coding gene	gene with protein product	lysophosphatidic acid acyltransferase, zeta	608143	1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)		NA	12938015	Standard	NM_178819	NM_178819	NA	Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.*3132A>G	chr8.hg19:g.41481652A>G		NA	Q86V89	hg19	CCDS6117.1	0.02	1.775028	CCCxGCC	COVERED																																																																																			NOVEL	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377158.1	14	7.21924	KEEP	1	0	0	24	681	AA	0.999909	0.996634	0		+	4	60	136	0	0	9.191823	54	60	1625	135	ENST00000396987.3	0.068966	0.996724
ANK1	286	__UNKNOWN__	__UNKNOWN__	8	41681139	41681139	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41681139G>A	ENST00000265709.8	-	2	408					NM_001142446.1	NP_001135918.1	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	NA		NA			axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			aaaattagccgggcatggtgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534	286		Ankyrin repeat domain containing	492	protein-coding gene	gene with protein product		612641		ANK	NA	1689849	Standard	NM_020475	NM_001142445	NA	Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000265709.8:c.127-65484C>T	chr8.hg19:g.41681139G>A		NA	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	hg19	CCDS47849.1	0.02	-0.245618	GCCxGGC	COVERED																																																																																			NOVEL	ANK1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377171.1	9	3.008225	KEEP	0	0	0	10	296	GG	0.992708	0.63667	0		-	3	60	93	0	0	6.592904	25	60	819	57	ENST00000265709.8	0.107143	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	41945098	41945098	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:41945098T>G			NA	NA				KAT6A (35593 upstream) : RP11-589C21.6 (51880 downstream)						NA		NA									NA						cagcactttgtgaggctgagg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.41945098T>G		NA		hg19		0.02	-0.201738	TTGxGAG	COVERED																																																																																			NOVEL					0			14	3.609382	KEEP	0	0	0	12	334	TT	0.993634	0.549368	0			4	60	129	0	0	10.36878	17	60	514	47		0.190476	0.552887
AP3M2	10947	__UNKNOWN__	__UNKNOWN__	8	42020260	42020260	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42020260T>C	ENST00000518421.1	+	5	874				AP3M2_ENST00000517922.1_Intron|AP3M2_ENST00000396926.3_Intron|AP3M2_ENST00000520685.1_Intron|AP3M2_ENST00000174653.3_Intron	NM_001134296.1	NP_001127768.1	P53677	AP3M2_HUMAN	adaptor-related protein complex 3, mu 2 subunit	NA		NA			anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|prostate(1)|stomach(1)	17	all_cancers(6;8.14e-25)|all_epithelial(6;2.41e-27)|all_lung(13;5.09e-13)|Lung NSC(13;8.38e-12)|Ovarian(28;0.00438)|Prostate(17;0.0119)|Colorectal(14;0.0221)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Esophageal squamous(32;0.0954)|Renal(179;0.0983)	BRCA - Breast invasive adenocarcinoma(8;5.23e-10)|Colorectal(10;0.00165)|OV - Ovarian serous cystadenocarcinoma(14;0.00346)|Lung(22;0.00467)|COAD - Colon adenocarcinoma(11;0.0171)|LUSC - Lung squamous cell carcinoma(45;0.024)			cccaggagtttaagaccagcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D38293	CCDS6125.1	8p11.2	2008-07-07			ENSG00000070718	ENSG00000070718	10947			570	protein-coding gene	gene with protein product		610469			NA	7601449	Standard		NM_006803	NA	Approved	CLA20, AP47B	uc003xoo.3	P53677	OTTHUMG00000164060	ENST00000518421.1:c.583+324T>C	chr8.hg19:g.42020260T>C		NA	B2RCR0|D3DSY2|Q7Z472	hg19	CCDS6125.1	0.02	-0.19289	GTTxAAG	COVERED																																																																																			NOVEL	AP3M2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376996.1	5	3.307464	KEEP	2	0	0	11	292	TT	0.99254	0.454342	0		+	3	60	100	0	0	7.833899	16	60	442	49	ENST00000518421.1	0.157895	0.457757
RP11-231D20.2	0	__UNKNOWN__	__UNKNOWN__	8	42105395	42105395	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42105395A>G	ENST00000523459.1	-	0	405										NA		NA									NA						ggtggatcacaaggtcaggag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000523459.1:	chr8.hg19:g.42105395A>G		NA		hg19		0.02	-0.149085	CACxAGG	COVERED																																																																																			NOVEL	RP11-231D20.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000377111.1	7	3.609262	KEEP	0	0	0	12	333	AA	0.993634	0.290142	0		-	3	60	97	0	1	7.872618	12	60	341	41	ENST00000523459.1	0.2	0.292001
IKBKB	3551	__UNKNOWN__	__UNKNOWN__	8	42130206	42130206	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42130206T>C	ENST00000520810.1	+	2	291				IKBKB_ENST00000379708.3_Intron|IKBKB_ENST00000520835.1_Intron|IKBKB_ENST00000416505.2_Intron|IKBKB_ENST00000519735.1_Intron|IKBKB_ENST00000522147.1_Intron	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	NA		NA			B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	acctgtaatctcagcactttg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365	3551			5960	protein-coding gene	gene with protein product		603258			NA	9878263, 9763654	Standard		NM_001556	NA	Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.105+483T>C	chr8.hg19:g.42130206T>C		NA	B4DZ30|B4E0U4|O75327	hg19	CCDS6128.1	0.02	-0.157871	ATCxCAG	COVERED																																																																																			NOVEL	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377214.1	11	3.308679	KEEP	0	0	0	11	307	TT	0.993072	0.32057	0		+	3	60	95	0	1	8.001136	9	60	275	36	ENST00000520810.1	0.25	0.322807
SLC20A2	6575	__UNKNOWN__	__UNKNOWN__	8	42365449	42365449	__UNKNOWN__	Intron	SNP	G	G	A	rs376527275		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42365449G>A	ENST00000342228.3	-	1	106				SLC20A2_ENST00000520179.1_Intron	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	NA		NA			ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)			breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			aggctgaggcgggcggatcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575	6575		Solute carriers	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2	NA	7745689, 16790504	Standard		NM_001257180	NA	Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.263+31514C>T	chr8.hg19:g.42365449G>A		NA		hg19	CCDS6132.1	0.02	-0.201761	GGCxGGC	COVERED																																																																																			NOVEL	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377578.1	5	3.610725	KEEP	3	0	0	12	368	GG	0.992708	0.486967	0		-	3	60	88	0	0	6.492816	18	60	606	61	ENST00000342228.3	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	42425673	42425673	__UNKNOWN__	IGR	SNP	A	A	G	rs73633616	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42425673A>G			NA	NA				RP11-503E24.3 (15337 upstream) : CHRNB3 (126845 downstream)						NA		NA									NA						ttgggaggccaaggcaggtgg	0.488		NA											a|||	3441	0.687101	0.8555	0.6153	5008	,	,	NA	16744	0.5427	NA	0.6123	False	NA	,,,	NA	NA	NA	2504	0.7362	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.42425673A>G		NA		hg19		0.02	-0.210498	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			10	2.404951	KEEP	3	0	0	8	209	AA	0	0	0			12	60	372	0	0	37.077748	8	60	233	46		0.6	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	42641384	42641384	__UNKNOWN__	IGR	SNP	A	A	G	rs577049712		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42641384A>G			NA	NA				CHRNA6 (17455 upstream) : THAP1 (50432 downstream)						NA		NA									NA						aaggaaggaaagaaggaagga	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.42641384A>G		NA		hg19		0.02	-0.3508	GAAxGAA	COVERED																																																																																			NOVEL					0			7	2.40511	KEEP	0	0	0	8	216	AA	0.99257	0.871187	0			3	60	100	0	0	6.87624	35	60	1036	70		0.078947	0.877708
HOOK3	84376	__UNKNOWN__	__UNKNOWN__	8	42855270	42855270	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42855270A>G	ENST00000307602.4	+	17	1820					NM_032410.3	NP_115786.1	Q86VS8	HOOK3_HUMAN	hook microtubule-tethering protein 3	NA		NA			cytoplasmic microtubule organization (GO:0031122)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|Golgi localization (GO:0051645)|interkinetic nuclear migration (GO:0022027)|lysosome organization (GO:0007040)|microtubule anchoring at centrosome (GO:0034454)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|protein localization to centrosome (GO:0071539)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|FHF complex (GO:0070695)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|pericentriolar material (GO:0000242)	identical protein binding (GO:0042802)|microtubule binding (GO:0008017)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	31	Ovarian(28;0.01)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.000105)|Lung NSC(58;0.000419)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.048)|LUSC - Lung squamous cell carcinoma(45;0.114)			cagcctgggcaacagagcgag	0.498		NA	T	RET	papillary thyroid																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8p11.21	84376	hook homolog 3		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK090540	CCDS6139.1	8p11.21	2013-08-21	2013-08-21		ENSG00000168172	ENSG00000168172	84376			23576	protein-coding gene	gene with protein product		607825	hook homolog 3 (Drosophila)		NA	9927460	Standard	NM_032410	NM_032410	NA	Approved	HK3	uc003xpr.3	Q86VS8	OTTHUMG00000165278	ENST00000307602.4:c.1621-1980A>G	chr8.hg19:g.42855270A>G		NA	D3DSY8|Q8NBH0|Q9BY13	hg19	CCDS6139.1	0.02	-0.37713	GGCxACA	COVERED																																																																																			NOVEL	HOOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383172.2	7	2.739176	KEEP	1	1	28	19	531	AA	0.999863	0.908944	0		+	3	60	99	0	0	6.74071	36	60	1056	76	ENST00000307602.4	0.076923	0.909069
FNTA	2339	__UNKNOWN__	__UNKNOWN__	8	42918358	42918358	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42918358T>G	ENST00000302279.3	+	3	480				FNTA_ENST00000524546.1_Intron|FNTA_ENST00000342116.4_Intron|FNTA_ENST00000529687.1_Intron|RP11-598P20.5_ENST00000534420.1_Intron	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	NA		NA			apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|phototransduction, visible light (GO:0007603)|positive regulation of deacetylase activity (GO:0090045)|positive regulation of tubulin deacetylation (GO:0090044)|protein farnesylation (GO:0018343)|protein geranylgeranylation (GO:0018344)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transforming growth factor beta receptor signaling pathway (GO:0007179)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	alpha-tubulin binding (GO:0043014)|CAAX-protein geranylgeranyltransferase activity (GO:0004662)|microtubule binding (GO:0008017)|protein farnesyltransferase activity (GO:0004660)|protein geranylgeranyltransferase activity (GO:0004661)			cervix(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	16	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			cgagtagctgtgactgcaggc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L10413	CCDS6140.1	8p11.21	2011-06-27			ENSG00000168522	ENSG00000168522	2339		Prenyltransferase alpha subunit repeat containing	3782	protein-coding gene	gene with protein product	protein prenyltransferase alpha subunit repeat containing 2	134635			NA	8276393	Standard	NM_002027	NR_033698	NA	Approved	FPTA, PGGT1A, PTAR2	uc003xps.3	P49354	OTTHUMG00000165279	ENST00000302279.3:c.287-886T>G	chr8.hg19:g.42918358T>G		NA	A6NJW0|Q53XJ9|Q9UDC1	hg19	CCDS6140.1	0.02	-0.298173	CTGxGAC	COVERED																																																																																			NOVEL	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383178.1	12	3.337468	KEEP	0	1	28	21	554	TT	0.999879	0.780965	0		+	3	60	94	0	0	6.598669	27	60	770	70	ENST00000302279.3	0.1	0.78106
POMK	84197	__UNKNOWN__	__UNKNOWN__	8	42978449	42978449	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:42978449T>C	ENST00000331373.5	+	0	1737					NM_001277971.1|NM_032237.3	NP_001264900.1|NP_115613.1	Q9H5K3	SG196_HUMAN	protein-O-mannose kinase	NA		NA			brain development (GO:0007420)|carbohydrate phosphorylation (GO:0046835)|learning or memory (GO:0007611)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|protein O-linked glycosylation (GO:0006493)|sensory perception of pain (GO:0019233)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|carbohydrate kinase activity (GO:0019200)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|protein kinase activity (GO:0004672)				NA						tcccaaagtgttgggattaca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6141.1	8p11.21	2013-08-22			ENSG00000185900	ENSG00000185900	84197			26267	protein-coding gene	gene with protein product		615247			NA	16879967, 23519211	Standard	NM_032237	NM_001277971	NA	Approved	FLJ23356, SgK196		Q9H5K3	OTTHUMG00000164100	ENST00000331373.5:c.*429T>C	chr8.hg19:g.42978449T>C		NA		hg19	CCDS6141.1	0.02	3.77499	GTGxTGG	COVERED																																																																																			NOVEL	POMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377291.2	31	3.569683	KEEP	3	2	54	31	847	TT	0.999997	0.999997	0		+	6	60	208	0	0	13.193211	120	60	3583	264	ENST00000331373.5	0.047619	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	43822425	43822425	__UNKNOWN__	IGR	SNP	T	T	C	rs200336493		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:43822425T>C			NA	NA				AC134698.1 (406509 upstream) : None (None downstream)						NA		NA									NA						agtggatatttggatagattt	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.43822425T>C		NA		hg19		0.02	1.312573	ATTxGGA	COVERED																																																																																			NOVEL					0			72	8.186031	KEEP	82	2	59	48	1356	TT	0.999997	0.99996	0			8	44	249	0	0	18.884167	46	45	1355	312		0.148148	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46843731	46843731	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:46843731C>G			NA	NA				None (None upstream) : RNU6-656P (898940 downstream)						NA		NA									NA						tgtctgcgttcaagtcacaga	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46843731C>G		NA		hg19		0.02	-0.140353	GTTxAAG	COVERED																																																																																			NOVEL					0			11	3.911572	KEEP	5	0	0	13	396	CC	0.994391	0.259501	0			3	23	101	0	0	8.27205	12	47	394	51		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46844277	46844277	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:46844277T>G			NA	NA				None (None upstream) : RNU6-656P (898394 downstream)						NA		NA									NA						gatacagcagttttgaaccac	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46844277T>G		NA		hg19		0.02	-0.236833	CAGxTTT	COVERED																																																																																			NOVEL					0			17	7.517884	KEEP	59	0	0	25	677	TT	0.992708	0.63667	0			3	22	110	0	0	8.393978	23	22	709	135		0.115385	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	46849310	46849310	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:46849310C>G			NA	NA				None (None upstream) : RNU6-656P (893361 downstream)						NA		NA									NA						gcagcattctcagaaacttct	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.46849310C>G		NA		hg19		0.02	-0.368453	TCTxAGA	COVERED																																																																																			NOVEL					0			7	6.318305	KEEP	38	0	0	21	634	CC	0.993634	0.893588	0			3	22	105	0	0	7.374875	35	22	1199	130		0.078947	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	48088636	48088636	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48088636A>G			NA	NA				RNU6-819P (45126 upstream) : RP11-1134I14.8 (13758 downstream)						NA		NA									NA						tggctaacatagtgaaacccc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.48088636A>G		NA		hg19		0.02	-0.40344	CATxGTG	COVERED																																																																																			NOVEL					0			15	4.643071	KEEP	0	1	30	26	707	AA	0.999997	0.934489	0			5	60	178	0	0	13.474962	38	60	1126	105		0.116279	0.934492
SPIDR	23514	__UNKNOWN__	__UNKNOWN__	8	48533731	48533731	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48533731A>C	ENST00000518074.1	+	10	1535				SPIDR_ENST00000521214.1_Intron|SPIDR_ENST00000297423.4_Intron|SPIDR_ENST00000541342.1_Intron	NM_001282919.1	NP_001269848.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	NA		NA			cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)					NA						gttggccaggatggtctcgat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808	23514			28971	protein-coding gene	gene with protein product		615384	KIAA0146	KIAA0146	NA	8590280, 23509288	Standard	NM_001080394	XM_005251189	NA	Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000518074.1:c.1364+21973A>C	chr8.hg19:g.48533731A>C		NA	B4DFV2|B4E0Y6|Q96BI5	hg19		0.02	-0.201735	AGGxTGG	UNCOVERED																																																																																			NOVEL	SPIDR-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000377614.1	9	2.70632	KEEP	7	0	0	9	240	AA	0	0	0		+	3	24	105	0	0	8.06462	20	60	607	44	ENST00000518074.1	0.130435	0.522161
SPIDR	23514	__UNKNOWN__	__UNKNOWN__	8	48587638	48587638	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48587638A>G	ENST00000518074.1	+	11	1676				SPIDR_ENST00000521214.1_Intron|SPIDR_ENST00000297423.4_Intron|SPIDR_ENST00000517693.1_Intron|SPIDR_ENST00000541342.1_Intron	NM_001282919.1	NP_001269848.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	NA		NA			cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)					NA						cgctcttgttacccaggctgg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808	23514			28971	protein-coding gene	gene with protein product		615384	KIAA0146	KIAA0146	NA	8590280, 23509288	Standard	NM_001080394	XM_005251189	NA	Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000518074.1:c.1505+1135A>G	chr8.hg19:g.48587638A>G		NA	B4DFV2|B4E0Y6|Q96BI5	hg19		0.02	-0.236801	GTTxCCC	COVERED																																																																																			NOVEL	SPIDR-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000377614.1	10	4.510471	KEEP	1	0	0	15	398	AA	0.99649	0.610258	0		+	3	60	101	0	0	7.494603	23	60	676	64	ENST00000518074.1	0.115385	0.612407
SPIDR	23514	__UNKNOWN__	__UNKNOWN__	8	48643557	48643557	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48643557T>C	ENST00000518074.1	+	18	2596				SPIDR_ENST00000521214.1_Intron|SPIDR_ENST00000518060.1_Intron|SPIDR_ENST00000297423.4_Intron|SPIDR_ENST00000517693.1_Intron|SPIDR_ENST00000541342.1_Intron	NM_001282919.1	NP_001269848.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	NA		NA			cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)					NA						tggtggctcatgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808	23514			28971	protein-coding gene	gene with protein product		615384	KIAA0146	KIAA0146	NA	8590280, 23509288	Standard	NM_001080394	XM_005251189	NA	Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000518074.1:c.2425+1893T>C	chr8.hg19:g.48643557T>C		NA	B4DFV2|B4E0Y6|Q96BI5	hg19		0.02	-0.280662	TCAxGCC	COVERED																																																																																			NOVEL	SPIDR-002	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000377614.1	14	3.608965	KEEP	4	0	0	12	329	TT	0.992708	0.734278	0		+	4	42	132	0	0	10.05734	25	60	744	72	ENST00000518074.1	0.137931	0.739671
PRKDC	5591	__UNKNOWN__	__UNKNOWN__	8	48848466	48848466	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48848466G>A	ENST00000523565.1	-	13	1335				PRKDC_ENST00000314191.2_Intron|PRKDC_ENST00000338368.3_Intron			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	NA		NA			B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	GGAACCTACCGGAAATAATCA	0.388		NA						Non-homologous end-joining													NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(79;1091 1253 12329 31680 40677)							NA				0													60	56	57			NA	NA	8		NA											NA				48848466		1877	4114	5991	SO:0001627	intron_variant				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	5591	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1	NA	7638222	Standard	NM_001081640	NM_001081640	NA	Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.12174-6C>T	chr8.hg19:g.48848466G>A		NA	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	hg19		0.02	1.289379	ACCxGAA	COVERED																																																																																			NOVEL	PRKDC-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000377896.1	2	2.406978	KEEP	0	0	0	8	242	GG	0.99257	0.991794	0		-	4	60	126	0	0	7.663438	74	60	2366	129	ENST00000523565.1	0.051282	0.999218
PRKDC	5591	__UNKNOWN__	__UNKNOWN__	8	48867761	48867761	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48867761A>G	ENST00000523565.1	-	4	456				PRKDC_ENST00000314191.2_Intron|PRKDC_ENST00000338368.3_Intron			P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	NA		NA			B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	ggtggctcacacctgtaatcc	0.537		NA						Non-homologous end-joining													NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(79;1091 1253 12329 31680 40677)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	5591	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1	NA	7638222	Standard	NM_001081640	NM_001081640	NA	Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000523565.1:c.13052+672T>C	chr8.hg19:g.48867761A>G		NA	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	hg19		0.02	-0.210479	CACxCCT	COVERED																																																																																			NOVEL	PRKDC-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000377896.1	8	5.408352	KEEP	6	0	0	18	460	AA	0.999366	0.52183	0		-	3	60	105	0	0	8.064778	20	60	575	68	ENST00000523565.1	0.130435	0.522161
UBE2V2	7336	__UNKNOWN__	__UNKNOWN__	8	48954604	48954604	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:48954604C>T	ENST00000521346.1	+	3	248				UBE2V2_ENST00000517630.1_Intron|UBE2V2_ENST00000523111.2_Intron|UBE2V2_ENST00000520809.1_5'UTR			Q15819	UB2V2_HUMAN	ubiquitin-conjugating enzyme E2 variant 2	NA		NA			cell proliferation (GO:0008283)|DNA double-strand break processing (GO:0000729)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of DNA repair (GO:0045739)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of synapse assembly (GO:0051965)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of DNA repair (GO:0006282)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|UBC13-MMS2 complex (GO:0031372)	acid-amino acid ligase activity (GO:0016881)			large_intestine(1)|lung(2)	3		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00171)|all_lung(136;0.00196)				ctgcctgcctcggcctcccaa	0.483		NA						Rad6 pathway													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X98091	CCDS43738.1	8q11.21	2008-02-05			ENSG00000169139	ENSG00000169139	7336		Ubiquitin-conjugating enzymes E2	12495	protein-coding gene	gene with protein product		603001			NA	9418904, 9199207	Standard	NM_003350	NM_003350	NA	Approved	UEV-2, DDVit-1, EDPF-1, MMS2	uc003xqm.3	Q15819	OTTHUMG00000164206	ENST00000521346.1:c.-104-989C>T	chr8.hg19:g.48954604C>T		NA		hg19		0.02	-0.342023	CCTxGGC	COVERED																																																																																			NOVEL	UBE2V2-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000377810.1	11	3.308589	KEEP	0	0	0	11	313	CC	0.993072	0.859748	0		+	4	60	99	0	0	6.47567	30	60	946	65	ENST00000521346.1	0.117647	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	49007526	49007526	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:49007526T>C			NA	NA				UBE2V2 (30258 upstream) : RNU6-295P (212960 downstream)						NA		NA									NA						gtgatctgcctgccttggcct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.49007526T>C		NA		hg19		0.02	-0.280664	GCCxGCC	COVERED																																																																																			NOVEL					0			11	3.006794	KEEP	3	0	0	10	269	TT	0.99254	0.734154	0			3	60	98	0	0	7.04452	26	60	776	61		0.103448	0.739671
RP11-770E5.1	0	__UNKNOWN__	__UNKNOWN__	8	49568190	49568190	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:49568190A>G	ENST00000522575.1	+	0	356										NA		NA									NA						tcaccatgttagccaggctgg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000522575.1:	chr8.hg19:g.49568190A>G		NA		hg19		0.02	-0.061358	GTTxGCC	UNCOVERED																																																																																			NOVEL	RP11-770E5.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000377771.1	5	3.007172	KEEP	2	0	0	10	269	AA	0.99254	0.04346	0		+	3	60	99	0	0	9.527283	3	60	79	23	ENST00000522575.1	0.5	0.043787
SNTG1	54212	__UNKNOWN__	__UNKNOWN__	8	50871137	50871137	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:50871137C>T	ENST00000522124.1	+	1	559				SNTG1_ENST00000518864.1_Intron|SNTG1_ENST00000517473.1_Intron|SNTG1_ENST00000520697.1_Intron	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	NA		NA			cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				cctgccaccacgcctggctaa	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481	54212			13740	protein-coding gene	gene with protein product		608714			NA	10747910	Standard		NM_018967	NA	Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.-103+46346C>T	chr8.hg19:g.50871137C>T		NA	Q2M3Q0|Q9NY98	hg19	CCDS6147.1	0.02	-0.157883	CCAxGCC	UNCOVERED																																																																																			NOVEL	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377964.1	8	2.405938	KEEP	2	0	0	8	222	CC	0	0	0		+	3	60	89	0	0	6.979046	13	60	419	34	ENST00000522124.1	0.1875	0.322807
SNTG1	54212	__UNKNOWN__	__UNKNOWN__	8	51367150	51367150	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:51367150C>T	ENST00000522124.1	+	8	1024				SNTG1_ENST00000276467.5_Intron|SNTG1_ENST00000518864.1_Intron|SNTG1_ENST00000517473.1_Intron	NM_018967.2	NP_061840.1	Q9NSN8	SNTG1_HUMAN	syntrophin, gamma 1	NA		NA			cell communication (GO:0007154)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)|syntrophin complex (GO:0016013)	protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(36)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	66		all_cancers(86;0.00754)|all_epithelial(80;9.76e-05)|Lung NSC(129;0.000865)|all_lung(136;0.00249)|Colorectal(162;0.22)				gcctgtaatcccagcactttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ003030	CCDS6147.1, CCDS75737.1	8q11-q12	2008-07-03				ENSG00000147481	54212			13740	protein-coding gene	gene with protein product		608714			NA	10747910	Standard		NM_018967	NA	Approved	SYN4, G1SYN	uc003xqs.1	Q9NSN8		ENST00000522124.1:c.363+3861C>T	chr8.hg19:g.51367150C>T		NA	Q2M3Q0|Q9NY98	hg19	CCDS6147.1	0.02	-0.20161	ATCxCAG	COVERED																																																																																			NOVEL	SNTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377964.1	7	3.30983	KEEP	0	0	0	11	337	CC	0.993072	0.487146	0		+	3	60	94	0	0	6.966116	20	60	650	50	ENST00000522124.1	0.130435	0.490544
PXDNL	137902	__UNKNOWN__	__UNKNOWN__	8	52279428	52279428	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:52279428C>T	ENST00000356297.4	-	19	4002				PXDNL_ENST00000543296.1_Intron	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	NA		NA			hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				tttgggaggccgaggcaggca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485	137902		Immunoglobulin superfamily / I-set domain containing	26359	protein-coding gene	gene with protein product	polysomal ribonuclease 1 homolog (Xenopus)	615904	peroxidasin homolog-like (Drosophila)		NA	22543864	Standard	NM_144651	NM_144651	NA	Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3901+5004G>A	chr8.hg19:g.52279428C>T		NA	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	hg19	CCDS47855.1	0.02	-0.18421	GGCxGAG	COVERED																																																																																			NOVEL	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377905.1	12	2.707414	KEEP	2	0	0	9	265	CC	0.99254	0.420319	0		-	3	60	91	0	0	7.010328	15	60	489	44	ENST00000356297.4	0.166667	0.423478
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52731894	52731894	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:52731894C>G	ENST00000360540.5	-	0	2497				PCMTD1_ENST00000544451.1_3'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	NA		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				AATGTAGGCTCAGCCCTACCT	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.*1017G>C	chr8.hg19:g.52731894C>G		NA	Q96FK9	hg19	CCDS6148.1	0.02	1.654495	GCTxAGC	COVERED																																																																																			NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	0	3.007077	KEEP	2	0	0	10	285	CC	0.992708	0.982326	0		-	4	59	124	0	0	8.224074	47	60	1529	87	ENST00000360540.5	0.078431	0.989542
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52731959	52731959	__UNKNOWN__	3'UTR	SNP	G	G	A	rs111392823		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:52731959G>A	ENST00000360540.5	-	0	2432				PCMTD1_ENST00000544451.1_3'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	NA		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				AAGTGCATCCGCTGACCAGGT	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.*952C>T	chr8.hg19:g.52731959G>A		NA	Q96FK9	hg19	CCDS6148.1	0.02	4.753229	TCCxCTG	COVERED																																																																																			NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	9	4.745287	KEEP	3	1	29	26	768	GG	0.999988	0.999988	0		-	9	59	279	0	0	20.039349	70	60	2264	336	ENST00000360540.5	0.113924	1
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52733144	52733144	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs200246241		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:52733144C>T	ENST00000360540.5	-	7	1247	c.841G>A	c.(841-843)Gtt>Att	p.V281I	PCMTD1_ENST00000522514.1_Missense_Mutation_p.V281I|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.V205I	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	281		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CTCTGTTTAACTCTCTTTCTT	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.841G>A	chr8.hg19:g.52733144C>T	ENSP00000353739:p.Val281Ile	NA	Q96FK9	hg19	CCDS6148.1	0.02	1.449863	TAAxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	11.99	1.803545	0.31869	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.46451	0.87;0.87;0.87	5.97	5.97	0.96955	.	0.260164	0.36972	N	0.002316	T	0.37128	0.0992	L	0.42245	1.32	0.27985	N	0.935891	B;B;B	0.32467	0.039;0.372;0.001	B;B;B	0.35770	0.024;0.21;0.002	T	0.27905	-1.0060	10	0.21540	T	0.41	-33.7683	13.3218	0.60436	0.2592:0.7408:0.0:0.0	.	151;205;281	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	I	281;205;281	ENSP00000353739:V281I;ENSP00000444026:V205I;ENSP00000428099:V281I	ENSP00000353739:V281I	V	-	1	0	PCMTD1	52895697	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	5.921000	0.70028	2.828000	0.97474	0.655000	0.94253	GTT	NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	7	3.91165	KEEP	7	0	0	13	398	CC	0.993634	0.991545	0		-	4	57	128	0	0	8.360703	55	60	1860	132	ENST00000360540.5	0.067797	0.997898
PCMTD1	115294	__UNKNOWN__	__UNKNOWN__	8	52733228	52733228	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs73592211		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:52733228G>A	ENST00000360540.5	-	7	1163	c.757C>T	c.(757-759)Cgc>Tgc	p.R253C	PCMTD1_ENST00000522514.1_Missense_Mutation_p.R253C|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.R177C	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	253		NA				cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)			NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				CTAAGTGTGCGTCGAATGTAA	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300	115294			30483	protein-coding gene	gene with protein product		NA			NA		Standard	NM_052937	XM_005251146	NA	Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.757C>T	chr8.hg19:g.52733228G>A	ENSP00000353739:p.Arg253Cys	NA	Q96FK9	hg19	CCDS6148.1	0.02	-0.359632	TGCxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	G	20.8	4.044757	0.75732	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.47869	1.43;0.83;1.43	5.76	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.62060	0.2397	L	0.60455	1.87	0.80722	D	1	D;B;B	0.89917	1.0;0.333;0.231	P;B;B	0.62184	0.899;0.061;0.081	T	0.64300	-0.6440	10	0.52906	T	0.07	-15.7151	14.8982	0.70659	0.0689:0.0:0.9311:0.0	.	123;177;253	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	C	253;177;253	ENSP00000353739:R253C;ENSP00000444026:R177C;ENSP00000428099:R253C	ENSP00000353739:R253C	R	-	1	0	PCMTD1	52895781	1.000000	0.71417	0.985000	0.45067	0.970000	0.65996	8.903000	0.92573	1.438000	0.47492	0.650000	0.86243	CGC	NOVEL	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377909.2	0	2.706127	KEEP	0	0	0	9	246	GG	0.99254	0.882244	0		-	4	49	115	0	0	7.766929	36	60	1151	70	ENST00000360540.5	0.1	0.888875
FAM150A	389658	__UNKNOWN__	__UNKNOWN__	8	53457491	53457491	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:53457491T>C	ENST00000358543.4	-	2	441				FAM150A_ENST00000523939.1_Intron	NM_207413.3	NP_997296.1	Q6UXT8	F150A_HUMAN	family with sequence similarity 150, member A	NA		NA				extracellular region (GO:0005576)				lung(1)	1		Lung NSC(129;0.0919)|all_epithelial(80;0.125)|all_lung(136;0.17)				Attttgtttttttgagacagg	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6150.1	8q11.23	2007-12-18			ENSG00000196711	ENSG00000196711	389658			33775	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207413	NM_207413	NA	Approved	UNQ9433	uc003xrd.3	Q6UXT8	OTTHUMG00000164256	ENST00000358543.4:c.191-2486A>G	chr8.hg19:g.53457491T>C		NA	B7ZMG9	hg19	CCDS6150.1	0.02	-0.078938	TTTxTTG	UNCOVERED																																																																																			NOVEL	FAM150A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377959.1	8	2.706074	KEEP	2	0	0	9	237	TT	0.99257	0.076761	0		-	3	60	95	0	0	9.125136	3	60	87	24	ENST00000358543.4	0.5	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	53642870	53642870	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:53642870C>T			NA	NA				CTD-3214K23.1 (7169 upstream) : NPBWR1 (208120 downstream)						NA		NA									NA						ctcatgcctgcaatcccagca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.53642870C>T		NA		hg19		0.02	-0.175403	CTGxAAT	COVERED																																																																																			NOVEL					0			8	3.610546	KEEP	1	0	0	12	363	CC	0.993072	0.384723	0			4	60	109	1	0	8.781363	13	60	419	41		0.235294	0.387407
LYPLA1	10434	__UNKNOWN__	__UNKNOWN__	8	54996426	54996426	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:54996426G>A	ENST00000316963.3	-	2	295				LYPLA1_ENST00000522007.1_Intron|LYPLA1_ENST00000343231.6_Intron|LYPLA1_ENST00000519926.1_Intron	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	NA		NA			fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			ggccgggcacggtggctcacg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	10434	3.1.1.5		6737	protein-coding gene	gene with protein product		605599			NA	10064899	Standard		NM_006330	NA	Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.101+17041C>T	chr8.hg19:g.54996426G>A		NA	O43202|Q9UQF9	hg19	CCDS6157.1	0.02	-0.245546	CACxGTG	UNCOVERED																																																																																			NOVEL	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378238.1	7	2.707467	KEEP	4	0	0	9	263	GG	0	0	0		-	4	60	120	0	0	9.295456	19	60	581	58	ENST00000316963.3	0.173913	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	55064928	55064928	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:55064928A>G			NA	NA				MRPL15 (4467 upstream) : RNU6ATAC32P (438 downstream)						NA		NA									NA						cgcccgcctcagcctcccaaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.55064928A>G		NA		hg19		0.02	-0.210512	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.406258	KEEP	3	0	0	8	223	AA	0	0	0			3	60	99	0	0	7.464917	20	60	612	50		0.130435	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	55240084	55240084	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:55240084A>G			NA	NA				RNU6ATAC32P (174642 upstream) : RNU105C (3162 downstream)						NA		NA									NA						ggttgctcacacctataatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.55240084A>G		NA		hg19		0.02	-0.122767	CACxCCT	COVERED																																																																																			NOVEL					0			4	2.405797	KEEP	0	0	0	8	219	AA	0.99257	0.194853	0			3	60	96	0	0	7.873282	11	60	312	30		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	55240088	55240088	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:55240088A>G			NA	NA				RNU6ATAC32P (174646 upstream) : RNU105C (3158 downstream)						NA		NA									NA						gctcacacctataatcccagc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.55240088A>G		NA		hg19		0.02	-0.11401	CCTxTAA	UNCOVERED																																																																																			NOVEL					0			4	2.406086	KEEP	0	0	0	8	220	AA	0.99257	0.16126	0			3	60	102	0	0	8.582227	10	60	289	30		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	55284656	55284656	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:55284656C>T			NA	NA				RNU105C (41201 upstream) : RN7SL250P (48371 downstream)						NA		NA									NA						ctgcaacctccgcctcccggg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.55284656C>T		NA		hg19		0.02	-0.12278	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			11	2.406833	KEEP	4	0	0	8	238	CG	0	0	0			3	49	83	1	0	6.68226	10	60	310	36		0.230769	0.196312
TMEM68	137695	__UNKNOWN__	__UNKNOWN__	8	56659698	56659698	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:56659698G>A	ENST00000523073.1	-	4	428				TMEM68_ENST00000434581.2_Intron|TMEM68_ENST00000519784.1_Intron|TMEM68_ENST00000334667.2_Intron			Q96MH6	TMM68_HUMAN	transmembrane protein 68	NA		NA				integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups (GO:0016746)			NS(1)|kidney(1)|lung(2)|ovary(1)|skin(1)	6			Epithelial(17;0.000361)|all cancers(17;0.00326)			caaggcaggtggatcacttga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056932	CCDS6161.1, CCDS75740.1, CCDS75741.1, CCDS75742.1	8q12.1	2011-12-12			ENSG00000167904	ENSG00000167904	137695			26510	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152417	XM_005251150	NA	Approved	FLJ32370	uc003xsh.1	Q96MH6	OTTHUMG00000164293	ENST00000523073.1:c.346-2018C>T	chr8.hg19:g.56659698G>A		NA	Q658X6|Q8WUD2	hg19		0.02	-0.254401	GGTxGAT	COVERED																																																																																			NOVEL	TMEM68-016	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000378141.1	11	4.513465	KEEP	7	0	0	15	462	GG	0.993634	0.664267	0		-	3	60	92	0	0	6.59516	23	60	784	75	ENST00000523073.1	0.115385	0.668523
TGS1	96764	__UNKNOWN__	__UNKNOWN__	8	56734831	56734831	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:56734831T>G	ENST00000260129.5	+	13	2916					NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	NA		NA			7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			gggttttaccttgtttgccag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(34;275 823 4842 34837 48447)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	96764	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	nuclear receptor coactivator 6 interacting protein, trimethylguanosine synthase homolog (S. cerevisiae)	NCOA6IP	NA	11517327, 11983179, 19307714	Standard	NM_024831	NM_024831	NA	Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.2440-2309T>G	chr8.hg19:g.56734831T>G		NA	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	hg19	CCDS34894.1	0.02	-0.105249	ACCxTGT	UNCOVERED																																																																																			NOVEL	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378152.1	4	2.406437	KEEP	0	0	0	8	225	TT	0.99257	0.138793	0		+	3	54	90	0	0	7.501176	9	60	271	26	ENST00000260129.5	0.25	0.139832
LYN	4067	__UNKNOWN__	__UNKNOWN__	8	56891844	56891844	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:56891844A>G	ENST00000519728.1	+	10	1346				LYN_ENST00000520220.2_Intron|LYN_ENST00000420292.1_Intron	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	NA		NA			B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	caggtgatccacccgcctcgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087	4067		SH2 domain containing	6735	protein-coding gene	gene with protein product		165120	v-yes-1 Yamaguchi sarcoma viral related oncogene homolog		NA	3561390	Standard	NM_002350	NM_002350	NA	Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1050+9492A>G	chr8.hg19:g.56891844A>G		NA	A0AVQ5	hg19	CCDS6162.1	0.02	-0.096461	TCCxCCC	UNCOVERED																																																																																			NOVEL	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378155.1	3	2.644968	KEEP	3	0	0	9	229	AA	0.99254	0.119538	0		+	3	60	92	0	0	7.979082	7	60	195	38	ENST00000519728.1	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	56969681	56969681	__UNKNOWN__	IGR	SNP	G	G	A	rs4360268	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:56969681G>A			NA	NA				RN7SL323P (34809 upstream) : RPS20 (10172 downstream)						NA		NA									NA						actttgggaggctgaggcggg	0.468		NA											G|||	434	0.0866613	0.0219	0.1527	5008	,	,	NA	16308	0.001	NA	0.2217	False	NA	,,,	NA	NA	NA	2504	0.0767	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.56969681G>A		NA		hg19		0.02	-0.122796	GAGxCTG	UNCOVERED																																																																																			NOVEL					0			9	2.7072	KEEP	11	0	0	9	265	GG	0	0	0			5	60	143	0	0	13.144291	7	60	242	43		0.416667	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	56976414	56976414	__UNKNOWN__	IGR	SNP	C	C	T	rs113266469	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:56976414C>T			NA	NA				RN7SL323P (41542 upstream) : RPS20 (3439 downstream)						NA		NA									NA						agtgcagtggcgtgatctcgg	0.512		NA											C|||	113	0.0225639	0.0151	0.036	5008	,	,	NA	12461	0.006	NA	0.0308	False	NA	,,,	NA	NA	NA	2504	0.0317	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.56976414C>T		NA		hg19		0.02	-0.087692	TGGxGTG	UNCOVERED																																																																																			NOVEL					0			7	3.00859	KEEP	9	0	0	10	305	CC	0	0	0			3	60	77	0	0	6.642594	6	60	199	36		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	58026785	58026785	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:58026785A>G			NA	NA				IMPAD1 (120382 upstream) : RNA5SP266 (12428 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.58026785A>G		NA		hg19		0.02	-0.157761	GGCxTGA	COVERED																																																																																			NOVEL					0			7	2.405779	KEEP	0	0	0	8	218	AA	0.99257	0.320408	0			3	60	103	0	0	8.292811	14	60	386	37		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	58341241	58341241	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:58341241T>C			NA	NA				RP11-756K15.2 (63825 upstream) : RP11-246K15.1 (64201 downstream)						NA		NA									NA						catgagccactgcgcccggcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.58341241T>C		NA		hg19		0.02	-0.324513	CACxGCG	COVERED																																																																																			NOVEL					0			9	5.41436	KEEP	6	0	0	18	510	TT	0.999366	0.835186	0			3	60	94	0	0	6.388638	32	60	962	92		0.085714	0.835716
RP11-388G22.1	0	__UNKNOWN__	__UNKNOWN__	8	58525292	58525292	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:58525292C>T	ENST00000520426.1	-	0	273										NA		NA									NA						ttttggaggccgaggtgggtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000520426.1:	chr8.hg19:g.58525292C>T		NA		hg19		0.02	-0.175441	GGCxGAG	COVERED																																																																																			NOVEL	RP11-388G22.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000378045.1	7	3.308947	KEEP	4	0	0	11	321	CC	0.99254	0.384517	0		-	4	60	120	0	0	9.768241	14	60	471	46	ENST00000520426.1	0.222222	0.387407
RP11-388G22.1	0	__UNKNOWN__	__UNKNOWN__	8	58525413	58525413	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:58525413T>C	ENST00000520426.1	-	0	273										NA		NA									NA						cctgtagtcctagctacttgg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000520426.1:	chr8.hg19:g.58525413T>C		NA		hg19		0.02	-0.184187	TCCxAGC	UNCOVERED																																																																																			NOVEL	RP11-388G22.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000378045.1	3	2.405732	KEEP	1	0	0	8	214	TT	0	0	0		-	3	60	99	0	0	7.660965	17	60	513	39	ENST00000520426.1	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	60058479	60058479	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:60058479G>A			NA	NA				SNORA51 (8418 upstream) : RNA5SP267 (309964 downstream)						NA		NA									NA						ggcagatcacgaagtcaagag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.60058479G>A		NA		hg19		0.02	-0.175435	CACxAAG	COVERED																																																																																			NOVEL					0			9	2.40702	KEEP	0	0	0	8	243	GG	0.99257	0.384528	0			3	60	85	0	0	6.579307	13	60	429	40		0.1875	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	60368760	60368760	__UNKNOWN__	IGR	SNP	T	T	G	rs58048385		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:60368760T>G			NA	NA				RNA5SP267 (191 upstream) : RP11-379I19.1 (105125 downstream)						NA		NA									NA						ctgcctgccttccttccttcc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.60368760T>G		NA		hg19		0.02	-0.122732	CCTxCCT	UNCOVERED																																																																																			NOVEL					0			9	2.404902	KEEP	6	0	0	8	206	TT	0	0	0			3	60	89	0	0	7.174238	11	60	305	32		0.214286	0.196312
CA8	767	__UNKNOWN__	__UNKNOWN__	8	61183740	61183740	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:61183740C>A	ENST00000317995.4	-	3	557					NM_004056.4	NP_004047.3	P35219	CAH8_HUMAN	carbonic anhydrase VIII	NA		NA			one-carbon metabolic process (GO:0006730)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasm (GO:0005737)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|prostate(2)|skin(1)	16		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)			Zonisamide(DB00909)	ctgtctctaccaaaaatttaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L04656	CCDS6174.1	8q12.1	2012-08-21			ENSG00000178538	ENSG00000178538	767		Carbonic anhydrases	1382	protein-coding gene	gene with protein product		114815		CALS	NA	17219437	Standard		NM_004056	NA	Approved	CARP	uc003xtz.1	P35219	OTTHUMG00000165325	ENST00000317995.4:c.293-5132G>T	chr8.hg19:g.61183740C>A		NA	A8K0A5|B3KQZ7|Q32MY2	hg19	CCDS6174.1	0.02	-0.175441	TACxAAA	COVERED																																																																																			NOVEL	CA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383445.1	9	3.009151	KEEP	0	0	0	10	312	CC	0.992708	0.384582	0		-	3	60	89	0	0	6.891928	14	60	470	39	ENST00000317995.4	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	61249504	61249504	__UNKNOWN__	IGR	SNP	A	A	G	rs2086394	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:61249504A>G			NA	NA				CA8 (55533 upstream) : RP11-163N6.2 (66266 downstream)						NA		NA									NA						tcaggagatcaagaccatcct	0.567		NA											A|||	1109	0.221446	0.0356	0.3343	5008	,	,	NA	15753	0.3274	NA	0.2803	False	NA	,,,	NA	NA	NA	2504	0.2229	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.61249504A>G		NA		hg19		0.02	-0.105262	ATCxAGA	UNCOVERED																																																																																			NOVEL					0			5	2.404932	KEEP	14	0	0	8	207	AA	0	0	0			6	40	194	0	0	19.339544	4	57	120	42		0.6	0.139832
CHD7	55636	__UNKNOWN__	__UNKNOWN__	8	61765587	61765587	__UNKNOWN__	Silent	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:61765587G>C	ENST00000423902.2	+	31	6782	c.6303G>C	c.(6301-6303)ctG>ctC	p.L2101L	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2101		NA			adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			GAGACTTGCTGGTTGGTGCTG	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													100	111	107			NA	NA	8		NA											NA				61765587		2074	4208	6282	SO:0001819	synonymous_variant			AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316	55636			20626	protein-coding gene	gene with protein product		608892	CHARGE association	CRG	NA	15300250, 18834967	Standard	XM_098762	NM_017780	NA	Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6303G>C	chr8.hg19:g.61765587G>C		NA	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	hg19	CCDS47865.1	0.02	3.306109	GCTxGTT	COVERED																																																																																			NOVEL	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383468.2	2	4.209493	KEEP	0	0	0	14	417	GG	0.995343	0.995343	0		+	26	60	822	0	0	65.430495	114	60	3832	222	ENST00000423902.2	0.185714	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	61818548	61818548	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:61818548T>C			NA	NA				CHD7 (39083 upstream) : AC022182.1 (12991 downstream)						NA		NA									NA						gctgggattataggcgtgagc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.61818548T>C		NA		hg19		0.02	-0.14907	TTAxAGG	COVERED																																																																																			NOVEL					0			6	2.406462	KEEP	0	0	0	8	227	TT	0.99257	0.289832	0			3	60	96	0	0	7.679563	13	60	381	36		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	61902432	61902432	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:61902432A>C			NA	NA				AC022182.3 (22098 upstream) : RP11-787D18.2 (274750 downstream)						NA		NA									NA						tgcctgtaataccagcacttt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.61902432A>C		NA		hg19		0.02	-0.175413	AATxCCA	COVERED																																																																																			NOVEL					0			6	2.405929	KEEP	0	0	0	8	218	AA	0.99257	0.384528	0			3	60	100	0	0	7.910175	15	60	443	42		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	64283342	64283342	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:64283342G>T			NA	NA				RN7SL135P (135873 upstream) : CTD-3046C4.1 (14054 downstream)						NA		NA									NA						agtggcgcgagctcggctcac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.64283342G>T		NA		hg19		0.02	-0.219308	CGAxCTC	COVERED																																																																																			NOVEL					0			6	4.212336	KEEP	2	0	0	14	431	GG	0.995343	0.550313	0			3	60	95	0	0	7.192102	18	60	622	63		0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	65803795	65803795	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:65803795T>C			NA	NA				RP11-1D12.2 (73665 upstream) : CTD-3025N20.2 (635447 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.65803795T>C		NA		hg19		0.02	-0.254354	TCAxGCC	COVERED																																																																																			NOVEL					0			10	2.406437	KEEP	3	0	0	8	228	TT	0.99257	0.663556	0			3	60	91	0	0	6.549796	22	60	665	59		0.12	0.668523
PDE7A	5150	__UNKNOWN__	__UNKNOWN__	8	66650947	66650947	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:66650947T>C	ENST00000401827.3	-	6	1039				PDE7A_ENST00000396642.3_Intron|PDE7A_ENST00000379419.4_Intron|PDE7A_ENST00000518667.1_Intron	NM_001242318.2	NP_001229247.1	Q13946	PDE7A_HUMAN	phosphodiesterase 7A	NA		NA			cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			large_intestine(5)|lung(3)|stomach(1)|urinary_tract(1)	10			Epithelial(68;0.0509)|BRCA - Breast invasive adenocarcinoma(89;0.111)|all cancers(69;0.168)|OV - Ovarian serous cystadenocarcinoma(28;0.238)		Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	ggattacaggtgtgagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L12052	CCDS34901.1, CCDS56538.1	8q13	2008-03-18				ENSG00000205268	5150	3.1.4.17	Phosphodiesterases	8791	protein-coding gene	gene with protein product		171885			NA	8389765, 9521885	Standard		NM_001242318	NA	Approved	HCP1	uc003xvq.3	Q13946		ENST00000401827.3:c.595+789A>G	chr8.hg19:g.66650947T>C		NA	A0AVH6|A8K436|A8K9G5|O15380|Q96T72	hg19	CCDS56538.1	0.02	-0.19295	AGGxGTG	COVERED																																																																																			NOVEL	PDE7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378905.1	6	3.007306	KEEP	0	0	0	10	270	TT	0.992708	0.454419	0		-	3	60	108	0	0	8.491925	18	60	528	48	ENST00000401827.3	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	66880761	66880761	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:66880761T>C			NA	NA				CTD-2532N20.1 (125195 upstream) : DNAJC5B (53033 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.66880761T>C		NA		hg19		0.02	-0.228009	TCAxGCC	COVERED																																																																																			NOVEL					0			5	2.706642	KEEP	1	0	0	9	245	TT	0.99257	0.578599	0			3	60	100	0	0	7.565089	20	60	579	60		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	67328114	67328114	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:67328114G>A			NA	NA				LINC00967 (218564 upstream) : RP11-346I3.4 (3709 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.67328114G>A		NA		hg19		0.02	-0.210524	CACxCCT	COVERED																																																																																			NOVEL					0			8	3.308238	KEEP	0	0	0	11	313	GG	0.993072	0.518544	0			3	60	89	0	0	6.528137	19	60	629	51		0.136364	0.522161
SGK3	23678	__UNKNOWN__	__UNKNOWN__	8	67637211	67637211	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:67637211T>C	ENST00000521198.2	+	1	416				C8orf44-SGK3_ENST00000520044.1_Intron|C8orf44-SGK3_ENST00000519289.1_Intron	NM_001033578.2	NP_001028750.1	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	NA		NA			ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			cctgtaatcctagcactttgg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205	23678			10812	protein-coding gene	gene with protein product		607591	serum/glucocorticoid regulated kinase-like	SGK2, SGKL	NA	10585774, 10548550	Standard		NM_013257	NA	Approved		uc003xwr.3	Q96BR1		ENST00000521198.2:c.-122+12143T>C	chr8.hg19:g.67637211T>C		NA	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	hg19	CCDS6195.1	0.02	-0.28061	TCCxAGC	COVERED																																																																																			NOVEL	SGK3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379232.3	13	3.608615	KEEP	5	0	0	12	322	TT	0.992708	0.734278	0		+	3	60	103	0	1	7.592512	25	60	730	71	ENST00000521198.2	0.107143	0.739671
SGK3	23678	__UNKNOWN__	__UNKNOWN__	8	67649294	67649294	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:67649294A>T	ENST00000521198.2	+	1	416				C8orf44-SGK3_ENST00000520044.1_Intron|C8orf44-SGK3_ENST00000519289.1_Intron	NM_001033578.2	NP_001028750.1	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	NA		NA			ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			attacaggcaagagccactgt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205	23678			10812	protein-coding gene	gene with protein product		607591	serum/glucocorticoid regulated kinase-like	SGK2, SGKL	NA	10585774, 10548550	Standard		NM_013257	NA	Approved		uc003xwr.3	Q96BR1		ENST00000521198.2:c.-122+24226A>T	chr8.hg19:g.67649294A>T		NA	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	hg19	CCDS6195.1	0.02	-0.140338	GCAxGAG	COVERED																																																																																			NOVEL	SGK3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379232.3	2	3.007577	KEEP	0	0	0	10	275	AA	0.992708	0.259062	0		+	3	60	86	0	0	6.772494	12	60	376	39	ENST00000521198.2	0.2	0.260965
MCMDC2	157777	__UNKNOWN__	__UNKNOWN__	8	67833166	67833166	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:67833166T>C	ENST00000422365.2	+	0	3979				MCMDC2_ENST00000541540.1_3'UTR	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	NA		NA			DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						cttcccagtgttgggattaca	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460	157777			26368	protein-coding gene	gene with protein product		NA	chromosome 8 open reading frame 45	C8orf45	NA		Standard	NM_173518	NM_173518	NA	Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.*1762T>C	chr8.hg19:g.67833166T>C		NA	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	hg19	CCDS6197.2	0.02	-0.298216	GTGxTGG	COVERED																																																																																			NOVEL	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347350.1	1	2.406686	KEEP	0	0	0	8	230	TT	0.99257	0.775257	0		+	4	60	128	0	0	9.41791	29	60	882	61	ENST00000422365.2	0.121212	0.78106
PPP1R42	286187	__UNKNOWN__	__UNKNOWN__	8	67952618	67952618	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:67952618A>G	ENST00000517834.1	-	2	198							Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	NA		NA			regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)				NA						agctggtctcaaactcctgac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125	286187		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	33732	protein-coding gene	gene with protein product	testis leucine-rich repeat	NA	leucine rich repeat containing 67	LRRC67	NA		Standard	NM_001013626	NM_001013626	NA	Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000517834.1:c.412+10846T>C	chr8.hg19:g.67952618A>G		NA		hg19		0.02	-0.122799	CTCxAAC	COVERED																																																																																			NOVEL	PPP1R42-013	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000381490.1	4	2.405855	KEEP	0	0	0	8	218	AA	0.99257	0.194853	0		-	3	60	103	0	0	8.572793	11	60	335	33	ENST00000517834.1	0.214286	0.196312
ARFGEF1	10565	__UNKNOWN__	__UNKNOWN__	8	68200778	68200778	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:68200778G>A	ENST00000262215.3	-	7	1306					NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	NA		NA			endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			gaccagcctggccaacatggt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777	10565			15772	protein-coding gene	gene with protein product		604141			NA	10212200, 8917509	Standard	NM_006421	NM_006421	NA	Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.917-478C>T	chr8.hg19:g.68200778G>A		NA	Q9NV46|Q9UFV2|Q9UNL0	hg19	CCDS6199.1	0.02	-0.157902	CTGxCCA	COVERED																																																																																			NOVEL	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379441.4	2	2.406674	KEEP	0	0	0	8	231	GG	0.99257	0.320408	0		-	3	60	88	0	0	6.878937	13	60	451	35	ENST00000262215.3	0.1875	0.322807
ARFGEF1	10565	__UNKNOWN__	__UNKNOWN__	8	68232227	68232227	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:68232227G>A	ENST00000262215.3	-	2	514					NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	NA		NA			endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			aggccgaggcgggtggatcac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777	10565			15772	protein-coding gene	gene with protein product		604141			NA	10212200, 8917509	Standard	NM_006421	NM_006421	NA	Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.125-17526C>T	chr8.hg19:g.68232227G>A		NA	Q9NV46|Q9UFV2|Q9UNL0	hg19	CCDS6199.1	0.02	-0.15788	GGCxGGT	COVERED																																																																																			NOVEL	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379441.4	6	2.707945	KEEP	0	0	0	9	280	GT	0.992708	0.351366	0		-	3	60	87	0	0	6.872546	12	60	383	48	ENST00000262215.3	0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	68292159	68292159	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:68292159T>C			NA	NA				RP11-7F18.2 (34837 upstream) : CPA6 (42245 downstream)						NA		NA									NA						cagagtcttgttctgtctccc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.68292159T>C		NA		hg19		0.02	-0.131536	TTGxTCT	COVERED																																																																																			NOVEL					0			7	3.007282	KEEP	3	0	0	10	270	TT	0.99257	0.22747	0			3	60	102	0	0	8.473281	11	60	308	31		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	68314578	68314578	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:68314578G>A			NA	NA				RP11-7F18.2 (57256 upstream) : CPA6 (19826 downstream)						NA		NA									NA						cgcctgcctcggcctcccaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.68314578G>A		NA		hg19		0.02	-0.175447	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			8	2.708221	KEEP	7	0	0	9	283	GG	0	0	0			3	60	87	0	0	6.610697	15	60	535	50		0.166667	0.387407
PREX2	80243	__UNKNOWN__	__UNKNOWN__	8	69030377	69030377	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:69030377T>C	ENST00000288368.4	+	27	3603					NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	NA		NA			adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						gatcacaaggtcaggagatgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889	80243		Rho guanine nucleotide exchange factors	22950	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 129	612139	DEP domain containing 2	DEPDC2	NA	15304342, 15304343	Standard	NM_025170	NM_024870	NA	Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3327-408T>C	chr8.hg19:g.69030377T>C		NA	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	hg19	CCDS6201.1	0.02	-0.192899	AGGxCAG	UNCOVERED																																																																																			NOVEL	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378620.1	9	3.304654	KEEP	8	0	0	11	277	TT	0	0	0		+	4	46	143	0	0	11.679919	18	60	531	56	ENST00000288368.4	0.181818	0.457757
PREX2	80243	__UNKNOWN__	__UNKNOWN__	8	69073594	69073594	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:69073594T>C	ENST00000288368.4	+	35	4623					NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	NA		NA			adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						tcctaaagtgttgggattaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889	80243		Rho guanine nucleotide exchange factors	22950	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 129	612139	DEP domain containing 2	DEPDC2	NA	15304342, 15304343	Standard	NM_025170	NM_024870	NA	Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4346+3923T>C	chr8.hg19:g.69073594T>C		NA	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	hg19	CCDS6201.1	0.02	-0.219255	GTGxTGG	COVERED																																																																																			NOVEL	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378620.1	8	3.309262	KEEP	0	0	0	11	321	TT	0.993072	0.549057	0		+	3	60	106	0	0	8.164746	20	60	599	52	ENST00000288368.4	0.130435	0.552887
SULF1	23213	__UNKNOWN__	__UNKNOWN__	8	70467631	70467631	__UNKNOWN__	Intron	SNP	G	G	A	rs368177276		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:70467631G>A	ENST00000260128.4	+	4	584				SULF1_ENST00000402687.4_Intron|SULF1_ENST00000458141.2_Intron|SULF1_ENST00000419716.3_Intron	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	NA		NA			apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			ggtggctcacgcctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573	23213			20391	protein-coding gene	gene with protein product		610012			NA	12368295	Standard	NM_015170	NM_015170	NA	Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.-133-8143G>A	chr8.hg19:g.70467631G>A		NA	Q86YV8|Q8NCA2|Q9UPS5	hg19	CCDS6204.1	0.02	-0.219282	CACxCCT	COVERED																																																																																			NOVEL	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378885.2	11	3.008486	KEEP	1	0	0	10	296	GG	0.99254	0.548763	0		+	3	60	91	1	0	6.549793	22	60	698	48	ENST00000260128.4	0.12	0.552887
SULF1	23213	__UNKNOWN__	__UNKNOWN__	8	70548523	70548523	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:70548523A>G	ENST00000260128.4	+	20	3001				SULF1_ENST00000402687.4_Intron|SULF1_ENST00000521946.1_Intron|SULF1_ENST00000458141.2_Intron|SULF1_ENST00000419716.3_Intron	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	NA		NA			apoptotic process (GO:0006915)|bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			tgtaatcccaacactttggga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573	23213			20391	protein-coding gene	gene with protein product		610012			NA	12368295	Standard	NM_015170	NM_015170	NA	Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.2285-2214A>G	chr8.hg19:g.70548523A>G		NA	Q86YV8|Q8NCA2|Q9UPS5	hg19	CCDS6204.1	0.02	-0.184179	CCAxCAC	UNCOVERED																																																																																			NOVEL	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378885.2	5	2.406014	KEEP	1	0	0	8	219	AA	0	0	0		+	3	60	94	0	0	7.234157	16	60	475	45	ENST00000260128.4	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	71004157	71004157	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:71004157C>T			NA	NA				RNU1-101P (13890 upstream) : NCOA2 (17839 downstream)						NA		NA									NA						aggctggtctcgaactcctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.71004157C>T		NA		hg19		0.02	1.401123	TCTxGAA	COVERED																																																																																			NOVEL					0			16	4.512434	KEEP	0	0	0	15	437	CC	0.99649	0.976088	0			4	60	121	0	0	8.034595	44	60	1405	102		0.083333	0.979526
NCOA2	10499	__UNKNOWN__	__UNKNOWN__	8	71123553	71123553	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:71123553A>G	ENST00000452400.2	-	4	441					NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	NA		NA			cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			aattagctggacgtggtggcg	0.552		NA	T	RUNXBP2, HEY1	AML, Chondrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396	10499		Chromatin-modifying enzymes / K-acetyltransferases, Basic helix-loop-helix proteins	7669	protein-coding gene	gene with protein product		601993			NA	9111344, 8670870	Standard		XM_005251128	NA	Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.259+2584T>C	chr8.hg19:g.71123553A>G		NA	Q14CD2	hg19	CCDS47872.1	0.02	-0.122769	TGGxCGT	COVERED																																																																																			NOVEL	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379696.1	5	2.707237	KEEP	3	0	0	9	256	AA	0.99254	0.194847	0		-	3	45	96	0	0	7.982369	10	60	280	34	ENST00000452400.2	0.230769	0.196312
NCOA2	10499	__UNKNOWN__	__UNKNOWN__	8	71123673	71123673	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:71123673A>G	ENST00000452400.2	-	4	441					NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	NA		NA			cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			cagcctgggcaacagagcaag	0.463		NA	T	RUNXBP2, HEY1	AML, Chondrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396	10499		Chromatin-modifying enzymes / K-acetyltransferases, Basic helix-loop-helix proteins	7669	protein-coding gene	gene with protein product		601993			NA	9111344, 8670870	Standard		XM_005251128	NA	Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.259+2464T>C	chr8.hg19:g.71123673A>G		NA	Q14CD2	hg19	CCDS47872.1	0.02	-0.263045	GGCxACA	COVERED																																																																																			NOVEL	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379696.1	12	3.607756	KEEP	0	0	0	12	315	AA	0.993634	0.689252	0		-	3	60	100	0	0	7.505951	21	60	587	57	ENST00000452400.2	0.125	0.693668
NCOA2	10499	__UNKNOWN__	__UNKNOWN__	8	71221993	71221993	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:71221993A>C	ENST00000452400.2	-	2	106					NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	NA		NA			cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)		PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			ccagaccagcatgggcaacat	0.507		NA	T	RUNXBP2, HEY1	AML, Chondrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396	10499		Chromatin-modifying enzymes / K-acetyltransferases, Basic helix-loop-helix proteins	7669	protein-coding gene	gene with protein product		601993			NA	9111344, 8670870	Standard		XM_005251128	NA	Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.76-12958T>G	chr8.hg19:g.71221993A>C		NA	Q14CD2	hg19	CCDS47872.1	0.02	-0.24559	AGCxTGG	COVERED																																																																																			NOVEL	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379696.1	11	2.406111	KEEP	0	0	0	8	222	AA	0.99257	0.636582	0		-	3	60	114	1	0	8.741793	24	60	723	45	ENST00000452400.2	0.111111	0.641347
RP11-382J12.1	0	__UNKNOWN__	__UNKNOWN__	8	71573129	71573129	__UNKNOWN__	Silent	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:71573129T>C	ENST00000499227.2	+	4	1331	c.333T>C	c.(331-333)ctT>ctC	p.L111L	LACTB2_ENST00000276590.4_Intron|LACTB2_ENST00000522447.1_Intron						NA		NA									NA						ctgcccaccttagcctcccga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant											NA			NA				NA			NA					NA						ENST00000499227.2:c.333T>C	chr8.hg19:g.71573129T>C		NA		hg19		0.02	1.482232	CCTxAGC	COVERED																																																																																			NOVEL	RP11-382J12.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000378742.2	12	5.411177	KEEP	0	0	0	18	464	TT	0.999859	0.99974	0		+	5	60	171	0	0	11.205696	81	60	2322	148	ENST00000499227.2	0.05814	0.999881
EYA1	2138	__UNKNOWN__	__UNKNOWN__	8	72145537	72145537	__UNKNOWN__	Intron	SNP	T	T	C	rs186925733	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:72145537T>C	ENST00000340726.3	-	12	1780				EYA1_ENST00000388742.4_Intron|EYA1_ENST00000388741.2_Intron|EYA1_ENST00000388740.3_Intron|EYA1_ENST00000388743.2_Intron|EYA1_ENST00000303824.7_Intron|EYA1_ENST00000419131.1_Intron	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	NA		NA			anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			cggtggctcatgcctgtaatc	0.448		NA											t|||	10	0.00199681	0.0	0.0	5008	,	,	NA	15558	0.003	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313	2138		Protein tyrosine phosphatases / Asp-based PTPs	3519	protein-coding gene	gene with protein product		601653	eyes absent (Drosophila) homolog 1, eyes absent homolog 1 (Drosophila)	BOR	NA	9020840	Standard	NM_000503, NM_172060	XM_005251184	NA	Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1140+11300A>G	chr8.hg19:g.72145537T>C		NA	A6NHQ0|G5E9R4|Q0P516|Q8WX80	hg19	CCDS34906.1	0.02	-0.21926	TCAxGCC	COVERED																																																																																			NOVEL	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313788.2	7	2.405841	KEEP	8	0	0	8	217	TT	0.99257	0.54878	0		-	3	60	96	2	0	7.106028	21	60	622	61	ENST00000340726.3	0.125	0.552887
EYA1	2138	__UNKNOWN__	__UNKNOWN__	8	72180072	72180072	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:72180072C>T	ENST00000340726.3	-	11	1690				EYA1_ENST00000388742.4_Intron|EYA1_ENST00000388741.2_Intron|EYA1_ENST00000388740.3_Intron|EYA1_ENST00000388743.2_Intron|EYA1_ENST00000303824.7_Intron|EYA1_ENST00000419131.1_Intron	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	NA		NA			anatomical structure morphogenesis (GO:0009653)|aorta morphogenesis (GO:0035909)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|double-strand break repair (GO:0006302)|embryonic skeletal system morphogenesis (GO:0048704)|establishment of mitotic spindle orientation (GO:0000132)|establishment or maintenance of apical/basal cell polarity (GO:0035088)|histone dephosphorylation (GO:0016576)|lung epithelial cell differentiation (GO:0060487)|metanephros development (GO:0001656)|middle ear morphogenesis (GO:0042474)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neuron fate specification (GO:0048665)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of DNA repair (GO:0045739)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of neuron differentiation (GO:0045664)|response to ionizing radiation (GO:0010212)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|RNA binding (GO:0003723)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(15)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	44	Breast(64;0.046)		Epithelial(68;0.0837)|all cancers(69;0.247)			catgagccaccgcgcccggcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ000098	CCDS34906.1, CCDS34907.1, CCDS47873.1, CCDS75750.1	8q13.3	2014-06-19	2014-06-19		ENSG00000104313	ENSG00000104313	2138		Protein tyrosine phosphatases / Asp-based PTPs	3519	protein-coding gene	gene with protein product		601653	eyes absent (Drosophila) homolog 1, eyes absent homolog 1 (Drosophila)	BOR	NA	9020840	Standard	NM_000503, NM_172060	XM_005251184	NA	Approved		uc003xys.4	Q99502	OTTHUMG00000149894	ENST00000340726.3:c.1050+1902G>A	chr8.hg19:g.72180072C>T		NA	A6NHQ0|G5E9R4|Q0P516|Q8WX80	hg19	CCDS34906.1	0.02	-0.289044	CACxGCG	COVERED																																																																																			NOVEL	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313788.2	12	4.211714	KEEP	7	0	0	14	413	CC	0.994391	0.756619	0		-	5	60	129	0	0	9.5293	24	60	784	79	ENST00000340726.3	0.172414	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	72678350	72678350	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:72678350T>C			NA	NA				RP11-1144P22.1 (63329 upstream) : RP11-281N10.1 (13489 downstream)						NA		NA									NA						tggctcacgcttgtaatccca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.72678350T>C		NA		hg19		0.02	-0.236827	CGCxTGT	COVERED																																																																																			NOVEL					0			8	3.60923	KEEP	2	0	0	12	332	TT	0.993072	0.608164	0			3	60	106	0	0	8.105216	21	60	640	61		0.125	0.612407
RP11-383H13.1	0	__UNKNOWN__	__UNKNOWN__	8	72820473	72820473	__UNKNOWN__	Intron	SNP	C	C	T	rs180827384		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:72820473C>T	ENST00000524152.1	+	2	144				RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000521467.1_Intron						NA		NA								lung(1)	1						tgagccaccgcgcctggccaa	0.493		NA											-|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15206	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000524152.1:c.-90-54685C>T	chr8.hg19:g.72820473C>T		NA		hg19		0.02	-0.271919	CCGxGCC	COVERED																																																																																			NOVEL	RP11-383H13.1-004	PUTATIVE	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000378995.1	9	3.607841	KEEP	13	0	0	12	318	CC	0.99254	0.711964	0		+	3	60	94	0	0	6.644657	26	60	857	74	ENST00000524152.1	0.103448	0.717315
RP11-383H13.1	0	__UNKNOWN__	__UNKNOWN__	8	72914641	72914641	__UNKNOWN__	Intron	SNP	G	G	A	rs148062941	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:72914641G>A	ENST00000524152.1	+	3	396				RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron						NA		NA								lung(1)	1						TGAAGACGTCGTTATTTTAGT	0.413		NA											G|||	9	0.00179712	0.0053	0.0014	5008	,	,	NA	18446	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000524152.1:c.162+36872G>A	chr8.hg19:g.72914641G>A		NA		hg19		0.02	0.701752	GTCxTTA	COVERED																																																																																			NOVEL	RP11-383H13.1-004	PUTATIVE	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000378995.1	9	9.325241	KEEP	0	0	0	31	894	GG	0.999997	0.999859	0		+	5	60	134	0	0	7.396422	86	60	2857	167	ENST00000524152.1	0.054945	0.999862
TRPA1	8989	__UNKNOWN__	__UNKNOWN__	8	72975410	72975410	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:72975410A>T	ENST00000262209.4	-	6	869					NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	NA		NA			calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	aggtcaggagatcgagaccag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321	8989		Voltage-gated ion channels / Transient receptor potential cation channels, Ankyrin repeat domain containing	497	protein-coding gene	gene with protein product		604775	ankyrin-like with transmembrane domains 1	ANKTM1	NA	16382100	Standard	NM_007332	NM_007332	NA	Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.662-231T>A	chr8.hg19:g.72975410A>T		NA	A6NIN6	hg19	CCDS34908.1	0.02	-0.236799	GAGxTCG	COVERED																																																																																			NOVEL	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379079.2	4	3.307021	KEEP	0	0	0	11	286	AA	0.993072	0.608164	0		-	3	59	93	1	0	6.74962	22	60	639	59	ENST00000262209.4	0.12	0.612407
KCNB2	9312	__UNKNOWN__	__UNKNOWN__	8	73780543	73780543	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:73780543A>G	ENST00000523207.1	+	3	1167					NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	NA		NA			potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	ggccgggcgcagtggctcaca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674	9312		Potassium channels, Voltage-gated ion channels / Potassium channels	6232	protein-coding gene	gene with protein product		607738			NA	9612272, 16382104	Standard	NM_004770	NM_004770	NA	Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.580-67627A>G	chr8.hg19:g.73780543A>G		NA	Q7Z7D0|Q9BXD3	hg19	CCDS6209.1	0.02	-0.289408	CGCxGTG	COVERED																																																																																			NOVEL	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378998.1	7	2.707028	KEEP	0	0	0	9	251	AA	0.99254	0.755211	0		+	3	60	93	0	0	6.500605	27	60	807	63	ENST00000523207.1	0.1	0.760887
RP11-531A24.3	0	__UNKNOWN__	__UNKNOWN__	8	73859513	73859513	__UNKNOWN__	lincRNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:73859513A>C	ENST00000564832.1	+	0	129										NA		NA									NA						gcctcagcctaccaaagtgct	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000564832.1:	chr8.hg19:g.73859513A>C		NA		hg19		0.02	-0.271884	CCTxCCA	COVERED																																																																																			NOVEL	RP11-531A24.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000379092.2	10	3.00747	KEEP	2	0	0	10	275	AA	0.99254	0.755211	0		+	3	40	100	0	0	7.197779	27	60	797	66	ENST00000564832.1	0.1	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	73919561	73919561	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:73919561C>T			NA	NA				RP11-531A24.3 (56881 upstream) : TERF1 (1537 downstream)						NA		NA									NA						ctcggctcaccgcaatctccg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.73919561C>T		NA		hg19		0.02	-0.166613	CACxGCA	COVERED																																																																																			NOVEL					0			7	3.575289	KEEP	1	0	0	12	326	CC	0.993072	0.351495	0			3	60	85	0	0	6.334958	16	60	481	43		0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	73920182	73920182	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:73920182G>T			NA	NA				RP11-531A24.3 (57502 upstream) : TERF1 (916 downstream)						NA		NA									NA						ttgtggctcaggcctgtaaac	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.73920182G>T		NA		hg19		0.02	-0.19298	TCAxGCC	COVERED																																																																																			NOVEL					0			6	2.406308	KEEP	0	0	0	8	235	GG	0.99257	0.454356	0			3	60	93	0	0	6.992411	18	60	595	36		0.142857	0.457757
TERF1	7013	__UNKNOWN__	__UNKNOWN__	8	73937609	73937609	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:73937609G>C	ENST00000276603.5	+	5	797				TERF1_ENST00000276602.6_Intron	NM_017489.2	NP_059523.2	P54274	TERF1_HUMAN	telomeric repeat binding factor (NIMA-interacting) 1	NA		NA			age-dependent telomere shortening (GO:0001309)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of DNA replication (GO:0008156)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of apoptotic process (GO:0043065)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of mitosis (GO:0045840)|positive regulation of mitotic cell cycle (GO:0045931)|protein homooligomerization (GO:0051260)|response to drug (GO:0042493)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded telomeric DNA binding (GO:0003691)|microtubule binding (GO:0008017)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			central_nervous_system(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9	Breast(64;0.218)		Epithelial(68;0.0984)			tgcctgtaatgctagcacttt	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U74382	CCDS6210.1, CCDS6211.1	8q21.11	2011-05-24			ENSG00000147601	ENSG00000147601	7013			11728	protein-coding gene	gene with protein product		600951		TRBF1	NA	9391075	Standard	NM_017489	NM_003218	NA	Approved	PIN2, TRF1, TRF	uc003xzd.2	P54274	OTTHUMG00000164522	ENST00000276603.5:c.774+403G>C	chr8.hg19:g.73937609G>C		NA	A7XP29|Q15553|Q8NHT6|Q93029	hg19	CCDS6211.1	0.02	-0.333347	AATxCTA	COVERED																																																																																			NOVEL	TERF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379093.1	9	2.708301	KEEP	0	0	0	9	283	GG	0.99254	0.845628	0		+	4	60	126	0	0	9.333875	27	60	911	67	ENST00000276603.5	0.129032	0.851984
RP11-531A24.5	0	__UNKNOWN__	__UNKNOWN__	8	73965076	73965076	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:73965076A>G	ENST00000517664.1	+	0	664										NA		NA									NA						gattacaggcatgagccacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000517664.1:	chr8.hg19:g.73965076A>G		NA		hg19		0.02	-0.306948	GGCxTGA	COVERED																																																																																			NOVEL	RP11-531A24.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000379313.1	8	3.007998	KEEP	2	0	0	10	284	AA	0.99254	0.794276	0		+	4	60	122	0	0	8.875997	28	60	823	70	ENST00000517664.1	0.125	0.800245
RDH10	157506	__UNKNOWN__	__UNKNOWN__	8	74236131	74236131	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74236131T>C	ENST00000240285.5	+	0	2564				RP11-434I12.2_ENST00000517475.1_RNA|RP11-434I12.2_ENST00000514599.1_RNA	NM_172037.4	NP_742034.1	Q8IZV5	RDH10_HUMAN	retinol dehydrogenase 10 (all-trans)	NA		NA			bud elongation involved in lung branching (GO:0060449)|ear development (GO:0043583)|embryonic camera-type eye development (GO:0031076)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|gonad development (GO:0008406)|in utero embryonic development (GO:0001701)|metanephros development (GO:0001656)|neural crest cell development (GO:0014032)|nose development (GO:0043584)|phototransduction, visible light (GO:0007603)|primary lung bud formation (GO:0060431)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	11	Breast(64;0.0954)		Epithelial(68;0.0105)|all cancers(69;0.0465)|BRCA - Breast invasive adenocarcinoma(89;0.0608)			gtgatccacctgcctcggcct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF456765	CCDS6213.1	8q21.11	2011-09-20			ENSG00000121039	ENSG00000121039	157506	1.1.1.-	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	19975	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 16C, member 4	607599			NA	12407145, 19027726	Standard		NM_172037	NA	Approved	SDR16C4	uc003xzi.3	Q8IZV5	OTTHUMG00000164492	ENST00000240285.5:c.*860T>C	chr8.hg19:g.74236131T>C		NA		hg19	CCDS6213.1	0.02	-0.333263	ACCxGCC	COVERED																																																																																			NOVEL	RDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000378982.1	12	3.909397	KEEP	0	0	0	13	355	TT	0.994391	0.847205	0		+	4	41	137	0	0	10.374215	28	60	810	62	ENST00000240285.5	0.125	0.851984
RP11-434I12.2	0	__UNKNOWN__	__UNKNOWN__	8	74262997	74262997	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74262997T>C	ENST00000514599.1	-	0	170				RP11-434I12.2_ENST00000517475.1_RNA						NA		NA									NA						accatgttggtcaggatggtc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000514599.1:	chr8.hg19:g.74262997T>C		NA		hg19		0.02	-0.341978	TGGxCAG	UNCOVERED																																																																																			NOVEL	RP11-434I12.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000378988.1	13	2.405317	KEEP	2	0	0	8	211	TT	0	0	0		-	3	60	105	1	0	7.487084	32	60	917	62	ENST00000514599.1	0.085714	0.865745
STAU2	27067	__UNKNOWN__	__UNKNOWN__	8	74374703	74374703	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74374703C>T	ENST00000524300.1	-	14	1881				STAU2_ENST00000523558.1_Intron|STAU2_ENST00000521210.1_Intron|STAU2_ENST00000522695.1_Intron	NM_001164380.1|NM_001164381.1	NP_001157852.1|NP_001157853.1	Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	NA		NA			transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			tgatcatggcccactgcaacc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341	27067			11371	protein-coding gene	gene with protein product		605920	staufen (Drosophila, RNA-binding protein) homolog 2, staufen, RNA binding protein, homolog 2 (Drosophila)		NA	10585778	Standard	NM_001164380	NM_014393	NA	Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000524300.1:c.1531-39766G>A	chr8.hg19:g.74374703C>T		NA	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	hg19	CCDS55247.1	0.02	-0.236177	GGCxCAC	COVERED																																																																																			NOVEL	STAU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379000.2	14	3.910183	KEEP	0	0	0	13	382	CC	0.994391	0.608972	0		-	4	60	109	0	0	8.203276	19	60	596	48	ENST00000524300.1	0.173913	0.612407
RP11-463D19.2	0	__UNKNOWN__	__UNKNOWN__	8	74661727	74661727	__UNKNOWN__	Intron	SNP	G	G	A	rs550314824	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74661727G>A	ENST00000358757.5	-	6	474										NA		NA									NA						agaaaaaaaagaaaaaaaatc	0.473		NA											G|||	13	0.00259585	0.003	0.0014	5008	,	,	NA	19793	0.006	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000358757.5:c.443-9624C>T	chr8.hg19:g.74661727G>A		NA		hg19		0.02	-0.149097	AAAxAAA	COVERED																																																																																			NOVEL	RP11-463D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000413292.2	7	3.008333	KEEP	0	0	0	10	294	GG	0.992708	0.289872	0		-	3	60	84	0	0	6.572773	12	60	374	35	ENST00000358757.5	0.2	0.292001
RP11-463D19.2	0	__UNKNOWN__	__UNKNOWN__	8	74752331	74752331	__UNKNOWN__	Intron	SNP	G	G	A	rs532156321		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74752331G>A	ENST00000358757.5	-	2	47				UBE2W_ENST00000453587.2_Intron|UBE2W_ENST00000517608.1_Intron|UBE2W_ENST00000602593.1_Intron|UBE2W_ENST00000419880.3_Intron|UBE2W_ENST00000602969.1_Intron						NA		NA									NA						ttgctctgtcgcccaggctgg	0.527		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	19323	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000358757.5:c.16-9624C>T	chr8.hg19:g.74752331G>A		NA		hg19		0.02	-0.192981	GTCxCCC	COVERED																																																																																			NOVEL	RP11-463D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000413292.2	5	3.911403	KEEP	0	0	0	13	395	GG	0.994391	0.455189	0		-	3	60	86	0	0	6.361736	17	60	573	51	ENST00000358757.5	0.15	0.457757
RP11-463D19.2	0	__UNKNOWN__	__UNKNOWN__	8	74781613	74781613	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74781613T>G	ENST00000358757.5	-	1	47				UBE2W_ENST00000453587.2_Intron|UBE2W_ENST00000517608.1_Intron|UBE2W_ENST00000602593.1_Intron|UBE2W_ENST00000419880.3_Intron|UBE2W_ENST00000602969.1_Intron						NA		NA									NA						ccaacatggttaaaccccgtc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000358757.5:c.15+9429A>C	chr8.hg19:g.74781613T>G		NA		hg19		0.02	-0.122794	GGTxAAA	COVERED																																																																																			NOVEL	RP11-463D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000413292.2	10	2.705611	KEEP	2	0	0	9	232	TT	0.99254	0.194847	0		-	3	21	100	0	0	8.272907	11	60	329	31	ENST00000358757.5	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	74809078	74809078	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74809078T>C			NA	NA				UBE2W (17933 upstream) : TCEB1 (42325 downstream)						NA		NA									NA						cgagatggcatcactgcactc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.74809078T>C		NA		hg19		0.02	-0.333271	GCAxCAC	COVERED																																																																																			NOVEL					0			8	2.406011	KEEP	0	0	0	8	219	TT	0.99257	0.859313	0			4	60	133	1	0	9.808816	31	60	911	66		0.114286	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	74818202	74818202	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74818202A>C			NA	NA				UBE2W (27057 upstream) : TCEB1 (33201 downstream)						NA		NA									NA						gatgaaacccagtctctacac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.74818202A>C		NA		hg19		0.02	-0.245509	CCCxGTC	COVERED																																																																																			NOVEL					0			10	3.609275	KEEP	1	0	0	12	334	AA	0.993072	0.688863	0			3	60	95	0	0	6.895594	23	60	651	51		0.115385	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	74843263	74843263	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74843263T>C			NA	NA				UBE2W (52118 upstream) : TCEB1 (8140 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.74843263T>C		NA		hg19		0.02	-0.19295	TCAxGCC	COVERED																																																																																			NOVEL					0			7	3.909255	KEEP	2	0	0	13	354	TT	0.994391	0.455189	0			3	60	97	0	0	7.533444	16	60	473	58		0.157895	0.457757
TMEM70	54968	__UNKNOWN__	__UNKNOWN__	8	74891516	74891516	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:74891516G>A	ENST00000312184.5	+	2	389				TMEM70_ENST00000517439.1_Intron	NM_001040613.2|NM_017866.5	NP_001035703.1|NP_060336.3	Q9BUB7	TMM70_HUMAN	transmembrane protein 70	NA		NA			mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)				breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8	Breast(64;0.0311)		Epithelial(68;0.0186)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0564)			cacccacctcggcctcccaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC002748	CCDS6215.1, CCDS47876.1	8q21.11	2013-05-23				ENSG00000175606	54968			26050	protein-coding gene	gene with protein product		612418			NA	21945727, 22986587	Standard	NM_017866	NM_017866	NA	Approved	FLJ20533	uc003yab.3	Q9BUB7		ENST00000312184.5:c.316+420G>A	chr8.hg19:g.74891516G>A		NA	E9PDY9|Q9NWY5	hg19	CCDS6215.1	0.02	-0.280637	CTCxGCC	COVERED																																																																																			NOVEL	TMEM70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379028.1	11	3.008082	KEEP	0	0	0	10	292	GG	0.992708	0.734278	0		+	4	60	118	0	0	8.79275	23	60	728	61	ENST00000312184.5	0.148148	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	76244881	76244881	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:76244881T>C			NA	NA				CASC9 (54185 upstream) : HNF4G (75267 downstream)						NA		NA									NA						gctgggattataggcaagagc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.76244881T>C		NA		hg19		0.02	-0.192948	TTAxAGG	COVERED																																																																																			NOVEL					0			4	2.405744	KEEP	0	0	0	8	214	TT	0.99257	0.454356	0			3	60	91	0	0	6.8619	17	60	500	36		0.15	0.457757
HNF4G	3174	__UNKNOWN__	__UNKNOWN__	8	76394882	76394882	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:76394882T>C	ENST00000354370.1	+	2	127				HNF4G_ENST00000494318.1_Intron			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	NA		NA			endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ggattacaggtgtgagccacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749	3174		Nuclear hormone receptors	5026	protein-coding gene	gene with protein product		605966			NA	8622695, 12220494	Standard	NM_004133	NM_004133	NA	Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.-143-7442T>C	chr8.hg19:g.76394882T>C		NA	Q7Z2V9|Q9UH81|Q9UIS6	hg19		0.02	-0.201705	AGGxGTG	COVERED																																																																																			NOVEL	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000313914.2	16	3.904998	KEEP	4	0	0	13	327	TT	0.994391	0.487793	0		+	5	60	172	0	0	14.466116	17	60	480	55	ENST00000354370.1	0.227273	0.490544
ZFHX4-AS1	100192378	__UNKNOWN__	__UNKNOWN__	8	77452586	77452586	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:77452586A>G	ENST00000522961.1	-	0	105									ZFHX4 antisense RNA 1	NA		NA									NA						tgatccacccacctcagcctc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC037827		8q21.11	2012-10-12	2012-08-15		ENSG00000253661	ENSG00000253661	100192378		Long non-coding RNAs	44165	non-coding RNA	RNA, long non-coding		NA	ZFHX4 antisense RNA 1 (non-protein coding)		NA		Standard	NR_024360	NR_024360	NA	Approved		uc003yas.4		OTTHUMG00000164554	ENST00000522961.1:	chr8.hg19:g.77452586A>G		NA		hg19		0.02	-0.289361	CCCxCCT	COVERED																																																																																			NOVEL	ZFHX4-AS1-005	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000379190.1	13	3.910027	KEEP	7	0	0	13	361	AA	0.99254	0.755211	0		-	4	60	113	0	0	8.036412	27	60	772	70	ENST00000522961.1	0.129032	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	78908131	78908131	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:78908131C>G			NA	NA				RP11-38H17.1 (458605 upstream) : RP11-91P17.1 (152204 downstream)						NA		NA									NA						ctcccaaagtcctgggattac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.78908131C>G		NA		hg19		0.02	-0.210547	AGTxCTG	COVERED																																																																																			NOVEL					0			7	2.407488	KEEP	1	0	0	8	257	AC	0.99254	0.518266	0			3	60	108	0	0	8.560203	17	60	598	53		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	79553688	79553688	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:79553688A>G			NA	NA				RP11-594N15.3 (31748 upstream) : ZC2HC1A (24593 downstream)						NA		NA									NA						actccagcctaggcaacaaga	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.79553688A>G		NA		hg19		0.02	-0.114028	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			8	2.707003	KEEP	4	0	0	9	250	AA	0.99257	0.16126	0			3	60	106	0	0	9.101221	9	60	269	36		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	79999096	79999096	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:79999096A>G			NA	NA				RP11-79H23.3 (246339 upstream) : AC009941.1 (10501 downstream)						NA		NA									NA						agcactttggaaggccgaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.79999096A>G		NA		hg19		0.02	-0.14908	TGGxAGG	COVERED																																																																																			NOVEL					0			4	2.707506	KEEP	0	0	0	9	261	AA	0.99254	0.289823	0			3	60	81	0	0	6.373827	11	60	334	37		0.214286	0.292001
RP11-26J3.1	0	__UNKNOWN__	__UNKNOWN__	8	80717288	80717288	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:80717288T>C	ENST00000502766.2	-	0	349										NA		NA									NA						cagtggctcattcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502766.2:	chr8.hg19:g.80717288T>C		NA		hg19		0.02	-0.184154	TCAxTCC	COVERED																																																																																			NOVEL	RP11-26J3.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000379270.1	6	2.405345	KEEP	0	0	0	8	214	TT	0.99257	0.420331	0		-	4	60	123	0	0	9.963216	15	60	430	40	ENST00000502766.2	0.210526	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	80793762	80793762	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:80793762C>G			NA	NA				RP11-26J3.1 (9790 upstream) : MRPS28 (37189 downstream)						NA		NA									NA						ggatcacaagctcaggagttc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.80793762C>G		NA		hg19		0.02	-0.236747	AAGxTCA	COVERED																																																																																			NOVEL					0			12	2.708076	KEEP	3	0	0	9	278	CC	0.99257	0.607857	0			3	60	95	0	0	6.895766	23	60	763	54		0.115385	0.612407
MRPS28	28957	__UNKNOWN__	__UNKNOWN__	8	80857188	80857188	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:80857188C>T	ENST00000276585.4	-	3	418				MRPS28_ENST00000521605.1_Intron|MRPS28_ENST00000521434.1_Intron	NM_014018.2	NP_054737.1	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28	NA		NA				mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			cctccgcctcccaaagtgctg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB061209	CCDS6226.1	8q21.1-q21.2	2012-09-13			ENSG00000147586	ENSG00000147586	28957		Mitochondrial ribosomal proteins / small subunits	14513	protein-coding gene	gene with protein product		611990			NA	11279123, 11042152	Standard	NM_014018	NM_014018	NA	Approved	MRP-S28, HSPC007, MRPS35	uc003ybp.3	Q9Y2Q9	OTTHUMG00000164642	ENST00000276585.4:c.396-25805G>A	chr8.hg19:g.80857188C>T		NA	B2RDZ7|Q96Q21	hg19	CCDS6226.1	0.02	-0.29784	CTCxCAA	COVERED																																																																																			NOVEL	MRPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379526.1	12	2.405644	KEEP	0	0	0	8	239	CC	0.99257	0.775257	0		-	3	60	97	0	1	6.946585	26	60	857	59	ENST00000276585.4	0.103448	0.78106
MRPS28	28957	__UNKNOWN__	__UNKNOWN__	8	80857210	80857210	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:80857210A>G	ENST00000276585.4	-	3	418				MRPS28_ENST00000521605.1_Intron|MRPS28_ENST00000521434.1_Intron	NM_014018.2	NP_054737.1	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28	NA		NA				mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			gattacaggcatgagccacca	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB061209	CCDS6226.1	8q21.1-q21.2	2012-09-13			ENSG00000147586	ENSG00000147586	28957		Mitochondrial ribosomal proteins / small subunits	14513	protein-coding gene	gene with protein product		611990			NA	11279123, 11042152	Standard	NM_014018	NM_014018	NA	Approved	MRP-S28, HSPC007, MRPS35	uc003ybp.3	Q9Y2Q9	OTTHUMG00000164642	ENST00000276585.4:c.396-25827T>C	chr8.hg19:g.80857210A>G		NA	B2RDZ7|Q96Q21	hg19	CCDS6226.1	0.02	-0.29817	GGCxTGA	COVERED																																																																																			NOVEL	MRPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379526.1	12	2.40451	KEEP	0	0	0	8	203	AA	0.99257	0.775257	0		-	4	60	122	0	0	9.124185	24	60	695	59	ENST00000276585.4	0.142857	0.78106
MRPS28	28957	__UNKNOWN__	__UNKNOWN__	8	80933427	80933427	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:80933427A>G	ENST00000276585.4	-	1	236				TPD52_ENST00000537855.1_Intron|MRPS28_ENST00000521605.1_Intron|MRPS28_ENST00000521434.1_Intron|MRPS28_ENST00000522987.1_Intron	NM_014018.2	NP_054737.1	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S28	NA		NA				mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5	Lung NSC(7;1.86e-06)|all_lung(9;6.91e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00769)|Epithelial(68;0.0208)|all cancers(69;0.0805)			tagtaaagacagggtttcacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB061209	CCDS6226.1	8q21.1-q21.2	2012-09-13			ENSG00000147586	ENSG00000147586	28957		Mitochondrial ribosomal proteins / small subunits	14513	protein-coding gene	gene with protein product		611990			NA	11279123, 11042152	Standard	NM_014018	NM_014018	NA	Approved	MRP-S28, HSPC007, MRPS35	uc003ybp.3	Q9Y2Q9	OTTHUMG00000164642	ENST00000276585.4:c.213+8843T>C	chr8.hg19:g.80933427A>G		NA	B2RDZ7|Q96Q21	hg19	CCDS6226.1	0.02	-0.157869	GACxGGG	COVERED																																																																																			NOVEL	MRPS28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379526.1	8	4.210015	KEEP	0	0	0	14	382	AA	0.995343	0.321303	0		-	3	60	94	0	0	7.310416	15	60	449	38	ENST00000276585.4	0.166667	0.322807
TPD52	7163	__UNKNOWN__	__UNKNOWN__	8	80944126	80944126	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:80944126A>G	ENST00000537855.1	-	5	877							P55327	TPD52_HUMAN	tumor protein D52	NA		NA			anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			ggtggctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554	7163			12005	protein-coding gene	gene with protein product		604068			NA	7796418	Standard	NM_005079	NM_001287144	NA	Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000537855.1:c.555+10728T>C	chr8.hg19:g.80944126A>G		NA	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	hg19		0.02	-0.236773	CACxCCT	UNCOVERED																																																																																			NOVEL	TPD52-202	KNOWN	basic	protein_coding	NA	protein_coding		15	2.406457	KEEP	3	0	0	8	229	AA	0	0	0		-	3	60	104	0	0	7.84893	22	60	631	48	ENST00000537855.1	0.12	0.612407
TPD52	7163	__UNKNOWN__	__UNKNOWN__	8	81076259	81076259	__UNKNOWN__	Intron	SNP	C	C	G	rs66668699|rs58566558|rs201388277|rs201828072|rs722901|rs372391752	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81076259C>G	ENST00000379096.5	-	1	134				TPD52_ENST00000518937.1_Intron|TPD52_ENST00000519303.2_Intron	NM_005079.2	NP_005070.1	P55327	TPD52_HUMAN	tumor protein D52	NA		NA			anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			gagagagagacagagagagag	0.403		NA											-|||	3160	0.63099	0.8669	0.5202	5008	,	,	NA	15300	0.7143	NA	0.4602	False	NA	,,,	NA	NA	NA	2504	0.4806	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554	7163			12005	protein-coding gene	gene with protein product		604068			NA	7796418	Standard	NM_005079	NM_001287144	NA	Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000379096.5:c.19+7400G>C	chr8.hg19:g.81076259C>G		NA	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	hg19	CCDS55249.1	0.02	-0.078954	AGAxAGA	UNCOVERED																																																																																			NOVEL	TPD52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379380.2	18	4.512922	KEEP	21	0	0	15	445	CC	0	0	0		-	4	60	143	1	0	15.121569	1	60	35	44	ENST00000379096.5	0.8	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	81098529	81098529	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81098529G>A			NA	NA				TPD52 (14635 upstream) : RN7SL41P (18311 downstream)						NA		NA									NA						cacctgcctcggcctcccaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.81098529G>A		NA		hg19		0.02	-0.385984	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			12	3.008789	KEEP	5	0	0	10	304	GG	0	0	0			4	60	124	0	0	8.619197	37	60	1262	89		0.097561	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	81117864	81117864	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81117864T>C			NA	NA				RN7SL41P (729 upstream) : MIR5708 (35759 downstream)						NA		NA									NA						cctgtaatcctagcacttttg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.81117864T>C		NA		hg19		0.02	-0.280678	TCCxAGC	COVERED																																																																																			NOVEL					0			8	3.006703	KEEP	0	0	0	10	264	TT	0.992708	0.734278	0			3	60	96	0	0	6.844513	26	60	788	53		0.103448	0.739671
RP11-941H19.3	0	__UNKNOWN__	__UNKNOWN__	8	81207087	81207087	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81207087C>T	ENST00000522044.1	+	0	404										NA		NA									NA						ggattacaggcgtgagccacc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000522044.1:	chr8.hg19:g.81207087C>T		NA		hg19		0.02	-0.289462	AGGxGTG	COVERED																																																																																			NOVEL	RP11-941H19.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000379180.1	13	2.707624	KEEP	3	0	0	9	264	CC	0.99254	0.755211	0		+	4	60	116	0	0	8.334984	27	60	874	63	ENST00000522044.1	0.129032	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	81264321	81264321	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81264321A>G			NA	NA				RP11-941H19.3 (12246 upstream) : RNU6-1213P (53429 downstream)						NA		NA									NA						tgggattacaagtgtgagcca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.81264321A>G		NA		hg19		0.02	-0.280685	ACAxGTG	COVERED																																																																																			NOVEL					0			6	3.007384	KEEP	1	0	0	10	276	AA	0.992708	0.734278	0			3	60	101	0	0	7.442363	24	60	746	67		0.111111	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	81351111	81351111	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81351111T>C			NA	NA				RNU6-1213P (33267 upstream) : Y_RNA (45684 downstream)						NA		NA									NA						acctgggaggtggaggttgca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.81351111T>C		NA		hg19		0.02	-0.289368	AGGxGGA	COVERED																																																																																			NOVEL					0			12	3.608702	KEEP	0	0	0	12	329	TT	0.993634	0.776087	0			3	60	96	0	0	6.753722	28	60	793	62		0.096774	0.78106
PAG1	55824	__UNKNOWN__	__UNKNOWN__	8	81919597	81919597	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81919597C>T	ENST00000220597.4	-	4	631					NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			gcctataatcccagcactttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30				55824			30043	protein-coding gene	gene with protein product	Csk-binding protein, transmembrane adaptor protein PAG	605767	phosphoprotein associated with glycosphingolipid microdomains 1		NA	10790433	Standard	NM_018440	XM_006716461	NA	Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.80-14055G>A	chr8.hg19:g.81919597C>T		NA	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	hg19	CCDS6227.1	0.02	-0.333338	ATCxCAG	UNCOVERED																																																																																			NOVEL	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379352.3	9	2.407187	KEEP	2	0	0	8	246	CC	0	0	0		-	3	60	93	0	0	6.453346	28	60	955	74	ENST00000220597.4	0.096774	0.851984
PAG1	55824	__UNKNOWN__	__UNKNOWN__	8	81964092	81964092	__UNKNOWN__	Intron	SNP	G	G	A	rs567349072		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:81964092G>A	ENST00000220597.4	-	2	537					NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TTggccgggcgcggtggctca	0.483		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14474	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30				55824			30043	protein-coding gene	gene with protein product	Csk-binding protein, transmembrane adaptor protein PAG	605767	phosphoprotein associated with glycosphingolipid microdomains 1		NA	10790433	Standard	NM_018440	XM_006716461	NA	Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.173+18254C>T	chr8.hg19:g.81964092G>A		NA	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	hg19	CCDS6227.1	0.02	-0.210518	GGCxCGG	COVERED																																																																																			NOVEL	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379352.3	6	3.007423	KEEP	0	0	0	10	277	GG	0.992708	0.518353	0		-	3	60	88	0	0	6.42783	19	60	600	45	ENST00000220597.4	0.136364	0.522161
IMPA1P	650747	__UNKNOWN__	__UNKNOWN__	8	82538578	82538578	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:82538578A>G	ENST00000522318.1	-	0	193									inositol(myo)-1(or 4)-monophosphatase 1 pseudogene	NA		NA									NA						ggtggctcacacctgtaatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							8q21.13	2014-03-18			ENSG00000251521	ENSG00000251521	650747			33956	pseudogene	pseudogene		NA			NA		Standard		NG_007612	NA	Approved				OTTHUMG00000164680	ENST00000522318.1:	chr8.hg19:g.82538578A>G		NA		hg19		0.02	-0.298191	CACxCCT	COVERED																																																																																			NOVEL	IMPA1P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000379721.1	11	2.404779	KEEP	3	0	0	8	209	AA	0.99257	0.812384	0		-	3	60	100	0	0	7.109378	29	60	857	65	ENST00000522318.1	0.09375	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	82569729	82569729	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:82569729C>T			NA	NA				IMPA1P (26360 upstream) : IMPA1 (466 downstream)						NA		NA									NA						ggtgggaggactgcttgagcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.82569729C>T		NA		hg19		0.02	-0.219297	GGAxTGC	COVERED																																																																																			NOVEL					0			9	2.708245	KEEP	0	0	0	9	281	CC	0.99254	0.548763	0			3	60	88	0	0	6.428217	19	60	625	43		0.136364	0.552887
ZFAND1	79752	__UNKNOWN__	__UNKNOWN__	8	82625637	82625637	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:82625637T>C	ENST00000220669.5	-	6	499				ZFAND1_ENST00000517588.1_Intron|ZFAND1_ENST00000523096.1_Intron|ZFAND1_ENST00000522520.1_Intron|ZFAND1_ENST00000519523.1_Intron|ZFAND1_ENST00000521895.1_Intron|ZFAND1_ENST00000521287.1_Intron	NM_024699.2	NP_078975.2	Q8TCF1	ZFAN1_HUMAN	zinc finger, AN1-type domain 1	NA		NA					zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						ggattacaggtgtgagccacc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6232.1, CCDS55250.1, CCDS55251.1	8q21.13	2006-07-07					79752		Zinc fingers, AN1-type domain containing	25858	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024699	NM_024699	NA	Approved	FLJ14007	uc003ycj.2	Q8TCF1		ENST00000220669.5:c.480+515A>G	chr8.hg19:g.82625637T>C		NA	E5RIG0|E5RJ99|Q658R7|Q6IA32|Q6PGQ6|Q9H810	hg19	CCDS6232.1	0.02	-0.201728	AGGxGTG	COVERED																																																																																			NOVEL	ZFAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379739.1	8	3.908792	KEEP	1	0	0	13	359	TT	0.993634	0.487421	0		-	3	60	90	0	0	6.761432	17	60	511	57	ENST00000220669.5	0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	82635688	82635688	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:82635688G>A			NA	NA				ZFAND1 (2153 upstream) : CHMP4C (8980 downstream)						NA		NA									NA						aggctgaggcgggtggatcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.82635688G>A		NA		hg19		0.02	-0.236856	GGCxGGT	COVERED																																																																																			NOVEL					0			8	3.309749	KEEP	3	0	0	11	335	GG	0.993072	0.608164	0			3	60	90	0	0	6.565394	20	60	682	62		0.130435	0.612407
RP11-354A14.1	0	__UNKNOWN__	__UNKNOWN__	8	82832522	82832522	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:82832522T>C	ENST00000534675.1	+	0	64										NA		NA									NA						ggattacaggtgtgagccact	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000534675.1:	chr8.hg19:g.82832522T>C		NA		hg19		0.02	-0.210388	AGGxGTG	COVERED																																																																																			NOVEL	RP11-354A14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000382823.1	12	4.201454	KEEP	1	0	0	14	340	TT	0.995343	0.519729	0		+	3	60	105	0	0	8.261635	17	60	462	54	ENST00000534675.1	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	82943663	82943663	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:82943663T>A			NA	NA				RP11-354A14.1 (108235 upstream) : RP11-99H20.1 (67022 downstream)						NA		NA									NA						cacccacctctgcctcccaaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.82943663T>A		NA		hg19		0.02	-0.122792	CTCxGCC	COVERED																																																																																			NOVEL					0			3	2.707078	KEEP	1	0	0	9	253	TT	0.99254	0.227464	0			3	60	92	0	0	7.47299	11	60	329	45		0.214286	0.229173
RP11-653B10.1	0	__UNKNOWN__	__UNKNOWN__	8	83526196	83526196	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:83526196A>G	ENST00000522776.1	-	0	149										NA		NA									NA						cgcccgcctcagcctcccaaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000522776.1:	chr8.hg19:g.83526196A>G		NA		hg19		0.02	-0.245598	CTCxGCC	COVERED																																																																																			NOVEL	RP11-653B10.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000380599.1	12	3.910247	KEEP	5	0	0	13	368	AA	0.99254	0.636563	0		-	3	60	96	0	0	6.995027	23	60	708	59	ENST00000522776.1	0.115385	0.641347
RP11-731N10.1	0	__UNKNOWN__	__UNKNOWN__	8	83800122	83800122	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:83800122T>C	ENST00000522123.1	-	0	130										NA		NA									NA						cgcctgtaattccagcacttt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000522123.1:	chr8.hg19:g.83800122T>C		NA		hg19		0.02	-0.192971	AATxCCA	UNCOVERED																																																																																			NOVEL	RP11-731N10.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000379374.1	5	2.406098	KEEP	2	0	0	8	221	TT	0	0	0		-	3	60	103	0	0	8.209978	15	60	454	48	ENST00000522123.1	0.166667	0.457757
RALYL	138046	__UNKNOWN__	__UNKNOWN__	8	85131589	85131589	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:85131589T>C	ENST00000521268.1	+	1	1082				RALYL_ENST00000521695.1_Intron|RALYL_ENST00000517638.1_Intron|RALYL_ENST00000518566.1_Intron|RALYL_ENST00000522455.1_Intron	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	NA		NA					nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						ttccccttcttcttctgccat	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672	138046		RNA binding motif (RRM) containing	27036	protein-coding gene	gene with protein product		614648			NA	12688537	Standard		NM_001100391	NA	Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.-24+34930T>C	chr8.hg19:g.85131589T>C		NA	B3KTH2|G3V129|Q6ZW87|Q8N1C2	hg19	CCDS55253.1	0.02	-0.377165	TCTxCTT	COVERED																																																																																			NOVEL	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379448.1	8	5.414502	KEEP	1	0	0	18	508	TT	0.999859	0.908941	0		+	3	60	103	1	1	7.367316	30	60	910	100	ENST00000521268.1	0.090909	0.909069
E2F5	1875	__UNKNOWN__	__UNKNOWN__	8	86093091	86093091	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:86093091A>G	ENST00000418930.2	+	1	430				E2F5_ENST00000256117.5_Intron|E2F5_ENST00000416274.2_Intron|E2F5_ENST00000519128.1_Intron			Q15329	E2F5_HUMAN	E2F transcription factor 5, p130-binding	NA		NA			gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	8						tgggattacaagcgtgagcca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X86097	CCDS47885.1, CCDS47886.1, CCDS55254.1	8q21.2	2004-01-29			ENSG00000133740	ENSG00000133740	1875			3119	protein-coding gene	gene with protein product		600967			NA	7892279	Standard	NM_001951	NM_001083588	NA	Approved		uc003ycz.4	Q15329	OTTHUMG00000164785	ENST00000418930.2:c.234+3202A>G	chr8.hg19:g.86093091A>G		NA	E9PBN9|Q16601|Q92756	hg19	CCDS47886.1	0.02	-0.333213	ACAxGCG	COVERED																																																																																			NOVEL	E2F5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380273.1	22	4.511053	KEEP	13	0	0	15	419	AA	0.994391	0.847205	0		+	3	60	103	0	0	7.367221	30	60	887	93	ENST00000418930.2	0.090909	0.851984
RP11-219B4.5	0	__UNKNOWN__	__UNKNOWN__	8	86140556	86140556	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:86140556T>C	ENST00000546501.1	-	1	50				RP11-219B4.5_ENST00000549291.1_Intron|CA13_ENST00000517298.1_Intron						NA		NA									NA						gtggctcacgtctgtaatccc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000546501.1:c.62+639A>G	chr8.hg19:g.86140556T>C		NA		hg19		0.02	-0.359572	ACGxCTG	COVERED																																																																																			NOVEL	RP11-219B4.5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000407345.1	19	3.306679	KEEP	0	0	0	11	291	TT	0.993072	0.882717	0		-	3	60	99	0	0	6.740713	36	60	1046	67	ENST00000546501.1	0.076923	0.888875
WWP1	11059	__UNKNOWN__	__UNKNOWN__	8	87383139	87383139	__UNKNOWN__	Intron	SNP	G	G	T	rs4961189	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:87383139G>T	ENST00000517970.1	+	2	286				WWP1_ENST00000523863.1_Intron	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	NA		NA			central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						ctgttgcccaggctggagtgc	0.398		NA											G|||	1822	0.363818	0.1778	0.3271	5008	,	,	NA	10164	0.4167	NA	0.5139	False	NA	,,,	NA	NA	NA	2504	0.4325	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124	11059			17004	protein-coding gene	gene with protein product		602307			NA	9169421, 9647693	Standard	NM_007013	NM_007013	NA	Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.-22+1879G>T	chr8.hg19:g.87383139G>T		NA	O00307|Q5YLC1|Q96BP4	hg19	CCDS6242.1	0.02	-0.035081	CCAxGCT	UNCOVERED																																																																																			NOVEL	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374755.1	6	2.406805	KEEP	6	0	0	8	234	GG	0	0	0		+	2	60	59	0	0	6.853101	0	0	0	16	ENST00000517970.1	1	0.019982
WWP1	11059	__UNKNOWN__	__UNKNOWN__	8	87408608	87408608	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:87408608G>A	ENST00000517970.1	+	6	641				WWP1_ENST00000341922.2_Intron|WWP1_ENST00000349423.2_Intron|WWP1_ENST00000265428.4_Intron	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	NA		NA			central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						gattacaggcgtgagccactg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124	11059			17004	protein-coding gene	gene with protein product		602307			NA	9169421, 9647693	Standard	NM_007013	NM_007013	NA	Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.335-1963G>A	chr8.hg19:g.87408608G>A		NA	O00307|Q5YLC1|Q96BP4	hg19	CCDS6242.1	0.02	-0.403522	GGCxTGA	COVERED																																																																																			NOVEL	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374755.1	7	3.008359	KEEP	1	0	0	10	293	GG	0.99254	0.927521	0		+	3	60	95	0	0	6.306791	37	60	1243	82	ENST00000517970.1	0.075	0.934492
WWP1	11059	__UNKNOWN__	__UNKNOWN__	8	87458266	87458266	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:87458266A>T	ENST00000517970.1	+	19	2305				WWP1_ENST00000341922.2_Intron|WWP1_ENST00000349423.2_Intron|WWP1_ENST00000265428.4_Intron	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	NA		NA			central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						gctggagtgcagtggcatgat	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124	11059			17004	protein-coding gene	gene with protein product		602307			NA	9169421, 9647693	Standard	NM_007013	NM_007013	NA	Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.1999-2111A>T	chr8.hg19:g.87458266A>T		NA	O00307|Q5YLC1|Q96BP4	hg19	CCDS6242.1	0.02	-0.15787	TGCxGTG	UNCOVERED																																																																																			NOVEL	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374755.1	8	2.405512	KEEP	2	0	0	8	214	AA	0	0	0		+	3	40	93	0	0	7.379051	13	60	385	33	ENST00000517970.1	0.1875	0.322807
CPNE3	8895	__UNKNOWN__	__UNKNOWN__	8	87543200	87543200	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:87543200A>G	ENST00000521271.1	+	5	474				CPNE3_ENST00000198765.4_Intron	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	NA		NA			lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						gattacaggcatgagccactg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719	8895			2316	protein-coding gene	gene with protein product		604207			NA	9430674	Standard		NM_003909	NA	Approved		uc003ydv.2	O75131		ENST00000521271.1:c.313-183A>G	chr8.hg19:g.87543200A>G		NA	A8KA47|Q8IYA1	hg19	CCDS6243.1	0.02	-0.263122	GGCxTGA	COVERED																																																																																			NOVEL	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374994.1	6	3.308315	KEEP	0	0	0	11	301	AA	0.993072	0.688863	0		+	3	60	100	0	0	7.394609	23	60	682	60	ENST00000521271.1	0.115385	0.693668
CNBD1	168975	__UNKNOWN__	__UNKNOWN__	8	87885597	87885597	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:87885597A>G	ENST00000518476.1	+	1	139					NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	NA		NA								breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						ccaaagtgctaggattacagg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093121	CCDS55259.1	8q21.3	2005-08-09				ENSG00000176571	168975			26663	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173538	NM_173538	NA	Approved	FLJ35802	uc003ydy.2	Q8NA66		ENST00000518476.1:c.88+6786A>G	chr8.hg19:g.87885597A>G		NA		hg19	CCDS55259.1	0.02	-0.219117	GCTxGGA	COVERED																																																																																			NOVEL	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000375113.2	8	4.209125	KEEP	2	0	0	14	375	AA	0.995343	0.550313	0		+	4	60	140	0	0	11.381042	18	60	520	66	ENST00000518476.1	0.181818	0.552887
AF121898.3	0	__UNKNOWN__	__UNKNOWN__	8	88740186	88740186	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:88740186C>G	ENST00000517711.1	-	0	69				AF121898.3_ENST00000518494.1_RNA|AF121898.3_ENST00000440763.2_RNA						NA		NA									NA						tacttgggagcctgaggtagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000517711.1:	chr8.hg19:g.88740186C>G		NA		hg19		0.02	-0.157875	GAGxCTG	COVERED																																																																																			NOVEL	AF121898.3-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000375298.1	7	2.707664	KEEP	0	0	0	9	266	CC	0.99254	0.320398	0		-	3	60	92	0	0	7.192012	14	60	466	33	ENST00000517711.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	90237618	90237618	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:90237618T>C			NA	NA				RP11-642C5.1 (416481 upstream) : RP11-37B2.1 (492037 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.90237618T>C		NA		hg19		0.02	-0.19288	AGGxGTG	COVERED																																																																																			NOVEL					0			10	3.607116	KEEP	0	0	0	12	320	TT	0.993634	0.454842	0			3	60	96	0	0	7.361772	17	60	499	49		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	90876754	90876754	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:90876754T>C			NA	NA				RIPK2 (73463 upstream) : RNU6-925P (36194 downstream)						NA		NA									NA						gtgatccacctgcctcagcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.90876754T>C		NA		hg19		0.02	-0.210482	ACCxGCC	UNCOVERED																																																																																			NOVEL					0			9	2.706839	KEEP	4	0	0	9	249	TT	0	0	0			3	60	91	0	0	6.793429	18	60	542	52		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	93328847	93328847	__UNKNOWN__	IGR	SNP	A	A	G	rs144736371	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:93328847A>G			NA	NA				RUNX1T1 (213393 upstream) : RP11-700E23.2 (86925 downstream)						NA		NA									NA						gaagaagaagaagaagaagaa	0.403		NA											-|||	217	0.0433307	0.1445	0.0144	5008	,	,	NA	15977	0.0069	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.93328847A>G		NA		hg19		0.02	1.657977	AAGxAGA	COVERED																																																																																			NOVEL					0			20	10.857597	KEEP	8	1	28	46	1248	AA	1	0.997553	0			5	60	136	1	0	8.473996	57	60	1652	160		0.080645	0.997553
RP11-587H10.2	0	__UNKNOWN__	__UNKNOWN__	8	93616787	93616787	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:93616787T>C	ENST00000523284.1	-	0	395										NA		NA									NA						ttgggaccagtctgggcaaca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000523284.1:	chr8.hg19:g.93616787T>C		NA		hg19		0.02	-0.140334	CAGxCTG	COVERED																																																																																			NOVEL	RP11-587H10.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000377512.1	10	3.910359	KEEP	0	0	0	13	367	TT	0.994391	0.259501	0		-	3	60	100	0	0	8.172258	12	60	358	43	ENST00000523284.1	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	94208175	94208175	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:94208175A>G			NA	NA				C8orf87 (29096 upstream) : LINC00535 (17355 downstream)						NA		NA									NA						ctggagtgcaatggtgcaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.94208175A>G		NA		hg19		0.02	-0.192952	GCAxTGG	COVERED																																																																																			NOVEL					0			8	5.713395	KEEP	3	0	0	19	509	AA	0.999366	0.457467	0			3	60	94	0	0	7.233638	16	60	474	62		0.157895	0.457757
PDP1	54704	__UNKNOWN__	__UNKNOWN__	8	94885188	94885188	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:94885188A>G	ENST00000523021.1	+	1	388							Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	NA		NA			cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						gcttacacctataatcccagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	54704	3.1.3.43	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	9279	protein-coding gene	gene with protein product		605993	protein phosphatase 2C, magnesium-dependent, catalytic subunit	PPM2C	NA	8396421	Standard	NM_018444	NM_001161779	NA	Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000523021.1:c.388+14766A>G	chr8.hg19:g.94885188A>G		NA	B3KX71|J3KPU0|Q5U5K1	hg19		0.02	-0.192908	CCTxTAA	COVERED																																																																																			NOVEL	PDP1-005	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000378414.1	7	2.705958	KEEP	0	0	0	9	236	AA	0.99254	0.454342	0		+	3	60	108	0	0	8.561004	17	60	470	43	ENST00000523021.1	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	95039276	95039276	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:95039276T>C			NA	NA				AC105081.1 (53125 upstream) : KB-1184D12.1 (70715 downstream)						NA		NA									NA						ctccgcctcctgggttcaagt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.95039276T>C		NA		hg19		0.02	-0.166619	TCCxGGG	COVERED																																																																																			NOVEL					0			5	3.006751	KEEP	0	0	0	10	264	TT	0.992708	0.384582	0			4	60	114	0	0	9.28148	13	60	376	33		0.235294	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	95623937	95623937	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:95623937T>C			NA	NA				RP11-267M23.4 (41964 upstream) : RP11-22C11.2 (25575 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.95623937T>C		NA		hg19		0.02	-0.184176	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			9	2.706806	KEEP	4	0	0	9	250	TT	0	0	0			3	49	101	0	0	8.010097	15	60	448	47		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	95648653	95648653	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:95648653C>T			NA	NA				RP11-267M23.4 (66680 upstream) : RP11-22C11.2 (859 downstream)						NA		NA									NA						ggtttcaccacgttggccagg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.95648653C>T		NA		hg19		0.02	-0.210526	CCAxGTT	COVERED																																																																																			NOVEL					0			10	2.405932	KEEP	0	0	0	8	224	CC	0.99257	0.518282	0			3	60	87	0	0	6.461441	17	60	566	42		0.15	0.522161
INTS8	55656	__UNKNOWN__	__UNKNOWN__	8	95843111	95843111	__UNKNOWN__	Intron	SNP	T	T	C	rs11778250	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:95843111T>C	ENST00000523731.1	+	6	703				INTS8_ENST00000447247.1_Intron	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	NA		NA			snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					ctgcaacctctgcctcccggg	0.488		NA											C|||	837	0.167133	0.2761	0.1138	5008	,	,	NA	19989	0.0496	NA	0.2078	False	NA	,,,	NA	NA	NA	2504	0.137	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941	55656			26048	protein-coding gene	gene with protein product		611351	chromosome 8 open reading frame 52	C8orf52	NA	16239144	Standard	NM_017864	NM_017864	NA	Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.571-1109T>C	chr8.hg19:g.95843111T>C		NA	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	hg19	CCDS34925.1	0.02	-0.105247	CTCxGCC	UNCOVERED																																																																																			NOVEL	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379794.1	8	2.406381	KEEP	4	0	0	8	225	TT	0	0	0		+	9	60	290	0	0	31.028961	2	60	55	29	ENST00000523731.1	0.818182	0.139832
CCNE2	9134	__UNKNOWN__	__UNKNOWN__	8	95893863	95893863	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:95893863G>C	ENST00000520509.1	-	12	1464	c.1212C>G	c.(1210-1212)caC>caG	p.H404Q	CCNE2_ENST00000308108.4_Missense_Mutation_p.H404Q|INTS8_ENST00000523731.1_3'UTR|CCNE2_ENST00000396133.3_3'UTR			O96020	CCNE2_HUMAN	cyclin E2	404		NA			cell cycle checkpoint (GO:0000075)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|prostate(1)	11	Breast(36;8.75e-07)					ATCTTCTTTAGTGTTTTCCTG	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													280	261	267			NA	NA	8		NA											NA				95893863		2203	4300	6503	SO:0001583	missense			AF091433	CCDS6264.1	8q22.1	2005-10-18			ENSG00000175305	ENSG00000175305	9134			1590	protein-coding gene	gene with protein product		603775			NA	9840927, 9840943	Standard	NM_057749, NM_004702	NM_057749	NA	Approved	CYCE2	uc003yhc.3	O96020	OTTHUMG00000164696	ENST00000520509.1:c.1212C>G	chr8.hg19:g.95893863G>C	ENSP00000429089:p.His404Gln	NA	O95439	hg19	CCDS6264.1	0.02	4.011496	TTAxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447618	0.26074	.	.	ENSG00000175305	ENST00000520509;ENST00000308108;ENST00000542725	T;T	0.23552	1.9;1.9	5.84	4.96	0.65561	.	0.477105	0.21345	N	0.076079	T	0.18964	0.0455	L	0.36672	1.1	0.23969	N	0.99632	B	0.15141	0.012	B	0.15052	0.012	T	0.17379	-1.0371	10	0.23302	T	0.38	.	8.8587	0.35245	0.1682:0.0:0.8318:0.0	.	404	O96020	CCNE2_HUMAN	Q	404;404;296	ENSP00000429089:H404Q;ENSP00000309181:H404Q	ENSP00000309181:H404Q	H	-	3	2	CCNE2	95963039	1.000000	0.71417	0.968000	0.41197	0.874000	0.50279	2.207000	0.42788	1.481000	0.48307	0.655000	0.94253	CAC	NOVEL	CCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379808.1	6	7.823024	KEEP	0	0	0	26	791	GG	0.999957	0.99995	0		-	56	60	1943	0	0	189.507752	49	60	1703	207	ENST00000520509.1	0.533333	0.999993
NDUFAF6	137682	__UNKNOWN__	__UNKNOWN__	8	96004454	96004454	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:96004454A>G	ENST00000396113.1	+	6	817				NDUFAF6_ENST00000542894.1_Intron|NDUFAF6_ENST00000396111.2_Intron			Q330K2	NDUF6_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 6	NA		NA			biosynthetic process (GO:0009058)|mitochondrial respiratory chain complex I assembly (GO:0032981)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	transferase activity (GO:0016740)				NA						ggtggctcacacctgtaatcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC028166	CCDS6266.2	8q22.1	2013-10-21	2012-05-08	2012-05-08	ENSG00000156170	ENSG00000156170	137682		Mitochondrial respiratory chain complex assembly factors	28625	protein-coding gene	gene with protein product		612392	chromosome 8 open reading frame 38	C8orf38	NA	22019594, 23509070	Standard	NM_152416	NM_152416	NA	Approved	MGC40214	uc003yhj.3	Q330K2	OTTHUMG00000150173	ENST00000396113.1:c.-234+11253A>G	chr8.hg19:g.96004454A>G		NA	A8MT28|A8MWF0|B4DQ45|Q8N6U6	hg19		0.02	-0.236776	CACxCCT	UNCOVERED																																																																																			NOVEL	NDUFAF6-003	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000316699.1	7	2.406148	KEEP	4	0	0	8	221	AA	0	0	0		+	3	53	106	0	0	8.048813	22	60	635	64	ENST00000396113.1	0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	96134072	96134072	__UNKNOWN__	IGR	SNP	T	T	G	rs115932795	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:96134072T>G			NA	NA				RP11-320N21.2 (33920 upstream) : PLEKHF2 (11959 downstream)						NA		NA									NA						actttgggagtctgagAAAAA	0.383		NA											G|||	15	0.00299521	0.0113	0.0	5008	,	,	NA	14029	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.96134072T>G		NA		hg19		0.02	-0.245594	GAGxCTG	COVERED																																																																																			NOVEL					0			7	2.706215	KEEP	0	0	0	9	240	TT	0.99254	0.636563	0			3	60	108	1	0	8.091817	25	60	761	57		0.107143	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	96198392	96198392	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:96198392T>C			NA	NA				PLEKHF2 (29480 upstream) : KB-1047C11.1 (20842 downstream)						NA		NA									NA						tggctgatttttgcctttttt	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.96198392T>C		NA		hg19		0.02	-0.24552	TTTxTGC	COVERED																																																																																			NOVEL					0			8	3.306323	KEEP	0	0	0	11	294	TT	0.993072	0.636904	0			9	60	308	0	0	28.002588	16	60	443	52		0.36	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	97102168	97102168	__UNKNOWN__	IGR	SNP	G	G	A	rs2319512	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:97102168G>A			NA	NA				RP11-31K23.2 (96837 upstream) : KB-1043D8.8 (50631 downstream)						NA		NA									NA						actccagcctgggcaacaaga	0.483		NA											G|||	2434	0.486022	0.239	0.6744	5008	,	,	NA	13493	0.6617	NA	0.5537	False	NA	,,,	NA	NA	NA	2504	0.4356	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.97102168G>A		NA		hg19		0.02	-0.140347	CCTxGGC	COVERED																																																																																			NOVEL					0			13	4.513099	KEEP	5	0	0	15	453	GG	0.994391	0.259501	0			9	60	268	0	0	27.128284	5	60	175	50		0.642857	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	97414679	97414679	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:97414679A>G			NA	NA				KB-1448A5.1 (15803 upstream) : RNU6-1172P (28602 downstream)						NA		NA									NA						ctggagtgcaatgacacgatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.97414679A>G		NA		hg19		0.02	-0.21925	GCAxTGA	COVERED																																																																																			NOVEL					0			9	6.01368	KEEP	3	0	0	20	536	AA	0.99986	0.55281	0			4	60	125	0	0	9.714563	20	60	591	71		0.166667	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	98378075	98378075	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98378075A>C			NA	NA				U3 (7373 upstream) : MTDH (278331 downstream)						NA		NA									NA						ccttgtgatcaccctgcctcg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.98378075A>C		NA		hg19		0.02	-0.13155	ATCxCCC	COVERED																																																																																			NOVEL					0			9	3.007321	KEEP	0	0	0	10	275	AA	0.992708	0.227502	0			3	60	93	0	0	7.573161	11	60	322	33		0.214286	0.229173
MTDH	92140	__UNKNOWN__	__UNKNOWN__	8	98704147	98704147	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98704147T>G	ENST00000519934.1	+	6	1009				MTDH_ENST00000336273.3_Intron			Q86UE4	LYRIC_HUMAN	metadherin	NA		NA			lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			ttgctctgtctcccaggctgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649	92140			29608	protein-coding gene	gene with protein product	astrocyte elevated gene 1	610323			NA	15093543	Standard		NM_178812	NA	Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000519934.1:c.979+731T>G	chr8.hg19:g.98704147T>G		NA	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	hg19		0.02	-0.201743	GTCxCCC	COVERED																																																																																			NOVEL	MTDH-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000379773.2	9	3.609586	KEEP	3	0	0	12	337	TT	0.993072	0.518544	0		+	3	60	101	0	0	7.726772	19	60	582	54	ENST00000519934.1	0.136364	0.522161
MTDH	92140	__UNKNOWN__	__UNKNOWN__	8	98735355	98735355	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98735355A>G	ENST00000519934.1	+	10	1540				MTDH_ENST00000336273.3_Intron			Q86UE4	LYRIC_HUMAN	metadherin	NA		NA			lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			ggccaggcgcagtggctcacg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649	92140			29608	protein-coding gene	gene with protein product	astrocyte elevated gene 1	610323			NA	15093543	Standard		NM_178812	NA	Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000519934.1:c.1510+92A>G	chr8.hg19:g.98735355A>G		NA	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	hg19		0.02	-0.280675	CGCxGTG	COVERED																																																																																			NOVEL	MTDH-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000379773.2	8	2.406409	KEEP	1	0	0	8	225	AA	0.99257	0.734176	0		+	3	60	100	0	0	7.109282	29	60	883	59	ENST00000519934.1	0.09375	0.739671
MATN2	4147	__UNKNOWN__	__UNKNOWN__	8	98887151	98887151	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98887151A>G	ENST00000521689.1	+	1	448				MATN2_ENST00000254898.5_Intron|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000524308.1_Intron			O00339	MATN2_HUMAN	matrilin 2	NA		NA				proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			tcaccatgttagtcaggctgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15					4147			6908	protein-coding gene	gene with protein product		602108			NA	9083061, 11852232	Standard		XM_005250920	NA	Approved		uc003yic.3	O00339		ENST00000521689.1:c.-27+5636A>G	chr8.hg19:g.98887151A>G		NA	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	hg19	CCDS55265.1	0.02	-0.122774	GTTxGTC	COVERED																																																																																			NOVEL	MATN2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380327.1	4	2.405127	KEEP	0	0	0	8	208	AA	0.99257	0.194853	0		+	3	60	89	0	0	7.401416	9	60	265	31	ENST00000521689.1	0.25	0.196312
MATN2	4147	__UNKNOWN__	__UNKNOWN__	8	98896969	98896969	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98896969T>A	ENST00000521689.1	+	2	448				MATN2_ENST00000254898.5_Intron|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000524308.1_Intron			O00339	MATN2_HUMAN	matrilin 2	NA		NA				proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			actgcactcctgcctgggcga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15					4147			6908	protein-coding gene	gene with protein product		602108			NA	9083061, 11852232	Standard		XM_005250920	NA	Approved		uc003yic.3	O00339		ENST00000521689.1:c.-26-3334T>A	chr8.hg19:g.98896969T>A		NA	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	hg19	CCDS55265.1	0.02	-0.429779	TCCxGCC	COVERED																																																																																			NOVEL	MATN2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380327.1	6	4.812535	KEEP	0	0	0	16	448	TT	0.997832	0.957778	0		+	4	60	122	1	0	8.250683	41	60	1243	99	ENST00000521689.1	0.088889	0.959859
MATN2	4147	__UNKNOWN__	__UNKNOWN__	8	98939594	98939594	__UNKNOWN__	Intron	SNP	G	G	A	rs1840372	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98939594G>A	ENST00000521689.1	+	3	616				MATN2_ENST00000254898.5_Intron|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000520016.1_Intron|MATN2_ENST00000524308.1_Intron			O00339	MATN2_HUMAN	matrilin 2	NA		NA				proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			ctccatgttggtcaggctggt	0.473		NA											G|||	3619	0.722644	0.5053	0.7522	5008	,	,	NA	15085	0.9335	NA	0.667	False	NA	,,,	NA	NA	NA	2504	0.8354	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15					4147			6908	protein-coding gene	gene with protein product		602108			NA	9083061, 11852232	Standard		XM_005250920	NA	Approved		uc003yic.3	O00339		ENST00000521689.1:c.143-3587G>A	chr8.hg19:g.98939594G>A		NA	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	hg19	CCDS55265.1	0.02	-0.070173	TTGxTCA	UNCOVERED																																																																																			NOVEL	MATN2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380327.1	7	2.4067	KEEP	5	0	0	8	233	GG	0	0	0		+	6	60	188	0	0	20.414761	1	6	31	27	ENST00000521689.1	0.857143	0.054137
MATN2	4147	__UNKNOWN__	__UNKNOWN__	8	98999348	98999348	__UNKNOWN__	Intron	SNP	C	C	T	rs565863589		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:98999348C>T	ENST00000521689.1	+	7	1555				MATN2_ENST00000254898.5_Intron|MATN2_ENST00000524308.1_Intron|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000520016.1_Intron			O00339	MATN2_HUMAN	matrilin 2	NA		NA				proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			ggattacaggcgtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15					4147			6908	protein-coding gene	gene with protein product		602108			NA	9083061, 11852232	Standard		XM_005250920	NA	Approved		uc003yic.3	O00339		ENST00000521689.1:c.1082-7360C>T	chr8.hg19:g.98999348C>T		NA	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	hg19	CCDS55265.1	0.02	-0.184207	AGGxGTG	UNCOVERED																																																																																			NOVEL	MATN2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380327.1	5	2.405958	KEEP	1	0	0	8	226	CC	0	0	0		+	3	60	88	0	0	6.634008	16	60	524	46	ENST00000521689.1	0.157895	0.457757
MATN2	4147	__UNKNOWN__	__UNKNOWN__	8	99037952	99037952	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:99037952C>T	ENST00000521689.1	+	14	2416				MATN2_ENST00000254898.5_Intron|MATN2_ENST00000524308.1_Intron|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000520016.1_Intron|RPL30_ENST00000518164.1_5'UTR			O00339	MATN2_HUMAN	matrilin 2	NA		NA				proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			ccagcctgggcgacacagcaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15					4147			6908	protein-coding gene	gene with protein product		602108			NA	9083061, 11852232	Standard		XM_005250920	NA	Approved		uc003yic.3	O00339		ENST00000521689.1:c.1943-1692C>T	chr8.hg19:g.99037952C>T		NA	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	hg19	CCDS55265.1	0.02	1.102745	GGGxGAC	COVERED																																																																																			NOVEL	MATN2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380327.1	16	10.830226	KEEP	0	0	0	36	1070	CC	0.999999	0.99988	0		+	5	60	146	1	1	8.930989	73	60	2398	180	ENST00000521689.1	0.064103	0.999881
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	99059282	99059282	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:99059282A>G			NA	NA				RPL30 (1464 upstream) : RNU6-703P (1801 downstream)						NA		NA									NA						ctgggcgacaaagcgagactc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.99059282A>G		NA		hg19		0.02	-0.359563	ACAxAGC	COVERED																																																																																			NOVEL					0			10	3.308098	KEEP	1	0	0	11	299	AA	0.993072	0.882717	0			3	60	105	0	0	7.411367	34	60	1002	77		0.081081	0.888875
NIPAL2	79815	__UNKNOWN__	__UNKNOWN__	8	99220897	99220897	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:99220897A>G	ENST00000430223.2	-	7	854				NIPAL2_ENST00000520545.1_Intron|NIPAL2_ENST00000341166.3_Intron			Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	NA		NA				integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						ggctggtctcaaactcctgac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361	79815			25854	protein-coding gene	gene with protein product		NA		NPAL2	NA	14702039	Standard	NM_024759	NM_024759	NA	Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000430223.2:c.656-3423T>C	chr8.hg19:g.99220897A>G		NA	A2RTY8	hg19		0.02	-0.149086	CTCxAAC	COVERED																																																																																			NOVEL	NIPAL2-002	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000379678.2	10	2.406098	KEEP	1	0	0	8	221	AA	0.99257	0.289832	0		-	3	60	93	0	0	7.292288	14	60	409	37	ENST00000430223.2	0.176471	0.292001
VPS13B	157680	__UNKNOWN__	__UNKNOWN__	8	100030511	100030511	__UNKNOWN__	Intron	SNP	C	C	G	rs188955410	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:100030511C>G	ENST00000358544.2	+	2	258				VPS13B_ENST00000357162.2_Intron|VPS13B_ENST00000395996.1_Intron|VPS13B_ENST00000355155.1_Intron|VPS13B_ENST00000441350.2_Intron	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	NA		NA			protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			ctacttgggacgctggggcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(161;2205 2542 7338 31318)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549	157680			2183	protein-coding gene	gene with protein product		607817	Cohen syndrome 1	CHS1, COH1	NA	7920642, 15498460	Standard	NM_184042	NM_181661	NA	Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.147+4348C>G	chr8.hg19:g.100030511C>G		NA	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	hg19	CCDS6280.1	0.02	-0.096493	GGAxGCT	UNCOVERED																																																																																			NOVEL	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277138.1	7	3.608597	KEEP	0	0	0	12	339	CC	0.993634	0.138942	0		+	3	43	100	0	1	8.943432	6	60	202	36	ENST00000358544.2	0.333333	0.139832
VPS13B	157680	__UNKNOWN__	__UNKNOWN__	8	100709973	100709973	__UNKNOWN__	Intron	SNP	G	G	A	rs540747610	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:100709973G>A	ENST00000358544.2	+	36	6232				VPS13B_ENST00000357162.2_Intron|VPS13B_ENST00000395996.1_Intron	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	NA		NA			protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GGGCGCGCCCGTAGGGGAGAA	0.592		NA											g|||	2	0.000399361	0.0	0.0	5008	,	,	NA	22243	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Colon(161;2205 2542 7338 31318)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549	157680			2183	protein-coding gene	gene with protein product		607817	Cohen syndrome 1	CHS1, COH1	NA	7920642, 15498460	Standard	NM_184042	NM_181661	NA	Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.6122-1780G>A	chr8.hg19:g.100709973G>A		NA	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	hg19	CCDS6280.1	0.02	-0.377148	CCCxTAG	COVERED																																																																																			NOVEL	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277138.1	2	2.406635	KEEP	0	0	0	8	230	GG	0.99257	0.902315	0		+	4	60	107	0	0	6.881162	38	60	1232	60	ENST00000358544.2	0.095238	0.909069
RGS22	26166	__UNKNOWN__	__UNKNOWN__	8	100994019	100994019	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:100994019A>G	ENST00000523437.1	-	22	3365				RGS22_ENST00000360863.6_Intron|RGS22_ENST00000523287.1_Intron			Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	NA		NA			positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			caaactcctgagctcaaacaa	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554	26166		Regulators of G-protein signaling	24499	protein-coding gene	gene with protein product		615650	regulator of G-protein signalling 22		NA		Standard	NM_015668	XM_005250856	NA	Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000523437.1:c.3324+145T>C	chr8.hg19:g.100994019A>G		NA	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	hg19		0.02	-0.19298	CTGxGCT	COVERED																																																																																			NOVEL	RGS22-006	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380369.1	15	3.609087	KEEP	3	0	0	12	332	AA	0.992708	0.454419	0		-	3	60	103	0	0	8.060528	17	60	533	47	ENST00000523437.1	0.15	0.457757
RGS22	26166	__UNKNOWN__	__UNKNOWN__	8	101057303	101057303	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:101057303A>G	ENST00000523437.1	-	11	1828				RGS22_ENST00000360863.6_Intron|RGS22_ENST00000523287.1_Intron			Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	NA		NA			positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			ccaggagttcaagaccagcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554	26166		Regulators of G-protein signaling	24499	protein-coding gene	gene with protein product		615650	regulator of G-protein signalling 22		NA		Standard	NM_015668	XM_005250856	NA	Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000523437.1:c.1787+2387T>C	chr8.hg19:g.101057303A>G		NA	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	hg19		0.02	-0.324224	TTCxAGA	COVERED																																																																																			NOVEL	RGS22-006	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380369.1	12	3.307928	KEEP	0	0	0	11	301	AA	0.993072	0.846082	0		-	3	60	101	0	0	7.127901	31	60	891	75	ENST00000523437.1	0.088235	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	101258880	101258880	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:101258880T>C			NA	NA				SPAG1 (4750 upstream) : RNF19A (10407 downstream)						NA		NA									NA						atcctcctgcttcagcctccc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.101258880T>C		NA		hg19		0.02	-0.210517	TGCxTCA	COVERED																																																																																			NOVEL					0			6	4.210391	KEEP	0	0	0	14	387	TT	0.995343	0.519729	0			4	60	136	0	0	10.894249	19	60	586	60		0.173913	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	101263567	101263567	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:101263567T>G			NA	NA				SPAG1 (9437 upstream) : RNF19A (5720 downstream)						NA		NA									NA						gggttcaagctattctcctgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.101263567T>G		NA		hg19		0.02	-0.201706	AGCxATT	COVERED																																																																																			NOVEL					0			11	5.109514	KEEP	0	0	0	17	442	CT	0.99986	0.55281	0			3	60	91	0	0	6.793266	18	60	526	64		0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	101913496	101913496	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:101913496C>G			NA	NA				RNU4-83P (69408 upstream) : RP11-521I2.3 (11978 downstream)						NA		NA									NA						attgcttgagcccaggagttt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.101913496C>G		NA		hg19		0.02	-0.201749	GAGxCCA	COVERED																																																																																			NOVEL					0			8	3.30972	KEEP	0	0	0	11	339	CC	0.993072	0.518544	0			3	60	87	0	0	6.395122	18	60	618	49		0.142857	0.522161
YWHAZ	7534	__UNKNOWN__	__UNKNOWN__	8	101929718	101929718	__UNKNOWN__	3'UTR	SNP	T	T	C	rs142848129		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:101929718T>C	ENST00000395957.2	-	0	4282							P63104	1433Z_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta	NA		NA			apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|gene expression (GO:0010467)|histamine secretion by mast cell (GO:0002553)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting to mitochondrion (GO:0006626)|response to drug (GO:0042493)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mast cell granule (GO:0042629)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			large_intestine(1)|lung(2)	3	all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197)		Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05)			gaggccgaggtgggcggatca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U28964	CCDS6290.1	8q22.3	2013-12-03	2013-12-03		ENSG00000164924	ENSG00000164924	7534			12855	protein-coding gene	gene with protein product	14-3-3 zeta, 14-3-3 delta	601288	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, delta polypeptide, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	YWHAD	NA	8617504, 7890696	Standard	NM_145690	NM_003406	NA	Approved	KCIP-1, 14-3-3-zeta	uc010mbr.2	P63104	OTTHUMG00000134291	ENST00000395957.2:c.*3203A>G	chr8.hg19:g.101929718T>C		NA	A8K1N0|B7Z465|P29213|P29312|Q32P43|Q5XJ08|Q6GPI2|Q6IN74|Q6NUR9|Q6P3U9|Q86V33	hg19	CCDS6290.1	0.02	-0.166638	AGGxGGG	COVERED																																																																																			NOVEL	YWHAZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259017.2	9	2.706704	KEEP	5	0	0	9	246	TT	0.99254	0.351306	0		-	3	60	88	0	0	6.711235	15	60	455	49	ENST00000395957.2	0.166667	0.353947
YWHAZ	7534	__UNKNOWN__	__UNKNOWN__	8	101940725	101940725	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:101940725T>C	ENST00000522542.1	-	2	86				YWHAZ_ENST00000419477.2_Intron|YWHAZ_ENST00000395951.3_Intron|YWHAZ_ENST00000353245.3_Intron|YWHAZ_ENST00000522819.1_Intron|YWHAZ_ENST00000395956.3_Intron|YWHAZ_ENST00000521309.1_Intron|YWHAZ_ENST00000395958.2_Intron|YWHAZ_ENST00000395953.2_Intron|YWHAZ_ENST00000395957.2_Intron|YWHAZ_ENST00000457309.1_Intron|YWHAZ_ENST00000395948.2_Intron			P63104	1433Z_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta	NA		NA			apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|gene expression (GO:0010467)|histamine secretion by mast cell (GO:0002553)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting to mitochondrion (GO:0006626)|response to drug (GO:0042493)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mast cell granule (GO:0042629)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			large_intestine(1)|lung(2)	3	all_cancers(14;7.43e-06)|all_epithelial(15;2.77e-08)|Lung NSC(17;6.08e-05)|all_lung(17;0.000197)		Epithelial(11;2.79e-11)|all cancers(13;5.45e-09)|OV - Ovarian serous cystadenocarcinoma(57;4.75e-05)			tttgggaggctgaggcgggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U28964	CCDS6290.1	8q22.3	2013-12-03	2013-12-03		ENSG00000164924	ENSG00000164924	7534			12855	protein-coding gene	gene with protein product	14-3-3 zeta, 14-3-3 delta	601288	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, delta polypeptide, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	YWHAD	NA	8617504, 7890696	Standard	NM_145690	NM_003406	NA	Approved	KCIP-1, 14-3-3-zeta	uc010mbr.2	P63104	OTTHUMG00000134291	ENST00000522542.1:c.70-3458A>G	chr8.hg19:g.101940725T>C		NA	A8K1N0|B7Z465|P29213|P29312|Q32P43|Q5XJ08|Q6GPI2|Q6IN74|Q6NUR9|Q6P3U9|Q86V33	hg19		0.02	-0.140331	GGCxGAG	COVERED																																																																																			NOVEL	YWHAZ-013	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380239.1	8	2.707335	KEEP	1	0	0	9	256	TT	0.99257	0.259026	0		-	3	60	98	0	0	7.878954	13	60	388	37	ENST00000522542.1	0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	102320046	102320046	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:102320046C>G			NA	NA				RNU7-67P (390 upstream) : NACAP1 (53975 downstream)						NA		NA									NA						aaactcctggcctcaagtgat	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.102320046C>G		NA		hg19		0.02	-0.157894	TGGxCTC	COVERED																																																																																			NOVEL					0			4	3.008184	KEEP	0	0	0	10	291	CC	0.992708	0.320453	0			3	60	95	2	0	7.772989	11	60	371	44		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	102369546	102369546	__UNKNOWN__	IGR	SNP	C	C	A	rs10109873	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:102369546C>A			NA	NA				RNU7-67P (49890 upstream) : NACAP1 (4475 downstream)						NA		NA									NA						gcctgggcaacagagtgagac	0.468		NA											C|||	930	0.185703	0.2511	0.1427	5008	,	,	NA	11516	0.0526	NA	0.2356	False	NA	,,,	NA	NA	NA	2504	0.2137	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.102369546C>A		NA		hg19		0.02	-0.043844	CAAxAGA	UNCOVERED																																																																																			NOVEL					0			8	3.008658	KEEP	2	0	0	10	300	CC	0.99257	0.036492	0			3	60	80	0	0	8.452355	1	60	29	19		0.75	0.036766
RRM2B	50484	__UNKNOWN__	__UNKNOWN__	8	103243864	103243864	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:103243864T>C	ENST00000251810.3	-	2	448				RRM2B_ENST00000519317.1_Intron|RRM2B_ENST00000519962.1_Intron|RRM2B_ENST00000395912.2_Intron	NM_001172478.1|NM_015713.4	NP_001165949.1|NP_056528.2	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)	NA		NA			deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleoside triphosphate metabolic process (GO:0009200)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA repair (GO:0006281)|kidney development (GO:0001822)|mitochondrial DNA replication (GO:0006264)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|renal system process (GO:0003014)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	9	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)		Cladribine(DB00242)	tttgggaggctgaggcaggtg	0.468		NA						Modulation of nucleotide pools													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB036532	CCDS34932.1, CCDS55267.1	8q23.1	2014-09-17			ENSG00000048392	ENSG00000048392	50484			17296	protein-coding gene	gene with protein product		604712			NA	10716435, 10980602, 17486094	Standard		NM_015713	NA	Approved	p53R2	uc022azl.1	Q7LG56	OTTHUMG00000164776	ENST00000251810.3:c.204+512A>G	chr8.hg19:g.103243864T>C		NA	B4E2N4|Q17R22|Q75PQ6|Q75PQ7|Q75PY8|Q75PY9|Q86YE3|Q9NPD6|Q9NTD8|Q9NUW3	hg19	CCDS34932.1	0.02	-0.140333	GGCxGAG	COVERED																																																																																			NOVEL	RRM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380191.3	6	4.51182	KEEP	5	0	0	15	420	TT	0.993634	0.290142	0		-	3	44	99	0	0	8.172957	11	60	327	51	ENST00000251810.3	0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	103431083	103431083	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:103431083T>C			NA	NA				UBR5 (6014 upstream) : RNU6ATAC8P (2341 downstream)						NA		NA									NA						gctgggattataggtgtgagc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.103431083T>C		NA		hg19		0.02	-0.324486	TTAxAGG	COVERED																																																																																			NOVEL					0			4	3.308018	KEEP	0	0	0	11	297	TT	0.993072	0.829926	0			5	60	161	0	0	12.617525	25	60	720	72		0.166667	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	103537374	103537374	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:103537374A>T			NA	NA				RNU6ATAC8P (103824 upstream) : KB-1980E6.3 (3593 downstream)						NA		NA									NA						ttttttttttagagacagggt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.103537374A>T		NA		hg19		0.02	-0.26256	TTTxGAG	COVERED																																																																																			NOVEL					0			16	4.208868	KEEP	0	0	0	14	367	AA	0.995343	0.690438	0			3	55	92	1	0	6.599036	23	60	660	62		0.115385	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	103614563	103614563	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:103614563T>C			NA	NA				ODF1 (41318 upstream) : KLF10 (46443 downstream)						NA		NA									NA						gctgggattataggcatgagc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.103614563T>C		NA		hg19		0.02	-0.131571	TTAxAGG	COVERED																																																																																			NOVEL					0			4	2.406016	KEEP	0	0	0	8	220	TT	0.99257	0.22747	0			3	60	105	0	0	9.001213	9	60	270	37		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	103815661	103815661	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:103815661T>C			NA	NA				AP003356.1 (69714 upstream) : KB-1732A1.1 (3388 downstream)						NA		NA									NA						gtggctcacatctgtaatccc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.103815661T>C		NA		hg19		0.02	-0.298203	ACAxCTG	UNCOVERED																																																																																			NOVEL					0			11	2.406086	KEEP	5	0	0	8	222	TT	0	0	0			3	60	102	0	0	7.352574	28	60	833	66		0.096774	0.78106
KB-1507C5.2	0	__UNKNOWN__	__UNKNOWN__	8	103956611	103956611	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:103956611T>C	ENST00000517996.1	+	3	604										NA		NA									NA						aggccgggtgtggtggctcat	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000517996.1:c.604+2330T>C	chr8.hg19:g.103956611T>C		NA		hg19		0.02	-0.228002	GTGxGGT	COVERED																																																																																			NOVEL	KB-1507C5.2-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000380497.1	8	3.006562	KEEP	2	0	0	10	263	TT	0.99254	0.578582	0		+	3	60	103	0	0	7.805708	21	60	594	52	ENST00000517996.1	0.125	0.58293
ATP6V1C1	528	__UNKNOWN__	__UNKNOWN__	8	104074459	104074459	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104074459T>C	ENST00000395862.3	+	9	800				ATP6V1C1_ENST00000518738.1_Intron|ATP6V1C1_ENST00000518857.1_Intron|ATP6V1C1_ENST00000521514.1_Intron	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			agtgcagtggtgcaatctcag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	528	3.6.3.14	ATPases / V-type	856	protein-coding gene	gene with protein product		603097	ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD, ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1	ATP6D, ATP6C	NA	8250920, 14580332	Standard	NM_001695	NM_001695	NA	Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.642-724T>C	chr8.hg19:g.104074459T>C		NA		hg19	CCDS6296.1	0.02	-0.184127	TGGxGCA	COVERED																																																																																			NOVEL	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380101.1	14	2.406198	KEEP	0	0	0	8	222	AT	0.99254	0.420319	0		+	3	60	96	0	0	7.59246	14	60	384	33	ENST00000395862.3	0.176471	0.423478
ATP6V1C1	528	__UNKNOWN__	__UNKNOWN__	8	104074468	104074468	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104074468A>G	ENST00000395862.3	+	9	800				ATP6V1C1_ENST00000518738.1_Intron|ATP6V1C1_ENST00000518857.1_Intron|ATP6V1C1_ENST00000521514.1_Intron	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			gtgcaatctcagctcactgta	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	528	3.6.3.14	ATPases / V-type	856	protein-coding gene	gene with protein product		603097	ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD, ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1	ATP6D, ATP6C	NA	8250920, 14580332	Standard	NM_001695	NM_001695	NA	Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.642-715A>G	chr8.hg19:g.104074468A>G		NA		hg19	CCDS6296.1	0.02	-0.192954	CTCxGCT	COVERED																																																																																			NOVEL	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380101.1	15	2.706752	KEEP	0	0	0	9	246	AA	0.99254	0.454342	0		+	3	60	105	0	0	8.333178	16	60	477	34	ENST00000395862.3	0.157895	0.457757
ATP6V1C1	528	__UNKNOWN__	__UNKNOWN__	8	104084054	104084054	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104084054G>A	ENST00000395862.3	+	0	4387					NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			tatgttgcccgggctggtctc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	528	3.6.3.14	ATPases / V-type	856	protein-coding gene	gene with protein product		603097	ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD, ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1	ATP6D, ATP6C	NA	8250920, 14580332	Standard	NM_001695	NM_001695	NA	Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.*3079G>A	chr8.hg19:g.104084054G>A		NA		hg19	CCDS6296.1	0.02	1.365923	CCCxGGC	COVERED																																																																																			NOVEL	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380101.1	11	3.141776	KEEP	1	1	24	19	574	GG	0.999863	0.987808	0		+	5	60	149	0	0	10.056685	49	60	1602	118	ENST00000395862.3	0.092593	0.987943
RP11-318M2.2	0	__UNKNOWN__	__UNKNOWN__	8	104299396	104299396	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104299396T>C	ENST00000521383.1	-	0	415				RP11-318M2.2_ENST00000523614.2_RNA|RP11-318M2.2_ENST00000522856.1_RNA						NA		NA									NA						ggattacaggtgtgagccacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000521383.1:	chr8.hg19:g.104299396T>C		NA		hg19		0.02	-0.377089	AGGxGTG	COVERED																																																																																			NOVEL	RP11-318M2.2-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000380352.1	11	3.909125	KEEP	2	0	0	13	353	TT	0.993634	0.903281	0		-	3	60	99	0	0	6.812176	34	60	989	86	ENST00000521383.1	0.081081	0.909069
FZD6	8323	__UNKNOWN__	__UNKNOWN__	8	104330046	104330046	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104330046T>C	ENST00000358755.4	+	3	494				FZD6_ENST00000523739.1_Intron|FZD6_ENST00000540287.1_Intron|FZD6_ENST00000522566.1_Intron	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	NA		NA			angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			agagcaagactctgtctcaaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930	8323		GPCR / Class F : Frizzled receptors	4044	protein-coding gene	gene with protein product		603409	frizzled (Drosophila) homolog 6, frizzled homolog 6 (Drosophila), frizzled 6, seven transmembrane spanning receptor, frizzled family receptor 6		NA	9480858, 14747478	Standard	NM_003506	NM_003506	NA	Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.178-772T>C	chr8.hg19:g.104330046T>C		NA	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	hg19	CCDS6298.1	0.02	-0.140345	GACxCTG	COVERED																																																																																			NOVEL	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380560.1	15	4.511773	KEEP	3	0	0	15	417	TT	0.995343	0.25975	0		+	3	60	105	0	0	8.672071	12	60	366	52	ENST00000358755.4	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	104371266	104371266	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104371266T>C			NA	NA				FZD6 (26179 upstream) : CTHRC1 (12476 downstream)						NA		NA									NA						CTAggctgggtacggtggctc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.104371266T>C		NA		hg19		0.02	-0.245372	GGGxACG	COVERED																																																																																			NOVEL					0			9	3.005081	KEEP	0	0	0	10	247	TT	0.992708	0.63667	0			3	60	111	0	0	8.495408	23	60	611	53		0.115385	0.641347
DCAF13	25879	__UNKNOWN__	__UNKNOWN__	8	104429639	104429639	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104429639A>G	ENST00000297579.5	+	1	803				DCAF13_ENST00000519682.1_Intron|DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000521971.1_Intron|DCAF13_ENST00000521716.1_Intron	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	NA		NA			protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ggaggccgagacgggcggatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934	25879		WD repeat domain containing, DDB1 and CUL4 associated factors	24535	protein-coding gene	gene with protein product		NA	WD repeats and SOF1 domain containing	WDSOF1	NA	11042152	Standard	NM_015420	NM_015420	NA	Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.526+1895A>G	chr8.hg19:g.104429639A>G		NA	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	hg19	CCDS34934.1	0.02	-0.245535	GAGxCGG	UNCOVERED																																																																																			NOVEL	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380797.2	5	2.405712	KEEP	2	0	0	8	216	AA	0	0	0		+	3	60	106	0	0	7.994589	23	60	651	51	ENST00000297579.5	0.115385	0.641347
RIMS2	9699	__UNKNOWN__	__UNKNOWN__	8	104624999	104624999	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:104624999A>C	ENST00000406091.3	+	2	176					NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	NA		NA			calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			agggtttcacaatgttggcca	0.552		NA								HNSCC(12;0.0054)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14			9699			17283	protein-coding gene	gene with protein product		606630	RAB3 interacting protein 3	RAB3IP3	NA	9872452, 12578829	Standard	NM_001100117	NM_014677	NA	Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.177-84315A>C	chr8.hg19:g.104624999A>C		NA	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	hg19	CCDS55269.1	0.02	-0.149083	CACxATG	COVERED																																																																																			NOVEL	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		3	2.705821	KEEP	0	0	0	9	236	AA	0.99254	0.289823	0		+	3	60	96	0	0	7.679206	13	60	384	36	ENST00000406091.3	0.1875	0.292001
LRP12	29967	__UNKNOWN__	__UNKNOWN__	8	105513899	105513899	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:105513899C>T	ENST00000276654.5	-	4	381				LRP12_ENST00000424843.2_Intron	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	NA		NA			endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			accactgcaccccagcctggg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650	29967		Low density lipoprotein receptors	31708	protein-coding gene	gene with protein product		NA			NA	12809483, 14676824	Standard	NM_013437	NM_013437	NA	Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.273-2152G>A	chr8.hg19:g.105513899C>T		NA	A8K137|B4DRQ2	hg19	CCDS6303.1	0.02	-0.219294	CACxCCA	COVERED																																																																																			NOVEL	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380821.1	7	3.610633	KEEP	1	0	0	12	364	CC	0.993634	0.608508	0		-	3	60	87	0	0	6.327975	19	60	617	52	ENST00000276654.5	0.136364	0.612407
LRP12	29967	__UNKNOWN__	__UNKNOWN__	8	105526883	105526883	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:105526883A>G	ENST00000276654.5	-	3	245				LRP12_ENST00000424843.2_Intron	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	NA		NA			endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			cagcctgggcaacagagcaag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650	29967		Low density lipoprotein receptors	31708	protein-coding gene	gene with protein product		NA			NA	12809483, 14676824	Standard	NM_013437	NM_013437	NA	Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.137-5581T>C	chr8.hg19:g.105526883A>G		NA	A8K137|B4DRQ2	hg19	CCDS6303.1	0.02	-0.210457	GGCxACA	COVERED																																																																																			NOVEL	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380821.1	11	3.90857	KEEP	0	0	0	13	345	AA	0.994391	0.519232	0		-	3	60	95	0	0	7.192834	18	60	503	53	ENST00000276654.5	0.142857	0.522161
ZFPM2	23414	__UNKNOWN__	__UNKNOWN__	8	106798037	106798037	__UNKNOWN__	Intron	SNP	G	G	A	rs146068138	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:106798037G>A	ENST00000407775.2	+	6	782				ZFPM2_ENST00000522296.1_Intron|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000520492.1_Intron|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000518932.1_RNA|ZFPM2_ENST00000517361.1_Intron	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	NA		NA			blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ttgggaggccgaggcgggtgg	0.493		NA											G|||	50	0.00998403	0.0348	0.0058	5008	,	,	NA	15047	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946	23414		Zinc fingers, C2H2-type, Zinc fingers, C2HC-type containing	16700	protein-coding gene	gene with protein product		603693	zinc finger protein, multitype 2		NA	9927675, 10438528	Standard		NM_012082	NA	Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.533-2909G>A	chr8.hg19:g.106798037G>A		NA	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	hg19	CCDS47908.1	0.02	-0.20173	GCCxAGG	COVERED																																																																																			NOVEL	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380614.1	7	2.404213	KEEP	0	0	0	8	227	GG	0.99257	0.4869	0		+	3	60	87	0	0	6.533961	16	60	517	42	ENST00000407775.2	0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	107179597	107179597	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:107179597A>G			NA	NA				RP11-152P17.2 (106845 upstream) : RP11-778D12.2 (98065 downstream)						NA		NA									NA						cccgggaggcagaggttgcag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.107179597A>G		NA		hg19		0.02	-0.166644	GGCxGAG	COVERED																																																																																			NOVEL					0			6	2.706966	KEEP	1	0	0	9	250	AA	0.99254	0.351306	0			3	60	91	0	0	7.010652	15	60	451	36		0.166667	0.353947
ABRA	137735	__UNKNOWN__	__UNKNOWN__	8	107772913	107772913	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:107772913A>C	ENST00000311955.3	-	0	1552					NM_139166.4	NP_631905.1			actin-binding Rho activating protein	NA		NA								breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			aatcccagctacttgggaggc	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429	137735			30655	protein-coding gene	gene with protein product	striated muscle activator of Rho-dependent signaling	609747			NA	11983702	Standard	NM_139166	NM_139166	NA	Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.*352T>G	chr8.hg19:g.107772913A>C		NA		hg19	CCDS6305.1	0.02	-0.210462	GCTxCTT	COVERED																																																																																			NOVEL	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380416.1	4	2.637684	KEEP	1	1	29	19	507	AA	0.99986	0.522088	0		-	3	60	92	0	0	6.827885	19	60	541	48	ENST00000311955.3	0.136364	0.522161
EIF3E	3646	__UNKNOWN__	__UNKNOWN__	8	109232081	109232081	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:109232081G>A	ENST00000220849.5	-	8	785				EIF3E_ENST00000519517.1_Intron|EIF3E_ENST00000519030.1_Intron	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E	NA		NA							EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			aaagaaaaaaGAAAATGTAgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(15;360 410 8460 34179 52246)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408	3646			3277	protein-coding gene	gene with protein product		602210	eukaryotic translation initiation factor 3, subunit 6 48kDa	INT6, EIF3S6	NA	9403073, 9295280	Standard	NM_001568	NM_001568	NA	Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.723-2392C>T	chr8.hg19:g.109232081G>A		NA		hg19	CCDS6308.1	0.02	-0.105256	AAAxAAA	UNCOVERED																																																																																			NOVEL	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380612.2	4	3.911681	KEEP	0	0	0	13	402	GG	0.994391	0.139048	0		-	3	60	80	0	0	6.631863	8	60	288	40	ENST00000220849.5	0.272727	0.139832
KCNV1	27012	__UNKNOWN__	__UNKNOWN__	8	110977248	110977248	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:110977248T>C	ENST00000524391.1	-	0	5604							Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	NA		NA			potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			AGAAAGtggctaacacggtga	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794	27012		Potassium channels, Voltage-gated ion channels / Potassium channels	18861	protein-coding gene	gene with protein product		608164			NA	8670833, 16382104	Standard	NM_014379	NM_014379	NA	Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.*3069A>G	chr8.hg19:g.110977248T>C		NA	Q9UHJ4	hg19	CCDS6314.1	0.02	1.690145	GGCxAAC	COVERED																																																																																			NOVEL	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385525.1	29	16.304358	KEEP	0	2	62	76	2076	TT	1	0.999862	0		-	4	60	137	1	0	8.608199	81	70	2438	244	ENST00000524391.1	0.047059	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	111608626	111608626	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:111608626G>A			NA	NA				RP11-211F2.1 (246790 upstream) : RP11-238I10.1 (12843 downstream)						NA		NA									NA						cgcccgcctcggcctcccaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.111608626G>A		NA		hg19		0.02	-0.122068	CTCxGCC	COVERED																																																																																			NOVEL					0			11	5.414398	KEEP	8	0	0	18	522	GG	0.994391	0.19521	0			3	60	87	0	0	6.982677	11	60	337	49		0.214286	0.196312
TRPS1	7227	__UNKNOWN__	__UNKNOWN__	8	116627734	116627734	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:116627734C>T	ENST00000395715.3	-	3	1544				TRPS1_ENST00000220888.5_Intron|TRPS1_ENST00000520276.1_Intron|TRPS1_ENST00000519674.1_Intron|TRPS1_ENST00000519076.1_Intron	NM_001282902.1|NM_001282903.1|NM_014112.2	NP_001269831.1|NP_001269832.1|NP_054831.2	Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	NA		NA			chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			cggtggctcacgcctgtaatc	0.488		NA							Langer-Giedion syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447	7227		GATA zinc finger domain containing, Zinc fingers, C2H2-type	12340	protein-coding gene	gene with protein product		604386			NA	8530105, 10615131, 10647898	Standard	NM_014112	NM_001282903	NA	Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000395715.3:c.966+3624G>A	chr8.hg19:g.116627734C>T		NA	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	hg19	CCDS6318.2	0.02	-0.166656	TCAxGCC	COVERED																																																																																			NOVEL	TRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286435.3	8	4.512819	KEEP	1	0	0	15	442	CC	0.99649	0.352705	0		-	3	60	87	0	0	6.779249	13	60	426	47	ENST00000395715.3	0.1875	0.353947
LINC00536	100859921	__UNKNOWN__	__UNKNOWN__	8	117000972	117000972	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:117000972A>G	ENST00000505156.2	-	0	1558					NR_046215.1				long intergenic non-protein coding RNA 536	NA		NA									NA						caaagtgctgagattacaggc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC040336		8q23.3	2012-10-12			ENSG00000249917	ENSG00000249917	100859921		Long non-coding RNAs	43645	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_046215	NA	Approved		uc031tcc.1		OTTHUMG00000164936	ENST00000505156.2:	chr8.hg19:g.117000972A>G		NA		hg19		0.02	-0.166666	CTGxGAT	COVERED																																																																																			NOVEL	LINC00536-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000381020.1	7	2.40637	KEEP	1	0	0	8	225	AA	0.99257	0.351317	0		-	3	60	103	0	0	8.378641	13	60	408	40	ENST00000505156.2	0.1875	0.353947
UTP23	84294	__UNKNOWN__	__UNKNOWN__	8	117819397	117819397	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:117819397A>G	ENST00000517820.1	+	1	220				UTP23_ENST00000520733.1_Intron			Q9BRU9	UTP23_HUMAN	UTP23, small subunit (SSU) processome component, homolog (yeast)	NA		NA			rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	12						tcaggagttcaagaccagcct	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6320.1	8q24.11	2008-06-12	2008-06-12	2008-06-12		ENSG00000147679	84294			28224	protein-coding gene	gene with protein product		NA	chromosome 8 open reading frame 53	C8orf53	NA	16769905	Standard	NM_032334	NM_032334	NA	Approved	MGC14595	uc003yoc.3	Q9BRU9		ENST00000517820.1:c.188+40367A>G	chr8.hg19:g.117819397A>G		NA	B2RE25|Q96NJ8	hg19		0.02	-0.113981	TTCxAGA	UNCOVERED																																																																																			NOVEL	UTP23-008	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000381179.1	6	2.40651	KEEP	2	0	0	8	227	AA	0	0	0		+	3	60	88	0	0	7.301483	9	60	252	25	ENST00000517820.1	0.25	0.162467
EXT1	2131	__UNKNOWN__	__UNKNOWN__	8	118839825	118839825	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:118839825A>G	ENST00000378204.2	-	4	2091					NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	NA		NA			axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			aggccgaggcaggcagatcac	0.517		NA	Mis, N, F, S			exostoses, osteosarcoma			Langer-Giedion syndrome;Hereditary Multiple Exostoses												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2131	2.4.1.224, 2.4.1.225	Exostosin glycosyltransferase family	3512	protein-coding gene	gene with protein product	Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase, N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase	608177	Langer-Giedion syndrome chromosome region, exostoses (multiple) 1, exostosin 1	LGCR, LGS	NA		Standard	NM_000127	NM_000127	NA	Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1284+2643T>C	chr8.hg19:g.118839825A>G		NA	B2R7V2|Q9BVI9	hg19	CCDS6324.1	0.02	-0.201725	GGCxGGC	COVERED																																																																																			NOVEL	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132768.3	7	3.609566	KEEP	4	0	0	12	338	AA	0.99254	0.486885	0		-	3	60	92	0	0	6.893251	18	60	545	62	ENST00000378204.2	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	119933517	119933517	__UNKNOWN__	IGR	SNP	C	C	T	rs147144922	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:119933517C>T			NA	NA				SAMD12 (299325 upstream) : TNFRSF11B (2278 downstream)						NA		NA									NA						TAAGTCAggccgggcgcggtg	0.522		NA											-|||	280	0.0559105	0.0204	0.0274	5008	,	,	NA	13392	0.1359	NA	0.0219	False	NA	,,,	NA	NA	NA	2504	0.0767	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.119933517C>T		NA		hg19		0.02	-0.157881	GGCxGGG	COVERED																																																																																			NOVEL					0			4	2.573662	KEEP	27	2	49	26	758	CC	0.992708	0.320453	0			5	60	145	0	0	12.738254	10	60	328	68		0.333333	0.322807
DEPTOR	64798	__UNKNOWN__	__UNKNOWN__	8	121041914	121041914	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:121041914C>T	ENST00000286234.5	+	9	1231				DEPTOR_ENST00000518057.1_Intron|DEPTOR_ENST00000523492.1_Intron	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	NA		NA			intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						ggattacaggcgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792	64798			22953	protein-coding gene	gene with protein product		612974	DEP domain containing 6	DEPDC6	NA	19446321	Standard	NM_022783	NM_022783	NA	Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.1102-19901C>T	chr8.hg19:g.121041914C>T		NA	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	hg19	CCDS6331.1	0.02	-0.324506	AGGxGTG	COVERED																																																																																			NOVEL	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381601.1	11	3.610471	KEEP	1	0	0	12	362	CC	0.993072	0.846082	0		+	4	60	101	0	0	6.727886	29	60	958	78	ENST00000286234.5	0.121212	0.851984
RP11-760H22.2	0	__UNKNOWN__	__UNKNOWN__	8	121068093	121068093	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:121068093G>A	ENST00000574086.1	+	0	245										NA		NA									NA						tcaccatgttggccaggatgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000574086.1:	chr8.hg19:g.121068093G>A		NA		hg19		0.02	-0.149128	GTTxGCC	COVERED																																																																																			NOVEL	RP11-760H22.2-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000438120.1	10	3.606032	KEEP	4	0	0	12	342	GG	0.993072	0.32057	0		+	3	60	85	0	0	6.492189	14	60	488	46	ENST00000574086.1	0.176471	0.322807
COL14A1	7373	__UNKNOWN__	__UNKNOWN__	8	121297689	121297689	__UNKNOWN__	Intron	SNP	C	C	T	rs4871055	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:121297689C>T	ENST00000297848.3	+	33	4237				COL14A1_ENST00000247781.3_Intron|COL14A1_ENST00000309791.4_Intron	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1	NA		NA								NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			ggtgacagagcgagactccat	0.458		NA											C|||	3112	0.621406	0.7602	0.5922	5008	,	,	NA	10569	0.5794	NA	0.5775	False	NA	,,,	NA	NA	NA	2504	0.5429	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955	7373		Collagens, Fibronectin type III domain containing	2191	protein-coding gene	gene with protein product		120324	undulin	UND	NA	1716629, 9427527	Standard	NM_021110	NM_021110	NA	Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3968-411C>T	chr8.hg19:g.121297689C>T		NA		hg19	CCDS34938.1	0.02	-0.078939	GAGxGAG	UNCOVERED																																																																																			NOVEL	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313657.2	9	2.406921	KEEP	12	0	0	8	237	CC	0	0	0		+	4	40	117	0	0	11.199289	4	60	131	25	ENST00000297848.3	0.5	0.077336
COL14A1	7373	__UNKNOWN__	__UNKNOWN__	8	121340272	121340272	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:121340272A>G	ENST00000297848.3	+	41	4929				COL14A1_ENST00000247781.3_Intron|COL14A1_ENST00000309791.4_Intron	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1	NA		NA								NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			caaagtgctgagattacaggc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955	7373		Collagens, Fibronectin type III domain containing	2191	protein-coding gene	gene with protein product		120324	undulin	UND	NA	1716629, 9427527	Standard	NM_021110	NM_021110	NA	Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4660-4108A>G	chr8.hg19:g.121340272A>G		NA		hg19	CCDS34938.1	0.02	-0.148118	CTGxGAT	COVERED																																																																																			NOVEL	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313657.2	9	3.308524	KEEP	0	0	0	11	307	AA	0.993072	0.289978	0		+	3	60	98	0	0	7.890007	13	60	366	36	ENST00000297848.3	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	122491636	122491636	__UNKNOWN__	IGR	SNP	G	G	A	rs13260680	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:122491636G>A			NA	NA				AC027238.1 (292504 upstream) : AC022909.1 (63500 downstream)						NA		NA									NA						ccgcctcctgggttcaagcga	0.488		NA											G|||	2208	0.440895	0.652	0.2421	5008	,	,	NA	15312	0.3591	NA	0.329	False	NA	,,,	NA	NA	NA	2504	0.4959	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.122491636G>A		NA		hg19		0.02	-0.035089	CTGxGTT	UNCOVERED																																																																																			NOVEL					0			7	2.407133	KEEP	6	0	0	8	243	GG	0	0	0			2	60	65	0	0	6.62458	1	8	36	19		0.666667	0.019982
DERL1	79139	__UNKNOWN__	__UNKNOWN__	8	124032492	124032492	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:124032492A>G	ENST00000259512.4	-	7	807				DERL1_ENST00000523036.1_Intron|DERL1_ENST00000405944.3_Intron|DERL1_ENST00000519018.1_Intron|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000419562.2_Intron	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	NA		NA			endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			ggccaaggtgagcggatcatt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986	79139			28454	protein-coding gene	gene with protein product		608813	Der1-like domain family, member 1		NA	12975309, 15215855	Standard	NM_024295	NM_024295	NA	Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.507-947T>C	chr8.hg19:g.124032492A>G		NA	B3KW41|E9PH19	hg19	CCDS6337.1	0.02	-0.192963	GTGxGCG	COVERED																																																																																			NOVEL	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381714.2	8	2.706924	KEEP	0	0	0	9	248	AA	0.99254	0.454342	0		-	3	60	95	0	0	7.192584	18	60	553	46	ENST00000259512.4	0.142857	0.457757
FAM83A	84985	__UNKNOWN__	__UNKNOWN__	8	124206992	124206992	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:124206992A>G	ENST00000518448.1	+	4	2787				FAM83A_ENST00000536633.1_Intron|FAM83A_ENST00000546351.1_Intron|FAM83A_ENST00000318462.6_Intron|FAM83A_ENST00000276699.6_Intron|FAM83A_ENST00000522648.1_Intron			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	NA		NA								breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			caaagtgctgagattagaggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689	84985			28210	protein-coding gene	gene with protein product		NA			NA	22886303	Standard	NM_032899	XM_005251087	NA	Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.773+604A>G	chr8.hg19:g.124206992A>G		NA	Q71HL2|Q8N7I1|Q96I47	hg19	CCDS6340.1	0.02	-0.201733	CTGxGAT	COVERED																																																																																			NOVEL	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381737.1	8	4.812709	KEEP	0	0	0	16	449	AA	0.997832	0.489481	0		+	3	60	103	0	0	8.133187	16	60	483	59	ENST00000518448.1	0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	124302767	124302767	__UNKNOWN__	IGR	SNP	G	G	A	rs565971818		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:124302767G>A			NA	NA				ZHX1 (14986 upstream) : ATAD2 (29322 downstream)						NA		NA									NA						ggctgggcgcggtggctcacg	0.537		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17436	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.124302767G>A		NA		hg19		0.02	1.249694	CGCxGTG	COVERED																																																																																			NOVEL					0			15	6.917474	KEEP	0	0	0	23	670	GG	0.999892	0.990857	0			5	60	147	0	0	9.774589	51	60	1652	124		0.089286	0.990964
ATAD2	29028	__UNKNOWN__	__UNKNOWN__	8	124339351	124339351	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:124339351A>G	ENST00000521903.1	-	26	4206				ATAD2_ENST00000287394.5_Intron			Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	NA		NA			ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			gtttcaccatataggccaggc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802	29028		ATPases / AAA-type	30123	protein-coding gene	gene with protein product		611941			NA	12477932	Standard	NM_014109	NM_014109	NA	Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000521903.1:c.1822+1078T>C	chr8.hg19:g.124339351A>G		NA	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	hg19		0.02	-0.035084	CATxTAG	UNCOVERED																																																																																			NOVEL	ATAD2-002	PUTATIVE	upstream_uORF|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000381767.2	4	2.405859	KEEP	1	0	0	8	216	AA	0	0	0		-	2	45	72	0	0	6.950496	2	60	55	15	ENST00000521903.1	0.5	0.019982
WDYHV1	55093	__UNKNOWN__	__UNKNOWN__	8	124449469	124449469	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:124449469G>T	ENST00000523356.1	+	5	440	c.403G>T	c.(403-405)Gca>Tca	p.A135S	WDYHV1_ENST00000523984.1_Missense_Mutation_p.A75S|WDYHV1_ENST00000287387.2_Missense_Mutation_p.A135S|WDYHV1_ENST00000518125.1_5'UTR|WDYHV1_ENST00000517609.1_3'UTR			Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	135		NA			cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)	p.A135S(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						AGTGATCCGTGCAGATTCATA	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	lung(1)											76	77	77			NA	NA	8		NA											NA				124449469		2203	4300	6503	SO:0001583	missense			AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795	55093			25490	protein-coding gene	gene with protein product		NA	chromosome 8 open reading frame 32	C8orf32	NA	12477932	Standard	NM_018024	NM_018024	NA	Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000523356.1:c.403G>T	chr8.hg19:g.124449469G>T	ENSP00000428615:p.Ala135Ser	NA	B4DE68|Q9NW95	hg19		0.02	1.379677	CGTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.0	4.087307	0.76642	.	.	ENSG00000156795	ENST00000287387;ENST00000523984;ENST00000523356	T;T;T	0.19669	2.13;2.13;2.13	5.48	5.48	0.80851	Protein N-terminal glutamine amidohydrolase, alpha beta roll (1);Protein N-terminal glutamine amidohydrolase (1);	0.057106	0.64402	D	0.000001	T	0.53981	0.1830	M	0.89601	3.045	0.80722	D	1	P	0.51537	0.946	D	0.64042	0.921	T	0.60816	-0.7188	10	0.52906	T	0.07	-6.2969	18.1223	0.89576	0.0:0.0:1.0:0.0	.	135	Q96HA8	NTAQ1_HUMAN	S	135;75;135	ENSP00000287387:A135S;ENSP00000430427:A75S;ENSP00000428615:A135S	ENSP00000287387:A135S	A	+	1	0	WDYHV1	124518650	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	6.168000	0.71908	2.567000	0.86603	0.591000	0.81541	GCA	NOVEL	WDYHV1-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000381779.1	0	4.513602	KEEP	0	0	0	15	464	GG	0.99649	0.99581	0		+	15	60	459	0	0	36.384677	64	60	2217	154	ENST00000523356.1	0.189873	0.999317
FER1L6	654463	__UNKNOWN__	__UNKNOWN__	8	124914224	124914224	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:124914224A>G	ENST00000522917.1	+	1	199					NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	NA		NA				integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			ctccccaagtactgggattac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814	654463			28065	protein-coding gene	gene with protein product		NA	fer-1-like 6 (C. elegans)		NA		Standard	NM_001039112	NM_001039112	NA	Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.-8+49799A>G	chr8.hg19:g.124914224A>G		NA		hg19	CCDS43767.1	0.02	-0.113893	AGTxCTG	COVERED																																																																																			NOVEL	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381400.1	9	2.705154	KEEP	1	0	0	9	237	AA	0.99254	0.194847	0		+	3	60	98	0	0	8.303286	9	60	248	32	ENST00000522917.1	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	125264677	125264677	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:125264677A>G			NA	NA				RP11-37N22.1 (5038 upstream) : RNU6-756P (8209 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.125264677A>G		NA		hg19		0.02	-0.236783	CACxCCT	COVERED																																																																																			NOVEL					0			7	2.705611	KEEP	0	0	0	9	245	AA	0.99254	0.636563	0			3	60	93	0	0	6.865641	20	60	571	47		0.130435	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	125763625	125763625	__UNKNOWN__	IGR	SNP	A	A	G	rs368986051	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:125763625A>G			NA	NA				MTSS1 (22895 upstream) : RP11-1082L8.4 (60234 downstream)						NA		NA									NA						tcaggagatcaagaccatcct	0.532		NA											A|||	7	0.00139776	0.0	0.0014	5008	,	,	NA	6481	0.0	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.125763625A>G		NA		hg19		0.02	-0.13154	ATCxAGA	UNCOVERED																																																																																			NOVEL					0			5	3.007119	KEEP	7	0	0	10	270	AA	0	0	0			3	43	91	0	0	7.373415	11	44	312	41		0.214286	0.229173
NSMCE2	286053	__UNKNOWN__	__UNKNOWN__	8	126296134	126296134	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:126296134G>A	ENST00000287437.3	+	6	634				NSMCE2_ENST00000517315.1_Intron|NSMCE2_ENST00000522563.1_Intron	NM_173685.2	NP_775956.1	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog (S. cerevisiae)	NA		NA			cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|protein sumoylation (GO:0016925)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			breast(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	9	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			agtggctcacgcctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057002	CCDS6356.1	8q24.13	2013-01-28	2006-12-21	2006-07-05	ENSG00000156831	ENSG00000156831	286053		Zinc fingers, MIZ-type	26513	protein-coding gene	gene with protein product	zinc finger, MIZ-type containing 7	NA	chromosome 8 open reading frame 36, non-SMC element 2 homolog (MMS21, S. cerevisiae)	C8orf36	NA	12477932	Standard	NM_173685	NM_173685	NA	Approved	FLJ32440, MMS21, NSE2, ZMIZ7	uc003yrw.2	Q96MF7	OTTHUMG00000164993	ENST00000287437.3:c.419-73327G>A	chr8.hg19:g.126296134G>A		NA	Q8N549	hg19	CCDS6356.1	0.02	-0.201626	CACxCCT	UNCOVERED																																																																																			NOVEL	NSMCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381378.1	8	2.406613	KEEP	4	0	0	8	232	GG	0	0	0		+	3	60	88	0	0	6.4287	19	60	607	52	ENST00000287437.3	0.136364	0.490544
NSMCE2	286053	__UNKNOWN__	__UNKNOWN__	8	126296150	126296150	__UNKNOWN__	Intron	SNP	T	T	C	rs562373975	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:126296150T>C	ENST00000287437.3	+	6	634				NSMCE2_ENST00000517315.1_Intron|NSMCE2_ENST00000522563.1_Intron	NM_173685.2	NP_775956.1	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog (S. cerevisiae)	NA		NA			cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|protein sumoylation (GO:0016925)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			breast(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	9	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			aatcccagcattttgggaggc	0.483		NA											T|||	3	0.000599042	0.0	0.0	5008	,	,	NA	16672	0.003	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057002	CCDS6356.1	8q24.13	2013-01-28	2006-12-21	2006-07-05	ENSG00000156831	ENSG00000156831	286053		Zinc fingers, MIZ-type	26513	protein-coding gene	gene with protein product	zinc finger, MIZ-type containing 7	NA	chromosome 8 open reading frame 36, non-SMC element 2 homolog (MMS21, S. cerevisiae)	C8orf36	NA	12477932	Standard	NM_173685	NM_173685	NA	Approved	FLJ32440, MMS21, NSE2, ZMIZ7	uc003yrw.2	Q96MF7	OTTHUMG00000164993	ENST00000287437.3:c.419-73311T>C	chr8.hg19:g.126296150T>C		NA	Q8N549	hg19	CCDS6356.1	0.02	-0.228006	GCAxTTT	COVERED																																																																																			NOVEL	NSMCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381378.1	10	3.007753	KEEP	4	0	0	10	278	TT	0.99254	0.578582	0		+	4	60	133	0	0	10.513892	20	60	583	58	ENST00000287437.3	0.166667	0.58293
NSMCE2	286053	__UNKNOWN__	__UNKNOWN__	8	126371274	126371274	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:126371274C>T	ENST00000287437.3	+	7	842				NSMCE2_ENST00000517315.1_Intron|NSMCE2_ENST00000522563.1_Intron	NM_173685.2	NP_775956.1	Q96MF7	NSE2_HUMAN	non-SMC element 2, MMS21 homolog (S. cerevisiae)	NA		NA			cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|protein sumoylation (GO:0016925)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)			breast(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	9	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			tttgggaggccgaggcgggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057002	CCDS6356.1	8q24.13	2013-01-28	2006-12-21	2006-07-05	ENSG00000156831	ENSG00000156831	286053		Zinc fingers, MIZ-type	26513	protein-coding gene	gene with protein product	zinc finger, MIZ-type containing 7	NA	chromosome 8 open reading frame 36, non-SMC element 2 homolog (MMS21, S. cerevisiae)	C8orf36	NA	12477932	Standard	NM_173685	NM_173685	NA	Approved	FLJ32440, MMS21, NSE2, ZMIZ7	uc003yrw.2	Q96MF7	OTTHUMG00000164993	ENST00000287437.3:c.626+1214C>T	chr8.hg19:g.126371274C>T		NA	Q8N549	hg19	CCDS6356.1	0.02	-0.184198	GGCxGAG	COVERED																																																																																			NOVEL	NSMCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381378.1	3	3.008466	KEEP	2	0	0	10	299	CC	0.992708	0.42039	0		+	3	60	86	0	0	6.434331	16	60	512	51	ENST00000287437.3	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	126434203	126434203	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:126434203T>C			NA	NA				NSMCE2 (54841 upstream) : TRIB1 (8359 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.126434203T>C		NA		hg19		0.02	-0.315737	TCAxGCC	COVERED																																																																																			NOVEL					0			12	2.405919	KEEP	3	0	0	8	219	TT	0.99257	0.812384	0			5	60	170	0	0	13.153644	30	60	891	66		0.142857	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	126658009	126658009	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:126658009T>C			NA	NA				RP11-136O12.2 (115281 upstream) : RP11-697B24.1 (103289 downstream)						NA		NA									NA						tgagccactgtgcccggccTA	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.126658009T>C		NA		hg19		0.02	-0.1754	CTGxGCC	COVERED																																																																																			NOVEL					0			5	3.007895	KEEP	0	0	0	10	281	TT	0.992708	0.384582	0			3	60	92	0	0	7.111113	15	60	445	43		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	126701672	126701672	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:126701672A>G			NA	NA				RP11-136O12.2 (158944 upstream) : RP11-697B24.1 (59626 downstream)						NA		NA									NA						gggttcaagcaattctcctgc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.126701672A>G		NA		hg19		0.02	-0.21922	AGCxATT	COVERED																																																																																			NOVEL					0			11	3.307322	KEEP	3	0	0	11	290	AA	0.992708	0.548856	0			4	60	117	0	0	9.080797	18	60	503	45		0.181818	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	127961320	127961320	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:127961320T>C			NA	NA				RP11-351C8.1 (158438 upstream) : PCAT1 (64078 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.127961320T>C		NA		hg19		0.02	-0.219253	TCAxGCC	COVERED																																																																																			NOVEL					0			8	3.007938	KEEP	2	0	0	10	282	TT	0.992708	0.548856	0			3	60	102	0	0	7.705593	21	60	612	54		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	128574552	128574552	__UNKNOWN__	IGR	SNP	G	G	A	rs56310971	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:128574552G>A			NA	NA				CASC8 (80168 upstream) : CASC11 (124035 downstream)						NA		NA									NA						acacacacacgcacacacaca	0.507		NA											A|||	886	0.176917	0.3041	0.1715	5008	,	,	NA	17560	0.0258	NA	0.2207	False	NA	,,,	NA	NA	NA	2504	0.1196	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.128574552G>A		NA		hg19		0.02	-0.192927	CACxCAC	COVERED																																																																																			NOVEL					0			5	2.706766	KEEP	0	0	0	9	250	GG	0.99254	0.454342	0			4	60	119	0	0	9.463697	16	60	522	47		0.2	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	128774281	128774281	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:128774281A>G			NA	NA				MYC (20607 upstream) : PVT1 (33926 downstream)						NA		NA									NA						aggagtttgaaaccagcctgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.128774281A>G		NA		hg19		0.02	-0.078353	TGAxACC	UNCOVERED																																																																																			NOVEL					0			6	2.405433	KEEP	2	0	0	8	211	AA	0	0	0			3	60	74	0	0	6.355386	6	60	157	23		0.333333	0.077336
ASAP1	50807	__UNKNOWN__	__UNKNOWN__	8	131167863	131167863	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:131167863G>A	ENST00000518721.1	-	13	1238				ASAP1_ENST00000357668.1_Intron	NM_001247996.1|NM_018482.3	NP_001234925.1|NP_060952.2	Q9ULH1	ASAP1_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 1	NA		NA			cilium morphogenesis (GO:0060271)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(22)|ovary(6)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	68						aaagtgttgggattacaggca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033075	CCDS6362.1, CCDS75788.1	8q24.1-q24.2	2013-01-11	2008-09-22	2008-09-22	ENSG00000153317	ENSG00000153317	50807		ADP-ribosylation factor GTPase activating proteins, Pleckstrin homology (PH) domain containing, Ankyrin repeat domain containing	2720	protein-coding gene	gene with protein product	centaurin, beta 4	605953	development and differentiation enhancing factor 1	DDEF1	NA	9819391	Standard	NM_018482	NM_018482	NA	Approved	PAP, KIAA1249, ZG14P, CENTB4	uc003yta.2	Q9ULH1	OTTHUMG00000164772	ENST00000518721.1:c.1011-2812C>T	chr8.hg19:g.131167863G>A		NA	B2RNV3	hg19	CCDS6362.1	0.02	-0.228055	TGGxATT	COVERED																																																																																			NOVEL	ASAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380170.1	8	2.708088	KEEP	1	0	0	9	279	GG	0.99254	0.578582	0		-	4	60	100	0	0	7.216326	20	60	685	51	ENST00000518721.1	0.166667	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	132571823	132571823	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:132571823T>C			NA	NA				SNORA72 (126707 upstream) : EFR3A (344511 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.132571823T>C		NA		hg19		0.02	-0.105257	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			2	3.608799	KEEP	3	0	0	12	328	TT	0.99254	0.138789	0			3	60	105	0	0	9.443786	6	60	179	39		0.333333	0.139832
TG	7038	__UNKNOWN__	__UNKNOWN__	8	133902078	133902078	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:133902078A>G	ENST00000220616.4	+	10	2801				TG_ENST00000377869.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	NA		NA			hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		ctggagtgcaatggagcgatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832	7038			11764	protein-coding gene	gene with protein product		188450			NA		Standard	NM_003235	NM_003235	NA	Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2761+1265A>G	chr8.hg19:g.133902078A>G		NA	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	hg19	CCDS34944.1	0.02	-0.026316	GCAxTGG	UNCOVERED																																																																																			NOVEL	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379606.1	8	2.706802	KEEP	0	0	0	9	246	AA	0.99254	0	0		+	2	60	68	0	0	6.924809	1	60	31	14	ENST00000220616.4	0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	134762954	134762954	__UNKNOWN__	IGR	SNP	A	A	G	rs2958826	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:134762954A>G			NA	NA				SNORA40 (105986 upstream) : CTD-2588J1.1 (20697 downstream)						NA		NA									NA						tgatccacccacctcggcctc	0.527		NA											-|||	3983	0.795327	0.8026	0.7795	5008	,	,	NA	15157	0.6558	NA	0.9225	False	NA	,,,	NA	NA	NA	2504	0.8098	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.134762954A>G		NA		hg19		0.02	-0.148677	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			12	3.609036	KEEP	19	0	0	12	329	AA	0	0	0			7	60	189	0	0	17.444393	9	60	273	54		0.4375	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	134981829	134981829	__UNKNOWN__	IGR	SNP	T	T	C	rs567596783	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:134981829T>C			NA	NA				RP11-157E21.1 (67179 upstream) : RP11-513H8.1 (242278 downstream)						NA		NA									NA						ggcgcggtggttcacgcctgt	0.498		NA											T|||	7	0.00139776	0.0008	0.0	5008	,	,	NA	15622	0.002	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.134981829T>C		NA		hg19		0.02	-0.140322	TGGxTCA	COVERED																																																																																			NOVEL					0			7	3.307968	KEEP	3	0	0	11	298	TT	0.99254	0.259018	0			3	60	102	0	0	8.473087	11	60	315	38		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	135381344	135381344	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:135381344A>G			NA	NA				RP11-513H8.1 (48654 upstream) : ZFAT (108686 downstream)						NA		NA									NA						caaagtgctgagattacaggt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.135381344A>G		NA		hg19		0.02	-0.19296	CTGxGAT	COVERED																																																																																			NOVEL					0			8	3.008377	KEEP	2	0	0	10	289	AA	0.99254	0.454342	0			3	60	102	0	0	8.11007	15	60	456	50		0.166667	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	135759378	135759378	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:135759378T>C			NA	NA				CTD-2342N23.3 (23186 upstream) : AC083843.1 (44884 downstream)						NA		NA									NA						gttgcccaggttggagtgcag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.135759378T>C		NA		hg19		0.02	-0.139911	AGGxTGG	COVERED																																																																																			NOVEL					0			10	2.405333	KEEP	0	0	0	8	211	TT	0.99257	0.259026	0			4	60	117	0	0	9.82679	11	60	328	31		0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	136028067	136028067	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:136028067T>C			NA	NA				RP11-1057B8.2 (133925 upstream) : RP11-452N4.1 (218306 downstream)						NA		NA									NA						tgtggtggcttatgcctgtaa	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.136028067T>C		NA		hg19		0.02	-0.228024	GCTxATG	COVERED																																																																																			NOVEL					0			10	3.006136	KEEP	2	0	0	10	261	TT	0.99254	0.578582	0			4	60	135	0	0	10.794684	19	60	546	55		0.173913	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	137366128	137366128	__UNKNOWN__	IGR	SNP	T	T	C	rs61001770|rs71298298|rs9694120		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:137366128T>C			NA	NA				RP11-149P24.1 (187890 upstream) : RP11-431D12.1 (135562 downstream)						NA		NA									NA						tcttcttctttttcttcttct	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.137366128T>C		NA		hg19		0.02	-0.052481	CTTxTTC	UNCOVERED																																																																																			NOVEL					0			12	2.4057	KEEP	11	0	0	8	218	TT	0	0	0			4	60	139	0	1	14.750838	1	11	13	25		0.8	0.036766
RP11-489O18.1	0	__UNKNOWN__	__UNKNOWN__	8	139081446	139081446	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:139081446C>T	ENST00000521793.1	+	0	256				RP11-238K6.1_ENST00000518973.1_lincRNA						NA		NA									NA						cgtgagccaccgcacccggGC	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000521793.1:	chr8.hg19:g.139081446C>T		NA		hg19		0.02	-0.200768	CACxGCA	COVERED																																																																																			NOVEL	RP11-489O18.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000377598.1	8	3.309358	KEEP	1	0	0	11	325	CC	0.993072	0.487146	0		+	3	60	88	0	0	6.570058	17	60	537	54	ENST00000521793.1	0.15	0.490544
TRAPPC9	83696	__UNKNOWN__	__UNKNOWN__	8	141240485	141240485	__UNKNOWN__	Intron	SNP	A	A	G	rs4286928|rs386730821	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:141240485A>G	ENST00000389328.4	-	17	2740				TRAPPC9_ENST00000438773.2_Intron|TRAPPC9_ENST00000389327.3_Intron	NM_031466.5	NP_113654.4	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	NA		NA			cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						aggcaggtggatcgcctgagg	0.493		NA											A|||	3050	0.609026	0.5038	0.7565	5008	,	,	NA	19764	0.5317	NA	0.6948	False	NA	,,,	NA	NA	NA	2504	0.638	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632	83696		Trafficking protein particle complex	30832	protein-coding gene	gene with protein product	TRAPP 120 kDa subunit, tularik gene 1	611966			NA	11572484	Standard	NM_031466	NM_031466	NA	Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000389328.4:c.2726-8803T>C	chr8.hg19:g.141240485A>G		NA	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	hg19	CCDS34946.1	0.02	-0.078946	TGGxTCG	UNCOVERED																																																																																			NOVEL	TRAPPC9-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377711.3	6	2.405527	KEEP	6	0	0	8	217	AA	0	0	0		-	5	60	178	0	0	17.501019	4	60	116	26	ENST00000389328.4	0.555556	0.077336
AGO2	27161	__UNKNOWN__	__UNKNOWN__	8	141583556	141583556	__UNKNOWN__	Intron	SNP	C	C	T	rs530932377	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:141583556C>T	ENST00000220592.5	-	3	328				AGO2_ENST00000519980.1_Intron|AGO2_ENST00000517293.1_Intron	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)				NA						gaattacaggcgtgagccacc	0.493		NA											C|||	2	0.000399361	0.0	0.0	5008	,	,	NA	17013	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908	27161		Argonaute/PIWI family	3263	protein-coding gene	gene with protein product	argonaute 2	606229	eukaryotic translation initiation factor 2C, 2	EIF2C2	NA	10534406, 12906857	Standard		NM_012154	NA	Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.216-525G>A	chr8.hg19:g.141583556C>T		NA	Q8TCZ5|Q8WV58|Q96ID1	hg19	CCDS6380.1	0.02	-0.122792	AGGxGTG	COVERED																																																																																			NOVEL	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377866.4	5	2.406384	KEEP	0	0	0	8	231	CC	0.99257	0.194853	0		-	3	60	80	0	0	6.382092	10	60	324	30	ENST00000220592.5	0.230769	0.196312
AGO2	27161	__UNKNOWN__	__UNKNOWN__	8	141614617	141614617	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:141614617T>C	ENST00000220592.5	-	2	135				AGO2_ENST00000519980.1_Intron|AGO2_ENST00000517293.1_Intron	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)				NA						tggtgaaacctcatctctact	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908	27161		Argonaute/PIWI family	3263	protein-coding gene	gene with protein product	argonaute 2	606229	eukaryotic translation initiation factor 2C, 2	EIF2C2	NA	10534406, 12906857	Standard		NM_012154	NA	Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.23-19207A>G	chr8.hg19:g.141614617T>C		NA	Q8TCZ5|Q8WV58|Q96ID1	hg19	CCDS6380.1	0.02	-0.227936	ACCxCAT	COVERED																																																																																			NOVEL	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377866.4	18	7.218252	KEEP	1	0	0	24	664	TT	0.999909	0.582877	0		-	3	60	97	0	0	7.265898	20	60	601	66	ENST00000220592.5	0.130435	0.58293
PTK2	5747	__UNKNOWN__	__UNKNOWN__	8	141681809	141681809	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:141681809A>G	ENST00000430260.2	-	8	1097				PTK2_ENST00000340930.3_Intron|PTK2_ENST00000538769.1_Intron|PTK2_ENST00000522684.1_Intron|PTK2_ENST00000521059.1_Intron|PTK2_ENST00000519419.1_Intron|PTK2_ENST00000535192.1_Intron|PTK2_ENST00000517887.1_Intron|PTK2_ENST00000519465.1_Intron|PTK2_ENST00000395218.2_Intron			Q05397	FAK1_HUMAN	protein tyrosine kinase 2	NA		NA			angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			tcaggagatcaagaccatcct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	5747	2.7.10.1	Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	9611	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 71	600758	PTK2 protein tyrosine kinase 2		NA	8422239	Standard	NM_005607	NM_153831	NA	Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000430260.2:c.639+2587T>C	chr8.hg19:g.141681809A>G		NA	B4E2N6|F5H4S4|Q14291|Q9UD85	hg19		0.02	-0.131547	ATCxAGA	COVERED																																																																																			NOVEL	PTK2-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000378058.2	6	3.606434	KEEP	9	0	0	12	305	AA	0.99257	0.22747	0		-	3	60	88	0	0	7.073261	11	60	316	48	ENST00000430260.2	0.214286	0.229173
DENND3	22898	__UNKNOWN__	__UNKNOWN__	8	142166468	142166468	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:142166468T>C	ENST00000519811.1	+	8	1266				DENND3_ENST00000262585.2_Intron|DENND3_ENST00000424248.1_Intron			A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	NA		NA			cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			ggattacaggtgtgagccacc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339	22898		DENN/MADD domain containing, WD repeat domain containing	29134	protein-coding gene	gene with protein product		NA			NA	10048485	Standard	NM_014957	NM_014957	NA	Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000519811.1:c.1196+399T>C	chr8.hg19:g.142166468T>C		NA	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	hg19		0.02	-0.184179	AGGxGTG	COVERED																																																																																			NOVEL	DENND3-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000380189.3	5	3.007986	KEEP	3	0	0	10	281	TT	0.99254	0.420319	0		+	3	60	86	0	0	6.362709	17	60	517	52	ENST00000519811.1	0.15	0.423478
SLC45A4	57210	__UNKNOWN__	__UNKNOWN__	8	142314405	142314405	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:142314405G>C	ENST00000521804.1	-	1	197							Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	NA		NA			transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			AGActataatgccagcacttc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22					57210		Solute carriers	29196	protein-coding gene	gene with protein product		NA			NA		Standard	XM_050325	NM_001080431	NA	Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000521804.1:c.529+3789C>G	chr8.hg19:g.142314405G>C		NA	Q6ZRI2|Q9ULU3	hg19		0.02	-0.114041	AATxCCA	UNCOVERED																																																																																			NOVEL	SLC45A4-006	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000378941.1	6	2.407155	KEEP	0	0	0	8	244	GG	0.99257	0.16126	0		-	3	60	96	0	0	8.10094	9	60	302	28	ENST00000521804.1	0.25	0.162467
TSNARE1	203062	__UNKNOWN__	__UNKNOWN__	8	143455777	143455777	__UNKNOWN__	Intron	SNP	C	C	T	rs548541003	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:143455777C>T	ENST00000524325.1	-	2	137				TSNARE1_ENST00000307180.3_Intron|TSNARE1_ENST00000519651.1_Intron			Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	NA		NA			intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					cggtggctcacgcctgtaatc	0.507		NA											C|||	4	0.000798722	0.0008	0.0014	5008	,	,	NA	15135	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					8q24.3	2005-08-18					203062			26437	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_145003	XM_005250828	NA	Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000524325.1:c.39-19653G>A	chr8.hg19:g.143455777C>T		NA	B7ZLB0|Q14D03	hg19		0.02	-0.192974	TCAxGCC	COVERED																																																																																			NOVEL	TSNARE1-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000380678.1	5	4.510313	KEEP	1	0	0	15	415	CC	0.99649	0.45615	0		-	3	60	87	0	0	6.328084	19	60	619	51	ENST00000524325.1	0.136364	0.457757
LY6K	54742	__UNKNOWN__	__UNKNOWN__	8	143783297	143783297	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:143783297C>T	ENST00000519387.1	+	2	631				LY6K_ENST00000522591.1_3'UTR|LY6K_ENST00000292430.6_Intron|LY6K_ENST00000519390.1_Intron|LY6K_ENST00000561179.1_Intron|LY6K_ENST00000518841.1_Intron			Q17RY6	LY6K_HUMAN	lymphocyte antigen 6 complex, locus K	NA		NA				anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)	10	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ggtgtgatctcggctcactgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092545	CCDS6385.1, CCDS6385.2, CCDS59114.1	8q24.3	2009-08-06				ENSG00000160886	54742			24225	protein-coding gene	gene with protein product	cancer/testis antigen 97	615093			NA	12516096	Standard	NM_017527	NM_017527	NA	Approved	HSJ001348, FLJ35226, CT97	uc011ljv.2	Q17RY6		ENST00000519387.1:c.217+166C>T	chr8.hg19:g.143783297C>T		NA	G3V116|O15227|Q9BVD7	hg19	CCDS59114.1	0.02	1.131519	TCTxGGC	COVERED																																																																																			NOVEL	LY6K-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379957.2	31	4.898367	KEEP	1	6	157	72	2020	CC	1	0.999956	0		+	6	60	177	0	0	11.187644	78	60	2459	257	ENST00000519387.1	0.071429	0.999956
CTD-2292P10.4	0	__UNKNOWN__	__UNKNOWN__	8	143793861	143793861	__UNKNOWN__	RNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:143793861T>G	ENST00000520572.1	-	0	252					NR_038925.1					NA		NA									NA						ggaggccgagtcgggaagatc	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000520572.1:	chr8.hg19:g.143793861T>G		NA		hg19		0.02	1.941312	GAGxCGG	COVERED																																																																																			NOVEL	CTD-2292P10.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000379959.1	9	4.810306	KEEP	0	0	0	16	426	TT	0.997832	0.961684	0		-	5	60	174	0	0	12.775332	44	60	1307	101	ENST00000520572.1	0.102041	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	144180949	144180949	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:144180949T>C			NA	NA				RP11-520P18.5 (16531 upstream) : LY6H (58381 downstream)						NA		NA									NA						ccagcctgggtgacagagcaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.144180949T>C		NA		hg19		0.02	-0.140314	GGGxGAC	COVERED																																																																																			NOVEL					0			4	2.406472	KEEP	0	0	0	8	226	TT	0.99254	0.259018	0			4	45	119	0	0	10.171292	10	60	296	36		0.285714	0.260965
EPPK1	83481	__UNKNOWN__	__UNKNOWN__	8	144940290	144940290	__UNKNOWN__	Missense_Mutation	SNP	C	C	G	rs201976887		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:144940290C>G	ENST00000525985.1	-	2	7203	c.7132G>C	c.(7132-7134)Gac>Cac	p.D2378H				P58107	EPIPL_HUMAN	epiplakin 1	2378		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCGCTGGGGTCGGCCAGGACG	0.682		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C	HIS/ASP	51,4341	20.2+/-43.8	0,51,2145	315	292	300		7132	3.6	0.8	8		300	22,8530	7.1+/-27.0	0,22,4254	no	missense	EPPK1	NM_031308.1	81	0,73,6399	GG,GC,CC	NA	0.2572,1.1612,0.564	probably-damaging	2378/2420	144940290	73,12871	2196	4276	6472	SO:0001583	missense			AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150	83481			15577	protein-coding gene	gene with protein product	epidermal autoantigen 450K	607553			NA	11278896, 15671067	Standard	NM_031308	NM_031308	NA	Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7132G>C	chr8.hg19:g.144940290C>G	ENSP00000436337:p.Asp2378His	NA	Q76E58|Q9NSU9	hg19		0.02	11.610029	GGTxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279155	0.80692	0.011612	0.002572	ENSG00000227184	ENST00000525985	T	0.74737	-0.87	4.43	3.56	0.40772	.	.	.	.	.	D	0.83133	0.5188	M	0.89785	3.06	0.42176	D	0.991666	D	0.89917	1.0	D	0.91635	0.999	D	0.86316	0.1689	9	0.62326	D	0.03	.	10.4012	0.44231	0.0:0.9038:0.0:0.0962	.	2378	E9PPU0	.	H	2378	ENSP00000436337:D2378H	ENSP00000436337:D2378H	D	-	1	0	EPPK1	145012278	1.000000	0.71417	0.773000	0.31616	0.942000	0.58702	7.555000	0.82223	1.223000	0.43536	0.591000	0.81541	GAC	NOVEL	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000382675.1	0	12.028833	KEEP	3	0	0	40	1153	CC	1	1	0		-	27	60	913	0	0	64.030595	292	60	9352	555	ENST00000525985.1	0.084639	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	145173253	145173253	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:145173253T>C			NA	NA				KIAA1875 (35 upstream) : FAM203A (19418 downstream)						NA		NA									NA						Aggccgggtgtggtggctcac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.145173253T>C		NA		hg19		0.02	1.618477	GTGxGGT	COVERED																																																																																			NOVEL					0			33	7.851143	KEEP	5	3	84	56	1509	TT	1	0.999768	0			5	60	161	0	0	10.346053	76	60	2256	193		0.061728	0.999768
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	145591492	145591492	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:145591492C>T			NA	NA				SLC52A2 (6560 upstream) : ADCK5 (6033 downstream)						NA		NA									NA						agtgatccacctgcctcagcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.145591492C>T		NA		hg19		0.02	-0.228082	CACxTGC	COVERED																																																																																			NOVEL					0			6	3.008907	KEEP	0	0	0	10	308	CC	0.992708	0.578679	0			3	32	89	0	0	6.465526	20	60	693	51		0.130435	0.58293
ZNF7	7553	__UNKNOWN__	__UNKNOWN__	8	146058391	146058391	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:146058391A>T	ENST00000528130.1	+	2	176				ZNF7_ENST00000532393.1_Intron|ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000529819.1_Intron|ZNF7_ENST00000544249.1_Intron|ZNF7_ENST00000325241.6_Intron|ZNF7_ENST00000446747.2_Intron|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000528372.1_Intron			P17097	ZNF7_HUMAN	zinc finger protein 7	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		gagaccagccaggccaacatg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789	7553		Zinc fingers, C2H2-type, -	13139	protein-coding gene	gene with protein product		194531	zinc finger protein 7 (KOX 4, clone HF.16)		NA	2106481, 1946370	Standard	NM_003416	NM_003416	NA	Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528130.1:c.130+3402A>T	chr8.hg19:g.146058391A>T		NA	B4DT08|D3DWN6|P17015|Q8N8Y4	hg19		0.02	-0.131554	GCCxGGC	UNCOVERED																																																																																			NOVEL	ZNF7-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000382661.1	5	2.706971	KEEP	3	0	0	9	249	AA	0	0	0		+	3	60	87	0	0	6.97318	11	60	325	36	ENST00000528130.1	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	8	146178707	146178707	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr8:146178707A>G			NA	NA				ZNF16 (2433 upstream) : ZNF252P (20267 downstream)						NA		NA									NA						gtgagccaccacgcccggctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr8.hg19:g.146178707A>G		NA		hg19		0.02	-0.236638	ACCxCGC	COVERED																																																																																			NOVEL					0			11	2.404902	KEEP	0	0	0	8	206	AC	0.99254	0.607839	0			3	60	108	0	0	8.365808	20	60	563	50		0.130435	0.612407
C9orf66	157983	__UNKNOWN__	__UNKNOWN__	9	213291	213291	__UNKNOWN__	3'UTR	SNP	G	G	A	rs680144	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:213291G>A	ENST00000382387.2	-	0	2602					NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	NA		NA								central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CTGAAACCAGGAAGGAAGGCT	0.438		NA											A|||	1913	0.381989	0.4864	0.3516	5008	,	,	NA	16460	0.3254	NA	0.3569	False	NA	,,,	NA	NA	NA	2504	0.3466	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784	157983			26436	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152569	NM_152569	NA	Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.*1218C>T	chr9.hg19:g.213291G>A		NA	Q96NB0	hg19	CCDS6439.1	0.02	-0.298139	CAGxAAG	COVERED																																																																																			NOVEL	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055436.1	1	3.00868	KEEP	0	0	0	10	300	GG	0.992708	0.775364	0		-	10	60	276	0	0	23.57745	23	60	748	65	ENST00000382387.2	0.30303	0.78106
C9orf66	157983	__UNKNOWN__	__UNKNOWN__	9	213999	213999	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:213999C>T	ENST00000382387.2	-	0	1894					NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	NA		NA								central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		gtgctgggatcacaggcgtga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784	157983			26436	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152569	NM_152569	NA	Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.*510G>A	chr9.hg19:g.213999C>T		NA	Q96NB0	hg19	CCDS6439.1	0.02	-0.21052	GATxACA	COVERED																																																																																			NOVEL	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055436.1	2	4.814187	KEEP	0	0	0	16	487	CC	0.997832	0.521029	0		-	3	60	87	0	0	6.327932	19	60	634	57	ENST00000382387.2	0.136364	0.522161
DOCK8	81704	__UNKNOWN__	__UNKNOWN__	9	384805	384805	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:384805A>G	ENST00000469391.1	+	21	2653				DOCK8_ENST00000382329.1_Intron|DOCK8_ENST00000382331.1_Intron|DOCK8_ENST00000453981.1_Intron|DOCK8_ENST00000432829.2_Intron	NM_001190458.1|NM_001193536.1	NP_001177387.1|NP_001180465.1	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	NA		NA			blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		aatcccagctactcaggaggc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099	81704			19191	protein-coding gene	gene with protein product		611432			NA	11214971	Standard	XM_036307	NM_203447	NA	Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000469391.1:c.2574+2120A>G	chr9.hg19:g.384805A>G		NA	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	hg19	CCDS55284.1	0.02	-0.035064	GCTxCTC	UNCOVERED																																																																																			NOVEL	DOCK8-012	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354646.1	4	2.703812	KEEP	14	0	0	9	218	AC	0	0	0		+	2	22	67	0	0	6.451207	2	13	49	33	ENST00000469391.1	0.5	0.019982
KANK1	23189	__UNKNOWN__	__UNKNOWN__	9	730490	730490	__UNKNOWN__	Intron	SNP	G	G	A	rs141670064	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:730490G>A	ENST00000382303.1	+	8	3548				KANK1_ENST00000489369.1_Intron|KANK1_ENST00000382297.2_Intron|KANK1_ENST00000382293.3_Intron	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	NA		NA			negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		ccaggagttcgagaccagcct	0.527		NA											G|||	134	0.0267572	0.0923	0.013	5008	,	,	NA	17119	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104	23189		KN motif and ankyrin repeat domain containing, Ankyrin repeat domain containing	19309	protein-coding gene	gene with protein product		607704	ankyrin repeat domain 15	ANKRD15	NA	12133830, 17996375, 19554261	Standard	NM_015158	NM_015158	NA	Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.2896+242G>A	chr9.hg19:g.730490G>A		NA	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	hg19	CCDS34976.1	0.02	-0.412248	TTCxAGA	COVERED																																																																																			NOVEL	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051484.2	6	2.705119	KEEP	1	3	76	36	1060	GG	1	0.941741	0		+	4	60	109	0	0	6.95625	41	60	1312	104	ENST00000382303.1	0.088889	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	1059872	1059872	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:1059872G>A			NA	NA				DMRT2 (2320 upstream) : RNA5SP279 (273964 downstream)						NA		NA									NA						ggccgggcgcggtggctcacg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.1059872G>A		NA		hg19		0.02	-0.157893	CGCxGTG	COVERED																																																																																			NOVEL					0			4	2.707522	KEEP	3	0	0	9	268	GG	0.99257	0.320408	0			3	60	92	0	0	7.110233	15	60	489	45		0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	1074695	1074695	__UNKNOWN__	IGR	SNP	C	C	T	rs111272599		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:1074695C>T			NA	NA				DMRT2 (17143 upstream) : RNA5SP279 (259141 downstream)						NA		NA									NA						actacaggtgcccgccaccac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.1074695C>T		NA		hg19		0.02	-0.096488	GTGxCCG	UNCOVERED																																																																																			NOVEL					0			5	2.708379	KEEP	2	0	0	9	289	CC	0	0	0			3	52	90	0	0	7.778445	7	60	235	32		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	2715005	2715005	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:2715005A>G			NA	NA				VLDLR (54952 upstream) : KCNV2 (2496 downstream)						NA		NA									NA						ctcctgagtaactgggattac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.2715005A>G		NA		hg19		0.02	-0.052627	GTAxCTG	UNCOVERED																																																																																			NOVEL					0			0	3.007105	KEEP	0	0	0	10	271	AA	0.992708	0.036498	0			2	60	69	0	0	6.650479	2	60	56	22		0.5	0.036766
RFX3	5991	__UNKNOWN__	__UNKNOWN__	9	3424413	3424413	__UNKNOWN__	Intron	SNP	G	G	C	rs142545170	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:3424413G>C	ENST00000382004.3	-	3	304				RFX3_ENST00000302303.1_Intron	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	NA		NA			cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		ccaggctggagtgcagtggcg	0.507		NA											g|||	931	0.185903	0.3918	0.1628	5008	,	,	NA	8688	0.1319	NA	0.0785	False	NA	,,,	NA	NA	NA	2504	0.09	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298	5991			9984	protein-coding gene	gene with protein product		601337			NA	8289803	Standard	NM_002919	XM_005251534	NA	Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.8-28817C>G	chr9.hg19:g.3424413G>C		NA	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	hg19	CCDS6449.1	0.02	-0.07895	GGAxTGC	UNCOVERED																																																																																			NOVEL	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051545.1	7	3.309763	KEEP	18	0	0	11	336	GG	0	0	0		-	3	60	101	0	0	9.043458	6	40	198	42	ENST00000382004.3	0.333333	0.077336
RFX3	5991	__UNKNOWN__	__UNKNOWN__	9	3448706	3448706	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:3448706G>T	ENST00000382004.3	-	2	304				RFX3_ENST00000302303.1_Intron	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	NA		NA			cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		tttttgtaaggaaggaatctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298	5991			9984	protein-coding gene	gene with protein product		601337			NA	8289803	Standard	NM_002919	XM_005251534	NA	Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.7+41572C>A	chr9.hg19:g.3448706G>T		NA	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	hg19	CCDS6449.1	0.02	-0.096486	AAGxAAG	UNCOVERED																																																																																			NOVEL	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051545.1	7	2.406917	KEEP	0	0	0	8	239	GG	0.99257	0.119541	0		-	3	60	82	0	0	7.142852	6	60	201	24	ENST00000382004.3	0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	6031259	6031259	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:6031259C>T			NA	NA				RANBP6 (15641 upstream) : RP11-218I7.2 (16100 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.6031259C>T		NA		hg19		0.02	-0.114032	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			5	3.307478	KEEP	1	0	0	11	300	CC	0.992708	0.161282	0			3	60	83	0	0	6.932049	8	60	274	36		0.272727	0.162467
RP11-390F4.6	0	__UNKNOWN__	__UNKNOWN__	9	6657941	6657941	__UNKNOWN__	lincRNA	SNP	G	G	A	rs190268272	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:6657941G>A	ENST00000413145.1	+	0	130										NA		NA									NA						gattacaggcgtgagccacca	0.522		NA											G|||	9	0.00179712	0.0053	0.0029	5008	,	,	NA	14881	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000413145.1:	chr9.hg19:g.6657941G>A		NA		hg19		0.02	-0.219295	GGCxTGA	COVERED																																																																																			NOVEL	RP11-390F4.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000051688.1	6	3.008763	KEEP	1	0	0	10	302	GG	0.99254	0.548763	0		+	3	60	88	0	0	6.427783	19	60	624	51	ENST00000413145.1	0.136364	0.552887
KDM4C	23081	__UNKNOWN__	__UNKNOWN__	9	6817471	6817471	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:6817471T>C	ENST00000381309.3	+	4	1000				KDM4C_ENST00000536108.1_Intron|KDM4C_ENST00000489243.1_Intron|KDM4C_ENST00000381306.3_Intron|KDM4C_ENST00000535193.1_Intron|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000543771.1_Intron	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	NA		NA			histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						tcccaaagtgttgggattaca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077	23081		Chromatin-modifying enzymes / K-demethylases, Tudor domain containing	17071	protein-coding gene	gene with protein product	tudor domain containing 14C	605469	jumonji domain containing 2C	JMJD2C	NA	9872452, 15138608	Standard	NM_015061	NM_015061	NA	Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.435+2726T>C	chr9.hg19:g.6817471T>C		NA	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	hg19	CCDS6471.1	0.02	-0.280659	GTGxTGG	COVERED																																																																																			NOVEL	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051692.1	8	4.509475	KEEP	0	0	0	15	406	TT	0.99649	0.737075	0		+	3	60	97	0	0	6.945529	26	60	784	66	ENST00000381309.3	0.103448	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	8240440	8240440	__UNKNOWN__	IGR	SNP	G	G	C	rs62533916	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:8240440G>C			NA	NA				RP11-29B9.2 (279360 upstream) : PTPRD (73805 downstream)						NA		NA									NA						cagacctggtggtgggtgcct	0.527		NA											G|||	837	0.167133	0.2405	0.0706	5008	,	,	NA	16639	0.2292	NA	0.0915	False	NA	,,,	NA	NA	NA	2504	0.1503	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.8240440G>C		NA		hg19		0.02	-0.070131	GGTxGTG	UNCOVERED																																																																																			NOVEL					0			5	2.407131	KEEP	0	0	0	8	243	GG	0.99257	0.053735	0			4	60	116	0	0	11.426953	3	60	96	21		0.571429	0.054137
PTPRD	5789	__UNKNOWN__	__UNKNOWN__	9	8483763	8483763	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:8483763G>A	ENST00000381196.4	-	27	3957				PTPRD_ENST00000358503.5_Intron|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000540109.1_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000356435.5_Intron|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	NA		NA			heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		tgggtgacagggcgagactcc	0.458		NA								TSP Lung(15;0.13)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707	5789		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	9668	protein-coding gene	gene with protein product		601598			NA	7896816, 8355697	Standard		NM_002839	NA	Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3413+355C>T	chr9.hg19:g.8483763G>A		NA	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	hg19	CCDS43786.1	0.02	-0.157884	CAGxGCG	COVERED																																																																																			NOVEL	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055395.3	2	2.407329	KEEP	0	0	0	8	251	GG	0.99257	0.320408	0		-	3	36	88	0	0	6.792648	14	60	468	38	ENST00000381196.4	0.176471	0.322807
PTPRD	5789	__UNKNOWN__	__UNKNOWN__	9	9747796	9747796	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:9747796A>G	ENST00000381196.4	-	4	219				PTPRD_ENST00000463477.1_Intron	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	NA		NA			heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		caggtgatctacctgcctcgg	0.478		NA								TSP Lung(15;0.13)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707	5789		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	9668	protein-coding gene	gene with protein product		601598			NA	7896816, 8355697	Standard		NM_002839	NA	Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.325-13225T>C	chr9.hg19:g.9747796A>G		NA	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	hg19	CCDS43786.1	0.02	-0.149083	TCTxCCT	COVERED																																																																																			NOVEL	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055395.3	9	2.405166	KEEP	0	0	0	8	207	AA	0.99257	0.289832	0		-	3	60	96	0	0	7.679206	13	60	372	36	ENST00000381196.4	0.1875	0.292001
PTPRD	5789	__UNKNOWN__	__UNKNOWN__	9	10149981	10149981	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:10149981G>A	ENST00000463477.1	-	4	199							P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	NA		NA			heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		cacctgcctcggcctcccaaa	0.438		NA								TSP Lung(15;0.13)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707	5789		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	9668	protein-coding gene	gene with protein product		601598			NA	7896816, 8355697	Standard		NM_002839	NA	Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000463477.1:c.616-116191C>T	chr9.hg19:g.10149981G>A		NA	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	hg19		0.02	-0.061375	CTCxGCC	UNCOVERED																																																																																			NOVEL	PTPRD-001	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000055393.2	6	2.404001	KEEP	0	0	0	8	223	GG	0.99257	0.043461	0		-	3	60	92	1	0	8.555845	4	60	122	19	ENST00000463477.1	0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	12244090	12244090	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:12244090C>T			NA	NA				RP11-74C3.1 (84943 upstream) : RNU2-47P (56175 downstream)						NA		NA									NA						cgtgagccaccgtgcctggcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.12244090C>T		NA		hg19		0.02	-0.236819	CACxGTG	COVERED																																																																																			NOVEL					0			7	3.007976	KEEP	0	0	0	10	286	CC	0.992708	0.607941	0			3	60	94	0	0	6.965276	20	60	629	58		0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	12569375	12569375	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:12569375T>C			NA	NA				RNU2-47P (268924 upstream) : TYRP1 (124010 downstream)						NA		NA									NA						caggttcaagtgattctcctg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.12569375T>C		NA		hg19		0.02	-0.11401	AAGxGAT	UNCOVERED																																																																																			NOVEL					0			5	3.00602	KEEP	2	0	0	10	270	TT	0.99257	0.16126	0			3	60	95	1	0	8.001324	9	60	264	35		0.25	0.162467
RP11-3L8.3	0	__UNKNOWN__	__UNKNOWN__	9	12762875	12762875	__UNKNOWN__	RNA	SNP	G	G	A	rs529433170	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:12762875G>A	ENST00000417638.1	-	0	199										NA		NA									NA						gattacaggcgtaagccaccg	0.428		NA											G|||	15	0.00299521	0.0113	0.0	5008	,	,	NA	13357	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000417638.1:	chr9.hg19:g.12762875G>A		NA		hg19		0.02	-0.298262	GGCxTAA	COVERED																																																																																			NOVEL	RP11-3L8.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000051732.1	8	3.006266	KEEP	2	0	0	10	278	GG	0.99254	0.775233	0		-	3	60	94	0	0	6.598055	27	60	907	70	ENST00000417638.1	0.1	0.78106
LURAP1L	286343	__UNKNOWN__	__UNKNOWN__	9	12781096	12781096	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:12781096G>A	ENST00000319264.3	+	1	1007				RP11-3L8.3_ENST00000417638.1_RNA	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	NA		NA									NA						tcagcctcccgagtagctggg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714	286343			31452	protein-coding gene	gene with protein product	similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed	NA	chromosome 9 open reading frame 150	C9orf150	NA	12766061	Standard	NM_203403	NM_203403	NA	Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.312+5070G>A	chr9.hg19:g.12781096G>A		NA	Q5VZX7|Q8N923|Q8NCG2	hg19	CCDS6473.1	0.02	-0.12278	CCCxAGT	COVERED																																																																																			NOVEL	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051730.1	5	2.405139	KEEP	0	0	0	8	225	GG	0.99257	0.194853	0		+	3	60	83	0	0	6.68208	10	60	321	25	ENST00000319264.3	0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	14066486	14066486	__UNKNOWN__	IGR	SNP	A	A	G	rs199799143		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:14066486A>G			NA	NA				RP11-284P20.3 (36372 upstream) : NFIB (15355 downstream)						NA		NA									NA						gatcacttgaacccaggagtt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.14066486A>G		NA		hg19		0.02	-0.140325	TGAxCCC	COVERED																																																																																			NOVEL					0			10	2.405203	KEEP	1	0	0	8	211	AA	0.99257	0.259026	0			3	60	98	0	0	8.073138	11	60	323	33		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	15312554	15312554	__UNKNOWN__	IGR	SNP	G	G	A	rs532279276		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:15312554G>A			NA	NA				TTC39B (5196 upstream) : RN7SL157P (35611 downstream)						NA		NA									NA						ccagccgggcgcagtggctca	0.478		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	18094	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.15312554G>A		NA		hg19		0.02	-0.219292	GGCxCAG	COVERED																																																																																			NOVEL					0			8	3.608669	KEEP	1	0	0	12	328	GG	0.993634	0.549368	0			3	60	90	0	0	6.76126	17	60	538	55		0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	15325111	15325111	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:15325111T>C			NA	NA				TTC39B (17753 upstream) : RN7SL157P (23054 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.15325111T>C		NA		hg19		0.02	-0.245587	GCAxTTT	COVERED																																																																																			NOVEL					0			5	2.70693	KEEP	1	0	0	9	249	TT	0.99257	0.636582	0			6	60	191	0	0	16.102402	18	60	538	55		0.25	0.641347
SNAPC3	6619	__UNKNOWN__	__UNKNOWN__	9	15463316	15463316	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:15463316G>A	ENST00000380821.3	+	0	4864					NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	NA		NA			gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		tctgcctcccgggttcaagca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975	6619			11136	protein-coding gene	gene with protein product		602348	small nuclear RNA activating complex, polypeptide 3, 50kD		NA	9003788	Standard	NM_001039697	XR_428427	NA	Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.*3452G>A	chr9.hg19:g.15463316G>A		NA	D3DRI8|Q2VPI6|Q5T285	hg19	CCDS6478.1	0.02	-0.394667	CCCxGGT	COVERED																																																																																			NOVEL	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051763.2	8	4.242128	KEEP	5	1	28	24	673	GG	0.999892	0.92654	0		+	4	60	105	0	0	6.683057	38	60	1193	89	ENST00000380821.3	0.095238	0.92664
CCDC171	203238	__UNKNOWN__	__UNKNOWN__	9	15864551	15864551	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:15864551C>T	ENST00000380701.3	+	24	3796				CCDC171_ENST00000297641.3_Intron	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	NA		NA									NA						tgagtgagaacatgcggtgtt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989	203238			29828	protein-coding gene	gene with protein product	myosin tail domain containing protein	NA	chromosome 9 open reading frame 93	C9orf93	NA	14702039	Standard	NM_173550	NM_173550	NA	Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3469-9979C>T	chr9.hg19:g.15864551C>T		NA	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	hg19	CCDS6481.1	0.02	1.188299	GAAxATG	COVERED																																																																																			NOVEL	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051768.4	7	6.907463	KEEP	1	0	0	23	659	CC	0.999892	0.996125	0		+	7	60	187	0	0	12.219124	62	60	2031	110	ENST00000380701.3	0.101449	0.996233
CCDC171	203238	__UNKNOWN__	__UNKNOWN__	9	15864573	15864573	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:15864573C>T	ENST00000380701.3	+	24	3796				CCDC171_ENST00000297641.3_Intron	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	NA		NA									NA						ggttttttgtccttgcgatag	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989	203238			29828	protein-coding gene	gene with protein product	myosin tail domain containing protein	NA	chromosome 9 open reading frame 93	C9orf93	NA	14702039	Standard	NM_173550	NM_173550	NA	Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3469-9957C>T	chr9.hg19:g.15864573C>T		NA	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	hg19	CCDS6481.1	0.02	1.190409	TGTxCTT	COVERED																																																																																			NOVEL	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051768.4	12	8.124905	KEEP	1	0	0	27	858	CC	0.999988	0.999206	0		+	6	60	180	1	0	11.616634	74	60	2455	156	ENST00000380701.3	0.075	0.999218
BNC2	54796	__UNKNOWN__	__UNKNOWN__	9	16523235	16523235	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:16523235C>T	ENST00000380672.4	-	5	727				BNC2_ENST00000545497.1_Intron|BNC2_ENST00000380667.2_Intron|BNC2_ENST00000380666.2_Intron	NM_017637.5	NP_060107.3			basonuclin 2	NA		NA								NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		tttgggaggccgaggtgggtg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068	54796		Zinc fingers, C2H2-type	30988	protein-coding gene	gene with protein product		608669			NA	14702039	Standard	NM_017637	XM_006716784	NA	Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.669+29292G>A	chr9.hg19:g.16523235C>T		NA		hg19	CCDS6482.2	0.02	-0.131572	GGCxGAG	COVERED																																																																																			NOVEL	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216901.5	4	2.706905	KEEP	1	0	0	9	259	CC	0.99254	0.227464	0		-	3	60	88	0	0	7.432225	8	60	263	40	ENST00000380672.4	0.272727	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	16948502	16948502	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:16948502A>G			NA	NA				BNC2 (77716 upstream) : RP11-132E11.2 (100414 downstream)						NA		NA									NA						gcctcccaaaatgctgggatt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.16948502A>G		NA		hg19		0.02	-0.20172	AAAxTGC	UNCOVERED																																																																																			NOVEL					0			3	2.405112	KEEP	1	0	0	8	208	AA	0	0	0			3	60	90	0	0	6.693342	18	60	531	49		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	18430062	18430062	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:18430062G>A			NA	NA				RP11-570H19.2 (67844 upstream) : ADAMTSL1 (43829 downstream)						NA		NA									NA						tgctgggattgcaggcatgag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.18430062G>A		NA		hg19		0.02	-0.21054	ATTxCAG	COVERED																																																																																			NOVEL					0			6	3.911877	KEEP	1	0	0	13	406	GG	0.994391	0.519232	0			3	60	90	0	1	6.565469	20	60	692	59		0.130435	0.522161
ADAMTSL1	92949	__UNKNOWN__	__UNKNOWN__	9	18686144	18686144	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:18686144C>G	ENST00000276935.6	+	13	1574				ADAMTSL1_ENST00000380548.4_Intron			Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	NA		NA				proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		gtctcaaactcctgacctcaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031	92949		Immunoglobulin superfamily / I-set domain containing	14632	protein-coding gene	gene with protein product	punctin	609198	chromosome 9 open reading frame 94	C9orf94	NA	9628581, 11805097	Standard		NM_001040272	NA	Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000276935.6:c.1574+1346C>G	chr9.hg19:g.18686144C>G		NA	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	hg19		0.02	-0.149128	ACTxCTG	COVERED																																																																																			NOVEL	ADAMTSL1-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000051804.5	8	2.407286	KEEP	0	0	0	8	252	CC	0.99257	0.289832	0		+	3	59	99	0	0	7.978771	13	60	437	34	ENST00000276935.6	0.1875	0.292001
HAUS6	54801	__UNKNOWN__	__UNKNOWN__	9	19054549	19054549	__UNKNOWN__	3'UTR	SNP	T	T	G	rs151216206		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19054549T>G	ENST00000380502.3	-	0	5127					NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	NA		NA			centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AACAATGTGATTTTTACAAAT	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874	54801		HAUS augmin-like complex subunits	25948	protein-coding gene	gene with protein product		613433	family with sequence similarity 29, member A	FAM29A	NA	10997877, 19427217	Standard	NM_017645	NM_001270890	NA	Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.*1792A>C	chr9.hg19:g.19054549T>G		NA	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	hg19	CCDS6489.1	0.02	3.748651	TGAxTTT	COVERED																																																																																			NOVEL	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051825.1	5	7.350787	KEEP	0	1	30	35	979	TT	0.999999	0.999999	0		-	14	60	488	0	0	35.860029	123	60	3684	254	ENST00000380502.3	0.10219	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	19226504	19226504	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19226504T>C			NA	NA				PLIN2 (77216 upstream) : DENND4C (3928 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.19226504T>C		NA		hg19		0.02	-0.271807	TCAxGCC	COVERED																																																																																			NOVEL					0			3	3.609526	KEEP	2	0	0	12	340	TT	0.993072	0.712346	0			3	60	104	0	0	7.644379	26	60	740	71		0.103448	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	19229153	19229153	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19229153A>G			NA	NA				PLIN2 (79865 upstream) : DENND4C (1279 downstream)						NA		NA									NA						cgcccgcctcagcctcccaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.19229153A>G		NA		hg19		0.02	-0.245535	CTCxGCC	COVERED																																																																																			NOVEL					0			7	2.706809	KEEP	0	0	0	9	249	AA	0.99254	0.636563	0			3	60	104	0	0	8.027228	19	60	554	54		0.136364	0.641347
DENND4C	55667	__UNKNOWN__	__UNKNOWN__	9	19331481	19331481	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19331481A>G	ENST00000602925.1	+	17	2669				DENND4C_ENST00000380432.2_Intron|DENND4C_ENST00000434457.2_Intron	NM_017925.5	NP_060395.5	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	NA		NA			cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ttacaggcataagccactgca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145	55667		DENN/MADD domain containing	26079	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 55B, chromosome 9 open reading frame 55	C9orf55B, C9orf55	NA	12906859	Standard	NM_017925	NM_017925	NA	Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000602925.1:c.2254-495A>G	chr9.hg19:g.19331481A>G		NA	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	hg19	CCDS6491.3	0.02	-0.228027	CATxAGC	COVERED																																																																																			NOVEL	DENND4C-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000099627.4	7	2.405677	KEEP	1	0	0	8	214	AA	0.99257	0.578599	0		+	3	60	102	0	0	7.705587	21	60	613	52	ENST00000602925.1	0.125	0.58293
DENND4C	55667	__UNKNOWN__	__UNKNOWN__	9	19351753	19351753	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19351753C>T	ENST00000602925.1	+	24	4764				DENND4C_ENST00000380432.2_Intron|DENND4C_ENST00000434457.2_Intron	NM_017925.5	NP_060395.5	Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	NA		NA			cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						tgcagtgagccgagattgtac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145	55667		DENN/MADD domain containing	26079	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 55B, chromosome 9 open reading frame 55	C9orf55B, C9orf55	NA	12906859	Standard	NM_017925	NM_017925	NA	Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000602925.1:c.4349-318C>T	chr9.hg19:g.19351753C>T		NA	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	hg19	CCDS6491.3	0.02	-0.157886	AGCxGAG	COVERED																																																																																			NOVEL	DENND4C-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000099627.4	9	3.609831	KEEP	4	0	0	12	349	CC	0.99254	0.320398	0		+	3	60	84	0	0	6.392654	14	60	461	46	ENST00000602925.1	0.176471	0.322807
RPS6	6194	__UNKNOWN__	__UNKNOWN__	9	19378905	19378905	__UNKNOWN__	Silent	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19378905G>T	ENST00000380394.4	-	3	208	c.150C>A	c.(148-150)gtC>gtA	p.V50V	RPS6_ENST00000380384.1_Silent_p.V19V|RPS6_ENST00000380381.3_3'UTR|RPS6_ENST00000315377.4_Silent_p.V19V	NM_001010.2	NP_001001.2	P62753	RS6_HUMAN	ribosomal protein S6	50		NA			activation-induced cell death of T cells (GO:0006924)|cellular protein metabolic process (GO:0044267)|erythrocyte development (GO:0048821)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|oogenesis stage (GO:0022605)|placenta development (GO:0001890)|positive regulation of apoptotic process (GO:0043065)|ribosomal small subunit assembly (GO:0000028)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell differentiation in thymus (GO:0033077)|T cell proliferation involved in immune response (GO:0002309)|TOR signaling (GO:0031929)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|dendrite (GO:0030425)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural constituent of ribosome (GO:0003735)			endometrium(3)|lung(2)|ovary(1)|urinary_tract(1)	7		Colorectal(97;3.46e-05)|Myeloproliferative disorder(762;0.0255)		Lung(42;0.161)|LUSC - Lung squamous cell carcinoma(42;0.234)		CACTGATTCGGACCACATAAC	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													34	30	31			NA	NA	9		NA											NA				19378905		2203	4300	6503	SO:0001819	synonymous_variant				CCDS6492.1	9p21	2011-04-05			ENSG00000137154	ENSG00000137154	6194		S ribosomal proteins	10429	protein-coding gene	gene with protein product	40S ribosomal protein S6, phosphoprotein NP33	180460			NA	1577483	Standard	NM_001010	NM_001010	NA	Approved	S6	uc003znv.1	P62753	OTTHUMG00000019642	ENST00000380394.4:c.150C>A	chr9.hg19:g.19378905G>T		NA	P08227|P10660|Q4VBY7|Q8N6Z7	hg19	CCDS6492.1	0.02	3.02264	TCGxACC	COVERED																																																																																			NOVEL	RPS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051858.1	9	17.150988	KEEP	1	0	0	57	1746	GG	1	1	0		-	25	60	729	0	0	57.384973	103	60	3444	295	ENST00000380394.4	0.195312	1
SLC24A2	25769	__UNKNOWN__	__UNKNOWN__	9	19529872	19529872	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19529872T>C	ENST00000341998.2	-	8	1541				SLC24A2_ENST00000286344.3_Intron	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	NA		NA			cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)			endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		ctcagcctcctgagtagctgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886	25769		Solute carriers	10976	protein-coding gene	gene with protein product		609838			NA	10662833	Standard	NM_020344	NM_020344	NA	Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.1480-1736A>G	chr9.hg19:g.19529872T>C		NA	B7ZLL8|Q9NTN5|Q9NZQ4	hg19	CCDS6493.1	0.02	-0.298205	TCCxGAG	COVERED																																																																																			NOVEL	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051866.2	5	3.006282	KEEP	0	0	0	10	263	TT	0.992708	0.775364	0		-	4	60	123	0	0	9.094775	26	60	781	65	ENST00000341998.2	0.133333	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	19846913	19846913	__UNKNOWN__	IGR	SNP	G	G	A	rs371419372		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:19846913G>A			NA	NA				AL158077.1 (17068 upstream) : RP11-378I6.1 (79178 downstream)						NA		NA									NA						ccagctactcgggaggctgag	0.507		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16968	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.19846913G>A		NA		hg19		0.02	-0.210527	CTCxGGA	COVERED																																																																																			NOVEL					0			10	2.372799	KEEP	0	0	0	8	227	GG	0.99257	0.518282	0			3	60	92	0	0	6.89248	18	60	583	43		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	21224163	21224163	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:21224163T>C			NA	NA				IFNA16 (6853 upstream) : IFNA17 (3078 downstream)						NA		NA									NA						Tggccgggcgtggtggctcac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.21224163T>C		NA		hg19		0.02	-0.201714	GCGxGGT	UNCOVERED																																																																																			NOVEL					0			5	2.406093	KEEP	2	0	0	8	221	TT	0	0	0			3	60	106	0	0	8.292056	18	60	525	55		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	21612649	21612649	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:21612649G>A			NA	NA				MIR31HG (52981 upstream) : RN7SL151P (86663 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.21612649G>A		NA		hg19		0.02	-0.175437	CACxCCT	COVERED																																																																																			NOVEL					0			7	3.007555	KEEP	5	0	0	10	293	GG	0.99257	0.384528	0			4	60	116	0	0	9.262661	15	60	493	50		0.210526	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	25786120	25786120	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:25786120A>G			NA	NA				RP11-33G16.1 (1560 upstream) : AL442639.1 (827917 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.25786120A>G		NA		hg19		0.02	-0.227986	GGCxTGA	COVERED																																																																																			NOVEL					0			9	3.907903	KEEP	2	0	0	13	340	AA	0.993634	0.608508	0			3	60	96	0	0	6.995605	23	60	680	66		0.115385	0.612407
IFT74	80173	__UNKNOWN__	__UNKNOWN__	9	26981375	26981375	__UNKNOWN__	Intron	SNP	G	G	A	rs146856046	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:26981375G>A	ENST00000443698.1	+	4	476				IFT74_ENST00000433700.1_Intron|IFT74_ENST00000380062.5_Intron|IFT74_ENST00000429045.2_Intron	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	NA		NA			cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		ttcccaaagtgctgggattat	0.517		NA											G|||	237	0.0473243	0.0045	0.0259	5008	,	,	NA	16572	0.0288	NA	0.0537	False	NA	,,,	NA	NA	NA	2504	0.1329	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872	80173		Intraflagellar transport homologs	21424	protein-coding gene	gene with protein product	capillary morphogenesis protein 1	608040	coiled-coil domain containing 2, intraflagellar transport 74 homolog (Chlamydomonas)	CCDC2	NA	11683410	Standard	NM_025103	NM_001099223	NA	Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.305+758G>A	chr9.hg19:g.26981375G>A		NA	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	hg19	CCDS43793.1	0.02	-0.078933	AGTxCTG	UNCOVERED																																																																																			NOVEL	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055476.2	1	2.406298	KEEP	0	0	0	8	229	GG	0.99257	0.076761	0		+	5	60	138	0	0	13.497577	4	60	143	22	ENST00000443698.1	0.555556	0.077336
IFT74	80173	__UNKNOWN__	__UNKNOWN__	9	27030477	27030477	__UNKNOWN__	Intron	SNP	C	C	T	rs57770546	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:27030477C>T	ENST00000443698.1	+	13	1225				IFT74_ENST00000433700.1_Intron|IFT74_ENST00000380062.5_Intron|IFT74_ENST00000429045.2_Intron	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	NA		NA			cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		acccaggaggcggaggttgca	0.478		NA											C|||	597	0.119209	0.0946	0.072	5008	,	,	NA	13582	0.0308	NA	0.1451	False	NA	,,,	NA	NA	NA	2504	0.2505	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872	80173		Intraflagellar transport homologs	21424	protein-coding gene	gene with protein product	capillary morphogenesis protein 1	608040	coiled-coil domain containing 2, intraflagellar transport 74 homolog (Chlamydomonas)	CCDC2	NA	11683410	Standard	NM_025103	NM_001099223	NA	Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.1054+1375C>T	chr9.hg19:g.27030477C>T		NA	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	hg19	CCDS43793.1	0.02	-0.061268	AGGxGGA	UNCOVERED																																																																																			NOVEL	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055476.2	8	2.707434	KEEP	6	0	0	9	262	CC	0	0	0		+	6	60	152	0	0	16.79623	1	43	32	29	ENST00000443698.1	0.857143	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	27302968	27302968	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:27302968C>T			NA	NA				EQTN (5831 upstream) : MOB3B (22238 downstream)						NA		NA									NA						ggagacagagcgagactccgt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.27302968C>T		NA		hg19		0.02	-0.157897	GAGxGAG	COVERED																																																																																			NOVEL					0			12	3.911554	KEEP	7	0	0	13	396	CC	0.992708	0.320453	0			3	43	96	1	1	7.678723	13	60	422	55		0.1875	0.322807
LINGO2	158038	__UNKNOWN__	__UNKNOWN__	9	28467124	28467124	__UNKNOWN__	Intron	SNP	C	C	A	rs562839147	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:28467124C>A	ENST00000379992.2	-	2	172					NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		cctgggttcacgccattctcc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482	158038		Immunoglobulin superfamily / I-set domain containing	21207	protein-coding gene	gene with protein product		609793	leucine rich repeat neuronal 6C	LRRN6C	NA	14686891	Standard	NM_152570	NM_152570	NA	Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.277+8813G>T	chr9.hg19:g.28467124C>A		NA	A8K4K7|B2RPM5|Q6ZMD0	hg19	CCDS6524.1	0.02	-0.105236	TCAxGCC	UNCOVERED																																																																																			NOVEL	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051978.2	4	3.006771	KEEP	3	0	0	10	266	CC	0.99254	0.138789	0		-	3	60	77	0	0	6.47805	7	60	214	28	ENST00000379992.2	0.3	0.139832
LINGO2	158038	__UNKNOWN__	__UNKNOWN__	9	28548655	28548655	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:28548655T>C	ENST00000379992.2	-	2	86					NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		tgagccgagattgagccactg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482	158038		Immunoglobulin superfamily / I-set domain containing	21207	protein-coding gene	gene with protein product		609793	leucine rich repeat neuronal 6C	LRRN6C	NA	14686891	Standard	NM_152570	NM_152570	NA	Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.364-72632A>G	chr9.hg19:g.28548655T>C		NA	A8K4K7|B2RPM5|Q6ZMD0	hg19	CCDS6524.1	0.02	-0.070157	AGAxTGA	UNCOVERED																																																																																			NOVEL	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051978.2	6	3.006537	KEEP	4	0	0	10	262	TT	0.99257	0.053735	0		-	3	43	87	0	0	8.054126	4	60	124	27	ENST00000379992.2	0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	31688158	31688158	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:31688158A>G			NA	NA				RP11-271O3.1 (306670 upstream) : RNA5SP281 (605397 downstream)						NA		NA									NA						gggtttcaccatgttggccag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.31688158A>G		NA		hg19		0.02	-0.122774	ACCxTGT	COVERED																																																																																			NOVEL					0			8	3.005747	KEEP	5	0	0	10	258	AA	0.99254	0.194847	0			3	60	87	0	0	7.082274	10	60	295	37		0.230769	0.196312
APTX	54840	__UNKNOWN__	__UNKNOWN__	9	33020898	33020898	__UNKNOWN__	Intron	SNP	C	C	T	rs539338953		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33020898C>T	ENST00000473270.1	-	1	307							Q7Z2E3	APTX_HUMAN	aprataxin	NA		NA			cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|dephosphorylation (GO:0016311)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA ligation (GO:0006266)|double-strand break repair (GO:0006302)|polynucleotide 3' dephosphorylation (GO:0098506)|regulation of protein stability (GO:0031647)|response to hydrogen peroxide (GO:0042542)|single strand break repair (GO:0000012)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA 5'-adenosine monophosphate hydrolase activity (GO:0033699)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|phosphoglycolate phosphatase activity (GO:0008967)|phosphoprotein binding (GO:0051219)|polynucleotide 3'-phosphatase activity (GO:0046403)|protein N-terminus binding (GO:0047485)			endometrium(1)|lung(1)|ovary(2)|prostate(2)	6			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		gaggccgaggcgggcagatca	0.522		NA						Editing and processing nucleases					C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17502	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000164	CCDS47956.1, CCDS56568.1, CCDS75827.1	9p13.3	2014-01-28	2003-04-03		ENSG00000137074	ENSG00000137074	54840			15984	protein-coding gene	gene with protein product		606350	ataxia 1, early onset with hypoalbuminemia	AXA1	NA	11586299, 11586300	Standard	NM_017692	NM_175069	NA	Approved	FLJ20157, AOA, AOA1, EAOH, EOAHA	uc003zry.3	Q7Z2E3	OTTHUMG00000019759	ENST00000473270.1:c.338+3903G>A	chr9.hg19:g.33020898C>T		NA	A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	hg19		0.02	-0.175427	AGGxGGG	UNCOVERED																																																																																			NOVEL	APTX-023	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000355329.1	4	2.406437	KEEP	1	0	0	8	230	CC	0	0	0		-	3	60	88	0	0	6.710834	15	60	501	41	ENST00000473270.1	0.166667	0.387407
SMU1	55234	__UNKNOWN__	__UNKNOWN__	9	33045079	33045079	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33045079G>T	ENST00000397149.3	-	0	3804					NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		AGCAACAGAAGTGTTCCCTAA	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692	55234		WD repeat domain containing	18247	protein-coding gene	gene with protein product	functional spliceosome-associated protein 57	NA			NA	11438655, 11410362	Standard	NM_018225	NM_018225	NA	Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.*2212C>A	chr9.hg19:g.33045079G>T		NA	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	hg19	CCDS6534.1	0.02	1.505332	GAAxTGT	COVERED																																																																																			NOVEL	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052022.1	2	4.513153	KEEP	0	0	0	15	456	GG	0.99649	0.995603	0		-	14	60	419	0	0	32.728698	63	60	2161	138	ENST00000397149.3	0.181818	0.99911
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	33098240	33098240	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33098240C>G			NA	NA				SMU1 (21575 upstream) : B4GALT1 (5839 downstream)						NA		NA									NA						cgccatgttgcccagactggt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.33098240C>G		NA		hg19		0.02	-0.184219	TTGxCCA	COVERED																																																																																			NOVEL					0			6	2.996597	KEEP	0	0	0	10	280	CC	0.992708	0.42039	0			3	60	100	0	0	7.991504	14	60	457	36		0.176471	0.423478
RP11-326F20.5	0	__UNKNOWN__	__UNKNOWN__	9	33169771	33169771	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33169771G>A	ENST00000442432.1	+	0	72				RP11-326F20.5_ENST00000426270.1_RNA						NA		NA									NA						cgcccgcctcggcctcccaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000442432.1:	chr9.hg19:g.33169771G>A		NA		hg19		0.02	-0.298064	CTCxGCC	COVERED																																																																																			NOVEL	RP11-326F20.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000052037.1	17	6.594559	KEEP	18	0	0	22	636	GG	0.993634	0.776087	0		+	3	53	93	0	0	6.545383	26	60	830	96	ENST00000442432.1	0.103448	0.78106
RP11-326F20.5	0	__UNKNOWN__	__UNKNOWN__	9	33170246	33170246	__UNKNOWN__	RNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33170246T>G	ENST00000442432.1	+	0	72				RP11-326F20.5_ENST00000426270.1_RNA						NA		NA									NA						gggattacagttgtgagccac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000442432.1:	chr9.hg19:g.33170246T>G		NA		hg19		0.02	-0.201644	CAGxTGT	COVERED																																																																																			NOVEL	RP11-326F20.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000052037.1	6	2.707241	KEEP	1	0	0	9	257	AT	0.992708	0.486967	0		+	4	60	127	0	0	10.363396	15	60	437	52	ENST00000442432.1	0.210526	0.490544
NFX1	4799	__UNKNOWN__	__UNKNOWN__	9	33301808	33301808	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33301808G>A	ENST00000379540.3	+	3	1254				NFX1_ENST00000318524.6_Intron|NFX1_ENST00000379521.4_Intron	NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	NA		NA			inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		gatggctcacgcctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102	4799			7803	protein-coding gene	gene with protein product		603255			NA	7964459, 2511169	Standard		NM_002504	NA	Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.1192+389G>A	chr9.hg19:g.33301808G>A		NA	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	hg19	CCDS6538.1	0.02	-0.131579	CACxCCT	COVERED																																																																																			NOVEL	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052069.1	3	2.404207	KEEP	0	0	0	8	212	GG	0.99257	0.22747	0		+	3	60	88	0	0	7.300957	9	60	304	37	ENST00000379540.3	0.25	0.229173
AQP7	364	__UNKNOWN__	__UNKNOWN__	9	33386144	33386144	__UNKNOWN__	Silent	SNP	G	G	A	rs76209395	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33386144G>A	ENST00000537089.1	-	5	498	c.180C>T	c.(178-180)gtC>gtT	p.V60V	AQP7_ENST00000377425.4_Silent_p.V95V|AQP7_ENST00000539936.1_Silent_p.V152V|AQP7_ENST00000541274.1_Intron			O14520	AQP7_HUMAN	aquaporin 7	152		NA			excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		CAGCTGTAGCGACGGGACCGG	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													86	80	82			NA	NA	9		NA											NA				33386144		2203	4300	6503	SO:0001819	synonymous_variant			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269	364		Ion channels / Aquaporins	640	protein-coding gene	gene with protein product		602974		AQP7L	NA	9252401	Standard	NM_001170	NM_001170	NA	Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.180C>T	chr9.hg19:g.33386144G>A		NA	Q08E94|Q5T5L9|Q8NHM3	hg19		0.02	1.42105	AGCxACG	COVERED																																																																																			NOVEL	AQP7-202	KNOWN	basic	protein_coding	NA	protein_coding		0	2.40578	KEEP	0	0	0	8	227	GG	0.99257	0.98632	0		-	4	40	124	0	0	7.816811	60	60	1873	103	ENST00000537089.1	0.0625	0.993703
AQP7	364	__UNKNOWN__	__UNKNOWN__	9	33386146	33386146	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs76608797		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33386146C>A	ENST00000537089.1	-	5	496	c.178G>T	c.(178-180)Gtc>Ttc	p.V60F	AQP7_ENST00000377425.4_Missense_Mutation_p.V95F|AQP7_ENST00000539936.1_Missense_Mutation_p.V152F|AQP7_ENST00000541274.1_Intron			O14520	AQP7_HUMAN	aquaporin 7	152		NA			excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		GCTGTAGCGACGGGACCGGTC	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													86	80	82			NA	NA	9		NA											NA				33386146		2203	4300	6503	SO:0001583	missense			AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269	364		Ion channels / Aquaporins	640	protein-coding gene	gene with protein product		602974		AQP7L	NA	9252401	Standard	NM_001170	NM_001170	NA	Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.178G>T	chr9.hg19:g.33386146C>A	ENSP00000441619:p.Val60Phe	NA	Q08E94|Q5T5L9|Q8NHM3	hg19		0.02	1.429677	CGAxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	-	9.634	1.137210	0.21123	.	.	ENSG00000165269	ENST00000537089;ENST00000379507;ENST00000447660;ENST00000297988;ENST00000377425;ENST00000439678;ENST00000379506;ENST00000539936;ENST00000379503	D;D;D;D;D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04;-2.04	3.98	-1.55	0.08558	Aquaporin-like (2);	1.211120	0.05677	N	0.589625	T	0.69233	0.3088	N	0.16166	0.38	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.13407	0.003;0.002;0.009;0.002	T	0.52223	-0.8604	10	0.17369	T	0.5	2.1417	4.6196	0.12444	0.0:0.225:0.4403:0.3347	.	151;152;95;152	Q5T5M0;B7Z4U2;Q6P5T0;O14520	.;.;.;AQP7_HUMAN	F	60;151;20;152;95;60;151;152;88	ENSP00000441619:V60F;ENSP00000368821:V151F;ENSP00000412868:V20F;ENSP00000297988:V152F;ENSP00000396111:V95F;ENSP00000410138:V60F;ENSP00000368820:V151F;ENSP00000439534:V152F;ENSP00000368817:V88F	ENSP00000297988:V152F	V	-	1	0	AQP7	33376146	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	0.006000	0.13152	-0.272000	0.09259	-0.320000	0.08662	GTC	NOVEL	AQP7-202	KNOWN	basic	protein_coding	NA	protein_coding		0	2.406981	KEEP	0	0	0	8	240	CC	0.99257	0.98632	0		-	4	40	123	0	0	7.744748	59	60	1965	103	ENST00000537089.1	0.063492	0.993703
UBE2R2	54926	__UNKNOWN__	__UNKNOWN__	9	33823610	33823610	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33823610A>G	ENST00000263228.3	+	1	368					NM_017811.3	NP_060281.2	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme E2R 2	NA		NA			protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		ctgacctcagatgatctaccc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000426	CCDS6546.1	9p11.2	2008-02-05			ENSG00000107341	ENSG00000107341	54926		Ubiquitin-conjugating enzymes E2	19907	protein-coding gene	gene with protein product		612506			NA	12037680	Standard	NM_017811	XM_005251496	NA	Approved	UBC3B, CDC34B, FLJ20419, MGC10481	uc003ztm.3	Q712K3	OTTHUMG00000019797	ENST00000263228.3:c.177+5678A>G	chr9.hg19:g.33823610A>G		NA	D3DRL5|Q9NX64	hg19	CCDS6546.1	0.02	-0.184161	CAGxTGA	COVERED																																																																																			NOVEL	UBE2R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052118.1	7	2.705609	KEEP	0	0	0	9	240	AA	0.99254	0.420319	0		+	3	60	93	0	0	7.292742	14	60	403	42	ENST00000263228.3	0.176471	0.423478
UBE2R2	54926	__UNKNOWN__	__UNKNOWN__	9	33845941	33845941	__UNKNOWN__	Intron	SNP	C	C	G	rs145239060	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:33845941C>G	ENST00000263228.3	+	1	368					NM_017811.3	NP_060281.2	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme E2R 2	NA		NA			protein K48-linked ubiquitination (GO:0070936)|protein monoubiquitination (GO:0006513)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8			LUSC - Lung squamous cell carcinoma(29;0.0176)	GBM - Glioblastoma multiforme(74;0.188)		gagatcaagaccatggtgaaa	0.527		NA											C|||	228	0.0455272	0.0045	0.0447	5008	,	,	NA	15413	0.006	NA	0.1322	False	NA	,,,	NA	NA	NA	2504	0.0532	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000426	CCDS6546.1	9p11.2	2008-02-05			ENSG00000107341	ENSG00000107341	54926		Ubiquitin-conjugating enzymes E2	19907	protein-coding gene	gene with protein product		612506			NA	12037680	Standard	NM_017811	XM_005251496	NA	Approved	UBC3B, CDC34B, FLJ20419, MGC10481	uc003ztm.3	Q712K3	OTTHUMG00000019797	ENST00000263228.3:c.177+28009C>G	chr9.hg19:g.33845941C>G		NA	D3DRL5|Q9NX64	hg19	CCDS6546.1	0.02	-0.148702	AGAxCAT	COVERED																																																																																			NOVEL	UBE2R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052118.1	4	2.706451	KEEP	0	0	0	9	259	CC	0.99254	0.289823	0		+	6	60	203	0	0	18.3806	11	60	340	38	ENST00000263228.3	0.352941	0.292001
UBAP2	55833	__UNKNOWN__	__UNKNOWN__	9	34002950	34002950	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34002950C>T	ENST00000379238.1	-	3	217				UBAP2_ENST00000449054.1_Intron|UBAP2_ENST00000360802.1_Intron|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000480885.1_Intron|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000539807.1_Intron					ubiquitin associated protein 2	NA		NA								endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		cctcccaaagcgctaggatta	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073	55833			14185	protein-coding gene	gene with protein product		NA			NA	8871400	Standard	NM_018449	NM_018449	NA	Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.100-4088G>A	chr9.hg19:g.34002950C>T		NA		hg19	CCDS6547.1	0.02	-0.140354	AAGxGCT	COVERED																																																																																			NOVEL	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001071.1	6	2.707814	KEEP	0	0	0	9	270	CC	0.99254	0.259018	0		-	3	60	88	0	0	7.181848	10	60	337	37	ENST00000379238.1	0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	34080617	34080617	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34080617C>T			NA	NA				RN7SKP114 (30375 upstream) : RP11-537H15.3 (3712 downstream)						NA		NA									NA						gaaaccccgtctctattaaaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.34080617C>T		NA		hg19		0.02	-0.184219	CGTxTCT	COVERED																																																																																			NOVEL					0			22	3.611143	KEEP	10	0	0	12	385	CC	0.992708	0.42039	0			3	38	86	0	0	6.981862	10	60	340	54		0.230769	0.423478
UBAP1	51271	__UNKNOWN__	__UNKNOWN__	9	34199801	34199801	__UNKNOWN__	Intron	SNP	T	T	C	rs61409484		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34199801T>C	ENST00000297661.4	+	1	228				UBAP1_ENST00000545103.1_Intron|UBAP1_ENST00000540348.1_Intron|UBAP1_ENST00000379186.4_Intron|UBAP1_ENST00000536252.1_Intron|UBAP1_ENST00000543944.1_Intron	NM_016525.4	NP_057609.2	Q9NZ09	UBAP1_HUMAN	ubiquitin associated protein 1	NA		NA			protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)	ubiquitin binding (GO:0043130)			endometrium(4)|kidney(2)|lung(6)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(29;0.00272)			gcctggctgattttttttttt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(109;1074 1634 14978 20375 39620)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF222043	CCDS6550.1	9p13.3	2008-05-15	2002-08-27	2002-08-30	ENSG00000165006	ENSG00000165006	51271			12461	protein-coding gene	gene with protein product		609787	ubiquitin associated protein	UBAP	NA		Standard		NM_001171201	NA	Approved		uc011loj.2	Q9NZ09	OTTHUMG00000000430	ENST00000297661.4:c.-8+20563T>C	chr9.hg19:g.34199801T>C		NA	B7Z348|B7Z8N9|D3DRL7|F5GXE2|F5H0J8|Q4V759|Q53FP7|Q5T7B3|Q6FI75|Q8NC52|Q8NCG6|Q8NCH9	hg19	CCDS6550.1	0.02	-0.157773	TGAxTTT	COVERED																																																																																			NOVEL	UBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001084.1	12	3.006961	KEEP	0	0	0	10	265	TT	0.992708	0.320453	0		+	3	43	98	0	0	8.07299	11	60	319	38	ENST00000297661.4	0.214286	0.322807
UBAP1	51271	__UNKNOWN__	__UNKNOWN__	9	34220741	34220741	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34220741A>G	ENST00000297661.4	+	2	228				UBAP1_ENST00000545103.1_Intron|UBAP1_ENST00000359544.2_Intron|UBAP1_ENST00000540348.1_Intron|UBAP1_ENST00000379186.4_Intron|UBAP1_ENST00000536252.1_Intron|UBAP1_ENST00000543944.1_Intron	NM_016525.4	NP_057609.2	Q9NZ09	UBAP1_HUMAN	ubiquitin associated protein 1	NA		NA			protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)	ubiquitin binding (GO:0043130)			endometrium(4)|kidney(2)|lung(6)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(29;0.00272)			gattacaggcatgagccacag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(109;1074 1634 14978 20375 39620)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF222043	CCDS6550.1	9p13.3	2008-05-15	2002-08-27	2002-08-30	ENSG00000165006	ENSG00000165006	51271			12461	protein-coding gene	gene with protein product		609787	ubiquitin associated protein	UBAP	NA		Standard		NM_001171201	NA	Approved		uc011loj.2	Q9NZ09	OTTHUMG00000000430	ENST00000297661.4:c.-7-165A>G	chr9.hg19:g.34220741A>G		NA	B7Z348|B7Z8N9|D3DRL7|F5GXE2|F5H0J8|Q4V759|Q53FP7|Q5T7B3|Q6FI75|Q8NC52|Q8NCG6|Q8NCH9	hg19	CCDS6550.1	0.02	1.335981	GGCxTGA	COVERED																																																																																			NOVEL	UBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000001084.1	12	5.746901	KEEP	0	1	28	29	807	AA	0.999997	0.999675	0		+	5	60	156	0	0	9.815397	77	60	2300	166	ENST00000297661.4	0.060976	0.999678
KIF24	347240	__UNKNOWN__	__UNKNOWN__	9	34293252	34293252	__UNKNOWN__	Intron	SNP	C	C	T	rs10814093	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34293252C>T	ENST00000402558.2	-	4	936				KIF24_ENST00000345050.2_Intron|KIF24_ENST00000379166.2_Intron|KIF24_ENST00000379174.3_Intron			Q5T7B8	KIF24_HUMAN	kinesin family member 24	NA		NA			ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)	centriole (GO:0005814)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(13)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	32			LUSC - Lung squamous cell carcinoma(29;0.0107)			ctgaggcaggcggatcacttg	0.522		NA											C|||	2060	0.411342	0.1067	0.5	5008	,	,	NA	15322	0.3363	NA	0.6223	False	NA	,,,	NA	NA	NA	2504	0.6207	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001795	CCDS6551.2	9p13.3	2013-01-10			ENSG00000186638	ENSG00000186638	347240		Kinesins, Sterile alpha motif (SAM) domain containing	19916	protein-coding gene	gene with protein product		613747	chromosome 9 open reading frame 48	C9orf48	NA	12477932	Standard		NM_194313	NA	Approved	bA571F15.4, FLJ10933, FLJ43884	uc003zua.4	Q5T7B8	OTTHUMG00000019810	ENST00000402558.2:c.912-2865G>A	chr9.hg19:g.34293252C>T		NA	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	hg19	CCDS6551.2	0.02	-0.157888	AGGxGGA	UNCOVERED																																																																																			NOVEL	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052150.5	5	2.407331	KEEP	1	0	0	8	250	CC	0	0	0		-	9	60	276	0	0	26.78772	8	60	261	44	ENST00000402558.2	0.529412	0.322807
NUDT2	318	__UNKNOWN__	__UNKNOWN__	9	34330382	34330382	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34330382G>A	ENST00000379158.2	+	1	94				NUDT2_ENST00000346365.4_Intron|NUDT2_ENST00000379155.5_Intron	NM_001161.4	NP_001152.1	P50583	AP4A_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 2	NA		NA			apoptotic process (GO:0006915)|nucleobase-containing compound metabolic process (GO:0006139)	mitochondrion (GO:0005739)	bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity (GO:0004081)|bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity (GO:0008803)|GTP binding (GO:0005525)			lung(3)	3			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		cagcctgggcgacagagcgag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(95;1683 1957 4276 39813)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U30313	CCDS6552.1	9p13	2008-07-21			ENSG00000164978	ENSG00000164978	318		Nudix motif containing	8049	protein-coding gene	gene with protein product	Ap4A hydrolase 1, Ap4Aase, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical), diadenosine tetraphosphatase, diadenosine 5',5''-P1,P4-tetraphosphate pyrophosphohydrolase	602852		APAH1	NA	7487923, 9479504	Standard	NM_001161	NM_001161	NA	Approved		uc022bga.1	P50583	OTTHUMG00000019817	ENST00000379158.2:c.-265+785G>A	chr9.hg19:g.34330382G>A		NA	D3DRM0|Q5T589	hg19	CCDS6552.1	0.02	-0.157769	GGCxACA	COVERED																																																																																			NOVEL	NUDT2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052160.2	9	2.406665	KEEP	1	0	0	8	236	GG	0.99257	0.320408	0		+	3	57	89	0	2	6.979025	13	60	413	36	ENST00000379158.2	0.1875	0.322807
FAM219A	203259	__UNKNOWN__	__UNKNOWN__	9	34422902	34422902	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34422902A>G	ENST00000379089.1	-	2	349				FAM219A_ENST00000297620.4_Intron|FAM219A_ENST00000379081.1_Intron|FAM219A_ENST00000379078.1_Intron|FAM219A_ENST00000379080.1_Intron|FAM219A_ENST00000379087.1_Intron|FAM219A_ENST00000445726.1_Intron|FAM219A_ENST00000379084.1_Intron			Q8IW50	F219A_HUMAN	family with sequence similarity 219, member A	NA		NA									NA						ggtggctcacacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096350	CCDS6556.1, CCDS55304.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164970	ENSG00000164970	203259			19920	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 25	C9orf25	NA	9110174, 8619474	Standard	NM_001184940	NM_147202	NA	Approved	bA573M23.5, FLJ39031	uc011lok.2	Q8IW50	OTTHUMG00000019822	ENST00000379089.1:c.58-16940T>C	chr9.hg19:g.34422902A>G		NA	A2A364|B4DFE1|B4DSR8|Q5T590|Q5T591|Q5T592|Q5T594|Q5T595|Q8TAZ8	hg19		0.02	-0.254269	CACxCCT	COVERED																																																																																			NOVEL	FAM219A-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000052179.1	8	2.707035	KEEP	0	0	0	9	254	AA	0.99254	0.663536	0		-	3	60	102	0	0	7.444457	26	60	743	56	ENST00000379089.1	0.103448	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	34681543	34681543	__UNKNOWN__	IGR	SNP	C	C	G	rs2772557	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:34681543C>G			NA	NA				RP11-195F19.9 (248 upstream) : CCL19 (8020 downstream)						NA		NA									NA						tgtggtggctcacacctgtaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.34681543C>G		NA		hg19		0.02	-0.263168	GCTxACA	COVERED																																																																																			NOVEL					0			11	3.610658	KEEP	0	0	0	12	366	CC	0.993634	0.689252	0			3	60	106	0	0	8.048349	22	60	723	59		0.12	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	35135774	35135774	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:35135774T>C			NA	NA				FAM214B (19436 upstream) : UNC13B (26224 downstream)						NA		NA									NA						gtggctcacatctgtaatcct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.35135774T>C		NA		hg19		0.02	-0.280622	ACAxCTG	COVERED																																																																																			NOVEL					0			11	3.307297	KEEP	0	0	0	11	295	TT	0.993072	0.734547	0			3	60	99	0	0	7.242857	24	60	694	59		0.111111	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	35148246	35148246	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:35148246G>A			NA	NA				FAM214B (31908 upstream) : UNC13B (13752 downstream)						NA		NA									NA						CACATTTGTAGGGTTTCTCTC	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.35148246G>A		NA		hg19		0.02	1.593037	GTAxGGT	COVERED																																																																																			NOVEL					0			5	2.406856	KEEP	0	0	0	8	235	GG	0.99257	0.988289	0			4	25	129	0	0	8.206588	64	60	2207	107		0.058824	0.995687
ARHGEF39	84904	__UNKNOWN__	__UNKNOWN__	9	35661791	35661791	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:35661791A>G	ENST00000378387.3	-	0	1318				ARHGEF39_ENST00000343259.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|ARHGEF39_ENST00000490970.1_5'UTR	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	NA		NA			positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)				NA						gattacaggcatgagccactg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135	84904			25909	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 100	C9orf100	NA	22327280	Standard	NM_032818	XR_242516	NA	Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.*193T>C	chr9.hg19:g.35661791A>G		NA	Q49AG0|Q6TPQ2|Q96ST6	hg19	CCDS6584.2	0.02	1.438426	GGCxTGA	COVERED																																																																																			NOVEL	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052330.1	14	3.669869	KEEP	1	5	144	63	1751	AA	1	0.999956	0		-	4	60	131	0	1	7.948776	84	60	2489	211	ENST00000378387.3	0.045455	0.999956
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	35855412	35855412	__UNKNOWN__	IGR	SNP	C	C	T	rs192367588		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:35855412C>T			NA	NA				TMEM8B (568 upstream) : OR13J1 (13962 downstream)						NA		NA									NA						ttttttgagacggagttttgc	0.473		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17596	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.35855412C>T		NA		hg19		0.02	-0.201705	AGAxGGA	COVERED																																																																																			NOVEL					0			9	2.406447	KEEP	1	0	0	8	229	CC	0.99257	0.4869	0			3	60	90	0	0	6.628042	19	60	586	46		0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	35947925	35947925	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:35947925G>A			NA	NA				RP11-327L3.3 (10777 upstream) : OR2S2 (9179 downstream)						NA		NA									NA						gcccaggctggtctccaacta	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.35947925G>A		NA		hg19		0.02	-0.12277	CTGxTCT	COVERED																																																																																			NOVEL					0			9	4.212757	KEEP	0	0	0	14	438	GG	0.995343	0.195397	0			4	60	110	0	0	9.775984	7	60	231	38		0.363636	0.196312
GNE	10020	__UNKNOWN__	__UNKNOWN__	9	36245015	36245015	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36245015T>C	ENST00000539208.1	-	2	577				GNE_ENST00000543356.2_Intron|GNE_ENST00000396594.3_Intron|GNE_ENST00000447283.2_Intron|GNE_ENST00000377902.5_Intron|GNE_ENST00000539815.1_Intron	NM_001190384.1	NP_001177313.1	Q9Y223	GLCNE_HUMAN	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase	NA		NA			carbohydrate phosphorylation (GO:0046835)|cell adhesion (GO:0007155)|N-acetylglucosamine biosynthetic process (GO:0006045)|N-acetylneuraminate metabolic process (GO:0006054)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|metal ion binding (GO:0046872)|N-acylmannosamine kinase activity (GO:0009384)|UDP-N-acetylglucosamine 2-epimerase activity (GO:0008761)			endometrium(8)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			STAD - Stomach adenocarcinoma(86;0.228)			tggctcacgcttgtaatccca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(184;106 2118 20004 35750 50727)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF051852	CCDS6602.1, CCDS47965.1, CCDS55308.1, CCDS55309.1, CCDS55310.1	9p13.1	2008-02-05	2003-12-01		ENSG00000159921	ENSG00000159921	10020			23657	protein-coding gene	gene with protein product		603824	UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase	IBM2	NA	9305887, 9305888	Standard	NM_005476	NM_005476	NA	Approved	Uae1	uc010mli.3	Q9Y223	OTTHUMG00000019899	ENST00000539208.1:c.439+1012A>G	chr9.hg19:g.36245015T>C		NA	A6PZH2|A6PZH3|A7UNU7|B2R6E1|B7Z372|B7Z428|D3DRP7|F5H499|H0YFA7|Q0VA94	hg19	CCDS55308.1	0.02	-0.245593	CGCxTGT	COVERED																																																																																			NOVEL	GNE-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052413.2	13	3.303301	KEEP	2	0	0	11	287	TT	0.992708	0.663648	0		-	3	60	101	0	0	7.548885	22	60	663	52	ENST00000539208.1	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	36405011	36405011	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36405011C>T			NA	NA				RNF38 (3816 upstream) : MELK (167847 downstream)						NA		NA									NA						ctcacacctgcaatcccagca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.36405011C>T		NA		hg19		0.02	-0.149124	CTGxAAT	UNCOVERED																																																																																			NOVEL					0			8	2.407124	KEEP	2	0	0	8	243	CC	0	0	0			3	60	91	0	0	7.272112	12	60	411	39		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	36489868	36489868	__UNKNOWN__	IGR	SNP	G	G	A	rs10758375	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36489868G>A			NA	NA				RNF38 (88673 upstream) : MELK (82990 downstream)						NA		NA									NA						ggccgaggcggggggatcacc	0.517		NA											G|||	3009	0.600839	0.4342	0.696	5008	,	,	NA	16214	0.7639	NA	0.6282	False	NA	,,,	NA	NA	NA	2504	0.5624	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.36489868G>A		NA		hg19		0.02	-0.157886	GCGxGGG	COVERED																																																																																			NOVEL					0			10	3.308815	KEEP	3	0	0	11	331	GG	0.992708	0.320453	0			5	60	139	0	0	11.969076	11	60	379	46		0.3125	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	36507182	36507182	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36507182A>C			NA	NA				RNF38 (105987 upstream) : MELK (65676 downstream)						NA		NA									NA						ctctgcctccaaaagtgctgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.36507182A>C		NA		hg19		0.02	-0.166654	TCCxAAA	COVERED																																																																																			NOVEL					0			6	2.406457	KEEP	0	0	0	8	228	AA	0.99257	0.351317	0			3	60	104	0	0	8.309975	15	60	451	40		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	36527418	36527418	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36527418T>C			NA	NA				RNF38 (126223 upstream) : MELK (45440 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.36527418T>C		NA		hg19		0.02	-0.245502	AGGxGTG	COVERED																																																																																			NOVEL					0			12	2.70367	KEEP	0	0	0	9	227	TT	0.99254	0.636563	0			3	60	94	0	0	6.693926	25	60	698	42		0.107143	0.641347
MELK	9833	__UNKNOWN__	__UNKNOWN__	9	36589423	36589423	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36589423T>C	ENST00000298048.2	+	4	328				MELK_ENST00000541717.1_Intron|MELK_ENST00000487398.1_Intron|MELK_ENST00000536329.1_Intron|MELK_ENST00000536860.1_Intron|MELK_ENST00000538311.1_Intron|MELK_ENST00000536987.1_Intron|MELK_ENST00000545008.1_Intron|MELK_ENST00000543751.1_Intron	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			ggattacaggtgtgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(82;980 1317 7225 14391 18624)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304	9833			16870	protein-coding gene	gene with protein product		607025			NA	8724849, 9136115	Standard	NM_014791	NM_001256689	NA	Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.145-110T>C	chr9.hg19:g.36589423T>C		NA	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	hg19	CCDS6606.1	0.02	1.491031	AGGxGTG	COVERED																																																																																			NOVEL	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052428.3	19	3.171343	KEEP	1	2	52	29	804	TT	0.999997	0.999859	0		+	4	60	133	0	0	8.251455	79	60	2276	187	ENST00000298048.2	0.048193	0.999862
MELK	9833	__UNKNOWN__	__UNKNOWN__	9	36643150	36643150	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36643150T>C	ENST00000298048.2	+	11	1105				MELK_ENST00000541717.1_Intron|MELK_ENST00000536329.1_Intron|MELK_ENST00000536860.1_Intron|MELK_ENST00000538311.1_Intron|MELK_ENST00000536987.1_Intron|MELK_ENST00000545008.1_Intron|MELK_ENST00000543751.1_Intron	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			gaggccgaggtgggaggatca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(82;980 1317 7225 14391 18624)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304	9833			16870	protein-coding gene	gene with protein product		607025			NA	8724849, 9136115	Standard	NM_014791	NM_001256689	NA	Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.921+70T>C	chr9.hg19:g.36643150T>C		NA	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	hg19	CCDS6606.1	0.02	-0.201707	AGGxGGG	COVERED																																																																																			NOVEL	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052428.3	7	2.705558	KEEP	2	0	0	9	237	TT	0.99254	0.518266	0		+	4	60	122	0	1	9.86312	15	60	438	40	ENST00000298048.2	0.210526	0.522161
MELK	9833	__UNKNOWN__	__UNKNOWN__	9	36661909	36661909	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:36661909A>G	ENST00000298048.2	+	14	1360				MELK_ENST00000541717.1_Intron|MELK_ENST00000536329.1_Intron|MELK_ENST00000536860.1_Intron|MELK_ENST00000538311.1_Intron|MELK_ENST00000536987.1_Intron|MELK_ENST00000545008.1_Intron|MELK_ENST00000543751.1_Intron	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	NA		NA			apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			actccagcctaggtgacagag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(82;980 1317 7225 14391 18624)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304	9833			16870	protein-coding gene	gene with protein product		607025			NA	8724849, 9136115	Standard	NM_014791	NM_001256689	NA	Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.1177-3438A>G	chr9.hg19:g.36661909A>G		NA	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	hg19	CCDS6606.1	0.02	-0.026315	CCTxGGT	UNCOVERED																																																																																			NOVEL	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052428.3	4	2.397777	KEEP	2	0	0	8	193	AA	0	0	0		+	2	40	65	0	0	6.624752	1	33	30	16	ENST00000298048.2	0.666667	0
ZBTB5	9925	__UNKNOWN__	__UNKNOWN__	9	37444414	37444414	__UNKNOWN__	Intron	SNP	T	T	C	rs309448		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:37444414T>C	ENST00000307750.4	-	2	185					NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		tcaggctggttttgaactcct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795	9925		-, BTB/POZ domain containing, Zinc fingers, C2H2-type	23836	protein-coding gene	gene with protein product		NA			NA	9205841	Standard	NM_014872	NM_014872	NA	Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.4-1862A>G	chr9.hg19:g.37444414T>C		NA		hg19	CCDS6610.1	0.02	-0.105216	GGTxTTG	UNCOVERED																																																																																			NOVEL	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052462.1	5	2.405052	KEEP	0	0	0	8	207	TT	0.99257	0.138793	0		-	3	60	95	0	0	8.001781	9	60	244	30	ENST00000307750.4	0.25	0.139832
POLR1E	64425	__UNKNOWN__	__UNKNOWN__	9	37500218	37500218	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:37500218A>G	ENST00000377798.4	+	10	999				POLR1E_ENST00000377792.3_Intron|POLR1E_ENST00000442009.2_Intron	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	NA		NA			gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		gtctcactctattgcccaggc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(116;843 1620 18506 32459 34463)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054	64425		RNA polymerase subunits	17631	protein-coding gene	gene with protein product	RNA polymerase I associated factor 53	NA	polymerase (RNA) I associated factor 1	PRAF1	NA	8641287	Standard	NM_022490	XM_005251547	NA	Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.887-619A>G	chr9.hg19:g.37500218A>G		NA	O75395|Q5JTE3	hg19	CCDS6611.1	0.02	-0.09646	TCTxTTG	UNCOVERED																																																																																			NOVEL	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052464.1	6	2.706315	KEEP	1	0	0	9	239	AA	0.99254	0.119538	0		+	3	40	97	0	0	8.479213	7	60	191	26	ENST00000377798.4	0.3	0.120436
RP11-613M10.9	0	__UNKNOWN__	__UNKNOWN__	9	37800389	37800389	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:37800389C>A	ENST00000540557.1	-	9	1696										NA		NA									NA						tgggcgacagcgcgagactcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000540557.1:c.892-16329G>T	chr9.hg19:g.37800389C>A		NA		hg19		0.02	-0.31581	CAGxGCG	COVERED																																																																																			NOVEL	RP11-613M10.9-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000401856.1	4	4.211903	KEEP	0	0	0	14	421	CC	0.995343	0.814653	0		-	3	60	98	0	0	6.82663	31	60	1048	63	ENST00000540557.1	0.088235	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	38261042	38261042	__UNKNOWN__	IGR	SNP	T	T	C	rs10123320		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:38261042T>C			NA	NA				snoU13 (70538 upstream) : RP11-113O24.3 (99381 downstream)						NA		NA									NA						tctttctttctttccttcctt	0.289		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.38261042T>C		NA		hg19		0.02	-0.096479	TTCxTTC	UNCOVERED																																																																																			NOVEL					0			9	2.405784	KEEP	10	0	0	8	217	TT	0	0	0			3	60	105	0	0	9.27893	7	47	203	35		0.3	0.120436
ANKRD18A	253650	__UNKNOWN__	__UNKNOWN__	9	38599573	38599573	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:38599573T>C	ENST00000399703.5	-	8	1311					NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	NA		NA								NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						gcaattctcctgcctcagcct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071	253650		Ankyrin repeat domain containing	23643	protein-coding gene	gene with protein product		NA			NA		Standard		NM_147195	NA	Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.936+1554A>G	chr9.hg19:g.38599573T>C		NA	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	hg19	CCDS55311.1	0.02	-0.114033	TCCxGCC	UNCOVERED																																																																																			NOVEL	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052506.3	5	2.700356	KEEP	4	0	0	9	217	TT	0.99254	0.161255	0		-	3	21	96	0	0	7.981887	10	60	313	33	ENST00000399703.5	0.230769	0.162467
ANKRD18A	253650	__UNKNOWN__	__UNKNOWN__	9	38599574	38599574	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:38599574G>A	ENST00000399703.5	-	8	1311					NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	NA		NA								NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						caattctcctgcctcagcctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071	253650		Ankyrin repeat domain containing	23643	protein-coding gene	gene with protein product		NA			NA		Standard		NM_147195	NA	Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.936+1553C>T	chr9.hg19:g.38599574G>A		NA	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	hg19	CCDS55311.1	0.02	-0.114042	CCTxCCT	UNCOVERED																																																																																			NOVEL	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052506.3	5	2.706746	KEEP	4	0	0	9	251	GG	0.99254	0.161255	0		-	3	21	90	0	0	7.381763	10	60	351	34	ENST00000399703.5	0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	38933023	38933023	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:38933023A>C			NA	NA				RP11-402N8.1 (81110 upstream) : CNTNAP3 (139740 downstream)						NA		NA									NA						cctgtaatccaagcactttgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.38933023A>C		NA		hg19		0.02	-0.052625	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			6	2.704305	KEEP	1	0	0	9	228	AA	0.99254	0.036491	0			2	60	71	0	0	6.593136	3	60	85	20		0.4	0.036766
CNTNAP3	79937	__UNKNOWN__	__UNKNOWN__	9	39146642	39146642	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:39146642T>C	ENST00000297668.6	-	11	1723				CNTNAP3_ENST00000377659.1_Intron|CNTNAP3_ENST00000323947.7_Intron|CNTNAP3_ENST00000358144.2_Intron|CNTNAP3_ENST00000377656.2_Intron	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	NA		NA			cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		gccgagatcgtgccactgcac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714	79937			13834	protein-coding gene	gene with protein product	cell recognition molecule CASPR3 (FLJ14195, KIAA1714)	610517			NA	12093160	Standard	NM_033655	NM_033655	NA	Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.1650-2299A>G	chr9.hg19:g.39146642T>C		NA	B1AMA0|Q9C0E9	hg19	CCDS6616.1	0.02	-0.105238	TCGxGCC	UNCOVERED																																																																																			NOVEL	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052511.1	6	2.706979	KEEP	3	0	0	9	253	TT	0	0	0		-	3	60	100	0	0	8.632852	8	60	223	30	ENST00000297668.6	0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	40739448	40739448	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:40739448A>G			NA	NA				FAM74A3 (16769 upstream) : RP11-395E19.7 (1327 downstream)						NA		NA									NA						ccaagtagctaggattacagg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.40739448A>G		NA		hg19		0.02	-0.061346	GCTxGGA	UNCOVERED																																																																																			NOVEL					0			7	2.40466	KEEP	1	0	0	8	204	AA	0	0	0			3	27	94	0	0	8.757109	4	60	103	17		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	43541271	43541271	__UNKNOWN__	IGR	SNP	G	G	A	rs201253580		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:43541271G>A			NA	NA				RP11-327I22.8 (351860 upstream) : SPATA31A6 (83235 downstream)						NA		NA									NA						ctcgtgatccgcccacctcgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.43541271G>A		NA		hg19		0.02	-0.114037	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			8	2.406761	KEEP	11	0	0	8	237	GG	0	0	0			5	46	152	1	0	14.045189	7	47	241	42		0.416667	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	44175535	44175535	__UNKNOWN__	IGR	SNP	T	T	C	rs55633393	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:44175535T>C			NA	NA				RNU6-599P (67616 upstream) : RP11-175I6.5 (81044 downstream)						NA		NA									NA						CTGGACATGATTACCATGCTG	0.428		NA											t|||	585	0.116813	0.0265	0.1599	5008	,	,	NA	24200	0.0516	NA	0.2147	False	NA	,,,	NA	NA	NA	2504	0.1748	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.44175535T>C		NA		hg19		0.02	-0.298201	TGAxTAC	UNCOVERED																																																																																			NOVEL					0			6	2.405213	KEEP	35	0	0	8	211	TT	0	0	0			18	60	588	0	0	57.178604	16	60	466	98		0.529412	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	45765432	45765432	__UNKNOWN__	IGR	SNP	C	C	T	rs202006028		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:45765432C>T			NA	NA				Y_RNA (10082 upstream) : SNORA70 (277348 downstream)						NA		NA									NA						agcaatgctcccacatcagcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.45765432C>T		NA		hg19		0.02	-0.061404	CTCxCAC	UNCOVERED																																																																																			NOVEL					0			8	3.309278	KEEP	12	0	0	11	330	CC	0	0	0			4	22	126	0	0	12.43177	3	21	98	28		0.571429	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	46329503	46329503	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:46329503G>T			NA	NA				RP11-292F9.1 (54575 upstream) : RP11-292F9.2 (29738 downstream)						NA		NA									NA						aggagttcaagaccagcctgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.46329503G>T		NA		hg19		0.02	-0.184219	CAAxACC	COVERED																																																																																			NOVEL					0			15	3.31021	KEEP	10	0	0	11	351	GG	0.992708	0.42039	0			5	46	152	0	0	12.96685	13	48	447	59		0.277778	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	65604944	65604944	__UNKNOWN__	IGR	SNP	G	G	T	rs62561577		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:65604944G>T			NA	NA				SPATA31A7 (95334 upstream) : RP11-118H15.1 (275588 downstream)						NA		NA									NA						cctattggccgggcacggtgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.65604944G>T		NA		hg19		0.02	-0.114028	GCCxGGC	UNCOVERED																																																																																			NOVEL					0			8	3.609137	KEEP	28	0	0	12	333	GG	0	0	0			4	25	117	0	0	10.123533	9	25	287	65		0.307692	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66457259	66457259	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:66457259G>T			NA	NA				RP11-118H15.1 (573374 upstream) : RP11-262H14.1 (29 downstream)						NA		NA									NA						gagCACCACAGTagagcgcga	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66457259G>T		NA		hg19		0.02	1.347639	ACAxTAG	COVERED																																																																																			NOVEL					0			21	8.424243	KEEP	3	3	82	57	1750	GG	1	0.99993	0			7	60	207	0	0	15.063149	46	60	1503	217		0.132075	0.99993
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66469786	66469786	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:66469786G>T			NA	NA				RP11-262H14.1 (476 upstream) : RP11-262H14.7 (47419 downstream)						NA		NA									NA						gagtgcagtggtgcaatcttg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66469786G>T		NA		hg19		0.02	-0.149109	GTGxTGC	COVERED																																																																																			NOVEL					0			7	3.911077	KEEP	10	0	0	13	381	GG	0.99254	0.289823	0			3	60	84	0	0	6.781939	10	60	337	44		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66484582	66484582	__UNKNOWN__	IGR	SNP	T	T	C	rs7870190	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:66484582T>C			NA	NA				RP11-262H14.1 (15272 upstream) : RP11-262H14.7 (32623 downstream)						NA		NA									NA						accaacatggtgaatccctgt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66484582T>C		NA		hg19		0.02	-0.14033	TGGxGAA	COVERED																																																																																			NOVEL					0			16	3.608968	KEEP	3	0	0	12	330	TT	0.993634	0.259304	0			5	49	171	0	0	15.17067	11	60	326	39		0.3125	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66506027	66506027	__UNKNOWN__	IGR	SNP	T	T	C	rs62563473		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:66506027T>C			NA	NA				RP11-262H14.1 (36717 upstream) : RP11-262H14.7 (11178 downstream)						NA		NA									NA						ttaatagagatggggtttcgc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66506027T>C		NA		hg19		0.02	-0.16663	AGAxGGG	COVERED																																																																																			NOVEL					0			8	3.308292	KEEP	5	0	0	11	304	TT	0.992708	0.351366	0			6	49	189	0	0	16.96998	11	50	313	46		0.352941	0.353947
RP11-262H14.3	0	__UNKNOWN__	__UNKNOWN__	9	66524393	66524393	__UNKNOWN__	lincRNA	SNP	C	C	A	rs539258840	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:66524393C>A	ENST00000445604.2	-	0	784										NA		NA									NA						ggtggctcacccctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000445604.2:	chr9.hg19:g.66524393C>A		NA		hg19		0.02	-0.131583	CACxCCT	COVERED																																																																																			NOVEL	RP11-262H14.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000037074.2	12	2.681006	KEEP	1	0	0	9	240	CG	0.992708	0.289872	0		-	4	40	118	0	0	10.223356	9	60	312	40	ENST00000445604.2	0.307692	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	66800792	66800792	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:66800792G>C			NA	NA				RP11-318K12.2 (41420 upstream) : AL353626.1 (57744 downstream)						NA		NA									NA						tgttgaaaaaggaaatatctt	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.66800792G>C		NA		hg19		0.02	3.171439	AAAxGAA	COVERED																																																																																			NOVEL					0			93	14.312358	KEEP	88	5	149	100	3135	GG	1	1	0			5	50	163	2	0	12.323527	32	60	1111	510		0.135135	1
RP11-195B21.3	0	__UNKNOWN__	__UNKNOWN__	9	67974341	67974341	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:67974341C>G	ENST00000417488.1	+	3	220										NA		NA								breast(1)	1						gagccgagatcatgccactgc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000417488.1:c.-19-3097C>G	chr9.hg19:g.67974341C>G		NA		hg19		0.02	-0.061411	GATxATG	UNCOVERED																																																																																			NOVEL	RP11-195B21.3-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic	protein_coding	NA	protein_coding	OTTHUMT00000144022.2	6	3.009023	KEEP	25	0	0	10	307	CC	0	0	0		+	3	40	101	0	0	9.455072	4	24	144	51	ENST00000417488.1	0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68382585	68382585	__UNKNOWN__	IGR	SNP	A	A	T	rs62545623	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68382585A>T			NA	NA				RP11-149F8.5 (41941 upstream) : RP11-764K9.1 (15292 downstream)						NA		NA									NA						gctggagtgcagtggcatgat	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68382585A>T		NA		hg19		0.02	-0.157776	TGCxGTG	UNCOVERED																																																																																			NOVEL					0			10	3.909476	KEEP	21	0	0	13	352	AA	0	0	0			4	40	102	1	0	8.471053	10	41	283	57		0.285714	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68397182	68397182	__UNKNOWN__	IGR	SNP	C	C	T	rs375567432		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68397182C>T			NA	NA				RP11-149F8.5 (56538 upstream) : RP11-764K9.1 (695 downstream)						NA		NA									NA						ggcacagtggctcacgcctgt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68397182C>T		NA		hg19		0.02	1.390008	TGGxTCA	COVERED																																																																																			NOVEL					0			16	5.760523	KEEP	17	1	13	24	752	AC	0.999909	0.963687	0			5	60	138	0	0	10.482371	23	51	786	142		0.178571	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68414556	68414556	__UNKNOWN__	IGR	SNP	G	G	T	rs145693434		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68414556G>T			NA	NA				RP11-764K9.1 (4663 upstream) : MIR4477B (751 downstream)						NA		NA									NA						cagcacatctgttaatagcat	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68414556G>T		NA		hg19		0.02	-0.29822	TCTxTTA	COVERED																																																																																			NOVEL					0			28	2.707213	KEEP	1	0	0	9	256	GG	0.99257	0.775257	0			5	60	133	0	0	10.680531	16	60	525	43		0.238095	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68414700	68414700	__UNKNOWN__	IGR	SNP	G	G	A	rs142306528	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68414700G>A			NA	NA				RP11-764K9.1 (4807 upstream) : MIR4477B (607 downstream)						NA		NA									NA						ttgggaggctgaggatcacct	0.418		NA											.|||	481	0.0960463	0.1112	0.0908	5008	,	,	NA	92042	0.0883	NA	0.1014	False	NA	,,,	NA	NA	NA	2504	0.0818	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68414700G>A		NA		hg19		0.02	1.300812	GCTxAGG	COVERED																																																																																			NOVEL					0			32	3.140155	KEEP	3	4	97	45	1359	GG	1	0.999835	0			4	60	120	0	1	7.826244	47	60	1544	209		0.078431	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415293	68415293	__UNKNOWN__	IGR	SNP	T	T	C	rs35922576		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68415293T>C			NA	NA				RP11-764K9.1 (5400 upstream) : MIR4477B (14 downstream)						NA		NA									NA						ccattaatcctttcatgatat	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415293T>C		NA		hg19		0.02	4.172736	TCCxTTC	COVERED																																																																																			NOVEL					0			3	4.512582	KEEP	0	0	0	15	435	TT	0.99649	0.996468	0			6	60	214	0	0	14.436398	93	60	2948	203		0.060606	0.999978
MIR4477B	100616194	__UNKNOWN__	__UNKNOWN__	9	68415352	68415352	__UNKNOWN__	RNA	SNP	A	A	G	rs77109690		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68415352A>G	ENST00000581659.1	+	0	45					NR_039688.1|NR_039689.1				microRNA 4477b	NA		NA									NA						caatccttaaatgccattaag	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							9	2011-09-12					100616194		ncRNAs / Micro RNAs	41898	non-coding RNA	RNA, micro		NA			NA		Standard	NR_039689	NR_039689	NA	Approved	hsa-mir-4477b				ENST00000581659.1:	chr9.hg19:g.68415352A>G		NA		hg19		0.02	1.529014	TAAxTGC	COVERED																																																																																			NOVEL	MIR4477B-201	KNOWN	basic	miRNA	NA	miRNA		1	2.704723	KEEP	0	0	0	9	239	AA	0.99254	0.985519	0		+	4	60	128	0	0	8.423257	53	60	1505	97	ENST00000581659.1	0.070175	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415693	68415693	__UNKNOWN__	IGR	SNP	T	T	C	rs76015020		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68415693T>C			NA	NA				MIR4477B (305 upstream) : CR786580.2 (96652 downstream)						NA		NA									NA						gaatattccataaacctagtt	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415693T>C		NA		hg19		0.02	7.757025	CCAxAAA	COVERED																																																																																			NOVEL					0			16	5.944943	KEEP	9	1	29	30	810	TT	0.999997	0.999997	0			7	60	243	0	0	14.885911	168	60	4940	376		0.04	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415727	68415727	__UNKNOWN__	IGR	SNP	G	G	A	rs145008376		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68415727G>A			NA	NA				MIR4477B (339 upstream) : CR786580.2 (96618 downstream)						NA		NA									NA						cagggtttgagagggtttact	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415727G>A		NA		hg19		0.02	4.814266	TGAxAGG	COVERED																																																																																			NOVEL					0			16	3.576885	KEEP	9	2	48	29	914	GG	0.999988	0.999988	0			21	60	645	0	0	47.218892	144	60	4923	373		0.127273	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68415756	68415756	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68415756C>T			NA	NA				MIR4477B (368 upstream) : CR786580.2 (96589 downstream)						NA		NA									NA						gaaagaagttctactgttgat	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68415756C>T		NA		hg19		0.02	3.13941	GTTxTAC	COVERED																																																																																			NOVEL					0			10	3.644713	KEEP	3	1	31	23	708	CC	0.999879	0.999879	0			6	60	183	0	0	11.316355	94	60	3234	234		0.06	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68416840	68416840	__UNKNOWN__	IGR	SNP	C	C	G	rs113583286		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68416840C>G			NA	NA				MIR4477B (1452 upstream) : CR786580.2 (95505 downstream)						NA		NA									NA						gatcgtgccactgcactcctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68416840C>G		NA		hg19		0.02	1.733871	CCAxTGC	COVERED																																																																																			NOVEL					0			32	3.343996	KEEP	4	4	119	53	1628	CC	1	0.999726	0			10	60	355	0	0	29.406859	40	60	1347	220		0.2	0.999726
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68422498	68422498	__UNKNOWN__	IGR	SNP	G	G	A	rs1143480	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68422498G>A			NA	NA				MIR4477B (7110 upstream) : CR786580.2 (89847 downstream)						NA		NA									NA						gaccatcctggctaacacggt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68422498G>A		NA		hg19		0.02	1.328609	CTGxCTA	COVERED																																																																																			NOVEL					0			17	2.437744	KEEP	6	1	28	18	545	GG	0.999366	0.970205	0			5	60	138	0	0	9.480465	38	60	1293	105		0.116279	0.97082
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68422581	68422581	__UNKNOWN__	IGR	SNP	C	C	T	rs1143483	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68422581C>T			NA	NA				MIR4477B (7193 upstream) : CR786580.2 (89764 downstream)						NA		NA									NA						cccagctactcgggaggctga	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68422581C>T		NA		hg19		0.02	-0.245569	ACTxGGG	COVERED																																																																																			NOVEL					0			6	3.007173	KEEP	2	0	0	10	285	CC	0.99254	0.688494	0			10	60	277	1	0	24.739317	17	60	537	55		0.37037	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68422611	68422611	__UNKNOWN__	IGR	SNP	C	C	A	rs532238610		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68422611C>A			NA	NA				MIR4477B (7223 upstream) : CR786580.2 (89734 downstream)						NA		NA									NA						atgctgtcaacctgggaggcg	0.507		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	27925	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68422611C>A		NA		hg19		0.02	-0.32457	CAAxCTG	COVERED																																																																																			NOVEL					0			8	2.407161	KEEP	0	0	0	8	247	CT	0.99254	0.829482	0			4	60	117	0	0	8.318751	29	60	981	67		0.121212	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68427740	68427740	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68427740A>T			NA	NA				MIR4477B (12352 upstream) : CR786580.2 (84605 downstream)						NA		NA									NA						ATCCTGGTTAAACTAGCTACT	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68427740A>T		NA		hg19		0.02	3.839033	TTAxACT	COVERED																																																																																			NOVEL					0			0	5.646932	KEEP	14	1	26	28	793	AA	0.999988	0.999988	0			7	59	207	0	0	11.300664	168	60	5211	316		0.04	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68427801	68427801	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68427801T>C			NA	NA				MIR4477B (12413 upstream) : CR786580.2 (84544 downstream)						NA		NA									NA						AAGCATTTCCTCTGAATATTT	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68427801T>C		NA		hg19		0.02	13.381675	TCCxCTG	COVERED																																																																																			NOVEL					0			8	11.523874	KEEP	35	3	90	70	1913	TT	1	1	0			27	60	922	0	0	63.387316	335	60	10155	726		0.074586	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68427803	68427803	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68427803T>C			NA	NA				MIR4477B (12415 upstream) : CR786580.2 (84542 downstream)						NA		NA									NA						GCATTTCCTCTGAATATTTTA	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68427803T>C		NA		hg19		0.02	12.819304	CTCxGAA	COVERED																																																																																			NOVEL					0			8	5.072222	KEEP	34	5	148	69	1911	TT	1	1	0			21	60	689	0	0	44.313099	334	60	10205	729		0.059155	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68427957	68427957	__UNKNOWN__	IGR	SNP	T	T	A	rs576698474	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68427957T>A			NA	NA				MIR4477B (12569 upstream) : CR786580.2 (84388 downstream)						NA		NA									NA						TATATTCAATTGCTACTAAAT	0.244		NA											.|||	6	0.00119808	0.0015	0.0	5008	,	,	NA	16877	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68427957T>A		NA		hg19		0.02	-0.324499	AATxGCT	COVERED																																																																																			NOVEL					0			2	3.307266	KEEP	3	0	0	11	301	TT	0.992708	0.829622	0			4	60	111	0	0	7.721439	29	60	874	55		0.121212	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68429363	68429363	__UNKNOWN__	IGR	SNP	C	C	T	rs144295139		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68429363C>T			NA	NA				MIR4477B (13975 upstream) : CR786580.2 (82982 downstream)						NA		NA									NA						gcagatcactcgaggtcagga	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68429363C>T		NA		hg19		0.02	3.125281	ACTxGAG	COVERED																																																																																			NOVEL					0			42	7.685804	KEEP	21	2	58	46	1327	CC	1	0.999992	0			9	60	265	2	0	18.584901	71	60	2273	247		0.1125	0.999992
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68429913	68429913	__UNKNOWN__	IGR	SNP	G	G	A	rs200589227	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68429913G>A			NA	NA				MIR4477B (14525 upstream) : CR786580.2 (82432 downstream)						NA		NA									NA						ACGTTGTGTTGCCTCTTCTTG	0.458		NA											.|||	3	0.000599042	0.0	0.0	5008	,	,	NA	31100	0.003	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68429913G>A		NA		hg19		0.02	1.223343	GTTxCCT	COVERED																																																																																			NOVEL					0			33	6.283564	KEEP	2	2	54	40	1192	GG	1	0.993703	0			7	60	199	0	0	14.871373	37	60	1257	130		0.159091	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68429932	68429932	__UNKNOWN__	IGR	SNP	T	T	G	rs569987772	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68429932T>G			NA	NA				MIR4477B (14544 upstream) : CR786580.2 (82413 downstream)						NA		NA									NA						TGTCCATCAGttttcattttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68429932T>G		NA		hg19		0.02	1.464759	CAGxTTT	COVERED																																																																																			NOVEL					0			46	9.18199	KEEP	2	2	61	52	1365	TT	1	0.999907	0			4	60	135	0	0	8.914444	60	60	1721	199		0.0625	0.999907
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68431163	68431163	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68431163G>A			NA	NA				MIR4477B (15775 upstream) : CR786580.2 (81182 downstream)						NA		NA									NA						CCAAGTACTTGACTAACCAAA	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68431163G>A		NA		hg19		0.02	2.477346	CTTxACT	COVERED																																																																																			NOVEL					0			3	8.723897	KEEP	14	0	0	29	856	GG	0.999988	0.999988	0			5	48	148	1	0	9.403845	64	60	2117	256		0.072464	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68431169	68431169	__UNKNOWN__	IGR	SNP	C	C	A	rs368717033		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68431169C>A			NA	NA				MIR4477B (15781 upstream) : CR786580.2 (81176 downstream)						NA		NA									NA						ACTTGACTAACCAAAGAGACC	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68431169C>A		NA		hg19		0.02	2.780662	TAAxCAA	COVERED																																																																																			NOVEL					0			3	4.545865	KEEP	14	1	31	26	757	CC	0.999931	0.999931	0			7	48	209	0	0	14.552528	59	60	1984	229		0.106061	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68431179	68431179	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68431179C>A			NA	NA				MIR4477B (15791 upstream) : CR786580.2 (81166 downstream)						NA		NA									NA						CCAAAGAGACCCAGAAAACTT	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68431179C>A		NA		hg19		0.02	2.866228	GACxCAG	COVERED																																																																																			NOVEL					0			3	7.219877	KEEP	13	0	0	24	701	CC	0.999879	0.999876	0			10	60	290	0	0	21.957081	51	60	1716	189		0.163934	0.999997
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68433464	68433464	__UNKNOWN__	IGR	SNP	C	C	T	rs79004307		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68433464C>T			NA	NA				MIR4477B (18076 upstream) : CR786580.2 (78881 downstream)						NA		NA									NA						GTCATCATTACCTTGATCATT	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68433464C>T		NA		hg19		0.02	8.182029	TTAxCTT	COVERED																																																																																			NOVEL					0			9	11.767127	KEEP	9	1	28	49	1494	CC	1	1	0			18	60	546	0	0	35.862674	210	65	7085	485		0.078947	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68433568	68433568	__UNKNOWN__	IGR	SNP	T	T	C	rs139880713		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68433568T>C			NA	NA				MIR4477B (18180 upstream) : CR786580.2 (78777 downstream)						NA		NA									NA						CATTTTCCCCTAAGTGAAACA	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68433568T>C		NA		hg19		0.02	7.820962	CCCxAAG	COVERED																																																																																			NOVEL					0			10	3.47044	KEEP	37	2	61	33	896	TT	0.999997	0.999997	0			11	60	379	1	0	27.146221	110	60	3322	412		0.090909	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68433588	68433588	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68433588A>T			NA	NA				MIR4477B (18200 upstream) : CR786580.2 (78757 downstream)						NA		NA									NA						AAAATAACAAAATAGCCATGA	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68433588A>T		NA		hg19		0.02	6.265531	CAAxATA	COVERED																																																																																			NOVEL					0			13	6.249984	KEEP	34	1	29	31	899	AA	0.999997	0.999997	0			17	60	515	0	0	38.293236	104	60	3191	418		0.140496	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68439591	68439591	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68439591G>T			NA	NA				MIR4477B (24203 upstream) : CR786580.2 (72754 downstream)						NA		NA									NA						ctcccaaagtgctgggattac	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68439591G>T		NA		hg19		0.02	2.774118	AGTxCTG	COVERED																																																																																			NOVEL					0			40	8.993639	KEEP	22	2	60	51	1553	GG	1	0.999984	0			7	60	169	0	0	11.168757	49	60	1659	244		0.125	0.999984
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68452988	68452988	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68452988C>T			NA	NA				MIR4477B (37600 upstream) : CR786580.2 (59357 downstream)						NA		NA									NA						cttatctttgctctttttctt	0.294		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68452988C>T		NA		hg19		0.02	-0.324573	TTGxTCT	COVERED																																																																																			NOVEL					0			7	3.911868	KEEP	7	0	0	13	405	CC	0.993072	0.829926	0			8	36	245	0	0	20.379926	25	60	838	65		0.242424	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68482560	68482560	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68482560G>T			NA	NA				MIR4477B (67172 upstream) : CR786580.2 (29785 downstream)						NA		NA									NA						taggaggatcgcttgagccca	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68482560G>T		NA		hg19		0.02	-0.359646	ATCxCTT	COVERED																																																																																			NOVEL					0			23	5.145441	KEEP	14	1	28	27	774	GG	0.999909	0.908987	0			4	49	119	0	0	8.695014	26	60	875	111		0.133333	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68484625	68484625	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68484625C>T			NA	NA				MIR4477B (69237 upstream) : CR786580.2 (27720 downstream)						NA		NA									NA						cttccaactcctggcctcaag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68484625C>T		NA		hg19		0.02	3.081265	CTCxTGG	COVERED																																																																																			NOVEL					0			74	20.890362	KEEP	16	1	27	79	2427	CC	1	0.999996	0			5	47	154	0	0	10.393512	53	60	1824	289		0.086207	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68681852	68681852	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68681852C>A			NA	NA				CR786580.1 (168665 upstream) : AL353763.2 (315556 downstream)						NA		NA									NA						tggggtctcactttattgccc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68681852C>A		NA		hg19		0.02	1.295942	TCAxTTT	COVERED																																																																																			NOVEL					0			37	4.911933	KEEP	26	3	84	46	1362	CC	1	0.995686	0			4	49	122	0	0	7.674539	58	51	1907	166		0.064516	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68681946	68681946	__UNKNOWN__	IGR	SNP	G	G	A	rs368013472		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68681946G>A			NA	NA				CR786580.1 (168759 upstream) : AL353763.2 (315462 downstream)						NA		NA									NA						gagccaccatgcccagtccta	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68681946G>A		NA		hg19		0.02	1.118079	CATxCCC	COVERED																																																																																			NOVEL					0			39	2.470946	KEEP	33	5	129	54	1622	GG	1	0.998867	0			7	60	192	0	0	12.762356	61	50	2077	228		0.102941	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728799	68728799	__UNKNOWN__	IGR	SNP	A	A	T	rs4928724	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68728799A>T			NA	NA				CR786580.1 (215612 upstream) : AL353763.2 (268609 downstream)						NA		NA									NA						ACACAAATCAATATACTTAAA	0.264		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728799A>T		NA		hg19		0.02	1.091938	TCAxTAT	COVERED																																																																																			NOVEL					0			0	3.027211	KEEP	4	1	25	19	483	AA	0.999863	0.999081	0			9	60	231	0	0	23.000903	6	60	177	104		0.6	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728896	68728896	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68728896T>G			NA	NA				CR786580.1 (215709 upstream) : AL353763.2 (268512 downstream)						NA		NA									NA						gaaACCCAGCTTGATATGTTG	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728896T>G		NA		hg19		0.02	17.012253	AGCxTGA	COVERED																																																																																			NOVEL					0			39	54.986151	KEEP	71	2	66	206	5826	TT	1	1	0			12	47	421	0	0	23.911655	430	60	13311	1264		0.027149	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728922	68728922	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68728922G>A			NA	NA				CR786580.1 (215735 upstream) : AL353763.2 (268486 downstream)						NA		NA									NA						TCAGTTTTCAGTGCTTTATTC	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728922G>A		NA		hg19		0.02	14.213981	TCAxTGC	COVERED																																																																																			NOVEL					0			35	4.659029	KEEP	76	17	465	180	5564	GG	1	1	0			33	60	976	0	0	62.61192	404	60	14173	1204		0.075515	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728952	68728952	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68728952T>C			NA	NA				CR786580.1 (215765 upstream) : AL353763.2 (268456 downstream)						NA		NA									NA						TTAACATTTCTTGAGATCTCA	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728952T>C		NA		hg19		0.02	12.078801	TTCxTGA	COVERED																																																																																			NOVEL					0			18	5.81087	KEEP	68	9	281	118	3326	TT	1	1	0			23	59	808	1	0	56.300475	284	60	8835	710		0.074919	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	68728997	68728997	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:68728997T>C			NA	NA				CR786580.1 (215810 upstream) : AL353763.2 (268411 downstream)						NA		NA									NA						ATTTATGATGTATTCATATTT	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.68728997T>C		NA		hg19		0.02	1.634516	ATGxATT	COVERED																																																																																			NOVEL					0			1	3.735504	KEEP	15	1	30	23	583	TT	0.999869	0.999547	0			7	40	230	0	0	16.242842	68	50	1931	123		0.093333	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69007505	69007505	__UNKNOWN__	IGR	SNP	C	C	A	rs369301876		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69007505C>A			NA	NA				MIR1299 (5184 upstream) : PGM5P2 (72734 downstream)						NA		NA									NA						aaaaattagccaggcttggtg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69007505C>A		NA		hg19		0.02	-0.228071	AGCxAGG	COVERED																																																																																			NOVEL					0			17	5.717085	KEEP	14	0	0	19	585	CC	0.994391	0.57966	0			5	60	154	0	0	12.665483	17	60	575	72		0.227273	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69007611	69007611	__UNKNOWN__	IGR	SNP	T	T	C	rs529174685	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69007611T>C			NA	NA				MIR1299 (5290 upstream) : PGM5P2 (72628 downstream)						NA		NA									NA						attgcaccactgcactccagc	0.483		NA											.|||	680	0.135783	0.2224	0.1441	5008	,	,	NA	18768	0.0149	NA	0.2266	False	NA	,,,	NA	NA	NA	2504	0.044	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69007611T>C		NA		hg19		0.02	-0.403443	CACxGCA	COVERED																																																																																			NOVEL					0			26	8.420957	KEEP	16	0	0	28	775	TT	0.999879	0.934379	0			3	60	96	0	0	6.710256	29	60	863	109		0.09375	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69067929	69067929	__UNKNOWN__	IGR	SNP	G	G	A	rs113676670		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69067929G>A			NA	NA				MIR1299 (65608 upstream) : PGM5P2 (12310 downstream)						NA		NA									NA						TGATATGTTGGTGAGTCAGTT	0.279		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69067929G>A		NA		hg19		0.02	3.221186	TTGxTGA	COVERED																																																																																			NOVEL					0			19	6.485606	KEEP	85	2	55	41	1257	GG	0.999988	0.999987	0			20	51	620	0	0	48.14708	99	60	3363	384		0.168067	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69073538	69073538	__UNKNOWN__	IGR	SNP	A	A	C	rs374347188		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69073538A>C			NA	NA				MIR1299 (71217 upstream) : PGM5P2 (6701 downstream)						NA		NA									NA						ttttgtagagatgggggtctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69073538A>C		NA		hg19		0.02	-0.149114	GAGxTGG	COVERED																																																																																			NOVEL					0			33	2.971159	KEEP	51	2	63	32	869	AA	0.993072	0.289978	0			3	25	108	0	0	9.181932	10	40	305	109		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69073583	69073583	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69073583C>T			NA	NA				MIR1299 (71262 upstream) : PGM5P2 (6656 downstream)						NA		NA									NA						aactcctgggcttaagtgatt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69073583C>T		NA		hg19		0.02	-0.149133	GGGxTTA	COVERED																																																																																			NOVEL					0			24	3.377276	KEEP	40	2	53	30	939	CC	0.993634	0.290142	0			4	40	119	0	0	10.030686	11	49	390	93		0.266667	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69073596	69073596	__UNKNOWN__	IGR	SNP	C	C	T	rs374645410		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69073596C>T			NA	NA				MIR1299 (71275 upstream) : PGM5P2 (6643 downstream)						NA		NA									NA						aagtgattctcctgcttccac	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69073596C>T		NA		hg19		0.02	-0.140348	TCTxCTG	COVERED																																																																																			NOVEL					0			23	4.078598	KEEP	34	2	46	30	899	CC	0.994391	0.259501	0			4	40	115	0	0	9.501284	12	60	401	82		0.25	0.260965
CR769776.1	0	__UNKNOWN__	__UNKNOWN__	9	69378666	69378666	__UNKNOWN__	Intron	SNP	A	A	G	rs62559754		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69378666A>G	ENST00000414341.2	-	2	1305										NA		NA									NA						aggccgaggcaggtagatcat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000414341.2:c.418-52T>C	chr9.hg19:g.69378666A>G		NA		hg19		0.02	-0.087717	GGCxGGT	UNCOVERED																																																																																			NOVEL	CR769776.1-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		6	2.406607	KEEP	3	0	0	8	229	AA	0	0	0		-	3	25	100	0	0	8.778644	7	60	216	27	ENST00000414341.2	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69432113	69432113	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69432113C>G			NA	NA				ANKRD20A4 (6553 upstream) : AL445665.2 (155264 downstream)						NA		NA									NA						tgtggtggctcacacctgtaa	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69432113C>G		NA		hg19		0.02	-0.263172	GCTxACA	COVERED																																																																																			NOVEL					0			14	6.292889	KEEP	31	0	0	21	631	CC	0.99254	0.711964	0			3	44	105	0	0	8.409798	15	46	506	115		0.166667	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	69834691	69834691	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:69834691T>C			NA	NA				AL359955.1 (12850 upstream) : RNU6-1293P (58095 downstream)						NA		NA									NA						gtgatccgcctgcctcggcct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.69834691T>C		NA		hg19		0.02	-0.140343	GCCxGCC	COVERED																																																																																			NOVEL					0			3	3.909282	KEEP	2	0	0	13	366	TT	0.994391	0.259501	0			3	60	106	0	0	8.981945	10	60	304	52		0.230769	0.260965
RP11-274B18.4	0	__UNKNOWN__	__UNKNOWN__	9	71195556	71195556	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:71195556A>G	ENST00000413269.3	+	0	460										NA		NA									NA						tgggattacaagcatgagcca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000413269.3:	chr9.hg19:g.71195556A>G		NA		hg19		0.02	-0.210511	ACAxGCA	COVERED																																																																																			NOVEL	RP11-274B18.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000052555.2	10	3.007145	KEEP	2	0	0	10	273	AA	0.992708	0.518353	0		+	3	60	105	0	0	8.064549	20	60	613	50	ENST00000413269.3	0.130435	0.522161
RP11-274B18.4	0	__UNKNOWN__	__UNKNOWN__	9	71209876	71209876	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:71209876T>C	ENST00000413269.3	+	0	460										NA		NA									NA						ggattacaggtgtgagccact	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000413269.3:	chr9.hg19:g.71209876T>C		NA		hg19		0.02	-0.184135	AGGxGTG	UNCOVERED																																																																																			NOVEL	RP11-274B18.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000052555.2	11	3.306212	KEEP	12	0	0	11	286	TT	0	0	0		+	3	45	96	0	0	7.592562	14	60	408	51	ENST00000413269.3	0.176471	0.423478
FXN	2395	__UNKNOWN__	__UNKNOWN__	9	71673977	71673977	__UNKNOWN__	Intron	SNP	T	T	C	rs35739047		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:71673977T>C	ENST00000377270.3	+	3	908				FXN_ENST00000498653.1_Intron|FXN_ENST00000396366.2_Intron|FXN_ENST00000396364.3_Intron	NM_000144.4	NP_000135.2	Q16595	FRDA_HUMAN	frataxin	NA		NA			adult walking behavior (GO:0007628)|aerobic respiration (GO:0009060)|cellular iron ion homeostasis (GO:0006879)|cellular response to hydrogen peroxide (GO:0070301)|embryo development ending in birth or egg hatching (GO:0009792)|heme biosynthetic process (GO:0006783)|ion transport (GO:0006811)|iron incorporation into metallo-sulfur cluster (GO:0018283)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|oxidative phosphorylation (GO:0006119)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)|proprioception (GO:0019230)|protein autoprocessing (GO:0016540)|regulation of ferrochelatase activity (GO:0010722)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)|iron chaperone activity (GO:0034986)|iron-sulfur cluster binding (GO:0051536)			large_intestine(1)|lung(1)	2						gagcgagacttcatcttaaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U43752	CCDS6626.1, CCDS43834.1, CCDS55313.1	9q21.11	2014-09-17	2004-08-16	2004-08-19	ENSG00000165060	ENSG00000165060	2395			3951	protein-coding gene	gene with protein product		606829	Friedreich ataxia	FRDA	NA	8596916, 8841185	Standard	NM_000144	NM_000144	NA	Approved	FA, FARR, X25, CyaY	uc004aha.2	Q16595	OTTHUMG00000019977	ENST00000377270.3:c.384+5801T>C	chr9.hg19:g.71673977T>C		NA	A8MXJ6|C9JJ89|O15545|O95656|Q15294|Q5VZ01	hg19	CCDS6626.1	0.02	-0.42043	ACTxCAT	COVERED																																																																																			NOVEL	FXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052568.2	13	4.743804	KEEP	0	1	29	26	718	TT	0.999988	0.94839	0		+	3	60	107	2	0	7.378763	41	60	1201	118	ENST00000377270.3	0.068182	0.948402
FXN	2395	__UNKNOWN__	__UNKNOWN__	9	71695156	71695156	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:71695156C>T	ENST00000396364.3	+	4	702					NM_001161706.1	NP_001155178.1	Q16595	FRDA_HUMAN	frataxin	NA		NA			adult walking behavior (GO:0007628)|aerobic respiration (GO:0009060)|cellular iron ion homeostasis (GO:0006879)|cellular response to hydrogen peroxide (GO:0070301)|embryo development ending in birth or egg hatching (GO:0009792)|heme biosynthetic process (GO:0006783)|ion transport (GO:0006811)|iron incorporation into metallo-sulfur cluster (GO:0018283)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|oxidative phosphorylation (GO:0006119)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)|proprioception (GO:0019230)|protein autoprocessing (GO:0016540)|regulation of ferrochelatase activity (GO:0010722)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)|iron chaperone activity (GO:0034986)|iron-sulfur cluster binding (GO:0051536)			large_intestine(1)|lung(1)	2						agtgagactccatctcaaaaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U43752	CCDS6626.1, CCDS43834.1, CCDS55313.1	9q21.11	2014-09-17	2004-08-16	2004-08-19	ENSG00000165060	ENSG00000165060	2395			3951	protein-coding gene	gene with protein product		606829	Friedreich ataxia	FRDA	NA	8596916, 8841185	Standard	NM_000144	NM_000144	NA	Approved	FA, FARR, X25, CyaY	uc004aha.2	Q16595	OTTHUMG00000019977	ENST00000396364.3:c.482+15205C>T	chr9.hg19:g.71695156C>T		NA	A8MXJ6|C9JJ89|O15545|O95656|Q15294|Q5VZ01	hg19	CCDS55313.1	0.02	-0.087708	CTCxATC	UNCOVERED																																																																																			NOVEL	FXN-201	KNOWN	basic|CCDS	protein_coding	NA	protein_coding		5	2.707973	KEEP	4	0	0	9	275	CC	0	0	0		+	3	22	82	0	0	6.978033	7	60	232	29	ENST00000396364.3	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	71730132	71730132	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:71730132A>G			NA	NA				FXN (15038 upstream) : TJP2 (6091 downstream)						NA		NA									NA						ctggagtgcaatggtgtgatc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.71730132A>G		NA		hg19		0.02	-0.10524	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			9	4.204237	KEEP	5	0	0	14	362	AA	0.993072	0.138863	0			3	60	106	0	0	9.379169	7	60	194	38		0.3	0.139832
TJP2	9414	__UNKNOWN__	__UNKNOWN__	9	71800177	71800177	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:71800177C>T	ENST00000377245.4	+	1	268				TJP2_ENST00000265384.7_Intron|TJP2_ENST00000377259.1_Intron|TJP2_ENST00000453658.2_Intron|TJP2_ENST00000348208.4_Intron	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	NA		NA			apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						agggtttcaccatgttggcca	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139	9414			11828	protein-coding gene	gene with protein product	Friedreich ataxia region gene X104 (tight junction protein ZO-2), zona occludens 2	607709	deafness, autosomal dominant 51	DFNA51	NA	7951235, 20602916	Standard	NM_201629	NM_001170630	NA	Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.60+10829C>T	chr9.hg19:g.71800177C>T		NA	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	hg19	CCDS6627.1	0.02	-0.140344	CACxATG	UNCOVERED																																																																																			NOVEL	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052572.2	8	2.707819	KEEP	10	0	0	9	272	CC	0	0	0		+	3	20	87	0	0	6.872384	12	60	398	39	ENST00000377245.4	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	72017147	72017147	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:72017147G>T			NA	NA				FAM189A2 (9776 upstream) : APBA1 (25298 downstream)						NA		NA									NA						acagagtctcgctctgttgcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.72017147G>T		NA		hg19		0.02	-0.087715	CTCxCTC	UNCOVERED																																																																																			NOVEL					0			11	2.70658	KEEP	8	0	0	9	252	GG	0	0	0			3	22	97	0	0	8.643506	6	50	201	27		0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	72025431	72025431	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:72025431G>A			NA	NA				FAM189A2 (18060 upstream) : APBA1 (17014 downstream)						NA		NA									NA						cagcctgggcgacagagtgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.72025431G>A		NA		hg19		0.02	-0.131553	GGCxACA	UNCOVERED																																																																																			NOVEL					0			5	2.40601	KEEP	1	0	0	8	222	GG	0	0	0			3	60	89	0	1	7.072641	12	60	370	28		0.2	0.229173
APBA1	320	__UNKNOWN__	__UNKNOWN__	9	72151768	72151768	__UNKNOWN__	Intron	SNP	T	T	C	rs183092413	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:72151768T>C	ENST00000265381.4	-	2	154					NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	NA		NA			axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						tgcactccagtctgggtgaca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282	320			578	protein-coding gene	gene with protein product		602414		MINT1	NA	7678331, 7719031	Standard	NM_001163	NM_001163	NA	Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.69-19573A>G	chr9.hg19:g.72151768T>C		NA	O14914|O60570|Q5VYR8	hg19	CCDS6630.1	0.02	-0.096484	CAGxCTG	UNCOVERED																																																																																			NOVEL	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052589.2	7	2.706735	KEEP	0	0	0	9	245	TT	0.99254	0.119538	0		-	4	60	136	0	0	12.823625	5	60	145	30	ENST00000265381.4	0.444444	0.120436
TRPM3	80036	__UNKNOWN__	__UNKNOWN__	9	73989262	73989262	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:73989262T>C	ENST00000357533.2	-	1	183				TRPM3_ENST00000423814.3_Intron			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	NA		NA			calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						tgcactccagtctgggcaaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067	80036		Voltage-gated ion channels / Transient receptor potential cation channels	17992	protein-coding gene	gene with protein product	melastatin 2	608961			NA	16382100	Standard	NM_206945	NM_206946	NA	Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000357533.2:c.183+72306A>G	chr9.hg19:g.73989262T>C		NA	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	hg19		0.02	-0.140337	CAGxCTG	COVERED																																																																																			NOVEL	TRPM3-014	PUTATIVE	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000214163.1	4	2.405191	KEEP	1	0	0	8	210	TT	0.99257	0.259026	0		-	3	60	104	0	0	8.572207	12	60	354	39	ENST00000357533.2	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	74256156	74256156	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:74256156G>A			NA	NA				TRPM3 (194405 upstream) : TMEM2 (42125 downstream)						NA		NA									NA						aggctgaggtgggaggatcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.74256156G>A		NA		hg19		0.02	-0.140347	GGTxGGA	COVERED																																																																																			NOVEL					0			7	3.008806	KEEP	0	0	0	10	304	GG	0.992708	0.259062	0			3	60	86	0	0	6.981935	10	60	330	35		0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	74438991	74438991	__UNKNOWN__	IGR	SNP	C	C	A	rs7870238	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:74438991C>A			NA	NA				TMEM2 (55191 upstream) : ABHD17B (38376 downstream)						NA		NA									NA						tcactgcaacctctgcctcct	0.433		NA											C|||	4120	0.822684	0.6059	0.8833	5008	,	,	NA	12123	0.9415	NA	0.8459	False	NA	,,,	NA	NA	NA	2504	0.9264	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.74438991C>A		NA		hg19		0.02	-0.210541	AACxTCT	COVERED																																																																																			NOVEL					0			17	3.912026	KEEP	10	0	0	13	412	CC	0.993072	0.518544	0			4	60	122	0	0	10.623421	9	38	316	68		0.307692	0.522161
C9orf85	138241	__UNKNOWN__	__UNKNOWN__	9	74597720	74597720	__UNKNOWN__	Silent	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:74597720C>T	ENST00000377031.3	+	4	661	c.471C>T	c.(469-471)atC>atT	p.I157I	C9orf85_ENST00000486911.2_Intron			Q96MD7	CI085_HUMAN	chromosome 9 open reading frame 85	157		NA								kidney(2)|large_intestine(1)|lung(4)	7						cccagctaatctttgtatttt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			BC010179	CCDS6639.1	9q21.2	2012-03-16			ENSG00000155621	ENSG00000155621	138241			28784	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182505	NM_182505	NA	Approved	MGC61599	uc004ain.3	Q96MD7	OTTHUMG00000020002	ENST00000377031.3:c.471C>T	chr9.hg19:g.74597720C>T		NA	Q5W0N1|Q5W0N3|Q6PJW9|Q86U95	hg19		0.02	-0.131563	AATxTTT	COVERED																																																																																			NOVEL	C9orf85-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000052628.2	4	2.406737	KEEP	0	0	0	8	233	CC	0.99257	0.22747	0		+	3	60	82	1	2	6.473207	11	60	355	25	ENST00000377031.3	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	74665662	74665662	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:74665662C>A			NA	NA				C9orf85 (64692 upstream) : C9orf57 (629 downstream)						NA		NA									NA						aaaaaaaaaacaaaaacaaaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.74665662C>A		NA		hg19		0.02	-0.131572	AAAxAAA	COVERED																																																																																			NOVEL					0			2	2.70832	KEEP	1	0	0	9	284	CC	0.99254	0.227464	0			3	60	89	0	0	7.282004	10	60	327	42		0.230769	0.229173
GDA	9615	__UNKNOWN__	__UNKNOWN__	9	74829483	74829483	__UNKNOWN__	Intron	SNP	T	T	C	rs11143173	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:74829483T>C	ENST00000358399.3	+	5	671				GDA_ENST00000376986.1_Intron|GDA_ENST00000376989.3_Intron|GDA_ENST00000477618.1_Intron|GDA_ENST00000238018.4_Intron|GDA_ENST00000545168.1_Intron	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	NA		NA			guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		gtgctgagattacaggcgtga	0.517		NA											T|||	1433	0.286142	0.0991	0.2406	5008	,	,	NA	13067	0.5298	NA	0.2286	False	NA	,,,	NA	NA	NA	2504	0.3793	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125	9615			4212	protein-coding gene	gene with protein product		139260			NA	10075721, 3966794	Standard		NM_001242507	NA	Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.578+576T>C	chr9.hg19:g.74829483T>C		NA	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	hg19	CCDS6641.1	0.02	-0.209133	GATxACA	COVERED																																																																																			NOVEL	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052633.1	7	2.403124	KEEP	0	0	0	8	206	TT	0.99257	0.518282	0		+	11	60	386	0	0	37.948196	9	60	225	47	ENST00000358399.3	0.55	0.522161
TMC1	117531	__UNKNOWN__	__UNKNOWN__	9	75154215	75154215	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:75154215G>A	ENST00000297784.5	+	1	113					NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	NA		NA			auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						ccagttactcgggaggctgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(75;173 1345 14232 34245 43413)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091	117531			16513	protein-coding gene	gene with protein product		606706	transmembrane, cochlear expressed, 1	DFNA36, DFNB7, DFNB11	NA	11850618, 11850623	Standard		NM_138691	NA	Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.-428+17386G>A	chr9.hg19:g.75154215G>A		NA	A8MVZ2|B1AM91	hg19	CCDS6643.1	0.02	-0.11402	CTCxGGA	UNCOVERED																																																																																			NOVEL	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052655.1	8	4.511751	KEEP	1	0	0	15	435	GG	0.995343	0.16171	0		+	3	60	91	0	0	7.601224	9	60	287	38	ENST00000297784.5	0.25	0.162467
TMC1	117531	__UNKNOWN__	__UNKNOWN__	9	75164788	75164788	__UNKNOWN__	Intron	SNP	G	G	A	rs575830991		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:75164788G>A	ENST00000297784.5	+	1	113					NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	NA		NA			auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						ttggcctcccgaagtgctggg	0.502		NA											g|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16616	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Pancreas(75;173 1345 14232 34245 43413)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091	117531			16513	protein-coding gene	gene with protein product		606706	transmembrane, cochlear expressed, 1	DFNA36, DFNB7, DFNB11	NA	11850618, 11850623	Standard		NM_138691	NA	Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.-428+27959G>A	chr9.hg19:g.75164788G>A		NA	A8MVZ2|B1AM91	hg19	CCDS6643.1	0.02	-0.149122	CCCxAAG	COVERED																																																																																			NOVEL	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052655.1	9	3.008544	KEEP	0	0	0	10	307	GG	0.992708	0.289872	0		+	3	60	89	0	0	6.979016	13	60	430	39	ENST00000297784.5	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	77096361	77096361	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:77096361T>C			NA	NA				RP11-171A24.2 (97915 upstream) : RP11-171A24.3 (4105 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.77096361T>C		NA		hg19		0.02	-0.140289	TCAxGCC	COVERED																																																																																			NOVEL					0			2	3.909614	KEEP	0	0	0	13	355	TT	0.994391	0.259501	0			3	60	87	0	0	6.873411	12	60	336	45		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	77545861	77545861	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:77545861C>A			NA	NA				TRPM6 (42851 upstream) : C9orf40 (15635 downstream)						NA		NA									NA						aaaaaacaaacaaaaaaaaCT	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.77545861C>A		NA		hg19		0.02	-0.157894	AAAxAAA	COVERED																																																																																			NOVEL					0			9	3.00824	KEEP	0	0	0	10	290	CC	0.992708	0.320453	0			3	60	89	2	0	6.891995	14	60	471	39		0.176471	0.322807
OSTF1	26578	__UNKNOWN__	__UNKNOWN__	9	77719442	77719442	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:77719442T>C	ENST00000346234.6	+	2	184					NM_012383.4	NP_036515.4	Q92882	OSTF1_HUMAN	osteoclast stimulating factor 1	NA		NA			ossification (GO:0001503)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)				endometrium(1)|skin(1)	2						ggtgacagagtgagaccctgt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U63717	CCDS6651.1	9q13-q21.2	2013-01-10			ENSG00000134996	ENSG00000134996	26578		Ankyrin repeat domain containing	8510	protein-coding gene	gene with protein product		610180			NA	10092216	Standard	NM_012383	NM_012383	NA	Approved	SH3P2, OSF, bA235O14.1	uc004ajv.4	Q92882	OTTHUMG00000020033	ENST00000346234.6:c.35-12978T>C	chr9.hg19:g.77719442T>C		NA	Q5W126|Q96IJ4	hg19	CCDS6651.1	0.02	-0.131561	GAGxGAG	COVERED																																																																																			NOVEL	OSTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052704.1	6	2.406146	KEEP	0	0	0	8	221	TT	0.99257	0.22747	0		+	3	47	100	0	0	8.272951	11	60	335	34	ENST00000346234.6	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	77774535	77774535	__UNKNOWN__	IGR	SNP	A	A	G	rs530271684		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:77774535A>G			NA	NA				OSTF1 (12354 upstream) : Y_RNA (21900 downstream)						NA		NA									NA						cacccgcctcagcctcccaaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.77774535A>G		NA		hg19		0.02	-0.08771	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			6	3.308898	KEEP	5	0	0	11	315	AA	0	0	0			3	60	91	0	0	8.232785	5	60	148	32		0.375	0.120436
PCSK5	5125	__UNKNOWN__	__UNKNOWN__	9	78790187	78790187	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs10118321	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:78790187G>C	ENST00000376767.3	+	14	2554	c.2042G>C	c.(2041-2043)tGg>tCg	p.W681S	PCSK5_ENST00000376752.4_Intron|PCSK5_ENST00000545128.1_Intron			Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	0	CRM (Cys-rich motif).	NA			anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ggaatggaatggaatcgaatc	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139	5125			8747	protein-coding gene	gene with protein product		600488			NA	7782070	Standard		NM_001190482	NA	Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000376767.3:c.2042G>C	chr9.hg19:g.78790187G>C	ENSP00000365958:p.Trp681Ser	NA	F5H2G7|Q13527|Q96EP4	hg19		0.02	-0.096489	AATxGAA	UNCOVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	0.135|0.135	-1.109232|-1.109232	0.01813|0.01813	.|.	.|.	ENSG00000099139|ENSG00000099139	ENST00000396108|ENST00000376767	.|T	.|0.78126	.|-1.15	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.69043|0.69043	0.3067|0.3067	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|P	.|0.44006	.|0.824	.|B	.|0.42959	.|0.403	T|T	0.60073|0.60073	-0.7334|-0.7334	4|7	0.14252|0.72032	T|D	0.57|0.01	.|.	4.6597|4.6597	0.12636|0.12636	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs10118321|rs10118321	.|681	.|B1AMG5	.|.	I|S	679|681	.|ENSP00000365958:W681S	ENSP00000379415:M679I|ENSP00000365958:W681S	M|W	+|+	3|2	0|0	PCSK5|PCSK5	77980007|77980007	0.006000|0.006000	0.16342|0.16342	0.095000|0.095000	0.20976|0.20976	0.096000|0.096000	0.18686|0.18686	-1.253000|-1.253000	0.02877|0.02877	-0.000000|-0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	ATG|TGG	NOVEL	PCSK5-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000052718.1	10	3.008622	KEEP	11	0	0	10	297	GG	0	0	0		+	3	60	95	0	0	8.443497	6	60	188	28	ENST00000376767.3	0.333333	0.120436
GCNT1	2650	__UNKNOWN__	__UNKNOWN__	9	79114106	79114106	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:79114106T>C	ENST00000376730.4	+	3	194				GCNT1_ENST00000444201.2_Intron|GCNT1_ENST00000442371.1_Intron|GCNT1_ENST00000536223.1_Intron|GCNT1_ENST00000488136.1_Intron	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	NA		NA			cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						tgcagtggcatgatcttggct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2650	2.4.1.102	Glucosaminyl (N-acetyl) transferase and xylosyltransferase family	4203	protein-coding gene	gene with protein product	core 2 beta1,6 N-acetylglucosaminyltransferase-I, beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase	600391	glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)	NACGT2	NA	8449405, 9915862	Standard	NM_001097634	NM_001490	NA	Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.-289-1726T>C	chr9.hg19:g.79114106T>C		NA	Q6DJZ4	hg19	CCDS6653.1	0.02	-0.140134	GCAxGAT	COVERED																																																																																			NOVEL	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052725.1	4	2.406363	KEEP	0	0	0	8	225	TT	0.99257	0.259026	0		+	3	60	97	0	0	7.7813	13	60	369	36	ENST00000376730.4	0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	79203817	79203817	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:79203817C>T			NA	NA				AL161626.1 (17030 upstream) : PRUNE2 (22474 downstream)						NA		NA									NA						ccacccgcctcggcctcccaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.79203817C>T		NA		hg19		0.02	-0.175432	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			11	3.008319	KEEP	11	0	0	10	293	CC	0	0	0			3	60	85	0	0	6.411385	15	60	499	52		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	80297766	80297766	__UNKNOWN__	IGR	SNP	C	C	T	rs11792972	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:80297766C>T			NA	NA				GNA14 (34543 upstream) : GNAQ (33236 downstream)						NA		NA									NA						gtgatccgcccgcctcggcct	0.537		NA											-|||	2362	0.471645	0.1498	0.5548	5008	,	,	NA	11796	0.4603	NA	0.7107	False	NA	,,,	NA	NA	NA	2504	0.6135	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.80297766C>T		NA		hg19		0.02	-0.105261	GCCxGCC	UNCOVERED																																																																																			NOVEL					0			10	2.439613	KEEP	25	1	22	16	488	CC	0	0	0			3	60	89	0	0	7.678341	7	60	234	55		0.3	0.139832
GNAQ	2776	__UNKNOWN__	__UNKNOWN__	9	80333166	80333166	__UNKNOWN__	3'UTR	SNP	C	C	T	rs74472483		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:80333166C>T	ENST00000286548.4	-	0	4375					NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	NA		NA			action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						ACGCTTATAACGCTTGCAATC	0.413		NA	Mis		uveal melanoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		9	9q21	2776	guanine nucleotide binding protein (G protein), q polypeptide		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052	2776			4390	protein-coding gene	gene with protein product		600998			NA	8825633	Standard	NM_002072	NM_002072	NA	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.*3073G>A	chr9.hg19:g.80333166C>T		NA	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	hg19	CCDS6658.1	0.02	1.327368	TAAxGCT	COVERED																																																																																			NOVEL	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052761.1	7	10.453574	KEEP	0	1	26	44	1217	CC	1	0.999726	0		-	11	60	318	0	0	22.719198	76	60	2390	172	ENST00000286548.4	0.126437	0.999726
GNAQ	2776	__UNKNOWN__	__UNKNOWN__	9	80566211	80566211	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:80566211T>A	ENST00000286548.4	-	2	359					NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	NA		NA			action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						acggggtttctccatgttggc	0.537		NA	Mis		uveal melanoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		9	9q21	2776	guanine nucleotide binding protein (G protein), q polypeptide		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052	2776			4390	protein-coding gene	gene with protein product		600998			NA	8825633	Standard	NM_002072	NM_002072	NA	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.137-28950A>T	chr9.hg19:g.80566211T>A		NA	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	hg19	CCDS6658.1	0.02	-0.114007	TTCxCCA	COVERED																																																																																			NOVEL	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052761.1	7	2.705777	KEEP	3	0	0	9	235	TT	0.99257	0.22747	0		-	3	60	85	0	0	7.001303	9	60	266	33	ENST00000286548.4	0.25	0.229173
GNAQ	2776	__UNKNOWN__	__UNKNOWN__	9	80646212	80646212	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:80646212A>G	ENST00000286548.4	-	0	162					NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	NA		NA			action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)			NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						GCGCACACACACCCTCCCGCC	0.761		NA	Mis		uveal melanoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		9	9q21	2776	guanine nucleotide binding protein (G protein), q polypeptide		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052	2776			4390	protein-coding gene	gene with protein product		600998			NA	8825633	Standard	NM_002072	NM_002072	NA	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.-61T>C	chr9.hg19:g.80646212A>G		NA	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	hg19	CCDS6658.1	0.02	1.842176	CACxCCC	COVERED																																																																																			NOVEL	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052761.1	4	8.742694	KEEP	3	1	5	31	804	AA	1	0.963774	0		-	5	60	164	0	0	11.687019	46	60	1168	158	ENST00000286548.4	0.098039	0.963774
CEP78	84131	__UNKNOWN__	__UNKNOWN__	9	80887114	80887114	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:80887114A>G	ENST00000424347.2	+	0	3706							Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						gattacaggcatgagccactg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019	84131			25740	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 81	C9orf81	NA	14654843	Standard	XM_095991	NM_001098802	NA	Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.*1347A>G	chr9.hg19:g.80887114A>G		NA	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	hg19		0.02	-0.192962	GGCxTGA	COVERED																																																																																			NOVEL	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000052766.2	12	3.30839	KEEP	1	0	0	11	303	AA	0.993072	0.454585	0		+	3	60	101	0	1	7.933233	16	60	481	46	ENST00000424347.2	0.157895	0.457757
CEP78	84131	__UNKNOWN__	__UNKNOWN__	9	80890586	80890586	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:80890586T>C	ENST00000424347.2	+	0	7178							Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						gtggctcatgtctgtaatccc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019	84131			25740	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 81	C9orf81	NA	14654843	Standard	XM_095991	NM_001098802	NA	Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.*4819T>C	chr9.hg19:g.80890586T>C		NA	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	hg19		0.02	6.079213	ATGxCTG	COVERED																																																																																			NOVEL	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000052766.2	42	7.876399	KEEP	1	5	147	78	2132	TT	1	1	0		+	7	60	245	0	0	15.668213	138	70	4065	338	ENST00000424347.2	0.048276	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	82430418	82430418	__UNKNOWN__	IGR	SNP	G	G	A	rs7039819	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:82430418G>A			NA	NA				TLE4 (88760 upstream) : RP11-403N16.2 (59192 downstream)						NA		NA									NA						gcctcccaaagtgctgggatt	0.463		NA											G|||	3164	0.631789	0.6747	0.6066	5008	,	,	NA	18684	0.6786	NA	0.5944	False	NA	,,,	NA	NA	NA	2504	0.5818	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.82430418G>A		NA		hg19		0.02	-0.219279	AAAxTGC	UNCOVERED																																																																																			NOVEL					0			4	2.407222	KEEP	1	0	0	8	247	GG	0	0	0			16	60	481	0	0	49.095381	8	60	260	49		0.666667	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	83982943	83982943	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:83982943T>C			NA	NA				RP11-289F5.1 (496733 upstream) : TLE1 (215654 downstream)						NA		NA									NA						gcctggccaatatggtgaaac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.83982943T>C		NA		hg19		0.02	-0.070154	CAAxATG	UNCOVERED																																																																																			NOVEL					0			5	2.706418	KEEP	1	0	0	9	242	TT	0.99254	0.053733	0			2	40	71	1	0	6.39626	4	60	111	27		0.333333	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	84119667	84119667	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:84119667A>G			NA	NA				RP11-289F5.1 (633457 upstream) : TLE1 (78930 downstream)						NA		NA									NA						caaggtgctgagattacaggt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.84119667A>G		NA		hg19		0.02	-0.254355	CTGxGAT	COVERED																																																																																			NOVEL					0			7	3.609451	KEEP	1	0	0	12	335	AA	0.993634	0.664267	0			3	60	103	0	0	7.642336	24	60	735	64		0.111111	0.668523
TLE1	7088	__UNKNOWN__	__UNKNOWN__	9	84254124	84254124	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:84254124G>A	ENST00000376499.3	-	7	1437				TLE1_ENST00000376463.1_Intron|TLE1_ENST00000376472.1_Intron	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	NA		NA			multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						tacaggtgtgggccactgtgc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781	7088		WD repeat domain containing	11837	protein-coding gene	gene with protein product	enhancer of split groucho 1	600189	transducin-like enhancer of split 1, homolog of Drosophila E(sp1)		NA	8365415, 8808280	Standard	NM_005077	NM_005077	NA	Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.373-4908C>T	chr9.hg19:g.84254124G>A		NA	A8K495|Q5T3G4|Q969V9	hg19	CCDS6661.1	0.02	-0.140357	GTGxGCC	COVERED																																																																																			NOVEL	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055407.1	8	2.707833	KEEP	0	0	0	9	268	GG	0.99254	0.259018	0		-	3	60	93	0	0	7.681773	10	60	339	34	ENST00000376499.3	0.230769	0.260965
TLE1	7088	__UNKNOWN__	__UNKNOWN__	9	84256933	84256933	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:84256933A>G	ENST00000376499.3	-	7	1437				TLE1_ENST00000376463.1_Intron|TLE1_ENST00000376472.1_Intron	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	NA		NA			multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						gcaaaactccatctcCAAaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781	7088		WD repeat domain containing	11837	protein-coding gene	gene with protein product	enhancer of split groucho 1	600189	transducin-like enhancer of split 1, homolog of Drosophila E(sp1)		NA	8365415, 8808280	Standard	NM_005077	NM_005077	NA	Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.373-7717T>C	chr9.hg19:g.84256933A>G		NA	A8K495|Q5T3G4|Q969V9	hg19	CCDS6661.1	0.02	-0.192948	TCCxTCT	COVERED																																																																																			NOVEL	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055407.1	6	3.308116	KEEP	1	0	0	11	299	AA	0.993072	0.454585	0		-	3	60	97	2	0	7.53367	16	60	468	52	ENST00000376499.3	0.157895	0.457757
TLE1	7088	__UNKNOWN__	__UNKNOWN__	9	84303843	84303843	__UNKNOWN__	5'UTR	SNP	G	G	A	rs367779642		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:84303843G>A	ENST00000376499.3	-	0	377					NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	NA		NA			multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						GGCGCGCCGGGAGGCGGCTCG	0.726		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781	7088		WD repeat domain containing	11837	protein-coding gene	gene with protein product	enhancer of split groucho 1	600189	transducin-like enhancer of split 1, homolog of Drosophila E(sp1)		NA	8365415, 8808280	Standard	NM_005077	NM_005077	NA	Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.-688C>T	chr9.hg19:g.84303843G>A		NA	A8K495|Q5T3G4|Q969V9	hg19	CCDS6661.1	0.02	2.478696	CGGxAGG	COVERED																																																																																			NOVEL	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055407.1	0	16.850574	KEEP	0	0	0	56	1761	GG	1	1	0		-	12	55	348	0	0	22.429234	137	60	4575	314	ENST00000376499.3	0.080537	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	84454557	84454557	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:84454557T>C			NA	NA				AL158154.1 (33561 upstream) : RNA5SP287 (45853 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.84454557T>C		NA		hg19		0.02	-0.122757	AGAxGGG	COVERED																																																																																			NOVEL					0			8	2.404846	KEEP	0	0	0	8	207	TT	0.99257	0.194853	0			3	60	95	0	0	7.882339	10	60	284	24		0.230769	0.196312
FRMD3	257019	__UNKNOWN__	__UNKNOWN__	9	85969061	85969061	__UNKNOWN__	Intron	SNP	G	G	A	rs184207638	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:85969061G>A	ENST00000304195.3	-	4	502				FRMD3_ENST00000376438.1_Intron	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	NA		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						ggctggtctcgaactcctgac	0.502		NA											G|||	14	0.00279553	0.0	0.0	5008	,	,	NA	17981	0.0139	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159	257019			24125	protein-coding gene	gene with protein product		607619			NA	12601556	Standard	NM_174938	NM_174938	NA	Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.296-4389C>T	chr9.hg19:g.85969061G>A		NA	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	hg19	CCDS43840.1	0.02	-0.140342	CTCxAAC	UNCOVERED																																																																																			NOVEL	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157355.1	10	2.406219	KEEP	4	0	0	8	225	GG	0	0	0		-	3	43	88	0	0	7.07289	11	60	354	34	ENST00000304195.3	0.214286	0.260965
FRMD3	257019	__UNKNOWN__	__UNKNOWN__	9	86122357	86122357	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:86122357T>C	ENST00000304195.3	-	1	354				FRMD3_ENST00000376438.1_Intron	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	NA		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						ccgaggcgggtggatcacaag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159	257019			24125	protein-coding gene	gene with protein product		607619			NA	12601556	Standard	NM_174938	NM_174938	NA	Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.147+30642A>G	chr9.hg19:g.86122357T>C		NA	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	hg19	CCDS43840.1	0.02	-0.184158	GGGxGGA	COVERED																																																																																			NOVEL	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157355.1	8	2.940173	KEEP	9	1	20	17	478	TT	0.99649	0.421991	0		-	3	35	90	0	0	6.762318	17	60	499	62	ENST00000304195.3	0.15	0.423478
FRMD3	257019	__UNKNOWN__	__UNKNOWN__	9	86122376	86122376	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:86122376A>T	ENST00000304195.3	-	1	354				FRMD3_ENST00000376438.1_Intron	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	NA		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						aggtcaggagatcgagaccat	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159	257019			24125	protein-coding gene	gene with protein product		607619			NA	12601556	Standard	NM_174938	NM_174938	NA	Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.147+30623T>A	chr9.hg19:g.86122376A>T		NA	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	hg19	CCDS43840.1	0.02	-0.184141	GAGxTCG	COVERED																																																																																			NOVEL	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157355.1	10	5.11001	KEEP	8	0	0	17	434	AA	0.99649	0.421991	0		-	3	46	87	0	0	6.393485	18	60	508	61	ENST00000304195.3	0.142857	0.423478
GKAP1	80318	__UNKNOWN__	__UNKNOWN__	9	86410056	86410056	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:86410056A>G	ENST00000376371.2	-	4	761				GKAP1_ENST00000376365.3_Intron	NM_025211.3	NP_079487.2	Q5VSY0	GKAP1_HUMAN	G kinase anchoring protein 1	NA		NA			signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)	14						gggcgacaagagcgagactcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014476	CCDS35049.1, CCDS47988.1	9q22.1	2008-02-05			ENSG00000165113	ENSG00000165113	80318			17496	protein-coding gene	gene with protein product	cGMP-dependent protein kinase anchoring protein 42kDa	611356			NA		Standard	NM_025211	NM_025211	NA	Approved	GKAP42, FKSG21	uc004amy.3	Q5VSY0	OTTHUMG00000020106	ENST00000376371.2:c.360+4043T>C	chr9.hg19:g.86410056A>G		NA	Q96LI0|Q9BYI1|Q9BYI2|Q9H225	hg19	CCDS35049.1	0.02	-0.052598	AAGxGCG	UNCOVERED																																																																																			NOVEL	GKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052839.2	6	3.007335	KEEP	1	0	0	10	271	AA	0.99254	0.036491	0		-	2	60	71	1	0	6.594075	3	50	81	20	ENST00000376371.2	0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	86650973	86650973	__UNKNOWN__	IGR	SNP	C	C	T	rs370175406|rs7847758|rs200044956	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:86650973C>T			NA	NA				RMI1 (31988 upstream) : RP11-158D2.2 (27384 downstream)						NA		NA									NA						gaacttcttcctcttaaactc	0.468		NA											C|||	4115	0.821685	0.7398	0.8444	5008	,	,	NA	14880	0.9653	NA	0.7654	False	NA	,,,	NA	NA	NA	2504	0.8262	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.86650973C>T		NA		hg19		0.02	-0.131574	TTCxTCT	COVERED																																																																																			NOVEL					0			4	2.406626	KEEP	0	0	0	8	238	CC	0.99257	0.22747	0			8	60	247	0	0	24.363001	6	60	198	31		0.571429	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	86884604	86884604	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:86884604G>A			NA	NA				RP11-158D2.2 (175112 upstream) : SLC28A3 (5767 downstream)						NA		NA									NA						tgggattacaggcgtgagcca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.86884604G>A		NA		hg19		0.02	-0.219312	ACAxGCG	COVERED																																																																																			NOVEL					0			8	3.911695	KEEP	6	0	0	13	402	GG	0.992708	0.548856	0			3	43	89	0	0	6.406398	21	60	731	63		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	87021994	87021994	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:87021994T>C			NA	NA				SLC28A3 (66322 upstream) : NTRK2 (261471 downstream)						NA		NA									NA						cctcagcctctcaaagtgctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.87021994T>C		NA		hg19		0.02	-0.122784	CTCxCAA	COVERED																																																																																			NOVEL					0			4	2.707098	KEEP	0	0	0	9	252	TT	0.99254	0.194847	0			3	60	102	0	0	8.701265	9	60	274	34		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	87125061	87125061	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:87125061G>T			NA	NA				SLC28A3 (169389 upstream) : NTRK2 (158404 downstream)						NA		NA									NA						tacacactttgatgatttttt	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.87125061G>T		NA		hg19		0.02	-0.061396	TTTxATG	UNCOVERED																																																																																			NOVEL					0			6	2.404328	KEEP	0	0	0	8	230	GG	0.99257	0.043461	0			3	60	82	0	1	7.554074	4	60	137	20		0.428571	0.043787
GOLM1	51280	__UNKNOWN__	__UNKNOWN__	9	88691530	88691530	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:88691530T>C	ENST00000388712.3	-	3	478				GOLM1_ENST00000388711.3_Intron|GOLM1_ENST00000257504.6_Intron	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	NA		NA			nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						cctgtaatcctagcactctgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052	51280			15451	protein-coding gene	gene with protein product		606804	golgi phosphoprotein 2, chromosome 9 open reading frame 155	GOLPH2, C9orf155	NA	10831838, 18953438, 22542941	Standard	NM_177937	NM_016548	NA	Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.309+796A>G	chr9.hg19:g.88691530T>C		NA	Q6IAF4|Q9NRB9	hg19	CCDS35054.1	0.02	-0.201731	TCCxAGC	COVERED																																																																																			NOVEL	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052904.2	14	3.608816	KEEP	1	0	0	12	327	TT	0.993072	0.487146	0		-	3	57	98	0	0	7.7918	14	60	420	50	ENST00000388712.3	0.176471	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	88822948	88822948	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:88822948A>G			NA	NA				GOLM1 (107884 upstream) : C9orf153 (12231 downstream)						NA		NA									NA						aggccgaggcaggtggatcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.88822948A>G		NA		hg19		0.02	-0.14033	GGCxGGT	COVERED																																																																																			NOVEL					0			6	3.308518	KEEP	2	0	0	11	308	AA	0.993072	0.259157	0			3	60	98	0	0	8.301327	9	60	267	47		0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	88829768	88829768	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:88829768A>G			NA	NA				GOLM1 (114704 upstream) : C9orf153 (5411 downstream)						NA		NA									NA						gctcatgcctataatcccagc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.88829768A>G		NA		hg19		0.02	-0.166613	CCTxTAA	COVERED																																																																																			NOVEL					0			6	2.706422	KEEP	2	0	0	9	241	AA	0.99257	0.351317	0			3	60	106	1	0	8.591996	14	60	396	44		0.176471	0.353947
ZCCHC6	79670	__UNKNOWN__	__UNKNOWN__	9	88944425	88944425	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:88944425C>T	ENST00000375963.3	-	11	1628				ZCCHC6_ENST00000375960.2_Intron|ZCCHC6_ENST00000375961.2_Intron|ZCCHC6_ENST00000277141.6_Intron	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	NA		NA			RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						gcaacaagagcgaaactccat	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223	79670		Zinc fingers, CCHC domain containing	25817	protein-coding gene	gene with protein product	TUTase7	NA			NA	11214970	Standard	NM_024617	NM_001185059	NA	Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.1456-1018G>A	chr9.hg19:g.88944425C>T		NA	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	hg19	CCDS35057.1	0.02	-0.140344	GAGxGAA	COVERED																																																																																			NOVEL	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000052918.1	10	2.707768	KEEP	3	0	0	9	271	CC	0.99254	0.259018	0		-	3	40	82	0	0	6.372618	12	60	404	43	ENST00000375963.3	0.2	0.260965
ROR2	4920	__UNKNOWN__	__UNKNOWN__	9	94370957	94370957	__UNKNOWN__	Intron	SNP	G	G	A	rs181771031	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:94370957G>A	ENST00000375715.1	-	13	2754							Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	NA		NA			cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						cacctgcctcggcctcccaaa	0.458		NA											G|||	4	0.000798722	0.003	0.0	5008	,	,	NA	17726	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071	4920		Immunoglobulin superfamily / I-set domain containing	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1	NA	1334494, 10700182	Standard		NM_004560	NA	Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375715.1:c.2113-45346C>T	chr9.hg19:g.94370957G>A		NA	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	hg19		0.02	-0.122801	CTCxGCC	UNCOVERED																																																																																			NOVEL	ROR2-002	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000053041.1	10	3.008002	KEEP	7	0	0	10	286	GG	0	0	0		-	3	60	84	1	0	6.901004	9	60	293	40	ENST00000375715.1	0.25	0.260965
ROR2	4920	__UNKNOWN__	__UNKNOWN__	9	94490964	94490964	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:94490964T>C	ENST00000375708.3	-	8	1382				ROR2_ENST00000550066.1_Intron|ROR2_ENST00000375715.1_Intron	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	NA		NA			cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						ccgcctgccttggcctcccaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071	4920		Immunoglobulin superfamily / I-set domain containing	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1	NA	1334494, 10700182	Standard		NM_004560	NA	Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.1184-1939A>G	chr9.hg19:g.94490964T>C		NA	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	hg19	CCDS6691.1	0.02	-0.149076	CCTxGGC	COVERED																																																																																			NOVEL	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053040.1	6	4.210907	KEEP	2	0	0	14	390	TT	0.994391	0.290363	0		-	3	60	96	0	0	7.679264	13	60	375	50	ENST00000375708.3	0.1875	0.292001
SPTLC1	10558	__UNKNOWN__	__UNKNOWN__	9	94817298	94817298	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:94817298A>G	ENST00000262554.2	-	8	786					NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	cttgagcccaagagtttgaga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	10558	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	hereditary sensory neuropathy, type 1	HSN1	NA	9363775	Standard	NM_006415	NM_006415	NA	Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.780+388T>C	chr9.hg19:g.94817298A>G		NA	A8K681|Q5VWB4|Q96IX6	hg19	CCDS6692.1	0.02	-0.210491	CCAxGAG	COVERED																																																																																			NOVEL	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055553.1	10	4.21085	KEEP	0	0	0	14	389	AA	0.995343	0.519729	0		-	5	60	168	0	0	14.180874	16	60	474	53	ENST00000262554.2	0.238095	0.522161
SPTLC1	10558	__UNKNOWN__	__UNKNOWN__	9	94841575	94841575	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:94841575T>C	ENST00000262554.2	-	5	433				SPTLC1_ENST00000337841.4_3'UTR|SPTLC1_ENST00000482632.1_Intron	NM_006415.2	NP_006406.1	O15269	SPTC1_HUMAN	serine palmitoyltransferase, long chain base subunit 1	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)|SPOTS complex (GO:0035339)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14					L-Serine(DB00133)	ccaggctggttttgaactcct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y08685	CCDS6692.1, CCDS6693.1	9q22.31	2014-09-17	2003-12-02		ENSG00000090054	ENSG00000090054	10558	2.3.1.50		11277	protein-coding gene	gene with protein product		605712	hereditary sensory neuropathy, type 1	HSN1	NA	9363775	Standard	NM_006415	NM_006415	NA	Approved	LCB1, SPTI, HSAN1, hLCB1	uc004arl.1	O15269	OTTHUMG00000021047	ENST00000262554.2:c.427+722A>G	chr9.hg19:g.94841575T>C		NA	A8K681|Q5VWB4|Q96IX6	hg19	CCDS6692.1	0.02	-0.157843	GGTxTTG	COVERED																																																																																			NOVEL	SPTLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055553.1	4	3.240591	KEEP	0	1	17	17	447	TT	0.999859	0.322761	0		-	3	60	91	0	0	7.179416	13	60	360	43	ENST00000262554.2	0.1875	0.322807
CENPP	401541	__UNKNOWN__	__UNKNOWN__	9	95180289	95180289	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:95180289T>C	ENST00000375587.3	+	5	1079				OMD_ENST00000375550.4_Intron	NM_001012267.1	NP_001012267.1	Q6IPU0	CENPP_HUMAN	centromere protein P	NA		NA			CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(1)	16						ggattacaggtgtgagccacc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091247	CCDS35063.1, CCDS69618.1	9q22.31	2013-11-05			ENSG00000188312	ENSG00000188312	401541			32933	protein-coding gene	gene with protein product		611505			NA	16622419, 16622420	Standard	NM_001012267	NM_001286969	NA	Approved	RP11-19J3.3, CENP-P	uc004arz.3	Q6IPU0	OTTHUMG00000020228	ENST00000375587.3:c.564+38148T>C	chr9.hg19:g.95180289T>C		NA	B3KRA5|B3KS17|Q5T9F8|Q5T9F9	hg19	CCDS35063.1	0.02	-0.219227	AGGxGTG	COVERED																																																																																			NOVEL	CENPP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053098.1	8	2.938967	KEEP	1	1	26	19	522	TT	0.99986	0.582848	0		+	4	60	129	0	1	10.114143	20	60	574	64	ENST00000375587.3	0.166667	0.58293
BICD2	23299	__UNKNOWN__	__UNKNOWN__	9	95504961	95504961	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:95504961G>A	ENST00000356884.6	-	2	308				BICD2_ENST00000375512.3_Intron	NM_001003800.1	NP_001003800.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	NA		NA			cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						cactgtgcccggcctaattcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963	23299			17208	protein-coding gene	gene with protein product		609797			NA	9734811	Standard	NM_015250	NM_001003800	NA	Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000356884.6:c.241-13443C>T	chr9.hg19:g.95504961G>A		NA	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	hg19	CCDS35064.1	0.02	-0.122803	CCCxGCC	COVERED																																																																																			NOVEL	BICD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055507.1	2	2.406843	KEEP	0	0	0	8	238	GG	0.99257	0.194853	0		-	4	60	116	0	0	9.870782	10	60	335	33	ENST00000356884.6	0.285714	0.196312
ANKRD19P	138649	__UNKNOWN__	__UNKNOWN__	9	95580757	95580757	__UNKNOWN__	RNA	SNP	T	T	C	rs200777355	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:95580757T>C	ENST00000473204.1	+	0	879							Q9H560	ANR19_HUMAN	ankyrin repeat domain 19, pseudogene	NA		NA				extracellular vesicular exosome (GO:0070062)					NA						tttttttttttCCTAAAAACC	0.284		NA											.|||	20	0.00399361	0.0	0.0115	5008	,	,	NA	12632	0.001	NA	0.0099	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													36	30	32			NA	NA	9		NA											NA				95580757		692	1588	2280					BC038951		9q22.32	2011-04-27	2011-04-27	2011-04-27	ENSG00000187984	ENSG00000187984	138649			22567	pseudogene	pseudogene		NA	ankyrin repeat domain 19, ankyrin repeat domain 19 pseudogene	ANKRD19	NA		Standard	NR_026868	NR_026868	NA	Approved	FLJ36178	uc011lua.1	Q9H560	OTTHUMG00000020237	ENST00000473204.1:	chr9.hg19:g.95580757T>C		NA	A8K853|Q17RD3	hg19		0.02	-0.149117	TTTxCCT	COVERED																																																																																			NOVEL	ANKRD19P-004	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000053116.3	2	4.209509	KEEP	0	0	0	14	373	TT	0.995343	0.290641	0		+	9	60	290	0	0	28.188852	8	60	243	35	ENST00000473204.1	0.529412	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	96925016	96925016	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:96925016T>C			NA	NA				PTPDC1 (52878 upstream) : RP11-2B6.3 (3554 downstream)						NA		NA									NA						ccgaggtgggtggatcacgag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.96925016T>C		NA		hg19		0.02	-0.210495	GGGxGGA	COVERED																																																																																			NOVEL					0			4	4.209216	KEEP	3	0	0	14	372	TT	0.993634	0.518837	0			3	60	87	0	0	6.462396	17	60	509	60		0.15	0.522161
ERCC6L2	375748	__UNKNOWN__	__UNKNOWN__	9	98730335	98730335	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:98730335C>T	ENST00000288985.7	+	0	3777				ERCC6L2_ENST00000437817.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	NA		NA			DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)				NA						ATCAGGATGACAGGTTATTAA	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150	375748			26922	protein-coding gene	gene with protein product		615667	chromosome 9 open reading frame 102, excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2	C9orf102	NA		Standard	NM_001010895	NM_001010895	NA	Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.*1333C>T	chr9.hg19:g.98730335C>T		NA	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	hg19	CCDS35072.1	0.02	-0.24562	TGAxAGG	COVERED																																																																																			NOVEL	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053247.2	12	4.211942	KEEP	0	0	0	14	414	CC	0.995343	0.638361	0		+	3	60	93	0	0	6.592896	25	60	860	55	ENST00000288985.7	0.107143	0.641347
SLC35D2	11046	__UNKNOWN__	__UNKNOWN__	9	99095369	99095369	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:99095369T>C	ENST00000253270.7	-	9	815				SLC35D2_ENST00000375259.4_Intron	NM_007001.2	NP_008932.2	Q76EJ3	S35D2_HUMAN	solute carrier family 35 (UDP-GlcNAc/UDP-glucose transporter), member D2	NA		NA			carbohydrate derivative transport (GO:1901264)|carbohydrate metabolic process (GO:0005975)|carbohydrate transport (GO:0008643)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|nucleotide transmembrane transport (GO:1901679)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)			endometrium(3)|large_intestine(3)|lung(4)|skin(2)	12		Acute lymphoblastic leukemia(62;0.0167)				ttagtagagatggggtttcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB122077	CCDS6717.1, CCDS69625.1	9q22.33	2013-07-17	2013-07-17		ENSG00000130958	ENSG00000130958	11046		Solute carriers	20799	protein-coding gene	gene with protein product		609182	solute carrier family 35, member D2		NA	15607426	Standard		NM_007001	NA	Approved	UGTrel8, SQV7L	uc004awc.3	Q76EJ3	OTTHUMG00000020293	ENST00000253270.7:c.752+3629A>G	chr9.hg19:g.99095369T>C		NA	O95454|Q498C1|Q75W21|Q7Z5X5	hg19	CCDS6717.1	0.02	-0.113984	AGAxGGG	UNCOVERED																																																																																			NOVEL	SLC35D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053261.1	9	3.005018	KEEP	4	0	0	10	253	TT	0.99254	0.161255	0		-	4	49	117	0	0	10.685562	6	60	156	32	ENST00000253270.7	0.4	0.162467
ZNF782	158431	__UNKNOWN__	__UNKNOWN__	9	99583112	99583112	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:99583112A>G	ENST00000481138.1	-	6	906				ZNF782_ENST00000466833.1_Intron|ZNF782_ENST00000535338.1_Intron	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				gattacaggcatgagccacca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597	158431		Zinc fingers, C2H2-type, -	33110	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001001662	NM_001001662	NA	Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.245-1052T>C	chr9.hg19:g.99583112A>G		NA	B2RNR0	hg19	CCDS35075.1	0.02	-0.105236	GGCxTGA	UNCOVERED																																																																																			NOVEL	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000356810.1	6	3.307445	KEEP	0	0	0	11	299	AA	0.993072	0.138863	0		-	3	60	86	0	1	7.543279	6	60	179	34	ENST00000481138.1	0.333333	0.139832
HIATL2	84278	__UNKNOWN__	__UNKNOWN__	9	99711159	99711159	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:99711159A>C	ENST00000602917.1	-	4	609				HIATL2_ENST00000506067.1_Intron			Q5VZR4	HIAL2_HUMAN	hippocampus abundant transcript-like 2	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)				NA						cctgcctcggactcccgagta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005058		9q22.33	2008-09-12	2008-09-12		ENSG00000196312	ENSG00000196312	84278			23672	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032318	NR_002894	NA	Approved	MGC12945	uc004aws.3	Q5VZR4	OTTHUMG00000020317	ENST00000602917.1:c.395+677T>G	chr9.hg19:g.99711159A>C		NA	Q9BSG7	hg19		0.02	1.757148	CGGxCTC	COVERED																																																																																			NOVEL	HIATL2-001	PUTATIVE	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000053305.3	25	5.040039	KEEP	1	4	117	58	1583	AA	1	0.997553	0		-	5	60	168	0	0	11.500213	61	60	1830	199	ENST00000602917.1	0.075758	0.997553
HIATL2	84278	__UNKNOWN__	__UNKNOWN__	9	99714639	99714639	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:99714639C>T	ENST00000602917.1	-	4	481				HIATL2_ENST00000375223.4_Intron			Q5VZR4	HIAL2_HUMAN	hippocampus abundant transcript-like 2	NA		NA			transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)				NA						gagctgagatcgtgccattgc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005058		9q22.33	2008-09-12	2008-09-12		ENSG00000196312	ENSG00000196312	84278			23672	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032318	NR_002894	NA	Approved	MGC12945	uc004aws.3	Q5VZR4	OTTHUMG00000020317	ENST00000602917.1:c.268-2675G>A	chr9.hg19:g.99714639C>T		NA	Q9BSG7	hg19		0.02	-0.175388	GATxGTG	COVERED																																																																																			NOVEL	HIATL2-001	PUTATIVE	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000053305.3	54	9.556965	KEEP	37	1	23	40	1143	CC	0.999892	0.423432	0		-	5	22	126	0	0	10.366182	13	60	417	85	ENST00000602917.1	0.277778	0.423478
TMOD1	7111	__UNKNOWN__	__UNKNOWN__	9	100358093	100358093	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:100358093A>G	ENST00000259365.4	+	10	1228				TMOD1_ENST00000395211.2_Intron|TMOD1_ENST00000375175.1_Intron	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	NA		NA			adult locomotory behavior (GO:0008344)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)	cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|membrane (GO:0016020)|myofibril (GO:0030016)				breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(2)|urinary_tract(1)	11		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		ggtggctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6726.1	9q22	2008-07-21		2003-03-21	ENSG00000136842	ENSG00000136842	7111			11871	protein-coding gene	gene with protein product		190930		D9S57E, TMOD	NA	1370827, 8661028	Standard	NM_003275	NM_003275	NA	Approved	ETMOD	uc004axl.2	P28289	OTTHUMG00000020325	ENST00000259365.4:c.1016-3823A>G	chr9.hg19:g.100358093A>G		NA	B2RB77|Q5T7W3|Q9BUF1	hg19	CCDS6726.1	0.02	-0.09629	CACxCCT	UNCOVERED																																																																																			NOVEL	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053320.2	6	2.706786	KEEP	4	0	0	9	247	AA	0.99257	0.119541	0		+	3	60	101	0	0	8.882824	7	60	192	30	ENST00000259365.4	0.3	0.120436
TSTD2	158427	__UNKNOWN__	__UNKNOWN__	9	100381834	100381834	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:100381834A>G	ENST00000341170.4	-	4	865				TSTD2_ENST00000354801.2_Intron	NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	NA		NA								large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						tgttgcccagactggtcttga	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925	158427			30087	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 97	C9orf97	NA	12477932	Standard	NM_139246	NM_139246	NA	Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.483-1675T>C	chr9.hg19:g.100381834A>G		NA	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	hg19	CCDS6727.2	0.02	-0.122786	CAGxCTG	COVERED																																																																																			NOVEL	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053325.4	7	5.112655	KEEP	0	0	0	17	465	AA	0.999366	0.196187	0		-	3	60	105	0	0	9.001443	9	60	258	50	ENST00000341170.4	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	100627691	100627691	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:100627691G>C			NA	NA				FOXE1 (8705 upstream) : C9orf156 (39079 downstream)						NA		NA									NA						cctgcctcaggctcctgagta	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.100627691G>C		NA		hg19		0.02	-0.052636	CAGxCTC	UNCOVERED																																																																																			NOVEL					0			7	2.708003	KEEP	0	0	0	9	274	GG	0.99254	0.036491	0			2	60	67	0	0	6.44999	2	60	68	15		0.5	0.036766
GABBR2	9568	__UNKNOWN__	__UNKNOWN__	9	101325276	101325276	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:101325276C>T	ENST00000259455.2	-	2	919					NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	cgcttgagcccgggaaatgga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928	9568		GABA receptors, GPCR / Class C : GABA(B) receptors	4507	protein-coding gene	gene with protein product		607340	G protein-coupled receptor 51	GPR51	NA	10087195	Standard		NM_005458	NA	Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.459+14940G>A	chr9.hg19:g.101325276C>T		NA	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	hg19	CCDS6736.1	0.02	-0.070172	GCCxGGG	UNCOVERED																																																																																			NOVEL	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053373.1	6	2.406923	KEEP	0	0	0	8	244	CC	0.99257	0.053735	0		-	3	60	90	0	0	8.624585	3	60	94	20	ENST00000259455.2	0.5	0.054137
GALNT12	79695	__UNKNOWN__	__UNKNOWN__	9	101591391	101591391	__UNKNOWN__	Intron	SNP	G	G	A	rs549703728	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:101591391G>A	ENST00000375011.3	+	3	731					NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	NA		NA			cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				gattacaggcgtgagccactg	0.448		NA											G|||	3	0.000599042	0.0	0.0	5008	,	,	NA	18956	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	79695	2.4.1.41	Glycosyltransferase family 2 domain containing	19877	protein-coding gene	gene with protein product	polypeptide GalNAc transferase 12	610290	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)		NA	12135769	Standard	NM_024642	NM_024642	NA	Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.731+2168G>A	chr9.hg19:g.101591391G>A		NA	Q5TCF7|Q8NG54|Q96CT9|Q9H771	hg19	CCDS6737.1	0.02	-0.157695	GGCxTGA	COVERED																																																																																			NOVEL	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053382.1	5	2.405174	KEEP	0	0	0	8	212	GG	0.99257	0.320408	0		+	3	60	90	0	1	6.912337	15	60	471	37	ENST00000375011.3	0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	104107403	104107403	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:104107403A>G			NA	NA				LPPR1 (19986 upstream) : BAAT (15295 downstream)						NA		NA									NA						gctgaggcagaagaatcactt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.104107403A>G		NA		hg19		0.02	-0.035084	CAGxAGA	UNCOVERED																																																																																			NOVEL					0			5	2.706792	KEEP	2	0	0	9	249	AA	0.99257	0.019833	0			2	40	67	0	0	6.45026	2	60	57	19		0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	107256810	107256810	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:107256810C>T			NA	NA				RP11-86L19.2 (216703 upstream) : OR13F1 (9644 downstream)						NA		NA									NA						ttagtagagacgggggtttca	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.107256810C>T		NA		hg19		0.02	-0.096486	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			27	5.113786	KEEP	18	0	0	17	492	CC	0.993634	0.119669	0			3	60	86	0	0	7.954586	4	60	129	50		0.428571	0.120436
SLC44A1	23446	__UNKNOWN__	__UNKNOWN__	9	108157539	108157539	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:108157539C>T	ENST00000374720.3	+	0	8423				SLC44A1_ENST00000343170.7_Intron|SLC44A1_ENST00000374723.1_3'UTR|SLC44A1_ENST00000374724.1_Intron	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	NA		NA			choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	ctcgctctatcgccagcttag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214	23446		CD molecules, Solute carriers	18798	protein-coding gene	gene with protein product		606105	CDW92 antigen	CDW92	NA	11698453, 10677542	Standard	NM_080546	NM_080546	NA	Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.*6202C>T	chr9.hg19:g.108157539C>T		NA	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	hg19	CCDS6763.1	0.02	-0.184165	TATxGCC	COVERED																																																																																			NOVEL	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053500.1	2	4.503684	KEEP	0	0	0	15	400	CC	0.99649	0.421991	0		+	3	60	87	0	0	6.393547	18	60	538	42	ENST00000374720.3	0.142857	0.423478
RP11-308N19.1	0	__UNKNOWN__	__UNKNOWN__	9	109161134	109161134	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:109161134T>C	ENST00000435485.1	+	0	171										NA		NA									NA						gggcagatcatgaggtcagga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000435485.1:	chr9.hg19:g.109161134T>C		NA		hg19		0.02	-0.08771	TCAxGAG	UNCOVERED																																																																																			NOVEL	RP11-308N19.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000053526.1	4	2.70656	KEEP	6	0	0	9	244	TT	0	0	0		+	3	60	86	0	0	7.543171	6	60	189	33	ENST00000435485.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	110157829	110157829	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:110157829A>G			NA	NA				RAD23B (63354 upstream) : RP11-363D24.1 (24735 downstream)						NA		NA									NA						ccagcactttaggaggccgag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.110157829A>G		NA		hg19		0.02	-0.052631	TTTxGGA	UNCOVERED																																																																																			NOVEL					0			8	2.40519	KEEP	7	0	0	8	214	AA	0	0	0			2	60	71	0	0	6.395813	4	60	122	23		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	110838977	110838977	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:110838977T>G			NA	NA				RNA5SP293 (157718 upstream) : RP11-505C13.1 (175456 downstream)						NA		NA									NA						caaagtgctgtgattacaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.110838977T>G		NA		hg19		0.02	-0.043861	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			3	2.707417	KEEP	1	0	0	9	257	TT	0.99257	0.023895	0			2	55	72	0	0	6.692951	3	60	93	20		0.4	0.024074
PALM2	114299	__UNKNOWN__	__UNKNOWN__	9	112460834	112460834	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:112460834T>C	ENST00000374531.2	+	1	79				PALM2_ENST00000448454.2_Intron	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	NA		NA			regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						attgggattataggcgtgagc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444	114299			15845	protein-coding gene	gene with protein product		NA			NA	11478809	Standard	NM_001037293	NM_001037293	NA	Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.5+57688T>C	chr9.hg19:g.112460834T>C		NA	A9Z1X9|Q8N9D5|Q96DU1	hg19	CCDS35099.1	0.02	-0.061397	TTAxAGG	UNCOVERED																																																																																			NOVEL	PALM2-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053604.1	3	2.70666	KEEP	0	0	0	9	245	TT	0.99254	0.04346	0		+	2	60	70	0	0	6.492959	3	60	90	25	ENST00000374531.2	0.4	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	114282941	114282941	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114282941T>C			NA	NA				KIAA0368 (35916 upstream) : ZNF483 (4497 downstream)						NA		NA									NA						agggtttcactatgttggcca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.114282941T>C		NA		hg19		0.02	-0.070161	CACxATG	UNCOVERED																																																																																			NOVEL					0			4	2.70531	KEEP	2	0	0	9	235	TT	0.99254	0.053733	0			3	60	94	0	0	8.533027	5	60	144	24		0.375	0.054137
PTGR1	22949	__UNKNOWN__	__UNKNOWN__	9	114340100	114340100	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114340100A>G	ENST00000407693.2	-	7	914				PTGR1_ENST00000238248.3_Intron|ZNF483_ENST00000358151.4_3'UTR|PTGR1_ENST00000309195.5_Intron|PTGR1_ENST00000538962.1_Intron	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	NA		NA			arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						actccagcctaggtgacagag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(200;132 2151 7551 19220 46064)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	22949	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	zinc binding alcohol dehydrogenase domain containing 3	601274	leukotriene B4 12-hydroxydehydrogenase	LTB4DH	NA	8576264, 17449869	Standard		NM_001146109	NA	Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.651+975T>C	chr9.hg19:g.114340100A>G		NA	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	hg19	CCDS6779.1	0.02	3.751005	CCTxGGT	COVERED																																																																																			NOVEL	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053647.2	32	15.732242	KEEP	0	6	187	118	3225	AA	1	0.999998	0		-	5	60	169	1	0	10.500934	103	60	3091	377	ENST00000407693.2	0.046296	0.999998
PTGR1	22949	__UNKNOWN__	__UNKNOWN__	9	114358849	114358849	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114358849A>G	ENST00000407693.2	-	2	369				PTGR1_ENST00000238248.3_Intron|PTGR1_ENST00000309195.5_Intron|PTGR1_ENST00000538962.1_Intron	NM_001146108.1	NP_001139580.1	Q14914	PTGR1_HUMAN	prostaglandin reductase 1	NA		NA			arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|leukotriene metabolic process (GO:0006691)|lipoxin metabolic process (GO:2001300)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)|2-alkenal reductase [NAD(P)] activity (GO:0032440)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)	11						tggccaacacagtgaaactcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(200;132 2151 7551 19220 46064)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D49387	CCDS6779.1, CCDS55331.1	9q32	2008-06-04	2008-06-02	2008-06-02	ENSG00000106853	ENSG00000106853	22949	1.3.1.74, 1.3.1.48		18429	protein-coding gene	gene with protein product	zinc binding alcohol dehydrogenase domain containing 3	601274	leukotriene B4 12-hydroxydehydrogenase	LTB4DH	NA	8576264, 17449869	Standard		NM_001146109	NA	Approved	ZADH3	uc004bfh.2	Q14914	OTTHUMG00000020493	ENST00000407693.2:c.106+747T>C	chr9.hg19:g.114358849A>G		NA	A8K0N2|B4DPK3|F5GY50|Q8IYQ0|Q9H1X6	hg19	CCDS6779.1	0.02	-0.096473	CACxGTG	UNCOVERED																																																																																			NOVEL	PTGR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053647.2	8	2.406188	KEEP	3	0	0	8	223	AA	0	0	0		-	3	60	93	0	0	7.932456	8	60	235	25	ENST00000407693.2	0.272727	0.120436
C9orf84	158401	__UNKNOWN__	__UNKNOWN__	9	114519629	114519629	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114519629A>G	ENST00000394777.4	-	3	644				C9orf84_ENST00000374287.3_Intron|C9orf84_ENST00000374283.5_Intron|C9orf84_ENST00000394779.3_Intron|C9orf84_ENST00000318737.4_Intron			Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	NA		NA								breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						tgatctgcccacctcggcctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181	158401			26535	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173521	XM_005251738	NA	Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000394777.4:c.399+734T>C	chr9.hg19:g.114519629A>G		NA	A2A2V3|Q2M1H8|Q96M73	hg19		0.02	-0.114006	CCCxCCT	COVERED																																																																																			NOVEL	C9orf84-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000316570.1	4	3.096267	KEEP	5	1	7	13	367	AA	0.995343	0.195397	0		-	3	60	97	0	0	8.332787	8	60	227	51	ENST00000394777.4	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	114621073	114621073	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114621073G>T			NA	NA				RNU6-1013P (18859 upstream) : UGCG (37972 downstream)						NA		NA									NA						ggccgaggcgggtggatcacg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.114621073G>T		NA		hg19		0.02	-0.114036	GCGxGTG	UNCOVERED																																																																																			NOVEL					0			9	3.30963	KEEP	5	0	0	11	340	GG	0.99257	0.16126	0			3	50	91	0	0	7.48184	10	60	345	37		0.230769	0.162467
SUSD1	64420	__UNKNOWN__	__UNKNOWN__	9	114916681	114916681	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114916681A>C	ENST00000374270.3	-	2	390				SUSD1_ENST00000374263.3_Intron|SUSD1_ENST00000374264.2_Intron	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	NA		NA				integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)		SUSD1/ROD1(2)	central_nervous_system(1)|endometrium(4)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						gtagtcccagatactcaggag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137432	CCDS6783.1, CCDS65105.1, CCDS65106.1	9q31.3-q33.1	2008-02-05			ENSG00000106868	ENSG00000106868	64420			25413	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_022486	NM_022486	NA	Approved	DKFZP761E1824	uc004bfu.3	Q6UWL2	OTTHUMG00000020499	ENST00000374270.3:c.217+3098T>G	chr9.hg19:g.114916681A>C		NA	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	hg19	CCDS6783.1	0.02	-0.114022	CAGxTAC	UNCOVERED																																																																																			NOVEL	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053668.3	8	2.706065	KEEP	0	0	0	9	241	AA	0.99254	0.161255	0		-	3	60	104	0	0	8.901252	9	60	270	27	ENST00000374270.3	0.25	0.162467
PTBP3	9991	__UNKNOWN__	__UNKNOWN__	9	114982572	114982572	__UNKNOWN__	3'UTR	SNP	G	G	A	rs192657315		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:114982572G>A	ENST00000374257.1	-	0	5382				PTBP3_ENST00000334318.6_3'UTR|PTBP3_ENST00000458258.1_3'UTR	NM_001163788.2|NM_001244896.1|NM_001244897.1	NP_001157260.1|NP_001231825.1|NP_001231826.1	O95758	PTBP3_HUMAN	polypyrimidine tract binding protein 3	NA		NA			anatomical structure morphogenesis (GO:0009653)|erythrocyte maturation (GO:0043249)|mRNA processing (GO:0006397)|negative regulation of RNA splicing (GO:0033119)|regulation of cell differentiation (GO:0045595)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)				NA						AGAgccaggcgtggtggctca	0.488		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18008	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													15	14	15			NA	NA	9		NA											NA				114982572		876	1990	2866	SO:0001624	3_prime_UTR_variant			AB023967	CCDS6784.1, CCDS55332.1, CCDS55333.1, CCDS59140.1, CCDS59141.1	9q32	2013-07-16	2011-11-16	2011-11-16	ENSG00000119314	ENSG00000119314	9991		RNA binding motif (RRM) containing	10253	protein-coding gene	gene with protein product		607527	regulator of differentiation (in S. pombe) 1, ROD1 regulator of differentiation 1 (S. pombe)	ROD1	NA	10207106	Standard		NM_005156	NA	Approved	DKFZp781I1117	uc004bfx.3	O95758	OTTHUMG00000020503	ENST00000374257.1:c.*3559C>T	chr9.hg19:g.114982572G>A		NA	B1ALY2|B1ALY3|B1ALY5|B1ALY6|B3KME7|Q68DB9|Q86YB3|Q86YH9	hg19	CCDS55332.1	0.02	3.078677	GGCxTGG	COVERED																																																																																			NOVEL	PTBP3-004	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053677.1	40	5.338923	KEEP	0	10	257	109	3214	GG	1	0.999981	0		-	5	60	156	0	0	9.51079	89	60	2933	325	ENST00000374257.1	0.053191	0.999981
SNX30	401548	__UNKNOWN__	__UNKNOWN__	9	115581826	115581826	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:115581826T>C	ENST00000374232.3	+	3	623					NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	NA		NA			apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						ggattacaggtgtgagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158	401548		Sorting nexins	23685	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001012994	NA	Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.459+1731T>C	chr9.hg19:g.115581826T>C		NA		hg19	CCDS43865.1	0.02	-0.131538	AGGxGTG	COVERED																																																																																			NOVEL	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053700.1	4	2.70715	KEEP	0	0	0	9	252	TT	0.99254	0.227464	0		+	3	60	86	0	0	7.101401	9	60	261	38	ENST00000374232.3	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	116072504	116072504	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:116072504G>A			NA	NA				RNF183 (6953 upstream) : WDR31 (2997 downstream)						NA		NA									NA						gtgagccaccgtgcccggccC	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.116072504G>A		NA		hg19		0.02	-0.166652	ACCxTGC	COVERED																																																																																			NOVEL					0			10	5.114469	KEEP	1	0	0	17	506	GG	0.997832	0.353179	0			3	60	86	0	0	6.679165	13	60	437	50		0.1875	0.353947
WDR31	114987	__UNKNOWN__	__UNKNOWN__	9	116092671	116092671	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:116092671A>G	ENST00000374193.4	-	4	496				WDR31_ENST00000341761.4_Intron|WDR31_ENST00000374195.3_Intron|WDR31_ENST00000461942.1_Intron	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	NA		NA								NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						gtgagccaccacacccggccC	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225	114987		WD repeat domain containing	21421	protein-coding gene	gene with protein product	similar to spermatid WD-repeat protein	NA			NA		Standard	NM_145241	NM_145241	NA	Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.249+592T>C	chr9.hg19:g.116092671A>G		NA	Q5W0T9|Q96EG8	hg19	CCDS35110.1	0.02	-0.175311	ACCxCAC	COVERED																																																																																			NOVEL	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053734.2	7	3.006237	KEEP	1	0	0	10	263	AA	0.99254	0.384517	0		-	3	60	108	0	0	8.634083	16	60	449	41	ENST00000374193.4	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	116197142	116197142	__UNKNOWN__	IGR	SNP	G	G	A	rs1093666	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:116197142G>A			NA	NA				C9orf43 (5178 upstream) : RGS3 (9868 downstream)						NA		NA									NA						gggattacaggcgtgagccac	0.443		NA											-|||	214	0.0427316	0.0091	0.0965	5008	,	,	NA	17838	0.0	NA	0.1183	False	NA	,,,	NA	NA	NA	2504	0.0164	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.116197142G>A		NA		hg19		0.02	-0.114034	CAGxCGT	UNCOVERED																																																																																			NOVEL					0			4	2.708073	KEEP	4	0	0	9	277	GG	0	0	0			6	60	186	0	0	17.849269	6	60	202	39		0.5	0.162467
COL27A1	85301	__UNKNOWN__	__UNKNOWN__	9	117006367	117006367	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:117006367A>G	ENST00000356083.3	+	23	3325					NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	NA		NA			extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						caccacgcccagctaattttt	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739	85301		Collagens	22986	protein-coding gene	gene with protein product		608461			NA	12766169	Standard	NM_032888	NM_032888	NA	Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.2934+527A>G	chr9.hg19:g.117006367A>G		NA	Q66K43|Q96JF7	hg19	CCDS6802.1	0.02	-0.052632	CCCxGCT	UNCOVERED																																																																																			NOVEL	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053763.1	9	3.006788	KEEP	0	0	0	10	269	AA	0.992708	0.036498	0		+	2	60	72	0	0	6.495807	4	60	125	23	ENST00000356083.3	0.333333	0.036766
AKNA	80709	__UNKNOWN__	__UNKNOWN__	9	117155706	117155706	__UNKNOWN__	Intron	SNP	T	T	C	rs10817599	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:117155706T>C	ENST00000307564.4	-	1	49					NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						agggtttcactgtgttagcca	0.537		NA											C|||	2144	0.428115	0.2095	0.5014	5008	,	,	NA	11643	0.4861	NA	0.5129	False	NA	,,,	NA	NA	NA	2504	0.5245	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948	80709			24108	protein-coding gene	gene with protein product		605729			NA	11268217, 11853319	Standard	NM_030767	NM_030767	NA	Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.112+930A>G	chr9.hg19:g.117155706T>C		NA	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	hg19	CCDS6805.1	0.02	-0.043858	CACxGTG	UNCOVERED																																																																																			NOVEL	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053767.2	3	2.705761	KEEP	11	0	0	9	235	AT	0	0	0		-	3	40	101	0	0	10.069997	2	40	58	24	ENST00000307564.4	0.6	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	117416867	117416867	__UNKNOWN__	IGR	SNP	C	C	T	rs9775036	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:117416867C>T			NA	NA				C9orf91 (8165 upstream) : RP11-402G3.5 (1716 downstream)						NA		NA									NA						aggccgggcgcggtagctcac	0.537		NA											C|||	203	0.0405351	0.0023	0.0245	5008	,	,	NA	15226	0.131	NA	0.0308	False	NA	,,,	NA	NA	NA	2504	0.0204	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.117416867C>T		NA		hg19		0.02	-0.087717	GCGxGGT	UNCOVERED																																																																																			NOVEL					0			2	2.407081	KEEP	0	0	0	8	250	CC	0.99257	0.09898	0			3	60	86	0	0	7.378209	7	60	235	27		0.3	0.099721
ASTN2	23245	__UNKNOWN__	__UNKNOWN__	9	119878030	119878030	__UNKNOWN__	Intron	SNP	C	C	T	rs557120428		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:119878030C>T	ENST00000361209.2	-	4	1147				ASTN2_ENST00000361477.3_Intron|ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000373996.3_Intron	NM_014010.4	NP_054729.3	O75129	ASTN2_HUMAN	astrotactin 2	NA		NA			negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						GCTggccgggcgcggtggctc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219	23245			17021	protein-coding gene	gene with protein product		612856			NA	9734811	Standard	NM_014010	NM_014010	NA	Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000361209.2:c.1016-19600G>A	chr9.hg19:g.119878030C>T		NA	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	hg19	CCDS6815.1	0.02	-0.157891	GGGxGCG	COVERED																																																																																			NOVEL	ASTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055428.2	11	3.007617	KEEP	2	0	0	10	289	CC	0.99254	0.320398	0		-	3	46	83	0	0	6.472529	12	60	397	39	ENST00000361209.2	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	122773185	122773185	__UNKNOWN__	IGR	SNP	C	C	T	rs547960154	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:122773185C>T			NA	NA				RP11-360A18.1 (36585 upstream) : MIR147A (234071 downstream)						NA		NA									NA						tgcagtgagccgagatcatgc	0.542		NA											c|||	4	0.000798722	0.0	0.0	5008	,	,	NA	16874	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.122773185C>T		NA		hg19		0.02	-0.052628	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			0	2.7066	KEEP	0	0	0	9	261	CC	0.99254	0.036491	0			3	60	90	0	0	8.969241	2	60	61	24		0.6	0.036766
GSN	2934	__UNKNOWN__	__UNKNOWN__	9	124085712	124085712	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:124085712A>G	ENST00000373823.3	+	19	2230				GSN_ENST00000449733.1_Intron|GSN_ENST00000373807.1_Intron|GSN_ENST00000373818.4_Intron|GSN_ENST00000545652.1_Intron|GSN_ENST00000394353.2_Intron|GSN_ENST00000341272.2_Intron|GSN_ENST00000412819.1_Intron|GSN_ENST00000373808.2_Intron|GSN_ENST00000436847.1_Intron			P06396	GELS_HUMAN	gelsolin	NA		NA			actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						cagtggcatgatctcggctca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180	2934			4620	protein-coding gene	gene with protein product	amyloidosis, Finnish type	137350	gelsolin (amyloidosis, Finnish type)		NA	1652889	Standard	NM_000177	NM_001127662	NA	Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373823.3:c.1326-1120A>G	chr9.hg19:g.124085712A>G		NA	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	hg19	CCDS6829.1	0.02	-0.131555	ATGxTCT	COVERED																																																																																			NOVEL	GSN-013	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254323.3	8	3.006657	KEEP	5	0	0	10	264	AA	0.99257	0.22747	0		+	3	30	95	0	0	8.001274	9	60	267	35	ENST00000373823.3	0.25	0.229173
GSN	2934	__UNKNOWN__	__UNKNOWN__	9	124085717	124085717	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:124085717G>A	ENST00000373823.3	+	19	2230				GSN_ENST00000449733.1_Intron|GSN_ENST00000373807.1_Intron|GSN_ENST00000373818.4_Intron|GSN_ENST00000545652.1_Intron|GSN_ENST00000394353.2_Intron|GSN_ENST00000341272.2_Intron|GSN_ENST00000412819.1_Intron|GSN_ENST00000373808.2_Intron|GSN_ENST00000436847.1_Intron			P06396	GELS_HUMAN	gelsolin	NA		NA			actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						gcatgatctcggctcactgca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180	2934			4620	protein-coding gene	gene with protein product	amyloidosis, Finnish type	137350	gelsolin (amyloidosis, Finnish type)		NA	1652889	Standard	NM_000177	NM_001127662	NA	Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373823.3:c.1326-1115G>A	chr9.hg19:g.124085717G>A		NA	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	hg19	CCDS6829.1	0.02	-0.131563	CTCxGCT	COVERED																																																																																			NOVEL	GSN-013	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254323.3	8	3.008652	KEEP	5	0	0	10	298	GG	0.99257	0.22747	0		+	3	30	84	0	0	6.901151	9	60	280	34	ENST00000373823.3	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	124297399	124297399	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:124297399T>C			NA	NA				GGTA1P (35363 upstream) : AL357936.1 (4755 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.124297399T>C		NA		hg19		0.02	-0.087701	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			8	3.007234	KEEP	0	0	0	10	270	TT	0.992708	0.098994	0			3	60	103	0	0	9.24406	6	60	171	29		0.333333	0.099721
DAB2IP	153090	__UNKNOWN__	__UNKNOWN__	9	124526152	124526152	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:124526152C>T	ENST00000309989.1	+	6	1229	c.1082C>T	c.(1081-1083)tCc>tTc	p.S361F	DAB2IP_ENST00000408936.3_Missense_Mutation_p.S485F|DAB2IP_ENST00000259371.2_Missense_Mutation_p.S457F	NM_138709.1	NP_619723.1	Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	485		NA			activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						ATCATCAACTCCTACTGGTCA	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													114	92	100			NA	NA	9		NA											NA				124526152		2203	4300	6503	SO:0001583	missense			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848	153090			17294	protein-coding gene	gene with protein product	nGAP-like protein, DOC-2/DAB2 interactive protein, ASK-interacting protein, ASK1-interacting protein 1	609205			NA	11944990, 11812785	Standard	NM_032552	XM_005251721	NA	Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000309989.1:c.1082C>T	chr9.hg19:g.124526152C>T	ENSP00000310827:p.Ser361Phe	NA	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	hg19	CCDS6832.1	0.02	1.610641	ACTxCTA	COVERED	.	.	.	.	.	.	.	.	.	.	C	28.2	4.897832	0.91962	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.94175	0.8131	H	0.96175	3.78	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.95742	0.8784	10	0.87932	D	0	.	18.238	0.89956	0.0:1.0:0.0:0.0	.	457	G3XA90	.	F	457;485;394;361	ENSP00000259371:S457F;ENSP00000386183:S485F;ENSP00000362887:S394F;ENSP00000310827:S361F	ENSP00000259371:S457F	S	+	2	0	DAB2IP	123565973	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.619000	0.88677	0.561000	0.74099	TCC	NOVEL	DAB2IP-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053898.1	1	4.513232	KEEP	0	0	0	15	457	CC	0.99649	0.990932	0		+	34	60	1029	0	0	99.259578	32	60	1075	115	ENST00000309989.1	0.515152	0.994422
DENND1A	57706	__UNKNOWN__	__UNKNOWN__	9	126160929	126160929	__UNKNOWN__	Intron	SNP	A	A	T	rs544476433		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:126160929A>T	ENST00000373624.2	-	20	1779				DENND1A_ENST00000542603.1_Intron|DENND1A_ENST00000473039.1_Intron|DENND1A_ENST00000394219.3_Intron	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	NA		NA			endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						gtgctgggataacaggcgtga	0.532		NA											A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15294	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522	57706		DENN/MADD domain containing	29324	protein-coding gene	gene with protein product		613633	KIAA1608	KIAA1608	NA	10997877	Standard	NM_024820	XM_005252109	NA	Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1577+4751T>A	chr9.hg19:g.126160929A>T		NA	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	hg19	CCDS35133.1	0.02	-0.149075	GATxACA	UNCOVERED																																																																																			NOVEL	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000053997.1	4	3.307555	KEEP	5	0	0	11	293	AA	0	0	0		-	3	60	88	0	0	6.972833	12	60	334	45	ENST00000373624.2	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	126867385	126867385	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:126867385C>T			NA	NA				LHX2 (71805 upstream) : NEK6 (152499 downstream)						NA		NA									NA						aggctggtctcgaactcctga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.126867385C>T		NA		hg19		0.02	-0.10526	TCTxGAA	UNCOVERED																																																																																			NOVEL					0			6	2.707003	KEEP	1	0	0	9	251	CC	0.99257	0.138793	0			3	60	92	0	0	7.701036	9	60	288	30		0.25	0.139832
GPR144	347088	__UNKNOWN__	__UNKNOWN__	9	127235067	127235067	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:127235067A>G	ENST00000334810.1	+	17	2679							Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						gattacaggcatgagccaccg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264	347088		-, GPCR / Class B : Orphans	18651	protein-coding gene	gene with protein product		NA			NA		Standard	NM_182611	XM_006710216	NA	Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.2679+2174A>G	chr9.hg19:g.127235067A>G		NA	Q86SL4|Q8NH12	hg19	CCDS48016.1	0.02	-0.131548	GGCxTGA	COVERED																																																																																			NOVEL	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054026.2	6	2.40646	KEEP	0	0	0	8	226	AA	0.99257	0.22747	0		+	3	60	105	0	0	8.773086	11	60	317	35	ENST00000334810.1	0.214286	0.229173
NR6A1	2649	__UNKNOWN__	__UNKNOWN__	9	127392515	127392515	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:127392515A>G	ENST00000487099.2	-	3	300				NR6A1_ENST00000416460.2_Intron|NR6A1_ENST00000373584.3_Intron|NR6A1_ENST00000344523.4_Intron	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	NA		NA			cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						tttttttgagacggagttttg	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(192;272 2884 6208 20560)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200	2649		Nuclear hormone receptors	7985	protein-coding gene	gene with protein product		602778		GCNF	NA	9134503, 8982251	Standard		NM_001489	NA	Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.143-75666T>C	chr9.hg19:g.127392515A>G		NA	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	hg19	CCDS35137.1	0.02	-0.052625	GAGxCGG	UNCOVERED																																																																																			NOVEL	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054043.4	6	3.005321	KEEP	6	0	0	10	262	AA	0.99257	0.036492	0		-	2	38	72	0	0	6.495979	4	48	114	25	ENST00000487099.2	0.333333	0.036766
OLFML2A	169611	__UNKNOWN__	__UNKNOWN__	9	127540408	127540408	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:127540408A>G	ENST00000373580.3	+	1	90					NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	NA		NA			extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						ggaggccgagacgggcggatc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585	169611			27270	protein-coding gene	gene with protein product		615899			NA	12477932	Standard	NM_182487	NM_001282715	NA	Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.90+769A>G	chr9.hg19:g.127540408A>G		NA	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	hg19	CCDS6857.2	0.02	-0.184201	GAGxCGG	COVERED																																																																																			NOVEL	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054046.2	6	3.038679	KEEP	12	1	25	19	515	AA	0.995343	0.421506	0		+	4	31	144	0	0	11.962752	16	60	485	68	ENST00000373580.3	0.2	0.423478
SCAI	286205	__UNKNOWN__	__UNKNOWN__	9	127835691	127835691	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:127835691A>C	ENST00000336505.6	-	3	157				SCAI_ENST00000373549.4_Intron	NM_001144877.2	NP_001138349.1	Q8N9R8	SCAI_HUMAN	suppressor of cancer cell invasion	NA		NA			negative regulation of cell migration (GO:0030336)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(5)|stomach(1)|urinary_tract(1)	35						ccctatttttaattttttgag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093983	CCDS43877.1, CCDS48017.1	9q34.11	2009-11-06	2009-07-09	2009-07-09	ENSG00000173611	ENSG00000173611	286205			26709	protein-coding gene	gene with protein product		NA	chromosome 9 open reading frame 126	C9orf126	NA		Standard	NM_173690	NM_173690	NA	Approved	FLJ36664, NET40	uc004bpd.3	Q8N9R8	OTTHUMG00000020667	ENST00000336505.6:c.99-17405T>G	chr9.hg19:g.127835691A>C		NA	Q3SXZ1|Q3SXZ2|Q5T163|Q8N1I4	hg19	CCDS48017.1	0.02	-0.114	TTTxATT	UNCOVERED																																																																																			NOVEL	SCAI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054055.3	8	2.702344	KEEP	4	0	0	9	225	AA	0.99254	0.161255	0		-	4	30	138	0	0	12.224698	9	60	243	35	ENST00000336505.6	0.307692	0.162467
MAPKAP1	79109	__UNKNOWN__	__UNKNOWN__	9	128242997	128242997	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:128242997A>T	ENST00000350766.3	-	8	1401				MAPKAP1_ENST00000373511.2_Intron|MAPKAP1_ENST00000373497.5_Intron|MAPKAP1_ENST00000373498.1_Intron|MAPKAP1_ENST00000265960.3_Intron|MAPKAP1_ENST00000394063.1_Intron|MAPKAP1_ENST00000373503.3_Intron	NM_024117.3	NP_077022.1	Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						cacgcctgtaatcccagcact	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487	79109			18752	protein-coding gene	gene with protein product	stress-activated protein kinase-interacting 1	610558			NA	15363842	Standard		NM_001006620	NA	Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000350766.3:c.1099+3724T>A	chr9.hg19:g.128242997A>T		NA	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	hg19	CCDS6864.1	0.02	-0.245574	GTAxTCC	COVERED																																																																																			NOVEL	MAPKAP1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054090.1	12	2.938923	KEEP	18	1	26	19	519	AA	0.99649	0.639096	0		-	6	25	167	1	0	13.4643	20	60	612	86	ENST00000350766.3	0.230769	0.641347
MAPKAP1	79109	__UNKNOWN__	__UNKNOWN__	9	128243062	128243062	__UNKNOWN__	Intron	SNP	T	T	C	rs541118657		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:128243062T>C	ENST00000350766.3	-	8	1401				MAPKAP1_ENST00000373511.2_Intron|MAPKAP1_ENST00000373497.5_Intron|MAPKAP1_ENST00000373498.1_Intron|MAPKAP1_ENST00000265960.3_Intron|MAPKAP1_ENST00000394063.1_Intron|MAPKAP1_ENST00000373503.3_Intron	NM_024117.3	NP_077022.1	Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						ccatcctggctaacatggtga	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487	79109			18752	protein-coding gene	gene with protein product	stress-activated protein kinase-interacting 1	610558			NA	15363842	Standard		NM_001006620	NA	Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000350766.3:c.1099+3659A>G	chr9.hg19:g.128243062T>C		NA	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	hg19	CCDS6864.1	0.02	-0.236822	GGCxAAC	UNCOVERED																																																																																			NOVEL	MAPKAP1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054090.1	11	3.307847	KEEP	20	0	0	11	297	TT	0	0	0		-	3	44	96	0	1	7.106046	21	40	639	78	ENST00000350766.3	0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	128774842	128774842	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:128774842T>C			NA	NA				PBX3 (45186 upstream) : RP11-343J18.2 (45016 downstream)						NA		NA									NA						cctcctgccttagcctcctga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.128774842T>C		NA		hg19		0.02	-0.192917	CCTxAGC	COVERED																																																																																			NOVEL					0			6	3.00666	KEEP	1	0	0	10	262	TT	0.99254	0.454342	0			3	60	105	0	0	8.261003	17	60	483	44		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	129503615	129503615	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:129503615A>C			NA	NA				AL161731.1 (23003 upstream) : ZBTB43 (63669 downstream)						NA		NA									NA						ggattacaggagtgagccact	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.129503615A>C		NA		hg19		0.02	-0.114023	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			4	2.706497	KEEP	1	0	0	9	242	AA	0.99257	0.16126	0			3	60	88	0	0	7.182043	10	60	304	32		0.230769	0.162467
ZBTB43	23099	__UNKNOWN__	__UNKNOWN__	9	129579670	129579670	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:129579670A>G	ENST00000373464.4	+	2	241				ZBTB43_ENST00000449886.1_Intron	NM_014007.3	NP_054726.1	O43298	ZBT43_HUMAN	zinc finger and BTB domain containing 43	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						gattacaggcatgagccacca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF049907	CCDS6867.1	9q33.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000169155	ENSG00000169155	23099		-, BTB/POZ domain containing, Zinc fingers, C2H2-type	17908	protein-coding gene	gene with protein product		NA	zinc finger protein 297B	ZNF297B	NA		Standard	NM_001135776	NM_014007	NA	Approved	KIAA0414, ZNF-X, FLJ22470, ZBTB22B	uc010mxf.3	O43298	OTTHUMG00000020693	ENST00000373464.4:c.-24+8476A>G	chr9.hg19:g.129579670A>G		NA	Q5JU96	hg19	CCDS6867.1	0.02	-0.271843	GGCxTGA	COVERED																																																																																			NOVEL	ZBTB43-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054124.1	13	5.71298	KEEP	3	0	0	19	509	AA	0.999366	0.716861	0		+	3	57	104	0	0	7.848852	22	60	631	70	ENST00000373464.4	0.12	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	129673109	129673109	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:129673109T>C			NA	NA				ZBTB34 (24952 upstream) : RALGPS1 (3943 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.129673109T>C		NA		hg19		0.02	-0.070161	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			5	2.405768	KEEP	2	0	0	8	220	TT	0	0	0			2	60	72	0	0	6.335933	5	60	139	25		0.285714	0.054137
ZNF79	7633	__UNKNOWN__	__UNKNOWN__	9	130206121	130206121	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130206121A>G	ENST00000342483.5	+	5	734				ZNF79_ENST00000543471.1_Intron	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						cggaggttgcagtgagctgag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152	7633		Zinc fingers, C2H2-type	13153	protein-coding gene	gene with protein product		194552	zinc finger protein 79 (pT7)		NA	8478004	Standard	NM_007135	NM_007135	NA	Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.329-187A>G	chr9.hg19:g.130206121A>G		NA	Q5VVW1|Q96NV1	hg19	CCDS6871.1	0.02	-0.14033	TGCxGTG	COVERED																																																																																			NOVEL	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054188.1	17	6.917714	KEEP	10	0	0	23	636	AA	0.997832	0.291368	0		+	3	20	94	0	1	7.479049	13	60	383	59	ENST00000342483.5	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	130365045	130365045	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130365045T>G			NA	NA				FAM129B (23777 upstream) : STXBP1 (9498 downstream)						NA		NA									NA						tgttgcccagtctggtctcaa	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.130365045T>G		NA		hg19		0.02	-0.166637	CAGxCTG	COVERED																																																																																			NOVEL					0			9	4.510608	KEEP	1	0	0	15	408	TT	0.995343	0.352299	0			3	60	97	0	1	7.691961	14	60	411	50		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	130366572	130366572	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130366572A>G			NA	NA				FAM129B (25304 upstream) : STXBP1 (7971 downstream)						NA		NA									NA						cccgaggtcaagagttcgaga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.130366572A>G		NA		hg19		0.02	-0.140337	TCAxGAG	COVERED																																																																																			NOVEL					0			7	2.706774	KEEP	0	0	0	9	246	AA	0.99254	0.259018	0			3	60	93	0	0	7.472493	12	60	371	40		0.2	0.260965
STXBP1	6812	__UNKNOWN__	__UNKNOWN__	9	130398283	130398283	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130398283A>G	ENST00000373302.3	+	2	176				STXBP1_ENST00000373299.1_Intron	NM_003165.3	NP_003156.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	NA		NA			axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						tttggagatgaagtctcactc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854	6812			11444	protein-coding gene	gene with protein product	syntaxin-binding protein 1	602926			NA	9545644	Standard	NM_003165	NM_001032221	NA	Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373302.3:c.38-15599A>G	chr9.hg19:g.130398283A>G		NA	B1AM97|Q28208|Q62759|Q64320|Q96TG8	hg19	CCDS6874.1	0.02	-0.087697	ATGxAGT	UNCOVERED																																																																																			NOVEL	STXBP1-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054228.1	15	3.006562	KEEP	4	0	0	10	260	AA	0.99257	0.09898	0		+	3	60	94	1	0	9.369334	2	60	56	25	ENST00000373302.3	0.6	0.099721
STXBP1	6812	__UNKNOWN__	__UNKNOWN__	9	130401112	130401112	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130401112T>G	ENST00000373302.3	+	2	176				STXBP1_ENST00000373299.1_Intron	NM_003165.3	NP_003156.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	NA		NA			axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						aaagtgctggtattacaggcg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854	6812			11444	protein-coding gene	gene with protein product	syntaxin-binding protein 1	602926			NA	9545644	Standard	NM_003165	NM_001032221	NA	Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373302.3:c.38-12770T>G	chr9.hg19:g.130401112T>G		NA	B1AM97|Q28208|Q62759|Q64320|Q96TG8	hg19	CCDS6874.1	0.02	-0.070172	TGGxATT	UNCOVERED																																																																																			NOVEL	STXBP1-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054228.1	5	2.405788	KEEP	0	0	0	8	215	TT	0.99257	0.053735	0		+	2	60	71	0	0	6.395828	4	60	122	25	ENST00000373302.3	0.333333	0.054137
STXBP1	6812	__UNKNOWN__	__UNKNOWN__	9	130437604	130437604	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130437604C>T	ENST00000373302.3	+	14	1249				STXBP1_ENST00000373299.1_Intron|STXBP1_ENST00000481942.1_Intron	NM_003165.3	NP_003156.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	NA		NA			axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						gtagctgggactacaggcatg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854	6812			11444	protein-coding gene	gene with protein product	syntaxin-binding protein 1	602926			NA	9545644	Standard	NM_003165	NM_001032221	NA	Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373302.3:c.1111-479C>T	chr9.hg19:g.130437604C>T		NA	B1AM97|Q28208|Q62759|Q64320|Q96TG8	hg19	CCDS6874.1	0.02	-0.140358	GGAxTAC	COVERED																																																																																			NOVEL	STXBP1-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054228.1	5	3.308348	KEEP	1	0	0	11	334	CC	0.992708	0.259062	0		+	3	60	92	0	0	7.581747	10	60	346	39	ENST00000373302.3	0.230769	0.260965
ST6GALNAC4	27090	__UNKNOWN__	__UNKNOWN__	9	130671592	130671592	__UNKNOWN__	Intron	SNP	C	C	T	rs187824020	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130671592C>T	ENST00000335791.5	-	5	995				ST6GALNAC4_ENST00000343609.2_Intron|ST6GALNAC4_ENST00000495983.1_Intron	NM_175039.3	NP_778204.1	Q9H4F1	SIA7D_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4	NA		NA			cellular protein metabolic process (GO:0044267)|glycolipid metabolic process (GO:0006664)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	(alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity (GO:0047290)|sialyltransferase activity (GO:0008373)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7						cgcttgaacccgggaggtgga	0.502		NA											C|||	9	0.00179712	0.0008	0.0	5008	,	,	NA	12035	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035172	CCDS6883.1	9q34	2013-03-01	2005-02-07	2005-02-07	ENSG00000136840	ENSG00000136840	27090	2.4.99.7	Sialyltransferases	17846	protein-coding gene	gene with protein product		606378	sialyltransferase 7D ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)	SIAT7D	NA	10207017, 11062056	Standard	NM_175040	XM_005251922	NA	Approved	ST6GALNACIV, SIAT3C	uc004bss.3	Q9H4F1	OTTHUMG00000020724	ENST00000335791.5:c.719+637G>A	chr9.hg19:g.130671592C>T		NA	Q5T9D0|Q9NWU6|Q9UKU1|Q9ULB9|Q9Y3G3|Q9Y3G4	hg19	CCDS6883.1	0.02	-0.140348	ACCxGGG	COVERED																																																																																			NOVEL	ST6GALNAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054317.2	11	3.308195	KEEP	4	0	0	11	318	CC	0.99254	0.259018	0		-	3	43	87	0	0	6.972888	11	60	363	41	ENST00000335791.5	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	130757727	130757727	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130757727T>C			NA	NA				FAM102A (14935 upstream) : RP11-379C10.1 (43686 downstream)						NA		NA									NA						ggcatggtggttcacacctgt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.130757727T>C		NA		hg19		0.02	-0.236801	TGGxTCA	COVERED																																																																																			NOVEL					0			5	3.90906	KEEP	0	0	0	13	349	TT	0.994391	0.608972	0			3	60	97	0	0	7.206069	21	60	617	58		0.125	0.612407
RP11-379C10.1	0	__UNKNOWN__	__UNKNOWN__	9	130819082	130819082	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130819082T>C	ENST00000414976.1	-	0	207										NA		NA									NA						ggattgcaggtatgagccact	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000414976.1:	chr9.hg19:g.130819082T>C		NA		hg19		0.02	-0.052631	AGGxATG	UNCOVERED																																																																																			NOVEL	RP11-379C10.1-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000054329.1	5	3.604534	KEEP	0	0	0	12	304	TT	0.993634	0.036532	0		-	2	60	70	0	0	6.750208	2	60	61	20	ENST00000414976.1	0.5	0.036766
SLC25A25	114789	__UNKNOWN__	__UNKNOWN__	9	130843995	130843995	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:130843995G>C	ENST00000373068.2	+	1	380				SLC25A25_ENST00000373069.5_Intron	NM_001006641.3	NP_001006642.1	Q6KCM7	SCMC2_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25	NA		NA			adipose tissue development (GO:0060612)|ATP metabolic process (GO:0046034)|calcium ion transmembrane transport (GO:0070588)|camera-type eye development (GO:0043010)|cellular respiration (GO:0045333)|multicellular organism growth (GO:0035264)|response to activity (GO:0014823)|response to dietary excess (GO:0002021)|response to food (GO:0032094)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)	10						attgcttgaggccaggagttc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ619963	CCDS6890.1, CCDS35151.1, CCDS48031.1, CCDS59146.1	9q34	2013-05-22			ENSG00000148339	ENSG00000148339	114789		Solute carriers, EF-hand domain containing	20663	protein-coding gene	gene with protein product		608745			NA	15123600	Standard	NM_052901	NM_052901	NA	Approved	KIAA1896, PCSCL, MCSC	uc004btb.4	Q6KCM7	OTTHUMG00000020736	ENST00000373068.2:c.261+13136G>C	chr9.hg19:g.130843995G>C		NA	Q5SYW7|Q5SYW8|Q5SYX3|Q5VWU2|Q5VWU3|Q5VWU4|Q6KCM4|Q6KCM6|Q6UX48|Q705K2|Q96PZ1|Q9BSA6	hg19	CCDS35151.1	0.02	-0.114043	GAGxCCA	COVERED																																																																																			NOVEL	SLC25A25-004	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054409.2	6	4.814104	KEEP	1	0	0	16	490	GG	0.999366	0.229028	0		+	3	60	101	0	0	8.600921	9	60	308	52	ENST00000373068.2	0.25	0.229173
SPTAN1	6709	__UNKNOWN__	__UNKNOWN__	9	131352045	131352045	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:131352045G>A	ENST00000372731.4	+	21	3116				SPTAN1_ENST00000358161.5_Intron|SPTAN1_ENST00000372739.3_Intron	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	NA		NA			actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						tagtagagacggggtttcacc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(120;833 1744 2558 35612 37579)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694	6709		EF-hand domain containing	11273	protein-coding gene	gene with protein product	alpha-fodrin	182810			NA	3336352	Standard	NM_003127	NM_003127	NA	Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3006+823G>A	chr9.hg19:g.131352045G>A		NA	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	hg19	CCDS6905.1	0.02	-0.122449	GACxGGG	UNCOVERED																																																																																			NOVEL	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054472.1	8	3.306102	KEEP	7	0	0	11	289	GG	0	0	0		+	5	35	117	0	0	10.104524	9	48	271	33	ENST00000372731.4	0.357143	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	131430481	131430481	__UNKNOWN__	IGR	SNP	G	G	A	rs573016191	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:131430481G>A			NA	NA				HMGA1P4 (4624 upstream) : SET (15452 downstream)						NA		NA									NA						cttgtgatccgcccgccttgg	0.562		NA											N|||	3	0.000599042	0.0	0.0	5008	,	,	NA	15755	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.131430481G>A		NA		hg19		0.02	-0.131579	TCCxCCC	COVERED																																																																																			NOVEL					0			7	3.30889	KEEP	4	0	0	11	331	GG	0.992708	0.227502	0			3	46	93	0	0	7.572752	11	60	361	43		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	131431364	131431364	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:131431364G>A			NA	NA				HMGA1P4 (5507 upstream) : SET (14569 downstream)						NA		NA									NA						atataattgggccgggtgtgg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.131431364G>A		NA		hg19		0.02	-0.175444	TGGxCCG	COVERED																																																																																			NOVEL					0			12	2.33992	KEEP	3	1	26	17	522	GG	0.999366	0.387161	0			3	50	85	0	0	6.492135	14	60	481	61		0.176471	0.387407
SET	6418	__UNKNOWN__	__UNKNOWN__	9	131456888	131456888	__UNKNOWN__	Intron	SNP	C	C	T	rs548111975		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:131456888C>T	ENST00000322030.8	+	8	1167				SET_ENST00000372692.4_Intron|SET_ENST00000372688.4_Intron|SET_ENST00000409104.3_Intron	NM_003011.3	NP_003002.2	Q01105	SET_HUMAN	SET nuclear proto-oncogene	NA		NA			DNA replication (GO:0006260)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of catalytic activity (GO:0043086)|negative regulation of histone acetylation (GO:0035067)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|nucleosome disassembly (GO:0006337)|regulation of catalytic activity (GO:0050790)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone binding (GO:0042393)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(2)|kidney(1)|lung(2)	5		Myeloproliferative disorder(178;0.204)		GBM - Glioblastoma multiforme(294;3.1e-09)		CAGCATTAATCCTGAAGATTA	0.438		NA	T	NUP214	AML								C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16019	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA			Dom	yes		9	9q34	6418	SET translocation		L	0													128	126	127			NA	NA	9		NA											NA				131456888		2203	4300	6503	SO:0001627	intron_variant			M93651	CCDS6907.1, CCDS48037.1, CCDS59149.1, CCDS59150.1	9q34	2014-06-25	2014-06-25		ENSG00000119335	ENSG00000119335	6418			10760	protein-coding gene	gene with protein product	protein phosphatase type 2A inhibitor, Template-Activating Factor-I, chromatin remodelling factor	600960	SET translocation (myeloid leukemia-associated)		NA	1630450, 8626647	Standard	NM_001122821	NM_003011	NA	Approved	PHAPII, 2PP2A, IPP2A2	uc022bol.1	Q01105	OTTHUMG00000020755	ENST00000322030.8:c.811-32C>T	chr9.hg19:g.131456888C>T		NA	A5A5H4|A6NGV1|B4DUE2|Q15541|Q5VXV1|Q5VXV2|Q6FHZ5	hg19	CCDS6907.1	0.02	1.047875	AATxCTG	COVERED																																																																																			NOVEL	SET-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054477.2	5	10.527681	KEEP	0	0	0	35	1025	CC	0.999999	0.999621	0		+	5	60	147	0	0	8.864953	79	60	2682	175	ENST00000322030.8	0.059524	0.999622
PKN3	29941	__UNKNOWN__	__UNKNOWN__	9	131478877	131478877	__UNKNOWN__	Intron	SNP	A	A	T	rs79568039	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:131478877A>T	ENST00000291906.4	+	16	2201				PKN3_ENST00000485301.1_Intron	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	NA		NA			epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						actgtgtctcaaaaaaaaaaa	0.517		NA											A|||	1123	0.224241	0.1475	0.2939	5008	,	,	NA	15111	0.2659	NA	0.2416	False	NA	,,,	NA	NA	NA	2504	0.2178	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447	29941			17999	protein-coding gene	gene with protein product		610714			NA	10441506	Standard	NM_013355	NM_013355	NA	Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1809-149A>T	chr9.hg19:g.131478877A>T		NA	Q9UM03	hg19	CCDS6908.1	0.02	-0.078919	CTCxAAA	UNCOVERED																																																																																			NOVEL	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054487.1	6	2.401246	KEEP	0	0	0	8	182	AA	0.99257	0.076761	0		+	3	60	82	2	1	7.554227	4	60	118	20	ENST00000291906.4	0.428571	0.077336
NUP188	23511	__UNKNOWN__	__UNKNOWN__	9	131737737	131737737	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:131737737G>A	ENST00000372577.2	+	12	1224					NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	NA		NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						tcctgacctcgtgatccgccc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319	23511			17859	protein-coding gene	gene with protein product		615587	KIAA0169	KIAA0169	NA	11029043	Standard		NM_015354	NA	Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.1203+2209G>A	chr9.hg19:g.131737737G>A		NA	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	hg19	CCDS35156.1	0.02	-0.096486	CTCxTGA	UNCOVERED																																																																																			NOVEL	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054529.2	5	3.307597	KEEP	2	0	0	11	302	GG	0.99254	0.119538	0		+	3	60	90	0	0	7.778463	7	60	221	29	ENST00000372577.2	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	132011694	132011694	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:132011694T>C			NA	NA				AL158151.1 (18698 upstream) : RP11-344B5.4 (8938 downstream)						NA		NA									NA						aaaccaggcatggtggctcat	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.132011694T>C		NA		hg19		0.02	-0.043853	GCAxGGT	UNCOVERED																																																																																			NOVEL					0			6	2.405151	KEEP	1	0	0	8	211	TT	0	0	0			2	60	69	0	0	6.650424	2	60	55	18		0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	132223702	132223702	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:132223702T>C			NA	NA				RP11-65J3.3 (14133 upstream) : AL353803.1 (17132 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.132223702T>C		NA		hg19		0.02	-0.24555	TCAxGCC	COVERED																																																																																			NOVEL					0			5	3.608417	KEEP	0	0	0	12	323	TT	0.993634	0.637264	0			3	60	97	0	0	7.095104	23	60	666	55		0.115385	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	132240662	132240662	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:132240662T>C			NA	NA				RP11-65J3.3 (31093 upstream) : AL353803.1 (172 downstream)						NA		NA									NA						ggtgtggtggttcacacctgt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.132240662T>C		NA		hg19		0.02	-0.105248	TGGxTCA	UNCOVERED																																																																																			NOVEL					0			3	2.706362	KEEP	0	0	0	9	245	TT	0.99254	0.138789	0			3	60	99	0	0	8.401287	9	60	265	33		0.25	0.139832
PRRX2	51450	__UNKNOWN__	__UNKNOWN__	9	132478923	132478923	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:132478923T>G	ENST00000372469.4	+	2	486				RP11-483H20.6_ENST00000440413.1_RNA	NM_016307.3	NP_057391.1	Q99811	PRRX2_HUMAN	paired related homeobox 2	NA		NA			artery morphogenesis (GO:0048844)|cartilage development (GO:0051216)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|inner ear morphogenesis (GO:0042472)|middle ear morphogenesis (GO:0042474)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(2)|pancreas(1)	3		Ovarian(14;0.00556)				tagtagagactgggttttgcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF061970	CCDS6926.1	9q34.11	2011-06-20			ENSG00000167157	ENSG00000167157	51450		Homeoboxes / PRD class	21338	protein-coding gene	gene with protein product		604675			NA	11063257	Standard	NM_016307	NM_016307	NA	Approved	PRX2, PMX2	uc004byh.3	Q99811	OTTHUMG00000020790	ENST00000372469.4:c.260-2587T>G	chr9.hg19:g.132478923T>G		NA	Q5SZB5|Q9UIB3	hg19	CCDS6926.1	0.02	-0.122797	GACxGGG	COVERED																																																																																			NOVEL	PRRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054598.2	3	2.706488	KEEP	5	0	0	9	248	AT	0.99257	0.22747	0		+	3	40	94	0	0	7.901165	9	60	272	42	ENST00000372469.4	0.25	0.229173
GPR107	57720	__UNKNOWN__	__UNKNOWN__	9	132875757	132875757	__UNKNOWN__	Intron	SNP	A	A	G	rs556003145	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:132875757A>G	ENST00000347136.6	+	14	1813				GPR107_ENST00000372406.1_Intron|GPR107_ENST00000372410.3_Intron	NM_020960.4	NP_066011.2	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	NA		NA				integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				tgatccacccacctcggcctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358	57720		GPCR / Unclassified : 7TM orphan receptors	17830	protein-coding gene	gene with protein product		NA			NA		Standard		NM_020960	NA	Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000347136.6:c.1306+5939A>G	chr9.hg19:g.132875757A>G		NA	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	hg19	CCDS35162.1	0.02	-0.175387	CCCxCCT	COVERED																																																																																			NOVEL	GPR107-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054645.1	5	3.909705	KEEP	0	0	0	13	361	AA	0.994391	0.385234	0		+	3	60	97	0	0	7.533753	16	60	457	46	ENST00000347136.6	0.157895	0.387407
HMCN2	256158	__UNKNOWN__	__UNKNOWN__	9	133306737	133306737	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:133306737C>G	ENST00000428715.1	+	12	1778				HMCN2_ENST00000302481.1_Intron			Q8NDA2	HMCN2_HUMAN	hemicentin 2	NA		NA			response to stimulus (GO:0050896)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)				NA						CCTGCCCCACCCCCATGCCCG	0.687		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074396		9q34.11	2013-01-29			ENSG00000148357	ENSG00000148357	256158		Fibulins, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	21293	protein-coding gene	gene with protein product		NA			NA		Standard	XM_175125	XM_006710218	NA	Approved	DKFZp434P0216, FLJ23816		Q8NDA2	OTTHUMG00000140096	ENST00000428715.1:c.1778-17C>G	chr9.hg19:g.133306737C>G		NA	Q8N225|Q8TCI8	hg19		0.02	-0.368399	CACxCCC	COVERED																																																																																			NOVEL	HMCN2-001	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000054661.2	2	2.406464	KEEP	0	0	0	8	234	CC	0.99257	0.892632	0		+	21	60	656	0	0	62.970251	21	60	728	71	ENST00000428715.1	0.5	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	134202068	134202068	__UNKNOWN__	IGR	SNP	C	C	G	rs2478857	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:134202068C>G			NA	NA				PPAPDC3 (17419 upstream) : PRRC2B (67411 downstream)						NA		NA									NA						gggtggatcacgaggtcagga	0.517		NA											c|||	2189	0.437101	0.5151	0.3674	5008	,	,	NA	14768	0.5744	NA	0.3231	False	NA	,,,	NA	NA	NA	2504	0.3569	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.134202068C>G		NA		hg19		0.02	-0.070177	TCAxGAG	UNCOVERED																																																																																			NOVEL					0			12	2.406267	KEEP	8	0	0	8	227	CC	0	0	0			2	60	73	0	1	6.435648	5	60	158	28		0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	134229820	134229820	__UNKNOWN__	IGR	SNP	T	T	G	rs11243366	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:134229820T>G			NA	NA				PPAPDC3 (45171 upstream) : PRRC2B (39659 downstream)						NA		NA									NA						atcccagcactttgggaggcc	0.517		NA											G|||	2917	0.582468	0.6536	0.5951	5008	,	,	NA	11898	0.4871	NA	0.6133	False	NA	,,,	NA	NA	NA	2504	0.544	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.134229820T>G		NA		hg19		0.02	-0.157827	CACxTTG	COVERED																																																																																			NOVEL					0			9	2.706574	KEEP	6	0	0	9	252	TT	0.99254	0.320398	0			3	60	89	0	0	7.1737	11	60	311	45		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	134229830	134229830	__UNKNOWN__	IGR	SNP	C	C	T	rs138881655	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:134229830C>T			NA	NA				PPAPDC3 (45181 upstream) : PRRC2B (39649 downstream)						NA		NA									NA						tttgggaggccaaggcgggcg	0.512		NA											C|||	331	0.0660942	0.0401	0.0548	5008	,	,	NA	10909	0.0923	NA	0.0934	False	NA	,,,	NA	NA	NA	2504	0.0542	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.134229830C>T		NA		hg19		0.02	-0.140148	GGCxAAG	COVERED																																																																																			NOVEL					0			7	2.407237	KEEP	6	0	0	8	249	CC	0.99257	0.259026	0			3	60	82	0	0	6.700907	9	60	310	41		0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	134229831	134229831	__UNKNOWN__	IGR	SNP	A	A	G	rs10901048	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:134229831A>G			NA	NA				PPAPDC3 (45182 upstream) : PRRC2B (39648 downstream)						NA		NA									NA						ttgggaggccaaggcgggcgg	0.512		NA											G|||	3224	0.64377	0.5719	0.6844	5008	,	,	NA	10860	0.7292	NA	0.6412	False	NA	,,,	NA	NA	NA	2504	0.6268	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.134229831A>G		NA		hg19		0.02	-0.140308	GCCxAGG	COVERED																																																																																			NOVEL					0			7	2.405298	KEEP	6	0	0	8	212	AA	0.99257	0.259026	0			3	60	84	0	0	6.901192	9	60	271	41		0.25	0.260965
SETX	23064	__UNKNOWN__	__UNKNOWN__	9	135218187	135218187	__UNKNOWN__	Splice_Site	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:135218187C>T	ENST00000224140.5	-	5	571		c.e5-1		SETX_ENST00000393220.1_Splice_Site|SETX_ENST00000372169.2_Splice_Site	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	NA		NA			cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CATAACTCGTCTAAAAAGAAA	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													84	89	87			NA	NA	9		NA											NA				135218187		2203	4300	6503	SO:0001630	splice_region_variant			AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290	23064			445	protein-coding gene	gene with protein product		608465	amyotrophic lateral sclerosis 4, spinocerebellar ataxia, recessive, non-Friedreich type 1	ALS4, SCAR1	NA	9497266, 11022012	Standard	NM_015046	NM_015046	NA	Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.389-1G>A	chr9.hg19:g.135218187C>T		NA	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	hg19	CCDS6947.1	0.02	-0.350895	CGTxTAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.53	2.860654	0.51482	.	.	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2409	0.93883	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETX	134208008	1.000000	0.71417	0.984000	0.44739	0.472000	0.32918	5.417000	0.66423	2.788000	0.95919	0.557000	0.71058	.	NOVEL	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054774.3	0	2.707701	KEEP	0	0	0	9	276	CC	0.99254	0.87116	0	Intron	-	4	60	115	1	0	7.766942	36	60	1234	59	ENST00000224140.5	0.1	0.877708
C9orf9	11092	__UNKNOWN__	__UNKNOWN__	9	135764446	135764446	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:135764446A>C	ENST00000350499.6	+	4	649				C9orf9_ENST00000372136.3_3'UTR|C9orf9_ENST00000356311.5_3'UTR	NM_018956.3	NP_061829.3	Q96E40	CI009_HUMAN	chromosome 9 open reading frame 9	NA		NA				cytoplasmic microtubule (GO:0005881)		p.?(1)		cervix(1)|large_intestine(1)|lung(1)|prostate(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|GBM - Glioblastoma multiforme(294;4.84e-07)|Epithelial(140;1.28e-06)		cgtgagccacagcgcccggcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Unknown(1)	bone(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS6955.1	9q34.13	2012-03-06			ENSG00000165698	ENSG00000165698	11092			1367	protein-coding gene	gene with protein product		NA			NA		Standard	NM_018956	NM_018956	NA	Approved		uc004cby.1	Q96E40	OTTHUMG00000020847	ENST00000350499.6:c.495+622A>C	chr9.hg19:g.135764446A>C		NA	Q9UGQ0	hg19	CCDS6955.1	0.02	-0.254356	CACxGCG	COVERED																																																																																			NOVEL	C9orf9-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054808.1	2	5.715201	KEEP	0	0	0	19	534	AA	0.99986	0.693571	0		+	3	60	96	0	0	6.844508	26	60	784	57	ENST00000350499.6	0.103448	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	135935631	135935631	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:135935631C>A			NA	NA				GTF3C5 (1741 upstream) : CEL (1733 downstream)						NA		NA									NA						ccagcctggccaacatggtga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.135935631C>A		NA		hg19		0.02	-0.114036	GGCxAAC	UNCOVERED																																																																																			NOVEL					0			6	2.407017	KEEP	3	0	0	8	241	CC	0	0	0			3	60	86	0	0	7.100934	9	60	307	30		0.25	0.162467
CEL	1056	__UNKNOWN__	__UNKNOWN__	9	135939976	135939976	__UNKNOWN__	Intron	SNP	G	G	A	rs8193019	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:135939976G>A	ENST00000372080.4	+	2	242				CEL_ENST00000351304.7_Intron	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	NA		NA			cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		GCCCTGCGGCGGGGCGGGTGA	0.652		NA											G|||	142	0.0283546	0.0197	0.0029	5008	,	,	NA	15739	0.0526	NA	0.0139	False	NA	,,,	NA	NA	NA	2504	0.0481	NA	NA	NA								NA				0								G		53,3935		1,51,1942	39	47	44			-8.3	0	9	dbSNP_117	44	117,8195		0,117,4039	no	intron	CEL	NM_001807.3		1,168,5981	AA,AG,GG	NA	1.4076,1.329,1.3821			135939976	170,12130	1994	4156	6150	SO:0001627	intron_variant			M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	1056	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	bile salt-stimulated lipase	114840			NA	1676983	Standard		NM_001807	NA	Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.226+35G>A	chr9.hg19:g.135939976G>A		NA	Q16398|Q5T7U7|Q9UCH1|Q9UP41	hg19	CCDS43896.1	0.02	1.193023	GGCxGGG	COVERED																																																																																			NOVEL	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054823.1	2	2.407224	KEEP	0	0	0	8	247	GG	0.99257	0.992433	0		+	42	60	1226	0	0	115.352307	49	60	1565	125	ENST00000372080.4	0.461538	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	136061121	136061121	__UNKNOWN__	IGR	SNP	G	G	C	rs11788544	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:136061121G>C			NA	NA				GBGT1 (21789 upstream) : OBP2B (19542 downstream)						NA		NA									NA						cactttgggaggatgaggtag	0.463		NA											G|||	966	0.192891	0.1732	0.3357	5008	,	,	NA	16751	0.0089	NA	0.332	False	NA	,,,	NA	NA	NA	2504	0.1646	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.136061121G>C		NA		hg19		0.02	-0.070177	GGAxGAT	UNCOVERED																																																																																			NOVEL					0			3	3.008639	KEEP	0	0	0	10	300	GG	0.992708	0.053742	0			4	60	129	0	0	12.731858	3	60	103	26		0.571429	0.054137
OLFM1	10439	__UNKNOWN__	__UNKNOWN__	9	137982234	137982234	__UNKNOWN__	Intron	SNP	G	G	T	rs10672761|rs397744056|rs199972738	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:137982234G>T	ENST00000371796.3	+	2	333				OLFM1_ENST00000392991.4_Intron|OLFM1_ENST00000252854.4_Intron|OLFM1_ENST00000277415.11_Intron|OLFM1_ENST00000371793.3_Intron	NM_001282612.1	NP_001269541.1	Q99784	NOE1_HUMAN	olfactomedin 1	NA		NA			negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of neuron migration (GO:2001223)|nervous system development (GO:0007399)|protein oligomerization (GO:0051259)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)	21		Myeloproliferative disorder(178;0.0333)		Epithelial(140;5.49e-08)|OV - Ovarian serous cystadenocarcinoma(145;9.68e-08)|all cancers(34;1.88e-07)		gtgtgtgtttgtgtgtgtgtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													73	53	60			NA	NA	9		NA											NA				137982234		2203	4300	6503	SO:0001627	intron_variant			AF035301	CCDS6986.1, CCDS6987.1, CCDS65183.1, CCDS65184.1	9q34.3	2014-01-20			ENSG00000130558	ENSG00000130558	10439			17187	protein-coding gene	gene with protein product	pancortin	605366			NA	9039501	Standard	NM_014279	NM_006334	NA	Approved	NOE1, OlfA, AMY, NOELIN	uc004cfl.4	Q99784	OTTHUMG00000020897	ENST00000371796.3:c.219+44G>T	chr9.hg19:g.137982234G>T		NA	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	hg19		0.02	-0.394696	TTTxTGT	COVERED																																																																																			NOVEL	OLFM1-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000054973.1	6	8.931034	KEEP	0	1	6	32	948	GG	0.999998	0.926638	0		+	5	60	134	0	0	9.247259	35	70	1155	100	ENST00000371796.3	0.125	0.92664
KIAA1984	0	__UNKNOWN__	__UNKNOWN__	9	139692793	139692793	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:139692793G>A	ENST00000338005.6	+	2	105				KIAA1984_ENST00000371682.3_Intron|RP11-216L13.17_ENST00000456614.2_Intron	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		NA		NA								biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		tcattctgtcgtccaggtgga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000338005.6:c.71-761G>A	chr9.hg19:g.139692793G>A		NA	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	hg19	CCDS43906.1	0.02	-0.105214	GTCxTCC	UNCOVERED																																																																																			NOVEL	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354899.1	2	2.707031	KEEP	0	0	0	9	257	GG	0.99254	0.138789	0		+	3	60	88	0	0	7.301747	9	60	265	29	ENST00000338005.6	0.25	0.139832
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139997126	139997126	__UNKNOWN__	Intron	SNP	A	A	T	rs554634366	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:139997126A>T	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TGTTACACACATTCACACTGT	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1002A>T	chr9.hg19:g.139997126A>T		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	2.754472	CACxTTC	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	13	2.369163	KEEP	4	2	51	26	715	AA	0.999988	0.999988	0		+	13	60	363	2	0	24.7492	105	60	3042	230	ENST00000371589.4	0.110169	1
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139997224	139997224	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:139997224G>A	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TTGCAGGCGTGCAGGTCGGTG	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1100G>A	chr9.hg19:g.139997224G>A		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	10.261733	CGTxCAG	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	49	7.891585	KEEP	32	8	190	94	2865	GG	1	1	0		+	19	60	525	0	0	30.815935	285	60	9735	762	ENST00000371589.4	0.0625	1
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139997554	139997554	__UNKNOWN__	Intron	SNP	G	G	T	rs577478453	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:139997554G>T	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		CAGGTCGGTGGTGTTACACAC	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1430G>T	chr9.hg19:g.139997554G>T		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	5.312548	GTGxTGT	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	30	12.033102	KEEP	23	3	79	68	2041	GG	1	1	0		+	9	40	245	0	0	12.75541	199	60	6690	472	ENST00000371589.4	0.043269	1
MAN1B1	11253	__UNKNOWN__	__UNKNOWN__	9	139997625	139997625	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:139997625C>T	ENST00000371589.4	+	8	1327				MAN1B1_ENST00000474902.1_Intron	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	NA		NA			cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		GCGTGCAGGTCGGTGGTACAC	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239	11253			6823	protein-coding gene	gene with protein product	endoplasmic reticulum alpha-mannosidase 1, alpha 1,2-mannosidase, endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1, ER alpha 1,2-mannosidase, Man9GlcNAc2-specific processing alpha-mannosidase	604346			NA	10409699, 10521544	Standard	NM_016219	NM_016219	NA	Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.1254+1501C>T	chr9.hg19:g.139997625C>T		NA	Q5VSG3|Q9BRS9|Q9Y5K7	hg19	CCDS7029.1	0.02	4.791283	GGTxGGT	COVERED																																																																																			NOVEL	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055294.2	19	12.594492	KEEP	19	2	48	59	1644	CC	1	1	0		+	10	60	297	0	0	18.692081	135	60	4273	355	ENST00000371589.4	0.068966	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	9	140496137	140496137	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:140496137A>G			NA	NA				ZMYND19 (11195 upstream) : ARRDC1 (3968 downstream)						NA		NA									NA						gggattacagatgtgagccac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr9.hg19:g.140496137A>G		NA		hg19		0.02	-0.210483	CAGxTGT	COVERED																																																																																			NOVEL					0			10	2.706535	KEEP	0	0	0	9	244	AA	0.99254	0.518266	0			3	60	96	0	0	7.292514	18	60	526	50		0.142857	0.522161
EHMT1	79813	__UNKNOWN__	__UNKNOWN__	9	140633561	140633561	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:140633561T>C	ENST00000462484.1	+	5	860				EHMT1_ENST00000371394.2_Intron|EHMT1_ENST00000460843.1_Intron|EHMT1_ENST00000334856.6_Intron	NM_001145527.1	NP_001138999.1	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	NA		NA			chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		cggtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	79813	2.1.1.43	Chromatin-modifying enzymes / K-methyltransferases, Ankyrin repeat domain containing	24650	protein-coding gene	gene with protein product		607001	euchromatic histone methyltransferase 1		NA	11347906, 12004135	Standard	NM_024757	NM_024757	NA	Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000462484.1:c.824-4262T>C	chr9.hg19:g.140633561T>C		NA	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	hg19	CCDS56595.1	0.02	-0.140328	TCAxGCC	UNCOVERED																																																																																			NOVEL	EHMT1-004	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348982.1	7	2.405329	KEEP	7	0	0	8	211	TT	0	0	0		+	3	60	95	0	0	7.882186	10	60	291	46	ENST00000462484.1	0.230769	0.260965
TUBBP5	643224	__UNKNOWN__	__UNKNOWN__	9	141070213	141070213	__UNKNOWN__	RNA	SNP	A	A	G	rs184986292		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr9:141070213A>G	ENST00000503395.1	+	0	1293									tubulin, beta pseudogene 5	NA		NA									NA						AGGGCAGCTCAAAATCCAGGA	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247	643224			23674	pseudogene	pseudogene		NA	tubulin, beta polypeptide pseudogene 5		NA	11731935	Standard	NR_027156	NR_027156	NA	Approved		uc010ncq.3		OTTHUMG00000021001	ENST00000503395.1:	chr9.hg19:g.141070213A>G		NA		hg19		0.02	1.745252	CTCxAAA	COVERED																																																																																			NOVEL	TUBBP5-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000373087.1	5	4.210743	KEEP	6	0	0	14	387	AA	0.993634	0.984655	0		+	15	60	476	0	0	39.982734	46	60	1354	118	ENST00000503395.1	0.245902	0.990964
ZMYND11	10771	__UNKNOWN__	__UNKNOWN__	10	251438	251438	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:251438A>T	ENST00000397962.3	+	3	544				ZMYND11_ENST00000381604.4_Intron|ZMYND11_ENST00000509513.2_Intron|ZMYND11_ENST00000602682.1_Intron|ZMYND11_ENST00000397959.3_Intron|ZMYND11_ENST00000381584.1_Intron|ZMYND11_ENST00000309776.4_Intron|ZMYND11_ENST00000381591.1_Intron|ZMYND11_ENST00000558098.2_Intron|ZMYND11_ENST00000403354.1_Intron|ZMYND11_ENST00000381602.4_Intron|ZMYND11_ENST00000381607.4_Intron|ZMYND11_ENST00000402736.1_Intron			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	NA		NA			cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		gagaccagccagggcaacata	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171	10771		Zinc fingers, MYND-type	16966	protein-coding gene	gene with protein product		608668	zinc finger, MYND domain containing 11		NA	7621829, 10734313	Standard	NM_006624	NM_006624	NA	Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.117-4391A>T	chr10.hg19:g.251438A>T		NA	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	hg19	CCDS7052.2	0.02	-0.157877	GCCxGGG	COVERED																																																																																			NOVEL	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046382.4	5	3.007906	KEEP	0	0	0	10	280	AA	0.992708	0.320453	0		+	3	60	90	0	1	7.172372	12	60	367	38	ENST00000397962.3	0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	1891311	1891311	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:1891311A>G			NA	NA				ADARB2 (111641 upstream) : LINC00700 (156355 downstream)						NA		NA									NA						agtggctcacacctgtaattc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.1891311A>G		NA		hg19		0.02	-0.149106	CACxCCT	COVERED																																																																																			NOVEL					0			4	2.706587	KEEP	1	0	0	9	245	AA	0.99254	0.289823	0			3	60	95	0	0	7.491874	14	60	418	43		0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	3980805	3980805	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:3980805A>C			NA	NA				RP11-464C19.3 (2800 upstream) : RP11-433J20.2 (86326 downstream)						NA		NA									NA						gtcaggagatagagaccagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.3980805A>C		NA		hg19		0.02	-0.114005	GATxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.705298	KEEP	1	0	0	9	235	AA	0.992708	0.161282	0			3	60	96	0	0	7.982304	10	60	290	28		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	4013892	4013892	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:4013892T>G			NA	NA				RP11-464C19.3 (35887 upstream) : RP11-433J20.2 (53239 downstream)						NA		NA									NA						ctcccaaagttctgggattac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.4013892T>G		NA		hg19		0.02	-0.131519	AGTxCTG	UNCOVERED																																																																																			NOVEL					0			6	2.669885	KEEP	2	0	0	9	220	TT	0	0	0			3	60	85	0	0	6.774188	11	60	322	36		0.214286	0.229173
CALML3-AS1	100132159	__UNKNOWN__	__UNKNOWN__	10	5558026	5558026	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:5558026C>G	ENST00000543008.1	-	0	2711									CALML3 antisense RNA 1	NA		NA									NA						TGTCCTGAGGCGCCGAGCCTT	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					DA220455, DA770774		10p15.1	2012-12-04			ENSG00000205488	ENSG00000205488	100132159		Long non-coding RNAs	44682	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_120497	NA	Approved				OTTHUMG00000168090	ENST00000543008.1:	chr10.hg19:g.5558026C>G		NA		hg19		0.02	1.900539	AGGxGCC	COVERED																																																																																			NOVEL	CALML3-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000398076.1	1	3.907982	KEEP	0	0	0	13	357	CC	0.995343	0.99045	0		-	16	60	548	0	0	46.440965	51	60	1642	112	ENST00000543008.1	0.238806	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	5655183	5655183	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:5655183C>G			NA	NA				RP11-336A10.5 (2427 upstream) : RP11-336A10.4 (3641 downstream)						NA		NA									NA						gggaggccgacgtgggcagat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.5655183C>G		NA		hg19		0.02	-0.184202	CGAxGTG	COVERED																																																																																			NOVEL					0			5	3.008771	KEEP	1	0	0	10	304	CC	0.992708	0.42039	0			3	60	85	0	0	6.411558	15	60	501	46		0.166667	0.423478
FAM208B	54906	__UNKNOWN__	__UNKNOWN__	10	5771140	5771140	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:5771140C>T	ENST00000328090.5	+	11	1112				RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	NA		NA									NA						ggtgaaaccccatctctacta	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021	54906			23484	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 18	C10orf18	NA	12477932	Standard	NM_017782	NM_017782	NA	Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.488-1310C>T	chr10.hg19:g.5771140C>T		NA	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	hg19	CCDS41485.1	0.02	-0.131004	CCCxATC	COVERED																																																																																			NOVEL	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046571.2	9	2.708015	KEEP	3	0	0	9	273	CC	0.99254	0.227464	0		+	3	60	84	0	0	7.03209	8	60	258	29	ENST00000328090.5	0.272727	0.229173
FAM208B	54906	__UNKNOWN__	__UNKNOWN__	10	5771141	5771141	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:5771141A>G	ENST00000328090.5	+	11	1112				RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	NA		NA									NA						gtgaaaccccatctctactaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021	54906			23484	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 18	C10orf18	NA	12477932	Standard	NM_017782	NM_017782	NA	Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.488-1309A>G	chr10.hg19:g.5771141A>G		NA	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	hg19	CCDS41485.1	0.02	-0.140254	CCCxTCT	COVERED																																																																																			NOVEL	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046571.2	10	2.405172	KEEP	3	0	0	8	209	AA	0.99257	0.259026	0		+	3	60	88	0	0	7.433306	8	60	210	30	ENST00000328090.5	0.272727	0.260965
FBXO18	84893	__UNKNOWN__	__UNKNOWN__	10	5950811	5950811	__UNKNOWN__	Intron	SNP	C	C	T	rs183768833	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:5950811C>T	ENST00000362091.4	+	4	868				FBXO18_ENST00000397269.3_Intron|FBXO18_ENST00000379999.5_Intron|FBXO18_ENST00000470089.1_Intron	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	NA		NA			DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						tgacctcaggcgatctgcccg	0.438		NA											T|||	30	0.00599042	0.0219	0.0014	5008	,	,	NA	19194	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452	84893		F-boxes /  other	13620	protein-coding gene	gene with protein product		607222	F-box only protein 18		NA	10531037, 11956208	Standard	NM_032807	NM_032807	NA	Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.754-77C>T	chr10.hg19:g.5950811C>T		NA	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	hg19	CCDS7072.1	0.02	2.552297	AGGxGAT	COVERED																																																																																			NOVEL	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046596.1	27	9.995069	KEEP	0	3	75	60	1767	CC	1	0.999999	0		+	7	60	201	0	0	12.31672	97	70	3257	276	ENST00000362091.4	0.067308	0.999999
PFKFB3	5209	__UNKNOWN__	__UNKNOWN__	10	6228691	6228691	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:6228691T>C	ENST00000379789.4	+	2	80				PFKFB3_ENST00000540253.1_Intron|PFKFB3_ENST00000536985.1_Intron	NM_001145443.1|NM_001282630.1	NP_001138915.1|NP_001269559.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NA		NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						aaactcctggtctcaagccat	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525	5209			8874	protein-coding gene	gene with protein product		605319			NA	9146922, 10072580	Standard		NM_004566	NA	Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379789.4:c.17-26895T>C	chr10.hg19:g.6228691T>C		NA	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	hg19	CCDS44353.1	0.02	-0.245572	TGGxCTC	COVERED																																																																																			NOVEL	PFKFB3-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046646.1	15	3.608951	KEEP	3	0	0	12	329	GT	0.997832	0.738068	0		+	3	60	104	0	0	7.848829	22	60	639	70	ENST00000379789.4	0.12	0.739671
PFKFB3	5209	__UNKNOWN__	__UNKNOWN__	10	6254747	6254747	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:6254747A>G	ENST00000379775.4	+	2	406				PFKFB3_ENST00000540253.1_Intron|PFKFB3_ENST00000379785.1_Intron|PFKFB3_ENST00000536985.1_Intron|PFKFB3_ENST00000317350.4_Intron|PFKFB3_ENST00000360521.2_Intron|PFKFB3_ENST00000379789.4_Intron|PFKFB3_ENST00000379782.3_Intron	NM_004566.3	NP_004557.1	Q16875	F263_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3	NA		NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|liver(2)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)	22						acaggcatgaaccaccgcgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7078.1, CCDS44353.1, CCDS60479.1	10p15.1	2008-05-14			ENSG00000170525	ENSG00000170525	5209			8874	protein-coding gene	gene with protein product		605319			NA	9146922, 10072580	Standard		NM_004566	NA	Approved		uc001ije.3	Q16875	OTTHUMG00000017621	ENST00000379775.4:c.77-839A>G	chr10.hg19:g.6254747A>G		NA	B7Z955|O43622|O75902|Q5VX15|Q5VX18|Q5VX19	hg19	CCDS7078.1	0.02	-0.149089	TGAxCCA	COVERED																																																																																			NOVEL	PFKFB3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046647.1	6	2.705717	KEEP	0	0	0	9	235	AA	0.99254	0.289823	0		+	3	60	109	0	0	8.978904	13	60	375	39	ENST00000379775.4	0.1875	0.292001
PRKCQ	5588	__UNKNOWN__	__UNKNOWN__	10	6509351	6509351	__UNKNOWN__	Intron	SNP	C	C	G	rs142808742|rs139579346		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:6509351C>G	ENST00000263125.5	-	13	1453				PRKCQ_ENST00000397176.2_Intron|PRKCQ_ENST00000539722.1_Intron	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	NA		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	gagagacagacagagagagag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(50;572 1126 10530 25349 30594)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	5588	2.7.11.1		9410	protein-coding gene	gene with protein product		600448			NA	8444877	Standard	NM_006257	NM_001282645	NA	Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.1354-2985G>C	chr10.hg19:g.6509351C>G		NA	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	hg19	CCDS7079.1	0.02	2.023901	AGAxAGA	COVERED																																																																																			NOVEL	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046665.1	93	5.934909	KEEP	81	4	114	60	1739	CC	0.999909	0.973877	0		-	3	60	101	1	1	8.87878	7	60	228	227	ENST00000263125.5	0.3	0.973965
SFMBT2	57713	__UNKNOWN__	__UNKNOWN__	10	7355540	7355540	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:7355540A>G	ENST00000361972.4	-	5	527				SFMBT2_ENST00000397167.1_Intron|SFMBT2_ENST00000379713.3_Intron	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	NA		NA			negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						caaagtgctgagattacaggc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879	57713		Sterile alpha motif (SAM) domain containing	20256	protein-coding gene	gene with protein product		615392	Scm-related gene containing four mbt domains 2		NA	10997877	Standard	NM_001029880	NM_001029880	NA	Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.437-27624T>C	chr10.hg19:g.7355540A>G		NA	A7MD09|Q9HCF5	hg19	CCDS31138.1	0.02	-0.166648	CTGxGAT	COVERED																																																																																			NOVEL	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046673.1	11	2.839745	KEEP	0	1	27	19	539	AA	0.999863	0.387354	0		-	3	60	96	0	0	7.510694	15	60	458	51	ENST00000361972.4	0.166667	0.387407
SFMBT2	57713	__UNKNOWN__	__UNKNOWN__	10	7394434	7394434	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:7394434A>G	ENST00000361972.4	-	4	527				SFMBT2_ENST00000397160.3_Intron|SFMBT2_ENST00000379711.2_Intron|SFMBT2_ENST00000397167.1_Intron|SFMBT2_ENST00000379713.3_Intron	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	NA		NA			negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)			NS(2)|breast(3)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(26)|lung(34)|ovary(5)|pancreas(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	99						acaggcatgcaccaccacacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046837	CCDS31138.1	10p15.1	2013-01-10	2003-11-14		ENSG00000198879	ENSG00000198879	57713		Sterile alpha motif (SAM) domain containing	20256	protein-coding gene	gene with protein product		615392	Scm-related gene containing four mbt domains 2		NA	10997877	Standard	NM_001029880	NM_001029880	NA	Approved	KIAA1617	uc009xio.2	Q5VUG0	OTTHUMG00000017630	ENST00000361972.4:c.436+15176T>C	chr10.hg19:g.7394434A>G		NA	A7MD09|Q9HCF5	hg19	CCDS31138.1	0.02	-0.184151	TGCxCCA	COVERED																																																																																			NOVEL	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046673.1	9	2.702009	KEEP	0	0	0	9	232	AA	0.99254	0.420319	0		-	3	60	93	0	0	7.211109	15	60	433	41	ENST00000361972.4	0.166667	0.423478
ITIH2	3698	__UNKNOWN__	__UNKNOWN__	10	7771027	7771027	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:7771027A>T	ENST00000379587.4	+	11	1281				ITIH2_ENST00000358415.4_Intron			P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	NA		NA			hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						ctgtaatcccagcactttggg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655	3698			6167	protein-coding gene	gene with protein product		146640	inter-alpha (globulin) inhibitor, H2 polypeptide		NA	1385302, 10100603	Standard	NM_002216	NM_002216	NA	Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000379587.4:c.1247-888A>T	chr10.hg19:g.7771027A>T		NA	Q14659|Q15484|Q5T986	hg19		0.02	-0.157881	CCCxGCA	COVERED																																																																																			NOVEL	ITIH2-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000046679.2	13	5.714035	KEEP	12	0	0	19	521	AA	0.993072	0.32057	0		+	4	48	125	0	2	10.381045	13	60	399	58	ENST00000379587.4	0.235294	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	8240433	8240433	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:8240433C>T			NA	NA				GATA3 (123272 upstream) : LINC00708 (60860 downstream)						NA		NA									NA						AAACTTACTACTATTTTTGAA	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.8240433C>T		NA		hg19		0.02	-0.18421	CTAxTAT	COVERED																																																																																			NOVEL					0			10	2.707089	KEEP	0	0	0	9	262	CC	0.99254	0.420319	0			3	60	87	0	0	6.5341	16	60	526	41		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	10974995	10974995	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:10974995T>C			NA	NA				SFTA1P (138118 upstream) : LINC00710 (1491 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.10974995T>C		NA		hg19		0.02	-0.184167	TCAxGCC	COVERED																																																																																			NOVEL					0			8	3.007333	KEEP	1	0	0	10	275	TT	0.992708	0.42039	0			3	60	95	0	0	7.333686	16	60	465	44		0.157895	0.423478
USP6NL	9712	__UNKNOWN__	__UNKNOWN__	10	11586076	11586076	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:11586076T>C	ENST00000609104.1	-	3	399				USP6NL_ENST00000379237.2_Intron	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	NA		NA			Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						tcccaaagtgttgggattaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429	9712			16858	protein-coding gene	gene with protein product	related to the N terminus of tre	605405	USP6NL intronic transcript 1 (non-protein coding)	USP6NL-IT1	NA	8700515, 8700527, 12399475	Standard	NM_014688	XR_247492	NA	Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.5-16510A>G	chr10.hg19:g.11586076T>C		NA	A8KA79|Q15400|Q5VV10|Q7L0K9	hg19	CCDS53492.1	0.02	-0.201731	GTGxTGG	UNCOVERED																																																																																			NOVEL	USP6NL-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046764.3	4	2.706446	KEEP	3	0	0	9	242	TT	0	0	0		-	4	60	136	0	0	10.894414	19	60	572	50	ENST00000609104.1	0.173913	0.490544
PROSER2	254427	__UNKNOWN__	__UNKNOWN__	10	11885436	11885436	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:11885436C>T	ENST00000277570.5	+	2	73				PROSER2_ENST00000474155.1_Intron	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	NA		NA									NA						cctgtaatcccagcactttgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426	254427			23728	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 47, proline and serine-rich protein 2	C10orf47	NA	12477932	Standard	NM_153256	NM_153256	NA	Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.-81-8560C>T	chr10.hg19:g.11885436C>T		NA	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	hg19	CCDS7085.1	0.02	-0.280714	TCCxAGC	COVERED																																																																																			NOVEL	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090189.2	19	7.221631	KEEP	8	0	0	24	740	CC	0.999869	0.739575	0		+	4	23	113	1	0	8.095844	26	60	900	92	ENST00000277570.5	0.133333	0.739671
DHTKD1	55526	__UNKNOWN__	__UNKNOWN__	10	12160445	12160445	__UNKNOWN__	Intron	SNP	G	G	A	rs61274534	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:12160445G>A	ENST00000263035.4	+	15	2464					NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	NA		NA			cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			gcagtggcacgatcttggctc	0.547		NA											G|||	1077	0.215056	0.2731	0.2565	5008	,	,	NA	13023	0.2569	NA	0.1799	False	NA	,,,	NA	NA	NA	2504	0.1002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192	55526			23537	protein-coding gene	gene with protein product		614984			NA	10997877	Standard	NM_018706	NM_018706	NA	Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2403-303G>A	chr10.hg19:g.12160445G>A		NA	Q68CU5|Q9BUM8|Q9HCE2	hg19	CCDS7087.1	0.02	-0.087703	CACxATC	UNCOVERED																																																																																			NOVEL	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046777.1	4	2.406711	KEEP	3	0	0	8	235	CG	0.99257	0.09898	0		+	3	47	85	0	0	7.443245	6	60	184	27	ENST00000263035.4	0.333333	0.099721
DHTKD1	55526	__UNKNOWN__	__UNKNOWN__	10	12160602	12160602	__UNKNOWN__	Intron	SNP	T	T	C	rs11257543	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:12160602T>C	ENST00000263035.4	+	15	2464					NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	NA		NA			cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			aggatggtcttgatttcctga	0.527		NA											C|||	3505	0.69988	0.3828	0.7709	5008	,	,	NA	14824	0.8532	NA	0.7614	False	NA	,,,	NA	NA	NA	2504	0.8569	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192	55526			23537	protein-coding gene	gene with protein product		614984			NA	10997877	Standard	NM_018706	NM_018706	NA	Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2403-146T>C	chr10.hg19:g.12160602T>C		NA	Q68CU5|Q9BUM8|Q9HCE2	hg19	CCDS7087.1	0.02	-0.149058	TCTxGAT	COVERED																																																																																			NOVEL	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046777.1	4	2.403808	KEEP	1	0	0	8	204	TT	0.99257	0.289832	0		+	3	40	92	0	0	7.372964	12	60	323	32	ENST00000263035.4	0.2	0.292001
NUDT5	11164	__UNKNOWN__	__UNKNOWN__	10	12211054	12211054	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:12211054A>G	ENST00000491614.1	-	10	946				NUDT5_ENST00000378937.3_Intron|SEC61A2_ENST00000304267.8_Intron|NUDT5_ENST00000537776.1_Intron|NUDT5_ENST00000378952.3_Intron|SEC61A2_ENST00000495368.1_Intron			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	NA		NA			D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				gagccaccgcacccggccAGC	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609	11164		Nudix motif containing	8052	protein-coding gene	gene with protein product		609230			NA	10373642	Standard		NM_014142	NA	Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.551-1244T>C	chr10.hg19:g.12211054A>G		NA	A8K516|Q6IAG0|Q9UH49	hg19	CCDS7089.1	0.02	-0.2104	CGCxCCC	COVERED																																																																																			NOVEL	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046811.1	9	3.608019	KEEP	1	0	0	12	318	AA	0.993072	0.518544	0		-	3	60	102	0	0	7.765479	20	60	541	48	ENST00000491614.1	0.130435	0.522161
CAMK1D	57118	__UNKNOWN__	__UNKNOWN__	10	12503427	12503427	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:12503427C>T	ENST00000378847.3	+	2	429				CAMK1D_ENST00000487696.1_Intron|CAMK1D_ENST00000378845.1_Intron	NM_153498.2	NP_705718.1	Q8IU85	KCC1D_HUMAN	calcium/calmodulin-dependent protein kinase ID	NA		NA			inflammatory response (GO:0006954)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis (GO:0050766)|positive regulation of respiratory burst (GO:0060267)|regulation of dendrite development (GO:0050773)|regulation of granulocyte chemotaxis (GO:0071622)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)	16				GBM - Glioblastoma multiforme(1;3.16e-05)		cagtggctcacgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF286366	CCDS7091.1, CCDS7092.1	10p13	2003-11-05			ENSG00000183049	ENSG00000183049	57118			19341	protein-coding gene	gene with protein product		607957			NA	11050006	Standard	NM_020397	XM_006717481	NA	Approved	CKLiK	uc001ilo.3	Q8IU85	OTTHUMG00000017683	ENST00000378847.3:c.93-91797C>T	chr10.hg19:g.12503427C>T		NA	B0YIY0|Q9HD31	hg19	CCDS7091.1	0.02	-0.184188	TCAxGCC	COVERED																																																																																			NOVEL	CAMK1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046820.1	4	2.405902	KEEP	0	0	0	8	228	CC	0.99257	0.454356	0		+	3	60	91	0	0	6.792696	18	60	587	44	ENST00000378847.3	0.142857	0.457757
OPTN	10133	__UNKNOWN__	__UNKNOWN__	10	13172373	13172373	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:13172373C>A	ENST00000378748.3	+	14	1763				OPTN_ENST00000378747.3_Intron|OPTN_ENST00000378757.2_Intron|OPTN_ENST00000378752.3_Intron|OPTN_ENST00000263036.5_Intron|OPTN_ENST00000378764.2_Intron	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	NA		NA			cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						tgcagtgagccgagatcatgc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240	10133			17142	protein-coding gene	gene with protein product		602432	glaucoma 1, open angle, E (adult-onset)	GLC1E	NA	11834836, 9488477	Standard	NM_021980	NM_001008211	NA	Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.1402-1694C>A	chr10.hg19:g.13172373C>A		NA	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	hg19	CCDS7094.1	0.02	-0.114035	AGCxGAG	UNCOVERED																																																																																			NOVEL	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046834.1	12	4.813882	KEEP	9	0	0	16	482	CC	0.993072	0.161341	0		+	3	57	90	0	0	7.500968	9	60	298	43	ENST00000378748.3	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	13191609	13191609	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:13191609A>G			NA	NA				OPTN (11318 upstream) : MCM10 (11944 downstream)						NA		NA									NA						gaccagcctgagcaacatagg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.13191609A>G		NA		hg19		0.02	-0.324523	CTGxGCA	COVERED																																																																																			NOVEL					0			9	3.307089	KEEP	0	0	0	11	298	AA	0.993072	0.829926	0			3	60	96	0	0	6.667813	30	60	915	64		0.090909	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	13404029	13404029	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:13404029A>C			NA	NA				SEPHS1 (13732 upstream) : RP11-445K13.2 (53172 downstream)						NA		NA									NA						aatcccagcaatttgggaggc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.13404029A>C		NA		hg19		0.02	-0.114013	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			3	2.70696	KEEP	0	0	0	9	253	AA	0.99254	0.161255	0			3	60	96	0	0	7.982181	10	60	302	27		0.230769	0.162467
FRMD4A	55691	__UNKNOWN__	__UNKNOWN__	10	13855416	13855416	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:13855416T>G	ENST00000357447.2	-	4	480				FRMD4A_ENST00000358621.4_Intron|FRMD4A_ENST00000342409.2_Intron|FRMD4A_ENST00000378503.1_Intron	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	NA		NA			establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						actccagccttggcaacagag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474	55691			25491	protein-coding gene	gene with protein product		NA	FERM domain containing 4	FRMD4	NA	10718198	Standard	NM_018027	NM_018027	NA	Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.112-2508A>C	chr10.hg19:g.13855416T>G		NA	A7E2Y3|Q5T377	hg19	CCDS7101.1	0.02	-0.061394	CCTxGGC	UNCOVERED																																																																																			NOVEL	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046889.1	3	2.405592	KEEP	0	0	0	8	220	TT	0.99257	0.043461	0		-	2	60	72	0	0	6.496094	4	60	114	22	ENST00000357447.2	0.333333	0.043787
CDNF	441549	__UNKNOWN__	__UNKNOWN__	10	14868034	14868034	__UNKNOWN__	Intron	SNP	A	A	G	rs201887135		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:14868034A>G	ENST00000378442.1	-	5	441				CDNF_ENST00000378441.2_Intron			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor	NA		NA				extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						gaaggagaagaagaagaagaa	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267	441549			24913	protein-coding gene	gene with protein product	conserved dopamine neurotrophic factor	611233	arginine-rich, mutated in early stage tumors-like 1	ARMETL1	NA	17611540	Standard	NM_001029954	NM_001029954	NA	Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.63-415T>C	chr10.hg19:g.14868034A>G		NA	A2RUU0|B4DVW3	hg19		0.02	-0.140328	AAGxAGA	UNCOVERED																																																																																			NOVEL	CDNF-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000046919.1	11	3.306868	KEEP	9	0	0	11	290	AA	0	0	0		-	3	60	93	0	1	7.472444	12	60	353	49	ENST00000378442.1	0.2	0.292001
DCLRE1C	64421	__UNKNOWN__	__UNKNOWN__	10	14950006	14950006	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:14950006A>G	ENST00000378246.2	-	0	2508				DCLRE1C_ENST00000378289.4_Intron|DCLRE1C_ENST00000453695.2_3'UTR	NM_022487.2	NP_071932.2	Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	NA		NA			B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						gattacaggcatgagccaccg	0.542		NA						Non-homologous end-joining													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457	64421			17642	protein-coding gene	gene with protein product	PSO2 homolog (S. cerevisiae)	605988	severe combined immunodeficiency, type a (Athabascan), DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)	SCIDA	NA	11336668, 9443881	Standard	NM_022487	XM_005252558	NA	Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378246.2:c.*401T>C	chr10.hg19:g.14950006A>G		NA	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	hg19	CCDS7105.1	0.02	-0.359582	GGCxTGA	COVERED																																																																																			NOVEL	DCLRE1C-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046926.1	11	6.314662	KEEP	0	0	0	21	562	AA	0.999869	0.888759	0		-	4	60	125	0	0	8.858461	34	60	1018	86	ENST00000378246.2	0.105263	0.888875
DCLRE1C	64421	__UNKNOWN__	__UNKNOWN__	10	14950277	14950277	__UNKNOWN__	3'UTR	SNP	A	A	G	rs562179937		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:14950277A>G	ENST00000378278.2	-	0	2246				DCLRE1C_ENST00000396817.2_3'UTR|DCLRE1C_ENST00000378289.4_Intron|DCLRE1C_ENST00000378254.1_3'UTR|DCLRE1C_ENST00000378242.1_3'UTR|DCLRE1C_ENST00000453695.2_3'UTR|DCLRE1C_ENST00000378246.2_3'UTR|DCLRE1C_ENST00000378258.1_3'UTR|DCLRE1C_ENST00000357717.2_3'UTR|DCLRE1C_ENST00000378249.1_3'UTR|DCLRE1C_ENST00000378255.1_3'UTR			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	NA		NA			B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						tgggattacaagtgtgagcca	0.418		NA						Non-homologous end-joining					A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17534	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457	64421			17642	protein-coding gene	gene with protein product	PSO2 homolog (S. cerevisiae)	605988	severe combined immunodeficiency, type a (Athabascan), DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)	SCIDA	NA	11336668, 9443881	Standard	NM_022487	XM_005252558	NA	Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.*130T>C	chr10.hg19:g.14950277A>G		NA	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	hg19	CCDS31149.1	0.02	1.71318	ACAxGTG	COVERED																																																																																			NOVEL	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046934.1	16	10.291978	KEEP	0	2	62	56	1568	AA	1	0.998867	0		-	4	60	141	1	0	9.253419	70	60	2201	186	ENST00000378278.2	0.054054	0.998867
NMT2	9397	__UNKNOWN__	__UNKNOWN__	10	15151324	15151324	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:15151324G>A	ENST00000378165.4	-	12	1557				NMT2_ENST00000535341.1_Intron|RPP38_ENST00000451677.1_Intron|NMT2_ENST00000378150.1_Intron|NMT2_ENST00000466201.1_Intron|NMT2_ENST00000540259.1_Intron	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	NA		NA			intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						ctgtaatcccggcactttggg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(117;1345 1645 4130 12688 30625)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465	9397			7858	protein-coding gene	gene with protein product		603801			NA	9506952	Standard	NM_004808	NM_004808	NA	Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.1477-110C>T	chr10.hg19:g.15151324G>A		NA	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	hg19	CCDS7109.1	0.02	-0.210525	CCCxGCA	COVERED																																																																																			NOVEL	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046958.2	3	3.30908	KEEP	0	0	0	11	323	GG	0.993072	0.518544	0		-	4	60	117	0	0	8.99487	19	60	623	36	ENST00000378165.4	0.173913	0.522161
FAM171A1	221061	__UNKNOWN__	__UNKNOWN__	10	15269266	15269266	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:15269266T>C	ENST00000378116.4	-	6	761				FAM171A1_ENST00000477161.1_Intron	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						tcccaaagtgtagggattata	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468	221061			23522	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 38	C10orf38	NA		Standard	XM_167709	NM_001010924	NA	Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.755-6207A>G	chr10.hg19:g.15269266T>C		NA	D3DRT9|Q32M49|Q8N4I0	hg19	CCDS31154.1	0.02	-0.149095	GTGxAGG	COVERED																																																																																			NOVEL	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046984.1	7	2.404372	KEEP	0	0	0	8	205	TT	0.99257	0.289832	0		-	3	60	102	0	0	8.191795	14	60	407	33	ENST00000378116.4	0.176471	0.292001
FAM171A1	221061	__UNKNOWN__	__UNKNOWN__	10	15379914	15379914	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:15379914T>C	ENST00000378116.4	-	1	104					NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						cgtgccactgtactccagcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468	221061			23522	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 38	C10orf38	NA		Standard	XM_167709	NM_001010924	NA	Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.97+33040A>G	chr10.hg19:g.15379914T>C		NA	D3DRT9|Q32M49|Q8N4I0	hg19	CCDS31154.1	0.02	-0.131539	CTGxACT	COVERED																																																																																			NOVEL	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046984.1	6	2.405116	KEEP	2	0	0	8	206	TT	0.99257	0.22747	0		-	3	60	108	0	0	9.073171	11	60	303	35	ENST00000378116.4	0.214286	0.229173
FAM171A1	221061	__UNKNOWN__	__UNKNOWN__	10	15402036	15402036	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:15402036C>T	ENST00000378116.4	-	1	104					NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						caggctcaagcgatccttcca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468	221061			23522	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 38	C10orf38	NA		Standard	XM_167709	NM_001010924	NA	Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.97+10918G>A	chr10.hg19:g.15402036C>T		NA	D3DRT9|Q32M49|Q8N4I0	hg19	CCDS31154.1	0.02	-0.105256	AAGxGAT	UNCOVERED																																																																																			NOVEL	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000046984.1	8	2.406765	KEEP	0	0	0	8	235	CC	0.99257	0.138793	0		-	3	60	83	0	0	6.932098	8	60	265	28	ENST00000378116.4	0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	15550242	15550242	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:15550242T>C			NA	NA				FAM171A1 (137184 upstream) : ITGA8 (5705 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.15550242T>C		NA		hg19		0.02	-0.166638	AGGxGTG	COVERED																																																																																			NOVEL					0			5	3.591666	KEEP	2	0	0	12	306	TT	0.993072	0.351495	0			3	60	98	0	0	7.972422	12	60	349	46		0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	15762719	15762719	__UNKNOWN__	IGR	SNP	C	C	T	rs145417087		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:15762719C>T			NA	NA				ITGA8 (595 upstream) : FAM188A (57449 downstream)						NA		NA									NA						ggttaattttctaattttttt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.15762719C>T		NA		hg19		0.02	-0.096468	TTTxTAA	UNCOVERED																																																																																			NOVEL					0			12	2.70792	KEEP	0	0	0	9	275	CC	0.99254	0.119538	0			4	60	104	0	0	9.383657	6	60	209	25		0.4	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	16386495	16386495	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:16386495T>A			NA	NA				RP11-461K13.1 (48638 upstream) : snoU13 (54158 downstream)						NA		NA									NA						ctggtctcgatctcctgacct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.16386495T>A		NA		hg19		0.02	-0.157858	CGAxCTC	UNCOVERED																																																																																			NOVEL					0			16	3.307821	KEEP	11	0	0	11	294	TT	0	0	0			3	60	86	0	0	6.679518	13	60	380	53		0.1875	0.353947
TRDMT1	1787	__UNKNOWN__	__UNKNOWN__	10	17202761	17202761	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:17202761C>T	ENST00000377799.3	-	6	437				TRDMT1_ENST00000351358.4_Intron|TRDMT1_ENST00000358282.7_Intron|TRDMT1_ENST00000412821.3_Intron|TRDMT1_ENST00000457442.2_Intron|TRDMT1_ENST00000452380.2_Intron|TRDMT1_ENST00000377766.5_Intron|TRDMT1_ENST00000488990.1_Intron	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	NA		NA			C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	tgagccaccgcgcccggccCA	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	1787	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	DNA (cytosine-5-)-methyltransferase 2	DNMT2	NA	9425235, 9763678, 16424344	Standard	NM_004412	NM_004412	NA	Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.390-388G>A	chr10.hg19:g.17202761C>T		NA	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	hg19	CCDS7114.1	0.02	-0.16667	CCGxGCC	COVERED																																																																																			NOVEL	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047024.3	7	3.30896	KEEP	4	0	0	11	321	CC	0.993072	0.351495	0		-	3	60	94	0	0	7.233336	16	60	531	50	ENST00000377799.3	0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	17585323	17585323	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:17585323A>G			NA	NA				ST8SIA6 (88994 upstream) : PTPLA (46634 downstream)						NA		NA									NA						acgtagctggaaccacaggtg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.17585323A>G		NA		hg19		0.02	-0.14034	TGGxACC	COVERED																																																																																			NOVEL					0			6	3.007123	KEEP	0	0	0	10	271	AA	0.992708	0.259062	0			3	60	102	0	0	8.27877	13	60	393	33		0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	17608155	17608155	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:17608155T>C			NA	NA				ST8SIA6 (111826 upstream) : PTPLA (23802 downstream)						NA		NA									NA						tgcagtggcgtgatctcggct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.17608155T>C		NA		hg19		0.02	-0.175403	GCGxGAT	UNCOVERED																																																																																			NOVEL					0			12	2.403774	KEEP	3	0	0	8	208	TT	0	0	0			3	60	94	0	0	7.479163	13	60	377	36		0.1875	0.387407
CACNB2	783	__UNKNOWN__	__UNKNOWN__	10	18517743	18517743	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:18517743G>A	ENST00000324631.7	+	2	273				CACNB2_ENST00000282343.8_Intron|CACNB2_ENST00000377331.2_Intron|CACNB2_ENST00000352115.6_Intron|CACNB2_ENST00000377328.1_Intron	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	NA		NA			axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	atcccagctcgctgcagcctc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995	783		Calcium channel subunits	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2	NA	9254841, 8494331	Standard	NM_000724	NM_201596	NA	Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.213+77839G>A	chr10.hg19:g.18517743G>A		NA	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	hg19	CCDS7125.1	0.02	-0.114024	CTCxCTG	UNCOVERED																																																																																			NOVEL	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047072.2	8	3.007846	KEEP	2	0	0	10	285	GG	0.99254	0.161255	0		+	3	60	89	0	0	7.401171	9	60	291	32	ENST00000324631.7	0.25	0.162467
CACNB2	783	__UNKNOWN__	__UNKNOWN__	10	18627905	18627905	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:18627905A>G	ENST00000324631.7	+	3	273				CACNB2_ENST00000282343.8_Intron|CACNB2_ENST00000377331.2_Intron|CACNB2_ENST00000377319.3_Intron|CACNB2_ENST00000352115.6_Intron|CACNB2_ENST00000377328.1_Intron|CACNB2_ENST00000396576.2_Intron	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	NA		NA			axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ctgggctcaaatgatcctccc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995	783		Calcium channel subunits	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2	NA	9254841, 8494331	Standard	NM_000724	NM_201596	NA	Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.214-62948A>G	chr10.hg19:g.18627905A>G		NA	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	hg19	CCDS7125.1	0.02	-0.157866	CAAxTGA	COVERED																																																																																			NOVEL	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047072.2	8	3.308075	KEEP	0	0	0	11	299	AA	0.993072	0.32057	0		+	3	60	87	0	0	6.77948	13	60	387	39	ENST00000324631.7	0.1875	0.322807
CACNB2	783	__UNKNOWN__	__UNKNOWN__	10	18685031	18685031	__UNKNOWN__	Intron	SNP	A	A	G	rs4748459	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:18685031A>G	ENST00000324631.7	+	3	273				CACNB2_ENST00000282343.8_Intron|CACNB2_ENST00000377329.4_Intron|CACNB2_ENST00000377331.2_Intron|CACNB2_ENST00000377319.3_Intron|CACNB2_ENST00000352115.6_Intron|CACNB2_ENST00000377328.1_Intron|CACNB2_ENST00000396576.2_Intron	NM_201593.2|NM_201596.2	NP_963887.2|NP_963890.2	Q08289	CACB2_HUMAN	calcium channel, voltage-dependent, beta 2 subunit	NA		NA			axon guidance (GO:0007411)|calcium ion import (GO:0070509)|neuromuscular junction development (GO:0007528)|positive regulation of calcium ion transport (GO:0051928)|synaptic transmission (GO:0007268)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|voltage-gated calcium channel complex (GO:0005891)	calcium channel activity (GO:0005262)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|prostate(1)|skin(3)|stomach(2)	31					Amlodipine(DB00381)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	gaccacaggcacctgccacca	0.547		NA											a|||	3455	0.689896	0.6914	0.5648	5008	,	,	NA	17014	0.7579	NA	0.674	False	NA	,,,	NA	NA	NA	2504	0.7229	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U95019	CCDS7125.1, CCDS7126.1, CCDS7127.1, CCDS7128.1, CCDS7129.1, CCDS41493.1, CCDS41494.1	10p12	2014-09-17			ENSG00000165995	ENSG00000165995	783		Calcium channel subunits	1402	protein-coding gene	gene with protein product		600003		MYSB, CACNLB2	NA	9254841, 8494331	Standard	NM_000724	NM_201596	NA	Approved		uc001ipr.2	Q08289	OTTHUMG00000017764	ENST00000324631.7:c.214-5822A>G	chr10.hg19:g.18685031A>G		NA	A6PVM5|A6PVM7|A6PVM8|O00304|Q5QJ99|Q5QJA0|Q5VVG9|Q5VVH0|Q5VWV6|Q6TME1|Q6TME2|Q6TME3|Q8WX81|Q96NZ3|Q96NZ4|Q96NZ5|Q9BWU2|Q9HD32|Q9Y340|Q9Y341	hg19	CCDS7125.1	0.02	-0.035076	GGCxCCT	UNCOVERED																																																																																			NOVEL	CACNB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047072.2	4	2.704084	KEEP	3	0	0	9	232	AA	0	0	0		+	2	60	67	0	0	6.825324	1	60	26	19	ENST00000324631.7	0.666667	0.019982
NSUN6	221078	__UNKNOWN__	__UNKNOWN__	10	18933747	18933747	__UNKNOWN__	Intron	SNP	C	C	T	rs548758321		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:18933747C>T	ENST00000377304.4	-	3	650				RP11-139J15.7_ENST00000606425.1_Intron	NM_182543.2	NP_872349.1	Q8TEA1	NSUN6_HUMAN	NOP2/Sun domain family, member 6	NA		NA					methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15						ccagcctgggcgacagagcga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035778	CCDS7130.1	10p13	2014-06-23	2009-11-23	2004-08-26	ENSG00000241058	ENSG00000241058	221078		NOP2/Sun domain containing	23529	protein-coding gene	gene with protein product		NA	NOL1/NOP2/Sun domain family 6, NOL1/NOP2/Sun domain family, member 6, ARL5B antisense RNA 1	NOPD1, ARL5B-AS1	NA		Standard	NM_182543	XM_005252394	NA	Approved	FLJ23743	uc010qcp.1	Q8TEA1	OTTHUMG00000017767	ENST00000377304.4:c.232-2263G>A	chr10.hg19:g.18933747C>T		NA	B0YJ54	hg19	CCDS7130.1	0.02	-0.13148	GGGxGAC	COVERED																																																																																			NOVEL	NSUN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047083.1	8	2.707288	KEEP	5	0	0	9	263	CG	0.99257	0.22747	0		-	3	60	82	0	1	6.583339	10	60	321	39	ENST00000377304.4	0.230769	0.229173
C10orf112	0	__UNKNOWN__	__UNKNOWN__	10	20019758	20019758	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:20019758T>C	ENST00000454679.2	+	23	4341				C10orf112_ENST00000455457.2_Intron			Q5VYJ5	MALR1_HUMAN		NA		NA			cholesterol homeostasis (GO:0042632)|negative regulation of bile acid biosynthetic process (GO:0070858)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|lung(2)	3						tgcacacacatacaaacacac	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000454679.2:c.4341+48T>C	chr10.hg19:g.20019758T>C		NA	B7ZBP2	hg19		0.02	-0.228008	ACAxACA	COVERED																																																																																			NOVEL	C10orf112-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		9	2.405847	KEEP	0	0	0	8	216	GT	0.99254	0.578582	0		+	3	60	100	0	0	7.627387	19	60	537	40	ENST00000454679.2	0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	21556323	21556323	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:21556323A>G			NA	NA				NEBL-AS1 (92346 upstream) : RNU6-15P (54566 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.21556323A>G		NA		hg19		0.02	-0.149081	GGCxTGA	COVERED																																																																																			NOVEL					0			2	3.006708	KEEP	3	0	0	10	267	AA	0.99257	0.289832	0			3	50	86	0	0	6.772948	12	60	341	38		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	21587926	21587926	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:21587926A>G			NA	NA				NEBL-AS1 (123949 upstream) : RNU6-15P (22963 downstream)						NA		NA									NA						tgcaatcccaacactttggga	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.21587926A>G		NA		hg19		0.02	-0.184196	CCAxCAC	COVERED																																																																																			NOVEL					0			3	2.406367	KEEP	0	0	0	8	226	AA	0.99257	0.420331	0			3	60	99	0	0	7.733404	16	60	487	44		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	21609106	21609106	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:21609106T>C			NA	NA				NEBL-AS1 (145129 upstream) : RNU6-15P (1783 downstream)						NA		NA									NA						atactctggctgggcacggtg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.21609106T>C		NA		hg19		0.02	-0.113997	GGCxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.707182	KEEP	0	0	0	9	254	TT	0.99254	0.161255	0			3	60	109	0	0	9.282406	10	60	294	34		0.230769	0.162467
MLLT10	8028	__UNKNOWN__	__UNKNOWN__	10	21992725	21992725	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:21992725A>G	ENST00000307729.7	+	14	1877				MLLT10_ENST00000446906.2_Intron|MLLT10_ENST00000377059.3_Intron|MLLT10_ENST00000377072.3_Intron			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						cgcccgcctcagcctcccaaa	0.473		NA	T	MLL, PICALM, CDK6	AL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		10	10p12	8028	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403	8028		Zinc fingers, PHD-type	16063	protein-coding gene	gene with protein product		602409	myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10		NA	7888665	Standard		NM_004641	NA	Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.1700-9976A>G	chr10.hg19:g.21992725A>G		NA	B1ANA8|Q5JT37|Q5VX90|Q66K63	hg19	CCDS55708.1	0.02	-0.184204	CTCxGCC	UNCOVERED																																																																																			NOVEL	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047136.1	7	2.406001	KEEP	2	0	0	8	220	AA	0	0	0		+	4	60	140	0	0	11.468492	17	60	525	41	ENST00000307729.7	0.190476	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	22473808	22473808	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:22473808A>G			NA	NA				DNAJC1 (181110 upstream) : EBLN1 (23934 downstream)						NA		NA									NA						ggctggtctcaaactcctggg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.22473808A>G		NA		hg19		0.02	-0.192962	CTCxAAC	COVERED																																																																																			NOVEL					0			5	3.008168	KEEP	1	0	0	10	285	AA	0.992708	0.486967	0			3	60	94	0	0	7.233604	16	60	486	51		0.157895	0.490544
MSRB2	22921	__UNKNOWN__	__UNKNOWN__	10	23397156	23397156	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:23397156G>A	ENST00000376510.3	+	3	322					NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	NA		NA			actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	caaagtgctgggattacaggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(89;1240 1363 4973 30188 42299)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450	22921			17061	protein-coding gene	gene with protein product		613782	methionine sulfoxide reductase B	MSRB	NA	8749308, 10375640	Standard	NM_012228	NM_012228	NA	Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.220-2015G>A	chr10.hg19:g.23397156G>A		NA	Q17R44|Q4G1C7|Q9Y5W6	hg19	CCDS41495.1	0.02	-0.19298	CTGxGAT	UNCOVERED																																																																																			NOVEL	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047205.1	11	3.310133	KEEP	8	0	0	11	349	GG	0	0	0		+	3	60	91	1	0	7.091916	14	60	462	53	ENST00000376510.3	0.176471	0.457757
C10orf67	256815	__UNKNOWN__	__UNKNOWN__	10	23606924	23606924	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:23606924A>G	ENST00000323327.4	-	0	1540					NM_153714.2	NP_714925.2	Q8IYJ2	CJ067_HUMAN	chromosome 10 open reading frame 67	NA		NA								central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5						ccagctactcaggaggctgag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC035732	CCDS44365.1	10p12.31	2012-05-31			ENSG00000179133	ENSG00000179133	256815			28716	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_153714	NM_153714	NA	Approved	MGC46732	uc010qcx.2	Q8IYJ2	OTTHUMG00000017818	ENST00000323327.4:c.*915T>C	chr10.hg19:g.23606924A>G		NA	A8MUP9|Q5SWD4	hg19	CCDS44365.1	0.02	1.254495	CTCxGGA	COVERED																																																																																			NOVEL	C10orf67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047213.1	33	3.726278	KEEP	0	4	109	51	1405	AA	1	0.999559	0		-	5	60	136	0	0	8.030864	72	60	2195	188	ENST00000323327.4	0.064935	0.999559
KIAA1217	56243	__UNKNOWN__	__UNKNOWN__	10	24712489	24712489	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:24712489C>A	ENST00000376454.3	+	4	583				KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000458595.1_Intron	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	NA		NA			embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						cccaggttcacgtgattctcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549	56243			25428	protein-coding gene	gene with protein product	sickle tail	NA			NA	10574462	Standard	NM_019590	XM_005252500	NA	Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.554-9435C>A	chr10.hg19:g.24712489C>A		NA	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	hg19	CCDS31165.1	0.02	-0.105258	TCAxGTG	UNCOVERED																																																																																			NOVEL	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047223.2	7	2.403599	KEEP	0	0	0	8	200	CG	0.99254	0.138789	0		+	3	49	86	0	0	7.378195	7	60	231	27	ENST00000376454.3	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	25037748	25037748	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:25037748A>C			NA	NA				ARHGAP21 (25151 upstream) : PRTFDC1 (99787 downstream)						NA		NA									NA						ggattacaggagtgagccacc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.25037748A>C		NA		hg19		0.02	-0.122794	AGGxGTG	COVERED																																																																																			NOVEL					0			7	3.909328	KEEP	0	0	0	13	360	AA	0.995343	0.195397	0			3	60	92	0	0	7.832463	8	60	239	41		0.272727	0.196312
PRTFDC1	56952	__UNKNOWN__	__UNKNOWN__	10	25196282	25196282	__UNKNOWN__	Intron	SNP	C	C	G	rs577532914	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:25196282C>G	ENST00000320152.6	-	3	368				PRTFDC1_ENST00000376378.1_Intron	NM_020200.5	NP_064585.1	Q9NRG1	PRDC1_HUMAN	phosphoribosyl transferase domain containing 1	NA		NA			nucleoside metabolic process (GO:0009116)	cytosol (GO:0005829)	magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9						ccagcactttcggaggctgag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF226056	CCDS7145.1, CCDS60506.1	10p12.31	2003-11-10			ENSG00000099256	ENSG00000099256	56952			23333	protein-coding gene	gene with protein product		610751			NA		Standard	NM_020200	XM_005252537	NA	Approved	HHGP	uc001ise.1	Q9NRG1	OTTHUMG00000017829	ENST00000320152.6:c.339+29830G>C	chr10.hg19:g.25196282C>G		NA	B7Z1Z3|Q53HA7|Q59EL9|Q5VV18|Q5VV20	hg19	CCDS7145.1	0.02	-0.140309	TTTxGGA	COVERED																																																																																			NOVEL	PRTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047243.2	7	2.708033	KEEP	1	0	0	9	274	CC	0.99257	0.259026	0		-	3	60	99	0	0	8.173292	11	60	344	33	ENST00000320152.6	0.214286	0.260965
GPR158	57512	__UNKNOWN__	__UNKNOWN__	10	25875621	25875621	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:25875621T>C	ENST00000376351.3	+	8	2112					NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	NA		NA			protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						ggattacaggtgtgagccacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025	57512		GPCR / Class C : Orphans	23689	protein-coding gene	gene with protein product		614573			NA		Standard	XM_166110	NM_020752	NA	Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.1754-2315T>C	chr10.hg19:g.25875621T>C		NA	Q6QR81|Q9ULT3	hg19	CCDS31166.1	0.02	-0.15788	AGGxGTG	COVERED																																																																																			NOVEL	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047248.2	7	3.909022	KEEP	0	0	0	13	354	TT	0.994391	0.320996	0		+	3	60	106	0	0	8.591591	14	60	417	46	ENST00000376351.3	0.176471	0.322807
MYO3A	53904	__UNKNOWN__	__UNKNOWN__	10	26495598	26495598	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:26495598A>G	ENST00000265944.5	+	34	4896				MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	NA		NA			ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ggctggtctcaaactcctgac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777	53904		Myosins / Myosin superfamily : Class III	7601	protein-coding gene	gene with protein product		606808	deafness, autosomal recessive 30	DFNB30	NA	10936054	Standard	NM_017433	NM_017433	NA	Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4730+3562A>G	chr10.hg19:g.26495598A>G		NA	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	hg19	CCDS7148.1	0.02	-0.175403	CTCxAAC	UNCOVERED																																																																																			NOVEL	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047259.1	12	3.909706	KEEP	18	0	0	13	357	AA	0	0	0		+	3	60	86	0	0	6.362435	17	60	509	62	ENST00000265944.5	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	26900319	26900319	__UNKNOWN__	IGR	SNP	C	C	T	rs10829034	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:26900319C>T			NA	NA				LINC00264 (17066 upstream) : LINC00202-2 (31778 downstream)						NA		NA									NA						Aggcctggcgcggtggctcac	0.433		NA											-|||	1822	0.363818	0.1641	0.5576	5008	,	,	NA	14176	0.4494	NA	0.4443	False	NA	,,,	NA	NA	NA	2504	0.3252	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.26900319C>T		NA		hg19		0.02	-0.087716	GCGxGGT	UNCOVERED																																																																																			NOVEL					0			2	2.406335	KEEP	8	0	0	8	233	CC	0	0	0			4	60	118	0	0	10.784949	6	60	199	37		0.4	0.099721
PDSS1	23590	__UNKNOWN__	__UNKNOWN__	10	27020790	27020790	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:27020790G>A	ENST00000376215.5	+	9	884				PDSS1_ENST00000376203.5_Intron	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	NA		NA			isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						gcacgatctcggctcactgca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459	23590			17759	protein-coding gene	gene with protein product	coenzyme Q1 homolog (yeast)	607429	trans-prenyltransferase	TPRT	NA	10972372	Standard		NM_014317	NA	Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.832-3379G>A	chr10.hg19:g.27020790G>A		NA	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	hg19	CCDS31168.1	0.02	-0.210506	CTCxGCT	COVERED																																																																																			NOVEL	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047276.1	12	3.609687	KEEP	9	0	0	12	364	GG	0.99254	0.518266	0		+	3	60	90	0	0	6.627639	19	60	607	58	ENST00000376215.5	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	27153529	27153529	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:27153529T>C			NA	NA				ABI1 (3513 upstream) : snoU13 (3564 downstream)						NA		NA									NA						ttcgggaggctgaggcgggca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.27153529T>C		NA		hg19		0.02	-0.184198	GGCxGAG	COVERED																																																																																			NOVEL					0			6	2.406345	KEEP	0	0	0	8	227	TT	0.99257	0.420331	0			3	60	103	0	0	8.060646	17	60	518	41		0.15	0.423478
ANKRD26	22852	__UNKNOWN__	__UNKNOWN__	10	27336525	27336525	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:27336525A>G	ENST00000376087.4	-	18	1980				ANKRD26_ENST00000376070.3_Intron|ANKRD26_ENST00000436985.2_Intron	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	NA		NA			glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						actccagcctaggcaacaaaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890	22852		Ankyrin repeat domain containing	29186	protein-coding gene	gene with protein product		610855	thrombocytopenia 2 (autosomal dominant)	THC2	NA	10470851, 21211618	Standard		NM_014915	NA	Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1815-1073T>C	chr10.hg19:g.27336525A>G		NA	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	hg19	CCDS41499.1	0.02	-0.096477	CCTxGGC	UNCOVERED																																																																																			NOVEL	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047296.1	5	2.406183	KEEP	0	0	0	8	221	AA	0.99257	0.119541	0		-	3	60	101	0	0	8.878889	7	60	209	30	ENST00000376087.4	0.3	0.120436
YME1L1	10730	__UNKNOWN__	__UNKNOWN__	10	27401879	27401879	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:27401879G>A	ENST00000376016.3	-	19	2189				YME1L1_ENST00000375972.3_Intron|YME1L1_ENST00000326799.3_Intron	NM_014263.3	NP_055078.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	NA		NA			cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						ggctgggtgcggtggctcaca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758	10730		ATPases / AAA-type	12843	protein-coding gene	gene with protein product		607472	YME1 (S.cerevisiae)-like 1, YME1-like 1 (S. cerevisiae)		NA	22262461	Standard	NM_139312	NM_139312	NA	Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000376016.3:c.2008-830C>T	chr10.hg19:g.27401879G>A		NA	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	hg19	CCDS7151.1	0.02	-0.236834	TGCxGTG	COVERED																																																																																			NOVEL	YME1L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047305.1	13	6.016093	KEEP	2	0	0	20	579	GG	0.99986	0.641257	0		-	3	60	90	0	0	6.395624	23	60	736	68	ENST00000376016.3	0.115385	0.641347
ACBD5	91452	__UNKNOWN__	__UNKNOWN__	10	27495972	27495972	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:27495972T>C	ENST00000396271.3	-	10	1531				ACBD5_ENST00000476758.1_Intron|ACBD5_ENST00000375897.3_Intron|ACBD5_ENST00000375905.4_Intron|ACBD5_ENST00000375888.1_Intron|ACBD5_ENST00000375901.1_Intron	NM_001271512.1|NM_145698.3	NP_001258441.1|NP_663736.2	Q5T8D3	ACBD5_HUMAN	acyl-CoA binding domain containing 5	NA		NA			peroxisome degradation (GO:0030242)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisome (GO:0005777)	fatty-acyl-CoA binding (GO:0000062)|lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(3)|lung(7)|prostate(1)	13						tttgggaggctgaggcgggtg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF505653	CCDS7154.1, CCDS44368.1, CCDS73079.1	10p12.1	2010-04-30	2010-04-30		ENSG00000107897	ENSG00000107897	91452			23338	protein-coding gene	gene with protein product		NA	acyl-Coenzyme A binding domain containing 5		NA	12056414	Standard	NM_145698	NR_024150	NA	Approved	DKFZp434A2417, KIAA1996	uc010qdp.2	Q5T8D3	OTTHUMG00000017854	ENST00000396271.3:c.1404+1202A>G	chr10.hg19:g.27495972T>C		NA	B3KQ56|D3DRW0|Q5T8D4|Q5T8E1|Q5T8E2|Q86UV1|Q8N6E3|Q9UFB5	hg19	CCDS44368.1	0.02	-0.175427	GGCxGAG	UNCOVERED																																																																																			NOVEL	ACBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047310.1	8	2.406021	KEEP	4	0	0	8	219	TT	0	0	0		-	3	60	103	0	0	8.133188	16	60	486	43	ENST00000396271.3	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	27922286	27922286	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:27922286T>C			NA	NA				RAB18 (91143 upstream) : MKX (39517 downstream)						NA		NA									NA						ccacctcggcttcccaaagtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.27922286T>C		NA		hg19		0.02	-0.131552	GGCxTCC	COVERED																																																																																			NOVEL					0			3	3.908582	KEEP	1	0	0	13	356	TT	0.994391	0.227888	0			3	60	89	0	0	7.173268	11	60	333	44		0.214286	0.229173
ARMC4	55130	__UNKNOWN__	__UNKNOWN__	10	28170332	28170332	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:28170332A>T	ENST00000305242.5	-	18	2703				ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000537576.1_Intron	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	NA		NA			cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						atcccagcacattgggaggcc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126	55130		Armadillo repeat containing	25583	protein-coding gene	gene with protein product		615408			NA	11230166	Standard	NM_018076	XM_005252485	NA	Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2611-18781T>A	chr10.hg19:g.28170332A>T		NA	A8K906|B7Z7I1|Q9H0C0	hg19	CCDS7157.1	0.02	-0.166221	CACxTTG	COVERED																																																																																			NOVEL	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047339.1	9	4.210906	KEEP	0	0	0	14	394	AA	0.995343	0.352299	0		-	3	60	90	0	0	6.996537	14	60	397	46	ENST00000305242.5	0.176471	0.353947
ARMC4	55130	__UNKNOWN__	__UNKNOWN__	10	28228415	28228415	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:28228415A>C	ENST00000305242.5	-	14	2190				ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000537576.1_Intron	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	NA		NA			cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						gaggctgaggagggagaatca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126	55130		Armadillo repeat containing	25583	protein-coding gene	gene with protein product		615408			NA	11230166	Standard	NM_018076	XM_005252485	NA	Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2097+410T>G	chr10.hg19:g.28228415A>C		NA	A8K906|B7Z7I1|Q9H0C0	hg19	CCDS7157.1	0.02	-0.184021	AGGxGGG	COVERED																																																																																			NOVEL	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047339.1	7	3.309055	KEEP	1	0	0	11	314	AA	0.992708	0.42039	0		-	3	60	105	0	1	8.334723	16	60	453	48	ENST00000305242.5	0.157895	0.423478
ARMC4	55130	__UNKNOWN__	__UNKNOWN__	10	28228416	28228416	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:28228416G>A	ENST00000305242.5	-	14	2190				ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000537576.1_Intron	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	NA		NA			cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						aggctgaggagggagaatcac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126	55130		Armadillo repeat containing	25583	protein-coding gene	gene with protein product		615408			NA	11230166	Standard	NM_018076	XM_005252485	NA	Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2097+409C>T	chr10.hg19:g.28228416G>A		NA	A8K906|B7Z7I1|Q9H0C0	hg19	CCDS7157.1	0.02	-0.184204	GGAxGGA	COVERED																																																																																			NOVEL	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047339.1	7	3.009325	KEEP	0	0	0	10	320	GG	0.992708	0.42039	0		-	3	60	91	0	1	6.933636	16	60	522	47	ENST00000305242.5	0.157895	0.423478
RP11-351M16.3	0	__UNKNOWN__	__UNKNOWN__	10	28761634	28761634	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:28761634T>C	ENST00000421132.1	-	0	93										NA		NA									NA						cagtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000421132.1:	chr10.hg19:g.28761634T>C		NA		hg19		0.02	-0.140331	TCAxGCC	COVERED																																																																																			NOVEL	RP11-351M16.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000047354.1	9	2.706687	KEEP	3	0	0	9	246	AT	0.99257	0.259026	0		-	4	60	130	0	0	11.131373	11	60	323	34	ENST00000421132.1	0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	28806226	28806226	__UNKNOWN__	IGR	SNP	G	G	A	rs12411640	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:28806226G>A			NA	NA				RP11-351M16.3 (21484 upstream) : WAC-AS1 (5354 downstream)						NA		NA									NA						ctcgtgatccgcccgcctcag	0.483		NA											G|||	983	0.196286	0.031	0.2507	5008	,	,	NA	14387	0.2411	NA	0.3002	False	NA	,,,	NA	NA	NA	2504	0.228	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.28806226G>A		NA		hg19		0.02	-0.105186	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			1	2.405986	KEEP	1	0	0	8	220	GG	0	0	0			6	60	156	0	0	15.167616	5	60	144	36		0.545455	0.139832
C10orf126	283080	__UNKNOWN__	__UNKNOWN__	10	29137914	29137914	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:29137914T>C	ENST00000375520.1	+	3	352					NM_001278522.1	NP_001265451.1	Q8N4M7	CJ126_HUMAN	chromosome 10 open reading frame 126	NA		NA								haematopoietic_and_lymphoid_tissue(1)	1						gaggccgaggtgggtggatca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC033839	CCDS60510.1	10p12.1	2014-08-13			ENSG00000204365	ENSG00000204365	283080			28693	protein-coding gene	gene with protein product		NA			NA	12477932	Standard		NM_001278522	NA	Approved	MGC45541, bA492M23.1		Q8N4M7	OTTHUMG00000017878	ENST00000375520.1:c.174+619T>C	chr10.hg19:g.29137914T>C		NA	Q5T2Z8	hg19		0.02	-0.096481	AGGxGGG	UNCOVERED																																																																																			NOVEL	C10orf126-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000047379.1	5	2.706473	KEEP	5	0	0	9	245	TT	0	0	0		+	3	60	95	0	0	8.132467	8	60	242	37	ENST00000375520.1	0.272727	0.120436
SVIL	6840	__UNKNOWN__	__UNKNOWN__	10	29857766	29857766	__UNKNOWN__	Intron	SNP	T	T	G	rs111524641		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:29857766T>G	ENST00000355867.4	-	2	611				SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	NA		NA			cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				gtgtgtgtgtttgtgtatgtg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321	6840			11480	protein-coding gene	gene with protein product	archvillin	604126			NA	9382871	Standard		NM_003174	NA	Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.141+417A>C	chr10.hg19:g.29857766T>G		NA	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	hg19	CCDS7164.1	0.02	-0.16659	TGTxTGT	COVERED																																																																																			NOVEL	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047395.1	6	3.005058	KEEP	0	0	0	10	245	TT	0.993072	0.351495	0		-	6	60	189	1	0	16.971075	11	60	300	40	ENST00000355867.4	0.352941	0.353947
SVIL	6840	__UNKNOWN__	__UNKNOWN__	10	29918645	29918645	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:29918645A>G	ENST00000355867.4	-	1	553				SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Intron	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	NA		NA			cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ggtggctcacacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321	6840			11480	protein-coding gene	gene with protein product	archvillin	604126			NA	9382871	Standard		NM_003174	NA	Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.199+4703T>C	chr10.hg19:g.29918645A>G		NA	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	hg19	CCDS7164.1	0.02	-0.087269	CACxCCT	UNCOVERED																																																																																			NOVEL	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047395.1	5	2.706766	KEEP	0	0	0	9	247	AA	0.99254	0.098977	0		-	2	60	72	0	0	6.343969	5	60	127	27	ENST00000355867.4	0.285714	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	30710528	30710528	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:30710528T>A			NA	NA				MTPAP (47158 upstream) : MAP3K8 (12337 downstream)						NA		NA									NA						atcccaacactttgggaggcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.30710528T>A		NA		hg19		0.02	-0.157884	CACxTTG	COVERED																																																																																			NOVEL					0			14	4.811793	KEEP	5	0	0	16	434	TT	0.993634	0.320751	0			4	60	118	0	0	9.8014	12	60	381	51		0.25	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	30760540	30760540	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:30760540T>C			NA	NA				MAP3K8 (9778 upstream) : RP11-253D19.1 (82242 downstream)						NA		NA									NA						gctgggattataggtgtgagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.30760540T>C		NA		hg19		0.02	-0.228002	TTAxAGG	COVERED																																																																																			NOVEL					0			15	3.907	KEEP	0	0	0	13	335	TT	0.994391	0.57966	0			3	60	97	0	0	7.779115	13	60	371	45		0.1875	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	30806199	30806199	__UNKNOWN__	IGR	SNP	T	T	A	rs2009810	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:30806199T>A			NA	NA				MAP3K8 (55437 upstream) : RP11-253D19.1 (36583 downstream)						NA		NA									NA						CTTTTTTTTTTTTTTTTTAAA	0.363		NA											T|||	1531	0.305711	0.3245	0.2579	5008	,	,	NA	18718	0.3462	NA	0.2545	False	NA	,,,	NA	NA	NA	2504	0.3252	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.30806199T>A		NA		hg19		0.02	-0.254329	TTTxTTT	COVERED																																																																																			NOVEL					0			2	2.705322	KEEP	1	0	0	9	229	TT	0.99254	0.663536	0			11	60	319	0	0	28.787618	18	60	529	56		0.37931	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	30997792	30997792	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:30997792T>C			NA	NA				SVILP1 (10400 upstream) : RP11-14C22.6 (14387 downstream)						NA		NA									NA						cggagtctcattctgttgccc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.30997792T>C		NA		hg19		0.02	-0.114026	TCAxTCT	UNCOVERED																																																																																			NOVEL					0			3	3.007671	KEEP	1	0	0	10	277	TT	0.99254	0.161255	0			3	60	99	0	0	8.281992	10	60	301	35		0.230769	0.162467
ARHGAP12	94134	__UNKNOWN__	__UNKNOWN__	10	32176853	32176853	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:32176853A>G	ENST00000375250.5	-	3	926				ARHGAP12_ENST00000344936.2_Intron|ARHGAP12_ENST00000311380.4_Intron|ARHGAP12_ENST00000396144.4_Intron|ARHGAP12_ENST00000375245.4_Intron	NM_001270696.1|NM_001270698.1	NP_001257625.1|NP_001257627.1	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	NA		NA			morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				ccaaagtgctaggattacagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322	94134		Rho GTPase activating proteins, Pleckstrin homology (PH) domain containing	16348	protein-coding gene	gene with protein product		610577			NA	11854031	Standard		NM_001270695	NA	Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000375250.5:c.684+20246T>C	chr10.hg19:g.32176853A>G		NA	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	hg19	CCDS59215.1	0.02	-0.17543	GCTxGGA	COVERED																																																																																			NOVEL	ARHGAP12-008	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047464.1	5	2.706829	KEEP	0	0	0	9	247	AA	0.99254	0.384517	0		-	3	60	105	0	0	8.409871	15	60	457	40	ENST00000375250.5	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	32439333	32439333	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:32439333T>C			NA	NA				Y_RNA (93566 upstream) : RNU7-22P (23278 downstream)						NA		NA									NA						gacggggttttaccatgttgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.32439333T>C		NA		hg19		0.02	-0.07012	TTTxACC	UNCOVERED																																																																																			NOVEL					0			5	3.006521	KEEP	0	0	0	10	261	TT	0.992708	0.053742	0			3	60	93	0	0	8.434171	5	60	135	28		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	32477390	32477390	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:32477390G>C			NA	NA				RNU7-22P (14718 upstream) : RP11-166N17.1 (77826 downstream)						NA		NA									NA						CAACCACTCAGTCTTGGCAGT	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.32477390G>C		NA		hg19		0.02	-0.421097	TCAxTCT	UNCOVERED																																																																																			NOVEL					0			3	3.008969	KEEP	19	0	0	10	305	GG	0	0	0			4	25	136	0	0	9.531239	44	50	1538	109		0.083333	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	32484250	32484250	__UNKNOWN__	IGR	SNP	G	G	A	rs2998070	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:32484250G>A			NA	NA				RNU7-22P (21578 upstream) : RP11-166N17.1 (70966 downstream)						NA		NA									NA						gtaagccaccgtgcccggcct	0.453		NA											g|||	1317	0.262979	0.0809	0.2046	5008	,	,	NA	15169	0.5069	NA	0.2763	False	NA	,,,	NA	NA	NA	2504	0.2853	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.32484250G>A		NA		hg19		0.02	-0.140343	ACCxTGC	COVERED																																																																																			NOVEL					0			7	2.707629	KEEP	0	0	0	9	265	GG	0.99254	0.259018	0			8	60	245	0	0	24.553327	5	60	166	35		0.615385	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	33676520	33676520	__UNKNOWN__	IGR	SNP	C	C	T	rs2804458	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:33676520C>T			NA	NA				RP11-90B22.1 (45687 upstream) : RP11-476F14.1 (191338 downstream)						NA		NA									NA						aaggtttcaccgtgttagcca	0.552		NA											c|||	1044	0.208466	0.0242	0.2666	5008	,	,	NA	14176	0.1042	NA	0.3598	False	NA	,,,	NA	NA	NA	2504	0.3681	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.33676520C>T		NA		hg19		0.02	-0.043853	CACxGTG	UNCOVERED																																																																																			NOVEL					0			4	2.406305	KEEP	2	0	0	8	224	CC	0	0	0			3	60	88	0	0	8.769143	2	34	60	14		0.6	0.024074
PARD3	56288	__UNKNOWN__	__UNKNOWN__	10	34919623	34919623	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:34919623T>C	ENST00000374789.3	-	2	548				PARD3_ENST00000374790.3_Intron|PARD3_ENST00000340077.5_Intron|PARD3_ENST00000545260.1_Intron|PARD3_ENST00000346874.4_Intron|PARD3_ENST00000545693.1_Intron|PARD3_ENST00000374788.3_Intron|PARD3_ENST00000374776.1_Intron|PARD3_ENST00000374794.3_Intron|PARD3_ENST00000350537.4_Intron|PARD3_ENST00000374773.1_Intron	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	NA		NA			apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				cctcccaccttggcctcccaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498	56288			16051	protein-coding gene	gene with protein product	atypical PKC isotype-specific interacting protein, par-3 family cell polarity regulator alpha, protein phosphatase 1, regulatory subunit 118	606745	par-3 (partitioning defective 3, C.elegans) homolog, par-3 partitioning defective 3 homolog (C. elegans)		NA	10934474	Standard	NM_019619	NM_001184790	NA	Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.222+65622A>G	chr10.hg19:g.34919623T>C		NA	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	hg19	CCDS7178.1	0.02	-0.131572	CCTxGGC	COVERED																																																																																			NOVEL	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047527.1	7	2.706783	KEEP	1	0	0	9	250	TT	0.99257	0.22747	0		-	3	60	100	0	0	8.501122	9	60	276	35	ENST00000374789.3	0.25	0.229173
PARD3	56288	__UNKNOWN__	__UNKNOWN__	10	35039886	35039886	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:35039886T>G	ENST00000374789.3	-	2	446				PARD3_ENST00000374790.3_Intron|PARD3_ENST00000340077.5_Intron|PARD3_ENST00000545260.1_Intron|PARD3_ENST00000346874.4_Intron|PARD3_ENST00000545693.1_Intron|PARD3_ENST00000374788.3_Intron|PARD3_ENST00000374776.1_Intron|PARD3_ENST00000374794.3_Intron|PARD3_ENST00000350537.4_Intron|PARD3_ENST00000374773.1_Intron	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	NA		NA			apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				caaagtgctgtgattacaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498	56288			16051	protein-coding gene	gene with protein product	atypical PKC isotype-specific interacting protein, par-3 family cell polarity regulator alpha, protein phosphatase 1, regulatory subunit 118	606745	par-3 (partitioning defective 3, C.elegans) homolog, par-3 partitioning defective 3 homolog (C. elegans)		NA	10934474	Standard	NM_019619	NM_001184790	NA	Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.121-54539A>C	chr10.hg19:g.35039886T>G		NA	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	hg19	CCDS7178.1	0.02	-0.114024	CTGxGAT	UNCOVERED																																																																																			NOVEL	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047527.1	6	2.40645	KEEP	0	0	0	8	226	TT	0.99257	0.16126	0		-	3	60	109	0	0	9.532697	8	60	236	32	ENST00000374789.3	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	35231577	35231577	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:35231577G>T			NA	NA				RNU6-847P (15767 upstream) : RNU6-193P (319 downstream)						NA		NA									NA						tttgttttttgtttttttgag	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.35231577G>T		NA		hg19		0.02	-0.175448	TTTxTTT	COVERED																																																																																			NOVEL					0			9	3.310093	KEEP	3	0	0	11	345	GG	0.993072	0.384723	0			3	60	87	0	0	6.778938	13	60	457	49		0.1875	0.387407
CCNY	219771	__UNKNOWN__	__UNKNOWN__	10	35735958	35735958	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:35735958T>C	ENST00000374704.4	+	2	334				CCNY_ENST00000374706.1_Intron|CCNY_ENST00000265375.9_Intron|CCNY_ENST00000339497.5_Intron|CCNY_ENST00000492478.1_Intron	NM_145012.4	NP_659449.3	Q8ND76	CCNY_HUMAN	cyclin Y	NA		NA			cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	8						gtaatcccagtactttgggag	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF413522, AY504868	CCDS7189.1, CCDS7190.1, CCDS60513.1	10p11.22	2011-01-25	2007-02-09	2007-02-09	ENSG00000108100	ENSG00000108100	219771			23354	protein-coding gene	gene with protein product		612786	chromosome 10 open reading frame 9	C10orf9	NA	20441050	Standard	NM_181698	XM_005252388	NA	Approved	CFP1, CBCP1	uc001iyw.4	Q8ND76	OTTHUMG00000017955	ENST00000374704.4:c.155-36374T>C	chr10.hg19:g.35735958T>C		NA	B7ZKX9|D3DRY9|Q2M3V4|Q2TU96|Q6NT86|Q7Z4U7|Q8TEX2|Q8TEX3|Q96M99|Q96P45	hg19	CCDS7189.1	0.02	-0.149088	CAGxACT	COVERED																																																																																			NOVEL	CCNY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047568.2	7	2.706443	KEEP	3	0	0	9	245	TT	0.99254	0.289823	0		+	3	60	105	1	0	8.579002	13	60	368	46	ENST00000374704.4	0.1875	0.292001
CCNY	219771	__UNKNOWN__	__UNKNOWN__	10	35774420	35774420	__UNKNOWN__	Intron	SNP	A	A	G	rs188943544	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:35774420A>G	ENST00000374704.4	+	2	409				CCNY_ENST00000374706.1_Intron|CCNY_ENST00000265375.9_Intron|CCNY_ENST00000339497.5_Intron|CCNY_ENST00000492478.1_Intron	NM_145012.4	NP_659449.3	Q8ND76	CCNY_HUMAN	cyclin Y	NA		NA			cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytoplasmic cyclin-dependent protein kinase holoenzyme complex (GO:0000308)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			cervix(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	8						ttgggaggccaaggcgggtgg	0.448		NA											A|||	34	0.00678914	0.0023	0.0072	5008	,	,	NA	16026	0.0	NA	0.0229	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF413522, AY504868	CCDS7189.1, CCDS7190.1, CCDS60513.1	10p11.22	2011-01-25	2007-02-09	2007-02-09	ENSG00000108100	ENSG00000108100	219771			23354	protein-coding gene	gene with protein product		612786	chromosome 10 open reading frame 9	C10orf9	NA	20441050	Standard	NM_181698	XM_005252388	NA	Approved	CFP1, CBCP1	uc001iyw.4	Q8ND76	OTTHUMG00000017955	ENST00000374704.4:c.229+2014A>G	chr10.hg19:g.35774420A>G		NA	B7ZKX9|D3DRY9|Q2M3V4|Q2TU96|Q6NT86|Q7Z4U7|Q8TEX2|Q8TEX3|Q96M99|Q96P45	hg19	CCDS7189.1	0.02	-0.157846	GCCxAGG	UNCOVERED																																																																																			NOVEL	CCNY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047568.2	10	3.307348	KEEP	7	0	0	11	304	AA	0	0	0		+	3	60	87	0	0	6.780372	13	60	379	42	ENST00000374704.4	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	35910390	35910390	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:35910390T>C			NA	NA				GJD4 (12527 upstream) : FZD8 (16786 downstream)						NA		NA									NA						cgggttcaagtgattctcctg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.35910390T>C		NA		hg19		0.02	-0.236771	AAGxGAT	COVERED																																																																																			NOVEL					0			44	3.072837	KEEP	16	2	65	33	913	TT	0.999997	0.641345	0			4	43	129	0	0	10.668946	14	60	403	95		0.222222	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	36071709	36071709	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:36071709T>C			NA	NA				FZD8 (141347 upstream) : RP11-309N24.1 (114092 downstream)						NA		NA									NA						CCAggccgggtgcggtggctc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.36071709T>C		NA		hg19		0.02	-0.420994	GGGxGCG	COVERED																																																																																			NOVEL					0			20	3.036011	KEEP	1	1	31	21	552	TT	0.999869	0.954366	0			4	60	135	0	0	9.674542	38	60	1134	96		0.095238	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	37031541	37031541	__UNKNOWN__	IGR	SNP	A	A	G	rs375359080		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:37031541A>G			NA	NA				Y_RNA (116475 upstream) : RP11-322I2.1 (197495 downstream)						NA		NA									NA						aagaagaagaagaagaagaag	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.37031541A>G		NA		hg19		0.02	-0.061401	AGAxGAA	UNCOVERED																																																																																			NOVEL					0			17	2.404896	KEEP	9	0	0	8	207	AA	0	0	0			3	60	100	0	0	9.625288	3	43	88	24		0.5	0.043787
ANKRD30A	91074	__UNKNOWN__	__UNKNOWN__	10	37520514	37520514	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:37520514G>T	ENST00000602533.1	+	0	4242				ANKRD30A_ENST00000374660.1_3'UTR|ANKRD30A_ENST00000361713.1_3'UTR			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	NA		NA			regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CCAATAGTCTGTGTCAACAGA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513	91074		Ankyrin repeat domain containing	17234	protein-coding gene	gene with protein product	breast cancer antigen NY-BR-1	610856			NA	11280766	Standard	NM_052997	NM_052997	NA	Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.*117G>T	chr10.hg19:g.37520514G>T		NA	Q5W025	hg19		0.02	1.663247	TCTxTGT	COVERED																																																																																			NOVEL	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000047588.2	1	2.708161	KEEP	0	0	0	9	278	GG	0.99254	0.980573	0		+	22	60	678	0	0	61.170388	38	60	1298	107	ENST00000602533.1	0.366667	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	38183046	38183046	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:38183046A>G			NA	NA				RP11-162G10.5 (35008 upstream) : ZNF25 (55453 downstream)						NA		NA									NA						cgaagtgctgagattacaggt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.38183046A>G		NA		hg19		0.02	-0.096473	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			6	2.795027	KEEP	1	1	7	12	334	AA	0.994391	0.119761	0			3	60	90	0	0	7.778602	7	60	204	36		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	38939346	38939346	__UNKNOWN__	IGR	SNP	T	T	C	rs367868476	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:38939346T>C			NA	NA				RP11-291L22.4 (184242 upstream) : None (None downstream)						NA		NA									NA						AAGGTCCTTGTAGCCATTCAA	0.274		NA											.|||	290	0.0579073	0.0431	0.0879	5008	,	,	NA	28003	0.0625	NA	0.0477	False	NA	,,,	NA	NA	NA	2504	0.0624	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.38939346T>C		NA		hg19		0.02	-0.38586	TTGxAGC	COVERED																																																																																			NOVEL					0			4	3.006961	KEEP	4	0	0	10	265	TT	0.99257	0.911349	0			8	27	263	0	0	21.147751	35	46	997	56		0.186047	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	39138152	39138152	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:39138152C>T			NA	NA				RP11-291L22.4 (383048 upstream) : None (None downstream)						NA		NA									NA						atggaatggactcgaatggaa	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.39138152C>T		NA		hg19		0.02	4.354483	GGAxTCG	COVERED																																																																																			NOVEL					0			160	13.300059	KEEP	96	5	129	90	2732	CC	1	1	0			5	40	145	0	0	11.359252	21	60	713	452		0.192308	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42384770	42384770	__UNKNOWN__	IGR	SNP	A	A	G	rs148873058|rs147070410		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42384770A>G			NA	NA				None (None upstream) : AL031601.1 (345580 downstream)						NA		NA									NA						aatcgaatggaatcatcaaat	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42384770A>G		NA		hg19		0.02	-0.131541	TGGxATC	COVERED																																																																																			NOVEL					0			20	3.601046	KEEP	12	0	0	12	303	AA	0.99257	0.22747	0			3	50	97	0	0	8.832914	5	47	153	45		0.375	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385215	42385215	__UNKNOWN__	IGR	SNP	G	G	A	rs28760987		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42385215G>A			NA	NA				None (None upstream) : AL031601.1 (345135 downstream)						NA		NA									NA						ggaattgaatggaatcatcga	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385215G>A		NA		hg19		0.02	5.824013	AATxGAA	COVERED																																																																																			NOVEL					0			83	21.827377	KEEP	14	5	137	121	3653	GG	1	1	0			8	60	244	0	0	15.206475	121	60	4070	558		0.062016	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385255	42385255	__UNKNOWN__	IGR	SNP	G	G	A	rs71230978		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42385255G>A			NA	NA				None (None upstream) : AL031601.1 (345095 downstream)						NA		NA									NA						ttatcaaatggaatcgaatgg	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385255G>A		NA		hg19		0.02	6.910808	ATGxAAT	COVERED																																																																																			NOVEL					0			80	19.31998	KEEP	16	5	138	113	3402	GG	1	1	0			11	60	334	1	1	21.424346	144	60	4766	523		0.070968	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385257	42385257	__UNKNOWN__	IGR	SNP	A	A	G	rs71230978		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42385257A>G			NA	NA				None (None upstream) : AL031601.1 (345093 downstream)						NA		NA									NA						atcaaatggaatcgaatggaa	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385257A>G		NA		hg19		0.02	7.923923	GGAxTCG	COVERED																																																																																			NOVEL					0			78	17.199444	KEEP	15	5	153	111	3058	AA	1	1	0			10	60	344	1	1	23.134217	143	60	4315	516		0.065359	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42385610	42385610	__UNKNOWN__	IGR	SNP	T	T	A	rs60571574		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42385610T>A			NA	NA				None (None upstream) : AL031601.1 (344740 downstream)						NA		NA									NA						ttcaaaggaatcatcatcaaa	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42385610T>A		NA		hg19		0.02	3.3707	GAAxCAT	COVERED																																																																																			NOVEL					0			38	3.668557	KEEP	49	3	84	42	1133	TT	0.999997	0.999995	0			9	49	275	2	0	18.545552	94	60	2799	283		0.087379	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42388344	42388344	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42388344T>A			NA	NA				None (None upstream) : AL031601.1 (342006 downstream)						NA		NA									NA						atcatgaaattgaaatggatg	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42388344T>A		NA		hg19		0.02	1.543906	AATxGAA	COVERED																																																																																			NOVEL					0			29	3.992203	KEEP	84	3	84	43	1166	TT	0.999879	0.963657	0			5	43	149	0	0	10.578349	38	47	1103	237		0.116279	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42392318	42392318	__UNKNOWN__	IGR	SNP	A	A	T	rs148932631		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42392318A>T			NA	NA				None (None upstream) : AL031601.1 (338032 downstream)						NA		NA									NA						gaatggaaacaccatcgaatt	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42392318A>T		NA		hg19		0.02	-0.3859	AACxCCA	COVERED																																																																																			NOVEL					0			35	11.729853	KEEP	76	0	0	39	1086	AA	0.99649	0.923388	0			3	22	92	0	0	6.961295	17	53	503	222		0.15	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42535214	42535214	__UNKNOWN__	IGR	SNP	C	C	T	rs377750180		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42535214C>T			NA	NA				None (None upstream) : AL031601.1 (195136 downstream)						NA		NA									NA						cacttgcagactttacaaata	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42535214C>T		NA		hg19		0.02	-0.096499	AGAxTTT	UNCOVERED																																																																																			NOVEL					0			12	2.741415	KEEP	29	1	28	19	581	CC	0.99257	0.119541	0			3	60	93	0	0	8.243243	6	28	210	75		0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42599630	42599630	__UNKNOWN__	IGR	SNP	A	A	G	rs144050204		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42599630A>G			NA	NA				None (None upstream) : AL031601.1 (130720 downstream)						NA		NA									NA						atcatcatcgaatggaaatga	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42599630A>G		NA		hg19		0.02	6.764547	TCGxATG	COVERED																																																																																			NOVEL					0			109	26.700754	KEEP	34	1	32	100	2772	AA	1	1	0			7	21	228	2	0	15.069807	95	60	2831	480		0.068627	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42599734	42599734	__UNKNOWN__	IGR	SNP	G	G	A	rs113426781		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42599734G>A			NA	NA				None (None upstream) : AL031601.1 (130616 downstream)						NA		NA									NA						aacattgaacggaattgaatg	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42599734G>A		NA		hg19		0.02	3.183469	AACxGAA	COVERED																																																																																			NOVEL					0			19	5.505791	KEEP	48	3	81	47	1287	GG	1	0.999999	0			5	27	152	0	0	10.486978	46	50	1417	268		0.098039	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42599767	42599767	__UNKNOWN__	IGR	SNP	A	A	C	rs139875229		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42599767A>C			NA	NA				None (None upstream) : AL031601.1 (130583 downstream)						NA		NA									NA						aatgaattgaatgcaatcatc	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42599767A>C		NA		hg19		0.02	5.689363	TGAxTGC	COVERED																																																																																			NOVEL					0			52	9.620606	KEEP	57	3	91	64	1769	AA	1	1	0			6	49	202	1	0	13.406331	87	54	2607	349		0.064516	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	42618156	42618156	__UNKNOWN__	IGR	SNP	A	A	C	rs140620412		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:42618156A>C			NA	NA				None (None upstream) : AL031601.1 (112194 downstream)						NA		NA									NA						aggcagaagaatcacttgaag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.42618156A>C		NA		hg19		0.02	-0.175429	AGAxTCA	COVERED																																																																																			NOVEL					0			10	2.4055	KEEP	7	0	0	8	213	AA	0.99257	0.384528	0			4	40	140	0	0	12.131308	11	60	331	47		0.266667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	43364696	43364696	__UNKNOWN__	IGR	SNP	G	G	A	rs538285481		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:43364696G>A			NA	NA				BMS1 (34311 upstream) : RP11-124O11.1 (2272 downstream)						NA		NA									NA						ctcccaaagtgctgggattac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.43364696G>A		NA		hg19		0.02	-0.157898	AGTxCTG	COVERED																																																																																			NOVEL					0			12	4.212499	KEEP	2	0	0	14	430	GG	0.993634	0.320751	0			3	39	85	0	0	6.672377	12	60	407	48		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	43775251	43775251	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:43775251A>G			NA	NA				RASGEF1A (12884 upstream) : RP11-168L22.2 (43861 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.43775251A>G		NA		hg19		0.02	-0.184173	GGCxTGA	COVERED																																																																																			NOVEL					0			10	3.298204	KEEP	1	0	0	11	280	AA	0.992708	0.42039	0			3	60	103	0	0	8.060853	17	60	496	44		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	43874461	43874461	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:43874461A>T			NA	NA				FXYD4 (2681 upstream) : HNRNPF (6603 downstream)						NA		NA									NA						aaaccctgtcactactaaaaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.43874461A>T		NA		hg19		0.02	-0.149075	GTCxCTA	COVERED																																																																																			NOVEL					0			5	2.406049	KEEP	0	0	0	8	219	AA	0.99257	0.289832	0			3	60	84	0	0	6.480443	13	60	377	32		0.1875	0.292001
ZNF487	642819	__UNKNOWN__	__UNKNOWN__	10	43957048	43957048	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:43957048T>C	ENST00000437590.2	+	2	137				ZNF487_ENST00000431662.1_Intron			B1APH4	ZN487_HUMAN	zinc finger protein 487	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						ggattacaggtatgagccact	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					10q11.21	2013-06-03	2013-03-06	2013-03-06	ENSG00000243660	ENSG00000243660	642819			23488	other	unknown		NA	KRAB domain only 1, zinc finger protein 487, pseudogene	KRBO1, ZNF487P	NA		Standard	XM_926224	NR_026693	NA	Approved			B1APH4	OTTHUMG00000185507	ENST00000437590.2:c.-90-14121T>C	chr10.hg19:g.43957048T>C		NA	B1APH5|B7Z7S5	hg19		0.02	-0.166599	AGGxATG	COVERED																																																																																			NOVEL	ZNF487-003	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000317659.3	9	3.006158	KEEP	0	0	0	10	257	TT	0.992708	0.351366	0		+	3	60	99	0	0	8.072849	12	60	331	44	ENST00000437590.2	0.2	0.353947
ZNF487	642819	__UNKNOWN__	__UNKNOWN__	10	43978725	43978725	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:43978725A>G	ENST00000431662.1	+	6	1293							B1APH4	ZN487_HUMAN	zinc finger protein 487	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						tttcgctcttattgcccaggc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					10q11.21	2013-06-03	2013-03-06	2013-03-06	ENSG00000243660	ENSG00000243660	642819			23488	other	unknown		NA	KRAB domain only 1, zinc finger protein 487, pseudogene	KRBO1, ZNF487P	NA		Standard	XM_926224	NR_026693	NA	Approved			B1APH4	OTTHUMG00000185507	ENST00000431662.1:c.1293+134A>G	chr10.hg19:g.43978725A>G		NA	B1APH5|B7Z7S5	hg19		0.02	-0.07894	CTTxTTG	UNCOVERED																																																																																			NOVEL	ZNF487-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		5	2.705932	KEEP	0	0	0	9	236	AA	0.99254	0.076759	0		+	4	60	135	0	0	13.000379	4	60	118	24	ENST00000431662.1	0.5	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	45233982	45233982	__UNKNOWN__	IGR	SNP	G	G	A	rs150351775	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:45233982G>A			NA	NA				RP11-733D4.1 (136430 upstream) : TMEM72-AS1 (72489 downstream)						NA		NA									NA						ggctgggtgcggtggctcacg	0.453		NA											G|||	5	0.000998403	0.0008	0.0014	5008	,	,	NA	15621	0.0	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.45233982G>A		NA		hg19		0.02	-0.192975	TGCxGTG	COVERED																																																																																			NOVEL					0			9	5.714274	KEEP	6	0	0	19	541	GG	0.997832	0.456764	0			3	22	87	0	0	6.393037	18	60	585	60		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	45585149	45585149	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:45585149C>T			NA	NA				CEP164P1 (18113 upstream) : RSU1P2 (10464 downstream)						NA		NA									NA						catgagccaccgcacccagct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.45585149C>T		NA		hg19		0.02	-0.236844	CACxGCA	COVERED																																																																																			NOVEL					0			13	3.60685	KEEP	1	0	0	12	316	CC	0.993072	0.608164	0			3	60	93	0	0	6.805936	21	60	681	54		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	46949942	46949942	__UNKNOWN__	IGR	SNP	G	G	A	rs55758447	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:46949942G>A			NA	NA				RP11-38L15.2 (11446 upstream) : RP11-38L15.3 (1529 downstream)						NA		NA									NA						aggcttaggtgagcctctcgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.46949942G>A		NA		hg19		0.02	-0.192955	GGTxAGC	COVERED																																																																																			NOVEL					0			12	2.708422	KEEP	0	0	0	9	288	GG	0.99254	0.454342	0			9	60	257	0	0	24.014095	11	60	367	45		0.45	0.457757
RP11-38L15.3	0	__UNKNOWN__	__UNKNOWN__	10	46952758	46952758	__UNKNOWN__	RNA	SNP	G	G	T	rs3120431	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:46952758G>T	ENST00000506914.1	+	0	312				RP11-38L15.3_ENST00000430188.1_RNA						NA		NA									NA						ctaaactttcgatttcatttt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000506914.1:	chr10.hg19:g.46952758G>T		NA		hg19		0.02	-0.359574	TTCxATT	COVERED																																																																																			NOVEL	RP11-38L15.3-002	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000367006.1	1	3.007227	KEEP	7	0	0	10	284	GG	0.992708	0.892756	0		+	5	27	143	0	0	10.148034	35	60	1096	84	ENST00000506914.1	0.125	0.899314
RP11-38L15.3	0	__UNKNOWN__	__UNKNOWN__	10	46952802	46952802	__UNKNOWN__	RNA	SNP	T	T	C	rs480119		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:46952802T>C	ENST00000506914.1	+	0	312				RP11-38L15.3_ENST00000430188.1_RNA						NA		NA									NA						ctcccccaagtctggcccagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000506914.1:	chr10.hg19:g.46952802T>C		NA		hg19		0.02	1.865579	AAGxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	C	2.800	-0.249421	0.05867	.	.	ENSG00000204176	ENST00000416127	.	.	.	1.43	0.323	0.15893	.	.	.	.	.	T	0.33962	0.0881	.	.	.	.	.	.	.	.	.	.	.	.	T	0.40175	-0.9577	4	0.54805	T	0.06	.	1.9401	0.03345	0.3158:0.4623:0.0:0.222	.	.	.	.	G	336	.	ENSP00000412323:D336G	D	-	2	0	SYT15	46372808	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.269000	0.08596	-0.271000	0.09272	-0.642000	0.03964	GAC	NOVEL	RP11-38L15.3-002	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000367006.1	3	2.536923	KEEP	15	1	30	19	514	TT	0.99986	0.997023	0		+	13	27	441	0	0	35.715877	57	60	1658	154	ENST00000506914.1	0.185714	0.997163
SYT15	83849	__UNKNOWN__	__UNKNOWN__	10	46960374	46960374	__UNKNOWN__	3'UTR	SNP	G	G	A	rs576807935		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:46960374G>A	ENST00000374323.4	-	0	3608				RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000449358.2_Intron|SYT15_ENST00000503753.1_Intron|SYT15_ENST00000374325.3_Intron			Q9BQS2	SYT15_HUMAN	synaptotagmin XV	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						cagcctgggcgacagagcaag	0.478		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	36113	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Ovarian(57;1152 1428 19651 37745)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176	83849		Synaptotagmins	17167	protein-coding gene	gene with protein product		608081			NA	11543631	Standard	NM_031912	NM_031912	NA	Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374323.4:c.*1596C>T	chr10.hg19:g.46960374G>A		NA	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	hg19		0.02	3.002714	GGCxACA	COVERED																																																																																			NOVEL	SYT15-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000123282.3	9	16.326458	KEEP	3	3	81	83	2244	GG	1	0.999999	0		-	8	60	247	2	2	16.457039	91	70	2818	242	ENST00000374323.4	0.080808	0.999999
SYT15	83849	__UNKNOWN__	__UNKNOWN__	10	46961964	46961964	__UNKNOWN__	3'UTR	SNP	G	G	A	rs9422211	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:46961964G>A	ENST00000374321.4	-	0	1338				RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_3'UTR|SYT15_ENST00000503753.1_Intron|SYT15_ENST00000374325.3_Intron	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	NA		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGTGCTGGGCGAAGGGTCAGG	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(57;1152 1428 19651 37745)							NA				0								G	,	106,4100		0,106,1997	56	67	63		,	-2.8	0	10	dbSNP_134	63	1059,7397		2,1055,3171	no	utr-3,intron	SYT15	NM_031912.4,NM_181519.2	,	2,1161,5168	AA,AG,GG	NA	12.5237,2.5202,9.2008	,	,	46961964	1165,11497	2103	4228	6331	SO:0001624	3_prime_UTR_variant			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176	83849		Synaptotagmins	17167	protein-coding gene	gene with protein product		608081			NA	11543631	Standard	NM_031912	NM_031912	NA	Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.*6C>T	chr10.hg19:g.46961964G>A		NA	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	hg19	CCDS44376.1	0.02	4.229394	GGCxAAG	COVERED																																																																																			NOVEL	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367008.1	4	4.811876	KEEP	21	0	0	16	456	GG	0.993634	0.993634	0		-	39	50	1108	0	0	90.345915	125	51	4043	290	ENST00000374321.4	0.237805	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	47072089	47072089	__UNKNOWN__	IGR	SNP	C	C	G	rs578182520|rs12359033	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:47072089C>G			NA	NA				GPRIN2 (66446 upstream) : NPY4R (11444 downstream)						NA		NA									NA						tgcagtgagccgagatcacgc	0.522		NA											C|||	1505	0.300519	0.2557	0.2003	5008	,	,	NA	29311	0.4306	NA	0.2793	False	NA	,,,	NA	NA	NA	2504	0.32	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.47072089C>G		NA		hg19		0.02	-0.105258	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.405912	KEEP	5	0	0	8	223	CC	0	0	0			4	60	126	0	0	11.191207	8	60	257	31		0.333333	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	47073566	47073566	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:47073566T>C			NA	NA				GPRIN2 (67923 upstream) : NPY4R (9967 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.47073566T>C		NA		hg19		0.02	-0.315732	AGAxGGG	COVERED																																																																																			NOVEL					0			5	2.404061	KEEP	0	0	0	8	201	TT	0.99257	0.829507	0			3	60	102	0	0	7.226679	31	60	902	56		0.088235	0.835716
RBP3	5949	__UNKNOWN__	__UNKNOWN__	10	48389870	48389870	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:48389870G>A	ENST00000224600.4	-	1	1121	c.1008C>T	c.(1006-1008)gtC>gtT	p.V336V		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	336	4 X approximate tandem repeats.	NA			lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	AGTCCTTCAGGACCTCCTGGA	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													39	38	38			NA	NA	10		NA											NA				48389870		2203	4300	6503	SO:0001819	synonymous_variant			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203	5949			9921	protein-coding gene	gene with protein product		180290	retinol-binding protein 3, interstitial		NA		Standard	NM_002900	NM_002900	NA	Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.1008C>T	chr10.hg19:g.48389870G>A		NA	Q0QD34|Q5VSR0|Q8IXN0	hg19	CCDS7218.1	0.02	1.04611	CAGxACC	COVERED																																																																																			NOVEL	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047888.1	6	3.007269	KEEP	0	0	0	10	287	GG	0.992708	0.990921	0		-	5	60	136	0	0	8.117897	67	60	2218	107	ENST00000224600.4	0.069444	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	49501857	49501857	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:49501857T>G			NA	NA				FRMPD2 (18916 upstream) : MAPK8 (12875 downstream)						NA		NA									NA						ctcccaaagttctgggattac	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.49501857T>G		NA		hg19		0.02	-0.298208	AGTxCTG	COVERED																																																																																			NOVEL					0			12	4.511321	KEEP	2	0	0	15	418	TT	0.995343	0.777423	0			3	60	102	0	0	7.309198	29	60	886	72		0.09375	0.78106
CHAT	1103	__UNKNOWN__	__UNKNOWN__	10	50824577	50824577	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:50824577C>A	ENST00000337653.2	+	2	469	c.316C>A	c.(316-318)Ctc>Atc	p.L106I	CHAT_ENST00000351556.3_5'UTR|CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000339797.1_5'UTR|CHAT_ENST00000395562.2_Missense_Mutation_p.L24I|CHAT_ENST00000395559.2_5'UTR|CHAT_ENST00000455728.2_5'UTR	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	106		NA			adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	TGCACCAGGACTCACCAAGAC	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													102	73	83			NA	NA	10		NA											NA				50824577		2203	4300	6503	SO:0001583	missense			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	1103	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	choline acetyltransferase		NA	1840566	Standard	NM_020549	NM_020984	NA	Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.316C>A	chr10.hg19:g.50824577C>A	ENSP00000337103:p.Leu106Ile	NA	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	hg19	CCDS7232.1	0.02	1.479037	GGAxTCA	COVERED	.	.	.	.	.	.	.	.	.	.	C	1.259	-0.616450	0.03663	.	.	ENSG00000070748	ENST00000337653;ENST00000395562	D;D	0.84660	-1.88;-1.88	4.06	1.08	0.20341	.	0.665977	0.13424	N	0.388884	T	0.65417	0.2689	N	0.08118	0	0.23215	N	0.998102	B	0.02656	0.0	B	0.04013	0.001	T	0.51268	-0.8727	10	0.27082	T	0.32	-10.85	4.3008	0.10923	0.2968:0.1798:0.5234:0.0	.	106	P28329	CLAT_HUMAN	I	106;24	ENSP00000337103:L106I;ENSP00000378929:L24I	ENSP00000337103:L106I	L	+	1	0	CHAT	50494583	0.000000	0.05858	0.244000	0.24202	0.031000	0.12232	-0.060000	0.11712	0.255000	0.21593	-0.165000	0.13383	CTC	NOVEL	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000047997.1	3	5.114939	KEEP	0	0	0	17	525	CC	0.999366	0.998684	0		+	27	60	815	0	0	72.714811	50	60	1729	151	ENST00000337653.2	0.350649	0.999317
C10orf53	282966	__UNKNOWN__	__UNKNOWN__	10	50917264	50917264	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:50917264C>A	ENST00000374112.3	+	0	1087				C10orf53_ENST00000535836.1_3'UTR	NM_182554.2	NP_872360.2	Q8N6V4	CJ053_HUMAN	chromosome 10 open reading frame 53	NA		NA								endometrium(1)|lung(6)	7		all_neural(218;0.107)				aatgcactggccctagacctc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC028127	CCDS31202.1, CCDS41521.1	10q11.23	2012-05-24			ENSG00000178645	ENSG00000178645	282966			27421	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182554	NM_182554	NA	Approved	Em:AC069546.1	uc001jid.1	Q8N6V4	OTTHUMG00000018199	ENST00000374112.3:c.*601C>A	chr10.hg19:g.50917264C>A		NA	A6NI81|A6NLE0|B9ZVK6	hg19	CCDS31202.1	0.02	1.449902	TGGxCCT	COVERED																																																																																			NOVEL	C10orf53-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048006.1	0	3.008607	KEEP	0	0	0	10	298	CC	0.992708	0.990621	0		+	18	60	535	0	0	44.381996	55	60	1888	127	ENST00000374112.3	0.246575	0.997898
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	51019868	51019868	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:51019868A>G			NA	NA				OGDHL (49443 upstream) : PARG (6456 downstream)						NA		NA									NA						tcaccatgttagccaggatgg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.51019868A>G		NA		hg19		0.02	-0.210489	GTTxGCC	COVERED																																																																																			NOVEL					0			15	2.337261	KEEP	15	1	29	18	487	AA	0.993072	0.518544	0			3	54	98	0	0	7.365315	20	60	587	72		0.130435	0.522161
MSMB	4477	__UNKNOWN__	__UNKNOWN__	10	51556189	51556189	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:51556189T>C	ENST00000358559.2	+	2	196				MSMB_ENST00000298239.6_Intron|MSMB_ENST00000474170.1_Intron	NM_002443.3	NP_002434.1	P08118	MSMB_HUMAN	microseminoprotein, beta-	NA		NA				extracellular space (GO:0005615)|nucleus (GO:0005634)				lung(4)|ovary(2)|prostate(1)	7						tcccaaagtgttgggattaca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005257	CCDS73095.1, CCDS73096.1	10q11.2	2014-05-06			ENSG00000138294	ENSG00000263639	4477			7372	protein-coding gene	gene with protein product		157145			NA	1783399	Standard	NM_002443, NM_138634	NM_002443	NA	Approved	PSP-94, PSP57, PSP94, IGBF, MSP, MSPB, PN44, PRPS, PSP	uc001jiq.3	P08118	OTTHUMG00000188315	ENST00000358559.2:c.109+353T>C	chr10.hg19:g.51556189T>C		NA	B1API6|P11999|Q13125|Q6IAY9|Q9UC59	hg19	CCDS7235.1	0.02	-0.131562	GTGxTGG	COVERED																																																																																			NOVEL	MSMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048034.1	2	2.405618	KEEP	0	0	0	8	215	TT	0.99257	0.22747	0		+	3	60	97	0	0	7.872363	12	60	360	37	ENST00000358559.2	0.2	0.229173
ASAH2	56624	__UNKNOWN__	__UNKNOWN__	10	51946709	51946709	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:51946709C>T	ENST00000395526.4	-	0	2708					NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	NA		NA			apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						ATTAGTGAGCCATTCTCACTA	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611	56624			18860	protein-coding gene	gene with protein product		611202			NA	10781606	Standard	NM_019893	NM_019893	NA	Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.*366G>A	chr10.hg19:g.51946709C>T		NA	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	hg19	CCDS7239.2	0.02	-0.070155	AGCxATT	UNCOVERED																																																																																			NOVEL	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048061.3	2	3.609962	KEEP	4	0	0	12	346	CC	0.992708	0.053742	0		-	3	25	83	0	0	7.432341	5	25	151	22	ENST00000395526.4	0.375	0.054137
ASAH2	56624	__UNKNOWN__	__UNKNOWN__	10	51946825	51946825	__UNKNOWN__	3'UTR	SNP	G	G	A	rs61856759		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:51946825G>A	ENST00000395526.4	-	0	2592					NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	NA		NA			apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ceramidase activity (GO:0017040)			large_intestine(1)|lung(9)|urinary_tract(1)	11						GGCTGCTGGAGCAAGATATAT	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF250847	CCDS7239.2, CCDS44398.1	10q11.23	2008-08-11			ENSG00000188611	ENSG00000188611	56624			18860	protein-coding gene	gene with protein product		611202			NA	10781606	Standard	NM_019893	NM_019893	NA	Approved		uc001jjd.3	Q9NR71	OTTHUMG00000018223	ENST00000395526.4:c.*250C>T	chr10.hg19:g.51946825G>A		NA	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	hg19	CCDS7239.2	0.02	4.400776	GGAxCAA	COVERED																																																																																			NOVEL	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048061.3	72	11.059613	KEEP	19	10	269	132	4027	GG	1	1	0		-	8	33	224	2	0	12.44487	155	60	5273	454	ENST00000395526.4	0.04908	1
PRKG1	5592	__UNKNOWN__	__UNKNOWN__	10	52781693	52781693	__UNKNOWN__	Intron	SNP	G	G	A	rs571298619	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:52781693G>A	ENST00000373985.1	+	1	287				PRKG1_ENST00000401604.2_Intron	NM_001098512.2	NP_001091982.1	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	NA		NA			actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		cacctgcctcggcctcccaaa	0.493		NA											G|||	4	0.000798722	0.0	0.0	5008	,	,	NA	16886	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	5592	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B	NA	2792381, 1544322	Standard		NM_001098512	NA	Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000373985.1:c.230+30289G>A	chr10.hg19:g.52781693G>A		NA	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	hg19		0.02	-0.149118	CTCxGCC	COVERED																																																																																			NOVEL	PRKG1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000048102.1	12	5.114783	KEEP	4	0	0	17	525	GG	0.99649	0.290976	0		+	3	60	89	0	0	6.979197	13	60	420	52	ENST00000373985.1	0.1875	0.292001
PRKG1	5592	__UNKNOWN__	__UNKNOWN__	10	53243107	53243107	__UNKNOWN__	Intron	SNP	C	C	T	rs293319	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:53243107C>T	ENST00000373980.4	+	3	1009				PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_006258.3	NP_006249.1	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	NA		NA			actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TTTTGGTGCCCTTATGCAGGG	0.473		NA											T|||	3984	0.795527	0.7186	0.817	5008	,	,	NA	16402	0.871	NA	0.8121	False	NA	,,,	NA	NA	NA	2504	0.7894	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	5592	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B	NA	2792381, 1544322	Standard		NM_001098512	NA	Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000373980.4:c.592+15511C>T	chr10.hg19:g.53243107C>T		NA	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	hg19	CCDS7244.1	0.02	-0.078951	GCCxTTA	UNCOVERED																																																																																			NOVEL	PRKG1-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048103.1	2	2.708126	KEEP	0	0	0	9	278	CC	0.99254	0.076759	0		+	4	60	124	0	0	11.62275	5	60	177	29	ENST00000373980.4	0.444444	0.077336
PRKG1	5592	__UNKNOWN__	__UNKNOWN__	10	53755808	53755808	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:53755808T>C	ENST00000373980.4	+	6	1179				PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_006258.3	NP_006249.1	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	NA		NA			actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		cacggtggcttacgcctgtaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	5592	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B	NA	2792381, 1544322	Standard		NM_001098512	NA	Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000373980.4:c.763-58436T>C	chr10.hg19:g.53755808T>C		NA	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	hg19	CCDS7244.1	0.02	-0.219101	GCTxACG	COVERED																																																																																			NOVEL	PRKG1-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048103.1	8	3.608135	KEEP	0	0	0	12	316	TT	0.993634	0.549368	0		+	4	60	135	0	0	10.796157	19	60	519	55	ENST00000373980.4	0.173913	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	54998435	54998435	__UNKNOWN__	IGR	SNP	C	C	T	rs10824955	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:54998435C>T			NA	NA				RP11-319F12.2 (262860 upstream) : RP11-71J2.1 (52396 downstream)						NA		NA									NA						gcaggtggatcacaaggtcaa	0.463		NA											C|||	1503	0.30012	0.2496	0.3573	5008	,	,	NA	16076	0.4514	NA	0.2873	False	NA	,,,	NA	NA	NA	2504	0.1851	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.54998435C>T		NA		hg19		0.02	-0.096488	GATxACA	UNCOVERED																																																																																			NOVEL					0			6	2.407213	KEEP	2	0	0	8	248	CC	0	0	0			4	60	116	0	0	10.584674	6	60	202	28		0.4	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	55544411	55544411	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:55544411A>G			NA	NA				RNA5SP318 (326363 upstream) : PCDH15 (18119 downstream)						NA		NA									NA						cagcactttgagaggccgagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.55544411A>G		NA		hg19		0.02	-0.131578	TTGxGAG	COVERED																																																																																			NOVEL					0			8	2.706717	KEEP	2	0	0	9	248	AA	0.99257	0.22747	0			3	60	97	0	0	8.332381	8	60	248	39		0.272727	0.229173
PCDH15	65217	__UNKNOWN__	__UNKNOWN__	10	56345327	56345327	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:56345327A>G	ENST00000373965.2	-	3	486				PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373955.1_Intron|PCDH15_ENST00000395433.1_Intron|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395438.1_Intron|RP11-257I14.1_ENST00000422842.1_RNA|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395430.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000320301.6_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395432.2_Intron	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	NA		NA			equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				TAGTTAACAAATAATTCATTC	0.318		NA								HNSCC(58;0.16)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275	65217		Cadherins / Cadherin-related	14674	protein-coding gene	gene with protein product	cadherin-related family member 15	605514	deafness, autosomal recessive 23, protocadherin 15	USH1F, DFNB23	NA	11398101, 14570705	Standard	NM_033056	NM_033056	NA	Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000373965.2:c.92-57690T>C	chr10.hg19:g.56345327A>G		NA	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	hg19		0.02	-0.342063	CAAxTAA	COVERED																																																																																			NOVEL	PCDH15-008	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000291336.1	0	2.40633	KEEP	0	0	0	8	225	AA	0.99257	0.859313	0		-	9	60	299	0	0	25.046179	30	70	908	64	ENST00000373965.2	0.230769	0.865745
PCDH15	65217	__UNKNOWN__	__UNKNOWN__	10	56521435	56521435	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:56521435T>G	ENST00000373965.2	-	1	367				PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373955.1_Intron|PCDH15_ENST00000395433.1_Intron|PCDH15_ENST00000437009.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395438.1_Intron|PCDH15_ENST00000414778.1_Intron|PCDH15_ENST00000395430.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000320301.6_Intron|PCDH15_ENST00000409834.1_Intron|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_Intron|PCDH15_ENST00000395445.1_Intron|PCDH15_ENST00000395432.2_Intron	NM_001142771.1|NM_001142772.1	NP_001136243.1|NP_001136244.1	Q96QU1	PCD15_HUMAN	protocadherin-related 15	NA		NA			equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				atagcgagactctgtctcaaa	0.423		NA								HNSCC(58;0.16)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275	65217		Cadherins / Cadherin-related	14674	protein-coding gene	gene with protein product	cadherin-related family member 15	605514	deafness, autosomal recessive 23, protocadherin 15	USH1F, DFNB23	NA	11398101, 14570705	Standard	NM_033056	NM_033056	NA	Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000373965.2:c.27+39249A>C	chr10.hg19:g.56521435T>G		NA	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	hg19		0.02	-0.105262	GACxCTG	UNCOVERED																																																																																			NOVEL	PCDH15-008	NOVEL	not_organism_supported|basic	protein_coding	NA	protein_coding	OTTHUMT00000291336.1	12	3.006279	KEEP	4	0	0	10	270	CT	0.99257	0.138793	0		-	3	44	108	0	0	10.155633	4	60	119	32	ENST00000373965.2	0.428571	0.139832
PCDH15	65217	__UNKNOWN__	__UNKNOWN__	10	56612758	56612758	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:56612758C>T	ENST00000373957.3	-	4	334							Q96QU1	PCD15_HUMAN	protocadherin-related 15	NA		NA			equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				caatggctcacgcctgtaatc	0.438		NA								HNSCC(58;0.16)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275	65217		Cadherins / Cadherin-related	14674	protein-coding gene	gene with protein product	cadherin-related family member 15	605514	deafness, autosomal recessive 23, protocadherin 15	USH1F, DFNB23	NA	11398101, 14570705	Standard	NM_033056	NM_033056	NA	Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000373957.3:c.27+44451G>A	chr10.hg19:g.56612758C>T		NA	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	hg19		0.02	-0.105263	TCAxGCC	UNCOVERED																																																																																			NOVEL	PCDH15-019	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000291346.4	6	2.707771	KEEP	2	0	0	9	267	CC	0	0	0		-	3	60	92	0	0	7.832275	8	60	257	28	ENST00000373957.3	0.272727	0.139832
TFAM	7019	__UNKNOWN__	__UNKNOWN__	10	60157794	60157794	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:60157794T>C	ENST00000487519.1	+	0	4227					NM_001270782.1|NM_003201.2	NP_001257711.1|NP_003192.1	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial	NA		NA			DNA-dependent DNA replication (GO:0006261)|gene expression (GO:0010467)|mitochondrial respiratory chain complex assembly (GO:0033108)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|mitochondrial light strand promoter sense binding (GO:0070363)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						gctgggattataggtgtgagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC018628	CCDS7253.1, CCDS59217.1	10q21	2010-09-24			ENSG00000108064	ENSG00000108064	7019			11741	protein-coding gene	gene with protein product		600438		TCF6, TCF6L2	NA	7789991	Standard	NM_003201	NM_003201	NA	Approved		uc001jkf.4	Q00059	OTTHUMG00000018270	ENST00000487519.1:c.*2960T>C	chr10.hg19:g.60157794T>C		NA	A8MRB2|A9QXC6|B5BU05|Q5U0C6	hg19	CCDS7253.1	0.02	5.879888	TTAxAGG	COVERED																																																																																			NOVEL	TFAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048146.1	59	11.145343	KEEP	1	7	204	109	2930	TT	1	1	0		+	7	60	243	1	0	15.491356	137	60	3971	386	ENST00000487519.1	0.048611	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	60751367	60751367	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:60751367G>A			NA	NA				RN7SKP196 (122079 upstream) : LINC00844 (8018 downstream)						NA		NA									NA						gattacaggcgtgagccactg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.60751367G>A		NA		hg19		0.02	1.374665	GGCxTGA	COVERED																																																																																			NOVEL					0			12	4.443931	KEEP	3	1	29	25	714	GG	0.999909	0.986064	0			5	60	147	0	0	9.857156	49	60	1599	127		0.092593	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	61327180	61327180	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:61327180T>C			NA	NA				FAM13C (204519 upstream) : RP11-135D11.2 (21727 downstream)						NA		NA									NA						gttggccgggtgcggtggctc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.61327180T>C		NA		hg19		0.02	-0.210432	GGGxGCG	COVERED																																																																																			NOVEL					0			7	5.406523	KEEP	0	0	0	18	465	TT	0.999859	0.522088	0			3	60	101	0	0	7.792435	18	60	506	60		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	61707274	61707274	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:61707274G>T			NA	NA				CCDC6 (40860 upstream) : C10orf40 (7913 downstream)						NA		NA									NA						gcgccattttggctcactgca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.61707274G>T		NA		hg19		0.02	-0.114026	TTTxGCT	UNCOVERED																																																																																			NOVEL					0			7	2.40702	KEEP	3	0	0	8	242	GG	0	0	0			3	60	83	0	0	6.931893	8	60	277	32		0.272727	0.162467
ANK3	288	__UNKNOWN__	__UNKNOWN__	10	61841122	61841122	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:61841122A>G	ENST00000280772.2	-	36	4542				ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	NA		NA			axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						ccaaagtgctaggattacagg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150	288		Ankyrin repeat domain containing	494	protein-coding gene	gene with protein product	ankyrin-3, node of Ranvier, ankyrin-G	600465			NA	7665168	Standard	NM_020987	NM_020987	NA	Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.4351-746T>C	chr10.hg19:g.61841122A>G		NA	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	hg19	CCDS7258.1	0.02	1.652595	GCTxGGA	COVERED																																																																																			NOVEL	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048201.4	20	2.569067	KEEP	4	2	61	30	802	AA	0.999997	0.999556	0		-	4	60	140	0	0	9.03933	75	60	2210	153	ENST00000280772.2	0.050633	0.999559
ANK3	288	__UNKNOWN__	__UNKNOWN__	10	62252604	62252604	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:62252604A>G	ENST00000373827.2	-	2	267				ANK3_ENST00000503366.1_Intron	NM_001204403.1	NP_001191332.1	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	NA		NA			axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						ggaggccgagacaggcagatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150	288		Ankyrin repeat domain containing	494	protein-coding gene	gene with protein product	ankyrin-3, node of Ranvier, ankyrin-G	600465			NA	7665168	Standard	NM_020987	NM_020987	NA	Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000373827.2:c.96+122339T>C	chr10.hg19:g.62252604A>G		NA	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	hg19	CCDS55712.1	0.02	-0.122793	GAGxCAG	COVERED																																																																																			NOVEL	ANK3-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359307.2	4	2.705473	KEEP	1	0	0	9	245	AA	0.99257	0.194853	0		-	3	60	96	0	0	8.101236	9	60	266	36	ENST00000373827.2	0.25	0.196312
ZNF365	22891	__UNKNOWN__	__UNKNOWN__	10	64245030	64245030	__UNKNOWN__	Intron	SNP	T	T	C	rs71472213		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:64245030T>C	ENST00000410046.3	+	4	1261					NM_199451.2	NP_955523.1	Q70YC4	TALAN_HUMAN	zinc finger protein 365	NA		NA								breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27	Prostate(12;0.0297)|all_hematologic(501;0.228)					cggtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020651	CCDS7264.1, CCDS7265.1, CCDS31209.1, CCDS41531.1	10q21.2	2008-10-28			ENSG00000138311	ENSG00000138311	22891		Zinc fingers, C2H2-type	18194	protein-coding gene	gene with protein product	Talanin	607818			NA	10048485, 12740763	Standard	NM_014951	NM_199450	NA	Approved	KIAA0844, UAN	uc001jmc.2	Q70YC4	OTTHUMG00000018302	ENST00000410046.3:c.981+25474T>C	chr10.hg19:g.64245030T>C		NA		hg19	CCDS7264.1	0.02	-0.245585	TCAxGCC	COVERED																																																																																			NOVEL	ZNF365-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277038.1	6	3.007382	KEEP	2	0	0	10	273	TT	0.99257	0.636582	0		+	3	60	99	0	0	7.349005	22	60	658	55	ENST00000410046.3	0.12	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	64855787	64855787	__UNKNOWN__	IGR	SNP	T	T	C	rs35154680	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:64855787T>C			NA	NA				EGR2 (176127 upstream) : RNU6-543P (14111 downstream)						NA		NA									NA						ctgggcaacatagcaagaccc	0.522		NA											T|||	91	0.0181709	0.0023	0.0317	5008	,	,	NA	15080	0.0	NA	0.0388	False	NA	,,,	NA	NA	NA	2504	0.0276	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.64855787T>C		NA		hg19		0.02	-0.17542	ACAxAGC	COVERED																																																																																			NOVEL					0			5	3.909724	KEEP	0	0	0	13	355	TT	0.994391	0.385234	0			3	60	100	0	0	7.76079	17	60	508	47		0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	64876939	64876939	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:64876939G>A			NA	NA				RNU6-543P (6933 upstream) : RP11-144G16.1 (6758 downstream)						NA		NA									NA						GCcctggtgcggtggctcacg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.64876939G>A		NA		hg19		0.02	-0.175389	TGCxGTG	COVERED																																																																																			NOVEL					0			14	4.812277	KEEP	1	0	0	16	461	GG	0.997832	0.386567	0			3	60	86	0	0	6.511308	15	60	448	48		0.166667	0.387407
JMJD1C	221037	__UNKNOWN__	__UNKNOWN__	10	64980658	64980658	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:64980658G>A	ENST00000399262.2	-	4	666				JMJD1C_ENST00000399251.1_Intron|JMJD1C_ENST00000489372.2_Intron|JMJD1C_ENST00000402544.1_Intron|JMJD1C_ENST00000542921.1_Intron	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	NA		NA			blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					cacaaggtcaggagatcgaga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988	221037			12313	protein-coding gene	gene with protein product		604503	thyroid hormone receptor interactor 8	TRIP8	NA	7776974	Standard	NM_004241	XM_005269624	NA	Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.448-915C>T	chr10.hg19:g.64980658G>A		NA	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	hg19	CCDS41532.1	0.02	-0.175449	TCAxGAG	COVERED																																																																																			NOVEL	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048249.2	10	3.907803	KEEP	13	0	0	13	381	GG	0.993072	0.384723	0		-	3	48	89	0	0	6.661187	17	60	588	68	ENST00000399262.2	0.15	0.387407
JMJD1C	221037	__UNKNOWN__	__UNKNOWN__	10	65040748	65040748	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:65040748T>C	ENST00000399262.2	-	3	552				JMJD1C_ENST00000399251.1_Intron	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	NA		NA			blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					gacggagtcttgctgtgtcgc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988	221037			12313	protein-coding gene	gene with protein product		604503	thyroid hormone receptor interactor 8	TRIP8	NA	7776974	Standard	NM_004241	XM_005269624	NA	Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.334-16224A>G	chr10.hg19:g.65040748T>C		NA	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	hg19	CCDS41532.1	0.02	-0.087713	TCTxGCT	UNCOVERED																																																																																			NOVEL	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048249.2	6	2.405141	KEEP	0	0	0	8	215	TT	0.99257	0.09898	0		-	3	52	100	0	0	9.133089	5	60	147	26	ENST00000399262.2	0.375	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	65248888	65248888	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:65248888A>G			NA	NA				JMJD1C-AS1 (22565 upstream) : REEP3 (32234 downstream)						NA		NA									NA						ggccgggcgcagtggctcacg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.65248888A>G		NA		hg19		0.02	-0.105257	CGCxGTG	UNCOVERED																																																																																			NOVEL					0			3	3.007661	KEEP	2	0	0	10	276	AA	0.99254	0.138789	0			3	60	102	0	0	8.832504	8	60	240	36		0.272727	0.139832
REEP3	221035	__UNKNOWN__	__UNKNOWN__	10	65330629	65330629	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:65330629C>G	ENST00000298249.4	+	2	288				REEP3_ENST00000373758.4_Intron			Q6NUK4	REEP3_HUMAN	receptor accessory protein 3	NA		NA			mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)				endometrium(1)|large_intestine(2)|lung(3)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					aatcccagcactttgggaggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC057832	CCDS44411.1	10q21.3	2011-01-05	2006-02-07	2006-02-07	ENSG00000165476	ENSG00000165476	221035		Receptor accessory proteins	23711	protein-coding gene	gene with protein product		609348	chromosome 10 open reading frame 74	C10orf74	NA	16271481, 15550249	Standard	NM_001001330	NM_001001330	NA	Approved		uc001jmt.3	Q6NUK4	OTTHUMG00000018318	ENST00000298249.4:c.60+4459C>G	chr10.hg19:g.65330629C>G		NA	Q5JQR5|Q5QGT2|Q6PEW8|Q6PJY4	hg19		0.02	-0.175448	GCAxTTT	COVERED																																																																																			NOVEL	REEP3-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000048263.3	10	2.40702	KEEP	0	0	0	8	240	CC	0.99257	0.384528	0		+	3	60	101	0	0	8.00974	15	60	521	38	ENST00000298249.4	0.166667	0.387407
RP11-222A11.1	0	__UNKNOWN__	__UNKNOWN__	10	67355200	67355200	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:67355200C>T	ENST00000433152.4	+	0	706										NA		NA									NA						ctactaacaacacaaaaatta	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000433152.4:	chr10.hg19:g.67355200C>T		NA		hg19		0.02	-0.096485	CAAxACA	UNCOVERED																																																																																			NOVEL	RP11-222A11.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000048275.4	4	2.407063	KEEP	0	0	0	8	242	CC	0.99257	0.119541	0		+	3	60	87	1	0	7.332252	8	60	258	26	ENST00000433152.4	0.272727	0.120436
CTNNA3	29119	__UNKNOWN__	__UNKNOWN__	10	68286047	68286047	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:68286047G>A	ENST00000433211.2	-	11	1549				CTNNA3_ENST00000373744.4_Intron	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						aggctcaagcgatcctcccac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230	29119			2511	protein-coding gene	gene with protein product		607667			NA	12596047, 11590244	Standard	NM_013266	XM_005269717	NA	Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1375-5516C>T	chr10.hg19:g.68286047G>A		NA		hg19	CCDS7269.1	0.02	-0.09645	AGCxATC	UNCOVERED																																																																																			NOVEL	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048282.2	4	2.707992	KEEP	0	0	0	9	275	GG	0.99254	0.119538	0		-	3	60	79	0	0	6.678387	7	60	209	30	ENST00000433211.2	0.3	0.120436
CTNNA3	29119	__UNKNOWN__	__UNKNOWN__	10	68678621	68678621	__UNKNOWN__	Intron	SNP	C	C	T	rs185642660	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:68678621C>T	ENST00000433211.2	-	8	1222				CTNNA3_ENST00000373744.4_Intron	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						Tggctgggtgcggtggctcat	0.478		NA											C|||	6	0.00119808	0.0008	0.0	5008	,	,	NA	15688	0.0	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230	29119			2511	protein-coding gene	gene with protein product		607667			NA	12596047, 11590244	Standard	NM_013266	XM_005269717	NA	Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1048-143339G>A	chr10.hg19:g.68678621C>T		NA		hg19	CCDS7269.1	0.02	-0.157883	GTGxGGT	COVERED																																																																																			NOVEL	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048282.2	7	3.910714	KEEP	7	0	0	13	375	CC	0.993072	0.32057	0		-	3	60	87	0	0	6.973004	11	60	361	56	ENST00000433211.2	0.214286	0.322807
CTNNA3	29119	__UNKNOWN__	__UNKNOWN__	10	68678664	68678664	__UNKNOWN__	Intron	SNP	C	C	T	rs569837145	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:68678664C>T	ENST00000433211.2	-	8	1222				CTNNA3_ENST00000373744.4_Intron	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						gaggctgaggcgggcagatca	0.493		NA											C|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	16362	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230	29119			2511	protein-coding gene	gene with protein product		607667			NA	12596047, 11590244	Standard	NM_013266	XM_005269717	NA	Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.1048-143382G>A	chr10.hg19:g.68678664C>T		NA		hg19	CCDS7269.1	0.02	-0.166638	AGGxGGG	COVERED																																																																																			NOVEL	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048282.2	5	3.605836	KEEP	7	0	0	12	337	CC	0.992708	0.351366	0		-	3	45	88	0	0	6.972335	12	60	405	56	ENST00000433211.2	0.2	0.353947
CTNNA3	29119	__UNKNOWN__	__UNKNOWN__	10	69267053	69267053	__UNKNOWN__	Intron	SNP	C	C	T	rs566009946	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:69267053C>T	ENST00000433211.2	-	5	754				CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000545309.1_Intron	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						tttgggaggccgaggcaggtg	0.468		NA											C|||	4	0.000798722	0.003	0.0	5008	,	,	NA	15734	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230	29119			2511	protein-coding gene	gene with protein product		607667			NA	12596047, 11590244	Standard	NM_013266	XM_005269717	NA	Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.579+14546G>A	chr10.hg19:g.69267053C>T		NA		hg19	CCDS7269.1	0.02	-0.148375	GGCxGAG	COVERED																																																																																			NOVEL	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048282.2	8	4.513506	KEEP	0	0	0	15	463	CC	0.99649	0.321674	0		-	3	60	83	0	0	6.472687	12	60	399	50	ENST00000433211.2	0.2	0.322807
CTNNA3	29119	__UNKNOWN__	__UNKNOWN__	10	69268823	69268823	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:69268823G>A	ENST00000433211.2	-	5	754				CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000545309.1_Intron	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3	NA		NA								breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						tagtagagacggggtttcacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230	29119			2511	protein-coding gene	gene with protein product		607667			NA	12596047, 11590244	Standard	NM_013266	XM_005269717	NA	Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.579+12776C>T	chr10.hg19:g.69268823G>A		NA		hg19	CCDS7269.1	0.02	-0.140327	GACxGGG	UNCOVERED																																																																																			NOVEL	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048282.2	9	2.406472	KEEP	2	0	0	8	232	GG	0	0	0		-	3	40	91	0	0	7.272508	12	60	365	29	ENST00000433211.2	0.2	0.260965
DNAJC12	56521	__UNKNOWN__	__UNKNOWN__	10	69590064	69590064	__UNKNOWN__	Intron	SNP	G	G	A	rs181186658		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:69590064G>A	ENST00000225171.2	-	2	231				DNAJC12_ENST00000483798.2_Intron|DNAJC12_ENST00000339758.7_Intron	NM_021800.2	NP_068572.1	Q9UKB3	DJC12_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 12	NA		NA								breast(2)|kidney(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	12						gcaagactccgtctcaaaaaa	0.562		NA											g|||	1	0.000199681	0.0	0.0	5008	,	,	NA	11835	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF176012	CCDS7271.1, CCDS7272.1	10q21.3	2011-09-02			ENSG00000108176	ENSG00000108176	56521		Heat shock proteins / DNAJ (HSP40)	28908	protein-coding gene	gene with protein product	J domain protein 1	606060			NA	10760603	Standard	NM_021800	NM_021800	NA	Approved	JDP1	uc001jnb.3	Q9UKB3	OTTHUMG00000018339	ENST00000225171.2:c.79-6914C>T	chr10.hg19:g.69590064G>A		NA	Q5JVQ1|Q9UKB2	hg19	CCDS7271.1	0.02	-0.175421	TCCxTCT	COVERED																																																																																			NOVEL	DNAJC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048291.1	10	2.706999	KEEP	1	0	0	9	254	GG	0.99257	0.384528	0		-	3	59	87	0	0	6.610705	15	60	488	35	ENST00000225171.2	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	69630134	69630134	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:69630134T>C			NA	NA				RP11-57G10.8 (19630 upstream) : SIRT1 (14292 downstream)						NA		NA									NA						tgaggtgaggtgggtggatca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.69630134T>C		NA		hg19		0.02	-0.061398	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			6	2.705569	KEEP	1	0	0	9	242	TT	0.99257	0.043461	0			2	60	71	0	0	6.395921	4	60	118	19		0.333333	0.043787
HERC4	26091	__UNKNOWN__	__UNKNOWN__	10	69829735	69829735	__UNKNOWN__	Intron	SNP	G	G	C	rs556259544		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:69829735G>C	ENST00000395198.3	-	3	474				HERC4_ENST00000373700.4_Intron|HERC4_ENST00000395187.2_Intron|HERC4_ENST00000412272.2_Intron|HERC4_ENST00000492996.2_3'UTR	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	NA		NA			cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						ggaggcggaggttgcagtgag	0.498		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15081	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634	26091			24521	protein-coding gene	gene with protein product		609248	hect domain and RLD 4		NA	10997877	Standard	NM_015601	NM_022079	NA	Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.226+2904C>G	chr10.hg19:g.69829735G>C		NA	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	hg19	CCDS41533.1	0.02	-0.298232	GAGxTTG	COVERED																																																																																			NOVEL	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359262.1	6	3.911141	KEEP	2	0	0	13	393	GG	0.993634	0.795151	0		-	3	60	95	0	0	6.653193	28	60	901	51	ENST00000395198.3	0.096774	0.800245
MYPN	84665	__UNKNOWN__	__UNKNOWN__	10	69873190	69873190	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:69873190T>C	ENST00000358913.5	+	1	487				MYPN_ENST00000373675.3_Intron|MYPN_ENST00000540630.1_Intron|MYPN_ENST00000354393.2_Intron	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	NA		NA			sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						cggtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347	84665		Immunoglobulin superfamily / I-set domain containing	23246	protein-coding gene	gene with protein product	sarcomeric protein myopalladin, 145 kDa	608517			NA	11309420, 12482578	Standard	NM_032578	NM_032578	NA	Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.-2+3710T>C	chr10.hg19:g.69873190T>C		NA	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	hg19	CCDS7275.1	0.02	-0.166643	TCAxGCC	COVERED																																																																																			NOVEL	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048307.1	6	3.3072	KEEP	2	0	0	11	291	TT	0.99254	0.384517	0		+	4	60	132	0	0	11.201782	12	60	347	45	ENST00000358913.5	0.25	0.387407
RUFY2	55680	__UNKNOWN__	__UNKNOWN__	10	70143144	70143144	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70143144G>A	ENST00000602465.1	-	10	1040				RUFY2_ENST00000454950.2_Intron|RUFY2_ENST00000399200.2_Intron|RUFY2_ENST00000388768.2_Intron|RUFY2_ENST00000472394.2_Intron			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	NA		NA				nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						gggaggccaagataggcagat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130	55680		Zinc fingers, FYVE domain containing	19761	protein-coding gene	gene with protein product		610328			NA	11877430	Standard	NM_017987	NM_001042417	NA	Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.939+410C>T	chr10.hg19:g.70143144G>A		NA	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	hg19		0.02	-0.175431	CAAxATA	COVERED																																																																																			NOVEL	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000467567.1	9	3.009299	KEEP	0	0	0	10	319	GG	0.992708	0.384582	0		-	3	60	86	0	0	6.592502	14	60	459	39	ENST00000602465.1	0.176471	0.387407
RUFY2	55680	__UNKNOWN__	__UNKNOWN__	10	70147527	70147527	__UNKNOWN__	Intron	SNP	C	C	T	rs200943084		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70147527C>T	ENST00000602465.1	-	8	751				RUFY2_ENST00000454950.2_Intron|RUFY2_ENST00000399200.2_Intron|RUFY2_ENST00000388768.2_Intron|RUFY2_ENST00000472394.2_Intron			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	NA		NA				nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						tttgggaggccgaggcgggca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130	55680		Zinc fingers, FYVE domain containing	19761	protein-coding gene	gene with protein product		610328			NA	11877430	Standard	NM_017987	NM_001042417	NA	Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.651-1642G>A	chr10.hg19:g.70147527C>T		NA	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	hg19		0.02	-0.157878	GGCxGAG	COVERED																																																																																			NOVEL	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000467567.1	5	2.406943	KEEP	1	0	0	8	241	CC	0.99257	0.320408	0		-	3	60	90	0	0	7.07914	13	60	415	42	ENST00000602465.1	0.1875	0.322807
SLC25A16	8034	__UNKNOWN__	__UNKNOWN__	10	70280696	70280696	__UNKNOWN__	Intron	SNP	T	T	G	rs550025035		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70280696T>G	ENST00000609923.1	-	2	229				SLC25A16_ENST00000539557.1_Intron	NM_152707.3	NP_689920.1	P16260	GDC_HUMAN	solute carrier family 25 (mitochondrial carrier), member 16	NA		NA			coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	antiporter activity (GO:0015297)			endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	7						atcgagaccatcctggctaac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M31659	CCDS7280.1	10q21.3-q22.1	2014-06-17	2014-06-17		ENSG00000122912	ENSG00000122912	8034		Solute carriers	10986	protein-coding gene	gene with protein product	Graves disease autoantigen	139080			NA	8444471, 2575220	Standard		NM_152707	NA	Approved	GDA, D10S105E, HGT.1, ML7	uc001joi.3	P16260	OTTHUMG00000018354	ENST00000609923.1:c.131-4096A>C	chr10.hg19:g.70280696T>G		NA	Q8N2U1	hg19	CCDS7280.1	0.02	-0.184168	CCAxCCT	COVERED																																																																																			NOVEL	SLC25A16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048347.2	6	3.607151	KEEP	0	0	0	12	317	TT	0.993634	0.420782	0		-	3	60	90	0	0	6.911106	15	60	446	42	ENST00000609923.1	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	70294060	70294060	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70294060C>T			NA	NA				SLC25A16 (6829 upstream) : TET1 (26352 downstream)						NA		NA									NA						gttggatcacctgaggttggg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.70294060C>T		NA		hg19		0.02	-0.11404	CACxTGA	UNCOVERED																																																																																			NOVEL					0			4	2.406428	KEEP	2	0	0	8	245	CC	0	0	0			3	60	90	0	0	7.381789	10	60	352	33		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	70296712	70296712	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70296712A>G			NA	NA				SLC25A16 (9481 upstream) : TET1 (23700 downstream)						NA		NA									NA						aaagtgctggaattacaggca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.70296712A>G		NA		hg19		0.02	-0.192954	TGGxATT	COVERED																																																																																			NOVEL					0			7	2.406026	KEEP	0	0	0	8	219	AA	0.99257	0.454356	0			3	60	90	0	0	6.693003	18	60	539	42		0.142857	0.457757
TET1	80312	__UNKNOWN__	__UNKNOWN__	10	70336985	70336985	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70336985A>G	ENST00000373644.4	+	2	2123					NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	NA		NA			chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						tgtatttttaatagagacagg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336	80312			29484	protein-coding gene	gene with protein product	leukemia-associated protein with a CXXC domain, ten-eleven translocation-1	607790	CXXC zinc finger 6, tet oncogene 1	CXXC6	NA	12124344, 12646957	Standard	NM_030625	NM_030625	NA	Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.1914+2976A>G	chr10.hg19:g.70336985A>G		NA	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	hg19	CCDS7281.1	0.02	-0.131559	TTAxTAG	COVERED																																																																																			NOVEL	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048354.1	4	2.705923	KEEP	1	0	0	9	237	AA	0.99254	0.227464	0		+	3	60	96	0	0	7.982173	10	60	292	35	ENST00000373644.4	0.230769	0.229173
TET1	80312	__UNKNOWN__	__UNKNOWN__	10	70416520	70416520	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70416520C>T	ENST00000373644.4	+	6	4670					NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	NA		NA			chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						aggtggctcacgcctgtaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336	80312			29484	protein-coding gene	gene with protein product	leukemia-associated protein with a CXXC domain, ten-eleven translocation-1	607790	CXXC zinc finger 6, tet oncogene 1	CXXC6	NA	12124344, 12646957	Standard	NM_030625	NM_030625	NA	Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4461+4169C>T	chr10.hg19:g.70416520C>T		NA	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	hg19	CCDS7281.1	0.02	-0.149118	TCAxGCC	COVERED																																																																																			NOVEL	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048354.1	11	3.0088	KEEP	1	0	0	10	300	CC	0.992708	0.289872	0		+	3	60	84	0	0	6.392313	14	60	457	36	ENST00000373644.4	0.176471	0.292001
CCAR1	55749	__UNKNOWN__	__UNKNOWN__	10	70531906	70531906	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70531906T>G	ENST00000265872.6	+	18	2657				CCAR1_ENST00000543719.1_Intron|CCAR1_ENST00000535016.1_Intron	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	NA		NA			apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						aaagtgctggtattacagatg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339	55749			24236	protein-coding gene	gene with protein product		612569			NA	12816952	Standard	NM_018237	NM_018237	NA	Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.2538+704T>G	chr10.hg19:g.70531906T>G		NA	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	hg19	CCDS7282.1	0.02	-0.22802	TGGxATT	COVERED																																																																																			NOVEL	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048356.2	10	2.705336	KEEP	0	0	0	9	233	TT	0.99254	0.607839	0		+	3	60	90	0	0	6.451023	22	60	641	49	ENST00000265872.6	0.12	0.612407
CCAR1	55749	__UNKNOWN__	__UNKNOWN__	10	70541038	70541038	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70541038A>G	ENST00000265872.6	+	20	2769				CCAR1_ENST00000543719.1_Intron|CCAR1_ENST00000535016.1_Intron	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	NA		NA			apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						ggtggctcatacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339	55749			24236	protein-coding gene	gene with protein product		612569			NA	12816952	Standard	NM_018237	NM_018237	NA	Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.2651-4855A>G	chr10.hg19:g.70541038A>G		NA	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	hg19	CCDS7282.1	0.02	-0.070155	CATxCCT	UNCOVERED																																																																																			NOVEL	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048356.2	4	3.006439	KEEP	0	0	0	10	262	AA	0.992708	0.053742	0		+	2	60	72	0	0	6.496263	4	60	107	30	ENST00000265872.6	0.333333	0.054137
STOX1	219736	__UNKNOWN__	__UNKNOWN__	10	70623946	70623946	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70623946T>C	ENST00000298596.6	+	2	393				STOX1_ENST00000399169.4_Intron|STOX1_ENST00000421961.2_Intron|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	NA		NA				cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						tcccaaagtgttgggattaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730	219736			23508	protein-coding gene	gene with protein product		609397	chromosome 10 open reading frame 24	C10orf24	NA		Standard	NM_152709	NM_152709	NA	Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.311-17768T>C	chr10.hg19:g.70623946T>C		NA	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	hg19	CCDS41535.1	0.02	-0.201692	GTGxTGG	COVERED																																																																																			NOVEL	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276849.3	4	3.910414	KEEP	2	0	0	13	366	TT	0.993072	0.487146	0		+	3	60	95	0	0	7.065848	20	60	581	55	ENST00000298596.6	0.130435	0.490544
DDX21	9188	__UNKNOWN__	__UNKNOWN__	10	70717981	70717981	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70717981C>T	ENST00000354185.4	+	2	185					NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	NA		NA			ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						ccgcccacctcggcctcccaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732	9188		DEAD-boxes	2744	protein-coding gene	gene with protein product		606357	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21, DEAD (Asp-Glu-Ala-Asp) box polypeptide 21		NA	8614622, 18180292	Standard	NM_004728	NM_004728	NA	Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.88-1581C>T	chr10.hg19:g.70717981C>T		NA	B2RDL0|Q13436|Q5VX41|Q68D35	hg19	CCDS31211.1	0.02	-0.289475	CCTxGGC	COVERED																																																																																			NOVEL	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048374.1	10	5.71556	KEEP	1	0	0	19	559	CC	0.999859	0.76078	0		+	4	60	120	0	0	8.733937	27	60	887	76	ENST00000354185.4	0.129032	0.760887
KIAA1279	26128	__UNKNOWN__	__UNKNOWN__	10	70762156	70762156	__UNKNOWN__	Intron	SNP	C	C	T	rs183469937	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70762156C>T	ENST00000361983.4	+	2	627					NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	NA		NA			cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						tcaagtgatccgcccacctca	0.498		NA											C|||	14	0.00279553	0.0098	0.0014	5008	,	,	NA	15235	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954	26128			23419	protein-coding gene	gene with protein product		609367			NA		Standard	NM_015634	NM_015634	NA	Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.525+1878C>T	chr10.hg19:g.70762156C>T		NA	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	hg19	CCDS7284.1	0.02	-0.078951	ATCxGCC	UNCOVERED																																																																																			NOVEL	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048370.1	5	3.00792	KEEP	2	0	0	10	289	CC	0.99257	0.076761	0		+	3	60	93	1	0	8.65486	4	60	136	29	ENST00000361983.4	0.428571	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	70842916	70842916	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:70842916A>G			NA	NA				KIAA1279 (66178 upstream) : SRGN (4945 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.70842916A>G		NA		hg19		0.02	-0.166637	GGCxTGA	COVERED																																																																																			NOVEL					0			3	2.706659	KEEP	0	0	0	9	247	AA	0.99254	0.351306	0			3	60	103	0	0	8.291797	14	60	400	42		0.176471	0.353947
HK1	3098	__UNKNOWN__	__UNKNOWN__	10	71108304	71108304	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71108304T>C	ENST00000359426.6	+	2	330				HK1_ENST00000404387.2_Intron|HK1_ENST00000494253.1_Intron|HK1_ENST00000448642.2_Intron|HK1_ENST00000360289.2_Intron|HK1_ENST00000298649.3_Intron	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						cggtggctcatgcctgtaatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	3098	2.7.1.1		4922	protein-coding gene	gene with protein product		142600			NA		Standard	NM_000188	NM_033496	NA	Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.226+4559T>C	chr10.hg19:g.71108304T>C		NA	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	hg19	CCDS7292.1	0.02	-0.105251	TCAxGCC	UNCOVERED																																																																																			NOVEL	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048429.2	3	2.706195	KEEP	1	0	0	9	240	TT	0.99257	0.138793	0		+	3	60	97	0	0	8.332594	8	60	236	29	ENST00000359426.6	0.272727	0.139832
HK1	3098	__UNKNOWN__	__UNKNOWN__	10	71152831	71152831	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71152831G>A	ENST00000359426.6	+	15	2323				HK1_ENST00000404387.2_Intron|HK1_ENST00000448642.2_Intron|HK1_ENST00000360289.2_Intron|HK1_ENST00000298649.3_Intron	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						tccacctcccgggttcaagca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	3098	2.7.1.1		4922	protein-coding gene	gene with protein product		142600			NA		Standard	NM_000188	NM_033496	NA	Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.2219+767G>A	chr10.hg19:g.71152831G>A		NA	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	hg19	CCDS7292.1	0.02	-0.12279	CCCxGGT	COVERED																																																																																			NOVEL	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048429.2	7	2.707571	KEEP	1	0	0	9	267	GG	0.99257	0.194853	0		+	3	60	83	1	0	6.801132	9	60	286	28	ENST00000359426.6	0.25	0.196312
RP11-343J3.2	0	__UNKNOWN__	__UNKNOWN__	10	71335580	71335580	__UNKNOWN__	RNA	SNP	T	T	C	rs375949009|rs145552653		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71335580T>C	ENST00000428753.1	+	0	18										NA		NA									NA						cctcctcctcttcttcttctt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000428753.1:	chr10.hg19:g.71335580T>C		NA		hg19		0.02	-0.166578	CTCxTCT	COVERED																																																																																			NOVEL	RP11-343J3.2-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000048457.1	3	2.706861	KEEP	4	0	0	9	251	TT	0.99257	0.351317	0		+	4	60	129	0	0	10.668405	14	60	422	48	ENST00000428753.1	0.222222	0.353947
RP11-343J3.2	0	__UNKNOWN__	__UNKNOWN__	10	71335583	71335583	__UNKNOWN__	RNA	SNP	T	T	C	rs375949009|rs138755888		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71335583T>C	ENST00000428753.1	+	0	21										NA		NA									NA						cctcctcttcttcttcttctt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000428753.1:	chr10.hg19:g.71335583T>C		NA		hg19		0.02	-0.1661	TTCxTCT	COVERED																																																																																			NOVEL	RP11-343J3.2-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000048457.1	2	2.707223	KEEP	4	0	0	9	254	TT	0.99257	0.351317	0		+	4	60	135	0	0	11.268351	14	60	421	48	ENST00000428753.1	0.222222	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	71438790	71438790	__UNKNOWN__	IGR	SNP	A	A	G	rs2927383	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71438790A>G			NA	NA				C10orf35 (45438 upstream) : RP11-242G20.1 (5864 downstream)						NA		NA									NA						aggctgaggcaggcggatcac	0.493		NA											G|||	4812	0.960863	0.8585	0.987	5008	,	,	NA	16326	1.0	NA	1.0	False	NA	,,,	NA	NA	NA	2504	1.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.71438790A>G		NA		hg19		0.02	-0.043857	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			6	2.406488	KEEP	9	0	0	8	227	AA	0	0	0			2	40	70	0	0	6.750262	2	43	59	29		0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	71946948	71946948	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71946948C>T			NA	NA				SAR1A (16669 upstream) : PPA1 (15637 downstream)						NA		NA									NA						ctcctgacctcgtgatctgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.71946948C>T		NA		hg19		0.02	-0.131571	CCTxGTG	UNCOVERED																																																																																			NOVEL					0			10	2.707165	KEEP	8	0	0	9	263	CC	0	0	0			3	60	90	0	0	7.172359	12	60	385	45		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	71954587	71954587	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71954587C>G			NA	NA				SAR1A (24308 upstream) : PPA1 (7998 downstream)						NA		NA									NA						ctcactgcaacctccgcctcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.71954587C>G		NA		hg19		0.02	-0.087718	CAAxCTC	UNCOVERED																																																																																			NOVEL					0			17	4.807013	KEEP	9	0	0	16	454	CC	0.995343	0.119875	0			4	60	126	0	0	12.099867	4	60	129	41		0.5	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	71955396	71955396	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71955396T>C			NA	NA				SAR1A (25117 upstream) : PPA1 (7189 downstream)						NA		NA									NA						gaggccgaggtgggtggatca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.71955396T>C		NA		hg19		0.02	-0.078942	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			7	2.405072	KEEP	4	0	0	8	218	TT	0	0	0			2	60	73	0	0	6.300804	6	60	182	28		0.25	0.077336
PPA1	5464	__UNKNOWN__	__UNKNOWN__	10	71989956	71989956	__UNKNOWN__	Intron	SNP	C	C	T	rs371023462	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:71989956C>T	ENST00000373232.3	-	2	223				PPA1_ENST00000495346.1_Intron|PPA1_ENST00000608321.1_Intron	NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	NA		NA			diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						tgagccaccacgcccagccTA	0.493		NA											C|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	18480	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	5464	3.6.1.1		9226	protein-coding gene	gene with protein product	cytosolic inorganic pyrophosphatase, inorganic pyrophosphatase 1, pyrophosphate phospho-hydrolase	179030	pyrophosphatase (inorganic)	PP	NA	10542310, 975879	Standard	NM_021129	NM_021129	NA	Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.123+140G>A	chr10.hg19:g.71989956C>T		NA	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	hg19	CCDS7299.1	0.02	-0.429823	CCAxGCC	COVERED																																																																																			NOVEL	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048490.2	8	7.821254	KEEP	1	0	0	26	752	CC	0.999957	0.95445	0		-	4	60	119	0	0	7.91209	42	60	1387	108	ENST00000373232.3	0.086957	0.954491
ADAMTS14	140766	__UNKNOWN__	__UNKNOWN__	10	72469508	72469508	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:72469508A>G	ENST00000373208.1	+	4	870				ADAMTS14_ENST00000373207.1_Intron	NM_139155.2	NP_631894.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	NA		NA			collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						cgcccgcctcagcctcccaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316	140766		ADAM metallopeptidases with thrombospondin type 1 motif	14899	protein-coding gene	gene with protein product		607506	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14		NA	11779638	Standard	NM_080722	NM_139155	NA	Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373208.1:c.870+974A>G	chr10.hg19:g.72469508A>G		NA	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	hg19	CCDS7307.1	0.02	-0.236816	CTCxGCC	UNCOVERED																																																																																			NOVEL	ADAMTS14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048521.1	9	2.707003	KEEP	4	0	0	9	250	AA	0	0	0		+	3	60	105	0	0	7.894287	23	60	690	53	ENST00000373208.1	0.115385	0.612407
SGPL1	8879	__UNKNOWN__	__UNKNOWN__	10	72633282	72633282	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:72633282G>A	ENST00000373202.3	+	12	1434	c.1234G>A	c.(1234-1236)Ggt>Agt	p.G412S		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	412		NA			androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)			large_intestine(4)	4						GATGCACTTCGGTGAGAACGG	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(151;1054 2458 6676 40971)							NA				0													141	125	131			NA	NA	10		NA											NA				72633282		2203	4300	6503	SO:0001583	missense			AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224	8879			10817	protein-coding gene	gene with protein product		603729			NA	9464245, 17090686	Standard	NM_003901	NM_003901	NA	Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.1234G>A	chr10.hg19:g.72633282G>A	ENSP00000362298:p.Gly412Ser	NA	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	hg19	CCDS31216.1	0.02	1.377074	TTCxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	36	5.748353	0.96882	.	.	ENSG00000166224	ENST00000373202	T	0.78364	-1.17	5.73	5.73	0.89815	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.91994	0.7464	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93555	0.6890	10	0.87932	D	0	-16.8428	19.9064	0.97008	0.0:0.0:1.0:0.0	.	412	O95470	SGPL1_HUMAN	S	412	ENSP00000362298:G412S	ENSP00000362298:G412S	G	+	1	0	SGPL1	72303288	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.615000	0.83006	2.693000	0.91896	0.655000	0.94253	GGT	NOVEL	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048533.1	0	3.0085	KEEP	0	0	0	10	298	GG	0.992708	0.989456	0		+	4	60	126	0	0	7.881367	65	60	2125	118	ENST00000373202.3	0.057971	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	73136815	73136815	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:73136815G>A			NA	NA				SLC29A3 (13673 upstream) : CDH23 (19875 downstream)						NA		NA									NA						gagccaccgcgcccggccCTG	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.73136815G>A		NA		hg19		0.02	-0.131583	CGCxCCC	COVERED																																																																																			NOVEL					0			2	2.406461	KEEP	0	0	0	8	230	GG	0.99257	0.22747	0			3	60	92	0	0	7.372137	12	60	401	37		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	73613467	73613467	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:73613467G>A			NA	NA				PSAP (2341 upstream) : RP11-472G21.2 (24646 downstream)						NA		NA									NA						tgcctgccttggcctcccaaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.73613467G>A		NA		hg19		0.02	-0.149124	CTTxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.406698	KEEP	1	0	0	8	239	GG	0	0	0			3	60	82	0	0	6.581906	10	60	344	38		0.230769	0.292001
ASCC1	51008	__UNKNOWN__	__UNKNOWN__	10	73891895	73891895	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:73891895A>G	ENST00000394919.1	-	8	1059				ASCC1_ENST00000342444.4_Intron|ASCC1_ENST00000394915.3_Intron|ASCC1_ENST00000317126.4_Intron|ASCC1_ENST00000545550.1_Intron|ASCC1_ENST00000317168.6_Intron	NM_001198798.2	NP_001185727.1	Q8N9N2	ASCC1_HUMAN	activating signal cointegrator 1 complex subunit 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|transcription factor complex (GO:0005667)	catalytic activity (GO:0003824)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	7						ccaaagtgctaggattacagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY013290	CCDS31219.1, CCDS55713.1	10q22.1	2012-09-20			ENSG00000138303	ENSG00000138303	51008			24268	protein-coding gene	gene with protein product		614215			NA	10810093, 12077347	Standard	NM_015947	NM_001198799	NA	Approved	CGI-18, ASC1p50, Em:AC022392.3	uc001jst.2	Q8N9N2	OTTHUMG00000018434	ENST00000394919.1:c.871+919T>C	chr10.hg19:g.73891895A>G		NA	Q5SW06|Q5SW07|Q96EI8|Q9Y307	hg19	CCDS31219.1	0.02	-0.11401	GCTxGGA	UNCOVERED																																																																																			NOVEL	ASCC1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384352.1	2	3.307717	KEEP	0	0	0	11	295	AA	0.993072	0.161341	0		-	3	60	106	0	0	9.101513	9	60	263	34	ENST00000394919.1	0.25	0.162467
ASCC1	51008	__UNKNOWN__	__UNKNOWN__	10	73913436	73913436	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:73913436A>G	ENST00000394919.1	-	7	814				ASCC1_ENST00000342444.4_Intron|ASCC1_ENST00000394915.3_Intron|ASCC1_ENST00000317126.4_Intron|ASCC1_ENST00000545550.1_Intron|ASCC1_ENST00000317168.6_Intron	NM_001198798.2	NP_001185727.1	Q8N9N2	ASCC1_HUMAN	activating signal cointegrator 1 complex subunit 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|transcription factor complex (GO:0005667)	catalytic activity (GO:0003824)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	7						tgcccgcctcagcctcccaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY013290	CCDS31219.1, CCDS55713.1	10q22.1	2012-09-20			ENSG00000138303	ENSG00000138303	51008			24268	protein-coding gene	gene with protein product		614215			NA	10810093, 12077347	Standard	NM_015947	NM_001198799	NA	Approved	CGI-18, ASC1p50, Em:AC022392.3	uc001jst.2	Q8N9N2	OTTHUMG00000018434	ENST00000394919.1:c.627-690T>C	chr10.hg19:g.73913436A>G		NA	Q5SW06|Q5SW07|Q96EI8|Q9Y307	hg19	CCDS31219.1	0.02	-0.157889	CTCxGCC	COVERED																																																																																			NOVEL	ASCC1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384352.1	7	3.609432	KEEP	4	0	0	12	334	AA	0.99254	0.320398	0		-	3	51	108	0	0	8.8786	13	60	399	46	ENST00000394919.1	0.1875	0.322807
OIT3	170392	__UNKNOWN__	__UNKNOWN__	10	74687144	74687144	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:74687144T>C	ENST00000334011.5	+	7	1585					NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	NA		NA				nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					gtgatccacctgcctcggcct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(7;19 345 13446 17537)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315	170392			29953	protein-coding gene	gene with protein product		609330			NA	12975309, 12939600	Standard	NM_152635	NM_152635	NA	Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.1367+2742T>C	chr10.hg19:g.74687144T>C		NA	A0AVP3|Q8N1M8	hg19	CCDS7318.1	0.02	-0.131554	ACCxGCC	COVERED																																																																																			NOVEL	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048596.1	5	2.405954	KEEP	0	0	0	8	219	TT	0.99257	0.22747	0		+	3	60	92	1	0	7.701423	9	60	261	36	ENST00000334011.5	0.25	0.229173
USP54	159195	__UNKNOWN__	__UNKNOWN__	10	75318996	75318996	__UNKNOWN__	Intron	SNP	C	C	T	rs549256253		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75318996C>T	ENST00000339859.4	-	3	341				USP54_ENST00000319786.7_Intron|USP54_ENST00000394811.2_Intron|USP54_ENST00000408019.1_Intron|USP54_ENST00000428547.1_Intron			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	NA		NA			ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					ccggccaacacggtgaaaccc	0.542		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	14124	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Colon(195;880 2046 8854 25025 38456)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348	159195		Ubiquitin-specific peptidases	23513	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 29, ubiquitin specific protease 54	C10orf29	NA	14715245	Standard	NM_152586	NM_152586	NA	Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.240+12182G>A	chr10.hg19:g.75318996C>T		NA	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	hg19	CCDS7329.2	0.02	-0.166657	ACAxGGT	COVERED																																																																																			NOVEL	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316563.2	8	3.309421	KEEP	0	0	0	11	326	CC	0.993072	0.351495	0		-	3	59	85	0	0	6.579239	13	60	419	39	ENST00000339859.4	0.1875	0.353947
USP54	159195	__UNKNOWN__	__UNKNOWN__	10	75363997	75363997	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75363997G>C	ENST00000339859.4	-	1	84							Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	NA		NA			ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(5)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	30	Prostate(51;0.0112)					cagagcgagagtccatctcaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(195;880 2046 8854 25025 38456)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ583820	CCDS7329.2	10q22.3	2006-09-26	2005-08-08	2004-01-30	ENSG00000166348	ENSG00000166348	159195		Ubiquitin-specific peptidases	23513	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 29, ubiquitin specific protease 54	C10orf29	NA	14715245	Standard	NM_152586	NM_152586	NA	Approved	FLJ37318, bA137L10.3, bA137L10.4	uc001juo.3	Q70EL1	OTTHUMG00000018469	ENST00000339859.4:c.16+21327C>G	chr10.hg19:g.75363997G>C		NA	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	hg19	CCDS7329.2	0.02	-0.166666	AGAxTCC	COVERED																																																																																			NOVEL	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316563.2	6	3.610728	KEEP	0	0	0	12	369	GG	0.993634	0.351693	0		-	3	60	96	0	0	7.591929	14	60	483	49	ENST00000339859.4	0.176471	0.353947
ZSWIM8	23053	__UNKNOWN__	__UNKNOWN__	10	75555964	75555964	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75555964G>A	ENST00000605216.1	+	15	3235				ZSWIM8_ENST00000604524.1_Intron|ZSWIM8_ENST00000603114.1_Intron|ZSWIM8_ENST00000604729.1_Intron|ZSWIM8_ENST00000398706.2_Intron	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	NA		NA					zinc ion binding (GO:0008270)				NA						aaaattagccgggcatggtgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655	23053		Zinc fingers, SWIM-type	23528	protein-coding gene	gene with protein product		NA	KIAA0913	KIAA0913	NA		Standard	NM_001242487	NM_015037	NA	Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.3018+543G>A	chr10.hg19:g.75555964G>A		NA	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	hg19		0.02	-0.131518	GCCxGGC	COVERED																																																																																			NOVEL	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000468545.1	13	3.609606	KEEP	3	0	0	12	346	GG	0.993072	0.227586	0		+	3	60	87	0	0	7.201824	9	60	280	35	ENST00000605216.1	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	75668343	75668343	__UNKNOWN__	IGR	SNP	A	A	G	rs528523847		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75668343A>G			NA	NA				CAMK2G (34000 upstream) : C10orf55 (1383 downstream)						NA		NA									NA						GGggccgggcacggtggctca	0.488		NA											A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	14718	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.75668343A>G		NA		hg19		0.02	-0.245545	GGCxCGG	UNCOVERED																																																																																			NOVEL					0			16	3.004371	KEEP	6	0	0	10	256	AA	0	0	0			3	60	94	0	0	6.796495	23	60	669	57		0.115385	0.641347
VCL	7414	__UNKNOWN__	__UNKNOWN__	10	75817445	75817445	__UNKNOWN__	Intron	SNP	T	T	C	rs542748129		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75817445T>C	ENST00000372755.3	+	3	333				VCL_ENST00000478896.2_Intron|VCL_ENST00000417648.2_Intron|VCL_ENST00000211998.4_Intron	NM_003373.3	NP_003364.1	P18206	VINC_HUMAN	vinculin	NA		NA			adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					atcccagcactttgggaggct	0.438		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	19207	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403	7414			12665	protein-coding gene	gene with protein product	metavinculin	193065			NA	1339348	Standard	NM_003373, NM_014000	NM_014000	NA	Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000372755.3:c.240-12983T>C	chr10.hg19:g.75817445T>C		NA	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	hg19	CCDS7340.1	0.02	-0.184198	CACxTTG	COVERED																																																																																			NOVEL	VCL-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048751.1	4	2.706811	KEEP	0	0	0	9	248	TT	0.99254	0.420319	0		+	3	60	96	0	0	7.360901	17	60	521	44	ENST00000372755.3	0.15	0.423478
VCL	7414	__UNKNOWN__	__UNKNOWN__	10	75865643	75865643	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75865643T>C	ENST00000372755.3	+	16	2528				VCL_ENST00000417648.2_Intron|VCL_ENST00000211998.4_Intron	NM_003373.3	NP_003364.1	P18206	VINC_HUMAN	vinculin	NA		NA			adherens junction assembly (GO:0034333)|apical junction assembly (GO:0043297)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|epithelial cell-cell adhesion (GO:0090136)|lamellipodium assembly (GO:0030032)|morphogenesis of an epithelium (GO:0002009)|muscle contraction (GO:0006936)|negative regulation of cell migration (GO:0030336)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|protein localization to cell surface (GO:0034394)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cell-substrate junction (GO:0030055)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	actin binding (GO:0003779)|alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)		VCL/ALK(4)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	20	Prostate(51;0.0112)					ggattacaggtgtgagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M33308	CCDS7340.1, CCDS7341.1	10q22.1-q23	2014-09-17			ENSG00000035403	ENSG00000035403	7414			12665	protein-coding gene	gene with protein product	metavinculin	193065			NA	1339348	Standard	NM_003373, NM_014000	NM_014000	NA	Approved		uc001jwd.3	P18206	OTTHUMG00000018498	ENST00000372755.3:c.2434+532T>C	chr10.hg19:g.75865643T>C		NA	Q16450|Q5SWX2|Q7Z3B8|Q8IXU7	hg19	CCDS7340.1	0.02	-0.43828	AGGxGTG	COVERED																																																																																			NOVEL	VCL-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048751.1	22	9.019092	KEEP	1	0	0	30	782	TT	0.999997	0.959856	0		+	3	60	96	0	0	6.628135	31	60	867	113	ENST00000372755.3	0.088235	0.959859
AP3M1	26985	__UNKNOWN__	__UNKNOWN__	10	75891589	75891589	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:75891589C>T	ENST00000355264.4	-	5	895				AP3M1_ENST00000372745.1_Intron	NM_012095.4	NP_036227.1	Q9Y2T2	AP3M1_HUMAN	adaptor-related protein complex 3, mu 1 subunit	NA		NA			anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|protein targeting to lysosome (GO:0006622)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	Rab GTPase binding (GO:0017137)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	13	Prostate(51;0.0112)					tgtgagccaccgtgcctggcA	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF092092	CCDS7342.1	10q22.1-q22.3	2008-07-07			ENSG00000185009	ENSG00000185009	26985			569	protein-coding gene	gene with protein product		610366			NA	10024875	Standard		NM_207012	NA	Approved		uc001jwh.3	Q9Y2T2	OTTHUMG00000018497	ENST00000355264.4:c.584-1839G>A	chr10.hg19:g.75891589C>T		NA	Q5JQ12|Q9H5L2	hg19	CCDS7342.1	0.02	-0.140331	CACxGTG	COVERED																																																																																			NOVEL	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048747.1	2	3.007853	KEEP	0	0	0	10	284	CC	0.992708	0.259062	0		-	3	60	90	0	0	7.079166	13	60	394	33	ENST00000355264.4	0.1875	0.260965
ADK	132	__UNKNOWN__	__UNKNOWN__	10	76454498	76454498	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:76454498A>C	ENST00000286621.2	+	11	1014				ADK_ENST00000541550.1_Intron|ADK_ENST00000372734.3_Intron|ADK_ENST00000539909.1_Intron	NM_006721.3	NP_006712.2	P55263	ADK_HUMAN	adenosine kinase	NA		NA			adenosine metabolic process (GO:0046085)|AMP salvage (GO:0044209)|circadian regulation of gene expression (GO:0032922)|dATP biosynthetic process (GO:0006175)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of T cell proliferation (GO:0042102)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenosine kinase activity (GO:0004001)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	8	Prostate(51;0.0112)|Ovarian(15;0.148)				Abacavir(DB01048)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Adenosine(DB00640)|Ribavirin(DB00811)	cctcaacctcacaaagtgctg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U50196	CCDS7343.1, CCDS7344.1, CCDS55716.1, CCDS55717.1	10q22.2	2006-02-21			ENSG00000156110	ENSG00000156110	132	2.7.1.20		257	protein-coding gene	gene with protein product	adenosine 5'-phosphotransferase	102750			NA	8577746	Standard	NM_001123, NM_006721	NM_001123	NA	Approved	AK	uc001jwi.3	P55263	OTTHUMG00000018506	ENST00000286621.2:c.965-13581A>C	chr10.hg19:g.76454498A>C		NA	B7Z783|B7Z800|O00741|O00742|Q16710|Q5JQ10|Q5JQ11|Q9BTN2	hg19	CCDS7343.1	0.02	-0.219242	CTCxCAA	COVERED																																																																																			NOVEL	ADK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048763.1	2	3.607598	KEEP	0	0	0	12	313	AA	0.993634	0.549368	0		+	3	60	93	0	0	6.866379	20	60	580	53	ENST00000286621.2	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	76478952	76478952	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:76478952T>C			NA	NA				ADK (9891 upstream) : RP11-222G7.2 (102415 downstream)						NA		NA									NA						cctcccaccttagcctccaaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.76478952T>C		NA		hg19		0.02	-0.184167	CCTxAGC	COVERED																																																																																			NOVEL					0			11	3.006245	KEEP	0	0	0	10	262	TT	0.992708	0.42039	0			3	60	98	0	0	7.492393	18	60	524	42		0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	77196499	77196499	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:77196499C>T			NA	NA				RP11-399K21.10 (5153 upstream) : MIR606 (115716 downstream)						NA		NA									NA						agtgctgggactacaggcatg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.77196499C>T		NA		hg19		0.02	-0.184219	GGAxTAC	COVERED																																																																																			NOVEL					0			6	2.407259	KEEP	0	0	0	8	247	AC	0.99254	0.420319	0			4	60	122	0	0	9.968136	14	60	478	40		0.222222	0.423478
C10orf11	83938	__UNKNOWN__	__UNKNOWN__	10	77554892	77554892	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:77554892A>G	ENST00000372499.1	+	1	262				C10orf11_ENST00000593699.1_Intron	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	NA		NA			melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					agtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655	83938			23405	protein-coding gene	gene with protein product	oculocutaneous albinism 7, autosomal recessive	614537			NA	23395477	Standard	NM_032024	NM_032024	NA	Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.47+12112A>G	chr10.hg19:g.77554892A>G		NA	B1AVW6	hg19	CCDS7351.1	0.02	-0.140342	CACxCCT	COVERED																																																																																			NOVEL	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048839.1	7	2.707003	KEEP	4	0	0	9	252	AA	0.99257	0.259026	0		+	3	29	94	0	0	7.672852	11	60	339	37	ENST00000372499.1	0.214286	0.260965
C10orf11	83938	__UNKNOWN__	__UNKNOWN__	10	77554903	77554903	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:77554903C>T	ENST00000372499.1	+	1	262				C10orf11_ENST00000593699.1_Intron	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	NA		NA			melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					cctgtaatcccagcactttgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655	83938			23405	protein-coding gene	gene with protein product	oculocutaneous albinism 7, autosomal recessive	614537			NA	23395477	Standard	NM_032024	NM_032024	NA	Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.47+12123C>T	chr10.hg19:g.77554903C>T		NA	B1AVW6	hg19	CCDS7351.1	0.02	-0.149122	TCCxAGC	COVERED																																																																																			NOVEL	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048839.1	8	3.309762	KEEP	5	0	0	11	334	CC	0.99254	0.289823	0		+	3	40	84	1	0	6.572476	12	60	400	41	ENST00000372499.1	0.2	0.292001
KCNMA1	3778	__UNKNOWN__	__UNKNOWN__	10	78943402	78943402	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:78943402G>A	ENST00000286627.5	-	5	1649				KCNMA1_ENST00000372443.1_Intron|KCNMA1_ENST00000372440.1_Intron|KCNMA1_ENST00000404857.1_Intron|KCNMA1_ENST00000406533.3_Intron|KCNMA1_ENST00000286628.8_Intron|KCNMA1_ENST00000354353.5_Intron|KCNMA1_ENST00000404771.3_Intron	NM_001271519.1|NM_002247.3	NP_001258448.1|NP_002238.2	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	NA		NA			blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	GGgccaccacgcccggctaat	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113	3778		Potassium channels, Voltage-gated ion channels / Potassium channels, calcium-activated	6284	protein-coding gene	gene with protein product	BK channel alpha subunit	600150		SLO	NA	7987297, 16382103	Standard	NM_002247	NM_002247	NA	Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286627.5:c.697-112C>T	chr10.hg19:g.78943402G>A		NA	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	hg19	CCDS7352.1	0.02	-0.333326	CACxCCC	COVERED																																																																																			NOVEL	KCNMA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048877.3	4	3.61052	KEEP	0	0	0	12	361	GG	0.993634	0.84656	0		-	4	60	112	1	0	7.819906	29	60	947	61	ENST00000286627.5	0.121212	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	79485641	79485641	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:79485641C>T			NA	NA				KCNMA1 (87288 upstream) : RNU6-1266P (51067 downstream)						NA		NA									NA						gccgagatcgcgccattgcac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.79485641C>T		NA		hg19		0.02	-0.096485	TCGxGCC	UNCOVERED																																																																																			NOVEL					0			6	2.708235	KEEP	0	0	0	9	280	CC	0.99254	0.119538	0			3	60	86	0	0	7.73223	5	60	170	30		0.375	0.120436
POLR3A	11128	__UNKNOWN__	__UNKNOWN__	10	79738709	79738709	__UNKNOWN__	Intron	SNP	C	C	T	rs541880193		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:79738709C>T	ENST00000372371.3	-	30	4162					NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	NA		NA			defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			cgtgagccaccgcgcccggcc	0.532		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	13606	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606	11128		RNA polymerase subunits	30074	protein-coding gene	gene with protein product		614258			NA	9331371, 12391170	Standard	NM_007055	NM_007055	NA	Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.4024+1189G>A	chr10.hg19:g.79738709C>T		NA	Q8IW34|Q8TCW5	hg19	CCDS7354.1	0.02	-0.236837	CACxGCG	COVERED																																																																																			NOVEL	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048923.1	17	3.911075	KEEP	7	0	0	13	385	CC	0.993072	0.636904	0		-	3	60	88	0	0	6.306944	21	60	680	64	ENST00000372371.3	0.125	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	81225548	81225548	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:81225548A>G			NA	NA				ZCCHC24 (20165 upstream) : RP11-342M3.1 (38280 downstream)						NA		NA									NA						ggaggctgagacgggcggatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.81225548A>G		NA		hg19		0.02	-0.201736	GAGxCGG	UNCOVERED																																																																																			NOVEL					0			8	2.706966	KEEP	8	0	0	9	251	AA	0	0	0			3	37	100	0	0	7.833288	16	60	480	54		0.157895	0.490544
TMEM254-AS1	219347	__UNKNOWN__	__UNKNOWN__	10	81816795	81816795	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:81816795T>A	ENST00000412298.1	-	0	313				TMEM254-AS1_ENST00000432070.2_RNA|TMEM254-AS1_ENST00000448729.2_RNA	NR_027428.1				TMEM254 antisense RNA 1	NA		NA									NA						aggctgaggctggagaatata	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							10q22.3	2012-11-15			ENSG00000230091	ENSG00000230091	219347		Long non-coding RNAs	27340	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_027428	NA	Approved		uc001kbi.4		OTTHUMG00000018601	ENST00000412298.1:	chr10.hg19:g.81816795T>A		NA		hg19		0.02	-0.13156	GGCxGGA	COVERED																																																																																			NOVEL	TMEM254-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000049027.1	3	3.00828	KEEP	2	0	0	10	288	TT	0.99254	0.227464	0		-	4	60	114	0	0	9.671006	10	60	306	40	ENST00000412298.1	0.285714	0.229173
TMEM254	80195	__UNKNOWN__	__UNKNOWN__	10	81844854	81844854	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:81844854A>G	ENST00000372281.3	+	3	281				TMEM254_ENST00000372274.1_Intron|TMEM254_ENST00000467529.1_Intron|TMEM254_ENST00000372275.1_Intron|TMEM254_ENST00000372277.3_Intron	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	NA		NA				integral component of membrane (GO:0016021)					NA						gggattacagacgtgagccac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678	80195			25804	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 57	C10orf57	NA	14702039	Standard	NM_025125	NM_025125	NA	Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.251+2894A>G	chr10.hg19:g.81844854A>G		NA	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	hg19	CCDS7363.1	0.02	-0.219279	CAGxCGT	COVERED																																																																																			NOVEL	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049030.1	8	3.006887	KEEP	0	0	0	10	265	AA	0.992708	0.548856	0		+	3	60	104	0	0	8.309891	15	60	458	49	ENST00000372281.3	0.166667	0.552887
ANXA11	311	__UNKNOWN__	__UNKNOWN__	10	81913880	81913880	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:81913880A>G	ENST00000438331.1	-	0	3729				ANXA11_ENST00000372231.3_3'UTR	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	NA		NA			cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			tttttgagacagagtctcact	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359	311		Annexins	535	protein-coding gene	gene with protein product		602572		ANX11	NA	7508441, 9503022	Standard	NM_145869	NM_001157	NA	Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.*1729T>C	chr10.hg19:g.81913880A>G		NA	B4DVE7	hg19	CCDS7364.1	0.02	4.809184	GACxGAG	COVERED																																																																																			NOVEL	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049044.1	60	29.336482	KEEP	1	6	171	158	4176	AA	1	1	0		-	6	60	196	1	0	11.346416	155	70	4503	523	ENST00000438331.1	0.037267	1
ANXA11	311	__UNKNOWN__	__UNKNOWN__	10	81950607	81950607	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:81950607A>G	ENST00000438331.1	-	2	230				ANXA11_ENST00000537102.1_Intron|ANXA11_ENST00000463657.1_Intron|ANXA11_ENST00000422982.3_Intron|ANXA11_ENST00000372231.3_Intron|ANXA11_ENST00000360615.4_Intron|ANXA11_ENST00000535999.1_Intron|ANXA11_ENST00000265447.4_Intron	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	NA		NA			cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			agcactttggaaggccaaggt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359	311		Annexins	535	protein-coding gene	gene with protein product		602572		ANX11	NA	7508441, 9503022	Standard	NM_145869	NM_001157	NA	Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.253-9715T>C	chr10.hg19:g.81950607A>G		NA	B4DVE7	hg19	CCDS7364.1	0.02	-0.175439	TGGxAGG	COVERED																																																																																			NOVEL	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049044.1	9	3.008611	KEEP	1	0	0	10	295	AA	0.99254	0.384517	0		-	3	60	107	0	0	8.532951	16	60	505	43	ENST00000438331.1	0.157895	0.387407
NRG3	10718	__UNKNOWN__	__UNKNOWN__	10	83967433	83967433	__UNKNOWN__	Intron	SNP	C	C	T	rs10748922	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:83967433C>T	ENST00000372141.2	+	2	850				NRG3_ENST00000404576.2_Intron|NRG3_ENST00000404547.1_Intron|NRG3_ENST00000372142.2_Intron|NRG3_ENST00000556918.1_Intron	NM_001010848.3|NM_001165972.1	NP_001010848.2|NP_001159444.1	P56975	NRG3_HUMAN	neuregulin 3	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		tgggaaggctcaggaaacaca	0.483		NA											C|||	2241	0.447484	0.3797	0.4452	5008	,	,	NA	18683	0.2827	NA	0.6481	False	NA	,,,	NA	NA	NA	2504	0.5041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737	10718			7999	protein-coding gene	gene with protein product		605533			NA	9275162	Standard	XM_166086	NM_001010848	NA	Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000372141.2:c.824-151062C>T	chr10.hg19:g.83967433C>T		NA	A4D7U1|Q0PEH2|Q5VYH3	hg19	CCDS31233.1	0.02	-0.105257	GCTxAGG	UNCOVERED																																																																																			NOVEL	NRG3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412261.1	5	2.407125	KEEP	1	0	0	8	244	CC	0.99257	0.138793	0		+	3	60	87	0	0	7.47828	7	60	230	27	ENST00000372141.2	0.3	0.139832
NRG3	10718	__UNKNOWN__	__UNKNOWN__	10	83967446	83967446	__UNKNOWN__	Intron	SNP	A	A	G	rs10786964	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:83967446A>G	ENST00000372141.2	+	2	850				NRG3_ENST00000404576.2_Intron|NRG3_ENST00000404547.1_Intron|NRG3_ENST00000372142.2_Intron|NRG3_ENST00000556918.1_Intron	NM_001010848.3|NM_001165972.1	NP_001010848.2|NP_001159444.1	P56975	NRG3_HUMAN	neuregulin 3	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		gaaacacacaatcatggcgaa	0.458		NA											A|||	2070	0.413339	0.3222	0.4395	5008	,	,	NA	18348	0.2391	NA	0.6392	False	NA	,,,	NA	NA	NA	2504	0.4652	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737	10718			7999	protein-coding gene	gene with protein product		605533			NA	9275162	Standard	XM_166086	NM_001010848	NA	Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000372141.2:c.824-151049A>G	chr10.hg19:g.83967446A>G		NA	A4D7U1|Q0PEH2|Q5VYH3	hg19	CCDS31233.1	0.02	-0.131535	ACAxTCA	COVERED																																																																																			NOVEL	NRG3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412261.1	5	2.406462	KEEP	0	0	0	8	227	AA	0.99257	0.22747	0		+	3	60	107	0	0	9.082498	10	60	273	30	ENST00000372141.2	0.230769	0.229173
NRG3	10718	__UNKNOWN__	__UNKNOWN__	10	84629575	84629575	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:84629575C>A	ENST00000372141.2	+	4	1081				NRG3_ENST00000537893.1_Intron|NRG3_ENST00000404576.2_Intron|NRG3_ENST00000404547.1_Intron|NRG3_ENST00000545131.1_Intron|NRG3_ENST00000372142.2_Intron|NRG3_ENST00000556918.1_Intron	NM_001010848.3|NM_001165972.1	NP_001010848.2|NP_001159444.1	P56975	NRG3_HUMAN	neuregulin 3	NA		NA			activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		cgtgttagcccggatggtctc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737	10718			7999	protein-coding gene	gene with protein product		605533			NA	9275162	Standard	XM_166086	NM_001010848	NA	Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000372141.2:c.1054+4382C>A	chr10.hg19:g.84629575C>A		NA	A4D7U1|Q0PEH2|Q5VYH3	hg19	CCDS31233.1	0.02	-0.061394	GCCxGGA	UNCOVERED																																																																																			NOVEL	NRG3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412261.1	5	3.308954	KEEP	0	0	0	11	319	CC	0.993072	0.043483	0		+	4	44	115	0	0	11.330602	3	60	101	23	ENST00000372141.2	0.571429	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	85578687	85578687	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:85578687T>C			NA	NA				RNU6-129P (54467 upstream) : RP11-219F10.1 (92722 downstream)						NA		NA									NA						tgtctctctctctctctctct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.85578687T>C		NA		hg19		0.02	-0.035089	CTCxCTC	UNCOVERED																																																																																			NOVEL					0			8	2.406023	KEEP	5	0	0	8	222	TT	0	0	0			3	60	100	0	0	10.454205	1	60	31	19		0.75	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	85842631	85842631	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:85842631C>T			NA	NA				RNU1-65P (79396 upstream) : RP11-338I21.1 (55544 downstream)						NA		NA									NA						tatttcattccattctcttct	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.85842631C>T		NA		hg19		0.02	-0.113709	TTCxATT	UNCOVERED																																																																																			NOVEL					0			4	2.406939	KEEP	0	0	0	8	246	CC	0.99257	0.16126	0			3	60	88	0	0	7.585066	7	60	215	27		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	85882554	85882554	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:85882554A>G			NA	NA				RNU1-65P (119319 upstream) : RP11-338I21.1 (15621 downstream)						NA		NA									NA						gtgaaaccccatctctactaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.85882554A>G		NA		hg19		0.02	-0.113952	CCCxTCT	UNCOVERED																																																																																			NOVEL					0			6	2.704334	KEEP	5	0	0	9	232	AA	0.99257	0.16126	0			3	42	90	1	0	7.383082	10	60	269	31		0.230769	0.162467
CCSER2	54462	__UNKNOWN__	__UNKNOWN__	10	86275443	86275443	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:86275443A>G	ENST00000224756.8	+	0	4834					NM_001284243.1|NM_018999.2	NP_001271172.1|NP_061872.2	Q9H7U1	CCSE2_HUMAN	coiled-coil serine-rich protein 2	NA		NA			microtubule bundle formation (GO:0001578)	microtubule cytoskeleton (GO:0015630)					NA						caagtgatccacccacctcgT	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS31235.1, CCDS60582.1, CCDS60583.1, CCDS73159.1	10q23.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000107771	ENSG00000107771	54462			29197	protein-coding gene	gene with protein product		NA	KIAA1128, family with sequence similarity 190, member B	KIAA1128, FAM190B	NA	10574461	Standard	NM_018999	XM_005269905	NA	Approved		uc001kdh.1	Q9H7U1	OTTHUMG00000018641	ENST00000224756.8:c.*2144A>G	chr10.hg19:g.86275443A>G		NA	B4DFY4|B4DQU9|B7WPE8|D3DWE2|Q8N6E9|Q9H2S0|Q9ULU1	hg19	CCDS31235.1	0.02	1.888726	TCCxCCC	COVERED																																																																																			NOVEL	CCSER2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049132.2	10	6.916942	KEEP	0	0	0	23	632	AA	0.999892	0.98185	0		+	4	60	136	0	0	9.690354	40	60	1191	105	ENST00000224756.8	0.090909	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	88171763	88171763	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88171763A>G			NA	NA				GRID1 (45528 upstream) : WAPAL (23249 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.88171763A>G		NA		hg19		0.02	-0.131563	CCAxCAC	COVERED																																																																																			NOVEL					0			6	3.909343	KEEP	0	0	0	13	349	AA	0.994391	0.227888	0			3	60	90	0	0	7.273102	11	60	334	43		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	88317889	88317889	__UNKNOWN__	IGR	SNP	G	G	T	rs112154019	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88317889G>T			NA	NA				RP11-77P6.2 (33031 upstream) : OPN4 (96424 downstream)						NA		NA									NA						actcctgaccgcaagtgatcc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.88317889G>T		NA		hg19		0.02	-0.13158	ACCxCAA	COVERED																																																																																			NOVEL					0			8	2.706427	KEEP	1	0	0	9	254	GG	0.99254	0.227464	0			3	40	90	2	0	7.172213	12	60	404	35		0.2	0.229173
LDB3	11155	__UNKNOWN__	__UNKNOWN__	10	88457574	88457574	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88457574T>G	ENST00000361373.4	+	6	917				LDB3_ENST00000429277.2_Intron|LDB3_ENST00000372056.4_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000310944.6_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000542786.1_Intron|LDB3_ENST00000372066.3_Intron|LDB3_ENST00000263066.6_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3	NA		NA								breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						ctcccaaagttctgggattac	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367	11155			15710	protein-coding gene	gene with protein product	cypher, oracle, Z-band alternatively spliced PDZ motif protein	605906	cardiomyopathy, dilated 1C (autosomal dominant)	CMD1C	NA	10427098, 23271734, 23996002, 14662268	Standard		NM_001080114	NA	Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.896+5246T>G	chr10.hg19:g.88457574T>G		NA		hg19	CCDS7377.1	0.02	-0.166639	AGTxCTG	COVERED																																																																																			NOVEL	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049160.2	8	2.406497	KEEP	0	0	0	8	226	TT	0.99257	0.351317	0		+	3	60	107	0	0	8.973101	11	60	317	37	ENST00000361373.4	0.214286	0.353947
LDB3	11155	__UNKNOWN__	__UNKNOWN__	10	88473292	88473292	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88473292G>A	ENST00000361373.4	+	9	1252				LDB3_ENST00000429277.2_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000352360.5_Intron|LDB3_ENST00000263066.6_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3	NA		NA								breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						gtgagccaccgcgcccagccA	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367	11155			15710	protein-coding gene	gene with protein product	cypher, oracle, Z-band alternatively spliced PDZ motif protein	605906	cardiomyopathy, dilated 1C (autosomal dominant)	CMD1C	NA	10427098, 23271734, 23996002, 14662268	Standard		NM_001080114	NA	Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1232-2792G>A	chr10.hg19:g.88473292G>A		NA		hg19	CCDS7377.1	0.02	-0.175368	ACCxCGC	COVERED																																																																																			NOVEL	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049160.2	5	2.706949	KEEP	0	0	0	9	259	GG	0.99254	0.384517	0		+	3	60	89	0	0	6.734419	16	60	515	45	ENST00000361373.4	0.157895	0.387407
BMPR1A	657	__UNKNOWN__	__UNKNOWN__	10	88545304	88545304	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88545304T>C	ENST00000372037.3	+	1	270					NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	NA		NA			BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						tcaggtgatctgcccacttgg	0.512		NA	Mis, N, F			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2												NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(190;603 2086 22044 30335 47971)	yes	Rec		Juvenile polyposis	10	10q22.3	657	bone morphogenetic protein receptor, type IA		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779	657		CD molecules	1076	protein-coding gene	gene with protein product		601299		ACVRLK3	NA	8397373, 9730621	Standard	NM_004329	NM_004329	NA	Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.-268+28628T>C	chr10.hg19:g.88545304T>C		NA	A8K6U9|Q8NEN8	hg19	CCDS7378.1	0.02	-0.140303	ATCxGCC	COVERED																																																																																			NOVEL	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049170.3	4	2.707571	KEEP	0	0	0	9	260	TT	0.99254	0.259018	0		+	3	60	98	0	0	7.879261	13	60	377	35	ENST00000372037.3	0.1875	0.260965
BMPR1A	657	__UNKNOWN__	__UNKNOWN__	10	88595072	88595072	__UNKNOWN__	Intron	SNP	T	T	C	rs200531003		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88595072T>C	ENST00000372037.3	+	2	270					NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	NA		NA			BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						cctgtaatcctagcactttgg	0.428		NA	Mis, N, F			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2												NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(190;603 2086 22044 30335 47971)	yes	Rec		Juvenile polyposis	10	10q22.3	657	bone morphogenetic protein receptor, type IA		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779	657		CD molecules	1076	protein-coding gene	gene with protein product		601299		ACVRLK3	NA	8397373, 9730621	Standard	NM_004329	NM_004329	NA	Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.-267-3550T>C	chr10.hg19:g.88595072T>C		NA	A8K6U9|Q8NEN8	hg19	CCDS7378.1	0.02	-0.157841	TCCxAGC	COVERED																																																																																			NOVEL	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049170.3	9	3.608889	KEEP	2	0	0	12	329	TT	0.993634	0.320751	0		+	3	60	107	0	0	8.691691	14	60	408	42	ENST00000372037.3	0.176471	0.322807
BMPR1A	657	__UNKNOWN__	__UNKNOWN__	10	88614951	88614951	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88614951A>G	ENST00000372037.3	+	2	385				BMPR1A_ENST00000480152.1_Intron	NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	NA		NA			BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						gtgagccaccacaccctgcGT	0.448		NA	Mis, N, F			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2												NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(190;603 2086 22044 30335 47971)	yes	Rec		Juvenile polyposis	10	10q22.3	657	bone morphogenetic protein receptor, type IA		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779	657		CD molecules	1076	protein-coding gene	gene with protein product		601299		ACVRLK3	NA	8397373, 9730621	Standard	NM_004329	NM_004329	NA	Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.-153+16215A>G	chr10.hg19:g.88614951A>G		NA	A8K6U9|Q8NEN8	hg19	CCDS7378.1	0.02	-0.359603	ACCxCAC	COVERED																																																																																			NOVEL	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049170.3	5	4.510527	KEEP	0	0	0	15	405	AA	0.99649	0.885755	0		+	3	60	101	0	0	7.011917	34	60	1029	75	ENST00000372037.3	0.081081	0.888875
BMPR1A	657	__UNKNOWN__	__UNKNOWN__	10	88684222	88684222	__UNKNOWN__	3'UTR	SNP	A	A	G	rs61856965	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88684222A>G	ENST00000372037.3	+	0	2882					NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	NA		NA			BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						GCCAAGGCCAAAAGAAGTTTA	0.378		NA	Mis, N, F			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2												NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(190;603 2086 22044 30335 47971)	yes	Rec		Juvenile polyposis	10	10q22.3	657	bone morphogenetic protein receptor, type IA		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779	657		CD molecules	1076	protein-coding gene	gene with protein product		601299		ACVRLK3	NA	8397373, 9730621	Standard	NM_004329	NM_004329	NA	Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.*746A>G	chr10.hg19:g.88684222A>G		NA	A8K6U9|Q8NEN8	hg19	CCDS7378.1	0.02	1.909389	CCAxAAG	COVERED																																																																																			NOVEL	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049170.3	4	3.910137	KEEP	63	0	0	13	362	AA	0.99257	0.987034	0		+	7	47	248	0	0	18.497872	58	60	1750	202	ENST00000372037.3	0.107692	0.994422
MMRN2	79812	__UNKNOWN__	__UNKNOWN__	10	88699014	88699014	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88699014A>T	ENST00000372027.5	-	7	2789					NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	NA		NA			angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						aggtcaggagatagagaccag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269	79812		EMI domain containing	19888	protein-coding gene	gene with protein product		608925	elastin microfibril interfacer 3	EMILIN3	NA	11559704	Standard	NM_024756	NM_024756	NA	Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.2468-2132T>A	chr10.hg19:g.88699014A>T		NA	Q504V7|Q6P2N2	hg19	CCDS7379.1	0.02	-0.096452	GAGxTAG	UNCOVERED																																																																																			NOVEL	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049179.2	7	2.704929	KEEP	1	0	0	9	228	AA	0.99257	0.119541	0		-	3	60	75	0	0	6.63131	5	60	145	26	ENST00000372027.5	0.375	0.120436
AGAP11	119385	__UNKNOWN__	__UNKNOWN__	10	88768039	88768039	__UNKNOWN__	RNA	SNP	A	A	G	rs36104328	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88768039A>G	ENST00000444431.1	+	0	2711				RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.5_ENST00000433214.2_RNA			Q8TF27	AGA11_HUMAN	ankyrin repeat and GTPase domain Arf GTPase activating protein 11	NA		NA			regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)				NA						TTAAAAGGTAATTGTGAGCTG	0.473		NA											a|||	832	0.166134	0.2368	0.2089	5008	,	,	NA	14414	0.0952	NA	0.1223	False	NA	,,,	NA	NA	NA	2504	0.1585	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							10q23.2	2013-01-11			ENSG00000151303	ENSG00000151303	119385		ADP-ribosylation factor GTPase activating proteins, Ankyrin repeat domain containing	29421	protein-coding gene	gene with protein product		NA			NA	11853319	Standard	NM_133447	NM_133447	NA	Approved	KIAA1975	uc001kee.2	Q8TF27	OTTHUMG00000018667	ENST00000444431.1:	chr10.hg19:g.88768039A>G		NA	B9EIP7|D3DWE4	hg19		0.02	-0.175363	GTAxTTG	COVERED																																																																																			NOVEL	AGAP11-001	KNOWN	basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000049193.1	9	2.705998	KEEP	2	0	0	9	237	AA	0.99254	0.384517	0		+	8	60	268	0	0	25.515394	9	44	236	41	ENST00000444431.1	0.470588	0.387407
GLUD1	2746	__UNKNOWN__	__UNKNOWN__	10	88817849	88817849	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88817849C>T	ENST00000277865.4	-	11	1499				GLUD1_ENST00000544149.1_Intron|GLUD1_ENST00000537649.1_Intron	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	NA		NA			cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	atggtctcgacctcctgacct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	2746	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD	NA	2757358	Standard	NM_005271	NM_005271	NA	Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.1403-310G>A	chr10.hg19:g.88817849C>T		NA	B3KV55|B4DGN5|Q5TBU3	hg19	CCDS7382.1	0.02	-0.078938	CGAxCTC	UNCOVERED																																																																																			NOVEL	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049188.1	2	2.406882	KEEP	2	0	0	8	250	AC	0.99257	0.076761	0		-	3	60	83	0	0	7.242588	6	60	208	31	ENST00000277865.4	0.333333	0.077336
GLUD1	2746	__UNKNOWN__	__UNKNOWN__	10	88829975	88829975	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88829975C>T	ENST00000277865.4	-	5	743				GLUD1_ENST00000544149.1_Intron|GLUD1_ENST00000537649.1_Intron	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	NA		NA			cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	tttgggaggccgaggcaggag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	2746	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD	NA	2757358	Standard	NM_005271	NM_005271	NA	Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.647-2061G>A	chr10.hg19:g.88829975C>T		NA	B3KV55|B4DGN5|Q5TBU3	hg19	CCDS7382.1	0.02	-0.131576	GGCxGAG	COVERED																																																																																			NOVEL	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049188.1	10	3.309818	KEEP	2	0	0	11	336	CC	0.993072	0.227586	0		-	3	60	88	0	0	6.972334	12	60	394	36	ENST00000277865.4	0.2	0.229173
GLUD1	2746	__UNKNOWN__	__UNKNOWN__	10	88831140	88831140	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88831140T>C	ENST00000277865.4	-	4	743				GLUD1_ENST00000544149.1_Intron|GLUD1_ENST00000537649.1_Intron	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	NA		NA			cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	gacggggttttaccatgttgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	2746	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD	NA	2757358	Standard	NM_005271	NM_005271	NA	Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.646+3167A>G	chr10.hg19:g.88831140T>C		NA	B3KV55|B4DGN5|Q5TBU3	hg19	CCDS7382.1	0.02	-0.122765	TTTxACC	UNCOVERED																																																																																			NOVEL	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049188.1	11	2.404688	KEEP	4	0	0	8	204	TT	0	0	0		-	5	60	149	0	0	13.523523	8	60	226	31	ENST00000277865.4	0.384615	0.196312
FAM35A	54537	__UNKNOWN__	__UNKNOWN__	10	88915892	88915892	__UNKNOWN__	Intron	SNP	C	C	T	rs61858926	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:88915892C>T	ENST00000298784.1	+	4	1639				FAM35A_ENST00000298786.4_Intron	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	NA		NA								endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						ggcgcgatctcggctcactgc	0.507		NA											C|||	741	0.147963	0.1384	0.2896	5008	,	,	NA	12066	0.1151	NA	0.1282	False	NA	,,,	NA	NA	NA	2504	0.1145	NA	NA	NA	Ovarian(175;703 2004 25460 32514 43441)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376	54537			28773	protein-coding gene	gene with protein product		NA			NA	8619474, 9110174	Standard	NM_019054	NM_019054	NA	Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.1526-1913C>T	chr10.hg19:g.88915892C>T		NA	O95885|Q9H991	hg19	CCDS7383.1	0.02	-0.131564	TCTxGGC	COVERED																																																																																			NOVEL	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049196.2	16	4.812675	KEEP	9	0	0	16	459	CC	0.994391	0.227888	0		+	4	47	115	0	0	9.771091	10	60	315	47	ENST00000298784.1	0.285714	0.229173
RNLS	55328	__UNKNOWN__	__UNKNOWN__	10	90333696	90333696	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:90333696G>A	ENST00000331772.4	-	4	390				RNLS_ENST00000371947.3_Intron|RNLS_ENST00000466945.1_Intron|RNLS_ENST00000437752.1_Intron	NM_001031709.2	NP_001026879.2	Q5VYX0	RNLS_HUMAN	renalase, FAD-dependent amine oxidase	NA		NA			cardiac left ventricle morphogenesis (GO:0003214)|dopamine metabolic process (GO:0042417)|epinephrine metabolic process (GO:0042414)|heart contraction (GO:0060047)|norepinephrine metabolic process (GO:0042415)|phosphate ion homeostasis (GO:0055062)|regulation of systemic arterial blood pressure (GO:0003073)|response to epinephrine (GO:0071871)|response to ischemia (GO:0002931)|response to norepinephrine (GO:0071873)|response to salt (GO:1902074)	extracellular space (GO:0005615)	oxidoreductase activity (GO:0016491)			breast(1)|kidney(1)|lung(3)|ovary(1)|prostate(1)	7						tcaggagtttgagaccagcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005364	CCDS7388.1, CCDS31239.1	10q23.31	2009-04-22	2009-04-22	2009-04-22	ENSG00000184719	ENSG00000184719	55328			25641	protein-coding gene	gene with protein product		609360	chromosome 10 open reading frame 59	C10orf59	NA	15841207, 17565281	Standard	NM_018363	NM_001031709	NA	Approved	FLJ11218, renalase	uc001kfe.3	Q5VYX0	OTTHUMG00000018692	ENST00000331772.4:c.368-878C>T	chr10.hg19:g.90333696G>A		NA	Q9BS33|Q9NUP8	hg19	CCDS31239.1	0.02	-0.140308	TTTxAGA	COVERED																																																																																			NOVEL	RNLS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049250.1	9	5.114631	KEEP	4	0	0	17	507	GG	0.994391	0.259501	0		-	3	41	83	0	0	6.682339	10	60	323	46	ENST00000331772.4	0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	92452457	92452457	__UNKNOWN__	IGR	SNP	T	T	C	rs2489292	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:92452457T>C			NA	NA				RP11-15K3.1 (151895 upstream) : HTR7 (48120 downstream)						NA		NA									NA						gtttttttgtttttttttttt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.92452457T>C		NA		hg19		0.02	-0.052631	TGTxTTT	UNCOVERED																																																																																			NOVEL					0			8	2.705003	KEEP	3	0	0	9	231	TT	0	0	0			3	60	100	0	0	9.969974	2	60	58	20		0.6	0.036766
HTR7	3363	__UNKNOWN__	__UNKNOWN__	10	92604456	92604456	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:92604456C>T	ENST00000371719.2	-	1	566				HTR7_ENST00000277874.6_Intron|HTR7_ENST00000371721.3_Intron|HTR7_ENST00000336152.3_Intron	NM_019860.3	NP_062874.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	NA		NA			blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	tgcactccagcctgggcaaca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680	3363		5-HT (serotonin) receptors, GPCR / Class A : 5-HT (serotonin) receptors, GPCR only	5302	protein-coding gene	gene with protein product		182137	5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)		NA	8226867	Standard	NM_000872	NM_000872	NA	Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000371719.2:c.539+12433G>A	chr10.hg19:g.92604456C>T		NA	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	hg19	CCDS7410.1	0.02	-0.087712	CAGxCTG	UNCOVERED																																																																																			NOVEL	HTR7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049345.1	13	2.706357	KEEP	9	0	0	9	251	CC	0	0	0		-	3	30	81	0	0	7.042802	6	51	200	27	ENST00000371719.2	0.333333	0.099721
TNKS2	80351	__UNKNOWN__	__UNKNOWN__	10	93598693	93598693	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:93598693C>T	ENST00000371627.4	+	14	1906					NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	NA		NA			multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				tgcacgatctcggctcacagc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854	80351		Poly (ADP-ribose) polymerases, Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	15677	protein-coding gene	gene with protein product		607128			NA		Standard	NM_025235	NM_025235	NA	Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.1528-1625C>T	chr10.hg19:g.93598693C>T		NA	B2RBD3|Q9H8F2|Q9HAS4	hg19	CCDS7417.1	0.02	-0.122717	TCTxGGC	COVERED																																																																																			NOVEL	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049374.1	6	2.706466	KEEP	1	0	0	9	268	CC	0.99254	0.194847	0		+	3	60	86	0	0	6.874064	11	60	325	35	ENST00000371627.4	0.214286	0.196312
TNKS2	80351	__UNKNOWN__	__UNKNOWN__	10	93615142	93615142	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:93615142G>A	ENST00000371627.4	+	23	3292					NM_025235.3	NP_079511.1	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2	NA		NA			multicellular organism growth (GO:0035264)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein polyubiquitination (GO:0000209)|regulation of multicellular organism growth (GO:0040014)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			biliary_tract(1)|breast(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	48		Colorectal(252;0.162)				atggggtttcgccatgttgcc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF342982	CCDS7417.1	10q23.3	2013-01-10			ENSG00000107854	ENSG00000107854	80351		Poly (ADP-ribose) polymerases, Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	15677	protein-coding gene	gene with protein product		607128			NA		Standard	NM_025235	NM_025235	NA	Approved	TNKL, TANK2, PARP-5b, PARP-5c, PARP5B, PARP5C, pART6	uc001khp.3	Q9H2K2	OTTHUMG00000018747	ENST00000371627.4:c.2914-229G>A	chr10.hg19:g.93615142G>A		NA	B2RBD3|Q9H8F2|Q9HAS4	hg19	CCDS7417.1	0.02	-0.192989	TTCxCCA	COVERED																																																																																			NOVEL	TNKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049374.1	9	3.00865	KEEP	1	0	0	10	304	GG	0.99254	0.454342	0		+	3	60	91	0	0	6.933564	16	60	540	49	ENST00000371627.4	0.157895	0.457757
FGFBP3	143282	__UNKNOWN__	__UNKNOWN__	10	93667258	93667258	__UNKNOWN__	3'UTR	SNP	C	C	T	rs113262917	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:93667258C>T	ENST00000311575.5	-	0	1632					NM_152429.4	NP_689642.3	Q8TAT2	FGFP3_HUMAN	fibroblast growth factor binding protein 3	NA		NA			positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of vascular permeability (GO:0043117)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	fibroblast growth factor binding (GO:0017134)|heparin binding (GO:0008201)			large_intestine(1)|prostate(1)	2		Colorectal(252;0.162)				gactagccaccgcactccagc	0.463		NA											C|||	32	0.00638978	0.0234	0.0014	5008	,	,	NA	14665	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK075410	CCDS7418.1	10q23.33	2006-12-14	2006-12-14	2006-12-14	ENSG00000174721	ENSG00000174721	143282			23428	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 13	C10orf13	NA		Standard	NM_152429	NM_152429	NA	Approved	MGC39320	uc001khq.4	Q8TAT2	OTTHUMG00000018751	ENST00000311575.5:c.*692G>A	chr10.hg19:g.93667258C>T		NA	B2RD68|Q8NBN0	hg19	CCDS7418.1	0.02	1.491611	CACxGCA	COVERED																																																																																			NOVEL	FGFBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049379.1	11	9.758971	KEEP	0	1	27	42	1211	CC	1	0.984161	0		-	4	60	122	0	0	7.956797	49	60	1543	132	ENST00000311575.5	0.075472	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	93680407	93680407	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:93680407A>G			NA	NA				FGFBP3 (11167 upstream) : BTAF1 (3118 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.93680407A>G		NA		hg19		0.02	-0.350818	GGCxTGA	COVERED																																																																																			NOVEL					0			22	2.471453	KEEP	3	2	56	28	785	AA	0.999997	0.877705	0			3	60	103	0	0	7.326438	31	60	924	102		0.088235	0.877708
CPEB3	22849	__UNKNOWN__	__UNKNOWN__	10	93880728	93880728	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:93880728G>A	ENST00000265997.4	-	7	1626				CPEB3_ENST00000412050.4_Intron	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	NA		NA			3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				aaagtgctgggattacaggca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864	22849		RNA binding motif (RRM) containing	21746	protein-coding gene	gene with protein product		610606			NA	10231032, 12672660	Standard	NM_014912	NM_014912	NA	Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.1454-9777C>T	chr10.hg19:g.93880728G>A		NA	Q5T389|Q9NQJ7|Q9Y2E9	hg19	CCDS31246.1	0.02	-0.22805	TGGxATT	COVERED																																																																																			NOVEL	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049387.2	13	4.812545	KEEP	6	0	0	16	479	GG	0.995343	0.580216	0		-	4	40	118	0	0	9.179892	18	60	590	59	ENST00000265997.4	0.181818	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	94120250	94120250	__UNKNOWN__	IGR	SNP	G	G	A	rs188087990	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:94120250G>A			NA	NA				MARCH5 (6529 upstream) : AL161652.1 (80717 downstream)						NA		NA									NA						tggaggttgcggtgagccaag	0.473		NA											g|||	2	0.000399361	0.0	0.0029	5008	,	,	NA	17824	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.94120250G>A		NA		hg19		0.02	-0.166652	TGCxGTG	COVERED																																																																																			NOVEL					0			5	2.707061	KEEP	0	0	0	9	256	GG	0.99254	0.351306	0			3	60	84	0	0	6.392542	14	60	449	40		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	94145158	94145158	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:94145158A>G			NA	NA				MARCH5 (31437 upstream) : AL161652.1 (55809 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.94145158A>G		NA		hg19		0.02	-0.166619	GGCxTGA	COVERED																																																																																			NOVEL					0			9	3.910047	KEEP	4	0	0	13	361	AT	0.995343	0.352299	0			3	60	87	1	0	6.693284	14	60	404	56		0.176471	0.353947
IDE	3416	__UNKNOWN__	__UNKNOWN__	10	94269432	94269432	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:94269432T>C	ENST00000265986.6	-	6	954					NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	NA		NA			beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)	aatcccagcattttgggaggc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912	3416			5381	protein-coding gene	gene with protein product	insulysin	146680			NA	2293021	Standard	NM_004969	NM_004969	NA	Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.897+374A>G	chr10.hg19:g.94269432T>C		NA	B2R721|B7ZAU2|D3DR35|Q5T5N2	hg19	CCDS7421.1	0.02	-0.157857	GCAxTTT	COVERED																																																																																			NOVEL	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049393.1	7	5.111962	KEEP	0	0	0	17	458	TT	0.999366	0.322602	0		-	3	60	98	0	0	7.792076	14	60	408	44	ENST00000265986.6	0.176471	0.322807
KIF11	3832	__UNKNOWN__	__UNKNOWN__	10	94413663	94413663	__UNKNOWN__	3'UTR	SNP	G	G	A	rs41290170	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:94413663G>A	ENST00000260731.3	+	0	3371					NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TATATCAgccgggcgcggtgg	0.458		NA											G|||	16	0.00319489	0.0	0.0043	5008	,	,	NA	16190	0.0	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA	Colon(47;212 1003 2764 4062 8431)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160	3832		Kinesins	6388	protein-coding gene	gene with protein product		148760	kinesin-like 1	KNSL1	NA	1505978, 8548803	Standard	NM_004523	NM_004523	NA	Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.*110G>A	chr10.hg19:g.94413663G>A		NA	A0AV49|B2RMV3|Q15716|Q5VWX0	hg19	CCDS7422.1	0.02	4.499671	GCCxGGC	COVERED																																																																																			NOVEL	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049401.1	55	22.529139	KEEP	1	2	54	94	2808	GG	1	1	0		+	9	60	278	0	0	17.377611	139	60	4532	377	ENST00000260731.3	0.060811	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	94496330	94496330	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:94496330A>G			NA	NA				Y_RNA (25965 upstream) : EXOC6 (94604 downstream)						NA		NA									NA						ctgaggtcagaagttcgagac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.94496330A>G		NA		hg19		0.02	-0.219268	CAGxAGT	COVERED																																																																																			NOVEL					0			7	2.706121	KEEP	2	0	0	9	240	AA	0.99254	0.548763	0			3	36	103	0	0	7.92686	19	60	562	56		0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	95035938	95035938	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95035938T>G			NA	NA				CYP26A1 (198291 upstream) : MYOF (30248 downstream)						NA		NA									NA						caggtgatcctcccgcctcag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.95035938T>G		NA		hg19		0.02	-0.210477	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			9	2.405687	KEEP	3	0	0	8	215	TT	0	0	0			3	60	93	0	0	6.865647	20	60	582	49		0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	95048192	95048192	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95048192A>G			NA	NA				CYP26A1 (210545 upstream) : MYOF (17994 downstream)						NA		NA									NA						caccacgcccagctaattttt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.95048192A>G		NA		hg19		0.02	-0.157806	CCCxGCT	COVERED																																																																																			NOVEL					0			5	2.405926	KEEP	2	0	0	8	218	AA	0.99257	0.320408	0			3	40	85	0	0	6.580123	13	60	373	37		0.1875	0.322807
MYOF	26509	__UNKNOWN__	__UNKNOWN__	10	95208515	95208515	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95208515A>G	ENST00000359263.4	-	3	236				MYOF_ENST00000371501.4_Intron|MYOF_ENST00000371488.3_Intron|MYOF_ENST00000371489.1_Intron|MYOF_ENST00000371502.4_Intron|MYOF_ENST00000358334.5_Intron	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	NA		NA			blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						actttgggagaccaaggtggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119	26509			3656	protein-coding gene	gene with protein product	fer-1-like family member 3	604603	fer-1 (C.elegans)-like 3 (myoferlin), fer-1-like 3, myoferlin (C. elegans)	FER1L3	NA	10607832, 10995573, 17702744	Standard	NM_013451	NM_013451	NA	Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.236+3291T>C	chr10.hg19:g.95208515A>G		NA	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	hg19	CCDS41551.1	0.02	-0.078939	GAGxCCA	UNCOVERED																																																																																			NOVEL	MYOF-005	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049423.2	4	2.406559	KEEP	1	0	0	8	228	AA	0.99257	0.076761	0		-	3	60	99	0	0	9.03298	5	60	149	23	ENST00000359263.4	0.375	0.077336
MYOF	26509	__UNKNOWN__	__UNKNOWN__	10	95218228	95218228	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95218228G>C	ENST00000359263.4	-	2	88				MYOF_ENST00000371501.4_Intron|MYOF_ENST00000371488.3_Intron|MYOF_ENST00000371489.1_Intron|MYOF_ENST00000371502.4_Intron|MYOF_ENST00000358334.5_Intron	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	NA		NA			blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						tgcggtggctgacacctgtaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119	26509			3656	protein-coding gene	gene with protein product	fer-1-like family member 3	604603	fer-1 (C.elegans)-like 3 (myoferlin), fer-1-like 3, myoferlin (C. elegans)	FER1L3	NA	10607832, 10995573, 17702744	Standard	NM_013451	NM_013451	NA	Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.89-1534C>G	chr10.hg19:g.95218228G>C		NA	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	hg19	CCDS41551.1	0.02	-0.140361	GCTxACA	COVERED																																																																																			NOVEL	MYOF-005	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049423.2	4	2.407124	KEEP	0	0	0	8	247	GG	0.99257	0.259026	0		-	4	60	133	0	0	11.301248	12	60	406	35	ENST00000359263.4	0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	95598562	95598562	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95598562C>T			NA	NA				LGI1 (40646 upstream) : SLC35G1 (55167 downstream)						NA		NA									NA						tggtggctcacgcctctaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.95598562C>T		NA		hg19		0.02	-0.157893	TCAxGCC	COVERED																																																																																			NOVEL					0			5	2.707753	KEEP	0	0	0	9	270	CC	0.99254	0.351306	0			3	60	91	0	0	7.09189	14	60	467	43		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	95598567	95598567	__UNKNOWN__	IGR	SNP	C	C	G	rs2901715	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95598567C>G			NA	NA				LGI1 (40651 upstream) : SLC35G1 (55162 downstream)						NA		NA									NA						gctcacgcctctaatcccagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.95598567C>G		NA		hg19		0.02	-0.175442	CCTxTAA	COVERED																																																																																			NOVEL					0			5	2.708034	KEEP	0	0	0	9	279	CC	0.99254	0.420319	0			4	60	127	0	0	10.701173	12	60	421	47		0.25	0.423478
PLCE1	51196	__UNKNOWN__	__UNKNOWN__	10	95961516	95961516	__UNKNOWN__	Intron	SNP	G	G	A	rs577126145	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:95961516G>A	ENST00000371380.3	+	4	2044				PLCE1_ENST00000371375.1_Intron|PLCE1_ENST00000260766.3_Intron|PLCE1_ENST00000371385.3_Intron			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	NA		NA			activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				gattacaggcgtgagccacca	0.468		NA											G|||	2	0.000399361	0.0008	0.0014	5008	,	,	NA	16685	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	51196	3.1.4.11		17175	protein-coding gene	gene with protein product	nephrosis type 3	608414			NA	11022047, 11022048	Standard	NM_016341	NM_016341	NA	Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.1810-25547G>A	chr10.hg19:g.95961516G>A		NA	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	hg19	CCDS41552.1	0.02	-0.140349	GGCxTGA	UNCOVERED																																																																																			NOVEL	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049469.3	7	2.708208	KEEP	4	0	0	9	280	GG	0	0	0		+	3	60	88	0	0	7.072967	11	60	368	38	ENST00000371380.3	0.214286	0.260965
RP11-119K6.6	0	__UNKNOWN__	__UNKNOWN__	10	96367733	96367733	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:96367733C>T	ENST00000432120.1	+	0	207										NA		NA									NA						ctgcccacctcggcctcccaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432120.1:	chr10.hg19:g.96367733C>T		NA		hg19		0.02	2.127314	CCTxGGC	COVERED	.	.	.	.	.	.	.	.	.	.	C	3.719	-0.057994	0.07317	.	.	ENSG00000119969	ENST00000371327	T	0.01933	4.55	0.401	-0.667	0.11395	.	.	.	.	.	T	0.02970	0.0088	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.41963	-0.9479	5	0.87932	D	0	.	.	.	.	.	.	.	.	L	295	ENSP00000360378:S295L	ENSP00000360378:S295L	S	+	2	0	HELLS	96357723	0.007000	0.16637	0.002000	0.10522	0.002000	0.02628	-0.309000	0.08145	-0.440000	0.07211	-0.436000	0.05848	TCG	NOVEL	RP11-119K6.6-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000049474.1	54	21.325225	KEEP	0	5	127	116	3500	CC	1	1	0		+	6	60	166	0	0	8.952271	123	60	4009	359	ENST00000432120.1	0.046512	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	96761120	96761120	__UNKNOWN__	IGR	SNP	C	C	T	rs547387378	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:96761120C>T			NA	NA				CYP2C9 (11973 upstream) : CYP2C8 (35409 downstream)						NA		NA									NA						ctggctaacacggtgaaaccc	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.96761120C>T		NA		hg19		0.02	-0.105241	ACAxGGT	UNCOVERED																																																																																			NOVEL					0			4	2.404908	KEEP	8	0	0	8	211	CC	0	0	0			3	40	82	0	0	6.701217	9	43	271	28		0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	97350675	97350675	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:97350675T>C			NA	NA				SORBS1 (29504 upstream) : ALDH18A1 (15020 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.97350675T>C		NA		hg19		0.02	-0.157866	TCAxGCC	COVERED																																																																																			NOVEL					0			2	4.209707	KEEP	1	0	0	14	382	TT	0.995343	0.321303	0			3	60	95	0	0	7.492221	14	60	412	52		0.176471	0.322807
ENTPD1	953	__UNKNOWN__	__UNKNOWN__	10	97507691	97507691	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:97507691C>T	ENST00000453258.2	+	1	215					NM_001098175.1	NP_001091645.1	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	NA		NA			ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		tgcagtggcaccatctcggct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185	953		CD molecules	3363	protein-coding gene	gene with protein product		601752		CD39	NA	9226376, 24482476	Standard	NM_001776	NM_001098175	NA	Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000453258.2:c.37+35941C>T	chr10.hg19:g.97507691C>T		NA	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	hg19	CCDS41554.1	0.02	-0.148795	GCAxCAT	COVERED																																																																																			NOVEL	ENTPD1-005	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049563.1	7	3.910918	KEEP	0	0	0	13	386	CC	0.994391	0.290363	0		+	3	60	89	0	0	6.895429	14	60	444	47	ENST00000453258.2	0.176471	0.292001
PIK3AP1	118788	__UNKNOWN__	__UNKNOWN__	10	98412308	98412308	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:98412308A>C	ENST00000339364.5	-	4	832				PIK3AP1_ENST00000371110.2_Intron|PIK3AP1_ENST00000468783.1_Intron	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	NA		NA			negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		ccagcctgggagacagagcga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629	118788			30034	protein-coding gene	gene with protein product		607942			NA	1251844, 11163197	Standard	NM_152309	NM_152309	NA	Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.712+146T>G	chr10.hg19:g.98412308A>C		NA	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	hg19	CCDS31259.1	0.02	-0.298154	GGGxGAC	COVERED																																																																																			NOVEL	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049619.2	6	2.706317	KEEP	1	0	0	9	247	AA	0.99254	0.794276	0		-	5	60	135	2	1	9.797302	28	60	832	56	ENST00000339364.5	0.151515	0.800245
ARHGAP19-SLIT1	100533184	__UNKNOWN__	__UNKNOWN__	10	98971770	98971770	__UNKNOWN__	Intron	SNP	G	G	C	rs377609609		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:98971770G>C	ENST00000453547.2	-	11	1474									ARHGAP19-SLIT1 readthrough (NMD candidate)	NA		NA									NA						ctgggcaacagagcaagactc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					10q24.1	2013-05-10			ENSG00000269891	ENSG00000269891	100533184			48348	other	readthrough		NA			NA		Standard		NR_037909	NA	Approved				OTTHUMG00000184018	ENST00000453547.2:c.1474+17133C>G	chr10.hg19:g.98971770G>C		NA		hg19		0.02	-0.105273	ACAxAGC	UNCOVERED																																																																																			NOVEL	ARHGAP19-SLIT1-203	KNOWN	basic	protein_coding	NA	protein_coding		5	2.401619	KEEP	1	0	0	8	239	GG	0.99257	0.16126	0		-	3	60	104	0	1	9.532822	5	60	172	33	ENST00000453547.2	0.375	0.162467
RP11-452K12.7	0	__UNKNOWN__	__UNKNOWN__	10	99165130	99165130	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99165130C>T	ENST00000422848.1	+	0	259										NA		NA									NA						tctcagcactctgggaggccg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000422848.1:	chr10.hg19:g.99165130C>T		NA		hg19		0.02	-0.263155	ACTxTGG	COVERED																																																																																			NOVEL	RP11-452K12.7-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000049679.1	12	2.741145	KEEP	1	1	28	19	573	CC	0.99986	0.693571	0		+	4	60	118	0	0	8.792843	23	60	778	72	ENST00000422848.1	0.148148	0.693668
RP11-452K12.7	0	__UNKNOWN__	__UNKNOWN__	10	99170593	99170593	__UNKNOWN__	RNA	SNP	G	G	A	rs10444014	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99170593G>A	ENST00000422848.1	+	0	259										NA		NA									NA						aggctgaggcgggtggatcac	0.507		NA											G|||	2217	0.442692	0.6407	0.3516	5008	,	,	NA	15123	0.3502	NA	0.3439	False	NA	,,,	NA	NA	NA	2504	0.4366	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000422848.1:	chr10.hg19:g.99170593G>A		NA		hg19		0.02	-0.184214	GGCxGGT	UNCOVERED																																																																																			NOVEL	RP11-452K12.7-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000049679.1	2	2.407165	KEEP	3	0	0	8	245	GG	0	0	0		+	4	60	120	0	0	9.56295	16	60	536	53	ENST00000422848.1	0.2	0.423478
MMS19	64210	__UNKNOWN__	__UNKNOWN__	10	99245287	99245287	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99245287T>C	ENST00000438925.2	-	2	448				MMS19_ENST00000327277.7_Intron|MMS19_ENST00000483626.1_Intron|MMS19_ENST00000327238.10_Intron|MMS19_ENST00000370782.2_Intron|MMS19_ENST00000355839.6_Intron	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		ccaggctggttttgaactcct	0.512		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229	64210			13824	protein-coding gene	gene with protein product	MET18 homolog (S. cerevisiae)	614777		MMS19L	NA	11071939	Standard		NM_022362	NA	Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.113-1379A>G	chr10.hg19:g.99245287T>C		NA	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	hg19	CCDS7464.1	0.02	-0.166623	GGTxTTG	COVERED																																																																																			NOVEL	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049706.2	5	3.002179	KEEP	1	0	0	10	254	TT	0.99254	0.384517	0		-	4	60	131	0	0	10.763016	15	60	422	41	ENST00000438925.2	0.210526	0.387407
UBTD1	80019	__UNKNOWN__	__UNKNOWN__	10	99304488	99304488	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99304488G>C	ENST00000370664.3	+	2	406					NM_024954.3	NP_079230.1	Q9HAC8	UBTD1_HUMAN	ubiquitin domain containing 1	NA		NA								central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		Colorectal(252;0.162)		Epithelial(162;3.04e-10)|all cancers(201;2.86e-08)		tggctcatgcgtgtaatccca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(100;169 2668 32720)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007331	CCDS7465.1	10q24.2	2005-09-22			ENSG00000165886	ENSG00000165886	80019			25683	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024954	NM_024954	NA	Approved	FLJ11807	uc001knv.1	Q9HAC8	OTTHUMG00000018856	ENST00000370664.3:c.71-23183G>C	chr10.hg19:g.99304488G>C		NA	D3DR57|Q53HI3	hg19	CCDS7465.1	0.02	-0.03509	TGCxTGT	UNCOVERED																																																																																			NOVEL	UBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049701.1	3	2.405863	KEEP	0	0	0	8	226	AG	0.99254	0.023894	0		+	2	60	68	0	0	6.550028	2	60	66	19	ENST00000370664.3	0.5	0.024074
ZFYVE27	118813	__UNKNOWN__	__UNKNOWN__	10	99510780	99510780	__UNKNOWN__	Intron	SNP	G	G	A	rs7897888	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99510780G>A	ENST00000359980.3	+	8	991				ZFYVE27_ENST00000357540.4_Intron|ZFYVE27_ENST00000356257.4_Intron|ZFYVE27_ENST00000453958.2_Intron|ZFYVE27_ENST00000370610.3_Intron|ZFYVE27_ENST00000337540.7_Intron|ZFYVE27_ENST00000370613.3_Intron|ZFYVE27_ENST00000393677.4_Intron	NM_001002262.3	NP_001002262.1	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	NA		NA			cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		gattacaggcgtgagccactg	0.537		NA											G|||	39	0.00778754	0.0287	0.0014	5008	,	,	NA	19333	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256	118813		Zinc fingers, FYVE domain containing	26559	protein-coding gene	gene with protein product	protrudin	610243			NA	14702039	Standard	NM_144588	NM_144588	NA	Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000359980.3:c.805-368G>A	chr10.hg19:g.99510780G>A		NA	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	hg19	CCDS31264.1	0.02	-0.166662	GGCxTGA	COVERED																																																																																			NOVEL	ZFYVE27-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049748.2	7	2.707659	KEEP	1	0	0	9	267	GG	0.99257	0.351317	0		+	3	60	85	0	0	6.334762	16	60	543	41	ENST00000359980.3	0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	99543602	99543602	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99543602C>T			NA	NA				SFRP5 (11893 upstream) : LINC00866 (44632 downstream)						NA		NA									NA						atgatccacccgccttggcct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.99543602C>T		NA		hg19		0.02	-0.166663	ACCxGCC	COVERED																																																																																			NOVEL					0			4	2.700325	KEEP	0	0	0	9	254	AC	0.992708	0.351366	0			5	60	144	0	0	12.16664	13	60	440	40		0.277778	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	99544611	99544611	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99544611T>C			NA	NA				SFRP5 (12902 upstream) : LINC00866 (43623 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.99544611T>C		NA		hg19		0.02	-0.175425	TCCxAGC	COVERED																																																																																			NOVEL					0			9	2.405039	KEEP	0	0	0	8	209	TT	0.99257	0.384528	0			3	57	105	0	0	8.409956	15	60	455	41		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	99557047	99557047	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:99557047T>C			NA	NA				SFRP5 (25338 upstream) : LINC00866 (31187 downstream)						NA		NA									NA						aggctggtcttaaactcctgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.99557047T>C		NA		hg19		0.02	-0.149045	TCTxAAA	COVERED																																																																																			NOVEL					0			6	3.308418	KEEP	0	0	0	11	302	TT	0.993072	0.289978	0			3	60	85	0	0	6.58036	13	60	364	42		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	100110117	100110117	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:100110117A>G			NA	NA				LOXL4 (82110 upstream) : PYROXD2 (33204 downstream)						NA		NA									NA						tgggattacaagtgtgagcca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.100110117A>G		NA		hg19		0.02	-0.184182	ACAxGTG	COVERED																																																																																			NOVEL					0			8	2.972871	KEEP	1	0	0	10	258	AA	0.992708	0.42039	0			3	60	99	0	0	7.89191	14	60	423	44		0.176471	0.423478
HPSE2	60495	__UNKNOWN__	__UNKNOWN__	10	100929219	100929219	__UNKNOWN__	Intron	SNP	A	A	G	rs12355829	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:100929219A>G	ENST00000370552.3	-	3	508				HPSE2_ENST00000404542.1_Intron|HPSE2_ENST00000370549.1_Intron|HPSE2_ENST00000370546.1_Intron	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		ccaagatggcaccactgcact	0.473		NA											G|||	2491	0.497404	0.2277	0.4942	5008	,	,	NA	12770	0.6389	NA	0.6233	False	NA	,,,	NA	NA	NA	2504	0.589	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987	60495			18374	protein-coding gene	gene with protein product		613469	urofacial syndrome, heparanase 2	UFS	NA	11027606, 20605132, 9199567, 20576607	Standard	NM_021828	NM_021828	NA	Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.449-25063T>C	chr10.hg19:g.100929219A>G		NA	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	hg19	CCDS7477.1	0.02	-0.078927	GGCxCCA	UNCOVERED																																																																																			NOVEL	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049789.1	21	4.209455	KEEP	15	0	0	14	372	AA	0	0	0		-	4	60	121	0	0	11.322399	5	60	147	33	ENST00000370552.3	0.444444	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	101332320	101332320	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101332320C>G			NA	NA				NKX2-3 (36042 upstream) : snoU13 (29216 downstream)						NA		NA									NA						gccgggcgcgctggctcacgc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.101332320C>G		NA		hg19		0.02	-0.263188	GCGxTGG	COVERED																																																																																			NOVEL					0			3	2.708027	KEEP	1	0	0	9	277	CC	0.99257	0.688515	0			3	60	106	0	0	7.891648	25	60	877	63		0.107143	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	101341813	101341813	__UNKNOWN__	IGR	SNP	G	G	A	rs7090137	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101341813G>A			NA	NA				NKX2-3 (45535 upstream) : snoU13 (19723 downstream)						NA		NA									NA						caggtgatccgcccacctcgg	0.517		NA											G|||	1764	0.352236	0.3669	0.3242	5008	,	,	NA	15379	0.3175	NA	0.4364	False	NA	,,,	NA	NA	NA	2504	0.3016	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.101341813G>A		NA		hg19		0.02	-0.228044	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			10	2.707155	KEEP	5	0	0	9	264	GG	0	0	0			10	60	292	0	0	26.889891	14	60	454	58		0.416667	0.612407
DNMBP	23268	__UNKNOWN__	__UNKNOWN__	10	101701288	101701288	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101701288C>T	ENST00000324109.4	-	4	2352				DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Intron	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	NA		NA			intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		tgcaatggcacgatctcggct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554	23268		Rho guanine nucleotide exchange factors	30373	protein-coding gene	gene with protein product	scaffold protein TUBA	611282			NA	10231032, 14506234	Standard	NM_015221	NM_015221	NA	Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.2260+13682G>A	chr10.hg19:g.101701288C>T		NA	Q8IVY3|Q9Y2L3	hg19	CCDS7485.1	0.02	-0.114013	GCAxGAT	UNCOVERED																																																																																			NOVEL	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049832.2	8	3.007392	KEEP	3	0	0	10	284	CC	0.99257	0.16126	0		-	3	60	86	0	0	7.378209	7	60	229	36	ENST00000324109.4	0.3	0.162467
CPN1	1369	__UNKNOWN__	__UNKNOWN__	10	101806570	101806570	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101806570T>C	ENST00000370418.3	-	8	1482					NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	NA		NA			response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		gtggctcacgtctgtaatcct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	1369	3.4.17.3		2312	protein-coding gene	gene with protein product	anaphylatoxin inactivator, arginine carboxypeptidase, carboxypeptidase K, kininase I, lysine carboxypeptidase	603103	carboxypeptidase N, polypeptide 1, 50kD		NA	9628828, 2912725	Standard	NM_001308	NM_001308	NA	Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1230+1944A>G	chr10.hg19:g.101806570T>C		NA	B1AP59	hg19	CCDS7486.1	0.02	-0.210504	ACGxCTG	COVERED																																																																																			NOVEL	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049828.1	4	3.60116	KEEP	1	0	0	12	305	TT	0.993634	0.518837	0		-	3	60	108	0	0	8.426603	19	60	570	55	ENST00000370418.3	0.136364	0.522161
CPN1	1369	__UNKNOWN__	__UNKNOWN__	10	101835796	101835796	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101835796G>C	ENST00000370418.3	-	2	543	c.292C>G	c.(292-294)Cag>Gag	p.Q98E		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	98	Catalytic.	NA			response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		TCCGACAGCTGCAGCATCAGC	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													135	112	120			NA	NA	10		NA											NA				101835796		2203	4300	6503	SO:0001583	missense			X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	1369	3.4.17.3		2312	protein-coding gene	gene with protein product	anaphylatoxin inactivator, arginine carboxypeptidase, carboxypeptidase K, kininase I, lysine carboxypeptidase	603103	carboxypeptidase N, polypeptide 1, 50kD		NA	9628828, 2912725	Standard	NM_001308	NM_001308	NA	Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.292C>G	chr10.hg19:g.101835796G>C	ENSP00000359446:p.Gln98Glu	NA	B1AP59	hg19	CCDS7486.1	0.02	1.833538	GCTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	12.52	1.962639	0.34659	.	.	ENSG00000120054	ENST00000370418	T	0.03212	4.01	5.59	5.59	0.84812	Peptidase M14, carboxypeptidase A (3);	0.211812	0.50627	D	0.000112	T	0.05090	0.0136	L	0.35593	1.075	0.41527	D	0.988433	P	0.35307	0.494	B	0.34991	0.193	T	0.52909	-0.8512	10	0.33141	T	0.24	-18.3026	19.5966	0.95541	0.0:0.0:1.0:0.0	.	98	P15169	CBPN_HUMAN	E	98	ENSP00000359446:Q98E	ENSP00000359446:Q98E	Q	-	1	0	CPN1	101825786	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	3.845000	0.55880	2.647000	0.89833	0.655000	0.94253	CAG	NOVEL	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049828.1	1	2.407125	KEEP	0	0	0	8	245	GG	0.99257	0.99225	0		-	29	60	964	0	0	86.36308	57	60	1974	130	ENST00000370418.3	0.337209	0.999678
CHUK	1147	__UNKNOWN__	__UNKNOWN__	10	101959152	101959152	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101959152T>C	ENST00000370397.7	-	16	1816					NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	NA		NA			anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	ggtgtgatcttggctcactgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(159;52 1904 10536 35305 37148)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341	1147			1974	protein-coding gene	gene with protein product		600664		TCF16	NA	7558004, 16902410	Standard	NM_001278	XR_246062	NA	Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1729+575A>G	chr10.hg19:g.101959152T>C		NA	O14666|Q13132|Q5W0I4|Q92467	hg19	CCDS7488.1	0.02	-0.114028	TCTxGGC	UNCOVERED																																																																																			NOVEL	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049836.1	4	2.705696	KEEP	1	0	0	9	240	TT	0.99254	0.161255	0		-	3	60	100	0	0	8.50117	9	60	275	32	ENST00000370397.7	0.25	0.162467
CWF19L1	55280	__UNKNOWN__	__UNKNOWN__	10	101996112	101996112	__UNKNOWN__	Intron	SNP	C	C	T	rs115598142	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:101996112C>T	ENST00000370379.1	-	5	522				CWF19L1_ENST00000478047.1_Intron|CWF19L1_ENST00000354105.4_Intron			Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	NA		NA					catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		gtgctcctcccgcctcagcct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485	55280			25613	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_018294	NM_018294	NA	Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000370379.1:c.520-591G>A	chr10.hg19:g.101996112C>T		NA	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	hg19		0.02	-0.149106	TCCxGCC	COVERED																																																																																			NOVEL	CWF19L1-007	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000049849.3	1	2.406074	KEEP	0	0	0	8	228	CC	0.99257	0.289832	0		-	3	60	84	0	0	6.572744	12	60	387	36	ENST00000370379.1	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	102131708	102131708	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:102131708T>C			NA	NA				SCD (7117 upstream) : LINC00263 (1663 downstream)						NA		NA									NA						gagacagagttttgctcttgt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.102131708T>C		NA		hg19		0.02	-0.245483	AGTxTTG	COVERED																																																																																			NOVEL					0			7	3.607371	KEEP	0	0	0	12	320	TT	0.993634	0.637264	0			3	60	90	0	0	6.452293	22	60	648	57		0.12	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	102151981	102151981	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:102151981A>G			NA	NA				LINC00263 (8856 upstream) : Y_RNA (6127 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.102151981A>G		NA		hg19		0.02	-0.236792	CACxCCT	COVERED																																																																																			NOVEL					0			10	3.308958	KEEP	2	0	0	11	312	AA	0.992708	0.607941	0			3	50	95	0	0	6.949576	22	60	647	60		0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	102203330	102203330	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:102203330A>G			NA	NA				RP11-285F16.1 (30152 upstream) : WNT8B (19467 downstream)						NA		NA									NA						Ggccaggcacagtggctcaca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.102203330A>G		NA		hg19		0.02	-0.28946	CACxGTG	COVERED																																																																																			NOVEL					0			46	7.25011	KEEP	27	1	25	33	908	AA	0.999892	0.760805	0			3	31	99	0	0	7.192633	25	60	776	109		0.107143	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	102204828	102204828	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:102204828A>G			NA	NA				RP11-285F16.1 (31650 upstream) : WNT8B (17969 downstream)						NA		NA									NA						ctggagtgcaatggcgcgatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.102204828A>G		NA		hg19		0.02	-0.087695	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			12	6.315269	KEEP	9	0	0	21	567	AA	0.999366	0.099658	0			3	60	91	0	0	7.878672	7	48	199	45		0.3	0.099721
C10orf2	56652	__UNKNOWN__	__UNKNOWN__	10	102749798	102749798	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:102749798C>T	ENST00000311916.2	+	2	1669				C10orf2_ENST00000370228.1_Intron|C10orf2_ENST00000473656.1_Intron	NM_001163813.1|NM_021830.4	NP_001157285.1|NP_068602.2	Q96RR1	PEO1_HUMAN	chromosome 10 open reading frame 2	NA		NA			cell death (GO:0008219)|DNA unwinding involved in DNA replication (GO:0006268)|mitochondrial DNA replication (GO:0006264)|protein hexamerization (GO:0034214)|protein homooligomerization (GO:0051260)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial nucleoid (GO:0042645)	5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|stomach(1)	24		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;7.18e-11)|all cancers(201;8.75e-09)|BRCA - Breast invasive adenocarcinoma(275;0.224)		cactggctcacgcctgtaatc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF292004	CCDS7506.1, CCDS53570.1	10q24	2013-05-13			ENSG00000107815	ENSG00000107815	56652			1160	protein-coding gene	gene with protein product	twinkle, T7 helicase-related protein with intramitochondrial nucleoid localization	606075	infantile onset spinocerebellar ataxia (autosomal recessive)	IOSCA	NA	11431692, 10645945, 16135556	Standard	NM_021830	NM_021830	NA	Approved	PEO, PEO1, TWINKLE, FLJ21832, TWINL	uc001ksf.2	Q96RR1	OTTHUMG00000018917	ENST00000311916.2:c.1484+157C>T	chr10.hg19:g.102749798C>T		NA	B2CQL2|Q6MZX2|Q6PJP5|Q96RR0	hg19	CCDS7506.1	0.02	-0.28063	TCAxGCC	COVERED																																																																																			NOVEL	C10orf2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000049886.1	4	3.307893	KEEP	0	0	0	11	298	CC	0.993072	0.755616	0		+	4	60	119	0	0	8.824337	24	60	714	50	ENST00000311916.2	0.142857	0.760887
SFXN3	81855	__UNKNOWN__	__UNKNOWN__	10	102800521	102800521	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:102800521C>T	ENST00000393459.1	+	0	2618				SFXN3_ENST00000224807.5_3'UTR			Q9BWM7	SFXN3_HUMAN	sideroflexin 3	NA		NA			iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		gtatttttagcagagatgggg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK074707	CCDS7508.2	10q24.32	2008-09-04			ENSG00000107819	ENSG00000107819	81855		Sideroflexins	16087	protein-coding gene	gene with protein product		615571			NA		Standard	NM_030971	NM_030971	NA	Approved	SFX3	uc001ksp.3	Q9BWM7	OTTHUMG00000018921	ENST00000393459.1:c.*1179C>T	chr10.hg19:g.102800521C>T		NA	Q8NCJ0|Q9NTP4	hg19		0.02	2.521407	TAGxAGA	COVERED																																																																																			NOVEL	SFXN3-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000049913.1	30	2.429013	KEEP	0	7	180	72	2183	CC	1	1	0		+	6	70	172	0	1	9.429265	129	60	4455	331	ENST00000393459.1	0.044444	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	103108377	103108377	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:103108377C>T			NA	NA				RP11-107I14.5 (25226 upstream) : BTRC (5442 downstream)						NA		NA									NA						CTTggccgggcgcagtggctc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.103108377C>T		NA		hg19		0.02	-0.201749	GGGxGCA	UNCOVERED																																																																																			NOVEL					0			7	2.407023	KEEP	4	0	0	8	242	CC	0	0	0			3	60	95	0	0	7.12708	19	60	632	52		0.136364	0.490544
C10orf76	79591	__UNKNOWN__	__UNKNOWN__	10	103606444	103606444	__UNKNOWN__	3'UTR	SNP	T	T	C	rs534119742		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:103606444T>C	ENST00000370033.4	-	0	3030				C10orf76_ENST00000495001.1_5'UTR	NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		ACTggctgggtgtggtggctc	0.502		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16207	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029	79591			25788	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_024541	NM_024541	NA	Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.*841A>G	chr10.hg19:g.103606444T>C		NA	Q2TB87|Q9H8Z9	hg19	CCDS41563.1	0.02	1.818523	GGGxGTG	COVERED																																																																																			NOVEL	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050007.1	4	3.239892	KEEP	2	1	26	20	561	TT	0.999869	0.993573	0		-	4	60	137	0	0	9.199885	57	60	1688	115	ENST00000370033.4	0.065574	0.993703
C10orf76	79591	__UNKNOWN__	__UNKNOWN__	10	103606456	103606456	__UNKNOWN__	3'UTR	SNP	C	C	T	rs556471830		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:103606456C>T	ENST00000370033.4	-	0	3018				C10orf76_ENST00000495001.1_5'UTR	NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		tggtggctcacgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029	79591			25788	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_024541	NM_024541	NA	Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.*829G>A	chr10.hg19:g.103606456C>T		NA	Q2TB87|Q9H8Z9	hg19	CCDS41563.1	0.02	1.581529	TCAxGCC	COVERED																																																																																			NOVEL	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050007.1	5	5.714682	KEEP	2	0	0	19	539	CC	0.999863	0.984026	0		-	4	60	122	0	0	7.955403	49	60	1533	108	ENST00000370033.4	0.075472	0.984161
C10orf76	79591	__UNKNOWN__	__UNKNOWN__	10	103691035	103691035	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:103691035A>G	ENST00000370033.4	-	23	1901					NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		tgtaatcccaacactttggga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029	79591			25788	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_024541	NM_024541	NA	Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.1781+8584T>C	chr10.hg19:g.103691035A>G		NA	Q2TB87|Q9H8Z9	hg19	CCDS41563.1	0.02	-0.184147	CCAxCAC	COVERED																																																																																			NOVEL	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050007.1	5	2.40635	KEEP	0	0	0	8	224	AA	0.99257	0.420331	0		-	3	60	96	0	0	7.772996	12	60	337	45	ENST00000370033.4	0.2	0.423478
C10orf76	79591	__UNKNOWN__	__UNKNOWN__	10	103809570	103809570	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:103809570C>T	ENST00000370033.4	-	1	109				C10orf76_ENST00000311122.5_Intron	NM_024541.2	NP_078817.2	Q5T2E6	CJ076_HUMAN	chromosome 10 open reading frame 76	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|upper_aerodigestive_tract(2)	24		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		cacctaggccccccaaagtgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023176	CCDS41563.1	10q24.32	2008-10-21			ENSG00000120029	ENSG00000120029	79591			25788	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_024541	NM_024541	NA	Approved	FLJ13114	uc009xwy.1	Q5T2E6	OTTHUMG00000018943	ENST00000370033.4:c.10+6271G>A	chr10.hg19:g.103809570C>T		NA	Q2TB87|Q9H8Z9	hg19	CCDS41563.1	0.02	-0.263176	GCCxCCC	COVERED																																																																																			NOVEL	C10orf76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050007.1	7	3.61118	KEEP	0	0	0	12	382	CC	0.993634	0.689252	0		-	3	60	94	0	0	6.742762	24	60	824	61	ENST00000370033.4	0.111111	0.693668
PPRC1	23082	__UNKNOWN__	__UNKNOWN__	10	103895383	103895383	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:103895383A>G	ENST00000278070.2	+	2	192				PPRC1_ENST00000413464.2_Intron	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		tgatccacccacctcagcctc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840	23082		RNA binding motif (RRM) containing	30025	protein-coding gene	gene with protein product		NA	peroxisome proliferative activated receptor, gamma, coactivator-related 1		NA	9628581, 11340167	Standard	NM_015062	XM_005269656	NA	Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.154-2224A>G	chr10.hg19:g.103895383A>G		NA	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	hg19	CCDS7529.1	0.02	-0.236761	CCCxCCT	COVERED																																																																																			NOVEL	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050021.1	6	3.308449	KEEP	4	0	0	11	306	AA	0.992708	0.607941	0		+	3	60	97	0	0	7.149584	22	60	643	64	ENST00000278070.2	0.12	0.612407
GBF1	8729	__UNKNOWN__	__UNKNOWN__	10	104035732	104035732	__UNKNOWN__	Intron	SNP	G	G	A	rs544793357		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104035732G>A	ENST00000369983.3	+	3	423					NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	NA		NA			COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		ggtggctcacgcctgtaatcc	0.493		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17349	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862	8729			4181	protein-coding gene	gene with protein product		603698	golgi-specific brefeldin A resistance factor 1		NA	9828135	Standard		NM_004193	NA	Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.163+15859G>A	chr10.hg19:g.104035732G>A		NA	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	hg19	CCDS7533.1	0.02	-0.149126	CACxCCT	COVERED																																																																																			NOVEL	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050051.1	11	3.007182	KEEP	5	0	0	10	274	GG	0.99254	0.289823	0		+	3	60	95	0	0	7.772718	11	60	366	41	ENST00000369983.3	0.214286	0.292001
GBF1	8729	__UNKNOWN__	__UNKNOWN__	10	104051898	104051898	__UNKNOWN__	Intron	SNP	G	G	A	rs562668970		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104051898G>A	ENST00000369983.3	+	3	423					NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	NA		NA			COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		tgcccgcctcggcctcccaaa	0.502		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	13424	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862	8729			4181	protein-coding gene	gene with protein product		603698	golgi-specific brefeldin A resistance factor 1		NA	9828135	Standard		NM_004193	NA	Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.163+32025G>A	chr10.hg19:g.104051898G>A		NA	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	hg19	CCDS7533.1	0.02	-0.271933	CTCxGCC	COVERED																																																																																			NOVEL	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050051.1	15	3.242055	KEEP	11	1	26	20	606	GG	0.99649	0.714798	0		+	4	44	117	1	0	8.623863	24	60	796	83	ENST00000369983.3	0.142857	0.717315
GBF1	8729	__UNKNOWN__	__UNKNOWN__	10	104121963	104121963	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104121963A>G	ENST00000369983.3	+	15	1943					NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	NA		NA			COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		acaggtgcccaccaccacgcc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862	8729			4181	protein-coding gene	gene with protein product		603698	golgi-specific brefeldin A resistance factor 1		NA	9828135	Standard		NM_004193	NA	Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.1684-269A>G	chr10.hg19:g.104121963A>G		NA	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	hg19	CCDS7533.1	0.02	-0.0877	CCCxCCA	UNCOVERED																																																																																			NOVEL	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050051.1	4	2.405489	KEEP	3	0	0	8	215	AA	0	0	0		+	3	40	89	0	0	7.843256	6	60	178	23	ENST00000369983.3	0.333333	0.099721
TMEM180	79847	__UNKNOWN__	__UNKNOWN__	10	104227615	104227615	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104227615G>A	ENST00000238936.4	+	3	162				TMEM180_ENST00000369931.3_Intron|TMEM180_ENST00000366277.2_Intron|TMEM180_ENST00000450947.2_Intron	NM_024789.3	NP_079065.2	Q14CX5	TM180_HUMAN	transmembrane protein 180	NA		NA				integral component of membrane (GO:0016021)				breast(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|skin(1)	13		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		gggtttcaccgtgttggccag	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK026182	CCDS7535.1	10q24.32	2011-02-09	2006-10-12	2006-10-12	ENSG00000138111	ENSG00000138111	79847			26196	protein-coding gene	gene with protein product		NA		C10orf77	NA	12477932	Standard	NM_024789	XM_006717971	NA	Approved	FLJ22529, bA18I14.8	uc001kvt.3	Q14CX5	OTTHUMG00000018961	ENST00000238936.4:c.-75-1097G>A	chr10.hg19:g.104227615G>A		NA	Q6NWM8|Q6NWM9|Q6PEZ7|Q9H679	hg19	CCDS7535.1	0.02	-0.131553	ACCxTGT	COVERED																																																																																			NOVEL	TMEM180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050075.2	8	3.610561	KEEP	6	0	0	12	362	GG	0.99257	0.22747	0		+	3	60	89	0	0	7.072583	12	60	387	44	ENST00000238936.4	0.2	0.229173
SUFU	51684	__UNKNOWN__	__UNKNOWN__	10	104374375	104374375	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104374375A>G	ENST00000369902.3	+	9	1188				SUFU_ENST00000369899.2_Intron|SUFU_ENST00000423559.2_Intron	NM_016169.3	NP_057253.2	Q9UMX1	SUFU_HUMAN	suppressor of fused homolog (Drosophila)	NA		NA			cytoplasmic sequestering of transcription factor (GO:0042994)|heart looping (GO:0001947)|multicellular organismal development (GO:0007275)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|skin development (GO:0043588)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|primary cilium (GO:0072372)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(7)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(2)	24		Colorectal(252;0.207)		Epithelial(162;1.36e-08)|all cancers(201;3.81e-07)|BRCA - Breast invasive adenocarcinoma(275;0.242)		gctcacgcctataatcccagc	0.507		NA	D, F, S		medulloblastoma	medulloblastoma			Medulloblastoma, associated with Germline SUFU Mutation												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Medulloblastoma predisposition	10	10q24.32	51684	suppressor of fused homolog (Drosophila)		O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database		AF175770	CCDS7537.1, CCDS53571.1	10q24.32	2014-09-17			ENSG00000107882	ENSG00000107882	51684			16466	protein-coding gene	gene with protein product		607035			NA	15367681	Standard	NM_016169	NM_016169	NA	Approved	SUFUH, SUFUXL, PRO1280	uc001kvy.2	Q9UMX1	OTTHUMG00000018966	ENST00000369902.3:c.1023-650A>G	chr10.hg19:g.104374375A>G		NA	Q7LCP7|Q9NT90|Q9NZ07|Q9UHK2|Q9UHM8|Q9UMY0	hg19	CCDS7537.1	0.02	-0.184125	CCTxTAA	COVERED																																																																																			NOVEL	SUFU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050089.1	9	3.906676	KEEP	1	0	0	13	326	AA	0.994391	0.421102	0		+	3	60	104	0	0	8.3923	14	60	378	52	ENST00000369902.3	0.176471	0.423478
WBP1L	54838	__UNKNOWN__	__UNKNOWN__	10	104515540	104515540	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104515540T>C	ENST00000448841.1	+	1	174					NM_001083913.1	NP_001077382.1	Q9NX94	WBP1L_HUMAN	WW domain binding protein 1-like	NA		NA				integral component of membrane (GO:0016021)					NA						cggtggctcatgcctgtaatt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056285	CCDS7540.1, CCDS44473.1	10q24.33	2012-05-02	2012-05-02	2012-05-02	ENSG00000166272	ENSG00000166272	54838			23510	protein-coding gene	gene with protein product	outcome predictor in acute leukemia 1	611129	chromosome 10 open reading frame 26	C10orf26	NA		Standard	NM_017787	NM_017787	NA	Approved	FLJ20154, OPAL1	uc001kwf.4	Q9NX94	OTTHUMG00000018968	ENST00000448841.1:c.90+11640T>C	chr10.hg19:g.104515540T>C		NA	B3KPF4|B7Z6S7|D3DR90|Q1EG70|Q2HIY7|Q5F2G6	hg19	CCDS44473.1	0.02	-0.228043	TCAxGCC	UNCOVERED																																																																																			NOVEL	WBP1L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		6	2.706437	KEEP	3	0	0	9	243	TT	0	0	0		+	3	60	95	0	0	7.127294	19	60	560	59	ENST00000448841.1	0.136364	0.58293
CNNM2	54805	__UNKNOWN__	__UNKNOWN__	10	104730699	104730699	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:104730699A>G	ENST00000369878.4	+	1	1809				CNNM2_ENST00000433628.2_Intron	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	NA		NA			magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		tataatcccaacactttggga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842	54805			103	protein-coding gene	gene with protein product		607803	cyclin M2	ACDP2	NA	21393841, 24699222	Standard	NM_017649	NM_017649	NA	Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1621+50841A>G	chr10.hg19:g.104730699A>G		NA	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	hg19	CCDS44474.1	0.02	-0.140343	CCAxCAC	COVERED																																																																																			NOVEL	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050113.3	6	2.406243	KEEP	0	0	0	8	222	AA	0.99257	0.259026	0		+	3	60	102	0	0	8.472808	11	60	333	34	ENST00000369878.4	0.214286	0.260965
SH3PXD2A	9644	__UNKNOWN__	__UNKNOWN__	10	105393127	105393127	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:105393127C>T	ENST00000369774.4	-	9	881				SH3PXD2A_ENST00000538130.1_Intron|SH3PXD2A_ENST00000315994.6_Intron|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000540321.1_Intron|SH3PXD2A_ENST00000355946.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	NA		NA			superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		tgagccaagaccatgccattg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957	9644			23664	protein-coding gene	gene with protein product	five SH3 domains	NA	SH3 multiple domains 1	SH3MD1	NA	9687503	Standard	NM_014631	XM_005270297	NA	Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.605-6168G>A	chr10.hg19:g.105393127C>T		NA	D3DR98|O43302|Q5TCZ2|Q5TDQ8	hg19		0.02	-0.122686	AGAxCAT	COVERED																																																																																			NOVEL	SH3PXD2A-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050178.1	4	2.405406	KEEP	0	0	0	8	231	CC	0.99257	0.194853	0		-	3	60	89	0	0	7.283618	10	60	311	30	ENST00000369774.4	0.230769	0.196312
SH3PXD2A	9644	__UNKNOWN__	__UNKNOWN__	10	105440319	105440319	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:105440319A>G	ENST00000369774.4	-	7	704				SH3PXD2A_ENST00000315994.6_Intron|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000355946.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	NA		NA			superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		acaggcgtgaaccaccacacc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957	9644			23664	protein-coding gene	gene with protein product	five SH3 domains	NA	SH3 multiple domains 1	SH3MD1	NA	9687503	Standard	NM_014631	XM_005270297	NA	Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.428-11909T>C	chr10.hg19:g.105440319A>G		NA	D3DR98|O43302|Q5TCZ2|Q5TDQ8	hg19		0.02	-0.157864	TGAxCCA	COVERED																																																																																			NOVEL	SH3PXD2A-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050178.1	7	2.405622	KEEP	0	0	0	8	213	AA	0.99257	0.320408	0		-	3	60	107	0	0	8.872297	12	60	343	34	ENST00000369774.4	0.2	0.322807
SLK	9748	__UNKNOWN__	__UNKNOWN__	10	105746644	105746644	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:105746644C>T	ENST00000369755.3	+	2	695				SLK_ENST00000335753.4_Intron	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	NA		NA			apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		ccatgttggccaggctggtct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(111;540 1651 1927 4474 17706)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613	9748			11088	protein-coding gene	gene with protein product		NA	SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast), STE20-like kinase (yeast)		NA	3526554	Standard	NM_014720	NM_014720	NA	Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.151-3789C>T	chr10.hg19:g.105746644C>T		NA	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	hg19	CCDS7553.1	0.02	-0.184218	GGCxAGG	COVERED																																																																																			NOVEL	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050188.1	15	3.609704	KEEP	6	0	0	12	353	CC	0.99257	0.420331	0		+	3	30	89	1	0	6.592644	18	60	615	48	ENST00000369755.3	0.142857	0.423478
WDR96	0	__UNKNOWN__	__UNKNOWN__	10	105989215	105989215	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:105989215A>T	ENST00000278064.2	-	2	435				WDR96_ENST00000369720.1_Intron|WDR96_ENST00000357060.3_Intron|WDR96_ENST00000369719.1_Intron|WDR96_ENST00000428666.1_Intron						NA		NA								NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						gttcgagaccagcctggccaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000278064.2:c.109+1132T>A	chr10.hg19:g.105989215A>T		NA		hg19		0.02	-0.035081	ACCxGCC	UNCOVERED																																																																																			NOVEL	WDR96-003	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050200.1	2	2.707153	KEEP	1	0	0	9	252	AA	0.99254	0.019833	0		-	3	60	89	0	0	9.353918	1	60	28	18	ENST00000278064.2	0.75	0.019982
SORCS1	114815	__UNKNOWN__	__UNKNOWN__	10	108383268	108383268	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:108383268T>C	ENST00000263054.6	-	20	2670				SORCS1_ENST00000344440.6_Intron|SORCS1_ENST00000369698.1_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	NA		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		tcccaaagtgttgggattaca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018	114815			16697	protein-coding gene	gene with protein product		606283			NA	11499680	Standard	NM_052918	NM_001206570	NA	Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2663-2949A>G	chr10.hg19:g.108383268T>C		NA	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	hg19	CCDS7559.1	0.02	-0.184201	GTGxTGG	COVERED																																																																																			NOVEL	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050232.4	10	4.511406	KEEP	6	0	0	15	412	TT	0.994391	0.421102	0		-	5	46	177	0	0	15.770428	11	60	331	59	ENST00000263054.6	0.3125	0.423478
SORCS1	114815	__UNKNOWN__	__UNKNOWN__	10	108443816	108443816	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:108443816G>A	ENST00000263054.6	-	10	1568				SORCS1_ENST00000344440.6_Intron|SORCS1_ENST00000369698.1_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	NA		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CAGATAggccgggcacggtgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018	114815			16697	protein-coding gene	gene with protein product		606283			NA	11499680	Standard	NM_052918	NM_001206570	NA	Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.1560+4133C>T	chr10.hg19:g.108443816G>A		NA	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	hg19	CCDS7559.1	0.02	-0.122803	GCCxGGC	COVERED																																																																																			NOVEL	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050232.4	5	3.307409	KEEP	0	0	0	11	296	GG	0.993072	0.194952	0		-	3	60	91	0	0	7.481922	10	60	323	35	ENST00000263054.6	0.230769	0.196312
SORCS1	114815	__UNKNOWN__	__UNKNOWN__	10	108502390	108502390	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:108502390G>A	ENST00000263054.6	-	6	967				SORCS1_ENST00000344440.6_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	NA		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		cacctgcctcggcctcccaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018	114815			16697	protein-coding gene	gene with protein product		606283			NA	11499680	Standard	NM_052918	NM_001206570	NA	Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.960-12518C>T	chr10.hg19:g.108502390G>A		NA	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	hg19	CCDS7559.1	0.02	-0.157894	CTCxGCC	COVERED																																																																																			NOVEL	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050232.4	6	2.7072	KEEP	2	0	0	9	259	GG	0.99257	0.320408	0		-	3	60	87	0	0	6.779133	13	60	438	37	ENST00000263054.6	0.1875	0.322807
SORCS1	114815	__UNKNOWN__	__UNKNOWN__	10	108585266	108585266	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:108585266G>T	ENST00000263054.6	-	3	734				SORCS1_ENST00000344440.6_Intron	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	NA		NA			neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		tcctgacctcgtgatccaccc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018	114815			16697	protein-coding gene	gene with protein product		606283			NA	11499680	Standard	NM_052918	NM_001206570	NA	Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.726+4065C>A	chr10.hg19:g.108585266G>T		NA	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	hg19	CCDS7559.1	0.02	-0.14912	CTCxTGA	COVERED																																																																																			NOVEL	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050232.4	6	2.405782	KEEP	1	0	0	8	216	GG	0.99257	0.351317	0		-	3	60	93	0	1	7.378859	13	60	416	48	ENST00000263054.6	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	108997160	108997160	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:108997160G>T			NA	NA				SORCS1 (72868 upstream) : RNA5SP326 (224157 downstream)						NA		NA									NA						ggccaaggcaggaggatcgct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.108997160G>T		NA		hg19		0.02	-0.192971	GCAxGAG	COVERED																																																																																			NOVEL					0			12	3.009247	KEEP	0	0	0	10	318	GG	0.992708	0.454419	0			3	60	87	0	0	6.779159	13	60	429	42		0.1875	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	111350453	111350453	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:111350453A>G			NA	NA				RNU6-839P (350949 upstream) : XPNPEP1 (274070 downstream)						NA		NA									NA						cagcctgggcaacagagtgag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.111350453A>G		NA		hg19		0.02	-0.140324	GGCxACA	UNCOVERED																																																																																			NOVEL					0			6	2.406085	KEEP	3	0	0	8	221	AA	0	0	0			4	60	126	0	0	10.871415	10	60	292	39		0.285714	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	111613975	111613975	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:111613975T>C			NA	NA				RNU6-839P (614471 upstream) : XPNPEP1 (10548 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.111613975T>C		NA		hg19		0.02	-0.280668	TCAxGCC	COVERED																																																																																			NOVEL					0			7	4.209699	KEEP	0	0	0	14	377	TT	0.995343	0.736227	0			3	60	103	0	0	7.592175	25	60	744	70		0.107143	0.739671
ADD3	120	__UNKNOWN__	__UNKNOWN__	10	111894012	111894012	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:111894012T>G	ENST00000277900.8	+	0	3026				ADD3_ENST00000360162.3_3'UTR	NM_001121.2	NP_001112.2	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	NA		NA				cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		TCCTTTTTTATTAGTTTAGAA	0.254		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700	120			245	protein-coding gene	gene with protein product		601568		ADDL	NA	8893809	Standard	NM_019903	XM_005269529	NA	Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000277900.8:c.*636T>G	chr10.hg19:g.111894012T>G		NA	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	hg19	CCDS7562.1	0.02	-0.420981	TTAxTAG	COVERED																																																																																			NOVEL	ADD3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050290.1	0	3.906917	KEEP	0	0	0	13	329	TT	0.994391	0.943082	0		+	15	70	502	0	0	44.411712	33	60	971	75	ENST00000277900.8	0.3125	0.948402
MXI1	4601	__UNKNOWN__	__UNKNOWN__	10	111976685	111976685	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:111976685A>C	ENST00000332674.5	+	1	478				MXI1_ENST00000361248.4_Intron	NM_130439.3	NP_569157.2	P50539	MXI1_HUMAN	MAX interactor 1, dimerization protein	NA		NA			cytoplasmic sequestering of transcription factor (GO:0042994)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(1)	10		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;1.33e-05)|all cancers(201;0.000277)|BRCA - Breast invasive adenocarcinoma(275;0.127)		ctcggcctccaaaagtgctgg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016678	CCDS7563.1, CCDS7564.2, CCDS31284.1	10q24-q25	2012-11-15	2012-11-15		ENSG00000119950	ENSG00000119950	4601		MAX dimerization proteins, Basic helix-loop-helix proteins	7534	protein-coding gene	gene with protein product		600020	MAX interacting protein 1, MAX interactor 1		NA	7959753	Standard	NM_130439	NM_130439	NA	Approved	MXD2, MAD2, MXI, bHLHc11	uc001kyy.3	P50539	OTTHUMG00000019033	ENST00000332674.5:c.274+8845A>C	chr10.hg19:g.111976685A>C		NA	B1ANN7|D3DR25|D3DRA9|Q15887|Q6FHW2|Q96E53	hg19	CCDS7563.1	0.02	-0.166631	TCCxAAA	COVERED																																																																																			NOVEL	MXI1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050314.1	8	3.006288	KEEP	1	0	0	10	261	AA	0.992708	0.351366	0		+	3	60	95	0	0	7.579174	13	60	374	42	ENST00000332674.5	0.1875	0.353947
RBM20	282996	__UNKNOWN__	__UNKNOWN__	10	112531015	112531015	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:112531015G>C	ENST00000369519.3	+	2	249					NM_001134363.1	NP_001127835.1	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	NA		NA			heart development (GO:0007507)|mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(4)|kidney(3)|large_intestine(1)|ovary(1)|skin(2)	12						tcccgagtaggtgggactaca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648563	CCDS44477.1	10q25.3	2014-09-17			ENSG00000203867	ENSG00000203867	282996		RNA binding motif (RRM) containing	27424	protein-coding gene	gene with protein product		613171			NA		Standard	NM_001134363	NM_001134363	NA	Approved		uc001kzf.2	Q5T481	OTTHUMG00000019043	ENST00000369519.3:c.192-9544G>C	chr10.hg19:g.112531015G>C		NA	A6NIP5|B5A868|Q5JVI1	hg19	CCDS44477.1	0.02	-0.131576	TAGxTGG	COVERED																																																																																			NOVEL	RBM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050339.2	3	2.407407	KEEP	0	0	0	8	253	GG	0.99257	0.22747	0		+	3	60	94	0	0	7.672889	11	60	368	30	ENST00000369519.3	0.214286	0.229173
ADRA2A	150	__UNKNOWN__	__UNKNOWN__	10	112837956	112837956	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:112837956C>T	ENST00000280155.2	+	1	1167	c.202C>T	c.(202-204)Ctc>Ttc	p.L68F		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	53		NA			actin cytoskeleton organization (GO:0030036)|activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|acute inflammatory response (GO:0002526)|adenylate cyclase-inhibiting adrenergic receptor signaling pathway (GO:0071881)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|DNA replication (GO:0006260)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|fear response (GO:0042596)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intestinal absorption (GO:0050892)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of adrenergic receptor signaling pathway (GO:0071878)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of insulin secretion (GO:0046676)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|phospholipase C-activating adrenergic receptor signaling pathway (GO:0071882)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of vasodilation (GO:0045909)|positive regulation of wound healing (GO:0090303)|Ras protein signal transduction (GO:0007265)|regulation of insulin secretion (GO:0050796)|regulation of vasoconstriction (GO:0019229)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|thermoception (GO:0050955)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	alpha-1B adrenergic receptor binding (GO:0031692)|alpha-2C adrenergic receptor binding (GO:0031696)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|heterotrimeric G-protein binding (GO:0032795)|norepinephrine binding (GO:0051380)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			breast(1)|cervix(3)|endometrium(6)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Dexmedetomidine(DB00633)|Dihydroergotamine(DB00320)|Dipivefrin(DB00449)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupirtine(DB06623)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Lofexidine(DB04948)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Naphazoline(DB06711)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pramipexole(DB00413)|Prazosin(DB00457)|Propericiazine(DB01608)|Pseudoephedrine(DB00852)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CGGCAACGTGCTCGTCATCAT	0.687		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(173;605 2658 7278 49362)							NA				0													45	40	42			NA	NA	10		NA											NA				112837956		2202	4300	6502	SO:0001583	missense			AF284095	CCDS7569.2	10q25.2	2012-08-08	2012-05-09		ENSG00000150594	ENSG00000150594	150		GPCR / Class A : Adrenoceptors : alpha	281	protein-coding gene	gene with protein product	alpha-2AAR subtype C10,  alpha-2A-adrenergic receptor	104210	adrenergic, alpha-2A-, receptor	ADRA2, ADRA2R	NA		Standard	NM_000681	NM_000681	NA	Approved	ADRAR	uc001kzo.3	P08913	OTTHUMG00000019050	ENST00000280155.2:c.202C>T	chr10.hg19:g.112837956C>T	ENSP00000280155:p.Leu68Phe	NA	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	hg19	CCDS7569.2	0.02	3.192179	GTGxTCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043997	0.75732	.	.	ENSG00000150594	ENST00000280155	T	0.78481	-1.18	4.8	2.89	0.33648	GPCR, rhodopsin-like superfamily (1);	0.088711	0.47455	U	0.000226	T	0.77336	0.4115	M	0.78285	2.405	0.51767	D	0.999936	P	0.37441	0.595	B	0.41646	0.362	T	0.74051	-0.3789	10	0.56958	D	0.05	.	7.3913	0.26911	0.3016:0.6217:0.0:0.0767	.	53	P08913	ADA2A_HUMAN	F	68	ENSP00000280155:L68F	ENSP00000280155:L68F	L	+	1	0	ADRA2A	112827946	1.000000	0.71417	0.867000	0.34043	0.990000	0.78478	4.959000	0.63666	0.414000	0.25790	0.555000	0.69702	CTC	NOVEL	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050372.2	0	4.513287	KEEP	0	0	0	15	459	CC	0.99649	0.99649	0		+	40	60	1127	0	0	97.91544	84	60	2878	195	ENST00000280155.2	0.322581	0.999999
GPAM	57678	__UNKNOWN__	__UNKNOWN__	10	113909876	113909876	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:113909876A>C	ENST00000348367.4	-	0	6116				GPAM_ENST00000423155.1_3'UTR			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	NA		NA			acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		AATCTCTTTCAAATGCAATCA	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(161;1017 2606 18293 52943)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927	57678			24865	protein-coding gene	gene with protein product	glycerol-3-phosphate acyltransferase 1, mitochondrial	602395			NA	10997877, 8369314	Standard	NM_020918	NM_020918	NA	Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.*3432T>G	chr10.hg19:g.113909876A>C		NA	Q5VW51|Q86TA3	hg19	CCDS7570.1	0.02	-0.280676	TTCxAAT	COVERED																																																																																			NOVEL	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050377.1	0	2.706657	KEEP	0	0	0	9	247	AA	0.99254	0.734154	0		-	4	60	133	0	0	9.974129	28	60	858	58	ENST00000348367.4	0.125	0.739671
ACSL5	51703	__UNKNOWN__	__UNKNOWN__	10	114152103	114152103	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:114152103A>G	ENST00000393081.1	+	2	278				ACSL5_ENST00000433418.1_Intron|ACSL5_ENST00000356116.1_Intron|ACSL5_ENST00000354655.4_Intron|ACSL5_ENST00000354273.4_Intron|ACSL5_ENST00000479936.1_Intron	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	NA		NA			cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		ggtggctcacacctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142	51703		Acyl-CoA synthetase family	16526	protein-coding gene	gene with protein product	FACL5 for fatty acid coenzyme A ligase 5, long-chain acyl-CoA synthetase 5, long-chain fatty acid coenzyme A ligase 5, fatty-acid-Coenzyme A ligase, long-chain 5	605677	fatty-acid-Coenzyme A ligase, long-chain 5	FACL5	NA	11127823	Standard	NM_016234	NM_016234	NA	Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.-29-2573A>G	chr10.hg19:g.114152103A>G		NA	A6GV77|D3DRB3|Q6UX44|Q9UIU4	hg19	CCDS7573.1	0.02	-0.33315	CACxCCT	COVERED																																																																																			NOVEL	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050386.1	16	3.006703	KEEP	9	0	0	10	268	AA	0.99254	0.845628	0		+	3	60	97	0	0	6.649783	33	60	940	75	ENST00000393081.1	0.083333	0.851984
TCF7L2	6934	__UNKNOWN__	__UNKNOWN__	10	114731348	114731348	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:114731348T>C	ENST00000369397.4	+	3	686				TCF7L2_ENST00000349937.2_Intron|TCF7L2_ENST00000352065.5_Intron|TCF7L2_ENST00000538897.1_Intron|TCF7L2_ENST00000355717.4_Intron|TCF7L2_ENST00000542695.1_Intron|TCF7L2_ENST00000369395.1_Intron|TCF7L2_ENST00000534894.1_Intron|TCF7L2_ENST00000355995.4_Intron|TCF7L2_ENST00000543371.1_Intron|TCF7L2_ENST00000536810.1_Intron|TCF7L2_ENST00000545257.1_Intron	NM_001198525.1|NM_001198527.1|NM_001198528.1|NM_030756.4	NP_001185454.1|NP_001185456.1|NP_001185457.1|NP_110383.2	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	NA		NA			blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		ggattacaggtgtgagccacc	0.527		NA	T	VTI1A	colorectal																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737	6934			11641	protein-coding gene	gene with protein product		602228		TCF4	NA	1741298	Standard	NM_030756	NM_001146283	NA	Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000369397.4:c.381+19982T>C	chr10.hg19:g.114731348T>C		NA	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	hg19	CCDS7576.1	0.02	-0.323802	AGGxGTG	COVERED																																																																																			NOVEL	TCF7L2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050413.1	13	5.089004	KEEP	2	0	0	17	420	TT	0.999366	0.851444	0		+	5	60	143	0	0	10.530228	29	60	801	83	ENST00000369397.4	0.147059	0.851984
TCF7L2	6934	__UNKNOWN__	__UNKNOWN__	10	114740637	114740637	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:114740637A>G	ENST00000369397.4	+	3	686				TCF7L2_ENST00000349937.2_Intron|TCF7L2_ENST00000352065.5_Intron|TCF7L2_ENST00000538897.1_Intron|TCF7L2_ENST00000355717.4_Intron|TCF7L2_ENST00000542695.1_Intron|TCF7L2_ENST00000369395.1_Intron|TCF7L2_ENST00000534894.1_Intron|TCF7L2_ENST00000355995.4_Intron|TCF7L2_ENST00000543371.1_Intron|TCF7L2_ENST00000536810.1_Intron|TCF7L2_ENST00000545257.1_Intron	NM_001198525.1|NM_001198527.1|NM_001198528.1|NM_030756.4	NP_001185454.1|NP_001185456.1|NP_001185457.1|NP_110383.2	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	NA		NA			blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		cgcccgcctcagcctcccaaa	0.483		NA	T	VTI1A	colorectal																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		10	10q25.3	6934	transcription factor 7-like 2		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737	6934			11641	protein-coding gene	gene with protein product		602228		TCF4	NA	1741298	Standard	NM_030756	NM_001146283	NA	Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000369397.4:c.381+29271A>G	chr10.hg19:g.114740637A>G		NA	B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	hg19	CCDS7576.1	0.02	-0.201723	CTCxGCC	COVERED																																																																																			NOVEL	TCF7L2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050413.1	4	3.90994	KEEP	2	0	0	13	359	AA	0.993072	0.487146	0		+	3	60	93	0	0	6.867026	20	60	606	54	ENST00000369397.4	0.130435	0.490544
ABLIM1	3983	__UNKNOWN__	__UNKNOWN__	10	116282905	116282905	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:116282905A>G	ENST00000277895.5	-	6	992				ABLIM1_ENST00000369252.4_Intron|ABLIM1_ENST00000369253.2_Intron|ABLIM1_ENST00000392952.3_Intron|ABLIM1_ENST00000533213.2_Intron|ABLIM1_ENST00000369266.3_Intron	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	NA		NA			axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		gcaagactccatctcaaaaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204	3983			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM	NA	9245787	Standard		NM_002313	NA	Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.894+21858T>C	chr10.hg19:g.116282905A>G		NA	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	hg19	CCDS7590.1	0.02	-0.175412	TCCxTCT	COVERED																																																																																			NOVEL	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050469.3	8	2.704102	KEEP	2	0	0	9	238	AA	0.99257	0.384528	0		-	3	60	101	0	0	8.010155	15	60	441	43	ENST00000277895.5	0.166667	0.387407
ABLIM1	3983	__UNKNOWN__	__UNKNOWN__	10	116291555	116291555	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:116291555G>A	ENST00000277895.5	-	6	992				ABLIM1_ENST00000369252.4_Intron|ABLIM1_ENST00000533213.2_Intron	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	NA		NA			axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		gattacaggcgtgagccaccg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204	3983			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM	NA	9245787	Standard		NM_002313	NA	Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.894+13208C>T	chr10.hg19:g.116291555G>A		NA	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	hg19	CCDS7590.1	0.02	-0.122814	GGCxTGA	COVERED																																																																																			NOVEL	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050469.3	5	2.707241	KEEP	8	0	0	9	258	GG	0.99257	0.194853	0		-	3	60	92	0	0	7.581779	10	60	339	40	ENST00000277895.5	0.230769	0.196312
FAM160B1	57700	__UNKNOWN__	__UNKNOWN__	10	116596938	116596938	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:116596938T>C	ENST00000369248.4	+	5	857				FAM160B1_ENST00000369250.3_Intron	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	NA		NA								NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						tctggtattataggtgtgagc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553	57700			29320	protein-coding gene	gene with protein product		NA	KIAA1600	KIAA1600	NA	10997877	Standard	XM_049351	NM_020940	NA	Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.522+933T>C	chr10.hg19:g.116596938T>C		NA	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	hg19	CCDS31290.1	0.02	-0.166593	TTAxAGG	COVERED																																																																																			NOVEL	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050499.1	6	3.00506	KEEP	0	0	0	10	258	TT	0.992708	0.351366	0		+	3	60	97	0	0	7.610593	15	60	420	39	ENST00000369248.4	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	117792394	117792394	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:117792394C>T			NA	NA				ATRNL1 (83891 upstream) : GFRA1 (24049 downstream)						NA		NA									NA						ccgcccgcctcggcctcccaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.117792394C>T		NA		hg19		0.02	-0.131553	CCTxGGC	COVERED																																																																																			NOVEL					0			4	2.406821	KEEP	0	0	0	8	239	CC	0.99257	0.22747	0			3	59	83	0	0	6.472834	12	60	381	35		0.2	0.229173
KIAA1598	57698	__UNKNOWN__	__UNKNOWN__	10	118704387	118704387	__UNKNOWN__	Intron	SNP	C	C	T	rs368077003	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:118704387C>T	ENST00000260777.10	-	8	997				KIAA1598_ENST00000497044.1_Intron|KIAA1598_ENST00000355371.4_Intron|KIAA1598_ENST00000392901.4_Intron|KIAA1598_ENST00000392903.2_Intron	NM_018330.6	NP_060800.2	A0MZ66	SHOT1_HUMAN	KIAA1598	NA		NA			axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		ggtgacagagcgagactctgt	0.507		NA											C|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	17627	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0								C	,	0,4406		0,0,2203	51	50	50		,	-0.9	0	10		50	4,8596	3.7+/-12.6	0,4,4296	no	intron,intron	KIAA1598	NM_001127211.1,NM_018330.5	,	0,4,6499	TT,TC,CC	NA	0.0465,0.0,0.0308	,	,	118704387	4,13002	2203	4300	6503	SO:0001627	intron_variant			BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164	57698			29319	protein-coding gene	gene with protein product		611171			NA	10997877, 17030985	Standard	NM_018330	NM_001127211	NA	Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000260777.10:c.711+47G>A	chr10.hg19:g.118704387C>T		NA	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	hg19	CCDS31293.1	0.02	1.204016	GAGxGAG	COVERED																																																																																			NOVEL	KIAA1598-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050553.1	11	6.048623	KEEP	1	1	28	30	890	CC	0.999997	0.981953	0		-	5	60	135	0	0	8.662517	49	60	1625	116	ENST00000260777.10	0.092593	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	119342940	119342940	__UNKNOWN__	IGR	SNP	T	T	A	rs10787778	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:119342940T>A			NA	NA				CTA-109P11.1 (10972 upstream) : RP11-328K15.1 (151883 downstream)						NA		NA									NA						agtggcatgatcatagctcac	0.478		NA											T|||	2381	0.475439	0.2405	0.5259	5008	,	,	NA	13440	0.5337	NA	0.66	False	NA	,,,	NA	NA	NA	2504	0.5072	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.119342940T>A		NA		hg19		0.02	-0.13156	TGAxCAT	UNCOVERED																																																																																			NOVEL					0			10	2.405951	KEEP	3	0	0	8	218	TT	0	0	0			7	60	213	0	0	20.424213	7	60	216	31		0.5	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	120339080	120339080	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:120339080C>T			NA	NA				AL356865.2 (33404 upstream) : PRLHR (13835 downstream)						NA		NA									NA						tcccaaagtgctgggattaca	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.120339080C>T		NA		hg19		0.02	-0.210544	GTGxTGG	COVERED																																																																																			NOVEL					0			13	4.813845	KEEP	0	0	0	16	490	CC	0.997832	0.521029	0			3	60	92	0	0	6.827195	19	60	660	55		0.136364	0.522161
EIF3A	8661	__UNKNOWN__	__UNKNOWN__	10	120797462	120797462	__UNKNOWN__	Intron	SNP	C	C	T	rs573923952	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:120797462C>T	ENST00000369144.3	-	20	3856				EIF3A_ENST00000541549.1_Intron	NM_003750.2	NP_003741.1	P56537	IF6_HUMAN	eukaryotic translation initiation factor 3, subunit A	NA		NA			mature ribosome assembly (GO:0042256)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal subunit export from nucleus (GO:0000054)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lamin filament (GO:0005638)|nucleus (GO:0005634)	ribosomal large subunit binding (GO:0043023)|ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)			endometrium(8)|kidney(4)|large_intestine(14)|lung(22)|prostate(1)|skin(4)|urinary_tract(3)	56		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0236)		gagttttgctcttgttgccca	0.473		NA											.|||	8	0.00159744	0.0023	0.0	5008	,	,	NA	11080	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U78311	CCDS7608.1	10q26.11	2007-08-03	2007-07-27	2007-07-27	ENSG00000107581	ENSG00000107581	8661			3271	protein-coding gene	gene with protein product		602039	eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa	EIF3, EIF3S10	NA	9054404, 8590280	Standard	NM_003750	NM_003750	NA	Approved	eIF3-theta, eIF3-p170, KIAA0139, eIF3a, TIF32	uc001ldu.3	Q14152	OTTHUMG00000019144	ENST00000369144.3:c.3728+287G>A	chr10.hg19:g.120797462C>T		NA	B7ZBG9|Q6IBN8|Q96TD5	hg19	CCDS7608.1	0.02	-0.131426	GCTxTTG	UNCOVERED																																																																																			NOVEL	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050634.1	13	2.407169	KEEP	9	0	0	8	245	CC	0	0	0		-	4	30	123	0	0	10.573971	10	60	317	33	ENST00000369144.3	0.285714	0.229173
FAM45A	404636	__UNKNOWN__	__UNKNOWN__	10	120867722	120867722	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:120867722C>T	ENST00000361432.2	+	2	278				FAM45A_ENST00000535029.1_Intron|FAM45A_ENST00000544016.1_Intron	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	NA		NA								breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		ATAggctgggcgcggtggctc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													29	31	30			NA	NA	10		NA											NA				120867722		2203	4297	6500	SO:0001627	intron_variant			AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979	404636			31793	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207009	NM_207009	NA	Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.252+46C>T	chr10.hg19:g.120867722C>T		NA	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	hg19	CCDS7609.1	0.02	1.499886	GGGxGCG	COVERED																																																																																			NOVEL	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050623.1	7	3.139502	KEEP	0	1	30	21	592	CC	0.999879	0.979408	0		+	4	60	124	0	0	8.120931	50	60	1626	109	ENST00000361432.2	0.074074	0.979526
FAM45A	404636	__UNKNOWN__	__UNKNOWN__	10	120894689	120894689	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:120894689A>G	ENST00000361432.2	+	9	923				FAM45A_ENST00000489988.1_Intron|FAM45A_ENST00000535029.1_Intron|FAM45A_ENST00000544016.1_Intron	NM_207009.2	NP_996892.1	Q8TCE6	FA45A_HUMAN	family with sequence similarity 45, member A	NA		NA								breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	14		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0293)		aaaaaaaaaaaaaaaaaaaaa	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF168713	CCDS7609.1	10q25	2008-09-04			ENSG00000119979	ENSG00000119979	404636			31793	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207009	NM_207009	NA	Approved			Q8TCE6	OTTHUMG00000019143	ENST00000361432.2:c.898-1294A>G	chr10.hg19:g.120894689A>G		NA	B1AMV6|B4DDC3|D3DRC8|Q9NXW4	hg19	CCDS7609.1	0.02	-0.09647	AAAxAAA	UNCOVERED																																																																																			NOVEL	FAM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050623.1	5	2.406001	KEEP	3	0	0	8	218	AA	0	0	0		+	3	60	90	0	0	7.943367	6	60	178	30	ENST00000361432.2	0.333333	0.139832
SFXN4	119559	__UNKNOWN__	__UNKNOWN__	10	120915660	120915660	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:120915660C>A	ENST00000355697.2	-	10	636				SFXN4_ENST00000330036.6_Intron|SFXN4_ENST00000461438.1_Intron	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	NA		NA			iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		TAGggccaggcgcggtggctc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605	119559		Sideroflexins	16088	protein-coding gene	gene with protein product		615564			NA	14756423	Standard	XM_058406	NM_213649	NA	Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.616+529G>T	chr10.hg19:g.120915660C>A		NA	Q6WSU4|Q86TD9	hg19	CCDS7610.1	0.02	-0.140323	AGGxGCG	COVERED																																																																																			NOVEL	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050642.3	5	2.407029	KEEP	0	0	0	8	241	CC	0.99257	0.259026	0		-	3	60	81	0	0	6.373821	11	60	372	35	ENST00000355697.2	0.214286	0.260965
SFXN4	119559	__UNKNOWN__	__UNKNOWN__	10	120918550	120918550	__UNKNOWN__	Intron	SNP	C	C	G	rs567992959		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:120918550C>G	ENST00000355697.2	-	6	380				SFXN4_ENST00000330036.6_Intron|SFXN4_ENST00000461438.1_Intron	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	NA		NA			iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		ccagcactttcggaggccaag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605	119559		Sideroflexins	16088	protein-coding gene	gene with protein product		615564			NA	14756423	Standard	XM_058406	NM_213649	NA	Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.360+689G>C	chr10.hg19:g.120918550C>G		NA	Q6WSU4|Q86TD9	hg19	CCDS7610.1	0.02	-0.131575	TTTxGGA	COVERED																																																																																			NOVEL	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050642.3	3	3.862531	KEEP	1	0	0	13	343	CC	0.994391	0.227888	0		-	3	60	103	0	0	8.572754	11	60	343	41	ENST00000355697.2	0.214286	0.229173
GRK5	2869	__UNKNOWN__	__UNKNOWN__	10	121093796	121093796	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:121093796A>G	ENST00000392870.2	+	2	477					NM_005308.2	NP_005299.1	P34947	GRK5_HUMAN	G protein-coupled receptor kinase 5	NA		NA			adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|protein autophosphorylation (GO:0046777)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|phospholipid binding (GO:0005543)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(5)|lung(15)|skin(3)|stomach(1)|urinary_tract(1)	27		Lung NSC(174;0.0971)|all_lung(145;0.127)|Ovarian(717;0.249)		all cancers(201;0.0227)		gctccagcctaggtgacagag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L15388	CCDS7612.1	10q26.11	2013-09-19	2004-02-04	2004-02-06	ENSG00000198873	ENSG00000198873	2869			4544	protein-coding gene	gene with protein product		600870		GPRK5	NA	7685906	Standard	NM_005308	NM_005308	NA	Approved		uc001led.3	P34947	OTTHUMG00000019149	ENST00000392870.2:c.148+7673A>G	chr10.hg19:g.121093796A>G		NA	D3DRD0|Q5T059	hg19	CCDS7612.1	0.02	-0.359573	CCTxGGT	COVERED																																																																																			NOVEL	GRK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050652.2	3	4.510562	KEEP	0	0	0	15	400	AA	0.99649	0.885755	0		+	3	60	106	0	0	7.439885	36	60	1060	81	ENST00000392870.2	0.076923	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	121392237	121392237	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:121392237T>C			NA	NA				TIAL1 (35696 upstream) : BAG3 (18644 downstream)						NA		NA									NA						cgtggtggcttatgcctgtaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.121392237T>C		NA		hg19		0.02	-0.114015	GCTxATG	UNCOVERED																																																																																			NOVEL					0			4	3.007256	KEEP	0	0	0	10	271	TT	0.992708	0.161282	0			3	60	105	0	0	9.279076	7	60	200	34		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	121392239	121392239	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:121392239T>C			NA	NA				TIAL1 (35698 upstream) : BAG3 (18642 downstream)						NA		NA									NA						tggtggcttatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.121392239T>C		NA		hg19		0.02	-0.122785	TTAxGCC	COVERED																																																																																			NOVEL					0			4	3.308452	KEEP	0	0	0	11	307	TT	0.993072	0.194952	0			3	60	95	0	0	8.132386	8	60	243	37		0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	121478850	121478850	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:121478850G>A			NA	NA				BAG3 (41519 upstream) : INPP5F (6758 downstream)						NA		NA									NA						ttacaggcatgagccaccacg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.121478850G>A		NA		hg19		0.02	-0.219314	CATxAGC	COVERED																																																																																			NOVEL					0			8	3.308889	KEEP	0	0	0	11	317	GG	0.993072	0.549057	0			3	40	95	1	0	7.005642	21	60	717	54		0.125	0.552887
SEC23IP	11196	__UNKNOWN__	__UNKNOWN__	10	121694749	121694749	__UNKNOWN__	Intron	SNP	G	G	A	rs2420649	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:121694749G>A	ENST00000369075.3	+	18	3095				SEC23IP_ENST00000543134.1_Intron	NM_007190.3	NP_009121.1	Q9Y6Y8	S23IP_HUMAN	SEC23 interacting protein	NA		NA			acrosome assembly (GO:0001675)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|single fertilization (GO:0007338)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear endoplasmic reticulum (GO:0097038)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	36		Lung NSC(174;0.109)|all_lung(145;0.142)|all_neural(114;0.234)		all cancers(201;0.00515)		gaggcaggtggattacttgag	0.453		NA											G|||	584	0.116613	0.0023	0.0274	5008	,	,	NA	18116	0.1984	NA	0.0537	False	NA	,,,	NA	NA	NA	2504	0.3149	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB019435	CCDS7618.1	10q26.11-q26.12	2013-01-10			ENSG00000107651	ENSG00000107651	11196		Sterile alpha motif (SAM) domain containing	17018	protein-coding gene	gene with protein product		NA			NA	10400679	Standard		NM_007190	NA	Approved	p125	uc001leu.2	Q9Y6Y8	OTTHUMG00000019161	ENST00000369075.3:c.3000+1450G>A	chr10.hg19:g.121694749G>A		NA	D3DRD2|Q8IXH5|Q9BUK5	hg19	CCDS7618.1	0.02	-0.131571	GTGxATT	UNCOVERED																																																																																			NOVEL	SEC23IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050688.1	6	2.406811	KEEP	3	0	0	8	235	GG	0	0	0		+	4	60	111	0	0	9.523124	9	60	309	34	ENST00000369075.3	0.307692	0.229173
PPAPDC1A	196051	__UNKNOWN__	__UNKNOWN__	10	122323055	122323055	__UNKNOWN__	Intron	SNP	G	G	A	rs75325606	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:122323055G>A	ENST00000369073.3	+	6	415				PPAPDC1A_ENST00000398250.1_Intron|PPAPDC1A_ENST00000439221.1_Intron|PPAPDC1A_ENST00000541332.1_Intron|PPAPDC1A_ENST00000398248.1_Intron			Q5VZY2	PPC1A_HUMAN	phosphatidic acid phosphatase type 2 domain containing 1A	NA		NA			Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|phospholipid dephosphorylation (GO:0046839)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	20		Lung NSC(174;0.1)|all_lung(145;0.132)		all cancers(201;0.0117)		gctcacgcctgtaatcccagc	0.463		NA											-|||	826	0.164936	0.0439	0.1916	5008	,	,	NA	12485	0.1915	NA	0.2366	False	NA	,,,	NA	NA	NA	2504	0.2086	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098668	CCDS41573.1	10q26.13	2008-02-05		2005-07-15	ENSG00000203805	ENSG00000203805	196051			23531	protein-coding gene	gene with protein product		NA	phosphatidic acid phosphatase type 2 domain containing 1	PPAPDC1	NA		Standard	XM_113641	XM_005269592	NA	Approved		uc001lev.1	Q5VZY2	OTTHUMG00000019168	ENST00000369073.3:c.416-11588G>A	chr10.hg19:g.122323055G>A		NA	A2RU82|Q08EQ2|Q0IIP2|Q495B4|Q5VZY1	hg19		0.02	-0.105245	CCTxTAA	UNCOVERED																																																																																			NOVEL	PPAPDC1A-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050701.1	5	2.707897	KEEP	10	0	0	9	272	GG	0	0	0		+	6	60	166	0	0	16.536357	4	60	139	40	ENST00000369073.3	0.6	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	123130356	123130356	__UNKNOWN__	IGR	SNP	G	G	C	rs11199933	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:123130356G>C			NA	NA				RP11-159H3.2 (184876 upstream) : RN7SKP167 (40073 downstream)						NA		NA									NA						ttgaacctgggagtcggaggt	0.512		NA											G|||	1450	0.289537	0.1626	0.2421	5008	,	,	NA	16572	0.3948	NA	0.3867	False	NA	,,,	NA	NA	NA	2504	0.2863	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.123130356G>C		NA		hg19		0.02	-0.052633	TGGxAGT	UNCOVERED																																																																																			NOVEL					0			5	2.407179	KEEP	0	0	0	8	245	GG	0.99257	0.036492	0			2	45	69	1	0	6.650192	2	60	62	20		0.5	0.036766
FGFR2	2263	__UNKNOWN__	__UNKNOWN__	10	123241631	123241631	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:123241631A>G	ENST00000457416.2	-	17	2896				FGFR2_ENST00000369056.1_3'UTR|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000358487.5_Intron|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000360144.3_3'UTR|FGFR2_ENST00000351936.6_Intron|FGFR2_ENST00000346997.2_Intron|FGFR2_ENST00000478859.1_Intron|FGFR2_ENST00000369059.1_Intron|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000369060.4_Intron	NM_022970.3	NP_075259.4	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	NA		NA			angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	gattacaggcatgagccactg	0.493		5	Mis		gastric. NSCLC, endometrial		Crouzon, Pfeiffer, and Apert syndromes		Saethre-Chotzen syndrome;Apert syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	0													77	69	71			NA	NA	10		NA											NA				123241631		692	1591	2283	SO:0001627	intron_variant	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468	2263		CD molecules, Immunoglobulin superfamily / I-set domain containing	3689	protein-coding gene	gene with protein product	Crouzon syndrome, Pfeiffer syndrome	176943	bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Jackson-Weiss syndrome	KGFR, BEK, CFD1, JWS	NA		Standard	NM_022976, NM_000141	NM_022970	NA	Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000457416.2:c.2304+1580T>C	chr10.hg19:g.123241631A>G		NA	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	hg19	CCDS7620.2	0.02	5.253374	GGCxTGA	COVERED																																																																																			NOVEL	FGFR2-010	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050724.1	58	13.488227	KEEP	1	8	224	124	3416	AA	1	1	0		-	10	60	329	1	0	21.465449	149	60	4397	462	ENST00000457416.2	0.062893	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	123410066	123410066	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:123410066A>G			NA	NA				RP11-62L18.3 (34713 upstream) : RP11-78A18.2 (85751 downstream)						NA		NA									NA						catggctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.123410066A>G		NA		hg19		0.02	-0.16658	CACxCCT	COVERED																																																																																			NOVEL					0			10	4.208104	KEEP	0	0	0	14	359	AA	0.995343	0.352299	0			3	60	88	0	0	6.635433	16	60	435	44		0.157895	0.353947
BTBD16	118663	__UNKNOWN__	__UNKNOWN__	10	124094316	124094316	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:124094316T>C	ENST00000260723.4	+	14	1415				BTBD16_ENST00000368994.2_Intron|BTBD16_ENST00000495370.2_Intron	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	NA		NA								breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				ggattacaggtgtgaaccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152	118663		BTB/POZ domain containing	26340	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 87	C10orf87	NA		Standard	NM_144587	NM_144587	NA	Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1165-80T>C	chr10.hg19:g.124094316T>C		NA	A6NM63|Q4VXL1|Q96LN0	hg19	CCDS31301.1	0.02	3.672284	AGGxGTG	COVERED																																																																																			NOVEL	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050780.3	43	13.892193	KEEP	1	5	147	98	2684	TT	1	1	0		+	5	60	172	0	0	10.758456	105	60	2993	336	ENST00000260723.4	0.045455	1
BTBD16	118663	__UNKNOWN__	__UNKNOWN__	10	124094321	124094321	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:124094321A>G	ENST00000260723.4	+	14	1415				BTBD16_ENST00000368994.2_Intron|BTBD16_ENST00000495370.2_Intron	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	NA		NA								breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				acaggtgtgaaccaccacgcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152	118663		BTB/POZ domain containing	26340	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 87	C10orf87	NA		Standard	NM_144587	NM_144587	NA	Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1165-75A>G	chr10.hg19:g.124094321A>G		NA	A6NM63|Q4VXL1|Q96LN0	hg19	CCDS31301.1	0.02	3.776317	TGAxCCA	COVERED																																																																																			NOVEL	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050780.3	45	5.938729	KEEP	2	7	211	94	2567	AA	1	1	0		+	7	60	240	0	0	15.815426	111	60	3239	353	ENST00000260723.4	0.059322	1
RP11-282I1.1	0	__UNKNOWN__	__UNKNOWN__	10	125177610	125177610	__UNKNOWN__	lincRNA	SNP	A	A	G	rs139301981	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:125177610A>G	ENST00000448347.1	+	0	586										NA		NA									NA						gacctcaggtaatccgcctgc	0.478		NA											A|||	138	0.0275559	0.0045	0.0418	5008	,	,	NA	16734	0.0	NA	0.0865	False	NA	,,,	NA	NA	NA	2504	0.0164	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000448347.1:	chr10.hg19:g.125177610A>G		NA		hg19		0.02	-0.070158	GGTxATC	UNCOVERED																																																																																			NOVEL	RP11-282I1.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000050847.1	14	3.306974	KEEP	14	0	0	11	285	AA	0	0	0		+	4	40	122	0	0	12.031348	3	60	88	39	ENST00000448347.1	0.571429	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	126119067	126119067	__UNKNOWN__	IGR	SNP	A	A	G	rs7894266	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126119067A>G			NA	NA				OAT (11522 upstream) : RP13-238F13.5 (14740 downstream)						NA		NA									NA						ggcatgagccaccaagcccag	0.458		NA											A|||	4190	0.836661	0.6566	0.8069	5008	,	,	NA	15119	0.9881	NA	0.835	False	NA	,,,	NA	NA	NA	2504	0.9468	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.126119067A>G		NA		hg19		0.02	-0.114002	GCCxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.405832	KEEP	0	0	0	8	216	AA	0.99257	0.16126	0			4	60	134	0	0	12.38643	6	60	167	31		0.4	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	126132668	126132668	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126132668T>C			NA	NA				OAT (25123 upstream) : RP13-238F13.5 (1139 downstream)						NA		NA									NA						agaagaattgtttgaacctag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.126132668T>C		NA		hg19		0.02	-0.271736	TTGxTTG	COVERED																																																																																			NOVEL					0			3	3.236842	KEEP	1	1	23	19	494	TT	0.99986	0.717215	0			3	60	92	0	0	6.399577	27	60	716	59		0.1	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	126132730	126132730	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126132730T>C			NA	NA				OAT (25185 upstream) : RP13-238F13.5 (1077 downstream)						NA		NA									NA						ccagcctgggtgacagagtga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.126132730T>C		NA		hg19		0.02	1.382783	GGGxGAC	COVERED																																																																																			NOVEL					0			24	10.277794	KEEP	1	2	59	55	1438	TT	1	0.999895	0			4	60	130	1	0	7.82852	85	60	2505	210		0.044944	0.999895
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	126132817	126132817	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126132817T>C			NA	NA				OAT (25272 upstream) : RP13-238F13.5 (990 downstream)						NA		NA									NA						AATCTtggcttatgcctgtaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.126132817T>C		NA		hg19		0.02	1.637607	GCTxATG	COVERED																																																																																			NOVEL					0			42	8.238445	KEEP	1	4	124	71	1874	TT	1	0.99994	0			4	60	136	0	0	8.330816	90	60	2609	228		0.042553	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	126142000	126142000	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126142000C>T			NA	NA				NKX1-2 (3247 upstream) : LHPP (8402 downstream)						NA		NA									NA						ggattacaggcgtgagctacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.126142000C>T		NA		hg19		0.02	-0.175436	AGGxGTG	COVERED																																																																																			NOVEL					0			11	2.406458	KEEP	0	0	0	8	233	CC	0.99257	0.384528	0			3	60	86	0	0	6.361602	17	60	559	35		0.15	0.387407
FAM53B	9679	__UNKNOWN__	__UNKNOWN__	10	126409639	126409639	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126409639T>C	ENST00000280780.6	-	2	257				FAM53B_ENST00000392754.3_Intron|RP11-12J10.3_ENST00000494792.1_Intron|FAM53B_ENST00000337318.3_Intron			Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	NA		NA								cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		ggcatggtggtgcatgcctgt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319	9679			28968	protein-coding gene	gene with protein product		NA	KIAA0140	KIAA0140	NA	8590280	Standard	NM_014661	NM_014661	NA	Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000280780.6:c.174-14183A>G	chr10.hg19:g.126409639T>C		NA	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	hg19		0.02	-0.271891	TGGxGCA	COVERED																																																																																			NOVEL	FAM53B-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000050881.1	11	3.608728	KEEP	1	0	0	12	325	TT	0.993634	0.712749	0		-	3	60	103	0	0	7.452549	28	60	835	60	ENST00000280780.6	0.096774	0.717315
RP11-12J10.3	0	__UNKNOWN__	__UNKNOWN__	10	126439302	126439302	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126439302A>G	ENST00000494792.1	-	6	628										NA		NA									NA						gctcacacctataatcccagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000494792.1:c.602+9652T>C	chr10.hg19:g.126439302A>G		NA		hg19		0.02	-0.210484	CCTxTAA	COVERED																																																																																			NOVEL	RP11-12J10.3-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000411896.1	9	2.706632	KEEP	0	0	0	9	244	AA	0.99254	0.518266	0		-	5	60	159	0	0	13.166051	17	60	503	47	ENST00000494792.1	0.227273	0.522161
METTL10	399818	__UNKNOWN__	__UNKNOWN__	10	126450952	126450952	__UNKNOWN__	Silent	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:126450952C>G	ENST00000368836.2	-	6	828	c.792G>C	c.(790-792)ctG>ctC	p.L264L	RP11-12J10.3_ENST00000494792.1_Intron	NM_212554.2	NP_997719.2	Q5JPI9	MET10_HUMAN	methyltransferase like 10	264		NA					methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(1)	5		all_lung(145;0.0186)|Lung NSC(174;0.0295)|all_neural(114;0.116)|Colorectal(57;0.172)		Colorectal(40;0.101)|COAD - Colon adenocarcinoma(40;0.111)		ccaggagttccagaccagcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													23	24	23			NA	NA	10		NA											NA				126450952		1327	2309	3636	SO:0001819	synonymous_variant				CCDS31307.1	10q26.13	2010-01-15			ENSG00000203791	ENSG00000203791	399818			33787	protein-coding gene	gene with protein product		NA	chromosome 10 open reading frame 138	C10orf138	NA		Standard	NM_212554	NM_212554	NA	Approved	Em:AC068896.3	uc001lhy.1	Q5JPI9	OTTHUMG00000019217	ENST00000368836.2:c.792G>C	chr10.hg19:g.126450952C>G		NA	A8MPY7	hg19	CCDS31307.1	0.02	1.566769	TTCxAGA	COVERED																																																																																			NOVEL	METTL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050884.1	18	4.210936	KEEP	2	3	82	43	1292	CC	1	0.997553	0		-	5	60	148	0	0	9.573751	59	60	1988	153	ENST00000368836.2	0.078125	0.997553
DHX32	55760	__UNKNOWN__	__UNKNOWN__	10	127556043	127556043	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:127556043C>T	ENST00000284690.3	-	2	773				DHX32_ENST00000284688.6_Intron	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	NA		NA				mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|stomach(1)	29		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				tggtggctcacgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7652.1	10q26.11-q26.2	2008-01-07	2004-01-29	2004-01-30	ENSG00000089876	ENSG00000089876	55760		DEAH-boxes	16717	protein-coding gene	gene with protein product		607960	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32	DDX32	NA		Standard	NM_018180	NM_018180	NA	Approved	FLJ10889, FLJ10694, DHLP1	uc001ljf.1	Q7L7V1	OTTHUMG00000019238	ENST00000284690.3:c.283-291G>A	chr10.hg19:g.127556043C>T		NA	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	hg19	CCDS7652.1	0.02	-0.210521	TCAxGCC	COVERED																																																																																			NOVEL	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000050945.2	7	2.406767	KEEP	1	0	0	8	233	CC	0.99254	0.518266	0		-	3	60	88	0	0	6.428219	19	60	624	54	ENST00000284690.3	0.136364	0.522161
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127588033	127588033	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:127588033T>G	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				tcctgcctcgtcctcccaaag	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+2809T>G	chr10.hg19:g.127588033T>G		NA	Q6UXY9|Q6X7T6	hg19		0.02	1.944475	TCGxCCT	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	36	6.610718	KEEP	6	3	85	52	1439	TT	1	0.990964	0		+	4	60	138	0	0	10.063521	36	60	1069	180	ENST00000368695.1	0.1	0.990964
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127593421	127593421	__UNKNOWN__	Intron	SNP	G	G	A	rs113021570		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:127593421G>A	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				CTggccgggcgcggtggctca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+8197G>A	chr10.hg19:g.127593421G>A		NA	Q6UXY9|Q6X7T6	hg19		0.02	1.465761	GGCxCGG	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	37	2.472322	KEEP	6	2	56	28	824	GG	0.999997	0.98794	0		+	6	60	185	0	0	13.577627	41	60	1328	139	ENST00000368695.1	0.12766	0.987943
FANK1	92565	__UNKNOWN__	__UNKNOWN__	10	127608054	127608054	__UNKNOWN__	Intron	SNP	T	T	G	rs77002387		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:127608054T>G	ENST00000368695.1	+	1	117				FANK1_ENST00000449042.2_Intron|FANK1_ENST00000368693.1_Intron	NM_145235.3	NP_660278.3	Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				ggattacaggtgtgagccact	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780	92565		Ankyrin repeat domain containing, Fibronectin type III domain containing	23527	protein-coding gene	gene with protein product		611640	fibronectin type 3 and ankyrin repeat domains 1		NA	12477932	Standard	NM_145235	NM_145235	NA	Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368695.1:c.-6+22830T>G	chr10.hg19:g.127608054T>G		NA	Q6UXY9|Q6X7T6	hg19		0.02	-0.342085	AGGxGTG	COVERED																																																																																			NOVEL	FANK1-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000050950.1	24	4.20164	KEEP	7	2	36	27	725	TT	0.999997	0.888873	0		+	7	60	236	0	0	20.363405	19	60	580	103	ENST00000368695.1	0.269231	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	128385881	128385881	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:128385881G>C			NA	NA				C10orf90 (26802 upstream) : SNORD60 (82389 downstream)						NA		NA									NA						gaccccatctgtacaaaaaaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.128385881G>C		NA		hg19		0.02	-0.140351	TCTxTAC	COVERED																																																																																			NOVEL					0			5	2.40724	KEEP	0	0	0	8	248	GG	0.99257	0.289832	0			3	60	93	0	0	7.472313	12	60	401	33		0.2	0.292001
DOCK1	1793	__UNKNOWN__	__UNKNOWN__	10	128601024	128601024	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:128601024G>A	ENST00000280333.6	+	1	155					NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	NA		NA			apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		gaccgggcgcggtggctcacg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760	1793			2987	protein-coding gene	gene with protein product	DOwnstream of CrK	601403	dedicator of cyto-kinesis 1		NA	8657152, 8661160	Standard	NM_001380	XM_006717681	NA	Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.46+6892G>A	chr10.hg19:g.128601024G>A		NA	A9Z1Z5	hg19		0.02	-0.157891	CGCxGTG	COVERED																																																																																			NOVEL	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000050979.2	11	3.610456	KEEP	0	0	0	12	359	GG	0.993634	0.320751	0		+	3	60	84	0	0	6.67294	11	60	366	43	ENST00000280333.6	0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	129647164	129647164	__UNKNOWN__	IGR	SNP	G	G	C	rs61874846	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:129647164G>C			NA	NA				FOXI2 (107714 upstream) : CLRN3 (28940 downstream)						NA		NA									NA						acgaggtcaggagatcgagac	0.592		NA											C|||	1030	0.205671	0.2057	0.2464	5008	,	,	NA	11545	0.0823	NA	0.2763	False	NA	,,,	NA	NA	NA	2504	0.2311	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.129647164G>C		NA		hg19		0.02	-0.052638	CAGxAGA	UNCOVERED																																																																																			NOVEL					0			11	3.610952	KEEP	21	0	0	12	374	GG	0	0	0			2	60	68	0	0	6.549968	2	4	71	48		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	129929089	129929089	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:129929089C>T			NA	NA				MKI67 (4440 upstream) : RP11-264E18.1 (185456 downstream)						NA		NA									NA						catgagccaccgcacccggcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.129929089C>T		NA		hg19		0.02	-0.228046	CACxGCA	COVERED																																																																																			NOVEL					0			12	3.87546	KEEP	0	0	0	13	353	CC	0.994391	0.57966	0			3	60	92	0	0	7.03373	16	60	500	48		0.157895	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	129978014	129978014	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:129978014G>A			NA	NA				MKI67 (53365 upstream) : RP11-264E18.1 (136531 downstream)						NA		NA									NA						ctgggttcaagcaattctcct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.129978014G>A		NA		hg19		0.02	-0.078945	CAAxCAA	UNCOVERED																																																																																			NOVEL					0			12	2.707759	KEEP	9	0	0	9	267	GG	0	0	0			3	29	84	0	0	7.532092	5	60	174	31		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	130851599	130851599	__UNKNOWN__	IGR	SNP	A	A	G	rs12411639	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:130851599A>G			NA	NA				RP11-442O18.1 (93273 upstream) : RP11-168C9.1 (224915 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.468		NA											N|||	566	0.113019	0.0038	0.2406	5008	,	,	NA	15661	0.2183	NA	0.0527	False	NA	,,,	NA	NA	NA	2504	0.1237	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.130851599A>G		NA		hg19		0.02	-0.227948	GGCxTGA	COVERED																																																																																			NOVEL					0			6	4.812056	KEEP	1	0	0	16	438	AA	0.99649	0.580884	0			3	60	100	0	0	7.565481	20	60	576	66		0.130435	0.58293
LINC00959	387723	__UNKNOWN__	__UNKNOWN__	10	131895311	131895311	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:131895311A>G	ENST00000456581.1	-	0	380									long intergenic non-protein coding RNA 959	NA		NA									NA						tgtaacctctacctcctgggt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							10q26.3	2013-06-06			ENSG00000237489	ENSG00000237489	387723		Long non-coding RNAs	48677	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_034125	NA	Approved				OTTHUMG00000019268	ENST00000456581.1:	chr10.hg19:g.131895311A>G		NA		hg19		0.02	-0.061377	TCTxCCT	UNCOVERED																																																																																			NOVEL	LINC00959-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000051025.1	8	2.404569	KEEP	3	0	0	8	202	AT	0	0	0		-	2	33	71	0	0	6.3964	4	60	108	20	ENST00000456581.1	0.333333	0.043787
GLRX3	10539	__UNKNOWN__	__UNKNOWN__	10	131947065	131947065	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:131947065A>G	ENST00000368644.1	+	2	223				GLRX3_ENST00000331244.5_Intron	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	NA		NA			cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		agtggctcacacctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010	10539			15987	protein-coding gene	gene with protein product	glutaredoxin 4	612754	thioredoxin-like 2	TXNL2	NA	10636891, 11124703	Standard	NM_006541	NM_006541	NA	Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.201+3482A>G	chr10.hg19:g.131947065A>G		NA	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	hg19	CCDS7661.1	0.02	-0.122792	CACxCCT	COVERED																																																																																			NOVEL	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051021.1	3	2.406362	KEEP	0	0	0	8	224	AA	0.99257	0.194853	0		+	3	60	101	0	0	8.482063	10	60	298	29	ENST00000368644.1	0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	133772319	133772319	__UNKNOWN__	IGR	SNP	G	G	A	rs377070130		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:133772319G>A			NA	NA				PPP2R2D (2300 upstream) : BNIP3 (9258 downstream)						NA		NA									NA						TGTGGAGATGGAGGCGTGTGC	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.133772319G>A		NA		hg19		0.02	1.401063	ATGxAGG	COVERED																																																																																			NOVEL					0			6	6.751375	KEEP	1	1	24	31	924	GG	0.999997	0.979524	0			5	60	123	0	0	7.790143	42	60	1370	124		0.106383	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	10	133911652	133911652	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:133911652G>A			NA	NA				BNIP3 (116217 upstream) : JAKMIP3 (6522 downstream)						NA		NA									NA						cgatcctcccgcctcagcctc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr10.hg19:g.133911652G>A		NA		hg19		0.02	-0.096491	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			3	2.406897	KEEP	0	0	0	8	237	CG	0.99254	0.119538	0			3	60	87	0	0	7.478168	7	60	240	22		0.3	0.120436
JAKMIP3	282973	__UNKNOWN__	__UNKNOWN__	10	133940851	133940851	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:133940851C>T	ENST00000298622.4	+	3	771					NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	NA		NA				Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		ctcagcctcccaagtagctgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385	282973			23523	protein-coding gene	gene with protein product	neuroendocrine long coiled-coil 2	611198	chromosome 10 open reading frame 39, chromosome 10 open reading frame 14	C10orf39, C10orf14	NA	15277531, 17572408	Standard	NM_194303	NM_001105521	NA	Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.634-5965C>T	chr10.hg19:g.133940851C>T		NA	A6PW00|Q69YM6|Q6ZT29	hg19	CCDS44494.1	0.02	-0.122805	TCCxAAG	COVERED																																																																																			NOVEL	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051049.3	10	2.706955	KEEP	1	0	0	9	272	CC	0.99254	0.194847	0		+	3	60	88	0	0	7.072855	11	60	365	30	ENST00000298622.4	0.214286	0.196312
JAKMIP3	282973	__UNKNOWN__	__UNKNOWN__	10	133940852	133940852	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:133940852A>G	ENST00000298622.4	+	3	771					NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	NA		NA				Golgi apparatus (GO:0005794)				breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		tcagcctcccaagtagctggg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832756	CCDS44494.1	10q26.3	2009-04-23	2009-04-23	2008-01-28	ENSG00000188385	ENSG00000188385	282973			23523	protein-coding gene	gene with protein product	neuroendocrine long coiled-coil 2	611198	chromosome 10 open reading frame 39, chromosome 10 open reading frame 14	C10orf39, C10orf14	NA	15277531, 17572408	Standard	NM_194303	NM_001105521	NA	Approved	FLJ37857, NECC2, KIAA4091, bA140A10.5	uc001lkx.4	Q5VZ66	OTTHUMG00000150167	ENST00000298622.4:c.634-5964A>G	chr10.hg19:g.133940852A>G		NA	A6PW00|Q69YM6|Q6ZT29	hg19	CCDS44494.1	0.02	-0.122782	CCCxAGT	COVERED																																																																																			NOVEL	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000051049.3	10	2.707003	KEEP	1	0	0	9	251	AA	0.99254	0.194847	0		+	3	60	91	0	0	7.482217	10	60	290	30	ENST00000298622.4	0.230769	0.196312
FRG2B	441581	__UNKNOWN__	__UNKNOWN__	10	135439049	135439049	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs200347477		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr10:135439049G>C	ENST00000425520.1	-	4	443	c.391C>G	c.(391-393)Cct>Gct	p.P131A	FRG2B_ENST00000443774.1_Missense_Mutation_p.P132A	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	131		NA				nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTGTGCACAGGAGTGGAGGAT	0.537		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15405	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													57	67	64			NA	NA	10		NA											NA				135439049		2164	4277	6441	SO:0001583	missense			AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899	441581			33518	protein-coding gene	gene with protein product		NA			NA	15520407	Standard	NM_001080998	NM_001080998	NA	Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.391C>G	chr10.hg19:g.135439049G>C	ENSP00000401310:p.Pro131Ala	NA	Q5VSQ1	hg19	CCDS44502.1	0.02	1.926867	CAGxAGT	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.070	-1.203939	0.01581	.	.	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.39056	1.1;1.1	.	.	.	.	3.000390	0.01542	N	0.019277	T	0.14356	0.0347	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	8	0.07644	T	0.81	0.8293	.	.	.	.	131	Q96QU4	FRG2B_HUMAN	A	132;131	ENSP00000408343:P132A;ENSP00000401310:P131A	ENSP00000401310:P131A	P	-	1	0	FRG2B	135289039	0.014000	0.17966	0.057000	0.19452	0.057000	0.15508	-0.781000	0.04648	-1.905000	0.01090	-2.023000	0.00429	CCT	NOVEL	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467780.1	2	2.4071	KEEP	5	0	0	8	245	GG	0.99257	0.985548	0		-	5	40	150	0	0	10.250787	47	60	1568	108	ENST00000425520.1	0.096154	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	120854	120854	__UNKNOWN__	IGR	SNP	A	A	C	rs372791874		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:120854A>C			NA	NA				None (None upstream) : RP11-304M2.6 (424 downstream)						NA		NA									NA						ctggagtgtaatggtgagatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.120854A>C		NA		hg19		0.02	-0.139906	GTAxTGG	COVERED																																																																																			NOVEL					0			1	2.705794	KEEP	6	0	0	9	235	AA	0.99257	0.289832	0			5	40	171	0	0	15.737389	8	48	204	41		0.384615	0.292001
PTDSS2	81490	__UNKNOWN__	__UNKNOWN__	11	486834	486834	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:486834C>T	ENST00000308020.5	+	5	611					NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	ggcgacagagcgagactccat	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915	81490			15463	protein-coding gene	gene with protein product		612793			NA	14984733	Standard		NM_030783	NA	Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.436-105C>T	chr11.hg19:g.486834C>T		NA		hg19	CCDS7696.1	0.02	-0.33326	GAGxGAG	COVERED																																																																																			NOVEL	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000239301.2	9	2.501352	KEEP	0	3	72	34	979	CC	1	0.851984	0		+	6	60	169	0	0	13.059211	26	60	849	104	ENST00000308020.5	0.1875	0.851984
DEAF1	10522	__UNKNOWN__	__UNKNOWN__	11	658194	658194	__UNKNOWN__	Intron	SNP	T	T	C	rs4963173	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:658194T>C	ENST00000382409.3	-	11	1988				DEAF1_ENST00000525904.1_Intron|DEAF1_ENST00000338675.6_Intron	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	NA		NA			anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		tttgggaggctgaggcaggcg	0.458		NA											C|||	3970	0.792732	0.857	0.6657	5008	,	,	NA	19092	0.9365	NA	0.6988	False	NA	,,,	NA	NA	NA	2504	0.7444	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030	10522		Zinc fingers, MYND-type	14677	protein-coding gene	gene with protein product		602635	deformed epidermal autoregulatory factor 1 (Drosophila)		NA	9773984	Standard	NM_021008	XR_428838	NA	Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1504-4143A>G	chr11.hg19:g.658194T>C		NA	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	hg19	CCDS31327.1	0.02	-0.0614	GGCxGAG	UNCOVERED																																																																																			NOVEL	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000383614.3	7	3.910384	KEEP	7	0	0	13	369	TT	0.99257	0.043461	0		-	3	60	95	0	0	9.124764	3	60	92	31	ENST00000382409.3	0.5	0.043787
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016756	1016756	__UNKNOWN__	Silent	SNP	G	G	A	rs537530758	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1016756G>A	ENST00000421673.2	-	31	6095	c.6045C>T	c.(6043-6045)tcC>tcT	p.S2015S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2015	Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGTCACCAAGGAGGTGGAGA	0.542		NA											G|||	13	0.00259585	0.0	0.0072	5008	,	,	NA	28170	0.0	NA	0.008	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													879	819	839			NA	NA	11		NA											NA				1016756		2203	4296	6499	SO:0001819	synonymous_variant			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.6045C>T	chr11.hg19:g.1016756G>A		NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	3.212449	CAAxGAG	COVERED																																																																																			NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	29	6.081977	KEEP	21	8	211	95	2918	GG	1	1	0		-	16	60	486	0	0	37.779012	76	60	2529	322	ENST00000421673.2	0.173913	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016818	1016818	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1016818A>G	ENST00000421673.2	-	31	6033	c.5983T>C	c.(5983-5985)Tat>Cat	p.Y1995H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1995	Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGGTTGGATAGGTAGTGGTG	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5983T>C	chr11.hg19:g.1016818A>G	ENSP00000406861:p.Tyr1995His	NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	11.393636	GATxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	A	1.618	-0.522280	0.04171	.	.	ENSG00000184956	ENST00000421673	T	0.19806	2.12	3.08	-6.16	0.02098	.	.	.	.	.	T	0.04272	0.0118	N	0.00823	-1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32771	-0.9894	9	0.15066	T	0.55	.	4.0713	0.09884	0.251:0.1308:0.4892:0.129	.	1995	Q6W4X9	MUC6_HUMAN	H	1995	ENSP00000406861:Y1995H	ENSP00000406861:Y1995H	Y	-	1	0	MUC6	1006818	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-3.876000	0.00344	-2.305000	0.00654	-0.760000	0.03462	TAT	NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	101	18.457119	KEEP	23	20	610	276	7334	AA	1	1	0		-	12	60	419	0	0	28.113056	181	60	5284	920	ENST00000421673.2	0.062176	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016819	1016819	__UNKNOWN__	Silent	SNP	G	G	T	rs369828826		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1016819G>T	ENST00000421673.2	-	31	6032	c.5982C>A	c.(5980-5982)acC>acA	p.T1994T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1994	Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTTGGATAGGTAGTGGTGG	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													1471	1465	1467			NA	NA	11		NA											NA				1016819		2203	4298	6501	SO:0001819	synonymous_variant			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5982C>A	chr11.hg19:g.1016819G>T		NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	8.981882	ATAxGTA	COVERED																																																																																			NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	101	2.393908	KEEP	24	29	759	277	8445	GG	1	1	0		-	38	60	1087	0	0	84.889137	159	60	5452	938	ENST00000421673.2	0.192893	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1016835	1016835	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1016835A>G	ENST00000421673.2	-	31	6016	c.5966T>C	c.(5965-5967)tTc>tCc	p.F1989S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1989	Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.F1989Y(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGTGGTCTGGAAGGATGTTGC	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	lung(2)											1541	1526	1531			NA	NA	11		NA											NA				1016835		2203	4299	6502	SO:0001583	missense			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5966T>C	chr11.hg19:g.1016835A>G	ENSP00000406861:p.Phe1989Ser	NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	13.557186	TGGxAGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	12.65	2.002866	0.35320	.	.	ENSG00000184956	ENST00000421673	T	0.18657	2.2	3.08	-0.788	0.10939	.	.	.	.	.	T	0.12390	0.0301	L	0.38531	1.155	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.41106	-0.9527	9	0.07644	T	0.81	.	6.7728	0.23602	0.4725:0.0:0.5275:0.0	.	1989	Q6W4X9	MUC6_HUMAN	S	1989	ENSP00000406861:F1989S	ENSP00000406861:F1989S	F	-	2	0	MUC6	1006835	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.386000	0.07370	-0.019000	0.14055	0.254000	0.18369	TTC	NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	108	28.698826	KEEP	13	20	604	308	8331	AA	1	1	0		-	10	60	343	0	0	21.840457	190	60	5641	1021	ENST00000421673.2	0.05	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1017401	1017401	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1017401G>A	ENST00000421673.2	-	31	5450	c.5400C>T	c.(5398-5400)caC>caT	p.H1800H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1800	Approximate repeats.|Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TAGGTGGGGAGTGTGTGGTGA	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													627	625	626			NA	NA	11		NA											NA				1017401		2202	4298	6500	SO:0001819	synonymous_variant			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5400C>T	chr11.hg19:g.1017401G>A		NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	5.471813	GGAxTGT	COVERED																																																																																			NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	83	43.248201	KEEP	22	10	248	232	6906	GG	1	1	0		-	10	60	286	0	0	17.533228	137	60	4622	618	ENST00000421673.2	0.068027	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1017417	1017417	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1017417G>A	ENST00000421673.2	-	31	5434	c.5384C>T	c.(5383-5385)aCa>aTa	p.T1795I		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1795	Approximate repeats.|Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGTGAAGGGTGTGGGTAGCCT	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5384C>T	chr11.hg19:g.1017417G>A	ENSP00000406861:p.Thr1795Ile	NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	5.194307	GGTxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.70	2.612249	0.46631	.	.	ENSG00000184956	ENST00000421673	T	0.22539	1.95	3.21	2.27	0.28462	.	.	.	.	.	T	0.39358	0.1075	M	0.64404	1.975	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.05099	-1.0906	9	0.51188	T	0.08	.	9.0622	0.36442	0.1201:0.0:0.8799:0.0	.	1795	Q6W4X9	MUC6_HUMAN	I	1795	ENSP00000406861:T1795I	ENSP00000406861:T1795I	T	-	2	0	MUC6	1007417	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.582000	0.23834	1.760000	0.52011	0.313000	0.20887	ACA	NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	64	5.705682	KEEP	23	18	432	173	5067	GG	1	1	0		-	20	60	529	0	0	37.334227	123	60	4074	568	ENST00000421673.2	0.13986	1
MUC6	4588	__UNKNOWN__	__UNKNOWN__	11	1017988	1017988	__UNKNOWN__	Missense_Mutation	SNP	G	G	T	rs112579249		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1017988G>T	ENST00000421673.2	-	31	4863	c.4813C>A	c.(4813-4815)Cca>Aca	p.P1605T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1605	Pro-rich.|Thr-rich.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTGTGATGGGGTTGGATAG	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													440	415	424			NA	NA	11		NA											NA				1017988		2181	4271	6452	SO:0001583	missense			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956	4588		Mucins	7517	protein-coding gene	gene with protein product		158374	mucin 6, gastric		NA	7680650	Standard	XM_290540	NM_005961	NA	Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4813C>A	chr11.hg19:g.1017988G>T	ENSP00000406861:p.Pro1605Thr	NA	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	hg19	CCDS44513.1	0.02	1.362301	ATGxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	G	1.148	-0.647618	0.03506	.	.	ENSG00000184956	ENST00000421673	T	0.25579	1.79	2.39	-0.213	0.13165	.	.	.	.	.	T	0.28333	0.0700	L	0.35341	1.055	0.09310	N	1	D	0.71674	0.998	D	0.73708	0.981	T	0.18209	-1.0344	9	0.29301	T	0.29	.	0.7847	0.01046	0.1618:0.2393:0.3558:0.2431	.	1605	Q6W4X9	MUC6_HUMAN	T	1605	ENSP00000406861:P1605T	ENSP00000406861:P1605T	P	-	1	0	MUC6	1007988	0.001000	0.12720	0.002000	0.10522	0.020000	0.10135	0.017000	0.13399	0.255000	0.21593	0.297000	0.19635	CCA	NOVEL	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382120.2	23	10.294028	KEEP	13	2	53	53	1587	GG	1	0.999487	0		-	5	50	157	0	0	11.724103	32	60	1051	178	ENST00000421673.2	0.135135	0.999487
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1092884	1092884	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs201415503		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1092884C>T	ENST00000441003.2	+	30	4730	c.4703C>T	c.(4702-4704)aCg>aTg	p.T1568M	MUC2_ENST00000359061.5_Missense_Mutation_p.T1569M|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1569M(2)|p.T1568M(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCACCACCACGGTGacccca	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				4	Substitution - Missense(4)	large_intestine(2)|skin(2)											129	172	157			NA	NA	11		NA											NA				1092884		1964	3669	5633	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4703C>T	chr11.hg19:g.1092884C>T	ENSP00000415183:p.Thr1568Met	NA	Q14878	hg19		0.02	12.563288	CCAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	2.409	-0.335727	0.05278	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14893	2.5;2.47	1.63	0.367	0.16140	.	25.055600	0.00797	U	0.001394	T	0.21841	0.0526	.	.	.	0.09310	N	1	D	0.76494	0.999	P	0.48425	0.577	T	0.35301	-0.9794	9	0.45353	T	0.12	.	8.9064	0.35526	0.0:0.7681:0.2319:0.0	.	1568	E7EUV1	.	M	1568;1569	ENSP00000415183:T1568M;ENSP00000351956:T1569M	ENSP00000351956:T1569M	T	+	2	0	MUC2	1082884	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.878000	0.28126	0.945000	0.37605	0.121000	0.15741	ACG	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	231	70.778534	KEEP	189	23	600	448	13269	CC	1	1	0		+	14	60	406	0	0	20.772231	401	60	13082	1649	ENST00000441003.2	0.033735	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1092891	1092891	__UNKNOWN__	Silent	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1092891C>A	ENST00000441003.2	+	30	4737	c.4710C>A	c.(4708-4710)acC>acA	p.T1570T	MUC2_ENST00000359061.5_Silent_p.T1571T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1571T(1)|p.T1570T(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCACGGTGaccccaaccccaa	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - coding silent(2)	ovary(2)											116	157	142			NA	NA	11		NA											NA				1092891		1961	3652	5613	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4710C>A	chr11.hg19:g.1092891C>A		NA	Q14878	hg19		0.02	12.664857	GACxCCA	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	218	3.890173	KEEP	208	43	1137	416	12796	CC	1	1	0		+	13	60	378	1	0	19.183269	387	60	13033	1627	ENST00000441003.2	0.0325	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1092910	1092910	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1092910G>A	ENST00000441003.2	+	30	4756	c.4729G>A	c.(4729-4731)Ggc>Agc	p.G1577S	MUC2_ENST00000359061.5_Missense_Mutation_p.G1578S|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.G1577S(1)|p.G1578S(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccggcacacagac	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	prostate(2)											85	125	111			NA	NA	11		NA											NA				1092910		1937	3603	5540	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4729G>A	chr11.hg19:g.1092910G>A	ENSP00000415183:p.Gly1577Ser	NA	Q14878	hg19		0.02	13.286048	ACCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	g	2.787	-0.252217	0.05829	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11169	2.8;2.9	1.49	-2.97	0.05530	.	1.221530	0.07178	U	0.853623	T	0.04092	0.0114	.	.	.	0.09310	N	1	B	0.24882	0.113	B	0.11329	0.006	T	0.37798	-0.9690	9	0.07175	T	0.84	.	4.8921	0.13731	0.6336:0.1684:0.198:0.0	.	1577	E7EUV1	.	S	1577;1578	ENSP00000415183:G1577S;ENSP00000351956:G1578S	ENSP00000351956:G1578S	G	+	1	0	MUC2	1082910	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.266000	0.02842	-2.620000	0.00440	-1.713000	0.00713	GGC	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	219	41.858956	KEEP	244	30	810	426	12436	GG	1	1	0		+	20	60	592	0	0	34.044316	393	60	12505	1548	ENST00000441003.2	0.048426	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1092948	1092948	__UNKNOWN__	Silent	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1092948C>G	ENST00000441003.2	+	30	4794	c.4767C>G	c.(4765-4767)acC>acG	p.T1589T	MUC2_ENST00000359061.5_Silent_p.T1590T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1590T(2)|p.T1589T(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	tcaccaccaccactacggtga	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				4	Substitution - coding silent(4)	endometrium(2)|kidney(2)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4767C>G	chr11.hg19:g.1092948C>G		NA	Q14878	hg19		0.02	12.020853	CACxACT	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	182	80.214719	KEEP	245	9	244	353	10477	CC	1	1	0		+	12	59	357	0	0	19.084588	324	60	10508	1193	ENST00000441003.2	0.035714	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093066	1093066	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs56365200	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093066C>A	ENST00000441003.2	+	30	4912	c.4885C>A	c.(4885-4887)Cca>Aca	p.P1629T	MUC2_ENST00000359061.5_Missense_Mutation_p.P1596T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	gaccccaaccccaacagccat	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													123	163	149			NA	NA	11		NA											NA				1093066		1876	3602	5478	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4885C>A	chr11.hg19:g.1093066C>A	ENSP00000415183:p.Pro1629Thr	NA	Q14878	hg19		0.02	4.739491	ACCxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.903	-0.721580	0.03182	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12879	2.64;3.49	1.75	-3.49	0.04724	.	16.324000	0.00424	N	0.000074	T	0.04407	0.0121	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25502	-1.0130	9	0.05620	T	0.96	.	2.5689	0.04790	0.221:0.4621:0.0:0.317	rs56365200	1629	E7EUV1	.	T	1629;1596	ENSP00000415183:P1629T;ENSP00000351956:P1596T	ENSP00000351956:P1596T	P	+	1	0	MUC2	1083066	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.774000	0.00187	-0.960000	0.03613	-3.899000	0.00016	CCA	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	48	12.919895	KEEP	16	6	167	102	3063	CC	1	1	0		+	10	60	309	0	0	21.655413	88	60	2813	365	ENST00000441003.2	0.102041	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093094	1093094	__UNKNOWN__	Missense_Mutation	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093094T>G	ENST00000441003.2	+	30	4940	c.4913T>G	c.(4912-4914)gTg>gGg	p.V1638G	MUC2_ENST00000359061.5_Missense_Mutation_p.V1605G|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.V1605G(1)|p.V1638G(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accactacggtgaccccaacc	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	lung(2)											70	127	107			NA	NA	11		NA											NA				1093094		1817	3454	5271	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4913T>G	chr11.hg19:g.1093094T>G	ENSP00000415183:p.Val1638Gly	NA	Q14878	hg19		0.02	3.801734	CGGxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	T	2.324	-0.355023	0.05138	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14022	2.54;3.16	1.66	-3.31	0.04988	.	0.262594	0.13470	U	0.385509	T	0.06462	0.0166	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29822	-0.9999	9	0.41790	T	0.15	.	0.1958	0.00139	0.2143:0.1839:0.2436:0.3582	.	1638	E7EUV1	.	G	1638;1605	ENSP00000415183:V1638G;ENSP00000351956:V1605G	ENSP00000351956:V1605G	V	+	2	0	MUC2	1083094	0.003000	0.15002	0.000000	0.03702	0.171000	0.22731	1.577000	0.36515	-1.792000	0.01259	0.102000	0.15555	GTG	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	78	7.918289	KEEP	96	10	288	128	3318	TT	1	1	0		+	9	60	309	0	0	21.941589	94	60	2591	402	ENST00000441003.2	0.087379	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093236	1093236	__UNKNOWN__	Silent	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093236C>A	ENST00000441003.2	+	30	5082	c.5055C>A	c.(5053-5055)acC>acA	p.T1685T	MUC2_ENST00000359061.5_Silent_p.T1652T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ctacGGTGaccccaaccccaa	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													87	147	126			NA	NA	11		NA											NA				1093236		1819	3302	5121	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5055C>A	chr11.hg19:g.1093236C>A		NA	Q14878	hg19		0.02	2.795584	GACxCCA	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	63	24.866054	KEEP	84	3	83	112	3393	CC	1	0.999999	0		+	6	40	170	0	0	9.946935	97	60	3223	352	ENST00000441003.2	0.058252	0.999999
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093272	1093272	__UNKNOWN__	Silent	SNP	A	A	C	rs56230143		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093272A>C	ENST00000441003.2	+	30	5118	c.5091A>C	c.(5089-5091)acA>acC	p.T1697T	MUC2_ENST00000359061.5_Silent_p.T1664T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1664T(2)|p.T1697T(2)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	agaccccaacatcgacaccca	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				4	Substitution - coding silent(4)	kidney(2)|endometrium(2)											128	167	153			NA	NA	11		NA											NA				1093272		1845	3351	5196	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5091A>C	chr11.hg19:g.1093272A>C		NA	Q14878	hg19		0.02	5.393176	AACxTCG	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	113	42.707976	KEEP	143	4	122	185	4973	AA	1	1	0		+	11	58	333	0	0	21.787458	139	60	3956	597	ENST00000441003.2	0.073333	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093274	1093274	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs11245949	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093274C>T	ENST00000441003.2	+	30	5120	c.5093C>T	c.(5092-5094)tCg>tTg	p.S1698L	MUC2_ENST00000359061.5_Missense_Mutation_p.S1665L|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accccaacatcgacacccatc	0.637		NA											N|||	2435	0.486222	0.4826	0.4899	5008	,	,	NA	22392	0.631	NA	0.3608	False	NA	,,,	NA	NA	NA	2504	0.4683	NA	NA	NA								NA				0													129	167	154			NA	NA	11		NA											NA				1093274		1842	3364	5206	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5093C>T	chr11.hg19:g.1093274C>T	ENSP00000415183:p.Ser1698Leu	NA	Q14878	hg19		0.02	3.886112	CATxGAC	COVERED	.	.	.	.	.	.	.	.	.	.	T	1.748	-0.490089	0.04322	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.08370	3.13;3.1	0.851	-1.7	0.08159	.	227.466000	0.04577	U	0.394340	T	0.06005	0.0156	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40979	-0.9534	9	0.30854	T	0.27	.	5.5277	0.16967	0.0:0.5285:0.0:0.4715	rs11245949;rs59265712	1698	E7EUV1	.	L	1698;1665	ENSP00000415183:S1698L;ENSP00000351956:S1665L	ENSP00000351956:S1665L	S	+	2	0	MUC2	1083274	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.256000	0.18351	-1.248000	0.02503	-2.819000	0.00109	TCG	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	113	21.842352	KEEP	152	12	314	184	5328	CC	1	1	0		+	19	60	509	0	0	35.201236	133	60	4096	615	ENST00000441003.2	0.125	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093295	1093295	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs200837746|rs200145328		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093295C>T	ENST00000441003.2	+	30	5141	c.5114C>T	c.(5113-5115)aCt>aTt	p.T1705I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1672I|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1705I(1)|p.T1672I(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	accaccaccactacggtgacc	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	large_intestine(2)											113	161	144			NA	NA	11		NA											NA				1093295		1882	3466	5348	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5114C>T	chr11.hg19:g.1093295C>T	ENSP00000415183:p.Thr1705Ile	NA	Q14878	hg19		0.02	6.669937	CCAxTAC	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.775	-0.764347	0.02996	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11277	3.02;2.79	1.6	-0.698	0.11280	.	0.547305	0.11728	U	0.535177	T	0.05868	0.0153	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38457	-0.9660	9	0.34782	T	0.22	.	3.0673	0.06219	0.0:0.5189:0.2842:0.1969	.	1705	E7EUV1	.	I	1705;1672	ENSP00000415183:T1705I;ENSP00000351956:T1672I	ENSP00000351956:T1672I	T	+	2	0	MUC2	1083295	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.065000	0.14466	-0.392000	0.07751	-1.238000	0.01547	ACT	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	138	28.968855	KEEP	169	15	376	230	6904	CC	1	1	0		+	18	60	501	1	0	32.087606	191	60	6295	800	ENST00000441003.2	0.086124	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093368	1093368	__UNKNOWN__	Silent	SNP	G	G	A	rs111440994		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093368G>A	ENST00000441003.2	+	30	5214	c.5187G>A	c.(5185-5187)acG>acA	p.T1729T	MUC2_ENST00000359061.5_Silent_p.T1696T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.T17T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1696T(3)|p.T1729T(3)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccactacggtgaccccaa	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				6	Substitution - coding silent(6)	prostate(6)											175	224	207			NA	NA	11		NA											NA				1093368		1971	3826	5797	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5187G>A	chr11.hg19:g.1093368G>A		NA	Q14878	hg19		0.02	12.016317	TACxGTG	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	175	11.74906	KEEP	146	29	770	312	8921	GG	1	1	0		+	27	60	801	0	0	51.827879	320	60	10138	1181	ENST00000441003.2	0.07781	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093393	1093393	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs199525790		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093393G>A	ENST00000441003.2	+	30	5239	c.5212G>A	c.(5212-5214)Ggc>Agc	p.G1738S	MUC2_ENST00000359061.5_Missense_Mutation_p.G1705S|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.G26S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.	NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	aacacccaccggcacacagac	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													167	217	200			NA	NA	11		NA											NA				1093393		1999	3870	5869	SO:0001583	missense			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5212G>A	chr11.hg19:g.1093393G>A	ENSP00000415183:p.Gly1738Ser	NA	Q14878	hg19		0.02	11.873807	ACCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	G	0.322	-0.961495	0.02249	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.16743	3.21;3.25;2.32	0.677	-1.35	0.09114	.	381.381000	0.01358	N	0.012136	T	0.08537	0.0212	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21861	-1.0233	9	0.12430	T	0.62	.	4.7623	0.13113	0.7467:0.0:0.2533:0.0	.	1738	E7EUV1	.	S	1738;1705;26	ENSP00000415183:G1738S;ENSP00000351956:G1705S;ENSP00000331373:G26S	ENSP00000331373:G26S	G	+	1	0	MUC2	1083393	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.042000	0.13949	-0.796000	0.04456	-1.112000	0.02068	GGC	NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	219	25.775436	KEEP	187	28	764	356	10284	GG	1	1	0		+	26	60	733	0	0	45.674454	323	60	10288	1290	ENST00000441003.2	0.074499	1
MUC2	4583	__UNKNOWN__	__UNKNOWN__	11	1093434	1093434	__UNKNOWN__	Silent	SNP	C	C	T	rs12786901		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1093434C>T	ENST00000441003.2	+	30	5280	c.5253C>T	c.(5251-5253)acC>acT	p.T1751T	MUC2_ENST00000359061.5_Silent_p.T1718T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.T39T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0		NA			cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccaccacggtgaccc	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								T		10,4082		0,10,2036	196	223	214		5250	-3.5	0	11	dbSNP_121	214	15,8043		0,15,4014	no	coding-synonymous	MUC2	NM_002457.2		0,25,6050	TT,TC,CC	NA	0.1862,0.2444,0.2058		1750/2813	1093434	25,12125	2046	4029	6075	SO:0001819	synonymous_variant			L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788	4583		Mucins	7512	protein-coding gene	gene with protein product		158370	mucin 2, intestinal/tracheal		NA	15081123	Standard	NM_002457	NM_002457	NA	Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5253C>T	chr11.hg19:g.1093434C>T		NA	Q14878	hg19		0.02	8.063546	CACxACG	COVERED																																																																																			NOVEL	MUC2-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000345894.2	165	74.452501	KEEP	152	8	201	319	9707	CC	1	1	0		+	11	60	296	0	2	14.759397	271	60	8867	1074	ENST00000441003.2	0.039007	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1212810	1212810	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1212810T>C	ENST00000358378.6	+	0	51							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		CTGGAACTACTCCCAGCCCTG	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*48T>C	chr11.hg19:g.1212810T>C		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	5.084353	TACxCCC	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	83	32.40967	KEEP	68	8	227	188	4903	TT	1	1	0		+	6	25	187	0	0	12.922323	58	60	1630	496	ENST00000358378.6	0.09375	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1212895	1212895	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1212895C>G	ENST00000358378.6	+	0	136							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		aacctctggtcctggaactac	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*133C>G	chr11.hg19:g.1212895C>G		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	14.613776	GGTxCTG	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	155	39.9782	KEEP	97	26	790	411	12381	CC	1	1	0		+	17	60	561	0	0	43.156504	100	60	3286	1172	ENST00000358378.6	0.145299	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1213115	1213115	__UNKNOWN__	3'UTR	SNP	C	C	T	rs113511365	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1213115C>T	ENST00000358378.6	+	0	356							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		TCTGCTCCTACAACCAGCACG	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													114	110	112			NA	NA	11		NA											NA				1213115		875	1990	2865	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*353C>T	chr11.hg19:g.1213115C>T		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	4.270123	CTAxAAC	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	84	28.21139	KEEP	35	7	187	160	4826	CC	1	1	0		+	9	60	258	0	0	18.268507	64	60	2169	512	ENST00000358378.6	0.123288	1
MUC5AC	4586	__UNKNOWN__	__UNKNOWN__	11	1213142	1213142	__UNKNOWN__	3'UTR	SNP	C	C	G	rs200544156		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1213142C>G	ENST00000358378.6	+	0	383							P98088	MUC5A_HUMAN	mucin 5AC, oligomeric mucus/gel-forming	NA		NA			cellular protein metabolic process (GO:0044267)|extracellular fibril organization (GO:0043206)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|fibril (GO:0043205)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(7)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(5)|kidney(9)|large_intestine(19)|liver(1)|lung(89)|ovary(7)|prostate(8)|skin(9)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	203		all_cancers(49;2.94e-05)|Breast(177;0.00257)|all_epithelial(84;0.00314)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00146)|Lung(200;0.0612)|LUSC - Lung squamous cell carcinoma(625;0.0724)		GGTCCTGGAACTACTCCCAGC	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													144	140	141			NA	NA	11		NA											NA				1213142		875	1990	2865	SO:0001624	3_prime_UTR_variant			AJ001402, AJ298317		11p15.5	2007-04-23	2006-03-14		ENSG00000215182	ENSG00000215182	4586		Mucins	7515	protein-coding gene	gene with protein product		158373	mucin 5, subtypes A and C, tracheobronchial/gastric		NA	7826332, 9588204	Standard	XM_001130382	XM_006709945	NA	Approved	MUC5	uc001lsz.3	P98088	OTTHUMG00000154270	ENST00000358378.6:c.*380C>G	chr11.hg19:g.1213142C>G		NA	O60460|O76065|Q13792|Q14425|Q658Q1|Q7M4S5|Q8N4M9|Q8WWQ3|Q8WWQ4|Q8WWQ5	hg19		0.02	5.52539	GAAxTAC	COVERED																																																																																			NOVEL	MUC5AC-002	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000396096.2	63	14.349458	KEEP	18	7	214	123	3603	CC	1	1	0		+	6	60	198	0	0	13.587731	69	60	2329	428	ENST00000358378.6	0.08	1
KRTAP5-AS1	338651	__UNKNOWN__	__UNKNOWN__	11	1614626	1614626	__UNKNOWN__	RNA	SNP	C	C	A	rs79656866		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1614626C>A	ENST00000424148.1	+	0	328				KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NR_021489.1				KRTAP5-1/KRTAP5-2 antisense RNA 1	NA		NA									NA						gactgtatctcaaaaaaaaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							11p15.5	2013-05-31			ENSG00000233930	ENSG00000233930	338651		Long non-coding RNAs	27877	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_021489	NA	Approved				OTTHUMG00000165546	ENST00000424148.1:	chr11.hg19:g.1614626C>A		NA		hg19		0.02	-0.192785	TCTxAAA	COVERED																																																																																			NOVEL	KRTAP5-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000384772.1	5	3.911868	KEEP	0	0	0	13	405	CC	0.994391	0.455189	0		+	3	60	86	2	1	6.3637	17	60	549	61	ENST00000424148.1	0.15	0.457757
IFITM10	402778	__UNKNOWN__	__UNKNOWN__	11	1760221	1760221	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:1760221T>C	ENST00000340134.4	-	3	686				IFITM10_ENST00000482459.1_Intron	NM_001170820.3	NP_001164291.2	A6NMD0	IFM10_HUMAN	interferon induced transmembrane protein 10	NA		NA			response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)					NA						agggcagaggttgcagtgagc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS53593.1, CCDS53593.2	11p15.5	2011-05-06			ENSG00000244242	ENSG00000244242	402778			40022	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001170820	NM_001170820	NA	Approved		uc021qbs.2	A6NMD0	OTTHUMG00000043933	ENST00000340134.4:c.538-3562A>G	chr11.hg19:g.1760221T>C		NA	A6NEU7	hg19	CCDS53593.2	0.02	-0.026319	AGGxTGC	UNCOVERED																																																																																			NOVEL	IFITM10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000102341.5	8	2.403307	KEEP	4	0	0	8	196	TT	0	0	0		-	2	51	73	0	0	7.424921	1	45	33	14	ENST00000340134.4	0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	2080254	2080254	__UNKNOWN__	IGR	SNP	A	A	G	rs11042465	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:2080254A>G			NA	NA				H19 (62180 upstream) : IGF2 (70087 downstream)						NA		NA									NA						gcgtgatctcagctcactgca	0.438		NA											a|||	3745	0.747804	0.9236	0.8444	5008	,	,	NA	17246	0.5992	NA	0.7306	False	NA	,,,	NA	NA	NA	2504	0.6125	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.2080254A>G		NA		hg19		0.02	-0.052632	CTCxGCT	UNCOVERED																																																																																			NOVEL					0			5	2.405314	KEEP	3	0	0	8	219	AA	0	0	0			4	60	133	1	0	13.549656	2	60	61	21		0.666667	0.036766
CARS	833	__UNKNOWN__	__UNKNOWN__	11	3055773	3055773	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:3055773C>T	ENST00000380525.4	-	7	871				CARS-AS1_ENST00000499962.1_RNA|CARS_ENST00000401769.3_Intron|CARS_ENST00000397111.5_Intron|CARS_ENST00000397114.3_Intron|CARS_ENST00000278224.9_Intron	NM_001014437.2|NM_001194997.1	NP_001014437.1|NP_001181926.1	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	NA		NA			cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)		CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	AAttttttttctttttgagac	0.567		NA	T	ALK	ALCL																NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(61;932 1157 5961 20446 52152)		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	833	6.1.1.16	Aminoacyl tRNA synthetases / Class I	1493	protein-coding gene	gene with protein product	cysteine tRNA ligase 1, cytoplasmic	123859			NA	8468064	Standard	NM_001751	NM_139273	NA	Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000380525.4:c.801+3506G>A	chr11.hg19:g.3055773C>T		NA	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	hg19	CCDS41600.1	0.02	-0.105263	TTTxTTT	UNCOVERED																																																																																			NOVEL	CARS-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000030118.3	6	2.681592	KEEP	0	0	0	9	249	CC	0.99254	0.138789	0		-	3	60	85	2	0	7.000909	9	60	309	29	ENST00000380525.4	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	3093474	3093474	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:3093474G>A			NA	NA				CARS (14631 upstream) : OSBPL5 (14871 downstream)						NA		NA									NA						cacctgcctcggcctcccaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.3093474G>A		NA		hg19		0.02	-0.122792	CTCxGCC	COVERED																																																																																			NOVEL					0			9	2.371841	KEEP	1	0	0	8	207	GG	0.99257	0.194853	0			3	59	87	1	0	7.081945	10	60	319	26		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	3485557	3485557	__UNKNOWN__	IGR	SNP	T	T	C	rs541179386	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:3485557T>C			NA	NA				TSSC2 (55349 upstream) : RP13-726E6.1 (4991 downstream)						NA		NA									NA						cccacctcggtctcccaaagt	0.428		NA											N|||	2	0.000399361	0.0	0.0	5008	,	,	NA	12010	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.3485557T>C		NA		hg19		0.02	-0.096488	CGGxCTC	UNCOVERED																																																																																			NOVEL					0			7	2.406013	KEEP	2	0	0	8	222	GT	0.99254	0.119538	0			3	60	103	0	0	9.078712	7	60	215	32		0.3	0.120436
HBG2	3048	__UNKNOWN__	__UNKNOWN__	11	5413924	5413924	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:5413924C>T	ENST00000380259.2	-	5	677				HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA			P69892	HBG2_HUMAN	hemoglobin, gamma G	NA		NA			blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	13		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		gggtggatcacgaggtcagga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC029387	CCDS7755.1	11p15.5	2014-05-19			ENSG00000196565	ENSG00000196565	3048			4832	protein-coding gene	gene with protein product		142250			NA	2649166	Standard	NM_000184	NM_000184	NA	Approved	HBG-T1		P69892	OTTHUMG00000066673	ENST00000380259.2:c.564-46795G>A	chr11.hg19:g.5413924C>T		NA	A8MZE0|P02096|P62027|Q14491|Q68NH9|Q96FH6|Q96FH7	hg19	CCDS7755.1	0.02	-0.157869	TCAxGAG	COVERED																																																																																			NOVEL	HBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000142967.2	3	3.308355	KEEP	3	0	0	11	309	CC	0.99254	0.320398	0		-	3	40	92	0	0	7.192052	14	60	440	45	ENST00000380259.2	0.176471	0.322807
CCKBR	887	__UNKNOWN__	__UNKNOWN__	11	6293289	6293289	__UNKNOWN__	3'UTR	SNP	G	G	A	rs147405755	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:6293289G>A	ENST00000334619.2	+	0	2053				CCKBR_ENST00000525462.1_3'UTR|CCKBR_ENST00000532715.1_3'UTR	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	NA		NA			cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	GTTAAGGACCGTGGCCCTGCC	0.468		NA											G|||	13	0.00259585	0.0038	0.0029	5008	,	,	NA	24486	0.0	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148	887		GPCR / Class A : Cholecystokinin receptors	1571	protein-coding gene	gene with protein product		118445			NA	1280419	Standard	NM_176875	NM_176875	NA	Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.*516G>A	chr11.hg19:g.6293289G>A		NA	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	hg19	CCDS7761.1	0.02	-0.289463	ACCxTGG	COVERED																																																																																			NOVEL	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257230.2	0	2.707832	KEEP	0	0	0	9	270	GG	0.99254	0.755211	0		+	5	60	155	0	0	11.792323	28	60	897	62	ENST00000334619.2	0.151515	0.760887
ARFIP2	23647	__UNKNOWN__	__UNKNOWN__	11	6496973	6496973	__UNKNOWN__	3'UTR	SNP	A	A	G	rs141459407		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:6496973A>G	ENST00000254584.2	-	0	2479					NM_012402.3	NP_036534.1	P53365	ARFP2_HUMAN	ADP-ribosylation factor interacting protein 2	NA		NA			actin cytoskeleton organization (GO:0030036)|cellular component movement (GO:0006928)|lamellipodium assembly (GO:0030032)|ruffle organization (GO:0031529)|small GTPase mediated signal transduction (GO:0007264)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|Rac GTPase binding (GO:0048365)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(2)	15		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;3.41e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		gcagtggcgcaatcttggctc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(119;796 1674 9049 20480 24794)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC000392	CCDS7765.1, CCDS55739.1, CCDS55740.1, CCDS73250.1	11p15	2008-08-01	2008-08-01		ENSG00000132254	ENSG00000132254	23647			17160	protein-coding gene	gene with protein product	arfaptin 2	601638			NA	8670882, 9038142	Standard	NM_012402	NM_012402	NA	Approved	POR1	uc010ran.2	P53365	OTTHUMG00000133406	ENST00000254584.2:c.*1370T>C	chr11.hg19:g.6496973A>G		NA	B4DX86|B4E306|D3DQT5	hg19	CCDS7765.1	0.02	-0.210428	CGCxATC	COVERED																																																																																			NOVEL	ARFIP2-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387044.1	7	3.006873	KEEP	0	0	0	10	268	AA	0.992708	0.518353	0		-	3	44	87	0	0	6.328674	19	60	542	41	ENST00000254584.2	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	6719310	6719310	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:6719310T>C			NA	NA				MRPL17 (14678 upstream) : GVINP1 (15456 downstream)						NA		NA									NA						tggctcatgcttgtaatccca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.6719310T>C		NA		hg19		0.02	-0.078942	TGCxTGT	UNCOVERED																																																																																			NOVEL					0			6	2.706764	KEEP	0	0	0	9	249	TT	0.99254	0.076759	0			3	60	94	0	0	8.343459	6	60	184	22		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	7178766	7178766	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:7178766C>G			NA	NA				RBMXL2 (66387 upstream) : RP11-324J3.1 (65397 downstream)						NA		NA									NA						gtctcaaactcctgacctcgt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.7178766C>G		NA		hg19		0.02	-0.070177	ACTxCTG	UNCOVERED																																																																																			NOVEL					0			6	3.009255	KEEP	2	0	0	10	318	CC	0.99254	0.053733	0			2	24	72	0	0	6.495799	4	60	127	27		0.333333	0.054137
PPFIBP2	8495	__UNKNOWN__	__UNKNOWN__	11	7628331	7628331	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:7628331C>T	ENST00000530181.1	+	1	278				PPFIBP2_ENST00000533792.1_Intron|PPFIBP2_ENST00000299492.4_Intron|PPFIBP2_ENST00000528883.1_Intron	NM_001256569.1	NP_001243498	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	NA		NA			cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		ttagtagagacggggtttcac	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387	8495		Sterile alpha motif (SAM) domain containing	9250	protein-coding gene	gene with protein product		603142			NA	9624153	Standard	NM_003621	NM_003621	NA	Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000530181.1:c.57+1085C>T	chr11.hg19:g.7628331C>T		NA	B7Z433|E9PK77|O75337|Q8WW26	hg19	CCDS58117.1	0.02	-0.052608	AGAxGGG	UNCOVERED																																																																																			NOVEL	PPFIBP2-008	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385403.2	4	2.407065	KEEP	2	0	0	8	241	CC	0	0	0		+	3	22	78	0	0	7.767619	2	60	63	21	ENST00000530181.1	0.6	0.036766
PPFIBP2	8495	__UNKNOWN__	__UNKNOWN__	11	7628348	7628348	__UNKNOWN__	Intron	SNP	C	C	G	rs568429467		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:7628348C>G	ENST00000530181.1	+	1	278				PPFIBP2_ENST00000533792.1_Intron|PPFIBP2_ENST00000299492.4_Intron|PPFIBP2_ENST00000528883.1_Intron	NM_001256569.1	NP_001243498	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	NA		NA			cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		tcaccatgttcgtcaggatgg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387	8495		Sterile alpha motif (SAM) domain containing	9250	protein-coding gene	gene with protein product		603142			NA	9624153	Standard	NM_003621	NM_003621	NA	Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000530181.1:c.57+1102C>G	chr11.hg19:g.7628348C>G		NA	B7Z433|E9PK77|O75337|Q8WW26	hg19	CCDS58117.1	0.02	-0.070165	GTTxGTC	UNCOVERED																																																																																			NOVEL	PPFIBP2-008	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385403.2	3	2.406574	KEEP	0	0	0	8	232	CC	0.99257	0.053735	0		+	3	40	102	0	0	9.555671	4	60	116	26	ENST00000530181.1	0.428571	0.054137
TRIM66	9866	__UNKNOWN__	__UNKNOWN__	11	8636765	8636765	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:8636765C>T	ENST00000402157.2	-	0	6904				TRIM66_ENST00000299550.6_3'UTR			O15016	TRI66_HUMAN	tripartite motif containing 66	NA		NA				aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						cgtgagccaccgcgcccagcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436	9866		Tripartite motif containing / Tripartite motif containing, Zinc fingers, PHD-type	29005	protein-coding gene	gene with protein product		612000	chromosome 11 open reading frame 29, tripartite motif-containing 66	C11orf29	NA	9205841	Standard	XM_084529	NM_014818	NA	Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000402157.2:c.*2726G>A	chr11.hg19:g.8636765C>T		NA	Q9BQQ4	hg19		0.02	1.368279	CACxGCG	COVERED																																																																																			NOVEL	TRIM66-001	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000318299.2	15	3.63998	KEEP	0	4	107	50	1470	CC	1	0.997163	0		-	5	60	151	0	0	10.018665	55	60	1831	179	ENST00000402157.2	0.083333	0.997163
TRIM66	9866	__UNKNOWN__	__UNKNOWN__	11	8636767	8636767	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:8636767C>T	ENST00000402157.2	-	0	6902				TRIM66_ENST00000299550.6_3'UTR			O15016	TRI66_HUMAN	tripartite motif containing 66	NA		NA				aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						tgagccaccgcgcccagccaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436	9866		Tripartite motif containing / Tripartite motif containing, Zinc fingers, PHD-type	29005	protein-coding gene	gene with protein product		612000	chromosome 11 open reading frame 29, tripartite motif-containing 66	C11orf29	NA	9205841	Standard	XM_084529	NM_014818	NA	Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000402157.2:c.*2724G>A	chr11.hg19:g.8636767C>T		NA	Q9BQQ4	hg19		0.02	1.359505	CCGxGCC	COVERED																																																																																			NOVEL	TRIM66-001	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000318299.2	15	4.241647	KEEP	0	4	104	51	1508	CC	1	0.997898	0		-	5	60	145	0	0	9.346296	57	60	1908	179	ENST00000402157.2	0.080645	0.997898
DENND5A	23258	__UNKNOWN__	__UNKNOWN__	11	9261770	9261770	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:9261770A>G	ENST00000530044.1	-	1	127				DENND5A_ENST00000328194.3_Intron			Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	NA		NA			positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						gtgaaaccccatctctactaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014	23258		DENN/MADD domain containing	19344	protein-coding gene	gene with protein product		NA	RAB6 interacting protein 1	RAB6IP1	NA	10470851	Standard	NM_015213	NM_015213	NA	Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000530044.1:c.109+24737T>C	chr11.hg19:g.9261770A>G		NA	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	hg19	CCDS58119.1	0.02	-0.08767	CCCxTCT	UNCOVERED																																																																																			NOVEL	DENND5A-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385912.1	1	2.405357	KEEP	5	0	0	8	214	AA	0	0	0		-	3	60	89	0	0	7.679167	7	60	185	28	ENST00000530044.1	0.3	0.099721
IPO7	10527	__UNKNOWN__	__UNKNOWN__	11	9434754	9434754	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:9434754A>T	ENST00000379719.3	+	5	621					NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	NA		NA			innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		ATACttttttattttttttga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339	10527		Importins	9852	protein-coding gene	gene with protein product		605586	RAN binding protein 7	RANBP7	NA	9214382	Standard	NM_006391	NM_006391	NA	Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.480-1048A>T	chr11.hg19:g.9434754A>T		NA	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	hg19	CCDS31425.1	0.02	-0.149084	TTTxTTT	COVERED																																																																																			NOVEL	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386022.1	5	5.41235	KEEP	0	0	0	18	478	AA	0.999859	0.29196	0		+	3	60	88	0	1	6.972705	12	60	341	55	ENST00000379719.3	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	9581344	9581344	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:9581344G>A			NA	NA				ZNF143 (31273 upstream) : WEE1 (13883 downstream)						NA		NA									NA						tgcccgcctcggcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.9581344G>A		NA		hg19		0.02	-0.131586	CTCxGCC	COVERED																																																																																			NOVEL					0			16	6.01754	KEEP	11	0	0	20	611	GG	0.99649	0.228369	0			4	60	123	0	0	10.890958	8	60	281	57		0.333333	0.229173
WEE1	7465	__UNKNOWN__	__UNKNOWN__	11	9604152	9604152	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:9604152T>C	ENST00000450114.2	+	6	1541				WEE1_ENST00000299613.6_Intron	NM_003390.3	NP_003381.1	P30291	WEE1_HUMAN	WEE1 G2 checkpoint kinase	NA		NA			blood coagulation (GO:0007596)|establishment of cell polarity (GO:0030010)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|neuron projection morphogenesis (GO:0048812)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	23				all cancers(16;4.59e-09)|Epithelial(150;3.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0484)		ctcgctctgttgcccaggctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X62048	CCDS7800.1, CCDS44536.1	11p15.4	2013-10-21	2013-10-21		ENSG00000166483	ENSG00000166483	7465			12761	protein-coding gene	gene with protein product		193525	wee1+ (S. pombe) homolog, WEE1 homolog (S. pombe)		NA	1840647	Standard	NM_003390	NM_003390	NA	Approved		uc001mhs.3	P30291	OTTHUMG00000165863	ENST00000450114.2:c.1288+927T>C	chr11.hg19:g.9604152T>C		NA	B3KVE1|D3DQV0	hg19	CCDS7800.1	0.02	-0.096462	TGTxGCC	UNCOVERED																																																																																			NOVEL	WEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386757.1	6	3.007353	KEEP	3	0	0	10	271	TT	0.992708	0.119558	0		+	3	60	86	0	0	7.378576	7	60	198	31	ENST00000450114.2	0.3	0.120436
SBF2	81846	__UNKNOWN__	__UNKNOWN__	11	10306669	10306669	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:10306669T>C	ENST00000256190.8	-	1	193					NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	NA		NA			cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		ccagcctgggtaacatggtga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812	81846		Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins, DENN/MADD domain containing, Pleckstrin homology (PH) domain containing	2135	protein-coding gene	gene with protein product	myotubularin related 13	607697	Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding), DENN/MADD domain containing 7B	CMT4B2	NA	10644431	Standard	NM_030962	NM_030962	NA	Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.55+8892A>G	chr11.hg19:g.10306669T>C		NA	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	hg19	CCDS31427.1	0.02	-0.043857	GGGxAAC	UNCOVERED																																																																																			NOVEL	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386911.2	3	2.704899	KEEP	0	0	0	9	232	TT	0.99254	0.023894	0		-	2	60	73	0	0	6.79309	3	60	87	19	ENST00000256190.8	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	10729937	10729937	__UNKNOWN__	IGR	SNP	T	T	C	rs151064630		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:10729937T>C			NA	NA				MRVI1 (14402 upstream) : Y_RNA (17512 downstream)						NA		NA									NA						cctcctcctcttcctcctcct	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.10729937T>C		NA		hg19		0.02	-0.070168	CTCxTCC	UNCOVERED																																																																																			NOVEL					0			5	4.811519	KEEP	0	0	0	16	430	TT	0.997832	0.05402	0			2	60	74	1	0	6.53568	5	60	155	36		0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	10772196	10772196	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:10772196T>C			NA	NA				Y_RNA (24645 upstream) : CTR9 (337 downstream)						NA		NA									NA						ccgcccgccttggcctcccaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.10772196T>C		NA		hg19		0.02	-0.087705	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			5	4.811852	KEEP	1	0	0	16	442	TT	0.997832	0.099505	0			3	60	91	0	0	7.878616	7	60	205	42		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	12112821	12112821	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:12112821G>A			NA	NA				RP13-631K18.5 (1833 upstream) : MICAL2 (2721 downstream)						NA		NA									NA						ttgtatttttggcagagacga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.12112821G>A		NA		hg19		0.02	-0.1228	TTTxGCA	COVERED																																																																																			NOVEL					0			9	2.40709	KEEP	0	0	0	8	242	GG	0.99257	0.194853	0			4	60	116	0	0	9.870908	10	60	332	27		0.285714	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	12112823	12112823	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:12112823C>T			NA	NA				RP13-631K18.5 (1835 upstream) : MICAL2 (2719 downstream)						NA		NA									NA						gtatttttggcagagacgaag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.12112823C>T		NA		hg19		0.02	-0.122798	TGGxAGA	COVERED																																																																																			NOVEL					0			9	2.407061	KEEP	0	0	0	8	243	CC	0.99257	0.194853	0			4	60	113	0	0	9.723024	9	60	308	27		0.307692	0.196312
TEAD1	7003	__UNKNOWN__	__UNKNOWN__	11	12905326	12905326	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:12905326C>T	ENST00000526600.1	+	4	634				TEAD1_ENST00000527575.1_Intron|TEAD1_ENST00000527636.1_Intron|TEAD1_ENST00000334310.6_Intron|TEAD1_ENST00000361985.2_Intron|TEAD1_ENST00000361905.4_Intron			P28347	TEAD1_HUMAN	TEA domain family member 1 (SV40 transcriptional enhancer factor)	NA		NA			gene expression (GO:0010467)|hippo signaling (GO:0035329)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)	17				Epithelial(150;0.00223)|BRCA - Breast invasive adenocarcinoma(625;0.236)		tttgggaggccgaggcaggtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X84839	CCDS7810.1, CCDS7810.2	11p15.4	2008-11-12				ENSG00000187079	7003			11714	protein-coding gene	gene with protein product		189967	atrophia areata, peripapillary chorioretinal degeneration	TCF13, AA	NA	1851669, 9889009, 15016762	Standard	NM_021961	NM_021961	NA	Approved	TEF-1	uc021qdx.1	P28347		ENST00000526600.1:c.411+654C>T	chr11.hg19:g.12905326C>T		NA	A4FUP2|E7EV65	hg19		0.02	-0.1228	GGCxGAG	COVERED																																																																																			NOVEL	TEAD1-007	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000387220.1	7	2.406226	KEEP	2	0	0	8	232	CC	0.99257	0.194853	0		+	3	20	89	0	0	7.28198	10	60	328	37	ENST00000526600.1	0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	13963766	13963766	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:13963766G>A			NA	NA				RP11-231N3.1 (17356 upstream) : SPON1 (20147 downstream)						NA		NA									NA						tagcctccccggtagctggga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.13963766G>A		NA		hg19		0.02	-0.131559	CCCxGTA	COVERED																																																																																			NOVEL					0			5	2.405203	KEEP	0	0	0	8	216	GG	0.99257	0.22747	0			3	60	84	0	0	6.673043	11	60	354	29		0.214286	0.229173
PDE3B	5140	__UNKNOWN__	__UNKNOWN__	11	14766646	14766646	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:14766646T>C	ENST00000455098.2	+	2	1223				PDE3B_ENST00000282096.4_Intron|PDE3B_ENST00000534317.1_Intron			Q13370	PDE3B_HUMAN	phosphodiesterase 3B, cGMP-inhibited	NA		NA			angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of lipid catabolic process (GO:0050995)|regulation of insulin secretion (GO:0050796)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)|protein kinase B binding (GO:0043422)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39					Caffeine(DB00201)	actgggattataggcgtgagc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U38178	CCDS7817.1	11p15.2	2008-03-18			ENSG00000152270	ENSG00000152270	5140	3.1.4.17	Phosphodiesterases	8779	protein-coding gene	gene with protein product		602047			NA	8884271, 16395595	Standard	NM_000922	NM_000922	NA	Approved	HcGIP1	uc001mln.3	Q13370	OTTHUMG00000165898	ENST00000455098.2:c.979-26837T>C	chr11.hg19:g.14766646T>C		NA	B7ZM37|O00639|Q14408|Q6SEI4	hg19		0.02	-0.035088	TTAxAGG	UNCOVERED																																																																																			NOVEL	PDE3B-002	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000386975.1	4	2.406014	KEEP	0	0	0	8	218	TT	0.99257	0.019833	0		+	2	60	71	0	0	6.850256	2	60	60	18	ENST00000455098.2	0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	15551533	15551533	__UNKNOWN__	IGR	SNP	G	G	A	rs143610857	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:15551533G>A			NA	NA				snoMBII-202 (48094 upstream) : RP11-531H8.1 (22867 downstream)						NA		NA									NA						aggttgcagtgagccgagatg	0.418		NA											G|||	514	0.102636	0.0204	0.0865	5008	,	,	NA	12837	0.1171	NA	0.1551	False	NA	,,,	NA	NA	NA	2504	0.1564	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.15551533G>A		NA		hg19		0.02	-0.219124	AGTxAGC	COVERED																																																																																			NOVEL					0			31	3.439257	KEEP	14	1	21	19	513	GG	0.993072	0.549057	0			6	60	153	0	0	12.707614	15	23	453	52		0.285714	0.552887
C11orf58	10944	__UNKNOWN__	__UNKNOWN__	11	16677837	16677837	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:16677837A>C	ENST00000527893.1	+	2	404							O00193	SMAP_HUMAN	chromosome 11 open reading frame 58	NA		NA								NS(1)|endometrium(1)|lung(3)|prostate(1)|skin(1)	7						gttggccaggatggtctcaat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007103	CCDS7822.1	11p15.1	2012-05-30			ENSG00000110696	ENSG00000110696	10944			16990	protein-coding gene	gene with protein product	small acidic protein	NA			NA	9263035	Standard	NM_014267	NM_014267	NA	Approved	SMAP	uc001mmk.2	O00193	OTTHUMG00000165910	ENST00000527893.1:c.404+9981A>C	chr11.hg19:g.16677837A>C		NA	B2RD28	hg19		0.02	-0.16665	AGGxTGG	COVERED																																																																																			NOVEL	C11orf58-011	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000387235.1	8	3.007757	KEEP	2	0	0	10	278	AA	0.993072	0.351495	0		+	4	60	128	1	0	10.462759	15	60	456	45	ENST00000527893.1	0.210526	0.353947
PLEKHA7	144100	__UNKNOWN__	__UNKNOWN__	11	17028099	17028099	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:17028099C>T	ENST00000531066.1	-	3	263				PLEKHA7_ENST00000532079.1_Intron|PLEKHA7_ENST00000355661.3_Intron|PLEKHA7_ENST00000448080.2_Intron			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	NA		NA			epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						cgcttgaacccgggaagcaga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689	144100		Pleckstrin homology (PH) domain containing	27049	protein-coding gene	gene with protein product		612686			NA	12477932	Standard	NM_175058	NM_175058	NA	Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000531066.1:c.221+7436G>A	chr11.hg19:g.17028099C>T		NA	B4DK33|B4DWC3|Q86VZ7	hg19		0.02	-0.026316	ACCxGGG	UNCOVERED																																																																																			NOVEL	PLEKHA7-002	PUTATIVE	not_organism_supported|basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000387236.1	4	2.406331	KEEP	0	0	0	8	231	CC	0.99257	0	0		-	2	60	62	0	0	6.324455	1	28	35	17	ENST00000531066.1	0.666667	0
PIK3C2A	5286	__UNKNOWN__	__UNKNOWN__	11	17123429	17123429	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:17123429C>T	ENST00000265970.7	-	24	3851				PIK3C2A_ENST00000540361.1_Intron|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	NA		NA			clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ggattacaggcgtgagccact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	5286	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	phosphoinositide-3-kinase, class 2, alpha polypeptide		NA	9337861	Standard	NM_002645	NM_002645	NA	Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.3852-448G>A	chr11.hg19:g.17123429C>T		NA	B0LPH2|B4E2G4|Q14CQ9	hg19	CCDS7824.1	0.02	-0.122807	AGGxGTG	UNCOVERED																																																																																			NOVEL	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387553.1	9	3.006794	KEEP	13	0	0	10	271	CC	0	0	0		-	3	60	91	0	0	7.732253	8	60	262	51	ENST00000265970.7	0.272727	0.196312
NUCB2	4925	__UNKNOWN__	__UNKNOWN__	11	17320452	17320452	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:17320452T>G	ENST00000529010.1	+	4	471				NUCB2_ENST00000458064.2_Intron|NUCB2_ENST00000323688.6_Intron	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	NA		NA				cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						tgccatgttgtccaggctggt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF052642	CCDS41623.1	11p15.1	2013-01-10					4925		EF-hand domain containing	8044	protein-coding gene	gene with protein product		608020			NA	7811391	Standard	NM_005013	NM_005013	NA	Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.252+2694T>G	chr11.hg19:g.17320452T>G		NA	A8K642|D3DQX5|Q8NFT5	hg19	CCDS41623.1	0.02	-0.078924	TTGxCCA	UNCOVERED																																																																																			NOVEL	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387614.2	3	2.405357	KEEP	1	0	0	8	212	TT	0	0	0		+	3	51	103	0	0	9.433673	5	60	135	22	ENST00000529010.1	0.375	0.077336
ABCC8	6833	__UNKNOWN__	__UNKNOWN__	11	17458570	17458570	__UNKNOWN__	Intron	SNP	G	G	A	rs199585049		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:17458570G>A	ENST00000389817.3	-	11	1699				ABCC8_ENST00000302539.4_Intron|ABCC8_ENST00000528202.1_Intron			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	NA		NA			carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	cccaggaggcggaggttgcag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071	6833		ATP binding cassette transporters / subfamily C	59	protein-coding gene	gene with protein product	sulfonylurea receptor (hyperinsulinemia)	600509		SUR, HRINS	NA	7920639, 7716548	Standard	NM_000352	NM_000352	NA	Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.1631-4779C>T	chr11.hg19:g.17458570G>A		NA	A6NMX8|E3UYX6|O75948|Q16583	hg19	CCDS31437.1	0.02	-0.131558	GGCxGAG	COVERED																																																																																			NOVEL	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389093.1	19	3.60698	KEEP	8	0	0	12	311	GG	0.99257	0.22747	0		-	5	49	145	0	0	13.123264	8	60	241	37	ENST00000389817.3	0.384615	0.229173
ABCC8	6833	__UNKNOWN__	__UNKNOWN__	11	17458592	17458592	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:17458592C>G	ENST00000389817.3	-	11	1699				ABCC8_ENST00000302539.4_Intron|ABCC8_ENST00000528202.1_Intron			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	NA		NA			carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	gagccgagatcgcgccactgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071	6833		ATP binding cassette transporters / subfamily C	59	protein-coding gene	gene with protein product	sulfonylurea receptor (hyperinsulinemia)	600509		SUR, HRINS	NA	7920639, 7716548	Standard	NM_000352	NM_000352	NA	Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.1631-4801G>C	chr11.hg19:g.17458592C>G		NA	A6NMX8|E3UYX6|O75948|Q16583	hg19	CCDS31437.1	0.02	-0.149102	GATxGCG	COVERED																																																																																			NOVEL	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389093.1	27	5.415111	KEEP	16	0	0	18	526	CC	0.992708	0.289872	0		-	3	24	94	0	0	7.572415	12	60	387	50	ENST00000389817.3	0.2	0.292001
SAA2	6289	__UNKNOWN__	__UNKNOWN__	11	18264296	18264296	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:18264296A>G	ENST00000528349.1	-	4	337	c.301T>C	c.(301-303)Ttc>Ctc	p.F101L	SAA2-SAA4_ENST00000524555.1_RNA|SAA2_ENST00000530400.1_Intron|SAA2_ENST00000414546.2_Intron			P0DJI9	SAA2_HUMAN	serum amyloid A2	0		NA			acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						aagaggctgaagtgggaggat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense			M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339	6289			10514	protein-coding gene	gene with protein product		104751			NA	7686132	Standard	NM_030754	NM_030754	NA	Approved			P0DJI9	OTTHUMG00000166484	ENST00000528349.1:c.301T>C	chr11.hg19:g.18264296A>G	ENSP00000435659:p.Phe101Leu	NA	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	hg19		0.02	5.815172	TGAxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	3.282	-0.146730	0.06627	.	.	ENSG00000134339	ENST00000528349	T	0.14022	2.54	0.158	0.158	0.14942	.	.	.	.	.	T	0.15392	0.0371	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25779	-1.0122	5	0.87932	D	0	.	.	.	.	.	.	.	.	L	101	ENSP00000435659:F101L	ENSP00000435659:F101L	F	-	1	0	SAA2	18220872	0.122000	0.22280	0.064000	0.19789	0.065000	0.16274	0.241000	0.18065	0.175000	0.19841	0.172000	0.16884	TTC	NOVEL	SAA2-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000389980.1	76	34.888258	KEEP	0	4	116	157	4216	AA	1	1	0		-	6	60	201	0	0	12.220235	134	60	3990	427	ENST00000528349.1	0.042857	1
UEVLD	55293	__UNKNOWN__	__UNKNOWN__	11	18597855	18597855	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:18597855C>T	ENST00000541984.1	-	3	190				UEVLD_ENST00000543987.1_Intron|UEVLD_ENST00000540666.1_Intron|UEVLD_ENST00000535484.1_Intron|UEVLD_ENST00000320750.6_Intron|UEVLD_ENST00000396197.3_Intron|UEVLD_ENST00000300038.7_Intron|UEVLD_ENST00000379387.4_Intron	NM_001261386.1	NP_001248315.1			UEV and lactate/malate dehyrogenase domains	NA		NA								endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						atcccagcaccttgggaggct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116	55293			30866	protein-coding gene	gene with protein product		610985			NA	12427560	Standard	NM_018314	NM_001040697	NA	Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000541984.1:c.128-896G>A	chr11.hg19:g.18597855C>T		NA		hg19	CCDS58125.1	0.02	-0.184218	CACxTTG	COVERED																																																																																			NOVEL	UEVLD-015	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395928.1	4	4.212898	KEEP	0	0	0	14	441	CC	0.995343	0.421506	0		-	3	60	85	1	0	6.492173	14	60	495	47	ENST00000541984.1	0.176471	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	18674777	18674777	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:18674777G>A			NA	NA				SPTY2D1 (18439 upstream) : TMEM86A (39891 downstream)						NA		NA									NA						cgaggtgggcggatcacgaga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.18674777G>A		NA		hg19		0.02	-0.087721	GGCxGAT	UNCOVERED																																																																																			NOVEL					0			8	2.706156	KEEP	4	0	0	9	254	GG	0.99257	0.09898	0			3	60	88	0	0	7.578238	7	60	240	30		0.3	0.099721
ZDHHC13	54503	__UNKNOWN__	__UNKNOWN__	11	19196914	19196914	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:19196914G>A	ENST00000446113.2	+	17	1851				ZDHHC13_ENST00000399351.3_Intron	NM_019028.2	NP_061901.2	Q8IUH4	ZDH13_HUMAN	zinc finger, DHHC-type containing 13	NA		NA			metabolic process (GO:0008152)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	magnesium ion transmembrane transporter activity (GO:0015095)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6						tccagcctgggtgacagagcg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB024495	CCDS44550.1, CCDS44551.1	11p15.1	2013-01-10			ENSG00000177054	ENSG00000177054	54503		Zinc fingers, DHHC-type, Ankyrin repeat domain containing	18413	protein-coding gene	gene with protein product		612815			NA	18794299	Standard	NM_019028	NM_001001483	NA	Approved	FLJ10852, FLJ10941, HIP14L	uc001mpi.3	Q8IUH4	OTTHUMG00000166099	ENST00000446113.2:c.1731-455G>A	chr11.hg19:g.19196914G>A		NA	Q7Z2D3|Q86VK2|Q9NV30|Q9NV99	hg19	CCDS44550.1	0.02	-0.070177	TGGxTGA	UNCOVERED																																																																																			NOVEL	ZDHHC13-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387821.1	10	2.407206	KEEP	10	0	0	8	247	GG	0	0	0		+	3	22	93	0	0	8.432625	5	60	168	26	ENST00000446113.2	0.375	0.054137
RP11-428C19.4	0	__UNKNOWN__	__UNKNOWN__	11	19269197	19269197	__UNKNOWN__	RNA	SNP	A	A	G	rs6483587	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:19269197A>G	ENST00000527978.1	+	0	292										NA		NA									NA						cctgggaggcagaggttgcag	0.493		NA											A|||	2191	0.4375	0.3775	0.5346	5008	,	,	NA	15128	0.375	NA	0.5149	False	NA	,,,	NA	NA	NA	2504	0.4346	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000527978.1:	chr11.hg19:g.19269197A>G		NA		hg19		0.02	-0.061403	GGCxGAG	UNCOVERED																																																																																			NOVEL	RP11-428C19.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000387829.1	4	2.406666	KEEP	3	0	0	8	230	AA	0	0	0		+	3	60	96	0	0	9.569562	2	42	63	25	ENST00000527978.1	0.6	0.043787
NAV2	89797	__UNKNOWN__	__UNKNOWN__	11	19784438	19784438	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:19784438A>G	ENST00000360655.4	+	2	304				NAV2_ENST00000349880.4_Intron|NAV2_ENST00000396085.1_Intron|NAV2_ENST00000396087.3_Intron	NM_001111018.1	NP_001104488.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	NA		NA			glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						gattacaggcatgagccacta	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	89797	3.6.1.1		15997	protein-coding gene	gene with protein product	pore membrane and/or filament interacting like protein 2, retinoic acid inducible gene in neuroblastoma 1, helicase, APC down-regulated 1	607026			NA	12079279, 12062803	Standard	NM_145117	NM_145117	NA	Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000360655.4:c.76-69592A>G	chr11.hg19:g.19784438A>G		NA	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	hg19	CCDS53612.1	0.02	-0.350786	GGCxTGA	COVERED																																																																																			NOVEL	NAV2-008	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389876.1	9	2.405906	KEEP	1	0	0	8	218	AA	0.99257	0.871187	0		+	3	60	94	0	0	6.313707	34	60	982	68	ENST00000360655.4	0.081081	0.877708
NAV2	89797	__UNKNOWN__	__UNKNOWN__	11	20028527	20028527	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:20028527T>A	ENST00000360655.4	+	11	2805				NAV2_ENST00000349880.4_Intron|NAV2_ENST00000527559.2_Intron|NAV2_ENST00000396085.1_Intron|NAV2_ENST00000396087.3_Intron|NAV2_ENST00000540292.1_Intron	NM_001111018.1	NP_001104488.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	NA		NA			glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						ttggagacagtgtctcactct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	89797	3.6.1.1		15997	protein-coding gene	gene with protein product	pore membrane and/or filament interacting like protein 2, retinoic acid inducible gene in neuroblastoma 1, helicase, APC down-regulated 1	607026			NA	12079279, 12062803	Standard	NM_145117	NM_145117	NA	Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000360655.4:c.2576+22734T>A	chr11.hg19:g.20028527T>A		NA	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	hg19	CCDS53612.1	0.02	-0.157776	CAGxGTC	COVERED																																																																																			NOVEL	NAV2-008	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389876.1	11	2.706855	KEEP	1	0	0	9	249	TT	0.99254	0.351306	0		+	3	60	83	0	0	6.573888	11	60	298	37	ENST00000360655.4	0.214286	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	20146487	20146487	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:20146487C>T			NA	NA				NAV2 (3343 upstream) : DBX1 (31213 downstream)						NA		NA									NA						ctctctctgtcacccaggctg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.20146487C>T		NA		hg19		0.02	-0.140328	TGTxACC	COVERED																																																																																			NOVEL					0			5	2.407097	KEEP	0	0	0	8	243	CC	0.99257	0.259026	0			3	60	83	0	0	6.932494	8	60	245	31		0.272727	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	20146488	20146488	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:20146488A>G			NA	NA				NAV2 (3344 upstream) : DBX1 (31212 downstream)						NA		NA									NA						tctctctgtcacccaggctgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.20146488A>G		NA		hg19		0.02	-0.140288	GTCxCCC	COVERED																																																																																			NOVEL					0			5	2.404338	KEEP	0	0	0	8	200	AA	0.99257	0.259026	0			3	60	101	0	0	8.879438	7	60	190	31		0.3	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	20371555	20371555	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:20371555T>C			NA	NA				DBX1 (189396 upstream) : HTATIP2 (13675 downstream)						NA		NA									NA						accagcctggtcaacatagca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.20371555T>C		NA		hg19		0.02	-0.105253	TGGxCAA	COVERED																																																																																			NOVEL					0			5	3.308312	KEEP	0	0	0	11	304	TT	0.993072	0.194952	0			3	60	99	0	0	8.532527	8	60	241	36		0.272727	0.196312
PRMT3	10196	__UNKNOWN__	__UNKNOWN__	11	20455206	20455206	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:20455206T>G	ENST00000331079.6	+	10	1210				PRMT3_ENST00000437750.2_Intron	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	NA		NA			histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						tcactctgtctcccaggctgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238	10196		Protein arginine methyltransferases	30163	protein-coding gene	gene with protein product		603190	HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)	HRMT1L3	NA	9642256	Standard	NM_005788	NM_005788	NA	Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.993+6795T>G	chr11.hg19:g.20455206T>G		NA	B4DUC7	hg19	CCDS7853.1	0.02	-0.166639	GTCxCCC	COVERED																																																																																			NOVEL	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387489.1	7	3.007253	KEEP	0	0	0	10	271	TT	0.992708	0.454419	0		+	3	60	99	0	0	7.733524	16	60	478	45	ENST00000331079.6	0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	21964938	21964938	__UNKNOWN__	IGR	SNP	G	G	A	rs552859092	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:21964938G>A			NA	NA				NELL1 (367711 upstream) : CTD-2019O4.1 (170055 downstream)						NA		NA									NA						tgatccgcccgcctcggcctc	0.527		NA											-|||	9	0.00179712	0.0061	0.0014	5008	,	,	NA	13075	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.21964938G>A		NA		hg19		0.02	-0.149121	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			7	2.405254	KEEP	4	0	0	8	242	GG	0	0	0			3	60	87	0	0	6.779063	13	60	442	34		0.1875	0.292001
RP11-17A1.3	0	__UNKNOWN__	__UNKNOWN__	11	22902789	22902789	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:22902789G>A	ENST00000499625.1	+	0	484				RP11-17A1.3_ENST00000528701.1_RNA						NA		NA									NA						ggtggctcacgcctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000499625.1:	chr11.hg19:g.22902789G>A		NA		hg19		0.02	-0.140332	CACxCCT	UNCOVERED																																																																																			NOVEL	RP11-17A1.3-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000388547.1	6	2.40699	KEEP	2	0	0	8	239	GG	0	0	0		+	3	60	84	0	0	6.572887	12	60	395	40	ENST00000499625.1	0.2	0.260965
RP11-266A24.1	0	__UNKNOWN__	__UNKNOWN__	11	23211103	23211103	__UNKNOWN__	lincRNA	SNP	G	G	A	rs145338016	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:23211103G>A	ENST00000533591.1	+	0	343										NA		NA									NA						actttcacaaggtaatgtcat	0.493		NA											G|||	151	0.0301518	0.1029	0.0202	5008	,	,	NA	13805	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000533591.1:	chr11.hg19:g.23211103G>A		NA		hg19		0.02	-0.105236	CAAxGTA	UNCOVERED																																																																																			NOVEL	RP11-266A24.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000387734.1	7	2.407433	KEEP	22	0	0	8	255	GG	0	0	0		+	9	40	263	0	0	27.660089	3	25	87	47	ENST00000533591.1	0.75	0.139832
BDNF-AS	497258	__UNKNOWN__	__UNKNOWN__	11	27537919	27537919	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:27537919T>C	ENST00000499008.3	+	0	47				BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000502161.2_RNA|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000530686.1_RNA|BDNF-AS_ENST00000500662.2_RNA	NR_002832.2				BDNF antisense RNA	NA		NA									NA						tgagatcagcttgggcaacat	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AY054391		11p14.1	2014-01-23	2012-08-15	2012-05-03	ENSG00000245573	ENSG00000245573	497258		Long non-coding RNAs	20608	non-coding RNA	RNA, long non-coding	non-protein coding RNA 49, BDNF antisense RNA 1 (non-protein coding)	611468	BDNF opposite strand (non-protein coding), BDNF antisense RNA (non-protein coding)	BDNFOS	NA	15666411, 22446693	Standard	NR_002832	NR_002832	NA	Approved	BT2A, BT2B, BT2C, BT2D, NCRNA00049, BDNF-AS1	uc001mrm.3			ENST00000499008.3:	chr11.hg19:g.27537919T>C		NA		hg19		0.02	-0.289448	AGCxTGG	COVERED																																																																																			NOVEL	BDNF-AS-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000388068.1	14	4.812614	KEEP	0	0	0	16	452	TT	0.997832	0.759237	0		+	4	60	137	0	0	10.622703	24	60	734	61	ENST00000499008.3	0.142857	0.760887
METTL15	196074	__UNKNOWN__	__UNKNOWN__	11	28354322	28354322	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:28354322C>T	ENST00000407364.3	+	0	3510				METTL15_ENST00000342303.5_3'UTR|METTL15_ENST00000303459.6_3'UTR|METTL15_ENST00000406787.3_3'UTR			A6NJ78	MET15_HUMAN	methyltransferase like 15	NA		NA					methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						gccaacatggcgaaaacccat	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519	196074			26606	protein-coding gene	gene with protein product		NA	methyltransferase 5 domain containing 1	METT5D1	NA	12477932	Standard	NM_152636	NM_152636	NA	Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.*1934C>T	chr11.hg19:g.28354322C>T		NA	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	hg19	CCDS44559.1	0.02	2.947547	TGGxGAA	COVERED																																																																																			NOVEL	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318135.2	21	5.075505	KEEP	0	5	121	60	1770	CC	1	0.999998	0		+	9	50	233	2	0	14.369354	94	60	3070	257	ENST00000407364.3	0.087379	0.999998
METTL15	196074	__UNKNOWN__	__UNKNOWN__	11	28354327	28354327	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:28354327A>C	ENST00000407364.3	+	0	3515				METTL15_ENST00000342303.5_3'UTR|METTL15_ENST00000303459.6_3'UTR|METTL15_ENST00000406787.3_3'UTR			A6NJ78	MET15_HUMAN	methyltransferase like 15	NA		NA					methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						catggcgaaaacccatctcta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519	196074			26606	protein-coding gene	gene with protein product		NA	methyltransferase 5 domain containing 1	METT5D1	NA	12477932	Standard	NM_152636	NM_152636	NA	Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.*1939A>C	chr11.hg19:g.28354327A>C		NA	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	hg19	CCDS44559.1	0.02	3.619551	AAAxCCC	COVERED																																																																																			NOVEL	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318135.2	25	2.566583	KEEP	0	5	146	60	1650	AA	1	1	0		+	5	49	169	2	0	10.341624	111	60	3253	277	ENST00000407364.3	0.043103	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	29990142	29990142	__UNKNOWN__	IGR	SNP	G	G	A	rs566932	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:29990142G>A			NA	NA				CTD-3138F19.1 (86881 upstream) : RP11-215H22.1 (11517 downstream)						NA		NA									NA						cacccacctcggcctcccaaa	0.463		NA											G|||	1380	0.275559	0.3767	0.1758	5008	,	,	NA	11859	0.2302	NA	0.2644	False	NA	,,,	NA	NA	NA	2504	0.2679	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.29990142G>A		NA		hg19		0.02	-0.122801	CTCxGCC	COVERED																																																																																			NOVEL					0			5	2.37989	KEEP	3	0	0	8	211	GG	0.99257	0.194853	0			6	60	181	0	0	17.064652	7	60	237	39		0.461538	0.196312
ARL14EP	120534	__UNKNOWN__	__UNKNOWN__	11	30356040	30356040	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:30356040T>C	ENST00000282032.3	+	3	769					NM_152316.1	NP_689529.1	Q8N8R7	AL14E_HUMAN	ADP-ribosylation factor-like 14 effector protein	NA		NA				cytoplasm (GO:0005737)					NA						ggattacaggtgtgagccacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096287	CCDS7869.1	11p14.1	2014-09-17	2012-07-09	2012-07-09	ENSG00000152219	ENSG00000152219	120534			26798	protein-coding gene	gene with protein product		612295	chromosome 11 open reading frame 46	C11orf46	NA	21458045	Standard	NM_152316	XM_005252792	NA	Approved	FLJ38968, ARF7EP	uc001mso.1	Q8N8R7	OTTHUMG00000166154	ENST00000282032.3:c.554+1500T>C	chr11.hg19:g.30356040T>C		NA	Q5HYH9	hg19	CCDS7869.1	0.02	-0.359567	AGGxGTG	UNCOVERED																																																																																			NOVEL	ARL14EP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388129.1	6	2.706961	KEEP	2	0	0	9	249	TT	0	0	0		+	3	60	97	0	0	6.687911	32	60	942	77	ENST00000282032.3	0.085714	0.888875
WT1	7490	__UNKNOWN__	__UNKNOWN__	11	32414333	32414333	__UNKNOWN__	Intron	SNP	G	G	T	rs2234593	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:32414333G>T	ENST00000379079.2	-	8	887				WT1_ENST00000530998.1_Intron|WT1_ENST00000448076.3_Intron|WT1_ENST00000332351.3_Intron	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	NA		NA			adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)		EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			ATTTGAAAATGATACTGGAAA	0.443		NA	D, Mis, N, F, S	EWSR1	Wilms, desmoplastic small round cell tumor	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome				G|||	613	0.122404	0.2632	0.0605	5008	,	,	NA	19619	0.0238	NA	0.0885	False	NA	,,,	NA	NA	NA	2504	0.1125	NA	NA	NA		yes	Rec	yes	Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor	11	11p13	7490	Wilms tumour 1 gene		O	0								G	,,,,	1015,3389	376.3+/-322.0	122,771,1309	71	68	69		,,,,	-2	0	11	dbSNP_98	69	801,7797	186.3+/-233.8	42,717,3540	no	intron,intron,intron,intron,intron	WT1	NM_000378.4,NM_001198551.1,NM_001198552.1,NM_024424.3,NM_024426.4	,,,,	164,1488,4849	TT,TG,GG	NA	9.3161,23.0472,13.9671	,,,,	,,,,	32414333	1816,11186	2202	4299	6501	SO:0001627	intron_variant	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937	7490		Zinc fingers, C2H2-type	12796	protein-coding gene	gene with protein product		607102		GUD	NA	14681303	Standard	NM_000378	NM_024424	NA	Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.614-32C>A	chr11.hg19:g.32414333G>T		NA	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	hg19	CCDS55751.1	0.02	-0.43857	AATxATA	COVERED																																																																																			NOVEL	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000095434.1	0	2.707956	KEEP	0	0	0	9	273	GG	0.99254	0.952699	0		-	30	60	900	0	0	89.690966	20	60	677	87	ENST00000379079.2	0.6	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	32903565	32903565	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:32903565A>C			NA	NA				PRRG4 (23896 upstream) : QSER1 (11158 downstream)						NA		NA									NA						tggctcatgcatgtaatccca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.32903565A>C		NA		hg19		0.02	-0.201725	TGCxTGT	COVERED																																																																																			NOVEL					0			7	2.707753	KEEP	2	0	0	9	265	AA	0.99254	0.486885	0			3	60	95	0	0	7.491941	14	60	425	48		0.176471	0.490544
CSTF3-AS1	338739	__UNKNOWN__	__UNKNOWN__	11	33186750	33186750	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:33186750G>A	ENST00000500025.2	+	0	94				CSTF3-AS1_ENST00000531870.1_RNA	NR_034027.1				CSTF3 antisense RNA 1 (head to head)	NA		NA									NA						gcatgcctgtggtcccagctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							11p13	2013-07-05			ENSG00000247151	ENSG00000247151	338739		Long non-coding RNAs	27882	non-coding RNA	RNA, long non-coding		NA			NA	12477932	Standard	NR_034027	NR_034027	NA	Approved		uc001muk.3		OTTHUMG00000166243	ENST00000500025.2:	chr11.hg19:g.33186750G>A		NA		hg19		0.02	-0.236849	TGTxGTC	COVERED																																																																																			NOVEL	CSTF3-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000388660.1	13	2.39965	KEEP	0	0	0	8	225	GG	0.99257	0.607857	0		+	3	48	95	0	0	6.894803	23	60	780	42	ENST00000500025.2	0.115385	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	33261194	33261194	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:33261194T>C			NA	NA				Y_RNA (43011 upstream) : HIPK3 (17023 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.33261194T>C		NA		hg19		0.02	-0.289418	AATxCCA	COVERED																																																																																			NOVEL					0			14	5.413418	KEEP	2	0	0	18	496	TT	0.999859	0.76078	0			3	60	101	1	0	7.442727	24	60	701	72		0.111111	0.760887
HIPK3	10114	__UNKNOWN__	__UNKNOWN__	11	33302708	33302708	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:33302708T>A	ENST00000379016.3	+	2	303				HIPK3_ENST00000456517.1_Intron|HIPK3_ENST00000525975.1_Intron|HIPK3_ENST00000303296.4_Intron	NM_001048200.1|NM_001278162.1|NM_001278163.1	NP_001041665.1|NP_001265091.1|NP_001265092.1	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	NA		NA			apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						ctccacctcctgggttcaagc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422	10114			4915	protein-coding gene	gene with protein product		604424	homeodomain-interacting protein kinase 3		NA	9373137, 9748262	Standard	NM_005734	NM_005734	NA	Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000379016.3:c.-2-5251T>A	chr11.hg19:g.33302708T>A		NA	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	hg19	CCDS41634.1	0.02	-0.11402	TCCxGGG	UNCOVERED																																																																																			NOVEL	HIPK3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255359.1	6	3.308876	KEEP	1	0	0	11	312	TT	0.993072	0.161341	0		+	3	42	87	0	0	7.082092	10	60	303	35	ENST00000379016.3	0.230769	0.162467
LMO2	4005	__UNKNOWN__	__UNKNOWN__	11	33892887	33892887	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:33892887C>A	ENST00000257818.2	-	3	559					NM_005574.3	NP_005565.2	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	NA		NA			cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						cttgtgatcccagcactttgg	0.453		NA	T	TRD@	T-ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363	4005			6642	protein-coding gene	gene with protein product	T-cell translocation gene 2, rhombotin-like 1	180385		RBTNL1	NA	2034676	Standard	NM_005574	NM_005574	NA	Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000257818.2:c.271-1354G>T	chr11.hg19:g.33892887C>A		NA	Q9HD58	hg19	CCDS7888.2	0.02	-0.350412	TCCxAGC	COVERED																																																																																			NOVEL	LMO2-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347776.1	8	3.309755	KEEP	0	0	0	11	335	CC	0.993634	0.87212	0		-	10	60	304	0	0	26.078269	25	60	825	70	ENST00000257818.2	0.285714	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	33934972	33934972	__UNKNOWN__	IGR	SNP	G	G	T	rs386752295|rs2038604	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:33934972G>T			NA	NA				LMO2 (21136 upstream) : CAPRIN1 (138257 downstream)						NA		NA									NA						tgggtgcggtggctcacgcct	0.512		NA											T|||	2667	0.532548	0.5287	0.4611	5008	,	,	NA	14978	0.497	NA	0.5557	False	NA	,,,	NA	NA	NA	2504	0.6012	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.33934972G>T		NA		hg19		0.02	-0.149129	GGTxGCT	UNCOVERED																																																																																			NOVEL					0			6	2.708021	KEEP	8	0	0	9	274	GG	0	0	0			5	60	151	0	0	13.522232	9	60	311	49		0.357143	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	33994698	33994698	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:33994698A>G			NA	NA				LMO2 (80862 upstream) : CAPRIN1 (78531 downstream)						NA		NA									NA						ccagcactttaggaggccaag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.33994698A>G		NA		hg19		0.02	-0.149113	TTTxGGA	COVERED																																																																																			NOVEL					0			10	2.706446	KEEP	6	0	0	9	244	AA	0.99257	0.289832	0			3	60	99	0	0	8.072185	12	60	366	45		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	34032516	34032516	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:34032516A>G			NA	NA				LMO2 (118680 upstream) : CAPRIN1 (40713 downstream)						NA		NA									NA						ctggagtgcaatggtgcgatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.34032516A>G		NA		hg19		0.02	-0.228003	GCAxTGG	COVERED																																																																																			NOVEL					0			12	3.307259	KEEP	1	0	0	11	288	AA	0.993072	0.578892	0			3	60	100	0	0	7.449197	22	60	619	52		0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	35110704	35110704	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:35110704G>A			NA	NA				PDHX (68566 upstream) : AL356215.1 (39386 downstream)						NA		NA									NA						cacacctatagtcccagcact	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.35110704G>A		NA		hg19		0.02	-0.412272	ATAxTCC	COVERED																																																																																			NOVEL					0			6	4.814393	KEEP	1	0	0	16	491	GG	0.99649	0.938436	0			4	60	116	1	0	7.824105	37	60	1240	101		0.097561	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	36924612	36924612	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:36924612T>C			NA	NA				C11orf74 (229789 upstream) : SNORA31 (799062 downstream)						NA		NA									NA						gagactctgtttcaaaaacaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.36924612T>C		NA		hg19		0.02	-0.114022	TGTxTCA	UNCOVERED																																																																																			NOVEL					0			8	3.30838	KEEP	2	0	0	11	304	TT	0.99254	0.161255	0			3	60	92	1	1	7.582054	10	60	304	36		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	39044252	39044252	__UNKNOWN__	IGR	SNP	C	C	T	rs11035051	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:39044252C>T			NA	NA				RP11-64I17.1 (348461 upstream) : RNU6-99P (238404 downstream)						NA		NA									NA						gatctcctgacctcatgatcc	0.532		NA											-|||	616	0.123003	0.0855	0.1398	5008	,	,	NA	13255	0.0506	NA	0.2843	False	NA	,,,	NA	NA	NA	2504	0.0706	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.39044252C>T		NA		hg19		0.02	-0.070164	TGAxCTC	UNCOVERED																																																																																			NOVEL					0			3	2.407464	KEEP	13	0	0	8	256	CC	0	0	0			3	59	83	0	0	7.923743	3	40	100	34		0.5	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	39489611	39489611	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:39489611C>T			NA	NA				RNU6-99P (206848 upstream) : AC027806.1 (262747 downstream)						NA		NA									NA						cgggttcaagcgattctcctg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.39489611C>T		NA		hg19		0.02	-0.10525	AAGxGAT	UNCOVERED																																																																																			NOVEL					0			7	3.305676	KEEP	4	0	0	11	289	CC	0	0	0			3	49	85	0	0	7.001015	9	50	292	28		0.25	0.139832
HSD17B12	51144	__UNKNOWN__	__UNKNOWN__	11	43752843	43752843	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:43752843A>G	ENST00000395700.4	+	2	207				HSD17B12_ENST00000529261.1_Intron|HSD17B12_ENST00000278353.4_Intron			Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12	NA		NA			cellular lipid metabolic process (GO:0044255)|estrogen biosynthetic process (GO:0006703)|extracellular matrix organization (GO:0030198)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cell-substrate adhesion (GO:0010811)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|heparin binding (GO:0008201)			endometrium(2)|large_intestine(4)|lung(4)	10						cactgcgcccagccTAAAATC	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(58;548 1143 13948 16572 34258)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF078850	CCDS7905.1	11q11	2011-09-20				ENSG00000149084	51144	1.1.1.62	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	18646	protein-coding gene	gene with protein product	3-ketoacyl-CoA reductase, short chain dehydrogenase/reductase family 12C, member 1	609574			NA	12482854, 19027726	Standard		NM_016142	NA	Approved	KAR, SDR12C1	uc001mxq.4	Q53GQ0		ENST00000395700.4:c.161-19618A>G	chr11.hg19:g.43752843A>G		NA	A8K9B0|D3DR23|Q96EA9|Q96JU2|Q9Y6G8	hg19		0.02	-0.175412	CCCxGCC	COVERED																																																																																			NOVEL	HSD17B12-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000389595.1	14	3.608886	KEEP	3	0	0	12	325	AA	0.993072	0.384723	0		+	3	60	98	0	0	7.63349	16	60	469	42	ENST00000395700.4	0.157895	0.387407
ALKBH3	221120	__UNKNOWN__	__UNKNOWN__	11	43936642	43936642	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:43936642C>T	ENST00000302708.4	+	9	1080				ALKBH3-AS1_ENST00000527960.1_RNA|ALKBH3-AS1_ENST00000528285.1_RNA|ALKBH3_ENST00000532410.1_Intron|ALKBH3-AS1_ENST00000534287.1_RNA|ALKBH3-AS1_ENST00000499194.1_RNA	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	NA		NA			cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	cctgtaatcccagctactcgg	0.532		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199	221120		Alkylation repair homologs	30141	protein-coding gene	gene with protein product		610603			NA	22055184	Standard	NM_139178	NM_139178	NA	Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.670-3946C>T	chr11.hg19:g.43936642C>T		NA	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	hg19	CCDS7906.1	0.02	-0.114031	TCCxAGC	UNCOVERED																																																																																			NOVEL	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389693.1	7	2.407254	KEEP	0	0	0	8	248	CC	0.99257	0.16126	0		+	3	24	90	0	0	7.381914	10	60	323	29	ENST00000302708.4	0.230769	0.162467
TSPAN18	90139	__UNKNOWN__	__UNKNOWN__	11	44810275	44810275	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:44810275A>G	ENST00000520358.2	+	2	263				TSPAN18_ENST00000340160.3_Intron			Q96SJ8	TSN18_HUMAN	tetraspanin 18	NA		NA				integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						gggattacagacttgagccac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570	90139		Tetraspanins	20660	protein-coding gene	gene with protein product		NA			NA	11756464	Standard	NM_130783	NM_130783	NA	Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.-153+24213A>G	chr11.hg19:g.44810275A>G		NA	Q6UY44|Q8NBI9	hg19	CCDS7910.1	0.02	-0.149102	CAGxCTT	COVERED																																																																																			NOVEL	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376197.3	6	2.70575	KEEP	0	0	0	9	235	AA	0.99254	0.289823	0		+	3	60	105	0	0	8.491711	14	60	412	37	ENST00000520358.2	0.176471	0.292001
PRDM11	56981	__UNKNOWN__	__UNKNOWN__	11	45159032	45159032	__UNKNOWN__	Intron	SNP	C	C	T	rs185083093		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:45159032C>T	ENST00000530656.1	+	1	96				PRDM11_ENST00000263765.4_Intron			Q9NQV5	PRD11_HUMAN	PR domain containing 11	NA		NA					methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						ctgggtgtggcggctcatgcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(118;1511 1736 6472 36603 43224)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485	56981			13996	protein-coding gene	gene with protein product	PR-domain containing protein 11	NA			NA		Standard	NM_020229	NM_001256695	NA	Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.96+41580C>T	chr11.hg19:g.45159032C>T		NA	Q8N9F1	hg19		0.02	-0.192957	TGGxGGC	COVERED																																																																																			NOVEL	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000389928.1	13	2.406043	KEEP	0	0	0	8	224	CC	0.99257	0.454356	0		+	3	60	92	0	0	6.82752	19	60	582	41	ENST00000530656.1	0.136364	0.457757
PRDM11	56981	__UNKNOWN__	__UNKNOWN__	11	45159053	45159053	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:45159053A>G	ENST00000530656.1	+	1	96				PRDM11_ENST00000263765.4_Intron			Q9NQV5	PRD11_HUMAN	PR domain containing 11	NA		NA					methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						tgtaatcccaacactttagga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(118;1511 1736 6472 36603 43224)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485	56981			13996	protein-coding gene	gene with protein product	PR-domain containing protein 11	NA			NA		Standard	NM_020229	NM_001256695	NA	Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.96+41601A>G	chr11.hg19:g.45159053A>G		NA	Q8N9F1	hg19		0.02	-0.201716	CCAxCAC	COVERED																																																																																			NOVEL	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000389928.1	13	2.405709	KEEP	0	0	0	8	217	AA	0.99257	0.4869	0		+	4	60	128	0	0	10.179753	18	60	525	40	ENST00000530656.1	0.181818	0.490544
RP11-430H10.2	0	__UNKNOWN__	__UNKNOWN__	11	45399357	45399357	__UNKNOWN__	lincRNA	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:45399357C>A	ENST00000528390.1	+	0	1444										NA		NA									NA						tcactgcaacctccacctccc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000528390.1:	chr11.hg19:g.45399357C>A		NA		hg19		0.02	-0.175445	AACxTCC	UNCOVERED																																																																																			NOVEL	RP11-430H10.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000390118.1	12	2.4072	KEEP	3	0	0	8	247	CC	0	0	0		+	3	60	89	0	0	6.733679	16	60	553	40	ENST00000528390.1	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	45821597	45821597	__UNKNOWN__	IGR	SNP	G	G	A	rs539515606	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:45821597G>A			NA	NA				CTD-2210P24.4 (27688 upstream) : SLC35C1 (4025 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.488		NA											G|||	2	0.000399361	0.0	0.0014	5008	,	,	NA	11915	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.45821597G>A		NA		hg19		0.02	-0.175437	GGCxTGA	COVERED																																																																																			NOVEL					0			7	3.309567	KEEP	4	0	0	11	329	GG	0.99254	0.384517	0			3	60	93	0	0	7.133454	16	60	521	50		0.157895	0.387407
CREB3L1	90993	__UNKNOWN__	__UNKNOWN__	11	46305222	46305222	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46305222A>G	ENST00000529193.1	+	1	553				CREB3L1_ENST00000288400.3_Intron			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	NA		NA			regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)		FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		cttgaggccaagagtttgaga	0.468		NA	T	FUS	myxofibrosarcoma																NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(3;159 194 19597 26278 47995)		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS53620.1	11q11	2013-01-10				ENSG00000157613	90993		basic leucine zipper proteins	18856	protein-coding gene	gene with protein product	BBF-2 homolog (drosophila)	NA			NA		Standard	NM_052854	NM_052854	NA	Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.102+5458A>G	chr11.hg19:g.46305222A>G		NA	Q8N2D5|Q96CP0	hg19	CCDS53620.1	0.02	-0.219274	CCAxGAG	COVERED																																																																																			NOVEL	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389702.1	12	2.707263	KEEP	1	0	0	9	254	AC	0.99254	0.548763	0		+	3	60	106	0	0	8.164541	20	60	596	50	ENST00000529193.1	0.130435	0.552887
DGKZ	8525	__UNKNOWN__	__UNKNOWN__	11	46396592	46396592	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46396592G>A	ENST00000454345.1	+	20	2396	c.2271G>A	c.(2269-2271)tcG>tcA	p.S757S	DGKZ_ENST00000318201.8_Silent_p.S546S|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Silent_p.S573S|DGKZ_ENST00000421244.2_Silent_p.S569S|DGKZ_ENST00000395574.3_Silent_p.S535S|DGKZ_ENST00000528615.1_Silent_p.S347S|DGKZ_ENST00000456247.2_Silent_p.S568S|DGKZ_ENST00000527911.1_Silent_p.S569S|DGKZ_ENST00000343674.6_Silent_p.S585S	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	757		NA			blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		CCATGACGTCGTTGGTGAGTG	0.657		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													37	34	35			NA	NA	11		NA											NA				46396592		2200	4298	6498	SO:0001819	synonymous_variant			U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	8525	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	diacylglycerol kinase, zeta 104kDa		NA	8626588	Standard	NM_001105540	NM_003646	NA	Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.2271G>A	chr11.hg19:g.46396592G>A		NA	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	hg19	CCDS41640.1	0.02	0.933926	GTCxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	9.190	1.025720	0.19512	.	.	ENSG00000149091	ENST00000524869	.	.	.	4.86	-2.29	0.06805	.	.	.	.	.	T	0.39462	0.1079	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30592	-0.9973	4	.	.	.	.	1.7273	0.02925	0.2053:0.4046:0.2018:0.1882	.	.	.	.	H	124	.	.	R	+	2	0	DGKZ	46353168	0.073000	0.21202	0.814000	0.32528	0.739000	0.42172	-0.542000	0.06091	-0.275000	0.09219	-0.228000	0.12330	CGT	NOVEL	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389772.1	0	3.00898	KEEP	0	0	0	10	305	GG	0.992708	0.992656	0		+	6	60	165	0	0	9.582679	92	60	3015	161	ENST00000454345.1	0.061224	0.999948
AMBRA1	55626	__UNKNOWN__	__UNKNOWN__	11	46568603	46568603	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46568603C>T	ENST00000314845.3	-	4	738				AMBRA1_ENST00000533727.1_Intron|AMBRA1_ENST00000528950.1_Intron|AMBRA1_ENST00000298834.3_Intron|AMBRA1_ENST00000458649.2_Intron|AMBRA1_ENST00000534300.1_Intron|AMBRA1_ENST00000426438.1_Intron	NM_017749.3	NP_060219.2	Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	NA		NA			autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		agcgagactccgtctcaaaaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497	55626		WD repeat domain containing, DDB1 and CUL4 associated factors	25990	protein-coding gene	gene with protein product	WD repeat domain 94, DDB1 and CUL4 associated factor 3	611359			NA	17622796, 17603510, 17589504	Standard	NM_017749	NM_001267782	NA	Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000314845.3:c.378+59G>A	chr11.hg19:g.46568603C>T		NA	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	hg19	CCDS31475.1	0.02	-0.429797	CTCxGTC	COVERED																																																																																			NOVEL	AMBRA1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390099.1	5	5.64821	KEEP	0	1	26	28	828	CC	0.999997	0.954488	0		-	4	60	108	0	0	6.778619	43	60	1401	111	ENST00000314845.3	0.085106	0.954491
HARBI1	283254	__UNKNOWN__	__UNKNOWN__	11	46631683	46631683	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46631683A>G	ENST00000326737.3	-	2	918					NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	NA		NA				centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclease activity (GO:0004518)			large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)	3						gattacaggcatgagtcacag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057237	CCDS7920.1	11p11.2	2008-07-10	2008-07-01	2008-07-01	ENSG00000180423	ENSG00000180423	283254			26522	protein-coding gene	gene with protein product		615086	chromosome 11 open reading frame 77	C11orf77	NA	15169610, 18339812	Standard	NM_173811	NM_173811	NA	Approved	FLJ32675	uc001ncy.3	Q96MB7	OTTHUMG00000166537	ENST00000326737.3:c.670+5434T>C	chr11.hg19:g.46631683A>G		NA	D3DQP9	hg19	CCDS7920.1	0.02	-0.122795	GGCxTGA	COVERED																																																																																			NOVEL	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390291.1	6	2.706993	KEEP	2	0	0	9	250	AA	0.99257	0.194853	0		-	3	60	102	0	0	8.978774	7	60	208	36	ENST00000326737.3	0.3	0.196312
ATG13	9776	__UNKNOWN__	__UNKNOWN__	11	46646348	46646348	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46646348T>C	ENST00000530500.1	+	1	328				ATG13_ENST00000524625.1_Intron|ATG13_ENST00000528494.1_Intron|ATG13_ENST00000359513.4_Intron|ATG13_ENST00000529655.1_Intron|ATG13_ENST00000434074.1_Intron|ATG13_ENST00000526508.1_Intron|ATG13_ENST00000451945.1_Intron|ATG13_ENST00000312040.4_Intron	NM_001205122.1	NP_001192051.1	O75143	ATG13_HUMAN	autophagy related 13	NA		NA			autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						tttgggaggctgaggtgagag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224	9776			29091	protein-coding gene	gene with protein product		615088	KIAA0652, ATG13 autophagy related 13 homolog (S. cerevisiae)	KIAA0652	NA	15169610, 18339812, 17204848	Standard	NM_014741	NM_001205120	NA	Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000530500.1:c.-169+6908T>C	chr11.hg19:g.46646348T>C		NA	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	hg19	CCDS55761.1	0.02	-0.096477	GGCxGAG	UNCOVERED																																																																																			NOVEL	ATG13-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390296.1	9	2.405762	KEEP	1	0	0	8	217	TT	0	0	0		+	3	60	96	0	0	8.378788	7	60	209	21	ENST00000530500.1	0.3	0.120436
ATG13	9776	__UNKNOWN__	__UNKNOWN__	11	46654848	46654848	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46654848A>G	ENST00000530500.1	+	2	328				ATG13_ENST00000524625.1_Intron|ATG13_ENST00000528494.1_Intron|ATG13_ENST00000359513.4_Intron|ATG13_ENST00000529655.1_Intron|ATG13_ENST00000434074.1_Intron|ATG13_ENST00000526508.1_Intron|ATG13_ENST00000451945.1_Intron|ATG13_ENST00000312040.4_Intron	NM_001205122.1	NP_001192051.1	O75143	ATG13_HUMAN	autophagy related 13	NA		NA			autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						tgggattacaagcgtgagcca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224	9776			29091	protein-coding gene	gene with protein product		615088	KIAA0652, ATG13 autophagy related 13 homolog (S. cerevisiae)	KIAA0652	NA	15169610, 18339812, 17204848	Standard	NM_014741	NM_001205120	NA	Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000530500.1:c.-168-12041A>G	chr11.hg19:g.46654848A>G		NA	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	hg19	CCDS55761.1	0.02	-0.096487	ACAxGCG	UNCOVERED																																																																																			NOVEL	ATG13-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390296.1	5	3.006641	KEEP	0	0	0	10	270	AA	0.992708	0.119558	0		+	3	60	102	0	0	9.143649	6	60	184	29	ENST00000530500.1	0.333333	0.120436
ATG13	9776	__UNKNOWN__	__UNKNOWN__	11	46668490	46668490	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46668490T>A	ENST00000530500.1	+	3	529				ATG13_ENST00000524625.1_Intron|ATG13_ENST00000528494.1_Intron|ATG13_ENST00000359513.4_Intron|ATG13_ENST00000529655.1_Intron|ATG13_ENST00000434074.1_Intron|ATG13_ENST00000526508.1_Intron|ATG13_ENST00000451945.1_Intron|ATG13_ENST00000312040.4_Intron	NM_001205122.1	NP_001192051.1	O75143	ATG13_HUMAN	autophagy related 13	NA		NA			autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						ttgtattttttgtagagatgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224	9776			29091	protein-coding gene	gene with protein product		615088	KIAA0652, ATG13 autophagy related 13 homolog (S. cerevisiae)	KIAA0652	NA	15169610, 18339812, 17204848	Standard	NM_014741	NM_001205120	NA	Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000530500.1:c.33+951T>A	chr11.hg19:g.46668490T>A		NA	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	hg19	CCDS55761.1	0.02	-0.157852	TTTxGTA	COVERED																																																																																			NOVEL	ATG13-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390296.1	9	3.308026	KEEP	4	0	0	11	297	TT	0.993072	0.32057	0		+	3	46	83	0	0	6.573495	11	60	321	45	ENST00000530500.1	0.214286	0.322807
F2	2147	__UNKNOWN__	__UNKNOWN__	11	46757222	46757222	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46757222T>C	ENST00000311907.5	+	13	1710				F2_ENST00000530231.1_Intron	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	NA		NA			acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)			endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	cctgtaatcctagcactttgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(147;1147 1808 2148 38609 51144)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	2147	3.4.21.5	Endogenous ligands	3535	protein-coding gene	gene with protein product	prepro-coagulation factor II	176930			NA		Standard		NM_000506	NA	Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.1655-3376T>C	chr11.hg19:g.46757222T>C		NA	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	hg19	CCDS31476.1	0.02	-0.157838	TCCxAGC	COVERED																																																																																			NOVEL	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317706.1	7	3.60806	KEEP	0	0	0	12	317	TT	0.993634	0.320751	0		+	3	60	97	0	0	7.692612	14	60	409	44	ENST00000311907.5	0.176471	0.322807
CKAP5	9793	__UNKNOWN__	__UNKNOWN__	11	46865062	46865062	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46865062C>A	ENST00000529230.1	-	1	10				CKAP5_ENST00000415402.1_Intron|CKAP5_ENST00000312055.5_Intron			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	NA		NA			centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						caaaaggatcccttgagccca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(4;85 273 2202 4844 13323)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216	9793			28959	protein-coding gene	gene with protein product		611142			NA	7788527, 8536682	Standard	NM_014756	NM_014756	NA	Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.36+2708G>T	chr11.hg19:g.46865062C>A		NA	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	hg19	CCDS31477.1	0.02	-0.184208	ATCxCTT	COVERED																																																																																			NOVEL	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390679.1	4	3.009025	KEEP	1	0	0	10	310	CC	0.99254	0.420319	0		-	3	60	84	0	0	6.479353	13	60	437	48	ENST00000529230.1	0.1875	0.423478
C11orf49	79096	__UNKNOWN__	__UNKNOWN__	11	46959691	46959691	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:46959691T>C	ENST00000378615.3	+	1	74				C11orf49_ENST00000395460.2_Intron|C11orf49_ENST00000543718.1_Intron|C11orf49_ENST00000278460.7_Intron|C11orf49_ENST00000536126.1_Intron|C11orf49_ENST00000378618.2_Intron			Q9H6J7	CK049_HUMAN	chromosome 11 open reading frame 49	NA		NA				nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(1)	11						tcccaaagtgttgggattaca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136575	CCDS7925.1, CCDS31479.1, CCDS31480.1, CCDS41641.1	11p11.2	2006-02-02			ENSG00000149179	ENSG00000149179	79096			28720	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024113	NM_001003677	NA	Approved	FLJ22210, MGC4707	uc001ndr.4	Q9H6J7	OTTHUMG00000166725	ENST00000378615.3:c.46+1289T>C	chr11.hg19:g.46959691T>C		NA	D3DQQ8|E9PAX7|Q7L077|Q96CS8|Q9BQH4|Q9BUW5	hg19	CCDS31480.1	0.02	-0.192944	GTGxTGG	COVERED																																																																																			NOVEL	C11orf49-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391223.1	6	2.70661	KEEP	3	0	0	9	246	TT	0.99257	0.454356	0		+	3	60	97	1	0	7.328062	19	60	566	55	ENST00000378615.3	0.136364	0.457757
C11orf49	79096	__UNKNOWN__	__UNKNOWN__	11	47075247	47075247	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47075247T>C	ENST00000378615.3	+	3	308				C11orf49_ENST00000395460.2_Intron|C11orf49_ENST00000543718.1_Intron|C11orf49_ENST00000278460.7_Intron|C11orf49_ENST00000527268.1_Intron|C11orf49_ENST00000536126.1_Intron|C11orf49_ENST00000378618.2_Intron			Q9H6J7	CK049_HUMAN	chromosome 11 open reading frame 49	NA		NA				nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(1)	11						aatcccagcattttgggagcc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136575	CCDS7925.1, CCDS31479.1, CCDS31480.1, CCDS41641.1	11p11.2	2006-02-02			ENSG00000149179	ENSG00000149179	79096			28720	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024113	NM_001003677	NA	Approved	FLJ22210, MGC4707	uc001ndr.4	Q9H6J7	OTTHUMG00000166725	ENST00000378615.3:c.280+1178T>C	chr11.hg19:g.47075247T>C		NA	D3DQQ8|E9PAX7|Q7L077|Q96CS8|Q9BQH4|Q9BUW5	hg19	CCDS31480.1	0.02	-0.201698	GCAxTTT	COVERED																																																																																			NOVEL	C11orf49-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391223.1	13	3.608932	KEEP	0	0	0	12	330	TT	0.993634	0.487421	0		+	3	60	96	1	0	7.292809	18	60	531	44	ENST00000378615.3	0.142857	0.490544
NR1H3	10062	__UNKNOWN__	__UNKNOWN__	11	47283668	47283668	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47283668T>C	ENST00000467728.1	+	6	2226				NR1H3_ENST00000405853.3_Intron|NR1H3_ENST00000407404.1_Intron|NR1H3_ENST00000527949.1_Intron|NR1H3_ENST00000405576.1_Intron|NR1H3_ENST00000395397.3_Intron|NR1H3_ENST00000529540.1_Intron|NR1H3_ENST00000441012.2_Intron|NR1H3_ENST00000481889.2_Intron			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	NA		NA			apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						cggtggctcatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434	10062		Nuclear hormone receptors	7966	protein-coding gene	gene with protein product	liver X receptor-alpha	602423			NA	8621574, 7744246	Standard		NM_005693	NA	Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.988+99T>C	chr11.hg19:g.47283668T>C		NA	A8K3J9|D3DQR1|Q8IW13|Q96H87	hg19	CCDS7929.1	0.02	1.745273	TCAxGCC	COVERED																																																																																			NOVEL	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319214.3	13	3.639097	KEEP	0	4	110	51	1417	TT	1	0.992926	0		+	4	60	136	0	0	9.286122	51	60	1506	154	ENST00000467728.1	0.072727	0.992926
MADD	8567	__UNKNOWN__	__UNKNOWN__	11	47342250	47342250	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47342250T>A	ENST00000311027.5	+	31	4542				MADD_ENST00000407859.3_Intron|MADD_ENST00000349238.3_Intron|MADD_ENST00000402192.2_Intron|MADD_ENST00000405573.2_Intron|MADD_ENST00000402799.1_Intron|MADD_ENST00000406482.1_Intron|MADD_ENST00000395344.3_Intron|MADD_ENST00000342922.4_Intron|MADD_ENST00000395336.3_Intron	NM_003682.3	NP_003673.3			MAP-kinase activating death domain	NA		NA								breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		aggtgggaggttcgcttgagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514	8567		DENN/MADD domain containing	6766	protein-coding gene	gene with protein product		603584			NA	9115275, 9796103	Standard		NM_130476	NA	Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4378-2972T>A	chr11.hg19:g.47342250T>A		NA		hg19	CCDS7930.1	0.02	-0.201709	AGGxTCG	COVERED																																																																																			NOVEL	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317746.1	7	3.006746	KEEP	0	0	0	10	275	TT	0.992708	0.486967	0		+	3	60	90	0	0	6.692926	18	60	530	48	ENST00000311027.5	0.142857	0.490544
KBTBD4	55709	__UNKNOWN__	__UNKNOWN__	11	47597046	47597046	__UNKNOWN__	Intron	SNP	A	A	G	rs371348946		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47597046A>G	ENST00000526005.1	-	3	850				KBTBD4_ENST00000533290.1_Intron|NDUFS3_ENST00000533507.1_Intron|KBTBD4_ENST00000430070.2_Intron|KBTBD4_ENST00000395288.2_Intron			Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4	NA		NA								NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	24						acgacagagcaagactccatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151086	CCDS7940.1, CCDS44594.1	11p11.2	2013-01-08	2003-12-12	2003-12-17	ENSG00000123444	ENSG00000123444	55709		BTB/POZ domain containing	23761	protein-coding gene	gene with protein product		NA	BTB and kelch domain containing 4	BKLHD4	NA	11042152	Standard	NM_016506	NM_018095	NA	Approved	FLJ10450, HSPC252	uc001nfz.3	Q9NVX7	OTTHUMG00000166894	ENST00000526005.1:c.696+98T>C	chr11.hg19:g.47597046A>G		NA	D3DQS1|D3DQS2|Q6IA85|Q9BUC3|Q9NV76	hg19	CCDS7940.1	0.02	1.499674	AGCxAGA	COVERED																																																																																			NOVEL	KBTBD4-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391763.1	11	3.235244	KEEP	0	4	105	48	1325	AA	1	0.999835	0		-	4	60	129	0	0	8.105135	68	60	2010	191	ENST00000526005.1	0.055556	0.999835
NDUFS3	4722	__UNKNOWN__	__UNKNOWN__	11	47602733	47602733	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47602733A>G	ENST00000263774.4	+	4	463				NDUFS3_ENST00000533507.1_Intron|NDUFS3_ENST00000528192.1_Silent_p.E129E|NDUFS3_ENST00000534716.2_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	tttagacggaatcttgctctg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(15;551 601 22438 23457 52512)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	4722	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7710	protein-coding gene	gene with protein product	complex I 30kDa subunit, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial	603846	NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)		NA	9763677	Standard	NM_004551	NM_004551	NA	Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.381+197A>G	chr11.hg19:g.47602733A>G		NA	B2R9J1|B4DFM8|Q9UNQ8	hg19	CCDS7941.1	0.02	-0.359466	GGAxTCT	COVERED																																																																																			NOVEL	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391749.1	11	3.440192	KEEP	0	1	30	22	593	AA	0.999892	0.888779	0		+	3	60	98	2	1	6.71272	34	60	922	81	ENST00000263774.4	0.081081	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	47611090	47611090	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47611090C>T			NA	NA				FAM180B (344 upstream) : C1QTNF4 (125 downstream)						NA		NA									NA						ACCTCCTCACCCTCCCAGGGT	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.47611090C>T		NA		hg19		0.02	1.129214	CACxCTC	COVERED																																																																																			NOVEL					0			4	8.423659	KEEP	0	0	0	28	837	CC	0.999997	0.999723	0			27	60	776	0	0	67.565529	57	60	1921	153		0.321429	0.999726
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	47633913	47633913	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:47633913A>T			NA	NA				C1QTNF4 (17702 upstream) : Y_RNA (2536 downstream)						NA		NA									NA						aggtcaggagatcaagaccat	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.47633913A>T		NA		hg19		0.02	-0.166432	GAGxTCA	UNCOVERED																																																																																			NOVEL					0			5	2.404398	KEEP	6	0	0	8	202	AA	0	0	0			4	60	98	0	0	7.46982	15	60	433	48		0.210526	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	48453777	48453777	__UNKNOWN__	IGR	SNP	T	T	C	rs199850755	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:48453777T>C			NA	NA				OR4C5 (65760 upstream) : OR4A47 (56491 downstream)						NA		NA									NA						ATTTATTTGTTACCTGAAATG	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.48453777T>C		NA		hg19		0.02	1.470511	TGTxACC	COVERED																																																																																			NOVEL					0			24	5.705196	KEEP	3	0	0	19	472	TT	0.99986	0.999267	0			8	39	260	0	0	18.483234	73	60	2108	148		0.098765	0.999407
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	48526533	48526533	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:48526533T>C			NA	NA				OR4A47 (15201 upstream) : TRIM49B (523970 downstream)						NA		NA									NA						gaggccaaggtgggaggatca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.48526533T>C		NA		hg19		0.02	-0.228053	AGGxGGG	COVERED																																																																																			NOVEL					0			15	4.812289	KEEP	3	0	0	16	446	TT	0.995343	0.580216	0			4	60	137	0	0	10.994377	19	60	579	61		0.173913	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	48526537	48526537	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:48526537A>T			NA	NA				OR4A47 (15205 upstream) : TRIM49B (523966 downstream)						NA		NA									NA						ccaaggtgggaggatcacctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.48526537A>T		NA		hg19		0.02	-0.236819	GGGxGGA	COVERED																																																																																			NOVEL					0			15	4.509473	KEEP	3	0	0	15	406	AA	0.995343	0.609555	0			3	34	91	0	0	6.549761	22	60	670	61		0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	56513498	56513498	__UNKNOWN__	IGR	SNP	G	G	A	rs4525253	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:56513498G>A			NA	NA				OR9G4 (2211 upstream) : OR5G5P (56061 downstream)						NA		NA									NA						ggccgggcgcggtggctcacg	0.507		NA											-|||	435	0.086861	0.0371	0.0951	5008	,	,	NA	14786	0.119	NA	0.0964	False	NA	,,,	NA	NA	NA	2504	0.1053	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.56513498G>A		NA		hg19		0.02	-0.14034	CGCxGTG	UNCOVERED																																																																																			NOVEL					0			2	2.706799	KEEP	9	0	0	9	255	GG	0	0	0			10	60	305	0	0	31.12254	5	60	158	43		0.666667	0.260965
CLP1	10978	__UNKNOWN__	__UNKNOWN__	11	57429133	57429133	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:57429133G>C	ENST00000302731.4	+	0	1431				CLP1_ENST00000529430.1_3'UTR|CLP1_ENST00000533682.1_3'UTR	NM_001142597.1|NM_006831.2	NP_001136069.1|NP_006822.1	Q5KU26	COL12_HUMAN	cleavage and polyadenylation factor I subunit 1	NA		NA			carbohydrate mediated signaling (GO:0009756)|defense response (GO:0006952)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|protein homooligomerization (GO:0051260)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galactose binding (GO:0005534)|low-density lipoprotein particle binding (GO:0030169)|metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|stomach(1)	15						GACCACCTAAGATGCCACTTT	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC000446	CCDS7964.1, CCDS44600.1	11q12.1	2012-10-02	2012-10-02		ENSG00000172409	ENSG00000172409	10978	2.7.1.78		16999	protein-coding gene	gene with protein product	ATP/GTPbinding protein, polyribonucleotide 5'-hydroxyl-kinase	608757	CLP1, cleavage and polyadenylation factor I subunit, homolog (S. cerevisiae)		NA	8896421, 11060040	Standard	NM_006831	NM_006831	NA	Approved	HEAB, hClp1	uc001nkw.3	Q92989	OTTHUMG00000167146	ENST00000302731.4:c.*225G>C	chr11.hg19:g.57429133G>C		NA	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	hg19	CCDS44600.1	0.02	1.847838	TAAxATG	COVERED																																																																																			NOVEL	CLP1-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393465.1	2	5.416441	KEEP	0	0	0	18	562	GG	0.99986	0.997758	0		+	15	60	528	0	0	44.05877	56	60	1947	151	ENST00000302731.4	0.211268	0.997898
OR6Q1	219952	__UNKNOWN__	__UNKNOWN__	11	57799295	57799295	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:57799295C>T	ENST00000302622.3	+	1	894	c.871C>T	c.(871-873)Cct>Tct	p.P291S	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	291		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CATGCTCAATCCTCTCATCTA	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													100	98	99			NA	NA	11		NA											NA				57799295		2201	4296	6497	SO:0001583	missense			AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381	219952		GPCR / Class A : Olfactory receptors	15302	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001005186	NM_001005186	NA	Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.871C>T	chr11.hg19:g.57799295C>T	ENSP00000307734:p.Pro291Ser	NA	B9EKW1|Q6IFH1|Q96R34	hg19	CCDS31541.1	0.02	1.502594	AATxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138519	0.77775	.	.	ENSG00000172381	ENST00000302622	T	0.63417	-0.04	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38164	N	0.001791	D	0.84524	0.5491	M	0.93241	3.395	0.51012	D	0.999908	D	0.89917	1.0	D	0.85130	0.997	D	0.88967	0.3398	10	0.87932	D	0	.	17.1987	0.86900	0.0:1.0:0.0:0.0	.	291	Q8NGQ2	OR6Q1_HUMAN	S	291	ENSP00000307734:P291S	ENSP00000307734:P291S	P	+	1	0	OR6Q1	57555871	1.000000	0.71417	0.926000	0.36857	0.724000	0.41520	7.039000	0.76544	2.336000	0.79503	0.655000	0.94253	CCT	NOVEL	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401257.1	3	3.609912	KEEP	0	0	0	12	352	CC	0.993634	0.988748	0		+	16	60	472	0	0	38.960742	50	60	1629	105	ENST00000302622.3	0.242424	0.995084
TCN1	6947	__UNKNOWN__	__UNKNOWN__	11	59627727	59627727	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:59627727T>C	ENST00000257264.3	-	5	661				TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	NA		NA			cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ctcagcctcctgagtagctgg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827	6947			11652	protein-coding gene	gene with protein product	haptocorin, haptocorrin	189905			NA		Standard	NM_001062	NM_001062	NA	Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.557-987A>G	chr11.hg19:g.59627727T>C		NA	A8KAC5|Q8WV77	hg19	CCDS7978.1	0.02	-0.087718	TCCxGAG	UNCOVERED																																																																																			NOVEL	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394503.1	4	2.406033	KEEP	1	0	0	8	224	TT	0	0	0		-	3	60	105	0	0	9.443727	6	60	183	30	ENST00000257264.3	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	59914185	59914185	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:59914185A>G			NA	NA				MS4A2 (50741 upstream) : AP001257.1 (12974 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.59914185A>G		NA		hg19		0.02	-0.114028	GCTxGGA	UNCOVERED																																																																																			NOVEL					0			9	3.609146	KEEP	0	0	0	12	330	AA	0.993634	0.161432	0			3	60	105	0	0	9.278806	7	60	208	35		0.3	0.162467
MS4A6A	64231	__UNKNOWN__	__UNKNOWN__	11	59949219	59949219	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:59949219G>C	ENST00000533023.1	-	2	54				MS4A6A_ENST00000528851.1_Intron|MS4A6A_ENST00000530839.1_Intron|MS4A6A_ENST00000532169.1_Intron|MS4A6A_ENST00000323961.3_Intron|MS4A6A_ENST00000426738.2_Intron|MS4A6A_ENST00000529054.1_Intron|MS4A6A_ENST00000412309.2_Intron|MS4A6A_ENST00000420732.2_Intron			Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	NA		NA				integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGCCAACTATGTAAGAAAAAA	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													144	134	137			NA	NA	11		NA											NA				59949219		2201	4295	6496	SO:0001627	intron_variant			AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077	64231			13375	protein-coding gene	gene with protein product		606548		MS4A6	NA	11245982, 11401424	Standard		NM_152852	NA	Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000533023.1:c.14-5C>G	chr11.hg19:g.59949219G>C		NA	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	hg19		0.02	1.704339	TATxTAA	COVERED																																																																																			NOVEL	MS4A6A-014	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000394274.1	7	6.318875	KEEP	0	0	0	21	644	GG	0.999869	0.998862	0		-	22	60	745	0	0	65.439629	52	60	1776	151	ENST00000533023.1	0.297297	0.998993
CD6	923	__UNKNOWN__	__UNKNOWN__	11	60781244	60781244	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:60781244T>G	ENST00000313421.7	+	8	1477				CD6_ENST00000545105.1_Intron|CD6_ENST00000452451.2_Intron|CD6_ENST00000352009.5_Intron|CD6_ENST00000344028.5_Intron|CD6_ENST00000346437.4_Intron	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	NA		NA			cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						gtgcctgtgtttgtgtgtgtg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(169;904 2017 4767 38890 42505)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725	923		CD molecules	1691	protein-coding gene	gene with protein product		186720	CD6 antigen		NA	9013954	Standard	NM_006725	NM_006725	NA	Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1292-147T>G	chr11.hg19:g.60781244T>G		NA	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	hg19	CCDS7999.1	0.02	-0.184052	TGTxTGT	COVERED																																																																																			NOVEL	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396449.1	0	2.705552	KEEP	0	0	0	9	233	TT	0.99254	0.454342	0		+	3	60	95	1	0	7.262201	17	60	449	40	ENST00000313421.7	0.15	0.457757
PGA3	643834	__UNKNOWN__	__UNKNOWN__	11	60973439	60973439	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:60973439C>A	ENST00000325558.6	+	3	404					NM_001079807.1	NP_001073275.1	P0DJD8	PEPA3_HUMAN	pepsinogen 3, group I (pepsinogen A)	NA		NA			digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|lung(1)|ovary(1)|skin(2)	5						actgcactcccgcctggacaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832946	CCDS31574.1	11q13	2006-12-13			ENSG00000229859	ENSG00000229859	643834	3.4.23.1		8885	protein-coding gene	gene with protein product		169710			NA	6300126	Standard	NM_001079807	NM_001079807	NA	Approved		uc001nqx.3	P0DJD8	OTTHUMG00000168071	ENST00000325558.6:c.220-543C>A	chr11.hg19:g.60973439C>A		NA	A8K749|B2R7D6|B7ZW75|P00790|Q7M4R0|Q8N1E3	hg19	CCDS31574.1	0.02	4.526633	TCCxGCC	COVERED																																																																																			NOVEL	PGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397955.2	46	3.648905	KEEP	21	11	308	121	3681	CC	1	1	0		+	7	60	219	0	0	13.097012	137	60	4546	446	ENST00000325558.6	0.048611	1
CYB561A3	220002	__UNKNOWN__	__UNKNOWN__	11	61119463	61119463	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61119463T>G	ENST00000539890.1	-	2	272				CYB561A3_ENST00000426130.2_Intron|CYB561A3_ENST00000536915.1_Intron|CYB561A3_ENST00000540317.1_Intron|CYB561A3_ENST00000294072.4_Intron|CYB561A3_ENST00000447532.2_Intron|CYB561A3_ENST00000546151.1_3'UTR|CYB561A3_ENST00000544118.1_Intron			Q8NBI2	CYAC3_HUMAN	cytochrome b561 family, member A3	NA		NA				integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)				NA						tcagcctccctagtagctggg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024953	CCDS8004.1, CCDS53639.1, CCDS73296.1	11q12.2	2013-03-14	2013-03-14	2013-03-14		ENSG00000162144	220002		Cytochrome b genes	23014	protein-coding gene	gene with protein product		NA	cytochrome b, ascorbate dependent 3	CYBASC3	NA	23249217	Standard	NM_153611	NM_153611	NA	Approved		uc001nrf.4	Q8NBI2		ENST00000539890.1:c.185-844A>C	chr11.hg19:g.61119463T>G		NA	B3KPU2|B4DLN9|J3KQH4|Q6PK96	hg19		0.02	-0.333259	CCCxAGT	COVERED																																																																																			NOVEL	CYB561A3-021	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399149.1	6	6.615984	KEEP	0	0	0	22	604	TT	0.999892	0.865652	0		-	3	60	96	0	0	6.587987	32	60	932	89	ENST00000539890.1	0.085714	0.865745
TMEM138	51524	__UNKNOWN__	__UNKNOWN__	11	61133814	61133814	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61133814C>T	ENST00000278826.6	+	3	859				TMEM138_ENST00000542946.1_3'UTR|TMEM138_ENST00000540194.1_Intron|TMEM138_ENST00000381787.2_Intron	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	NA		NA			cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)				central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						gcctcccaagctcaagcaatt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483	51524			26944	protein-coding gene	gene with protein product		614459			NA		Standard	NM_016464	NM_016464	NA	Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.300+126C>T	chr11.hg19:g.61133814C>T		NA	A6NGA7|B4E044|Q5JPE1	hg19	CCDS8005.1	0.02	1.041367	AAGxTCA	COVERED																																																																																			NOVEL	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398399.2	19	13.736344	KEEP	1	3	80	74	2188	CC	1	0.99994	0		+	5	60	138	0	0	7.825737	85	60	2800	185	ENST00000278826.6	0.055556	0.99994
TMEM216	51259	__UNKNOWN__	__UNKNOWN__	11	61159415	61159415	__UNKNOWN__	5'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61159415G>A	ENST00000515837.2	+	0	257							Q9P0N5	TM216_HUMAN	transmembrane protein 216	NA		NA			cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						ccatcacctcggcctcccaaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049	51259			25018	protein-coding gene	gene with protein product		613277	cerebello-oculo-renal syndrome 2, Meckel syndrome, type 2	CORS2, MKS2	NA	11042152, 20036350, 20512146	Standard	NM_016499	NM_016499	NA	Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.-689G>A	chr11.hg19:g.61159415G>A		NA	A8MZ23|B7Z8N1	hg19	CCDS53640.1	0.02	1.194018	CTCxGCC	COVERED																																																																																			NOVEL	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398430.1	8	9.154692	KEEP	1	1	24	39	1118	GG	1	0.999862	0		+	5	60	149	1	0	9.041631	80	60	2514	189	ENST00000515837.2	0.058824	0.999862
RP11-286N22.8	0	__UNKNOWN__	__UNKNOWN__	11	61240704	61240704	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61240704T>C	ENST00000543044.1	+	5	658				RP11-286N22.8_ENST00000544880.1_Intron						NA		NA									NA						cttactctgttgcccaggctg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000543044.1:c.463-8550T>C	chr11.hg19:g.61240704T>C		NA		hg19		0.02	-0.35073	TGTxGCC	COVERED																																																																																			NOVEL	RP11-286N22.8-006	KNOWN	basic|appris_candidate|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000398485.1	5	3.440836	KEEP	0	1	30	22	606	TT	0.999892	0.877613	0		+	3	60	93	0	0	6.32817	31	60	915	81	ENST00000543044.1	0.088235	0.877708
FADS2	9415	__UNKNOWN__	__UNKNOWN__	11	61593596	61593596	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61593596A>G	ENST00000522056.1	+	1	293				FADS2_ENST00000522639.1_Silent_p.P13P|FADS2_ENST00000574708.1_Silent_p.P13P|FADS2_ENST00000517839.1_Intron|FADS2_ENST00000257261.6_Intron			O95864	FADS2_HUMAN	fatty acid desaturase 2	NA		NA			alpha-linolenic acid metabolic process (GO:0036109)|linoleic acid metabolic process (GO:0043651)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			breast(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20					Alpha-Linolenic Acid(DB00132)	ACGGATGTCCAAGCCTCCTCC	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF084559	CCDS8012.1, CCDS60807.1, CCDS60808.1	11q12.2	2013-01-25			ENSG00000134824	ENSG00000134824	9415	1.14.19.3	Fatty acid desaturases	3575	protein-coding gene	gene with protein product	delta-6-desaturase	606149		LLCDL2	NA		Standard	NM_004265	NM_004265	NA	Approved	FADSD6, D6D, TU13, DES6, SLL0262	uc001nsl.1	O95864	OTTHUMG00000163794	ENST00000522056.1:c.114+9428A>G	chr11.hg19:g.61593596A>G		NA	A8K2M6|B7Z634|Q6MZQ7|Q96H07|Q96SV8|Q9H3G3|Q9Y3X4	hg19		0.02	3.531779	TCCxAGC	COVERED																																																																																			NOVEL	FADS2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000375583.1	5	15.333746	KEEP	0	0	0	51	1358	AA	1	1	0		+	34	60	1110	0	0	93.645083	105	60	3117	281	ENST00000522056.1	0.244604	1
FADS2	9415	__UNKNOWN__	__UNKNOWN__	11	61627321	61627321	__UNKNOWN__	Intron	SNP	G	G	C	rs174607	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61627321G>C	ENST00000522056.1	+	7	968				FADS2_ENST00000257261.6_Intron|FADS2_ENST00000521849.1_Intron|FADS2_ENST00000278840.4_Intron			O95864	FADS2_HUMAN	fatty acid desaturase 2	NA		NA			alpha-linolenic acid metabolic process (GO:0036109)|linoleic acid metabolic process (GO:0043651)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			breast(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20					Alpha-Linolenic Acid(DB00132)	agcctggcatggtggtgtgca	0.537		NA											G|||	524	0.104633	0.0439	0.183	5008	,	,	NA	18766	0.0149	NA	0.2654	False	NA	,,,	NA	NA	NA	2504	0.0583	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF084559	CCDS8012.1, CCDS60807.1, CCDS60808.1	11q12.2	2013-01-25			ENSG00000134824	ENSG00000134824	9415	1.14.19.3	Fatty acid desaturases	3575	protein-coding gene	gene with protein product	delta-6-desaturase	606149		LLCDL2	NA		Standard	NM_004265	NM_004265	NA	Approved	FADSD6, D6D, TU13, DES6, SLL0262	uc001nsl.1	O95864	OTTHUMG00000163794	ENST00000522056.1:c.789+2319G>C	chr11.hg19:g.61627321G>C		NA	A8K2M6|B7Z634|Q6MZQ7|Q96H07|Q96SV8|Q9H3G3|Q9Y3X4	hg19		0.02	-0.043862	CATxGTG	UNCOVERED																																																																																			NOVEL	FADS2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000375583.1	5	3.009076	KEEP	3	0	0	10	310	GG	0.99257	0.023895	0		+	2	60	67	0	0	6.449985	2	60	67	25	ENST00000522056.1	0.5	0.024074
FTH1	2495	__UNKNOWN__	__UNKNOWN__	11	61735059	61735059	__UNKNOWN__	5'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61735059A>C	ENST00000529191.1	-	0	44				FTH1_ENST00000529631.1_5'UTR|FTH1_ENST00000526640.1_5'UTR|FTH1_ENST00000273550.7_5'UTR			P02794	FRIH_HUMAN	ferritin, heavy polypeptide 1	NA		NA			cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|intracellular sequestering of iron ion (GO:0006880)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)|iron ion binding (GO:0005506)			NS(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8					Iron Dextran(DB00893)	CCGTCCAAGCACTGTTGAAGC	0.697		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS41655.1	11q13	2012-10-02			ENSG00000167996	ENSG00000167996	2495			3976	protein-coding gene	gene with protein product	apoferritin, placenta immunoregulatory factor, proliferation-inducing protein 15	134770		FTHL6	NA	3020541	Standard	NM_002032	NM_002032	NA	Approved	FTH, PLIF, PIG15, FHC	uc001nsu.3	P02794		ENST00000529191.1:c.-162T>G	chr11.hg19:g.61735059A>C		NA	B3KNR5|Q3KRA8|Q3SWW1	hg19		0.02	3.862605	AGCxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	18.43	3.623016	0.66901	.	.	ENSG00000167996	ENST00000406545	.	.	.	4.85	3.7	0.42460	.	.	.	.	.	T	0.51753	0.1693	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34229	-0.9837	5	0.15952	T	0.53	.	10.8574	0.46806	0.8585:0.0:0.0:0.1415	.	.	.	.	G	8	.	ENSP00000384656:V8G	V	-	2	0	FTH1	61491635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.887000	0.63156	0.759000	0.33084	0.454000	0.30748	GTG	NOVEL	FTH1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000388520.1	20	4.33473	KEEP	0	7	218	91	2480	AA	1	1	0		-	9	58	300	0	0	20.925069	97	60	2879	332	ENST00000529191.1	0.084906	1
FTH1	2495	__UNKNOWN__	__UNKNOWN__	11	61735080	61735080	__UNKNOWN__	5'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61735080G>T	ENST00000529191.1	-	0	23				FTH1_ENST00000529631.1_5'UTR|FTH1_ENST00000273550.7_5'UTR			P02794	FRIH_HUMAN	ferritin, heavy polypeptide 1	NA		NA			cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|intracellular sequestering of iron ion (GO:0006880)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of fibroblast proliferation (GO:0048147)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)|iron ion binding (GO:0005506)			NS(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8					Iron Dextran(DB00893)	AGGAAACCCCGACGACTCTCG	0.701		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant				CCDS41655.1	11q13	2012-10-02			ENSG00000167996	ENSG00000167996	2495			3976	protein-coding gene	gene with protein product	apoferritin, placenta immunoregulatory factor, proliferation-inducing protein 15	134770		FTHL6	NA	3020541	Standard	NM_002032	NM_002032	NA	Approved	FTH, PLIF, PIG15, FHC	uc001nsu.3	P02794		ENST00000529191.1:c.-183C>A	chr11.hg19:g.61735080G>T		NA	B3KNR5|Q3KRA8|Q3SWW1	hg19		0.02	4.587495	CCCxACG	COVERED	.	.	.	.	.	.	.	.	.	.	.	15.66	2.900201	0.52227	.	.	ENSG00000167996	ENST00000406545	.	.	.	4.85	3.67	0.42095	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.9295	0.05795	0.2202:0.0:0.4593:0.3205	.	.	.	.	X	1	.	ENSP00000384656:S1X	S	-	2	0	FTH1	61491656	0.861000	0.29849	1.000000	0.80357	0.895000	0.52256	0.548000	0.23314	2.366000	0.80165	0.555000	0.69702	TCG	NOVEL	FTH1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000388520.1	18	15.362372	KEEP	0	7	195	120	3491	GG	1	1	0		-	11	58	329	0	0	21.464992	128	60	4122	404	ENST00000529191.1	0.079137	1
INCENP	3619	__UNKNOWN__	__UNKNOWN__	11	61903312	61903312	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:61903312T>C	ENST00000394818.3	+	5	1265				INCENP_ENST00000278849.4_Intron	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	NA		NA			chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						gatggagtcttgctctgttgc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503	3619			6058	protein-coding gene	gene with protein product		604411	inner centromere protein antigens (135kD, 155kD)		NA	1860899, 11453556	Standard	NM_020238	NM_001040694	NA	Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1064-1992T>C	chr11.hg19:g.61903312T>C		NA	A8MQD2|Q5Y192	hg19	CCDS44624.1	0.02	-0.227988	TCTxGCT	COVERED																																																																																			NOVEL	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394723.2	10	2.703999	KEEP	1	0	0	9	235	TT	0.99257	0.578599	0		+	3	60	92	0	0	6.766058	20	60	575	50	ENST00000394818.3	0.130435	0.58293
ASRGL1	80150	__UNKNOWN__	__UNKNOWN__	11	62153431	62153431	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62153431C>T	ENST00000415229.2	+	5	706				ASRGL1_ENST00000301776.5_Intron|ASRGL1_ENST00000535727.1_Intron	NM_001083926.1	NP_001077395.1	Q7L266	ASGL1_HUMAN	asparaginase like 1	NA		NA			asparagine catabolic process via L-aspartate (GO:0033345)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	asparaginase activity (GO:0004067)|beta-aspartyl-peptidase activity (GO:0008798)			endometrium(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	7					L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)	gtcaggagttcgagaccagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8019.1	11q12.3	2008-07-18			ENSG00000162174	ENSG00000162174	80150			16448	protein-coding gene	gene with protein product	asparaginase-like 1 protein	609212			NA		Standard	NM_001083926	NM_025080	NA	Approved	FLJ22316, ALP1, ALP	uc001ntf.4	Q7L266	OTTHUMG00000167513	ENST00000415229.2:c.492-3174C>T	chr11.hg19:g.62153431C>T		NA	B2R7Q0|Q567Q4|Q6P1P0|Q8NI34|Q9H6F7	hg19	CCDS8019.1	0.02	-0.122796	GTTxGAG	COVERED																																																																																			NOVEL	ASRGL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394865.1	3	3.007643	KEEP	0	0	0	10	279	CC	0.992708	0.19488	0		+	3	60	85	0	0	7.001045	9	60	288	33	ENST00000415229.2	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	62171036	62171036	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62171036T>C			NA	NA				ASRGL1 (10154 upstream) : SCGB1A1 (1538 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.62171036T>C		NA		hg19		0.02	-0.201727	TCAxGCC	COVERED																																																																																			NOVEL					0			5	2.705481	KEEP	1	0	0	9	239	TT	0.99254	0.486885	0			4	60	134	0	0	10.779563	18	60	531	50		0.181818	0.490544
SCGB1A1	7356	__UNKNOWN__	__UNKNOWN__	11	62183936	62183936	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62183936A>G	ENST00000534397.1	+	2	67							P11684	UTER_HUMAN	secretoglobin, family 1A, member 1 (uteroglobin)	NA		NA			embryo implantation (GO:0007566)|female pregnancy (GO:0007565)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-13 production (GO:0032696)|negative regulation of interleukin-4 production (GO:0032713)|negative regulation of interleukin-5 production (GO:0032714)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of inflammatory response (GO:0050727)|regulation of mRNA stability (GO:0043488)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fibroblast growth factor (GO:0071774)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to silicon dioxide (GO:0034021)|response to xenobiotic stimulus (GO:0009410)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nuclear envelope (GO:0005635)|rough endoplasmic reticulum (GO:0005791)|secretory granule (GO:0030141)	phospholipase A2 inhibitor activity (GO:0019834)			lung(1)	1						cacccgcctcagcctcccaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8020.1	11q12.3	2011-12-14	2002-03-22	2002-03-22	ENSG00000149021	ENSG00000149021	7356		Secretoglobins	12523	protein-coding gene	gene with protein product	Uteroglobin (Clara-cell specific 10-kD protein)	192020	uteroglobin	UGB	NA	1284526, 22155607	Standard	NM_003357	NM_003357	NA	Approved	CC10, CCSP, CC16	uc001ntj.3	P11684	OTTHUMG00000167526	ENST00000534397.1:c.-124-100A>G	chr11.hg19:g.62183936A>G		NA	B2R5F2|Q6FHH3|Q9UCM2|Q9UCM4	hg19		0.02	-0.271902	CTCxGCC	COVERED																																																																																			NOVEL	SCGB1A1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000394924.2	12	3.007859	KEEP	0	0	0	10	278	AA	0.992708	0.712085	0		+	3	53	106	0	0	7.942106	24	60	720	55	ENST00000534397.1	0.111111	0.717315
GANAB	23193	__UNKNOWN__	__UNKNOWN__	11	62395937	62395937	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62395937G>A	ENST00000346178.4	-	18	2262				GANAB_ENST00000540933.1_Intron|GANAB_ENST00000356638.3_Intron|GANAB_ENST00000534779.1_Intron	NM_001278192.1|NM_198335.2	NP_001265121.1|NP_938149.2	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	NA		NA			cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	tgcccacctcggcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(23;1005 1074 15747 18937)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	23193	3.2.1.20		4138	protein-coding gene	gene with protein product		104160			NA	10764838, 6342981	Standard	NM_198334	NM_198335	NA	Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000346178.4:c.2246+303C>T	chr11.hg19:g.62395937G>A		NA	A6NC20|Q8WTS9|Q9P0X0	hg19	CCDS41656.1	0.02	-0.192938	CTCxGCC	COVERED																																																																																			NOVEL	GANAB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395688.2	15	3.60979	KEEP	12	0	0	12	352	GG	0.99257	0.454356	0		-	3	43	91	0	0	7.092315	14	60	448	65	ENST00000346178.4	0.176471	0.457757
C11orf83	0	__UNKNOWN__	__UNKNOWN__	11	62438521	62438521	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62438521T>A	ENST00000531323.1	+	2	81				C11orf48_ENST00000431002.2_5'UTR|C11orf48_ENST00000354588.3_Intron|C11orf48_ENST00000532208.1_Intron			Q6UW78	CK083_HUMAN		NA		NA				extracellular region (GO:0005576)				cervix(1)|lung(1)|prostate(1)	3						cagtgagccatgatcgcgcca	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000531323.1:c.-462-235T>A	chr11.hg19:g.62438521T>A		NA	Q5FVD5	hg19	CCDS41658.1	0.02	7.235341	CCAxGAT	COVERED																																																																																			NOVEL	C11orf83-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394992.2	56	14.204666	KEEP	1	16	419	196	5060	TT	1	1	0		+	14	60	406	0	0	23.083044	271	60	7587	617	ENST00000531323.1	0.049123	1
LRRN4CL	221091	__UNKNOWN__	__UNKNOWN__	11	62454342	62454342	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62454342C>T	ENST00000317449.4	-	0	2116					NM_203422.2	NP_981967.1	Q8ND94	LRN4L_HUMAN	LRRN4 C-terminal like	NA		NA				integral component of membrane (GO:0016021)				cervix(1)|kidney(1)	2						ggggtttcaccgtgttagcca	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK291334	CCDS8030.1	11q12.3	2013-02-11				ENSG00000177363	221091		Fibronectin type III domain containing	33724	protein-coding gene	gene with protein product		NA			NA		Standard	NM_203422	NM_203422	NA	Approved		uc001nun.3	Q8ND94		ENST00000317449.4:c.*922G>A	chr11.hg19:g.62454342C>T		NA	A8K5L9	hg19	CCDS8030.1	0.02	-0.184186	CACxGTG	COVERED																																																																																			NOVEL	LRRN4CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395168.1	4	3.008446	KEEP	4	0	0	10	292	CC	0.99254	0.420319	0		-	3	43	87	0	0	6.461759	17	60	535	42	ENST00000317449.4	0.15	0.423478
HNRNPUL2-BSCL2	100534595	__UNKNOWN__	__UNKNOWN__	11	62461940	62461940	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62461940C>G	ENST00000403734.2	-	17	3150				BSCL2_ENST00000433053.1_Intron|BSCL2_ENST00000407022.3_Intron|BSCL2_ENST00000360796.5_Intron|BSCL2_ENST00000421906.1_Intron|BSCL2_ENST00000405837.1_Intron|BSCL2_ENST00000403550.1_Intron|BSCL2_ENST00000278893.7_Intron					HNRNPUL2-BSCL2 readthrough	NA		NA									NA						gcctcccaaactgctgggatt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					11q12.3	2013-09-25			ENSG00000234857	ENSG00000234857	100534595			49189	other	readthrough		NA			NA		Standard		NR_037946	NA	Approved				OTTHUMG00000167772	ENST00000403734.2:c.2238+99G>C	chr11.hg19:g.62461940C>G		NA		hg19		0.02	-0.140363	AAAxTGC	COVERED																																																																																			NOVEL	HNRNPUL2-BSCL2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000396207.1	8	2.394965	KEEP	0	0	0	8	225	AC	0.99254	0.259018	0		-	3	60	104	0	0	8.672549	11	60	371	30	ENST00000403734.2	0.214286	0.260965
STX5	6811	__UNKNOWN__	__UNKNOWN__	11	62597983	62597983	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62597983A>G	ENST00000294179.3	-	2	379				STX5_ENST00000541317.1_Intron|STX5_ENST00000377897.4_Intron|STX5_ENST00000394690.1_Intron	NM_001244666.1|NM_003164.4	NP_001231595.1|NP_003155.2	Q13190	STX5_HUMAN	syntaxin 5	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle targeting (GO:0006903)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|SNARE complex (GO:0031201)	protein N-terminus binding (GO:0047485)|SNAP receptor activity (GO:0005484)			breast(2)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	18						tcacaccactacactccagcc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U26648	CCDS8038.2, CCDS58140.1	11q12.3	2008-02-05	2006-04-25	2006-04-25	ENSG00000162236	ENSG00000162236	6811			11440	protein-coding gene	gene with protein product		603189	syntaxin 5A	STX5A	NA	9188044, 11959998	Standard	NM_003164	NM_003164	NA	Approved	SED5	uc001nvh.3	Q13190	OTTHUMG00000143864	ENST00000294179.3:c.225+507T>C	chr11.hg19:g.62597983A>G		NA	B2R8T2|F8W8Q9|Q5U0D4|Q7Z3T6|Q9BUG1	hg19	CCDS8038.2	0.02	-0.412203	ACTxCAC	COVERED																																																																																			NOVEL	STX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000290113.1	7	5.344091	KEEP	0	1	29	28	749	AA	0.999997	0.941738	0		-	3	60	98	1	0	6.44812	42	60	1230	109	ENST00000294179.3	0.066667	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	62739712	62739712	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62739712A>G			NA	NA				RN7SL259P (36006 upstream) : SLC22A6 (4356 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.62739712A>G		NA		hg19		0.02	-0.114015	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			6	2.70711	KEEP	1	0	0	9	253	AA	0.99257	0.16126	0			3	60	102	0	0	8.582146	10	60	290	29		0.230769	0.162467
SLC22A6	9356	__UNKNOWN__	__UNKNOWN__	11	62746353	62746353	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:62746353T>C	ENST00000360421.4	-	8	1654				SLC22A6_ENST00000458333.2_Intron|SLC22A6_ENST00000421062.2_Intron|SLC22A6_ENST00000377871.3_Intron	NM_153276.2|NM_153277.2	NP_695008.1|NP_695009.1	Q4U2R8	S22A6_HUMAN	solute carrier family 22 (organic anion transporter), member 6	NA		NA			alpha-ketoglutarate transport (GO:0015742)|organic anion transport (GO:0015711)|protein homooligomerization (GO:0051260)|renal tubular secretion (GO:0097254)|response to methotrexate (GO:0031427)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride ion binding (GO:0031404)|inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(18)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36					Acetaminophen(DB00316)|Acetazolamide(DB00819)|Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Aciclovir(DB00787)|Adefovir Dipivoxil(DB00718)|Aminohippurate(DB00345)|Aminophenazone(DB01424)|Amoxicillin(DB01060)|Antipyrine(DB01435)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bromodiphenhydramine(DB01237)|Bumetanide(DB00887)|Captopril(DB01197)|Carbenicillin(DB00578)|Carprofen(DB00821)|Caspofungin(DB00520)|Cefacetrile(DB01414)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Cefotiam(DB00229)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftriaxone(DB01212)|Cephalexin(DB00567)|Chloramphenicol(DB00446)|Chlorothiazide(DB00880)|Chlorpropamide(DB00672)|Cidofovir(DB00369)|Cilastatin(DB01597)|Cimetidine(DB00501)|Cinoxacin(DB00827)|Cloxacillin(DB01147)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Cyclothiazide(DB00606)|Dabrafenib(DB08912)|Diclofenac(DB00586)|Didanosine(DB00900)|Diflunisal(DB00861)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Enalapril(DB00584)|Ethacrynic acid(DB00903)|Etodolac(DB00749)|Fluorescein(DB00693)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Foscarnet(DB00529)|Furosemide(DB00695)|Ganciclovir(DB01004)|Gentamicin(DB00798)|Glyburide(DB01016)|Hydrochlorothiazide(DB00999)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Losartan(DB00678)|Meclofenamic acid(DB00939)|Methazolamide(DB00703)|Methotrexate(DB00563)|Minocycline(DB01017)|Nafcillin(DB00607)|Nalidixic Acid(DB00779)|Naproxen(DB00788)|Nateglinide(DB00731)|Norfloxacin(DB01059)|Novobiocin(DB01051)|Ofloxacin(DB01165)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piperacillin(DB00319)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Riboflavin(DB00140)|Salicylic acid(DB00936)|Stavudine(DB00649)|Streptomycin(DB01082)|Sulindac(DB00605)|Tenofovir(DB00300)|Tetracycline(DB00759)|Tolbutamide(DB01124)|Tolmetin(DB00500)|Trifluridine(DB00432)|Valaciclovir(DB00577)|Valproic Acid(DB00313)|Vancomycin(DB00512)|Zalcitabine(DB00943)|Zidovudine(DB00495)	tgagccaccgtgcccggccgg	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF057039	CCDS8041.1, CCDS31591.1, CCDS44631.1, CCDS44632.1	11q12.3	2013-07-15			ENSG00000197901	ENSG00000197901	9356		Solute carriers	10970	protein-coding gene	gene with protein product		607582			NA	9762842, 9950961	Standard	NM_004790	NM_004790	NA	Approved	ROAT1, PAHT, OAT1	uc001nwk.3	Q4U2R8	OTTHUMG00000167767	ENST00000360421.4:c.1361+606A>G	chr11.hg19:g.62746353T>C		NA	A8MY93|B2D0R6|O95187|O95742|Q7LDA0|Q8N192|Q9NQA6|Q9NQC2|Q9UBG6|Q9UEQ8	hg19	CCDS8041.1	0.02	-0.219195	CCGxGCC	COVERED																																																																																			NOVEL	SLC22A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396184.1	8	2.537018	KEEP	5	1	24	17	457	TT	0.99649	0.550947	0		-	3	60	104	0	0	7.905588	21	60	599	62	ENST00000360421.4	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	63579704	63579704	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:63579704G>A			NA	NA				RN7SL596P (14161 upstream) : C11orf84 (1155 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.63579704G>A		NA		hg19		0.02	-0.149126	CACxCCT	COVERED																																																																																			NOVEL					0			7	2.707613	KEEP	1	0	0	9	268	GG	0.99254	0.289823	0			3	60	93	0	0	7.572685	11	60	373	38		0.214286	0.292001
BAD	572	__UNKNOWN__	__UNKNOWN__	11	64045497	64045497	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64045497T>C	ENST00000394531.3	-	3	218				BAD_ENST00000309032.3_Intron|BAD_ENST00000544785.1_Intron|BAD_ENST00000394532.3_Intron			Q92934	BAD_HUMAN	BCL2-associated agonist of cell death	NA		NA			activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						tggtggctcatgcctgtaatc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330	572			936	protein-coding gene	gene with protein product		603167			NA	8929532	Standard	NM_032989	NM_004322	NA	Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394531.3:c.188-982A>G	chr11.hg19:g.64045497T>C		NA	O14803|Q6FH21	hg19		0.02	-0.105243	TCAxGCC	UNCOVERED																																																																																			NOVEL	BAD-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000259181.1	5	2.706851	KEEP	0	0	0	9	249	TT	0.99254	0.138789	0		-	3	60	105	0	0	9.444044	6	60	169	32	ENST00000394531.3	0.333333	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	64182154	64182154	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64182154C>T			NA	NA				AP003774.6 (18851 upstream) : AP003774.5 (5708 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.64182154C>T		NA		hg19		0.02	-0.184216	AGAxGGG	COVERED																																																																																			NOVEL					0			9	3.60997	KEEP	2	0	0	12	350	CC	0.993634	0.420782	0			3	60	87	0	0	6.610592	15	60	513	49		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	64280171	64280171	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64280171G>A			NA	NA				AP005273.1 (7313 upstream) : SLC22A11 (42926 downstream)						NA		NA									NA						tttgagaccagcctgggtaac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.64280171G>A		NA		hg19		0.02	-0.149133	CCAxCCT	COVERED																																																																																			NOVEL					0			6	3.009182	KEEP	0	0	0	10	318	GG	0.992708	0.320453	0			5	60	156	0	0	13.669659	11	60	382	38		0.3125	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	64590566	64590566	__UNKNOWN__	IGR	SNP	T	T	C	rs534758679		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64590566T>C			NA	NA				MEN1 (11800 upstream) : CDC42BPG (292 downstream)						NA		NA									NA						cttttcttttttttttttttt	0.512		NA											T|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17026	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.64590566T>C		NA		hg19		0.02	-0.052625	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			9	3.006332	KEEP	3	0	0	10	260	TT	0.99257	0.036492	0			2	49	70	0	0	6.750208	2	60	61	21		0.5	0.036766
EHD1	10938	__UNKNOWN__	__UNKNOWN__	11	64628244	64628244	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64628244G>A	ENST00000320631.3	-	3	757				EHD1_ENST00000359393.2_Intron	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	NA		NA			blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						ctgtaatcccgacactttggg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047	10938		EF-hand domain containing	3242	protein-coding gene	gene with protein product	testilin	605888		PAST1	NA	10395801, 10673336	Standard	NM_006795	NM_001282444	NA	Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.503-436C>T	chr11.hg19:g.64628244G>A		NA	O14611|Q2M3Q4|Q9UNR3	hg19	CCDS8084.1	0.02	-0.070162	CCCxACA	UNCOVERED																																																																																			NOVEL	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000143229.2	3	2.707496	KEEP	0	0	0	9	262	GG	0.99254	0.053733	0		-	3	60	80	0	0	7.353979	4	60	127	23	ENST00000320631.3	0.428571	0.054137
RP11-399J13.3	0	__UNKNOWN__	__UNKNOWN__	11	64792570	64792570	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64792570G>A	ENST00000301886.3	+	4	365										NA		NA									NA						ccaaagtgctgggattacagg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000301886.3:c.340-2220G>A	chr11.hg19:g.64792570G>A		NA		hg19		0.02	-0.166671	GCTxGGA	COVERED																																																																																			NOVEL	RP11-399J13.3-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000471510.1	8	2.407488	KEEP	0	0	0	8	256	GG	0.99257	0.351317	0		+	3	60	88	0	0	6.63406	16	60	551	39	ENST00000301886.3	0.157895	0.353947
CAPN1	823	__UNKNOWN__	__UNKNOWN__	11	64969237	64969237	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:64969237T>C	ENST00000527323.1	+	10	1405				CAPN1_ENST00000524773.1_Intron|CAPN1_ENST00000533129.1_Intron|CAPN1_ENST00000279247.6_Intron|CAPN1_ENST00000533820.1_Intron			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	NA		NA			extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		gatccgcccgtctcggcctcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	823	3.4.22.52	EF-hand domain containing	1476	protein-coding gene	gene with protein product		114220			NA	3017764, 2209092	Standard		NM_005186	NA	Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.1166-2917T>C	chr11.hg19:g.64969237T>C		NA	Q2TTR0|Q6DHV4	hg19	CCDS44644.1	0.02	-0.10525	CCGxCTC	UNCOVERED																																																																																			NOVEL	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385325.1	4	3.006597	KEEP	6	0	0	10	262	TT	0	0	0		+	3	33	102	0	0	8.832609	8	60	235	40	ENST00000527323.1	0.272727	0.139832
FRMD8	83786	__UNKNOWN__	__UNKNOWN__	11	65180711	65180711	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:65180711A>G	ENST00000317568.5	+	0	3438				FRMD8_ENST00000355991.5_3'UTR	NM_031904.3	NP_114110.1	Q9BZ67	FRMD8_HUMAN	FERM domain containing 8	NA		NA				cytoskeleton (GO:0005856)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|urinary_tract(1)	17						gcccgcctcaacctcccaaag	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK074850	CCDS8102.1, CCDS73320.1	11q13.1	2007-08-14			ENSG00000126391	ENSG00000126391	83786			25462	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_031904	NM_031904	NA	Approved	FLJ90369, FKSG44	uc001odu.4	Q9BZ67	OTTHUMG00000166275	ENST00000317568.5:c.*1880A>G	chr11.hg19:g.65180711A>G		NA	B4E2P1|Q86V56|Q8NCB5	hg19	CCDS8102.1	0.02	-0.403478	TCAxCCT	COVERED																																																																																			NOVEL	FRMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388833.1	5	6.547488	KEEP	0	1	29	32	868	AA	0.999998	0.93449	0		+	3	60	103	0	0	7.140136	36	60	1091	99	ENST00000317568.5	0.076923	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	65211794	65211794	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:65211794A>G			NA	NA				FRMD8 (30798 upstream) : NEAT1 (134 downstream)						NA		NA									NA						gtgtgtgtgtAAAAGAGAGAA	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.65211794A>G		NA		hg19		0.02	1.782756	TGTxAAA	COVERED																																																																																			NOVEL					0			8	10.51344	KEEP	2	0	0	35	872	AA	0.999998	0.984159	0			4	60	125	1	1	8.25754	49	60	1306	122		0.075472	0.984161
PACS1	55690	__UNKNOWN__	__UNKNOWN__	11	65867280	65867280	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:65867280A>G	ENST00000320580.4	+	1	389					NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	NA		NA			protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)		RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						gcctcccaaaatgctgggatt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115	55690			30032	protein-coding gene	gene with protein product		607492			NA	12855553, 14608369	Standard	NM_018026	NM_018026	NA	Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.356+28967A>G	chr11.hg19:g.65867280A>G		NA	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	hg19	CCDS8129.1	0.02	-0.192962	AAAxTGC	COVERED																																																																																			NOVEL	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391690.2	5	3.007812	KEEP	0	0	0	10	277	AA	0.992708	0.454419	0		+	3	60	96	0	0	7.360955	17	60	518	46	ENST00000320580.4	0.15	0.457757
PACS1	55690	__UNKNOWN__	__UNKNOWN__	11	65977612	65977612	__UNKNOWN__	Intron	SNP	G	G	C	rs539704417	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:65977612G>C	ENST00000320580.4	+	3	477					NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	NA		NA			protein targeting to Golgi (GO:0000042)|protein targeting to plasma membrane (GO:0072661)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	COPI-coated vesicle (GO:0030137)|cytosol (GO:0005829)	ion channel binding (GO:0044325)		RBM14/PACS1(2)	breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(8)|ovary(6)|skin(2)|urinary_tract(1)	37						agtgatcctcgcacctcagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033001	CCDS8129.1	11q13.1-q13.2	2008-02-05			ENSG00000175115	ENSG00000175115	55690			30032	protein-coding gene	gene with protein product		607492			NA	12855553, 14608369	Standard	NM_018026	NM_018026	NA	Approved	FLJ10209, KIAA1175	uc001oha.2	Q6VY07	OTTHUMG00000166889	ENST00000320580.4:c.445-221G>C	chr11.hg19:g.65977612G>C		NA	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	hg19	CCDS8129.1	0.02	-0.149115	CTCxCAC	COVERED																																																																																			NOVEL	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391690.2	11	2.406335	KEEP	0	0	0	8	227	GG	0.99257	0.289832	0		+	3	60	89	0	0	6.892259	14	60	462	30	ENST00000320580.4	0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	66087011	66087011	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66087011C>T			NA	NA				RP11-867G23.13 (303 upstream) : RIN1 (12521 downstream)						NA		NA									NA						ccagcctgggcgacagagcaa	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.66087011C>T		NA		hg19		0.02	-0.236806	GGGxGAC	COVERED																																																																																			NOVEL					0			5	3.910873	KEEP	0	0	0	13	384	CC	0.994391	0.608972	0			4	60	108	0	0	7.938307	21	60	677	61		0.16	0.612407
RP11-867G23.8	0	__UNKNOWN__	__UNKNOWN__	11	66127812	66127812	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66127812T>C	ENST00000531602.1	+	2	121				RP11-867G23.8_ENST00000580881.1_Intron						NA		NA								kidney(1)	1						ccttggcctctcaaggtgctg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000531602.1:c.-12-2928T>C	chr11.hg19:g.66127812T>C		NA		hg19		0.02	-0.096489	CTCxCAA	UNCOVERED																																																																																			NOVEL	RP11-867G23.8-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000391898.1	7	2.400559	KEEP	1	0	0	8	210	TT	0.99257	0.119541	0		+	3	60	101	0	0	8.732431	8	60	248	30	ENST00000531602.1	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	66151441	66151441	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66151441A>G			NA	NA				SLC29A2 (11756 upstream) : RNU1-84P (9478 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.66151441A>G		NA		hg19		0.02	-0.438527	GGCxTGA	COVERED																																																																																			NOVEL					0			13	4.796368	KEEP	0	0	0	16	418	AA	0.997832	0.957778	0			3	60	101	0	0	6.840358	39	60	1174	92		0.071429	0.959859
CTD-3074O7.11	0	__UNKNOWN__	__UNKNOWN__	11	66294586	66294586	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66294586G>A	ENST00000419755.3	+	13	1528				ZDHHC24_ENST00000526986.1_Intron|BBS1_ENST00000393994.2_Intron|BBS1_ENST00000318312.7_Intron|BBS1_ENST00000529766.1_Intron|BBS1_ENST00000455748.2_Intron						NA		NA									NA						ggtggctcacgcctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000419755.3:c.1450+308G>A	chr11.hg19:g.66294586G>A		NA		hg19		0.02	-0.263156	CACxCCT	COVERED																																																																																			NOVEL	CTD-3074O7.11-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000395848.2	6	3.905446	KEEP	1	0	0	13	372	GG	0.994391	0.689777	0		+	3	60	93	0	0	6.643076	24	60	786	52	ENST00000419755.3	0.111111	0.693668
ZDHHC24	254359	__UNKNOWN__	__UNKNOWN__	11	66302616	66302616	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66302616A>G	ENST00000526986.1	-	3	791							Q6UX98	ZDH24_HUMAN	zinc finger, DHHC-type containing 24	NA		NA				integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|ovary(1)|prostate(1)|skin(1)	7						cgcctgcctcagcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005015	CCDS8143.1	11q13.2	2008-05-02				ENSG00000174165	254359		Zinc fingers, DHHC-type	27387	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207340	NM_207340	NA	Approved		uc001oin.1	Q6UX98		ENST00000526986.1:c.560-5657T>C	chr11.hg19:g.66302616A>G		NA	Q6PEW7|Q9BSJ0	hg19		0.02	1.652101	CTCxGCC	COVERED																																																																																			NOVEL	ZDHHC24-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000393088.2	24	5.947711	KEEP	1	1	32	31	870	AA	0.999998	0.999557	0		-	4	60	137	0	0	8.761884	74	60	2233	179	ENST00000526986.1	0.051282	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	66345160	66345160	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66345160A>G			NA	NA				CTSF (9093 upstream) : CCDC87 (12479 downstream)						NA		NA									NA						cagctacttgagaggctgagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.66345160A>G		NA		hg19		0.02	-0.114011	TTGxGAG	UNCOVERED																																																																																			NOVEL					0			8	3.007121	KEEP	0	0	0	10	270	AA	0.992708	0.161282	0			3	44	96	0	0	7.982203	10	60	295	30		0.230769	0.162467
CCS	9973	__UNKNOWN__	__UNKNOWN__	11	66364969	66364969	__UNKNOWN__	Intron	SNP	T	T	A	rs184696484	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66364969T>A	ENST00000533244.1	+	3	553				CCS_ENST00000310190.4_Intron	NM_005125.1	NP_005116.1	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	NA		NA			copper ion transmembrane transport (GO:0035434)|intracellular copper ion transport (GO:0015680)|positive regulation of oxidoreductase activity (GO:0051353)|removal of superoxide radicals (GO:0019430)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|protein disulfide oxidoreductase activity (GO:0015035)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|large_intestine(2)|lung(3)|stomach(1)	9						catgcctgtattcccagcact	0.522		NA											t|||	5	0.000998403	0.0008	0.0014	5008	,	,	NA	18441	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF002210	CCDS8146.1	11q13.2	2012-09-20			ENSG00000173992	ENSG00000173992	9973			1613	protein-coding gene	gene with protein product		603864			NA	9295278	Standard	NM_005125	NM_005125	NA	Approved		uc001oir.3	O14618	OTTHUMG00000167238	ENST00000533244.1:c.113-1618T>A	chr11.hg19:g.66364969T>A		NA	Q2M366|Q8NEV0	hg19	CCDS8146.1	0.02	-0.236814	GTAxTCC	COVERED																																																																																			NOVEL	CCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393826.1	5	2.705661	KEEP	4	0	0	9	238	TT	0.99257	0.607857	0		+	3	60	91	0	0	6.727595	19	60	575	61	ENST00000533244.1	0.136364	0.612407
C11orf80	79703	__UNKNOWN__	__UNKNOWN__	11	66569049	66569049	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66569049A>G	ENST00000532565.2	+	8	700				C11orf80_ENST00000346672.4_Intron|C11orf80_ENST00000527634.1_Intron|C11orf80_ENST00000360962.4_Intron|C11orf80_ENST00000525449.2_Intron|C11orf80_ENST00000540737.1_Intron			Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	NA		NA								autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						gctcatgcctataatcccagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715	79703			26197	protein-coding gene	gene with protein product		NA			NA	18160775	Standard	NM_024650	NM_024650	NA	Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000532565.2:c.188+476A>G	chr11.hg19:g.66569049A>G		NA	Q9H677	hg19		0.02	-0.14909	CCTxTAA	COVERED																																																																																			NOVEL	C11orf80-001	NOVEL	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000393513.5	3	2.705518	KEEP	1	0	0	9	234	AA	0.99257	0.289832	0		+	5	60	166	0	0	14.670851	11	60	311	38	ENST00000532565.2	0.3125	0.292001
C11orf80	79703	__UNKNOWN__	__UNKNOWN__	11	66594474	66594474	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:66594474C>T	ENST00000532565.2	+	14	1427				C11orf80_ENST00000346672.4_Intron|C11orf80_ENST00000527634.1_Intron|C11orf80_ENST00000360962.4_Intron|C11orf80_ENST00000525449.2_Intron|C11orf80_ENST00000540737.1_Intron			Q8N6T0	CK080_HUMAN	chromosome 11 open reading frame 80	NA		NA								autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	14						ttttttgagacggagtttcgc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					11q13.2	2012-05-30			ENSG00000173715	ENSG00000173715	79703			26197	protein-coding gene	gene with protein product		NA			NA	18160775	Standard	NM_024650	NM_024650	NA	Approved	FLJ22531	uc021qmd.1	Q8N6T0	OTTHUMG00000167164	ENST00000532565.2:c.916-1263C>T	chr11.hg19:g.66594474C>T		NA	Q9H677	hg19		0.02	-0.105265	AGAxGGA	UNCOVERED																																																																																			NOVEL	C11orf80-001	NOVEL	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000393513.5	17	4.210796	KEEP	8	0	0	14	395	CC	0.993072	0.138863	0		+	3	55	91	0	0	7.87836	7	59	232	40	ENST00000532565.2	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	67243114	67243114	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:67243114T>C			NA	NA				TMEM134 (6371 upstream) : AIP (7397 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.67243114T>C		NA		hg19		0.02	-0.148979	AGGxGTG	COVERED																																																																																			NOVEL					0			11	3.607374	KEEP	3	0	0	12	312	TT	0.993072	0.32057	0			3	60	88	0	0	7.183982	10	60	263	40		0.230769	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	67575531	67575531	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:67575531A>G			NA	NA				FAM86C2P (10391 upstream) : RP11-119D9.1 (78435 downstream)						NA		NA									NA						acaggcgtgaaccaccgcgcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.67575531A>G		NA		hg19		0.02	-0.157864	TGAxCCA	COVERED																																																																																			NOVEL					0			8	2.70565	KEEP	3	0	0	9	235	AA	0.99257	0.320408	0			3	60	103	0	0	8.29182	14	60	407	39		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	67629543	67629543	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:67629543T>C			NA	NA				FAM86C2P (64403 upstream) : RP11-119D9.1 (24423 downstream)						NA		NA									NA						gcaacaagagtgaaactccgt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.67629543T>C		NA		hg19		0.02	-0.157881	GAGxGAA	COVERED																																																																																			NOVEL					0			11	3.007721	KEEP	4	0	0	10	279	TT	0.992708	0.320453	0			3	60	102	1	0	8.191652	14	60	430	49		0.176471	0.322807
UNC93B1	81622	__UNKNOWN__	__UNKNOWN__	11	67768908	67768908	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:67768908G>T	ENST00000530331.1	-	3	472				UNC93B1_ENST00000227471.2_Intron			Q9H1C4	UN93B_HUMAN	unc-93 homolog B1 (C. elegans)	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	early phagosome (GO:0032009)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)					NA						ggctggggcgggtgaatttga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ271326	CCDS73334.1	11q13.2	2014-09-17	2001-11-28		ENSG00000110057	ENSG00000110057	81622			13481	protein-coding gene	gene with protein product		608204	unc93 (C. elegans) homolog B1		NA	11867227	Standard	NM_030930	NM_030930	NA	Approved	UNC93	uc001omw.1	Q9H1C4	OTTHUMG00000167472	ENST00000530331.1:c.1843+1583C>A	chr11.hg19:g.67768908G>T		NA	O95764|Q569H6|Q710D4	hg19		0.02	-0.078936	GCGxGTG	UNCOVERED																																																																																			NOVEL	UNC93B1-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000394726.1	2	2.708509	KEEP	0	0	0	9	295	GG	0.99254	0.076759	0		-	3	60	86	0	0	7.543146	6	60	197	27	ENST00000530331.1	0.333333	0.077336
NDUFS8	4728	__UNKNOWN__	__UNKNOWN__	11	67799050	67799050	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:67799050G>A	ENST00000313468.5	+	2	107				NDUFS8_ENST00000528492.1_Intron	NM_002496.3	NP_002487.1	O00217	NDUS8_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzyme Q reductase)	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(1)|lung(5)|skin(1)	8						cctgacctcaggtgatccacc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(116;1205 2770 20054)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U65579	CCDS8176.1	11q13.2	2011-07-04	2002-08-29		ENSG00000110717	ENSG00000110717	4728	1.6.5.3	Mitochondrial respiratory chain complex / Complex I	7715	protein-coding gene	gene with protein product	complex I 23kDa subunit, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial	602141	NADH dehydrogenase (ubiquinone) Fe-S protein 8 (23kD) (NADH-coenzyme Q reductase)		NA	9666055, 9116042	Standard	NM_002496	NM_002496	NA	Approved	TYKY, CI-23k	uc001onc.3	O00217	OTTHUMG00000167331	ENST00000313468.5:c.0-569G>A	chr11.hg19:g.67799050G>A		NA	B2RB86|Q0VDA8	hg19	CCDS8176.1	0.02	-0.184216	TCAxGTG	COVERED																																																																																			NOVEL	NDUFS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394193.1	9	3.009161	KEEP	4	0	0	10	312	GG	0.99257	0.420331	0		+	3	60	89	0	0	6.661239	17	60	572	47	ENST00000313468.5	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	68060237	68060237	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:68060237G>A			NA	NA				C11orf24 (20768 upstream) : LRP5 (19839 downstream)						NA		NA									NA						cacgcctgtagtcccagcact	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.68060237G>A		NA		hg19		0.02	-0.236863	GTAxTCC	COVERED																																																																																			NOVEL					0			9	5.115596	KEEP	0	0	0	17	534	GG	0.999366	0.612019	0			3	60	90	0	0	6.395446	23	60	805	68		0.115385	0.612407
SHANK2	22941	__UNKNOWN__	__UNKNOWN__	11	70362911	70362911	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:70362911T>C	ENST00000409161.1	-	3	294				SHANK2_ENST00000357171.3_Intron|SHANK2_ENST00000423696.2_Intron|SHANK2_ENST00000449116.2_Intron|SHANK2_ENST00000449833.2_Intron|SHANK2_ENST00000338508.4_Intron|SHANK2_ENST00000409530.1_Intron			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	NA		NA			adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			tggtggctcatgcttgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105	22941		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	14295	protein-coding gene	gene with protein product		603290	cortactin binding protein 1	CORTBP1	NA	10506216	Standard	NM_012309	XM_005277930	NA	Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000409161.1:c.295-13875A>G	chr11.hg19:g.70362911T>C		NA	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	hg19		0.02	-0.157876	TCAxGCT	COVERED																																																																																			NOVEL	SHANK2-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000259184.1	8	3.909785	KEEP	0	0	0	13	356	TT	0.994391	0.320996	0		-	3	60	105	0	0	8.772832	11	60	328	43	ENST00000409161.1	0.214286	0.322807
SHANK2	22941	__UNKNOWN__	__UNKNOWN__	11	70362914	70362914	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:70362914T>C	ENST00000409161.1	-	3	294				SHANK2_ENST00000357171.3_Intron|SHANK2_ENST00000423696.2_Intron|SHANK2_ENST00000449116.2_Intron|SHANK2_ENST00000449833.2_Intron|SHANK2_ENST00000338508.4_Intron|SHANK2_ENST00000409530.1_Intron			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	NA		NA			adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			tggctcatgcttgtaatccca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105	22941		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	14295	protein-coding gene	gene with protein product		603290	cortactin binding protein 1	CORTBP1	NA	10506216	Standard	NM_012309	XM_005277930	NA	Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000409161.1:c.295-13878A>G	chr11.hg19:g.70362914T>C		NA	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	hg19		0.02	-0.157877	TGCxTGT	COVERED																																																																																			NOVEL	SHANK2-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000259184.1	8	3.910247	KEEP	0	0	0	13	365	TT	0.994391	0.320996	0		-	3	60	103	0	0	8.572739	11	60	339	45	ENST00000409161.1	0.214286	0.322807
ENPP7P8	100421860	__UNKNOWN__	__UNKNOWN__	11	71426460	71426460	__UNKNOWN__	RNA	SNP	T	T	C	rs371897629		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:71426460T>C	ENST00000529093.1	+	0	262									ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 8	NA		NA									NA						gacagagtcttgctctgttgc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							11q13.4	2013-06-06			ENSG00000255319	ENSG00000255319	100421860			48691	pseudogene	pseudogene		NA			NA		Standard		NG_024528	NA	Approved				OTTHUMG00000167461	ENST00000529093.1:	chr11.hg19:g.71426460T>C		NA		hg19		0.02	-0.140334	TCTxGCT	COVERED																																																																																			NOVEL	ENPP7P8-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000394697.1	6	2.707114	KEEP	4	0	0	9	252	TT	0.99254	0.259018	0		+	3	24	87	0	0	7.082091	10	60	303	47	ENST00000529093.1	0.230769	0.260965
FAM86C1	55199	__UNKNOWN__	__UNKNOWN__	11	71507205	71507205	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs57679800	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:71507205C>T	ENST00000359244.4	+	4	427	c.404C>T	c.(403-405)cCg>cTg	p.P135L	FAM86C1_ENST00000426628.2_Missense_Mutation_p.P128L|FAM86C1_ENST00000346333.6_Missense_Mutation_p.P101L	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	135		NA	P -> L (in dbSNP:rs57679800).							lung(1)	1						TGTTCACCACCGAGCTATGTG	0.637		NA											.|||	414	0.0826677	0.2247	0.036	5008	,	,	NA	17898	0.0159	NA	0.0278	False	NA	,,,	NA	NA	NA	2504	0.0491	NA	NA	NA								NA				0								C	LEU/PRO,LEU/PRO,LEU/PRO	749,3651		38,673,1489	109	120	116		383,404,302	-3	0	11	dbSNP_129	116	108,8478		0,108,4185	yes	missense,missense,missense	FAM86C1	NM_001099653.1,NM_018172.2,NM_152563.2	98,98,98	38,781,5674	TT,TC,CC	NA	1.2579,17.0227,6.5994	benign,benign,benign	128/159,135/166,101/132	71507205	857,12129	2200	4293	6493	SO:0001583	missense			AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483	55199			25561	protein-coding gene	gene with protein product		NA	family with sequence similarity 86, member C	FAM86C	NA	12477932	Standard	NM_152563	NM_152563	NA	Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.404C>T	chr11.hg19:g.71507205C>T	ENSP00000352182:p.Pro135Leu	NA	Q8N5D3	hg19	CCDS41686.1	0.02	1.420973	CACxGAG	COVERED	142	0.06501831501831502	94	0.1910569105691057	16	0.04419889502762431	7	0.012237762237762238	25	0.032981530343007916	.	7.137	0.580963	0.13686	0.170227	0.012579	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.16597	2.38;2.62;2.39;2.33	1.49	-2.98	0.05513	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	N	0.999999	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26430	-1.0103	8	0.02654	T	1	.	1.3057	0.02087	0.2011:0.2321:0.4001:0.1667	rs57679800;rs61889009	128;101;135	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	L	101;135;128;101	ENSP00000325662:P101L;ENSP00000352182:P135L;ENSP00000391329:P128L;ENSP00000436598:P101L	ENSP00000325662:P101L	P	+	2	0	FAM86C1	71184853	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.873000	0.01637	-1.543000	0.01723	-1.238000	0.01547	CCG	NOVEL	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361120.1	2	2.707981	KEEP	0	0	0	9	274	CC	0.99254	0.98629	0		+	5	50	153	0	0	10.107055	58	60	1880	101	ENST00000359244.4	0.079365	0.993703
RP11-849H4.2	0	__UNKNOWN__	__UNKNOWN__	11	71631256	71631256	__UNKNOWN__	Intron	SNP	A	A	G	rs564099630	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:71631256A>G	ENST00000529513.1	-	3	240				RP11-849H4.2_ENST00000528511.2_Intron|RP11-849H4.2_ENST00000529844.1_Intron						NA		NA									NA						cgcccgcctcagcctcccaaa	0.498		NA											A|||	5	0.000998403	0.0	0.0	5008	,	,	NA	13759	0.003	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000529513.1:c.46-1184T>C	chr11.hg19:g.71631256A>G		NA		hg19		0.02	-0.236817	CTCxGCC	COVERED																																																																																			NOVEL	RP11-849H4.2-006	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000394954.1	7	2.406626	KEEP	0	0	0	8	229	AA	0.99257	0.607857	0		-	3	60	107	0	0	8.094183	23	60	697	55	ENST00000529513.1	0.115385	0.612407
RNF121	55298	__UNKNOWN__	__UNKNOWN__	11	71684482	71684482	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:71684482G>A	ENST00000393713.3	+	3	233				RNF121_ENST00000490867.1_Intron|RNF121_ENST00000533380.1_Intron|RNF121_ENST00000530137.1_Intron|RNF121_ENST00000545854.1_Intron|RNF121_ENST00000361756.3_Intron			Q9H920	RN121_HUMAN	ring finger protein 121	NA		NA				integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|urinary_tract(1)	13						ggctgcagtgggctgtgattg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001961	CCDS8203.1, CCDS73343.1	11q13.3	2008-02-05			ENSG00000137522	ENSG00000137522	55298		RING-type (C3HC4) zinc fingers	21070	protein-coding gene	gene with protein product		NA			NA		Standard	NM_018320	NM_018320	NA	Approved	FLJ11099	uc001ora.3	Q9H920	OTTHUMG00000157023	ENST00000393713.3:c.148-9325G>A	chr11.hg19:g.71684482G>A		NA	B3KSW8|Q6IA57|Q6P449|Q96DB4	hg19		0.02	-0.219299	GTGxGCT	COVERED																																																																																			NOVEL	RNF121-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000347133.2	5	2.6732	KEEP	0	0	0	9	244	GG	0.99254	0.548763	0		+	3	60	88	0	0	6.36602	20	60	661	43	ENST00000393713.3	0.130435	0.552887
NUMA1	4926	__UNKNOWN__	__UNKNOWN__	11	71768854	71768854	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:71768854G>A	ENST00000393695.3	-	2	300				NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1	NA		NA								central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						ggtggctcacgcctgtaatcc	0.463		NA	T	RARA	APL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497	4926			8059	protein-coding gene	gene with protein product		164009			NA	8406455	Standard		NM_006185	NA	Approved		uc001orl.1	Q14980		ENST00000393695.3:c.31+12033C>T	chr11.hg19:g.71768854G>A		NA		hg19	CCDS31633.1	0.02	-0.30697	CACxCCT	COVERED																																																																																			NOVEL	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395769.1	22	6.919711	KEEP	2	0	0	23	679	GG	0.999892	0.800159	0		-	4	60	116	0	0	8.334744	27	60	879	87	ENST00000393695.3	0.129032	0.800245
LAMTOR1	55004	__UNKNOWN__	__UNKNOWN__	11	71807472	71807472	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:71807472T>C	ENST00000545249.1	-	4	415				LRTOMT_ENST00000324866.7_3'UTR|LRTOMT_ENST00000307198.7_Intron|LAMTOR1_ENST00000535107.1_Intron|LRTOMT_ENST00000435085.1_Intron|LRTOMT_ENST00000447974.1_Intron|LRTOMT_ENST00000541614.1_Intron|LRTOMT_ENST00000289488.2_3'UTR|LRTOMT_ENST00000439209.1_Intron|LRTOMT_ENST00000419228.1_Intron			Q6IAA8	LTOR1_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1	NA		NA			cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|cholesterol homeostasis (GO:0042632)|endosome localization (GO:0032439)|endosome organization (GO:0007032)|lysosome localization (GO:0032418)|lysosome organization (GO:0007040)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of TOR signaling (GO:0032008)|regulation of cholesterol efflux (GO:0010874)|regulation of cholesterol esterification (GO:0010872)|regulation of cholesterol import (GO:0060620)|regulation of receptor recycling (GO:0001919)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|Ragulator complex (GO:0071986)				cervix(1)	1						ttagtagagatggggtttcgc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000632	CCDS8209.1	11q13.4	2011-05-18	2011-02-15	2011-02-15	ENSG00000149357	ENSG00000149357	55004			26068	protein-coding gene	gene with protein product	p27kip1 releasing factor from RhoA, protein associated with DRMs and endosomes	613510	chromosome 11 open reading frame 59	C11orf59	NA	12358155	Standard	NM_017907	NM_017907	NA	Approved	FLJ20625, p18, p27RF-Rho, Pdro, Ragulator1	uc001ort.3	Q6IAA8	OTTHUMG00000167869	ENST00000545249.1:c.393+1862A>G	chr11.hg19:g.71807472T>C		NA	Q8WZ09|Q9NWT0	hg19		0.02	-0.376872	AGAxGGG	COVERED																																																																																			NOVEL	LAMTOR1-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000396730.1	5	2.435662	KEEP	2	1	28	18	468	TT	0.999859	0.908941	0		-	4	60	122	0	0	8.421675	37	60	986	72	ENST00000545249.1	0.097561	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	72243170	72243170	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:72243170A>G			NA	NA				CLPB (97478 upstream) : RP11-169D4.1 (38533 downstream)						NA		NA									NA						tgcctgcctcagcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.72243170A>G		NA		hg19		0.02	-0.157883	CTCxGCC	COVERED																																																																																			NOVEL					0			5	2.406108	KEEP	4	0	0	8	223	AA	0.99257	0.320408	0			3	60	101	0	0	8.091629	14	60	425	43		0.176471	0.322807
RELT	84957	__UNKNOWN__	__UNKNOWN__	11	73103451	73103451	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs35892397		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73103451G>A	ENST00000064780.2	+	6	824	c.563G>A	c.(562-564)cGg>cAg	p.R188Q	RELT_ENST00000393580.2_Missense_Mutation_p.R188Q	NM_152222.1	NP_689408.1	Q969Z4	TR19L_HUMAN	RELT tumor necrosis factor receptor	188		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	12						CTCCTCAAGCGGAAGGGCTAC	0.682		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													52	55	54			NA	NA	11		NA											NA				73103451		2200	4293	6493	SO:0001583	missense			AF319553	CCDS8222.1	11q13.2	2013-05-22	2007-06-14	2007-06-14		ENSG00000054967	84957		Tumor necrosis factor receptor superfamily	13764	protein-coding gene	gene with protein product		611211	tumor necrosis factor receptor superfamily, member 19-like	TNFRSF19L	NA	11313261, 16547002, 16950202, 16389068	Standard	NM_032871	NM_032871	NA	Approved	FLJ14993	uc001otv.3	Q969Z4		ENST00000064780.2:c.563G>A	chr11.hg19:g.73103451G>A	ENSP00000064780:p.Arg188Gln	NA	Q86V34|Q96JU1|Q9BUX7	hg19	CCDS8222.1	0.02	2.621113	AGCxGAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	32	5.112630	0.94339	.	.	ENSG00000054967	ENST00000064780;ENST00000393580	T;T	0.76839	-1.05;-1.05	5.69	3.48	0.39840	.	0.180739	0.46442	D	0.000299	T	0.69133	0.3077	N	0.19112	0.55	0.33363	D	0.572542	D	0.59357	0.985	P	0.51487	0.671	T	0.76408	-0.2970	10	0.59425	D	0.04	-31.1134	7.7908	0.29119	0.2531:0.0:0.7469:0.0	rs35892397	188	Q969Z4	TR19L_HUMAN	Q	188	ENSP00000064780:R188Q;ENSP00000377207:R188Q	ENSP00000064780:R188Q	R	+	2	0	RELT	72781099	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.933000	0.56545	1.403000	0.46800	0.561000	0.74099	CGG	NOVEL	RELT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397380.2	0	6.017017	KEEP	0	0	0	20	601	GG	0.999863	0.999863	0		+	6	60	171	0	0	9.201547	136	60	4481	242	ENST00000064780.2	0.042254	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	73383747	73383747	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73383747A>G			NA	NA				Y_RNA (8105 upstream) : RAB6A (2935 downstream)						NA		NA									NA						caaagtgctgagattacaggt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.73383747A>G		NA		hg19		0.02	-0.219289	CTGxGAT	COVERED																																																																																			NOVEL					0			6	2.406444	KEEP	1	0	0	8	226	AA	0.99257	0.54878	0			3	60	102	0	0	7.826742	19	60	585	48		0.136364	0.552887
RAB6A	5870	__UNKNOWN__	__UNKNOWN__	11	73464431	73464431	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73464431A>G	ENST00000310653.6	-	1	572				RAB6A_ENST00000336083.3_Intron|RAB6A_ENST00000541588.1_Intron|RAB6A_ENST00000536566.1_Intron	NM_001077637.1|NM_002869.4	NP_001071105.1|NP_002860.2	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						tagtagagacagggtttcacc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582	5870		RAB, member RAS oncogene	9786	protein-coding gene	gene with protein product		179513		RAB6	NA		Standard		NM_001243718	NA	Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000310653.6:c.70+7179T>C	chr11.hg19:g.73464431A>G		NA	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	hg19	CCDS8223.1	0.02	-0.114004	GACxGGG	UNCOVERED																																																																																			NOVEL	RAB6A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259240.3	5	4.51166	KEEP	0	0	0	15	418	AA	0.99649	0.161897	0		-	3	60	93	0	0	7.80131	9	60	266	33	ENST00000310653.6	0.25	0.162467
RAB6A	5870	__UNKNOWN__	__UNKNOWN__	11	73467125	73467125	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73467125T>C	ENST00000310653.6	-	1	572				RAB6A_ENST00000336083.3_Intron|RAB6A_ENST00000541588.1_Intron|RAB6A_ENST00000536566.1_Intron	NM_001077637.1|NM_002869.4	NP_001071105.1|NP_002860.2	P20340	RAB6A_HUMAN	RAB6A, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|early endosome to Golgi transport (GO:0034498)|GTP catabolic process (GO:0006184)|minus-end-directed organelle transport along microtubule (GO:0072385)|peptidyl-cysteine methylation (GO:0018125)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|protein domain specific binding (GO:0019904)			large_intestine(2)|lung(2)	4						Tggccaggcgtggtggctcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF130986	CCDS8223.1, CCDS8224.1, CCDS58155.1, CCDS58156.1	11q13.3	2008-08-08			ENSG00000175582	ENSG00000175582	5870		RAB, member RAS oncogene	9786	protein-coding gene	gene with protein product		179513		RAB6	NA		Standard		NM_001243718	NA	Approved		uc001ouf.3	P20340	OTTHUMG00000134308	ENST00000310653.6:c.70+4485A>G	chr11.hg19:g.73467125T>C		NA	A8K133|B7Z772|F5H668|Q1W5D8|Q5U0A8|Q9UBE4	hg19	CCDS8223.1	0.02	-0.25424	GCGxGGT	COVERED																																																																																			NOVEL	RAB6A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259240.3	6	3.905831	KEEP	0	0	0	13	332	TT	0.994391	0.664773	0		-	3	60	94	0	0	6.966083	20	60	574	61	ENST00000310653.6	0.130435	0.668523
PAAF1	80227	__UNKNOWN__	__UNKNOWN__	11	73606896	73606896	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73606896G>A	ENST00000544909.1	+	3	542				PAAF1_ENST00000535604.1_Intron|PAAF1_ENST00000310571.3_Intron|PAAF1_ENST00000541951.1_Intron|PAAF1_ENST00000544552.1_Intron|PAAF1_ENST00000543079.1_Intron|PAAF1_ENST00000536003.1_Intron|PAAF1_ENST00000376384.5_Intron			Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1	NA		NA			viral process (GO:0016032)	proteasome complex (GO:0000502)				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(11;7.42e-05)					tcacgcctgtgatcctagcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006142	CCDS8226.1, CCDS58157.1, CCDS58158.1	11q13.4	2013-05-21	2007-08-16	2007-08-16	ENSG00000175575	ENSG00000175575	80227		WD repeat domain containing	25687	protein-coding gene	gene with protein product		NA	WD repeat domain 71	WDR71	NA	15831487, 17317272, 17289585	Standard	NM_025155	NM_001267803	NA	Approved	FLJ11848, Rpn14	uc001ouk.2	Q9BRP4	OTTHUMG00000168062	ENST00000544909.1:c.286-3295G>A	chr11.hg19:g.73606896G>A		NA	A6NDR5|B4DPB0|B7ZAS9|Q4G165|Q53HS9|Q7Z500|Q8TBU6|Q9HAB6	hg19		0.02	-0.149126	TGTxATC	COVERED																																																																																			NOVEL	PAAF1-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000397896.1	7	3.009025	KEEP	1	0	0	10	312	GG	0.992708	0.289872	0		+	3	60	90	0	0	7.38177	10	60	345	41	ENST00000544909.1	0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	73643133	73643133	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73643133A>C			NA	NA				RP11-707G14.7 (1716 upstream) : DNAJB13 (18230 downstream)						NA		NA									NA						cccgcctcagactcccaaagt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.73643133A>C		NA		hg19		0.02	-0.166651	CAGxCTC	COVERED																																																																																			NOVEL					0			8	2.705697	KEEP	0	0	0	9	234	AA	0.99254	0.384517	0			3	60	98	0	0	7.791776	14	60	426	41		0.176471	0.387407
DNAJB13	374407	__UNKNOWN__	__UNKNOWN__	11	73678169	73678169	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73678169A>G	ENST00000339764.1	+	5	1357				DNAJB13_ENST00000543947.1_Intron|DNAJB13_ENST00000537753.1_Intron|RP11-167N4.2_ENST00000537019.1_RNA	NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	NA		NA			protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					aagtgctgggattacaggcgt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726	374407		Heat shock proteins / DNAJ (HSP40)	30718	protein-coding gene	gene with protein product	radial spoke 16 homolog A (Chlamydomonas)	610263	DnaJ (Hsp40) related, subfamily B, member 13		NA		Standard	NM_153614	NM_153614	NA	Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.606+873A>G	chr11.hg19:g.73678169A>G		NA	B3LEP4|Q8IZW5	hg19	CCDS8227.1	0.02	-0.315753	GGGxTTA	COVERED																																																																																			NOVEL	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398100.1	22	4.51007	KEEP	10	0	0	15	400	AA	0.995343	0.814653	0		+	5	40	172	0	0	13.491509	28	60	834	83	ENST00000339764.1	0.151515	0.818465
C2CD3	26005	__UNKNOWN__	__UNKNOWN__	11	73818093	73818093	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73818093G>A	ENST00000313663.7	-	13	2189				C2CD3_ENST00000334126.7_Intron	NM_015531.4	NP_056346.3	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	NA		NA			brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					taggctgggcgcggtggccca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014	26005			24564	protein-coding gene	gene with protein product		615944			NA		Standard	NM_015531	XM_005273897	NA	Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000313663.7:c.1963-555C>T	chr11.hg19:g.73818093G>A		NA	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	hg19	CCDS31636.1	0.02	-0.114024	GGCxCGG	UNCOVERED																																																																																			NOVEL	C2CD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398210.1	2	2.706653	KEEP	0	0	0	9	252	GG	0.99254	0.161255	0		-	3	60	91	0	0	7.732466	8	60	253	35	ENST00000313663.7	0.272727	0.162467
C2CD3	26005	__UNKNOWN__	__UNKNOWN__	11	73830961	73830961	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:73830961A>G	ENST00000313663.7	-	9	1592				C2CD3_ENST00000334126.7_Intron	NM_015531.4	NP_056346.3	Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	NA		NA			brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					gattacaggcatgagccacca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014	26005			24564	protein-coding gene	gene with protein product		615944			NA		Standard	NM_015531	XM_005273897	NA	Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000313663.7:c.1366-1534T>C	chr11.hg19:g.73830961A>G		NA	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	hg19	CCDS31636.1	0.02	-0.087706	GGCxTGA	UNCOVERED																																																																																			NOVEL	C2CD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398210.1	5	2.403848	KEEP	0	0	0	8	205	AA	0.99257	0.09898	0		-	3	60	102	0	0	8.978907	7	60	204	25	ENST00000313663.7	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	74281050	74281050	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:74281050A>G			NA	NA				AP001372.2 (71472 upstream) : POLD3 (22524 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.74281050A>G		NA		hg19		0.02	-0.184174	GGCxTGA	COVERED																																																																																			NOVEL					0			10	4.182464	KEEP	3	0	0	14	350	AA	0.993634	0.420782	0			3	60	105	0	0	8.333276	16	60	462	47		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	74281061	74281061	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:74281061T>C			NA	NA				AP001372.2 (71483 upstream) : POLD3 (22513 downstream)						NA		NA									NA						tgagccaccatgcccagAATT	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.74281061T>C		NA		hg19		0.02	-0.175389	CCAxGCC	COVERED																																																																																			NOVEL					0			9	3.609147	KEEP	2	0	0	12	331	TT	0.992708	0.384582	0			3	60	87	0	0	6.53511	16	60	473	42		0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	74300825	74300825	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:74300825A>G			NA	NA				AP001372.2 (91247 upstream) : POLD3 (2749 downstream)						NA		NA									NA						cccgggaggcagaggttgcag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.74300825A>G		NA		hg19		0.02	-0.078942	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			9	2.707112	KEEP	4	0	0	9	253	AA	0	0	0			3	40	97	0	0	8.83295	5	60	150	26		0.375	0.077336
NEU3	10825	__UNKNOWN__	__UNKNOWN__	11	74715376	74715376	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:74715376A>G	ENST00000294064.4	+	3	1233				NEU3_ENST00000529024.1_Intron|NEU3_ENST00000532963.1_Intron|NEU3_ENST00000544263.1_Intron|NEU3_ENST00000531509.1_Intron|NEU3_ENST00000531619.1_Silent_p.R111R|NEU3_ENST00000545272.1_Intron	NM_006656.5	NP_006647.3	Q9UQ49	NEUR3_HUMAN	sialidase 3 (membrane sialidase)	NA		NA			carbohydrate metabolic process (GO:0005975)|ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-sialidase activity (GO:0016997)|exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			kidney(2)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						tgttgcccagactggtctcaa	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB008185	CCDS44682.1	11q13.5	2008-02-05				ENSG00000162139	10825			7760	protein-coding gene	gene with protein product		604617			NA	10405317	Standard	NM_006656	NM_006656	NA	Approved		uc001ovw.3	Q9UQ49		ENST00000294064.4:c.307-1082A>G	chr11.hg19:g.74715376A>G		NA	A8K327|Q9NQE1	hg19	CCDS44682.1	0.02	-0.359624	CAGxCTG	COVERED																																																																																			NOVEL	NEU3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384595.1	7	5.413268	KEEP	1	0	0	18	498	AA	0.999859	0.88875	0		+	3	60	109	0	0	7.848019	33	60	1012	71	ENST00000294064.4	0.083333	0.888875
UVRAG	7405	__UNKNOWN__	__UNKNOWN__	11	75710670	75710670	__UNKNOWN__	Intron	SNP	G	G	A	rs555123180	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:75710670G>A	ENST00000533454.1	+	4	286				UVRAG_ENST00000539288.1_Intron|UVRAG_ENST00000356136.3_Intron|UVRAG_ENST00000532130.1_Intron|UVRAG_ENST00000528420.1_Intron|UVRAG_ENST00000531818.1_Intron			Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	NA		NA			DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						tgatctgcccgccttggcctc	0.468		NA											g|||	4	0.000798722	0.003	0.0	5008	,	,	NA	14944	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382	7405			12640	protein-coding gene	gene with protein product	beclin 1 binding protein	602493	UV radiation resistance associated gene		NA	9169138, 16799551, 18843052	Standard	NM_003369	NM_003369	NA	Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000533454.1:c.-466-4379G>A	chr11.hg19:g.75710670G>A		NA	B3KTC1|O00392	hg19		0.02	-0.114039	CCCxCCT	UNCOVERED																																																																																			NOVEL	UVRAG-005	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000383434.1	9	4.212164	KEEP	6	0	0	14	426	GG	0.993634	0.161432	0		+	4	33	120	0	0	10.590888	8	60	277	49	ENST00000533454.1	0.333333	0.162467
ACER3	55331	__UNKNOWN__	__UNKNOWN__	11	76733893	76733893	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:76733893G>A	ENST00000532485.1	+	0	3430				ACER3_ENST00000544113.1_3'UTR	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	NA		NA			ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						GGGCATggtggcagagcgaga	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	55331	3.5.1.23	Alkaline ceramidase	16066	protein-coding gene	gene with protein product	alkaline phytoceramidase	NA	phytoceramidase, alkaline	PHCA	NA	11356846, 18619555	Standard	NM_018367	XM_005274090	NA	Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.*2522G>A	chr11.hg19:g.76733893G>A		NA	B2RC99	hg19	CCDS8247.1	0.02	-0.210469	GTGxCAG	COVERED																																																																																			NOVEL	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382770.2	3	4.51185	KEEP	2	0	0	15	433	GG	0.99649	0.520328	0		+	3	60	90	0	0	6.69315	18	70	581	56	ENST00000532485.1	0.142857	0.522161
ACER3	55331	__UNKNOWN__	__UNKNOWN__	11	76733897	76733897	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:76733897A>G	ENST00000532485.1	+	0	3434				ACER3_ENST00000544113.1_3'UTR	NM_018367.5	NP_060837.3	Q9NUN7	ACER3_HUMAN	alkaline ceramidase 3	NA		NA			ceramide metabolic process (GO:0006672)|phytosphingosine biosynthetic process (GO:0071602)|positive regulation of cell proliferation (GO:0008284)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of Golgi membrane (GO:0030173)	phytoceramidase activity (GO:0070774)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	9						ATggtggcagagcgagactcc	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF214454	CCDS8247.1, CCDS73352.1	11q13.5	2013-01-25	2008-12-19	2008-12-19	ENSG00000078124	ENSG00000078124	55331	3.5.1.23	Alkaline ceramidase	16066	protein-coding gene	gene with protein product	alkaline phytoceramidase	NA	phytoceramidase, alkaline	PHCA	NA	11356846, 18619555	Standard	NM_018367	XM_005274090	NA	Approved	FLJ11238, APHC	uc009yum.1	Q9NUN7	OTTHUMG00000165225	ENST00000532485.1:c.*2526A>G	chr11.hg19:g.76733897A>G		NA	B2RC99	hg19	CCDS8247.1	0.02	-0.219276	CAGxGCG	COVERED																																																																																			NOVEL	ACER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382770.2	3	5.112095	KEEP	2	0	0	17	459	AA	0.999366	0.552537	0		+	3	60	108	0	0	8.42658	19	70	569	58	ENST00000532485.1	0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	77192459	77192459	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:77192459T>C			NA	NA				DKFZP434E1119 (4385 upstream) : RNU7-59P (85519 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.77192459T>C		NA		hg19		0.02	-0.149066	TCAxGCC	COVERED																																																																																			NOVEL					0			8	2.234681	KEEP	5	1	30	18	470	TT	0.997832	0.291368	0			3	60	87	0	0	6.874009	12	60	352	52		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	77299526	77299526	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:77299526C>T			NA	NA				RNU7-59P (21487 upstream) : AQP11 (909 downstream)						NA		NA									NA						gtttttgagacggagtttcgc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.77299526C>T		NA		hg19		0.02	-0.140355	AGAxGGA	COVERED																																																																																			NOVEL					0			10	3.008804	KEEP	0	0	0	10	301	CC	0.992708	0.259062	0			3	60	90	0	0	7.078902	13	60	436	38		0.1875	0.260965
CLNS1A	1207	__UNKNOWN__	__UNKNOWN__	11	77337424	77337424	__UNKNOWN__	Intron	SNP	G	G	A	rs563216618		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:77337424G>A	ENST00000525428.1	-	3	353				CLNS1A_ENST00000525064.1_Intron|CLNS1A_ENST00000528364.1_Intron|CLNS1A_ENST00000532069.1_Intron|CLNS1A_ENST00000263309.3_Intron	NM_001293.2	NP_001284.1	P54105	ICLN_HUMAN	chloride channel, nucleotide-sensitive, 1A	NA		NA			cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	5	all_cancers(14;5.43e-17)|all_epithelial(13;1.78e-19)		Epithelial(5;1.02e-48)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			ggtggctcacgcctgtaatcc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U17899	CCDS8252.1	11q13.5-q14	2008-05-02					1207			2080	protein-coding gene	gene with protein product		602158		CLCI	NA	7887970, 8975725	Standard	NM_001293	NM_001293	NA	Approved	ICln	uc001oyk.3	P54105		ENST00000525428.1:c.263-561C>T	chr11.hg19:g.77337424G>A		NA	B2RCS9|Q0VDK6|Q9NRD2|Q9NRD3	hg19	CCDS8252.1	0.02	-0.254399	CACxCCT	COVERED																																																																																			NOVEL	CLNS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382156.2	6	2.706542	KEEP	1	0	0	9	252	GG	0.99254	0.663536	0		-	3	60	91	0	0	6.393326	25	60	843	59	ENST00000525428.1	0.107143	0.668523
RSF1	51773	__UNKNOWN__	__UNKNOWN__	11	77472279	77472279	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:77472279T>C	ENST00000308488.6	-	2	582				RSF1_ENST00000360355.2_Intron			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	NA		NA			CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			ccaccgcacctggccACATTA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649	51773		Zinc fingers, PHD-type	18118	protein-coding gene	gene with protein product		608522	hepatitis B virus x associated protein	HBXAP	NA	11788598, 12972596	Standard	NM_016578	NM_016578	NA	Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.279+3363A>G	chr11.hg19:g.77472279T>C		NA	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	hg19	CCDS8253.1	0.02	-0.17541	ACCxGGC	COVERED																																																																																			NOVEL	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318075.2	5	2.406599	KEEP	0	0	0	8	229	TT	0.99257	0.384528	0		-	3	60	106	0	0	8.433223	16	60	471	42	ENST00000308488.6	0.157895	0.387407
KCTD14	65987	__UNKNOWN__	__UNKNOWN__	11	77739440	77739440	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:77739440A>G	ENST00000533144.1	-	2	226				NDUFC2-KCTD14_ENST00000528251.1_Intron|NDUFC2-KCTD14_ENST00000530054.1_Intron			Q9BQ13	KCD14_HUMAN	potassium channel tetramerization domain containing 14	NA		NA			protein homooligomerization (GO:0051260)					endometrium(2)|kidney(1)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	15	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1e-24)			catgaggtcaagagttcaata	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(86;414 1416 18100 32729 49271)|Esophageal Squamous(156;1132 1858 11406 36132 46748)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001062	CCDS8255.2, CCDS60908.1	11q13.4	2013-06-20	2013-06-20		ENSG00000151364	ENSG00000151364	65987			23295	protein-coding gene	gene with protein product		NA	potassium channel tetramerisation domain containing 14		NA	12477932	Standard	NM_023930	NM_023930	NA	Approved	MGC2376	uc001oyw.4	Q9BQ13	OTTHUMG00000150224	ENST00000533144.1:c.0+10269T>C	chr11.hg19:g.77739440A>G		NA	B2R9R8	hg19		0.02	-0.105247	TCAxGAG	UNCOVERED																																																																																			NOVEL	KCTD14-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000390937.1	3	2.706485	KEEP	2	0	0	9	241	AA	0	0	0		-	3	60	91	0	0	7.878653	7	60	208	30	ENST00000533144.1	0.3	0.139832
NARS2	79731	__UNKNOWN__	__UNKNOWN__	11	78275214	78275214	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:78275214A>G	ENST00000528850.1	-	4	769				NARS2_ENST00000281038.5_Intron			Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	NA		NA			asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	ccaaagtgctaggattacagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	79731	6.1.1.22	Aminoacyl tRNA synthetases / Class II	26274	protein-coding gene	gene with protein product	asparagine tRNA ligase 2, mitochondrial (putative)	612803			NA	15779907	Standard	NM_024678	NM_024678	NA	Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000528850.1:c.167+1963T>C	chr11.hg19:g.78275214A>G		NA	G3V178	hg19	CCDS58164.1	0.02	-0.114007	GCTxGGA	UNCOVERED																																																																																			NOVEL	NARS2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391139.1	10	2.40553	KEEP	0	0	0	8	211	AA	0.99257	0.16126	0		-	3	60	106	0	0	9.232978	8	60	222	26	ENST00000528850.1	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	80203084	80203084	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:80203084G>A			NA	NA				CTD-2555I5.1 (164129 upstream) : RNU6-544P (35919 downstream)						NA		NA									NA						aaaattagccgggtgtggtgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.80203084G>A		NA		hg19		0.02	-0.140344	GCCxGGT	UNCOVERED																																																																																			NOVEL					0			9	2.407155	KEEP	3	0	0	8	246	GG	0	0	0			3	36	82	0	0	6.372605	12	60	398	32		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	80738055	80738055	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:80738055C>T			NA	NA				RP11-686G23.2 (264186 upstream) : RP11-179A16.1 (852840 downstream)						NA		NA									NA						tttgggaggccgaggcgggca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.80738055C>T		NA		hg19		0.02	-0.122792	GGCxGAG	COVERED																																																																																			NOVEL					0			4	3.008783	KEEP	0	0	0	10	304	CC	0.992708	0.19488	0			3	60	87	0	0	7.332409	8	60	249	31		0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	81144032	81144032	__UNKNOWN__	IGR	SNP	A	A	G	rs10897817	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:81144032A>G			NA	NA				RP11-686G23.2 (670163 upstream) : RP11-179A16.1 (446863 downstream)						NA		NA									NA						cgcccgcctcagcctcccaaa	0.483		NA											-|||	3646	0.728035	0.7799	0.6715	5008	,	,	NA	8615	0.9544	NA	0.495	False	NA	,,,	NA	NA	NA	2504	0.7045	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.81144032A>G		NA		hg19		0.02	-0.113598	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			4	3.007483	KEEP	18	0	0	10	274	AA	0	0	0			4	60	135	0	0	12.091495	8	60	236	48		0.333333	0.162467
DLG2	1740	__UNKNOWN__	__UNKNOWN__	11	83769699	83769699	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:83769699T>C	ENST00000532653.1	-	6	907				DLG2_ENST00000398309.2_Intron|DLG2_ENST00000524982.1_Intron|DLG2_ENST00000537455.1_Intron|DLG2_ENST00000330014.6_Intron|DLG2_ENST00000398301.2_Intron|DLG2_ENST00000543673.1_Intron|DLG2_ENST00000280241.8_Intron|DLG2_ENST00000376104.2_Intron|DLG2_ENST00000531015.1_Intron|DLG2_ENST00000376106.3_Intron|DLG2_ENST00000418306.2_Intron			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	NA		NA			nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				cactgcactctagcctgggca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672	1740		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	2901	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 58	603583	discs, large homolog 2, chapsyn-110 (Drosophila)		NA	8755482, 9806853	Standard	NM_001364	NM_001142702	NA	Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.604+658A>G	chr11.hg19:g.83769699T>C		NA	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	hg19		0.02	-0.08771	CTCxAGC	UNCOVERED																																																																																			NOVEL	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000259253.2	6	3.006114	KEEP	0	0	0	10	256	TT	0.992708	0.098994	0		-	3	60	97	0	0	8.643737	6	60	176	30	ENST00000532653.1	0.333333	0.099721
DLG2	1740	__UNKNOWN__	__UNKNOWN__	11	83782429	83782429	__UNKNOWN__	Intron	SNP	C	C	T	rs538922318		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:83782429C>T	ENST00000532653.1	-	6	737				DLG2_ENST00000398309.2_Intron|DLG2_ENST00000524982.1_Intron|DLG2_ENST00000537455.1_Intron|DLG2_ENST00000330014.6_Intron|DLG2_ENST00000398301.2_Intron|DLG2_ENST00000543673.1_Intron|DLG2_ENST00000280241.8_Intron|DLG2_ENST00000376104.2_Intron|DLG2_ENST00000531015.1_Intron|DLG2_ENST00000376106.3_Intron|DLG2_ENST00000418306.2_Intron			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	NA		NA			nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				attacaggcgcgagctaccat	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672	1740		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	2901	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 58	603583	discs, large homolog 2, chapsyn-110 (Drosophila)		NA	8755482, 9806853	Standard	NM_001364	NM_001142702	NA	Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.435-11902G>A	chr11.hg19:g.83782429C>T		NA	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	hg19		0.02	-0.105257	GCGxGAG	UNCOVERED																																																																																			NOVEL	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000259253.2	3	2.706879	KEEP	0	0	0	9	255	CC	0.99254	0.138789	0		-	3	60	85	0	0	7.132216	8	60	256	27	ENST00000532653.1	0.272727	0.139832
DLG2	1740	__UNKNOWN__	__UNKNOWN__	11	84131868	84131868	__UNKNOWN__	Intron	SNP	C	C	T	rs181726453		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:84131868C>T	ENST00000532653.1	-	2	507				DLG2_ENST00000398309.2_Intron|DLG2_ENST00000524982.1_Intron|DLG2_ENST00000543673.1_Intron|DLG2_ENST00000376104.2_Intron			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	NA		NA			nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				tgcgccaccacgcccggctaa	0.597		NA											-|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	4086	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672	1740		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	2901	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 58	603583	discs, large homolog 2, chapsyn-110 (Drosophila)		NA	8755482, 9806853	Standard	NM_001364	NM_001142702	NA	Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.204+113744G>A	chr11.hg19:g.84131868C>T		NA	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	hg19		0.02	-0.184189	CCAxGCC	COVERED																																																																																			NOVEL	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	NA	protein_coding	OTTHUMT00000259253.2	11	4.512606	KEEP	10	0	0	15	447	CC	0.99257	0.420331	0		-	4	40	108	0	0	8.801313	12	60	394	51	ENST00000532653.1	0.25	0.423478
CTD-2005H7.2	0	__UNKNOWN__	__UNKNOWN__	11	86455485	86455485	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:86455485C>T	ENST00000532979.1	+	0	168										NA		NA									NA						tttgggaggccgaggtgggtg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000532979.1:	chr11.hg19:g.86455485C>T		NA		hg19		0.02	-0.175437	GGCxGAG	COVERED																																																																																			NOVEL	CTD-2005H7.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000393803.1	10	3.911031	KEEP	9	0	0	13	392	CC	0.993072	0.384723	0		+	3	41	93	0	0	7.291794	14	60	463	59	ENST00000532979.1	0.176471	0.387407
TMEM135	65084	__UNKNOWN__	__UNKNOWN__	11	87015222	87015222	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:87015222A>G	ENST00000305494.5	+	8	737				TMEM135_ENST00000340353.7_Intron|TMEM135_ENST00000532959.1_Intron|TMEM135_ENST00000535167.1_Intron	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	NA		NA			peroxisome organization (GO:0007031)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				agaccagcctaggcaacatag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648678	CCDS8280.1, CCDS53692.1	11q14.2	2006-03-09			ENSG00000166575	ENSG00000166575	65084			26167	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_022918	NM_022918	NA	Approved	FLJ22104	uc001pch.3	Q86UB9	OTTHUMG00000167248	ENST00000305494.5:c.698+1738A>G	chr11.hg19:g.87015222A>G		NA	Q6AW91|Q8ND01|Q9H6M3	hg19	CCDS8280.1	0.02	1.94127	CCTxGGC	COVERED																																																																																			NOVEL	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393875.1	19	4.243618	KEEP	1	1	31	25	698	AA	0.999957	0.963732	0		+	4	60	135	0	0	9.50886	42	60	1266	113	ENST00000305494.5	0.086957	0.963774
CTSC	1075	__UNKNOWN__	__UNKNOWN__	11	88055880	88055880	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:88055880G>A	ENST00000227266.5	-	3	433				CTSC_ENST00000524463.1_3'UTR	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	NA		NA			aging (GO:0007568)|immune response (GO:0006955)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of proteolysis involved in cellular protein catabolic process (GO:1903052)|proteolysis (GO:0006508)|response to organic substance (GO:0010033)|T cell mediated cytotoxicity (GO:0001913)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)	chaperone binding (GO:0051087)|chloride ion binding (GO:0031404)|cysteine-type peptidase activity (GO:0008234)|peptidase activator activity involved in apoptotic process (GO:0016505)|phosphatase binding (GO:0019902)|serine-type endopeptidase activity (GO:0004252)			large_intestine(7)|lung(8)|ovary(2)|prostate(3)|skin(2)	22		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				tcccaagactgaatcaggaag	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK223038	CCDS8282.1, CCDS31654.1, CCDS44693.1	11q14.2	2014-09-17			ENSG00000109861	ENSG00000109861	1075	3.4.14.1	Cathepsins	2528	protein-coding gene	gene with protein product	dipeptidyl peptidase 1	602365		PLS, PALS	NA	7649281, 9092576	Standard	NM_001814	NM_148170	NA	Approved	DPP1	uc001pck.4	P53634	OTTHUMG00000167290	ENST00000227266.5:c.319-10158C>T	chr11.hg19:g.88055880G>A		NA	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	hg19	CCDS8282.1	0.02	0.903394	ACTxAAT	COVERED																																																																																			NOVEL	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394019.2	10	7.518139	KEEP	0	0	0	25	703	GG	0.999931	0.981888	0		-	5	60	122	0	0	7.288138	51	60	1621	85	ENST00000227266.5	0.089286	0.981955
GRM5	2915	__UNKNOWN__	__UNKNOWN__	11	88314046	88314046	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:88314046C>T	ENST00000305447.4	-	6	1840				GRM5_ENST00000455756.2_Intron|GRM5_ENST00000305432.5_Intron|GRM5_ENST00000418177.2_Intron|GRM5_ENST00000393297.1_Intron	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	NA		NA			activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	cagtggctcacgcctgtaatc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959	2915		GPCR / Class C : Glutamate receptors, metabotropic, Glutamate receptors	4597	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 86	604102			NA	7908515	Standard	NM_000842	NM_001143831	NA	Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1690+9722G>A	chr11.hg19:g.88314046C>T		NA	Q6J164	hg19	CCDS44694.1	0.02	-0.087719	TCAxGCC	UNCOVERED																																																																																			NOVEL	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259226.1	4	2.407018	KEEP	2	0	0	8	241	CC	0	0	0		-	3	60	87	0	0	7.832231	5	60	173	28	ENST00000305447.4	0.375	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	89056479	89056479	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:89056479T>C			NA	NA				TYR (27552 upstream) : NOX4 (1044 downstream)						NA		NA									NA						Ggggcaggcgtggtggctcac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.89056479T>C		NA		hg19		0.02	-0.087697	GCGxGGT	UNCOVERED																																																																																			NOVEL					0			5	2.403065	KEEP	1	0	0	8	201	TT	0	0	0			3	60	98	1	0	8.578992	7	60	198	24		0.3	0.099721
NOX4	50507	__UNKNOWN__	__UNKNOWN__	11	89059714	89059714	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:89059714A>T	ENST00000263317.4	-	0	2185				NOX4_ENST00000527626.1_3'UTR|NOX4_ENST00000343727.5_3'UTR|NOX4_ENST00000532825.1_3'UTR|NOX4_ENST00000525196.1_3'UTR|NOX4_ENST00000535633.1_3'UTR|NOX4_ENST00000542487.1_3'UTR|NOX4_ENST00000527956.1_3'UTR|NOX4_ENST00000534731.1_3'UTR|NOX4_ENST00000424319.1_3'UTR			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	NA		NA			bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TCATCACATCAAATATTCTTC	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991	50507			7891	protein-coding gene	gene with protein product		605261			NA		Standard	NM_016931	NM_001143837	NA	Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.*210T>A	chr11.hg19:g.89059714A>T		NA	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	hg19	CCDS8285.1	0.02	1.406217	ATCxAAT	COVERED																																																																																			NOVEL	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394054.1	4	11.428236	KEEP	2	0	0	38	1047	AA	1	0.998992	0		-	29	60	843	0	0	75.776184	49	60	1471	165	ENST00000263317.4	0.371795	0.998993
NAALAD2	10003	__UNKNOWN__	__UNKNOWN__	11	89911621	89911621	__UNKNOWN__	Intron	SNP	T	T	C	rs7924405	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:89911621T>C	ENST00000534061.1	+	16	2088				NAALAD2_ENST00000321955.4_Intron|NAALAD2_ENST00000375944.3_Intron	NM_005467.3	NP_005458.1	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	NA		NA			neurotransmitter catabolic process (GO:0042135)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|N-formylglutamate deformylase activity (GO:0050129)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(32)|pancreas(1)|prostate(3)|skin(5)|stomach(2)	59		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				gggcagatgatgaggtcagga	0.493		NA											C|||	2567	0.51258	0.6831	0.5317	5008	,	,	NA	14695	0.4177	NA	0.3668	False	NA	,,,	NA	NA	NA	2504	0.5164	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ012370	CCDS8288.1, CCDS73364.1	11q14.3-q21	2011-08-16			ENSG00000077616	ENSG00000077616	10003	3.4.17.21		14526	protein-coding gene	gene with protein product	glutamate carboxypeptidase III	611636			NA	10085079	Standard	NM_005467	NM_005467	NA	Approved	NAALADASE2, NAADALASE2, GPCIII	uc001pdf.4	Q9Y3Q0	OTTHUMG00000166368	ENST00000534061.1:c.1858+336T>C	chr11.hg19:g.89911621T>C		NA	B3KQR4|Q4KKV4|Q4VAM9	hg19	CCDS8288.1	0.02	-0.078924	TGAxGAG	UNCOVERED																																																																																			NOVEL	NAALAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389424.2	3	3.007634	KEEP	2	0	0	10	277	TT	0.99257	0.076761	0		+	6	60	176	0	0	17.972795	3	60	88	31	ENST00000534061.1	0.666667	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	90060955	90060955	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:90060955T>G			NA	NA				AP002364.1 (2903 upstream) : DISC1FP1 (161522 downstream)						NA		NA									NA						atcacttgagtccaggaattt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.90060955T>G		NA		hg19		0.02	-0.096485	GAGxCCA	UNCOVERED																																																																																			NOVEL					0			7	2.706509	KEEP	1	0	0	9	243	TT	0.99254	0.119538	0			3	60	99	0	0	8.53246	8	60	246	30		0.272727	0.120436
CCDC67	159989	__UNKNOWN__	__UNKNOWN__	11	93124128	93124128	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:93124128A>G	ENST00000525646.1	+	3	395				CCDC67_ENST00000298050.3_Intron			Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	NA		NA			cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)	cytoplasm (GO:0005737)|deuterosome (GO:0098536)				endometrium(3)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		Acute lymphoblastic leukemia(157;2.35e-05)|all_hematologic(158;0.00824)				ggcgcctgtaatcccagctac	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK058122	CCDS44707.1	11q21	2014-02-20				ENSG00000165325	159989			26344	protein-coding gene	gene with protein product		NA			NA	24240477	Standard	NM_181645	NM_181645	NA	Approved	FLJ25393	uc001pdq.3	Q05D60		ENST00000525646.1:c.267+1837A>G	chr11.hg19:g.93124128A>G		NA	Q8NEF1|Q96LL7	hg19		0.02	-0.070159	GTAxTCC	UNCOVERED																																																																																			NOVEL	CCDC67-006	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000394627.1	4	2.704396	KEEP	1	0	0	9	231	AA	0.99257	0.053735	0		+	2	49	72	0	0	6.335898	5	60	142	23	ENST00000525646.1	0.285714	0.054137
C11orf54	28970	__UNKNOWN__	__UNKNOWN__	11	93495043	93495043	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:93495043T>C	ENST00000331239.4	+	0	1316				C11orf54_ENST00000528288.1_3'UTR|C11orf54_ENST00000354421.3_3'UTR|C11orf54_ENST00000528099.1_3'UTR|C11orf54_ENST00000540113.1_3'UTR			Q9H0W9	CK054_HUMAN	chromosome 11 open reading frame 54	NA		NA			metabolic process (GO:0008152)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(5)	8		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				tgagaccagcttgggcaacat	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF092133	CCDS8294.1, CCDS66204.1, CCDS73365.1, CCDS73366.1	11q21	2012-08-09			ENSG00000182919	ENSG00000182919	28970			30204	protein-coding gene	gene with protein product		615810			NA	16522806	Standard	NM_014039	NM_014039	NA	Approved	PTD012	uc001pef.3	Q9H0W9	OTTHUMG00000167452	ENST00000331239.4:c.*189T>C	chr11.hg19:g.93495043T>C		NA	A8K850|Q6FI88|Q6XYB0|Q96EI3|Q96IX1|Q9Y6B4	hg19		0.02	-0.298178	AGCxTGG	COVERED																																																																																			NOVEL	C11orf54-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000394671.1	7	4.843693	KEEP	1	1	31	27	734	TT	0.999997	0.781058	0		+	4	60	133	0	0	10.03325	27	60	787	80	ENST00000331239.4	0.129032	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	93662336	93662336	__UNKNOWN__	IGR	SNP	A	A	G	rs545909060	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:93662336A>G			NA	NA				VSTM5 (78639 upstream) : HEPHL1 (92190 downstream)						NA		NA									NA						tcctgacctcatgatccaccc	0.517		NA											-|||	12	0.00239617	0.0008	0.0043	5008	,	,	NA	13663	0.0	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.93662336A>G		NA		hg19		0.02	-0.131527	CTCxTGA	UNCOVERED																																																																																			NOVEL					0			5	2.40622	KEEP	9	0	0	8	222	AA	0	0	0			4	60	123	0	0	10.431662	11	60	313	40		0.266667	0.260965
PANX1	24145	__UNKNOWN__	__UNKNOWN__	11	93888254	93888254	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:93888254T>C	ENST00000227638.3	+	2	706				PANX1_ENST00000436171.2_Intron	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	NA		NA			calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	cggtggctcatgcctgtaatc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218	24145		Ion channels / Pannexins	8599	protein-coding gene	gene with protein product	innexin	608420			NA	14597722	Standard	NM_015368	NM_015368	NA	Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.321+1458T>C	chr11.hg19:g.93888254T>C		NA	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	hg19	CCDS8296.1	0.02	-0.385913	TCAxGCC	COVERED																																																																																			NOVEL	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396121.1	10	4.812244	KEEP	3	0	0	16	443	TT	0.99649	0.914948	0		+	4	60	137	0	0	10.057165	34	60	1020	92	ENST00000227638.3	0.105263	0.918171
AMOTL1	154810	__UNKNOWN__	__UNKNOWN__	11	94542372	94542372	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:94542372A>G	ENST00000433060.2	+	3	1262				AMOTL1_ENST00000317837.9_Intron|AMOTL1_ENST00000317829.8_Intron	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	NA		NA			establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				cctgacctcaagtgatccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025	154810			17811	protein-coding gene	gene with protein product	junction-enriched and associated protein	614657			NA	11733531	Standard	NM_130847	XM_005273798	NA	Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1121+8895A>G	chr11.hg19:g.94542372A>G		NA	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	hg19	CCDS44712.1	0.02	-0.043862	TCAxGTG	UNCOVERED																																																																																			NOVEL	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396474.3	5	2.406215	KEEP	0	0	0	8	222	AA	0.99257	0.023895	0		+	2	28	68	1	0	6.550055	2	60	64	18	ENST00000433060.2	0.5	0.024074
MAML2	84441	__UNKNOWN__	__UNKNOWN__	11	95926511	95926511	__UNKNOWN__	Intron	SNP	C	C	T	rs12274886	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:95926511C>T	ENST00000524717.1	-	2	1798					NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	NA		NA			gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				ccagcctgggcgacagggcga	0.488		NA	T	MECT1, CRTC3	salivary gland mucoepidermoid								C|||	1021	0.203874	0.1831	0.232	5008	,	,	NA	17279	0.1062	NA	0.329	False	NA	,,,	NA	NA	NA	2504	0.184	NA	NA	NA			Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384	84441			16259	protein-coding gene	gene with protein product		607537	mastermind (Drosophila)-like 2		NA	12370315, 12386158	Standard		NM_032427	NA	Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.514-99830G>A	chr11.hg19:g.95926511C>T		NA	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	hg19	CCDS44714.1	0.02	-0.087146	GGGxGAC	UNCOVERED																																																																																			NOVEL	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395540.1	0	2.40698	KEEP	1	0	0	8	243	CC	0.99257	0.09898	0		-	4	60	91	0	0	8.280652	5	60	161	34	ENST00000524717.1	0.444444	0.099721
MAML2	84441	__UNKNOWN__	__UNKNOWN__	11	96008713	96008713	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:96008713A>G	ENST00000524717.1	-	1	1798					NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	NA		NA			gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gattacaggcatgagccacca	0.463		NA	T	MECT1, CRTC3	salivary gland mucoepidermoid																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384	84441			16259	protein-coding gene	gene with protein product		607537	mastermind (Drosophila)-like 2		NA	12370315, 12386158	Standard		NM_032427	NA	Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.513+65833T>C	chr11.hg19:g.96008713A>G		NA	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	hg19	CCDS44714.1	0.02	-0.289434	GGCxTGA	COVERED																																																																																			NOVEL	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395540.1	13	3.608845	KEEP	2	0	0	12	330	AA	0.993072	0.755616	0		-	3	60	104	0	0	7.597309	27	60	806	71	ENST00000524717.1	0.1	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	96080814	96080814	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:96080814G>A			NA	NA				MAML2 (4470 upstream) : CCDC82 (5118 downstream)						NA		NA									NA						gcagtggcacgatctcagctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.96080814G>A		NA		hg19		0.02	-0.096455	CACxATC	UNCOVERED																																																																																			NOVEL					0			3	2.708125	KEEP	3	0	0	9	276	GG	0.99257	0.119541	0			3	60	90	0	0	7.632874	8	60	249	38		0.272727	0.120436
ARHGAP42	143872	__UNKNOWN__	__UNKNOWN__	11	100664532	100664532	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:100664532A>G	ENST00000524892.2	+	3	276				ARHGAP42_ENST00000534060.1_Intron|ARHGAP42_ENST00000298815.8_Intron			A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	NA		NA			signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						gcccggtgcaatggctcatgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895	143872		Rho GTPase activating proteins	26545	protein-coding gene	gene with protein product		615936			NA	18954304	Standard	NM_152432	NM_152432	NA	Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000524892.2:c.251-1304A>G	chr11.hg19:g.100664532A>G		NA	Q96M56	hg19		0.02	-0.078938	GCAxTGG	UNCOVERED																																																																																			NOVEL	ARHGAP42-003	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000395131.2	6	2.707275	KEEP	0	0	0	9	254	AA	0.99254	0.076759	0		+	3	60	95	0	0	8.443291	6	60	184	25	ENST00000524892.2	0.333333	0.077336
ARHGAP42	143872	__UNKNOWN__	__UNKNOWN__	11	100675509	100675509	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:100675509C>G	ENST00000524892.2	+	3	338				ARHGAP42_ENST00000534060.1_Intron|ARHGAP42_ENST00000298815.8_Intron			A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	NA		NA			signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						tccaaaagtgctgggattaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895	143872		Rho GTPase activating proteins	26545	protein-coding gene	gene with protein product		615936			NA	18954304	Standard	NM_152432	NM_152432	NA	Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000524892.2:c.312+9612C>G	chr11.hg19:g.100675509C>G		NA	Q96M56	hg19		0.02	-0.157909	GTGxTGG	COVERED																																																																																			NOVEL	ARHGAP42-003	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000395131.2	6	3.30659	KEEP	2	0	0	11	333	CC	0.992708	0.320453	0		+	3	42	96	0	0	7.77197	12	60	418	40	ENST00000524892.2	0.2	0.322807
KIAA1377	57562	__UNKNOWN__	__UNKNOWN__	11	101870717	101870717	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:101870717T>G	ENST00000263468.8	+	0	5967					NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	NA		NA								breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		atcaagaccatcctggccaac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318	57562			29264	protein-coding gene	gene with protein product		614634			NA	10718198	Standard	NM_020802	XM_005271627	NA	Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.*2343T>G	chr11.hg19:g.101870717T>G		NA	Q4G0U6	hg19	CCDS31658.1	0.02	-0.403428	CCAxCCT	COVERED																																																																																			NOVEL	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394140.1	2	3.171314	KEEP	1	2	58	31	848	TT	0.999998	0.954489	0		+	3	40	101	0	0	6.717793	43	60	1280	97	ENST00000263468.8	0.065217	0.954491
TMEM123	114908	__UNKNOWN__	__UNKNOWN__	11	102329294	102329294	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:102329294C>T	ENST00000525577.1	-	2	211				RP11-315O6.1_ENST00000528717.1_RNA			Q8N131	PORIM_HUMAN	transmembrane protein 123	NA		NA			oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		aaaaattagccgggcatggtg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558	114908			30138	protein-coding gene	gene with protein product	pro oncosis receptor inducing membrane injury gene	606356			NA	11481458, 24318988	Standard	NM_052932	NM_052932	NA	Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000525577.1:c.340-9695G>A	chr11.hg19:g.102329294C>T		NA	Q8IWS2|Q96QV2	hg19		0.02	-0.192977	AGCxGGG	COVERED																																																																																			NOVEL	TMEM123-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000394182.1	9	2.406557	KEEP	1	0	0	8	241	CC	0.99257	0.454356	0		-	4	60	120	0	0	9.468901	17	60	551	43	ENST00000525577.1	0.190476	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	102875013	102875013	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:102875013A>C			NA	NA				MMP13 (48550 upstream) : RP11-690D19.3 (46402 downstream)						NA		NA									NA						ggattacaggagtgagccact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.102875013A>C		NA		hg19		0.02	-0.201727	AGGxGTG	COVERED																																																																																			NOVEL					0			9	2.406589	KEEP	0	0	0	8	229	AT	0.99254	0.607839	0			3	60	104	0	0	8.026814	19	60	572	49		0.136364	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	102888690	102888690	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:102888690G>A			NA	NA				MMP13 (62227 upstream) : RP11-690D19.3 (32725 downstream)						NA		NA									NA						gcatgatctcggctcagtgca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.102888690G>A		NA		hg19		0.02	-0.131582	CTCxGCT	COVERED																																																																																			NOVEL					0			5	2.707924	KEEP	0	0	0	9	271	GG	0.99254	0.227464	0			3	60	91	0	0	7.600933	9	60	308	38		0.25	0.229173
DYNC2H1	79659	__UNKNOWN__	__UNKNOWN__	11	103178478	103178478	__UNKNOWN__	Missense_Mutation	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:103178478C>G	ENST00000375735.2	+	78	11555	c.11411C>G	c.(11410-11412)aCc>aGc	p.T3804S	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.T3811S|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3804	AAA 6. {ECO:0000250}.	NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCTAAAGATACCTTTCGTCTT	0.294		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													65	59	61			NA	NA	11		NA											NA				103178478		1845	4088	5933	SO:0001583	missense			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240	79659		Cytoplasmic dyneins	2962	protein-coding gene	gene with protein product		603297	dynein, cytoplasmic, heavy polypeptide 2	DNCH2	NA	9763680, 9373155	Standard	XM_370652	NM_001080463	NA	Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.11411C>G	chr11.hg19:g.103178478C>G	ENSP00000364887:p.Thr3804Ser	NA	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	hg19	CCDS53701.1	0.02	2.131801	ATAxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	7.831	0.719852	0.15372	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621	T;T	0.07688	3.17;3.17	5.53	2.46	0.29980	Dynein heavy chain (1);	0.466000	0.25506	N	0.030206	T	0.02767	0.0083	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44742	-0.9308	10	0.23891	T	0.37	.	7.716	0.28704	0.3186:0.3198:0.3616:0.0	.	3804;3811	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	S	3804;3811;50	ENSP00000364887:T3804S;ENSP00000381167:T3811S	ENSP00000364887:T3804S	T	+	2	0	DYNC2H1	102683688	0.875000	0.30112	0.994000	0.49952	0.699000	0.40488	1.374000	0.34283	1.312000	0.45043	0.561000	0.74099	ACC	NOVEL	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387196.1	2	4.212053	KEEP	0	0	0	14	421	CC	0.995343	0.96292	0		+	15	60	535	0	0	47.549399	34	60	1161	104	ENST00000375735.2	0.306122	0.967425
RP11-886D15.1	0	__UNKNOWN__	__UNKNOWN__	11	104467174	104467174	__UNKNOWN__	lincRNA	SNP	A	A	C	rs11226434	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:104467174A>C	ENST00000536529.1	-	0	60										NA		NA									NA						accaccaccaacaacaacaac	0.443		NA											a|||	1037	0.207069	0.2738	0.1268	5008	,	,	NA	14591	0.1915	NA	0.173	False	NA	,,,	NA	NA	NA	2504	0.2249	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000536529.1:	chr11.hg19:g.104467174A>C		NA		hg19		0.02	-0.149097	CCAxCAA	COVERED																																																																																			NOVEL	RP11-886D15.1-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000387394.1	9	3.608389	KEEP	1	0	0	12	322	AA	0.993634	0.320751	0		-	3	60	93	0	0	7.379147	13	60	380	46	ENST00000536529.1	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	105861160	105861160	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:105861160A>G			NA	NA				GRIA4 (8341 upstream) : MSANTD4 (5189 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.105861160A>G		NA		hg19		0.02	-0.228048	CTGxGAT	COVERED																																																																																			NOVEL					0			8	2.707646	KEEP	0	0	0	9	262	AA	0.99254	0.578582	0			3	60	103	1	0	7.805426	21	60	648	51		0.125	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	106014273	106014273	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:106014273G>A			NA	NA				RP11-677I18.4 (11430 upstream) : RP11-680E19.1 (106472 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.106014273G>A		NA		hg19		0.02	-0.157884	CACxCCT	UNCOVERED																																																																																			NOVEL					0			10	2.407251	KEEP	1	0	0	8	248	GG	0	0	0			3	60	87	0	0	6.779155	13	60	411	39		0.1875	0.322807
CWF19L2	143884	__UNKNOWN__	__UNKNOWN__	11	107313374	107313374	__UNKNOWN__	Intron	SNP	C	C	T	rs61906058	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:107313374C>T	ENST00000282251.5	-	4	478				CWF19L2_ENST00000433523.1_Intron	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	NA		NA					catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		tgtgccactgcggcccagcct	0.532		NA											C|||	969	0.19349	0.1581	0.1542	5008	,	,	NA	8823	0.1855	NA	0.2068	False	NA	,,,	NA	NA	NA	2504	0.2638	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404	143884			26508	protein-coding gene	gene with protein product		NA			NA	14702039	Standard	NM_152434	NM_152434	NA	Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.450+290G>A	chr11.hg19:g.107313374C>T		NA	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	hg19	CCDS8336.2	0.02	-0.061393	CTGxGGC	UNCOVERED																																																																																			NOVEL	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328825.2	6	2.706995	KEEP	0	0	0	9	255	CC	0.99254	0.04346	0		-	4	60	118	0	0	13.705929	0	0	0	20	ENST00000282251.5	1	0.043787
CUL5	8065	__UNKNOWN__	__UNKNOWN__	11	107938677	107938677	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:107938677C>T	ENST00000393094.2	+	8	1396					NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	NA		NA			calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		ttttttgagacggagttttgc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266	8065			2556	protein-coding gene	gene with protein product		601741			NA	8681378, 9037604	Standard		XM_005271682	NA	Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.781-2146C>T	chr11.hg19:g.107938677C>T		NA	A8K960|O14766|Q9BZC6	hg19	CCDS31668.1	0.02	-0.149113	AGAxGGA	COVERED																																																																																			NOVEL	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389429.1	3	2.406329	KEEP	1	0	0	8	229	CC	0.99257	0.289832	0		+	3	60	90	0	0	7.172384	12	60	389	42	ENST00000393094.2	0.2	0.292001
NPAT	4863	__UNKNOWN__	__UNKNOWN__	11	108065508	108065508	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:108065508C>T	ENST00000278612.8	-	3	262				NPAT_ENST00000610253.1_Intron	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		tcccacagtgctgggattaaa	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308	4863			7896	protein-coding gene	gene with protein product		601448			NA	9205109	Standard	NM_002519	NM_002519	NA	Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.157-764G>A	chr11.hg19:g.108065508C>T		NA	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	hg19	CCDS41710.1	0.02	-0.149127	GTGxTGG	COVERED																																																																																			NOVEL	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389506.2	13	2.406729	KEEP	0	0	0	8	232	CC	0.99257	0.289832	0		-	3	60	90	0	0	6.991829	14	60	471	31	ENST00000278612.8	0.176471	0.292001
ATM	472	__UNKNOWN__	__UNKNOWN__	11	108156846	108156846	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:108156846A>G	ENST00000452508.2	+	28	4182				ATM_ENST00000278616.4_Intron			Q13315	ATM_HUMAN	ATM serine/threonine kinase	NA		NA			brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	atcacctgagatcaggagttc	0.522		NA	D, Mis, N, F, S		T-PLL	leukemia, lymphoma, medulloblastoma, glioma		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)											NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		L, O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311	472			795	protein-coding gene	gene with protein product	TEL1, telomere maintenance 1, homolog (S. cerevisiae)	607585	ataxia telangiectasia mutated (includes complementation groups A, C and D), ataxia telangiectasia mutated	ATA, ATDC, ATC, ATD	NA		Standard	NM_000051	XM_005271561	NA	Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3994-1481A>G	chr11.hg19:g.108156846A>G		NA	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	hg19	CCDS31669.1	0.02	-0.175402	GAGxTCA	COVERED																																																																																			NOVEL	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389938.1	6	3.307875	KEEP	3	0	0	11	297	AA	0.99257	0.384528	0		+	3	60	98	0	0	7.561028	17	60	497	44	ENST00000452508.2	0.15	0.387407
EXPH5	23086	__UNKNOWN__	__UNKNOWN__	11	108446438	108446438	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:108446438T>C	ENST00000265843.4	-	1	230				EXPH5_ENST00000525344.1_Intron	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	NA		NA			intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		cggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723	23086			30578	protein-coding gene	gene with protein product	synaptotagmin-like homologue lacking C2 domains b	612878			NA	9734811, 11773082	Standard	NM_015065	NM_015065	NA	Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.119+17706A>G	chr11.hg19:g.108446438T>C		NA	Q2KHM1|Q9Y4D6	hg19	CCDS8341.1	0.02	-0.184174	TCAxGCC	COVERED																																																																																			NOVEL	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390279.1	8	3.609105	KEEP	4	0	0	12	333	TT	0.992708	0.42039	0		-	3	60	103	0	0	8.06082	17	60	494	52	ENST00000265843.4	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	108526217	108526217	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:108526217A>C			NA	NA				EXPH5 (61752 upstream) : DDX10 (9534 downstream)						NA		NA									NA						gtaatcccagaactttgggag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.108526217A>C		NA		hg19		0.02	-0.105247	CAGxACT	UNCOVERED																																																																																			NOVEL					0			6	2.405986	KEEP	0	0	0	8	219	AA	0.99257	0.138793	0			3	60	96	0	0	8.101275	9	60	265	27		0.25	0.139832
RP11-708B6.2	0	__UNKNOWN__	__UNKNOWN__	11	109340475	109340475	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:109340475T>C	ENST00000532929.1	-	0	252				RP11-708B6.2_ENST00000532992.1_RNA						NA		NA									NA						aactatactataaggctacag	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000532929.1:	chr11.hg19:g.109340475T>C		NA		hg19		0.02	-0.236665	CTAxAAG	COVERED																																																																																			NOVEL	RP11-708B6.2-002	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000390402.1	8	4.210857	KEEP	1	0	0	14	389	TT	0.994391	0.608972	0		-	3	60	103	0	0	7.695365	23	60	671	61	ENST00000532929.1	0.115385	0.612407
ZC3H12C	85463	__UNKNOWN__	__UNKNOWN__	11	110010811	110010811	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:110010811A>G	ENST00000528673.1	+	2	855				ZC3H12C_ENST00000278590.3_Intron|ZC3H12C_ENST00000453089.2_Intron			Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	NA		NA					endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		tggatcacttaaggccaggag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289	85463		Zinc fingers, CCCH-type domain containing	29362	protein-coding gene	gene with protein product	MCP induced protein 3	615001			NA	11214970, 18178554	Standard	NM_033390	NM_033390	NA	Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000528673.1:c.776+2672A>G	chr11.hg19:g.110010811A>G		NA	B4DI65|B4DR47	hg19		0.02	-0.184142	CTTxAGG	UNCOVERED																																																																																			NOVEL	ZC3H12C-003	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000390492.1	6	2.40628	KEEP	2	0	0	8	223	AA	0	0	0		+	3	60	93	1	0	7.292643	14	60	397	47	ENST00000528673.1	0.176471	0.423478
RDX	5962	__UNKNOWN__	__UNKNOWN__	11	110050718	110050718	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:110050718A>C	ENST00000528498.1	-	16	2156					NM_001260493.1	NP_001247422.1	P35241	RADI_HUMAN	radixin	NA		NA			actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		cctccgcctcacaggttcaag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(55;25 1062 11040 28755 44273)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710	5962			9944	protein-coding gene	gene with protein product		179410	deafness, autosomal recessive 24	DFNB24	NA	8486357, 17226784	Standard	NM_002906	NM_001260492	NA	Approved		uc031qdy.1	P35241		ENST00000528498.1:c.1813-4759T>G	chr11.hg19:g.110050718A>C		NA	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	hg19	CCDS58174.1	0.02	-0.113979	CTCxCAG	UNCOVERED																																																																																			NOVEL	RDX-006	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390531.1	3	3.607928	KEEP	0	0	0	12	316	AA	0.994391	0.161555	0		-	3	60	84	0	0	7.032993	8	60	222	31	ENST00000528498.1	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	110440088	110440088	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:110440088T>C			NA	NA				FDX1 (104483 upstream) : ARHGAP20 (7677 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.110440088T>C		NA		hg19		0.02	-0.210476	TCAxGCC	COVERED																																																																																			NOVEL					0			8	3.608538	KEEP	0	0	0	12	323	TT	0.994391	0.519232	0			3	60	94	0	0	7.161475	17	60	491	51		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	111118467	111118467	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:111118467G>A			NA	NA				RP11-89C3.4 (150386 upstream) : C11orf53 (8239 downstream)						NA		NA									NA						agctgagatcgtgccactgca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.111118467G>A		NA		hg19		0.02	-0.166653	ATCxTGC	COVERED																																																																																			NOVEL					0			6	2.695732	KEEP	0	0	0	9	255	GG	0.99254	0.351306	0			3	60	94	0	0	7.391852	14	60	461	46		0.176471	0.353947
SIK2	23235	__UNKNOWN__	__UNKNOWN__	11	111526644	111526644	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:111526644C>T	ENST00000304987.3	+	4	489					NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	NA		NA			insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						cagtggctcacacctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145	23235			21680	protein-coding gene	gene with protein product		608973	SNF1-like kinase 2	SNF1LK2	NA	15067358	Standard	NM_015191	NM_015191	NA	Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.317-32081C>T	chr11.hg19:g.111526644C>T		NA	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	hg19	CCDS8347.1	0.02	-0.122809	TCAxACC	UNCOVERED																																																																																			NOVEL	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319352.3	5	2.407004	KEEP	1	0	0	8	239	CC	0	0	0		+	3	60	91	0	0	7.600973	9	60	298	30	ENST00000304987.3	0.25	0.196312
PPP2R1B	5519	__UNKNOWN__	__UNKNOWN__	11	111599278	111599278	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:111599278A>G	ENST00000426998.2	-	14	1744				SIK2_ENST00000304987.3_3'UTR|PPP2R1B_ENST00000530787.1_Intron|PPP2R1B_ENST00000311129.5_Intron	NM_181700.1	NP_859051.1	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	NA		NA			apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		ctcccaaagtactgggattac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	5519	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits	9303	protein-coding gene	gene with protein product	PP2A-A-beta, protein phosphatase 2A, regulatory subunit A, beta isoform	603113	protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform, protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform		NA	2159327, 9795170	Standard	NM_002716	NM_181699	NA	Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741	ENST00000426998.2:c.1720-1497T>C	chr11.hg19:g.111599278A>G		NA	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	hg19	CCDS53706.1	0.02	3.68976	AGTxCTG	COVERED																																																																																			NOVEL	PPP2R1B-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391297.1	23	10.914187	KEEP	2	3	87	67	1749	AA	1	0.999999	0		-	8	60	274	0	1	18.613487	107	60	3082	299	ENST00000426998.2	0.069565	0.999999
IL18	3606	__UNKNOWN__	__UNKNOWN__	11	112017693	112017693	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:112017693G>A	ENST00000533858.1	-	5	623				IL18_ENST00000280357.7_Intron|IL18_ENST00000524595.1_Intron|IL18_ENST00000528832.1_Intron|SDHD_ENST00000532699.1_Intron			Q14116	IL18_HUMAN	interleukin 18	NA		NA			angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|cellular response to organic cyclic compound (GO:0071407)|chemokine biosynthetic process (GO:0042033)|granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0042253)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma biosynthetic process (GO:0042095)|interleukin-13 biosynthetic process (GO:0042231)|interleukin-2 biosynthetic process (GO:0042094)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|natural killer cell activation (GO:0030101)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of tissue remodeling (GO:0034105)|regulation of cell adhesion (GO:0030155)|sleep (GO:0030431)|T-helper 1 type immune response (GO:0042088)|type 2 immune response (GO:0042092)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)				NA		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|Epithelial(105;8.15e-07)|all cancers(92;1.43e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.055)		tgctcttgttgcccaggctgg	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U90434	CCDS44731.1, CCDS58180.1	11q22.2-q22.3	2014-04-04	2014-04-04		ENSG00000150782	ENSG00000150782	3606		Interleukins and interleukin receptors	5986	protein-coding gene	gene with protein product	interferon-gamma-inducing factor	600953	interleukin 18 (interferon-gamma-inducing factor)		NA	7477296, 9693051	Standard	NM_001562	NM_001562	NA	Approved	IGIF, IL1F4, IL-1g, IL-18	uc001pnb.2	Q14116	OTTHUMG00000167006	ENST00000533858.1:c.135+1632C>T	chr11.hg19:g.112017693G>A		NA	O75599|Q6FGY3|Q6WWJ7	hg19		0.02	-0.149089	GTTxCCC	COVERED																																																																																			NOVEL	IL18-005	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000392413.1	5	3.008847	KEEP	0	0	0	10	302	GG	0.992708	0.289872	0		-	4	60	118	0	0	10.070872	10	60	342	34	ENST00000533858.1	0.285714	0.292001
TEX12	56158	__UNKNOWN__	__UNKNOWN__	11	112039313	112039313	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:112039313T>C	ENST00000280358.4	+	2	116				TEX12_ENST00000530752.1_Intron|SDHD_ENST00000525468.1_Intron|SDHD_ENST00000532699.1_Intron|RP11-356J5.4_ENST00000527589.1_RNA	NM_031275.4	NP_112565.1	Q9BXU0	TEX12_HUMAN	testis expressed 12	NA		NA			meiotic DNA repair synthesis (GO:0000711)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				endometrium(1)|large_intestine(2)|lung(1)	4		all_cancers(61;5.7e-14)|all_epithelial(67;3.4e-08)|Melanoma(852;8.81e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;1.2e-06)|BRCA - Breast invasive adenocarcinoma(274;1.4e-06)|all cancers(92;1.97e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0512)		ctcgctctgttgcccaggctg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF285600	CCDS31679.1	11q23.1	2013-09-20	2007-03-13				56158			11734	protein-coding gene	gene with protein product		605791	testis expressed sequence 12		NA	11279525	Standard		NM_031275	NA	Approved		uc001pnc.3	Q9BXU0		ENST00000280358.4:c.-16-663T>C	chr11.hg19:g.112039313T>C		NA	A6NDL9|B0YIX3	hg19	CCDS31679.1	0.02	-0.18419	TGTxGCC	UNCOVERED																																																																																			NOVEL	TEX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000392417.1	4	2.405936	KEEP	2	0	0	8	221	TT	0	0	0		+	3	60	92	0	1	7.11051	15	60	457	51	ENST00000280358.4	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	113482039	113482039	__UNKNOWN__	IGR	SNP	C	C	T	rs59811748	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:113482039C>T			NA	NA				DRD2 (135928 upstream) : TMPRSS5 (76232 downstream)						NA		NA									NA						ctctgtcacccaggctggagt	0.473		NA											C|||	824	0.164537	0.2753	0.111	5008	,	,	NA	10885	0.1508	NA	0.1342	False	NA	,,,	NA	NA	NA	2504	0.0982	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.113482039C>T		NA		hg19		0.02	-0.078937	ACCxAGG	UNCOVERED																																																																																			NOVEL					0			4	3.309678	KEEP	7	0	0	11	331	CC	0	0	0			3	60	89	0	0	7.843447	6	60	183	29		0.333333	0.077336
ZW10	9183	__UNKNOWN__	__UNKNOWN__	11	113641010	113641010	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:113641010C>T	ENST00000200135.3	-	2	250					NM_004724.3	NP_004715.1	O43264	ZW10_HUMAN	zw10 kinetochore protein	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic metaphase plate congression (GO:0007080)|mitotic sister chromatid segregation (GO:0000070)|protein complex assembly (GO:0006461)|protein localization to kinetochore (GO:0034501)|protein transport (GO:0015031)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|nucleus (GO:0005634)|spindle pole (GO:0000922)	centromeric DNA binding (GO:0019237)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	18		all_cancers(61;3.84e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000237)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.94e-06)|Epithelial(105;0.000103)|all cancers(92;0.000786)		agggtttcaccatgttggcca	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U54996	CCDS8363.1	11q23	2013-01-17	2012-12-13		ENSG00000086827	ENSG00000086827	9183			13194	protein-coding gene	gene with protein product		603954	ZW10 (Drosophila) homolog, centromere/kinetochore protein, ZW10, kinetochore associated, homolog (Drosophila)		NA	9298984	Standard	NM_004724	NM_004724	NA	Approved	KNTC1AP	uc001poe.3	O43264	OTTHUMG00000168190	ENST00000200135.3:c.106-1321G>A	chr11.hg19:g.113641010C>T		NA	A1A528	hg19	CCDS8363.1	0.02	-0.157902	CACxATG	UNCOVERED																																																																																			NOVEL	ZW10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398700.1	15	2.707206	KEEP	8	0	0	9	264	CC	0	0	0		-	3	22	89	0	0	7.072225	12	60	405	45	ENST00000200135.3	0.2	0.322807
HTR3B	9177	__UNKNOWN__	__UNKNOWN__	11	113781406	113781406	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:113781406T>C	ENST00000260191.2	+	2	470				HTR3B_ENST00000537778.1_Intron	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	NA		NA			cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	aagtgatccatctgcctcggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305	9177		5-HT (serotonin) receptors, Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic	5298	protein-coding gene	gene with protein product		604654	5-hydroxytryptamine (serotonin) receptor 3B		NA	9950429, 10521471	Standard	NM_006028	NM_006028	NA	Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.213+1229T>C	chr11.hg19:g.113781406T>C		NA	B0YJ23|Q0VJC3	hg19	CCDS8364.1	0.02	-0.27188	CCAxCTG	UNCOVERED																																																																																			NOVEL	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398842.1	9	2.405535	KEEP	3	0	0	8	215	TT	0	0	0		+	3	60	97	0	0	7.043001	24	60	707	62	ENST00000260191.2	0.111111	0.717315
HTR3B	9177	__UNKNOWN__	__UNKNOWN__	11	113815006	113815006	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:113815006T>C	ENST00000260191.2	+	8	1164				HTR3B_ENST00000537778.1_Intron	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	NA		NA			cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	tcccaaagtgttgggattaca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305	9177		5-HT (serotonin) receptors, Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic	5298	protein-coding gene	gene with protein product		604654	5-hydroxytryptamine (serotonin) receptor 3B		NA	9950429, 10521471	Standard	NM_006028	NM_006028	NA	Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.908-289T>C	chr11.hg19:g.113815006T>C		NA	B0YJ23|Q0VJC3	hg19	CCDS8364.1	0.02	-0.166624	GTGxTGG	COVERED																																																																																			NOVEL	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398842.1	12	3.907526	KEEP	2	0	0	13	338	TT	0.993072	0.351495	0		+	4	60	130	0	0	10.881427	13	60	371	45	ENST00000260191.2	0.235294	0.353947
HTR3B	9177	__UNKNOWN__	__UNKNOWN__	11	113815204	113815204	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:113815204T>C	ENST00000260191.2	+	8	1164				HTR3B_ENST00000537778.1_Intron	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	NA		NA			cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	gcttgggcaatagagcaagac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305	9177		5-HT (serotonin) receptors, Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic	5298	protein-coding gene	gene with protein product		604654	5-hydroxytryptamine (serotonin) receptor 3B		NA	9950429, 10521471	Standard	NM_006028	NM_006028	NA	Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.908-91T>C	chr11.hg19:g.113815204T>C		NA	B0YJ23|Q0VJC3	hg19	CCDS8364.1	0.02	-0.403338	CAAxAGA	COVERED																																																																																			NOVEL	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398842.1	7	2.834335	KEEP	1	1	21	17	426	TT	0.999366	0.9339	0		+	4	60	136	1	1	9.81888	37	60	1023	83	ENST00000260191.2	0.097561	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	113921883	113921883	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:113921883A>G			NA	NA				HTR3A (60848 upstream) : ZBTB16 (8431 downstream)						NA		NA									NA						cagcctgggcaacagagcgac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.113921883A>G		NA		hg19		0.02	-0.087716	GGCxACA	UNCOVERED																																																																																			NOVEL					0			8	2.405681	KEEP	0	0	0	8	217	AA	0.99257	0.09898	0			2	26	72	0	2	6.692951	3	60	93	25		0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	114541325	114541325	__UNKNOWN__	IGR	SNP	G	G	A	rs200640237		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:114541325G>A			NA	NA				NXPE4 (74841 upstream) : NXPE2 (7782 downstream)						NA		NA									NA						gaggcaggaggatcacttgaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.114541325G>A		NA		hg19		0.02	-0.122813	GAGxATC	COVERED																																																																																			NOVEL					0			7	3.309876	KEEP	1	0	0	11	340	GG	0.993072	0.194952	0			3	60	91	0	0	7.60093	9	60	306	36		0.25	0.196312
PCSK7	9159	__UNKNOWN__	__UNKNOWN__	11	117078378	117078378	__UNKNOWN__	Intron	SNP	C	C	T	rs2269396	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:117078378C>T	ENST00000320934.3	-	14	2417				PCSK7_ENST00000540028.1_3'UTR|PCSK7_ENST00000529458.1_Intron	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	NA		NA			peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		acctgcctaccggggctggcc	0.473		NA	T	IGH@	MLCLS																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613	9159			8748	protein-coding gene	gene with protein product		604872			NA	8615762, 9820811	Standard	NM_004716	XM_006718938	NA	Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1786+307G>A	chr11.hg19:g.117078378C>T		NA	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	hg19	CCDS8382.1	0.02	1.324457	TACxGGG	COVERED																																																																																			NOVEL	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000385529.2	4	3.038906	KEEP	0	1	28	20	582	CC	0.999869	0.998565	0		-	13	50	389	0	0	30.170489	61	51	1988	138	ENST00000320934.3	0.175676	0.998696
TMPRSS4-AS1	100526771	__UNKNOWN__	__UNKNOWN__	11	117920344	117920344	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:117920344A>G	ENST00000606951.1	-	0	195				TMPRSS4-AS1_ENST00000527695.1_RNA|TMPRSS4-AS1_ENST00000527329.1_RNA	NR_038318.1				TMPRSS4 antisense RNA 1	NA		NA									NA						gattacaggcatgagccaccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							11q23.3	2012-10-12	2012-08-15		ENSG00000255274	ENSG00000255274	100526771		Long non-coding RNAs	44179	non-coding RNA	RNA, long non-coding		NA	TMPRSS4 antisense RNA 1 (non-protein coding)		NA		Standard	NR_038318	NR_038318	NA	Approved		uc001pry.1		OTTHUMG00000166993	ENST00000606951.1:	chr11.hg19:g.117920344A>G		NA		hg19		0.02	-0.201713	GGCxTGA	COVERED																																																																																			NOVEL	TMPRSS4-AS1-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000470982.1	6	2.706547	KEEP	1	0	0	9	244	AA	0.99254	0.486885	0		-	3	60	96	0	0	7.227358	19	60	556	49	ENST00000606951.1	0.136364	0.490544
CD3D	915	__UNKNOWN__	__UNKNOWN__	11	118210458	118210458	__UNKNOWN__	Intron	SNP	A	A	C	rs61900915	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118210458A>C	ENST00000529594.1	-	2	227				CD3D_ENST00000300692.4_Intron|CD3D_ENST00000392884.2_Intron			P04234	CD3D_HUMAN	CD3d molecule, delta (CD3-TCR complex)	NA		NA			cell surface receptor signaling pathway (GO:0007166)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive thymic T cell selection (GO:0045059)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)	Muromonab(DB00075)	cacacacacaaacacacTCTC	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X01451	CCDS8394.1, CCDS41724.1	11q23	2014-09-17	2006-03-28		ENSG00000167286	ENSG00000167286	915		CD molecules	1673	protein-coding gene	gene with protein product		186790	CD3d antigen, delta polypeptide (TiT3 complex)	T3D	NA		Standard	NM_000732	NM_000732	NA	Approved		uc001pss.1	P04234	OTTHUMG00000166970	ENST00000529594.1:c.187+31T>G	chr11.hg19:g.118210458A>C		NA	A8MVP6	hg19		0.02	3.708442	ACAxACA	COVERED																																																																																			NOVEL	CD3D-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000392130.1	15	11.740581	KEEP	0	3	81	68	1780	AA	1	0.999999	0		-	8	60	272	0	0	18.577	102	60	2878	273	ENST00000529594.1	0.072727	0.999999
RP11-770J1.4	0	__UNKNOWN__	__UNKNOWN__	11	118305187	118305187	__UNKNOWN__	3'UTR	SNP	A	A	G	rs368036346|rs148542925|rs72046909	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118305187A>G	ENST00000532619.1	-	0	734										NA		NA									NA						gagagagagaaagagagagag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000532619.1:c.*190T>C	chr11.hg19:g.118305187A>G		NA		hg19		0.02	-0.342026	AGAxAGA	COVERED																																																																																			NOVEL	RP11-770J1.4-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000389622.1	4	6.445901	KEEP	0	1	21	29	775	AA	0.999997	0.865743	0		-	5	60	149	0	1	10.926403	32	60	938	71	ENST00000532619.1	0.135135	0.865745
KMT2A	4297	__UNKNOWN__	__UNKNOWN__	11	118370231	118370231	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118370231T>G	ENST00000534358.1	+	23	6102				KMT2A_ENST00000354520.4_Intron|KMT2A_ENST00000389506.5_Intron	NM_001197104.1|NM_005933.3	NP_001184033.1|NP_005924.2	Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	NA		NA			anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)				NA						aggtgtggtgtctcacgcctg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058	4297		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	7132	protein-coding gene	gene with protein product		159555	myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog), myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)	MLL	NA	1720549	Standard	NM_005933	NM_001197104	NA	Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000534358.1:c.6079+96T>G	chr11.hg19:g.118370231T>G		NA	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	hg19	CCDS55791.1	0.02	-0.228049	GTGxCTC	COVERED																																																																																			NOVEL	KMT2A-001	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389228.2	4	2.706847	KEEP	1	0	0	9	250	TT	0.99254	0.578582	0		+	3	60	95	0	0	7.127559	19	60	580	45	ENST00000534358.1	0.136364	0.58293
KMT2A	4297	__UNKNOWN__	__UNKNOWN__	11	118370443	118370443	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118370443T>C	ENST00000534358.1	+	24	6102				KMT2A_ENST00000354520.4_Intron|KMT2A_ENST00000389506.5_Intron	NM_001197104.1|NM_005933.3	NP_001184033.1|NP_005924.2	Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	NA		NA			anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)				NA						tgcagtgagctgagattgcgc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058	4297		Chromatin-modifying enzymes / K-methyltransferases, Zinc fingers, PHD-type	7132	protein-coding gene	gene with protein product		159555	myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog), myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)	MLL	NA	1720549	Standard	NM_005933	NM_001197104	NA	Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000534358.1:c.6080-107T>C	chr11.hg19:g.118370443T>C		NA	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	hg19	CCDS55791.1	0.02	-0.17542	AGCxGAG	COVERED																																																																																			NOVEL	KMT2A-001	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389228.2	6	4.209331	KEEP	0	0	0	14	375	TT	0.995343	0.385603	0		+	3	60	94	0	0	7.310306	15	60	451	36	ENST00000534358.1	0.166667	0.387407
IFT46	56912	__UNKNOWN__	__UNKNOWN__	11	118430879	118430879	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118430879A>G	ENST00000264021.3	-	3	384				IFT46_ENST00000530872.1_Intron|IFT46_ENST00000527868.1_5'UTR|IFT46_ENST00000264020.2_Intron	NM_001168618.1	NP_001162089.1	Q9NQC8	IFT46_HUMAN	intraflagellar transport 46	NA		NA			cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)|protein stabilization (GO:0050821)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)	protein C-terminus binding (GO:0008022)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	9						tataatcccaacactttggga	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136934	CCDS8399.1, CCDS53718.1	11q23.3	2014-07-18	2014-07-03	2010-04-22	ENSG00000118096	ENSG00000118096	56912		Intraflagellar transport homologs	26146	protein-coding gene	gene with protein product	cilia and flagella associated protein 32	NA	chromosome 11 open reading frame 60, intraflagellar transport 46 homolog (Chlamydomonas)	C11orf60	NA	10873569, 19253336	Standard	NM_020153	NM_020153	NA	Approved	C11orf2, FLJ21827, CFAP32	uc001pto.2	Q9NQC8	OTTHUMG00000166408	ENST00000264021.3:c.35-300T>C	chr11.hg19:g.118430879A>G		NA	A8K0F6|Q9H6V5	hg19	CCDS53718.1	0.02	-0.385888	CCAxCAC	COVERED																																																																																			NOVEL	IFT46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389627.1	7	6.94454	KEEP	0	1	25	32	848	AA	0.999998	0.918169	0		-	5	60	150	0	0	10.964414	33	60	976	87	ENST00000264021.3	0.131579	0.918171
ARCN1	372	__UNKNOWN__	__UNKNOWN__	11	118455801	118455801	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118455801G>A	ENST00000359415.4	+	6	1106				ARCN1_ENST00000264028.4_Intron|ARCN1_ENST00000392859.3_Intron|ARCN1_ENST00000534182.2_Intron			P48444	COPD_HUMAN	archain 1	NA		NA			adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		tcagcctcccgaagtgctggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139	372			649	protein-coding gene	gene with protein product		600820	coatomer protein complex, subunit delta	COPD	NA	7782067, 8854871	Standard		NM_001655	NA	Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000359415.4:c.941+442G>A	chr11.hg19:g.118455801G>A		NA	B4E1X2|E9PEU4|Q52M80	hg19		0.02	-0.149118	CCCxAAG	COVERED																																																																																			NOVEL	ARCN1-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000389275.1	6	2.406304	KEEP	0	0	0	8	227	GG	0.99257	0.289832	0		+	4	60	118	0	0	9.801358	12	60	390	33	ENST00000359415.4	0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	118745289	118745289	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118745289C>T			NA	NA				Y_RNA (38470 upstream) : CXCR5 (9185 downstream)						NA		NA									NA						aattatgccactgcactccag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.118745289C>T		NA		hg19		0.02	-0.149123	CCAxTGC	COVERED																																																																																			NOVEL					0			10	2.406864	KEEP	0	0	0	8	236	CC	0.99257	0.289832	0			3	60	85	0	0	6.579277	13	60	437	33		0.1875	0.292001
CXCR5	643	__UNKNOWN__	__UNKNOWN__	11	118757872	118757872	__UNKNOWN__	Intron	SNP	C	C	T	rs144594581	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118757872C>T	ENST00000292174.4	+	1	227				RP11-158I9.5_ENST00000498872.2_RNA	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	NA		NA			B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		GCAGAGTCTCCGTCAGGAACT	0.552		NA											C|||	5	0.000998403	0.0038	0.0	5008	,	,	NA	18477	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683	643		CD molecules, GPCR / Class A : Chemokine receptors : C-X-C motif	1060	protein-coding gene	gene with protein product		601613	Burkitt lymphoma receptor 1, GTP-binding protein, Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)	BLR1	NA	1425907	Standard	NM_001716	NM_001716	NA	Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.51+3171C>T	chr11.hg19:g.118757872C>T		NA	Q14811	hg19	CCDS8402.1	0.02	1.420931	CTCxGTC	COVERED																																																																																			NOVEL	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389309.1	1	2.707172	KEEP	0	0	0	9	261	CC	0.99254	0.98629	0		+	4	60	124	0	0	7.816422	60	60	1971	115	ENST00000292174.4	0.0625	0.993703
UPK2	7379	__UNKNOWN__	__UNKNOWN__	11	118828694	118828694	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118828694G>A	ENST00000264031.2	+	5	453				UPK2_ENST00000534788.1_Intron	NM_006760.3	NP_006751.1	O00526	UPK2_HUMAN	uroplakin 2	NA		NA			epithelial cell differentiation (GO:0030855)|membrane organization (GO:0061024)|multicellular organismal development (GO:0007275)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)				kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		tggctggctggctggctggct	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y13645	CCDS8404.1	11q23	2008-07-21				ENSG00000110375	7379			12579	protein-coding gene	gene with protein product	uroplakin II, uroplakin-2	611558			NA	9515818, 9846985	Standard	NM_006760	NM_006760	NA	Approved	UP2, UPII, MGC138598	uc001puh.3	O00526		ENST00000264031.2:c.419-113G>A	chr11.hg19:g.118828694G>A		NA	B0YJ92|O00457|Q53YV0	hg19	CCDS8404.1	0.02	-0.385942	CTGxCTG	COVERED																																																																																			NOVEL	UPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389311.1	0	2.406477	KEEP	0	0	0	8	231	GG	0.99257	0.911349	0		+	17	60	513	0	0	46.661224	27	60	881	61	ENST00000264031.2	0.386364	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	118836821	118836821	__UNKNOWN__	IGR	SNP	G	G	A	rs7112758	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118836821G>A			NA	NA				UPK2 (7552 upstream) : Y_RNA (4386 downstream)						NA		NA									NA						gtagagacggggtttcaccat	0.537		NA											G|||	1779	0.355232	0.261	0.5821	5008	,	,	NA	14226	0.1141	NA	0.4722	False	NA	,,,	NA	NA	NA	2504	0.4499	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.118836821G>A		NA		hg19		0.02	-0.201739	CGGxGTT	COVERED																																																																																			NOVEL					0			8	2.407609	KEEP	0	0	0	8	262	GG	0.99257	0.4869	0			9	60	267	0	0	25.282853	10	60	339	44		0.473684	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	118852964	118852964	__UNKNOWN__	IGR	SNP	C	C	T	rs368571032		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118852964C>T			NA	NA				FOXR1 (963 upstream) : RN7SL529P (12079 downstream)						NA		NA									NA						ggagtctcaccctgttgccca	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.118852964C>T		NA		hg19		0.02	-0.140332	CACxCTG	COVERED																																																																																			NOVEL					0			8	3.911121	KEEP	2	0	0	13	400	CC	0.994391	0.259501	0			4	60	111	0	0	9.230861	11	60	367	45		0.266667	0.260965
HINFP	25988	__UNKNOWN__	__UNKNOWN__	11	118995648	118995648	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:118995648T>C	ENST00000527410.1	+	2	24				HINFP_ENST00000350777.2_Intron|HINFP_ENST00000527354.1_Intron			Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	NA		NA			DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						cgccactgcattccagcctgg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273	25988		Zinc fingers, C2H2-type	17850	protein-coding gene	gene with protein product	histone nuclear factor P	607099	MBD2-interacting zinc finger 1, MBD2-interacting zinc finger	MIZF	NA	11553631	Standard	NM_015517	NM_015517	NA	Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000527410.1:c.-10-1997T>C	chr11.hg19:g.118995648T>C		NA	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	hg19	CCDS58188.1	0.02	1.511578	GCAxTCC	COVERED																																																																																			NOVEL	HINFP-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388205.1	38	3.099789	KEEP	0	6	187	76	2070	TT	1	0.999962	0		+	9	60	288	0	0	20.397264	81	60	2373	269	ENST00000527410.1	0.1	0.999962
HINFP	25988	__UNKNOWN__	__UNKNOWN__	11	119000453	119000453	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:119000453C>T	ENST00000527410.1	+	3	215				HINFP_ENST00000350777.2_Intron|HINFP_ENST00000527354.1_Intron			Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	NA		NA			DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						ggattacaggcgtgagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273	25988		Zinc fingers, C2H2-type	17850	protein-coding gene	gene with protein product	histone nuclear factor P	607099	MBD2-interacting zinc finger 1, MBD2-interacting zinc finger	MIZF	NA	11553631	Standard	NM_015517	NM_015517	NA	Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000527410.1:c.182-982C>T	chr11.hg19:g.119000453C>T		NA	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	hg19	CCDS58188.1	0.02	-0.184208	AGGxGTG	COVERED																																																																																			NOVEL	HINFP-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388205.1	7	4.212105	KEEP	3	0	0	14	427	CC	0.993634	0.420782	0		+	3	60	87	0	0	6.610583	15	60	498	56	ENST00000527410.1	0.166667	0.423478
HINFP	25988	__UNKNOWN__	__UNKNOWN__	11	119002012	119002012	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:119002012C>T	ENST00000527410.1	+	4	445				HINFP_ENST00000350777.2_Intron|HINFP_ENST00000527354.1_Intron			Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	NA		NA			DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						ttgcccaggccggtctcgaac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273	25988		Zinc fingers, C2H2-type	17850	protein-coding gene	gene with protein product	histone nuclear factor P	607099	MBD2-interacting zinc finger 1, MBD2-interacting zinc finger	MIZF	NA	11553631	Standard	NM_015517	NM_015517	NA	Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000527410.1:c.412-233C>T	chr11.hg19:g.119002012C>T		NA	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	hg19	CCDS58188.1	0.02	1.54399	GGCxGGT	COVERED																																																																																			NOVEL	HINFP-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388205.1	17	7.345316	KEEP	0	1	27	34	939	CC	0.999999	0.963773	0		+	5	60	145	0	1	9.881033	44	60	1447	127	ENST00000527410.1	0.102041	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	119008950	119008950	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:119008950T>C			NA	NA				HINFP (2198 upstream) : ABCG4 (10771 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.119008950T>C		NA		hg19		0.02	-0.22794	TCAxGCC	COVERED																																																																																			NOVEL					0			5	3.307522	KEEP	1	0	0	11	296	TT	0.993072	0.578892	0			3	60	106	0	0	8.106004	21	60	591	58		0.125	0.58293
NLRX1	79671	__UNKNOWN__	__UNKNOWN__	11	119047156	119047156	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:119047156A>G	ENST00000409109.1	+	6	2258				NLRX1_ENST00000525863.1_Intron|NLRX1_ENST00000292199.2_Intron|NLRX1_ENST00000409265.4_Intron|NLRX1_ENST00000409991.1_Intron	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	NA		NA			innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		agccgggtgcagtggctcacg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703	79671		Nucleotide-binding domain and leucine rich repeat containing	29890	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat containing X1, NOD-like receptor X1, NLR family, X1	611947			NA	12766759	Standard	NM_170722	XM_005271669	NA	Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.1671+1173A>G	chr11.hg19:g.119047156A>G		NA	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	hg19	CCDS8416.1	0.02	-0.131573	TGCxGTG	COVERED																																																																																			NOVEL	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335403.1	3	2.40607	KEEP	0	0	0	8	223	AA	0.99257	0.22747	0		+	3	60	92	0	0	7.472857	11	60	342	33	ENST00000409109.1	0.214286	0.229173
NLRX1	79671	__UNKNOWN__	__UNKNOWN__	11	119054586	119054586	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:119054586G>A	ENST00000409109.1	+	0	3953				NLRX1_ENST00000525863.1_Nonsense_Mutation_p.W888*|NLRX1_ENST00000292199.2_3'UTR|NLRX1_ENST00000409265.4_Nonsense_Mutation_p.W888*|NLRX1_ENST00000409991.1_3'UTR	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	NA		NA			innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		GCTCACCTGTGGACACCGAGG	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													112	111	111			NA	NA	11		NA											NA				119054586		2136	4258	6394	SO:0001624	3_prime_UTR_variant			AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703	79671		Nucleotide-binding domain and leucine rich repeat containing	29890	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat containing X1, NOD-like receptor X1, NLR family, X1	611947			NA	12766759	Standard	NM_170722	XM_005271669	NA	Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.*438G>A	chr11.hg19:g.119054586G>A		NA	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	hg19	CCDS8416.1	0.02	1.219161	TGTxGAC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.661055|5.661055	0.96734|0.96734	.|.	.|.	ENSG00000160703|ENSG00000160703	ENST00000397884|ENST00000409265;ENST00000525863	.|.	.|.	.|.	4.45|4.45	2.47|2.47	0.30058|0.30058	.|.	.|.	.|.	.|.	.|.	T|.	0.55401|.	0.1918|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.47573|.	-0.9107|.	5|.	0.87932|.	D|.	0|.	.|.	7.3352|7.3352	0.26605|0.26605	0.0:0.1866:0.6202:0.1932|0.0:0.1866:0.6202:0.1932	.|.	.|.	.|.	.|.	R|X	89|888	.|.	ENSP00000380981:G89R|.	G|W	+|+	1|2	0|0	NLRX1|NLRX1	118559796|118559796	0.004000|0.004000	0.15560|0.15560	0.028000|0.028000	0.17463|0.17463	0.125000|0.125000	0.20455|0.20455	0.233000|0.233000	0.17911|0.17911	0.571000|0.571000	0.29365|0.29365	-0.241000|-0.241000	0.12123|0.12123	GGA|TGG	NOVEL	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335403.1	5	8.425452	KEEP	0	0	0	28	870	GG	0.999997	0.999765	0		+	16	60	474	0	0	37.184628	69	60	2371	179	ENST00000409109.1	0.188235	0.999768
GRIK4	2900	__UNKNOWN__	__UNKNOWN__	11	120741559	120741559	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:120741559G>C	ENST00000527524.2	+	10	1193				GRIK4_ENST00000438375.2_Intron|RP11-640N11.2_ENST00000505153.2_RNA	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	NA		NA			glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		aggttcaagcgattctcctgc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403	2900		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4582	protein-coding gene	gene with protein product		600282		GRIK	NA		Standard	NM_014619	NM_001282470	NA	Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.907-3216G>C	chr11.hg19:g.120741559G>C		NA	A8K9L1	hg19	CCDS8433.1	0.02	1.739575	AGCxATT	COVERED																																																																																			NOVEL	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109760.4	14	5.441947	KEEP	0	1	28	28	786	GG	0.999997	0.999215	0		+	4	60	129	0	0	8.207374	64	60	1974	136	ENST00000527524.2	0.058824	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	121133568	121133568	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:121133568T>C			NA	NA				TECTA (71366 upstream) : SC5D (29593 downstream)						NA		NA									NA						ggattacaggtgtgagccacg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.121133568T>C		NA		hg19		0.02	-0.245551	AGGxGTG	COVERED																																																																																			NOVEL					0			8	2.406365	KEEP	0	0	0	8	224	TT	0.99257	0.636582	0			3	60	106	0	0	8.291951	18	60	532	53		0.142857	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	121181371	121181371	__UNKNOWN__	IGR	SNP	G	G	A	rs182670074		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:121181371G>A			NA	NA				SC5D (1968 upstream) : RP11-730K11.1 (136668 downstream)						NA		NA									NA						gggtttcaccgtgttagccag	0.552		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	15711	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.121181371G>A		NA		hg19		0.02	-0.289459	ACCxTGT	UNCOVERED																																																																																			NOVEL					0			10	2.705486	KEEP	6	0	0	9	238	GG	0	0	0			4	40	117	0	0	8.43442	27	60	867	56		0.129032	0.760887
SORL1	6653	__UNKNOWN__	__UNKNOWN__	11	121367721	121367721	__UNKNOWN__	Missense_Mutation	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:121367721A>C	ENST00000260197.7	+	6	1031	c.902A>C	c.(901-903)cAg>cCg	p.Q301P	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	301		NA			cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		AGAGATTTTCAGCTTCGGGAC	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													99	96	97			NA	NA	11		NA											NA				121367721		2203	4299	6502	SO:0001583	missense			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642	6653		Fibronectin type III domain containing	11185	protein-coding gene	gene with protein product	LDLR relative with 11 ligand-binding repeats	602005	chromosome 11 open reading frame 32, sortilin-related receptor, L(DLR class) A repeats-containing	C11orf32	NA	9157966, 8940146	Standard	NM_003105	NM_003105	NA	Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.902A>C	chr11.hg19:g.121367721A>C	ENSP00000260197:p.Gln301Pro	NA	B2RNX7|Q92856	hg19	CCDS8436.1	0.02	5.760037	TTCxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484261	0.84854	.	.	ENSG00000137642	ENST00000260197	T	0.29142	1.58	5.7	5.7	0.88788	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.51686	0.1689	L	0.55481	1.735	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	T	0.51980	-0.8636	10	0.62326	D	0.03	.	15.9745	0.80049	1.0:0.0:0.0:0.0	.	301	Q92673	SORL_HUMAN	P	301	ENSP00000260197:Q301P	ENSP00000260197:Q301P	Q	+	2	0	SORL1	120872931	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.047000	0.93823	2.168000	0.68352	0.533000	0.62120	CAG	NOVEL	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387626.2	4	5.714582	KEEP	0	0	0	19	526	AA	0.99986	0.99986	0		+	29	60	923	0	0	71.789552	149	60	4523	303	ENST00000260197.7	0.162921	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	121845024	121845024	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:121845024A>G			NA	NA				SORL1 (340622 upstream) : RNU6-256P (30038 downstream)						NA		NA									NA						ggccaggtgcagtggctcatg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.121845024A>G		NA		hg19		0.02	-0.263147	TGCxGTG	COVERED																																																																																			NOVEL					0			4	2.406342	KEEP	0	0	0	8	225	AA	0.99257	0.688515	0			3	60	101	0	0	7.494593	23	60	708	59		0.115385	0.693668
RP11-820L6.1	0	__UNKNOWN__	__UNKNOWN__	11	122118376	122118376	__UNKNOWN__	RNA	SNP	G	G	A	rs546001876		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122118376G>A	ENST00000527474.1	-	0	898										NA		NA									NA						atagagtctcgctctgtcacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000527474.1:	chr11.hg19:g.122118376G>A		NA		hg19		0.02	-0.306966	CTCxCTC	UNCOVERED																																																																																			NOVEL	RP11-820L6.1-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000387551.1	9	2.406274	KEEP	1	0	0	8	228	GG	0	0	0		-	4	60	118	0	0	8.418853	29	60	914	62	ENST00000527474.1	0.121212	0.800245
RP11-820L6.1	0	__UNKNOWN__	__UNKNOWN__	11	122155444	122155444	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122155444G>A	ENST00000527474.1	-	0	898										NA		NA									NA						ggctggtctcgaactcctgac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000527474.1:	chr11.hg19:g.122155444G>A		NA		hg19		0.02	-0.236744	CTCxAAC	UNCOVERED																																																																																			NOVEL	RP11-820L6.1-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000387551.1	10	2.401075	KEEP	1	0	0	8	197	GG	0	0	0		-	4	60	99	0	0	6.966912	22	60	649	54	ENST00000527474.1	0.153846	0.612407
RP11-820L6.1	0	__UNKNOWN__	__UNKNOWN__	11	122234711	122234711	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122234711A>G	ENST00000527474.1	-	0	478										NA		NA									NA						cgcccacctcagcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000527474.1:	chr11.hg19:g.122234711A>G		NA		hg19		0.02	-0.219285	CTCxGCC	COVERED																																																																																			NOVEL	RP11-820L6.1-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000387551.1	6	2.707482	KEEP	4	0	0	9	259	AA	0.99257	0.54878	0		-	3	60	99	0	0	7.661114	17	60	522	57	ENST00000527474.1	0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	122445622	122445622	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122445622T>C			NA	NA				RNU4ATAC5P (123315 upstream) : RNU6-592P (4290 downstream)						NA		NA									NA						gtaatcccagtactttgggag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.122445622T>C		NA		hg19		0.02	-0.315727	CAGxACT	COVERED																																																																																			NOVEL					0			12	4.209105	KEEP	4	0	0	14	367	TT	0.993072	0.812795	0			3	60	102	0	0	7.44415	26	60	756	75		0.103448	0.818465
UBASH3B	84959	__UNKNOWN__	__UNKNOWN__	11	122579068	122579068	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122579068C>T	ENST00000284273.5	+	1	536				UBASH3B_ENST00000525711.1_Intron	NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	NA		NA			negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ggcacaatctcggctcactgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127	84959			29884	protein-coding gene	gene with protein product	SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate	609201			NA	11853319, 12370296	Standard	NM_032873	NM_032873	NA	Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.161+52150C>T	chr11.hg19:g.122579068C>T		NA	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	hg19	CCDS31694.1	0.02	-0.24527	TCTxGGC	UNCOVERED																																																																																			NOVEL	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387499.1	12	2.708075	KEEP	8	0	0	9	276	CC	0	0	0		+	3	53	93	0	0	6.697311	23	60	717	60	ENST00000284273.5	0.115385	0.693668
UBASH3B	84959	__UNKNOWN__	__UNKNOWN__	11	122579085	122579085	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122579085C>T	ENST00000284273.5	+	1	536				UBASH3B_ENST00000525711.1_Intron	NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	NA		NA			negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ctgcaacctccgcctcccagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127	84959			29884	protein-coding gene	gene with protein product	SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate	609201			NA	11853319, 12370296	Standard	NM_032873	NM_032873	NA	Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.161+52167C>T	chr11.hg19:g.122579085C>T		NA	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	hg19	CCDS31694.1	0.02	-0.254357	CTCxGCC	UNCOVERED																																																																																			NOVEL	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387499.1	14	2.707602	KEEP	8	0	0	9	268	CC	0	0	0		+	3	39	93	0	0	6.54493	26	60	829	59	ENST00000284273.5	0.103448	0.668523
C11orf63	79864	__UNKNOWN__	__UNKNOWN__	11	122782732	122782732	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122782732T>C	ENST00000531316.1	+	2	956				C11orf63_ENST00000227349.2_Intron			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	NA		NA			axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		tggtggctcatgcctgtaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944	79864			26288	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024806	NM_024806	NA	Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.864+7580T>C	chr11.hg19:g.122782732T>C		NA	A8K6G0|Q96GB5|Q9H5D6	hg19	CCDS8438.1	0.02	1.780338	TCAxGCC	COVERED																																																																																			NOVEL	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387511.1	19	4.509845	KEEP	3	0	0	15	406	TT	0.995343	0.979578	0		+	4	60	134	0	0	9.152967	49	60	1450	102	ENST00000531316.1	0.075472	0.984161
CLMP	79827	__UNKNOWN__	__UNKNOWN__	11	122943080	122943080	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122943080A>G	ENST00000448775.2	-	0	2564					NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	NA		NA			digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						gcaatggcataatcttggctc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250	79827		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	24039	protein-coding gene	gene with protein product	adipocyte-specific adhesion molecule, coxsackie- and adenovirus receptor-like membrane protein, adipocyte adhesion molecule	611693			NA	12851705, 14573622	Standard	NM_024769	NM_024769	NA	Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.*1102T>C	chr11.hg19:g.122943080A>G		NA		hg19	CCDS8441.1	0.02	-0.429693	CATxATC	COVERED																																																																																			NOVEL	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387542.1	10	3.002946	KEEP	0	0	0	10	250	AA	0.992708	0.947531	0		-	4	60	138	0	0	10.063445	36	60	1026	73	ENST00000448775.2	0.1	0.954491
CLMP	79827	__UNKNOWN__	__UNKNOWN__	11	122994954	122994954	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122994954C>G	ENST00000448775.2	-	2	369					NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	NA		NA			digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						gaactcctggcctcaagtgat	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250	79827		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	24039	protein-coding gene	gene with protein product	adipocyte-specific adhesion molecule, coxsackie- and adenovirus receptor-like membrane protein, adipocyte adhesion molecule	611693			NA	12851705, 14573622	Standard	NM_024769	NM_024769	NA	Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.29-26294G>C	chr11.hg19:g.122994954C>G		NA		hg19	CCDS8441.1	0.02	1.897356	TGGxCTC	COVERED																																																																																			NOVEL	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387542.1	13	5.415781	KEEP	0	0	0	18	552	CC	0.999859	0.979388	0		-	4	60	127	0	0	8.491263	48	60	1639	113	ENST00000448775.2	0.076923	0.979526
CLMP	79827	__UNKNOWN__	__UNKNOWN__	11	122998492	122998492	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:122998492T>C	ENST00000448775.2	-	2	369					NM_024769.2	NP_079045.1	Q9H6B4	CLMP_HUMAN	CXADR-like membrane protein	NA		NA			digestive tract development (GO:0048565)	cell surface (GO:0009986)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	14						cgcctgtaattccagcacttt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009371	CCDS8441.1	11q24	2013-01-29			ENSG00000166250	ENSG00000166250	79827		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	24039	protein-coding gene	gene with protein product	adipocyte-specific adhesion molecule, coxsackie- and adenovirus receptor-like membrane protein, adipocyte adhesion molecule	611693			NA	12851705, 14573622	Standard	NM_024769	NM_024769	NA	Approved	ASAM, FLJ22415, ACAM	uc001pyt.3	Q9H6B4		ENST00000448775.2:c.29-29832A>G	chr11.hg19:g.122998492T>C		NA		hg19	CCDS8441.1	0.02	-0.280666	AATxCCA	COVERED																																																																																			NOVEL	CLMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387542.1	8	3.007592	KEEP	1	0	0	10	275	TT	0.992708	0.734278	0		-	4	51	144	0	0	11.390754	23	60	680	58	ENST00000448775.2	0.148148	0.739671
CTD-2216M2.1	0	__UNKNOWN__	__UNKNOWN__	11	123083882	123083882	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123083882A>G	ENST00000531681.1	+	0	411										NA		NA									NA						ccaaagtgctagaattacagg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000531681.1:	chr11.hg19:g.123083882A>G		NA		hg19		0.02	-0.228041	GCTxGAA	COVERED																																																																																			NOVEL	CTD-2216M2.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000387548.1	9	2.706789	KEEP	0	0	0	9	246	AA	0.99254	0.578582	0		+	4	60	140	0	0	11.563008	16	60	471	47	ENST00000531681.1	0.2	0.58293
CTD-2216M2.1	0	__UNKNOWN__	__UNKNOWN__	11	123091677	123091677	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123091677T>C	ENST00000531681.1	+	0	411										NA		NA									NA						ggattacaggtgtgagccact	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000531681.1:	chr11.hg19:g.123091677T>C		NA		hg19		0.02	-0.2368	AGGxGTG	COVERED																																																																																			NOVEL	CTD-2216M2.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000387548.1	10	4.210289	KEEP	6	0	0	14	387	TT	0.99257	0.607857	0		+	3	60	94	0	0	7.161501	17	60	504	61	ENST00000531681.1	0.15	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	123123936	123123936	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123123936T>C			NA	NA				CTD-2216M2.1 (24951 upstream) : U8 (48161 downstream)						NA		NA									NA						gctgggattataggcgtgagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.123123936T>C		NA		hg19		0.02	-0.245151	TTAxAGG	COVERED																																																																																			NOVEL					0			6	2.705567	KEEP	2	0	0	9	232	TT	0.99257	0.636582	0			3	60	96	0	0	7.295861	18	60	505	56		0.142857	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	123188916	123188916	__UNKNOWN__	IGR	SNP	A	A	G	rs4935833	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123188916A>G			NA	NA				RP11-109E10.1 (3441 upstream) : MIR4493 (63231 downstream)						NA		NA									NA						aagaagaagaagaggaggagg	0.398		NA											-|||	292	0.0583067	0.0991	0.0836	5008	,	,	NA	14146	0.0417	NA	0.0447	False	NA	,,,	NA	NA	NA	2504	0.0164	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.123188916A>G		NA		hg19		0.02	-0.420987	AGAxGAG	COVERED																																																																																			NOVEL					0			21	5.112065	KEEP	13	0	0	17	461	AA	0.993634	0.942364	0			4	60	128	1	0	8.850184	41	60	1228	94		0.088889	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	123299697	123299697	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123299697T>C			NA	NA				MIR4493 (47477 upstream) : AP000783.1 (1360 downstream)						NA		NA									NA						gccaggagtttgagaccagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.123299697T>C		NA		hg19		0.02	-0.350529	GTTxGAG	COVERED																																																																																			NOVEL					0			11	4.511297	KEEP	1	0	0	15	416	TT	0.995343	0.87362	0			3	57	101	0	0	7.012971	34	60	1029	85		0.081081	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	123348765	123348765	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123348765T>G			NA	NA				LINC01059 (17647 upstream) : GRAMD1B (47578 downstream)						NA		NA									NA						ctcccaaagttctgggattac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.123348765T>G		NA		hg19		0.02	-0.324478	AGTxCTG	COVERED																																																																																			NOVEL					0			9	2.707211	KEEP	0	0	0	9	254	TT	0.99254	0.829482	0			3	60	98	0	0	6.827716	31	60	897	68		0.088235	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	123348784	123348784	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123348784A>G			NA	NA				LINC01059 (17666 upstream) : GRAMD1B (47559 downstream)						NA		NA									NA						acaggcgtgaaccaccacacc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.123348784A>G		NA		hg19		0.02	-0.368343	TGAxCCA	COVERED																																																																																			NOVEL					0			10	3.308277	KEEP	0	0	0	11	301	AA	0.993072	0.893084	0			3	60	104	0	0	7.240046	36	60	1058	81		0.076923	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	123527627	123527627	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123527627C>G			NA	NA				SCN3B (2312 upstream) : RP11-634B22.4 (11579 downstream)						NA		NA									NA						ttgttgcccacgctggagtgc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.123527627C>G		NA		hg19		0.02	-0.33335	CCAxGCT	COVERED																																																																																			NOVEL					0			15	3.309865	KEEP	0	0	0	11	337	CC	0.993072	0.846082	0			4	60	127	0	0	9.057768	34	60	1138	66		0.105263	0.851984
RP11-634B22.4	0	__UNKNOWN__	__UNKNOWN__	11	123539693	123539693	__UNKNOWN__	lincRNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:123539693T>G	ENST00000532961.1	+	0	487										NA		NA									NA						ctgctgccattattgtaagtt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000532961.1:	chr11.hg19:g.123539693T>G		NA		hg19		0.02	-0.298207	CATxATT	COVERED																																																																																			NOVEL	RP11-634B22.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000387416.1	5	2.706886	KEEP	0	0	0	9	249	TT	0.99254	0.775233	0		+	3	60	107	0	0	7.766758	30	60	898	59	ENST00000532961.1	0.090909	0.78106
SLC37A2	219855	__UNKNOWN__	__UNKNOWN__	11	124957807	124957807	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:124957807T>C	ENST00000308074.4	+	19	1579				SLC37A2_ENST00000298280.5_Intron|SLC37A2_ENST00000403796.2_Intron	NM_198277.2	NP_938018.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	NA		NA			carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		ggattacaggtgtgagccacc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(11;373 620 21213 26083 47768)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955	219855		Solute carriers	20644	protein-coding gene	gene with protein product		NA	solute carrier family 37 (glycerol-3-phosphate transporter), member 2		NA		Standard	XM_166184	NM_198277	NA	Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000308074.4:c.1516-208T>C	chr11.hg19:g.124957807T>C		NA	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	hg19	CCDS31714.1	0.02	-0.429661	AGGxGTG	COVERED																																																																																			NOVEL	SLC37A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386840.1	7	3.592558	KEEP	1	0	0	12	300	TT	0.993634	0.953748	0		+	3	60	96	0	0	6.341797	39	60	1094	74	ENST00000308074.4	0.071429	0.959859
AP000708.1	0	__UNKNOWN__	__UNKNOWN__	11	125367266	125367266	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125367266A>G	ENST00000527818.1	+	0	1265										NA		NA									NA						agaccagcctaggcaacatag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000527818.1:c.*559A>G	chr11.hg19:g.125367266A>G		NA		hg19		0.02	1.774735	CCTxGGC	COVERED																																																																																			NOVEL	AP000708.1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000257496.3	18	3.138337	KEEP	4	1	30	21	558	AA	0.999869	0.997032	0		+	5	60	161	0	0	10.837681	60	60	1730	130	ENST00000527818.1	0.076923	0.997163
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	125394599	125394599	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125394599A>G			NA	NA				AP000708.1 (25175 upstream) : EI24 (44512 downstream)						NA		NA									NA						gtgaaactccatctcaaaaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.125394599A>G		NA		hg19		0.02	-0.420993	TCCxTCT	COVERED																																																																																			NOVEL					0			14	3.307975	KEEP	1	0	0	11	296	AA	0.992708	0.941486	0			3	60	100	0	1	6.617982	43	60	1287	86		0.065217	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	125437507	125437507	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125437507C>T			NA	NA				AP000708.1 (68083 upstream) : EI24 (1604 downstream)						NA		NA									NA						ggtgaaaccccgtctctacta	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.125437507C>T		NA		hg19		0.02	-0.140325	CCCxGTC	UNCOVERED																																																																																			NOVEL					0			8	2.404895	KEEP	5	0	0	8	212	CC	0	0	0			3	39	91	0	1	7.373088	11	60	344	34		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	125639142	125639142	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125639142A>G			NA	NA				PATE1 (19380 upstream) : PATE2 (6865 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.125639142A>G		NA		hg19		0.02	-0.306943	CACxCCT	COVERED																																																																																			NOVEL					0			4	2.405722	KEEP	1	0	0	8	219	AA	0.99257	0.7943	0			3	40	99	0	0	6.968232	30	60	874	75		0.090909	0.800245
RP11-680F20.5	0	__UNKNOWN__	__UNKNOWN__	11	125810683	125810683	__UNKNOWN__	lincRNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125810683T>A	ENST00000530834.1	+	0	148				RP11-680F20.4_ENST00000524467.1_lincRNA						NA		NA									NA						tttttgagactgagtctttct	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000530834.1:	chr11.hg19:g.125810683T>A		NA		hg19		0.02	2.58544	GACxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	T	0.798	-0.756504	0.03019	.	.	ENSG00000254790	ENST00000524467	.	.	.	0.235	-0.47	0.12131	.	.	.	.	.	T	0.43831	0.1265	.	.	.	.	.	.	.	.	.	.	.	.	T	0.50668	-0.8801	3	0.87932	D	0	.	.	.	.	.	.	.	.	L	23	.	ENSP00000434502:Q23L	Q	-	2	0	RP11-680F20.4	125315893	0.000000	0.05858	0.008000	0.14137	0.015000	0.08874	-0.168000	0.09925	-0.738000	0.04817	-0.736000	0.03550	CAG	NOVEL	RP11-680F20.5-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000386742.1	49	6.309854	KEEP	3	3	76	48	1324	TT	1	1	0		+	7	60	211	2	2	12.524818	127	60	3616	314	ENST00000530834.1	0.052239	1
RP11-680F20.6	0	__UNKNOWN__	__UNKNOWN__	11	125821763	125821763	__UNKNOWN__	RNA	SNP	C	C	T	rs12797894	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125821763C>T	ENST00000531193.1	+	0	77				RP11-680F20.6_ENST00000524962.2_RNA|RP11-680F20.6_ENST00000529072.1_RNA						NA		NA									NA						GGGACCAGTTCATCATGCTGA	0.657		NA											C|||	588	0.117412	0.0038	0.1571	5008	,	,	NA	17154	0.0714	NA	0.2087	False	NA	,,,	NA	NA	NA	2504	0.1963	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000531193.1:	chr11.hg19:g.125821763C>T		NA		hg19		0.02	0.977913	GTTxATC	COVERED																																																																																			NOVEL	RP11-680F20.6-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000386745.1	0	2.707486	KEEP	0	0	0	9	261	CC	0.99254	0.992435	0		+	19	60	504	0	0	39.025246	74	60	2373	114	ENST00000531193.1	0.204301	0.999895
CDON	50937	__UNKNOWN__	__UNKNOWN__	11	125851906	125851906	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125851906T>C	ENST00000392693.3	-	17	3123				CDON_ENST00000531738.1_Intron|CDON_ENST00000263577.7_Intron	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	NA		NA			anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		gagatggagtttcgctcttgt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309	50937		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	17104	protein-coding gene	gene with protein product	cell adhesion molecule-related/down-regulated by oncogenes	608707	Cdon homolog (mouse)		NA	9214393	Standard	NM_016952	NM_016952	NA	Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.2996-682A>G	chr11.hg19:g.125851906T>C		NA	O14631	hg19	CCDS58192.1	0.02	-0.192893	AGTxTCG	COVERED																																																																																			NOVEL	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386749.2	26	8.11951	KEEP	23	0	0	27	749	TT	0.994391	0.455189	0		-	3	60	92	0	0	6.895588	18	60	506	62	ENST00000392693.3	0.142857	0.457757
CDON	50937	__UNKNOWN__	__UNKNOWN__	11	125910453	125910453	__UNKNOWN__	Intron	SNP	A	A	G	rs542242932		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:125910453A>G	ENST00000392693.3	-	2	67				CDON_ENST00000263577.7_Intron	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	NA		NA			anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		gctcacgcctataatcccagc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309	50937		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	17104	protein-coding gene	gene with protein product	cell adhesion molecule-related/down-regulated by oncogenes	608707	Cdon homolog (mouse)		NA	9214393	Standard	NM_016952	NM_016952	NA	Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.61-17021T>C	chr11.hg19:g.125910453A>G		NA	O14631	hg19	CCDS58192.1	0.02	-0.280655	CCTxTAA	COVERED																																																																																			NOVEL	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386749.2	10	5.713352	KEEP	7	0	0	19	507	AA	0.999366	0.739203	0		-	4	60	139	0	0	10.693887	26	60	762	86	ENST00000392693.3	0.133333	0.739671
RP11-50B3.2	0	__UNKNOWN__	__UNKNOWN__	11	126038593	126038593	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:126038593G>A	ENST00000532357.1	+	0	132										NA		NA									NA						cctgacctcaggtgatccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000532357.1:	chr11.hg19:g.126038593G>A		NA		hg19		0.02	-0.412216	TCAxGTG	COVERED																																																																																			NOVEL	RP11-50B3.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000386334.1	12	3.309245	KEEP	1	0	0	11	329	GG	0.992708	0.934874	0		+	4	60	114	1	0	7.454306	41	60	1357	80	ENST00000532357.1	0.088889	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	126050333	126050333	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:126050333T>C			NA	NA				RP11-50B3.2 (4403 upstream) : RPUSD4 (21659 downstream)						NA		NA									NA						tttgggaggctgaggcaggcg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.126050333T>C		NA		hg19		0.02	-0.236805	GGCxGAG	COVERED																																																																																			NOVEL					0			7	2.406472	KEEP	0	0	0	8	228	TT	0.99257	0.607857	0			3	60	94	0	0	7.027682	19	60	570	49		0.136364	0.612407
FAM118B	79607	__UNKNOWN__	__UNKNOWN__	11	126103352	126103352	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:126103352G>C	ENST00000533050.1	+	3	486				FAM118B_ENST00000360194.4_Intron|FAM118B_ENST00000529731.1_Intron|FAM118B_ENST00000525728.1_Intron	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	NA		NA								breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00948)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		tgcactccaggctgggcaaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798	79607			26110	protein-coding gene	gene with protein product		NA			NA	24569877	Standard	NM_024556	NM_024556	NA	Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.-7-1538G>C	chr11.hg19:g.126103352G>C		NA	Q9H7B0	hg19	CCDS8470.1	0.02	-0.131583	CAGxCTG	COVERED																																																																																			NOVEL	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386346.1	3	3.309652	KEEP	0	0	0	11	335	GG	0.993072	0.227586	0		+	3	60	104	0	0	8.781818	10	60	332	40	ENST00000533050.1	0.230769	0.229173
KIRREL3	84623	__UNKNOWN__	__UNKNOWN__	11	126325421	126325421	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:126325421T>C	ENST00000525144.2	-	7	1098				KIRREL3_ENST00000525704.2_Intron|KIRREL3_ENST00000529097.2_Intron	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	NA		NA			hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		cggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571	84623		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	23204	protein-coding gene	gene with protein product		607761			NA	12424224, 11347906	Standard	NM_032531	NM_032531	NA	Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.848+822A>G	chr11.hg19:g.126325421T>C		NA	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	hg19	CCDS53723.1	0.02	-0.35083	TCAxGCC	COVERED																																																																																			NOVEL	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386479.2	10	4.210668	KEEP	3	0	0	14	385	TT	0.994391	0.872784	0		-	3	60	101	0	0	7.011767	34	60	1014	91	ENST00000525144.2	0.081081	0.877708
ETS1	2113	__UNKNOWN__	__UNKNOWN__	11	128329990	128329990	__UNKNOWN__	3'UTR	SNP	C	C	A	rs369942096|rs577176917		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:128329990C>A	ENST00000392668.4	-	0	3808				ETS1_ENST00000345075.4_3'UTR|ETS1_ENST00000535549.1_3'UTR	NM_001143820.1	NP_001137292.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	NA		NA			angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		cacacacacacacacacacac	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954	2113			3488	protein-coding gene	gene with protein product	Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1, ets protein	164720		EWSR2	NA	1522903	Standard	NM_005238	NM_005238	NA	Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000392668.4:c.*2266G>T	chr11.hg19:g.128329990C>A		NA	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	hg19	CCDS44767.1	0.02	1.584294	ACAxACA	COVERED																																																																																			NOVEL	ETS1-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386267.2	9	7.821738	KEEP	0	0	0	26	759	CC	0.999957	0.996681	0		-	6	60	182	0	1	12.464246	57	70	1884	111	ENST00000392668.4	0.095238	0.996724
KCNJ1	3758	__UNKNOWN__	__UNKNOWN__	11	128709833	128709833	__UNKNOWN__	Nonsense_Mutation	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:128709833A>T	ENST00000392665.2	-	2	450	c.306T>A	c.(304-306)tgT>tgA	p.C102*	KCNJ1_ENST00000392664.2_Nonsense_Mutation_p.C121*|KCNJ1_ENST00000392666.1_Nonsense_Mutation_p.C102*|KCNJ1_ENST00000324036.3_Nonsense_Mutation_p.C102*|KCNJ1_ENST00000440599.2_Nonsense_Mutation_p.C102*	NM_153764.2	NP_722448.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	121		NA			cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	TATTCTCCACACAGGGAGTGT	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													87	86	86			NA	NA	11		NA											NA				128709833		2201	4297	6498	SO:0001587	stop_gained			BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704	3758		Potassium channels, Voltage-gated ion channels / Potassium channels, Inwardly rectifying	6255	protein-coding gene	gene with protein product		600359			NA	7680431, 8190102, 16382105	Standard	NM_000220	NM_153765	NA	Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392665.2:c.306T>A	chr11.hg19:g.128709833A>T	ENSP00000376433:p.Cys102*	NA	B2RMR4|Q6LD67	hg19	CCDS8477.1	0.02	4.847379	CACxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	A	38	6.688506	0.97764	.	.	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664;ENST00000324003	.	.	.	6.03	-4.48	0.03515	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4381	0.83884	0.4314:0.0:0.5686:0.0	.	.	.	.	X	102;102;102;102;121;102	.	ENSP00000316136:C102X	C	-	3	2	KCNJ1	128215043	0.702000	0.27816	0.814000	0.32528	0.828000	0.46876	0.059000	0.14322	-0.887000	0.03961	0.455000	0.32223	TGT	NOVEL	KCNJ1-005	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386231.1	4	4.208145	KEEP	0	0	0	14	374	AA	0.995343	0.995343	0		-	24	60	712	0	0	54.100198	125	60	3712	234	ENST00000392665.2	0.161074	1
BARX2	8538	__UNKNOWN__	__UNKNOWN__	11	129292327	129292327	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:129292327A>G	ENST00000281437.4	+	2	283					NM_003658.4	NP_003649.2	Q9UMQ3	BARX2_HUMAN	BARX homeobox 2	NA		NA			cartilage condensation (GO:0001502)|catagen (GO:0042637)|myotube differentiation (GO:0014902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	20	all_hematologic(175;0.0749)	Lung NSC(97;0.000383)|all_lung(97;0.000824)|Breast(109;0.000962)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.00929)|Lung(977;0.0245)|LUSC - Lung squamous cell carcinoma(976;0.0253)		ccaagtagctaggactacagg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF031924	CCDS8481.1	11q24.3	2011-06-20	2007-07-09		ENSG00000043039	ENSG00000043039	8538		Homeoboxes / ANTP class : NKL subclass	956	protein-coding gene	gene with protein product		604823	BarH-like homeobox 2		NA	10644443	Standard	NM_003658	NM_003658	NA	Approved		uc001qfc.4	Q9UMQ3	OTTHUMG00000165776	ENST00000281437.4:c.188-14319A>G	chr11.hg19:g.129292327A>G		NA	O43518|Q6NT51	hg19	CCDS8481.1	0.02	-0.289443	GCTxGGA	COVERED																																																																																			NOVEL	BARX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386153.1	15	3.30774	KEEP	1	0	0	11	293	AA	0.992708	0.755338	0		+	5	60	167	0	0	13.381252	23	60	695	52	ENST00000281437.4	0.178571	0.760887
TMEM45B	120224	__UNKNOWN__	__UNKNOWN__	11	129686925	129686925	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:129686925A>G	ENST00000281441.3	+	1	80				TMEM45B_ENST00000525709.1_Intron	NM_138788.3	NP_620143.1	Q96B21	TM45B_HUMAN	transmembrane protein 45B	NA		NA				integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		acaggcgtgaaccaccgcgcc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715	120224			25194	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_138788	NM_138788	NA	Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000281441.3:c.-9+1132A>G	chr11.hg19:g.129686925A>G		NA	A8K2L8	hg19	CCDS8482.1	0.02	-0.333269	TGAxCCA	UNCOVERED																																																																																			NOVEL	TMEM45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386058.1	10	3.00676	KEEP	7	0	0	10	264	AA	0	0	0		+	3	60	104	0	0	7.467193	30	60	880	82	ENST00000281441.3	0.090909	0.851984
PRDM10	56980	__UNKNOWN__	__UNKNOWN__	11	129786313	129786313	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:129786313C>T	ENST00000360871.3	-	16	2557				PRDM10_ENST00000358825.5_Intron|PRDM10_ENST00000304538.6_Intron|PRDM10_ENST00000526082.1_Intron|PRDM10_ENST00000528746.1_Intron|PRDM10_ENST00000423662.2_Intron	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		gaggccgaggcgggcgatcac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325	56980		Zinc fingers, C2H2-type	13995	protein-coding gene	gene with protein product	PRDM zinc finger transcription factor, PR-domain family member 7, tristanin	NA			NA	12175877	Standard	NM_199437	NM_020228	NA	Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2326-558G>A	chr11.hg19:g.129786313C>T		NA	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	hg19	CCDS8484.1	0.02	-0.254379	AGGxGGG	COVERED																																																																																			NOVEL	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000386076.1	6	3.911243	KEEP	0	0	0	13	389	CC	0.994391	0.664773	0		-	3	60	92	0	2	6.595288	23	60	756	70	ENST00000360871.3	0.115385	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	129883465	129883465	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:129883465A>G			NA	NA				LINC00167 (9214 upstream) : AP003041.2 (53370 downstream)						NA		NA									NA						ggccaggtgcagtggctcatg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.129883465A>G		NA		hg19		0.02	-0.26312	TGCxGTG	COVERED																																																																																			NOVEL					0			10	3.607366	KEEP	0	0	0	12	324	AA	0.993634	0.689252	0			3	60	95	1	0	7.006034	21	60	628	55		0.125	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	11	129929137	129929137	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:129929137T>C			NA	NA				LINC00167 (54886 upstream) : AP003041.2 (7698 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr11.hg19:g.129929137T>C		NA		hg19		0.02	-0.192824	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			7	2.404279	KEEP	2	0	0	8	208	TT	0	0	0			3	60	97	0	0	7.693127	14	60	371	44		0.176471	0.457757
RP11-121M22.1	0	__UNKNOWN__	__UNKNOWN__	11	130214491	130214491	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:130214491T>C	ENST00000532116.3	+	0	343										NA		NA									NA						gattgcgccattgcactccag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000532116.3:	chr11.hg19:g.130214491T>C		NA		hg19		0.02	-0.368334	CCAxTGC	UNCOVERED																																																																																			NOVEL	RP11-121M22.1-004	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000468111.1	7	2.40531	KEEP	2	0	0	8	209	TT	0	0	0		+	3	48	99	0	0	6.776379	35	60	1016	74	ENST00000532116.3	0.078947	0.899314
OPCML	4978	__UNKNOWN__	__UNKNOWN__	11	132489506	132489506	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:132489506A>G	ENST00000331898.7	-	2	979				OPCML_ENST00000529038.1_Intron|OPCML_ENST00000524381.1_Intron|OPCML_ENST00000541867.1_Intron|OPCML_ENST00000374778.4_Intron	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	NA		NA			cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		aggccgaggcagacggatcac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715	4978		Immunoglobulin superfamily / I-set domain containing	8143	protein-coding gene	gene with protein product	IgLON family member 1	600632	opioid-binding protein/cell adhesion molecule-like		NA	8244387	Standard	NM_001012393	XM_005271578	NA	Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.400+37475T>C	chr11.hg19:g.132489506A>G		NA	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	hg19	CCDS8492.1	0.02	-0.236781	GGCxGAC	COVERED																																																																																			NOVEL	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374689.3	10	3.007809	KEEP	1	0	0	10	278	AA	0.992708	0.607941	0		-	3	52	100	0	0	7.505813	21	60	612	57	ENST00000331898.7	0.125	0.612407
OPCML	4978	__UNKNOWN__	__UNKNOWN__	11	132489508	132489508	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:132489508A>G	ENST00000331898.7	-	2	979				OPCML_ENST00000529038.1_Intron|OPCML_ENST00000524381.1_Intron|OPCML_ENST00000541867.1_Intron|OPCML_ENST00000374778.4_Intron	NM_002545.3	NP_002536.1	Q14982	OPCM_HUMAN	opioid binding protein/cell adhesion molecule-like	NA		NA			cell adhesion (GO:0007155)|neuron recognition (GO:0008038)|opioid receptor signaling pathway (GO:0038003)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	opioid receptor activity (GO:0004985)			endometrium(5)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|skin(2)|urinary_tract(8)	47	all_hematologic(175;0.019)	all_cancers(12;5.86e-24)|all_epithelial(12;2.65e-17)|all_lung(97;2.89e-05)|Lung NSC(97;6.16e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0269)|all_neural(223;0.0326)|Esophageal squamous(93;0.129)		all cancers(11;4.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.012)		gccgaggcagacggatcacga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX537377	CCDS8492.1, CCDS31722.1	11q25	2013-01-11	2001-11-28		ENSG00000183715	ENSG00000183715	4978		Immunoglobulin superfamily / I-set domain containing	8143	protein-coding gene	gene with protein product	IgLON family member 1	600632	opioid-binding protein/cell adhesion molecule-like		NA	8244387	Standard	NM_001012393	XM_005271578	NA	Approved	OPCM, OBCAM, IGLON1	uc001qgs.3	Q14982	OTTHUMG00000163658	ENST00000331898.7:c.400+37473T>C	chr11.hg19:g.132489508A>G		NA	B2CZX2|B7ZLQ1|Q17RN7|Q7Z3W6	hg19	CCDS8492.1	0.02	-0.245488	CAGxCGG	COVERED																																																																																			NOVEL	OPCML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000374689.3	10	3.007131	KEEP	1	0	0	10	269	AA	0.992708	0.63667	0		-	3	52	102	0	0	7.706164	21	60	594	57	ENST00000331898.7	0.125	0.641347
JAM3	83700	__UNKNOWN__	__UNKNOWN__	11	133997332	133997332	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:133997332A>G	ENST00000441717.3	+	2	89				JAM3_ENST00000529443.2_Intron|JAM3_ENST00000524969.1_Intron|JAM3_ENST00000299106.4_Intron	NM_001205329.1	NP_001192258.1	Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	NA		NA			adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		ggtggctcacacctgtaatcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086	83700		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	15532	protein-coding gene	gene with protein product		606871			NA		Standard	NM_032801	NM_032801	NA	Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000441717.3:c.77-12414A>G	chr11.hg19:g.133997332A>G		NA	B3KWG9|Q8WWL8|Q96FL1	hg19	CCDS55799.1	0.02	-0.289442	CACxCCT	UNCOVERED																																																																																			NOVEL	JAM3-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393304.3	9	2.40614	KEEP	1	0	0	8	221	AA	0	0	0		+	3	60	107	0	0	7.897131	27	60	814	68	ENST00000441717.3	0.1	0.78106
GLB1L3	112937	__UNKNOWN__	__UNKNOWN__	11	134178111	134178111	__UNKNOWN__	Intron	SNP	T	T	C	rs62636435		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr11:134178111T>C	ENST00000431683.2	+	10	961					NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	NA		NA			carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		accaccaccatcaccatcacc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105	112937			25147	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_138416	NM_001080407	NA	Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.961+1009T>C	chr11.hg19:g.134178111T>C		NA	A6NEM0|A6NN15|Q6P3S3|Q96FF8	hg19	CCDS44780.1	0.02	-0.122217	CCAxCAC	COVERED																																																																																			NOVEL	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000393625.1	9	2.405172	KEEP	1	0	0	8	208	TT	0.99257	0.194853	0		+	3	60	99	1	0	8.690671	7	60	167	32	ENST00000431683.2	0.3	0.196312
IQSEC3	440073	__UNKNOWN__	__UNKNOWN__	12	254269	254269	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:254269A>G	ENST00000538872.1	+	5	2271				RP11-598F7.4_ENST00000508953.2_RNA|RP11-598F7.4_ENST00000505893.2_RNA|IQSEC3_ENST00000382841.2_Intron|IQSEC3_ENST00000326261.4_Intron			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	NA		NA			actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		aaaatgctggaattacaggca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645	440073			29193	protein-coding gene	gene with protein product		612118			NA	10470851	Standard	XM_495902	NM_001170738	NA	Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2153+3818A>G	chr12.hg19:g.254269A>G		NA	A6NIF2|A6NKV9|Q8TB43	hg19	CCDS53728.1	0.02	-0.219242	TGGxATT	COVERED																																																																																			NOVEL	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397382.3	3	3.00729	KEEP	0	0	0	10	271	AA	0.992708	0.548856	0		+	3	60	95	0	1	7.066041	20	60	573	47	ENST00000538872.1	0.130435	0.552887
KDM5A	5927	__UNKNOWN__	__UNKNOWN__	12	442336	442336	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:442336A>G	ENST00000399788.2	-	12	2016				KDM5A_ENST00000382815.4_Intron	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	NA		NA			chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						tgtaatcccaacactttggga	0.408		NA	T	NUP98	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		12	12p11	5927	lysine (K)-specific demethylase 5A, JARID1A		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614	5927		Chromatin-modifying enzymes / K-demethylases, Zinc fingers, PHD-type	9886	protein-coding gene	gene with protein product		180202	retinoblastoma-binding protein 2, Jumonji, AT rich interactive domain 1A (RBBP2-like), jumonji, AT rich interactive domain 1A	RBBP2, JARID1A	NA	1857421	Standard	NM_005056	NM_001042603	NA	Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.1653+316T>C	chr12.hg19:g.442336A>G		NA	A8MV76|Q4LE72|Q86XZ1	hg19	CCDS41736.1	0.02	-0.227992	CCAxCAC	COVERED																																																																																			NOVEL	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397812.1	10	2.406696	KEEP	0	0	0	8	233	AA	0.99257	0.578599	0		-	3	60	98	0	0	7.249406	22	60	638	46	ENST00000399788.2	0.12	0.58293
KDM5A	5927	__UNKNOWN__	__UNKNOWN__	12	442551	442551	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:442551C>T	ENST00000399788.2	-	12	2016				KDM5A_ENST00000382815.4_Intron	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	NA		NA			chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						tgccgctgcactccagcctgg	0.468		NA	T	NUP98	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		12	12p11	5927	lysine (K)-specific demethylase 5A, JARID1A		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614	5927		Chromatin-modifying enzymes / K-demethylases, Zinc fingers, PHD-type	9886	protein-coding gene	gene with protein product		180202	retinoblastoma-binding protein 2, Jumonji, AT rich interactive domain 1A (RBBP2-like), jumonji, AT rich interactive domain 1A	RBBP2, JARID1A	NA	1857421	Standard	NM_005056	NM_001042603	NA	Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.1653+101G>A	chr12.hg19:g.442551C>T		NA	A8MV76|Q4LE72|Q86XZ1	hg19	CCDS41736.1	0.02	1.313454	GCAxTCC	COVERED																																																																																			NOVEL	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397812.1	9	6.947778	KEEP	1	1	25	32	886	CC	0.999998	0.99442	0		-	5	60	139	0	0	9.023125	50	60	1616	112	ENST00000399788.2	0.090909	0.994422
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	823647	823647	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:823647G>A			NA	NA				RP11-218M22.2 (30354 upstream) : WNK1 (38111 downstream)						NA		NA									NA						aaaaaaaaaagaaaaaTACTT	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.823647G>A		NA		hg19		0.02	-0.271907	AAAxAAA	COVERED																																																																																			NOVEL					0			15	5.104732	KEEP	0	0	0	17	486	GG	0.999366	0.716861	0			4	60	120	0	0	8.991974	23	60	744	69		0.148148	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	852393	852393	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:852393A>G			NA	NA				RP11-218M22.2 (59100 upstream) : WNK1 (9365 downstream)						NA		NA									NA						actttgggagaccaagttggg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.852393A>G		NA		hg19		0.02	-0.201594	GAGxCCA	COVERED																																																																																			NOVEL					0			5	2.406156	KEEP	0	0	0	8	222	AA	0.99257	0.4869	0			3	60	106	0	0	8.293034	18	60	510	48		0.142857	0.490544
WNK1	65125	__UNKNOWN__	__UNKNOWN__	12	875982	875982	__UNKNOWN__	Intron	SNP	G	G	A	rs564666281		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:875982G>A	ENST00000315939.6	+	1	1402				WNK1_ENST00000530271.2_Intron|WNK1_ENST00000537687.1_Intron|WNK1_ENST00000447667.2_Intron|WNK1_ENST00000535572.1_Intron	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	NA		NA			intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			ttgctctgtcgcccaggctgg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(19;451 567 6672 12618 28860)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237	65125			14540	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 167	605232	protein kinase, lysine deficient 1, hereditary sensory neuropathy, type II	PRKWNK1, HSN2	NA		Standard	NM_018979	NM_001184985	NA	Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.759+12492G>A	chr12.hg19:g.875982G>A		NA	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	hg19	CCDS8506.1	0.02	-0.245595	GTCxCCC	COVERED																																																																																			NOVEL	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206683.1	9	5.71453	KEEP	2	0	0	19	545	GG	0.999859	0.641257	0		+	4	60	111	0	0	8.314765	20	60	647	66	ENST00000315939.6	0.166667	0.641347
WNK1	65125	__UNKNOWN__	__UNKNOWN__	12	879429	879429	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:879429T>C	ENST00000315939.6	+	1	1402				WNK1_ENST00000530271.2_Intron|WNK1_ENST00000537687.1_Intron|WNK1_ENST00000447667.2_Intron|WNK1_ENST00000535572.1_Intron	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	NA		NA			intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			cgtgagccactgcgcccggcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(19;451 567 6672 12618 28860)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237	65125			14540	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 167	605232	protein kinase, lysine deficient 1, hereditary sensory neuropathy, type II	PRKWNK1, HSN2	NA		Standard	NM_018979	NM_001184985	NA	Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.759+15939T>C	chr12.hg19:g.879429T>C		NA	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	hg19	CCDS8506.1	0.02	-0.175432	CACxGCG	COVERED																																																																																			NOVEL	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206683.1	8	3.008117	KEEP	2	0	0	10	284	TT	0.99257	0.384528	0		+	3	60	98	0	0	7.791665	14	60	433	45	ENST00000315939.6	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	1653946	1653946	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:1653946T>C			NA	NA				LINC00942 (37462 upstream) : FBXL14 (21212 downstream)						NA		NA									NA						tttgggaggctgaggcgggcg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.1653946T>C		NA		hg19		0.02	-0.175396	GGCxGAG	COVERED																																																																																			NOVEL					0			6	3.007617	KEEP	0	0	0	10	274	TT	0.993072	0.384723	0			3	60	99	0	0	7.733564	16	60	475	44		0.157895	0.387407
WNT5B	81029	__UNKNOWN__	__UNKNOWN__	12	1741858	1741858	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:1741858A>T	ENST00000542408.1	+	2	155	c.115A>T	c.(115-117)Atg>Ttg	p.M39L	WNT5B_ENST00000537031.1_Missense_Mutation_p.M39L|WNT5B_ENST00000397196.2_Missense_Mutation_p.M39L|WNT5B_ENST00000310594.3_Missense_Mutation_p.M39L			Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family, member 5B	39		NA			cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fat cell differentiation (GO:0045444)|lens fiber cell development (GO:0070307)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor binding (GO:0005102)			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			GAGACCCGAGATGTTTATCAT	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													117	122	120			NA	NA	12		NA											NA				1741858		2203	4300	6503	SO:0001583	missense			AB060966	CCDS8510.1	12p13.3	2008-07-07			ENSG00000111186	ENSG00000111186	81029		Wingless-type MMTV integration sites	16265	protein-coding gene	gene with protein product		606361			NA	11445850	Standard		NM_030775	NA	Approved		uc001qjk.3	Q9H1J7	OTTHUMG00000090375	ENST00000542408.1:c.115A>T	chr12.hg19:g.1741858A>T	ENSP00000440600:p.Met39Leu	NA	A8K315|D3DUP9|Q96S49|Q9BV04	hg19		0.02	1.114221	GAGxTGT	COVERED	.	.	.	.	.	.	.	.	.	.	A	11.48	1.651508	0.29336	.	.	ENSG00000111186	ENST00000539198;ENST00000545811;ENST00000537031;ENST00000310594;ENST00000397196;ENST00000543071;ENST00000542408	T;D;T;T;T;D;T	0.87029	-0.97;-1.67;-0.88;-0.88;-0.88;-2.2;0.03	5.31	-0.355	0.12587	.	2.541260	0.01781	N	0.031781	T	0.76097	0.3940	N	0.20401	0.57	0.43569	D	0.995894	B	0.02656	0.0	B	0.04013	0.001	T	0.61168	-0.7117	10	0.10111	T	0.7	.	6.116	0.20127	0.6103:0.2522:0.1375:0.0	.	39	Q9H1J7	WNT5B_HUMAN	L	39	ENSP00000438414:M39L;ENSP00000445395:M39L;ENSP00000439312:M39L;ENSP00000308887:M39L;ENSP00000380379:M39L;ENSP00000442348:M39L;ENSP00000440600:M39L	ENSP00000308887:M39L	M	+	1	0	WNT5B	1612119	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	2.071000	0.41500	0.000000	0.14550	0.460000	0.39030	ATG	NOVEL	WNT5B-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000397943.1	2	5.112298	KEEP	0	0	0	17	460	AA	0.999366	0.999329	0		+	32	60	886	0	0	76.809172	67	60	1974	163	ENST00000542408.1	0.323232	0.999962
WNT5B	81029	__UNKNOWN__	__UNKNOWN__	12	1752560	1752560	__UNKNOWN__	Intron	SNP	C	C	T	rs11061892	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:1752560C>T	ENST00000542408.1	+	3	368				WNT5B_ENST00000537031.1_Intron|WNT5B_ENST00000397196.2_Intron|WNT5B_ENST00000310594.3_Intron			Q9H1J7	WNT5B_HUMAN	wingless-type MMTV integration site family, member 5B	NA		NA			cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fat cell differentiation (GO:0045444)|lens fiber cell development (GO:0070307)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of fat cell differentiation (GO:0045600)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor binding (GO:0005102)			skin(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00109)			gacggagtttcgctcttgttg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB060966	CCDS8510.1	12p13.3	2008-07-07			ENSG00000111186	ENSG00000111186	81029		Wingless-type MMTV integration sites	16265	protein-coding gene	gene with protein product		606361			NA	11445850	Standard		NM_030775	NA	Approved		uc001qjk.3	Q9H1J7	OTTHUMG00000090375	ENST00000542408.1:c.329-2400C>T	chr12.hg19:g.1752560C>T		NA	A8K315|D3DUP9|Q96S49|Q9BV04	hg19		0.02	-0.359628	TTTxGCT	COVERED																																																																																			NOVEL	WNT5B-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000397943.1	11	5.41462	KEEP	2	0	0	18	520	CC	0.999366	0.888312	0		+	4	60	104	1	0	6.815532	33	60	1107	90	ENST00000542408.1	0.108108	0.888875
ADIPOR2	79602	__UNKNOWN__	__UNKNOWN__	12	1861374	1861374	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:1861374C>T	ENST00000357103.4	+	2	165					NM_024551.2	NP_078827.2	Q86V24	ADR2_HUMAN	adiponectin receptor 2	NA		NA			adiponectin-activated signaling pathway (GO:0033211)|fatty acid oxidation (GO:0019395)|female pregnancy (GO:0007565)|heart development (GO:0007507)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of cell growth (GO:0030308)|positive regulation of glucose import (GO:0046326)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(3)|lung(7)|stomach(1)	12	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000382)			ggattacaggcgtgagccact	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY424280	CCDS8511.1	12p13	2012-08-22			ENSG00000006831	ENSG00000006831	79602		GPCR / Unclassified : Adiponectin receptors	24041	protein-coding gene	gene with protein product		607946			NA	12802337	Standard	NM_024551	NM_024551	NA	Approved	PAQR2, ACDCR2	uc001qjm.3	Q86V24	OTTHUMG00000130139	ENST00000357103.4:c.-86-2050C>T	chr12.hg19:g.1861374C>T		NA	Q53YY5|Q9H737	hg19	CCDS8511.1	0.02	-0.157887	AGGxGTG	COVERED																																																																																			NOVEL	ADIPOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252447.2	18	3.007242	KEEP	3	0	0	10	278	CC	0.99254	0.320398	0		+	4	43	113	0	0	9.723274	9	60	301	39	ENST00000357103.4	0.307692	0.322807
CACNA2D4	93589	__UNKNOWN__	__UNKNOWN__	12	1919543	1919543	__UNKNOWN__	Intron	SNP	C	C	T	rs2286377	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:1919543C>T	ENST00000382722.5	-	29	3021				CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000586184.1_Intron|CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000538450.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000538027.2_Intron	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	NA		NA			calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		ATGCCAGGGCCCTCACCCACC	0.612		NA											C|||	2315	0.46226	0.23	0.4452	5008	,	,	NA	19800	0.5714	NA	0.6123	False	NA	,,,	NA	NA	NA	2504	0.5215	NA	NA	NA	Colon(2;101 179 21030 23310 28141)							NA				0								C		1267,2761		221,825,968	26	31	30			0.2	0	12	dbSNP_100	30	5259,3091		1680,1899,596	no	intron	CACNA2D4	NM_172364.4		1901,2724,1564	TT,TC,CC	NA	37.018,31.4548,47.2774			1919543	6526,5852	2014	4175	6189	SO:0001627	intron_variant			AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062	93589		Calcium channel subunits	20202	protein-coding gene	gene with protein product		608171			NA	12181424	Standard		NM_172364	NA	Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2659-37G>A	chr12.hg19:g.1919543C>T		NA	Q7Z3S8|Q86XZ5|Q8IZS9	hg19	CCDS44785.1	0.02	-0.359608	GGCxCTC	COVERED																																																																																			NOVEL	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398230.2	1	3.008649	KEEP	0	0	0	10	297	CC	0.992708	0.882393	0		-	28	60	841	0	0	86.84017	12	60	387	62	ENST00000382722.5	0.7	0.888875
CACNA2D4	93589	__UNKNOWN__	__UNKNOWN__	12	1976018	1976018	__UNKNOWN__	Intron	SNP	C	C	T	rs571657546	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:1976018C>T	ENST00000382722.5	-	19	2241				CACNA2D4_ENST00000587995.1_Intron|CACNA2D4_ENST00000585708.1_Intron|CACNA2D4_ENST00000588077.1_Intron|CACNA2D4_ENST00000585732.1_Intron|CACNA2D4_ENST00000539048.2_Intron|CACNA2D4_ENST00000586184.1_Intron	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	NA		NA			calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		aggctggtcacgaactcctgg	0.488		NA											C|||	6	0.00119808	0.0	0.0014	5008	,	,	NA	14676	0.0	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Colon(2;101 179 21030 23310 28141)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062	93589		Calcium channel subunits	20202	protein-coding gene	gene with protein product		608171			NA	12181424	Standard		NM_172364	NA	Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1879-6646G>A	chr12.hg19:g.1976018C>T		NA	Q7Z3S8|Q86XZ5|Q8IZS9	hg19	CCDS44785.1	0.02	-0.280693	TCAxGAA	COVERED																																																																																			NOVEL	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398230.2	12	3.608905	KEEP	0	0	0	12	335	CC	0.993634	0.734962	0		-	3	60	88	0	0	6.427805	19	60	612	66	ENST00000382722.5	0.136364	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	2125865	2125865	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:2125865A>G			NA	NA				RP5-1096D14.6 (5307 upstream) : CACNA1C-IT1 (1513 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.2125865A>G		NA		hg19		0.02	-0.149098	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			5	2.406051	KEEP	1	0	0	8	220	AA	0	0	0			3	60	95	0	0	7.672615	12	60	362	37		0.2	0.292001
FKBP4	2288	__UNKNOWN__	__UNKNOWN__	12	2910798	2910798	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:2910798C>T	ENST00000001008.4	+	9	1459				RP4-816N1.7_ENST00000547042.1_RNA|RP4-816N1.6_ENST00000547834.1_RNA	NM_002014.3	NP_002005.1	Q02790	FKBP4_HUMAN	FK506 binding protein 4, 59kDa	NA		NA			androgen receptor signaling pathway (GO:0030521)|chaperone-mediated protein folding (GO:0061077)|copper ion transport (GO:0006825)|embryo implantation (GO:0007566)|male sex differentiation (GO:0046661)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)|negative regulation of neuron projection development (GO:0010977)|prostate gland development (GO:0030850)|protein complex localization (GO:0031503)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|steroid hormone receptor complex assembly (GO:0006463)	axonal growth cone (GO:0044295)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|FK506 binding (GO:0005528)|GTP binding (GO:0005525)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(1)	14			OV - Ovarian serous cystadenocarcinoma(31;0.00105)			ctcacacctgcaatcccagca	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M88279	CCDS8512.1	12p13.33	2013-01-10	2002-08-29		ENSG00000004478	ENSG00000004478	2288		Tetratricopeptide (TTC) repeat domain containing	3720	protein-coding gene	gene with protein product		600611	FK506-binding protein 4 (59kD)		NA	1279700	Standard		NM_002014	NA	Approved	FKBP59, FKBP52	uc001qkz.3	Q02790	OTTHUMG00000090429	ENST00000001008.4:c.1272+276C>T	chr12.hg19:g.2910798C>T		NA	D3DUQ1|Q9UCP1|Q9UCV7	hg19	CCDS8512.1	0.02	1.109352	CTGxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	4.083	0.013379	0.07912	.	.	ENSG00000004478	ENST00000539181	.	.	.	0.699	-0.956	0.10353	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	X	67	.	.	Q	+	1	0	FKBP4	2781059	.	.	0.001000	0.08648	0.003000	0.03518	.	.	-0.414000	0.07495	-0.339000	0.08088	CAA	NOVEL	FKBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206861.1	5	6.684244	KEEP	0	2	53	41	1206	CC	1	0.998993	0		+	6	60	162	0	0	10.18571	64	60	2134	144	ENST00000001008.4	0.085714	0.998993
AC005841.1	0	__UNKNOWN__	__UNKNOWN__	12	2960107	2960107	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:2960107A>G	ENST00000382678.3	-	3	644										NA		NA									NA						caaagtgctgagattacaagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000382678.3:c.645-1416T>C	chr12.hg19:g.2960107A>G		NA		hg19		0.02	-0.087704	CTGxGAT	UNCOVERED																																																																																			NOVEL	AC005841.1-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		5	2.404823	KEEP	0	0	0	8	212	AA	0.99257	0.09898	0		-	3	60	98	0	0	8.932903	5	60	155	27	ENST00000382678.3	0.375	0.099721
TULP3	7289	__UNKNOWN__	__UNKNOWN__	12	3022529	3022529	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:3022529C>T	ENST00000397132.2	+	2	134				TULP3_ENST00000448120.2_Intron	NM_001160408.1	NP_001153880.1	O75386	TULP3_HUMAN	tubby like protein 3	NA		NA			anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			tcctcccaccccagcctccca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246	7289		Intraflagellar transport homologs	12425	protein-coding gene	gene with protein product		604730			NA	9828123	Standard	NM_003324	NM_003324	NA	Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000397132.2:c.93+3783C>T	chr12.hg19:g.3022529C>T		NA	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	hg19	CCDS53737.1	0.02	-0.192962	ACCxCAG	COVERED																																																																																			NOVEL	TULP3-004	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398469.1	9	3.910211	KEEP	0	0	0	13	381	CC	0.994391	0.455189	0		+	3	60	90	0	0	6.692769	18	60	571	45	ENST00000397132.2	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	3168471	3168471	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:3168471G>A			NA	NA				RP11-253E3.3 (14355 upstream) : TSPAN9 (18049 downstream)						NA		NA									NA						cgccatctcggctcactgcaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.3168471G>A		NA		hg19		0.02	-0.096487	TCGxCTC	UNCOVERED																																																																																			NOVEL					0			3	2.406759	KEEP	2	0	0	8	233	GG	0	0	0			3	40	83	0	0	7.078113	7	60	238	20		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	3176022	3176022	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:3176022T>C			NA	NA				RP11-253E3.3 (21906 upstream) : TSPAN9 (10498 downstream)						NA		NA									NA						aggatggtcttgatctcctga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.3176022T>C		NA		hg19		0.02	-0.122792	TCTxGAT	UNCOVERED																																																																																			NOVEL					0			12	2.405969	KEEP	15	0	0	8	219	TT	0	0	0			3	40	92	0	0	7.582095	10	60	295	52		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	3449828	3449828	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:3449828A>G			NA	NA				RP5-1063M23.2 (15319 upstream) : RP11-476M19.2 (27170 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.3449828A>G		NA		hg19		0.02	-0.210505	GGCxTGA	COVERED																																																																																			NOVEL					0			6	3.308217	KEEP	3	0	0	11	300	AA	0.99254	0.518266	0			3	60	100	0	0	7.760815	17	60	509	54		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	4477327	4477327	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:4477327A>G			NA	NA				C12orf5 (14989 upstream) : FGF23 (65 downstream)						NA		NA									NA						gtgacagagcaagactccatc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.4477327A>G		NA		hg19		0.02	-0.411407	AGCxAGA	COVERED																																																																																			NOVEL					0			11	4.811336	KEEP	4	0	0	16	433	AA	0.997832	0.946346	0			3	40	102	1	0	7.043564	36	60	1017	102		0.076923	0.948402
AKAP3	10566	__UNKNOWN__	__UNKNOWN__	12	4749234	4749234	__UNKNOWN__	Intron	SNP	G	G	A	rs540205224		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:4749234G>A	ENST00000545990.2	-	3	525				RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Intron	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	NA		NA			acrosome reaction (GO:0007340)|cellular component movement (GO:0006928)|protein localization (GO:0008104)|single fertilization (GO:0007338)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	acrosomal vesicle (GO:0001669)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	protein kinase A binding (GO:0051018)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|liver(1)|lung(17)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	51						cacccgcctcggcctcccaaa	0.502		NA											g|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15917	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U85715	CCDS8531.1	12p13.3	2009-03-12				ENSG00000111254	10566		A-kinase anchor proteins	373	protein-coding gene	gene with protein product	Fibrous Sheath Protein of 95 kDa, cancer/testis antigen 82	604689			NA	10334916, 10319321	Standard	NM_006422	NM_001278309	NA	Approved	FSP95, SOB1, AKAP110, CT82	uc001qnb.4	O75969		ENST00000545990.2:c.0+1830C>T	chr12.hg19:g.4749234G>A		NA	O75945|Q86X01|Q9UM61	hg19	CCDS8531.1	0.02	-0.166669	CTCxGCC	UNCOVERED																																																																																			NOVEL	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398911.2	9	2.407139	KEEP	11	0	0	8	250	GG	0	0	0		-	3	59	90	0	0	6.910306	15	60	499	57	ENST00000545990.2	0.166667	0.353947
RP11-234B24.6	0	__UNKNOWN__	__UNKNOWN__	12	4814281	4814281	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:4814281C>T	ENST00000544741.2	+	3	240				RP11-234B24.2_ENST00000527518.1_lincRNA						NA		NA									NA						gtcaggagttcgagaccagcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000544741.2:c.240+19790C>T	chr12.hg19:g.4814281C>T		NA		hg19		0.02	-0.175412	GTTxGAG	UNCOVERED																																																																																			NOVEL	RP11-234B24.6-002	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000399387.3	14	2.706686	KEEP	7	0	0	9	251	CG	0	0	0		+	3	60	85	0	1	6.4926	14	60	436	41	ENST00000544741.2	0.176471	0.387407
GALNT8	26290	__UNKNOWN__	__UNKNOWN__	12	4834972	4834972	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:4834972G>A	ENST00000252318.2	+	2	548				RP11-234B24.6_ENST00000544741.2_Intron	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	NA		NA			cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						cgcccacctcggcctcccaaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(108;631 1558 7270 20097 39846)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	26290	2.4.1.41	Glycosyltransferase family 2 domain containing	4130	protein-coding gene	gene with protein product	polypeptide GalNAc transferase 8	606250	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)		NA	10767557	Standard	NM_017417	NM_017417	NA	Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.212-726G>A	chr12.hg19:g.4834972G>A		NA	B2RU02	hg19	CCDS8533.1	0.02	-0.2193	CTCxGCC	COVERED																																																																																			NOVEL	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388277.2	7	3.308942	KEEP	2	0	0	11	321	GG	0.992708	0.548856	0		+	3	60	92	0	0	6.892409	18	60	594	54	ENST00000252318.2	0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	4911924	4911924	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:4911924T>C			NA	NA				GALNT8 (30032 upstream) : RP11-234B24.4 (3783 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.4911924T>C		NA		hg19		0.02	-0.201419	AGGxGTG	COVERED																																																																																			NOVEL					0			9	4.509519	KEEP	0	0	0	15	410	TT	0.99649	0.488823	0			3	60	96	0	0	7.513355	15	60	444	59		0.166667	0.490544
CD9	928	__UNKNOWN__	__UNKNOWN__	12	6317145	6317145	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6317145T>C	ENST00000382515.2	+	1	177				CD9_ENST00000009180.4_Intron|CD9_ENST00000382518.1_Intron			P21926	CD9_HUMAN	CD9 molecule	NA		NA			blood coagulation (GO:0007596)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|negative regulation of cell proliferation (GO:0008285)|oligodendrocyte development (GO:0014003)|paranodal junction assembly (GO:0030913)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|response to water deprivation (GO:0009414)|single fertilization (GO:0007338)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|vesicle (GO:0031982)				endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	8						aatcccagcattttgggaggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M38690	CCDS8540.1	12p13	2013-02-14	2006-03-28		ENSG00000010278	ENSG00000010278	928		CD molecules, Tetraspanins	1709	protein-coding gene	gene with protein product	motility related protein-1	143030	CD9 antigen (p24)	MIC3	NA	6198179	Standard		NM_001769	NA	Approved	BA2, P24, TSPAN29, MRP-1	uc001qnq.2	P21926	OTTHUMG00000044400	ENST00000382515.2:c.-142+7006T>C	chr12.hg19:g.6317145T>C		NA	D3DUQ9|Q5J7W6|Q96ES4	hg19		0.02	-0.175414	GCAxTTT	COVERED																																																																																			NOVEL	CD9-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000103347.2	7	2.405792	KEEP	0	0	0	8	217	TT	0.99257	0.384528	0		+	3	60	100	0	0	7.910287	15	60	441	41	ENST00000382515.2	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	6366220	6366220	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6366220A>G			NA	NA				CD9 (18795 upstream) : PLEKHG6 (53381 downstream)						NA		NA									NA						caacaagagcaaaactccgtc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.6366220A>G		NA		hg19		0.02	-0.166605	AGCxAAA	COVERED																																																																																			NOVEL					0			4	2.405345	KEEP	1	0	0	8	212	AA	0.99257	0.351317	0			3	60	89	0	0	6.812462	15	60	429	42		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	6403566	6403566	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6403566A>C			NA	NA				CD9 (56141 upstream) : PLEKHG6 (16035 downstream)						NA		NA									NA						tggtggctcaagcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.6403566A>C		NA		hg19		0.02	-0.280613	TCAxGCC	COVERED																																																																																			NOVEL					0			13	3.305872	KEEP	2	0	0	11	283	AT	0.994391	0.813874	0			4	60	117	0	0	8.625633	24	60	711	63		0.142857	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	6508301	6508301	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6508301C>T			NA	NA				RP1-102E24.8 (4066 upstream) : CD27-AS1 (40025 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.6508301C>T		NA		hg19		0.02	-0.210379	AGGxGTG	COVERED																																																																																			NOVEL					0			6	3.309362	KEEP	2	0	0	11	328	CC	0.992708	0.518353	0			3	60	87	0	0	6.329063	19	60	569	51		0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	6508803	6508803	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6508803A>C			NA	NA				RP1-102E24.8 (4568 upstream) : CD27-AS1 (39523 downstream)						NA		NA									NA						ccaggctggtattgaactcct	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.6508803A>C		NA		hg19		0.02	-0.131535	GGTxTTG	COVERED																																																																																			NOVEL					0			12	3.608185	KEEP	1	0	0	12	319	AA	0.993634	0.227714	0			3	28	97	0	0	8.082516	10	60	277	39		0.230769	0.229173
TAPBPL	55080	__UNKNOWN__	__UNKNOWN__	12	6567296	6567296	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6567296A>G	ENST00000544021.1	+	4	725				TAPBPL_ENST00000266556.7_Intron|TAPBPL_ENST00000545700.1_Intron			Q9BX59	TPSNR_HUMAN	TAP binding protein-like	NA		NA			negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						gctcacacctataatcccagc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001005	CCDS8546.1	12p13.31	2013-01-11					55080		Immunoglobulin superfamily / C1-set domain containing	30683	protein-coding gene	gene with protein product		607081			NA	11920573	Standard	NM_018009	NM_018009	NA	Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000544021.1:c.548+386A>G	chr12.hg19:g.6567296A>G		NA	Q9NWB8	hg19		0.02	-0.139908	CCTxTAA	COVERED																																																																																			NOVEL	TAPBPL-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000399262.1	6	3.006763	KEEP	0	0	0	10	264	AA	0.992708	0.259062	0		+	3	60	102	0	0	8.478554	11	60	300	40	ENST00000544021.1	0.214286	0.260965
NCAPD2	9918	__UNKNOWN__	__UNKNOWN__	12	6612676	6612676	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6612676A>G	ENST00000315579.5	+	3	926				NCAPD2_ENST00000545962.1_Intron	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	NA		NA			mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						ggtggctcacacctgtaatcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292	9918			24305	protein-coding gene	gene with protein product	chromosome condensation related SMC associated protein 1	615638			NA	8590280, 10958694	Standard	NM_014865	NM_014865	NA	Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.128-6207A>G	chr12.hg19:g.6612676A>G		NA	D3DUR4|Q8N6U3	hg19	CCDS8548.1	0.02	-0.27189	CACxCCT	UNCOVERED																																																																																			NOVEL	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399964.1	5	3.30818	KEEP	5	0	0	11	302	AA	0	0	0		+	3	60	107	0	0	8.04213	24	60	708	73	ENST00000315579.5	0.111111	0.717315
NCAPD2	9918	__UNKNOWN__	__UNKNOWN__	12	6625418	6625418	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6625418T>C	ENST00000315579.5	+	10	1786				NCAPD2_ENST00000545962.1_Intron	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	NA		NA			mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						gcctataatctcagcactttg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292	9918			24305	protein-coding gene	gene with protein product	chromosome condensation related SMC associated protein 1	615638			NA	8590280, 10958694	Standard	NM_014865	NM_014865	NA	Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.988-576T>C	chr12.hg19:g.6625418T>C		NA	D3DUR4|Q8N6U3	hg19	CCDS8548.1	0.02	-0.23683	ATCxCAG	COVERED																																																																																			NOVEL	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399964.1	12	2.660725	KEEP	1	0	0	9	221	TT	0.99254	0.607839	0		+	4	60	132	0	0	10.413432	20	60	612	52	ENST00000315579.5	0.166667	0.612407
NCAPD2	9918	__UNKNOWN__	__UNKNOWN__	12	6628148	6628148	__UNKNOWN__	Intron	SNP	T	T	C	rs7978597	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6628148T>C	ENST00000315579.5	+	13	2388				NCAPD2_ENST00000545962.1_Intron	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	NA		NA			mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						acctcctgggttcacgccatt	0.532		NA											T|||	1094	0.21845	0.1536	0.2089	5008	,	,	NA	13601	0.3671	NA	0.1809	False	NA	,,,	NA	NA	NA	2504	0.1984	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292	9918			24305	protein-coding gene	gene with protein product	chromosome condensation related SMC associated protein 1	615638			NA	8590280, 10958694	Standard	NM_014865	NM_014865	NA	Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.1589+1023T>C	chr12.hg19:g.6628148T>C		NA	D3DUR4|Q8N6U3	hg19	CCDS8548.1	0.02	-0.131524	GGGxTCA	UNCOVERED																																																																																			NOVEL	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399964.1	7	2.406255	KEEP	6	0	0	8	222	TT	0	0	0		+	6	60	201	0	0	19.352192	6	48	166	43	ENST00000315579.5	0.5	0.229173
NCAPD2	9918	__UNKNOWN__	__UNKNOWN__	12	6631169	6631169	__UNKNOWN__	Silent	SNP	C	C	A	rs917634	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6631169C>A	ENST00000315579.5	+	15	2719	c.1920C>A	c.(1918-1920)atC>atA	p.I640I	NCAPD2_ENST00000545962.1_Silent_p.I595I	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	640		NA			mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						CCATTGGCATCATCAGCAAGA	0.423		NA											C|||	2662	0.53155	0.5961	0.6225	5008	,	,	NA	17799	0.5704	NA	0.4742	False	NA	,,,	NA	NA	NA	2504	0.3988	NA	NA	NA								NA				0								C		2566,1840	635.7+/-396.4	758,1050,395	82	83	83		1920	5	1	12	dbSNP_86	83	3915,4685	547.1+/-385.1	903,2109,1288	no	coding-synonymous	NCAPD2	NM_014865.3		1661,3159,1683	AA,AC,CC	NA	45.5233,41.7612,49.8308		640/1402	6631169	6481,6525	2203	4300	6503	SO:0001819	synonymous_variant			D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292	9918			24305	protein-coding gene	gene with protein product	chromosome condensation related SMC associated protein 1	615638			NA	8590280, 10958694	Standard	NM_014865	NM_014865	NA	Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.1920C>A	chr12.hg19:g.6631169C>A		NA	D3DUR4|Q8N6U3	hg19	CCDS8548.1	0.02	1.222132	CATxATC	COVERED																																																																																			NOVEL	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399964.1	5	3.309361	KEEP	0	0	0	11	331	CC	0.993072	0.993029	0		+	58	60	1638	0	0	163.039412	39	60	1335	164	ENST00000315579.5	0.597938	0.999956
IFFO1	25900	__UNKNOWN__	__UNKNOWN__	12	6654196	6654196	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6654196T>C	ENST00000356896.4	-	8	1499				IFFO1_ENST00000336604.4_Intron|IFFO1_ENST00000436152.2_Intron|IFFO1_ENST00000396840.2_Intron|IFFO1_ENST00000465801.1_Intron	NM_001039670.2|NM_001193457.1	NP_001034759.1|NP_001180386.1	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	NA		NA				intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						ctggctaacatggtgaaaccc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295	25900		Intermediate filament family orphans	24970	protein-coding gene	gene with protein product		610495	intermediate filament family orphan	IFFO	NA	8771189, 3052284	Standard	NM_080730	NM_001193457	NA	Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000356896.4:c.1455+3034A>G	chr12.hg19:g.6654196T>C		NA	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	hg19	CCDS41741.1	0.02	-0.236779	ACAxGGT	COVERED																																																																																			NOVEL	IFFO1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413898.1	5	2.706549	KEEP	5	0	0	9	247	TT	0.99257	0.607857	0		-	4	40	117	1	0	8.914588	20	60	591	51	ENST00000356896.4	0.166667	0.612407
IFFO1	25900	__UNKNOWN__	__UNKNOWN__	12	6662832	6662832	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6662832A>G	ENST00000356896.4	-	1	817				IFFO1_ENST00000336604.4_Intron|IFFO1_ENST00000396840.2_Intron	NM_001039670.2|NM_001193457.1	NP_001034759.1|NP_001180386.1	Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	NA		NA				intermediate filament (GO:0005882)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						cagctactcaagaggctgagg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295	25900		Intermediate filament family orphans	24970	protein-coding gene	gene with protein product		610495	intermediate filament family orphan	IFFO	NA	8771189, 3052284	Standard	NM_080730	NM_001193457	NA	Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000356896.4:c.773+1590T>C	chr12.hg19:g.6662832A>G		NA	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	hg19	CCDS41741.1	0.02	1.713448	TCAxGAG	COVERED																																																																																			NOVEL	IFFO1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413898.1	17	3.372889	KEEP	0	2	59	32	883	AA	0.999998	0.998865	0		-	5	60	147	0	0	9.264288	66	60	1928	155	ENST00000356896.4	0.070423	0.998867
CHD4	1108	__UNKNOWN__	__UNKNOWN__	12	6703088	6703088	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6703088A>G	ENST00000544484.1	-	16	2451				CHD4_ENST00000544040.1_Intron|CHD4_ENST00000309577.6_Intron|CHD4_ENST00000357008.2_Intron			Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						tgcaacctccacctcccgggt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(32;586 792 4568 16848 45314)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642	1108		Zinc fingers, PHD-type	1919	protein-coding gene	gene with protein product		603277			NA	7575689, 8843877	Standard	NM_001273	XM_006718958	NA	Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000544484.1:c.2305-306T>C	chr12.hg19:g.6703088A>G		NA	Q8IXZ5	hg19		0.02	-0.122704	TCCxCCT	COVERED																																																																																			NOVEL	CHD4-013	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000402631.1	10	4.510593	KEEP	10	0	0	15	413	AA	0.99254	0.194847	0		-	3	60	89	0	0	7.17475	11	60	302	50	ENST00000544484.1	0.214286	0.196312
ZNF384	171017	__UNKNOWN__	__UNKNOWN__	12	6792928	6792928	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6792928C>T	ENST00000355772.4	-	3	147				ZNF384_ENST00000396799.2_Intron|ZNF384_ENST00000396801.3_Intron|ZNF384_ENST00000361959.3_Intron|ZNF384_ENST00000319770.3_Intron|ZNF384_ENST00000396795.1_Intron	NM_001039920.2	NP_001035009.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	NA		NA			nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						ctcatgcctgcaatcccagca	0.443		NA	T	EWSR1, TAF15 	ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746	171017		Zinc fingers, C2H2-type	11955	protein-coding gene	gene with protein product		609951	trinucleotide repeat containing 1	TNRC1	NA	9225980, 11149472	Standard		NM_001135734	NA	Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000355772.4:c.5-4237G>A	chr12.hg19:g.6792928C>T		NA	O15407|Q7Z722|Q8N938	hg19	CCDS31732.1	0.02	-0.149127	CTGxAAT	COVERED																																																																																			NOVEL	ZNF384-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400714.1	6	2.407148	KEEP	1	0	0	8	247	CC	0.99257	0.289832	0		-	3	60	90	0	0	7.272723	11	60	382	35	ENST00000355772.4	0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	6814463	6814463	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6814463T>C			NA	NA				PIANP (4497 upstream) : RNU6-781P (4154 downstream)						NA		NA									NA						tctcgatctcttgacctcgtg	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.6814463T>C		NA		hg19		0.02	-0.166634	CTCxTGA	UNCOVERED																																																																																			NOVEL					0			5	2.405066	KEEP	5	0	0	8	211	TT	0	0	0			3	60	84	0	0	6.3113	15	60	448	48		0.166667	0.353947
MLF2	8079	__UNKNOWN__	__UNKNOWN__	12	6865885	6865885	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6865885A>G	ENST00000539187.1	-	2	335							Q15773	MLF2_HUMAN	myeloid leukemia factor 2	NA		NA			defense response (GO:0006952)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(2)|large_intestine(3)|lung(4)	9						tgcccgcctcagcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U57342	CCDS8559.1	12p13.31	2014-09-11			ENSG00000089693	ENSG00000089693	8079			7126	protein-coding gene	gene with protein product		601401			NA	8661158	Standard		NM_005439	NA	Approved	NTN4	uc010sfi.2	Q15773	OTTHUMG00000168717	ENST00000539187.1:c.28-4357T>C	chr12.hg19:g.6865885A>G		NA		hg19	CCDS8559.1	0.02	-0.254357	CTCxGCC	COVERED																																																																																			NOVEL	MLF2-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402979.1	9	5.113832	KEEP	7	0	0	17	484	AA	0.995343	0.66541	0		-	3	60	103	0	0	7.748835	22	60	666	73	ENST00000539187.1	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	6891073	6891073	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6891073G>A			NA	NA				LAG3 (3454 upstream) : RN7SL380P (1946 downstream)						NA		NA									NA						gattacaggcgtgaaccacca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.6891073G>A		NA		hg19		0.02	-0.245586	GGCxTGA	COVERED																																																																																			NOVEL					0			12	3.910526	KEEP	0	0	0	13	378	GG	0.994391	0.63775	0			3	60	90	0	0	6.344987	24	60	788	57		0.111111	0.641347
GNB3	2784	__UNKNOWN__	__UNKNOWN__	12	6955873	6955873	__UNKNOWN__	Intron	SNP	C	C	A	rs373734079|rs199825311		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:6955873C>A	ENST00000229264.3	+	11	1321				CDCA3_ENST00000422785.3_3'UTR|CDCA3_ENST00000604599.1_5'UTR|GNB3_ENST00000435982.2_Intron	NM_002075.2	NP_002066.1	P16520	GBB3_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 3	NA		NA			cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|stomach(1)	20						acccacacacccacacataca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8564.1, CCDS73427.1	12p13	2013-01-10			ENSG00000111664	ENSG00000111664	2784		WD repeat domain containing	4400	protein-coding gene	gene with protein product		139130			NA	11770079, 16600389	Standard	NM_002075	XM_005253680	NA	Approved		uc001qrd.3	P16520	OTTHUMG00000168517	ENST00000229264.3:c.917-83C>A	chr12.hg19:g.6955873C>A		NA	Q96B71|Q9BQC0	hg19	CCDS8564.1	0.02	3.011224	CACxCAC	COVERED																																																																																			NOVEL	GNB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400006.1	25	10.697969	KEEP	0	2	58	56	1708	CC	1	0.999999	0		+	8	70	245	2	1	15.686264	108	70	3629	246	ENST00000229264.3	0.068966	0.999999
LRRC23	10233	__UNKNOWN__	__UNKNOWN__	12	7002817	7002817	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:7002817T>C	ENST00000433346.1	+	2	429				LRRC23_ENST00000449039.1_Intron			Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	NA		NA								NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						Tggccaggcatggtggctcac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626	10233			19138	protein-coding gene	gene with protein product		NA			NA	11830501, 11826754	Standard	NM_006992	NM_201650	NA	Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000433346.1:c.-50+9734T>C	chr12.hg19:g.7002817T>C		NA	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	hg19		0.02	-0.210504	GCAxGGT	COVERED																																																																																			NOVEL	LRRC23-011	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000345224.1	1	2.405163	KEEP	0	0	0	8	209	TT	0.99257	0.518282	0		+	3	60	92	0	0	6.96172	17	60	521	49	ENST00000433346.1	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	7052472	7052472	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:7052472C>A			NA	NA				ATN1 (988 upstream) : C12orf57 (123 downstream)						NA		NA									NA						gtctcaaaaacaaaaaacaaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.7052472C>A		NA		hg19		0.02	1.45271	AAAxAAA	COVERED																																																																																			NOVEL					0			28	5.247804	KEEP	0	4	106	55	1695	CC	1	0.999559	0			6	60	182	0	1	11.81603	74	60	2545	202		0.075	0.999559
RP11-273B20.3	0	__UNKNOWN__	__UNKNOWN__	12	7332735	7332735	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:7332735A>G	ENST00000545794.1	-	0	279				RP11-273B20.3_ENST00000543061.1_RNA						NA		NA									NA						gttcacgcctataatcccagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000545794.1:	chr12.hg19:g.7332735A>G		NA		hg19		0.02	-0.219266	CCTxTAA	COVERED																																																																																			NOVEL	RP11-273B20.3-002	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000398610.1	10	3.30839	KEEP	1	0	0	11	304	AA	0.993072	0.549057	0		-	3	60	95	0	0	7.127538	19	60	564	54	ENST00000545794.1	0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	7720646	7720646	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:7720646A>T			NA	NA				CD163 (64157 upstream) : APOBEC1 (81349 downstream)						NA		NA									NA						agagtgagacaccgtctcaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.7720646A>T		NA		hg19		0.02	-0.17541	GACxCCG	COVERED																																																																																			NOVEL					0			3	3.90953	KEEP	0	0	0	13	355	AA	0.994391	0.385234	0			3	60	88	0	0	6.792407	14	60	416	48		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	7833630	7833630	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:7833630T>C			NA	NA				APOBEC1 (15141 upstream) : GDF3 (8747 downstream)						NA		NA									NA						ggtgtggtggttcacacctgt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.7833630T>C		NA		hg19		0.02	-0.271802	TGGxTCA	COVERED																																																																																			NOVEL					0			15	3.910681	KEEP	1	0	0	13	375	TT	0.993634	0.712749	0			4	60	110	0	0	8.065069	22	60	647	52		0.153846	0.717315
SLC2A14	144195	__UNKNOWN__	__UNKNOWN__	12	7978097	7978097	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:7978097T>C	ENST00000340749.5	-	9	1265				SLC2A14_ENST00000396589.2_Intron|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000431042.2_Intron|SLC2A14_ENST00000535295.1_Intron|SLC2A14_ENST00000543909.1_Intron|SLC2A14_ENST00000539924.1_Intron|SLC2A14_ENST00000542546.1_Intron			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		cggtggctcatgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262	144195		Solute carriers	18301	protein-coding gene	gene with protein product		611039	solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3	SLC2A3P3	NA	12504846	Standard	NM_153449	NM_001286234	NA	Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000340749.5:c.864+1993A>G	chr12.hg19:g.7978097T>C		NA	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	hg19		0.02	-0.184153	TCAxGCC	COVERED																																																																																			NOVEL	SLC2A14-006	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000399936.2	10	2.707629	KEEP	2	0	0	9	263	TT	0.99254	0.420319	0		-	3	56	86	0	0	6.680008	13	60	392	46	ENST00000340749.5	0.1875	0.423478
NANOGP1	404635	__UNKNOWN__	__UNKNOWN__	12	8052026	8052026	__UNKNOWN__	RNA	SNP	G	G	T	rs148134990		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:8052026G>T	ENST00000607111.1	+	0	1129							Q8N7R0	NANG2_HUMAN	Nanog homeobox pseudogene 1	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|lung(4)|prostate(1)	6						ctcgggaggcggaggttgcag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AY455283		12p13.31	2014-03-20			ENSG00000176654	ENSG00000176654	404635		Homeoboxes / ANTP class : NKL subclass	23099	pseudogene	pseudogene		NA			NA	15108323, 15233988	Standard		NG_006522	NA	Approved	NANOG2	uc001qtp.1	Q8N7R0	OTTHUMG00000166020	ENST00000607111.1:	chr12.hg19:g.8052026G>T		NA		hg19		0.02	-0.359453	GGCxGAG	COVERED																																																																																			NOVEL	NANOGP1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000470953.1	16	8.413631	KEEP	8	0	0	28	752	GG	0.999988	0.909058	0		+	4	60	105	0	0	6.821438	35	60	1034	85	ENST00000607111.1	0.102564	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	8263732	8263732	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:8263732G>T			NA	NA				NECAP1 (13365 upstream) : CLEC4A (12495 downstream)						NA		NA									NA						cctcccaaagggctgggatta	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.8263732G>T		NA		hg19		0.02	-0.262995	AAGxGCT	COVERED																																																																																			NOVEL					0			8	3.610674	KEEP	2	0	0	12	364	GG	0.993634	0.689252	0			4	40	106	0	0	7.597754	23	60	759	65		0.148148	0.693668
MFAP5	8076	__UNKNOWN__	__UNKNOWN__	12	8810450	8810450	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:8810450A>G	ENST00000359478.2	-	4	282				MFAP5_ENST00000535336.1_Intron|MFAP5_ENST00000540087.1_Intron|MFAP5_ENST00000396549.2_Intron|MFAP5_ENST00000433590.2_Intron|MFAP5_ENST00000543369.1_Intron|MFAP5_ENST00000538107.1_Intron	NM_003480.2	NP_003471.1	Q13361	MFAP5_HUMAN	microfibrillar associated protein 5	NA		NA			extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|microfibril (GO:0001527)	extracellular matrix structural constituent (GO:0005201)			breast(1)|endometrium(2)|large_intestine(4)|lung(5)|skin(1)	13	Lung SC(5;0.184)					ttacaggcataagccaccatg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK124368	CCDS8595.1, CCDS73437.1	12p13.1-p12.3	2004-04-05				ENSG00000197614	8076			29673	protein-coding gene	gene with protein product		601103			NA	9792630, 8557636	Standard	NM_003480	XM_005253485	NA	Approved	MAGP2, MP25	uc001qut.1	Q13361		ENST00000359478.2:c.95-2024T>C	chr12.hg19:g.8810450A>G		NA	B0AZL6|D3DUV1|Q7Z490	hg19	CCDS8595.1	0.02	-0.271863	CATxAGC	COVERED																																																																																			NOVEL	MFAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400656.2	10	3.007194	KEEP	0	0	0	10	271	AA	0.992708	0.712085	0		-	3	60	97	0	0	7.095622	23	60	659	58	ENST00000359478.2	0.115385	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	8843944	8843944	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:8843944A>C			NA	NA				RP11-20D14.3 (22337 upstream) : RIMKLB (6551 downstream)						NA		NA									NA						gtggctcacgactgtaatccc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.8843944A>C		NA		hg19		0.02	-0.21917	ACGxCTG	COVERED																																																																																			NOVEL					0			12	3.279549	KEEP	1	0	0	11	261	AA	0.993072	0.549057	0			3	60	97	0	0	7.328019	19	60	526	48		0.136364	0.552887
RIMKLB	57494	__UNKNOWN__	__UNKNOWN__	12	8886207	8886207	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:8886207G>A	ENST00000538135.1	+	3	1000				RIMKLB_ENST00000535829.1_Intron|RIMKLB_ENST00000357529.3_Intron|RIMKLB_ENST00000299673.5_Intron			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	NA		NA			cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ggtggctcacgcctgtaatcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	57494	6.3.2.N6		29228	protein-coding gene	gene with protein product	N-acetylaspartyl-glutamate synthetase	614054	family with sequence similarity 80, member B	FAM80B	NA	10574462, 20643647	Standard	NM_020734	XM_006719116	NA	Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.176-16251G>A	chr12.hg19:g.8886207G>A		NA	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	hg19	CCDS41748.1	0.02	-0.385955	CACxCCT	COVERED																																																																																			NOVEL	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398874.1	16	3.910646	KEEP	2	0	0	13	378	GG	0.995343	0.913895	0		+	4	60	128	0	1	9.018783	37	60	1198	78	ENST00000538135.1	0.097561	0.918171
A2ML1	144568	__UNKNOWN__	__UNKNOWN__	12	9000474	9000474	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9000474G>A	ENST00000299698.7	+	15	2013				A2ML1_ENST00000539547.1_Intron|A2ML1_ENST00000540049.1_Intron	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1	NA		NA								NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ggtggctcacgcctgtaatcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535	144568			23336	protein-coding gene	gene with protein product		610627	C3 and PZP-like, alpha-2-macroglobulin domain containing 9	CPAMD9	NA	16298998	Standard	NM_144670	NM_144670	NA	Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.1833+180G>A	chr12.hg19:g.9000474G>A		NA		hg19	CCDS8596.2	0.02	-0.350871	CACxCCT	COVERED																																																																																			NOVEL	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250304.3	8	3.007543	KEEP	0	0	0	10	281	GG	0.992708	0.871307	0		+	4	60	120	0	0	8.509883	31	60	1018	73	ENST00000299698.7	0.114286	0.877708
A2ML1	144568	__UNKNOWN__	__UNKNOWN__	12	9024504	9024504	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9024504A>G	ENST00000299698.7	+	34	4401				A2ML1_ENST00000539547.1_Intron	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1	NA		NA								NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						ggccgggcgcagtggctcatg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535	144568			23336	protein-coding gene	gene with protein product		610627	C3 and PZP-like, alpha-2-macroglobulin domain containing 9	CPAMD9	NA	16298998	Standard	NM_144670	NM_144670	NA	Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.4222-2517A>G	chr12.hg19:g.9024504A>G		NA		hg19	CCDS8596.2	0.02	-0.298209	CGCxGTG	COVERED																																																																																			NOVEL	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250304.3	8	5.112104	KEEP	2	0	0	17	464	AA	0.997832	0.779366	0		+	3	60	100	0	0	7.152745	28	60	837	70	ENST00000299698.7	0.096774	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9058218	9058218	__UNKNOWN__	IGR	SNP	C	C	T	rs1073159	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9058218C>T			NA	NA				A2ML1 (28837 upstream) : PHC1 (8930 downstream)						NA		NA									NA						actcttgttgcccaggctgca	0.408		NA											C|||	1696	0.338658	0.0764	0.3746	5008	,	,	NA	-128	0.4365	NA	0.4294	False	NA	,,,	NA	NA	NA	2504	0.4734	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9058218C>T		NA		hg19		0.02	-0.175426	TTGxCCA	UNCOVERED																																																																																			NOVEL					0			8	2.407147	KEEP	3	0	0	8	244	CC	0	0	0			7	60	207	0	0	19.036374	10	60	324	42		0.411765	0.387407
PHC1	1911	__UNKNOWN__	__UNKNOWN__	12	9074694	9074694	__UNKNOWN__	Intron	SNP	A	A	G	rs111526877		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9074694A>G	ENST00000543824.1	+	6	788				PHC1_ENST00000544916.1_Intron|PHC1_ENST00000433083.2_Intron|PHC1_ENST00000433847.2_Intron|PHC1_ENST00000536844.1_Intron			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	NA		NA			cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						acaggcgtgaaccaccgcgcc	0.532		NA											A|||	865	0.172724	0.1952	0.3213	5008	,	,	NA	-128	0.0278	NA	0.2197	False	NA	,,,	NA	NA	NA	2504	0.138	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752	1911		Sterile alpha motif (SAM) domain containing	3182	protein-coding gene	gene with protein product		602978	early development regulator 1 (homolog of polyhomeotic 1), polyhomeotic-like 1 (Drosophila)	EDR1	NA	9121482	Standard	NM_004426	XM_005253334	NA	Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.456+348A>G	chr12.hg19:g.9074694A>G		NA	D3DUV4|Q8WVM3|Q9BU63	hg19	CCDS8597.1	0.02	-0.262687	TGAxCCA	COVERED																																																																																			NOVEL	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399115.1	8	3.005574	KEEP	1	0	0	10	269	AA	0.99254	0.688494	0		+	4	60	110	0	0	8.248525	20	60	578	59	ENST00000543824.1	0.166667	0.693668
KLRG1	10219	__UNKNOWN__	__UNKNOWN__	12	9132755	9132755	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9132755T>C	ENST00000538029.1	+	2	112							Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	NA		NA			cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						cctcagcctctcaaagtgctg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187	10219		Killer cell lectin-like receptors, C-type lectin domain containing	6380	protein-coding gene	gene with protein product	C-type lectin domain family 15, member A	604874			NA	9862378, 9842918, 16461340, 16140789	Standard	NM_005810	NM_005810	NA	Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000538029.1:c.113-28816T>C	chr12.hg19:g.9132755T>C		NA	B7ZAM2|O43198|O75613	hg19		0.02	-0.228064	CTCxCAA	COVERED																																																																																			NOVEL	KLRG1-003	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000399142.1	11	2.406322	KEEP	0	0	0	8	225	TT	0.99257	0.578599	0		+	4	60	142	0	0	11.579091	18	60	553	43	ENST00000538029.1	0.181818	0.58293
A2M	2	__UNKNOWN__	__UNKNOWN__	12	9268710	9268710	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9268710C>T	ENST00000318602.7	-	0	43					NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	NA		NA			blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	ATTCCCATTCCCGTAAGAGCT	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899	2			7	protein-coding gene	gene with protein product		103950			NA		Standard	NM_000014	XM_006719056	NA	Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.-265G>A	chr12.hg19:g.9268710C>T		NA	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	hg19	CCDS44827.1	0.02	1.531679	TTCxCGT	COVERED																																																																																			NOVEL	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317233.2	5	10.530948	KEEP	0	0	0	35	1080	CC	0.999999	0.998464	0		-	32	60	981	0	0	91.628773	41	60	1406	173	ENST00000318602.7	0.438356	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	9573223	9573223	__UNKNOWN__	IGR	SNP	C	C	A	rs4763936	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:9573223C>A			NA	NA				RP13-735L24.1 (23010 upstream) : SNORA75 (24430 downstream)						NA		NA									NA						AGAAACCACACCGCACAGGTT	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													125	129	128			NA	NA	12		NA											NA				9573223		692	1591	2283	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.9573223C>A		NA		hg19		0.02	1.175325	ACAxCGC	COVERED																																																																																			NOVEL					0			12	4.512212	KEEP	1	0	0	15	451	CC	0.99649	0.996385	0			20	50	574	0	0	46.133361	71	60	2407	162		0.21978	0.999895
PRB2	653247	__UNKNOWN__	__UNKNOWN__	12	11546808	11546808	__UNKNOWN__	Silent	SNP	A	A	G	rs1921331		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:11546808A>G	ENST00000389362.4	-	3	239	c.204T>C	c.(202-204)ccT>ccC	p.P68P	PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	68	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].	NA		P -> S (in Ref. 2; BX484538). {ECO:0000305}.		extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGGGACCTTGAGGCTGGTTGC	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													126	142	136			NA	NA	12		NA											NA				11546808		2163	4250	6413	SO:0001819	synonymous_variant			K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335	653247			9338	protein-coding gene	gene with protein product		168810			NA	8554050	Standard	NM_006248	NM_006248	NA	Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.204T>C	chr12.hg19:g.11546808A>G		NA	O00599|P02811|P04281	hg19	CCDS41757.2	0.02	-0.438441	TTGxGGC	COVERED																																																																																			NOVEL	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000346925.2	5	3.536415	KEEP	23	1	26	21	558	AA	0.99649	0.95649	0		-	3	40	102	0	0	6.705929	47	60	1345	129	ENST00000389362.4	0.06	0.959859
LRP6	4040	__UNKNOWN__	__UNKNOWN__	12	12377864	12377864	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:12377864G>C	ENST00000543091.1	-	2	483				LRP6_ENST00000261349.4_Intron			O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	NA		NA			anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				AATggccaggggcggtggctc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018	4040		Low density lipoprotein receptors	6698	protein-coding gene	gene with protein product		603507			NA	9704021	Standard		NM_002336	NA	Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000543091.1:c.449+19331C>G	chr12.hg19:g.12377864G>C		NA	Q17RZ2	hg19		0.02	-0.061411	AGGxGCG	UNCOVERED																																																																																			NOVEL	LRP6-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000400140.1	2	2.405453	KEEP	0	0	0	8	234	GG	0.99257	0.043461	0		-	2	60	72	0	0	6.335528	5	60	174	26	ENST00000543091.1	0.285714	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	13000516	13000516	__UNKNOWN__	IGR	SNP	C	C	T	rs12809196	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:13000516C>T			NA	NA				DDX47 (17601 upstream) : GPRC5A (43199 downstream)						NA		NA									NA						ccaaggcgggcggatcaggag	0.532		NA											c|||	2032	0.405751	0.348	0.3501	5008	,	,	NA	14752	0.4881	NA	0.4374	False	NA	,,,	NA	NA	NA	2504	0.4059	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.13000516C>T		NA		hg19		0.02	-0.140328	GGGxGGA	COVERED																																																																																			NOVEL					0			4	3.610542	KEEP	5	0	0	12	369	CC	0.99257	0.259026	0			6	60	171	0	0	15.807881	8	60	263	48		0.428571	0.260965
RP11-377D9.3	0	__UNKNOWN__	__UNKNOWN__	12	13190316	13190316	__UNKNOWN__	lincRNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:13190316T>G	ENST00000543321.1	+	0	1173										NA		NA									NA						agacggggtttcaccatgttg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000543321.1:	chr12.hg19:g.13190316T>G		NA		hg19		0.02	-0.227956	GTTxCAC	COVERED																																																																																			NOVEL	RP11-377D9.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000401005.1	8	3.908657	KEEP	3	0	0	13	342	TT	0.992708	0.578679	0		+	3	25	101	0	0	7.665424	20	60	532	48	ENST00000543321.1	0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	14217611	14217611	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:14217611A>G			NA	NA				GRIN2B (84558 upstream) : RN7SL46P (148416 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.14217611A>G		NA		hg19		0.02	-0.184182	CACxCCT	COVERED																																																																																			NOVEL					0			5	2.706811	KEEP	1	0	0	9	250	AA	0.99257	0.454356	0			3	60	94	0	0	7.233825	16	60	473	49		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	14401701	14401701	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:14401701A>G			NA	NA				RP11-134N1.2 (27470 upstream) : RNU6-491P (1464 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.14401701A>G		NA		hg19		0.02	-0.210474	CACxCCT	COVERED																																																																																			NOVEL					0			6	4.208865	KEEP	0	0	0	14	377	AA	0.995343	0.519729	0			3	60	96	0	0	7.227461	19	60	548	61		0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	14439352	14439352	__UNKNOWN__	IGR	SNP	A	A	G	rs4531566	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:14439352A>G			NA	NA				RNU6-491P (36077 upstream) : RN7SL676P (24924 downstream)						NA		NA									NA						tgggaggccaaggtgggcaga	0.478		NA											a|||	1615	0.322484	0.2012	0.4582	5008	,	,	NA	16668	0.253	NA	0.3141	False	NA	,,,	NA	NA	NA	2504	0.4703	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.14439352A>G		NA		hg19		0.02	-0.070178	CCAxGGT	UNCOVERED																																																																																			NOVEL					0			2	2.405649	KEEP	3	0	0	8	218	AA	0	0	0			4	60	139	0	0	13.7322	3	60	97	32		0.571429	0.054137
PLBD1	79887	__UNKNOWN__	__UNKNOWN__	12	14679881	14679881	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:14679881T>G	ENST00000240617.5	-	6	1497					NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	NA		NA			glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						actccagccttggcaacaaga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316	79887			26215	protein-coding gene	gene with protein product	PLB homolog 1 (Dictyostelium)	NA			NA	15193148, 19019078	Standard	NM_024829	NM_024829	NA	Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.844+8711A>C	chr12.hg19:g.14679881T>G		NA	A8K4E9|Q9BVV3|Q9H625	hg19	CCDS31751.1	0.02	-0.236817	CCTxGGC	COVERED																																																																																			NOVEL	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401203.1	6	3.941817	KEEP	1	1	31	24	659	TT	0.999909	0.612352	0		-	4	60	140	0	0	11.562991	16	60	466	63	ENST00000240617.5	0.2	0.612407
C12orf60	144608	__UNKNOWN__	__UNKNOWN__	12	15058964	15058964	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:15058964A>G	ENST00000527783.1	+	0	2314							Q5U649	CL060_HUMAN	chromosome 12 open reading frame 60	NA		NA								breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	9						ccaccaccacacccagctaat	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC038836	CCDS8667.1	12p12.3	2012-08-16			ENSG00000182993	ENSG00000182993	144608			28726	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_175874	NM_175874	NA	Approved	MGC47869	uc001rcj.4	Q5U649	OTTHUMG00000167473	ENST00000527783.1:c.*2311A>G	chr12.hg19:g.15058964A>G		NA	A8K1M7|Q5XKK8|Q8IXY2	hg19		0.02	-0.1403	CACxCCC	COVERED																																																																																			NOVEL	C12orf60-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000394737.1	6	2.704444	KEEP	0	0	0	9	228	AA	0.99254	0.259018	0		+	3	27	94	0	0	7.479388	13	60	380	35	ENST00000527783.1	0.1875	0.260965
ERP27	121506	__UNKNOWN__	__UNKNOWN__	12	15078743	15078743	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:15078743T>C	ENST00000540097.1	-	1	181				ERP27_ENST00000266397.2_Intron			Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	NA		NA				endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						gtggctcacgtctgtaatccc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055	121506		Protein disulfide isomerases	26495	protein-coding gene	gene with protein product	protein disulfide isomerase family A, member 8	610642	chromosome 12 open reading frame 46, endoplasmic reticulum protein 27 kDa	C12orf46	NA	12975309, 16940051	Standard	NM_152321	XM_005253303	NA	Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000540097.1:c.30+3135A>G	chr12.hg19:g.15078743T>C		NA		hg19		0.02	-0.149102	ACGxCTG	COVERED																																																																																			NOVEL	ERP27-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000400869.1	8	3.308928	KEEP	0	0	0	11	312	TT	0.993072	0.289978	0		-	4	60	142	0	0	12.201777	12	60	353	38	ENST00000540097.1	0.25	0.292001
RERG	85004	__UNKNOWN__	__UNKNOWN__	12	15365239	15365239	__UNKNOWN__	Intron	SNP	C	C	T	rs369635927		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:15365239C>T	ENST00000256953.2	-	2	398				RERG_ENST00000537647.1_Intron|RERG_ENST00000538313.1_Intron|RERG_ENST00000546331.1_Intron|RERG_ENST00000536465.1_Intron	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	NA		NA			negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to hormone (GO:0009725)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	estrogen receptor binding (GO:0030331)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16						atgatccacccgcctcggcct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF339750	CCDS8673.1, CCDS53753.1	12p13.1	2014-05-09			ENSG00000134533	ENSG00000134533	85004			15980	protein-coding gene	gene with protein product		612664			NA	11533059	Standard	NM_032918	NM_032918	NA	Approved	MGC15754	uc001rct.3	Q96A58	OTTHUMG00000168745	ENST00000256953.2:c.61+5123G>A	chr12.hg19:g.15365239C>T		NA	B2R9R0|B4DI02	hg19	CCDS8673.1	0.02	-0.13158	ACCxGCC	UNCOVERED																																																																																			NOVEL	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400882.1	10	3.309863	KEEP	10	0	0	11	339	CC	0	0	0		-	3	40	89	0	0	7.072248	12	60	401	46	ENST00000256953.2	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	15426364	15426364	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:15426364C>T			NA	NA				RERG (52013 upstream) : PTPRO (48966 downstream)						NA		NA									NA						tgtgagccaccgcgcccggcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.15426364C>T		NA		hg19		0.02	-0.219273	CACxGCG	COVERED																																																																																			NOVEL					0			5	2.707175	KEEP	2	0	0	9	257	CC	0.99257	0.54878	0			3	60	92	0	0	6.827482	19	60	603	50		0.136364	0.552887
EPS8	2059	__UNKNOWN__	__UNKNOWN__	12	15818316	15818316	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:15818316G>A	ENST00000281172.5	-	8	1173				EPS8_ENST00000543523.1_Intron|EPS8_ENST00000543612.1_Intron	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	NA		NA			actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		tccaggctggggtgcaatggc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491	2059			3420	protein-coding gene	gene with protein product		600206			NA	8084614	Standard		NM_004447	NA	Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.736+373C>T	chr12.hg19:g.15818316G>A		NA	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	hg19	CCDS31753.1	0.02	-0.070163	TGGxGTG	UNCOVERED																																																																																			NOVEL	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401093.1	1	2.707988	KEEP	0	0	0	9	274	GG	0.99254	0.053733	0		-	3	60	83	0	0	7.65377	4	60	136	26	ENST00000281172.5	0.428571	0.054137
PIK3C2G	5288	__UNKNOWN__	__UNKNOWN__	12	18548038	18548038	__UNKNOWN__	Intron	SNP	A	A	T	rs60631635	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:18548038A>T	ENST00000266497.5	+	13	2041				PIK3C2G_ENST00000433979.1_Intron|PIK3C2G_ENST00000538779.1_Intron			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	NA		NA			chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				tctttctttcattctttcttt	0.368		NA											A|||	639	0.127596	0.1172	0.2507	5008	,	,	NA	13864	0.1786	NA	0.0924	False	NA	,,,	NA	NA	NA	2504	0.0378	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	5288	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	phosphoinositide-3-kinase, class 2, gamma polypeptide		NA	9878262	Standard	NM_004570	XM_005253393	NA	Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2003+3852A>T	chr12.hg19:g.18548038A>T		NA	A1L3U0	hg19	CCDS44839.1	0.02	-0.140295	TTCxTTC	COVERED																																																																																			NOVEL	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401316.1	3	2.627885	KEEP	0	1	29	19	455	AA	0.999863	0.260929	0		+	3	60	84	1	0	6.573421	12	60	337	40	ENST00000266497.5	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	19130790	19130790	__UNKNOWN__	IGR	SNP	G	G	A	rs192393322	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:19130790G>A			NA	NA				CAPZA3 (238669 upstream) : PLEKHA5 (151857 downstream)						NA		NA									NA						ggtttaggccgggcacggtgg	0.463		NA											G|||	17	0.00339457	0.0083	0.0029	5008	,	,	NA	13906	0.001	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.19130790G>A		NA		hg19		0.02	-0.113939	GCCxGGC	UNCOVERED																																																																																			NOVEL					0			7	3.309189	KEEP	2	0	0	11	324	GG	0.993072	0.161341	0			3	60	94	0	0	7.902563	9	60	272	40		0.25	0.162467
PLEKHA5	54477	__UNKNOWN__	__UNKNOWN__	12	19290008	19290008	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:19290008A>G	ENST00000429027.2	+	3	259				PLEKHA5_ENST00000538714.1_Intron|PLEKHA5_ENST00000359180.3_Intron|PLEKHA5_ENST00000355397.3_Intron|PLEKHA5_ENST00000539256.1_Intron|PLEKHA5_ENST00000309364.4_Intron|PLEKHA5_ENST00000540972.1_Intron|PLEKHA5_ENST00000317589.4_Intron|PLEKHA5_ENST00000299275.6_Intron	NM_001256470.1	NP_001243399.1	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	NA		NA			reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					acggagtttcactcttgttgc	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(196;329 2193 11246 14234 19524)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126	54477		Pleckstrin homology (PH) domain containing	30036	protein-coding gene	gene with protein product		607770			NA	11214970, 11001876	Standard	NM_019012	NM_001143821	NA	Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000429027.2:c.227+4624A>G	chr12.hg19:g.19290008A>G		NA	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	hg19	CCDS58213.1	0.02	-0.140255	TTCxCTC	COVERED																																																																																			NOVEL	PLEKHA5-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397012.1	5	3.007592	KEEP	0	0	0	10	275	AA	0.992708	0.259062	0		+	4	60	110	0	0	9.271019	10	60	274	32	ENST00000429027.2	0.285714	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	20419107	20419107	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:20419107G>A			NA	NA				CTC-465D4.1 (136360 upstream) : RP11-284H19.1 (95558 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.20419107G>A		NA		hg19		0.02	-0.157888	CACxCCT	COVERED																																																																																			NOVEL					0			7	4.211542	KEEP	1	0	0	14	405	GG	0.995343	0.321303	0			3	60	86	0	0	6.872971	11	60	361	47		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	20506261	20506261	__UNKNOWN__	IGR	SNP	A	A	C	rs145508986	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:20506261A>C			NA	NA				CTC-465D4.1 (223514 upstream) : RP11-284H19.1 (8404 downstream)						NA		NA									NA						gctggagtgcagtggcgcgat	0.502		NA											-|||	1430	0.285543	0.1271	0.2579	5008	,	,	NA	16470	0.5754	NA	0.1571	False	NA	,,,	NA	NA	NA	2504	0.3528	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.20506261A>C		NA		hg19		0.02	-0.131569	TGCxGTG	UNCOVERED																																																																																			NOVEL					0			5	2.406377	KEEP	6	0	0	8	224	AA	0	0	0			4	60	135	0	0	12.277311	7	60	208	38		0.363636	0.229173
SLCO1B1	10599	__UNKNOWN__	__UNKNOWN__	12	21310795	21310795	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:21310795C>A	ENST00000256958.2	+	3	180					NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	NA		NA			bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	cggcctcccacagtgctggga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538	10599		Solute carriers	10959	protein-coding gene	gene with protein product		604843	solute carrier family 21 (organic anion transporter), member 6	SLC21A6	NA	10358072	Standard	NM_006446	NM_006446	NA	Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.85-14789C>A	chr12.hg19:g.21310795C>A		NA	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	hg19	CCDS8685.1	0.02	-0.122808	CCAxAGT	COVERED																																																																																			NOVEL	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402070.1	5	2.407311	KEEP	1	0	0	8	249	CC	0.99257	0.194853	0		+	3	60	87	0	0	7.200879	9	60	315	35	ENST00000256958.2	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	21403185	21403185	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:21403185T>C			NA	NA				SLCO1B1 (11005 upstream) : SLCO1A2 (14348 downstream)						NA		NA									NA						cgtgagccactgcgcccagcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.21403185T>C		NA		hg19		0.02	-0.140322	CACxGCG	COVERED																																																																																			NOVEL					0			6	2.707417	KEEP	0	0	0	9	257	TT	0.992708	0.259062	0			3	60	86	0	0	6.679967	13	60	395	40		0.1875	0.260965
SLCO1A2	6579	__UNKNOWN__	__UNKNOWN__	12	21503541	21503541	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:21503541C>T	ENST00000307378.6	-	3	659				SLCO1A2_ENST00000473830.1_Intron|SLCO1A2_ENST00000537524.1_Intron	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	NA		NA			bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	gaggccgaggcgggtggatca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453	6579		Solute carriers	10956	protein-coding gene	gene with protein product		602883	solute carrier family 21 (organic anion transporter), member 3	SLC21A3	NA	9007731	Standard	NM_021094	NM_134431	NA	Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.62-15898G>A	chr12.hg19:g.21503541C>T		NA	Q9UGP7|Q9UL38	hg19	CCDS8686.1	0.02	-0.140334	AGGxGGG	COVERED																																																																																			NOVEL	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000343648.3	10	3.309604	KEEP	1	0	0	11	338	CC	0.993072	0.259157	0		-	3	59	82	0	0	6.582021	10	60	336	42	ENST00000307378.6	0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	22194706	22194706	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:22194706A>C			NA	NA				ABCC9 (100370 upstream) : CMAS (4401 downstream)						NA		NA									NA						atggtgaaacactgtctctac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.22194706A>C		NA		hg19		0.02	-0.087701	AACxCTG	UNCOVERED																																																																																			NOVEL					0			6	3.303491	KEEP	3	0	0	11	269	AA	0.99254	0.119538	0			2	47	73	0	0	6.436036	5	60	138	30		0.285714	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	22265703	22265703	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:22265703T>C			NA	NA				CMAS (47106 upstream) : ST8SIA1 (80621 downstream)						NA		NA									NA						tggtcttgaattcctgacctc	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.22265703T>C		NA		hg19		0.02	-0.149087	GAAxTCC	COVERED																																																																																			NOVEL					0			4	2.406295	KEEP	0	0	0	8	225	TT	0.99257	0.289832	0			3	60	100	0	0	8.273136	11	60	323	41		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	25130364	25130364	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:25130364G>A			NA	NA				RP11-662I13.2 (17272 upstream) : C12orf77 (15993 downstream)						NA		NA									NA						tttgagacagggtctcgctct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.25130364G>A		NA		hg19		0.02	-0.10524	CAGxGTC	UNCOVERED																																																																																			NOVEL					0			2	2.70794	KEEP	0	0	0	9	280	GG	0.99254	0.138789	0			3	60	88	0	0	7.301299	9	60	294	32		0.25	0.139832
C12orf77	196415	__UNKNOWN__	__UNKNOWN__	12	25148072	25148072	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:25148072C>T	ENST00000549828.1	-	3	612				C12orf77_ENST00000549262.1_3'UTR	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	NA		NA								endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						ggcagggtcacaggacaatag	0.303		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC046192	CCDS44846.1	12p12.1	2009-09-30			ENSG00000226397	ENSG00000226397	196415			27282	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_001101339	NM_001101339	NA	Approved		uc001rgf.3	C9JDV5	OTTHUMG00000170185	ENST00000549828.1:c.407+668G>A	chr12.hg19:g.25148072C>T		NA		hg19	CCDS44846.1	0.02	-0.184188	TCAxAGG	COVERED																																																																																			NOVEL	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407827.1	7	2.707718	KEEP	0	0	0	9	271	CC	0.99254	0.420319	0		-	5	46	154	0	0	12.780667	16	60	511	37	ENST00000549828.1	0.238095	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	25580002	25580002	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:25580002T>C			NA	NA				RNU4-67P (22640 upstream) : IFLTD1 (49013 downstream)						NA		NA									NA						tggggcactctagcctgggca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.25580002T>C		NA		hg19		0.02	-0.052633	CTCxAGC	UNCOVERED																																																																																			NOVEL					0			5	2.406231	KEEP	2	0	0	8	223	TT	0.99257	0.036492	0			2	60	68	0	0	6.550097	2	60	62	23		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	25995904	25995904	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:25995904A>G			NA	NA				RP11-443N24.3 (8788 upstream) : RP11-443N24.4 (39983 downstream)						NA		NA									NA						caccatgttgaccaggctggt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.25995904A>G		NA		hg19		0.02	-0.069924	TTGxCCA	UNCOVERED																																																																																			NOVEL					0			2	3.308509	KEEP	1	0	0	11	304	AA	0.992708	0.053742	0			3	38	100	0	0	9.1402	5	60	140	24		0.375	0.054137
RASSF8	11228	__UNKNOWN__	__UNKNOWN__	12	26167957	26167957	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:26167957A>G	ENST00000405154.2	+	2	91				RASSF8_ENST00000381352.3_Intron|RASSF8_ENST00000538081.1_Intron|RASSF8_ENST00000541490.1_Intron|RASSF8_ENST00000542865.1_Intron	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	NA		NA			signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					tgggcaacatagtgagacccc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094	11228			13232	protein-coding gene	gene with protein product		608231	chromosome 12 open reading frame 2	C12orf2	NA		Standard	NM_007211	NM_007211	NA	Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.-108-40212A>G	chr12.hg19:g.26167957A>G		NA	A8K1Z0|O95647|Q5SCI2|Q76KB6	hg19	CCDS53765.1	0.02	-0.263071	CATxGTG	COVERED																																																																																			NOVEL	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402209.2	14	6.914163	KEEP	4	0	0	23	591	AA	0.999863	0.693573	0		+	3	60	100	0	0	7.449463	22	60	631	74	ENST00000405154.2	0.12	0.693668
RASSF8	11228	__UNKNOWN__	__UNKNOWN__	12	26178266	26178266	__UNKNOWN__	Intron	SNP	A	A	G	rs2669553	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:26178266A>G	ENST00000405154.2	+	2	91				RASSF8_ENST00000381352.3_Intron|RASSF8_ENST00000541490.1_Intron|RASSF8_ENST00000542865.1_Intron	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	NA		NA			signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					cgaggcgggcagatcacgagg	0.547		NA											G|||	3646	0.728035	0.6785	0.7277	5008	,	,	NA	14682	0.744	NA	0.7197	False	NA	,,,	NA	NA	NA	2504	0.7873	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094	11228			13232	protein-coding gene	gene with protein product		608231	chromosome 12 open reading frame 2	C12orf2	NA		Standard	NM_007211	NM_007211	NA	Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.-108-29903A>G	chr12.hg19:g.26178266A>G		NA	A8K1Z0|O95647|Q5SCI2|Q76KB6	hg19	CCDS53765.1	0.02	-0.113874	GGCxGAT	UNCOVERED																																																																																			NOVEL	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402209.2	5	2.706635	KEEP	6	0	0	9	245	AA	0	0	0		+	9	60	295	0	0	30.325143	4	60	100	38	ENST00000405154.2	0.692308	0.162467
ARNTL2	56938	__UNKNOWN__	__UNKNOWN__	12	27521065	27521065	__UNKNOWN__	Intron	SNP	A	A	C	rs71541521		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:27521065A>C	ENST00000546179.1	+	2	217				ARNTL2_ENST00000266503.5_Intron|ARNTL2_ENST00000261178.5_Intron|ARNTL2_ENST00000544915.1_Intron|ARNTL2_ENST00000395901.2_Intron|ARNTL2_ENST00000311001.5_Intron	NM_001248005.1	NP_001234934.1	Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	NA		NA			circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					catgagccacagcgcctggcc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153	56938		Basic helix-loop-helix proteins	18984	protein-coding gene	gene with protein product		614517			NA	10864977, 10964693	Standard	NM_020183	NM_020183	NA	Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000546179.1:c.65-130A>C	chr12.hg19:g.27521065A>C		NA	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	hg19	CCDS58222.1	0.02	-0.236825	CACxGCG	COVERED																																																																																			NOVEL	ARNTL2-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403159.1	10	3.609576	KEEP	0	0	0	12	339	AA	0.993634	0.637264	0		+	3	60	96	0	0	7.510171	15	60	460	54	ENST00000546179.1	0.166667	0.641347
PPFIBP1	8496	__UNKNOWN__	__UNKNOWN__	12	27717084	27717084	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:27717084G>A	ENST00000228425.6	+	2	110				PPFIBP1_ENST00000545334.1_Intron|PPFIBP1_ENST00000535047.1_Intron|PPFIBP1_ENST00000541633.1_Intron|PPFIBP1_ENST00000318304.8_Intron|PPFIBP1_ENST00000542629.1_Intron|PPFIBP1_ENST00000537927.1_Intron	NM_003622.3	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	NA		NA			cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					gattacaggcgtgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10					8496		Sterile alpha motif (SAM) domain containing	9249	protein-coding gene	gene with protein product		603141			NA	9624153, 11836260	Standard	NM_003622	NM_003622	NA	Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000228425.6:c.-123-14001G>A	chr12.hg19:g.27717084G>A		NA	O75336|Q86X70|Q9NY03|Q9ULJ0	hg19	CCDS8713.1	0.02	-0.219264	GGCxTGA	COVERED																																																																																			NOVEL	PPFIBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402880.1	10	2.406929	KEEP	4	0	0	8	240	GT	0.99254	0.548763	0		+	3	60	88	0	0	6.427917	19	60	604	54	ENST00000228425.6	0.136364	0.552887
PPFIBP1	8496	__UNKNOWN__	__UNKNOWN__	12	27846634	27846634	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:27846634A>G	ENST00000228425.6	+	0	4070				PPFIBP1_ENST00000318304.8_3'UTR|PPFIBP1_ENST00000537927.1_3'UTR	NM_003622.3	NP_003613	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	NA		NA			cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					ACttttttttaagatggagtc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10					8496		Sterile alpha motif (SAM) domain containing	9249	protein-coding gene	gene with protein product		603141			NA	9624153, 11836260	Standard	NM_003622	NM_003622	NA	Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000228425.6:c.*819A>G	chr12.hg19:g.27846634A>G		NA	O75336|Q86X70|Q9NY03|Q9ULJ0	hg19	CCDS8713.1	0.02	-0.289395	TTTxAGA	COVERED																																																																																			NOVEL	PPFIBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402880.1	10	5.112289	KEEP	1	0	0	17	459	AA	0.999366	0.760405	0		+	3	60	105	0	0	7.652594	28	60	800	73	ENST00000228425.6	0.096774	0.760887
KLHL42	57542	__UNKNOWN__	__UNKNOWN__	12	27953292	27953292	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:27953292T>G	ENST00000381271.2	+	0	4022				RP11-860B13.3_ENST00000543527.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	NA		NA			mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)					NA						ggggtgtgtgtgtgtgtgtgt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448	57542		Kelch-like	29252	protein-coding gene	gene with protein product		NA	kelch domain containing 5	KLHDC5	NA	19261606	Standard	NM_020782	NM_020782	NA	Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.*2193T>G	chr12.hg19:g.27953292T>G		NA	Q2VPK1|Q8N334	hg19	CCDS31763.1	0.02	-0.350759	GTGxGTG	COVERED																																																																																			NOVEL	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402904.1	5	4.810688	KEEP	0	0	0	16	423	TT	0.997832	0.875805	0		+	4	60	123	1	0	8.658994	34	60	965	66	ENST00000381271.2	0.105263	0.877708
TMTC1	83857	__UNKNOWN__	__UNKNOWN__	12	29819191	29819191	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:29819191C>T	ENST00000551659.1	-	6	1084				TMTC1_ENST00000552618.1_Intron|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000539277.1_Intron|TMTC1_ENST00000381224.2_Intron			Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	NA		NA				integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					gacggagtctcgctctgtcac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687	83857		Tetratricopeptide (TTC) repeat domain containing	24099	protein-coding gene	gene with protein product		615855			NA	24764305	Standard	NM_031920	NM_001193451	NA	Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000551659.1:c.939-5373G>A	chr12.hg19:g.29819191C>T		NA	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	hg19		0.02	1.418554	TCTxGCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.623	-0.820325	0.02755	.	.	ENSG00000133687	ENST00000540901	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.29783	0.0744	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.27536	-1.0071	3	.	.	.	.	.	.	.	.	.	.	.	Q	4	.	.	R	-	2	0	TMTC1	29710458	0.002000	0.14202	0.003000	0.11579	0.003000	0.03518	-0.932000	0.03963	0.192000	0.20272	0.195000	0.17529	CGA	NOVEL	TMTC1-010	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000403505.1	8	6.706676	KEEP	6	3	84	52	1392	CC	1	0.973965	0		-	4	60	122	0	0	8.210944	42	60	1278	128	ENST00000551659.1	0.086957	0.973965
TMTC1	83857	__UNKNOWN__	__UNKNOWN__	12	29819200	29819200	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:29819200A>G	ENST00000551659.1	-	6	1084				TMTC1_ENST00000552618.1_Intron|TMTC1_ENST00000256062.5_Intron|TMTC1_ENST00000539277.1_Intron|TMTC1_ENST00000381224.2_Intron			Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	NA		NA				integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					tcgctctgtcacccaggctgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687	83857		Tetratricopeptide (TTC) repeat domain containing	24099	protein-coding gene	gene with protein product		615855			NA	24764305	Standard	NM_031920	NM_001193451	NA	Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000551659.1:c.939-5382T>C	chr12.hg19:g.29819200A>G		NA	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	hg19		0.02	-0.403166	GTCxCCC	COVERED	.	.	.	.	.	.	.	.	.	.	A	1.433	-0.569709	0.03910	.	.	ENSG00000133687	ENST00000540901	.	.	.	0.354	0.354	0.16063	.	.	.	.	.	T	0.31231	0.0790	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.27839	-1.0062	3	.	.	.	.	.	.	.	.	.	.	.	A	1	.	.	V	-	2	0	TMTC1	29710467	0.031000	0.19500	0.007000	0.13788	0.007000	0.05969	-0.306000	0.08178	0.338000	0.23692	0.329000	0.21502	GTG	NOVEL	TMTC1-010	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000403505.1	7	4.093363	KEEP	5	3	80	42	1032	AA	1	0.941741	0		-	5	60	166	1	0	12.444691	35	60	907	108	ENST00000551659.1	0.125	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	31307356	31307356	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:31307356T>C			NA	NA				RP11-551L14.1 (36951 upstream) : FAM60A (126161 downstream)						NA		NA						p.K242E(2)			NA						ATTTGGGTTTTCCCTTGCACA	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	lung(2)											69	69	69			NA	NA	12		NA											NA				31307356		1841	4091	5932	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.31307356T>C		NA		hg19		0.02	2.032166	TTTxCCC	COVERED																																																																																			NOVEL					0			4	2.406278	KEEP	1	0	0	8	226	TT	0.99257	0.960237	0			4	27	133	0	0	9.158783	46	60	1394	91		0.08	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	31311258	31311258	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:31311258A>G			NA	NA				RP11-551L14.1 (40853 upstream) : FAM60A (122259 downstream)						NA		NA									NA						acggagtttcactctgttgcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.31311258A>G		NA		hg19		0.02	-0.096489	TTCxCTC	UNCOVERED																																																																																			NOVEL					0			7	2.406114	KEEP	6	0	0	8	223	AA	0	0	0			3	50	98	0	1	8.432396	8	50	252	32		0.272727	0.120436
FAM60A	58516	__UNKNOWN__	__UNKNOWN__	12	31462878	31462878	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:31462878A>G	ENST00000337682.4	-	2	349				FAM60A_ENST00000395766.1_Intron|FAM60A_ENST00000536836.1_Intron|FAM60A_ENST00000539409.1_Intron|FAM60A_ENST00000454658.2_Intron|FAM60A_ENST00000542983.1_Intron	NM_001135812.1	NP_001129284.1	Q9NP50	FA60A_HUMAN	family with sequence similarity 60, member A	NA		NA			negative regulation of cell migration (GO:0030336)	Sin3 complex (GO:0016580)				large_intestine(1)|lung(2)	3	all_cancers(9;5.22e-13)|all_epithelial(9;4e-13)|all_lung(12;1.2e-11)|Lung NSC(12;2.17e-09)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0207)|Lung SC(12;0.0592)|Esophageal squamous(101;0.162)					tgggattacaagcgtgagcca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF212220	CCDS8723.1	12p11.21	2012-11-30	2005-04-07	2005-04-07	ENSG00000139146	ENSG00000139146	58516			30702	protein-coding gene	gene with protein product		615027	chromosome 12 open reading frame 14	C12orf14	NA	11042152, 22984288, 22865885	Standard	NM_021238	NM_021238	NA	Approved	TERA	uc001rke.3	Q9NP50	OTTHUMG00000168586	ENST00000337682.4:c.20-11720T>C	chr12.hg19:g.31462878A>G		NA	D3DUV8|Q9BSZ8	hg19	CCDS8723.1	0.02	-0.139913	ACAxGCG	COVERED																																																																																			NOVEL	FAM60A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400347.1	6	2.706881	KEEP	0	0	0	9	248	AA	0.99254	0.259018	0		-	3	60	90	0	0	7.388253	10	60	283	37	ENST00000337682.4	0.230769	0.260965
DENND5B	160518	__UNKNOWN__	__UNKNOWN__	12	31585451	31585451	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:31585451T>C	ENST00000389082.5	-	8	2371				DENND5B_ENST00000536562.1_Intron|DENND5B_ENST00000354285.4_3'UTR|DENND5B_ENST00000306833.6_Intron	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	NA		NA			positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						gtaatcccaatactttgggag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456	160518		DENN/MADD domain containing	28338	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_144973	NM_144973	NA	Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.2106+637A>G	chr12.hg19:g.31585451T>C		NA	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	hg19	CCDS44857.1	0.02	-0.394634	CAAxACT	COVERED																																																																																			NOVEL	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402040.1	3	2.737403	KEEP	1	1	28	19	512	TT	0.99986	0.92651	0		-	3	60	103	0	0	7.008438	40	60	1152	82	ENST00000389082.5	0.069767	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	31982064	31982064	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:31982064G>A			NA	NA				SNORA25 (17940 upstream) : RP11-428G5.5 (47948 downstream)						NA		NA									NA						cctgaggtcaggagttcaagt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.31982064G>A		NA		hg19		0.02	-0.149125	TCAxGAG	COVERED																																																																																			NOVEL					0			7	3.309233	KEEP	0	0	0	11	323	GG	0.993072	0.289978	0			3	60	89	0	0	6.979007	13	60	438	34		0.1875	0.292001
BICD1	636	__UNKNOWN__	__UNKNOWN__	12	32473327	32473327	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:32473327A>G	ENST00000281474.5	+	5	1108				BICD1_ENST00000548411.1_Intron	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	NA		NA			anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			tgtaatcccaacactttggga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746	636			1049	protein-coding gene	gene with protein product		602204	Bicaudal D (Drosophila) homolog 1		NA	9367685	Standard	NM_001714	NM_001714	NA	Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1006-7068A>G	chr12.hg19:g.32473327A>G		NA	A8K2C3|F8W113|O43892|O43893	hg19	CCDS8726.1	0.02	-0.18406	CCAxCAC	COVERED																																																																																			NOVEL	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403380.1	8	4.210394	KEEP	3	0	0	14	383	AA	0.993634	0.420782	0		+	4	47	141	0	0	11.664519	16	60	456	50	ENST00000281474.5	0.2	0.423478
DNM1L	10059	__UNKNOWN__	__UNKNOWN__	12	32848516	32848516	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:32848516G>T	ENST00000266481.6	+	2	163				DNM1L_ENST00000358214.5_Intron|DNM1L_ENST00000381000.4_Intron|DNM1L_ENST00000548671.1_Intron|DNM1L_ENST00000414834.2_Intron|DNM1L_ENST00000553257.1_Intron|DNM1L_ENST00000452533.2_Intron|DNM1L_ENST00000549701.1_Intron|DNM1L_ENST00000547312.1_Intron	NM_005690.3	NP_005681.2	O00429	DNM1L_HUMAN	dynamin 1-like	NA		NA			apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dynamin polymerization involved in mitochondrial fission (GO:0003374)|endocytosis (GO:0006897)|GTP catabolic process (GO:0006184)|membrane fission involved in mitochondrial fission (GO:0090149)|membrane fusion (GO:0061025)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrion morphogenesis (GO:0070584)|necroptotic process (GO:0070266)|peroxisome fission (GO:0016559)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homotetramerization (GO:0051289)|protein localization to mitochondrion (GO:0070585)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|regulation of protein oligomerization (GO:0032459)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|protein complex (GO:0043234)|synapse (GO:0045202)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	23	Lung NSC(5;2.15e-06)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					accagcctgggcaacatgggg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF000430	CCDS8728.1, CCDS8729.1, CCDS8730.1, CCDS61095.1, CCDS61096.1, CCDS61098.1, CCDS61099.1	12p11.21	2012-10-02			ENSG00000087470	ENSG00000087470	10059			2973	protein-coding gene	gene with protein product		603850			NA	9348079, 9731200	Standard	NM_012062	NM_012062	NA	Approved	DRP1, DVLP, HDYNIV, DYMPLE, VPS1	uc001rld.2	O00429	OTTHUMG00000169451	ENST00000266481.6:c.103-5833G>T	chr12.hg19:g.32848516G>T		NA	A8K4X9|B4DGC9|B4DSU8|J3KPI2|O14541|O60709|Q59GN9|Q7L6B3|Q8TBT7|Q9BWM1|Q9Y5J2	hg19	CCDS8728.1	0.02	-0.175447	TGGxCAA	COVERED																																																																																			NOVEL	DNM1L-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404127.1	8	2.406692	KEEP	0	0	0	8	241	GG	0.99257	0.384528	0		+	3	60	93	0	0	7.133354	16	60	534	36	ENST00000266481.6	0.157895	0.387407
PKP2	5318	__UNKNOWN__	__UNKNOWN__	12	33019224	33019224	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:33019224T>C	ENST00000340811.4	-	4	1279				PKP2_ENST00000070846.6_Intron	NM_001005242.2	NP_001005242.2	Q99959	PKP2_HUMAN	plakophilin 2	NA		NA			adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					tggtggctcatgcctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294	5318		Armadillo repeat containing	9024	protein-coding gene	gene with protein product		602861			NA	8922383	Standard	NM_004572	NM_001005242	NA	Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000340811.4:c.1170+2636A>G	chr12.hg19:g.33019224T>C		NA	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	hg19	CCDS31771.1	0.02	-0.228004	TCAxGCC	COVERED																																																																																			NOVEL	PKP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404448.2	7	3.307946	KEEP	0	0	0	11	297	TT	0.993072	0.578892	0		-	3	60	88	0	0	6.493816	18	60	512	49	ENST00000340811.4	0.142857	0.58293
PKP2	5318	__UNKNOWN__	__UNKNOWN__	12	33019238	33019238	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:33019238T>G	ENST00000340811.4	-	4	1279				PKP2_ENST00000070846.6_Intron	NM_001005242.2	NP_001005242.2	Q99959	PKP2_HUMAN	plakophilin 2	NA		NA			adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					tgtaatcccatcactttggga	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294	5318		Armadillo repeat containing	9024	protein-coding gene	gene with protein product		602861			NA	8922383	Standard	NM_004572	NM_001005242	NA	Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000340811.4:c.1170+2622A>C	chr12.hg19:g.33019238T>G		NA	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	hg19	CCDS31771.1	0.02	-0.210504	CCAxCAC	COVERED																																																																																			NOVEL	PKP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404448.2	8	3.308133	KEEP	0	0	0	11	300	TT	0.993072	0.518544	0		-	3	60	105	0	0	8.333128	16	60	478	52	ENST00000340811.4	0.157895	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	39310268	39310268	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:39310268A>G			NA	NA				AC067735.1 (3140 upstream) : RP11-554L12.1 (171246 downstream)						NA		NA									NA						aaaggctcacacctgtaatcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.39310268A>G		NA		hg19		0.02	-0.122799	CACxCCT	COVERED																																																																																			NOVEL					0			4	2.706327	KEEP	1	0	0	9	244	AA	0.99257	0.194853	0			3	60	95	0	0	8.132349	8	60	252	37		0.272727	0.196312
KIF21A	55605	__UNKNOWN__	__UNKNOWN__	12	39817523	39817523	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:39817523T>C	ENST00000361418.5	-	1	60				KIF21A_ENST00000361961.3_Intron|KIF21A_ENST00000544797.2_Intron|KIF21A_ENST00000395670.3_Intron|KIF21A_ENST00000541463.2_Intron			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	NA		NA			ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				tggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10					55605		Kinesins, WD repeat domain containing	19349	protein-coding gene	gene with protein product		608283	fibrosis of the extraocular muscles, congenital, 1	FEOM1	NA	10225949	Standard	NM_017641	NM_017641	NA	Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.44+19205A>G	chr12.hg19:g.39817523T>C		NA	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	hg19	CCDS53776.1	0.02	-0.070165	TCAxGCC	UNCOVERED																																																																																			NOVEL	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403581.1	8	2.706565	KEEP	2	0	0	9	245	TT	0.99257	0.076761	0		-	3	40	100	0	0	9.133151	5	60	144	23	ENST00000361418.5	0.375	0.077336
LRRK2	120892	__UNKNOWN__	__UNKNOWN__	12	40703080	40703080	__UNKNOWN__	Intron	SNP	C	C	G	rs201348262		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:40703080C>G	ENST00000298910.7	+	30	4375					NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	NA		NA			activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				ATTCAtgtgtctgtgtgcgtg	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													35	30	32			NA	NA	12		NA											NA				40703080		2203	4300	6503	SO:0001627	intron_variant			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906	120892		Parkinson disease	18618	protein-coding gene	gene with protein product		609007	Parkinson disease (autosomal dominant) 8	PARK8	NA	15541308	Standard	XM_058513	NM_198578	NA	Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4317+45C>G	chr12.hg19:g.40703080C>G		NA	A6NJU2|Q6ZS50|Q8NCX9	hg19	CCDS31774.1	0.02	-0.289262	TGTxTGT	COVERED																																																																																			NOVEL	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000277179.1	5	6.318389	KEEP	0	0	0	21	633	CC	0.999879	0.780965	0		+	3	60	104	0	0	7.59706	27	60	913	72	ENST00000298910.7	0.1	0.78106
CNTN1	1272	__UNKNOWN__	__UNKNOWN__	12	41096012	41096012	__UNKNOWN__	Intron	SNP	A	A	G	rs9783468	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:41096012A>G	ENST00000551295.2	+	1	41				CNTN1_ENST00000547702.1_Intron	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				tactgggattacaggcatgag	0.458		NA											A|||	3268	0.652556	0.4539	0.7032	5008	,	,	NA	16386	0.8313	NA	0.6312	False	NA	,,,	NA	NA	NA	2504	0.7229	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236	1272		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing, Endogenous ligands	2171	protein-coding gene	gene with protein product	glycoprotein gP135	600016			NA	7959734, 8586965	Standard	NM_001843	NM_001843	NA	Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.-77+9618A>G	chr12.hg19:g.41096012A>G		NA	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	hg19	CCDS8737.1	0.02	-0.114009	ATTxCAG	UNCOVERED																																																																																			NOVEL	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403692.2	6	2.405305	KEEP	0	0	0	8	208	AA	0.99257	0.16126	0		+	3	60	98	0	0	8.744002	6	60	166	29	ENST00000551295.2	0.333333	0.162467
CNTN1	1272	__UNKNOWN__	__UNKNOWN__	12	41305150	41305150	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:41305150A>G	ENST00000551295.2	+	3	211				CNTN1_ENST00000547849.1_Intron|CNTN1_ENST00000348761.2_Intron|CNTN1_ENST00000360099.3_Intron|CNTN1_ENST00000547702.1_Intron|CNTN1_ENST00000347616.1_Intron	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				ccaaagagctaggattacagg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236	1272		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing, Endogenous ligands	2171	protein-coding gene	gene with protein product	glycoprotein gP135	600016			NA	7959734, 8586965	Standard	NM_001843	NM_001843	NA	Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.94+1243A>G	chr12.hg19:g.41305150A>G		NA	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	hg19	CCDS8737.1	0.02	-0.1403	GCTxGGA	COVERED																																																																																			NOVEL	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403692.2	4	3.307856	KEEP	2	0	0	11	296	AA	0.99254	0.259018	0		+	3	60	92	0	0	7.279571	13	60	382	35	ENST00000551295.2	0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	42107122	42107122	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:42107122C>T			NA	NA				RNA5SP360 (54527 upstream) : RP11-630C16.1 (50902 downstream)						NA		NA									NA						cgtgagccaccgcgcccggcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.42107122C>T		NA		hg19		0.02	-0.201753	CACxGCG	COVERED																																																																																			NOVEL					0			7	2.707491	KEEP	0	0	0	9	266	CC	0.99254	0.486885	0			3	60	90	0	0	6.83365	16	60	528	48		0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	42123308	42123308	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:42123308A>G			NA	NA				RNA5SP360 (70713 upstream) : RP11-630C16.1 (34716 downstream)						NA		NA									NA						gcggatcacgaggtcaggaga	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.42123308A>G		NA		hg19		0.02	-0.149091	ACGxGGT	UNCOVERED																																																																																			NOVEL					0			7	3.908841	KEEP	10	0	0	13	347	AA	0	0	0			3	49	106	0	0	8.591768	14	60	403	53		0.176471	0.292001
RP11-630C16.2	0	__UNKNOWN__	__UNKNOWN__	12	42262080	42262080	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:42262080C>T	ENST00000550874.1	-	0	471										NA		NA									NA						tgacctcaggcgatctgcctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550874.1:	chr12.hg19:g.42262080C>T		NA		hg19		0.02	-0.131558	AGGxGAT	COVERED																																																																																			NOVEL	RP11-630C16.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000403776.1	1	2.708245	KEEP	1	0	0	9	281	CC	0.99257	0.22747	0		-	3	60	81	0	0	6.373281	11	60	362	39	ENST00000550874.1	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	42543473	42543473	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:42543473T>C			NA	NA				GXYLT1 (4792 upstream) : YAF2 (7432 downstream)						NA		NA									NA						tgtggtggcttatgcctgtaa	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.42543473T>C		NA		hg19		0.02	-0.122738	GCTxATG	COVERED																																																																																			NOVEL					0			5	2.406151	KEEP	0	0	0	8	220	TT	0.99257	0.194853	0			3	60	85	0	0	6.882866	10	60	288	36		0.230769	0.196312
PPHLN1	51535	__UNKNOWN__	__UNKNOWN__	12	42697865	42697865	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:42697865A>G	ENST00000549190.1	+	2	215							Q8NEY8	PPHLN_HUMAN	periphilin 1	NA		NA			keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		gattacaggcatgagccaccg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283	51535			19369	protein-coding gene	gene with protein product		608150			NA		Standard	NM_201515	NM_016488	NA	Approved		uc001rng.1	Q8NEY8		ENST00000549190.1:c.35-31820A>G	chr12.hg19:g.42697865A>G		NA	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	hg19		0.02	-0.228045	GGCxTGA	UNCOVERED																																																																																			NOVEL	PPHLN1-001	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000404039.1	4	2.390653	KEEP	3	0	0	8	205	AA	0	0	0		+	3	60	100	0	0	7.564812	20	60	601	54	ENST00000549190.1	0.130435	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	43112319	43112319	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:43112319T>C			NA	NA				RP11-25I15.3 (1666 upstream) : RP11-547C5.1 (247605 downstream)						NA		NA									NA						tgcagtgagctatgatcatgc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.43112319T>C		NA		hg19		0.02	-0.113459	AGCxATG	UNCOVERED																																																																																			NOVEL					0			5	2.702606	KEEP	0	0	0	9	228	TT	0.99254	0.161255	0			3	60	93	0	0	7.690265	10	60	272	32		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	43242780	43242780	__UNKNOWN__	IGR	SNP	G	G	C	rs10785386	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:43242780G>C			NA	NA				RP11-25I15.3 (132127 upstream) : RP11-547C5.1 (117144 downstream)						NA		NA									NA						ttacaggcgtgagccaccgcg	0.493		NA											G|||	2822	0.563498	0.3283	0.4524	5008	,	,	NA	15616	0.5764	NA	0.7435	False	NA	,,,	NA	NA	NA	2504	0.7618	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.43242780G>C		NA		hg19		0.02	-0.087727	CGTxAGC	UNCOVERED																																																																																			NOVEL					0			8	2.842749	KEEP	26	1	33	21	639	GG	0.992708	0.098994	0			3	60	102	0	0	10.169669	2	44	69	80		0.6	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	44041716	44041716	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:44041716T>C			NA	NA				ADAMTS20 (95992 upstream) : RP11-350F4.2 (71079 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.44041716T>C		NA		hg19		0.02	-0.184186	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.406664	KEEP	1	0	0	8	232	TT	0	0	0			3	60	93	0	0	7.210532	15	60	445	46		0.166667	0.423478
ANO6	196527	__UNKNOWN__	__UNKNOWN__	12	45816574	45816574	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:45816574G>C	ENST00000423947.3	+	20	2720				ANO6_ENST00000320560.8_Intron|ANO6_ENST00000441606.2_Intron|ANO6_ENST00000435642.1_Intron|ANO6_ENST00000425752.2_Intron	NM_001204803.1	NP_001191732.1	Q4KMQ2	ANO6_HUMAN	anoctamin 6	NA		NA			activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ccaggctggtgtcgcactcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28			196527		Ion channels / Chloride channels : Calcium activated : Anoctamins	25240	protein-coding gene	gene with protein product		608663	transmembrane protein 16F	TMEM16F	NA	15067359, 24692353	Standard	XM_113743	NM_001025356	NA	Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000423947.3:c.2484-166G>C	chr12.hg19:g.45816574G>C		NA	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	hg19	CCDS55819.1	0.02	-0.324572	GGTxTCG	COVERED																																																																																			NOVEL	ANO6-005	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404820.1	6	3.609857	KEEP	1	0	0	12	347	GG	0.993072	0.846082	0		+	4	60	132	0	0	9.761912	30	60	998	62	ENST00000423947.3	0.117647	0.851984
ANO6	196527	__UNKNOWN__	__UNKNOWN__	12	45834183	45834183	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:45834183T>C	ENST00000425752.2	+	0	3554				ANO6_ENST00000435642.1_3'UTR	NM_001142679.1	NP_001136151.1	Q4KMQ2	ANO6_HUMAN	anoctamin 6	NA		NA			activation of blood coagulation via clotting cascade (GO:0002543)|blood coagulation (GO:0007596)|bone mineralization involved in bone maturation (GO:0035630)|calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|dendritic cell chemotaxis (GO:0002407)|ion transmembrane transport (GO:0034220)|phosphatidylserine exposure on blood platelet (GO:0097045)|phospholipid scrambling (GO:0017121)|positive regulation of endothelial cell apoptotic process (GO:2000353)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)	cell surface (GO:0009986)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)|voltage-gated chloride channel activity (GO:0005247)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						ccaccatgcctggctaatttt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL832340	CCDS31782.1, CCDS44865.1, CCDS44866.1, CCDS55819.1	12q12-q13.11	2014-09-17	2008-08-28	2008-08-28			196527		Ion channels / Chloride channels : Calcium activated : Anoctamins	25240	protein-coding gene	gene with protein product		608663	transmembrane protein 16F	TMEM16F	NA	15067359, 24692353	Standard	XM_113743	NM_001025356	NA	Approved	DKFZp313M0720	uc010slf.2	Q4KMQ2	OTTHUMG00000169564	ENST00000425752.2:c.*462T>C	chr12.hg19:g.45834183T>C		NA	A6NNM6|B9EGG0|E7ENK4|E9PB30|E9PCT2|Q8N3Q2	hg19	CCDS44865.1	0.02	1.783442	GCCxGGC	COVERED																																																																																			NOVEL	ANO6-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404819.1	7	3.640777	KEEP	2	1	28	22	609	TT	0.999892	0.996125	0		+	7	60	222	0	0	15.900281	58	60	1705	125	ENST00000425752.2	0.107692	0.996233
ARID2	196528	__UNKNOWN__	__UNKNOWN__	12	46236284	46236284	__UNKNOWN__	Intron	SNP	A	A	G	rs543270205		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:46236284A>G	ENST00000334344.6	+	11	1670				ARID2_ENST00000479608.1_Intron|ARID2_ENST00000422737.1_Intron|ARID2_ENST00000444670.1_Intron	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	NA		NA			chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		gctcatgcctataatcccagc	0.388		NA	N, S, F		hepatocellular carcinoma								A|||	1	0.000199681	0.0	0.0	5008	,	,	NA	13366	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA			Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079	196528		-	18037	protein-coding gene	gene with protein product		609539			NA		Standard	XM_350875	NM_152641	NA	Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.1498+3005A>G	chr12.hg19:g.46236284A>G		NA	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	hg19	CCDS31783.1	0.02	-0.070175	CCTxTAA	UNCOVERED																																																																																			NOVEL	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318380.2	6	3.007149	KEEP	1	0	0	10	271	AA	0.99254	0.053733	0		+	3	40	104	0	0	9.533041	5	60	153	25	ENST00000334344.6	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	47239581	47239581	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:47239581G>T			NA	NA				SLC38A4 (19801 upstream) : AMIGO2 (229908 downstream)						NA		NA									NA						gaggtggagggtgcagtgagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.47239581G>T		NA		hg19		0.02	-0.140314	AGGxTGC	COVERED																																																																																			NOVEL					0			8	3.610701	KEEP	0	0	0	12	369	GG	0.993634	0.259304	0			4	60	104	0	0	8.401259	12	60	408	39		0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	47374407	47374407	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:47374407G>T			NA	NA				SLC38A4 (154627 upstream) : AMIGO2 (95082 downstream)						NA		NA									NA						agtgctgggagtacaggcatg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.47374407G>T		NA		hg19		0.02	-0.166672	GGAxTAC	COVERED																																																																																			NOVEL					0			2	2.407416	KEEP	0	0	0	8	255	GG	0.99257	0.351317	0			3	60	89	0	0	6.733653	16	60	544	41		0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	47877117	47877117	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:47877117T>C			NA	NA				RP1-90J4.1 (63155 upstream) : RPAP3 (179952 downstream)						NA		NA									NA						accttagccttccaaagtgct	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.47877117T>C		NA		hg19		0.02	-0.070174	CCTxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.406591	KEEP	3	0	0	8	230	TT	0	0	0			2	60	70	0	0	6.492907	3	60	94	27		0.4	0.054137
VDR	7421	__UNKNOWN__	__UNKNOWN__	12	48247269	48247269	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:48247269T>C	ENST00000550325.1	-	7	1278				VDR_ENST00000229022.3_Intron|VDR_ENST00000549336.1_Intron|VDR_ENST00000395324.2_Intron|VDR_ENST00000535672.1_Intron	NM_001017536.1	NP_001017536.1	P11473	VDR_HUMAN	vitamin D (1,25- dihydroxyvitamin D3) receptor	NA		NA			bile acid signaling pathway (GO:0038183)|calcium ion transport (GO:0006816)|cell morphogenesis (GO:0000902)|cellular calcium ion homeostasis (GO:0006874)|decidualization (GO:0046697)|gene expression (GO:0010467)|intestinal absorption (GO:0050892)|lactation (GO:0007595)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vitamin D 24-hydroxylase activity (GO:0010980)|regulation of calcidiol 1-monooxygenase activity (GO:0060558)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vitamin D receptor signaling pathway (GO:0070561)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcitriol binding (GO:1902098)|calcitriol receptor activity (GO:0008434)|DNA binding (GO:0003677)|lithocholic acid binding (GO:1902121)|lithocholic acid receptor activity (GO:0038186)|retinoid X receptor binding (GO:0046965)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(3)|skin(2)	22		Acute lymphoblastic leukemia(13;0.109)|all_hematologic(14;0.214)		GBM - Glioblastoma multiforme(48;0.17)	Alfacalcidol(DB01436)|Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Cholecalciferol(DB00169)|Dihydrotachysterol(DB01070)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	ggcgtggtggttcatgcctgt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J03258	CCDS8757.1, CCDS55820.1	12q12-q14	2014-06-13				ENSG00000111424	7421		Nuclear hormone receptors	12679	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 163	601769			NA	1662663	Standard		NM_001017536	NA	Approved	NR1I1, PPP1R163	uc001rql.3	P11473		ENST00000550325.1:c.905+2143A>G	chr12.hg19:g.48247269T>C		NA	B2R5Q1|G3V1V9|Q5PSV3	hg19	CCDS55820.1	0.02	-0.245535	TGGxTCA	COVERED																																																																																			NOVEL	VDR-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406435.1	11	5.712865	KEEP	0	0	0	19	511	TT	0.99986	0.641257	0		-	3	60	93	0	0	6.865656	20	60	588	61	ENST00000550325.1	0.130435	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	48998493	48998493	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:48998493G>T			NA	NA				LALBA (34644 upstream) : KANSL2 (48691 downstream)						NA		NA									NA						atcccagcacgttgggaggcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.48998493G>T		NA		hg19		0.02	-0.140344	CACxTTG	UNCOVERED																																																																																			NOVEL					0			5	2.406632	KEEP	1	0	0	8	230	GG	0	0	0			4	60	123	0	0	10.571092	10	60	321	33		0.285714	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	48998646	48998646	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:48998646T>C			NA	NA				LALBA (34797 upstream) : KANSL2 (48538 downstream)						NA		NA									NA						ccgaggcgggtggatcacctg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.48998646T>C		NA		hg19		0.02	-0.166627	GGGxGGA	COVERED																																																																																			NOVEL					0			5	3.545166	KEEP	1	0	0	12	294	TT	0.993072	0.351495	0			3	60	87	0	0	6.611265	15	60	450	40		0.166667	0.353947
ADCY6	112	__UNKNOWN__	__UNKNOWN__	12	49160046	49160046	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49160046A>C	ENST00000550422.1	-	0	5811				ADCY6_ENST00000357869.3_3'UTR|RP11-579D7.2_ENST00000548742.1_RNA	NM_020983.2	NP_066193.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						ATGGTTCACCATCCTCCCCCA	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	112	4.6.1.1	Adenylate cyclases	237	protein-coding gene	gene with protein product		600294			NA		Standard	NM_020983	NM_015270	NA	Approved	AC6	uc001rsh.4	O43306		ENST00000550422.1:c.*2328T>G	chr12.hg19:g.49160046A>C		NA	Q9NR75|Q9UDB0	hg19	CCDS8768.1	0.02	-0.394708	ACCxTCC	COVERED																																																																																			NOVEL	ADCY6-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408862.1	2	4.745515	KEEP	0	0	0	16	402	AA	0.997832	0.924631	0		-	9	60	297	0	0	24.314631	35	60	1065	96	ENST00000550422.1	0.204545	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	49289747	49289747	__UNKNOWN__	IGR	SNP	A	A	G	rs543841767		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49289747A>G			NA	NA				RNU6-600P (3736 upstream) : RP11-302B13.5 (7538 downstream)						NA		NA									NA						caggagaatcacttgaacccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.49289747A>G		NA		hg19		0.02	-0.228022	ATCxCTT	COVERED																																																																																			NOVEL					0			8	2.705753	KEEP	2	0	0	9	241	AA	0.99257	0.578599	0			4	60	126	0	0	9.73732	21	60	619	41		0.16	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	49294563	49294563	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49294563G>A			NA	NA				RNU6-600P (8552 upstream) : RP11-302B13.5 (2722 downstream)						NA		NA									NA						ggctgggcacggtggctcacg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.49294563G>A		NA		hg19		0.02	-0.219295	CACxGTG	COVERED																																																																																			NOVEL					0			5	4.513082	KEEP	2	0	0	15	453	GG	0.995343	0.550313	0			3	60	90	0	0	6.692679	18	60	580	61		0.142857	0.552887
CCDC65	85478	__UNKNOWN__	__UNKNOWN__	12	49307660	49307660	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49307660T>C	ENST00000320516.4	+	3	488				CCDC65_ENST00000266984.5_Intron|RP11-302B13.5_ENST00000398092.4_Intron	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	NA		NA								breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						ctgcccaccttggcctcccaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537	85478			29937	protein-coding gene	gene with protein product		611088			NA	17089017, 21700706	Standard	NM_033124	NM_033124	NA	Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.301-527T>C	chr12.hg19:g.49307660T>C		NA	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	hg19	CCDS8772.1	0.02	-0.175406	CCTxGGC	COVERED																																																																																			NOVEL	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408922.1	14	3.907037	KEEP	5	0	0	13	334	TT	0.99254	0.384517	0		+	3	36	91	0	0	6.861559	17	60	498	46	ENST00000320516.4	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	49352194	49352194	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49352194G>A			NA	NA				ARF3 (860 upstream) : snoU13 (2326 downstream)						NA		NA									NA						tctgcctcccgggttcaagcg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.49352194G>A		NA		hg19		0.02	-0.324509	CCCxGGT	COVERED																																																																																			NOVEL					0			63	12.798899	KEEP	38	2	55	62	1831	GG	1	0.835716	0			4	60	100	0	1	6.519591	31	60	1011	156		0.114286	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	49354308	49354308	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49354308G>A			NA	NA				ARF3 (2974 upstream) : snoU13 (212 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.49354308G>A		NA		hg19		0.02	-0.12281	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			9	2.406508	KEEP	5	0	0	8	231	GG	0	0	0			3	60	93	0	0	7.681814	10	60	331	36		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	49387181	49387181	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49387181A>G			NA	NA				WNT1 (11722 upstream) : DDN (1750 downstream)						NA		NA									NA						cacccaggctagagtgcagtg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.49387181A>G		NA		hg19		0.02	-0.087716	GCTxGAG	UNCOVERED																																																																																			NOVEL					0			3	2.40612	KEEP	0	0	0	8	221	AA	0.99257	0.09898	0			3	60	101	0	0	9.043685	6	60	181	25		0.333333	0.099721
RP11-161H23.9	0	__UNKNOWN__	__UNKNOWN__	12	49710811	49710811	__UNKNOWN__	RNA	SNP	T	T	C	rs564658753	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49710811T>C	ENST00000553259.1	-	0	278										NA		NA									NA						cgcggtggcttacgcctgtaa	0.517		NA											T|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	13224	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000553259.1:	chr12.hg19:g.49710811T>C		NA		hg19		0.02	-0.131496	GCTxACG	COVERED																																																																																			NOVEL	RP11-161H23.9-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000405659.1	5	2.404822	KEEP	0	0	0	8	206	TT	0.99257	0.22747	0		-	3	60	96	0	0	7.982936	10	60	283	37	ENST00000553259.1	0.230769	0.229173
SPATS2	65244	__UNKNOWN__	__UNKNOWN__	12	49821776	49821776	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49821776T>C	ENST00000547865.1	+	3	104				SPATS2_ENST00000553127.1_Intron|SPATS2_ENST00000552918.1_Intron|SPATS2_ENST00000321898.6_Intron			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	NA		NA				cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						cggtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023179	CCDS31794.1	12q13.12	2009-06-12					65244			18650	protein-coding gene	gene with protein product		611667			NA	11944913, 17989879	Standard	NM_023071	NM_023071	NA	Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000547865.1:c.-330-13737T>C	chr12.hg19:g.49821776T>C		NA	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	hg19		0.02	-0.219258	TCAxGCC	COVERED																																																																																			NOVEL	SPATS2-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000404025.1	9	3.00742	KEEP	7	0	0	10	272	TT	0.99254	0.548763	0		+	3	60	103	0	0	7.926857	19	60	557	65	ENST00000547865.1	0.136364	0.552887
SPATS2	65244	__UNKNOWN__	__UNKNOWN__	12	49909690	49909690	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:49909690T>C	ENST00000553127.1	+	11	1411				SPATS2_ENST00000552918.1_Intron|SPATS2_ENST00000321898.6_Intron			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	NA		NA				cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						tttgggaggctgaggcgggca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023179	CCDS31794.1	12q13.12	2009-06-12					65244			18650	protein-coding gene	gene with protein product		611667			NA	11944913, 17989879	Standard	NM_023071	NM_023071	NA	Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.898+1294T>C	chr12.hg19:g.49909690T>C		NA	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	hg19	CCDS31794.1	0.02	-0.192972	GGCxGAG	COVERED																																																																																			NOVEL	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404023.1	6	2.706515	KEEP	0	0	0	9	247	TT	0.99254	0.454342	0		+	4	60	131	0	0	10.868305	14	60	428	44	ENST00000553127.1	0.222222	0.457757
RP11-70F11.8	0	__UNKNOWN__	__UNKNOWN__	12	50313117	50313117	__UNKNOWN__	lincRNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:50313117C>G	ENST00000546821.1	+	0	131										NA		NA									NA						aaactcctggcctcaagcgat	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000546821.1:	chr12.hg19:g.50313117C>G		NA		hg19		0.02	-0.289301	TGGxCTC	COVERED																																																																																			NOVEL	RP11-70F11.8-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000405534.1	12	6.319174	KEEP	4	0	0	21	654	CC	0.999879	0.760795	0		+	3	60	100	1	0	7.198409	27	60	901	85	ENST00000546821.1	0.1	0.760887
FAM186A	121006	__UNKNOWN__	__UNKNOWN__	12	50772080	50772080	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:50772080G>A	ENST00000327337.5	-	2	192				FAM186A_ENST00000543111.1_Intron	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	NA		NA									NA						ttgggaggccgaggtgggtgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(138;1796 1887 12511 19463 37884)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958	121006			26980	protein-coding gene	gene with protein product		NA			NA		Standard	XM_001718353	NM_001145475	NA	Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.193-14933C>T	chr12.hg19:g.50772080G>A		NA		hg19	CCDS44878.1	0.02	-0.184217	GCCxAGG	COVERED																																																																																			NOVEL	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000396838.1	11	2.707546	KEEP	3	0	0	9	267	GG	0.99257	0.420331	0		-	3	60	89	0	0	6.661275	17	60	571	44	ENST00000327337.5	0.15	0.423478
ATF1	466	__UNKNOWN__	__UNKNOWN__	12	51194609	51194609	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:51194609G>A	ENST00000262053.3	+	3	216				ATF1_ENST00000539132.1_Intron	NM_005171.4	NP_005162.1	P18846	ATF1_HUMAN	activating transcription factor 1	NA		NA			cellular protein complex assembly (GO:0043623)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to cobalt ion (GO:0032025)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/ATF1(347)|FUS/ATF1(4)	breast(1)|large_intestine(1)|ovary(2)	4					Pseudoephedrine(DB00852)	atggctgggcgcggtggctca	0.507		NA	T	EWSR1, FUS	malignant melanoma of soft parts , angiomatoid fibrous histiocytoma 																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		12	12q13	466	activating transcription factor 1		E, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC029619	CCDS8803.1	12q13	2014-05-13			ENSG00000123268	ENSG00000123268	466		basic leucine zipper proteins	783	protein-coding gene	gene with protein product		123803			NA	8401579	Standard	NM_005171	NM_005171	NA	Approved	TREB36	uc001rww.4	P18846		ENST00000262053.3:c.194+4817G>A	chr12.hg19:g.51194609G>A		NA	B4DRF9|P25168|Q9H4A8	hg19	CCDS8803.1	0.02	-0.175434	GGCxCGG	COVERED																																																																																			NOVEL	ATF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404285.1	7	2.70663	KEEP	3	0	0	9	249	GG	0.99257	0.384528	0		+	4	60	119	0	0	9.562642	15	60	486	45	ENST00000262053.3	0.210526	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	51291002	51291002	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:51291002A>C			NA	NA				TMPRSS12 (9335 upstream) : METTL7A (26252 downstream)						NA		NA									NA						ttttgggaggatgaggcagga	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.51291002A>C		NA		hg19		0.02	-0.254325	AGGxTGA	COVERED																																																																																			NOVEL					0			14	4.207585	KEEP	0	0	0	14	381	AA	0.995343	0.66541	0			3	60	95	0	0	6.793542	25	60	753	61		0.107143	0.668523
TFCP2	7024	__UNKNOWN__	__UNKNOWN__	12	51502362	51502362	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:51502362G>A	ENST00000257915.5	-	6	1176				TFCP2_ENST00000549867.1_Intron|TFCP2_ENST00000548115.1_Intron|TFCP2_ENST00000307660.4_Intron	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	NA		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						ttcaaggccagcctgggcaac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457	7024			11748	protein-coding gene	gene with protein product		189889			NA	8157699	Standard	NM_005653	NM_005653	NA	Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.717+541C>T	chr12.hg19:g.51502362G>A		NA	A8K5E9|Q12801|Q9UD75|Q9UD77	hg19	CCDS8808.1	0.02	-0.1228	CCAxCCT	COVERED																																																																																			NOVEL	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405119.1	9	3.611149	KEEP	0	0	0	12	383	GG	0.993634	0.195062	0		-	3	60	88	0	0	7.18199	10	60	328	34	ENST00000257915.5	0.230769	0.196312
TFCP2	7024	__UNKNOWN__	__UNKNOWN__	12	51558148	51558148	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:51558148G>A	ENST00000257915.5	-	1	581				TFCP2_ENST00000549867.1_Intron|TFCP2_ENST00000548115.1_Intron|TFCP2_ENST00000307660.4_Intron	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	NA		NA			regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						ttgggaggccgaggcgggcag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457	7024			11748	protein-coding gene	gene with protein product		189889			NA	8157699	Standard	NM_005653	NM_005653	NA	Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.122+7935C>T	chr12.hg19:g.51558148G>A		NA	A8K5E9|Q12801|Q9UD75|Q9UD77	hg19	CCDS8808.1	0.02	-0.289463	GCCxAGG	COVERED																																																																																			NOVEL	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405119.1	15	7.521325	KEEP	5	0	0	25	744	GG	0.999879	0.760795	0		-	4	60	116	0	0	8.524028	24	60	769	89	ENST00000257915.5	0.142857	0.760887
SMAGP	57228	__UNKNOWN__	__UNKNOWN__	12	51654187	51654187	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:51654187G>A	ENST00000603798.1	-	2	707				SMAGP_ENST00000605627.1_Intron|SMAGP_ENST00000603864.1_Intron|SMAGP_ENST00000398453.3_Intron|SMAGP_ENST00000604188.1_Intron|SMAGP_ENST00000603838.1_Intron|DAZAP2_ENST00000604900.1_Intron	NM_001031628.1	NP_001026798.1	Q0VAQ4	SMAGP_HUMAN	small cell adhesion glycoprotein	NA		NA				cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)					NA						ttgagacggagtctcgctctg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS44889.1	12q13.13	2010-02-17			ENSG00000170545	ENSG00000170545	57228			26918	protein-coding gene	gene with protein product	small trans-membrane and glycosylated protein	NA			NA	15021913	Standard	NM_020467	NM_001031628	NA	Approved	MGC149453, MGC149454, hSMAGP	uc001rye.1	Q0VAQ4		ENST00000603798.1:c.34+8841C>T	chr12.hg19:g.51654187G>A		NA	A6NIL5	hg19	CCDS44889.1	0.02	-0.157897	GGAxTCT	COVERED																																																																																			NOVEL	SMAGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000469789.1	8	3.310082	KEEP	4	0	0	11	347	GG	0.99254	0.320398	0		-	4	60	117	0	0	9.830783	11	60	370	41	ENST00000603798.1	0.266667	0.322807
SMAGP	57228	__UNKNOWN__	__UNKNOWN__	12	51655090	51655090	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:51655090A>T	ENST00000603798.1	-	2	707				SMAGP_ENST00000605627.1_Intron|SMAGP_ENST00000603864.1_Intron|SMAGP_ENST00000398453.3_Intron|SMAGP_ENST00000604188.1_Intron|SMAGP_ENST00000603838.1_Intron|DAZAP2_ENST00000604900.1_Intron	NM_001031628.1	NP_001026798.1	Q0VAQ4	SMAGP_HUMAN	small cell adhesion glycoprotein	NA		NA				cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)					NA						catgttggccaggctggtctc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS44889.1	12q13.13	2010-02-17			ENSG00000170545	ENSG00000170545	57228			26918	protein-coding gene	gene with protein product	small trans-membrane and glycosylated protein	NA			NA	15021913	Standard	NM_020467	NM_001031628	NA	Approved	MGC149453, MGC149454, hSMAGP	uc001rye.1	Q0VAQ4		ENST00000603798.1:c.34+7938T>A	chr12.hg19:g.51655090A>T		NA	A6NIL5	hg19	CCDS44889.1	0.02	-0.201727	GCCxGGC	COVERED																																																																																			NOVEL	SMAGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000469789.1	5	3.609394	KEEP	1	0	0	12	336	AA	0.993634	0.487421	0		-	3	52	92	0	0	7.033716	16	60	483	52	ENST00000603798.1	0.157895	0.490544
SCN8A	6334	__UNKNOWN__	__UNKNOWN__	12	52057764	52057764	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:52057764G>A	ENST00000354534.6	+	2	454				SCN8A_ENST00000550891.1_Intron|SCN8A_ENST00000545061.1_Intron	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	NA		NA			adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	cgtgatctcagctcactgcaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876	6334		Sodium channels, Voltage-gated ion channels / Sodium channels	10596	protein-coding gene	gene with protein product		600702	sodium channel, voltage gated, type VIII, alpha polypeptide	MED	NA	7670495, 9828131, 16382098	Standard	NM_014191	NM_014191	NA	Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.276+887G>A	chr12.hg19:g.52057764G>A		NA	B9VWG8|O95788|Q9NYX2|Q9UPB2	hg19	CCDS44891.1	0.02	-0.087696	TCAxCTC	UNCOVERED																																																																																			NOVEL	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404372.3	11	2.707968	KEEP	9	0	0	9	273	GG	0	0	0		+	3	28	77	0	0	6.478012	7	60	232	29	ENST00000354534.6	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	52275209	52275209	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:52275209T>C			NA	NA				RP11-923I11.5 (28696 upstream) : ANKRD33 (6534 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.52275209T>C		NA		hg19		0.02	-0.149114	TCAxGCC	COVERED																																																																																			NOVEL					0			3	3.308422	KEEP	0	0	0	11	306	TT	0.993072	0.289978	0			3	60	101	0	0	8.372836	11	60	330	42		0.214286	0.292001
GRASP	160622	__UNKNOWN__	__UNKNOWN__	12	52407104	52407104	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:52407104G>A	ENST00000293662.4	+	5	534				GRASP_ENST00000552963.1_Intron|GRASP_ENST00000552049.1_Intron|GRASP_ENST00000380039.2_Intron	NM_181711.2	NP_859062.1	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides 1)-associated scaffold protein	NA		NA			protein localization (GO:0008104)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				central_nervous_system(1)|large_intestine(1)|lung(1)|skin(2)	5				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ctcgtgatccgcccgcctcgg	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC019244	CCDS8817.1, CCDS61124.1	12q13.13	2011-09-02			ENSG00000161835	ENSG00000161835	160622			18707	protein-coding gene	gene with protein product		612027			NA	10828067	Standard		NM_001271856	NA	Approved		uc001rzo.2	Q7Z6J2	OTTHUMG00000169595	ENST00000293662.4:c.455-367G>A	chr12.hg19:g.52407104G>A		NA	Q6PIF8|Q7Z741	hg19	CCDS8817.1	0.02	-0.13156	TCCxCCC	UNCOVERED																																																																																			NOVEL	GRASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404972.1	3	2.405036	KEEP	7	0	0	8	213	GG	0	0	0		+	3	60	87	0	1	6.872646	12	60	374	45	ENST00000293662.4	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	52562725	52562725	__UNKNOWN__	IGR	SNP	G	G	C	rs199847695		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:52562725G>C			NA	NA				AC078864.2 (54929 upstream) : KRT80 (54 downstream)						NA		NA									NA						tacacacacagacacacacac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.52562725G>C		NA		hg19		0.02	-0.236832	ACAxACA	COVERED																																																																																			NOVEL					0			5	2.407119	KEEP	0	0	0	8	242	GG	0.99257	0.607857	0			3	60	90	1	0	6.628164	19	60	624	42		0.136364	0.612407
KRT86	3892	__UNKNOWN__	__UNKNOWN__	12	52699590	52699590	__UNKNOWN__	Intron	SNP	C	C	G	rs200865593		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:52699590C>G	ENST00000423955.2	+	8	1204				KRT86_ENST00000293525.5_Intron|KRT86_ENST00000544024.1_Intron			O43790	KRT86_HUMAN	keratin 86	NA		NA				extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCATCTGTGCCCAAGGTCAGA	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													95	85	88			NA	NA	12		NA											NA				52699590		2203	4300	6503	SO:0001627	intron_variant			X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442	3892		-, Intermediate filaments type II, keratins (basic)	6463	protein-coding gene	gene with protein product	hard keratin type II 6	601928	keratin, hair, basic, 6 (monilethrix)	KRTHB6	NA	9241275, 16831889	Standard	NM_002284	NM_002284	NA	Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.1026+18C>G	chr12.hg19:g.52699590C>G		NA	P78387	hg19	CCDS41785.1	0.02	1.555191	TGCxCAA	COVERED																																																																																			NOVEL	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404911.1	1	2.707045	KEEP	2	0	0	9	255	CC	0.99254	0.982161	0		+	5	40	157	0	0	10.578893	56	60	1853	93	ENST00000423955.2	0.081967	0.989542
EIF4B	1975	__UNKNOWN__	__UNKNOWN__	12	53403142	53403142	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:53403142C>T	ENST00000420463.3	+	1	41				EIF4B_ENST00000262056.9_Intron|EIF4B_ENST00000551527.1_Intron|EIF4B_ENST00000416762.3_Intron			P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						acccagtctccactaaaaata	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046	1975		RNA binding motif (RRM) containing	3285	protein-coding gene	gene with protein product		603928			NA		Standard	NM_001417	XM_005268709	NA	Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000420463.3:c.13+2862C>T	chr12.hg19:g.53403142C>T		NA	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	hg19		0.02	-0.149123	CTCxACT	COVERED																																																																																			NOVEL	EIF4B-007	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000404914.1	4	3.309894	KEEP	0	0	0	11	340	CC	0.993072	0.289978	0		+	3	60	90	0	0	7.17223	12	60	398	42	ENST00000420463.3	0.2	0.292001
SOAT2	8435	__UNKNOWN__	__UNKNOWN__	12	53497949	53497949	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:53497949C>T	ENST00000301466.3	+	2	157	c.97C>T	c.(97-99)Cac>Tac	p.H33Y		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	33		NA			cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)			endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	CACTGAGACGCACAGAGCCCC	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													106	97	100			NA	NA	12		NA											NA				53497949		2203	4300	6503	SO:0001583	missense			AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	8435	2.3.1.26		11178	protein-coding gene	gene with protein product		601311			NA	9756920	Standard		NM_003578	NA	Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.97C>T	chr12.hg19:g.53497949C>T	ENSP00000301466:p.His33Tyr	NA	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	hg19	CCDS8847.1	0.02	1.517798	ACGxACA	COVERED	.	.	.	.	.	.	.	.	.	.	C	14.63	2.592555	0.46214	.	.	ENSG00000167780	ENST00000551896;ENST00000301466	T;T	0.47177	0.85;1.95	5.01	3.16	0.36331	.	0.954902	0.08738	N	0.901015	T	0.48059	0.1479	L	0.57536	1.79	0.09310	N	1	B	0.26975	0.165	B	0.31751	0.135	T	0.41592	-0.9500	10	0.31617	T	0.26	-2.1435	11.9532	0.52966	0.0:0.6382:0.3618:0.0	.	33	O75908	SOAT2_HUMAN	Y	33	ENSP00000450120:H33Y;ENSP00000301466:H33Y	ENSP00000301466:H33Y	H	+	1	0	SOAT2	51784216	0.003000	0.15002	0.001000	0.08648	0.494000	0.33585	0.982000	0.29539	0.802000	0.34089	0.655000	0.94253	CAC	NOVEL	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405817.1	26	24.066634	KEEP	0	0	0	80	2346	CC	1	1	0		+	7	60	174	0	0	8.857279	127	60	4328	293	ENST00000301466.3	0.052239	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	53758404	53758404	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:53758404T>G			NA	NA				SP7 (28238 upstream) : SP1 (15573 downstream)						NA		NA									NA						gcctcccaaattgctgggatt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.53758404T>G		NA		hg19		0.02	-0.157859	AAAxTGC	COVERED																																																																																			NOVEL					0			6	3.004244	KEEP	0	0	0	10	252	TT	0.992708	0.320453	0			3	60	98	0	0	7.710323	15	60	428	39		0.166667	0.322807
RP11-793H13.10	0	__UNKNOWN__	__UNKNOWN__	12	53920671	53920671	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:53920671C>G	ENST00000591834.1	-	10	977				ATF7_ENST00000548446.2_Intron|ATF7_ENST00000415113.1_Intron|ATF7_ENST00000456903.4_Intron|ATF7_ENST00000420353.2_Intron|ATF7_ENST00000328463.7_Intron						NA		NA									NA						ggccgggcgccgtggctcacg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000591834.1:c.928-2126G>C	chr12.hg19:g.53920671C>G		NA		hg19		0.02	-0.245577	CGCxGTG	COVERED																																																																																			NOVEL	RP11-793H13.10-001	PUTATIVE	not_organism_supported|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000460684.1	10	2.703594	KEEP	1	0	0	9	246	AC	0.992708	0.663648	0		-	4	58	120	0	0	9.139247	21	60	659	53	ENST00000591834.1	0.16	0.668523
RP11-793H13.10	0	__UNKNOWN__	__UNKNOWN__	12	53933877	53933877	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:53933877T>C	ENST00000591834.1	-	5	314				ATF7_ENST00000548446.2_Intron|ATF7_ENST00000415113.1_Intron|ATF7_ENST00000456903.4_Intron|ATF7_ENST00000420353.2_Intron|ATF7_ENST00000328463.7_Intron						NA		NA									NA						tggctcatgcttgtaatccca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000591834.1:c.265-2541A>G	chr12.hg19:g.53933877T>C		NA		hg19		0.02	-0.219248	TGCxTGT	COVERED																																																																																			NOVEL	RP11-793H13.10-001	PUTATIVE	not_organism_supported|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000460684.1	9	3.609703	KEEP	0	0	0	12	340	TT	0.993634	0.549368	0		-	3	60	94	0	0	6.850572	22	60	651	53	ENST00000591834.1	0.12	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	54025550	54025550	__UNKNOWN__	IGR	SNP	A	A	G	rs12809705		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54025550A>G			NA	NA				ATF7 (5351 upstream) : ATP5G2 (959 downstream)						NA		NA									NA						tgggattacaagcatgagcca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.54025550A>G		NA		hg19		0.02	-0.131544	ACAxGCA	COVERED																																																																																			NOVEL					0			3	3.308295	KEEP	1	0	0	11	300	AA	0.993072	0.227586	0			3	60	89	0	0	7.07301	12	60	354	37		0.2	0.229173
ATP5G2	517	__UNKNOWN__	__UNKNOWN__	12	54036853	54036853	__UNKNOWN__	Intron	SNP	G	G	A	rs370266608		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54036853G>A	ENST00000550241.1	-	2	65							Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						ccaggaggccgaggtgggagg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390	517		Mitochondrial respiratory chain complex / Complex V, ATPases / F-type	842	protein-coding gene	gene with protein product		603193	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2, ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)		NA	8328972	Standard	NM_005176	NM_005176	NA	Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000550241.1:c.342-10003C>T	chr12.hg19:g.54036853G>A		NA	B3KQQ6	hg19		0.02	-0.140345	GCCxAGG	COVERED																																																																																			NOVEL	ATP5G2-009	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000407401.1	7	2.706789	KEEP	0	0	0	9	249	GG	0.99254	0.259018	0		-	3	60	86	0	0	6.679148	13	60	424	31	ENST00000550241.1	0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	54309296	54309296	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54309296G>C			NA	NA				RN7SKP289 (99033 upstream) : HOXC-AS5 (19815 downstream)						NA		NA									NA						tcttgttgccgaggctggagt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.54309296G>C		NA		hg19		0.02	-0.131573	GCCxAGG	COVERED																																																																																			NOVEL					0			4	2.406023	KEEP	0	0	0	8	227	GG	0.99257	0.22747	0			3	60	102	0	1	8.581935	10	60	311	31		0.230769	0.229173
RP11-834C11.3	0	__UNKNOWN__	__UNKNOWN__	12	54468672	54468672	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54468672G>T	ENST00000515617.1	+	0	311					NR_026655.1					NA		NA									NA						agcactttgggaggccaaggc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000515617.1:	chr12.hg19:g.54468672G>T		NA		hg19		0.02	-0.245636	TGGxAGG	COVERED																																																																																			NOVEL	RP11-834C11.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000358961.1	9	3.310121	KEEP	1	0	0	11	348	GG	0.993072	0.636904	0		+	3	40	96	0	0	6.994602	23	60	795	60	ENST00000515617.1	0.115385	0.641347
CBX5	23468	__UNKNOWN__	__UNKNOWN__	12	54627611	54627611	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54627611G>A	ENST00000209875.4	-	0	8640					NM_012117.2	NP_036249.1	P45973	CBX5_HUMAN	chromobox homolog 5	NA		NA			blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						agtcccagctgcttgggaggc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(153;588 2459 18334 48613)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916	23468			1555	protein-coding gene	gene with protein product	HP1 alpha homolog (Drosophila)	604478	chromobox homolog 5 (Drosophila HP1 alpha), chromobox homolog 5 (HP1 alpha homolog, Drosophila)		NA	8663349	Standard	NM_012117	NM_012117	NA	Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000209875.4:c.*7928C>T	chr12.hg19:g.54627611G>A		NA	B2R8T9	hg19	CCDS8875.1	0.02	2.666003	GCTxCTT	COVERED																																																																																			NOVEL	CBX5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405467.1	15	8.390027	KEEP	0	2	45	44	1309	GG	1	0.999987	0		-	6	60	165	0	0	9.527495	94	60	3166	196	ENST00000209875.4	0.06	0.999987
CBX5	23468	__UNKNOWN__	__UNKNOWN__	12	54629329	54629329	__UNKNOWN__	3'UTR	SNP	T	T	C	rs551960061	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54629329T>C	ENST00000209875.4	-	0	6922					NM_012117.2	NP_036249.1	P45973	CBX5_HUMAN	chromobox homolog 5	NA		NA			blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						acccgggaggtggagcttgca	0.552		NA											C|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	16117	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA	Colon(153;588 2459 18334 48613)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916	23468			1555	protein-coding gene	gene with protein product	HP1 alpha homolog (Drosophila)	604478	chromobox homolog 5 (Drosophila HP1 alpha), chromobox homolog 5 (HP1 alpha homolog, Drosophila)		NA	8663349	Standard	NM_012117	NM_012117	NA	Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000209875.4:c.*6210A>G	chr12.hg19:g.54629329T>C		NA	B2R8T9	hg19	CCDS8875.1	0.02	-0.271414	AGGxGGA	COVERED																																																																																			NOVEL	CBX5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405467.1	3	4.20608	KEEP	2	0	0	14	342	TT	0.99649	0.714798	0		-	4	60	104	0	0	7.303752	25	60	647	55	ENST00000209875.4	0.137931	0.717315
RP11-968A15.8	0	__UNKNOWN__	__UNKNOWN__	12	54701992	54701992	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54701992A>G	ENST00000553061.1	+	0	545										NA		NA									NA						cgcctgcctcagcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000553061.1:	chr12.hg19:g.54701992A>G		NA		hg19		0.02	-0.219262	CTCxGCC	COVERED																																																																																			NOVEL	RP11-968A15.8-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000406596.1	9	2.244177	KEEP	13	1	15	13	380	AA	0.99254	0.548763	0		+	3	60	90	0	0	6.565816	20	60	609	73	ENST00000553061.1	0.130435	0.552887
RP11-753H16.3	0	__UNKNOWN__	__UNKNOWN__	12	54748023	54748023	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54748023T>C	ENST00000550474.1	+	0	47				RP11-753H16.5_ENST00000552785.1_RNA						NA		NA									NA						cctcagcctcttgagtagctg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550474.1:	chr12.hg19:g.54748023T>C		NA		hg19		0.02	-0.166654	CTCxTGA	COVERED																																																																																			NOVEL	RP11-753H16.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000406597.1	6	3.308325	KEEP	0	0	0	11	304	TT	0.993072	0.351495	0		+	3	60	96	0	0	7.591885	14	60	434	39	ENST00000550474.1	0.176471	0.353947
NCKAP1L	3071	__UNKNOWN__	__UNKNOWN__	12	54925953	54925953	__UNKNOWN__	Splice_Site	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:54925953G>C	ENST00000293373.6	+	26	2860		c.e26-1		NCKAP1L_ENST00000545638.2_Splice_Site	NM_005337.4	NP_005328.2	P55160	NCKPL_HUMAN	NCK-associated protein 1-like	NA		NA			actin polymerization-dependent cell motility (GO:0070358)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|chemotaxis (GO:0006935)|cortical actin cytoskeleton organization (GO:0030866)|erythrocyte development (GO:0048821)|maintenance of cell polarity (GO:0030011)|myeloid cell homeostasis (GO:0002262)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of myosin-light-chain-phosphatase activity (GO:0035509)|neutrophil chemotaxis (GO:0030593)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of CD8-positive, alpha-beta T cell differentiation (GO:0043378)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of lymphocyte differentiation (GO:0045621)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of T cell proliferation (GO:0042102)|protein complex assembly (GO:0006461)|response to drug (GO:0042493)|T cell homeostasis (GO:0043029)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)|protein kinase activator activity (GO:0030295)|Rac GTPase activator activity (GO:0030675)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(37)|ovary(3)|prostate(3)|skin(3)|stomach(2)	80						CTTTCCTCCAGGTTTTCTCCT	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													142	121	128			NA	NA	12		NA											NA				54925953		2203	4300	6503	SO:0001630	splice_region_variant			AI924363	CCDS31813.1, CCDS53799.1	12q13.1	2005-10-11	2005-10-11	2005-10-11		ENSG00000123338	3071			4862	protein-coding gene	gene with protein product		141180	hematopoietic protein 1	HEM1	NA	1932118	Standard	NM_005337	NM_005337	NA	Approved		uc001sgc.4	P55160	OTTHUMG00000169843	ENST00000293373.6:c.2782-1G>C	chr12.hg19:g.54925953G>C		NA	B4DUT5|Q52LW0	hg19	CCDS31813.1	0.02	1.678029	CCAxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	13.56	2.273449	0.40194	.	.	ENSG00000123338	ENST00000293373;ENST00000545638	.	.	.	4.27	4.27	0.50696	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5927	0.68378	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NCKAP1L	53212220	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	8.268000	0.89876	2.390000	0.81377	0.563000	0.77884	.	NOVEL	NCKAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406195.1	9	7.221354	KEEP	0	0	0	24	728	GG	0.999909	0.999227	0	Intron	+	20	60	650	0	0	54.882332	61	60	2063	145	ENST00000293373.6	0.246914	0.999317
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	55807293	55807293	__UNKNOWN__	IGR	SNP	A	A	G	rs3887805	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:55807293A>G			NA	NA				OR6C65 (12004 upstream) : OR6C76 (12744 downstream)						NA		NA									NA						TGGGACTGCCAGTGCTGGAAC	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.55807293A>G		NA		hg19		0.02	-0.342062	GCCxGTG	COVERED																																																																																			NOVEL					0			8	6.94938	KEEP	3	1	22	31	859	AA	0.999997	0.865743	0			5	40	142	0	0	10.104092	34	51	1042	97		0.128205	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	56059894	56059894	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56059894C>T			NA	NA				RP11-644F5.16 (6315 upstream) : METTL7B (15435 downstream)						NA		NA									NA						agagcaagaccctgtctcaaa	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.56059894C>T		NA		hg19		0.02	-0.157478	GACxCTG	COVERED																																																																																			NOVEL					0			13	3.845303	KEEP	0	1	29	23	720	CC	0.999909	0.322777	0			3	60	92	0	0	7.283543	13	60	418	67		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	56068080	56068080	__UNKNOWN__	IGR	SNP	C	C	T	rs7136558	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56068080C>T			NA	NA				RP11-644F5.16 (14501 upstream) : METTL7B (7249 downstream)						NA		NA									NA						aaccctgtctctactaaaaat	0.532		NA											C|||	3475	0.69389	0.6778	0.6729	5008	,	,	NA	16526	0.6131	NA	0.7197	False	NA	,,,	NA	NA	NA	2504	0.7873	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.56068080C>T		NA		hg19		0.02	-0.087711	TCTxTAC	UNCOVERED																																																																																			NOVEL					0			7	2.40669	KEEP	2	0	0	8	243	CC	0.99257	0.09898	0			4	60	116	0	0	10.5849	6	60	193	25		0.4	0.099721
RP11-762I7.5	0	__UNKNOWN__	__UNKNOWN__	12	56215585	56215585	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56215585A>G	ENST00000546837.1	-	6	973				DNAJC14_ENST00000317287.5_3'UTR|DNAJC14_ENST00000357606.3_3'UTR|DNAJC14_ENST00000317269.3_3'UTR|RP11-762I7.5_ENST00000552719.1_Intron|ORMDL2_ENST00000243045.5_3'UTR						NA		NA									NA						aggttgcagtaagctgagatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000546837.1:c.973+199T>C	chr12.hg19:g.56215585A>G		NA		hg19		0.02	-0.377107	AGTxAGC	COVERED																																																																																			NOVEL	RP11-762I7.5-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409202.1	2	3.308133	KEEP	0	0	0	11	298	AA	0.993634	0.903281	0		-	3	60	100	0	0	6.949077	33	60	954	71	ENST00000546837.1	0.083333	0.909069
RP11-762I7.5	0	__UNKNOWN__	__UNKNOWN__	12	56215635	56215635	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56215635A>G	ENST00000546837.1	-	6	973				DNAJC14_ENST00000317287.5_3'UTR|DNAJC14_ENST00000357606.3_3'UTR|DNAJC14_ENST00000317269.3_3'UTR|RP11-762I7.5_ENST00000552719.1_Intron|ORMDL2_ENST00000243045.5_3'UTR						NA		NA									NA						gcaagactccatctcaaaaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000546837.1:c.973+149T>C	chr12.hg19:g.56215635A>G		NA		hg19		0.02	1.464607	TCCxTCT	COVERED																																																																																			NOVEL	RP11-762I7.5-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest|readthrough_transcript|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409202.1	24	10.189527	KEEP	0	2	57	54	1487	AA	1	0.999907	0		-	4	60	137	2	0	8.693583	77	60	2282	208	ENST00000546837.1	0.049383	0.999907
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	56251957	56251957	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56251957G>A			NA	NA				MMP19 (15223 upstream) : RNU1-69P (16504 downstream)						NA		NA									NA						caagcctgtagtcccagcact	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.56251957G>A		NA		hg19		0.02	-0.228067	GTAxTCC	COVERED																																																																																			NOVEL					0			5	3.309834	KEEP	0	0	0	11	334	GG	0.993072	0.578892	0			4	60	113	0	0	8.680254	18	60	614	46		0.181818	0.58293
WIBG	84305	__UNKNOWN__	__UNKNOWN__	12	56301693	56301693	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56301693A>G	ENST00000398213.4	-	2	37				WIBG_ENST00000408946.2_Intron|WIBG_ENST00000302533.6_Intron|WIBG_ENST00000547925.1_Intron|WIBG_ENST00000557259.1_Intron	NM_001143853.1	NP_001137325.1	Q9BRP8	WIBG_HUMAN	within bgcn homolog (Drosophila)	NA		NA			nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|exon-exon junction complex (GO:0035145)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	5						ttgcactccaacctgggcaac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014976	CCDS41795.1, CCDS44916.1	12q13.2	2008-02-05				ENSG00000170473	84305			30258	protein-coding gene	gene with protein product		NA			NA	12438415, 12483225	Standard	NM_032345	NM_032345	NA	Approved	PYM	uc001sif.1	Q9BRP8	OTTHUMG00000170220	ENST00000398213.4:c.35-4429T>C	chr12.hg19:g.56301693A>G		NA	B6ZDM5|Q8IXJ8|Q8N8E7	hg19	CCDS44916.1	0.02	-0.140301	CCAxCCT	COVERED																																																																																			NOVEL	WIBG-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408080.1	10	2.435803	KEEP	0	1	28	18	478	AA	0.99986	0.260928	0		-	3	60	90	0	0	7.079746	13	60	371	48	ENST00000398213.4	0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	56438215	56438215	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56438215T>C			NA	NA				RPS26 (99 upstream) : ERBB3 (35429 downstream)						NA		NA									NA						gcaacctccgtctcccgggtt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.56438215T>C		NA		hg19		0.02	-0.289394	CCGxCTC	COVERED																																																																																			NOVEL					0			4	3.539925	KEEP	0	1	23	20	540	TT	0.999869	0.760787	0			3	70	94	0	0	6.743865	24	70	694	56		0.111111	0.760887
ERBB3	2065	__UNKNOWN__	__UNKNOWN__	12	56496644	56496644	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56496644T>C	ENST00000267101.3	+	0	5274				RP11-603J24.9_ENST00000548861.1_Intron|ERBB3_ENST00000549832.1_3'UTR	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	NA		NA			cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			cagtggctcatgcctgtaatc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361	2065			3431	protein-coding gene	gene with protein product		190151	lethal congenital contracture syndrome 2	LCCS2	NA		Standard		NM_001982	NA	Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.*805T>C	chr12.hg19:g.56496644T>C		NA	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	hg19	CCDS31833.1	0.02	-0.29817	TCAxGCC	COVERED																																																																																			NOVEL	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407619.3	15	15.221214	KEEP	1	3	80	79	2135	TT	1	0.78106	0		+	3	60	100	0	0	7.198035	27	60	783	121	ENST00000267101.3	0.1	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	56658820	56658820	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56658820A>G			NA	NA				ANKRD52 (6645 upstream) : COQ10A (1821 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.56658820A>G		NA		hg19		0.02	-0.271906	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			12	2.406213	KEEP	3	0	0	8	223	AA	0	0	0			4	60	135	0	0	10.422785	24	60	730	59		0.142857	0.717315
CS	1431	__UNKNOWN__	__UNKNOWN__	12	56689044	56689044	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56689044T>C	ENST00000542324.2	-	2	171				CS_ENST00000351328.3_Intron|RP11-977G19.10_ENST00000549318.1_Intron|CS_ENST00000548567.1_Intron			O75390	CISY_HUMAN	citrate synthase	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		cggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	1431	2.3.3.1		2422	protein-coding gene	gene with protein product		118950			NA		Standard	NM_004077	NM_004077	NA	Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000542324.2:c.84-3954A>G	chr12.hg19:g.56689044T>C		NA	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	hg19		0.02	-0.14032	TCAxGCC	COVERED																																																																																			NOVEL	CS-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000408590.2	7	3.605503	KEEP	1	0	0	12	308	TT	0.993634	0.259304	0		-	3	60	91	0	0	7.601367	9	60	259	39	ENST00000542324.2	0.25	0.260965
CS	1431	__UNKNOWN__	__UNKNOWN__	12	56689061	56689061	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56689061T>C	ENST00000542324.2	-	2	171				CS_ENST00000351328.3_Intron|RP11-977G19.10_ENST00000549318.1_Intron|CS_ENST00000548567.1_Intron			O75390	CISY_HUMAN	citrate synthase	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		aatcccagcattttgggaggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	1431	2.3.3.1		2422	protein-coding gene	gene with protein product		118950			NA		Standard	NM_004077	NM_004077	NA	Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000542324.2:c.84-3971A>G	chr12.hg19:g.56689061T>C		NA	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	hg19		0.02	-0.122794	GCAxTTT	COVERED																																																																																			NOVEL	CS-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000408590.2	2	2.405954	KEEP	1	0	0	8	217	TT	0.99257	0.22747	0		-	3	60	103	0	0	8.932675	8	60	231	37	ENST00000542324.2	0.272727	0.229173
APOF	319	__UNKNOWN__	__UNKNOWN__	12	56754588	56754588	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56754588T>C	ENST00000398189.3	-	0	1479				APOF_ENST00000541105.1_3'UTR	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	NA		NA			cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						aggctgatcttgaactcctga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336	319		Apolipoproteins	615	protein-coding gene	gene with protein product		107760			NA	8093033	Standard		NM_001638	NA	Approved		uc001sle.1	Q13790		ENST00000398189.3:c.*421A>G	chr12.hg19:g.56754588T>C		NA	Q8TC13	hg19	CCDS44923.1	0.02	1.804182	TCTxGAA	COVERED																																																																																			NOVEL	APOF-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410076.1	13	2.531203	KEEP	0	4	112	48	1288	TT	1	0.998993	0		-	4	60	135	0	0	8.631409	71	60	2075	159	ENST00000398189.3	0.053333	0.998993
TIMELESS	8914	__UNKNOWN__	__UNKNOWN__	12	56835389	56835389	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56835389T>C	ENST00000553532.1	-	2	90				TIMELESS_ENST00000554616.1_Intron|TIMELESS_ENST00000229201.4_Intron					timeless circadian clock	NA		NA								NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						ccagcctgggtaacagagtga	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602	8914			11813	protein-coding gene	gene with protein product	Tof1 homolog (S. cerevisiae), timeless circadian clock 1	603887	timeless (Drosophila) homolog, timeless homolog (Drosophila)		NA	9856465	Standard	NM_003920	NM_003920	NA	Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.61-7374A>G	chr12.hg19:g.56835389T>C		NA		hg19	CCDS8918.1	0.02	-0.140328	GGGxAAC	COVERED																																																																																			NOVEL	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409771.1	8	2.706163	KEEP	4	0	0	9	244	TT	0.99257	0.259026	0		-	3	60	103	0	0	8.572973	11	60	316	45	ENST00000553532.1	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	56898278	56898278	__UNKNOWN__	IGR	SNP	G	G	A	rs548411591	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:56898278G>A			NA	NA				GLS2 (16097 upstream) : RBMS2 (17434 downstream)						NA		NA									NA						ggccaggcgcggtggctcaca	0.498		NA											G|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	14576	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.56898278G>A		NA		hg19		0.02	-0.201738	CGCxGTG	COVERED																																																																																			NOVEL					0			7	2.707152	KEEP	1	0	0	9	259	GG	0.99257	0.4869	0			3	60	91	0	0	6.727511	19	60	609	46		0.136364	0.490544
PTGES3	10728	__UNKNOWN__	__UNKNOWN__	12	57063274	57063274	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:57063274T>C	ENST00000262033.6	-	5	676				PTGES3_ENST00000448157.2_Intron|PTGES3_ENST00000456859.2_Intron|PTGES3_ENST00000537473.1_Intron|PTGES3_ENST00000414274.3_Intron|PTGES3_ENST00000436399.2_Intron	NM_006601.5	NP_006592.3	Q15185	TEBP_HUMAN	prostaglandin E synthase 3 (cytosolic)	NA		NA			arachidonic acid metabolic process (GO:0019369)|cell proliferation (GO:0008283)|chaperone cofactor-dependent protein refolding (GO:0070389)|cyclooxygenase pathway (GO:0019371)|glucocorticoid receptor signaling pathway (GO:0042921)|glycogen biosynthetic process (GO:0005978)|lung saccule development (GO:0060430)|prostaglandin biosynthetic process (GO:0001516)|RNA-dependent DNA replication (GO:0006278)|signal transduction (GO:0007165)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	prostaglandin-E synthase activity (GO:0050220)|telomerase activity (GO:0003720)|unfolded protein binding (GO:0051082)			large_intestine(1)|lung(1)	2						accatgttggtcaggctggtc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC003005	CCDS31836.1, CCDS61158.1, CCDS61159.1, CCDS61160.1, CCDS73485.1	12q13.13	2012-03-14			ENSG00000110958	ENSG00000110958	10728			16049	protein-coding gene	gene with protein product		607061			NA	8114727, 12077419	Standard	NM_006601	XR_245889	NA	Approved	p23, TEBP, cPGES	uc001slu.4	Q15185	OTTHUMG00000170217	ENST00000262033.6:c.375+784A>G	chr12.hg19:g.57063274T>C		NA	A8K7D0|B4DHP2|B4DP11|B4DP21|Q8WU70	hg19	CCDS31836.1	0.02	-0.114008	TGGxCAG	UNCOVERED																																																																																			NOVEL	PTGES3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408054.1	8	2.705366	KEEP	5	0	0	9	230	TT	0	0	0		-	5	40	160	0	2	15.094573	6	60	165	29	ENST00000262033.6	0.454545	0.162467
HSD17B6	8630	__UNKNOWN__	__UNKNOWN__	12	57148858	57148858	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:57148858G>C	ENST00000556481.1	+	1	125				HSD17B6_ENST00000555159.1_Intron|HSD17B6_ENST00000554643.1_Intron|HSD17B6_ENST00000554150.1_Intron|HSD17B6_ENST00000555805.1_Intron			O14756	H17B6_HUMAN	hydroxysteroid (17-beta) dehydrogenase 6	NA		NA			androgen biosynthetic process (GO:0006702)|androgen catabolic process (GO:0006710)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|intracellular (GO:0005622)|membrane (GO:0016020)	catalytic activity (GO:0003824)|electron carrier activity (GO:0009055)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|oxidoreductase activity (GO:0016491)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			endometrium(1)|large_intestine(2)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10					Succinic acid(DB00139)	cgcctgtaatgccagcacttt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF016509	CCDS8925.1	12q13.3	2012-12-07	2012-12-07		ENSG00000025423	ENSG00000025423	8630	1.1.1.62, 1.1.1.63, 1.1.1.105	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2	23316	protein-coding gene	gene with protein product	oxidative 3-alpha-hydroxysteroid-dehydrogenase, 3(alpha->beta)-hydroxysteroid epimerasel, retinol dehydrogenase, oxidoreductase, NAD+ -dependent 3 alpha-hydroxysteroid dehydrogenase, 3-hydroxysteroid epimerase, short chain dehydrogenase/reductase family 9C, member 6	606623	hydroxysteroid (17-beta) dehydrogenase 6, hydroxysteroid (17-beta) dehydrogenase 6 homolog (mouse)		NA	11165032, 19027726	Standard	NM_003725	XM_005269207	NA	Approved	HSE, RODH, SDR9C6	uc001smg.1	O14756	OTTHUMG00000170854	ENST00000556481.1:c.125+2493G>C	chr12.hg19:g.57148858G>C		NA	O43275	hg19		0.02	-0.105275	AATxCCA	UNCOVERED																																																																																			NOVEL	HSD17B6-008	PUTATIVE	mRNA_end_NF|basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000410783.1	6	2.407125	KEEP	0	0	0	8	245	GT	0.99254	0.138789	0		+	3	60	107	0	0	9.33226	8	60	273	30	ENST00000556481.1	0.272727	0.139832
MYO1A	4640	__UNKNOWN__	__UNKNOWN__	12	57432273	57432273	__UNKNOWN__	Silent	SNP	C	C	T	rs201712790		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:57432273C>T	ENST00000442789.2	-	18	1970	c.1683G>A	c.(1681-1683)ccG>ccA	p.P561P	MYO1A_ENST00000544473.1_Silent_p.P399P|MYO1A_ENST00000476795.1_5'UTR|MYO1A_ENST00000300119.3_Silent_p.P561P	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	561	Myosin motor.	NA			microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.P561P(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						CCCCAGCAGTCGGGGGGCGTT	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - coding silent(1)	lung(1)											50	50	50			NA	NA	12		NA											NA				57432273		2203	4300	6503	SO:0001819	synonymous_variant			L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866	4640		Myosins / Myosin superfamily : Class I	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48	NA	8884266, 12736868	Standard	NM_005379	NM_001256041	NA	Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.1683G>A	chr12.hg19:g.57432273C>T		NA	Q9UQD7	hg19	CCDS8929.1	0.02	-0.377152	AGTxGGG	COVERED																																																																																			NOVEL	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313833.2	1	3.308331	KEEP	0	0	0	11	315	CC	0.993072	0.902771	0		-	10	60	286	0	0	23.361207	32	60	1022	75	ENST00000442789.2	0.238095	0.909069
INHBC	3626	__UNKNOWN__	__UNKNOWN__	12	57834865	57834865	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:57834865T>G	ENST00000309668.2	+	1	440					NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	NA		NA			growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)			breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						Agccgggtgctgtggctcacg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS8938.1	12q13	2008-02-05				ENSG00000175189	3626			6068	protein-coding gene	gene with protein product		601233			NA	7826378	Standard	NM_005538	NM_005538	NA	Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.313+5883T>G	chr12.hg19:g.57834865T>G		NA	A1L3Y2	hg19	CCDS8938.1	0.02	-0.219264	TGCxGTG	COVERED																																																																																			NOVEL	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406770.1	11	3.006835	KEEP	0	0	0	10	268	TT	0.992708	0.578679	0		+	3	60	97	0	0	7.46112	17	60	503	47	ENST00000309668.2	0.15	0.58293
PIP4K2C	79837	__UNKNOWN__	__UNKNOWN__	12	57990007	57990007	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:57990007A>G	ENST00000354947.5	+	4	529				PIP4K2C_ENST00000550465.1_Intron|PIP4K2C_ENST00000540759.2_Intron|PIP4K2C_ENST00000422156.3_Intron			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	NA		NA				cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					agtggctcacacctgtagtcc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908	79837			23786	protein-coding gene	gene with protein product		NA	phosphatidylinositol-4-phosphate 5-kinase, type II, gamma	PIP5K2C	NA	9367159	Standard	NM_024779	NM_024779	NA	Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.513+193A>G	chr12.hg19:g.57990007A>G		NA	B2RDL3|B4DM11|B4DY44|Q9H6N2	hg19	CCDS8946.1	0.02	-0.184166	CACxCCT	COVERED																																																																																			NOVEL	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407644.1	3	3.006361	KEEP	1	0	0	10	261	AA	0.99254	0.420319	0		+	3	60	89	0	0	6.979574	13	60	382	42	ENST00000354947.5	0.1875	0.423478
CDK4	1019	__UNKNOWN__	__UNKNOWN__	12	58142484	58142484	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:58142484C>T	ENST00000257904.6	-	8	1185				CDK4_ENST00000549606.1_Intron|CDK4_ENST00000312990.6_Intron|TSPAN31_ENST00000547992.1_3'UTR|CDK4_ENST00000540325.1_Intron	NM_000075.3	NP_000066.1	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	NA		NA			cell division (GO:0051301)|circadian rhythm (GO:0007623)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle arrest (GO:0071157)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of translation (GO:0045727)|protein phosphorylation (GO:0006468)|regulation of gene expression (GO:0010468)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to lead ion (GO:0010288)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	21	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			GAGCtttcttcttttttcttt	0.458		NA	Mis			melanoma			Hereditary Melanoma												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Dom		Familial malignant melanoma	12	12q14	1019	cyclin-dependent kinase 4		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Familial Atypical Multiple Mole Melanoma sydrome, FAMMM, Familial Dysplastic Nevus syndrome	M14505	CCDS8953.1	12q13	2014-09-17				ENSG00000135446	1019		Cyclin-dependent kinases	1773	protein-coding gene	gene with protein product		123829			NA	8275715	Standard	NM_000075	NM_000075	NA	Approved	PSK-J3	uc001spv.3	P11802		ENST00000257904.6:c.820-84G>A	chr12.hg19:g.58142484C>T		NA	B2R9A0|B4DNF9|O00576|Q6FG61	hg19	CCDS8953.1	0.02	5.000542	CTTxTTT	COVERED																																																																																			NOVEL	CDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408790.2	88	8.027489	KEEP	0	15	265	123	3527	CC	1	1	0		-	9	60	235	2	1	12.379838	190	60	5866	534	ENST00000257904.6	0.045226	1
TSFM	10102	__UNKNOWN__	__UNKNOWN__	12	58198549	58198549	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:58198549G>C	ENST00000548851.1	+	6	586				AVIL_ENST00000537081.1_Intron|AVIL_ENST00000550083.1_Intron|AVIL_ENST00000257861.3_Intron					Ts translation elongation factor, mitochondrial	NA		NA								endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)	8	all_cancers(7;6.31e-80)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					ccaagatcgcgccactgcact	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L37936	CCDS8958.2, CCDS53809.1, CCDS53810.1, CCDS53811.1	12q14.1	2006-06-10			ENSG00000123297	ENSG00000123297	10102			12367	protein-coding gene	gene with protein product		604723			NA	7615523	Standard	NM_005726	NM_005726	NA	Approved	EF-Tsmt, EF-TS	uc001sqh.3	P43897	OTTHUMG00000153042	ENST00000548851.1:c.572-3098G>C	chr12.hg19:g.58198549G>C		NA		hg19		0.02	-0.070176	CGCxCCA	UNCOVERED																																																																																			NOVEL	TSFM-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409344.1	6	2.406749	KEEP	6	0	0	8	232	GG	0	0	0		+	2	58	72	0	0	6.335672	5	60	157	29	ENST00000548851.1	0.285714	0.054137
RP11-620J15.2	0	__UNKNOWN__	__UNKNOWN__	12	58277982	58277982	__UNKNOWN__	lincRNA	SNP	G	G	A	rs188168189	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:58277982G>A	ENST00000499481.2	-	0	2743										NA		NA									NA						gggaggctgaggcagggggat	0.463		NA											G|||	6	0.00119808	0.0008	0.0014	5008	,	,	NA	15571	0.0	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000499481.2:	chr12.hg19:g.58277982G>A		NA		hg19		0.02	-0.175423	TGAxGCA	COVERED																																																																																			NOVEL	RP11-620J15.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409363.1	8	3.008947	KEEP	4	0	0	10	306	GG	0.99257	0.384528	0		-	7	60	204	0	0	18.513562	11	60	382	44	ENST00000499481.2	0.388889	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	60384663	60384663	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:60384663A>G			NA	NA				SLC16A7 (208268 upstream) : AC091517.1 (35888 downstream)						NA		NA									NA						agcactttggaaggccgaggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.60384663A>G		NA		hg19		0.02	-0.122791	TGGxAGG	UNCOVERED																																																																																			NOVEL					0			3	2.405986	KEEP	2	0	0	8	218	AA	0	0	0			3	60	99	0	0	8.172944	11	60	325	35		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	61900885	61900885	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:61900885C>T			NA	NA				None (None upstream) : FAM19A2 (201154 downstream)						NA		NA									NA						gccattgcaccccagcctggg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.61900885C>T		NA		hg19		0.02	-0.035085	CACxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.708197	KEEP	0	0	0	9	283	CC	0.99254	0.019833	0			2	60	59	0	0	6.852933	0	0	0	18		1	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	62822963	62822963	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:62822963A>G			NA	NA				USP15 (23064 upstream) : MON2 (37633 downstream)						NA		NA									NA						cgaggcgggcagatcacaagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.62822963A>G		NA		hg19		0.02	-0.175414	GGCxGAT	COVERED																																																																																			NOVEL					0			7	5.715198	KEEP	3	0	0	19	534	AA	0.999366	0.387161	0			3	60	92	0	0	7.110669	15	60	447	62		0.166667	0.387407
MON2	23041	__UNKNOWN__	__UNKNOWN__	12	62886619	62886619	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:62886619C>T	ENST00000552738.1	+	3	535				MON2_ENST00000393632.2_Intron|MON2_ENST00000546600.1_Intron|MON2_ENST00000393629.2_Intron|MON2_ENST00000280379.6_Intron|MON2_ENST00000552115.1_Intron|MON2_ENST00000549378.1_Intron|MON2_ENST00000393630.3_Intron			Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	NA		NA			actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		attagccgggcgtggtggtgc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987	23041			29177	protein-coding gene	gene with protein product		NA	MON2 homolog (yeast)		NA	16301316, 24285343	Standard	NM_015026	NM_015026	NA	Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000552738.1:c.176-1076C>T	chr12.hg19:g.62886619C>T		NA	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	hg19		0.02	-0.114032	GGGxGTG	UNCOVERED																																																																																			NOVEL	MON2-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000406847.2	10	6.012683	KEEP	11	0	0	20	575	CC	0.995343	0.16171	0		+	3	39	94	0	0	8.032364	8	60	257	50	ENST00000552738.1	0.272727	0.162467
MON2	23041	__UNKNOWN__	__UNKNOWN__	12	62924042	62924042	__UNKNOWN__	Intron	SNP	G	G	A	rs368154977		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:62924042G>A	ENST00000552738.1	+	12	1760				MON2_ENST00000393632.2_Intron|MON2_ENST00000546600.1_Intron|MON2_ENST00000393629.2_Intron|MON2_ENST00000280379.6_Intron|MON2_ENST00000552115.1_Intron|MON2_ENST00000393630.3_Intron			Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	NA		NA			actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		acggagtctcgctctgtcacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987	23041			29177	protein-coding gene	gene with protein product		NA	MON2 homolog (yeast)		NA	16301316, 24285343	Standard	NM_015026	NM_015026	NA	Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000552738.1:c.1401-2176G>A	chr12.hg19:g.62924042G>A		NA	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	hg19		0.02	-0.052621	CTCxCTC	UNCOVERED																																																																																			NOVEL	MON2-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000406847.2	6	2.707015	KEEP	4	0	0	9	257	GG	0.99257	0.036492	0		+	3	40	82	0	0	7.823677	3	48	99	20	ENST00000552738.1	0.5	0.036766
PPM1H	57460	__UNKNOWN__	__UNKNOWN__	12	63051894	63051894	__UNKNOWN__	Intron	SNP	C	C	T	rs11174585	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:63051894C>T	ENST00000228705.6	-	9	1698				PPM1H_ENST00000551214.1_Intron	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	NA		NA					phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		cacctgcaatcccagcacttt	0.423		NA											C|||	1910	0.38139	0.292	0.2954	5008	,	,	NA	12632	0.4573	NA	0.3757	False	NA	,,,	NA	NA	NA	2504	0.4908	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	57460	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	18583	protein-coding gene	gene with protein product	neurite extension-related protein phosphatase related to PP2C	NA	ras homolog gene family, member C like 1, protein phosphatase 1H (PP2C domain containing)	ARHCL1	NA		Standard	NM_020700	NM_020700	NA	Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.1397+9063G>A	chr12.hg19:g.63051894C>T		NA	B1Q2A9|B2RXG4|Q6PI86	hg19	CCDS44934.1	0.02	-0.105269	AATxCCA	UNCOVERED																																																																																			NOVEL	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406760.2	7	2.407222	KEEP	1	0	0	8	249	CC	0	0	0		-	3	60	93	0	0	7.932189	8	60	273	29	ENST00000228705.6	0.272727	0.139832
PPM1H	57460	__UNKNOWN__	__UNKNOWN__	12	63240211	63240211	__UNKNOWN__	Intron	SNP	C	C	T	rs544823814	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:63240211C>T	ENST00000228705.6	-	2	546					NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	NA		NA					phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)	18			GBM - Glioblastoma multiforme(1;0.000443)|BRCA - Breast invasive adenocarcinoma(9;0.209)	GBM - Glioblastoma multiforme(28;0.0126)		acccaggaggcggaggttgca	0.458		NA											C|||	2	0.000399361	0.0	0.0	5008	,	,	NA	14366	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032983	CCDS44934.1	12q14.1	2012-04-17	2010-03-05	2004-03-26	ENSG00000111110	ENSG00000111110	57460	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	18583	protein-coding gene	gene with protein product	neurite extension-related protein phosphatase related to PP2C	NA	ras homolog gene family, member C like 1, protein phosphatase 1H (PP2C domain containing)	ARHCL1	NA		Standard	NM_020700	NM_020700	NA	Approved	KIAA1157, FLJ13253, NERPP-2C	uc001srk.3	Q9ULR3	OTTHUMG00000169990	ENST00000228705.6:c.246-14152G>A	chr12.hg19:g.63240211C>T		NA	B1Q2A9|B2RXG4|Q6PI86	hg19	CCDS44934.1	0.02	-0.105247	AGGxGGA	UNCOVERED																																																																																			NOVEL	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406760.2	6	2.407036	KEEP	2	0	0	8	242	CC	0	0	0		-	3	60	81	0	0	6.601007	9	60	296	30	ENST00000228705.6	0.25	0.139832
RP11-1022B3.1	0	__UNKNOWN__	__UNKNOWN__	12	63687288	63687288	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:63687288A>G	ENST00000551729.1	-	0	162										NA		NA									NA						ctggagtgcaatggtgcaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000551729.1:	chr12.hg19:g.63687288A>G		NA		hg19		0.02	-0.043855	GCAxTGG	UNCOVERED																																																																																			NOVEL	RP11-1022B3.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000406727.1	7	2.706233	KEEP	4	0	0	9	239	AA	0	0	0		-	2	57	69	0	1	6.393058	3	60	86	21	ENST00000551729.1	0.4	0.024074
TMEM5-AS1	0	__UNKNOWN__	__UNKNOWN__	12	64215188	64215188	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:64215188T>C	ENST00000546214.1	-	0	228									TMEM5 antisense RNA 1	NA		NA									NA						tggccgggcgtggtggctcac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					DB026756		12q14.2	2013-07-04			ENSG00000255850	ENSG00000255850	NA		Long non-coding RNAs	48910	non-coding RNA	RNA, long non-coding		NA			NA		Standard			NA	Approved				OTTHUMG00000168731	ENST00000546214.1:	chr12.hg19:g.64215188T>C		NA		hg19		0.02	-0.149058	GCGxGGT	COVERED																																																																																			NOVEL	TMEM5-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000400829.1	5	3.307974	KEEP	0	0	0	11	298	TT	0.993072	0.289978	0		-	3	60	98	0	0	7.972833	12	60	319	36	ENST00000546214.1	0.2	0.292001
SRGAP1	57522	__UNKNOWN__	__UNKNOWN__	12	64298464	64298464	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:64298464C>A	ENST00000355086.3	+	1	591				SRGAP1_ENST00000357825.3_Intron	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	NA		NA			axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		taatcccagccctttgggagg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935	57522		Rho GTPase activating proteins	17382	protein-coding gene	gene with protein product		606523			NA	11672528	Standard		NM_020762	NA	Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.67+59801C>A	chr12.hg19:g.64298464C>A		NA	Q9H8A3|Q9P2P2	hg19	CCDS8967.1	0.02	-0.166667	AGCxCTT	COVERED																																																																																			NOVEL	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400896.1	3	3.610923	KEEP	0	0	0	12	374	CC	0.993634	0.351693	0		+	3	60	91	0	0	7.010399	15	60	497	50	ENST00000355086.3	0.166667	0.353947
SRGAP1	57522	__UNKNOWN__	__UNKNOWN__	12	64363312	64363312	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:64363312A>G	ENST00000355086.3	+	2	591				SRGAP1_ENST00000357825.3_Intron	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	NA		NA			axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		agtggctcacacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935	57522		Rho GTPase activating proteins	17382	protein-coding gene	gene with protein product		606523			NA	11672528	Standard		NM_020762	NA	Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.68-14415A>G	chr12.hg19:g.64363312A>G		NA	Q9H8A3|Q9P2P2	hg19	CCDS8967.1	0.02	-0.157871	CACxCCT	COVERED																																																																																			NOVEL	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400896.1	9	2.705912	KEEP	3	0	0	9	235	AA	0.99257	0.320408	0		+	3	60	98	0	0	7.97232	12	60	358	45	ENST00000355086.3	0.2	0.322807
SRGAP1	57522	__UNKNOWN__	__UNKNOWN__	12	64373070	64373070	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:64373070G>A	ENST00000355086.3	+	2	591				SRGAP1_ENST00000357825.3_Intron	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	NA		NA			axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		cacctgcctcggcctcccaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935	57522		Rho GTPase activating proteins	17382	protein-coding gene	gene with protein product		606523			NA	11672528	Standard		NM_020762	NA	Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.68-4657G>A	chr12.hg19:g.64373070G>A		NA	Q9H8A3|Q9P2P2	hg19	CCDS8967.1	0.02	-0.19289	CTCxGCC	COVERED																																																																																			NOVEL	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400896.1	8	3.610577	KEEP	2	0	0	12	367	GG	0.992708	0.454419	0		+	3	60	91	0	0	6.934438	16	60	509	49	ENST00000355086.3	0.157895	0.457757
SRGAP1	57522	__UNKNOWN__	__UNKNOWN__	12	64470708	64470708	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:64470708T>C	ENST00000355086.3	+	9	1649				SRGAP1_ENST00000543397.1_Intron|RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000357825.3_Intron	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	NA		NA			axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		caggtgtgagtcaccacgccc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935	57522		Rho GTPase activating proteins	17382	protein-coding gene	gene with protein product		606523			NA	11672528	Standard		NM_020762	NA	Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1126-1991T>C	chr12.hg19:g.64470708T>C		NA	Q9H8A3|Q9P2P2	hg19	CCDS8967.1	0.02	-0.105261	GAGxCAC	UNCOVERED																																																																																			NOVEL	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400896.1	8	3.007036	KEEP	0	0	0	10	266	TT	0.992708	0.138812	0		+	3	60	107	1	0	9.833088	5	60	154	32	ENST00000355086.3	0.375	0.139832
C12orf56	115749	__UNKNOWN__	__UNKNOWN__	12	64701902	64701902	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:64701902C>G	ENST00000543942.2	-	6	1595				C12orf56_ENST00000333722.5_Intron|RPS11P6_ENST00000535684.1_RNA	NM_001170633.1	NP_001164104.1	Q8IXR9	CL056_HUMAN	chromosome 12 open reading frame 56	NA		NA								NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)	15			GBM - Glioblastoma multiforme(3;0.000582)	GBM - Glioblastoma multiforme(28;0.0259)		atttcgagaccagcctgggca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS44935.1, CCDS61182.1	12q14.2	2012-08-15			ENSG00000185306	ENSG00000185306	115749			26967	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001099676	NM_001099676	NA	Approved		uc021qzu.1	Q8IXR9	OTTHUMG00000168782	ENST00000543942.2:c.969-4343G>C	chr12.hg19:g.64701902C>G		NA		hg19		0.02	-0.114037	GACxAGC	UNCOVERED																																																																																			NOVEL	C12orf56-008	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000401058.2	6	3.009064	KEEP	0	0	0	10	311	CC	0.992708	0.161282	0		-	4	60	125	0	0	11.091044	8	60	268	33	ENST00000543942.2	0.333333	0.162467
WIF1	11197	__UNKNOWN__	__UNKNOWN__	12	65471897	65471897	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:65471897T>C	ENST00000286574.4	-	3	663					NM_007191.4	NP_009122.2	Q9Y5W5	WIF1_HUMAN	WNT inhibitory factor 1	NA		NA			multicellular organismal development (GO:0007275)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)				cervix(1)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|stomach(1)|urinary_tract(1)	21			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0231)		cttgctctgttgcccaggctg	0.463		NA	T	HMGA2	pleomorphic salivary gland adenoma																NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(148;1595 1816 48559 49439 49664)		Dom	yes		12	12q14.3	11197	WNT inhibitory factor 1		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF122922	CCDS8971.1	12q14.2	2008-04-11			ENSG00000156076	ENSG00000156076	11197			18081	protein-coding gene	gene with protein product		605186			NA	10201374	Standard		NM_007191	NA	Approved		uc001ssk.3	Q9Y5W5	OTTHUMG00000168832	ENST00000286574.4:c.289-263A>G	chr12.hg19:g.65471897T>C		NA	Q6UXI1|Q8WVG4	hg19	CCDS8971.1	0.02	-0.140318	TGTxGCC	UNCOVERED																																																																																			NOVEL	WIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401258.2	11	2.405728	KEEP	6	0	0	8	215	TT	0	0	0		-	3	38	96	0	0	7.772491	12	60	347	42	ENST00000286574.4	0.2	0.260965
LEMD3	23592	__UNKNOWN__	__UNKNOWN__	12	65607279	65607279	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:65607279T>A	ENST00000308330.2	+	3	1586					NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	NA		NA			negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of cell cycle (GO:0051726)|skeletal muscle cell differentiation (GO:0035914)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	36			LUAD - Lung adenocarcinoma(6;0.0234)|LUSC - Lung squamous cell carcinoma(43;0.0975)	GBM - Glioblastoma multiforme(28;0.0104)		acttgggatttcaggtgtgag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF263918	CCDS8972.1	12q14	2008-02-05			ENSG00000174106	ENSG00000174106	23592			28887	protein-coding gene	gene with protein product		607844			NA	10671519, 15489854	Standard		NM_014319	NA	Approved	MAN1	uc001ssl.2	Q9Y2U8	OTTHUMG00000168840	ENST00000308330.2:c.1561-2478T>A	chr12.hg19:g.65607279T>A		NA	Q9NT47|Q9NYA5	hg19	CCDS8972.1	0.02	-0.166636	ATTxCAG	COVERED																																																																																			NOVEL	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401312.2	9	4.211177	KEEP	0	0	0	14	393	TT	0.995343	0.352299	0		+	4	60	114	0	0	9.168722	14	60	418	45	ENST00000308330.2	0.222222	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	66111446	66111446	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:66111446T>C			NA	NA				RP11-221N13.4 (69811 upstream) : RPSAP52 (40353 downstream)						NA		NA									NA						ctcggcctcctaaagtgctgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.66111446T>C		NA		hg19		0.02	-0.289446	TCCxAAA	UNCOVERED																																																																																			NOVEL					0			6	2.404215	KEEP	1	0	0	8	203	TT	0	0	0			5	60	174	0	0	13.838947	26	60	774	61		0.16129	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	66126266	66126266	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:66126266T>C			NA	NA				RP11-221N13.4 (84631 upstream) : RPSAP52 (25533 downstream)						NA		NA									NA						ggtgcggtggttcacgcctgt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.66126266T>C		NA		hg19		0.02	-0.122763	TGGxTCA	COVERED																																																																																			NOVEL					0			6	3.006882	KEEP	0	0	0	10	266	TT	0.992708	0.19488	0			3	60	105	0	0	8.882505	10	60	281	31		0.230769	0.196312
HELB	92797	__UNKNOWN__	__UNKNOWN__	12	66704440	66704440	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:66704440A>G	ENST00000247815.4	+	4	1739					NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	NA		NA			DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		ggccgggcacagtggctcacg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													21	25	23			NA	NA	12		NA											NA				66704440		1313	2307	3620	SO:0001627	intron_variant			AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311	92797			17196	protein-coding gene	gene with protein product		614539			NA	12181327	Standard		NM_033647	NA	Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1680+52A>G	chr12.hg19:g.66704440A>G		NA	A8K4C9|Q4G0T2|Q9H7L5	hg19	CCDS8976.1	0.02	1.836066	CACxGTG	COVERED																																																																																			NOVEL	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401919.1	2	2.538385	KEEP	0	1	30	19	521	AA	0.999863	0.991958	0		+	4	60	136	0	0	9.099965	57	70	1690	107	ENST00000247815.4	0.065574	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	68650459	68650459	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:68650459T>C			NA	NA				IL22 (3072 upstream) : MDM1 (37888 downstream)						NA		NA									NA						tttgggaggctgaggtgggca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.68650459T>C		NA		hg19		0.02	-0.166631	GGCxGAG	COVERED																																																																																			NOVEL					0			9	2.406676	KEEP	2	0	0	8	230	TT	0.99257	0.351317	0			3	60	91	0	0	7.092514	14	60	422	41		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	68751832	68751832	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:68751832T>C			NA	NA				RP11-71J4.2 (8093 upstream) : RAP1B (252786 downstream)						NA		NA									NA						ctgcctgccttggcctcccaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.68751832T>C		NA		hg19		0.02	-0.114015	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			3	2.706562	KEEP	1	0	0	9	247	TT	0.99257	0.16126	0			3	60	95	0	0	8.278753	7	60	205	32		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	68806542	68806542	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:68806542A>G			NA	NA				RP11-71J4.2 (62803 upstream) : RAP1B (198076 downstream)						NA		NA									NA						aaagtgctggaattacaggtg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.68806542A>G		NA		hg19		0.02	-0.192964	TGGxATT	COVERED																																																																																			NOVEL					0			9	6.314358	KEEP	1	0	0	21	568	AA	0.999863	0.457694	0			3	60	104	0	0	8.233122	16	60	493	63		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	68806551	68806551	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:68806551T>C			NA	NA				RP11-71J4.2 (62812 upstream) : RAP1B (198067 downstream)						NA		NA									NA						gaattacaggtgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.68806551T>C		NA		hg19		0.02	-0.236753	AGGxGTG	COVERED																																																																																			NOVEL					0			9	7.210935	KEEP	1	0	0	24	613	TT	0.999892	0.612341	0			3	60	98	0	0	7.30713	21	60	589	73		0.125	0.612407
SLC35E3	55508	__UNKNOWN__	__UNKNOWN__	12	69171664	69171664	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:69171664A>G	ENST00000538043.1	+	2	40							Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	NA		NA				integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			ttgggaggccaaggtgggcgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF148713, AY358943	CCDS41808.1	12q15	2014-09-04			ENSG00000175782	ENSG00000175782	55508		Solute carriers	20864	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_018656	XM_005269006	NA	Approved	BLOV1	uc001suh.3	Q7Z769	OTTHUMG00000169282	ENST00000538043.1:c.41-15404A>G	chr12.hg19:g.69171664A>G		NA	A8K0T0|Q0P5Y5|Q9P0V1	hg19		0.02	-0.271868	GCCxAGG	COVERED																																																																																			NOVEL	SLC35E3-004	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000403244.1	9	3.007586	KEEP	0	0	0	10	280	AA	0.992708	0.712085	0		+	3	60	94	0	0	6.743979	24	60	698	61	ENST00000538043.1	0.111111	0.717315
SLC35E3	55508	__UNKNOWN__	__UNKNOWN__	12	69184452	69184452	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:69184452A>G	ENST00000538043.1	+	2	40							Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	NA		NA				integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			agccgagatcacgccattgca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF148713, AY358943	CCDS41808.1	12q15	2014-09-04			ENSG00000175782	ENSG00000175782	55508		Solute carriers	20864	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_018656	XM_005269006	NA	Approved	BLOV1	uc001suh.3	Q7Z769	OTTHUMG00000169282	ENST00000538043.1:c.41-2616A>G	chr12.hg19:g.69184452A>G		NA	A8K0T0|Q0P5Y5|Q9P0V1	hg19		0.02	-0.228043	ATCxCGC	COVERED																																																																																			NOVEL	SLC35E3-004	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000403244.1	11	3.307709	KEEP	3	0	0	11	296	AA	0.992708	0.578679	0		+	3	60	99	0	0	7.29508	23	60	698	57	ENST00000538043.1	0.115385	0.58293
MDM2	4193	__UNKNOWN__	__UNKNOWN__	12	69234166	69234166	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:69234166C>T	ENST00000462284.1	+	0	2333				MDM2_ENST00000258149.5_3'UTR|MDM2_ENST00000540827.1_3'UTR|MDM2_ENST00000428863.2_3'UTR|MDM2_ENST00000356290.4_3'UTR	NM_002392.4	NP_002383.2	Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	NA		NA			cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			cctcgtgatccgcccacctcg	0.498		NA	A		sarcoma, glioma, colorectal, other																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		M, O, E, L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679	4193			6973	protein-coding gene	gene with protein product		164785	mouse double minute 2, human homolog of; p53-binding protein, Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse), Mdm2 p53 binding protein homolog (mouse)		NA	1614537, 16905769	Standard	NM_006880	NM_002392	NA	Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000462284.1:c.*537C>T	chr12.hg19:g.69234166C>T		NA	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	hg19	CCDS8986.2	0.02	2.411732	ATCxGCC	COVERED																																																																																			NOVEL	MDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286419.1	22	6.649612	KEEP	4	4	95	56	1659	CC	1	1	0		+	6	60	168	0	0	9.118696	125	70	4011	247	ENST00000462284.1	0.045802	1
MDM2	4193	__UNKNOWN__	__UNKNOWN__	12	69234204	69234204	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:69234204A>G	ENST00000462284.1	+	0	2371				MDM2_ENST00000258149.5_3'UTR|MDM2_ENST00000540827.1_3'UTR|MDM2_ENST00000428863.2_3'UTR|MDM2_ENST00000356290.4_3'UTR	NM_002392.4	NP_002383.2	Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	NA		NA			cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			gattacaggcatgagccaccg	0.453		NA	A		sarcoma, glioma, colorectal, other																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		M, O, E, L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679	4193			6973	protein-coding gene	gene with protein product		164785	mouse double minute 2, human homolog of; p53-binding protein, Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse), Mdm2 p53 binding protein homolog (mouse)		NA	1614537, 16905769	Standard	NM_006880	NM_002392	NA	Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000462284.1:c.*575A>G	chr12.hg19:g.69234204A>G		NA	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	hg19	CCDS8986.2	0.02	5.156802	GGCxTGA	COVERED																																																																																			NOVEL	MDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286419.1	54	28.904889	KEEP	4	1	28	106	2931	AA	1	1	0		+	8	60	255	0	0	14.937668	182	70	5438	450	ENST00000462284.1	0.042105	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	69515663	69515663	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:69515663A>G			NA	NA				AC139931.1 (4231 upstream) : RP11-324P9.1 (90239 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.69515663A>G		NA		hg19		0.02	-0.219255	CACxCCT	UNCOVERED																																																																																			NOVEL					0			6	2.406395	KEEP	1	0	0	8	226	AA	0	0	0			3	60	96	0	0	7.433809	16	60	466	49		0.157895	0.552887
CCT2	10576	__UNKNOWN__	__UNKNOWN__	12	69982973	69982973	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:69982973A>G	ENST00000299300.6	+	7	634				CCT2_ENST00000543146.2_Intron|CCT2_ENST00000544368.2_Intron	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			ccaaagtgctaggattacagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02					10576		Heat Shock Proteins / Chaperonins	1615	protein-coding gene	gene with protein product		605139			NA	9819444	Standard	NM_006431	NM_001198842	NA	Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.447-292A>G	chr12.hg19:g.69982973A>G		NA	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	hg19	CCDS8991.1	0.02	-0.184197	GCTxGGA	COVERED																																																																																			NOVEL	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403818.1	13	2.40489	KEEP	1	0	0	8	214	AA	0.99257	0.420331	0		+	4	60	134	0	1	11.531331	11	60	327	38	ENST00000299300.6	0.266667	0.423478
RP11-611E13.2	0	__UNKNOWN__	__UNKNOWN__	12	70487258	70487258	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:70487258G>A	ENST00000549419.1	-	0	144										NA		NA									NA						ggtggctcacgcctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000549419.1:	chr12.hg19:g.70487258G>A		NA		hg19		0.02	-0.175437	CACxCCT	COVERED																																																																																			NOVEL	RP11-611E13.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000404075.1	14	3.610076	KEEP	0	0	0	12	350	GG	0.993634	0.38494	0		-	3	60	84	0	0	6.310861	15	60	501	38	ENST00000549419.1	0.166667	0.387407
KCNMB4	27345	__UNKNOWN__	__UNKNOWN__	12	70801449	70801449	__UNKNOWN__	Intron	SNP	G	G	A	rs787935	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:70801449G>A	ENST00000258111.4	+	2	923					NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	NA		NA			action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)			kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	gggtttcaccgtgttagccag	0.592		NA											G|||	862	0.172125	0.1808	0.1023	5008	,	,	NA	12489	0.3452	NA	0.0467	False	NA	,,,	NA	NA	NA	2504	0.1605	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643	27345		Potassium channels	6289	protein-coding gene	gene with protein product		605223			NA	10692449, 10828459	Standard	NM_014505	NM_014505	NA	Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.464+7333G>A	chr12.hg19:g.70801449G>A		NA	Q8IVR3|Q9NPA4|Q9P0G5	hg19	CCDS8997.1	0.02	-0.070172	ACCxTGT	UNCOVERED																																																																																			NOVEL	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395208.1	3	2.405445	KEEP	12	0	0	8	212	GG	0	0	0		+	4	40	120	0	0	11.831363	3	40	97	33	ENST00000258111.4	0.571429	0.054137
KCNMB4	27345	__UNKNOWN__	__UNKNOWN__	12	70814604	70814604	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:70814604C>T	ENST00000258111.4	+	3	923					NM_014505.5	NP_055320.4	Q86W47	KCMB4_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 4	NA		NA			action potential (GO:0001508)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|neuronal action potential (GO:0019228)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of neurotransmitter secretion (GO:0046928)|regulation of vasoconstriction (GO:0019229)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)			kidney(1)|large_intestine(4)|lung(5)	10	Renal(347;0.236)		Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00243)|STAD - Stomach adenocarcinoma(21;0.0118)		Miconazole(DB01110)|Procaine(DB00721)	tttgggaggccgaggcgggcg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF207992	CCDS8997.1	12q15	2006-06-10			ENSG00000135643	ENSG00000135643	27345		Potassium channels	6289	protein-coding gene	gene with protein product		605223			NA	10692449, 10828459	Standard	NM_014505	NM_014505	NA	Approved		uc001svx.3	Q86W47	OTTHUMG00000167586	ENST00000258111.4:c.465-9661C>T	chr12.hg19:g.70814604C>T		NA	Q8IVR3|Q9NPA4|Q9P0G5	hg19	CCDS8997.1	0.02	-0.245615	GGCxGAG	UNCOVERED																																																																																			NOVEL	KCNMB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395208.1	7	2.406745	KEEP	6	0	0	8	237	CC	0	0	0		+	3	60	92	0	0	6.493077	25	60	827	65	ENST00000258111.4	0.107143	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	75230067	75230067	__UNKNOWN__	IGR	SNP	G	G	T	rs71460103	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:75230067G>T			NA	NA				ATXN7L3B (294844 upstream) : RP11-81K13.1 (184681 downstream)						NA		NA									NA						agactggagtgcagtggcgtg	0.493		NA											G|||	715	0.142772	0.0098	0.1628	5008	,	,	NA	17986	0.125	NA	0.2207	False	NA	,,,	NA	NA	NA	2504	0.2464	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.75230067G>T		NA		hg19		0.02	-0.096487	AGTxCAG	UNCOVERED																																																																																			NOVEL					0			4	3.008986	KEEP	1	0	0	10	306	GG	0.992708	0.138812	0			4	60	124	0	0	12.231521	3	60	105	35		0.571429	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	75402249	75402249	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:75402249T>C			NA	NA				ATXN7L3B (467026 upstream) : RP11-81K13.1 (12499 downstream)						NA		NA									NA						cttcttctttttttttttttt	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.75402249T>C		NA		hg19		0.02	-0.043842	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			6	2.705048	KEEP	1	0	0	9	228	TT	0.99254	0.023894	0			2	60	67	1	0	6.450759	2	60	52	20		0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	75869845	75869845	__UNKNOWN__	IGR	SNP	A	A	G	rs10879920		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:75869845A>G			NA	NA				GLIPR1L2 (43377 upstream) : GLIPR1 (4614 downstream)						NA		NA									NA						aaaaaaaaaaaaaaagaaaag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.75869845A>G		NA		hg19		0.02	-0.043859	AAAxAAA	UNCOVERED																																																																																			NOVEL					0			8	2.704681	KEEP	3	0	0	9	227	AA	0	0	0			3	60	98	0	0	11.230643	0	0	0	20		1	0.024074
GLIPR1	11010	__UNKNOWN__	__UNKNOWN__	12	75882313	75882313	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:75882313G>A	ENST00000266659.3	+	3	621				RP11-585P4.5_ENST00000547326.1_RNA	NM_006851.2	NP_006842.2	P48060	GLIP1_HUMAN	GLI pathogenesis-related 1	NA		NA			cellular lipid metabolic process (GO:0044255)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	14						gcaaaactccgtctcaaaaac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U16307	CCDS9011.1	12q14.1	2008-08-15	2008-08-15			ENSG00000139278	11010			17001	protein-coding gene	gene with protein product		602692	GLI pathogenesis-related 1 (glioma)		NA	7607567, 8973356	Standard	NM_006851	NM_006851	NA	Approved	RTVP1, GliPR	uc001sxs.3	P48060	OTTHUMG00000169757	ENST00000266659.3:c.421-1873G>A	chr12.hg19:g.75882313G>A		NA	A7YET6|F8VUC2|Q15409|Q969K2	hg19	CCDS9011.1	0.02	-0.149126	TCCxTCT	COVERED																																																																																			NOVEL	GLIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405722.1	6	2.706598	KEEP	3	0	0	9	248	GG	0.99257	0.289832	0		+	3	60	92	0	0	7.472728	11	60	373	39	ENST00000266659.3	0.214286	0.292001
OSBPL8	114882	__UNKNOWN__	__UNKNOWN__	12	76808318	76808318	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:76808318G>C	ENST00000261183.3	-	5	697				OSBPL8_ENST00000393249.2_Intron|OSBPL8_ENST00000393250.4_Intron	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	NA		NA			fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						ctgcagcctcgacctcctgta	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039	114882		Oxysterol binding proteins, Pleckstrin homology (PH) domain containing	16396	protein-coding gene	gene with protein product		606736			NA	1735225, 17991739	Standard	NM_020841	NM_020841	NA	Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.218-3904C>G	chr12.hg19:g.76808318G>C		NA	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	hg19	CCDS31862.1	0.02	-0.105257	CTCxACC	UNCOVERED																																																																																			NOVEL	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406357.1	10	3.007349	KEEP	1	0	0	10	281	GG	0.992708	0.161282	0		-	3	60	97	0	0	8.832549	5	60	162	32	ENST00000261183.3	0.375	0.162467
OSBPL8	114882	__UNKNOWN__	__UNKNOWN__	12	76901865	76901865	__UNKNOWN__	Intron	SNP	C	C	T	rs11829924	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:76901865C>T	ENST00000261183.3	-	2	413				OSBPL8_ENST00000393249.2_Intron|OSBPL8_ENST00000552178.1_Intron|OSBPL8_ENST00000393250.4_Intron	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	NA		NA			fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						gcaggggaatcgcttgaacct	0.512		NA											C|||	729	0.145567	0.1596	0.1268	5008	,	,	NA	16878	0.0923	NA	0.2326	False	NA	,,,	NA	NA	NA	2504	0.1053	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039	114882		Oxysterol binding proteins, Pleckstrin homology (PH) domain containing	16396	protein-coding gene	gene with protein product		606736			NA	1735225, 17991739	Standard	NM_020841	NM_020841	NA	Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.67-20467G>A	chr12.hg19:g.76901865C>T		NA	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	hg19	CCDS31862.1	0.02	-0.140303	AATxGCT	COVERED																																																																																			NOVEL	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406357.1	18	4.813389	KEEP	14	0	0	16	464	CC	0.99257	0.289832	0		-	4	60	111	0	0	10.321948	5	60	147	52	ENST00000261183.3	0.444444	0.292001
NAV3	89795	__UNKNOWN__	__UNKNOWN__	12	78537176	78537176	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:78537176T>C	ENST00000536525.2	+	21	4856				NAV3_ENST00000266692.7_Silent_p.A1385A|NAV3_ENST00000228327.6_Silent_p.A1562A|NAV3_ENST00000397909.2_Intron	NM_014903.4	NP_055718.4	Q8IVL0	NAV3_HUMAN	neuron navigator 3	NA		NA				membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						tttgggaggctgaggcgggtg	0.488		NA								HNSCC(70;0.22)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798	89795			15998	protein-coding gene	gene with protein product	pore membrane and/or filament interacting like protein 1, steerin 3	611629			NA	12079279, 12062803	Standard	NM_001024383	XM_005269215	NA	Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000536525.2:c.4684-2973T>C	chr12.hg19:g.78537176T>C		NA	Q8NFW7|Q9Y2E7	hg19	CCDS41815.1	0.02	1.827259	GGCxGAG	COVERED																																																																																			NOVEL	NAV3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406811.1	12	3.836631	KEEP	2	4	108	51	1409	TT	1	0.992926	0		+	4	60	132	1	0	8.98805	48	60	1437	152	ENST00000536525.2	0.076923	0.992926
RP11-530C5.1	0	__UNKNOWN__	__UNKNOWN__	12	80138482	80138482	__UNKNOWN__	lincRNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:80138482A>C	ENST00000551995.1	+	0	253										NA		NA									NA						cagggtttcaacatgttggcc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000551995.1:	chr12.hg19:g.80138482A>C		NA		hg19		0.02	-0.052624	TCAxCAT	UNCOVERED																																																																																			NOVEL	RP11-530C5.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000407185.1	3	2.405108	KEEP	0	0	0	8	212	AA	0.99257	0.036492	0		+	3	60	95	0	0	9.124498	3	60	91	21	ENST00000551995.1	0.5	0.036766
POC1B	282809	__UNKNOWN__	__UNKNOWN__	12	89874657	89874657	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:89874657A>G	ENST00000313546.3	-	5	581				POC1B_ENST00000541909.1_Intron|POC1B_ENST00000378528.2_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000549504.1_Intron	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	NA		NA			cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						gattacaggcatgagccacca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323	282809		WD repeat domain containing	30836	protein-coding gene	gene with protein product		614784	WD repeat domain 51B, POC1 centriolar protein homolog B (Chlamydomonas)	WDR51B	NA	19109428	Standard	NM_172240	NM_172240	NA	Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.453-8605T>C	chr12.hg19:g.89874657A>G		NA	G3V1X0	hg19	CCDS31869.1	0.02	-0.149113	GGCxTGA	COVERED																																																																																			NOVEL	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406637.1	5	3.910372	KEEP	4	0	0	13	368	AA	0.993634	0.290142	0		-	3	60	99	0	0	7.9788	13	60	393	54	ENST00000313546.3	0.1875	0.292001
NUDT4	11163	__UNKNOWN__	__UNKNOWN__	12	93786252	93786252	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:93786252T>C	ENST00000337179.5	+	2	539				NUDT4_ENST00000415493.2_Intron|NUDT4_ENST00000549992.1_Intron|NUDT4_ENST00000548662.1_Intron|NUDT4_ENST00000547014.1_Intron	NM_199040.2	NP_950241.1	Q9NZJ9	NUDT4_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 4	NA		NA			calcium-mediated signaling (GO:0019722)|cyclic nucleotide metabolic process (GO:0009187)|cyclic-nucleotide-mediated signaling (GO:0019935)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|regulation of RNA export from nucleus (GO:0046831)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)	diphosphoinositol-polyphosphate diphosphatase activity (GO:0008486)|inositol diphosphate tetrakisphosphate diphosphatase activity (GO:0052840)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity (GO:0052846)|inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052847)|inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity (GO:0052843)|inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity (GO:0052848)|inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity (GO:0052844)|inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity (GO:0052845)|metal ion binding (GO:0046872)|snoRNA binding (GO:0030515)			endometrium(2)|kidney(1)|lung(2)	5						aggctggtcttgaactcctga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF067803	CCDS9044.1, CCDS44952.1, CCDS73504.1	12q21	2008-09-04			ENSG00000173598	ENSG00000173598	11163		Nudix motif containing	8051	protein-coding gene	gene with protein product	diphosphoinositol polyphosphate phosphohydrolase type 2	609229			NA	10777568, 11376937	Standard	NM_019094	XM_005268595	NA	Approved	DIPP2, HDCMB47P, KIAA0487, DIPP2alpha, DIPP2beta	uc001tcm.3	Q9NZJ9	OTTHUMG00000170155	ENST00000337179.5:c.100-2133T>C	chr12.hg19:g.93786252T>C		NA	B7Z916|Q4AEJ6|Q53EZ2|Q68DD7|Q9NPC5|Q9NS30|Q9NZK0|Q9NZK1	hg19	CCDS9044.1	0.02	-0.157857	TCTxGAA	COVERED																																																																																			NOVEL	NUDT4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407701.1	15	4.811143	KEEP	10	0	0	16	431	TT	0.992708	0.320453	0		+	3	47	96	0	0	7.679122	13	60	371	53	ENST00000337179.5	0.1875	0.322807
UBE2N	7334	__UNKNOWN__	__UNKNOWN__	12	93799781	93799781	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:93799781C>T	ENST00000548946.1	-	2	177							P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	NA		NA			cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						cggtggctcacgcctgtaatc	0.507		NA						Direct reversal of damage;Rad6 pathway													NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(197;738 2228 30225 32034 33454)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889	7334		Ubiquitin-conjugating enzymes E2	12492	protein-coding gene	gene with protein product		603679	ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13), ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)		NA	8902611	Standard	NM_003348	NM_003348	NA	Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000548946.1:c.316-18G>A	chr12.hg19:g.93799781C>T		NA	Q16781|Q53Y81	hg19		0.02	-0.122724	TCAxGCC	COVERED																																																																																			NOVEL	UBE2N-006	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000407709.1	5	3.30741	KEEP	3	0	0	11	293	CC	0.992708	0.19488	0		-	3	60	83	0	0	6.933351	8	60	230	39	ENST00000548946.1	0.272727	0.196312
UBE2N	7334	__UNKNOWN__	__UNKNOWN__	12	93824959	93824959	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:93824959T>C	ENST00000549833.1	-	2	113				UBE2N_ENST00000552442.1_Intron|UBE2N_ENST00000550657.1_Intron|UBE2N_ENST00000318066.2_Intron			P61088	UBE2N_HUMAN	ubiquitin-conjugating enzyme E2N	NA		NA			cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|DNA double-strand break processing (GO:0000729)|double-strand break repair via homologous recombination (GO:0000724)|Fc-epsilon receptor signaling pathway (GO:0038095)|histone ubiquitination (GO:0016574)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone modification (GO:0031058)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|postreplication repair (GO:0006301)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of DNA repair (GO:0006282)|regulation of histone ubiquitination (GO:0033182)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)|UBC13-MMS2 complex (GO:0031372)|UBC13-UEV1A complex (GO:0035370)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|liver(2)|lung(5)	10						gccgagatcgtgccattgcac	0.532		NA						Direct reversal of damage;Rad6 pathway													NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(197;738 2228 30225 32034 33454)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D83004	CCDS31875.1	12q22	2011-05-19	2011-05-19			ENSG00000177889	7334		Ubiquitin-conjugating enzymes E2	12492	protein-coding gene	gene with protein product		603679	ubiquitin-conjugating enzyme E2N (homologous to yeast UBC13), ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)		NA	8902611	Standard	NM_003348	NM_003348	NA	Approved	UbcH-ben, UBC13, MGC8489	uc001tcp.3	P61088	OTTHUMG00000170156	ENST00000549833.1:c.280-6793A>G	chr12.hg19:g.93824959T>C		NA	Q16781|Q53Y81	hg19		0.02	-0.157839	TCGxGCC	COVERED																																																																																			NOVEL	UBE2N-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000407712.1	6	4.209541	KEEP	1	0	0	14	372	TT	0.995343	0.321303	0		-	3	60	94	0	0	7.392418	14	60	396	46	ENST00000549833.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	93852771	93852771	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:93852771A>G			NA	NA				UBE2N (16733 upstream) : Y_RNA (1729 downstream)						NA		NA									NA						aggcacagtgactcatgcctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.93852771A>G		NA		hg19		0.02	-0.07017	GTGxCTC	UNCOVERED																																																																																			NOVEL					0			4	2.405916	KEEP	0	0	0	8	220	AA	0.99257	0.053735	0			2	60	73	0	0	6.595939	4	60	118	23		0.333333	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	93919968	93919968	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:93919968T>A			NA	NA				RN7SL737P (16424 upstream) : SOCS2-AS1 (16270 downstream)						NA		NA									NA						ctcaggctggtgtgcagtggt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.93919968T>A		NA		hg19		0.02	-0.105246	TGGxGTG	UNCOVERED																																																																																			NOVEL					0			9	3.00708	KEEP	0	0	0	10	276	TT	0.992708	0.138812	0			3	60	91	0	0	7.601273	9	60	266	34		0.25	0.139832
CRADD	8738	__UNKNOWN__	__UNKNOWN__	12	94118926	94118926	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:94118926A>G	ENST00000542893.2	+	2	616				CRADD_ENST00000548483.1_Intron|CRADD_ENST00000541813.1_Intron|CRADD_ENST00000332896.3_Intron|RP11-887P2.5_ENST00000550287.1_RNA|CRADD_ENST00000552033.1_Intron|CRADD_ENST00000552983.1_Intron|RP11-887P2.5_ENST00000551107.1_RNA			P78560	CRADD_HUMAN	CASP2 and RIPK1 domain containing adaptor with death domain	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death domain binding (GO:0070513)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)	8						gtgagccaccacgcccggccc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U84388	CCDS9048.1	12q21.33-q23.1	2008-08-04				ENSG00000169372	8738			2340	protein-coding gene	gene with protein product	RIP-associated ICH1/CED3-homologous protein with death domain	603454			NA	8985253, 9044836	Standard	NM_003805	NM_003805	NA	Approved	RAIDD	uc001tda.3	P78560		ENST00000542893.2:c.298+46078A>G	chr12.hg19:g.94118926A>G		NA	B7Z2Q5	hg19	CCDS9048.1	0.02	-0.227978	ACCxCGC	UNCOVERED																																																																																			NOVEL	CRADD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408515.1	6	2.70416	KEEP	4	0	0	9	224	AA	0	0	0		+	3	60	96	1	0	7.165971	20	60	568	52	ENST00000542893.2	0.130435	0.58293
TMPO	7112	__UNKNOWN__	__UNKNOWN__	12	98920508	98920508	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:98920508T>C	ENST00000556029.1	+	2	635				TMPO_ENST00000266732.4_Intron|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000343315.5_Intron|TMPO_ENST00000261210.5_Intron	NM_001032283.2	NP_001027454.1	P42167	LAP2B_HUMAN	thymopoietin	NA		NA				cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)|lamin binding (GO:0005521)			breast(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						gaggctgaggtgggcagataa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9064.1, CCDS31879.1, CCDS31880.1	12q22	2014-09-17			ENSG00000120802	ENSG00000120802	7112			11875	protein-coding gene	gene with protein product	LEM domain containing 4	188380			NA	7517549	Standard	NM_003276	NM_003276	NA	Approved	TP, LAP2, LEMD4	uc001tfh.2	P42166	OTTHUMG00000170210	ENST00000556029.1:c.280-1156T>C	chr12.hg19:g.98920508T>C		NA	A2T926|Q14861	hg19	CCDS31879.1	0.02	-0.12279	AGGxGGG	COVERED																																																																																			NOVEL	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407973.2	5	3.608869	KEEP	1	0	0	12	330	TT	0.993634	0.195062	0		+	3	42	91	0	0	7.60121	9	60	272	42	ENST00000556029.1	0.25	0.196312
IKBIP	121457	__UNKNOWN__	__UNKNOWN__	12	99018873	99018873	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:99018873C>T	ENST00000299157.4	-	0	2342				IKBIP_ENST00000420861.1_Intron|IKBIP_ENST00000342502.2_Intron|IKBIP_ENST00000393042.3_Intron	NM_153687.3	NP_710154.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	NA		NA			response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						tgagccactgcgcctggccTA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130	121457			26430	protein-coding gene	gene with protein product	I kappa B kinase interacting protein	609861			NA	15389287	Standard	NM_153687	NM_153687	NA	Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000299157.4:c.*835G>A	chr12.hg19:g.99018873C>T		NA	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	hg19	CCDS9068.1	0.02	-0.236846	CTGxGCC	COVERED																																																																																			NOVEL	IKBIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408005.2	13	6.617687	KEEP	1	0	0	22	626	CC	0.999879	0.612333	0		-	3	60	91	0	0	6.443288	24	60	787	69	ENST00000299157.4	0.111111	0.612407
ANKS1B	56899	__UNKNOWN__	__UNKNOWN__	12	99150787	99150787	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:99150787A>G	ENST00000547776.2	-	25	3504				ANKS1B_ENST00000546568.1_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000332712.7_Intron|ANKS1B_ENST00000333732.7_Intron|ANKS1B_ENST00000549025.2_Intron|ANKS1B_ENST00000549558.2_Intron|ANKS1B_ENST00000549493.2_Intron|ANKS1B_ENST00000547446.1_Intron|ANKS1B_ENST00000546960.1_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000550693.2_Intron|ANKS1B_ENST00000341752.7_Intron	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	NA		NA				cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		gattacaggcatgagccaccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10					56899		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	24600	protein-coding gene	gene with protein product		607815			NA	10490826, 12415113	Standard	NM_020140	NM_020140	NA	Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3505-5487T>C	chr12.hg19:g.99150787A>G		NA	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	hg19	CCDS55872.1	0.02	-0.148904	GGCxTGA	COVERED																																																																																			NOVEL	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408421.3	6	3.608757	KEEP	0	0	0	12	327	AA	0.993634	0.290142	0		-	3	60	90	0	0	7.174932	12	60	334	43	ENST00000547776.2	0.2	0.292001
ACTR6	64431	__UNKNOWN__	__UNKNOWN__	12	100613796	100613796	__UNKNOWN__	Silent	SNP	G	G	A	rs140292829		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:100613796G>A	ENST00000188312.2	+	10	1698	c.933G>A	c.(931-933)ccG>ccA	p.P311P	ACTR6_ENST00000551617.1_Intron|ACTR6_ENST00000546902.1_Silent_p.P229P|ACTR6_ENST00000552376.1_Intron	NM_022496.4	NP_071941.1	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog (yeast)	311		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14						AAATGCAGCCGCATTTTTTTA	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								G		0,4404		0,0,2202	65	66	65		933	-2.1	1	12	dbSNP_134	65	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ACTR6	NM_022496.3		0,2,6500	AA,AG,GG	NA	0.0233,0.0,0.0154		311/397	100613796	2,13002	2202	4300	6502	SO:0001819	synonymous_variant			AF212251	CCDS9074.1	12q23.1	2012-07-09			ENSG00000075089	ENSG00000075089	64431			24025	protein-coding gene	gene with protein product		NA			NA	11368909	Standard	NM_022496	NM_022496	NA	Approved	ARP6, FLJ13433	uc001thb.2	Q9GZN1	OTTHUMG00000170245	ENST00000188312.2:c.933G>A	chr12.hg19:g.100613796G>A		NA	B3KW37|B4DLG9|Q53GH2|Q9BY39|Q9H8H6	hg19	CCDS9074.1	0.02	-0.263151	GCCxCAT	COVERED																																																																																			NOVEL	ACTR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408159.1	0	2.403262	KEEP	0	0	0	8	201	GG	0.99257	0.688515	0		+	3	60	94	0	0	6.598168	27	60	872	54	ENST00000188312.2	0.1	0.693668
SLC5A8	160728	__UNKNOWN__	__UNKNOWN__	12	101549325	101549325	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:101549325T>C	ENST00000536262.2	-	0	4123					NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8	NA		NA								breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						agtgcagtggtgtaatcatag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(60;420 1056 13605 22380 47675)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870	160728		Solute carriers	19119	protein-coding gene	gene with protein product		608044	solute carrier family 5 (iodide transporter), member 8		NA	12107270, 12829793	Standard	NM_145913	NM_145913	NA	Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.*1732A>G	chr12.hg19:g.101549325T>C		NA		hg19	CCDS9080.1	0.02	-0.350717	TGGxGTA	COVERED																																																																																			NOVEL	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409401.1	18	11.549483	KEEP	0	1	27	48	1239	TT	1	0.877708	0		-	3	60	96	0	0	6.477276	35	60	987	115	ENST00000536262.2	0.078947	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	101916566	101916566	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:101916566T>C			NA	NA				SPIC (35791 upstream) : MYBPC1 (72060 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.101916566T>C		NA		hg19		0.02	-0.184115	AGGxGTG	COVERED																																																																																			NOVEL					0			6	4.210353	KEEP	2	0	0	14	397	TT	0.994391	0.421102	0			3	60	98	0	0	7.710976	15	60	430	54		0.166667	0.423478
DRAM1	55332	__UNKNOWN__	__UNKNOWN__	12	102284749	102284749	__UNKNOWN__	Intron	SNP	G	G	T	rs4764829	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:102284749G>T	ENST00000544152.1	+	2	238				DRAM1_ENST00000258534.8_Intron			Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	NA		NA			apoptotic process (GO:0006915)|autophagy (GO:0006914)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12						ggatggtctcgatctcttgac	0.577		NA											G|||	3630	0.72484	0.8805	0.585	5008	,	,	NA	10688	0.9127	NA	0.5149	False	NA	,,,	NA	NA	NA	2504	0.636	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC018435, DA721965	CCDS41823.1	12q23.2	2014-02-12	2009-06-12		ENSG00000136048	ENSG00000136048	55332			25645	protein-coding gene	gene with protein product	damage-regulated autophagy modulator	610776			NA	16839881	Standard	NM_018370	NM_018370	NA	Approved	FLJ11259, DRAM	uc001tix.3	Q8N682		ENST00000544152.1:c.132-6892G>T	chr12.hg19:g.102284749G>T		NA	B7Z4T0|Q7L3E3|Q9NUN1	hg19		0.02	1.140676	CTCxATC	COVERED																																																																																			NOVEL	DRAM1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409196.1	48	9.523968	KEEP	112	3	80	60	1787	GG	1	0.999948	0		+	5	60	147	0	0	12.769932	11	50	325	386	ENST00000544152.1	0.3125	0.999948
DRAM1	55332	__UNKNOWN__	__UNKNOWN__	12	102309363	102309363	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:102309363T>C	ENST00000544152.1	+	4	449				DRAM1_ENST00000258534.8_Intron			Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	NA		NA			apoptotic process (GO:0006915)|autophagy (GO:0006914)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12						ccttgttgcctaggctggagt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC018435, DA721965	CCDS41823.1	12q23.2	2014-02-12	2009-06-12		ENSG00000136048	ENSG00000136048	55332			25645	protein-coding gene	gene with protein product	damage-regulated autophagy modulator	610776			NA	16839881	Standard	NM_018370	NM_018370	NA	Approved	FLJ11259, DRAM	uc001tix.3	Q8N682		ENST00000544152.1:c.343-5631T>C	chr12.hg19:g.102309363T>C		NA	B7Z4T0|Q7L3E3|Q9NUN1	hg19		0.02	-0.078943	GCCxAGG	UNCOVERED																																																																																			NOVEL	DRAM1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409196.1	6	2.70555	KEEP	1	0	0	9	235	TT	0.99257	0.076761	0		+	2	60	71	0	0	6.395919	4	60	117	28	ENST00000544152.1	0.333333	0.077336
RP11-554E23.4	0	__UNKNOWN__	__UNKNOWN__	12	102466028	102466028	__UNKNOWN__	RNA	SNP	T	T	G	rs11111148	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:102466028T>G	ENST00000552707.1	+	0	67										NA		NA									NA						tagaggtgggttttcaacatg	0.512		NA											G|||	1294	0.258387	0.2186	0.245	5008	,	,	NA	17178	0.4246	NA	0.2157	False	NA	,,,	NA	NA	NA	2504	0.1943	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000552707.1:	chr12.hg19:g.102466028T>G		NA		hg19		0.02	-0.09649	GGGxTTT	UNCOVERED																																																																																			NOVEL	RP11-554E23.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000409328.1	5	2.403749	KEEP	0	0	0	8	198	TT	0.99257	0.119541	0		+	6	60	213	0	0	21.675415	3	60	87	25	ENST00000552707.1	0.666667	0.120436
NUP37	79023	__UNKNOWN__	__UNKNOWN__	12	102471846	102471846	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:102471846T>C	ENST00000552283.1	-	7	680				NUP37_ENST00000251074.1_Intron			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	NA		NA			carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						tggctcacgcttgtaatccca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188	79023		WD repeat domain containing	29929	protein-coding gene	gene with protein product		609264			NA	12196509	Standard	NM_024057	NM_024057	NA	Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.541-565A>G	chr12.hg19:g.102471846T>C		NA	Q9H644	hg19	CCDS9089.1	0.02	-0.210523	CGCxTGT	COVERED																																																																																			NOVEL	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409330.1	10	2.406375	KEEP	1	0	0	8	225	TT	0.99257	0.518282	0		-	3	60	105	0	0	8.260485	17	60	532	53	ENST00000552283.1	0.15	0.522161
STAB2	55576	__UNKNOWN__	__UNKNOWN__	12	104039912	104039912	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:104039912T>C	ENST00000388887.2	+	10	1244					NM_017564.9	NP_060034.9			stabilin 2	NA		NA								NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						gatcacgccattgcactccag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011	55576			18629	protein-coding gene	gene with protein product	hyaluronic acid receptor for endocytosis	608561			NA	11829752, 12077138	Standard		XR_429107	NA	Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.1041-2556T>C	chr12.hg19:g.104039912T>C		NA		hg19	CCDS31888.1	0.02	-0.070178	CCAxTGC	UNCOVERED																																																																																			NOVEL	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407089.1	6	3.910007	KEEP	0	0	0	13	367	TT	0.994391	0.053834	0		+	2	60	72	0	0	6.495736	4	60	129	31	ENST00000388887.2	0.333333	0.054137
TDG	6996	__UNKNOWN__	__UNKNOWN__	12	104359763	104359763	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:104359763C>T	ENST00000392872.3	+	0	182				TDG_ENST00000266775.9_5'UTR|TDG_ENST00000544861.1_5'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	NA		NA			base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CTACAGAGACCGGCTGCCCGT	0.677		NA						Base excision repair (BER), DNA glycosylases													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													3	7	6			NA	NA	12		NA											NA				104359763		559	1341	1900	SO:0001623	5_prime_UTR_variant			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	6996	3.2.2.29		11700	protein-coding gene	gene with protein product	G/T mismatch-specific thymine DNA glycosylase	601423			NA	8662714, 9299239	Standard		NM_003211	NA	Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.-53C>T	chr12.hg19:g.104359763C>T		NA	Q8IUZ6|Q8IZM3	hg19	CCDS9095.1	0.02	-0.429819	GACxGGC	COVERED																																																																																			NOVEL	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399673.2	2	9.023689	KEEP	0	0	0	30	862	CC	0.999997	0.954488	0		+	11	60	320	0	0	25.917633	38	60	1257	104	ENST00000392872.3	0.22449	0.954491
TDG	6996	__UNKNOWN__	__UNKNOWN__	12	104359779	104359779	__UNKNOWN__	5'UTR	SNP	C	C	T	rs372823872		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:104359779C>T	ENST00000392872.3	+	0	198				TDG_ENST00000266775.9_5'UTR|TDG_ENST00000544861.1_5'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	NA		NA			base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		CCCGTGTGCCCGGCAGGTGGA	0.687		NA						Base excision repair (BER), DNA glycosylases													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													5	7	6			NA	NA	12		NA											NA				104359779		2049	4006	6055	SO:0001623	5_prime_UTR_variant			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	6996	3.2.2.29		11700	protein-coding gene	gene with protein product	G/T mismatch-specific thymine DNA glycosylase	601423			NA	8662714, 9299239	Standard		NM_003211	NA	Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.-37C>T	chr12.hg19:g.104359779C>T		NA	Q8IUZ6|Q8IZM3	hg19	CCDS9095.1	0.02	1.534958	GCCxGGC	COVERED																																																																																			NOVEL	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399673.2	2	10.228579	KEEP	0	0	0	34	1015	CC	0.999998	0.967423	0		+	10	60	294	0	0	23.211851	41	60	1403	126	ENST00000392872.3	0.196078	0.967425
TDG	6996	__UNKNOWN__	__UNKNOWN__	12	104366824	104366824	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:104366824C>T	ENST00000392872.3	+	2	257				TDG_ENST00000266775.9_Intron|TDG_ENST00000544861.1_Intron	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	NA		NA			base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AGGTAGATTGCCTTCCTGACC	0.388		NA						Base excision repair (BER), DNA glycosylases													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	6996	3.2.2.29		11700	protein-coding gene	gene with protein product	G/T mismatch-specific thymine DNA glycosylase	601423			NA	8662714, 9299239	Standard		NM_003211	NA	Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.24-3872C>T	chr12.hg19:g.104366824C>T		NA	Q8IUZ6|Q8IZM3	hg19	CCDS9095.1	0.02	3.782258	TTGxCTT	COVERED																																																																																			NOVEL	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399673.2	116	39.631985	KEEP	0	1	26	141	4195	CC	1	1	0		+	8	60	230	0	0	13.138135	148	60	4939	410	ENST00000392872.3	0.051282	1
GLT8D2	83468	__UNKNOWN__	__UNKNOWN__	12	104455679	104455679	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:104455679A>G	ENST00000548660.1	-	1	235							Q9H1C3	GL8D2_HUMAN	glycosyltransferase 8 domain containing 2	NA		NA				integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						gcttgaacctaggaggtggag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC022343	CCDS9096.1	12q23.3	2013-02-22			ENSG00000120820	ENSG00000120820	83468		Glycosyltransferase family 8 domain containing	24890	protein-coding gene	gene with protein product		NA			NA		Standard	NM_031302	NM_031302	NA	Approved	FLJ31494	uc001tkh.1	Q9H1C3	OTTHUMG00000170120	ENST00000548660.1:c.421+2047T>C	chr12.hg19:g.104455679A>G		NA	Q96KA2	hg19	CCDS9096.1	0.02	-0.096482	CCTxGGA	UNCOVERED																																																																																			NOVEL	GLT8D2-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000407373.1	4	2.705067	KEEP	0	0	0	9	236	AA	0.99254	0.119538	0		-	3	60	88	0	0	7.578414	7	60	216	29	ENST00000548660.1	0.3	0.120436
ALDH1L2	160428	__UNKNOWN__	__UNKNOWN__	12	105431824	105431824	__UNKNOWN__	Intron	SNP	C	C	T	rs374647962		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:105431824C>T	ENST00000258494.9	-	18	2286				C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	NA		NA			10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						ggattacaggcgtgagccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	160428	1.5.1.6	Aldehyde dehydrogenases	26777	protein-coding gene	gene with protein product	mitochondrial 10-formyltetrahydrofolate dehydrogenase	613584			NA	20498374	Standard	XM_090294	NM_001034173	NA	Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2145+56G>A	chr12.hg19:g.105431824C>T		NA	Q3SY68|Q68D62|Q6AI55|Q8N922	hg19	CCDS31891.1	0.02	1.427255	AGGxGTG	COVERED																																																																																			NOVEL	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000406098.1	12	9.024366	KEEP	1	0	0	30	869	CC	0.999997	0.973962	0		-	4	60	117	0	0	7.792477	40	60	1329	111	ENST00000258494.9	0.090909	0.973965
WSCD2	9671	__UNKNOWN__	__UNKNOWN__	12	108643977	108643977	__UNKNOWN__	3'UTR	SNP	A	A	G	rs60876553		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:108643977A>G	ENST00000332082.4	+	0	4373				WSCD2_ENST00000261400.3_3'UTR			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	NA		NA				integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						gtgtgtgtgtatgagagagag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035	9671			29117	protein-coding gene	gene with protein product		NA			NA		Standard	NM_014653	NM_014653	NA	Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.*1857A>G	chr12.hg19:g.108643977A>G		NA	B2RN48|B4DES1|Q8IY35|Q9Y4B7	hg19	CCDS41828.1	0.02	-0.235257	TGTxTGA	COVERED																																																																																			NOVEL	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405554.1	1	3.170616	KEEP	0	1	29	21	496	AA	0.999879	0.64127	0		+	3	60	101	0	0	7.556429	22	60	548	59	ENST00000332082.4	0.12	0.641347
SSH1	54434	__UNKNOWN__	__UNKNOWN__	12	109203105	109203105	__UNKNOWN__	Intron	SNP	T	T	C	rs373130936		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:109203105T>C	ENST00000326495.5	-	7	630				SSH1_ENST00000360239.3_Intron|SSH1_ENST00000551165.1_Intron|SSH1_ENST00000326470.5_Intron	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	NA		NA			actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						tggtggcgcatgcctgtagtc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112	54434		Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots	30579	protein-coding gene	gene with protein product		606778	slingshot homolog 1 (Drosophila)		NA	10718198, 11832213	Standard	NM_018984	NM_018984	NA	Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.536+363A>G	chr12.hg19:g.109203105T>C		NA	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	hg19	CCDS9121.1	0.02	-0.12277	GCAxGCC	COVERED																																																																																			NOVEL	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403724.1	6	5.412732	KEEP	1	0	0	18	486	TT	0.999366	0.196187	0		-	3	60	84	0	0	6.78242	10	60	290	43	ENST00000326495.5	0.230769	0.196312
DAO	1610	__UNKNOWN__	__UNKNOWN__	12	109273636	109273636	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:109273636G>C	ENST00000551281.1	+	2	104				DAO_ENST00000548052.1_3'UTR			P14920	OXDA_HUMAN	D-amino-acid oxidase	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|D-alanine catabolic process (GO:0055130)|D-serine catabolic process (GO:0036088)|D-serine metabolic process (GO:0070178)|dopamine biosynthetic process (GO:0042416)|glyoxylate metabolic process (GO:0046487)|leucine metabolic process (GO:0006551)|proline catabolic process (GO:0006562)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-amino-acid oxidase activity (GO:0003884)|FAD binding (GO:0071949)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(2)|skin(1)	26					Flavin adenine dinucleotide(DB03147)	TCTCCAGCTGGCCAGAGAGAC	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D11370	CCDS9122.1	12q24.11	2013-09-20			ENSG00000110887	ENSG00000110887	1610	1.4.3.3		2671	protein-coding gene	gene with protein product		124050			NA	1356107, 8182053	Standard		NM_001917	NA	Approved	DAMOX	uc001tnr.4	P14920	OTTHUMG00000169360	ENST00000551281.1:c.-9-5138G>C	chr12.hg19:g.109273636G>C		NA	B2R7I5|Q16758|Q8N6R2	hg19		0.02	1.715868	CTGxCCA	COVERED																																																																																			NOVEL	DAO-006	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000403680.1	6	2.707979	KEEP	0	0	0	9	274	GG	0.99254	0.9667	0		+	4	60	130	0	0	8.719449	50	60	1667	85	ENST00000551281.1	0.074074	0.973965
ACACB	32	__UNKNOWN__	__UNKNOWN__	12	109561244	109561244	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:109561244T>C	ENST00000338432.7	+	1	110				RP11-968O1.5_ENST00000541704.2_RNA			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	NA		NA			acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	catctgtaattccagcacttt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	32	6.4.1.2		85	protein-coding gene	gene with protein product	acetyl-CoA carboxylase 2	601557	acetyl-Coenzyme A carboxylase beta		NA	8670171	Standard	NM_001093	NM_001093	NA	Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.-10+6735T>C	chr12.hg19:g.109561244T>C		NA	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	hg19	CCDS31898.1	0.02	-0.061403	AATxCCA	UNCOVERED																																																																																			NOVEL	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403077.1	2	2.706443	KEEP	0	0	0	9	242	TT	0.99254	0.04346	0		+	2	60	72	0	0	6.692999	3	60	90	24	ENST00000338432.7	0.4	0.043787
ANAPC7	51434	__UNKNOWN__	__UNKNOWN__	12	110818440	110818440	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:110818440G>A	ENST00000455511.3	-	8	1235				ANAPC7_ENST00000450008.2_Intron	NM_016238.2	NP_057322.2	Q9UJX3	APC7_HUMAN	anaphase promoting complex subunit 7	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)	19						tgggtgacagggcgagactct	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF191340	CCDS9145.2, CCDS44971.1	12q13.12	2013-01-10			ENSG00000196510	ENSG00000196510	51434		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	17380	protein-coding gene	gene with protein product		606949			NA		Standard	NM_016238	NM_016238	NA	Approved	APC7	uc001tqo.2	Q9UJX3	OTTHUMG00000157009	ENST00000455511.3:c.1234+1116C>T	chr12.hg19:g.110818440G>A		NA	Q96AC4|Q96GF4|Q9BU24|Q9NT16	hg19	CCDS9145.2	0.02	-0.114028	CAGxGCG	UNCOVERED																																																																																			NOVEL	ANAPC7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347075.3	4	2.406368	KEEP	1	0	0	8	229	GG	0.99257	0.16126	0		-	3	60	85	0	0	7.442642	6	60	209	30	ENST00000455511.3	0.333333	0.162467
RP11-478C19.2	0	__UNKNOWN__	__UNKNOWN__	12	110851373	110851373	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:110851373T>C	ENST00000550231.1	-	0	97										NA		NA									NA						cggtggctcatgcctgtaatc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550231.1:	chr12.hg19:g.110851373T>C		NA		hg19		0.02	-0.271905	TCAxGCC	COVERED																																																																																			NOVEL	RP11-478C19.2-001	KNOWN	basic|readthrough_transcript	retained_intron	NA	processed_transcript	OTTHUMT00000404601.1	13	3.910177	KEEP	2	0	0	13	362	TT	0.993072	0.712346	0		-	3	60	99	0	0	7.465048	20	60	606	62	ENST00000550231.1	0.130435	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	110890207	110890207	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:110890207T>C			NA	NA				ARPC3 (1995 upstream) : GPN3 (81 downstream)						NA		NA									NA						ctcggcctcctaaagtgctgg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.110890207T>C		NA		hg19		0.02	-0.070176	TCCxAAA	UNCOVERED																																																																																			NOVEL					0			4	2.706676	KEEP	0	0	0	9	248	TT	0.99254	0.053733	0			2	51	72	0	0	6.49586	4	60	120	24		0.333333	0.054137
VPS29	51699	__UNKNOWN__	__UNKNOWN__	12	110930679	110930679	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:110930679T>C	ENST00000549970.1	-	4	581				VPS29_ENST00000447578.2_Intron|VPS29_ENST00000360579.7_Intron|VPS29_ENST00000546588.1_Intron|VPS29_ENST00000549578.1_Intron|VPS29_ENST00000552130.2_Intron			Q9UBQ0	VPS29_HUMAN	vacuolar protein sorting 29 homolog (S. cerevisiae)	NA		NA			protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphoserine phosphatase activity (GO:0004647)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						cctgccctggtctcccgaagt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF193795	CCDS41832.1, CCDS53832.1, CCDS73525.1	12q24	2006-12-19	2006-12-19			ENSG00000111237	51699			14340	protein-coding gene	gene with protein product		606932	vacuolar protein sorting 29 (yeast homolog), vacuolar protein sorting 29 (yeast)		NA	11062004	Standard		NM_001282151	NA	Approved	PEP11, DC7, DC15	uc001tqx.3	Q9UBQ0	OTTHUMG00000169527	ENST00000549970.1:c.146+121A>G	chr12.hg19:g.110930679T>C		NA	Q502Y5|Q6FIF8|Q6IAH3|Q9H0W0|Q9NRP1|Q9NRU7	hg19		0.02	-0.340568	TGGxCTC	COVERED																																																																																			NOVEL	VPS29-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000404628.1	7	6.61366	KEEP	0	0	0	22	569	TT	0.999879	0.86564	0		-	3	60	101	0	0	7.055925	33	60	873	71	ENST00000549970.1	0.083333	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	111043184	111043184	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:111043184C>T			NA	NA				PPTC7 (22059 upstream) : TCTN1 (8647 downstream)						NA		NA									NA						gatggtgccactgcactccag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.111043184C>T		NA		hg19		0.02	-0.096462	CCAxTGC	UNCOVERED																																																																																			NOVEL					0			4	2.407155	KEEP	1	0	0	8	245	CC	0.99257	0.119541	0			3	60	79	0	0	6.677136	7	60	246	30		0.3	0.120436
HVCN1	84329	__UNKNOWN__	__UNKNOWN__	12	111100489	111100489	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:111100489A>G	ENST00000548312.1	-	4	230				HVCN1_ENST00000439744.2_Intron|HVCN1_ENST00000242607.8_Intron|HVCN1_ENST00000356742.5_Intron			Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	NA		NA			cellular response to pH (GO:0071467)|cellular response to zinc ion (GO:0071294)|multicellular organism reproduction (GO:0032504)|proton transport (GO:0015992)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	voltage-gated cation channel activity (GO:0022843)|voltage-gated proton channel activity (GO:0030171)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	19						cagcctgggcaacaggttgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007277	CCDS31900.1, CCDS58278.1	12q24.11	2011-12-09	2006-03-24	2006-03-24	ENSG00000122986	ENSG00000122986	84329		Voltage-gated ion channels / Hydrogen voltage-gated channel	28240	protein-coding gene	gene with protein product	voltage sensor domain-only protein	611227			NA	20961760, 16556803, 18356202, 22020278	Standard	NM_032369	NM_032369	NA	Approved	MGC15619, Hv1, VSOP	uc001trs.2	Q96D96		ENST00000548312.1:c.22-1236T>C	chr12.hg19:g.111100489A>G		NA	A8MQ37|B4DEB3|F8WCH5|Q6UW11|Q96IS5	hg19		0.02	1.552271	GGCxACA	COVERED																																																																																			NOVEL	HVCN1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000404651.1	24	15.632457	KEEP	0	3	79	80	2190	AA	1	0.999559	0		-	4	60	130	0	0	8.132452	71	60	2136	227	ENST00000548312.1	0.053333	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	111151204	111151204	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:111151204T>C			NA	NA				HVCN1 (23621 upstream) : PPP1CC (6280 downstream)						NA		NA									NA						tcacaaagtgttgggattaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.111151204T>C		NA		hg19		0.02	-0.254315	GTGxTGG	COVERED																																																																																			NOVEL					0			13	2.740269	KEEP	1	1	31	20	567	TT	0.999863	0.668432	0			4	60	138	0	0	10.862355	22	60	645	74		0.153846	0.668523
PPP1CC	5501	__UNKNOWN__	__UNKNOWN__	12	111170151	111170151	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:111170151A>G	ENST00000335007.5	-	2	246				PPP1CC_ENST00000546933.1_5'UTR|PPP1CC_ENST00000551690.1_Intron|PPP1CC_ENST00000340766.5_Intron|PPP1CC_ENST00000551676.1_Intron|PPP1CC_ENST00000550991.1_Intron	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	NA		NA			cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|large_intestine(2)|lung(3)	6						gcagtgagccaagatcgcgcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	5501	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase, catalytic subunits	9283	protein-coding gene	gene with protein product		176914	protein phosphatase 1, catalytic subunit, gamma isoform		NA		Standard		NM_002710	NA	Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.56-445T>C	chr12.hg19:g.111170151A>G		NA		hg19	CCDS9150.1	0.02	-0.16664	GCCxAGA	COVERED																																																																																			NOVEL	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404659.1	3	3.007649	KEEP	3	0	0	10	276	AA	0.99257	0.351317	0		-	3	60	93	0	0	7.210661	15	60	440	33	ENST00000335007.5	0.166667	0.353947
CUX2	23316	__UNKNOWN__	__UNKNOWN__	12	111544212	111544212	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:111544212T>C	ENST00000261726.6	+	1	217					NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	NA		NA			cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						tcacccaccttggcctcccaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249	23316		Homeoboxes / CUT class	19347	protein-coding gene	gene with protein product		610648	cut-like 2 (Drosophila)	CUTL2	NA		Standard	NM_015267	NM_015267	NA	Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.63+72168T>C	chr12.hg19:g.111544212T>C		NA	A7E2Y4	hg19	CCDS41837.1	0.02	-0.157816	CCTxGGC	COVERED																																																																																			NOVEL	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000404765.1	8	3.307444	KEEP	0	0	0	11	299	TT	0.993072	0.32057	0		+	3	60	101	0	0	8.179487	13	60	364	42	ENST00000261726.6	0.1875	0.322807
RP3-473L9.4	0	__UNKNOWN__	__UNKNOWN__	12	111808108	111808108	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:111808108T>C	ENST00000552663.1	+	0	39										NA		NA									NA						tcccaagtagttgggactaca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000552663.1:	chr12.hg19:g.111808108T>C		NA		hg19		0.02	-0.245507	TAGxTGG	COVERED																																																																																			NOVEL	RP3-473L9.4-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000404776.1	7	4.509796	KEEP	2	0	0	15	399	TT	0.997832	0.639957	0		+	3	60	99	0	0	7.295325	23	60	634	63	ENST00000552663.1	0.115385	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	112051315	112051315	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:112051315T>C			NA	NA				RP11-686G8.2 (13255 upstream) : BRAP (28634 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.112051315T>C		NA		hg19		0.02	-0.201713	AGGxGTG	COVERED																																																																																			NOVEL					0			5	2.702008	KEEP	0	0	0	9	221	TT	0.99254	0.486885	0			3	60	106	0	0	8.360786	17	60	484	45		0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	112070284	112070284	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:112070284A>G			NA	NA				RP11-686G8.2 (32224 upstream) : BRAP (9665 downstream)						NA		NA									NA						taggccgggcacggtggctca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.112070284A>G		NA		hg19		0.02	-0.228019	GGCxCGG	COVERED																																																																																			NOVEL					0			13	3.006726	KEEP	5	0	0	10	266	AA	0.99257	0.578599	0			3	60	91	0	0	6.550439	22	60	639	56		0.12	0.58293
ACAD10	80724	__UNKNOWN__	__UNKNOWN__	12	112142693	112142693	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:112142693A>G	ENST00000313698.4	+	4	491				ACAD10_ENST00000455480.2_Intron|ACAD10_ENST00000413681.3_Intron|ACAD10_ENST00000549590.1_Intron|ACAD10_ENST00000392636.2_Intron	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	NA		NA				mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						gggtttcaccatgttagccag	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271	80724			21597	protein-coding gene	gene with protein product		611181	acyl-Coenzyme A dehydrogenase family, member 10		NA	15560374	Standard	NM_025247	NM_025247	NA	Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.337-849A>G	chr12.hg19:g.112142693A>G		NA	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	hg19	CCDS31903.1	0.02	-0.07894	ACCxTGT	UNCOVERED																																																																																			NOVEL	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368307.1	9	2.405537	KEEP	3	0	0	8	215	AA	0	0	0		+	3	53	93	0	0	8.432769	5	60	152	23	ENST00000313698.4	0.375	0.077336
ACAD10	80724	__UNKNOWN__	__UNKNOWN__	12	112190682	112190682	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:112190682T>G	ENST00000313698.4	+	19	2972				ACAD10_ENST00000455480.2_Intron	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	NA		NA				mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|hydrolase activity (GO:0016787)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(17)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(5)	47						gtgtggtggttcatgcctgta	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY323912	CCDS31903.1, CCDS44973.1	12q24.12	2012-10-02	2010-04-30		ENSG00000111271	ENSG00000111271	80724			21597	protein-coding gene	gene with protein product		611181	acyl-Coenzyme A dehydrogenase family, member 10		NA	15560374	Standard	NM_025247	NM_025247	NA	Approved	MGC5601	uc009zvx.3	Q6JQN1	OTTHUMG00000169602	ENST00000313698.4:c.2818-894T>G	chr12.hg19:g.112190682T>G		NA	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	hg19	CCDS31903.1	0.02	-0.4296	GGTxCAT	COVERED																																																																																			NOVEL	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000368307.1	8	10.521606	KEEP	1	0	0	35	914	TT	0.999998	0.954489	0		+	3	60	101	0	0	6.7479	42	60	1179	114	ENST00000313698.4	0.066667	0.954491
DTX1	1840	__UNKNOWN__	__UNKNOWN__	12	113495646	113495646	__UNKNOWN__	5'UTR	SNP	G	G	A	rs1732786	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:113495646G>A	ENST00000257600.3	+	0	152					NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	NA		NA			cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						GAGACAACACGGAAGAGGCTG	0.647		NA											G|||	2992	0.597444	0.4092	0.6873	5008	,	,	NA	14266	0.6468	NA	0.7366	False	NA	,,,	NA	NA	NA	2504	0.5941	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144	1840			3060	protein-coding gene	gene with protein product		602582	deltex homolog 1 (Drosophila)		NA	9590294, 12670957	Standard		NM_004416	NA	Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.-352G>A	chr12.hg19:g.113495646G>A		NA	O60630|Q9BS04	hg19	CCDS9164.1	0.02	1.599122	CACxGAA	COVERED																																																																																			NOVEL	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000405045.2	3	2.708277	KEEP	0	0	0	9	283	GG	0.992708	0.972383	0		+	41	60	1204	0	0	126.396423	14	60	435	98	ENST00000257600.3	0.745455	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	113581819	113581819	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:113581819T>G			NA	NA				RASAL1 (7775 upstream) : CCDC42B (5843 downstream)						NA		NA									NA						ccagcacttttggaggccaag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.113581819T>G		NA		hg19		0.02	-0.131518	TTTxGGA	COVERED																																																																																			NOVEL					0			6	2.405894	KEEP	0	0	0	8	216	TT	0.99257	0.259026	0			3	60	102	0	0	8.473425	11	60	323	33		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	114238426	114238426	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:114238426G>A			NA	NA				RP11-438N16.1 (26938 upstream) : RBM19 (16116 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.114238426G>A		NA		hg19		0.02	-0.122798	CACxCCT	UNCOVERED																																																																																			NOVEL					0			9	2.707472	KEEP	4	0	0	9	266	GG	0	0	0			3	60	83	0	0	6.682013	10	60	331	36		0.230769	0.196312
MED13L	23389	__UNKNOWN__	__UNKNOWN__	12	116662761	116662761	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:116662761G>C	ENST00000281928.3	-	2	517				MED13L_ENST00000551197.1_Intron	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	NA		NA				mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		ctcagcctccgaaagtgctgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066	23389			22962	protein-coding gene	gene with protein product		608771	thyroid hormone receptor associated protein 2	THRAP2	NA		Standard		NM_015335	NA	Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.310+12511C>G	chr12.hg19:g.116662761G>C		NA	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	hg19	CCDS9177.1	0.02	-0.017544	TCCxAAA	UNCOVERED																																																																																			NOVEL	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403879.3	2	2.708012	KEEP	1	0	0	9	274	GG	0.99257	0	0		-	2	60	63	0	0	7.253623	0	0	0	16	ENST00000281928.3	1	0
RNFT2	84900	__UNKNOWN__	__UNKNOWN__	12	117206598	117206598	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:117206598T>C	ENST00000257575.4	+	6	961				RNFT2_ENST00000407967.3_Intron|RNFT2_ENST00000392549.2_Intron|RNFT2_ENST00000319176.7_Intron			Q96EX2	RNFT2_HUMAN	ring finger protein, transmembrane 2	NA		NA				integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.034)		tgcagtggtgtgatctcggct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027533	CCDS9180.2, CCDS44987.1	12q24.22	2013-01-09	2008-02-26	2008-02-26	ENSG00000135119	ENSG00000135119	84900		RING-type (C3HC4) zinc fingers	25905	protein-coding gene	gene with protein product		NA	transmembrane protein 118	TMEM118	NA	12477932	Standard	NM_032814	NM_032814	NA	Approved	FLJ14627	uc009zwn.3	Q96EX2	OTTHUMG00000150882	ENST00000257575.4:c.728+1879T>C	chr12.hg19:g.117206598T>C		NA	E9PAM7|Q96SU5	hg19	CCDS44987.1	0.02	-0.035086	GTGxGAT	UNCOVERED																																																																																			NOVEL	RNFT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320417.1	6	2.40541	KEEP	5	0	0	8	218	TT	0	0	0		+	2	60	65	0	0	6.624759	1	60	31	17	ENST00000257575.4	0.666667	0.019982
NOS1	4842	__UNKNOWN__	__UNKNOWN__	12	117649598	117649598	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:117649598T>C	ENST00000317775.6	-	0	8506					NM_000620.4|NM_001204218.1	NP_000611.1|NP_001191147.1	Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	NA		NA			cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		Tggctgggcgtggtggctcat	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(162;1748 2599 51982 52956)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	4842	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS	NA	1385308, 7682706	Standard		NM_001204213	NA	Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000317775.6:c.*3516A>G	chr12.hg19:g.117649598T>C		NA		hg19	CCDS41842.1	0.02	-0.31573	GCGxGGT	COVERED																																																																																			NOVEL	NOS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268052.1	9	3.608741	KEEP	0	0	0	12	327	TT	0.993634	0.813254	0		-	3	60	100	0	0	7.109404	29	60	855	58	ENST00000317775.6	0.09375	0.818465
KSR2	283455	__UNKNOWN__	__UNKNOWN__	12	118356384	118356384	__UNKNOWN__	Intron	SNP	G	G	A	rs549505018		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:118356384G>A	ENST00000339824.5	-	1	908				KSR2_ENST00000425217.1_Intron			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	NA		NA			intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					acctgaggtcgggagtttgag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435	283455			18610	protein-coding gene	gene with protein product		610737			NA	12471243	Standard	NM_173598	NM_173598	NA	Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.180+49496C>T	chr12.hg19:g.118356384G>A		NA	A0PJT2|Q3B828|Q8N775	hg19		0.02	-0.10526	GTCxGGA	UNCOVERED																																																																																			NOVEL	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000401987.2	5	2.406467	KEEP	4	0	0	8	232	GG	0	0	0		-	3	49	90	0	0	7.632278	8	60	259	33	ENST00000339824.5	0.272727	0.139832
KSR2	283455	__UNKNOWN__	__UNKNOWN__	12	118400532	118400532	__UNKNOWN__	Intron	SNP	G	G	C	rs112662385	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:118400532G>C	ENST00000339824.5	-	1	908				KSR2_ENST00000425217.1_Intron			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	NA		NA			intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(25)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ttacaggcgtgagccactgtg	0.463		NA											T|||	498	0.0994409	0.2186	0.0634	5008	,	,	NA	13694	0.0	NA	0.0845	False	NA	,,,	NA	NA	NA	2504	0.0818	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY345972	CCDS61250.1	12q24.22-q24.23	2014-08-12			ENSG00000171435	ENSG00000171435	283455			18610	protein-coding gene	gene with protein product		610737			NA	12471243	Standard	NM_173598	NM_173598	NA	Approved	FLJ25965	uc001two.2	Q6VAB6	OTTHUMG00000169020	ENST00000339824.5:c.180+5348C>G	chr12.hg19:g.118400532G>C		NA	A0PJT2|Q3B828|Q8N775	hg19		0.02	-0.078952	CGTxAGC	UNCOVERED																																																																																			NOVEL	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000401987.2	7	2.40727	KEEP	5	0	0	8	248	GG	0	0	0		-	3	60	96	0	0	9.224835	3	60	101	27	ENST00000339824.5	0.5	0.077336
VSIG10	54621	__UNKNOWN__	__UNKNOWN__	12	118504037	118504037	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:118504037G>C	ENST00000359236.5	-	0	2306					NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	NA		NA				integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						ggcaatagagggagactccgt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834	54621		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	26078	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_019086	NM_019086	NA	Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.*407C>G	chr12.hg19:g.118504037G>C		NA	Q9NWQ7	hg19	CCDS44992.1	0.02	-0.184203	GAGxGAG	COVERED																																																																																			NOVEL	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401273.2	7	8.123732	KEEP	1	0	0	27	817	GG	0.999988	0.423472	0		-	4	40	134	0	0	11.280952	13	70	411	53	ENST00000359236.5	0.235294	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	118992533	118992533	__UNKNOWN__	IGR	SNP	T	T	C	rs183203263	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:118992533T>C			NA	NA				SUDS3 (136693 upstream) : RP11-121J20.1 (90586 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.488		NA											t|||	2	0.000399361	0.0	0.0029	5008	,	,	NA	16890	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.118992533T>C		NA		hg19		0.02	-0.140329	AGGxGTG	COVERED																																																																																			NOVEL					0			4	3.308132	KEEP	0	0	0	11	299	TT	0.993634	0.259304	0			3	60	98	0	0	8.073106	11	60	321	44		0.214286	0.260965
SRRM4	84530	__UNKNOWN__	__UNKNOWN__	12	119550595	119550595	__UNKNOWN__	Intron	SNP	T	T	C	rs139206565	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:119550595T>C	ENST00000267260.4	+	3	666				RP11-364C11.2_ENST00000537730.1_RNA	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	NA		NA			cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						catcacacactggggcctgtt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767	84530			29389	protein-coding gene	gene with protein product	neural-specific SR-related protein of 100 kDa	613103	KIAA1853	KIAA1853	NA	19737518	Standard	NM_194286	NM_194286	NA	Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.279-1488T>C	chr12.hg19:g.119550595T>C		NA	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	hg19	CCDS44994.1	0.02	-0.114021	CACxGGG	UNCOVERED																																																																																			NOVEL	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401640.2	2	2.405974	KEEP	0	0	0	8	218	TT	0.99257	0.16126	0		+	3	60	99	0	0	8.282061	10	60	298	31	ENST00000267260.4	0.230769	0.162467
CIT	11113	__UNKNOWN__	__UNKNOWN__	12	120127758	120127758	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:120127758G>A	ENST00000392521.2	-	47	6242				CIT_ENST00000537607.1_Intron|CIT_ENST00000261833.7_Intron	NM_001206999.1	NP_001193928.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	NA		NA			cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		tgctgggattgcaggcgtgag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966	11113			1985	protein-coding gene	gene with protein product	serine/threonine kinase 21	605629	citron (rho-interacting, serine/threonine kinase 21)		NA	9792683	Standard	NM_007174	NM_001206999	NA	Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000392521.2:c.6186+197C>T	chr12.hg19:g.120127758G>A		NA	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	hg19	CCDS55891.1	0.02	-0.315755	ATTxCAG	COVERED																																																																																			NOVEL	CIT-005	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401847.1	7	2.708328	KEEP	0	0	0	9	284	GG	0.99254	0.812359	0		-	4	60	113	0	0	8.035166	27	60	897	70	ENST00000392521.2	0.129032	0.818465
DYNLL1	8655	__UNKNOWN__	__UNKNOWN__	12	120920377	120920377	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:120920377G>A	ENST00000392509.2	+	1	255				DYNLL1_ENST00000548342.1_Intron	NM_001037494.1	NP_001032583.1	P63167	DYL1_HUMAN	dynein, light chain, LC8-type 1	NA		NA			actin cytoskeleton organization (GO:0030036)|anatomical structure morphogenesis (GO:0009653)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic process (GO:0006915)|female gamete generation (GO:0007292)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|regulation of transcription, DNA-templated (GO:0006355)|substantia nigra development (GO:0021762)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	motor activity (GO:0003774)|nitric-oxide synthase regulator activity (GO:0030235)				NA	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					cgcctgcctcggcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U32944	CCDS9200.1	12q24.23	2013-05-30	2005-11-25	2005-11-25	ENSG00000088986	ENSG00000088986	8655		Cytoplasmic dyneins	15476	protein-coding gene	gene with protein product		601562	dynein, cytoplasmic, light polypeptide 1	DNCL1	NA	8628263, 8864115, 16260502	Standard	NM_003746	NM_001037494	NA	Approved	hdlc1, DLC1, PIN, LC8, DLC8	uc001tym.3	P63167	OTTHUMG00000169368	ENST00000392509.2:c.-7+12470G>A	chr12.hg19:g.120920377G>A		NA	Q15701	hg19	CCDS9200.1	0.02	-0.131551	CTCxGCC	COVERED																																																																																			NOVEL	DYNLL1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403709.1	8	3.911141	KEEP	2	0	0	13	393	GG	0.993634	0.227714	0		+	3	60	82	1	0	6.700986	9	60	295	39	ENST00000392509.2	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	121111732	121111732	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:121111732T>C			NA	NA				CABP1 (6605 upstream) : MLEC (12939 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.121111732T>C		NA		hg19		0.02	-0.122785	AATxCCA	COVERED																																																																																			NOVEL					0			10	2.405555	KEEP	0	0	0	8	212	TT	0.99257	0.194853	0			3	60	98	0	0	8.182138	10	60	293	27		0.230769	0.196312
HNF1A	6927	__UNKNOWN__	__UNKNOWN__	12	121426780	121426780	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:121426780G>A	ENST00000257555.6	+	2	697	c.471G>A	c.(469-471)caG>caA	p.Q157Q	HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000541395.1_Silent_p.Q157Q|HNF1A_ENST00000402929.1_Silent_p.Q157Q|HNF1A_ENST00000544413.1_Silent_p.Q157Q|HNF1A_ENST00000543427.1_Silent_p.Q40Q|HNF1A_ENST00000400024.2_Silent_p.Q157Q			P20823	HNF1A_HUMAN	HNF1 homeobox A	157	Interaction with DNA.	NA			glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGAAGACGCAGAAGCGGGCCG	0.622		NA							Hepatic Adenoma, Familial Clustering of												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													141	111	121			NA	NA	12		NA											NA				121426780		2203	4300	6503	SO:0001819	synonymous_variant	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100	6927		Homeoboxes / HNF class	11621	protein-coding gene	gene with protein product		142410	transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor	MODY3, TCF1	NA	1535333, 7795649	Standard	NM_000545	NM_000545	NA	Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.471G>A	chr12.hg19:g.121426780G>A		NA	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	hg19	CCDS9209.1	0.02	2.940943	GCAxAAG	COVERED																																																																																			NOVEL	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320957.5	2	6.921061	KEEP	0	0	0	23	723	GG	0.999892	0.999892	0		+	8	60	245	0	0	15.36187	119	60	4044	223	ENST00000257555.6	0.062992	1
RNF34	80196	__UNKNOWN__	__UNKNOWN__	12	121844171	121844171	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:121844171G>A	ENST00000392464.2	+	1	75				RNF34_ENST00000392465.3_Intron|RNF34_ENST00000361234.5_Intron|RNF34_ENST00000555076.1_Intron					ring finger protein 34, E3 ubiquitin protein ligase	NA		NA								breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		gctcactgcagcctccgcctc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633	80196		RING-type (C3HC4) zinc fingers	17297	protein-coding gene	gene with protein product		608299	ring finger protein 34		NA	12118383	Standard	NM_194271	NM_025126	NA	Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.6+6150G>A	chr12.hg19:g.121844171G>A		NA		hg19		0.02	-0.122795	GCAxCCT	COVERED																																																																																			NOVEL	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000413892.1	3	3.610636	KEEP	0	0	0	12	365	GG	0.993634	0.195062	0		+	3	60	79	0	0	6.401007	9	60	302	39	ENST00000392464.2	0.25	0.196312
KDM2B	84678	__UNKNOWN__	__UNKNOWN__	12	121934631	121934631	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:121934631G>A	ENST00000377071.4	-	12	1720				KDM2B_ENST00000377069.4_Intron|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Intron|KDM2B_ENST00000538046.2_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	NA		NA			embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						tgctgggattgcaggtgtgag	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094	84678		F-boxes / Leucine-rich repeats, Chromatin-modifying enzymes / K-demethylases	13610	protein-coding gene	gene with protein product	jumonji C domain-containing histone demethylase 1B	609078	F-box and leucine-rich repeat protein 10	FBXL10	NA	10799292	Standard	NM_032590	NM_032590	NA	Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.1648-2163C>T	chr12.hg19:g.121934631G>A		NA	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	hg19	CCDS41850.1	0.02	-0.166668	ATTxCAG	COVERED																																																																																			NOVEL	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402132.2	6	2.407191	KEEP	0	0	0	8	249	GG	0.99257	0.351317	0		-	4	60	114	0	0	9.280822	13	60	440	34	ENST00000377071.4	0.235294	0.353947
ORAI1	84876	__UNKNOWN__	__UNKNOWN__	12	122067157	122067157	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122067157G>C	ENST00000330079.7	+	1	502					NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	NA		NA			blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		gctgggattagaggcgtgagc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045	84876		ORAI calcium release-activated calcium modulators	25896	protein-coding gene	gene with protein product	calcium release-activated calcium modulator 1	610277	transmembrane protein 142A	TMEM142A	NA	16582901	Standard	NM_032790	NM_032790	NA	Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.309+2201G>C	chr12.hg19:g.122067157G>C		NA	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	hg19	CCDS41851.1	0.02	-0.219319	TTAxAGG	COVERED																																																																																			NOVEL	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402151.1	2	2.407289	KEEP	0	0	0	8	250	GG	0.99257	0.54878	0		+	3	60	108	0	0	8.248181	22	60	752	55	ENST00000330079.7	0.12	0.552887
MORN3	283385	__UNKNOWN__	__UNKNOWN__	12	122093677	122093677	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122093677T>C	ENST00000355329.3	-	3	474					NM_173855.4	NP_776254.3	Q6PF18	MORN3_HUMAN	MORN repeat containing 3	NA		NA				nucleus (GO:0005634)				breast(2)|large_intestine(1)|lung(4)|skin(1)|stomach(1)	9	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000409)|Epithelial(86;0.00145)		tggctcacgcttgtaatccca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC057760	CCDS31917.1	12q24.31	2006-01-17			ENSG00000139714	ENSG00000139714	283385			29807	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173855	NM_173855	NA	Approved		uc001uax.3	Q6PF18	OTTHUMG00000169075	ENST00000355329.3:c.304-1338A>G	chr12.hg19:g.122093677T>C		NA	Q86YQ9	hg19	CCDS31917.1	0.02	-0.201719	CGCxTGT	COVERED																																																																																			NOVEL	MORN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402154.1	10	2.539748	KEEP	2	1	33	20	559	TT	0.99986	0.490476	0		-	3	40	98	0	0	7.427119	19	60	565	65	ENST00000355329.3	0.136364	0.490544
HPD	3242	__UNKNOWN__	__UNKNOWN__	12	122290195	122290195	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122290195A>G	ENST00000289004.4	-	7	450				HPD_ENST00000543163.1_Intron	NM_002150.2	NP_002141	P32754	HPPD_HUMAN	4-hydroxyphenylpyruvate dioxygenase	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|urinary_tract(1)	18	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)	caaattgctgagattacaggt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014790	CCDS9224.1, CCDS53839.1	12q24.31	2013-09-19			ENSG00000158104	ENSG00000158104	3242	1.13.11.27		5147	protein-coding gene	gene with protein product	glyoxalase domain containing 3	609695		PPD	NA		Standard	NM_002150	NM_001171993	NA	Approved	4-HPPD, 4HPPD, GLOD3	uc001ubj.3	P32754	OTTHUMG00000169081	ENST00000289004.4:c.414+2413T>C	chr12.hg19:g.122290195A>G		NA	A8K461|B3KQ63|Q13234	hg19	CCDS9224.1	0.02	-0.105208	CTGxGAT	UNCOVERED																																																																																			NOVEL	HPD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402184.1	9	3.007153	KEEP	0	0	0	10	271	AA	0.992708	0.138812	0		-	3	60	104	0	0	9.179348	7	60	199	28	ENST00000289004.4	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	122325118	122325118	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122325118A>G			NA	NA				HPD (23616 upstream) : PSMD9 (1518 downstream)						NA		NA									NA						CTGCTAATTAATTATTAtttt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.122325118A>G		NA		hg19		0.02	-0.114017	TTAxTTA	UNCOVERED																																																																																			NOVEL					0			9	2.405819	KEEP	0	0	0	8	218	AA	0.99257	0.16126	0			3	46	101	0	0	8.87879	7	60	222	26		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	122508380	122508380	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122508380C>T			NA	NA				AC156455.1 (4652 upstream) : MLXIP (8247 downstream)						NA		NA									NA						tgagccaccgcgcccggccCt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.122508380C>T		NA		hg19		0.02	-0.096469	CCGxGCC	UNCOVERED																																																																																			NOVEL					0			4	3.008716	KEEP	1	0	0	10	305	CC	0.99254	0.119538	0			3	60	81	0	0	7.231491	5	60	176	30		0.375	0.120436
MLXIP	22877	__UNKNOWN__	__UNKNOWN__	12	122616749	122616749	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122616749A>G	ENST00000319080.7	+	8	1132									MLX interacting protein	NA		NA								NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		gattacaggcatgagccaccg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(105;787 1493 16200 18566 52466)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727	22877		Basic helix-loop-helix proteins	17055	protein-coding gene	gene with protein product		608090			NA	10048485, 11073985	Standard	NM_014938	XM_006719290	NA	Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1001-90A>G	chr12.hg19:g.122616749A>G		NA		hg19		0.02	1.710181	GGCxTGA	COVERED																																																																																			NOVEL	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000401718.2	16	4.583307	KEEP	0	2	41	30	832	AA	0.999998	0.995082	0		+	6	60	205	0	0	14.849716	55	60	1629	140	ENST00000319080.7	0.098361	0.995084
B3GNT4	79369	__UNKNOWN__	__UNKNOWN__	12	122689353	122689353	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122689353A>G	ENST00000535274.1	+	0	207				B3GNT4_ENST00000545141.1_Intron|B3GNT4_ENST00000546192.1_Intron|B3GNT4_ENST00000324189.4_Intron			Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		ttgggaggccaaggcgggagg	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AB049586	CCDS9227.1	12q24	2013-02-19					79369		Beta 3-glycosyltransferases	15683	protein-coding gene	gene with protein product		605864			NA	11042166	Standard	NM_030765	NM_030765	NA	Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000535274.1:c.-1521A>G	chr12.hg19:g.122689353A>G		NA	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	hg19		0.02	1.632089	GCCxAGG	COVERED																																																																																			NOVEL	B3GNT4-003	KNOWN	alternative_5_UTR|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000401600.1	13	7.273672	KEEP	1	2	56	44	1150	AA	1	0.998696	0		+	5	60	141	1	0	8.917288	64	60	1809	163	ENST00000535274.1	0.072464	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	122916535	122916535	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:122916535C>T			NA	NA				CLIP1 (9356 upstream) : ZCCHC8 (40881 downstream)						NA		NA									NA						caagactccacctcaaaataa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.122916535C>T		NA		hg19		0.02	-0.140347	CCAxCTC	COVERED																																																																																			NOVEL					0			5	2.707933	KEEP	0	0	0	9	271	CC	0.99254	0.259018	0			3	60	84	0	0	6.479285	13	60	429	32		0.1875	0.260965
HCAR1	27198	__UNKNOWN__	__UNKNOWN__	12	123113451	123113451	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123113451C>T	ENST00000356987.2	-	4	2321							Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	NA		NA			response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						tgcagtgagccaagattgtgc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917	27198		GPCR / Class A : Hydroxy-carboxylic acid receptors	4532	protein-coding gene	gene with protein product	lactate receptor 1	606923	G protein-coupled receptor 104, G protein-coupled receptor 81	GPR104, GPR81	NA	11574155, 19047060, 18952058, 21454438	Standard		NM_032554	NA	Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000356987.2:c.1038+6594G>A	chr12.hg19:g.123113451C>T		NA	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	hg19	CCDS9236.1	0.02	-0.078946	AGCxAAG	UNCOVERED																																																																																			NOVEL	HCAR1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		10	3.610026	KEEP	1	0	0	12	356	CC	0.993072	0.0768	0		-	3	30	84	0	0	7.532063	5	60	178	25	ENST00000356987.2	0.375	0.077336
HCAR1	27198	__UNKNOWN__	__UNKNOWN__	12	123113464	123113464	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123113464C>T	ENST00000356987.2	-	4	2321							Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	NA		NA			response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						gattgtgccactgcactccag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917	27198		GPCR / Class A : Hydroxy-carboxylic acid receptors	4532	protein-coding gene	gene with protein product	lactate receptor 1	606923	G protein-coupled receptor 104, G protein-coupled receptor 81	GPR104, GPR81	NA	11574155, 19047060, 18952058, 21454438	Standard		NM_032554	NA	Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000356987.2:c.1038+6581G>A	chr12.hg19:g.123113464C>T		NA	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	hg19	CCDS9236.1	0.02	-0.078947	CCAxTGC	UNCOVERED																																																																																			NOVEL	HCAR1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		8	2.407251	KEEP	0	0	0	8	248	CC	0.99257	0.076761	0		-	3	30	87	0	0	7.832283	5	60	173	19	ENST00000356987.2	0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	123392516	123392516	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123392516T>C			NA	NA				VPS37B (11525 upstream) : ABCB9 (12981 downstream)						NA		NA									NA						tttcaatctcttgacctcatg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.123392516T>C		NA		hg19		0.02	-0.078932	CTCxTGA	UNCOVERED																																																																																			NOVEL					0			8	3.909225	KEEP	2	0	0	13	350	TT	0.993634	0.076843	0			3	60	87	0	0	7.643241	6	60	178	34		0.333333	0.077336
PITPNM2	57605	__UNKNOWN__	__UNKNOWN__	12	123472845	123472845	__UNKNOWN__	Missense_Mutation	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123472845G>C	ENST00000542749.1	-	18	2996	c.2933C>G	c.(2932-2934)tCg>tGg	p.S978W	PITPNM2_ENST00000280562.5_Missense_Mutation_p.S972W|PITPNM2_ENST00000392428.1_Missense_Mutation_p.S699W|PITPNM2_ENST00000320201.4_Missense_Mutation_p.S978W			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	978		NA			metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		GGTGAACACCGACACTTCCTT	0.652		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													132	130	131			NA	NA	12		NA											NA				123472845		2203	4300	6503	SO:0001583	missense			AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975	57605			21044	protein-coding gene	gene with protein product		608920			NA	10022914	Standard	NM_020845	XM_005253582	NA	Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.2933C>G	chr12.hg19:g.123472845G>C	ENSP00000437611:p.Ser978Trp	NA	Q9P271	hg19	CCDS9242.1	0.02	1.786651	ACCxACA	COVERED	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372751	0.82573	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000392428;ENST00000542749	T;T;T;T	0.49432	1.11;1.1;0.78;1.1	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.69360	0.3102	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.986	T	0.72054	-0.4406	10	0.87932	D	0	-16.8423	18.9357	0.92584	0.0:0.0:1.0:0.0	.	972;978	Q9BZ72-2;Q9BZ72	.;PITM2_HUMAN	W	972;978;699;978	ENSP00000280562:S972W;ENSP00000322218:S978W;ENSP00000376223:S699W;ENSP00000437611:S978W	ENSP00000280562:S972W	S	-	2	0	PITPNM2	122038798	1.000000	0.71417	0.910000	0.35882	0.479000	0.33129	7.719000	0.84751	2.717000	0.92951	0.484000	0.47621	TCG	NOVEL	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000401342.1	1	5.415284	KEEP	0	0	0	18	533	GG	0.999859	0.999078	0		-	38	60	1292	0	0	123.580022	41	60	1294	137	ENST00000542749.1	0.481013	0.999218
SBNO1	55206	__UNKNOWN__	__UNKNOWN__	12	123808091	123808091	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123808091T>C	ENST00000602398.1	-	16	2253				SBNO1_ENST00000602750.1_Intron|SBNO1_ENST00000420886.2_Intron|SBNO1_ENST00000267176.4_Intron			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	NA		NA			regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		tcagtagagatggggtttcac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697	55206			22973	protein-coding gene	gene with protein product		614274	sno, strawberry notch homolog 1 (Drosophila)		NA		Standard	NM_018183	NM_018183	NA	Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.2125+135A>G	chr12.hg19:g.123808091T>C		NA	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	hg19	CCDS53844.1	0.02	-0.157786	AGAxGGG	COVERED																																																																																			NOVEL	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467684.1	4	3.304278	KEEP	3	0	0	11	273	TT	0.992708	0.320453	0		-	3	34	89	0	0	6.893224	14	60	370	35	ENST00000602398.1	0.176471	0.322807
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123875311	123875311	__UNKNOWN__	Silent	SNP	C	C	T	rs74356260		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123875311C>T	ENST00000402868.3	+	3	693	c.267C>T	c.(265-267)gcC>gcT	p.A89A	SETD8_ENST00000330479.4_Silent_p.A89A|SETD8_ENST00000478781.2_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	130		NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)	p.A89A(4)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AACCATTAGCCGGAATCTACA	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				4	Substitution - coding silent(4)	prostate(3)|central_nervous_system(1)											105	100	101			NA	NA	12		NA											NA				123875311		2203	4300	6503	SO:0001819	synonymous_variant			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.267C>T	chr12.hg19:g.123875311C>T		NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	1.484981	AGCxGGA	COVERED																																																																																			NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	3	8.123293	KEEP	1	0	0	27	803	CC	0.999988	0.99622	0		+	5	60	145	0	0	9.171057	62	60	2040	155	ENST00000402868.3	0.074627	0.996233
SETD8	387893	__UNKNOWN__	__UNKNOWN__	12	123892186	123892186	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs61955127		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:123892186T>C	ENST00000402868.3	+	8	1421	c.995T>C	c.(994-996)cTc>cCc	p.L332P	SETD8_ENST00000330479.4_Missense_Mutation_p.L332P			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	373	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.	NA			histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		GGGGAGGAGCTCCTGTATGAC	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													54	43	47			NA	NA	12		NA											NA				123892186		2203	4299	6502	SO:0001583	missense			AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955	387893		Chromatin-modifying enzymes / K-methyltransferases	29489	protein-coding gene	gene with protein product		607240			NA	15933070, 12086618, 12121615	Standard	NM_020382	NM_020382	NA	Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.995T>C	chr12.hg19:g.123892186T>C	ENSP00000384629:p.Leu332Pro	NA	A8K9D0|Q86W83|Q8TD09	hg19	CCDS9247.1	0.02	6.09645	AGCxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	T	23.4	4.413887	0.83449	.	.	ENSG00000183955	ENST00000402868;ENST00000330479	D;D	0.88741	-2.42;-2.42	5.12	5.12	0.69794	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.97123	0.9060	H	0.99516	4.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98816	1.0745	10	0.72032	D	0.01	-14.6681	15.2321	0.73398	0.0:0.0:0.0:1.0	rs61955127	373;332	Q9NQR1;Q9NQR1-2	SETD8_HUMAN;.	P	332	ENSP00000384629:L332P;ENSP00000332995:L332P	ENSP00000332995:L332P	L	+	2	0	SETD8	122458139	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.063000	0.61619	0.533000	0.62120	CTC	NOVEL	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318263.1	3	3.012584	KEEP	1	1	28	20	523	TT	0.999869	0.999869	0		+	44	50	1466	0	0	127.295652	112	52	3428	231	ENST00000402868.3	0.282051	1
TMED2	10959	__UNKNOWN__	__UNKNOWN__	12	124078325	124078325	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:124078325G>A	ENST00000262225.3	+	4	587				TMED2_ENST00000509052.2_Intron	NM_006815.3	NP_006806.1	Q15363	TMED2_HUMAN	transmembrane emp24 domain trafficking protein 2	NA		NA			cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPII vesicle coating (GO:0048208)|embryonic morphogenesis (GO:0048598)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|maternal placenta development (GO:0001893)|negative regulation of GTPase activity (GO:0034260)|protein targeting to plasma membrane (GO:0072661)	COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|zymogen granule membrane (GO:0042589)				kidney(1)|large_intestine(4)|lung(1)|prostate(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		gattacaggcgtgagccacca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X92098	CCDS9250.1	12q24.31	2006-03-27			ENSG00000086598	ENSG00000086598	10959			16996	protein-coding gene	gene with protein product		NA			NA	8663407	Standard	NM_006815	NM_006815	NA	Approved	RNP24, P24A	uc001ufg.3	Q15363	OTTHUMG00000168694	ENST00000262225.3:c.482-2827G>A	chr12.hg19:g.124078325G>A		NA		hg19	CCDS9250.1	0.02	-0.149108	GGCxTGA	COVERED																																																																																			NOVEL	TMED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400606.1	5	2.70648	KEEP	1	0	0	9	252	GG	0.99254	0.289823	0		+	3	47	88	0	0	6.792218	14	60	444	38	ENST00000262225.3	0.176471	0.292001
EIF2B1	1967	__UNKNOWN__	__UNKNOWN__	12	124108256	124108256	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:124108256G>A	ENST00000539951.1	-	6	539				EIF2B1_ENST00000424014.2_Intron			Q14232	EI2BA_HUMAN	eukaryotic translation initiation factor 2B, subunit 1 alpha, 26kDa	NA		NA			cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme regulator activity (GO:0030234)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|translation initiation factor activity (GO:0003743)			breast(1)|kidney(3)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.67e-05)|Epithelial(86;0.000353)|all cancers(50;0.00489)		cctgacctcagatgatctacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X95648	CCDS31924.1	12q24.3	1998-10-16	2002-08-29		ENSG00000111361	ENSG00000111361	1967			3257	protein-coding gene	gene with protein product		606686	eukaryotic translation initiation factor 2B, subunit 1 (alpha, 26kD)	EIF2B	NA		Standard	NM_001414	NM_001414	NA	Approved	EIF-2Balpha, EIF-2B, EIF2BA	uc001ufm.3	Q14232	OTTHUMG00000168696	ENST00000539951.1:c.513-948C>T	chr12.hg19:g.124108256G>A		NA	A6NLY9|B4DGX0|Q3SXP4	hg19		0.02	-0.026311	TCAxATG	UNCOVERED																																																																																			NOVEL	EIF2B1-004	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000400630.1	4	2.708139	KEEP	4	0	0	9	282	GG	0	0	0		-	2	60	57	0	0	6.652805	0	0	0	18	ENST00000539951.1	1	0
GTF2H3	2967	__UNKNOWN__	__UNKNOWN__	12	124146546	124146546	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:124146546G>C	ENST00000543341.2	+	0	2722					NM_001271867.1|NM_001516.3	NP_001258796.1|NP_001507.2	Q13889	TF2H3_HUMAN	general transcription factor IIH, polypeptide 3, 34kDa	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|translation (GO:0006412)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)		cgtggtggcaggtgcctgtaa	0.502		NA						Nucleotide excision repair (NER)													NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(176;111 2022 3038 14733 36962)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Z30093	CCDS9252.1, CCDS61275.1, CCDS73544.1	12q24.31	2012-11-05	2002-08-29		ENSG00000111358	ENSG00000111358	2967		General transcription factors, General transcription factor IIH complex subunits	4657	protein-coding gene	gene with protein product		601750	general transcription factor IIH, polypeptide 3 (34kD subunit)		NA	8194529	Standard	NM_001516	NM_001516	NA	Approved	BTF2, TFIIH, P34	uc001ufo.2	Q13889	OTTHUMG00000168697	ENST00000543341.2:c.*1764G>C	chr12.hg19:g.124146546G>C		NA	B2R819|B4DNZ6|Q7L0G0|Q96AT7	hg19	CCDS9252.1	0.02	-0.342096	GCAxGTG	COVERED																																																																																			NOVEL	GTF2H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400641.2	6	5.415005	KEEP	1	0	0	18	531	GG	0.999863	0.877587	0		+	3	60	93	0	0	6.369727	30	60	959	68	ENST00000543341.2	0.090909	0.877708
ATP6V0A2	23545	__UNKNOWN__	__UNKNOWN__	12	124243359	124243359	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:124243359A>G	ENST00000330342.3	+	0	3599					NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	NA		NA			ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		gtgagccaccatgcctggccA	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344	23545		ATPases / V-type	18481	protein-coding gene	gene with protein product	infantile malignant osteopetrosis	611716	infantile malignant osteopetrosis, ATPase, H+ transporting, lysosomal V0 subunit a isoform 2, ATPase, H+ transporting, lysosomal V0 subunit A2		NA	2247090, 18157129	Standard	NM_012463	NM_012463	NA	Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.*780A>G	chr12.hg19:g.124243359A>G		NA	A8K026|Q6NUM0	hg19	CCDS9254.1	0.02	-0.280633	ACCxTGC	COVERED																																																																																			NOVEL	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400765.2	14	3.541313	KEEP	1	1	29	22	610	AA	0.999879	0.739582	0		+	3	60	105	0	0	7.89448	23	60	673	76	ENST00000330342.3	0.115385	0.739671
DNAH10	196385	__UNKNOWN__	__UNKNOWN__	12	124281448	124281448	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:124281448C>T	ENST00000409039.3	+	12	1834					NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		gatggagtctcgctctgtcgc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653	196385		Axonemal dyneins	2941	protein-coding gene	gene with protein product		605884	dynein, axonemal, heavy polypeptide 10		NA		Standard		NM_207437	NA	Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1809+69C>T	chr12.hg19:g.124281448C>T		NA	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	hg19	CCDS9255.2	0.02	-0.096453	TCTxGCT	UNCOVERED																																																																																			NOVEL	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335420.3	9	4.210733	KEEP	5	0	0	14	393	CC	0.993072	0.119602	0		+	4	54	106	0	0	9.583652	6	60	179	32	ENST00000409039.3	0.4	0.120436
DNAH10	196385	__UNKNOWN__	__UNKNOWN__	12	124339917	124339917	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:124339917T>C	ENST00000409039.3	+	36	6109					NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	NA		NA			microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		cctgtaatcctagcactttcg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653	196385		Axonemal dyneins	2941	protein-coding gene	gene with protein product		605884	dynein, axonemal, heavy polypeptide 10		NA		Standard		NM_207437	NA	Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.6085-1686T>C	chr12.hg19:g.124339917T>C		NA	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	hg19	CCDS9255.2	0.02	-0.166661	TCCxAGC	COVERED																																																																																			NOVEL	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335420.3	10	3.607649	KEEP	2	0	0	12	316	TT	0.992708	0.351366	0		+	4	60	140	0	0	11.880979	13	60	394	42	ENST00000409039.3	0.235294	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	125103473	125103473	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:125103473C>T			NA	NA				NCOR2 (83324 upstream) : SCARB1 (157928 downstream)						NA		NA									NA						cagtggctcacgcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.125103473C>T		NA		hg19		0.02	-0.166659	TCAxGCC	COVERED																																																																																			NOVEL					0			4	2.707573	KEEP	3	0	0	9	265	CC	0.99257	0.351317	0			3	60	86	0	0	6.679358	13	60	422	46		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	125378377	125378377	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:125378377C>T			NA	NA				SCARB1 (13370 upstream) : RNU6-927P (7680 downstream)						NA		NA									NA						tcccagctacccaggaggctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.125378377C>T		NA		hg19		0.02	-0.114043	TACxCAG	UNCOVERED																																																																																			NOVEL					0			7	3.309703	KEEP	0	0	0	11	332	CC	0.993072	0.161341	0			3	60	96	0	0	8.100912	9	60	311	31		0.25	0.162467
AACS	65985	__UNKNOWN__	__UNKNOWN__	12	125562535	125562535	__UNKNOWN__	Intron	SNP	C	C	T	rs113887304	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:125562535C>T	ENST00000316519.6	+	3	564				AACS_ENST00000261686.6_Intron	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	NA		NA			adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		ggattacaggcgtgagccacc	0.507		NA											c|||	38	0.00758786	0.0265	0.0014	5008	,	,	NA	19151	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	65985	6.2.1.16	Acyl-CoA synthetase family	21298	protein-coding gene	gene with protein product	acyl-CoA synthetase family member 1	614364			NA	12623130, 17762044	Standard	NM_023928	NM_023928	NA	Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.358+1378C>T	chr12.hg19:g.125562535C>T		NA	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	hg19	CCDS9263.1	0.02	-0.210514	AGGxGTG	COVERED																																																																																			NOVEL	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400202.1	4	4.04402	KEEP	0	1	27	23	677	CC	0.999909	0.522114	0		+	4	60	112	0	0	8.76344	16	60	525	61	ENST00000316519.6	0.2	0.522161
AACS	65985	__UNKNOWN__	__UNKNOWN__	12	125586590	125586590	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:125586590T>C	ENST00000316519.6	+	6	776				AACS_ENST00000261686.6_Intron	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	NA		NA			adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		ggattacaggtgtaagccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	65985	6.2.1.16	Acyl-CoA synthetase family	21298	protein-coding gene	gene with protein product	acyl-CoA synthetase family member 1	614364			NA	12623130, 17762044	Standard	NM_023928	NM_023928	NA	Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.571-635T>C	chr12.hg19:g.125586590T>C		NA	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	hg19	CCDS9263.1	0.02	1.553598	AGGxGTA	COVERED																																																																																			NOVEL	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000400202.1	24	11.030325	KEEP	0	2	60	58	1356	TT	1	0.999559	0		+	5	60	144	0	0	8.954515	69	60	1732	180	ENST00000316519.6	0.067568	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	126482276	126482276	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:126482276A>T			NA	NA				RP5-916L7.2 (11496 upstream) : RP3-446N13.1 (98261 downstream)						NA		NA									NA						aacctctgccacctgggttca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.126482276A>T		NA		hg19		0.02	-0.078926	GCCxCCT	UNCOVERED																																																																																			NOVEL					0			1	2.403834	KEEP	0	0	0	8	203	AA	0.99257	0.076761	0			3	60	87	0	0	7.832705	5	60	143	25		0.375	0.077336
RP11-407A16.4	0	__UNKNOWN__	__UNKNOWN__	12	127134299	127134299	__UNKNOWN__	lincRNA	SNP	A	A	G	rs140287547|rs12814809		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:127134299A>G	ENST00000541769.1	-	0	288										NA		NA									NA						aggaaggaagaaaggaaggaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000541769.1:	chr12.hg19:g.127134299A>G		NA		hg19		0.02	-0.087708	AAGxAAG	UNCOVERED																																																																																			NOVEL	RP11-407A16.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000399858.1	5	2.405064	KEEP	0	0	0	8	210	AA	0.99257	0.09898	0		-	2	25	71	1	0	6.850832	2	60	53	22	ENST00000541769.1	0.5	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	12	129261970	129261970	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:129261970T>C			NA	NA				TMEM132C (69510 upstream) : SLC15A4 (15768 downstream)						NA		NA									NA						tagctgggactacaggtgtgt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr12.hg19:g.129261970T>C		NA		hg19		0.02	-0.149111	GACxACA	COVERED																																																																																			NOVEL					0			4	3.608732	KEEP	4	0	0	12	324	TT	0.99254	0.289823	0			3	60	105	0	0	8.67213	12	60	361	44		0.2	0.292001
SLC15A4	121260	__UNKNOWN__	__UNKNOWN__	12	129298797	129298797	__UNKNOWN__	Intron	SNP	G	G	A	rs71072405|rs201494823	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:129298797G>A	ENST00000266771.5	-	2	882				SLC15A4_ENST00000539703.1_Intron	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	NA		NA			ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		GGACCTGACCGCTGTATGATG	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370	121260		Solute carriers	23090	protein-coding gene	gene with protein product		615806	solute carrier family 15, member 4		NA	11741232	Standard	NM_145648	NM_145648	NA	Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.842+522C>T	chr12.hg19:g.129298797G>A		NA	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	hg19	CCDS9264.1	0.02	2.497672	ACCxCTG	COVERED																																																																																			NOVEL	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399663.1	18	4.908032	KEEP	9	3	75	43	1227	GG	1	0.999995	0		-	13	60	330	0	0	22.387133	88	60	2908	276	ENST00000266771.5	0.128713	0.999995
SLC15A4	121260	__UNKNOWN__	__UNKNOWN__	12	129298817	129298817	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:129298817G>A	ENST00000266771.5	-	2	882				SLC15A4_ENST00000539703.1_Intron	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	NA		NA			ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		GGACCTGACCGCCGTATGATG	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370	121260		Solute carriers	23090	protein-coding gene	gene with protein product		615806	solute carrier family 15, member 4		NA	11741232	Standard	NM_145648	NM_145648	NA	Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.842+502C>T	chr12.hg19:g.129298817G>A		NA	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	hg19	CCDS9264.1	0.02	2.393278	ACCxCCG	COVERED																																																																																			NOVEL	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399663.1	14	9.297394	KEEP	7	2	42	46	1336	GG	1	0.999999	0		-	7	60	192	0	0	11.27716	102	60	3306	277	ENST00000266771.5	0.06422	0.999999
TMEM132D	121256	__UNKNOWN__	__UNKNOWN__	12	129990083	129990083	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:129990083T>C	ENST00000422113.2	-	3	1442					NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	NA		NA			negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		ccaccacgcctggcctgttcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952	121256			29411	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 153	611257			NA	11853319, 12966072	Standard	NM_133448	NM_133448	NA	Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.1115+25520A>G	chr12.hg19:g.129990083T>C		NA	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	hg19	CCDS9266.1	0.02	-0.114018	GCCxGGC	UNCOVERED																																																																																			NOVEL	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399592.1	4	3.309254	KEEP	1	0	0	11	320	TT	0.993072	0.161341	0		-	3	60	91	0	0	7.732464	8	60	242	38	ENST00000422113.2	0.272727	0.162467
PIWIL1	9271	__UNKNOWN__	__UNKNOWN__	12	130848185	130848185	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:130848185T>C	ENST00000245255.3	+	18	2467					NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	NA		NA			gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		ttttttgagatggagtctcgc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207	9271		Argonaute/PIWI family	9007	protein-coding gene	gene with protein product		605571	piwi (Drosophila)-like 1, piwi-like 1 (Drosophila)		NA	9851978, 12906857	Standard		NM_004764	NA	Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.2195+496T>C	chr12.hg19:g.130848185T>C		NA	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	hg19	CCDS9268.1	0.02	-0.096471	AGAxGGA	UNCOVERED																																																																																			NOVEL	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000399510.1	9	2.406328	KEEP	5	0	0	8	225	TT	0	0	0		+	4	27	133	0	1	12.286265	6	60	169	28	ENST00000245255.3	0.4	0.120436
RAN	5901	__UNKNOWN__	__UNKNOWN__	12	131358672	131358672	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:131358672A>G	ENST00000543796.1	+	5	505				RAN_ENST00000541630.1_Intron|RAN_ENST00000392367.3_Intron|RAN_ENST00000392369.2_Intron|RAN_ENST00000254675.3_Intron			P62826	RAN_HUMAN	RAN, member RAS oncogene family	NA		NA			actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|cellular protein complex localization (GO:0034629)|DNA metabolic process (GO:0006259)|gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(2)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		gggattacagacgtgagccac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M31469	CCDS9271.1, CCDS73546.1	12q24.33	2014-05-09			ENSG00000132341	ENSG00000132341	5901			9846	protein-coding gene	gene with protein product		601179			NA	8421051	Standard	NM_006325	XM_005253592	NA	Approved	ARA24, TC4, Gsp1	uc001uir.3	P62826	OTTHUMG00000134328	ENST00000543796.1:c.248-419A>G	chr12.hg19:g.131358672A>G		NA	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	hg19	CCDS9271.1	0.02	-0.350836	CAGxCGT	COVERED																																																																																			NOVEL	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259441.2	9	9.022888	KEEP	0	0	0	30	835	AA	0.999997	0.877705	0		+	3	60	101	0	0	7.048951	33	60	1008	106	ENST00000543796.1	0.083333	0.877708
GOLGA3	2802	__UNKNOWN__	__UNKNOWN__	12	133390557	133390557	__UNKNOWN__	Intron	SNP	G	G	A	rs111944392	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:133390557G>A	ENST00000450791.2	-	3	590				GOLGA3_ENST00000204726.3_Intron|GOLGA3_ENST00000456883.2_Intron|GOLGA3_ENST00000545875.1_Intron|GOLGA3_ENST00000537452.1_Intron			Q08378	GOGA3_HUMAN	golgin A3	NA		NA			intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		tgatccacccgcctcggcctc	0.517		NA											G|||	531	0.10603	0.0091	0.1037	5008	,	,	NA	13750	0.1151	NA	0.165	False	NA	,,,	NA	NA	NA	2504	0.1687	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615	2802			4426	protein-coding gene	gene with protein product	SY2/SY10 protein, Golgi complex-associated protein of 170 kD	602581	golgi autoantigen, golgin subfamily a, 3		NA	8315394, 15829563	Standard	NM_005895	NM_001172557	NA	Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.407-552C>T	chr12.hg19:g.133390557G>A		NA	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	hg19	CCDS9281.1	0.02	-0.122797	CCCxCCT	COVERED																																																																																			NOVEL	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397569.2	13	5.112939	KEEP	14	0	0	17	499	GG	0.992708	0.19488	0		-	3	60	82	0	0	6.473101	11	45	368	57	ENST00000450791.2	0.214286	0.196312
CHFR	55743	__UNKNOWN__	__UNKNOWN__	12	133417311	133417311	__UNKNOWN__	3'UTR	SNP	C	C	G	rs75167846		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:133417311C>G	ENST00000443047.2	-	0	2616				CHFR_ENST00000537522.1_3'UTR|CHFR_ENST00000541341.1_Intron|CHFR_ENST00000266880.7_3'UTR|CHFR_ENST00000450056.2_3'UTR|CHFR_ENST00000315585.7_3'UTR	NM_001161347.1	NP_001154819.1	Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	NA		NA			mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		GTCACTCACACAAGGGAGCAG	0.701		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609	55743		RING-type (C3HC4) zinc fingers	20455	protein-coding gene	gene with protein product		605209	checkpoint with forkhead and ring finger domains		NA	10935642, 11807090	Standard		NM_001161344	NA	Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000443047.2:c.*829G>C	chr12.hg19:g.133417311C>G		NA	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	hg19	CCDS53847.1	0.02	6.073146	ACAxAAG	COVERED																																																																																			NOVEL	CHFR-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397240.2	4	5.582861	KEEP	0	2	64	41	1250	CC	1	1	0		-	25	60	834	0	0	65.518032	131	60	4506	331	ENST00000443047.2	0.160256	1
CHFR	55743	__UNKNOWN__	__UNKNOWN__	12	133447273	133447273	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:133447273T>G	ENST00000443047.2	-	4	412				CHFR_ENST00000266880.7_Intron|CHFR_ENST00000450056.2_Intron|CHFR_ENST00000432561.2_Intron|CHFR_ENST00000541837.2_Intron|CHFR_ENST00000315585.7_Intron	NM_001161347.1	NP_001154819.1	Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	NA		NA			mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		CTATAGCTCCTAACATGCACC	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													269	217	235			NA	NA	12		NA											NA				133447273		2203	4300	6503	SO:0001627	intron_variant			AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609	55743		RING-type (C3HC4) zinc fingers	20455	protein-coding gene	gene with protein product		605209	checkpoint with forkhead and ring finger domains		NA	10935642, 11807090	Standard		NM_001161344	NA	Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000443047.2:c.343+1597A>C	chr12.hg19:g.133447273T>G		NA	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	hg19	CCDS53847.1	0.02	3.950266	TCCxAAC	COVERED																																																																																			NOVEL	CHFR-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397240.2	30	25.262719	KEEP	0	0	0	84	2324	TT	1	0.999998	0		-	53	70	1717	0	0	165.687308	51	60	1535	275	ENST00000443047.2	0.509615	0.999998
ZNF268	10795	__UNKNOWN__	__UNKNOWN__	12	133760011	133760011	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr12:133760011A>G	ENST00000536435.2	+	2	363				ZNF268_ENST00000416488.1_Intron|ZNF268_ENST00000541009.2_Intron|ZNF268_ENST00000539248.2_Intron|ZNF268_ENST00000542711.2_Intron|ZNF268_ENST00000228289.5_Intron|ZNF268_ENST00000592241.1_Intron|ZNF268_ENST00000537565.1_Intron|ZNF268_ENST00000536899.2_Intron|ZNF268_ENST00000542986.2_Intron|CTD-2140B24.4_ENST00000540096.2_Intron|ZNF268_ENST00000541211.2_Intron	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	NA		NA			cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		gcttgaacccaggaggcagag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612	10795		Zinc fingers, C2H2-type, -	13061	protein-coding gene	gene with protein product		604753			NA	7865130	Standard	NM_152943	NM_003415	NA	Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.33+1395A>G	chr12.hg19:g.133760011A>G		NA	Q8TDG8|Q96RH4|Q9BZJ9	hg19	CCDS45012.1	0.02	-0.184167	CCCxGGA	COVERED																																																																																			NOVEL	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397191.2	5	3.00736	KEEP	1	0	0	10	272	AA	0.99254	0.420319	0		+	3	60	103	0	0	8.060889	17	60	490	42	ENST00000536435.2	0.15	0.423478
TPTE2	93492	__UNKNOWN__	__UNKNOWN__	13	20077352	20077352	__UNKNOWN__	Intron	SNP	T	T	C	rs201812089	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:20077352T>C	ENST00000382978.1	-	1	54				TPTE2_ENST00000457266.2_Intron|TPTE2_ENST00000390680.2_Intron|TPTE2_ENST00000382977.4_Intron|TPTE2_ENST00000255310.6_Intron|TPTE2_ENST00000382975.4_Intron|TPTE2_ENST00000400230.2_Intron|TPTE2_ENST00000400103.2_Intron			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		GACACATGTATGCATAACTCA	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													165	135	145			NA	NA	13		NA											NA				20077352		2203	4300	6503	SO:0001627	intron_variant			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958	93492		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	17299	protein-coding gene	gene with protein product		606791			NA	11716755, 12717346, 15057823	Standard	NM_199254	NM_130785	NA	Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000382978.1:c.11+11A>G	chr13.hg19:g.20077352T>C		NA	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	hg19		0.02	1.891888	GTAxGCA	COVERED																																																																																			NOVEL	TPTE2-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000044022.1	2	3.038334	KEEP	2	1	28	20	542	TT	0.999869	0.995556	0		-	8	40	264	0	0	19.579293	59	60	1755	122	ENST00000382978.1	0.119403	0.995687
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20277291	20277291	__UNKNOWN__	3'UTR	SNP	A	A	G	rs2125722	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:20277291A>G	ENST00000338910.4	-	0	1755					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TTTTTTTTCTAGATAGCCAGG	0.363		NA											A|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	18318	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.*24T>C	chr13.hg19:g.20277291A>G		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	1.813063	TCTxGAT	COVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	10	7.046282	KEEP	0	1	30	34	904	AA	0.999999	0.998866	0		-	4	33	132	0	0	8.333373	71	60	2064	158	ENST00000338910.4	0.053333	0.998867
PSPC1	55269	__UNKNOWN__	__UNKNOWN__	13	20277293	20277293	__UNKNOWN__	3'UTR	SNP	A	A	G	rs9508852		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:20277293A>G	ENST00000338910.4	-	0	1753					NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	NA		NA			negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		TTTTTTCTAGATAGCCAGGAA	0.368		NA											A|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	18322	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													43	44	44			NA	NA	13		NA											NA				20277293		1834	4090	5924	SO:0001624	3_prime_UTR_variant			AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390	55269		RNA binding motif (RRM) containing	20320	protein-coding gene	gene with protein product		612408			NA	11790299	Standard		NM_001042414	NA	Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.*22T>C	chr13.hg19:g.20277293A>G		NA	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	hg19	CCDS41870.1	0.02	1.795455	TAGxTAG	COVERED																																																																																			NOVEL	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044037.2	10	7.34562	KEEP	0	1	30	35	926	AA	0.999999	0.999109	0		-	4	33	134	0	0	8.509976	72	60	2100	159	ENST00000338910.4	0.052632	0.99911
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	20497527	20497527	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:20497527G>A			NA	NA				snoU13 (48102 upstream) : AL591925.1 (7416 downstream)						NA		NA									NA						aaaaaaaGGAGAAAAAAAGTC	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.20497527G>A		NA		hg19		0.02	-0.043847	GGAxAAA	UNCOVERED																																																																																			NOVEL					0			4	2.406731	KEEP	0	0	0	8	232	GG	0.99257	0.023895	0			2	60	54	1	0	6.352508	0	0	0	18		1	0.024074
CRYL1	51084	__UNKNOWN__	__UNKNOWN__	13	20997997	20997997	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:20997997T>C	ENST00000298248.7	-	5	696				CRYL1_ENST00000382812.1_Intron	NM_015974.2	NP_057058.2	Q9Y2S2	CRYL1_HUMAN	crystallin, lambda 1	NA		NA			fatty acid metabolic process (GO:0006631)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|L-gulonate 3-dehydrogenase activity (GO:0050104)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)			NS(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		gcaacctctgtctcccaggtt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF077049	CCDS41871.1	13q11	2008-07-18			ENSG00000165475	ENSG00000165475	51084			18246	protein-coding gene	gene with protein product	crystallin, lamda 1, L-gulonate 3-dehydrogenase, lambda-crystallin homolog	609877			NA	12527201	Standard	NM_015974	NM_015974	NA	Approved	GDH, lambda-CRY, MGC149525, MGC149526	uc001une.3	Q9Y2S2	OTTHUMG00000016516	ENST00000298248.7:c.633+8243A>G	chr13.hg19:g.20997997T>C		NA	A0PJ43|B3KN92|Q0VDI1|Q7Z4Z9|Q9P0G7	hg19	CCDS41871.1	0.02	-0.078947	CTGxCTC	UNCOVERED																																																																																			NOVEL	CRYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044071.1	10	3.007746	KEEP	7	0	0	10	277	TT	0	0	0		-	3	60	100	0	0	9.355333	4	42	122	33	ENST00000298248.7	0.428571	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	21791882	21791882	__UNKNOWN__	IGR	SNP	A	A	G	rs188862954		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:21791882A>G			NA	NA				MRP63 (38659 upstream) : LINC01046 (16824 downstream)						NA		NA									NA						ccagcactttaggaggccgag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.21791882A>G		NA		hg19		0.02	-0.114027	TTTxGGA	UNCOVERED																																																																																			NOVEL					0			10	3.308237	KEEP	3	0	0	11	301	AA	0.992708	0.161282	0			3	60	105	1	0	9.278706	7	60	214	39		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	23560798	23560798	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:23560798G>A			NA	NA				AL157931.1 (8662 upstream) : RNY3P4 (165926 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.23560798G>A		NA		hg19		0.02	-0.114032	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			7	3.309561	KEEP	1	0	0	11	332	GG	0.993072	0.161341	0			3	60	88	0	0	7.181905	10	60	326	35		0.230769	0.162467
SGCG	6445	__UNKNOWN__	__UNKNOWN__	13	23815075	23815075	__UNKNOWN__	Intron	SNP	G	G	A	rs75949657	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:23815075G>A	ENST00000218867.3	+	3	421				SGCG_ENST00000537476.1_Intron|SGCG_ENST00000545013.1_Intron	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	NA		NA			muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		ggcggatcacgaggtcaggag	0.517		NA											G|||	99	0.0197684	0.0	0.0	5008	,	,	NA	12237	0.0843	NA	0.0109	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683	6445			10809	protein-coding gene	gene with protein product	Maghrebian myopathy (autosomal recessive), 35kD dystrophin-associated glycoprotein, limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive), gamma sarcoglycan	608896	sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)	DMDA1, MAM, LGMD2C	NA	8968757	Standard	NM_000231	NM_000231	NA	Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.297+6224G>A	chr13.hg19:g.23815075G>A		NA	Q32M32|Q5T9J6	hg19	CCDS9299.1	0.02	-0.140338	CACxAGG	UNCOVERED																																																																																			NOVEL	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044151.1	7	3.008592	KEEP	6	0	0	10	300	GG	0	0	0		+	3	60	85	0	0	6.579299	13	60	412	38	ENST00000218867.3	0.1875	0.260965
SGCG	6445	__UNKNOWN__	__UNKNOWN__	13	23852073	23852073	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:23852073A>G	ENST00000218867.3	+	5	509				SGCG_ENST00000537476.1_Intron|SGCG_ENST00000545013.1_Intron	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	NA		NA			muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		tcctgacctcatgatccgcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683	6445			10809	protein-coding gene	gene with protein product	Maghrebian myopathy (autosomal recessive), 35kD dystrophin-associated glycoprotein, limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive), gamma sarcoglycan	608896	sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)	DMDA1, MAM, LGMD2C	NA	8968757	Standard	NM_000231	NM_000231	NA	Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.386-1425A>G	chr13.hg19:g.23852073A>G		NA	Q32M32|Q5T9J6	hg19	CCDS9299.1	0.02	-0.149096	CTCxTGA	UNCOVERED																																																																																			NOVEL	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044151.1	6	2.707544	KEEP	7	0	0	9	260	AA	0	0	0		+	3	46	98	0	0	8.073085	11	60	330	43	ENST00000218867.3	0.214286	0.292001
SACS	26278	__UNKNOWN__	__UNKNOWN__	13	23936983	23936983	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:23936983T>C	ENST00000382292.3	-	5	731				SACS_ENST00000382298.3_Intron|SACS_ENST00000402364.1_Intron			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	NA		NA			cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		cctcagcctctcaaagtgctg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835	26278		Heat shock proteins / DNAJ (HSP40)	10519	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 138	604490	spastic ataxia of Charlevoix-Saguenay (sacsin)		NA	10610707, 15057823, 21726565	Standard	NM_014363	NM_001278055	NA	Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.457+2321A>G	chr13.hg19:g.23936983T>C		NA	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	hg19	CCDS9300.2	0.02	-0.087721	CTCxCAA	UNCOVERED																																																																																			NOVEL	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044148.3	2	2.406654	KEEP	1	0	0	8	230	TT	0	0	0		-	4	60	138	0	0	13.02343	5	60	156	27	ENST00000382292.3	0.444444	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	24549086	24549086	__UNKNOWN__	IGR	SNP	T	T	C	rs139102015	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:24549086T>C			NA	NA				ANKRD20A19P (28165 upstream) : RP11-307N16.6 (4752 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.567		NA											t|||	122	0.024361	0.0	0.0029	5008	,	,	NA	12248	0.0972	NA	0.003	False	NA	,,,	NA	NA	NA	2504	0.0194	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.24549086T>C		NA		hg19		0.02	-0.052605	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			5	3.005151	KEEP	3	0	0	10	253	TT	0.99254	0.036491	0			2	40	66	0	0	6.350379	2	60	55	21		0.5	0.036766
ATP8A2	51761	__UNKNOWN__	__UNKNOWN__	13	26053249	26053249	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:26053249A>G	ENST00000381655.2	+	2	363				ATP8A2_ENST00000255283.8_Intron	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	NA		NA			aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		ctcccaaagtactgggattac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	51761	3.6.3.1	ATPases / P-type	13533	protein-coding gene	gene with protein product		605870	ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2, ATPase, aminophospholipid transporter-like, class I, type 8A, member 2		NA	11015572, 19778899	Standard	NM_016529	NM_016529	NA	Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.221+9990A>G	chr13.hg19:g.26053249A>G		NA	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	hg19	CCDS41873.1	0.02	-0.096474	AGTxCTG	UNCOVERED																																																																																			NOVEL	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044236.2	7	2.405725	KEEP	0	0	0	8	214	AA	0.99257	0.119541	0		+	3	60	102	0	0	9.333416	5	60	139	27	ENST00000381655.2	0.375	0.120436
RNF6	6049	__UNKNOWN__	__UNKNOWN__	13	26733512	26733512	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:26733512C>T	ENST00000468480.1	-	6	768							Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	NA		NA			negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		cctgtaatcccagcactttgg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870	6049		RING-type (C3HC4) zinc fingers	10069	protein-coding gene	gene with protein product	RING-H2 protein RNF-6	604242			NA	10331950	Standard	NM_005977	NM_005977	NA	Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000468480.1:c.338-26923G>A	chr13.hg19:g.26733512C>T		NA	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	hg19		0.02	-0.157909	TCCxAGC	COVERED																																																																																			NOVEL	RNF6-007	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000044247.2	6	3.911846	KEEP	0	0	0	13	405	CC	0.994391	0.320996	0		-	3	60	92	0	0	7.191648	14	60	495	45	ENST00000468480.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	28269487	28269487	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:28269487T>C			NA	NA				POLR1D (27939 upstream) : GSX1 (97292 downstream)						NA		NA									NA						gatcgcaccattgcactccag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.28269487T>C		NA		hg19		0.02	-0.210474	CCAxTGC	COVERED																																																																																			NOVEL					0			18	4.342917	KEEP	1	1	30	25	683	TT	0.999931	0.522125	0			3	60	104	0	0	8.16091	17	60	488	74		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	29154983	29154983	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:29154983A>G			NA	NA				FLT1 (85718 upstream) : POMP (78257 downstream)						NA		NA									NA						gcctgccttgacctcccaaag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.29154983A>G		NA		hg19		0.02	-0.149116	TTGxCCT	COVERED																																																																																			NOVEL					0			7	3.607099	KEEP	0	0	0	12	318	AA	0.993634	0.290142	0			3	60	95	0	0	7.672206	12	60	371	42		0.2	0.292001
KATNAL1	84056	__UNKNOWN__	__UNKNOWN__	13	30779982	30779982	__UNKNOWN__	3'UTR	SNP	A	A	G	rs112146305		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:30779982A>G	ENST00000380615.3	-	0	4335					NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1	NA		NA								autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		gtgtgtgtgtatgtgtgtgta	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781	84056		ATPases / AAA-type	28361	protein-coding gene	gene with protein product		614764			NA	12477932	Standard	NM_032116	NM_001014380	NA	Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.*2695T>C	chr13.hg19:g.30779982A>G		NA		hg19	CCDS31956.1	0.02	5.565416	TGTxTGT	COVERED																																																																																			NOVEL	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044346.2	70	16.207743	KEEP	0	10	268	149	3851	AA	1	1	0		-	10	60	332	0	0	22.094482	138	60	3806	418	ENST00000380615.3	0.067568	1
KATNAL1	84056	__UNKNOWN__	__UNKNOWN__	13	30779992	30779992	__UNKNOWN__	3'UTR	SNP	A	A	G	rs9508676		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:30779992A>G	ENST00000380615.3	-	0	4325					NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1	NA		NA								autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		atgtgtgtgtatgtgtgtctg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781	84056		ATPases / AAA-type	28361	protein-coding gene	gene with protein product		614764			NA	12477932	Standard	NM_032116	NM_001014380	NA	Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.*2685T>C	chr13.hg19:g.30779992A>G		NA		hg19	CCDS31956.1	0.02	5.528604	TGTxTGT	COVERED																																																																																			NOVEL	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044346.2	82	30.67172	KEEP	0	7	192	170	4488	AA	1	1	0		-	7	60	239	0	0	14.94354	144	60	4142	446	ENST00000380615.3	0.046358	1
USPL1	10208	__UNKNOWN__	__UNKNOWN__	13	31224530	31224530	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:31224530G>A	ENST00000255304.4	+	8	1580					NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	NA		NA			Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		cctggccaacgtggtgaaacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(60;318 1180 1554 28110 31601)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952	10208			20294	protein-coding gene	gene with protein product		NA	chromosome 13 open reading frame 22	C13orf22	NA	22878415	Standard	NM_005800	NM_005800	NA	Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1239-2755G>A	chr13.hg19:g.31224530G>A		NA	Q14109|Q6AI45|Q8IY30|Q8IYE8	hg19	CCDS9336.1	0.02	-0.131555	AACxTGG	COVERED																																																																																			NOVEL	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044369.1	11	2.406232	KEEP	0	0	0	8	225	GG	0.99257	0.22747	0		+	3	60	84	0	0	6.673194	11	60	344	25	ENST00000255304.4	0.214286	0.229173
FRY	10129	__UNKNOWN__	__UNKNOWN__	13	32696556	32696556	__UNKNOWN__	Intron	SNP	A	A	G	rs113349777	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:32696556A>G	ENST00000380250.3	+	5	960					NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	NA		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		tccagcctggacgacagagtg	0.488		NA											G|||	284	0.0567093	0.1286	0.0403	5008	,	,	NA	14102	0.003	NA	0.0656	False	NA	,,,	NA	NA	NA	2504	0.0174	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910	10129			20367	protein-coding gene	gene with protein product		614818	chromosome 13 open reading frame 14	C13orf14	NA	14702039, 8812419	Standard	NM_023037	NM_023037	NA	Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.465-1867A>G	chr13.hg19:g.32696556A>G		NA	Q9Y3N6	hg19	CCDS41875.1	0.02	-0.0877	TGGxCGA	UNCOVERED																																																																																			NOVEL	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044405.1	5	3.307821	KEEP	0	0	0	11	294	AA	0.993072	0.09903	0		+	3	60	104	0	1	9.344135	6	60	167	28	ENST00000380250.3	0.333333	0.099721
FRY	10129	__UNKNOWN__	__UNKNOWN__	13	32849241	32849241	__UNKNOWN__	Intron	SNP	T	T	C	rs547338861		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:32849241T>C	ENST00000380250.3	+	56	8782				FRY_ENST00000542859.1_Intron	NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	NA		NA				cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		TCTggccgggtgcggtggctc	0.557		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	13945	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910	10129			20367	protein-coding gene	gene with protein product		614818	chromosome 13 open reading frame 14	C13orf14	NA	14702039, 8812419	Standard	NM_023037	NM_023037	NA	Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.8286+113T>C	chr13.hg19:g.32849241T>C		NA	Q9Y3N6	hg19	CCDS41875.1	0.02	1.60804	GGGxGCG	COVERED																																																																																			NOVEL	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044405.1	25	10.821872	KEEP	2	2	62	58	1510	TT	1	0.999804	0		+	4	60	142	1	0	9.282847	73	60	2125	224	ENST00000380250.3	0.051948	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	33154512	33154512	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:33154512A>G			NA	NA				N4BP2L2 (41576 upstream) : PDS5B (6051 downstream)						NA		NA									NA						ctcatgatccacccgccttgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.33154512A>G		NA		hg19		0.02	-0.070164	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			5	3.607768	KEEP	5	0	0	12	321	AA	0.992708	0.053742	0			2	40	71	0	0	6.395989	4	60	116	40		0.333333	0.054137
STARD13	90627	__UNKNOWN__	__UNKNOWN__	13	33691293	33691293	__UNKNOWN__	Intron	SNP	C	C	T	rs575741011	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:33691293C>T	ENST00000336934.5	-	8	2398				STARD13_ENST00000255486.4_Intron|STARD13_ENST00000399365.3_Intron	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		tcacccaggccggagtgcagt	0.463		NA											C|||	2	0.000399361	0.0	0.0	5008	,	,	NA	19584	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121	90627		Rho GTPase activating proteins, StAR-related lipid transfer (START) domain containing	19164	protein-coding gene	gene with protein product		609866	START domain containing 13, long intergenic non-protein coding RNA 464	LINC00464	NA	8812419	Standard	NM_001243466	NM_178006	NA	Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.2281+908G>A	chr13.hg19:g.33691293C>T		NA	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	hg19	CCDS9348.1	0.02	-0.140305	GGCxGGA	COVERED																																																																																			NOVEL	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276118.2	5	3.00895	KEEP	0	0	0	10	306	CC	0.992708	0.259062	0		-	3	60	93	0	0	7.682546	10	60	311	41	ENST00000336934.5	0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	34704184	34704184	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:34704184G>C			NA	NA				SNORA25 (29209 upstream) : RP11-16D22.2 (217995 downstream)						NA		NA									NA						gaactcctgagctcaagtgat	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.34704184G>C		NA		hg19		0.02	-0.070183	TGAxCTC	UNCOVERED																																																																																			NOVEL					0			1	2.407346	KEEP	1	0	0	8	251	GG	0	0	0			2	60	72	0	0	6.335535	5	60	174	24		0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	39037038	39037038	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:39037038G>A			NA	NA				UFM1 (99898 upstream) : LINC00437 (70441 downstream)						NA		NA									NA						tcaggagttcgagaccagcct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.39037038G>A		NA		hg19		0.02	-0.149115	TTCxAGA	COVERED																																																																																			NOVEL					0			5	3.91166	KEEP	2	0	0	13	398	GG	0.994391	0.290363	0			4	60	117	0	0	9.580946	13	60	417	48		0.235294	0.292001
LHFP	10186	__UNKNOWN__	__UNKNOWN__	13	40008960	40008960	__UNKNOWN__	Intron	SNP	G	G	A	rs9594332	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:40008960G>A	ENST00000379589.3	-	3	848					NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	NA		NA				integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		ttgggaggccgaggcgggtgg	0.483		NA	T	HMGA2	lipoma								-|||	978	0.195288	0.152	0.1744	5008	,	,	NA	16893	0.3254	NA	0.2237	False	NA	,,,	NA	NA	NA	2504	0.1053	NA	NA	NA			Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722	10186			6586	protein-coding gene	gene with protein product		606710			NA	10329012	Standard	NM_005780	NM_005780	NA	Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.386-56297C>T	chr13.hg19:g.40008960G>A		NA	B2R7M2|Q53FC0|Q96SH5	hg19	CCDS9369.1	0.02	-0.114019	GCCxAGG	UNCOVERED																																																																																			NOVEL	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044619.1	4	2.407048	KEEP	9	0	0	8	241	GG	0	0	0		-	10	60	294	0	0	31.116682	3	60	104	45	ENST00000379589.3	0.769231	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	40651331	40651331	__UNKNOWN__	IGR	SNP	G	G	A	rs113676851|rs12871070	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:40651331G>A			NA	NA				SNORD116 (219967 upstream) : LINC00332 (104614 downstream)						NA		NA									NA						tagggaagcgggggaggaagg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.40651331G>A		NA		hg19		0.02	-0.078693	GCGxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.406992	KEEP	0	0	0	8	242	GG	0.99257	0.076761	0			3	60	92	2	0	8.554948	4	60	127	38		0.428571	0.077336
MRPS31	10240	__UNKNOWN__	__UNKNOWN__	13	41332007	41332007	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:41332007A>G	ENST00000323563.6	-	4	636					NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	NA		NA				mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		ggccgggtgcagtggctcacg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738	10240		Mitochondrial ribosomal proteins / small subunits	16632	protein-coding gene	gene with protein product		611992			NA	11279123, 8567980	Standard		NM_005830	NA	Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.600-858T>C	chr13.hg19:g.41332007A>G		NA	B2RCS3|Q5VYC8|Q8WTV8	hg19	CCDS9372.1	0.02	-0.157885	TGCxGTG	COVERED																																																																																			NOVEL	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044640.2	4	3.308318	KEEP	0	0	0	11	306	AA	0.993072	0.32057	0		-	3	60	102	0	0	8.191589	14	60	427	46	ENST00000323563.6	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	41472566	41472566	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:41472566T>C			NA	NA				TPTE2P5 (43439 upstream) : SUGT1P3 (13456 downstream)						NA		NA									NA						gaggccgaggtgggtggatca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.41472566T>C		NA		hg19		0.02	-0.087668	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.707302	KEEP	7	0	0	9	259	TT	0	0	0			3	60	82	0	0	6.977092	7	60	215	37		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	41761798	41761798	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:41761798T>C			NA	NA				snoU13 (7575 upstream) : KBTBD7 (2170 downstream)						NA		NA									NA						TCTggctgggtgcggtggctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.41761798T>C		NA		hg19		0.02	-0.078921	GGGxGCG	UNCOVERED																																																																																			NOVEL					0			3	3.007697	KEEP	1	0	0	10	278	TT	0.99254	0.076759	0			3	60	102	0	0	9.144264	6	60	170	30		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	41771567	41771567	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:41771567G>A			NA	NA				KBTBD7 (2865 upstream) : MTRF1 (18937 downstream)						NA		NA									NA						ggctaacacggtgaaaccctg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.41771567G>A		NA		hg19		0.02	-0.122793	ACGxTGA	UNCOVERED																																																																																			NOVEL					0			13	2.707864	KEEP	7	0	0	9	272	GG	0	0	0			3	32	83	0	0	6.6821	10	60	319	32		0.230769	0.196312
VWA8	23078	__UNKNOWN__	__UNKNOWN__	13	42371420	42371420	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:42371420C>T	ENST00000379310.3	-	18	2132				VWA8_ENST00000281496.6_Intron	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	NA		NA				extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)				NA						tcatgatccacccacctcggc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763	23078			29071	protein-coding gene	gene with protein product		NA	KIAA0564	KIAA0564	NA	9628581	Standard	NM_015058	NM_015058	NA	Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.2064-9741G>A	chr13.hg19:g.42371420C>T		NA	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	hg19	CCDS41881.1	0.02	-0.271949	CCAxCCA	COVERED																																																																																			NOVEL	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354828.2	10	4.513564	KEEP	1	0	0	15	467	CC	0.99649	0.714798	0		-	3	40	95	0	0	6.894865	23	60	792	69	ENST00000379310.3	0.115385	0.717315
DGKH	160851	__UNKNOWN__	__UNKNOWN__	13	42785585	42785585	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:42785585A>G	ENST00000337343.4	+	24	3035				DGKH_ENST00000498255.2_Intron|DGKH_ENST00000538674.1_Intron|DGKH_ENST00000379274.2_Intron|DGKH_ENST00000261491.5_Intron|DGKH_ENST00000540693.1_Intron|DGKH_ENST00000536612.1_Intron	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	NA		NA			blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		tgtaatcccaacactttggga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780	160851		Sterile alpha motif (SAM) domain containing, Pleckstrin homology (PH) domain containing	2854	protein-coding gene	gene with protein product		604071			NA	8702685	Standard	NM_178009	XM_005266271	NA	Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3014+684A>G	chr13.hg19:g.42785585A>G		NA	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	hg19	CCDS9381.1	0.02	-0.087706	CCAxCAC	UNCOVERED																																																																																			NOVEL	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044699.2	5	3.609153	KEEP	0	0	0	12	331	AA	0.993634	0.099086	0		+	3	45	103	0	0	9.243977	6	60	174	35	ENST00000337343.4	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	43314282	43314282	__UNKNOWN__	IGR	SNP	T	T	C	rs185678989	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:43314282T>C			NA	NA				TNFSF11 (132133 upstream) : FAM216B (41403 downstream)						NA		NA									NA						tggctcatgcttgtaatccca	0.393		NA											T|||	5	0.000998403	0.0	0.0072	5008	,	,	NA	11339	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.43314282T>C		NA		hg19		0.02	-0.096486	TGCxTGT	UNCOVERED																																																																																			NOVEL					0			5	3.007371	KEEP	0	0	0	10	273	TT	0.992708	0.119558	0			3	60	103	0	0	8.932504	8	60	242	29		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	44497286	44497286	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:44497286G>A			NA	NA				LACC1 (29218 upstream) : LINC00284 (102168 downstream)						NA		NA									NA						gattataggcgtgagccacca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.44497286G>A		NA		hg19		0.02	-0.114025	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			7	2.707633	KEEP	1	0	0	9	265	GG	0.99257	0.16126	0			3	60	82	0	0	6.832109	8	60	262	35		0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	45287079	45287079	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:45287079A>G			NA	NA				LINC00407 (11927 upstream) : LINC00330 (86559 downstream)						NA		NA									NA						ggccaaggcaagtggattgct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.45287079A>G		NA		hg19		0.02	-0.078947	GCAxGTG	UNCOVERED																																																																																			NOVEL					0			3	3.008124	KEEP	0	0	0	10	284	AA	0.992708	0.076772	0			3	60	103	0	0	9.243651	6	60	186	26		0.333333	0.077336
GTF2F2	2963	__UNKNOWN__	__UNKNOWN__	13	45808035	45808035	__UNKNOWN__	Intron	SNP	G	G	A	rs534271831	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:45808035G>A	ENST00000340473.6	+	6	527				GTF2F2_ENST00000494087.1_Intron	NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		gcaacagagcgcgtctctgtc	0.473		NA											G|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	19285	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342	2963		General transcription factors	4653	protein-coding gene	gene with protein product		189969	general transcription factor IIF, polypeptide 1 (74kD subunit)		NA	8162052	Standard	NM_004128	NM_004128	NA	Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.387-18971G>A	chr13.hg19:g.45808035G>A		NA	A6NNS5|Q5W0H3	hg19	CCDS9395.1	0.02	-0.078941	AGCxCGT	UNCOVERED																																																																																			NOVEL	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044767.2	8	2.407288	KEEP	0	0	0	8	248	GG	0.99257	0.076761	0		+	3	60	84	0	0	7.532191	5	60	165	20	ENST00000340473.6	0.375	0.077336
GTF2F2	2963	__UNKNOWN__	__UNKNOWN__	13	45808037	45808037	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:45808037G>A	ENST00000340473.6	+	6	527				GTF2F2_ENST00000494087.1_Intron	NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		aacagagcgcgtctctgtctc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342	2963		General transcription factors	4653	protein-coding gene	gene with protein product		189969	general transcription factor IIF, polypeptide 1 (74kD subunit)		NA	8162052	Standard	NM_004128	NM_004128	NA	Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.387-18969G>A	chr13.hg19:g.45808037G>A		NA	A6NNS5|Q5W0H3	hg19	CCDS9395.1	0.02	-0.078936	CGCxTCT	UNCOVERED																																																																																			NOVEL	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044767.2	8	2.407263	KEEP	0	0	0	8	247	GG	0.99257	0.076761	0		+	3	60	85	0	0	7.632402	5	60	156	20	ENST00000340473.6	0.375	0.077336
GTF2F2	2963	__UNKNOWN__	__UNKNOWN__	13	45847093	45847093	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:45847093A>G	ENST00000340473.6	+	7	771					NM_004128.2	NP_004119.1	P13984	T2FB_HUMAN	general transcription factor IIF, polypeptide 2, 30kDa	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|prostate(1)|upper_aerodigestive_tract(1)	10		Lung NSC(96;0.00115)|Prostate(109;0.00578)|Breast(139;0.0192)|Lung SC(185;0.0367)|Hepatocellular(98;0.133)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000647)		acggagtctcactctgttgcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X16901	CCDS9395.1	13q14	2012-01-23	2002-08-29		ENSG00000188342	ENSG00000188342	2963		General transcription factors	4653	protein-coding gene	gene with protein product		189969	general transcription factor IIF, polypeptide 1 (74kD subunit)		NA	8162052	Standard	NM_004128	NM_004128	NA	Approved	TFIIF, BTF4, RAP30	uc001uzw.3	P13984	OTTHUMG00000016849	ENST00000340473.6:c.630+5582A>G	chr13.hg19:g.45847093A>G		NA	A6NNS5|Q5W0H3	hg19	CCDS9395.1	0.02	-0.052583	CTCxCTC	UNCOVERED																																																																																			NOVEL	GTF2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044767.2	9	3.004936	KEEP	7	0	0	10	254	AC	0	0	0		+	2	60	68	0	0	6.550327	2	47	56	23	ENST00000340473.6	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	45896931	45896931	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:45896931C>T			NA	NA				AL138963.1 (22696 upstream) : SNORA31 (13517 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.45896931C>T		NA		hg19		0.02	-0.131514	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			4	2.406538	KEEP	3	0	0	8	236	CC	0	0	0			3	60	87	0	0	7.643171	6	60	200	37		0.333333	0.229173
LRRC63	220416	__UNKNOWN__	__UNKNOWN__	13	46839041	46839041	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:46839041T>C	ENST00000595396.1	+	8	1310				LRRC63_ENST00000446175.1_Intron			Q05C16	LRC63_HUMAN	leucine rich repeat containing 63	NA		NA								lung(1)|ovary(1)	2						cctgtaatcctagcactttgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS61325.1	13q14.12	2014-02-12			ENSG00000173988	ENSG00000173988	220416			34296	protein-coding gene	gene with protein product		NA			NA		Standard	XM_001718341	NM_001282460	NA	Approved	RP11-139H14.4	uc001vbc.3	Q05C16	OTTHUMG00000016866	ENST00000595396.1:c.1311-1827T>C	chr13.hg19:g.46839041T>C		NA	Q5TBN0	hg19		0.02	-0.087708	TCCxAGC	UNCOVERED																																																																																			NOVEL	LRRC63-002	NOVEL	not_organism_supported|basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000463266.1	6	3.008023	KEEP	0	0	0	10	282	TT	0.992708	0.098994	0		+	3	60	102	0	0	9.143889	6	60	174	29	ENST00000595396.1	0.333333	0.099721
LRCH1	23143	__UNKNOWN__	__UNKNOWN__	13	47158050	47158050	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:47158050T>C	ENST00000389797.3	+	1	444				LRCH1_ENST00000311191.6_Intron|LRCH1_ENST00000389798.3_Intron	NM_001164211.1	NP_001157683	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	NA		NA								breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		cgtgagccactgcgcccagcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141	23143			20309	protein-coding gene	gene with protein product		610368	calponin homology (CH) domain containing 1	CHDC1	NA	10231032	Standard	NM_015116	NM_015116	NA	Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389797.3:c.307+30212T>C	chr13.hg19:g.47158050T>C		NA	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	hg19	CCDS53865.1	0.02	-0.105259	CACxGCG	UNCOVERED																																																																																			NOVEL	LRCH1-004	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354618.1	7	4.812682	KEEP	8	0	0	16	451	TT	0.993072	0.138863	0		+	3	60	96	0	0	8.378578	7	60	217	51	ENST00000389797.3	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	48463653	48463653	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:48463653C>T			NA	NA				RP11-279N8.1 (53562 upstream) : LINC00444 (15810 downstream)						NA		NA									NA						cgcttgaacccgggaggcaga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.48463653C>T		NA		hg19		0.02	-0.114036	ACCxGGG	COVERED																																																																																			NOVEL					0			20	4.813371	KEEP	11	0	0	16	475	CC	0.992708	0.19488	0			3	27	92	0	1	7.832265	8	60	273	45		0.272727	0.196312
RB1	5925	__UNKNOWN__	__UNKNOWN__	13	48965858	48965858	__UNKNOWN__	Intron	SNP	G	G	A	rs144911815	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:48965858G>A	ENST00000267163.4	+	17	1833					NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	NA		NA			androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(4)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"Insulin(DB00071)|Insulin Regular(DB00030)	gggttcaagcgattctcctgc	0.488		6	D, Mis, N, F, S		retinoblastoma, sarcoma, breast, small cell lung	retinoblastoma, sarcoma, breast, small cell lung			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			G|||	31	0.0061901	0.0227	0.0014	5008	,	,	NA	15489	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA		yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		L, E, M, O	19	Whole gene deletion(15)|Unknown(4)	bone(10)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database		M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687	5925		Endogenous ligands	9884	protein-coding gene	gene with protein product	prepro-retinoblastoma-associated protein, protein phosphatase 1, regulatory subunit 130	614041	osteosarcoma	OSRC	NA	1857421, 15057823	Standard		NM_000321	NA	Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1695+10279G>A	chr13.hg19:g.48965858G>A		NA	A8K5E3|P78499|Q5VW46|Q8IZL4	hg19	CCDS31973.1	0.02	-0.052629	AGCxATT	UNCOVERED																																																																																			NOVEL	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044884.1	3	2.707895	KEEP	4	0	0	9	269	GG	0	0	0		+	3	60	88	0	0	8.768972	2	60	66	26	ENST00000267163.4	0.6	0.036766
FNDC3A	22862	__UNKNOWN__	__UNKNOWN__	13	49646885	49646885	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:49646885A>G	ENST00000492622.2	+	3	404				FNDC3A_ENST00000541916.1_Intron	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	NA		NA			fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		ctcccaaagtattgggattac	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531	22862		Fibronectin type III domain containing	20296	protein-coding gene	gene with protein product		615794	fibronectin type III domain containing 3	FNDC3	NA		Standard	NM_014923	NM_001079673	NA	Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.100-2540A>G	chr13.hg19:g.49646885A>G		NA	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	hg19	CCDS41886.1	0.02	-0.192931	AGTxTTG	COVERED																																																																																			NOVEL	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354845.2	11	4.811074	KEEP	1	0	0	16	426	AA	0.99649	0.45615	0		+	4	60	133	1	0	11.181385	13	60	365	58	ENST00000492622.2	0.235294	0.457757
SETDB2	83852	__UNKNOWN__	__UNKNOWN__	13	50047487	50047487	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:50047487G>A	ENST00000317257.8	+	7	1166				SETDB2_ENST00000258672.5_Intron|SETDB2_ENST00000354234.4_Intron	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2	NA		NA			chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		ggagtttgaggctagcctggg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169	83852		Chromatin-modifying enzymes / K-methyltransferases	20263	protein-coding gene	gene with protein product		607865	chromosome 13 open reading frame 4	C13orf4	NA	11306461	Standard	NM_031915	NM_031915	NA	Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.342-3125G>A	chr13.hg19:g.50047487G>A		NA	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	hg19	CCDS9417.1	0.02	-0.096488	GAGxCTA	UNCOVERED																																																																																			NOVEL	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044925.1	7	3.309704	KEEP	1	0	0	11	333	GG	0.992708	0.119558	0		+	3	60	87	0	1	7.83226	5	60	175	29	ENST00000317257.8	0.375	0.120436
ARL11	115761	__UNKNOWN__	__UNKNOWN__	13	50205433	50205433	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:50205433T>C	ENST00000282026.1	+	0	1185				ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		cccagctacttgggaggctga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213	115761		ADP-ribosylation factors-like, ADP-ribosylation factors	24046	protein-coding gene	gene with protein product		609351			NA	12477932	Standard	NM_138450	NM_138450	NA	Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.*259T>C	chr13.hg19:g.50205433T>C		NA		hg19	CCDS9419.1	0.02	1.727738	ACTxGGG	COVERED																																																																																			NOVEL	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044929.2	19	2.427371	KEEP	2	4	107	46	1237	TT	1	0.993703	0		+	5	60	156	0	0	10.595924	53	60	1572	137	ENST00000282026.1	0.086207	0.993703
SPRYD7	57213	__UNKNOWN__	__UNKNOWN__	13	50508436	50508436	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:50508436A>G	ENST00000361840.3	-	1	211				SPRYD7_ENST00000492258.1_Intron|SPRYD7_ENST00000378195.2_Intron	NM_020456.2	NP_065189.1	Q5W111	SPRY7_HUMAN	SPRY domain containing 7	NA		NA								haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)	6						gctcacccctataatcccagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF055016	CCDS9422.1, CCDS45046.1	13q14.3	2011-05-25	2011-05-25	2011-05-25	ENSG00000123178	ENSG00000123178	57213			14297	protein-coding gene	gene with protein product		607866	chromosome 13 open reading frame 1	C13orf1	NA	11306461, 11771308	Standard	NM_020456	NM_020456	NA	Approved	CLLD6	uc001vdl.2	Q5W111	OTTHUMG00000016924	ENST00000361840.3:c.106+1829T>C	chr13.hg19:g.50508436A>G		NA	A8K3G1|O60648|Q8TBG8|Q96T69	hg19	CCDS9422.1	0.02	-0.140327	CCTxTAA	COVERED																																																																																			NOVEL	SPRYD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000044942.2	5	2.705916	KEEP	0	0	0	9	237	AA	0.99254	0.259018	0		-	3	60	108	0	0	9.301449	9	60	255	37	ENST00000361840.3	0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	50530795	50530795	__UNKNOWN__	IGR	SNP	C	C	A	rs56273425	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:50530795C>A			NA	NA				AL136123.1 (4045 upstream) : MIR3613 (39755 downstream)						NA		NA									NA						ttccttccttctttcctttcc	0.498		NA											C|||	36	0.0071885	0.0008	0.0086	5008	,	,	NA	13796	0.0	NA	0.0199	False	NA	,,,	NA	NA	NA	2504	0.0092	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.50530795C>A		NA		hg19		0.02	-0.061127	CTTxTTT	UNCOVERED																																																																																			NOVEL					0			8	2.404196	KEEP	0	0	0	8	225	CC	0.99257	0.043461	0			4	60	93	0	0	9.519462	2	60	55	28		0.666667	0.043787
RP11-327P2.5	0	__UNKNOWN__	__UNKNOWN__	13	52386775	52386775	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:52386775T>C	ENST00000456688.1	+	0	505										NA		NA									NA						tgcttgaggctaggagtttga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000456688.1:	chr13.hg19:g.52386775T>C		NA		hg19		0.02	-0.280664	GGCxAGG	COVERED																																																																																			NOVEL	RP11-327P2.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000045041.1	15	3.238918	KEEP	2	1	29	21	559	TT	0.999869	0.739575	0		+	3	60	96	0	0	6.893038	25	60	741	71	ENST00000456688.1	0.107143	0.739671
RP11-327P2.5	0	__UNKNOWN__	__UNKNOWN__	13	52386783	52386783	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:52386783T>C	ENST00000456688.1	+	0	505										NA		NA									NA						gctaggagtttgagaccagcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000456688.1:	chr13.hg19:g.52386783T>C		NA		hg19		0.02	-0.315689	GTTxGAG	COVERED																																																																																			NOVEL	RP11-327P2.5-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000045041.1	16	7.518462	KEEP	2	0	0	25	685	TT	0.999909	0.818391	0		+	3	60	98	0	0	6.953396	28	60	799	87	ENST00000456688.1	0.096774	0.818465
VPS36	51028	__UNKNOWN__	__UNKNOWN__	13	53006450	53006450	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:53006450C>T	ENST00000378060.4	-	6	556					NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	NA		NA			endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		cgagccactgcactccagcct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100	51028			20312	protein-coding gene	gene with protein product		610903	chromosome 13 open reading frame 9, vacuolar protein sorting 36 homolog (yeast)	C13orf9	NA	11278625, 15755741	Standard		NM_016075	NA	Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.528+1346G>A	chr13.hg19:g.53006450C>T		NA	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	hg19	CCDS9434.1	0.02	-0.122805	CTGxACT	COVERED																																																																																			NOVEL	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045059.3	10	3.309486	KEEP	0	0	0	11	326	CC	0.993072	0.194952	0		-	3	24	87	0	0	7.200965	9	60	298	32	ENST00000378060.4	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	55083087	55083087	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:55083087C>T			NA	NA				LINC00458 (376086 upstream) : AL512655.1 (296914 downstream)						NA		NA									NA						tgagccaccgcgcccggccag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.55083087C>T		NA		hg19		0.02	-0.113903	CCGxGCC	UNCOVERED																																																																																			NOVEL					0			7	3.309298	KEEP	0	0	0	11	325	CC	0.993072	0.161341	0			3	60	91	0	0	7.60311	9	60	262	32		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	57196315	57196315	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:57196315T>C			NA	NA				snoU13 (62456 upstream) : RN7SKP6 (263102 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.57196315T>C		NA		hg19		0.02	-0.192939	TCAxGCC	COVERED																																																																																			NOVEL					0			11	4.811776	KEEP	4	0	0	16	438	TT	0.99649	0.45615	0			4	60	127	0	0	10.701777	12	60	346	50		0.25	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	57229840	57229840	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:57229840T>C			NA	NA				snoU13 (95981 upstream) : RN7SKP6 (229577 downstream)						NA		NA									NA						caggtgtgagtcaccgcgccc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.57229840T>C		NA		hg19		0.02	-0.052629	GAGxCAC	UNCOVERED																																																																																			NOVEL					0			4	3.007275	KEEP	1	0	0	10	270	TT	0.99254	0.036491	0			2	60	71	0	0	6.593079	3	60	87	21		0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	61199151	61199151	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:61199151A>G			NA	NA				RNA5SP31 (11283 upstream) : LINC00378 (60181 downstream)						NA		NA									NA						acaagagcgaaactccatctc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.61199151A>G		NA		hg19		0.02	-0.043851	CGAxACT	UNCOVERED																																																																																			NOVEL					0			12	3.006888	KEEP	9	0	0	10	269	AA	0	0	0			2	40	68	0	0	6.550409	2	51	56	25		0.5	0.024074
LINC00395	100874157	__UNKNOWN__	__UNKNOWN__	13	64304825	64304825	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:64304825T>C	ENST00000451570.1	-	0	110					NR_047011.1				long intergenic non-protein coding RNA 395	NA		NA									NA						cagtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							13q21.31	2012-10-12			ENSG00000231061	ENSG00000231061	100874157		Long non-coding RNAs	42723	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_047011	NA	Approved				OTTHUMG00000017022	ENST00000451570.1:	chr13.hg19:g.64304825T>C		NA		hg19		0.02	-0.078939	TCAxGCC	UNCOVERED																																																																																			NOVEL	LINC00395-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000045195.1	6	2.706308	KEEP	1	0	0	9	240	TT	0.99254	0.076759	0		-	3	60	103	0	0	9.243859	6	60	173	27	ENST00000451570.1	0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	65670398	65670398	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:65670398G>A			NA	NA				None (None upstream) : AL354775.1 (767906 downstream)						NA		NA									NA						aacgaggtcaggagatcgaga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.65670398G>A		NA		hg19		0.02	-0.192946	TCAxGAG	COVERED																																																																																			NOVEL					0			10	2.407209	KEEP	0	0	0	8	248	GG	0.99257	0.454356	0			3	60	86	0	0	6.434294	16	60	512	39		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	66842118	66842118	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:66842118C>G			NA	NA				MIR4704 (49662 upstream) : PCDH9 (34848 downstream)						NA		NA									NA						ctcccaaagtcctgggattac	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.66842118C>G		NA		hg19		0.02	-0.157908	AGTxCTG	COVERED																																																																																			NOVEL					0			9	2.406777	KEEP	0	0	0	8	241	CC	0.99257	0.320408	0			3	60	108	0	0	8.878423	13	60	438	38		0.1875	0.322807
PIBF1	10464	__UNKNOWN__	__UNKNOWN__	13	73483908	73483908	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:73483908A>G	ENST00000326291.6	+	12	1977					NM_006346.2	NP_006337.2	Q8WXW3	PIBF1_HUMAN	progesterone immunomodulatory binding factor 1	NA		NA				centrosome (GO:0005813)				breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Prostate(6;0.00191)|Breast(118;0.0736)|Acute lymphoblastic leukemia(28;0.0865)		GBM - Glioblastoma multiforme(99;0.000664)		gggattacagacgtgagccac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF330046	CCDS31991.1	13q21.33	2014-02-20	2007-10-17	2007-10-17	ENSG00000083535	ENSG00000083535	10464			23352	protein-coding gene	gene with protein product	progesterone-induced blocking factor 1	607532	chromosome 13 open reading frame 24	C13orf24	NA	11935316	Standard	NM_006346	NM_006346	NA	Approved	CEP90	uc001vjc.3	Q8WXW3	OTTHUMG00000017071	ENST00000326291.6:c.1639+1089A>G	chr13.hg19:g.73483908A>G		NA	O95664|Q6U9V2|Q6UG50|Q86V07|Q96SF4	hg19	CCDS31991.1	0.02	-0.105252	CAGxCGT	UNCOVERED																																																																																			NOVEL	PIBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045255.1	3	2.705821	KEEP	0	0	0	9	236	AA	0.99254	0.138789	0		+	3	60	101	0	0	8.878822	7	60	208	29	ENST00000326291.6	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	73671550	73671550	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:73671550G>C			NA	NA				KLF5 (19874 upstream) : RNU6-66P (15501 downstream)						NA		NA									NA						aatcccagcagtttggggtgc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.73671550G>C		NA		hg19		0.02	-0.078957	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			7	2.406827	KEEP	0	0	0	8	237	GT	0.99254	0.076759	0			2	60	72	0	0	6.335538	5	60	172	23		0.285714	0.077336
COMMD6	170622	__UNKNOWN__	__UNKNOWN__	13	76103593	76103593	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:76103593C>G	ENST00000377619.5	-	2	390				COMMD6_ENST00000460675.1_Intron|COMMD6_ENST00000406936.3_Intron|COMMD6_ENST00000355801.4_Intron|COMMD6_ENST00000377615.3_Intron			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6	NA		NA			negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		ggaggcagagcttgcagtgag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243	170622			24015	protein-coding gene	gene with protein product		612377			NA	15799966	Standard	XM_085023	NM_203497	NA	Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377619.5:c.252+656G>C	chr13.hg19:g.76103593C>G		NA	A6NF28|B7ZLN0|Q5TBK4	hg19		0.02	-0.070182	GAGxTTG	UNCOVERED																																																																																			NOVEL	COMMD6-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000045290.2	12	3.309675	KEEP	16	0	0	11	333	CC	0	0	0		-	3	26	99	0	0	9.032697	5	43	176	37	ENST00000377619.5	0.375	0.054137
LMO7	4008	__UNKNOWN__	__UNKNOWN__	13	76311646	76311646	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:76311646C>T	ENST00000341547.4	+	4	1626				RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000377534.3_Intron|LMO7_ENST00000357063.3_Intron	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	NA		NA			protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		tcccagcactctgggaggccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153	4008			6646	protein-coding gene	gene with protein product	F-box only protein 20	604362	LIM domain only 7	FBXO20	NA	9826547, 10531035	Standard	NM_005358	NM_005358	NA	Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.366+10412C>T	chr13.hg19:g.76311646C>T		NA	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	hg19	CCDS9454.1	0.02	-0.18422	ACTxTGG	UNCOVERED																																																																																			NOVEL	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045297.1	2	3.310305	KEEP	9	0	0	11	353	CC	0	0	0		+	3	60	92	0	0	6.960978	17	60	587	61	ENST00000341547.4	0.15	0.423478
LMO7	4008	__UNKNOWN__	__UNKNOWN__	13	76325563	76325563	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:76325563A>T	ENST00000341547.4	+	5	1626				RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000377534.3_Intron|LMO7_ENST00000357063.3_Intron	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	NA		NA			protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		cccaaagtgcagggattacag	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153	4008			6646	protein-coding gene	gene with protein product	F-box only protein 20	604362	LIM domain only 7	FBXO20	NA	9826547, 10531035	Standard	NM_005358	NM_005358	NA	Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.367-9505A>T	chr13.hg19:g.76325563A>T		NA	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	hg19	CCDS9454.1	0.02	-0.192951	TGCxGGG	COVERED																																																																																			NOVEL	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045297.1	3	2.406049	KEEP	0	0	0	8	221	AA	0.99257	0.454356	0		+	3	60	88	0	0	6.634369	16	60	490	47	ENST00000341547.4	0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	77366679	77366679	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:77366679C>T			NA	NA				RN7SL571P (657319 upstream) : KCTD12 (87632 downstream)						NA		NA									NA						tcccaaagtgctgggattaca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.77366679C>T		NA		hg19		0.02	-0.236854	GTGxTGG	COVERED																																																																																			NOVEL					0			13	4.212024	KEEP	9	0	0	14	423	CC	0.992708	0.607941	0			3	60	90	0	0	6.565483	20	60	688	71		0.130435	0.612407
MYCBP2	23077	__UNKNOWN__	__UNKNOWN__	13	77824124	77824124	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:77824124C>T	ENST00000544440.2	-	15	2285				MYCBP2_ENST00000407578.2_Intron|MYCBP2_ENST00000360084.5_Intron|MYCBP2_ENST00000357337.6_Intron					MYC binding protein 2, E3 ubiquitin protein ligase	NA		NA								NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		tttgggaggccgaggcgggcg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810	23077			23386	protein-coding gene	gene with protein product		610392	MYC binding protein 2		NA	9689053, 15057823	Standard	NM_015057	NM_015057	NA	Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.2267+1161G>A	chr13.hg19:g.77824124C>T		NA		hg19		0.02	-0.140352	GGCxGAG	UNCOVERED																																																																																			NOVEL	MYCBP2-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000045326.1	3	2.407059	KEEP	6	0	0	8	247	CC	0	0	0		-	3	60	86	0	0	6.679205	13	60	452	44	ENST00000544440.2	0.1875	0.260965
RNF219-AS1	100874222	__UNKNOWN__	__UNKNOWN__	13	78926118	78926118	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:78926118G>A	ENST00000607862.1	+	0	315				RNF219-AS1_ENST00000430549.2_RNA|RNF219-AS1_ENST00000605996.1_RNA|RNF219-AS1_ENST00000606429.1_RNA|RNF219-AS1_ENST00000606803.1_RNA|RNF219-AS1_ENST00000607860.1_RNA|RNF219-AS1_ENST00000607205.1_RNA|RNF219-AS1_ENST00000606187.1_RNA|RNF219-AS1_ENST00000444769.3_RNA|RNF219-AS1_ENST00000606124.1_RNA|RNF219-AS1_ENST00000560209.2_RNA|RNF219-AS1_ENST00000606376.1_RNA|RNF219-AS1_ENST00000607220.1_RNA					RNF219 antisense RNA 1	NA		NA									NA						gggtttcaccgtgttagccag	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							13q31.1	2014-03-25	2013-02-22	2013-02-22	ENSG00000234377	ENSG00000234377	100874222		Long non-coding RNAs	42700	non-coding RNA	RNA, long non-coding		NA	POU4F1 antisense RNA 1	POU4F1-AS1	NA		Standard		NR_047001	NA	Approved		uc001vks.3		OTTHUMG00000185746	ENST00000607862.1:	chr13.hg19:g.78926118G>A		NA		hg19		0.02	-0.175429	ACCxTGT	COVERED																																																																																			NOVEL	RNF219-AS1-013	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000471155.1	5	2.706907	KEEP	1	0	0	9	255	GG	0.99254	0.384517	0		+	3	41	88	1	0	6.561497	17	60	541	37	ENST00000607862.1	0.15	0.387407
RBM26	64062	__UNKNOWN__	__UNKNOWN__	13	79965851	79965851	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:79965851A>G	ENST00000267229.7	-	2	85				RBM26_ENST00000438737.2_Intron|RBM26_ENST00000438724.1_Intron	NM_022118.3	NP_071401.3	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	NA		NA			mRNA processing (GO:0006397)|negative regulation of phosphatase activity (GO:0010923)		metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)		gagccaccgcacccagccgaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF116667	CCDS9462.1, CCDS66566.1, CCDS73591.1	13q31.1	2014-06-13	2006-06-22	2006-06-22	ENSG00000139746	ENSG00000139746	64062		Zinc fingers, CCCH-type domain containing, RNA binding motif (RRM) containing	20327	protein-coding gene	gene with protein product	acidic rich RS domain containing 2, protein phosphatase 1, regulatory 132	NA	chromosome 13 open reading frame 10	C13orf10	NA	11149944, 15741184	Standard	NM_022118	XM_005266497	NA	Approved	PRO1777, SE70-2, FLJ20957, ZC3H17, ARRS2, PPP1R132	uc001vky.2	Q5T8P6	OTTHUMG00000017133	ENST00000267229.7:c.72-12809T>C	chr13.hg19:g.79965851A>G		NA	B4DZE0|Q2NKM2|Q2NKQ2|Q5CZH8|Q5T8P5|Q5T8P8|Q5U5P5|Q5W0G7|Q8N3H5|Q96K92|Q96SZ3|Q9H2F8|Q9H7F9|Q9P1G7	hg19	CCDS9462.1	0.02	-0.315683	CGCxCCC	COVERED																																																																																			NOVEL	RBM26-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045371.4	9	2.404674	KEEP	0	0	0	8	208	AA	0.99257	0.812384	0		-	3	60	112	0	0	8.352316	28	60	780	66	ENST00000267229.7	0.096774	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	79999425	79999425	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:79999425A>G			NA	NA				RBM26-AS1 (962 upstream) : NDFIP2-AS1 (52073 downstream)						NA		NA									NA						ttttagtagaaatggggtttc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.79999425A>G		NA		hg19		0.02	-0.149067	AGAxATG	COVERED																																																																																			NOVEL					0			3	2.704854	KEEP	1	0	0	9	229	AA	0.99257	0.289832	0			3	50	92	0	0	7.58248	10	60	285	31		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	80239911	80239911	__UNKNOWN__	IGR	SNP	C	C	T	rs11293487|rs67012853|rs200235703|rs9601259	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:80239911C>T			NA	NA				LINC01068 (94928 upstream) : LINC01038 (138641 downstream)						NA		NA									NA						ttctttctttctttttttttt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.80239911C>T		NA		hg19		0.02	-0.131298	TTTxTTT	COVERED																																																																																			NOVEL					0			7	3.00866	KEEP	1	0	0	10	297	CC	0.992708	0.227502	0			4	60	93	1	0	7.714617	9	60	287	32		0.307692	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	83112232	83112232	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:83112232T>C			NA	NA				PTMAP5 (847025 upstream) : RNU6-67P (759973 downstream)						NA		NA									NA						ccacccgccttggcctcccaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.83112232T>C		NA		hg19		0.02	-0.122738	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			4	3.007503	KEEP	11	0	0	10	277	TT	0	0	0			3	60	92	0	0	7.702048	9	60	237	48		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	83158434	83158434	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:83158434T>C			NA	NA				PTMAP5 (893227 upstream) : RNU6-67P (713771 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.83158434T>C		NA		hg19		0.02	-0.201724	TCAxGCC	COVERED																																																																																			NOVEL					0			10	2.706585	KEEP	0	0	0	9	244	TT	0.99254	0.486885	0			3	60	100	0	0	7.833394	16	60	471	43		0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	84593509	84593509	__UNKNOWN__	IGR	SNP	G	G	A	rs573535034		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:84593509G>A			NA	NA				SLITRK1 (136981 upstream) : LINC00333 (542989 downstream)						NA		NA									NA						gtgagccaccgtgcccagcct	0.473		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15464	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.84593509G>A		NA		hg19		0.02	-0.191993	ACCxTGC	COVERED																																																																																			NOVEL					0			4	2.707949	KEEP	1	0	0	9	271	GG	0.99257	0.454356	0			3	60	93	0	0	7.142474	16	60	500	50		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	85625332	85625332	__UNKNOWN__	IGR	SNP	T	T	G	rs4040788	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:85625332T>G			NA	NA				LINC00333 (487961 upstream) : LINC00375 (13889 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.408		NA											T|||	842	0.168131	0.1944	0.1326	5008	,	,	NA	16871	0.1419	NA	0.1223	False	NA	,,,	NA	NA	NA	2504	0.2321	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.85625332T>G		NA		hg19		0.02	-0.061388	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			9	2.705203	KEEP	5	0	0	9	230	TT	0	0	0			3	60	96	0	0	9.569866	2	60	56	21		0.6	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	85638022	85638022	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:85638022C>T			NA	NA				LINC00333 (500651 upstream) : LINC00375 (1199 downstream)						NA		NA									NA						acctccgcctcccggattcaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.85638022C>T		NA		hg19		0.02	-0.087715	CCTxCCG	UNCOVERED																																																																																			NOVEL					0			4	3.007969	KEEP	0	0	0	10	294	CC	0.992708	0.098994	0			3	60	83	0	0	7.078096	7	60	239	27		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	87920216	87920216	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:87920216G>A			NA	NA				LINC00430 (330945 upstream) : RP11-342C20.2 (159238 downstream)						NA		NA									NA						atgaaccaccgcacctggccT	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.87920216G>A		NA		hg19		0.02	-0.14034	ACCxCAC	UNCOVERED																																																																																			NOVEL					0			4	2.40682	KEEP	5	0	0	8	236	GG	0	0	0			3	60	80	0	0	6.500975	9	60	297	41		0.25	0.260965
LINC01047	0	__UNKNOWN__	__UNKNOWN__	13	89868124	89868124	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:89868124G>A	ENST00000415193.1	-	0	297									long intergenic non-protein coding RNA 1047	NA		NA									NA						aggccaaggcgggcaaattgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BG183515		13q31.2	2013-08-15			ENSG00000232225	ENSG00000232225	NA		Long non-coding RNAs	49041	non-coding RNA	RNA, long non-coding		NA			NA		Standard			NA	Approved				OTTHUMG00000017173	ENST00000415193.1:	chr13.hg19:g.89868124G>A		NA		hg19		0.02	-0.184213	GGCxGGC	COVERED																																																																																			NOVEL	LINC01047-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000045423.2	7	2.40362	KEEP	0	0	0	8	207	GG	0.99257	0.420331	0		-	4	60	121	0	0	9.568785	17	60	571	40	ENST00000415193.1	0.190476	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	90898145	90898145	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:90898145T>C			NA	NA				MIR622 (14614 upstream) : LINC01049 (247395 downstream)						NA		NA									NA						gtggctcacatctgtaatctc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.90898145T>C		NA		hg19		0.02	-0.236785	ACAxCTG	COVERED																																																																																			NOVEL					0			10	3.007579	KEEP	0	0	0	10	277	TT	0.992708	0.607941	0			3	60	88	0	0	6.36661	20	60	589	56		0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	91901468	91901468	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:91901468T>C			NA	NA				LINC00379 (117849 upstream) : MIR17HG (101390 downstream)						NA		NA									NA						cctgctttggtctcccaaagt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.91901468T>C		NA		hg19		0.02	-0.061372	TGGxCTC	UNCOVERED																																																																																			NOVEL					0			4	2.406332	KEEP	0	0	0	8	225	TT	0.99257	0.043461	0			2	60	73	0	0	6.596623	4	60	101	21		0.333333	0.043787
GPC5	2262	__UNKNOWN__	__UNKNOWN__	13	92214953	92214953	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:92214953A>G	ENST00000377067.3	+	2	697					NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	NA		NA			carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				gattacaggcatgagccacca	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399	2262		Proteoglycans / Cell Surface : Glypicans	4453	protein-coding gene	gene with protein product	glypican proteoglycan 5	602446			NA	9070915, 20304703, 19556317, 15057823	Standard	NM_004466	NM_004466	NA	Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.325+113777A>G	chr13.hg19:g.92214953A>G		NA	B2R726|O60436|Q9BX27	hg19	CCDS9468.1	0.02	-0.140329	GGCxTGA	COVERED																																																																																			NOVEL	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045454.1	6	3.00598	KEEP	0	0	0	10	263	AA	0.992708	0.289872	0		+	3	60	100	0	0	8.272984	11	60	322	39	ENST00000377067.3	0.214286	0.292001
GPC5	2262	__UNKNOWN__	__UNKNOWN__	13	92647504	92647504	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:92647504A>C	ENST00000377067.3	+	6	1773					NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	NA		NA			carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ggattacaggagtgagccacc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399	2262		Proteoglycans / Cell Surface : Glypicans	4453	protein-coding gene	gene with protein product	glypican proteoglycan 5	602446			NA	9070915, 20304703, 19556317, 15057823	Standard	NM_004466	NM_004466	NA	Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1401+87193A>C	chr13.hg19:g.92647504A>C		NA	B2R726|O60436|Q9BX27	hg19	CCDS9468.1	0.02	-0.166656	AGGxGTG	COVERED																																																																																			NOVEL	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045454.1	6	2.406502	KEEP	0	0	0	8	228	AT	0.993072	0.384723	0		+	3	60	99	0	0	7.891654	14	60	434	47	ENST00000377067.3	0.176471	0.387407
GPC5	2262	__UNKNOWN__	__UNKNOWN__	13	93365584	93365584	__UNKNOWN__	Intron	SNP	G	G	A	rs554894228		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:93365584G>A	ENST00000377067.3	+	8	1933				GPC5-AS1_ENST00000451897.1_RNA|GPC5-AS1_ENST00000419288.1_RNA	NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	NA		NA			carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ggtggctcacgcttgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399	2262		Proteoglycans / Cell Surface : Glypicans	4453	protein-coding gene	gene with protein product	glypican proteoglycan 5	602446			NA	9070915, 20304703, 19556317, 15057823	Standard	NM_004466	NM_004466	NA	Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.1562-152951G>A	chr13.hg19:g.93365584G>A		NA	B2R726|O60436|Q9BX27	hg19	CCDS9468.1	0.02	-0.192561	CACxCTT	COVERED																																																																																			NOVEL	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045454.1	8	3.240437	KEEP	4	1	29	21	599	GG	0.999863	0.457694	0		+	3	60	90	0	0	6.696101	18	60	578	78	ENST00000377067.3	0.142857	0.457757
GPC6	10082	__UNKNOWN__	__UNKNOWN__	13	94735652	94735652	__UNKNOWN__	Intron	SNP	A	A	C	rs386773482|rs9589900	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:94735652A>C	ENST00000377047.4	+	4	1492					NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	NA		NA			carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				gattacaggcatgagccactg	0.448		NA											A|||	410	0.081869	0.0106	0.134	5008	,	,	NA	15819	0.001	NA	0.2406	False	NA	,,,	NA	NA	NA	2504	0.0613	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098	10082		Proteoglycans / Cell Surface : Glypicans	4454	protein-coding gene	gene with protein product	glypican proteoglycan 6	604404			NA	10329016	Standard	NM_005708	NM_005708	NA	Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.877+55504A>C	chr13.hg19:g.94735652A>C		NA	A8K279|Q96SG5|Q96SG8|Q9H1P4	hg19	CCDS9469.1	0.02	-0.114019	GGCxTGA	COVERED																																																																																			NOVEL	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045460.4	7	2.405712	KEEP	2	0	0	8	215	AG	0.99254	0.194847	0		+	3	60	100	0	0	8.501334	9	60	262	38	ENST00000377047.4	0.25	0.196312
ABCC4	10257	__UNKNOWN__	__UNKNOWN__	13	95748334	95748334	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:95748334T>C	ENST00000376887.4	-	21	2650				ABCC4_ENST00000412704.1_Intron|ABCC4_ENST00000431522.1_3'UTR|ABCC4_ENST00000536256.1_3'UTR	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	NA		NA			blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	cagtggctcatgcctataatc	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257	10257		ATP binding cassette transporters / subfamily C	55	protein-coding gene	gene with protein product	canalicular multispecific organic anion transporter (ABC superfamily), bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4), multidrug resistance-associated protein 4, multispecific organic anion transporter B	605250			NA	8894702, 9661885	Standard	NM_005845	NM_005845	NA	Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.2536-12790A>G	chr13.hg19:g.95748334T>C		NA	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	hg19	CCDS9474.1	0.02	-0.271788	TCAxGCC	COVERED																																																																																			NOVEL	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045478.2	4	3.004604	KEEP	0	0	0	10	245	TT	0.992708	0.712085	0		-	3	60	97	0	0	6.94517	26	60	723	50	ENST00000376887.4	0.103448	0.717315
ABCC4	10257	__UNKNOWN__	__UNKNOWN__	13	95943044	95943044	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:95943044A>C	ENST00000376887.4	-	1	189				ABCC4_ENST00000538287.1_Intron|ABCC4_ENST00000412704.1_Intron|ABCC4_ENST00000431522.1_Intron|ABCC4_ENST00000536256.1_Intron	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	NA		NA			blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	gcctgggcaaaaagagcaaaa	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257	10257		ATP binding cassette transporters / subfamily C	55	protein-coding gene	gene with protein product	canalicular multispecific organic anion transporter (ABC superfamily), bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4), multidrug resistance-associated protein 4, multispecific organic anion transporter B	605250			NA	8894702, 9661885	Standard	NM_005845	NM_005845	NA	Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.74+10450T>G	chr13.hg19:g.95943044A>C		NA	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	hg19	CCDS9474.1	0.02	-0.192913	CAAxAAG	COVERED																																																																																			NOVEL	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045478.2	11	6.008932	KEEP	0	0	0	20	522	AA	0.999863	0.457694	0		-	4	60	132	0	0	10.579949	18	60	506	55	ENST00000376887.4	0.181818	0.457757
UGGT2	55757	__UNKNOWN__	__UNKNOWN__	13	96598884	96598884	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:96598884T>C	ENST00000376747.3	-	15	1748					NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	NA		NA			cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						cttggcctcctaaaatgctgg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595	55757			15664	protein-coding gene	gene with protein product	UDP-glucose:glycoprotein glucosyltransferase 2	605898	UDP-glucose ceramide glucosyltransferase-like 2	UGCGL2	NA	10694380	Standard	NM_020121	NM_020121	NA	Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.1677+406A>G	chr13.hg19:g.96598884T>C		NA	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	hg19	CCDS9480.1	0.02	-0.219276	TCCxAAA	COVERED																																																																																			NOVEL	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045507.1	8	2.406193	KEEP	0	0	0	8	222	TT	0.99257	0.54878	0		-	3	60	97	1	0	7.461022	17	60	512	46	ENST00000376747.3	0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	98751167	98751167	__UNKNOWN__	IGR	SNP	T	T	C	rs645702	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:98751167T>C			NA	NA				IPO5 (74616 upstream) : FARP1 (43648 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.468		NA											T|||	1341	0.267772	0.0121	0.3242	5008	,	,	NA	15837	0.5923	NA	0.2147	False	NA	,,,	NA	NA	NA	2504	0.2935	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.98751167T>C		NA		hg19		0.02	-0.254364	ATCxCAG	UNCOVERED																																																																																			NOVEL					0			9	2.705538	KEEP	3	0	0	9	243	TT	0	0	0			3	60	103	0	0	7.694545	23	60	705	59		0.115385	0.668523
FARP1	10160	__UNKNOWN__	__UNKNOWN__	13	98966784	98966784	__UNKNOWN__	Intron	SNP	G	G	A	rs138626833	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:98966784G>A	ENST00000319562.6	+	3	436				FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376586.2_Intron	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	NA		NA			dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			tgcccgcctcggcctcccaaa	0.468		NA											G|||	945	0.188698	0.0371	0.2133	5008	,	,	NA	15799	0.2937	NA	0.159	False	NA	,,,	NA	NA	NA	2504	0.2986	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767	10160		Rho guanine nucleotide exchange factors, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Pleckstrin homology (PH) domain containing	3591	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 75	602654			NA	9425278	Standard	NM_005766	NM_005766	NA	Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.172-29232G>A	chr13.hg19:g.98966784G>A		NA	Q5JVI9|Q6IQ29	hg19	CCDS9487.1	0.02	-0.131554	CTCxGCC	UNCOVERED																																																																																			NOVEL	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045541.3	10	3.610052	KEEP	14	0	0	12	356	GG	0	0	0		+	6	60	176	0	0	16.564973	7	60	224	50	ENST00000319562.6	0.461538	0.229173
SLC15A1	6564	__UNKNOWN__	__UNKNOWN__	13	99373199	99373199	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:99373199A>G	ENST00000376503.5	-	7	612					NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	NA		NA			digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	ccagctactcaggaggctgag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386	6564		Solute carriers	10920	protein-coding gene	gene with protein product	peptide transporter HPEPT1, bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1), solute carrier family 15 oligopeptide transporter member 1	600544			NA	7896779	Standard	NM_005073	NM_005073	NA	Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.556+549T>C	chr13.hg19:g.99373199A>G		NA	Q5VW82	hg19	CCDS9489.1	0.02	-0.342047	CTCxGGA	COVERED																																																																																			NOVEL	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045560.3	2	2.835573	KEEP	2	1	24	18	472	AA	0.999863	0.865627	0		-	4	60	120	0	0	8.459203	32	60	947	68	ENST00000376503.5	0.111111	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	99748755	99748755	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:99748755A>G			NA	NA				DOCK9-AS2 (7876 upstream) : UBAC2-AS1 (99875 downstream)						NA		NA									NA						Cgccgggtgcagtggctcacg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.99748755A>G		NA		hg19		0.02	-0.350789	TGCxGTG	COVERED																																																																																			NOVEL					0			14	4.21011	KEEP	0	0	0	14	379	AA	0.995343	0.87362	0			3	59	96	0	0	6.550296	33	60	955	71		0.083333	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	99780003	99780003	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:99780003A>G			NA	NA				DOCK9-AS2 (39124 upstream) : UBAC2-AS1 (68627 downstream)						NA		NA									NA						gaccagcctgaccaacatggt	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.99780003A>G		NA		hg19		0.02	-0.114007	CTGxCCA	UNCOVERED																																																																																			NOVEL					0			4	2.706236	KEEP	3	0	0	9	238	AA	0.99254	0.161255	0			3	29	94	0	0	7.782268	10	60	283	35		0.230769	0.162467
CLYBL	171425	__UNKNOWN__	__UNKNOWN__	13	100351696	100351696	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:100351696T>C	ENST00000376360.1	+	2	89				CLYBL_ENST00000444838.2_Intron|CLYBL_ENST00000339105.4_Intron|CLYBL_ENST00000376355.3_Intron|CLYBL_ENST00000376354.1_Intron			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	NA		NA				mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					gcctgtaatctcagcactttg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246	171425			18355	protein-coding gene	gene with protein product		609686			NA		Standard		XM_005254030	NA	Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.63-73382T>C	chr13.hg19:g.100351696T>C		NA	Q5W0F7|Q8TDH8	hg19	CCDS32002.1	0.02	-0.166652	ATCxCAG	COVERED																																																																																			NOVEL	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045611.1	5	2.706679	KEEP	1	0	0	9	245	TT	0.99254	0.351306	0		+	3	60	104	0	0	8.30998	15	60	451	41	ENST00000376360.1	0.166667	0.353947
CLYBL	171425	__UNKNOWN__	__UNKNOWN__	13	100406070	100406070	__UNKNOWN__	Intron	SNP	C	C	T	rs192976492		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:100406070C>T	ENST00000376360.1	+	2	89				CLYBL_ENST00000444838.2_Intron|CLYBL_ENST00000339105.4_Intron|CLYBL_ENST00000376355.3_Intron|CLYBL_ENST00000376354.1_Intron			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	NA		NA				mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					Tggccgggcgcggtggctcat	0.507		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	15559	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246	171425			18355	protein-coding gene	gene with protein product		609686			NA		Standard		XM_005254030	NA	Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.63-19008C>T	chr13.hg19:g.100406070C>T		NA	Q5W0F7|Q8TDH8	hg19	CCDS32002.1	0.02	-0.192987	GCGxGGT	COVERED																																																																																			NOVEL	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045611.1	11	3.911248	KEEP	4	0	0	13	386	CC	0.993634	0.454842	0		+	3	60	89	0	0	6.661286	17	60	567	47	ENST00000376360.1	0.15	0.457757
PCCA	5095	__UNKNOWN__	__UNKNOWN__	13	100787444	100787444	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:100787444G>A	ENST00000376285.1	+	5	338				PCCA_ENST00000376279.3_Intron|PCCA_ENST00000376286.4_Intron	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	NA		NA			biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	ccaggagtttgagaccagcct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	5095	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	propionyl Coenzyme A carboxylase, alpha polypeptide		NA	1427880	Standard		NM_000282	NA	Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.301-19789G>A	chr13.hg19:g.100787444G>A		NA	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	hg19	CCDS9496.2	0.02	-0.122807	TTTxAGA	COVERED																																																																																			NOVEL	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045627.2	4	4.814389	KEEP	0	0	0	16	491	GG	0.997832	0.195886	0		+	3	60	81	0	0	6.37297	11	60	387	43	ENST00000376285.1	0.214286	0.196312
PCCA	5095	__UNKNOWN__	__UNKNOWN__	13	100804923	100804923	__UNKNOWN__	Intron	SNP	G	G	A	rs2893017	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:100804923G>A	ENST00000376285.1	+	5	338				PCCA_ENST00000376279.3_Intron|PCCA_ENST00000376286.4_Intron|PCCA_ENST00000485946.1_Intron	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	NA		NA			biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	gatggtctcggtctcctgacc	0.547		NA											A|||	4284	0.855431	0.8411	0.8213	5008	,	,	NA	14331	0.9802	NA	0.7485	False	NA	,,,	NA	NA	NA	2504	0.8804	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	5095	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	propionyl Coenzyme A carboxylase, alpha polypeptide		NA	1427880	Standard		NM_000282	NA	Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.301-2310G>A	chr13.hg19:g.100804923G>A		NA	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	hg19	CCDS9496.2	0.02	-0.070161	TCGxTCT	UNCOVERED																																																																																			NOVEL	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045627.2	4	2.407346	KEEP	1	0	0	8	252	GG	0.99257	0.053735	0		+	5	47	142	0	0	14.763521	2	60	71	27	ENST00000376285.1	0.714286	0.054137
PCCA	5095	__UNKNOWN__	__UNKNOWN__	13	101069147	101069147	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:101069147C>G	ENST00000376285.1	+	20	1784				PCCA_ENST00000376279.3_Intron|PCCA_ENST00000376286.4_Intron	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	NA		NA			biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	gtccaggctgcagtgcaatgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	5095	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	propionyl Coenzyme A carboxylase, alpha polypeptide		NA	1427880	Standard		NM_000282	NA	Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1747-8740C>G	chr13.hg19:g.101069147C>G		NA	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	hg19	CCDS9496.2	0.02	-0.210543	CTGxAGT	COVERED																																																																																			NOVEL	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045627.2	5	3.911405	KEEP	0	0	0	13	391	CC	0.994391	0.519232	0		+	3	60	97	0	0	7.326953	19	60	655	50	ENST00000376285.1	0.136364	0.522161
NALCN	259232	__UNKNOWN__	__UNKNOWN__	13	101957034	101957034	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:101957034C>T	ENST00000251127.6	-	8	881				NALCN_ENST00000470333.1_Intron|NALCN_ENST00000376196.3_Intron	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	NA		NA			calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					agcggtccacccaccttggcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452	259232		Ion channels / Sodium leak channels, non-selective	19082	protein-coding gene	gene with protein product		611549	voltage gated channel like 1	VGCNL1	NA	17448995	Standard	NM_052867	XM_006719943	NA	Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.800-12317G>A	chr13.hg19:g.101957034C>T		NA	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	hg19	CCDS9498.1	0.02	-0.184189	CACxCAC	COVERED																																																																																			NOVEL	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045663.2	8	2.406725	KEEP	0	0	0	8	236	CC	0.99257	0.420331	0		-	3	60	90	0	0	6.692778	18	60	589	39	ENST00000251127.6	0.142857	0.423478
FGF14	2259	__UNKNOWN__	__UNKNOWN__	13	102392408	102392408	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:102392408C>G	ENST00000376143.4	-	4	408				FGF14_ENST00000376131.4_Intron	NM_004115.3	NP_004106.1	Q92915	FGF14_HUMAN	fibroblast growth factor 14	NA		NA			adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cell-cell signaling (GO:0007267)|JNK cascade (GO:0007254)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)	29	all_neural(89;0.0239)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					acccctgtcacgtatccccta	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9500.1, CCDS9501.1	13q34	2008-02-05			ENSG00000102466	ENSG00000102466	2259			3671	protein-coding gene	gene with protein product		601515			NA	8790420, 17236779	Standard		NM_175929	NA	Approved	FHF4, SCA27	uc001vpf.2	Q92915	OTTHUMG00000017303	ENST00000376143.4:c.409-13248G>C	chr13.hg19:g.102392408C>G		NA	Q86YN7|Q96QX6	hg19	CCDS9501.1	0.02	1.997035	TCAxGTA	COVERED																																																																																			NOVEL	FGF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045679.2	1	3.309208	KEEP	0	0	0	11	325	CC	0.993072	0.972741	0		-	11	60	375	0	0	30.797651	44	60	1419	101	ENST00000376143.4	0.2	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	103803907	103803907	__UNKNOWN__	IGR	SNP	C	C	T	rs138301698	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:103803907C>T			NA	NA				SLC10A2 (84711 upstream) : RP11-123H22.1 (273642 downstream)						NA		NA									NA						cggtggctcacgcctgtaatc	0.502		NA											C|||	7	0.00139776	0.0045	0.0	5008	,	,	NA	16451	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.103803907C>T		NA		hg19		0.02	-0.087709	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.405536	KEEP	0	0	0	8	226	CC	0.99257	0.09898	0			3	60	84	0	0	7.342866	6	60	199	23		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	106328670	106328670	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:106328670C>T			NA	NA				DAOA-AS1 (170640 upstream) : LINC00343 (30323 downstream)						NA		NA									NA						gtagctgggactacaggcacc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.106328670C>T		NA		hg19		0.02	-0.070136	GGAxTAC	UNCOVERED																																																																																			NOVEL					0			5	3.008333	KEEP	4	0	0	10	293	CC	0.99257	0.053735	0			4	35	107	0	0	10.195675	4	60	134	25		0.5	0.054137
EFNB2	1948	__UNKNOWN__	__UNKNOWN__	13	107145439	107145439	__UNKNOWN__	Silent	SNP	G	G	A	rs566875957		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:107145439G>A	ENST00000245323.4	-	5	1100	c.951C>T	c.(949-951)atC>atT	p.I317I		NM_004093.3	NP_004084.1	P52799	EFNB2_HUMAN	ephrin-B2	317		NA			anatomical structure morphogenesis (GO:0009653)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)|lymph vessel development (GO:0001945)|negative regulation of keratinocyte proliferation (GO:0010839)|organ morphogenesis (GO:0009887)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|regulation of chemotaxis (GO:0050920)|viral process (GO:0016032)	focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	13	Lung NSC(43;0.015)|all_neural(89;0.0741)|Lung SC(71;0.14)|Medulloblastoma(90;0.169)					TCTCCTGGACGATGTACACCG	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													73	66	68			NA	NA	13		NA											NA				107145439		2203	4300	6503	SO:0001819	synonymous_variant			L38734	CCDS9507.1	13q33	2011-03-09			ENSG00000125266	ENSG00000125266	1948		Ephrins	3227	protein-coding gene	gene with protein product	HTK ligand, ligand of eph-related kinase 5, eph-related receptor tyrosine kinase ligand 5	600527		EPLG5	NA	7833926	Standard	NM_004093	NM_004093	NA	Approved	LERK5, Htk-L, HTKL, MGC126226, MGC126227, MGC126228	uc001vqi.3	P52799	OTTHUMG00000017324	ENST00000245323.4:c.951C>T	chr13.hg19:g.107145439G>A		NA	Q5JV56	hg19	CCDS9507.1	0.02	1.125108	GACxATG	COVERED																																																																																			NOVEL	EFNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045733.4	2	8.719812	KEEP	0	0	0	29	825	GG	0.999997	0.9937	0		-	5	60	139	0	0	8.641771	60	60	1914	122	ENST00000245323.4	0.076923	0.993703
TNFSF13B	10673	__UNKNOWN__	__UNKNOWN__	13	108959240	108959240	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:108959240C>T	ENST00000375887.4	+	6	990	c.812C>T	c.(811-813)tCa>tTa	p.S271L	TNFSF13B_ENST00000430559.1_Missense_Mutation_p.S252L	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	271		NA			B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	GCACAAATATCACTGGATGGA	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													142	122	129			NA	NA	13		NA											NA				108959240		2203	4300	6503	SO:0001583	missense			AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524	10673		Tumor necrosis factor (ligand) superfamily, CD molecules	11929	protein-coding gene	gene with protein product		603969		TNFSF20	NA	10331498, 10359578	Standard		NM_006573	NA	Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.812C>T	chr13.hg19:g.108959240C>T	ENSP00000365048:p.Ser271Leu	NA	E0ADT7|Q6FHD6|Q7Z5J2	hg19	CCDS9509.1	0.02	0.781613	TATxACT	COVERED	.	.	.	.	.	.	.	.	.	.	C	12.80	2.047691	0.36085	.	.	ENSG00000102524	ENST00000430559;ENST00000375887	T;T	0.29397	1.57;1.57	5.49	4.65	0.58169	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.000000	0.85682	D	0.000000	T	0.33235	0.0856	M	0.74258	2.255	0.80722	D	1	P;B	0.35542	0.508;0.085	B;B	0.31547	0.132;0.072	T	0.14924	-1.0455	9	.	.	.	-13.7874	13.9094	0.63857	0.0:0.9264:0.0:0.0736	.	252;271	Q9Y275-2;Q9Y275	.;TN13B_HUMAN	L	252;271	ENSP00000389540:S252L;ENSP00000365048:S271L	.	S	+	2	0	TNFSF13B	107757241	0.966000	0.33281	0.028000	0.17463	0.763000	0.43281	2.265000	0.43311	1.445000	0.47624	-0.216000	0.12614	TCA	NOVEL	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045739.3	27	12.936883	KEEP	0	0	0	43	1277	CC	1	0.999895	0		+	6	60	168	0	0	10.046293	86	60	2822	187	ENST00000375887.4	0.065217	0.999895
MYO16	23026	__UNKNOWN__	__UNKNOWN__	13	109350322	109350322	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:109350322T>C	ENST00000357550.2	+	2	267				MYO16_ENST00000356711.2_Intron|MYO16_ENST00000251041.5_Intron	NM_001198950.1	NP_001185879.1			myosin XVI	NA		NA								NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			ccacccgccttggcctcccaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515	23026		Myosins / Myosin superfamily : Class XVI, Ankyrin repeat domain containing	29822	protein-coding gene	gene with protein product	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3, protein phosphatase 1, regulatory subunit 107	615479			NA	11588169, 17029291, 21946561	Standard	NM_015011	NM_001198950	NA	Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.227-14687T>C	chr13.hg19:g.109350322T>C		NA		hg19	CCDS32008.1	0.02	-0.105255	CCTxGGC	UNCOVERED																																																																																			NOVEL	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045746.1	6	3.308569	KEEP	5	0	0	11	306	TT	0.99257	0.138793	0		+	3	60	103	0	0	8.801208	9	60	268	41	ENST00000357550.2	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	110513809	110513809	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:110513809A>G			NA	NA				IRS2 (74894 upstream) : RN7SKP10 (53633 downstream)						NA		NA									NA						cactttgggaagctgaggagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.110513809A>G		NA		hg19		0.02	-0.140336	GGAxGCT	COVERED																																																																																			NOVEL					0			7	2.406462	KEEP	0	0	0	8	227	AA	0.99257	0.259026	0			3	60	90	0	0	7.272958	11	60	338	33		0.214286	0.260965
COL4A1	1282	__UNKNOWN__	__UNKNOWN__	13	110875069	110875069	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:110875069G>A	ENST00000375820.4	-	3	266				COL4A1_ENST00000543140.1_Intron	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	NA		NA			axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			gcagtgagccgagatcgtgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498	1282		Collagens	2202	protein-coding gene	gene with protein product		120130			NA	3691802	Standard		NM_001845	NA	Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.145-8707C>T	chr13.hg19:g.110875069G>A		NA	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	hg19	CCDS9511.1	0.02	-0.122441	GCCxAGA	COVERED																																																																																			NOVEL	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045759.3	6	3.30941	KEEP	3	0	0	11	326	GG	0.992708	0.19488	0		-	5	60	118	0	0	10.402538	8	60	258	43	ENST00000375820.4	0.384615	0.196312
ARHGEF7	8874	__UNKNOWN__	__UNKNOWN__	13	111790700	111790700	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:111790700T>C	ENST00000317133.5	+	2	1073				ARHGEF7_ENST00000375741.2_Intron|ARHGEF7_ENST00000370623.3_Intron|ARHGEF7-IT1_ENST00000423329.1_RNA|ARHGEF7_ENST00000375739.2_Intron			Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	NA		NA			apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			tggtggctcatgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606	8874		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	15607	protein-coding gene	gene with protein product	SH3 domain-containing proline-rich protein, PAK-interacting exchange factor beta, rho, guanine nucleotide exchange factor 7	605477			NA	9207241, 9726964	Standard	NM_001113511	NM_003899	NA	Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000317133.5:c.166-15552T>C	chr13.hg19:g.111790700T>C		NA	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	hg19	CCDS32009.1	0.02	-0.219267	TCAxGCC	COVERED																																																																																			NOVEL	ARHGEF7-008	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000355033.1	13	5.71402	KEEP	8	0	0	19	519	TT	0.995343	0.550313	0		+	3	60	96	0	0	7.361065	17	60	505	70	ENST00000317133.5	0.15	0.552887
ARHGEF7	8874	__UNKNOWN__	__UNKNOWN__	13	111816102	111816102	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:111816102T>A	ENST00000218789.5	+	1	278				ARHGEF7_ENST00000375741.2_Intron|ARHGEF7_ENST00000375736.4_Intron|ARHGEF7_ENST00000370623.3_Intron|ARHGEF7_ENST00000317133.5_Intron|ARHGEF7_ENST00000375739.2_Intron|ARHGEF7_ENST00000544132.1_Intron			Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	NA		NA			apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ggctgatctctaactcctggg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606	8874		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	15607	protein-coding gene	gene with protein product	SH3 domain-containing proline-rich protein, PAK-interacting exchange factor beta, rho, guanine nucleotide exchange factor 7	605477			NA	9207241, 9726964	Standard	NM_001113511	NM_003899	NA	Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000218789.5:c.-220+9764T>A	chr13.hg19:g.111816102T>A		NA	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	hg19		0.02	-0.149072	CTCxAAC	COVERED																																																																																			NOVEL	ARHGEF7-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000045805.3	10	4.190487	KEEP	0	0	0	14	365	TT	0.99649	0.290976	0		+	3	60	83	0	0	6.574052	11	60	331	46	ENST00000218789.5	0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	113285657	113285657	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:113285657A>G			NA	NA				TUBGCP3 (43176 upstream) : C13orf35 (15700 downstream)						NA		NA									NA						gggcgcggtgactcatacctg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.113285657A>G		NA		hg19		0.02	-0.175417	GTGxCTC	COVERED																																																																																			NOVEL					0			7	3.9102	KEEP	0	0	0	13	364	AA	0.994391	0.385234	0			3	60	102	1	0	8.110126	15	60	453	52		0.166667	0.387407
PROZ	8858	__UNKNOWN__	__UNKNOWN__	13	113818501	113818501	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:113818501C>T	ENST00000342783.4	+	6	446				PROZ_ENST00000375547.2_Intron	NM_001256134.1	NP_001243063.1	P22891	PROZ_HUMAN	protein Z, vitamin K-dependent plasma glycoprotein	NA		NA			blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(2)|skin(2)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.216)	all cancers(43;0.104)		Menadione(DB00170)	accatgttggccaggctggtc	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M55670	CCDS9531.1, CCDS58300.1	13q34	2008-07-18			ENSG00000126231	ENSG00000126231	8858			9460	protein-coding gene	gene with protein product		176895			NA	2244898, 2403355	Standard	NM_003891	NM_001256134	NA	Approved	PZ	uc010agr.2	P22891	OTTHUMG00000017376	ENST00000342783.4:c.440-326C>T	chr13.hg19:g.113818501C>T		NA	A6NMB4|Q15213|Q5JVF5|Q5JVF6	hg19	CCDS58300.1	0.02	-0.377195	TGGxCAG	COVERED																																																																																			NOVEL	PROZ-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045846.1	51	7.371009	KEEP	31	2	52	43	1313	CC	0.999988	0.909058	0		+	4	60	115	0	0	8.235306	27	60	913	142	ENST00000342783.4	0.129032	0.909069
LAMP1	3916	__UNKNOWN__	__UNKNOWN__	13	113958190	113958190	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:113958190A>T	ENST00000332556.4	+	2	255				LAMP1_ENST00000397181.3_Intron	NM_005561.3	NP_005552.3	P11279	LAMP1_HUMAN	lysosomal-associated membrane protein 1	NA		NA			autophagic cell death (GO:0048102)|autophagy (GO:0006914)|establishment of protein localization to organelle (GO:0072594)|Golgi to lysosome transport (GO:0090160)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|protein stabilization (GO:0050821)|regulation of organelle transport along microtubule (GO:1902513)	alveolar lamellar body (GO:0097208)|cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|phagolysosome membrane (GO:0061474)|sarcolemma (GO:0042383)	enzyme binding (GO:0019899)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|skin(1)|stomach(2)	16	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.025)|GBM - Glioblastoma multiforme(44;0.206)|Epithelial(84;0.246)			gaggagttggagaccagcctg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J03263	CCDS41909.1	13q34	2011-11-24			ENSG00000185896	ENSG00000185896	3916		CD molecules	6499	protein-coding gene	gene with protein product		153330			NA		Standard		NM_005561	NA	Approved	CD107a	uc001vtm.1	P11279	OTTHUMG00000017380	ENST00000332556.4:c.62-2610A>T	chr13.hg19:g.113958190A>T		NA	B4DWL3|Q8WU33|Q96I40|Q9BRD2|Q9NP13	hg19	CCDS41909.1	0.02	-0.13156	TGGxGAC	COVERED																																																																																			NOVEL	LAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045876.2	2	2.706515	KEEP	0	0	0	9	243	AA	0.99254	0.227464	0		+	3	60	97	0	0	7.972983	11	60	322	35	ENST00000332556.4	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	114026631	114026631	__UNKNOWN__	IGR	SNP	T	T	G	rs28526818	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:114026631T>G			NA	NA				GRTP1 (8185 upstream) : ADPRHL1 (49628 downstream)						NA		NA									NA						gtttcaccgttttagccggga	0.577		NA											N|||	2139	0.427117	0.6831	0.3516	5008	,	,	NA	7924	0.1806	NA	0.4105	False	NA	,,,	NA	NA	NA	2504	0.4059	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.114026631T>G		NA		hg19		0.02	-0.070145	CGTxTTA	UNCOVERED																																																																																			NOVEL					0			13	3.909195	KEEP	15	0	0	13	351	TT	0.99257	0.053735	0			3	25	83	0	0	7.923012	3	31	86	44		0.5	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	114026638	114026638	__UNKNOWN__	IGR	SNP	G	G	A	rs28522331	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:114026638G>A			NA	NA				GRTP1 (8192 upstream) : ADPRHL1 (49621 downstream)						NA		NA									NA						cgttttagccgggatggtctc	0.562		NA											N|||	2140	0.427316	0.6838	0.3516	5008	,	,	NA	8296	0.1806	NA	0.4105	False	NA	,,,	NA	NA	NA	2504	0.4059	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.114026638G>A		NA		hg19		0.02	-0.070165	GCCxGGA	UNCOVERED																																																																																			NOVEL					0			13	3.90896	KEEP	15	0	0	13	376	GG	0.99257	0.053735	0			3	25	82	0	0	7.823722	3	31	101	45		0.5	0.054137
TFDP1	7027	__UNKNOWN__	__UNKNOWN__	13	114246502	114246502	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:114246502T>C	ENST00000375370.5	+	2	224				TFDP1_ENST00000538138.1_Intron|TFDP1_ENST00000465174.1_Intron|TFDP1_ENST00000544902.1_Intron	NM_007111.4	NP_009042.1	Q14186	TFDP1_HUMAN	transcription factor Dp-1	NA		NA			anoikis (GO:0043276)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA biosynthetic process (GO:2000278)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(10)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.132)|all_epithelial(44;0.0731)|all_lung(25;0.149)|Breast(118;0.153)	all cancers(43;0.0576)			cggagtttcgttcttgttgcc	0.478		NA								TSP Lung(29;0.18)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011685	CCDS9538.1	13q34	2008-07-18			ENSG00000198176	ENSG00000198176	7027			11749	protein-coding gene	gene with protein product		189902			NA	8413592, 9027491	Standard	NM_007111	NM_007111	NA	Approved	Dp-1, DRTF1, DP1	uc001vtw.3	Q14186	OTTHUMG00000017388	ENST00000375370.5:c.12+6338T>C	chr13.hg19:g.114246502T>C		NA	B4DLQ9|Q5JSB4|Q8IZL5	hg19	CCDS9538.1	0.02	-0.149101	TCGxTCT	COVERED																																																																																			NOVEL	TFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045918.3	6	3.006164	KEEP	0	0	0	10	269	TT	0.992708	0.289872	0		+	3	60	107	1	0	8.778821	13	60	388	43	ENST00000375370.5	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	13	114922778	114922778	__UNKNOWN__	IGR	SNP	C	C	T	rs112228838	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr13:114922778C>T			NA	NA				RASA3 (24692 upstream) : CDC16 (77583 downstream)						NA		NA									NA						tgagccaccacgcccagccAG	0.577		NA											c|||	50	0.00998403	0.0325	0.0072	5008	,	,	NA	16904	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr13.hg19:g.114922778C>T		NA		hg19		0.02	-0.149108	CCAxGCC	COVERED																																																																																			NOVEL					0			4	3.00799	KEEP	3	0	0	10	291	CC	0.99254	0.289823	0			3	60	88	0	0	6.879164	13	60	424	47		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19079823	19079823	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19079823C>A			NA	NA				None (None upstream) : RP11-754I20.1 (30479 downstream)						NA		NA									NA						gagcaagaatccatctccaaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19079823C>A		NA		hg19		0.02	-0.105244	AATxCAT	UNCOVERED																																																																																			NOVEL					0			5	2.407259	KEEP	1	0	0	8	247	CC	0	0	0			5	37	139	0	0	12.992398	6	60	190	27		0.454545	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19439973	19439973	__UNKNOWN__	IGR	SNP	C	C	T	rs145189418		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19439973C>T			NA	NA				RP11-536C10.16 (26075 upstream) : MED15P1 (59872 downstream)						NA		NA									NA						GATAAAGGTGCGTGAATGAGA	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19439973C>T		NA		hg19		0.02	0.89559	GTGxGTG	COVERED																																																																																			NOVEL					0			2	2.406836	KEEP	3	0	0	8	235	CC	0.99257	0.991794	0			5	27	131	1	0	7.412554	74	60	2468	143		0.063291	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19444083	19444083	__UNKNOWN__	IGR	SNP	T	T	G	rs28513337		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19444083T>G			NA	NA				RP11-536C10.16 (30185 upstream) : MED15P1 (55762 downstream)						NA		NA									NA						TTTTCAGTCCTATTTGGCAGA	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19444083T>G		NA		hg19		0.02	3.578202	TCCxATT	COVERED																																																																																			NOVEL					0			8	4.543599	KEEP	8	1	31	26	710	TT	0.999957	0.999953	0			13	49	427	0	0	31.500289	98	60	2918	224		0.117117	0.999996
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19472816	19472816	__UNKNOWN__	IGR	SNP	C	C	T	rs370680122		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19472816C>T			NA	NA				RP11-536C10.16 (58918 upstream) : MED15P1 (27029 downstream)						NA		NA									NA						caaaacaaaacgaaacaaaac	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19472816C>T		NA		hg19		0.02	-0.201741	AAAxGAA	COVERED																																																																																			NOVEL					0			15	4.512229	KEEP	1	0	0	15	432	CC	0.995343	0.48826	0			3	49	89	2	0	6.661367	17	51	550	54		0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19476226	19476226	__UNKNOWN__	IGR	SNP	C	C	T	rs61969335		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19476226C>T			NA	NA				RP11-536C10.16 (62328 upstream) : MED15P1 (23619 downstream)						NA		NA									NA						TGTGTTGGTCCGGTCAATAAT	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19476226C>T		NA		hg19		0.02	1.388497	GTCxGGT	COVERED																																																																																			NOVEL					0			2	2.40681	KEEP	10	0	0	8	238	CC	0.99257	0.991794	0			5	25	152	0	0	9.471959	75	48	2441	149		0.0625	0.999218
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19503050	19503050	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19503050A>C			NA	NA				MED15P1 (754 upstream) : CTD-2311B13.1 (2820 downstream)						NA		NA									NA						aaaaaaaagaaaagaaaAGGG	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19503050A>C		NA		hg19		0.02	-0.210465	AGAxAAG	COVERED																																																																																			NOVEL					0			16	3.306034	KEEP	0	0	0	11	279	AA	0.993072	0.518544	0			3	60	86	0	0	6.435066	16	60	464	46		0.157895	0.522161
CTD-2311B13.1	0	__UNKNOWN__	__UNKNOWN__	14	19509304	19509304	__UNKNOWN__	lincRNA	SNP	A	A	C	rs61969931		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19509304A>C	ENST00000551565.1	+	0	453										NA		NA									NA						ggcctcccaaagtgctggaat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000551565.1:	chr14.hg19:g.19509304A>C		NA		hg19		0.02	3.803709	CAAxGTG	COVERED																																																																																			NOVEL	CTD-2311B13.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000408574.1	27	6.077404	KEEP	5	2	62	42	1147	AA	1	0.999994	0		+	7	49	224	0	0	14.797748	91	60	2763	244	ENST00000551565.1	0.071429	0.999994
POTEG	404785	__UNKNOWN__	__UNKNOWN__	14	19553524	19553524	__UNKNOWN__	Silent	SNP	G	G	A	rs142702316	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19553524G>A	ENST00000409832.3	+	1	160	c.108G>A	c.(106-108)agG>agA	p.R36R		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	36		NA								cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						CCTGGTGCAGGGGGAGCGGCA	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													18	29	25			NA	NA	14		NA											NA				19553524		1543	3281	4824	SO:0001819	synonymous_variant				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036	404785		POTE ankyrin domain containing, Ankyrin repeat domain containing	33896	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 4	608916	ANKRD26-like family C, member 2	A26C2	NA		Standard	NM_001005356	NR_027480	NA	Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.108G>A	chr14.hg19:g.19553524G>A		NA	A1L153|A6NMI9|Q6S5H6|Q6S8J2	hg19	CCDS32018.1	0.02	2.876883	CAGxGGG	COVERED																																																																																			NOVEL	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408579.1	5	3.911579	KEEP	51	0	0	13	394	GG	0.99257	0.99257	0		+	12	47	365	0	0	25.028138	114	48	3894	259	ENST00000409832.3	0.095238	1
POTEG	404785	__UNKNOWN__	__UNKNOWN__	14	19554500	19554500	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19554500A>G	ENST00000409832.3	+	1	573					NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	NA		NA								cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						ggtggctcacacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036	404785		POTE ankyrin domain containing, Ankyrin repeat domain containing	33896	protein-coding gene	gene with protein product	cancer/testis antigen family 104, member 4	608916	ANKRD26-like family C, member 2	A26C2	NA		Standard	NM_001005356	NR_027480	NA	Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.521+563A>G	chr14.hg19:g.19554500A>G		NA	A1L153|A6NMI9|Q6S5H6|Q6S8J2	hg19	CCDS32018.1	0.02	-0.306906	CACxCCT	COVERED																																																																																			NOVEL	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000408579.1	14	3.040493	KEEP	34	1	28	20	566	AA	0.994391	0.795757	0		+	3	40	101	1	0	7.127	31	59	919	136	ENST00000409832.3	0.088235	0.800245
AL589743.1	0	__UNKNOWN__	__UNKNOWN__	14	19656098	19656098	__UNKNOWN__	lincRNA	SNP	A	A	T	rs2495191		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19656098A>T	ENST00000418499.3	+	0	585										NA		NA									NA						gtctcgctgtattgcccaggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000418499.3:	chr14.hg19:g.19656098A>T		NA		hg19		0.02	-0.350695	TGTxTTG	COVERED																																																																																			NOVEL	AL589743.1-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000317887.3	14	5.207022	KEEP	11	1	24	26	654	AA	0.999892	0.877613	0		+	4	51	114	0	0	7.761694	34	53	929	103	ENST00000418499.3	0.105263	0.877708
AL589743.1	0	__UNKNOWN__	__UNKNOWN__	14	19677268	19677268	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19677268C>T	ENST00000418499.3	+	0	711										NA		NA									NA						ggctacagagcgagactctgt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000418499.3:	chr14.hg19:g.19677268C>T		NA		hg19		0.02	-0.10519	GAGxGAG	UNCOVERED																																																																																			NOVEL	AL589743.1-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000317887.3	6	2.404565	KEEP	2	0	0	8	209	CC	0.99257	0.16126	0		+	3	51	84	0	0	7.033392	8	48	237	30	ENST00000418499.3	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19695868	19695868	__UNKNOWN__	IGR	SNP	T	T	C	rs61968622		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19695868T>C			NA	NA				AL589743.1 (8303 upstream) : RP11-496I2.2 (44164 downstream)						NA		NA									NA						aaaaAATCggttgggcacagt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19695868T>C		NA		hg19		0.02	-0.254359	CGGxTGG	COVERED																																																																																			NOVEL					0			22	6.746176	KEEP	38	1	30	33	879	TT	0.99986	0.668429	0			4	27	135	0	0	10.491115	23	50	695	111		0.148148	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	19811556	19811556	__UNKNOWN__	IGR	SNP	A	A	G	rs371034477		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:19811556A>G			NA	NA				RP11-496I2.2 (68812 upstream) : RP11-146E13.4 (619 downstream)						NA		NA									NA						AATGTAggccaagcatggtgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.19811556A>G		NA		hg19		0.02	-0.254358	GCCxAGC	COVERED																																																																																			NOVEL					0			13	2.840506	KEEP	3	1	30	20	570	AA	0.999863	0.668432	0			5	47	148	0	1	11.956886	18	60	542	70		0.217391	0.668523
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20092220	20092220	__UNKNOWN__	RNA	SNP	G	G	A	rs138599944		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20092220G>A	ENST00000548261.1	+	0	245										NA		NA									NA						ccaaagtgctgggattacagg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20092220G>A		NA		hg19		0.02	-0.368437	GCTxGGA	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	16	5.717698	KEEP	4	0	0	19	605	GG	0.999859	0.899187	0		+	7	47	211	1	0	16.386405	33	48	1136	98	ENST00000548261.1	0.175	0.899314
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20098673	20098673	__UNKNOWN__	RNA	SNP	G	G	A	rs9652317|rs184246378	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20098673G>A	ENST00000548261.1	+	0	245										NA		NA									NA						ACCAACTTTTGGAGACTGATG	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20098673G>A		NA		hg19		0.02	1.074215	TTTxGAG	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	0	3.309037	KEEP	6	0	0	11	326	GG	0.993072	0.992484	0		+	6	24	167	0	0	10.298853	75	50	2593	136	ENST00000548261.1	0.074074	0.999407
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20098703	20098703	__UNKNOWN__	RNA	SNP	C	C	T	rs9652318	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20098703C>T	ENST00000548261.1	+	0	245										NA		NA									NA						TGTAGCGTTACATACTTGGTT	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20098703C>T		NA		hg19		0.02	2.949733	TTAxATA	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	1	5.416563	KEEP	12	0	0	18	568	CC	0.999859	0.999859	0		+	16	46	447	0	0	31.584022	109	51	3777	238	ENST00000548261.1	0.128	1
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20098718	20098718	__UNKNOWN__	RNA	SNP	G	G	A	rs79698788		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20098718G>A	ENST00000548261.1	+	0	245										NA		NA									NA						TTGGTTCCATGAGCCGTGCCT	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20098718G>A		NA		hg19		0.02	2.85054	CATxAGC	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	4	3.744673	KEEP	47	1	27	22	690	GG	0.999859	0.999859	0		+	16	46	489	0	0	35.7745	109	51	3780	301	ENST00000548261.1	0.128	1
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20120247	20120247	__UNKNOWN__	RNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20120247A>C	ENST00000548261.1	+	0	245										NA		NA									NA						TACTATCATTATTTCTCTTCG	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20120247A>C		NA		hg19		0.02	5.844603	ATTxTTT	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	8	4.072705	KEEP	73	2	61	35	947	AA	0.999988	0.999988	0		+	12	46	408	0	0	27.957652	150	48	4476	397	ENST00000548261.1	0.074074	1
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20125598	20125598	__UNKNOWN__	RNA	SNP	A	A	G	rs200677953		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20125598A>G	ENST00000548261.1	+	0	343										NA		NA									NA						GTCACAGCTGATGGCCAGGTA	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20125598A>G		NA		hg19		0.02	3.891872	CTGxTGG	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	2	3.308892	KEEP	3	0	0	11	311	AA	0.993072	0.993041	0		+	7	36	243	0	0	16.662844	92	60	2788	167	ENST00000548261.1	0.070707	0.999968
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20137028	20137028	__UNKNOWN__	RNA	SNP	G	G	A	rs201263842	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20137028G>A	ENST00000548261.1	+	0	391										NA		NA									NA						CCCTCGGACGGGCAGGCTGGG	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20137028G>A		NA		hg19		0.02	1.414787	ACGxGCA	UNCOVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	4	2.705937	KEEP	36	0	0	9	259	GG	0	0	0		+	10	49	306	0	0	22.464307	67	60	2246	160	ENST00000548261.1	0.12987	0.998867
RP11-597A11.1	0	__UNKNOWN__	__UNKNOWN__	14	20137384	20137384	__UNKNOWN__	RNA	SNP	G	G	T	rs570646805	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20137384G>T	ENST00000548261.1	+	0	391										NA		NA									NA						TGCCCTCGCCGCATGCACAGC	0.647		NA											.|||	283	0.0565096	0.0794	0.0288	5008	,	,	NA	45173	0.0367	NA	0.0417	False	NA	,,,	NA	NA	NA	2504	0.0808	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000548261.1:	chr14.hg19:g.20137384G>T		NA		hg19		0.02	3.008555	GCCxCAT	COVERED																																																																																			NOVEL	RP11-597A11.1-003	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409571.1	5	3.309312	KEEP	3	0	0	11	326	GG	0.99257	0.992564	0		+	12	60	359	0	0	25.22422	97	60	3130	157	ENST00000548261.1	0.110092	0.999994
RP11-597A11.6	0	__UNKNOWN__	__UNKNOWN__	14	20146601	20146601	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20146601G>A	ENST00000555580.1	-	0	225										NA		NA									NA						CGTCAGTTACGCCCAGGACTT	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555580.1:	chr14.hg19:g.20146601G>A		NA		hg19		0.02	5.872969	TACxCCC	COVERED																																																																																			NOVEL	RP11-597A11.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409767.1	13	8.853156	KEEP	15	1	27	39	1099	GG	0.999998	0.999998	0		-	10	49	304	1	0	17.613607	206	60	6633	368	ENST00000555580.1	0.046296	1
RP11-597A11.6	0	__UNKNOWN__	__UNKNOWN__	14	20147110	20147110	__UNKNOWN__	lincRNA	SNP	A	A	T	rs8015035		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147110A>T	ENST00000555580.1	-	0	65										NA		NA									NA						CTGGTTTCTGAAAAGCAGGTT	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555580.1:	chr14.hg19:g.20147110A>T		NA		hg19		0.02	1.085466	CTGxAAA	UNCOVERED																																																																																			NOVEL	RP11-597A11.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409767.1	3	2.404001	KEEP	9	0	0	8	201	AA	0	0	0		-	8	47	223	0	0	14.423586	82	60	2403	142	ENST00000555580.1	0.088889	0.999881
RP11-597A11.6	0	__UNKNOWN__	__UNKNOWN__	14	20147118	20147118	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147118G>A	ENST00000555580.1	-	0	57										NA		NA									NA						TGAAAAGCAGGTTGAAGTCAA	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555580.1:	chr14.hg19:g.20147118G>A		NA		hg19		0.02	1.230867	CAGxTTG	COVERED																																																																																			NOVEL	RP11-597A11.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409767.1	3	2.706456	KEEP	9	0	0	9	247	GG	0.99257	0.992519	0		-	10	60	296	0	0	20.452514	86	60	2811	157	ENST00000555580.1	0.104167	0.999948
RP11-597A11.6	0	__UNKNOWN__	__UNKNOWN__	14	20147146	20147146	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147146T>C	ENST00000555580.1	-	0	29										NA		NA									NA						CTTGTTCCAGTTTCAGGGGAT	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555580.1:	chr14.hg19:g.20147146T>C		NA		hg19		0.02	1.529194	CAGxTTC	UNCOVERED																																																																																			NOVEL	RP11-597A11.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000409767.1	6	2.706004	KEEP	10	0	0	9	236	TT	0	0	0		-	8	60	257	0	0	17.532397	89	60	2586	161	ENST00000555580.1	0.082474	0.999948
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	20147236	20147236	__UNKNOWN__	IGR	SNP	G	G	A	rs572115899	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147236G>A			NA	NA				RP11-597A11.6 (61 upstream) : RP11-597A11.2 (2342 downstream)						NA		NA									NA						AAGTGCAAAGGCCCTGTACGT	0.473		NA											.|||	237	0.0473243	0.0499	0.0245	5008	,	,	NA	58412	0.0268	NA	0.0408	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.20147236G>A		NA		hg19		0.02	3.099086	AAGxCCC	COVERED																																																																																			NOVEL					0			4	4.212367	KEEP	0	0	0	14	423	GG	0.995343	0.995338	0			7	60	214	0	0	13.466406	102	60	3404	176		0.06422	0.999995
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	20147239	20147239	__UNKNOWN__	IGR	SNP	C	C	T	rs545881368	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147239C>T			NA	NA				RP11-597A11.6 (64 upstream) : RP11-597A11.2 (2339 downstream)						NA		NA									NA						TGCAAAGGCCCTGTACGTCAA	0.468		NA											.|||	237	0.0473243	0.0499	0.0245	5008	,	,	NA	56261	0.0268	NA	0.0408	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.20147239C>T		NA		hg19		0.02	3.125389	GCCxTGT	COVERED																																																																																			NOVEL					0			4	4.212502	KEEP	0	0	0	14	429	CC	0.995343	0.995335	0			7	60	217	0	0	13.852164	99	60	3315	174		0.066038	0.999992
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	20147287	20147287	__UNKNOWN__	IGR	SNP	G	G	A	rs2999996		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147287G>A			NA	NA				RP11-597A11.6 (112 upstream) : RP11-597A11.2 (2291 downstream)						NA		NA									NA						TAATGAATGAGTTTACTAATA	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.20147287G>A		NA		hg19		0.02	1.179516	TGAxTTT	COVERED																																																																																			NOVEL					0			2	3.310168	KEEP	0	0	0	11	350	GG	0.993072	0.989819	0			6	49	159	0	0	9.971944	62	60	2128	121		0.088235	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	20147838	20147838	__UNKNOWN__	IGR	SNP	A	A	G	rs201855591		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20147838A>G			NA	NA				RP11-597A11.6 (663 upstream) : RP11-597A11.2 (1740 downstream)						NA		NA									NA						AATCTGTCCAAGGTTATACCA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.20147838A>G		NA		hg19		0.02	1.698841	CCAxGGT	COVERED																																																																																			NOVEL					0			6	2.238903	KEEP	26	1	30	18	514	AA	0.999859	0.999694	0			17	60	570	0	0	46.175558	73	60	2271	206		0.188889	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	20148274	20148274	__UNKNOWN__	IGR	SNP	C	C	T	rs374056919		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20148274C>T			NA	NA				RP11-597A11.6 (1099 upstream) : RP11-597A11.2 (1304 downstream)						NA		NA									NA						ACCCTGTGTGCGCTGTGTGTG	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.20148274C>T		NA		hg19		0.02	3.055173	GTGxGCT	COVERED																																																																																			NOVEL					0			1	3.309396	KEEP	4	0	0	11	330	CC	0.993072	0.99307	0			8	60	235	0	0	14.730738	107	50	3481	207		0.069565	0.999998
PARP2	10038	__UNKNOWN__	__UNKNOWN__	14	20825656	20825656	__UNKNOWN__	Silent	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:20825656C>G	ENST00000429687.3	+	15	1590	c.1530C>G	c.(1528-1530)ccC>ccG	p.P510P	PARP2_ENST00000250416.5_Silent_p.P523P|PARP2_ENST00000527915.1_Silent_p.P523P			Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	523	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.	NA			base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		AGATGGCTCCCAGTTCTGCCC	0.488		NA						Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													65	63	64			NA	NA	14		NA											NA				20825656		1916	4118	6034	SO:0001819	synonymous_variant			AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484	10038		Poly (ADP-ribose) polymerases	272	protein-coding gene	gene with protein product		607725	ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2, poly (ADP-ribose) polymerase family, member 2	ADPRTL2	NA	10329013, 18353725	Standard		NM_005484	NA	Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000429687.3:c.1530C>G	chr14.hg19:g.20825656C>G		NA	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	hg19	CCDS45077.1	0.02	1.646145	TCCxAGT	COVERED																																																																																			NOVEL	PARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387845.2	2	4.512763	KEEP	0	0	0	15	450	CC	0.99649	0.99642	0		+	40	60	1273	0	0	118.778289	53	60	1795	155	ENST00000429687.3	0.430108	0.99993
HNRNPC	3183	__UNKNOWN__	__UNKNOWN__	14	21721962	21721962	__UNKNOWN__	Intron	SNP	G	G	C	rs143335891	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:21721962G>C	ENST00000555914.1	-	2	133				HNRNPC_ENST00000430246.2_Intron|HNRNPC_ENST00000556142.1_Intron|HNRNPC_ENST00000320084.7_Intron|HNRNPC_ENST00000556897.1_Intron|HNRNPC_ENST00000556513.1_Intron|HNRNPC_ENST00000554969.1_Intron|HNRNPC_ENST00000553300.1_Intron|HNRNPC_ENST00000557201.1_Intron|HNRNPC_ENST00000554455.1_Intron|HNRNPC_ENST00000420743.2_Intron|HNRNPC_ENST00000336053.6_Intron|HNRNPC_ENST00000555309.1_Intron|HNRNPC_ENST00000556628.1_Intron|HNRNPC_ENST00000449098.1_Intron|HNRNPC_ENST00000553753.1_Intron|HNRNPC_ENST00000555883.1_Intron			P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	NA		NA			3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		cggtggctcaggcctgtaatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(108;607 2244 12726 38757)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199	3183		RNA binding motif (RRM) containing	5035	protein-coding gene	gene with protein product		164020		HNRPC	NA	3457372	Standard		NM_031314	NA	Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000555914.1:c.35+9507C>G	chr14.hg19:g.21721962G>C		NA	D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	hg19		0.02	-0.157901	TCAxGCC	UNCOVERED																																																																																			NOVEL	HNRNPC-011	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000410228.1	4	2.407087	KEEP	2	0	0	8	241	GG	0	0	0		-	3	60	102	0	0	8.191453	14	60	468	35	ENST00000555914.1	0.176471	0.322807
CHD8	57680	__UNKNOWN__	__UNKNOWN__	14	21853496	21853496	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:21853496G>T	ENST00000430710.3	-	0	7276				CHD8_ENST00000399982.2_3'UTR	NM_020920.3	NP_065971.2	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	NA		NA			ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GTTAATGGAGGTGACTAGGGA	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888	57680			20153	protein-coding gene	gene with protein product		610528	helicase with SNF2 domain 1	HELSNF1	NA	10997877	Standard	NM_020920	NM_020920	NA	Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000430710.3:c.*276C>A	chr14.hg19:g.21853496G>T		NA	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	hg19	CCDS45081.1	0.02	-0.429814	GAGxTGA	COVERED																																																																																			NOVEL	CHD8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410276.2	1	4.212377	KEEP	0	0	0	14	430	GG	0.995343	0.950046	0		-	14	60	416	0	0	35.847203	33	60	1113	93	ENST00000430710.3	0.297872	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	22009467	22009467	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:22009467C>T			NA	NA				SALL2 (4117 upstream) : OR10G3 (28466 downstream)						NA		NA									NA						cctgtaatcccagcactttgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.22009467C>T		NA		hg19		0.02	-0.175449	TCCxAGC	COVERED																																																																																			NOVEL					0			3	3.008997	KEEP	2	0	0	10	307	CC	0.992708	0.384582	0			3	60	89	0	0	6.891858	14	60	480	46		0.176471	0.387407
MRPL52	122704	__UNKNOWN__	__UNKNOWN__	14	23303771	23303771	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:23303771C>T	ENST00000355151.5	+	0	643				MRPL52_ENST00000311892.6_3'UTR|MRPL52_ENST00000555345.1_3'UTR|MRPL52_ENST00000557221.1_3'UTR|MRPL52_ENST00000397496.3_3'UTR	NM_178336.2|NM_180982.2|NM_181306.2	NP_848026.1|NP_851313.1|NP_851823.1	Q86TS9	RM52_HUMAN	mitochondrial ribosomal protein L52	NA		NA			translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	structural constituent of ribosome (GO:0003735)				NA	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)		TAgctgggtgcggtggctcac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000450	CCDS9575.1, CCDS9576.1, CCDS41917.1, CCDS41918.1	14q11.2	2012-09-13			ENSG00000172590	ENSG00000172590	122704		Mitochondrial ribosomal proteins / large subunits	16655	protein-coding gene	gene with protein product		611856			NA	11551941, 11943462	Standard	NM_180982	NM_178336	NA	Approved		uc001wgw.4	Q86TS9	OTTHUMG00000028703	ENST00000355151.5:c.*241C>T	chr14.hg19:g.23303771C>T		NA	A6NMQ8|A8MXK5|A8MYI6|G3XCN9|Q6NVH8	hg19	CCDS41917.1	0.02	-0.289485	GTGxGGT	COVERED																																																																																			NOVEL	MRPL52-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000071657.4	9	11.128675	KEEP	1	0	0	37	1049	CC	0.999999	0.760886	0		+	3	60	96	0	0	6.752951	28	60	936	98	ENST00000355151.5	0.096774	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	23976419	23976419	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:23976419T>C			NA	NA				NGDN (28387 upstream) : RP11-66N24.4 (4549 downstream)						NA		NA									NA						gcggaggttgtagtgagccaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.23976419T>C		NA		hg19		0.02	-0.052631	TTGxAGT	UNCOVERED																																																																																			NOVEL					0			3	2.402447	KEEP	0	0	0	8	192	TT	0.99257	0.036492	0			2	47	72	0	0	6.693034	3	60	89	20		0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	24065526	24065526	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:24065526T>C			NA	NA				JPH4 (17517 upstream) : DHRS2 (33797 downstream)						NA		NA									NA						gtgatccacctgccttggcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.24065526T>C		NA		hg19		0.02	-0.105255	ACCxGCC	UNCOVERED																																																																																			NOVEL					0			8	3.609297	KEEP	6	0	0	12	334	TT	0.992708	0.138812	0			3	60	94	0	0	8.178598	7	60	212	40		0.3	0.139832
NRL	4901	__UNKNOWN__	__UNKNOWN__	14	24579604	24579604	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:24579604T>C	ENST00000561028.1	-	1	293							P54845	NRL_HUMAN	neural retina leucine zipper	NA		NA			positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of rhodopsin gene expression (GO:0007468)|response to stimulus (GO:0050896)|retinal rod cell development (GO:0046548)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(2)	2				GBM - Glioblastoma multiforme(265;0.0181)		aggtgtgagctaccacgccTA	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9608.1	14q11.1-q11.2	2013-01-08			ENSG00000129535	ENSG00000129535	4901			8002	protein-coding gene	gene with protein product		162080			NA	1427865, 10192380	Standard		NM_006177	NA	Approved	D14S46E, RP27, NRL-MAF	uc021rrk.1	P54845	OTTHUMG00000028789	ENST00000561028.1:c.26+4326A>G	chr14.hg19:g.24579604T>C		NA	A8MX14|Q53XD0	hg19	CCDS9608.1	0.02	1.58172	AGCxACC	COVERED																																																																																			NOVEL	NRL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415595.1	19	13.428485	KEEP	0	3	77	72	1963	TT	1	0.999881	0		-	5	60	170	0	0	11.081229	82	60	2424	252	ENST00000561028.1	0.057471	0.999881
STXBP6	29091	__UNKNOWN__	__UNKNOWN__	14	25400095	25400095	__UNKNOWN__	Intron	SNP	A	A	G	rs34298539	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:25400095A>G	ENST00000323944.5	-	2	606				STXBP6_ENST00000419632.2_Intron|STXBP6_ENST00000358326.2_Intron|STXBP6_ENST00000546511.1_Intron|STXBP6_ENST00000396700.1_Intron|STXBP6_ENST00000548724.1_Intron|STXBP6_ENST00000550887.1_Intron			Q8NFX7	STXB6_HUMAN	syntaxin binding protein 6 (amisyn)	NA		NA			negative regulation of exocytosis (GO:0045920)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|large_intestine(3)	7				GBM - Glioblastoma multiforme(265;0.0296)		aggcgggtggatcatgaggtc	0.547		NA											-|||	1316	0.26278	0.3608	0.2032	5008	,	,	NA	12445	0.2738	NA	0.2306	False	NA	,,,	NA	NA	NA	2504	0.1943	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF161505	CCDS9634.1	14q11.2	2002-12-18			ENSG00000168952	ENSG00000168952	29091			19666	protein-coding gene	gene with protein product		607958			NA	12145319	Standard		NM_014178	NA	Approved	amisyn, HSPC156	uc001wpu.3	Q8NFX7	OTTHUMG00000140186	ENST00000323944.5:c.154+43775T>C	chr14.hg19:g.25400095A>G		NA	D3DS78|Q8N3H1|Q8N8D5|Q96GF3|Q9P008	hg19	CCDS9634.1	0.02	-0.035056	TGGxTCA	UNCOVERED																																																																																			NOVEL	STXBP6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409166.1	6	2.404926	KEEP	9	0	0	8	207	AA	0	0	0		-	2	60	72	0	0	6.951863	2	60	44	23	ENST00000323944.5	0.5	0.019982
RP11-314P15.2	0	__UNKNOWN__	__UNKNOWN__	14	26569276	26569276	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:26569276T>C	ENST00000546412.1	-	0	258										NA		NA									NA						aggatggtcttgatctcctga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000546412.1:	chr14.hg19:g.26569276T>C		NA		hg19		0.02	-0.087686	TCTxGAT	UNCOVERED																																																																																			NOVEL	RP11-314P15.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000408476.1	4	3.307121	KEEP	0	0	0	11	289	TT	0.993072	0.09903	0		-	3	60	88	0	0	7.743871	6	60	161	32	ENST00000546412.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	29722879	29722879	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:29722879A>G			NA	NA				RP11-148E17.1 (224910 upstream) : RP11-562L8.1 (11151 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.29722879A>G		NA		hg19		0.02	-0.149084	CACxCCT	COVERED																																																																																			NOVEL					0			6	3.909557	KEEP	0	0	0	13	354	AA	0.994391	0.290363	0			3	60	97	0	0	7.872535	12	60	337	42		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	32449281	32449281	__UNKNOWN__	IGR	SNP	T	T	C	rs8007850	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:32449281T>C			NA	NA				RP11-187E13.1 (29693 upstream) : RP11-187E13.2 (26826 downstream)						NA		NA									NA						cctgacctcgtgatccgcccg	0.537		NA											T|||	1110	0.221645	0.1936	0.2781	5008	,	,	NA	11579	0.1875	NA	0.1531	False	NA	,,,	NA	NA	NA	2504	0.3252	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.32449281T>C		NA		hg19		0.02	-0.105224	TCGxGAT	UNCOVERED																																																																																			NOVEL					0			10	3.006129	KEEP	8	0	0	10	257	TT	0	0	0			3	44	104	0	0	9.033013	8	60	220	39		0.272727	0.139832
ARHGAP5	394	__UNKNOWN__	__UNKNOWN__	14	32615378	32615378	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:32615378G>A	ENST00000345122.3	+	4	4180				ARHGAP5_ENST00000539826.2_Intron|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000432921.1_Intron|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000556611.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	NA		NA			cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		tggcctcccagagtgctggga	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(9;77 350 3443 29227 41353)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05					394		Rho GTPase activating proteins	675	protein-coding gene	gene with protein product		602680	growth factor independent 2	GFI2	NA	8537347	Standard	NM_001030055	XM_005267635	NA	Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.3866-91G>A	chr14.hg19:g.32615378G>A		NA	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	hg19	CCDS32062.1	0.02	-0.157907	CCAxAGT	COVERED																																																																																			NOVEL	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000409735.1	4	5.11519	KEEP	0	0	0	17	524	GG	0.999366	0.322602	0		+	3	60	94	0	0	7.478665	13	60	447	46	ENST00000345122.3	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	34502633	34502633	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:34502633T>C			NA	NA				AL358340.1 (56036 upstream) : EGLN3-AS1 (6669 downstream)						NA		NA									NA						tttgggaggctgaggcgggca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.34502633T>C		NA		hg19		0.02	-0.070177	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			2	2.707445	KEEP	1	0	0	9	259	TT	0.99257	0.076761	0			2	60	72	0	0	6.335668	5	60	155	30		0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	34851223	34851223	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:34851223G>A			NA	NA				EGLN3 (251973 upstream) : SPTSSA (50771 downstream)						NA		NA									NA						gagccactgcgcccggccTTG	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.34851223G>A		NA		hg19		0.02	-0.192991	TGCxCCC	COVERED																																																																																			NOVEL					0			1	3.00856	KEEP	0	0	0	10	299	GG	0.992708	0.454419	0			3	60	92	0	0	6.892365	18	60	606	50		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	34956088	34956088	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:34956088T>C			NA	NA				SPTSSA (24526 upstream) : EAPP (29046 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.34956088T>C		NA		hg19		0.02	-0.157875	AGGxGTG	COVERED																																																																																			NOVEL					0			7	3.906325	KEEP	0	0	0	13	336	TT	0.994391	0.320996	0			3	40	101	0	0	8.272271	12	60	357	44		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	34963422	34963422	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:34963422T>C			NA	NA				SPTSSA (31860 upstream) : EAPP (21712 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.34963422T>C		NA		hg19		0.02	-0.157844	GTGxTGG	UNCOVERED																																																																																			NOVEL					0			3	2.405986	KEEP	1	0	0	8	218	TT	0	0	0			3	60	91	0	0	7.273184	12	60	341	39		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	35017667	35017667	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:35017667C>A			NA	NA				RNU1-27P (1584 upstream) : RNU1-28P (7764 downstream)						NA		NA									NA						GTTggccaggcacggtggctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.35017667C>A		NA		hg19		0.02	-0.131567	AGGxACG	COVERED																																																																																			NOVEL					0			16	6.617354	KEEP	0	0	0	22	642	CC	0.999892	0.229148	0			3	60	81	0	0	6.373165	11	60	357	49		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	35200630	35200630	__UNKNOWN__	IGR	SNP	A	A	T	rs1953426	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:35200630A>T			NA	NA				CFL2 (16734 upstream) : BAZ1A (21306 downstream)						NA		NA									NA						aaaattacaaaaattagccgg	0.547		NA											a|||	2170	0.433307	0.4652	0.2695	5008	,	,	NA	16051	0.8085	NA	0.175	False	NA	,,,	NA	NA	NA	2504	0.3855	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.35200630A>T		NA		hg19		0.02	-0.09643	CAAxAAT	UNCOVERED																																																																																			NOVEL					0			4	2.40492	KEEP	1	0	0	8	215	AA	0.99257	0.119541	0			3	60	87	0	0	7.833742	5	60	130	28		0.375	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	35200639	35200639	__UNKNOWN__	IGR	SNP	G	G	A	rs1953427	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:35200639G>A			NA	NA				CFL2 (16743 upstream) : BAZ1A (21297 downstream)						NA		NA									NA						aaaattagccgggtgtggtgg	0.552		NA											g|||	2170	0.433307	0.4652	0.2695	5008	,	,	NA	16868	0.8085	NA	0.175	False	NA	,,,	NA	NA	NA	2504	0.3855	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.35200639G>A		NA		hg19		0.02	-0.052628	GCCxGGT	UNCOVERED																																																																																			NOVEL					0			5	3.609555	KEEP	1	0	0	12	348	GG	0.993634	0.053793	0			3	60	91	0	0	9.55367	1	60	31	32		0.75	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	35352320	35352320	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:35352320T>C			NA	NA				RP11-73E17.2 (6655 upstream) : RP11-85K15.2 (37743 downstream)						NA		NA									NA						cctgcaatcctagcactttgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.35352320T>C		NA		hg19		0.02	-0.175424	TCCxAGC	COVERED																																																																																			NOVEL					0			10	3.909042	KEEP	1	0	0	13	352	TT	0.994391	0.385234	0			3	60	102	0	0	8.109997	15	60	455	48		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	35375523	35375523	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:35375523G>T			NA	NA				RP11-73E17.2 (29858 upstream) : RP11-85K15.2 (14540 downstream)						NA		NA									NA						attacaggcaggagccaccac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.35375523G>T		NA		hg19		0.02	-0.140352	GCAxGAG	COVERED																																																																																			NOVEL					0			4	3.309933	KEEP	0	0	0	11	340	GG	0.993072	0.259157	0			3	60	87	0	0	7.081867	10	60	337	41		0.230769	0.260965
KIAA0391	9692	__UNKNOWN__	__UNKNOWN__	14	35723626	35723626	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:35723626T>C	ENST00000557565.1	+	6	1656				KIAA0391_ENST00000605870.1_Intron|KIAA0391_ENST00000603544.1_Intron|KIAA0391_ENST00000604948.1_Intron|KIAA0391_ENST00000321130.10_Intron|KIAA0391_ENST00000250377.7_Intron|KIAA0391_ENST00000534898.4_Intron	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	NA		NA			tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		gagatggagtttcgctcttgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890	9692			19958	protein-coding gene	gene with protein product	mitochondrial RNase P subunit 3, proteinaceous RNase P	609947			NA	9205841, 18984158	Standard	NM_014672	NM_001256678	NA	Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.1276-12307T>C	chr14.hg19:g.35723626T>C		NA	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	hg19	CCDS32063.1	0.02	-0.122795	AGTxTCG	COVERED																																																																																			NOVEL	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000411280.1	8	3.607442	KEEP	1	0	0	12	317	TT	0.993072	0.194952	0		+	3	60	105	0	0	9.278915	7	60	202	39	ENST00000557565.1	0.3	0.196312
RP11-116N8.1	0	__UNKNOWN__	__UNKNOWN__	14	36459694	36459694	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:36459694T>C	ENST00000550089.1	+	0	242										NA		NA									NA						tttgggaggctgaggcgggca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550089.1:	chr14.hg19:g.36459694T>C		NA		hg19		0.02	-0.131564	GGCxGAG	COVERED																																																																																			NOVEL	RP11-116N8.1-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000409615.1	15	5.714849	KEEP	8	0	0	19	533	TT	0.99649	0.228369	0		+	3	60	94	0	0	7.782035	10	60	304	55	ENST00000550089.1	0.230769	0.229173
SLC25A21	89874	__UNKNOWN__	__UNKNOWN__	14	37280605	37280605	__UNKNOWN__	Intron	SNP	T	T	C	rs538004532		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:37280605T>C	ENST00000331299.5	-	3	719				SLC25A21_ENST00000555449.1_Intron|RP11-81F13.2_ENST00000557642.1_RNA	NM_030631.3	NP_085134.1	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial oxoadipate carrier), member 21	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|pancreas(1)|prostate(1)|skin(1)	9	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)		cctgtaatcctagcactttgg	0.473		NA											T|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16224	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ278148	CCDS9663.1, CCDS55913.1	14q13.3	2014-01-28	2012-03-29		ENSG00000183032	ENSG00000183032	89874		Solute carriers	14411	protein-coding gene	gene with protein product		607571	solute carrier family 25 (mitochondrial oxodicarboxylate carrier), member 21		NA	11083877	Standard	NM_030631	NM_030631	NA	Approved	ODC1, ODC	uc001wtz.2	Q9BQT8	OTTHUMG00000140250	ENST00000331299.5:c.203+2517A>G	chr14.hg19:g.37280605T>C		NA	A8K0L0|G3V4L5|Q3MJ99	hg19	CCDS9663.1	0.02	-0.105244	TCCxAGC	UNCOVERED																																																																																			NOVEL	SLC25A21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276732.2	5	2.705759	KEEP	0	0	0	9	244	TT	0.99254	0.138789	0		-	3	60	98	0	0	8.743969	6	60	170	29	ENST00000331299.5	0.333333	0.139832
TTC6	319089	__UNKNOWN__	__UNKNOWN__	14	38094493	38094493	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:38094493T>C	ENST00000553443.1	+	1	939							Q86TZ1	TTC6_HUMAN	tetratricopeptide repeat domain 6	NA		NA								central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	14	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;1.59e-06)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0543)|all cancers(34;0.108)|BRCA - Breast invasive adenocarcinoma(188;0.156)|LUSC - Lung squamous cell carcinoma(13;0.176)	GBM - Glioblastoma multiforme(112;0.00551)		tggctcacgcttgtaatccca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014342		14q13.1	2013-01-10			ENSG00000139865	ENSG00000139865	319089		Tetratricopeptide (TTC) repeat domain containing	19739	protein-coding gene	gene with protein product		NA	non-protein coding RNA 291, chromosome 14 open reading frame 25	NCRNA00291, C14orf25	NA		Standard	XM_002343299	XM_006709976	NA	Approved		uc001wuj.3	Q86TZ1	OTTHUMG00000157369	ENST00000553443.1:c.939+2285T>C	chr14.hg19:g.38094493T>C		NA	Q3SY88|Q96CE6	hg19		0.02	-0.131564	CGCxTGT	COVERED																																																																																			NOVEL	TTC6-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000348620.4	7	3.00758	KEEP	7	0	0	10	274	TT	0.99257	0.22747	0		+	5	60	165	0	0	14.922864	9	60	269	43	ENST00000553443.1	0.357143	0.229173
SEC23A	10484	__UNKNOWN__	__UNKNOWN__	14	39562351	39562351	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:39562351A>G	ENST00000307712.6	-	3	797				SEC23A_ENST00000548032.2_Missense_Mutation_p.C107R|SEC23A_ENST00000536508.1_Intron|SEC23A_ENST00000545328.2_Intron	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		gattacaggcatgagccactg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													46	45	45			NA	NA	14		NA											NA				39562351		2201	4298	6499	SO:0001627	intron_variant			X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934	10484			10701	protein-coding gene	gene with protein product		610511	Sec23 (S. cerevisiae) homolog A		NA	8898360, 10329445	Standard		NM_006364	NA	Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.279+39T>C	chr14.hg19:g.39562351A>G		NA	B2R5P4|B3KXI2|Q8NE16	hg19	CCDS9668.1	0.02	3.595762	GGCxTGA	COVERED	.	.	.	.	.	.	.	.	.	.	A	3.130	-0.178531	0.06380	.	.	ENSG00000100934	ENST00000548032	D	0.88509	-2.39	0.392	-0.783	0.10958	.	.	.	.	.	T	0.80347	0.4606	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.65569	-0.6136	4	.	.	.	.	.	.	.	.	.	.	.	R	107	ENSP00000447489:C107R	.	C	-	1	0	SEC23A	38632102	0.083000	0.21467	0.012000	0.15200	0.011000	0.07611	-2.355000	0.01088	-0.832000	0.04251	-0.862000	0.03010	TGC	NOVEL	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276728.2	28	3.765151	KEEP	6	8	219	90	2495	AA	1	0.999995	0		-	5	60	168	1	0	10.483554	99	60	2936	318	ENST00000307712.6	0.048077	0.999995
SEC23A	10484	__UNKNOWN__	__UNKNOWN__	14	39571164	39571164	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:39571164A>G	ENST00000553970.1	-	1	212				SEC23A_ENST00000548032.2_Intron|SEC23A_ENST00000536508.1_Intron|SEC23A_ENST00000545328.2_Intron|SEC23A_ENST00000307712.6_Intron|SEC23A_ENST00000557280.1_Intron			Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ggccgggcgcagtggctcatg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934	10484			10701	protein-coding gene	gene with protein product		610511	Sec23 (S. cerevisiae) homolog A		NA	8898360, 10329445	Standard		NM_006364	NA	Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000553970.1:c.20+1071T>C	chr14.hg19:g.39571164A>G		NA	B2R5P4|B3KXI2|Q8NE16	hg19		0.02	-0.17542	CGCxGTG	COVERED																																																																																			NOVEL	SEC23A-012	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409973.1	7	3.007677	KEEP	1	0	0	10	275	AA	0.992708	0.384582	0		-	4	60	141	0	0	11.981066	13	60	389	42	ENST00000553970.1	0.235294	0.387407
RP11-407N17.3	0	__UNKNOWN__	__UNKNOWN__	14	39809325	39809325	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:39809325A>G	ENST00000553728.1	+	25	3649				CTAGE5_ENST00000348007.3_Intron|CTAGE5_ENST00000557038.1_Intron|CTAGE5_ENST00000341749.3_Intron|CTAGE5_ENST00000553352.1_Intron|CTAGE5_ENST00000280083.3_Intron|CTAGE5_ENST00000396165.4_Intron|RP11-407N17.3_ENST00000603904.1_Intron|CTAGE5_ENST00000341502.5_Intron|CTAGE5_ENST00000556148.1_Intron|CTAGE5_ENST00000396158.2_Intron						NA		NA									NA						gggattacagacgtgagccac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000553728.1:c.3437-5783A>G	chr14.hg19:g.39809325A>G		NA		hg19		0.02	-0.043853	CAGxCGT	UNCOVERED																																																																																			NOVEL	RP11-407N17.3-001	NOVEL	not_organism_supported|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000410208.1	7	2.70522	KEEP	1	0	0	9	233	AA	0.99257	0.023895	0		+	2	60	70	0	0	6.493141	3	60	88	16	ENST00000553728.1	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	45166708	45166708	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:45166708T>C			NA	NA				snoU13 (130499 upstream) : RP11-398E10.1 (65651 downstream)						NA		NA									NA						ccgcccgccttggcctcccaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.45166708T>C		NA		hg19		0.02	-0.105251	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			3	3.307489	KEEP	1	0	0	11	298	TT	0.993072	0.138863	0			3	60	93	0	0	7.801136	9	60	276	38		0.25	0.139832
FAM179B	23116	__UNKNOWN__	__UNKNOWN__	14	45539167	45539167	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:45539167C>T	ENST00000361462.2	+	18	5152				FAM179B_ENST00000361577.3_Intron|FAM179B_ENST00000382233.2_Intron			Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	NA		NA								endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						aggcagatcacgaggtcagga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718	23116			19959	protein-coding gene	gene with protein product		NA	KIAA0423	KIAA0423	NA		Standard	XM_113781	XM_005267451	NA	Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361462.2:c.4969+1321C>T	chr14.hg19:g.45539167C>T		NA	Q68D66|Q6PG27	hg19		0.02	-0.157885	TCAxGAG	COVERED																																																																																			NOVEL	FAM179B-002	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000276792.1	7	3.910418	KEEP	6	0	0	13	376	CC	0.992708	0.320453	0		+	3	38	91	0	0	7.272322	12	60	387	49	ENST00000361462.2	0.2	0.322807
PRPF39	55015	__UNKNOWN__	__UNKNOWN__	14	45570850	45570850	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:45570850G>A	ENST00000355765.6	+	5	739					NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						tgtatttttagtagagatggg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246	55015			20314	protein-coding gene	gene with protein product		614907	PRP39 pre-mRNA processing factor 39 homolog (yeast), PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)		NA		Standard		NM_017922	NA	Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.570-882G>A	chr14.hg19:g.45570850G>A		NA	Q08AL1|Q08AL2|Q9NUU5	hg19	CCDS9682.2	0.02	-0.23686	TTAxTAG	COVERED																																																																																			NOVEL	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319683.2	9	7.219782	KEEP	1	0	0	24	706	GG	0.999892	0.612341	0		+	3	60	93	0	0	6.865037	20	60	690	70	ENST00000355765.6	0.130435	0.612407
PRPF39	55015	__UNKNOWN__	__UNKNOWN__	14	45570912	45570912	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:45570912A>G	ENST00000355765.6	+	5	739					NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						catgtgctggaattacaggtg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246	55015			20314	protein-coding gene	gene with protein product		614907	PRP39 pre-mRNA processing factor 39 homolog (yeast), PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)		NA		Standard		NM_017922	NA	Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.570-820A>G	chr14.hg19:g.45570912A>G		NA	Q08AL1|Q08AL2|Q9NUU5	hg19	CCDS9682.2	0.02	1.997126	TGGxATT	COVERED																																																																																			NOVEL	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319683.2	15	11.726657	KEEP	0	0	0	39	1041	AA	1	0.979526	0		+	4	60	137	0	0	9.522146	47	60	1379	122	ENST00000355765.6	0.078431	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	49832778	49832778	__UNKNOWN__	IGR	SNP	C	C	A	rs377046449|rs145823797	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:49832778C>A			NA	NA				RP11-816J8.1 (288555 upstream) : RNA5SP384 (186572 downstream)						NA		NA									NA						aaaaaaaacacacacacacac	0.478		NA											C|||	1063	0.21226	0.1611	0.3934	5008	,	,	NA	17945	0.003	NA	0.4066	False	NA	,,,	NA	NA	NA	2504	0.1687	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.49832778C>A		NA		hg19		0.02	-0.105266	ACAxACA	UNCOVERED																																																																																			NOVEL					0			5	2.40722	KEEP	1	0	0	8	246	CC	0	0	0			4	60	118	2	0	10.390798	8	60	281	29		0.333333	0.139832
RPS29	6235	__UNKNOWN__	__UNKNOWN__	14	50058072	50058072	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50058072G>T	ENST00000557111.1	-	2	291							P62273	RS29_HUMAN	ribosomal protein S29	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|small ribosomal subunit (GO:0015935)	structural constituent of ribosome (GO:0003735)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(1)|ovary(1)	4	all_epithelial(31;0.00214)|Breast(41;0.0124)					caggctggagggcaatggtgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L31610	CCDS9685.1, CCDS32072.1	14q21.3	2011-04-06			ENSG00000213741	ENSG00000213741	6235		S ribosomal proteins	10419	protein-coding gene	gene with protein product		603633			NA	8781548, 7772601	Standard	NM_001030001	NM_001032	NA	Approved	S29	uc001wwl.4	P62273	OTTHUMG00000140272	ENST00000557111.1:c.198-5305C>A	chr14.hg19:g.50058072G>T		NA	A8MZ73|P30054	hg19		0.02	-0.087694	GAGxGCA	UNCOVERED																																																																																			NOVEL	RPS29-010	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000410501.1	8	2.405946	KEEP	0	0	0	8	230	GG	0.99257	0.09898	0		-	3	60	74	0	0	6.53083	5	60	172	23	ENST00000557111.1	0.375	0.099721
POLE2	5427	__UNKNOWN__	__UNKNOWN__	14	50142069	50142069	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50142069A>T	ENST00000216367.5	-	4	345				POLE2_ENST00000539565.2_Intron|POLE2_ENST00000556584.1_Intron|POLE2_ENST00000554396.1_Intron	NM_002692.3	NP_002683.2	P56282	DPOE2_HUMAN	polymerase (DNA directed), epsilon 2, accessory subunit	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	epsilon DNA polymerase complex (GO:0008622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	10	all_epithelial(31;0.0021)|Breast(41;0.0124)				Cladribine(DB00242)	cccaaagtgcagggattacag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF025840	CCDS32073.1, CCDS55914.1, CCDS55915.1	14q21-q22	2012-05-18	2012-05-18		ENSG00000100479	ENSG00000100479	5427		DNA polymerases	9178	protein-coding gene	gene with protein product	DNA polymerase epsilon subunit B	602670	polymerase (DNA directed), epsilon 2 (p59 subunit)		NA	9405441, 9443964	Standard	NM_002692	NM_002692	NA	Approved	DPE2	uc001wwu.3	P56282	OTTHUMG00000170813	ENST00000216367.5:c.246-924T>A	chr14.hg19:g.50142069A>T		NA	A0AV55|A4FU92|A4LBB7|A6NH58|B4DDE6|O43560	hg19	CCDS32073.1	0.02	-0.184191	TGCxGGG	COVERED																																																																																			NOVEL	POLE2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410512.1	5	3.308888	KEEP	2	0	0	11	311	AA	0.99254	0.420319	0		-	3	60	90	0	0	6.692778	18	60	548	48	ENST00000216367.5	0.142857	0.423478
NEMF	9147	__UNKNOWN__	__UNKNOWN__	14	50275159	50275159	__UNKNOWN__	Intron	SNP	T	T	C	rs574841956		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50275159T>C	ENST00000298310.5	-	19	2194				NEMF_ENST00000546046.1_Intron|NEMF_ENST00000556925.1_Intron|NEMF_ENST00000545773.1_Intron			O60524	NEMF_HUMAN	nuclear export mediator factor	NA		NA			nuclear export (GO:0051168)	nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(13)|liver(1)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	36						tcccaaagtgttgggattaca	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF039687	CCDS9694.1	14q21.3	2012-11-19	2011-01-31	2011-01-31	ENSG00000165525	ENSG00000165525	9147			10663	protein-coding gene	gene with protein product		608378	serologically defined colon cancer antigen 1	SDCCAG1	NA	9610721, 10575219	Standard	NM_004713	XR_429334	NA	Approved	NY-CO-1, FLJ10051	uc001wxc.3	O60524	OTTHUMG00000170857	ENST00000298310.5:c.1745-2308A>G	chr14.hg19:g.50275159T>C		NA	A0JLQ3|B3KSK1|B4DDL3|B4DHA9|B4E3F3|Q32Q66|Q8WW70|Q9NWG1	hg19	CCDS9694.1	0.02	-0.149109	GTGxTGG	COVERED																																																																																			NOVEL	NEMF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410798.1	8	2.70736	KEEP	1	0	0	9	259	TT	0.99257	0.351317	0		-	6	60	200	0	0	18.478752	9	60	272	41	ENST00000298310.5	0.4	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	50333053	50333053	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50333053A>G			NA	NA				RN7SL2 (3486 upstream) : ARF6 (26756 downstream)						NA		NA									NA						cacccgcctcagcctcccaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.50333053A>G		NA		hg19		0.02	-0.096477	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.707197	KEEP	0	0	0	9	256	AT	0.992708	0.119558	0			3	60	96	0	0	8.378583	7	60	210	29		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	50478889	50478889	__UNKNOWN__	IGR	SNP	T	T	C	rs540046188	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50478889T>C			NA	NA				C14orf182 (4651 upstream) : RP11-58E21.3 (25423 downstream)						NA		NA									NA						gccgagatcatgccactgcac	0.527		NA											T|||	13	0.00259585	0.0091	0.0014	5008	,	,	NA	11607	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.50478889T>C		NA		hg19		0.02	-0.175395	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			7	2.706529	KEEP	9	0	0	9	243	TT	0	0	0			3	60	92	0	0	7.033889	16	60	456	50		0.157895	0.387407
SOS2	6655	__UNKNOWN__	__UNKNOWN__	14	50635768	50635768	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50635768G>A	ENST00000543680.1	-	8	995				SOS2_ENST00000216373.5_Intron|SOS2_ENST00000555794.1_Intron			Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	NA		NA			apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					agtggctcacgcctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485	6655		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11188	protein-coding gene	gene with protein product		601247	son of sevenless (Drosophilia) homolog 2		NA	8276400	Standard		NM_006939	NA	Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000543680.1:c.970-7441C>T	chr14.hg19:g.50635768G>A		NA	B7ZKT6|D3DSB4|Q15503|Q17RN1	hg19		0.02	-0.175439	CACxCCT	COVERED																																																																																			NOVEL	SOS2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000410706.1	8	3.008461	KEEP	0	0	0	10	296	GG	0.992708	0.384582	0		-	4	60	117	0	0	9.70122	12	60	411	48	ENST00000543680.1	0.25	0.387407
SOS2	6655	__UNKNOWN__	__UNKNOWN__	14	50662677	50662677	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50662677G>A	ENST00000543680.1	-	4	536				SOS2_ENST00000216373.5_Intron			Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	NA		NA			apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					cctgggaggcggaggttgcag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485	6655		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11188	protein-coding gene	gene with protein product		601247	son of sevenless (Drosophilia) homolog 2		NA	8276400	Standard		NM_006939	NA	Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000543680.1:c.510+3731C>T	chr14.hg19:g.50662677G>A		NA	B7ZKT6|D3DSB4|Q15503|Q17RN1	hg19		0.02	-0.105242	GGCxGAG	UNCOVERED																																																																																			NOVEL	SOS2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000410706.1	6	3.60845	KEEP	3	0	0	12	326	GG	0.992708	0.138812	0		-	3	60	89	0	0	7.678527	7	60	221	32	ENST00000543680.1	0.3	0.139832
L2HGDH	79944	__UNKNOWN__	__UNKNOWN__	14	50713368	50713368	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:50713368T>G	ENST00000261699.4	-	10	1214				L2HGDH_ENST00000421284.3_Intron|L2HGDH_ENST00000267436.4_3'UTR			Q9H9P8	L2HDH_HUMAN	L-2-hydroxyglutarate dehydrogenase	NA		NA			2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2-hydroxyglutarate dehydrogenase activity (GO:0047545)			kidney(1)|large_intestine(4)|lung(3)|ovary(2)	10	all_epithelial(31;0.000599)|Breast(41;0.0102)					gcccaggctgttctcaaactc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9698.1	14q22.1	2006-04-28	2005-05-25	2005-05-25	ENSG00000087299	ENSG00000087299	79944	1.1.99.2		20499	protein-coding gene	gene with protein product	2-hydroxyglutarate dehydrogenase	609584	chromosome 14 open reading frame 160	C14orf160	NA	16005139	Standard	NM_024884	NM_024884	NA	Approved	FLJ12618	uc001wxu.3	Q9H9P8	OTTHUMG00000140289	ENST00000261699.4:c.1197-8925A>C	chr14.hg19:g.50713368T>G		NA	Q9BRR1	hg19		0.02	-0.368341	CTGxTCT	COVERED																																																																																			NOVEL	L2HGDH-002	KNOWN	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000276871.1	12	3.338905	KEEP	0	1	31	22	593	TT	0.999892	0.899217	0		-	3	60	98	0	0	6.676413	35	60	1019	98	ENST00000261699.4	0.078947	0.899314
ATL1	51062	__UNKNOWN__	__UNKNOWN__	14	51097705	51097705	__UNKNOWN__	Intron	SNP	G	G	A	rs143125272		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:51097705G>A	ENST00000441560.2	+	14	2032				ATL1_ENST00000354525.4_Intron|ATL1_ENST00000358385.6_Intron|ATL1_ENST00000357032.3_Intron	NM_001127713.1	NP_001121185.1	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	NA		NA			axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						ggccaggcgcggtggctcacg	0.493		NA											G|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17487	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513	51062			11231	protein-coding gene	gene with protein product	atlastin	606439	spastic paraplegia 3A (autosomal dominant)	SPG3, SPG3A	NA	8252041, 7825576	Standard		NM_015915	NA	Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000441560.2:c.1552-1242G>A	chr14.hg19:g.51097705G>A		NA	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	hg19	CCDS32077.1	0.02	1.201965	CGCxGTG	COVERED																																																																																			NOVEL	ATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410925.1	20	5.379983	KEEP	2	2	54	37	1087	GG	1	0.999835	0		+	5	60	152	0	0	9.417054	77	60	2482	182	ENST00000441560.2	0.060976	0.999835
SAV1	60485	__UNKNOWN__	__UNKNOWN__	14	51101117	51101117	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:51101117C>G	ENST00000324679.4	-	0	2299					NM_021818.3	NP_068590.1	Q9H4B6	SAV1_HUMAN	salvador family WW domain containing protein 1	NA		NA			hair follicle development (GO:0001942)|hippo signaling (GO:0035329)|intestinal epithelial cell differentiation (GO:0060575)|keratinocyte differentiation (GO:0030216)|lung epithelial cell differentiation (GO:0060487)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of epithelial cell proliferation (GO:0050680)|positive regulation of apoptotic process (GO:0043065)|regulation of stem cell maintenance (GO:2000036)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|kidney(2)|lung(2)|prostate(1)	6	all_epithelial(31;0.000611)|Breast(41;0.0333)					tctcaggctgcagtgcaagtg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK023071	CCDS9701.1	14q13-q23	2014-04-14	2014-04-14		ENSG00000151748	ENSG00000151748	60485			17795	protein-coding gene	gene with protein product	WW domain-containing adaptor 45	607203	salvador homolog 1 (Drosophila)		NA	12202036, 11027580	Standard		NM_021818	NA	Approved	WW45, WWP4, salvador	uc001wyh.2	Q9H4B6	OTTHUMG00000140293	ENST00000324679.4:c.*784G>C	chr14.hg19:g.51101117C>G		NA	A8K4B8|D3DSB6|Q6IA58|Q9H949|Q9HAK9	hg19	CCDS9701.1	0.02	1.932453	CTGxAGT	COVERED																																																																																			NOVEL	SAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276879.1	19	9.625609	KEEP	0	0	0	32	982	CC	0.999997	0.967423	0		-	4	60	136	0	0	9.648503	41	60	1391	124	ENST00000324679.4	0.088889	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	51141643	51141643	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:51141643G>T			NA	NA				SAV1 (6594 upstream) : NIN (44837 downstream)						NA		NA									NA						ttttgtttttgtttttgagac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.51141643G>T		NA		hg19		0.02	-0.114028	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			7	2.407234	KEEP	1	0	0	8	251	GG	0	0	0			3	60	80	0	1	6.500877	9	60	315	32		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	51178146	51178146	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:51178146T>C			NA	NA				SAV1 (43097 upstream) : NIN (8334 downstream)						NA		NA									NA						cccagctacttgggaggctga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.51178146T>C		NA		hg19		0.02	-0.166644	ACTxGGG	UNCOVERED																																																																																			NOVEL					0			11	2.40575	KEEP	3	0	0	8	216	TT	0	0	0			3	41	97	0	0	7.533452	16	60	476	38		0.157895	0.353947
FRMD6	122786	__UNKNOWN__	__UNKNOWN__	14	52194619	52194619	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:52194619G>A	ENST00000395718.2	+	14	2002	c.1717G>A	c.(1717-1719)Ggc>Agc	p.G573S	FRMD6_ENST00000356218.4_Missense_Mutation_p.G573S|FRMD6_ENST00000554167.1_Missense_Mutation_p.G504S|FRMD6_ENST00000344768.5_Missense_Mutation_p.G581S|FRMD6_ENST00000553556.1_Missense_Mutation_p.G223S	NM_001267046.1|NM_152330.3	NP_001253975.1|NP_689543.1	Q96NE9	FRMD6_HUMAN	FERM domain containing 6	581		NA			apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					GGATGAGGAAGGCCTCTATTG	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													126	100	109			NA	NA	14		NA											NA				52194619		2203	4300	6503	SO:0001583	missense			BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926	122786			19839	protein-coding gene	gene with protein product	expanded homolog	614555	chromosome 14 open reading frame 31	C14orf31	NA		Standard	NM_152330	NM_152330	NA	Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000395718.2:c.1717G>A	chr14.hg19:g.52194619G>A	ENSP00000379068:p.Gly573Ser	NA	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	hg19	CCDS9704.1	0.02	-0.421041	GAAxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858693	0.71834	.	.	ENSG00000139926	ENST00000356218;ENST00000395718;ENST00000344768;ENST00000554167;ENST00000553556	T;T;T;T	0.78481	-1.18;-1.18;-0.96;-0.77	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.69070	0.3070	N	0.22421	0.69	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.08055	0.003;0.002;0.003	T	0.62134	-0.6918	10	0.42905	T	0.14	.	19.4915	0.95052	0.0:0.0:1.0:0.0	.	504;581;573	G3V4T7;Q96NE9;Q96NE9-2	.;FRMD6_HUMAN;.	S	573;573;581;504;223	ENSP00000348550:G573S;ENSP00000379068:G573S;ENSP00000343899:G581S;ENSP00000451977:G504S	ENSP00000343899:G581S	G	+	1	0	FRMD6	51264369	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	3.493000	0.53266	2.717000	0.92951	0.655000	0.94253	GGC	NOVEL	FRMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276880.1	0	4.51325	KEEP	0	0	0	15	454	GG	0.99649	0.945073	0		+	14	60	433	0	0	37.548234	33	60	1087	87	ENST00000395718.2	0.297872	0.948402
RP11-280K24.4	0	__UNKNOWN__	__UNKNOWN__	14	52284476	52284476	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:52284476T>C	ENST00000553312.1	+	0	3943										NA		NA									NA						tggctcatgcttgtaatccca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000553312.1:	chr14.hg19:g.52284476T>C		NA		hg19		0.02	-0.201746	TGCxTGT	COVERED																																																																																			NOVEL	RP11-280K24.4-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000411576.1	5	2.70732	KEEP	0	0	0	9	256	TT	0.99254	0.486885	0		+	3	60	102	0	0	8.033164	16	60	492	48	ENST00000553312.1	0.157895	0.490544
TXNDC16	57544	__UNKNOWN__	__UNKNOWN__	14	53018161	53018161	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:53018161G>A	ENST00000281741.4	-	1	191				TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	NA		NA			cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					ctacagcctgggcgacagagc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301	57544			19965	protein-coding gene	gene with protein product		NA	KIAA1344	KIAA1344	NA		Standard	XM_051699	NM_020784	NA	Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.180+872C>T	chr14.hg19:g.53018161G>A		NA	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	hg19	CCDS32083.1	0.02	-0.157889	CTGxGCG	COVERED																																																																																			NOVEL	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411681.1	9	3.548443	KEEP	0	0	0	12	346	GG	0.993634	0.320751	0		-	3	60	84	0	0	6.479264	13	60	437	45	ENST00000281741.4	0.1875	0.322807
ERO1L	30001	__UNKNOWN__	__UNKNOWN__	14	53116726	53116726	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:53116726A>G	ENST00000395686.3	-	13	1349					NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	NA		NA			4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					cttgaggccaagaattcaaga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930	30001			13280	protein-coding gene	gene with protein product		615435	ERO1 (S. cerevisiae)-like		NA	10671517	Standard	NM_014584	NM_014584	NA	Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.1125+2230T>C	chr14.hg19:g.53116726A>G		NA	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	hg19	CCDS9709.1	0.02	-0.210519	CCAxGAA	COVERED																																																																																			NOVEL	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276892.1	11	3.308333	KEEP	0	0	0	11	302	AA	0.993072	0.518544	0		-	3	60	108	0	0	8.491699	18	60	560	47	ENST00000395686.3	0.142857	0.522161
ERO1L	30001	__UNKNOWN__	__UNKNOWN__	14	53116729	53116729	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:53116729A>G	ENST00000395686.3	-	13	1349					NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	NA		NA			4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					gaggccaagaattcaagacca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930	30001			13280	protein-coding gene	gene with protein product		615435	ERO1 (S. cerevisiae)-like		NA	10671517	Standard	NM_014584	NM_014584	NA	Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.1125+2227T>C	chr14.hg19:g.53116729A>G		NA	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	hg19	CCDS9709.1	0.02	-0.201738	AGAxTTC	COVERED																																																																																			NOVEL	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276892.1	12	3.608257	KEEP	0	0	0	12	320	AA	0.993634	0.487421	0		-	3	60	108	0	0	8.560498	17	60	516	49	ENST00000395686.3	0.15	0.490544
PSMC6	5706	__UNKNOWN__	__UNKNOWN__	14	53193626	53193626	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:53193626T>C	ENST00000445930.2	+	14	1099				PSMC6_ENST00000557557.1_Intron|PSMC6_ENST00000606149.1_Intron			P62333	PRS10_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 6	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein binding, bridging (GO:0030674)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	19	Breast(41;0.176)					tcccaaagtgttgggattaca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9710.2	14q22.1	2010-04-21			ENSG00000100519	ENSG00000100519	5706		Proteasome (prosome, macropain) subunits, ATPases / AAA-type	9553	protein-coding gene	gene with protein product		602708			NA	8674546, 9473509	Standard	NM_002806	NM_002806	NA	Approved	p42	uc010tqx.2	P62333	OTTHUMG00000152333	ENST00000445930.2:c.1094-591T>C	chr14.hg19:g.53193626T>C		NA	B2R975|P49719|Q6IBU3|Q92524	hg19	CCDS9710.2	0.02	-0.245563	GTGxTGG	COVERED																																																																																			NOVEL	PSMC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276904.2	7	3.006797	KEEP	1	0	0	10	276	TT	0.99254	0.636563	0		+	3	60	109	0	0	8.294284	23	60	672	55	ENST00000445930.2	0.115385	0.641347
RP11-589M4.3	0	__UNKNOWN__	__UNKNOWN__	14	53263086	53263086	__UNKNOWN__	lincRNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:53263086T>G	ENST00000554548.1	-	0	110										NA		NA									NA						actttgggagtctgaggcggg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554548.1:	chr14.hg19:g.53263086T>G		NA		hg19		0.02	-0.201727	GAGxCTG	COVERED																																																																																			NOVEL	RP11-589M4.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000411943.1	7	2.992546	KEEP	3	0	0	10	265	TT	0.99257	0.4869	0		-	3	60	91	0	0	6.862125	17	60	518	50	ENST00000554548.1	0.15	0.490544
DDHD1	80821	__UNKNOWN__	__UNKNOWN__	14	53533423	53533423	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:53533423G>A	ENST00000323669.5	-	7	1503				DDHD1_ENST00000357758.3_Intron|DDHD1_ENST00000395606.1_Intron	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	NA		NA			cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					agtggctcacgcctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523	80821			19714	protein-coding gene	gene with protein product	phosphatidic acid-preferring phospholipase A1	614603	spastic paraplegia 28 (autosomal recessive)	SPG28	NA	11214970, 20359546	Standard		NM_030637	NA	Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.1504-3500C>T	chr14.hg19:g.53533423G>A		NA	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	hg19	CCDS53895.1	0.02	-0.131561	CACxCCT	COVERED																																																																																			NOVEL	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276901.1	8	2.406993	KEEP	0	0	0	8	244	GG	0.99257	0.22747	0		-	3	49	90	0	0	7.632373	8	60	257	33	ENST00000323669.5	0.272727	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	54361765	54361765	__UNKNOWN__	IGR	SNP	T	T	C	rs556993282	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:54361765T>C			NA	NA				AL162759.1 (44165 upstream) : MIR5580 (53379 downstream)						NA		NA									NA						tccctccctttctttcttcct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.54361765T>C		NA		hg19		0.02	-0.166626	CTTxCTT	COVERED																																																																																			NOVEL					0			4	2.405665	KEEP	0	0	0	8	214	TT	0.99257	0.384528	0			3	60	103	0	0	8.133424	16	60	455	39		0.157895	0.387407
CGRRF1	10668	__UNKNOWN__	__UNKNOWN__	14	54987944	54987944	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:54987944T>C	ENST00000216420.7	+	2	236				CGRRF1_ENST00000557512.1_Intron	NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	NA		NA			cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						tttgggaggctgaggtgggcg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532	10668		RING-type (C3HC4) zinc fingers	15528	protein-coding gene	gene with protein product		606138			NA	8968090	Standard	NM_006568	NM_006568	NA	Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308	ENST00000216420.7:c.105-1228T>C	chr14.hg19:g.54987944T>C		NA	Q96BX2	hg19	CCDS9719.1	0.02	-0.254304	GGCxGAG	COVERED																																																																																			NOVEL	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276905.2	10	4.812295	KEEP	3	0	0	16	448	TT	0.995343	0.66541	0		+	3	60	99	0	0	7.295256	23	60	669	68	ENST00000216420.7	0.115385	0.668523
WDHD1	11169	__UNKNOWN__	__UNKNOWN__	14	55450498	55450498	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:55450498G>A	ENST00000360586.3	-	15	1972				WDHD1_ENST00000359167.4_Intron|WDHD1_ENST00000420358.2_Intron|WDHD1_ENST00000421192.1_Intron	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	NA		NA			heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						cggcctcccagagtgctggga	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554	11169		WD repeat domain containing	23170	protein-coding gene	gene with protein product	CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)	608126			NA	9175701, 20028748	Standard	NM_007086	NM_007086	NA	Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.1906+942C>T	chr14.hg19:g.55450498G>A		NA	C9JW18|F6W0U7	hg19	CCDS9721.1	0.02	-0.122783	CCAxAGT	COVERED																																																																																			NOVEL	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276897.2	6	3.309763	KEEP	0	0	0	11	336	GG	0.993072	0.194952	0		-	4	60	103	0	0	8.570503	10	60	344	39	ENST00000360586.3	0.285714	0.196312
WDHD1	11169	__UNKNOWN__	__UNKNOWN__	14	55475550	55475550	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:55475550A>G	ENST00000360586.3	-	5	407				WDHD1_ENST00000420358.2_Intron|WDHD1_ENST00000421192.1_Intron	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	NA		NA			heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						acggagtctcactctgtcacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554	11169		WD repeat domain containing	23170	protein-coding gene	gene with protein product	CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)	608126			NA	9175701, 20028748	Standard	NM_007086	NM_007086	NA	Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.342-113T>C	chr14.hg19:g.55475550A>G		NA	C9JW18|F6W0U7	hg19	CCDS9721.1	0.02	-0.367963	CTCxCTC	COVERED																																																																																			NOVEL	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276897.2	8	2.234183	KEEP	0	1	30	18	456	AA	0.99986	0.908941	0		-	3	60	103	0	0	7.327795	31	60	771	70	ENST00000360586.3	0.088235	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	55540101	55540101	__UNKNOWN__	IGR	SNP	A	A	G	rs56725788	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:55540101A>G			NA	NA				MAPK1IP1L (3191 upstream) : LGALS3 (55660 downstream)						NA		NA									NA						caccacgcccagactccaggt	0.498		NA											G|||	2300	0.459265	0.7897	0.3156	5008	,	,	NA	15484	0.2014	NA	0.4245	False	NA	,,,	NA	NA	NA	2504	0.4162	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.55540101A>G		NA		hg19		0.02	-0.087695	CCCxGAC	UNCOVERED																																																																																			NOVEL					0			2	2.403938	KEEP	1	0	0	8	207	AA	0	0	0			4	60	119	0	0	11.3987	4	60	123	23		0.5	0.099721
KTN1-AS1	100129075	__UNKNOWN__	__UNKNOWN__	14	56001381	56001381	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:56001381T>C	ENST00000554558.1	-	0	364							Q86SY8	KTAS1_HUMAN	KTN1 antisense RNA 1	NA		NA									NA						tgctatgttgtccaggctggt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							14q22.3	2012-10-12	2012-08-15	2011-12-07	ENSG00000186615	ENSG00000186615	100129075		Long non-coding RNAs	19842	non-coding RNA	RNA, long non-coding		NA	chromosome 14 open reading frame 33, KTN1 antisense RNA 1 (non-protein coding)	C14orf33	NA		Standard	NR_027123	NR_027123	NA	Approved		uc001xbz.2	Q86SY8	OTTHUMG00000171057	ENST00000554558.1:	chr14.hg19:g.56001381T>C		NA		hg19		0.02	-0.184171	TTGxCCA	COVERED																																																																																			NOVEL	KTN1-AS1-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000411452.1	14	4.209914	KEEP	0	0	0	14	378	TT	0.995343	0.421506	0		-	4	60	138	0	0	11.268907	17	60	505	51	ENST00000554558.1	0.190476	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	56569600	56569600	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:56569600T>C			NA	NA				AL163952.2 (27316 upstream) : PELI2 (15492 downstream)						NA		NA									NA						ctgcccgccttggcctcccaa	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.56569600T>C		NA		hg19		0.02	-0.175409	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			13	2.4058	KEEP	5	0	0	8	217	TT	0	0	0			3	60	100	0	0	7.76087	17	60	496	44		0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	57247963	57247963	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:57247963C>T			NA	NA				RP11-1085N6.4 (15488 upstream) : RP11-1085N6.6 (18659 downstream)						NA		NA									NA						ctgcccacctcggcctcccaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.57247963C>T		NA		hg19		0.02	-0.175425	CCTxGGC	COVERED																																																																																			NOVEL					0			9	4.208689	KEEP	8	0	0	14	385	CC	0.99254	0.384517	0			3	46	88	0	0	6.710741	15	60	478	50		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	57639501	57639501	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:57639501G>A			NA	NA				OTX2-AS1 (20606 upstream) : EXOC5 (31016 downstream)						NA		NA									NA						caaagtgctgggataacaggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.57639501G>A		NA		hg19		0.02	-0.192992	CTGxGAT	COVERED																																																																																			NOVEL					0			6	3.61077	KEEP	0	0	0	12	370	GG	0.993634	0.454842	0			3	54	91	0	0	7.010204	15	60	517	52		0.166667	0.457757
C14orf105	55195	__UNKNOWN__	__UNKNOWN__	14	57937275	57937275	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:57937275T>C	ENST00000216445.3	-	0	1825					NM_001283057.1|NM_018168.2	NP_001269986.1|NP_060638.2	Q9NVL8	CN105_HUMAN	chromosome 14 open reading frame 105	NA		NA								breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						aggctggtcttgaactcctga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001512	CCDS9730.1, CCDS61458.1, CCDS61459.1	14q22.2	2012-09-25			ENSG00000100557	ENSG00000100557	55195			20189	protein-coding gene	gene with protein product		NA			NA		Standard	NM_018168	XM_005267806	NA	Approved	FLJ10650	uc001xcy.2	Q9NVL8	OTTHUMG00000140317	ENST00000216445.3:c.*798A>G	chr14.hg19:g.57937275T>C		NA	Q53G04	hg19	CCDS9730.1	0.02	-0.280073	TCTxGAA	COVERED																																																																																			NOVEL	C14orf105-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276921.2	0	5.414036	KEEP	0	0	0	18	500	TT	0.999859	0.739567	0		-	4	60	109	0	0	7.965737	22	60	646	67	ENST00000216445.3	0.153846	0.739671
SLC35F4	341880	__UNKNOWN__	__UNKNOWN__	14	58067177	58067177	__UNKNOWN__	Intron	SNP	A	A	G	rs11847126	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:58067177A>G	ENST00000556826.1	-	2	340				SLC35F4_ENST00000557430.1_Intron	NM_001206920.1	NP_001193849.1	A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	NA		NA			transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ttgggaggccaaggtgggcgg	0.478		NA											N|||	2976	0.594249	0.5363	0.745	5008	,	,	NA	11970	0.3333	NA	0.7863	False	NA	,,,	NA	NA	NA	2504	0.637	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812	341880		Solute carriers	19845	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 36	C14orf36	NA		Standard	XM_292260	NM_001206920	NA	Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000556826.1:c.104-6335T>C	chr14.hg19:g.58067177A>G		NA	A6NDQ3	hg19		0.02	-0.114021	GCCxAGG	UNCOVERED																																																																																			NOVEL	SLC35F4-004	NOVEL	not_organism_supported|upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000412973.1	13	4.210207	KEEP	19	0	0	14	382	AA	0.99257	0.16126	0		-	5	60	162	0	0	15.045929	7	40	214	58	ENST00000556826.1	0.416667	0.162467
SLC35F4	341880	__UNKNOWN__	__UNKNOWN__	14	58067181	58067181	__UNKNOWN__	Intron	SNP	T	T	C	rs11851484	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:58067181T>C	ENST00000556826.1	-	2	340				SLC35F4_ENST00000557430.1_Intron	NM_001206920.1	NP_001193849.1	A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	NA		NA			transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						gaggccaaggtgggcggatca	0.498		NA											N|||	4091	0.816893	0.7973	0.8329	5008	,	,	NA	11877	0.756	NA	0.8946	False	NA	,,,	NA	NA	NA	2504	0.8149	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812	341880		Solute carriers	19845	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 36	C14orf36	NA		Standard	XM_292260	NM_001206920	NA	Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000556826.1:c.104-6339A>G	chr14.hg19:g.58067181T>C		NA	A6NDQ3	hg19		0.02	-0.105254	AGGxGGG	UNCOVERED																																																																																			NOVEL	SLC35F4-004	NOVEL	not_organism_supported|upstream_uORF|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000412973.1	12	4.210644	KEEP	18	0	0	14	385	TT	0.99257	0.138793	0		-	5	60	165	0	0	15.346155	7	40	205	55	ENST00000556826.1	0.416667	0.139832
ACTR10	55860	__UNKNOWN__	__UNKNOWN__	14	58699353	58699353	__UNKNOWN__	Intron	SNP	C	C	T	rs1951203	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:58699353C>T	ENST00000254286.4	+	12	1152					NM_018477.2	NP_060947.1	Q9NZ32	ARP10_HUMAN	actin-related protein 10 homolog (S. cerevisiae)	NA		NA			microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|dynactin complex (GO:0005869)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	13						aggatggtctcgatctcttga	0.507		NA											C|||	1707	0.340855	0.2126	0.281	5008	,	,	NA	13859	0.3651	NA	0.4543	False	NA	,,,	NA	NA	NA	2504	0.4151	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF220190	CCDS32090.1	14q23.1	2014-08-08			ENSG00000131966	ENSG00000131966	55860			17372	protein-coding gene	gene with protein product		NA			NA	12857853	Standard		NM_018477	NA	Approved	HARP11, ACTR11, Arp11	uc001xdf.3	Q9NZ32	OTTHUMG00000171049	ENST00000254286.4:c.1072+368C>T	chr14.hg19:g.58699353C>T		NA	Q9H9Y5|Q9NWY2	hg19	CCDS32090.1	0.02	-0.070177	TCTxGAT	UNCOVERED																																																																																			NOVEL	ACTR10-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411405.1	5	2.708042	KEEP	9	0	0	9	274	CC	0	0	0		+	3	54	89	0	0	8.032374	5	60	174	36	ENST00000254286.4	0.375	0.054137
TIMM9	26520	__UNKNOWN__	__UNKNOWN__	14	58878884	58878884	__UNKNOWN__	Intron	SNP	C	C	T	rs568610679		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:58878884C>T	ENST00000556007.2	-	3	149				TIMM9_ENST00000216463.4_Intron|TIMM9_ENST00000555593.1_Intron|TIMM9_ENST00000555404.1_Intron|RP11-517O13.1_ENST00000556734.1_RNA|TIMM9_ENST00000395159.2_Intron			Q9Y5J7	TIM9_HUMAN	translocase of inner mitochondrial membrane 9 homolog (yeast)	NA		NA			cellular protein metabolic process (GO:0044267)|chaperone-mediated protein transport (GO:0072321)|protein import into mitochondrial inner membrane (GO:0045039)|protein targeting to mitochondrion (GO:0006626)|sensory perception of sound (GO:0007605)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)|mitochondrion (GO:0005739)	chaperone binding (GO:0051087)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			kidney(2)|skin(1)	3						ttttttgagacggagtctcac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF150100	CCDS9735.1	14q22.3-q24	2008-07-04	2001-11-28		ENSG00000100575	ENSG00000100575	26520			11819	protein-coding gene	gene with protein product		607384	translocase of inner mitochondrial membrane 9 (yeast) homolog		NA	10552927, 14726512	Standard		NM_012460	NA	Approved	TIM9A	uc001xds.3	Q9Y5J7	OTTHUMG00000140322	ENST00000556007.2:c.26-195G>A	chr14.hg19:g.58878884C>T		NA	B2R584	hg19		0.02	1.219294	AGAxGGA	COVERED																																																																																			NOVEL	TIMM9-009	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000412360.2	10	10.649117	KEEP	1	1	30	46	1244	CC	1	0.999768	0		-	5	60	153	0	0	9.543908	76	60	2331	190	ENST00000556007.2	0.061728	0.999768
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	59850768	59850768	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:59850768G>A			NA	NA				DAAM1 (12645 upstream) : AL159140.1 (15972 downstream)						NA		NA									NA						cacctgccttggcctcccaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.59850768G>A		NA		hg19		0.02	-0.192989	CTTxGCC	COVERED																																																																																			NOVEL					0			10	5.114753	KEEP	3	0	0	17	524	GG	0.997832	0.456764	0			3	60	87	0	0	6.533814	16	60	546	55		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	60367018	60367018	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:60367018T>C			NA	NA				RTN1 (29334 upstream) : RP11-62H20.1 (19122 downstream)						NA		NA									NA						gccgagatcgtgccattgcac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.60367018T>C		NA		hg19		0.02	-0.131552	TCGxGCC	COVERED																																																																																			NOVEL					0			6	3.307605	KEEP	3	0	0	11	293	TT	0.993072	0.227586	0			3	60	99	0	0	8.282275	10	60	283	41		0.230769	0.229173
PPM1A	5494	__UNKNOWN__	__UNKNOWN__	14	60760406	60760406	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:60760406T>G	ENST00000395076.4	+	0	2785					NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	NA		NA			cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		gtgtgtgtgtttgtgagtgtg	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	5494	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	9275	protein-coding gene	gene with protein product	phosphatase 2C alpha, protein phosphatase 2C, alpha isoform	606108	protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform		NA	1311954	Standard	NM_021003	NM_177952	NA	Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.*1206T>G	chr14.hg19:g.60760406T>G		NA	B5BU11|J3KNM0|O75551	hg19	CCDS9744.1	0.02	3.739295	TGTxTGT	COVERED																																																																																			NOVEL	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276949.2	21	9.952584	KEEP	0	1	31	44	1202	TT	1	0.999992	0		+	8	60	265	1	0	18.183317	93	60	2764	231	ENST00000395076.4	0.079208	0.999992
PPM1A	5494	__UNKNOWN__	__UNKNOWN__	14	60760411	60760411	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:60760411A>T	ENST00000395076.4	+	0	2790					NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	NA		NA			cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		tgtgtttgtgagtgtgtgtTT	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	5494	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	9275	protein-coding gene	gene with protein product	phosphatase 2C alpha, protein phosphatase 2C, alpha isoform	606108	protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform		NA	1311954	Standard	NM_021003	NM_177952	NA	Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.*1211A>T	chr14.hg19:g.60760411A>T		NA	B5BU11|J3KNM0|O75551	hg19	CCDS9744.1	0.02	3.035577	GTGxGTG	COVERED																																																																																			NOVEL	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276949.2	21	3.702369	KEEP	0	3	81	41	1122	AA	1	0.999991	0		+	8	60	240	0	0	15.79749	90	60	2659	223	ENST00000395076.4	0.081633	0.999991
TMEM30B	161291	__UNKNOWN__	__UNKNOWN__	14	61747371	61747371	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:61747371G>A	ENST00000555868.1	-	1	1187	c.495C>T	c.(493-495)atC>atT	p.I165I	TMEM30B_ENST00000557163.1_5'UTR|TMEM30B_ENST00000355702.2_Silent_p.I165I	NM_001017970.2	NP_001017970.1	Q3MIR4	CC50B_HUMAN	transmembrane protein 30B	165		NA			lipid transport (GO:0006869)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(108;0.107)|BRCA - Breast invasive adenocarcinoma(234;0.181)		GGCTGTTGGCGATGGCGCCGC	0.726		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													4	4	4			NA	NA	14		NA											NA				61747371		1885	3791	5676	SO:0001819	synonymous_variant			AK091169	CCDS32093.1	14q23.1	2006-09-20				ENSG00000182107	161291			27254	protein-coding gene	gene with protein product		611029			NA	15375526	Standard	XM_090844	NM_001017970	NA	Approved	CDC50B	uc001xfl.3	Q3MIR4		ENST00000555868.1:c.495C>T	chr14.hg19:g.61747371G>A		NA	B3KR84|Q14D00	hg19	CCDS32093.1	0.02	1.493915	GGCxATG	COVERED																																																																																			NOVEL	TMEM30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413358.1	0	3.008151	KEEP	0	0	0	10	291	GG	0.992708	0.988426	0		-	26	60	731	0	0	65.854374	42	60	1309	101	ENST00000555868.1	0.382353	0.995687
RP11-47I22.4	0	__UNKNOWN__	__UNKNOWN__	14	62106228	62106228	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:62106228C>T	ENST00000556347.1	+	4	419				RP11-47I22.3_ENST00000556569.1_Intron						NA		NA									NA						cggtggctcacgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000556347.1:c.420-18095C>T	chr14.hg19:g.62106228C>T		NA		hg19		0.02	-0.192972	TCAxGCC	UNCOVERED																																																																																			NOVEL	RP11-47I22.4-001	PUTATIVE	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000413996.1	0	2.407028	KEEP	2	0	0	8	241	CC	0	0	0		+	3	60	90	0	0	6.8339	16	60	522	51	ENST00000556347.1	0.157895	0.457757
SNAPC1	6617	__UNKNOWN__	__UNKNOWN__	14	62230778	62230778	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:62230778G>A	ENST00000216294.4	+	1	232				RP11-618G20.1_ENST00000555937.1_RNA	NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	NA		NA			gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		tcagcctcccgagtagctggg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(27;223 907 37180 39193 46568)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608	6617			11134	protein-coding gene	gene with protein product		600591	small nuclear RNA activating complex, polypeptide 1, 43kD		NA	9644240	Standard	NM_003082	NM_003082	NA	Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.128+1472G>A	chr14.hg19:g.62230778G>A		NA		hg19	CCDS9755.1	0.02	-0.096467	CCCxAGT	UNCOVERED																																																																																			NOVEL	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276976.2	1	2.406825	KEEP	0	0	0	8	240	GG	0.99257	0.119541	0		+	3	60	80	0	0	6.632006	8	60	256	27	ENST00000216294.4	0.272727	0.120436
SNAPC1	6617	__UNKNOWN__	__UNKNOWN__	14	62262677	62262677	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:62262677A>G	ENST00000216294.4	+	0	2187					NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	NA		NA			gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		ctcccaaagtactgggattat	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(27;223 907 37180 39193 46568)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608	6617			11134	protein-coding gene	gene with protein product		600591	small nuclear RNA activating complex, polypeptide 1, 43kD		NA	9644240	Standard	NM_003082	NM_003082	NA	Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.*976A>G	chr14.hg19:g.62262677A>G		NA		hg19	CCDS9755.1	0.02	-0.428937	AGTxCTG	COVERED																																																																																			NOVEL	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276976.2	7	2.632667	KEEP	1	1	29	19	480	AA	0.999863	0.95436	0		+	3	60	96	1	1	6.317612	40	60	1125	88	ENST00000216294.4	0.069767	0.954491
CTD-2277K2.1	0	__UNKNOWN__	__UNKNOWN__	14	62405839	62405839	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:62405839T>C	ENST00000554436.1	+	0	482										NA		NA									NA						ggcaacagagtgagacttggt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554436.1:	chr14.hg19:g.62405839T>C		NA		hg19		0.02	-0.043859	GAGxGAG	UNCOVERED																																																																																			NOVEL	CTD-2277K2.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000411882.1	5	2.406701	KEEP	0	0	0	8	231	TT	0.99257	0.036492	0		+	2	26	70	0	0	6.75019	2	60	62	21	ENST00000554436.1	0.5	0.036766
PPP2R5E	5529	__UNKNOWN__	__UNKNOWN__	14	63851820	63851820	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:63851820A>G	ENST00000555899.1	-	12	1601				PPP2R5E_ENST00000553266.1_Intron|PPP2R5E_ENST00000422769.2_Intron|PPP2R5E_ENST00000337537.3_Intron			Q16537	2A5E_HUMAN	protein phosphatase 2, regulatory subunit B', epsilon isoform	NA		NA			regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)	15				OV - Ovarian serous cystadenocarcinoma(108;0.00197)|all cancers(60;0.0153)|BRCA - Breast invasive adenocarcinoma(234;0.128)		caaggcaggcagatcacttga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L76703	CCDS9758.1, CCDS61467.1, CCDS61468.1	14q23.2	2010-06-18	2007-01-22		ENSG00000154001	ENSG00000154001	5529		Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits	9313	protein-coding gene	gene with protein product		601647	protein phosphatase 2, regulatory subunit B (B56), epsilon isoform		NA	7592815	Standard	NM_006246	NM_006246	NA	Approved		uc001xgd.1	Q16537	OTTHUMG00000140341	ENST00000555899.1:c.1075-531T>C	chr14.hg19:g.63851820A>G		NA	A4FU37|B7ZAW5|B7ZKK8|B7ZKK9|J3KQN6|Q52LW4	hg19		0.02	-0.131578	GGCxGAT	COVERED																																																																																			NOVEL	PPP2R5E-008	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000411877.1	7	3.308204	KEEP	2	0	0	11	306	AA	0.993072	0.227586	0		-	3	60	100	0	0	8.381884	10	60	313	41	ENST00000555899.1	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	64044503	64044503	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64044503G>A			NA	NA				CTD-2302E22.4 (33121 upstream) : WDR89 (19253 downstream)						NA		NA									NA						tttttttgaggcagagtctct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.64044503G>A		NA		hg19		0.02	-0.175386	GAGxCAG	COVERED																																																																																			NOVEL					0			7	2.707889	KEEP	0	0	0	9	269	GG	0.99254	0.384517	0			4	60	101	0	0	7.665074	16	60	528	41		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	64290578	64290578	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64290578T>C			NA	NA				RNU7-116P (87355 upstream) : Y_RNA (24400 downstream)						NA		NA									NA						tggtctcaaattcctgggctc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.64290578T>C		NA		hg19		0.02	-0.26312	AAAxTCC	COVERED																																																																																			NOVEL					0			10	4.210795	KEEP	1	0	0	14	388	TT	0.995343	0.690438	0			3	60	94	0	0	6.850474	22	60	658	67		0.12	0.693668
SYNE2	23224	__UNKNOWN__	__UNKNOWN__	14	64387579	64387579	__UNKNOWN__	Intron	SNP	T	T	C	rs201914570		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64387579T>C	ENST00000554584.1	+	1	130				SYNE2_ENST00000344113.4_Intron|SYNE2_ENST00000358025.3_Intron|SYNE2_ENST00000357395.3_Intron|SYNE2_ENST00000341472.5_Intron|SYNE2_ENST00000356081.3_Intron			Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	NA		NA			centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		tgcctgtaattccagcacttt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654	23224			17084	protein-coding gene	gene with protein product	nuclear envelope spectrin repeat-2, nucleus and actin connecting element	608442			NA	10231032, 10878022	Standard	NM_182914	NM_182910	NA	Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000554584.1:c.79+11634T>C	chr14.hg19:g.64387579T>C		NA	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	hg19		0.02	-0.210501	AATxCCA	COVERED																																																																																			NOVEL	SYNE2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000411905.1	8	2.706988	KEEP	0	0	0	9	251	TT	0.99254	0.518266	0		+	4	60	123	0	0	9.962983	15	60	444	48	ENST00000554584.1	0.210526	0.522161
SYNE2	23224	__UNKNOWN__	__UNKNOWN__	14	64577821	64577821	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64577821T>C	ENST00000554584.1	+	66	12705				SYNE2_ENST00000344113.4_Intron|SYNE2_ENST00000358025.3_Intron|SYNE2_ENST00000357395.3_Intron|SYNE2_ENST00000394768.2_Intron|SYNE2_ENST00000555002.1_Intron|ESR2_ENST00000542956.1_Intron			Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	NA		NA			centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		tggtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654	23224			17084	protein-coding gene	gene with protein product	nuclear envelope spectrin repeat-2, nucleus and actin connecting element	608442			NA	10231032, 10878022	Standard	NM_182914	NM_182910	NA	Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000554584.1:c.12655-2238T>C	chr14.hg19:g.64577821T>C		NA	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	hg19		0.02	-0.24558	TCAxGCC	COVERED																																																																																			NOVEL	SYNE2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000411905.1	4	3.007875	KEEP	3	0	0	10	280	TT	0.99257	0.636582	0		+	3	60	98	0	0	7.305827	21	60	619	62	ENST00000554584.1	0.125	0.641347
SYNE2	23224	__UNKNOWN__	__UNKNOWN__	14	64661160	64661160	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64661160A>C	ENST00000554584.1	+	99	17896				SYNE2_ENST00000344113.4_Intron|SYNE2_ENST00000358025.3_Intron|SYNE2_ENST00000357395.3_Intron|SYNE2_ENST00000394768.2_Intron|SYNE2_ENST00000555002.1_Intron|ESR2_ENST00000542956.1_Intron			Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	NA		NA			centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		acaagcacacaccaccatgcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654	23224			17084	protein-coding gene	gene with protein product	nuclear envelope spectrin repeat-2, nucleus and actin connecting element	608442			NA	10231032, 10878022	Standard	NM_182914	NM_182910	NA	Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000554584.1:c.17845+3322A>C	chr14.hg19:g.64661160A>C		NA	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	hg19		0.02	-0.184214	CACxCCA	COVERED																																																																																			NOVEL	SYNE2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000411905.1	7	2.706608	KEEP	0	0	0	9	246	AA	0.99254	0.420319	0		+	13	60	434	0	0	44.98286	5	60	154	39	ENST00000554584.1	0.722222	0.423478
MTHFD1	4522	__UNKNOWN__	__UNKNOWN__	14	64913512	64913512	__UNKNOWN__	Intron	SNP	G	G	A	rs370454598	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64913512G>A	ENST00000545908.1	+	23	2575				MTHFD1_ENST00000216605.8_Intron|CTD-2555O16.2_ENST00000556640.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	NA		NA			folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	cacccgcctcggcctcccaaa	0.522		NA											G|||	4	0.000798722	0.003	0.0	5008	,	,	NA	17589	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	4522	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD	NA	3053686, 2786332	Standard		NM_005956	NA	Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2347-1423G>A	chr14.hg19:g.64913512G>A		NA	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	hg19		0.02	-0.271919	CTCxGCC	COVERED																																																																																			NOVEL	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000412167.1	6	3.309148	KEEP	0	0	0	11	322	GG	0.993072	0.712346	0		+	4	60	121	0	0	9.09232	23	60	769	58	ENST00000545908.1	0.148148	0.717315
MTHFD1	4522	__UNKNOWN__	__UNKNOWN__	14	64915758	64915758	__UNKNOWN__	Intron	SNP	T	T	C	rs368148978		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64915758T>C	ENST00000545908.1	+	24	2676				MTHFD1_ENST00000216605.8_Intron			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	NA		NA			folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	acctcgtgattctcccacctc	0.498		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17936	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	4522	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD	NA	3053686, 2786332	Standard		NM_005956	NA	Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2448-405T>C	chr14.hg19:g.64915758T>C		NA	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	hg19		0.02	-0.201667	GATxCTC	COVERED																																																																																			NOVEL	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000412167.1	9	3.608303	KEEP	3	0	0	12	319	TT	0.993634	0.487421	0		+	3	59	101	0	0	7.792773	18	60	515	58	ENST00000545908.1	0.142857	0.490544
ZBTB25	7597	__UNKNOWN__	__UNKNOWN__	14	64947035	64947035	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:64947035C>T	ENST00000555424.1	-	2	256				ZBTB25_ENST00000555220.1_Intron|ZBTB25_ENST00000608382.1_3'UTR			P24278	ZBT25_HUMAN	zinc finger and BTB domain containing 25	NA		NA			gene expression (GO:0010467)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|skin(2)	10				all cancers(60;0.00865)|OV - Ovarian serous cystadenocarcinoma(108;0.0102)|BRCA - Breast invasive adenocarcinoma(234;0.0469)		agcaagactccatctcaaaaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X16576	CCDS9765.1	14q23-q24	2013-01-08	2005-05-22	2005-05-22	ENSG00000089775	ENSG00000089775	7597		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	13112	protein-coding gene	gene with protein product		194541	zinc finger protein 46 (KUP), chromosome 14 open reading frame 51	ZNF46, C14orf51	NA		Standard	NM_006977	NM_006977	NA	Approved	KUP	uc001xhf.3	P24278	OTTHUMG00000141310	ENST00000555424.1:c.256+6796G>A	chr14.hg19:g.64947035C>T		NA	B3KUX6|Q8IYH9	hg19		0.02	-0.342085	CTCxATC	COVERED																																																																																			NOVEL	ZBTB25-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000414209.1	1	2.640019	KEEP	3	1	26	18	530	CC	0.999366	0.865197	0		-	3	40	93	0	0	6.865123	20	60	655	60	ENST00000555424.1	0.130435	0.865745
PPP1R36	145376	__UNKNOWN__	__UNKNOWN__	14	65023389	65023389	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65023389T>G	ENST00000298705.1	+	3	278				RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	NA		NA			negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)				NA						ctacttgggatgctgaggtgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807	145376		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	20097	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 50	C14orf50	NA		Standard	NM_172365	NM_172365	NA	Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.182+3810T>G	chr14.hg19:g.65023389T>G		NA	Q6NTH6	hg19	CCDS9767.1	0.02	-0.131357	GGAxGCT	COVERED																																																																																			NOVEL	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280667.1	3	2.705403	KEEP	0	0	0	9	232	TT	0.99254	0.227464	0		+	5	60	172	0	0	15.830835	8	60	207	31	ENST00000298705.1	0.384615	0.229173
PPP1R36	145376	__UNKNOWN__	__UNKNOWN__	14	65054742	65054742	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65054742A>G	ENST00000298705.1	+	11	986				RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	NA		NA			negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)				NA						gattacaggcatgagccactg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807	145376		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	20097	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 50	C14orf50	NA		Standard	NM_172365	NM_172365	NA	Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.891-80A>G	chr14.hg19:g.65054742A>G		NA	Q6NTH6	hg19	CCDS9767.1	0.02	-0.377127	GGCxTGA	COVERED																																																																																			NOVEL	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280667.1	9	4.944065	KEEP	0	1	21	24	661	AA	0.999931	0.909006	0		+	3	60	103	0	0	7.140116	36	60	1064	88	ENST00000298705.1	0.076923	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	65601200	65601200	__UNKNOWN__	IGR	SNP	C	C	T	rs552861124		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65601200C>T			NA	NA				RNU2-14P (9940 upstream) : CTD-2509G16.2 (78410 downstream)						NA		NA									NA						ccgaggcgggcagatcatgag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.65601200C>T		NA		hg19		0.02	-0.184212	GGGxAGA	COVERED																																																																																			NOVEL					0			4	3.008277	KEEP	2	0	0	10	297	CC	0.99254	0.420319	0			3	60	93	0	0	7.060968	17	60	581	45		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	65715424	65715424	__UNKNOWN__	IGR	SNP	A	A	G	rs61987801	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65715424A>G			NA	NA				CTD-2509G16.2 (26359 upstream) : CTD-2509G16.5 (4994 downstream)						NA		NA									NA						cagcactttgagaggccgagg	0.468		NA											G|||	2183	0.435903	0.4871	0.3401	5008	,	,	NA	18525	0.6022	NA	0.2266	False	NA	,,,	NA	NA	NA	2504	0.4785	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.65715424A>G		NA		hg19		0.02	-0.210516	TTGxGAG	COVERED																																																																																			NOVEL					0			12	3.910645	KEEP	6	0	0	13	373	AA	0.993072	0.518544	0			3	60	105	0	0	8.191872	18	60	551	56		0.142857	0.522161
CTD-2509G16.5	0	__UNKNOWN__	__UNKNOWN__	14	65732038	65732038	__UNKNOWN__	lincRNA	SNP	G	G	A	rs551042204	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65732038G>A	ENST00000553754.1	-	0	368										NA		NA									NA						cacccgcctcggcctcccaaa	0.473		NA											g|||	3	0.000599042	0.0023	0.0	5008	,	,	NA	17312	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000553754.1:	chr14.hg19:g.65732038G>A		NA		hg19		0.02	-0.157883	CTCxGCC	COVERED																																																																																			NOVEL	CTD-2509G16.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000412041.1	5	3.008877	KEEP	0	0	0	10	308	GG	0.992708	0.320453	0		-	3	60	87	0	0	6.69234	14	60	457	38	ENST00000553754.1	0.176471	0.322807
CTD-2509G16.5	0	__UNKNOWN__	__UNKNOWN__	14	65733748	65733748	__UNKNOWN__	lincRNA	SNP	C	C	T	rs59867793|rs71126722|rs61987805	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65733748C>T	ENST00000553754.1	-	0	368										NA		NA									NA						Cctttctttccttctttcttt	0.348		NA											N|||	328	0.0654952	0.0348	0.1369	5008	,	,	NA	16304	0.003	NA	0.1093	False	NA	,,,	NA	NA	NA	2504	0.0757	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000553754.1:	chr14.hg19:g.65733748C>T		NA		hg19		0.02	1.347396	TTCxTTC	COVERED																																																																																			NOVEL	CTD-2509G16.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000412041.1	8	3.797038	KEEP	1	3	86	43	1303	CC	1	0.99993	0		-	5	60	161	2	1	10.033132	88	60	3008	203	ENST00000553754.1	0.053763	0.99993
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	65842580	65842580	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65842580G>A			NA	NA				MIR4708 (40679 upstream) : FUT8 (34729 downstream)						NA		NA									NA						aggccaaggcgggcagatcac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.65842580G>A		NA		hg19		0.02	-0.175435	GGCxGGC	COVERED																																																																																			NOVEL					0			7	2.406986	KEEP	3	0	0	8	243	GG	0.99257	0.384528	0			3	60	94	0	0	7.391774	14	60	443	48		0.176471	0.387407
FUT8	2530	__UNKNOWN__	__UNKNOWN__	14	65975077	65975077	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:65975077T>C	ENST00000358307.2	+	2	305				FUT8_ENST00000557164.1_Intron|FUT8_ENST00000394586.2_Intron|FUT8_ENST00000394585.1_Intron|FUT8_ENST00000360689.5_Intron			Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	NA		NA			cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		cgtgagccactgtgcccggcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170	2530		Fucosyltransferases	4019	protein-coding gene	gene with protein product		602589			NA	9368041	Standard	NM_004480	NM_178155	NA	Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000358307.2:c.-287+52641T>C	chr14.hg19:g.65975077T>C		NA	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	hg19		0.02	-0.175421	CACxGTG	COVERED																																																																																			NOVEL	FUT8-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000286407.1	6	3.007975	KEEP	0	0	0	10	281	TT	0.992708	0.384582	0		+	3	60	100	0	0	7.833289	16	60	478	42	ENST00000358307.2	0.157895	0.387407
FUT8	2530	__UNKNOWN__	__UNKNOWN__	14	66078621	66078621	__UNKNOWN__	Intron	SNP	T	T	C	rs1140001		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:66078621T>C	ENST00000358307.2	+	3	305				FUT8_ENST00000557164.1_Intron|FUT8_ENST00000394586.2_Intron|FUT8_ENST00000394585.1_Intron|FUT8_ENST00000360689.5_Intron			Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	NA		NA			cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		tcaggtgatctgcctgcctca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170	2530		Fucosyltransferases	4019	protein-coding gene	gene with protein product		602589			NA	9368041	Standard	NM_004480	NM_178155	NA	Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000358307.2:c.-286-4075T>C	chr14.hg19:g.66078621T>C		NA	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	hg19		0.02	-0.140336	ATCxGCC	UNCOVERED																																																																																			NOVEL	FUT8-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000286407.1	6	2.706703	KEEP	3	0	0	9	250	TT	0	0	0		+	3	60	96	0	0	7.772207	12	60	368	36	ENST00000358307.2	0.2	0.260965
RAD51B	5890	__UNKNOWN__	__UNKNOWN__	14	68450906	68450906	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:68450906T>G	ENST00000471583.1	+	7	804				RAD51B_ENST00000487270.1_Intron|RAD51B_ENST00000488612.1_Intron|RAD51B_ENST00000487861.1_Intron|RAD51B_ENST00000390683.3_Intron|RAD51B_ENST00000469165.2_Intron	NM_133510.3	NP_598194.1	O15315	RA51B_HUMAN	RAD51 paralog B	NA		NA			ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						tgcctgcctctgcctcccaaa	0.478		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185	5890			9822	protein-coding gene	gene with protein product		602948	RAD51 (S. cerevisiae)-like 1, RAD51-like 1 (S. cerevisiae), RAD51 homolog B (S. cerevisiae)	RAD51L1	NA	6261043, 9207106	Standard		NM_002877	NA	Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000471583.1:c.756+96985T>G	chr14.hg19:g.68450906T>G		NA	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	hg19	CCDS9790.1	0.02	-0.25437	CTCxGCC	COVERED																																																																																			NOVEL	RAD51B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349062.1	10	2.707195	KEEP	2	0	0	9	254	AT	0.99254	0.663536	0		+	3	60	99	0	0	7.348974	22	60	676	60	ENST00000471583.1	0.12	0.668523
RAD51B	5890	__UNKNOWN__	__UNKNOWN__	14	68504206	68504206	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:68504206A>G	ENST00000471583.1	+	7	804				RAD51B_ENST00000487270.1_Intron|RAD51B_ENST00000488612.1_Intron|RAD51B_ENST00000487861.1_Intron|RAD51B_ENST00000390683.3_Intron|RAD51B_ENST00000469165.2_Intron	NM_133510.3	NP_598194.1	O15315	RA51B_HUMAN	RAD51 paralog B	NA		NA			ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						aaagtgctggaattacaggtg	0.443		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185	5890			9822	protein-coding gene	gene with protein product		602948	RAD51 (S. cerevisiae)-like 1, RAD51-like 1 (S. cerevisiae), RAD51 homolog B (S. cerevisiae)	RAD51L1	NA	6261043, 9207106	Standard		NM_002877	NA	Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000471583.1:c.756+150285A>G	chr14.hg19:g.68504206A>G		NA	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	hg19	CCDS9790.1	0.02	-0.166645	TGGxATT	COVERED																																																																																			NOVEL	RAD51B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000349062.1	10	3.909449	KEEP	2	0	0	13	351	AA	0.994391	0.351961	0		+	5	60	180	0	0	15.767781	13	60	379	48	ENST00000471583.1	0.277778	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	69335120	69335120	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:69335120G>A			NA	NA				RN7SL224P (22348 upstream) : ACTN1 (5739 downstream)						NA		NA									NA						ccaggagttcgagaccagcct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.69335120G>A		NA		hg19		0.02	-0.157884	TTCxAGA	COVERED																																																																																			NOVEL					0			7	4.512623	KEEP	3	0	0	15	439	GG	0.994391	0.320996	0			3	60	86	0	0	6.510879	15	60	479	43		0.166667	0.322807
EXD2	55218	__UNKNOWN__	__UNKNOWN__	14	69680002	69680002	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:69680002C>T	ENST00000409018.3	+	2	461				EXD2_ENST00000492815.1_Intron|EXD2_ENST00000312994.5_Intron|EXD2_ENST00000409242.1_Intron|EXD2_ENST00000409675.1_Intron|EXD2_ENST00000409014.1_Intron|RP11-363J20.1_ENST00000554898.1_lincRNA|EXD2_ENST00000409949.1_Intron|EXD2_ENST00000449989.1_Intron	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	NA		NA					3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						caggctggtcccaaactccta	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177	55218			20217	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 114, exonuclease 3'-5' domain-like 2	C14orf114, EXDL2	NA		Standard		NM_018199	NA	Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.333+3482C>T	chr14.hg19:g.69680002C>T		NA	B4DIH6|G5E947|Q6AWB6|Q8N3D3	hg19	CCDS53902.1	0.02	-0.192991	GTCxCAA	COVERED																																																																																			NOVEL	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335504.1	4	4.212706	KEEP	0	0	0	14	434	CC	0.995343	0.455625	0		+	3	60	92	0	0	6.961023	17	60	565	52	ENST00000409018.3	0.15	0.457757
EXD2	55218	__UNKNOWN__	__UNKNOWN__	14	69681833	69681833	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:69681833C>T	ENST00000409018.3	+	2	461				EXD2_ENST00000492815.1_Intron|EXD2_ENST00000312994.5_Intron|EXD2_ENST00000409242.1_Intron|EXD2_ENST00000409675.1_Intron|EXD2_ENST00000409014.1_Intron|EXD2_ENST00000409949.1_Intron|EXD2_ENST00000449989.1_Intron	NM_001193361.1	NP_001180290.1	Q9NVH0	EXD2_HUMAN	exonuclease 3'-5' domain containing 2	NA		NA					3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|urinary_tract(1)	14						ggtgaaaccccgtctctacta	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001600	CCDS9793.1, CCDS53902.1	14q24.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000081177	ENSG00000081177	55218			20217	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 114, exonuclease 3'-5' domain-like 2	C14orf114, EXDL2	NA		Standard		NM_018199	NA	Approved	FLJ10738	uc001xkv.3	Q9NVH0	OTTHUMG00000154496	ENST00000409018.3:c.333+5313C>T	chr14.hg19:g.69681833C>T		NA	B4DIH6|G5E947|Q6AWB6|Q8N3D3	hg19	CCDS53902.1	0.02	-0.105242	CCCxGTC	UNCOVERED																																																																																			NOVEL	EXD2-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335504.1	7	2.405687	KEEP	1	0	0	8	218	CC	0.99257	0.138793	0		+	3	60	86	0	0	7.101214	9	60	287	25	ENST00000409018.3	0.25	0.139832
ERH	2079	__UNKNOWN__	__UNKNOWN__	14	69855996	69855996	__UNKNOWN__	Intron	SNP	G	G	A	rs141629507	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:69855996G>A	ENST00000557016.1	-	3	485				ERH_ENST00000555373.1_Intron|ERH_ENST00000216520.6_Intron	NM_004450.2	NP_004441.1	P84090	ERH_HUMAN	enhancer of rudimentary homolog (Drosophila)	NA		NA			cell cycle (GO:0007049)|nucleobase-containing compound metabolic process (GO:0006139)|osteoblast differentiation (GO:0001649)|pyrimidine nucleoside metabolic process (GO:0006213)	membrane (GO:0016020)|midbody (GO:0030496)	poly(A) RNA binding (GO:0044822)				NA				all cancers(60;0.00365)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0507)		cacccgcgtcggcctcccaaa	0.488		NA											G|||	26	0.00519169	0.0	0.0	5008	,	,	NA	16901	0.0258	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014301	CCDS9794.1	14q24.1	2011-05-18	2001-11-28		ENSG00000100632	ENSG00000100632	2079			3447	protein-coding gene	gene with protein product		601191	enhancer of rudimentary (Drosophila) homolog		NA	8786099, 9074495	Standard	NM_004450	NM_004450	NA	Approved	DROER	uc001xlc.2	P84090		ENST00000557016.1:c.92-2196C>T	chr14.hg19:g.69855996G>A		NA	B2R5H2|P70659|Q14259	hg19	CCDS9794.1	0.02	-0.114021	GTCxGCC	UNCOVERED																																																																																			NOVEL	ERH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412990.1	8	3.609762	KEEP	2	0	0	12	357	GG	0.993634	0.161432	0		-	3	60	84	0	0	7.343219	6	60	186	37	ENST00000557016.1	0.333333	0.162467
SLC39A9	55334	__UNKNOWN__	__UNKNOWN__	14	69874335	69874335	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:69874335T>C	ENST00000556605.1	+	1	776				SLC39A9_ENST00000031146.4_Intron|SLC39A9_ENST00000555245.1_Intron|SLC39A9_ENST00000557046.1_Intron|SLC39A9_ENST00000336643.5_Intron	NM_001252150.1	NP_001239079.1	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	NA		NA			zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		cgtgagccactgcgcccggcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364	55334		Solute carriers	20182	protein-coding gene	gene with protein product		NA			NA		Standard	NM_018375	NM_018375	NA	Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000556605.1:c.96+8153T>C	chr14.hg19:g.69874335T>C		NA	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	hg19	CCDS58327.1	0.02	-0.289397	CACxGCG	COVERED																																																																																			NOVEL	SLC39A9-004	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412445.1	5	2.7065	KEEP	1	0	0	9	241	TT	0.99254	0.755211	0		+	3	60	107	0	0	7.852216	28	60	827	62	ENST00000556605.1	0.096774	0.760887
SLC39A9	55334	__UNKNOWN__	__UNKNOWN__	14	69926512	69926512	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:69926512C>G	ENST00000556605.1	+	7	1373				SLC39A9_ENST00000031146.4_3'UTR|SLC39A9_ENST00000336643.5_3'UTR	NM_001252150.1	NP_001239079.1	Q9NUM3	S39A9_HUMAN	solute carrier family 39, member 9	NA		NA			zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|skin(1)|stomach(1)	14				all cancers(60;0.00299)|BRCA - Breast invasive adenocarcinoma(234;0.0145)|OV - Ovarian serous cystadenocarcinoma(108;0.0373)		CCACAATTTGCTGCTTACTGC	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9795.1, CCDS58327.1, CCDS58328.1	14q24.1	2013-07-17	2013-07-17			ENSG00000029364	55334		Solute carriers	20182	protein-coding gene	gene with protein product		NA			NA		Standard	NM_018375	NM_018375	NA	Approved	FLJ11274	uc001xle.3	Q9NUM3		ENST00000556605.1:c.694-1902C>G	chr14.hg19:g.69926512C>G		NA	G3V5J8|Q53HN3|Q5MJQ0|Q6P2Q1|Q86WY2	hg19	CCDS58327.1	0.02	1.874187	TTGxTGC	COVERED																																																																																			NOVEL	SLC39A9-004	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412445.1	2	6.920734	KEEP	0	0	0	23	712	CC	0.999892	0.996616	0		+	19	60	635	0	0	54.791729	51	60	1751	135	ENST00000556605.1	0.271429	0.996724
SRSF5	6430	__UNKNOWN__	__UNKNOWN__	14	70197370	70197370	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:70197370T>C	ENST00000553521.1	+	1	292							Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						catgagccactgcgcccggcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650	6430		Serine/arginine-rich splicing factors, RNA binding motif (RRM) containing	10787	protein-coding gene	gene with protein product	SR splicing factor 5	600914	splicing factor, arginine/serine-rich 5	SFRS5	NA	7686911, 20516191	Standard	NM_001039465	XM_005267998	NA	Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.-1162+3462T>C	chr14.hg19:g.70197370T>C		NA	O14797|Q16662|Q49AD6|Q6FGE0	hg19	CCDS32109.1	0.02	-0.210505	CACxGCG	COVERED																																																																																			NOVEL	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412456.1	5	3.307573	KEEP	1	0	0	11	298	TT	0.993072	0.518544	0		+	3	60	95	0	0	7.127979	19	60	581	52	ENST00000553521.1	0.136364	0.522161
SRSF5	6430	__UNKNOWN__	__UNKNOWN__	14	70197372	70197372	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:70197372C>T	ENST00000553521.1	+	1	292							Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						tgagccactgcgcccggcctt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650	6430		Serine/arginine-rich splicing factors, RNA binding motif (RRM) containing	10787	protein-coding gene	gene with protein product	SR splicing factor 5	600914	splicing factor, arginine/serine-rich 5	SFRS5	NA	7686911, 20516191	Standard	NM_001039465	XM_005267998	NA	Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.-1162+3464C>T	chr14.hg19:g.70197372C>T		NA	O14797|Q16662|Q49AD6|Q6FGE0	hg19	CCDS32109.1	0.02	-0.210521	CTGxGCC	COVERED																																																																																			NOVEL	SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412456.1	5	3.309076	KEEP	1	0	0	11	322	CC	0.993072	0.518544	0		+	3	60	89	0	0	6.527643	19	60	614	52	ENST00000553521.1	0.136364	0.522161
SLC8A3	6547	__UNKNOWN__	__UNKNOWN__	14	70577648	70577648	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:70577648C>T	ENST00000381269.2	-	3	2538				SLC8A3_ENST00000356921.2_Intron|SLC8A3_ENST00000357887.3_Intron|SLC8A3_ENST00000534137.1_Intron|SLC8A3_ENST00000528359.1_Intron	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	NA		NA			blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		ctgcctgcctcggcctcccaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678	6547		Solute carriers	11070	protein-coding gene	gene with protein product		607991			NA	8798769	Standard		XM_005268017	NA	Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.1785-49992G>A	chr14.hg19:g.70577648C>T		NA	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	hg19	CCDS35498.1	0.02	-0.157853	CCTxGGC	COVERED																																																																																			NOVEL	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390736.1	4	3.910559	KEEP	4	0	0	13	391	CC	0.993072	0.32057	0		-	3	60	88	0	0	6.879482	13	60	421	50	ENST00000381269.2	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	72281479	72281479	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:72281479T>C			NA	NA				SIPA1L1 (73533 upstream) : RP6-114E22.1 (33843 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.72281479T>C		NA		hg19		0.02	-0.175403	AGGxGTG	COVERED																																																																																			NOVEL					0			10	3.308091	KEEP	2	0	0	11	300	TT	0.993072	0.384723	0			3	60	102	0	0	8.110055	15	60	445	48		0.166667	0.387407
RGS6	9628	__UNKNOWN__	__UNKNOWN__	14	72753530	72753530	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:72753530T>C	ENST00000355512.6	+	2	84				RGS6_ENST00000343854.6_Intron|RGS6_ENST00000407322.4_Intron|RGS6_ENST00000404301.2_Intron|RGS6_ENST00000556437.1_Intron|RGS6_ENST00000406236.4_Intron|RGS6_ENST00000553525.1_Intron|RGS6_ENST00000555571.1_Intron|RGS6_ENST00000402788.2_Intron|RGS6_ENST00000553530.1_Intron			P49758	RGS6_HUMAN	regulator of G-protein signaling 6	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		ttcactctgttgcccaggctg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(143;1926 2468 21071 48641)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732	9628		Regulators of G-protein signaling	10002	protein-coding gene	gene with protein product		603894	regulator of G-protein signalling 6		NA	10083744, 14734556	Standard		NM_004296	NA	Approved		uc010ttn.2	P49758		ENST00000355512.6:c.85-65273T>C	chr14.hg19:g.72753530T>C		NA	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	hg19		0.02	-0.175405	TGTxGCC	COVERED																																																																																			NOVEL	RGS6-006	NOVEL	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000413036.1	8	2.402815	KEEP	0	0	0	8	208	TT	0.99257	0.384528	0		+	3	60	85	0	0	6.672792	12	60	356	38	ENST00000355512.6	0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	73515416	73515416	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:73515416C>G			NA	NA				RN7SL586P (7794 upstream) : RP11-109N23.4 (9722 downstream)						NA		NA									NA						tttcactcttcttgcccaggc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.73515416C>G		NA		hg19		0.02	-0.254392	CTTxTTG	COVERED																																																																																			NOVEL					0			6	2.40714	KEEP	0	0	0	8	244	CC	0.99257	0.688515	0			3	60	100	1	0	7.342271	24	60	782	57		0.111111	0.693668
RBM25	58517	__UNKNOWN__	__UNKNOWN__	14	73532514	73532514	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:73532514T>C	ENST00000261973.7	+	2	270				RBM25_ENST00000525321.1_Intron|RBM25_ENST00000540173.1_Intron|RBM25_ENST00000527432.1_Intron|RBM25_ENST00000526754.1_Intron	NM_021239.2	NP_067062.1	P49756	RBM25_HUMAN	RNA binding motif protein 25	NA		NA			mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of apoptotic process (GO:0042981)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(6)|ovary(2)|pancreas(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00362)|OV - Ovarian serous cystadenocarcinoma(108;0.0688)		ctgcccgccttggcctcccaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX647116	CCDS32113.1	14q24.3	2013-02-12	2004-04-23	2004-04-29	ENSG00000119707	ENSG00000119707	58517		RNA binding motif (RRM) containing	23244	protein-coding gene	gene with protein product	functional spliceosome-associated protein 94	612427	RNA-binding region (RNP1, RRM) containing 7	RNPC7	NA	9847074, 7596406	Standard	XM_027330	NM_021239	NA	Approved	S164, fSAP94, NET52, Snu71	uc001xno.3	P49756	OTTHUMG00000167540	ENST00000261973.7:c.-15-5821T>C	chr14.hg19:g.73532514T>C		NA	A0PJL9|B2RNA8|B3KT03|Q2TA72|Q5XJ17|Q6P665|Q9H6A1|Q9UEQ5|Q9UIE9	hg19	CCDS32113.1	0.02	-0.140327	CCTxGGC	UNCOVERED																																																																																			NOVEL	RBM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394966.1	4	2.405408	KEEP	3	0	0	8	214	TT	0	0	0		+	3	60	89	0	0	7.173125	11	60	322	37	ENST00000261973.7	0.214286	0.292001
PSEN1	5663	__UNKNOWN__	__UNKNOWN__	14	73655537	73655537	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:73655537T>C	ENST00000406768.1	+	4	2094				PSEN1_ENST00000557511.1_Intron|PSEN1_ENST00000324501.5_Intron|PSEN1_ENST00000357710.4_Intron|PSEN1_ENST00000261970.3_Intron|PSEN1_ENST00000344094.3_Intron|PSEN1_ENST00000394164.1_Intron			P49768	PSN1_HUMAN	presenilin 1	NA		NA			activation of MAPKK activity (GO:0000186)|amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|autophagic vacuole assembly (GO:0000045)|beta-amyloid formation (GO:0034205)|beta-amyloid metabolic process (GO:0050435)|blood vessel development (GO:0001568)|brain morphogenesis (GO:0048854)|Cajal-Retzius cell differentiation (GO:0021870)|calcium ion transmembrane transport (GO:0070588)|canonical Wnt signaling pathway (GO:0060070)|cell fate specification (GO:0001708)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex cell migration (GO:0021795)|choline transport (GO:0015871)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|L-glutamate transport (GO:0015813)|membrane protein ectodomain proteolysis (GO:0006509)|memory (GO:0007613)|mitochondrial transport (GO:0006839)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of axonogenesis (GO:0050771)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of receptor recycling (GO:0001921)|post-embryonic development (GO:0009791)|protein glycosylation (GO:0006486)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of phosphorylation (GO:0042325)|regulation of protein binding (GO:0043393)|regulation of resting membrane potential (GO:0060075)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)|skeletal system morphogenesis (GO:0048705)|skin morphogenesis (GO:0043589)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|somitogenesis (GO:0001756)|synaptic vesicle targeting (GO:0016080)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary rootlet (GO:0035253)|cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|gamma-secretase complex (GO:0070765)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)|perinuclear region of cytoplasm (GO:0048471)|rough endoplasmic reticulum (GO:0005791)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|calcium channel activity (GO:0005262)|endopeptidase activity (GO:0004175)|PDZ domain binding (GO:0030165)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.075)		cactctgtcatccaggctgga	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ008005	CCDS9812.1, CCDS9813.1	14q24.3	2014-09-17	2008-07-28		ENSG00000080815	ENSG00000080815	5663			9508	protein-coding gene	gene with protein product		104311	Alzheimer disease 3	AD3	NA	1411576	Standard		NM_007318	NA	Approved	FAD, S182, PS1	uc001xnr.3	P49768	OTTHUMG00000141279	ENST00000406768.1:c.272+1909T>C	chr14.hg19:g.73655537T>C		NA	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	hg19		0.02	-0.078934	TCAxCCA	UNCOVERED																																																																																			NOVEL	PSEN1-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000280504.3	5	3.008038	KEEP	0	0	0	10	284	TT	0.992708	0.076772	0		+	2	60	70	0	0	6.493136	3	60	86	29	ENST00000406768.1	0.4	0.077336
HEATR4	399671	__UNKNOWN__	__UNKNOWN__	14	73946194	73946194	__UNKNOWN__	Intron	SNP	G	G	A	rs182540933		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:73946194G>A	ENST00000553558.1	-	18	3166				HEATR4_ENST00000566478.1_Intron|HEATR4_ENST00000334988.2_Intron|HEATR4_ENST00000560393.1_Intron	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	NA		NA								breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		cccaggctggggtgcaatggt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105	399671			16761	protein-coding gene	gene with protein product		NA			NA	15489334	Standard	NM_203309	NM_203309	NA	Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2845-647C>T	chr14.hg19:g.73946194G>A		NA	B7Z7V9|E9KL41	hg19	CCDS9815.2	0.02	-0.166666	TGGxGTG	COVERED																																																																																			NOVEL	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414422.2	11	2.706768	KEEP	0	0	0	9	268	GG	0.99254	0.351306	0		-	3	24	93	0	0	7.210181	15	60	501	40	ENST00000553558.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	74064035	74064035	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:74064035G>A			NA	NA				ACOT4 (835 upstream) : RP3-414A15.10 (19376 downstream)						NA		NA									NA						tgatccacccgcctcggcctc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.74064035G>A		NA		hg19		0.02	-0.297986	CCCxCCT	COVERED																																																																																			NOVEL					0			11	4.210058	KEEP	7	0	0	14	390	GG	0.992708	0.775364	0			3	60	92	0	0	6.311563	29	60	905	73		0.09375	0.78106
PTGR2	145482	__UNKNOWN__	__UNKNOWN__	14	74353180	74353180	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:74353180G>A	ENST00000555661.1	+	0	3501				RP5-1021I20.4_ENST00000556551.2_Intron			Q8N8N7	PTGR2_HUMAN	prostaglandin reductase 2	NA		NA			prostaglandin metabolic process (GO:0006693)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	13-prostaglandin reductase activity (GO:0036132)|15-oxoprostaglandin 13-oxidase activity (GO:0047522)			NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(2)	9					Indomethacin(DB00328)	TTTGATAAATGTTTAAGCAGT	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(98;1155 1417 16452 47043 47872)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096410	CCDS9820.1	14q24.1-q24.2	2008-06-04	2008-06-02	2008-06-03		ENSG00000140043	145482			20149	protein-coding gene	gene with protein product		608642	zinc binding alcohol dehydrogenase domain containing 1	ZADH1	NA	17449869	Standard		NM_152444	NA	Approved	FLJ39091	uc001xow.3	Q8N8N7		ENST00000555661.1:c.*2300G>A	chr14.hg19:g.74353180G>A		NA	Q3L8A4|Q6MZH8	hg19	CCDS9820.1	0.02	1.365899	AATxTTT	COVERED																																																																																			NOVEL	PTGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412575.1	1	6.918775	KEEP	0	0	0	23	668	GG	0.999892	0.987837	0		+	11	60	305	0	0	23.428483	48	60	1612	109	ENST00000555661.1	0.186441	0.987943
ZNF410	57862	__UNKNOWN__	__UNKNOWN__	14	74368399	74368399	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:74368399C>T	ENST00000540593.1	+	5	809				ZNF410_ENST00000555044.1_Intron|ZNF410_ENST00000442160.3_Intron|RP5-1021I20.5_ENST00000554009.1_RNA|RP5-1021I20.4_ENST00000556551.2_Intron|ZNF410_ENST00000324593.6_Intron|ZNF410_ENST00000334521.4_Intron|ZNF410_ENST00000412490.3_Intron	NM_001242927.1	NP_001229856.1	Q86VK4	ZN410_HUMAN	zinc finger protein 410	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.00369)		tttgggtggccgaggcgggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U90919	CCDS9821.1, CCDS55929.1, CCDS55930.1, CCDS55931.1	14q24.3	2013-01-08				ENSG00000119725	57862		Zinc fingers, C2H2-type	20144	protein-coding gene	gene with protein product		NA			NA	12370286	Standard	NM_021188	NM_001242924	NA	Approved	APA1, APA-1	uc010arz.2	Q86VK4		ENST00000540593.1:c.362-2264C>T	chr14.hg19:g.74368399C>T		NA	B4DDV5|B4DR78|O00153|Q9BQ19	hg19	CCDS55931.1	0.02	-0.210513	GGCxGAG	COVERED																																																																																			NOVEL	ZNF410-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412583.1	4	2.405161	KEEP	0	0	0	8	224	CC	0.99257	0.518282	0		+	4	60	116	0	0	9.069857	17	60	573	44	ENST00000540593.1	0.190476	0.522161
COQ6	51004	__UNKNOWN__	__UNKNOWN__	14	74422987	74422987	__UNKNOWN__	Intron	SNP	C	C	T	rs569736386		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:74422987C>T	ENST00000554920.1	+	4	506				COQ6_ENST00000394026.4_Intron|COQ6_ENST00000555552.1_Intron|COQ6_ENST00000334571.2_Intron|COQ6_ENST00000238709.4_Intron			Q9Y2Z9	COQ6_HUMAN	coenzyme Q6 monooxygenase	NA		NA			small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	cell projection (GO:0042995)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(234;0.00337)		gccgagatcacgccactgcac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF132944	CCDS9823.1, CCDS9824.1, CCDS9824.2	14q24.1	2013-05-01	2013-05-01		ENSG00000119723	ENSG00000119723	51004			20233	protein-coding gene	gene with protein product		614647	coenzyme Q6 homolog (yeast), coenzyme Q6 homolog, monooxygenase (yeast), coenzyme Q6 homolog, monooxygenase (S. cerevisiae)		NA	21540551	Standard		NM_182476	NA	Approved	CGI-10	uc001xph.3	Q9Y2Z9	OTTHUMG00000171260	ENST00000554920.1:c.481+356C>T	chr14.hg19:g.74422987C>T		NA	B7Z3K8|Q53GG6|Q86U30|Q96CA1|Q96CK2	hg19		0.02	1.093998	TCAxGCC	COVERED																																																																																			NOVEL	COQ6-019	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000412620.1	8	5.444275	KEEP	10	4	95	52	1506	CC	1	0.999881	0		+	7	60	201	1	0	13.103235	74	60	2411	167	ENST00000554920.1	0.08642	0.999881
ENTPD5	957	__UNKNOWN__	__UNKNOWN__	14	74426463	74426463	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:74426463A>G	ENST00000557325.1	-	16	1552				COQ6_ENST00000394026.4_Intron|COQ6_ENST00000554920.1_Intron|COQ6_ENST00000334571.2_Intron|COQ6_ENST00000238709.4_Intron			O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	NA		NA			'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		agtagagatgaggtttcacca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097	957			3367	protein-coding gene	gene with protein product		603162	proto-oncogene CPH	CD39L4, PCPH	NA	9271669, 9676430	Standard	NM_001249	NM_001249	NA	Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000557325.1:c.1201-207T>C	chr14.hg19:g.74426463A>G		NA	A1L4C5|Q96RX0	hg19		0.02	-0.122797	ATGxGGT	UNCOVERED																																																																																			NOVEL	ENTPD5-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000412635.1	6	2.405657	KEEP	4	0	0	8	216	AA	0	0	0		-	3	40	88	0	0	7.182022	10	60	313	35	ENST00000557325.1	0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	74933921	74933921	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:74933921T>C			NA	NA				SYNDIG1L (41116 upstream) : RP3-449M8.9 (4711 downstream)						NA		NA									NA						cctcccaccttggcctcccaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.74933921T>C		NA		hg19		0.02	-0.131553	CCTxGGC	COVERED																																																																																			NOVEL					0			7	3.308267	KEEP	1	0	0	11	301	TT	0.993072	0.227586	0			3	60	91	0	0	7.373163	11	60	321	40		0.214286	0.229173
NEK9	91754	__UNKNOWN__	__UNKNOWN__	14	75572797	75572797	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:75572797A>G	ENST00000238616.5	-	13	1687					NM_033116.4	NP_149107.4	Q8TD19	NEK9_HUMAN	NIMA-related kinase 9	NA		NA			mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	31				BRCA - Breast invasive adenocarcinoma(234;0.00718)		ggtggctcacacctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY048580	CCDS9839.1	14q24.2	2012-11-15	2012-11-15		ENSG00000119638	ENSG00000119638	91754			18591	protein-coding gene	gene with protein product		609798	NIMA (never in mitosis gene a)- related kinase 9		NA	11864968	Standard	NM_033116	NM_033116	NA	Approved	Nek8, NERCC, DKFZp434D0935, MGC16714	uc001xrl.3	Q8TD19	OTTHUMG00000171768	ENST00000238616.5:c.1529-98T>C	chr14.hg19:g.75572797A>G		NA	Q52LK6|Q8NCN0|Q8TCY4|Q9UPI4|Q9Y6S4|Q9Y6S5|Q9Y6S6	hg19	CCDS9839.1	0.02	-0.420926	CACxCCT	COVERED																																																																																			NOVEL	NEK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415021.1	8	3.635048	KEEP	0	1	31	23	579	AA	0.999931	0.954425	0		-	5	60	169	0	0	12.471295	40	60	1127	92	ENST00000238616.5	0.111111	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	75670113	75670113	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:75670113T>C			NA	NA				RNU4ATAC14P (1241 upstream) : RP11-293M10.1 (35205 downstream)						NA		NA									NA						aatcccagcattttgggaggc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.75670113T>C		NA		hg19		0.02	-0.131568	GCAxTTT	COVERED																																																																																			NOVEL					0			5	2.405875	KEEP	0	0	0	8	216	TT	0.99257	0.22747	0			3	60	93	0	0	7.57292	11	60	335	35		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	75864710	75864710	__UNKNOWN__	IGR	SNP	A	A	G	rs7401950	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:75864710A>G			NA	NA				RP11-293M10.5 (101369 upstream) : RP11-293M10.6 (25675 downstream)						NA		NA									NA						aggctggagtacagtggcgtg	0.428		NA											G|||	1667	0.332867	0.2859	0.3934	5008	,	,	NA	14771	0.4861	NA	0.172	False	NA	,,,	NA	NA	NA	2504	0.3609	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.75864710A>G		NA		hg19		0.02	-0.114014	AGTxCAG	UNCOVERED																																																																																			NOVEL					0			9	2.405301	KEEP	0	0	0	8	209	AA	0.99257	0.16126	0			3	60	98	0	0	8.301327	9	60	262	30		0.25	0.162467
TTLL5	23093	__UNKNOWN__	__UNKNOWN__	14	76170619	76170619	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:76170619T>C	ENST00000557636.1	+	8	800				TTLL5_ENST00000298832.9_Intron|TTLL5_ENST00000286650.5_Intron|TTLL5_ENST00000555422.1_Intron			Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	NA		NA			fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		cagtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685	23093		Tubulin tyrosine ligase-like family	19963	protein-coding gene	gene with protein product		612268	KIAA0998	KIAA0998	NA	15890843	Standard	NM_015072	NM_015072	NA	Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000557636.1:c.586-2742T>C	chr14.hg19:g.76170619T>C		NA	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	hg19		0.02	-0.192593	TCAxGCC	COVERED																																																																																			NOVEL	TTLL5-016	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000414451.1	7	2.405816	KEEP	2	0	0	8	216	TT	0.99257	0.454356	0		+	3	60	103	0	1	8.063776	17	60	465	43	ENST00000557636.1	0.15	0.457757
TTLL5	23093	__UNKNOWN__	__UNKNOWN__	14	76251811	76251811	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:76251811T>C	ENST00000557636.1	+	27	3243				TTLL5_ENST00000298832.9_Intron|TTLL5_ENST00000556893.1_Intron|TTLL5_ENST00000554510.1_Intron			Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	NA		NA			fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		cgtgagccactgcgcccggcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685	23093		Tubulin tyrosine ligase-like family	19963	protein-coding gene	gene with protein product		612268	KIAA0998	KIAA0998	NA	15890843	Standard	NM_015072	NM_015072	NA	Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000557636.1:c.3028+1938T>C	chr14.hg19:g.76251811T>C		NA	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	hg19		0.02	-0.228035	CACxGCG	COVERED																																																																																			NOVEL	TTLL5-016	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000414451.1	2	3.007103	KEEP	1	0	0	10	270	TT	0.992708	0.578679	0		+	3	60	90	0	0	6.628013	19	60	565	52	ENST00000557636.1	0.136364	0.58293
ESRRB	2103	__UNKNOWN__	__UNKNOWN__	14	76882117	76882117	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:76882117C>T	ENST00000556177.1	+	1	59				ESRRB_ENST00000261532.7_Intron|ESRRB_ENST00000380887.2_Intron|ESRRB_ENST00000509242.1_Intron|ESRRB_ENST00000507951.1_Intron			O95718	ERR2_HUMAN	estrogen-related receptor beta	NA		NA			gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		cccaaagtgccgggattacag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715	2103		Nuclear hormone receptors	3473	protein-coding gene	gene with protein product		602167	deafness, autosomal recessive 35	ESRL2, DFNB35	NA	3267207, 9344655, 18179891	Standard		NM_004452	NA	Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000556177.1:c.-14+8178C>T	chr14.hg19:g.76882117C>T		NA	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	hg19		0.02	-0.166649	TGCxGGG	COVERED																																																																																			NOVEL	ESRRB-006	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000414484.1	6	3.008968	KEEP	0	0	0	10	310	CC	0.992708	0.351366	0		+	3	60	92	0	0	7.110437	15	60	495	46	ENST00000556177.1	0.166667	0.353947
ESRRB	2103	__UNKNOWN__	__UNKNOWN__	14	76910651	76910651	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:76910651T>C	ENST00000556177.1	+	2	469				ESRRB_ENST00000261532.7_Intron|ESRRB_ENST00000380887.2_Intron|ESRRB_ENST00000509242.1_Intron|ESRRB_ENST00000507951.1_Intron			O95718	ERR2_HUMAN	estrogen-related receptor beta	NA		NA			gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|trophectodermal cell proliferation (GO:0001834)|trophectodermal cellular morphogenesis (GO:0001831)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(4)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(234;0.0213)		gctgggattataggcgtgagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X51417	CCDS9850.1, CCDS9850.2	14q24.3	2013-01-16				ENSG00000119715	2103		Nuclear hormone receptors	3473	protein-coding gene	gene with protein product		602167	deafness, autosomal recessive 35	ESRL2, DFNB35	NA	3267207, 9344655, 18179891	Standard		NM_004452	NA	Approved	ERR2, ERRbeta, NR3B2, ERRb	uc001xsr.3	O95718		ENST00000556177.1:c.397+4558T>C	chr14.hg19:g.76910651T>C		NA	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	hg19		0.02	-0.166641	TTAxAGG	COVERED																																																																																			NOVEL	ESRRB-006	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000414484.1	6	3.006518	KEEP	0	0	0	10	260	TT	0.992708	0.351366	0		+	3	60	103	0	0	8.133291	16	60	470	43	ENST00000556177.1	0.157895	0.353947
RP11-187O7.3	0	__UNKNOWN__	__UNKNOWN__	14	76995325	76995325	__UNKNOWN__	lincRNA	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:76995325C>A	ENST00000554926.1	-	0	310										NA		NA									NA						tttgcctaggctggtcttgaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554926.1:	chr14.hg19:g.76995325C>A		NA		hg19		0.02	-0.131589	AGGxTGG	COVERED																																																																																			NOVEL	RP11-187O7.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000414485.1	7	2.70826	KEEP	0	0	0	9	283	CC	0.99254	0.227464	0		-	3	60	92	0	0	7.581744	10	60	348	37	ENST00000554926.1	0.230769	0.229173
ANGEL1	23357	__UNKNOWN__	__UNKNOWN__	14	77271160	77271160	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:77271160C>T	ENST00000251089.2	-	6	1493					NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	NA		NA								breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	22			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0285)		cgagaccagcctggccaacat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111169	CCDS9852.1	14q24.3	2014-06-17		2005-08-04	ENSG00000013523	ENSG00000013523	23357			19961	protein-coding gene	gene with protein product		NA		KIAA0759	NA	11943475	Standard	NM_015305	NM_015305	NA	Approved	Ccr4e	uc001xsv.3	Q9UNK9	OTTHUMG00000171494	ENST00000251089.2:c.1381-905G>A	chr14.hg19:g.77271160C>T		NA	B4DWL7|O94859|Q8NCS9	hg19	CCDS9852.1	0.02	-0.052636	AGCxTGG	UNCOVERED																																																																																			NOVEL	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413712.2	1	2.707533	KEEP	1	0	0	9	269	CC	0.99257	0.036492	0		-	2	60	66	0	0	6.349948	2	60	68	19	ENST00000251089.2	0.5	0.036766
RP11-7F17.4	0	__UNKNOWN__	__UNKNOWN__	14	77543209	77543209	__UNKNOWN__	lincRNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:77543209T>G	ENST00000554043.1	-	0	219										NA		NA									NA						agtggctcactcctgtaatcc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554043.1:	chr14.hg19:g.77543209T>G		NA		hg19		0.02	-0.254345	CACxCCT	COVERED																																																																																			NOVEL	RP11-7F17.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000414301.1	10	3.0074	KEEP	0	0	0	10	271	TT	0.993072	0.663892	0		-	3	60	98	0	0	7.194832	23	60	690	52	ENST00000554043.1	0.115385	0.668523
SPTLC2	9517	__UNKNOWN__	__UNKNOWN__	14	77973941	77973941	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:77973941T>C	ENST00000216484.2	-	0	6568					NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	tcccaaagtgttgggattaca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	9517	2.3.1.50		11278	protein-coding gene	gene with protein product		605713			NA	8921873, 9363775	Standard	NM_004863	NM_004863	NA	Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.*4686A>G	chr14.hg19:g.77973941T>C		NA	Q16685	hg19	CCDS9865.1	0.02	-0.184176	GTGxTGG	COVERED																																																																																			NOVEL	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414030.1	7	2.405784	KEEP	0	0	0	8	216	TT	0.99257	0.420331	0		-	3	60	99	0	0	7.66106	17	60	501	39	ENST00000216484.2	0.15	0.423478
SPTLC2	9517	__UNKNOWN__	__UNKNOWN__	14	77991661	77991661	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:77991661A>G	ENST00000216484.2	-	10	1497					NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	TGAgccaggcacggtggctca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	9517	2.3.1.50		11278	protein-coding gene	gene with protein product		605713			NA	8921873, 9363775	Standard	NM_004863	NM_004863	NA	Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.1304-3737T>C	chr14.hg19:g.77991661A>G		NA	Q16685	hg19	CCDS9865.1	0.02	-0.122784	GGCxCGG	COVERED																																																																																			NOVEL	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414030.1	2	3.007289	KEEP	1	0	0	10	274	AA	0.99254	0.194847	0		-	3	60	105	0	1	9.001438	9	60	262	34	ENST00000216484.2	0.25	0.196312
SPTLC2	9517	__UNKNOWN__	__UNKNOWN__	14	78060915	78060915	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:78060915G>C	ENST00000216484.2	-	2	521					NM_004863.3	NP_004854.1	O15270	SPTC2_HUMAN	serine palmitoyltransferase, long chain base subunit 2	NA		NA			ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphinganine biosynthetic process (GO:0046511)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(5)	19			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0346)	L-Serine(DB00133)	accagcctgggcaacatggcg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011098	CCDS9865.1	14q24.3	2014-09-17			ENSG00000100596	ENSG00000100596	9517	2.3.1.50		11278	protein-coding gene	gene with protein product		605713			NA	8921873, 9363775	Standard	NM_004863	NM_004863	NA	Approved	KIAA0526, LCB2, LCB2A, hLCB2a	uc001xub.3	O15270		ENST00000216484.2:c.327+2613C>G	chr14.hg19:g.78060915G>C		NA	Q16685	hg19	CCDS9865.1	0.02	-0.096497	TGGxCAA	UNCOVERED																																																																																			NOVEL	SPTLC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414030.1	10	3.610618	KEEP	0	0	0	12	366	GG	0.993634	0.119669	0		-	3	60	97	0	0	8.643365	6	60	208	28	ENST00000216484.2	0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	78503137	78503137	__UNKNOWN__	IGR	SNP	G	G	A	rs535127044		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:78503137G>A			NA	NA				ADCK1 (102840 upstream) : RNA5SP388 (141008 downstream)						NA		NA									NA						gtgcaatggcgcgatcttggc	0.483		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16859	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.78503137G>A		NA		hg19		0.02	-0.07016	GGCxCGA	UNCOVERED																																																																																			NOVEL					0			4	3.309515	KEEP	1	0	0	11	328	GG	0.992708	0.053742	0			3	60	85	0	0	7.632442	5	60	152	25		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	78710044	78710044	__UNKNOWN__	IGR	SNP	G	G	A	rs11626446	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:78710044G>A			NA	NA				RNA5SP388 (65780 upstream) : RP11-332E19.2 (35870 downstream)						NA		NA									NA						GGACCCTGTGGTGAGCGTCCC	0.582		NA											G|||	1001	0.19988	0.0938	0.1643	5008	,	,	NA	19064	0.2292	NA	0.2883	False	NA	,,,	NA	NA	NA	2504	0.2474	NA	NA	NA								NA				0								G		197,1555		8,181,687	90	86	87			3.1	0	14	dbSNP_120	87	1075,2907		148,779,1064	no	intergenic				156,960,1751	AA,AG,GG	NA	26.9965,11.2443,22.1835			78710044	1272,4462	876	1991	2867	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.78710044G>A		NA		hg19		0.02	1.718905	GTGxTGA	COVERED	485	0.22206959706959706	46	0.09349593495934959	74	0.20441988950276244	131	0.229020979020979	234	0.3087071240105541	G	12.23	1.874813	0.33069	0.112443	0.269965	ENSG00000021645	ENST00000330071;ENST00000332068	.	.	.	6.16	3.14	0.36123	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.24323	P	0.9950343	.	.	.	.	.	.	T	0.26643	-1.0097	3	.	.	.	.	10.7098	0.45977	0.0802:0.2946:0.6252:0.0	rs11626446;rs57440596;rs11626446	.	.	.	D	203	.	.	G	+	2	0	NRXN3	77779797	0.024000	0.19004	0.042000	0.18584	0.955000	0.61496	2.594000	0.46189	1.626000	0.50381	0.650000	0.86243	GGT	NOVEL					0			2	2.407378	KEEP	0	0	0	8	253	GG	0.99257	0.98632	0			33	60	963	0	0	92.470182	32	60	1090	108		0.507692	0.993703
CEP128	145508	__UNKNOWN__	__UNKNOWN__	14	81224605	81224605	__UNKNOWN__	Intron	SNP	C	C	G	rs8023233	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:81224605C>G	ENST00000555265.1	-	18	2929				CEP128_ENST00000281129.3_Intron			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	NA		NA				centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	51						gtggctcacgcctgtaatccc	0.458		NA											C|||	1464	0.292332	0.1203	0.3444	5008	,	,	NA	17545	0.3343	NA	0.4056	False	NA	,,,	NA	NA	NA	2504	0.3282	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056756	CCDS32130.1	14q31.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000100629	ENSG00000100629	145508			20359	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 61, chromosome 14 open reading frame 145	C14orf61, C14orf145	NA	21399614	Standard	NM_152446	NM_152446	NA	Approved		uc001xux.2	Q6ZU80		ENST00000555265.1:c.2554-1310G>C	chr14.hg19:g.81224605C>G		NA	B9EK52|Q86X97|Q96ML4	hg19	CCDS32130.1	0.02	-0.22809	ACGxCTG	UNCOVERED																																																																																			NOVEL	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413415.1	8	2.40722	KEEP	4	0	0	8	246	CC	0	0	0		-	5	60	175	0	0	14.552236	19	60	656	58	ENST00000555265.1	0.208333	0.58293
TSHR	7253	__UNKNOWN__	__UNKNOWN__	14	81514269	81514269	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:81514269T>C	ENST00000541158.2	+	3	492				TSHR_ENST00000298171.2_Intron|TSHR_ENST00000342443.6_Intron|TSHR_ENST00000554435.1_Intron|TSHR_ENST00000554263.1_Intron			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	NA		NA			adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	ggattacaggtgtgagccacc	0.488		NA	Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism														NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409	7253		GPCR / Class A : Gonadotropin and TSH receptors	12373	protein-coding gene	gene with protein product		603372			NA	2558651, 2610690	Standard	NM_000369	NM_001018036	NA	Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.171-14223T>C	chr14.hg19:g.81514269T>C		NA	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	hg19	CCDS9872.1	0.02	-0.2104	AGGxGTG	COVERED																																																																																			NOVEL	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413364.1	14	4.209034	KEEP	3	0	0	14	376	TT	0.993634	0.518837	0		+	3	60	97	0	0	7.265822	20	60	575	57	ENST00000541158.2	0.130435	0.522161
RP11-114N19.3	0	__UNKNOWN__	__UNKNOWN__	14	81620456	81620456	__UNKNOWN__	RNA	SNP	G	G	A	rs181642849	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:81620456G>A	ENST00000557775.1	-	0	495										NA		NA									NA						cagcctaagcgacatggcaaa	0.498		NA											G|||	14	0.00279553	0.0	0.0	5008	,	,	NA	15288	0.0129	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000557775.1:	chr14.hg19:g.81620456G>A		NA		hg19		0.02	-0.052618	AGCxACA	UNCOVERED																																																																																			NOVEL	RP11-114N19.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000413374.1	6	2.708058	KEEP	0	0	0	9	276	GG	0.99254	0.036491	0		-	3	60	85	0	0	8.123548	3	60	96	20	ENST00000557775.1	0.5	0.036766
STON2	85439	__UNKNOWN__	__UNKNOWN__	14	81856864	81856864	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:81856864C>T	ENST00000555447.1	-	4	786				STON2_ENST00000267540.2_Intron	NM_001256430.1	NP_001243359.1	Q8WXE9	STON2_HUMAN	stonin 2	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		gctgggatcgcgccactgcac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022	85439			30652	protein-coding gene	gene with protein product	stoned B homolog 2 (Drosophila)	608467			NA	11381094, 11454741	Standard	NM_033104	NM_033104	NA	Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000555447.1:c.373+5373G>A	chr14.hg19:g.81856864C>T		NA	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	hg19	CCDS58332.1	0.02	-0.157878	TCGxGCC	COVERED																																																																																			NOVEL	STON2-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413314.1	11	2.707797	KEEP	0	0	0	9	267	CC	0.99254	0.351306	0		-	3	60	84	0	0	6.572654	12	60	395	38	ENST00000555447.1	0.2	0.353947
SEL1L	6400	__UNKNOWN__	__UNKNOWN__	14	81997947	81997947	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:81997947G>A	ENST00000336735.4	-	1	187				SEL1L_ENST00000555824.1_Intron	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	NA		NA			Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		gtccaggctggagtgcagtgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537	6400			10717	protein-coding gene	gene with protein product	sel-1 suppressor of lin-12-like 1 (C. elegans)	602329	sel-1 (suppressor of lin-12, C.elegans)-like		NA	9417916, 10051412, 16331677	Standard	NM_005065	NM_005065	NA	Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.70+2071C>T	chr14.hg19:g.81997947G>A		NA	Q6UWT6|Q9P1T9|Q9UHK7	hg19	CCDS9876.1	0.02	-0.096485	CTGxAGT	UNCOVERED																																																																																			NOVEL	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413325.1	6	2.407178	KEEP	1	0	0	8	247	GG	0.99257	0.138793	0		-	3	54	84	0	0	7.178202	7	60	229	30	ENST00000336735.4	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	82112565	82112565	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:82112565C>T			NA	NA				RP11-799P8.1 (23160 upstream) : RP11-226P1.2 (81558 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.82112565C>T		NA		hg19		0.02	-0.166671	AGGxGTG	COVERED																																																																																			NOVEL					0			4	3.008566	KEEP	0	0	0	10	294	CC	0.992708	0.351366	0			3	60	92	0	0	7.19182	14	60	460	50		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	84339122	84339122	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:84339122T>C			NA	NA				RNU6ATAC28P (122277 upstream) : RP11-353P15.1 (34093 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.84339122T>C		NA		hg19		0.02	-0.035085	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			2	2.405009	KEEP	2	0	0	8	209	TT	0	0	0			2	46	66	0	0	6.350199	2	60	58	16		0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	86403793	86403793	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:86403793T>C			NA	NA				FLRT2 (308759 upstream) : CTD-2341M24.1 (46496 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.86403793T>C		NA		hg19		0.02	-0.385915	TCAxGCC	COVERED																																																																																			NOVEL					0			10	5.714724	KEEP	1	0	0	19	532	TT	0.999859	0.918042	0			3	53	101	0	0	6.940344	36	60	1078	97		0.076923	0.918171
PTPN21	11099	__UNKNOWN__	__UNKNOWN__	14	88961380	88961380	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:88961380A>G	ENST00000556564.1	-	10	1217				PTPN21_ENST00000328736.3_Intron|PTPN21_ENST00000554628.1_Intron	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						aaaaaaaaaaaaaagaagagt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778	11099		Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor	9651	protein-coding gene	gene with protein product		603271			NA	7519780	Standard		NM_007039	NA	Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.932+1376T>C	chr14.hg19:g.88961380A>G		NA		hg19	CCDS9884.1	0.02	-0.052621	AAAxAAA	UNCOVERED																																																																																			NOVEL	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410303.1	4	3.306649	KEEP	0	0	0	11	284	AA	0.993072	0.036511	0		-	2	60	66	0	0	7.553807	0	0	0	23	ENST00000556564.1	1	0.036766
ZC3H14	79882	__UNKNOWN__	__UNKNOWN__	14	89040855	89040855	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:89040855A>G	ENST00000555755.1	+	7	957				ZC3H14_ENST00000359301.3_Intron|ZC3H14_ENST00000393514.5_Intron|ZC3H14_ENST00000302216.8_Intron|ZC3H14_ENST00000556945.1_Intron|ZC3H14_ENST00000251038.5_Intron|ZC3H14_ENST00000557607.1_Intron|ZC3H14_ENST00000557605.1_3'UTR|ZC3H14_ENST00000336693.4_Intron			Q6PJT7	ZC3HE_HUMAN	zinc finger CCCH-type containing 14	NA		NA				cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(2)	21						ccaaagtgctaggattacaga	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155107	CCDS32133.1, CCDS32134.1, CCDS32135.1, CCDS32136.1, CCDS55938.1	14q31.3	2014-08-12			ENSG00000100722	ENSG00000100722	79882		Zinc fingers, CCCH-type domain containing	20509	protein-coding gene	gene with protein product		613279			NA	10508479	Standard	NM_024824	NM_024824	NA	Approved	FLJ11806, UKp68, NY-REN-37	uc001xww.3	Q6PJT7	OTTHUMG00000170803	ENST00000555755.1:c.862-182A>G	chr14.hg19:g.89040855A>G		NA	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	hg19	CCDS55938.1	0.02	-0.175427	GCTxGGA	COVERED																																																																																			NOVEL	ZC3H14-007	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410397.1	7	2.405916	KEEP	0	0	0	8	220	AA	0.99257	0.384528	0		+	3	60	103	0	0	8.378733	13	60	392	42	ENST00000555755.1	0.1875	0.387407
FOXN3	1112	__UNKNOWN__	__UNKNOWN__	14	89783040	89783040	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:89783040T>C	ENST00000345097.4	-	3	797				FOXN3_ENST00000555658.1_Intron|FOXN3_ENST00000261302.5_Intron|FOXN3_ENST00000557258.1_Intron|FOXN3_ENST00000555353.1_Intron	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	NA		NA			mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						gatggagtcttgctctgtcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254	1112		Forkhead boxes	1928	protein-coding gene	gene with protein product		602628	chromosome 14 open reading frame 116, checkpoint suppressor 1	C14orf116, CHES1	NA	9154802	Standard	NM_005197	NM_005197	NA	Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.680+33975A>G	chr14.hg19:g.89783040T>C		NA	Q96II7|Q9UIE7	hg19	CCDS41977.1	0.02	-0.289433	TCTxGCT	COVERED																																																																																			NOVEL	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410902.2	10	4.801796	KEEP	1	0	0	16	411	TT	0.997832	0.759237	0		-	4	60	120	1	1	8.924156	24	60	722	78	ENST00000345097.4	0.142857	0.760887
FOXN3	1112	__UNKNOWN__	__UNKNOWN__	14	89842362	89842362	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:89842362A>G	ENST00000345097.4	-	3	660				FOXN3_ENST00000261302.5_Intron|FOXN3_ENST00000557258.1_Intron|FOXN3_ENST00000555353.1_Intron	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	NA		NA			mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						cctgacctcaaatgatccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254	1112		Forkhead boxes	1928	protein-coding gene	gene with protein product		602628	chromosome 14 open reading frame 116, checkpoint suppressor 1	C14orf116, CHES1	NA	9154802	Standard	NM_005197	NM_005197	NA	Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.544-25210T>C	chr14.hg19:g.89842362A>G		NA	Q96II7|Q9UIE7	hg19	CCDS41977.1	0.02	-0.157888	TCAxATG	COVERED																																																																																			NOVEL	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410902.2	17	3.607671	KEEP	8	0	0	12	319	AA	0.99254	0.320398	0		-	3	22	108	0	0	8.878613	13	60	399	47	ENST00000345097.4	0.1875	0.322807
FOXN3	1112	__UNKNOWN__	__UNKNOWN__	14	89893919	89893919	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:89893919T>C	ENST00000345097.4	-	2	103				FOXN3_ENST00000555353.1_Intron|RP11-33N16.3_ENST00000555070.1_RNA	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	NA		NA			mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						gcctcggccttccaaagtgct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254	1112		Forkhead boxes	1928	protein-coding gene	gene with protein product		602628	chromosome 14 open reading frame 116, checkpoint suppressor 1	C14orf116, CHES1	NA	9154802	Standard	NM_005197	NM_005197	NA	Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.14-15085A>G	chr14.hg19:g.89893919T>C		NA	Q96II7|Q9UIE7	hg19	CCDS41977.1	0.02	-0.184191	CCTxCCA	COVERED																																																																																			NOVEL	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410902.2	7	2.406208	KEEP	0	0	0	8	225	TT	0.99257	0.420331	0		-	3	60	103	0	0	8.291658	14	60	430	41	ENST00000345097.4	0.176471	0.423478
RP11-33N16.3	0	__UNKNOWN__	__UNKNOWN__	14	90158493	90158493	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:90158493G>A	ENST00000555070.1	-	0	170										NA		NA									NA						gagccaccgcgcccagcctaa	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555070.1:	chr14.hg19:g.90158493G>A		NA		hg19		0.02	-0.131577	CGCxCCC	COVERED																																																																																			NOVEL	RP11-33N16.3-001	KNOWN	basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000411023.1	5	3.008652	KEEP	2	0	0	10	298	GG	0.99257	0.22747	0		-	3	60	91	0	0	7.481928	10	60	328	36	ENST00000555070.1	0.230769	0.229173
TDP1	55775	__UNKNOWN__	__UNKNOWN__	14	90452127	90452127	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:90452127T>C	ENST00000335725.4	+	10	1381				TDP1_ENST00000357382.3_Intron|TDP1_ENST00000393454.2_Intron|TDP1_ENST00000555880.1_Intron|TDP1_ENST00000393452.3_Intron	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	NA		NA			cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		aatcccagcattttgggaggc	0.448		NA						Repair of DNA-protein crosslinks													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088	55775			18884	protein-coding gene	gene with protein product		607198			NA	11839309, 12244316	Standard	NM_018319	XM_005267847	NA	Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1131+573T>C	chr14.hg19:g.90452127T>C		NA	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	hg19	CCDS9888.1	0.02	-0.201713	GCAxTTT	COVERED																																																																																			NOVEL	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411239.1	6	3.609301	KEEP	0	0	0	12	334	TT	0.993634	0.487421	0		+	4	60	131	0	0	10.762988	15	60	438	49	ENST00000335725.4	0.210526	0.490544
PSMC1	5700	__UNKNOWN__	__UNKNOWN__	14	90726824	90726824	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:90726824C>T	ENST00000261303.8	+	3	257				PSMC1_ENST00000543772.2_Intron	NM_002802.2	NP_002793.2	P62191	PRS4_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 1	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|upper_aerodigestive_tract(2)	6		all_cancers(154;0.142)		COAD - Colon adenocarcinoma(157;0.21)		gcctgtaatcccagcactttg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L02426	CCDS32139.1	14q32.11	2010-04-21			ENSG00000100764	ENSG00000100764	5700		Proteasome (prosome, macropain) subunits, ATPases / AAA-type	9547	protein-coding gene	gene with protein product		602706			NA	9473509	Standard	NM_002802	NM_002802	NA	Approved	S4, p56	uc001xyf.3	P62191		ENST00000261303.8:c.154+269C>T	chr14.hg19:g.90726824C>T		NA	B4DR63|P49014|Q03527|Q6IAW0|Q6NW36|Q96AZ3	hg19	CCDS32139.1	0.02	-0.228088	ATCxCAG	COVERED																																																																																			NOVEL	PSMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411253.1	4	2.70801	KEEP	3	0	0	9	275	CC	0.99257	0.578599	0		+	3	40	92	0	0	6.827165	19	60	657	57	ENST00000261303.8	0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	90828784	90828784	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:90828784C>A			NA	NA				NRDE2 (30303 upstream) : AL512791.1 (18757 downstream)						NA		NA									NA						aagatgaggacgaggaggagg	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.90828784C>A		NA		hg19		0.02	-0.245608	GGAxGAG	COVERED																																																																																			NOVEL					0			8	2.536534	KEEP	0	1	27	18	484	CC	0.99986	0.693571	0			3	60	91	2	0	6.549777	22	60	724	66		0.12	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	90945812	90945812	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:90945812T>C			NA	NA				LINC00642 (20564 upstream) : RP11-1078H9.6 (9543 downstream)						NA		NA									NA						agattacaggtgtgagccact	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.90945812T>C		NA		hg19		0.02	-0.140307	AGGxGTG	COVERED																																																																																			NOVEL					0			6	3.308489	KEEP	0	0	0	11	305	TT	0.993072	0.259157	0			3	60	92	0	0	7.582502	10	60	291	40		0.230769	0.260965
TTC7B	145567	__UNKNOWN__	__UNKNOWN__	14	91223008	91223008	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:91223008G>A	ENST00000328459.6	-	4	567				TTC7B_ENST00000357056.2_Intron	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	NA		NA								NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				caaagtgctgggattacaggt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914	145567		Tetratricopeptide (TTC) repeat domain containing	19858	protein-coding gene	gene with protein product		NA	tetratricopeptide repeat domain 7 like 1	TTC7L1	NA		Standard		XM_005267367	NA	Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.446-11742C>T	chr14.hg19:g.91223008G>A		NA	Q86U24|Q86VT3	hg19	CCDS32140.1	0.02	-0.201771	CTGxGAT	COVERED																																																																																			NOVEL	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411364.2	10	4.812451	KEEP	6	0	0	16	472	GG	0.99649	0.488823	0		-	3	60	99	0	0	7.660541	17	60	585	68	ENST00000328459.6	0.15	0.490544
TTC7B	145567	__UNKNOWN__	__UNKNOWN__	14	91223018	91223018	__UNKNOWN__	Intron	SNP	T	T	C	rs549559847		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:91223018T>C	ENST00000328459.6	-	4	567				TTC7B_ENST00000357056.2_Intron	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	NA		NA								NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				ggattacaggtgtgagccacc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914	145567		Tetratricopeptide (TTC) repeat domain containing	19858	protein-coding gene	gene with protein product		NA	tetratricopeptide repeat domain 7 like 1	TTC7L1	NA		Standard		XM_005267367	NA	Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.446-11752A>G	chr14.hg19:g.91223018T>C		NA	Q86U24|Q86VT3	hg19	CCDS32140.1	0.02	-0.210485	AGGxGTG	COVERED																																																																																			NOVEL	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411364.2	7	4.148698	KEEP	4	0	0	14	363	TT	0.995343	0.519729	0		-	3	60	102	0	0	7.892247	18	60	533	66	ENST00000328459.6	0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	91302364	91302364	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:91302364T>G			NA	NA				CTD-3035D6.2 (7892 upstream) : RPS6KA5 (34434 downstream)						NA		NA									NA						atcaagaccatcctggctaac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.91302364T>G		NA		hg19		0.02	-0.131553	CCAxCCT	UNCOVERED																																																																																			NOVEL					0			2	2.706948	KEEP	3	0	0	9	248	TT	0	0	0			3	60	97	0	0	8.082223	10	60	290	36		0.230769	0.229173
RPS6KA5	9252	__UNKNOWN__	__UNKNOWN__	14	91517053	91517053	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:91517053G>A	ENST00000261991.3	-	1	277				RPS6KA5_ENST00000536315.2_Intron|RPS6KA5_ENST00000418736.2_Intron	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	NA		NA			axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		gattacaggcgtgagccaccg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784	9252			10434	protein-coding gene	gene with protein product		603607	ribosomal protein S6 kinase, 90kD, polypeptide 5		NA	9687510, 10702687	Standard	NM_004755	NM_004755	NA	Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.103+9622C>T	chr14.hg19:g.91517053G>A		NA	O95316|Q96AF7	hg19	CCDS9893.1	0.02	-0.131562	GGCxTGA	COVERED																																																																																			NOVEL	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411442.2	4	3.309289	KEEP	0	0	0	11	325	GG	0.993072	0.227586	0		-	3	60	85	1	0	6.882142	10	60	324	38	ENST00000261991.3	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	92013976	92013976	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:92013976G>A			NA	NA				SMEK1 (37154 upstream) : AL133373.1 (24811 downstream)						NA		NA									NA						ccaggagttcgagaccagcct	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.92013976G>A		NA		hg19		0.02	-0.307017	TTCxAGA	COVERED																																																																																			NOVEL					0			17	3.141476	KEEP	1	1	24	19	576	GG	0.999863	0.800136	0			3	60	91	0	0	6.443434	24	60	779	85		0.111111	0.800245
CATSPERB	79820	__UNKNOWN__	__UNKNOWN__	14	92072348	92072348	__UNKNOWN__	Intron	SNP	C	C	T	rs143448686	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:92072348C>T	ENST00000256343.3	-	22	2866					NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	NA		NA			cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				ggtgaaaccccgtctctacta	0.562		NA											C|||	41	0.0081869	0.0295	0.0029	5008	,	,	NA	15574	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962	79820			20500	protein-coding gene	gene with protein product		611169	chromosome 14 open reading frame 161, cation channel, sperm-associated, beta	C14orf161	NA	17478420	Standard	NM_024764	NM_024764	NA	Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.2709+2289G>A	chr14.hg19:g.92072348C>T		NA	A0AV51	hg19	CCDS32142.1	0.02	-0.087706	CCCxGTC	UNCOVERED																																																																																			NOVEL	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411769.1	5	2.406274	KEEP	2	0	0	8	227	CC	0	0	0		-	3	60	81	1	0	7.454154	4	60	127	22	ENST00000256343.3	0.428571	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	92237402	92237402	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:92237402A>T			NA	NA				RP11-747H7.3 (11260 upstream) : TC2N (8692 downstream)						NA		NA									NA						aaaaaaaaaaagagccaggca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.92237402A>T		NA		hg19		0.02	-0.122787	AAAxGAG	COVERED																																																																																			NOVEL					0			21	5.708595	KEEP	7	0	0	19	493	AA	0.993634	0.195062	0			5	42	159	0	0	14.746326	7	60	211	36		0.416667	0.196312
TC2N	123036	__UNKNOWN__	__UNKNOWN__	14	92318564	92318564	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:92318564G>T	ENST00000435962.2	-	1	268					NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	NA		NA			regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		ctgaggttgggaatttgagac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929	123036			19859	protein-coding gene	gene with protein product	C2 calcium-dependent domain containing 1	NA	chromosome 14 open reading frame 47, membrane targeting (tandem) C2 domain containing 1	C14orf47, MTAC2D1	NA	11526914	Standard	NM_152332	NM_001128596	NA	Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.55+15041C>A	chr14.hg19:g.92318564G>T		NA		hg19	CCDS9897.1	0.02	-0.070171	TGGxAAT	UNCOVERED																																																																																			NOVEL	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411778.1	2	2.407387	KEEP	2	0	0	8	257	GG	0	0	0		-	4	60	118	0	0	11.299236	4	60	131	26	ENST00000435962.2	0.5	0.054137
ATXN3	4287	__UNKNOWN__	__UNKNOWN__	14	92528610	92528610	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:92528610C>A	ENST00000393287.5	-	0	3197				ATXN3_ENST00000545170.1_3'UTR|ATXN3_ENST00000429774.2_3'UTR			P54252	ATX3_HUMAN	ataxin 3	NA		NA			actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		caaaaaaaaacaaaaacaaaa	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(190;752 2094 29897 44875 49530)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427	4287		Ataxins	7106	protein-coding gene	gene with protein product		607047	Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)	SCA3, MJD	NA	8358439	Standard	NM_004993	NM_004993	NA	Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000393287.5:c.*2054G>T	chr14.hg19:g.92528610C>A		NA	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	hg19	CCDS9900.1	0.02	-0.324361	AAAxAAA	COVERED																																																																																			NOVEL	ATXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367922.3	11	5.749501	KEEP	0	1	25	28	848	CC	0.999997	0.851982	0		-	4	60	98	0	0	6.402951	30	60	1013	92	ENST00000393287.5	0.117647	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	92664704	92664704	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:92664704C>T			NA	NA				CPSF2 (33949 upstream) : RP11-472N19.3 (55132 downstream)						NA		NA									NA						tcccagctctctgggaggcca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.92664704C>T		NA		hg19		0.02	-0.122811	TCTxTGG	COVERED																																																																																			NOVEL					0			7	2.407162	KEEP	0	0	0	8	247	CC	0.99257	0.194853	0			3	50	89	0	0	7.532137	8	60	273	30		0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	93633579	93633579	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:93633579A>G			NA	NA				ITPK1 (51316 upstream) : MOAP1 (14961 downstream)						NA		NA									NA						gattacaggcatgagccacca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.93633579A>G		NA		hg19		0.02	-0.210442	GGCxTGA	COVERED																																																																																			NOVEL					0			10	5.413983	KEEP	0	0	0	18	503	AA	0.999859	0.522088	0			3	60	100	0	0	7.627349	19	60	532	57		0.136364	0.522161
UBR7	55148	__UNKNOWN__	__UNKNOWN__	14	93677579	93677579	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:93677579A>G	ENST00000013070.6	+	3	581				RP11-371E8.4_ENST00000557048.1_Intron|RP11-371E8.4_ENST00000557574.1_Intron|UBR7_ENST00000416753.1_Intron	NM_175748.3	NP_786924.2	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin 7 (putative)	NA		NA					ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1)	19						gcaagactccatctcaaaaca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001345	CCDS9909.1	14q32.12	2008-06-23	2008-06-23	2008-06-23		ENSG00000012963	55148		Ubiquitin protein ligase E3 component n-recognins	20344	protein-coding gene	gene with protein product		613816	chromosome 14 open reading frame 130	C14orf130	NA	18162545	Standard	NM_175748	NM_175748	NA	Approved		uc001ybm.4	Q8N806		ENST00000013070.6:c.345+525A>G	chr14.hg19:g.93677579A>G		NA	Q86U21|Q86UA9|Q96BY0|Q9NVV6	hg19	CCDS9909.1	0.02	-0.324515	TCCxTCT	COVERED																																																																																			NOVEL	UBR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412693.1	14	3.91024	KEEP	0	0	0	13	363	AA	0.994391	0.831028	0		+	3	60	101	0	0	7.126685	31	60	916	70	ENST00000013070.6	0.088235	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	94353282	94353282	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:94353282G>A			NA	NA				PRIMA1 (98455 upstream) : FAM181A-AS1 (17793 downstream)						NA		NA									NA						aagtgctggggttacaggcat	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.94353282G>A		NA		hg19		0.02	-0.210522	GGGxTTA	COVERED																																																																																			NOVEL					0			6	2.40718	KEEP	0	0	0	8	244	GG	0.99257	0.518282	0			3	60	89	0	0	6.733739	16	60	534	45		0.157895	0.522161
PPP4R4	57718	__UNKNOWN__	__UNKNOWN__	14	94642454	94642454	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:94642454T>C	ENST00000304338.3	+	2	335	c.181T>C	c.(181-183)Tat>Cat	p.Y61H	PPP4R4_ENST00000555690.1_3'UTR|PPP4R4_ENST00000328839.3_Missense_Mutation_p.Y61H	NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	61		NA			negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						AAGGGCTGTTTATCTGCTCAG	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													225	225	225			NA	NA	14		NA											NA				94642454		2203	4300	6503	SO:0001583	missense			AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698	57718		Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits	23788	protein-coding gene	gene with protein product	cilia and flagella associated protein 14	NA	KIAA1622	KIAA1622	NA	18715871	Standard	NM_058237	NM_020958	NA	Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.181T>C	chr14.hg19:g.94642454T>C	ENSP00000305924:p.Tyr61His	NA	Q9BUF8|Q9HCF0	hg19	CCDS9921.1	0.02	1.760278	GTTxATC	COVERED	.	.	.	.	.	.	.	.	.	.	T	19.76	3.888244	0.72524	.	.	ENSG00000119698	ENST00000304338;ENST00000328839	.	.	.	4.95	4.95	0.65309	Armadillo-like helical (1);Armadillo-type fold (1);	0.066927	0.64402	D	0.000007	T	0.70710	0.3255	M	0.64997	1.995	0.35024	D	0.75813	B;D	0.69078	0.452;0.997	B;D	0.65010	0.164;0.931	T	0.80334	-0.1426	9	0.66056	D	0.02	-6.996	13.5816	0.61907	0.0:0.0:0.0:1.0	.	61;61	Q6NUP7;Q6NUP7-2	PP4R4_HUMAN;.	H	61	.	ENSP00000305924:Y61H	Y	+	1	0	PPP4R4	93712207	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.391000	0.73208	2.079000	0.62486	0.402000	0.26972	TAT	NOVEL	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413056.1	4	6.61466	KEEP	0	0	0	22	591	TT	0.999879	0.999366	0		+	25	60	856	0	0	75.791623	56	60	1630	160	ENST00000304338.3	0.308642	0.999487
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	95971122	95971122	__UNKNOWN__	IGR	SNP	A	A	G	rs179161	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:95971122A>G			NA	NA				SYNE3 (28949 upstream) : RP11-1070N10.3 (11350 downstream)						NA		NA									NA						gttcgagatcagcctgaacaa	0.438		NA											G|||	2814	0.561901	0.7776	0.4928	5008	,	,	NA	18929	0.3234	NA	0.6093	False	NA	,,,	NA	NA	NA	2504	0.5164	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.95971122A>G		NA		hg19		0.02	-0.175431	ATCxGCC	COVERED																																																																																			NOVEL					0			13	4.511419	KEEP	6	0	0	15	414	AA	0.993072	0.384723	0			4	60	137	0	0	11.831164	11	60	336	49		0.266667	0.387407
AK7	122481	__UNKNOWN__	__UNKNOWN__	14	96893321	96893321	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:96893321G>A	ENST00000267584.4	+	5	653					NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	NA		NA			axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		ggtggctcacgcctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057	122481		Adenylate kinases	20091	protein-coding gene	gene with protein product		615364			NA		Standard		NM_152327	NA	Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.609+6052G>A	chr14.hg19:g.96893321G>A		NA	Q8IYP6	hg19	CCDS9945.1	0.02	-0.210522	CACxCCT	COVERED																																																																																			NOVEL	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000413340.1	6	3.911492	KEEP	1	0	0	13	394	GG	0.993634	0.518837	0		+	3	60	88	0	0	6.427849	19	60	623	59	ENST00000267584.4	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	99441769	99441769	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:99441769G>C			NA	NA				RP11-1127D7.1 (47627 upstream) : AL162151.4 (182983 downstream)						NA		NA									NA						gtaatcccaggactttgggag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.99441769G>C		NA		hg19		0.02	-0.149138	CAGxACT	COVERED																																																																																			NOVEL					0			7	2.708333	KEEP	2	0	0	9	284	GG	0.99257	0.320408	0			3	60	108	0	0	8.971812	12	60	418	40		0.2	0.322807
RP11-638I2.4	0	__UNKNOWN__	__UNKNOWN__	14	100686306	100686306	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:100686306G>A	ENST00000554537.1	-	0	85										NA		NA									NA						tccacctcccgggttcaagca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554537.1:	chr14.hg19:g.100686306G>A		NA		hg19		0.02	-0.105243	CCCxGGT	UNCOVERED																																																																																			NOVEL	RP11-638I2.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000414045.1	6	3.308851	KEEP	0	0	0	11	317	GG	0.993072	0.138863	0		-	3	60	78	0	0	6.431857	8	60	266	27	ENST00000554537.1	0.272727	0.139832
RP11-638I2.4	0	__UNKNOWN__	__UNKNOWN__	14	100697630	100697630	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:100697630C>T	ENST00000554537.1	-	0	85										NA		NA									NA						ggggtttcgccatgttggcca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000554537.1:	chr14.hg19:g.100697630C>T		NA		hg19		0.02	-0.087699	CGCxATG	UNCOVERED																																																																																			NOVEL	RP11-638I2.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000414045.1	5	2.407012	KEEP	0	0	0	8	246	CC	0.99257	0.09898	0		-	3	60	89	0	0	8.032404	5	60	172	26	ENST00000554537.1	0.375	0.099721
WARS	7453	__UNKNOWN__	__UNKNOWN__	14	100801990	100801990	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:100801990A>G	ENST00000355338.2	-	11	1873				WARS_ENST00000392882.2_Intron|RP11-638I2.8_ENST00000557226.1_RNA|WARS_ENST00000556645.1_Intron|WARS_ENST00000358655.4_Intron|WARS_ENST00000344102.5_Intron|WARS_ENST00000557135.1_Intron	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	NA		NA			angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	ccaaagtgctaggattacagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	7453	6.1.1.2	Aminoacyl tRNA synthetases / Class I	12729	protein-coding gene	gene with protein product	tryptophan tRNA ligase 1, cytoplasmic	191050		IFI53	NA	1537332, 1763065	Standard	NM_004184	NM_004184	NA	Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.1255-617T>C	chr14.hg19:g.100801990A>G		NA	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	hg19	CCDS9960.1	0.02	-0.157548	GCTxGGA	COVERED																																																																																			NOVEL	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414236.1	5	2.70611	KEEP	0	0	0	9	241	AA	0.99254	0.320398	0		-	4	60	134	0	0	11.28606	13	60	368	38	ENST00000355338.2	0.235294	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	101900386	101900386	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:101900386T>C			NA	NA				LINC00524 (26127 upstream) : RP11-168L7.3 (8026 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.101900386T>C		NA		hg19		0.02	-0.140311	AGGxGTG	COVERED																																																																																			NOVEL					0			11	3.619105	KEEP	2	1	25	21	537	TT	0.999869	0.260931	0			3	60	97	0	0	7.872654	12	60	341	49		0.2	0.260965
RP11-1029J19.5	0	__UNKNOWN__	__UNKNOWN__	14	102146568	102146568	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:102146568T>C	ENST00000557778.1	-	0	55										NA		NA									NA						cggtggctcatgcctgtaatc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000557778.1:	chr14.hg19:g.102146568T>C		NA		hg19		0.02	-0.140333	TCAxGCC	COVERED																																																																																			NOVEL	RP11-1029J19.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000414793.2	7	3.007435	KEEP	0	0	0	10	273	TT	0.992708	0.259062	0		-	3	60	104	0	0	8.782035	10	60	297	38	ENST00000557778.1	0.230769	0.260965
PPP2R5C	5527	__UNKNOWN__	__UNKNOWN__	14	102357378	102357378	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:102357378A>G	ENST00000334743.5	+	6	737				PPP2R5C_ENST00000328724.5_Intron|PPP2R5C_ENST00000422945.2_Intron|PPP2R5C_ENST00000557095.1_Intron|PPP2R5C_ENST00000445439.3_Intron|PPP2R5C_ENST00000350249.3_Intron	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	NA		NA			DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						caaagtgctgagattacaggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304	5527		Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits	9311	protein-coding gene	gene with protein product		601645	protein phosphatase 2, regulatory subunit B (B56), gamma isoform, protein phosphatase 2, regulatory subunit B', gamma isoform		NA	7592815	Standard	NM_002719	NM_002719	NA	Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.689+745A>G	chr14.hg19:g.102357378A>G		NA	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	hg19	CCDS9964.1	0.02	-0.175432	CTGxGAT	COVERED																																																																																			NOVEL	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414373.2	7	3.007891	KEEP	2	0	0	10	279	AA	0.992708	0.384582	0		+	3	46	102	0	1	8.109963	15	60	459	47	ENST00000334743.5	0.166667	0.387407
DYNC1H1	1778	__UNKNOWN__	__UNKNOWN__	14	102457517	102457517	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:102457517C>A	ENST00000360184.4	+	11	3032					NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ctcaaaaaaacaaaaaGCAAA	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102	1778		Cytoplasmic dyneins	2961	protein-coding gene	gene with protein product		600112	dynein, cytoplasmic, heavy polypeptide 1	DNECL, DNCL, DNCH1	NA	16260502, 8666668	Standard	NM_001376	NM_001376	NA	Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.2869-347C>A	chr14.hg19:g.102457517C>A		NA	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	hg19	CCDS9966.1	0.02	-0.166678	AAAxAAA	COVERED																																																																																			NOVEL	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414574.1	8	3.007342	KEEP	0	0	0	10	297	CC	0.992708	0.351366	0		+	3	60	90	0	0	6.910249	15	60	525	40	ENST00000360184.4	0.166667	0.353947
MOK	5891	__UNKNOWN__	__UNKNOWN__	14	102760521	102760521	__UNKNOWN__	Intron	SNP	T	T	C	rs148782624	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:102760521T>C	ENST00000361847.2	-	2	239				MOK_ENST00000193029.6_Intron|MOK_ENST00000522874.1_Intron|MOK_ENST00000524214.1_Intron	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	NA		NA			protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)				NA						cggtggctcatgcctgtaatc	0.522		NA											T|||	305	0.0609026	0.1324	0.0317	5008	,	,	NA	13899	0.0377	NA	0.0388	False	NA	,,,	NA	NA	NA	2504	0.0317	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823	5891			9833	protein-coding gene	gene with protein product		605762	renal tumor antigen	RAGE	NA	8781117, 10421840	Standard		NM_014226	NA	Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.8-10592A>G	chr14.hg19:g.102760521T>C		NA	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	hg19	CCDS9971.1	0.02	-0.254331	TCAxGCC	COVERED																																																																																			NOVEL	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380848.3	9	3.308689	KEEP	2	0	0	11	308	TT	0.992708	0.663648	0		-	3	60	91	0	0	6.394574	25	60	732	62	ENST00000361847.2	0.107143	0.668523
TECPR2	9895	__UNKNOWN__	__UNKNOWN__	14	102949211	102949211	__UNKNOWN__	Intron	SNP	C	C	T	rs11626549	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:102949211C>T	ENST00000359520.7	+	18	4015					NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	NA		NA			autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						gacggagtctcgctctgtcgc	0.512		NA											C|||	698	0.139377	0.0363	0.1513	5008	,	,	NA	10168	0.1438	NA	0.2376	False	NA	,,,	NA	NA	NA	2504	0.1646	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663	9895			19957	protein-coding gene	gene with protein product		615000	KIAA0329	KIAA0329	NA	9205841	Standard	NM_014844	NM_014844	NA	Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3790-14105C>T	chr14.hg19:g.102949211C>T		NA	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	hg19	CCDS32162.1	0.02	-0.087719	TCTxGCT	UNCOVERED																																																																																			NOVEL	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415056.2	14	3.44262	KEEP	16	1	27	21	626	CC	0.995343	0.099257	0		+	3	40	88	1	0	7.743149	6	47	202	46	ENST00000359520.7	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	102985422	102985422	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:102985422T>C			NA	NA				ANKRD9 (9286 upstream) : MIR4309 (20558 downstream)						NA		NA									NA						gttaggagtttgagaccagcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.102985422T>C		NA		hg19		0.02	-0.131542	GTTxGAG	COVERED																																																																																			NOVEL					0			9	3.308178	KEEP	2	0	0	11	301	TT	0.99254	0.259018	0			4	60	125	0	0	10.924229	9	60	257	37		0.307692	0.260965
CTD-2555C10.3	0	__UNKNOWN__	__UNKNOWN__	14	103013018	103013018	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103013018T>C	ENST00000559946.1	+	0	323										NA		NA									NA						GGGTAgggcatggtggctcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559946.1:	chr14.hg19:g.103013018T>C		NA		hg19		0.02	-0.104995	GCAxGGT	UNCOVERED																																																																																			NOVEL	CTD-2555C10.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000415849.1	12	4.210125	KEEP	2	0	0	14	380	TT	0.994391	0.139048	0		+	3	60	95	0	0	8.443673	6	60	179	37	ENST00000559946.1	0.333333	0.139832
RCOR1	23186	__UNKNOWN__	__UNKNOWN__	14	103084204	103084204	__UNKNOWN__	Intron	SNP	C	C	T	rs538025884		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103084204C>T	ENST00000262241.6	+	2	587				RCOR1_ENST00000570597.1_Intron	NM_015156.3	NP_055971.2	Q9UKL0	RCOR1_HUMAN	REST corepressor 1	NA		NA			blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						ggattacaggcgtgagccacc	0.453		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	16186	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902	23186			17441	protein-coding gene	gene with protein product		607675	REST corepressor	RCOR	NA	10449787	Standard	NM_015156	NM_015156	NA	Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000262241.6:c.361+24542C>T	chr14.hg19:g.103084204C>T		NA	Q15044|Q6P2I9|Q86VG5	hg19	CCDS9974.2	0.02	-0.184206	AGGxGTG	UNCOVERED																																																																																			NOVEL	RCOR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415058.3	5	2.406515	KEEP	1	0	0	8	231	CC	0	0	0		+	3	60	89	0	0	6.733762	16	60	515	41	ENST00000262241.6	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	103208319	103208319	__UNKNOWN__	IGR	SNP	C	C	T	rs575515455		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103208319C>T			NA	NA				RCOR1 (11406 upstream) : RP11-661D19.3 (28057 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.488		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16292	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.103208319C>T		NA		hg19		0.02	-0.166671	AGGxGTG	COVERED																																																																																			NOVEL					0			7	3.910361	KEEP	4	0	0	13	374	CC	0.994391	0.351961	0			3	60	89	0	0	6.891913	14	60	465	56		0.176471	0.353947
TRAF3	7187	__UNKNOWN__	__UNKNOWN__	14	103371090	103371090	__UNKNOWN__	Intron	SNP	T	T	C	rs2092971	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103371090T>C	ENST00000560371.1	+	11	1352				TRAF3_ENST00000392745.2_Intron|TRAF3_ENST00000539721.1_Intron|TRAF3_ENST00000351691.5_Intron|TRAF3_ENST00000347662.4_Intron	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	NA		NA			apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		gagcttgcagtgagccgagat	0.577		NA											T|||	1489	0.297324	0.3933	0.3674	5008	,	,	NA	13694	0.4008	NA	0.1869	False	NA	,,,	NA	NA	NA	2504	0.1247	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323	7187			12033	protein-coding gene	gene with protein product		601896			NA	7530216, 7859281	Standard	NM_145725	NM_145725	NA	Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1136-460T>C	chr14.hg19:g.103371090T>C		NA	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	hg19	CCDS9975.1	0.02	-0.11402	CAGxGAG	UNCOVERED																																																																																			NOVEL	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415735.1	9	2.404035	KEEP	10	0	0	8	199	TT	0	0	0		+	5	60	174	0	0	16.246645	7	40	202	37	ENST00000560371.1	0.416667	0.162467
CDC42BPB	9578	__UNKNOWN__	__UNKNOWN__	14	103502694	103502694	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103502694A>G	ENST00000361246.2	-	1	464					NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)	NA		NA								NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		gggtttcaccatgttagccag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752	9578			1738	protein-coding gene	gene with protein product		614062	CDC42-binding protein kinase beta (DMPK-like)		NA	10198171	Standard	NM_006035	NM_006035	NA	Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.175+20641T>C	chr14.hg19:g.103502694A>G		NA		hg19	CCDS9978.1	0.02	-0.157873	ACCxTGT	UNCOVERED																																																																																			NOVEL	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415711.1	6	3.60919	KEEP	11	0	0	12	331	AA	0	0	0		-	3	40	91	0	0	7.092055	14	48	418	47	ENST00000361246.2	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	103763069	103763069	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103763069T>C			NA	NA				RAP2CP1 (16777 upstream) : RP11-45P15.4 (34941 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.103763069T>C		NA		hg19		0.02	-0.157856	AGGxGTG	COVERED																																																																																			NOVEL					0			8	2.706365	KEEP	1	0	0	9	246	TT	0.99254	0.320398	0			3	60	95	2	0	7.492243	14	60	404	34		0.176471	0.322807
MARK3	4140	__UNKNOWN__	__UNKNOWN__	14	103861368	103861368	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:103861368C>T	ENST00000429436.2	+	1	561				MARK3_ENST00000440884.3_Intron|MARK3_ENST00000416682.2_Intron|MARK3_ENST00000335102.5_Intron|MARK3_ENST00000303622.9_Intron|MARK3_ENST00000553942.1_Intron|MARK3_ENST00000216288.7_Intron	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	NA		NA				plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			ccacctgcctcggcctcccaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413	4140			6897	protein-coding gene	gene with protein product		602678			NA	9533022	Standard	NM_001128918	NM_002376	NA	Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.51+8951C>T	chr14.hg19:g.103861368C>T		NA	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	hg19	CCDS45165.1	0.02	-0.271928	CCTxGGC	COVERED																																																																																			NOVEL	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415144.1	13	3.309353	KEEP	0	0	0	11	327	CC	0.993072	0.712346	0		+	4	60	116	0	0	8.592026	23	60	759	60	ENST00000429436.2	0.148148	0.717315
BAG5	9529	__UNKNOWN__	__UNKNOWN__	14	104027762	104027762	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104027762G>A	ENST00000445922.2	-	2	219				BAG5_ENST00000337322.4_Intron|BAG5_ENST00000299204.4_Intron|RP11-894P9.2_ENST00000556332.1_RNA	NM_004873.3	NP_004864.1	Q9UL15	BAG5_HUMAN	BCL2-associated athanogene 5	NA		NA			negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein refolding (GO:0061084)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|neuron death (GO:0070997)|protein folding (GO:0006457)|regulation of inclusion body assembly (GO:0090083)	inclusion body (GO:0016234)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chaperone binding (GO:0051087)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	24		Melanoma(154;0.155)	Epithelial(46;0.144)			cagacgatccgcccgcctccg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(171;1832 2055 18950 31566 41632)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF095195	CCDS9982.1, CCDS41995.1	14q32	2008-08-01				ENSG00000166170	9529			941	protein-coding gene	gene with protein product		603885			NA	9873016, 15603737	Standard		NM_001015048	NA	Approved		uc001ynh.2	Q9UL15		ENST00000445922.2:c.28-233C>T	chr14.hg19:g.104027762G>A		NA	O94950|Q86W59	hg19	CCDS9982.1	0.02	-0.166659	TCCxCCC	COVERED																																																																																			NOVEL	BAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414990.1	6	3.308409	KEEP	0	0	0	11	303	GG	0.993072	0.351495	0		-	3	60	88	0	0	6.710564	15	60	476	45	ENST00000445922.2	0.166667	0.353947
KLC1	3831	__UNKNOWN__	__UNKNOWN__	14	104133735	104133735	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104133735T>C	ENST00000445352.4	+	6	990				RP11-73M18.2_ENST00000472726.2_Intron|KLC1_ENST00000555836.1_Intron|KLC1_ENST00000380038.3_Intron|KLC1_ENST00000347839.6_Intron|KLC1_ENST00000389744.4_Intron|KLC1_ENST00000553286.1_Intron|KLC1_ENST00000554280.1_Intron|KLC1_ENST00000348520.6_Intron|KLC1_ENST00000334553.6_Intron|KLC1_ENST00000557450.1_Intron|KLC1_ENST00000246489.7_Intron|KLC1_ENST00000452929.2_Intron|KLC1_ENST00000557575.1_Intron	NM_005552.4	NP_005543.2	Q07866	KLC1_HUMAN	kinesin light chain 1	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				tgagccaccgtgcccagccTT	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214	3831		Tetratricopeptide (TTC) repeat domain containing	6387	protein-coding gene	gene with protein product		600025	kinesin 2 60/70kDa, kinesin 2	KNS2	NA	8274221, 11106729	Standard	NM_005552	NM_005552	NA	Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000445352.4:c.792-2113T>C	chr14.hg19:g.104133735T>C		NA	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	hg19		0.02	-0.271855	CCGxGCC	UNCOVERED																																																																																			NOVEL	KLC1-015	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000414871.1	12	2.406288	KEEP	1	0	0	8	225	TT	0	0	0		+	3	60	96	0	0	7.049471	22	60	636	50	ENST00000445352.4	0.12	0.717315
ZFYVE21	79038	__UNKNOWN__	__UNKNOWN__	14	104194029	104194029	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104194029G>C	ENST00000216602.6	+	3	301				ZFYVE21_ENST00000311141.2_Intron	NM_001198953.1	NP_001185882.1	Q9BQ24	ZFY21_HUMAN	zinc finger, FYVE domain containing 21	NA		NA				cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(2)	8		Melanoma(154;0.226)		Epithelial(152;0.245)		GGCCACACCCGGGGCCGCTTG	0.721		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057816	CCDS9985.1, CCDS55948.1	14q32.33	2011-09-07					79038		Zinc fingers, FYVE domain containing	20760	protein-coding gene	gene with protein product		613504			NA	21768110	Standard	NM_024071	NM_024071	NA	Approved	MGC2550, ZF21	uc001yod.3	Q9BQ24		ENST00000216602.6:c.190-54G>C	chr14.hg19:g.104194029G>C		NA	A8K3A4|Q86T05|Q96LT1	hg19	CCDS55948.1	0.02	3.78597	CCCxGGG	COVERED																																																																																			NOVEL	ZFYVE21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414614.1	1	10.526944	KEEP	0	0	0	35	1037	GG	0.999999	0.999994	0		+	11	60	363	0	0	25.934494	101	60	3340	227	ENST00000216602.6	0.098214	0.999995
PPP1R13B	23368	__UNKNOWN__	__UNKNOWN__	14	104227925	104227925	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104227925A>C	ENST00000202556.9	-	5	637					NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	NA		NA			intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				atggtgaaacactgtctctac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808	23368		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Ankyrin repeat domain containing	14950	protein-coding gene	gene with protein product		606455	protein phosphatase 1, regulatory (inhibitor) subunit 13B		NA	9872452	Standard	NM_015316	NM_015316	NA	Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.355-3837T>G	chr14.hg19:g.104227925A>C		NA	B2RMX5|O94870	hg19	CCDS41997.1	0.02	-0.140277	AACxCTG	COVERED																																																																																			NOVEL	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414591.1	3	2.405809	KEEP	1	0	0	8	217	AA	0.99257	0.259026	0		-	3	51	100	0	0	8.079513	13	60	349	32	ENST00000202556.9	0.1875	0.260965
PPP1R13B	23368	__UNKNOWN__	__UNKNOWN__	14	104278122	104278122	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104278122A>G	ENST00000202556.9	-	2	292					NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	NA		NA			intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				ggccgggcgcagtggctcaca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808	23368		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Ankyrin repeat domain containing	14950	protein-coding gene	gene with protein product		606455	protein phosphatase 1, regulatory (inhibitor) subunit 13B		NA	9872452	Standard	NM_015316	NM_015316	NA	Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.10-14267T>C	chr14.hg19:g.104278122A>G		NA	B2RMX5|O94870	hg19	CCDS41997.1	0.02	-0.280669	CGCxGTG	COVERED																																																																																			NOVEL	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414591.1	10	5.413675	KEEP	0	0	0	18	498	AA	0.999859	0.76078	0		-	3	60	97	0	1	7.095404	23	60	689	82	ENST00000202556.9	0.115385	0.760887
CTD-2134A5.4	0	__UNKNOWN__	__UNKNOWN__	14	104330157	104330157	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104330157G>A	ENST00000555967.1	-	0	403										NA		NA									NA						cagcactttgggaggccgaag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000555967.1:	chr14.hg19:g.104330157G>A		NA		hg19		0.02	-0.131584	TTGxGAG	COVERED																																																																																			NOVEL	CTD-2134A5.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000414608.1	4	3.008504	KEEP	0	0	0	10	295	GG	0.992708	0.227502	0		-	3	60	90	0	0	7.27275	11	60	374	32	ENST00000555967.1	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	104373415	104373415	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104373415A>G			NA	NA				CTD-2134A5.4 (26967 upstream) : C14orf2 (5209 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.104373415A>G		NA		hg19		0.02	-0.192933	GGCxTGA	COVERED																																																																																			NOVEL					0			9	2.70232	KEEP	1	0	0	9	234	AA	0.99257	0.454356	0			4	60	117	0	0	9.169659	17	60	489	47		0.190476	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	104373652	104373652	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104373652C>T			NA	NA				CTD-2134A5.4 (27204 upstream) : C14orf2 (4972 downstream)						NA		NA									NA						gggcggatcacgaggtccaga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.104373652C>T		NA		hg19		0.02	-0.104704	TCAxGAG	UNCOVERED																																																																																			NOVEL					0			0	2.406237	KEEP	0	0	0	8	230	CC	0.99257	0.138793	0			3	60	84	0	0	7.042153	8	60	245	33		0.272727	0.139832
C14orf2	9556	__UNKNOWN__	__UNKNOWN__	14	104379775	104379775	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104379775T>C	ENST00000554880.1	-	3	302				C14orf2_ENST00000557040.1_Intron|C14orf2_ENST00000286953.3_Intron|C14orf2_ENST00000555030.1_Intron|C14orf2_ENST00000553449.1_Intron|C14orf2_ENST00000554713.1_3'UTR|C14orf2_ENST00000414262.2_Intron|C14orf2_ENST00000553430.1_3'UTR			P56378	68MP_HUMAN	chromosome 14 open reading frame 2	NA		NA				integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)				kidney(1)	1				Epithelial(152;0.223)		tgtgaaaccctatctctacta	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF054175	CCDS9986.1, CCDS45169.1	14q32.33	2013-02-18			ENSG00000156411	ENSG00000156411	9556			1188	protein-coding gene	gene with protein product	6.8 kDa mitochondrial proteolipid	604573			NA	9653160	Standard	NM_001127393	NM_001127393	NA	Approved	MP68	uc001yoi.4	P56378	OTTHUMG00000171601	ENST00000554880.1:c.148+522A>G	chr14.hg19:g.104379775T>C		NA	B2R588|G3V5Q3|Q86TT7	hg19	CCDS9986.1	0.02	3.719282	CCCxATC	COVERED																																																																																			NOVEL	C14orf2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414398.1	46	3.346442	KEEP	1	8	220	89	2320	TT	1	1	0		-	10	60	315	0	1	21.084608	117	60	3401	278	ENST00000554880.1	0.07874	1
TDRD9	122402	__UNKNOWN__	__UNKNOWN__	14	104457818	104457818	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104457818T>C	ENST00000409874.4	+	9	1228				TDRD9_ENST00000339063.5_Intron	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	NA		NA			cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ggcacgatcttggctcactgc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414	122402		Tudor domain containing	20122	protein-coding gene	gene with protein product		NA	chromosome 14 open reading frame 75	C14orf75	NA		Standard	NM_153046	NM_153046	NA	Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1180+257T>C	chr14.hg19:g.104457818T>C		NA	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	hg19	CCDS9987.2	0.02	-0.166652	TCTxGGC	COVERED																																																																																			NOVEL	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328325.3	6	3.007771	KEEP	1	0	0	10	277	TT	0.992708	0.351366	0		+	3	60	100	0	0	7.991736	14	60	421	39	ENST00000409874.4	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	104930938	104930938	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:104930938A>G			NA	NA				RNU6-684P (63553 upstream) : C14orf180 (115082 downstream)						NA		NA									NA						tcaccatgttagccaggatgg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.104930938A>G		NA		hg19		0.02	-0.070165	GTTxGCC	UNCOVERED																																																																																			NOVEL					0			2	3.308101	KEEP	4	0	0	11	300	AA	0.99254	0.053733	0			3	40	90	0	0	8.132731	5	60	149	32		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	105285338	105285338	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105285338C>T			NA	NA				ZBTB42 (14289 upstream) : LINC00638 (2199 downstream)						NA		NA									NA						cggtggctcacgcctataatc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.105285338C>T		NA		hg19		0.02	-0.166676	TCAxGCC	COVERED																																																																																			NOVEL					0			8	2.707903	KEEP	0	0	0	9	271	CC	0.99254	0.351306	0			3	60	94	0	0	7.478731	13	60	437	41		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	105295189	105295189	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105295189G>A			NA	NA				LINC00638 (5134 upstream) : CTD-3051D23.1 (13810 downstream)						NA		NA									NA						cacgcctgtagtcccagcact	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.105295189G>A		NA		hg19		0.02	-0.175431	GTAxTCC	COVERED																																																																																			NOVEL					0			14	5.114575	KEEP	0	0	0	17	501	GG	0.999366	0.387161	0			4	60	114	0	0	9.168362	14	60	467	44		0.222222	0.387407
GPR132	29933	__UNKNOWN__	__UNKNOWN__	14	105515873	105515873	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105515873G>T	ENST00000392585.2	-	0	2747				GPR132_ENST00000329797.3_3'UTR	NM_001278695.1	NP_001265624.1	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	NA		NA			G1/S transition of mitotic cell cycle (GO:0000082)|response to stress (GO:0006950)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	18		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		gtgctgggatgacaggcgtga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF083955	CCDS9997.1, CCDS61567.1	14q32.3	2012-08-21			ENSG00000183484	ENSG00000183484	29933		GPCR / Class A : Orphans	17482	protein-coding gene	gene with protein product	G2 accumulation	606167			NA	12086852	Standard	NM_013345	NM_013345	NA	Approved	G2A	uc001yqd.3	Q9UNW8	OTTHUMG00000140173	ENST00000392585.2:c.*1458C>A	chr14.hg19:g.105515873G>T		NA	A8K7X7|B4E144|Q9BSU2	hg19		0.02	2.475771	GATxACA	COVERED																																																																																			NOVEL	GPR132-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000409279.1	31	4.777346	KEEP	0	5	127	61	1866	GG	1	1	0		-	7	60	199	0	0	11.400976	124	60	4189	297	ENST00000392585.2	0.053435	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	105575840	105575840	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105575840G>A			NA	NA				RP11-44N21.1 (10499 upstream) : JAG2 (31477 downstream)						NA		NA									NA						gcggtggctcgtgcctgtaat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.105575840G>A		NA		hg19		0.02	-0.157816	CTCxTGC	COVERED																																																																																			NOVEL					0			8	2.406397	KEEP	0	0	0	8	233	GG	0.99257	0.320408	0			3	60	86	0	0	6.679958	13	60	413	33		0.1875	0.322807
BRF1	2972	__UNKNOWN__	__UNKNOWN__	14	105693722	105693722	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105693722A>C	ENST00000546474.1	-	8	15748				BRF1_ENST00000379932.4_Intron|BRF1_ENST00000392557.4_Intron|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000551787.1_Intron|BRF1_ENST00000446501.2_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	NA		NA			gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		gtgccactgtactccagcctg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024	2972		General transcription factors	11551	protein-coding gene	gene with protein product		604902	TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2, BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)	TAF3B2, TAF3C, GTF3B	NA	7624363, 8943358	Standard	NM_001519	NM_145685	NA	Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.789-625T>G	chr14.hg19:g.105693722A>C		NA	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	hg19	CCDS10001.1	0.02	1.906219	TGTxCTC	COVERED																																																																																			NOVEL	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000074548.4	17	6.314924	KEEP	0	0	0	21	565	AA	0.999879	0.976747	0		-	5	28	174	0	0	12.639443	47	60	1385	90	ENST00000546474.1	0.096154	0.976865
BRF1	2972	__UNKNOWN__	__UNKNOWN__	14	105769454	105769454	__UNKNOWN__	5'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105769454T>C	ENST00000546474.1	-	0	12472				BRF1_ENST00000327359.3_Intron|PACS2_ENST00000430725.2_Intron|BRF1_ENST00000440513.3_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	NA		NA			gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		ttagtagagatggggtttcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024	2972		General transcription factors	11551	protein-coding gene	gene with protein product		604902	TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2, BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)	TAF3B2, TAF3C, GTF3B	NA	7624363, 8943358	Standard	NM_001519	NM_145685	NA	Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.-2488A>G	chr14.hg19:g.105769454T>C		NA	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	hg19	CCDS10001.1	0.02	3.426816	AGAxGGG	COVERED																																																																																			NOVEL	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000074548.4	15	8.591663	KEEP	3	6	159	85	2158	TT	1	0.999999	0		-	5	60	164	0	0	9.981812	104	60	2843	248	ENST00000546474.1	0.045872	0.999999
BRF1	2972	__UNKNOWN__	__UNKNOWN__	14	105769705	105769705	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105769705C>T	ENST00000546474.1	-	0	12221				BRF1_ENST00000327359.3_Intron|PACS2_ENST00000430725.2_Intron|BRF1_ENST00000440513.3_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	NA		NA			gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		ctcagcctcccaagtagctgg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024	2972		General transcription factors	11551	protein-coding gene	gene with protein product		604902	TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2, BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)	TAF3B2, TAF3C, GTF3B	NA	7624363, 8943358	Standard	NM_001519	NM_145685	NA	Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.-2739G>A	chr14.hg19:g.105769705C>T		NA	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	hg19	CCDS10001.1	0.02	-0.201751	TCCxAAG	COVERED																																																																																			NOVEL	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000074548.4	5	6.016765	KEEP	1	0	0	20	589	CC	0.999863	0.490477	0		-	3	60	88	0	0	6.427757	19	60	627	47	ENST00000546474.1	0.136364	0.490544
BRF1	2972	__UNKNOWN__	__UNKNOWN__	14	105774435	105774435	__UNKNOWN__	5'UTR	SNP	G	G	A	rs587673421		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105774435G>A	ENST00000546474.1	-	0	7491				BRF1_ENST00000327359.3_Intron|PACS2_ENST00000430725.2_Intron|BRF1_ENST00000440513.3_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	NA		NA			gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		caggagaatcgcttgaaccca	0.493		NA											G|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	20082	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024	2972		General transcription factors	11551	protein-coding gene	gene with protein product		604902	TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2, BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)	TAF3B2, TAF3C, GTF3B	NA	7624363, 8943358	Standard	NM_001519	NM_145685	NA	Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.-7469C>T	chr14.hg19:g.105774435G>A		NA	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	hg19	CCDS10001.1	0.02	1.243166	ATCxCTT	COVERED																																																																																			NOVEL	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000074548.4	9	3.767536	KEEP	0	2	55	32	871	GG	0.999998	0.998463	0		-	5	60	145	0	0	9.010224	67	60	2074	139	ENST00000546474.1	0.069444	0.998465
MTA1	9112	__UNKNOWN__	__UNKNOWN__	14	105928912	105928912	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:105928912C>A	ENST00000405646.1	+	10	989				MTA1_ENST00000331320.7_Intron|MTA1_ENST00000406191.1_Intron			Q13330	MTA1_HUMAN	metastasis associated 1	NA		NA			circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		gtctcaaaaacaaaaaTGGCT	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979	9112		GATA zinc finger domain containing	7410	protein-coding gene	gene with protein product		603526			NA	8083195, 7607577	Standard		NM_004689	NA	Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000405646.1:c.892-609C>A	chr14.hg19:g.105928912C>A		NA	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	hg19		0.02	-0.149115	AAAxAAA	COVERED																																																																																			NOVEL	MTA1-003	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000317851.1	12	4.2116	KEEP	0	0	0	14	416	CC	0.995343	0.290641	0		+	3	60	85	0	1	6.579166	13	60	435	41	ENST00000405646.1	0.1875	0.292001
IGHG3	3502	__UNKNOWN__	__UNKNOWN__	14	106236593	106236593	__UNKNOWN__	RNA	SNP	C	C	T	rs367634229		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:106236593C>T	ENST00000390551.2	-	0	435							P01860	IGHG3_HUMAN	immunoglobulin heavy constant gamma 3 (G3m marker)	NA		NA			complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)				NA						GCTCTTGTCCCGCCTTGAGCT	0.622		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								T		1,3793		0,1,1896	79	78	79			-0.3	0	14		79	17,8159		0,17,4071	no	intergenic				0,18,5967	TT,TC,CC	NA	0.2079,0.0264,0.1504			106236593	18,11952	1897	4088	5985					M12958		14q32.33	2012-10-02			ENSG00000211897	ENSG00000211897	3502		Immunoglobulins / IGH locus	5527	other	immunoglobulin gene		147120			NA	6808505	Standard	NG_001019	NG_001019	NA	Approved			P01860	OTTHUMG00000152539	ENST00000390551.2:	chr14.hg19:g.106236593C>T		NA	A2NU35	hg19		0.02	-0.340653	TCCxGCC	COVERED																																																																																			NOVEL	IGHG3-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	NA	IG_C_gene	OTTHUMT00000326654.1	2	2.707715	KEEP	8	0	0	9	271	CC	0.99257	0.859313	0		-	5	27	144	0	0	10.313684	34	60	1058	71	ENST00000390551.2	0.128205	0.865745
IGHV3-7	28452	__UNKNOWN__	__UNKNOWN__	14	106518704	106518704	__UNKNOWN__	RNA	SNP	C	C	T	rs199995238		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:106518704C>T	ENST00000390598.2	-	0	125									immunoglobulin heavy variable 3-7	NA		NA									NA						ACACTGGACACCTGCAAACAA	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													151	143	145			NA	NA	14		NA											NA				106518704		1885	4101	5986					M99649		14q32.33	2012-02-08			ENSG00000211938	ENSG00000211938	28452		Immunoglobulins / IGH locus	5620	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000152271	ENST00000390598.2:	chr14.hg19:g.106518704C>T		NA		hg19		0.02	1.360486	ACAxCTG	COVERED																																																																																			NOVEL	IGHV3-7-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000325659.1	16	6.686212	KEEP	18	2	56	42	1288	CC	0.999999	0.997552	0		-	6	51	175	0	0	11.523088	63	60	2107	187	ENST00000390598.2	0.086957	0.997553
IGHV3-48	28424	__UNKNOWN__	__UNKNOWN__	14	106993959	106993959	__UNKNOWN__	RNA	SNP	T	T	G	rs553838567		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:106993959T>G	ENST00000390624.2	-	0	284									immunoglobulin heavy variable 3-48	NA		NA									NA						ACTACTAATGTATGAAACCCA	0.502		NA											T|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	15418	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													134	150	145			NA	NA	14		NA											NA				106993959		1859	4092	5951					M99675		14q32.33	2012-02-08			ENSG00000211964	ENSG00000211964	28424		Immunoglobulins / IGH locus	5606	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151959	ENST00000390624.2:	chr14.hg19:g.106993959T>G		NA		hg19		0.02	1.593355	ATGxATG	COVERED																																																																																			NOVEL	IGHV3-48-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324605.1	6	2.706757	KEEP	7	0	0	9	247	TT	0.99254	0.988259	0		-	7	40	225	0	0	16.405056	54	60	1503	116	ENST00000390624.2	0.114754	0.995687
IGHV3-48	28424	__UNKNOWN__	__UNKNOWN__	14	106993964	106993964	__UNKNOWN__	RNA	SNP	A	A	G	rs572393864	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:106993964A>G	ENST00000390624.2	-	0	279									immunoglobulin heavy variable 3-48	NA		NA									NA						TAATGTATGAAACCCACTCCA	0.522		NA											N|||	3	0.000599042	0.0015	0.0	5008	,	,	NA	15812	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													130	147	142			NA	NA	14		NA											NA				106993964		1854	4089	5943					M99675		14q32.33	2012-02-08			ENSG00000211964	ENSG00000211964	28424		Immunoglobulins / IGH locus	5606	other	immunoglobulin gene		NA			NA		Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151959	ENST00000390624.2:	chr14.hg19:g.106993964A>G		NA		hg19		0.02	1.792193	TGAxACC	COVERED																																																																																			NOVEL	IGHV3-48-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324605.1	5	2.703634	KEEP	6	0	0	9	228	AA	0.99254	0.988259	0		-	7	40	229	0	0	16.803725	54	60	1623	118	ENST00000390624.2	0.114754	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	107099393	107099393	__UNKNOWN__	IGR	SNP	G	G	T	rs76492778	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:107099393G>T			NA	NA				IGHV4-61 (3731 upstream) : IGHV3-64 (14347 downstream)						NA		NA									NA						CCCCAGGCTGGACCAAGCCTT	0.562		NA											.|||	3041	0.607228	0.8359	0.4496	5008	,	,	NA	11296	0.5278	NA	0.4036	False	NA	,,,	NA	NA	NA	2504	0.7014	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.107099393G>T		NA		hg19		0.02	-0.289442	CTGxACC	COVERED																																																																																			NOVEL					0			3	4.212094	KEEP	5	0	0	14	417	GG	0.993072	0.755616	0			9	49	257	0	0	21.737274	23	60	759	65		0.28125	0.760887
IGHV1-69	28461	__UNKNOWN__	__UNKNOWN__	14	107170077	107170077	__UNKNOWN__	RNA	SNP	C	C	T	rs11845244	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:107170077C>T	ENST00000390633.2	-	0	265									immunoglobulin heavy variable 1-69	NA		NA									NA						GGGATGATCCCTCCCATCCAC	0.562		NA											.|||	2103	0.419928	0.3162	0.4078	5008	,	,	NA	24767	0.4752	NA	0.3628	False	NA	,,,	NA	NA	NA	2504	0.5706	NA	NA	NA								NA				0								C		950,3176		76,798,1189	216	172	186			-0.5	0	14	dbSNP_120	186	2826,5570		528,1770,1900	no	intergenic				604,2568,3089	TT,TC,CC	NA	33.6589,23.0247,30.1549			107170077	3776,8746	2063	4198	6261					L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973	28461		Immunoglobulins / IGH locus	5558	other	immunoglobulin gene		NA		IGHV1-E	NA	8469934	Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151862	ENST00000390633.2:	chr14.hg19:g.107170077C>T		NA		hg19		0.02	3.271138	TCCxTCC	COVERED																																																																																			NOVEL	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324207.1	2	3.310053	KEEP	0	0	0	11	345	CC	0.993072	0.993069	0		-	34	60	981	0	0	86.297216	67	60	2216	173	ENST00000390633.2	0.336634	0.999997
IGHV1-69	28461	__UNKNOWN__	__UNKNOWN__	14	107170128	107170128	__UNKNOWN__	RNA	SNP	C	C	T	rs11558005	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:107170128C>T	ENST00000390633.2	-	0	214									immunoglobulin heavy variable 1-69	NA		NA									NA						CAGCTGATAGCATAGCTGCTG	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C		583,3417		7,569,1424	181	142	155			-0.5	0	14	dbSNP_120	155	1567,6729		137,1293,2718	no	intergenic				144,1862,4142	TT,TC,CC	NA	18.8886,14.575,17.4854			107170128	2150,10146	2000	4148	6148					L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973	28461		Immunoglobulins / IGH locus	5558	other	immunoglobulin gene		NA		IGHV1-E	NA	8469934	Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151862	ENST00000390633.2:	chr14.hg19:g.107170128C>T		NA		hg19		0.02	1.245552	TAGxATA	COVERED																																																																																			NOVEL	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324207.1	0	2.406943	KEEP	0	0	0	8	243	CC	0.99257	0.992195	0		-	27	60	784	0	0	69.426563	51	60	1764	138	ENST00000390633.2	0.346154	0.999622
IGHV1-69	28461	__UNKNOWN__	__UNKNOWN__	14	107170247	107170247	__UNKNOWN__	RNA	SNP	A	A	G	rs369341963		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:107170247A>G	ENST00000390633.2	-	0	107									immunoglobulin heavy variable 1-69	NA		NA									NA						TGTGGAGAGGACACAGGGGTG	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													90	72	78			NA	NA	14		NA											NA				107170247		1923	4127	6050					L22582		14q32.33	2012-02-10			ENSG00000211973	ENSG00000211973	28461		Immunoglobulins / IGH locus	5558	other	immunoglobulin gene		NA		IGHV1-E	NA	8469934	Standard	NG_001019	NG_001019	NA	Approved				OTTHUMG00000151862	ENST00000390633.2:	chr14.hg19:g.107170247A>G		NA		hg19		0.02	1.783428	AGGxCAC	COVERED																																																																																			NOVEL	IGHV1-69-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	IG_V_gene	NA	IG_V_gene	OTTHUMT00000324207.1	3	2.706422	KEEP	0	0	0	9	243	AA	0.99254	0.988801	0		-	10	60	345	0	0	26.874425	59	60	1740	113	ENST00000390633.2	0.144928	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	14	107183575	107183575	__UNKNOWN__	IGR	SNP	G	G	T	rs371950679		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr14:107183575G>T			NA	NA				IGHV2-70 (4237 upstream) : IGHV3-72 (15356 downstream)						NA		NA									NA						GCCCCTTCCCGGGAGCCTGGC	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr14.hg19:g.107183575G>T		NA		hg19		0.02	1.234286	CCCxGGA	COVERED																																																																																			NOVEL					0			3	2.40648	KEEP	2	0	0	8	231	GG	0.99257	0.991275	0			5	47	148	0	0	9.247053	69	60	2242	132		0.067568	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20141870	20141870	__UNKNOWN__	IGR	SNP	A	A	C	rs200849888		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20141870A>C			NA	NA				RNU6-978P (52901 upstream) : IGHV1OR15-9 (28048 downstream)						NA		NA									NA						ctttatcataaattgtttatt	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20141870A>C		NA		hg19		0.02	-0.096492	ATAxATT	UNCOVERED																																																																																			NOVEL					0			6	2.405076	KEEP	5	0	0	8	212	AA	0	0	0			3	45	103	0	0	9.432901	5	60	161	30		0.375	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20407911	20407911	__UNKNOWN__	IGR	SNP	T	T	C	rs3933731	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20407911T>C			NA	NA				RP11-173D3.1 (54705 upstream) : CHEK2P2 (80085 downstream)						NA		NA									NA						ggattacagatatgagccaca	0.498		NA											C|||	2510	0.501198	0.5507	0.4726	5008	,	,	NA	35288	0.4921	NA	0.4851	False	NA	,,,	NA	NA	NA	2504	0.4806	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20407911T>C		NA		hg19		0.02	-0.157883	AGAxATG	COVERED																																																																																			NOVEL					0			4	2.405819	KEEP	0	0	0	8	215	TT	0.99257	0.320408	0			3	27	96	0	0	7.591861	14	51	429	38		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20443891	20443891	__UNKNOWN__	IGR	SNP	T	T	C	rs4102015	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20443891T>C			NA	NA				RP11-173D3.1 (90685 upstream) : CHEK2P2 (44105 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.413		NA											C|||	1754	0.35024	0.5045	0.3012	5008	,	,	NA	41400	0.2202	NA	0.3479	False	NA	,,,	NA	NA	NA	2504	0.3129	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20443891T>C		NA		hg19		0.02	-0.289418	TCAxGCC	COVERED																																																																																			NOVEL					0			6	2.405677	KEEP	2	0	0	8	215	TT	0.99257	0.755234	0			8	60	257	0	0	21.703661	24	60	700	62		0.25	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20448295	20448295	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20448295C>T			NA	NA				RP11-173D3.1 (95089 upstream) : CHEK2P2 (39701 downstream)						NA		NA									NA						tttgggaggccgaggcaggtg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20448295C>T		NA		hg19		0.02	2.985135	GGCxGAG	COVERED																																																																																			NOVEL					0			19	5.170429	KEEP	3	5	141	67	1865	CC	1	1	0			9	60	268	0	0	17.617225	100	60	3098	242		0.082569	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20452980	20452980	__UNKNOWN__	IGR	SNP	G	G	T	rs373969992		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20452980G>T			NA	NA				RP11-173D3.1 (99774 upstream) : CHEK2P2 (35016 downstream)						NA		NA									NA						agaggaggaaggatgagagga	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20452980G>T		NA		hg19		0.02	-0.105258	GAAxGAT	UNCOVERED																																																																																			NOVEL					0			6	2.407107	KEEP	1	0	0	8	244	GG	0	0	0			4	60	122	0	0	11.422768	5	60	161	29		0.444444	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20452984	20452984	__UNKNOWN__	IGR	SNP	G	G	A	rs376084464		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20452984G>A			NA	NA				RP11-173D3.1 (99778 upstream) : CHEK2P2 (35012 downstream)						NA		NA									NA						gaggaaggatgagaggagagg	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20452984G>A		NA		hg19		0.02	-0.096484	GATxAGA	UNCOVERED																																																																																			NOVEL					0			5	2.407149	KEEP	1	0	0	8	243	GG	0	0	0			4	60	123	0	0	11.523178	5	60	155	28		0.444444	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20454835	20454835	__UNKNOWN__	IGR	SNP	G	G	A	rs533567628	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20454835G>A			NA	NA				RP11-173D3.1 (101629 upstream) : CHEK2P2 (33161 downstream)						NA		NA									NA						cacccagctcggcctcccaaa	0.537		NA											g|||	138	0.0275559	0.0204	0.0879	5008	,	,	NA	51173	0.003	NA	0.0229	False	NA	,,,	NA	NA	NA	2504	0.0245	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20454835G>A		NA		hg19		0.02	-0.175434	CTCxGCC	COVERED																																																																																			NOVEL					0			6	2.407288	KEEP	0	0	0	8	249	GG	0.99257	0.384528	0			3	60	93	0	0	7.29182	14	60	441	40		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20460316	20460316	__UNKNOWN__	IGR	SNP	G	G	A	rs4932064	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20460316G>A			NA	NA				RP11-173D3.1 (107110 upstream) : CHEK2P2 (27680 downstream)						NA		NA									NA						ttgctctgtcgcccaggctgg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20460316G>A		NA		hg19		0.02	-0.157863	GTCxCCC	COVERED																																																																																			NOVEL					0			6	2.703678	KEEP	2	0	0	9	240	GG	0.99254	0.320398	0			4	60	105	0	1	8.63029	11	60	381	41		0.266667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20460397	20460397	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20460397A>G			NA	NA				RP11-173D3.1 (107191 upstream) : CHEK2P2 (27599 downstream)						NA		NA									NA						caagtagctgagactacaggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20460397A>G		NA		hg19		0.02	-0.263121	CTGxGAC	COVERED																																																																																			NOVEL					0			11	7.218247	KEEP	1	0	0	24	660	AA	0.999909	0.693605	0			5	49	163	0	0	12.897606	24	60	714	69		0.172414	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20462367	20462367	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20462367A>G			NA	NA				RP11-173D3.1 (109161 upstream) : CHEK2P2 (25629 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20462367A>G		NA		hg19		0.02	-0.315731	GGCxTGA	COVERED																																																																																			NOVEL					0			11	2.739491	KEEP	1	1	28	19	533	AA	0.99986	0.81835	0			4	60	125	0	0	9.175176	28	60	819	82		0.125	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20464212	20464212	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20464212C>G			NA	NA				RP11-173D3.1 (111006 upstream) : CHEK2P2 (23784 downstream)						NA		NA									NA						actttgggagcccgaggcagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20464212C>G		NA		hg19		0.02	-0.271953	GAGxCCG	COVERED																																																																																			NOVEL					0			10	3.309831	KEEP	0	0	0	11	340	CC	0.993072	0.712346	0			3	60	102	0	0	7.443701	26	60	890	66		0.103448	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20464473	20464473	__UNKNOWN__	IGR	SNP	A	A	G	rs57410305		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20464473A>G			NA	NA				RP11-173D3.1 (111267 upstream) : CHEK2P2 (23523 downstream)						NA		NA									NA						aaaaaGggccaggtgcagtgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20464473A>G		NA		hg19		0.02	-0.332693	GCCxGGT	COVERED																																																																																			NOVEL					0			30	8.413016	KEEP	4	0	0	28	742	AA	0.999957	0.851947	0			4	60	110	1	0	8.67362	15	60	419	82		0.210526	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20464778	20464778	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20464778A>G			NA	NA				RP11-173D3.1 (111572 upstream) : CHEK2P2 (23218 downstream)						NA		NA									NA						ATATATATATAGCTTCTCCTA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20464778A>G		NA		hg19		0.02	14.925375	TATxGCT	COVERED																																																																																			NOVEL					0			257	19.496459	KEEP	29	27	840	360	9820	AA	1	1	0			13	39	434	0	0	25.034845	367	60	10837	1164		0.034211	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20465087	20465087	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20465087G>C			NA	NA				RP11-173D3.1 (111881 upstream) : CHEK2P2 (22909 downstream)						NA		NA									NA						aaactcctgggctcaagtgat	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20465087G>C		NA		hg19		0.02	1.625355	TGGxCTC	COVERED																																																																																			NOVEL					0			35	10.566337	KEEP	23	1	34	47	1453	GG	1	0.999804	0			4	60	140	0	0	9.08258	73	60	2541	224		0.051948	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20467242	20467242	__UNKNOWN__	IGR	SNP	C	C	T	rs59808209		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20467242C>T			NA	NA				RP11-173D3.1 (114036 upstream) : CHEK2P2 (20754 downstream)						NA		NA									NA						GCTGGGCGTCCGACAAGCCTG	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20467242C>T		NA		hg19		0.02	1.42103	GTCxGAC	UNCOVERED																																																																																			NOVEL					0			3	2.399492	KEEP	24	0	0	8	222	CC	0	0	0			11	60	330	0	0	25.419238	54	60	1646	130		0.169231	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20467720	20467720	__UNKNOWN__	IGR	SNP	A	A	T	rs4427770	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20467720A>T			NA	NA				RP11-173D3.1 (114514 upstream) : CHEK2P2 (20276 downstream)						NA		NA									NA						acctcaggtgatccacccgct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20467720A>T		NA		hg19		0.02	-0.105234	GTGxTCC	UNCOVERED																																																																																			NOVEL					0			9	3.307754	KEEP	2	0	0	11	297	AA	0.993072	0.138863	0			3	60	83	0	0	6.932234	8	60	245	34		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20470720	20470720	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20470720T>C			NA	NA				RP11-173D3.1 (117514 upstream) : CHEK2P2 (17276 downstream)						NA		NA									NA						gagctgagactgagccattgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20470720T>C		NA		hg19		0.02	-0.087715	GACxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.70639	KEEP	4	0	0	9	241	TT	0	0	0			3	28	93	0	0	8.078542	7	60	217	24		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20475029	20475029	__UNKNOWN__	IGR	SNP	C	C	G	rs7403506	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20475029C>G			NA	NA				RP11-173D3.1 (121823 upstream) : CHEK2P2 (12967 downstream)						NA		NA									NA						gaagtgggagcatcaactgag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20475029C>G		NA		hg19		0.02	-0.228077	GAGxATC	COVERED																																																																																			NOVEL					0			11	2.407205	KEEP	2	0	0	8	246	CC	0.99257	0.578599	0			3	50	107	0	0	8.32639	19	60	655	53		0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20476141	20476141	__UNKNOWN__	IGR	SNP	G	G	A	rs8030110	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20476141G>A			NA	NA				RP11-173D3.1 (122935 upstream) : CHEK2P2 (11855 downstream)						NA		NA									NA						gtgagccactgtgcccagcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20476141G>A		NA		hg19		0.02	-0.175446	ACTxTGC	UNCOVERED																																																																																			NOVEL					0			4	2.406802	KEEP	1	0	0	8	239	GG	0	0	0			5	60	152	0	0	12.96684	13	60	440	44		0.277778	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20476942	20476942	__UNKNOWN__	IGR	SNP	C	C	T	rs4983659	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20476942C>T			NA	NA				RP11-173D3.1 (123736 upstream) : CHEK2P2 (11054 downstream)						NA		NA									NA						ACTGAAAAGTCGATGTCTTTC	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20476942C>T		NA		hg19		0.02	2.949911	AGTxGAT	COVERED																																																																																			NOVEL					0			5	2.938904	KEEP	0	1	26	19	533	CC	0.999863	0.999862	0			20	60	551	0	0	40.642435	107	60	3410	199		0.15748	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20502405	20502405	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20502405G>A			NA	NA				CHEK2P2 (5594 upstream) : snoU13 (54933 downstream)						NA		NA									NA						tgggattacaggcatgagcca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20502405G>A		NA		hg19		0.02	-0.28071	ACAxGCA	COVERED																																																																																			NOVEL					0			8	6.619759	KEEP	3	0	0	22	675	GG	0.999869	0.739575	0			3	60	92	0	0	6.39849	27	60	906	85		0.1	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20539858	20539858	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20539858A>G			NA	NA				CHEK2P2 (43047 upstream) : snoU13 (17480 downstream)						NA		NA									NA						caaagtgctgagatgacaggc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20539858A>G		NA		hg19		0.02	-0.438526	CTGxGAT	COVERED																																																																																			NOVEL					0			14	6.315713	KEEP	5	0	0	21	576	AA	0.99986	0.959724	0			4	60	128	1	0	8.770997	43	60	1316	115		0.085106	0.959859
RP11-509A17.3	0	__UNKNOWN__	__UNKNOWN__	15	20561192	20561192	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20561192C>T	ENST00000557528.1	+	0	760										NA		NA									NA						ggcgtgatctcggctcactgc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000557528.1:	chr15.hg19:g.20561192C>T		NA		hg19		0.02	1.047988	TCTxGGC	COVERED																																																																																			NOVEL	RP11-509A17.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000414658.1	18	14.133571	KEEP	6	0	0	47	1324	CC	1	0.999622	0		+	5	60	138	1	0	8.165834	72	60	2248	184	ENST00000557528.1	0.064935	0.999622
HERC2P3	283755	__UNKNOWN__	__UNKNOWN__	15	20591017	20591017	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20591017T>C	ENST00000428453.1	-	0	4041							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3	NA		NA					metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						cccgcctcagtctcccaaagt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229	283755			4871	pseudogene	pseudogene		NA			NA	9730612	Standard	NG_008269	NR_036432	NA	Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175	ENST00000428453.1:	chr15.hg19:g.20591017T>C		NA		hg19		0.02	-0.166664	CAGxCTC	COVERED																																																																																			NOVEL	HERC2P3-014	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000347772.2	7	2.706893	KEEP	3	0	0	9	249	TT	0.99254	0.351306	0		-	3	49	100	1	0	7.910059	15	60	472	51	ENST00000428453.1	0.166667	0.353947
HERC2P3	283755	__UNKNOWN__	__UNKNOWN__	15	20599588	20599588	__UNKNOWN__	RNA	SNP	C	C	T	rs12592472	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20599588C>T	ENST00000428453.1	-	0	4041							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3	NA		NA					metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						agcattgaaactgtaaatcac	0.318		NA											C|||	345	0.0688898	0.0038	0.0605	5008	,	,	NA	51364	0.123	NA	0.0676	False	NA	,,,	NA	NA	NA	2504	0.1084	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229	283755			4871	pseudogene	pseudogene		NA			NA	9730612	Standard	NG_008269	NR_036432	NA	Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175	ENST00000428453.1:	chr15.hg19:g.20599588C>T		NA		hg19		0.02	-0.236802	AAAxTGT	COVERED																																																																																			NOVEL	HERC2P3-014	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000347772.2	0	3.00842	KEEP	1	0	0	10	292	CC	0.992708	0.607941	0		-	5	60	142	0	0	10.969238	22	60	680	40	ENST00000428453.1	0.185185	0.612407
HERC2P3	283755	__UNKNOWN__	__UNKNOWN__	15	20694935	20694935	__UNKNOWN__	RNA	SNP	A	A	C	rs370356072		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20694935A>C	ENST00000428453.1	-	0	157							Q9BVR0	HRC23_HUMAN	hect domain and RLD 2 pseudogene 3	NA		NA					metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(1)|lung(14)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	35						caagcgatccacccgcctcag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF041081		15q11.2	2010-08-02			ENSG00000180229	ENSG00000180229	283755			4871	pseudogene	pseudogene		NA			NA	9730612	Standard	NG_008269	NR_036432	NA	Approved	D15F37S4, LOC283755	uc001ytg.3	Q9BVR0	OTTHUMG00000157175	ENST00000428453.1:	chr15.hg19:g.20694935A>C		NA		hg19		0.02	-0.201593	TCCxCCC	UNCOVERED																																																																																			NOVEL	HERC2P3-014	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000347772.2	8	2.405978	KEEP	4	0	0	8	223	AA	0	0	0		-	4	47	135	0	0	11.064652	16	48	450	55	ENST00000428453.1	0.2	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	20859386	20859386	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:20859386G>C			NA	NA				AC131280.1 (81934 upstream) : NBEAP1 (10667 downstream)						NA		NA									NA						gtctcaaactgctgacctcgt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.20859386G>C		NA		hg19		0.02	-0.254401	ACTxCTG	COVERED																																																																																			NOVEL					0			10	3.912082	KEEP	1	0	0	13	412	GG	0.994391	0.664773	0			3	36	98	0	0	7.194647	23	60	787	61		0.115385	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	21912753	21912753	__UNKNOWN__	IGR	SNP	G	G	A	rs1401548		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:21912753G>A			NA	NA				RP11-854K16.3 (577329 upstream) : RP11-32B5.7 (28393 downstream)						NA		NA									NA						ctgcagcctcgacctctcagg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.21912753G>A		NA		hg19		0.02	-0.122738	CTCxACC	COVERED																																																																																			NOVEL					0			12	2.406329	KEEP	0	0	0	8	229	GG	0.99257	0.194853	0			5	60	148	0	0	13.895102	6	60	176	28		0.454545	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	21934350	21934350	__UNKNOWN__	IGR	SNP	C	C	T	rs8030398	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:21934350C>T			NA	NA				RP11-854K16.3 (598926 upstream) : RP11-32B5.7 (6796 downstream)						NA		NA									NA						AGGTAACTATCGAAGAAGTTG	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.21934350C>T		NA		hg19		0.02	3.128079	TATxGAA	COVERED																																																																																			NOVEL					0			3	4.812535	KEEP	0	0	0	16	460	CC	0.997832	0.99783	0			24	60	720	0	0	57.478349	95	60	3056	200		0.201681	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	21935194	21935194	__UNKNOWN__	IGR	SNP	C	C	A	rs1996585	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:21935194C>A			NA	NA				RP11-854K16.3 (599770 upstream) : RP11-32B5.7 (5952 downstream)						NA		NA									NA						TGTTTTTTTACATTAATAGTC	0.289		NA											c|||	2509	0.500998	0.4697	0.5533	5008	,	,	NA	47544	0.504	NA	0.5159	False	NA	,,,	NA	NA	NA	2504	0.4877	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.21935194C>A		NA		hg19		0.02	1.420632	TTAxATT	COVERED																																																																																			NOVEL					0			2	3.008672	KEEP	0	0	0	10	297	CC	0.992708	0.992664	0			39	60	1168	0	0	106.79206	59	60	2003	154		0.397959	0.999956
RP11-69H14.6	0	__UNKNOWN__	__UNKNOWN__	15	22319295	22319295	__UNKNOWN__	RNA	SNP	T	T	C	rs4779264	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:22319295T>C	ENST00000558896.1	+	0	194										NA		NA									NA						TGGGCCACAGTAGGATAGCTG	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000558896.1:	chr15.hg19:g.22319295T>C		NA		hg19		0.02	-0.43852	CAGxAGG	COVERED																																																																																			NOVEL	RP11-69H14.6-001	KNOWN	basic	sense_overlapping	NA	sense_overlapping	OTTHUMT00000417625.1	3	3.608565	KEEP	0	0	0	12	322	TT	0.993634	0.953748	0		+	17	60	589	0	0	53.276718	32	60	947	83	ENST00000558896.1	0.346939	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22531641	22531641	__UNKNOWN__	IGR	SNP	C	C	T	rs28494164		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:22531641C>T			NA	NA				MIR1268A (18361 upstream) : MIR4509-2 (143506 downstream)						NA		NA									NA						ggtgtggtggcgcatgccttt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22531641C>T		NA		hg19		0.02	-0.201689	TGGxGCA	COVERED																																																																																			NOVEL					0			3	2.406241	KEEP	0	0	0	8	229	CC	0.99257	0.4869	0			8	60	214	0	0	19.152989	13	60	412	43		0.380952	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22581755	22581755	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:22581755A>G			NA	NA				MIR1268A (68475 upstream) : MIR4509-2 (93392 downstream)						NA		NA									NA						gcatgatctcagctcactgca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22581755A>G		NA		hg19		0.02	-0.122801	CTCxGCT	COVERED																																																																																			NOVEL					0			4	2.706103	KEEP	4	0	0	9	241	AA	0.99257	0.194853	0			3	48	100	0	0	8.501168	9	54	272	37		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	22688131	22688131	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:22688131T>C			NA	NA				MIR4509-2 (12890 upstream) : GOLGA8DP (16589 downstream)						NA		NA									NA						gatcacaccattgcactccag	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.22688131T>C		NA		hg19		0.02	-0.166646	CCAxTGC	COVERED																																																																																			NOVEL					0			7	3.907388	KEEP	3	0	0	13	333	TT	0.993072	0.351495	0			3	47	101	0	0	8.010071	15	48	453	42		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	23891834	23891834	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:23891834G>C			NA	NA				MAGEL2 (659 upstream) : NDN (38730 downstream)						NA		NA									NA						GCGGGCCCTGGGGAACCTGCG	0.682		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													2	2	2			NA	NA	15		NA											NA				23891834		513	1291	1804	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.23891834G>C		NA		hg19		0.02	1.721923	CTGxGGA	COVERED																																																																																			NOVEL					0			2	3.008859	KEEP	0	0	0	10	307	GG	0.992708	0.991413	0			22	60	723	0	0	63.238367	52	60	1781	130		0.297297	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	24068623	24068623	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:24068623A>G			NA	NA				RNU6-741P (45933 upstream) : RP11-484P15.1 (88932 downstream)						NA		NA									NA						ctcgtgatccacctgcctcgg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.24068623A>G		NA		hg19		0.02	-0.105219	TCCxCCT	UNCOVERED																																																																																			NOVEL					0			3	3.007527	KEEP	8	0	0	10	276	AA	0	0	0			3	60	98	0	0	8.301765	9	60	247	38		0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	24089326	24089326	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:24089326G>A			NA	NA				RNU6-741P (66636 upstream) : RP11-484P15.1 (68229 downstream)						NA		NA									NA						cggcctcccagagtgctggga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.24089326G>A		NA		hg19		0.02	-0.122814	CCAxAGT	COVERED																																																																																			NOVEL					0			8	2.708327	KEEP	1	0	0	9	285	GG	0.99254	0.194847	0			3	60	91	0	0	7.481773	10	60	344	34		0.230769	0.196312
UBE3A	7337	__UNKNOWN__	__UNKNOWN__	15	25656716	25656716	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:25656716A>G	ENST00000566215.1	-	2	117				SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000232165.3_Intron			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	NA		NA			androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		cagcctgggcaacagagcaag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	7337	6.3.2.19		12496	protein-coding gene	gene with protein product	Angelman syndrome	601623	human papilloma virus E6-associated protein	EPVE6AP, HPVE6A	NA	8221889	Standard	NM_000462	NM_130838	NA	Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000566215.1:c.468+338T>C	chr15.hg19:g.25656716A>G		NA	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	hg19	CCDS32177.1	0.02	-0.403463	GGCxACA	COVERED																																																																																			NOVEL	UBE3A-002	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434202.1	12	7.518685	KEEP	0	0	0	25	689	AA	0.999931	0.941676	0		-	3	60	104	1	0	7.140264	39	60	1171	102	ENST00000566215.1	0.071429	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	25841491	25841491	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:25841491C>T			NA	NA				AC124997.1 (17553 upstream) : ATP10A (80928 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.25841491C>T		NA		hg19		0.02	-0.070156	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			5	3.00686	KEEP	0	0	0	10	287	CC	0.992708	0.053742	0			3	60	86	0	0	7.954173	4	60	123	24		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	26484274	26484274	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:26484274A>G			NA	NA				LINC00929 (112756 upstream) : AC009878.2 (155944 downstream)						NA		NA									NA						gccaatcccaacactttggga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.26484274A>G		NA		hg19		0.02	-0.087695	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			3	2.405398	KEEP	0	0	0	8	214	AA	0.99257	0.09898	0			3	60	96	0	0	8.378984	7	60	196	27		0.3	0.099721
GABRG3	2567	__UNKNOWN__	__UNKNOWN__	15	27778215	27778215	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:27778215T>C	ENST00000333743.6	+	0	1846				RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	NA		NA			gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	cacacacacatacatacacac	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(114;800 1656 7410 37729 45293)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256	2567		GABA receptors, Ligand-gated ion channels / GABA(A) receptors	4088	protein-coding gene	gene with protein product	GABA(G) receptor, gamma 3	600233			NA	7601451	Standard		NM_033223	NA	Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.*188T>C	chr15.hg19:g.27778215T>C		NA	G3V594|Q9HD46|Q9NYT2	hg19	CCDS45195.1	0.02	1.537854	ACAxACA	COVERED																																																																																			NOVEL	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000103584.2	34	5.578207	KEEP	0	2	49	36	983	TT	1	0.99994	0		+	5	60	172	0	0	11.305321	81	60	2429	201	ENST00000333743.6	0.05814	0.99994
HERC2	8924	__UNKNOWN__	__UNKNOWN__	15	28477454	28477454	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:28477454C>T	ENST00000261609.7	-	30	4784					NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2	NA		NA								NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		tttgggaggccgaggcaggca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731	8924			4868	protein-coding gene	gene with protein product		605837	hect domain and RLD 2		NA	9949213	Standard	NM_004667	NM_004667	NA	Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.4675+837G>A	chr15.hg19:g.28477454C>T		NA		hg19	CCDS10021.1	0.02	-0.192984	GGCxGAG	COVERED																																																																																			NOVEL	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251358.2	7	3.610657	KEEP	4	0	0	12	374	CC	0.993072	0.454585	0		-	3	42	92	0	0	6.89254	18	60	600	57	ENST00000261609.7	0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	30221007	30221007	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:30221007T>A			NA	NA				RP11-680F8.3 (104723 upstream) : RP11-143J24.1 (76638 downstream)						NA		NA									NA						tagctgggcgtggtggtgggc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.30221007T>A		NA		hg19		0.02	-0.087701	GCGxGGT	UNCOVERED																																																																																			NOVEL					0			12	3.007071	KEEP	12	0	0	10	266	TT	0	0	0			3	20	90	0	0	7.943699	6	51	171	38		0.333333	0.099721
TRPM1	4308	__UNKNOWN__	__UNKNOWN__	15	31448228	31448228	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:31448228C>T	ENST00000542188.1	-	1	368					NM_001252020.1	NP_001238949.1			transient receptor potential cation channel, subfamily M, member 1	NA		NA								NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		ggtgaaaccccgtctctacta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160	4308		Voltage-gated ion channels / Transient receptor potential cation channels	7146	protein-coding gene	gene with protein product		603576	melastatin 1	MLSN1	NA	9806836, 9537257, 16382100	Standard	NM_002420	NM_001252020	NA	Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000542188.1:c.54+4880G>A	chr15.hg19:g.31448228C>T		NA		hg19	CCDS58347.1	0.02	-0.096456	CCCxGTC	UNCOVERED																																																																																			NOVEL	TRPM1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding		5	2.406633	KEEP	2	0	0	8	233	CG	0.99254	0.119538	0		-	3	60	83	0	0	7.243314	6	60	182	29	ENST00000542188.1	0.333333	0.120436
OTUD7A	161725	__UNKNOWN__	__UNKNOWN__	15	31810472	31810472	__UNKNOWN__	Intron	SNP	C	C	A	rs12440031	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:31810472C>A	ENST00000307050.4	-	6	965				OTUD7A_ENST00000382902.1_Intron	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	NA		NA			protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		gtcaggagatcgagaccatcc	0.507		NA											C|||	1002	0.20008	0.0424	0.3055	5008	,	,	NA	20150	0.3671	NA	0.1968	False	NA	,,,	NA	NA	NA	2504	0.1697	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918	161725		OTU domain containing	20718	protein-coding gene	gene with protein product		612024	chromosome 15 open reading frame 16, OTU domain containing 7, OTU domain containing 7A	C15orf16, OTUD7	NA	23827681	Standard	NM_130901	NM_130901	NA	Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.872+8079G>T	chr15.hg19:g.31810472C>A		NA	Q8IWK5	hg19	CCDS10026.1	0.02	-0.201734	GATxGAG	COVERED																																																																																			NOVEL	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251393.2	24	3.674347	KEEP	18	2	53	31	900	CC	0.999892	0.490492	0		-	11	60	316	0	0	30.222235	11	60	358	98	ENST00000307050.4	0.5	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	32310536	32310536	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:32310536C>T			NA	NA				SNORA18 (89899 upstream) : CHRNA7 (12154 downstream)						NA		NA									NA						ctggctaacacggtgaaaccc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.32310536C>T		NA		hg19		0.02	-0.070167	ACAxGGT	UNCOVERED																																																																																			NOVEL					0			4	2.706378	KEEP	1	0	0	9	245	CC	0.99254	0.053733	0			3	40	87	0	0	8.054664	4	60	125	23		0.428571	0.054137
AC123768.4	0	__UNKNOWN__	__UNKNOWN__	15	32901467	32901467	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:32901467T>C	ENST00000576873.1	-	0	724										NA		NA									NA						ccggtcgcagtggctcacacc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000576873.1:	chr15.hg19:g.32901467T>C		NA		hg19		0.02	-0.175407	CAGxGGC	COVERED																																																																																			NOVEL	AC123768.4-201	NOVEL	basic	lincRNA	NA	lincRNA		6	3.909809	KEEP	1	0	0	13	357	TT	0.993634	0.38494	0		-	3	27	95	0	1	7.333634	16	60	469	44	ENST00000576873.1	0.157895	0.387407
RYR3	6263	__UNKNOWN__	__UNKNOWN__	15	33632058	33632058	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:33632058C>G	ENST00000389232.4	+	1	121				RYR3_ENST00000415757.3_Intron	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	NA		NA			calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		ccactgcactccagcctgggc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838	6263		Ion channels / Ryanodine receptors, EF-hand domain containing	10485	protein-coding gene	gene with protein product		180903			NA	8276408	Standard		NM_001036	NA	Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.51+28761C>G	chr15.hg19:g.33632058C>G		NA	O15175|Q15412	hg19	CCDS45210.1	0.02	-0.052633	ACTxCAG	UNCOVERED																																																																																			NOVEL	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417514.1	8	2.407114	KEEP	7	0	0	8	243	CC	0	0	0		+	2	34	74	0	0	6.892928	3	48	95	22	ENST00000389232.4	0.4	0.036766
AVEN	57099	__UNKNOWN__	__UNKNOWN__	15	34242955	34242955	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:34242955T>C	ENST00000306730.3	-	2	575					NM_020371.2	NP_065104.1	Q9NQS1	AVEN_HUMAN	apoptosis, caspase activation inhibitor	NA		NA			apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	intracellular (GO:0005622)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)|stomach(1)	7		all_lung(180;1.78e-08)		all cancers(64;1.66e-15)|GBM - Glioblastoma multiforme(113;1.42e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0359)		acctgtaatctcagcactttg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF283508	CCDS10030.1	15q13.1	2011-10-19		2008-07-07	ENSG00000169857	ENSG00000169857	57099			13509	protein-coding gene	gene with protein product	cell death regulator aven, programmed cell death 12	605265			NA	10949025	Standard	NM_020371	XM_005254563	NA	Approved	PDCD12	uc001zhj.3	Q9NQS1	OTTHUMG00000129371	ENST00000306730.3:c.445+52277A>G	chr15.hg19:g.34242955T>C		NA		hg19	CCDS10030.1	0.02	-0.184201	ATCxCAG	COVERED																																																																																			NOVEL	AVEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251523.2	7	4.511359	KEEP	0	0	0	15	414	TT	0.99649	0.421991	0		-	3	60	98	0	0	7.633271	16	60	503	54	ENST00000306730.3	0.157895	0.423478
CHRM5	1133	__UNKNOWN__	__UNKNOWN__	15	34333001	34333001	__UNKNOWN__	Intron	SNP	C	C	T	rs2684943	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:34333001C>T	ENST00000383263.5	+	2	263				CHRM5_ENST00000557872.1_Intron	NM_012125.3	NP_036257.1	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	NA		NA			adenylate cyclase-inhibiting G-protein coupled acetylcholine receptor signaling pathway (GO:0007197)|cell proliferation (GO:0008283)|dopamine transport (GO:0015872)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|gastric acid secretion (GO:0001696)|metabolic process (GO:0008152)|regulation of phosphatidylinositol dephosphorylation (GO:0060304)|transmission of nerve impulse (GO:0019226)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|skin(1)	20		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Darifenacin(DB00496)|Desipramine(DB01151)|Doxepin(DB01142)|Fesoterodine(DB06702)|Homatropine Methylbromide(DB00725)|Imipramine(DB00458)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paroxetine(DB00715)|Pethidine(DB00454)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Tolterodine(DB01036)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Ziprasidone(DB00246)	tgcctatagtcccactacttg	0.473		NA											C|||	2066	0.41254	0.0605	0.5677	5008	,	,	NA	19041	0.4821	NA	0.5915	False	NA	,,,	NA	NA	NA	2504	0.5225	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10031.1	15q26	2012-08-08			ENSG00000184984	ENSG00000184984	1133		Cholinergic receptors, GPCR / Class A : Cholinergic receptors, muscarinic	1954	protein-coding gene	gene with protein product	acetylcholine receptor, muscarinic 5	118496			NA		Standard		NM_012125	NA	Approved		uc001zhk.1	P08912	OTTHUMG00000129369	ENST00000383263.5:c.-407-5740C>T	chr15.hg19:g.34333001C>T		NA	Q96RG7	hg19	CCDS10031.1	0.02	-0.096492	AGTxCCA	UNCOVERED																																																																																			NOVEL	CHRM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251521.2	1	2.708139	KEEP	0	0	0	9	278	CC	0.99254	0.119538	0		+	4	60	124	0	0	11.385197	6	60	196	34	ENST00000383263.5	0.4	0.120436
EMC4	51234	__UNKNOWN__	__UNKNOWN__	15	34521157	34521157	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:34521157A>G	ENST00000559421.1	+	3	250				EMC4_ENST00000267750.4_Intron|EMC4_ENST00000559078.1_Intron|EMC4_ENST00000249209.4_Intron			Q5J8M3	EMC4_HUMAN	ER membrane protein complex subunit 4	NA		NA			apoptotic process (GO:0006915)	ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)					NA						ccaaagtgctaggattacagg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC016348	CCDS10035.1, CCDS66732.1	15q14	2012-05-23	2012-05-23	2012-05-23	ENSG00000128463	ENSG00000128463	51234			28032	protein-coding gene	gene with protein product		NA	transmembrane protein 85	TMEM85	NA	18586032, 22119785	Standard	NM_016454	NM_001286420	NA	Approved	FLJ90746, MGC24415, PIG17	uc001zhq.3	Q5J8M3	OTTHUMG00000129411	ENST00000559421.1:c.202-797A>G	chr15.hg19:g.34521157A>G		NA	A8K3A9|B4DJQ4|Q96KX9|Q9BUI5|Q9P0T9	hg19		0.02	1.643028	GCTxGGA	COVERED																																																																																			NOVEL	EMC4-012	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417985.1	38	4.535832	KEEP	0	6	161	72	2001	AA	1	0.999678	0		+	4	60	133	0	0	8.407989	72	60	2196	263	ENST00000559421.1	0.052632	0.999678
GOLGA8A	23015	__UNKNOWN__	__UNKNOWN__	15	34879864	34879864	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:34879864G>A	ENST00000543376.1	-	1	113							A7E2F4	GOG8A_HUMAN	golgin A8 family, member A	NA		NA				Golgi apparatus (GO:0005794)|membrane (GO:0016020)					NA		all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		tgatccacctgcctcggcctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648160	CCDS10038.1	15q14	2011-10-25	2010-02-12		ENSG00000175265	ENSG00000175265	23015			31972	protein-coding gene	gene with protein product		NA	golgi autoantigen, golgin subfamily a, 8A		NA	10660574, 10677249	Standard	NM_181076	NM_181077	NA	Approved	GM88, GOLGIN-67	uc001zii.3	A7E2F4	OTTHUMG00000129447	ENST00000543376.1:c.2641+727C>T	chr15.hg19:g.34879864G>A		NA	A7MCY9|B7ZMK5|O94937|Q52M46|Q68DK6|Q9NZG8|Q9NZW0|Q9NZW3	hg19		0.02	-0.11403	CCTxCCT	UNCOVERED																																																																																			NOVEL	GOLGA8A-203	KNOWN	basic|appris_candidate	protein_coding	NA	protein_coding		5	2.407059	KEEP	0	0	0	8	242	GG	0.99257	0.16126	0		-	4	60	109	0	0	9.490321	8	60	283	29	ENST00000543376.1	0.333333	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	35019892	35019892	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35019892T>C			NA	NA				CTD-2125J1.1 (71927 upstream) : GJD2 (23340 downstream)						NA		NA									NA						ggtgaaaccctgtctctacta	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.35019892T>C		NA		hg19		0.02	-0.09647	CCCxGTC	UNCOVERED																																																																																			NOVEL					0			4	3.910354	KEEP	0	0	0	13	370	TT	0.994391	0.119761	0			3	60	89	0	0	7.532403	8	60	238	33		0.272727	0.120436
AQR	9716	__UNKNOWN__	__UNKNOWN__	15	35229478	35229478	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35229478A>G	ENST00000156471.5	-	9	944					NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	NA		NA			mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		cacccacctcagcctcccaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776	9716			29513	protein-coding gene	gene with protein product	functional spliceosome-associated protein 164	610548	aquarius homolog (mouse)		NA	9626505, 16949364	Standard	NM_014691	NM_014691	NA	Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.718+1459T>C	chr15.hg19:g.35229478A>G		NA	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	hg19	CCDS42013.1	0.02	-0.201723	CTCxGCC	COVERED																																																																																			NOVEL	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417526.2	6	2.406457	KEEP	1	0	0	8	228	AA	0.99257	0.4869	0		-	3	60	101	0	0	7.664841	20	60	596	47	ENST00000156471.5	0.130435	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	35375452	35375452	__UNKNOWN__	IGR	SNP	T	T	C	rs200313061		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35375452T>C			NA	NA				RP11-463I20.2 (72060 upstream) : RP11-323I15.5 (15770 downstream)						NA		NA									NA						ATTTACTCATTGAAACACTCG	0.303		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.35375452T>C		NA		hg19		0.02	1.534793	CATxGAA	COVERED																																																																																			NOVEL					0			49	25.33022	KEEP	16	2	53	103	2900	TT	1	0.999678	0			24	49	738	0	0	63.283816	61	60	1786	241		0.282353	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	35375498	35375498	__UNKNOWN__	IGR	SNP	G	G	T	rs111578807		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35375498G>T			NA	NA				RP11-463I20.2 (72106 upstream) : RP11-323I15.5 (15724 downstream)						NA		NA									NA						AGGAAAAATAGTTGTTTCATT	0.289		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.35375498G>T		NA		hg19		0.02	5.437921	ATAxTTG	COVERED																																																																																			NOVEL					0			35	20.484321	KEEP	15	4	104	105	3012	GG	1	1	0			69	51	2038	0	0	188.728343	93	60	3148	359		0.425926	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	35385608	35385608	__UNKNOWN__	IGR	SNP	C	C	G	rs535411142	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35385608C>G			NA	NA				RP11-463I20.2 (82216 upstream) : RP11-323I15.5 (5614 downstream)						NA		NA									NA						gggcgcggtgcctcacgcctg	0.463		NA											C|||	3	0.000599042	0.0015	0.0	5008	,	,	NA	14657	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.35385608C>G		NA		hg19		0.02	-0.307036	GTGxCTC	COVERED																																																																																			NOVEL					0			7	3.009109	KEEP	2	0	0	10	310	CC	0.99254	0.794276	0			3	60	106	0	0	7.79691	27	60	918	66		0.1	0.800245
DPH6	89978	__UNKNOWN__	__UNKNOWN__	15	35761191	35761191	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35761191T>C	ENST00000256538.4	-	4	339					NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	NA		NA			peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)				NA						atcgcttgaatccgggaggcg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	89978	6.3.1.14		30543	protein-coding gene	gene with protein product	diphthine--ammonia ligase	NA	ATP binding domain 4, DPH6 homolog (S. cerevisiae)	ATPBD4	NA	23169644, 23468660	Standard	NM_080650	NM_080650	NA	Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.313-14170A>G	chr15.hg19:g.35761191T>C		NA	B3KWG1|Q96HJ6	hg19	CCDS10043.1	0.02	-0.13155	GAAxCCG	COVERED																																																																																			NOVEL	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251973.1	4	2.401639	KEEP	0	0	0	8	201	TT	0.99257	0.22747	0		-	3	60	89	0	0	7.282207	10	60	295	33	ENST00000256538.4	0.230769	0.229173
DPH6-AS1	100507466	__UNKNOWN__	__UNKNOWN__	15	35935704	35935704	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:35935704T>C	ENST00000501169.2	+	0	279					NR_038251.1				DPH6 antisense RNA 1 (head to head)	NA		NA									NA						aacagaaaactaaataccaca	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC025664		15q14	2013-05-02	2013-05-02	2013-05-02	ENSG00000248079	ENSG00000248079	100507466		Long non-coding RNAs	44147	non-coding RNA	RNA, long non-coding		NA	ATPBD4 antisense RNA 1 (non-protein coding), ATPBD4 antisense RNA 1, ATPBD4 antisense RNA 1 (head to head)	ATPBD4-AS1	NA		Standard	NR_038251	NR_038251	NA	Approved				OTTHUMG00000172347	ENST00000501169.2:	chr15.hg19:g.35935704T>C		NA		hg19		0.02	-0.210488	AACxAAA	COVERED																																																																																			NOVEL	DPH6-AS1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000418019.1	5	2.705785	KEEP	0	0	0	9	235	TT	0.99254	0.518266	0		+	3	60	96	0	0	7.106943	21	60	635	46	ENST00000501169.2	0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	36686297	36686297	__UNKNOWN__	IGR	SNP	A	A	G	rs4381550	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:36686297A>G			NA	NA				RP11-475A13.2 (49930 upstream) : RP11-475A13.1 (44875 downstream)						NA		NA									NA						gggtttcaccatgttggccag	0.582		NA											a|||	4350	0.86861	0.9455	0.8329	5008	,	,	NA	14594	0.995	NA	0.7058	False	NA	,,,	NA	NA	NA	2504	0.8272	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.36686297A>G		NA		hg19		0.02	-0.122766	ACCxTGT	UNCOVERED																																																																																			NOVEL					0			14	3.908056	KEEP	13	0	0	13	344	AA	0	0	0			3	39	86	0	0	6.982435	10	44	281	45		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	37913215	37913215	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:37913215A>G			NA	NA				RP11-720L8.1 (130206 upstream) : TMCO5A (313611 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.37913215A>G		NA		hg19		0.02	-0.1754	GGCxTGA	COVERED																																																																																			NOVEL					0			6	2.706941	KEEP	0	0	0	9	251	AA	0.99254	0.384517	0			4	60	137	1	0	11.263177	16	60	457	42		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	38039532	38039532	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:38039532A>G			NA	NA				RP11-720L8.1 (256523 upstream) : TMCO5A (187294 downstream)						NA		NA									NA						caggagaattacttgaacctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.38039532A>G		NA		hg19		0.02	-0.07891	ATTxCTT	UNCOVERED																																																																																			NOVEL					0			2	2.404937	KEEP	0	0	0	8	206	AA	0.99254	0.076759	0			3	60	92	0	0	8.333075	5	60	139	24		0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	38718239	38718239	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:38718239T>C			NA	NA				SPRED1 (68789 upstream) : FAM98B (28088 downstream)						NA		NA									NA						tatgtccaggtgcggtggctc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.38718239T>C		NA		hg19		0.02	-0.052585	AGGxGCG	UNCOVERED																																																																																			NOVEL					0			2	2.405412	KEEP	0	0	0	8	215	TT	0.99257	0.036492	0			2	60	71	0	0	6.594463	3	60	77	21		0.4	0.036766
RP11-275I4.2	0	__UNKNOWN__	__UNKNOWN__	15	38969699	38969699	__UNKNOWN__	lincRNA	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:38969699A>T	ENST00000557946.1	+	0	287										NA		NA									NA						tgcctcagccacccgagtagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000557946.1:	chr15.hg19:g.38969699A>T		NA		hg19		0.02	-0.122787	GCCxCCC	COVERED																																																																																			NOVEL	RP11-275I4.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000418238.1	10	3.609006	KEEP	0	0	0	12	330	AA	0.993634	0.195062	0		+	3	60	87	0	0	6.973127	11	60	330	28	ENST00000557946.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	40614010	40614010	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:40614010T>A			NA	NA				RP11-133K1.6 (5175 upstream) : LINC00984 (3406 downstream)						NA		NA									NA						atggtctcaatctcctgacct	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.40614010T>A		NA		hg19		0.02	-0.148237	CAAxCTC	UNCOVERED																																																																																			NOVEL					0			4	2.404036	KEEP	1	0	0	8	201	TT	0	0	0			3	60	91	0	0	7.188808	13	60	317	33		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	40880384	40880384	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:40880384A>G			NA	NA				RPUSD2 (13725 upstream) : CASC5 (5833 downstream)						NA		NA									NA						acaggcgtgaaccaccgtgcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.40880384A>G		NA		hg19		0.02	-0.201713	TGAxCCA	COVERED																																																																																			NOVEL					0			7	2.70575	KEEP	2	0	0	9	241	AA	0.99257	0.4869	0			3	60	105	1	0	8.260812	17	60	487	49		0.15	0.490544
CASC5	57082	__UNKNOWN__	__UNKNOWN__	15	40941563	40941563	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:40941563T>A	ENST00000346991.5	+	19	6562				CASC5_ENST00000399668.2_Intron			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	NA		NA			acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		gcatgatctctgctcactgca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812	57082		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	24054	protein-coding gene	gene with protein product	cancer/testis antigen 29, kinetochore null 1 homolog (C. elegans), blinkin, bub-linking kinetochore protein, protein phosphatase 1, regulatory subunit 55	609173			NA	10980622, 10780384, 18045986	Standard	NM_144508	NM_170589	NA	Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.6173-936T>A	chr15.hg19:g.40941563T>A		NA	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	hg19	CCDS42023.1	0.02	-0.078934	CTCxGCT	UNCOVERED																																																																																			NOVEL	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000390224.2	6	3.609394	KEEP	1	0	0	12	336	GT	0.994391	0.076902	0		+	3	60	89	0	0	7.843477	6	60	176	33	ENST00000346991.5	0.333333	0.077336
RAD51	5888	__UNKNOWN__	__UNKNOWN__	15	40999535	40999535	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:40999535C>T	ENST00000267868.3	+	4	611				RAD51_ENST00000532743.1_Intron|RAD51_ENST00000423169.2_Intron|RAD51_ENST00000557850.1_Intron|RAD51_ENST00000382643.3_Intron	NM_002875.4	NP_002866.2	Q06609	RAD51_HUMAN	RAD51 recombinase	NA		NA			ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA unwinding involved in DNA replication (GO:0006268)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|mitotic recombination (GO:0006312)|positive regulation of DNA ligation (GO:0051106)|protein homooligomerization (GO:0051260)|reciprocal meiotic recombination (GO:0007131)|regulation of double-strand break repair via homologous recombination (GO:0010569)	condensed chromosome (GO:0000793)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|lateral element (GO:0000800)|mitochondrion (GO:0005739)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|PML body (GO:0016605)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA polymerase binding (GO:0070182)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|single-stranded DNA binding (GO:0003697)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		gacagagtctcactctgttac	0.532		NA						Homologous recombination													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13804	CCDS10062.1, CCDS53931.1, CCDS53932.1	15q15.1	2014-06-12	2013-07-02		ENSG00000051180	ENSG00000051180	5888			9817	protein-coding gene	gene with protein product	BRCA1/BRCA2-containing complex, subunit 5	179617	RAD51 (S. cerevisiae) homolog (E coli RecA homolog), RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae), RAD51 homolog (S. cerevisiae)	RAD51A, RECA	NA	8358431, 8479919	Standard	NM_002875, NM_133487	NM_002875	NA	Approved	HsRad51, HsT16930, BRCC5	uc010bbx.3	Q06609	OTTHUMG00000130067	ENST00000267868.3:c.343+1043C>T	chr15.hg19:g.40999535C>T		NA	B0FXP0|B2R8T6|Q6FHX9|Q6ZNA8|Q9BV60	hg19	CCDS10062.1	0.02	-0.087687	TCTxACT	UNCOVERED																																																																																			NOVEL	RAD51-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252358.1	3	2.707844	KEEP	1	0	0	9	268	CC	0.99257	0.09898	0		+	3	60	74	0	0	6.530277	5	60	167	29	ENST00000267868.3	0.375	0.099721
RAD51	5888	__UNKNOWN__	__UNKNOWN__	15	41006095	41006095	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41006095T>C	ENST00000267868.3	+	5	703				RAD51_ENST00000532743.1_Intron|RAD51_ENST00000423169.2_Intron|RAD51_ENST00000557850.1_Intron|RAD51_ENST00000382643.3_Intron	NM_002875.4	NP_002866.2	Q06609	RAD51_HUMAN	RAD51 recombinase	NA		NA			ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA unwinding involved in DNA replication (GO:0006268)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|mitotic recombination (GO:0006312)|positive regulation of DNA ligation (GO:0051106)|protein homooligomerization (GO:0051260)|reciprocal meiotic recombination (GO:0007131)|regulation of double-strand break repair via homologous recombination (GO:0010569)	condensed chromosome (GO:0000793)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|lateral element (GO:0000800)|mitochondrion (GO:0005739)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|PML body (GO:0016605)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA polymerase binding (GO:0070182)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|single-stranded DNA binding (GO:0003697)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.45e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000421)|COAD - Colon adenocarcinoma(120;0.163)		tgagccaccgtgcctggcTGG	0.478		NA						Homologous recombination													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13804	CCDS10062.1, CCDS53931.1, CCDS53932.1	15q15.1	2014-06-12	2013-07-02		ENSG00000051180	ENSG00000051180	5888			9817	protein-coding gene	gene with protein product	BRCA1/BRCA2-containing complex, subunit 5	179617	RAD51 (S. cerevisiae) homolog (E coli RecA homolog), RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae), RAD51 homolog (S. cerevisiae)	RAD51A, RECA	NA	8358431, 8479919	Standard	NM_002875, NM_133487	NM_002875	NA	Approved	HsRad51, HsT16930, BRCC5	uc010bbx.3	Q06609	OTTHUMG00000130067	ENST00000267868.3:c.435+4781T>C	chr15.hg19:g.41006095T>C		NA	B0FXP0|B2R8T6|Q6FHX9|Q6ZNA8|Q9BV60	hg19	CCDS10062.1	0.02	-0.131558	CCGxGCC	COVERED																																																																																			NOVEL	RAD51-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252358.1	6	2.406233	KEEP	0	0	0	8	223	TT	0.99257	0.22747	0		+	3	60	87	0	0	6.872674	12	60	361	30	ENST00000267868.3	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	41025344	41025344	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41025344G>A			NA	NA				RAD51 (990 upstream) : RMDN3 (2737 downstream)						NA		NA									NA						cctgggaggcggagggtgcgg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.41025344G>A		NA		hg19		0.02	-0.359579	GGCxGAG	COVERED																																																																																			NOVEL					0			100	14.667636	KEEP	107	1	26	58	1672	GG	0.99986	0.88875	0			4	60	115	0	0	8.638481	21	60	683	226		0.16	0.888875
INO80	54617	__UNKNOWN__	__UNKNOWN__	15	41344133	41344133	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41344133T>G	ENST00000361937.3	-	20	2699				INO80_ENST00000401393.3_Intron			Q9ULG1	INO80_HUMAN	INO80 complex subunit	NA		NA			ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						tccagcctggtcgacagagca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	54617	3.6.1.3	INO80 complex subunits	26956	protein-coding gene	gene with protein product	INO80 complex subunit A	610169	INO80 complex homolog 1 (S. cerevisiae), INO80 homolog (S. cerevisiae)	INOC1	NA	16298340, 16230350, 20237820	Standard	NM_017553	NM_017553	NA	Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.2275-1833A>C	chr15.hg19:g.41344133T>G		NA	A6H8X4|Q9NTG6	hg19	CCDS10071.1	0.02	-0.05263	TGGxCGA	UNCOVERED																																																																																			NOVEL	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252527.2	3	2.406014	KEEP	1	0	0	8	219	TT	0	0	0		-	2	44	72	0	0	6.495856	4	60	120	22	ENST00000361937.3	0.333333	0.036766
INO80	54617	__UNKNOWN__	__UNKNOWN__	15	41390328	41390328	__UNKNOWN__	Intron	SNP	G	G	A	rs542362227	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41390328G>A	ENST00000361937.3	-	2	382				INO80_ENST00000401393.3_Intron			Q9ULG1	INO80_HUMAN	INO80 complex subunit	NA		NA			ATP catabolic process (GO:0006200)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of cell growth (GO:0030307)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|spindle assembly (GO:0051225)|UV-damage excision repair (GO:0070914)	Ino80 complex (GO:0031011)|microtubule (GO:0005874)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			NS(1)|breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						gattacaggcgtgagccacca	0.448		NA											G|||	6	0.00119808	0.0008	0.0014	5008	,	,	NA	14149	0.0	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033085	CCDS10071.1	15q15.1	2013-08-21	2013-08-21	2008-08-07	ENSG00000128908	ENSG00000128908	54617	3.6.1.3	INO80 complex subunits	26956	protein-coding gene	gene with protein product	INO80 complex subunit A	610169	INO80 complex homolog 1 (S. cerevisiae), INO80 homolog (S. cerevisiae)	INOC1	NA	16298340, 16230350, 20237820	Standard	NM_017553	NM_017553	NA	Approved	KIAA1259, Ino80, hINO80, INO80A	uc001zni.3	Q9ULG1	OTTHUMG00000130209	ENST00000361937.3:c.43-1777C>T	chr15.hg19:g.41390328G>A		NA	A6H8X4|Q9NTG6	hg19	CCDS10071.1	0.02	-0.131574	GGCxTGA	COVERED																																																																																			NOVEL	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252527.2	9	3.911264	KEEP	3	0	0	13	386	GG	0.993634	0.227714	0		-	3	60	86	0	0	7.232274	8	60	257	43	ENST00000361937.3	0.272727	0.229173
EXD1	161829	__UNKNOWN__	__UNKNOWN__	15	41507878	41507878	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41507878C>T	ENST00000458580.2	-	6	713				EXD1_ENST00000314992.5_Intron			Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	NA		NA					3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						agcaagactccgtctcaaaaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997	161829			28507	protein-coding gene	gene with protein product		NA	exonuclease 3'-5' domain-like 1	EXDL1	NA	12477932	Standard	NM_152596	NM_001286441	NA	Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000458580.2:c.447+94G>A	chr15.hg19:g.41507878C>T		NA	A8K909|B7Z839|Q6ZW94	hg19		0.02	1.358074	CTCxGTC	COVERED																																																																																			NOVEL	EXD1-002	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000418943.1	9	4.810314	KEEP	1	3	79	44	1291	CC	1	0.989542	0		-	6	60	179	1	0	12.438622	51	60	1676	143	ENST00000458580.2	0.105263	0.989542
NUSAP1	51203	__UNKNOWN__	__UNKNOWN__	15	41657543	41657543	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41657543T>C	ENST00000450592.2	+	6	678				NUSAP1_ENST00000558123.1_Intron|NUSAP1_ENST00000450318.1_Intron|NUSAP1_ENST00000559596.1_Intron|NUSAP1_ENST00000414849.2_Intron|NUSAP1_ENST00000560747.1_Intron|NUSAP1_ENST00000260359.6_Intron|NUSAP1_ENST00000560177.1_Intron			Q9BXS6	NUSAP_HUMAN	nucleolar and spindle associated protein 1	NA		NA			establishment of mitotic spindle localization (GO:0040001)|mitotic chromosome condensation (GO:0007076)|mitotic cytokinesis (GO:0000281)|mitotic sister chromatid segregation (GO:0000070)|positive regulation of mitosis (GO:0045840)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	13		all_cancers(109;5.07e-19)|all_epithelial(112;2.43e-16)|Lung NSC(122;1.81e-11)|all_lung(180;4.81e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;9.63e-17)|GBM - Glioblastoma multiforme(113;1.59e-06)|BRCA - Breast invasive adenocarcinoma(123;0.168)		ttagtagagatggggtttcac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF290612	CCDS45234.1, CCDS45236.1, CCDS58356.1, CCDS58357.1, CCDS58358.1, CCDS73708.1	15q14	2008-02-05				ENSG00000137804	51203			18538	protein-coding gene	gene with protein product		612818			NA	12963707	Standard	NM_016359	NM_016359	NA	Approved	FLJ13421, LNP, ANKT, NuSAP1, SAPL, BM037, PRO0310p1, Q0310	uc001zns.4	Q9BXS6		ENST00000450592.2:c.592-60T>C	chr15.hg19:g.41657543T>C		NA	B4DDF1|E7ERR5|J3KN21|Q53GW2|Q8TBT4|Q96E58|Q96FJ1|Q9GZM9|Q9NZ85|Q9UI70	hg19	CCDS58358.1	0.02	-0.368233	AGAxGGG	COVERED																																																																																			NOVEL	NUSAP1-005	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419426.1	2	3.907055	KEEP	0	0	0	13	330	TT	0.994391	0.894269	0		+	3	60	97	1	2	6.507923	37	60	1017	58	ENST00000450592.2	0.075	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	41704048	41704048	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41704048C>T			NA	NA				NDUFAF1 (9406 upstream) : RTF1 (5253 downstream)						NA		NA									NA						gccacgagttcgagaccagcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.41704048C>T		NA		hg19		0.02	-0.192964	GTTxGAG	COVERED																																																																																			NOVEL					0			10	4.512833	KEEP	0	0	0	15	446	CC	0.99649	0.45615	0			3	60	85	0	0	6.49307	14	60	444	57		0.176471	0.457757
RPAP1	26015	__UNKNOWN__	__UNKNOWN__	15	41826356	41826356	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41826356T>C	ENST00000561603.1	-	6	878				RPAP1_ENST00000304330.4_Intron			Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	NA		NA				nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		tggctcatgcttgtaatccta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932	26015			24567	protein-coding gene	gene with protein product		611475			NA	10718198	Standard	NM_015540	XM_005254297	NA	Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000561603.1:c.763+555A>G	chr15.hg19:g.41826356T>C		NA	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	hg19		0.02	-0.069443	TGCxTGT	UNCOVERED																																																																																			NOVEL	RPAP1-004	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420208.1	6	3.006838	KEEP	2	0	0	10	271	TT	0.99254	0.053733	0		-	2	45	71	1	0	6.413418	4	60	99	25	ENST00000561603.1	0.333333	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	41849274	41849274	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:41849274C>T			NA	NA				RPAP1 (12817 upstream) : TYRO3 (598 downstream)						NA		NA									NA						CCTGATGCCACGTATGTCAAA	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.41849274C>T		NA		hg19		0.02	-0.298237	CCAxGTA	COVERED																																																																																			NOVEL					0			0	2.706962	KEEP	0	0	0	9	256	CC	0.99254	0.775233	0			3	60	96	0	0	6.667797	30	60	993	70		0.090909	0.78106
SPTBN5	51332	__UNKNOWN__	__UNKNOWN__	15	42171120	42171120	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:42171120C>T	ENST00000320955.6	-	17	3410					NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	NA		NA			actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		aaaaattagccaggcatggtg	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877	51332			15680	protein-coding gene	gene with protein product	beta V spectrin	605916			NA	10764729	Standard	NM_016642	NM_016642	NA	Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.3183-293G>A	chr15.hg19:g.42171120C>T		NA		hg19		0.02	-0.122809	AGCxAGG	COVERED																																																																																			NOVEL	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000420237.1	16	3.309985	KEEP	10	0	0	11	341	CC	0.992708	0.19488	0		-	4	46	119	0	0	10.3234	9	60	308	50	ENST00000320955.6	0.307692	0.196312
SNAP23	8773	__UNKNOWN__	__UNKNOWN__	15	42789302	42789302	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:42789302G>A	ENST00000564153.1	+	1	80				SNAP23_ENST00000249647.3_Intron|SNAP23_ENST00000567094.1_Intron|SNAP23_ENST00000349777.1_Intron|SNAP23_ENST00000566141.1_Intron			O00161	SNP23_HUMAN	synaptosomal-associated protein, 23kDa	NA		NA			exocytosis (GO:0006887)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	azurophil granule (GO:0042582)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|synapse (GO:0045202)				large_intestine(1)|lung(1)	2		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)		gtgcagtggcgcgatcttggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y09567	CCDS10087.1, CCDS10088.1	15q14	2004-01-19	2002-08-29		ENSG00000092531	ENSG00000092531	8773			11131	protein-coding gene	gene with protein product		602534	synaptosomal-associated protein, 23kD		NA	9070898, 8663154	Standard	NM_003825	NM_003825	NA	Approved	SNAP23A, SNAP23B, HsT17016	uc001zpz.2	O00161	OTTHUMG00000130625	ENST00000564153.1:c.-15+1391G>A	chr15.hg19:g.42789302G>A		NA	O00162|Q13602|Q6IAE3	hg19		0.02	-0.078909	GGCxCGA	UNCOVERED																																																																																			NOVEL	SNAP23-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000423107.1	6	3.006536	KEEP	0	0	0	10	278	GG	0.992708	0.076772	0		+	3	60	76	0	0	6.731075	5	60	182	23	ENST00000564153.1	0.375	0.077336
TTBK2	146057	__UNKNOWN__	__UNKNOWN__	15	43175318	43175318	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43175318A>G	ENST00000567274.1	-	2	325				TTBK2_ENST00000267890.6_Intron|TTBK2_ENST00000567485.1_Intron|TTBK2_ENST00000567840.1_Intron			Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	NA		NA			cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		ggtggctcacacctgtaatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881	146057			19141	protein-coding gene	gene with protein product		611695	spinocerebellar ataxia 11	SCA11	NA	10048485	Standard	NM_173500	NM_173500	NA	Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000567274.1:c.67-4436T>C	chr15.hg19:g.43175318A>G		NA	O94932|Q6ZN52|Q8IVV1	hg19		0.02	-0.192912	CACxCCT	COVERED																																																																																			NOVEL	TTBK2-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000431432.2	13	3.90967	KEEP	1	0	0	13	354	AA	0.993634	0.454842	0		-	3	54	94	0	0	7.161154	17	60	507	46	ENST00000567274.1	0.15	0.457757
UBR1	197131	__UNKNOWN__	__UNKNOWN__	15	43247167	43247167	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43247167T>C	ENST00000290650.4	-	45	4914				UBR1_ENST00000382177.2_Intron	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	NA		NA			cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		gagttcaagatcagcctggcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459	197131		Ubiquitin protein ligase E3 component n-recognins	16808	protein-coding gene	gene with protein product		605981			NA	9653112	Standard	NM_174916	NM_174916	NA	Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4836-2521A>G	chr15.hg19:g.43247167T>C		NA	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	hg19	CCDS10091.1	0.02	-0.043858	AGAxCAG	UNCOVERED																																																																																			NOVEL	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253202.1	4	2.405784	KEEP	0	0	0	8	216	TT	0.99257	0.023895	0		-	3	60	101	0	0	10.069784	2	60	60	17	ENST00000290650.4	0.6	0.024074
UBR1	197131	__UNKNOWN__	__UNKNOWN__	15	43384230	43384230	__UNKNOWN__	Intron	SNP	G	G	T	rs535743392		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43384230G>T	ENST00000290650.4	-	2	160				UBR1_ENST00000382177.2_Intron	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	NA		NA			cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		gtcagtgagcggagatcatgc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459	197131		Ubiquitin protein ligase E3 component n-recognins	16808	protein-coding gene	gene with protein product		605981			NA	9653112	Standard	NM_174916	NM_174916	NA	Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.82-5792C>A	chr15.hg19:g.43384230G>T		NA	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	hg19	CCDS10091.1	0.02	-0.368398	AGCxGAG	COVERED																																																																																			NOVEL	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253202.1	6	2.768811	KEEP	1	2	47	26	719	CG	0.999999	0.926639	0		-	4	60	117	0	0	8.059545	34	60	1085	100	ENST00000290650.4	0.105263	0.92664
TMEM62	80021	__UNKNOWN__	__UNKNOWN__	15	43447531	43447531	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43447531C>A	ENST00000260403.2	+	9	1461					NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	NA		NA				integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		cgcatctcaacaaaaaaataa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842	80021			26269	protein-coding gene	gene with protein product		NA			NA		Standard	NM_024956	NM_024956	NA	Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1182+502C>A	chr15.hg19:g.43447531C>A		NA	Q6I9Y5|Q9H5J6	hg19	CCDS32210.1	0.02	-0.157902	CAAxAAA	COVERED																																																																																			NOVEL	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000432227.1	9	3.009016	KEEP	0	0	0	10	309	CC	0.992708	0.320453	0		+	3	60	87	0	0	6.778975	13	60	445	39	ENST00000260403.2	0.1875	0.322807
EPB42	2038	__UNKNOWN__	__UNKNOWN__	15	43508004	43508004	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43508004A>C	ENST00000441366.2	-	2	422				EPB42_ENST00000300215.3_Intron|EPB42_ENST00000540029.1_Intron	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	NA		NA			cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		aagtgattctactgcctcagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947	2038		Transglutaminases	3381	protein-coding gene	gene with protein product	Erythrocyte surface protein band 4.2	177070			NA	1284644	Standard	NM_000119	NM_000119	NA	Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.196+461T>G	chr15.hg19:g.43508004A>C		NA	Q4KKX0|Q4VB97	hg19	CCDS45249.1	0.02	-0.043852	TCTxCTG	UNCOVERED																																																																																			NOVEL	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000432219.1	2	2.402871	KEEP	0	0	0	8	199	AA	0.99257	0.023895	0		-	2	60	67	0	0	6.450308	2	60	56	18	ENST00000441366.2	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	43616826	43616826	__UNKNOWN__	IGR	SNP	C	C	A	rs544407695		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43616826C>A			NA	NA				RP11-402F9.3 (21856 upstream) : LCMT2 (3147 downstream)						NA		NA									NA						cgtctcaaaacaaaaaacaaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.43616826C>A		NA		hg19		0.02	-0.122784	AAAxAAA	COVERED																																																																																			NOVEL					0			9	3.00161	KEEP	0	0	0	10	290	CC	0.992708	0.19488	0			3	60	87	1	0	6.973151	11	60	370	35		0.214286	0.196312
CATSPER2	117155	__UNKNOWN__	__UNKNOWN__	15	43922744	43922744	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:43922744A>G	ENST00000396879.1	-	0	1854				STRC_ENST00000541030.1_Intron	NM_001282309.1	NP_001269238.1	Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	NA		NA			calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		tagtagagacagggtttcacc	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762	117155		Voltage-gated ion channels / Cation channels, sperm associated	18810	protein-coding gene	gene with protein product		607249			NA	11675491, 16382101	Standard	NM_054020	NM_172095	NA	Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000396879.1:c.*155T>C	chr15.hg19:g.43922744A>G		NA	Q8NHT9|Q96P54|Q96P55	hg19	CCDS32216.1	0.02	5.823856	GACxGGG	COVERED																																																																																			NOVEL	CATSPER2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133150.2	41	13.099012	KEEP	2	5	140	93	2652	AA	1	1	0		-	8	60	270	0	0	17.459179	134	60	4087	400	ENST00000396879.1	0.056338	1
RP11-296A16.1	0	__UNKNOWN__	__UNKNOWN__	15	44080353	44080353	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:44080353A>G	ENST00000417761.2	-	7	768				SERF2_ENST00000381359.1_Intron						NA		NA									NA						gattacaggcatgagccacca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000417761.2:c.326+7232T>C	chr15.hg19:g.44080353A>G		NA		hg19		0.02	-0.166642	GGCxTGA	COVERED																																																																																			NOVEL	RP11-296A16.1-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000439768.1	5	3.308815	KEEP	0	0	0	11	312	AA	0.993072	0.351495	0		-	3	60	99	0	0	7.891782	14	60	413	48	ENST00000417761.2	0.176471	0.353947
WDR76	79968	__UNKNOWN__	__UNKNOWN__	15	44132336	44132336	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:44132336T>C	ENST00000381246.2	+	5	811				WDR76_ENST00000263795.6_Intron			Q9H967	WDR76_HUMAN	WD repeat domain 76	NA		NA								breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)	20		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		ggattacaggtgtgagccact	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023035	CCDS10106.1, CCDS53938.1	15q15.3	2013-01-09			ENSG00000092470	ENSG00000092470	79968		WD repeat domain containing	25773	protein-coding gene	gene with protein product		NA			NA	12860291	Standard	NM_024908	NM_024908	NA	Approved	FLJ12973	uc001zti.2	Q9H967	OTTHUMG00000060143	ENST00000381246.2:c.540+410T>C	chr15.hg19:g.44132336T>C		NA	A0MNP5|Q05CI4	hg19	CCDS53938.1	0.02	-0.245507	AGGxGTG	COVERED																																																																																			NOVEL	WDR76-002	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133483.4	8	3.307296	KEEP	1	0	0	11	303	TT	0.993072	0.636904	0		+	3	60	95	0	0	6.95085	22	60	611	61	ENST00000381246.2	0.12	0.641347
SPG11	80208	__UNKNOWN__	__UNKNOWN__	15	44867709	44867709	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:44867709T>C	ENST00000261866.7	-	31	5883				SPG11_ENST00000427534.2_Intron|SPG11_ENST00000535302.2_Intron|SPG11_ENST00000558319.1_Intron	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	NA		NA			cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		ttttttttttttgagatggag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133	80208			11226	protein-coding gene	gene with protein product	spatacsin	610844	KIAA1840	KIAA1840	NA	10408536, 17322883	Standard		NM_001160227	NA	Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.5867-470A>G	chr15.hg19:g.44867709T>C		NA	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	hg19	CCDS10112.1	0.02	-0.122785	TTTxTGA	UNCOVERED																																																																																			NOVEL	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253927.1	9	2.70645	KEEP	5	0	0	9	241	TT	0	0	0		-	2	21	72	0	0	6.335796	5	60	146	37	ENST00000261866.7	0.285714	0.196312
SPG11	80208	__UNKNOWN__	__UNKNOWN__	15	44892626	44892626	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:44892626A>G	ENST00000261866.7	-	21	3703				SPG11_ENST00000427534.2_Intron|SPG11_ENST00000535302.2_Intron|SPG11_ENST00000558319.1_Intron	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	NA		NA			cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		acaggtgtgaaccactgtacc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													38	45	43			NA	NA	15		NA											NA				44892626		2198	4298	6496	SO:0001627	intron_variant				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133	80208			11226	protein-coding gene	gene with protein product	spatacsin	610844	KIAA1840	KIAA1840	NA	10408536, 17322883	Standard		NM_001160227	NA	Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3686+38T>C	chr15.hg19:g.44892626A>G		NA	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	hg19	CCDS10112.1	0.02	1.529108	TGAxCCA	COVERED																																																																																			NOVEL	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253927.1	30	10.788978	KEEP	1	2	54	55	1518	AA	1	0.999948	0		-	4	60	136	0	0	8.348862	89	60	2725	226	ENST00000261866.7	0.043011	0.999948
SPG11	80208	__UNKNOWN__	__UNKNOWN__	15	44946774	44946774	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:44946774C>T	ENST00000261866.7	-	5	886				SPG11_ENST00000559193.1_Intron|SPG11_ENST00000427534.2_Intron|SPG11_ENST00000535302.2_Intron|SPG11_ENST00000558319.1_Intron	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	NA		NA			cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		cggtggctcacgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133	80208			11226	protein-coding gene	gene with protein product	spatacsin	610844	KIAA1840	KIAA1840	NA	10408536, 17322883	Standard		NM_001160227	NA	Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.870-2310G>A	chr15.hg19:g.44946774C>T		NA	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	hg19	CCDS10112.1	0.02	-0.263144	TCAxGCC	COVERED																																																																																			NOVEL	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000253927.1	6	3.00799	KEEP	0	0	0	10	290	CG	0.993072	0.688863	0		-	3	60	94	0	0	6.692887	25	60	805	59	ENST00000261866.7	0.107143	0.693668
DUOXA2	405753	__UNKNOWN__	__UNKNOWN__	15	45409859	45409859	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:45409859G>C	ENST00000323030.5	+	6	1054				DUOXA1_ENST00000267803.4_Missense_Mutation_p.P436A|DUOXA1_ENST00000430224.2_Missense_Mutation_p.P391A|DUOXA1_ENST00000558996.1_3'UTR|DUOXA1_ENST00000559014.1_Missense_Mutation_p.P436A	NM_207581.3	NP_997464.2	Q1HG44	DOXA2_HUMAN	dual oxidase maturation factor 2	NA		NA			hydrogen peroxide metabolic process (GO:0042743)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)					NA		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;2.88e-18)|GBM - Glioblastoma multiforme(94;3.95e-07)|COAD - Colon adenocarcinoma(120;0.0652)|Colorectal(133;0.0659)		accagcctgggcaacatagcC	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													58	55	56			NA	NA	15		NA											NA				45409859		2198	4298	6496	SO:0001627	intron_variant			BX537581	CCDS10118.2	15q21.1	2008-10-30		2006-07-25	ENSG00000140274	ENSG00000140274	405753			32698	protein-coding gene	gene with protein product		612772			NA	16651268	Standard	NM_207581	NM_207581	NA	Approved		uc001zuo.3	Q1HG44	OTTHUMG00000131354	ENST00000323030.5:c.770-55G>C	chr15.hg19:g.45409859G>C		NA	B2RPI9|H0YNQ6	hg19	CCDS10118.2	0.02	3.602723	TGGxCAA	COVERED	.	.	.	.	.	.	.	.	.	.	G	14.79	2.641040	0.47153	.	.	ENSG00000140254	ENST00000267803;ENST00000430224	T;T	0.61274	0.55;0.12	2.39	1.26	0.21427	.	0.853776	0.09984	N	0.730594	T	0.33933	0.0880	N	0.19112	0.55	0.18873	N	0.999984	P;B	0.37594	0.601;0.209	B;B	0.17722	0.019;0.011	T	0.12091	-1.0561	10	0.87932	D	0	.	7.1448	0.25577	0.0:0.5056:0.4944:0.0	.	391;436	B5M0C0;A8K9Q6	.;.	A	436;391	ENSP00000267803:P436A;ENSP00000415512:P391A	ENSP00000267803:P436A	P	-	1	0	DUOXA1	43197151	0.000000	0.05858	0.011000	0.14972	0.410000	0.31052	-0.070000	0.11523	0.124000	0.18369	0.491000	0.48974	CCC	NOVEL	DUOXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254142.1	34	14.978372	KEEP	1	4	117	91	2787	GG	1	1	0		+	5	60	171	0	1	10.34394	122	60	4136	334	ENST00000323030.5	0.03937	1
SHF	90525	__UNKNOWN__	__UNKNOWN__	15	45492142	45492142	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:45492142G>A	ENST00000290894.8	-	1	449				RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000318390.6_Intron	NM_138356.2	NP_612365			Src homology 2 domain containing F	NA		NA								endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		acagagcgaggctccatctca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606	90525		SH2 domain containing	25116	protein-coding gene	gene with protein product		NA			NA	11095946	Standard	NM_138356	NM_138356	NA	Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.45+782C>T	chr15.hg19:g.45492142G>A		NA		hg19	CCDS10120.2	0.02	-0.175401	GAGxCTC	COVERED																																																																																			NOVEL	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254141.2	33	3.480949	KEEP	19	1	26	21	618	GG	0.997832	0.386567	0		-	3	23	90	0	1	7.77922	7	60	230	59	ENST00000290894.8	0.3	0.387407
SHF	90525	__UNKNOWN__	__UNKNOWN__	15	45492143	45492143	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:45492143C>T	ENST00000290894.8	-	1	449				RP11-519G16.2_ENST00000560034.1_RNA|SHF_ENST00000318390.6_Intron	NM_138356.2	NP_612365			Src homology 2 domain containing F	NA		NA								endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(2)	12		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		cagagcgaggctccatctcaa	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007586	CCDS10120.2, CCDS73721.1	15q21.1	2013-02-14			ENSG00000138606	ENSG00000138606	90525		SH2 domain containing	25116	protein-coding gene	gene with protein product		NA			NA	11095946	Standard	NM_138356	NM_138356	NA	Approved		uc001zuy.3	Q7M4L6	OTTHUMG00000131353	ENST00000290894.8:c.45+781G>A	chr15.hg19:g.45492143C>T		NA		hg19	CCDS10120.2	0.02	-0.175445	AGGxTCC	COVERED																																																																																			NOVEL	SHF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254141.2	34	6.885612	KEEP	20	0	0	23	669	CC	0.997832	0.386567	0		-	3	23	87	0	1	7.47819	7	60	245	60	ENST00000290894.8	0.3	0.387407
SPATA5L1	79029	__UNKNOWN__	__UNKNOWN__	15	45704030	45704030	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:45704030T>C	ENST00000305560.6	+	3	1533				SPATA5L1_ENST00000559860.1_Intron	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	NA		NA				cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		catggtggcttacacctgtaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763	79029		ATPases / AAA-type	28762	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024063	NM_024063	NA	Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1434+1302T>C	chr15.hg19:g.45704030T>C		NA	C9JHR5|Q9H8W7|Q9HA41	hg19	CCDS10123.1	0.02	-0.122779	GCTxACA	UNCOVERED																																																																																			NOVEL	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254218.1	5	2.404672	KEEP	1	0	0	8	205	TT	0	0	0		+	3	60	97	0	0	8.082222	10	60	287	31	ENST00000305560.6	0.230769	0.196312
RP11-718O11.1	0	__UNKNOWN__	__UNKNOWN__	15	46138627	46138627	__UNKNOWN__	lincRNA	SNP	T	T	C	rs145894650	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:46138627T>C	ENST00000560705.1	+	0	556										NA		NA									NA						ctttgggaggttgaggtgggt	0.483		NA											T|||	18	0.00359425	0.0129	0.0014	5008	,	,	NA	16956	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000560705.1:	chr15.hg19:g.46138627T>C		NA		hg19		0.02	-0.17541	AGGxTGA	UNCOVERED																																																																																			NOVEL	RP11-718O11.1-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000416555.1	7	3.007332	KEEP	4	0	0	10	270	TT	0	0	0		+	3	60	96	0	0	7.361698	17	60	508	48	ENST00000560705.1	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	46341554	46341554	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:46341554A>T			NA	NA				RP11-718O11.1 (200471 upstream) : SNORD11 (302305 downstream)						NA		NA									NA						atgagaacacatggacacagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.46341554A>T		NA		hg19		0.02	-0.184182	CACxTGG	UNCOVERED																																																																																			NOVEL					0			9	3.307625	KEEP	8	0	0	11	295	AA	0	0	0			3	39	88	0	0	6.633979	16	60	479	45		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	46341584	46341584	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:46341584G>A			NA	NA				RP11-718O11.1 (200501 upstream) : SNORD11 (302275 downstream)						NA		NA									NA						atcacacaccggggcctgttg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.46341584G>A		NA		hg19		0.02	-0.192957	ACCxGGG	UNCOVERED																																																																																			NOVEL					0			6	2.40635	KEEP	6	0	0	8	233	GG	0	0	0			4	40	117	0	0	9.169263	17	60	553	48		0.190476	0.457757
SEMA6D	80031	__UNKNOWN__	__UNKNOWN__	15	47541174	47541174	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:47541174T>C	ENST00000558014.1	+	1	318					NM_001198999.1	NP_001185928.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	NA		NA			axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		cctgtaatcctagcactttgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872	80031		Semaphorins	16770	protein-coding gene	gene with protein product		609295			NA	12110693, 14977921	Standard	NM_024966	NM_020858	NA	Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000558014.1:c.-239+64559T>C	chr15.hg19:g.47541174T>C		NA	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	hg19	CCDS32224.1	0.02	-0.140327	TCCxAGC	COVERED																																																																																			NOVEL	SEMA6D-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416860.1	3	3.007853	KEEP	1	0	0	10	279	TT	0.992708	0.259062	0		+	4	60	126	0	0	10.601657	12	60	355	40	ENST00000558014.1	0.25	0.260965
MYEF2	50804	__UNKNOWN__	__UNKNOWN__	15	48462072	48462072	__UNKNOWN__	Intron	SNP	G	G	A	rs8030158	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:48462072G>A	ENST00000324324.7	-	2	441				MYEF2_ENST00000267836.6_Intron	NM_016132.3	NP_057216	Q9P2K5	MYEF2_HUMAN	myelin expression factor 2	NA		NA			myotube differentiation (GO:0014902)|neuron differentiation (GO:0030182)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31		all_lung(180;0.00217)		all cancers(107;3.73e-10)|GBM - Glioblastoma multiforme(94;7.81e-07)		gattacaggcgtgagccacca	0.453		NA											G|||	7	0.00139776	0.0053	0.0	5008	,	,	NA	16374	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037762	CCDS32230.1, CCDS73722.1	15q15.1	2013-07-16				ENSG00000104177	50804		RNA binding motif (RRM) containing	17940	protein-coding gene	gene with protein product		NA			NA	10718198, 2601707	Standard	NM_016132	XM_005254422	NA	Approved	MEF-2, FLJ11213, KIAA1341, HsT18564	uc001zwi.4	Q9P2K5		ENST00000324324.7:c.162-1036C>T	chr15.hg19:g.48462072G>A		NA	A7MCZ9|C9J921|C9K0J4|Q6NUM5|Q7L388|Q7Z4B7|Q9H922|Q9NUQ1	hg19	CCDS32230.1	0.02	-0.140353	GGCxTGA	COVERED																																																																																			NOVEL	MYEF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416909.2	4	3.00879	KEEP	0	0	0	10	300	GG	0.992708	0.259062	0		-	3	59	91	0	0	7.178866	13	60	433	37	ENST00000324324.7	0.1875	0.260965
SLC12A1	6557	__UNKNOWN__	__UNKNOWN__	15	48517694	48517694	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:48517694T>C	ENST00000330289.6	+	4	814				SLC12A1_ENST00000380993.3_Intron|SLC12A1_ENST00000558405.1_Intron|SLC12A1_ENST00000396577.3_Intron			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	NA		NA			cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	gaggctgaggtaggaggatga	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803	6557		Solute carriers	10910	protein-coding gene	gene with protein product		600839			NA	8640224	Standard		NM_000338	NA	Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000330289.6:c.629-979T>C	chr15.hg19:g.48517694T>C		NA	A8JYA2|E9PDW4	hg19		0.02	-0.324303	AGGxAGG	COVERED																																																																																			NOVEL	SLC12A1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417130.1	10	2.260017	KEEP	0	2	58	28	686	TT	0.999997	0.835714	0		+	3	60	104	0	0	7.598306	27	60	725	86	ENST00000330289.6	0.1	0.835716
SLC12A1	6557	__UNKNOWN__	__UNKNOWN__	15	48517711	48517711	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:48517711G>C	ENST00000330289.6	+	4	814				SLC12A1_ENST00000380993.3_Intron|SLC12A1_ENST00000558405.1_Intron|SLC12A1_ENST00000396577.3_Intron			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	NA		NA			cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	atgacttgaggccaggagttt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803	6557		Solute carriers	10910	protein-coding gene	gene with protein product		600839			NA	8640224	Standard		NM_000338	NA	Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000330289.6:c.629-962G>C	chr15.hg19:g.48517711G>C		NA	A8JYA2|E9PDW4	hg19		0.02	-0.394741	GAGxCCA	COVERED																																																																																			NOVEL	SLC12A1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417130.1	14	4.980749	KEEP	0	2	55	36	1098	GG	1	0.92664	0		+	3	60	99	0	0	6.775546	35	60	1159	113	ENST00000330289.6	0.078947	0.92664
SLC12A1	6557	__UNKNOWN__	__UNKNOWN__	15	48556070	48556070	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:48556070T>A	ENST00000396577.3	+	18	2369				SLC12A1_ENST00000380993.3_Intron|SLC12A1_ENST00000558405.1_Intron	NM_001184832.1	NP_001171761.1	Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	NA		NA			cell death (GO:0008219)|chemical homeostasis (GO:0048878)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|kidney development (GO:0001822)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:potassium:chloride symporter activity (GO:0008511)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|prostate(2)|skin(1)	59		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Potassium Chloride(DB00761)|Quinethazone(DB01325)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	ttgtattttttgtagagacag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10129.2, CCDS53940.1	15q15-q21	2013-07-18	2013-07-18		ENSG00000074803	ENSG00000074803	6557		Solute carriers	10910	protein-coding gene	gene with protein product		600839			NA	8640224	Standard		NM_000338	NA	Approved	NKCC2	uc010bem.3	Q13621	OTTHUMG00000131495	ENST00000396577.3:c.2155-3688T>A	chr15.hg19:g.48556070T>A		NA	A8JYA2|E9PDW4	hg19	CCDS53940.1	0.02	-0.078903	TTTxGTA	UNCOVERED																																																																																			NOVEL	SLC12A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254341.1	10	3.007727	KEEP	3	0	0	10	276	TT	0	0	0		+	3	60	77	0	0	6.831422	5	60	147	23	ENST00000396577.3	0.375	0.077336
FBN1	2200	__UNKNOWN__	__UNKNOWN__	15	48720745	48720745	__UNKNOWN__	Intron	SNP	G	G	C	rs376562288		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:48720745G>C	ENST00000316623.5	-	57	7327					NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	NA		NA			extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		tccttccttcgttccttcctt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147	2200			3603	protein-coding gene	gene with protein product	Marfan syndrome	134797	fibrillin 1 (Marfan syndrome)	FBN, MFS1, WMS	NA	10036187, 12525539	Standard		NM_000138	NA	Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6872-77C>G	chr15.hg19:g.48720745G>C		NA	B2RUU0|D2JYH6|Q15972|Q75N87	hg19	CCDS32232.1	0.02	-0.30702	TTCxTTC	COVERED																																																																																			NOVEL	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417355.1	2	5.715902	KEEP	0	0	0	19	556	GG	0.999863	0.800136	0		-	3	60	95	1	0	6.492811	32	60	1080	73	ENST00000316623.5	0.085714	0.800245
FBN1	2200	__UNKNOWN__	__UNKNOWN__	15	48755394	48755394	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:48755394G>T	ENST00000316623.5	-	42	5564	c.5109C>A	c.(5107-5109)aaC>aaA	p.N1703K		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1703	TB 7.	NA			extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CACAGGTCTGGTTGTCAGCAT	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													135	129	131			NA	NA	15		NA											NA				48755394		2198	4296	6494	SO:0001583	missense			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147	2200			3603	protein-coding gene	gene with protein product	Marfan syndrome	134797	fibrillin 1 (Marfan syndrome)	FBN, MFS1, WMS	NA	10036187, 12525539	Standard		NM_000138	NA	Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5109C>A	chr15.hg19:g.48755394G>T	ENSP00000325527:p.Asn1703Lys	NA	B2RUU0|D2JYH6|Q15972|Q75N87	hg19	CCDS32232.1	0.02	1.505516	CTGxTTG	COVERED	.	.	.	.	.	.	.	.	.	.	G	15.42	2.828921	0.50845	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.92149	-2.98	5.96	5.96	0.96718	Matrix fibril-associated (2);TGF-beta binding (1);	0.000000	0.85682	D	0.000000	D	0.94988	0.8378	M	0.78637	2.42	0.80722	D	1	D	0.63880	0.993	D	0.66196	0.942	D	0.93584	0.6915	10	0.36615	T	0.2	.	11.6757	0.51427	0.1107:0.0:0.8893:0.0	.	1703	P35555	FBN1_HUMAN	K	1703;271;593	ENSP00000325527:N1703K	ENSP00000325527:N1703K	N	-	3	2	FBN1	46542686	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.911000	0.48774	2.830000	0.97506	0.585000	0.79938	AAC	NOVEL	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417355.1	2	6.920428	KEEP	0	0	0	23	699	GG	0.999892	0.998885	0		-	27	60	779	0	0	69.295718	49	60	1658	149	ENST00000316623.5	0.355263	0.998993
SECISBP2L	9728	__UNKNOWN__	__UNKNOWN__	15	49282503	49282503	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:49282503T>G	ENST00000559471.1	-	0	5507				SECISBP2L_ENST00000261847.3_3'UTR	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	NA		NA					poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTAAATTCACTTTTAAGACTG	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593	9728			28997	protein-coding gene	gene with protein product		615756			NA		Standard	NM_014701	NM_001193489	NA	Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.*1938A>C	chr15.hg19:g.49282503T>G		NA	Q8N767	hg19	CCDS53942.1	0.02	-0.394663	CACxTTT	COVERED																																																																																			NOVEL	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417277.1	0	3.00754	KEEP	0	0	0	10	277	TT	0.992708	0.919883	0		-	18	60	591	0	0	54.531618	27	60	832	79	ENST00000559471.1	0.4	0.92664
SECISBP2L	9728	__UNKNOWN__	__UNKNOWN__	15	49305771	49305771	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:49305771C>T	ENST00000559471.1	-	12	1825				SECISBP2L_ENST00000261847.3_Intron	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	NA		NA					poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						ggattacaggcgtgagccact	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593	9728			28997	protein-coding gene	gene with protein product		615756			NA		Standard	NM_014701	NM_001193489	NA	Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.1562-757G>A	chr15.hg19:g.49305771C>T		NA	Q8N767	hg19	CCDS53942.1	0.02	-0.192904	AGGxGTG	COVERED																																																																																			NOVEL	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417277.1	4	2.406231	KEEP	0	0	0	8	229	CC	0.99257	0.4869	0		-	3	60	87	0	0	6.462499	17	60	545	43	ENST00000559471.1	0.15	0.490544
ATP8B4	79895	__UNKNOWN__	__UNKNOWN__	15	50335922	50335922	__UNKNOWN__	Intron	SNP	A	A	G	rs8028408	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:50335922A>G	ENST00000284509.6	-	5	442				ATP8B4_ENST00000559829.1_Intron|ATP8B4_ENST00000558959.1_Intron	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	NA		NA				Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		aggccgaggcaggtggatcat	0.507		NA											-|||	4063	0.811302	0.9576	0.7089	5008	,	,	NA	14151	0.9891	NA	0.5278	False	NA	,,,	NA	NA	NA	2504	0.7945	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043	79895		ATPases / P-type	13536	protein-coding gene	gene with protein product		609123	ATPase, Class I, type 8B, member 4		NA	11015572	Standard	NM_024837	NM_024837	NA	Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.300+868T>C	chr15.hg19:g.50335922A>G		NA	Q9H727	hg19	CCDS32238.1	0.02	-0.061397	GGCxGGT	UNCOVERED																																																																																			NOVEL	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418100.1	6	2.706802	KEEP	13	0	0	9	246	AA	0	0	0		-	4	60	127	0	0	12.532289	3	60	86	33	ENST00000284509.6	0.571429	0.043787
GABPB1	2553	__UNKNOWN__	__UNKNOWN__	15	50635161	50635161	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:50635161G>A	ENST00000380877.3	-	1	424				GABPB1_ENST00000429662.2_Intron|GABPB1_ENST00000560825.1_Intron|GABPB1_ENST00000220429.8_Intron|GABPB1_ENST00000543881.1_Intron|GABPB1_ENST00000396464.3_Intron|GABPB1_ENST00000359031.4_Intron	NM_005254.5|NM_016654.4	NP_005245.2|NP_057738.1	Q06547	GABP1_HUMAN	GA binding protein transcription factor, beta subunit 1	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|endometrium(1)|large_intestine(7)|lung(5)	14						gcagtggcacgatcttggctc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13316	CCDS10135.1, CCDS10136.1, CCDS32239.1, CCDS45258.1	15q21.2	2013-01-10	2008-02-25	2008-02-25	ENSG00000104064	ENSG00000104064	2553		Ankyrin repeat domain containing	4074	protein-coding gene	gene with protein product		600610	GA binding protein transcription factor, beta subunit 2	GABPB2	NA	7958862	Standard		NM_016655	NA	Approved	E4TF1-47, GABPB	uc001zyb.3	Q06547	OTTHUMG00000131642	ENST00000380877.3:c.0+12020C>T	chr15.hg19:g.50635161G>A		NA	A8IE52|Q06545|Q12940|Q12941|Q12942|Q8IYD0	hg19	CCDS10135.1	0.02	-0.087719	CACxATC	UNCOVERED																																																																																			NOVEL	GABPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254537.2	5	3.608839	KEEP	3	0	0	12	335	GG	0.99254	0.098977	0		-	3	59	87	0	0	7.478232	7	60	238	32	ENST00000380877.3	0.3	0.099721
USP8	9101	__UNKNOWN__	__UNKNOWN__	15	50784950	50784950	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs78143971	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:50784950C>T	ENST00000425032.3	+	12	2162	c.1969C>T	c.(1969-1971)Cgg>Tgg	p.R657W	USP8_ENST00000433963.1_Missense_Mutation_p.R763W|USP8_ENST00000307179.4_Missense_Mutation_p.R763W|USP8_ENST00000396444.3_Missense_Mutation_p.R763W	NM_001283049.1	NP_001269978.1	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	763		NA			cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TTCTCAGATTCGGAACCTCAA	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													133	120	125			NA	NA	15		NA											NA				50784950		2196	4294	6490	SO:0001583	missense			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592	9101		Ubiquitin-specific peptidases	12631	protein-coding gene	gene with protein product		603158	ubiquitin specific protease 8		NA	12838346, 9582025, 24482476	Standard	NM_005154	NM_005154	NA	Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000425032.3:c.1969C>T	chr15.hg19:g.50784950C>T	ENSP00000412682:p.Arg657Trp	NA	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	hg19		0.02	1.227997	ATTxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	C	25.3	4.628030	0.87560	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.21031	2.03;2.03;2.03;2.07	5.22	5.22	0.72569	.	0.556073	0.19308	N	0.117479	T	0.32255	0.0823	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.995;0.999	P;P	0.61477	0.889;0.889	T	0.02320	-1.1177	10	0.56958	D	0.05	-12.0933	15.5388	0.76024	0.1385:0.8615:0.0:0.0	.	657;763	B4DKA8;P40818	.;UBP8_HUMAN	W	763;763;763;657	ENSP00000379721:R763W;ENSP00000405537:R763W;ENSP00000302239:R763W;ENSP00000412682:R657W	ENSP00000302239:R763W	R	+	1	2	USP8	48572242	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.586000	0.53950	2.593000	0.87608	0.650000	0.86243	CGG	NOVEL	USP8-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000418317.1	3	4.846292	KEEP	0	1	31	27	779	CC	0.999997	0.999723	0		+	7	50	201	0	0	12.995286	77	60	2471	175	ENST00000425032.3	0.083333	0.999726
USP8	9101	__UNKNOWN__	__UNKNOWN__	15	50784955	50784955	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs74840283		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:50784955C>A	ENST00000425032.3	+	12	2167	c.1974C>A	c.(1972-1974)aaC>aaA	p.N658K	USP8_ENST00000433963.1_Missense_Mutation_p.N764K|USP8_ENST00000307179.4_Missense_Mutation_p.N764K|USP8_ENST00000396444.3_Missense_Mutation_p.N764K	NM_001283049.1	NP_001269978.1	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	764		NA			cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AGATTCGGAACCTCAATCCTG	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													135	121	126			NA	NA	15		NA											NA				50784955		2196	4294	6490	SO:0001583	missense			D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592	9101		Ubiquitin-specific peptidases	12631	protein-coding gene	gene with protein product		603158	ubiquitin specific protease 8		NA	12838346, 9582025, 24482476	Standard	NM_005154	NM_005154	NA	Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000425032.3:c.1974C>A	chr15.hg19:g.50784955C>A	ENSP00000412682:p.Asn658Lys	NA	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	hg19		0.02	1.236683	GAAxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650128	0.67472	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.18174	2.23;2.23;2.23;2.27	5.22	2.26	0.28386	.	0.395808	0.31859	N	0.006953	T	0.09069	0.0224	N	0.24115	0.695	0.48696	D	0.999694	B;B	0.26672	0.083;0.156	B;B	0.21546	0.035;0.03	T	0.19224	-1.0312	10	0.10902	T	0.67	-18.6446	9.071	0.36493	0.0:0.5813:0.0:0.4187	.	658;764	B4DKA8;P40818	.;UBP8_HUMAN	K	764;764;764;658	ENSP00000379721:N764K;ENSP00000405537:N764K;ENSP00000302239:N764K;ENSP00000412682:N658K	ENSP00000302239:N764K	N	+	3	2	USP8	48572247	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.755000	0.26405	0.695000	0.31675	0.650000	0.86243	AAC	NOVEL	USP8-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000418317.1	3	5.048282	KEEP	0	1	29	27	822	CC	0.999997	0.999675	0		+	7	50	219	0	0	14.820553	76	60	2563	170	ENST00000425032.3	0.084337	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	50843443	50843443	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:50843443T>C			NA	NA				USP50 (4538 upstream) : RP11-120K9.2 (6354 downstream)						NA		NA									NA						gctgggattataggtgtgagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.50843443T>C		NA		hg19		0.02	-0.192941	TTAxAGG	COVERED																																																																																			NOVEL					0			3	3.307285	KEEP	0	0	0	11	292	TT	0.993072	0.454585	0			3	60	99	0	0	7.592415	18	60	522	46		0.142857	0.457757
SPPL2A	84888	__UNKNOWN__	__UNKNOWN__	15	51037979	51037979	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:51037979A>G	ENST00000261854.5	-	5	859					NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	NA		NA			membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		cgggcacggtagctcacgcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(50;790 1209 4069 22965 33125)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600	84888			30227	protein-coding gene	gene with protein product	intramembrane protease 3, presenilin-like protein 2	608238			NA	12077416, 12139484	Standard	NM_032802	NM_032802	NA	Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.584+1712T>C	chr15.hg19:g.51037979A>G		NA	B2RDS0|Q8TAW1|Q96SZ8	hg19	CCDS10138.1	0.02	-0.157893	GGTxGCT	COVERED																																																																																			NOVEL	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254543.3	7	3.298454	KEEP	1	0	0	11	282	AA	0.993072	0.32057	0		-	3	60	101	0	0	8.091561	14	60	436	43	ENST00000261854.5	0.176471	0.322807
AP4E1	23431	__UNKNOWN__	__UNKNOWN__	15	51211405	51211405	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:51211405T>C	ENST00000261842.5	+	3	452				AP4E1_ENST00000560508.1_Intron	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	NA		NA			intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ccagcctgggtaacagagtga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014	23431			573	protein-coding gene	gene with protein product		607244			NA	10436028, 21620353	Standard		NM_007347	NA	Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.346+3637T>C	chr15.hg19:g.51211405T>C		NA	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	hg19	CCDS32240.1	0.02	-0.175298	GGGxAAC	COVERED																																																																																			NOVEL	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418656.1	8	3.607433	KEEP	3	0	0	12	313	TT	0.993634	0.38494	0		+	3	60	104	1	0	8.392618	14	60	385	52	ENST00000261842.5	0.176471	0.387407
AP4E1	23431	__UNKNOWN__	__UNKNOWN__	15	51239272	51239272	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:51239272T>A	ENST00000261842.5	+	11	1282				AP4E1_ENST00000560508.1_Intron	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	NA		NA			intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		tagcctgggctacagagtgag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014	23431			573	protein-coding gene	gene with protein product		607244			NA	10436028, 21620353	Standard		NM_007347	NA	Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.1177-945T>A	chr15.hg19:g.51239272T>A		NA	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	hg19	CCDS32240.1	0.02	-0.149058	GGCxACA	COVERED																																																																																			NOVEL	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418656.1	11	4.207262	KEEP	0	0	0	14	376	TT	0.99649	0.421991	0		+	4	60	114	1	0	9.402225	12	60	339	47	ENST00000261842.5	0.25	0.423478
CYP19A1	1588	__UNKNOWN__	__UNKNOWN__	15	51510868	51510868	__UNKNOWN__	Intron	SNP	A	A	C	rs4324076	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:51510868A>C	ENST00000396402.1	-	6	782				CYP19A1_ENST00000396404.4_Intron|RP11-108K3.1_ENST00000559909.1_lincRNA|CYP19A1_ENST00000260433.2_Intron|CYP19A1_ENST00000559878.1_Intron	NM_000103.3	NP_000094.2	P11511	CP19A_HUMAN	cytochrome P450, family 19, subfamily A, polypeptide 1	NA		NA			androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|prostate gland growth (GO:0060736)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)	aromatase activity (GO:0070330)|electron carrier activity (GO:0009055)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			endometrium(1)|kidney(4)|large_intestine(9)|lung(11)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	33				all cancers(107;0.000372)|GBM - Glioblastoma multiforme(94;0.0128)	Aminoglutethimide(DB00357)|Anastrozole(DB01217)|Betamethasone(DB00443)|Bifonazole(DB04794)|Buserelin(DB06719)|Carbimazole(DB00389)|Chlorphenesin(DB00856)|Clomifene(DB00882)|Clotrimazole(DB00257)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Dinoprostone(DB00917)|Drostanolone(DB00858)|Econazole(DB01127)|Edetic Acid(DB00974)|Etomidate(DB00292)|Exemestane(DB00990)|Ketoconazole(DB01026)|Letrozole(DB01006)|Levomethadyl Acetate(DB01227)|Levonorgestrel(DB00367)|Mefloquine(DB00358)|Melatonin(DB01065)|Methadone(DB00333)|Methyltestosterone(DB06710)|Miconazole(DB01110)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nicotine(DB00184)|Paclitaxel(DB01229)|Raloxifene(DB00481)|Sulfathiazole(DB06147)|Tamoxifen(DB00675)|Terbinafine(DB00857)|Testolactone(DB00894)|Testosterone(DB00624)|Tioconazole(DB01007)|Trastuzumab(DB00072)	GGAAAAAAAAACACACATACA	0.408		NA											A|||	1839	0.367212	0.2035	0.3415	5008	,	,	NA	20737	0.5208	NA	0.4881	False	NA	,,,	NA	NA	NA	2504	0.3241	NA	NA	NA	Melanoma(142;1016 1807 39614 48966 51721)							NA				0								A	,	976,3416		139,698,1359	36	35	36		,	2.6	0	15	dbSNP_111	36	4184,4402		1143,1898,1252	no	intron,intron	CYP19A1	NM_000103.3,NM_031226.2	,	1282,2596,2611	CC,CA,AA	NA	48.7305,22.2222,39.7596	,	,	51510868	5160,7818	2196	4293	6489	SO:0001627	intron_variant			D14473	CCDS10139.1	15q21	2009-01-26	2003-02-14	2003-02-28	ENSG00000137869	ENSG00000137869	1588		Cytochrome P450s	2594	protein-coding gene	gene with protein product		107910	cytochrome P450, subfamily XIX (aromatization of androgens)	CYP19	NA	8477708	Standard		NM_031226	NA	Approved	ARO, P-450AROM, CPV1, ARO1, CYAR, aromatase	uc001zza.4	P11511	OTTHUMG00000131747	ENST00000396402.1:c.629-16T>G	chr15.hg19:g.51510868A>C		NA	Q16731|Q3B764|Q58FA0|Q8IYJ7	hg19	CCDS10139.1	0.02	2.014645	AAAxCAC	COVERED																																																																																			NOVEL	CYP19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254669.1	2	2.405832	KEEP	0	0	0	8	216	AA	0.99257	0.966729	0		-	27	60	886	0	0	85.22154	27	60	812	92	ENST00000396402.1	0.5	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	51946225	51946225	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:51946225T>C			NA	NA				DMXL2 (31195 upstream) : SCG3 (27324 downstream)						NA		NA									NA						cacctgtaattccagcacttt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.51946225T>C		NA		hg19		0.02	-0.043858	AATxCCA	UNCOVERED																																																																																			NOVEL					0			4	2.406021	KEEP	0	0	0	8	219	GT	0.99254	0.023894	0			2	60	70	0	0	7.124915	1	60	31	22		0.666667	0.024074
TMOD2	29767	__UNKNOWN__	__UNKNOWN__	15	52086677	52086677	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:52086677C>T	ENST00000249700.4	+	8	953				TMOD2_ENST00000435126.2_Intron|TMOD2_ENST00000539962.2_Intron	NM_001142885.1|NM_014548.3	NP_001136357.1|NP_055363.1	Q9NZR1	TMOD2_HUMAN	tropomodulin 2 (neuronal)	NA		NA			learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuron-neuron synaptic transmission (GO:0007270)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)	tropomyosin binding (GO:0005523)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16				all cancers(107;0.00435)		tttgggaggccgaggcaggag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF177169	CCDS10144.1, CCDS45260.1	15q21.2	2008-05-14			ENSG00000128872	ENSG00000128872	29767			11872	protein-coding gene	gene with protein product		602928			NA	10662549	Standard		NM_014548	NA	Approved	NTMOD	uc002abk.3	Q9NZR1	OTTHUMG00000131805	ENST00000249700.4:c.733-3717C>T	chr15.hg19:g.52086677C>T		NA	B4DEW6	hg19	CCDS10144.1	0.02	-0.140346	GGCxGAG	COVERED																																																																																			NOVEL	TMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254742.2	5	2.708011	KEEP	0	0	0	9	275	CC	0.99254	0.259018	0		+	3	60	84	0	0	6.572579	12	60	394	34	ENST00000249700.4	0.2	0.260965
TMOD2	29767	__UNKNOWN__	__UNKNOWN__	15	52093436	52093436	__UNKNOWN__	Intron	SNP	A	A	T	rs546562505|rs58571819|rs56194324		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:52093436A>T	ENST00000249700.4	+	8	1097				TMOD2_ENST00000435126.2_Intron|TMOD2_ENST00000539962.2_Intron	NM_001142885.1|NM_014548.3	NP_001136357.1|NP_055363.1	Q9NZR1	TMOD2_HUMAN	tropomodulin 2 (neuronal)	NA		NA			learning or memory (GO:0007611)|nervous system development (GO:0007399)|neuron-neuron synaptic transmission (GO:0007270)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)	tropomyosin binding (GO:0005523)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16				all cancers(107;0.00435)		tctctctctcacacacacaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF177169	CCDS10144.1, CCDS45260.1	15q21.2	2008-05-14			ENSG00000128872	ENSG00000128872	29767			11872	protein-coding gene	gene with protein product		602928			NA	10662549	Standard		NM_014548	NA	Approved	NTMOD	uc002abk.3	Q9NZR1	OTTHUMG00000131805	ENST00000249700.4:c.876+2899A>T	chr15.hg19:g.52093436A>T		NA	B4DEW6	hg19	CCDS10144.1	0.02	-0.070156	CTCxCAC	UNCOVERED																																																																																			NOVEL	TMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254742.2	10	2.405153	KEEP	7	0	0	8	210	AA	0	0	0		+	3	60	91	0	0	8.455342	4	60	112	28	ENST00000249700.4	0.428571	0.054137
TMOD3	29766	__UNKNOWN__	__UNKNOWN__	15	52164409	52164409	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:52164409T>C	ENST00000308580.7	+	3	564				TMOD3_ENST00000544199.1_Intron	NM_014547.4	NP_055362.1	Q9NYL9	TMOD3_HUMAN	tropomodulin 3 (ubiquitous)	NA		NA				striated muscle thin filament (GO:0005865)	tropomyosin binding (GO:0005523)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|stomach(1)	14				all cancers(107;0.00194)		ctggccaacatggtgaaaccc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(122;1837 2251 18387 22826)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF177171	CCDS10145.1	15q21.1-q21.2	2008-05-14			ENSG00000138594	ENSG00000138594	29766			11873	protein-coding gene	gene with protein product		605112			NA	10662549	Standard		NM_014547	NA	Approved	UTMOD	uc002abn.3	Q9NYL9	OTTHUMG00000131803	ENST00000308580.7:c.283+2839T>C	chr15.hg19:g.52164409T>C		NA	B2R6G7|Q9NT43|Q9NZR0	hg19	CCDS10145.1	0.02	-0.026315	ACAxGGT	UNCOVERED																																																																																			NOVEL	TMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254740.3	2	2.706249	KEEP	3	0	0	9	241	TT	0	0	0		+	2	60	65	0	0	6.624872	1	60	29	21	ENST00000308580.7	0.666667	0
MAPK6	5597	__UNKNOWN__	__UNKNOWN__	15	52326612	52326612	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:52326612C>T	ENST00000558841.1	+	2	111				MAPK6_ENST00000261845.5_Intron|RP11-430B1.1_ENST00000561207.1_RNA			Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	NA		NA			cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		cgggttcaagcagtcctccca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956	5597		Mitogen-activated protein kinase cascade / Kinases	6879	protein-coding gene	gene with protein product		602904		PRKM6	NA	8875998	Standard	NM_002748	NM_002748	NA	Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000558841.1:c.112-11415C>T	chr15.hg19:g.52326612C>T		NA	B2R945|B5BU65|Q68DH4|Q8IYN8	hg19		0.02	-0.131565	AAGxAGT	COVERED																																																																																			NOVEL	MAPK6-005	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000419353.1	5	2.708064	KEEP	0	0	0	9	276	CC	0.99254	0.227464	0		+	5	60	138	0	0	12.422577	8	60	264	32	ENST00000558841.1	0.384615	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	54187287	54187287	__UNKNOWN__	IGR	SNP	G	G	A	rs2725623	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:54187287G>A			NA	NA				RNU6-449P (130780 upstream) : RP11-643A5.2 (53055 downstream)						NA		NA									NA						GAggctgggcgtggtggctca	0.433		NA											g|||	1176	0.234824	0.2731	0.2695	5008	,	,	NA	13511	0.2887	NA	0.1461	False	NA	,,,	NA	NA	NA	2504	0.1943	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.54187287G>A		NA		hg19		0.02	-0.236837	GGCxTGG	COVERED																																																																																			NOVEL					0			8	2.707518	KEEP	1	0	0	9	262	GG	0.99257	0.636582	0			8	60	245	0	0	22.699553	11	60	358	59		0.421053	0.641347
RAB27A	5873	__UNKNOWN__	__UNKNOWN__	15	55499956	55499956	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:55499956T>C	ENST00000396307.2	-	6	719				RAB27A_ENST00000336787.1_Intron|RAB27A_ENST00000564609.1_Intron|RAB27A_ENST00000569493.1_Intron	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	NA		NA			antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		tattggctcattgcaacctct	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974	5873		RAB, member RAS oncogene	9766	protein-coding gene	gene with protein product		603868			NA	7592656	Standard	NM_004580, NM_183236	NM_183235	NA	Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.468-2053A>G	chr15.hg19:g.55499956T>C		NA	O00195|Q6FI40|Q9UIR9|Q9Y5U3	hg19	CCDS10153.1	0.02	-0.087711	TCAxTGC	UNCOVERED																																																																																			NOVEL	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254918.1	5	2.706804	KEEP	0	0	0	9	247	TT	0.99254	0.098977	0		-	2	60	71	0	0	6.396048	4	60	116	28	ENST00000396307.2	0.333333	0.099721
CCPG1	9236	__UNKNOWN__	__UNKNOWN__	15	55678353	55678353	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:55678353T>C	ENST00000442196.3	-	3	108				CCPG1_ENST00000425574.3_Intron|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000310958.6_Intron|CCPG1_ENST00000569205.1_Intron			Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	NA		NA			cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		tttgggaggctgaggccggtg	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916	9236			24227	protein-coding gene	gene with protein product		611326			NA	9383053, 10574462	Standard	NM_004748	NM_004748	NA	Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000442196.3:c.61-441A>G	chr15.hg19:g.55678353T>C		NA	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	hg19	CCDS55966.1	0.02	-0.228043	GGCxGAG	COVERED																																																																																			NOVEL	CCPG1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419849.1	7	3.007473	KEEP	1	0	0	10	275	TT	0.992708	0.578679	0		-	3	60	101	1	0	7.726946	19	60	578	57	ENST00000442196.3	0.136364	0.58293
CCPG1	9236	__UNKNOWN__	__UNKNOWN__	15	55686425	55686425	__UNKNOWN__	Intron	SNP	C	C	T	rs60168254	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:55686425C>T	ENST00000442196.3	-	2	39				CCPG1_ENST00000425574.3_Intron|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000310958.6_Intron|CCPG1_ENST00000569205.1_Intron			Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	NA		NA			cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		ctcaagtgatccacccacctc	0.453		NA											C|||	740	0.147764	0.034	0.1787	5008	,	,	NA	17256	0.0575	NA	0.333	False	NA	,,,	NA	NA	NA	2504	0.182	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916	9236			24227	protein-coding gene	gene with protein product		611326			NA	9383053, 10574462	Standard	NM_004748	NM_004748	NA	Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000442196.3:c.9-4794G>A	chr15.hg19:g.55686425C>T		NA	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	hg19	CCDS55966.1	0.02	-0.131573	GATxCAC	COVERED																																																																																			NOVEL	CCPG1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419849.1	4	2.407256	KEEP	1	0	0	8	251	CC	0.99257	0.22747	0		-	4	60	121	0	0	10.523508	9	60	302	35	ENST00000442196.3	0.307692	0.229173
PYGO1	26108	__UNKNOWN__	__UNKNOWN__	15	55834864	55834864	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:55834864T>C	ENST00000302000.6	-	0	4711					NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		cgtggtggcttacacctgtaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016	26108		Zinc fingers, PHD-type	30256	protein-coding gene	gene with protein product		606902	pygopus homolog 1 (Drosophila)		NA	11988739	Standard	NM_015617	NM_015617	NA	Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.*3357A>G	chr15.hg19:g.55834864T>C		NA	A7Y2D6	hg19	CCDS10155.1	0.02	-0.368275	GCTxACA	COVERED																																																																																			NOVEL	PYGO1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254977.2	11	2.435415	KEEP	1	1	31	19	491	TT	0.99986	0.899188	0		-	3	60	97	0	0	6.612653	34	60	948	80	ENST00000302000.6	0.081081	0.899314
PYGO1	26108	__UNKNOWN__	__UNKNOWN__	15	55880176	55880176	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:55880176G>A	ENST00000302000.6	-	1	144					NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		GGCCGCTGCGGCTGCGAGGCA	0.706		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016	26108		Zinc fingers, PHD-type	30256	protein-coding gene	gene with protein product		606902	pygopus homolog 1 (Drosophila)		NA	11988739	Standard	NM_015617	NM_015617	NA	Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.49+825C>T	chr15.hg19:g.55880176G>A		NA	A7Y2D6	hg19	CCDS10155.1	0.02	1.276008	GCGxCTG	COVERED																																																																																			NOVEL	PYGO1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254977.2	1	6.350169	KEEP	0	1	25	30	893	GG	0.999997	0.986151	0		-	11	60	304	0	0	23.32788	48	60	1600	115	ENST00000302000.6	0.186441	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	57642959	57642959	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:57642959T>C			NA	NA				RP11-358M11.3 (26853 upstream) : CGNL1 (25743 downstream)						NA		NA									NA						tgagccaccgtgcccagccTC	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.57642959T>C		NA		hg19		0.02	-0.166628	CCGxGCC	UNCOVERED																																																																																			NOVEL					0			7	2.405974	KEEP	2	0	0	8	218	TT	0	0	0			3	60	97	0	0	7.533626	16	60	462	39		0.157895	0.353947
POLR2M	81488	__UNKNOWN__	__UNKNOWN__	15	58009404	58009404	__UNKNOWN__	3'UTR	SNP	C	C	T	rs2414518		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:58009404C>T	ENST00000299638.3	+	0	3848				POLR2M_ENST00000380557.4_3'UTR|POLR2M_ENST00000380563.2_Intron	NM_015532.3	NP_056347.1	P0CAP2	GRL1A_HUMAN	polymerase (RNA) II (DNA directed) polypeptide M	NA		NA			maintenance of ER location (GO:0051685)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)	DNA-directed RNA polymerase activity (GO:0003899)				NA						GTTTTTTCTACACTGTCAATA	0.303		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF326773	CCDS32252.1, CCDS42045.1	15q21.3	2013-01-21	2011-11-07	2011-11-07		ENSG00000255529	81488		RNA polymerase subunits	14862	protein-coding gene	gene with protein product		606485	glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A	GRINL1A	NA	16769904, 22850672	Standard		NM_015532	NA	Approved	Gdown, Gdown1, GCOM1	uc002aev.1	P0CAP2	OTTHUMG00000166486	ENST00000299638.3:c.*2527C>T	chr15.hg19:g.58009404C>T		NA	Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5|Q9Y3V6	hg19	CCDS32252.1	0.02	2.687862	CTAxACT	COVERED																																																																																			NOVEL	POLR2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255719.2	7	8.691084	KEEP	0	2	42	44	1331	CC	1	0.999999	0		+	10	49	272	0	0	16.901417	114	60	3866	242	ENST00000299638.3	0.080645	0.999999
LIPC	3990	__UNKNOWN__	__UNKNOWN__	15	58845761	58845761	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:58845761T>C	ENST00000414170.3	+	7	1338				LIPC_ENST00000299022.5_Intron|LIPC_ENST00000433326.2_Intron|LIPC_ENST00000356113.6_Intron			P11150	LIPC_HUMAN	lipase, hepatic	NA		NA			cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		cactgcactctagcctgggtg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3990	3.1.1.3		6619	protein-coding gene	gene with protein product		151670			NA		Standard		NM_000236	NA	Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000414170.3:c.1051+4990T>C	chr15.hg19:g.58845761T>C		NA	A2RUB4|A8K9B6|O43571|P78529|Q99465	hg19		0.02	-0.122799	CTCxAGC	UNCOVERED																																																																																			NOVEL	LIPC-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000416210.1	4	2.405863	KEEP	1	0	0	8	219	TT	0	0	0		+	3	60	103	0	0	8.801188	9	60	270	33	ENST00000414170.3	0.25	0.196312
FAM63B	54629	__UNKNOWN__	__UNKNOWN__	15	59145437	59145437	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59145437G>C	ENST00000559228.1	+	9	1819				FAM63B_ENST00000450403.2_Intron			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	NA		NA								central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						caggtgtgaggcaccacgcct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09					54629			26954	protein-coding gene	gene with protein product		NA			NA	10574461	Standard	NM_019092	NM_001040450	NA	Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.1738-1244G>C	chr15.hg19:g.59145437G>C		NA	B2RTT8|Q9ULQ6	hg19	CCDS42046.1	0.02	-0.210545	GAGxCAC	COVERED																																																																																			NOVEL	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416230.1	5	2.706519	KEEP	0	0	0	9	258	GG	0.99254	0.518266	0		+	3	60	101	0	0	7.860473	17	60	584	48	ENST00000559228.1	0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	59246080	59246080	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59246080T>C			NA	NA				SLTM (20228 upstream) : RNF111 (33773 downstream)						NA		NA									NA						gtggctcacgtctgtaatccc	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.59246080T>C		NA		hg19		0.02	-0.192961	ACGxCTG	COVERED																																																																																			NOVEL					0			3	2.706351	KEEP	0	0	0	9	243	TT	0.99254	0.454342	0			4	60	135	0	0	10.968734	17	60	506	47		0.190476	0.457757
MYO1E	4643	__UNKNOWN__	__UNKNOWN__	15	59505711	59505711	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59505711A>C	ENST00000288235.4	-	12	1675					NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	NA		NA			actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		gttgcctaggatggagtgcag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483	4643		Myosins / Myosin superfamily : Class I	7599	protein-coding gene	gene with protein product	myosin-IC	601479			NA	8884266	Standard	NM_004998	NM_004998	NA	Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1275+715T>G	chr15.hg19:g.59505711A>C		NA	Q14778	hg19	CCDS32254.1	0.02	-0.096426	AGGxTGG	UNCOVERED																																																																																			NOVEL	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416024.1	1	2.406233	KEEP	0	0	0	8	225	AA	0.99257	0.119541	0		-	3	60	87	1	0	7.477576	7	60	197	26	ENST00000288235.4	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	59709687	59709687	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59709687T>C			NA	NA				Y_RNA (8473 upstream) : FAM81A (20684 downstream)						NA		NA									NA						gacaggtcacttgaggtcagg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.59709687T>C		NA		hg19		0.02	-0.438579	CACxTGA	COVERED																																																																																			NOVEL					0			10	2.436588	KEEP	0	1	31	19	524	TT	0.999863	0.959727	0			3	60	107	1	1	7.376582	41	60	1270	107		0.068182	0.959859
FAM81A	145773	__UNKNOWN__	__UNKNOWN__	15	59734773	59734773	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59734773G>A	ENST00000288228.5	+	1	110				FAM81A_ENST00000557895.1_Intron	NM_152450.2	NP_689663.2	Q8TBF8	FA81A_HUMAN	family with sequence similarity 81, member A	NA		NA								endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10						ctgagatcgcgccactgcact	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45269.1	15q22.2	2012-10-02			ENSG00000157470	ENSG00000157470	145773			28379	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152450	NM_152450	NA	Approved	MGC26690	uc002agc.2	Q8TBF8	OTTHUMG00000171915	ENST00000288228.5:c.-78+4292G>A	chr15.hg19:g.59734773G>A		NA		hg19	CCDS45269.1	0.02	-0.114025	CGCxCCA	UNCOVERED																																																																																			NOVEL	FAM81A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415876.1	7	2.405857	KEEP	7	0	0	8	220	GG	0	0	0		+	3	60	94	0	0	7.901068	9	60	286	31	ENST00000288228.5	0.25	0.162467
FAM81A	145773	__UNKNOWN__	__UNKNOWN__	15	59786046	59786046	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59786046A>C	ENST00000288228.5	+	4	600					NM_152450.2	NP_689663.2	Q8TBF8	FA81A_HUMAN	family with sequence similarity 81, member A	NA		NA								endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10						ctcggcctccaagagtgctgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45269.1	15q22.2	2012-10-02			ENSG00000157470	ENSG00000157470	145773			28379	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152450	NM_152450	NA	Approved	MGC26690	uc002agc.2	Q8TBF8	OTTHUMG00000171915	ENST00000288228.5:c.413+1458A>C	chr15.hg19:g.59786046A>C		NA		hg19	CCDS45269.1	0.02	-0.157868	TCCxAGA	COVERED																																																																																			NOVEL	FAM81A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415876.1	5	2.405043	KEEP	0	0	0	8	208	AA	0.99257	0.320408	0		+	3	60	103	0	1	8.378907	13	60	382	39	ENST00000288228.5	0.1875	0.322807
GCNT3	9245	__UNKNOWN__	__UNKNOWN__	15	59907856	59907856	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59907856A>T	ENST00000396065.1	+	2	198				GCNT3_ENST00000560580.1_Intron|GCNT3_ENST00000560585.1_Intron	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	NA		NA			carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ccgaggtgggaggatcacttg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	9245	2.4.1.102, 2.4.1.150	Glucosaminyl (N-acetyl) transferase and xylosyltransferase family	4205	protein-coding gene	gene with protein product		606836			NA	9915862, 9988682	Standard	NM_004751	NM_004751	NA	Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.-250-1035A>T	chr15.hg19:g.59907856A>T		NA		hg19	CCDS10172.1	0.02	-0.263085	GGGxGGA	COVERED																																																																																			NOVEL	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256068.1	8	2.405303	KEEP	0	0	0	8	214	AA	0.99257	0.688515	0		+	4	60	112	0	0	8.264037	22	60	639	53	ENST00000396065.1	0.153846	0.693668
BNIP2	663	__UNKNOWN__	__UNKNOWN__	15	59973936	59973936	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59973936G>A	ENST00000607373.1	-	2	253				BNIP2_ENST00000415213.2_Intron|BNIP2_ENST00000267859.3_Intron	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	NA		NA			apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						gtgagccaccgcacctggccA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(174;1936 1978 6671 8240 38212)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299	663			1083	protein-coding gene	gene with protein product		603292	BCL2/adenovirus E1B 19kD-interacting protein 2		NA	7954800	Standard	NM_004330	NM_004330	NA	Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.50+670C>T	chr15.hg19:g.59973936G>A		NA	B4DS94	hg19		0.02	-0.192978	ACCxCAC	COVERED																																																																																			NOVEL	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000470740.1	6	2.706967	KEEP	2	0	0	9	255	GG	0.99257	0.454356	0		-	3	60	95	0	0	7.33337	16	60	520	46	ENST00000607373.1	0.157895	0.457757
BNIP2	663	__UNKNOWN__	__UNKNOWN__	15	59975786	59975786	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:59975786T>C	ENST00000607373.1	-	2	146				BNIP2_ENST00000415213.2_Intron|BNIP2_ENST00000267859.3_Intron	NM_004330.2	NP_004321.2	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 2	NA		NA			apoptotic process (GO:0006915)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|positive regulation of GTPase activity (GO:0043547)|positive regulation of muscle cell differentiation (GO:0051149)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)			NS(1)|large_intestine(2)|lung(5)|ovary(1)	9						gaggccgaggtgggcggatca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(174;1936 1978 6671 8240 38212)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U15173	CCDS10174.2	15q21.3	2008-07-18	2002-08-29		ENSG00000140299	ENSG00000140299	663			1083	protein-coding gene	gene with protein product		603292	BCL2/adenovirus E1B 19kD-interacting protein 2		NA	7954800	Standard	NM_004330	NM_004330	NA	Approved	Nip2, BNIP-2	uc010uhc.2	Q12982	OTTHUMG00000132727	ENST00000607373.1:c.57-1073A>G	chr15.hg19:g.59975786T>C		NA	B4DS94	hg19		0.02	-0.15789	AGGxGGG	COVERED																																																																																			NOVEL	BNIP2-012	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000470740.1	4	2.707063	KEEP	3	0	0	9	253	TT	0.99257	0.320408	0		-	3	60	104	0	0	8.478634	13	60	402	46	ENST00000607373.1	0.1875	0.322807
ANXA2	302	__UNKNOWN__	__UNKNOWN__	15	60640709	60640709	__UNKNOWN__	Intron	SNP	C	C	T	rs35182260	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:60640709C>T	ENST00000396024.3	-	13	1120				ANXA2_ENST00000421017.2_Intron|ANXA2_ENST00000451270.2_Intron|ANXA2_ENST00000332680.4_Intron	NM_001136015.2	NP_001129487.1	P07355	ANXA2_HUMAN	annexin A2	NA		NA			angiogenesis (GO:0001525)|body fluid secretion (GO:0007589)|cellular response to acid chemical (GO:0071229)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|membrane budding (GO:0006900)|membrane raft assembly (GO:0001765)|negative regulation of catalytic activity (GO:0043086)|osteoclast development (GO:0036035)|positive regulation of binding (GO:0051099)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vesicle fusion (GO:0031340)|protein heterotetramerization (GO:0051290)|protein targeting to plasma membrane (GO:0072661)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell surface (GO:0009986)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|late endosome membrane (GO:0031902)|lipid particle (GO:0005811)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)|midbody (GO:0030496)|myelin sheath adaxonal region (GO:0035749)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|sarcolemma (GO:0042383)|Schmidt-Lanterman incisure (GO:0043220)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phospholipase A2 inhibitor activity (GO:0019834)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			kidney(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9					Tenecteplase(DB00031)	tttgggaggccgaggcgggcg	0.517		NA											C|||	786	0.156949	0.0121	0.219	5008	,	,	NA	17970	0.1121	NA	0.325	False	NA	,,,	NA	NA	NA	2504	0.182	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D00017	CCDS10175.1, CCDS32256.1	15q22.2	2012-10-02			ENSG00000182718	ENSG00000182718	302		Annexins	537	protein-coding gene	gene with protein product	annexin II	151740		ANX2, ANX2L4, CAL1H, LPC2D	NA	7961821	Standard	NM_001002857	NM_001136015	NA	Approved	LIP2	uc002agm.3	P07355	OTTHUMG00000132763	ENST00000396024.3:c.960+564G>A	chr15.hg19:g.60640709C>T		NA	Q567R4|Q6N0B3|Q8TBV2|Q96DD5|Q9UDH8	hg19	CCDS10175.1	0.02	-0.394694	GGCxGAG	COVERED																																																																																			NOVEL	ANXA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256135.1	20	12.496433	KEEP	158	2	58	62	1800	CC	0.99986	0.92651	0		-	7	60	219	0	0	19.435811	14	20	423	339	ENST00000396024.3	0.333333	0.92664
RORA	6095	__UNKNOWN__	__UNKNOWN__	15	60958656	60958656	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:60958656C>T	ENST00000335670.6	-	2	297				RORA_ENST00000560004.1_Intron	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	NA		NA			angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						agtgctgggactacaggcatg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667	6095		Nuclear hormone receptors	10258	protein-coding gene	gene with protein product		600825			NA	7926749	Standard		NM_134261	NA	Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.196+12199G>A	chr15.hg19:g.60958656C>T		NA	P35397|P35399|P45445|Q495X4|Q96H83	hg19	CCDS10177.1	0.02	-0.201769	GGAxTAC	COVERED																																																																																			NOVEL	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256142.2	7	2.708135	KEEP	0	0	0	9	280	CC	0.99254	0.486885	0		-	3	60	93	0	0	7.133373	16	60	554	45	ENST00000335670.6	0.157895	0.490544
RORA	6095	__UNKNOWN__	__UNKNOWN__	15	61295068	61295068	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:61295068C>T	ENST00000335670.6	-	1	267					NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	NA		NA			angiogenesis (GO:0001525)|cellular response to hypoxia (GO:0071456)|cellular response to sterol (GO:0036315)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|circadian regulation of gene expression (GO:0032922)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|muscle cell differentiation (GO:0042692)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cholesterol homeostasis (GO:2000188)|regulation of glucose metabolic process (GO:0010906)|regulation of macrophage activation (GO:0043030)|regulation of smoothened signaling pathway (GO:0008589)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription involved in cell fate commitment (GO:0060850)|regulation of transcription, DNA-templated (GO:0006355)|T-helper 17 cell differentiation (GO:0072539)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	direct ligand regulated sequence-specific DNA binding transcription factor activity (GO:0098531)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|oxysterol binding (GO:0008142)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator binding (GO:0001223)|transcription corepressor binding (GO:0001222)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	21						tggtggctcacgcctgtaatc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U04897	CCDS10177.1, CCDS10178.1, CCDS10179.1, CCDS45271.1	15q21-q22	2013-01-16			ENSG00000069667	ENSG00000069667	6095		Nuclear hormone receptors	10258	protein-coding gene	gene with protein product		600825			NA	7926749	Standard		NM_134261	NA	Approved	RZRA, ROR1, ROR2, ROR3, NR1F1	uc002agv.3	P35398	OTTHUMG00000132769	ENST00000335670.6:c.166+226183G>A	chr15.hg19:g.61295068C>T		NA	P35397|P35399|P45445|Q495X4|Q96H83	hg19	CCDS10177.1	0.02	-0.166583	TCAxGCC	COVERED																																																																																			NOVEL	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256142.2	4	3.309935	KEEP	1	0	0	11	339	CC	0.992708	0.351366	0		-	3	60	91	0	0	6.934378	16	60	498	48	ENST00000335670.6	0.157895	0.353947
RP11-507B12.2	0	__UNKNOWN__	__UNKNOWN__	15	61825016	61825016	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:61825016C>T	ENST00000559783.1	-	0	123										NA		NA									NA						gtcaggctggcctcgaactcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559783.1:	chr15.hg19:g.61825016C>T		NA		hg19		0.02	-0.087713	TGGxCTC	UNCOVERED																																																																																			NOVEL	RP11-507B12.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000418692.1	3	2.407191	KEEP	0	0	0	8	245	CC	0.99257	0.09898	0		-	3	38	82	0	0	7.142845	6	60	202	25	ENST00000559783.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	62613784	62613784	__UNKNOWN__	IGR	SNP	G	G	A	rs35519125	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:62613784G>A			NA	NA				RP11-299H22.7 (36579 upstream) : TLN2 (239779 downstream)						NA		NA									NA						cagaagaatcgcttaaaccct	0.473		NA											G|||	602	0.120208	0.0287	0.0576	5008	,	,	NA	15895	0.2738	NA	0.1312	False	NA	,,,	NA	NA	NA	2504	0.1186	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.62613784G>A		NA		hg19		0.02	-0.157865	ATCxCTT	COVERED																																																																																			NOVEL					0			6	2.404141	KEEP	1	0	0	8	214	GG	0.99257	0.320408	0			6	60	177	0	0	15.76924	11	60	331	31		0.352941	0.322807
HERC1	8925	__UNKNOWN__	__UNKNOWN__	15	63927514	63927514	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:63927514T>C	ENST00000443617.2	-	66	12502					NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	NA		NA			cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						tcccaaagtgttaggattaca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657	8925		WD repeat domain containing	4867	protein-coding gene	gene with protein product		605109	hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1		NA	8861955, 9233772	Standard	NM_003922	NM_003922	NA	Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12415-427A>G	chr15.hg19:g.63927514T>C		NA	Q8IW65	hg19	CCDS45277.1	0.02	-0.131575	GTGxTAG	COVERED																																																																																			NOVEL	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418523.1	3	3.608661	KEEP	0	0	0	12	327	TT	0.993634	0.259304	0		-	3	60	102	1	0	8.832496	8	60	244	40	ENST00000443617.2	0.272727	0.260965
PPIB	5479	__UNKNOWN__	__UNKNOWN__	15	64453667	64453667	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:64453667C>G	ENST00000300026.3	-	2	468				PPIB_ENST00000558492.1_Intron	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)	NA		NA			bone development (GO:0060348)|chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|positive regulation of multicellular organism growth (GO:0040018)|protein peptidyl-prolyl isomerization (GO:0000413)|protein stabilization (GO:0050821)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(6)	10					L-Proline(DB00172)	gctcacacctctaatcccagc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(105;399 1481 32889 33051 36637)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10191.1	15q21-q22	2014-09-17			ENSG00000166794	ENSG00000166794	5479	5.2.1.8		9255	protein-coding gene	gene with protein product		123841			NA	2000394, 20089953	Standard		NM_000942	NA	Approved	CYPB, OI9	uc002and.3	P23284	OTTHUMG00000133018	ENST00000300026.3:c.249+572G>C	chr15.hg19:g.64453667C>G		NA	A8K534|Q6IBH5|Q9BVK5	hg19	CCDS10191.1	0.02	-0.166683	CCTxTAA	COVERED																																																																																			NOVEL	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256604.1	5	3.009388	KEEP	0	0	0	10	323	CC	0.992708	0.351366	0		-	3	60	105	0	0	8.409676	15	60	515	46	ENST00000300026.3	0.166667	0.353947
TRIP4	9325	__UNKNOWN__	__UNKNOWN__	15	64744202	64744202	__UNKNOWN__	Intron	SNP	T	T	G	rs556403727		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:64744202T>G	ENST00000261884.3	+	13	1738					NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						ctgttgcccatgctggagtgc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671	9325		-	12310	protein-coding gene	gene with protein product	zinc finger, C2HC5-type	604501			NA	7776974	Standard	NM_016213	NM_016213	NA	Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.1679-2994T>G	chr15.hg19:g.64744202T>G		NA	B2RAS0|Q96ED7|Q9UKH0	hg19	CCDS10194.1	0.02	-0.149086	CCAxGCT	COVERED																																																																																			NOVEL	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256635.2	5	3.00757	KEEP	0	0	0	10	276	TT	0.992708	0.289872	0		+	4	60	140	0	0	12.27156	10	60	292	38	ENST00000261884.3	0.285714	0.292001
ZNF609	23060	__UNKNOWN__	__UNKNOWN__	15	64877298	64877298	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:64877298A>C	ENST00000326648.3	+	2	875					NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	NA		NA				nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ccaaggcgggaggatcacttg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357	23060		Zinc fingers, C2H2-type	29003	protein-coding gene	gene with protein product		NA			NA	9205841	Standard	XM_042833	NM_015042	NA	Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.748-37728A>C	chr15.hg19:g.64877298A>C		NA	Q0D2I2	hg19	CCDS32270.1	0.02	-0.166636	GGGxGGA	COVERED																																																																																			NOVEL	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418130.1	10	2.405786	KEEP	1	0	0	8	220	AA	0.99257	0.4869	0		+	3	60	89	0	0	6.811185	15	60	445	43	ENST00000326648.3	0.166667	0.490544
SPG21	51324	__UNKNOWN__	__UNKNOWN__	15	65256125	65256125	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:65256125G>T	ENST00000416889.2	-	8	1000				SPG21_ENST00000204566.2_Intron|SPG21_ENST00000559199.1_Intron|SPG21_ENST00000433215.2_Intron	NM_001127890.1	NP_001121362.1	Q9NZD8	SPG21_HUMAN	spastic paraplegia 21 (autosomal recessive, Mast syndrome)	NA		NA			antigen receptor-mediated signaling pathway (GO:0050851)|cell death (GO:0008219)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network transport vesicle (GO:0030140)	CD4 receptor binding (GO:0042609)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10						gagctggagtgtcactcttgt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													22	23	22			NA	NA	15		NA											NA				65256125		2202	4299	6501	SO:0001627	intron_variant			AF208861	CCDS10198.1, CCDS45279.1	15q21-q22	2008-02-05	2007-04-23		ENSG00000090487	ENSG00000090487	51324			20373	protein-coding gene	gene with protein product	maspardin	608181			NA	11113139, 14564668	Standard	NM_016630	XM_006720564	NA	Approved	ACP33, GL010, BM-019, MAST	uc002aoe.3	Q9NZD8	OTTHUMG00000133098	ENST00000416889.2:c.730-48C>A	chr15.hg19:g.65256125G>T		NA	B4DW44|Q6ZMB6	hg19	CCDS45279.1	0.02	-0.184212	AGTxTCA	COVERED																																																																																			NOVEL	SPG21-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418144.1	5	4.211306	KEEP	0	0	0	14	406	GG	0.99649	0.421991	0		-	3	60	86	0	0	6.362417	17	60	582	48	ENST00000416889.2	0.15	0.423478
UBAP1L	390595	__UNKNOWN__	__UNKNOWN__	15	65386131	65386131	__UNKNOWN__	Intron	SNP	C	C	T	rs183782023	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:65386131C>T	ENST00000559089.1	-	6	1232				UBAP1L_ENST00000502113.2_Intron			F5GYI3	UBA1L_HUMAN	ubiquitin associated protein 1-like	NA		NA								breast(1)|endometrium(1)|kidney(1)	3						cctgtaatcccagcactttgg	0.572		NA											C|||	20	0.00399361	0.0	0.0072	5008	,	,	NA	17754	0.0069	NA	0.004	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS53948.1	15q22.31	2011-08-15			ENSG00000246922	ENSG00000246922	390595			40028	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001163692	NM_001163692	NA	Approved		uc010uit.2	F5GYI3		ENST00000559089.1:c.1012-562G>A	chr15.hg19:g.65386131C>T		NA		hg19	CCDS53948.1	0.02	-0.166673	TCCxAGC	COVERED																																																																																			NOVEL	UBAP1L-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418469.1	8	5.415939	KEEP	6	0	0	18	546	CC	0.994391	0.351961	0		-	5	60	155	0	0	13.413014	12	60	407	57	ENST00000559089.1	0.294118	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	65427446	65427446	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:65427446G>A			NA	NA				PDCD7 (1272 upstream) : CLPX (13110 downstream)						NA		NA									NA						aagtgctggggttacaggtgt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.65427446G>A		NA		hg19		0.02	-0.166667	GGGxTTA	COVERED																																																																																			NOVEL					0			11	4.212321	KEEP	0	0	0	14	421	GG	0.995343	0.352299	0			3	60	91	0	0	7.010334	15	60	493	44		0.166667	0.353947
DENND4A	10260	__UNKNOWN__	__UNKNOWN__	15	66032696	66032696	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:66032696T>C	ENST00000431932.2	-	5	840				DENND4A_ENST00000443035.3_Intron	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	NA		NA			positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						gcctgtaatctcagcactttg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27			10260		DENN/MADD domain containing	24321	protein-coding gene	gene with protein product		600382	c-myc promoter binding protein	MYCPBP	NA	8056341, 12906859	Standard	NM_005848	NM_005848	NA	Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.631+1356A>G	chr15.hg19:g.66032696T>C		NA	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	hg19	CCDS45285.1	0.02	-0.30699	ATCxCAG	COVERED																																																																																			NOVEL	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419611.1	10	3.308604	KEEP	0	0	0	11	312	TT	0.993072	0.794702	0		-	3	60	95	0	0	6.746051	26	60	799	65	ENST00000431932.2	0.103448	0.800245
DIS3L	115752	__UNKNOWN__	__UNKNOWN__	15	66617533	66617533	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:66617533G>A	ENST00000319212.4	+	12	1717				DIS3L_ENST00000319194.5_Intron|DIS3L_ENST00000441424.2_Intron|RP11-352G18.2_ENST00000565993.1_RNA	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	NA		NA			RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ggagtttgaggccagcctggg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938	115752			28698	protein-coding gene	gene with protein product		614183	DIS3 mitotic control homolog (S. cerevisiae)-like		NA	20531386	Standard	NM_133375	NM_001143688	NA	Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.1668-636G>A	chr15.hg19:g.66617533G>A		NA	Q8N1N8|Q8WTU9|Q96CM7	hg19	CCDS45286.1	0.02	-0.157893	GAGxCCA	COVERED																																																																																			NOVEL	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000382792.2	5	3.310148	KEEP	0	0	0	11	352	GG	0.993072	0.32057	0		+	3	40	86	0	0	6.592259	14	60	470	43	ENST00000319212.4	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	66663337	66663337	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:66663337C>T			NA	NA				TIPIN (14283 upstream) : TIPIN (8270 downstream)						NA		NA									NA						tcacttgaggccaggagttcg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.66663337C>T		NA		hg19		0.02	-0.166667	AGGxCAG	UNCOVERED																																																																																			NOVEL					0			6	2.407483	KEEP	1	0	0	8	256	CC	0	0	0			3	60	90	0	0	6.991896	14	60	474	37		0.176471	0.353947
RPL4	6124	__UNKNOWN__	__UNKNOWN__	15	66792100	66792100	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:66792100G>A	ENST00000568588.1	-	11	1534				RPL4_ENST00000307961.6_Intron			P36578	RL4_HUMAN	ribosomal protein L4	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						ggtggctcacgcctgtaatcc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444	6124		L ribosomal proteins	10353	protein-coding gene	gene with protein product	60S ribosomal protein L4	180479			NA	9582194, 8268230	Standard	NM_000968	NM_000968	NA	Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000568588.1:c.757-110C>T	chr15.hg19:g.66792100G>A		NA	A8K502|P39029|Q4VBR0|Q969Z9	hg19		0.02	-0.298203	CACxCCT	COVERED																																																																																			NOVEL	RPL4-020	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420737.1	4	3.309186	KEEP	2	0	0	11	322	GG	0.993072	0.775649	0		-	5	60	133	0	0	9.525082	29	60	962	64	ENST00000568588.1	0.147059	0.78106
RP11-798K3.4	0	__UNKNOWN__	__UNKNOWN__	15	67214348	67214348	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:67214348A>G	ENST00000559904.1	+	0	110										NA		NA									NA						accatgcccaactaatttttt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559904.1:	chr15.hg19:g.67214348A>G		NA		hg19		0.02	-0.210483	CCAxCTA	COVERED																																																																																			NOVEL	RP11-798K3.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000417722.1	14	3.741523	KEEP	0	1	30	23	635	AA	0.999909	0.522114	0		+	3	60	108	0	1	8.305322	21	60	608	62	ENST00000559904.1	0.125	0.522161
RP11-798K3.4	0	__UNKNOWN__	__UNKNOWN__	15	67214454	67214454	__UNKNOWN__	lincRNA	SNP	C	C	A	rs113415983	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:67214454C>A	ENST00000559904.1	+	0	110										NA		NA									NA						agccccccaacgtgctgggat	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559904.1:	chr15.hg19:g.67214454C>A		NA		hg19		0.02	-0.184213	CAAxGTG	COVERED																																																																																			NOVEL	RP11-798K3.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000417722.1	11	3.010637	KEEP	0	1	31	21	540	CC	0.999879	0.457701	0		+	3	60	94	0	0	7.310087	15	60	495	57	ENST00000559904.1	0.166667	0.457757
AAGAB	79719	__UNKNOWN__	__UNKNOWN__	15	67521568	67521568	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:67521568A>G	ENST00000561452.1	-	5	724				AAGAB_ENST00000542650.1_Intron|AAGAB_ENST00000261880.5_Intron			Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin binding protein	NA		NA			protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9						tcaagagttcaagaccagcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136715	CCDS42050.1, CCDS61679.1	15q22.33-q23	2014-02-12	2009-07-20		ENSG00000103591	ENSG00000103591	79719			25662	protein-coding gene	gene with protein product		614888			NA	11230166, 10477754	Standard	NM_024666	NM_024666	NA	Approved	FLJ11506, p34	uc002aqk.5	Q6PD74	OTTHUMG00000172246	ENST00000561452.1:c.208+2583T>C	chr15.hg19:g.67521568A>G		NA	B4DG44|Q6FI86|Q7Z5X9|Q9H0P1|Q9HAK0	hg19		0.02	-0.12275	TTCxAGA	UNCOVERED																																																																																			NOVEL	AAGAB-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417474.1	9	2.404702	KEEP	5	0	0	8	206	AA	0	0	0		-	3	60	85	0	0	6.773685	11	60	305	37	ENST00000561452.1	0.214286	0.196312
MAP2K5	5607	__UNKNOWN__	__UNKNOWN__	15	67883422	67883422	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:67883422T>C	ENST00000178640.5	+	7	1058				MAP2K5_ENST00000354498.5_Intron|MAP2K5_ENST00000560591.1_Intron|MAP2K5_ENST00000395476.2_Intron	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	NA		NA			activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						tggtggctcatgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764	5607		Mitogen-activated protein kinase cascade / Kinase kinases	6845	protein-coding gene	gene with protein product		602520		PRKMK5	NA	7759517	Standard	NM_145162	NM_002757	NA	Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.432-1842T>C	chr15.hg19:g.67883422T>C		NA	B4DE43|Q92961|Q92962	hg19	CCDS10224.1	0.02	-0.271879	TCAxGCC	COVERED																																																																																			NOVEL	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257041.1	15	3.596504	KEEP	7	0	0	12	305	TT	0.992708	0.712085	0		+	3	60	101	0	0	7.442704	24	60	692	68	ENST00000178640.5	0.111111	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	68110015	68110015	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:68110015A>G			NA	NA				MAP2K5 (10554 upstream) : SKOR1 (2026 downstream)						NA		NA									NA						gccaggcgccatggctcatgc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.68110015A>G		NA		hg19		0.02	-0.114016	GCCxTGG	UNCOVERED																																																																																			NOVEL					0			3	2.4064	KEEP	0	0	0	8	226	AA	0.99257	0.16126	0			3	60	96	0	0	7.982135	10	60	293	30		0.230769	0.162467
RP11-34F13.3	0	__UNKNOWN__	__UNKNOWN__	15	68134589	68134589	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:68134589G>A	ENST00000558889.1	+	0	121										NA		NA									NA						gctggagtgcggtggtgtgat	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000558889.1:	chr15.hg19:g.68134589G>A		NA		hg19		0.02	-0.166649	TGCxGTG	UNCOVERED																																																																																			NOVEL	RP11-34F13.3-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000417505.1	6	2.406883	KEEP	2	0	0	8	237	GG	0	0	0		+	3	60	83	0	0	6.573174	11	60	354	39	ENST00000558889.1	0.214286	0.353947
PIAS1	8554	__UNKNOWN__	__UNKNOWN__	15	68358666	68358666	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:68358666T>C	ENST00000249636.6	+	1	172				PIAS1_ENST00000545237.1_Intron	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	NA		NA			androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						aggctggtcttgaactgctga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800	8554		Zinc fingers, MIZ-type	2752	protein-coding gene	gene with protein product	zinc finger, MIZ-type containing 3	603566	DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1	DDXBP1	NA	9724754, 9177271	Standard		XM_005254735	NA	Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.24+11978T>C	chr15.hg19:g.68358666T>C		NA	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	hg19	CCDS45290.1	0.02	-0.149095	TCTxGAA	COVERED																																																																																			NOVEL	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419642.2	4	2.406103	KEEP	0	0	0	8	223	TT	0.99257	0.289832	0		+	3	60	100	0	0	7.991858	14	60	410	36	ENST00000249636.6	0.176471	0.292001
FEM1B	10116	__UNKNOWN__	__UNKNOWN__	15	68583512	68583512	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs568876101		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:68583512C>T	ENST00000306917.4	+	2	2431	c.1816C>T	c.(1816-1818)Cgg>Tgg	p.R606W		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	606		NA			apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						CCGAGCAGTTCGGGCTAATGA	0.418		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	19084	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													55	55	55			NA	NA	15		NA											NA				68583512		2200	4298	6498	SO:0001583	missense				CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018	10116		Ankyrin repeat domain containing	3649	protein-coding gene	gene with protein product		613539	FEM-1 (C. elegans) homolog b		NA	10623617	Standard		NM_015322	NA	Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.1816C>T	chr15.hg19:g.68583512C>T	ENSP00000307298:p.Arg606Trp	NA	O43146	hg19	CCDS10228.1	0.02	1.155363	GTTxGGG	COVERED	.	.	.	.	.	.	.	.	.	.	C	17.34	3.366156	0.61513	.	.	ENSG00000169018	ENST00000306917	T	0.50001	0.76	5.75	5.75	0.90469	.	0.054495	0.85682	D	0.000000	T	0.55497	0.1924	M	0.64170	1.965	0.80722	D	1	D	0.67145	0.996	P	0.47603	0.551	T	0.60026	-0.7343	10	0.66056	D	0.02	-22.3165	18.9194	0.92519	0.0:1.0:0.0:0.0	.	606	Q9UK73	FEM1B_HUMAN	W	606	ENSP00000307298:R606W	ENSP00000307298:R606W	R	+	1	2	FEM1B	66370566	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.756000	0.55205	2.720000	0.93068	0.491000	0.48974	CGG	NOVEL	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257065.1	2	3.139495	KEEP	0	1	27	20	560	CC	0.999869	0.999428	0		+	5	60	136	0	0	7.774488	79	60	2551	151	ENST00000306917.4	0.059524	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	69399264	69399264	__UNKNOWN__	IGR	SNP	C	C	T	rs4776430	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:69399264C>T			NA	NA				RP11-809H16.5 (6989 upstream) : GLCE (53708 downstream)						NA		NA									NA						tgcggtgagccgagatcgcac	0.502		NA											C|||	1958	0.390974	0.0673	0.5144	5008	,	,	NA	15115	0.5258	NA	0.5706	False	NA	,,,	NA	NA	NA	2504	0.4172	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.69399264C>T		NA		hg19		0.02	-0.087718	AGCxGAG	UNCOVERED																																																																																			NOVEL					0			16	4.813079	KEEP	19	0	0	16	482	CC	0	0	0			4	60	124	0	0	12.649232	2	60	61	43		0.666667	0.099721
PAQR5	54852	__UNKNOWN__	__UNKNOWN__	15	69639413	69639413	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:69639413G>A	ENST00000340965.3	+	2	553				PAQR5_ENST00000561153.1_Intron|PAQR5_ENST00000395407.2_Intron	NM_001104554.1	NP_001098024.1	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	NA		NA			multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)|steroid binding (GO:0005496)			endometrium(3)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|skin(1)	11						cacctgcctcggcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10232.1	15q22.31	2012-08-10			ENSG00000137819	ENSG00000137819	54852			29645	protein-coding gene	gene with protein product	membrane progestin receptor gamma	607781			NA	12574519	Standard	NM_017705	NM_001104554	NA	Approved	FLJ20190, MPRG	uc002arz.2	Q9NXK6	OTTHUMG00000133322	ENST00000340965.3:c.-116+9573G>A	chr15.hg19:g.69639413G>A		NA	Q8IXU2	hg19	CCDS10232.1	0.02	-0.122804	CTCxGCC	COVERED																																																																																			NOVEL	PAQR5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416671.1	4	2.406684	KEEP	0	0	0	8	235	GG	0.99257	0.194853	0		+	3	60	88	0	0	7.432144	8	60	268	34	ENST00000340965.3	0.272727	0.196312
PAQR5	54852	__UNKNOWN__	__UNKNOWN__	15	69698945	69698945	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:69698945T>C	ENST00000340965.3	+	0	4445				RP11-253M7.1_ENST00000558107.1_RNA|RP11-253M7.1_ENST00000558617.1_RNA|RP11-253M7.1_ENST00000560539.1_RNA|PAQR5_ENST00000395407.2_3'UTR	NM_001104554.1	NP_001098024.1	Q9NXK6	MPRG_HUMAN	progestin and adipoQ receptor family member V	NA		NA			multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)|steroid binding (GO:0005496)			endometrium(3)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|skin(1)	11						cagtggctcatgcctgtaatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS10232.1	15q22.31	2012-08-10			ENSG00000137819	ENSG00000137819	54852			29645	protein-coding gene	gene with protein product	membrane progestin receptor gamma	607781			NA	12574519	Standard	NM_017705	NM_001104554	NA	Approved	FLJ20190, MPRG	uc002arz.2	Q9NXK6	OTTHUMG00000133322	ENST00000340965.3:c.*2784T>C	chr15.hg19:g.69698945T>C		NA	Q8IXU2	hg19	CCDS10232.1	0.02	5.666505	TCAxGCC	COVERED																																																																																			NOVEL	PAQR5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000416671.1	38	6.634935	KEEP	2	7	201	93	2515	TT	1	1	0		+	9	60	300	0	0	19.362335	147	60	4264	377	ENST00000340965.3	0.057692	1
RP11-279F6.1	0	__UNKNOWN__	__UNKNOWN__	15	69839834	69839834	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:69839834T>C	ENST00000560882.1	+	0	278										NA		NA									NA						aggatggtcttgatctcctga	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000560882.1:	chr15.hg19:g.69839834T>C		NA		hg19		0.02	-0.09649	TCTxGAT	UNCOVERED																																																																																			NOVEL	RP11-279F6.1-006	KNOWN	mRNA_end_NF|basic	lincRNA	NA	lincRNA	OTTHUMT00000416818.1	11	2.707055	KEEP	4	0	0	9	251	TT	0	0	0		+	3	44	100	0	0	8.632381	8	60	252	31	ENST00000560882.1	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	70068580	70068580	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:70068580A>G			NA	NA				AC009677.1 (45419 upstream) : AC021818.1 (9173 downstream)						NA		NA									NA						ttacaggcataagccaccgca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.70068580A>G		NA		hg19		0.02	-0.236799	CATxAGC	COVERED																																																																																			NOVEL					0			4	2.405311	KEEP	0	0	0	8	211	AA	0.99257	0.607857	0			3	60	101	0	0	7.860982	17	60	491	55		0.15	0.612407
LRRC49	54839	__UNKNOWN__	__UNKNOWN__	15	71309210	71309210	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:71309210T>C	ENST00000560691.1	+	16	2151				LRRC49_ENST00000443425.2_Intron|LRRC49_ENST00000260382.5_Intron|LRRC49_ENST00000560158.2_Intron|LRRC49_ENST00000436542.2_Intron|LRRC49_ENST00000544974.2_Intron|LRRC49_ENST00000560369.1_Intron			Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	NA		NA				cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						tttgggaggctgaggcaggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821	54839			25965	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_017691	NM_001199017	NA	Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000560691.1:c.821+3958T>C	chr15.hg19:g.71309210T>C		NA	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	hg19		0.02	-0.201727	GGCxGAG	COVERED																																																																																			NOVEL	LRRC49-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417216.1	17	5.113086	KEEP	8	0	0	17	480	TT	0.995343	0.48826	0		+	3	60	96	0	0	7.292592	18	60	543	60	ENST00000560691.1	0.142857	0.490544
THSD4	79875	__UNKNOWN__	__UNKNOWN__	15	71703108	71703108	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:71703108T>C	ENST00000355327.3	+	7	1149				THSD4_ENST00000261862.6_Intron			Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	NA		NA			elastic fiber assembly (GO:0048251)	extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						tggtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023772	CCDS10238.2, CCDS66817.1	15q23	2009-11-09			ENSG00000187720	ENSG00000187720	79875			25835	protein-coding gene	gene with protein product		614476			NA	19734141	Standard	NM_024817	NM_001286429	NA	Approved	FVSY9334, PRO34005, FLJ13710, ADAMTSL6	uc002atb.1	Q6ZMP0	OTTHUMG00000133389	ENST00000355327.3:c.1016-918T>C	chr15.hg19:g.71703108T>C		NA	B2RTY3|B4DR13|Q6MZI3|Q6UXZ8|Q9H8E4	hg19	CCDS10238.2	0.02	-0.157875	TCAxGCC	COVERED																																																																																			NOVEL	THSD4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257253.2	4	2.405938	KEEP	1	0	0	8	218	TT	0.99257	0.320408	0		+	3	60	98	0	0	7.878939	13	60	385	42	ENST00000355327.3	0.1875	0.322807
MYO9A	4649	__UNKNOWN__	__UNKNOWN__	15	72284387	72284387	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:72284387T>C	ENST00000564571.1	-	11	1747				MYO9A_ENST00000563542.1_Intron|RP11-390D11.1_ENST00000568391.1_RNA|MYO9A_ENST00000566885.1_Intron|MYO9A_ENST00000356056.5_Intron|MYO9A_ENST00000444904.1_Intron|MYO9A_ENST00000424560.1_Intron			B2RTY4	MYO9A_HUMAN	myosin IXA	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						tgagccaccgtgcccggccAG	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933	4649		Myosins / Myosin superfamily : Class IX	7608	protein-coding gene	gene with protein product		604875			NA	10409426	Standard	NM_006901	NM_006901	NA	Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000564571.1:c.1588-809A>G	chr15.hg19:g.72284387T>C		NA	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	hg19		0.02	-0.140338	CCGxGCC	COVERED																																																																																			NOVEL	MYO9A-015	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420905.1	5	3.007303	KEEP	2	0	0	10	273	TT	0.99254	0.259018	0		-	3	60	97	0	0	7.972886	11	60	333	37	ENST00000564571.1	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	72451110	72451110	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:72451110G>A			NA	NA				RP11-2I17.4 (3310 upstream) : GRAMD2 (1037 downstream)						NA		NA									NA						tatttttagtggagacagggt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.72451110G>A		NA		hg19		0.02	-0.114022	AGTxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.708229	KEEP	0	0	0	9	281	GG	0.99254	0.161255	0			3	60	83	0	0	7.078091	7	60	237	34		0.3	0.162467
ARIH1	25820	__UNKNOWN__	__UNKNOWN__	15	72780660	72780660	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:72780660T>C	ENST00000379887.4	+	1	689					NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						tcaaacgatcttcccacctca	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233	25820			689	protein-coding gene	gene with protein product	ariadne, Drosophila, homolog of	605624	ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1, ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)		NA	10521492, 24058416	Standard	NM_005744	NM_005744	NA	Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.375+13305T>C	chr15.hg19:g.72780660T>C		NA	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	hg19	CCDS10244.1	0.02	-0.131546	ATCxTCC	COVERED																																																																																			NOVEL	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257350.1	10	3.307682	KEEP	1	0	0	11	299	TT	0.992708	0.227502	0		+	3	60	97	0	0	8.478856	7	60	208	34	ENST00000379887.4	0.3	0.229173
NEO1	4756	__UNKNOWN__	__UNKNOWN__	15	73374238	73374238	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:73374238T>C	ENST00000339362.5	+	2	577				NEO1_ENST00000261908.6_Intron|NEO1_ENST00000558964.1_Intron|NEO1_ENST00000560262.1_Intron			Q92859	NEO1_HUMAN	neogenin 1	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						gatggagtcttgctctgtcac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141	4756		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	7754	protein-coding gene	gene with protein product	immunoglobulin superfamily, DCC subclass, member 2	601907	neogenin (chicken) homolog 1		NA	9121761	Standard	NM_002499	NM_002499	NA	Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.130+29092T>C	chr15.hg19:g.73374238T>C		NA	B7ZKM9|B7ZKN0|O00340|Q17RX1	hg19	CCDS10247.1	0.02	-0.192955	TCTxGCT	COVERED																																																																																			NOVEL	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257472.2	5	3.307645	KEEP	0	0	0	11	305	TT	0.993072	0.454585	0		+	3	60	91	0	0	6.93391	16	60	481	43	ENST00000339362.5	0.157895	0.457757
CD276	80381	__UNKNOWN__	__UNKNOWN__	15	74003558	74003558	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:74003558G>C	ENST00000318443.5	+	9	1884				CD276_ENST00000564751.1_Intron|CD276_ENST00000561213.1_3'UTR|CD276_ENST00000537340.2_Intron|CD276_ENST00000318424.5_Intron	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	NA		NA			cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCACACATCTGTGTGTGAGAG	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													104	91	95			NA	NA	15		NA											NA				74003558		2198	4297	6495	SO:0001627	intron_variant			AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855	80381		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing	19137	protein-coding gene	gene with protein product		605715	CD276 antigen		NA	11224528, 12055244	Standard	NM_025240	XM_005254699	NA	Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.1582+47G>C	chr15.hg19:g.74003558G>C		NA	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	hg19	CCDS32288.1	0.02	1.909259	TCTxTGT	COVERED																																																																																			NOVEL	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268979.1	5	4.512374	KEEP	0	0	0	15	441	GG	0.99649	0.990932	0		+	14	60	483	0	0	40.487964	49	60	1671	126	ENST00000318443.5	0.222222	0.994422
CD276	80381	__UNKNOWN__	__UNKNOWN__	15	74003583	74003583	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:74003583T>G	ENST00000318443.5	+	9	1884				CD276_ENST00000564751.1_Intron|CD276_ENST00000561213.1_3'UTR|CD276_ENST00000537340.2_Intron|CD276_ENST00000318424.5_Intron	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	NA		NA			cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						AGAGGGTGGGTAGGCATCATC	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													100	95	97			NA	NA	15		NA											NA				74003583		687	1588	2275	SO:0001627	intron_variant			AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855	80381		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing	19137	protein-coding gene	gene with protein product		605715	CD276 antigen		NA	11224528, 12055244	Standard	NM_025240	XM_005254699	NA	Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.1582+72T>G	chr15.hg19:g.74003583T>G		NA	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	hg19	CCDS32288.1	0.02	1.970812	GGGxAGG	COVERED																																																																																			NOVEL	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268979.1	3	3.607723	KEEP	0	0	0	12	312	TT	0.993634	0.979875	0		+	10	60	332	0	0	26.827098	43	60	1235	111	ENST00000318443.5	0.188679	0.986153
PML	5371	__UNKNOWN__	__UNKNOWN__	15	74292452	74292452	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:74292452A>G	ENST00000268058.3	+	2	698				PML_ENST00000565898.1_Intron|PML_ENST00000569477.1_Intron|PML_ENST00000436891.3_Intron|PML_ENST00000435786.2_Intron|PML_ENST00000569965.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000354026.6_Intron|PML_ENST00000564428.1_Intron|PML_ENST00000563500.1_Intron|PML_ENST00000359928.4_Intron|PML_ENST00000268059.6_Intron|PML_ENST00000567543.1_Intron	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						gattacaggcatgagccacca	0.468		NA	T	RARA, PAX5	APL, ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		15	15q22	5371	promyelocytic leukemia		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464	5371		Tripartite motif containing / Tripartite motif containing, RING-type (C3HC4) zinc fingers	9113	protein-coding gene	gene with protein product		102578			NA		Standard	NM_002675	NM_033244	NA	Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.602+1635A>G	chr15.hg19:g.74292452A>G		NA	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	hg19	CCDS10255.1	0.02	-0.096477	GGCxTGA	UNCOVERED																																																																																			NOVEL	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269021.3	8	2.40504	KEEP	1	0	0	8	210	AA	0.99257	0.119541	0		+	3	60	101	0	0	8.878774	7	60	209	29	ENST00000268058.3	0.3	0.120436
SCAMP2	10066	__UNKNOWN__	__UNKNOWN__	15	75164025	75164025	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75164025T>A	ENST00000268099.9	-	1	167					NM_005697.3	NP_005688.2	O15127	SCAM2_HUMAN	secretory carrier membrane protein 2	NA		NA			post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)|trans-Golgi network membrane (GO:0032588)|transport vesicle (GO:0030133)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	9						cccaggaggctgaggttgcag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF005038	CCDS10271.1	15q23-q25	2013-02-21			ENSG00000140497	ENSG00000140497	10066		Secretory carrier membrane proteins	10564	protein-coding gene	gene with protein product		606912			NA	9378760	Standard	NM_005697	NM_005697	NA	Approved		uc002azb.1	O15127	OTTHUMG00000142817	ENST00000268099.9:c.57+1514A>T	chr15.hg19:g.75164025T>A		NA	B2RDF0|Q9BQE8	hg19	CCDS10271.1	0.02	-0.166643	GGCxGAG	COVERED																																																																																			NOVEL	SCAMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286403.3	6	2.405363	KEEP	2	0	0	8	214	GT	0.993072	0.384723	0		-	3	40	95	0	0	7.491924	14	60	410	43	ENST00000268099.9	0.176471	0.387407
COX5A	9377	__UNKNOWN__	__UNKNOWN__	15	75227618	75227618	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75227618G>A	ENST00000567270.1	-	1	166				COX5A_ENST00000564811.1_Intron|COX5A_ENST00000568783.1_Intron|COX5A_ENST00000322347.6_Intron|COX5A_ENST00000562233.1_Intron|COX5A_ENST00000568517.1_Intron			P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	NA		NA			cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						atgacagagcgagaccctgtc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	9377	1.9.3.1	Mitochondrial respiratory chain complex / Complex IV	2267	protein-coding gene	gene with protein product		603773			NA	10072584, 2853101	Standard	NM_004255	NM_004255	NA	Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000567270.1:c.100+2637C>T	chr15.hg19:g.75227618G>A		NA	P30045|Q8TB65	hg19		0.02	-0.254377	AGCxAGA	COVERED																																																																																			NOVEL	COX5A-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420148.1	9	3.309197	KEEP	0	0	0	11	319	GG	0.993072	0.663892	0		-	3	60	91	0	0	6.443366	24	60	766	54	ENST00000567270.1	0.111111	0.668523
COX5A	9377	__UNKNOWN__	__UNKNOWN__	15	75228513	75228513	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75228513C>T	ENST00000567270.1	-	1	166				COX5A_ENST00000564811.1_Intron|COX5A_ENST00000568783.1_Intron|COX5A_ENST00000322347.6_Intron|COX5A_ENST00000562233.1_Intron|COX5A_ENST00000568517.1_Intron			P20674	COX5A_HUMAN	cytochrome c oxidase subunit Va	NA		NA			cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|pancreas(1)	3						gtgcctgtaaccccagctact	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M22760	CCDS10273.1	15q25	2011-07-04			ENSG00000178741	ENSG00000178741	9377	1.9.3.1	Mitochondrial respiratory chain complex / Complex IV	2267	protein-coding gene	gene with protein product		603773			NA	10072584, 2853101	Standard	NM_004255	NM_004255	NA	Approved		uc002azi.4	P20674	OTTHUMG00000142825	ENST00000567270.1:c.100+1742G>A	chr15.hg19:g.75228513C>T		NA	P30045|Q8TB65	hg19		0.02	-0.175398	TAAxCCC	COVERED																																																																																			NOVEL	COX5A-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000420148.1	2	2.407176	KEEP	0	0	0	8	245	CC	0.99257	0.384528	0		-	4	60	99	0	0	7.56399	15	60	492	32	ENST00000567270.1	0.210526	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	75261830	75261830	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75261830G>T			NA	NA				RPP25 (12025 upstream) : Y_RNA (13784 downstream)						NA		NA									NA						aggctggtctggaactcctgg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.75261830G>T		NA		hg19		0.02	-0.166666	TCTxGAA	COVERED																																																																																			NOVEL					0			7	2.707817	KEEP	0	0	0	9	269	GG	0.99254	0.486885	0			3	60	89	0	0	6.892024	14	60	457	46		0.176471	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	75456080	75456080	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75456080C>T			NA	NA				SCARNA20 (42073 upstream) : C15orf39 (35152 downstream)						NA		NA									NA						aggctggtctcaaactcctgg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.75456080C>T		NA		hg19		0.02	-0.114029	TCTxAAA	UNCOVERED																																																																																			NOVEL					0			11	3.008868	KEEP	9	0	0	10	303	CC	0	0	0			3	43	81	0	0	6.600931	9	60	306	43		0.25	0.162467
CSPG4	1464	__UNKNOWN__	__UNKNOWN__	15	75982271	75982271	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs141212136		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75982271C>T	ENST00000308508.5	-	3	1227	c.1135G>A	c.(1135-1137)Ggc>Agc	p.G379S		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	379	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.	NA			activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGCCTGCAGCCGGCTGCCATG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													11	13	12			NA	NA	15		NA											NA				75982271		2041	4052	6093	SO:0001583	missense			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546	1464		Proteoglycans / Cell surface : Other	2466	protein-coding gene	gene with protein product	melanoma-associated chondroitin sulfate proteoglycan	601172	chondroitin sulfate proteoglycan 4 (melanoma-associated)		NA	8790396, 16407841	Standard	NM_001897	NM_001897	NA	Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1135G>A	chr15.hg19:g.75982271C>T	ENSP00000312506:p.Gly379Ser	NA	D3DW77|Q92675	hg19	CCDS10284.1	0.02	1.403561	AGCxGGC	COVERED	60	0.027472527472527472	55	0.11178861788617886	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	.	16.24	3.068368	0.55539	.	.	ENSG00000173546	ENST00000308508	T	0.71817	-0.6	5.26	5.26	0.73747	Concanavalin A-like lectin/glucanase (1);Laminin G domain (1);	0.000000	0.64402	D	0.000003	T	0.08758	0.0217	L	0.61218	1.895	0.48236	D	0.999619	D	0.89917	1.0	D	0.70016	0.967	T	0.50474	-0.8824	10	0.40728	T	0.16	.	17.856	0.88762	0.0:1.0:0.0:0.0	.	379	Q6UVK1	CSPG4_HUMAN	S	379	ENSP00000312506:G379S	ENSP00000312506:G379S	G	-	1	0	CSPG4	73769326	1.000000	0.71417	0.944000	0.38274	0.097000	0.18754	4.544000	0.60691	2.463000	0.83235	0.555000	0.69702	GGC	NOVEL	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286472.1	0	3.008868	KEEP	5	0	0	10	306	CC	0.992708	0.987827	0		-	7	48	211	0	0	14.753113	59	60	1838	124	ENST00000308508.5	0.106061	0.995084
CSPG4	1464	__UNKNOWN__	__UNKNOWN__	15	75982275	75982275	__UNKNOWN__	Silent	SNP	T	T	C	rs146234778		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:75982275T>C	ENST00000308508.5	-	3	1223	c.1131A>G	c.(1129-1131)gcA>gcG	p.A377A		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	377	Globular or compact configuration stabilized by disulfide bonds.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.|Neurite growth inhibition. {ECO:0000250}.	NA			activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						TGCAGCCGGCTGCCATGTTGC	0.622		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													10	12	12			NA	NA	15		NA											NA				75982275		2044	4033	6077	SO:0001819	synonymous_variant			X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546	1464		Proteoglycans / Cell surface : Other	2466	protein-coding gene	gene with protein product	melanoma-associated chondroitin sulfate proteoglycan	601172	chondroitin sulfate proteoglycan 4 (melanoma-associated)		NA	8790396, 16407841	Standard	NM_001897	NM_001897	NA	Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1131A>G	chr15.hg19:g.75982275T>C		NA	D3DW77|Q92675	hg19	CCDS10284.1	0.02	1.818732	GGCxGCC	COVERED																																																																																			NOVEL	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286472.1	0	3.008145	KEEP	5	0	0	10	284	TT	0.992708	0.986456	0		-	7	48	199	0	0	13.686943	57	60	1668	123	ENST00000308508.5	0.109375	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	76012223	76012223	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:76012223A>G			NA	NA				CSPG4 (7034 upstream) : ODF3L1 (4094 downstream)						NA		NA									NA						tgggattacaagcatgagcca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.76012223A>G		NA		hg19		0.02	-0.17543	ACAxGCA	COVERED																																																																																			NOVEL					0			2	3.609005	KEEP	0	0	0	12	328	AA	0.993634	0.38494	0			3	60	103	0	0	8.291593	14	60	428	50		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	76131980	76131980	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:76131980T>C			NA	NA				SNORD112 (22476 upstream) : UBE2Q2 (3641 downstream)						NA		NA									NA						gttgcccaggttggagtgcag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.76131980T>C		NA		hg19		0.02	-0.04386	AGGxTGG	UNCOVERED																																																																																			NOVEL					0			3	2.405787	KEEP	0	0	0	8	216	TT	0.99257	0.023895	0			2	60	73	0	0	6.792993	3	60	92	20		0.4	0.024074
NRG4	145957	__UNKNOWN__	__UNKNOWN__	15	76255861	76255861	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:76255861T>C	ENST00000394907.3	-	4	286				NRG4_ENST00000535975.1_Intron	NM_138573.3	NP_612640.1	Q8WWG1	NRG4_HUMAN	neuregulin 4	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	5						tggctcacgcttgtaatccca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017568	CCDS10288.1	15q23	2005-10-30			ENSG00000169752	ENSG00000169752	145957			29862	protein-coding gene	gene with protein product		610894			NA	12477932	Standard	NM_138573	NM_138573	NA	Approved	HRG4	uc002bbo.3	Q8WWG1	OTTHUMG00000142917	ENST00000394907.3:c.105-1546A>G	chr15.hg19:g.76255861T>C		NA	A6NIE8	hg19	CCDS10288.1	0.02	-0.184195	CGCxTGT	COVERED																																																																																			NOVEL	NRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286632.1	9	3.307979	KEEP	3	0	0	11	296	TT	0.99254	0.420319	0		-	3	44	100	0	0	7.760796	17	60	517	42	ENST00000394907.3	0.15	0.423478
ETFA	2108	__UNKNOWN__	__UNKNOWN__	15	76577246	76577246	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:76577246A>G	ENST00000557943.1	-	7	745				ETFA_ENST00000433983.2_Intron|ETFA_ENST00000560816.1_Intron|ETFA_ENST00000559602.1_Intron|ETFA_ENST00000560726.1_Intron	NM_000126.3	NP_000117.1	P13804	ETFA_HUMAN	electron-transfer-flavoprotein, alpha polypeptide	NA		NA			cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9						actccagcctaggcaacaaga	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04058	CCDS32299.1, CCDS45311.1	15q23-q25	2012-04-04	2008-08-01		ENSG00000140374	ENSG00000140374	2108			3481	protein-coding gene	gene with protein product	glutaric aciduria II	608053			NA		Standard	NM_000126	NM_000126	NA	Approved	GA2, EMA, MADD	uc002bbt.2	P13804	OTTHUMG00000172586	ENST00000557943.1:c.664+731T>C	chr15.hg19:g.76577246A>G		NA	B4DT43|Q53XN3	hg19	CCDS32299.1	0.02	1.599261	CCTxGGC	COVERED																																																																																			NOVEL	ETFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419302.2	25	2.66911	KEEP	1	5	157	64	1777	AA	1	0.999835	0		-	5	60	161	0	0	10.290218	78	60	2301	249	ENST00000557943.1	0.060241	0.999835
SCAPER	49855	__UNKNOWN__	__UNKNOWN__	15	76711801	76711801	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:76711801T>C	ENST00000563290.1	-	26	3407				SCAPER_ENST00000324767.7_Intron|SCAPER_ENST00000538941.2_Intron			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	NA		NA				endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						gtggctcatgtctgtaatccc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386	49855		Zinc fingers, C2H2-type	13081	protein-coding gene	gene with protein product		611611	zinc finger protein 291	ZNF291	NA	17698606	Standard	NM_020843	NM_020843	NA	Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.3311+14617A>G	chr15.hg19:g.76711801T>C		NA	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	hg19	CCDS53962.1	0.02	-0.17543	ATGxCTG	COVERED																																																																																			NOVEL	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419698.1	9	3.307759	KEEP	0	0	0	11	298	TT	0.993072	0.384723	0		-	3	60	99	0	0	7.978955	13	60	400	40	ENST00000563290.1	0.1875	0.387407
SCAPER	49855	__UNKNOWN__	__UNKNOWN__	15	76733502	76733502	__UNKNOWN__	Intron	SNP	T	T	C	rs284886	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:76733502T>C	ENST00000563290.1	-	26	3174				SCAPER_ENST00000324767.7_Intron|SCAPER_ENST00000538941.2_Intron			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	NA		NA				endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						gacctcgtgatccacccgcct	0.512		NA											T|||	1583	0.316094	0.4962	0.219	5008	,	,	NA	15563	0.128	NA	0.3807	False	NA	,,,	NA	NA	NA	2504	0.2689	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386	49855		Zinc fingers, C2H2-type	13081	protein-coding gene	gene with protein product		611611	zinc finger protein 291	ZNF291	NA	17698606	Standard	NM_020843	NM_020843	NA	Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.3079-6851A>G	chr15.hg19:g.76733502T>C		NA	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	hg19	CCDS53962.1	0.02	-0.086725	TGAxCCA	UNCOVERED																																																																																			NOVEL	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419698.1	5	2.406073	KEEP	9	0	0	8	220	TT	0	0	0		-	4	60	144	0	0	13.623969	5	60	143	43	ENST00000563290.1	0.444444	0.099721
SCAPER	49855	__UNKNOWN__	__UNKNOWN__	15	77039583	77039583	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:77039583A>G	ENST00000563290.1	-	15	1962				SCAPER_ENST00000324767.7_Intron|SCAPER_ENST00000538941.2_Intron			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	NA		NA				endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(16)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	39						ggtggctcacacctgtaatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040887, AF242528	CCDS53961.1, CCDS53962.1	15q24.3	2012-10-05	2009-03-11	2007-08-20	ENSG00000140386	ENSG00000140386	49855		Zinc fingers, C2H2-type	13081	protein-coding gene	gene with protein product		611611	zinc finger protein 291	ZNF291	NA	17698606	Standard	NM_020843	NM_020843	NA	Approved	Zfp291	uc002bby.3	Q9BY12	OTTHUMG00000172655	ENST00000563290.1:c.1866+6565T>C	chr15.hg19:g.77039583A>G		NA	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	hg19	CCDS53962.1	0.02	-0.122342	CACxCCT	COVERED																																																																																			NOVEL	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419698.1	3	2.705423	KEEP	0	0	0	9	243	AA	0.99254	0.194847	0		-	3	60	83	0	0	6.808025	9	60	251	35	ENST00000563290.1	0.25	0.196312
PEAK1	79834	__UNKNOWN__	__UNKNOWN__	15	77567797	77567797	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:77567797T>C	ENST00000560626.2	-	3	202				PEAK1_ENST00000567337.1_Intron|PEAK1_ENST00000558305.1_Intron			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	NA		NA			cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)				NA						tggtggctcatgcctataatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517	79834			29431	protein-coding gene	gene with protein product		614248			NA	16879967, 20534451	Standard		NM_024776	NA	Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.274-22929A>G	chr15.hg19:g.77567797T>C		NA	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	hg19	CCDS42062.1	0.02	-0.166642	TCAxGCC	UNCOVERED																																																																																			NOVEL	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419483.3	4	2.40565	KEEP	4	0	0	8	215	TT	0	0	0		-	3	60	92	0	0	7.110856	15	60	449	43	ENST00000560626.2	0.166667	0.353947
TBC1D2B	23102	__UNKNOWN__	__UNKNOWN__	15	78368890	78368890	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:78368890T>C	ENST00000300584.3	-	1	360				TBC1D2B_ENST00000409931.3_Intron	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	NA		NA					Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						agttcgagactagcctgggca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202	23102			29183	protein-coding gene	gene with protein product		NA			NA	10470851	Standard	NM_015079	NM_015079	NA	Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.360+744A>G	chr15.hg19:g.78368890T>C		NA	A7MD42|Q8N1F9|Q9NXM0	hg19	CCDS45314.1	0.02	-0.21048	GACxAGC	COVERED																																																																																			NOVEL	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328369.3	8	3.606097	KEEP	1	0	0	12	304	TT	0.993634	0.518837	0		-	4	60	136	0	0	10.813632	20	60	578	52	ENST00000300584.3	0.166667	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	78539766	78539766	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:78539766T>C			NA	NA				ACSBG1 (1736 upstream) : RP11-762H8.3 (3077 downstream)						NA		NA									NA						gaccctgtctttacaaaaaat	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.78539766T>C		NA		hg19		0.02	-0.20165	TCTxTAC	COVERED																																																																																			NOVEL					0			11	3.308054	KEEP	0	0	0	11	298	TT	0.993072	0.487146	0			3	60	101	0	0	7.861433	17	60	496	47		0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	78604612	78604612	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:78604612A>T			NA	NA				WDR61 (12476 upstream) : CRABP1 (28053 downstream)						NA		NA									NA						tgtctcaaacacctgacctca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.78604612A>T		NA		hg19		0.02	-0.184173	AACxCCT	COVERED																																																																																			NOVEL					0			10	2.405103	KEEP	0	0	0	8	209	AA	0.99257	0.420331	0			3	60	86	0	0	6.361981	17	60	505	41		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	78693948	78693948	__UNKNOWN__	IGR	SNP	C	C	T	rs558825136		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:78693948C>T			NA	NA				CRABP1 (53376 upstream) : IREB2 (36582 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.78693948C>T		NA		hg19		0.02	-0.149116	AGGxGTG	COVERED																																																																																			NOVEL					0			10	4.512506	KEEP	7	0	0	15	444	CC	0.994391	0.290363	0			3	60	85	1	0	6.579205	13	60	428	52		0.1875	0.292001
MORF4L1	10933	__UNKNOWN__	__UNKNOWN__	15	79157405	79157405	__UNKNOWN__	Intron	SNP	G	G	A	rs4491476	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:79157405G>A	ENST00000379535.4	+	3	679							Q9UBU8	MO4L1_HUMAN	mortality factor 4 like 1	NA		NA			cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|double-strand break repair via homologous recombination (GO:0000724)|histone deacetylation (GO:0016575)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|Sin3 complex (GO:0016580)	chromatin binding (GO:0003682)|protein N-terminus binding (GO:0047485)			breast(1)|large_intestine(3)|lung(4)|prostate(1)|urinary_tract(1)	10						tctccatgttggtcaggctgg	0.532		NA											G|||	1021	0.203874	0.1067	0.2507	5008	,	,	NA	14079	0.0248	NA	0.4155	False	NA	,,,	NA	NA	NA	2504	0.2689	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF100615	CCDS10307.1, CCDS32304.1, CCDS58393.1	15q25.1	2009-07-13			ENSG00000185787	ENSG00000185787	10933			16989	protein-coding gene	gene with protein product	MORF-related gene on chromosome 15, Esa1p-associated factor 3 homolog (S. cerevisiae)	607303			NA	8619474, 9110174	Standard	NM_006791	NM_006791	NA	Approved	MRG15, MORFRG15, HsT17725, Eaf3, MEAF3	uc002bel.4	Q9UBU8	OTTHUMG00000143865	ENST00000379535.4:c.116-13150G>A	chr15.hg19:g.79157405G>A		NA	B4DKN6|B7Z6R1|D3DW88|O95899|Q5QTS1|Q6NVX8|Q86YT7|Q9HBP6|Q9NSW5	hg19		0.02	-0.096495	GTTxGTC	UNCOVERED																																																																																			NOVEL	MORF4L1-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000417833.1	4	2.708049	KEEP	4	0	0	9	276	GG	0	0	0		+	3	48	91	0	0	8.043221	6	40	204	30	ENST00000379535.4	0.333333	0.120436
RP11-752G15.3	0	__UNKNOWN__	__UNKNOWN__	15	83319622	83319622	__UNKNOWN__	RNA	SNP	G	G	A	rs7495972	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:83319622G>A	ENST00000560650.1	+	0	1328					NR_046096.1					NA		NA									NA						ggccaggcgcggtggctcatg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000560650.1:	chr15.hg19:g.83319622G>A		NA		hg19		0.02	-0.149122	CGCxGTG	COVERED																																																																																			NOVEL	RP11-752G15.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000418253.1	3	2.707549	KEEP	0	0	0	9	267	GG	0.99254	0.289823	0		+	3	60	91	0	0	7.178909	13	60	422	38	ENST00000560650.1	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	83409825	83409825	__UNKNOWN__	IGR	SNP	G	G	A	rs190810769		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:83409825G>A			NA	NA				RP11-752G15.9 (2457 upstream) : RP11-752G15.8 (3149 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.83409825G>A		NA		hg19		0.02	1.429749	GGCxTGA	COVERED																																																																																			NOVEL					0			60	9.902044	KEEP	20	2	39	47	1366	GG	1	0.992926	0			7	60	217	0	0	16.453018	40	60	1321	195		0.148936	0.992926
HDGFRP3	0	__UNKNOWN__	__UNKNOWN__	15	83809514	83809514	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:83809514C>T	ENST00000299633.4	-	6	1210					NM_016073.3	NP_057157.1	Q9Y3E1	HDGR3_HUMAN		NA		NA			cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						ggattacaggcgtgagccacc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000299633.4:c.607-1487G>A	chr15.hg19:g.83809514C>T		NA		hg19	CCDS32314.1	0.02	-0.105265	AGGxGTG	UNCOVERED																																																																																			NOVEL	HDGFRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000419898.1	5	2.406841	KEEP	0	0	0	8	239	CC	0.99257	0.138793	0		-	3	60	86	0	0	7.100884	9	60	315	28	ENST00000299633.4	0.25	0.139832
RP11-382A20.4	0	__UNKNOWN__	__UNKNOWN__	15	84017227	84017227	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:84017227A>G	ENST00000565495.1	+	0	264										NA		NA									NA						tttgagcccaagagttcgagt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000565495.1:	chr15.hg19:g.84017227A>G		NA		hg19		0.02	-0.131577	CCAxGAG	COVERED																																																																																			NOVEL	RP11-382A20.4-003	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000419906.1	5	2.706738	KEEP	0	0	0	9	248	AA	0.99254	0.227464	0		+	3	60	103	0	0	8.801105	9	60	278	41	ENST00000565495.1	0.25	0.229173
ADAMTSL3	57188	__UNKNOWN__	__UNKNOWN__	15	84338209	84338209	__UNKNOWN__	Intron	SNP	T	T	C	rs71156089		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:84338209T>C	ENST00000286744.5	+	2	293				ADAMTSL3_ENST00000567476.1_Intron	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	NA		NA				proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGTGAGGtttttttttttttt	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218	57188		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	14633	protein-coding gene	gene with protein product		609199			NA	9628581, 10574462	Standard	NM_207517	NM_207517	NA	Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.69+13627T>C	chr15.hg19:g.84338209T>C		NA	A1A566|A1A567|Q9ULI7	hg19	CCDS10326.1	0.02	-0.07016	TTTxTTT	UNCOVERED																																																																																			NOVEL	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000304007.2	14	4.209355	KEEP	7	0	0	14	367	TT	0.99254	0.053733	0		+	2	60	70	0	0	7.125169	1	60	28	29	ENST00000286744.5	0.666667	0.054137
ADAMTSL3	57188	__UNKNOWN__	__UNKNOWN__	15	84571301	84571301	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:84571301T>C	ENST00000286744.5	+	15	1924				ADAMTSL3_ENST00000567476.1_Intron	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	NA		NA				proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			ggattacaggtgtgagccacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218	57188		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	14633	protein-coding gene	gene with protein product		609199			NA	9628581, 10574462	Standard	NM_207517	NM_207517	NA	Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.1700+2818T>C	chr15.hg19:g.84571301T>C		NA	A1A566|A1A567|Q9ULI7	hg19	CCDS10326.1	0.02	-0.14034	AGGxGTG	COVERED																																																																																			NOVEL	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000304007.2	4	2.980815	KEEP	0	0	0	10	253	TT	0.992708	0.259062	0		+	3	60	98	0	0	8.072845	11	60	333	40	ENST00000286744.5	0.214286	0.260965
UBE2Q2P1	388165	__UNKNOWN__	__UNKNOWN__	15	85106429	85106429	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:85106429C>T	ENST00000339094.1	-	0	1291					NR_003661.2				ubiquitin-conjugating enzyme E2Q family member 2 pseudogene 1	NA		NA									NA						Tggccgggtgcggtggctcac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							15q25.2	2013-11-05	2009-12-17	2009-12-17	ENSG00000189136	ENSG00000189136	388165			37439	pseudogene	pseudogene		NA	ubiquitin-conjugating enzyme E2Q family pseudogene 1	UBE2QP1	NA		Standard	NR_003661	NR_003661	NA	Approved	FLJ43276	uc002bkn.1		OTTHUMG00000148662	ENST00000339094.1:	chr15.hg19:g.85106429C>T		NA		hg19		0.02	-0.166668	GTGxGGT	COVERED																																																																																			NOVEL	UBE2Q2P1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000308970.2	7	3.309413	KEEP	0	0	0	11	329	CC	0.993634	0.38494	0		-	3	60	86	1	0	6.510633	15	60	509	46	ENST00000339094.1	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	85262531	85262531	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:85262531C>T			NA	NA				SEC11A (2584 upstream) : ZNF592 (29334 downstream)						NA		NA									NA						tttgggaggccgaggcagatg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.85262531C>T		NA		hg19		0.02	-0.184119	GGCxGAG	COVERED																																																																																			NOVEL					0			9	3.005136	KEEP	1	0	0	10	280	CC	0.992708	0.42039	0			3	60	95	0	0	7.334164	16	60	507	45		0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	85275587	85275587	__UNKNOWN__	IGR	SNP	G	G	C	rs1245331		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:85275587G>C			NA	NA				SEC11A (15640 upstream) : ZNF592 (16278 downstream)						NA		NA									NA						tctcggctcagtgcaacctct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.85275587G>C		NA		hg19		0.02	-0.122804	TCAxTGC	COVERED																																																																																			NOVEL					0			8	3.310246	KEEP	1	0	0	11	351	GG	0.993072	0.194952	0			3	60	98	0	0	8.072812	11	60	364	38		0.214286	0.196312
PDE8A	5151	__UNKNOWN__	__UNKNOWN__	15	85536481	85536481	__UNKNOWN__	Intron	SNP	T	T	C	rs12913418	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:85536481T>C	ENST00000310298.4	+	2	438				PDE8A_ENST00000339708.5_Intron|PDE8A_ENST00000557957.1_Intron|PDE8A_ENST00000394553.1_Intron			O60658	PDE8A_HUMAN	phosphodiesterase 8A	NA		NA			cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	aagaccatcctggctaacacg	0.557		NA											T|||	294	0.0587061	0.0068	0.062	5008	,	,	NA	13856	0.001	NA	0.1541	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	5151	3.1.4.17	Phosphodiesterases	8793	protein-coding gene	gene with protein product		602972			NA	9618252	Standard	NM_002605	NM_001243137	NA	Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.186+10902T>C	chr15.hg19:g.85536481T>C		NA	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	hg19	CCDS10336.1	0.02	-0.122791	TCCxGGC	COVERED																																																																																			NOVEL	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309018.1	6	3.608644	KEEP	7	0	0	12	324	TT	0.99257	0.194853	0		+	8	60	256	0	0	26.099945	4	60	112	43	ENST00000310298.4	0.666667	0.196312
PDE8A	5151	__UNKNOWN__	__UNKNOWN__	15	85620150	85620150	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:85620150A>G	ENST00000310298.4	+	6	798				PDE8A_ENST00000339708.5_Intron|PDE8A_ENST00000557957.1_Intron|PDE8A_ENST00000394553.1_Intron|PDE8A_ENST00000557819.2_Intron			O60658	PDE8A_HUMAN	phosphodiesterase 8A	NA		NA			cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	ggtggctcatacctgtaatcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	5151	3.1.4.17	Phosphodiesterases	8793	protein-coding gene	gene with protein product		602972			NA	9618252	Standard	NM_002605	NM_001243137	NA	Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.546+132A>G	chr15.hg19:g.85620150A>G		NA	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	hg19	CCDS10336.1	0.02	-0.210376	CATxCCT	COVERED																																																																																			NOVEL	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309018.1	3	2.704618	KEEP	0	0	0	9	233	AA	0.99254	0.548763	0		+	3	60	104	0	0	8.09303	18	60	477	47	ENST00000310298.4	0.142857	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	85885931	85885931	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:85885931G>T			NA	NA				RP11-561C5.5 (12470 upstream) : AKAP13 (37939 downstream)						NA		NA									NA						gtcaggagttggagaccagcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.85885931G>T		NA		hg19		0.02	-0.096492	GTTxGAG	UNCOVERED																																																																																			NOVEL					0			2	2.380577	KEEP	0	0	0	8	215	GG	0.99257	0.138793	0			3	60	93	0	0	7.932264	8	60	270	30		0.272727	0.139832
NTRK3	4916	__UNKNOWN__	__UNKNOWN__	15	88626707	88626707	__UNKNOWN__	Intron	SNP	T	T	C	rs60903671	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:88626707T>C	ENST00000542733.2	-	11	1262				NTRK3_ENST00000317501.3_Intron|NTRK3_ENST00000558676.1_Intron|NTRK3_ENST00000394480.2_Intron|NTRK3_ENST00000558306.1_Intron|NTRK3_ENST00000355254.2_Intron|NTRK3_ENST00000360948.2_Intron|NTRK3_ENST00000557856.1_Intron|NTRK3_ENST00000357724.2_Intron|NTRK3_ENST00000540489.2_Intron			Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	NA		NA			activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			cctgcctcagtctcccaaagt	0.483		NA	T	ETV6	congenital fibrosarcoma, Secretory breast 					TSP Lung(13;0.10)			T|||	98	0.0195687	0.0711	0.0043	5008	,	,	NA	18741	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA			Dom	yes		15	15q25	4916	neurotrophic tyrosine kinase, receptor, type 3		E, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	4916	2.7.10.1	Immunoglobulin superfamily / I-set domain containing	8033	protein-coding gene	gene with protein product		191316			NA	7806211	Standard		NM_001012338	NA	Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000542733.2:c.1102+42794A>G	chr15.hg19:g.88626707T>C		NA	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	hg19		0.02	-0.149101	CAGxCTC	COVERED																																																																																			NOVEL	NTRK3-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000415277.1	5	2.406357	KEEP	0	0	0	8	225	TT	0.99257	0.289832	0		-	3	60	102	0	0	8.372327	12	60	354	38	ENST00000542733.2	0.2	0.292001
NTRK3	4916	__UNKNOWN__	__UNKNOWN__	15	88755338	88755338	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:88755338A>G	ENST00000394480.2	-	4	570				NTRK3_ENST00000317501.3_Intron|NTRK3_ENST00000558676.1_Intron|NTRK3_ENST00000355254.2_Intron|NTRK3_ENST00000360948.2_Intron|NTRK3_ENST00000557856.1_Intron|NTRK3_ENST00000357724.2_Intron|NTRK3_ENST00000540489.2_Intron	NM_001243101.1|NM_002530.3	NP_001230030.1|NP_002521.2	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	NA		NA			activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			ggtggctcacacctgtaatcc	0.473		NA	T	ETV6	congenital fibrosarcoma, Secretory breast 					TSP Lung(13;0.10)											NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		15	15q25	4916	neurotrophic tyrosine kinase, receptor, type 3		E, M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	4916	2.7.10.1	Immunoglobulin superfamily / I-set domain containing	8033	protein-coding gene	gene with protein product		191316			NA	7806211	Standard		NM_001012338	NA	Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000394480.2:c.249-27808T>C	chr15.hg19:g.88755338A>G		NA	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	hg19	CCDS10340.1	0.02	-0.184151	CACxCCT	UNCOVERED																																																																																			NOVEL	NTRK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309066.2	9	2.405675	KEEP	4	0	0	8	216	AA	0	0	0		-	3	60	99	0	0	7.979326	13	60	367	45	ENST00000394480.2	0.1875	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	89304906	89304906	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:89304906T>C			NA	NA				ISG20 (105192 upstream) : RP11-343B18.2 (35737 downstream)						NA		NA									NA						aggatggtcttgatctcctga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.89304906T>C		NA		hg19		0.02	-0.096471	TCTxGAT	UNCOVERED																																																																																			NOVEL					0			11	2.401422	KEEP	8	0	0	8	205	TT	0	0	0			3	60	87	0	0	7.478543	7	60	208	34		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	89310375	89310375	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:89310375T>C			NA	NA				ISG20 (110661 upstream) : RP11-343B18.2 (30268 downstream)						NA		NA									NA						aggtgtgagctactgcacccg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.89310375T>C		NA		hg19		0.02	-0.096486	AGCxACT	UNCOVERED																																																																																			NOVEL					0			7	2.402674	KEEP	2	0	0	8	209	TT	0.99257	0.119541	0			3	60	99	0	1	8.532441	8	60	245	29		0.272727	0.120436
HAPLN3	145864	__UNKNOWN__	__UNKNOWN__	15	89420578	89420578	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:89420578G>T	ENST00000359595.3	-	0	1920					NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	NA		NA			cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	ACACCTGAGGGCCCCTCCCCA	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511	145864		Immunoglobulin superfamily / V-set domain containing	21446	protein-coding gene	gene with protein product		NA	extracellular link domain containing, 1	EXLD1	NA	12663660	Standard	NM_178232	NM_178232	NA	Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.*623C>A	chr15.hg19:g.89420578G>T		NA	A8K7P0	hg19	CCDS10346.1	0.02	1.654514	AGGxCCC	COVERED																																																																																			NOVEL	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309070.1	3	4.212539	KEEP	0	0	0	14	430	GG	0.995343	0.984934	0		-	15	60	434	0	0	35.781405	46	60	1555	106	ENST00000359595.3	0.245902	0.989542
ABHD2	11057	__UNKNOWN__	__UNKNOWN__	15	89660476	89660476	__UNKNOWN__	Intron	SNP	T	T	C	rs293393	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:89660476T>C	ENST00000352732.5	+	3	714				ABHD2_ENST00000355100.3_Intron|ABHD2_ENST00000565973.1_Intron	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	NA		NA			negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					aggctggtcttgaactcctga	0.527		NA											T|||	1609	0.321286	0.3684	0.2709	5008	,	,	NA	18275	0.1518	NA	0.3926	False	NA	,,,	NA	NA	NA	2504	0.3947	NA	NA	NA	Colon(11;252 417 24570 33239 41878)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526	11057		Abhydrolase domain containing	18717	protein-coding gene	gene with protein product		612196			NA		Standard		NM_152924	NA	Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.194+724T>C	chr15.hg19:g.89660476T>C		NA	Q53G48|Q53GU0|Q5FVD9|Q8TC79	hg19	CCDS10348.1	0.02	-0.052627	TCTxGAA	UNCOVERED																																																																																			NOVEL	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000309074.2	8	3.308477	KEEP	14	0	0	11	306	TT	0	0	0		+	3	43	93	0	0	9.269579	2	28	60	37	ENST00000352732.5	0.6	0.036766
AP3S2	10239	__UNKNOWN__	__UNKNOWN__	15	90375744	90375744	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90375744G>A	ENST00000336418.4	-	0	3977					NM_005829.4	NP_005820.1	P59780	AP3S2_HUMAN	adaptor-related protein complex 3, sigma 2 subunit	NA		NA			anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)	protein transporter activity (GO:0008565)			NS(1)|kidney(1)|lung(2)|ovary(1)|urinary_tract(1)	6	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			tttttgagacggagtcttgct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X99459	CCDS10357.1	15q26.1	2010-08-13			ENSG00000157823	ENSG00000157823	10239			571	protein-coding gene	gene with protein product		602416			NA	9118953	Standard		NM_005829	NA	Approved	sigma3b		P59780	OTTHUMG00000149811	ENST00000336418.4:c.*3003C>T	chr15.hg19:g.90375744G>A		NA	B2R677|B4DGQ3|O09077|O09149|Q53H83|Q99589	hg19	CCDS10357.1	0.02	1.543752	GACxGAG	COVERED																																																																																			NOVEL	AP3S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313422.1	5	5.347852	KEEP	4	1	26	27	801	GG	0.999988	0.967413	0		-	4	60	120	0	0	8.133479	39	60	1263	98	ENST00000336418.4	0.093023	0.967425
CTD-2315E11.1	0	__UNKNOWN__	__UNKNOWN__	15	90660147	90660147	__UNKNOWN__	lincRNA	SNP	C	C	T	rs566841597		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90660147C>T	ENST00000561101.1	+	0	188										NA		NA									NA						cgcaagccaccgtgcctggcc	0.478		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	19544	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000561101.1:	chr15.hg19:g.90660147C>T		NA		hg19		0.02	-0.175434	CACxGTG	COVERED																																																																																			NOVEL	CTD-2315E11.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000417311.1	7	3.008773	KEEP	0	0	0	10	302	CC	0.992708	0.384582	0		+	3	60	88	0	0	6.633932	16	60	518	44	ENST00000561101.1	0.157895	0.387407
CTD-2315E11.1	0	__UNKNOWN__	__UNKNOWN__	15	90661081	90661081	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90661081T>C	ENST00000561101.1	+	0	188										NA		NA									NA						tgctatgttgtccaggctggt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000561101.1:	chr15.hg19:g.90661081T>C		NA		hg19		0.02	-0.219264	TTGxCCA	COVERED																																																																																			NOVEL	CTD-2315E11.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000417311.1	8	4.210427	KEEP	0	0	0	14	382	TT	0.99649	0.550947	0		+	3	60	102	0	0	7.649003	22	60	658	55	ENST00000561101.1	0.12	0.552887
RP11-697E2.6	0	__UNKNOWN__	__UNKNOWN__	15	90794636	90794636	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90794636A>G	ENST00000561573.1	+	3	521				TTLL13_ENST00000438251.1_Intron|TTLL13_ENST00000339615.5_Intron						NA		NA									NA						gattacaggcatgagccaccg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000561573.1:c.258-150A>G	chr15.hg19:g.90794636A>G		NA		hg19		0.02	5.525107	GGCxTGA	COVERED																																																																																			NOVEL	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000435855.1	38	3.630138	KEEP	2	10	277	110	3050	AA	1	1	0		+	6	60	207	0	0	12.870392	131	60	3953	390	ENST00000561573.1	0.043796	1
RP11-697E2.6	0	__UNKNOWN__	__UNKNOWN__	15	90803998	90803998	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90803998G>A	ENST00000561573.1	+	9	1183				TTLL13_ENST00000438251.1_Intron						NA		NA									NA						caggagaatcgcttgaaccca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000561573.1:c.652-1240G>A	chr15.hg19:g.90803998G>A		NA		hg19		0.02	-0.157864	ATCxCTT	COVERED																																																																																			NOVEL	RP11-697E2.6-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000435855.1	13	4.812761	KEEP	10	0	0	16	455	GG	0.994391	0.320996	0		+	3	33	86	0	0	6.592455	14	60	422	52	ENST00000561573.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	90846694	90846694	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90846694G>A			NA	NA				AC091167.1 (8339 upstream) : GABARAPL3 (44124 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.90846694G>A		NA		hg19		0.02	-0.184179	GGCxTGA	COVERED																																																																																			NOVEL					0			11	4.813918	KEEP	8	0	0	16	477	GG	0.992708	0.42039	0			3	60	94	0	0	7.310479	15	60	480	52		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	90858082	90858082	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90858082T>G			NA	NA				AC091167.1 (19727 upstream) : GABARAPL3 (32736 downstream)						NA		NA									NA						aggccgaggttggtggatcac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.90858082T>G		NA		hg19		0.02	-0.227987	GGTxGGT	UNCOVERED																																																																																			NOVEL					0			10	2.405859	KEEP	4	0	0	8	223	TT	0	0	0			5	60	149	0	0	11.855001	20	60	576	48		0.2	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	90858085	90858085	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90858085T>C			NA	NA				AC091167.1 (19730 upstream) : GABARAPL3 (32733 downstream)						NA		NA									NA						ccgaggttggtggatcacaag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.90858085T>C		NA		hg19		0.02	-0.219179	TGGxGGA	UNCOVERED																																																																																			NOVEL					0			9	2.40612	KEEP	4	0	0	8	225	TT	0	0	0			3	60	94	0	0	6.906879	21	60	598	49		0.125	0.552887
ZNF774	342132	__UNKNOWN__	__UNKNOWN__	15	90904288	90904288	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:90904288G>C	ENST00000379090.5	+	4	302				ZNF774_ENST00000354377.3_Missense_Mutation_p.G409R			Q6NX45	ZN774_HUMAN	zinc finger protein 774	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TGGAGAGTGTGGGAAGAGCTT	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													75	69	71			NA	NA	15		NA											NA				90904288		2199	4298	6497	SO:0001627	intron_variant			BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391	342132		Zinc fingers, C2H2-type	33108	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004309	NM_001004309	NA	Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000379090.5:c.212-1489G>C	chr15.hg19:g.90904288G>C		NA	A8K020	hg19		0.02	1.742603	TGTxGGA	COVERED	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221563	0.79464	.	.	ENSG00000196391	ENST00000354377	T	0.22743	1.94	5.53	5.53	0.82687	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36303	N	0.002672	T	0.52549	0.1741	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.58634	-0.7602	10	0.87932	D	0	.	16.9262	0.86177	0.0:0.0:1.0:0.0	.	409	Q6NX45	ZN774_HUMAN	R	409	ENSP00000346348:G409R	ENSP00000346348:G409R	G	+	1	0	ZNF774	88705292	1.000000	0.71417	0.923000	0.36655	0.941000	0.58515	7.582000	0.82546	2.592000	0.87571	0.655000	0.94253	GGG	NOVEL	ZNF774-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000418051.1	4	7.51985	KEEP	0	0	0	25	729	GG	0.999931	0.999553	0		+	25	60	814	0	0	71.117694	59	60	1979	159	ENST00000379090.5	0.297619	0.999622
IQGAP1	8826	__UNKNOWN__	__UNKNOWN__	15	91009229	91009229	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:91009229G>A	ENST00000268182.5	+	16	1900				IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	NA		NA			cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTAATGATATGTAGGAAATCC	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													124	121	122			NA	NA	15		NA											NA				91009229		2198	4298	6496	SO:0001627	intron_variant			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575	8826			6110	protein-coding gene	gene with protein product	RasGAP-like with IQ motifs	603379			NA	8051149, 8670801	Standard	NM_003870	XM_005254984	NA	Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.1777-4G>A	chr15.hg19:g.91009229G>A		NA	A7MBM3	hg19	CCDS10362.1	0.02	1.54446	TATxTAG	COVERED																																																																																			NOVEL	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313493.1	0	3.910393	KEEP	0	0	0	13	379	GG	0.994391	0.958368	0		+	11	60	332	0	0	26.911565	40	60	1334	91	ENST00000268182.5	0.215686	0.963774
RP11-387D10.2	0	__UNKNOWN__	__UNKNOWN__	15	91249238	91249238	__UNKNOWN__	RNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:91249238G>T	ENST00000559531.1	-	0	294										NA		NA									NA						cttgctctgtggcccaggcta	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559531.1:	chr15.hg19:g.91249238G>T		NA		hg19		0.02	-0.087688	TGTxGCC	UNCOVERED																																																																																			NOVEL	RP11-387D10.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000417937.1	10	3.009112	KEEP	0	0	0	10	311	CG	0.993072	0.09903	0		-	4	60	106	0	0	10.096451	4	60	134	28	ENST00000559531.1	0.5	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	91382414	91382414	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:91382414A>G			NA	NA				BLM (23722 upstream) : CTD-3094K11.1 (539 downstream)						NA		NA									NA						gggattacagacatgagccac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.91382414A>G		NA		hg19		0.02	-0.14911	CAGxCAT	COVERED																																																																																			NOVEL					0			6	2.705587	KEEP	0	0	0	9	232	AA	0.99254	0.289823	0			3	60	101	0	0	8.272225	12	60	364	36		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	91442322	91442322	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:91442322C>T			NA	NA				FES (3316 upstream) : MAN2A2 (3899 downstream)						NA		NA									NA						ggtgaaaccccgtctctacta	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.91442322C>T		NA		hg19		0.02	-0.166656	CCCxGTC	UNCOVERED																																																																																			NOVEL					0			5	2.40648	KEEP	1	0	0	8	232	CC	0	0	0			3	60	89	1	0	6.892095	14	60	444	36		0.176471	0.353947
SV2B	9899	__UNKNOWN__	__UNKNOWN__	15	91803955	91803955	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:91803955A>G	ENST00000394232.1	+	6	1478				SV2B_ENST00000545111.2_Intron|SV2B_ENST00000330276.4_Intron	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	NA		NA			neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			aagaaaaagaagtttaattgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518	9899			16874	protein-coding gene	gene with protein product		185861			NA	9872452, 7681585	Standard	NM_014848	NM_014848	NA	Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1008+316A>G	chr15.hg19:g.91803955A>G		NA	B4DH30|C6G489|O94840|Q6IAR8	hg19	CCDS10370.1	0.02	-0.148984	AGAxGTT	COVERED																																																																																			NOVEL	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313494.3	2	2.405728	KEEP	0	0	0	8	215	AA	0.99257	0.289832	0		+	3	60	92	0	0	7.193462	14	60	408	32	ENST00000394232.1	0.176471	0.292001
SLCO3A1	28232	__UNKNOWN__	__UNKNOWN__	15	92475908	92475908	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:92475908G>A	ENST00000424469.2	+	2	699				SLCO3A1_ENST00000318445.6_Intron	NM_001145044.1	NP_001138516.1	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	NA		NA			sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	25	Lung NSC(78;0.0158)|all_lung(78;0.0255)		BRCA - Breast invasive adenocarcinoma(143;0.0841)		Alprostadil(DB00770)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Iloprost(DB01088)|Methotrexate(DB00563)	cctgacctcaggtgatctgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB031050	CCDS10371.1, CCDS45354.1	15q26	2013-05-22	2003-11-25	2003-11-26	ENSG00000176463	ENSG00000176463	28232		Solute carriers	10952	protein-coding gene	gene with protein product		612435	solute carrier family 21 (organic anion transporter), member 11	SLC21A11	NA		Standard	NM_013272	NM_001145044	NA	Approved	OATP-D, OATP3A1	uc002bqx.2	Q9UIG8	OTTHUMG00000149846	ENST00000424469.2:c.646+16220G>A	chr15.hg19:g.92475908G>A		NA	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	hg19	CCDS45354.1	0.02	-0.192982	TCAxGTG	COVERED																																																																																			NOVEL	SLCO3A1-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000414816.1	6	2.708498	KEEP	5	0	0	9	292	GG	0.99257	0.454356	0		+	3	60	87	0	0	6.327912	19	60	649	50	ENST00000424469.2	0.136364	0.457757
FAM174B	400451	__UNKNOWN__	__UNKNOWN__	15	93346564	93346564	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:93346564T>C	ENST00000555971.1	-	1	216							Q3ZCQ3	F174B_HUMAN	family with sequence similarity 174, member B	NA		NA				integral component of membrane (GO:0016021)				endometrium(2)|lung(1)	3						cctcggcctctcaaagtgctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45355.1	15q26.1	2012-10-03			ENSG00000185442	ENSG00000185442	400451			34339	protein-coding gene	gene with protein product		NA			NA		Standard	NM_207446	NM_207446	NA	Approved	LOC400451, MGC102891	uc010boe.3	Q3ZCQ3	OTTHUMG00000171744	ENST00000555971.1:c.264+6311A>G	chr15.hg19:g.93346564T>C		NA	Q3ZCR9|Q8NBH7	hg19		0.02	-0.149118	CTCxCAA	COVERED																																																																																			NOVEL	FAM174B-016	KNOWN	mRNA_end_NF|basic	processed_transcript	NA	protein_coding	OTTHUMT00000471211.1	9	2.707447	KEEP	2	0	0	9	258	TT	0.99257	0.289832	0		-	3	60	104	0	0	8.572067	12	60	369	36	ENST00000555971.1	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	95722010	95722010	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:95722010T>G			NA	NA				RP11-255M2.2 (45922 upstream) : CTD-2536I1.1 (100502 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.95722010T>G		NA		hg19		0.02	-0.02627	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			11	3.306047	KEEP	7	0	0	11	276	TT	0.99254	0	0			2	60	55	0	0	6.452165	0	0	0	18		1	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	95722016	95722016	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:95722016T>G			NA	NA				RP11-255M2.2 (45928 upstream) : CTD-2536I1.1 (100496 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.95722016T>G		NA		hg19		0.02	-0.026235	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			12	3.907127	KEEP	5	0	0	13	329	TT	0.992708	0	0			2	60	58	0	0	6.752649	0	0	0	21		1	0
NR2F2-AS1	644192	__UNKNOWN__	__UNKNOWN__	15	96799659	96799659	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:96799659T>C	ENST00000560800.1	-	0	220									NR2F2 antisense RNA 1	NA		NA									NA						ggcgcggtggttcacgcctgt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK000872		15q26.2	2012-10-12	2012-08-15		ENSG00000247809	ENSG00000247809	644192		Long non-coding RNAs	44222	non-coding RNA	RNA, long non-coding		NA	NR2F2 antisense RNA 1 (non-protein coding)		NA		Standard	XR_109225	NR_102743	NA	Approved		uc002bto.2		OTTHUMG00000171855	ENST00000560800.1:	chr15.hg19:g.96799659T>C		NA		hg19		0.02	-0.140327	TGGxTCA	COVERED																																																																																			NOVEL	NR2F2-AS1-006	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000415484.1	5	3.907406	KEEP	0	0	0	13	333	TT	0.994391	0.259501	0		-	3	60	103	0	0	8.682161	10	60	294	43	ENST00000560800.1	0.230769	0.260965
RP11-522B15.5	0	__UNKNOWN__	__UNKNOWN__	15	96986650	96986650	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:96986650T>C	ENST00000559214.1	+	0	235										NA		NA									NA						tgagccactgtgcctggccct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559214.1:	chr15.hg19:g.96986650T>C		NA		hg19		0.02	-0.184181	CTGxGCC	COVERED																																																																																			NOVEL	RP11-522B15.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000415473.1	5	3.007941	KEEP	0	0	0	10	283	TT	0.992708	0.42039	0		+	3	60	87	0	0	6.779799	13	60	389	46	ENST00000559214.1	0.1875	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	99177242	99177242	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:99177242T>C			NA	NA				FAM169B (119631 upstream) : RP11-35O15.1 (12937 downstream)						NA		NA									NA						ttttttgagatggagtcttgc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.99177242T>C		NA		hg19		0.02	-0.05261	AGAxGGA	UNCOVERED																																																																																			NOVEL					0			5	2.404822	KEEP	2	0	0	8	217	TT	0	0	0			3	40	99	0	0	10.354147	1	40	32	17		0.75	0.036766
IGF1R	3480	__UNKNOWN__	__UNKNOWN__	15	99407294	99407294	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:99407294T>C	ENST00000558762.1	+	3	1178				IGF1R_ENST00000268035.6_Intron			P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	NA		NA			axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)	tgggaccagcttgggcaacat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443	3480		CD molecules, Fibronectin type III domain containing	5465	protein-coding gene	gene with protein product		147370			NA	1316909	Standard	NM_000875	XM_006720486	NA	Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000558762.1:c.641-27260T>C	chr15.hg19:g.99407294T>C		NA	B1B5Y2|Q14CV2|Q9UCC0	hg19		0.02	-0.235462	AGCxTGG	COVERED																																																																																			NOVEL	IGF1R-002	NOVEL	NAGNAG_splice_site|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000415271.1	12	3.607606	KEEP	0	0	0	12	322	TT	0.993634	0.608508	0		+	3	60	104	0	0	7.857644	22	60	638	52	ENST00000558762.1	0.12	0.612407
RP11-654A16.3	0	__UNKNOWN__	__UNKNOWN__	15	99510207	99510207	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:99510207A>G	ENST00000559468.1	-	0	266										NA		NA									NA						tgatccgcccacctcagcctc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559468.1:	chr15.hg19:g.99510207A>G		NA		hg19		0.02	-0.140333	CCCxCCT	COVERED																																																																																			NOVEL	RP11-654A16.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000415701.1	12	2.706351	KEEP	2	0	0	9	242	AA	0.99257	0.259026	0		-	3	60	93	0	0	7.573135	11	60	335	33	ENST00000559468.1	0.214286	0.260965
RP11-654A16.3	0	__UNKNOWN__	__UNKNOWN__	15	99590580	99590580	__UNKNOWN__	RNA	SNP	G	G	A	rs551785742		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:99590580G>A	ENST00000559468.1	-	0	266										NA		NA									NA						gattacaggcgtgagccactg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000559468.1:	chr15.hg19:g.99590580G>A		NA		hg19		0.02	-0.12281	GGCxTGA	COVERED																																																																																			NOVEL	RP11-654A16.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000415701.1	8	3.008476	KEEP	0	0	0	10	294	GG	0.992708	0.19488	0		-	3	60	91	0	0	7.372747	11	60	370	35	ENST00000559468.1	0.214286	0.196312
LRRC28	123355	__UNKNOWN__	__UNKNOWN__	15	99842697	99842697	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:99842697A>G	ENST00000331450.5	+	3	485				LRRC28_ENST00000447360.2_Intron|LRRC28_ENST00000559399.1_Intron|LRRC28_ENST00000301981.3_Intron|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000442993.2_Intron|LRRC28_ENST00000422500.2_Intron			Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	NA		NA								endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			cggttcaagcaattctcctgc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904	123355			28355	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_144598	XM_005254861	NA	Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000331450.5:c.209+25876A>G	chr15.hg19:g.99842697A>G		NA	A8KA22|Q6UY49|Q6ZSS6	hg19		0.02	-0.105206	AGCxATT	UNCOVERED																																																																																			NOVEL	LRRC28-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000415753.1	6	2.40293	KEEP	2	0	0	8	200	AA	0	0	0		+	3	60	90	0	0	7.501879	9	60	244	28	ENST00000331450.5	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	100882241	100882241	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:100882241C>T			NA	NA				ADAMTS17 (31 upstream) : SPATA41 (2441 downstream)						NA		NA									NA						CGTGGTAAACCCCAAGCCCCG	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.100882241C>T		NA		hg19		0.02	1.517413	AACxCCA	COVERED																																																																																			NOVEL					0			0	7.221869	KEEP	0	0	0	24	754	CC	0.999909	0.973877	0			13	60	387	0	0	32.080683	40	60	1370	117		0.245283	0.973965
RP11-168G16.2	0	__UNKNOWN__	__UNKNOWN__	15	100926690	100926690	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:100926690T>C	ENST00000560718.1	+	0	54										NA		NA									NA						atcctcctgcttcggcctccc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000560718.1:	chr15.hg19:g.100926690T>C		NA		hg19		0.02	-0.140332	TGCxTCG	COVERED																																																																																			NOVEL	RP11-168G16.2-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000417771.1	9	5.413297	KEEP	3	0	0	18	494	TT	0.99649	0.260049	0		+	3	60	93	0	0	7.573149	11	60	326	52	ENST00000560718.1	0.214286	0.260965
RP11-89K11.1	0	__UNKNOWN__	__UNKNOWN__	15	102279895	102279895	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:102279895A>G	ENST00000560292.2	-	2	364				RP11-89K11.1_ENST00000558592.1_Intron						NA		NA								lung(1)	1						agctacttagaaggctgaggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000560292.2:c.133-2323T>C	chr15.hg19:g.102279895A>G		NA		hg19		0.02	-0.271913	TAGxAGG	COVERED																																																																																			NOVEL	RP11-89K11.1-002	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000417118.2	12	4.810558	KEEP	0	0	0	16	441	AA	0.997832	0.71576	0		-	3	60	98	0	0	7.142557	24	60	743	68	ENST00000560292.2	0.111111	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	15	102286845	102286845	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr15:102286845C>G			NA	NA				RP11-89K11.1 (932 upstream) : DNM1P47 (4389 downstream)						NA		NA									NA						ccagcctgggcgacagagcga	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr15.hg19:g.102286845C>G		NA		hg19		0.02	-0.201737	GGGxGAC	COVERED																																																																																			NOVEL					0			3	3.008047	KEEP	2	0	0	10	285	CT	0.995343	0.519729	0			4	21	138	0	1	11.268708	17	60	518	50		0.190476	0.522161
POLR3K	51728	__UNKNOWN__	__UNKNOWN__	16	96462	96462	__UNKNOWN__	3'UTR	SNP	C	C	T	rs182283632	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:96462C>T	ENST00000293860.5	-	0	1336					NM_016310.3	NP_057394.2	Q9Y2Y1	RPC10_HUMAN	polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa	NA		NA			defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(1)|skin(1)	3		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)				cagtggctcacgcctgtaatc	0.458		NA											.|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	14598	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF051316	CCDS10395.1	16p13.3	2013-01-21	2002-08-29		ENSG00000161980	ENSG00000161980	51728		RNA polymerase subunits	14121	protein-coding gene	gene with protein product		606007	polymerase (RNA) III (DNA directed) polypeptide K (12.3 kDa)		NA	9869639, 10079944	Standard	NM_016310	NM_016310	NA	Approved	RPC11	uc002cfi.2	Q9Y2Y1	OTTHUMG00000060722	ENST00000293860.5:c.*968G>A	chr16.hg19:g.96462C>T		NA	Q1W6H4|Q96S35	hg19	CCDS10395.1	0.02	3.241896	TCAxGCC	COVERED																																																																																			NOVEL	POLR3K-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000134192.1	29	11.565278	KEEP	1	1	27	48	1425	CC	1	0.999989	0		-	7	60	209	0	0	13.365478	89	60	2934	239	ENST00000293860.5	0.072917	0.999989
NPRL3	8131	__UNKNOWN__	__UNKNOWN__	16	177855	177855	__UNKNOWN__	Intron	SNP	G	G	A	rs2857996	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:177855G>A	ENST00000405960.3	-	3	474				NPRL3_ENST00000399953.3_Intron|NPRL3_ENST00000399951.3_Intron			Q12980	NPRL3_HUMAN	nitrogen permease regulator-like 3 (S. cerevisiae)	NA		NA			aorta morphogenesis (GO:0035909)|cardiac muscle tissue development (GO:0048738)|palate development (GO:0060021)|ventricular septum development (GO:0003281)		GTPase activator activity (GO:0005096)			endometrium(1)|large_intestine(3)|ovary(2)	6						gggtttcaccgtgttagccag	0.587		NA											A|||	2172	0.433706	0.702	0.4669	5008	,	,	NA	14007	0.3532	NA	0.2803	False	NA	,,,	NA	NA	NA	2504	0.2883	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS73794.1, CCDS73795.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000103148	ENSG00000103148	8131			14124	protein-coding gene	gene with protein product	conserved gene telomeric to alpha globin cluster	600928	chromosome 16 open reading frame 35	C16orf35	NA	8575760	Standard	NM_001039476	NM_001243247	NA	Approved	CGTHBA, RMD11, NPR3, MARE, HS-40	uc002cfr.3	Q12980	OTTHUMG00000047792	ENST00000405960.3:c.2406+2665C>T	chr16.hg19:g.177855G>A		NA	D3DU40|Q1W6H0|Q4TT56|Q92469	hg19		0.02	-0.035073	ACCxTGT	UNCOVERED																																																																																			NOVEL	NPRL3-015	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000467385.1	3	2.405951	KEEP	0	0	0	8	222	CG	0.99254	0.019833	0		-	3	60	87	0	0	9.154761	1	60	24	16	ENST00000405960.3	0.75	0.019982
RAB11FIP3	9727	__UNKNOWN__	__UNKNOWN__	16	498341	498341	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:498341T>C	ENST00000262305.4	+	2	1102				RAB11FIP3_ENST00000457159.1_Intron	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	NA		NA			cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				cagtggctcatgcctgtaatc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(160;2366 2595 4474 8099)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565	9727		EF-hand domain containing	17224	protein-coding gene	gene with protein product		608738			NA	9734811, 11481332	Standard	NM_014700	NM_014700	NA	Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.715-13063T>C	chr16.hg19:g.498341T>C		NA	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	hg19	CCDS32351.1	0.02	-0.210498	TCAxGCC	COVERED																																																																																			NOVEL	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109066.4	9	3.909506	KEEP	2	0	0	13	359	TT	0.993072	0.518544	0		+	3	60	104	0	0	8.026784	19	60	569	53	ENST00000262305.4	0.136364	0.522161
RAB40C	57799	__UNKNOWN__	__UNKNOWN__	16	675332	675332	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:675332G>T	ENST00000248139.3	+	4	467				RAB40C_ENST00000539661.1_Intron|RAB40C_ENST00000538492.1_Intron|RAB40C_ENST00000535977.1_Intron	NM_021168.4	NP_066991.3	Q96S21	RB40C_HUMAN	RAB40C, member RAS oncogene family	NA		NA			protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	6		Hepatocellular(780;0.0218)				AGCATCCTTGGCCCTGCCCGG	0.657		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(123;1631 1690 28262 44104 44957)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z84779	CCDS10413.1	16p13.3	2008-07-28	2003-10-14		ENSG00000197562	ENSG00000197562	57799		RAB, member RAS oncogene	18285	protein-coding gene	gene with protein product		NA	RAS-like, family 8, member C	RASL8C	NA	11697911, 18485483	Standard	NM_021168	NM_021168	NA	Approved	RARL	uc021szv.1	Q96S21	OTTHUMG00000047854	ENST00000248139.3:c.265-100G>T	chr16.hg19:g.675332G>T		NA	A2IDE2|D3DU54|O60795|Q4TT41|Q5PXE8|Q6PIU5	hg19	CCDS10413.1	0.02	1.276019	TTGxCCC	COVERED																																																																																			NOVEL	RAB40C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109079.4	3	6.183749	KEEP	0	1	9	24	751	GG	0.999931	0.986085	0		+	13	60	356	0	0	28.293511	46	60	1556	117	ENST00000248139.3	0.220339	0.986153
LMF1	64788	__UNKNOWN__	__UNKNOWN__	16	975463	975463	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:975463T>C	ENST00000262301.11	-	3	533				LMF1_ENST00000543238.1_Intron|LMF1_ENST00000399843.2_Intron|LA16c-366D3.1_ENST00000567820.1_RNA|LA16c-366D3.1_ENST00000569574.1_RNA|LMF1_ENST00000568897.1_Intron|LMF1_ENST00000539379.1_Intron	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	NA		NA			chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				tggtggctcatgcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227	64788			14154	protein-coding gene	gene with protein product		611761	chromosome 16 open reading frame 26, transmembrane protein 112	C16orf26, TMEM112	NA	11157797, 17994020	Standard	NM_022773	NM_022773	NA	Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.514+8780A>G	chr16.hg19:g.975463T>C		NA	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	hg19	CCDS45373.1	0.02	-0.061381	TCAxGCC	UNCOVERED																																																																																			NOVEL	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109071.3	5	2.405574	KEEP	0	0	0	8	217	TT	0.99257	0.043461	0		-	2	60	70	0	0	6.493611	3	60	79	23	ENST00000262301.11	0.4	0.043787
UNKL	64718	__UNKNOWN__	__UNKNOWN__	16	1436282	1436282	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:1436282G>A	ENST00000508903.2	-	10	1086				UNKL_ENST00000389221.4_Intron|UNKL_ENST00000397462.1_Intron			Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	NA		NA			protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Hepatocellular(780;0.0893)				ggccgggcgcggtggctcaca	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011924	CCDS32359.1, CCDS53980.1, CCDS61787.1	16p13.3	2014-03-10	2013-10-17		ENSG00000059145	ENSG00000059145	64718		Zinc fingers, CCCH-type domain containing	14184	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 28, unkempt homolog (Drosophila)-like	C16orf28	NA	20148946	Standard	NM_001037125	NM_001193389	NA	Approved	ZC3HDC5L, ZC3H5L, FLJ23360	uc031qup.1	Q9H9P5	OTTHUMG00000128553	ENST00000508903.2:c.1087-896C>T	chr16.hg19:g.1436282G>A		NA	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	hg19		0.02	-0.157897	CGCxGTG	COVERED																																																																																			NOVEL	UNKL-002	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000362481.2	13	3.008403	KEEP	0	0	0	10	297	GG	0.992708	0.320453	0		-	4	45	119	0	0	9.901239	12	60	406	40	ENST00000508903.2	0.25	0.322807
HN1L	90861	__UNKNOWN__	__UNKNOWN__	16	1747399	1747399	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:1747399C>A	ENST00000382710.4	+	4	454				HN1L_ENST00000382711.5_Intron|HN1L_ENST00000561516.1_Intron|HN1L_ENST00000569256.1_Intron|HN1L_ENST00000562684.1_Intron|HN1L_ENST00000248098.3_Intron|HN1L_ENST00000569765.1_Intron			Q9H910	HN1L_HUMAN	hematological and neurological expressed 1-like	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|kidney(2)|lung(3)|upper_aerodigestive_tract(1)	9						ctgtagtccccactactcggg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023154	CCDS10441.1	16p13.3	2006-12-13	2006-12-13	2006-12-13	ENSG00000206053	ENSG00000206053	90861			14137	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 34	C16orf34	NA	15094197	Standard	NM_144570	NM_144570	NA	Approved	FLJ13092, L11, KIAA1426	uc002cmg.3	Q9H910	OTTHUMG00000047859	ENST00000382710.4:c.301-414C>A	chr16.hg19:g.1747399C>A		NA	B1AJY2|Q6EIC7	hg19		0.02	-0.087712	CCCxACT	UNCOVERED																																																																																			NOVEL	HN1L-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000432999.1	7	2.406993	KEEP	0	0	0	8	240	CC	0.99257	0.09898	0		+	3	60	91	0	0	8.232659	5	60	160	23	ENST00000382710.4	0.375	0.099721
HN1L	90861	__UNKNOWN__	__UNKNOWN__	16	1747400	1747400	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:1747400A>G	ENST00000382710.4	+	4	454				HN1L_ENST00000382711.5_Intron|HN1L_ENST00000561516.1_Intron|HN1L_ENST00000569256.1_Intron|HN1L_ENST00000562684.1_Intron|HN1L_ENST00000248098.3_Intron|HN1L_ENST00000569765.1_Intron			Q9H910	HN1L_HUMAN	hematological and neurological expressed 1-like	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|kidney(2)|lung(3)|upper_aerodigestive_tract(1)	9						tgtagtccccactactcggga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023154	CCDS10441.1	16p13.3	2006-12-13	2006-12-13	2006-12-13	ENSG00000206053	ENSG00000206053	90861			14137	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 34	C16orf34	NA	15094197	Standard	NM_144570	NM_144570	NA	Approved	FLJ13092, L11, KIAA1426	uc002cmg.3	Q9H910	OTTHUMG00000047859	ENST00000382710.4:c.301-413A>G	chr16.hg19:g.1747400A>G		NA	B1AJY2|Q6EIC7	hg19		0.02	-0.08771	CCCxCTA	UNCOVERED																																																																																			NOVEL	HN1L-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000432999.1	7	2.404611	KEEP	0	0	0	8	212	AA	0.99257	0.09898	0		+	3	60	102	0	0	9.333249	5	60	146	23	ENST00000382710.4	0.375	0.099721
MAPK8IP3	23162	__UNKNOWN__	__UNKNOWN__	16	1780485	1780485	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:1780485C>A	ENST00000250894.4	+	4	759				MAPK8IP3_ENST00000356010.5_Intron	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	NA		NA			activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						tcacgcctgtcattccagcac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834	23162			6884	protein-coding gene	gene with protein product	homolog of Drosophila Sunday driver 2	605431			NA	10523642, 10629060	Standard	NM_001040439	XM_005255187	NA	Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.602+906C>A	chr16.hg19:g.1780485C>A		NA	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	hg19	CCDS10442.2	0.02	-0.13148	TGTxATT	COVERED																																																																																			NOVEL	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250508.2	7	3.007364	KEEP	2	0	0	10	287	CC	0.99254	0.227464	0		+	3	53	82	0	0	6.473063	11	60	381	37	ENST00000250894.4	0.214286	0.229173
MEIOB	254528	__UNKNOWN__	__UNKNOWN__	16	1899173	1899173	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:1899173A>G	ENST00000325962.3	-	8	788				MEIOB_ENST00000470044.1_Intron|MEIOB_ENST00000452149.2_Intron|MEIOB_ENST00000412554.2_Intron|MEIOB_ENST00000397344.3_Intron			Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	NA		NA			double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)				NA						tgtaatcccaacactttggga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039	254528			28569	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 73	C16orf73	NA	12477932	Standard	NM_152764	NM_152764	NA	Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000325962.3:c.778+3866T>C	chr16.hg19:g.1899173A>G		NA	B1AK39|C9J0S1|Q96RY0	hg19	CCDS53983.1	0.02	-0.149011	CCAxCAC	COVERED																																																																																			NOVEL	MEIOB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000347846.1	3	3.607556	KEEP	2	0	0	12	318	AA	0.993072	0.289978	0		-	3	60	102	0	0	8.583078	10	60	284	45	ENST00000325962.3	0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	1984373	1984373	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:1984373G>A			NA	NA				HS3ST6 (15932 upstream) : MSRB1 (3837 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.1984373G>A		NA		hg19		0.02	-0.236827	GGCxTGA	COVERED																																																																																			NOVEL					0			12	5.068092	KEEP	2	0	0	17	467	GG	0.997832	0.611079	0			3	60	92	0	0	6.649537	22	60	699	64		0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	2061453	2061453	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2061453T>C			NA	NA				ZNF598 (1629 upstream) : RN7SL219P (1728 downstream)						NA		NA									NA						tgagccactgtgcctggccaa	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.2061453T>C		NA		hg19		0.02	-0.201741	CTGxGCC	COVERED																																																																																			NOVEL					0			7	2.706996	KEEP	1	0	0	9	252	TT	0.99254	0.486885	0			3	60	94	0	0	7.027281	19	60	585	47		0.136364	0.490544
TSC2	7249	__UNKNOWN__	__UNKNOWN__	16	2100214	2100214	__UNKNOWN__	Intron	SNP	C	C	T	rs560889892	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2100214C>T	ENST00000219476.3	+	3	768				TSC2_ENST00000568454.1_Intron|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000439673.2_Intron|TSC2_ENST00000350773.4_Intron|TSC2_ENST00000401874.2_Intron|TSC2_ENST00000353929.4_Intron	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	NA		NA			acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				tgccttggccccccaaagtgc	0.488		NA	D, Mis, N, F, S			hamartoma, renal cell			Tuberous Sclerosis				T|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	17268	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA		yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		E, O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197	7249			12363	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 160	191092		TSC4	NA	1303246, 7558029	Standard	NM_000548	NM_001077183	NA	Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.139-187C>T	chr16.hg19:g.2100214C>T		NA	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	hg19	CCDS10458.1	0.02	-0.166661	GCCxCCC	COVERED																																																																																			NOVEL	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250657.2	1	2.390092	KEEP	0	0	0	8	205	CC	0.99257	0.351317	0		+	3	60	85	0	0	6.334332	16	60	523	29	ENST00000219476.3	0.157895	0.353947
TSC2	7249	__UNKNOWN__	__UNKNOWN__	16	2115433	2115433	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2115433A>G	ENST00000219476.3	+	16	2229				TSC2_ENST00000568454.1_Intron|TSC2_ENST00000382538.6_Intron|TSC2_ENST00000439673.2_Intron|TSC2_ENST00000350773.4_Intron|TSC2_ENST00000401874.2_Intron|TSC2_ENST00000353929.4_Intron	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	NA		NA			acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				aaaaaaaaaaaaaaaGGTGTT	0.498		NA	D, Mis, N, F, S			hamartoma, renal cell			Tuberous Sclerosis												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		E, O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197	7249			12363	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 160	191092		TSC4	NA	1303246, 7558029	Standard	NM_000548	NM_001077183	NA	Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.1600-87A>G	chr16.hg19:g.2115433A>G		NA	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	hg19	CCDS10458.1	0.02	5.833136	AAAxAAA	COVERED																																																																																			NOVEL	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250657.2	67	31.570159	KEEP	3	0	0	105	2780	AA	1	1	0		+	6	60	209	0	0	13.729814	101	60	2875	375	ENST00000219476.3	0.056075	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	2323244	2323244	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2323244G>A			NA	NA				MIR940 (1403 upstream) : MIR4717 (1376 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.2323244G>A		NA		hg19		0.02	-0.184089	GGCxTGA	COVERED																																																																																			NOVEL					0			10	4.512275	KEEP	0	0	0	15	430	GG	0.99649	0.421991	0			3	60	87	0	0	6.611742	15	60	481	46		0.166667	0.423478
ABCA3	21	__UNKNOWN__	__UNKNOWN__	16	2370213	2370213	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2370213C>T	ENST00000382381.3	-	8	1325				ABCA3_ENST00000301732.5_Intron			Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	NA		NA			response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	gattctcctgcctcagcctcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972	21		ATP binding cassette transporters / subfamily A	33	protein-coding gene	gene with protein product		601615		ABC3	NA	8706931	Standard	NM_001089	NM_001089	NA	Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000382381.3:c.614-372G>A	chr16.hg19:g.2370213C>T		NA	B2RU09|Q54A95|Q6P5P9|Q92473	hg19		0.02	-0.210532	CTGxCTC	UNCOVERED																																																																																			NOVEL	ABCA3-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000435440.1	11	2.707965	KEEP	5	0	0	9	272	CC	0	0	0		-	3	40	89	0	0	6.733659	16	60	541	48	ENST00000382381.3	0.157895	0.522161
AC141586.5	0	__UNKNOWN__	__UNKNOWN__	16	2658353	2658353	__UNKNOWN__	RNA	SNP	T	T	A	rs560438643		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2658353T>A	ENST00000399702.1	+	0	378					NR_015441.1					NA		NA									NA						atggggtttctccatgttggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000399702.1:	chr16.hg19:g.2658353T>A		NA		hg19		0.02	-0.096481	TTCxCCA	UNCOVERED																																																																																			NOVEL	AC141586.5-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000250833.2	6	2.405436	KEEP	2	0	0	8	212	TT	0.99257	0.138793	0		+	3	60	90	0	0	7.77855	7	60	215	29	ENST00000399702.1	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	2731352	2731352	__UNKNOWN__	IGR	SNP	C	C	T	rs539149499	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2731352C>T			NA	NA				ERVK13-1 (7910 upstream) : KCTD5 (1123 downstream)						NA		NA									NA						ctcactctgtcgcccaggcta	0.463		NA											.|||	3	0.000599042	0.0	0.0	5008	,	,	NA	17432	0.003	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.2731352C>T		NA		hg19		0.02	-0.210492	TGTxGCC	COVERED																																																																																			NOVEL					0			8	5.113024	KEEP	2	0	0	17	494	CC	0.997832	0.521029	0			3	60	91	0	0	6.861337	17	60	523	54		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	2863287	2863287	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2863287G>A			NA	NA				PRSS41 (8154 upstream) : PRSS21 (3876 downstream)						NA		NA									NA						gtgaaaccccgtctctactaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.2863287G>A		NA		hg19		0.02	-0.157869	CCCxTCT	COVERED																																																																																			NOVEL					0			11	2.999242	KEEP	3	0	0	10	279	GG	0.99254	0.320398	0			4	46	110	1	0	9.001575	12	60	374	37		0.25	0.322807
PRSS21	10942	__UNKNOWN__	__UNKNOWN__	16	2873984	2873984	__UNKNOWN__	Intron	SNP	A	A	G	rs565764325	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2873984A>G	ENST00000575739.1	+	2	43							Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	NA		NA			spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						ccaaagtgctaggattacagg	0.453		NA											G|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	20123	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038	10942		Serine peptidases / Serine peptidases	9485	protein-coding gene	gene with protein product		608159			NA	10397266, 9826525	Standard	NM_006799	NM_006799	NA	Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000575739.1:c.44-1987A>G	chr16.hg19:g.2873984A>G		NA	Q9NS34|Q9P2V6	hg19		0.02	-0.184204	GCTxGGA	COVERED																																																																																			NOVEL	PRSS21-010	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000436459.1	6	3.308399	KEEP	1	0	0	11	305	AA	0.993072	0.420544	0		+	4	60	135	0	0	11.268292	14	60	428	53	ENST00000575739.1	0.222222	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	2898655	2898655	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:2898655T>C			NA	NA				PRSS30P (5944 upstream) : PRSS22 (4072 downstream)						NA		NA									NA						gatctcaccattgcactccag	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.2898655T>C		NA		hg19		0.02	-0.122787	CCAxTGC	COVERED																																																																																			NOVEL					0			8	3.007796	KEEP	2	0	0	10	280	TT	0.99254	0.194847	0			3	60	94	0	0	7.901262	9	60	268	33		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	3034694	3034694	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3034694G>A			NA	NA				PKMYT1 (4154 upstream) : LINC00514 (5500 downstream)						NA		NA									NA						cacccgcctcggcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.3034694G>A		NA		hg19		0.02	-0.13158	CTCxGCC	COVERED																																																																																			NOVEL					0			5	4.21069	KEEP	1	0	0	14	406	GG	0.995343	0.228106	0			3	60	85	1	0	6.772914	11	60	384	49		0.214286	0.229173
RP11-473M20.9	0	__UNKNOWN__	__UNKNOWN__	16	3135261	3135261	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3135261A>G	ENST00000571404.1	-	0	210										NA		NA									NA						gctcacacctataatcccagc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000571404.1:	chr16.hg19:g.3135261A>G		NA		hg19		0.02	-0.27184	CCTxTAA	COVERED																																																																																			NOVEL	RP11-473M20.9-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000437122.1	6	3.006771	KEEP	1	0	0	10	262	AT	0.993072	0.712346	0		-	3	60	105	0	0	7.894688	23	60	662	62	ENST00000571404.1	0.115385	0.717315
ZNF205-AS1	81854	__UNKNOWN__	__UNKNOWN__	16	3160900	3160900	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3160900G>A	ENST00000572691.1	-	0	779				ZNF205-AS1_ENST00000576943.1_RNA	NR_024166.1|NR_024167.1				ZNF205 antisense RNA 1	NA		NA									NA						cggaggttggggtgagctgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							16p13.3	2012-11-06			ENSG00000263214	ENSG00000263214	81854		Long non-coding RNAs	28586	non-coding RNA	RNA, long non-coding		NA			NA	12477932	Standard	NR_024166	NR_024166	NA	Approved	MGC3771	uc010btd.2		OTTHUMG00000177517	ENST00000572691.1:	chr16.hg19:g.3160900G>A		NA		hg19		0.02	1.137779	TGGxGTG	COVERED																																																																																			NOVEL	ZNF205-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000437319.1	21	8.559245	KEEP	1	4	115	69	2155	GG	1	0.999678	0		-	5	60	146	0	0	8.903183	74	60	2535	236	ENST00000572691.1	0.063291	0.999678
ZNF205-AS1	81854	__UNKNOWN__	__UNKNOWN__	16	3161053	3161053	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3161053G>A	ENST00000572691.1	-	0	724				ZNF205-AS1_ENST00000576943.1_RNA	NR_024166.1|NR_024167.1				ZNF205 antisense RNA 1	NA		NA									NA						ggtggctcacgcctgtaatcc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							16p13.3	2012-11-06			ENSG00000263214	ENSG00000263214	81854		Long non-coding RNAs	28586	non-coding RNA	RNA, long non-coding		NA			NA	12477932	Standard	NR_024166	NR_024166	NA	Approved	MGC3771	uc010btd.2		OTTHUMG00000177517	ENST00000572691.1:	chr16.hg19:g.3161053G>A		NA		hg19		0.02	-0.315659	CACxCCT	COVERED																																																																																			NOVEL	ZNF205-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000437319.1	12	5.647041	KEEP	4	1	23	27	777	GG	0.999957	0.818429	0		-	5	60	133	0	0	9.822043	25	60	778	77	ENST00000572691.1	0.166667	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	3223331	3223331	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3223331G>A			NA	NA				RP11-473M20.16 (15847 upstream) : AJ003147.8 (7901 downstream)						NA		NA									NA						tgcccacctcggcctcccaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.3223331G>A		NA		hg19		0.02	-0.184174	CTCxGCC	COVERED																																																																																			NOVEL					0			8	2.706954	KEEP	2	0	0	9	253	GG	0.99257	0.420331	0			3	60	91	0	0	7.092268	14	60	438	46		0.176471	0.423478
NAA60	79903	__UNKNOWN__	__UNKNOWN__	16	3527837	3527837	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3527837G>A	ENST00000360862.5	+	2	189				NAA60_ENST00000572942.1_Intron|NAA60_ENST00000424546.2_Intron|NAA60_ENST00000610180.1_Intron|NAA60_ENST00000577013.1_Intron|NAA60_ENST00000570551.1_Intron|NAA60_ENST00000576916.1_Intron|NAA60_ENST00000572584.1_Intron|NAA60_ENST00000414063.2_Intron|LA16c-306E5.3_ENST00000574423.2_RNA|NAA60_ENST00000407558.4_Intron|NAA60_ENST00000573580.1_Intron|NAA60_ENST00000608993.1_Intron|NAA60_ENST00000608722.1_Intron|NAA60_ENST00000575076.1_Intron|NAA60_ENST00000570819.1_Intron|NAA60_ENST00000421765.3_Intron			Q9H7X0	NAA60_HUMAN	N(alpha)-acetyltransferase 60, NatF catalytic subunit	NA		NA			cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|histone H4 acetylation (GO:0043967)|N-terminal peptidyl-methionine acetylation (GO:0017196)|nucleosome assembly (GO:0006334)	Golgi membrane (GO:0000139)	H4 histone acetyltransferase activity (GO:0010485)|peptide alpha-N-acetyltransferase activity (GO:0004596)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)	7						aggccgaggcgggtggatcac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45396.1	16p13.3	2012-07-13	2011-08-02	2011-08-02	ENSG00000122390	ENSG00000122390	79903	2.3.1.48, 2.3.1.88	N(alpha)-acetyltransferase subunits	25875	protein-coding gene	gene with protein product		614246	N-acetyltransferase 15 (GCN5-related, putative)	NAT15	NA	12975309, 21750686	Standard	NM_024845	NM_001083600	NA	Approved	FLJ14154	uc010btm.3	Q9H7X0	OTTHUMG00000150268	ENST00000360862.5:c.-85-1634G>A	chr16.hg19:g.3527837G>A		NA	B3KRQ0|B4DLZ0|B4DPZ8|B4DYC4|D3DUC2|E7EQ65|Q6IA31|Q6UX26	hg19		0.02	-0.157893	GGCxGGT	UNCOVERED																																																																																			NOVEL	NAA60-003	PUTATIVE	NMD_exception|non_canonical_U12|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000437863.1	3	2.406951	KEEP	1	0	0	8	239	GG	0	0	0		+	3	60	87	0	0	6.610557	15	60	504	36	ENST00000360862.5	0.166667	0.322807
CLUAP1	23059	__UNKNOWN__	__UNKNOWN__	16	3582027	3582027	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3582027C>T	ENST00000576634.1	+	11	1180				CLUAP1_ENST00000341633.5_Intron|CLUAP1_ENST00000571025.1_Intron|CLUAP1_ENST00000572600.1_Intron|CLUAP1_ENST00000445795.2_Intron|CLUAP1_ENST00000417763.2_Intron	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	NA		NA			cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ttagtagagacggggtttcac	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351	23059		Intraflagellar transport homologs	19009	protein-coding gene	gene with protein product	flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas), cilia and flagella associated protein 22	NA			NA	15480429, 9734811, 19253336	Standard	NM_024793	NM_015041	NA	Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.1037-759C>T	chr16.hg19:g.3582027C>T		NA	O75138|Q65ZA3|Q9H8R4|Q9H8T1	hg19	CCDS32381.1	0.02	-0.140344	AGAxGGG	COVERED																																																																																			NOVEL	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000437883.2	12	3.609976	KEEP	10	0	0	12	348	CG	0.993072	0.259157	0		+	3	45	83	0	0	6.681972	10	60	331	49	ENST00000576634.1	0.230769	0.260965
SLX4	84464	__UNKNOWN__	__UNKNOWN__	16	3643456	3643456	__UNKNOWN__	Intron	SNP	C	C	T	rs138396495	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3643456C>T	ENST00000294008.3	-	11	2801					NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	NA		NA			DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						tggcctcaagcgatcctccca	0.532		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827	84464		Fanconi anemia, complementation groups, BTB/POZ domain containing	23845	protein-coding gene	gene with protein product	Fanconi anemia, complementation group P	613278	BTB (POZ) domain containing 12, SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	BTBD12	NA	11347906, 19595721	Standard	NM_032444	NM_032444	NA	Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2161-590G>A	chr16.hg19:g.3643456C>T		NA	Q69YT8|Q8TF15|Q96JP1	hg19	CCDS10506.2	0.02	-0.122788	AAGxGAT	COVERED																																																																																			NOVEL	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157301.3	6	2.406645	KEEP	0	0	0	8	241	CC	0.99257	0.194853	0		-	3	60	80	0	0	6.500988	9	60	298	29	ENST00000294008.3	0.25	0.196312
SLX4	84464	__UNKNOWN__	__UNKNOWN__	16	3655430	3655430	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3655430T>C	ENST00000294008.3	-	3	1401					NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	NA		NA			DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						cactatgttgtccaggctggt	0.532		NA						Direct reversal of damage													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827	84464		Fanconi anemia, complementation groups, BTB/POZ domain containing	23845	protein-coding gene	gene with protein product	Fanconi anemia, complementation group P	613278	BTB (POZ) domain containing 12, SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)	BTBD12	NA	11347906, 19595721	Standard	NM_032444	NM_032444	NA	Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.760+1044A>G	chr16.hg19:g.3655430T>C		NA	Q69YT8|Q8TF15|Q96JP1	hg19	CCDS10506.2	0.02	-0.201715	TTGxCCA	COVERED																																																																																			NOVEL	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157301.3	6	2.406073	KEEP	0	0	0	8	220	TT	0.99257	0.4869	0		-	4	60	118	1	0	9.363533	16	60	473	44	ENST00000294008.3	0.2	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	3947316	3947316	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3947316T>C			NA	NA				CREBBP (16589 upstream) : RP11-462G12.2 (33901 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.3947316T>C		NA		hg19		0.02	-0.201724	TCCxAGC	COVERED																																																																																			NOVEL					0			7	3.609081	KEEP	0	0	0	12	329	TT	0.993634	0.487421	0			5	60	171	0	0	14.256757	18	60	531	51		0.217391	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	3958362	3958362	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:3958362T>A			NA	NA				CREBBP (27635 upstream) : RP11-462G12.2 (22855 downstream)						NA		NA									NA						atggtctcgatctcctgacct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.3958362T>A		NA		hg19		0.02	-0.184153	CGAxCTC	COVERED																																																																																			NOVEL					0			6	3.006504	KEEP	2	0	0	10	265	TT	0.99254	0.420319	0			3	60	87	0	0	6.462315	17	60	486	49		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	4305333	4305333	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4305333T>C			NA	NA				RP11-95P2.1 (1543 upstream) : TFAP4 (1853 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.4305333T>C		NA		hg19		0.02	-0.210451	AGGxGTG	COVERED																																																																																			NOVEL					0			4	2.403911	KEEP	2	0	0	8	219	TT	0.99257	0.518282	0			3	60	87	0	0	6.400344	18	60	544	49		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	4350435	4350435	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4350435A>G			NA	NA				TFAP4 (27359 upstream) : GLIS2 (14326 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.4350435A>G		NA		hg19		0.02	-0.236732	CACxCCT	COVERED																																																																																			NOVEL					0			10	6.915877	KEEP	0	0	0	23	629	AA	0.999892	0.612341	0			4	60	124	0	0	9.537386	21	60	602	67		0.16	0.612407
ANKS3	124401	__UNKNOWN__	__UNKNOWN__	16	4757906	4757906	__UNKNOWN__	Intron	SNP	C	C	G	rs141178819	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4757906C>G	ENST00000304283.4	-	8	1004				ANKS3_ENST00000450067.2_Intron|ANKS3_ENST00000446014.2_Intron|ANKS3_ENST00000585773.1_Intron	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	NA		NA								endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						gaggtcaggacttcaagacca	0.527		NA											C|||	43	0.00858626	0.0	0.0144	5008	,	,	NA	14758	0.002	NA	0.0288	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096	124401		Sterile alpha motif (SAM) domain containing, Ankyrin repeat domain containing	29422	protein-coding gene	gene with protein product		NA			NA	11853319	Standard	NM_133450	NM_133450	NA	Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.710-2652G>C	chr16.hg19:g.4757906C>G		NA	B4DWU4|D3DUE2|Q8TF25	hg19	CCDS10520.1	0.02	-0.131581	GGAxTTC	COVERED																																																																																			NOVEL	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251642.3	3	2.708105	KEEP	1	0	0	9	278	CC	0.99254	0.227464	0		-	3	60	99	0	0	8.281787	10	60	342	36	ENST00000304283.4	0.230769	0.229173
ZNF500	26048	__UNKNOWN__	__UNKNOWN__	16	4800770	4800770	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4800770A>G	ENST00000219478.6	-	0	3349				RP11-127I20.7_ENST00000588099.1_RNA			O60304	ZN500_HUMAN	zinc finger protein 500	NA		NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						tgggattacaagcgtgagcca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199	26048		Zinc fingers, C2H2-type, -, -, -	23716	protein-coding gene	gene with protein product		NA			NA	9628581	Standard	XM_085507	XM_005255243	NA	Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.*1607T>C	chr16.hg19:g.4800770A>G		NA	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	hg19	CCDS32383.1	0.02	-0.052629	ACAxGCG	UNCOVERED																																																																																			NOVEL	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000432461.1	4	2.40612	KEEP	0	0	0	8	220	AA	0.99257	0.036492	0		-	2	58	70	0	0	6.492977	3	60	92	18	ENST00000219478.6	0.4	0.036766
GLYR1	84656	__UNKNOWN__	__UNKNOWN__	16	4857109	4857109	__UNKNOWN__	Intron	SNP	T	T	C	rs2880222	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4857109T>C	ENST00000321919.9	-	16	1664				GLYR1_ENST00000591451.1_Intron|GLYR1_ENST00000381983.3_Intron|GLYR1_ENST00000436648.5_Intron	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	NA		NA			pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						gcctggccCCttttttttttt	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632	84656			24434	protein-coding gene	gene with protein product	nuclear protein 60kDa	610660			NA	16352664	Standard	NM_032569	NM_032569	NA	Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.1588-1798A>G	chr16.hg19:g.4857109T>C		NA	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	hg19	CCDS10524.1	0.02	-0.19297	CCCxTTT	COVERED																																																																																			NOVEL	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251717.2	19	2.224432	KEEP	6	1	33	19	479	TT	0.997832	0.456764	0		-	5	60	180	1	0	18.087236	3	60	95	64	ENST00000321919.9	0.625	0.457757
GLYR1	84656	__UNKNOWN__	__UNKNOWN__	16	4892972	4892972	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4892972G>A	ENST00000321919.9	-	3	232				GLYR1_ENST00000591451.1_Intron|GLYR1_ENST00000381983.3_Intron|GLYR1_ENST00000436648.5_Intron	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	NA		NA			pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						aagtgctggggttacaggcat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632	84656			24434	protein-coding gene	gene with protein product	nuclear protein 60kDa	610660			NA	16352664	Standard	NM_032569	NM_032569	NA	Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.155+2102C>T	chr16.hg19:g.4892972G>A		NA	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	hg19	CCDS10524.1	0.02	-0.184218	GGGxTTA	COVERED																																																																																			NOVEL	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251717.2	7	3.911452	KEEP	1	0	0	13	394	GG	0.994391	0.455189	0		-	3	60	90	0	0	6.692709	18	60	618	54	ENST00000321919.9	0.142857	0.457757
UBN1	29855	__UNKNOWN__	__UNKNOWN__	16	4904292	4904292	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4904292T>C	ENST00000396658.4	+	1	952				UBN1_ENST00000262376.6_Intron|UBN1_ENST00000545171.1_Intron|UBN1_ENST00000590769.1_Intron	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	NA		NA			chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						ccttggcctctcaaagtgctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900	29855			12506	protein-coding gene	gene with protein product		609771			NA	10725330	Standard	NM_016936	XM_005255277	NA	Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.249+1125T>C	chr16.hg19:g.4904292T>C		NA	B7Z6D3|D3DUE8|Q13079|Q9P1P7	hg19	CCDS10525.1	0.02	-0.210506	CTCxCAA	COVERED																																																																																			NOVEL	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251719.1	11	3.307019	KEEP	2	0	0	11	293	TT	0.99254	0.518266	0		+	3	60	97	0	0	7.393355	18	60	547	47	ENST00000396658.4	0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	4995657	4995657	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:4995657T>G			NA	NA				PPL (8521 upstream) : Y_RNA (6116 downstream)						NA		NA									NA						ctcctgcctctgccacccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.4995657T>G		NA		hg19		0.02	-0.140336	CTCxGCC	COVERED																																																																																			NOVEL					0			9	2.707015	KEEP	0	0	0	9	250	TT	0.99254	0.259018	0			3	60	98	0	0	8.182035	10	60	301	31		0.230769	0.260965
RP11-420N3.2	0	__UNKNOWN__	__UNKNOWN__	16	5877311	5877311	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:5877311A>G	ENST00000569895.1	+	0	403										NA		NA									NA						tgaggcaggaaaattgcttga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000569895.1:	chr16.hg19:g.5877311A>G		NA		hg19		0.02	-0.061401	GGAxAAT	UNCOVERED																																																																																			NOVEL	RP11-420N3.2-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000435404.2	7	3.908305	KEEP	0	0	0	13	343	AA	0.994391	0.043541	0		+	3	60	104	0	0	9.755512	4	60	123	23	ENST00000569895.1	0.428571	0.043787
RP11-420N3.2	0	__UNKNOWN__	__UNKNOWN__	16	5877315	5877315	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:5877315T>C	ENST00000569895.1	+	0	403										NA		NA									NA						gcaggaaaattgcttgagccc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000569895.1:	chr16.hg19:g.5877315T>C		NA		hg19		0.02	-0.087701	AATxGCT	UNCOVERED																																																																																			NOVEL	RP11-420N3.2-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000435404.2	9	3.908896	KEEP	0	0	0	13	347	TT	0.994391	0.099162	0		+	4	60	130	0	0	11.986131	6	60	166	26	ENST00000569895.1	0.4	0.099721
RBFOX1	54715	__UNKNOWN__	__UNKNOWN__	16	6353714	6353714	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:6353714T>C	ENST00000547372.1	+	2	309				RP11-420N3.2_ENST00000569895.1_RNA|RBFOX1_ENST00000553186.1_Intron|RBFOX1_ENST00000422070.4_Intron|RBFOX1_ENST00000550418.1_Intron			Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	NA		NA			mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						cagtggctcatgcctgtaatc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(157;934 2567 15163 39509)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328	54715		RNA binding motif (RRM) containing	18222	protein-coding gene	gene with protein product	ataxin 2-binding protein 1, hexaribonucleotide binding protein 1	605104			NA	10814712, 16260614	Standard	NM_145891	NM_018723	NA	Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000547372.1:c.4-13282T>C	chr16.hg19:g.6353714T>C		NA	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	hg19		0.02	-0.140341	TCAxGCC	UNCOVERED																																																																																			NOVEL	RBFOX1-010	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000409494.2	5	2.406397	KEEP	1	0	0	8	226	TT	0	0	0		+	4	60	141	0	0	12.1016	12	60	361	35	ENST00000547372.1	0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	8763431	8763431	__UNKNOWN__	IGR	SNP	C	C	T	rs2312961	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:8763431C>T			NA	NA				METTL22 (23352 upstream) : ABAT (4990 downstream)						NA		NA									NA						aatggcacaaccttggctcac	0.498		NA											T|||	367	0.0732827	0.0113	0.1427	5008	,	,	NA	19569	0.0883	NA	0.0437	False	NA	,,,	NA	NA	NA	2504	0.1227	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.8763431C>T		NA		hg19		0.02	-0.122792	CAAxCTT	COVERED																																																																																			NOVEL					0			4	2.406795	KEEP	0	0	0	8	235	CC	0.99257	0.194853	0			4	60	111	0	0	9.52303	9	60	296	30		0.307692	0.196312
ABAT	18	__UNKNOWN__	__UNKNOWN__	16	8798763	8798763	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:8798763G>A	ENST00000268251.8	+	1	147					NM_020686.5	NP_065737.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	NA		NA			behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	ggctggtctcgaactcctggc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	18	2.6.1.19		23	protein-coding gene	gene with protein product	4-aminobutyrate transaminase	137150			NA	7721088	Standard	NM_020686	NM_020686	NA	Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000268251.8:c.-42+30195G>A	chr16.hg19:g.8798763G>A		NA	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	hg19	CCDS10534.1	0.02	-0.210515	CTCxAAC	COVERED																																																																																			NOVEL	ABAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109648.2	13	4.212037	KEEP	7	0	0	14	420	GG	0.993634	0.518837	0		+	3	60	89	0	0	6.661774	17	60	556	64	ENST00000268251.8	0.15	0.522161
ABAT	18	__UNKNOWN__	__UNKNOWN__	16	8805980	8805980	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:8805980T>C	ENST00000268251.8	+	2	147					NM_020686.5	NP_065737.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	NA		NA			behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	cccagctacttgggaggctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	18	2.6.1.19		23	protein-coding gene	gene with protein product	4-aminobutyrate transaminase	137150			NA	7721088	Standard	NM_020686	NM_020686	NA	Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000268251.8:c.-41-23576T>C	chr16.hg19:g.8805980T>C		NA	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	hg19	CCDS10534.1	0.02	-0.114016	ACTxGGG	UNCOVERED																																																																																			NOVEL	ABAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109648.2	7	3.608597	KEEP	1	0	0	12	321	TT	0.993072	0.161341	0		+	3	60	95	0	0	8.00116	9	60	274	34	ENST00000268251.8	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	8975820	8975820	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:8975820T>C			NA	NA				RP11-77H9.6 (11931 upstream) : USP7 (10130 downstream)						NA		NA									NA						gtgatctgcctgcctcggcct	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.8975820T>C		NA		hg19		0.02	-0.157888	GCCxGCC	UNCOVERED																																																																																			NOVEL					0			10	2.405492	KEEP	6	0	0	8	216	TT	0	0	0			3	60	103	0	0	8.209913	15	60	459	44		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	9082420	9082420	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:9082420G>A			NA	NA				RP11-77H9.8 (21573 upstream) : RP11-473I1.6 (79990 downstream)						NA		NA									NA						cacccgcctcggcctcccaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.9082420G>A		NA		hg19		0.02	-0.228049	CTCxGCC	COVERED																																																																																			NOVEL					0			12	3.309558	KEEP	5	0	0	11	333	GG	0.99254	0.607839	0			3	60	92	0	0	6.765415	20	60	642	59		0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	9174941	9174941	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:9174941G>A			NA	NA				RP11-473I1.6 (8672 upstream) : C16orf72 (10563 downstream)						NA		NA									NA						cagcctgggcgacagagtgag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.9174941G>A		NA		hg19		0.02	-0.078814	GGCxACA	UNCOVERED																																																																																			NOVEL					0			5	2.40652	KEEP	1	0	0	8	232	GG	0	0	0			3	60	84	0	0	7.758679	4	60	108	23		0.428571	0.077336
C16orf72	29035	__UNKNOWN__	__UNKNOWN__	16	9215034	9215034	__UNKNOWN__	3'UTR	SNP	T	T	C	rs528761498		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:9215034T>C	ENST00000327827.7	+	0	5490					NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72	NA		NA								endometrium(4)|large_intestine(2)|lung(2)	8						cagtcttgaattcctgacctt	0.488		NA											T|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	16287	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK123266	CCDS10538.1	16p13.2	2012-11-19			ENSG00000182831	ENSG00000182831	29035			30103	protein-coding gene	gene with protein product		NA			NA	8889548	Standard	NM_014117	NM_014117	NA	Approved	FLJ41272, PRO0149	uc002czm.3	Q14CZ0	OTTHUMG00000178147	ENST00000327827.7:c.*4265T>C	chr16.hg19:g.9215034T>C		NA		hg19	CCDS10538.1	0.02	-0.157813	GAAxTCC	UNCOVERED																																																																																			NOVEL	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440760.2	4	2.405575	KEEP	1	0	0	8	212	TT	0	0	0		+	3	60	95	0	0	7.492577	14	60	395	38	ENST00000327827.7	0.176471	0.322807
GRIN2A	2903	__UNKNOWN__	__UNKNOWN__	16	9928436	9928436	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:9928436G>A	ENST00000396573.2	-	9	1961				GRIN2A_ENST00000330684.3_Intron|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000535259.1_Intron|GRIN2A_ENST00000396575.2_Intron	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	NA		NA			directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	acggggtttcgccatgttgcc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454	2903		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4585	protein-coding gene	gene with protein product		138253		NMDAR2A	NA	9480759	Standard		XM_005255267	NA	Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.1652-349C>T	chr16.hg19:g.9928436G>A		NA	O00669|Q17RZ6	hg19	CCDS10539.1	0.02	-0.105251	TTCxCCA	UNCOVERED																																																																																			NOVEL	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251930.3	10	3.30908	KEEP	4	0	0	11	325	GG	0.99254	0.138789	0		-	3	60	90	0	0	7.632417	8	60	252	31	ENST00000396573.2	0.272727	0.139832
GRIN2A	2903	__UNKNOWN__	__UNKNOWN__	16	10129006	10129006	__UNKNOWN__	Intron	SNP	T	T	C	rs373689491		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:10129006T>C	ENST00000396573.2	-	4	724				GRIN2A_ENST00000330684.3_Intron|GRIN2A_ENST00000404927.2_Intron|RP11-895K13.2_ENST00000569218.1_RNA|GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000396575.2_Intron	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	NA		NA			directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	cctcaacctcttgagtagctg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454	2903		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4585	protein-coding gene	gene with protein product		138253		NMDAR2A	NA	9480759	Standard		XM_005255267	NA	Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.415-96598A>G	chr16.hg19:g.10129006T>C		NA	O00669|Q17RZ6	hg19	CCDS10539.1	0.02	-0.131575	CTCxTGA	COVERED																																																																																			NOVEL	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000251930.3	5	2.406502	KEEP	0	0	0	8	228	TT	0.99257	0.22747	0		-	3	60	104	0	0	8.572061	12	60	372	31	ENST00000396573.2	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	10439249	10439249	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:10439249T>C			NA	NA				RN7SL493P (123319 upstream) : RP11-609N14.1 (6047 downstream)						NA		NA									NA						aatctcggcttactgcaacct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.10439249T>C		NA		hg19		0.02	-0.061355	GCTxACT	UNCOVERED																																																																																			NOVEL					0			5	2.404188	KEEP	6	0	0	8	201	TT	0	0	0			3	60	92	0	0	8.555551	4	60	105	27		0.428571	0.043787
CLEC16A	23274	__UNKNOWN__	__UNKNOWN__	16	11102581	11102581	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:11102581T>C	ENST00000409790.1	+	11	1533				CLEC16A_ENST00000409552.3_Intron	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A	NA		NA								breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ggtgcggtggttcacgcctgt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532	23274		C-type lectin domain containing	29013	protein-coding gene	gene with protein product		611303	KIAA0350	KIAA0350	NA	9205841, 17632545	Standard	NM_015226	NM_015226	NA	Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1303+5419T>C	chr16.hg19:g.11102581T>C		NA		hg19	CCDS45409.1	0.02	-0.201713	TGGxTCA	COVERED																																																																																			NOVEL	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328540.2	8	2.405436	KEEP	1	0	0	8	211	TT	0.99257	0.4869	0		+	3	60	103	0	0	7.864836	20	60	587	51	ENST00000409790.1	0.130435	0.490544
CLEC16A	23274	__UNKNOWN__	__UNKNOWN__	16	11195784	11195784	__UNKNOWN__	Intron	SNP	C	C	T	rs531971399		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:11195784C>T	ENST00000409790.1	+	20	2346				CLEC16A_ENST00000409552.3_Intron|CLEC16A_ENST00000465491.1_Intron	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A	NA		NA						p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ctcagccccccgagtagctgg	0.498		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15541	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532	23274		C-type lectin domain containing	29013	protein-coding gene	gene with protein product		611303	KIAA0350	KIAA0350	NA	9205841, 17632545	Standard	NM_015226	NM_015226	NA	Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2117-18688C>T	chr16.hg19:g.11195784C>T		NA		hg19	CCDS45409.1	0.02	-0.166629	CCCxGAG	COVERED																																																																																			NOVEL	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000328540.2	12	5.114065	KEEP	1	0	0	17	495	CC	0.999366	0.353723	0		+	3	60	88	0	0	6.792387	14	60	442	50	ENST00000409790.1	0.176471	0.353947
RMI2	116028	__UNKNOWN__	__UNKNOWN__	16	11423533	11423533	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:11423533A>G	ENST00000572173.1	+	4	751				RMI2_ENST00000381820.2_Intron			Q96E14	RMI2_HUMAN	RecQ mediated genome instability 2	NA		NA			DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.0?(1)		endometrium(1)|kidney(1)|ovary(1)	3						tcagcctcccaagtagctggg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK123764	CCDS10548.1	16p13.13	2013-06-10	2013-06-10	2011-06-09	ENSG00000175643	ENSG00000175643	116028			28349	protein-coding gene	gene with protein product		612426	chromosome 16 open reading frame 75, RMI2, RecQ mediated genome instability 2, homolog (S. cerevisiae)	C16orf75	NA	18923083, 20826341	Standard	NM_152308	NM_152308	NA	Approved	MGC24665, BLAP18	uc002daw.1	Q96E14	OTTHUMG00000129793	ENST00000572173.1:c.106+12792A>G	chr16.hg19:g.11423533A>G		NA	B3KVZ6|Q49AE2|Q8TBL0	hg19		0.02	-0.078882	CCCxAGT	UNCOVERED																																																																																			NOVEL	RMI2-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000436708.1	4	2.707118	KEEP	2	0	0	9	251	AA	0.99254	0.076759	0		+	3	60	90	0	0	7.944363	6	60	157	27	ENST00000572173.1	0.333333	0.077336
RMI2	116028	__UNKNOWN__	__UNKNOWN__	16	11424362	11424362	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:11424362T>C	ENST00000572173.1	+	4	751				RMI2_ENST00000381820.2_Intron			Q96E14	RMI2_HUMAN	RecQ mediated genome instability 2	NA		NA			DNA replication (GO:0006260)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.0?(1)		endometrium(1)|kidney(1)|ovary(1)	3						gggttacaggtgtgagccact	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK123764	CCDS10548.1	16p13.13	2013-06-10	2013-06-10	2011-06-09	ENSG00000175643	ENSG00000175643	116028			28349	protein-coding gene	gene with protein product		612426	chromosome 16 open reading frame 75, RMI2, RecQ mediated genome instability 2, homolog (S. cerevisiae)	C16orf75	NA	18923083, 20826341	Standard	NM_152308	NM_152308	NA	Approved	MGC24665, BLAP18	uc002daw.1	Q96E14	OTTHUMG00000129793	ENST00000572173.1:c.106+13621T>C	chr16.hg19:g.11424362T>C		NA	B3KVZ6|Q49AE2|Q8TBL0	hg19		0.02	-0.201722	AGGxGTG	COVERED																																																																																			NOVEL	RMI2-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000436708.1	8	2.405574	KEEP	0	0	0	8	215	TT	0.99257	0.4869	0		+	4	60	124	0	0	9.779779	18	60	526	43	ENST00000572173.1	0.181818	0.490544
RP11-166B2.1	0	__UNKNOWN__	__UNKNOWN__	16	12037584	12037584	__UNKNOWN__	Intron	SNP	G	G	A	rs190972529		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:12037584G>A	ENST00000532936.1	-	4	306										NA		NA								lung(2)	2						agccaggcacggtggctcatg	0.542		NA											g|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16768	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000532936.1:c.269-6059C>T	chr16.hg19:g.12037584G>A		NA		hg19		0.02	-0.201699	CACxGTG	UNCOVERED																																																																																			NOVEL	RP11-166B2.1-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000388782.1	8	2.406276	KEEP	4	0	0	8	228	GG	0	0	0		-	3	60	90	0	0	6.833889	16	60	508	48	ENST00000532936.1	0.157895	0.490544
SNX29	92017	__UNKNOWN__	__UNKNOWN__	16	12130241	12130241	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:12130241G>C	ENST00000566228.1	+	5	316					NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	NA		NA				extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						gcccaggctggagtgcagtgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471	92017		Sorting nexins	30542	protein-coding gene	gene with protein product		NA	RUN domain containing 2A	RUNDC2A	NA	16782399	Standard		XM_005255682	NA	Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.248-6513G>C	chr16.hg19:g.12130241G>C		NA	B5MDW2|Q8N2X2|Q9HA26	hg19	CCDS10553.2	0.02	-0.12281	CTGxAGT	COVERED																																																																																			NOVEL	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422622.1	5	2.407306	KEEP	1	0	0	8	250	AG	0.99254	0.194847	0		+	3	60	100	0	0	8.381817	10	60	329	29	ENST00000566228.1	0.230769	0.196312
SNX29	92017	__UNKNOWN__	__UNKNOWN__	16	12146294	12146294	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:12146294A>G	ENST00000566228.1	+	8	1193				SNX29_ENST00000323433.4_Intron|SNX29_ENST00000306030.3_Intron	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	NA		NA				extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						ggctggtctcaaactcctgac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471	92017		Sorting nexins	30542	protein-coding gene	gene with protein product		NA	RUN domain containing 2A	RUNDC2A	NA	16782399	Standard		XM_005255682	NA	Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1124+215A>G	chr16.hg19:g.12146294A>G		NA	B5MDW2|Q8N2X2|Q9HA26	hg19	CCDS10553.2	0.02	-0.324471	CTCxAAC	COVERED																																																																																			NOVEL	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422622.1	7	3.440457	KEEP	2	1	24	20	554	AA	0.999863	0.835601	0		+	3	60	95	0	0	6.698716	27	60	794	67	ENST00000566228.1	0.1	0.835716
SNX29	92017	__UNKNOWN__	__UNKNOWN__	16	12147066	12147066	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:12147066C>G	ENST00000566228.1	+	8	1193				SNX29_ENST00000323433.4_Intron|SNX29_ENST00000306030.3_Intron	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	NA		NA				extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						gcaggagaatcgcttgaatat	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471	92017		Sorting nexins	30542	protein-coding gene	gene with protein product		NA	RUN domain containing 2A	RUNDC2A	NA	16782399	Standard		XM_005255682	NA	Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1124+987C>G	chr16.hg19:g.12147066C>G		NA	B5MDW2|Q8N2X2|Q9HA26	hg19	CCDS10553.2	0.02	1.411885	AATxGCT	COVERED																																																																																			NOVEL	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422622.1	48	16.507146	KEEP	0	2	51	73	2094	CC	1	0.999962	0		+	4	60	140	0	0	8.80566	86	60	2707	207	ENST00000566228.1	0.044444	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	12973384	12973384	__UNKNOWN__	IGR	SNP	C	C	T	rs149541178	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:12973384C>T			NA	NA				SNORA27 (36917 upstream) : SHISA9 (22092 downstream)						NA		NA									NA						gatctgcctgccttggcctcc	0.507		NA											C|||	23	0.00459265	0.0	0.0058	5008	,	,	NA	17651	0.0	NA	0.0109	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.12973384C>T		NA		hg19		0.02	-0.140349	CTGxCTT	COVERED																																																																																			NOVEL					0			11	3.309819	KEEP	4	0	0	11	336	CC	0.99254	0.259018	0			6	60	177	0	0	16.40919	8	60	276	44		0.428571	0.260965
U91319.1	0	__UNKNOWN__	__UNKNOWN__	16	13614194	13614194	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:13614194C>T	ENST00000571619.1	+	0	552										NA		NA									NA						tggtggctcacgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000571619.1:	chr16.hg19:g.13614194C>T		NA		hg19		0.02	-0.175436	TCAxGCC	COVERED																																																																																			NOVEL	U91319.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000436324.1	8	2.706897	KEEP	0	0	0	9	252	CC	0.99254	0.384517	0		+	3	60	90	0	0	6.833728	16	60	529	39	ENST00000571619.1	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	13812308	13812308	__UNKNOWN__	IGR	SNP	G	G	T	rs139776700	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:13812308G>T			NA	NA				U91319.1 (155533 upstream) : U95743.1 (11685 downstream)						NA		NA									NA						ctcccaaagtgctgggattac	0.388		NA											G|||	354	0.0706869	0.0068	0.0403	5008	,	,	NA	17393	0.0655	NA	0.0924	False	NA	,,,	NA	NA	NA	2504	0.1616	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.13812308G>T		NA		hg19		0.02	-0.122808	AGTxCTG	COVERED																																																																																			NOVEL					0			9	3.309762	KEEP	1	0	0	11	333	GG	0.992708	0.19488	0			4	60	120	0	0	10.776595	7	60	237	33		0.363636	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	13976657	13976657	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:13976657T>C			NA	NA				U95743.1 (103052 upstream) : ERCC4 (37356 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.13976657T>C		NA		hg19		0.02	-0.175419	AATxCCA	COVERED																																																																																			NOVEL					0			8	3.007059	KEEP	0	0	0	10	270	TT	0.992708	0.384582	0			4	60	134	0	0	11.16839	14	60	422	41		0.222222	0.387407
ERCC4	2072	__UNKNOWN__	__UNKNOWN__	16	14027048	14027048	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:14027048G>A	ENST00000311895.7	+	6	1111				CTD-2135D7.2_ENST00000570663.1_RNA|CTD-2135D7.2_ENST00000575137.1_RNA|ERCC4_ENST00000575156.1_3'UTR	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	NA		NA			DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						ctatactccagcctgggtgac	0.403		NA	Mis, N, F			skin basal cell, skin squamous cell, melanoma		Nucleotide excision repair (NER)	Xeroderma Pigmentosum												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	excision repair cross-complementing rodent repair deficiency, complementation group 4		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595	2072			3436	protein-coding gene	gene with protein product	xeroderma pigmentosum, complementation group F	133520	excision repair cross-complementing rodent repair deficiency, complementation group 4	XPF	NA	9579555, 8887684	Standard	NM_005236	NM_005236	NA	Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.1102+906G>A	chr16.hg19:g.14027048G>A		NA	A5PKV6|A8K111|O00140|Q8TD83	hg19	CCDS32390.1	0.02	0.929826	CCAxCCT	COVERED																																																																																			NOVEL	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109634.2	12	8.698156	KEEP	0	0	0	29	828	GG	0.999997	0.9937	0		+	5	60	132	0	0	8.087874	56	60	1894	114	ENST00000311895.7	0.081967	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	14156017	14156017	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:14156017A>T			NA	NA				CTD-2135D7.4 (41083 upstream) : MKL2 (9161 downstream)						NA		NA									NA						tggcacaatcacagctcactg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.14156017A>T		NA		hg19		0.02	-0.166638	ATCxCAG	COVERED																																																																																			NOVEL					0			9	2.406173	KEEP	2	0	0	8	222	AA	0.99257	0.351317	0			3	33	94	0	0	7.391956	14	60	415	40		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	14465447	14465447	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:14465447C>T			NA	NA				RP11-65J21.1 (1324 upstream) : RP11-65J21.4 (36448 downstream)						NA		NA									NA						gtcaggagttcgagaccagcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.14465447C>T		NA		hg19		0.02	-0.131566	GTTxGAG	COVERED																																																																																			NOVEL					0			7	3.607521	KEEP	1	0	0	12	323	CC	0.993072	0.227586	0			3	60	89	0	0	7.072423	12	60	370	36		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	14481243	14481243	__UNKNOWN__	IGR	SNP	G	G	A	rs549621871	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:14481243G>A			NA	NA				RP11-65J21.1 (17120 upstream) : RP11-65J21.4 (20652 downstream)						NA		NA									NA						gcttgaacccgggaggcagag	0.512		NA											G|||	7	0.00139776	0.0038	0.0	5008	,	,	NA	16163	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.14481243G>A		NA		hg19		0.02	-0.09649	CCCxGGA	UNCOVERED																																																																																			NOVEL					0			5	2.406039	KEEP	0	0	0	8	223	GG	0.99257	0.119541	0			3	60	90	0	0	7.778375	7	60	228	27		0.3	0.120436
PLA2G10	8399	__UNKNOWN__	__UNKNOWN__	16	14779608	14779608	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:14779608A>G	ENST00000438167.3	-	3	795					NM_003561.1	NP_003552.1	O15496	PA2GX_HUMAN	phospholipase A2, group X	NA		NA			arachidonic acid metabolic process (GO:0019369)|axon guidance (GO:0007411)|cholesterol homeostasis (GO:0042632)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|lysophospholipid transport (GO:0051977)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of prostaglandin secretion (GO:0032308)|regulation of macrophage activation (GO:0043030)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)|phospholipase activity (GO:0004620)				NA						ctggagtgcaatggtgcagtc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U95301	CCDS10555.1	16p13.1-p12	2008-09-19			ENSG00000069764	ENSG00000069764	8399	3.1.1.4		9029	protein-coding gene	gene with protein product		603603			NA	9188469	Standard	NM_003561	NM_003561	NA	Approved	GXPLA2	uc002dcq.3	O15496	OTTHUMG00000048069	ENST00000438167.3:c.355+2413T>C	chr16.hg19:g.14779608A>G		NA	Q14DU3|Q6NT23	hg19	CCDS10555.1	0.02	-0.096477	GCAxTGG	UNCOVERED																																																																																			NOVEL	PLA2G10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109393.3	5	2.405756	KEEP	0	0	0	8	217	AA	0.99257	0.119541	0		-	3	60	106	0	0	9.23271	8	60	231	25	ENST00000438167.3	0.272727	0.120436
NOMO1	23420	__UNKNOWN__	__UNKNOWN__	16	14931158	14931158	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:14931158G>A	ENST00000287667.7	+	2	336					NM_014287.3	NP_055102.3	Q15155	NOMO1_HUMAN	NODAL modulator 1	NA		NA				integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(6)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|skin(2)	30						gagccaccatgcctggccGCA	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X57398	CCDS10556.1	16p13.11	2008-02-05			ENSG00000103512	ENSG00000103512	23420			30060	protein-coding gene	gene with protein product		609157			NA	1310294, 15257293	Standard		NM_014287	NA	Approved	PM5	uc002dcv.3	Q15155	OTTHUMG00000090541	ENST00000287667.7:c.166-1106G>A	chr16.hg19:g.14931158G>A		NA	P78421|Q8IW21|Q96DG0	hg19	CCDS10556.1	0.02	-0.29821	CATxCCT	COVERED																																																																																			NOVEL	NOMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207065.1	3	3.309484	KEEP	0	0	0	11	329	GG	0.993072	0.775649	0		+	4	25	107	0	0	7.268378	30	60	981	55	ENST00000287667.7	0.117647	0.78106
NTAN1	123803	__UNKNOWN__	__UNKNOWN__	16	15138715	15138715	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:15138715C>A	ENST00000287706.3	-	5	452				PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	NA		NA			adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						cagtggctcacgcctgtaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045	123803			29909	protein-coding gene	gene with protein product		615367			NA	8910481	Standard	NM_173474	NM_173474	NA	Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.360-451G>T	chr16.hg19:g.15138715C>A		NA	Q7Z4Z0	hg19	CCDS10558.1	0.02	-0.210306	TCAxGCC	COVERED																																																																																			NOVEL	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252089.1	18	2.939023	KEEP	9	1	26	19	537	CC	0.999859	0.55281	0		-	4	48	118	0	0	9.097061	19	60	599	73	ENST00000287706.3	0.173913	0.552887
RRN3	54700	__UNKNOWN__	__UNKNOWN__	16	15158751	15158751	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:15158751C>T	ENST00000198767.6	-	16	1790				RRN3_ENST00000429751.2_Intron|RRN3_ENST00000563559.1_Intron|RRN3_ENST00000540462.1_Intron|RRN3_ENST00000327307.7_Intron|PDXDC1_ENST00000535621.2_Intron	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	NA		NA			cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						Tggccgggcgcggtggctcac	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721	54700			30346	protein-coding gene	gene with protein product		605121	RRN3 RNA polymerase I transcription factor homolog (yeast)		NA	10758157, 11250903	Standard	NM_018427	XM_005255375	NA	Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.1706+324G>A	chr16.hg19:g.15158751C>T		NA	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	hg19	CCDS10559.1	0.02	-0.298248	GCGxGGT	COVERED																																																																																			NOVEL	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252087.2	9	6.017351	KEEP	4	0	0	20	602	CC	0.999859	0.78095	0		-	4	40	116	0	0	8.334538	27	60	918	85	ENST00000198767.6	0.129032	0.78106
C16orf45	89927	__UNKNOWN__	__UNKNOWN__	16	15628197	15628197	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:15628197C>T	ENST00000566490.1	+	2	409				C16orf45_ENST00000300006.4_Intron|C16orf45_ENST00000561692.1_Intron|C16orf45_ENST00000452191.2_Intron			Q96MC5	CP045_HUMAN	chromosome 16 open reading frame 45	NA		NA								endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)	11						cggtggctcacgtctgtaatc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057180	CCDS10561.1, CCDS45422.1	16p13.2	2012-10-09			ENSG00000166780	ENSG00000166780	89927			19213	protein-coding gene	gene with protein product		NA			NA		Standard	NM_033201	NM_033201	NA	Approved	FLJ32618	uc002ddo.3	Q96MC5	OTTHUMG00000129883	ENST00000566490.1:c.230+18912C>T	chr16.hg19:g.15628197C>T		NA	O00223|O75769|Q8IZ36|Q96H25	hg19		0.02	-0.122793	TCAxGTC	COVERED																																																																																			NOVEL	C16orf45-004	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000422455.1	9	4.208678	KEEP	2	0	0	14	377	CC	0.993634	0.195062	0		+	3	60	81	0	0	6.732123	8	60	255	38	ENST00000566490.1	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	16003988	16003988	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:16003988C>T			NA	NA				FOPNL (21506 upstream) : ABCC1 (39445 downstream)						NA		NA									NA						aggctggtctcgaacttctga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.16003988C>T		NA		hg19		0.02	-0.157878	TCTxGAA	COVERED																																																																																			NOVEL					0			10	3.008943	KEEP	0	0	0	10	304	CC	0.992708	0.320453	0			3	60	93	0	0	7.210361	15	60	471	39		0.166667	0.322807
ABCC1	4363	__UNKNOWN__	__UNKNOWN__	16	16209799	16209799	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:16209799G>A	ENST00000399410.3	+	23	3565				ABCC1_ENST00000349029.5_Intron|ABCC1_ENST00000346370.5_Intron|ABCC1_ENST00000399408.2_Intron|ABCC1_ENST00000351154.5_Intron|ABCC1_ENST00000345148.5_Intron	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	NA		NA			arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	tcgctctgtcgcccaggctgg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222	4363		ATP binding cassette transporters / subfamily C	51	protein-coding gene	gene with protein product		158343	multidrug resistance associated protein 1	MRP, MRP1	NA	8098549, 1360704	Standard	NM_004996	NM_004996	NA	Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.3390+866G>A	chr16.hg19:g.16209799G>A		NA	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	hg19	CCDS42122.1	0.02	-0.149064	GTCxCCC	COVERED																																																																																			NOVEL	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109701.1	8	3.007657	KEEP	2	0	0	10	287	GG	0.99254	0.289823	0		+	3	60	88	0	0	6.792621	14	60	448	36	ENST00000399410.3	0.176471	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	16591199	16591199	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:16591199C>T			NA	NA				NPIPA7 (103388 upstream) : RN7SL90P (139912 downstream)						NA		NA									NA						ttttttgagacggagtttcgc	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.16591199C>T		NA		hg19		0.02	-0.166298	AGAxGGA	UNCOVERED																																																																																			NOVEL					0			10	2.405606	KEEP	6	0	0	8	222	CC	0	0	0			3	49	94	0	0	7.236758	16	43	457	46		0.157895	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	17075029	17075029	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:17075029T>C			NA	NA				RP11-14N9.2 (317037 upstream) : XYLT1 (120596 downstream)						NA		NA									NA						gagacggagtttcgctcttgt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.17075029T>C		NA		hg19		0.02	-0.438484	AGTxTCG	COVERED																																																																																			NOVEL					0			10	5.111672	KEEP	0	0	0	17	451	TT	0.999366	0.959251	0			3	60	98	0	0	6.389875	44	60	1264	101		0.06383	0.959859
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	17932313	17932313	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:17932313A>G			NA	NA				CTD-3229J4.1 (11550 upstream) : CTA-481E9.4 (128936 downstream)						NA		NA									NA						ctgggcaacaaagtgagactc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.17932313A>G		NA		hg19		0.02	-0.052618	ACAxAGT	UNCOVERED																																																																																			NOVEL					0			6	2.405238	KEEP	1	0	0	8	214	AA	0.99257	0.036492	0			2	60	71	0	0	6.396138	4	60	113	19		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	18448311	18448311	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:18448311T>C			NA	NA				NPIPA8 (7180 upstream) : RP11-1212A22.4 (3631 downstream)						NA		NA									NA						gtaatcccagtactttgggag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.18448311T>C		NA		hg19		0.02	-0.271883	CAGxACT	COVERED																																																																																			NOVEL					0			14	3.005674	KEEP	5	0	0	10	257	TT	0.99254	0.734154	0			4	44	139	0	0	10.822799	24	60	697	70		0.142857	0.739671
NOMO2	283820	__UNKNOWN__	__UNKNOWN__	16	18532173	18532173	__UNKNOWN__	Silent	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:18532173A>G	ENST00000330537.6	-	19	2357	c.2187T>C	c.(2185-2187)ggT>ggC	p.G729G	NOMO2_ENST00000381474.3_Silent_p.G729G|NOMO2_ENST00000543392.1_Silent_p.G562G	NM_173614.2	NP_775885.1	Q5JPE7	NOMO2_HUMAN	NODAL modulator 2	729		NA				endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(4)|kidney(1)|large_intestine(2)|liver(3)|lung(5)|ovary(3)|prostate(1)|skin(1)	20						TTCTTTCTTCACCTTCCTCAT	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													284	288	287			NA	NA	16		NA											NA				18532173		2196	4298	6494	SO:0001819	synonymous_variant			AL512687	CCDS10570.1, CCDS32394.1	16p12.3	2008-02-05			ENSG00000185164	ENSG00000185164	283820			22652	protein-coding gene	gene with protein product		609158			NA	15257293	Standard	NM_001004060	NM_001004060	NA	Approved	NOMO, PM5	uc002dfe.3	Q5JPE7	OTTHUMG00000131366	ENST00000330537.6:c.2187T>C	chr16.hg19:g.18532173A>G		NA	Q4G177	hg19	CCDS10570.1	0.02	-0.201719	TTCxCCT	UNCOVERED																																																																																			NOVEL	NOMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254155.1	1	2.406001	KEEP	24	0	0	8	220	AA	0	0	0		-	3	27	90	0	0	6.566042	20	48	597	56	ENST00000330537.6	0.130435	0.490544
SMG1	23049	__UNKNOWN__	__UNKNOWN__	16	18879282	18879282	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:18879282T>A	ENST00000446231.2	-	22	3608				SMG1_ENST00000389467.3_Intron			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	NA		NA			DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						cgcccacctctgcctcccaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106	23049			30045	protein-coding gene	gene with protein product	phosphatidylinositol 3-kinase-related kinase	607032	smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)		NA	9455477, 11331269, 17229728	Standard	NM_015092	NM_015092	NA	Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.3195+229A>T	chr16.hg19:g.18879282T>A		NA	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	hg19	CCDS45430.1	0.02	-0.131564	CTCxGCC	UNCOVERED																																																																																			NOVEL	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391817.1	5	2.707472	KEEP	9	0	0	9	259	TT	0	0	0		-	3	60	94	0	0	7.901173	9	60	271	43	ENST00000446231.2	0.25	0.229173
SMG1	23049	__UNKNOWN__	__UNKNOWN__	16	18921680	18921680	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:18921680A>G	ENST00000446231.2	-	2	505				SMG1_ENST00000389467.3_Intron			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	NA		NA			DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						agcctcccaaatagctgggat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106	23049			30045	protein-coding gene	gene with protein product	phosphatidylinositol 3-kinase-related kinase	607032	smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)		NA	9455477, 11331269, 17229728	Standard	NM_015092	NM_015092	NA	Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.93-13402T>C	chr16.hg19:g.18921680A>G		NA	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	hg19	CCDS45430.1	0.02	-0.149087	CAAxTAG	UNCOVERED																																																																																			NOVEL	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000391817.1	9	2.705145	KEEP	5	0	0	9	237	AA	0	0	0		-	4	40	128	0	0	11.391531	8	60	236	40	ENST00000446231.2	0.333333	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	18966375	18966375	__UNKNOWN__	IGR	SNP	G	G	A	rs28380402	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:18966375G>A			NA	NA				CTD-2288F12.1 (18010 upstream) : TMC7 (28880 downstream)						NA		NA									NA						agaccagcctggccaacatgg	0.537		NA											G|||	2671	0.533347	0.4327	0.487	5008	,	,	NA	19176	0.6845	NA	0.5746	False	NA	,,,	NA	NA	NA	2504	0.5041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.18966375G>A		NA		hg19		0.02	-0.087709	CCTxGCC	UNCOVERED																																																																																			NOVEL					0			9	3.911884	KEEP	5	0	0	13	406	GG	0.992708	0.098994	0			3	60	82	0	0	7.142734	6	60	198	34		0.333333	0.099721
TMC7	79905	__UNKNOWN__	__UNKNOWN__	16	19056804	19056804	__UNKNOWN__	Intron	SNP	T	T	C	rs553652412		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19056804T>C	ENST00000304381.5	+	11	1683				TMC7_ENST00000421369.3_Intron|TMC7_ENST00000569532.1_Intron	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	NA		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						ACcacacacatgcacacacac	0.502		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16923	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													56	46	49			NA	NA	16		NA											NA				19056804		2197	4300	6497	SO:0001627	intron_variant			AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537	79905			23000	protein-coding gene	gene with protein product		NA			NA	12812529, 12906855	Standard	NM_024847	XM_005255597	NA	Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1553+44T>C	chr16.hg19:g.19056804T>C		NA	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	hg19	CCDS10573.1	0.02	-0.157826	ACAxGCA	COVERED																																																																																			NOVEL	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254276.3	2	3.274307	KEEP	0	0	0	11	290	TT	0.993072	0.32057	0		+	3	60	100	1	0	7.992307	14	60	398	40	ENST00000304381.5	0.176471	0.322807
TMC7	79905	__UNKNOWN__	__UNKNOWN__	16	19059301	19059301	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19059301G>A	ENST00000304381.5	+	12	1870				TMC7_ENST00000421369.3_Intron|TMC7_ENST00000569532.1_Intron	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	NA		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						gattacaggcgtgagccaccg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537	79905			23000	protein-coding gene	gene with protein product		NA			NA	12812529, 12906855	Standard	NM_024847	XM_005255597	NA	Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1740+730G>A	chr16.hg19:g.19059301G>A		NA	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	hg19	CCDS10573.1	0.02	-0.184208	GGCxTGA	COVERED																																																																																			NOVEL	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254276.3	7	2.407141	KEEP	2	0	0	8	244	GG	0.99257	0.420331	0		+	3	60	90	0	0	6.761236	17	60	544	43	ENST00000304381.5	0.15	0.423478
TMC7	79905	__UNKNOWN__	__UNKNOWN__	16	19064787	19064787	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19064787G>A	ENST00000304381.5	+	13	2001				TMC7_ENST00000421369.3_Intron|TMC7_ENST00000569532.1_Intron	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	NA		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						gtgcagtggcgcgatcttggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537	79905			23000	protein-coding gene	gene with protein product		NA			NA	12812529, 12906855	Standard	NM_024847	XM_005255597	NA	Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1871+1649G>A	chr16.hg19:g.19064787G>A		NA	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	hg19	CCDS10573.1	0.02	-0.17544	GGCxCGA	COVERED																																																																																			NOVEL	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254276.3	11	5.416156	KEEP	8	0	0	18	555	GG	0.997832	0.386567	0		+	3	60	90	0	0	7.078876	13	60	438	69	ENST00000304381.5	0.1875	0.387407
TMC7	79905	__UNKNOWN__	__UNKNOWN__	16	19070479	19070479	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19070479T>C	ENST00000304381.5	+	15	2157				TMC7_ENST00000421369.3_Intron|TMC7_ENST00000569532.1_Intron	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	NA		NA			ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						ggattacaggtgtgagccact	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537	79905			23000	protein-coding gene	gene with protein product		NA			NA	12812529, 12906855	Standard	NM_024847	XM_005255597	NA	Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.2028-259T>C	chr16.hg19:g.19070479T>C		NA	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	hg19	CCDS10573.1	0.02	-0.298067	AGGxGTG	COVERED																																																																																			NOVEL	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254276.3	9	3.907599	KEEP	2	0	0	13	353	TT	0.993634	0.795151	0		+	3	60	92	0	0	6.354811	28	60	777	71	ENST00000304381.5	0.096774	0.800245
ITPRIPL2	162073	__UNKNOWN__	__UNKNOWN__	16	19126487	19126487	__UNKNOWN__	Missense_Mutation	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19126487C>A	ENST00000381440.3	+	1	1234	c.704C>A	c.(703-705)gCc>gAc	p.A235D	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	235		NA				integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TTTGCTGATGCCTTCTGCGTG	0.657		NA									OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)									NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													71	76	74			NA	NA	16		NA											NA				19126487		2197	4300	6497	SO:0001583	missense				CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730	162073			27257	protein-coding gene	gene with protein product		NA	inositol 1,4,5-triphosphate receptor interacting protein-like 2		NA		Standard	NM_001034841	NM_001034841	NA	Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.704C>A	chr16.hg19:g.19126487C>A	ENSP00000370849:p.Ala235Asp	730		hg19	CCDS32395.1	0.02	4.455864	ATGxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	6.241	0.412514	0.11812	.	.	ENSG00000205730	ENST00000381440	T	0.14640	2.49	4.71	1.48	0.22813	.	1.068630	0.07462	U	0.900886	T	0.06781	0.0173	N	0.08118	0	0.24836	N	0.992499	B	0.16166	0.016	B	0.12156	0.007	T	0.42582	-0.9443	10	0.12103	T	0.63	-2.7195	8.4746	0.33005	0.0834:0.301:0.6155:0.0	.	235	Q3MIP1	IPIL2_HUMAN	D	235	ENSP00000370849:A235D	ENSP00000370849:A235D	A	+	2	0	ITPRIPL2	19033988	0.999000	0.42202	0.966000	0.40874	0.983000	0.72400	1.958000	0.40402	0.355000	0.24131	-0.147000	0.13772	GCC	NOVEL	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435827.3	4	16.546895	KEEP	0	0	0	55	1654	CC	1	1	0		+	56	60	1603	0	0	139.873318	116	60	4012	317	ENST00000381440.3	0.325581	1
TMC5	79838	__UNKNOWN__	__UNKNOWN__	16	19470996	19470996	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19470996C>T	ENST00000541464.1	+	6	1590				TMC5_ENST00000542583.2_Intron|TMC5_ENST00000564959.1_Intron|TMC5_ENST00000219821.5_Intron|TMC5_ENST00000381414.4_Intron|TMC5_ENST00000396229.2_Intron|TMC5_ENST00000561503.1_Intron			Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	NA		NA			ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						cccagctactctggaggctga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534	79838			22999	protein-coding gene	gene with protein product		NA			NA	12812529, 12906855	Standard	NM_024780	NM_024780	NA	Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000541464.1:c.1049-561C>T	chr16.hg19:g.19470996C>T		NA	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	hg19		0.02	-0.236855	ACTxTGG	COVERED																																																																																			NOVEL	TMC5-007	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000435887.1	12	4.212408	KEEP	2	0	0	14	424	CC	0.994391	0.608972	0		+	4	60	117	1	0	8.836644	21	60	723	54	ENST00000541464.1	0.16	0.612407
C16orf62	57020	__UNKNOWN__	__UNKNOWN__	16	19615324	19615324	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19615324T>G	ENST00000438132.3	+	9	1099				C16orf62_ENST00000448695.1_Intron|C16orf62_ENST00000538853.1_Intron|C16orf62_ENST00000417362.2_Intron|C16orf62_ENST00000251143.5_Intron|C16orf62_ENST00000542263.1_Intron|C16orf62_ENST00000543152.1_Intron	NM_020314.5	NP_064710.4	Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	NA		NA				integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						aaagtgctggtattacaggca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544	57020			24641	protein-coding gene	gene with protein product		NA			NA	10493829	Standard	NM_020314	NM_020314	NA	Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000438132.3:c.1051+2279T>G	chr16.hg19:g.19615324T>G		NA	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	hg19	CCDS32397.2	0.02	-0.131565	TGGxATT	COVERED																																																																																			NOVEL	C16orf62-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397058.2	8	2.405894	KEEP	0	0	0	8	216	TT	0.99257	0.259026	0		+	3	60	101	0	0	8.601218	9	60	268	30	ENST00000438132.3	0.25	0.260965
C16orf62	57020	__UNKNOWN__	__UNKNOWN__	16	19627019	19627019	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:19627019T>A	ENST00000438132.3	+	13	1338				C16orf62_ENST00000448695.1_Intron|C16orf62_ENST00000417362.2_Intron|C16orf62_ENST00000251143.5_Intron|C16orf62_ENST00000542263.1_Intron|C16orf62_ENST00000543152.1_Intron	NM_020314.5	NP_064710.4	Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	NA		NA				integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						ggccgggcgctgtggctcaca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544	57020			24641	protein-coding gene	gene with protein product		NA			NA	10493829	Standard	NM_020314	NM_020314	NA	Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000438132.3:c.1291-417T>A	chr16.hg19:g.19627019T>A		NA	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	hg19	CCDS32397.2	0.02	-0.254326	CGCxGTG	COVERED																																																																																			NOVEL	C16orf62-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397058.2	10	3.909341	KEEP	1	0	0	13	354	GT	0.995343	0.713975	0		+	3	60	92	0	0	6.543481	24	60	708	64	ENST00000438132.3	0.111111	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	20418121	20418121	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:20418121G>A			NA	NA				PDILT (2062 upstream) : ACSM5 (2734 downstream)						NA		NA									NA						gattacaggcgtgagccactg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.20418121G>A		NA		hg19		0.02	-0.122811	GGCxTGA	COVERED																																																																																			NOVEL					0			5	3.309968	KEEP	1	0	0	11	343	GG	0.993072	0.194952	0			3	60	93	0	0	7.681806	10	60	331	42		0.230769	0.196312
AC004381.6	0	__UNKNOWN__	__UNKNOWN__	16	20839988	20839988	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:20839988T>C	ENST00000261377.6	+	11	1367				AC004381.6_ENST00000564274.1_Intron|AC004381.6_ENST00000348433.6_Intron|ERI2_ENST00000564349.1_Intron	NM_001199053.1|NM_030941.2	NP_001185982.1|NP_112203.2				NA		NA									NA						cagtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000261377.6:c.1158+129T>C	chr16.hg19:g.20839988T>C		NA		hg19	CCDS10591.1	0.02	-0.297469	TCAxGCC	COVERED																																																																																			NOVEL	AC004381.6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254418.2	13	4.511548	KEEP	3	0	0	15	417	TT	0.995343	0.777423	0		+	3	60	98	0	0	7.002113	27	60	779	72	ENST00000261377.6	0.1	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	21519540	21519540	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:21519540A>G			NA	NA				MIR3680-1 (2084 upstream) : SCARNA6 (79407 downstream)						NA		NA									NA						ttttgagacgaagtctccctc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.21519540A>G		NA		hg19		0.02	-0.140331	ACGxAGT	COVERED																																																																																			NOVEL					0			10	3.608189	KEEP	0	0	0	12	320	AA	0.993634	0.259304	0			3	60	92	0	0	7.473075	11	60	325	42		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	21557786	21557786	__UNKNOWN__	IGR	SNP	C	C	G	rs62044168		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:21557786C>G			NA	NA				MIR3680-1 (40330 upstream) : SCARNA6 (41161 downstream)						NA		NA									NA						cggtgattcacgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.21557786C>G		NA		hg19		0.02	-0.131587	TCAxGCC	COVERED																																																																																			NOVEL					0			6	3.308886	KEEP	8	0	0	11	316	CC	0.99254	0.259018	0			5	49	174	0	0	15.639226	10	50	332	48		0.333333	0.260965
RP11-101E7.2	0	__UNKNOWN__	__UNKNOWN__	16	22102990	22102990	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:22102990A>G	ENST00000568603.1	-	0	24										NA		NA									NA						gggattacagacatgagccac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000568603.1:	chr16.hg19:g.22102990A>G		NA		hg19		0.02	-0.149055	CAGxCAT	COVERED																																																																																			NOVEL	RP11-101E7.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000430046.1	7	2.704694	KEEP	0	0	0	9	225	AA	0.99254	0.320398	0		-	3	60	100	0	1	8.079436	13	60	352	36	ENST00000568603.1	0.1875	0.322807
VWA3A	146177	__UNKNOWN__	__UNKNOWN__	16	22129993	22129993	__UNKNOWN__	Intron	SNP	C	C	T	rs188128967	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:22129993C>T	ENST00000389398.5	+	12	1086				VWA3A_ENST00000389397.4_Intron	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	NA		NA				extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		ggtgacagagcgagactccat	0.562		NA											c|||	26	0.00519169	0.0	0.0346	5008	,	,	NA	16925	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267	146177			27088	protein-coding gene	gene with protein product		NA			NA	12477932	Standard		XM_006721021	NA	Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.991-230C>T	chr16.hg19:g.22129993C>T		NA	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	hg19	CCDS45441.1	0.02	-0.184201	GAGxGAG	COVERED																																																																																			NOVEL	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000430052.1	11	3.008352	KEEP	1	0	0	10	295	CC	0.992708	0.42039	0		+	3	60	91	0	0	7.010388	15	60	481	44	ENST00000389398.5	0.166667	0.423478
RP11-368J21.3	0	__UNKNOWN__	__UNKNOWN__	16	22581407	22581407	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:22581407T>C	ENST00000550753.1	+	0	2211					NR_003676.2					NA		NA									NA						gtaatcccagttacttgggag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000550753.1:	chr16.hg19:g.22581407T>C		NA		hg19		0.02	-0.078938	CAGxTAC	UNCOVERED																																																																																			NOVEL	RP11-368J21.3-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000409041.1	8	2.405843	KEEP	14	0	0	8	218	TT	0	0	0		+	3	27	99	0	0	9.032917	5	50	156	36	ENST00000550753.1	0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	22663463	22663463	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:22663463T>C			NA	NA				RN7SL245P (15398 upstream) : HS3ST2 (162034 downstream)						NA		NA									NA						gcctgtaatctcagcactttg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.22663463T>C		NA		hg19		0.02	-0.219279	ATCxCAG	COVERED																																																																																			NOVEL					0			17	4.812356	KEEP	6	0	0	16	443	TT	0.995343	0.550313	0			3	60	103	0	0	7.864646	20	60	608	59		0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	22666488	22666488	__UNKNOWN__	IGR	SNP	C	C	T	rs562205345	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:22666488C>T			NA	NA				RN7SL245P (18423 upstream) : HS3ST2 (159009 downstream)						NA		NA									NA						ctcggcctcccgaagggctgg	0.498		NA											C|||	25	0.00499201	0.0174	0.0029	5008	,	,	NA	34347	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.22666488C>T		NA		hg19		0.02	-0.245605	TCCxGAA	COVERED																																																																																			NOVEL					0			11	6.317841	KEEP	0	0	0	21	624	CC	0.999869	0.641263	0			3	60	91	0	0	6.665442	20	60	668	72		0.130435	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	22700688	22700688	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:22700688T>C			NA	NA				RN7SL245P (52623 upstream) : HS3ST2 (124809 downstream)						NA		NA									NA						aactcctgacttcaagtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.22700688T>C		NA		hg19		0.02	-0.140345	GACxTCA	UNCOVERED																																																																																			NOVEL					0			8	2.406196	KEEP	3	0	0	8	221	TT	0	0	0			3	60	104	0	0	8.901158	9	60	273	38		0.25	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	23012061	23012061	__UNKNOWN__	IGR	SNP	C	C	T	rs11642173	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23012061C>T			NA	NA				HS3ST2 (84402 upstream) : RP11-20G6.2 (19596 downstream)						NA		NA									NA						tatgattgtaccactgcactc	0.493		NA											C|||	2975	0.59405	0.8464	0.4611	5008	,	,	NA	13966	0.2302	NA	0.5656	False	NA	,,,	NA	NA	NA	2504	0.7515	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.23012061C>T		NA		hg19		0.02	-0.061399	GTAxCAC	UNCOVERED																																																																																			NOVEL					0			1	2.406812	KEEP	0	0	0	8	235	CC	0.99257	0.043461	0			3	60	86	0	0	7.954412	4	60	135	22		0.428571	0.043787
USP31	57478	__UNKNOWN__	__UNKNOWN__	16	23150700	23150700	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23150700G>C	ENST00000219689.7	-	1	633					NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	NA		NA			ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		ccactgcactgcagcctgggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404	57478		Ubiquitin-specific peptidases	20060	protein-coding gene	gene with protein product		NA	ubiquitin specific protease 31		NA	12838346	Standard	NM_020718	NM_020718	NA	Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.633+9258C>G	chr16.hg19:g.23150700G>C		NA	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	hg19	CCDS10607.1	0.02	-0.087727	ACTxCAG	UNCOVERED																																																																																			NOVEL	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000211607.1	5	2.708191	KEEP	0	0	0	9	279	GG	0.99254	0.098977	0		-	3	60	109	0	1	9.67856	7	60	239	26	ENST00000219689.7	0.3	0.099721
SCNN1G	6340	__UNKNOWN__	__UNKNOWN__	16	23209812	23209812	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23209812A>G	ENST00000300061.2	+	6	1220				CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	NA		NA			excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	agcactttggaaggccaaggt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828	6340		Ion channels / Sodium channel, nonvoltage-gated, Sodium channels	10602	protein-coding gene	gene with protein product		600761	sodium channel, nonvoltage-gated 1, gamma, sodium channel, non-voltage-gated 1, gamma		NA	7490094	Standard	NM_001039	NM_001039	NA	Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1077+1064A>G	chr16.hg19:g.23209812A>G		NA	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	hg19	CCDS10608.1	0.02	-0.166637	TGGxAGG	COVERED																																																																																			NOVEL	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254496.1	11	3.609247	KEEP	1	0	0	12	332	AA	0.993634	0.351693	0		+	3	51	99	0	0	7.810234	15	60	440	42	ENST00000300061.2	0.166667	0.353947
SCNN1B	6338	__UNKNOWN__	__UNKNOWN__	16	23293279	23293279	__UNKNOWN__	Intron	SNP	G	G	A	rs78856554	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23293279G>A	ENST00000569789.1	+	2	110							P51168	SCNNB_HUMAN	sodium channel, non-voltage-gated 1, beta subunit	NA		NA			excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(48;0.0465)	Amiloride(DB00594)|Triamterene(DB00384)	ttgggaggccgaggtgggtga	0.498		NA											G|||	732	0.146166	0.1006	0.0937	5008	,	,	NA	17416	0.2798	NA	0.0775	False	NA	,,,	NA	NA	NA	2504	0.1779	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X87159	CCDS10609.1	16p12.2-p12.1	2012-02-28	2012-02-28		ENSG00000168447	ENSG00000168447	6338		Ion channels / Sodium channel, nonvoltage-gated, Sodium channels	10600	protein-coding gene	gene with protein product	Liddle syndrome	600760	sodium channel, nonvoltage-gated 1, beta, sodium channel, non-voltage-gated 1, beta		NA		Standard		NM_000336	NA	Approved	ENaCbeta	uc002dln.3	P51168	OTTHUMG00000131608	ENST00000569789.1:c.111-1779G>A	chr16.hg19:g.23293279G>A		NA	C5HTZ2|O60891|Q96KG2|Q9UJ32|Q9UMU5	hg19		0.02	-0.105242	GCCxAGG	UNCOVERED																																																																																			NOVEL	SCNN1B-008	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000434809.1	9	4.211135	KEEP	3	0	0	14	402	GG	0.993634	0.138942	0		+	3	60	87	0	0	7.332519	8	60	249	39	ENST00000569789.1	0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	23472181	23472181	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23472181T>C			NA	NA				CTD-2270L9.4 (3272 upstream) : GGA2 (2681 downstream)						NA		NA									NA						tcaagaccagtctggccaaca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.23472181T>C		NA		hg19		0.02	-0.11403	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			10	2.405784	KEEP	0	0	0	8	217	TT	0.99257	0.16126	0			3	60	99	0	0	8.401144	9	60	276	26		0.25	0.162467
PALB2	79728	__UNKNOWN__	__UNKNOWN__	16	23626213	23626213	__UNKNOWN__	Intron	SNP	C	C	T	rs551129720	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23626213C>T	ENST00000261584.4	-	11	3266				CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	NA		NA			DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		cctcgtgatccgcccgcctcg	0.542		NA	F, N, Mis			Wilms tumor, medulloblastoma, AML ,breast		Involved in tolerance or repair of DNA crosslinks					-|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	13115	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA		yes	Rec		Fanconi anaemia N, breast cancer susceptibility 	16	16p12.1	79728	partner and localizer of BRCA2		L, O, E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093	79728		Fanconi anemia, complementation groups	26144	protein-coding gene	gene with protein product	Fanconi anemia, complementation group N	610355			NA	16793542, 17200672	Standard	NM_024675	NM_024675	NA	Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.3114-801G>A	chr16.hg19:g.23626213C>T		NA	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	hg19	CCDS32406.1	0.02	-0.131552	ATCxGCC	UNCOVERED																																																																																			NOVEL	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435287.2	14	4.807506	KEEP	22	0	0	16	452	CC	0	0	0		-	3	44	93	0	0	7.472489	12	40	359	56	ENST00000261584.4	0.2	0.229173
ERN2	10595	__UNKNOWN__	__UNKNOWN__	16	23711415	23711415	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:23711415T>C	ENST00000457008.2	-	12	1408				ERN2_ENST00000256797.4_Intron					endoplasmic reticulum to nucleus signaling 2	NA		NA								large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		tttgggaggctaaggtgggag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398	10595			16942	protein-coding gene	gene with protein product		604034	ER to nucleus signalling 2		NA	9755171, 11175748	Standard		NM_033266	NA	Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1369+444A>G	chr16.hg19:g.23711415T>C		NA		hg19		0.02	-0.157877	GGCxAAG	COVERED																																																																																			NOVEL	ERN2-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000434886.1	4	3.608027	KEEP	0	0	0	12	320	TT	0.993634	0.320751	0		-	3	60	93	0	0	7.379004	13	60	391	35	ENST00000457008.2	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	24468116	24468116	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:24468116T>C			NA	NA				AC008938.1 (17708 upstream) : CTD-2313J23.1 (16002 downstream)						NA		NA									NA						cacctataattccagcacttt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.24468116T>C		NA		hg19		0.02	-0.210485	AATxCCA	COVERED																																																																																			NOVEL					0			11	3.308546	KEEP	1	0	0	11	305	GT	0.993634	0.518837	0			3	60	94	0	0	7.093081	18	60	526	54		0.142857	0.522161
RBBP6	5930	__UNKNOWN__	__UNKNOWN__	16	24577277	24577277	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:24577277C>T	ENST00000319715.4	+	14	2021				RBBP6_ENST00000381039.3_Intron|RBBP6_ENST00000348022.2_Intron	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	NA		NA			embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		tcccagctacctgggaggctg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257	5930			9889	protein-coding gene	gene with protein product	proliferation potential-related protein	600938	retinoblastoma-binding protein 6		NA	8595913, 16396680	Standard	NM_006910	NM_006910	NA	Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.1589+1091C>T	chr16.hg19:g.24577277C>T		NA	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	hg19	CCDS10621.1	0.02	-0.11404	TACxTGG	UNCOVERED																																																																																			NOVEL	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000214067.2	8	4.212284	KEEP	0	0	0	14	420	CC	0.995343	0.16171	0		+	3	60	90	0	0	7.500889	9	60	313	36	ENST00000319715.4	0.25	0.162467
AC012317.1	0	__UNKNOWN__	__UNKNOWN__	16	24676288	24676288	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:24676288G>T	ENST00000414816.1	-	0	194										NA		NA									NA						CAGAATCACGGGATGGTTGCA	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000414816.1:	chr16.hg19:g.24676288G>T		NA		hg19		0.02	1.522968	ACGxGAT	COVERED																																																																																			NOVEL	AC012317.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000254547.2	4	9.327174	KEEP	0	0	0	31	947	GG	0.999997	0.998693	0		-	16	60	455	0	0	36.359934	58	60	1917	156	ENST00000414816.1	0.216216	0.998696
ARHGAP17	55114	__UNKNOWN__	__UNKNOWN__	16	25018789	25018789	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:25018789C>T	ENST00000289968.6	-	1	123				ARHGAP17_ENST00000575975.1_Intron|ARHGAP17_ENST00000303665.5_Intron|ARHGAP17_ENST00000441763.2_Intron	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	NA		NA			regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		caggctcaagcgatcctccca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750	55114		Rho GTPase activating proteins	18239	protein-coding gene	gene with protein product		608293			NA	10967100, 11431473	Standard	NM_018054	XM_005255413	NA	Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.53+7740G>A	chr16.hg19:g.25018789C>T		NA	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	hg19	CCDS32409.1	0.02	-0.114033	AAGxGAT	UNCOVERED																																																																																			NOVEL	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000436548.3	6	2.706406	KEEP	0	0	0	9	249	CC	0.99254	0.161255	0		-	4	60	119	0	0	10.491023	8	60	260	31	ENST00000289968.6	0.333333	0.162467
LCMT1	51451	__UNKNOWN__	__UNKNOWN__	16	25174528	25174528	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:25174528G>A	ENST00000399069.3	+	7	724				LCMT1_ENST00000572869.1_Intron|LCMT1_ENST00000380966.4_Intron	NM_016309.2	NP_057393.2	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1	NA		NA			C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|negative regulation of protein complex assembly (GO:0031333)|protein methylation (GO:0006479)|regulation of apoptotic process (GO:0042981)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	cytosol (GO:0005829)	protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)				NA				GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	ggtggctcacgcctgtaatcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(200;565 2072 24396 47922 50898)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF037601	CCDS45445.1, CCDS45446.1	16p12.1	2014-08-01			ENSG00000205629	ENSG00000205629	51451			17557	protein-coding gene	gene with protein product	protein phosphatase methyltransferase 1	610286			NA	10810093	Standard	NM_016309	XM_005255354	NA	Approved	CGI-68, PPMT1	uc002dnx.1	Q9UIC8	OTTHUMG00000177182	ENST00000399069.3:c.570-1391G>A	chr16.hg19:g.25174528G>A		NA	A6NL89|A8K770|Q53FC5|Q96CI5|Q9H6I9|Q9NTG4|Q9Y378	hg19	CCDS45445.1	0.02	-0.254372	CACxCCT	COVERED																																																																																			NOVEL	LCMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435747.4	8	3.309091	KEEP	1	0	0	11	319	GG	0.992708	0.663648	0		+	3	60	94	0	0	6.795001	23	60	743	54	ENST00000399069.3	0.115385	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	25287266	25287266	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:25287266T>C			NA	NA				ZKSCAN2 (18014 upstream) : CTA-249B10.1 (143868 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.25287266T>C		NA		hg19		0.02	-0.114028	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			2	2.706644	KEEP	2	0	0	9	245	TT	0.99254	0.161255	0			3	60	102	0	0	8.701185	9	60	271	35		0.25	0.162467
HS3ST4	9951	__UNKNOWN__	__UNKNOWN__	16	25874651	25874651	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:25874651T>C	ENST00000331351.5	+	1	1126					NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	NA		NA			heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		atctgcccgcttcagcctccc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	9951	2.8.2.23	Sulfotransferases, membrane-bound	5200	protein-coding gene	gene with protein product		604059			NA	9988767	Standard	NM_006040	NM_006040	NA	Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.734+170179T>C	chr16.hg19:g.25874651T>C		NA	Q5QI42|Q8NDC2	hg19	CCDS53995.1	0.02	-0.052633	CGCxTCA	UNCOVERED																																																																																			NOVEL	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133286.2	4	3.609366	KEEP	0	0	0	12	339	TT	0.993634	0.036532	0		+	2	43	72	0	0	6.495786	4	60	126	29	ENST00000331351.5	0.333333	0.036766
HS3ST4	9951	__UNKNOWN__	__UNKNOWN__	16	26110748	26110748	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:26110748T>A	ENST00000331351.5	+	2	1126				HS3ST4_ENST00000475436.1_Intron	NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	NA		NA			heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		aagtgctgggtttacaggcgt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	9951	2.8.2.23	Sulfotransferases, membrane-bound	5200	protein-coding gene	gene with protein product		604059			NA	9988767	Standard	NM_006040	NM_006040	NA	Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.735-36185T>A	chr16.hg19:g.26110748T>A		NA	Q5QI42|Q8NDC2	hg19	CCDS53995.1	0.02	-0.087705	GGGxTTA	UNCOVERED																																																																																			NOVEL	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000133286.2	3	2.706739	KEEP	0	0	0	9	253	TT	0.99254	0.098977	0		+	3	60	92	0	0	8.143558	6	60	183	27	ENST00000331351.5	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	26898356	26898356	__UNKNOWN__	IGR	SNP	G	G	A	rs143624564		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:26898356G>A			NA	NA				AC009035.1 (150718 upstream) : C16orf82 (179671 downstream)						NA		NA									NA						gaaagagagagagagagagag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.26898356G>A		NA		hg19		0.02	-0.07016	AGAxAGA	UNCOVERED																																																																																			NOVEL					0			11	4.211807	KEEP	3	0	0	14	414	GG	0.993634	0.053793	0			3	60	81	1	0	7.231665	5	60	163	33		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	27093815	27093815	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:27093815G>A			NA	NA				C16orf82 (13329 upstream) : RP11-673P17.4 (75959 downstream)						NA		NA									NA						tctgcctcccgggttcaaacg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.27093815G>A		NA		hg19		0.02	-0.114016	CCCxGGT	UNCOVERED																																																																																			NOVEL					0			7	3.008888	KEEP	1	0	0	10	304	GG	0.992708	0.161282	0			3	60	81	0	0	6.731872	8	60	266	27		0.272727	0.162467
IL21R-AS1	283888	__UNKNOWN__	__UNKNOWN__	16	27463025	27463025	__UNKNOWN__	RNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:27463025T>G	ENST00000563191.1	-	0	477					NR_037158.1				IL21R antisense RNA 1	NA		NA									NA						gggtcacagatcaagaccctg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK093371		16p12.1	2012-10-12	2012-08-15		ENSG00000259954	ENSG00000259954	283888		Long non-coding RNAs	27551	non-coding RNA	RNA, long non-coding		NA	IL21R antisense RNA 1 (non-protein coding)		NA		Standard	NR_037158	NR_037158	NA	Approved		uc002dot.3		OTTHUMG00000176806	ENST00000563191.1:	chr16.hg19:g.27463025T>G		NA		hg19		0.02	-0.271849	AGAxCAA	COVERED																																																																																			NOVEL	IL21R-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000433868.1	7	3.006271	KEEP	1	0	0	10	274	TT	0.992708	0.712085	0		-	3	60	106	0	0	7.892279	25	60	723	58	ENST00000563191.1	0.107143	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	28246167	28246167	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:28246167T>G			NA	NA				XPO6 (22977 upstream) : RP11-57A19.2 (50038 downstream)						NA		NA									NA						caaagtgctgtgattacaggt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.28246167T>G		NA		hg19		0.02	-0.114018	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			4	2.406759	KEEP	0	0	0	8	233	TT	0.99257	0.16126	0			3	60	99	0	0	8.282105	10	60	294	30		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	28252617	28252617	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:28252617A>G			NA	NA				XPO6 (29427 upstream) : RP11-57A19.2 (43588 downstream)						NA		NA									NA						gcacgatctcagctcactgca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.28252617A>G		NA		hg19		0.02	-0.184163	CTCxGCT	COVERED																																																																																			NOVEL					0			8	3.306214	KEEP	4	0	0	11	282	AA	0.992708	0.42039	0			3	60	93	0	0	7.21072	15	60	436	38		0.166667	0.423478
SULT1A1	6817	__UNKNOWN__	__UNKNOWN__	16	28630608	28630608	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:28630608G>C	ENST00000350842.4	-	2	527				SULT1A1_ENST00000395609.1_Intron	NM_177536.3	NP_803880.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	NA		NA			3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)			endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	gttgggattagaggcgtgagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	6817	2.8.2.1	Sulfotransferases, cytosolic	11453	protein-coding gene	gene with protein product		171150		STP, STP1	NA	8288252, 8912648	Standard	NM_001055	NM_177534	NA	Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000350842.4:c.138+775C>G	chr16.hg19:g.28630608G>C		NA	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	hg19	CCDS10637.1	0.02	-0.139933	TTAxAGG	COVERED																																																																																			NOVEL	SULT1A1-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254693.1	7	2.708153	KEEP	1	0	0	9	278	GG	0.99257	0.259026	0		-	3	60	101	0	0	8.378276	11	60	346	34	ENST00000350842.4	0.214286	0.260965
SH2B1	25970	__UNKNOWN__	__UNKNOWN__	16	28880667	28880667	__UNKNOWN__	Silent	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:28880667G>T	ENST00000545570.1	+	4	529	c.342G>T	c.(340-342)ctG>ctT	p.L114L	SH2B1_ENST00000322610.8_Silent_p.L424L|SH2B1_ENST00000337120.5_Silent_p.L424L|SH2B1_ENST00000538342.1_Silent_p.L88L|SH2B1_ENST00000359285.5_Silent_p.L424L|SH2B1_ENST00000395532.4_Silent_p.L424L|SH2B1_ENST00000563674.1_Intron			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	424	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.|Interaction with RAC1. {ECO:0000250}.|Required for NGF signaling. {ECO:0000250}.	NA			blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						AGGACCTGCTGCTTGGACCCA	0.622		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													47	45	46			NA	NA	16		NA											NA				28880667		2197	4300	6497	SO:0001819	synonymous_variant			AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14					25970		Pleckstrin homology (PH) domain containing, SH2 domain containing	30417	protein-coding gene	gene with protein product	SH2-B homolog	608937			NA	11827956, 10594240	Standard	NM_015503	NM_001145812	NA	Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000545570.1:c.342G>T	chr16.hg19:g.28880667G>T		NA	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	hg19		0.02	1.344611	GCTxCTT	COVERED																																																																																			NOVEL	SH2B1-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000432669.1	0	5.415931	KEEP	0	0	0	18	548	GG	0.999859	0.999481	0		+	23	60	689	0	0	58.4593	61	60	2109	155	ENST00000545570.1	0.27381	0.999622
SH2B1	25970	__UNKNOWN__	__UNKNOWN__	16	28880673	28880673	__UNKNOWN__	Silent	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:28880673A>G	ENST00000545570.1	+	4	535	c.348A>G	c.(346-348)ggA>ggG	p.G116G	SH2B1_ENST00000322610.8_Silent_p.G426G|SH2B1_ENST00000337120.5_Silent_p.G426G|SH2B1_ENST00000538342.1_Silent_p.G90G|SH2B1_ENST00000359285.5_Silent_p.G426G|SH2B1_ENST00000395532.4_Silent_p.G426G|SH2B1_ENST00000563674.1_Intron			Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1	426	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation). {ECO:0000250}.|Interaction with RAC1. {ECO:0000250}.|Required for NGF signaling. {ECO:0000250}.	NA			blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|intracellular signal transduction (GO:0035556)|lamellipodium assembly (GO:0030032)|positive regulation of mitosis (GO:0045840)|regulation of DNA biosynthetic process (GO:2000278)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25						TGCTGCTTGGACCCAGCGAGA	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													46	44	45			NA	NA	16		NA											NA				28880673		2197	4300	6497	SO:0001819	synonymous_variant			AK055104	CCDS32424.1, CCDS53996.1, CCDS53997.1	16p11.2	2013-02-14					25970		Pleckstrin homology (PH) domain containing, SH2 domain containing	30417	protein-coding gene	gene with protein product	SH2-B homolog	608937			NA	11827956, 10594240	Standard	NM_015503	NM_001145812	NA	Approved	FLJ30542, SH2B	uc002drl.3	Q9NRF2		ENST00000545570.1:c.348A>G	chr16.hg19:g.28880673A>G		NA	A8K2R7|Q96FK3|Q96SX3|Q9NRF1|Q9NRF3|Q9P2P7|Q9Y3Y3	hg19		0.02	1.760308	TGGxCCC	COVERED																																																																																			NOVEL	SH2B1-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000432669.1	0	5.710527	KEEP	0	0	0	19	488	AA	0.99986	0.999347	0		+	23	60	801	0	0	69.803686	60	60	1753	153	ENST00000545570.1	0.277108	0.999487
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	29008999	29008999	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29008999G>C			NA	NA				LAT (6895 upstream) : CTB-134H23.2 (40923 downstream)						NA		NA									NA						tctcggctcagtgcaacctcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.29008999G>C		NA		hg19		0.02	-0.140347	TCAxTGC	COVERED																																																																																			NOVEL					0			5	2.707737	KEEP	0	0	0	9	267	GG	0.99254	0.259018	0			3	60	98	0	0	8.072764	11	60	381	35		0.214286	0.260965
NPIPB11	728888	__UNKNOWN__	__UNKNOWN__	16	29413980	29413980	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29413980T>A	ENST00000524087.1	-	2	195				SNX29P2_ENST00000398878.3_lincRNA			E5RHQ5	NPB11_HUMAN	nuclear pore complex interacting protein family, member B11	NA		NA				integral component of membrane (GO:0016021)					NA						gccaagattgtgccactgcac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					16p11.2	2013-06-11			ENSG00000254206	ENSG00000254206	728888			37453	protein-coding gene	gene with protein product		NA			NA		Standard	XM_002343430	XM_006721110	NA	Approved			E5RHQ5	OTTHUMG00000170467	ENST00000524087.1:c.120+1023A>T	chr16.hg19:g.29413980T>A		NA		hg19		0.02	-0.149091	TTGxGCC	COVERED																																																																																			NOVEL	NPIPB11-001	PUTATIVE	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000374094.1	6	2.706631	KEEP	3	0	0	9	248	CT	0.99257	0.320408	0		-	3	60	93	0	1	7.379138	13	60	395	42	ENST00000524087.1	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	29631665	29631665	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29631665G>C			NA	NA				MIR3680-2 (21079 upstream) : SPN (42634 downstream)						NA		NA									NA						ggccaggtgtggtggctcatg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.29631665G>C		NA		hg19		0.02	-0.280708	TGTxGTG	COVERED																																																																																			NOVEL					0			17	6.619668	KEEP	5	0	0	22	672	GG	0.999863	0.760782	0			4	60	135	0	0	10.635867	21	60	692	84		0.16	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	29645172	29645172	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29645172C>A			NA	NA				MIR3680-2 (34586 upstream) : SPN (29127 downstream)						NA		NA									NA						CCCCAGCAAGCGATTACCTTT	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.29645172C>A		NA		hg19		0.02	4.613761	AAGxGAT	COVERED																																																																																			NOVEL					0			33	21.052516	KEEP	4	0	0	70	1955	CC	1	1	0			41	49	1252	0	0	106.144368	112	60	3610	325		0.267974	1
SPN	6693	__UNKNOWN__	__UNKNOWN__	16	29678824	29678824	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29678824T>C	ENST00000360121.3	+	0	3867					NM_001030288.2|NM_003123.4	NP_001025459.1|NP_003114.1	O75398	DEAF1_HUMAN	sialophorin	NA		NA			anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|stomach(1)	15						ACAggccgggtgcggtggctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			J04536	CCDS10650.1	16p11.2	2008-07-31	2008-07-31		ENSG00000197471	ENSG00000197471	6693		CD molecules	11249	protein-coding gene	gene with protein product	leukosialin	182160	sialophorin (gpL115, leukosialin, CD43)		NA	2784859, 2521952	Standard		NM_001030288	NA	Approved	LSN, CD43, GPL115	uc002dtm.4	P16150	OTTHUMG00000097765	ENST00000360121.3:c.*2572T>C	chr16.hg19:g.29678824T>C		NA	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	hg19	CCDS10650.1	0.02	-0.324486	GGGxGCG	COVERED																																																																																			NOVEL	SPN-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215001.2	10	4.209362	KEEP	3	0	0	14	374	TT	0.994391	0.831028	0		+	3	60	100	0	0	6.987605	32	60	933	70	ENST00000360121.3	0.085714	0.835716
QPRT	23475	__UNKNOWN__	__UNKNOWN__	16	29709286	29709286	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29709286T>C	ENST00000395384.4	+	0	1609					NM_014298.3	NP_055113.2	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	NA		NA			NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|protein oligomerization (GO:0051259)|quinolinate catabolic process (GO:0034213)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9					Niacin(DB00627)	gcctgggtgatagagcgagac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D78177	CCDS10651.1	16p11.2	2008-07-31	2008-07-31		ENSG00000103485	ENSG00000103485	23475	2.4.2.19		9755	protein-coding gene	gene with protein product	nicotinate-nucleotide pyrophosphorylase (carboxylating)	606248			NA	9473669	Standard	NM_014298	NM_014298	NA	Approved	QPRTase	uc002dto.3	Q15274	OTTHUMG00000097770	ENST00000395384.4:c.*554T>C	chr16.hg19:g.29709286T>C		NA	Q53XW7|Q96G22|Q9BSG6	hg19	CCDS10651.1	0.02	1.880042	TGAxAGA	COVERED																																																																																			NOVEL	QPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000215011.2	15	7.516366	KEEP	0	0	0	25	665	TT	0.999931	0.984093	0		+	5	60	169	0	0	12.097204	48	60	1375	127	ENST00000395384.4	0.09434	0.984161
KCTD13	253980	__UNKNOWN__	__UNKNOWN__	16	29926710	29926710	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29926710C>T	ENST00000568000.1	-	3	1416					NM_178863.3	NP_849194.1	Q8WZ19	BACD1_HUMAN	potassium channel tetramerization domain containing 13	NA		NA			cell migration (GO:0016477)|DNA replication (GO:0006260)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nucleus (GO:0005634)	GTP-Rho binding (GO:0017049)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	7						cagtggctcacgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF289573	CCDS10661.1	16p11.2	2013-06-20	2013-06-20		ENSG00000174943	ENSG00000174943	253980			22234	protein-coding gene	gene with protein product	polymerase delta-interacting protein 1, TNFAIP1-like	608947	potassium channel tetramerisation domain containing 13		NA	11593007	Standard	NM_178863	NM_178863	NA	Approved	PDIP1, FKSG86, POLDIP1	uc002duv.4	Q8WZ19	OTTHUMG00000132120	ENST00000568000.1:c.415-3340G>A	chr16.hg19:g.29926710C>T		NA	A8K0R5|Q96P93|Q96SA1	hg19	CCDS10661.1	0.02	-0.201765	TCAxGCC	UNCOVERED																																																																																			NOVEL	KCTD13-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255162.2	4	2.70802	KEEP	4	0	0	9	273	CC	0	0	0		-	3	60	94	0	0	7.092231	18	60	601	50	ENST00000568000.1	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	29948307	29948307	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29948307A>G			NA	NA				CTD-2574D22.2 (8053 upstream) : TMEM219 (3898 downstream)						NA		NA									NA						agaccagcctaggcaacacag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.29948307A>G		NA		hg19		0.02	-0.350804	CCTxGGC	COVERED																																																																																			NOVEL					0			11	3.238136	KEEP	0	1	29	21	552	AA	0.999879	0.877601	0			4	60	132	0	0	9.606609	33	60	956	95		0.108108	0.877708
TMEM219	124446	__UNKNOWN__	__UNKNOWN__	16	29976755	29976755	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:29976755T>C	ENST00000566848.1	+	2	822				TMEM219_ENST00000414689.2_Intron|TMEM219_ENST00000279396.6_Intron|TMEM219_ENST00000561899.2_Intron			Q86XT9	TM219_HUMAN	transmembrane protein 219	NA		NA			apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(1)|prostate(2)	4						agtgtacagttAGggccggat	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42145.1	16p11.2	2008-08-08			ENSG00000149932	ENSG00000149932	124446			25201	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001083613	NM_194280	NA	Approved		uc010bzk.1	Q86XT9		ENST00000566848.1:c.355+1845T>C	chr16.hg19:g.29976755T>C		NA	D5FK14|Q8WVV8	hg19	CCDS42145.1	0.02	-0.14032	AGTxAGG	COVERED																																																																																			NOVEL	TMEM219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435307.1	7	2.705864	KEEP	0	0	0	9	235	TT	0.99254	0.259018	0		+	6	60	201	0	0	18.366721	10	60	278	35	ENST00000566848.1	0.375	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	30147762	30147762	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30147762G>A			NA	NA				MAPK3 (13132 upstream) : CORO1A (46980 downstream)						NA		NA									NA						tcactctgtcgcccaggctgg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.30147762G>A		NA		hg19		0.02	-0.140351	GTCxCCC	COVERED																																																																																			NOVEL					0			27	5.047416	KEEP	19	1	26	26	784	GG	0.99649	0.260049	0			3	40	85	0	0	6.772909	11	60	373	56		0.214286	0.260965
ZNF785	146540	__UNKNOWN__	__UNKNOWN__	16	30592011	30592011	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30592011T>C	ENST00000395216.2	-	0	3247				ZNF785_ENST00000470110.1_Intron|AC002310.7_ENST00000492040.1_RNA|AC002310.7_ENST00000486926.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9						ttagtagagatggggtttcac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC040642	CCDS10685.1	16p11.2	2013-01-08			ENSG00000197162	ENSG00000197162	146540		Zinc fingers, C2H2-type, -	26496	protein-coding gene	gene with protein product		NA			NA	10493829	Standard	NM_152458	NM_152458	NA	Approved	FLJ32130	uc002dyu.3	A8K8V0	OTTHUMG00000132398	ENST00000395216.2:c.*1870A>G	chr16.hg19:g.30592011T>C		NA	O75701|Q8IW91|Q8WV14|Q96MN0	hg19	CCDS10685.1	0.02	-0.280441	AGAxGGG	COVERED																																																																																			NOVEL	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255529.2	11	9.018055	KEEP	3	0	0	30	790	TT	0.999997	0.739669	0		-	5	60	148	0	0	11.660384	21	60	580	84	ENST00000395216.2	0.192308	0.739671
ZNF785	146540	__UNKNOWN__	__UNKNOWN__	16	30592241	30592241	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30592241A>C	ENST00000395216.2	-	0	3017				ZNF785_ENST00000470110.1_Intron|AC002310.7_ENST00000492040.1_RNA|AC002310.7_ENST00000486926.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	9						gtaatcccagaactttgggag	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC040642	CCDS10685.1	16p11.2	2013-01-08			ENSG00000197162	ENSG00000197162	146540		Zinc fingers, C2H2-type, -	26496	protein-coding gene	gene with protein product		NA			NA	10493829	Standard	NM_152458	NM_152458	NA	Approved	FLJ32130	uc002dyu.3	A8K8V0	OTTHUMG00000132398	ENST00000395216.2:c.*1640T>G	chr16.hg19:g.30592241A>C		NA	O75701|Q8IW91|Q8WV14|Q96MN0	hg19	CCDS10685.1	0.02	1.783529	CAGxACT	COVERED																																																																																			NOVEL	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255529.2	11	6.237611	KEEP	0	1	29	31	773	AA	0.999998	0.996722	0		-	5	60	172	0	0	11.934106	60	60	1687	142	ENST00000395216.2	0.076923	0.996724
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	30647323	30647323	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30647323C>T			NA	NA				ZNF689 (11990 upstream) : PRR14 (14864 downstream)						NA		NA									NA						gatggagtctcgctcttgttg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.30647323C>T		NA		hg19		0.02	-0.219279	TCTxGCT	COVERED																																																																																			NOVEL					0			6	2.405805	KEEP	0	0	0	8	223	CC	0.99257	0.54878	0			3	60	89	0	0	6.465754	20	60	639	44		0.130435	0.552887
CTF1	1489	__UNKNOWN__	__UNKNOWN__	16	30913118	30913118	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30913118T>C	ENST00000279804.2	+	3	181				CTF1_ENST00000395019.3_Intron	NM_001142544.1|NM_001330.3	NP_001136016.1|NP_001321.1	Q16619	CTF1_HUMAN	cardiotrophin 1	NA		NA			cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|leukemia inhibitory factor signaling pathway (GO:0048861)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	leukemia inhibitory factor receptor binding (GO:0005146)			large_intestine(1)|urinary_tract(1)	2			Colorectal(24;0.198)			ttgcctaggctggtctcgaac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U43030	CCDS10694.1, CCDS45464.1	16p11.2	2014-09-17			ENSG00000150281	ENSG00000150281	1489			2499	protein-coding gene	gene with protein product		600435			NA	8833032	Standard	NM_001330	NM_001330	NA	Approved	CT-1, CT1	uc002dzw.3	Q16619	OTTHUMG00000132413	ENST00000279804.2:c.145-281T>C	chr16.hg19:g.30913118T>C		NA	A8MVX4|Q5U5Y7	hg19	CCDS10694.1	0.02	-0.254359	GGCxGGT	COVERED																																																																																			NOVEL	CTF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255550.1	12	5.99572	KEEP	2	0	0	20	541	TT	0.99986	0.668429	0		+	3	22	93	0	0	6.865247	20	60	614	75	ENST00000279804.2	0.130435	0.668523
CTF1	1489	__UNKNOWN__	__UNKNOWN__	16	30913125	30913125	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30913125G>A	ENST00000279804.2	+	3	181				CTF1_ENST00000395019.3_Intron	NM_001142544.1|NM_001330.3	NP_001136016.1|NP_001321.1	Q16619	CTF1_HUMAN	cardiotrophin 1	NA		NA			cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|leukemia inhibitory factor signaling pathway (GO:0048861)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	leukemia inhibitory factor receptor binding (GO:0005146)			large_intestine(1)|urinary_tract(1)	2			Colorectal(24;0.198)			ggctggtctcgaacccctggg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U43030	CCDS10694.1, CCDS45464.1	16p11.2	2014-09-17			ENSG00000150281	ENSG00000150281	1489			2499	protein-coding gene	gene with protein product		600435			NA	8833032	Standard	NM_001330	NM_001330	NA	Approved	CT-1, CT1	uc002dzw.3	Q16619	OTTHUMG00000132413	ENST00000279804.2:c.145-274G>A	chr16.hg19:g.30913125G>A		NA	A8MVX4|Q5U5Y7	hg19	CCDS10694.1	0.02	-0.236783	CTCxAAC	COVERED																																																																																			NOVEL	CTF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255550.1	11	2.739916	KEEP	1	1	25	18	523	GG	0.99986	0.612321	0		+	4	60	115	0	0	8.795065	19	60	615	72	ENST00000279804.2	0.173913	0.612407
ORAI3	93129	__UNKNOWN__	__UNKNOWN__	16	30965788	30965788	__UNKNOWN__	Intron	SNP	G	G	A	rs546698883		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30965788G>A	ENST00000562699.1	+	2	366				ORAI3_ENST00000566237.1_3'UTR|ORAI3_ENST00000318663.4_3'UTR			Q9BRQ5	ORAI3_HUMAN	ORAI calcium release-activated calcium modulator 3	NA		NA			store-operated calcium entry (GO:0002115)	integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6						ctcccgcctcggcctcccaaa	0.488		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	6822	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006126	CCDS10697.1	16p11.2	2007-08-14	2007-08-14	2007-08-14	ENSG00000175938	ENSG00000175938	93129		ORAI calcium release-activated calcium modulators	28185	protein-coding gene	gene with protein product		610930	transmembrane protein 142C	TMEM142C	NA	16582901	Standard	NM_152288	NM_152288	NA	Approved	MGC13024	uc002eac.3	Q9BRQ5	OTTHUMG00000132409	ENST00000562699.1:c.229-1733G>A	chr16.hg19:g.30965788G>A		NA	Q96BI8	hg19		0.02	1.412224	CTCxGCC	COVERED																																																																																			NOVEL	ORAI3-005	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000433645.1	12	3.172325	KEEP	1	2	55	30	862	GG	0.999997	0.995081	0		+	5	60	141	1	0	8.988956	56	60	1778	115	ENST00000562699.1	0.081967	0.995084
SETD1A	9739	__UNKNOWN__	__UNKNOWN__	16	30978754	30978754	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30978754A>C	ENST00000262519.8	+	10	3368					NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	NA		NA			histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						ggattacaggagtgagccacc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381	9739		Chromatin-modifying enzymes / K-methyltransferases, RNA binding motif (RRM) containing	29010	protein-coding gene	gene with protein product		611052			NA	9205841, 12670868	Standard	NM_014712	XM_005255723	NA	Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2683-68A>C	chr16.hg19:g.30978754A>C		NA	A6NP62|Q6PIF3|Q8TAJ6	hg19	CCDS32435.1	0.02	3.564655	AGGxGTG	COVERED																																																																																			NOVEL	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318244.2	32	3.839446	KEEP	0	4	111	52	1457	AT	1	1	0		+	9	60	291	0	0	19.560927	110	60	3369	273	ENST00000262519.8	0.07563	1
SETD1A	9739	__UNKNOWN__	__UNKNOWN__	16	30979624	30979624	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:30979624A>T	ENST00000262519.8	+	10	3456					NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	NA		NA			histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						cttgggaggcagaggcacgag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381	9739		Chromatin-modifying enzymes / K-methyltransferases, RNA binding motif (RRM) containing	29010	protein-coding gene	gene with protein product		611052			NA	9205841, 12670868	Standard	NM_014712	XM_005255723	NA	Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2770+715A>T	chr16.hg19:g.30979624A>T		NA	A6NP62|Q6PIF3|Q8TAJ6	hg19	CCDS32435.1	0.02	-0.131551	GGCxGAG	COVERED																																																																																			NOVEL	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318244.2	3	3.008312	KEEP	0	0	0	10	289	AA	0.992708	0.227502	0		+	3	60	85	0	0	6.773286	11	60	326	38	ENST00000262519.8	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	31039417	31039417	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:31039417T>C			NA	NA				STX1B (17468 upstream) : STX4 (4998 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.31039417T>C		NA		hg19		0.02	-0.28063	AGGxGTG	COVERED																																																																																			NOVEL					0			12	3.038281	KEEP	7	1	25	19	515	TT	0.999366	0.760405	0			3	60	100	0	0	7.395022	23	60	656	83		0.115385	0.760887
CTD-2014E2.6	0	__UNKNOWN__	__UNKNOWN__	16	31561297	31561297	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:31561297C>T	ENST00000567765.1	-	0	423										NA		NA									NA						aatctcagcactttgggaggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000567765.1:	chr16.hg19:g.31561297C>T		NA		hg19		0.02	-0.149109	GCAxTTT	COVERED																																																																																			NOVEL	CTD-2014E2.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000438859.1	14	3.911799	KEEP	3	0	0	13	402	CC	0.993072	0.289978	0		-	3	60	84	0	0	6.479392	13	60	426	46	ENST00000567765.1	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	31987302	31987302	__UNKNOWN__	IGR	SNP	C	C	A	rs2077134		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:31987302C>A			NA	NA				ZNF267 (58634 upstream) : RP11-1166P10.1 (5888 downstream)						NA		NA									NA						CCCCACACCCCCAGCCCCACC	0.652		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.31987302C>A		NA		hg19		0.02	1.109318	CCCxCAG	COVERED																																																																																			NOVEL					0			2	4.212603	KEEP	3	0	0	14	436	CC	0.995343	0.99434	0			16	49	455	0	0	36.049116	61	60	2107	152		0.207792	0.998993
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	31987322	31987322	__UNKNOWN__	IGR	SNP	G	G	A	rs74331035		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:31987322G>A			NA	NA				ZNF267 (58654 upstream) : RP11-1166P10.1 (5868 downstream)						NA		NA									NA						CCTTTCCCTCGCTGCCCAGTC	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.31987322G>A		NA		hg19		0.02	1.240949	CTCxCTG	COVERED																																																																																			NOVEL					0			1	2.707026	KEEP	3	0	0	9	267	GG	0.99254	0.984693	0			13	49	353	0	0	27.782366	48	60	1592	111		0.213115	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32136101	32136101	__UNKNOWN__	IGR	SNP	T	T	C	rs12102357		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:32136101T>C			NA	NA				RP11-1166P10.6 (39995 upstream) : HERC2P4 (45203 downstream)						NA		NA									NA						aggctaatttttgtatattta	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32136101T>C		NA		hg19		0.02	-0.271923	TTTxTGT	COVERED																																																																																			NOVEL					0			24	3.641941	KEEP	28	1	34	24	659	TT	0.99649	0.714798	0			5	44	177	0	0	14.558618	21	49	651	98		0.192308	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32164484	32164484	__UNKNOWN__	IGR	SNP	C	C	T	rs62042680		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:32164484C>T			NA	NA				RP11-1166P10.6 (68378 upstream) : HERC2P4 (16820 downstream)						NA		NA									NA						caacctccacctcccaggttc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32164484C>T		NA		hg19		0.02	-0.07018	CACxTCC	UNCOVERED																																																																																			NOVEL					0			8	3.610825	KEEP	9	0	0	12	371	CC	0.99257	0.053735	0			3	47	93	0	0	8.432523	5	47	178	36		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32357849	32357849	__UNKNOWN__	IGR	SNP	A	A	T	rs62043129		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:32357849A>T			NA	NA				RP11-17M15.2 (35973 upstream) : RP11-626K17.3 (108083 downstream)						NA		NA									NA						aggcaggtggatcactagagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32357849A>T		NA		hg19		0.02	-0.166606	TGGxTCA	COVERED																																																																																			NOVEL					0			12	2.706323	KEEP	2	0	0	9	243	AA	0.99254	0.351306	0			4	45	114	0	0	9.401912	12	60	346	41		0.25	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32357883	32357883	__UNKNOWN__	IGR	SNP	T	T	C	rs2550081		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:32357883T>C			NA	NA				RP11-17M15.2 (36007 upstream) : RP11-626K17.3 (108049 downstream)						NA		NA									NA						agcagcctggtcaacataggg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32357883T>C		NA		hg19		0.02	-0.122802	TGGxCAA	COVERED																																																																																			NOVEL					0			9	3.006401	KEEP	1	0	0	10	273	TT	0.992708	0.227502	0			7	45	233	0	0	22.424707	7	60	216	35		0.5	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32418117	32418117	__UNKNOWN__	IGR	SNP	C	C	T	rs28576978		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:32418117C>T			NA	NA				RP11-17M15.2 (96241 upstream) : RP11-626K17.3 (47815 downstream)						NA		NA									NA						tcacttgaacccaggaggcgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32418117C>T		NA		hg19		0.02	-0.219315	AACxCAG	COVERED																																																																																			NOVEL					0			13	3.342624	KEEP	7	1	25	20	618	CC	0.999859	0.55281	0			3	60	95	0	0	7.005649	21	60	720	71		0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	32436680	32436680	__UNKNOWN__	IGR	SNP	C	C	A	rs79930738		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:32436680C>A			NA	NA				RP11-17M15.2 (114804 upstream) : RP11-626K17.3 (29252 downstream)						NA		NA									NA						gatggggtttcattatgttgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.32436680C>A		NA		hg19		0.02	-0.175437	TTTxATT	COVERED																																																																																			NOVEL					0			8	3.306195	KEEP	4	0	0	11	303	CC	0.992708	0.384582	0			3	49	87	0	0	6.610794	15	60	503	48		0.166667	0.387407
RP11-19N8.4	0	__UNKNOWN__	__UNKNOWN__	16	33060167	33060167	__UNKNOWN__	lincRNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33060167A>C	ENST00000561541.1	-	0	291										NA		NA									NA						agagaatggtaaaagggagga	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000561541.1:	chr16.hg19:g.33060167A>C		NA		hg19		0.02	-0.11401	GGTxAAA	UNCOVERED																																																																																			NOVEL	RP11-19N8.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000432096.1	15	2.436755	KEEP	9	1	34	20	520	AA	0.99649	0.161897	0		-	3	29	95	0	0	8.001369	9	50	258	48	ENST00000561541.1	0.25	0.162467
RP11-19N8.4	0	__UNKNOWN__	__UNKNOWN__	16	33060185	33060185	__UNKNOWN__	lincRNA	SNP	G	G	A	rs200872170		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33060185G>A	ENST00000561541.1	-	0	291										NA		NA									NA						ggaaggcacagaaacaaagaa	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000561541.1:	chr16.hg19:g.33060185G>A		NA		hg19		0.02	-0.175442	ACAxAAA	COVERED																																																																																			NOVEL	RP11-19N8.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000432096.1	19	3.041978	KEEP	11	1	28	20	615	GG	0.99649	0.386047	0		-	3	22	89	0	0	6.810351	15	50	507	60	ENST00000561541.1	0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33294297	33294297	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33294297G>T			NA	NA				RP11-1437A8.5 (20141 upstream) : RP11-23E10.3 (41985 downstream)						NA		NA									NA						tggctggcttggctgtcttgg	0.652		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33294297G>T		NA		hg19		0.02	-0.087684	CTTxGCT	UNCOVERED																																																																																			NOVEL					0			12	3.008268	KEEP	1	0	0	10	299	GG	0.99254	0.098977	0			3	60	81	0	0	7.041653	6	60	200	22		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33309184	33309184	__UNKNOWN__	IGR	SNP	A	A	G	rs78650422		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33309184A>G			NA	NA				RP11-1437A8.5 (35028 upstream) : RP11-23E10.3 (27098 downstream)						NA		NA									NA						gtgacagagcaagactccgta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33309184A>G		NA		hg19		0.02	-0.122792	AGCxAGA	COVERED																																																																																			NOVEL					0			5	3.007096	KEEP	1	0	0	10	269	AA	0.992708	0.19488	0			3	48	100	0	0	8.382042	10	60	299	37		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33383661	33383661	__UNKNOWN__	IGR	SNP	G	G	C	rs9935328		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33383661G>C			NA	NA				RP11-23E10.4 (16848 upstream) : BMS1P8 (113501 downstream)						NA		NA									NA						ttgagatggagtttagctctt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33383661G>C		NA		hg19		0.02	-0.166676	GGAxTTT	COVERED																																																																																			NOVEL					0			13	3.009015	KEEP	10	0	0	10	308	GG	0.99257	0.351317	0			5	50	171	0	0	14.730269	14	60	477	47		0.263158	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33391966	33391966	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33391966G>A			NA	NA				RP11-23E10.4 (25153 upstream) : BMS1P8 (105196 downstream)						NA		NA									NA						ttgaaacggggtctcactgtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33391966G>A		NA		hg19		0.02	-0.368403	GGGxTCT	COVERED																																																																																			NOVEL					0			8	9.626244	KEEP	1	0	0	32	946	GG	0.999997	0.899312	0			5	47	149	0	0	10.687283	36	60	1158	99		0.121951	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33392044	33392044	__UNKNOWN__	IGR	SNP	G	G	T	rs80350834		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33392044G>T			NA	NA				RP11-23E10.4 (25231 upstream) : BMS1P8 (105118 downstream)						NA		NA									NA						gagtagctgggactataggca	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33392044G>T		NA		hg19		0.02	3.002463	TGGxACT	COVERED																																																																																			NOVEL					0			12	6.014379	KEEP	5	3	76	47	1392	GG	1	0.999999	0			9	54	247	0	0	15.28456	107	60	3547	230		0.077586	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33393866	33393866	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33393866G>A			NA	NA				RP11-23E10.4 (27053 upstream) : BMS1P8 (103296 downstream)						NA		NA									NA						tttttgagacggagtctcact	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33393866G>A		NA		hg19		0.02	2.644106	GACxGAG	COVERED																																																																																			NOVEL					0			25	3.804393	KEEP	1	6	156	68	1970	GG	1	1	0			6	60	183	1	0	11.061893	104	60	3342	270		0.054545	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33394037	33394037	__UNKNOWN__	IGR	SNP	C	C	T	rs7192819	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33394037C>T			NA	NA				RP11-23E10.4 (27224 upstream) : BMS1P8 (103125 downstream)						NA		NA									NA						actatgttgcccaggctggtc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33394037C>T		NA		hg19		0.02	-0.236848	TGCxCAG	COVERED																																																																																			NOVEL					0			10	3.911911	KEEP	0	0	0	13	407	CC	0.994391	0.608972	0			8	60	253	0	0	22.147352	18	60	596	61		0.307692	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33394222	33394222	__UNKNOWN__	IGR	SNP	T	T	G	rs7190001	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33394222T>G			NA	NA				RP11-23E10.4 (27409 upstream) : BMS1P8 (102940 downstream)						NA		NA									NA						aacctccgcctcctgggttca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33394222T>G		NA		hg19		0.02	-0.122777	GCCxCCT	COVERED																																																																																			NOVEL					0			2	3.307311	KEEP	2	0	0	11	297	TT	0.99254	0.194847	0			5	60	162	0	0	14.623623	9	60	255	32		0.357143	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33406247	33406247	__UNKNOWN__	IGR	SNP	T	T	C	rs62029434	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33406247T>C			NA	NA				RP11-23E10.4 (39434 upstream) : BMS1P8 (90915 downstream)						NA		NA									NA						TGTAAAAAGGtttttgtagag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33406247T>C		NA		hg19		0.02	-0.245493	AGGxTTT	COVERED																																																																																			NOVEL					0			18	5.410551	KEEP	9	0	0	18	466	TT	0.997832	0.639957	0			7	60	238	0	0	20.704446	18	60	484	66		0.28	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33406316	33406316	__UNKNOWN__	IGR	SNP	C	C	T	rs62029435	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33406316C>T			NA	NA				RP11-23E10.4 (39503 upstream) : BMS1P8 (90846 downstream)						NA		NA									NA						agcgatcctccttcctctgtc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33406316C>T		NA		hg19		0.02	-0.271944	CTCxTTC	COVERED																																																																																			NOVEL					0			10	5.11569	KEEP	2	0	0	17	536	CC	0.999366	0.716861	0			9	60	282	0	0	24.53514	21	60	720	77		0.3	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33410819	33410819	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33410819C>T			NA	NA				RP11-23E10.4 (44006 upstream) : BMS1P8 (86343 downstream)						NA		NA									NA						Gtgtcttagtccatgtgggct	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33410819C>T		NA		hg19		0.02	3.393847	AGTxCAT	COVERED																																																																																			NOVEL					0			6	6.016271	KEEP	5	0	0	20	592	CC	0.999863	0.999831	0			15	60	462	0	0	35.005337	85	60	2803	168		0.15	0.999968
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33414771	33414771	__UNKNOWN__	IGR	SNP	C	C	T	rs2632791	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33414771C>T			NA	NA				RP11-23E10.4 (47958 upstream) : BMS1P8 (82391 downstream)						NA		NA									NA						ggggtctcaccgtgttagcca	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33414771C>T		NA		hg19		0.02	-0.236837	CACxGTG	COVERED																																																																																			NOVEL					0			6	3.308072	KEEP	0	0	0	11	310	CC	0.993072	0.608164	0			5	54	143	0	0	11.159586	21	60	695	45		0.192308	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33534563	33534563	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33534563C>A			NA	NA				BMS1P8 (35471 upstream) : IGHV3OR16-12 (70667 downstream)						NA		NA									NA						ccagcctgggcaacagtgagt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33534563C>A		NA		hg19		0.02	1.260604	GGGxAAC	COVERED																																																																																			NOVEL					0			20	3.241295	KEEP	6	4	111	50	1500	CC	1	0.997898	0			6	55	173	0	0	11.39988	61	60	2026	158		0.089552	0.997898
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33539535	33539535	__UNKNOWN__	IGR	SNP	T	T	C	rs55950724	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33539535T>C			NA	NA				BMS1P8 (40443 upstream) : IGHV3OR16-12 (65695 downstream)						NA		NA									NA						GAAAATAATATAAAAAATGAG	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33539535T>C		NA		hg19		0.02	1.927105	ATAxAAA	COVERED																																																																																			NOVEL					0			0	3.005115	KEEP	2	0	0	10	259	TT	0.99254	0.985519	0			4	47	137	0	0	9.67055	43	60	1169	97		0.085106	0.992926
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33539673	33539673	__UNKNOWN__	IGR	SNP	A	A	C	rs77818975		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33539673A>C			NA	NA				BMS1P8 (40581 upstream) : IGHV3OR16-12 (65557 downstream)						NA		NA									NA						AAAAAGATACAACAAAAATGA	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33539673A>C		NA		hg19		0.02	1.880022	TACxACA	COVERED																																																																																			NOVEL					0			4	3.306761	KEEP	16	0	0	11	288	AA	0.992708	0.976984	0			4	27	133	0	0	9.158672	46	60	1289	115		0.08	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33935715	33935715	__UNKNOWN__	IGR	SNP	A	A	G	rs74793003	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33935715A>G			NA	NA				RP11-812E19.3 (157971 upstream) : AC136932.2 (10233 downstream)						NA		NA									NA						AAGGAGACAGAAAAAAGCAAA	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33935715A>G		NA		hg19		0.02	3.86536	CAGxAAA	COVERED																																																																																			NOVEL					0			11	2.568984	KEEP	6	2	61	30	802	AA	0.999997	0.999978	0			11	60	346	0	2	29.234565	32	60	907	192		0.255814	0.999981
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33939904	33939904	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33939904T>C			NA	NA				RP11-812E19.3 (162160 upstream) : AC136932.2 (6044 downstream)						NA		NA									NA						GGTCAAAGAATGAAAGACAAT	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33939904T>C		NA		hg19		0.02	-0.28937	GAAxGAA	COVERED																																																																																			NOVEL					0			6	2.704759	KEEP	0	0	0	9	226	TT	0.99254	0.755211	0			3	60	97	1	0	6.944673	26	60	730	44		0.103448	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33939927	33939927	__UNKNOWN__	IGR	SNP	A	A	T	rs694592	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33939927A>T			NA	NA				RP11-812E19.3 (162183 upstream) : AC136932.2 (6021 downstream)						NA		NA									NA						GGAAAAGCCAATCTTCAAATA	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33939927A>T		NA		hg19		0.02	1.520152	CCAxTCT	COVERED																																																																																			NOVEL					0			12	3.337262	KEEP	1	1	25	20	522	AA	0.999869	0.993573	0			9	60	255	0	0	19.649272	40	60	1231	96		0.183673	0.993703
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33940664	33940664	__UNKNOWN__	IGR	SNP	G	G	A	rs79869205	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33940664G>A			NA	NA				RP11-812E19.3 (162920 upstream) : AC136932.2 (5284 downstream)						NA		NA									NA						ACAAACAATGGCAGTTACTAT	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33940664G>A		NA		hg19		0.02	7.680182	ATGxCAG	COVERED																																																																																			NOVEL					0			6	2.438422	KEEP	0	4	110	47	1424	GG	1	1	0			11	60	314	0	0	17.700797	210	60	7215	528		0.049774	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33940742	33940742	__UNKNOWN__	IGR	SNP	A	A	G	rs78622517	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33940742A>G			NA	NA				RP11-812E19.3 (162998 upstream) : AC136932.2 (5206 downstream)						NA		NA									NA						GATATTAAGTAAAAAATGAAA	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33940742A>G		NA		hg19		0.02	1.412216	AGTxAAA	COVERED																																																																																			NOVEL					0			2	2.532462	KEEP	0	1	27	18	444	AA	0.99986	0.999822	0			8	60	243	0	0	17.710688	55	60	1513	124		0.126984	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33940812	33940812	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33940812G>A			NA	NA				RP11-812E19.3 (163068 upstream) : AC136932.2 (5136 downstream)						NA		NA									NA						AATGAGCATGGCATAAGTCCC	0.289		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33940812G>A		NA		hg19		0.02	4.662972	ATGxCAT	COVERED																																																																																			NOVEL					0			12	6.92071	KEEP	0	0	0	23	708	GG	0.999892	0.999892	0			11	60	337	0	0	22.748514	115	60	3853	290		0.087302	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33941008	33941008	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33941008C>A			NA	NA				RP11-812E19.3 (163264 upstream) : AC136932.2 (4940 downstream)						NA		NA									NA						CCAGGTCTACCATGGCCCTGC	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33941008C>A		NA		hg19		0.02	4.315595	TACxATG	COVERED																																																																																			NOVEL					0			4	9.025105	KEEP	4	0	0	30	889	CC	0.999997	0.999997	0			10	45	296	0	0	19.326515	113	60	3777	308		0.081301	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33941044	33941044	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33941044C>T			NA	NA				RP11-812E19.3 (163300 upstream) : AC136932.2 (4904 downstream)						NA		NA									NA						AGAAAGTGGCCTCACTCATGC	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33941044C>T		NA		hg19		0.02	6.060779	GGCxTCA	COVERED																																																																																			NOVEL					0			4	6.553278	KEEP	3	1	29	32	998	CC	0.999997	0.999997	0			9	48	271	0	0	16.494228	146	60	5029	393		0.058065	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33941046	33941046	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33941046C>T			NA	NA				RP11-812E19.3 (163302 upstream) : AC136932.2 (4902 downstream)						NA		NA									NA						AAAGTGGCCTCACTCATGCTC	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33941046C>T		NA		hg19		0.02	5.755891	CCTxACT	COVERED																																																																																			NOVEL					0			4	6.351963	KEEP	4	1	28	31	950	CC	0.999997	0.999997	0			9	48	258	0	0	15.229465	145	60	4850	389		0.058442	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33941086	33941086	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33941086C>T			NA	NA				RP11-812E19.3 (163342 upstream) : AC136932.2 (4862 downstream)						NA		NA									NA						TATCAAGAGTCACACATAACA	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33941086C>T		NA		hg19		0.02	3.803827	AGTxACA	COVERED																																																																																			NOVEL					0			3	4.647514	KEEP	3	1	30	26	800	CC	0.999988	0.999988	0			11	50	324	0	0	20.687647	136	60	4553	305		0.07483	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33942063	33942063	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33942063T>C			NA	NA				RP11-812E19.3 (164319 upstream) : AC136932.2 (3885 downstream)						NA		NA									NA						GTCTTGAAAATGTAGCATTTG	0.289		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33942063T>C		NA		hg19		0.02	1.970739	AAAxGTA	UNCOVERED																																																																																			NOVEL					0			5	3.007816	KEEP	37	0	0	10	278	TT	0	0	0			4	27	129	0	0	8.556256	52	60	1619	163		0.071429	0.986153
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33946383	33946383	__UNKNOWN__	IGR	SNP	G	G	A	rs112055332		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33946383G>A			NA	NA				AC136932.2 (362 upstream) : LINC00273 (14668 downstream)						NA		NA									NA						caattttgaaggaagttctac	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33946383G>A		NA		hg19		0.02	3.400016	GAAxGAA	COVERED																																																																																			NOVEL					0			8	5.717088	KEEP	1	0	0	19	589	GG	0.99986	0.999859	0			8	49	228	1	0	14.650115	92	60	3157	219		0.08	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33946398	33946398	__UNKNOWN__	IGR	SNP	G	G	A	rs143417285		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33946398G>A			NA	NA				AC136932.2 (377 upstream) : LINC00273 (14653 downstream)						NA		NA									NA						ttctactgtggataaaatgct	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33946398G>A		NA		hg19		0.02	1.140263	GTGxATA	COVERED																																																																																			NOVEL					0			2	2.707871	KEEP	1	0	0	9	273	GG	0.99254	0.99248	0			10	60	284	0	0	20.390384	65	60	2153	148		0.133333	0.99994
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33946426	33946426	__UNKNOWN__	IGR	SNP	G	G	T	rs141432699		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33946426G>T			NA	NA				AC136932.2 (405 upstream) : LINC00273 (14625 downstream)						NA		NA									NA						agcatcacatgctacagggaa	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33946426G>T		NA		hg19		0.02	1.634145	CATxCTA	COVERED																																																																																			NOVEL					0			3	3.308828	KEEP	0	0	0	11	317	GG	0.993072	0.960723	0			6	60	162	0	1	12.023587	30	60	970	72		0.166667	0.967425
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33947968	33947968	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33947968C>A			NA	NA				AC136932.2 (1947 upstream) : LINC00273 (13083 downstream)						NA		NA									NA						attgttctaccacagcctcct	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33947968C>A		NA		hg19		0.02	-0.3859	TACxACA	COVERED																																																																																			NOVEL					0			48	6.853136	KEEP	10	1	23	31	946	CC	0.999997	0.918168	0			5	47	158	0	0	12.568943	22	60	703	102		0.185185	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33950613	33950613	__UNKNOWN__	IGR	SNP	C	C	A	rs12165010		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33950613C>A			NA	NA				AC136932.2 (4592 upstream) : LINC00273 (10438 downstream)						NA		NA									NA						AAAACCCACCCCACCCTCCAC	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33950613C>A		NA		hg19		0.02	-0.324548	ACCxCAC	COVERED																																																																																			NOVEL					0			23	2.270772	KEEP	7	2	55	27	783	CC	0.999988	0.877697	0			3	60	92	0	0	7.472806	11	60	355	92		0.214286	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33955581	33955581	__UNKNOWN__	IGR	SNP	G	G	C	rs374857149|rs62643063		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33955581G>C			NA	NA				AC136932.2 (9560 upstream) : LINC00273 (5470 downstream)						NA		NA									NA						ctgtctctttgtgtctgtctg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33955581G>C		NA		hg19		0.02	-0.324511	TTTxTGT	COVERED																																																																																			NOVEL					0			7	5.283504	KEEP	8	2	61	39	1205	GG	0.999999	0.835715	0			4	24	132	0	0	12.423085	5	60	173	92		0.444444	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	33957634	33957634	__UNKNOWN__	IGR	SNP	A	A	G	rs79755069	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33957634A>G			NA	NA				AC136932.2 (11613 upstream) : LINC00273 (3417 downstream)						NA		NA									NA						TTTCCTGAGCACGCCCTTCCT	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.33957634A>G		NA		hg19		0.02	3.737307	AGCxCGC	COVERED																																																																																			NOVEL					0			104	2.769028	KEEP	18	9	257	100	2551	AA	1	1	0			6	60	198	0	0	17.523092	13	60	354	296		0.315789	1
LINC00273	649159	__UNKNOWN__	__UNKNOWN__	16	33961602	33961602	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33961602G>A	ENST00000539813.1	-	0	901					NR_038368.1				long intergenic non-protein coding RNA 273	NA		NA								lung(1)	1						GGCTGAGGTCGCTTCGGGGTC	0.711		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AY587847		16p11.2	2013-06-03	2011-08-11	2011-08-11	ENSG00000256642	ENSG00000256642	649159		Long non-coding RNAs	38595	other	unknown	non-protein coding RNA 273-1	NA	non-protein coding RNA 273	NCRNA00273	NA		Standard	NR_038368	NR_038368	NA	Approved	TOP, NCRNA00273-1	uc021thl.1		OTTHUMG00000176379	ENST00000539813.1:	chr16.hg19:g.33961602G>A		NA		hg19		0.02	13.669668	GTCxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	N	0.058	-1.230130	0.01518	.	.	ENSG00000256642	ENST00000539813	.	.	.	0.113	-0.226	0.13106	.	.	.	.	.	T	0.20618	0.0496	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23084	-1.0198	3	.	.	.	.	.	.	.	.	.	.	.	V	280	.	.	A	-	2	0	AC136932.2	33869103	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-1.632000	0.02024	-1.133000	0.02903	-1.132000	0.01976	GCG	NOVEL	LINC00273-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000431840.1	14	4.629693	KEEP	13	8	201	87	2400	GG	1	1	0		-	13	60	388	1	0	25.858031	136	60	4376	799	ENST00000539813.1	0.087248	1
LINC00273	649159	__UNKNOWN__	__UNKNOWN__	16	33961792	33961792	__UNKNOWN__	lincRNA	SNP	C	C	T	rs75294993		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:33961792C>T	ENST00000539813.1	-	0	711					NR_038368.1				long intergenic non-protein coding RNA 273	NA		NA								lung(1)	1						TCTGCGGGCTCCCGGGTGCCC	0.692		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AY587847		16p11.2	2013-06-03	2011-08-11	2011-08-11	ENSG00000256642	ENSG00000256642	649159		Long non-coding RNAs	38595	other	unknown	non-protein coding RNA 273-1	NA	non-protein coding RNA 273	NCRNA00273	NA		Standard	NR_038368	NR_038368	NA	Approved	TOP, NCRNA00273-1	uc021thl.1		OTTHUMG00000176379	ENST00000539813.1:	chr16.hg19:g.33961792C>T		NA		hg19		0.02	-0.324502	GCTxCCG	COVERED	.	.	.	.	.	.	.	.	.	.	t	7.233	0.599757	0.13939	.	.	ENSG00000256642	ENST00000539813	.	.	.	.	.	.	.	.	.	.	.	T	0.29355	0.0731	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26467	-1.0102	2	.	.	.	.	.	.	.	.	.	.	.	K	217	.	.	E	-	1	0	AC136932.2	33869293	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	-1.933000	0.01553	0.119000	0.18210	0.121000	0.15741	GAG	NOVEL	LINC00273-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000431840.1	3	3.0064	KEEP	1	0	0	10	281	CC	0.992708	0.829622	0		-	5	60	137	0	0	10.857852	18	60	570	55	ENST00000539813.1	0.217391	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	34175669	34175669	__UNKNOWN__	IGR	SNP	C	C	A	rs367812236		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:34175669C>A			NA	NA				RNA5-8SP2 (210092 upstream) : CTD-2144E22.8 (37445 downstream)						NA		NA									NA						catgagccaccgcgctgggtc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.34175669C>A		NA		hg19		0.02	-0.25439	CACxGCG	COVERED																																																																																			NOVEL					0			19	5.407742	KEEP	20	0	0	18	469	CT	0.99649	0.691234	0			4	60	126	0	1	9.979312	18	60	589	85		0.181818	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	34175671	34175671	__UNKNOWN__	IGR	SNP	C	C	T	rs150947775	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:34175671C>T			NA	NA				RNA5-8SP2 (210094 upstream) : CTD-2144E22.8 (37443 downstream)						NA		NA									NA						tgagccaccgcgctgggtcct	0.493		NA											.|||	4	0.000798722	0.0	0.0	5008	,	,	NA	16286	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.34175671C>T		NA		hg19		0.02	-0.236834	CCGxGCT	COVERED																																																																																			NOVEL					0			19	3.137156	KEEP	20	1	30	21	562	CC	0.99649	0.610258	0			4	54	124	0	1	10.062537	15	60	488	78		0.210526	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46395190	46395190	__UNKNOWN__	IGR	SNP	A	A	T	rs4250144		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:46395190A>T			NA	NA				None (None upstream) : ANKRD26P1 (108062 downstream)						NA		NA									NA						atctcattcgatgatgattcc	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46395190A>T		NA		hg19		0.02	-0.131557	TCGxTGA	UNCOVERED																																																																																			NOVEL					0			9	5.113535	KEEP	24	0	0	17	482	AA	0	0	0			3	40	85	0	0	6.882165	10	48	299	65		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	46407013	46407013	__UNKNOWN__	IGR	SNP	T	T	G	rs4436803	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:46407013T>G			NA	NA				None (None upstream) : ANKRD26P1 (96239 downstream)						NA		NA									NA						ttacattccatgacgattccg	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.46407013T>G		NA		hg19		0.02	-0.131549	CCAxGAC	COVERED																																																																																			NOVEL					0			11	2.336978	KEEP	10	1	29	18	489	TT	0.993634	0.227714	0			3	27	100	0	0	8.273104	11	50	315	41		0.214286	0.229173
NETO2	81831	__UNKNOWN__	__UNKNOWN__	16	47128655	47128655	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:47128655G>A	ENST00000562435.1	-	8	1268				NETO2_ENST00000303155.5_Intron	NM_018092.4	NP_060562.3	Q8NC67	NETO2_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 2	NA		NA			regulation of kainate selective glutamate receptor activity (GO:2000312)	kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)				breast(1)|cervix(1)|endometrium(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	29		all_cancers(37;0.00114)|all_lung(18;0.00432)|Lung NSC(13;0.0384)|Breast(268;0.174)				tttgagacggggtcttgctct	0.552		NA								HNSCC(25;0.065)											NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001292	CCDS10727.1, CCDS58460.1	16q11.2	2008-08-04			ENSG00000171208	ENSG00000171208	81831			14644	protein-coding gene	gene with protein product		607974			NA	11943477	Standard	NM_018092	NM_018092	NA	Approved	FLJ10430, NEOT2	uc002eer.2	Q8NC67	OTTHUMG00000133101	ENST00000562435.1:c.884-8405C>T	chr16.hg19:g.47128655G>A		NA	J3KNF1|Q7Z381|Q8ND51|Q96SP4|Q9NVY8	hg19	CCDS10727.1	0.02	-0.192988	CGGxGTC	COVERED																																																																																			NOVEL	NETO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256766.2	3	4.21298	KEEP	0	0	0	14	445	GG	0.99649	0.45615	0		-	3	60	91	0	0	6.792506	18	60	609	53	ENST00000562435.1	0.142857	0.457757
PHKB	5257	__UNKNOWN__	__UNKNOWN__	16	47563536	47563536	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:47563536A>G	ENST00000566044.1	+	7	762				RP11-177N22.3_ENST00000573040.1_RNA|PHKB_ENST00000455779.1_Intron|PHKB_ENST00000323584.5_Intron|PHKB_ENST00000567402.1_Intron|PHKB_ENST00000299167.8_Intron	NM_001031835.2	NP_001027005.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	NA		NA			carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				gattacaggcatgagccaccg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	5257	2.7.11.19		8927	protein-coding gene	gene with protein product		172490			NA		Standard		NM_000293	NA	Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000566044.1:c.573+14024A>G	chr16.hg19:g.47563536A>G		NA	Q8N4T5	hg19	CCDS42161.1	0.02	-0.245585	GGCxTGA	COVERED																																																																																			NOVEL	PHKB-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000430412.1	3	3.006415	KEEP	1	0	0	10	262	AA	0.992708	0.63667	0		+	3	60	104	1	0	7.96463	20	60	595	60	ENST00000566044.1	0.130435	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	48491406	48491406	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:48491406A>G			NA	NA				RP11-44I10.6 (9097 upstream) : snoU13 (34902 downstream)						NA		NA									NA						agcactttggaaggccaaggt	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.48491406A>G		NA		hg19		0.02	-0.157883	TGGxAGG	COVERED																																																																																			NOVEL					0			1	2.406562	KEEP	0	0	0	8	229	AA	0.99257	0.320408	0			3	60	90	0	0	7.382073	10	60	309	38		0.230769	0.322807
HEATR3	55027	__UNKNOWN__	__UNKNOWN__	16	50130001	50130001	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:50130001T>C	ENST00000299192.7	+	12	1790				HEATR3_ENST00000285767.4_Intron	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	NA		NA								cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						tttgggaggctgaggcgggca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393	55027			26087	protein-coding gene	gene with protein product		614951			NA	12477932	Standard	NM_182922	XM_005256013	NA	Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1599+1297T>C	chr16.hg19:g.50130001T>C		NA	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	hg19	CCDS10739.1	0.02	-0.192947	GGCxGAG	COVERED																																																																																			NOVEL	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256880.2	11	4.512115	KEEP	0	0	0	15	425	TT	0.99649	0.488823	0		+	3	60	96	1	0	7.293185	18	60	539	50	ENST00000299192.7	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	50156823	50156823	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:50156823A>G			NA	NA				RP11-429P3.5 (969 upstream) : SNORA70 (28729 downstream)						NA		NA									NA						cactttgggaagccgaggtgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.50156823A>G		NA		hg19		0.02	-0.201731	GGAxGCC	UNCOVERED																																																																																			NOVEL					0			7	2.406484	KEEP	4	0	0	8	228	AA	0	0	0			3	60	91	0	0	6.793364	18	60	547	49		0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	51986811	51986811	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:51986811T>C			NA	NA				RP11-7O14.1 (179727 upstream) : C16orf97 (52587 downstream)						NA		NA									NA						ttagtagagatggggtttcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.51986811T>C		NA		hg19		0.02	-0.15782	AGAxGGG	COVERED																																																																																			NOVEL					0			4	2.404552	KEEP	0	0	0	8	206	TT	0.99257	0.320408	0			4	60	129	0	0	10.902023	12	60	334	30		0.25	0.322807
TOX3	27324	__UNKNOWN__	__UNKNOWN__	16	52535347	52535347	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:52535347G>A	ENST00000219746.9	-	2	372				TOX3_ENST00000407228.3_Intron	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	NA		NA			apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						actttgggaggctgaggcggg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460	27324		Trinucleotide (CAG) repeat containing	11972	protein-coding gene	gene with protein product		611416	trinucleotide repeat containing 9	TNRC9	NA	9225980	Standard	XM_049037	NM_001080430	NA	Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.88-32861C>T	chr16.hg19:g.52535347G>A		NA	B4DRD0|B5MCW4	hg19	CCDS54009.1	0.02	-0.122815	GAGxCTG	UNCOVERED																																																																																			NOVEL	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422534.1	10	2.40705	KEEP	6	0	0	8	243	GG	0	0	0		-	3	40	93	0	0	7.800881	9	60	317	38	ENST00000219746.9	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	52861078	52861078	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:52861078A>G			NA	NA				RP11-297L17.4 (197808 upstream) : RP11-467J12.2 (115614 downstream)						NA		NA									NA						aggccgaggcaggcggatcac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.52861078A>G		NA		hg19		0.02	-0.105253	GGCxGGC	UNCOVERED																																																																																			NOVEL					0			5	2.707427	KEEP	3	0	0	9	257	AT	0.99257	0.138793	0			3	60	103	0	0	8.932583	8	60	236	35		0.272727	0.139832
CHD9	80205	__UNKNOWN__	__UNKNOWN__	16	53141129	53141129	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:53141129C>T	ENST00000564582.1	+	1	89				CHD9_ENST00000566029.1_Intron|CHD9_ENST00000447540.1_Intron			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	NA		NA			cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				cccagcacttcgggaggccaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200	80205			25701	protein-coding gene	gene with protein product		NA			NA	9205841	Standard	NM_025134	XM_005256168	NA	Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000564582.1:c.89+7949C>T	chr16.hg19:g.53141129C>T		NA	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	hg19		0.02	-0.078924	CTTxGGG	UNCOVERED																																																																																			NOVEL	CHD9-009	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000422341.1	5	2.406609	KEEP	0	0	0	8	238	CC	0.99257	0.076761	0		+	3	60	78	0	0	6.742595	6	60	190	22	ENST00000564582.1	0.333333	0.077336
CHD9	80205	__UNKNOWN__	__UNKNOWN__	16	53233969	53233969	__UNKNOWN__	Intron	SNP	A	A	G	rs34730170		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:53233969A>G	ENST00000566029.1	+	3	1661				CHD9_ENST00000564845.1_Intron|CHD9_ENST00000447540.1_Intron|CHD9_ENST00000398510.3_Intron			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	NA		NA			cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				ccaacatggcaaaaccctgtc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200	80205			25701	protein-coding gene	gene with protein product		NA			NA	9205841	Standard	NM_025134	XM_005256168	NA	Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000566029.1:c.1453-9425A>G	chr16.hg19:g.53233969A>G		NA	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	hg19	CCDS45485.1	0.02	-0.114029	GGCxAAA	UNCOVERED																																																																																			NOVEL	CHD9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422338.1	7	3.007514	KEEP	0	0	0	10	276	AA	0.992708	0.161282	0		+	3	60	103	1	0	8.932499	8	60	241	32	ENST00000566029.1	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	53609481	53609481	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:53609481A>G			NA	NA				AKTIP (72318 upstream) : RPGRIP1L (22113 downstream)						NA		NA									NA						tgatctgcccacctcagcctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.53609481A>G		NA		hg19		0.02	-0.122756	CCCxCCT	COVERED																																																																																			NOVEL					0			4	2.405942	KEEP	0	0	0	8	217	AA	0.99257	0.194853	0			3	60	92	0	0	7.832528	8	60	234	31		0.272727	0.196312
FTO	79068	__UNKNOWN__	__UNKNOWN__	16	53740576	53740576	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:53740576A>G	ENST00000471389.1	+	1	267				FTO_ENST00000394647.3_Intron	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	NA		NA			adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						tacccaaagtactgggattat	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718	79068		Alkylation repair homologs	24678	protein-coding gene	gene with protein product	AlkB homolog 9, alpha-ketoglutarate-dependent dioxygenase	610966			NA	17434869, 17991826, 22002720	Standard	NM_001080432	NM_001080432	NA	Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.45+2435A>G	chr16.hg19:g.53740576A>G		NA	A2RUH1|B2RNS0|Q0P676|Q7Z785	hg19	CCDS32448.1	0.02	-0.228008	AGTxCTG	COVERED																																																																																			NOVEL	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000352196.1	4	2.706105	KEEP	0	0	0	9	239	AA	0.99254	0.578582	0		+	3	60	94	0	0	7.092879	18	60	505	52	ENST00000471389.1	0.142857	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	55372063	55372063	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:55372063A>C			NA	NA				RP11-26L20.3 (4563 upstream) : MMP2 (51548 downstream)						NA		NA									NA						gttggccaggatggtctggat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.55372063A>C		NA		hg19		0.02	-0.105241	AGGxTGG	UNCOVERED																																																																																			NOVEL					0			4	2.704828	KEEP	0	0	0	9	239	AA	0.99254	0.138789	0			3	60	94	0	0	8.032701	8	60	233	30		0.272727	0.139832
GNAO1	2775	__UNKNOWN__	__UNKNOWN__	16	56388327	56388327	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:56388327T>C	ENST00000262493.6	+	8	1723					NM_020988.2	NP_066268.1	P09471	GNAO_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O	NA		NA			adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|dopamine receptor signaling pathway (GO:0007212)|forebrain development (GO:0030900)|locomotory behavior (GO:0007626)|muscle contraction (GO:0006936)|negative regulation of calcium ion transport (GO:0051926)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|regulation of heart contraction (GO:0008016)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to morphine (GO:0043278)	heterotrimeric G-protein complex (GO:0005834)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	corticotropin-releasing hormone receptor 1 binding (GO:0051430)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|mu-type opioid receptor binding (GO:0031852)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)	17		all_neural(199;0.159)				gtggctcacgtctgtaatccc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10756.1, CCDS10757.1	16q13	2008-08-01			ENSG00000087258	ENSG00000087258	2775			4389	protein-coding gene	gene with protein product		139311			NA	1899283, 11395521	Standard	NM_020988	NM_020988	NA	Approved	G-ALPHA-o	uc002eit.4	P09471	OTTHUMG00000133241	ENST00000262493.6:c.878-451T>C	chr16.hg19:g.56388327T>C		NA	P29777|Q8TD72|Q9UMV4	hg19	CCDS10756.1	0.02	-0.122802	ACGxCTG	UNCOVERED																																																																																			NOVEL	GNAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256981.2	3	2.406502	KEEP	1	0	0	8	228	TT	0	0	0		+	3	60	98	0	0	8.181945	10	60	307	34	ENST00000262493.6	0.230769	0.196312
NUDT21	11051	__UNKNOWN__	__UNKNOWN__	16	56474923	56474923	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:56474923C>A	ENST00000300291.5	-	4	554					NM_007006.2	NP_008937.1	O43809	CPSF5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 21	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	AU-rich element binding (GO:0017091)|histone deacetylase binding (GO:0042826)|hydrolase activity (GO:0016787)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)	7						aagtgctgggcttacaggcat	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ001810	CCDS10760.1	16q12.2	2013-06-18	2005-07-11	2005-07-11	ENSG00000167005	ENSG00000167005	11051		Nudix motif containing	13870	protein-coding gene	gene with protein product	cleavage factor Im complex 25 kDa subunit	604978	cleavage and polyadenylation specific factor 5, 25 kDa, cleavage and polyadenylation specific factor 5, 25 kD subunit	CPSF5	NA	9659921	Standard	NM_007006	NM_007006	NA	Approved	CFIM25	uc002eja.3	O43809	OTTHUMG00000133240	ENST00000300291.5:c.382-1265G>T	chr16.hg19:g.56474923C>A		NA	Q6IB85|Q6NE84	hg19	CCDS10760.1	0.02	-0.078939	GGGxTTA	UNCOVERED																																																																																			NOVEL	NUDT21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256980.3	4	3.009066	KEEP	0	0	0	10	310	CC	0.992708	0.076772	0		-	3	45	87	0	0	7.832421	5	60	167	28	ENST00000300291.5	0.375	0.077336
NUDT21	11051	__UNKNOWN__	__UNKNOWN__	16	56475069	56475069	__UNKNOWN__	Intron	SNP	A	A	C	rs4784668	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:56475069A>C	ENST00000300291.5	-	4	554					NM_007006.2	NP_008937.1	O43809	CPSF5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 21	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	AU-rich element binding (GO:0017091)|histone deacetylase binding (GO:0042826)|hydrolase activity (GO:0016787)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)	7						cctcagccccacaaagcactg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ001810	CCDS10760.1	16q12.2	2013-06-18	2005-07-11	2005-07-11	ENSG00000167005	ENSG00000167005	11051		Nudix motif containing	13870	protein-coding gene	gene with protein product	cleavage factor Im complex 25 kDa subunit	604978	cleavage and polyadenylation specific factor 5, 25 kDa, cleavage and polyadenylation specific factor 5, 25 kD subunit	CPSF5	NA	9659921	Standard	NM_007006	NM_007006	NA	Approved	CFIM25	uc002eja.3	O43809	OTTHUMG00000133240	ENST00000300291.5:c.382-1411T>G	chr16.hg19:g.56475069A>C		NA	Q6IB85|Q6NE84	hg19	CCDS10760.1	0.02	-0.236669	CCCxCAA	COVERED																																																																																			NOVEL	NUDT21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256980.3	11	5.713201	KEEP	0	0	0	19	517	AA	0.99986	0.612321	0		-	3	60	95	0	0	6.950246	22	60	618	63	ENST00000300291.5	0.12	0.612407
OGFOD1	55239	__UNKNOWN__	__UNKNOWN__	16	56507804	56507804	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:56507804T>C	ENST00000566157.1	+	11	1408				OGFOD1_ENST00000568397.1_Intron	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	NA		NA			cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	ctgcaacctctgcctcccagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263	55239			25585	protein-coding gene	gene with protein product	TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)	615857			NA	10997877	Standard	NM_018233	NM_018233	NA	Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.1286-936T>C	chr16.hg19:g.56507804T>C		NA	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	hg19	CCDS10761.2	0.02	-0.122796	CTCxGCC	COVERED																																																																																			NOVEL	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256976.3	3	3.307437	KEEP	0	0	0	11	292	TT	0.993072	0.194952	0		+	3	60	94	0	0	7.672907	11	60	333	39	ENST00000566157.1	0.214286	0.196312
OGFOD1	55239	__UNKNOWN__	__UNKNOWN__	16	56507805	56507805	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:56507805G>A	ENST00000566157.1	+	11	1408				OGFOD1_ENST00000568397.1_Intron	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	NA		NA			cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	tgcaacctctgcctcccaggt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263	55239			25585	protein-coding gene	gene with protein product	TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)	615857			NA	10997877	Standard	NM_018233	NM_018233	NA	Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.1286-935G>A	chr16.hg19:g.56507805G>A		NA	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	hg19	CCDS10761.2	0.02	-0.122807	TCTxCCT	COVERED																																																																																			NOVEL	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256976.3	3	3.309262	KEEP	0	0	0	11	320	GG	0.993072	0.194952	0		+	3	60	84	0	0	6.672898	11	60	375	39	ENST00000566157.1	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	56577495	56577495	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:56577495A>G			NA	NA				BBS2 (23300 upstream) : MT4 (21465 downstream)						NA		NA									NA						gctcacgcctataatcccagc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.56577495A>G		NA		hg19		0.02	-0.201685	CCTxTAA	COVERED																																																																																			NOVEL					0			6	2.706441	KEEP	1	0	0	9	242	AA	0.99257	0.4869	0			3	60	103	0	0	8.210508	15	60	416	48		0.166667	0.490544
NLRC5	84166	__UNKNOWN__	__UNKNOWN__	16	57097871	57097871	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:57097871C>T	ENST00000262510.6	+	33	4379				NLRC5_ENST00000539144.1_Intron|NLRC5_ENST00000308149.7_Intron|NLRC5_ENST00000436936.1_Intron	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	NA		NA			defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				aggatggtctcgatctcctga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853	84166		Nucleotide-binding domain and leucine rich repeat containing	29933	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5, NOD-like receptor C5	613537			NA	12615073	Standard	NM_032206	NM_032206	NA	Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4155-1253C>T	chr16.hg19:g.57097871C>T		NA	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	hg19	CCDS10773.1	0.02	-0.12278	TCTxGAT	UNCOVERED																																																																																			NOVEL	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257346.1	5	2.407249	KEEP	2	0	0	8	250	CC	0	0	0		+	3	40	81	0	0	6.601215	9	60	283	33	ENST00000262510.6	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	58089859	58089859	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58089859T>C			NA	NA				MMP15 (9054 upstream) : Y_RNA (27112 downstream)						NA		NA									NA						tgcagtggcatgatctcggca	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.58089859T>C		NA		hg19		0.02	-0.201604	GCAxGAT	COVERED																																																																																			NOVEL					0			4	2.706782	KEEP	3	0	0	9	247	TT	0.99257	0.4869	0			4	60	104	0	0	7.968918	16	60	472	44		0.2	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	58145979	58145979	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58145979G>A			NA	NA				Y_RNA (28907 upstream) : C16orf80 (1516 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.58145979G>A		NA		hg19		0.02	-0.157885	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			5	2.406688	KEEP	5	0	0	8	236	GG	0	0	0			3	60	84	0	0	6.479281	13	60	435	45		0.1875	0.322807
RP11-459F6.3	0	__UNKNOWN__	__UNKNOWN__	16	58185346	58185346	__UNKNOWN__	RNA	SNP	C	C	T	rs150368651	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58185346C>T	ENST00000569580.1	+	0	235										NA		NA									NA						gagccgagatcgcgccactgc	0.547		NA											C|||	2	0.000399361	0.0	0.0	5008	,	,	NA	15167	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000569580.1:	chr16.hg19:g.58185346C>T		NA		hg19		0.02	-0.192973	GATxGCG	COVERED																																																																																			NOVEL	RP11-459F6.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000422610.1	5	3.911083	KEEP	3	0	0	13	383	CC	0.993634	0.518837	0		+	3	60	84	1	0	6.392418	14	60	450	60	ENST00000569580.1	0.176471	0.522161
CCDC113	29070	__UNKNOWN__	__UNKNOWN__	16	58315789	58315789	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58315789A>C	ENST00000219299.4	+	0	3321				CCDC113_ENST00000443128.2_3'UTR|PRSS54_ENST00000567164.1_Intron|PRSS54_ENST00000543437.1_Intron|PRSS54_ENST00000219301.4_Intron	NM_014157.3	NP_054876.2	Q9H0I3	CC113_HUMAN	coiled-coil domain containing 113	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)				large_intestine(4)|lung(6)|ovary(1)|urinary_tract(1)	12						ctctgtccccaaggctggagt	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL136785	CCDS10795.1, CCDS45497.1	16q21	2008-02-05			ENSG00000103021	ENSG00000103021	29070			25002	protein-coding gene	gene with protein product		NA			NA	11230166, 11042152	Standard	NM_014157	NM_014157	NA	Approved	HSPC065, DKFZp434N1418	uc002ene.3	Q9H0I3	OTTHUMG00000133489	ENST00000219299.4:c.*2108A>C	chr16.hg19:g.58315789A>C		NA	B2RAQ7|B4DR20|Q9NZX2	hg19	CCDS10795.1	0.02	-0.41218	CCCxAGG	COVERED																																																																																			NOVEL	CCDC113-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257387.2	13	7.81696	KEEP	0	0	0	26	683	AA	0.999988	0.94173	0		+	3	60	97	0	0	6.44176	39	60	1131	97	ENST00000219299.4	0.071429	0.941741
NDRG4	65009	__UNKNOWN__	__UNKNOWN__	16	58524923	58524923	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58524923A>G	ENST00000394282.4	+	2	539				NDRG4_ENST00000394279.2_Intron|NDRG4_ENST00000258187.5_Intron	NM_001130487.1	NP_001123959.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	NA		NA			cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						gctcacacctataatcccagc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034	65009			14466	protein-coding gene	gene with protein product		614463			NA	11352569, 16408304	Standard		NM_020465	NA	Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000394282.4:c.132+3169A>G	chr16.hg19:g.58524923A>G		NA	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	hg19	CCDS45500.1	0.02	-0.315657	CCTxTAA	COVERED																																																																																			NOVEL	NDRG4-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257383.5	10	5.412132	KEEP	1	0	0	18	473	AA	0.999859	0.818349	0		+	4	60	136	0	0	10.16248	30	60	826	77	ENST00000394282.4	0.117647	0.818465
NDRG4	65009	__UNKNOWN__	__UNKNOWN__	16	58540062	58540062	__UNKNOWN__	Intron	SNP	C	C	G	rs56908844|rs2550426|rs200871998|rs528969454|rs72499708	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58540062C>G	ENST00000568640.1	+	6	568				NDRG4_ENST00000394279.2_Intron|NDRG4_ENST00000569923.1_Intron|NDRG4_ENST00000570248.1_Intron|NDRG4_ENST00000394282.4_Intron|NDRG4_ENST00000356752.4_Intron|NDRG4_ENST00000566192.1_Intron|NDRG4_ENST00000563799.1_Intron|NDRG4_ENST00000258187.5_Intron|NDRG4_ENST00000562999.1_Intron			Q9ULP0	NDRG4_HUMAN	NDRG family member 4	NA		NA			cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						gtgtgtgtgtctgtgtgtgtg	0.398		NA											G|||	3665	0.731829	0.8517	0.6499	5008	,	,	NA	4355	0.9266	NA	0.4632	False	NA	,,,	NA	NA	NA	2504	0.7035	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034	65009			14466	protein-coding gene	gene with protein product		614463			NA	11352569, 16408304	Standard		NM_020465	NA	Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000568640.1:c.427-229C>G	chr16.hg19:g.58540062C>G		NA	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	hg19	CCDS58465.1	0.02	3.80355	TGTxTGT	COVERED																																																																																			NOVEL	NDRG4-006	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422667.3	12	4.510416	KEEP	0	3	88	46	1403	CC	1	0.999994	0		+	6	60	207	0	1	13.657211	96	60	3135	227	ENST00000568640.1	0.058824	0.999994
CNOT1	23019	__UNKNOWN__	__UNKNOWN__	16	58583669	58583669	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58583669G>T	ENST00000317147.5	-	25	3808	c.3476C>A	c.(3475-3477)cCt>cAt	p.P1159H	CNOT1_ENST00000245138.4_Missense_Mutation_p.P49H|CNOT1_ENST00000441024.2_Missense_Mutation_p.P1159H|CNOT1_ENST00000569240.1_Missense_Mutation_p.P1154H	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1159	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.	NA			gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GTTAAATTCAGGATTCTTCAG	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													141	139	140			NA	NA	16		NA											NA				58583669		2198	4300	6498	SO:0001583	missense			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107	23019			7877	protein-coding gene	gene with protein product		604917		NOT1	NA	14702039	Standard	NM_016284	NM_016284	NA	Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.3476C>A	chr16.hg19:g.58583669G>T	ENSP00000320949:p.Pro1159His	NA	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	hg19	CCDS10799.1	0.02	1.300945	TCAxGAT	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.91|17.91	3.505040|3.505040	0.64410|0.64410	.|.	.|.	ENSG00000125107|ENSG00000125107	ENST00000422872|ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	.|T;T	.|0.17370	.|2.28;2.28	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.053701	.|0.85682	.|D	.|0.000000	.|T	.|0.37019	.|0.0988	M|M	0.82056|0.82056	2.57|2.57	0.80722|0.80722	D|D	1|1	.|P;D;P;P	.|0.59357	.|0.808;0.985;0.856;0.654	.|B;P;B;P	.|0.55999	.|0.344;0.789;0.319;0.605	.|T	.|0.16217	.|-1.0410	.|10	.|0.59425	.|D	.|0.04	.|.	12.6973|12.6973	0.57012|0.57012	0.0756:0.0:0.9244:0.0|0.0756:0.0:0.9244:0.0	.|.	.|49;1159;1159;1154	.|B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.|.;.;CNOT1_HUMAN;.	.|H	-1|1159;49;1154;1159	.|ENSP00000320949:P1159H;ENSP00000413113:P1159H	.|ENSP00000245138:P49H	.|P	-|-	.|2	.|0	CNOT1|CNOT1	57141170|57141170	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	6.807000|6.807000	0.75201|0.75201	2.583000|2.583000	0.87209|0.87209	0.561000|0.561000	0.74099|0.74099	.|CCT	NOVEL	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257385.3	0	5.717237	KEEP	0	0	0	19	587	GG	0.99986	0.999695	0		-	15	60	421	0	0	31.829724	73	60	2530	165	ENST00000317147.5	0.170455	0.999835
CNOT1	23019	__UNKNOWN__	__UNKNOWN__	16	58610239	58610239	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58610239T>C	ENST00000317147.5	-	14	2037				CNOT1_ENST00000441024.2_Intron|CNOT1_ENST00000569240.1_Intron	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	NA		NA			gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		tggtctcgaattcctgacctt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107	23019			7877	protein-coding gene	gene with protein product		604917		NOT1	NA	14702039	Standard	NM_016284	NM_016284	NA	Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.1704+127A>G	chr16.hg19:g.58610239T>C		NA	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	hg19	CCDS10799.1	0.02	-0.263078	GAAxTCC	COVERED																																																																																			NOVEL	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257385.3	12	3.908402	KEEP	1	0	0	13	343	TT	0.993634	0.689252	0		-	3	60	91	0	0	6.444784	24	60	682	53	ENST00000317147.5	0.111111	0.693668
SLC38A7	55238	__UNKNOWN__	__UNKNOWN__	16	58701867	58701867	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58701867C>T	ENST00000564100.1	-	8	1751				SLC38A7_ENST00000564010.1_Intron|SLC38A7_ENST00000566953.1_Intron|SLC38A7_ENST00000570101.1_Intron|SLC38A7_ENST00000219320.4_Intron			Q9NVC3	S38A7_HUMAN	solute carrier family 38, member 7	NA		NA			sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	L-alanine transmembrane transporter activity (GO:0015180)|L-amino acid transmembrane transporter activity (GO:0015179)|L-asparagine transmembrane transporter activity (GO:0015182)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|L-glutamine transmembrane transporter activity (GO:0015186)|L-histidine transmembrane transporter activity (GO:0005290)|L-leucine transmembrane transporter activity (GO:0015190)|L-methionine transmembrane transporter activity (GO:0015191)|L-serine transmembrane transporter activity (GO:0015194)			endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	13						gtcaggagttcgagaccagcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001961	CCDS10800.1	16q21	2013-05-22			ENSG00000103042	ENSG00000103042	55238		Solute carriers	25582	protein-coding gene	gene with protein product		614236			NA		Standard	NM_018231	XM_006721229	NA	Approved	FLJ10815	uc002eod.1	Q9NVC3	OTTHUMG00000133491	ENST00000564100.1:c.884-476G>A	chr16.hg19:g.58701867C>T		NA	Q53GJ9|Q9H9I5	hg19		0.02	-0.148326	GTTxGAG	COVERED																																																																																			NOVEL	SLC38A7-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000422205.1	6	2.7075	KEEP	0	0	0	9	260	CC	0.99254	0.289823	0		-	3	60	91	0	0	7.187192	13	60	391	35	ENST00000564100.1	0.1875	0.292001
RP11-410D17.2	0	__UNKNOWN__	__UNKNOWN__	16	58863758	58863758	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:58863758G>A	ENST00000500117.1	+	0	679										NA		NA									NA						ccaaagtgctgggattatagg	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000500117.1:	chr16.hg19:g.58863758G>A		NA		hg19		0.02	-0.149122	GCTxGGA	COVERED																																																																																			NOVEL	RP11-410D17.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000422091.1	14	3.009289	KEEP	2	0	0	10	318	GG	0.992708	0.289872	0		+	3	52	85	0	0	6.672417	12	60	400	40	ENST00000500117.1	0.2	0.292001
RP11-410D17.2	0	__UNKNOWN__	__UNKNOWN__	16	59062948	59062948	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:59062948C>T	ENST00000500117.1	+	0	679										NA		NA									NA						tttgggaggccgaggcgggtg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000500117.1:	chr16.hg19:g.59062948C>T		NA		hg19		0.02	-0.114036	GGCxGAG	UNCOVERED																																																																																			NOVEL	RP11-410D17.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000422091.1	8	2.707154	KEEP	4	0	0	9	263	CC	0	0	0		+	3	60	91	0	0	7.600975	9	60	297	33	ENST00000500117.1	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	61385772	61385772	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:61385772T>C			NA	NA				RP11-51O6.1 (295904 upstream) : CDH8 (295373 downstream)						NA		NA									NA						gggtggatcatgaggtcagga	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.61385772T>C		NA		hg19		0.02	-0.052617	TCAxGAG	UNCOVERED																																																																																			NOVEL					0			4	2.405804	KEEP	3	0	0	8	218	TT	0	0	0			3	60	92	0	1	8.825102	3	60	83	21		0.5	0.036766
RP11-95H3.1	0	__UNKNOWN__	__UNKNOWN__	16	65208439	65208439	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:65208439T>C	ENST00000563754.1	-	0	406										NA		NA									NA						ggattacaggtgtgagccacc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000563754.1:	chr16.hg19:g.65208439T>C		NA		hg19		0.02	-0.210486	AGGxGTG	COVERED																																																																																			NOVEL	RP11-95H3.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000420596.2	9	3.007881	KEEP	2	0	0	10	280	TT	0.99254	0.518266	0		-	4	60	114	0	0	8.780836	18	60	537	52	ENST00000563754.1	0.181818	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	65892297	65892297	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:65892297T>G			NA	NA				RP11-351A20.1 (211447 upstream) : RP11-513N24.1 (2717 downstream)						NA		NA									NA						tccctatgtttcccaggctgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.65892297T>G		NA		hg19		0.02	-0.131563	GTTxCCC	COVERED																																																																																			NOVEL					0			4	2.405991	KEEP	0	0	0	8	220	TT	0.99257	0.22747	0			3	60	102	0	0	8.372236	12	60	356	33		0.2	0.229173
CDH5	1003	__UNKNOWN__	__UNKNOWN__	16	66418617	66418617	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:66418617A>C	ENST00000341529.3	+	3	358				CDH5_ENST00000563425.2_Intron	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	NA		NA			adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	acctgtaatcacagcactttg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776	1003		CD molecules, Cadherins / Major cadherins	1764	protein-coding gene	gene with protein product	VE-cadherin	601120	cadherin 5, type 2, VE-cadherin (vascular epithelium)		NA	2059658	Standard	NM_001795	NM_001795	NA	Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.211-2095A>C	chr16.hg19:g.66418617A>C		NA	Q4VAI5|Q4VAI6	hg19	CCDS10804.1	0.02	-0.140324	ATCxCAG	UNCOVERED																																																																																			NOVEL	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268767.1	12	3.006684	KEEP	3	0	0	10	264	AA	0	0	0		+	4	40	127	0	0	10.971569	10	60	289	31	ENST00000341529.3	0.285714	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	66622595	66622595	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:66622595A>G			NA	NA				CMTM2 (417 upstream) : CMTM3 (15339 downstream)						NA		NA									NA						cactcttgttacccaggctgg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.66622595A>G		NA		hg19		0.02	-0.096484	GTTxCCC	UNCOVERED																																																																																			NOVEL					0			3	2.405974	KEEP	0	0	0	8	218	AA	0.99257	0.119541	0			3	60	107	0	0	9.643921	6	60	173	30		0.333333	0.120436
CMTM4	146223	__UNKNOWN__	__UNKNOWN__	16	66668081	66668081	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:66668081A>G	ENST00000394106.2	-	2	545				CMTM4_ENST00000563952.1_Intron|CMTM4_ENST00000330687.4_Intron			Q8IZR5	CKLF4_HUMAN	CKLF-like MARVEL transmembrane domain containing 4	NA		NA			chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0811)|Epithelial(162;0.214)		ggtggctcacacctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF479814	CCDS10817.1, CCDS42170.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000183723	ENSG00000183723	146223			19175	protein-coding gene	gene with protein product		607887	chemokine-like factor super family 4, chemokine-like factor superfamily 4	CKLFSF4	NA	12782130	Standard		NM_178818	NA	Approved		uc002epz.3	Q8IZR5	OTTHUMG00000137500	ENST00000394106.2:c.363+2226T>C	chr16.hg19:g.66668081A>G		NA	Q52M40|Q8IZR4|Q8IZV1	hg19	CCDS42170.1	0.02	-0.201713	CACxCCT	COVERED																																																																																			NOVEL	CMTM4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421030.1	8	3.308701	KEEP	2	0	0	11	309	AA	0.992708	0.486967	0		-	3	60	104	0	0	8.233339	16	60	464	48	ENST00000394106.2	0.157895	0.490544
CCDC79	283847	__UNKNOWN__	__UNKNOWN__	16	66795499	66795499	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:66795499T>G	ENST00000558713.2	-	16	1853				CCDC79_ENST00000432602.1_Intron|CCDC79_ENST00000433574.1_Intron|CCDC79_ENST00000415744.1_Intron|CCDC79_ENST00000433154.1_Intron			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	NA		NA			meiotic telomere clustering (GO:0045141)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|skin(2)	7						ttcaagaccatcctgggcaac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093213		16q22.1	2012-10-03			ENSG00000249961	ENSG00000249961	283847			26675	protein-coding gene	gene with protein product		NA			NA		Standard		NM_001136505	NA	Approved	FLJ35894	uc010viv.2	Q8NA31	OTTHUMG00000133562	ENST00000558713.2:c.1781-2306A>C	chr16.hg19:g.66795499T>G		NA	A0AUW1	hg19		0.02	-0.140325	CCAxCCT	COVERED																																																																																			NOVEL	CCDC79-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000418864.2	10	3.608665	KEEP	0	0	0	12	324	TT	0.993634	0.259304	0		-	4	60	123	0	0	10.431144	11	60	323	40	ENST00000558713.2	0.266667	0.260965
PDP2	57546	__UNKNOWN__	__UNKNOWN__	16	66922246	66922246	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:66922246A>G	ENST00000568720.1	+	2	59				RP11-61A14.2_ENST00000561475.1_lincRNA			Q9P2J9	PDP2_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 2	NA		NA			cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|magnesium-dependent protein serine/threonine phosphatase activity (GO:0004724)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.088)|Epithelial(162;0.204)		gatgataggcatgagccaccg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037769	CCDS10822.1	16q22.1	2012-04-17			ENSG00000172840	ENSG00000172840	57546		Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	30263	protein-coding gene	gene with protein product	protein phosphatase 2C, magnesium-dependent, catalytic subunit 2	615499			NA	9651365	Standard	NM_020786	NM_020786	NA	Approved	KIAA1348, PPM2C2	uc002eqk.2	Q9P2J9	OTTHUMG00000137512	ENST00000568720.1:c.60-4211A>G	chr16.hg19:g.66922246A>G		NA	A8K924	hg19		0.02	-0.201716	GGCxTGA	COVERED																																																																																			NOVEL	PDP2-008	PUTATIVE	basic	processed_transcript	NA	protein_coding	OTTHUMT00000421191.1	10	3.007602	KEEP	1	0	0	10	275	AA	0.992708	0.486967	0		+	3	60	99	0	0	7.733449	16	60	473	46	ENST00000568720.1	0.157895	0.490544
CES3	23491	__UNKNOWN__	__UNKNOWN__	16	67002545	67002545	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:67002545G>A	ENST00000543856.1	+	1	425				CES3_ENST00000303334.4_Intron|CES3_ENST00000394037.1_Intron	NM_001185176.1	NP_001172105.1	Q6UWW8	EST3_HUMAN	carboxylesterase 3	NA		NA				endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		Agccgggtgcggtggctcatg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828	23491		Carboxylesterases	1865	protein-coding gene	gene with protein product	esterase 31, brain carboxylesterase BR3	605279	carboxylesterase 3 (brain)		NA	10518925, 14581373, 15100172, 20931200	Standard	NM_024922	NM_001185176	NA	Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000543856.1:c.-22+743G>A	chr16.hg19:g.67002545G>A		NA	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	hg19	CCDS54023.1	0.02	-0.140345	TGCxGTG	COVERED																																																																																			NOVEL	CES3-003	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000431986.1	3	2.405863	KEEP	0	0	0	8	229	GG	0.99257	0.259026	0		+	3	60	92	0	0	7.472863	11	60	347	35	ENST00000543856.1	0.214286	0.260965
C16orf70	80262	__UNKNOWN__	__UNKNOWN__	16	67157222	67157222	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:67157222T>G	ENST00000219139.3	+	3	335				C16orf70_ENST00000569600.1_Intron|C16orf70_ENST00000569683.1_Intron	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	NA		NA								cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		gctcatgcctttaatcccagc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149	80262			29564	protein-coding gene	gene with protein product		NA	chromosome 16 open reading frame 6	C16orf6, LIN10	NA	12477932	Standard	NM_025187	NM_025187	NA	Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.148-2640T>G	chr16.hg19:g.67157222T>G		NA	Q9HA86	hg19	CCDS10828.1	0.02	-0.192957	CCTxTAA	COVERED																																																																																			NOVEL	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268829.2	2	3.006792	KEEP	0	0	0	10	263	TT	0.992708	0.454419	0		+	3	60	94	0	0	7.02734	19	60	570	49	ENST00000219139.3	0.136364	0.457757
CTCF	10664	__UNKNOWN__	__UNKNOWN__	16	67644521	67644521	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:67644521T>C	ENST00000264010.4	+	3	435				CTCF_ENST00000401394.1_Intron	NM_006565.3	NP_006556.1	P49711	CTCF_HUMAN	CCCTC-binding factor (zinc finger protein)	NA		NA			chromatin modification (GO:0016568)|chromosome segregation (GO:0007059)|DNA methylation (GO:0006306)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome positioning (GO:0016584)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone acetylation (GO:0035065)|regulation of histone methylation (GO:0031060)|regulation of molecular function, epigenetic (GO:0040030)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin insulator sequence binding (GO:0043035)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(6)|central_nervous_system(2)|cervix(1)|endometrium(34)|haematopoietic_and_lymphoid_tissue(7)|kidney(3)|large_intestine(9)|liver(1)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	79		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0166)|Epithelial(162;0.0577)		cctcccaaagtgctgggatta	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(175;1200 1966 6945 23069 27405)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U25435	CCDS10841.1, CCDS54029.1	16q21-q22.3	2013-01-08			ENSG00000102974	ENSG00000102974	10664		Zinc fingers, C2H2-type	13723	protein-coding gene	gene with protein product	11 zinc finger transcriptional repressor	604167			NA	8649389, 18550811	Standard	NM_006565	NM_006565	NA	Approved		uc002etl.3	P49711	OTTHUMG00000137539	ENST00000264010.4:c.-9-206T>C	chr16.hg19:g.67644521T>C		NA	B5MC38|Q53XI7|Q59EL8	hg19	CCDS10841.1	0.02	-0.192953	AAGxGCT	UNCOVERED																																																																																			NOVEL	CTCF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268870.2	5	2.405832	KEEP	4	0	0	8	220	TT	0	0	0		+	3	40	106	0	0	8.291987	18	60	539	49	ENST00000264010.4	0.142857	0.457757
GFOD2	81577	__UNKNOWN__	__UNKNOWN__	16	67721314	67721314	__UNKNOWN__	Intron	SNP	C	C	T	rs112206338	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:67721314C>T	ENST00000268797.7	-	2	259				GFOD2_ENST00000602377.1_Intron	NM_030819.3	NP_110446.3	Q3B7J2	GFOD2_HUMAN	glucose-fructose oxidoreductase domain containing 2	NA		NA			extracellular matrix organization (GO:0030198)	proteinaceous extracellular matrix (GO:0005578)	oxidoreductase activity (GO:0016491)			breast(2)|endometrium(1)|large_intestine(4)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	19		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0151)|Epithelial(162;0.0505)|all cancers(182;0.242)		gaggccgaggcgggcggatca	0.468		NA											C|||	21	0.00419329	0.0159	0.0	5008	,	,	NA	12649	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074382	CCDS10845.1, CCDS59268.1	16q22.1	2008-02-05			ENSG00000141098	ENSG00000141098	81577			28159	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_030819	NM_030819	NA	Approved	FLJ23802, MGC11335	uc002eub.3	Q3B7J2	OTTHUMG00000137537	ENST00000268797.7:c.87-1609G>A	chr16.hg19:g.67721314C>T		NA	Q69YL9|Q6UXX6|Q7L648|Q8TE86|Q9BQ07|R4GNG5	hg19	CCDS10845.1	0.02	-0.175428	AGGxGGG	UNCOVERED																																																																																			NOVEL	GFOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268868.2	7	3.00858	KEEP	6	0	0	10	302	CC	0	0	0		-	3	60	85	0	0	6.492371	14	60	466	48	ENST00000268797.7	0.176471	0.387407
RANBP10	57610	__UNKNOWN__	__UNKNOWN__	16	67799098	67799098	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:67799098A>G	ENST00000317506.3	-	3	516				RANBP10_ENST00000536251.1_Intron|RANBP10_ENST00000448631.2_Intron|RANBP10_ENST00000602677.1_Intron|RANBP10_ENST00000602887.1_Intron|RANBP10_ENST00000411657.2_Intron|RANBP10_ENST00000425512.2_Intron	NM_020850.1	NP_065901.1	Q6VN20	RBP10_HUMAN	RAN binding protein 10	NA		NA			microtubule cytoskeleton organization (GO:0000226)	cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			endometrium(5)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23		Acute lymphoblastic leukemia(13;4.34e-06)|all_hematologic(13;0.000643)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00522)|Epithelial(162;0.025)|all cancers(182;0.157)		gcaagactccatctcaaaaaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040897	CCDS32469.1	16q22	2008-02-05				ENSG00000141084	57610			29285	protein-coding gene	gene with protein product		614031			NA	14684163	Standard	NM_020850	NM_020850	NA	Approved	KIAA1464	uc002eud.3	Q6VN20		ENST00000317506.3:c.400+6838T>C	chr16.hg19:g.67799098A>G		NA	A4FTY2|B4DID0|B4DQH9|E7EW27|Q9P264	hg19	CCDS32469.1	0.02	-0.02631	TCCxTCT	UNCOVERED																																																																																			NOVEL	RANBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000467896.1	7	2.706042	KEEP	6	0	0	9	246	AA	0	0	0		-	2	38	68	1	0	7.753897	0	0	0	16	ENST00000317506.3	1	0
CENPT	80152	__UNKNOWN__	__UNKNOWN__	16	67871386	67871386	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:67871386T>C	ENST00000562787.1	-	2	58					NM_025082.3	NP_079358.3	Q96BT3	CENPT_HUMAN	centromere protein T	NA		NA			chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|lung(6)|urinary_tract(1)	10		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00429)|Epithelial(162;0.019)|all cancers(182;0.124)		ccgaggcaggtggatcacaag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056097	CCDS42182.1	16q22.1	2013-11-05	2006-06-15	2006-06-15		ENSG00000102901	80152			25787	protein-coding gene	gene with protein product		611510	chromosome 16 open reading frame 56	C16orf56	NA	16622420, 16622419	Standard	NM_025082	NM_025082	NA	Approved	FLJ13111, CENP-T	uc002eun.4	Q96BT3		ENST00000562787.1:c.491-1825A>G	chr16.hg19:g.67871386T>C		NA	Q96I29|Q96IC6|Q96NK9|Q9H901	hg19	CCDS42182.1	0.02	-0.122792	AGGxGGA	COVERED																																																																																			NOVEL	CENPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000422020.1	6	3.307189	KEEP	5	0	0	11	292	TT	0.99254	0.194847	0		-	3	60	94	0	0	7.782067	10	60	302	44	ENST00000562787.1	0.230769	0.196312
PLA2G15	23659	__UNKNOWN__	__UNKNOWN__	16	68287466	68287466	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:68287466T>C	ENST00000413021.2	+	2	250				PLA2G15_ENST00000444212.2_Intron|PLA2G15_ENST00000219345.5_Intron|PLA2G15_ENST00000566188.1_Intron			Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	NA		NA			ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						ttagtagagatggggtttcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066	23659			17163	protein-coding gene	gene with protein product		609362	lysophospholipase 3 (lysosomal phospholipase A2)	LYPLA3	NA	10092508, 16973413	Standard	NM_012320	XM_005255886	NA	Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000413021.2:c.128-1356T>C	chr16.hg19:g.68287466T>C		NA	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	hg19		0.02	-0.254331	AGAxGGG	COVERED																																																																																			NOVEL	PLA2G15-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000433095.1	7	3.006193	KEEP	0	0	0	10	257	TT	0.992708	0.663648	0		+	3	60	95	1	0	6.949621	22	60	650	49	ENST00000413021.2	0.12	0.668523
SLC7A6OS	84138	__UNKNOWN__	__UNKNOWN__	16	68343250	68343250	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:68343250C>T	ENST00000263997.6	-	2	490					NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		cctcccaaagcgctgggatta	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061	84138			25807	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032178	NM_032178	NA	Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.471+987G>A	chr16.hg19:g.68343250C>T		NA	Q8TCZ3|Q9H8R8	hg19	CCDS10865.1	0.02	-0.131583	AAGxGCT	COVERED																																																																																			NOVEL	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268894.3	3	3.609682	KEEP	0	0	0	12	357	CC	0.993634	0.227714	0		-	3	60	93	0	0	7.472114	12	60	402	42	ENST00000263997.6	0.2	0.229173
TANGO6	79613	__UNKNOWN__	__UNKNOWN__	16	68901783	68901783	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:68901783A>G	ENST00000261778.1	+	4	1006					NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	NA		NA				integral component of membrane (GO:0016021)					NA						ggtggctcacacctgtaatcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047	79613			25749	protein-coding gene	gene with protein product		NA	transmembrane and coiled-coil domains 7	TMCO7	NA	11214970	Standard	XM_928235.2	NM_024562	NA	Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.994+660A>G	chr16.hg19:g.68901783A>G		NA	Q569F9|Q9H9K1	hg19	CCDS45516.1	0.02	-0.210488	CACxCCT	COVERED																																																																																			NOVEL	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000433471.2	9	4.208805	KEEP	1	0	0	14	364	AA	0.994391	0.519232	0		+	3	60	101	0	0	7.792136	18	60	533	51	ENST00000261778.1	0.142857	0.522161
SNTB2	6645	__UNKNOWN__	__UNKNOWN__	16	69285664	69285664	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69285664A>G	ENST00000528525.1	+	2	319				SNTB2_ENST00000336278.4_Intron			Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	NA		NA				cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		cagcctgggcaacaagagtga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807	6645			11169	protein-coding gene	gene with protein product		600027	syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)	SNT2B2, SNTL, D16S2531E	NA	8576247, 8183929	Standard		NM_006750	NA	Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000528525.1:c.319+5946A>G	chr16.hg19:g.69285664A>G		NA	Q9BY09	hg19		0.02	-0.289429	GGCxACA	COVERED																																																																																			NOVEL	SNTB2-006	KNOWN	NMD_likely_if_extended|basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000390959.1	12	3.910091	KEEP	2	0	0	13	360	AA	0.993072	0.755616	0		+	3	58	102	1	0	7.352588	28	60	836	65	ENST00000528525.1	0.096774	0.760887
VPS4A	27183	__UNKNOWN__	__UNKNOWN__	16	69356704	69356704	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69356704A>G	ENST00000254950.11	+	10	1368				COG8_ENST00000564419.1_Intron	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)	NA		NA								NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				caggcatggtagctcacgcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612	27183		ATPases / AAA-type	13488	protein-coding gene	gene with protein product		609982	vacuolar protein sorting 4A (yeast homolog), vacuolar protein sorting 4A (yeast)		NA	10637304, 11563910	Standard	NM_013245	NM_013245	NA	Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.1212+101A>G	chr16.hg19:g.69356704A>G		NA		hg19	CCDS45517.1	0.02	-0.254329	GGTxGCT	COVERED																																																																																			NOVEL	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000430563.3	6	5.713402	KEEP	1	0	0	19	509	AA	0.999859	0.693571	0		+	4	60	134	1	0	10.462317	22	60	639	64	ENST00000254950.11	0.153846	0.693668
TMED6	146456	__UNKNOWN__	__UNKNOWN__	16	69380405	69380405	__UNKNOWN__	Intron	SNP	A	A	G	rs544711218		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69380405A>G	ENST00000288025.3	-	3	545				RP11-343C2.7_ENST00000564737.1_Intron|RP11-343C2.9_ENST00000563634.1_Intron	NM_144676.3	NP_653277.2	Q8WW62	TMED6_HUMAN	transmembrane emp24 protein transport domain containing 6	NA		NA			transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	9						ggtggctcatacctgtaatcc	0.488		NA											A|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	19441	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC020827	CCDS10878.1	16q22.1	2008-02-05			ENSG00000157315	ENSG00000157315	146456			28331	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_144676	NM_144676	NA	Approved	MGC23911	uc002exc.2	Q8WW62	OTTHUMG00000137571	ENST00000288025.3:c.489+1285T>C	chr16.hg19:g.69380405A>G		NA	Q6UXN5	hg19	CCDS10878.1	0.02	-0.184173	CATxCCT	COVERED																																																																																			NOVEL	TMED6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268951.1	2	4.508348	KEEP	0	0	0	15	390	AA	0.99649	0.421991	0		-	3	60	100	0	0	7.833605	16	60	459	56	ENST00000288025.3	0.157895	0.423478
TERF2	7014	__UNKNOWN__	__UNKNOWN__	16	69414330	69414330	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69414330A>G	ENST00000254942.3	-	3	623				TERF2_ENST00000603068.1_Intron|TERF2_ENST00000569611.2_Intron|TERF2_ENST00000567296.2_Intron	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	NA		NA			age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				ttgggaggccaaggcgggtgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(13;63 524 30420 31710 34037)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604	7014			11729	protein-coding gene	gene with protein product		602027		TRBF2	NA	9326950, 10226653	Standard		NM_005652	NA	Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.606+4152T>C	chr16.hg19:g.69414330A>G		NA		hg19		0.02	-0.122779	GCCxAGG	COVERED																																																																																			NOVEL	TERF2-001	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000268944.2	2	2.405657	KEEP	0	0	0	8	216	AA	0.99257	0.194853	0		-	3	60	96	0	0	8.101477	9	60	256	29	ENST00000254942.3	0.25	0.196312
CYB5B	80777	__UNKNOWN__	__UNKNOWN__	16	69461997	69461997	__UNKNOWN__	Intron	SNP	A	A	G	rs544352720		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69461997A>G	ENST00000512062.1	+	1	333				CYB5B_ENST00000561792.1_Intron|CYB5B_ENST00000515314.1_Intron|CYB5B_ENST00000307892.8_Intron			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	NA		NA			oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				caaagtgctgagattacaggt	0.423		NA											A|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	15691	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018	80777			24374	protein-coding gene	gene with protein product		611964			NA	11867265, 14733950	Standard	NM_030579	NM_030579	NA	Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.162+3237A>G	chr16.hg19:g.69461997A>G		NA	A8K6B1|Q96CC3|Q9BT35	hg19		0.02	-0.1228	CTGxGAT	COVERED																																																																																			NOVEL	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000256606.2	10	2.406089	KEEP	0	0	0	8	221	AA	0.99257	0.194853	0		+	3	60	107	0	0	8.97277	11	60	335	26	ENST00000512062.1	0.214286	0.196312
CYB5B	80777	__UNKNOWN__	__UNKNOWN__	16	69477737	69477737	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69477737A>G	ENST00000512062.1	+	2	333				CYB5B_ENST00000515314.1_Intron|CYB5B_ENST00000307892.8_Intron|CYB5B_ENST00000561792.1_Intron			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	NA		NA			oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				cagcctgggcaacagagtgag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018	80777			24374	protein-coding gene	gene with protein product		611964			NA	11867265, 14733950	Standard	NM_030579	NM_030579	NA	Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.163-3316A>G	chr16.hg19:g.69477737A>G		NA	A8K6B1|Q96CC3|Q9BT35	hg19		0.02	-0.429755	GGCxACA	COVERED																																																																																			NOVEL	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000256606.2	9	4.210731	KEEP	1	0	0	14	387	AA	0.995343	0.950046	0		+	3	60	99	1	0	6.640647	39	60	1153	88	ENST00000512062.1	0.071429	0.954491
CYB5B	80777	__UNKNOWN__	__UNKNOWN__	16	69477752	69477752	__UNKNOWN__	Intron	SNP	C	C	T	rs9929098	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69477752C>T	ENST00000512062.1	+	2	333				CYB5B_ENST00000515314.1_Intron|CYB5B_ENST00000307892.8_Intron|CYB5B_ENST00000561792.1_Intron			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	NA		NA			oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				agtgagactccgtctcaaaac	0.478		NA											C|||	684	0.136581	0.1596	0.1182	5008	,	,	NA	21198	0.0099	NA	0.1769	False	NA	,,,	NA	NA	NA	2504	0.2076	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018	80777			24374	protein-coding gene	gene with protein product		611964			NA	11867265, 14733950	Standard	NM_030579	NM_030579	NA	Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.163-3301C>T	chr16.hg19:g.69477752C>T		NA	A8K6B1|Q96CC3|Q9BT35	hg19		0.02	1.392204	CTCxGTC	COVERED																																																																																			NOVEL	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000256606.2	13	5.113951	KEEP	0	0	0	17	500	CC	0.999366	0.981333	0		+	5	60	140	1	0	9.478334	42	60	1387	111	ENST00000512062.1	0.106383	0.981955
NFAT5	10725	__UNKNOWN__	__UNKNOWN__	16	69669184	69669184	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69669184T>G	ENST00000393742.2	+	2	293				NFAT5_ENST00000567239.1_Intron|NFAT5_ENST00000349945.1_Intron|NFAT5_ENST00000566899.1_Intron|NFAT5_ENST00000354436.2_Intron|NFAT5_ENST00000432919.1_Intron	NM_173214.2	NP_775321.1	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5, tonicity-responsive	NA		NA			cytokine production (GO:0001816)|excretion (GO:0007588)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of calcineurin-NFAT signaling cascade (GO:0070884)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						aaagtgctggtattacaggcg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF134870	CCDS10881.1, CCDS10882.1, CCDS45519.1	16q22.1	2009-11-24			ENSG00000102908	ENSG00000102908	10725		Nuclear factor of activated T-cells	7774	protein-coding gene	gene with protein product		604708			NA	10377394	Standard	NM_138714	NM_173214	NA	Approved	TONEBP, KIAA0827, NFATL1, OREBP, NFATZ, NF-AT5	uc002exl.2	O94916	OTTHUMG00000137572	ENST00000393742.2:c.-92+8753T>G	chr16.hg19:g.69669184T>G		NA	A2RRB4|A6H8V5|E9PHR7|O95693|Q7LA65|Q969Q8|Q96QH3|Q9UN18	hg19	CCDS10882.1	0.02	-0.192952	TGGxATT	UNCOVERED																																																																																			NOVEL	NFAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268953.2	8	2.405932	KEEP	2	0	0	8	221	TT	0	0	0		+	3	60	99	0	0	7.527062	19	60	560	48	ENST00000393742.2	0.136364	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	69789895	69789895	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69789895C>G			NA	NA				NOB1 (1052 upstream) : WWP2 (6313 downstream)						NA		NA									NA						ggtggctcacccctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.69789895C>G		NA		hg19		0.02	5.528055	CACxCCT	COVERED																																																																																			NOVEL					0			29	4.008832	KEEP	1	9	260	105	3192	CC	1	1	0			8	60	268	0	0	16.94554	147	60	5002	411		0.051613	1
CLEC18A	348174	__UNKNOWN__	__UNKNOWN__	16	69989095	69989095	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:69989095A>G	ENST00000288040.6	+	3	643				CLEC18A_ENST00000568461.1_Intron|CLEC18A_ENST00000393701.2_Intron|CLEC18A_ENST00000449317.2_Intron	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	NA		NA				extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						tagtagagacagggtttcacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322	348174		C-type lectin domain containing	30388	protein-coding gene	gene with protein product	mannose receptor-like	NA			NA	12975309	Standard	NM_182619	NM_001136214	NA	Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.456+619A>G	chr16.hg19:g.69989095A>G		NA	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	hg19	CCDS10886.1	0.02	-0.122784	GACxGGG	COVERED																																																																																			NOVEL	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268955.2	6	2.707138	KEEP	1	0	0	9	252	AA	0.99254	0.194847	0		+	3	40	91	0	0	7.601336	9	60	262	30	ENST00000288040.6	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	70108692	70108692	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70108692G>A			NA	NA				PDXDC2P (8841 upstream) : PDPR (38836 downstream)						NA		NA									NA						ttgtatttttggtagagatgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.70108692G>A		NA		hg19		0.02	-0.131568	TTTxGTA	COVERED																																																																																			NOVEL					0			9	2.708001	KEEP	1	0	0	9	274	GG	0.99254	0.227464	0			3	27	81	2	0	6.482066	10	60	325	31		0.230769	0.229173
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70160966	70160966	__UNKNOWN__	Intron	SNP	G	G	A	rs8044841		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70160966G>A	ENST00000288050.4	+	4	1184				PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		gaccaggctggtcgtaaaccc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.228-197G>A	chr16.hg19:g.70160966G>A		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	-0.157881	CTGxTCG	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	9	3.009111	KEEP	1	0	0	10	310	GG	0.992708	0.320453	0		+	4	60	112	0	0	9.081017	13	60	426	39	ENST00000288050.4	0.235294	0.322807
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70161468	70161468	__UNKNOWN__	Intron	SNP	G	G	A	rs551962415		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70161468G>A	ENST00000288050.4	+	4	1318				PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		cgaggcaggcggatcacgagg	0.498		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	23903	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.361+172G>A	chr16.hg19:g.70161468G>A		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	-0.280703	GGCxGAT	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	9	6.016526	KEEP	17	0	0	20	593	GG	0.99649	0.737075	0		+	4	60	119	0	0	8.758373	25	60	823	96	ENST00000288050.4	0.137931	0.739671
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70165739	70165739	__UNKNOWN__	Intron	SNP	C	C	T	rs201458502		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70165739C>T	ENST00000288050.4	+	9	1804				PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GGCTCTGCAACCCCCCTCTCT	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.848-315C>T	chr16.hg19:g.70165739C>T		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	2.486053	CAAxCCC	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	6	6.018657	KEEP	0	0	0	20	648	CC	0.999863	0.999863	0		+	12	60	337	1	0	21.510981	132	60	4532	256	ENST00000288050.4	0.083333	1
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70165746	70165746	__UNKNOWN__	Intron	SNP	C	C	T	rs202188872		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70165746C>T	ENST00000288050.4	+	9	1804				PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		CAACCCCCCTCTCTGTTAAAC	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.848-308C>T	chr16.hg19:g.70165746C>T		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	4.220308	CCTxTCT	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	6	6.01837	KEEP	0	0	0	20	632	CC	0.999863	0.999863	0		+	13	60	366	0	0	23.628755	137	60	4657	264	ENST00000288050.4	0.086667	1
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70165749	70165749	__UNKNOWN__	Intron	SNP	T	T	C	rs200381305		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70165749T>C	ENST00000288050.4	+	9	1804				PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		CCCCCCTCTCTGTTAAACTTT	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.848-305T>C	chr16.hg19:g.70165749T>C		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	5.607165	CTCxGTT	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	6	6.315143	KEEP	0	0	0	21	592	TT	0.999869	0.999869	0		+	14	60	466	0	0	32.997814	138	60	4196	262	ENST00000288050.4	0.092105	1
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70167914	70167914	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70167914A>G	ENST00000288050.4	+	9	1954				PDPR_ENST00000562100.1_Intron|PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		gggattacagacgtgagccac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.997+1711A>G	chr16.hg19:g.70167914A>G		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	-0.289429	CAGxCGT	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	9	3.007222	KEEP	2	0	0	10	270	AA	0.99254	0.775233	0		+	3	60	104	0	0	7.643886	26	60	774	65	ENST00000288050.4	0.103448	0.78106
PDPR	55066	__UNKNOWN__	__UNKNOWN__	16	70182325	70182325	__UNKNOWN__	Intron	SNP	T	T	C	rs55843501	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70182325T>C	ENST00000288050.4	+	17	2919				PDPR_ENST00000562100.1_Intron|PDPR_ENST00000567046.1_Intron|PDPR_ENST00000398122.3_Intron|PDPR_ENST00000568530.1_Intron|PDPR_ENST00000542659.1_Intron	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	NA		NA			cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		CCTTGACAAGTAATGTGAGTG	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													42	39	40			NA	NA	16		NA											NA				70182325		2005	4152	6157	SO:0001627	intron_variant				CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857	55066			30264	protein-coding gene	gene with protein product		NA			NA	9395502	Standard	NM_017990	NM_017990	NA	Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1963-42T>C	chr16.hg19:g.70182325T>C		NA	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	hg19	CCDS45520.1	0.02	1.707896	AAGxAAT	COVERED																																																																																			NOVEL	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434502.1	1	2.703786	KEEP	0	0	0	9	227	TT	0.99254	0.969578	0		+	5	40	137	0	0	9.150027	45	60	1229	91	ENST00000288050.4	0.1	0.976865
RP11-296I10.3	0	__UNKNOWN__	__UNKNOWN__	16	70201480	70201480	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70201480T>C	ENST00000502126.1	-	0	321				RP11-296I10.3_ENST00000566989.1_RNA						NA		NA									NA						tggctcatgattgtaatccca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000502126.1:	chr16.hg19:g.70201480T>C		NA		hg19		0.02	-0.114027	TGAxTGT	UNCOVERED																																																																																			NOVEL	RP11-296I10.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000434586.2	8	3.307112	KEEP	7	0	0	11	295	TT	0.99254	0.161255	0		-	3	25	97	0	0	8.201185	9	60	270	42	ENST00000502126.1	0.25	0.162467
AARS	16	__UNKNOWN__	__UNKNOWN__	16	70303416	70303416	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70303416A>G	ENST00000261772.8	-	7	1106					NM_001605.2	NP_001596.2			alanyl-tRNA synthetase	NA		NA								breast(3)|cervix(2)|endometrium(5)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)		cagcctgggcaacagagcaac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D32050	CCDS32474.1	16q22.1	2014-09-17			ENSG00000090861	ENSG00000090861	16	6.1.1.7	Aminoacyl tRNA synthetases / Class II	20	protein-coding gene	gene with protein product	alanine tRNA ligase 1, cytoplasmic	601065			NA	8595897	Standard	NM_001605	NM_001605	NA	Approved		uc002eyn.1	P49588	OTTHUMG00000177042	ENST00000261772.8:c.962+104T>C	chr16.hg19:g.70303416A>G		NA		hg19	CCDS32474.1	0.02	-0.412162	GGCxACA	COVERED																																																																																			NOVEL	AARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435021.2	9	3.339534	KEEP	0	1	28	21	571	AA	0.999879	0.941627	0		-	3	60	107	1	0	7.376964	41	60	1189	89	ENST00000261772.8	0.068182	0.941741
DDX19B	11269	__UNKNOWN__	__UNKNOWN__	16	70358692	70358692	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70358692T>C	ENST00000288071.6	+	6	737				DDX19B_ENST00000355992.3_Intron|DDX19B_ENST00000568625.1_Intron|DDX19B_ENST00000563392.1_Intron|DDX19B_ENST00000393657.2_Intron|DDX19B_ENST00000563206.1_Intron|RP11-529K1.3_ENST00000567706.1_Intron|DDX19B_ENST00000451014.3_Intron|RP11-529K1.2_ENST00000562077.1_RNA	NM_007242.5	NP_009173.1	Q9UMR2	DD19B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 19B	NA		NA			mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)	9		Ovarian(137;0.0694)				cagtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(26;382 757 1343 9728 15939)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ237946	CCDS10888.1, CCDS32475.1, CCDS42187.1, CCDS58478.1	16q22.3	2012-02-23	2012-02-23	2005-07-13	ENSG00000157349	ENSG00000157349	11269		DEAD-boxes	2742	protein-coding gene	gene with protein product		605812	DEAD (Asp-Glu-Ala-As) box polypeptide 19, DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (Dbp5, yeast, homolog)	DDX19	NA	10428971	Standard	NM_007242	NM_007242	NA	Approved	DBP5	uc002eyo.4	Q9UMR2	OTTHUMG00000137577	ENST00000288071.6:c.492+102T>C	chr16.hg19:g.70358692T>C		NA	B3KNE9|B4DXS6|E7EMK4|Q6FIB7|Q6IAE0|Q96KE7|Q9H0U0	hg19	CCDS10888.1	0.02	-0.279912	TCAxGCC	UNCOVERED																																																																																			NOVEL	DDX19B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268965.3	5	2.404763	KEEP	4	0	0	8	206	TT	0	0	0		+	4	60	133	0	0	10.099765	26	60	747	53	ENST00000288071.6	0.133333	0.739671
RP11-529K1.3	0	__UNKNOWN__	__UNKNOWN__	16	70373154	70373154	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70373154G>A	ENST00000567706.1	+	7	691				RP11-529K1.2_ENST00000562077.1_RNA						NA		NA								lung(1)	1						ggtggctcatgcctgtagtcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000567706.1:c.607+13563G>A	chr16.hg19:g.70373154G>A		NA		hg19		0.02	-0.245618	CATxCCT	COVERED																																																																																			NOVEL	RP11-529K1.3-002	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_candidate_longest|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000435149.1	11	3.30922	KEEP	0	0	0	11	328	GG	0.993072	0.636904	0		+	3	60	88	0	0	6.306719	21	60	705	58	ENST00000567706.1	0.125	0.641347
ST3GAL2	6483	__UNKNOWN__	__UNKNOWN__	16	70461486	70461486	__UNKNOWN__	Intron	SNP	C	C	T	rs376626726	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70461486C>T	ENST00000566097.1	-	1	289				ST3GAL2_ENST00000342907.2_Intron			Q16842	SIA4B_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 2	NA		NA			amino sugar metabolic process (GO:0006040)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)	11		Ovarian(137;0.0694)				gtgatccgcccgcctcagcct	0.542		NA											C|||	26	0.00519169	0.0189	0.0014	5008	,	,	NA	17600	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U63090	CCDS10890.1	16q22.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000157350	ENSG00000157350	6483	2.4.99.4	Sialyltransferases	10863	protein-coding gene	gene with protein product		607188	sialyltransferase 4B (beta-galactosidase alpha-2,3-sialytransferase)	SIAT4B	NA	9266697, 8920913	Standard	NM_006927	NM_006927	NA	Approved	ST3GALII, ST3GalA.2	uc002eyx.2	Q16842	OTTHUMG00000137580	ENST00000566097.1:c.615+11365G>A	chr16.hg19:g.70461486C>T		NA	O00654	hg19		0.02	-0.219254	GCCxGCC	UNCOVERED																																																																																			NOVEL	ST3GAL2-005	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000435177.1	12	3.609667	KEEP	13	0	0	12	346	CC	0	0	0		-	4	60	102	0	0	7.498323	19	60	623	60	ENST00000566097.1	0.173913	0.552887
COG4	25839	__UNKNOWN__	__UNKNOWN__	16	70530359	70530359	__UNKNOWN__	Intron	SNP	A	A	G	rs2303793	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70530359A>G	ENST00000323786.5	-	12	1503					NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	NA		NA			Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				TGCATAGAGGAATTGACAGTG	0.552		NA											G|||	2838	0.566693	0.621	0.4481	5008	,	,	NA	21269	0.5823	NA	0.4215	False	NA	,,,	NA	NA	NA	2504	0.7106	NA	NA	NA								NA				0								G	,	2479,1917	541.0+/-375.7	687,1105,406	49	42	44		,	2.2	0	16	dbSNP_100	44	3659,4941	615.8+/-396.4	796,2067,1437	no	intron,intron	COG4	NM_001195139.1,NM_015386.2	,	1483,3172,1843	GG,GA,AA	NA	42.5465,43.6078,47.2299	,	,	70530359	6138,6858	2198	4300	6498	SO:0001627	intron_variant			AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051	25839		Components of oligomeric golgi complex	18620	protein-coding gene	gene with protein product		606976			NA	11980916	Standard		NM_015386	NA	Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.1482-25T>C	chr16.hg19:g.70530359A>G		NA	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	hg19	CCDS10892.2	0.02	-0.429713	AGGxATT	COVERED																																																																																			NOVEL	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250326.3	1	3.00725	KEEP	0	0	0	10	269	AA	0.992708	0.947531	0		-	24	60	802	0	0	76.909264	25	60	697	82	ENST00000323786.5	0.489796	0.954491
COG4	25839	__UNKNOWN__	__UNKNOWN__	16	70535579	70535579	__UNKNOWN__	Intron	SNP	A	A	G	rs545796756	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70535579A>G	ENST00000323786.5	-	9	1083					NM_001195139.1|NM_015386.2	NP_001182068.1|NP_056201.2	Q9H9E3	COG4_HUMAN	component of oligomeric golgi complex 4	NA		NA			Golgi organization (GO:0007030)|Golgi vesicle prefusion complex stabilization (GO:0048213)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|pancreas(1)|prostate(2)	33		Ovarian(137;0.0694)				tttttgagacagagtcttgct	0.547		NA											A|||	2	0.000399361	0.0	0.0	5008	,	,	NA	16158	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050101	CCDS10892.2, CCDS73909.1	16q22.1	2013-09-20			ENSG00000103051	ENSG00000103051	25839		Components of oligomeric golgi complex	18620	protein-coding gene	gene with protein product		606976			NA	11980916	Standard		NM_015386	NA	Approved	COD1, DKFZP586E1519	uc002ezc.3	Q9H9E3	OTTHUMG00000128515	ENST00000323786.5:c.1062-585T>C	chr16.hg19:g.70535579A>G		NA	B4DMN8|C9JS23|Q96D40|Q9BRF0|Q9BVZ2|Q9H5Y4|Q9Y3W3	hg19	CCDS10892.2	0.02	-0.22802	GACxGAG	COVERED																																																																																			NOVEL	COG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250326.3	14	3.910356	KEEP	0	0	0	13	367	AA	0.994391	0.57966	0		-	3	60	96	2	0	7.592381	14	60	428	63	ENST00000323786.5	0.176471	0.58293
SF3B3	23450	__UNKNOWN__	__UNKNOWN__	16	70598024	70598024	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70598024G>A	ENST00000302516.5	+	18	2674					NM_012426.4	NP_036558.3	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3, 130kDa	NA		NA			gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|protein complex assembly (GO:0006461)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleic acid binding (GO:0003676)			breast(2)|endometrium(8)|kidney(2)|large_intestine(8)|liver(3)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	53		Ovarian(137;0.0694)				TAAACTGcccggcactttggg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ001443	CCDS10894.1	16q22	2008-08-01	2002-08-29		ENSG00000189091	ENSG00000189091	23450			10770	protein-coding gene	gene with protein product		605592	splicing factor 3b, subunit 3, 130kD		NA	10490618	Standard	NM_012426	NM_012426	NA	Approved	SAP130, SF3b130, RSE1, KIAA0017	uc002ezf.3	Q15393	OTTHUMG00000137582	ENST00000302516.5:c.2463+71G>A	chr16.hg19:g.70598024G>A		NA	Q6NTI8|Q96GC0|Q9BPY2|Q9UFX7|Q9UJ29	hg19	CCDS10894.1	0.02	1.359521	CCCxGCA	COVERED																																																																																			NOVEL	SF3B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268972.1	13	7.153181	KEEP	0	1	26	33	988	GG	0.999998	0.997551	0		+	5	60	155	1	1	10.270907	59	60	1930	143	ENST00000302516.5	0.078125	0.997553
IL34	146433	__UNKNOWN__	__UNKNOWN__	16	70615755	70615755	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70615755A>G	ENST00000429149.2	+	1	155					NM_001172771.1|NM_152456.2	NP_001166242.1|NP_689669.2	Q6ZMJ4	IL34_HUMAN	interleukin 34	NA		NA			inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						ggaggctgagatgggtggatt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368	146433		Interleukins and interleukin receptors	28529	protein-coding gene	gene with protein product		612081	chromosome 16 open reading frame 77	C16orf77	NA	18467591	Standard	NM_152456	NM_152456	NA	Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000429149.2:c.-401+1803A>G	chr16.hg19:g.70615755A>G		NA	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	hg19	CCDS10895.1	0.02	-0.271885	GAGxTGG	COVERED																																																																																			NOVEL	IL34-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		13	5.712355	KEEP	0	0	0	19	507	AA	0.99986	0.717215	0		+	3	60	94	0	0	6.743335	24	60	714	63	ENST00000429149.2	0.111111	0.717315
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	70898221	70898221	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70898221A>G	ENST00000393567.2	-	68	11622					NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				gtgacagagcaagactccggc	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11472-1136T>C	chr16.hg19:g.70898221A>G		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	-0.113876	AGCxAGA	UNCOVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	26	2.61936	KEEP	13	1	23	17	440	AA	0.99254	0.161255	0		-	4	25	107	1	0	9.470562	7	60	204	36	ENST00000393567.2	0.363636	0.162467
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	70898229	70898229	__UNKNOWN__	Intron	SNP	G	G	A	rs78552205		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70898229G>A	ENST00000393567.2	-	68	11622					NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				gcaagactccggctcaaaaaa	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.11472-1144C>T	chr16.hg19:g.70898229G>A		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	-0.105255	TCCxGCT	UNCOVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	30	6.239454	KEEP	15	0	0	21	529	GG	0.993072	0.138863	0		-	3	42	90	0	1	7.778386	7	60	230	41	ENST00000393567.2	0.3	0.139832
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	70957443	70957443	__UNKNOWN__	Intron	SNP	A	A	C	rs372116570	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70957443A>C	ENST00000393567.2	-	46	7309					NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				tggtggctcaagcctgtaatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7159-2323T>G	chr16.hg19:g.70957443A>C		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	-0.341279	TCAxGCC	COVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	16	6.915319	KEEP	0	0	0	23	620	AA	0.999892	0.865652	0		-	3	56	95	0	0	6.415959	34	60	1000	91	ENST00000393567.2	0.081081	0.865745
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	70962947	70962947	__UNKNOWN__	Intron	SNP	T	T	C	rs1798406		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70962947T>C	ENST00000393567.2	-	45	7309					NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				aatcccagcattttgggaggc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7158+6907A>G	chr16.hg19:g.70962947T>C		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	-0.157889	GCAxTTT	COVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	4	3.307471	KEEP	0	0	0	11	300	TT	0.993072	0.32057	0		-	4	60	128	0	0	11.07128	10	60	306	44	ENST00000393567.2	0.285714	0.322807
HYDIN	54768	__UNKNOWN__	__UNKNOWN__	16	70984887	70984887	__UNKNOWN__	Intron	SNP	T	T	C	rs62049591	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:70984887T>C	ENST00000393567.2	-	41	6682					NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	NA		NA			cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				atcctagttctttgggaggca	0.502		NA											T|||	2284	0.45607	0.1868	0.4611	5008	,	,	NA	19039	0.4375	NA	0.7475	False	NA	,,,	NA	NA	NA	2504	0.5358	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423	54768		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	19368	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 31	610812	hydrocephalus inducing, hydrocephalus inducing homolog (mouse)		NA	12719380, 23022101	Standard		NM_001198542	NA	Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6531+1436A>G	chr16.hg19:g.70984887T>C		NA	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	hg19	CCDS59269.1	0.02	-0.324505	TTCxTTG	COVERED																																																																																			NOVEL	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398624.3	8	3.008506	KEEP	1	0	0	10	292	TT	0.99254	0.829482	0		-	8	60	264	0	0	22.162539	26	60	780	68	ENST00000393567.2	0.235294	0.835716
RP11-510M2.1	0	__UNKNOWN__	__UNKNOWN__	16	71456757	71456757	__UNKNOWN__	lincRNA	SNP	T	T	C	rs8060176	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:71456757T>C	ENST00000567469.1	-	0	304										NA		NA									NA						atcctcctgctttggcctccc	0.512		NA											C|||	1697	0.338858	0.8638	0.2406	5008	,	,	NA	16857	0.0079	NA	0.3141	False	NA	,,,	NA	NA	NA	2504	0.0654	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000567469.1:	chr16.hg19:g.71456757T>C		NA		hg19		0.02	-0.061402	TGCxTTG	UNCOVERED																																																																																			NOVEL	RP11-510M2.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000433792.1	4	2.40631	KEEP	0	0	0	8	224	TT	0.99257	0.043461	0		-	3	60	100	0	0	9.355279	4	60	122	18	ENST00000567469.1	0.428571	0.043787
MARVELD3	91862	__UNKNOWN__	__UNKNOWN__	16	71667032	71667032	__UNKNOWN__	Intron	SNP	A	A	G	rs60580019		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:71667032A>G	ENST00000299952.4	+	2	638				MARVELD3_ENST00000268485.3_Intron|MARVELD3_ENST00000567501.1_Intron|MARVELD3_ENST00000565261.1_Intron	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	NA		NA			cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				ttgggaggccaaggcaggagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832	91862			30525	protein-coding gene	gene with protein product		614094	MARVEL (membrane-associating) domain containing 3	MRVLDC3	NA		Standard	NM_052858	NM_001017967	NA	Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.595+3635A>G	chr16.hg19:g.71667032A>G		NA	A8K820|H3BQM5|Q96MJ4	hg19	CCDS32478.1	0.02	-0.324527	GCCxAGG	COVERED																																																																																			NOVEL	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268990.1	11	3.910479	KEEP	1	0	0	13	368	AA	0.994391	0.831028	0		+	3	60	100	0	0	7.109395	29	60	872	77	ENST00000299952.4	0.09375	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	71864905	71864905	__UNKNOWN__	IGR	SNP	G	G	A	rs186902062	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:71864905G>A			NA	NA				AP1G1 (21801 upstream) : ATXN1L (14988 downstream)						NA		NA									NA						gattacaggcgtgagccactg	0.433		NA											G|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	14535	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.71864905G>A		NA		hg19		0.02	-0.210525	GGCxTGA	COVERED																																																																																			NOVEL					0			9	4.812745	KEEP	1	0	0	16	460	GG	0.997832	0.521029	0			3	60	88	0	0	6.427871	19	60	627	60		0.136364	0.522161
IST1	9798	__UNKNOWN__	__UNKNOWN__	16	71931677	71931677	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:71931677T>C	ENST00000378799.6	+	1	341				IST1_ENST00000538850.1_Intron|IST1_ENST00000535424.1_Intron|IST1_ENST00000544564.1_Intron|IST1_ENST00000538565.1_Intron|IST1_ENST00000329908.8_Intron|IST1_ENST00000541571.2_Intron|IST1_ENST00000606369.1_Intron|IST1_ENST00000378798.5_Intron			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	NA		NA			abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)				NA						ggtgaaaccctgtctctacta	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149	9798			28977	protein-coding gene	gene with protein product		NA	KIAA0174	KIAA0174	NA	8724849, 19129480	Standard	NM_014761	NM_001270975	NA	Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.-16+2185T>C	chr16.hg19:g.71931677T>C		NA	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	hg19	CCDS59272.1	0.02	-0.201719	CCCxGTC	UNCOVERED																																																																																			NOVEL	IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269005.2	9	2.40645	KEEP	4	0	0	8	226	TT	0	0	0		+	3	32	90	0	0	6.693019	18	60	530	42	ENST00000378799.6	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	73141826	73141826	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:73141826T>C			NA	NA				HCCAT5 (14153 upstream) : C16orf47 (18709 downstream)						NA		NA									NA						tttgggaggctgaggcgggcg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.73141826T>C		NA		hg19		0.02	-0.175424	GGCxGAG	COVERED																																																																																			NOVEL					0			5	3.308892	KEEP	2	0	0	11	312	TT	0.992708	0.384582	0			3	60	99	0	0	7.660831	17	60	519	47		0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	74091510	74091510	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:74091510A>G			NA	NA				RP11-53L24.1 (241557 upstream) : AC009120.4 (134780 downstream)						NA		NA									NA						ttgttgcccaagctggagtgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.74091510A>G		NA		hg19		0.02	-0.096484	CCAxGCT	UNCOVERED																																																																																			NOVEL					0			5	3.007214	KEEP	1	0	0	10	273	AA	0.992708	0.119558	0			3	60	100	0	0	8.77868	7	60	211	34		0.3	0.120436
RP11-252A24.2	0	__UNKNOWN__	__UNKNOWN__	16	74397125	74397125	__UNKNOWN__	RNA	SNP	G	G	A	rs556588461	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:74397125G>A	ENST00000429810.2	-	0	176										NA		NA									NA						tttttgagacggagtctcgct	0.507		NA											.|||	2	0.000399361	0.0	0.0	5008	,	,	NA	22087	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000429810.2:	chr16.hg19:g.74397125G>A		NA		hg19		0.02	-0.140342	GACxGAG	COVERED																																																																																			NOVEL	RP11-252A24.2-003	KNOWN	basic	retained_intron	NA	pseudogene	OTTHUMT00000434683.1	10	3.008907	KEEP	0	0	0	10	306	GG	0.992708	0.259062	0		-	4	60	112	0	0	9.330668	11	60	369	34	ENST00000429810.2	0.266667	0.260965
GLG1	2734	__UNKNOWN__	__UNKNOWN__	16	74504616	74504616	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:74504616A>G	ENST00000447066.2	-	14	2214				GLG1_ENST00000205061.5_Intron|GLG1_ENST00000422840.2_Intron	NM_001145666.1	NP_001139138.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	NA		NA			blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						aaagtgctggaattacaggcg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863	2734			4316	protein-coding gene	gene with protein product		600753	golgi apparatus protein 1		NA	8530051, 7531823	Standard	NM_012201	NM_012201	NA	Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000447066.2:c.2196+454T>C	chr16.hg19:g.74504616A>G		NA	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	hg19	CCDS45526.1	0.02	-0.263121	TGGxATT	COVERED																																																																																			NOVEL	GLG1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435751.1	9	4.511531	KEEP	1	0	0	15	416	AA	0.99649	0.691234	0		-	3	60	101	0	0	7.549207	22	60	658	62	ENST00000447066.2	0.12	0.693668
GLG1	2734	__UNKNOWN__	__UNKNOWN__	16	74632194	74632194	__UNKNOWN__	Intron	SNP	C	C	A	rs188870899	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:74632194C>A	ENST00000447066.2	-	1	456				GLG1_ENST00000205061.5_Intron|GLG1_ENST00000422840.2_Intron	NM_001145666.1	NP_001139138.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	NA		NA			blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						ccaaggcgggcggatcacgag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863	2734			4316	protein-coding gene	gene with protein product		600753	golgi apparatus protein 1		NA	8530051, 7531823	Standard	NM_012201	NM_012201	NA	Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000447066.2:c.438+8360G>T	chr16.hg19:g.74632194C>A		NA	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	hg19	CCDS45526.1	0.02	-0.236835	GGGxGGA	COVERED																																																																																			NOVEL	GLG1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000435751.1	11	3.910785	KEEP	7	0	0	13	385	CC	0.99254	0.607839	0		-	3	22	91	0	0	6.54959	22	60	708	65	ENST00000447066.2	0.12	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	74738075	74738075	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:74738075A>G			NA	NA				MLKL (3263 upstream) : FA2H (8777 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.74738075A>G		NA		hg19		0.02	-0.245572	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			11	2.706936	KEEP	5	0	0	9	250	AA	0	0	0			3	60	100	0	0	7.505668	21	60	614	59		0.125	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	74738609	74738609	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:74738609T>C			NA	NA				MLKL (3797 upstream) : FA2H (8243 downstream)						NA		NA									NA						ccgtggctcatgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.74738609T>C		NA		hg19		0.02	-0.175404	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			8	2.405376	KEEP	2	0	0	8	210	TT	0	0	0			3	60	97	0	0	7.533584	16	60	466	43		0.157895	0.387407
WDR59	79726	__UNKNOWN__	__UNKNOWN__	16	75017129	75017129	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:75017129A>G	ENST00000262144.6	-	1	185				WDR59_ENST00000562331.1_Intron	NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	NA		NA								breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						ccagcactttaggaggccaag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091	79726		WD repeat domain containing	25706	protein-coding gene	gene with protein product		NA			NA	11572484	Standard	NM_030581	XM_005256146	NA	Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.54+1732T>C	chr16.hg19:g.75017129A>G		NA	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	hg19	CCDS32488.1	0.02	-0.175409	TTTxGGA	COVERED																																																																																			NOVEL	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410601.3	9	2.70638	KEEP	0	0	0	9	245	AA	0.99254	0.384517	0		-	3	60	106	0	0	8.433223	16	60	466	36	ENST00000262144.6	0.157895	0.387407
ZNRF1	84937	__UNKNOWN__	__UNKNOWN__	16	75125935	75125935	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:75125935A>G	ENST00000320619.6	+	2	1059				ZNRF1_ENST00000566250.1_Intron|ZNRF1_ENST00000567962.1_Intron|ZNRF1_ENST00000335325.4_Intron|ZNRF1_ENST00000564320.1_Intron			Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase	NA		NA			proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						ggtggctcacacctgtaatcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187	84937		RING-type (C3HC4) zinc fingers	18452	protein-coding gene	gene with protein product		612060	zinc and ring finger 1		NA		Standard		NM_032268	NA	Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606	ENST00000320619.6:c.425-1535A>G	chr16.hg19:g.75125935A>G		NA	D3DUJ9|Q9H083	hg19		0.02	-0.184183	CACxCCT	COVERED																																																																																			NOVEL	ZNRF1-001	KNOWN	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000269019.2	8	2.706764	KEEP	0	0	0	9	249	AA	0.99254	0.420319	0		+	3	60	99	0	0	7.810168	15	60	447	39	ENST00000320619.6	0.166667	0.423478
CFDP1	10428	__UNKNOWN__	__UNKNOWN__	16	75464344	75464344	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:75464344A>C	ENST00000283882.3	-	1	197				RP11-77K12.1_ENST00000567194.1_Intron|CFDP1_ENST00000564286.1_Intron|RP11-77K12.1_ENST00000561887.1_Intron	NM_006324.2	NP_006315.1	Q9UEE9	CFDP1_HUMAN	craniofacial development protein 1	NA		NA			cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|negative regulation of fibroblast apoptotic process (GO:2000270)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)					endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5						gctgggattaaaggtgtgagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB009285	CCDS10916.1	16q22.2-q22.3	2011-08-12			ENSG00000153774	ENSG00000153774	10428			1873	protein-coding gene	gene with protein product	Bucentaur, centromere protein 29	608108			NA	9602175, 9006920, 11992732	Standard	NM_006324	NM_006324	NA	Approved	BCNT, p97, CP27, SWC5, Yeti, CENP-29	uc002fdy.3	Q9UEE9	OTTHUMG00000137615	ENST00000283882.3:c.64+2842T>G	chr16.hg19:g.75464344A>C		NA	O00393|O00404|Q9UEF0|Q9UEF1|Q9UEF8	hg19	CCDS10916.1	0.02	-0.228042	TTAxAGG	COVERED																																																																																			NOVEL	CFDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269031.2	8	2.406266	KEEP	0	0	0	8	223	AA	0.99257	0.607857	0		-	3	60	107	0	0	8.264533	20	60	598	48	ENST00000283882.3	0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	75534424	75534424	__UNKNOWN__	IGR	SNP	C	C	T	rs191100652	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:75534424C>T			NA	NA				RP11-77K12.4 (5119 upstream) : RP11-77K12.5 (4131 downstream)						NA		NA									NA						gatggagtttcgctcttgttg	0.438		NA											C|||	34	0.00678914	0.0242	0.0029	5008	,	,	NA	19031	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.75534424C>T		NA		hg19		0.02	-0.140348	TTTxGCT	COVERED																																																																																			NOVEL					0			5	3.008484	KEEP	1	0	0	10	297	CC	0.99254	0.259018	0			3	60	88	1	0	6.972357	12	60	393	41		0.2	0.260965
KARS	3735	__UNKNOWN__	__UNKNOWN__	16	75668768	75668768	__UNKNOWN__	Intron	SNP	C	C	T	rs58657577	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:75668768C>T	ENST00000319410.5	-	8	1001				KARS_ENST00000302445.3_Intron|KARS_ENST00000568378.1_Intron	NM_001130089.1	NP_001123561.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	NA		NA			cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	ccactgcgcccggccCAATTC	0.433		NA											C|||	624	0.124601	0.3608	0.0346	5008	,	,	NA	16935	0.0079	NA	0.0596	False	NA	,,,	NA	NA	NA	2504	0.0562	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	3735	6.1.1.6	Aminoacyl tRNA synthetases / Class II	6215	protein-coding gene	gene with protein product	lysine tRNA ligase	601421	deafness, autosomal recessive 89	DFNB89	NA	8812440, 9278442, 23768514	Standard	NM_005548	NM_005548	NA	Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000319410.5:c.880-578G>A	chr16.hg19:g.75668768C>T		NA	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	hg19	CCDS45532.1	0.02	-0.096484	GCCxGGC	UNCOVERED																																																																																			NOVEL	KARS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269024.1	6	2.406722	KEEP	1	0	0	8	236	CC	0.99257	0.119541	0		-	6	60	180	0	0	17.569872	5	60	163	30	ENST00000319410.5	0.545455	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	77172287	77172287	__UNKNOWN__	IGR	SNP	C	C	G	rs149277735	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:77172287C>G			NA	NA				CTD-2336H13.2 (210221 upstream) : MON1B (52528 downstream)						NA		NA									NA						ggggtttcaccatgttagcca	0.557		NA											C|||	817	0.163139	0.1256	0.2522	5008	,	,	NA	11148	0.1458	NA	0.1421	False	NA	,,,	NA	NA	NA	2504	0.1902	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.77172287C>G		NA		hg19		0.02	-0.157876	CACxATG	COVERED																																																																																			NOVEL					0			7	3.008691	KEEP	2	0	0	10	300	CC	0.99254	0.320398	0			6	60	179	0	0	15.968933	11	60	354	34		0.352941	0.322807
WWOX	51741	__UNKNOWN__	__UNKNOWN__	16	79036148	79036148	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:79036148T>C	ENST00000566780.1	+	9	1422				WWOX_ENST00000402655.2_Intron|WWOX_ENST00000406884.2_Intron|WWOX_ENST00000539474.2_Intron|RP11-319G9.5_ENST00000561938.1_RNA	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	NA		NA			cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		gagatggagtttcactcttct	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	51741	1.1.1.-	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2	12799	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 41C, member 1	605131	WW domain-containing oxidoreductase		NA	10786676, 10861292, 19027726	Standard		XR_243411	NA	Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.1057-209357T>C	chr16.hg19:g.79036148T>C		NA	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	hg19	CCDS42196.1	0.02	-0.052629	AGTxTCA	UNCOVERED																																																																																			NOVEL	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000434328.1	9	2.406038	KEEP	6	0	0	8	220	TT	0	0	0		+	2	60	72	0	0	6.693059	3	60	88	18	ENST00000566780.1	0.4	0.036766
GAN	8139	__UNKNOWN__	__UNKNOWN__	16	81389171	81389171	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:81389171C>T	ENST00000568107.2	+	3	795					NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	NA		NA			cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				tctcgctgtgctgcccaggct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(106;1239 1507 7582 9741 33976)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609	8139		Kelch-like, BTB/POZ domain containing	4137	protein-coding gene	gene with protein product	kelch-like family member 16	605379	giant axonal neuropathy (gigaxonin)		NA	9450783, 11062483	Standard		NM_022041	NA	Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.633+811C>T	chr16.hg19:g.81389171C>T		NA		hg19	CCDS10935.1	0.02	-0.184212	GTGxTGC	COVERED																																																																																			NOVEL	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269050.3	11	3.610417	KEEP	0	0	0	12	358	CC	0.993634	0.454842	0		+	4	60	112	0	0	8.669241	17	60	584	46	ENST00000568107.2	0.190476	0.457757
GAN	8139	__UNKNOWN__	__UNKNOWN__	16	81403455	81403455	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:81403455A>G	ENST00000568107.2	+	9	1664				GAN_ENST00000567335.1_Intron	NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	NA		NA			cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				gattacaggcatgagccaccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(106;1239 1507 7582 9741 33976)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609	8139		Kelch-like, BTB/POZ domain containing	4137	protein-coding gene	gene with protein product	kelch-like family member 16	605379	giant axonal neuropathy (gigaxonin)		NA	9450783, 11062483	Standard		NM_022041	NA	Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.1502+4372A>G	chr16.hg19:g.81403455A>G		NA		hg19	CCDS10935.1	0.02	-0.166623	GGCxTGA	COVERED																																																																																			NOVEL	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269050.3	3	3.307552	KEEP	4	0	0	11	294	AA	0.99257	0.351317	0		+	3	60	95	0	0	7.492136	14	60	398	48	ENST00000568107.2	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	81757706	81757706	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:81757706A>G			NA	NA				CMIP (12339 upstream) : RP11-960L18.1 (14980 downstream)						NA		NA									NA						ctcctaaagtactggggttac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.81757706A>G		NA		hg19		0.02	-0.131555	AGTxCTG	COVERED																																																																																			NOVEL					0			9	3.305755	KEEP	0	0	0	11	285	AA	0.993072	0.227586	0			3	60	94	1	0	7.782118	10	60	300	33		0.230769	0.229173
NECAB2	54550	__UNKNOWN__	__UNKNOWN__	16	84036325	84036325	__UNKNOWN__	3'UTR	SNP	A	A	G	rs3881	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:84036325A>G	ENST00000305202.4	+	0	1552				NECAB2_ENST00000565691.1_3'UTR	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	NA		NA				cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						GTAGTGCCCAACCTAGCCAGG	0.577		NA											A|||	1735	0.346446	0.3245	0.3703	5008	,	,	NA	17928	0.2163	NA	0.4374	False	NA	,,,	NA	NA	NA	2504	0.3998	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154	54550		N-terminal EF-hand calcium binding proteins, EF-hand domain containing	23746	protein-coding gene	gene with protein product		NA	EF-hand calcium binding protein 2	EFCBP2	NA	12044471	Standard	NM_019065	NM_019065	NA	Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.*374A>G	chr16.hg19:g.84036325A>G		NA	A2RRG3|O75547|Q6ZSK0	hg19	CCDS10940.1	0.02	-0.359524	CCAxCCT	COVERED																																																																																			NOVEL	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269077.2	3	2.705996	KEEP	0	0	0	9	239	AA	0.99254	0.882244	0		+	10	60	351	0	0	29.982438	31	60	876	78	ENST00000305202.4	0.243902	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	84570627	84570627	__UNKNOWN__	IGR	SNP	C	C	G	rs140954646	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:84570627C>G			NA	NA				TLDC1 (32263 upstream) : COTL1 (28572 downstream)						NA		NA									NA						ctcctgacctcaggtgatccg	0.517		NA											C|||	11	0.00219649	0.0	0.0029	5008	,	,	NA	15472	0.0	NA	0.006	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.84570627C>G		NA		hg19		0.02	-0.043865	CCTxAGG	UNCOVERED																																																																																			NOVEL					0			4	2.406805	KEEP	7	0	0	8	237	CC	0	0	0			4	59	139	0	0	14.721432	1	8	37	26		0.8	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	84731086	84731086	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:84731086G>A			NA	NA				KLHL36 (35166 upstream) : USP10 (2497 downstream)						NA		NA									NA						tagtagagacggggtttcacc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.84731086G>A		NA		hg19		0.02	-0.105206	GACxGGG	UNCOVERED																																																																																			NOVEL					0			6	3.607906	KEEP	1	0	0	12	322	GG	0.993072	0.138863	0			3	60	86	0	0	7.233084	8	60	223	28		0.272727	0.139832
CRISPLD2	83716	__UNKNOWN__	__UNKNOWN__	16	84929854	84929854	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:84929854C>T	ENST00000262424.5	+	14	1663				CRISPLD2_ENST00000567845.1_Intron	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	NA		NA			extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)			endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						gggatttcaccatgttggcca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196	83716			25248	protein-coding gene	gene with protein product		612434	LCCL domain containing cysteine-rich secretory protein 2	LCRISP2	NA	11230166	Standard	NM_031476	NM_031476	NA	Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.1439+6885C>T	chr16.hg19:g.84929854C>T		NA	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	hg19	CCDS10949.1	0.02	-0.140298	CACxATG	COVERED																																																																																			NOVEL	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269086.2	8	3.008498	KEEP	1	0	0	10	296	CC	0.992708	0.259062	0		+	3	60	86	0	0	6.773016	12	60	366	31	ENST00000262424.5	0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	85594008	85594008	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:85594008T>C			NA	NA				AC092377.1 (118910 upstream) : RP11-118F19.1 (19606 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.85594008T>C		NA		hg19		0.02	-0.140336	AGGxGTG	COVERED																																																																																			NOVEL					0			5	3.609103	KEEP	0	0	0	12	333	TT	0.993634	0.259304	0			4	60	132	0	0	11.624119	9	60	266	35		0.307692	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	85975075	85975075	__UNKNOWN__	IGR	SNP	G	G	A	rs12596295	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:85975075G>A			NA	NA				RP11-542M13.3 (5246 upstream) : RP11-542M13.2 (40280 downstream)						NA		NA									NA						tcgatctcctgaccttgtgat	0.527		NA											G|||	403	0.0804712	0.0113	0.0461	5008	,	,	NA	16004	0.1925	NA	0.0885	False	NA	,,,	NA	NA	NA	2504	0.0746	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.85975075G>A		NA		hg19		0.02	-0.070167	CCTxACC	UNCOVERED																																																																																			NOVEL					0			10	2.406453	KEEP	7	0	0	8	229	GG	0	0	0			5	60	148	0	0	15.36504	2	20	63	22		0.714286	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	16	86206921	86206921	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:86206921T>C			NA	NA				RP11-805I24.4 (14517 upstream) : RP11-805I24.3 (19477 downstream)						NA		NA									NA						tgagccaccatgcccagccGG	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr16.hg19:g.86206921T>C		NA		hg19		0.02	-0.061392	CCAxGCC	UNCOVERED																																																																																			NOVEL					0			1	2.405976	KEEP	4	0	0	8	219	TT	0	0	0			3	42	93	0	0	8.923898	3	60	93	29		0.5	0.043787
MAP1LC3B	81631	__UNKNOWN__	__UNKNOWN__	16	87424316	87424316	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:87424316A>G	ENST00000562778.1	+	3	304							Q9GZQ8	MLP3B_HUMAN	microtubule-associated protein 1 light chain 3 beta	NA		NA			autophagy (GO:0006914)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasmic vesicle (GO:0031410)|intracellular (GO:0005622)|microtubule (GO:0005874)|organelle membrane (GO:0031090)				endometrium(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(80;0.0249)		aaagtgctggaattacaggca	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF087871	CCDS10960.1	16q24.2	2014-02-12			ENSG00000140941	ENSG00000140941	81631			13352	protein-coding gene	gene with protein product		609604			NA		Standard		NM_022818	NA	Approved	ATG8F	uc002fjx.3	Q9GZQ8	OTTHUMG00000137654	ENST00000562778.1:c.305-888A>G	chr16.hg19:g.87424316A>G		NA	Q6NW02	hg19		0.02	-0.096479	TGGxATT	UNCOVERED																																																																																			NOVEL	MAP1LC3B-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000430808.1	3	2.406034	KEEP	0	0	0	8	220	AA	0.99257	0.119541	0		+	3	60	100	0	0	8.943746	6	60	175	29	ENST00000562778.1	0.333333	0.120436
MAP1LC3B	81631	__UNKNOWN__	__UNKNOWN__	16	87435634	87435634	__UNKNOWN__	Intron	SNP	G	G	A	rs191653859	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:87435634G>A	ENST00000268607.5	+	3	724				MAP1LC3B_ENST00000534986.1_Intron|MAP1LC3B_ENST00000565788.1_Intron	NM_022818.4	NP_073729.1	Q9GZQ8	MLP3B_HUMAN	microtubule-associated protein 1 light chain 3 beta	NA		NA			autophagy (GO:0006914)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasmic vesicle (GO:0031410)|intracellular (GO:0005622)|microtubule (GO:0005874)|organelle membrane (GO:0031090)				endometrium(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(80;0.0249)		gtagagatggggtttcaccat	0.567		NA											G|||	56	0.0111821	0.0038	0.0216	5008	,	,	NA	14808	0.0	NA	0.0308	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF087871	CCDS10960.1	16q24.2	2014-02-12			ENSG00000140941	ENSG00000140941	81631			13352	protein-coding gene	gene with protein product		609604			NA		Standard		NM_022818	NA	Approved	ATG8F	uc002fjx.3	Q9GZQ8	OTTHUMG00000137654	ENST00000268607.5:c.97-147G>A	chr16.hg19:g.87435634G>A		NA	Q6NW02	hg19	CCDS10960.1	0.02	-0.087688	TGGxGTT	UNCOVERED																																																																																			NOVEL	MAP1LC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269106.1	3	2.707579	KEEP	1	0	0	9	265	GG	0.99257	0.09898	0		+	6	60	171	0	0	17.473362	3	60	84	22	ENST00000268607.5	0.666667	0.099721
CA5A	763	__UNKNOWN__	__UNKNOWN__	16	87935932	87935932	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:87935932C>A	ENST00000309893.2	-	4	621					NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	NA		NA			bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	tgcactccagcctgtgtgaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	763	4.2.1.1	Carbonic anhydrases	1377	protein-coding gene	gene with protein product		114761		CA5	NA	8356065, 7490083	Standard	NM_001739	NM_001739	NA	Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.555+98G>T	chr16.hg19:g.87935932C>A		NA	B2RPF2	hg19	CCDS10965.1	0.02	-0.315808	CAGxCTG	COVERED																																																																																			NOVEL	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269164.1	3	8.120682	KEEP	1	0	0	27	764	CC	0.999997	0.818462	0		-	3	31	93	1	0	6.40998	29	60	965	73	ENST00000309893.2	0.09375	0.818465
CA5A	763	__UNKNOWN__	__UNKNOWN__	16	87936017	87936017	__UNKNOWN__	Intron	SNP	G	G	C	rs537022607	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:87936017G>C	ENST00000309893.2	-	4	621					NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	NA		NA			bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	ATCTACACCCGAGCAAGTGAT	0.433		NA											G|||	8	0.00159744	0.0015	0.0014	5008	,	,	NA	12645	0.002	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													67	57	60			NA	NA	16		NA											NA				87936017		2198	4300	6498	SO:0001627	intron_variant			L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	763	4.2.1.1	Carbonic anhydrases	1377	protein-coding gene	gene with protein product		114761		CA5	NA	8356065, 7490083	Standard	NM_001739	NM_001739	NA	Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.555+13C>G	chr16.hg19:g.87936017G>C		NA	B2RPF2	hg19	CCDS10965.1	0.02	3.487372	CCCxAGC	COVERED																																																																																			NOVEL	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269164.1	23	15.980248	KEEP	1	1	31	64	1928	GG	1	0.999996	0		-	5	33	166	0	0	10.179322	104	60	3349	261	ENST00000309893.2	0.045872	0.999996
ANKRD11	29123	__UNKNOWN__	__UNKNOWN__	16	89537135	89537135	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:89537135T>C	ENST00000301030.4	-	1	317				ANKRD11_ENST00000378330.2_Intron	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	NA		NA			bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		cggtggctcatgcctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522	29123		Ankyrin repeat domain containing	21316	protein-coding gene	gene with protein product		611192			NA	11483580	Standard	NM_013275	NM_001256182	NA	Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.143+19517A>G	chr16.hg19:g.89537135T>C		NA	Q6NTG1|Q6QMF8	hg19	CCDS32513.1	0.02	-0.166634	TCAxGCC	COVERED																																																																																			NOVEL	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000430462.3	9	3.910054	KEEP	0	0	0	13	362	TT	0.994391	0.351961	0		-	3	60	102	0	0	8.110054	15	60	446	43	ENST00000301030.4	0.166667	0.353947
TCF25	22980	__UNKNOWN__	__UNKNOWN__	16	89952397	89952397	__UNKNOWN__	Intron	SNP	C	C	T	rs79441750	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr16:89952397C>T	ENST00000263346.8	+	4	604				TCF25_ENST00000263347.7_Intron	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	NA		NA			heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		cccttctctgcggctgccctt	0.642		NA											C|||	891	0.177915	0.1921	0.0648	5008	,	,	NA	12743	0.2788	NA	0.0905	False	NA	,,,	NA	NA	NA	2504	0.2249	NA	NA	NA								NA				0								C		714,3682	285.7+/-278.4	54,606,1538	32	28	29			-3.2	0	16	dbSNP_131	29	911,7689	195.5+/-240.7	43,825,3432	no	intron	TCF25	NM_014972.2		97,1431,4970	TT,TC,CC	NA	10.593,16.242,12.5038			89952397	1625,11371	2198	4300	6498	SO:0001627	intron_variant			AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002	22980			29181	protein-coding gene	gene with protein product		612326			NA	12107429, 16574069	Standard	NM_014972	NM_014972	NA	Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.548+23C>T	chr16.hg19:g.89952397C>T		NA	Q2MK75|Q9UPV3	hg19	CCDS10987.1	0.02	-0.403465	CTGxGGC	COVERED																																																																																			NOVEL	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000272875.2	2	3.008029	KEEP	1	0	0	10	284	CC	0.992708	0.927678	0		+	15	60	439	0	0	38.442754	31	60	989	69	ENST00000263346.8	0.326087	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	242647	242647	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:242647A>G			NA	NA				RP11-1260E13.2 (35275 upstream) : AC108004.3 (11678 downstream)						NA		NA									NA						tgggattacaagtgtaagcca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.242647A>G		NA		hg19		0.02	-0.236833	ACAxGTG	COVERED																																																																																			NOVEL					0			10	2.707023	KEEP	0	0	0	9	251	AA	0.99254	0.607839	0			3	60	105	0	0	7.948525	22	60	683	48		0.12	0.612407
VPS53	55275	__UNKNOWN__	__UNKNOWN__	17	418822	418822	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:418822G>C	ENST00000437048.2	-	0	6191					NM_001128159.2	NP_001121631.1	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	NA		NA			protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		ttgtcttgaagtcctgggctc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252	55275			25608	protein-coding gene	gene with protein product		615850	vacuolar protein sorting 53 (yeast)		NA	15878329	Standard	NM_018289	NM_018289	NA	Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000437048.2:c.*3546C>G	chr17.hg19:g.418822G>C		NA	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	hg19	CCDS45558.1	0.02	-0.22808	GAAxTCC	COVERED																																																																																			NOVEL	VPS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000436930.5	15	3.008994	KEEP	0	0	0	10	309	GG	0.992708	0.578679	0		-	3	60	100	0	0	7.833137	16	60	535	50	ENST00000437048.2	0.157895	0.58293
RNMTL1	55178	__UNKNOWN__	__UNKNOWN__	17	685815	685815	__UNKNOWN__	Missense_Mutation	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:685815G>T	ENST00000304478.4	+	1	303	c.197G>T	c.(196-198)aGt>aTt	p.S66I		NM_018146.2	NP_060616.1			RNA methyltransferase like 1	NA		NA								breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (25;0.0219)		TCTGAGGCCAGTGCCCAGGAG	0.622		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													33	33	33			NA	NA	17		NA											NA				685815		2202	4300	6502	SO:0001583	missense			AF177344	CCDS10997.1	17p13.3	2008-02-05			ENSG00000171861	ENSG00000171861	55178			18485	protein-coding gene	gene with protein product		612600			NA	12296377	Standard	NM_018146	NM_018146	NA	Approved	FLJ10581, HC90	uc002frw.3	Q9HC36	OTTHUMG00000090285	ENST00000304478.4:c.197G>T	chr17.hg19:g.685815G>T	ENSP00000306080:p.Ser66Ile	NA		hg19	CCDS10997.1	0.02	4.551499	CCAxTGC	COVERED	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.58|14.58	2.578338|2.578338	0.45902|0.45902	.|.	.|.	ENSG00000171861|ENSG00000167699	ENST00000304478|ENST00000397393	T|.	0.19394|.	2.15|.	5.06|5.06	3.0|3.0	0.34707|0.34707	.|.	0.690264|.	0.15005|.	N|.	0.285893|.	T|T	0.33933|0.33933	0.0880|0.0880	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	B|.	0.26744|.	0.158|.	B|.	0.21917|.	0.037|.	T|T	0.26087|0.26087	-1.0113|-1.0113	9|6	.|0.87932	.|D	.|0	-1.3251|-1.3251	9.0431|9.0431	0.36329|0.36329	0.1911:0.0:0.8089:0.0|0.1911:0.0:0.8089:0.0	.|.	66|.	Q9HC36|.	RMTL1_HUMAN|.	I|N	66|101	ENSP00000306080:S66I|.	.|ENSP00000380548:T101N	S|T	+|-	2|2	0|0	RNMTL1|GLOD4	632565|632565	0.002000|0.002000	0.14202|0.14202	0.092000|0.092000	0.20876|0.20876	0.069000|0.069000	0.16628|0.16628	0.865000|0.865000	0.27940|0.27940	0.592000|0.592000	0.29728|0.29728	0.563000|0.563000	0.77884|0.77884	AGT|ACT	NOVEL	RNMTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206611.1	5	12.93731	KEEP	0	0	0	43	1293	GG	1	1	0		+	12	60	340	0	0	21.594876	138	60	4714	273	ENST00000304478.4	0.08	1
NXN	64359	__UNKNOWN__	__UNKNOWN__	17	730493	730493	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:730493T>C	ENST00000336868.3	-	2	452				NXN_ENST00000575801.1_Intron|NXN_ENST00000537628.2_Intron|NXN_ENST00000577098.1_Intron	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	NA		NA			cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		ccgaggtgggtggatcatgag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693	64359			18008	protein-coding gene	gene with protein product		612895			NA		Standard		NM_022463	NA	Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.361-1175A>G	chr17.hg19:g.730493T>C		NA	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	hg19	CCDS10998.1	0.02	-0.236704	GGGxGGA	COVERED																																																																																			NOVEL	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206669.1	9	3.305935	KEEP	2	0	0	11	287	TT	0.993072	0.608164	0		-	3	60	90	0	0	6.628721	19	60	496	53	ENST00000336868.3	0.136364	0.612407
NXN	64359	__UNKNOWN__	__UNKNOWN__	17	736394	736394	__UNKNOWN__	Intron	SNP	A	A	G	rs570542731	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:736394A>G	ENST00000336868.3	-	2	452				NXN_ENST00000575801.1_Intron|NXN_ENST00000537628.2_Intron|NXN_ENST00000577098.1_Intron	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	NA		NA			cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		gcctcccaaaatgctgggatt	0.483		NA											A|||	5	0.000998403	0.0	0.0058	5008	,	,	NA	17108	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693	64359			18008	protein-coding gene	gene with protein product		612895			NA		Standard		NM_022463	NA	Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.361-7076T>C	chr17.hg19:g.736394A>G		NA	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	hg19	CCDS10998.1	0.02	-0.298197	AAAxTGC	COVERED																																																																																			NOVEL	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206669.1	7	3.308097	KEEP	1	0	0	11	300	AA	0.992708	0.775364	0		-	4	60	129	0	0	9.634689	27	60	797	71	ENST00000336868.3	0.129032	0.78106
NXN	64359	__UNKNOWN__	__UNKNOWN__	17	867271	867271	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:867271C>G	ENST00000336868.3	-	1	452					NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	NA		NA			cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		gagccgagatcgcgccactgc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693	64359			18008	protein-coding gene	gene with protein product		612895			NA		Standard		NM_022463	NA	Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.360+15287G>C	chr17.hg19:g.867271C>G		NA	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	hg19	CCDS10998.1	0.02	-0.359497	GATxGCG	COVERED																																																																																			NOVEL	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206669.1	100	13.892172	KEEP	73	2	56	66	1774	CT	1	0.934492	0		-	4	31	118	0	0	8.20953	33	60	989	185	ENST00000336868.3	0.108108	0.934492
AC144836.1	0	__UNKNOWN__	__UNKNOWN__	17	1145980	1145980	__UNKNOWN__	lincRNA	SNP	A	A	G	rs577578974	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1145980A>G	ENST00000575911.1	-	0	87										NA		NA									NA						aggctggagtacagtggctca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000575911.1:	chr17.hg19:g.1145980A>G		NA		hg19		0.02	-0.245556	AGTxCAG	COVERED																																																																																			NOVEL	AC144836.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000437296.1	10	2.705083	KEEP	1	0	0	9	230	AA	0.99254	0.636563	0		-	3	60	96	0	0	7.229016	19	60	545	52	ENST00000575911.1	0.136364	0.641347
AC144836.1	0	__UNKNOWN__	__UNKNOWN__	17	1151851	1151851	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1151851C>T	ENST00000575911.1	-	0	87										NA		NA									NA						aactcctgacctcagatgatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000575911.1:	chr17.hg19:g.1151851C>T		NA		hg19		0.02	-0.192991	GACxTCA	COVERED																																																																																			NOVEL	AC144836.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000437296.1	10	2.708084	KEEP	1	0	0	9	275	CC	0.99254	0.454342	0		-	3	26	90	0	0	6.627397	19	60	642	46	ENST00000575911.1	0.136364	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	1231342	1231342	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1231342T>C			NA	NA				TUSC5 (27061 upstream) : YWHAE (16223 downstream)						NA		NA									NA						gtaatcccagtactttgggag	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.1231342T>C		NA		hg19		0.02	-0.219258	CAGxACT	COVERED																																																																																			NOVEL					0			3	2.705821	KEEP	0	0	0	9	236	TT	0.99254	0.548763	0			3	60	103	0	0	7.805531	21	60	606	50		0.125	0.552887
YWHAE	7531	__UNKNOWN__	__UNKNOWN__	17	1260334	1260334	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1260334A>T	ENST00000264335.8	-	5	846				YWHAE_ENST00000575977.1_Intron|YWHAE_ENST00000573026.1_Intron|YWHAE_ENST00000571732.1_Intron	NM_006761.4	NP_006752.1	P62258	1433E_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cerebral cortex development (GO:0021987)|G2/M transition of mitotic cell cycle (GO:0000086)|hippo signaling (GO:0035329)|hippocampus development (GO:0021766)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|mitotic cell cycle (GO:0000278)|negative regulation of peptidyl-serine dephosphorylation (GO:1902309)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|substantia nigra development (GO:0021762)|viral process (GO:0016032)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|kinesin complex (GO:0005871)|membrane (GO:0016020)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|ion channel binding (GO:0044325)|MHC class II protein complex binding (GO:0023026)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|poly(A) RNA binding (GO:0044822)|potassium channel regulator activity (GO:0015459)|protein heterodimerization activity (GO:0046982)			kidney(2)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(18;0.203)	UCEC - Uterine corpus endometrioid carcinoma (25;0.0887)		gaggccgaggagggcagatca	0.517		NA	T	FAM22a, FAM22B	edometrial stromal sarcoma		Miller-Dieker lissencephaly syndrome														NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		17	17p13.3	7531	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (14-3-3 epsilon)	yes	M	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U54778	CCDS11001.1	17p13.3	2013-12-03	2013-12-03		ENSG00000108953	ENSG00000108953	7531			12851	protein-coding gene	gene with protein product	14-3-3 epsilon	605066	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide		NA	9371399	Standard	NM_006761	NM_006761	NA	Approved	FLJ45465	uc002fsj.3	P62258	OTTHUMG00000134316	ENST00000264335.8:c.579-2693T>A	chr17.hg19:g.1260334A>T		NA	B3KY71|D3DTH5|P29360|P42655|Q4VJB6|Q53XZ5|Q63631|Q7M4R4	hg19	CCDS11001.1	0.02	-0.236784	AGGxGGG	COVERED																																																																																			NOVEL	YWHAE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259354.3	12	2.406138	KEEP	3	0	0	8	221	AA	0.99257	0.607857	0		-	3	60	93	1	0	6.806337	21	60	607	47	ENST00000264335.8	0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	1314418	1314418	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1314418C>T			NA	NA				YWHAE (10746 upstream) : CRK (9564 downstream)						NA		NA									NA						tctcgatctcctgacctcgtg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.1314418C>T		NA		hg19		0.02	-0.254401	CTCxTGA	COVERED																																																																																			NOVEL					0			11	5.113736	KEEP	0	0	0	17	524	CC	0.999366	0.6681	0			3	60	93	0	0	6.642937	24	60	819	68		0.111111	0.668523
SCARF1	8578	__UNKNOWN__	__UNKNOWN__	17	1539736	1539736	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1539736G>C	ENST00000263071.4	-	10	1683				SCARF1_ENST00000348987.3_Intron|SCARF1_ENST00000571272.1_Intron	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	NA		NA			cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ggtgaaacccggtctctacta	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660	8578			16820	protein-coding gene	gene with protein product	scavenger receptor expressed by endothelial cells, acetyl LDL receptor	607873			NA	9395444, 8590280	Standard	NM_003693	NM_003693	NA	Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1633+266C>G	chr17.hg19:g.1539736G>C		NA	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	hg19	CCDS11007.1	0.02	-0.184197	CCCxGTC	COVERED																																																																																			NOVEL	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207081.4	10	3.609449	KEEP	0	0	0	12	347	GG	0.993634	0.420782	0		-	3	60	88	0	0	6.634356	16	60	523	43	ENST00000263071.4	0.157895	0.423478
PRPF8	10594	__UNKNOWN__	__UNKNOWN__	17	1568951	1568951	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1568951G>C	ENST00000572621.1	-	24	4040				PRPF8_ENST00000304992.6_Intron			Q6P2Q9	PRP8_HUMAN	pre-mRNA processing factor 8	NA		NA			gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	poly(A) RNA binding (GO:0044822)|U5 snRNA binding (GO:0030623)|U6 snRNA binding (GO:0017070)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(13)|lung(24)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	77				UCEC - Uterine corpus endometrioid carcinoma (25;0.0855)		gcctggccaagatggtgaaac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007510	CCDS11010.1	17p13.3	2013-07-16	2013-06-10		ENSG00000174231	ENSG00000174231	10594			17340	protein-coding gene	gene with protein product		607300	PRP8 pre-mRNA processing factor 8 homolog (yeast), PRP8 pre-mRNA processing factor 8 homolog (S. cerevisiae)	RP13	NA	11468273, 10411133	Standard		NM_006445	NA	Approved	PRPC8, Prp8, hPrp8, SNRNP220	uc002fte.3	Q6P2Q9	OTTHUMG00000090553	ENST00000572621.1:c.3775-3504C>G	chr17.hg19:g.1568951G>C		NA	O14547|O75965	hg19	CCDS11010.1	0.02	-0.149124	CAAxATG	COVERED																																																																																			NOVEL	PRPF8-002	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438412.2	7	2.707799	KEEP	2	0	0	9	270	GG	0.99254	0.289823	0		-	4	60	132	0	0	11.080822	13	60	431	32	ENST00000572621.1	0.235294	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	1597059	1597059	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1597059A>T			NA	NA				PRPF8 (8883 upstream) : TLCD2 (14004 downstream)						NA		NA									NA						atcccaacacattgggaggcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.1597059A>T		NA		hg19		0.02	-0.210485	CACxTTG	COVERED																																																																																			NOVEL					0			6	2.405843	KEEP	0	0	0	8	220	AA	0.99257	0.518282	0			3	60	89	0	0	6.661674	17	60	490	49		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	1606955	1606955	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1606955A>G			NA	NA				PRPF8 (18779 upstream) : TLCD2 (4108 downstream)						NA		NA									NA						gtgagccaccacgcccggccT	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.1606955A>G		NA		hg19		0.02	-0.254334	ACCxCGC	COVERED																																																																																			NOVEL					0			4	3.307278	KEEP	0	0	0	11	290	AA	0.993072	0.663892	0			4	60	135	0	0	10.56229	22	60	643	58		0.153846	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	1609825	1609825	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1609825T>C			NA	NA				PRPF8 (21649 upstream) : TLCD2 (1238 downstream)						NA		NA									NA						tttgggaggctgaggtgggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.1609825T>C		NA		hg19		0.02	-0.210516	GGCxGAG	COVERED																																																																																			NOVEL					0			13	3.608061	KEEP	2	0	0	12	330	TT	0.992708	0.518353	0			3	60	99	0	0	7.733306	16	60	492	54		0.157895	0.522161
SERPINF2	5345	__UNKNOWN__	__UNKNOWN__	17	1648374	1648374	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1648374G>A	ENST00000324015.3	+	2	140				SERPINF2_ENST00000382061.4_Intron|SERPINF2_ENST00000450523.2_Intron	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	NA		NA			acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	CTGAAGTCAAGGTGGGGTGGG	0.652		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													30	29	29			NA	NA	17		NA											NA				1648374		2202	4300	6502	SO:0001627	intron_variant			D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711	5345		Serine (or cysteine) peptidase inhibitors	9075	protein-coding gene	gene with protein product	alpha-2-plasmin inhibitor, alpha-2-antiplasmin	613168	serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	PLI	NA	3416655, 24172014	Standard	NM_000934	NM_000934	NA	Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.63+22G>A	chr17.hg19:g.1648374G>A		NA	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	hg19	CCDS11011.1	0.02	1.329964	CAAxGTG	COVERED																																																																																			NOVEL	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207078.3	3	4.814136	KEEP	0	0	0	16	488	GG	0.997832	0.99778	0		+	23	60	687	0	0	56.603019	74	60	2481	151	ENST00000324015.3	0.237113	0.999948
SMYD4	114826	__UNKNOWN__	__UNKNOWN__	17	1691848	1691848	__UNKNOWN__	Intron	SNP	A	A	G	rs573422476		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1691848A>G	ENST00000305513.7	-	6	1705					NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	NA		NA					metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						gaccatcctgactaacacggt	0.547		NA											A|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	13676	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532	114826		Zinc fingers, MYND-type	21067	protein-coding gene	gene with protein product		NA			NA	11572484	Standard	XM_056082	NM_052928	NA	Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.1538-950T>C	chr17.hg19:g.1691848A>G		NA	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	hg19	CCDS11013.1	0.02	-0.157782	CTGxCTA	COVERED																																																																																			NOVEL	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207108.4	6	2.406014	KEEP	2	0	0	8	218	AA	0.99257	0.351317	0		-	3	60	87	0	0	6.780412	13	60	344	37	ENST00000305513.7	0.1875	0.353947
RPA1	6117	__UNKNOWN__	__UNKNOWN__	17	1793722	1793722	__UNKNOWN__	Intron	SNP	T	T	C	rs550479307		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1793722T>C	ENST00000254719.5	+	15	1661					NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	NA		NA			base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						tttgggaggctgaggcaggcg	0.502		NA						Nucleotide excision repair (NER)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383	6117			10289	protein-coding gene	gene with protein product		179835	replication protein A1 (70kD)		NA	8454588	Standard	NM_002945	NM_002945	NA	Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1552-1405T>C	chr17.hg19:g.1793722T>C		NA	A8K0Y9|Q59ES9	hg19	CCDS11014.1	0.02	-0.166661	GGCxGAG	COVERED																																																																																			NOVEL	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207118.2	7	2.406706	KEEP	1	0	0	8	233	TT	0.99257	0.351317	0		+	4	60	140	0	0	11.76822	14	60	434	41	ENST00000254719.5	0.222222	0.353947
RTN4RL1	146760	__UNKNOWN__	__UNKNOWN__	17	1842442	1842442	__UNKNOWN__	Intron	SNP	C	C	G	rs35303223	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1842442C>G	ENST00000331238.6	-	2	493					NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1	NA		NA								breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						gtcaggagatcgagaccatcc	0.517		NA											C|||	158	0.0315495	0.0045	0.062	5008	,	,	NA	9856	0.005	NA	0.0934	False	NA	,,,	NA	NA	NA	2504	0.0102	NA	NA	NA	GBM(68;949 1139 14865 32798 38342)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924	146760			21329	protein-coding gene	gene with protein product	nogo-66 receptor homolog 2	610461			NA		Standard	NM_178568	NM_178568	NA	Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.14-1340G>C	chr17.hg19:g.1842442C>G		NA		hg19	CCDS45569.1	0.02	-0.061407	GATxGAG	UNCOVERED																																																																																			NOVEL	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450155.2	7	2.406347	KEEP	5	0	0	8	230	CC	0	0	0		-	6	60	204	0	0	22.015476	1	7	31	25	ENST00000331238.6	0.857143	0.043787
RTN4RL1	146760	__UNKNOWN__	__UNKNOWN__	17	1842447	1842447	__UNKNOWN__	Intron	SNP	C	C	T	rs187111291	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1842447C>T	ENST00000331238.6	-	2	493					NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1	NA		NA								breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						gagatcgagaccatcctggct	0.532		NA											C|||	137	0.0273562	0.0061	0.0533	5008	,	,	NA	9908	0.001	NA	0.0755	False	NA	,,,	NA	NA	NA	2504	0.0153	NA	NA	NA	GBM(68;949 1139 14865 32798 38342)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924	146760			21329	protein-coding gene	gene with protein product	nogo-66 receptor homolog 2	610461			NA		Standard	NM_178568	NM_178568	NA	Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.14-1345G>A	chr17.hg19:g.1842447C>T		NA		hg19	CCDS45569.1	0.02	-0.061391	AGAxCAT	UNCOVERED																																																																																			NOVEL	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450155.2	7	2.707902	KEEP	5	0	0	9	274	CC	0	0	0		-	5	60	145	0	0	15.709071	1	7	31	26	ENST00000331238.6	0.833333	0.043787
RTN4RL1	146760	__UNKNOWN__	__UNKNOWN__	17	1852579	1852579	__UNKNOWN__	Intron	SNP	C	C	T	rs565385083		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1852579C>T	ENST00000331238.6	-	2	493					NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1	NA		NA								breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						ttagtagagacggggtttcac	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(68;949 1139 14865 32798 38342)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924	146760			21329	protein-coding gene	gene with protein product	nogo-66 receptor homolog 2	610461			NA		Standard	NM_178568	NM_178568	NA	Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.14-11477G>A	chr17.hg19:g.1852579C>T		NA		hg19	CCDS45569.1	0.02	-0.20175	AGAxGGG	COVERED																																																																																			NOVEL	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450155.2	9	3.609535	KEEP	6	0	0	12	343	CC	0.992708	0.486967	0		-	3	44	86	0	0	6.434034	16	60	522	57	ENST00000331238.6	0.157895	0.490544
RTN4RL1	146760	__UNKNOWN__	__UNKNOWN__	17	1867771	1867771	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1867771T>A	ENST00000331238.6	-	2	493					NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1	NA		NA								breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						tcacgcctgttatcccagcac	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(68;949 1139 14865 32798 38342)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924	146760			21329	protein-coding gene	gene with protein product	nogo-66 receptor homolog 2	610461			NA		Standard	NM_178568	NM_178568	NA	Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.14-26669A>T	chr17.hg19:g.1867771T>A		NA		hg19	CCDS45569.1	0.02	-0.35942	TGTxATC	COVERED																																																																																			NOVEL	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450155.2	14	2.836996	KEEP	0	1	27	19	495	TT	0.999863	0.888753	0		-	4	60	102	0	0	6.615733	33	60	946	87	ENST00000331238.6	0.108108	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	1930129	1930129	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1930129T>C			NA	NA				RTN4RL1 (1490 upstream) : DPH1 (3274 downstream)						NA		NA									NA						agagtgagactctgtctcaaa	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.1930129T>C		NA		hg19		0.02	-0.210482	GACxCTG	COVERED																																																																																			NOVEL					0			10	3.306628	KEEP	8	0	0	11	288	TT	0.99257	0.54878	0			3	60	102	2	0	8.278838	13	60	388	54		0.1875	0.552887
DPH1	1801	__UNKNOWN__	__UNKNOWN__	17	1942950	1942950	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:1942950C>T	ENST00000263083.6	+	7	740				DPH1_ENST00000570477.1_Intron	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	NA		NA			cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						ggattacaggcgtgagccacc	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963	1801			3003	protein-coding gene	gene with protein product	ovarian tumor suppressor candidate 1	603527	diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae), DPH-like 1 (S. cerevisiae), DPH1 homolog (S. cerevisiae)	DPH2L, DPH2L1	NA	8603384, 15485916, 22869748	Standard	NM_001383	NM_001383	NA	Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.696-99C>T	chr17.hg19:g.1942950C>T		NA	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	hg19	CCDS42228.1	0.02	4.198919	AGGxGTG	COVERED																																																																																			NOVEL	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438660.1	17	7.052682	KEEP	3	4	91	56	1684	CC	1	1	0		+	8	60	248	0	0	14.441285	171	70	5696	343	ENST00000263083.6	0.044693	1
SMG6	23293	__UNKNOWN__	__UNKNOWN__	17	2034683	2034683	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2034683G>A	ENST00000263073.6	-	13	3408				SMG6_ENST00000544865.1_Intron|SMG6_ENST00000536871.2_Intron|SMG6_ENST00000354901.4_Intron	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	NA		NA			gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						tccgcctcccgggttcaagcg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(59;28 1088 11621 25887 46638 50814)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366	23293			17809	protein-coding gene	gene with protein product	EST1 telomerase component homolog A (S. cerevisiae)	610963	chromosome 17 open reading frame 31, smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)	C17orf31	NA	12676087, 12699629	Standard		NM_017575	NA	Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.3357+41268C>T	chr17.hg19:g.2034683G>A		NA	B7Z874|O94837|Q86VH6|Q9UF60	hg19	CCDS11016.1	0.02	-0.087716	CCCxGGT	UNCOVERED																																																																																			NOVEL	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000437826.3	7	2.407186	KEEP	1	0	0	8	244	GG	0	0	0		-	3	60	87	0	0	7.478151	7	60	243	22	ENST00000263073.6	0.3	0.099721
SRR	63826	__UNKNOWN__	__UNKNOWN__	17	2225491	2225491	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2225491A>G	ENST00000344595.5	+	6	912				SRR_ENST00000576848.1_Intron	NM_021947.1	NP_068766.1	Q9GZT4	SRR_HUMAN	serine racemase	NA		NA			aging (GO:0007568)|brain development (GO:0007420)|D-serine biosynthetic process (GO:0070179)|D-serine metabolic process (GO:0070178)|L-serine metabolic process (GO:0006563)|protein homotetramerization (GO:0051289)|pyruvate biosynthetic process (GO:0042866)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|serine family amino acid metabolic process (GO:0009069)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|D-serine ammonia-lyase activity (GO:0008721)|glycine binding (GO:0016594)|L-serine ammonia-lyase activity (GO:0003941)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|serine racemase activity (GO:0030378)|threonine racemase activity (GO:0018114)			NS(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	L-Serine(DB00133)	ccaaagtgctaggattacagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF169974	CCDS11017.1	17p13	2007-01-18			ENSG00000167720	ENSG00000167720	63826			14398	protein-coding gene	gene with protein product		606477			NA	17067558, 15953485, 15193426	Standard	NM_021947	NM_021947	NA	Approved	ILV1, ISO1	uc002fue.1	Q9GZT4	OTTHUMG00000090583	ENST00000344595.5:c.594+581A>G	chr17.hg19:g.2225491A>G		NA	D3DTI5|Q6IA55	hg19	CCDS11017.1	0.02	-0.149106	GCTxGGA	COVERED																																																																																			NOVEL	SRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207129.2	6	3.00774	KEEP	1	0	0	10	277	AA	0.99254	0.289823	0		+	3	60	97	0	0	7.872369	12	60	358	38	ENST00000344595.5	0.2	0.292001
SGSM2	9905	__UNKNOWN__	__UNKNOWN__	17	2280739	2280739	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2280739C>G	ENST00000574563.1	+	20	2734				RP1-59D14.5_ENST00000574290.1_RNA|RP1-59D14.5_ENST00000573007.1_RNA|SGSM2_ENST00000268989.3_Intron|SGSM2_ENST00000426855.2_Intron			O43147	SGSM2_HUMAN	small G protein signaling modulator 2	NA		NA			late endosome to Golgi transport (GO:0034499)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(2;5.15e-05)|READ - Rectum adenocarcinoma(2;0.000115)		gatcacaccactgcactccag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC039204	CCDS32526.1, CCDS45570.1	17p13.3	2013-07-10	2007-08-14	2007-08-14		ENSG00000141258	9905		Small G protein signaling modulators	29026	protein-coding gene	gene with protein product		611418	RUN and TBC1 domain containing 1	RUTBC1	NA	9455477, 17509819, 21808068	Standard	NM_014853	NM_014853	NA	Approved	KIAA0397	uc002fum.4	O43147		ENST00000574563.1:c.2667+377C>G	chr17.hg19:g.2280739C>G		NA	A5LGW2|B4DH69|Q49AC2|Q6ZUY2|Q8IXU4	hg19		0.02	-0.08773	CCAxTGC	UNCOVERED																																																																																			NOVEL	SGSM2-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000438187.1	10	2.70801	KEEP	11	0	0	9	274	CC	0.99257	0.09898	0		+	3	60	108	0	0	9.743478	6	60	210	40	ENST00000574563.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	2425231	2425231	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2425231A>G			NA	NA				METTL16 (10046 upstream) : RN7SL33P (35864 downstream)						NA		NA									NA						ctggagtgcaatggtgcaatc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.2425231A>G		NA		hg19		0.02	-0.052613	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			4	2.405859	KEEP	3	0	0	8	216	AA	0.99257	0.036492	0			2	43	69	0	0	6.393393	3	60	79	23		0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	2428342	2428342	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2428342A>G			NA	NA				METTL16 (13157 upstream) : RN7SL33P (32753 downstream)						NA		NA									NA						tgatctgcccacctcggcctc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.2428342A>G		NA		hg19		0.02	-0.131559	CCCxCCT	UNCOVERED																																																																																			NOVEL					0			4	2.706308	KEEP	3	0	0	9	241	AA	0	0	0			3	60	97	0	0	7.87237	12	60	358	40		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	2445297	2445297	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2445297T>C			NA	NA				METTL16 (30112 upstream) : RN7SL33P (15798 downstream)						NA		NA									NA						cctgcctcggtctcccaaagt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.2445297T>C		NA		hg19		0.02	-0.096475	CGGxCTC	UNCOVERED																																																																																			NOVEL					0			5	2.405321	KEEP	1	0	0	8	215	TT	0	0	0			3	44	105	0	0	9.633157	5	60	150	26		0.375	0.120436
RAP1GAP2	23108	__UNKNOWN__	__UNKNOWN__	17	2704496	2704496	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:2704496T>C	ENST00000254695.8	+	2	170				RAP1GAP2_ENST00000366401.4_Intron|RAP1GAP2_ENST00000542807.1_Intron|RAP1GAP2_ENST00000540393.2_Intron	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	NA		NA			negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						Gggctgggcatggtggctcac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359	23108			29176	protein-coding gene	gene with protein product		NA	GTPase activating RANGAP domain-like 4, GTPase activating Rap/RanGAP domain-like 4	GARNL4	NA	15632203	Standard		NM_015085	NA	Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.80+652T>C	chr17.hg19:g.2704496T>C		NA	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	hg19	CCDS45573.1	0.02	-0.140292	GCAxGGT	UNCOVERED																																																																																			NOVEL	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438208.2	5	2.705841	KEEP	6	0	0	9	236	TT	0	0	0		+	3	60	105	0	0	8.57925	13	60	361	34	ENST00000254695.8	0.1875	0.260965
P2RX5-TAX1BP3	100533970	__UNKNOWN__	__UNKNOWN__	17	3582954	3582954	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs61748727	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:3582954C>T	ENST00000550383.1	-	11	1377	c.1189G>A	c.(1189-1191)Gag>Aag	p.E397K	P2RX5_ENST00000552050.1_Missense_Mutation_p.E337K|P2RX5_ENST00000225328.5_Missense_Mutation_p.E397K|P2RX5_ENST00000551178.1_Missense_Mutation_p.E372K|P2RX5_ENST00000345901.3_Missense_Mutation_p.E373K|P2RX5_ENST00000552276.1_Missense_Mutation_p.E396K|P2RX5_ENST00000547178.1_Missense_Mutation_p.E396K|P2RX5_ENST00000435558.1_Missense_Mutation_p.E397K					P2RX5-TAX1BP3 readthrough (NMD candidate)	NA		NA									NA						CGCTTCGCCTCGGGTGGCTCC	0.672		NA											C|||	92	0.0183706	0.0045	0.0086	5008	,	,	NA	18138	0.0486	NA	0.005	False	NA	,,,	NA	NA	NA	2504	0.0266	NA	NA	NA								NA				0								C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	20,4386	28.1+/-56.4	0,20,2183	75	54	61		1186,1117,1189,1114	-0.7	0	17	dbSNP_129	61	43,8557	27.4+/-76.7	0,43,4257	yes	missense,missense,missense,missense	P2RX5	NM_001204519.1,NM_001204520.1,NM_002561.3,NM_175080.2	56,56,56,56	0,63,6440	TT,TC,CC	NA	0.5,0.4539,0.4844	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	396/422,373/399,397/423,372/398	3582954	63,12943	2203	4300	6503	SO:0001583	missense					17p13.2	2013-09-25			ENSG00000257950	ENSG00000257950	100533970			49191	other	readthrough		NA			NA		Standard		NR_037928	NA	Approved				OTTHUMG00000169623	ENST00000550383.1:c.1189G>A	chr17.hg19:g.3582954C>T	ENSP00000455681:p.Glu397Lys	NA		hg19		0.02	1.245502	CCTxGGG	COVERED	30|30	0.013736263736263736|0.013736263736263736	5|5	0.01016260162601626|0.01016260162601626	4|4	0.011049723756906077|0.011049723756906077	20|20	0.03496503496503497|0.03496503496503497	1|1	0.0013192612137203166|0.0013192612137203166	C|C	10.98|10.98	1.503067|1.503067	0.26949|0.26949	0.004539|0.004539	0.005|0.005	ENSG00000083454|ENSG00000083454	ENST00000435558;ENST00000551178;ENST00000547178;ENST00000225328;ENST00000345901;ENST00000552050|ENST00000552723	T;T;T;T;T;T|.	0.07114|.	3.58;3.6;3.6;3.6;3.6;3.22|.	2.99|2.99	-0.74|-0.74	0.11115|0.11115	.|.	4.829560|.	0.00966|.	U|.	0.003163|.	T|T	0.04724|0.04724	0.0128|0.0128	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B|.	0.14012|.	0.005;0.009;0.009;0.009;0.005;0.009|.	B;B;B;B;B;B|.	0.10450|.	0.001;0.005;0.005;0.005;0.002;0.005|.	T|T	0.22765|0.22765	-1.0207|-1.0207	10|5	0.42905|.	T|.	0.14|.	-0.5454|-0.5454	3.8043|3.8043	0.08771|0.08771	0.0:0.3352:0.286:0.3788|0.0:0.3352:0.286:0.3788	.|.	337;373;396;372;397;397|.	B4DEG2;G5E981;Q93086-1;Q93086-2;Q93086;Q93086-4|.	.;.;.;.;P2RX5_HUMAN;.|.	K|Q	397;372;396;397;373;337|270	ENSP00000415370:E397K;ENSP00000447545:E372K;ENSP00000448355:E396K;ENSP00000225328:E397K;ENSP00000342161:E373K;ENSP00000450006:E337K|.	ENSP00000225328:E397K|.	E|R	-|-	1|2	0|0	P2RX5|P2RX5	3529703|3529703	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.318000|-0.318000	0.08050|0.08050	-0.056000|-0.056000	0.13221|0.13221	-0.432000|-0.432000	0.05891|0.05891	GAG|CGA	NOVEL	P2RX5-TAX1BP3-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000405135.1	5	5.104012	KEEP	0	0	0	17	467	CC	0.999366	0.998989	0		-	5	60	144	0	0	8.569003	79	60	2580	150	ENST00000550383.1	0.059524	0.999622
ZZEF1	23140	__UNKNOWN__	__UNKNOWN__	17	3918797	3918797	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:3918797G>A	ENST00000381638.2	-	49	8270					NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	NA		NA					calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ggtggctcacgcctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755	23140		Zinc fingers, ZZ-type, EF-hand domain containing	29027	protein-coding gene	gene with protein product		NA	zinc finger, ZZ-type with EF hand domain 1		NA	9455477	Standard	NM_015113	XM_005256560	NA	Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.8145+819C>T	chr17.hg19:g.3918797G>A		NA	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	hg19	CCDS11043.1	0.02	-0.087702	CACxCCT	UNCOVERED																																																																																			NOVEL	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207480.1	1	2.707994	KEEP	0	0	0	9	279	GG	0.99254	0.098977	0		-	4	60	114	1	0	10.384313	6	60	194	30	ENST00000381638.2	0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	4279645	4279645	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4279645T>C			NA	NA				UBE2G1 (9722 upstream) : SPNS3 (57337 downstream)						NA		NA									NA						ggctggagtgtagtggcacga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.4279645T>C		NA		hg19		0.02	-0.131515	GTGxAGT	COVERED																																																																																			NOVEL					0			7	2.405282	KEEP	1	0	0	8	209	TT	0.99257	0.22747	0			3	60	104	0	0	8.67353	11	60	296	34		0.214286	0.229173
RP11-141J13.5	0	__UNKNOWN__	__UNKNOWN__	17	4515710	4515710	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4515710T>C	ENST00000573270.1	+	0	385										NA		NA									NA						aggctggtcttgaactcctga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000573270.1:	chr17.hg19:g.4515710T>C		NA		hg19		0.02	-0.149102	TCTxGAA	UNCOVERED																																																																																			NOVEL	RP11-141J13.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000439132.1	14	2.405669	KEEP	13	0	0	8	214	TT	0	0	0		+	3	40	101	0	0	8.178874	13	60	382	46	ENST00000573270.1	0.1875	0.322807
INCA1	388324	__UNKNOWN__	__UNKNOWN__	17	4899500	4899500	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4899500C>T	ENST00000574617.1	-	2	193				INCA1_ENST00000576820.1_Intron|INCA1_ENST00000355025.3_Intron|INCA1_ENST00000396829.2_Intron|INCA1_ENST00000575780.1_Intron			Q0VD86	INCA1_HUMAN	inhibitor of CDK, cyclin A1 interacting protein 1	NA		NA			negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			upper_aerodigestive_tract(1)	1						ggcaacatggcgaaaccccct	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY601906, AAT09152	CCDS11064.1, CCDS54074.1	17p13.2	2010-03-19	2009-04-20		ENSG00000196388	ENSG00000196388	388324			32224	protein-coding gene	gene with protein product		NA			NA	15159402, 18756329	Standard	NM_213726	NM_213726	NA	Approved		uc002gak.3	Q0VD86		ENST00000574617.1:c.163-275G>A	chr17.hg19:g.4899500C>T		NA	Q6J273|Q6PKN9	hg19	CCDS54074.1	0.02	-0.114031	TGGxGAA	UNCOVERED																																																																																			NOVEL	INCA1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438886.1	3	3.609579	KEEP	0	0	0	12	345	CC	0.993634	0.161432	0		-	3	60	85	0	0	7.132152	8	60	264	35	ENST00000574617.1	0.272727	0.162467
KIF1C	10749	__UNKNOWN__	__UNKNOWN__	17	4929843	4929843	__UNKNOWN__	3'UTR	SNP	G	G	A	rs113609914	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4929843G>A	ENST00000320785.5	+	0	6066					NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	NA		NA			ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						ccaggagttcgagaccagcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(96;1023 1447 10250 19259 33730)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250	10749		Kinesins	6317	protein-coding gene	gene with protein product		603060	spastic ataxia 2 (autosomal recessive)	SAX2	NA	9685376, 24319291, 24482476	Standard		NM_006612	NA	Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.*2397G>A	chr17.hg19:g.4929843G>A		NA	D3DTL6|O75186|Q5U618	hg19	CCDS11065.1	0.02	-0.298197	TTCxAGA	COVERED																																																																																			NOVEL	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216916.1	11	2.770387	KEEP	0	2	53	28	801	GG	0.999997	0.781058	0		+	4	60	127	0	0	9.374653	28	60	870	83	ENST00000320785.5	0.125	0.78106
KIF1C	10749	__UNKNOWN__	__UNKNOWN__	17	4929863	4929863	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4929863A>G	ENST00000320785.5	+	0	6086					NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	NA		NA			ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						tgggcaacatagtgaaaccct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(96;1023 1447 10250 19259 33730)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250	10749		Kinesins	6317	protein-coding gene	gene with protein product		603060	spastic ataxia 2 (autosomal recessive)	SAX2	NA	9685376, 24319291, 24482476	Standard		NM_006612	NA	Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.*2417A>G	chr17.hg19:g.4929863A>G		NA	D3DTL6|O75186|Q5U618	hg19	CCDS11065.1	0.02	-0.333265	CATxGTG	COVERED																																																																																			NOVEL	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000216916.1	11	9.622977	KEEP	0	0	0	32	867	AA	0.999997	0.851982	0		+	3	60	108	0	0	7.711055	34	60	1005	100	ENST00000320785.5	0.081081	0.851984
RP11-46I8.3	0	__UNKNOWN__	__UNKNOWN__	17	4979852	4979852	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4979852T>C	ENST00000574352.1	-	0	227										NA		NA									NA						ccaggctggtttcgaactcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000574352.1:	chr17.hg19:g.4979852T>C		NA		hg19		0.02	-0.087716	GGTxTCG	UNCOVERED																																																																																			NOVEL	RP11-46I8.3-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000438978.1	5	2.704914	KEEP	1	0	0	9	232	TT	0.99257	0.09898	0		-	4	60	137	0	0	12.685914	6	60	179	30	ENST00000574352.1	0.4	0.099721
ZFP3	124961	__UNKNOWN__	__UNKNOWN__	17	4991905	4991905	__UNKNOWN__	Intron	SNP	G	G	A	rs9900450	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:4991905G>A	ENST00000318833.3	+	2	328					NM_153018.2	NP_694563.1	Q96NJ6	ZFP3_HUMAN	ZFP3 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(3)|prostate(1)	20						caccatgcccggctaattttt	0.552		NA											G|||	1253	0.2502	0.0477	0.4424	5008	,	,	NA	16132	0.1895	NA	0.4702	False	NA	,,,	NA	NA	NA	2504	0.2239	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX647638	CCDS11067.1	17p13.2	2013-01-08	2012-11-27		ENSG00000180787	ENSG00000180787	124961		Zinc fingers, C2H2-type	12861	protein-coding gene	gene with protein product		194480	zinc finger protein homologous to Zfp-3 in mouse, zinc finger protein 3 homolog (mouse)		NA		Standard	NM_153018	NM_153018	NA	Approved	FLJ30726, ZNF752	uc002gaq.3	Q96NJ6		ENST00000318833.3:c.-8-2887G>A	chr17.hg19:g.4991905G>A		NA	A5PLL4	hg19	CCDS11067.1	0.02	-0.157882	CCCxGCT	COVERED																																																																																			NOVEL	ZFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438979.1	18	4.244476	KEEP	13	1	28	24	713	GG	0.995343	0.321303	0		+	3	56	97	0	0	8.201096	9	60	284	64	ENST00000318833.3	0.25	0.322807
ZNF594	84622	__UNKNOWN__	__UNKNOWN__	17	5083545	5083545	__UNKNOWN__	3'UTR	SNP	C	C	T	rs529002531		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:5083545C>T	ENST00000399604.4	-	0	4147				ZNF594_ENST00000575779.1_3'UTR			Q96JF6	ZN594_HUMAN	zinc finger protein 594	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ttagtagagacggggttttag	0.502		NA											A|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17360	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626	84622		Zinc fingers, C2H2-type	29392	protein-coding gene	gene with protein product		NA			NA	11347906	Standard	XM_290737	NM_032530	NA	Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.*1583G>A	chr17.hg19:g.5083545C>T		NA	Q6RFS0	hg19	CCDS42241.1	0.02	2.56109	AGAxGGG	COVERED																																																																																			NOVEL	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000438996.1	47	32.420484	KEEP	2	1	26	117	3419	CC	1	0.999998	0		-	6	60	173	0	0	10.091581	103	60	3399	339	ENST00000399604.4	0.055046	0.999998
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	5844094	5844094	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:5844094A>G			NA	NA				WSCD1 (10078 upstream) : WSCD1 (128331 downstream)						NA		NA									NA						ttgaggtcagaagtttgagac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.5844094A>G		NA		hg19		0.02	-0.078935	CAGxAGT	UNCOVERED																																																																																			NOVEL					0			2	3.0074	KEEP	0	0	0	10	271	AA	0.992708	0.076772	0			3	24	101	0	0	9.043899	6	60	173	29		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	6091829	6091829	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:6091829T>C			NA	NA				WSCD1 (64082 upstream) : RP11-960B9.2 (944 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.6091829T>C		NA		hg19		0.02	-0.114022	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			6	2.406328	KEEP	0	0	0	8	224	TT	0.99257	0.16126	0			3	60	101	0	0	8.482039	10	60	296	29		0.230769	0.162467
PITPNM3	83394	__UNKNOWN__	__UNKNOWN__	17	6358803	6358803	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs371145698		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:6358803A>T	ENST00000262483.8	-	20	2867	c.2780T>A	c.(2779-2781)aTg>aAg	p.M927K	PITPNM3_ENST00000421306.3_Missense_Mutation_p.M891K|PITPNM3_ENST00000576664.1_5'UTR	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	927		NA			phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		CTGCACTGACATGGTTCTGCG	0.687		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													21	27	25			NA	NA	17		NA											NA				6358803		2190	4298	6488	SO:0001583	missense			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622	83394		GPCR / Class A : Chemokine receptors : Atypical	21043	protein-coding gene	gene with protein product	atypical chemokine receptor 6	608921	cone rod dystrophy 5	CORD5	NA	10022914	Standard	NM_031220	NM_031220	NA	Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.2780T>A	chr17.hg19:g.6358803A>T	ENSP00000262483:p.Met927Lys	NA	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	hg19	CCDS11076.1	0.02	4.99363	GACxTGG	COVERED	.	.	.	.	.	.	.	.	.	.	A	13.57	2.276732	0.40294	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.42131	0.98;0.98	4.76	4.76	0.60689	.	0.040493	0.85682	D	0.000000	T	0.39963	0.1098	M	0.63428	1.95	0.49051	D	0.999744	B;B	0.31153	0.246;0.31	B;B	0.37780	0.258;0.113	T	0.23154	-1.0196	10	0.02654	T	1	.	12.5741	0.56354	1.0:0.0:0.0:0.0	.	891;927	F8WEW5;Q9BZ71	.;PITM3_HUMAN	K	927;891	ENSP00000262483:M927K;ENSP00000407882:M891K	ENSP00000262483:M927K	M	-	2	0	PITPNM3	6299527	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.251000	0.95483	1.921000	0.55644	0.414000	0.27820	ATG	NOVEL	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000219824.2	2	7.518109	KEEP	0	0	0	25	673	AA	0.999931	0.999931	0		-	79	60	2310	0	0	221.723243	77	60	2195	252	ENST00000262483.8	0.50641	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	6943578	6943578	__UNKNOWN__	IGR	SNP	C	C	T	rs532086699		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:6943578C>T			NA	NA				SLC16A13 (138 upstream) : SLC16A11 (1370 downstream)						NA		NA									NA						ctccgcttcccgggttcaagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.6943578C>T		NA		hg19		0.02	-0.17542	TCCxGGG	COVERED																																																																																			NOVEL					0			7	3.910187	KEEP	2	0	0	13	368	CC	0.993634	0.38494	0			3	60	93	0	0	7.133596	16	60	488	40		0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	6990136	6990136	__UNKNOWN__	IGR	SNP	G	G	A	rs113508418	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:6990136G>A			NA	NA				CLEC10A (6510 upstream) : ASGR2 (14504 downstream)						NA		NA									NA						caaagtgctgggattacaggc	0.458		NA											a|||	1096	0.21885	0.5696	0.0893	5008	,	,	NA	13811	0.1458	NA	0.0795	False	NA	,,,	NA	NA	NA	2504	0.0552	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.6990136G>A		NA		hg19		0.02	-0.078946	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			4	2.706945	KEEP	6	0	0	9	263	GG	0.99257	0.09898	0			4	60	121	0	0	11.322656	5	60	167	38		0.444444	0.099721
SLC2A4	6517	__UNKNOWN__	__UNKNOWN__	17	7190722	7190722	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:7190722C>T	ENST00000317370.8	+	0	2572					NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	NA		NA			amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						ggattacaggcgtgagccacc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856	6517		Solute carriers	11009	protein-coding gene	gene with protein product		138190		GLUT4	NA		Standard		NM_001042	NA	Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.*774C>T	chr17.hg19:g.7190722C>T		NA	Q05BQ3|Q14CX2	hg19	CCDS11097.1	0.02	1.151384	AGGxGTG	COVERED																																																																																			NOVEL	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000220031.3	11	9.325294	KEEP	2	0	0	31	914	CC	0.999997	0.992091	0		+	5	60	134	0	0	8.329729	55	60	1822	129	ENST00000317370.8	0.083333	0.992094
SLC2A4	6517	__UNKNOWN__	__UNKNOWN__	17	7190732	7190732	__UNKNOWN__	3'UTR	SNP	C	C	T	rs534053868		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:7190732C>T	ENST00000317370.8	+	0	2582					NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	NA		NA			amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						cgtgagccaccgcgcctggcG	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856	6517		Solute carriers	11009	protein-coding gene	gene with protein product		138190		GLUT4	NA		Standard		NM_001042	NA	Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.*784C>T	chr17.hg19:g.7190732C>T		NA	Q05BQ3|Q14CX2	hg19	CCDS11097.1	0.02	1.438473	CACxGCG	COVERED																																																																																			NOVEL	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000220031.3	12	7.253409	KEEP	2	1	22	32	962	CC	0.999998	0.992092	0		+	4	60	125	0	0	8.031324	56	60	1832	134	ENST00000317370.8	0.066667	0.992094
TNFSF12-TNFSF13	407977	__UNKNOWN__	__UNKNOWN__	17	7457822	7457822	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:7457822C>T	ENST00000293826.4	+	6	428				TNFSF12_ENST00000462811.1_Intron|TNFSF12_ENST00000557233.1_Intron|TNFSF12_ENST00000293825.6_Intron	NM_172089.3	NP_742086.1			TNFSF12-TNFSF13 readthrough	NA		NA								central_nervous_system(1)|large_intestine(2)	3		Prostate(122;0.157)				ttagtagagacggggtttcac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY081051	CCDS11108.1	17p13.1	2011-05-31			ENSG00000248871	ENSG00000248871	407977			33537	other	readthrough		NA			NA	12411489	Standard		NM_172089	NA	Approved	TWE-PRIL	uc002ghi.1		OTTHUMG00000161573	ENST00000293826.4:c.374-2273C>T	chr17.hg19:g.7457822C>T		NA		hg19	CCDS11108.1	0.02	-0.096473	AGAxGGG	UNCOVERED																																																																																			NOVEL	TNFSF12-TNFSF13-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000365376.1	4	3.308112	KEEP	5	0	0	11	309	CC	0	0	0		+	3	48	80	0	0	6.632111	8	60	255	29	ENST00000293826.4	0.272727	0.120436
SHBG	6462	__UNKNOWN__	__UNKNOWN__	17	7520022	7520022	__UNKNOWN__	Intron	SNP	A	A	G	rs536516346		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:7520022A>G	ENST00000575314.1	+	1	48				SHBG_ENST00000576728.1_Intron|SHBG_ENST00000576478.1_Intron|SHBG_ENST00000572182.1_Intron|SHBG_ENST00000570547.1_Intron|SHBG_ENST00000574539.1_Intron|SHBG_ENST00000572262.1_Intron			P04278	SHBG_HUMAN	sex hormone-binding globulin	NA		NA			primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	ttgggaggccaagatgggtgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214	6462			10839	protein-coding gene	gene with protein product	androgen binding protein	182205			NA	2587256	Standard	NM_001040	NM_001146279	NA	Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000575314.1:c.-62+2593A>G	chr17.hg19:g.7520022A>G		NA	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	hg19		0.02	-0.219222	GCCxAGA	UNCOVERED																																																																																			NOVEL	SHBG-014	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000440064.1	9	2.40523	KEEP	1	0	0	8	210	AA	0	0	0		+	3	50	104	0	0	7.849067	22	60	620	44	ENST00000575314.1	0.12	0.552887
TP53	7157	__UNKNOWN__	__UNKNOWN__	17	7577539	7577539	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs397516437|rs121912651		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	248	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.	NA	NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:1394225, ECO:0000269|PubMed:7682763}.|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:2263646, ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:7887414}.|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1978757, ECO:0000269|PubMed:8829627}.		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R248W(544)|p.R155W(28)|p.R248G(12)|p.0?(8)|p.?(5)|p.N247_R248delNR(2)|p.R248fs*16(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248R(2)|p.R248fs*>39(1)|p.R248_P250delRRP(1)|p.unknown(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	111	Mis, N, F		breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types	breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)											NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	617	Substitution - Missense(585)|Whole gene deletion(8)|Deletion - In frame(7)|Unknown(6)|Insertion - Frameshift(3)|Deletion - Frameshift(3)|Complex - compound substitution(3)|Substitution - coding silent(2)	large_intestine(156)|breast(72)|ovary(42)|endometrium(38)|oesophagus(38)|skin(37)|haematopoietic_and_lymphoid_tissue(37)|central_nervous_system(35)|stomach(27)|lung(26)|upper_aerodigestive_tract(25)|urinary_tract(19)|biliary_tract(17)|pancreas(12)|prostate(10)|soft_tissue(6)|bone(6)|thyroid(4)|liver(4)|penis(2)|peritoneum(1)|vulva(1)|kidney(1)|cervix(1)	GRCh37	CM010465|CM900211	TP53	M	rs121912651						151	112	125			NA	NA	17		NA											NA				7577539		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510	7157			11998	protein-coding gene	gene with protein product	Li-Fraumeni syndrome	191170			NA	6396087, 3456488, 2047879	Standard	NM_000546	NM_001126115	NA	Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.742C>T	chr17.hg19:g.7577539G>A	ENSP00000269305:p.Arg248Trp	NA	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	hg19	CCDS11118.1	0.02	1.636968	TCCxGTT	COVERED	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710019	0.68730	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	4.62	2.56	0.30785	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.92507	3.315	0.58432	A	0.999997	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0	D	0.97208	0.9869	9	0.87932	D	0	-9.5643	7.568	0.27890	0.0893:0.0:0.7471:0.1636	.	248;248;155;248;248;248	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	W	248;248;248;248;248;248;237;155;116;155	ENSP00000410739:R248W;ENSP00000352610:R248W;ENSP00000269305:R248W;ENSP00000398846:R248W;ENSP00000391127:R248W;ENSP00000391478:R248W;ENSP00000425104:R116W;ENSP00000423862:R155W	ENSP00000269305:R248W	R	-	1	2	TP53	7518264	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.447000	0.35101	0.644000	0.30656	0.462000	0.41574	CGG	NOVEL	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367397.1	0	3.610532	KEEP	0	0	0	12	365	GG	0.993634	0.985778	0		-	24	60	723	0	0	65.774853	38	60	1280	117	ENST00000269305.4	0.387097	0.992094
CHD3	1107	__UNKNOWN__	__UNKNOWN__	17	7799189	7799189	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:7799189A>G	ENST00000380358.4	+	10	1885				CHD3_ENST00000330494.7_Intron|CHD3_ENST00000358181.4_Intron	NM_001005271.2	NP_001005271.2	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	NA		NA			centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				ttgggaggccaaggcaggagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004	1107		Zinc fingers, PHD-type	1918	protein-coding gene	gene with protein product		602120			NA	9326634, 7560064	Standard	NM_001005273	NM_001005271	NA	Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000380358.4:c.1884+329A>G	chr17.hg19:g.7799189A>G		NA	D3DTQ9|E9PG89|Q9Y4I0	hg19	CCDS32553.2	0.02	-0.289433	GCCxAGG	COVERED																																																																																			NOVEL	CHD3-003	NOVEL	not_organism_supported|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318052.1	8	5.413373	KEEP	0	0	0	18	494	AA	0.999859	0.76078	0		+	3	60	94	0	0	6.64674	26	60	782	69	ENST00000380358.4	0.103448	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	8183649	8183649	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:8183649G>A			NA	NA				RP11-849F2.9 (1895 upstream) : SLC25A35 (7431 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.8183649G>A		NA		hg19		0.02	-0.201749	CACxCCT	COVERED																																																																																			NOVEL					0			12	3.008718	KEEP	6	0	0	10	301	GG	0.99254	0.518266	0			3	60	88	0	0	6.427754	19	60	625	61		0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	8212183	8212183	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:8212183A>G			NA	NA				SLC25A35 (13522 upstream) : ARHGEF15 (1417 downstream)						NA		NA									NA						ctggagtgcaatggcacgatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.8212183A>G		NA		hg19		0.02	-0.122761	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			5	2.404876	KEEP	4	0	0	8	208	AA	0	0	0			3	60	104	0	0	9.032633	8	60	233	31		0.272727	0.196312
ODF4	146852	__UNKNOWN__	__UNKNOWN__	17	8247074	8247074	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:8247074T>C	ENST00000584943.1	+	2	291				ODF4_ENST00000328248.2_Intron			Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						cctcgtgatctgcccacctcg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650	146852			19056	protein-coding gene	gene with protein product	cancer/testis antigen 136	610097			NA		Standard		NM_153007	NA	Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000584943.1:c.110-1587T>C	chr17.hg19:g.8247074T>C		NA	Q8J021	hg19		0.02	-0.184158	ATCxGCC	COVERED																																																																																			NOVEL	ODF4-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000442316.1	14	4.812151	KEEP	10	0	0	16	445	TT	0.993634	0.420782	0		+	3	23	97	0	0	7.610606	15	60	441	64	ENST00000584943.1	0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	8338280	8338280	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:8338280A>C			NA	NA				RNF222 (37136 upstream) : NDEL1 (898 downstream)						NA		NA									NA						cccagctactagggaggctga	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.8338280A>C		NA		hg19		0.02	-0.096436	ACTxGGG	UNCOVERED																																																																																			NOVEL					0			4	2.406039	KEEP	2	0	0	8	219	AT	0	0	0			3	27	90	0	0	7.633025	8	60	225	29		0.272727	0.120436
NTN1	9423	__UNKNOWN__	__UNKNOWN__	17	9064127	9064127	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:9064127C>A	ENST00000173229.2	+	3	1125				NTN1_ENST00000546090.1_Intron|NTN1_ENST00000538852.1_Intron	NM_004822.2	NP_004813.2	O95631	NET1_HUMAN	netrin 1	NA		NA			anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|establishment of nucleus localization (GO:0040023)|inner ear morphogenesis (GO:0042472)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of axon extension (GO:0030517)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of cell proliferation (GO:0008284)|regulation of cell migration (GO:0030334)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)			NTN1/ACLY(2)	central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(5)	13						acaaaaaattcgctgggcatg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U75586	CCDS11148.1	17p13-p12	2013-03-01			ENSG00000065320	ENSG00000065320	9423		Netrins	8029	protein-coding gene	gene with protein product	Netrin-1	601614			NA	9950216	Standard		NM_004822	NA	Approved	NTN1L	uc002glw.4	O95631	OTTHUMG00000130257	ENST00000173229.2:c.1019-2003C>A	chr17.hg19:g.9064127C>A		NA	E9KL51	hg19	CCDS11148.1	0.02	-0.122799	ATTxGCT	COVERED																																																																																			NOVEL	NTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252583.1	8	3.00842	KEEP	0	0	0	10	296	CC	0.992708	0.227502	0		+	3	60	85	0	0	6.773012	11	60	354	36	ENST00000173229.2	0.214286	0.229173
STX8	9482	__UNKNOWN__	__UNKNOWN__	17	9251481	9251481	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:9251481A>G	ENST00000306357.4	-	7	1071				STX8_ENST00000574431.1_Intron	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8	NA		NA			endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						ggtggctcacacctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310	9482			11443	protein-coding gene	gene with protein product		604203			NA	9852078, 10198254	Standard	NM_004853	NM_004853	NA	Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.643+30387T>C	chr17.hg19:g.9251481A>G		NA	O60712|Q53XT8	hg19	CCDS32565.1	0.02	-0.105239	CACxCCT	UNCOVERED																																																																																			NOVEL	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439206.3	6	3.007863	KEEP	1	0	0	10	279	AA	0.99254	0.138789	0		-	3	60	98	0	0	8.743947	6	60	176	34	ENST00000306357.4	0.333333	0.139832
STX8	9482	__UNKNOWN__	__UNKNOWN__	17	9405065	9405065	__UNKNOWN__	Intron	SNP	C	C	T	rs113790503	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:9405065C>T	ENST00000306357.4	-	5	876				STX8_ENST00000574431.1_Intron	NM_004853.2	NP_004844.1	Q9UNK0	STX8_HUMAN	syntaxin 8	NA		NA			endosome to lysosome transport (GO:0008333)|intracellular protein transport (GO:0006886)|transport (GO:0006810)|vesicle fusion (GO:0006906)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(1)	12						ccgaggcaggcggatcacgag	0.537		NA											C|||	566	0.113019	0.0197	0.2738	5008	,	,	NA	19409	0.006	NA	0.2535	False	NA	,,,	NA	NA	NA	2504	0.091	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF115323	CCDS32565.1	17p13.1	2012-05-25			ENSG00000170310	ENSG00000170310	9482			11443	protein-coding gene	gene with protein product		604203			NA	9852078, 10198254	Standard	NM_004853	NM_004853	NA	Approved	CARB	uc002glx.3	Q9UNK0	OTTHUMG00000177844	ENST00000306357.4:c.448+3289G>A	chr17.hg19:g.9405065C>T		NA	O60712|Q53XT8	hg19	CCDS32565.1	0.02	-0.122793	AGGxGGA	COVERED																																																																																			NOVEL	STX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439206.3	5	2.707153	KEEP	3	0	0	9	259	CC	0.99257	0.194853	0		-	3	60	82	0	0	6.473139	11	60	352	34	ENST00000306357.4	0.214286	0.196312
GLP2R	9340	__UNKNOWN__	__UNKNOWN__	17	9736302	9736302	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:9736302A>G	ENST00000262441.5	+	2	702				GLP2R_ENST00000574745.1_Intron	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	NA		NA			adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|positive regulation of cell proliferation (GO:0008284)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|glucagon receptor activity (GO:0004967)			endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	GATCCGggccaggcgcggtgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF105367	CCDS11150.1	17p13.3	2012-08-10			ENSG00000065325	ENSG00000065325	9340		GPCR / Class B : Glucagon receptors	4325	protein-coding gene	gene with protein product		603659			NA	9990065	Standard		NM_004246	NA	Approved		uc002gmd.1	O95838	OTTHUMG00000130269	ENST00000262441.5:c.190-822A>G	chr17.hg19:g.9736302A>G		NA	Q4VAT3	hg19	CCDS11150.1	0.02	-0.078941	GCCxGGC	UNCOVERED																																																																																			NOVEL	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252601.4	9	3.00797	KEEP	2	0	0	10	282	AA	0.99254	0.076759	0		+	3	60	100	1	0	9.133072	5	60	148	27	ENST00000262441.5	0.375	0.077336
GAS7	8522	__UNKNOWN__	__UNKNOWN__	17	10093857	10093857	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:10093857T>A	ENST00000432992.2	-	1	344				GAS7_ENST00000540214.1_Intron	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	NA		NA			actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						agatcgtgcctttacactcca	0.512		NA	T	MLL	AML*																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		17	17p	8522	growth arrest-specific 7		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18					8522			4169	protein-coding gene	gene with protein product		603127			NA	9736752	Standard	NM_003644, NM_201432, NM_201433	NM_001130831	NA	Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.183+7667A>T	chr17.hg19:g.10093857T>A		NA	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	hg19	CCDS11152.1	0.02	-0.096475	GCCxTTA	UNCOVERED																																																																																			NOVEL	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439883.1	7	2.406076	KEEP	0	0	0	8	219	TT	0.99257	0.119541	0		-	3	44	83	0	0	7.078307	7	60	213	26	ENST00000432992.2	0.3	0.120436
MYH3	4621	__UNKNOWN__	__UNKNOWN__	17	10551098	10551098	__UNKNOWN__	Intron	SNP	G	G	A	rs3760433	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:10551098G>A	ENST00000583535.1	-	9	823				MYH3_ENST00000226209.7_Intron	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	NA		NA			actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						ttgacctcgtgatccgcccgc	0.522		NA											G|||	2325	0.464257	0.2383	0.5346	5008	,	,	NA	12584	0.375	NA	0.7584	False	NA	,,,	NA	NA	NA	2504	0.5092	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063	4621		Myosins / Myosin superfamily : Class II	7573	protein-coding gene	gene with protein product	myosin, skeletal, heavy chain, embryonic 1, muscle embryonic myosin heavy chain 3	160720	myosin, heavy polypeptide 3, skeletal muscle, embryonic		NA	2726495	Standard	NM_002470	NM_002470	NA	Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.736-355C>T	chr17.hg19:g.10551098G>A		NA	Q15492	hg19	CCDS11157.1	0.02	-0.131549	CGTxATC	UNCOVERED																																																																																			NOVEL	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252734.2	13	2.337601	KEEP	19	1	23	16	472	GG	0	0	0		-	9	60	246	0	0	24.504296	6	34	206	63	ENST00000583535.1	0.6	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	10841131	10841131	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:10841131A>G			NA	NA				RP11-963H4.3 (56919 upstream) : AC005284.1 (115973 downstream)						NA		NA									NA						caaagtgctgagattacagga	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.10841131A>G		NA		hg19		0.02	-0.114031	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			9	2.707031	KEEP	0	0	0	9	250	AA	0.99254	0.161255	0			4	60	132	0	0	11.791488	8	60	245	31		0.333333	0.162467
HS3ST3A1	9955	__UNKNOWN__	__UNKNOWN__	17	13489185	13489185	__UNKNOWN__	Intron	SNP	C	C	G	rs59129335|rs386795588		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:13489185C>G	ENST00000284110.1	-	1	1397					NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		ttttttttttctgacagagtc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	9955	2.8.2.23	Sulfotransferases, membrane-bound	5196	protein-coding gene	gene with protein product		604057			NA	9988767	Standard	NM_006042	NM_006042	NA	Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.599+14662G>C	chr17.hg19:g.13489185C>G		NA	A8K7N2	hg19	CCDS11165.1	0.02	-0.035092	TTTxTGA	UNCOVERED																																																																																			NOVEL	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000129952.1	6	2.703842	KEEP	3	0	0	9	272	CC	0.99254	0.019833	0		-	2	40	70	0	1	7.124783	1	60	36	18	ENST00000284110.1	0.666667	0.019982
HS3ST3A1	9955	__UNKNOWN__	__UNKNOWN__	17	13489186	13489186	__UNKNOWN__	Intron	SNP	T	T	A	rs58804128|rs386795588		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:13489186T>A	ENST00000284110.1	-	1	1397					NM_006042.1	NP_006033.1	Q9Y663	HS3SA_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)|sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_lung(20;0.114)		UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		tttttttttctgacagagtct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF105376	CCDS11165.1	17p12	2007-04-02			ENSG00000153976	ENSG00000153976	9955	2.8.2.23	Sulfotransferases, membrane-bound	5196	protein-coding gene	gene with protein product		604057			NA	9988767	Standard	NM_006042	NM_006042	NA	Approved	3OST3A1, 30ST3A1	uc002gob.1	Q9Y663	OTTHUMG00000058768	ENST00000284110.1:c.599+14661A>T	chr17.hg19:g.13489186T>A		NA	A8K7N2	hg19	CCDS11165.1	0.02	-0.035084	TTCxGAC	UNCOVERED																																																																																			NOVEL	HS3ST3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000129952.1	6	2.645264	KEEP	3	0	0	9	232	TT	0.99254	0.019833	0		-	2	40	62	0	1	6.324728	1	60	29	19	ENST00000284110.1	0.666667	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	14274507	14274507	__UNKNOWN__	IGR	SNP	T	T	C	rs139744427	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:14274507T>C			NA	NA				HS3ST3B1 (21786 upstream) : AC022816.2 (2948 downstream)						NA		NA									NA						ctgcctgccttagcctcccaa	0.448		NA											T|||	173	0.0345447	0.1248	0.0086	5008	,	,	NA	13464	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.14274507T>C		NA		hg19		0.02	-0.035079	CCTxAGC	UNCOVERED																																																																																			NOVEL					0			2	2.706074	KEEP	5	0	0	9	237	TT	0	0	0			2	60	67	0	0	6.450555	2	60	55	21		0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	14656386	14656386	__UNKNOWN__	IGR	SNP	C	C	T	rs551352695		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:14656386C>T			NA	NA				AC013248.2 (23383 upstream) : AC005863.1 (14513 downstream)						NA		NA									NA						tttgggaggccgaggcaggtg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.14656386C>T		NA		hg19		0.02	-0.139592	GGCxGAG	COVERED																																																																																			NOVEL					0			5	2.70764	KEEP	3	0	0	9	270	CC	0.99254	0.259018	0			3	60	85	0	0	6.782993	11	60	319	41		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	15202671	15202671	__UNKNOWN__	IGR	SNP	T	T	C	rs230957	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:15202671T>C			NA	NA				AC005703.2 (19877 upstream) : TEKT3 (4456 downstream)						NA		NA									NA						gaggccgaggtgggtggatca	0.552		NA											-|||	3947	0.788139	0.854	0.7507	5008	,	,	NA	13840	0.7252	NA	0.7684	False	NA	,,,	NA	NA	NA	2504	0.8108	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.15202671T>C		NA		hg19		0.02	-0.070167	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			10	3.306457	KEEP	19	0	0	11	282	TT	0	0	0			4	60	129	0	0	12.400085	4	40	118	45		0.5	0.054137
ZNF286A	57335	__UNKNOWN__	__UNKNOWN__	17	15603799	15603799	__UNKNOWN__	Intron	SNP	A	A	G	rs144866168		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:15603799A>G	ENST00000464847.2	+	1	590				ZNF286A_ENST00000593105.1_Intron|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000395893.2_Intron|ZNF286A_ENST00000395894.2_Intron|ZNF286A_ENST00000413242.2_Intron|ZNF286A_ENST00000580259.1_Intron|ZNF286A_ENST00000472486.1_Intron|ZNF286A_ENST00000585194.1_Intron|ZNF286A_ENST00000581529.1_Intron|ZNF286A_ENST00000421016.1_Intron|ZNF286A_ENST00000583566.1_Intron			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		TGTCTTGGGGATGGATGGGCT	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607	57335		Zinc fingers, C2H2-type, -	13501	protein-coding gene	gene with protein product		NA	zinc finger protein 286	ZNF286	NA	11347906	Standard	NM_020652	NM_020652	NA	Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.37+119A>G	chr17.hg19:g.15603799A>G		NA	B4DKF9|Q96JF3	hg19	CCDS11172.1	0.02	-0.105251	GGGxTGG	UNCOVERED																																																																																			NOVEL	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130696.4	2	3.005342	KEEP	13	0	0	10	255	AA	0	0	0		+	5	27	165	0	0	15.346395	7	27	200	32	ENST00000464847.2	0.416667	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	15844944	15844944	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:15844944G>A			NA	NA				AC015922.5 (82812 upstream) : ADORA2B (3286 downstream)						NA		NA									NA						tgggaggctggggtgggagga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.15844944G>A		NA		hg19		0.02	-0.096475	CTGxGGT	UNCOVERED																																																																																			NOVEL					0			6	2.406776	KEEP	0	0	0	8	238	GG	0.99257	0.138793	0			3	60	81	0	0	6.731791	8	60	278	27		0.272727	0.139832
NCOR1	9611	__UNKNOWN__	__UNKNOWN__	17	16096638	16096638	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16096638A>G	ENST00000268712.3	-	2	366				NCOR1_ENST00000395848.1_Intron|NCOR1_ENST00000395851.1_Intron	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	NA		NA			CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		tctgcctcccaggttcaagcg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027	9611			7672	protein-coding gene	gene with protein product	thyroid hormone- and retinoic acid receptor-associated corepressor 1, protein phosphatase 1, regulatory subunit 109	600849	nuclear receptor co-repressor 1		NA	7566114, 9724795	Standard	NM_006311	NM_006311	NA	Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.108+1137T>C	chr17.hg19:g.16096638A>G		NA	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	hg19	CCDS11175.1	0.02	-0.078936	CCCxGGT	UNCOVERED																																																																																			NOVEL	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131751.5	1	2.405436	KEEP	1	0	0	8	213	AA	0.99257	0.076761	0		-	3	60	89	0	0	8.032678	5	60	149	24	ENST00000268712.3	0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	16266480	16266480	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16266480T>C			NA	NA				CENPV (9667 upstream) : UBB (17632 downstream)						NA		NA									NA						ccacccaccttggcctcccaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.16266480T>C		NA		hg19		0.02	-0.166615	CCTxGGC	COVERED																																																																																			NOVEL					0			8	3.307867	KEEP	0	0	0	11	298	TT	0.993634	0.351693	0			3	60	102	0	0	8.110329	15	60	420	43		0.166667	0.353947
TRPV2	51393	__UNKNOWN__	__UNKNOWN__	17	16337553	16337553	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16337553C>A	ENST00000338560.7	+	13	2513				TRPV2_ENST00000577397.1_Intron	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	NA		NA			calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		gaggccgaggcgggcaaatca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688	51393		Voltage-gated ion channels / Transient receptor potential cation channels, Ankyrin repeat domain containing	18082	protein-coding gene	gene with protein product		606676			NA	10201375, 16382100	Standard	NM_016113	NM_016113	NA	Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.2114+541C>A	chr17.hg19:g.16337553C>A		NA	A6NML2|A8K0Z0|Q9Y670	hg19	CCDS32576.1	0.02	-0.149119	AGGxGGG	COVERED																																																																																			NOVEL	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130464.2	6	3.911069	KEEP	2	0	0	13	384	CC	0.994391	0.320996	0		+	3	35	94	0	0	7.391747	14	60	471	55	ENST00000338560.7	0.176471	0.322807
FAM211A	0	__UNKNOWN__	__UNKNOWN__	17	16380303	16380303	__UNKNOWN__	Intron	SNP	T	T	C	rs11870244	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16380303T>C	ENST00000409083.3	-	2	409				FAM211A_ENST00000470794.1_Intron|C17orf76-AS1_ENST00000580770.1_RNA	NM_207387.3	NP_997270.2				NA		NA								lung(1)	1						ccgcccgccttggcctcccaa	0.527		NA											T|||	2929	0.584864	0.6702	0.4885	5008	,	,	NA	16789	0.6825	NA	0.3648	False	NA	,,,	NA	NA	NA	2504	0.6636	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409083.3:c.247-14603A>G	chr17.hg19:g.16380303T>C		NA		hg19	CCDS11178.2	0.02	-0.105257	CCTxGGC	UNCOVERED																																																																																			NOVEL	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130461.2	10	2.707096	KEEP	15	0	0	9	255	TT	0	0	0		-	3	60	102	0	0	9.143788	6	60	177	48	ENST00000409083.3	0.333333	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	16402561	16402561	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16402561C>G			NA	NA				FAM211A (7094 upstream) : ZNF287 (52139 downstream)						NA		NA									NA						ttgggaggcccaggcaggctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.16402561C>G		NA		hg19		0.02	-0.114035	GCCxAGG	COVERED																																																																																			NOVEL					0			4	2.708203	KEEP	0	0	0	9	282	CC	0.99254	0.227464	0			3	60	90	0	0	7.500852	9	60	322	37		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	16483958	16483958	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16483958C>T			NA	NA				ZNF287 (11438 upstream) : ZNF624 (40092 downstream)						NA		NA									NA						gttggccgggcgcggtggctc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.16483958C>T		NA		hg19		0.02	-0.166669	GGGxGCG	COVERED																																																																																			NOVEL					0			9	4.211877	KEEP	6	0	0	14	420	CC	0.994391	0.351961	0			3	60	84	0	0	6.479195	13	60	449	57		0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	16589743	16589743	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16589743C>G			NA	NA				RP11-92B11.4 (31642 upstream) : CCDC144A (3802 downstream)						NA		NA									NA						ATTTTTATAACTCAAGGAGTT	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.16589743C>G		NA		hg19		0.02	-0.315816	TAAxTCA	COVERED																																																																																			NOVEL					0			7	5.114515	KEEP	0	0	0	17	502	CC	0.999366	0.817946	0			3	44	105	0	0	7.448084	33	60	1137	72		0.083333	0.818465
MPRIP	23164	__UNKNOWN__	__UNKNOWN__	17	16950249	16950249	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16950249A>T	ENST00000395807.2	+	1	212				MPRIP_ENST00000395804.3_Intron|MPRIP_ENST00000341712.4_Intron|MPRIP_ENST00000395806.1_Intron|MPRIP_ENST00000444976.1_Intron|MPRIP_ENST00000395811.5_Intron			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	NA		NA				actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						cccagcacttagggaggctga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030	23164		Pleckstrin homology (PH) domain containing	30321	protein-coding gene	gene with protein product	Rho interacting protein 3	612935			NA	10048485	Standard	NM_015134	NM_201274	NA	Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000395807.2:c.212+3964A>T	chr17.hg19:g.16950249A>T		NA	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	hg19		0.02	-0.087681	CTTxGGG	UNCOVERED																																																																																			NOVEL	MPRIP-006	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000131591.3	6	2.404941	KEEP	0	0	0	8	208	AA	0.99257	0.09898	0		+	4	60	101	0	0	9.08355	6	60	179	26	ENST00000395807.2	0.4	0.099721
MPRIP	23164	__UNKNOWN__	__UNKNOWN__	17	16953251	16953251	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:16953251T>C	ENST00000395807.2	+	1	212				MPRIP_ENST00000395804.3_Intron|MPRIP_ENST00000341712.4_Intron|MPRIP_ENST00000395806.1_Intron|MPRIP_ENST00000444976.1_Intron|MPRIP_ENST00000395811.5_Intron			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	NA		NA				actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						gcctgtaatttcagcactttg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030	23164		Pleckstrin homology (PH) domain containing	30321	protein-coding gene	gene with protein product	Rho interacting protein 3	612935			NA	10048485	Standard	NM_015134	NM_201274	NA	Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000395807.2:c.212+6966T>C	chr17.hg19:g.16953251T>C		NA	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	hg19		0.02	-0.19293	ATTxCAG	COVERED																																																																																			NOVEL	MPRIP-006	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000131591.3	4	2.706866	KEEP	1	0	0	9	249	TT	0.99254	0.454342	0		+	3	60	106	0	0	8.360846	17	60	502	46	ENST00000395807.2	0.15	0.457757
MPRIP	23164	__UNKNOWN__	__UNKNOWN__	17	17088483	17088483	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:17088483T>C	ENST00000395811.5	+	0	3481				RP11-45M22.3_ENST00000584203.1_RNA|MPRIP_ENST00000341712.4_3'UTR	NM_015134.3|NM_201274.3	NP_055949.2|NP_958431.2	Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	NA		NA				actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						GTGTTAGTCCTTTCCTGGCTG	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030	23164		Pleckstrin homology (PH) domain containing	30321	protein-coding gene	gene with protein product	Rho interacting protein 3	612935			NA	10048485	Standard	NM_015134	NM_201274	NA	Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000395811.5:c.*275T>C	chr17.hg19:g.17088483T>C		NA	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	hg19	CCDS42268.1	0.02	1.792214	TCCxTTC	COVERED																																																																																			NOVEL	MPRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131586.2	1	4.205001	KEEP	1	0	0	14	364	TT	0.995343	0.99105	0		+	4	27	130	0	0	8.333536	63	60	1887	123	ENST00000395811.5	0.059701	0.995687
COPS3	8533	__UNKNOWN__	__UNKNOWN__	17	17179363	17179363	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:17179363G>A	ENST00000439936.2	-	2	242	c.111C>T	c.(109-111)ggC>ggT	p.G37G	COPS3_ENST00000539941.2_Silent_p.G37G|COPS3_ENST00000268717.5_Silent_p.G57G			Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	57		NA			cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						CAGCAAGGACGCCCAAGGAGT	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													111	101	105			NA	NA	17		NA											NA				17179363		2203	4300	6503	SO:0001819	synonymous_variant			AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030	8533			2239	protein-coding gene	gene with protein product		604665	COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3, COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)		NA	9535219, 10191102	Standard		NM_003653	NA	Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000439936.2:c.111C>T	chr17.hg19:g.17179363G>A		NA	B2R683|B4DY81|O43191|Q7LDR6	hg19		0.02	-0.377206	GACxCCC	COVERED																																																																																			NOVEL	COPS3-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000131604.3	3	3.911738	KEEP	0	0	0	13	402	GG	0.994391	0.90397	0		-	3	60	97	0	0	6.50643	37	60	1224	90	ENST00000439936.2	0.075	0.909069
RP11-524F11.2	0	__UNKNOWN__	__UNKNOWN__	17	17499877	17499877	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:17499877A>G	ENST00000583662.1	+	0	275										NA		NA									NA						ttacaggcataagccaccacc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000583662.1:	chr17.hg19:g.17499877A>G		NA		hg19		0.02	-0.043856	CATxAGC	UNCOVERED																																																																																			NOVEL	RP11-524F11.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000446050.1	7	2.405135	KEEP	1	0	0	8	208	AA	0.99257	0.023895	0		+	2	60	71	0	0	6.850477	2	60	55	21	ENST00000583662.1	0.5	0.024074
LRRC48	83450	__UNKNOWN__	__UNKNOWN__	17	17879825	17879825	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:17879825T>C	ENST00000399187.1	+	3	201				LRRC48_ENST00000584166.1_Intron|LRRC48_ENST00000399182.1_Intron|LRRC48_ENST00000313838.8_Intron|LRRC48_ENST00000411504.2_Intron	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	NA		NA				cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					gaaaccccgtttctactaaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962	83450			25384	protein-coding gene	gene with protein product		NA			NA	11997338, 23354437	Standard	NM_031294	NM_001130090	NA	Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.-17-1071T>C	chr17.hg19:g.17879825T>C		NA	A8KAE6|Q86SF9|Q86W73|Q8IWG0	hg19	CCDS45622.1	0.02	-0.026309	CGTxTCT	UNCOVERED																																																																																			NOVEL	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000131945.3	5	2.405258	KEEP	3	0	0	8	215	TT	0	0	0		+	3	60	89	1	0	10.32944	0	0	0	15	ENST00000399187.1	1	0
SMCR8	140775	__UNKNOWN__	__UNKNOWN__	17	18220357	18220357	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	G	rs374947089		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:18220357C>G	ENST00000406438.3	+	1	1734	c.1254C>G	c.(1252-1254)taC>taG	p.Y418*		NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	418		NA				nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TTGGTTCTTACAAGTCCAGTG	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													108	101	103			NA	NA	17		NA											NA				18220357		2203	4300	6503	SO:0001587	stop_gained			AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994	140775			17921	protein-coding gene	gene with protein product		NA			NA	11997338, 23248642	Standard	NM_144775	NM_144775	NA	Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1254C>G	chr17.hg19:g.18220357C>G	ENSP00000385025:p.Tyr418*	NA	A5PKZ5|Q3ZCN0|Q6PJL3	hg19	CCDS11195.2	0.02	1.991481	TTAxAAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	40	8.284841	0.98742	.	.	ENSG00000176994	ENST00000406438	.	.	.	6.03	4.88	0.63580	.	0.368408	0.25964	N	0.027165	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-46.5651	16.1889	0.81972	0.0:0.9267:0.0:0.0733	.	.	.	.	X	418	.	ENSP00000385025:Y418X	Y	+	3	2	SMCR8	18161082	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.862000	0.48388	2.861000	0.98227	0.655000	0.94253	TAC	NOVEL	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132065.2	1	5.114281	KEEP	0	0	0	17	498	CC	0.999366	0.995602	0		+	21	60	704	0	0	62.326641	46	60	1533	119	ENST00000406438.3	0.313433	0.996233
RP1-178F10.3	0	__UNKNOWN__	__UNKNOWN__	17	18229171	18229171	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:18229171G>T	ENST00000577764.1	+	0	1636										NA		NA									NA						gtcaggagttggagaccagcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000577764.1:	chr17.hg19:g.18229171G>T		NA		hg19		0.02	-0.061394	GTTxGAG	UNCOVERED																																																																																			NOVEL	RP1-178F10.3-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000448452.1	9	3.008824	KEEP	6	0	0	10	303	GG	0	0	0		+	3	43	82	0	0	7.554039	4	60	134	27	ENST00000577764.1	0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	18269018	18269018	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:18269018C>T			NA	NA				SHMT1 (2209 upstream) : EVPLL (11957 downstream)						NA		NA									NA						cgcgcccggccgtgcacagct	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.18269018C>T		NA		hg19		0.02	-0.149113	GGCxGTG	COVERED																																																																																			NOVEL					0			3	2.40725	KEEP	0	0	0	8	251	CC	0.99257	0.289832	0			6	60	177	0	0	16.66464	7	60	235	37		0.461538	0.292001
RP1-37N7.3	0	__UNKNOWN__	__UNKNOWN__	17	18314830	18314830	__UNKNOWN__	lincRNA	SNP	T	T	C	rs62074236	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:18314830T>C	ENST00000577684.1	+	0	358										NA		NA									NA						ttcttcctcatcccgcaccct	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000577684.1:	chr17.hg19:g.18314830T>C		NA		hg19		0.02	-0.113292	TCAxCCC	UNCOVERED																																																																																			NOVEL	RP1-37N7.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000447480.1	7	3.906734	KEEP	2	0	0	13	324	TT	0.993634	0.161432	0		+	8	40	235	0	0	23.92114	4	60	112	30	ENST00000577684.1	0.666667	0.162467
TRIM16L	147166	__UNKNOWN__	__UNKNOWN__	17	18601403	18601403	__UNKNOWN__	5'UTR	SNP	G	G	C	rs12937368	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:18601403G>C	ENST00000449552.2	+	0	81				TRIM16L_ENST00000449697.3_3'UTR|TRIM16L_ENST00000395902.3_5'UTR|TRIM16L_ENST00000572555.1_5'UTR			Q309B1	TR16L_HUMAN	tripartite motif containing 16-like	NA		NA				cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	9						GTGTCTGGACGGGGGAGGAGC	0.647		NA											c|||	3230	0.644968	0.6437	0.7767	5008	,	,	NA	13645	0.5427	NA	0.8091	False	NA	,,,	NA	NA	NA	2504	0.4898	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			DQ232882	CCDS32588.1	17p11.2	2011-02-10	2011-01-25		ENSG00000108448	ENSG00000108448	147166			32670	protein-coding gene	gene with protein product		NA	tripartite motif-containing 16-like		NA		Standard	NM_001037330	XM_005256479	NA	Approved	TRIM70	uc002gui.1	Q309B1	OTTHUMG00000059050	ENST00000449552.2:c.-1404G>C	chr17.hg19:g.18601403G>C		NA	A0PK10|B2RUW6|B4DQK2|B4DWQ8	hg19	CCDS32588.1	0.02	-0.324551	GACxGGG	COVERED																																																																																			NOVEL	TRIM16L-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000130670.3	2	2.407127	KEEP	0	0	0	8	249	GG	0.99257	0.829507	0		+	8	60	274	0	0	22.82906	29	60	944	65	ENST00000449552.2	0.216216	0.835716
PRPSAP2	5636	__UNKNOWN__	__UNKNOWN__	17	18785114	18785114	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:18785114A>G	ENST00000268835.2	+	7	695				PRPSAP2_ENST00000542013.1_Intron|PRPSAP2_ENST00000536323.1_Intron|PRPSAP2_ENST00000419071.2_Intron	NM_002767.3	NP_002758.1	O60256	KPRB_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 2	NA		NA			bone development (GO:0060348)|negative regulation of catalytic activity (GO:0043086)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11						tcaaagtgctaggattacagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007851	CCDS11200.1, CCDS58525.1, CCDS58526.1, CCDS58527.1	17p12-p11.2	2008-05-14			ENSG00000141127	ENSG00000141127	5636			9467	protein-coding gene	gene with protein product		603762			NA	9806849	Standard	NM_002767	NM_002767	NA	Approved	PAP41	uc002gup.2	O60256	OTTHUMG00000059406	ENST00000268835.2:c.413-767A>G	chr17.hg19:g.18785114A>G		NA	B4E1M8|B4E329|B7ZKZ1|E7EMY2|Q6IAS2	hg19	CCDS11200.1	0.02	-0.16664	GCTxGGA	COVERED																																																																																			NOVEL	PRPSAP2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132112.3	6	4.2063	KEEP	0	0	0	14	373	AA	0.995343	0.352299	0		+	3	60	98	0	0	7.71021	15	60	445	43	ENST00000268835.2	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	19302857	19302857	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:19302857A>G			NA	NA				MFAP4 (12304 upstream) : RNF112 (11649 downstream)						NA		NA									NA						tgtgcctgtaatcccagctac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.19302857A>G		NA		hg19		0.02	-0.052632	GTAxTCC	UNCOVERED																																																																																			NOVEL					0			6	3.008217	KEEP	3	0	0	10	285	AA	0.99257	0.036492	0			2	60	71	0	0	6.592952	3	60	92	24		0.4	0.036766
CTB-187M2.3	0	__UNKNOWN__	__UNKNOWN__	17	19390956	19390956	__UNKNOWN__	lincRNA	SNP	C	C	T	rs370699981|rs201543378	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:19390956C>T	ENST00000582654.1	-	0	109										NA		NA									NA						ctttttctttctttttttttt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000582654.1:	chr17.hg19:g.19390956C>T		NA		hg19		0.02	-0.096158	TTTxTTT	UNCOVERED																																																																																			NOVEL	CTB-187M2.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000443475.3	11	2.404766	KEEP	1	0	0	8	225	CC	0.99257	0.138793	0		-	3	60	84	2	0	7.350929	6	60	177	27	ENST00000582654.1	0.333333	0.139832
AKAP10	11216	__UNKNOWN__	__UNKNOWN__	17	19871239	19871239	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:19871239T>C	ENST00000395536.3	-	2	136				AKAP10_ENST00000572155.1_Intron|AKAP10_ENST00000225737.6_Intron			O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	NA		NA			blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					TACggccgggtgcggtggctc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599	11216		A-kinase anchor proteins	368	protein-coding gene	gene with protein product	dual-specificity A-kinase anchoring protein 2, protein kinase A anchoring protein 10, mitochondrial A kinase PPKA anchor protein 10	604694			NA	9326583	Standard	NM_007202	NM_007202	NA	Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000395536.3:c.136+487A>G	chr17.hg19:g.19871239T>C		NA	B2R650|Q96AJ7	hg19	CCDS11214.1	0.02	-0.19292	GGGxGCG	COVERED																																																																																			NOVEL	AKAP10-005	NOVEL	non_canonical_TEC|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000441144.3	3	4.811487	KEEP	0	0	0	16	432	TT	0.997832	0.456764	0		-	3	60	95	0	0	7.2614	17	60	483	61	ENST00000395536.3	0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	19889274	19889274	__UNKNOWN__	IGR	SNP	A	A	T	rs111513543	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:19889274A>T			NA	NA				AKAP10 (7618 upstream) : RP11-209D14.2 (22089 downstream)						NA		NA									NA						acgcccAACAAtttttttttt	0.547		NA											T|||	1554	0.310304	0.4047	0.353	5008	,	,	NA	16345	0.1786	NA	0.3469	False	NA	,,,	NA	NA	NA	2504	0.2505	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.19889274A>T		NA		hg19		0.02	-0.043837	ACAxTTT	UNCOVERED																																																																																			NOVEL					0			6	2.705824	KEEP	2	0	0	9	242	AA	0	0	0			4	60	109	1	0	11.718404	1	45	30	21		0.8	0.024074
SPECC1	92521	__UNKNOWN__	__UNKNOWN__	17	20219963	20219963	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:20219963A>G	ENST00000395530.2	+	0	5757				AC004702.2_ENST00000580225.1_lincRNA	NM_001033555.2	NP_001028727.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	NA		NA			cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		gattacaggcatgagccactg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487	92521			30615	protein-coding gene	gene with protein product	sperm antigen HCMOGT 1, cytokinesis and spindle organization B, cytospin B	608793			NA	15602574, 18763323, 15087372	Standard	NM_152904	NM_001033553	NA	Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000395530.2:c.*2585A>G	chr17.hg19:g.20219963A>G		NA	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	hg19	CCDS42281.1	0.02	-0.280602	GGCxTGA	COVERED																																																																																			NOVEL	SPECC1-004	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000132368.3	9	4.041426	KEEP	2	1	30	24	651	AA	0.999909	0.739604	0		+	4	60	125	0	0	9.358431	25	60	710	84	ENST00000395530.2	0.137931	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	20587641	20587641	__UNKNOWN__	IGR	SNP	G	G	C	rs682169		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:20587641G>C			NA	NA				AC087499.10 (51094 upstream) : AC126365.1 (32152 downstream)						NA		NA									NA						ttttGGCTctgcctctgcctc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.20587641G>C		NA		hg19		0.02	-0.429861	TCTxCCT	COVERED																																																																																			NOVEL					0			2	5.394241	KEEP	0	0	0	18	510	GG	0.999859	0.954357	0			3	60	107	0	0	7.231629	46	60	1572	105		0.061224	0.954491
CCDC144NL	339184	__UNKNOWN__	__UNKNOWN__	17	20768692	20768692	__UNKNOWN__	3'UTR	SNP	A	A	G	rs4629022		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:20768692A>G	ENST00000327925.5	-	0	821				CCDC144NL_ENST00000539484.1_Intron	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	NA		NA								large_intestine(3)|lung(3)|skin(1)	7						TCTTAAAGGCAAAAGTTAATA	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													66	61	62			NA	NA	17		NA											NA				20768692		2203	4300	6503	SO:0001624	3_prime_UTR_variant				CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212	339184			33735	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004306	NM_001004306	NA	Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.*36T>C	chr17.hg19:g.20768692A>G		NA		hg19	CCDS32591.1	0.02	1.997044	GGCxAAA	COVERED																																																																																			NOVEL	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255361.2	3	4.210719	KEEP	1	0	0	14	389	AA	0.995343	0.974965	0		-	5	45	177	0	0	12.938959	47	60	1463	107	ENST00000327925.5	0.096154	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	20951889	20951889	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:20951889A>G			NA	NA				USP22 (4816 upstream) : AC087393.1 (26979 downstream)						NA		NA									NA						ctggagtgcaatggtgcgatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.20951889A>G		NA		hg19		0.02	-0.078905	GCAxTGG	UNCOVERED																																																																																			NOVEL					0			8	2.707188	KEEP	5	0	0	9	253	AA	0.99257	0.076761	0			3	54	88	0	0	7.741323	6	60	195	32		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21004591	21004591	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21004591T>C			NA	NA				AC087393.1 (10663 upstream) : DHRS7B (25373 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21004591T>C		NA		hg19		0.02	-0.157485	AGGxGTG	COVERED																																																																																			NOVEL					0			10	3.30638	KEEP	0	0	0	11	283	TT	0.993072	0.32057	0			3	60	101	0	0	8.485057	10	60	258	35		0.230769	0.322807
DHRS7B	25979	__UNKNOWN__	__UNKNOWN__	17	21032120	21032120	__UNKNOWN__	Intron	SNP	T	T	C	rs11204336	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21032120T>C	ENST00000395511.3	+	1	340				DHRS7B_ENST00000579303.1_Intron	NM_015510.4	NP_056325.2	Q6IAN0	DRS7B_HUMAN	dehydrogenase/reductase (SDR family) member 7B	NA		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|pancreas(2)	7						gaggcagaggttgcagtgagc	0.527		NA											T|||	1791	0.357628	0.3427	0.3703	5008	,	,	NA	13267	0.2867	NA	0.3907	False	NA	,,,	NA	NA	NA	2504	0.408	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC004126	CCDS11215.1	17p12	2011-09-20				ENSG00000109016	25979		Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	24547	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase family 32C, member 1	NA			NA	10810093, 11230166, 19027726	Standard	NM_015510	NM_015510	NA	Approved	DKFZp566O084, MGC8916, CGI-93, SDR32C1	uc002gyo.3	Q6IAN0		ENST00000395511.3:c.20+1816T>C	chr17.hg19:g.21032120T>C		NA	B5MEF4|Q6UX59|Q9BTF9|Q9UFM6|Q9Y3A1	hg19	CCDS11215.1	0.02	-0.061377	AGGxTGC	UNCOVERED																																																																																			NOVEL	DHRS7B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444066.3	4	2.404676	KEEP	2	0	0	8	205	TT	0	0	0		+	4	60	135	0	0	13.334104	3	60	77	21	ENST00000395511.3	0.571429	0.054137
MAP2K3	5606	__UNKNOWN__	__UNKNOWN__	17	21207813	21207813	__UNKNOWN__	Missense_Mutation	SNP	T	T	G	rs74575904	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21207813T>G	ENST00000342679.4	+	8	893	c.644T>G	c.(643-645)tTg>tGg	p.L215W	MAP2K3_ENST00000361818.5_Missense_Mutation_p.L186W|MAP2K3_ENST00000316920.6_Missense_Mutation_p.L186W	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	215	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA	L -> V (in colon cancer). {ECO:0000269|PubMed:11414763}.		activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)				NA				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		AGTGGCTACTTGGTGGACTCT	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													276	193	221			NA	NA	17		NA											NA				21207813		2203	4300	6503	SO:0001583	missense			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152	5606		Mitogen-activated protein kinase cascade / Kinase kinases	6843	protein-coding gene	gene with protein product	MAPK/ERK kinase 3, MAP kinase kinase 3, dual specificity mitogen activated protein kinase kinase 3	602315		PRKMK3	NA	9465908	Standard	NM_145109	NM_145109	NA	Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.644T>G	chr17.hg19:g.21207813T>G	ENSP00000345083:p.Leu215Trp	NA	B3KSK7|Q99441|Q9UE71|Q9UE72	hg19	CCDS11217.1	0.02	3.967901	ACTxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	T	25.4	4.629605	0.87660	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.48201	0.82;0.82	4.98	4.98	0.66077	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000058	T	0.76863	0.4047	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84230	0.0466	10	0.87932	D	0	-23.6514	14.7002	0.69150	0.0:0.0:0.0:1.0	.	215	P46734	MP2K3_HUMAN	W	215;186;186;219	ENSP00000345083:L215W;ENSP00000355081:L186W	ENSP00000319139:L219W	L	+	2	0	MAP2K3	21148406	1.000000	0.71417	0.994000	0.49952	0.988000	0.76386	7.898000	0.87363	1.877000	0.54381	0.460000	0.39030	TTG	NOVEL	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259374.2	5	2.338045	KEEP	0	1	29	18	498	TT	0.99986	0.999856	0		+	24	60	809	0	0	66.876824	90	60	2636	187	ENST00000342679.4	0.210526	0.999997
MAP2K3	5606	__UNKNOWN__	__UNKNOWN__	17	21207834	21207834	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs58609466	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21207834C>T	ENST00000342679.4	+	8	914	c.665C>T	c.(664-666)aCg>aTg	p.T222M	MAP2K3_ENST00000361818.5_Missense_Mutation_p.T193M|MAP2K3_ENST00000316920.6_Missense_Mutation_p.T193M	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	222	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)				NA				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GTGGCCAAGACGATGGATGCC	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													238	173	195			NA	NA	17		NA											NA				21207834		2203	4300	6503	SO:0001583	missense			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152	5606		Mitogen-activated protein kinase cascade / Kinase kinases	6843	protein-coding gene	gene with protein product	MAPK/ERK kinase 3, MAP kinase kinase 3, dual specificity mitogen activated protein kinase kinase 3	602315		PRKMK3	NA	9465908	Standard	NM_145109	NM_145109	NA	Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.665C>T	chr17.hg19:g.21207834C>T	ENSP00000345083:p.Thr222Met	NA	B3KSK7|Q99441|Q9UE71|Q9UE72	hg19	CCDS11217.1	0.02	3.034853	AGAxGAT	COVERED	656	0.30036630036630035	185	0.37601626016260165	93	0.2569060773480663	167	0.291958041958042	211	0.2783641160949868	C	26.4	4.735409	0.89482	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.68025	-0.3;-0.3	4.87	4.87	0.63330	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.79693	2.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00920	-1.1514	10	0.72032	D	0.01	-22.3871	18.0327	0.89290	0.0:1.0:0.0:0.0	rs58609466	222	P46734	MP2K3_HUMAN	M	222;193;193;226	ENSP00000345083:T222M;ENSP00000355081:T193M	ENSP00000319139:T226M	T	+	2	0	MAP2K3	21148427	1.000000	0.71417	0.971000	0.41717	0.990000	0.78478	7.677000	0.84024	2.242000	0.73789	0.563000	0.77884	ACG	NOVEL	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259374.2	6	5.114521	KEEP	0	0	0	17	512	CC	0.999366	0.999357	0		+	18	60	539	0	0	41.60317	87	60	2894	188	ENST00000342679.4	0.171429	0.999991
MAP2K3	5606	__UNKNOWN__	__UNKNOWN__	17	21218337	21218337	__UNKNOWN__	3'UTR	SNP	A	A	T	rs56254869	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21218337A>T	ENST00000342679.4	+	0	2088				MAP2K3_ENST00000361818.5_3'UTR	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	NA		NA			activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)				NA				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GGGGCCCAAGATCTCTGCTCA	0.582		NA											G|||	5	0.000998403	0.0	0.0	5008	,	,	NA	13106	0.005	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152	5606		Mitogen-activated protein kinase cascade / Kinase kinases	6843	protein-coding gene	gene with protein product	MAPK/ERK kinase 3, MAP kinase kinase 3, dual specificity mitogen activated protein kinase kinase 3	602315		PRKMK3	NA	9465908	Standard	NM_145109	NM_145109	NA	Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.*795A>T	chr17.hg19:g.21218337A>T		NA	B3KSK7|Q99441|Q9UE71|Q9UE72	hg19	CCDS11217.1	0.02	1.292197	AAGxTCT	COVERED																																																																																			NOVEL	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259374.2	1	3.608562	KEEP	0	0	0	12	322	AA	0.993634	0.993496	0		+	29	60	852	0	0	74.640403	60	60	1773	159	ENST00000342679.4	0.325843	0.999862
MAP2K3	5606	__UNKNOWN__	__UNKNOWN__	17	21218463	21218463	__UNKNOWN__	3'UTR	SNP	G	G	A	rs72838584	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21218463G>A	ENST00000342679.4	+	0	2214				MAP2K3_ENST00000361818.5_3'UTR	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	NA		NA			activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)				NA				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		ttGAAAAAACGACTGCCCATC	0.408		NA											G|||	2	0.000399361	0.0	0.0	5008	,	,	NA	14005	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152	5606		Mitogen-activated protein kinase cascade / Kinase kinases	6843	protein-coding gene	gene with protein product	MAPK/ERK kinase 3, MAP kinase kinase 3, dual specificity mitogen activated protein kinase kinase 3	602315		PRKMK3	NA	9465908	Standard	NM_145109	NM_145109	NA	Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.*921G>A	chr17.hg19:g.21218463G>A		NA	B3KSK7|Q99441|Q9UE71|Q9UE72	hg19	CCDS11217.1	0.02	-0.306957	AACxACT	COVERED																																																																																			NOVEL	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259374.2	2	3.005711	KEEP	0	0	0	10	262	GG	0.992708	0.79441	0		+	12	70	342	0	0	30.151898	23	60	709	58	ENST00000342679.4	0.342857	0.800245
MAP2K3	5606	__UNKNOWN__	__UNKNOWN__	17	21218498	21218498	__UNKNOWN__	3'UTR	SNP	G	G	T	rs62055368		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21218498G>T	ENST00000342679.4	+	0	2249				MAP2K3_ENST00000361818.5_3'UTR	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	NA		NA			activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)				NA				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		TGATGGGTTGGGGCAGTTACC	0.388		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	13483	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152	5606		Mitogen-activated protein kinase cascade / Kinase kinases	6843	protein-coding gene	gene with protein product	MAPK/ERK kinase 3, MAP kinase kinase 3, dual specificity mitogen activated protein kinase kinase 3	602315		PRKMK3	NA	9465908	Standard	NM_145109	NM_145109	NA	Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.*956G>T	chr17.hg19:g.21218498G>T		NA	B3KSK7|Q99441|Q9UE71|Q9UE72	hg19	CCDS11217.1	0.02	-0.201745	TTGxGGC	COVERED																																																																																			NOVEL	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259374.2	3	2.406443	KEEP	0	0	0	8	241	GG	0.99257	0.4869	0		+	8	60	234	0	0	20.95293	14	60	464	41	ENST00000342679.4	0.363636	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21514039	21514039	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21514039C>T			NA	NA				AC138710.1 (32868 upstream) : UBBP4 (215561 downstream)						NA		NA									NA						caaagcgagactccgtctcaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21514039C>T		NA		hg19		0.02	-0.175441	AGAxTCC	COVERED																																																																																			NOVEL					0			3	5.415124	KEEP	2	0	0	18	524	CC	0.999366	0.387161	0			3	33	87	0	0	6.972852	11	60	363	46		0.214286	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21530203	21530203	__UNKNOWN__	IGR	SNP	C	C	T	rs12603527		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21530203C>T			NA	NA				AC138710.1 (49032 upstream) : UBBP4 (199397 downstream)						NA		NA									NA						ctcagcctcccgagtagctgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21530203C>T		NA		hg19		0.02	-0.105265	TCCxGAG	UNCOVERED																																																																																			NOVEL					0			7	2.707527	KEEP	0	0	0	9	264	CC	0.99254	0.138789	0			3	60	91	0	0	7.732232	8	60	270	27		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21534040	21534040	__UNKNOWN__	IGR	SNP	C	C	T	rs67715708	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21534040C>T			NA	NA				AC138710.1 (52869 upstream) : UBBP4 (195560 downstream)						NA		NA									NA						cacacctggccgcctaactaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21534040C>T		NA		hg19		0.02	-0.070172	GGCxGCC	UNCOVERED																																																																																			NOVEL					0			4	3.608639	KEEP	1	0	0	12	340	CC	0.993072	0.053762	0			3	60	87	0	0	8.054558	4	60	136	30		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21535229	21535229	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21535229T>C			NA	NA				AC138710.1 (54058 upstream) : UBBP4 (194371 downstream)						NA		NA									NA						gtagctgggattacaggcgca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21535229T>C		NA		hg19		0.02	-0.122738	GGAxTAC	COVERED																																																																																			NOVEL					0			8	3.00613	KEEP	3	0	0	10	262	TT	0.99254	0.194847	0			3	52	87	0	0	7.082846	10	60	280	34		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21536022	21536022	__UNKNOWN__	IGR	SNP	T	T	G	rs9325913	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21536022T>G			NA	NA				AC138710.1 (54851 upstream) : UBBP4 (193578 downstream)						NA		NA									NA						GTCAAGTTCATGTTACCCTCC	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21536022T>G		NA		hg19		0.02	-0.350823	TCAxGTT	COVERED																																																																																			NOVEL					0			1	3.608043	KEEP	6	0	0	12	322	TT	0.993634	0.87212	0			4	40	131	0	0	9.410245	35	60	1057	80		0.102564	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21536104	21536104	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21536104C>T			NA	NA				AC138710.1 (54933 upstream) : UBBP4 (193496 downstream)						NA		NA									NA						TTTCCCAGCACCTGCCACCAG	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21536104C>T		NA		hg19		0.02	1.581435	GCAxCTG	COVERED																																																																																			NOVEL					0			2	2.741726	KEEP	7	1	28	19	594	CC	0.999366	0.983538	0			7	40	215	0	0	15.739374	48	60	1674	133		0.127273	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21538837	21538837	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21538837T>C			NA	NA				AC138710.1 (57666 upstream) : UBBP4 (190763 downstream)						NA		NA									NA						agtgcagtggtgcgatctcgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21538837T>C		NA		hg19		0.02	-0.114013	TGGxGCG	UNCOVERED																																																																																			NOVEL					0			6	3.909723	KEEP	3	0	0	13	357	TT	0.993072	0.161341	0			3	60	89	0	0	7.53254	8	60	232	40		0.272727	0.162467
UBBP4	23666	__UNKNOWN__	__UNKNOWN__	17	21730653	21730653	__UNKNOWN__	Intron	SNP	G	G	C	rs11656087	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21730653G>C	ENST00000584755.1	+	2	391				UBBP4_ENST00000583708.1_Intron|UBBP4_ENST00000584398.1_Intron					ubiquitin B pseudogene 4	NA		NA								endometrium(9)|kidney(4)|lung(4)|prostate(3)|urinary_tract(4)	24						GAAATACAATGATCCTGAGAT	0.393		NA											.|||	1267	0.252995	0.2738	0.3012	5008	,	,	NA	22594	0.1111	NA	0.3847	False	NA	,,,	NA	NA	NA	2504	0.2014	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X07499		17p11.2	2011-08-10				ENSG00000263563	23666			12467	pseudogene	pseudogene		NA			NA	2834222	Standard		NG_002285	NA	Approved		uc002gyy.3			ENST00000584755.1:c.-6-40G>C	chr17.hg19:g.21730653G>C		NA		hg19		0.02	-0.368439	AATxATC	COVERED																																																																																			NOVEL	UBBP4-001	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000444585.1	0	2.707911	KEEP	0	0	0	9	270	GG	0.99254	0.892605	0		+	11	60	377	0	0	32.460218	31	60	1039	77	ENST00000584755.1	0.261905	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21904919	21904919	__UNKNOWN__	IGR	SNP	G	G	T	rs146752896		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21904919G>T			NA	NA				FAM27L (78420 upstream) : RP11-744K17.9 (1497 downstream)						NA		NA									NA						CACCCGCTTCGCACCCCTCCT	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21904919G>T		NA		hg19		0.02	5.734339	TTCxCAC	COVERED																																																																																			NOVEL					0			12	8.791421	KEEP	22	2	56	49	1489	GG	1	1	0			8	60	251	0	0	13.693114	233	60	7917	490		0.033195	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21904927	21904927	__UNKNOWN__	IGR	SNP	C	C	T	rs138763326		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21904927C>T			NA	NA				FAM27L (78428 upstream) : RP11-744K17.9 (1489 downstream)						NA		NA									NA						TCGCACCCCTCCTCTTATGCC	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21904927C>T		NA		hg19		0.02	5.841913	CCTxCTC	COVERED																																																																																			NOVEL					0			12	11.667712	KEEP	24	1	29	49	1508	CC	1	1	0			9	60	279	0	0	15.550712	231	60	7941	475		0.0375	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21904955	21904955	__UNKNOWN__	IGR	SNP	G	G	A	rs150725531		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21904955G>A			NA	NA				FAM27L (78456 upstream) : RP11-744K17.9 (1461 downstream)						NA		NA									NA						GTGGCACGGCGCTGTATCCTG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21904955G>A		NA		hg19		0.02	5.215195	GGCxCTG	COVERED																																																																																			NOVEL					0			9	6.28079	KEEP	29	2	54	40	1176	GG	0.999998	0.999998	0			15	60	385	0	0	22.594473	185	60	6140	361		0.075	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	21906351	21906351	__UNKNOWN__	IGR	SNP	A	A	G	rs11150720	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:21906351A>G			NA	NA				FAM27L (79852 upstream) : RP11-744K17.9 (65 downstream)						NA		NA									NA						tgtcttaggaaccagtccccg	0.682		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.21906351A>G		NA		hg19		0.02	1.897953	GGAxCCA	COVERED																																																																																			NOVEL					0			0	3.004888	KEEP	0	0	0	10	250	AA	0.992708	0.972383	0			6	60	177	0	0	12.33271	50	60	1474	74		0.107143	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	22253144	22253144	__UNKNOWN__	IGR	SNP	T	T	C	rs4107688		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:22253144T>C			NA	NA				RP11-285M22.1 (60204 upstream) : None (None downstream)						NA		NA									NA						cttgggcctctctgaggattt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.22253144T>C		NA		hg19		0.02	3.581431	CTCxCTG	COVERED																																																																																			NOVEL					0			42	13.426443	KEEP	49	3	80	73	1982	TT	1	0.999999	0			5	46	152	0	0	11.566587	27	46	776	290		0.15625	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	25266435	25266435	__UNKNOWN__	IGR	SNP	G	G	A	rs199756207		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:25266435G>A			NA	NA				None (None upstream) : RP11-260A9.6 (49779 downstream)						NA		NA									NA						agaatggaatgtaatggaatg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.25266435G>A		NA		hg19		0.02	-0.18418	AATxTAA	COVERED																																																																																			NOVEL					0			7	4.210288	KEEP	2	0	0	14	394	GT	0.99649	0.421991	0			3	60	82	0	0	7.82423	3	60	89	47		0.5	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	25267383	25267383	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:25267383G>C			NA	NA				None (None upstream) : RP11-260A9.6 (48831 downstream)						NA		NA									NA						caatggaatggaatggaatgg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.25267383G>C		NA		hg19		0.02	-0.131581	ATGxAAT	COVERED																																																																																			NOVEL					0			33	3.643754	KEEP	18	1	31	23	687	GG	0.999859	0.260928	0			3	31	97	0	1	9.669668	2	40	63	65		0.6	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	25290992	25290992	__UNKNOWN__	IGR	SNP	G	G	A	rs60021950	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:25290992G>A			NA	NA				None (None upstream) : RP11-260A9.6 (25222 downstream)						NA		NA									NA						gttcacacctgttatcctgtc	0.443		NA											g|||	245	0.0489217	0.1082	0.0173	5008	,	,	NA	22020	0.006	NA	0.0606	False	NA	,,,	NA	NA	NA	2504	0.0235	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.25290992G>A		NA		hg19		0.02	-0.184184	CCTxTTA	COVERED																																																																																			NOVEL					0			9	3.610808	KEEP	8	0	0	12	368	GG	0.99254	0.420319	0			5	60	141	0	0	12.168286	11	60	372	47		0.3125	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	25649114	25649114	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:25649114A>G			NA	NA				RP11-173M1.8 (6162 upstream) : RP11-173M1.4 (11167 downstream)						NA		NA									NA						tgttgcccagactggtctcaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.25649114A>G		NA		hg19		0.02	-0.061394	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			6	2.405467	KEEP	1	0	0	8	213	AA	0	0	0			3	60	97	0	0	9.054872	4	60	119	20		0.428571	0.043787
RP11-173M1.4	0	__UNKNOWN__	__UNKNOWN__	17	25661967	25661967	__UNKNOWN__	lincRNA	SNP	T	T	C	rs9896774	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:25661967T>C	ENST00000581118.1	+	0	172										NA		NA									NA						ccaccacacctggccAACAtt	0.398		NA											T|||	1832	0.365815	0.2814	0.3228	5008	,	,	NA	10168	0.6508	NA	0.333	False	NA	,,,	NA	NA	NA	2504	0.2505	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000581118.1:	chr17.hg19:g.25661967T>C		NA		hg19		0.02	-0.035089	ACCxGGC	UNCOVERED																																																																																			NOVEL	RP11-173M1.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000445013.1	2	2.40634	KEEP	0	0	0	8	224	TT	0.99257	0.019833	0		+	2	60	68	0	0	6.550092	2	60	63	15	ENST00000581118.1	0.5	0.019982
KSR1	8844	__UNKNOWN__	__UNKNOWN__	17	25836595	25836595	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:25836595G>A	ENST00000398988.3	+	2	265				KSR1_ENST00000319524.6_Intron|KSR1_ENST00000268763.6_Intron|KSR1_ENST00000509603.2_Intron	NM_014238.1	NP_055053.1	Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	NA		NA			Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		gattacaggcgtgagccacca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(88;1120 1336 6324 10502 16832)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068	8844			6465	protein-coding gene	gene with protein product		601132	kinase suppressor of ras	KSR	NA	8521512	Standard	NM_014238	XM_006722151	NA	Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000398988.3:c.-181+25718G>A	chr17.hg19:g.25836595G>A		NA	F8WEA9|H7BYU0|Q13476	hg19	CCDS58532.1	0.02	-0.131566	GGCxTGA	COVERED																																																																																			NOVEL	KSR1-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255074.2	3	3.008473	KEEP	2	0	0	10	296	GG	0.992708	0.227502	0		+	3	60	91	0	0	7.482047	10	60	314	42	ENST00000398988.3	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	26251910	26251910	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:26251910G>T			NA	NA				LYRM9 (31501 upstream) : RP11-218F4.1 (4663 downstream)						NA		NA									NA						gtagagacggggtttctccat	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.26251910G>T		NA		hg19		0.02	-0.0877	CGGxGTT	UNCOVERED																																																																																			NOVEL					0			8	2.40647	KEEP	3	0	0	8	232	GG	0	0	0			5	58	143	0	0	13.997662	4	60	134	26		0.555556	0.099721
CTD-2008P7.3	0	__UNKNOWN__	__UNKNOWN__	17	26589896	26589896	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:26589896A>G	ENST00000578466.1	+	0	86										NA		NA									NA						ggctggtctcaaactcctgac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000578466.1:	chr17.hg19:g.26589896A>G		NA		hg19		0.02	-0.052632	CTCxAAC	UNCOVERED																																																																																			NOVEL	CTD-2008P7.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000445676.1	5	2.706218	KEEP	0	0	0	9	242	AA	0.99254	0.036491	0		+	2	60	71	0	0	6.395782	4	60	124	21	ENST00000578466.1	0.333333	0.036766
TMEM97	27346	__UNKNOWN__	__UNKNOWN__	17	26654053	26654053	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:26654053A>G	ENST00000226230.6	+	0	910				TMEM97_ENST00000336687.6_3'UTR	NM_014573.2	NP_055388.2	Q5BJF2	TMM97_HUMAN	transmembrane protein 97	NA		NA			cholesterol homeostasis (GO:0042632)|regulation of cell growth (GO:0001558)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)				endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	6	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		gggcagtggcatgatctcggc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC091504	CCDS11226.2	17q11.2	2014-01-28			ENSG00000109084	ENSG00000109084	27346			28106	protein-coding gene	gene with protein product		612912			NA	7694637, 15375745	Standard	NM_014573	NM_014573	NA	Approved	MAC30	uc002hat.3	Q5BJF2	OTTHUMG00000132497	ENST00000226230.6:c.*234A>G	chr17.hg19:g.26654053A>G		NA	B4DS02|Q07823	hg19	CCDS11226.2	0.02	3.690247	GGCxTGA	COVERED																																																																																			NOVEL	TMEM97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255675.2	15	22.434531	KEEP	0	3	80	103	2641	AA	1	0.999999	0		+	6	60	188	0	0	11.540332	105	70	2899	267	ENST00000226230.6	0.054054	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	26754134	26754134	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:26754134A>T			NA	NA				CTD-2350C19.2 (20320 upstream) : SLC13A2 (46176 downstream)						NA		NA									NA						ggtggctcatacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.26754134A>T		NA		hg19		0.02	-0.114005	CATxCCT	UNCOVERED																																																																																			NOVEL					0			1	2.705841	KEEP	0	0	0	9	235	AA	0.99254	0.161255	0			3	60	93	0	0	7.682296	10	60	284	37		0.230769	0.162467
UNC119	9094	__UNKNOWN__	__UNKNOWN__	17	26879583	26879583	__UNKNOWN__	5'UTR	SNP	C	C	T	rs531975581	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:26879583C>T	ENST00000335765.4	-	0	103				UNC119_ENST00000301032.4_5'UTR	NM_005148.3	NP_005139.1	Q13432	U119A_HUMAN	unc-119 homolog (C. elegans)	NA		NA			cytokinesis, completion of separation (GO:0007109)|endocytosis (GO:0006897)|lipoprotein transport (GO:0042953)|negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of clathrin-mediated endocytosis (GO:1900186)|phototransduction (GO:0007602)|positive regulation of protein tyrosine kinase activity (GO:0061098)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	lipid binding (GO:0008289)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	7	Lung NSC(42;0.00431)					CATGGCCTTGCGGGGCCGAGG	0.781		NA											C|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	6829	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U40998	CCDS11233.1, CCDS11234.1	17q11.2	2014-09-17	2001-11-28		ENSG00000109103	ENSG00000109103	9094			12565	protein-coding gene	gene with protein product	POC7 centriolar protein homolog A (Chlamydomonas)	604011	unc119 (C.elegans) homolog		NA	8576185, 9538874	Standard		NM_005148	NA	Approved	HRG4, POC7, POC7A	uc002hbk.2	Q13432	OTTHUMG00000132606	ENST00000335765.4:c.-8G>A	chr17.hg19:g.26879583C>T		NA	A8K8G4|F1T095|O95126	hg19	CCDS11233.1	0.02	-0.306965	TTGxGGG	COVERED																																																																																			NOVEL	UNC119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255842.2	1	3.309407	KEEP	0	0	0	11	333	CC	0.993072	0.794702	0		-	3	60	94	0	0	6.38814	32	60	1014	68	ENST00000335765.4	0.085714	0.800245
RPL23A	6147	__UNKNOWN__	__UNKNOWN__	17	27046769	27046769	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:27046769C>T	ENST00000422514.2	+	0	359					NM_000984.5	NP_000975.2	P62750	RL23A_HUMAN	ribosomal protein L23a	NA		NA			cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			endometrium(1)|lung(3)|ovary(1)	5	Lung NSC(42;0.00431)					ccagcctgggcgacagagcgc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U43701	CCDS11241.1	17q11.2	2011-04-06			ENSG00000198242	ENSG00000198242	6147		L ribosomal proteins	10317	protein-coding gene	gene with protein product		602326			NA	9417910	Standard	NM_000984	NM_000984	NA	Approved	L23A	uc002hci.3	P62750	OTTHUMG00000132684	ENST00000422514.2:c.-255C>T	chr17.hg19:g.27046769C>T		NA	B2R5B2|P29316|P39024|Q92774	hg19	CCDS11241.1	0.02	2.813537	GGGxGAC	COVERED																																																																																			NOVEL	RPL23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255975.1	36	36.567476	KEEP	1	12	299	228	6824	CC	1	0.999999	0		+	9	60	253	1	0	16.050259	102	60	3367	547	ENST00000422514.2	0.081081	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	27666752	27666752	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:27666752T>C			NA	NA				NUFIP2 (45616 upstream) : RP11-296K13.4 (12334 downstream)						NA		NA									NA						gagtggctcatgcctgtaatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.27666752T>C		NA		hg19		0.02	-0.087697	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			5	3.007083	KEEP	0	0	0	10	272	TT	0.992708	0.098994	0			3	60	99	0	0	8.679021	7	60	195	22		0.3	0.099721
SSH2	85464	__UNKNOWN__	__UNKNOWN__	17	27987549	27987549	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:27987549T>C	ENST00000269033.3	-	11	1103				RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Intron	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	NA		NA			actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						tcccaaagtgttgggattaca	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298	85464		Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots	30580	protein-coding gene	gene with protein product		606779	slingshot homolog 2 (Drosophila)		NA	11832213, 11214970	Standard	NM_033389	XM_005258059	NA	Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.952-4924A>G	chr17.hg19:g.27987549T>C		NA	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	hg19	CCDS11253.1	0.02	-0.114029	GTGxTGG	UNCOVERED																																																																																			NOVEL	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256116.1	5	2.405602	KEEP	0	0	0	8	221	TT	0.99257	0.16126	0		-	3	60	101	0	0	8.732524	8	60	245	29	ENST00000269033.3	0.272727	0.162467
EFCAB5	374786	__UNKNOWN__	__UNKNOWN__	17	28306097	28306097	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:28306097C>T	ENST00000394835.3	+	4	959				EFCAB5_ENST00000536908.2_Intron|EFCAB5_ENST00000320856.5_Intron|EFCAB5_ENST00000534836.2_Intron|EFCAB5_ENST00000378738.3_Intron|EFCAB5_ENST00000394832.2_Intron|EFCAB5_ENST00000541045.1_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	NA		NA					calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						Tggctgggcacggtggctcac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927	374786		EF-hand domain containing	24801	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198529	NM_198529	NA	Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.767+9712C>T	chr17.hg19:g.28306097C>T		NA	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	hg19	CCDS11254.2	0.02	-0.157893	GCAxGGT	COVERED																																																																																			NOVEL	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256120.4	6	3.008284	KEEP	1	0	0	10	289	CC	0.99254	0.320398	0		+	3	60	84	0	0	6.392494	14	60	470	42	ENST00000394835.3	0.176471	0.322807
NF1	4763	__UNKNOWN__	__UNKNOWN__	17	29446211	29446211	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:29446211G>A	ENST00000358273.4	+	1	443				NF1_ENST00000431387.4_Intron|NF1_ENST00000356175.3_Intron	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	NA		NA			actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		tgcccgcctcggcctcccaaa	0.512		NA	D, Mis, N, F, S, O		neurofibroma, glioma	neurofibroma, glioma			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)											NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|central_nervous_system(3)|autonomic_ganglia(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712	4763			7765	protein-coding gene	gene with protein product	neurofibromatosis, von Recklinghausen disease, Watson disease	613113			NA	1715669	Standard	NM_000267	NM_000267	NA	Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.60+23824G>A	chr17.hg19:g.29446211G>A		NA	O00662|Q14284|Q14930|Q14931|Q9UMK3	hg19	CCDS42292.1	0.02	-0.201761	CTCxGCC	COVERED																																																																																			NOVEL	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256351.2	8	4.512009	KEEP	1	0	0	15	441	GG	0.99649	0.488823	0		+	3	60	94	0	0	7.092255	18	60	609	56	ENST00000358273.4	0.142857	0.490544
NF1	4763	__UNKNOWN__	__UNKNOWN__	17	29706226	29706226	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:29706226A>G	ENST00000444181.2	+	16	2013							P21359	NF1_HUMAN	neurofibromin 1	NA		NA			actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.?(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		gtgaaaccccatctctactaa	0.542		NA	D, Mis, N, F, S, O		neurofibroma, glioma	neurofibroma, glioma			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)											NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	1	Unknown(1)	autonomic_ganglia(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712	4763			7765	protein-coding gene	gene with protein product	neurofibromatosis, von Recklinghausen disease, Watson disease	613113			NA	1715669	Standard	NM_000267	NM_000267	NA	Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000444181.2:c.1914+185A>G	chr17.hg19:g.29706226A>G		NA	O00662|Q14284|Q14930|Q14931|Q9UMK3	hg19		0.02	-0.175387	CCCxTCT	COVERED																																																																																			NOVEL	NF1-202	KNOWN	basic	protein_coding	NA	protein_coding		5	3.60724	KEEP	0	0	0	12	310	AA	0.993634	0.38494	0		+	3	60	98	0	0	7.633716	16	60	448	39	ENST00000444181.2	0.157895	0.387407
RAB11FIP4	84440	__UNKNOWN__	__UNKNOWN__	17	29748964	29748964	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:29748964A>G	ENST00000325874.8	+	2	388					NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	NA		NA			cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.?(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				ttgggaggctaaggcaggagg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Unknown(1)	autonomic_ganglia(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242	84440		EF-hand domain containing	30267	protein-coding gene	gene with protein product		611999			NA	11347906, 11468690	Standard	NM_032932	NM_032932	NA	Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.160-9867A>G	chr17.hg19:g.29748964A>G		NA	Q52LI1|Q8N829|Q8NDT7|Q969D8	hg19	CCDS11267.1	0.02	-0.131538	GCTxAGG	COVERED																																																																																			NOVEL	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256195.2	5	5.112118	KEEP	1	0	0	17	455	AA	0.997832	0.228676	0		+	3	60	105	0	0	8.672505	12	60	346	48	ENST00000325874.8	0.2	0.229173
RAB11FIP4	84440	__UNKNOWN__	__UNKNOWN__	17	29843732	29843732	__UNKNOWN__	Intron	SNP	C	C	T	rs182963350	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:29843732C>T	ENST00000325874.8	+	4	565				RAB11FIP4_ENST00000394744.2_Intron	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	NA		NA			cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				gtgatctgcccgccttggcct	0.532		NA											C|||	2	0.000399361	0.0	0.0	5008	,	,	NA	17703	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242	84440		EF-hand domain containing	30267	protein-coding gene	gene with protein product		611999			NA	11347906, 11468690	Standard	NM_032932	NM_032932	NA	Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.337-937C>T	chr17.hg19:g.29843732C>T		NA	Q52LI1|Q8N829|Q8NDT7|Q969D8	hg19	CCDS11267.1	0.02	1.436068	GCCxGCC	COVERED																																																																																			NOVEL	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256195.2	8	6.016962	KEEP	2	0	0	20	585	CC	0.999859	0.967289	0		+	4	60	117	0	0	7.877063	38	60	1224	88	ENST00000325874.8	0.095238	0.967425
UTP6	55813	__UNKNOWN__	__UNKNOWN__	17	30188380	30188380	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:30188380A>C	ENST00000261708.4	-	0	3929					NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	NA		NA			rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				tgcctataataccagcacttt	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651	55813			18279	protein-coding gene	gene with protein product	hepatocellular carcinoma associated antigen 66	NA	chromosome 17 open reading frame 40	C17orf40	NA	10843809, 16138909	Standard	NM_018428	NM_018428	NA	Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.*1998T>G	chr17.hg19:g.30188380A>C		NA	Q8IX96|Q96BL2|Q9NQ91	hg19	CCDS11269.1	0.02	1.655124	AATxCCA	COVERED																																																																																			NOVEL	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256265.2	31	5.689991	KEEP	0	6	173	80	2036	AA	1	0.999919	0		-	5	60	170	0	0	11.10692	81	60	2344	234	ENST00000261708.4	0.05814	0.999919
UTP6	55813	__UNKNOWN__	__UNKNOWN__	17	30189628	30189628	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:30189628T>C	ENST00000261708.4	-	0	2681					NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	NA		NA			rRNA processing (GO:0006364)	nucleolus (GO:0005730)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)	21		all_hematologic(16;0.0149)|Ovarian(249;0.021)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|Breast(31;0.231)				tcgctcttcttacccaggatg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF116631	CCDS11269.1	17q11.2	2010-06-24	2006-05-16	2006-05-16	ENSG00000108651	ENSG00000108651	55813			18279	protein-coding gene	gene with protein product	hepatocellular carcinoma associated antigen 66	NA	chromosome 17 open reading frame 40	C17orf40	NA	10843809, 16138909	Standard	NM_018428	NM_018428	NA	Approved	HCA66	uc002hgr.3	Q9NYH9	OTTHUMG00000132815	ENST00000261708.4:c.*750A>G	chr17.hg19:g.30189628T>C		NA	Q8IX96|Q96BL2|Q9NQ91	hg19	CCDS11269.1	0.02	-0.412153	TCTxACC	COVERED																																																																																			NOVEL	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256265.2	8	2.833661	KEEP	0	1	30	20	498	TT	0.999869	0.941618	0		-	3	60	100	0	0	6.740636	39	60	1125	101	ENST00000261708.4	0.071429	0.941741
LRRC37B	114659	__UNKNOWN__	__UNKNOWN__	17	30339768	30339768	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:30339768C>G	ENST00000543378.2	+	1	145							Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	NA		NA				cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				aggtgcggtgcctcacgcctg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158	114659			29070	protein-coding gene	gene with protein product	KIAA0563-related	NA			NA	11468690, 10843809	Standard	NM_052888	NM_052888	NA	Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000543378.2:c.-191+4617C>G	chr17.hg19:g.30339768C>G		NA	Q17RC9|Q5YKG6	hg19		0.02	-0.166684	GTGxCTC	COVERED																																																																																			NOVEL	LRRC37B-006	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446503.1	6	3.309198	KEEP	1	0	0	11	326	CC	0.992708	0.351366	0		+	3	60	104	0	0	8.478449	13	60	447	43	ENST00000543378.2	0.1875	0.353947
RHBDL3	162494	__UNKNOWN__	__UNKNOWN__	17	30633193	30633193	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:30633193A>G	ENST00000536287.1	+	5	710				RHBDL3_ENST00000538145.1_Intron|RHBDL3_ENST00000269051.4_Intron			P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	NA		NA				integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				ctgtaatcccagcactttggg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314	162494		EF-hand domain containing	16502	protein-coding gene	gene with protein product		NA	rhomboid, veinlet-like 4 (Drosophila)	RHBDL4	NA	11900977	Standard	NM_138328	XM_006721733	NA	Approved	VRHO	uc002hhe.1	P58872		ENST00000536287.1:c.588+733A>G	chr17.hg19:g.30633193A>G		NA	A6NMH1|Q495Y4|Q495Y5|Q495Y6	hg19		0.02	-0.184204	CCCxGCA	COVERED																																																																																			NOVEL	RHBDL3-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447122.2	9	3.910514	KEEP	6	0	0	13	368	AA	0.993072	0.420544	0		+	3	50	99	0	0	7.891601	14	60	439	61	ENST00000536287.1	0.176471	0.423478
MYO1D	4642	__UNKNOWN__	__UNKNOWN__	17	30824190	30824190	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:30824190C>T	ENST00000394649.4	-	24	3144				MYO1D_ENST00000318217.5_Intron|RP11-466A19.1_ENST00000581360.1_RNA			O94832	MYO1D_HUMAN	myosin ID	NA		NA			early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			gtggctcatgcttgtaatccc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658	4642		Myosins / Myosin superfamily : Class I	7598	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 108	606539			NA	8884266	Standard		NM_015194	NA	Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000394649.4:c.2601-2257G>A	chr17.hg19:g.30824190C>T		NA	A6H8V3|Q8NHP9	hg19		0.02	-0.035064	ATGxTTG	UNCOVERED																																																																																			NOVEL	MYO1D-004	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447459.2	3	2.70828	KEEP	0	0	0	9	285	CC	0.99254	0.019833	0		-	4	60	112	0	0	13.103807	0	0	0	20	ENST00000394649.4	1	0.019982
MYO1D	4642	__UNKNOWN__	__UNKNOWN__	17	31062309	31062309	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:31062309T>C	ENST00000394649.4	-	16	2026				MYO1D_ENST00000584232.1_Intron|MYO1D_ENST00000579584.1_Intron|MYO1D_ENST00000318217.5_Intron			O94832	MYO1D_HUMAN	myosin ID	NA		NA			early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			tgggttcaagtgattctcctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658	4642		Myosins / Myosin superfamily : Class I	7598	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 108	606539			NA	8884266	Standard		NM_015194	NA	Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000394649.4:c.1482+2961A>G	chr17.hg19:g.31062309T>C		NA	A6H8V3|Q8NHP9	hg19		0.02	-0.035082	AAGxGAT	UNCOVERED																																																																																			NOVEL	MYO1D-004	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447459.2	1	2.405954	KEEP	0	0	0	8	219	TT	0.99257	0.019833	0		-	2	60	67	0	0	6.450381	2	60	55	18	ENST00000394649.4	0.5	0.019982
ASIC2	40	__UNKNOWN__	__UNKNOWN__	17	31397582	31397582	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:31397582T>C	ENST00000359872.6	-	3	1596				ASIC2_ENST00000225823.2_Intron|ASIC2_ENST00000448983.1_Intron	NM_001094.4	NP_001085.2	Q16515	ASIC2_HUMAN	acid-sensing (proton-gated) ion channel 2	NA		NA			central nervous system development (GO:0007417)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|ion transmembrane transport (GO:0034220)|monovalent inorganic cation transport (GO:0015672)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|phototransduction (GO:0007602)|positive regulation of synapse assembly (GO:0051965)|protein localization to synapse (GO:0035418)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of membrane potential (GO:0042391)|regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback (GO:0003026)|regulation of vasoconstriction (GO:0019229)|response to acid chemical (GO:0001101)|response to acidic pH (GO:0010447)|sensory perception of sound (GO:0007605)|sensory perception of sour taste (GO:0050915)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)|voltage-gated sodium channel activity (GO:0005248)				NA					Amiloride(DB00594)	tctcgatctcttgaccttgtg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL834182	CCDS11276.1, CCDS42296.1	17q11.2-q12	2012-02-23	2012-02-22	2012-02-22	ENSG00000108684	ENSG00000108684	40		Ion channels / Acid-sensing (proton-gated) ion channels	99	protein-coding gene	gene with protein product	degenerin	601784	amiloride-sensitive cation channel 1, neuronal	ACCN, ACCN1	NA	8921408	Standard	NM_183377, NM_001094	NM_183377	NA	Approved	ASIC2a, BNC1, BNaC1, hBNaC1, MDEG	uc002hhu.3	Q16515	OTTHUMG00000132885	ENST00000359872.6:c.834+18298A>G	chr17.hg19:g.31397582T>C		NA	E9PBX2|Q13553|Q6DJU1|Q8N3E2	hg19	CCDS42296.1	0.02	-0.07894	CTCxTGA	UNCOVERED																																																																																			NOVEL	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447552.1	7	2.40628	KEEP	4	0	0	8	223	TT	0	0	0		-	3	42	94	0	0	8.343559	6	60	180	26	ENST00000359872.6	0.333333	0.077336
RFFL	117584	__UNKNOWN__	__UNKNOWN__	17	33334882	33334882	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:33334882G>A	ENST00000315249.7	-	0	5419				RFFL_ENST00000580569.1_Intron|RP5-837J1.2_ENST00000578488.1_RNA					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase	NA		NA								kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		cctcccaagtggctaagactt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871	117584		RING-type (C3HC4) zinc fingers	24821	protein-coding gene	gene with protein product		609735	ring finger and FYVE-like domain containing		NA	15229288	Standard	NM_057178	NR_037713	NA	Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.*4105C>T	chr17.hg19:g.33334882G>A		NA		hg19	CCDS11286.1	0.02	5.459364	AGTxGCT	COVERED																																																																																			NOVEL	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256460.2	111	72.009571	KEEP	0	6	160	296	9105	GG	1	1	0		-	8	60	236	0	0	12.911784	189	60	6421	779	ENST00000315249.7	0.040609	1
RFFL	117584	__UNKNOWN__	__UNKNOWN__	17	33335930	33335930	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:33335930G>A	ENST00000315249.7	-	0	4371				RP5-837J1.2_ENST00000578488.1_RNA					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase	NA		NA								kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		gattacaggcgtgagccaccg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871	117584		RING-type (C3HC4) zinc fingers	24821	protein-coding gene	gene with protein product		609735	ring finger and FYVE-like domain containing		NA	15229288	Standard	NM_057178	NR_037713	NA	Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.*3057C>T	chr17.hg19:g.33335930G>A		NA		hg19	CCDS11286.1	0.02	-0.271891	GGCxTGA	COVERED																																																																																			NOVEL	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256460.2	7	4.797659	KEEP	3	0	0	16	422	GG	0.99649	0.714798	0		-	3	60	92	0	0	6.445209	26	60	825	66	ENST00000315249.7	0.103448	0.717315
RFFL	117584	__UNKNOWN__	__UNKNOWN__	17	33367387	33367387	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:33367387A>G	ENST00000315249.7	-	2	215				RFFL_ENST00000378516.2_Intron|RAD51L3-RFFL_ENST00000593039.1_Intron|RFFL_ENST00000413582.2_Intron|RFFL_ENST00000394597.2_Intron|RFFL_ENST00000415395.2_Intron|RFFL_ENST00000447669.2_Intron|RFFL_ENST00000584655.1_Intron|RFFL_ENST00000268850.7_Intron					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase	NA		NA								kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		ttgggaggccaaggcgggcag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871	117584		RING-type (C3HC4) zinc fingers	24821	protein-coding gene	gene with protein product		609735	ring finger and FYVE-like domain containing		NA	15229288	Standard	NM_057178	NR_037713	NA	Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.8-13807T>C	chr17.hg19:g.33367387A>G		NA		hg19	CCDS11286.1	0.02	-0.184168	GCCxAGG	COVERED																																																																																			NOVEL	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256460.2	9	3.308716	KEEP	6	0	0	11	310	AA	0.992708	0.42039	0		-	3	60	101	0	0	7.933438	16	60	462	55	ENST00000315249.7	0.157895	0.423478
SLFN12	55106	__UNKNOWN__	__UNKNOWN__	17	33748053	33748053	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:33748053T>C	ENST00000394562.1	-	5	1563				SLFN12_ENST00000304905.5_Intron|SLFN12_ENST00000452764.3_Intron			Q8IYM2	SLN12_HUMAN	schlafen family member 12	NA		NA					ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		atggtgaaactccgtctctac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123	55106			25500	protein-coding gene	gene with protein product		614955			NA	12477932	Standard	NM_018042	NM_018042	NA	Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.1040-653A>G	chr17.hg19:g.33748053T>C		NA	A8K711|Q9NP47	hg19	CCDS11295.1	0.02	-0.061406	AACxCCG	UNCOVERED																																																																																			NOVEL	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256491.1	5	2.405681	KEEP	1	0	0	8	214	TT	0	0	0		-	2	29	72	0	0	6.335622	5	60	160	19	ENST00000394562.1	0.285714	0.043787
CCL23	6368	__UNKNOWN__	__UNKNOWN__	17	34342840	34342840	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:34342840A>G	ENST00000293280.2	-	2	147				CCL23_ENST00000591423.1_Intron	NM_005064.3	NP_005055.2	P55773	CCL23_HUMAN	chemokine (C-C motif) ligand 23	NA		NA			cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|negative regulation of C-C chemokine binding (GO:2001264)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)			large_intestine(2)|liver(1)|lung(2)|prostate(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ttgggaggccaaggcgggcgg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U58913	CCDS11305.1, CCDS59282.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000167236	ENSG00000274736	6368		Chemokine ligands, Endogenous ligands	10622	protein-coding gene	gene with protein product		602494	small inducible cytokine subfamily A (Cys-Cys), member 23	SCYA23	NA	9104803, 10409433	Standard	NM_005064, NM_145898	XR_429910	NA	Approved	Ckb-8, MPIF-1, MIP-3, CKb8	uc002hks.1	P55773	OTTHUMG00000188409	ENST00000293280.2:c.77-1407T>C	chr17.hg19:g.34342840A>G		NA	B7ZKQ3|O00174|O75950|Q52LD4	hg19	CCDS11305.1	0.02	-0.228016	GCCxAGG	UNCOVERED																																																																																			NOVEL	CCL23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256575.2	11	2.405434	KEEP	9	0	0	8	216	AA	0	0	0		-	3	60	101	1	0	7.727003	19	60	554	59	ENST00000293280.2	0.136364	0.58293
CTB-91J4.1	0	__UNKNOWN__	__UNKNOWN__	17	34465938	34465938	__UNKNOWN__	RNA	SNP	A	A	G	rs9912991	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:34465938A>G	ENST00000592460.1	+	0	41										NA		NA									NA						ggtggctcacacctgtaatcc	0.557		NA											.|||	463	0.0924521	0.323	0.0331	5008	,	,	NA	24028	0.0	NA	0.008	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000592460.1:	chr17.hg19:g.34465938A>G		NA		hg19		0.02	-0.210486	CACxCCT	COVERED																																																																																			NOVEL	CTB-91J4.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000450617.1	19	5.713157	KEEP	4	0	0	19	508	AA	0.999366	0.552537	0		+	3	60	98	0	1	7.365065	20	60	582	62	ENST00000592460.1	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	35018754	35018754	__UNKNOWN__	IGR	SNP	G	G	A	rs143610884		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:35018754G>A			NA	NA				CTB-75G16.3 (27598 upstream) : CTD-3194G12.1 (22448 downstream)						NA		NA									NA						ggaggctgaggtgggtgaatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.35018754G>A		NA		hg19		0.02	-0.184217	GAGxTGG	COVERED																																																																																			NOVEL					0			19	4.212398	KEEP	14	0	0	14	428	GG	0.99254	0.420319	0			3	42	89	0	0	6.810323	15	60	523	60		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	35018781	35018781	__UNKNOWN__	IGR	SNP	G	G	C	rs138201258		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:35018781G>C			NA	NA				CTB-75G16.3 (27625 upstream) : CTD-3194G12.1 (22421 downstream)						NA		NA									NA						tcaggagatcgagaccatcct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.35018781G>C		NA		hg19		0.02	-0.175449	ATCxAGA	COVERED																																																																																			NOVEL					0			20	4.512487	KEEP	13	0	0	15	438	GG	0.992708	0.42039	0			3	42	101	0	0	8.091449	14	60	465	57		0.176471	0.423478
TADA2A	6871	__UNKNOWN__	__UNKNOWN__	17	35803623	35803623	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:35803623A>G	ENST00000394395.2	+	7	704				TADA2A_ENST00000586023.1_Intron|TADA2A_ENST00000225396.6_Intron|TADA2A_ENST00000417170.1_Intron|TADA2A_ENST00000591992.1_Intron	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	NA		NA			chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						ccaaagtgctaggattacagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234	6871			11531	protein-coding gene	gene with protein product		602276	transcriptional adaptor 2 (ADA2 homolog, yeast)-like	TADA2L	NA	8552087	Standard	NM_001488	XM_006722043	NA	Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.531+870A>G	chr17.hg19:g.35803623A>G		NA	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	hg19	CCDS11319.1	0.02	-0.096467	GCTxGGA	UNCOVERED																																																																																			NOVEL	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256677.3	3	2.406258	KEEP	0	0	0	8	222	AA	0.99257	0.119541	0		+	2	60	74	0	0	6.401105	6	60	174	32	ENST00000394395.2	0.25	0.120436
DDX52	11056	__UNKNOWN__	__UNKNOWN__	17	35970198	35970198	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:35970198G>A	ENST00000349699.2	-	0	5986				RP11-697E22.1_ENST00000591689.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	NA		NA				membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				tttgagacagggtcttgctct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053	11056		DEAD-boxes	20038	protein-coding gene	gene with protein product		612500			NA	11124703	Standard	NM_152300	XM_006721650	NA	Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.*4143C>T	chr17.hg19:g.35970198G>A		NA	Q86YG1|Q8N213|Q9NVE0|Q9Y482	hg19	CCDS11323.1	0.02	-0.263117	CAGxGTC	COVERED																																																																																			NOVEL	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256795.1	6	2.439157	KEEP	0	1	22	16	473	GG	0.999366	0.693229	0		-	4	60	111	2	0	8.093347	23	60	717	56	ENST00000349699.2	0.148148	0.693668
DDX52	11056	__UNKNOWN__	__UNKNOWN__	17	35974119	35974119	__UNKNOWN__	3'UTR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:35974119A>C	ENST00000349699.2	-	0	2065				DDX52_ENST00000394367.3_3'UTR	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	NA		NA				membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				accagcctggacaacatggca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053	11056		DEAD-boxes	20038	protein-coding gene	gene with protein product		612500			NA	11124703	Standard	NM_152300	XM_006721650	NA	Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.*222T>G	chr17.hg19:g.35974119A>C		NA	Q86YG1|Q8N213|Q9NVE0|Q9Y482	hg19	CCDS11323.1	0.02	3.475994	TGGxCAA	COVERED																																																																																			NOVEL	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256795.1	61	20.64053	KEEP	0	12	362	196	5405	AA	1	1	0		-	7	60	239	0	0	15.481119	120	60	3620	572	ENST00000349699.2	0.055118	1
RP11-115K3.2	0	__UNKNOWN__	__UNKNOWN__	17	36214061	36214061	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:36214061C>T	ENST00000590732.1	-	0	391					NR_024178.1					NA		NA									NA						CCAAGCTGTTCTCTGCCACCT	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000590732.1:	chr17.hg19:g.36214061C>T		NA		hg19		0.02	-0.385839	GTTxTCT	COVERED																																																																																			NOVEL	RP11-115K3.2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000451947.1	7	3.008928	KEEP	0	0	0	10	307	CC	0.992708	0.911475	0		-	4	60	108	0	0	6.937822	39	60	1289	75	ENST00000590732.1	0.093023	0.918171
RP11-115K3.2	0	__UNKNOWN__	__UNKNOWN__	17	36214065	36214065	__UNKNOWN__	RNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:36214065G>T	ENST00000590732.1	-	0	387					NR_024178.1					NA		NA									NA						GCTGTTCTCTGCCACCTCCTT	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000590732.1:	chr17.hg19:g.36214065G>T		NA		hg19		0.02	-0.39475	TCTxCCA	COVERED																																																																																			NOVEL	RP11-115K3.2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000451947.1	7	3.009034	KEEP	0	0	0	10	310	GG	0.992708	0.919883	0		-	4	60	112	0	0	7.293895	40	60	1363	76	ENST00000590732.1	0.090909	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	36300228	36300228	__UNKNOWN__	IGR	SNP	A	A	T	rs4362438		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:36300228A>T			NA	NA				TBC1D3F (5314 upstream) : TBC1D3 (37482 downstream)						NA		NA									NA						caacctcccaaagtgttggga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.36300228A>T		NA		hg19		0.02	-0.14906	CCAxAGT	UNCOVERED																																																																																			NOVEL					0			8	3.007226	KEEP	9	0	0	10	271	AA	0	0	0			6	60	172	0	0	15.678539	9	50	253	45		0.4	0.292001
CWC25	54883	__UNKNOWN__	__UNKNOWN__	17	36960756	36960756	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:36960756A>C	ENST00000225428.5	-	9	1299				CWC25_ENST00000536127.1_Intron	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	NA		NA								central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						aaccccatctatattaaaaat	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559	54883			25989	protein-coding gene	gene with protein product		NA	coiled-coil domain containing 49	CCDC49	NA	19941820	Standard	NM_017748	NM_017748	NA	Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.1002-1642T>G	chr17.hg19:g.36960756A>C		NA	A0JLM3|Q68DK5	hg19	CCDS45663.1	0.02	-0.105237	TCTxTAT	UNCOVERED																																																																																			NOVEL	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442186.6	6	2.706099	KEEP	0	0	0	9	240	AA	0.99254	0.138789	0		-	3	60	97	1	1	8.201369	9	60	261	26	ENST00000225428.5	0.25	0.139832
PLXDC1	57125	__UNKNOWN__	__UNKNOWN__	17	37291701	37291701	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:37291701G>A	ENST00000315392.4	-	2	467				PLXDC1_ENST00000444911.2_Intron|PLXDC1_ENST00000394316.2_Intron|PLXDC1_ENST00000539608.1_Intron	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	NA		NA			angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)			kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						aggctgaggcgggtagatcac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381	57125			20945	protein-coding gene	gene with protein product	tumor endothelial marker 7 precursor	606826			NA	10947988, 11559528	Standard	NM_020405	NM_020405	NA	Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.255+4205C>T	chr17.hg19:g.37291701G>A		NA	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	hg19	CCDS11333.1	0.02	-0.087717	GGCxGGT	UNCOVERED																																																																																			NOVEL	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256892.2	5	3.309668	KEEP	1	0	0	11	333	GG	0.993072	0.09903	0		-	3	60	88	0	0	7.578331	7	60	229	35	ENST00000315392.4	0.3	0.099721
FBXL20	84961	__UNKNOWN__	__UNKNOWN__	17	37528512	37528512	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:37528512T>G	ENST00000264658.6	-	2	303				FBXL20_ENST00000583610.1_Intron|FBXL20_ENST00000577399.1_Intron|FBXL20_ENST00000394294.3_Intron	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	NA		NA			behavioral fear response (GO:0001662)	cytoplasm (GO:0005737)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22			LUAD - Lung adenocarcinoma(14;0.146)			ggtggctcactcctgtaatcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007557	CCDS32640.1, CCDS54116.1	17q21.2	2011-06-09				ENSG00000108306	84961		F-boxes / Leucine-rich repeats	24679	protein-coding gene	gene with protein product		609086			NA	12477932	Standard	NM_032875	NM_032875	NA	Approved	MGC15482, Fbl2, Fbl20	uc002hrt.3	Q96IG2		ENST00000264658.6:c.43-29018A>C	chr17.hg19:g.37528512T>G		NA	A8K729|Q38J52	hg19	CCDS32640.1	0.02	-0.10526	CACxCCT	UNCOVERED																																																																																			NOVEL	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444315.2	7	2.706966	KEEP	3	0	0	9	250	CT	0.99257	0.16126	0		-	3	60	100	0	0	8.943499	6	60	188	33	ENST00000264658.6	0.333333	0.162467
FBXL20	84961	__UNKNOWN__	__UNKNOWN__	17	37546471	37546471	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:37546471T>C	ENST00000264658.6	-	1	303				FBXL20_ENST00000583610.1_Intron|FBXL20_ENST00000577399.1_Intron|FBXL20_ENST00000394294.3_Intron	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	NA		NA			behavioral fear response (GO:0001662)	cytoplasm (GO:0005737)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22			LUAD - Lung adenocarcinoma(14;0.146)			tccaggagtttgagaccagcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC007557	CCDS32640.1, CCDS54116.1	17q21.2	2011-06-09				ENSG00000108306	84961		F-boxes / Leucine-rich repeats	24679	protein-coding gene	gene with protein product		609086			NA	12477932	Standard	NM_032875	NM_032875	NA	Approved	MGC15482, Fbl2, Fbl20	uc002hrt.3	Q96IG2		ENST00000264658.6:c.42+11142A>G	chr17.hg19:g.37546471T>C		NA	A8K729|Q38J52	hg19	CCDS32640.1	0.02	-0.166644	GTTxGAG	COVERED																																																																																			NOVEL	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444315.2	10	4.811858	KEEP	0	0	0	16	438	TT	0.997832	0.422559	0		-	3	60	92	0	0	7.279079	13	60	396	52	ENST00000264658.6	0.1875	0.423478
CDK12	51755	__UNKNOWN__	__UNKNOWN__	17	37666348	37666348	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:37666348C>T	ENST00000447079.4	+	7	2699				CDK12_ENST00000430627.2_Intron	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	NA		NA			mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						agccaccgcacctggGCAACA	0.493		NA	Mis, N, F		serous ovarian					TCGA Ovarian(9;0.13)											NA			NA			NA		NA	NA	NA			NA	NA	NA			Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258	51755		Cyclin-dependent kinases	24224	protein-coding gene	gene with protein product	CDC2 related protein kinase 7	615514	Cdc2-related kinase, arginine/serine-rich	CRKRS	NA	10048485, 11683387, 19884882	Standard	NM_016507	XM_005257456	NA	Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.2666+334C>T	chr17.hg19:g.37666348C>T		NA	A7E2B2|B4DYX4|B9EIQ6|O94978	hg19	CCDS11337.1	0.02	-0.087647	GCAxCTG	UNCOVERED																																																																																			NOVEL	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256941.4	11	3.309319	KEEP	0	0	0	11	321	CC	0.993072	0.09903	0		+	3	60	74	0	0	6.748769	4	60	135	23	ENST00000447079.4	0.428571	0.099721
MED24	9862	__UNKNOWN__	__UNKNOWN__	17	38175458	38175458	__UNKNOWN__	3'UTR	SNP	T	T	C	rs56369434		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:38175458T>C	ENST00000394128.2	-	0	3375				MED24_ENST00000394126.1_3'UTR|MED24_ENST00000394127.2_3'UTR|MED24_ENST00000356271.3_3'UTR	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	NA		NA			androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					cacacacacatacacacTTTG	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838	9862			22963	protein-coding gene	gene with protein product		607000	thyroid hormone receptor associated protein 4, cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa	THRAP4, CRSP4	NA		Standard	NM_014815	NM_001079518	NA	Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.*324A>G	chr17.hg19:g.38175458T>C		NA	A8K4S5|B3KMR9|Q14143|Q9NNY5	hg19	CCDS11359.1	0.02	-0.394592	ACAxACA	COVERED																																																																																			NOVEL	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257147.2	15	9.637675	KEEP	2	1	19	39	980	TT	1	0.934492	0		-	5	60	169	0	0	12.630209	37	60	1010	138	ENST00000394128.2	0.119048	0.934492
MED24	9862	__UNKNOWN__	__UNKNOWN__	17	38193954	38193954	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:38193954A>G	ENST00000394128.2	-	4	295				MED24_ENST00000394126.1_Intron|MED24_ENST00000394127.2_Intron|MED24_ENST00000356271.3_Intron|MED24_ENST00000479829.1_Intron|MED24_ENST00000501516.3_Intron	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	NA		NA			androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					catgaggtcaagagatcaaga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838	9862			22963	protein-coding gene	gene with protein product		607000	thyroid hormone receptor associated protein 4, cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa	THRAP4, CRSP4	NA		Standard	NM_014815	NM_001079518	NA	Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.214-1547T>C	chr17.hg19:g.38193954A>G		NA	A8K4S5|B3KMR9|Q14143|Q9NNY5	hg19	CCDS11359.1	0.02	-0.070171	TCAxGAG	UNCOVERED																																																																																			NOVEL	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257147.2	4	3.308604	KEEP	2	0	0	11	306	AA	0.993072	0.053762	0		-	3	48	104	0	0	9.533149	5	60	147	36	ENST00000394128.2	0.375	0.054137
RAPGEFL1	51195	__UNKNOWN__	__UNKNOWN__	17	38338083	38338083	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:38338083C>T	ENST00000456989.2	+	2	192				RAPGEFL1_ENST00000544503.1_Intron|RAPGEFL1_ENST00000540388.1_Intron|RAPGEFL1_ENST00000436615.3_Intron|RAPGEFL1_ENST00000264644.6_Intron			Q9UHV5	RPGFL_HUMAN	Rap guanine nucleotide exchange factor (GEF)-like 1	NA		NA			G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						cctgtaatcccagcactttgg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(28;274 750 6870 14218 42203)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF117946	CCDS11363.1	17q21.2	2006-08-01	2004-03-26		ENSG00000108352	ENSG00000108352	51195			17428	protein-coding gene	gene with protein product	Link guanine nucleotide exchange factor II	NA	RAP guanine-nucleotide-exchange factor (GEF)-like 1		NA		Standard	NM_016339	NM_016339	NA	Approved	Link-GEFII	uc010cwu.1	Q9UHV5	OTTHUMG00000133325	ENST00000456989.2:c.146+137C>T	chr17.hg19:g.38338083C>T		NA		hg19		0.02	-0.254406	TCCxAGC	COVERED																																																																																			NOVEL	RAPGEFL1-005	PUTATIVE	non_canonical_conserved|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000397518.1	4	4.513725	KEEP	2	0	0	15	468	CC	0.995343	0.66541	0		+	3	60	89	0	0	6.349801	22	60	769	61	ENST00000456989.2	0.12	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	38663480	38663480	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:38663480T>C			NA	NA				TNS4 (5631 upstream) : RP5-1028K7.2 (9797 downstream)						NA		NA									NA						ctcaggagtttgagaccagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.38663480T>C		NA		hg19		0.02	-0.11398	GTTxGAG	UNCOVERED																																																																																			NOVEL					0			5	3.306834	KEEP	0	0	0	11	288	TT	0.993072	0.161341	0			3	60	91	0	0	7.733202	8	60	233	32		0.272727	0.162467
KRTAP4-8	728224	__UNKNOWN__	__UNKNOWN__	17	39254054	39254054	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs76270529		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:39254054A>T	ENST00000333822.4	-	1	339	c.283T>A	c.(283-285)Tgc>Agc	p.C95S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].	NA			aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C95S(4)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ctggagatgcagcagcTAGGG	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				4	Substitution - Missense(4)	endometrium(3)|kidney(1)											7	11	10			NA	NA	17		NA											NA				39254054		685	1582	2267	SO:0001583	missense			AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880	728224		Keratin associated proteins	17230	protein-coding gene	gene with protein product		NA			NA	11279113	Standard	NM_031960	NM_031960	NA	Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.283T>A	chr17.hg19:g.39254054A>T	ENSP00000328444:p.Cys95Ser	NA	A8MSH3	hg19	CCDS45674.1	0.02	-0.298188	TGCxGCA	COVERED	.	.	.	.	.	.	.	.	.	.	.	15.18	2.755714	0.49362	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.02280	4.36	3.11	2.01	0.26516	.	0.000000	0.52532	U	0.000067	T	0.04497	0.0123	M	0.83223	2.63	0.25182	N	0.99019	B	0.21606	0.058	B	0.27887	0.084	T	0.21793	-1.0235	10	0.54805	T	0.06	.	6.3859	0.21559	0.8715:0.0:0.1285:0.0	.	95	Q9BYQ9	KRA48_HUMAN	S	95;80	ENSP00000328444:C95S	ENSP00000414561:C80S	C	-	1	0	KRTAP4-8	36507580	0.999000	0.42202	0.393000	0.26258	0.649000	0.38597	3.122000	0.50446	0.404000	0.25506	0.374000	0.22700	TGC	NOVEL	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257684.1	7	2.406519	KEEP	1	0	0	8	228	AA	0.99257	0.775257	0		-	5	55	145	0	0	10.793271	28	60	832	80	ENST00000333822.4	0.151515	0.78106
KRTAP4-11	653240	__UNKNOWN__	__UNKNOWN__	17	39274157	39274157	__UNKNOWN__	Silent	SNP	G	G	A	rs145503152		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:39274157G>A	ENST00000391413.2	-	1	449	c.411C>T	c.(409-411)ccC>ccT	p.P137P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	137	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].	NA				keratin filament (GO:0045095)		p.P137P(3)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			tgctgcagctggggtggcagc	0.672		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				3	Substitution - coding silent(3)	prostate(1)|lung(1)|endometrium(1)											8	13	12			NA	NA	17		NA											NA				39274157		684	1586	2270	SO:0001819	synonymous_variant			AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721	653240		Keratin associated proteins	18911	protein-coding gene	gene with protein product		NA	keratin associated protein 4-14	KRTAP4-14	NA		Standard		NM_033059	NA	Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.411C>T	chr17.hg19:g.39274157G>A		NA	A0AUY2	hg19	CCDS45675.1	0.02	-0.298245	GCTxGGG	COVERED																																																																																			NOVEL	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257690.1	1	2.707763	KEEP	1	0	0	9	270	GG	0.99257	0.775257	0		-	7	60	204	0	0	16.335426	26	60	887	66	ENST00000391413.2	0.212121	0.78106
KRTAP4-6	81871	__UNKNOWN__	__UNKNOWN__	17	39296167	39296167	__UNKNOWN__	Silent	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:39296167A>G	ENST00000345847.4	-	1	572	c.573T>C	c.(571-573)atT>atC	p.I191I		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	191		NA				keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GGCAGGTGGAAATGACACAGG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant			AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090	81871		Keratin associated proteins	18909	protein-coding gene	gene with protein product		NA	keratin associated protein 4-15	KRTAP4-15	NA		Standard		NM_030976	NA	Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.573T>C	chr17.hg19:g.39296167A>G		NA	Q9BYR1	hg19	CCDS54125.1	0.02	-0.377057	GGAxATG	COVERED																																																																																			NOVEL	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257779.1	4	5.411621	KEEP	0	0	0	18	471	AA	0.999859	0.908941	0		-	4	41	125	0	0	8.720794	37	60	1056	88	ENST00000345847.4	0.097561	0.909069
JUP	3728	__UNKNOWN__	__UNKNOWN__	17	39805487	39805487	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:39805487G>A	ENST00000540235.1	-	5	909							P14923	PLAK_HUMAN	junction plakoglobin	NA		NA			adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		caccacgcccggctaattttt	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(16;42 520 6044 17852 28530)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801	3728		Armadillo repeat containing	6207	protein-coding gene	gene with protein product		173325	catenin (cadherin-associated protein), gamma 80kDa	CTNNG	NA	1889810, 7604000	Standard		NM_021991	NA	Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000540235.1:c.910-26203C>T	chr17.hg19:g.39805487G>A		NA	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	hg19		0.02	-0.140341	CCCxGCT	UNCOVERED																																																																																			NOVEL	JUP-201	KNOWN	basic	protein_coding	NA	protein_coding		6	2.707623	KEEP	5	0	0	9	264	GG	0	0	0		-	3	40	90	0	0	7.2729	11	55	360	38	ENST00000540235.1	0.214286	0.260965
DNAJC7	7266	__UNKNOWN__	__UNKNOWN__	17	40158545	40158545	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:40158545G>A	ENST00000457167.4	-	2	314				DNAJC7_ENST00000316603.7_Intron|DNAJC7_ENST00000589547.1_Intron|DNAJC7_ENST00000426588.3_Intron	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	NA		NA			chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				ggctgggcacggtggctcacg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(63;618 1117 8600 10857 19751)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259	7266		Heat shock proteins / DNAJ (HSP40), Tetratricopeptide (TTC) repeat domain containing	12392	protein-coding gene	gene with protein product		601964		TTC2	NA	8836031, 11147971	Standard		NR_029431	NA	Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.78-5957C>T	chr17.hg19:g.40158545G>A		NA	Q7Z784	hg19	CCDS45677.1	0.02	-0.21925	CACxGTG	COVERED																																																																																			NOVEL	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453366.2	10	3.91087	KEEP	1	0	0	13	383	GG	0.993634	0.549368	0		-	4	60	114	0	0	8.61485	20	60	636	56	ENST00000457167.4	0.166667	0.552887
ZNF385C	201181	__UNKNOWN__	__UNKNOWN__	17	40199366	40199366	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:40199366A>T	ENST00000436535.3	-	2	251							Q66K41	Z385C_HUMAN	zinc finger protein 385C	NA		NA				nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				aatttttttgaatttttagta	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595	201181			33722	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013624	NM_001242704	NA	Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.251-9463T>A	chr17.hg19:g.40199366A>T		NA	Q4G0J1	hg19		0.02	-0.11401	TTGxATT	UNCOVERED																																																																																			NOVEL	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000347740.3	7	3.907383	KEEP	1	0	0	13	344	AA	0.994391	0.161555	0		-	4	60	110	1	0	9.776446	7	60	208	40	ENST00000436535.3	0.363636	0.162467
RP11-400F19.8	0	__UNKNOWN__	__UNKNOWN__	17	40707683	40707683	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:40707683T>C	ENST00000585572.1	+	0	379										NA		NA									NA						cagattcaagtgattctcctg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000585572.1:	chr17.hg19:g.40707683T>C		NA		hg19		0.02	-0.078938	AAGxGAT	UNCOVERED																																																																																			NOVEL	RP11-400F19.8-001	KNOWN	NMD_likely_if_extended|basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000450390.1	5	4.801799	KEEP	0	0	0	16	420	TT	0.997832	0.077168	0		+	3	60	91	0	0	8.043319	6	60	183	34	ENST00000585572.1	0.333333	0.077336
RAMP2-AS1	100190938	__UNKNOWN__	__UNKNOWN__	17	40906107	40906107	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:40906107G>A	ENST00000592670.1	-	0	2942					NR_024461.1				RAMP2 antisense RNA 1	NA		NA									NA						agtagagatggggtttcacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC018638, BC041021		17q21.31	2012-10-12			ENSG00000197291	ENSG00000197291	100190938		Long non-coding RNAs	44358	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_024461	NR_024461	NA	Approved		uc002ibf.4			ENST00000592670.1:	chr17.hg19:g.40906107G>A		NA		hg19		0.02	-0.096492	ATGxGGT	UNCOVERED																																																																																			NOVEL	RAMP2-AS1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000452372.1	13	3.309557	KEEP	8	0	0	11	327	GG	0	0	0		-	3	49	92	0	0	8.143349	6	60	196	35	ENST00000592670.1	0.333333	0.120436
CNTD1	124817	__UNKNOWN__	__UNKNOWN__	17	40958020	40958020	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:40958020T>A	ENST00000588527.1	+	4	543				CNTD1_ENST00000588408.1_Intron|CNTD1_ENST00000315066.5_Intron			Q8N815	CNTD1_HUMAN	cyclin N-terminal domain containing 1	NA		NA								central_nervous_system(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		ctgaggtaggtggatcacttg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK097456	CCDS11440.1	17q21.31	2014-07-03	2006-03-31	2006-03-31	ENSG00000176563	ENSG00000176563	124817			26847	protein-coding gene	gene with protein product		NA	cyclin N-terminal domain containing	CNTD	NA	24891606	Standard	NM_173478	NM_173478	NA	Approved	FLJ40137	uc002ibm.4	Q8N815		ENST00000588527.1:c.331+118T>A	chr17.hg19:g.40958020T>A		NA	Q658Q6|Q8NEP1	hg19		0.02	-0.157848	AGGxGGA	COVERED																																																																																			NOVEL	CNTD1-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000452402.1	10	3.306638	KEEP	3	0	0	11	307	TT	0.993072	0.351495	0		+	3	40	83	1	0	6.379827	13	60	382	50	ENST00000588527.1	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	41068375	41068375	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:41068375T>C			NA	NA				G6PC (2989 upstream) : RNY4P2 (16489 downstream)						NA		NA									NA						gcaggaggattacttgagcct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.41068375T>C		NA		hg19		0.02	-0.175353	GATxACT	COVERED																																																																																			NOVEL					0			7	3.007278	KEEP	1	0	0	10	273	TT	0.992708	0.42039	0			3	60	89	0	0	6.734717	16	60	446	48		0.157895	0.423478
BRCA1	672	__UNKNOWN__	__UNKNOWN__	17	41197111	41197111	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:41197111A>G	ENST00000357654.3	-	0	6294				BRCA1_ENST00000309486.4_3'UTR|BRCA1_ENST00000352993.3_3'UTR|BRCA1_ENST00000354071.3_3'UTR|BRCA1_ENST00000346315.3_3'UTR|BRCA1_ENST00000468300.1_3'UTR|BRCA1_ENST00000351666.3_3'UTR	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	NA		NA			androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		gtgagccaccatgcccagGTT	0.507		NA	D, Mis, N, F, S		ovarian	breast, ovarian		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)											NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant	Familial Cancer Database		U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048	672		RING-type (C3HC4) zinc fingers, Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	1100	protein-coding gene	gene with protein product	BRCA1/BRCA2-containing complex, subunit 1, protein phosphatase 1, regulatory subunit 53	113705			NA	1676470	Standard	NM_007294	NM_007300	NA	Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.*584T>C	chr17.hg19:g.41197111A>G		NA	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	hg19	CCDS11453.1	0.02	1.871118	ACCxTGC	COVERED																																																																																			NOVEL	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348798.2	9	10.525308	KEEP	0	0	0	35	952	AA	0.999999	0.986152	0		-	4	60	133	1	0	8.98655	51	60	1528	132	ENST00000357654.3	0.072727	0.986153
RP11-392O1.4	0	__UNKNOWN__	__UNKNOWN__	17	41668332	41668332	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:41668332A>G	ENST00000588996.1	+	0	109										NA		NA									NA						ggaggctgagacaggagaatt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000588996.1:	chr17.hg19:g.41668332A>G		NA		hg19		0.02	-0.035086	GAGxCAG	UNCOVERED																																																																																			NOVEL	RP11-392O1.4-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000453499.1	3	2.706357	KEEP	0	0	0	9	247	AA	0.99254	0.019833	0		+	2	60	66	0	0	6.350127	2	60	61	16	ENST00000588996.1	0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	42214700	42214700	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42214700T>C			NA	NA				RNU6-131P (1343 upstream) : C17orf53 (4573 downstream)						NA		NA									NA						gtagctgggattacaggtgtg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.42214700T>C		NA		hg19		0.02	-0.035087	GGAxTAC	UNCOVERED																																																																																			NOVEL					0			11	2.706948	KEEP	14	0	0	9	249	TT	0	0	0			2	25	71	0	0	6.850286	2	26	59	32		0.5	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	42214810	42214810	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42214810C>T			NA	NA				RNU6-131P (1453 upstream) : C17orf53 (4463 downstream)						NA		NA									NA						agattacaggcgtgagccacc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.42214810C>T		NA		hg19		0.02	-0.105203	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			11	3.910859	KEEP	1	0	0	13	383	CC	0.994391	0.139048	0			3	60	85	0	0	7.444398	6	60	190	38		0.333333	0.139832
RP5-1067M6.3	0	__UNKNOWN__	__UNKNOWN__	17	42406617	42406617	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42406617G>T	ENST00000588260.1	+	0	124										NA		NA									NA						ttttttttgagacggagtctc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000588260.1:	chr17.hg19:g.42406617G>T		NA		hg19		0.02	-0.08771	TGAxACG	UNCOVERED																																																																																			NOVEL	RP5-1067M6.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000457760.1	6	3.30992	KEEP	11	0	0	11	337	GG	0	0	0		+	3	40	80	0	0	7.353625	4	40	139	34	ENST00000588260.1	0.428571	0.099721
GPATCH8	23131	__UNKNOWN__	__UNKNOWN__	17	42524488	42524488	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42524488T>G	ENST00000591680.1	-	4	224				GPATCH8_ENST00000434000.1_Intron	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	NA		NA					metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		acaggtgtgatccaccgcacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566	23131		G patch domain containing	29066	protein-coding gene	gene with protein product		614396	KIAA0553	KIAA0553, GPATC8	NA	9628581	Standard	NM_001002909	NM_001002909	NA	Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.194-10575A>C	chr17.hg19:g.42524488T>G		NA	B9EGP9|O60300|Q8TB99	hg19	CCDS32666.1	0.02	-0.052572	TGAxCCA	UNCOVERED																																																																																			NOVEL	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000457797.1	2	2.404553	KEEP	0	0	0	8	202	TT	0.99257	0.036492	0		-	3	60	86	0	0	8.563338	2	60	60	20	ENST00000591680.1	0.6	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	42688904	42688904	__UNKNOWN__	IGR	SNP	C	C	A	rs8067486	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42688904C>A			NA	NA				FZD2 (51997 upstream) : RP11-1072C15.2 (34827 downstream)						NA		NA									NA						cctcggcctcccaaagtgctg	0.453		NA											C|||	2371	0.473442	0.6989	0.389	5008	,	,	NA	14049	0.2897	NA	0.4006	False	NA	,,,	NA	NA	NA	2504	0.4928	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.42688904C>A		NA		hg19		0.02	-0.052627	CTCxCAA	UNCOVERED																																																																																			NOVEL					0			6	2.407111	KEEP	5	0	0	8	246	CC	0	0	0			5	60	151	0	0	17.483298	0	0	0	21		1	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	42701262	42701262	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42701262G>A			NA	NA				FZD2 (64355 upstream) : RP11-1072C15.2 (22469 downstream)						NA		NA									NA						tgagcccaggggtttgagact	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.42701262G>A		NA		hg19		0.02	-0.131582	AGGxGTT	COVERED																																																																																			NOVEL					0			4	2.407106	KEEP	0	0	0	8	243	GG	0.99257	0.22747	0			3	60	90	0	0	7.500878	9	60	315	36		0.25	0.229173
CTC-296K1.3	0	__UNKNOWN__	__UNKNOWN__	17	42870666	42870666	__UNKNOWN__	lincRNA	SNP	G	G	A	rs12952284	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:42870666G>A	ENST00000585620.1	+	0	100										NA		NA									NA						cactgagcccggccCGTGttt	0.552		NA											G|||	1820	0.363419	0.1868	0.4553	5008	,	,	NA	10784	0.506	NA	0.4125	False	NA	,,,	NA	NA	NA	2504	0.3395	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000585620.1:	chr17.hg19:g.42870666G>A		NA		hg19		0.02	-0.403494	CCCxGCC	COVERED																																																																																			NOVEL	CTC-296K1.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000448655.1	52	14.98508	KEEP	107	2	48	67	1987	GG	0.999988	0.934481	0		+	9	60	266	0	0	27.404173	4	60	131	300	ENST00000585620.1	0.692308	0.934492
PLCD3	113026	__UNKNOWN__	__UNKNOWN__	17	43187618	43187618	__UNKNOWN__	5'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:43187618C>T	ENST00000540511.1	-	0	4822							Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	NA		NA			angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						tcgagaccagcctggccaaca	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	113026	3.1.4.11		9061	protein-coding gene	gene with protein product		608795			NA	10702670, 9056492	Standard	NM_133373	NM_133373	NA	Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000540511.1:c.-1284G>A	chr17.hg19:g.43187618C>T		NA	Q8TEC1|Q8TF37|Q96FL6	hg19		0.02	-0.114031	CAGxCTG	UNCOVERED																																																																																			NOVEL	PLCD3-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000397579.1	6	3.911114	KEEP	4	0	0	13	387	CC	0.992708	0.161282	0		-	3	47	93	0	0	7.80106	9	60	291	38	ENST00000540511.1	0.25	0.162467
PLCD3	113026	__UNKNOWN__	__UNKNOWN__	17	43203693	43203693	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:43203693A>G	ENST00000540511.1	-	2	251				PLCD3_ENST00000322765.5_Intron			Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	NA		NA			angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						gattacaggcatgagccactg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	113026	3.1.4.11		9061	protein-coding gene	gene with protein product		608795			NA	10702670, 9056492	Standard	NM_133373	NM_133373	NA	Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000540511.1:c.5856-4954T>C	chr17.hg19:g.43203693A>G		NA	Q8TEC1|Q8TF37|Q96FL6	hg19		0.02	-0.245573	GGCxTGA	COVERED																																																																																			NOVEL	PLCD3-001	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000397579.1	20	2.723399	KEEP	7	1	28	19	510	AA	0.997832	0.639957	0		-	3	23	98	0	0	7.972401	12	60	352	61	ENST00000540511.1	0.2	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	43660141	43660141	__UNKNOWN__	IGR	SNP	C	C	T	rs547420390	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:43660141C>T			NA	NA				RP11-798G7.6 (19545 upstream) : CRHR1-IT1 (37834 downstream)						NA		NA									NA						tcgagaccagcctggccaaca	0.557		NA											N|||	430	0.0858626	0.3116	0.0245	5008	,	,	NA	28038	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.43660141C>T		NA		hg19		0.02	-0.20176	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			5	2.4071	KEEP	3	0	0	8	243	CC	0	0	0			4	60	119	0	0	9.19468	19	60	638	43		0.173913	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	43668253	43668253	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:43668253G>T			NA	NA				RP11-798G7.6 (27657 upstream) : CRHR1-IT1 (29722 downstream)						NA		NA									NA						ggctcatgccggtaatcccag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.43668253G>T		NA		hg19		0.02	-0.1842	GCCxGTA	COVERED																																																																																			NOVEL					0			6	4.209432	KEEP	1	0	0	14	405	GG	0.994391	0.421102	0			4	60	124	0	0	10.401525	12	60	378	49		0.25	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	43694787	43694787	__UNKNOWN__	IGR	SNP	C	C	T	rs2526505		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:43694787C>T			NA	NA				RP11-798G7.6 (54191 upstream) : CRHR1-IT1 (3188 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.43694787C>T		NA		hg19		0.02	-0.342084	AGGxGTG	COVERED																																																																																			NOVEL					0			13	3.843979	KEEP	10	1	29	23	696	CC	0.999859	0.865624	0			8	50	237	0	0	19.580362	25	60	822	103		0.242424	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	43694797	43694797	__UNKNOWN__	IGR	SNP	C	C	T	rs2526504		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:43694797C>T			NA	NA				RP11-798G7.6 (54201 upstream) : CRHR1-IT1 (3178 downstream)						NA		NA									NA						cgtgagccaccgcgcccggcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.43694797C>T		NA		hg19		0.02	-0.324533	CACxGCG	COVERED																																																																																			NOVEL					0			13	3.142178	KEEP	10	1	30	21	632	CC	0.999366	0.835186	0			5	49	154	0	0	11.764758	27	60	862	96		0.15625	0.835716
KANSL1	284058	__UNKNOWN__	__UNKNOWN__	17	44219804	44219804	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44219804A>G	ENST00000575318.1	-	1	1323				KANSL1_ENST00000432791.1_Intron|KANSL1_ENST00000393476.3_Intron|KANSL1_ENST00000262419.6_Intron|KANSL1_ENST00000574590.1_Intron|KANSL1_ENST00000572904.1_Intron			Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	NA		NA			chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)					NA						aacagagcaaaaccccatctc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071	284058			24565	protein-coding gene	gene with protein product	centromere protein 36	612452	KIAA1267	KIAA1267	NA	10574462	Standard	NM_015443	NM_015443	NA	Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000575318.1:c.1289+28416T>C	chr17.hg19:g.44219804A>G		NA	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	hg19		0.02	-0.324459	CAAxACC	COVERED																																																																																			NOVEL	KANSL1-006	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000440272.1	17	5.409414	KEEP	2	0	0	18	461	AA	0.999859	0.835598	0		-	3	60	103	0	0	7.36741	30	60	846	79	ENST00000575318.1	0.090909	0.835716
KANSL1	284058	__UNKNOWN__	__UNKNOWN__	17	44286335	44286335	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44286335G>A	ENST00000574590.1	-	1	138					NM_001193465.1	NP_001180394.1	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	NA		NA			chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)					NA						tcaggagttcgagaccagcct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071	284058			24565	protein-coding gene	gene with protein product	centromere protein 36	612452	KIAA1267	KIAA1267	NA	10574462	Standard	NM_015443	NM_015443	NA	Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000574590.1:c.88+14701C>T	chr17.hg19:g.44286335G>A		NA	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	hg19	CCDS11503.1	0.02	-0.219275	TTCxAGA	COVERED																																																																																			NOVEL	KANSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440270.2	13	4.813239	KEEP	0	0	0	16	473	GG	0.997832	0.581666	0		-	3	60	95	0	0	7.260968	17	60	532	56	ENST00000574590.1	0.15	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44318590	44318590	__UNKNOWN__	IGR	SNP	T	T	A	rs192117373		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44318590T>A			NA	NA				KANSL1 (17416 upstream) : RP11-259G18.1 (25812 downstream)						NA		NA									NA						tttaaaaaaattttaaaaaag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44318590T>A		NA		hg19		0.02	-0.140319	AAAxTTT	UNCOVERED																																																																																			NOVEL					0			7	3.007841	KEEP	10	0	0	10	279	TT	0	0	0			5	60	141	1	0	12.521665	9	60	276	46		0.357143	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44323201	44323201	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44323201C>G			NA	NA				KANSL1 (22027 upstream) : RP11-259G18.1 (21201 downstream)						NA		NA									NA						gggagggaggcaggaaggaag	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44323201C>G		NA		hg19		0.02	-0.254256	AGGxAGG	UNCOVERED																																																																																			NOVEL					0			8	3.050901	KEEP	25	1	13	15	426	CC	0	0	0			6	48	185	0	1	15.631677	17	50	527	70		0.26087	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44336643	44336643	__UNKNOWN__	IGR	SNP	G	G	C	rs2950654		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44336643G>C			NA	NA				KANSL1 (35469 upstream) : RP11-259G18.1 (7759 downstream)						NA		NA									NA						GATCGGGTGGGGGTGGGATAA	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44336643G>C		NA		hg19		0.02	1.900502	TGGxGGT	COVERED																																																																																			NOVEL					0			5	2.340785	KEEP	22	1	32	19	576	GG	0.992708	0.987827	0			22	60	728	0	0	65.051761	44	60	1475	141		0.333333	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44336962	44336962	__UNKNOWN__	IGR	SNP	G	G	A	rs2429442	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44336962G>A			NA	NA				KANSL1 (35788 upstream) : RP11-259G18.1 (7440 downstream)						NA		NA									NA						ACCACAGGAGGTTGGCCCCAG	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44336962G>A		NA		hg19		0.02	1.625343	GAGxTTG	COVERED																																																																																			NOVEL					0			3	5.71721	KEEP	20	0	0	19	594	GG	0.999366	0.970205	0			21	49	623	0	0	57.081481	31	60	1076	143		0.403846	0.97082
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44337209	44337209	__UNKNOWN__	IGR	SNP	C	C	T	rs112008792		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44337209C>T			NA	NA				KANSL1 (36035 upstream) : RP11-259G18.1 (7193 downstream)						NA		NA									NA						CAGGGTAGCCCGAGCCCCTTG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44337209C>T		NA		hg19		0.02	2.830772	GCCxGAG	COVERED																																																																																			NOVEL					0			2	2.740156	KEEP	11	1	28	19	555	CC	0.99986	0.999858	0			18	60	530	0	0	39.641703	101	60	3256	213		0.151261	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44337291	44337291	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44337291C>T			NA	NA				KANSL1 (36117 upstream) : RP11-259G18.1 (7111 downstream)						NA		NA									NA						GAGGGACCCACAAGCTGCTGG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44337291C>T		NA		hg19		0.02	1.201627	CCAxAAG	COVERED																																																																																			NOVEL					0			0	3.610552	KEEP	6	0	0	12	364	CC	0.993634	0.99347	0			17	60	490	0	0	38.175219	73	60	2476	141		0.188889	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	44337903	44337903	__UNKNOWN__	IGR	SNP	C	C	G	rs112305366	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44337903C>G			NA	NA				KANSL1 (36729 upstream) : RP11-259G18.1 (6499 downstream)						NA		NA									NA						ATGCCTGTCTCCCTGACCCAC	0.607		NA											.|||	405	0.0808706	0.0129	0.147	5008	,	,	NA	17020	0.001	NA	0.2296	False	NA	,,,	NA	NA	NA	2504	0.0552	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.44337903C>G		NA		hg19		0.02	-0.157906	TCTxCCT	COVERED																																																																																			NOVEL					0			5	8.12311	KEEP	1	0	0	27	807	CC	0.999988	0.322803	0			3	40	99	0	0	7.80989	15	60	514	57		0.166667	0.322807
ARL17B	100506084	__UNKNOWN__	__UNKNOWN__	17	44357491	44357491	__UNKNOWN__	Intron	SNP	C	C	A	rs78729576	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44357491C>A	ENST00000570618.1	-	5	505							Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)			pancreas(1)	1						gtaatcccagcactttgggag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696	100506084		ADP-ribosylation factors-like, ADP-ribosylation factors	32387	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 17	ARL17	NA		Standard	NM_001039083	NM_001039083	NA	Approved			Q8IVW1	OTTHUMG00000178031	ENST00000570618.1:c.376-4707G>T	chr17.hg19:g.44357491C>A		NA	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	hg19	CCDS54137.1	0.02	-0.219297	CAGxACT	COVERED																																																																																			NOVEL	ARL17B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440291.1	6	2.707165	KEEP	0	0	0	9	263	CC	0.99254	0.548763	0		-	4	60	124	0	0	10.670881	10	60	350	53	ENST00000570618.1	0.285714	0.552887
ARL17B	100506084	__UNKNOWN__	__UNKNOWN__	17	44366025	44366025	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44366025G>A	ENST00000570618.1	-	4	505							Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)			pancreas(1)	1						ggtcactttcgtcaccatctt	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696	100506084		ADP-ribosylation factors-like, ADP-ribosylation factors	32387	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 17	ARL17	NA		Standard	NM_001039083	NM_001039083	NA	Approved			Q8IVW1	OTTHUMG00000178031	ENST00000570618.1:c.375+10866C>T	chr17.hg19:g.44366025G>A		NA	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	hg19	CCDS54137.1	0.02	-0.192958	TTCxTCA	UNCOVERED																																																																																			NOVEL	ARL17B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440291.1	9	2.402625	KEEP	1	0	0	8	199	GG	0	0	0		-	5	60	147	0	0	12.201979	15	60	458	31	ENST00000570618.1	0.25	0.457757
ARL17B	100506084	__UNKNOWN__	__UNKNOWN__	17	44369029	44369029	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:44369029A>G	ENST00000570618.1	-	4	505							Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)			pancreas(1)	1						gctcatgcctataatcccagc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696	100506084		ADP-ribosylation factors-like, ADP-ribosylation factors	32387	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 17	ARL17	NA		Standard	NM_001039083	NM_001039083	NA	Approved			Q8IVW1	OTTHUMG00000178031	ENST00000570618.1:c.375+7862T>C	chr17.hg19:g.44369029A>G		NA	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	hg19	CCDS54137.1	0.02	-0.166635	CCTxTAA	COVERED																																																																																			NOVEL	ARL17B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440291.1	7	2.406258	KEEP	0	0	0	8	223	AA	0.99257	0.351317	0		-	3	50	102	0	0	8.110193	15	60	436	37	ENST00000570618.1	0.166667	0.353947
RP11-156P1.2	0	__UNKNOWN__	__UNKNOWN__	17	45075323	45075323	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45075323T>C	ENST00000571841.1	+	8	736				LRRC37A17P_ENST00000570478.1_RNA|GOSR2_ENST00000439730.2_Intron						NA		NA									NA						gcaacaagagtgaaactccat	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000571841.1:c.677-26723T>C	chr17.hg19:g.45075323T>C		NA		hg19		0.02	-0.096469	GAGxGAA	UNCOVERED																																																																																			NOVEL	RP11-156P1.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000440447.1	14	4.49502	KEEP	9	0	0	15	365	TT	0.994391	0.119761	0		+	3	42	94	0	0	8.032676	8	60	232	44	ENST00000571841.1	0.272727	0.120436
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45214564	45214564	__UNKNOWN__	Missense_Mutation	SNP	A	A	T	rs201184967		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45214564A>T	ENST00000531206.1	-	14	1888	c.1885T>A	c.(1885-1887)Tgt>Agt	p.C629S	CDC27_ENST00000066544.3_Missense_Mutation_p.C623S|CDC27_ENST00000446365.2_Missense_Mutation_p.C562S|CDC27_ENST00000527547.1_Missense_Mutation_p.C622S			P30260	CDC27_HUMAN	cell division cycle 27	623		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TTTCGAAAACAAGCTAATGCT	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													59	61	60			NA	NA	17		NA											NA				45214564		2203	4300	6503	SO:0001583	missense			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000531206.1:c.1885T>A	chr17.hg19:g.45214564A>T	ENSP00000434614:p.Cys629Ser	NA	G3V1C4|Q16349|Q96F35	hg19	CCDS45720.1	0.02	13.765682	AACxAGC	COVERED	.	.	.	.	.	.	.	.	.	.	A	15.90	2.968854	0.53614	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.42245	0.1194	L	0.33485	1.01	0.80722	D	1	D;P;P;P	0.55172	0.97;0.698;0.698;0.936	P;B;B;P	0.56751	0.805;0.112;0.112;0.491	T	0.12889	-1.0530	10	0.25751	T	0.34	-10.7595	14.1085	0.65107	1.0:0.0:0.0:0.0	.	562;622;629;623	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	623;629;562;622	ENSP00000066544:C623S;ENSP00000434614:C629S;ENSP00000392802:C562S;ENSP00000437339:C622S	ENSP00000066544:C623S	C	-	1	0	CDC27	42569563	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.529000	0.81952	2.228000	0.72767	0.477000	0.44152	TGT	NOVEL	CDC27-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389745.1	19	7.813209	KEEP	3	3	85	56	1526	AA	1	1	0		-	9	60	279	0	0	24.086187	22	60	618	845	ENST00000531206.1	0.290323	1
CDC27	996	__UNKNOWN__	__UNKNOWN__	17	45266551	45266551	__UNKNOWN__	5'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45266551G>C	ENST00000066544.3	-	0	81				CDC27_ENST00000446365.2_5'UTR|CDC27_ENST00000527547.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	NA		NA			anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TCGAGGCTCAGGCCCACTTTC	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													35	33	34			NA	NA	17		NA											NA				45266551		2203	4300	6503	SO:0001623	5_prime_UTR_variant			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897	996		Anaphase promoting complex subunits, Tetratricopeptide (TTC) repeat domain containing	1728	protein-coding gene	gene with protein product	anaphase promoting complex subunit 3	116946	cell division cycle 27, cell division cycle 27 homolog (S. cerevisiae)	D0S1430E, D17S978E	NA	8234252	Standard		XM_005257892	NA	Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.-13C>G	chr17.hg19:g.45266551G>C		NA	G3V1C4|Q16349|Q96F35	hg19	CCDS11509.1	0.02	31.440543	TCAxGCC	COVERED																																																																																			NOVEL	CDC27-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000389742.2	98	28.737352	KEEP	3	23	671	332	9928	GG	1	1	0		-	20	68	665	0	0	42.522067	340	70	11767	1441	ENST00000066544.3	0.055556	1
EFCAB13	124989	__UNKNOWN__	__UNKNOWN__	17	45492366	45492366	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45492366G>A	ENST00000331493.2	+	23	2905				EFCAB13_ENST00000517484.1_Intron|CTD-2026D20.2_ENST00000523101.1_RNA	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)				NA						aggtccaacagtgatagactg	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852	124989		EF-hand domain containing	26864	protein-coding gene	gene with protein product		NA	chromosome 17 open reading frame 57	C17orf57	NA		Standard	NM_152347	NM_152347	NA	Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.2494+81G>A	chr17.hg19:g.45492366G>A		NA	G3V128|Q49AG9	hg19	CCDS11512.1	0.02	-0.421057	ACAxTGA	COVERED																																																																																			NOVEL	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000380147.4	9	7.054171	KEEP	0	1	27	33	1027	GG	0.999998	0.954489	0		+	8	60	225	0	0	17.174433	37	60	1293	119	ENST00000331493.2	0.177778	0.954491
NPEPPS	9520	__UNKNOWN__	__UNKNOWN__	17	45661361	45661361	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45661361T>C	ENST00000322157.4	+	5	885				NPEPPS_ENST00000544660.1_Intron|NPEPPS_ENST00000530173.1_Intron|NPEPPS_ENST00000525037.1_Intron	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	NA		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						ctgaggcaggtggatcatttg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	9520	3.4.11.2		7900	protein-coding gene	gene with protein product	puromycin-sensitive aminopeptidase, metalloproteinase MP100	606793			NA	9048733, 10329370	Standard	NM_006310	NM_006310	NA	Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.648+1146T>C	chr17.hg19:g.45661361T>C		NA	B7Z463|Q6P145|Q9NP16|Q9UEM2	hg19	CCDS45721.1	0.02	-0.043858	AGGxGGA	UNCOVERED																																																																																			NOVEL	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384269.1	9	3.003439	KEEP	4	0	0	10	246	TT	0.99257	0.036492	0		+	2	27	68	0	0	6.550166	2	60	61	25	ENST00000322157.4	0.5	0.036766
NPEPPS	9520	__UNKNOWN__	__UNKNOWN__	17	45694124	45694124	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45694124A>C	ENST00000322157.4	+	20	2532				RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000544660.1_Intron|NPEPPS_ENST00000530173.1_Intron	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	NA		NA			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						gcactccagcatgggcaacag	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	9520	3.4.11.2		7900	protein-coding gene	gene with protein product	puromycin-sensitive aminopeptidase, metalloproteinase MP100	606793			NA	9048733, 10329370	Standard	NM_006310	NM_006310	NA	Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.2296-1592A>C	chr17.hg19:g.45694124A>C		NA	B7Z463|Q6P145|Q9NP16|Q9UEM2	hg19	CCDS45721.1	0.02	-0.043849	AGCxTGG	UNCOVERED																																																																																			NOVEL	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384269.1	5	3.308592	KEEP	1	0	0	11	310	AA	0.992708	0.023898	0		+	2	60	68	0	0	6.550271	2	60	58	25	ENST00000322157.4	0.5	0.024074
KPNB1	3837	__UNKNOWN__	__UNKNOWN__	17	45754787	45754787	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45754787A>G	ENST00000540627.1	+	16	2185				KPNB1_ENST00000537679.1_Intron|KPNB1_ENST00000290158.4_Intron|KPNB1_ENST00000535458.2_Intron			Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	NA		NA			apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						gcagtgagccaagatcacgcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424	3837		Importins, Armadillo repeat containing	6400	protein-coding gene	gene with protein product	importin 1	602738			NA	7615630, 7627554	Standard	NM_002265	NM_002265	NA	Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000540627.1:c.1668+294A>G	chr17.hg19:g.45754787A>G		NA	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	hg19		0.02	-0.026317	GCCxAGA	UNCOVERED																																																																																			NOVEL	KPNB1-003	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000441351.1	5	2.405295	KEEP	0	0	0	8	214	AA	0.99257	0	0		+	2	37	70	0	0	7.125	1	60	30	14	ENST00000540627.1	0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	45833776	45833776	__UNKNOWN__	IGR	SNP	C	C	T	rs186371285		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45833776C>T			NA	NA				TBX21 (10291 upstream) : OSBPL7 (50961 downstream)						NA		NA									NA						AATTGTGggccgggcatggtg	0.468		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	19754	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.45833776C>T		NA		hg19		0.02	-0.131583	GGCxGGG	COVERED																																																																																			NOVEL					0			2	3.309568	KEEP	1	0	0	11	333	CC	0.992708	0.227502	0			3	60	90	0	0	7.172171	12	60	403	40		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	45965774	45965774	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:45965774G>A			NA	NA				RP11-6N17.2 (6010 upstream) : RP11-6N17.4 (2846 downstream)						NA		NA									NA						ttttagtagagacagtgtctc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.45965774G>A		NA		hg19		0.02	-0.122801	AGAxACA	COVERED																																																																																			NOVEL					0			8	2.407133	KEEP	0	0	0	8	244	GG	0.99257	0.194853	0			3	60	80	0	0	6.38196	10	60	342	27		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	46143393	46143393	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:46143393A>G			NA	NA				NFE2L1 (4544 upstream) : CBX1 (4020 downstream)						NA		NA									NA						tgtccgcctcagcctccaaag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.46143393A>G		NA		hg19		0.02	-0.157886	CTCxGCC	COVERED																																																																																			NOVEL					0			10	3.308489	KEEP	0	0	0	11	307	AA	0.993072	0.32057	0			3	60	106	0	2	8.77207	12	60	366	39		0.2	0.322807
HOXB13	10481	__UNKNOWN__	__UNKNOWN__	17	46806237	46806237	__UNKNOWN__	5'UTR	SNP	T	T	C	rs76765440|rs10673442|rs141988173|rs563081214		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:46806237T>C	ENST00000290295.7	-	0	303					NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	NA		NA			angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						ctctctctctttctctctctc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184	10481		Homeoboxes / ANTP class : HOXL subclass	5112	protein-coding gene	gene with protein product		604607	homeo box B13		NA	8756292, 9665387	Standard	NM_006361	NM_006361	NA	Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.-282A>G	chr17.hg19:g.46806237T>C		NA	B2R878|Q96QM4|Q99810	hg19	CCDS11536.1	0.02	-0.415072	TCTxTCT	COVERED																																																																																			NOVEL	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358087.3	71	13.894758	KEEP	74	1	32	58	1431	TT	0.999879	0.948287	0		-	4	60	113	0	1	8.016511	28	60	680	194	ENST00000290295.7	0.125	0.948402
RP11-463M16.4	0	__UNKNOWN__	__UNKNOWN__	17	46964907	46964907	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:46964907G>A	ENST00000508743.1	-	0	476										NA		NA									NA						cacctgccttggcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000508743.1:	chr17.hg19:g.46964907G>A		NA		hg19		0.02	-0.184216	CTTxGCC	COVERED																																																																																			NOVEL	RP11-463M16.4-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000361072.1	7	3.309881	KEEP	0	0	0	11	339	GG	0.993072	0.420544	0		-	4	60	123	0	0	9.962447	15	60	507	41	ENST00000508743.1	0.210526	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	47310487	47310487	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:47310487C>T			NA	NA				PHOSPHO1 (2359 upstream) : RP1-62O9.3 (15113 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.47310487C>T		NA		hg19		0.02	-0.087718	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			4	3.910103	KEEP	1	0	0	13	369	CC	0.993634	0.099086	0			3	60	89	0	0	7.678333	7	60	230	32		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	47323137	47323137	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:47323137T>C			NA	NA				PHOSPHO1 (15009 upstream) : RP1-62O9.3 (2463 downstream)						NA		NA									NA						cctggccgggtgcggtggctc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.47323137T>C		NA		hg19		0.02	-0.149108	GGGxGCG	COVERED																																																																																			NOVEL					0			6	3.604622	KEEP	2	0	0	12	303	TT	0.993634	0.290142	0			3	60	106	0	0	8.678758	13	60	386	49		0.1875	0.292001
ZNF652	22834	__UNKNOWN__	__UNKNOWN__	17	47387566	47387566	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:47387566T>C	ENST00000362063.2	-	5	1628				ZNF652_ENST00000430262.2_Intron	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			ccacccgccttggcctcccaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740	22834		Zinc fingers, C2H2-type	29147	protein-coding gene	gene with protein product		613907			NA	10231032	Standard	NM_014897	NM_014897	NA	Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.1309+1107A>G	chr17.hg19:g.47387566T>C		NA	A4QPD9|Q5H9Q0	hg19	CCDS32677.1	0.02	-0.10524	CCTxGGC	UNCOVERED																																																																																			NOVEL	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364524.1	7	4.507525	KEEP	3	0	0	15	397	TT	0.993634	0.138942	0		-	3	37	104	0	0	8.901453	9	60	257	42	ENST00000362063.2	0.25	0.139832
ZNF652	22834	__UNKNOWN__	__UNKNOWN__	17	47410867	47410867	__UNKNOWN__	Intron	SNP	C	C	T	rs372003636	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:47410867C>T	ENST00000362063.2	-	2	61				ZNF652_ENST00000430262.2_Intron	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			gtcaggagatcgagaccatcc	0.468		NA											C|||	33	0.00658946	0.0242	0.0014	5008	,	,	NA	7815	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740	22834		Zinc fingers, C2H2-type	29147	protein-coding gene	gene with protein product		613907			NA	10231032	Standard	NM_014897	NM_014897	NA	Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.258-15522G>A	chr17.hg19:g.47410867C>T		NA	A4QPD9|Q5H9Q0	hg19	CCDS32677.1	0.02	-0.087686	GATxGAG	UNCOVERED																																																																																			NOVEL	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364524.1	6	2.406454	KEEP	5	0	0	8	230	CC	0	0	0		-	3	60	81	0	0	6.878405	7	60	213	24	ENST00000362063.2	0.3	0.099721
RP11-893F2.5	0	__UNKNOWN__	__UNKNOWN__	17	48290182	48290182	__UNKNOWN__	lincRNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:48290182T>A	ENST00000509943.1	+	0	399										NA		NA									NA						ctgtaatccctgcactttggg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000509943.1:	chr17.hg19:g.48290182T>A		NA		hg19		0.02	-0.087706	CCCxGCA	UNCOVERED																																																																																			NOVEL	RP11-893F2.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000367043.1	1	3.309152	KEEP	0	0	0	11	319	TT	0.993072	0.09903	0		+	3	60	86	0	0	7.378234	7	60	218	35	ENST00000509943.1	0.3	0.099721
CACNA1G	8913	__UNKNOWN__	__UNKNOWN__	17	48684662	48684662	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:48684662G>T	ENST00000515411.1	+	24	4512				CACNA1G_ENST00000505165.1_Intron|CACNA1G_ENST00000354983.4_Intron|CACNA1G_ENST00000510366.1_Intron|CACNA1G_ENST00000515165.1_Intron|CACNA1G_ENST00000358244.5_Intron|CACNA1G_ENST00000514079.1_Intron|CACNA1G_ENST00000513964.1_Intron|CACNA1G_ENST00000507609.1_Intron|CACNA1G_ENST00000503485.1_Intron|CACNA1G_ENST00000513689.2_Intron|CACNA1G_ENST00000360761.4_Intron|CACNA1G_ENST00000507896.1_Intron|CACNA1G_ENST00000502264.1_Intron|CACNA1G_ENST00000352832.5_Intron|CACNA1G_ENST00000507510.2_Intron|CACNA1G_ENST00000510115.1_Intron|CACNA1G_ENST00000514181.1_Intron|CACNA1G_ENST00000429973.2_Intron|CACNA1G_ENST00000359106.5_Intron|CACNA1G_ENST00000515765.1_Intron|CACNA1G_ENST00000514717.1_Intron|CACNA1G_ENST00000507336.1_Intron|CACNA1G_ENST00000442258.2_Intron|CACNA1G_ENST00000512389.1_Intron	NM_001256324.1	NP_001243253.1	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	NA		NA			axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	gccaggagttggagaccagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283	8913		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1394	protein-coding gene	gene with protein product		604065			NA	9495342, 16382099	Standard	NM_018896	NM_001256334	NA	Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000515411.1:c.4512+312G>T	chr17.hg19:g.48684662G>T		NA	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	hg19	CCDS58568.1	0.02	1.254237	GTTxGAG	COVERED																																																																																			NOVEL	CACNA1G-034	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367938.1	30	12.570854	KEEP	0	4	87	73	2252	GG	1	0.999726	0		+	5	60	150	0	0	9.244782	76	60	2595	241	ENST00000515411.1	0.061728	0.999726
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	48871243	48871243	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:48871243A>G			NA	NA				LINC00483 (26325 upstream) : WFIKKN2 (40767 downstream)						NA		NA									NA						cgtggctcacacctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.48871243A>G		NA		hg19		0.02	-0.219216	CACxCCT	COVERED																																																																																			NOVEL					0			8	4.506708	KEEP	0	0	0	15	381	AA	0.99649	0.550947	0			3	60	101	0	0	7.861134	17	60	471	56		0.15	0.552887
COIL	8161	__UNKNOWN__	__UNKNOWN__	17	55020141	55020141	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:55020141C>T	ENST00000240316.4	-	6	1593					NM_004645.2	NP_004636.1	P38432	COIL_HUMAN	coilin	NA		NA				Cajal body (GO:0015030)|cytoplasm (GO:0005737)|female germ cell nucleus (GO:0001674)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	disulfide oxidoreductase activity (GO:0015036)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	15	Breast(9;6.15e-08)					cctcccaaagcgctgggatta	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U06632	CCDS11592.1	17q22	2012-10-02			ENSG00000121058	ENSG00000121058	8161			2184	protein-coding gene	gene with protein product		600272			NA	7971277	Standard		NM_004645	NA	Approved	CLN80, p80-coilin	uc002iuu.3	P38432	OTTHUMG00000178126	ENST00000240316.4:c.1559-657G>A	chr17.hg19:g.55020141C>T		NA	B2R931	hg19	CCDS11592.1	0.02	-0.219297	AAGxGCT	COVERED																																																																																			NOVEL	COIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440618.1	6	3.610454	KEEP	2	0	0	12	360	CC	0.993072	0.549057	0		-	3	60	88	0	1	6.427756	19	60	627	62	ENST00000240316.4	0.136364	0.552887
COIL	8161	__UNKNOWN__	__UNKNOWN__	17	55023367	55023367	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:55023367G>A	ENST00000240316.4	-	5	1593					NM_004645.2	NP_004636.1	P38432	COIL_HUMAN	coilin	NA		NA				Cajal body (GO:0015030)|cytoplasm (GO:0005737)|female germ cell nucleus (GO:0001674)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	disulfide oxidoreductase activity (GO:0015036)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	15	Breast(9;6.15e-08)					gtgagccaccgtgcccagcct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U06632	CCDS11592.1	17q22	2012-10-02			ENSG00000121058	ENSG00000121058	8161			2184	protein-coding gene	gene with protein product		600272			NA	7971277	Standard		NM_004645	NA	Approved	CLN80, p80-coilin	uc002iuu.3	P38432	OTTHUMG00000178126	ENST00000240316.4:c.1558+435C>T	chr17.hg19:g.55023367G>A		NA	B2R931	hg19	CCDS11592.1	0.02	-0.131567	ACCxTGC	COVERED																																																																																			NOVEL	COIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440618.1	7	3.610498	KEEP	0	0	0	12	363	GG	0.993634	0.227714	0		-	3	60	87	0	0	6.872507	12	60	389	37	ENST00000240316.4	0.2	0.229173
SCPEP1	59342	__UNKNOWN__	__UNKNOWN__	17	55075628	55075628	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:55075628T>C	ENST00000262288.3	+	10	935					NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	NA		NA			negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					gccgagatcgtgccactgcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064	59342			29507	protein-coding gene	gene with protein product	retinoid inducible serine carboxypeptidase	NA			NA	11447226, 12975309	Standard	NM_021626	NM_021626	NA	Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.881-118T>C	chr17.hg19:g.55075628T>C		NA	Q96A94|Q9H3F0	hg19	CCDS11593.1	0.02	-0.403361	TCGxGCC	COVERED																																																																																			NOVEL	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440622.1	7	3.66436	KEEP	1	2	59	33	817	TT	0.999999	0.934491	0		+	3	60	105	0	0	7.411612	34	60	934	105	ENST00000262288.3	0.081081	0.934492
CUEDC1	404093	__UNKNOWN__	__UNKNOWN__	17	55990425	55990425	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:55990425A>G	ENST00000577830.1	-	2	99				RP11-343K8.3_ENST00000580184.1_RNA|RP11-343K8.3_ENST00000579285.1_RNA|CUEDC1_ENST00000577840.1_Intron	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	NA		NA								endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						agtggctcacacctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000746	CCDS11599.1	17q23.2	2004-03-16				ENSG00000180891	404093			31350	protein-coding gene	gene with protein product		NA			NA		Standard	NM_017949	NM_001271875	NA	Approved		uc002ive.2	Q9NWM3		ENST00000577830.1:c.315-27185T>C	chr17.hg19:g.55990425A>G		NA	D3DTZ2|Q9NWD0	hg19	CCDS11599.1	0.02	-0.070167	CACxCCT	UNCOVERED																																																																																			NOVEL	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000443305.1	4	2.706477	KEEP	2	0	0	9	245	AA	0.99257	0.053735	0		-	3	60	92	0	0	8.332842	5	60	148	26	ENST00000577830.1	0.375	0.054137
RNF43	54894	__UNKNOWN__	__UNKNOWN__	17	56447530	56447530	__UNKNOWN__	Intron	SNP	C	C	T	rs143068999	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:56447530C>T	ENST00000584437.1	-	2	2331				BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Intron|RNF43_ENST00000500597.2_Intron|RNF43_ENST00000577625.1_Intron|RNF43_ENST00000577716.1_Intron|RNF43_ENST00000583753.1_Intron|RNF43_ENST00000407977.2_Intron			Q68DV7	RNF43_HUMAN	ring finger protein 43	NA		NA			negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					cctgggttcacaccattctcc	0.498		NA											C|||	64	0.0127796	0.0008	0.0115	5008	,	,	NA	16289	0.001	NA	0.0229	False	NA	,,,	NA	NA	NA	2504	0.0317	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11607.1	17q23.2	2013-01-09					54894		RING-type (C3HC4) zinc fingers	18505	protein-coding gene	gene with protein product		612482			NA		Standard	NM_017763	NM_017763	NA	Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.375+741G>A	chr17.hg19:g.56447530C>T		NA	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	hg19	CCDS11607.1	0.02	-0.087718	TCAxACC	UNCOVERED																																																																																			NOVEL	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444713.1	6	2.40705	KEEP	4	0	0	8	242	CC	0	0	0		-	3	60	86	0	0	7.954454	4	40	137	34	ENST00000584437.1	0.428571	0.099721
RP11-567L7.6	0	__UNKNOWN__	__UNKNOWN__	17	57530211	57530211	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:57530211T>C	ENST00000584262.1	-	0	583										NA		NA									NA						tagcctcaagtgatcctcctg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000584262.1:	chr17.hg19:g.57530211T>C		NA		hg19		0.02	-0.184184	AAGxGAT	COVERED																																																																																			NOVEL	RP11-567L7.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000446039.1	10	3.307457	KEEP	0	0	0	11	293	TT	0.993072	0.420544	0		-	3	60	102	0	0	8.278839	13	60	389	44	ENST00000584262.1	0.1875	0.423478
CLTC	1213	__UNKNOWN__	__UNKNOWN__	17	57772933	57772933	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:57772933T>G	ENST00000269122.3	+	0	7022					NM_004859.3	NP_004850.1	Q00610	CLH1_HUMAN	clathrin, heavy chain (Hc)	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|mitotic nuclear division (GO:0007067)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of protein localization to plasma membrane (GO:1903077)|osteoblast differentiation (GO:0001649)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|transferrin transport (GO:0033572)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	clathrin light chain binding (GO:0032051)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|structural molecule activity (GO:0005198)		CLTC/ALK(44)|CLTC/TFE3(2)	breast(2)|large_intestine(6)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					ggctgaggcatgagaatcact	0.468		NA	T	ALK, TFE3	ALCL, renal 																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		17	17q11-qter	1213	clathrin, heavy polypeptide (Hc)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X55878	CCDS32696.1, CCDS74115.1	17q23.1	2013-09-19	2006-09-29		ENSG00000141367	ENSG00000141367	1213			2092	protein-coding gene	gene with protein product		118955	clathrin, heavy polypeptide (Hc), clathrin, heavy chain, clathrin, heavy polypeptide-like 2	CLTCL2	NA	1765375, 7584026	Standard	NM_004859	NM_004859	NA	Approved	Hc	uc002ixq.1	Q00610	OTTHUMG00000134279	ENST00000269122.3:c.*1720T>G	chr17.hg19:g.57772933T>G		NA	D3DU00|Q6N0A0|Q86TF2	hg19	CCDS32696.1	0.02	-0.438562	GCAxGAG	COVERED																																																																																			NOVEL	CLTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000258859.1	21	5.311629	KEEP	0	3	95	51	1417	TT	1	0.959859	0		+	3	60	103	0	0	6.977135	41	60	1257	138	ENST00000269122.3	0.068182	0.959859
VMP1	81671	__UNKNOWN__	__UNKNOWN__	17	57875189	57875189	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:57875189A>G	ENST00000262291.4	+	8	1024				VMP1_ENST00000545362.1_Intron|VMP1_ENST00000536180.1_Intron|VMP1_ENST00000537567.1_Intron|VMP1_ENST00000539763.1_Intron	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	NA		NA			autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						gcagtgagctaagatcgcacc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716	81671			29559	protein-coding gene	gene with protein product	ectopic P-granules autophagy protein 3 homolog (C. elegans), transport and golgi organization 5 homolog (Drosophila)	611753	transmembrane protein 49	TMEM49	NA	11230166, 11785947	Standard	NM_030938	NM_030938	NA	Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.715-10968A>G	chr17.hg19:g.57875189A>G		NA	B4DVV9|Q9H0P4|Q9P089	hg19	CCDS11619.1	0.02	-0.061393	GCTxAGA	UNCOVERED																																																																																			NOVEL	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000448793.1	1	4.511022	KEEP	0	0	0	15	406	AA	0.99649	0.043633	0		+	3	60	95	0	0	8.855377	4	60	114	33	ENST00000262291.4	0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	58075770	58075770	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:58075770T>G			NA	NA				RP11-178C3.2 (1437 upstream) : TBC1D3P1-DHX40P1 (9718 downstream)						NA		NA									NA						aaggtcaggatatcgagacca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.58075770T>G		NA		hg19		0.02	-0.271815	GGAxATC	COVERED																																																																																			NOVEL					0			5	6.615147	KEEP	6	0	0	22	583	TT	0.999863	0.717217	0			4	60	113	0	0	8.160633	25	60	707	65		0.137931	0.717315
USP32	84669	__UNKNOWN__	__UNKNOWN__	17	58317375	58317375	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:58317375C>T	ENST00000300896.4	-	12	1331				USP32_ENST00000592339.1_Intron	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	NA		NA			protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ggattacaggcgtgggccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832	84669		Ubiquitin-specific peptidases, EF-hand domain containing	19143	protein-coding gene	gene with protein product		607740	ubiquitin specific protease 32		NA	12838346	Standard	NM_032582	NM_032582	NA	Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.1137-3774G>A	chr17.hg19:g.58317375C>T		NA	Q7Z5T3|Q9BX85|Q9Y591	hg19	CCDS32697.1	0.02	-0.061399	AGGxGTG	UNCOVERED																																																																																			NOVEL	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449235.2	3	2.687161	KEEP	0	0	0	9	243	CC	0.99254	0.04346	0		-	3	60	88	0	0	8.154702	4	60	130	24	ENST00000300896.4	0.428571	0.043787
USP32	84669	__UNKNOWN__	__UNKNOWN__	17	58388130	58388130	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:58388130T>C	ENST00000300896.4	-	3	381				USP32_ENST00000393003.3_Intron	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	NA		NA			protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			ggtgtggtggttcacgcctgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832	84669		Ubiquitin-specific peptidases, EF-hand domain containing	19143	protein-coding gene	gene with protein product		607740	ubiquitin specific protease 32		NA	12838346	Standard	NM_032582	NM_032582	NA	Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.187-9065A>G	chr17.hg19:g.58388130T>C		NA	Q7Z5T3|Q9BX85|Q9Y591	hg19	CCDS32697.1	0.02	-0.184177	TGGxTCA	COVERED																																																																																			NOVEL	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449235.2	12	5.712579	KEEP	1	0	0	19	503	TT	0.999859	0.423418	0		-	3	60	95	0	0	7.67255	12	60	342	50	ENST00000300896.4	0.2	0.423478
APPBP2	10513	__UNKNOWN__	__UNKNOWN__	17	58572626	58572626	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:58572626T>C	ENST00000083182.3	-	3	515					NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	NA		NA			intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			ggattacaggtgtgagccacc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725	10513			622	protein-coding gene	gene with protein product	protein interacting with APP tail 1	605324	amyloid beta precursor protein (cytoplasmic tail)-binding protein 2		NA	9843960	Standard	NM_006380	NM_006380	NA	Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.228-648A>G	chr17.hg19:g.58572626T>C		NA	A8K862|O95095|Q8WVC9	hg19	CCDS32699.1	0.02	-0.184169	AGGxGTG	UNCOVERED																																																																																			NOVEL	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449465.1	5	2.406624	KEEP	2	0	0	8	230	TT	0	0	0		-	3	60	98	0	0	7.710381	15	60	439	46	ENST00000083182.3	0.166667	0.423478
RP11-15E18.4	0	__UNKNOWN__	__UNKNOWN__	17	58654152	58654152	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:58654152C>T	ENST00000592917.1	+	3	188										NA		NA									NA						accatgttggccaggctggtc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000592917.1:c.55-406C>T	chr17.hg19:g.58654152C>T		NA		hg19		0.02	-0.157897	TGGxCAG	COVERED																																																																																			NOVEL	RP11-15E18.4-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000449472.1	12	4.500529	KEEP	14	0	0	15	430	CC	0.992708	0.320453	0		+	3	39	88	0	0	6.710464	15	45	502	61	ENST00000592917.1	0.166667	0.322807
BCAS3	54828	__UNKNOWN__	__UNKNOWN__	17	59157923	59157923	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:59157923A>G	ENST00000390652.5	+	22	2403				BCAS3_ENST00000589222.1_Intron|BCAS3_ENST00000585744.1_Intron|BCAS3_ENST00000588462.1_Intron|BCAS3_ENST00000407086.3_Intron|BCAS3_ENST00000408905.3_Intron|BCAS3_ENST00000588874.1_Intron	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3	NA		NA								NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ggccaacatgatgaaacccca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376	54828		WD repeat domain containing	14347	protein-coding gene	gene with protein product		607470			NA	12378525	Standard	NM_017679	NM_017679	NA	Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2372+2033A>G	chr17.hg19:g.59157923A>G		NA		hg19	CCDS45749.1	0.02	-0.05263	ATGxTGA	UNCOVERED																																																																																			NOVEL	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449578.1	1	2.40502	KEEP	2	0	0	8	211	AA	0	0	0		+	2	60	70	0	0	6.493022	3	60	91	20	ENST00000390652.5	0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	59616953	59616953	__UNKNOWN__	IGR	SNP	C	C	T	rs12948222	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:59616953C>T			NA	NA				TBX4 (54482 upstream) : NACA2 (50840 downstream)						NA		NA									NA						gctgggattacaggcatgcgc	0.463		NA											C|||	1651	0.329673	0.0893	0.5749	5008	,	,	NA	18065	0.1042	NA	0.5616	False	NA	,,,	NA	NA	NA	2504	0.4744	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.59616953C>T		NA		hg19		0.02	-0.035086	TTAxAGG	UNCOVERED																																																																																			NOVEL					0			3	2.407119	KEEP	1	0	0	8	242	CC	0	0	0			3	60	92	0	0	10.630197	0	0	0	17		1	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	59670341	59670341	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:59670341G>A			NA	NA				NACA2 (1778 upstream) : BRIP1 (88285 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.59670341G>A		NA		hg19		0.02	-0.148382	CACxCCT	UNCOVERED																																																																																			NOVEL					0			6	2.707776	KEEP	2	0	0	9	269	GG	0	0	0			3	60	84	0	0	6.682733	11	60	328	39		0.214286	0.292001
BRIP1	83990	__UNKNOWN__	__UNKNOWN__	17	59867655	59867655	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:59867655T>C	ENST00000259008.2	-	10	1741				BRIP1_ENST00000577598.1_Intron	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	NA		NA			DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						cctgtaatcctagcactttgg	0.453		NA	F, N, Mis			AML, leukemia, breast		Involved in tolerance or repair of DNA crosslinks													NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec		Fanconi anaemia J, breast cancer susceptiblity	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		L, E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492	83990		Fanconi anemia, complementation groups	20473	protein-coding gene	gene with protein product	BRCA1/BRCA2-associated helicase 1	605882			NA	11595410, 11301010	Standard	NM_032043	NM_032043	NA	Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.1473+3302A>G	chr17.hg19:g.59867655T>C		NA	Q3MJE2|Q8NCI5	hg19	CCDS11631.1	0.02	-0.052631	TCCxAGC	UNCOVERED																																																																																			NOVEL	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000445362.1	3	3.308258	KEEP	1	0	0	11	303	TT	0.992708	0.036498	0		-	2	60	70	0	0	6.750224	2	60	60	25	ENST00000259008.2	0.5	0.036766
INTS2	57508	__UNKNOWN__	__UNKNOWN__	17	59979159	59979159	__UNKNOWN__	Intron	SNP	G	G	A	rs548611135		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:59979159G>A	ENST00000251334.6	-	9	1663				INTS2_ENST00000444766.3_Intron			Q9H0H0	INT2_HUMAN	integrator complex subunit 2	NA		NA			snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						gggtttcaccgtgttagccag	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506	57508			29241	protein-coding gene	gene with protein product		611346	KIAA1287	KIAA1287	NA	16239144	Standard	NM_020748	NR_026641	NA	Approved	INT2	uc002izn.3	Q9H0H0		ENST00000251334.6:c.1307+2661C>T	chr17.hg19:g.59979159G>A		NA	Q9ULD3	hg19		0.02	-0.394692	ACCxTGT	COVERED																																																																																			NOVEL	INTS2-002	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000445369.1	68	3.803098	KEEP	44	3	83	42	1151	GG	0.999997	0.93449	0		-	4	49	119	2	0	8.634461	27	60	835	155	ENST00000251334.6	0.129032	0.934492
INTS2	57508	__UNKNOWN__	__UNKNOWN__	17	59979228	59979228	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:59979228G>A	ENST00000251334.6	-	9	1663				INTS2_ENST00000444766.3_Intron			Q9H0H0	INT2_HUMAN	integrator complex subunit 2	NA		NA			snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						caaagtgctgggattacaggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506	57508			29241	protein-coding gene	gene with protein product		611346	KIAA1287	KIAA1287	NA	16239144	Standard	NM_020748	NR_026641	NA	Approved	INT2	uc002izn.3	Q9H0H0		ENST00000251334.6:c.1307+2592C>T	chr17.hg19:g.59979228G>A		NA	Q9ULD3	hg19		0.02	-0.368437	CTGxGAT	COVERED																																																																																			NOVEL	INTS2-002	NOVEL	basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000445369.1	61	9.747565	KEEP	33	1	24	41	1209	GG	0.999997	0.899312	0		-	4	39	120	1	0	8.923465	24	60	812	140	ENST00000251334.6	0.142857	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	60016998	60016998	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:60016998C>T			NA	NA				INTS2 (11621 upstream) : MED13 (2967 downstream)						NA		NA									NA						tggtggctcacgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.60016998C>T		NA		hg19		0.02	-0.140336	TCAxGCC	COVERED																																																																																			NOVEL					0			4	3.007692	KEEP	0	0	0	10	286	CC	0.992708	0.259062	0			3	60	91	0	0	7.37303	11	60	346	41		0.214286	0.260965
EFCAB3	146779	__UNKNOWN__	__UNKNOWN__	17	60493752	60493752	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:60493752G>T	ENST00000305286.3	+	0	1457				EFCAB3_ENST00000450662.2_3'UTR	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	NA		NA					calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			CAAAATTATTGTTTCTTGCTT	0.289		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421	146779		EF-hand domain containing	26379	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173503	NM_173503	NA	Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.*62G>T	chr17.hg19:g.60493752G>T		NA	J3KQM8	hg19	CCDS11632.1	0.02	-0.368436	ATTxTTT	COVERED																																																																																			NOVEL	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379114.1	4	4.813394	KEEP	2	0	0	16	480	GG	0.99649	0.896158	0		+	4	60	111	0	0	7.322638	37	60	1278	78	ENST00000305286.3	0.097561	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	61690802	61690802	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:61690802G>A			NA	NA				TACO1 (5077 upstream) : MAP3K3 (8972 downstream)						NA		NA									NA						cagcctgggcgacagagcaag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.61690802G>A		NA		hg19		0.02	-0.08772	GGCxACA	UNCOVERED																																																																																			NOVEL					0			4	2.406774	KEEP	1	0	0	8	237	GG	0	0	0			3	60	91	0	0	8.043236	6	60	203	26		0.333333	0.099721
MAP3K3	4215	__UNKNOWN__	__UNKNOWN__	17	61737831	61737831	__UNKNOWN__	Intron	SNP	G	G	C	rs545805704		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:61737831G>C	ENST00000577395.1	+	5	431				MAP3K3_ENST00000579585.1_Intron|MAP3K3_ENST00000361733.3_Intron|MAP3K3_ENST00000584573.1_Intron|MAP3K3_ENST00000361357.3_Intron			Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	NA		NA			activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)			breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						tctcagcctcgcaaagtgctg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909	4215		Mitogen-activated protein kinase cascade / Kinase kinase kinases	6855	protein-coding gene	gene with protein product	MAP/ERK kinase kinase 3, MAPK/ERK kinase kinase 3	602539		MEKK3	NA	9006902	Standard	NM_002401	NM_002401	NA	Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000577395.1:c.381+2564G>C	chr17.hg19:g.61737831G>C		NA	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	hg19		0.02	-0.149129	CTCxCAA	COVERED																																																																																			NOVEL	MAP3K3-005	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000443869.1	9	3.610233	KEEP	0	0	0	12	354	GG	0.993634	0.290142	0		+	3	57	104	0	0	8.571969	12	60	389	38	ENST00000577395.1	0.2	0.292001
MAP3K3	4215	__UNKNOWN__	__UNKNOWN__	17	61737839	61737839	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:61737839C>T	ENST00000577395.1	+	5	431				MAP3K3_ENST00000579585.1_Intron|MAP3K3_ENST00000361733.3_Intron|MAP3K3_ENST00000584573.1_Intron|MAP3K3_ENST00000361357.3_Intron			Q99759	M3K3_HUMAN	mitogen-activated protein kinase kinase kinase 3	NA		NA			activation of MAPKK activity (GO:0000186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)			breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	28						tcgcaaagtgctgggattaca	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U78876	CCDS32701.1, CCDS32702.1	17q	2011-06-09				ENSG00000198909	4215		Mitogen-activated protein kinase cascade / Kinase kinase kinases	6855	protein-coding gene	gene with protein product	MAP/ERK kinase kinase 3, MAPK/ERK kinase kinase 3	602539		MEKK3	NA	9006902	Standard	NM_002401	NM_002401	NA	Approved	MAPKKK3	uc002jbf.3	Q99759		ENST00000577395.1:c.381+2572C>T	chr17.hg19:g.61737839C>T		NA	B2RCW2|D3DU15|Q5BKZ6|Q8N3I9	hg19		0.02	-0.157888	GTGxTGG	COVERED																																																																																			NOVEL	MAP3K3-005	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000443869.1	10	3.911643	KEEP	0	0	0	13	403	CC	0.994391	0.320996	0		+	3	57	84	0	0	6.479323	13	60	440	40	ENST00000577395.1	0.1875	0.322807
STRADA	92335	__UNKNOWN__	__UNKNOWN__	17	61798199	61798199	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:61798199G>A	ENST00000582137.1	-	3	136				STRADA_ENST00000245865.5_Intron|STRADA_ENST00000336174.6_Intron|RP11-51F16.8_ENST00000580553.1_Intron|STRADA_ENST00000375840.4_Intron|STRADA_ENST00000447001.3_Intron|STRADA_ENST00000580039.1_Intron|STRADA_ENST00000579340.1_Intron|STRADA_ENST00000392950.4_Intron			Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	NA		NA			activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						gctcacgcctgtaatcccagc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173	92335			30172	protein-coding gene	gene with protein product	STE20-like pseudokinase	608626			NA	12805220, 17921699	Standard		NM_153335	NA	Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000582137.1:c.37-6731C>T	chr17.hg19:g.61798199G>A		NA	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	hg19	CCDS58585.1	0.02	-0.184192	CCTxTAA	COVERED																																																																																			NOVEL	STRADA-006	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000443897.1	8	3.309116	KEEP	4	0	0	11	324	GG	0.99254	0.420319	0		-	4	54	100	0	0	7.470541	17	60	588	50	ENST00000582137.1	0.190476	0.423478
DDX42	11325	__UNKNOWN__	__UNKNOWN__	17	61880696	61880696	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:61880696T>C	ENST00000578681.1	+	8	1222				DDX42_ENST00000583590.1_Intron|DDX42_ENST00000359353.5_Intron|DDX42_ENST00000457800.2_Intron|DDX42_ENST00000389924.2_Intron	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	NA		NA			protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						tgcctgtaattccagcacttt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231	11325		DEAD-boxes	18676	protein-coding gene	gene with protein product	splicing factor 3b, subunit 8	613369	DEAD (Asp-Glu-Ala-Asp) box polypeptide 42		NA	10727850, 16397294	Standard	NM_007372	NM_007372	NA	Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.622-1735T>C	chr17.hg19:g.61880696T>C		NA	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	hg19	CCDS32704.1	0.02	-0.114022	AATxCCA	UNCOVERED																																																																																			NOVEL	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444368.1	7	3.308616	KEEP	0	0	0	11	307	TT	0.993072	0.161341	0		+	3	60	107	0	0	9.201281	9	60	264	32	ENST00000578681.1	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	62210553	62210553	__UNKNOWN__	IGR	SNP	G	G	A	rs113715096	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62210553G>A			NA	NA				ERN1 (2374 upstream) : SNORD104 (12889 downstream)						NA		NA									NA						tgaggtgggaggatggcttga	0.468		NA											g|||	127	0.0253594	0.0008	0.0389	5008	,	,	NA	19521	0.0089	NA	0.0596	False	NA	,,,	NA	NA	NA	2504	0.0307	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.62210553G>A		NA		hg19		0.02	-0.087712	GGAxGAT	UNCOVERED																																																																																			NOVEL					0			3	2.406228	KEEP	0	0	0	8	233	GG	0.99257	0.09898	0			4	60	128	0	0	11.785735	6	60	197	26		0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	62393450	62393450	__UNKNOWN__	IGR	SNP	C	C	T	rs553784579		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62393450C>T			NA	NA				TEX2 (52789 upstream) : MILR1 (68118 downstream)						NA		NA									NA						AACAACAggccgggcgcggtg	0.542		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16305	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.62393450C>T		NA		hg19		0.02	-0.140346	GGCxGGG	COVERED																																																																																			NOVEL					0			4	2.4064	KEEP	0	0	0	8	229	CC	0.99257	0.259026	0			3	60	92	0	0	7.581897	10	60	322	32		0.230769	0.260965
POLG2	11232	__UNKNOWN__	__UNKNOWN__	17	62489342	62489342	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62489342A>C	ENST00000539111.2	-	2	630					NM_007215.3	NP_009146.2	Q9UHN1	DPOG2_HUMAN	polymerase (DNA directed), gamma 2, accessory subunit	NA		NA			DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)	extracellular vesicular exosome (GO:0070062)|mitochondrial chromosome (GO:0000262)|mitochondrial nucleoid (GO:0042645)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(4)|skin(2)|stomach(1)|urinary_tract(1)	15	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;4.97e-11)			ctgagaccagactgggcaaca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(3;18 21 435 17652 48887)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U94703	CCDS32706.1	17q23.3	2012-05-18			ENSG00000256525	ENSG00000256525	11232		DNA polymerases	9180	protein-coding gene	gene with protein product		604983			NA	9153213	Standard	NM_007215	NM_007215	NA	Approved	MTPOLB, HP55	uc002jei.3	Q9UHN1		ENST00000539111.2:c.563-204T>G	chr17.hg19:g.62489342A>C		NA	O00419|Q0IJ81|Q96GW2|Q9UK35|Q9UK94	hg19	CCDS32706.1	0.02	-0.184166	CAGxCTG	COVERED																																																																																			NOVEL	POLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000443820.1	12	2.40542	KEEP	0	0	0	8	213	AA	0.99257	0.420331	0		-	3	60	103	0	0	8.133421	16	60	458	39	ENST00000539111.2	0.157895	0.423478
SMURF2	64750	__UNKNOWN__	__UNKNOWN__	17	62584854	62584854	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62584854T>C	ENST00000262435.9	-	5	588				SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	NA		NA			BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			tctcctgccttagcctcctga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854	64750			16809	protein-coding gene	gene with protein product		605532			NA	11016919	Standard	NM_022739	XM_005257585	NA	Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.400+2347A>G	chr17.hg19:g.62584854T>C		NA	Q52LL1|Q9H260	hg19	CCDS32707.1	0.02	-0.043853	CCTxAGC	UNCOVERED																																																																																			NOVEL	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000445227.1	4	2.705778	KEEP	0	0	0	9	233	TT	0.99254	0.023894	0		-	2	60	69	0	0	6.393134	3	60	85	19	ENST00000262435.9	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	62925197	62925197	__UNKNOWN__	IGR	SNP	G	G	A	rs113451961		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62925197G>A			NA	NA				LRRC37A3 (9611 upstream) : RP11-583F2.1 (1069 downstream)						NA		NA									NA						ctgggtacgggggctcacacc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.62925197G>A		NA		hg19		0.02	-0.140354	CGGxGGC	COVERED																																																																																			NOVEL					0			5	2.708269	KEEP	0	0	0	9	282	GG	0.992708	0.289872	0			8	60	250	0	0	23.999132	8	60	273	38		0.5	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	62973872	62973872	__UNKNOWN__	IGR	SNP	T	T	G	rs9903374		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62973872T>G			NA	NA				AMZ2P1 (2186 upstream) : GNA13 (32960 downstream)						NA		NA									NA						AGttttttttttttttttttt	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.62973872T>G		NA		hg19		0.02	-0.043858	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			8	2.702659	KEEP	4	0	0	9	215	TT	0	0	0			2	60	70	0	0	7.95396	0	0	0	16		1	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	62973875	62973875	__UNKNOWN__	IGR	SNP	T	T	G	rs9903377		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:62973875T>G			NA	NA				AMZ2P1 (2189 upstream) : GNA13 (32957 downstream)						NA		NA									NA						ttttttttttttttttttttt	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.62973875T>G		NA		hg19		0.02	-0.043853	TTTxTTT	UNCOVERED																																																																																			NOVEL					0			8	2.705063	KEEP	4	0	0	9	229	TT	0	0	0			2	60	70	0	0	7.95396	0	0	0	16		1	0.024074
CEP112	201134	__UNKNOWN__	__UNKNOWN__	17	63920374	63920374	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:63920374A>G	ENST00000392769.2	-	19	2199				CEP112_ENST00000541355.1_Intron|CEP112_ENST00000537949.1_Intron|CEP112_ENST00000535342.2_Intron	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	NA		NA			receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						gattacaggcatgagccaccg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240	201134			28514	protein-coding gene	gene with protein product		NA	coiled-coil domain containing 46	CCDC46	NA	21399614	Standard	NM_145036	NM_145036	NA	Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1980+3325T>C	chr17.hg19:g.63920374A>G		NA	Q6PIB5|Q8NCR4|Q8NFR4	hg19	CCDS32710.1	0.02	-0.114023	GGCxTGA	UNCOVERED																																																																																			NOVEL	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000446582.1	1	2.406038	KEEP	2	0	0	8	220	AA	0	0	0		-	3	60	90	0	0	7.943415	6	60	180	36	ENST00000392769.2	0.333333	0.162467
PRKCA	5578	__UNKNOWN__	__UNKNOWN__	17	64795332	64795332	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:64795332A>G	ENST00000413366.3	+	17	1880					NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	NA		NA			activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	ggtggtggtgatggtggtggt	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	5578	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA	NA		Standard		NM_002737	NA	Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1855-4659A>G	chr17.hg19:g.64795332A>G		NA	B5BU22|Q15137|Q32M72|Q96RE4	hg19	CCDS11664.1	0.02	-0.358231	GTGxTGG	COVERED																																																																																			NOVEL	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000446976.1	23	3.505668	KEEP	41	2	57	32	746	AA	0.999859	0.88875	0		+	3	21	93	2	1	6.874693	20	40	453	155	ENST00000413366.3	0.130435	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	65255429	65255429	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:65255429C>T			NA	NA				RP11-401F2.3 (13507 upstream) : RNA5SP447 (8796 downstream)						NA		NA									NA						tttgggaggacgaggcaggcg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.65255429C>T		NA		hg19		0.02	-0.13158	GGAxGAG	COVERED																																																																																			NOVEL					0			5	2.406793	KEEP	0	0	0	8	237	CC	0.99257	0.22747	0			3	60	88	0	0	7.300924	9	60	305	33		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	66051325	66051325	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:66051325C>T			NA	NA				KPNA2 (8367 upstream) : AC145343.2 (40861 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.66051325C>T		NA		hg19		0.02	-0.070165	AGGxGTG	UNCOVERED																																																																																			NOVEL					0			8	4.184065	KEEP	2	0	0	14	380	CC	0.993634	0.053793	0			3	45	91	0	0	8.232846	5	60	155	28		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	66081591	66081591	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:66081591A>G			NA	NA				KPNA2 (38633 upstream) : AC145343.2 (10595 downstream)						NA		NA									NA						tgcctgcctcagcctcccaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.66081591A>G		NA		hg19		0.02	-0.166653	CTCxGCC	COVERED																																																																																			NOVEL					0			6	2.707237	KEEP	1	0	0	9	255	AA	0.99257	0.351317	0			3	60	95	0	0	7.672259	12	60	369	40		0.2	0.353947
ARSG	22901	__UNKNOWN__	__UNKNOWN__	17	66397381	66397381	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:66397381T>C	ENST00000448504.2	+	11	2008				ARSG_ENST00000452479.2_Intron|ARSG_ENST00000582154.1_Intron	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	NA		NA			cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ccaggctggtttcaaactcct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337	22901		Arylsulfatase family	24102	protein-coding gene	gene with protein product		610008			NA	12461688, 16174644	Standard	NM_014960	NM_014960	NA	Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.1213-120T>C	chr17.hg19:g.66397381T>C		NA	Q6UXF2|Q9Y2K4	hg19	CCDS11676.1	0.02	-0.263087	GGTxTCA	COVERED																																																																																			NOVEL	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000448369.1	9	3.739547	KEEP	0	1	33	24	635	TT	0.999931	0.69362	0		+	3	60	98	0	0	7.044617	26	60	744	70	ENST00000448504.2	0.103448	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	68388045	68388045	__UNKNOWN__	IGR	SNP	G	G	A	rs529054120		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:68388045G>A			NA	NA				CTD-2378E21.1 (22988 upstream) : RP11-238F2.1 (386699 downstream)						NA		NA									NA						cgcccgcctcggcctcccaaa	0.468		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15255	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.68388045G>A		NA		hg19		0.02	-0.096493	CTCxGCC	UNCOVERED																																																																																			NOVEL					0			11	2.707108	KEEP	5	0	0	9	260	GT	0.99257	0.119541	0			3	40	93	0	0	8.078406	7	60	231	33		0.3	0.120436
C17orf80	55028	__UNKNOWN__	__UNKNOWN__	17	71229819	71229819	__UNKNOWN__	Intron	SNP	A	A	G	rs9910657	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:71229819A>G	ENST00000535032.2	+	1	106				C17orf80_ENST00000268942.8_Intron|C17orf80_ENST00000426147.2_Intron|C17orf80_ENST00000577615.1_Intron|FAM104A_ENST00000583178.1_Intron|C17orf80_ENST00000255557.4_Intron|C17orf80_ENST00000582793.1_Intron|C17orf80_ENST00000359042.2_Intron			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	NA		NA				extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			cctggccaacatggtgaaacc	0.602		NA											A|||	2460	0.491214	0.3835	0.487	5008	,	,	NA	16915	0.6379	NA	0.5586	False	NA	,,,	NA	NA	NA	2504	0.4192	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219	55028			29601	protein-coding gene	gene with protein product	sperm-expressed protein 1, migration-inducing protein 3	NA			NA	12477932	Standard	NM_017941	NM_017941	NA	Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.-8+355A>G	chr17.hg19:g.71229819A>G		NA	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	hg19	CCDS11694.1	0.02	-0.078935	AACxTGG	UNCOVERED																																																																																			NOVEL	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000441893.1	5	3.00573	KEEP	3	0	0	10	254	AA	0	0	0		+	5	60	157	0	0	15.787181	3	60	83	23	ENST00000535032.2	0.625	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	71261420	71261420	__UNKNOWN__	IGR	SNP	G	G	A	rs569752867	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:71261420G>A			NA	NA				CPSF4L (2929 upstream) : CDC42EP4 (18342 downstream)						NA		NA									NA						caggagaatcgcttgaaccca	0.458		NA											G|||	3	0.000599042	0.0023	0.0	5008	,	,	NA	13862	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.71261420G>A		NA		hg19		0.02	-0.105267	ATCxCTT	UNCOVERED																																																																																			NOVEL					0			7	3.610251	KEEP	0	0	0	12	354	GG	0.993634	0.138942	0			3	60	92	0	0	7.832201	8	60	270	33		0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	71654542	71654542	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:71654542A>G			NA	NA				SDK2 (14314 upstream) : RP11-277J6.3 (4164 downstream)						NA		NA									NA						gtgagccaccatgcccggccC	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.71654542A>G		NA		hg19		0.02	-0.070169	ACCxTGC	UNCOVERED																																																																																			NOVEL					0			6	3.006813	KEEP	0	0	0	10	267	AA	0.992708	0.053742	0			2	60	71	0	0	6.395888	4	60	119	26		0.333333	0.054137
TTYH2	94015	__UNKNOWN__	__UNKNOWN__	17	72255574	72255574	__UNKNOWN__	Intron	SNP	G	G	A	rs35589411	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:72255574G>A	ENST00000269346.4	+	14	1598				CTD-2514K5.4_ENST00000583018.1_RNA|TTYH2_ENST00000441391.2_Intron|TTYH2_ENST00000529107.1_Intron	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	NA		NA				chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						ggctggtctcgaactcctggg	0.468		NA											G|||	427	0.0852636	0.0204	0.1326	5008	,	,	NA	17919	0.0446	NA	0.1421	False	NA	,,,	NA	NA	NA	2504	0.1227	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540	94015			13877	protein-coding gene	gene with protein product		608855	tweety (Drosophila) homolog 2, tweety homolog 2 (Drosophila)		NA	11597145	Standard		XM_005257824	NA	Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1525-694G>A	chr17.hg19:g.72255574G>A		NA	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	hg19	CCDS32717.1	0.02	-0.035003	CTCxAAC	UNCOVERED																																																																																			NOVEL	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000387459.1	7	2.406414	KEEP	0	0	0	8	231	GG	0.99257	0.019833	0		+	4	60	101	0	0	11.994976	0	0	0	16	ENST00000269346.4	1	0.019982
DNAI2	64446	__UNKNOWN__	__UNKNOWN__	17	72295908	72295908	__UNKNOWN__	Missense_Mutation	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:72295908A>T	ENST00000311014.6	+	7	843	c.776A>T	c.(775-777)gAg>gTg	p.E259V	DNAI2_ENST00000307504.5_Missense_Mutation_p.E116V|DNAI2_ENST00000582036.1_Missense_Mutation_p.E259V|DNAI2_ENST00000446837.2_Missense_Mutation_p.E259V|DNAI2_ENST00000579490.1_Missense_Mutation_p.E316V			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	259		NA			cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TCCACCATTGAGTCCAGCCAC	0.617		NA							Kartagener syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													71	56	61			NA	NA	17		NA											NA				72295908		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595	64446		Axonemal dyneins, WD repeat domain containing	18744	protein-coding gene	gene with protein product	dynein intermediate chain 2	605483	dynein, axonemal, intermediate polypeptide 2		NA	11153919, 21953912	Standard	NM_023036	NM_023036	NA	Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.776A>T	chr17.hg19:g.72295908A>T	ENSP00000308312:p.Glu259Val	NA	C9J0S6|Q8IUW4|Q9H179|Q9NT53	hg19	CCDS11697.1	0.02	1.449997	TTGxGTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	26.2	4.716241	0.89205	.	.	ENSG00000171595	ENST00000311014;ENST00000307504;ENST00000446837	D;D;D	0.85861	-2.04;-2.04;-2.04	5.03	5.03	0.67393	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.93638	0.7968	M	0.92555	3.32	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	D	0.95005	0.8146	10	0.72032	D	0.01	-37.9913	14.4819	0.67590	1.0:0.0:0.0:0.0	.	259	Q9GZS0	DNAI2_HUMAN	V	259;116;259	ENSP00000308312:E259V;ENSP00000302929:E116V;ENSP00000400252:E259V	ENSP00000302929:E116V	E	+	2	0	DNAI2	69807503	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	8.916000	0.92745	1.897000	0.54924	0.363000	0.22086	GAG	NOVEL	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442537.1	0	3.910282	KEEP	0	0	0	13	364	AA	0.994391	0.9923	0		+	31	60	913	0	0	84.471741	42	60	1271	123	ENST00000311014.6	0.424658	0.997898
DNAI2	64446	__UNKNOWN__	__UNKNOWN__	17	72298209	72298209	__UNKNOWN__	Intron	SNP	A	A	G	rs201832227		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:72298209A>G	ENST00000311014.6	+	8	1054				DNAI2_ENST00000307504.5_Intron|DNAI2_ENST00000582036.1_Intron|DNAI2_ENST00000446837.2_Intron|DNAI2_ENST00000579490.1_Intron			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	NA		NA			cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						aaggaaggaaagaaggaagga	0.473		NA							Kartagener syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595	64446		Axonemal dyneins, WD repeat domain containing	18744	protein-coding gene	gene with protein product	dynein intermediate chain 2	605483	dynein, axonemal, intermediate polypeptide 2		NA	11153919, 21953912	Standard	NM_023036	NM_023036	NA	Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.987+902A>G	chr17.hg19:g.72298209A>G		NA	C9J0S6|Q8IUW4|Q9H179|Q9NT53	hg19	CCDS11697.1	0.02	-0.105249	GAAxGAA	UNCOVERED																																																																																			NOVEL	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442537.1	12	2.706022	KEEP	18	0	0	9	237	AA	0	0	0		+	3	60	95	0	0	8.632959	5	42	147	39	ENST00000311014.6	0.375	0.139832
CDR2L	30850	__UNKNOWN__	__UNKNOWN__	17	72995408	72995408	__UNKNOWN__	Intron	SNP	C	C	G	rs370557228|rs200504893		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:72995408C>G	ENST00000337231.5	+	2	491					NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	NA		NA									NA	all_lung(278;0.226)					cacacacacacacagacacac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11710.2	17q25.1	2006-03-28			ENSG00000109089	ENSG00000109089	30850			29999	protein-coding gene	gene with protein product	paraneoplastic antigen	NA			NA		Standard	NM_014603	NM_014603	NA	Approved	HUMPPA	uc002jml.4	Q86X02	OTTHUMG00000150435	ENST00000337231.5:c.80-191C>G	chr17.hg19:g.72995408C>G		NA	B4DFA7|Q15175	hg19	CCDS11710.2	0.02	1.508652	ACAxACA	COVERED																																																																																			NOVEL	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318080.1	3	3.441813	KEEP	0	1	27	21	607	CC	0.999879	0.979408	0		+	6	60	174	2	0	12.139906	47	60	1542	89	ENST00000337231.5	0.113208	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	73017808	73017808	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:73017808A>G			NA	NA				ICT1 (452 upstream) : RNU6-362P (9383 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.73017808A>G		NA		hg19		0.02	-0.175354	CACxCCT	COVERED																																																																																			NOVEL					0			3	3.304156	KEEP	1	0	0	11	273	AA	0.992708	0.384582	0			3	60	92	0	0	7.111109	15	60	398	43		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	73066838	73066838	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:73066838G>A			NA	NA				KCTD2 (4859 upstream) : SLC16A5 (16983 downstream)						NA		NA									NA						ctcaaaaaaagaaaaaaatat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.73066838G>A		NA		hg19		0.02	-0.096486	AAAxAAA	UNCOVERED																																																																																			NOVEL					0			6	2.707976	KEEP	0	0	0	9	273	GG	0.99254	0.119538	0			3	60	84	1	0	7.178146	7	60	233	24		0.3	0.120436
NUP85	79902	__UNKNOWN__	__UNKNOWN__	17	73212649	73212649	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:73212649C>T	ENST00000579298.1	+	6	517				NUP85_ENST00000449421.2_Intron|NUP85_ENST00000541827.1_Intron|NUP85_ENST00000245544.4_Intron|NUP85_ENST00000579324.1_Intron|NUP85_ENST00000447371.2_Intron			Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	NA		NA			carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			tgtgagccaccgtgcccagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450	79902			8734	protein-coding gene	gene with protein product		170285			NA	8124707	Standard	NM_024844	XM_005257690	NA	Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000579298.1:c.475+731C>T	chr17.hg19:g.73212649C>T		NA	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	hg19		0.02	-0.035087	CACxGTG	UNCOVERED																																																																																			NOVEL	NUP85-004	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446625.1	2	2.707076	KEEP	0	0	0	9	255	CC	0.99254	0.019833	0		+	2	60	62	0	0	6.324546	1	60	32	19	ENST00000579298.1	0.666667	0.019982
GRB2	2885	__UNKNOWN__	__UNKNOWN__	17	73326517	73326517	__UNKNOWN__	Intron	SNP	T	T	C	rs542000251		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:73326517T>C	ENST00000578961.1	-	2	351				GRB2_ENST00000392564.1_Intron|GRB2_ENST00000316615.5_Intron|GRB2_ENST00000392562.1_Intron|GRB2_ENST00000316804.5_Intron|GRB2_ENST00000392563.1_Intron			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	NA		NA			aging (GO:0007568)|anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to ionizing radiation (GO:0071479)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of MAPK cascade (GO:0043408)|signal transduction in response to DNA damage (GO:0042770)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Grb2-EGFR complex (GO:0070436)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|identical protein binding (GO:0042802)|insulin receptor substrate binding (GO:0043560)|neurotrophin TRKA receptor binding (GO:0005168)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	17	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)	tgcggtggcttacacctgtaa	0.498		NA											T|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	19854	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11721.1, CCDS11722.1	17q24-q25	2013-02-14			ENSG00000177885	ENSG00000177885	2885		SH2 domain containing	4566	protein-coding gene	gene with protein product		108355			NA		Standard		NM_002086	NA	Approved	NCKAP2	uc002jnx.4	P62993	OTTHUMG00000134332	ENST00000578961.1:c.176+2263A>G	chr17.hg19:g.73326517T>C		NA	P29354|Q14450|Q63057|Q63059	hg19		0.02	-0.175371	GCTxACA	COVERED																																																																																			NOVEL	GRB2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447295.1	7	5.110509	KEEP	0	0	0	17	441	TT	0.999366	0.387161	0		-	3	60	99	0	0	7.892256	14	60	388	52	ENST00000578961.1	0.176471	0.387407
TSEN54	283989	__UNKNOWN__	__UNKNOWN__	17	73515693	73515693	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:73515693T>G	ENST00000333213.6	+	6	557				TSEN54_ENST00000580013.1_Intron	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	NA		NA			mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			gcccaggctgtagtgcagtgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173	283989		tRNA splicing endonuclease subunits	27561	protein-coding gene	gene with protein product		608755	tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae), tRNA splicing endonuclease 54 homolog (S. cerevisiae)		NA	15109492	Standard	NM_207346	NM_207346	NA	Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.521+565T>G	chr17.hg19:g.73515693T>G		NA	Q86WV3|Q86XE4|Q8N9H2	hg19	CCDS11724.1	0.02	-0.043854	CTGxAGT	UNCOVERED																																																																																			NOVEL	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447618.1	2	2.705038	KEEP	0	0	0	9	228	TT	0.99254	0.023894	0		+	2	60	73	0	0	6.793178	3	60	84	21	ENST00000333213.6	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74069577	74069577	__UNKNOWN__	IGR	SNP	A	A	G	rs62090094		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:74069577A>G			NA	NA				SRP68 (843 upstream) : GALR2 (1297 downstream)						NA		NA									NA						gggtttcaccatgttggtcag	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74069577A>G		NA		hg19		0.02	-0.061389	ACCxTGT	UNCOVERED																																																																																			NOVEL					0			9	2.705823	KEEP	9	0	0	9	243	AA	0	0	0			4	40	125	0	0	12.33266	3	42	83	22		0.571429	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74559818	74559818	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:74559818A>T			NA	NA				SNHG16 (2031 upstream) : ST6GALNAC2 (1642 downstream)						NA		NA									NA						ttttttttttaacattttata	0.294		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74559818A>T		NA		hg19		0.02	1.267575	TTTxACA	COVERED																																																																																			NOVEL					0			26	4.899675	KEEP	1	7	176	79	1995	AA	1	0.987943	0			5	40	139	0	0	9.103562	48	60	1297	196		0.09434	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74560475	74560475	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:74560475A>G			NA	NA				SNHG16 (2688 upstream) : ST6GALNAC2 (985 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74560475A>G		NA		hg19		0.02	-0.219125	GCTxGGA	COVERED																																																																																			NOVEL					0			9	3.23808	KEEP	11	1	29	21	552	AA	0.99649	0.550947	0			5	60	171	0	0	14.154717	19	60	549	63		0.208333	0.552887
ST6GALNAC1	55808	__UNKNOWN__	__UNKNOWN__	17	74625904	74625904	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:74625904A>G	ENST00000156626.7	-	2	331				ST6GALNAC1_ENST00000590878.1_Intron	NM_018414.3	NP_060884.1	Q9NSC7	SIA7A_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1	NA		NA			oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	22						ttgctctgtcacccaggctgg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y11339	CCDS11748.1	17q25.3	2013-03-01	2005-02-07	2005-02-07	ENSG00000070526	ENSG00000070526	55808		Sialyltransferases	23614	protein-coding gene	gene with protein product		610138	sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) A	SIAT7A	NA		Standard	NM_018414	NM_001289107	NA	Approved	ST6GalNAcI	uc002jsh.3	Q9NSC7	OTTHUMG00000180369	ENST00000156626.7:c.132-111T>C	chr17.hg19:g.74625904A>G		NA	Q6UW90|Q9NSC6	hg19	CCDS11748.1	0.02	-0.219132	GTCxCCC	COVERED																																																																																			NOVEL	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450974.1	4	6.308349	KEEP	1	0	0	21	507	AA	0.999863	0.552812	0		-	3	60	99	0	0	7.465819	20	60	522	53	ENST00000156626.7	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	74812224	74812224	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:74812224C>A			NA	NA				CTD-2246P4.1 (10189 upstream) : LINC00868 (34033 downstream)						NA		NA									NA						cacgcctgtactcccagcact	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.74812224C>A		NA		hg19		0.02	-0.192968	GTAxTCC	COVERED																																																																																			NOVEL					0			6	3.309969	KEEP	0	0	0	11	341	CC	0.993072	0.454585	0			4	60	114	0	0	9.06279	15	60	492	47		0.210526	0.457757
SEC14L1	6397	__UNKNOWN__	__UNKNOWN__	17	75108795	75108795	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:75108795A>G	ENST00000392476.2	+	3	424				SEC14L1_ENST00000430767.4_Intron	NM_001204408.1	NP_001191337	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	NA		NA			transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						gtgaaaccccatctctactaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657	6397			10698	protein-coding gene	gene with protein product		601504	SEC14 (S. cerevisiae)-like 1	SEC14L	NA	8697811	Standard	NM_003003	NM_001143998	NA	Approved	PRELID4A	uc002jto.3	Q92503		ENST00000392476.2:c.-136+19366A>G	chr17.hg19:g.75108795A>G		NA	A8K4E8|B4DDI5|D5G3K1|Q99780	hg19	CCDS42385.1	0.02	-0.113956	CCCxTCT	UNCOVERED																																																																																			NOVEL	SEC14L1-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000436239.1	5	3.302613	KEEP	5	0	0	11	262	AA	0.99254	0.161255	0		+	3	40	90	0	0	7.383028	10	60	267	34	ENST00000392476.2	0.230769	0.162467
SEPT9	10801	__UNKNOWN__	__UNKNOWN__	17	75460955	75460955	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:75460955A>G	ENST00000423034.2	+	3	1008				SEPT9_ENST00000592481.1_Intron|SEPT9_ENST00000588690.1_Intron|SEPT9_ENST00000541152.2_Intron|SEPT9_ENST00000431235.2_Intron|SEPT9_ENST00000427674.2_Intron|SEPT9_ENST00000329047.8_Intron|SEPT9_ENST00000449803.2_Intron|SEPT9_ENST00000427177.1_Intron|SEPT9_ENST00000590294.1_Intron|SEPT9_ENST00000585930.1_Intron|SEPT9_ENST00000590917.1_Intron|SEPT9_ENST00000592951.1_Intron|SEPT9_ENST00000591088.1_Intron|SEPT9_ENST00000591198.1_Intron|SEPT9_ENST00000592420.1_Intron	NM_001113493.1	NP_001106965.1	Q9UHD8	SEPT9_HUMAN	septin 9	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			gattacaggcatgagccactg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640	10801		Septins	7323	protein-coding gene	gene with protein product	Ov/Br septin	604061	MLL septin-like fusion	MSF	NA	10339604, 10485469	Standard	NM_006640	NM_006640	NA	Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000423034.2:c.701-17271A>G	chr17.hg19:g.75460955A>G		NA	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	hg19	CCDS45792.1	0.02	-0.210488	GGCxTGA	COVERED																																																																																			NOVEL	SEPT9-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000436351.1	6	3.609325	KEEP	2	0	0	12	333	AA	0.993072	0.549057	0		+	3	60	93	0	0	6.806261	21	60	617	56	ENST00000423034.2	0.125	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	75635883	75635883	__UNKNOWN__	IGR	SNP	T	T	G	rs71160244|rs5021559|rs200353041		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:75635883T>G			NA	NA				RP11-13K12.5 (71106 upstream) : RP11-316M20.1 (83070 downstream)						NA		NA									NA						tgctgcttcttcttcttcttc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.75635883T>G		NA		hg19		0.02	1.590769	TCTxCTT	COVERED																																																																																			NOVEL					0			93	8.54876	KEEP	29	4	121	71	1952	TT	1	0.999862	0			5	60	155	0	1	9.599264	82	60	2495	259		0.057471	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	75749441	75749441	__UNKNOWN__	IGR	SNP	C	C	T	rs543428366		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:75749441C>T			NA	NA				RP11-316M20.1 (24800 upstream) : FLJ45079 (125667 downstream)						NA		NA									NA						tcgatcctcccgcctcagcct	0.498		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	21573	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.75749441C>T		NA		hg19		0.02	-0.017541	TCCxGCC	UNCOVERED																																																																																			NOVEL					0			5	2.406467	KEEP	0	0	0	8	233	CC	0.99257	0	0			2	60	59	0	0	6.853261	0	0	0	14		1	0
TNRC6C-AS1	100131096	__UNKNOWN__	__UNKNOWN__	17	76105667	76105667	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:76105667G>A	ENST00000589217.1	-	0	2213					NR_040071.1				TNRC6C antisense RNA 1	NA		NA									NA						agctgtgatcgtgccactgtg	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							17q25.3	2013-05-21			ENSG00000204282	ENSG00000204282	100131096		Long non-coding RNAs	44360	non-coding RNA	RNA, long non-coding		NA			NA		Standard		NR_040071	NA	Approved				OTTHUMG00000177654	ENST00000589217.1:	chr17.hg19:g.76105667G>A		NA		hg19		0.02	0.916425	ATCxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	G	31	5.070534	0.93950	.	.	ENSG00000204282	ENST00000374976	.	.	.	0.458	-0.916	0.10489	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	.	.	.	.	X	33	.	ENSP00000364115:R33X	R	-	1	2	AC021593.1	73617262	0.028000	0.19301	0.000000	0.03702	0.000000	0.00434	-0.569000	0.05902	-1.476000	0.01874	-1.512000	0.00943	CGA	NOVEL	TNRC6C-AS1-001	KNOWN	basic	antisense	NA	processed_transcript	OTTHUMT00000438267.1	18	19.752307	KEEP	0	3	77	93	2764	GG	1	0.999962	0		-	5	60	135	0	0	7.403086	90	60	2901	293	ENST00000589217.1	0.052632	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	76287309	76287309	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:76287309A>G			NA	NA				RP11-219G17.4 (12736 upstream) : AC061992.2 (24500 downstream)						NA		NA									NA						ctggagtgcaatggcatgatc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.76287309A>G		NA		hg19		0.02	-0.14033	GCAxTGG	COVERED																																																																																			NOVEL					0			8	3.006786	KEEP	0	0	0	10	266	AA	0.992708	0.259062	0			3	60	103	0	0	8.572889	11	60	324	38		0.214286	0.260965
DNAH17	8632	__UNKNOWN__	__UNKNOWN__	17	76499146	76499146	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:76499146T>A	ENST00000585328.1	-	32	5072				DNAH17_ENST00000389840.5_Intron	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	NA		NA			cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGCCTCTAGTTCCAATAATTT	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775	8632		Axonemal dyneins	2946	protein-coding gene	gene with protein product		610063	dynein, axonemal, heavy polypeptide 17, dynein, axonemal, heavy chain like 1, dynein, axonemal, heavy like 1	DNAHL1	NA	9545504	Standard	NM_173628	NM_173628	NA	Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4948-53A>T	chr17.hg19:g.76499146T>A		NA	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	hg19		0.02	-0.333216	AGTxCCA	COVERED																																																																																			NOVEL	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000318962.2	5	2.404429	KEEP	0	0	0	8	210	TT	0.99257	0.845654	0		-	19	60	518	0	0	49.417167	19	60	574	65	ENST00000585328.1	0.5	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	76631954	76631954	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:76631954A>G			NA	NA				CTD-2357A8.3 (3821 upstream) : CYTH1 (38175 downstream)						NA		NA									NA						cacccgcctcagcctcccaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.76631954A>G		NA		hg19		0.02	-0.140338	CTCxGCC	COVERED																																																																																			NOVEL					0			8	3.609683	KEEP	1	0	0	12	340	AA	0.993072	0.259157	0			3	58	93	0	0	7.37901	13	60	396	39		0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	76784537	76784537	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:76784537A>G			NA	NA				CYTH1 (6158 upstream) : USP36 (7197 downstream)						NA		NA									NA						gagccaccgcacccggccCTG	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.76784537A>G		NA		hg19		0.02	-0.210425	CGCxCCC	COVERED																																																																																			NOVEL					0			3	2.704977	KEEP	2	0	0	9	227	AA	0.99257	0.518282	0			3	60	96	0	0	7.227729	19	60	509	48		0.136364	0.522161
ENGASE	64772	__UNKNOWN__	__UNKNOWN__	17	77074381	77074381	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:77074381T>C	ENST00000579016.1	+	3	416				ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	NA		NA				cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						aagattgcactactgcactcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	64772	3.2.1.96		24622	protein-coding gene	gene with protein product	Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase, Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase	611898			NA	12114544, 18586680	Standard	NM_022759	NM_001042573	NA	Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.416+435T>C	chr17.hg19:g.77074381T>C		NA	Q659F0|Q8TB86|Q9H6U4	hg19	CCDS42394.1	0.02	-0.026317	CACxACT	UNCOVERED																																																																																			NOVEL	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395807.1	2	2.405388	KEEP	0	0	0	8	213	TT	0.99257	0	0		+	2	60	70	0	0	7.124915	1	60	31	17	ENST00000579016.1	0.666667	0
RNF213	57674	__UNKNOWN__	__UNKNOWN__	17	78256698	78256698	__UNKNOWN__	Intron	SNP	T	T	C	rs139117822	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:78256698T>C	ENST00000508628.2	+	4	553				RNF213_ENST00000319921.4_Intron|RNF213_ENST00000456466.1_Intron|RNF213_ENST00000582970.1_Intron			Q63HN8	RN213_HUMAN	ring finger protein 213	NA		NA			ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ggtttccccatgttggccagg	0.547		NA											T|||	88	0.0175719	0.003	0.0692	5008	,	,	NA	13614	0.0	NA	0.0219	False	NA	,,,	NA	NA	NA	2504	0.0143	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821	57674		RING-type (C3HC4) zinc fingers	14539	protein-coding gene	gene with protein product		613768	chromosome 17 open reading frame 27, KIAA1618, moyamoya disease 2, Moyamoya disease 2	C17orf27, KIAA1618, MYMY2	NA	10997877, 21048783, 21799892	Standard	NM_020914	NM_020954	NA	Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000508628.2:c.408+3989T>C	chr17.hg19:g.78256698T>C		NA	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	hg19		0.02	-0.096467	CCAxGTT	UNCOVERED																																																																																			NOVEL	RNF213-001	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000364861.3	9	2.405278	KEEP	3	0	0	8	210	TT	0	0	0		+	3	60	98	0	0	8.432813	8	60	228	25	ENST00000508628.2	0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	78468747	78468747	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:78468747G>A			NA	NA				NPTX1 (17104 upstream) : RPTOR (49871 downstream)						NA		NA									NA						aggaggctgaggcaggagaat	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.78468747G>A		NA		hg19		0.02	-0.078946	TGAxGCA	UNCOVERED																																																																																			NOVEL					0			12	2.407011	KEEP	5	0	0	8	245	GG	0	0	0			3	39	91	0	0	8.454845	4	60	129	24		0.428571	0.077336
AZI1	0	__UNKNOWN__	__UNKNOWN__	17	79176679	79176679	__UNKNOWN__	Intron	SNP	G	G	A	rs537949974		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:79176679G>A	ENST00000450824.2	-	7	808				AZI1_ENST00000269392.4_Intron|AZI1_ENST00000374782.3_Intron|AZI1_ENST00000575907.1_Intron|AZI1_ENST00000570482.2_Intron			Q9UPN4	CP131_HUMAN		NA		NA			cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			caggagaatcgcttgaacctg	0.488		NA											G|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16237	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000450824.2:c.630-481C>T	chr17.hg19:g.79176679G>A		NA	A6NHI8|B2RN11|Q96F50	hg19	CCDS45808.1	0.02	-0.105261	ATCxCTT	UNCOVERED																																																																																			NOVEL	AZI1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439201.1	9	2.7065	KEEP	8	0	0	9	252	GG	0	0	0		-	3	60	89	0	0	8.032495	5	60	165	31	ENST00000450824.2	0.375	0.139832
SLC38A10	124565	__UNKNOWN__	__UNKNOWN__	17	79221628	79221628	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:79221628A>G	ENST00000374759.3	-	15	2449					NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	NA		NA			amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			gcaacagagcaagaccctgtc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637	124565		Solute carriers	28237	protein-coding gene	gene with protein product		NA			NA		Standard	NM_138570	XM_005257019	NA	Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2066-767T>C	chr17.hg19:g.79221628A>G		NA	Q6ZRC5|Q8NA99|Q96C66	hg19	CCDS42397.1	0.02	-0.061397	AGCxAGA	UNCOVERED																																																																																			NOVEL	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000397747.1	4	2.705923	KEEP	1	0	0	9	239	AA	0.99254	0.04346	0		-	2	60	71	0	0	6.395979	4	60	118	24	ENST00000374759.3	0.333333	0.043787
TMEM105	284186	__UNKNOWN__	__UNKNOWN__	17	79299930	79299930	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:79299930C>T	ENST00000332900.1	-	1	531					NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	NA		NA				integral component of membrane (GO:0016021)				NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			ttgctcgagcccaggagtttg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK096111	CCDS11781.1	17q25.3	2008-04-21	2008-04-21	2008-04-21		ENSG00000185332	284186			26794	protein-coding gene	gene with protein product		NA			NA		Standard	NM_178520	NM_178520	NA	Approved	FLJ38792	uc002kad.2	Q8N8V8		ENST00000332900.1:c.18+4013G>A	chr17.hg19:g.79299930C>T		NA		hg19	CCDS11781.1	0.02	-0.184223	AGCxCAG	COVERED																																																																																			NOVEL	TMEM105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000439607.1	14	2.707999	KEEP	0	0	0	9	274	CC	0.99254	0.420319	0		-	3	60	92	0	0	6.892332	18	60	616	45	ENST00000332900.1	0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	79928708	79928708	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:79928708A>G			NA	NA				RP11-498C9.17 (4243 upstream) : ASPSCR1 (6717 downstream)						NA		NA									NA						tttttgagacagagtctcgct	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.79928708A>G		NA		hg19		0.02	-0.210459	GACxGAG	COVERED																																																																																			NOVEL					0			9	3.909105	KEEP	1	0	0	13	346	AA	0.993634	0.518837	0			3	60	98	0	0	7.492567	18	60	510	50		0.142857	0.522161
CCDC57	284001	__UNKNOWN__	__UNKNOWN__	17	80127257	80127257	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:80127257G>A	ENST00000392343.3	-	13	2237				CCDC57_ENST00000327026.3_Intron|CCDC57_ENST00000389641.4_Intron|CCDC57_ENST00000392347.1_Intron			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	NA		NA								endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			cacccacctcggcctcccaaa	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155	284001			27564	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_198082	XM_006722279	NA	Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000392343.3:c.1882+2319C>T	chr17.hg19:g.80127257G>A		NA	A6NP51|A8MQC7|Q8IWG2|Q8TER3	hg19		0.02	-0.157891	CTCxGCC	COVERED																																																																																			NOVEL	CCDC57-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000277183.1	13	3.609774	KEEP	9	0	0	12	356	GG	0.992708	0.320453	0		-	3	60	91	0	0	7.178964	13	60	426	56	ENST00000392343.3	0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	17	80473873	80473873	__UNKNOWN__	IGR	SNP	C	C	A	rs539277226		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:80473873C>A			NA	NA				NARF (25460 upstream) : FOXK2 (3717 downstream)						NA		NA									NA						gggcctcccacagtgctggga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr17.hg19:g.80473873C>A		NA		hg19		0.02	-0.157889	CCAxAGT	COVERED																																																																																			NOVEL					0			5	2.707619	KEEP	0	0	0	9	262	CC	0.99254	0.320398	0			3	60	86	0	0	6.59264	14	60	475	37		0.176471	0.322807
WDR45B	56270	__UNKNOWN__	__UNKNOWN__	17	80599118	80599118	__UNKNOWN__	Intron	SNP	C	C	A	rs72852071	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr17:80599118C>A	ENST00000392325.4	-	2	337					NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	NA		NA									NA						gctgggattacaggcgtgagc	0.473		NA											C|||	1073	0.214257	0.0938	0.3055	5008	,	,	NA	17009	0.1597	NA	0.2525	False	NA	,,,	NA	NA	NA	2504	0.3292	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580	56270		WD repeat domain containing	25072	protein-coding gene	gene with protein product		609226	WDR45-like	WDR45L	NA	12477932	Standard	NM_019613	NM_019613	NA	Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.142+2706G>T	chr17.hg19:g.80599118C>A		NA	O95328|Q2MCP6|Q6IBN2	hg19	CCDS11815.2	0.02	-0.070175	TTAxAGG	UNCOVERED																																																																																			NOVEL	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316536.1	4	2.407141	KEEP	2	0	0	8	245	CC	0	0	0		-	3	60	90	0	0	8.132399	5	60	170	26	ENST00000392325.4	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	108238	108238	__UNKNOWN__	IGR	SNP	C	C	G	rs139235934		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:108238C>G			NA	NA				RP11-683L23.1 (57998 upstream) : ROCK1P1 (826 downstream)						NA		NA									NA						tgatccaactcttgcctggtc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.108238C>G		NA		hg19		0.02	1.563997	ACTxTTG	COVERED																																																																																			NOVEL					0			37	8.815036	KEEP	0	3	93	62	1874	CC	1	0.999948	0			5	60	170	2	0	12.470413	42	60	1425	230		0.106383	0.999948
ENOSF1	55556	__UNKNOWN__	__UNKNOWN__	18	697484	697484	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:697484C>T	ENST00000251101.7	-	3	282				ENOSF1_ENST00000340116.7_Intron|ENOSF1_ENST00000383578.3_Intron|ENOSF1_ENST00000539164.1_Intron|ENOSF1_ENST00000580982.1_Intron	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	NA		NA			cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						ggcgcggtggctcatgcctgt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199	55556			30365	protein-coding gene	gene with protein product		607427			NA	14508106	Standard	NM_017512	NM_001126123	NA	Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.194-129G>A	chr18.hg19:g.697484C>T		NA	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	hg19	CCDS11822.1	0.02	-0.192992	TGGxTCA	COVERED																																																																																			NOVEL	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254312.2	8	2.407088	KEEP	0	0	0	8	242	CC	0.99257	0.454356	0		-	3	43	92	0	0	7.033704	16	60	546	39	ENST00000251101.7	0.157895	0.457757
YES1	7525	__UNKNOWN__	__UNKNOWN__	18	722984	722984	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:722984C>T	ENST00000584307.1	-	0	3242				YES1_ENST00000314574.4_3'UTR|YES1_ENST00000577961.1_3'UTR			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	NA		NA			blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	cccagctactcgggaggctga	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105	7525		SH2 domain containing	12841	protein-coding gene	gene with protein product		164880	v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1		NA	2983418	Standard	NM_005433	NM_005433	NA	Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.*1440G>A	chr18.hg19:g.722984C>T		NA	A6NLB3|D3DUH1	hg19	CCDS11824.1	0.02	-0.140268	ACTxGGG	UNCOVERED																																																																																			NOVEL	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440827.2	4	3.008619	KEEP	7	0	0	10	295	CC	0	0	0		-	5	40	126	0	0	10.667723	11	60	338	41	ENST00000584307.1	0.3125	0.260965
YES1	7525	__UNKNOWN__	__UNKNOWN__	18	757592	757592	__UNKNOWN__	Intron	SNP	G	G	A	rs544130074	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:757592G>A	ENST00000584307.1	-	2	163				YES1_ENST00000314574.4_Intron|YES1_ENST00000577611.1_Intron|YES1_ENST00000577961.1_Intron			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	NA		NA			blood coagulation (GO:0007596)|cellular protein modification process (GO:0006464)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glucose transport (GO:0015758)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|regulation of vascular permeability (GO:0043114)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)	17					Dasatinib(DB01254)	atgcctaggcggaccgatcac	0.468		NA											g|||	2	0.000399361	0.0	0.0	5008	,	,	NA	15774	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M15990	CCDS11824.1	18p11.31-p11.21	2014-06-26	2014-06-26		ENSG00000176105	ENSG00000176105	7525		SH2 domain containing	12841	protein-coding gene	gene with protein product		164880	v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1		NA	2983418	Standard	NM_005433	NM_005433	NA	Approved	Yes, c-yes, HsT441	uc002kky.3	P07947	OTTHUMG00000131472	ENST00000584307.1:c.8-757C>T	chr18.hg19:g.757592G>A		NA	A6NLB3|D3DUH1	hg19	CCDS11824.1	0.02	-0.166666	GGCxGAC	COVERED																																																																																			NOVEL	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000440827.2	7	3.910901	KEEP	0	0	0	13	381	GG	0.994391	0.351961	0		-	3	60	86	0	0	6.51073	15	60	498	43	ENST00000584307.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	828031	828031	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:828031T>C			NA	NA				RP11-672L10.6 (14274 upstream) : RP11-672L10.3 (66404 downstream)						NA		NA									NA						gtctctgtcatccaggctgga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.828031T>C		NA		hg19		0.02	-0.228033	TCAxCCA	COVERED																																																																																			NOVEL					0			10	4.210693	KEEP	0	0	0	14	387	TT	0.995343	0.609555	0			3	60	103	0	0	7.864746	20	60	592	64		0.130435	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	1812269	1812269	__UNKNOWN__	IGR	SNP	T	T	A	rs113945195	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:1812269T>A			NA	NA				CTD-2015H3.1 (30204 upstream) : RP11-161I6.2 (222410 downstream)						NA		NA									NA						cccagctaattttttgtattt	0.522		NA											T|||	546	0.109026	0.2405	0.1311	5008	,	,	NA	16100	0.002	NA	0.0875	False	NA	,,,	NA	NA	NA	2504	0.0481	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.1812269T>A		NA		hg19		0.02	-0.043841	AATxTTT	UNCOVERED																																																																																			NOVEL					0			6	2.404629	KEEP	5	0	0	8	209	TT	0	0	0			3	60	89	0	0	8.87025	2	60	50	18		0.6	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	2507251	2507251	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:2507251G>A			NA	NA				RP11-161I6.2 (267371 upstream) : METTL4 (30272 downstream)						NA		NA									NA						ccagcactttgggaggcgagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.2507251G>A		NA		hg19		0.02	-0.192926	TTTxGGA	COVERED																																																																																			NOVEL					0			3	2.407296	KEEP	1	0	0	8	250	GG	0.99257	0.454356	0			7	60	211	0	0	18.816899	13	60	429	46		0.35	0.457757
SMCHD1	23347	__UNKNOWN__	__UNKNOWN__	18	2661894	2661894	__UNKNOWN__	Intron	SNP	G	G	T	rs368692364		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:2661894G>T	ENST00000320876.6	+	2	524				SMCHD1_ENST00000261598.8_Intron	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	NA		NA			chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ggtggctcacgcctgtaatcc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596	23347			29090	protein-coding gene	gene with protein product		614982			NA	9734811	Standard		NM_015295	NA	Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.187-4262G>T	chr18.hg19:g.2661894G>T		NA	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	hg19	CCDS45822.1	0.02	-0.105264	CACxCCT	UNCOVERED																																																																																			NOVEL	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000441082.2	9	3.005271	KEEP	4	0	0	10	292	GG	0.992708	0.161282	0		+	3	60	90	0	0	7.632221	8	60	264	39	ENST00000320876.6	0.272727	0.162467
SMCHD1	23347	__UNKNOWN__	__UNKNOWN__	18	2661899	2661899	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:2661899T>G	ENST00000320876.6	+	2	524				SMCHD1_ENST00000261598.8_Intron	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	NA		NA			chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ctcacgcctgtaatcccagca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596	23347			29090	protein-coding gene	gene with protein product		614982			NA	9734811	Standard		NM_015295	NA	Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.187-4257T>G	chr18.hg19:g.2661899T>G		NA	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	hg19	CCDS45822.1	0.02	-0.105255	CTGxAAT	UNCOVERED																																																																																			NOVEL	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000441082.2	10	3.608387	KEEP	5	0	0	12	321	TT	0.992708	0.138812	0		+	3	60	103	0	0	8.932546	8	60	239	40	ENST00000320876.6	0.272727	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	3030198	3030198	__UNKNOWN__	IGR	SNP	A	A	G	rs59997343	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:3030198A>G			NA	NA				SNORA70 (4634 upstream) : MYOM1 (36606 downstream)						NA		NA									NA						GAggccgggcacggtggctca	0.512		NA											a|||	96	0.0191693	0.0673	0.0072	5008	,	,	NA	12049	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.3030198A>G		NA		hg19		0.02	-0.219248	GGCxCGG	COVERED																																																																																			NOVEL					0			12	4.508388	KEEP	0	0	0	15	393	AA	0.99649	0.550947	0			3	60	96	1	0	7.165366	20	60	577	54		0.130435	0.552887
MYOM1	8736	__UNKNOWN__	__UNKNOWN__	18	3090493	3090493	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:3090493T>C	ENST00000356443.4	-	27	4343				MYOM1_ENST00000261606.7_Intron|MYOM1_ENST00000400569.3_Intron	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	NA		NA			muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						gctgggattataggcatgagc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605	8736		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	7613	protein-coding gene	gene with protein product	skelemin	603508	myomesin 1 (skelemin) (185kD), myomesin 1 (skelemin) 185kDa, myomesin 1, 185kDa		NA	9806852	Standard	NM_003803	NM_019856	NA	Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4009+162A>G	chr18.hg19:g.3090493T>C		NA	Q14BD6|Q6H969|Q6ZUU0	hg19	CCDS45824.1	0.02	-0.201668	TTAxAGG	COVERED																																																																																			NOVEL	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000441037.2	2	3.006676	KEEP	0	0	0	10	269	TT	0.992708	0.486967	0		-	3	60	103	1	0	8.061205	17	60	467	43	ENST00000356443.4	0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	3395374	3395374	__UNKNOWN__	IGR	SNP	C	C	T	rs12958517	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:3395374C>T			NA	NA				RP11-838N2.3 (44817 upstream) : TGIF1 (16697 downstream)						NA		NA									NA						GGGGAGGTGTCTCTCCTCCCA	0.507		NA											C|||	987	0.197085	0.0946	0.1037	5008	,	,	NA	18528	0.3214	NA	0.1759	False	NA	,,,	NA	NA	NA	2504	0.2955	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.3395374C>T		NA		hg19		0.02	-0.254342	TGTxTCT	COVERED																																																																																			NOVEL					0			3	2.707314	KEEP	0	0	0	9	267	CC	0.99254	0.663536	0			6	60	158	0	0	12.244761	23	60	768	51		0.206897	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	3395400	3395400	__UNKNOWN__	IGR	SNP	C	C	A	rs12958641	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:3395400C>A			NA	NA				RP11-838N2.3 (44843 upstream) : TGIF1 (16671 downstream)						NA		NA									NA						AGTCATCCAGCCCTTCTCCCT	0.468		NA											C|||	987	0.197085	0.0946	0.1037	5008	,	,	NA	19569	0.3214	NA	0.1759	False	NA	,,,	NA	NA	NA	2504	0.2955	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.3395400C>A		NA		hg19		0.02	-0.271913	CAGxCCT	COVERED																																																																																			NOVEL					0			5	3.308229	KEEP	0	0	0	11	330	CC	0.993072	0.712346	0			5	60	147	0	0	11.298316	24	60	800	61		0.172414	0.717315
ZBTB14	7541	__UNKNOWN__	__UNKNOWN__	18	5290165	5290165	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:5290165C>T	ENST00000357006.4	-	0	2380					NM_001143823.2|NM_001243704.1	NP_001137295.1|NP_001230633.1	O43829	ZBT14_HUMAN	zinc finger and BTB domain containing 14	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)				NA						CAAGACCCCCCACCATCCCGG	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D89859	CCDS11837.1	18p11.31	2013-09-19	2013-01-08	2013-01-08	ENSG00000198081	ENSG00000198081	7541		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	12860	protein-coding gene	gene with protein product		602126	zinc finger protein 161 homolog (mouse), zinc finger protein 161, ZFP161 zinc finger protein	ZFP161	NA	9244432	Standard	NM_003409	NM_001243702	NA	Approved	ZNF478	uc010dkp.3	O43829	OTTHUMG00000131563	ENST00000357006.4:c.*692G>A	chr18.hg19:g.5290165C>T		NA	O00403|Q2TB80	hg19	CCDS11837.1	0.02	1.543814	CCCxACC	COVERED																																																																																			NOVEL	ZBTB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254425.1	1	4.813729	KEEP	0	0	0	16	474	CC	0.997832	0.961684	0		-	15	60	422	0	0	35.936776	36	60	1204	93	ENST00000357006.4	0.294118	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	5642522	5642522	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:5642522T>C			NA	NA				SNORD112 (63038 upstream) : AP001032.1 (19421 downstream)						NA		NA									NA						Gggctgggcgtggtggctcac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.5642522T>C		NA		hg19		0.02	-0.114019	GCGxGGT	UNCOVERED																																																																																			NOVEL					0			5	2.405317	KEEP	0	0	0	8	211	TT	0.99257	0.16126	0			3	60	100	0	0	8.382083	10	60	295	27		0.230769	0.162467
RP11-865B13.1	0	__UNKNOWN__	__UNKNOWN__	18	6588929	6588929	__UNKNOWN__	Intron	SNP	A	A	T	rs8094425	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:6588929A>T	ENST00000584361.1	+	4	455					NM_001243517.1	NP_001230446.1				NA		NA									NA						taaccagctcaccaggataaa	0.438		NA											T|||	2781	0.555312	0.9054	0.3516	5008	,	,	NA	17930	0.5159	NA	0.4066	False	NA	,,,	NA	NA	NA	2504	0.4202	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000584361.1:c.369+63A>T	chr18.hg19:g.6588929A>T		NA		hg19	CCDS58612.1	0.02	1.715986	CTCxCCA	COVERED																																																																																			NOVEL	RP11-865B13.1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442088.2	1	2.706477	KEEP	0	0	0	9	246	AA	0.99254	0.9667	0		+	28	60	841	0	0	81.538185	25	60	723	93	ENST00000584361.1	0.528302	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	6659817	6659817	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:6659817T>C			NA	NA				RP11-91I8.1 (17340 upstream) : RP11-91I8.3 (69002 downstream)						NA		NA									NA						ccacccgccttggcatcccaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.6659817T>C		NA		hg19		0.02	-0.078935	CCTxGGC	UNCOVERED																																																																																			NOVEL					0			7	2.405677	KEEP	1	0	0	8	215	TT	0.99257	0.076761	0			4	60	121	0	0	11.322935	5	60	147	23		0.444444	0.077336
PTPRM	5797	__UNKNOWN__	__UNKNOWN__	18	8352692	8352692	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:8352692T>C	ENST00000332175.8	+	21	4052				PTPRM_ENST00000580170.1_Intron|PTPRM_ENST00000400053.4_Intron|PTPRM_ENST00000444013.1_Intron|PTPRM_ENST00000400060.4_Intron	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	NA		NA			homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				ttttttgagatggagtctcac	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482	5797		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	9675	protein-coding gene	gene with protein product		176888		PTPRL1	NA	1655529, 8404049	Standard		NM_002845	NA	Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3015+9174T>C	chr18.hg19:g.8352692T>C		NA	A7MBN1|D3DUH8|J3QL11	hg19	CCDS11840.1	0.02	-0.175366	AGAxGGA	COVERED																																																																																			NOVEL	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254456.1	22	3.007444	KEEP	8	0	0	10	273	TT	0.99254	0.384517	0		+	3	46	102	0	0	8.372561	12	60	342	44	ENST00000332175.8	0.2	0.387407
PTPRM	5797	__UNKNOWN__	__UNKNOWN__	18	8352711	8352711	__UNKNOWN__	Intron	SNP	C	C	A	rs199629602		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:8352711C>A	ENST00000332175.8	+	21	4052				PTPRM_ENST00000580170.1_Intron|PTPRM_ENST00000400053.4_Intron|PTPRM_ENST00000444013.1_Intron|PTPRM_ENST00000400060.4_Intron	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	NA		NA			homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				actctgtcacccaggctggag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482	5797		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	9675	protein-coding gene	gene with protein product		176888		PTPRL1	NA	1655529, 8404049	Standard		NM_002845	NA	Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.3015+9193C>A	chr18.hg19:g.8352711C>A		NA	A7MBN1|D3DUH8|J3QL11	hg19	CCDS11840.1	0.02	-0.227337	CACxCAG	COVERED																																																																																			NOVEL	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254456.1	26	2.796554	KEEP	9	1	7	12	366	CC	0.992708	0.578679	0		+	3	46	89	0	0	6.733653	16	60	543	56	ENST00000332175.8	0.157895	0.58293
SOGA2	0	__UNKNOWN__	__UNKNOWN__	18	8780904	8780904	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:8780904A>G	ENST00000306329.11	+	5	1497				SOGA2_ENST00000359865.3_Intron|SOGA2_ENST00000306285.7_Intron|SOGA2_ENST00000517570.1_Intron|SOGA2_ENST00000400050.3_Intron						NA		NA									NA						ggtggctcatacctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000306329.11:c.1498-2624A>G	chr18.hg19:g.8780904A>G		NA		hg19		0.02	-0.14033	CATxCCT	COVERED																																																																																			NOVEL	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000444141.1	10	2.7065	KEEP	2	0	0	9	243	AA	0.99254	0.259018	0		+	4	60	137	0	0	11.971592	10	60	292	34	ENST00000306329.11	0.285714	0.260965
PPP4R1	9989	__UNKNOWN__	__UNKNOWN__	18	9603735	9603735	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:9603735A>G	ENST00000400556.3	-	3	126				PPP4R1_ENST00000400555.3_Intron	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	NA		NA			dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						ctcctgcctcaacctcccaaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(188;1232 2082 5061 11948 35994)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845	9989		Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits	9320	protein-coding gene	gene with protein product		604908			NA	10026142	Standard	NM_005134	NM_001042388	NA	Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.53-8584T>C	chr18.hg19:g.9603735A>G		NA	Q99774|Q9UNQ7	hg19	CCDS42412.1	0.02	-0.166637	CTCxACC	COVERED																																																																																			NOVEL	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000268571.1	9	3.006729	KEEP	0	0	0	10	271	AA	0.992708	0.351366	0		-	3	60	101	0	0	8.178932	13	60	383	40	ENST00000400556.3	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	10571431	10571431	__UNKNOWN__	IGR	SNP	G	G	T	rs9676160	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:10571431G>T			NA	NA				NAPG (18674 upstream) : RP11-883A18.3 (23155 downstream)						NA		NA									NA						ttacaggcgtgagccaccgcg	0.458		NA											G|||	1844	0.368211	0.4849	0.2781	5008	,	,	NA	15995	0.2619	NA	0.2922	False	NA	,,,	NA	NA	NA	2504	0.4622	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.10571431G>T		NA		hg19		0.02	-0.122543	CGTxAGC	UNCOVERED																																																																																			NOVEL					0			4	2.407367	KEEP	7	0	0	8	252	GG	0	0	0			4	60	114	0	0	10.392835	6	60	176	41		0.4	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	11915676	11915676	__UNKNOWN__	IGR	SNP	T	T	C	rs190465509	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:11915676T>C			NA	NA				RP11-820I16.1 (1333 upstream) : IMPA2 (65347 downstream)						NA		NA									NA						cgtggtggcttacacctgtaa	0.517		NA											N|||	3	0.000599042	0.0008	0.0	5008	,	,	NA	13893	0.001	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.11915676T>C		NA		hg19		0.02	-0.201712	GCTxACA	COVERED																																																																																			NOVEL					0			7	2.40612	KEEP	0	0	0	8	221	TT	0.99257	0.4869	0			3	40	96	0	0	7.29253	18	60	521	48		0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	11955187	11955187	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:11955187T>G			NA	NA				RP11-820I16.1 (40844 upstream) : IMPA2 (25836 downstream)						NA		NA									NA						gttgcagtgatctgagaactt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.11955187T>G		NA		hg19		0.02	-0.140332	TGAxCTG	COVERED																																																																																			NOVEL					0			4	2.405543	KEEP	0	0	0	8	213	TT	0.99257	0.259026	0			3	60	88	0	0	6.972538	12	60	364	34		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	12081321	12081321	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:12081321T>C			NA	NA				RP11-815J4.6 (4726 upstream) : RP11-815J4.1 (217 downstream)						NA		NA									NA						ggcgcgatcttgactcactgc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.12081321T>C		NA		hg19		0.02	-0.210496	TCTxGAC	COVERED																																																																																			NOVEL					0			5	3.60837	KEEP	0	0	0	12	322	TT	0.993634	0.518837	0			3	60	88	0	0	6.493172	18	60	533	45		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	12081323	12081323	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:12081323A>G			NA	NA				RP11-815J4.6 (4728 upstream) : RP11-815J4.1 (215 downstream)						NA		NA									NA						cgcgatcttgactcactgcaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.12081323A>G		NA		hg19		0.02	-0.210446	TTGxCTC	COVERED																																																																																			NOVEL					0			5	3.606442	KEEP	0	0	0	12	300	AA	0.993634	0.518837	0			4	60	133	0	0	10.680041	18	60	498	44		0.181818	0.522161
SLMO1	10650	__UNKNOWN__	__UNKNOWN__	18	12426361	12426361	__UNKNOWN__	Intron	SNP	G	G	A	rs9952699	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:12426361G>A	ENST00000440960.1	+	4	371				SLMO1_ENST00000592149.1_Intron|SLMO1_ENST00000336990.4_Intron|SLMO1_ENST00000587735.1_Intron|SLMO1_ENST00000590956.1_Intron	NM_001142405.1	NP_001135877.1	Q96N28	SLMO1_HUMAN	slowmo homolog 1 (Drosophila)	NA		NA			phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)			endometrium(1)	1						agaccatcctggctaacacgg	0.552		NA											A|||	2292	0.457668	0.2224	0.6009	5008	,	,	NA	12147	0.4415	NA	0.6481	False	NA	,,,	NA	NA	NA	2504	0.4949	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056046	CCDS11860.1	18p11.21	2007-02-20	2007-02-06	2007-02-06	ENSG00000141391	ENSG00000141391	10650			24639	protein-coding gene	gene with protein product	erythroid differentiation and denucleation factor 1	NA	chromosome 18 open reading frame 43	C18orf43	NA		Standard	NM_006553	NM_006553	NA	Approved	HFL-EDDG1, FLJ31484, PRELID3A	uc010wzu.2	Q96N28	OTTHUMG00000131694	ENST00000440960.1:c.292-679G>A	chr18.hg19:g.12426361G>A		NA	B0YJ10|B4E0C9|D3DUJ1|Q6AHX2	hg19	CCDS11860.1	0.02	-0.07895	CCTxGCT	UNCOVERED																																																																																			NOVEL	SLMO1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254602.2	5	2.407351	KEEP	4	0	0	8	251	GG	0	0	0		+	4	40	123	0	0	11.522748	5	51	174	30	ENST00000440960.1	0.444444	0.077336
SPIRE1	56907	__UNKNOWN__	__UNKNOWN__	18	12485394	12485394	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:12485394G>A	ENST00000409402.4	-	9	1499				SPIRE1_ENST00000453447.2_Intron|SPIRE1_ENST00000410092.3_Intron|SPIRE1_ENST00000309836.5_Intron|SPIRE1_ENST00000383356.2_Intron|SPIRE1_ENST00000464481.1_Intron	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1	NA		NA								breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						gtgagccaccgcgcccggccT	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278	56907			30622	protein-coding gene	gene with protein product		609216	spire homolog 1 (Drosophila), spire family actin nucleation factor 1		NA	10574461, 11747823	Standard	XM_290818	NM_001128626	NA	Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1231+563C>T	chr18.hg19:g.12485394G>A		NA		hg19	CCDS45829.1	0.02	-0.192981	ACCxCGC	COVERED																																																																																			NOVEL	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333109.2	5	2.707685	KEEP	1	0	0	9	265	GG	0.99254	0.454342	0		-	3	60	92	0	0	6.961022	17	60	570	47	ENST00000409402.4	0.15	0.457757
SPIRE1	56907	__UNKNOWN__	__UNKNOWN__	18	12617677	12617677	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:12617677A>G	ENST00000409402.4	-	2	640				SPIRE1_ENST00000410092.3_Intron|SPIRE1_ENST00000309836.5_Intron|SPIRE1_ENST00000453447.2_Intron|SPIRE1_ENST00000383356.2_Intron	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1	NA		NA								breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						ccaaagtgctaggattacagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278	56907			30622	protein-coding gene	gene with protein product		609216	spire homolog 1 (Drosophila), spire family actin nucleation factor 1		NA	10574461, 11747823	Standard	XM_290818	NM_001128626	NA	Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.372+17383T>C	chr18.hg19:g.12617677A>G		NA		hg19	CCDS45829.1	0.02	-0.140343	GCTxGGA	COVERED																																																																																			NOVEL	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333109.2	11	3.306384	KEEP	0	0	0	11	287	AA	0.993072	0.259157	0		-	4	60	133	1	0	11.571306	10	60	306	38	ENST00000409402.4	0.285714	0.260965
SPIRE1	56907	__UNKNOWN__	__UNKNOWN__	18	12641587	12641587	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:12641587T>C	ENST00000409402.4	-	2	605				SPIRE1_ENST00000410092.3_Intron|SPIRE1_ENST00000309836.5_Intron|SPIRE1_ENST00000453447.2_Intron|SPIRE1_ENST00000383356.2_Intron	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1	NA		NA								breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						aggatggtcttgatctcttga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278	56907			30622	protein-coding gene	gene with protein product		609216	spire homolog 1 (Drosophila), spire family actin nucleation factor 1		NA	10574461, 11747823	Standard	XM_290818	NM_001128626	NA	Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.338-6492A>G	chr18.hg19:g.12641587T>C		NA		hg19	CCDS45829.1	0.02	-0.175395	TCTxGAT	COVERED																																																																																			NOVEL	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000333109.2	12	4.210932	KEEP	11	0	0	14	390	TT	0.992708	0.384582	0		-	3	60	87	0	0	6.611215	15	60	434	62	ENST00000409402.4	0.166667	0.387407
CEP192	55125	__UNKNOWN__	__UNKNOWN__	18	13055249	13055249	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:13055249A>G	ENST00000506447.1	+	19	3269				CEP192_ENST00000430049.2_Intron|CEP192_ENST00000325971.8_Intron	NM_032142.3	NP_115518.3	Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	NA		NA			centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ttgcactccaacctgggcaac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639	55125		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	25515	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 62	NA			NA	11230166, 14654843	Standard	NM_032142	NM_032142	NA	Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000506447.1:c.3190-530A>G	chr18.hg19:g.13055249A>G		NA	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	hg19	CCDS32792.2	0.02	-0.140273	CCAxCCT	UNCOVERED																																																																																			NOVEL	CEP192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000361790.1	10	2.405776	KEEP	3	0	0	8	218	AA	0	0	0		+	3	45	103	0	0	8.682942	10	60	279	33	ENST00000506447.1	0.230769	0.260965
LDLRAD4	753	__UNKNOWN__	__UNKNOWN__	18	13272095	13272095	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:13272095G>A	ENST00000399848.3	+	2	202				LDLRAD4_ENST00000361205.4_Intron	NM_181482.3	NP_852147.1	O15165	LRAD4_HUMAN	low density lipoprotein receptor class A domain containing 4	NA		NA			negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	early endosome membrane (GO:0031901)|endosome (GO:0005768)|integral component of membrane (GO:0016021)	R-SMAD binding (GO:0070412)				NA						gggtttcaccgtgttagccag	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF009424, AF009428	CCDS32793.1, CCDS32794.1, CCDS32795.1, CCDS42415.1, CCDS62392.1, CCDS62393.1	18p11.21	2014-04-29	2012-10-24	2012-10-24	ENSG00000168675	ENSG00000168675	753			1224	protein-coding gene	gene with protein product	clone 22	606571	chromosome 18 open reading frame 1	C18orf1	NA	9479497, 9129712, 24627487	Standard	NM_181481	NM_181482	NA	Approved		uc002ksb.3	O15165	OTTHUMG00000181925	ENST00000399848.3:c.-466-6009G>A	chr18.hg19:g.13272095G>A		NA	B3KNT9|E9PAY9|K7EN38|O15166|O15167|O15168|Q5U646|Q6NXP3	hg19	CCDS32794.1	0.02	-0.149092	ACCxTGT	UNCOVERED																																																																																			NOVEL	LDLRAD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458325.1	5	2.706473	KEEP	6	0	0	9	244	GG	0	0	0		+	3	29	90	0	0	7.07932	13	60	390	39	ENST00000399848.3	0.1875	0.292001
ZNF519	162655	__UNKNOWN__	__UNKNOWN__	18	14105602	14105602	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:14105602T>C	ENST00000589498.1	-	3	281				ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000590202.1_Missense_Mutation_p.I313V			Q8TB69	ZN519_HUMAN	zinc finger protein 519	NA		NA			negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						CCAGTATGGATTCTCTGATGT	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													76	78	77			NA	NA	18		NA											NA				14105602		2203	4300	6503	SO:0001627	intron_variant			BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322	162655		Zinc fingers, C2H2-type, -	30574	protein-coding gene	gene with protein product	similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)	NA			NA	12477932	Standard	NM_145287	NM_145287	NA	Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000589498.1:c.131-3830A>G	chr18.hg19:g.14105602T>C		NA		hg19		0.02	-0.420969	GGAxTCT	COVERED	.	.	.	.	.	.	.	.	.	.	T	13.83	2.353365	0.41700	.	.	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31638	0.0803	N	0.10618	0.005	0.19300	N	0.999971	D	0.71674	0.998	D	0.66351	0.943	T	0.12993	-1.0526	8	0.54805	T	0.06	.	5.6281	0.17495	0.0:1.0E-4:0.0:0.9999	.	313	Q8TB69	ZN519_HUMAN	V	313	.	ENSP00000307908:I313V	I	-	1	0	ZNF519	14095602	0.000000	0.05858	0.917000	0.36280	0.542000	0.35054	0.475000	0.22164	0.552000	0.29026	0.076000	0.15429	ATC	NOVEL	ZNF519-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000459035.1	13	3.910092	KEEP	0	0	0	13	364	TT	0.994391	0.943082	0		-	3	52	101	0	0	6.747296	42	60	1251	85	ENST00000589498.1	0.066667	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	15209133	15209133	__UNKNOWN__	IGR	SNP	G	G	A	rs78137026	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:15209133G>A			NA	NA				RP11-454P7.3 (11405 upstream) : AP005901.1 (104421 downstream)						NA		NA									NA						aacccgggaggcagaggttgc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.15209133G>A		NA		hg19		0.02	-0.219304	GAGxCAG	COVERED																																																																																			NOVEL					0			4	5.416357	KEEP	5	0	0	18	562	GG	0.995343	0.550313	0			3	28	88	0	0	6.561425	17	60	581	62		0.15	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	15224591	15224591	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:15224591A>G			NA	NA				RP11-454P7.3 (26863 upstream) : AP005901.1 (88963 downstream)						NA		NA									NA						tacccacttcagcctcccaaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.15224591A>G		NA		hg19		0.02	-0.245601	TTCxGCC	COVERED																																																																																			NOVEL					0			21	2.238818	KEEP	19	1	30	18	517	AA	0.995343	0.638361	0			4	38	129	0	0	10.368641	17	60	530	84		0.190476	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	15264719	15264719	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:15264719A>G			NA	NA				RP11-454P7.3 (66991 upstream) : AP005901.1 (48835 downstream)						NA		NA									NA						cgcccgcctcagcctcccaaa	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.15264719A>G		NA		hg19		0.02	-0.192971	CTCxGCC	COVERED																																																																																			NOVEL					0			17	5.112538	KEEP	7	0	0	17	468	AA	0.994391	0.455189	0			3	51	105	0	0	8.33308	16	60	488	54		0.157895	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	18517151	18517151	__UNKNOWN__	IGR	SNP	A	A	C	rs374048578		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:18517151A>C			NA	NA				None (None upstream) : ROCK1 (9715 downstream)						NA		NA									NA						ctctttttgtagtatctggaa	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.18517151A>C		NA		hg19		0.02	5.390639	TGTxGTA	COVERED																																																																																			NOVEL					0			56	6.428601	KEEP	46	7	200	92	2474	AA	1	1	0			5	60	160	0	0	15.094045	6	60	178	403		0.454545	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	18517177	18517177	__UNKNOWN__	IGR	SNP	G	G	A	rs4391821		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:18517177G>A			NA	NA				None (None upstream) : ROCK1 (9689 downstream)						NA		NA									NA						catttggagcgctttgacgcc	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.18517177G>A		NA		hg19		0.02	4.721952	AGCxCTT	COVERED																																																																																			NOVEL					0			68	3.70261	KEEP	48	9	248	100	2922	GG	1	1	0			6	60	185	0	0	16.79336	10	60	292	495		0.375	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	18518460	18518460	__UNKNOWN__	IGR	SNP	A	A	T	rs201466213		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:18518460A>T			NA	NA				None (None upstream) : ROCK1 (8406 downstream)						NA		NA									NA						tgtcaaaagaaaggttcaatt	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.18518460A>T		NA		hg19		0.02	2.837184	AGAxAGG	COVERED																																																																																			NOVEL					0			35	8.108106	KEEP	26	3	79	55	1476	AA	1	0.999991	0			4	60	122	0	0	14.106903	0	0	0	263		1	0.999991
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	18787861	18787861	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:18787861T>C			NA	NA				RNU6-120P (87394 upstream) : RP11-699A5.2 (32774 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.18787861T>C		NA		hg19		0.02	-0.219217	AGGxGTG	COVERED																																																																																			NOVEL					0			6	3.007821	KEEP	3	0	0	10	279	TT	0.99254	0.548763	0			3	60	87	0	0	6.396436	18	60	534	54		0.142857	0.552887
SNRPD1	6632	__UNKNOWN__	__UNKNOWN__	18	19200186	19200186	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:19200186G>A	ENST00000582475.1	+	2	113				SNRPD1_ENST00000579618.1_Intron|SNRPD1_ENST00000300413.5_Intron			P62314	SMD1_HUMAN	small nuclear ribonucleoprotein D1 polypeptide 16kDa	NA		NA			gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			lung(2)|prostate(1)	3						aagtgctggggttacaggcat	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L36188	CCDS32801.1	18q11.2	2011-10-11	2002-08-29		ENSG00000167088	ENSG00000167088	6632			11158	protein-coding gene	gene with protein product		601063	small nuclear ribonucleoprotein D1 polypeptide (16kD)	SNRPD	NA	7527560, 1701240	Standard	NM_006938	NM_006938	NA	Approved	HsT2456, Sm-D1	uc002ktj.1	P62314		ENST00000582475.1:c.-41-3523G>A	chr18.hg19:g.19200186G>A		NA	B5BTZ1|P13641	hg19		0.02	-0.175016	GGGxTTA	COVERED																																																																																			NOVEL	SNRPD1-002	PUTATIVE	upstream_ATG|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000444022.1	9	3.89103	KEEP	0	0	0	13	366	GG	0.994391	0.385234	0		+	3	60	94	0	0	7.396098	14	60	445	46	ENST00000582475.1	0.176471	0.387407
RP11-13N13.2	0	__UNKNOWN__	__UNKNOWN__	18	19213104	19213104	__UNKNOWN__	lincRNA	SNP	T	T	C	rs570040574		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:19213104T>C	ENST00000577906.1	+	0	364										NA		NA									NA						agccaccgcgtccggccGAAC	0.438		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15900	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000577906.1:	chr18.hg19:g.19213104T>C		NA		hg19		0.02	-0.157851	GCGxCCG	COVERED																																																																																			NOVEL	RP11-13N13.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000444023.1	5	2.706889	KEEP	1	0	0	9	247	TT	0.99257	0.320408	0		+	3	60	91	0	0	7.092729	14	60	408	43	ENST00000577906.1	0.176471	0.322807
ABHD3	171586	__UNKNOWN__	__UNKNOWN__	18	19241966	19241966	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:19241966A>G	ENST00000289119.2	-	5	808				RP11-13N13.5_ENST00000584148.1_RNA|ABHD3_ENST00000580981.1_Intron|ABHD3_ENST00000578270.1_Intron	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	NA		NA				integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|prostate(2)	10						gtctcgctctattgcccaggc	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024880	CCDS32802.1	18q11.1	2011-02-16			ENSG00000158201	ENSG00000158201	171586		Abhydrolase domain containing	18718	protein-coding gene	gene with protein product		612197			NA		Standard		NM_138340	NA	Approved	LABH3	uc002ktl.2	Q8WU67		ENST00000289119.2:c.668+2112T>C	chr18.hg19:g.19241966A>G		NA	B0YIV0|B7Z5C2|O43411	hg19	CCDS32802.1	0.02	-0.306921	TCTxTTG	COVERED																																																																																			NOVEL	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444757.1	7	2.403278	KEEP	1	0	0	8	196	AA	0.99257	0.7943	0		-	3	60	98	0	0	6.788335	32	60	902	67	ENST00000289119.2	0.085714	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	19699111	19699111	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:19699111T>C			NA	NA				RP11-595B24.2 (20370 upstream) : RNU6ATAC20P (11452 downstream)						NA		NA									NA						tggtcttgaattcctgacctc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.19699111T>C		NA		hg19		0.02	-0.113969	GAAxTCC	UNCOVERED																																																																																			NOVEL					0			3	2.405413	KEEP	0	0	0	8	211	TT	0.99257	0.16126	0			3	60	79	0	0	6.5328	8	60	220	29		0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	19710047	19710047	__UNKNOWN__	IGR	SNP	C	C	T	rs71358458|rs146312442	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:19710047C>T			NA	NA				RP11-595B24.2 (31306 upstream) : RNU6ATAC20P (516 downstream)						NA		NA									NA						tttctttcttcctttctttct	0.468		NA											c|||	1754	0.35024	0.7587	0.3026	5008	,	,	NA	10119	0.2589	NA	0.0795	False	NA	,,,	NA	NA	NA	2504	0.2045	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.19710047C>T		NA		hg19		0.02	-0.122811	CTTxCTT	COVERED																																																																																			NOVEL					0			10	2.707169	KEEP	0	0	0	9	261	CC	0.99254	0.194847	0			3	60	92	0	0	7.472722	11	60	369	27		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	19897772	19897772	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:19897772G>C			NA	NA				snoU13 (57132 upstream) : RP11-535A5.1 (30036 downstream)						NA		NA									NA						gttgcccggggtggtcttgaa	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.19897772G>C		NA		hg19		0.02	-0.096491	GGGxTGG	UNCOVERED																																																																																			NOVEL					0			7	2.707149	KEEP	0	0	0	9	265	GG	0.99254	0.119538	0			3	60	93	0	0	8.078352	7	60	232	30		0.3	0.120436
TMEM241	85019	__UNKNOWN__	__UNKNOWN__	18	20876552	20876552	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:20876552G>A	ENST00000383233.3	-	0	2362				TMEM241_ENST00000450466.2_Intron|TMEM241_ENST00000475185.1_5'UTR	NM_032933.4	NP_116322.3	Q24JQ0	TM241_HUMAN	transmembrane protein 241	NA		NA				integral component of membrane (GO:0016021)					NA						gattataggcgtgagccactg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC082984	CCDS11876.2	18q11.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134490	ENSG00000134490	85019			31723	protein-coding gene	gene with protein product		615430	chromosome 18 open reading frame 45	C18orf45	NA	12477932	Standard	NM_032933	NM_032933	NA	Approved	MGC11386, FLJ44259	uc002kuf.3	Q24JQ0	OTTHUMG00000131771	ENST00000383233.3:c.*1419C>T	chr18.hg19:g.20876552G>A		NA	I0J130|Q6ZTS7|Q6ZW41	hg19	CCDS11876.2	0.02	-0.359624	GGCxTGA	COVERED																																																																																			NOVEL	TMEM241-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254702.3	9	5.414319	KEEP	2	0	0	18	518	GG	0.999366	0.888312	0		-	4	60	123	0	0	8.610984	35	60	1131	87	ENST00000383233.3	0.102564	0.888875
TMEM241	85019	__UNKNOWN__	__UNKNOWN__	18	20993112	20993112	__UNKNOWN__	Intron	SNP	C	C	T	rs573417297	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:20993112C>T	ENST00000383233.3	-	3	250				TMEM241_ENST00000399707.1_Intron|TMEM241_ENST00000450466.2_Intron|TMEM241_ENST00000542162.1_Intron	NM_032933.4	NP_116322.3	Q24JQ0	TM241_HUMAN	transmembrane protein 241	NA		NA				integral component of membrane (GO:0016021)					NA						ggattacaggcgtgagccacc	0.512		NA											C|||	3	0.000599042	0.0	0.0043	5008	,	,	NA	18785	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC082984	CCDS11876.2	18q11.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134490	ENSG00000134490	85019			31723	protein-coding gene	gene with protein product		615430	chromosome 18 open reading frame 45	C18orf45	NA	12477932	Standard	NM_032933	NM_032933	NA	Approved	MGC11386, FLJ44259	uc002kuf.3	Q24JQ0	OTTHUMG00000131771	ENST00000383233.3:c.197+8218G>A	chr18.hg19:g.20993112C>T		NA	I0J130|Q6ZTS7|Q6ZW41	hg19	CCDS11876.2	0.02	-0.210508	AGGxGTG	COVERED																																																																																			NOVEL	TMEM241-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254702.3	6	2.438051	KEEP	1	1	22	16	464	CC	0.997832	0.521029	0		-	3	60	89	0	0	6.527827	19	60	610	59	ENST00000383233.3	0.136364	0.522161
TMEM241	85019	__UNKNOWN__	__UNKNOWN__	18	20993123	20993123	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:20993123G>A	ENST00000383233.3	-	3	250				TMEM241_ENST00000399707.1_Intron|TMEM241_ENST00000450466.2_Intron|TMEM241_ENST00000542162.1_Intron	NM_032933.4	NP_116322.3	Q24JQ0	TM241_HUMAN	transmembrane protein 241	NA		NA				integral component of membrane (GO:0016021)					NA						gtgagccaccgtgcccagccT	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC082984	CCDS11876.2	18q11.2	2011-11-25	2011-11-25	2011-11-25	ENSG00000134490	ENSG00000134490	85019			31723	protein-coding gene	gene with protein product		615430	chromosome 18 open reading frame 45	C18orf45	NA	12477932	Standard	NM_032933	NM_032933	NA	Approved	MGC11386, FLJ44259	uc002kuf.3	Q24JQ0	OTTHUMG00000131771	ENST00000383233.3:c.197+8207C>T	chr18.hg19:g.20993123G>A		NA	I0J130|Q6ZTS7|Q6ZW41	hg19	CCDS11876.2	0.02	-0.175425	ACCxTGC	COVERED																																																																																			NOVEL	TMEM241-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254702.3	4	3.905347	KEEP	0	0	0	13	351	GG	0.994391	0.385234	0		-	3	60	86	0	0	6.434261	16	60	515	40	ENST00000383233.3	0.157895	0.387407
C18orf8	29919	__UNKNOWN__	__UNKNOWN__	18	21089803	21089803	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21089803G>A	ENST00000590868.1	+	3	364				C18orf8_ENST00000269221.3_Intron			Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	NA		NA				lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					gattacaggcgtgagccactg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452	29919			24326	protein-coding gene	gene with protein product	colon cancer associated protein Mic1, macrophage inhibitory cytokine 1	NA			NA	12477932	Standard	NM_013326	NM_013326	NA	Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000590868.1:c.264+2785G>A	chr18.hg19:g.21089803G>A		NA	Q9BU17|Q9Y5M0	hg19		0.02	-0.166662	GGCxTGA	COVERED																																																																																			NOVEL	C18orf8-004	NOVEL	non_canonical_conserved|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000445389.1	5	3.309027	KEEP	2	0	0	11	321	GG	0.993072	0.351495	0		+	3	60	88	1	0	6.633813	16	60	518	45	ENST00000590868.1	0.157895	0.353947
C18orf8	29919	__UNKNOWN__	__UNKNOWN__	18	21105601	21105601	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21105601A>C	ENST00000590868.1	+	11	1016				C18orf8_ENST00000269221.3_Intron			Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	NA		NA				lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					gttggccaggatggtctcgat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452	29919			24326	protein-coding gene	gene with protein product	colon cancer associated protein Mic1, macrophage inhibitory cytokine 1	NA			NA	12477932	Standard	NM_013326	NM_013326	NA	Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000590868.1:c.917-1000A>C	chr18.hg19:g.21105601A>C		NA	Q9BU17|Q9Y5M0	hg19		0.02	-0.087712	AGGxTGG	UNCOVERED																																																																																			NOVEL	C18orf8-004	NOVEL	non_canonical_conserved|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000445389.1	7	2.707083	KEEP	3	0	0	9	253	AA	0	0	0		+	3	40	101	0	0	9.043682	6	60	183	27	ENST00000590868.1	0.333333	0.099721
LAMA3	3909	__UNKNOWN__	__UNKNOWN__	18	21272487	21272487	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21272487T>C	ENST00000313654.9	+	1	535				LAMA3_ENST00000399516.3_Intron	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	NA		NA			cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					ccacccaccttggcctcccaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747	3909		Laminins	6483	protein-coding gene	gene with protein product		600805	laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)	LAMNA	NA	8077230	Standard	NM_000227, NM_198129	NM_000227	NA	Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.294+2546T>C	chr18.hg19:g.21272487T>C		NA	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	hg19	CCDS42419.1	0.02	-0.122779	CCTxGGC	COVERED																																																																																			NOVEL	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254824.3	7	2.706707	KEEP	1	0	0	9	245	TT	0.99254	0.194847	0		+	3	60	95	0	0	7.773138	11	60	313	34	ENST00000313654.9	0.214286	0.196312
OSBPL1A	114876	__UNKNOWN__	__UNKNOWN__	18	21790140	21790140	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21790140T>C	ENST00000319481.3	-	18	1808				OSBPL1A_ENST00000399443.3_Intron|OSBPL1A_ENST00000357041.4_Intron	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					cctgtaatcctagcactttgg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447	114876		Oxysterol binding proteins, Ankyrin repeat domain containing	16398	protein-coding gene	gene with protein product		606730	oxysterol binding protein-like 1B	OSBPL1B	NA	11279184, 10588946	Standard	NM_080597	NM_080597	NA	Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1602-13976A>G	chr18.hg19:g.21790140T>C		NA	B7Z7D3|Q9BZF5|Q9NW87	hg19	CCDS11884.1	0.02	-0.157877	TCCxAGC	COVERED																																																																																			NOVEL	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254902.1	7	2.706525	KEEP	2	0	0	9	245	TT	0.99254	0.320398	0		-	3	60	99	0	0	7.891881	14	60	424	42	ENST00000319481.3	0.176471	0.322807
OSBPL1A	114876	__UNKNOWN__	__UNKNOWN__	18	21864914	21864914	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21864914G>C	ENST00000319481.3	-	15	1381				OSBPL1A_ENST00000357041.4_Intron	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					tgcctgtaatgccaacacttt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447	114876		Oxysterol binding proteins, Ankyrin repeat domain containing	16398	protein-coding gene	gene with protein product		606730	oxysterol binding protein-like 1B	OSBPL1B	NA	11279184, 10588946	Standard	NM_080597	NM_080597	NA	Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1175-4002C>G	chr18.hg19:g.21864914G>C		NA	B7Z7D3|Q9BZF5|Q9NW87	hg19	CCDS11884.1	0.02	-0.06141	AATxCCA	UNCOVERED																																																																																			NOVEL	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254902.1	5	2.7081	KEEP	0	0	0	9	277	GG	0.99254	0.04346	0		-	2	60	72	0	0	6.335536	5	60	173	22	ENST00000319481.3	0.285714	0.043787
OSBPL1A	114876	__UNKNOWN__	__UNKNOWN__	18	21864918	21864918	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21864918A>G	ENST00000319481.3	-	15	1381				OSBPL1A_ENST00000357041.4_Intron	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					tgtaatgccaacactttggga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447	114876		Oxysterol binding proteins, Ankyrin repeat domain containing	16398	protein-coding gene	gene with protein product		606730	oxysterol binding protein-like 1B	OSBPL1B	NA	11279184, 10588946	Standard	NM_080597	NM_080597	NA	Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1175-4006T>C	chr18.hg19:g.21864918A>G		NA	B7Z7D3|Q9BZF5|Q9NW87	hg19	CCDS11884.1	0.02	-0.070173	CCAxCAC	UNCOVERED																																																																																			NOVEL	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254902.1	5	2.706585	KEEP	0	0	0	9	245	AA	0.99254	0.053733	0		-	2	60	73	0	0	6.300775	6	60	181	23	ENST00000319481.3	0.25	0.054137
OSBPL1A	114876	__UNKNOWN__	__UNKNOWN__	18	21881926	21881926	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:21881926C>T	ENST00000319481.3	-	14	1381				OSBPL1A_ENST00000357041.4_Intron	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					ggcgtggtggctcacgcctgt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447	114876		Oxysterol binding proteins, Ankyrin repeat domain containing	16398	protein-coding gene	gene with protein product		606730	oxysterol binding protein-like 1B	OSBPL1B	NA	11279184, 10588946	Standard	NM_080597	NM_080597	NA	Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.1174+1674G>A	chr18.hg19:g.21881926C>T		NA	B7Z7D3|Q9BZF5|Q9NW87	hg19	CCDS11884.1	0.02	-0.18422	TGGxTCA	COVERED																																																																																			NOVEL	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254902.1	11	2.707816	KEEP	0	0	0	9	268	CC	0.99254	0.420319	0		-	3	60	86	0	0	6.361513	17	60	587	39	ENST00000319481.3	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	22964945	22964945	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:22964945G>A			NA	NA				ZNF521 (32791 upstream) : RN7SL97P (433254 downstream)						NA		NA									NA						acggccgggcgcagtggctca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.22964945G>A		NA		hg19		0.02	-0.184164	GGCxCAG	COVERED																																																																																			NOVEL					0			5	2.707128	KEEP	0	0	0	9	260	GG	0.99254	0.420319	0			3	60	90	0	0	6.910774	15	60	473	45		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	23683256	23683256	__UNKNOWN__	IGR	SNP	C	C	T	rs377330995		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:23683256C>T			NA	NA				SS18 (12075 upstream) : PSMA8 (30559 downstream)						NA		NA									NA						tcccaaagtgctgggattaca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.23683256C>T		NA		hg19		0.02	-0.157908	GTGxTGG	COVERED																																																																																			NOVEL					0			7	3.91088	KEEP	2	0	0	13	390	CC	0.993634	0.320751	0			3	59	96	0	0	7.77198	12	60	420	46		0.2	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	26488174	26488174	__UNKNOWN__	IGR	SNP	T	T	A	rs112952694	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:26488174T>A			NA	NA				RP11-510D21.1 (118950 upstream) : RNU6-408P (140409 downstream)						NA		NA									NA						agagatggggtttcaccatct	0.527		NA											T|||	1849	0.369209	0.3865	0.3559	5008	,	,	NA	13019	0.4891	NA	0.1928	False	NA	,,,	NA	NA	NA	2504	0.4131	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.26488174T>A		NA		hg19		0.02	-0.096443	GGGxTTC	UNCOVERED																																																																																			NOVEL					0			11	2.404477	KEEP	8	0	0	8	204	TT	0	0	0			3	60	87	0	0	7.479024	7	60	191	29		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	27383457	27383457	__UNKNOWN__	IGR	SNP	C	C	A	rs7241830	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:27383457C>A			NA	NA				RP11-784B15.1 (265099 upstream) : RP11-675P14.1 (909783 downstream)						NA		NA									NA						gatctcggctcactgcaagct	0.522		NA											C|||	2409	0.48103	0.2731	0.4207	5008	,	,	NA	12552	0.6498	NA	0.4901	False	NA	,,,	NA	NA	NA	2504	0.6217	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.27383457C>A		NA		hg19		0.02	-0.07893	GCTxACT	UNCOVERED																																																																																			NOVEL					0			4	3.008938	KEEP	14	0	0	10	304	CC	0	0	0			5	53	138	0	0	14.363974	2	60	61	40		0.714286	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	27383676	27383676	__UNKNOWN__	IGR	SNP	A	A	G	rs2863744	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:27383676A>G			NA	NA				RP11-784B15.1 (265318 upstream) : RP11-675P14.1 (909564 downstream)						NA		NA									NA						gagccaccgcacccggccagt	0.478		NA											G|||	3461	0.691094	0.5363	0.6585	5008	,	,	NA	14903	0.745	NA	0.7416	False	NA	,,,	NA	NA	NA	2504	0.816	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.27383676A>G		NA		hg19		0.02	-0.070154	CGCxCCC	UNCOVERED																																																																																			NOVEL					0			9	3.006193	KEEP	1	0	0	10	260	AA	0.99254	0.053733	0			3	60	99	0	0	9.033511	5	60	136	24		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	28518879	28518879	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:28518879A>C			NA	NA				RP11-675P14.1 (224627 upstream) : RP11-25I11.1 (15906 downstream)						NA		NA									NA						aatcccagcaatttgggagac	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.28518879A>C		NA		hg19		0.02	-0.105241	GCAxTTT	UNCOVERED																																																																																			NOVEL					0			3	2.406415	KEEP	0	0	0	8	225	AA	0.99257	0.138793	0			3	60	96	0	0	8.378589	7	60	208	33		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	29400586	29400586	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29400586C>T			NA	NA				SLC25A52 (59743 upstream) : TRAPPC8 (8549 downstream)						NA		NA									NA						tcacctgaggccaggagttcg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.29400586C>T		NA		hg19		0.02	-0.087709	AGGxCAG	UNCOVERED																																																																																			NOVEL					0			10	2.407336	KEEP	4	0	0	8	252	CC	0	0	0			4	60	112	0	0	10.183973	6	60	214	26		0.4	0.099721
TRAPPC8	22878	__UNKNOWN__	__UNKNOWN__	18	29411053	29411053	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29411053C>T	ENST00000283351.4	-	29	4409				TRAPPC8_ENST00000582539.1_Intron	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	NA		NA			vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						cggtggctcacgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339	22878		Trafficking protein particle complex	29169	protein-coding gene	gene with protein product	general sporulation gene 1 homolog (S. cerevisiae)	614136	KIAA1012	KIAA1012	NA	10231032, 11230166	Standard	NM_014939	NM_014939	NA	Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.4074-101G>A	chr18.hg19:g.29411053C>T		NA	A0JP15|B3KME5|Q9H0L2	hg19	CCDS11901.1	0.02	-0.26301	TCAxGCC	COVERED																																																																																			NOVEL	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255355.1	9	3.309086	KEEP	2	0	0	11	320	CC	0.993072	0.688863	0		-	3	60	92	0	0	6.544216	24	60	722	50	ENST00000283351.4	0.111111	0.693668
RNF125	54941	__UNKNOWN__	__UNKNOWN__	18	29651136	29651136	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29651136T>C	ENST00000217740.3	+	0	3980				RP11-53I6.2_ENST00000583184.1_RNA	NM_017831.3	NP_060301.2	Q96EQ8	RN125_HUMAN	ring finger protein 125, E3 ubiquitin protein ligase	NA		NA			innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						cttgctctgttgcccaggctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK000463	CCDS11902.1	18q12.1	2013-01-09	2012-02-23		ENSG00000101695	ENSG00000101695	54941		RING-type (C3HC4) zinc fingers	21150	protein-coding gene	gene with protein product		610432	ring finger protein 125		NA		Standard	NM_017831	NM_017831	NA	Approved	FLJ20456	uc002kxf.1	Q96EQ8	OTTHUMG00000132266	ENST00000217740.3:c.*2789T>C	chr18.hg19:g.29651136T>C		NA	Q9NX39	hg19	CCDS11902.1	0.02	-0.157866	TGTxGCC	COVERED																																																																																			NOVEL	RNF125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255354.1	5	2.405863	KEEP	2	0	0	8	220	TT	0.99257	0.320408	0		+	5	60	153	0	0	13.53939	10	60	288	33	ENST00000217740.3	0.333333	0.322807
MEP1B	4225	__UNKNOWN__	__UNKNOWN__	18	29786826	29786826	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29786826A>G	ENST00000581447.1	+	8	593				MEP1B_ENST00000269202.6_Intron			Q16820	MEP1B_HUMAN	meprin A, beta	NA		NA			digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						gcctgcctcgacctcccaaag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	4225	3.4.24.18		7020	protein-coding gene	gene with protein product		600389			NA	7774936	Standard	NM_005925	NM_005925	NA	Approved		uc002kxj.4	Q16820		ENST00000581447.1:c.548-389A>G	chr18.hg19:g.29786826A>G		NA	B7ZM35|B9EGL6|Q670J1	hg19		0.02	-0.201719	TCGxCCT	COVERED																																																																																			NOVEL	MEP1B-002	NOVEL	NAGNAG_splice_site|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447756.1	7	3.909749	KEEP	2	0	0	13	358	AA	0.994391	0.487793	0		+	3	60	104	0	0	8.092119	18	60	528	55	ENST00000581447.1	0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	29836711	29836711	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29836711T>C			NA	NA				RP11-344B2.3 (7716 upstream) : Y_RNA (6386 downstream)						NA		NA									NA						acaggccgggtgcggtggctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.29836711T>C		NA		hg19		0.02	-0.236764	GGGxGCG	COVERED																																																																																			NOVEL					0			3	3.60742	KEEP	0	0	0	12	315	TT	0.993634	0.608508	0			3	60	108	0	0	8.248804	22	60	626	56		0.12	0.612407
GAREM	64762	__UNKNOWN__	__UNKNOWN__	18	29991868	29991868	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29991868C>T	ENST00000269209.6	-	2	125				GAREM_ENST00000399218.4_Intron			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	NA		NA			cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)				NA						TTCAGCGTCACGATCAGACTA	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441	64762			26136	protein-coding gene	gene with protein product	Grb2-associated and regulator of Erk/MAPK	NA	chromosome 18 open reading frame 11, family with sequence similarity 59, member A	C18orf11, FAM59A	NA	19509291	Standard	NM_022751	NM_001242409	NA	Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.122-18870G>A	chr18.hg19:g.29991868C>T		NA	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	hg19	CCDS56057.1	0.02	2.810741	TCAxGAT	COVERED																																																																																			NOVEL	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255365.1	9	3.073854	KEEP	6	2	53	29	854	CC	0.999997	0.999991	0		-	10	46	283	0	0	18.500404	101	60	3282	239	ENST00000269209.6	0.09009	0.999994
GAREM	64762	__UNKNOWN__	__UNKNOWN__	18	29991872	29991872	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:29991872C>G	ENST00000269209.6	-	2	125				GAREM_ENST00000399218.4_Intron			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	NA		NA			cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)				NA						GCGTCACGATCAGACTATTAC	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441	64762			26136	protein-coding gene	gene with protein product	Grb2-associated and regulator of Erk/MAPK	NA	chromosome 18 open reading frame 11, family with sequence similarity 59, member A	C18orf11, FAM59A	NA	19509291	Standard	NM_022751	NM_001242409	NA	Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.122-18874G>C	chr18.hg19:g.29991872C>G		NA	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	hg19	CCDS56057.1	0.02	3.794693	GATxAGA	COVERED																																																																																			NOVEL	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255365.1	9	2.772743	KEEP	6	2	62	31	901	CC	0.999997	0.999992	0		-	8	27	269	0	0	18.207848	104	60	3453	243	ENST00000269209.6	0.071429	0.999995
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	30055471	30055471	__UNKNOWN__	IGR	SNP	C	C	T	rs546657921		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:30055471C>T			NA	NA				GAREM (5024 upstream) : WBP11P1 (36154 downstream)						NA		NA									NA						agcaagactccgtctcaaaaa	0.468		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	15870	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.30055471C>T		NA		hg19		0.02	-0.210492	CTCxGTC	COVERED																																																																																			NOVEL					0			6	3.610318	KEEP	0	0	0	12	362	CC	0.993634	0.518837	0			4	60	99	0	0	7.371059	17	60	564	51		0.190476	0.522161
KLHL14	57565	__UNKNOWN__	__UNKNOWN__	18	30285429	30285429	__UNKNOWN__	Intron	SNP	C	C	T	rs148287023	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:30285429C>T	ENST00000359358.4	-	4	1508					NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	NA		NA				endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(20)|ovary(2)	31						ctcatgcctgcaatcccagca	0.408		NA											C|||	63	0.0125799	0.0136	0.0	5008	,	,	NA	14925	0.0089	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0368	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037805	CCDS32813.1	18q12.1	2013-10-15	2013-01-30		ENSG00000197705	ENSG00000197705	57565		Kelch-like, BTB/POZ domain containing	29266	protein-coding gene	gene with protein product	printor	613772	kelch-like 14 (Drosophila)		NA	10718198, 19535332	Standard		NM_020805	NA	Approved	KIAA1384	uc002kxm.1	Q9P2G3	OTTHUMG00000179819	ENST00000359358.4:c.1070-9914G>A	chr18.hg19:g.30285429C>T		NA	A6NNW1|B4DHA0|Q8WU41	hg19	CCDS32813.1	0.02	-0.114032	CTGxAAT	UNCOVERED																																																																																			NOVEL	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000448376.1	4	2.406995	KEEP	0	0	0	8	239	CC	0.99257	0.16126	0		-	3	60	88	0	0	7.181908	10	60	342	31	ENST00000359358.4	0.230769	0.162467
NOL4	8715	__UNKNOWN__	__UNKNOWN__	18	31638191	31638191	__UNKNOWN__	Intron	SNP	G	G	A	rs7229945	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:31638191G>A	ENST00000261592.5	-	5	1070				NOL4_ENST00000538587.1_Intron|NOL4_ENST00000589544.1_Intron|NOL4_ENST00000269185.4_Intron|NOL4_ENST00000535475.1_Intron	NM_001198546.1|NM_003787.4	NP_001185475.1|NP_003778.2	O94818	NOL4_HUMAN	nucleolar protein 4	NA		NA				nucleolus (GO:0005730)	RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	51						tccgcctcccgggttcacgcc	0.532		NA											G|||	2063	0.411941	0.4297	0.4841	5008	,	,	NA	15087	0.4375	NA	0.3877	False	NA	,,,	NA	NA	NA	2504	0.3354	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB017800	CCDS11907.2, CCDS56058.1, CCDS56059.1, CCDS59308.1	18q12	2010-05-04			ENSG00000101746	ENSG00000101746	8715			7870	protein-coding gene	gene with protein product	cancer/testis antigen 125	603577			NA	9813152	Standard	NM_003787	NM_003787	NA	Approved	NOLP, HRIHFB2255, CT125	uc010dmi.3	O94818	OTTHUMG00000132291	ENST00000261592.5:c.772+35237C>T	chr18.hg19:g.31638191G>A		NA	B4DSQ0|B7Z3Z7|F5H1E3|Q6IBS2|Q9BWF1	hg19	CCDS11907.2	0.02	-0.061404	CCCxGGT	UNCOVERED																																																																																			NOVEL	NOL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255386.1	11	3.008762	KEEP	7	0	0	10	302	GG	0	0	0		-	3	60	94	0	0	8.754984	4	60	132	22	ENST00000261592.5	0.428571	0.043787
DTNA	1837	__UNKNOWN__	__UNKNOWN__	18	32219080	32219080	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:32219080T>C	ENST00000399121.5	+	2	181				DTNA_ENST00000269190.7_Intron|DTNA_ENST00000598334.1_Intron|DTNA_ENST00000315456.6_Intron|DTNA_ENST00000595022.1_Intron|DTNA_ENST00000554864.3_Intron|DTNA_ENST00000283365.9_Intron|DTNA_ENST00000596745.1_Intron|DTNA_ENST00000399097.3_Intron	NM_001198939.1	NP_001185868.1	Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	NA		NA			neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						gttgggattataggcgtgagc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769	1837			3057	protein-coding gene	gene with protein product	dystrophin-related protein 3	601239			NA	8081380, 15834686	Standard	NM_001390	NM_001390	NA	Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399121.5:c.-126-40352T>C	chr18.hg19:g.32219080T>C		NA	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	hg19	CCDS56061.1	0.02	-0.131557	TTAxAGG	COVERED																																																																																			NOVEL	DTNA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255418.1	7	2.703927	KEEP	0	0	0	9	235	TT	0.99254	0.227464	0		+	3	60	98	0	0	8.301294	9	60	266	36	ENST00000399121.5	0.25	0.229173
ZNF397	84307	__UNKNOWN__	__UNKNOWN__	18	32824949	32824949	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:32824949C>G	ENST00000355632.4	+	3	691				ZNF397_ENST00000589420.1_Intron|ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000330501.7_Intron|ZNF397_ENST00000261333.6_Intron			Q8NF99	ZN397_HUMAN	zinc finger protein 397	NA		NA			transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|large_intestine(3)|lung(5)|skin(1)	12						agctgatgaacaggaatcagt	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC006172	CCDS32814.1, CCDS45852.1	18p12	2013-01-09	2003-07-22			ENSG00000186812	84307		-, Zinc fingers, C2H2-type	18818	protein-coding gene	gene with protein product		609601	zinc finger protein 47	ZNF47	NA		Standard	NM_032347	NM_032347	NA	Approved	ZSCAN15, MGC13250	uc010dmp.3	Q8NF99		ENST00000355632.4:c.556+1692C>G	chr18.hg19:g.32824949C>G		NA	Q9BRM2	hg19		0.02	-0.394737	GAAxAGG	COVERED																																																																																			NOVEL	ZNF397-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000442401.1	3	3.008344	KEEP	0	0	0	10	301	CC	0.992708	0.919883	0		+	13	60	450	0	0	39.605201	31	60	1047	77	ENST00000355632.4	0.295455	0.92664
ZNF271	10778	__UNKNOWN__	__UNKNOWN__	18	32887958	32887958	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:32887958A>G	ENST00000399070.3	+	0	2352					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(9)	12						tgtaatcccaacactttggga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267	10778		Zinc fingers, C2H2-type	13065	other	unknown		604754			NA	7865130, 11777961	Standard	NR_024565	NR_024565	NA	Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563	ENST00000399070.3:	chr18.hg19:g.32887958A>G		NA	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	hg19		0.02	-0.341979	CCAxCAC	COVERED																																																																																			NOVEL	ZNF271-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000255767.2	6	2.40413	KEEP	0	0	0	8	205	AA	0.99257	0.859313	0		+	3	60	99	0	0	6.81241	34	60	940	62	ENST00000399070.3	0.081081	0.865745
RPRD1A	55197	__UNKNOWN__	__UNKNOWN__	18	33587718	33587718	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:33587718C>T	ENST00000399022.4	-	7	961				RPRD1A_ENST00000357384.4_Intron|RPRD1A_ENST00000588737.1_Intron|RPRD1A_ENST00000590898.1_Intron|RPRD1A_ENST00000337059.5_Intron	NM_018170.3	NP_060640.2	Q96P16	RPR1A_HUMAN	regulation of nuclear pre-mRNA domain containing 1A	NA		NA			dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(2)	12						ctggccaacacggtgaaaccc	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF419845	CCDS11917.1	18q12.2	2012-02-09	2008-08-15		ENSG00000141425	ENSG00000141425	55197			25560	protein-coding gene	gene with protein product	cyclin-dependent kinase 2B-inhibitor-related protein, Cyclin-dependent kinase inhibitor 2B-related protein (p15INK4B-related protein)	610347			NA	12470661, 22231121	Standard	NM_018170	NM_018170	NA	Approved	P15RS, FLJ10656, HsT3101	uc002kzg.3	Q96P16	OTTHUMG00000132591	ENST00000399022.4:c.790-14455G>A	chr18.hg19:g.33587718C>T		NA	A8KA42|B2RBA3|Q7Z5G8|Q96FY9|Q9NVL4	hg19	CCDS11917.1	0.02	-0.149034	ACAxGGT	COVERED																																																																																			NOVEL	RPRD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255802.1	5	3.910194	KEEP	0	0	0	13	370	CC	0.994391	0.290363	0		-	3	40	91	1	0	7.179903	13	60	380	39	ENST00000399022.4	0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	33663206	33663206	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:33663206T>C			NA	NA				RPRD1A (15667 upstream) : SLC39A6 (25288 downstream)						NA		NA									NA						cgcggtggcttacgcctgtaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.33663206T>C		NA		hg19		0.02	-0.087713	GCTxACG	UNCOVERED																																																																																			NOVEL					0			6	4.809626	KEEP	2	0	0	16	417	TT	0.99649	0.099371	0			3	60	102	0	0	9.143755	6	60	178	41		0.333333	0.099721
FHOD3	80206	__UNKNOWN__	__UNKNOWN__	18	34193913	34193913	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:34193913A>G	ENST00000590592.1	+	9	957				FHOD3_ENST00000257209.4_Intron|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000445677.1_Intron|FHOD3_ENST00000359247.4_Intron	NM_001281740.1	NP_001268669.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	NA		NA			actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				tgggattacaagtgtgagcca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775	80206			26178	protein-coding gene	gene with protein product		609691			NA	11214970	Standard	XM_371114	NM_025135	NA	Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000590592.1:c.957+1855A>G	chr18.hg19:g.34193913A>G		NA	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	hg19	CCDS32816.1	0.02	-0.105254	ACAxGTG	UNCOVERED																																																																																			NOVEL	FHOD3-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460883.1	3	2.406108	KEEP	0	0	0	8	221	AA	0.99257	0.138793	0		+	3	60	104	0	0	9.178773	7	60	213	30	ENST00000590592.1	0.3	0.139832
FHOD3	80206	__UNKNOWN__	__UNKNOWN__	18	34226959	34226959	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:34226959G>A	ENST00000590592.1	+	11	1196				FHOD3_ENST00000257209.4_Intron|FHOD3_ENST00000591635.1_Intron|FHOD3_ENST00000445677.1_Intron|FHOD3_ENST00000359247.4_Intron	NM_001281740.1	NP_001268669.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	NA		NA			actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				cagcactttgggaggccaagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775	80206			26178	protein-coding gene	gene with protein product		609691			NA	11214970	Standard	XM_371114	NM_025135	NA	Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000590592.1:c.1197-2320G>A	chr18.hg19:g.34226959G>A		NA	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	hg19	CCDS32816.1	0.02	-0.18422	TTGxGAG	COVERED																																																																																			NOVEL	FHOD3-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460883.1	11	2.708285	KEEP	1	0	0	9	284	GG	0.99254	0.420319	0		+	4	26	120	0	0	9.468715	17	60	587	43	ENST00000590592.1	0.190476	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	38181420	38181420	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:38181420A>G			NA	NA				RNU7-145P (128574 upstream) : RP11-142I20.1 (878817 downstream)						NA		NA									NA						ttacaggcgtaagccactgcg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.38181420A>G		NA		hg19		0.02	-0.114009	CGTxAGC	UNCOVERED																																																																																			NOVEL					0			8	2.405562	KEEP	0	0	0	8	212	AA	0.99257	0.16126	0			4	60	132	0	0	12.185788	6	60	171	27		0.4	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	38543569	38543569	__UNKNOWN__	IGR	SNP	C	C	T	rs181563178		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:38543569C>T			NA	NA				RNU7-145P (490723 upstream) : RP11-142I20.1 (516668 downstream)						NA		NA									NA						gtatatgggccgggcgcagtg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.38543569C>T		NA		hg19		0.02	-0.149124	GGCxGGG	UNCOVERED																																																																																			NOVEL					0			6	2.707764	KEEP	3	0	0	9	272	CC	0	0	0			3	60	90	1	0	7.172223	12	60	398	40		0.2	0.292001
PIK3C3	5289	__UNKNOWN__	__UNKNOWN__	18	39665858	39665858	__UNKNOWN__	3'UTR	SNP	C	C	T	rs567720266		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:39665858C>T	ENST00000262039.4	+	0	7507				PIK3C3_ENST00000398870.3_3'UTR	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	NA		NA			autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						gagaccagcccgggcaacatg	0.463		NA								TSP Lung(28;0.18)			C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17933	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	NSCLC(37;552 1060 2683 16430 37914)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	5289	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	phosphoinositide-3-kinase, class 3		NA	7628435	Standard	NM_002647	NM_002647	NA	Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.*4757C>T	chr18.hg19:g.39665858C>T		NA	Q15134	hg19	CCDS11920.1	0.02	2.690299	GCCxGGG	COVERED																																																																																			NOVEL	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255804.1	57	9.423543	KEEP	0	6	160	88	2631	CC	1	1	0		+	7	60	213	1	0	13.038801	114	60	3751	329	ENST00000262039.4	0.057851	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	40802128	40802128	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:40802128T>C			NA	NA				RIT2 (106471 upstream) : SYT4 (45714 downstream)						NA		NA									NA						ggggtttcactgtgttagcca	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.40802128T>C		NA		hg19		0.02	-0.096399	CACxGTG	UNCOVERED																																																																																			NOVEL					0			7	3.006968	KEEP	3	0	0	10	267	TT	0.992708	0.119558	0			3	40	95	0	0	8.133997	8	60	217	29		0.272727	0.120436
SETBP1	26040	__UNKNOWN__	__UNKNOWN__	18	42499573	42499573	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:42499573T>A	ENST00000282030.5	+	4	836					NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	NA		NA				nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		tcagcctccctaagtgctggg	0.493		NA							Schinzel-Giedion syndrome												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217	26040			15573	protein-coding gene	gene with protein product		611060			NA	11231286	Standard	NM_001130110	NM_015559	NA	Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.541-30273T>A	chr18.hg19:g.42499573T>A		NA	A6H8W5|Q6P6C3|Q9UEF3	hg19	CCDS11923.2	0.02	-0.096469	CCCxAAG	UNCOVERED																																																																																			NOVEL	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255854.4	9	2.706522	KEEP	2	0	0	9	243	TT	0.99257	0.119541	0		+	3	60	84	2	0	7.178422	7	60	205	26	ENST00000282030.5	0.3	0.120436
SLC14A2	8170	__UNKNOWN__	__UNKNOWN__	18	42931539	42931539	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:42931539T>C	ENST00000586448.1	+	2	197					NM_001242692.1	NP_001229621.1	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	NA		NA			transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						aggctggtcttgaactcctgg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874	8170		Solute carriers	10919	protein-coding gene	gene with protein product		601611			NA	8647271	Standard		NM_007163	NA	Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000586448.1:c.-124-131659T>C	chr18.hg19:g.42931539T>C		NA	A8K8Q7|Q2TBD6|Q96PH5	hg19	CCDS11924.1	0.02	-0.105227	TCTxGAA	UNCOVERED																																																																																			NOVEL	SLC14A2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000444508.1	9	2.404752	KEEP	1	0	0	8	208	TT	0	0	0		+	3	60	103	0	0	9.243703	6	60	182	25	ENST00000586448.1	0.333333	0.139832
SLC14A2	8170	__UNKNOWN__	__UNKNOWN__	18	43262951	43262951	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:43262951T>C	ENST00000255226.6	+	0	4046				SLC14A2_ENST00000589658.1_3'UTR|RP11-116O18.3_ENST00000589510.1_RNA	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	NA		NA			transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						cccagctacttgggaggctga	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874	8170		Solute carriers	10919	protein-coding gene	gene with protein product		601611			NA	8647271	Standard		NM_007163	NA	Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.*467T>C	chr18.hg19:g.43262951T>C		NA	A8K8Q7|Q2TBD6|Q96PH5	hg19	CCDS11924.1	0.02	-0.131545	ACTxGGG	UNCOVERED																																																																																			NOVEL	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255858.1	3	2.702573	KEEP	6	0	0	9	221	TT	0	0	0		+	3	40	85	0	0	6.773373	11	60	315	31	ENST00000255226.6	0.214286	0.229173
SLC14A1	6563	__UNKNOWN__	__UNKNOWN__	18	43331481	43331481	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:43331481A>G	ENST00000321925.4	+	0	2967					NM_001128588.3|NM_001146036.2|NM_015865.6	NP_001122060.3|NP_001139508.2|NP_056949.4	Q13336	UT1_HUMAN	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)	NA		NA			transmembrane transport (GO:0055085)|urea transmembrane transport (GO:0071918)|urea transport (GO:0015840)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	urea channel activity (GO:0015265)|urea transmembrane transporter activity (GO:0015204)|water transmembrane transporter activity (GO:0005372)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(11)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	21						ACtggctcacacctgtaatcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC040128	CCDS11925.1, CCDS45860.1	18q11-q12	2014-07-19	2014-01-02		ENSG00000141469	ENSG00000141469	6563		Blood group antigens, Solute carriers	10918	protein-coding gene	gene with protein product		613868	Kidd blood group, solute carrier family 14 (urea transporter), member 1	JK	NA	7797558	Standard	NM_015865	NM_001146037	NA	Approved	HsT1341, RACH1, RACH2	uc010dnk.3	Q13336	OTTHUMG00000132617	ENST00000321925.4:c.*1565A>G	chr18.hg19:g.43331481A>G		NA	A8K0P3|B3KR62|B3KVX3|C9EHF2|Q86VM5	hg19	CCDS11925.1	0.02	3.233486	CACxCCT	COVERED																																																																																			NOVEL	SLC14A1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255860.2	21	2.822103	KEEP	0	4	118	51	1299	AA	1	0.999991	0		+	8	60	260	0	0	17.507739	98	60	2807	212	ENST00000321925.4	0.075472	0.999991
SIGLEC15	284266	__UNKNOWN__	__UNKNOWN__	18	43422409	43422409	__UNKNOWN__	3'UTR	SNP	A	A	T	rs533346380		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:43422409A>T	ENST00000389474.3	+	0	1461				SIGLEC15_ENST00000602118.2_3'UTR	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	NA		NA			cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						tgtgtgtgtgAGAGAGAGAGA	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046	284266		Sialic acid binding Ig-like lectins, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	27596	protein-coding gene	gene with protein product		NA	CD33 antigen-like 3, CD33 molecule-like 3	CD33L3	NA	17483134	Standard	NM_213602	NM_213602	NA	Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.*257A>T	chr18.hg19:g.43422409A>T		NA	A8K2Y5|B4DVQ9	hg19	CCDS32819.1	0.02	1.4011	GTGxGAG	COVERED																																																																																			NOVEL	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000410768.2	10	5.21752	KEEP	0	1	27	27	731	AA	0.999997	0.979523	0		+	5	60	138	2	0	9.138283	45	60	1350	135	ENST00000389474.3	0.1	0.979526
EPG5	57724	__UNKNOWN__	__UNKNOWN__	18	43462723	43462723	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:43462723G>A	ENST00000282041.5	-	31	5339				EPG5_ENST00000585906.1_Intron	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	NA		NA			autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						ctgtaatcccggcactttggg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223	57724			29331	protein-coding gene	gene with protein product		615068	KIAA1632	KIAA1632	NA	10997877, 20550938	Standard	NM_020964	XM_005258323	NA	Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.5305-271C>T	chr18.hg19:g.43462723G>A		NA	A2BDF3|Q9H8C8	hg19	CCDS11926.2	0.02	-0.114034	CCCxGCA	UNCOVERED																																																																																			NOVEL	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000445081.1	7	2.707805	KEEP	1	0	0	9	272	GG	0.99254	0.161255	0		-	3	60	91	0	0	7.600988	9	60	297	35	ENST00000282041.5	0.25	0.162467
HAUS1	115106	__UNKNOWN__	__UNKNOWN__	18	43700443	43700443	__UNKNOWN__	Intron	SNP	G	G	T	rs71364522	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:43700443G>T	ENST00000282058.6	+	4	556				HAUS1_ENST00000585518.1_Intron|HAUS1_ENST00000588704.1_Intron	NM_138443.3	NP_612452.1	Q96CS2	HAUS1_HUMAN	HAUS augmin-like complex, subunit 1	NA		NA			centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						caggtgatccgcccgcctcgg	0.517		NA											G|||	1269	0.253395	0.1823	0.2579	5008	,	,	NA	15326	0.0466	NA	0.3897	False	NA	,,,	NA	NA	NA	2504	0.4192	NA	NA	NA	NSCLC(79;183 1423 5813 15597 38427)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY360137	CCDS11928.1	18q21.1	2013-10-11	2009-04-20	2009-04-20	ENSG00000152240	ENSG00000152240	115106		HAUS augmin-like complex subunits	25174	protein-coding gene	gene with protein product		608775	coiled-coil domain containing 5 (spindle associated)	CCDC5	NA	19427217	Standard	NM_138443	NR_026978	NA	Approved	HEI-C, HsT1461, FLJ40084	uc002lbu.3	Q96CS2	OTTHUMG00000132638	ENST00000282058.6:c.476+417G>T	chr18.hg19:g.43700443G>T		NA	B2RDM7|Q8N837	hg19	CCDS11928.1	0.02	-0.183996	TCCxCCC	UNCOVERED																																																																																			NOVEL	HAUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255885.1	3	2.405911	KEEP	7	0	0	8	228	AG	0	0	0		+	4	60	119	0	0	9.562802	15	60	459	61	ENST00000282058.6	0.210526	0.457757
C18orf25	147339	__UNKNOWN__	__UNKNOWN__	18	43768592	43768592	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:43768592T>C	ENST00000282059.6	+	1	304				C18orf25_ENST00000321319.6_Intron	NM_145055.3	NP_659492	Q96B23	CR025_HUMAN	chromosome 18 open reading frame 25	NA		NA								central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)	11						agattacaggtgtgagccacc	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL713661	CCDS42430.1, CCDS42431.1	18q21.1	2014-01-03			ENSG00000152242	ENSG00000152242	147339			28172	protein-coding gene	gene with protein product	ARKadia-like 1	NA			NA	15722956	Standard	NM_145055	NM_001008239	NA	Approved	MGC12909, ARKL1, RNF111L1	uc002lbw.3	Q96B23		ENST00000282059.6:c.-71+14296T>C	chr18.hg19:g.43768592T>C		NA	A8K123|A8KAB6|Q5XG78|Q6N058|Q86TB5|Q8TCQ5	hg19	CCDS42430.1	0.02	-0.19291	AGGxGTG	COVERED																																																																																			NOVEL	C18orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000445242.1	10	4.209536	KEEP	0	0	0	14	380	TT	0.995343	0.455625	0		+	3	60	99	0	0	7.661277	17	60	497	45	ENST00000282059.6	0.15	0.457757
RNF165	494470	__UNKNOWN__	__UNKNOWN__	18	44031568	44031568	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:44031568A>G	ENST00000269439.7	+	6	867				RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	NA		NA					zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		gaccaacctgagcaaaatagt	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622	494470		RING-type (C3HC4) zinc fingers	31696	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152470	NR_046357	NA	Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.816+806A>G	chr18.hg19:g.44031568A>G		NA	B3KVD1	hg19	CCDS32823.1	0.02	-0.228067	CTGxGCA	COVERED																																																																																			NOVEL	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000445358.1	10	3.609576	KEEP	0	0	0	12	339	AA	0.993634	0.579219	0		+	3	60	101	0	0	7.548765	22	60	691	57	ENST00000269439.7	0.12	0.58293
ST8SIA5	29906	__UNKNOWN__	__UNKNOWN__	18	44319270	44319270	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:44319270T>C	ENST00000315087.7	-	1	792				ST8SIA5_ENST00000536490.1_Intron|ST8SIA5_ENST00000538168.1_Intron	NM_013305.4	NP_037437.2	O15466	SIA8E_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5	NA		NA			carbohydrate metabolic process (GO:0005975)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			kidney(1)|large_intestine(10)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	22						tttgggaggctgaggcgggtg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U91641	CCDS11930.1	18q12.3	2013-03-01	2003-01-14	2005-02-07	ENSG00000101638	ENSG00000101638	29906		Sialyltransferases	17827	protein-coding gene	gene with protein product	ST8Sia V	607162	sialyltransferase 8E (alpha-2, 8-polysialytransferase)	SIAT8E	NA	9199191	Standard	NM_013305	XM_005258250	NA	Approved		uc002lcj.1	O15466	OTTHUMG00000132643	ENST00000315087.7:c.131+17070A>G	chr18.hg19:g.44319270T>C		NA	B7Z1K9|Q6IAW7	hg19	CCDS11930.1	0.02	-0.201712	GGCxGAG	COVERED																																																																																			NOVEL	ST8SIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255892.1	4	3.609614	KEEP	2	0	0	12	339	TT	0.993072	0.518544	0		-	3	60	100	0	0	7.627161	19	60	577	57	ENST00000315087.7	0.136364	0.522161
KATNAL2	83473	__UNKNOWN__	__UNKNOWN__	18	44555051	44555051	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:44555051T>C	ENST00000592005.1	+	3	724				KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron|TCEB3C_ENST00000330682.2_Missense_Mutation_p.E388G					katanin p60 subunit A-like 2	NA		NA								central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						TTCATCTGTCTCTCGAGCGAG	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													317	295	302			NA	NA	18		NA											NA				44555051		1953	3941	5894	SO:0001627	intron_variant			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216	83473		ATPases / AAA-type	25387	protein-coding gene	gene with protein product		614697			NA	12477932	Standard	NM_031303	NM_031303	NA	Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.51+28165T>C	chr18.hg19:g.44555051T>C		NA		hg19		0.02	3.499933	GTCxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	t	14.97	2.694700	0.48202	.	.	ENSG00000183791	ENST00000330682	T	0.33865	1.39	1.75	1.75	0.24633	.	0.391329	0.21094	N	0.080275	T	0.27663	0.0680	L	0.52573	1.65	0.23366	N	0.997822	P	0.52316	0.952	B	0.39805	0.31	T	0.19582	-1.0301	10	0.59425	D	0.04	-12.2301	7.5569	0.27829	0.0:0.0:0.0:1.0	.	388	Q8NG57	ELOA3_HUMAN	G	388	ENSP00000328232:E388G	ENSP00000328232:E388G	E	-	2	0	TCEB3C	42809049	0.966000	0.33281	0.002000	0.10522	0.002000	0.02628	5.232000	0.65332	1.093000	0.41377	0.397000	0.26171	GAG	NOVEL	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446324.2	0	4.510972	KEEP	61	0	0	15	408	TT	0.994391	0.99439	0		+	5	47	166	0	0	9.914037	118	51	3433	263	ENST00000592005.1	0.04065	0.999999
KATNAL2	83473	__UNKNOWN__	__UNKNOWN__	18	44624587	44624587	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:44624587C>T	ENST00000592005.1	+	0	1082				KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron					katanin p60 subunit A-like 2	NA		NA								central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						agcaagactccgtctcaaaaa	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216	83473		ATPases / AAA-type	25387	protein-coding gene	gene with protein product		614697			NA	12477932	Standard	NM_031303	NM_031303	NA	Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.*91C>T	chr18.hg19:g.44624587C>T		NA		hg19		0.02	-0.114028	CTCxGTC	UNCOVERED	.	.	.	.	.	.	.	.	.	.	C	0.146	-1.096581	0.01843	.	.	ENSG00000167216	ENST00000454462	.	.	.	0.158	-0.317	0.12736	.	.	.	.	.	T	0.35248	0.0925	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.36212	-0.9757	4	0.87932	D	0	.	.	.	.	.	.	.	.	C	187	.	ENSP00000398354:R187C	R	+	1	0	KATNAL2	42878585	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	-0.827000	0.04424	-1.029000	0.03317	-1.021000	0.02439	CGT	NOVEL	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000446324.2	4	2.705251	KEEP	0	0	0	9	237	CC	0.99254	0.161255	0		+	3	60	92	0	0	7.701118	9	60	290	25	ENST00000592005.1	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	44739092	44739092	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:44739092T>C			NA	NA				IER3IP1 (36347 upstream) : SKOR2 (7200 downstream)						NA		NA									NA						acctgtaatctcagcactttg	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.44739092T>C		NA		hg19		0.02	-0.166632	ATCxCAG	COVERED																																																																																			NOVEL					0			12	3.308592	KEEP	3	0	0	11	306	TT	0.99257	0.351317	0			3	60	98	0	0	7.791961	14	60	410	39		0.176471	0.353947
CTIF	9811	__UNKNOWN__	__UNKNOWN__	18	46141531	46141531	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:46141531G>T	ENST00000256413.3	+	2	267				CTIF_ENST00000382998.4_Intron	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	NA		NA			nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						cctcccaaagggctgggatta	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030	9811			23925	protein-coding gene	gene with protein product		613178	KIAA0427	KIAA0427	NA	9455477, 19648179	Standard	NM_014772	NM_014772	NA	Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.-28-4378G>T	chr18.hg19:g.46141531G>T		NA	B3KTR8|Q8IVD5	hg19	CCDS11935.1	0.02	-0.18421	AAGxGCT	COVERED																																																																																			NOVEL	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255907.1	8	2.707903	KEEP	1	0	0	9	271	GG	0.99257	0.420331	0		+	4	60	115	0	0	9.063278	16	60	549	44	ENST00000256413.3	0.2	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	47001803	47001803	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:47001803G>A			NA	NA				DYM (14631 upstream) : C18orf32 (6224 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.47001803G>A		NA		hg19		0.02	-0.149074	GGCxTGA	COVERED																																																																																			NOVEL					0			12	2.437762	KEEP	4	1	25	17	474	GG	0.999859	0.29196	0			3	60	83	0	0	6.380811	13	60	401	48		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	47039494	47039494	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:47039494T>C			NA	NA				RP11-110H1.8 (11264 upstream) : LIPG (47574 downstream)						NA		NA									NA						tgcctgtaattccagcacttt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.47039494T>C		NA		hg19		0.02	-0.192959	AATxCCA	COVERED																																																																																			NOVEL					0			9	3.308596	KEEP	0	0	0	11	307	TT	0.993072	0.454585	0			3	46	97	0	0	7.533381	16	60	482	47		0.157895	0.457757
MYO5B	4645	__UNKNOWN__	__UNKNOWN__	18	47537452	47537452	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:47537452T>C	ENST00000285039.7	-	5	755					NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	NA		NA			endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		gtggctcacgtctgtaatccc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306	4645		Myosins / Myosin superfamily : Class V	7603	protein-coding gene	gene with protein product		606540			NA	8884266, 17462998	Standard		NM_001080467	NA	Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.456-9671A>G	chr18.hg19:g.47537452T>C		NA	B0I1R3|Q0P656|Q9H6Y6	hg19	CCDS42436.1	0.02	-0.2105	ACGxCTG	COVERED																																																																																			NOVEL	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000448515.2	6	3.308695	KEEP	7	0	0	11	309	TT	0.99254	0.518266	0		-	3	60	102	0	0	7.826845	19	60	568	61	ENST00000285039.7	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	47728889	47728889	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:47728889A>G			NA	NA				MYO5B (7426 upstream) : RN7SL310P (4480 downstream)						NA		NA									NA						cttgagcccaagagtttcaga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.47728889A>G		NA		hg19		0.02	-0.03509	CCAxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.701531	KEEP	0	0	0	9	240	AA	0.99254	0.019833	0			2	60	70	0	0	6.750122	2	60	64	18		0.5	0.019982
DCC	1630	__UNKNOWN__	__UNKNOWN__	18	50579453	50579453	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:50579453T>C	ENST00000581580.1	+	3	215				DCC_ENST00000580146.1_Intron|DCC_ENST00000412726.1_Intron|DCC_ENST00000442544.2_Intron			P43146	DCC_HUMAN	DCC netrin 1 receptor	NA		NA			anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		gtggaggttgtagtgagccga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323	1630		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	2701	protein-coding gene	gene with protein product	immunoglobulin superfamily, DCC subclass, member 1	120470	deleted in colorectal carcinoma		NA	2294591, 24400119	Standard	NM_005215	NM_005215	NA	Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000581580.1:c.-50-10222T>C	chr18.hg19:g.50579453T>C		NA		hg19		0.02	-0.157839	TTGxAGT	COVERED																																																																																			NOVEL	DCC-011	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447776.2	3	3.30564	KEEP	0	0	0	11	276	TT	0.993072	0.32057	0		+	3	60	90	0	0	6.992722	14	60	392	41	ENST00000581580.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	51649359	51649359	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:51649359A>G			NA	NA				AC090666.1 (36333 upstream) : MBD2 (29719 downstream)						NA		NA									NA						caacaagagcaaaactccatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.51649359A>G		NA		hg19		0.02	-0.201716	AGCxAAA	COVERED																																																																																			NOVEL					0			14	3.907147	KEEP	3	0	0	13	340	AA	0.993072	0.487146	0			3	60	92	1	0	7.192083	14	60	408	55		0.176471	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	52406423	52406423	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:52406423T>C			NA	NA				DYNAP (139699 upstream) : RAB27B (89006 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.52406423T>C		NA		hg19		0.02	-0.184187	TCAxGCC	COVERED																																																																																			NOVEL					0			7	3.307938	KEEP	3	0	0	11	298	TT	0.992708	0.42039	0			3	60	99	0	0	7.733407	16	60	476	55		0.157895	0.423478
CCDC68	80323	__UNKNOWN__	__UNKNOWN__	18	52585102	52585102	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:52585102T>A	ENST00000591504.1	-	10	1148				CCDC68_ENST00000432185.1_Intron|CCDC68_ENST00000337363.4_Intron	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	NA		NA								breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		acacacacactcacaccctca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													205	149	168			NA	NA	18		NA											NA				52585102		2203	4297	6500	SO:0001627	intron_variant				CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510	80323			24350	protein-coding gene	gene with protein product	cutaneous T-cell lymphoma associated antigen	NA			NA	11149944, 15142679	Standard	NM_025214	NM_025214	NA	Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.873+41A>T	chr18.hg19:g.52585102T>A		NA	B2R9I3	hg19	CCDS11959.1	0.02	1.537736	CACxCAC	COVERED																																																																																			NOVEL	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256006.1	12	4.241733	KEEP	0	1	25	23	626	TT	0.999957	0.992883	0		-	8	60	243	0	0	17.952958	51	60	1503	130	ENST00000591504.1	0.135593	0.992926
TCF4	6925	__UNKNOWN__	__UNKNOWN__	18	53033122	53033122	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:53033122C>T	ENST00000561992.1	-	3	378				TCF4_ENST00000568673.1_Intron|TCF4_ENST00000537578.1_Intron|TCF4_ENST00000566286.1_Intron|TCF4_ENST00000354452.3_Intron|TCF4_ENST00000565018.2_Intron|TCF4_ENST00000544241.2_Intron|TCF4_ENST00000570177.2_Intron|TCF4_ENST00000398339.1_Intron|TCF4_ENST00000564999.1_Intron|TCF4_ENST00000540999.1_Intron|TCF4_ENST00000564403.2_Intron|TCF4_ENST00000568740.1_Intron|TCF4_ENST00000537856.3_Intron|TCF4_ENST00000356073.4_Intron|TCF4_ENST00000564228.1_Intron|TCF4_ENST00000567880.1_Intron|TCF4_ENST00000566279.1_Intron|TCF4_ENST00000543082.1_Intron	NM_001243233.1	NP_001230162.1	P15884	ITF2_HUMAN	transcription factor 4	NA		NA			DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		aaactccatcccaaaaaaagc	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628	6925		Basic helix-loop-helix proteins	11634	protein-coding gene	gene with protein product		602272			NA	9302263, 2308860	Standard	NM_003199	NM_001083962	NA	Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000561992.1:c.21-14888G>A	chr18.hg19:g.53033122C>T		NA	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	hg19	CCDS58626.1	0.02	-0.210502	ATCxCAA	COVERED																																																																																			NOVEL	TCF4-010	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000421639.1	10	2.708364	KEEP	0	0	0	9	286	CC	0.99254	0.518266	0		-	4	60	109	0	0	8.280746	18	60	600	49	ENST00000561992.1	0.181818	0.522161
TCF4	6925	__UNKNOWN__	__UNKNOWN__	18	53253434	53253434	__UNKNOWN__	Intron	SNP	G	G	C	rs529440244		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:53253434G>C	ENST00000566279.1	-	2	240				TCF4_ENST00000537578.1_Intron|TCF4_ENST00000566286.1_Intron|TCF4_ENST00000354452.3_Intron|TCF4_ENST00000565018.2_Intron|TCF4_ENST00000398339.1_Intron|TCF4_ENST00000564999.1_Intron|TCF4_ENST00000564403.2_Intron|TCF4_ENST00000568740.1_Intron|TCF4_ENST00000356073.4_Intron|TCF4_ENST00000567880.1_Intron			P15884	ITF2_HUMAN	transcription factor 4	NA		NA			DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		agcagcagcagcagcagcagc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628	6925		Basic helix-loop-helix proteins	11634	protein-coding gene	gene with protein product		602272			NA	9302263, 2308860	Standard	NM_003199	NM_001083962	NA	Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000566279.1:c.72+841C>G	chr18.hg19:g.53253434G>C		NA	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	hg19		0.02	-0.377209	GCAxCAG	COVERED																																																																																			NOVEL	TCF4-045	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000421677.2	17	6.318163	KEEP	12	0	0	21	634	GG	0.999366	0.908493	0		-	4	60	127	0	0	8.919261	37	60	1262	98	ENST00000566279.1	0.097561	0.909069
CTD-2008L17.2	0	__UNKNOWN__	__UNKNOWN__	18	53723790	53723790	__UNKNOWN__	lincRNA	SNP	C	C	T	rs370529861		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:53723790C>T	ENST00000382897.2	-	0	899				RP11-456O19.2_ENST00000589450.1_lincRNA						NA		NA									NA						cccagctactcgggagattaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000382897.2:	chr18.hg19:g.53723790C>T		NA		hg19		0.02	-0.078933	ACTxGGG	UNCOVERED	.	.	.	.	.	.	.	.	.	.	C	2.401	-0.337526	0.05278	.	.	ENSG00000206129	ENST00000382897	.	.	.	0.225	-0.451	0.12214	.	.	.	.	.	T	0.29028	0.0721	.	.	.	.	.	.	.	.	.	.	.	.	T	0.33548	-0.9864	3	0.27785	T	0.31	.	.	.	.	.	.	.	.	Q	59	.	ENSP00000372353:R59Q	R	-	2	0	AC006305.1	51874788	0.065000	0.20965	0.195000	0.23364	0.201000	0.24016	-2.185000	0.01252	-0.779000	0.04560	-0.786000	0.03341	CGA	NOVEL	CTD-2008L17.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000449414.1	3	2.707262	KEEP	0	0	0	9	257	CC	0.99254	0.076759	0		-	3	60	90	0	0	8.132776	5	60	156	23	ENST00000382897.2	0.375	0.077336
WDR7	23335	__UNKNOWN__	__UNKNOWN__	18	54696383	54696383	__UNKNOWN__	3'UTR	SNP	T	T	C	rs1657397	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:54696383T>C	ENST00000254442.3	+	0	6629				WDR7-UT1_ENST00000592032.1_RNA|WDR7_ENST00000357574.3_3'UTR	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		AAATGTTCTGTGTGTCAGGAA	0.438		NA											T|||	1794	0.358227	0.5613	0.2795	5008	,	,	NA	17768	0.4345	NA	0.2644	False	NA	,,,	NA	NA	NA	2504	0.1575	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157	23335		WD repeat domain containing	13490	protein-coding gene	gene with protein product		613473			NA	10828621	Standard		XM_005266674	NA	Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.*1945T>C	chr18.hg19:g.54696383T>C		NA	A7E2C8|Q86UX5|Q86VP2|Q96PS7	hg19	CCDS11962.1	0.02	-0.368061	CTGxGTG	COVERED																																																																																			NOVEL	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256062.1	1	2.704785	KEEP	0	0	0	9	228	TT	0.99254	0.892605	0		+	12	60	406	0	0	35.569137	29	60	771	64	ENST00000254442.3	0.292683	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	55514270	55514270	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:55514270C>T			NA	NA				ATP8B1 (43943 upstream) : RP11-693L9.2 (114192 downstream)						NA		NA									NA						tttgggaggccgaggcaggtg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.55514270C>T		NA		hg19		0.02	-0.131556	GGCxGAG	COVERED																																																																																			NOVEL					0			6	3.007356	KEEP	3	0	0	10	283	CC	0.99254	0.227464	0			3	60	84	0	0	6.673486	11	60	359	36		0.214286	0.229173
MALT1	10892	__UNKNOWN__	__UNKNOWN__	18	56404449	56404449	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:56404449T>C	ENST00000348428.3	+	13	1861				RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Intron	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	NA		NA			activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						cagtggctcatgcctgtaatc	0.478		NA	T	BIRC3	MALT																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175	10892		Immunoglobulin superfamily / Immunoglobulin-like domain containing	6819	protein-coding gene	gene with protein product	paracaspase	604860		MLT	NA	10339464, 10406266, 10523859	Standard		NM_006785	NA	Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1603+1888T>C	chr18.hg19:g.56404449T>C		NA	Q9NTB7|Q9ULX4	hg19	CCDS11967.1	0.02	-0.166645	TCAxGCC	COVERED																																																																																			NOVEL	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256132.2	5	4.811561	KEEP	0	0	0	16	438	TT	0.999366	0.353723	0		+	3	60	102	0	0	8.372254	12	60	357	53	ENST00000348428.3	0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	56471939	56471939	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:56471939C>T			NA	NA				RN7SL112P (1378 upstream) : RNU6-219P (560 downstream)						NA		NA									NA						ccactgcactccagcctgggc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.56471939C>T		NA		hg19		0.02	-0.105261	ACTxCAG	UNCOVERED																																																																																			NOVEL					0			7	2.407422	KEEP	2	0	0	8	256	CC	0	0	0			3	54	85	0	0	7.27821	7	60	232	31		0.3	0.139832
CDH20	28316	__UNKNOWN__	__UNKNOWN__	18	59193168	59193168	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:59193168T>C	ENST00000262717.4	+	7	1415				CDH20_ENST00000536675.2_Intron|CDH20_ENST00000538374.1_Intron			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	NA		NA			homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				gtagctgggattacaggcaca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542	28316		Cadherins / Major cadherins	1760	protein-coding gene	gene with protein product		605807			NA	10995570	Standard	NM_031891	NM_031891	NA	Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1018-2032T>C	chr18.hg19:g.59193168T>C		NA	Q495S3	hg19	CCDS11977.1	0.02	-0.140329	GGAxTAC	UNCOVERED																																																																																			NOVEL	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256141.2	10	2.704058	KEEP	3	0	0	9	229	TT	0	0	0		+	3	24	98	0	0	8.301284	9	60	263	31	ENST00000262717.4	0.25	0.260965
CDH20	28316	__UNKNOWN__	__UNKNOWN__	18	59193174	59193174	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:59193174G>A	ENST00000262717.4	+	7	1415				CDH20_ENST00000536675.2_Intron|CDH20_ENST00000538374.1_Intron			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	NA		NA			homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				gggattacaggcacatgccac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542	28316		Cadherins / Major cadherins	1760	protein-coding gene	gene with protein product		605807			NA	10995570	Standard	NM_031891	NM_031891	NA	Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1018-2026G>A	chr18.hg19:g.59193174G>A		NA	Q495S3	hg19	CCDS11977.1	0.02	-0.140324	CAGxCAC	UNCOVERED																																																																																			NOVEL	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256141.2	10	2.707424	KEEP	3	0	0	9	261	GG	0	0	0		+	3	24	85	0	0	7.131973	8	60	256	30	ENST00000262717.4	0.272727	0.260965
RNF152	220441	__UNKNOWN__	__UNKNOWN__	18	59480550	59480550	__UNKNOWN__	3'UTR	SNP	T	T	C	rs113112635		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:59480550T>C	ENST00000312828.3	-	0	4246					NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	NA		NA			apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				cacacacacatacacaAGAAT	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641	220441		RING-type (C3HC4) zinc fingers	26811	protein-coding gene	gene with protein product		NA			NA		Standard	NM_173557	XM_005266650	NA	Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.*2535A>G	chr18.hg19:g.59480550T>C		NA	B3KV99|Q52LA4	hg19	CCDS11978.1	0.02	-0.350756	ACAxACA	COVERED																																																																																			NOVEL	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256180.1	23	4.858983	KEEP	1	2	53	35	897	TT	1	0.888875	0		-	3	60	107	1	0	7.809004	29	65	849	106	ENST00000312828.3	0.09375	0.888875
KIAA1468	57614	__UNKNOWN__	__UNKNOWN__	18	59957505	59957505	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:59957505G>A	ENST00000398130.2	+	27	3602				KIAA1468_ENST00000256858.6_Intron	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	NA		NA								autonomic_ganglia(1)|breast(4)|endometrium(4)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47		Colorectal(73;0.186)				ggtggctcacgcctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC011992	CCDS11979.2	18q21.33	2005-11-03			ENSG00000134444	ENSG00000134444	57614			29289	protein-coding gene	gene with protein product		NA			NA	11973628	Standard	NM_020854	NM_020854	NA	Approved	HsT885, HsT3308, FLJ33841	uc002lil.3	Q9P260	OTTHUMG00000132780	ENST00000398130.2:c.3371-1271G>A	chr18.hg19:g.59957505G>A		NA		hg19	CCDS11979.2	0.02	-0.114036	CACxCCT	UNCOVERED																																																																																			NOVEL	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256187.1	7	2.7066	KEEP	4	0	0	9	248	GG	0.99257	0.16126	0		+	3	60	89	0	0	7.400925	9	60	305	37	ENST00000398130.2	0.25	0.162467
PHLPP1	23239	__UNKNOWN__	__UNKNOWN__	18	60561618	60561618	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:60561618T>C	ENST00000262719.5	+	5	2300				PHLPP1_ENST00000400316.4_Intron			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	NA		NA			apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						ttggtagagatggggtttcac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913	23239		Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent, Pleckstrin homology (PH) domain containing	20610	protein-coding gene	gene with protein product		609396	pleckstrin homology domain containing, family E (with leucine rich repeats) member 1, PH domain and leucine rich repeat protein phosphatase	PLEKHE1, PHLPP	NA	10570941, 15808505	Standard	NM_194449	NM_194449	NA	Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.2067-626T>C	chr18.hg19:g.60561618T>C		NA	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	hg19	CCDS45881.2	0.02	-0.026315	AGAxGGG	UNCOVERED																																																																																			NOVEL	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319249.2	4	2.405772	KEEP	0	0	0	8	216	TT	0.99257	0	0		+	2	58	71	0	0	7.225193	1	7	28	16	ENST00000262719.5	0.666667	0
KDSR	2531	__UNKNOWN__	__UNKNOWN__	18	61005110	61005110	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:61005110A>G	ENST00000406396.3	-	8	1169				KDSR_ENST00000326575.5_Intron|KDSR_ENST00000589592.1_Intron	NM_002035.2	NP_002026.1	Q06136	KDSR_HUMAN	3-ketodihydrosphingosine reductase	NA		NA			3-keto-sphinganine metabolic process (GO:0006666)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-dehydrosphinganine reductase activity (GO:0047560)			endometrium(2)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	9						gcagtgagccaagatcgtgcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS11982.1	18q21	2011-09-20	2008-02-20	2008-02-20	ENSG00000119537	ENSG00000119537	2531	1.1.1.102	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	4021	protein-coding gene	gene with protein product	3-dehydrosphinganine reductase, short chain dehydrogenase/reductase family 35C, member 1	136440	follicular lymphoma variant translocation 1	FVT1	NA	8417785, 15328338, 17420465, 19027726	Standard		NM_002035	NA	Approved	DHSR, SDR35C1	uc010dpw.3	Q06136	OTTHUMG00000132792	ENST00000406396.3:c.777+922T>C	chr18.hg19:g.61005110A>G		NA	B2R5Y1|B4DMX0	hg19	CCDS11982.1	0.02	-0.140332	GCCxAGA	COVERED																																																																																			NOVEL	KDSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256200.2	5	3.007557	KEEP	2	0	0	10	275	AA	0.992708	0.259062	0		-	3	60	87	0	0	6.973096	11	60	333	42	ENST00000406396.3	0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	61241262	61241262	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:61241262A>G			NA	NA				SERPINB12 (7018 upstream) : SERPINB13 (13271 downstream)						NA		NA									NA						ttgcaccactacactccagcc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.61241262A>G		NA		hg19		0.02	-0.140316	ACTxCAC	COVERED																																																																																			NOVEL					0			8	3.606733	KEEP	1	0	0	12	306	AA	0.993634	0.259304	0			3	48	100	0	0	8.172455	12	60	343	38		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	62884484	62884484	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:62884484T>C			NA	NA				AC007631.1 (30230 upstream) : RP11-453M23.1 (206764 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.62884484T>C		NA		hg19		0.02	-0.140313	AGGxGTG	COVERED																																																																																			NOVEL					0			3	2.707004	KEEP	4	0	0	9	250	TT	0.99254	0.259018	0			3	60	99	0	0	8.072533	12	60	344	47		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	67516581	67516581	__UNKNOWN__	IGR	SNP	C	C	A	rs75203923	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:67516581C>A			NA	NA				DOK6 (258 upstream) : CD226 (13610 downstream)						NA		NA									NA						atggtgaaaccccgtctctac	0.547		NA											c|||	2269	0.453075	0.2413	0.5403	5008	,	,	NA	14145	0.5635	NA	0.5209	False	NA	,,,	NA	NA	NA	2504	0.4939	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.67516581C>A		NA		hg19		0.02	-0.131557	AACxCCG	UNCOVERED																																																																																			NOVEL					0			12	3.00869	KEEP	10	0	0	10	303	CC	0	0	0			5	60	134	0	0	11.821323	9	60	303	39		0.357143	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	69986828	69986828	__UNKNOWN__	IGR	SNP	A	A	T	rs150173536	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:69986828A>T			NA	NA				RP11-736G13.1 (375015 upstream) : CBLN2 (217086 downstream)						NA		NA									NA						taatcccagcactttgggagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.69986828A>T		NA		hg19		0.02	-0.131553	AGCxCTT	COVERED																																																																																			NOVEL					0			11	3.608305	KEEP	2	0	0	12	324	AA	0.993634	0.227714	0			3	60	81	0	0	6.373317	11	60	330	40		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	69986829	69986829	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:69986829C>A			NA	NA				RP11-736G13.1 (375016 upstream) : CBLN2 (217085 downstream)						NA		NA									NA						aatcccagcactttgggaggc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.69986829C>A		NA		hg19		0.02	-0.12281	GCAxTTT	COVERED																																																																																			NOVEL					0			11	3.610851	KEEP	2	0	0	12	372	CC	0.993634	0.227714	0			3	60	86	0	0	6.981831	10	60	345	40		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	69986830	69986830	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:69986830T>C			NA	NA				RP11-736G13.1 (375017 upstream) : CBLN2 (217084 downstream)						NA		NA									NA						atcccagcactttgggaggcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.69986830T>C		NA		hg19		0.02	-0.131569	CACxTTG	COVERED																																																																																			NOVEL					0			11	3.609334	KEEP	2	0	0	12	333	TT	0.993634	0.227714	0			3	60	108	0	0	9.072801	11	60	332	40		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	18	70790657	70790657	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:70790657C>G			NA	NA				RP11-676J15.1 (242025 upstream) : RP11-169F17.1 (35401 downstream)						NA		NA									NA						accagcctggccaacatggtg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr18.hg19:g.70790657C>G		NA		hg19		0.02	-0.06141	TGGxCAA	UNCOVERED																																																																																			NOVEL					0			1	2.406938	KEEP	0	0	0	8	238	CC	0.99257	0.043461	0			2	60	72	0	0	6.335548	5	60	171	18		0.285714	0.043787
CNDP2	55748	__UNKNOWN__	__UNKNOWN__	18	72188045	72188045	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:72188045A>G	ENST00000324262.4	+	0	2486				CNDP2_ENST00000579847.1_3'UTR|CNDP2_ENST00000324301.8_3'UTR	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	NA		NA			cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		gggcgacagaacgagacccca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	55748	3.4.13.18		24437	protein-coding gene	gene with protein product	cytosolic nonspecific dipeptidase	169800	peptidase A	PEPA	NA	12473676	Standard	NM_018235	NM_018235	NA	Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.*742A>G	chr18.hg19:g.72188045A>G		NA	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	hg19	CCDS12006.1	0.02	-0.166659	AGAxCGA	COVERED																																																																																			NOVEL	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256327.1	4	2.405792	KEEP	0	0	0	8	215	AA	0.99257	0.351317	0		+	3	60	105	0	0	8.491553	14	60	431	35	ENST00000324262.4	0.176471	0.353947
ADNP2	22850	__UNKNOWN__	__UNKNOWN__	18	77886490	77886490	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:77886490A>G	ENST00000262198.4	+	3	563					NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	NA		NA			cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		ccgagattgcaccactgcact	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544	22850		Homeoboxes / ZF class, Zinc fingers, C2H2-type	23803	protein-coding gene	gene with protein product		NA	zinc finger protein 508	ZNF508	NA		Standard	NM_014913	NM_014913	NA	Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.109-4496A>G	chr18.hg19:g.77886490A>G		NA	A8K951|O94943|Q9H9P3	hg19	CCDS32853.1	0.02	-0.14909	TGCxCCA	COVERED																																																																																			NOVEL	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000418979.1	9	2.406108	KEEP	0	0	0	8	220	AA	0.99257	0.289832	0		+	3	60	92	0	0	7.372652	12	60	347	37	ENST00000262198.4	0.2	0.292001
AC139100.2	0	__UNKNOWN__	__UNKNOWN__	18	77917149	77917149	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr18:77917149A>G	ENST00000586421.1	+	2	330				AC139100.2_ENST00000585422.1_Intron|AC139100.2_ENST00000587254.1_Intron|PARD6G_ENST00000353265.3_3'UTR|AC139100.2_ENST00000589574.1_Intron						NA		NA									NA						gggattacagacgtgagccac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000586421.1:c.97-3250A>G	chr18.hg19:g.77917149A>G		NA		hg19		0.02	-0.315751	CAGxCGT	COVERED																																																																																			NOVEL	AC139100.2-001	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000451060.1	2	5.111846	KEEP	0	0	0	17	453	AA	0.999366	0.817946	0		+	3	60	102	0	0	7.352554	28	60	845	74	ENST00000586421.1	0.096774	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	183690	183690	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:183690A>G			NA	NA				AC092192.1 (5777 upstream) : AC092299.8 (13384 downstream)						NA		NA									NA						aaagtgctggaattacaggtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.183690A>G		NA		hg19		0.02	-0.280658	TGGxATT	COVERED																																																																																			NOVEL					0			12	5.413936	KEEP	5	0	0	18	500	AA	0.999366	0.739203	0			3	60	101	0	0	7.252725	28	60	832	80		0.096774	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	479671	479671	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:479671G>A			NA	NA				ODF3L2 (4688 upstream) : MADCAM1 (9504 downstream)						NA		NA									NA						ccaaagtgctgggattacagg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.479671G>A		NA		hg19		0.02	1.42723	GCTxGGA	COVERED																																																																																			NOVEL					0			50	18.053193	KEEP	38	0	0	60	1820	GG	1	0.97082	0			4	60	121	0	0	8.557655	32	60	1095	191		0.111111	0.97082
AC009005.2	0	__UNKNOWN__	__UNKNOWN__	19	569461	569461	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:569461C>T	ENST00000589457.1	-	0	306				AC009005.2_ENST00000588290.1_RNA|AC009005.2_ENST00000590292.1_RNA|AC009005.2_ENST00000588908.1_RNA						NA		NA									NA						accctgtctccactaaaatac	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000589457.1:	chr19.hg19:g.569461C>T		NA		hg19		0.02	-0.087685	CTCxACT	UNCOVERED																																																																																			NOVEL	AC009005.2-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000452234.1	1	3.008564	KEEP	1	0	0	10	299	CC	0.992708	0.098994	0		-	3	49	78	0	1	6.741429	6	60	204	31	ENST00000589457.1	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	668132	668132	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:668132A>G			NA	NA				AC004156.3 (69 upstream) : FSTL3 (8259 downstream)						NA		NA									NA						agcactttggaaggccgaggt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.668132A>G		NA		hg19		0.02	-0.052623	TGGxAGG	UNCOVERED																																																																																			NOVEL					0			12	2.736425	KEEP	0	1	28	19	496	AA	0.999863	0.036761	0			2	60	71	0	0	6.396017	4	60	114	37		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	1022453	1022453	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1022453G>C			NA	NA				RNU6-2 (826 upstream) : CNN2 (3844 downstream)						NA		NA									NA						atccacccgcgtcagcctccc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.1022453G>C		NA		hg19		0.02	-0.061408	CGCxTCA	UNCOVERED																																																																																			NOVEL					0			4	2.704363	KEEP	0	0	0	9	253	GG	0.99254	0.04346	0			2	45	71	0	0	6.395717	4	60	132	21		0.333333	0.043787
ABCA7	10347	__UNKNOWN__	__UNKNOWN__	19	1044526	1044526	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1044526A>G	ENST00000435683.2	+	5	633				ABCA7_ENST00000433129.1_Intron|ABCA7_ENST00000263094.6_Intron			Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	NA		NA			apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gattacaggcatgagccactg	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													24	31	29			NA	NA	19		NA											NA				1044526		2200	4298	6498	SO:0001627	intron_variant			AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687	10347		ATP binding cassette transporters / subfamily A	37	protein-coding gene	gene with protein product		605414			NA		Standard	NM_019112	NM_019112	NA	Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000435683.2:c.634-50A>G	chr19.hg19:g.1044526A>G		NA	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	hg19		0.02	3.595828	GGCxTGA	COVERED																																																																																			NOVEL	ABCA7-002	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000395001.2	29	4.137945	KEEP	2	4	111	53	1461	AA	1	0.999995	0		+	6	60	206	0	0	13.480302	99	60	2926	249	ENST00000435683.2	0.057143	0.999995
STK11	6794	__UNKNOWN__	__UNKNOWN__	19	1200069	1200069	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1200069C>T	ENST00000585748.1	+	1	253							Q15831	STK11_HUMAN	serine/threonine kinase 11	NA		NA			activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		ctccacctcccgggctcaggt	0.483		14	D, Mis, N, F, S		NSCLC, pancreatic	jejunal harmartoma, ovarian, testicular, pancreatic			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)											NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		E, M, O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046	6794			11389	protein-coding gene	gene with protein product	polarization-related protein LKB1	602216	serine/threonine kinase 11 (Peutz-Jeghers syndrome)		NA	9425897	Standard	NM_000455	XM_005259617	NA	Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000585748.1:c.253+10411C>T	chr19.hg19:g.1200069C>T		NA	B2RBX7|E7EW76	hg19		0.02	-0.078945	TCCxGGG	UNCOVERED																																																																																			NOVEL	STK11-012	KNOWN	non_canonical_U12|mRNA_end_NF|basic	processed_transcript	NA	protein_coding	OTTHUMT00000450471.1	6	2.406747	KEEP	0	0	0	8	234	CC	0.99257	0.076761	0		+	3	60	89	0	0	7.843189	6	60	198	22	ENST00000585748.1	0.333333	0.077336
STK11	6794	__UNKNOWN__	__UNKNOWN__	19	1210899	1210899	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1210899C>T	ENST00000326873.7	+	1	1463				STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	NA		NA			activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(2)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		tggtggctcacgcctgtaatc	0.552		14	D, Mis, N, F, S		NSCLC, pancreatic	jejunal harmartoma, ovarian, testicular, pancreatic			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)											NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		E, M, O	22	Whole gene deletion(20)|Unknown(2)	cervix(15)|lung(3)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046	6794			11389	protein-coding gene	gene with protein product	polarization-related protein LKB1	602216	serine/threonine kinase 11 (Peutz-Jeghers syndrome)		NA	9425897	Standard	NM_000455	XM_005259617	NA	Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.290+3697C>T	chr19.hg19:g.1210899C>T		NA	B2RBX7|E7EW76	hg19	CCDS45896.1	0.02	-0.157884	TCAxGCC	COVERED																																																																																			NOVEL	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449839.3	5	6.014016	KEEP	0	0	0	20	546	CC	0.999863	0.322762	0		+	3	60	89	0	0	6.979074	13	60	411	52	ENST00000326873.7	0.1875	0.322807
MUM1	84939	__UNKNOWN__	__UNKNOWN__	19	1309222	1309222	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1309222T>C	ENST00000344663.3	+	1	32							Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	NA		NA			chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		tttgtagagatggggtttcac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953	84939			29641	protein-coding gene	gene with protein product		NA			NA	11042152, 7644523	Standard	NM_032853	NM_032853	NA	Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000344663.3:c.-70+23301T>C	chr19.hg19:g.1309222T>C		NA	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	hg19	CCDS12062.1	0.02	-0.052623	AGAxGGG	UNCOVERED																																																																																			NOVEL	MUM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		6	2.706378	KEEP	0	0	0	9	241	TT	0.99254	0.036491	0		+	2	60	70	0	0	6.750593	2	60	53	18	ENST00000344663.3	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	1481038	1481038	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1481038G>A			NA	NA				C19orf25 (1483 upstream) : PCSK4 (388 downstream)						NA		NA									NA						agtggctcacgcctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.1481038G>A		NA		hg19		0.02	-0.1842	CACxCCT	COVERED																																																																																			NOVEL					0			15	3.516032	KEEP	0	1	29	22	617	GG	0.999892	0.423432	0			3	60	86	0	0	6.361681	17	60	539	56		0.15	0.423478
TCF3	6929	__UNKNOWN__	__UNKNOWN__	19	1624886	1624886	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1624886T>C	ENST00000262965.5	-	7	844				TCF3_ENST00000453954.2_Intron|TCF3_ENST00000588136.1_Intron|TCF3_ENST00000395423.3_Intron|TCF3_ENST00000344749.5_Intron	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	NA		NA			anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gcgctgttgctcaggctggag	0.517		NA	T	PBX1, HLF, TFPT	pre B-ALL																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564	6929		Basic helix-loop-helix proteins	11633	protein-coding gene	gene with protein product	transcription factor E2-alpha, immunoglobulin transcription factor 1, kappa-E2-binding factor, E2A immunoglobulin enhancer-binding factor E12/E47, VDR interacting repressor	147141			NA	2308859, 1967983	Standard	NM_003200	NM_003200	NA	Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.499+688A>G	chr19.hg19:g.1624886T>C		NA	Q53R97|Q6PD70|Q9NP00	hg19	CCDS12074.1	0.02	-0.087699	TGCxCAG	UNCOVERED																																																																																			NOVEL	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449367.1	3	2.406101	KEEP	0	0	0	8	220	TT	0.99257	0.09898	0		-	3	60	104	0	0	9.179081	7	60	209	27	ENST00000262965.5	0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	1655111	1655111	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1655111C>T			NA	NA				TCF3 (2507 upstream) : AC005256.1 (93047 downstream)						NA		NA									NA						acgatcctcccgcctcagttt	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.1655111C>T		NA		hg19		0.02	-0.122808	TCCxGCC	COVERED																																																																																			NOVEL					0			1	2.406504	KEEP	0	0	0	8	233	CC	0.99257	0.194853	0			3	60	92	0	0	7.700992	9	60	297	34		0.25	0.196312
ATP8B3	148229	__UNKNOWN__	__UNKNOWN__	19	1798691	1798691	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:1798691C>T	ENST00000310127.6	-	14	1791				ATP8B3_ENST00000525591.1_Intron|ATP8B3_ENST00000539485.1_Intron	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	NA		NA			binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gagccgagatcgcgccactgc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270	148229		ATPases / P-type	13535	protein-coding gene	gene with protein product	aminophospholipid translocase ATP8B3, potential phospholipid-transporting ATPase IK	605866	ATPase, Class I, type 8B, member 3, ATPase, class I, type 8B, member 3		NA	11015572	Standard	NM_138813	NM_138813	NA	Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.1552+1254G>A	chr19.hg19:g.1798691C>T		NA	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	hg19	CCDS45901.1	0.02	-0.385863	GATxGCG	COVERED																																																																																			NOVEL	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388279.1	4	9.925914	KEEP	5	0	0	33	939	CC	0.999997	0.926638	0		-	5	60	128	0	0	8.896195	31	60	956	93	ENST00000310127.6	0.138889	0.92664
TMPRSS9	360200	__UNKNOWN__	__UNKNOWN__	19	2410284	2410284	__UNKNOWN__	Silent	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:2410284C>T	ENST00000332578.3	+	8	1044	c.1044C>T	c.(1042-1044)gcC>gcT	p.A348A		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	348	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.	NA			plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCAGAAAGCCACTGTGGAGC	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													113	98	103			NA	NA	19		NA											NA				2410284		2203	4300	6503	SO:0001819	synonymous_variant			AJ488946	CCDS12088.1	19p13.3	2010-04-13					360200		Serine peptidases / Transmembrane	30079	protein-coding gene	gene with protein product	polyserase 1	610477			NA	12886014	Standard	NM_182973	NM_182973	NA	Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1044C>T	chr19.hg19:g.2410284C>T		NA	Q6ZND6|Q7Z411	hg19	CCDS12088.1	0.02	1.315737	AGCxACT	COVERED																																																																																			NOVEL	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451330.3	0	3.610603	KEEP	0	0	0	12	363	CC	0.993634	0.992508	0		+	35	60	1013	0	0	95.210751	41	60	1407	127	ENST00000332578.3	0.460526	0.998867
GNG7	2788	__UNKNOWN__	__UNKNOWN__	19	2571654	2571654	__UNKNOWN__	Intron	SNP	T	T	C	rs539388489	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:2571654T>C	ENST00000382159.3	-	3	121					NM_052847.2	NP_443079.1	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein), gamma 7	NA		NA			behavioral fear response (GO:0001662)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of adenylate cyclase activity (GO:0045761)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			central_nervous_system(2)|large_intestine(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		agtgcagaggtgcggtctcgg	0.488		NA											T|||	18	0.00359425	0.0	0.0072	5008	,	,	NA	13481	0.0	NA	0.0119	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB010414	CCDS12091.1	19p13.3	2010-02-17			ENSG00000176533	ENSG00000176533	2788			4410	protein-coding gene	gene with protein product		604430			NA	9600093	Standard	NM_052847	NM_052847	NA	Approved	FLJ00058	uc002lwd.2	O60262		ENST00000382159.3:c.77-16468A>G	chr19.hg19:g.2571654T>C		NA	B2R496	hg19	CCDS12091.1	0.02	-0.087695	AGGxGCG	UNCOVERED																																																																																			NOVEL	GNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451345.1	8	2.405931	KEEP	0	0	0	8	218	TT	0.99257	0.09898	0		-	3	60	96	0	0	8.378993	7	60	197	24	ENST00000382159.3	0.3	0.099721
GNG7	2788	__UNKNOWN__	__UNKNOWN__	19	2624331	2624331	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:2624331T>G	ENST00000382159.3	-	2	121					NM_052847.2	NP_443079.1	O60262	GBG7_HUMAN	guanine nucleotide binding protein (G protein), gamma 7	NA		NA			behavioral fear response (GO:0001662)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of adenylate cyclase activity (GO:0045761)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			central_nervous_system(2)|large_intestine(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		atcgagaccatcctggctaac	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB010414	CCDS12091.1	19p13.3	2010-02-17			ENSG00000176533	ENSG00000176533	2788			4410	protein-coding gene	gene with protein product		604430			NA	9600093	Standard	NM_052847	NM_052847	NA	Approved	FLJ00058	uc002lwd.2	O60262		ENST00000382159.3:c.76+21890A>C	chr19.hg19:g.2624331T>G		NA	B2R496	hg19	CCDS12091.1	0.02	-0.070162	CCAxCCT	UNCOVERED																																																																																			NOVEL	GNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451345.1	7	3.60908	KEEP	2	0	0	12	328	TT	0.993634	0.053793	0		-	2	40	73	0	0	6.43579	5	60	151	34	ENST00000382159.3	0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	2706921	2706921	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:2706921G>A			NA	NA				GNG7 (4214 upstream) : DIRAS1 (7643 downstream)						NA		NA									NA						ttgggaggccgaggcgggcgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.2706921G>A		NA		hg19		0.02	1.526195	GCCxAGG	COVERED																																																																																			NOVEL					0			43	2.237908	KEEP	20	4	106	45	1357	GG	1	0.973965	0			5	41	151	1	0	11.002368	34	60	1120	162		0.128205	0.973965
ZNF556	80032	__UNKNOWN__	__UNKNOWN__	19	2868973	2868973	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:2868973T>C	ENST00000586426.1	+	1	90				ZNF556_ENST00000307635.2_Intron			Q9HAH1	ZN556_HUMAN	zinc finger protein 556	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		cacctcagcctcccaaagtgc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000	80032		Zinc fingers, C2H2-type, -	25669	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024967	XM_005259647	NA	Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000586426.1:c.3+1551T>C	chr19.hg19:g.2868973T>C		NA	Q96GM3	hg19		0.02	-0.096493	GCCxCCC	UNCOVERED																																																																																			NOVEL	ZNF556-002	NOVEL	NAGNAG_splice_site|basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000451639.2	8	2.406472	KEEP	6	0	0	8	228	TT	0	0	0		+	3	60	105	0	0	9.27864	7	60	221	35	ENST00000586426.1	0.3	0.120436
TLE6	79816	__UNKNOWN__	__UNKNOWN__	19	2992919	2992919	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:2992919T>G	ENST00000246112.4	+	15	1587				TLE6_ENST00000452088.1_Intron	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	NA		NA			regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gggcgcagtgtctcacgcctg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953	79816		WD repeat domain containing	30788	protein-coding gene	gene with protein product		612399	transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)		NA	11486032	Standard	NM_024760	NM_024760	NA	Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.1387-511T>G	chr19.hg19:g.2992919T>G		NA	J3KMZ1	hg19	CCDS45910.1	0.02	-0.184195	GTGxCTC	COVERED																																																																																			NOVEL	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345996.3	5	3.308422	KEEP	0	0	0	11	305	TT	0.993072	0.454585	0		+	3	60	103	0	0	8.291694	14	60	419	50	ENST00000246112.4	0.176471	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	3086471	3086471	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:3086471C>T			NA	NA				AES (23366 upstream) : GNA11 (7936 downstream)						NA		NA									NA						aggatggtctcgatctcctga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.3086471C>T		NA		hg19		0.02	-0.061394	TCTxGAT	UNCOVERED																																																																																			NOVEL					0			3	2.406999	KEEP	3	0	0	8	241	CG	0	0	0			3	40	84	0	0	7.754396	4	60	131	22		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	3169052	3169052	__UNKNOWN__	IGR	SNP	C	C	T	rs12610895	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:3169052C>T			NA	NA				GNA15 (5285 upstream) : S1PR4 (3291 downstream)						NA		NA									NA						cgtcagccaccgtgcccggtc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.3169052C>T		NA		hg19		0.02	-0.105256	CACxGTG	UNCOVERED																																																																																			NOVEL					0			8	2.406292	KEEP	3	0	0	8	233	CC	0.99257	0.138793	0			6	60	184	0	0	20.014003	1	60	36	30		0.857143	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	3703520	3703520	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:3703520C>T			NA	NA				PIP5K1C (3043 upstream) : TJP3 (4586 downstream)						NA		NA									NA						tgcactccagcctgggcgaca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.3703520C>T		NA		hg19		0.02	-0.087717	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			5	3.91107	KEEP	2	0	0	13	380	CC	0.993072	0.09903	0			3	53	89	0	0	7.843236	6	60	197	23		0.333333	0.099721
TJP3	27134	__UNKNOWN__	__UNKNOWN__	19	3720951	3720951	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:3720951A>G	ENST00000541714.2	+	2	453				TJP3_ENST00000539908.2_Intron	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	NA		NA			regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		tgtcgcccagactggagtgca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289	27134			11829	protein-coding gene	gene with protein product	zona occludens 3	612689			NA		Standard		NM_001267560	NA	Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.-9-7471A>G	chr19.hg19:g.3720951A>G		NA	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	hg19	CCDS32873.2	0.02	-0.035071	CAGxCTG	UNCOVERED																																																																																			NOVEL	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453434.1	2	2.404021	KEEP	0	0	0	8	200	AA	0.99257	0.019833	0		+	2	60	66	0	0	6.350895	2	60	52	12	ENST00000541714.2	0.5	0.019982
ZFR2	23217	__UNKNOWN__	__UNKNOWN__	19	3831499	3831499	__UNKNOWN__	Nonsense_Mutation	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:3831499A>T	ENST00000262961.4	-	5	664	c.654T>A	c.(652-654)taT>taA	p.Y218*	ZFR2_ENST00000591965.1_5'UTR	NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	218	Pro-rich.	NA					nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GCGCTGGAGGATAGAAAGGGC	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													9	10	10			NA	NA	19		NA											NA				3831499		1843	3941	5784	SO:0001587	stop_gained			AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278	23217			29189	protein-coding gene	gene with protein product		NA	KIAA1086	KIAA1086	NA	10470851	Standard	NM_015174	NM_015174	NA	Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.654T>A	chr19.hg19:g.3831499A>T	ENSP00000262961:p.Tyr218*	NA		hg19	CCDS45921.1	0.02	-0.385594	AGGxTAG	COVERED	.	.	.	.	.	.	.	.	.	.	a	15.93	2.979227	0.53827	.	.	ENSG00000105278	ENST00000262961;ENST00000438164	.	.	.	3.51	-3.65	0.04502	.	0.425981	0.21015	U	0.081602	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.0452	0.19755	0.3967:0.147:0.4563:0.0	.	.	.	.	X	218	.	ENSP00000262961:Y218X	Y	-	3	2	ZFR2	3782499	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-1.349000	0.02627	-1.194000	0.02684	0.449000	0.29647	TAT	NOVEL	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453648.2	2	4.489619	KEEP	0	0	0	15	376	AA	0.997832	0.924631	0		-	22	60	584	0	0	55.622957	22	60	624	93	ENST00000262961.4	0.5	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	3990838	3990838	__UNKNOWN__	IGR	SNP	C	C	T	rs545600807	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:3990838C>T			NA	NA				EEF2 (5371 upstream) : PIAS4 (16805 downstream)						NA		NA									NA						ccctccttccctccttccttc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.3990838C>T		NA		hg19		0.02	-0.184216	TCCxTCC	COVERED																																																																																			NOVEL					0			13	3.006908	KEEP	0	0	0	10	297	CC	0.992708	0.42039	0			3	60	91	0	0	6.861032	17	60	588	40		0.15	0.423478
CREB3L3	84699	__UNKNOWN__	__UNKNOWN__	19	4160104	4160104	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4160104G>C	ENST00000078445.2	+	4	723				CREB3L3_ENST00000602257.1_Intron|CREB3L3_ENST00000252587.3_Intron|CREB3L3_ENST00000602147.1_Intron|CREB3L3_ENST00000595923.1_Intron	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	NA		NA			positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		accagcctgggcaacatggtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566	84699		basic leucine zipper proteins	18855	protein-coding gene	gene with protein product		611998			NA	11353085	Standard	NM_032607	NM_032607	NA	Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.576+325G>C	chr19.hg19:g.4160104G>C		NA	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	hg19	CCDS12121.1	0.02	-0.122806	TGGxCAA	COVERED																																																																																			NOVEL	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000457922.1	4	2.707961	KEEP	2	0	0	9	274	GG	0.99257	0.194853	0		+	3	60	89	0	0	7.281872	10	60	342	32	ENST00000078445.2	0.230769	0.196312
STAP2	55620	__UNKNOWN__	__UNKNOWN__	19	4325722	4325722	__UNKNOWN__	Intron	SNP	C	C	G	rs553475592		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4325722C>G	ENST00000600324.1	-	10	897				STAP2_ENST00000594605.1_Intron|STAP2_ENST00000597593.1_Intron	NM_017720.2	NP_060190.2	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	NA		NA				cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		aatcccagcactttgggaggc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078	55620			30430	protein-coding gene	gene with protein product		607881			NA	10980601, 11441184	Standard	NM_001013841	XM_005259592	NA	Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000600324.1:c.830-180G>C	chr19.hg19:g.4325722C>G		NA	A6NKK3|Q9NXI2	hg19	CCDS12128.1	0.02	-0.078956	GCAxTTT	UNCOVERED																																																																																			NOVEL	STAP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458115.3	3	3.008571	KEEP	4	0	0	10	305	CC	0.99254	0.076759	0		-	2	60	72	0	0	6.335526	5	60	174	39	ENST00000600324.1	0.285714	0.077336
STAP2	55620	__UNKNOWN__	__UNKNOWN__	19	4331923	4331923	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4331923C>T	ENST00000600324.1	-	4	422				STAP2_ENST00000594605.1_Intron	NM_017720.2	NP_060190.2	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	NA		NA				cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		agcgagactccgtctcaaaaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078	55620			30430	protein-coding gene	gene with protein product		607881			NA	10980601, 11441184	Standard	NM_001013841	XM_005259592	NA	Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000600324.1:c.354+95G>A	chr19.hg19:g.4331923C>T		NA	A6NKK3|Q9NXI2	hg19	CCDS12128.1	0.02	1.348352	CTCxGTC	COVERED																																																																																			NOVEL	STAP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458115.3	13	5.656298	KEEP	3	2	51	37	1075	CC	1	0.990964	0		-	6	60	177	1	0	12.23975	51	60	1668	133	ENST00000600324.1	0.105263	0.990964
PLIN4	729359	__UNKNOWN__	__UNKNOWN__	19	4514925	4514925	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4514925C>T	ENST00000301286.3	-	3	213					NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	NA		NA				cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						cggtggctcacgcctgtaatc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676	729359		Perilipins	29393	protein-coding gene	gene with protein product		613247	KIAA1881	KIAA1881	NA	11572484, 19638644	Standard	XM_170901	NM_001080400	NA	Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.214-1209G>A	chr19.hg19:g.4514925C>T		NA	A6NEI2	hg19	CCDS45927.1	0.02	-0.236481	TCAxGCC	COVERED																																																																																			NOVEL	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000395095.1	14	4.811769	KEEP	5	0	0	16	441	CC	0.99649	0.639096	0		-	4	60	110	0	0	8.067429	22	60	672	70	ENST00000301286.3	0.153846	0.641347
TNFAIP8L1	126282	__UNKNOWN__	__UNKNOWN__	19	4653558	4653558	__UNKNOWN__	3'UTR	SNP	A	A	G	rs529460475	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4653558A>G	ENST00000536716.1	+	0	1823				TNFAIP8L1_ENST00000327473.4_3'UTR	NM_001167942.1	NP_001161414.1	Q8WVP5	TP8L1_HUMAN	tumor necrosis factor, alpha-induced protein 8-like 1	NA		NA			negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)				endometrium(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		cacaaggtcaagagatcgaga	0.517		NA											a|||	5	0.000998403	0.0	0.0	5008	,	,	NA	15705	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0031	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC017672	CCDS12132.1	19p13.3	2008-02-05				ENSG00000185361	126282			28279	protein-coding gene	gene with protein product		615869			NA	12477932	Standard	NM_152362	NM_001167942	NA	Approved	MGC17791	uc002max.3	Q8WVP5		ENST00000536716.1:c.*1116A>G	chr19.hg19:g.4653558A>G		NA	D6W627	hg19	CCDS12132.1	0.02	-0.166651	TCAxGAG	UNCOVERED																																																																																			NOVEL	TNFAIP8L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458662.1	13	3.608249	KEEP	15	0	0	12	327	AA	0	0	0		+	3	58	96	0	0	7.43342	16	60	483	60	ENST00000536716.1	0.157895	0.353947
MIR7-3HG	284424	__UNKNOWN__	__UNKNOWN__	19	4769978	4769978	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4769978G>A	ENST00000586721.1	+	0	340							Q8N6C7	PGSF1_HUMAN	MIR7-3 host gene (non-protein coding)	NA		NA									NA						gcagtggcacgatctcggctc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AB058892		19p13.3	2014-03-17	2011-09-01	2011-09-01	ENSG00000176840	ENSG00000176840	284424		Long non-coding RNAs	30049	non-coding RNA	RNA, long non-coding	pituitary gland specific factor 1a, pituitary gland specific factor 1b	NA	chromosome 19 open reading frame 30, non-protein coding RNA 306, long intergenic non-protein coding RNA 306	C19orf30, NCRNA00306, LINC00306	NA	11854097	Standard	NR_027148	NR_027148	NA	Approved	PGSF1, PGSF1a, PGSF1b, Huh7, uc002mbe.2	uc010xii.2	Q8N6C7	OTTHUMG00000150589	ENST00000586721.1:	chr19.hg19:g.4769978G>A		NA	D6W630|Q17RJ9|Q8N6C6	hg19		0.02	-0.078883	CACxATC	UNCOVERED																																																																																			NOVEL	MIR7-3HG-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000459345.1	5	3.006449	KEEP	1	0	0	10	269	GG	0.992708	0.098994	0		+	3	60	73	0	0	6.428701	5	60	157	25	ENST00000586721.1	0.375	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	4799670	4799670	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4799670A>G			NA	NA				AC005523.2 (4099 upstream) : TICAM1 (16273 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.4799670A>G		NA		hg19		0.02	-0.026318	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			2	2.406136	KEEP	4	0	0	8	222	AA	0	0	0			2	60	71	0	0	7.224953	1	60	31	21		0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	4832170	4832170	__UNKNOWN__	IGR	SNP	G	G	A	rs7249807	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4832170G>A			NA	NA				TICAM1 (454 upstream) : CTC-518P12.6 (6173 downstream)						NA		NA									NA						ggagtgcaatggcgcaatctc	0.438		NA											G|||	686	0.136981	0.2224	0.0937	5008	,	,	NA	15126	0.0427	NA	0.0527	False	NA	,,,	NA	NA	NA	2504	0.2362	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.4832170G>A		NA		hg19		0.02	-0.114015	AATxGCG	UNCOVERED																																																																																			NOVEL					0			7	2.708005	KEEP	0	0	0	9	275	GG	0.99254	0.161255	0			8	60	229	0	0	23.395376	4	60	144	29		0.666667	0.162467
PLIN3	10226	__UNKNOWN__	__UNKNOWN__	19	4849208	4849208	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4849208A>C	ENST00000592528.1	-	6	660				PLIN3_ENST00000221957.4_Intron|PLIN3_ENST00000585479.1_Intron			O60664	PLIN3_HUMAN	perilipin 3	NA		NA			vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	tggtcttgaaatcctggactc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355	10226		Perilipins	16893	protein-coding gene	gene with protein product	cargo selection protein (mannose 6 phosphate receptor binding protein), placental protein 17, MPR-BINDING PROTEIN, 47-KD	602702	mannose-6-phosphate receptor binding protein 1	M6PRBP1	NA	9590177, 6856484, 19638644	Standard	NM_005817	NM_005817	NA	Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000592528.1:c.599-1306T>G	chr19.hg19:g.4849208A>C		NA	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	hg19	CCDS59337.1	0.02	-0.043853	GAAxTCC	UNCOVERED																																																																																			NOVEL	PLIN3-007	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450437.1	7	3.908962	KEEP	0	0	0	13	343	AA	0.994391	0.023939	0		-	2	60	71	0	0	6.850652	2	60	55	28	ENST00000592528.1	0.5	0.024074
PLIN3	10226	__UNKNOWN__	__UNKNOWN__	19	4858719	4858719	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4858719T>G	ENST00000592528.1	-	4	410				PLIN3_ENST00000221957.4_Intron|PLIN3_ENST00000585479.1_Intron			O60664	PLIN3_HUMAN	perilipin 3	NA		NA			vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	tttggtttttttttttttttt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355	10226		Perilipins	16893	protein-coding gene	gene with protein product	cargo selection protein (mannose 6 phosphate receptor binding protein), placental protein 17, MPR-BINDING PROTEIN, 47-KD	602702	mannose-6-phosphate receptor binding protein 1	M6PRBP1	NA	9590177, 6856484, 19638644	Standard	NM_005817	NM_005817	NA	Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000592528.1:c.348+882A>C	chr19.hg19:g.4858719T>G		NA	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	hg19	CCDS59337.1	0.02	-0.114029	TTTxTTT	UNCOVERED																																																																																			NOVEL	PLIN3-007	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450437.1	7	3.035649	KEEP	0	1	5	12	325	TT	0.994391	0.161555	0		-	8	60	270	2	0	28.017041	3	60	90	38	ENST00000592528.1	0.727273	0.162467
UHRF1	29128	__UNKNOWN__	__UNKNOWN__	19	4926127	4926127	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:4926127T>C	ENST00000592666.1	+	0	729							Q96T88	UHRF1_HUMAN	ubiquitin-like with PHD and ring finger domains 1	NA		NA			cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|histone monoubiquitination (GO:0010390)|histone ubiquitination (GO:0016574)|maintenance of DNA methylation (GO:0010216)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity (GO:2000373)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autoubiquitination (GO:0051865)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|replication fork (GO:0005657)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|hemi-methylated DNA-binding (GO:0044729)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|upper_aerodigestive_tract(2)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0276)		aggctggtcttgaactcctga	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF129507	CCDS74262.1, CCDS74263.1	19p13.3	2012-04-20	2008-08-14		ENSG00000034063	ENSG00000276043	29128		RING-type (C3HC4) zinc fingers	12556	protein-coding gene	gene with protein product		607990			NA	10646863	Standard	NM_001048201	NM_001048201	NA	Approved	ICBP90, Np95, FLJ21925, RNF106	uc002mbo.3	Q96T88		ENST00000592666.1:	chr19.hg19:g.4926127T>C		NA	A0JBR2|A8K024|B2RBA9|Q2HIX7|Q8J022|Q9H6S6|Q9P115|Q9P1U7	hg19		0.02	-0.131518	TCTxGAA	UNCOVERED																																																																																			NOVEL	UHRF1-006	KNOWN	sequence_error|basic	processed_transcript	NA	processed_transcript	OTTHUMT00000450444.1	5	3.007696	KEEP	4	0	0	10	277	TT	0	0	0		+	3	59	93	0	0	7.573586	11	60	311	39	ENST00000592666.1	0.214286	0.260965
PTPRS	5802	__UNKNOWN__	__UNKNOWN__	19	5316640	5316640	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:5316640C>G	ENST00000588552.1	-	1	140				PTPRS_ENST00000357368.4_Intron|PTPRS_ENST00000262963.6_Intron|PTPRS_ENST00000372412.4_Intron|PTPRS_ENST00000348075.2_Intron|PTPRS_ENST00000353284.2_Intron			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	NA		NA			cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	ctgacctcaactgatccaccc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426	5802		Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	9681	protein-coding gene	gene with protein product		601576			NA	8954782, 8524829	Standard		NM_002850	NA	Approved		uc002mbv.3	Q13332		ENST00000588552.1:c.5303+24034G>C	chr19.hg19:g.5316640C>G		NA	O75255|O75870|Q15718|Q16341|Q2M3R7	hg19		0.02	-0.078942	CAAxTGA	UNCOVERED																																																																																			NOVEL	PTPRS-004	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000450761.2	2	2.407412	KEEP	1	0	0	8	254	CC	0.99257	0.076761	0		-	3	60	94	1	0	8.343493	6	60	195	30	ENST00000588552.1	0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	5574569	5574569	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:5574569A>G			NA	NA				TINCR (6524 upstream) : SAFB2 (12440 downstream)						NA		NA									NA						aggctggagtacagtggcatg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.5574569A>G		NA		hg19		0.02	-0.052579	AGTxCAG	UNCOVERED																																																																																			NOVEL					0			5	3.004917	KEEP	0	0	0	10	249	AA	0.992708	0.036498	0			2	48	71	0	0	6.397101	4	60	102	21		0.333333	0.036766
HSD11B1L	374875	__UNKNOWN__	__UNKNOWN__	19	5684307	5684307	__UNKNOWN__	5'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:5684307A>G	ENST00000581521.1	+	0	407				RPL36_ENST00000582380.2_Intron|HSD11B1L_ENST00000423665.2_Intron|RPL36_ENST00000579649.1_Intron|HSD11B1L_ENST00000577917.1_Intron|HSD11B1L_ENST00000581773.1_Intron|HSD11B1L_ENST00000342970.2_Intron|HSD11B1L_ENST00000581893.1_Intron|HSD11B1L_ENST00000422535.2_Intron|HSD11B1L_ENST00000301382.4_Intron|HSD11B1L_ENST00000583928.1_Intron|HSD11B1L_ENST00000339423.2_Intron|HSD11B1L_ENST00000411793.2_Intron|RPL36_ENST00000577222.1_Intron|HSD11B1L_ENST00000577701.1_Intron			Q7Z5J1	DHI1L_HUMAN	hydroxysteroid (11-beta) dehydrogenase 1-like	NA		NA				extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)				NA						gattccaggcatgagccacca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AY268353	CCDS12144.1, CCDS12145.1, CCDS12146.1, CCDS45931.1, CCDS45932.1, CCDS58641.1, CCDS58642.1, CCDS74266.1	19p13.3	2011-09-20				ENSG00000167733	374875	1.1.1.-	Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3	30419	protein-coding gene	gene with protein product	short chain dehydrogenase/reductase 10, short chain dehydrogenase/reductase family 26C, member 2	NA			NA	12477932	Standard	NM_198706	NM_001267868	NA	Approved	SCDR10, SDR26C2	uc010dug.4	Q7Z5J1		ENST00000581521.1:c.-69A>G	chr19.hg19:g.5684307A>G		NA	Q05D45|Q52LF4|Q7Z5I9|Q7Z5J0|Q7Z5P5|Q7Z5P6|Q7Z5P7|Q7Z5P8	hg19	CCDS12145.1	0.02	3.873857	GGCxTGA	COVERED																																																																																			NOVEL	HSD11B1L-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000442581.1	29	11.517553	KEEP	2	6	175	100	2743	AA	1	0.999978	0		+	7	60	218	1	0	14.309298	88	60	2617	310	ENST00000581521.1	0.073684	0.999978
CATSPERD	257062	__UNKNOWN__	__UNKNOWN__	19	5739580	5739580	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:5739580T>C	ENST00000381624.3	+	7	634				CATSPERD_ENST00000381614.2_Intron	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	NA		NA			multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)					NA						tggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898	257062			28598	protein-coding gene	gene with protein product		NA	transmembrane protein 146	TMEM146	NA	21224844	Standard	NM_152784	NM_152784	NA	Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.573+130T>C	chr19.hg19:g.5739580T>C		NA	Q6ZRP1	hg19	CCDS12149.2	0.02	-0.210457	TCAxGCC	COVERED																																																																																			NOVEL	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286953.2	8	2.406223	KEEP	2	0	0	8	223	GT	0.99257	0.518282	0		+	3	60	99	0	0	7.527414	19	60	557	45	ENST00000381624.3	0.136364	0.522161
AC104532.2	0	__UNKNOWN__	__UNKNOWN__	19	5912833	5912833	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:5912833G>T	ENST00000588891.1	+	2	241				AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000588776.1_5'UTR						NA		NA									NA						ttgcacaggcgggtctcaaac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000588891.1:c.192-1399G>T	chr19.hg19:g.5912833G>T		NA		hg19		0.02	-0.096493	GGCxGGT	UNCOVERED																																																																																			NOVEL	AC104532.2-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000452254.1	11	2.700361	KEEP	0	0	0	9	257	GG	0.99254	0.119538	0		+	3	60	91	0	0	7.87833	7	60	237	26	ENST00000588891.1	0.3	0.120436
CTC-232P5.1	0	__UNKNOWN__	__UNKNOWN__	19	5981878	5981878	__UNKNOWN__	RNA	SNP	T	T	G	rs80175951		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:5981878T>G	ENST00000587836.1	+	0	112					NR_046376.1					NA		NA									NA						aaaaaaaaaaTACACAATATg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000587836.1:	chr19.hg19:g.5981878T>G		NA		hg19		0.02	-0.12274	AAAxACA	COVERED																																																																																			NOVEL	CTC-232P5.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000452686.1	11	3.30733	KEEP	0	0	0	11	291	TT	0.993072	0.194952	0		+	3	60	102	1	0	8.979201	7	60	197	43	ENST00000587836.1	0.3	0.196312
GTF2F1	2962	__UNKNOWN__	__UNKNOWN__	19	6382381	6382381	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:6382381G>A	ENST00000394456.5	-	7	1147				GTF2F1_ENST00000429701.2_Intron	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	NA		NA			7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						ggtggctcacgcctgtaatcc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651	2962		General transcription factors	4652	protein-coding gene	gene with protein product		189968	general transcription factor IIF, polypeptide 1 (74kD subunit)		NA	1734284	Standard	NM_002096	NM_002096	NA	Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.683-520C>T	chr19.hg19:g.6382381G>A		NA	B2RCS0|Q9BWN0	hg19	CCDS12165.1	0.02	-0.149126	CACxCCT	COVERED																																																																																			NOVEL	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398033.1	4	3.309537	KEEP	0	0	0	11	332	GG	0.993072	0.289978	0		-	3	60	89	0	0	7.072231	12	60	400	42	ENST00000394456.5	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	6615552	6615552	__UNKNOWN__	IGR	SNP	C	C	T	rs8111231	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:6615552C>T			NA	NA				CD70 (24389 upstream) : TNFSF14 (47595 downstream)						NA		NA									NA						gtcaggagatcgagaccatcc	0.537		NA											C|||	1171	0.233826	0.146	0.2133	5008	,	,	NA	11733	0.2312	NA	0.3091	False	NA	,,,	NA	NA	NA	2504	0.2924	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.6615552C>T		NA		hg19		0.02	-0.087711	GATxGAG	UNCOVERED																																																																																			NOVEL					0			9	3.608745	KEEP	19	0	0	12	328	CC	0	0	0			3	60	96	0	0	8.378692	7	40	213	57		0.3	0.120436
SH2D3A	10045	__UNKNOWN__	__UNKNOWN__	19	6760079	6760079	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:6760079G>A	ENST00000245908.6	-	4	689				SH2D3A_ENST00000437152.3_Intron|SH2D3A_ENST00000599563.1_Intron	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	NA		NA			JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|urinary_tract(1)	24						gtgaaaccctgtctctactaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF124249	CCDS12173.1	19p13.3	2013-02-14	2002-01-14			ENSG00000125731	10045		SH2 domain containing	16885	protein-coding gene	gene with protein product		604721	SH2 domain-containing 3A		NA	10187783	Standard	NM_005490	NM_005490	NA	Approved	NSP1	uc002mft.3	Q9BRG2		ENST00000245908.6:c.420-398C>T	chr19.hg19:g.6760079G>A		NA	A8K9R6|B4DRS7|Q9Y2X4	hg19	CCDS12173.1	0.02	-0.394721	CCTxTCT	COVERED																																																																																			NOVEL	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458016.1	42	2.605807	KEEP	14	3	83	38	1134	GG	0.999998	0.926638	0		-	6	47	161	0	0	12.543969	23	60	768	128	ENST00000245908.6	0.206897	0.92664
VAV1	7409	__UNKNOWN__	__UNKNOWN__	19	6808068	6808068	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:6808068A>C	ENST00000602142.1	+	2	286				VAV1_ENST00000304076.2_Intron|VAV1_ENST00000539284.1_Intron|VAV1_ENST00000596764.1_Intron|VAV1_ENST00000599806.1_Intron	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	NA		NA			apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						tcaagcctataatcccagcac	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968	7409		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing, SH2 domain containing	12657	protein-coding gene	gene with protein product		164875	vav 1 oncogene	VAV	NA	9438848	Standard		NM_005428	NA	Approved		uc010xjh.2	P15498		ENST00000602142.1:c.205-12645A>C	chr19.hg19:g.6808068A>C		NA	B4DVK9|M0QXX6|Q15860	hg19	CCDS12174.1	0.02	-0.035079	TATxATC	UNCOVERED																																																																																			NOVEL	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458475.1	5	2.704505	KEEP	0	0	0	9	221	AT	0.992708	0.019836	0		+	2	51	70	0	0	6.750668	2	60	52	18	ENST00000602142.1	0.5	0.019982
INSR	3643	__UNKNOWN__	__UNKNOWN__	19	7182095	7182095	__UNKNOWN__	Intron	SNP	C	C	A	rs75923074	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:7182095C>A	ENST00000302850.5	-	3	1117				INSR_ENST00000341500.5_Intron	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	NA		NA			activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"Insulin(DB00071)|"Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)	gtaatcccagcactttgggag	0.458		NA											c|||	811	0.161941	0.0393	0.2205	5008	,	,	NA	13796	0.1379	NA	0.2584	False	NA	,,,	NA	NA	NA	2504	0.2117	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105	3643		CD molecules, Fibronectin type III domain containing	6091	protein-coding gene	gene with protein product		147670			NA	2983222	Standard		NM_000208	NA	Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.974+2231G>T	chr19.hg19:g.7182095C>A		NA	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	hg19	CCDS12176.1	0.02	-0.070178	CAGxACT	UNCOVERED																																																																																			NOVEL	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458544.1	11	3.008318	KEEP	6	0	0	10	303	CC	0.99257	0.053735	0		-	3	60	93	0	0	8.924636	3	60	104	28	ENST00000302850.5	0.5	0.054137
INSR	3643	__UNKNOWN__	__UNKNOWN__	19	7263919	7263919	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:7263919C>A	ENST00000302850.5	-	2	795				INSR_ENST00000341500.5_Intron	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	NA		NA			activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"Insulin(DB00071)|"Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)	ggtggctcacccctgtaatcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105	3643		CD molecules, Fibronectin type III domain containing	6091	protein-coding gene	gene with protein product		147670			NA	2983222	Standard		NM_000208	NA	Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.652+3436G>T	chr19.hg19:g.7263919C>A		NA	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	hg19	CCDS12176.1	0.02	-0.15789	CACxCCT	COVERED																																																																																			NOVEL	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458544.1	8	3.241727	KEEP	2	1	23	19	586	CC	0.999869	0.353901	0		-	3	40	88	1	0	6.879084	13	60	432	62	ENST00000302850.5	0.1875	0.353947
PEX11G	92960	__UNKNOWN__	__UNKNOWN__	19	7560499	7560499	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:7560499A>T	ENST00000593942.1	-	1	47							Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	NA		NA			peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						ggtctcaaacacctgggctca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883	92960			20208	protein-coding gene	gene with protein product		607583			NA	12417726	Standard	NM_080662	NM_080662	NA	Approved		uc002mgk.2	Q96HA9		ENST00000593942.1:c.455+1789T>A	chr19.hg19:g.7560499A>T		NA	Q8NDM0	hg19		0.02	-0.122643	AACxCCT	COVERED																																																																																			NOVEL	PEX11G-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000458966.1	12	3.305811	KEEP	1	0	0	11	283	AA	0.992708	0.19488	0		-	3	60	93	0	0	7.934889	8	60	217	33	ENST00000593942.1	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	7657896	7657896	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:7657896T>C			NA	NA				PNPLA6 (31246 upstream) : CAMSAP3 (2891 downstream)						NA		NA									NA						AACATCCggctgggcgcggtg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.7657896T>C		NA		hg19		0.02	-0.105236	GGCxGGG	UNCOVERED																																																																																			NOVEL					0			5	2.995382	KEEP	0	0	0	10	259	TT	0.992708	0.138812	0			3	60	102	0	0	8.701507	9	60	255	30		0.25	0.139832
CD209	30835	__UNKNOWN__	__UNKNOWN__	19	7806133	7806133	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:7806133G>A	ENST00000315599.7	-	0	3029				CD209_ENST00000301357.8_3'UTR	NM_001144895.1|NM_001144897.1|NM_021155.3	NP_001138367.1|NP_001138369.1|NP_066978.1	Q9NNX6	CD209_HUMAN	CD209 molecule	NA		NA			antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|heterophilic cell-cell adhesion (GO:0007157)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of T cell proliferation (GO:0042129)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|virion binding (GO:0046790)			endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						cgcggcgggcgaatcacgagg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			M98457	CCDS12186.1, CCDS45949.1, CCDS45950.1, CCDS45951.1, CCDS45952.1, CCDS59344.1, CCDS59345.1	19p13	2011-08-30	2006-03-28			ENSG00000090659	30835		C-type lectin domain containing, CD molecules	1641	protein-coding gene	gene with protein product		604672	CD209 antigen		NA	1518869	Standard	NM_021155	NM_021155	NA	Approved	DC-SIGN, CDSIGN, DC-SIGN1, CLEC4L	uc002mht.2	Q9NNX6		ENST00000315599.7:c.*1792C>T	chr19.hg19:g.7806133G>A		NA	A8KAM4|A8MVQ9|G5E9C4|Q2TB19|Q96QP7|Q96QP8|Q96QP9|Q96QQ0|Q96QQ1|Q96QQ2|Q96QQ3|Q96QQ4|Q96QQ5|Q96QQ6|Q96QQ7|Q96QQ8	hg19	CCDS12186.1	0.02	-0.385942	GGCxAAT	COVERED																																																																																			NOVEL	CD209-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462241.1	5	2.637864	KEEP	0	1	26	18	509	GG	0.99986	0.918042	0		-	4	60	114	0	0	7.666699	36	60	1148	80	ENST00000315599.7	0.1	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	8762630	8762630	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:8762630C>G			NA	NA				CTD-2586B10.1 (14527 upstream) : ACTL9 (45120 downstream)						NA		NA									NA						agtgattctcctgcctcagcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.8762630C>G		NA		hg19		0.02	-0.03509	CTCxTGC	UNCOVERED																																																																																			NOVEL					0			2	3.009008	KEEP	1	0	0	10	310	CC	0.992708	0.019836	0			2	60	70	1	0	6.750125	2	60	65	20		0.5	0.019982
MUC16	94025	__UNKNOWN__	__UNKNOWN__	19	9006385	9006385	__UNKNOWN__	Silent	SNP	A	A	G	rs201630633	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:9006385A>G	ENST00000397910.4	-	45	39836	c.39633T>C	c.(39631-39633)agT>agC	p.S13211S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13213	SEA 8. {ECO:0000255|PROSITE- ProRule:PRU00188}.	NA			cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GAGGGCCAACACTGGTGCTCT	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													104	86	92			NA	NA	19		NA											NA				9006385		2029	4189	6218	SO:0001819	synonymous_variant			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143	94025		Mucins	15582	protein-coding gene	gene with protein product		606154			NA	11369781	Standard	NM_024690	XM_006722941	NA	Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.39633T>C	chr19.hg19:g.9006385A>G		NA	Q6ZQW5|Q96RK2	hg19	CCDS54212.1	0.02	1.599295	AACxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	.	3.849	-0.032300	0.07543	.	.	ENSG00000181143	ENST00000542240	.	.	.	2.73	-1.45	0.08828	.	.	.	.	.	T	0.36166	0.0957	.	.	.	.	.	.	.	.	.	.	.	.	T	0.43491	-0.9388	3	.	.	.	-6.7364	6.3274	0.21251	0.5121:0.0:0.4879:0.0	.	.	.	.	A	51	.	.	V	-	2	0	MUC16	8867385	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.444000	0.02403	-0.357000	0.08175	0.254000	0.18369	GTG	NOVEL	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402806.1	19	3.759911	KEEP	2	2	64	35	958	AA	0.999999	0.999834	0		-	5	60	167	0	0	11.854343	49	60	1432	181	ENST00000397910.4	0.092593	0.999835
C3P1	388503	__UNKNOWN__	__UNKNOWN__	19	10159321	10159321	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10159321A>G	ENST00000495140.1	+	0	1342							Q6ZMU1	C3P1_HUMAN	complement component 3 precursor pseudogene	NA		NA				extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)			endometrium(4)|large_intestine(2)|lung(6)|urinary_tract(1)	13						aagaagaagaagaagaggagg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK131489		19p13.2	2009-04-08			ENSG00000167798	ENSG00000167798	388503			34414	pseudogene	pseudogene		NA			NA		Standard	NR_027300	NR_027300	NA	Approved	CPLP	uc010dwx.2	Q6ZMU1	OTTHUMG00000158555	ENST00000495140.1:	chr19.hg19:g.10159321A>G		NA		hg19		0.02	-0.175419	AGAxGAA	UNCOVERED																																																																																			NOVEL	C3P1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000351284.1	18	3.007183	KEEP	12	0	0	10	272	AA	0	0	0		+	3	60	94	1	1	7.392239	14	60	431	54	ENST00000495140.1	0.176471	0.387407
C3P1	388503	__UNKNOWN__	__UNKNOWN__	19	10159324	10159324	__UNKNOWN__	RNA	SNP	A	A	G	rs201429933		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10159324A>G	ENST00000495140.1	+	0	1342							Q6ZMU1	C3P1_HUMAN	complement component 3 precursor pseudogene	NA		NA				extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)			endometrium(4)|large_intestine(2)|lung(6)|urinary_tract(1)	13						aagaagaagaagaggaggagg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK131489		19p13.2	2009-04-08			ENSG00000167798	ENSG00000167798	388503			34414	pseudogene	pseudogene		NA			NA		Standard	NR_027300	NR_027300	NA	Approved	CPLP	uc010dwx.2	Q6ZMU1	OTTHUMG00000158555	ENST00000495140.1:	chr19.hg19:g.10159324A>G		NA		hg19		0.02	-0.192971	AGAxGAG	UNCOVERED																																																																																			NOVEL	C3P1-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000351284.1	19	2.699895	KEEP	9	0	0	9	238	AA	0	0	0		+	5	60	163	1	2	13.930559	14	60	424	56	ENST00000495140.1	0.263158	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	10333914	10333914	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10333914G>A			NA	NA				CTD-2369P2.2 (44 upstream) : S1PR2 (605 downstream)						NA		NA									NA						tgtaatcccagcactttggga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.10333914G>A		NA		hg19		0.02	-0.070168	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			12	2.238727	KEEP	9	1	27	17	494	GG	0.993072	0.053762	0			3	54	82	0	0	7.331948	5	40	170	37		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	10333915	10333915	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10333915C>T			NA	NA				CTD-2369P2.2 (45 upstream) : S1PR2 (604 downstream)						NA		NA									NA						gtaatcccagcactttgggag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.10333915C>T		NA		hg19		0.02	-0.070165	CAGxACT	UNCOVERED																																																																																			NOVEL					0			12	2.94075	KEEP	9	1	26	19	556	CC	0.994391	0.053834	0			3	54	85	0	0	7.632015	5	40	165	38		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	10351753	10351753	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10351753T>C			NA	NA				S1PR2 (9805 upstream) : MRPL4 (10886 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.10351753T>C		NA		hg19		0.02	-0.140275	TCAxGCC	COVERED																																																																																			NOVEL					0			4	2.706839	KEEP	2	0	0	9	248	TT	0.99257	0.259026	0			3	60	106	0	0	8.772721	12	60	347	41		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	10492463	10492463	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10492463A>G			NA	NA				TYK2 (1111 upstream) : CDC37 (9346 downstream)						NA		NA									NA						gagccaccgcacccggccCTT	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.10492463A>G		NA		hg19		0.02	-0.175386	CGCxCCC	COVERED																																																																																			NOVEL					0			9	3.306313	KEEP	0	0	0	11	284	AC	0.993634	0.38494	0			3	60	105	0	0	8.410307	15	60	430	45		0.166667	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	10595508	10595508	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10595508C>T			NA	NA				PDE4A (15203 upstream) : KEAP1 (1287 downstream)						NA		NA									NA						tgagccactgcgcccagccAT	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.10595508C>T		NA		hg19		0.02	-0.157885	CTGxGCC	COVERED																																																																																			NOVEL					0			10	4.209785	KEEP	1	0	0	14	406	CC	0.995343	0.321303	0			3	60	89	0	0	7.282036	10	60	313	47		0.230769	0.322807
KEAP1	9817	__UNKNOWN__	__UNKNOWN__	19	10599349	10599349	__UNKNOWN__	Intron	SNP	C	C	G	rs7247667	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10599349C>G	ENST00000171111.5	-	5	2256				KEAP1_ENST00000393623.2_Intron	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	NA		NA			cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	tggctcatgcctctaatccta	0.493		NA											C|||	1294	0.258387	0.2595	0.1859	5008	,	,	NA	18523	0.1964	NA	0.2545	False	NA	,,,	NA	NA	NA	2504	0.3763	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999	9817		Kelch-like, BTB/POZ domain containing	23177	protein-coding gene	gene with protein product	kelch-like family member 19	606016			NA		Standard	NM_012289	NM_012289	NA	Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1708+518G>C	chr19.hg19:g.10599349C>G		NA	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	hg19	CCDS12239.1	0.02	-0.122806	TGCxTCT	UNCOVERED																																																																																			NOVEL	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452000.1	7	2.407153	KEEP	2	0	0	8	246	CC	0	0	0		-	3	60	89	0	0	7.400934	9	60	309	32	ENST00000171111.5	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	10710629	10710629	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10710629C>T			NA	NA				AP1M2 (12638 upstream) : SLC44A2 (2556 downstream)						NA		NA									NA						tgtccaggtgcggtggctcat	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.10710629C>T		NA		hg19		0.02	-0.105257	GTGxGGT	UNCOVERED																																																																																			NOVEL					0			3	2.706453	KEEP	0	0	0	9	244	CC	0.99254	0.138789	0			3	60	89	0	0	7.532229	8	60	258	28		0.272727	0.139832
SLC44A2	57153	__UNKNOWN__	__UNKNOWN__	19	10728889	10728889	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10728889T>C	ENST00000407327.4	+	2	52					NM_001145056.1	NP_001138528.1	Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	NA		NA			choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	ctcgctctgttgcccaggctg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353	57153		Solute carriers	17292	protein-coding gene	gene with protein product		606106			NA	10677542, 15715662	Standard		NM_001145056	NA	Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000407327.4:c.32-8040T>C	chr19.hg19:g.10728889T>C		NA	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	hg19	CCDS54216.1	0.02	-0.078945	TGTxGCC	UNCOVERED																																																																																			NOVEL	SLC44A2-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452044.1	11	2.406547	KEEP	4	0	0	8	229	TT	0	0	0		+	3	60	104	0	0	9.343713	6	60	182	23	ENST00000407327.4	0.333333	0.077336
SLC44A2	57153	__UNKNOWN__	__UNKNOWN__	19	10734392	10734392	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10734392G>A	ENST00000407327.4	+	2	52					NM_001145056.1	NP_001138528.1	Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	NA		NA			choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	ttgaggcggagtctcgctctg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353	57153		Solute carriers	17292	protein-coding gene	gene with protein product		606106			NA	10677542, 15715662	Standard		NM_001145056	NA	Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000407327.4:c.32-2537G>A	chr19.hg19:g.10734392G>A		NA	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	hg19	CCDS54216.1	0.02	-0.149114	GGAxTCT	COVERED																																																																																			NOVEL	SLC44A2-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452044.1	5	3.008726	KEEP	0	0	0	10	298	GG	0.992708	0.289872	0		+	4	56	110	0	0	9.130698	11	60	365	38	ENST00000407327.4	0.266667	0.292001
SLC44A2	57153	__UNKNOWN__	__UNKNOWN__	19	10742940	10742940	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:10742940T>C	ENST00000335757.5	+	10	1199				SLC44A2_ENST00000586078.1_Intron|SLC44A2_ENST00000407327.4_Intron			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	NA		NA			choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	Aggccgggcgtggtggctcac	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353	57153		Solute carriers	17292	protein-coding gene	gene with protein product		606106			NA	10677542, 15715662	Standard		NM_001145056	NA	Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.823+108T>C	chr19.hg19:g.10742940T>C		NA	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	hg19	CCDS12245.1	0.02	-0.149053	GCGxGGT	UNCOVERED																																																																																			NOVEL	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452045.1	5	2.705696	KEEP	2	0	0	9	241	TT	0	0	0		+	3	60	88	0	0	7.073773	11	60	305	35	ENST00000335757.5	0.214286	0.292001
LDLR	3949	__UNKNOWN__	__UNKNOWN__	19	11217774	11217774	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11217774A>G	ENST00000558518.1	+	6	1004				LDLR_ENST00000455727.2_Intron|LDLR_ENST00000557933.1_Intron|LDLR_ENST00000545707.1_Intron|LDLR_ENST00000535915.1_Intron|LDLR_ENST00000558013.1_Intron	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	NA		NA			cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	ccaaagtgctaggattacagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(18;201 575 7820 21545)							NA				1	Unknown(1)	lung(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164	3949		Low density lipoprotein receptors	6547	protein-coding gene	gene with protein product	familial hypercholesterolemia	606945			NA		Standard		NM_000527	NA	Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.818-294A>G	chr19.hg19:g.11217774A>G		NA	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	hg19	CCDS12254.1	0.02	-0.096483	GCTxGGA	UNCOVERED																																																																																			NOVEL	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415973.2	5	4.207197	KEEP	2	0	0	14	364	AA	0.994391	0.119761	0		+	3	60	99	0	0	8.53251	8	60	239	37	ENST00000558518.1	0.272727	0.120436
LDLR	3949	__UNKNOWN__	__UNKNOWN__	19	11221105	11221105	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11221105A>G	ENST00000558518.1	+	7	1127				LDLR_ENST00000455727.2_Intron|LDLR_ENST00000557933.1_Intron|LDLR_ENST00000545707.1_Intron|LDLR_ENST00000535915.1_Intron|LDLR_ENST00000558013.1_Intron	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	NA		NA			cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	tcgtgccattacactccagcc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(18;201 575 7820 21545)							NA				1	Unknown(1)	lung(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164	3949		Low density lipoprotein receptors	6547	protein-coding gene	gene with protein product	familial hypercholesterolemia	606945			NA		Standard		NM_000527	NA	Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.941-223A>G	chr19.hg19:g.11221105A>G		NA	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	hg19	CCDS12254.1	0.02	-0.113999	ATTxCAC	UNCOVERED																																																																																			NOVEL	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000415973.2	4	3.307274	KEEP	2	0	0	11	288	AA	0.99254	0.161255	0		+	3	60	97	0	0	8.332897	8	60	223	36	ENST00000558518.1	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	11272099	11272099	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11272099A>G			NA	NA				SPC24 (5615 upstream) : KANK2 (2843 downstream)						NA		NA									NA						gtgagccaccacgcccggcca	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.11272099A>G		NA		hg19		0.02	-0.254338	ACCxCGC	COVERED																																																																																			NOVEL					0			8	8.418991	KEEP	1	0	0	28	744	AA	0.999997	0.668521	0			3	60	96	0	0	6.89299	25	60	739	83		0.107143	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	11380855	11380855	__UNKNOWN__	IGR	SNP	C	C	G	rs12971903	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11380855C>G			NA	NA				DOCK6 (7727 upstream) : TSPAN16 (25968 downstream)						NA		NA									NA						aggccaaggccggtggatcaa	0.542		NA											g|||	2651	0.529353	0.1142	0.6225	5008	,	,	NA	15386	0.6399	NA	0.7028	False	NA	,,,	NA	NA	NA	2504	0.7321	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.11380855C>G		NA		hg19		0.02	5.279343	GGCxGGT	COVERED																																																																																			NOVEL					0			236	40.210088	KEEP	248	7	211	208	6267	CC	1	1	0			11	60	354	0	0	36.867845	4	60	141	785		0.733333	1
CCDC159	126075	__UNKNOWN__	__UNKNOWN__	19	11459233	11459233	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11459233A>G	ENST00000588790.1	+	4	468				CCDC159_ENST00000458408.1_Intron			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	NA		NA								endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						ccaaagtgctaggattacagg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401	126075			26996	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001080503	NM_001080503	NA	Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.22-1097A>G	chr19.hg19:g.11459233A>G		NA	B4DEG3|B4DWR8|B4E133|B7ZAM4	hg19	CCDS45976.1	0.02	-0.429711	GCTxGGA	COVERED																																																																																			NOVEL	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000458761.1	10	3.532991	KEEP	1	1	29	22	584	AA	0.999892	0.954388	0		+	4	60	124	0	0	8.501552	40	60	1171	104	ENST00000588790.1	0.090909	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	11640549	11640549	__UNKNOWN__	IGR	SNP	A	A	G	rs10412437	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11640549A>G			NA	NA				ECSIT (560 upstream) : CNN1 (8982 downstream)						NA		NA									NA						tgtaatcccaacactttggga	0.512		NA											G|||	1049	0.209465	0.618	0.0605	5008	,	,	NA	14338	0.0694	NA	0.0239	False	NA	,,,	NA	NA	NA	2504	0.0982	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.11640549A>G		NA		hg19		0.02	-0.061403	CCAxCAC	UNCOVERED																																																																																			NOVEL					0			8	3.909219	KEEP	0	0	0	13	351	AA	0.994391	0.043541	0			3	60	103	0	0	9.655413	4	60	122	26		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	11706742	11706742	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11706742A>T			NA	NA				ACP5 (16941 upstream) : ZNF627 (1492 downstream)						NA		NA									NA						ctcgatctccagacctcgtga	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.11706742A>T		NA		hg19		0.02	-0.1228	TCCxGAC	COVERED																																																																																			NOVEL					0			5	3.007779	KEEP	2	0	0	10	280	AA	0.992708	0.19488	0			3	60	89	0	0	7.172904	11	60	344	38		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	11740473	11740473	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11740473G>C			NA	NA				ZNF627 (10523 upstream) : ZNF833P (10117 downstream)						NA		NA									NA						gctgaggcaggaggatcgctt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.11740473G>C		NA		hg19		0.02	-0.070182	CAGxAGG	UNCOVERED																																																																																			NOVEL					0			12	3.00859	KEEP	6	0	0	10	308	GG	0	0	0			2	31	72	0	0	6.335561	5	60	169	26		0.285714	0.054137
ZNF440	126070	__UNKNOWN__	__UNKNOWN__	19	11945205	11945205	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:11945205A>G	ENST00000304060.5	+	0	3378					NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						gcctcccaaaatgctgggatt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK095252	CCDS42503.1	19p13.13	2013-01-08	2006-08-14	2006-08-14	ENSG00000171295	ENSG00000171295	126070		Zinc fingers, C2H2-type, -	20874	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152357	NM_152357	NA	Approved	FLJ37933	uc002msp.1	Q8IYI8	OTTHUMG00000156403	ENST00000304060.5:c.*1426A>G	chr19.hg19:g.11945205A>G		NA	Q8N1R9	hg19	CCDS42503.1	0.02	1.774624	AAAxTGC	COVERED																																																																																			NOVEL	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344508.1	22	9.554962	KEEP	0	1	29	42	1148	AA	1	0.996724	0		+	4	60	135	0	0	9.121609	53	60	1589	166	ENST00000304060.5	0.070175	0.996724
ZNF700	90592	__UNKNOWN__	__UNKNOWN__	19	12057810	12057810	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12057810T>A	ENST00000254321.5	+	2	206				CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_5'UTR|ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000538752.1_Intron|ZNF763_ENST00000591944.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						tctcaaaaaataaataaataa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757	90592		Zinc fingers, C2H2-type, -	25292	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144566	NM_144566	NA	Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.64-186T>A	chr19.hg19:g.12057810T>A		NA	B9EGU4	hg19	CCDS32915.1	0.02	-0.385894	AAAxAAA	COVERED																																																																																			NOVEL	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000344126.2	15	9.890306	KEEP	0	0	0	33	889	TT	0.999998	0.918169	0		+	4	60	112	0	0	7.296427	40	60	1197	109	ENST00000254321.5	0.090909	0.918171
ZNF433	163059	__UNKNOWN__	__UNKNOWN__	19	12140875	12140875	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12140875T>C	ENST00000344980.6	-	1	174				ZNF433_ENST00000419886.2_Intron|CTD-2006C1.10_ENST00000547473.1_Intron|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						ccagcctgggtgacagagcaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647	163059		Zinc fingers, C2H2-type, -	20811	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152602	NM_001080411	NA	Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.3+5476A>G	chr19.hg19:g.12140875T>C		NA	Q86VX3	hg19	CCDS45983.1	0.02	1.616835	GGGxGAC	COVERED																																																																																			NOVEL	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403716.1	11	2.57109	KEEP	9	6	165	67	1610	TT	1	0.976865	0		-	4	40	132	1	0	9.332436	39	60	1070	139	ENST00000344980.6	0.093023	0.976865
ZNF433	163059	__UNKNOWN__	__UNKNOWN__	19	12140884	12140884	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12140884A>G	ENST00000344980.6	-	1	174				ZNF433_ENST00000419886.2_Intron|CTD-2006C1.10_ENST00000547473.1_Intron|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						gtgacagagcaagactccatc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647	163059		Zinc fingers, C2H2-type, -	20811	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152602	NM_001080411	NA	Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.3+5467T>C	chr19.hg19:g.12140884A>G		NA	Q86VX3	hg19	CCDS45983.1	0.02	1.493895	AGCxAGA	COVERED																																																																																			NOVEL	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403716.1	11	4.71648	KEEP	9	7	184	81	2222	AA	1	0.995687	0		-	4	60	120	0	0	8.011352	42	60	1246	166	ENST00000344980.6	0.086957	0.995687
CTD-2006C1.10	0	__UNKNOWN__	__UNKNOWN__	19	12152066	12152066	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12152066G>A	ENST00000547473.1	-	3	357				CTD-2006C1.2_ENST00000591838.1_RNA|CTD-2006C1.2_ENST00000591898.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA						NA		NA									NA						GTggccgggcgcggtggctca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000547473.1:c.191+5116C>T	chr19.hg19:g.12152066G>A		NA		hg19		0.02	-0.140344	GGCxCGG	COVERED																																																																																			NOVEL	CTD-2006C1.10-001	KNOWN	basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000403722.1	5	2.705399	KEEP	0	0	0	9	242	GG	0.99254	0.289823	0		-	3	60	88	0	0	7.301067	9	60	287	33	ENST00000547473.1	0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	12269550	12269550	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12269550C>T			NA	NA				ZNF625-ZNF20 (2004 upstream) : ZNF136 (4328 downstream)						NA		NA									NA						gtcaggagttcgagaccagcc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.12269550C>T		NA		hg19		0.02	-0.166536	GTTxGAG	COVERED																																																																																			NOVEL					0			16	5.41345	KEEP	6	0	0	18	499	CC	0.999366	0.353723	0			4	43	121	0	0	10.103401	12	60	359	59		0.25	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	12374545	12374545	__UNKNOWN__	IGR	SNP	C	C	G	rs9676932	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12374545C>G			NA	NA				ZNF44 (12927 upstream) : ZNF44 (8081 downstream)						NA		NA									NA						tcgagaccatcctggctaaca	0.537		NA											G|||	1120	0.223642	0.5953	0.1153	5008	,	,	NA	11373	0.0367	NA	0.1282	False	NA	,,,	NA	NA	NA	2504	0.089	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.12374545C>G		NA		hg19		0.02	-0.052636	CATxCTG	UNCOVERED																																																																																			NOVEL					0			8	2.707629	KEEP	10	0	0	9	266	CC	0	0	0			2	60	72	0	0	7.324987	1	23	31	31		0.666667	0.036766
CTD-2192J16.20	0	__UNKNOWN__	__UNKNOWN__	19	12671682	12671682	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12671682G>A	ENST00000593682.1	-	1	3472										NA		NA									NA						gcctcccaaagtgctgggatt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000593682.1:c.488+16635C>T	chr19.hg19:g.12671682G>A		NA		hg19		0.02	-0.184216	AAAxTGC	COVERED																																																																																			NOVEL	CTD-2192J16.20-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000461072.1	3	3.009152	KEEP	2	0	0	10	313	GG	0.992708	0.42039	0		-	3	60	100	0	0	7.99152	14	60	462	49	ENST00000593682.1	0.176471	0.423478
ZNF791	163049	__UNKNOWN__	__UNKNOWN__	19	12735612	12735612	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12735612T>C	ENST00000446165.1	+	2	292				ZNF490_ENST00000465656.1_Intron|ZNF791_ENST00000343325.4_Intron|ZNF791_ENST00000458122.3_Intron|ZNF791_ENST00000540038.1_Intron			Q3KP31	ZN791_HUMAN	zinc finger protein 791	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						acctgtaatctcagcactttg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875	163049		Zinc fingers, C2H2-type, -	26895	protein-coding gene	gene with protein product		NA			NA		Standard	NM_153358	NM_153358	NA	Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000446165.1:c.130+972T>C	chr19.hg19:g.12735612T>C		NA	B7Z586|Q8NC99	hg19		0.02	-0.236825	ATCxCAG	COVERED																																																																																			NOVEL	ZNF791-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000344141.1	4	4.51169	KEEP	0	0	0	15	418	TT	0.99649	0.610258	0		+	3	60	102	0	0	7.764792	20	60	609	56	ENST00000446165.1	0.130435	0.612407
MAST1	22983	__UNKNOWN__	__UNKNOWN__	19	12948658	12948658	__UNKNOWN__	Intron	SNP	A	A	G	rs369932486	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:12948658A>G	ENST00000591495.1	+	2	56									microtubule associated serine/threonine kinase 1	NA		NA								NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						tcctgcctcaacctcccaagt	0.483		NA											A|||	12	0.00239617	0.0038	0.0	5008	,	,	NA	18820	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613	22983			19034	protein-coding gene	gene with protein product		612256			NA		Standard	NM_014975	NM_014975	NA	Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000591495.1:c.40-425A>G	chr19.hg19:g.12948658A>G		NA		hg19		0.02	-0.201678	TCAxCCT	COVERED																																																																																			NOVEL	MAST1-005	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000451731.1	7	3.30471	KEEP	0	0	0	11	272	AA	0.993072	0.487146	0		+	3	60	90	0	0	6.762619	17	60	485	44	ENST00000591495.1	0.15	0.490544
STX10	8677	__UNKNOWN__	__UNKNOWN__	19	13260216	13260216	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:13260216G>A	ENST00000587230.1	-	3	365				STX10_ENST00000343587.5_Intron|STX10_ENST00000589083.1_Intron|STX10_ENST00000242770.5_Intron	NM_001271609.1	NP_001258538.1	O60499	STX10_HUMAN	syntaxin 10	NA		NA			Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|kidney(1)|lung(2)|prostate(1)	6			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			acagagcgaggctctgtctca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035531	CCDS32922.1, CCDS62569.1, CCDS62570.1, CCDS62571.1	19p13.13	2008-07-22				ENSG00000104915	8677			11428	protein-coding gene	gene with protein product		603765			NA	9446797	Standard	NM_003765	NM_003765	NA	Approved	hsyn10, SYN10	uc021upq.2	O60499		ENST00000587230.1:c.300+96C>T	chr19.hg19:g.13260216G>A		NA	A6NC41|Q6IAP4|Q96AE8	hg19	CCDS32922.1	0.02	-0.412284	GAGxCTC	COVERED																																																																																			NOVEL	STX10-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452918.1	5	10.760494	KEEP	4	1	26	45	1317	GG	1	0.941741	0		-	4	60	127	0	0	9.156993	32	70	1040	107	ENST00000587230.1	0.111111	0.941741
PODNL1	79883	__UNKNOWN__	__UNKNOWN__	19	14057612	14057612	__UNKNOWN__	Intron	SNP	T	T	C	rs551940452	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14057612T>C	ENST00000538371.2	-	1	274				PODNL1_ENST00000538517.2_Intron	NM_001146254.1	NP_001139726.1	Q6PEZ8	PONL1_HUMAN	podocan-like 1	NA		NA				proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			cgcctgtaattccagcacttt	0.463		NA											t|||	10	0.00199681	0.0045	0.0	5008	,	,	NA	17645	0.004	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05					79883			26275	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_024825	NM_024825	NA	Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000538371.2:c.18+6318A>G	chr19.hg19:g.14057612T>C		NA	B7Z564|Q9H5G9	hg19	CCDS54226.1	0.02	-0.070174	AATxCCA	UNCOVERED																																																																																			NOVEL	PODNL1-001	KNOWN	overlapping_uORF|basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000457969.1	6	2.706532	KEEP	3	0	0	9	242	TT	0.99254	0.053733	0		-	3	60	99	0	0	9.25521	4	60	126	30	ENST00000538371.2	0.428571	0.054137
PRKACA	5566	__UNKNOWN__	__UNKNOWN__	19	14216960	14216960	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14216960A>G	ENST00000308677.4	-	3	434				PRKACA_ENST00000589994.1_Intron|PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000350356.3_Intron	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	NA		NA			activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						ccaggagttcaagaccagcct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	5566	2.7.11.1		9380	protein-coding gene	gene with protein product		601639			NA	8884279	Standard	NM_002730	NM_002730	NA	Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.237+611T>C	chr19.hg19:g.14216960A>G		NA	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	hg19	CCDS12304.1	0.02	-0.298193	TTCxAGA	COVERED																																																																																			NOVEL	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459004.1	17	4.641351	KEEP	0	1	30	26	697	AA	0.999988	0.78105	0		-	3	60	100	0	0	7.109482	29	60	848	88	ENST00000308677.4	0.09375	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	14338344	14338344	__UNKNOWN__	IGR	SNP	A	A	G	rs8102651	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14338344A>G			NA	NA				RN7SL231P (14213 upstream) : CTD-2189E23.1 (26656 downstream)						NA		NA									NA						cgaggtgggcagatcacaagg	0.537		NA											G|||	3364	0.671725	0.5976	0.732	5008	,	,	NA	11327	0.744	NA	0.7386	False	NA	,,,	NA	NA	NA	2504	0.5859	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.14338344A>G		NA		hg19		0.02	-0.114032	GGCxGAT	UNCOVERED																																																																																			NOVEL					0			10	3.308	KEEP	6	0	0	11	300	AA	0.992708	0.161282	0			4	60	135	0	0	12.091537	8	60	244	44		0.333333	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	14338346	14338346	__UNKNOWN__	IGR	SNP	A	A	G	rs8102652	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14338346A>G			NA	NA				RN7SL231P (14215 upstream) : CTD-2189E23.1 (26654 downstream)						NA		NA									NA						aggtgggcagatcacaaggtc	0.542		NA											A|||	3355	0.669928	0.5908	0.732	5008	,	,	NA	11368	0.744	NA	0.7386	False	NA	,,,	NA	NA	NA	2504	0.5859	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.14338346A>G		NA		hg19		0.02	-0.114034	CAGxTCA	UNCOVERED																																																																																			NOVEL					0			10	3.306778	KEEP	6	0	0	11	288	AA	0.992708	0.161282	0			4	60	142	1	0	12.791667	8	60	243	43		0.333333	0.162467
CTC-548K16.2	0	__UNKNOWN__	__UNKNOWN__	19	14471180	14471180	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14471180A>G	ENST00000586698.1	-	0	119										NA		NA									NA						cggtgctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000586698.1:	chr19.hg19:g.14471180A>G		NA		hg19		0.02	-0.183448	CACxCCT	COVERED																																																																																			NOVEL	CTC-548K16.2-002	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000459814.1	9	3.308236	KEEP	1	0	0	11	301	AA	0.993072	0.420544	0		-	4	60	106	0	0	8.190931	16	60	476	46	ENST00000586698.1	0.2	0.423478
CD97	976	__UNKNOWN__	__UNKNOWN__	19	14507342	14507342	__UNKNOWN__	Intron	SNP	G	G	T	rs62122582		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14507342G>T	ENST00000242786.5	+	5	558				CD97_ENST00000587728.1_Intron|CD97_ENST00000358600.3_Intron|CD97_ENST00000357355.3_Intron	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	NA		NA			cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TGGAGCTGAGGCACGTCCTCC	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146	976		CD molecules, -, GPCR / Class B : Orphans	1711	protein-coding gene	gene with protein product	leukocyte antigen CD97, seven-span transmembrane protein, seven-transmembrane, heterodimeric receptor associated with inflammation, seven transmembrane helix receptor	601211	CD97 antigen		NA	7636245, 8786105	Standard	NM_078481	NM_078481	NA	Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.478+57G>T	chr19.hg19:g.14507342G>T		NA	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	hg19	CCDS32929.1	0.02	1.54639	GAGxCAC	COVERED																																																																																			NOVEL	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459821.2	0	6.318243	KEEP	2	0	0	21	639	GG	0.999869	0.990834	0		+	11	53	316	1	0	24.43915	49	60	1688	123	ENST00000242786.5	0.183333	0.990964
CD97	976	__UNKNOWN__	__UNKNOWN__	19	14507345	14507345	__UNKNOWN__	Intron	SNP	C	C	G	rs62122583		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14507345C>G	ENST00000242786.5	+	5	558				CD97_ENST00000587728.1_Intron|CD97_ENST00000358600.3_Intron|CD97_ENST00000357355.3_Intron	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	NA		NA			cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						AGCTGAGGCACGTCCTCCAAA	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146	976		CD molecules, -, GPCR / Class B : Orphans	1711	protein-coding gene	gene with protein product	leukocyte antigen CD97, seven-span transmembrane protein, seven-transmembrane, heterodimeric receptor associated with inflammation, seven transmembrane helix receptor	601211	CD97 antigen		NA	7636245, 8786105	Standard	NM_078481	NM_078481	NA	Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.478+60C>G	chr19.hg19:g.14507345C>G		NA	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	hg19	CCDS32929.1	0.02	1.961998	GCAxGTC	COVERED																																																																																			NOVEL	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459821.2	0	6.015157	KEEP	2	0	0	20	567	CC	0.999863	0.987808	0		+	10	53	299	1	0	23.098683	48	60	1538	115	ENST00000242786.5	0.172414	0.987943
CLEC17A	388512	__UNKNOWN__	__UNKNOWN__	19	14711754	14711754	__UNKNOWN__	Intron	SNP	A	A	T	rs10404521	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14711754A>T	ENST00000417570.1	+	12	932				CLEC17A_ENST00000547437.1_Intron|CLEC17A_ENST00000397439.2_Intron	NM_001204118.1	NP_001191047.1	Q6ZS10	CL17A_HUMAN	C-type lectin domain family 17, member A	NA		NA				cell surface (GO:0009986)|integral component of membrane (GO:0016021)	fucose binding (GO:0042806)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)				NA						tcactctgtcacccaggctgg	0.502		NA											a|||	854	0.170527	0.1422	0.1816	5008	,	,	NA	12880	0.0526	NA	0.2465	False	NA	,,,	NA	NA	NA	2504	0.2444	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK127809	CCDS46002.1, CCDS46002.2, CCDS56087.1	19p13.12	2009-06-26			ENSG00000187912	ENSG00000187912	388512		C-type lectin domain containing	34520	protein-coding gene	gene with protein product	prolectin	NA			NA	19419970	Standard	NM_207390	NM_207390	NA	Approved	FLJ45910	uc010dzn.2	Q6ZS10		ENST00000417570.1:c.894+760A>T	chr19.hg19:g.14711754A>T		NA	A8MX68|B2RTX0|B7ZMM4	hg19	CCDS56087.1	0.02	-0.140272	GTCxCCC	UNCOVERED																																																																																			NOVEL	CLEC17A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000403400.1	17	3.908562	KEEP	17	0	0	13	339	AA	0	0	0		+	3	60	89	0	0	7.678766	7	60	199	40	ENST00000417570.1	0.3	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	14982238	14982238	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:14982238C>T			NA	NA				OR7A10 (29549 upstream) : OR7A17 (8899 downstream)						NA		NA									NA						ttctcacttacaagtgggagc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.14982238C>T		NA		hg19		0.02	-0.122801	TTAxAAG	COVERED																																																																																			NOVEL					0			4	2.407315	KEEP	0	0	0	8	251	CC	0.99257	0.194853	0			3	60	81	0	0	6.373077	11	60	369	29		0.214286	0.196312
SLC1A6	6511	__UNKNOWN__	__UNKNOWN__	19	15075922	15075922	__UNKNOWN__	Intron	SNP	C	C	T	rs61260083	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:15075922C>T	ENST00000221742.3	-	4	556				SLC1A6_ENST00000600144.1_Intron|SLC1A6_ENST00000544886.2_Intron|SLC1A6_ENST00000430939.2_Intron|SLC1A6_ENST00000598504.1_Intron	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	NA		NA			aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						acctccacctcccgggttcaa	0.483		NA											-|||	2290	0.457268	0.4962	0.4496	5008	,	,	NA	16385	0.6022	NA	0.3419	False	NA	,,,	NA	NA	NA	2504	0.3793	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143	6511		Solute carriers	10944	protein-coding gene	gene with protein product		600637			NA	7791878	Standard	NM_005071	NM_005071	NA	Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.549-749G>A	chr19.hg19:g.15075922C>T		NA	Q8N753	hg19	CCDS12321.1	0.02	-0.061371	CCTxCCG	UNCOVERED																																																																																			NOVEL	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466283.1	4	2.406415	KEEP	5	0	0	8	227	CC	0	0	0		-	4	54	110	0	0	11.245367	2	60	66	26	ENST00000221742.3	0.666667	0.043787
NOTCH3	4854	__UNKNOWN__	__UNKNOWN__	19	15276150	15276150	__UNKNOWN__	Intron	SNP	G	G	A	rs368589806		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:15276150G>A	ENST00000263388.2	-	31	5891					NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	NA		NA			forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			CACCAACCCAGCTTAGACTTG	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								G		0,4406		0,0,2203	82	72	75			1.4	0	19		75	1,8599	1.2+/-3.3	0,1,4299	no	intron	NOTCH3	NM_000435.2		0,1,6502	AA,AG,GG	NA	0.0116,0.0,0.0077			15276150	1,13005	2203	4300	6503	SO:0001627	intron_variant			U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181	4854		Ankyrin repeat domain containing	7883	protein-coding gene	gene with protein product		600276	Notch (Drosophila) homolog 3, Notch homolog 3 (Drosophila)	CADASIL	NA	7835890	Standard	NM_000435	NM_000435	NA	Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.5815+28C>T	chr19.hg19:g.15276150G>A		NA	Q9UEB3|Q9UPL3|Q9Y6L8	hg19	CCDS12326.1	0.02	1.797863	CCAxCTT	COVERED																																																																																			NOVEL	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465714.1	1	3.009204	KEEP	0	0	0	10	315	GG	0.992708	0.972383	0		-	20	60	592	0	0	53.280118	34	60	1146	93	ENST00000263388.2	0.37037	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	15335963	15335963	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:15335963G>A			NA	NA				AC004257.1 (2855 upstream) : EPHX3 (1766 downstream)						NA		NA									NA						cacgcctgtagtcccagcact	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.15335963G>A		NA		hg19		0.02	-0.166662	GTAxTCC	COVERED																																																																																			NOVEL					0			7	4.51343	KEEP	1	0	0	15	463	GG	0.995343	0.352299	0			3	27	89	0	0	6.979032	13	60	434	49		0.1875	0.353947
OR10H1	26539	__UNKNOWN__	__UNKNOWN__	19	15918647	15918647	__UNKNOWN__	Silent	SNP	G	G	T	rs4081570	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:15918647G>T	ENST00000334920.2	-	1	289	c.201C>A	c.(199-201)tcC>tcA	p.S67S		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	67		NA				integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						TCTCGGAGACGGAGAGGGCGC	0.642		NA											.|||	1522	0.303914	0.4622	0.3184	5008	,	,	NA	20278	0.0417	NA	0.4145	False	NA	,,,	NA	NA	NA	2504	0.2362	NA	NA	NA								NA				0													103	93	96			NA	NA	19		NA											NA				15918647		2194	4278	6472	SO:0001819	synonymous_variant			AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723	26539		GPCR / Class A : Olfactory receptors	8172	protein-coding gene	gene with protein product		NA			NA		Standard		NM_013940	NA	Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.201C>A	chr19.hg19:g.15918647G>T		NA	Q6IFQ2|Q96R59	hg19	CCDS12335.1	0.02	1.280621	GACxGAG	COVERED																																																																																			NOVEL	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460364.1	2	6.016871	KEEP	1	0	0	20	597	GG	0.999863	0.99918	0		-	5	39	143	0	0	8.555849	76	60	2523	145	ENST00000334920.2	0.061728	0.999317
AC004791.2	0	__UNKNOWN__	__UNKNOWN__	19	15974892	15974892	__UNKNOWN__	RNA	SNP	A	A	G	rs11086004	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:15974892A>G	ENST00000589345.2	-	0	89										NA		NA									NA						cacccgtctcagcctcccaaa	0.572		NA											.|||	2544	0.507987	0.3676	0.5187	5008	,	,	NA	13590	0.756	NA	0.3956	False	NA	,,,	NA	NA	NA	2504	0.5501	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000589345.2:	chr19.hg19:g.15974892A>G		NA		hg19		0.02	-0.149112	CTCxGCC	UNCOVERED																																																																																			NOVEL	AC004791.2-001	KNOWN	basic	lincRNA	NA	processed_transcript	OTTHUMT00000460370.2	12	2.707456	KEEP	12	0	0	9	259	AA	0	0	0		-	5	60	162	0	0	14.269762	11	60	344	48	ENST00000589345.2	0.3125	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	16021083	16021083	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16021083C>T			NA	NA				CYP4F2 (12153 upstream) : CYP4F11 (2093 downstream)						NA		NA									NA						TGCAACAggccgggcgcggtg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.16021083C>T		NA		hg19		0.02	1.28934	GGCxGGG	COVERED																																																																																			NOVEL					0			12	7.354479	KEEP	0	1	27	34	1045	CC	0.999999	0.999217	0			4	60	126	1	0	7.686149	73	60	2437	174		0.051948	0.999218
FAM32A	26017	__UNKNOWN__	__UNKNOWN__	19	16297259	16297259	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16297259C>A	ENST00000588367.1	+	2	236				CTD-2562J15.4_ENST00000591038.1_RNA|FAM32A_ENST00000589852.1_Intron|FAM32A_ENST00000263384.7_Intron			Q9Y421	FA32A_HUMAN	family with sequence similarity 32, member A	NA		NA			apoptotic process (GO:0006915)|cell cycle (GO:0007049)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			lung(1)	1						tggtatttttcgtagagatgc	0.567		NA									OREG0025331	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)									NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC000639	CCDS12341.1	19p13.12-p13.11	2013-09-19			ENSG00000105058	ENSG00000105058	26017			24563	protein-coding gene	gene with protein product		614554			NA	11230166, 10810093	Standard	NM_014077	NM_014077	NA	Approved	DKFZP586O0120	uc002ndt.3	Q9Y421	OTTHUMG00000182279	ENST00000588367.1:c.216+683C>A	chr19.hg19:g.16297259C>A		709	Q9BT02	hg19		0.02	-0.070154	TTTxGTA	UNCOVERED																																																																																			NOVEL	FAM32A-003	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000460347.1	3	2.406729	KEEP	0	0	0	8	236	CC	0.99257	0.053735	0		+	3	60	76	0	0	6.73123	5	60	165	23	ENST00000588367.1	0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	16307742	16307742	__UNKNOWN__	IGR	SNP	A	A	G	rs12983884	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16307742A>G			NA	NA				FAM32A (4885 upstream) : AP1M1 (646 downstream)						NA		NA									NA						gtgagactccatctcaaaaaa	0.478		NA											a|||	3057	0.610423	0.3684	0.6758	5008	,	,	NA	11414	0.6885	NA	0.7873	False	NA	,,,	NA	NA	NA	2504	0.6288	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.16307742A>G		NA		hg19		0.02	-0.122796	TCCxTCT	UNCOVERED																																																																																			NOVEL					0			16	3.00831	KEEP	10	0	0	10	288	AA	0	0	0			4	60	128	0	0	11.391301	8	47	253	36		0.333333	0.196312
EPS15L1	58513	__UNKNOWN__	__UNKNOWN__	19	16473601	16473601	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16473601A>G	ENST00000455140.2	-	23	2447				EPS15L1_ENST00000594975.1_Intron|EPS15L1_ENST00000248070.6_Intron|EPS15L1_ENST00000535753.2_Intron	NM_001258374.1	NP_001245303.1	Q9UBC2	EP15R_HUMAN	epidermal growth factor receptor pathway substrate 15-like 1	NA		NA			endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	clathrin coat of coated pit (GO:0030132)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(4)|skin(2)	30						gattacaggcatgagccactg	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF110265	CCDS32944.1, CCDS58653.1, CCDS58654.1, CCDS59363.1	19p13.12	2013-01-10				ENSG00000127527	58513		EF-hand domain containing	24634	protein-coding gene	gene with protein product		NA			NA		Standard	NM_021235	NM_001258374	NA	Approved	eps15R	uc002ndx.4	Q9UBC2		ENST00000455140.2:c.2381-806T>C	chr19.hg19:g.16473601A>G		NA	A2RRF3|A5PL29|B4DKA3	hg19	CCDS58654.1	0.02	-0.184059	GGCxTGA	COVERED																																																																																			NOVEL	EPS15L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000461039.1	11	2.40553	KEEP	1	0	0	8	213	AA	0.99257	0.420331	0		-	3	60	104	0	0	8.392965	14	60	389	39	ENST00000455140.2	0.176471	0.423478
CTD-3222D19.2	0	__UNKNOWN__	__UNKNOWN__	19	16616741	16616741	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16616741T>C	ENST00000409035.1	-	8	1924				C19orf44_ENST00000594035.1_Intron|C19orf44_ENST00000221671.3_Intron						NA		NA									NA						gatctgcccatctcggcctcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409035.1:c.1282-10078A>G	chr19.hg19:g.16616741T>C		NA		hg19		0.02	-0.070161	CCAxCTC	UNCOVERED																																																																																			NOVEL	CTD-3222D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000461092.1	6	2.404604	KEEP	1	0	0	8	206	TT	0	0	0		-	2	59	72	1	0	6.335957	5	60	138	24	ENST00000409035.1	0.285714	0.077336
CTD-3222D19.2	0	__UNKNOWN__	__UNKNOWN__	19	16664814	16664814	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16664814A>G	ENST00000409035.1	-	6	1598				SLC35E1_ENST00000595753.1_Intron						NA		NA									NA						ggtggctcacacctgtaatcc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000409035.1:c.1282-94T>C	chr19.hg19:g.16664814A>G		NA		hg19		0.02	-0.342004	CACxCCT	UNCOVERED																																																																																			NOVEL	CTD-3222D19.2-001	KNOWN	basic|appris_principal|readthrough_transcript|exp_conf	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000461092.1	13	2.704564	KEEP	2	0	0	9	231	AA	0	0	0		-	3	60	99	0	0	6.967805	30	60	844	61	ENST00000409035.1	0.090909	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	16820791	16820791	__UNKNOWN__	IGR	SNP	G	G	A	rs2081043	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16820791G>A			NA	NA				TMEM38A (19951 upstream) : NWD1 (9999 downstream)						NA		NA									NA						ctcctgagtagctgggattac	0.532		NA											.|||	2208	0.440895	0.2784	0.6124	5008	,	,	NA	17337	0.3968	NA	0.5567	False	NA	,,,	NA	NA	NA	2504	0.4652	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.16820791G>A		NA		hg19		0.02	-0.087717	GTAxCTG	UNCOVERED																																																																																			NOVEL					0			6	3.308691	KEEP	4	0	0	11	316	GG	0.99257	0.09898	0			4	60	117	0	0	10.922359	5	60	172	29		0.444444	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	16823107	16823107	__UNKNOWN__	IGR	SNP	G	G	C	rs554577779		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16823107G>C			NA	NA				TMEM38A (22267 upstream) : NWD1 (7683 downstream)						NA		NA									NA						gattacaagcgtgagccacca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.16823107G>C		NA		hg19		0.02	1.438486	AGCxTGA	COVERED																																																																																			NOVEL					0			16	5.715696	KEEP	3	0	0	19	554	GG	0.999859	0.995546	0			4	60	127	0	0	8.322917	53	60	1704	123		0.070175	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	16826725	16826725	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16826725A>G			NA	NA				TMEM38A (25885 upstream) : NWD1 (4065 downstream)						NA		NA									NA						ttgctctgtcacccaggctgg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.16826725A>G		NA		hg19		0.02	-0.105208	GTCxCCC	UNCOVERED																																																																																			NOVEL					0			10	3.299968	KEEP	3	0	0	11	275	AA	0.99254	0.138789	0			3	60	86	0	0	7.378212	7	60	193	35		0.3	0.139832
NWD1	284434	__UNKNOWN__	__UNKNOWN__	19	16842367	16842367	__UNKNOWN__	Intron	SNP	C	C	T	rs77771742	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16842367C>T	ENST00000524140.2	+	3	499				NWD1_ENST00000523826.1_Intron|NWD1_ENST00000549814.1_Intron|NWD1_ENST00000552788.1_Intron|NWD1_ENST00000379808.3_Intron	NM_001007525.3	NP_001007526.3	Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	NA		NA					ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ctgcccgcctcggcctcccaa	0.532		NA											c|||	1137	0.227037	0.0461	0.2147	5008	,	,	NA	14501	0.2639	NA	0.3569	False	NA	,,,	NA	NA	NA	2504	0.3088	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039	284434		WD repeat domain containing	27619	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001007525	NM_001007525	NA	Approved		uc002neu.4	Q149M9		ENST00000524140.2:c.81+278C>T	chr19.hg19:g.16842367C>T		NA	C9J021|Q68CT3	hg19	CCDS32945.2	0.02	-0.14031	CCTxGGC	UNCOVERED																																																																																			NOVEL	NWD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379040.3	9	2.406948	KEEP	5	0	0	8	238	CC	0	0	0		+	8	60	223	0	0	21.611247	7	60	229	36	ENST00000524140.2	0.533333	0.260965
NWD1	284434	__UNKNOWN__	__UNKNOWN__	19	16869355	16869355	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:16869355A>T	ENST00000524140.2	+	7	2187				NWD1_ENST00000523826.1_Intron|NWD1_ENST00000339803.6_Intron|NWD1_ENST00000549814.1_Intron|NWD1_ENST00000552788.1_Intron|NWD1_ENST00000379808.3_Intron	NM_001007525.3	NP_001007526.3	Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	NA		NA					ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						cccaaagtgcagggattacag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039	284434		WD repeat domain containing	27619	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001007525	NM_001007525	NA	Approved		uc002neu.4	Q149M9		ENST00000524140.2:c.1770-681A>T	chr19.hg19:g.16869355A>T		NA	C9J021|Q68CT3	hg19	CCDS32945.2	0.02	-0.263107	TGCxGGG	COVERED																																																																																			NOVEL	NWD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000379040.3	3	2.706983	KEEP	1	0	0	9	252	AA	0.99257	0.688515	0		+	4	60	124	0	0	9.462684	22	60	649	62	ENST00000524140.2	0.153846	0.693668
CPAMD8	27151	__UNKNOWN__	__UNKNOWN__	19	17051972	17051972	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17051972G>A	ENST00000443236.1	-	23	2966					NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	NA		NA				extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						cgaactcctggcctcaggtga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111	27151			23228	protein-coding gene	gene with protein product		608841			NA	10574462	Standard	NM_015692	NM_015692	NA	Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2935-2716C>T	chr19.hg19:g.17051972G>A		NA	Q8NC09|Q9ULD7	hg19	CCDS42519.1	0.02	-0.114009	CTGxCCT	UNCOVERED																																																																																			NOVEL	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257531.2	7	3.00915	KEEP	4	0	0	10	312	GG	0.99254	0.161255	0		-	4	60	103	0	0	9.074848	7	60	246	35	ENST00000443236.1	0.363636	0.162467
MYO9B	4650	__UNKNOWN__	__UNKNOWN__	19	17291417	17291417	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17291417T>C	ENST00000594824.1	+	15	2366				MYO9B_ENST00000595618.1_Intron|MYO9B_ENST00000397274.2_Intron			Q13459	MYO9B_HUMAN	myosin IXB	NA		NA			actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						cctcggcctctcaaagtgctg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331	4650		Myosins / Myosin superfamily : Class IX	7609	protein-coding gene	gene with protein product		602129		CELIAC4	NA	9226381	Standard		NM_004145	NA	Approved		uc010eak.3	Q13459		ENST00000594824.1:c.2220-319T>C	chr19.hg19:g.17291417T>C		NA	O75314|Q9NUJ2|Q9UHN0	hg19		0.02	-0.149099	CTCxCAA	UNCOVERED																																																																																			NOVEL	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000463236.1	5	2.70717	KEEP	5	0	0	9	254	TT	0	0	0		+	3	60	91	0	0	7.092416	14	60	427	39	ENST00000594824.1	0.176471	0.292001
NR2F6	2063	__UNKNOWN__	__UNKNOWN__	19	17344799	17344799	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17344799T>C	ENST00000291442.3	-	4	1660					NM_005234.3	NP_005225.2	P10588	NR2F6_HUMAN	nuclear receptor subfamily 2, group F, member 6	NA		NA			detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|entrainment of circadian clock by photoperiod (GO:0043153)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						tttgggaggctgaggcgggca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X12794	CCDS12352.1	19p13.11	2013-09-20			ENSG00000160113	ENSG00000160113	2063		Nuclear hormone receptors	7977	protein-coding gene	gene with protein product		132880		ERBAL2	NA	2905047	Standard		NM_005234	NA	Approved	EAR-2	uc002nfq.3	P10588	OTTHUMG00000182728	ENST00000291442.3:c.941-1364A>G	chr19.hg19:g.17344799T>C		NA	B2RC68|Q5XGA0|Q6P586|Q9BUE8	hg19	CCDS12352.1	0.02	-0.192977	GGCxGAG	COVERED																																																																																			NOVEL	NR2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463325.1	5	3.007642	KEEP	2	0	0	10	277	TT	0.992708	0.454419	0		-	3	60	101	0	0	7.792014	18	60	560	57	ENST00000291442.3	0.142857	0.457757
ANKLE1	126549	__UNKNOWN__	__UNKNOWN__	19	17397479	17397479	__UNKNOWN__	3'UTR	SNP	G	G	T	rs11880549	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17397479G>T	ENST00000394458.3	+	0	2242				ANKLE1_ENST00000404085.1_3'UTR|ANKLE1_ENST00000598347.1_Silent_p.V583V|ANKLE1_ENST00000594072.1_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	NA		NA								large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						gtgtgtgtgtgtgtgtgtgtg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117	126549		Ankyrin repeat domain containing	26812	protein-coding gene	gene with protein product	LEM domain containing 6	NA	ankyrin repeat domain 41	ANKRD41	NA		Standard	NM_152363	NM_152363	NA	Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.*118G>T	chr19.hg19:g.17397479G>T		NA	A8VU82|Q8N8J8	hg19	CCDS12354.2	0.02	2.570453	TGTxTGT	COVERED																																																																																			NOVEL	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325392.2	17	9.907464	KEEP	3	2	39	47	1346	GG	1	0.999998	0		+	7	60	190	1	0	11.510308	88	60	2795	210	ENST00000394458.3	0.073684	0.999998
ANKLE1	126549	__UNKNOWN__	__UNKNOWN__	19	17397485	17397485	__UNKNOWN__	3'UTR	SNP	G	G	T	rs60712004		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17397485G>T	ENST00000394458.3	+	0	2248				ANKLE1_ENST00000404085.1_3'UTR|ANKLE1_ENST00000598347.1_Silent_p.V585V|ANKLE1_ENST00000594072.1_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	NA		NA								large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						gtgtgtgtgtgtgtgtgtgtg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117	126549		Ankyrin repeat domain containing	26812	protein-coding gene	gene with protein product	LEM domain containing 6	NA	ankyrin repeat domain 41	ANKRD41	NA		Standard	NM_152363	NM_152363	NA	Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.*124G>T	chr19.hg19:g.17397485G>T		NA	A8VU82|Q8N8J8	hg19	CCDS12354.2	0.02	2.259221	TGTxTGT	COVERED																																																																																			NOVEL	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000325392.2	20	7.017524	KEEP	3	3	63	46	1336	GG	1	1	0		+	13	60	317	1	0	20.698993	95	60	3085	237	ENST00000394458.3	0.12037	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	17578348	17578348	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17578348T>C			NA	NA				NXNL1 (6585 upstream) : SLC27A1 (1229 downstream)						NA		NA									NA						gtgcctcacgtctgtaatccc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.17578348T>C		NA		hg19		0.02	-0.192927	ACGxCTG	COVERED																																																																																			NOVEL					0			7	3.007736	KEEP	1	0	0	10	277	TT	0.99254	0.454342	0			3	60	104	0	0	8.160979	17	60	498	48		0.15	0.457757
CTD-3131K8.2	0	__UNKNOWN__	__UNKNOWN__	19	17620072	17620072	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17620072T>C	ENST00000596643.1	-	0	547										NA		NA									NA						cctcggcctctcaaagtgctg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000596643.1:	chr19.hg19:g.17620072T>C		NA		hg19		0.02	-0.192941	CTCxCAA	COVERED																																																																																			NOVEL	CTD-3131K8.2-003	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000464017.1	5	3.007645	KEEP	3	0	0	10	274	TT	0.99254	0.454342	0		-	3	60	102	0	0	7.960984	17	60	501	46	ENST00000596643.1	0.15	0.457757
FAM129C	199786	__UNKNOWN__	__UNKNOWN__	19	17659615	17659615	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17659615G>A	ENST00000335393.4	+	15	1897				FAM129C_ENST00000599124.1_Intron|FAM129C_ENST00000449408.2_Intron|FAM129C_ENST00000599164.1_Intron|FAM129C_ENST00000352727.3_Intron|FAM129C_ENST00000595684.1_Intron|FAM129C_ENST00000601861.1_Intron|FAM129C_ENST00000600871.1_Intron|FAM129C_ENST00000332386.5_Intron	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	NA		NA								autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						catgcctgtagtcccagctac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483	199786			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967			NA	12886250	Standard	NM_173544	NM_173544	NA	Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1760-638G>A	chr19.hg19:g.17659615G>A		NA	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	hg19	CCDS12362.1	0.02	-0.175446	GTAxTCC	COVERED																																																																																			NOVEL	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464206.1	14	3.04194	KEEP	10	1	28	20	609	GG	0.995343	0.385603	0		+	3	47	84	0	0	6.572461	12	60	420	68	ENST00000335393.4	0.2	0.387407
UNC13A	23025	__UNKNOWN__	__UNKNOWN__	19	17719567	17719567	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:17719567T>C	ENST00000519716.2	-	43	4811				UNC13A_ENST00000428389.2_Intron|UNC13A_ENST00000550896.1_Intron|UNC13A_ENST00000551649.1_Intron|UNC13A_ENST00000552293.1_Intron|UNC13A_ENST00000252773.7_Intron	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	NA		NA			beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						cctcgtgatctgcccgccttg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477	23025			23150	protein-coding gene	gene with protein product		609894			NA		Standard	XM_038604	NM_001080421	NA	Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.4811+1181A>G	chr19.hg19:g.17719567T>C		NA	E5RHY9	hg19	CCDS46013.2	0.02	-0.236808	ATCxGCC	COVERED																																																																																			NOVEL	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376169.2	14	4.812483	KEEP	18	0	0	16	445	TT	0.992708	0.607941	0		-	3	60	98	0	0	7.194849	23	60	687	87	ENST00000519716.2	0.115385	0.612407
PIK3R2	5296	__UNKNOWN__	__UNKNOWN__	19	18286902	18286902	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:18286902T>C	ENST00000593731.1	+	22	4666				IFI30_ENST00000407280.3_Intron			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	NA		NA			blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	ccgcctgccttggcctcccaa	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647	5296		SH2 domain containing	8980	protein-coding gene	gene with protein product		603157			NA	1314371	Standard	NM_005027	NM_005027	NA	Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.2184+395T>C	chr19.hg19:g.18286902T>C		NA	Q5EAT5|Q9UPH9	hg19	CCDS12371.1	0.02	-0.157859	CCTxGGC	COVERED																																																																																			NOVEL	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000466386.2	9	3.60751	KEEP	3	0	0	12	308	TT	0.993634	0.320751	0		+	3	41	91	0	0	7.179342	13	60	375	46	ENST00000593731.1	0.1875	0.322807
PGPEP1	54858	__UNKNOWN__	__UNKNOWN__	19	18472943	18472943	__UNKNOWN__	Intron	SNP	G	G	A	rs545293483		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:18472943G>A	ENST00000269919.6	+	5	532				PGPEP1_ENST00000597431.2_Intron|PGPEP1_ENST00000604499.2_Intron|PGPEP1_ENST00000252813.5_Intron	NM_017712.2	NP_060182.1	Q9NXJ5	PGPI_HUMAN	pyroglutamyl-peptidase I	NA		NA				cytosol (GO:0005829)	cysteine-type peptidase activity (GO:0008234)|pyroglutamyl-peptidase activity (GO:0016920)				NA						TAggccaggcgtggtggctca	0.527		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17464	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ278828	CCDS12375.1, CCDS74314.1	19p13.11	2012-07-25				ENSG00000130517	54858	3.4.19.3		13568	protein-coding gene	gene with protein product	pyroglutamyl aminopeptidase	610694			NA		Standard	NM_017712	XM_006722783	NA	Approved	PGP-I, Pcp, PGP, PGPI	uc002nis.1	Q9NXJ5		ENST00000269919.6:c.438-1258G>A	chr19.hg19:g.18472943G>A		NA	A8K1Q3|Q8IVT1	hg19	CCDS12375.1	0.02	-0.175437	GGCxTGG	COVERED																																																																																			NOVEL	PGPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466327.3	6	2.406504	KEEP	0	0	0	8	234	CG	0.99254	0.384517	0		+	3	60	92	0	0	7.033529	16	60	523	42	ENST00000269919.6	0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	18666842	18666842	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:18666842A>G			NA	NA				FKBP8 (12372 upstream) : KXD1 (1729 downstream)						NA		NA									NA						ggatggtctcaatctcctgac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.18666842A>G		NA		hg19		0.02	-0.166604	CTCxATC	COVERED																																																																																			NOVEL					0			5	3.005866	KEEP	2	0	0	10	260	AA	0.99254	0.351306	0			3	40	91	0	0	7.011965	15	60	429	37		0.166667	0.353947
GDF1	2657	__UNKNOWN__	__UNKNOWN__	19	18992866	18992866	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:18992866A>G	ENST00000247005.6	-	4	614				CERS1_ENST00000427170.2_Intron|CERS1_ENST00000542296.2_Intron|CERS1_ENST00000429504.2_Intron|AC005197.2_ENST00000597769.1_RNA			P27539	GDF1_HUMAN	growth differentiation factor 1	NA		NA			growth (GO:0040007)	extracellular space (GO:0005615)					NA						tgatccacccacctcggcctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M62302	CCDS42526.1	19p13.11	2014-01-30			ENSG00000130283	ENSG00000130283	2657		Endogenous ligands	4214	protein-coding gene	gene with protein product		602880			NA	2034669	Standard	NM_001492	NM_001492	NA	Approved			P27539		ENST00000247005.6:c.732-1622T>C	chr19.hg19:g.18992866A>G		NA	O43344	hg19	CCDS42526.1	0.02	1.906254	CCCxCCT	COVERED																																																																																			NOVEL	GDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465926.1	12	3.440104	KEEP	5	1	30	22	598	AA	0.999863	0.976731	0		-	4	60	126	0	0	8.693614	40	60	1182	106	ENST00000247005.6	0.090909	0.976865
COPE	11316	__UNKNOWN__	__UNKNOWN__	19	19018906	19018906	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19018906C>T	ENST00000262812.4	-	4	339				COPE_ENST00000598969.1_Intron|AC002985.3_ENST00000596918.1_Intron|COPE_ENST00000351079.4_Intron|COPE_ENST00000600932.1_Intron|COPE_ENST00000349893.4_Intron	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	NA		NA			COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						TGCCAGTTGTCGTAGCGTTGG	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669	11316			2234	protein-coding gene	gene with protein product		606942			NA	10469566	Standard	NM_007263	NM_007263	NA	Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.291-985G>A	chr19.hg19:g.19018906C>T		NA	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	hg19	CCDS12387.1	0.02	1.40097	TGTxGTA	COVERED																																																																																			NOVEL	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464801.1	5	3.008693	KEEP	0	0	0	10	302	CC	0.992708	0.972383	0		-	5	60	149	0	0	10.056568	49	60	1567	102	ENST00000262812.4	0.092593	0.979526
COPE	11316	__UNKNOWN__	__UNKNOWN__	19	19028789	19028789	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19028789A>G	ENST00000262812.4	-	1	175				AC002985.3_ENST00000596918.1_Intron|COPE_ENST00000351079.4_Intron|COPE_ENST00000600932.1_Intron|COPE_ENST00000349893.4_Intron	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	NA		NA			COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						cacaaggtcaagagatggaga	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669	11316			2234	protein-coding gene	gene with protein product		606942			NA	10469566	Standard	NM_007263	NM_007263	NA	Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.126+1242T>C	chr19.hg19:g.19028789A>G		NA	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	hg19	CCDS12387.1	0.02	-0.1228	TCAxGAG	COVERED																																																																																			NOVEL	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464801.1	10	2.406076	KEEP	1	0	0	8	219	AA	0.99257	0.194853	0		-	3	23	108	0	0	9.072764	11	60	332	32	ENST00000262812.4	0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	19061879	19061879	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19061879T>C			NA	NA				AC005932.1 (4239 upstream) : RN7SL70P (6889 downstream)						NA		NA									NA						acctgggaggtggagcttgca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.19061879T>C		NA		hg19		0.02	-0.113967	AGGxGGA	UNCOVERED																																																																																			NOVEL					0			7	2.704824	KEEP	7	0	0	9	235	TT	0	0	0			3	40	83	0	0	6.933102	8	60	216	36		0.272727	0.162467
TMEM161A	54929	__UNKNOWN__	__UNKNOWN__	19	19242586	19242586	__UNKNOWN__	Intron	SNP	C	C	T	rs113700466		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19242586C>T	ENST00000162044.9	-	5	508				TMEM161A_ENST00000450333.2_Intron|TMEM161A_ENST00000587583.2_Intron	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	NA		NA			cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			ccacctgcctcggcctcccaa	0.512		NA											C|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17674	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545	54929			26020	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_017814	NM_017814	NA	Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.443+574G>A	chr19.hg19:g.19242586C>T		NA	B3KUE0|G5E9M6|Q7L2Y1	hg19	CCDS12393.1	0.02	1.168934	CCTxGGC	COVERED																																																																																			NOVEL	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460089.2	47	5.949972	KEEP	19	1	29	30	885	CC	0.999931	0.987875	0		-	5	60	132	0	0	9.495166	28	60	912	144	ENST00000162044.9	0.151515	0.987943
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	19254871	19254871	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19254871A>G			NA	NA				TMEM161A (5569 upstream) : MEF2BNB-MEF2B (1504 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.19254871A>G		NA		hg19		0.02	-0.20173	GCTxGGA	COVERED																																																																																			NOVEL					0			11	4.81122	KEEP	1	0	0	16	431	AA	0.99649	0.488823	0			3	60	101	0	0	7.860876	17	60	508	50		0.15	0.490544
MAU2	23383	__UNKNOWN__	__UNKNOWN__	19	19467483	19467483	__UNKNOWN__	3'UTR	SNP	G	G	C	rs546665044		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19467483G>C	ENST00000392313.6	+	0	2913				MAU2_ENST00000262815.8_3'UTR	NM_015329.3	NP_056144.3	Q9Y6X3	SCC4_HUMAN	MAU2 sister chromatid cohesion factor	NA		NA			maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	protein N-terminus binding (GO:0047485)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	18						GGAGCCCAGGGACTTTCTTCC	0.632		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB020699	CCDS32969.2	19p13.11	2013-08-28	2013-08-28	2013-08-28	ENSG00000129933	ENSG00000129933	23383			29140	protein-coding gene	gene with protein product	sister chromatid cohesion 4	614560	KIAA0892, MAU2 chromatid cohesion factor homolog (C. elegans)	KIAA0892	NA	10048485	Standard	NM_015329	NM_015329	NA	Approved	MGC75361, mau-2, MAU2L, SCC4	uc002nmk.4	Q9Y6X3	OTTHUMG00000150188	ENST00000392313.6:c.*892G>C	chr19.hg19:g.19467483G>C		NA	Q66PT1|Q6P3S7|Q6ZTT2|Q9UFX8	hg19	CCDS32969.2	0.02	3.827454	AGGxACT	COVERED																																																																																			NOVEL	MAU2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316748.6	2	9.928122	KEEP	0	0	0	33	1004	GG	0.999998	0.999997	0		+	40	60	1364	0	0	120.481229	91	60	2959	231	ENST00000392313.6	0.305344	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	19491581	19491581	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19491581C>T			NA	NA				MAU2 (22018 upstream) : GATAD2A (5060 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.19491581C>T		NA		hg19		0.02	-0.113994	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			5	2.406507	KEEP	2	0	0	8	231	CC	0.99257	0.16126	0			4	60	96	0	0	8.189053	8	60	270	29		0.333333	0.162467
ATP13A1	57130	__UNKNOWN__	__UNKNOWN__	19	19756736	19756736	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19756736C>T	ENST00000357324.6	-	24	3333	c.3307G>A	c.(3307-3309)Gtc>Atc	p.V1103I	ATP13A1_ENST00000291503.5_Missense_Mutation_p.V985I	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	1103		NA				endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						ATGATGTAGACGGTGCTGTTG	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(142;920 1789 9047 14684 24777)							NA				0													256	224	235			NA	NA	19		NA											NA				19756736		2203	4300	6503	SO:0001583	missense			AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726	57130		ATPases / P-type	24215	protein-coding gene	gene with protein product	cation transporting ATPase	NA	ATPase type 13A	ATP13A	NA	11347906	Standard	NM_020410	NM_020410	NA	Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.3307G>A	chr19.hg19:g.19756736C>T	ENSP00000349877:p.Val1103Ile	NA	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	hg19	CCDS32970.2	0.02	2.747109	AGAxGGT	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.53	2.860889	0.51482	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	D;D	0.88664	-2.41;-2.41	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	D	0.89753	0.6806	L	0.48877	1.53	0.80722	D	1	D;D	0.69078	0.995;0.997	P;P	0.58331	0.699;0.837	D	0.86482	0.1792	10	0.15066	T	0.55	-14.2105	14.9595	0.71144	0.0:1.0:0.0:0.0	.	1103;985	Q9HD20;Q9HD20-2	AT131_HUMAN;.	I	985;1103	ENSP00000291503:V985I;ENSP00000349877:V1103I	ENSP00000291503:V985I	V	-	1	0	ATP13A1	19617736	1.000000	0.71417	0.938000	0.37757	0.765000	0.43378	7.209000	0.77916	2.384000	0.81235	0.491000	0.48974	GTC	NOVEL	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329005.1	11	6.04755	KEEP	0	1	25	29	826	CC	0.999997	0.999986	0		-	6	60	176	0	0	10.619289	94	60	3065	192	ENST00000357324.6	0.06	0.999989
ZNF101	94039	__UNKNOWN__	__UNKNOWN__	19	19791166	19791166	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19791166T>C	ENST00000592502.1	+	0	1478							Q8IZC7	ZN101_HUMAN	zinc finger protein 101	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						tggctcacgcttgtaatccca	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK097169	CCDS32971.1	19p13.11	2013-01-08	2004-02-10		ENSG00000181896	ENSG00000181896	94039		Zinc fingers, C2H2-type, -	12881	protein-coding gene	gene with protein product		603983	zinc finger protein 101 (Y2)		NA	11441184	Standard	NM_033204	XM_005260165	NA	Approved	HZF12, DKFZp570I0164	uc002nni.2	Q8IZC7	OTTHUMG00000167736	ENST00000592502.1:c.*57T>C	chr19.hg19:g.19791166T>C		NA	C9JU83|Q0VDG9	hg19	CCDS32971.1	0.02	-0.394659	CGCxTGT	COVERED																																																																																			NOVEL	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460559.1	15	4.810516	KEEP	3	0	0	16	427	TT	0.99649	0.923388	0		+	3	60	106	0	0	7.439869	36	60	1069	87	ENST00000592502.1	0.076923	0.92664
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	19849799	19849799	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19849799C>T			NA	NA				ZNF14 (5893 upstream) : CTC-559E9.4 (22047 downstream)						NA		NA									NA						cagccctctgccctcagccct	0.612		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.19849799C>T		NA		hg19		0.02	-0.1491	CTGxCCT	COVERED																																																																																			NOVEL					0			6	3.30987	KEEP	0	0	0	11	338	CC	0.993072	0.289978	0			6	60	170	0	0	15.264445	10	60	327	43		0.375	0.292001
CTC-559E9.4	0	__UNKNOWN__	__UNKNOWN__	19	19874636	19874636	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19874636C>T	ENST00000590274.1	-	0	116										NA		NA									NA						ggcacaatctcggctcactgc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000590274.1:	chr19.hg19:g.19874636C>T		NA		hg19		0.02	-0.087707	TCTxGGC	UNCOVERED																																																																																			NOVEL	CTC-559E9.4-001	KNOWN	basic|readthrough_transcript	lincRNA	NA	lincRNA	OTTHUMT00000460784.1	9	3.007108	KEEP	3	0	0	10	272	CC	0	0	0		-	3	60	87	0	0	7.643408	6	60	182	23	ENST00000590274.1	0.333333	0.099721
ZNF506	440515	__UNKNOWN__	__UNKNOWN__	19	19925827	19925827	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:19925827A>G	ENST00000450683.2	-	1	149				CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.4_ENST00000590274.1_lincRNA|ZNF506_ENST00000587461.1_Intron|ZNF506_ENST00000545006.1_Intron|ZNF506_ENST00000540806.2_Intron|ZNF506_ENST00000587452.1_Intron|ZNF506_ENST00000443905.2_Intron	NM_001145404.1	NP_001138876.1	Q5JVG8	ZN506_HUMAN	zinc finger protein 506	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						agcactttggaaggctgaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665	440515		Zinc fingers, C2H2-type, -	23780	protein-coding gene	gene with protein product		NA			NA		Standard	XM_036218	NM_001099269	NA	Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000450683.2:c.3+6582T>C	chr19.hg19:g.19925827A>G		NA	B3KTH6	hg19	CCDS46027.1	0.02	-0.228015	TGGxAGG	COVERED																																																																																			NOVEL	ZNF506-002	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460795.1	10	6.315296	KEEP	3	0	0	21	578	AA	0.999869	0.582854	0		-	3	60	96	0	0	7.227379	19	60	563	73	ENST00000450683.2	0.136364	0.58293
ZNF682	91120	__UNKNOWN__	__UNKNOWN__	19	20132718	20132718	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:20132718A>G	ENST00000397165.2	-	3	387				ZNF682_ENST00000597972.1_Intron|ZNF682_ENST00000593468.1_Intron|ZNF682_ENST00000358523.5_Intron|ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000397162.1_Intron|ZNF682_ENST00000595736.1_Intron	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						ggtggctcacacctgtaatcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124	91120		Zinc fingers, C2H2-type, -	28857	protein-coding gene	gene with protein product		NA			NA		Standard	NM_033196	NM_033196	NA	Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.226+1094T>C	chr19.hg19:g.20132718A>G		NA	B3KU64|E9PFJ5|Q96JV9	hg19	CCDS42533.1	0.02	-0.166644	CACxCCT	COVERED																																																																																			NOVEL	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462888.1	9	2.406229	KEEP	0	0	0	8	223	AA	0.99257	0.351317	0		-	3	60	102	0	0	8.278798	13	60	397	38	ENST00000397165.2	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	20907630	20907630	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:20907630A>G			NA	NA				ZNF626 (63228 upstream) : CTD-2626G11.2 (22098 downstream)						NA		NA									NA						gattacaggcatgagccaccg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.20907630A>G		NA		hg19		0.02	-0.043852	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			5	2.706826	KEEP	0	0	0	9	248	AA	0.99254	0.023894	0			2	60	67	0	0	6.45016	2	60	60	21		0.5	0.024074
ZNF714	148206	__UNKNOWN__	__UNKNOWN__	19	21300738	21300738	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:21300738T>C	ENST00000596143.1	+	5	1593	c.1268T>C	c.(1267-1269)cTc>cCc	p.L423P	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000291770.7_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	423		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						GGAGAGAAACTCTACAAATGT	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													38	41	40			NA	NA	19		NA											NA				21300738		2170	4287	6457	SO:0001583	missense			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352	148206		Zinc fingers, C2H2-type	27124	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_182515	NM_182515	NA	Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.1268T>C	chr19.hg19:g.21300738T>C	ENSP00000472368:p.Leu423Pro	NA	Q49AI1|Q86W65|Q8ND40	hg19	CCDS54239.1	0.02	1.800996	AACxCTA	COVERED	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.950278	0.00051	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	1.05	-2.11	0.07187	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05044	0.0135	N	0.00154	-1.97	0.19575	N	0.999962	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.24404	-1.0161	8	0.02654	T	1	.	7.1125	0.25399	0.0:0.6617:0.0:0.3383	.	424;423;424	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	P	423	.	ENSP00000291770:L423P	L	+	2	0	ZNF714	21092578	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.309000	0.19332	-1.683000	0.01444	-1.712000	0.00714	CTC	NOVEL	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463930.1	9	3.640357	KEEP	1	1	28	22	602	TT	0.999892	0.994976	0		+	4	60	130	1	0	8.418188	60	60	1812	129	ENST00000596143.1	0.0625	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	21568024	21568024	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:21568024T>C			NA	NA				ZNF738 (5920 upstream) : ZNF493 (11896 downstream)						NA		NA									NA						tttgggaggctgaggcaggca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.21568024T>C		NA		hg19		0.02	-0.149115	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.707138	KEEP	7	0	0	9	253	TT	0	0	0			3	60	102	0	0	8.278693	13	60	403	42		0.1875	0.292001
ZNF493	284443	__UNKNOWN__	__UNKNOWN__	19	21604419	21604419	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:21604419A>G	ENST00000392288.2	+	4	362				CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000596302.1_Intron|ZNF493_ENST00000355504.4_Intron	NM_001076678.2	NP_001070146.1	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						cacccacctcagcctcccaaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268	284443		Zinc fingers, C2H2-type, -	23708	protein-coding gene	gene with protein product		NA			NA		Standard	NM_175910	NM_001076678	NA	Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000392288.2:c.254-1296A>G	chr19.hg19:g.21604419A>G		NA	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	hg19	CCDS42536.1	0.02	-0.035086	CTCxGCC	UNCOVERED																																																																																			NOVEL	ZNF493-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280562.1	1	2.406179	KEEP	0	0	0	8	229	AA	0.99257	0.019833	0		+	2	60	62	0	0	6.324484	1	60	32	20	ENST00000392288.2	0.666667	0.019982
ZNF429	353088	__UNKNOWN__	__UNKNOWN__	19	21717921	21717921	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:21717921G>A	ENST00000358491.4	+	4	434				ZNF429_ENST00000597078.1_Intron|ZNF429_ENST00000594022.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						gagccaccgcgcccggccTTG	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013	353088		Zinc fingers, C2H2-type, -	20817	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001001415	NM_001001415	NA	Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.227-1161G>A	chr19.hg19:g.21717921G>A		NA	A6NLV7|Q9BZE6	hg19	CCDS42537.1	0.02	-0.157895	CGCxCCC	COVERED																																																																																			NOVEL	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463981.1	3	5.415366	KEEP	4	0	0	18	534	GG	0.999366	0.322602	0		+	3	60	88	0	0	6.792037	14	60	466	59	ENST00000358491.4	0.176471	0.322807
ZNF429	353088	__UNKNOWN__	__UNKNOWN__	19	21725407	21725407	__UNKNOWN__	Intron	SNP	G	G	A	rs12461802	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:21725407G>A	ENST00000597078.1	+	4	517							Q86V71	ZN429_HUMAN	zinc finger protein 429	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						ttgagatgaagtcttgctctg	0.393		NA											g|||	2806	0.560304	0.4902	0.5231	5008	,	,	NA	20365	0.6409	NA	0.5368	False	NA	,,,	NA	NA	NA	2504	0.6227	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013	353088		Zinc fingers, C2H2-type, -	20817	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001001415	NM_001001415	NA	Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000597078.1:c.349+719G>A	chr19.hg19:g.21725407G>A		NA	A6NLV7|Q9BZE6	hg19		0.02	-0.096486	GAAxTCT	UNCOVERED																																																																																			NOVEL	ZNF429-001	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000463983.1	10	2.407469	KEEP	1	0	0	8	257	GG	0	0	0		+	5	60	149	0	0	14.599003	4	60	141	25	ENST00000597078.1	0.555556	0.120436
RP11-678G14.3	0	__UNKNOWN__	__UNKNOWN__	19	21768612	21768612	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:21768612G>A	ENST00000596996.1	-	0	460										NA		NA									NA						caacaagagcgaaactccgtc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000596996.1:	chr19.hg19:g.21768612G>A		NA		hg19		0.02	-0.12272	AGCxAAA	COVERED																																																																																			NOVEL	RP11-678G14.3-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000464022.1	6	3.604364	KEEP	1	0	0	12	308	GG	0.993072	0.194952	0		-	3	60	80	0	0	6.502156	9	60	256	30	ENST00000596996.1	0.25	0.196312
ZNF99	7652	__UNKNOWN__	__UNKNOWN__	19	22940693	22940693	__UNKNOWN__	Missense_Mutation	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:22940693T>C	ENST00000596209.1	-	4	2108	c.2018A>G	c.(2017-2019)gAa>gGa	p.E673G	ZNF99_ENST00000397104.3_Missense_Mutation_p.E582G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	673		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGGTTTCTCTTCAGTATGAAT	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													48	51	50			NA	NA	19		NA											NA				22940693		2134	4256	6390	SO:0001583	missense			BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973	7652		Zinc fingers, C2H2-type, -	13175	protein-coding gene	gene with protein product		603981	zinc finger protein 99 (F8281), chromosome 19 open reading frame 9	C19orf9	NA		Standard	XM_065124	NM_001080409	NA	Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2018A>G	chr19.hg19:g.22940693T>C	ENSP00000472969:p.Glu673Gly	NA	M0R335	hg19	CCDS59369.1	0.02	-0.342026	TCTxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	N	0.003	-2.519673	0.00149	.	.	ENSG00000213973	ENST00000397104	T	0.11821	2.74	1.29	-2.57	0.06248	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02342	0.0072	N	0.00525	-1.395	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.25047	-1.0143	9	0.02654	T	1	.	4.0893	0.09962	0.0:0.3576:0.3633:0.2791	.	582	A8MXY4	ZNF99_HUMAN	G	582	ENSP00000380293:E582G	ENSP00000380293:E582G	E	-	2	0	ZNF99	22732533	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.204000	0.17335	-1.972000	0.01001	-2.181000	0.00316	GAA	NOVEL	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464591.1	5	5.113035	KEEP	0	0	0	17	471	TT	0.999366	0.865197	0		-	3	60	102	0	0	7.075553	35	60	1044	82	ENST00000596209.1	0.078947	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	23058521	23058521	__UNKNOWN__	IGR	SNP	G	G	C	rs11881726	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:23058521G>C			NA	NA				ZNF99 (91612 upstream) : CTD-2579N5.3 (31366 downstream)						NA		NA									NA						acaatggtgcgatcttggctc	0.458		NA											.|||	962	0.192093	0.3132	0.1225	5008	,	,	NA	11840	0.1726	NA	0.172	False	NA	,,,	NA	NA	NA	2504	0.1186	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.23058521G>C		NA		hg19		0.02	-0.114031	TGCxATC	UNCOVERED																																																																																			NOVEL					0			8	2.406572	KEEP	5	0	0	8	230	GT	0	0	0			4	60	138	0	0	12.785989	6	60	184	28		0.4	0.162467
ZNF724P	440519	__UNKNOWN__	__UNKNOWN__	19	23405158	23405158	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:23405158T>C	ENST00000418100.1	-	0	2006							A8MTY0	ZN724_HUMAN	zinc finger protein 724, pseudogene	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|lung(2)|ovary(2)	8						ggattacaggtgtgagccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					19p12	2014-02-14	2010-08-03		ENSG00000196081	ENSG00000196081	440519			32460	pseudogene	pseudogene		NA	zinc finger protein 724 pseudogene, zinc finger protein 724 (pseudogene)		NA		Standard		NR_045525	NA	Approved		uc021uru.1	A8MTY0	OTTHUMG00000183231	ENST00000418100.1:c.*29A>G	chr19.hg19:g.23405158T>C		NA		hg19		0.02	1.558327	AGGxGTG	COVERED																																																																																			NOVEL	ZNF724P-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000465743.1	12	7.245813	KEEP	4	1	31	35	926	TT	0.999998	0.997551	0		-	4	60	135	0	0	8.83273	63	60	1730	149	ENST00000418100.1	0.059701	0.997553
ZNF724P	440519	__UNKNOWN__	__UNKNOWN__	19	23405303	23405303	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:23405303C>T	ENST00000418100.1	-	4	1861	c.1744G>A	c.(1744-1746)Gta>Ata	p.V582I				A8MTY0	ZN724_HUMAN	zinc finger protein 724, pseudogene	582		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|lung(2)|ovary(2)	8						GTATGAATTACCTTATGTTTA	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					19p12	2014-02-14	2010-08-03		ENSG00000196081	ENSG00000196081	440519			32460	pseudogene	pseudogene		NA	zinc finger protein 724 pseudogene, zinc finger protein 724 (pseudogene)		NA		Standard		NR_045525	NA	Approved		uc021uru.1	A8MTY0	OTTHUMG00000183231	ENST00000418100.1:c.1744G>A	chr19.hg19:g.23405303C>T	ENSP00000413411:p.Val582Ile	NA		hg19		0.02	1.137799	TTAxCTT	COVERED	.	.	.	.	.	.	.	.	.	.	C	0.714	-0.786218	0.02907	.	.	ENSG00000196081	ENST00000418100	T	0.17054	2.3	1.08	-1.21	0.09524	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10594	0.0259	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.30416	-0.9979	8	0.44086	T	0.13	.	5.0646	0.14576	0.0:0.2321:0.0:0.7679	.	582	A8MTY0	ZN724_HUMAN	I	582	ENSP00000413411:V582I	ENSP00000413411:V582I	V	-	1	0	ZNF724P	23197143	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-4.618000	0.00207	-0.354000	0.08212	-0.350000	0.07774	GTA	NOVEL	ZNF724P-001	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000465743.1	11	8.122863	KEEP	0	0	0	27	816	CC	0.999988	0.999665	0		-	6	60	165	0	0	10.060303	76	60	2561	163	ENST00000418100.1	0.073171	0.999678
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	27732070	27732070	__UNKNOWN__	IGR	SNP	A	A	T	rs74197639	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:27732070A>T			NA	NA				None (None upstream) : CTB-151G24.1 (397320 downstream)						NA		NA									NA						gctagacagaagaattctcag	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.27732070A>T		NA		hg19		0.02	18.221279	AGAxGAA	COVERED																																																																																			NOVEL					0			255	47.822402	KEEP	95	16	456	320	9050	AA	1	1	0			21	60	625	0	0	40.904482	238	60	7355	1473		0.081081	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	27732199	27732199	__UNKNOWN__	IGR	SNP	A	A	C	rs74212594|rs74185391|rs74217232|rs74211471|rs74184378|rs74194881|rs74202978		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:27732199A>C			NA	NA				None (None upstream) : CTB-151G24.1 (397191 downstream)						NA		NA									NA						ctttgaggtcagtggtagaaa	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.27732199A>C		NA		hg19		0.02	5.789662	GTCxGTG	COVERED																																																																																			NOVEL					0			84	19.770045	KEEP	166	7	214	141	3836	AA	1	1	0			6	53	204	1	0	15.470101	41	60	1211	649		0.12766	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	27732223	27732223	__UNKNOWN__	IGR	SNP	G	G	C	rs74188557|rs74203016|rs34323974|rs74207383|rs74208816|rs35248962	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:27732223G>C			NA	NA				None (None upstream) : CTB-151G24.1 (397167 downstream)						NA		NA									NA						aaatatcttcgtataaaaact	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.27732223G>C		NA		hg19		0.02	10.426987	TTCxTAT	COVERED																																																																																			NOVEL					0			143	5.082	KEEP	217	17	536	205	6043	GG	1	1	0			9	49	316	0	0	22.483048	98	60	3240	1026		0.084112	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	27738438	27738438	__UNKNOWN__	IGR	SNP	T	T	G	rs200914145		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:27738438T>G			NA	NA				None (None upstream) : CTB-151G24.1 (390952 downstream)						NA		NA									NA						actctgtttgtaaagtctgca	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.27738438T>G		NA		hg19		0.02	3.447075	TTGxAAA	COVERED																																																																																			NOVEL					0			41	2.459836	KEEP	32	5	135	56	1441	TT	1	1	0			4	27	135	2	0	10.357805	25	60	698	297		0.137931	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	32991578	32991578	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:32991578C>T			NA	NA				DPY19L3 (14777 upstream) : AC005621.1 (183 downstream)						NA		NA									NA						acaacctctgcctcccaggtt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.32991578C>T		NA		hg19		0.02	-0.070175	CTGxCTC	UNCOVERED																																																																																			NOVEL					0			6	2.406496	KEEP	2	0	0	8	234	CC	0	0	0			3	41	88	0	0	7.932365	5	60	172	24		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	33056550	33056550	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33056550A>G			NA	NA				AC005621.1 (64703 upstream) : PDCD5 (15423 downstream)						NA		NA									NA						aaagtgctggaattacaggcg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.33056550A>G		NA		hg19		0.02	-0.157867	TGGxATT	COVERED																																																																																			NOVEL					0			4	3.007492	KEEP	3	0	0	10	276	AA	0.99254	0.320398	0			3	60	105	0	1	8.773024	11	60	321	43		0.214286	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	33087523	33087523	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33087523C>T			NA	NA				PDCD5 (9165 upstream) : ANKRD27 (389 downstream)						NA		NA									NA						gcactccagcctgggtgacag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.33087523C>T		NA		hg19		0.02	-0.175452	AGCxTGG	COVERED																																																																																			NOVEL					0			9	3.309379	KEEP	1	0	0	11	326	CC	0.992708	0.384582	0			3	27	91	0	0	7.010167	15	60	524	41		0.166667	0.387407
ANKRD27	84079	__UNKNOWN__	__UNKNOWN__	19	33115234	33115234	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33115234T>C	ENST00000306065.4	-	17	1788					NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	NA		NA			early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					gatcgtgccattgcactccag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186	84079		Ankyrin repeat domain containing	25310	protein-coding gene	gene with protein product	Vps9 domain and ankyrin-repeat-containing protein	NA			NA	11230166, 16525121	Standard	NM_032139	NM_032139	NA	Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.1629+1545A>G	chr19.hg19:g.33115234T>C		NA	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	hg19	CCDS32986.1	0.02	-0.149092	CCAxTGC	COVERED																																																																																			NOVEL	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450329.1	12	3.909437	KEEP	11	0	0	13	351	TT	0.99257	0.289832	0		-	3	60	96	0	0	7.679282	13	60	375	51	ENST00000306065.4	0.1875	0.292001
NUDT19	390916	__UNKNOWN__	__UNKNOWN__	19	33203521	33203521	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33203521T>A	ENST00000397061.3	+	0	1786					NM_001105570.1	NP_001099040.1	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 19	NA		NA				mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Esophageal squamous(110;0.137)					ctggtctcgatctcctgacct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS42543.1	19q13.11	2011-11-16			ENSG00000213965	ENSG00000213965	390916		Nudix motif containing	32036	protein-coding gene	gene with protein product		NA			NA		Standard	XM_372723	NM_001105570	NA	Approved	RP2	uc010edf.3	A8MXV4		ENST00000397061.3:c.*658T>A	chr19.hg19:g.33203521T>A		NA		hg19	CCDS42543.1	0.02	-0.105198	CGAxCTC	UNCOVERED																																																																																			NOVEL	NUDT19-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450338.3	7	2.404751	KEEP	1	0	0	8	206	TT	0	0	0		+	3	60	83	1	0	7.078371	7	60	203	30	ENST00000397061.3	0.3	0.139832
TDRD12	91646	__UNKNOWN__	__UNKNOWN__	19	33295357	33295357	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33295357C>T	ENST00000444215.2	+	21	2872							Q587J7	TDR12_HUMAN	tudor domain containing 12	NA		NA			cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			NS(1)|breast(1)|endometrium(3)|lung(2)|prostate(1)|skin(1)	9	Esophageal squamous(110;0.137)					cccagcacttcgggaggccga	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023134	CCDS46038.1	19q13.11	2013-01-23				ENSG00000173809	91646		Tudor domain containing	25044	protein-coding gene	gene with protein product		NA			NA	11441184	Standard	NM_001015890	NM_001110822	NA	Approved	ECAT8, FLJ13072	uc002ntq.2	Q587J7		ENST00000444215.2:c.2552+1309C>T	chr19.hg19:g.33295357C>T		NA		hg19		0.02	-0.105246	CTTxGGG	UNCOVERED																																																																																			NOVEL	TDRD12-001	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000435933.1	3	2.406831	KEEP	2	0	0	8	238	CC	0	0	0		+	3	60	81	0	0	6.732074	8	60	258	32	ENST00000444215.2	0.272727	0.139832
RHPN2	85415	__UNKNOWN__	__UNKNOWN__	19	33500263	33500263	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33500263A>G	ENST00000254260.3	-	7	629				RHPN2_ENST00000400226.4_Intron	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	NA		NA			signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					ttgggaggccaaggcggTATG	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941	85415			19974	protein-coding gene	gene with protein product		NA			NA	12221077	Standard	NM_033103	NM_033103	NA	Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.594-1177T>C	chr19.hg19:g.33500263A>G		NA	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	hg19	CCDS12427.1	0.02	3.429082	GCCxAGG	COVERED																																																																																			NOVEL	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450828.2	34	5.173957	KEEP	0	5	150	70	1932	AA	1	1	0		-	8	60	257	0	1	16.702842	114	60	3416	313	ENST00000254260.3	0.065574	1
RHPN2	85415	__UNKNOWN__	__UNKNOWN__	19	33505420	33505420	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33505420T>C	ENST00000254260.3	-	5	426				RHPN2_ENST00000400226.4_Intron	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	NA		NA			signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					ctatgttgcctaggctggtct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941	85415			19974	protein-coding gene	gene with protein product		NA			NA	12221077	Standard	NM_033103	NM_033103	NA	Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.391-1790A>G	chr19.hg19:g.33505420T>C		NA	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	hg19	CCDS12427.1	0.02	-0.306951	GCCxAGG	COVERED																																																																																			NOVEL	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000450828.2	20	5.713339	KEEP	13	0	0	19	509	TT	0.994391	0.795757	0		-	4	60	134	0	0	10.074302	28	60	828	86	ENST00000254260.3	0.125	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	33669934	33669934	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:33669934A>G			NA	NA				CTD-2540B15.10 (377 upstream) : LRP3 (15555 downstream)						NA		NA									NA						acaggtgtgaaccaccgtgcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.33669934A>G		NA		hg19		0.02	-0.184191	TGAxCCA	COVERED																																																																																			NOVEL					0			7	4.511439	KEEP	0	0	0	15	415	AA	0.99649	0.421991	0			3	60	106	0	0	8.360574	17	60	515	53		0.15	0.423478
LGI4	163175	__UNKNOWN__	__UNKNOWN__	19	35625945	35625945	__UNKNOWN__	5'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:35625945A>T	ENST00000310123.3	-	0	159				LGI4_ENST00000392225.3_5'UTR|LGI4_ENST00000493050.1_Intron	NM_139284.2	NP_644813.1	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	NA		NA			adult locomotory behavior (GO:0008344)|glial cell proliferation (GO:0014009)|myelination in peripheral nervous system (GO:0022011)|neuron maturation (GO:0042551)	extracellular space (GO:0005615)				endometrium(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)			TAtgtgtgtgagtgtatgtga	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001623	5_prime_UTR_variant			AJ487519	CCDS12444.1	19q13.13	2008-07-03			ENSG00000153902	ENSG00000153902	163175			18712	protein-coding gene	gene with protein product		608303			NA	12023020	Standard		NM_139284	NA	Approved		uc002nxx.2	Q8N135	OTTHUMG00000044558	ENST00000310123.3:c.-361T>A	chr19.hg19:g.35625945A>T		NA	B2RN53|B9EGS7|Q5M8T1	hg19	CCDS12444.1	0.02	2.850945	GTGxGTG	COVERED																																																																																			NOVEL	LGI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000103963.1	42	13.982426	KEEP	0	8	216	123	3384	AA	1	1	0		-	6	60	186	0	0	11.289813	107	60	3176	382	ENST00000310123.3	0.053097	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	35858216	35858216	__UNKNOWN__	IGR	SNP	G	G	A	rs386808925		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:35858216G>A			NA	NA				FFAR3 (6829 upstream) : GPR42 (3614 downstream)						NA		NA									NA						gagccaccacgcccagccttc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.35858216G>A		NA		hg19		0.02	-0.131226	CACxCCC	COVERED																																																																																			NOVEL					0			8	2.707932	KEEP	0	0	0	9	273	GG	0.99254	0.227464	0			3	60	83	0	0	6.801302	9	60	289	33		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	36071189	36071189	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36071189A>G			NA	NA				ATP4A (16629 upstream) : AC002115.5 (17619 downstream)						NA		NA									NA						atggagtctcactctgtcgcc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.36071189A>G		NA		hg19		0.02	-0.148929	CTCxCTC	COVERED																																																																																			NOVEL					0			5	2.70574	KEEP	0	0	0	9	235	AA	0.99254	0.289823	0			4	60	136	0	1	11.60457	12	60	311	37		0.25	0.292001
COX6B1	1340	__UNKNOWN__	__UNKNOWN__	19	36142996	36142996	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36142996A>G	ENST00000592141.1	+	2	371				COX6B1_ENST00000246554.3_Intron|COX6B1_ENST00000392201.1_Intron			P14854	CX6B1_HUMAN	cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous)	NA		NA			cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)			lung(6)|prostate(1)|stomach(1)	8	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			caatggtgcaatcttggctca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC001015	CCDS12469.1	19q13.1	2011-07-04	2010-01-07	2004-08-12	ENSG00000126267	ENSG00000126267	1340	1.9.3.1	Mitochondrial respiratory chain complex / Complex IV	2280	protein-coding gene	gene with protein product		124089	cytochrome c oxidase subunit Vib, cytochrome c oxidase subunit Vib polypeptide 1 (ubiquitous)	COX6B	NA	1650756	Standard	NM_001863	NM_001863	NA	Approved	COXG	uc002oav.3	P14854	OTTHUMG00000048112	ENST00000592141.1:c.106+745A>G	chr19.hg19:g.36142996A>G		NA	B2R5C9|Q6IBL4	hg19	CCDS12469.1	0.02	-0.131553	GCAxTCT	COVERED																																																																																			NOVEL	COX6B1-004	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459068.3	9	3.606986	KEEP	7	0	0	12	307	AA	0.99254	0.227464	0		+	3	21	104	0	0	8.67305	11	60	313	46	ENST00000592141.1	0.214286	0.229173
KMT2B	9757	__UNKNOWN__	__UNKNOWN__	19	36215392	36215392	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36215392C>T	ENST00000222270.7	+	9	3334				KMT2B_ENST00000420124.1_Intron|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	NA		NA			chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)				NA						agagcgagaccctgcctcaaa	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333	9757		Chromatin-modifying enzymes / K-methyltransferases	15840	protein-coding gene	gene with protein product	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4	606834			NA	10409430, 10637508	Standard	NM_014727	XM_006723513	NA	Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3335-146C>T	chr19.hg19:g.36215392C>T		NA	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	hg19	CCDS46055.1	0.02	-0.236683	GACxCTG	COVERED																																																																																			NOVEL	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		7	5.115429	KEEP	1	0	0	17	531	CC	0.999366	0.612019	0		+	3	60	90	0	0	6.396749	23	60	735	57	ENST00000222270.7	0.115385	0.612407
PRODH2	58510	__UNKNOWN__	__UNKNOWN__	19	36293715	36293715	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36293715T>C	ENST00000301175.3	-	9	1358					NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	NA		NA			proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			tcccaaagtgttgggattata	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799	58510			17325	protein-coding gene	gene with protein product		NA			NA		Standard	NM_021232	NM_021232	NA	Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.1340+154A>G	chr19.hg19:g.36293715T>C		NA		hg19	CCDS12478.1	0.02	-0.289337	GTGxTGG	COVERED																																																																																			NOVEL	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452552.2	4	2.405122	KEEP	0	0	0	8	208	TT	0.99257	0.755234	0		-	3	60	92	0	0	6.312334	29	60	803	47	ENST00000301175.3	0.09375	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	36308136	36308136	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36308136T>G			NA	NA				PRODH2 (3935 upstream) : NPHS1 (8729 downstream)						NA		NA									NA						ctcccaaagttctgggattac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.36308136T>G		NA		hg19		0.02	-0.210461	AGTxCTG	COVERED																																																																																			NOVEL					0			7	3.005137	KEEP	2	0	0	10	254	TT	0.992708	0.518353	0			4	60	122	0	0	9.495674	19	60	534	50		0.173913	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	36417555	36417555	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36417555A>G			NA	NA				TYROBP (18358 upstream) : LRFN3 (8704 downstream)						NA		NA									NA						tgatcctcccacctcagcctc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.36417555A>G		NA		hg19		0.02	-0.149094	CCCxCCT	COVERED																																																																																			NOVEL					0			5	3.307903	KEEP	0	0	0	11	295	AA	0.993072	0.289978	0			3	60	88	0	0	6.879793	13	60	390	40		0.1875	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	36768165	36768165	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:36768165T>C			NA	NA				ZNF565 (31006 upstream) : CTD-3162L10.1 (33094 downstream)						NA		NA									NA						tctccctctctcccttctcgc	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.36768165T>C		NA		hg19		0.02	-0.253189	CTCxCCC	COVERED																																																																																			NOVEL					0			29	3.83679	KEEP	11	1	29	23	612	TT	0.999366	0.6681	0			3	25	99	0	0	7.53599	19	60	505	70		0.136364	0.668523
ZNF260	339324	__UNKNOWN__	__UNKNOWN__	19	37002446	37002446	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:37002446A>G	ENST00000523638.1	-	0	4816				ZNF260_ENST00000592282.1_3'UTR	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					ccagctactcaagaggctgag	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004	339324		Zinc fingers, C2H2-type	13499	protein-coding gene	gene with protein product		613749			NA		Standard	NM_001012756	NM_001166036	NA	Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.*2456T>C	chr19.hg19:g.37002446A>G		NA	Q0VF43	hg19	CCDS33003.1	0.02	-0.17536	CTCxAGA	COVERED																																																																																			NOVEL	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109564.2	2	3.609334	KEEP	0	0	0	12	333	AA	0.993634	0.420782	0		-	3	60	88	0	0	6.711385	15	60	431	39	ENST00000523638.1	0.166667	0.423478
ZNF568	374900	__UNKNOWN__	__UNKNOWN__	19	37470033	37470033	__UNKNOWN__	3'UTR	SNP	G	G	C	rs10420859	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:37470033G>C	ENST00000586353.1	+	0	716				ZNF568_ENST00000427117.1_3'UTR|ZNF568_ENST00000455427.2_Intron			Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ttacaggcatgtgtcaccaca	0.547		NA											G|||	899	0.179513	0.2126	0.1499	5008	,	,	NA	14955	0.1567	NA	0.1551	False	NA	,,,	NA	NA	NA	2504	0.2045	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453	374900		Zinc fingers, C2H2-type, -	25392	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198539	NM_198539	NA	Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000586353.1:c.*17G>C	chr19.hg19:g.37470033G>C		NA	B4DS92|E7ER33|Q6N060|Q8NA64	hg19		0.02	-0.078951	CATxTGT	UNCOVERED																																																																																			NOVEL	ZNF568-009	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000457466.1	7	3.610034	KEEP	3	0	0	12	361	GG	0.99254	0.076759	0		+	3	60	103	0	0	9.432898	5	60	163	28	ENST00000586353.1	0.375	0.077336
ZNF420	147923	__UNKNOWN__	__UNKNOWN__	19	37585761	37585761	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:37585761G>A	ENST00000337995.3	+	4	351				ZNF420_ENST00000304239.7_Intron	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAggccaggcgcggtggctca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050	147923		Zinc fingers, C2H2-type, -	20649	protein-coding gene	gene with protein product		NA			NA		Standard	NM_144689	NM_144689	NA	Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.136+3738G>A	chr19.hg19:g.37585761G>A		NA	B2RDY6|Q96ML5	hg19	CCDS12498.1	0.02	-0.219237	GGCxCGG	COVERED																																																																																			NOVEL	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109587.3	7	2.40551	KEEP	1	0	0	8	219	GG	0.99257	0.54878	0		+	3	60	91	0	0	6.727917	19	60	610	48	ENST00000337995.3	0.136364	0.552887
ZNF585B	92285	__UNKNOWN__	__UNKNOWN__	19	37684021	37684021	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:37684021T>A	ENST00000532828.2	-	3	324				CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000586320.1_Intron|ZNF585B_ENST00000527838.1_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			tgggcgacagtgcaagactcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(93;882 1454 18863 28917 48427)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680	92285		Zinc fingers, C2H2-type, -	30948	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152279	NM_152279	NA	Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.73-2969A>T	chr19.hg19:g.37684021T>A		NA	Q8IZD3|Q96JW6	hg19	CCDS12500.1	0.02	-0.12278	CAGxGCA	COVERED																																																																																			NOVEL	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000388272.2	4	2.705686	KEEP	0	0	0	9	235	TT	0.99254	0.194847	0		-	3	41	93	0	0	7.932728	8	60	227	32	ENST00000532828.2	0.272727	0.196312
ZNF585B	92285	__UNKNOWN__	__UNKNOWN__	19	37704716	37704716	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:37704716A>G	ENST00000534363.1	-	1	536							Q52M93	Z585B_HUMAN	zinc finger protein 585B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			gggtttcatcatgttggccag	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(93;882 1454 18863 28917 48427)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680	92285		Zinc fingers, C2H2-type, -	30948	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152279	NM_152279	NA	Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000534363.1:c.60+3803T>C	chr19.hg19:g.37704716A>G		NA	Q8IZD3|Q96JW6	hg19		0.02	-0.175396	ATCxTGT	COVERED																																																																																			NOVEL	ZNF585B-005	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000388275.1	3	2.406203	KEEP	0	0	0	8	222	AA	0.99257	0.384528	0		-	3	40	97	0	0	7.779127	13	60	380	34	ENST00000534363.1	0.1875	0.387407
ZNF585B	92285	__UNKNOWN__	__UNKNOWN__	19	37704721	37704721	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:37704721G>A	ENST00000534363.1	-	1	536							Q52M93	Z585B_HUMAN	zinc finger protein 585B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			tcatcatgttggccaggatgg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(93;882 1454 18863 28917 48427)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680	92285		Zinc fingers, C2H2-type, -	30948	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152279	NM_152279	NA	Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000534363.1:c.60+3798C>T	chr19.hg19:g.37704721G>A		NA	Q8IZD3|Q96JW6	hg19		0.02	-0.201736	GTTxGCC	COVERED																																																																																			NOVEL	ZNF585B-005	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000388275.1	4	2.70812	KEEP	0	0	0	9	277	GG	0.99254	0.486885	0		-	3	40	88	0	0	6.63397	16	60	522	40	ENST00000534363.1	0.157895	0.490544
ZNF571	51276	__UNKNOWN__	__UNKNOWN__	19	38062379	38062379	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38062379G>C	ENST00000590751.1	-	4	320				ZNF571-AS1_ENST00000586139.1_RNA|ZNF571-AS1_ENST00000585578.1_RNA|ZNF571_ENST00000593133.1_Intron|ZNF571-AS1_ENST00000591430.1_RNA|ZNF571_ENST00000328550.2_Intron|ZNF540_ENST00000592533.1_Intron|ZNF571-AS1_ENST00000589802.1_RNA|ZNF571-AS1_ENST00000586013.1_RNA|ZNF571-AS1_ENST00000590838.1_RNA|ZNF571-AS1_ENST00000589750.1_RNA|ZNF571_ENST00000358744.3_Intron|ZNF571-AS1_ENST00000591177.1_RNA|ZNF571_ENST00000451802.2_Intron|ZNF571-AS1_ENST00000592392.1_RNA|ZNF571-AS1_ENST00000587121.1_RNA			Q7Z3V5	ZN571_HUMAN	zinc finger protein 571	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	25			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			gcctgggtgagagagcgagac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF161544	CCDS12505.1	19q13.12	2013-09-20			ENSG00000180479	ENSG00000180479	51276		Zinc fingers, C2H2-type, -	25000	protein-coding gene	gene with protein product		NA			NA	11042152	Standard	NM_016536	XM_005258977	NA	Approved	HSPC059	uc002ogt.3	Q7Z3V5	OTTHUMG00000182016	ENST00000590751.1:c.136+12492C>G	chr19.hg19:g.38062379G>C		NA	Q2HIY0|Q3ZCU3|Q9NZX7	hg19		0.02	-0.07018	TGAxAGA	UNCOVERED																																																																																			NOVEL	ZNF571-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000458666.1	5	2.407163	KEEP	0	0	0	8	248	GG	0.99257	0.053735	0		-	3	60	106	0	0	9.955345	4	60	129	22	ENST00000590751.1	0.428571	0.054137
ZFP30	22835	__UNKNOWN__	__UNKNOWN__	19	38135846	38135846	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38135846A>G	ENST00000351218.2	-	4	567				ZFP30_ENST00000514101.2_Intron|ZFP30_ENST00000392144.1_Intron|ZFP30_ENST00000589018.1_Intron	NM_014898.2	NP_055713.1	Q9Y2G7	ZFP30_HUMAN	ZFP30 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	21			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ggtggctcacacctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023178	CCDS33005.1	19q13.13	2013-01-08	2012-11-27		ENSG00000120784	ENSG00000120784	22835		Zinc fingers, C2H2-type, -	29555	protein-coding gene	gene with protein product		NA	zinc finger protein 30 homolog (mouse)		NA	10231032	Standard	NM_014898	NM_014898	NA	Approved	ZNF745, KIAA0961	uc002ogx.1	Q9Y2G7	OTTHUMG00000048177	ENST00000351218.2:c.10-209T>C	chr19.hg19:g.38135846A>G		NA	Q58EY8	hg19	CCDS33005.1	0.02	-0.140314	CACxCCT	COVERED																																																																																			NOVEL	ZFP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000109601.2	3	3.607991	KEEP	0	0	0	12	319	AA	0.993634	0.259304	0		-	3	60	100	0	0	8.172433	12	60	346	46	ENST00000351218.2	0.2	0.260965
ZNF781	163115	__UNKNOWN__	__UNKNOWN__	19	38178672	38178672	__UNKNOWN__	Intron	SNP	A	A	G	rs559065776	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38178672A>G	ENST00000590008.1	-	3	247				ZNF781_ENST00000358582.4_Intron|ZNF781_ENST00000593040.1_Intron|ZFP30_ENST00000586732.1_Intron			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						acaggcgtgaaccaccgcgcc	0.527		NA											A|||	6	0.00119808	0.0045	0.0	5008	,	,	NA	14734	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381	163115		Zinc fingers, C2H2-type	26745	protein-coding gene	gene with protein product		NA			NA		Standard	NM_152605	NM_152605	NA	Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.606-1249T>C	chr19.hg19:g.38178672A>G		NA	Q2VPJ8	hg19	CCDS12507.1	0.02	-0.105159	TGAxCCA	UNCOVERED																																																																																			NOVEL	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459495.2	4	2.405736	KEEP	8	0	0	8	220	AA	0	0	0		-	3	60	97	0	0	8.334226	8	60	222	38	ENST00000590008.1	0.272727	0.139832
SIPA1L3	23094	__UNKNOWN__	__UNKNOWN__	19	38428425	38428425	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38428425A>G	ENST00000222345.6	+	1	131				SIPA1L3_ENST00000476317.2_Intron	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ggtggctcacacctgtaatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738	23094			23801	protein-coding gene	gene with protein product		NA			NA		Standard	XM_032278	XM_005258671	NA	Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.-379+30427A>G	chr19.hg19:g.38428425A>G		NA	Q2TV87	hg19	CCDS33007.1	0.02	-0.192913	CACxCCT	COVERED																																																																																			NOVEL	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000156294.2	14	3.581294	KEEP	4	0	0	12	295	AA	0.993072	0.487146	0		+	3	60	102	0	1	8.701534	9	60	256	49	ENST00000222345.6	0.25	0.490544
SIPA1L3	23094	__UNKNOWN__	__UNKNOWN__	19	38428452	38428452	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38428452T>C	ENST00000222345.6	+	1	131				SIPA1L3_ENST00000476317.2_Intron	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			tttgggaggctgaggtgggca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738	23094			23801	protein-coding gene	gene with protein product		NA			NA		Standard	XM_032278	XM_005258671	NA	Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.-379+30454T>C	chr19.hg19:g.38428452T>C		NA	Q2TV87	hg19	CCDS33007.1	0.02	-0.149105	GGCxGAG	COVERED																																																																																			NOVEL	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000156294.2	9	3.308784	KEEP	2	0	0	11	310	TT	0.993072	0.32057	0		+	3	49	84	0	0	6.572554	12	60	382	43	ENST00000222345.6	0.2	0.322807
SIPA1L3	23094	__UNKNOWN__	__UNKNOWN__	19	38612146	38612146	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38612146C>T	ENST00000222345.6	+	9	3377					NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			tttgggaggccgaggtgggca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738	23094			23801	protein-coding gene	gene with protein product		NA			NA		Standard	XM_032278	XM_005258671	NA	Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2868+1624C>T	chr19.hg19:g.38612146C>T		NA	Q2TV87	hg19	CCDS33007.1	0.02	-0.210531	GGCxGAG	COVERED																																																																																			NOVEL	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000156294.2	16	3.309079	KEEP	9	0	0	11	326	CC	0.99254	0.518266	0		+	3	60	95	0	0	7.260816	17	60	567	58	ENST00000222345.6	0.15	0.522161
SIPA1L3	23094	__UNKNOWN__	__UNKNOWN__	19	38624885	38624885	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38624885G>A	ENST00000222345.6	+	10	3652					NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			cgacctcccagagtgctagga	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738	23094			23801	protein-coding gene	gene with protein product		NA			NA		Standard	XM_032278	XM_005258671	NA	Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3143+3473G>A	chr19.hg19:g.38624885G>A		NA	Q2TV87	hg19	CCDS33007.1	0.02	-0.122792	CCAxAGT	COVERED																																																																																			NOVEL	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000156294.2	9	3.008789	KEEP	0	0	0	10	301	GG	0.992708	0.19488	0		+	3	60	87	0	0	6.973048	11	60	352	31	ENST00000222345.6	0.214286	0.196312
SIPA1L3	23094	__UNKNOWN__	__UNKNOWN__	19	38642544	38642544	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38642544G>A	ENST00000222345.6	+	13	4042					NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ggaggttgcagtgagctgaga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738	23094			23801	protein-coding gene	gene with protein product		NA			NA		Standard	XM_032278	XM_005258671	NA	Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3534-936G>A	chr19.hg19:g.38642544G>A		NA	Q2TV87	hg19	CCDS33007.1	0.02	-0.105256	GCAxTGA	UNCOVERED																																																																																			NOVEL	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000156294.2	8	3.309539	KEEP	0	0	0	11	330	GG	0.993072	0.138863	0		+	3	60	82	0	0	7.331947	5	60	164	27	ENST00000222345.6	0.375	0.139832
SIPA1L3	23094	__UNKNOWN__	__UNKNOWN__	19	38652096	38652096	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38652096A>G	ENST00000222345.6	+	14	4170					NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			cgggtgcggtagctcacacct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738	23094			23801	protein-coding gene	gene with protein product		NA			NA		Standard	XM_032278	XM_005258671	NA	Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3662-797A>G	chr19.hg19:g.38652096A>G		NA	Q2TV87	hg19	CCDS33007.1	0.02	-0.157866	GGTxGCT	UNCOVERED																																																																																			NOVEL	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000156294.2	10	2.706409	KEEP	2	0	0	9	241	AA	0	0	0		+	3	60	104	0	0	8.391761	14	60	411	37	ENST00000222345.6	0.176471	0.322807
YIF1B	90522	__UNKNOWN__	__UNKNOWN__	19	38799635	38799635	__UNKNOWN__	Silent	SNP	C	C	T	rs369423923		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:38799635C>T	ENST00000339413.6	-	4	510	c.465G>A	c.(463-465)ccG>ccA	p.P155P	YIF1B_ENST00000592246.1_Silent_p.P89P|YIF1B_ENST00000591755.1_Silent_p.P152P|YIF1B_ENST00000587361.1_5'UTR|YIF1B_ENST00000592694.1_Silent_p.P124P|YIF1B_ENST00000337679.8_Silent_p.P152P|YIF1B_ENST00000591784.1_Silent_p.P124P|YIF1B_ENST00000329420.8_Silent_p.P140P|YIF1B_ENST00000392124.3_Silent_p.P124P	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	155		NA				integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGTAGAGGTCCGGGGCATTGA	0.657		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C	,,,,,,	1,4393		0,1,2196	60	68	65		420,465,456,414,372,456,372	-7.9	0.9	19		65	0,8552		0,0,4276	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YIF1B	NM_001039671.2,NM_001039672.2,NM_001039673.2,NM_001145461.1,NM_001145462.1,NM_001145463.1,NM_033557.3	,,,,,,	0,1,6472	TT,TC,CC	NA	0.0,0.0228,0.0077	,,,,,,	140/300,155/315,152/312,138/298,124/284,152/292,124/284	38799635	1,12945	2197	4276	6473	SO:0001819	synonymous_variant			AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05					90522			30511	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_033557	NM_001039672	NA	Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.465G>A	chr19.hg19:g.38799635C>T		NA	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	hg19	CCDS33010.1	0.02	1.012837	GTCxGGG	COVERED																																																																																			NOVEL	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460511.1	3	2.406835	KEEP	0	0	0	8	238	CC	0.99257	0.992376	0		-	5	60	141	0	0	8.191444	82	60	2709	146	ENST00000339413.6	0.057471	0.999804
CAPN12	147968	__UNKNOWN__	__UNKNOWN__	19	39233235	39233235	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:39233235C>G	ENST00000328867.4	-	3	616				CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	NA		NA			proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			gctcatgcctctaatcccagc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472	147968		EF-hand domain containing	13249	protein-coding gene	gene with protein product		608839			NA		Standard		NM_144691	NA	Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.308-67G>C	chr19.hg19:g.39233235C>G		NA		hg19	CCDS12519.1	0.02	-0.210537	CCTxTAA	COVERED																																																																																			NOVEL	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462151.1	3	2.407019	KEEP	0	0	0	8	243	CC	0.99257	0.518282	0		-	3	60	105	0	0	8.005062	21	60	711	42	ENST00000328867.4	0.125	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	39895213	39895213	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:39895213G>T			NA	NA				MED29 (3936 upstream) : ZFP36 (2239 downstream)						NA		NA									NA						ggagaatcacgtgaacccggg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.39895213G>T		NA		hg19		0.02	-0.087674	CACxTGA	UNCOVERED																																																																																			NOVEL					0			1	2.405076	KEEP	0	0	0	8	209	GG	0.99257	0.09898	0			3	60	81	0	0	7.043582	6	60	191	23		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	40340737	40340737	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:40340737T>A			NA	NA				FBL (3683 upstream) : FCGBP (13225 downstream)						NA		NA									NA						acggggtttctccatgttggt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.40340737T>A		NA		hg19		0.02	-0.13157	TTCxCCA	COVERED																																																																																			NOVEL					0			9	3.608707	KEEP	7	0	0	12	326	TT	0.99257	0.22747	0			3	40	85	0	0	6.881982	10	60	319	37		0.230769	0.229173
ZNF780A	284323	__UNKNOWN__	__UNKNOWN__	19	40591529	40591529	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:40591529T>C	ENST00000594395.1	-	2	70				ZNF780A_ENST00000450241.2_Intron|ZNF780A_ENST00000455521.1_Intron|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000595687.2_Intron|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000340963.5_Intron			O75290	Z780A_HUMAN	zinc finger protein 780A	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					tggctcacacttgtaatccca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782	284323		Zinc fingers, C2H2-type, -	27603	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001010880	NM_001142577	NA	Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000594395.1:c.45-824A>G	chr19.hg19:g.40591529T>C		NA	E9PB48|Q6ZN87	hg19	CCDS46079.1	0.02	-0.105262	CACxTGT	UNCOVERED																																																																																			NOVEL	ZNF780A-008	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462498.2	4	3.007786	KEEP	0	0	0	10	278	TT	0.992708	0.138812	0		-	3	60	99	0	0	8.5324	8	60	249	34	ENST00000594395.1	0.272727	0.139832
PLD3	23646	__UNKNOWN__	__UNKNOWN__	19	40860060	40860060	__UNKNOWN__	Intron	SNP	A	A	G	rs57885763	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:40860060A>G	ENST00000409587.1	+	1	84				PLD3_ENST00000356508.5_Intron|PLD3_ENST00000594085.1_Intron|PLD3_ENST00000409735.4_Intron|PLD3_ENST00000409419.1_Intron			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	NA		NA			cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			ggctcactgcaacttccacct	0.488		NA											a|||	807	0.161142	0.2534	0.1182	5008	,	,	NA	14249	0.1319	NA	0.1551	False	NA	,,,	NA	NA	NA	2504	0.1033	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223	23646			17158	protein-coding gene	gene with protein product		615698	phospholipase D3		NA	9140189, 15794758	Standard	NM_012268	XM_005258704	NA	Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.-314+5385A>G	chr19.hg19:g.40860060A>G		NA	Q92853|Q9BW87	hg19	CCDS33027.1	0.02	-0.078936	TGCxACT	UNCOVERED																																																																																			NOVEL	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000327721.1	9	2.446371	KEEP	3	1	13	13	335	AA	0.993072	0.0768	0		+	5	60	159	0	0	15.987096	3	60	85	27	ENST00000409587.1	0.625	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	41158747	41158747	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41158747A>G			NA	NA				LTBP4 (23022 upstream) : NUMBL (13848 downstream)						NA		NA									NA						gctcacacctataatcccagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.41158747A>G		NA		hg19		0.02	-0.219255	CCTxTAA	COVERED																																																																																			NOVEL					0			13	5.413496	KEEP	6	0	0	18	497	AA	0.997832	0.551689	0			3	60	100	0	0	7.564932	20	60	585	68		0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	41160369	41160369	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41160369T>C			NA	NA				LTBP4 (24644 upstream) : NUMBL (12226 downstream)						NA		NA									NA						ccatcctggctaacatggtga	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.41160369T>C		NA		hg19		0.02	-0.087678	GGCxAAC	UNCOVERED																																																																																			NOVEL					0			1	2.405685	KEEP	3	0	0	8	213	TT	0	0	0			3	43	98	0	0	8.579436	7	60	193	27		0.3	0.099721
NUMBL	9253	__UNKNOWN__	__UNKNOWN__	19	41176920	41176920	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41176920T>C	ENST00000252891.4	-	9	1204				NUMBL_ENST00000540131.1_Intron|NUMBL_ENST00000598779.1_Intron	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	NA		NA			adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			ctcgctctgttgcccaggctg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245	9253			8061	protein-coding gene	gene with protein product		604018	numb (Drosophila) homolog-like		NA	9225980, 9303539	Standard	NM_004756	XM_006723471	NA	Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.1037-995A>G	chr19.hg19:g.41176920T>C		NA	Q7Z4J9	hg19	CCDS12561.1	0.02	-0.131541	TGTxGCC	COVERED																																																																																			NOVEL	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462749.2	6	2.405543	KEEP	0	0	0	8	213	TT	0.99257	0.22747	0		-	3	60	88	0	0	7.182368	10	60	287	30	ENST00000252891.4	0.230769	0.229173
RAB4B-EGLN2	100529264	__UNKNOWN__	__UNKNOWN__	19	41301580	41301580	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41301580G>A	ENST00000594136.1	+	8	762				RAB4B-EGLN2_ENST00000601949.1_Intron|RAB4B_ENST00000357052.2_Intron					RAB4B-EGLN2 readthrough (NMD candidate)	NA		NA									NA						gattacaggcgtgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK291385		19q13.2	2013-05-09	2013-05-09		ENSG00000171570	ENSG00000171570	100529264			44465	other	readthrough	RAB4B-EGLN2 readthrough long non-coding RNA	NA			NA	23026137	Standard	NR_037791	NR_037791	NA	Approved	RERT-lncRNA			OTTHUMG00000182702	ENST00000594136.1:c.640-4664G>A	chr19.hg19:g.41301580G>A		NA		hg19	CCDS33030.1	0.02	-0.131574	GGCxTGA	COVERED																																																																																			NOVEL	RAB4B-EGLN2-003	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000464583.2	1	3.00793	KEEP	0	0	0	10	291	GG	0.992708	0.227502	0		+	3	60	89	0	0	7.281955	10	60	322	38	ENST00000594136.1	0.230769	0.229173
CTC-490E21.12	0	__UNKNOWN__	__UNKNOWN__	19	41325167	41325167	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41325167A>T	ENST00000601627.1	+	1	119										NA		NA									NA						cagcctgggcaacacagcaag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000601627.1:c.119+17847A>T	chr19.hg19:g.41325167A>T		NA		hg19		0.02	-0.16664	GGCxACA	COVERED																																																																																			NOVEL	CTC-490E21.12-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal|readthrough_transcript	nonsense_mediated_decay	NA	protein_coding	OTTHUMT00000463921.1	10	2.707191	KEEP	1	0	0	9	255	AA	0.99254	0.351306	0		+	4	45	122	0	0	9.862879	15	60	443	38	ENST00000601627.1	0.210526	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	41545179	41545179	__UNKNOWN__	IGR	SNP	T	T	C	rs11673238	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41545179T>C			NA	NA				CYP2B6 (20876 upstream) : CYP2A13 (49197 downstream)						NA		NA									NA						gctgagatcatgccaccgcac	0.448		NA											C|||	1234	0.246406	0.3298	0.1513	5008	,	,	NA	10505	0.3036	NA	0.1849	False	NA	,,,	NA	NA	NA	2504	0.2055	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.41545179T>C		NA		hg19		0.02	-0.087713	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			11	2.404558	KEEP	6	0	0	8	206	TT	0	0	0			5	60	169	0	0	16.60077	4	60	116	26		0.555556	0.099721
AXL	558	__UNKNOWN__	__UNKNOWN__	19	41731175	41731175	__UNKNOWN__	Intron	SNP	A	A	G	rs4803447	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41731175A>G	ENST00000301178.4	+	4	776				AXL_ENST00000359092.3_Intron	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	NA		NA			apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						ctcccaaagtactgggattac	0.522		NA											A|||	266	0.053115	0.0121	0.0706	5008	,	,	NA	20593	0.0198	NA	0.1173	False	NA	,,,	NA	NA	NA	2504	0.0644	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	558	2.7.10.1	Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	905	protein-coding gene	gene with protein product		109135			NA	1656220	Standard		NM_021913	NA	Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.586+3214A>G	chr19.hg19:g.41731175A>G		NA	Q8N5L2|Q9UD27	hg19	CCDS12575.1	0.02	-0.16661	AGTxCTG	COVERED																																																																																			NOVEL	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463323.2	5	3.007031	KEEP	1	0	0	10	265	AA	0.992708	0.351366	0		+	3	60	84	0	0	6.393546	14	60	398	46	ENST00000301178.4	0.176471	0.353947
TGFB1	7040	__UNKNOWN__	__UNKNOWN__	19	41847101	41847101	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41847101T>G	ENST00000221930.5	-	5	1727					NM_000660.4	NP_000651.3	P01137	TGFB1_HUMAN	transforming growth factor, beta 1	NA		NA			active induction of host immune response by virus (GO:0046732)|adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460)|aging (GO:0007568)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|branch elongation involved in mammary gland duct branching (GO:0060751)|cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|cellular calcium ion homeostasis (GO:0006874)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation (GO:0002062)|common-partner SMAD protein phosphorylation (GO:0007182)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|defense response to fungus, incompatible interaction (GO:0009817)|digestive tract development (GO:0048565)|embryo development (GO:0009790)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|evasion or tolerance of host defenses by virus (GO:0019049)|extracellular matrix assembly (GO:0085029)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|germ cell migration (GO:0008354)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymph node development (GO:0048535)|macrophage derived foam cell differentiation (GO:0010742)|mammary gland branching involved in thelarche (GO:0060744)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|modulation by virus of host morphology or physiology (GO:0019048)|mononuclear cell proliferation (GO:0032943)|myelination (GO:0042552)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA replication (GO:0008156)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of ossification (GO:0030279)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|ossification involved in bone remodeling (GO:0043932)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|phosphate-containing compound metabolic process (GO:0006796)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NAD+ ADP-ribosyltransferase activity (GO:1901666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of odontogenesis (GO:0042482)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein export from nucleus (GO:0006611)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|receptor catabolic process (GO:0032801)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of binding (GO:0051098)|regulation of blood vessel remodeling (GO:0060312)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of cartilage development (GO:0061035)|regulation of cell migration (GO:0030334)|regulation of DNA binding (GO:0051101)|regulation of miRNA metabolic process (GO:2000628)|regulation of protein import into nucleus (GO:0042306)|regulation of sodium ion transport (GO:0002028)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulatory T cell differentiation (GO:0045066)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|response to radiation (GO:0009314)|response to vitamin D (GO:0033280)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|T cell homeostasis (GO:0043029)|tolerance induction to self antigen (GO:0002513)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|viral life cycle (GO:0019058)	axon (GO:0030424)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	antigen binding (GO:0003823)|cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)	8					Hyaluronidase(DB00070)	gccgggcgcgttggctcacgc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X02812	CCDS33031.1	19q13.1	2014-01-30	2007-02-16			ENSG00000105329	7040		Endogenous ligands	11766	protein-coding gene	gene with protein product	Camurati-Engelmann disease, prepro-transforming growth factor beta-1	190180		TGFB, DPD1	NA	10631145, 10843814	Standard		NM_000660	NA	Approved	CED, TGFbeta	uc002oqh.2	P01137		ENST00000221930.5:c.860+686A>C	chr19.hg19:g.41847101T>G		NA	A8K792|Q9UCG4	hg19	CCDS33031.1	0.02	-0.192859	GCGxTGG	COVERED																																																																																			NOVEL	TGFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463500.2	7	3.306566	KEEP	1	0	0	11	281	TT	0.992708	0.454419	0		-	5	60	158	0	0	13.432126	14	60	407	45	ENST00000221930.5	0.263158	0.457757
TGFB1	7040	__UNKNOWN__	__UNKNOWN__	19	41849096	41849096	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41849096A>G	ENST00000221930.5	-	4	1501					NM_000660.4	NP_000651.3	P01137	TGFB1_HUMAN	transforming growth factor, beta 1	NA		NA			active induction of host immune response by virus (GO:0046732)|adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains (GO:0002460)|aging (GO:0007568)|ATP biosynthetic process (GO:0006754)|blood coagulation (GO:0007596)|branch elongation involved in mammary gland duct branching (GO:0060751)|cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cell-cell junction organization (GO:0045216)|cellular calcium ion homeostasis (GO:0006874)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to organic cyclic compound (GO:0071407)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chondrocyte differentiation (GO:0002062)|common-partner SMAD protein phosphorylation (GO:0007182)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|defense response to fungus, incompatible interaction (GO:0009817)|digestive tract development (GO:0048565)|embryo development (GO:0009790)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial to mesenchymal transition (GO:0001837)|evasion or tolerance of host defenses by virus (GO:0019049)|extracellular matrix assembly (GO:0085029)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|face morphogenesis (GO:0060325)|female pregnancy (GO:0007565)|frontal suture morphogenesis (GO:0060364)|germ cell migration (GO:0008354)|hematopoietic progenitor cell differentiation (GO:0002244)|hyaluronan catabolic process (GO:0030214)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|lens fiber cell differentiation (GO:0070306)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymph node development (GO:0048535)|macrophage derived foam cell differentiation (GO:0010742)|mammary gland branching involved in thelarche (GO:0060744)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|modulation by virus of host morphology or physiology (GO:0019048)|mononuclear cell proliferation (GO:0032943)|myelination (GO:0042552)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA replication (GO:0008156)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of extracellular matrix disassembly (GO:0010716)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of ossification (GO:0030279)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|ossification involved in bone remodeling (GO:0043932)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|phosphate-containing compound metabolic process (GO:0006796)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of extracellular matrix assembly (GO:1901203)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NAD+ ADP-ribosyltransferase activity (GO:1901666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of odontogenesis (GO:0042482)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein secretion (GO:0050714)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein export from nucleus (GO:0006611)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|receptor catabolic process (GO:0032801)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of binding (GO:0051098)|regulation of blood vessel remodeling (GO:0060312)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of cartilage development (GO:0061035)|regulation of cell migration (GO:0030334)|regulation of DNA binding (GO:0051101)|regulation of miRNA metabolic process (GO:2000628)|regulation of protein import into nucleus (GO:0042306)|regulation of sodium ion transport (GO:0002028)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulatory T cell differentiation (GO:0045066)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to laminar fluid shear stress (GO:0034616)|response to progesterone (GO:0032570)|response to radiation (GO:0009314)|response to vitamin D (GO:0033280)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|T cell homeostasis (GO:0043029)|tolerance induction to self antigen (GO:0002513)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|viral life cycle (GO:0019058)	axon (GO:0030424)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	antigen binding (GO:0003823)|cytokine activity (GO:0005125)|enzyme binding (GO:0019899)|glycoprotein binding (GO:0001948)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)	8					Hyaluronidase(DB00070)	ctggagtgcaatggcacgatc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X02812	CCDS33031.1	19q13.1	2014-01-30	2007-02-16			ENSG00000105329	7040		Endogenous ligands	11766	protein-coding gene	gene with protein product	Camurati-Engelmann disease, prepro-transforming growth factor beta-1	190180		TGFB, DPD1	NA	10631145, 10843814	Standard		NM_000660	NA	Approved	CED, TGFbeta	uc002oqh.2	P01137		ENST00000221930.5:c.635-944T>C	chr19.hg19:g.41849096A>G		NA	A8K792|Q9UCG4	hg19	CCDS33031.1	0.02	-0.236783	GCAxTGG	COVERED																																																																																			NOVEL	TGFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463500.2	18	3.527667	KEEP	8	1	26	21	550	AA	0.997832	0.611079	0		-	3	60	97	0	0	7.265225	20	60	567	70	ENST00000221930.5	0.130435	0.612407
TMEM91	641649	__UNKNOWN__	__UNKNOWN__	19	41877275	41877275	__UNKNOWN__	Intron	SNP	T	T	C	rs12459203		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:41877275T>C	ENST00000539627.1	+	2	292				TMEM91_ENST00000604123.1_Intron|TMEM91_ENST00000413014.2_Intron|CTC-435M10.3_ENST00000604424.1_Intron			Q6ZNR0	TMM91_HUMAN	transmembrane protein 91	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	5						tccttccttctttccttcctt	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK130820, BC063705	CCDS42571.1, CCDS42572.1, CCDS46082.1, CCDS46083.1, CCDS46084.1	19q13.2	2009-10-16					641649			32393	protein-coding gene	gene with protein product	interferon induced transmembrane protein domain containing 6	NA			NA	12477932	Standard		NM_001098824	NA	Approved	FLJ27310, IFITMD6		Q6ZNR0		ENST00000539627.1:c.-29-6911T>C	chr19.hg19:g.41877275T>C		NA	C9J9D1|C9JZ62|C9K046|Q6P434	hg19		0.02	-0.122783	TTCxTTC	COVERED																																																																																			NOVEL	TMEM91-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000398300.1	7	2.999343	KEEP	3	0	0	10	240	TT	0.99257	0.194853	0		+	3	60	91	0	0	7.732579	8	60	233	33	ENST00000539627.1	0.272727	0.196312
CEACAM6	4680	__UNKNOWN__	__UNKNOWN__	19	42260742	42260742	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs141329594	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:42260742C>T	ENST00000199764.6	+	2	517	c.299C>T	c.(298-300)aCa>aTa	p.T100I	CEA_ENST00000598976.1_Intron	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	100	Ig-like V-type.	NA			cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		GGTCGAGAGACAATATACCCC	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0								C	ILE/THR	4,4402	4.2+/-10.8	0,4,2199	314	297	303		299	-0.5	0.7	19	dbSNP_134	303	5,8595	2.2+/-6.3	0,5,4295	no	missense	CEACAM6	NM_002483.4	89	0,9,6494	TT,TC,CC	NA	0.0581,0.0908,0.0692	benign	100/345	42260742	9,12997	2203	4300	6503	SO:0001583	missense			M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548	4680		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	1818	protein-coding gene	gene with protein product		163980		NCA	NA		Standard		NM_002483	NA	Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.299C>T	chr19.hg19:g.42260742C>T	ENSP00000199764:p.Thr100Ile	NA	Q13774|Q14920|Q53XP7	hg19	CCDS12585.1	0.02	1.377373	AGAxAAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	7.727	0.698352	0.15106	9.08E-4	5.81E-4	ENSG00000086548	ENST00000199764	T	0.68479	-0.33	2.55	-0.464	0.12160	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.48429	0.1499	L	0.31752	0.955	0.09310	N	1	B	0.14805	0.011	B	0.16722	0.016	T	0.38001	-0.9681	9	0.46703	T	0.11	.	3.8844	0.09091	0.2271:0.612:0.0:0.1609	.	100	P40199	CEAM6_HUMAN	I	100	ENSP00000199764:T100I	ENSP00000199764:T100I	T	+	2	0	CEACAM6	46952582	0.002000	0.14202	0.736000	0.30914	0.051000	0.14879	-0.871000	0.04223	0.158000	0.19367	0.305000	0.20034	ACA	NOVEL	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321147.1	1	2.708303	KEEP	1	0	0	9	285	CC	0.99254	0.989288	0		+	5	49	158	0	0	10.434867	63	60	2108	124	ENST00000199764.6	0.073529	0.996724
GRIK5	2901	__UNKNOWN__	__UNKNOWN__	19	42565550	42565550	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:42565550T>C	ENST00000262895.3	-	4	508				GRIK5_ENST00000593562.1_Intron|GRIK5_ENST00000301218.4_Intron	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	NA		NA			cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				aggctggtcttgaactcctgg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737	2901		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4583	protein-coding gene	gene with protein product		600283		GRIK2	NA	7527545	Standard		NM_002088	NA	Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.508+1089A>G	chr19.hg19:g.42565550T>C		NA	Q8WWG8	hg19	CCDS12595.1	0.02	-0.306967	TCTxGAA	COVERED																																																																																			NOVEL	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463453.1	18	3.307512	KEEP	3	0	0	11	294	TT	0.992708	0.79441	0		-	3	60	102	0	0	7.226485	31	60	915	67	ENST00000262895.3	0.088235	0.800245
PAFAH1B3	5050	__UNKNOWN__	__UNKNOWN__	19	42805247	42805247	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:42805247G>A	ENST00000262890.3	-	3	430				PAFAH1B3_ENST00000538771.1_Intron	NM_002573.3	NP_002564.1	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa)	NA		NA			brain development (GO:0007420)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)			breast(1)|large_intestine(2)|ovary(1)	4		Prostate(69;0.0704)				gattacaggcgtaagccacca	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D63391	CCDS12602.1	19q13.1	2011-10-24	2010-02-10			ENSG00000079462	5050			8576	protein-coding gene	gene with protein product	PAF-AH1b alpha 1 subunit	603074	platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit (29kD), platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa, platelet-activating factor acetylhydrolase, isoform Ib, subunit 3 (29kDa)		NA	7669037	Standard	NM_002573	NM_002573	NA	Approved		uc010xwj.1	Q15102		ENST00000262890.3:c.169-808C>T	chr19.hg19:g.42805247G>A		NA	Q53X88	hg19	CCDS12602.1	0.02	-0.122791	GGCxTAA	COVERED																																																																																			NOVEL	PAFAH1B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463726.1	4	2.706789	KEEP	1	0	0	9	248	GG	0.99257	0.194853	0		-	3	60	81	0	0	6.482115	10	60	322	31	ENST00000262890.3	0.230769	0.196312
MEGF8	1954	__UNKNOWN__	__UNKNOWN__	19	42843089	42843089	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:42843089C>T	ENST00000334370.4	+	8	2148				MEGF8_ENST00000251268.6_Intron	NM_001410.2	NP_001401.2	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	NA		NA			BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				caggttcaagcgattctcctg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429	1954			3233	protein-coding gene	gene with protein product	HBV pre s2 binding protein 1	604267	EGF-like-domain, multiple 4, chromosome 19 open reading frame 49	EGFL4, C19orf49	NA	9693030	Standard	NM_001410	NM_001410	NA	Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000334370.4:c.1513+1731C>T	chr19.hg19:g.42843089C>T		NA	A8KAY0|O75097	hg19	CCDS12604.2	0.02	-0.122797	AAGxGAT	COVERED																																																																																			NOVEL	MEGF8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317695.1	11	2.706088	KEEP	5	0	0	9	241	CC	0.99254	0.227464	0		+	3	33	87	1	0	7.082019	10	60	326	40	ENST00000334370.4	0.230769	0.229173
LIPE-AS1	100996307	__UNKNOWN__	__UNKNOWN__	19	42932119	42932119	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:42932119T>A	ENST00000594688.1	+	0	1450				LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594624.2_RNA	NR_073179.1				LIPE antisense RNA 1	NA		NA									NA						aagtgctgggtttacaggtgt	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK096849, BM974950		19q13.2	2013-05-21			ENSG00000213904	ENSG00000213904	100996307		Long non-coding RNAs	48589	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_073179	NR_073179	NA	Approved				OTTHUMG00000182815	ENST00000594688.1:	chr19.hg19:g.42932119T>A		NA		hg19		0.02	-0.131543	GGGxTTA	COVERED																																																																																			NOVEL	LIPE-AS1-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000464099.1	3	2.406263	KEEP	0	0	0	8	225	TT	0.99257	0.22747	0		+	3	60	93	0	0	7.682339	10	60	284	31	ENST00000594688.1	0.230769	0.229173
LIPE-AS1	100996307	__UNKNOWN__	__UNKNOWN__	19	43062304	43062304	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:43062304T>C	ENST00000594688.1	+	0	1450				LIPE-AS1_ENST00000594624.2_RNA	NR_073179.1				LIPE antisense RNA 1	NA		NA									NA						cttgctctgttgcccaggctg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AK096849, BM974950		19q13.2	2013-05-21			ENSG00000213904	ENSG00000213904	100996307		Long non-coding RNAs	48589	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_073179	NR_073179	NA	Approved				OTTHUMG00000182815	ENST00000594688.1:	chr19.hg19:g.43062304T>C		NA		hg19		0.02	-0.148844	TGTxGCC	UNCOVERED																																																																																			NOVEL	LIPE-AS1-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000464099.1	6	2.405994	KEEP	4	0	0	8	220	TT	0	0	0		+	3	60	101	0	0	8.18179	13	60	356	43	ENST00000594688.1	0.1875	0.322807
PSG8	440533	__UNKNOWN__	__UNKNOWN__	19	43302069	43302069	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:43302069A>G	ENST00000401467.2	-	2	136							Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	NA		NA				extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				cgaggcgggcagatcacgagg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467	440533		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	9525	protein-coding gene	gene with protein product		176397			NA	1672663, 1572651	Standard		NM_182707	NA	Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000401467.2:c.65-33636T>C	chr19.hg19:g.43302069A>G		NA	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	hg19		0.02	-0.219252	GGCxGAT	UNCOVERED																																																																																			NOVEL	PSG8-009	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000464525.1	6	2.706457	KEEP	4	0	0	9	244	AA	0	0	0		-	3	60	90	0	0	6.627918	19	60	561	56	ENST00000401467.2	0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	43898914	43898914	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:43898914A>G			NA	NA				CTC-490G23.4 (25792 upstream) : TEX101 (6733 downstream)						NA		NA									NA						gagccactgcacccggccTTA	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.43898914A>G		NA		hg19		0.02	-0.131465	TGCxCCC	UNCOVERED																																																																																			NOVEL					0			5	2.404873	KEEP	1	0	0	8	210	AA	0	0	0			3	60	96	0	0	7.983447	10	60	260	31		0.230769	0.229173
PLAUR	5329	__UNKNOWN__	__UNKNOWN__	19	44154226	44154226	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:44154226C>T	ENST00000340093.3	-	7	984				PLAUR_ENST00000601723.1_Intron|PLAUR_ENST00000221264.4_Intron|PLAUR_ENST00000339082.3_Intron	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	NA		NA			attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)			endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	tgcagtggcacgatctcggct	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422	5329		CD molecules	9053	protein-coding gene	gene with protein product	urokinase-type plasminogen activator (uPA) receptor, urokinase plasminogen activator surface receptor	173391			NA		Standard	NM_002659	NM_002659	NA	Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.755-931G>A	chr19.hg19:g.44154226C>T		NA	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	hg19	CCDS12628.1	0.02	-0.166654	GCAxGAT	UNCOVERED																																																																																			NOVEL	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463571.1	6	2.407141	KEEP	4	0	0	8	246	CC	0	0	0		-	3	60	84	0	0	6.39244	14	60	446	44	ENST00000340093.3	0.176471	0.353947
PLAUR	5329	__UNKNOWN__	__UNKNOWN__	19	44166424	44166424	__UNKNOWN__	Intron	SNP	T	T	C	rs4251840	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:44166424T>C	ENST00000340093.3	-	3	540				PLAUR_ENST00000601723.1_Intron|PLAUR_ENST00000221264.4_Intron|PLAUR_ENST00000339082.3_Intron	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	NA		NA			attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)			endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	ccgaggtgggtggatcacgag	0.517		NA											t|||	3261	0.651158	0.6513	0.6657	5008	,	,	NA	13509	0.6994	NA	0.7068	False	NA	,,,	NA	NA	NA	2504	0.5337	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422	5329		CD molecules	9053	protein-coding gene	gene with protein product	urokinase-type plasminogen activator (uPA) receptor, urokinase plasminogen activator surface receptor	173391			NA		Standard	NM_002659	NM_002659	NA	Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.310+3043A>G	chr19.hg19:g.44166424T>C		NA	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	hg19	CCDS12628.1	0.02	-0.105257	GGGxGGA	UNCOVERED																																																																																			NOVEL	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000463571.1	10	3.909653	KEEP	9	0	0	13	357	TT	0.99254	0.138789	0		-	6	60	202	0	0	19.771302	5	60	150	42	ENST00000340093.3	0.545455	0.139832
ZNF155	7711	__UNKNOWN__	__UNKNOWN__	19	44490870	44490870	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:44490870A>G	ENST00000407951.2	+	2	52				ZNF155_ENST00000270014.2_Intron|ZNF155_ENST00000590615.1_Intron	NM_001260488.1	NP_001247417	Q12901	ZN155_HUMAN	zinc finger protein 155	NA		NA			transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				caaagtgctgagattacaggt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(61;554 1277 20909 42067 42312)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920	7711		Zinc fingers, C2H2-type, -	12940	protein-coding gene	gene with protein product		604086	zinc finger protein 155 (pHZ-96)		NA	7557990	Standard	NM_003445	NM_001260486	NA	Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000407951.2:c.-141-1741A>G	chr19.hg19:g.44490870A>G		NA	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	hg19	CCDS58668.1	0.02	-0.254378	CTGxGAT	COVERED																																																																																			NOVEL	ZNF155-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000460073.1	2	3.308972	KEEP	3	0	0	11	313	AA	0.992708	0.663648	0		+	3	60	97	0	0	7.149804	22	60	686	71	ENST00000407951.2	0.12	0.668523
ZNF227	7770	__UNKNOWN__	__UNKNOWN__	19	44731671	44731671	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:44731671C>G	ENST00000589707.1	+	3	176				ZNF227_ENST00000391961.2_Intron|ZNF227_ENST00000586228.1_Intron|ZNF227_ENST00000589237.1_Intron|ZNF227_ENST00000313040.7_Intron|ZNF227_ENST00000589005.1_Intron			Q86WZ6	ZN227_HUMAN	zinc finger protein 227	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				aaagtgctggcattacaggtg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08					7770		Zinc fingers, C2H2-type, -	13020	protein-coding gene	gene with protein product		NA			NA		Standard	NM_182490	XM_005259232	NA	Approved		uc002oyu.3	Q86WZ6		ENST00000589707.1:c.-93-928C>G	chr19.hg19:g.44731671C>G		NA	B3KRU7|B7Z5P9	hg19		0.02	-0.131582	TGGxATT	COVERED																																																																																			NOVEL	ZNF227-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000460721.1	2	3.008855	KEEP	0	0	0	10	306	CC	0.992708	0.227502	0		+	3	60	93	0	0	7.800922	9	60	310	37	ENST00000589707.1	0.25	0.229173
CTC-512J12.6	0	__UNKNOWN__	__UNKNOWN__	19	44864131	44864131	__UNKNOWN__	Intron	SNP	G	G	A	rs4239531	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:44864131G>A	ENST00000588212.1	-	3	99				ZNF112_ENST00000536500.1_Intron						NA		NA									NA						aggtctggccgggcacggtgg	0.448		NA											G|||	1550	0.309505	0.3964	0.3847	5008	,	,	NA	15340	0.251	NA	0.2823	False	NA	,,,	NA	NA	NA	2504	0.227	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000588212.1:c.16-19440C>T	chr19.hg19:g.44864131G>A		NA		hg19		0.02	-0.15789	GCCxGGC	COVERED																																																																																			NOVEL	CTC-512J12.6-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000460824.1	5	2.406725	KEEP	0	0	0	8	234	GG	0.99257	0.320408	0		-	5	60	159	0	0	14.139223	10	60	324	41	ENST00000588212.1	0.333333	0.322807
CTC-512J12.4	0	__UNKNOWN__	__UNKNOWN__	19	44915666	44915666	__UNKNOWN__	RNA	SNP	C	C	G	rs74498517		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:44915666C>G	ENST00000588655.1	-	0	488										NA		NA									NA						tgtcttcacccccagccctca	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000588655.1:	chr19.hg19:g.44915666C>G		NA		hg19		0.02	-0.043859	ACCxCCA	UNCOVERED																																																																																			NOVEL	CTC-512J12.4-001	KNOWN	NMD_likely_if_extended|basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000460829.1	8	2.407164	KEEP	5	0	0	8	246	CC	0	0	0		-	2	45	64	0	0	6.524217	1	60	36	13	ENST00000588655.1	0.666667	0.024074
PVRL2	5819	__UNKNOWN__	__UNKNOWN__	19	45371892	45371892	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45371892T>C	ENST00000252483.5	+	2	478				PVRL2_ENST00000252485.4_Intron	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	NA		NA			acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		ATCTTGAggctgggcgtggtg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202	5819		CD molecules, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	9707	protein-coding gene	gene with protein product		600798		HVEB	NA	7622062, 10196354	Standard	NM_002856	NM_001042724	NA	Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.478+2975T>C	chr19.hg19:g.45371892T>C		NA	A8K5L5|O75455|Q6IBI6|Q96J29	hg19	CCDS42576.1	0.02	-0.210502	GGCxGGG	COVERED																																																																																			NOVEL	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453231.1	9	2.704985	KEEP	2	0	0	9	242	TT	0.99257	0.518282	0		+	5	60	171	0	0	14.602126	15	60	438	49	ENST00000252483.5	0.25	0.522161
CLPTM1	1209	__UNKNOWN__	__UNKNOWN__	19	45462585	45462585	__UNKNOWN__	Intron	SNP	A	A	G	rs9710578		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45462585A>G	ENST00000541297.2	+	2	495				CLPTM1_ENST00000546079.1_Intron|CLPTM1_ENST00000337392.5_Intron			O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		ccaaagtgctaggattatagg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853	1209			2087	protein-coding gene	gene with protein product		604783			NA	9828125	Standard	NM_001294	NM_001294	NA	Approved		uc002pai.3	O96005		ENST00000541297.2:c.31-2635A>G	chr19.hg19:g.45462585A>G		NA	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	hg19		0.02	-0.271865	GCTxGGA	COVERED																																																																																			NOVEL	CLPTM1-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000453266.1	9	3.007173	KEEP	0	0	0	10	269	AA	0.992708	0.712085	0		+	3	60	94	0	0	6.645249	26	60	759	54	ENST00000541297.2	0.103448	0.717315
CLPTM1	1209	__UNKNOWN__	__UNKNOWN__	19	45462592	45462592	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45462592T>C	ENST00000541297.2	+	2	495				CLPTM1_ENST00000546079.1_Intron|CLPTM1_ENST00000337392.5_Intron			O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		gctaggattataggcatgagc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853	1209			2087	protein-coding gene	gene with protein product		604783			NA	9828125	Standard	NM_001294	NM_001294	NA	Approved		uc002pai.3	O96005		ENST00000541297.2:c.31-2628T>C	chr19.hg19:g.45462592T>C		NA	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	hg19		0.02	-0.263094	TTAxAGG	COVERED																																																																																			NOVEL	CLPTM1-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000453266.1	9	3.308054	KEEP	0	0	0	11	297	TT	0.993072	0.688863	0		+	3	60	105	0	0	7.792197	25	60	714	55	ENST00000541297.2	0.107143	0.693668
RELB	5971	__UNKNOWN__	__UNKNOWN__	19	45515283	45515283	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45515283C>T	ENST00000221452.8	+	4	403	c.253C>T	c.(253-255)Cgc>Tgc	p.R85C	RELB_ENST00000505236.1_Missense_Mutation_p.R82C|RELB_ENST00000540120.1_Missense_Mutation_p.R85C	NM_006509.3	NP_006500.2	Q01201	RELB_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog B	85		NA			antigen processing and presentation (GO:0019882)|circadian regulation of gene expression (GO:0032922)|myeloid dendritic cell differentiation (GO:0043011)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of gene expression (GO:0010628)|T-helper 1 cell differentiation (GO:0045063)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	core promoter binding (GO:0001047)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(3)|skin(1)	12		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00986)		CCTGGTGTCTCGCGGGGCTGC	0.726		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													7	8	8			NA	NA	19		NA											NA				45515283		1772	3865	5637	SO:0001583	missense			M83221	CCDS46110.1	19q13.32	2013-07-09	2013-07-09		ENSG00000104856	ENSG00000104856	5971			9956	protein-coding gene	gene with protein product		604758	v-rel avian reticuloendotheliosis viral oncogene homolog B (nuclear factor of kappa light polypeptide gene enhancer in B-cells 3)		NA	1531086	Standard		NM_006509	NA	Approved	REL-B	uc021uvp.1	Q01201	OTTHUMG00000162116	ENST00000221452.8:c.253C>T	chr19.hg19:g.45515283C>T	ENSP00000221452:p.Arg85Cys	NA	Q6GTX7|Q9UEI7	hg19	CCDS46110.1	0.02	-0.368332	TCTxGCG	COVERED	.	.	.	.	.	.	.	.	.	.	C	16.70	3.196911	0.58126	.	.	ENSG00000104856	ENST00000221452;ENST00000540120;ENST00000505236	T;T;T	0.53640	0.61;0.61;0.61	4.42	4.42	0.53409	.	0.431297	0.17349	N	0.177467	T	0.47783	0.1464	N	0.14661	0.345	0.45216	D	0.998222	D	0.89917	1.0	P	0.61800	0.894	T	0.53151	-0.8479	10	0.87932	D	0	-10.5648	12.3788	0.55295	0.0:1.0:0.0:0.0	.	82	D6R992	.	C	85;85;82	ENSP00000221452:R85C;ENSP00000445542:R85C;ENSP00000423287:R82C	ENSP00000221452:R85C	R	+	1	0	RELB	50207123	0.239000	0.23836	0.434000	0.26772	0.145000	0.21501	2.186000	0.42593	2.289000	0.77006	0.462000	0.41574	CGC	NOVEL	RELB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367361.2	1	2.705752	KEEP	0	0	0	9	248	CC	0.99254	0.892605	0		+	11	60	314	0	0	26.160979	31	60	935	62	ENST00000221452.8	0.261905	0.899314
CLASRP	11129	__UNKNOWN__	__UNKNOWN__	19	45572226	45572226	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45572226C>T	ENST00000221455.3	+	17	1866				CLASRP_ENST00000391953.4_Intron|CLASRP_ENST00000544944.2_Intron	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	NA		NA			mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						ccagcctgggcgacagagcga	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													8	9	9			NA	NA	19		NA											NA				45572226		690	1589	2279	SO:0001627	intron_variant			AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859	11129			17731	protein-coding gene	gene with protein product	Clk4 associating SR-related protein	NA	splicing factor, arginine/serine-rich 16	SFRS16	NA	12169693	Standard	NM_007056	NM_007056	NA	Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.1769-98C>T	chr19.hg19:g.45572226C>T		NA	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	hg19	CCDS12652.2	0.02	-0.368389	GGGxGAC	COVERED																																																																																			NOVEL	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316749.1	4	2.238517	KEEP	1	1	24	16	466	CC	0.999366	0.898744	0		+	4	60	101	0	1	6.899074	26	60	851	78	ENST00000221455.3	0.133333	0.899314
PPP1R37	284352	__UNKNOWN__	__UNKNOWN__	19	45628462	45628462	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45628462T>C	ENST00000221462.4	+	2	566				PPP1R37_ENST00000421905.1_Intron	NM_019121.1	NP_061994.1	O75864	PPR37_HUMAN	protein phosphatase 1, regulatory subunit 37	NA		NA			negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)				NA						gtggctcacgtctgtaatccc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC035704	CCDS56096.1	19q13.32	2012-04-17	2011-10-11	2011-10-11	ENSG00000104866	ENSG00000104866	284352		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits	27607	protein-coding gene	gene with protein product		NA	leucine rich repeat containing 68	LRRC68	NA	12477932	Standard	NM_173634	NM_019121	NA	Approved		uc021uvs.1	O75864	OTTHUMG00000168143	ENST00000221462.4:c.203-13310T>C	chr19.hg19:g.45628462T>C		NA	B5MDA4|Q8IWK3|Q8TF16	hg19	CCDS56096.1	0.02	-0.166649	ACGxCTG	COVERED																																																																																			NOVEL	PPP1R37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000398356.2	3	3.006258	KEEP	0	0	0	10	262	TT	0.992708	0.351366	0		+	4	60	136	0	0	11.481146	13	60	383	44	ENST00000221462.4	0.235294	0.353947
ERCC1	2067	__UNKNOWN__	__UNKNOWN__	19	45918881	45918881	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:45918881C>G	ENST00000591636.1	-	5	729				ERCC1_ENST00000013807.5_Intron|ERCC1_ENST00000589165.1_Intron|ERCC1_ENST00000340192.7_Intron|ERCC1_ENST00000423698.2_Intron|ERCC1_ENST00000300853.3_Intron			P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	NA		NA			cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		gcgacagagccagactccgtc	0.483		NA						Nucleotide excision repair (NER)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061	2067			3433	protein-coding gene	gene with protein product		126380	excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)		NA	6462228	Standard	NM_001983	NM_001983	NA	Approved	RAD10	uc002pbs.2	P07992		ENST00000591636.1:c.602+1197G>C	chr19.hg19:g.45918881C>G		NA	B2RC01|B3KRR0|Q7Z7F5|Q96S40	hg19		0.02	1.6137	AGCxAGA	COVERED																																																																																			NOVEL	ERCC1-013	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000459547.1	5	2.469826	KEEP	3	5	138	57	1665	AC	1	0.999487	0		-	6	60	178	1	1	12.066541	57	60	1917	165	ENST00000591636.1	0.095238	0.999487
OPA3	80207	__UNKNOWN__	__UNKNOWN__	19	46066607	46066607	__UNKNOWN__	Intron	SNP	G	G	A	rs1264231	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46066607G>A	ENST00000323060.3	-	1	220				OPA3_ENST00000544371.1_Intron|OPA3_ENST00000263275.4_Intron	NM_001017989.2	NP_001017989.2	Q9H6K4	OPA3_HUMAN	optic atrophy 3 (autosomal recessive, with chorea and spastic paraplegia)	NA		NA			growth (GO:0040007)|mitochondrion morphogenesis (GO:0070584)|neuromuscular process (GO:0050905)|regulation of lipid metabolic process (GO:0019216)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	mitochondrion (GO:0005739)				cervix(1)|large_intestine(1)|lung(2)	4		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)		tagtagagacggggtttcacc	0.557		NA											g|||	2662	0.53155	0.2481	0.6311	5008	,	,	NA	16687	0.7381	NA	0.5974	False	NA	,,,	NA	NA	NA	2504	0.5634	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025840	CCDS12668.1, CCDS33052.1	19q13.2-q13.3	2014-01-28				ENSG00000125741	80207			8142	protein-coding gene	gene with protein product		606580			NA	9097959, 11668429	Standard		NM_001017989	NA	Approved	FLJ22187, MGA3	uc002pcj.4	Q9H6K4		ENST00000323060.3:c.142+21273C>T	chr19.hg19:g.46066607G>A		NA	Q6P384|Q8N784	hg19	CCDS33052.1	0.02	-0.096489	GACxGGG	UNCOVERED																																																																																			NOVEL	OPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000459600.1	10	2.707056	KEEP	14	0	0	9	258	GG	0	0	0		-	6	60	179	0	0	17.469501	5	40	172	40	ENST00000323060.3	0.545455	0.120436
EML2	24139	__UNKNOWN__	__UNKNOWN__	19	46120551	46120551	__UNKNOWN__	Intron	SNP	C	C	T	rs554391479		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46120551C>T	ENST00000589876.1	-	13	1349				EML2_ENST00000245925.3_Intron|EML2_ENST00000587152.1_Intron|EML2_ENST00000536630.1_Intron			O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	NA		NA			negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		cggtggctcacgcctgtaatc	0.557		NA											C|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	14726	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746	24139		WD repeat domain containing	18035	protein-coding gene	gene with protein product	echinoderm MT-associated protein (EMAP)-like protein 70, microtubule-associated protein like echinoderm EMAP	NA			NA	11694528, 10521658	Standard	NM_012155	NM_012155	NA	Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000589876.1:c.1322+336G>A	chr19.hg19:g.46120551C>T		NA	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	hg19		0.02	-0.192972	TCAxGCC	COVERED																																																																																			NOVEL	EML2-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000459605.1	6	2.405895	KEEP	1	0	0	8	226	CC	0.99257	0.454356	0		-	3	60	89	0	0	6.661365	17	60	536	43	ENST00000589876.1	0.15	0.457757
MYPOP	339344	__UNKNOWN__	__UNKNOWN__	19	46397237	46397237	__UNKNOWN__	Intron	SNP	C	C	T	rs184439551	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46397237C>T	ENST00000322217.5	-	3	586					NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	NA		NA				nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						ttagtagagacggggtttcac	0.567		NA											C|||	163	0.0325479	0.0242	0.0389	5008	,	,	NA	11534	0.0813	NA	0.0139	False	NA	,,,	NA	NA	NA	2504	0.0082	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182	339344			20178	protein-coding gene	gene with protein product	p42 Myb-related transcription factor, partner of profilin	NA			NA	15615774	Standard	NM_001012643	NM_001012643	NA	Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.500-2656G>A	chr19.hg19:g.46397237C>T		NA		hg19	CCDS33055.1	0.02	-0.078936	AGAxGGG	UNCOVERED																																																																																			NOVEL	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000461684.1	3	2.706674	KEEP	9	0	0	9	255	CC	0	0	0		-	3	40	88	1	1	7.743322	6	44	191	31	ENST00000322217.5	0.333333	0.077336
HIF3A	64344	__UNKNOWN__	__UNKNOWN__	19	46843776	46843776	__UNKNOWN__	3'UTR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46843776T>G	ENST00000377670.4	+	0	2938				HIF3A_ENST00000339613.2_3'UTR	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	NA		NA			cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		ttttttttttttgacagagtc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440	64344		Basic helix-loop-helix proteins	15825	protein-coding gene	gene with protein product		609976			NA	11573933, 11734856	Standard		NM_152794	NA	Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.*897T>G	chr19.hg19:g.46843776T>G		NA	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	hg19	CCDS12681.2	0.02	-0.157863	TTTxTGA	COVERED																																																																																			NOVEL	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000280556.3	8	2.707405	KEEP	2	0	0	9	258	TT	0.99257	0.320408	0		+	3	60	89	0	0	6.810882	15	60	441	35	ENST00000377670.4	0.166667	0.322807
PPP5C	5536	__UNKNOWN__	__UNKNOWN__	19	46892717	46892717	__UNKNOWN__	Intron	SNP	C	C	G	rs8106592|rs201128440	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46892717C>G	ENST00000391919.1	+	11	1278				PPP5C_ENST00000012443.4_Intron	NM_001204284.1	NP_001191213.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	NA		NA			cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		cacacacacacaGTGTTGATC	0.498		NA											G|||	2763	0.551717	0.441	0.6801	5008	,	,	NA	15240	0.5694	NA	0.6799	False	NA	,,,	NA	NA	NA	2504	0.4601	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	5536	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase, catalytic subunits, Tetratricopeptide (TTC) repeat domain containing	9322	protein-coding gene	gene with protein product		600658		PPP5	NA	8666404	Standard	NM_006247	NM_006247	NA	Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000391919.1:c.972-591C>G	chr19.hg19:g.46892717C>G		NA	Q16722|Q53XV2	hg19		0.02	-0.156889	ACAxAGT	COVERED																																																																																			NOVEL	PPP5C-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000258970.1	69	12.232235	KEEP	89	3	95	74	2112	CC	0.999957	0.322793	0		+	6	60	188	0	0	16.895089	11	40	314	249	ENST00000391919.1	0.352941	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	46948603	46948603	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46948603T>C			NA	NA				CCDC8 (31762 upstream) : PNMAL1 (21144 downstream)						NA		NA									NA						gatccacctgtctcagcctcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.46948603T>C		NA		hg19		0.02	-0.1491	CTGxCTC	COVERED																																																																																			NOVEL					0			7	2.706948	KEEP	1	0	0	9	248	TT	0.99257	0.289832	0			3	56	109	0	0	9.172899	11	60	324	43		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	46959366	46959366	__UNKNOWN__	IGR	SNP	G	G	A	rs111957157	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:46959366G>A			NA	NA				CCDC8 (42525 upstream) : PNMAL1 (10381 downstream)						NA		NA									NA						gcgacagagcgagactccatc	0.468		NA											g|||	860	0.171725	0.3003	0.1571	5008	,	,	NA	9721	0.0298	NA	0.2316	False	NA	,,,	NA	NA	NA	2504	0.093	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.46959366G>A		NA		hg19		0.02	-0.035078	AGCxAGA	UNCOVERED																																																																																			NOVEL					0			6	2.707063	KEEP	5	0	0	9	256	GG	0	0	0			3	60	84	0	0	8.852566	1	40	34	16		0.75	0.019982
ZC3H4	23211	__UNKNOWN__	__UNKNOWN__	19	47582070	47582070	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:47582070G>T	ENST00000253048.5	-	11	1478				ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	NA		NA					metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		gagccgagatggtgccattgc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749	23211		Zinc fingers, CCCH-type domain containing	17808	protein-coding gene	gene with protein product		NA	chromosome 19 open reading frame 7	C19orf7	NA		Standard		NM_015168	NA	Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1440+2699C>A	chr19.hg19:g.47582070G>T		NA	Q9Y420	hg19	CCDS42582.1	0.02	-0.157898	GATxGTG	COVERED																																																																																			NOVEL	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466667.1	7	2.407215	KEEP	0	0	0	8	246	GG	0.99257	0.320408	0		-	3	60	84	0	0	6.39228	14	60	486	34	ENST00000253048.5	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	47738240	47738240	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:47738240T>C			NA	NA				BBC3 (2217 upstream) : CCDC9 (20996 downstream)						NA		NA									NA						cctgtaatcctagcactttgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.47738240T>C		NA		hg19		0.02	-0.192924	TCCxAGC	COVERED																																																																																			NOVEL					0			9	3.909127	KEEP	0	0	0	13	350	TT	0.994391	0.455189	0			3	60	105	0	0	8.260986	17	60	495	50		0.15	0.457757
MEIS3	56917	__UNKNOWN__	__UNKNOWN__	19	47911289	47911289	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:47911289C>T	ENST00000560253.1	-	4	414				MEIS3_ENST00000559524.1_Intron|MEIS3_ENST00000561293.1_Intron|MEIS3_ENST00000331559.5_Intron|MEIS3_ENST00000561096.1_Intron|MEIS3_ENST00000558555.1_Intron|MEIS3_ENST00000441740.2_Intron			Q99687	MEIS3_HUMAN	Meis homeobox 3	NA		NA			negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		gtctcgatctcctgacctcgt	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419	56917		Homeoboxes / TALE class	29537	protein-coding gene	gene with protein product		NA	Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)		NA	8950991	Standard	XM_085929	NM_020160	NA	Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000560253.1:c.647-604G>A	chr19.hg19:g.47911289C>T		NA	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	hg19		0.02	-0.087704	TCTxCTG	UNCOVERED																																																																																			NOVEL	MEIS3-012	KNOWN	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000417640.1	8	2.406838	KEEP	3	0	0	8	234	CC	0	0	0		-	3	60	80	0	0	6.777878	7	60	230	25	ENST00000560253.1	0.3	0.099721
MEIS3	56917	__UNKNOWN__	__UNKNOWN__	19	47916747	47916747	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:47916747G>T	ENST00000441740.2	-	6	780				MEIS3_ENST00000559524.1_Intron|MEIS3_ENST00000561293.1_Intron|MEIS3_ENST00000331559.5_Intron|MEIS3_ENST00000561096.1_Intron|MEIS3_ENST00000558555.1_Intron	NM_001009813.2	NP_001009813.1	Q99687	MEIS3_HUMAN	Meis homeobox 3	NA		NA			negative regulation of apoptotic signaling pathway (GO:2001234)|positive regulation of protein kinase B signaling (GO:0051897)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			breast(1)|large_intestine(5)|lung(11)|prostate(1)|skin(2)	20		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;0.000198)|OV - Ovarian serous cystadenocarcinoma(262;0.000439)|Epithelial(262;0.0113)|GBM - Glioblastoma multiforme(486;0.0223)		GTGTGGAGTGGGTGTGCGTGT	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC025404	CCDS33064.1, CCDS46132.1, CCDS74406.1	19q13.32	2012-10-02	2007-02-15		ENSG00000105419	ENSG00000105419	56917		Homeoboxes / TALE class	29537	protein-coding gene	gene with protein product		NA	Meis1, myeloid ecotropic viral integration site 1 homolog 3 (mouse)		NA	8950991	Standard	XM_085929	NM_020160	NA	Approved	MRG2, DKFZp547H236	uc002pgt.4	Q99687	OTTHUMG00000172280	ENST00000441740.2:c.546+1226C>A	chr19.hg19:g.47916747G>T		NA	A8K1N5|Q6NT73|Q8TC66|Q9NPW2	hg19	CCDS46132.1	0.02	-0.403435	GTGxGTG	COVERED																																																																																			NOVEL	MEIS3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417636.2	19	8.021339	KEEP	0	3	80	55	1653	GG	1	0.934492	0		-	4	60	118	0	0	7.852008	41	60	1323	130	ENST00000441740.2	0.088889	0.934492
SLC8A2	6543	__UNKNOWN__	__UNKNOWN__	19	47966125	47966125	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:47966125G>A	ENST00000236877.6	-	2	1071				SLC8A2_ENST00000542837.1_Intron|SLC8A2_ENST00000539381.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	NA		NA			blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		gattacaggcgtgagccactg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160	6543		Solute carriers	11069	protein-coding gene	gene with protein product		601901			NA	8021246	Standard		NM_015063	NA	Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.675+2860C>T	chr19.hg19:g.47966125G>A		NA	B4DYQ9	hg19	CCDS33065.1	0.02	-0.157896	GGCxTGA	COVERED																																																																																			NOVEL	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466997.1	4	2.40634	KEEP	1	0	0	8	225	GG	0.99257	0.320408	0		-	3	60	86	0	0	6.592183	14	60	472	38	ENST00000236877.6	0.176471	0.322807
ZNF541	84215	__UNKNOWN__	__UNKNOWN__	19	48024092	48024092	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48024092T>A	ENST00000391901.3	-	0	4429				ZNF541_ENST00000314121.4_3'UTR|ZNF541_ENST00000448976.1_3'UTR			Q9H0D2	ZN541_HUMAN	zinc finger protein 541	NA		NA			cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(1)|lung(2)|prostate(1)|skin(1)	9						GATCTCAAGGTTTTTTCCCAC	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL136846	CCDS46133.1, CCDS46133.2	19q13.33	2013-01-08			ENSG00000118156	ENSG00000118156	84215		Zinc fingers, C2H2-type	25294	protein-coding gene	gene with protein product		NA			NA	11230166	Standard	NM_032255	NM_001277075	NA	Approved	DKFZp434I1930	uc002phg.5	Q9H0D2	OTTHUMG00000141262	ENST00000391901.3:c.*389A>T	chr19.hg19:g.48024092T>A		NA	Q8NDK8	hg19		0.02	1.415179	AGGxTTT	COVERED																																																																																			NOVEL	ZNF541-001	KNOWN	basic|appris_candidate|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000280415.1	2	3.909215	KEEP	0	0	0	13	354	TT	0.994391	0.993264	0		-	20	60	574	0	0	48.194477	54	60	1533	139	ENST00000391901.3	0.27027	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	48106184	48106184	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48106184G>A			NA	NA				RN7SL322P (21608 upstream) : CTD-2571L23.8 (4596 downstream)						NA		NA									NA						ctccatctcagaaaaaaagaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.48106184G>A		NA		hg19		0.02	-0.11402	TCAxAAA	UNCOVERED																																																																																			NOVEL					0			6	2.640517	KEEP	2	1	23	17	519	GG	0.997832	0.162114	0			3	60	84	1	0	6.90096	9	60	300	41		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	48108578	48108578	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48108578C>T			NA	NA				RN7SL322P (24002 upstream) : CTD-2571L23.8 (2202 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.48108578C>T		NA		hg19		0.02	-0.113992	AGAxGGG	UNCOVERED																																																																																			NOVEL					0			5	3.008029	KEEP	4	0	0	10	285	CC	0.99254	0.161255	0			4	60	100	0	0	8.589222	8	60	263	33		0.333333	0.162467
EHD2	30846	__UNKNOWN__	__UNKNOWN__	19	48232069	48232069	__UNKNOWN__	Intron	SNP	C	C	T	rs539837254		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48232069C>T	ENST00000263277.3	+	4	1166				EHD2_ENST00000538399.1_Intron|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	NA		NA			blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		tcaggtgatccgcccgccttg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422	30846		EF-hand domain containing	3243	protein-coding gene	gene with protein product		605890		PAST2	NA	10673336	Standard		NM_014601	NA	Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.915+2588C>T	chr19.hg19:g.48232069C>T		NA	B2RDH9|B4DNU6|Q96CB6	hg19	CCDS12704.1	0.02	-0.175412	ATCxGCC	UNCOVERED																																																																																			NOVEL	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465851.1	6	2.40608	KEEP	4	0	0	8	230	CC	0	0	0		+	3	32	91	0	0	7.092117	14	60	449	43	ENST00000263277.3	0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	48276273	48276273	__UNKNOWN__	IGR	SNP	T	T	C	rs549467991		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48276273T>C			NA	NA				CTD-2571L23.6 (4176 upstream) : SEPW1 (5555 downstream)						NA		NA									NA						tctcctgccttagcctcctga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.48276273T>C		NA		hg19		0.02	-0.122787	CCTxAGC	COVERED																																																																																			NOVEL					0			8	3.007385	KEEP	4	0	0	10	272	TT	0.99254	0.194847	0			3	40	95	0	0	7.882155	10	60	292	35		0.230769	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	48459335	48459335	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48459335A>G			NA	NA				AC124853.1 (57262 upstream) : BSPH1 (11967 downstream)						NA		NA									NA						cgccatgttgaccaggctggt	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.48459335A>G		NA		hg19		0.02	-0.306774	TTGxCCA	COVERED																																																																																			NOVEL					0			7	2.368431	KEEP	16	2	57	28	755	AA	0.999909	0.800173	0			3	40	97	0	0	6.899048	27	40	798	90		0.1	0.800245
BSPH1	100131137	__UNKNOWN__	__UNKNOWN__	19	48492671	48492671	__UNKNOWN__	Intron	SNP	G	G	C	rs59162618	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48492671G>C	ENST00000344839.3	-	1	162					NM_001128326.2	NP_001121798.1	Q075Z2	BSPH1_HUMAN	binder of sperm protein homolog 1	NA		NA			single fertilization (GO:0007338)|sperm capacitation (GO:0048240)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)			stomach(2)	2						aaagtgctgggattacaggtg	0.527		NA											g|||	703	0.140375	0.087	0.219	5008	,	,	NA	14431	0.123	NA	0.1909	False	NA	,,,	NA	NA	NA	2504	0.1227	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			DQ227497	CCDS46135.1	19q13.32	2012-09-20				ENSG00000188334	100131137			33906	protein-coding gene	gene with protein product	epididymal sperm binding protein 2, bovine seminal plasma protein homolog 1	612213			NA	17085770, 18923155	Standard	NM_001128326	NM_001128326	NA	Approved	ELSPBP2, BSP1	uc002phs.1	Q075Z2		ENST00000344839.3:c.73+2594C>G	chr19.hg19:g.48492671G>C		NA	A6NIZ5	hg19	CCDS46135.1	0.02	-0.131592	TGGxATT	COVERED																																																																																			NOVEL	BSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465206.1	13	3.305208	KEEP	9	0	0	11	326	GG	0.99254	0.227464	0		-	4	60	140	0	0	12.777101	7	60	239	49	ENST00000344839.3	0.363636	0.229173
LIG1	3978	__UNKNOWN__	__UNKNOWN__	19	48627061	48627061	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48627061T>C	ENST00000263274.7	-	22	2424				CTC-453G23.5_ENST00000596839.1_RNA|CTC-453G23.5_ENST00000596563.1_RNA|LIG1_ENST00000427526.2_Intron|LIG1_ENST00000536218.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	NA		NA			anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	tcccaaagtgttgggattaca	0.483		NA						Nucleotide excision repair (NER)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	3978	6.5.1.1		6598	protein-coding gene	gene with protein product		126391			NA		Standard	NM_000234	XM_005258934	NA	Approved		uc002pia.1	P18858		ENST00000263274.7:c.2005-486A>G	chr19.hg19:g.48627061T>C		NA	B2RAI8|Q2TB12|Q32P23	hg19	CCDS12711.1	0.02	-0.192955	GTGxTGG	COVERED																																																																																			NOVEL	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465575.1	8	2.705897	KEEP	0	0	0	9	234	TT	0.99254	0.454342	0		-	3	60	101	0	0	7.933335	16	60	469	43	ENST00000263274.7	0.157895	0.457757
ZNF114	163071	__UNKNOWN__	__UNKNOWN__	19	48774084	48774084	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48774084T>C	ENST00000595607.1	+	2	118				ZNF114_ENST00000597695.1_Intron|CTC-241F20.4_ENST00000600941.1_lincRNA			Q8NC26	ZN114_HUMAN	zinc finger protein 114	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(6)|lung(11)	18		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)		gcctgtaatctcagcactttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC014935	CCDS12713.1, CCDS74412.1	19q13.32	2013-01-08			ENSG00000178150	ENSG00000178150	163071		Zinc fingers, C2H2-type, -	12894	protein-coding gene	gene with protein product		603996			NA		Standard	NM_153608	XM_005258580	NA	Approved	MGC17986	uc002pim.1	Q8NC26		ENST00000595607.1:c.-376-418T>C	chr19.hg19:g.48774084T>C		NA	A8K6B0|Q08AQ6	hg19	CCDS12713.1	0.02	-0.192973	ATCxCAG	COVERED																																																																																			NOVEL	ZNF114-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465601.1	12	3.910179	KEEP	0	0	0	13	362	TT	0.994391	0.455189	0		+	3	60	105	0	0	8.772859	11	60	325	43	ENST00000595607.1	0.214286	0.457757
TMEM143	55260	__UNKNOWN__	__UNKNOWN__	19	48840576	48840576	__UNKNOWN__	Intron	SNP	C	C	T	rs6509378	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:48840576C>T	ENST00000293261.3	-	7	1292				TMEM143_ENST00000541566.1_Intron|TMEM143_ENST00000436660.2_Intron|TMEM143_ENST00000435956.3_Intron|TMEM143_ENST00000377431.2_Intron	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN	transmembrane protein 143	NA		NA			hematopoietic progenitor cell differentiation (GO:0002244)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		gaggccgaggcgggcggatca	0.552		NA											C|||	1816	0.36262	0.2988	0.4107	5008	,	,	NA	16386	0.3462	NA	0.4503	False	NA	,,,	NA	NA	NA	2504	0.3415	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK129801	CCDS12716.1	19q13.32	2008-02-05				ENSG00000161558	55260			25603	protein-coding gene	gene with protein product		NA			NA	12975309	Standard	NM_018273	NM_018273	NA	Approved	FLJ10922	uc002pix.1	Q96AN5		ENST00000293261.3:c.976-3122G>A	chr19.hg19:g.48840576C>T		NA	A8K656|Q6UXY4|Q9NV49	hg19	CCDS12716.1	0.02	-0.385849	AGGxGGG	COVERED																																																																																			NOVEL	TMEM143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465622.1	43	5.450614	KEEP	49	4	98	53	1620	CC	0.999997	0.918168	0		-	7	60	204	1	0	15.447733	36	60	1208	191	ENST00000293261.3	0.162791	0.918171
RASIP1	54922	__UNKNOWN__	__UNKNOWN__	19	49235780	49235780	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:49235780A>G	ENST00000222145.4	-	4	1384				RASIP1_ENST00000594232.1_Intron	NM_017805.2	NP_060275.2	Q5U651	RAIN_HUMAN	Ras interacting protein 1	NA		NA			angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|negative regulation of autophagy (GO:0010507)|regulation of Rho GTPase activity (GO:0032319)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	Golgi apparatus (GO:0005794)				central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	21		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;9.98e-05)|all cancers(93;0.000272)|Epithelial(262;0.0155)|GBM - Glioblastoma multiforme(486;0.0222)		caaagtgctgagattacaggc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC028614	CCDS12731.1	19q13.33	2008-02-05				ENSG00000105538	54922			24716	protein-coding gene	gene with protein product		609623			NA	15031288	Standard	NM_017805	NM_017805	NA	Approved	FLJ20401, RAIN	uc002pki.3	Q5U651		ENST00000222145.4:c.1179+2672T>C	chr19.hg19:g.49235780A>G		NA	Q6U676	hg19	CCDS12731.1	0.02	-0.289449	CTGxGAT	COVERED																																																																																			NOVEL	RASIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466185.1	5	4.209873	KEEP	3	0	0	14	390	AA	0.994391	0.756619	0		-	3	60	106	0	0	7.708824	29	60	883	76	ENST00000222145.4	0.09375	0.760887
PLEKHA4	57664	__UNKNOWN__	__UNKNOWN__	19	49349463	49349463	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:49349463T>C	ENST00000263265.6	-	15	2122				PLEKHA4_ENST00000355496.5_Intron	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	NA		NA				cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		gtaatcccagtactttgggag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559	57664		Pleckstrin homology (PH) domain containing	14339	protein-coding gene	gene with protein product		607769	pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4		NA	11001876	Standard		NM_020904	NA	Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.1567-590A>G	chr19.hg19:g.49349463T>C		NA	Q8N4M8|Q8N658	hg19	CCDS12737.1	0.02	-0.192951	CAGxACT	COVERED																																																																																			NOVEL	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466216.1	8	2.704839	KEEP	0	0	0	9	225	TT	0.99254	0.454342	0		-	4	60	140	0	0	11.768535	14	60	404	43	ENST00000263265.6	0.222222	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	49740938	49740938	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:49740938C>T			NA	NA				TRPM4 (25845 upstream) : AC011450.1 (28801 downstream)						NA		NA									NA						gtgctgggatcacaggcgtga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.49740938C>T		NA		hg19		0.02	-0.131568	GATxACA	COVERED																																																																																			NOVEL					0			2	2.407006	KEEP	1	0	0	8	246	CC	0.99257	0.22747	0			3	60	81	0	0	6.373114	11	60	365	36		0.214286	0.229173
FLT3LG	2323	__UNKNOWN__	__UNKNOWN__	19	49985663	49985663	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:49985663A>G	ENST00000594009.1	+	7	808				FLT3LG_ENST00000600429.1_Intron|FLT3LG_ENST00000597551.1_Intron|FLT3LG_ENST00000596435.1_Intron|CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000204637.2_Intron|CTD-3148I10.9_ENST00000599536.1_Intron	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	NA		NA			embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		gattacaggcatgagccacca	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554	2323		Endogenous ligands	3766	protein-coding gene	gene with protein product		600007			NA	8145851, 7824267	Standard		NM_001204502	NA	Approved		uc010yau.2	P49771		ENST00000594009.1:c.705+1786A>G	chr19.hg19:g.49985663A>G		NA	A0AVC2|B9EGH2|Q05C96	hg19	CCDS12767.1	0.02	-0.192933	GGCxTGA	COVERED																																																																																			NOVEL	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000465305.1	9	3.308003	KEEP	2	0	0	11	298	AA	0.992708	0.454419	0		+	3	60	105	0	0	8.192163	18	60	516	49	ENST00000594009.1	0.142857	0.457757
PTOV1-AS1	100506033	__UNKNOWN__	__UNKNOWN__	19	50347983	50347983	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50347983T>C	ENST00000600742.1	-	0	2048				PTOV1-AS1_ENST00000596521.1_RNA					PTOV1 antisense RNA 1	NA		NA									NA						ggtgaaaccctgtctctacta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC043359		19q13.33	2012-10-12	2012-08-15			ENSG00000268006	100506033		Long non-coding RNAs	44174	non-coding RNA	RNA, long non-coding		NA	PTOV1 antisense RNA 1 (non-protein coding)		NA		Standard	NR_040037	NR_040037	NA	Approved		uc002ppy.4			ENST00000600742.1:	chr19.hg19:g.50347983T>C		NA		hg19		0.02	-0.070158	CCCxGTC	UNCOVERED																																																																																			NOVEL	PTOV1-AS1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000465822.1	4	2.406395	KEEP	2	0	0	8	226	TT	0.99257	0.053735	0		-	4	60	118	0	0	11.298578	4	60	122	23	ENST00000600742.1	0.5	0.054137
NUP62	23636	__UNKNOWN__	__UNKNOWN__	19	50410882	50410882	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50410882T>C	ENST00000422090.2	-	0	2678				NUP62_ENST00000413454.1_3'UTR|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000352066.3_3'UTR|IL4I1_ENST00000341114.3_Intron	NM_001193357.1	NP_001180286.1	P37198	NUP62_HUMAN	nucleoporin 62kDa	NA		NA			carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		caacacctcctgggttcaagt	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024	23636			8066	protein-coding gene	gene with protein product	nuclear pore glycoprotein p62	605815	nucleoporin 62kD		NA	1915414	Standard	NM_153719	NM_016553	NA	Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000422090.2:c.*614A>G	chr19.hg19:g.50410882T>C		NA	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	hg19	CCDS12788.1	0.02	-0.21048	TCCxGGG	COVERED																																																																																			NOVEL	NUP62-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464987.1	11	4.512176	KEEP	0	0	0	15	426	TT	0.99649	0.520328	0		-	3	60	103	0	0	7.926992	19	60	567	53	ENST00000422090.2	0.136364	0.522161
SIGLEC16	400709	__UNKNOWN__	__UNKNOWN__	19	50474960	50474960	__UNKNOWN__	RNA	SNP	C	C	G	rs201054007	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50474960C>G	ENST00000602139.1	+	0	1035							A6NMB1	SIG16_HUMAN	sialic acid binding Ig-like lectin 16 (gene/pseudogene)	NA		NA			cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.A337G(1)|p.A299G(1)		endometrium(2)|kidney(2)|lung(6)	10						GTTTCCCAAGCAAACAGGACA	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	endometrium(2)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC030222		19q13.33	2014-03-20	2008-08-04	2008-08-04	ENSG00000161643	ENSG00000161643	400709		Sialic acid binding Ig-like lectins, Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / C2-set domain containing	24851	protein-coding gene	gene with protein product		NA	sialic acid binding Ig-like lectin, pseudogene 16	SIGLECP16	NA	11986327, 18629938	Standard	NR_002825	NR_002825	NA	Approved	Siglec-P16	uc002prf.3	A6NMB1	OTTHUMG00000183074	ENST00000602139.1:	chr19.hg19:g.50474960C>G		NA		hg19		0.02	1.888556	AAGxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	C	8.640	0.895790	0.17686	.	.	ENSG00000161643	ENST00000417280;ENST00000456956	.	.	.	2.09	-4.17	0.03857	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.896444	0.09326	N	0.817572	T	0.25644	0.0624	.	.	.	0.09310	N	1	B	0.21309	0.054	B	0.23419	0.046	T	0.17228	-1.0376	8	0.39692	T	0.17	.	4.75	0.13056	0.3457:0.3082:0.3461:0.0	.	337	A6NMB1	SIG16_HUMAN	G	365;337	.	ENSP00000396157:A365G	A	+	2	0	SIGLEC16	55166772	0.000000	0.05858	0.000000	0.03702	0.910000	0.53928	-0.800000	0.04555	-1.793000	0.01258	0.407000	0.27541	GCA	NOVEL	SIGLEC16-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000464979.1	3	3.911515	KEEP	9	0	0	13	401	CC	0.993634	0.975704	0		+	4	50	137	0	0	9.321108	53	60	1817	126	ENST00000602139.1	0.070175	0.981955
IZUMO2	126123	__UNKNOWN__	__UNKNOWN__	19	50664458	50664458	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50664458C>T	ENST00000293405.3	-	2	308					NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	NA		NA				integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						ctcagctcaccgcaacctccg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY358196	CCDS12792.2	19q13.33	2014-02-17	2010-07-29	2010-07-29	ENSG00000161652	ENSG00000161652	126123		-	28518	protein-coding gene	gene with protein product		NA	chromosome 19 open reading frame 41	C19orf41	NA	19658160, 22957301	Standard	NM_152358	XM_006723007	NA	Approved	MGC33947, SCRL	uc002prp.1	Q6UXV1	OTTHUMG00000074063	ENST00000293405.3:c.307+1537G>A	chr19.hg19:g.50664458C>T		NA	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	hg19	CCDS12792.2	0.02	-0.0614	CACxGCA	UNCOVERED																																																																																			NOVEL	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157232.1	8	2.406504	KEEP	4	0	0	8	232	CC	0.99257	0.043461	0		-	3	60	90	0	0	8.624643	3	60	95	24	ENST00000293405.3	0.5	0.043787
POLD1	5424	__UNKNOWN__	__UNKNOWN__	19	50890187	50890187	__UNKNOWN__	Intron	SNP	G	G	C	rs143706589	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50890187G>C	ENST00000440232.2	+	1	52				POLD1_ENST00000599857.1_Intron	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	NA		NA			base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		cggtggctaaggcctgtaatc	0.562		NA						DNA polymerases (catalytic subunits)					c|||	120	0.0239617	0.062	0.0043	5008	,	,	NA	19389	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0348	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822	5424		DNA polymerases	9175	protein-coding gene	gene with protein product	CDC2 homolog (S. cerevisiae)	174761	polymerase (DNA directed), delta 1, catalytic subunit (125kD)	POLD	NA	1722322	Standard		NM_001256849	NA	Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.-2+2540G>C	chr19.hg19:g.50890187G>C		NA	Q8NER3|Q96H98	hg19	CCDS12795.1	0.02	-0.192	TAAxGCC	COVERED																																																																																			NOVEL	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464732.1	7	3.009084	KEEP	0	0	0	10	313	GG	0.992708	0.454419	0		+	3	60	100	0	0	7.769124	17	60	543	48	ENST00000440232.2	0.15	0.457757
POLD1	5424	__UNKNOWN__	__UNKNOWN__	19	50899244	50899244	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50899244A>G	ENST00000440232.2	+	2	52				POLD1_ENST00000599857.1_Intron	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	NA		NA			base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		caaagtgctgagattacaggc	0.413		NA						DNA polymerases (catalytic subunits)													NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822	5424		DNA polymerases	9175	protein-coding gene	gene with protein product	CDC2 homolog (S. cerevisiae)	174761	polymerase (DNA directed), delta 1, catalytic subunit (125kD)	POLD	NA	1722322	Standard		NM_001256849	NA	Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.-1-2864A>G	chr19.hg19:g.50899244A>G		NA	Q8NER3|Q96H98	hg19	CCDS12795.1	0.02	-0.105265	CTGxGAT	UNCOVERED																																																																																			NOVEL	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464732.1	6	3.608495	KEEP	0	0	0	12	325	AA	0.993634	0.138942	0		+	3	60	108	0	0	9.432417	8	60	255	29	ENST00000440232.2	0.272727	0.139832
MYBPC2	4606	__UNKNOWN__	__UNKNOWN__	19	50951747	50951747	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50951747T>C	ENST00000357701.5	+	13	1523					NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	NA		NA			cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		ttttttgagatggagttttgc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967	4606		Myosin binding proteins, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	7550	protein-coding gene	gene with protein product	fast-type muscle myosin-binding-protein C	160793	myosin-binding protein C, fast-type		NA	8375400	Standard	NM_004533	NM_004533	NA	Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.1472+100T>C	chr19.hg19:g.50951747T>C		NA	A1L4G9	hg19	CCDS46152.1	0.02	-0.201704	AGAxGGA	COVERED																																																																																			NOVEL	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464751.1	6	3.007372	KEEP	2	0	0	10	273	TT	0.99254	0.486885	0		+	3	60	92	0	0	6.827673	19	60	551	44	ENST00000357701.5	0.136364	0.490544
MYBPC2	4606	__UNKNOWN__	__UNKNOWN__	19	50951774	50951774	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50951774A>G	ENST00000357701.5	+	13	1523					NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	NA		NA			cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		tgcccaggctagagtgcaatg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967	4606		Myosin binding proteins, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	7550	protein-coding gene	gene with protein product	fast-type muscle myosin-binding-protein C	160793	myosin-binding protein C, fast-type		NA	8375400	Standard	NM_004533	NM_004533	NA	Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.1472+127A>G	chr19.hg19:g.50951774A>G		NA	A1L4G9	hg19	CCDS46152.1	0.02	-0.17539	GCTxGAG	COVERED																																																																																			NOVEL	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464751.1	7	2.706513	KEEP	2	0	0	9	242	AA	0.99257	0.384528	0		+	3	60	99	0	1	7.810424	15	60	429	38	ENST00000357701.5	0.166667	0.387407
MYBPC2	4606	__UNKNOWN__	__UNKNOWN__	19	50964269	50964269	__UNKNOWN__	Intron	SNP	T	T	C	rs11668639		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:50964269T>C	ENST00000357701.5	+	25	2982					NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	NA		NA			cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		taaattttttttttttttttg	0.488		NA									OREG0025636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)									NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967	4606		Myosin binding proteins, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	7550	protein-coding gene	gene with protein product	fast-type muscle myosin-binding-protein C	160793	myosin-binding protein C, fast-type		NA	8375400	Standard	NM_004533	NM_004533	NA	Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.2932-530T>C	chr19.hg19:g.50964269T>C		973	A1L4G9	hg19	CCDS46152.1	0.02	-0.105262	TTTxTTT	UNCOVERED																																																																																			NOVEL	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464751.1	6	2.40554	KEEP	0	0	0	8	214	TT	0.99257	0.138793	0		+	7	60	233	1	0	23.507949	4	60	122	28	ENST00000357701.5	0.636364	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	51008234	51008234	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:51008234G>A			NA	NA				CTD-2545M3.8 (17339 upstream) : JOSD2 (1020 downstream)						NA		NA									NA						tagtagagacggggtttcacc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.51008234G>A		NA		hg19		0.02	-0.096481	GACxGGG	UNCOVERED																																																																																			NOVEL					0			12	3.608714	KEEP	14	0	0	12	341	GG	0	0	0			3	49	95	0	0	8.443668	6	60	184	38		0.333333	0.120436
JOSD2	126119	__UNKNOWN__	__UNKNOWN__	19	51009801	51009801	__UNKNOWN__	Missense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:51009801C>T	ENST00000598418.1	-	4	554	c.301G>A	c.(301-303)Gta>Ata	p.V101I	JOSD2_ENST00000391815.3_Missense_Mutation_p.V101I|JOSD2_ENST00000595669.1_Missense_Mutation_p.V59I|JOSD2_ENST00000601423.1_Missense_Mutation_p.V101I	NM_001270639.1|NM_001270640.1	NP_001257568.1|NP_001257569.1	Q8TAC2	JOS2_HUMAN	Josephin domain containing 2	101	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.	NA			protein deubiquitination (GO:0016579)	cytoplasm (GO:0005737)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)			kidney(1)|lung(3)|prostate(1)	5		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00743)|GBM - Glioblastoma multiforme(134;0.0364)		AGCCCCAGTACCTGGGGCAGG	0.706		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													6	7	6			NA	NA	19		NA											NA				51009801		2048	3995	6043	SO:0001583	missense			AF247787	CCDS12797.1, CCDS59413.1	19q13.33	2008-02-05				ENSG00000161677	126119			28853	protein-coding gene	gene with protein product		615324			NA		Standard	NM_138334	NM_138334	NA	Approved	SBBI54	uc031rmi.1	Q8TAC2		ENST00000598418.1:c.301G>A	chr19.hg19:g.51009801C>T	ENSP00000468956:p.Val101Ile	NA	M0QX25	hg19	CCDS12797.1	0.02	1.333349	GTAxCTG	COVERED	.	.	.	.	.	.	.	.	.	.	c	0.028	-1.351630	0.01256	.	.	ENSG00000161677	ENST00000293431;ENST00000391815	T	0.42131	0.98	3.39	3.39	0.38822	.	0.173853	0.37530	U	0.002053	T	0.18087	0.0434	N	0.05199	-0.095	0.42602	D	0.993285	B;B	0.26902	0.163;0.088	B;B	0.33521	0.165;0.055	T	0.16778	-1.0391	10	0.02654	T	1	-8.5378	6.6976	0.23207	0.0:0.8702:0.0:0.1298	.	121;101	Q7Z7N5;Q8TAC2	.;JOS2_HUMAN	I	121;101	ENSP00000375691:V101I	ENSP00000293431:V121I	V	-	1	0	JOSD2	55701613	0.356000	0.24930	0.176000	0.23000	0.005000	0.04900	1.345000	0.33953	1.909000	0.55274	0.486000	0.48141	GTA	NOVEL	JOSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464902.1	0	3.008039	KEEP	0	0	0	10	289	CC	0.992708	0.991184	0		-	21	60	592	0	0	49.904739	54	60	1755	103	ENST00000598418.1	0.28	0.998465
SYT3	84258	__UNKNOWN__	__UNKNOWN__	19	51157874	51157874	__UNKNOWN__	Intron	SNP	T	T	C	rs566182215|rs200893812|rs148839100|rs372741216|rs369135987	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:51157874T>C	ENST00000544769.1	-	1	42				C19orf81_ENST00000425202.1_Intron			Q9BQG1	SYT3_HUMAN	synaptotagmin III	NA		NA			calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		ctccctcccttccttccttcc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023	84258		Synaptotagmins	11511	protein-coding gene	gene with protein product		600327			NA	7749232	Standard	NM_032298	NM_032298	NA	Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000544769.1:c.516+13735A>G	chr19.hg19:g.51157874T>C		NA	Q8N5Z1|Q8N640	hg19	CCDS12798.1	0.02	-0.175403	CCTxCCT	COVERED																																																																																			NOVEL	SYT3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464912.1	8	2.405511	KEEP	0	0	0	8	212	TT	0.99257	0.384528	0		-	3	60	102	0	0	8.278868	13	60	384	43	ENST00000544769.1	0.1875	0.387407
AC011523.2	0	__UNKNOWN__	__UNKNOWN__	19	51350329	51350329	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:51350329G>A	ENST00000598079.1	+	0	213										NA		NA									NA						ctggagtgcagtggcacaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000598079.1:	chr19.hg19:g.51350329G>A		NA		hg19		0.02	-0.166665	GCAxTGG	COVERED																																																																																			NOVEL	AC011523.2-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000465164.1	21	6.017705	KEEP	20	0	0	20	604	GG	0.993072	0.351495	0		+	3	40	83	0	0	6.37948	13	60	441	66	ENST00000598079.1	0.1875	0.353947
IGLON5	402665	__UNKNOWN__	__UNKNOWN__	19	51831738	51831738	__UNKNOWN__	Intron	SNP	C	C	T	rs188224245	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:51831738C>T	ENST00000270642.8	+	8	922					NM_001101372.1	NP_001094842.1	A6NGN9	IGLO5_HUMAN	IgLON family member 5	NA		NA				extracellular region (GO:0005576)				large_intestine(5)|lung(6)|prostate(1)	12						ggtgacagagcgagactccgt	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46158.1	19q13.33	2013-01-29			ENSG00000142549	ENSG00000142549	402665		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	34550	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001101372	NM_001101372	NA	Approved	LOC402665	uc002pwc.2	A6NGN9	OTTHUMG00000154422	ENST00000270642.8:c.923-187C>T	chr19.hg19:g.51831738C>T		NA		hg19	CCDS46158.1	0.02	0.886077	GAGxGAG	COVERED																																																																																			NOVEL	IGLON5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000335149.1	7	13.398229	KEEP	1	5	116	86	2477	CC	1	0.997163	0		+	6	60	154	0	0	9.995487	50	60	1602	176	ENST00000270642.8	0.107143	0.997163
ETFB	2109	__UNKNOWN__	__UNKNOWN__	19	51861827	51861827	__UNKNOWN__	Intron	SNP	C	C	T	rs546506317	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:51861827C>T	ENST00000309244.4	-	2	149				CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	NA		NA			cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		ccaaggtgggcggatcacctg	0.473		NA											C|||	22	0.00439297	0.0144	0.0029	5008	,	,	NA	16239	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379	2109			3482	protein-coding gene	gene with protein product		130410			NA		Standard		NM_001014763	NA	Approved		uc002pwg.3	P38117		ENST00000309244.4:c.58-4265G>A	chr19.hg19:g.51861827C>T		NA	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	hg19	CCDS12828.1	0.02	-0.210536	GGGxGGA	COVERED																																																																																			NOVEL	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464273.1	11	3.610399	KEEP	6	0	0	12	365	CC	0.99254	0.518266	0		-	3	44	89	0	0	6.661253	17	60	581	59	ENST00000309244.4	0.15	0.522161
PPP2R1A	5518	__UNKNOWN__	__UNKNOWN__	19	52715988	52715988	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:52715988G>A	ENST00000322088.6	+	5	611	c.553G>A	c.(553-555)Gca>Aca	p.A185T	PPP2R1A_ENST00000444322.2_Missense_Mutation_p.A130T|PPP2R1A_ENST00000462990.1_Missense_Mutation_p.A6T	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha	185	PP2A subunit B binding.|Polyoma small and medium T antigens Binding.|SV40 small T antigen binding.	NA			apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GCGGCGGGCCGCAGCCTCCAA	0.622		NA	Mis		clear cell ovarian carcinoma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom?	yes		19	19q13.41	5518	protein phosphatase 2, regulatory subunit A, alpha		E	0													78	59	66			NA	NA	19		NA											NA				52715988		2203	4300	6503	SO:0001583	missense				CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	5518	3.1.3.16	Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits	9302	protein-coding gene	gene with protein product	protein phosphatase 2A, regulatory subunit A, alpha isoform, protein phosphatase 2, 65kDa regulatory subunit A	605983	protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform, protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform		NA		Standard	NM_014225	NR_033500	NA	Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.553G>A	chr19.hg19:g.52715988G>A	ENSP00000324804:p.Ala185Thr	NA	Q13773|Q6ICQ3|Q96DH3	hg19	CCDS12849.1	0.02	1.181488	GCCxCAG	COVERED	.	.	.	.	.	.	.	.	.	.	G	32	5.124288	0.94429	.	.	ENSG00000105568	ENST00000423369;ENST00000391791;ENST00000322088;ENST00000444322	T;T	0.30182	1.54;1.54	4.5	4.5	0.54988	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000009	T	0.67543	0.2904	H	0.96239	3.79	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.77557	0.963;0.99;0.99	T	0.79047	-0.1963	10	0.87932	D	0	-6.472	15.1188	0.72426	0.0:0.0:1.0:0.0	.	130;185;185	F5H3X9;A8K7B7;P30153	.;.;2AAA_HUMAN	T	175;105;185;130	ENSP00000324804:A185T;ENSP00000415067:A130T	ENSP00000324804:A185T	A	+	1	0	PPP2R1A	57407800	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	8.489000	0.90461	2.503000	0.84419	0.655000	0.94253	GCA	NOVEL	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000267967.2	2	3.908038	KEEP	0	0	0	13	357	GG	0.994391	0.991133	0		+	24	60	660	0	0	57.948302	46	60	1301	110	ENST00000322088.6	0.342857	0.996724
ZNF610	162963	__UNKNOWN__	__UNKNOWN__	19	52849178	52849178	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:52849178C>T	ENST00000403906.3	+	2	199				ZNF610_ENST00000601151.1_Intron|ZNF610_ENST00000321287.8_Intron|ZNF610_ENST00000327920.8_Intron	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		aggatggtctcgatctcctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554	162963		Zinc fingers, C2H2-type, -	26687	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173530	NM_001161425	NA	Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.-257-1782C>T	chr19.hg19:g.52849178C>T		NA	A8K4C3|Q86YH8|Q8NDS9	hg19	CCDS12851.1	0.02	-0.175431	TCTxGAT	COVERED																																																																																			NOVEL	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462880.1	2	3.008671	KEEP	6	0	0	10	303	CC	0.99257	0.384528	0		+	3	60	91	0	0	7.010409	15	60	483	54	ENST00000403906.3	0.166667	0.387407
ZNF610	162963	__UNKNOWN__	__UNKNOWN__	19	52857717	52857717	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:52857717T>G	ENST00000403906.3	+	5	775				ZNF610_ENST00000601151.1_Intron|ZNF610_ENST00000321287.8_Intron|ZNF610_ENST00000327920.8_Intron	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		acccaggctgtagtgcagtgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554	162963		Zinc fingers, C2H2-type, -	26687	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173530	NM_001161425	NA	Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.319+85T>G	chr19.hg19:g.52857717T>G		NA	A8K4C3|Q86YH8|Q8NDS9	hg19	CCDS12851.1	0.02	-0.333218	CTGxAGT	COVERED																																																																																			NOVEL	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462880.1	5	5.713601	KEEP	0	0	0	19	515	TT	0.99986	0.851864	0		+	3	60	100	0	0	6.875874	35	60	1009	72	ENST00000403906.3	0.078947	0.851984
ZNF83	55769	__UNKNOWN__	__UNKNOWN__	19	53097823	53097823	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53097823A>G	ENST00000600714.1	-	6	565				ZNF83_ENST00000601257.1_Intron|ZNF137P_ENST00000597158.1_RNA			P51522	ZNF83_HUMAN	zinc finger protein 83	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		ctggagtgcaatggtgcgatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766	55769		Zinc fingers, C2H2-type	13158	protein-coding gene	gene with protein product		194558	zinc finger protein 83 (HPF1), zinc finger protein 816B	ZNF816B	NA	8088807	Standard	NM_018300	NM_018300	NA	Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000600714.1:c.283-266T>C	chr19.hg19:g.53097823A>G		NA	A8MT75|Q3ZCX0|Q6PI08	hg19		0.02	-0.122779	GCAxTGG	COVERED																																																																																			NOVEL	ZNF83-017	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000463754.1	5	3.307973	KEEP	0	0	0	11	299	AA	0.993072	0.194952	0		-	3	60	107	0	0	9.082239	10	60	283	34	ENST00000600714.1	0.230769	0.196312
ZNF611	81856	__UNKNOWN__	__UNKNOWN__	19	53207349	53207349	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53207349C>A	ENST00000602162.1	-	0	2812				ZNF611_ENST00000453741.2_3'UTR|ZNF611_ENST00000540744.1_3'UTR|ZNF611_ENST00000543227.1_3'UTR			Q8N823	ZN611_HUMAN	zinc finger protein 611	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		ggcctcccgacgtgctgggat	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020	81856		Zinc fingers, C2H2-type, -	28766	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_030972	NM_030972	NA	Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000602162.1:c.*841G>T	chr19.hg19:g.53207349C>A		NA	B3KRD5|Q69YG9	hg19	CCDS54312.1	0.02	1.566816	CGAxGTG	COVERED																																																																																			NOVEL	ZNF611-003	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000462990.1	21	4.176797	KEEP	0	2	48	31	920	CC	0.999998	0.997551	0		-	5	60	134	0	0	8.148737	60	60	1945	148	ENST00000602162.1	0.076923	0.997553
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	53293322	53293322	__UNKNOWN__	IGR	SNP	A	A	C	rs11670436	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53293322A>C			NA	NA				ZNF600 (3298 upstream) : ZNF28 (7339 downstream)						NA		NA									NA						aggaccggccatttacacttc	0.478		NA											-|||	2521	0.503395	0.6263	0.5591	5008	,	,	NA	19075	0.1865	NA	0.6412	False	NA	,,,	NA	NA	NA	2504	0.4826	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.53293322A>C		NA		hg19		0.02	-0.201714	GCCxTTT	COVERED																																																																																			NOVEL					0			2	2.70597	KEEP	7	0	0	9	240	AA	0.99257	0.4869	0			8	60	274	0	0	25.372265	12	60	336	64		0.4	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	53296240	53296240	__UNKNOWN__	IGR	SNP	C	C	T	rs536818497	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53296240C>T			NA	NA				ZNF600 (6216 upstream) : ZNF28 (4421 downstream)						NA		NA									NA						ccacccacctcggcctcccaa	0.498		NA											-|||	2	0.000399361	0.0008	0.0	5008	,	,	NA	16915	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.53296240C>T		NA		hg19		0.02	-0.166636	CCTxGGC	COVERED																																																																																			NOVEL					0			8	3.609758	KEEP	7	0	0	12	346	CC	0.99254	0.351306	0			3	26	86	0	0	6.872983	11	60	356	51		0.214286	0.353947
ZNF702P	79986	__UNKNOWN__	__UNKNOWN__	19	53493524	53493524	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53493524A>G	ENST00000270443.4	-	0	45					NR_003578.1		Q9H963	ZN702_HUMAN	zinc finger protein 702, pseudogene	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)				NA						gggcgcggtgactcacgcctg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							19q13.41	2010-08-03	2010-08-03	2008-07-03	ENSG00000242779	ENSG00000242779	79986			25775	pseudogene	pseudogene		NA	zinc finger protein 702, zinc finger protein 702 pseudogene, zinc finger protein 702 (pseudogene)	ZNF702	NA		Standard	NM_024924	NR_003578	NA	Approved	FLJ12985	uc002qan.4	Q9H963	OTTHUMG00000150515	ENST00000270443.4:	chr19.hg19:g.53493524A>G		NA	Q05BW1	hg19		0.02	-0.263077	GTGxCTC	COVERED																																																																																			NOVEL	ZNF702P-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000318717.1	14	4.808209	KEEP	3	0	0	16	395	AA	0.99649	0.714798	0		-	3	60	105	0	0	8.260944	17	60	479	60	ENST00000270443.4	0.15	0.717315
ZNF347	84671	__UNKNOWN__	__UNKNOWN__	19	53655270	53655270	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53655270C>G	ENST00000452676.2	-	2	442				ZNF347_ENST00000334197.7_Intron|ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Intron	NM_001172674.1	NP_001166145.1	Q96SE7	ZN347_HUMAN	zinc finger protein 347	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|prostate(3)|skin(1)	23				GBM - Glioblastoma multiforme(134;0.0179)		cgcttgaacccgggaggcaga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(64;205 1597 17324 45721)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY029765	CCDS33097.1, CCDS54314.1	19q13.3	2013-01-08				ENSG00000197937	84671		Zinc fingers, C2H2-type, -	16447	protein-coding gene	gene with protein product		NA			NA		Standard	NM_032584	NM_032584	NA	Approved	ZNF1111	uc010eql.2	Q96SE7		ENST00000452676.2:c.15+1715G>C	chr19.hg19:g.53655270C>G		NA	B3KU77|B9EG59|G5E9N4|Q8TCN1	hg19	CCDS54314.1	0.02	-0.096484	ACCxGGG	UNCOVERED																																																																																			NOVEL	ZNF347-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000464172.2	6	2.707461	KEEP	2	0	0	9	265	CC	0	0	0		-	4	27	128	0	0	11.577234	7	60	218	24	ENST00000452676.2	0.363636	0.120436
ZNF525	170958	__UNKNOWN__	__UNKNOWN__	19	53887539	53887539	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53887539T>C	ENST00000475179.1	+	4	256				ZNF525_ENST00000467003.1_3'UTR|ZNF525_ENST00000593918.1_Intron|ZNF525_ENST00000474037.1_3'UTR			Q8N782	ZN525_HUMAN	zinc finger protein 525	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(3)|lung(3)	9						gagtttgagatcagcctggac	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075859		19q13.42	2013-01-16			ENSG00000203326	ENSG00000203326	170958		Zinc fingers, C2H2-type, -	29423	protein-coding gene	gene with protein product		NA			NA	11853319	Standard	NR_003699	NR_003699	NA	Approved	KIAA1979	uc010eqn.3	Q8N782	OTTHUMG00000158277	ENST00000475179.1:c.143-684T>C	chr19.hg19:g.53887539T>C		NA	Q8TF23	hg19		0.02	1.713459	AGAxCAG	COVERED																																																																																			NOVEL	ZNF525-003	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000350553.1	20	2.369678	KEEP	0	2	57	28	770	TT	0.999997	0.99899	0		+	5	60	171	0	0	11.699903	64	60	1905	156	ENST00000475179.1	0.072464	0.998993
ZNF761	388561	__UNKNOWN__	__UNKNOWN__	19	53961038	53961038	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53961038T>C	ENST00000454407.1	+	0	3730							Q86XN6	ZN761_HUMAN	zinc finger protein 761	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	30				GBM - Glioblastoma multiforme(134;0.00786)		gtcaggagtttgagatcagcc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AB107355		19q13.42	2007-10-05	2006-08-11	2006-08-11	ENSG00000160336	ENSG00000160336	388561		Zinc fingers, C2H2-type	23179	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001008401	NM_001008401	NA	Approved	KIAA2033, FLJ16231, FLJ35333	uc010eqp.3	Q86XN6	OTTHUMG00000156999	ENST00000454407.1:	chr19.hg19:g.53961038T>C		NA	Q6ZNB9	hg19		0.02	3.791827	GTTxGAG	COVERED																																																																																			NOVEL	ZNF761-203	KNOWN	basic	processed_transcript	NA	processed_transcript		31	12.325884	KEEP	1	3	91	73	2013	TT	1	0.999968	0		+	5	60	166	0	0	10.508354	89	60	2625	263	ENST00000454407.1	0.053191	0.999968
ZNF813	126017	__UNKNOWN__	__UNKNOWN__	19	53997846	53997846	__UNKNOWN__	3'UTR	SNP	G	G	A	rs180735762	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53997846G>A	ENST00000396403.4	+	0	4488				ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		gctgtgagccgagattgcacc	0.458		NA											.|||	2	0.000399361	0.0015	0.0	5008	,	,	NA	14176	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346	126017		Zinc fingers, C2H2-type, -	33257	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004301	NM_001004301	NA	Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.*2506G>A	chr19.hg19:g.53997846G>A		NA		hg19	CCDS46172.1	0.02	-0.420911	GCCxAGA	COVERED																																																																																			NOVEL	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350638.1	9	14.39007	KEEP	2	0	0	48	1220	GG	1	0.948402	0		+	4	60	113	0	0	7.479582	38	60	1092	109	ENST00000396403.4	0.095238	0.948402
ZNF813	126017	__UNKNOWN__	__UNKNOWN__	19	53998014	53998014	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53998014G>C	ENST00000396403.4	+	0	4656				ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		cagtggctcaggcctgtaatc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346	126017		Zinc fingers, C2H2-type, -	33257	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004301	NM_001004301	NA	Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.*2674G>C	chr19.hg19:g.53998014G>C		NA		hg19	CCDS46172.1	0.02	5.736892	TCAxGCC	COVERED																																																																																			NOVEL	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350638.1	57	7.390587	KEEP	0	9	247	112	3361	GT	1	1	0		+	8	60	268	0	0	16.948203	147	60	4909	396	ENST00000396403.4	0.051613	1
ZNF813	126017	__UNKNOWN__	__UNKNOWN__	19	53998921	53998921	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:53998921T>C	ENST00000396403.4	+	0	5563				ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		aaaaattagctgggtgtggtg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346	126017		Zinc fingers, C2H2-type, -	33257	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001004301	NM_001004301	NA	Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.*3581T>C	chr19.hg19:g.53998921T>C		NA		hg19	CCDS46172.1	0.02	-0.140331	AGCxGGG	COVERED																																																																																			NOVEL	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000350638.1	6	3.909416	KEEP	1	0	0	13	355	TT	0.993634	0.290142	0		+	3	60	86	0	0	6.772795	12	60	369	35	ENST00000396403.4	0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	54206521	54206521	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54206521A>G			NA	NA				MIR518B (448 upstream) : MIR526A1 (2984 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.54206521A>G		NA		hg19		0.02	-0.070178	CTGxGAT	UNCOVERED																																																																																			NOVEL					0			5	2.406124	KEEP	0	0	0	8	222	AA	0.99257	0.053735	0			2	60	72	0	0	6.335634	5	60	158	20		0.285714	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	54356025	54356025	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54356025C>G			NA	NA				NLRP12 (28377 upstream) : AC008753.6 (1809 downstream)						NA		NA									NA						ccccatgttgcccaggctggt	0.592		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.54356025C>G		NA		hg19		0.02	-0.131586	TTGxCCA	COVERED																																																																																			NOVEL					0			9	3.008749	KEEP	0	0	0	10	299	CC	0.992708	0.227502	0			3	60	97	0	0	7.972659	11	60	374	31		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	54356064	54356064	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54356064T>C			NA	NA				NLRP12 (28416 upstream) : AC008753.6 (1770 downstream)						NA		NA									NA						gtgatccacctgcctcggcct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.54356064T>C		NA		hg19		0.02	-0.140324	ACCxGCC	COVERED																																																																																			NOVEL					0			7	2.40629	KEEP	0	0	0	8	225	TT	0.99257	0.259026	0			3	60	94	0	0	7.572486	12	60	350	30		0.2	0.260965
AC008753.6	0	__UNKNOWN__	__UNKNOWN__	19	54364202	54364202	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54364202A>G	ENST00000455835.2	-	0	297										NA		NA									NA						gattacaggcatgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000455835.2:	chr19.hg19:g.54364202A>G		NA		hg19		0.02	-0.201714	GGCxTGA	COVERED																																																																																			NOVEL	AC008753.6-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000134347.2	9	2.706822	KEEP	3	0	0	9	248	AA	0.99257	0.4869	0		-	4	60	131	0	0	10.394707	19	60	549	47	ENST00000455835.2	0.173913	0.490544
CACNG8	59283	__UNKNOWN__	__UNKNOWN__	19	54469632	54469632	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54469632A>G	ENST00000270458.2	+	1	386					NM_031895.5	NP_114101	Q8WXS5	CCG8_HUMAN	calcium channel, voltage-dependent, gamma subunit 8	NA		NA			calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			kidney(1)|large_intestine(3)|lung(8)|urinary_tract(1)	13	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.162)		gtgagccaccatgcctggcca	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF288388	CCDS33104.1	19q13.4	2008-05-02			ENSG00000142408	ENSG00000142408	59283		Calcium channel subunits	13628	protein-coding gene	gene with protein product		606900			NA	11170751	Standard		NM_031895	NA	Approved		uc002qcs.2	Q8WXS5	OTTHUMG00000064908	ENST00000270458.2:c.283+2953A>G	chr19.hg19:g.54469632A>G		NA	Q9BXT0|Q9BY23	hg19	CCDS33104.1	0.02	-0.280638	ACCxTGC	COVERED																																																																																			NOVEL	CACNG8-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139361.3	13	3.609262	KEEP	0	0	0	12	332	AA	0.993634	0.734962	0		+	3	60	101	0	0	7.297758	27	60	786	61	ENST00000270458.2	0.1	0.739671
NDUFA3	4696	__UNKNOWN__	__UNKNOWN__	19	54610676	54610676	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54610676T>C	ENST00000485876.1	+	0	764				NDUFA3_ENST00000391764.3_Intron|TFPT_ENST00000391759.1_Intron|TFPT_ENST00000391757.1_Intron|TFPT_ENST00000391758.1_Intron			O95167	NDUA3_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9kDa	NA		NA			cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(1)	2	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)					ccacctcagcttcccaagtag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF044955	CCDS12877.1	19q13.42	2011-07-04	2002-08-29		ENSG00000170906	ENSG00000170906	4696		Mitochondrial respiratory chain complex / Complex I	7686	protein-coding gene	gene with protein product	complex I B9 subunit	603832	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3 (9kD, B9)		NA	9878551	Standard	NM_004542	NM_004542	NA	Approved	B9	uc002qde.3	O95167	OTTHUMG00000064972	ENST00000485876.1:c.*467T>C	chr19.hg19:g.54610676T>C		NA		hg19	CCDS12877.1	0.02	3.525637	AGCxTCC	COVERED																																																																																			NOVEL	NDUFA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139509.5	50	5.667917	KEEP	2	5	154	73	1971	TT	1	0.999999	0		+	6	60	188	1	2	11.60965	102	60	3104	278	ENST00000485876.1	0.055556	0.999999
LILRA6	79168	__UNKNOWN__	__UNKNOWN__	19	54745989	54745989	__UNKNOWN__	Missense_Mutation	SNP	G	G	C	rs1052963	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54745989G>C	ENST00000396365.2	-	3	307	c.268C>G	c.(268-270)Cag>Gag	p.Q90E	LILRA6_ENST00000419410.2_Missense_Mutation_p.Q90E|LILRB3_ENST00000407860.2_Missense_Mutation_p.Q90E|LILRA6_ENST00000245621.5_Missense_Mutation_p.Q90E|LILRA6_ENST00000391735.3_Missense_Mutation_p.Q90E|LILRA6_ENST00000440558.2_Missense_Mutation_p.Q90E|LILRA6_ENST00000270464.5_Missense_Mutation_p.Q90E	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	90		NA			immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCATGGTGCTGTGTCATGGAT	0.557		NA											.|||	444	0.0886581	0.0393	0.0591	5008	,	,	NA	26213	0.2798	NA	0.0417	False	NA	,,,	NA	NA	NA	2504	0.0276	NA	NA	NA								NA				0								C	GLU/GLN	44,4314		3,38,2138	353	300	318		268	-6.8	0	19	dbSNP_86	318	96,8452		3,90,4181	no	missense	LILRA6	NM_024318.2	29	6,128,6319	CC,CG,GG	NA	1.1231,1.0096,1.0848		90/482	54745989	140,12766	2179	4274	6453	SO:0001583	missense			AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482	79168		Leukocyte immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	15495	protein-coding gene	gene with protein product		NA	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6	LILRB6	NA	10941842	Standard	NM_024318	NM_024318	NA	Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.268C>G	chr19.hg19:g.54745989G>C	ENSP00000379651:p.Gln90Glu	NA		hg19	CCDS42610.1	0.02	1.490747	GCTxTGT	COVERED	305	0.13965201465201466	21	0.042682926829268296	34	0.09392265193370165	180	0.3146853146853147	70	0.09234828496042216	g	0.001	-3.083109	0.00035	0.010096	0.011231	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.11063	2.81;2.81;2.81;2.81;2.81;2.81;2.81	3.4	-6.8	0.01709	Immunoglobulin-like fold (1);	2.768340	0.01040	N	0.004297	T	0.00012	0.0000	N	0.01529	-0.815	0.09310	N	1	B;B;B;B;B;B;B	0.14012	0.001;0.0;0.001;0.0;0.004;0.009;0.004	B;B;B;B;B;B;B	0.12837	0.003;0.001;0.004;0.004;0.007;0.001;0.008	T	0.15150	-1.0447	10	0.02654	T	1	.	1.7009	0.02872	0.2798:0.1249:0.3707:0.2246	rs16985555	90;90;90;90;90;90;90	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;D3YTC4	.;.;.;.;LIRA6_HUMAN;.;.	E	90	ENSP00000384274:Q90E;ENSP00000390120:Q90E;ENSP00000270464:Q90E;ENSP00000411227:Q90E;ENSP00000375615:Q90E;ENSP00000379651:Q90E;ENSP00000245621:Q90E	ENSP00000245621:Q90E	Q	-	1	0	LILRB3;LILRA6	59437801	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.130000	0.01312	-7.095000	0.00001	-4.115000	0.00011	CAG	NOVEL	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313725.1	5	2.708064	KEEP	7	0	0	9	275	GG	0.99254	0.992422	0		-	6	27	187	0	0	12.029696	83	60	2836	152	ENST00000396365.2	0.067416	0.999881
AC008984.2	0	__UNKNOWN__	__UNKNOWN__	19	54825033	54825033	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54825033T>A	ENST00000507363.1	-	0	753										NA		NA									NA						atggtctcgatctcctgacct	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000507363.1:	chr19.hg19:g.54825033T>A		NA		hg19		0.02	-0.105234	CGAxCTC	UNCOVERED																																																																																			NOVEL	AC008984.2-001	KNOWN	basic|readthrough_transcript	processed_transcript	NA	processed_transcript	OTTHUMT00000140230.1	6	2.672336	KEEP	3	0	0	9	224	TT	0.99257	0.138793	0		-	3	60	91	0	0	7.601463	9	60	257	33	ENST00000507363.1	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	54915667	54915667	__UNKNOWN__	IGR	SNP	G	G	A	rs200615898		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:54915667G>A			NA	NA				LAIR1 (33502 upstream) : TTYH1 (10937 downstream)						NA		NA									NA						gaacccgggaggcggaggttg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.54915667G>A		NA		hg19		0.02	-0.087723	GGAxGCG	UNCOVERED																																																																																			NOVEL					0			11	4.513325	KEEP	7	0	0	15	458	GG	0.993072	0.09903	0			3	38	92	0	0	8.332566	5	60	168	40		0.375	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	55009291	55009291	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55009291A>T			NA	NA				CDC42EP5 (24880 upstream) : LAIR2 (4721 downstream)						NA		NA									NA						TGGTCTCTCCACAGCGCAGGC	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.55009291A>T		NA		hg19		0.02	4.491078	TCCxCAG	COVERED																																																																																			NOVEL					0			3	6.314952	KEEP	9	0	0	21	582	AA	0.999863	0.999863	0			16	49	492	0	0	33.947274	151	51	4515	286		0.095808	1
KIR2DL1	3802	__UNKNOWN__	__UNKNOWN__	19	55294969	55294969	__UNKNOWN__	Silent	SNP	A	A	G	rs586234	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55294969A>G	ENST00000336077.6	+	7	889	c.849A>G	c.(847-849)ggA>ggG	p.G283G	KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000402254.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR2DL1_ENST00000291633.7_Silent_p.G309G|KIR2DL3_ENST00000434419.2_Silent_p.G283G	NM_014218.2	NP_055033.2	P43626	KI2L1_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 1	283		NA			immune response (GO:0006955)|natural killer cell inhibitory signaling pathway (GO:0002769)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17				GBM - Glioblastoma multiforme(193;0.0192)		AGTCTGCAGGAAACAGAACAG	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(72;624 1217 3963 34152 38303)							NA				0													192	191	191			NA	NA	19		NA											NA				55294969		2172	4194	6366	SO:0001819	synonymous_variant			L41267	CCDS12904.1	19q13.4	2013-01-29			ENSG00000125498	ENSG00000125498	3802		Killer cell immunoglobulin-like receptors, CD molecules, Immunoglobulin superfamily / Immunoglobulin-like domain containing	6329	protein-coding gene	gene with protein product		604936			NA	7749980, 7716543	Standard		NM_014218	NA	Approved	cl-42, nkat1, 47.11, p58.1, CD158A	uc002qhb.1	P43626	OTTHUMG00000065885	ENST00000336077.6:c.849A>G	chr19.hg19:g.55294969A>G		NA	O43470|Q32WE6|Q6IST4	hg19	CCDS12904.1	0.02	2.088021	AGGxAAC	COVERED																																																																																			NOVEL	KIR2DL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000141148.2	0	2.70728	KEEP	0	0	0	9	255	AA	0.99254	0.97463	0		+	27	60	893	0	0	86.545253	25	60	732	102	ENST00000336077.6	0.519231	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	55405398	55405398	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55405398T>G			NA	NA				CTB-61M7.2 (2612 upstream) : NCR1 (12109 downstream)						NA		NA									NA						caaaagtgcttggattacagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.55405398T>G		NA		hg19		0.02	-0.087714	GCTxGGA	UNCOVERED																																																																																			NOVEL					0			5	3.307029	KEEP	0	0	0	11	289	TT	0.993072	0.09903	0			4	60	135	0	0	12.723493	5	60	151	27		0.444444	0.099721
GP6	51206	__UNKNOWN__	__UNKNOWN__	19	55529375	55529375	__UNKNOWN__	Intron	SNP	A	A	T	rs148444706	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55529375A>T	ENST00000333884.2	-	5	698				GP6_ENST00000310373.3_Intron|GP6_ENST00000417454.1_Intron|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA	NM_001256017.1	NP_001242946	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	NA		NA			blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		agcagaggttacagtgagccg	0.517		NA											A|||	258	0.0515176	0.0061	0.0692	5008	,	,	NA	16739	0.0317	NA	0.0954	False	NA	,,,	NA	NA	NA	2504	0.0757	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053	51206		Immunoglobulin superfamily / Immunoglobulin-like domain containing	14388	protein-coding gene	gene with protein product		605546			NA	11027634	Standard		NM_001083899	NA	Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000333884.2:c.670+644T>A	chr19.hg19:g.55529375A>T		NA	Q9HCN7|Q9UIF2	hg19	CCDS58678.1	0.02	-0.105227	GTTxCAG	UNCOVERED																																																																																			NOVEL	GP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000357008.1	6	2.405293	KEEP	0	0	0	8	213	AA	0.99257	0.16126	0		-	4	60	114	0	0	10.385377	6	60	167	28	ENST00000333884.2	0.4	0.162467
EPS8L1	54869	__UNKNOWN__	__UNKNOWN__	19	55587658	55587658	__UNKNOWN__	Intron	SNP	G	G	A	rs62124197	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55587658G>A	ENST00000201647.6	+	2	19				EPS8L1_ENST00000592824.1_Intron|EPS8L1_ENST00000540810.1_Intron|EPS8L1_ENST00000586329.1_Intron	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	NA		NA			positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		tgggggcctggactcctgggc	0.662		NA											G|||	781	0.15595	0.1551	0.2075	5008	,	,	NA	12609	0.1002	NA	0.2475	False	NA	,,,	NA	NA	NA	2504	0.0838	NA	NA	NA	Ovarian(149;255 1863 3636 27051 29647)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037	54869			21295	protein-coding gene	gene with protein product		614987			NA	12620401	Standard	NM_017729	NM_133180	NA	Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.-37-118G>A	chr19.hg19:g.55587658G>A		NA	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	hg19	CCDS12914.1	0.02	-0.157345	CTGxACT	COVERED																																																																																			NOVEL	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451713.1	4	2.700865	KEEP	1	0	0	9	268	GG	0.99257	0.320408	0		+	8	60	228	0	0	21.203801	10	60	340	34	ENST00000201647.6	0.444444	0.322807
PPP1R12C	54776	__UNKNOWN__	__UNKNOWN__	19	55618551	55618551	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55618551A>G	ENST00000263433.3	-	4	587				PPP1R12C_ENST00000376393.2_Intron|PPP1R12C_ENST00000435544.2_Intron	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C	NA		NA								central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		gggggccgagacgggtggatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503	54776		Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits, Ankyrin repeat domain containing	14947	protein-coding gene	gene with protein product	myosin-binding subunit 85	613245	leukocyte receptor cluster (LRC) member 3, protein phosphatase 1, regulatory (inhibitor) subunit 12C	LENG3	NA	11399775	Standard	NM_017607	NM_017607	NA	Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.572-3615T>C	chr19.hg19:g.55618551A>G		NA		hg19	CCDS12916.1	0.02	-0.166593	GAGxCGG	COVERED																																																																																			NOVEL	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451814.2	10	2.694183	KEEP	0	0	0	9	223	AA	0.99254	0.351306	0		-	3	40	100	0	0	8.079322	13	60	352	37	ENST00000263433.3	0.1875	0.353947
TNNT1	7138	__UNKNOWN__	__UNKNOWN__	19	55647725	55647725	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55647725A>G	ENST00000588981.1	-	11	816				TNNT1_ENST00000587758.1_Intron|TNNT1_ENST00000587465.2_Intron|TNNT1_ENST00000291901.8_Intron|TNNT1_ENST00000536926.1_Intron|TNNT1_ENST00000588426.1_Intron|TNNT1_ENST00000356783.5_Intron|TNNT1_ENST00000585321.2_Intron	NM_003283.4	NP_003274.3	P13805	TNNT1_HUMAN	troponin T type 1 (skeletal, slow)	NA		NA			muscle filament sliding (GO:0030049)|negative regulation of muscle contraction (GO:0045932)|skeletal muscle contraction (GO:0003009)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	cytosol (GO:0005829)|troponin complex (GO:0005861)	tropomyosin binding (GO:0005523)			endometrium(2)|kidney(3)|lung(4)|ovary(1)	10			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		aaagtgctggaattacaggca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS12917.1, CCDS46185.1, CCDS59421.1	19q13.4	2014-09-17	2005-09-12			ENSG00000105048	7138			11948	protein-coding gene	gene with protein product	slow skeletal muscle troponin T, troponin T1, skeletal, slow, nemaline myopathy type 5	191041	troponin T1, skeletal, slow		NA	1505979	Standard	NM_003283	XM_006723343	NA	Approved	ANM, STNT, TNT, TNTS, FLJ98147, MGC104241, NEM5	uc002qjb.4	P13805		ENST00000588981.1:c.611+745T>C	chr19.hg19:g.55647725A>G		NA	O95472|Q16061|Q5U0E1	hg19	CCDS12917.1	0.02	-0.149095	TGGxATT	COVERED																																																																																			NOVEL	TNNT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000451825.2	8	3.006706	KEEP	4	0	0	10	266	AA	0.99257	0.289832	0		-	3	60	101	0	0	8.372919	11	60	325	46	ENST00000588981.1	0.214286	0.292001
PPP6R1	22870	__UNKNOWN__	__UNKNOWN__	19	55754610	55754610	__UNKNOWN__	Intron	SNP	A	A	G	rs377183170	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55754610A>G	ENST00000412770.2	-	6	1185				PPP6R1_ENST00000587283.1_Intron	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	NA		NA			regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						gtgaaaccccatctctactaa	0.562		NA											A|||	14	0.00279553	0.0	0.0029	5008	,	,	NA	14664	0.0	NA	0.0099	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063	22870		Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits	29195	protein-coding gene	gene with protein product		610875	KIAA1115, SAPS domain family, member 1	KIAA1115, SAPS1	NA	16769727	Standard	NM_014931	NM_014931	NA	Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.619-754T>C	chr19.hg19:g.55754610A>G		NA	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	hg19	CCDS46186.1	0.02	-0.131475	CCCxTCT	COVERED																																																																																			NOVEL	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000452663.1	13	4.505364	KEEP	12	0	0	15	377	AA	0.993072	0.227586	0		-	3	35	85	0	0	7.001984	9	60	239	42	ENST00000412770.2	0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	55842413	55842413	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55842413G>A			NA	NA				TMEM150B (5705 upstream) : SUV420H2 (8807 downstream)						NA		NA									NA						tggcctcccagagtgctggga	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.55842413G>A		NA		hg19		0.02	-0.210493	CCAxAGT	COVERED																																																																																			NOVEL					0			3	2.873985	KEEP	3	1	9	13	412	GG	0.993634	0.518837	0			4	60	104	0	0	7.69819	19	60	647	62		0.173913	0.522161
RPL28	6158	__UNKNOWN__	__UNKNOWN__	19	55897684	55897684	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55897684G>T	ENST00000560055.1	+	2	30				RPL28_ENST00000428193.2_Intron|RPL28_ENST00000431533.2_Intron|RPL28_ENST00000559463.1_5'UTR|RPL28_ENST00000558815.1_Intron|RPL28_ENST00000560583.1_Intron|RPL28_ENST00000344063.2_Intron			P46779	RL28_HUMAN	ribosomal protein L28	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		AGTTCTCTGTGTCTGACGCTT	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													21	20	20			NA	NA	19		NA											NA				55897684		2203	4300	6503	SO:0001627	intron_variant			U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107	6158		L ribosomal proteins	10330	protein-coding gene	gene with protein product	60S ribosomal protein L28	603638			NA	7772601, 9582194	Standard	NM_000991	NM_001136134	NA	Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000560055.1:c.-8-34G>T	chr19.hg19:g.55897684G>T		NA	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	hg19		0.02	1.487818	TGTxTCT	COVERED																																																																																			NOVEL	RPL28-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000416293.1	3	12.034565	KEEP	0	0	0	40	1194	GG	1	0.999218	0		+	24	60	706	0	0	60.826132	56	60	1903	166	ENST00000560055.1	0.3	0.999218
RPL28	6158	__UNKNOWN__	__UNKNOWN__	19	55909291	55909291	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55909291T>C	ENST00000560055.1	+	5	362							P46779	RL28_HUMAN	ribosomal protein L28	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6	Breast(117;0.191)	Renal(1328;0.245)	LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0443)		Aggttgggcgtggtggctcat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U14969	CCDS12924.1, CCDS46189.1, CCDS46190.1, CCDS46191.1, CCDS46192.1	19q13.4	2011-04-06				ENSG00000108107	6158		L ribosomal proteins	10330	protein-coding gene	gene with protein product	60S ribosomal protein L28	603638			NA	7772601, 9582194	Standard	NM_000991	NM_001136134	NA	Approved	FLJ43307, L28	uc010yga.2	P46779		ENST00000560055.1:c.325-5020T>C	chr19.hg19:g.55909291T>C		NA	B2R4A6|B4DEP9|C9JB50|E9PB24|G5E9L2|Q6IAY0|Q96FX1|Q9BWQ0	hg19		0.02	-0.184165	GCGxGGT	COVERED																																																																																			NOVEL	RPL28-007	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000416293.1	8	3.60488	KEEP	5	0	0	12	299	TT	0.99254	0.420319	0		+	3	60	98	0	0	7.633698	16	60	461	43	ENST00000560055.1	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	55933061	55933061	__UNKNOWN__	IGR	SNP	A	A	G	rs537937473	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55933061A>G			NA	NA				UBE2S (13916 upstream) : SHISA7 (7045 downstream)						NA		NA									NA						aggctgaggcaggaggatcac	0.483		NA											A|||	7	0.00139776	0.0053	0.0	5008	,	,	NA	17833	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.55933061A>G		NA		hg19		0.02	-0.201739	GGCxGGA	COVERED																																																																																			NOVEL					0			14	5.112507	KEEP	0	0	0	17	469	AA	0.999366	0.52183	0			3	60	91	0	0	6.79266	18	60	553	59		0.142857	0.522161
SHISA7	729956	__UNKNOWN__	__UNKNOWN__	19	55943594	55943594	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:55943594G>T	ENST00000376325.4	-	0	2545					NM_001145176.1	NP_001138648.1	A6NL88	SHSA7_HUMAN	shisa family member 7	NA		NA				integral component of membrane (GO:0016021)				skin(1)	1						ATCTTCCCTGGGGTGGTCCTG	0.607		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS46193.1	19q13.42	2013-07-31	2013-07-31				729956		Shisa homologs	35409	protein-coding gene	gene with protein product		NA	shisa homolog 7 (Xenopus laevis)		NA		Standard	NM_001145176	NM_001145176	NA	Approved		uc002qkz.3	A6NL88		ENST00000376325.4:c.*929C>A	chr19.hg19:g.55943594G>T		NA		hg19	CCDS46193.1	0.02	1.441189	CTGxGGT	COVERED																																																																																			NOVEL	SHISA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000334533.2	1	3.610567	KEEP	0	0	0	12	364	GG	0.993634	0.991846	0		-	23	60	662	0	0	57.252775	51	60	1724	118	ENST00000376325.4	0.310811	0.9982
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	56081382	56081382	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:56081382A>G			NA	NA				SBK3 (24473 upstream) : CTD-2537I9.5 (6753 downstream)						NA		NA									NA						atggtggctcatgcctgtaat	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.56081382A>G		NA		hg19		0.02	-0.078935	CTCxTGC	UNCOVERED																																																																																			NOVEL					0			5	2.405954	KEEP	0	0	0	8	220	AA	0.99257	0.076761	0			3	60	107	0	0	10.055689	4	60	116	23		0.428571	0.077336
U2AF2	11338	__UNKNOWN__	__UNKNOWN__	19	56184274	56184274	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:56184274A>G	ENST00000308924.4	+	12	1333				CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000450554.2_Intron|U2AF2_ENST00000590551.1_Intron			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	NA		NA			gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		ctcccaaagtactgggattac	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244	11338		RNA binding motif (RRM) containing	23156	protein-coding gene	gene with protein product	U2 small nuclear ribonucleoprotein auxiliary factor (65kD), splicing factor U2AF 65 kD subunit, U2 snRNP auxiliary factor large subunit	191318	U2 (RNU2) small nuclear RNA auxiliary factor 2		NA	1538748	Standard	NM_007279	XM_006722994	NA	Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1294-1026A>G	chr19.hg19:g.56184274A>G		NA	Q96HC5	hg19	CCDS12933.1	0.02	-0.19295	AGTxCTG	COVERED																																																																																			NOVEL	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000453599.1	6	3.307875	KEEP	0	0	0	11	296	AA	0.993072	0.454585	0		+	3	60	106	0	0	8.360715	17	60	495	45	ENST00000308924.4	0.15	0.457757
RFPL4A	342931	__UNKNOWN__	__UNKNOWN__	19	56273155	56273155	__UNKNOWN__	Intron	SNP	T	T	C	rs62126990		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:56273155T>C	ENST00000434937.2	+	2	162					NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	NA		NA					zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TTTTTTTCTATAGACATTTGC	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													7	5	6			NA	NA	19		NA											NA				56273155		608	1394	2002	SO:0001627	intron_variant				CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638	342931		RING-type (C3HC4) zinc fingers	16449	protein-coding gene	gene with protein product		612601	ret finger protein-like 4	RFPL4	NA	11850190	Standard	XM_292796	NM_001145014	NA	Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.-9-3T>C	chr19.hg19:g.56273155T>C		NA		hg19	CCDS46201.1	0.02	-0.298207	CTAxAGA	COVERED																																																																																			NOVEL	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000384184.1	3	3.307558	KEEP	2	0	0	11	292	TT	0.993072	0.775649	0		+	3	33	101	0	0	7.167941	30	60	902	68	ENST00000434937.2	0.090909	0.78106
NLRP11	204801	__UNKNOWN__	__UNKNOWN__	19	56346838	56346838	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:56346838G>A	ENST00000443188.1	-	1	427				NLRP11_ENST00000360133.3_Intron	NM_145007.3	NP_659444.2	P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	NA		NA					ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		aggccgaggcgggcagatcac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873	204801		Nucleotide-binding domain and leucine rich repeat containing	22945	protein-coding gene	gene with protein product	nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11	609664	NACHT, leucine rich repeat and PYD containing 11	NALP11	NA	12563287, 12019269	Standard	NM_145007	NM_145007	NA	Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000443188.1:c.283+863C>T	chr19.hg19:g.56346838G>A		NA	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	hg19	CCDS12935.1	0.02	-0.140318	GGCxGGC	UNCOVERED																																																																																			NOVEL	NLRP11-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		10	2.706787	KEEP	5	0	0	9	262	GG	0	0	0		-	4	29	119	0	0	10.031424	11	60	344	40	ENST00000443188.1	0.266667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	57522822	57522822	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:57522822T>C			NA	NA				MIMT1 (162898 upstream) : USP29 (108588 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.57522822T>C		NA		hg19		0.02	-0.122766	AGGxGTG	COVERED																																																																																			NOVEL					0			10	3.602982	KEEP	0	0	0	12	315	TT	0.993634	0.195062	0			3	60	85	0	0	6.882468	10	60	286	33		0.230769	0.196312
AC003002.4	0	__UNKNOWN__	__UNKNOWN__	19	57897383	57897383	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:57897383T>G	ENST00000597658.1	+	4	301										NA		NA									NA						ctcatgcctgtaatcccagca	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000597658.1:c.152-12415T>G	chr19.hg19:g.57897383T>G		NA		hg19		0.02	-0.201715	CTGxAAT	COVERED																																																																																			NOVEL	AC003002.4-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000465945.1	9	4.508954	KEEP	4	0	0	15	385	TT	0.993072	0.487146	0		+	3	30	102	0	0	7.892156	18	60	521	61	ENST00000597658.1	0.142857	0.490544
AC003006.7	0	__UNKNOWN__	__UNKNOWN__	19	58248903	58248903	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:58248903T>G	ENST00000594684.1	+	2	200				AC003006.7_ENST00000599221.1_Intron						NA		NA									NA						aaagtgctggtattacaggcg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000594684.1:c.34-13250T>G	chr19.hg19:g.58248903T>G		NA		hg19		0.02	-0.122779	TGGxATT	COVERED																																																																																			NOVEL	AC003006.7-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000466815.1	4	2.405835	KEEP	0	0	0	8	215	TT	0.99257	0.194853	0		+	3	60	89	0	0	7.401369	9	60	258	35	ENST00000594684.1	0.25	0.196312
ZNF587	84914	__UNKNOWN__	__UNKNOWN__	19	58374666	58374666	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:58374666A>T	ENST00000339656.5	+	0	5068				ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000419854.1_3'UTR|ZNF814_ENST00000597832.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		ttgtatttttagcagagacca	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(59;641 1233 1885 20055 50741)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466	84914		Zinc fingers, C2H2-type, -	30955	protein-coding gene	gene with protein product		NA			NA	10520746	Standard	NM_032828	NM_032828	NA	Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.*3158A>T	chr19.hg19:g.58374666A>T		NA	A0AV72|G3V0H5|Q6ZMK8	hg19	CCDS12964.1	0.02	-0.280603	TTTxGCA	COVERED																																																																																			NOVEL	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000337594.2	4	3.638086	KEEP	0	1	28	22	577	AA	0.999909	0.760818	0		+	8	60	238	0	0	20.492658	19	60	532	75	ENST00000339656.5	0.296296	0.760887
CTD-2368P22.1	0	__UNKNOWN__	__UNKNOWN__	19	58518205	58518205	__UNKNOWN__	3'UTR	SNP	G	G	A	rs142506380|rs386811372	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:58518205G>A	ENST00000550135.1	+	0	2043										NA		NA									NA						gcattgagccgagattgcgcc	0.478		NA											G|||	10	0.00199681	0.0061	0.0	5008	,	,	NA	17041	0.0	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000550135.1:c.*838G>A	chr19.hg19:g.58518205G>A		NA		hg19		0.02	0.934957	GCCxAGA	COVERED																																																																																			NOVEL	CTD-2368P22.1-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000405971.1	24	10.685265	KEEP	2	5	137	84	2353	GG	1	0.999948	0		+	5	60	131	1	0	7.319137	78	60	2468	237	ENST00000550135.1	0.060241	0.999948
CTD-2368P22.1	0	__UNKNOWN__	__UNKNOWN__	19	58521542	58521542	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:58521542C>T	ENST00000550135.1	+	0	5380										NA		NA									NA						aacctccgccccccaggttca	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant											NA			NA				NA			NA					NA						ENST00000550135.1:c.*4175C>T	chr19.hg19:g.58521542C>T		NA		hg19		0.02	-0.175436	GCCxCCC	COVERED																																																																																			NOVEL	CTD-2368P22.1-001	PUTATIVE	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000405971.1	2	3.610566	KEEP	0	0	0	12	365	CC	0.993634	0.38494	0		+	4	60	122	0	0	9.862572	15	60	492	41	ENST00000550135.1	0.210526	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	58672447	58672447	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:58672447A>G			NA	NA				ZNF329 (10302 upstream) : ZNF274 (21948 downstream)						NA		NA									NA						ccaggagttcaagaccagcct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.58672447A>G		NA		hg19		0.02	-0.122784	TTCxAGA	COVERED																																																																																			NOVEL					0			5	3.306065	KEEP	0	0	0	11	285	AA	0.993072	0.194952	0			3	60	98	0	0	8.073036	11	60	317	30		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	19	58835556	58835556	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr19:58835556A>G			NA	NA				ERVK3-1 (8533 upstream) : ZSCAN22 (2828 downstream)						NA		NA									NA						acaggcatgaaccaccgtgcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr19.hg19:g.58835556A>G		NA		hg19		0.02	-0.175411	TGAxCCA	COVERED																																																																																			NOVEL					0			8	3.307484	KEEP	5	0	0	11	295	AA	0.99254	0.384517	0			3	60	110	0	0	9.078845	13	60	382	47		0.1875	0.387407
CSNK2A1	1457	__UNKNOWN__	__UNKNOWN__	20	486026	486026	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:486026T>C	ENST00000217244.3	-	4	477				CSNK2A1_ENST00000400227.3_Intron|CSNK2A1_ENST00000400217.2_Intron|CSNK2A1_ENST00000349736.5_Intron	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	NA		NA			axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			tttttggagatggagtctcac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266	1457			2457	protein-coding gene	gene with protein product		115440			NA	2174700, 1766873	Standard	NM_001895	NM_177559	NA	Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.102-153A>G	chr20.hg19:g.486026T>C		NA	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	hg19	CCDS13003.1	0.02	-0.052624	AGAxGGA	UNCOVERED																																																																																			NOVEL	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077466.1	4	3.007944	KEEP	4	0	0	10	281	TT	0.99257	0.036492	0		-	2	58	72	0	0	6.950342	2	60	58	20	ENST00000217244.3	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	740672	740672	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:740672T>C			NA	NA				SCRT2 (83849 upstream) : SLC52A3 (51 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.740672T>C		NA		hg19		0.02	-0.359531	AGGxGTG	COVERED																																																																																			NOVEL					0			9	4.262391	KEEP	2	2	59	35	897	TT	0.999999	0.899313	0			3	60	101	0	0	7.011985	34	60	973	105		0.081081	0.899314
RSPO4	343637	__UNKNOWN__	__UNKNOWN__	20	947492	947492	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:947492A>G	ENST00000217260.4	-	3	506				RSPO4_ENST00000400634.2_Intron	NM_001029871.3	NP_001025042.2	Q2I0M5	RSPO4_HUMAN	R-spondin 4	NA		NA			Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	heparin binding (GO:0008201)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						gtgagaccctatctcaaacaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK122609	CCDS42845.1, CCDS42846.1	20p13	2014-01-30	2011-06-29	2005-08-08	ENSG00000101282	ENSG00000101282	343637		Endogenous ligands	16175	protein-coding gene	gene with protein product		610573	chromosome 20 open reading frame 182, R-spondin family, member 4	C20orf182	NA	15469841	Standard	XM_297816	NM_001029871	NA	Approved	dJ824F16.3	uc002wej.3	Q2I0M5	OTTHUMG00000031651	ENST00000217260.4:c.409+324T>C	chr20.hg19:g.947492A>G		NA	A2A2I6|Q9UGB2	hg19	CCDS42846.1	0.02	-0.043856	CCTxTCT	UNCOVERED																																																																																			NOVEL	RSPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077492.3	3	2.706535	KEEP	0	0	0	9	244	AA	0.99254	0.023894	0		-	2	60	70	0	0	6.750419	2	60	57	20	ENST00000217260.4	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	2237254	2237254	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:2237254C>T			NA	NA				RP11-128M1.1 (43457 upstream) : TGM3 (39392 downstream)						NA		NA									NA						ccaaggcgggcggatcacctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.2237254C>T		NA		hg19		0.02	-0.20175	GGGxGGA	COVERED																																																																																			NOVEL					0			25	3.641744	KEEP	23	1	28	22	650	CC	0.995343	0.48826	0			3	60	88	0	0	6.710555	15	60	496	91		0.166667	0.490544
C20orf194	25943	__UNKNOWN__	__UNKNOWN__	20	3253084	3253084	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:3253084A>G	ENST00000252032.9	-	30	2718				C20orf194_ENST00000453730.2_Intron	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	NA		NA								NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						tgttgcccagactggtctcaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854	25943			17721	protein-coding gene	gene with protein product		614146			NA		Standard	NM_001009984	NM_001009984	NA	Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.2651-1876T>C	chr20.hg19:g.3253084A>G		NA	Q66K86|Q6P2R9|Q9UFX9	hg19	CCDS42851.1	0.02	-0.061398	CAGxCTG	UNCOVERED																																																																																			NOVEL	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077734.1	5	3.608317	KEEP	0	0	0	12	318	AA	0.994391	0.043541	0		-	2	60	72	0	0	6.495941	4	60	120	29	ENST00000252032.9	0.333333	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	3697891	3697891	__UNKNOWN__	IGR	SNP	T	T	G	rs6076543	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:3697891T>G			NA	NA				SIGLEC1 (10116 upstream) : HSPA12B (15422 downstream)						NA		NA									NA						tcccagctactcgggaggctg	0.622		NA											C|||	2425	0.484225	0.4939	0.6081	5008	,	,	NA	15385	0.3026	NA	0.5199	False	NA	,,,	NA	NA	NA	2504	0.5337	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.3697891T>G		NA		hg19		0.02	-0.052632	TACxCGG	UNCOVERED																																																																																			NOVEL					0			21	3.07342	KEEP	20	2	59	31	880	TT	0.999859	0.03676	0			3	60	104	0	0	10.025285	3	60	91	65		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	3757446	3757446	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:3757446T>C			NA	NA				C20orf27 (8412 upstream) : SPEF1 (704 downstream)						NA		NA									NA						ctgcctcagcttcccaagtag	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.3757446T>C		NA		hg19		0.02	-0.0614	AGCxTCC	UNCOVERED																																																																																			NOVEL					0			5	2.404859	KEEP	0	0	0	8	211	TT	0.99257	0.043461	0			3	60	101	0	0	9.455292	4	60	121	19		0.428571	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	3863455	3863455	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:3863455A>G			NA	NA				MAVS (14175 upstream) : RP11-119B16.2 (5430 downstream)						NA		NA									NA						gcttgaacccaggaggcagag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.3863455A>G		NA		hg19		0.02	-0.114017	CCCxGGA	UNCOVERED																																																																																			NOVEL					0			4	2.706829	KEEP	0	0	0	9	247	AA	0.99254	0.161255	0			3	60	92	0	0	7.701158	9	60	273	30		0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	4569921	4569921	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:4569921T>C			NA	NA				RP5-1164C1.2 (64075 upstream) : PRNP (96960 downstream)						NA		NA									NA						ggcagatcacttgaggtcagg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.4569921T>C		NA		hg19		0.02	-0.078944	CACxTGA	UNCOVERED																																																																																			NOVEL					0			2	2.707412	KEEP	0	0	0	9	257	TT	0.99254	0.076759	0			3	60	105	1	0	9.443766	6	60	181	32		0.333333	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	4699497	4699497	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:4699497C>T			NA	NA				PRNP (17261 upstream) : PRND (3058 downstream)						NA		NA									NA						ctggctaacacggtgaaaccc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.4699497C>T		NA		hg19		0.02	-0.114015	ACAxGGT	UNCOVERED																																																																																			NOVEL					0			5	2.40236	KEEP	3	0	0	8	197	CC	0.99257	0.16126	0			3	46	86	0	0	6.98217	10	60	309	26		0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	5707376	5707376	__UNKNOWN__	IGR	SNP	C	C	G	rs6085255	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:5707376C>G			NA	NA				GPCPD1 (115704 upstream) : C20orf196 (23662 downstream)						NA		NA									NA						cctgtagtcccagctacttgg	0.547		NA											C|||	2476	0.494409	0.4289	0.5476	5008	,	,	NA	16021	0.371	NA	0.6243	False	NA	,,,	NA	NA	NA	2504	0.5389	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.5707376C>G		NA		hg19		0.02	-0.052632	TCCxAGC	UNCOVERED																																																																																			NOVEL					0			5	2.407238	KEEP	4	0	0	8	247	CC	0	0	0			3	60	94	0	0	9.853838	1	60	32	19		0.75	0.036766
C20orf196	149840	__UNKNOWN__	__UNKNOWN__	20	5804348	5804348	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:5804348C>T	ENST00000303142.6	+	3	265					NM_152504.2	NP_689717.2	Q8IYI0	CT196_HUMAN	chromosome 20 open reading frame 196	NA		NA								endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	9						cccacctcagcctcccacact	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK057796	CCDS13091.1	20p12.3	2006-07-07			ENSG00000171984	ENSG00000171984	149840			26318	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_152504	NM_152504	NA	Approved	FLJ25067	uc002wmf.3	Q8IYI0	OTTHUMG00000031813	ENST00000303142.6:c.179-39322C>T	chr20.hg19:g.5804348C>T		NA	A8K9J3|Q5TGA9|Q96LU1	hg19	CCDS13091.1	0.02	-0.052618	CAGxCTC	UNCOVERED																																																																																			NOVEL	C20orf196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077882.2	5	3.310015	KEEP	2	0	0	11	344	CC	0.992708	0.036498	0		+	3	60	84	0	0	8.023812	3	60	99	24	ENST00000303142.6	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	5983735	5983735	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:5983735A>G			NA	NA				RN7SL498P (1061 upstream) : CRLS1 (3000 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.5983735A>G		NA		hg19		0.02	-0.096485	CACxCCT	UNCOVERED																																																																																			NOVEL					0			6	2.393147	KEEP	0	0	0	8	197	AA	0.99257	0.119541	0			3	60	100	0	0	8.778709	7	60	213	28		0.3	0.120436
PLCB1	23236	__UNKNOWN__	__UNKNOWN__	20	8409134	8409134	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:8409134T>C	ENST00000338037.6	+	3	273				PLCB1_ENST00000378637.2_Intron|PLCB1_ENST00000378641.3_Intron	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	NA		NA			activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						tcccaaagtgttgggattata	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	23236	3.1.4.11		15917	protein-coding gene	gene with protein product		607120			NA	10760467, 11118617	Standard		NM_015192	NA	Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.246+57037T>C	chr20.hg19:g.8409134T>C		NA	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	hg19	CCDS13102.1	0.02	-0.184103	GTGxTGG	UNCOVERED																																																																																			NOVEL	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077938.3	6	2.404781	KEEP	3	0	0	8	214	TT	0	0	0		+	3	60	89	0	0	6.670097	17	60	512	49	ENST00000338037.6	0.15	0.423478
PLCB4	5332	__UNKNOWN__	__UNKNOWN__	20	9273868	9273868	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:9273868T>A	ENST00000334005.3	+	3	216				PLCB4_ENST00000278655.4_Intron|PLCB4_ENST00000378473.3_Intron			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	NA		NA			inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						gaaggaaggatggaaggaagg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	5332	3.1.4.11		9059	protein-coding gene	gene with protein product		600810			NA	8530101	Standard		NM_000933	NA	Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000334005.3:c.-15-14579T>A	chr20.hg19:g.9273868T>A		NA	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	hg19	CCDS13104.1	0.02	-0.22799	GGAxGGA	COVERED																																																																																			NOVEL	PLCB4-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding		7	5.143042	KEEP	0	1	19	24	630	TT	0.999931	0.612365	0		+	4	60	124	0	0	9.46307	22	60	621	70	ENST00000334005.3	0.153846	0.612407
SLX4IP	128710	__UNKNOWN__	__UNKNOWN__	20	10425047	10425047	__UNKNOWN__	Intron	SNP	C	C	G	rs6074142	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:10425047C>G	ENST00000334534.5	+	1	151					NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	NA		NA									NA						tttttttgagctggagtctcg	0.498		NA											G|||	1780	0.355431	0.2693	0.4611	5008	,	,	NA	16467	0.1518	NA	0.6034	False	NA	,,,	NA	NA	NA	2504	0.3517	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL035456	CCDS33439.1	20p12	2012-10-30	2012-10-30	2012-10-30	ENSG00000149346	ENSG00000149346	128710			16225	protein-coding gene	gene with protein product		615958	chromosome 20 open reading frame 94	C20orf94	NA	19596235	Standard	NM_001009608	XM_005260664	NA	Approved	dJ1099D15.3	uc010zre.2	Q5VYV7	OTTHUMG00000031873	ENST00000334534.5:c.-30+8946C>G	chr20.hg19:g.10425047C>G		NA	Q05CG2|Q05CT9	hg19	CCDS33439.1	0.02	-0.07895	GAGxTGG	UNCOVERED																																																																																			NOVEL	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078000.3	8	2.70828	KEEP	1	0	0	9	284	CC	0.99257	0.119541	0		+	4	60	137	0	0	12.923397	5	60	165	28	ENST00000334534.5	0.444444	0.120436
BTBD3	22903	__UNKNOWN__	__UNKNOWN__	20	11899644	11899644	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:11899644C>T	ENST00000405977.1	+	3	951				BTBD3_ENST00000399006.2_Intron|BTBD3_ENST00000254977.3_Intron|BTBD3_ENST00000378226.2_Intron	NM_001282550.1|NM_001282552.1|NM_001282554.1	NP_001269479.1|NP_001269481.1|NP_001269483.1	Q9Y2F9	BTBD3_HUMAN	BTB (POZ) domain containing 3	NA		NA			cerebral cortex development (GO:0021987)|dendrite morphogenesis (GO:0048813)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(18)|ovary(3)|skin(2)	34						TGTTGCTTAGCTTGCAAGTCT	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB023169	CCDS13113.1, CCDS13114.1	20p12.2	2013-01-08			ENSG00000132640	ENSG00000132640	22903		BTB/POZ domain containing	15854	protein-coding gene	gene with protein product		615566			NA		Standard		NM_001282551	NA	Approved	KIAA0952, dJ742J24.1	uc002wnz.3	Q9Y2F9	OTTHUMG00000031889	ENST00000405977.1:c.327-90C>T	chr20.hg19:g.11899644C>T		NA	D3DW19|Q5JY73	hg19	CCDS13113.1	0.02	1.196991	TAGxTTG	COVERED																																																																																			NOVEL	BTBD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078021.3	8	11.132173	KEEP	0	0	0	37	1131	CC	1	0.995686	0		+	6	60	180	0	0	12.178798	59	60	2049	156	ENST00000405977.1	0.092308	0.995687
TASP1	55617	__UNKNOWN__	__UNKNOWN__	20	13569957	13569957	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:13569957A>G	ENST00000337743.4	-	5	403				TASP1_ENST00000539805.1_Intron|TASP1_ENST00000480436.1_Intron	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	NA		NA			positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)			NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						cacccgcctcagcctcccaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	55617	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	chromosome 20 open reading frame 13	C20orf13	NA	14636557	Standard	NM_017714	XR_430268	NA	Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.283-1940T>C	chr20.hg19:g.13569957A>G		NA	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	hg19	CCDS13116.1	0.02	-0.070167	CTCxGCC	UNCOVERED																																																																																			NOVEL	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078041.2	7	2.40573	KEEP	5	0	0	8	220	AA	0	0	0		-	2	60	72	0	0	6.496078	4	60	118	26	ENST00000337743.4	0.333333	0.054137
SEL1L2	80343	__UNKNOWN__	__UNKNOWN__	20	13884919	13884919	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:13884919G>A	ENST00000284951.5	-	5	624				SEL1L2_ENST00000378072.5_Intron|SEL1L2_ENST00000486903.1_Intron			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	NA		NA				integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						tcacgcctgtgatcccagcac	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251	80343			15897	protein-coding gene	gene with protein product		614289	chromosome 20 open reading frame 50	C20orf50	NA		Standard	NM_025229	NM_001271539	NA	Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.549+9508C>T	chr20.hg19:g.13884919G>A		NA	B4DXX5	hg19		0.02	-0.087716	TGTxATC	UNCOVERED																																																																																			NOVEL	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078067.3	5	3.309869	KEEP	0	0	0	11	337	GG	0.993072	0.09903	0		-	3	60	85	0	0	7.443006	6	60	203	32	ENST00000284951.5	0.333333	0.099721
RRBP1	6238	__UNKNOWN__	__UNKNOWN__	20	17639804	17639804	__UNKNOWN__	Intron	SNP	T	T	C	rs375708430		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:17639804T>C	ENST00000360807.4	-	3	817				RRBP1_ENST00000377807.2_Intron|RRBP1_ENST00000377813.1_Missense_Mutation_p.K450R|RRBP1_ENST00000246043.4_Missense_Mutation_p.K450R|RRBP1_ENST00000455029.2_Intron	NM_004587.2	NP_004578	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	NA		NA			osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						CTCGGCCTTCTTGCCCTGGTT	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844	6238			10448	protein-coding gene	gene with protein product		601418	ribosome binding protein 1 (dog 180kD homolog), ribosome binding protein 1 homolog 180kDa (dog)		NA	8812507	Standard	NM_001042576	NM_001042576	NA	Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000360807.4:c.529-470A>G	chr20.hg19:g.17639804T>C		NA	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	hg19	CCDS13128.1	0.02	5.645614	TTCxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	T	14.87	2.663798	0.47572	.	.	ENSG00000125844	ENST00000377813;ENST00000246043	T;T	0.57907	0.37;0.37	4.75	1.01	0.19927	.	0.204964	0.24305	N	0.039685	T	0.45256	0.1333	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33189	-0.9878	7	0.35671	T	0.21	-24.6628	8.0916	0.30803	0.0:0.3461:0.0:0.6539	.	.	.	.	R	450	ENSP00000367044:K450R;ENSP00000246043:K450R	ENSP00000246043:K450R	K	-	2	0	RRBP1	17587804	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-1.465000	0.02357	0.036000	0.15547	-0.375000	0.07067	AAG	NOVEL	RRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078124.4	7	3.737831	KEEP	31	4	127	57	1540	TT	1	1	0		-	8	52	259	0	0	16.237042	139	60	4111	463	ENST00000360807.4	0.054422	1
RRBP1	6238	__UNKNOWN__	__UNKNOWN__	20	17639807	17639807	__UNKNOWN__	Intron	SNP	C	C	T	rs78244614	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:17639807C>T	ENST00000360807.4	-	3	817				RRBP1_ENST00000377807.2_Intron|RRBP1_ENST00000377813.1_Missense_Mutation_p.G449D|RRBP1_ENST00000246043.4_Missense_Mutation_p.G449D|RRBP1_ENST00000455029.2_Intron	NM_004587.2	NP_004578	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	NA		NA			osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						GGCCTTCTTGCCCTGGTTCTG	0.642		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844	6238			10448	protein-coding gene	gene with protein product		601418	ribosome binding protein 1 (dog 180kD homolog), ribosome binding protein 1 homolog 180kDa (dog)		NA	8812507	Standard	NM_001042576	NM_001042576	NA	Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000360807.4:c.529-473G>A	chr20.hg19:g.17639807C>T		NA	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	hg19	CCDS13128.1	0.02	3.961684	TTGxCCT	COVERED	.	.	.	.	.	.	.	.	.	.	C	15.26	2.781767	0.49891	.	.	ENSG00000125844	ENST00000377813;ENST00000246043	T;T	0.65549	-0.16;-0.16	4.75	3.78	0.43462	.	0.000000	0.36591	N	0.002516	T	0.58308	0.2113	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.52335	-0.8589	7	0.45353	T	0.12	-19.7075	8.2523	0.31735	0.0:0.8111:0.0:0.1889	.	.	.	.	D	449	ENSP00000367044:G449D;ENSP00000246043:G449D	ENSP00000246043:G449D	G	-	2	0	RRBP1	17587807	0.000000	0.05858	0.011000	0.14972	0.007000	0.05969	-0.437000	0.06914	1.293000	0.44690	0.561000	0.74099	GGC	NOVEL	RRBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078124.4	7	8.393217	KEEP	32	3	81	57	1724	CC	1	1	0		-	19	55	504	1	0	34.681819	132	60	4595	464	ENST00000360807.4	0.125828	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	18108819	18108819	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:18108819A>T			NA	NA				Y_RNA (14596 upstream) : PET117 (9697 downstream)						NA		NA									NA						accaacatggagaaaccccgt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.18108819A>T		NA		hg19		0.02	-0.087708	TGGxGAA	UNCOVERED																																																																																			NOVEL					0			1	3.608571	KEEP	2	0	0	12	326	AA	0.992708	0.098994	0			3	60	89	0	0	7.678527	7	60	210	28		0.3	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	18972823	18972823	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:18972823A>G			NA	NA				C20orf78 (162026 upstream) : AL136090.1 (133605 downstream)						NA		NA									NA						aacacagggaaaccccgtctc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.18972823A>G		NA		hg19		0.02	-0.131557	GGAxACC	COVERED																																																																																			NOVEL					0			7	7.217446	KEEP	0	0	0	24	655	AA	0.999909	0.229152	0			3	60	97	0	0	7.872391	12	60	353	60		0.2	0.229173
RIN2	54453	__UNKNOWN__	__UNKNOWN__	20	19918902	19918902	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:19918902A>G	ENST00000255006.6	+	3	454				RIN2_ENST00000484638.1_Intron|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	NA		NA			endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						tcactctgttacccaggctgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669	54453			18750	protein-coding gene	gene with protein product		610222			NA	11733506, 1849280, 16423831	Standard		NM_018993	NA	Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.305+3059A>G	chr20.hg19:g.19918902A>G		NA	Q00425|Q5TFT8|Q9BQL3|Q9H071	hg19	CCDS56182.1	0.02	-0.105251	GTTxCCC	UNCOVERED																																																																																			NOVEL	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078212.1	7	2.40508	KEEP	1	0	0	8	210	AA	0	0	0		+	3	60	108	0	0	9.743889	6	60	176	28	ENST00000255006.6	0.333333	0.139832
RIN2	54453	__UNKNOWN__	__UNKNOWN__	20	19966360	19966360	__UNKNOWN__	Intron	SNP	A	A	T	rs6046516	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:19966360A>T	ENST00000255006.6	+	9	2058				RIN2_ENST00000484638.1_Intron|RIN2_ENST00000440354.2_Intron	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	NA		NA			endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						tctcaacaacagcaacaacaa	0.468		NA											A|||	2529	0.504992	0.6672	0.4914	5008	,	,	NA	18537	0.6865	NA	0.2793	False	NA	,,,	NA	NA	NA	2504	0.3405	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669	54453			18750	protein-coding gene	gene with protein product		610222			NA	11733506, 1849280, 16423831	Standard		NM_018993	NA	Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.1910-4290A>T	chr20.hg19:g.19966360A>T		NA	Q00425|Q5TFT8|Q9BQL3|Q9H071	hg19	CCDS56182.1	0.02	-0.114025	AACxGCA	UNCOVERED																																																																																			NOVEL	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078212.1	5	2.70728	KEEP	0	0	0	9	258	AA	0.99254	0.161255	0		+	8	60	248	0	0	25.816197	3	60	91	34	ENST00000255006.6	0.727273	0.162467
RALGAPA2	57186	__UNKNOWN__	__UNKNOWN__	20	20651490	20651490	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:20651490G>C	ENST00000202677.7	-	3	278					NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	NA		NA			activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						ctactcaggaggctgaggcag	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559	57186			16207	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 74	C20orf74	NA	16490346, 19520869	Standard	NM_020343	NM_020343	NA	Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.270+5389C>G	chr20.hg19:g.20651490G>C		NA	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	hg19	CCDS46584.1	0.02	-0.114037	GGAxGCT	UNCOVERED																																																																																			NOVEL	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471941.1	6	2.406925	KEEP	1	0	0	8	244	GG	0	0	0		-	3	60	96	0	0	8.232217	8	60	272	26	ENST00000202677.7	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	21627945	21627945	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:21627945T>C			NA	NA				RP5-984P4.4 (116563 upstream) : PAX1 (58351 downstream)						NA		NA									NA						tttgggaggctgaggtgggtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.21627945T>C		NA		hg19		0.02	-0.157875	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			8	2.707644	KEEP	11	0	0	9	264	TT	0	0	0			4	59	131	1	0	10.980945	13	60	401	50		0.235294	0.322807
RP4-694B14.5	0	__UNKNOWN__	__UNKNOWN__	20	25622730	25622730	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:25622730C>T	ENST00000414393.1	+	0	443				RP4-694B14.5_ENST00000439498.1_RNA|RP4-694B14.5_ENST00000420803.1_RNA|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA						NA		NA									NA						ggattacaggcgtgagccacc	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000414393.1:	chr20.hg19:g.25622730C>T		NA		hg19		0.02	-0.219238	AGGxGTG	COVERED																																																																																			NOVEL	RP4-694B14.5-004	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000078450.1	4	3.308781	KEEP	3	0	0	11	320	CC	0.99254	0.548763	0		+	3	60	88	0	0	6.366447	20	60	647	48	ENST00000414393.1	0.130435	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	25893447	25893447	__UNKNOWN__	IGR	SNP	T	T	C	rs79211734	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:25893447T>C			NA	NA				FAM182B (44661 upstream) : RP4-760C5.5 (43000 downstream)						NA		NA									NA						ccacccaccttggcctcccaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.25893447T>C		NA		hg19		0.02	-0.228035	CCTxGGC	COVERED																																																																																			NOVEL					0			16	5.41394	KEEP	2	0	0	18	505	TT	0.999366	0.582561	0			4	40	121	0	0	9.479889	18	60	537	62		0.181818	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	25900293	25900293	__UNKNOWN__	IGR	SNP	C	C	T	rs201927378		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:25900293C>T			NA	NA				FAM182B (51507 upstream) : RP4-760C5.5 (36154 downstream)						NA		NA									NA						TTTGGTTTTGCTTTCTCAAAT	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.25900293C>T		NA		hg19		0.02	1.22791	TTGxTTT	COVERED																																																																																			NOVEL					0			7	5.147544	KEEP	4	1	25	26	780	CC	0.999988	0.999714	0			7	40	201	0	0	13.102996	74	60	2526	168		0.08642	0.999726
RP4-760C5.5	0	__UNKNOWN__	__UNKNOWN__	20	25942583	25942583	__UNKNOWN__	lincRNA	SNP	G	G	A	rs73599880		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:25942583G>A	ENST00000449316.1	+	0	183										NA		NA									NA						GGTGAAAGCAgccaagtgcgg	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000449316.1:	chr20.hg19:g.25942583G>A		NA		hg19		0.02	-0.105264	GCAxCCA	UNCOVERED																																																																																			NOVEL	RP4-760C5.5-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000316666.1	8	3.008948	KEEP	0	0	0	10	310	GG	0.992708	0.138812	0		+	5	60	155	0	0	14.874337	5	60	172	34	ENST00000449316.1	0.5	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	26256172	26256172	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:26256172G>A			NA	NA				MIR663A (67258 upstream) : None (None downstream)						NA		NA									NA						tctgaacccaggaggtggagg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.26256172G>A		NA		hg19		0.02	-0.087715	CCAxGAG	UNCOVERED																																																																																			NOVEL					0			8	2.646006	KEEP	3	0	0	9	255	GG	0.99257	0.09898	0			4	60	119	0	0	11.122486	5	60	168	27		0.444444	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29546781	29546781	__UNKNOWN__	IGR	SNP	G	G	T	rs77311797		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29546781G>T			NA	NA				Y_RNA (2979 upstream) : RP4-610C12.1 (11706 downstream)						NA		NA									NA						ttctcctggggccctcatact	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29546781G>T		NA		hg19		0.02	-0.429799	GGGxCCC	COVERED																																																																																			NOVEL					0			1	2.407184	KEEP	2	0	0	8	247	GG	0.99257	0.9474	0			4	40	111	0	0	7.114143	42	60	1369	70		0.086957	0.954491
RP4-610C12.1	0	__UNKNOWN__	__UNKNOWN__	20	29586512	29586512	__UNKNOWN__	RNA	SNP	C	C	T	rs73607111	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29586512C>T	ENST00000432067.1	-	0	152										NA		NA									NA						tgtgagccatcacaccaggcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432067.1:	chr20.hg19:g.29586512C>T		NA		hg19		0.02	-0.403537	CATxACA	COVERED																																																																																			NOVEL	RP4-610C12.1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000078489.3	19	2.539554	KEEP	9	1	27	18	527	CC	0.997832	0.939699	0		-	5	60	149	0	0	10.924771	32	60	1092	104	ENST00000432067.1	0.135135	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29600729	29600729	__UNKNOWN__	IGR	SNP	T	T	G	rs376108138		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29600729T>G			NA	NA				RP4-610C12.1 (4323 upstream) : FRG1B (11127 downstream)						NA		NA									NA						caaataaaaattccccaggta	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29600729T>G		NA		hg19		0.02	-0.18417	AAAxTCC	COVERED																																																																																			NOVEL					0			11	4.209276	KEEP	6	0	0	14	370	TT	0.992708	0.42039	0			3	44	92	0	0	7.372631	12	60	349	44		0.2	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29607592	29607592	__UNKNOWN__	IGR	SNP	A	A	G	rs74967047	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29607592A>G			NA	NA				RP4-610C12.1 (11186 upstream) : FRG1B (4264 downstream)						NA		NA									NA						tgccatgattataagtttcct	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29607592A>G		NA		hg19		0.02	-0.192962	ATTxTAA	UNCOVERED																																																																																			NOVEL					0			17	3.605355	KEEP	16	0	0	12	308	AA	0	0	0			5	24	168	0	0	15.424285	8	49	236	59		0.384615	0.457757
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29612923	29612923	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29612923C>T	ENST00000278882.3	+	1	257				FRG1B_ENST00000468180.2_3'UTR|FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AGCATTTCCTCCTGGCCTCCG	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.-124+810C>T	chr20.hg19:g.29612923C>T		NA	C4AME5	hg19		0.02	6.112771	CCTxCTG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	11	6.1519	KEEP	173	4	112	60	1865	CC	1	1	0		+	13	48	398	0	0	27.660186	117	60	3958	722	ENST00000278882.3	0.1	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29613033	29613033	__UNKNOWN__	Intron	SNP	C	C	G	rs113314585		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29613033C>G	ENST00000278882.3	+	1	257				FRG1B_ENST00000468180.2_3'UTR|FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AGGAGTCTGGCCTCATGAAGA	0.438		NA											.|||	1	0.000199681	0.0008	0.0	5008	,	,	NA	17963	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.-124+920C>G	chr20.hg19:g.29613033C>G		NA	C4AME5	hg19		0.02	-0.36831	TGGxCTC	UNCOVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	1	2.406787	KEEP	26	0	0	8	234	CC	0	0	0		+	6	33	199	0	0	15.80138	29	52	923	75	ENST00000278882.3	0.171429	0.899314
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29625832	29625832	__UNKNOWN__	Intron	SNP	T	T	C	rs75914051	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29625832T>C	ENST00000278882.3	+	5	496				FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAATTAATTTTCTCTCCGTTT	0.338		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.117-41T>C	chr20.hg19:g.29625832T>C		NA	C4AME5	hg19		0.02	17.605391	TTTxCTC	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	35	18.41923	KEEP	18	9	254	151	4060	TT	1	1	0		+	16	49	513	1	0	32.650143	252	70	7431	941	ENST00000278882.3	0.059701	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29625873	29625873	__UNKNOWN__	Splice_Site	SNP	A	A	C	rs78003242	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29625873A>C	ENST00000278882.3	+	5	497	c.117A>C	c.(115-117)agA>agC	p.R39S	FRG1B_ENST00000358464.4_Splice_Site_p.R39S|FRG1B_ENST00000439954.2_Splice_Site_p.R44S			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	39		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAATGTACAGAATCGCCCTGA	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001630	splice_region_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.117-1A>C	chr20.hg19:g.29625873A>C		NA	C4AME5	hg19		0.02	25.126353	CAGxATC	COVERED	.	.	.	.	.	.	.	.	.	.	a	10.74	1.435478	0.25813	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.47869	0.83	1.68	1.68	0.24146	.	0.000000	0.85682	D	0.000000	T	0.53738	0.1815	.	.	.	0.80722	D	1	P	0.44521	0.837	P	0.55749	0.783	T	0.50767	-0.8789	8	.	.	.	.	7.3757	0.26827	1.0:0.0:0.0:0.0	.	44	F5H5R5	.	S	39;44;39	ENSP00000408863:R44S	.	R	+	3	2	FRG1B	28239534	1.000000	0.71417	0.938000	0.37757	0.022000	0.10575	1.633000	0.37113	1.028000	0.39785	0.155000	0.16302	AGA	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	58	22.778915	KEEP	17	13	414	221	6137	AA	1	1	0	Missense_Mutation	+	34	70	1181	0	0	82.99967	388	70	11855	1361	ENST00000278882.3	0.080569	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29626013	29626013	__UNKNOWN__	Intron	SNP	T	T	C	rs76825953	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29626013T>C	ENST00000278882.3	+	5	608				FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TATAAAAACTTCCTGTCAGTT	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.228+29T>C	chr20.hg19:g.29626013T>C		NA	C4AME5	hg19		0.02	1.769027	ACTxCCT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	4	4.811303	KEEP	6	0	0	16	435	TT	0.994391	0.993801	0		+	14	56	442	0	0	38.005595	36	60	1078	101	ENST00000278882.3	0.28	0.999407
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29626021	29626021	__UNKNOWN__	Intron	SNP	G	G	A	rs80220317	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29626021G>A	ENST00000278882.3	+	5	608				FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CTTCCTGTCAGTTTAACAGAA	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.228+37G>A	chr20.hg19:g.29626021G>A		NA	C4AME5	hg19		0.02	1.214683	TCAxTTT	UNCOVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	4	2.406623	KEEP	4	0	0	8	230	GG	0	0	0		+	11	56	284	0	0	24.182082	24	60	796	76	ENST00000278882.3	0.314286	0.994422
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628251	29628251	__UNKNOWN__	Missense_Mutation	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29628251A>G	ENST00000278882.3	+	6	633	c.253A>G	c.(253-255)Aat>Gat	p.N85D	FRG1B_ENST00000358464.4_Missense_Mutation_p.N85D|FRG1B_ENST00000439954.2_Missense_Mutation_p.N90D			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	85		NA						p.N85D(2)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GTTGGCCTCAAATAGCTGCTT	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	kidney(2)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.253A>G	chr20.hg19:g.29628251A>G	ENSP00000278882:p.Asn85Asp	NA	C4AME5	hg19		0.02	19.460595	TCAxATA	COVERED	.	.	.	.	.	.	.	.	.	.	a	15.78	2.933773	0.52866	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.50277	0.75	2.08	2.08	0.27032	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.46619	0.1402	.	.	.	0.45390	D	0.998378	B;B	0.26809	0.086;0.16	B;B	0.40329	0.326;0.253	T	0.51553	-0.8691	9	0.66056	D	0.02	.	8.0833	0.30758	1.0:0.0:0.0:0.0	.	90;85	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	D	85;90;85	ENSP00000408863:N90D	ENSP00000278882:N85D	N	+	1	0	FRG1B	28241912	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	8.047000	0.89440	1.208000	0.43306	0.347000	0.21830	AAT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	28	10.788084	KEEP	51	8	242	121	3386	AA	1	1	0		+	36	60	1226	0	0	86.061021	394	60	12092	1173	ENST00000278882.3	0.083721	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628261	29628261	__UNKNOWN__	Missense_Mutation	SNP	T	T	C	rs111331725		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29628261T>C	ENST00000278882.3	+	6	643	c.263T>C	c.(262-264)tTt>tCt	p.F88S	FRG1B_ENST00000358464.4_Missense_Mutation_p.F88S|FRG1B_ENST00000439954.2_Missense_Mutation_p.F93S			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	88		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATAGCTGCTTTATTAGATGC	0.363		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.263T>C	chr20.hg19:g.29628261T>C	ENSP00000278882:p.Phe88Ser	NA	C4AME5	hg19		0.02	20.186892	GCTxTAT	COVERED	.	.	.	.	.	.	.	.	.	.	t	18.59	3.656788	0.67586	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.66995	-0.24	2.08	2.08	0.27032	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.78071	0.4226	.	.	.	0.58432	D	0.999995	D;D	0.89917	0.999;1.0	D;D	0.97110	0.998;1.0	T	0.78585	-0.2147	9	0.87932	D	0	.	8.0833	0.30758	0.0:0.0:0.0:1.0	.	93;88	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	S	88;93;88	ENSP00000408863:F93S	ENSP00000278882:F88S	F	+	2	0	FRG1B	28241922	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	6.955000	0.76007	1.208000	0.43306	0.347000	0.21830	TTT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	23	22.691509	KEEP	52	4	124	119	3388	TT	1	1	0		+	28	60	968	0	0	65.268391	400	60	12480	1091	ENST00000278882.3	0.065421	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29628334	29628334	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29628334A>G	ENST00000278882.3	+	6	713				FRG1B_ENST00000358464.4_Intron|FRG1B_ENST00000439954.2_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TGATCAAGGTAATGATGCCAT	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.333+3A>G	chr20.hg19:g.29628334A>G		NA	C4AME5	hg19		0.02	5.078202	GGTxATG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	3	8.8724	KEEP	29	2	55	49	1222	AA	1	1	0		+	8	31	248	0	0	15.343848	131	60	3664	289	ENST00000278882.3	0.057554	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632551	29632551	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29632551A>G	ENST00000278882.3	+	8	805				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TATAAATTTAATAGTAAATAT	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.426-60A>G	chr20.hg19:g.29632551A>G		NA	C4AME5	hg19		0.02	1.42117	TTAxTAG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	1	3.533141	KEEP	28	1	26	21	522	AA	0.999859	0.993563	0		+	5	40	148	0	0	9.7584	54	60	1527	114	ENST00000278882.3	0.084746	0.993703
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632638	29632638	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs9647043	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29632638C>A	ENST00000278882.3	+	8	833	c.453C>A	c.(451-453)caC>caA	p.H151Q	FRG1B_ENST00000358464.4_Missense_Mutation_p.H151Q			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	151		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TCCAAGACCACAAACTTAAAA	0.294		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.453C>A	chr20.hg19:g.29632638C>A	ENSP00000278882:p.His151Gln	NA	C4AME5	hg19		0.02	17.638455	CCAxAAA	COVERED	.	.	.	.	.	.	.	.	.	.	c	7.065	0.567065	0.13560	.	.	ENSG00000149531	ENST00000278882;ENST00000358464	.	.	.	1.44	0.459	0.16678	.	0.391955	0.28360	N	0.015622	T	0.23370	0.0565	.	.	.	0.19945	N	0.99994	B	0.19331	0.035	B	0.14578	0.011	T	0.11012	-1.0605	8	0.30078	T	0.28	.	5.6181	0.17442	0.0:0.799:0.0:0.201	rs9647043;rs57196803	151	Q9BZ01	FRG1B_HUMAN	Q	151	.	ENSP00000278882:H151Q	H	+	3	2	FRG1B	28246299	0.988000	0.35896	0.998000	0.56505	0.964000	0.63967	0.124000	0.15728	0.179000	0.19938	0.398000	0.26397	CAC	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	25	5.047856	KEEP	154	13	363	145	4471	CC	1	1	0		+	62	70	1949	1	0	147.74886	364	60	12516	1253	ENST00000278882.3	0.14554	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632704	29632704	__UNKNOWN__	Missense_Mutation	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29632704T>A	ENST00000278882.3	+	8	899	c.519T>A	c.(517-519)caT>caA	p.H173Q	FRG1B_ENST00000358464.4_Missense_Mutation_p.H173Q			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	173		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GATTTTTGCATGAGACGCTTC	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001583	missense					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.519T>A	chr20.hg19:g.29632704T>A	ENSP00000278882:p.His173Gln	NA	C4AME5	hg19		0.02	11.013669	GCAxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	t	13.62	2.292490	0.40594	.	.	ENSG00000149531	ENST00000278882;ENST00000358464	.	.	.	1.44	0.279	0.15677	.	0.000000	0.85682	U	0.000000	T	0.62441	0.2428	.	.	.	0.48632	D	0.999689	D	0.59357	0.985	P	0.57283	0.817	T	0.60357	-0.7279	8	0.87932	D	0	.	4.1229	0.10114	0.0:0.4216:0.0:0.5784	.	173	Q9BZ01	FRG1B_HUMAN	Q	173	.	ENSP00000278882:H173Q	H	+	3	2	FRG1B	28246365	1.000000	0.71417	0.996000	0.52242	0.851000	0.48451	0.492000	0.22435	0.057000	0.16193	0.327000	0.21459	CAT	NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	8	28.840502	KEEP	87	2	54	115	3259	TT	1	1	0		+	16	49	477	0	0	28.402843	278	60	8543	788	ENST00000278882.3	0.054422	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29632784	29632784	__UNKNOWN__	Intron	SNP	C	C	G	rs6087299		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29632784C>G	ENST00000278882.3	+	8	916				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ATGTAGAAAACCTATATTCTC	0.313		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.536+63C>G	chr20.hg19:g.29632784C>G		NA	C4AME5	hg19		0.02	3.543454	AAAxCTA	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	3	5.413311	KEEP	0	0	0	18	507	CC	0.999859	0.999858	0		+	5	60	158	0	0	9.934535	80	60	2532	138	ENST00000278882.3	0.058824	0.999998
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633816	29633816	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633816G>A	ENST00000278882.3	+	9	916				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						CAGTTTTAAAGCTTTTTATAT	0.244		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.537-82G>A	chr20.hg19:g.29633816G>A		NA	C4AME5	hg19		0.02	-0.376849	AAAxCTT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	0	2.707797	KEEP	3	0	0	9	268	GG	0.99254	0.902287	0		+	4	60	127	0	0	8.965981	36	60	1146	55	ENST00000278882.3	0.1	0.909069
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633850	29633850	__UNKNOWN__	Intron	SNP	G	G	C	rs2313265|rs374283656		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633850G>C	ENST00000278882.3	+	9	916				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AATATATATGGCATGTTTTAC	0.264		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.537-48G>C	chr20.hg19:g.29633850G>C		NA	C4AME5	hg19		0.02	3.751494	ATGxCAT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	0	2.840894	KEEP	7	1	27	19	566	GG	0.99986	0.999858	0		+	7	60	226	0	0	14.965081	92	60	3028	186	ENST00000278882.3	0.070707	0.999998
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633883	29633883	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633883C>A	ENST00000278882.3	+	9	916				FRG1B_ENST00000358464.4_Intron			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TACTATTTTTCTTTGTTTAAA	0.269		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.537-15C>A	chr20.hg19:g.29633883C>A		NA	C4AME5	hg19		0.02	4.350478	TTTxTTT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	3	10.530287	KEEP	28	0	0	35	1057	CC	0.999997	0.999997	0		+	8	60	251	0	0	15.715083	128	60	4200	344	ENST00000278882.3	0.058824	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633927	29633927	__UNKNOWN__	3'UTR	SNP	C	C	A	rs62196372	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633927C>A	ENST00000278882.3	+	0	946				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						ACAGATACTGCAAATGACTGG	0.284		NA											.|||	2505	0.5002	0.5	0.5	5008	,	,	NA	53540	0.5	NA	0.499	False	NA	,,,	NA	NA	NA	2504	0.502	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*17C>A	chr20.hg19:g.29633927C>A		NA	C4AME5	hg19		0.02	10.511708	CTGxAAA	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	9	6.884098	KEEP	41	5	133	70	2078	CC	1	1	0		+	12	60	348	0	0	19.68116	237	60	8049	571	ENST00000278882.3	0.048193	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633945	29633945	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633945G>A	ENST00000278882.3	+	0	964				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TGGAATTTTTGTTTCTGCCTT	0.279		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*35G>A	chr20.hg19:g.29633945G>A		NA	C4AME5	hg19		0.02	10.175933	TTTxTTT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	14	3.380316	KEEP	47	8	202	83	2512	GG	1	1	0		+	26	60	738	1	0	47.168297	292	60	9951	717	ENST00000278882.3	0.081761	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633983	29633983	__UNKNOWN__	3'UTR	SNP	A	A	G	rs76742789	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633983A>G	ENST00000278882.3	+	0	1002				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TTTTCTGAATAAAATATTCAG	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*73A>G	chr20.hg19:g.29633983A>G		NA	C4AME5	hg19		0.02	17.461214	AATxAAA	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	14	13.156063	KEEP	32	4	123	87	2358	AA	1	1	0		+	18	60	605	0	0	36.460043	423	70	12263	888	ENST00000278882.3	0.040816	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29633992	29633992	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29633992A>G	ENST00000278882.3	+	0	1011				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TAAAATATTCAGAGGAAATGC	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*82A>G	chr20.hg19:g.29633992A>G		NA	C4AME5	hg19		0.02	18.927671	TTCxGAG	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	20	22.825768	KEEP	35	2	57	96	2719	AA	1	1	0		+	16	60	538	1	0	30.94705	468	70	14403	980	ENST00000278882.3	0.033058	1
FRG1B	284802	__UNKNOWN__	__UNKNOWN__	20	29634002	29634002	__UNKNOWN__	3'UTR	SNP	C	C	A	rs371593782		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29634002C>A	ENST00000278882.3	+	0	1021				FRG1B_ENST00000358464.4_3'UTR			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	NA		NA								endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						AGAGGAAATGCTTTTACAGAG	0.313		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant					20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531	284802			15792	other	unknown		NA	chromosome 20 open reading frame 80	C20orf80	NA		Standard	NR_003579	NR_003579	NA	Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.*92C>A	chr20.hg19:g.29634002C>A		NA	C4AME5	hg19		0.02	14.651868	ATGxTTT	COVERED																																																																																			NOVEL	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000078494.2	19	14.607615	KEEP	34	5	131	95	2933	CC	1	1	0		+	28	60	819	0	0	48.421489	474	70	16555	1006	ENST00000278882.3	0.055777	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29634034	29634034	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29634034A>G			NA	NA				FRG1B (24 upstream) : AL441988.1 (3127 downstream)						NA		NA									NA						TTGTGAAATTATTGTTTAGCT	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29634034A>G		NA		hg19		0.02	16.887605	ATTxTTG	COVERED																																																																																			NOVEL					0			15	19.372469	KEEP	12	1	33	76	1993	AA	1	1	0			15	60	515	0	0	30.107846	436	70	12475	821		0.033259	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29634043	29634043	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29634043C>G			NA	NA				FRG1B (33 upstream) : AL441988.1 (3118 downstream)						NA		NA									NA						TATTGTTTAGCTAGTAGCTAG	0.308		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29634043C>G		NA		hg19		0.02	15.324884	TAGxTAG	COVERED																																																																																			NOVEL					0			14	7.954589	KEEP	11	4	106	64	1950	CC	1	1	0			23	70	739	1	0	46.567773	382	70	13173	717		0.05679	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29634075	29634075	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29634075T>A			NA	NA				FRG1B (65 upstream) : AL441988.1 (3086 downstream)						NA		NA									NA						TTAAACAAGTTTAATCAGGAT	0.313		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29634075T>A		NA		hg19		0.02	7.526488	AGTxTAA	COVERED																																																																																			NOVEL					0			7	4.575309	KEEP	6	2	50	33	922	TT	0.999999	0.999999	0			13	60	378	0	0	21.500699	253	60	7665	432		0.048872	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29636583	29636583	__UNKNOWN__	IGR	SNP	C	C	A	rs6118921		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29636583C>A			NA	NA				FRG1B (2573 upstream) : AL441988.1 (578 downstream)						NA		NA									NA						cctctgtaatcccagaacttt	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29636583C>A		NA		hg19		0.02	1.385959	AATxCCA	COVERED																																																																																			NOVEL					0			27	11.398345	KEEP	1	2	48	55	1682	CC	1	0.997163	0			6	60	177	0	0	13.685249	28	60	901	181		0.176471	0.997163
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29636602	29636602	__UNKNOWN__	IGR	SNP	A	A	T	rs534603781|rs144102995	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29636602A>T			NA	NA				FRG1B (2592 upstream) : AL441988.1 (559 downstream)						NA		NA									NA						tttagaggccaaggcaggagg	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29636602A>T		NA		hg19		0.02	1.271945	GCCxAGG	COVERED																																																																																			NOVEL					0			36	10.622025	KEEP	1	3	84	65	1803	AA	1	0.999559	0			4	60	118	0	0	7.977432	38	60	1140	236		0.095238	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29636692	29636692	__UNKNOWN__	IGR	SNP	G	G	A	rs201260108		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29636692G>A			NA	NA				FRG1B (2682 upstream) : AL441988.1 (469 downstream)						NA		NA									NA						ttagcgtggtgcaaaaagtaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29636692G>A		NA		hg19		0.02	-0.367601	GGTxCAA	COVERED																																																																																			NOVEL					0			19	6.951525	KEEP	0	1	22	31	896	GG	0.999998	0.899312	0			4	60	113	1	0	9.302557	12	60	375	87		0.25	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29637851	29637851	__UNKNOWN__	IGR	SNP	C	C	G	rs148007340		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29637851C>G			NA	NA				AL441988.1 (551 upstream) : DEFB115 (207615 downstream)						NA		NA									NA						TCTTGGATTTCTTTCAACACC	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29637851C>G		NA		hg19		0.02	1.792094	TTTxTTT	COVERED																																																																																			NOVEL					0			4	2.40699	KEEP	1	0	0	8	242	CT	0.99254	0.988259	0			5	60	173	0	0	12.628578	45	60	1490	106		0.1	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29637965	29637965	__UNKNOWN__	IGR	SNP	G	G	A	rs6119123	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29637965G>A			NA	NA				AL441988.1 (665 upstream) : DEFB115 (207501 downstream)						NA		NA									NA						GGTATGTGCAGAGACTTCCTG	0.408		NA											.|||	680	0.135783	0.354	0.1153	5008	,	,	NA	21896	0.001	NA	0.1054	False	NA	,,,	NA	NA	NA	2504	0.0256	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29637965G>A		NA		hg19		0.02	1.286893	GCAxAGA	COVERED																																																																																			NOVEL					0			3	2.707538	KEEP	4	0	0	9	265	GG	0.99257	0.988831	0			5	60	146	0	0	9.758137	49	60	1664	110		0.092593	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29645380	29645380	__UNKNOWN__	IGR	SNP	A	A	T	rs7351999		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29645380A>T			NA	NA				AL441988.1 (8080 upstream) : DEFB115 (200086 downstream)						NA		NA									NA						agcatggcacatgtatatata	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29645380A>T		NA		hg19		0.02	-0.377092	CACxTGT	COVERED																																																																																			NOVEL					0			1	5.043028	KEEP	1	1	26	26	702	AA	0.999957	0.90903	0			4	60	113	0	0	7.976673	28	60	820	74		0.125	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29645479	29645479	__UNKNOWN__	IGR	SNP	G	G	A	rs73610054		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29645479G>A			NA	NA				AL441988.1 (8179 upstream) : DEFB115 (199987 downstream)						NA		NA									NA						atgctggcaagactgtggaga	0.348		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29645479G>A		NA		hg19		0.02	4.733113	CAAxACT	COVERED																																																																																			NOVEL					0			48	10.229619	KEEP	9	6	170	94	2884	GG	1	1	0			9	60	265	0	0	17.20535	103	60	3473	405		0.080357	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29646370	29646370	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29646370C>G			NA	NA				AL441988.1 (9070 upstream) : DEFB115 (199096 downstream)						NA		NA									NA						ggggattatgcttatccatta	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29646370C>G		NA		hg19		0.02	1.941185	ATGxTTA	COVERED																																																																																			NOVEL					0			4	5.416025	KEEP	0	0	0	18	549	CC	0.999859	0.963638	0			3	60	107	0	0	8.326313	19	60	660	87		0.136364	0.963774
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29647425	29647425	__UNKNOWN__	IGR	SNP	T	T	C	rs77496274		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29647425T>C			NA	NA				AL441988.1 (10125 upstream) : DEFB115 (198041 downstream)						NA		NA									NA						ccatatccagtGGCAAAAAAA	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29647425T>C		NA		hg19		0.02	-0.298178	CAGxGGC	COVERED																																																																																			NOVEL					0			21	3.307977	KEEP	0	0	0	11	300	TT	0.993072	0.775649	0			6	60	199	0	2	17.165393	16	60	462	58		0.272727	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29647604	29647604	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29647604G>A			NA	NA				AL441988.1 (10304 upstream) : DEFB115 (197862 downstream)						NA		NA									NA						gagagggaaggaaggaagtag	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29647604G>A		NA		hg19		0.02	-0.280689	AAGxAAG	UNCOVERED																																																																																			NOVEL					0			18	2.707891	KEEP	11	0	0	9	270	GG	0	0	0			4	41	115	1	0	9.063265	16	60	527	59		0.2	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29648605	29648605	__UNKNOWN__	IGR	SNP	C	C	T	rs201009475		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29648605C>T			NA	NA				AL441988.1 (11305 upstream) : DEFB115 (196861 downstream)						NA		NA									NA						ccattttaaccttccaagtag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29648605C>T		NA		hg19		0.02	3.043702	AACxTTC	COVERED																																																																																			NOVEL					0			45	6.385457	KEEP	3	5	147	73	2238	CC	1	0.999989	0			4	60	123	0	0	9.513648	20	60	654	242		0.166667	0.999989
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29648721	29648721	__UNKNOWN__	IGR	SNP	C	C	T	rs140755767		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29648721C>T			NA	NA				AL441988.1 (11421 upstream) : DEFB115 (196745 downstream)						NA		NA									NA						tcaagcaatcctcctgcctcg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29648721C>T		NA		hg19		0.02	5.806649	ATCxTCC	COVERED																																																																																			NOVEL					0			103	13.737213	KEEP	2	9	253	135	4166	CC	1	1	0			7	60	210	0	0	13.094389	101	60	3484	567		0.064815	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	29649525	29649525	__UNKNOWN__	IGR	SNP	T	T	C	rs377297136		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:29649525T>C			NA	NA				AL441988.1 (12225 upstream) : DEFB115 (195941 downstream)						NA		NA									NA						attcttccaattgcatattgt	0.338		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	24774	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.29649525T>C		NA		hg19		0.02	1.742673	CAAxTGC	COVERED																																																																																			NOVEL					0			7	5.746674	KEEP	0	1	28	29	804	TT	0.999997	0.999619	0			5	60	167	0	0	12.170775	42	60	1303	165		0.106383	0.999622
HM13	81502	__UNKNOWN__	__UNKNOWN__	20	30122414	30122414	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:30122414T>C	ENST00000340852.5	+	3	406				HM13_ENST00000335574.5_Intron|HM13_ENST00000398174.3_Intron|HM13_ENST00000376127.3_Intron	NM_030789.2	NP_110416.1	Q8TCT9	HM13_HUMAN	histocompatibility (minor) 13	NA		NA			membrane protein proteolysis (GO:0033619)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	aspartic endopeptidase activity, intramembrane cleaving (GO:0042500)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	12	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			ggtgaaaccctgtctctacaa	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL110115	CCDS13182.1, CCDS13183.1, CCDS42861.1	20q11.21	2012-02-21			ENSG00000101294	ENSG00000101294	81502			16435	protein-coding gene	gene with protein product	signal peptide peptidase beta, presenilin-like protein 3, intramembrane protease, signal peptide peptidase like 1	607106			NA	12077416, 14704149	Standard	NM_178580	NM_030789	NA	Approved	H13, dJ324O17.1, SPP, PSL3, IMP1, IMPAS, PSENL3, SPPL1	uc002wwc.3	Q8TCT9	OTTHUMG00000032175	ENST00000340852.5:c.283-3568T>C	chr20.hg19:g.30122414T>C		NA	B2RAY5|E1P5L3|Q15K36|Q540H8|Q5JWP2|Q5JWP3|Q5JWP4|Q5JWP5|Q7Z4F2|Q86Y35|Q95H87|Q9H110|Q9H111	hg19	CCDS13182.1	0.02	-0.105251	CCCxGTC	UNCOVERED																																																																																			NOVEL	HM13-011	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078527.2	2	2.706277	KEEP	0	0	0	9	247	TT	0.99254	0.138789	0		+	3	60	92	0	0	7.701197	9	60	270	27	ENST00000340852.5	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	30163278	30163278	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:30163278T>C			NA	NA				HM13-AS1 (2212 upstream) : RNU6-384P (5613 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.30163278T>C		NA		hg19		0.02	-0.262801	TCAxGCC	COVERED																																																																																			NOVEL					0			11	3.341339	KEEP	2	1	31	22	612	TT	0.999879	0.693584	0			3	60	90	0	0	6.397877	23	60	668	84		0.115385	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	30182116	30182116	__UNKNOWN__	IGR	SNP	C	C	T	rs113558800	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:30182116C>T			NA	NA				RNU6-384P (13121 upstream) : ID1 (10969 downstream)						NA		NA									NA						cccaaagtgccgggattacag	0.527		NA											C|||	55	0.0109824	0.0378	0.0043	5008	,	,	NA	20562	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.30182116C>T		NA		hg19		0.02	-0.175432	TGCxGGG	COVERED																																																																																			NOVEL					0			9	2.70753	KEEP	0	0	0	9	264	CC	0.99254	0.384517	0			3	60	86	0	0	6.981876	10	60	334	36		0.230769	0.387407
CCM2L	140706	__UNKNOWN__	__UNKNOWN__	20	30611788	30611788	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:30611788A>G	ENST00000262659.8	+	6	1074				CCM2L_ENST00000300415.8_Intron	NM_080625.3	NP_542192.2	Q9NUG4	CCM2L_HUMAN	cerebral cavernous malformation 2-like	NA		NA									NA						tgcctgcctcagcctcccaaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL031658	CCDS13195.1	20q11.21	2012-10-30	2012-10-30	2012-10-30	ENSG00000101331	ENSG00000101331	140706			16153	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 160	C20orf160	NA		Standard	NM_080625	NM_080625	NA	Approved	dJ310O13.5	uc002wxf.2	Q9NUG4	OTTHUMG00000032197	ENST00000262659.8:c.1069+1190A>G	chr20.hg19:g.30611788A>G		NA	Q5JYR9|Q8N5F1|Q8N6G8|Q96MD5	hg19	CCDS13195.1	0.02	-0.140321	CTCxGCC	COVERED																																																																																			NOVEL	CCM2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078594.1	6	3.308808	KEEP	1	0	0	11	311	AA	0.993072	0.259157	0		+	3	60	86	0	0	6.873659	11	60	345	46	ENST00000262659.8	0.214286	0.260965
ASXL1	171023	__UNKNOWN__	__UNKNOWN__	20	30965478	30965478	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:30965478C>T	ENST00000375687.4	+	4	676				ASXL1_ENST00000306058.5_Intron|ASXL1_ENST00000542461.1_Intron|ASXL1_ENST00000470145.1_Intron	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	NA		NA			bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						ttttttgagacggagtctcac	0.458		NA	F, N, Mis		MDS, CMML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456	171023			18318	protein-coding gene	gene with protein product		612990	additional sex combs like 1 (Drosophila)		NA	12657473	Standard	NM_015338	NM_015338	NA	Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.252+8552C>T	chr20.hg19:g.30965478C>T		NA	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	hg19	CCDS13201.1	0.02	-0.078944	AGAxGGA	UNCOVERED																																																																																			NOVEL	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078624.2	5	2.406539	KEEP	1	0	0	8	229	CC	0	0	0		+	3	60	90	0	0	7.943031	6	60	202	24	ENST00000375687.4	0.333333	0.077336
ASXL1	171023	__UNKNOWN__	__UNKNOWN__	20	30967401	30967401	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:30967401T>G	ENST00000375687.4	+	4	676				ASXL1_ENST00000306058.5_Intron|ASXL1_ENST00000542461.1_Intron|ASXL1_ENST00000470145.1_Intron	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	NA		NA			bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						ggctgaggtgtgtggatcacc	0.507		NA	F, N, Mis		MDS, CMML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456	171023			18318	protein-coding gene	gene with protein product		612990	additional sex combs like 1 (Drosophila)		NA	12657473	Standard	NM_015338	NM_015338	NA	Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.252+10475T>G	chr20.hg19:g.30967401T>G		NA	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	hg19	CCDS13201.1	0.02	-0.03509	GTGxGTG	UNCOVERED																																																																																			NOVEL	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078624.2	4	2.406006	KEEP	0	0	0	8	222	TT	0.99257	0.019833	0		+	2	60	73	0	0	7.425065	1	60	30	17	ENST00000375687.4	0.666667	0.019982
C20orf112	0	__UNKNOWN__	__UNKNOWN__	20	31113838	31113838	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:31113838A>G	ENST00000201961.2	-	2	415				C20orf112_ENST00000375678.3_Intron			Q96MY1	NOL4L_HUMAN		NA		NA				cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						tgggattacaagcatgagcca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000201961.2:c.195+1722T>C	chr20.hg19:g.31113838A>G		NA	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	hg19		0.02	-0.263131	ACAxGCA	COVERED																																																																																			NOVEL	C20orf112-002	KNOWN	basic|appris_candidate_longest	protein_coding	NA	protein_coding	OTTHUMT00000078629.3	8	3.910299	KEEP	1	0	0	13	364	AA	0.994391	0.689777	0		-	3	60	107	0	0	8.094221	23	60	688	68	ENST00000201961.2	0.115385	0.693668
EFCAB8	388795	__UNKNOWN__	__UNKNOWN__	20	31488654	31488654	__UNKNOWN__	Intron	SNP	G	G	C	rs6120031	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:31488654G>C	ENST00000400522.4	+	11	1182							A8MWE9	EFCB8_HUMAN	EF-hand calcium binding domain 8	NA		NA					calcium ion binding (GO:0005509)			endometrium(2)	2						gattacaggcgtgagccacca	0.517		NA											G|||	1317	0.262979	0.416	0.1744	5008	,	,	NA	14553	0.2044	NA	0.2227	False	NA	,,,	NA	NA	NA	2504	0.2209	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					20q11.21	2013-01-10			ENSG00000215529	ENSG00000215529	388795		WD repeat domain containing, EF-hand domain containing	34532	protein-coding gene	gene with protein product		NA			NA		Standard	XM_371397	XM_006710086	NA	Approved			A8MWE9	OTTHUMG00000153693	ENST00000400522.4:c.1088+2225G>C	chr20.hg19:g.31488654G>C		NA		hg19		0.02	-0.201767	GGCxTGA	UNCOVERED																																																																																			NOVEL	EFCAB8-001	PUTATIVE	mRNA_end_NF|cds_end_NF|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000332144.2	6	2.406397	KEEP	3	0	0	8	230	GG	0	0	0		+	6	60	210	0	0	18.557116	14	60	470	52	ENST00000400522.4	0.3	0.522161
BPIFB4	149954	__UNKNOWN__	__UNKNOWN__	20	31695449	31695449	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:31695449G>A	ENST00000375483.3	+	15	1744				BPIFB4_ENST00000494121.1_Intron	NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	NA		NA				cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)				NA						ctcaaaaaaagaaaaaagaaa	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF549190	CCDS13213.2	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186191	ENSG00000186191	149954		BPI fold containing	16179	protein-coding gene	gene with protein product		615718	chromosome 20 open reading frame 186	C20orf186	NA	11971875, 21787333	Standard	NM_182519	NM_182519	NA	Approved	dJ726C3.5, LPLUNC4	uc010zue.2	P59827	OTTHUMG00000032235	ENST00000375483.3:c.1745-101G>A	chr20.hg19:g.31695449G>A		NA	Q5TDX6	hg19	CCDS13213.2	0.02	3.025385	AAAxAAA	COVERED																																																																																			NOVEL	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078655.5	45	4.80263	KEEP	3	6	161	73	2293	GG	1	1	0		+	8	60	235	2	1	14.628459	110	60	3758	338	ENST00000375483.3	0.067797	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	31915183	31915183	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:31915183T>C			NA	NA				BPIFB1 (17499 upstream) : BPIFB9P (23485 downstream)						NA		NA									NA						gtaatcccagtactttgggag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.31915183T>C		NA		hg19		0.02	-0.140335	CAGxACT	UNCOVERED																																																																																			NOVEL					0			6	2.405102	KEEP	2	0	0	8	210	TT	0	0	0			3	60	103	0	0	8.572922	11	60	323	36		0.214286	0.260965
CBFA2T2	9139	__UNKNOWN__	__UNKNOWN__	20	32097388	32097388	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32097388A>C	ENST00000342704.6	+	1	215				CBFA2T2_ENST00000375279.2_Intron	NM_001032999.2	NP_001028171.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	NA		NA			epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						aatcccagcaatttgggaggc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(174;142 1955 14837 21276 28041)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699	9139		Zinc fingers, MYND-type	1536	protein-coding gene	gene with protein product		603672			NA	9790752	Standard	NM_001032999	XM_006723886	NA	Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000342704.6:c.34+19281A>C	chr20.hg19:g.32097388A>C		NA	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	hg19	CCDS46590.1	0.02	-0.21039	GCAxTTT	COVERED																																																																																			NOVEL	CBFA2T2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000471953.1	8	2.405926	KEEP	1	0	0	8	220	AA	0.99257	0.518282	0		+	4	60	141	0	0	11.569967	17	60	504	47	ENST00000342704.6	0.190476	0.522161
CHMP4B	128866	__UNKNOWN__	__UNKNOWN__	20	32406997	32406997	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32406997T>C	ENST00000217402.2	+	1	355					NM_176812.4	NP_789782.1	Q9H444	CHM4B_HUMAN	charged multivesicular body protein 4B	NA		NA			endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|positive regulation of viral release from host cell (GO:1902188)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13						ggattacaggtgtgagccacc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050349	CCDS13228.1	20q11.22	2011-09-21	2011-09-21	2005-04-04	ENSG00000101421	ENSG00000101421	128866		Charged multivesicular body proteins	16171	protein-coding gene	gene with protein product		610897	chromosome 20 open reading frame 178, chromatin modifying protein 4B	C20orf178	NA	14678797	Standard		NM_176812	NA	Approved	dJ553F4.4, Shax1, SNF7-2, VPS32B	uc002xaa.3	Q9H444	OTTHUMG00000032272	ENST00000217402.2:c.190+7533T>C	chr20.hg19:g.32406997T>C		NA	E1P5N4|Q53ZD6	hg19	CCDS13228.1	0.02	-0.228045	AGGxGTG	COVERED																																																																																			NOVEL	CHMP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078738.2	7	2.406569	KEEP	0	0	0	8	228	TT	0.99257	0.578599	0		+	3	60	97	0	0	7.39235	18	60	540	49	ENST00000217402.2	0.142857	0.58293
CHMP4B	128866	__UNKNOWN__	__UNKNOWN__	20	32410170	32410170	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32410170C>G	ENST00000217402.2	+	1	355					NM_176812.4	NP_789782.1	Q9H444	CHM4B_HUMAN	charged multivesicular body protein 4B	NA		NA			endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|positive regulation of viral release from host cell (GO:1902188)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13						aggctggtctcgaactcctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050349	CCDS13228.1	20q11.22	2011-09-21	2011-09-21	2005-04-04	ENSG00000101421	ENSG00000101421	128866		Charged multivesicular body proteins	16171	protein-coding gene	gene with protein product		610897	chromosome 20 open reading frame 178, chromatin modifying protein 4B	C20orf178	NA	14678797	Standard		NM_176812	NA	Approved	dJ553F4.4, Shax1, SNF7-2, VPS32B	uc002xaa.3	Q9H444	OTTHUMG00000032272	ENST00000217402.2:c.190+10706C>G	chr20.hg19:g.32410170C>G		NA	E1P5N4|Q53ZD6	hg19	CCDS13228.1	0.02	-0.114027	TCTxGAA	UNCOVERED																																																																																			NOVEL	CHMP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078738.2	9	3.610039	KEEP	7	0	0	12	355	CC	0.99254	0.161255	0		+	3	49	100	0	0	8.501206	9	52	287	42	ENST00000217402.2	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	32479542	32479542	__UNKNOWN__	IGR	SNP	C	C	T	rs6120410|rs570017408	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32479542C>T			NA	NA				CHMP4B (37370 upstream) : RP5-1125A11.1 (100751 downstream)						NA		NA									NA						tctttctttccttccttcctt	0.413		NA											-|||	114	0.0227636	0.0461	0.0043	5008	,	,	NA	13273	0.001	NA	0.0109	False	NA	,,,	NA	NA	NA	2504	0.0389	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.32479542C>T		NA		hg19		0.02	-0.131585	TTCxTTC	COVERED																																																																																			NOVEL					0			7	3.008035	KEEP	1	0	0	10	294	CC	0.99254	0.227464	0			3	60	90	0	0	7.172171	12	60	409	36		0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	32750533	32750533	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32750533A>G			NA	NA				EIF2S2 (50395 upstream) : ASIP (31841 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.32750533A>G		NA		hg19		0.02	-0.140308	GGCxTGA	COVERED																																																																																			NOVEL					0			2	2.237104	KEEP	0	1	30	18	487	AA	0.99986	0.260928	0			3	60	92	0	0	7.373159	12	60	353	49		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	32923271	32923271	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32923271A>G			NA	NA				AHCY (23663 upstream) : ITCH (27769 downstream)						NA		NA									NA						gctcacgcctataatcccagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.32923271A>G		NA		hg19		0.02	-0.245471	CCTxTAA	COVERED																																																																																			NOVEL					0			7	4.209711	KEEP	0	0	0	14	372	AA	0.995343	0.66541	0			3	60	95	0	0	6.844487	24	60	672	60		0.111111	0.668523
ITCH	83737	__UNKNOWN__	__UNKNOWN__	20	32955814	32955814	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:32955814T>C	ENST00000374864.4	+	2	115				ITCH_ENST00000262650.6_Intron|ITCH_ENST00000535650.1_Intron	NM_001257137.1|NM_001257138.1|NM_031483.5	NP_001244066.1|NP_001244067.1|NP_113671.3	Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	NA		NA			apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of defense response to virus (GO:0050687)|negative regulation of JNK cascade (GO:0046329)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cell growth (GO:0001558)|regulation of protein deubiquitination (GO:0090085)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	CXCR chemokine receptor binding (GO:0045236)|ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(9)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(13)|skin(1)|upper_aerodigestive_tract(1)	36						cggtggctcatgcctgtaatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF095745	CCDS13234.1, CCDS58768.1, CCDS58769.1	20q11.22	2014-09-17	2012-02-23		ENSG00000078747	ENSG00000078747	83737			13890	protein-coding gene	gene with protein product		606409	itchy (mouse homolog) E3 ubiquitin protein ligase, itchy E3 ubiquitin protein ligase homolog (mouse)		NA	11318614	Standard		NM_001257137	NA	Approved	AIP4	uc010geu.2	Q96J02	OTTHUMG00000032300	ENST00000374864.4:c.-98-1386T>C	chr20.hg19:g.32955814T>C		NA	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	hg19	CCDS13234.1	0.02	-0.245588	TCAxGCC	COVERED																																																																																			NOVEL	ITCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078782.1	10	3.006572	KEEP	1	0	0	10	267	TT	0.992708	0.63667	0		+	3	60	89	0	0	6.407721	21	60	644	61	ENST00000374864.4	0.125	0.641347
ITCH	83737	__UNKNOWN__	__UNKNOWN__	20	33098144	33098144	__UNKNOWN__	3'UTR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33098144A>T	ENST00000374864.4	+	0	5347					NM_001257137.1|NM_001257138.1|NM_031483.5	NP_001244066.1|NP_001244067.1|NP_113671.3	Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	NA		NA			apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of defense response to virus (GO:0050687)|negative regulation of JNK cascade (GO:0046329)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cell growth (GO:0001558)|regulation of protein deubiquitination (GO:0090085)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	CXCR chemokine receptor binding (GO:0045236)|ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(9)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(13)|skin(1)|upper_aerodigestive_tract(1)	36						ATGGAAATAGATTTATTGTAA	0.284		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF095745	CCDS13234.1, CCDS58768.1, CCDS58769.1	20q11.22	2014-09-17	2012-02-23		ENSG00000078747	ENSG00000078747	83737			13890	protein-coding gene	gene with protein product		606409	itchy (mouse homolog) E3 ubiquitin protein ligase, itchy E3 ubiquitin protein ligase homolog (mouse)		NA	11318614	Standard		NM_001257137	NA	Approved	AIP4	uc010geu.2	Q96J02	OTTHUMG00000032300	ENST00000374864.4:c.*2545A>T	chr20.hg19:g.33098144A>T		NA	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	hg19	CCDS13234.1	0.02	-0.412196	TAGxTTT	COVERED																																																																																			NOVEL	ITCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078782.1	3	2.405879	KEEP	0	0	0	8	219	AA	0.99257	0.934744	0		+	18	60	542	0	0	49.200968	29	60	878	82	ENST00000374864.4	0.382979	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	33103920	33103920	__UNKNOWN__	IGR	SNP	G	G	A	rs111684887|rs572210930	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33103920G>A			NA	NA				ITCH (4722 upstream) : DYNLRB1 (293 downstream)						NA		NA									NA						ggctggtctcgaactcttggg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.33103920G>A		NA		hg19		0.02	-0.149112	CTCxAAC	COVERED																																																																																			NOVEL					0			15	3.309404	KEEP	0	0	0	11	323	GG	0.993634	0.290142	0			3	60	87	0	0	7.081934	10	60	324	38		0.230769	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	33103926	33103926	__UNKNOWN__	IGR	SNP	T	T	C	rs572210930		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33103926T>C			NA	NA				ITCH (4728 upstream) : DYNLRB1 (287 downstream)						NA		NA									NA						tctcgaactcttgggctcaag	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.33103926T>C		NA		hg19		0.02	-0.140309	CTCxTGG	COVERED																																																																																			NOVEL					0			14	3.608348	KEEP	0	0	0	12	329	TT	0.993634	0.259304	0			4	60	142	0	0	12.624879	9	60	263	37		0.307692	0.260965
MAP1LC3A	84557	__UNKNOWN__	__UNKNOWN__	20	33136770	33136770	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33136770G>A	ENST00000374837.3	+	2	63					NM_181509.2	NP_852610.1	Q9H492	MLP3A_HUMAN	microtubule-associated protein 1 light chain 3 alpha	NA		NA			autophagic vacuole assembly (GO:0000045)|mitochondrion degradation (GO:0000422)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|late endosome (GO:0005770)|microtubule (GO:0005874)|organelle membrane (GO:0031090)	phosphatidylethanolamine binding (GO:0008429)|phospholipid binding (GO:0005543)			cervix(1)|kidney(1)|large_intestine(1)|upper_aerodigestive_tract(2)	5						tcggcctcccgaagtgctggg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13237.1, CCDS13238.1	20q11.22	2014-02-12			ENSG00000101460	ENSG00000101460	84557			6838	protein-coding gene	gene with protein product		601242			NA	8833088, 17580304	Standard	NM_181509	NM_032514	NA	Approved	MAP1BLC3, MAP1ALC3, LC3, LC3A, ATG8E	uc002xaq.2	Q9H492	OTTHUMG00000032306	ENST00000374837.3:c.-73-939G>A	chr20.hg19:g.33136770G>A		NA	E1P5P4|E1P5P5|Q9BXW5	hg19	CCDS13237.1	0.02	-0.210516	CCCxAAG	COVERED																																																																																			NOVEL	MAP1LC3A-001	NOVEL	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078800.1	9	4.211308	KEEP	2	0	0	14	411	GG	0.995343	0.519729	0		+	3	60	91	0	0	6.72759	19	60	623	59	ENST00000374837.3	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	33687431	33687431	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33687431C>T			NA	NA				TRPC4AP (6757 upstream) : EDEM2 (15735 downstream)						NA		NA									NA						gtgatccacccgccttggctt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.33687431C>T		NA		hg19		0.02	-0.175443	ACCxGCC	COVERED																																																																																			NOVEL					0			5	3.61056	KEEP	0	0	0	12	363	CC	0.993634	0.38494	0			3	60	89	0	0	6.733664	16	60	535	49		0.157895	0.387407
MMP24	10893	__UNKNOWN__	__UNKNOWN__	20	33837675	33837675	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33837675T>C	ENST00000246186.6	+	3	480				EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000454184.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	NA		NA			cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	ggattacaggtgtgagccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966	10893			7172	protein-coding gene	gene with protein product	membrane-type 5 matrix metalloproteinase	604871	matrix metalloproteinase 24 (membrane-inserted)		NA	10363975	Standard	NM_006690	NM_006690	NA	Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.396-2033T>C	chr20.hg19:g.33837675T>C		NA	B7ZBG8|Q9H440	hg19	CCDS46593.1	0.02	-0.175421	AGGxGTG	COVERED																																																																																			NOVEL	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078851.4	8	3.909013	KEEP	7	0	0	13	355	TT	0.994391	0.385234	0		+	3	60	101	0	0	7.933255	16	60	480	62	ENST00000246186.6	0.157895	0.387407
EIF6	3692	__UNKNOWN__	__UNKNOWN__	20	33870869	33870869	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33870869A>C	ENST00000374450.3	-	3	458				EIF6_ENST00000374436.3_Intron|EIF6_ENST00000374443.3_Intron|EIF6_ENST00000462894.1_Intron	NM_002212.3	NP_002203.1			eukaryotic translation initiation factor 6	NA		NA								central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(18;0.00252)			ccgaggtgggaggatcacctg	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y11435	CCDS13249.1, CCDS13250.1	20q11.2	2008-01-18	2007-07-27	2007-07-27	ENSG00000242372	ENSG00000242372	3692			6159	protein-coding gene	gene with protein product		602912	integrin beta 4 binding protein	EIF3A, ITGB4BP	NA	9374518, 9740680	Standard	NM_002212	NM_181468	NA	Approved	p27BBP, b(2)gcn	uc002xbz.2	P56537	OTTHUMG00000032328	ENST00000374450.3:c.193+1109T>G	chr20.hg19:g.33870869A>C		NA		hg19	CCDS13249.1	0.02	-0.201731	GGGxGGA	UNCOVERED																																																																																			NOVEL	EIF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078848.3	8	2.372004	KEEP	4	0	0	8	204	AA	0	0	0		-	4	60	127	0	0	10.169241	17	60	516	49	ENST00000374450.3	0.190476	0.490544
UQCC1	55245	__UNKNOWN__	__UNKNOWN__	20	33988577	33988577	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:33988577T>C	ENST00000374380.2	-	2	92				UQCC1_ENST00000374377.5_Intron|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374385.5_Intron|UQCC1_ENST00000542501.1_Intron|UQCC1_ENST00000359226.2_Intron|UQCC1_ENST00000407996.2_Intron|UQCC1_ENST00000491125.1_Intron|UQCC1_ENST00000374384.2_Intron|UQCC1_ENST00000349714.5_Intron|UQCC1_ENST00000397554.1_Intron	NM_001184977.1	NP_001171906.1	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	NA		NA				cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)					NA						ggattacaggtgtgagccacc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019	55245		Mitochondrial respiratory chain complex assembly factors	15891	protein-coding gene	gene with protein product	Basic FGF-repressed Zic-binding protein, cytochrome B protein synthesis 3 homolog (S. cerevisiae)	611797	chromosome 20 open reading frame 44, ubiquinol-cytochrome c reductase complex chaperone	C20orf44, UQCC	NA		Standard	NM_018244	NM_018244	NA	Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374380.2:c.25-6578A>G	chr20.hg19:g.33988577T>C		NA	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	hg19	CCDS54458.1	0.02	-0.192956	AGGxGTG	COVERED																																																																																			NOVEL	UQCC1-018	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000125984.1	17	3.309247	KEEP	8	0	0	11	319	TT	0.99254	0.454342	0		-	3	60	89	0	0	6.734766	16	60	489	52	ENST00000374380.2	0.157895	0.457757
GDF5	8200	__UNKNOWN__	__UNKNOWN__	20	34033222	34033222	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34033222T>C	ENST00000374372.1	-	2	107							P43026	GDF5_HUMAN	growth differentiation factor 5	NA		NA			cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			cctgtaatcctagcactttgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965	8200			4220	protein-coding gene	gene with protein product	cartilage-derived morphogenetic protein-1	601146			NA	9288091, 9288098	Standard		NM_000557	NA	Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.397-4028A>G	chr20.hg19:g.34033222T>C		NA	E1P5Q2|Q96SB1	hg19	CCDS13254.1	0.02	-0.166633	TCCxAGC	COVERED																																																																																			NOVEL	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078875.2	12	3.006913	KEEP	1	0	0	10	269	TT	0.99254	0.351306	0		-	3	60	96	0	0	7.772856	12	60	355	38	ENST00000374372.1	0.2	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	34121196	34121196	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34121196G>A			NA	NA				C20orf173 (3715 upstream) : ERGIC3 (8573 downstream)						NA		NA									NA						tcaccatgttgaccaggatga	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.34121196G>A		NA		hg19		0.02	-0.114039	GTTxACC	UNCOVERED																																																																																			NOVEL					0			6	2.407086	KEEP	0	0	0	8	245	GG	0.99257	0.16126	0			3	60	93	0	0	7.800969	9	60	297	30		0.25	0.162467
FER1L4	80307	__UNKNOWN__	__UNKNOWN__	20	34174622	34174622	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34174622A>G	ENST00000430275.2	-	0	2640							A9Z1Z3	FR1L4_HUMAN	fer-1-like family member 4, pseudogene (functional)	NA		NA				integral component of membrane (GO:0016021)					NA						ttgtagagatagggtctcact	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AL121586		20q11.23	2014-09-11	2014-06-27		ENSG00000088340	ENSG00000088340	80307		-	15801	pseudogene	pseudogene		NA	fer-1-like 4 (C. elegans), fer-1-like 4 (C. elegans), pseudogene (functional)	C20orf124	NA	24063685, 24961353	Standard	NR_024377	XR_425236	NA	Approved	bA563A22B.1, dJ309K20.1	uc002xcx.3	A9Z1Z3	OTTHUMG00000032354	ENST00000430275.2:	chr20.hg19:g.34174622A>G		NA	Q9GZQ9|Q9H646|Q9H8L7	hg19		0.02	-0.19294	GATxGGG	COVERED																																																																																			NOVEL	FER1L4-016	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000443297.1	10	4.208173	KEEP	1	0	0	14	370	AA	0.994391	0.455189	0		-	3	60	88	0	0	6.493397	18	60	521	45	ENST00000430275.2	0.142857	0.457757
NFS1	9054	__UNKNOWN__	__UNKNOWN__	20	34268037	34268037	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34268037T>C	ENST00000374092.4	-	7	861				NFS1_ENST00000397425.1_Intron|NFS1_ENST00000374085.1_Intron|NFS1_ENST00000541387.1_Intron|NFS1_ENST00000540053.1_Intron	NM_021100.4	NP_066923.3	Q9Y697	NFS1_HUMAN	NFS1 cysteine desulfurase	NA		NA			cysteine metabolic process (GO:0006534)|iron incorporation into metallo-sulfur cluster (GO:0018283)|Mo-molybdopterin cofactor biosynthetic process (GO:0006777)|molybdopterin cofactor biosynthetic process (GO:0032324)|protein complex assembly (GO:0006461)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine desulfurase activity (GO:0031071)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	18	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.0886)		L-Alanine(DB00160)|L-Cysteine(DB00151)	ccatcctggctaacatggtga	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF097025	CCDS13262.1, CCDS56185.1	20q11.22	2013-08-06	2013-08-06		ENSG00000244005	ENSG00000244005	9054	2.8.1.7		15910	protein-coding gene	gene with protein product		603485	nitrogen fixation 1 (S. cerevisiae, homolog), NFS1 nitrogen fixation 1 homolog (S. cerevisiae)		NA	9885568, 16847322	Standard	NM_021100	NM_021100	NA	Approved	NifS, IscS	uc002xdw.2	Q9Y697	OTTHUMG00000032361	ENST00000374092.4:c.790+621A>G	chr20.hg19:g.34268037T>C		NA	B3KMA5|B4DXK9|E1P5R8|F5GYK5|Q6P0L8|Q9NTZ5|Q9Y481	hg19	CCDS13262.1	0.02	-0.122785	GGCxAAC	COVERED																																																																																			NOVEL	NFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078936.4	1	3.605766	KEEP	1	0	0	12	300	TT	0.993634	0.195062	0		-	3	60	90	0	0	7.2731	11	60	324	32	ENST00000374092.4	0.214286	0.196312
PHF20	51230	__UNKNOWN__	__UNKNOWN__	20	34402560	34402560	__UNKNOWN__	Intron	SNP	C	C	G	rs145039857	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34402560C>G	ENST00000374012.3	+	2	212				PHF20_ENST00000481202.1_Intron|PHF20_ENST00000439301.1_Intron			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	NA		NA			chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					ctttgggaggccgaggcaggt	0.502		NA											-|||	184	0.0367412	0.0908	0.0259	5008	,	,	NA	9771	0.0	NA	0.0388	False	NA	,,,	NA	NA	NA	2504	0.0072	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293	51230		Tudor domain containing, Zinc fingers, PHD-type	16098	protein-coding gene	gene with protein product	tudor domain containing 20A	610335	chromosome 20 open reading frame 104	C20orf104	NA		Standard	NM_016436	NM_016436	NA	Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.83+13033C>G	chr20.hg19:g.34402560C>G		NA	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	hg19	CCDS13268.1	0.02	-0.201777	AGGxCGA	COVERED																																																																																			NOVEL	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078949.2	21	5.851883	KEEP	30	1	30	30	949	CC	0.99649	0.488823	0		+	4	60	141	0	0	11.393818	19	60	666	107	ENST00000374012.3	0.173913	0.490544
PHF20	51230	__UNKNOWN__	__UNKNOWN__	20	34433249	34433249	__UNKNOWN__	Intron	SNP	G	G	A	rs576489227		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34433249G>A	ENST00000374012.3	+	4	384				PHF20_ENST00000481202.1_Intron|PHF20_ENST00000439301.1_Intron			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	NA		NA			chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					atatgtatacgtgtgccatgt	0.328		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	16565	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293	51230		Tudor domain containing, Zinc fingers, PHD-type	16098	protein-coding gene	gene with protein product	tudor domain containing 20A	610335	chromosome 20 open reading frame 104	C20orf104	NA		Standard	NM_016436	NM_016436	NA	Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.256-2023G>A	chr20.hg19:g.34433249G>A		NA	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	hg19	CCDS13268.1	0.02	-0.263127	TACxTGT	COVERED																																																																																			NOVEL	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000078949.2	4	3.008137	KEEP	1	0	0	10	291	GG	0.992708	0.68861	0		+	4	60	125	0	0	9.294561	26	60	797	53	ENST00000374012.3	0.133333	0.693668
LINC00657	647979	__UNKNOWN__	__UNKNOWN__	20	34638305	34638305	__UNKNOWN__	lincRNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34638305C>T	ENST00000565493.1	-	0	577					NR_027451.1				long intergenic non-protein coding RNA 657	NA		NA									NA						CGCTCACCTTCCAGGCCCCTT	0.597		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AI619767, AK090641, BC011592		20q11.23	2012-10-12			ENSG00000260032	ENSG00000260032	647979		Long non-coding RNAs	44311	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_027451	NR_027451	NA	Approved		uc002xet.3		OTTHUMG00000175580	ENST00000565493.1:	chr20.hg19:g.34638305C>T		NA		hg19		0.02	3.026046	CTTxCAG	COVERED																																																																																			NOVEL	LINC00657-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000430538.1	3	8.425619	KEEP	7	0	0	28	887	CC	0.999997	0.999989	0		-	12	39	347	0	0	24.027512	97	60	3285	224	ENST00000565493.1	0.110092	0.999992
DLGAP4	22839	__UNKNOWN__	__UNKNOWN__	20	34987165	34987165	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:34987165G>C	ENST00000373913.3	+	2	177							Q9Y2H0	DLGP4_HUMAN	discs, large (Drosophila) homolog-associated protein 4	NA		NA			cell-cell signaling (GO:0007267)	membrane (GO:0016020)|synapse (GO:0045202)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(20)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				gagccgagatggtgccactgc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF088030	CCDS13274.1, CCDS13275.1	20q11.23	2010-02-05			ENSG00000080845	ENSG00000080845	22839			24476	protein-coding gene	gene with protein product		NA			NA	9115257	Standard	NM_014902	XM_005260329	NA	Approved	DAP4, KIAA0964, SAPAP4	uc010zvp.2	Q9Y2H0	OTTHUMG00000032390	ENST00000373913.3:c.-303-8283G>C	chr20.hg19:g.34987165G>C		NA	E1P5T5|Q5QPG4|Q5T2Y4|Q5T2Y5|Q9H137|Q9H138|Q9H1L7	hg19	CCDS13274.1	0.02	-0.035092	GATxGTG	UNCOVERED																																																																																			NOVEL	DLGAP4-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079023.1	6	2.407006	KEEP	0	0	0	8	242	GG	0.99257	0.019833	0		+	2	27	72	0	0	6.950064	2	60	71	17	ENST00000373913.3	0.5	0.019982
NDRG3	57446	__UNKNOWN__	__UNKNOWN__	20	35303853	35303853	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35303853G>A	ENST00000349004.1	-	9	613				NDRG3_ENST00000373803.2_Intron|NDRG3_ENST00000373773.3_Intron|NDRG3_ENST00000359675.2_Intron|NDRG3_ENST00000540765.1_Intron	NM_032013.3	NP_114402.1	Q9UGV2	NDRG3_HUMAN	NDRG family member 3	NA		NA			cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Myeloproliferative disorder(115;0.00878)				gcaatggcacgatctcgactc	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL031662	CCDS13284.1, CCDS13285.1	20q11.21-q11.23	2008-07-28			ENSG00000101079	ENSG00000101079	57446			14462	protein-coding gene	gene with protein product		605273			NA	10831399, 17998568	Standard		NM_032013	NA	Approved		uc002xfw.3	Q9UGV2	OTTHUMG00000032398	ENST00000349004.1:c.532-4053C>T	chr20.hg19:g.35303853G>A		NA	A2A2S8|E1P5U7|E1P5U8|Q5TH32|Q96PL8|Q96SM2|Q9BXY7|Q9H3N7|Q9H411|Q9H8J6	hg19	CCDS13285.1	0.02	-0.175342	CACxATC	COVERED																																																																																			NOVEL	NDRG3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079053.2	7	3.610179	KEEP	5	0	0	12	355	GG	0.99254	0.384517	0		-	3	60	91	0	0	7.011258	15	60	471	49	ENST00000349004.1	0.166667	0.387407
NDRG3	57446	__UNKNOWN__	__UNKNOWN__	20	35324930	35324930	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35324930T>C	ENST00000349004.1	-	4	175				NDRG3_ENST00000373803.2_Intron|NDRG3_ENST00000373773.3_Intron|NDRG3_ENST00000359675.2_Intron|NDRG3_ENST00000540765.1_Intron	NM_032013.3	NP_114402.1	Q9UGV2	NDRG3_HUMAN	NDRG family member 3	NA		NA			cell differentiation (GO:0030154)|negative regulation of cell growth (GO:0030308)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12		Myeloproliferative disorder(115;0.00878)				cggagtcttgttctgtcacca	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL031662	CCDS13284.1, CCDS13285.1	20q11.21-q11.23	2008-07-28			ENSG00000101079	ENSG00000101079	57446			14462	protein-coding gene	gene with protein product		605273			NA	10831399, 17998568	Standard		NM_032013	NA	Approved		uc002xfw.3	Q9UGV2	OTTHUMG00000032398	ENST00000349004.1:c.94-7743A>G	chr20.hg19:g.35324930T>C		NA	A2A2S8|E1P5U7|E1P5U8|Q5TH32|Q96PL8|Q96SM2|Q9BXY7|Q9H3N7|Q9H411|Q9H8J6	hg19	CCDS13285.1	0.02	-0.342053	TTGxTCT	COVERED																																																																																			NOVEL	NDRG3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079053.2	12	3.909725	KEEP	0	0	0	13	357	TT	0.994391	0.860889	0		-	5	60	174	0	0	13.423783	32	60	944	78	ENST00000349004.1	0.135135	0.865745
DSN1	79980	__UNKNOWN__	__UNKNOWN__	20	35382357	35382357	__UNKNOWN__	Intron	SNP	C	C	T	rs375674263		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35382357C>T	ENST00000426836.1	-	10	1334				DSN1_ENST00000373745.3_Intron|DSN1_ENST00000473615.1_Intron|DSN1_ENST00000373750.4_Intron|DSN1_ENST00000448110.2_Intron|DSN1_ENST00000373734.4_Intron|DSN1_ENST00000373740.3_Intron	NM_001145316.1	NP_001138788.1	Q9H410	DSN1_HUMAN	DSN1, MIS12 kinetochore complex component	NA		NA			chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	16		Myeloproliferative disorder(115;0.00874)				tgcagtgagccgagatcgcac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023408	CCDS13286.1, CCDS46596.1, CCDS46597.1	20q11.23	2013-07-03	2013-07-03	2006-11-07	ENSG00000149636	ENSG00000149636	79980			16165	protein-coding gene	gene with protein product	kinetochore null 3 homolog (C. elegans)	609175	chromosome 20 open reading frame 172, DSN1, MIND kinetochore complex component, homolog (S. cerevisiae)	C20orf172	NA	16585270, 20819937	Standard	NM_024918	NM_001145315	NA	Approved	dJ469A13.2, MIS13, KNL3, hKNL-3	uc002xfz.3	Q9H410	OTTHUMG00000032396	ENST00000426836.1:c.961+808G>A	chr20.hg19:g.35382357C>T		NA	B4DWT2|E1P5U9|Q5JW55|Q5JW56|Q9H8P4	hg19	CCDS13286.1	0.02	-0.192958	AGCxGAG	COVERED																																																																																			NOVEL	DSN1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079043.2	10	3.910007	KEEP	1	0	0	13	373	CC	0.994391	0.487793	0		-	3	60	92	0	0	7.033718	16	60	495	50	ENST00000426836.1	0.157895	0.490544
DSN1	79980	__UNKNOWN__	__UNKNOWN__	20	35400563	35400563	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35400563G>A	ENST00000426836.1	-	2	358				DSN1_ENST00000373745.3_Intron|DSN1_ENST00000473615.1_Intron|DSN1_ENST00000373750.4_Intron|DSN1_ENST00000373734.4_Intron|DSN1_ENST00000373740.3_Intron|DSN1_ENST00000448110.2_Intron	NM_001145316.1	NP_001138788.1	Q9H410	DSN1_HUMAN	DSN1, MIS12 kinetochore complex component	NA		NA			chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	16		Myeloproliferative disorder(115;0.00874)				gattacaggcgtgagccacca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK023408	CCDS13286.1, CCDS46596.1, CCDS46597.1	20q11.23	2013-07-03	2013-07-03	2006-11-07	ENSG00000149636	ENSG00000149636	79980			16165	protein-coding gene	gene with protein product	kinetochore null 3 homolog (C. elegans)	609175	chromosome 20 open reading frame 172, DSN1, MIND kinetochore complex component, homolog (S. cerevisiae)	C20orf172	NA	16585270, 20819937	Standard	NM_024918	NM_001145315	NA	Approved	dJ469A13.2, MIS13, KNL3, hKNL-3	uc002xfz.3	Q9H410	OTTHUMG00000032396	ENST00000426836.1:c.15-687C>T	chr20.hg19:g.35400563G>A		NA	B4DWT2|E1P5U9|Q5JW55|Q5JW56|Q9H8P4	hg19	CCDS13286.1	0.02	-0.166656	GGCxTGA	COVERED																																																																																			NOVEL	DSN1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079043.2	8	3.008321	KEEP	0	0	0	10	292	GG	0.992708	0.351366	0		-	3	60	84	0	1	6.392453	14	60	460	38	ENST00000426836.1	0.176471	0.353947
SOGA1	140710	__UNKNOWN__	__UNKNOWN__	20	35409995	35409995	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35409995C>T	ENST00000237536.4	-	0	10220				SOGA1_ENST00000279034.6_Intron	NM_080627.2	NP_542194.2	O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	NA		NA			insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						ctgcctgtaaccccagcactt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639	140710			16111	protein-coding gene	gene with protein product	suppressor of glucose by autophagy, suppressor of glucose from autophagy	NA	chromosome 20 open reading frame 117, KIAA0889	C20orf117, KIAA0889	NA	20813965	Standard	NM_199181	NM_080627	NA	Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000237536.4:c.*4893G>A	chr20.hg19:g.35409995C>T		NA	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	hg19	CCDS54459.1	0.02	1.341976	TAAxCCC	COVERED																																																																																			NOVEL	SOGA1-005	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276635.1	14	5.112613	KEEP	0	3	82	46	1368	CC	1	0.9982	0		-	5	60	150	0	0	9.60405	64	60	2126	151	ENST00000237536.4	0.072464	0.9982
SOGA1	140710	__UNKNOWN__	__UNKNOWN__	20	35445408	35445408	__UNKNOWN__	Intron	SNP	A	A	G	rs540234541	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35445408A>G	ENST00000237536.4	-	4	1476				SOGA1_ENST00000357779.3_Intron|SOGA1_ENST00000279034.6_Intron	NM_080627.2	NP_542194.2	O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	NA		NA			insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						agtggctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639	140710			16111	protein-coding gene	gene with protein product	suppressor of glucose by autophagy, suppressor of glucose from autophagy	NA	chromosome 20 open reading frame 117, KIAA0889	C20orf117, KIAA0889	NA	20813965	Standard	NM_199181	NM_080627	NA	Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000237536.4:c.1134+401T>C	chr20.hg19:g.35445408A>G		NA	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	hg19	CCDS54459.1	0.02	-0.166644	CACxCCT	COVERED																																																																																			NOVEL	SOGA1-005	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276635.1	4	3.005508	KEEP	0	0	0	10	263	AA	0.992708	0.351366	0		-	3	60	103	0	0	8.291639	14	60	419	42	ENST00000237536.4	0.176471	0.353947
RBL1	5933	__UNKNOWN__	__UNKNOWN__	20	35658996	35658996	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35658996A>G	ENST00000373664.3	-	16	2449				RBL1_ENST00000344359.3_Intron	NM_002895.2	NP_002886.2	P28749	RBL1_HUMAN	retinoblastoma-like 1	NA		NA			chromatin modification (GO:0016568)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(7)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	42		Myeloproliferative disorder(115;0.00878)				ggtggctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L14812	CCDS13289.1, CCDS13290.1	20q11.23	2014-03-11	2014-03-11		ENSG00000080839	ENSG00000080839	5933			9893	protein-coding gene	gene with protein product		116957			NA	1833063	Standard	NM_002895	NM_183404	NA	Approved	p107, cp107, PRB1	uc002xgi.3	P28749	OTTHUMG00000032406	ENST00000373664.3:c.2382+2071T>C	chr20.hg19:g.35658996A>G		NA	A8K2W5|Q4VXA0|Q8N5K6|Q9H1L5|Q9H1M1	hg19	CCDS13289.1	0.02	-0.166629	CACxCCT	COVERED																																																																																			NOVEL	RBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079067.2	8	3.607342	KEEP	0	0	0	12	309	AA	0.993634	0.351693	0		-	3	60	103	0	0	8.29187	14	60	400	43	ENST00000373664.3	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	35878825	35878825	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:35878825T>C			NA	NA				RPN2 (8803 upstream) : GHRH (663 downstream)						NA		NA									NA						cctgtaatcctaacactttgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.35878825T>C		NA		hg19		0.02	-0.210497	TCCxAAC	COVERED																																																																																			NOVEL					0			11	2.706393	KEEP	1	0	0	9	245	TT	0.99257	0.518282	0			3	40	97	0	0	7.460995	17	60	504	44		0.15	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	36228043	36228043	__UNKNOWN__	IGR	SNP	C	C	T	rs4810919	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:36228043C>T			NA	NA				BLCAP (71710 upstream) : LINC00489 (19656 downstream)						NA		NA									NA						tgcctgtaatcccagcacttt	0.478		NA											.|||	3430	0.684904	0.6649	0.804	5008	,	,	NA	19033	0.7222	NA	0.7724	False	NA	,,,	NA	NA	NA	2504	0.499	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.36228043C>T		NA		hg19		0.02	-0.052629	AATxCCA	UNCOVERED																																																																																			NOVEL					0			4	2.406992	KEEP	1	0	0	8	240	CC	0	0	0			4	60	119	0	0	12.720303	1	60	36	19		0.8	0.036766
BPI	671	__UNKNOWN__	__UNKNOWN__	20	36892623	36892623	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:36892623T>C	ENST00000451435.1	+	1	182							P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	NA		NA			defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				ggtgacagagtgagactctgt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425	671		BPI fold containing	1095	protein-coding gene	gene with protein product	BPI fold containing family D, member 1	109195			NA	8432532	Standard	NM_001725	NM_001725	NA	Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000451435.1:c.71+3865T>C	chr20.hg19:g.36892623T>C		NA	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	hg19		0.02	-0.403423	GAGxGAG	COVERED																																																																																			NOVEL	BPI-008	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000079153.1	11	3.308162	KEEP	0	0	0	11	307	TT	0.993072	0.941832	0		+	3	60	101	0	0	6.873003	38	60	1121	88	ENST00000451435.1	0.073171	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	37406045	37406045	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:37406045T>C			NA	NA				ACTR5 (5211 upstream) : PPP1R16B (28302 downstream)						NA		NA									NA						tttgggaggctgaggcgggcg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.37406045T>C		NA		hg19		0.02	-0.245606	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			10	2.406155	KEEP	2	0	0	8	221	TT	0	0	0			3	60	100	0	0	7.394559	23	60	714	49		0.115385	0.641347
RP5-1031J8.1	0	__UNKNOWN__	__UNKNOWN__	20	38419617	38419617	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:38419617G>A	ENST00000444436.1	+	0	211										NA		NA									NA						tactaaaaatgcaaaaattaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000444436.1:	chr20.hg19:g.38419617G>A		NA		hg19		0.02	-0.052624	AATxCAA	UNCOVERED																																																																																			NOVEL	RP5-1031J8.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000079225.1	6	2.70813	KEEP	0	0	0	9	277	GG	0.99254	0.036491	0		+	3	60	84	0	0	8.023821	3	60	103	21	ENST00000444436.1	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	39615802	39615802	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:39615802A>G			NA	NA				RNA5SP484 (132933 upstream) : RNU2-52P (37042 downstream)						NA		NA									NA						tacaaggtcaagagttcgaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.39615802A>G		NA		hg19		0.02	-0.105247	TCAxGAG	UNCOVERED																																																																																			NOVEL					0			1	2.40639	KEEP	0	0	0	8	224	AA	0.99257	0.138793	0			3	60	86	0	0	7.101135	9	60	274	34		0.25	0.139832
LPIN3	64900	__UNKNOWN__	__UNKNOWN__	20	39988406	39988406	__UNKNOWN__	3'UTR	SNP	G	G	T	rs577528215	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:39988406G>T	ENST00000373257.3	+	0	3547					NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	NA		NA			fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				GGCTGCTGCCGCTGCCTCTCT	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793	64900			14451	protein-coding gene	gene with protein product		605520	lipin 3-like	LIPN3L	NA	11138012	Standard	NM_022896	XM_005260515	NA	Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.*900G>T	chr20.hg19:g.39988406G>T		NA	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	hg19	CCDS33469.1	0.02	1.321242	GCCxCTG	COVERED																																																																																			NOVEL	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080393.1	6	5.411312	KEEP	0	0	0	18	506	GG	0.999859	0.999815	0		+	33	60	988	0	0	87.176846	66	60	2122	163	ENST00000373257.3	0.333333	0.999956
SRSF6	6431	__UNKNOWN__	__UNKNOWN__	20	42089894	42089894	__UNKNOWN__	3'UTR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:42089894C>T	ENST00000244020.3	+	0	1332					NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	NA		NA			alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						GACCCTCTCCCTTCTTTGTAG	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193	6431		Serine/arginine-rich splicing factors, RNA binding motif (RRM) containing	10788	protein-coding gene	gene with protein product	pre-mRNA splicing factor SRP55, SR splicing factor 6	601944	splicing factor, arginine/serine-rich 6	SFRS6	NA	7556075, 20516191	Standard	NM_006275	NM_006275	NA	Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.*191C>T	chr20.hg19:g.42089894C>T		NA	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	hg19	CCDS13318.1	0.02	2.378642	TCCxTTC	COVERED																																																																																			NOVEL	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079292.1	30	30.085306	KEEP	0	0	0	100	2989	CC	1	1	0		+	6	60	181	0	0	10.093494	141	60	4760	326	ENST00000244020.3	0.040816	1
SGK2	10110	__UNKNOWN__	__UNKNOWN__	20	42207681	42207681	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:42207681A>G	ENST00000373100.1	+	13	1309				SGK2_ENST00000341458.4_Intron|SGK2_ENST00000426287.1_Intron|SGK2_ENST00000373077.1_Intron|SGK2_ENST00000423407.3_Intron|SGK2_ENST00000373092.3_Intron			Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	NA		NA			intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			tttttgagacagagtcttgct	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049	10110			13900	protein-coding gene	gene with protein product		607589			NA	10548550	Standard		NM_016276	NA	Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000373100.1:c.850-931A>G	chr20.hg19:g.42207681A>G		NA	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	hg19	CCDS13321.1	0.02	-0.12279	GACxGAG	UNCOVERED																																																																																			NOVEL	SGK2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080386.1	13	2.404872	KEEP	10	0	0	8	217	AA	0	0	0		+	4	40	131	0	0	12.600142	4	50	117	41	ENST00000373100.1	0.5	0.196312
MYBL2	4605	__UNKNOWN__	__UNKNOWN__	20	42300076	42300076	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:42300076A>G	ENST00000217026.4	+	2	147				MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			gattacaggtatgagtcaccg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057	4605			7548	protein-coding gene	gene with protein product		601415			NA	8812502	Standard	NM_002466	NM_002466	NA	Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.21-2370A>G	chr20.hg19:g.42300076A>G		NA	B2RBS5|B7Z8D9|F8W6N6|Q53F07	hg19	CCDS13322.1	0.02	-0.166634	GGTxTGA	COVERED																																																																																			NOVEL	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080408.1	9	2.705853	KEEP	0	0	0	9	234	AA	0.99254	0.351306	0		+	3	60	90	0	0	6.992463	14	60	415	46	ENST00000217026.4	0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	42524830	42524830	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:42524830C>G			NA	NA				RP5-1030M6.3 (722 upstream) : TOX2 (18673 downstream)						NA		NA									NA						gcctcccaaactgctgggatt	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.42524830C>G		NA		hg19		0.02	-0.122816	AAAxTGC	COVERED																																																																																			NOVEL					0			9	2.708059	KEEP	1	0	0	9	278	AC	0.992708	0.227502	0			2	60	73	0	0	6.300655	6	60	201	36		0.25	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	42949295	42949295	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:42949295A>G			NA	NA				FITM2 (9486 upstream) : R3HDML (16330 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.42949295A>G		NA		hg19		0.02	-0.201717	CACxCCT	COVERED																																																																																			NOVEL					0			5	2.70731	KEEP	4	0	0	9	257	AC	0.992708	0.486967	0			3	60	100	0	0	7.627128	19	60	559	58		0.136364	0.490544
HNF4A	3172	__UNKNOWN__	__UNKNOWN__	20	42998927	42998927	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:42998927G>A	ENST00000316673.4	+	1	154				HNF4A_ENST00000457232.1_Intron|HNF4A_ENST00000609795.1_Intron			P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	NA		NA			blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			tcggcctcccgaagtgctggg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(79;2 1269 8820 14841 52347)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076	3172		Nuclear hormone receptors	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1	NA	7926813, 9048927	Standard		NM_001030003	NA	Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316673.4:c.49+14434G>A	chr20.hg19:g.42998927G>A		NA	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	hg19	CCDS42876.1	0.02	-0.149106	CCCxAAG	COVERED																																																																																			NOVEL	HNF4A-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079362.2	2	3.008487	KEEP	1	0	0	10	298	GG	0.99254	0.289823	0		+	3	60	86	0	0	6.772618	12	60	376	44	ENST00000316673.4	0.2	0.292001
HNF4A	3172	__UNKNOWN__	__UNKNOWN__	20	43012457	43012457	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43012457C>G	ENST00000316673.4	+	2	154				HNF4A_ENST00000457232.1_Intron|HNF4A_ENST00000609795.1_Intron|RP5-881L22.4_ENST00000452481.1_RNA|RP5-881L22.4_ENST00000609152.1_RNA			P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	NA		NA			blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			gccccccaaactgctgggatt	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(79;2 1269 8820 14841 52347)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076	3172		Nuclear hormone receptors	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1	NA	7926813, 9048927	Standard		NM_001030003	NA	Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316673.4:c.50-22241C>G	chr20.hg19:g.43012457C>G		NA	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	hg19	CCDS42876.1	0.02	-0.201715	AAAxTGC	COVERED																																																																																			NOVEL	HNF4A-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079362.2	16	2.405988	KEEP	0	0	0	8	233	AC	0.99254	0.486885	0		+	3	60	93	0	0	6.928219	19	60	628	37	ENST00000316673.4	0.136364	0.490544
SERINC3	10955	__UNKNOWN__	__UNKNOWN__	20	43139786	43139786	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43139786C>T	ENST00000342374.4	-	4	633				SERINC3_ENST00000255175.1_Intron|SERINC3_ENST00000541235.1_Intron	NM_006811.2	NP_006802.1	Q13530	SERC3_HUMAN	serine incorporator 3	NA		NA			phosphatidylserine metabolic process (GO:0006658)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(4)|large_intestine(2)|lung(8)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			aactcctgacctcaggtgatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U49188	CCDS13333.1	20q13.12	2008-05-14	2005-11-15	2005-11-15	ENSG00000132824	ENSG00000132824	10955			11699	protein-coding gene	gene with protein product		607165	tumor differentially expressed 1	TDE1	NA	10559794	Standard	NM_006811	NM_006811	NA	Approved	DIFF33, TDE, SBBI99, TMS-1, AIGP1	uc002xme.3	Q13530	OTTHUMG00000033087	ENST00000342374.4:c.475+143G>A	chr20.hg19:g.43139786C>T		NA	B4DUE9|O43717|Q9BR33	hg19	CCDS13333.1	0.02	-0.210502	GACxTCA	COVERED																																																																																			NOVEL	SERINC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080544.3	6	2.407087	KEEP	0	0	0	8	244	CC	0.99257	0.518282	0		-	4	60	109	0	0	8.56323	15	60	493	38	ENST00000342374.4	0.210526	0.522161
PKIG	11142	__UNKNOWN__	__UNKNOWN__	20	43196589	43196589	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43196589T>C	ENST00000372889.1	+	2	70				PKIG_ENST00000372891.3_Intron|PKIG_ENST00000372892.3_Intron|PKIG_ENST00000372894.3_Intron|PKIG_ENST00000372887.1_Intron|PKIG_ENST00000477390.1_Intron|PKIG_ENST00000372882.3_Intron	NM_001281444.1	NP_001268373.1	Q9Y2B9	IPKG_HUMAN	protein kinase (cAMP-dependent, catalytic) inhibitor gamma	NA		NA			negative regulation of protein import into nucleus (GO:0042308)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|signal transduction (GO:0007165)		cAMP-dependent protein kinase inhibitor activity (GO:0004862)			breast(1)|urinary_tract(1)	2		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.001)|COAD - Colon adenocarcinoma(18;0.00189)			gtgtttgagatcagcctgggc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB019517	CCDS13334.1	20q13.12-q13.13	2008-07-03			ENSG00000168734	ENSG00000168734	11142			9019	protein-coding gene	gene with protein product		604932			NA	10880337	Standard		NM_181805	NA	Approved		uc002xmi.3	Q9Y2B9	OTTHUMG00000033065	ENST00000372889.1:c.-515-14637T>C	chr20.hg19:g.43196589T>C		NA		hg19	CCDS13334.1	0.02	-0.105253	AGAxCAG	UNCOVERED																																																																																			NOVEL	PKIG-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000127804.1	4	2.404771	KEEP	0	0	0	8	205	TT	0.99257	0.138793	0		+	4	60	132	0	0	11.977245	7	60	208	32	ENST00000372889.1	0.363636	0.139832
ADA	100	__UNKNOWN__	__UNKNOWN__	20	43275826	43275826	__UNKNOWN__	Intron	SNP	G	G	A	rs62207811		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43275826G>A	ENST00000537820.1	-	1	117				ADA_ENST00000372874.4_Intron			P00813	ADA_HUMAN	adenosine deaminase	NA		NA			adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	ctgtaatcccggcactttggg	0.542		NA							Adenosine Deaminase Deficiency												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	100	3.5.4.4		186	protein-coding gene	gene with protein product		608958			NA	6198240, 6090454	Standard	NM_000022	NM_000022	NA	Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000537820.1:c.33+4389C>T	chr20.hg19:g.43275826G>A		NA	Q53F92|Q6LA59	hg19		0.02	-0.228059	CCCxGCA	COVERED																																																																																			NOVEL	ADA-008	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000402954.1	8	3.610638	KEEP	1	0	0	12	364	GG	0.993634	0.579219	0		-	3	60	86	0	0	6.434047	16	60	528	61	ENST00000537820.1	0.157895	0.58293
STK4	6789	__UNKNOWN__	__UNKNOWN__	20	43610568	43610568	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43610568G>A	ENST00000372806.3	+	4	439	c.344G>A	c.(343-345)cGa>cAa	p.R115Q	STK4_ENST00000372801.1_Missense_Mutation_p.R115Q|STK4_ENST00000499879.2_Missense_Mutation_p.R115Q|STK4_ENST00000396731.4_Missense_Mutation_p.R115Q	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	115	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.	NA			apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|cell morphogenesis (GO:0000902)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|keratinocyte differentiation (GO:0030216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)				GATATCATTCGATTACGAAAT	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(187;1039 2137 11798 21916 33213)							NA				0													191	184	187			NA	NA	20		NA											NA				43610568		2203	4300	6503	SO:0001583	missense				CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109	6789			11408	protein-coding gene	gene with protein product	mammalian sterile 20-like 1, yeast Ste20-like, kinase responsive to stress 2	604965			NA	8816758, 9545236, 11517310	Standard	NM_006282	NM_006282	NA	Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.344G>A	chr20.hg19:g.43610568G>A	ENSP00000361892:p.Arg115Gln	NA	B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	hg19	CCDS13341.1	0.02	2.631327	TTCxATT	COVERED	.	.	.	.	.	.	.	.	.	.	G	31	5.067748	0.93950	.	.	ENSG00000101109	ENST00000372806;ENST00000396731;ENST00000372801;ENST00000499879	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.44	5.44	0.79542	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.67097	0.2857	N	0.13043	0.29	0.80722	D	1	D;P;P;P	0.89917	1.0;0.572;0.626;0.793	D;B;B;B	0.78314	0.991;0.108;0.174;0.242	T	0.70995	-0.4720	10	0.48119	T	0.1	.	19.2425	0.93889	0.0:0.0:1.0:0.0	.	115;115;115;115	F5H5B4;Q13043-2;A0PJ51;Q13043	.;.;.;STK4_HUMAN	Q	115	ENSP00000361892:R115Q;ENSP00000379957:R115Q;ENSP00000361887:R115Q;ENSP00000443514:R115Q	ENSP00000361887:R115Q	R	+	2	0	STK4	43043982	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.349000	0.97066	2.542000	0.85734	0.585000	0.79938	CGA	NOVEL	STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080401.4	1	6.016057	KEEP	0	0	0	20	579	GG	0.999863	0.999855	0		+	6	60	174	0	0	10.240222	101	60	3235	194	ENST00000372806.3	0.056075	0.999992
STK4	6789	__UNKNOWN__	__UNKNOWN__	20	43674487	43674487	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43674487G>A	ENST00000372806.3	+	10	1400				STK4_ENST00000372801.1_Intron|STK4_ENST00000499879.2_Intron|STK4_ENST00000396731.4_Intron	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	NA		NA			apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|cell morphogenesis (GO:0000902)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|keratinocyte differentiation (GO:0030216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)				tcgctctgtcgcccaggctgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(187;1039 2137 11798 21916 33213)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109	6789			11408	protein-coding gene	gene with protein product	mammalian sterile 20-like 1, yeast Ste20-like, kinase responsive to stress 2	604965			NA	8816758, 9545236, 11517310	Standard	NM_006282	NM_006282	NA	Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.1305+20716G>A	chr20.hg19:g.43674487G>A		NA	B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	hg19	CCDS13341.1	0.02	-0.140337	GTCxCCC	COVERED																																																																																			NOVEL	STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080401.4	6	3.008554	KEEP	1	0	0	10	295	GG	0.99254	0.259018	0		+	3	60	86	1	0	6.679316	13	60	419	34	ENST00000372806.3	0.1875	0.260965
STK4	6789	__UNKNOWN__	__UNKNOWN__	20	43707137	43707137	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:43707137T>C	ENST00000372806.3	+	0	4879				STK4_ENST00000499879.2_3'UTR	NM_006282.2	NP_006273.1	Q13043	STK4_HUMAN	serine/threonine kinase 4	NA		NA			apoptotic process (GO:0006915)|cell differentiation involved in embryonic placenta development (GO:0060706)|cell morphogenesis (GO:0000902)|central nervous system development (GO:0007417)|endocardium development (GO:0003157)|hepatocyte apoptotic process (GO:0097284)|hippo signaling (GO:0035329)|intracellular signal transduction (GO:0035556)|keratinocyte differentiation (GO:0030216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of organ growth (GO:0046621)|neural tube formation (GO:0001841)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|primitive hemopoiesis (GO:0060215)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Myeloproliferative disorder(115;0.0122)				tgagccaccttgcctggccAA	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(187;1039 2137 11798 21916 33213)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13341.1	20q11.2-q13.2	2014-09-17			ENSG00000101109	ENSG00000101109	6789			11408	protein-coding gene	gene with protein product	mammalian sterile 20-like 1, yeast Ste20-like, kinase responsive to stress 2	604965			NA	8816758, 9545236, 11517310	Standard	NM_006282	NM_006282	NA	Approved	MST1, KRS2, YSK3	uc002xnb.3	Q13043	OTTHUMG00000033059	ENST00000372806.3:c.*3320T>C	chr20.hg19:g.43707137T>C		NA	B2RCR8|Q15802|Q4G156|Q5H982|Q6PD60|Q9BR32|Q9NTZ4	hg19	CCDS13341.1	0.02	1.581818	CCTxGCC	COVERED																																																																																			NOVEL	STK4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080401.4	17	2.767226	KEEP	1	2	59	30	800	TT	0.999997	0.999878	0		+	4	60	129	0	1	7.963304	74	60	2151	184	ENST00000372806.3	0.051282	0.999881
WFDC3	140686	__UNKNOWN__	__UNKNOWN__	20	44398727	44398727	__UNKNOWN__	Intron	SNP	A	A	G	rs800679		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:44398727A>G	ENST00000481847.1	-	4	479							Q8IUB2	WFDC3_HUMAN	WAP four-disulfide core domain 3	NA		NA				extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|large_intestine(3)|prostate(1)	5		Myeloproliferative disorder(115;0.0122)				tgtaatcccaacactttggga	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050348	CCDS33478.1	20q13.12	2013-01-21			ENSG00000124116	ENSG00000124116	140686		WAP four-disulfide core domain containing	15957	protein-coding gene	gene with protein product		NA			NA	12206714, 10680116	Standard		NM_080614	NA	Approved	dJ447F3.3, WAP14	uc002xpf.1	Q8IUB2	OTTHUMG00000032614	ENST00000481847.1:c.511+4311T>C	chr20.hg19:g.44398727A>G		NA	A6PVF2|Q0P6A5|Q3T1C5|Q8TC52|Q9BQP3|Q9BQP4	hg19		0.02	-0.105256	CCAxCAC	UNCOVERED																																																																																			NOVEL	WFDC3-010	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000316861.1	6	2.707008	KEEP	0	0	0	9	250	AA	0.992708	0.138812	0		-	3	60	106	0	0	9.23257	8	60	243	33	ENST00000481847.1	0.272727	0.139832
DNTTIP1	116092	__UNKNOWN__	__UNKNOWN__	20	44421953	44421953	__UNKNOWN__	Intron	SNP	G	G	A	rs6073915	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:44421953G>A	ENST00000372622.3	+	2	244					NM_052951.2	NP_443183.1	Q9H147	TDIF1_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 1	NA		NA				nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9		Myeloproliferative disorder(115;0.0122)				tgtaatcccagcactttggga	0.443		NA											G|||	1752	0.34984	0.0484	0.5331	5008	,	,	NA	16974	0.3958	NA	0.5895	False	NA	,,,	NA	NA	NA	2504	0.3333	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB035676	CCDS13369.1	20q13.12	2003-09-10	2003-09-10	2003-09-12	ENSG00000101457	ENSG00000101457	116092			16160	protein-coding gene	gene with protein product	novel protein similar to synaptotagmin 1 (SYT1, P65) (isoform 1), TdT binding protein	611388	chromosome 20 open reading frame 167	C20orf167	NA	11473582	Standard	NM_052951	NM_052951	NA	Approved	dJ447F3.4, Tdif1	uc002xpk.3	Q9H147	OTTHUMG00000032610	ENST00000372622.3:c.176+567G>A	chr20.hg19:g.44421953G>A		NA	B2RA18|Q96DE3|Q9BQP2|Q9H148	hg19	CCDS13369.1	0.02	-0.166657	CCAxCAC	COVERED																																																																																			NOVEL	DNTTIP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079502.1	2	2.406866	KEEP	0	0	0	8	241	GG	0.99257	0.351317	0		+	6	60	179	0	0	16.16486	10	60	343	41	ENST00000372622.3	0.375	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	44623311	44623311	__UNKNOWN__	IGR	SNP	A	A	G	rs79132585	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:44623311A>G			NA	NA				ZNF335 (22478 upstream) : MMP9 (14235 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.44623311A>G		NA		hg19		0.02	-0.236791	GCTxGGA	COVERED																																																																																			NOVEL					0			8	4.208385	KEEP	5	0	0	14	371	AA	0.993634	0.608508	0			3	60	92	0	0	6.707488	21	60	629	68		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	44623332	44623332	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:44623332C>T			NA	NA				ZNF335 (22499 upstream) : MMP9 (14214 downstream)						NA		NA									NA						cgtgagccaccgcgcccagct	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.44623332C>T		NA		hg19		0.02	-0.271932	CACxGCG	COVERED																																																																																			NOVEL					0			11	5.411332	KEEP	5	0	0	18	512	CC	0.997832	0.71576	0			3	60	93	1	0	6.544718	26	60	852	77		0.103448	0.717315
MMP9	4318	__UNKNOWN__	__UNKNOWN__	20	44644365	44644365	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:44644365C>A	ENST00000372330.3	+	13	2024				RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	NA		NA			collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	gctgggattacaggcatgagc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	4318	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase), matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	CLG4B	NA	2158484	Standard		NM_004994	NA	Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.2006-524C>A	chr20.hg19:g.44644365C>A		NA	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	hg19	CCDS13390.1	0.02	-0.17545	TTAxAGG	COVERED																																																																																			NOVEL	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080337.1	12	4.814002	KEEP	8	0	0	16	480	CC	0.994391	0.421102	0		+	3	24	87	0	0	6.533751	16	60	561	62	ENST00000372330.3	0.157895	0.423478
ELMO2	63916	__UNKNOWN__	__UNKNOWN__	20	45049017	45049017	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:45049017A>T	ENST00000445496.2	-	1	172				ZNF663P_ENST00000400371.2_RNA			Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	NA		NA			apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				cctcccaaagagctgaaatca	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598	63916		Engulfment and cell motility proteins	17233	protein-coding gene	gene with protein product		606421	engulfment and cell motility 2 (ced-12 homolog, C. elegans)		NA	11595183	Standard	NM_022086	NM_133171	NA	Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000445496.2:c.469+12515T>A	chr20.hg19:g.45049017A>T		NA	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	hg19		0.02	-0.201744	AAGxGCT	COVERED																																																																																			NOVEL	ELMO2-203	KNOWN	basic	protein_coding	NA	protein_coding		9	2.40634	KEEP	0	0	0	8	225	AA	0.99257	0.4869	0		-	3	60	96	0	0	7.360866	17	60	529	43	ENST00000445496.2	0.15	0.490544
ZNF663P	100130934	__UNKNOWN__	__UNKNOWN__	20	45077165	45077165	__UNKNOWN__	RNA	SNP	C	C	T	rs60727400|rs142795769		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:45077165C>T	ENST00000400371.2	-	0	1985									zinc finger protein 663, pseudogene	NA		NA									NA						ttcttcttttctttttttttt	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							20q13.12	2014-03-13	2013-09-26	2013-09-26	ENSG00000215452	ENSG00000215452	100130934		Zinc fingers, C2H2-type	25342	pseudogene	pseudogene		NA	zinc finger protein 663	ZNF663	NA		Standard	NM_173643	NR_045983	NA	Approved	DKFZp547G0215	uc031rtv.1		OTTHUMG00000032648	ENST00000400371.2:	chr20.hg19:g.45077165C>T		NA		hg19		0.02	-0.149122	TTTxTTT	COVERED																																																																																			NOVEL	ZNF663P-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000079571.1	21	3.910999	KEEP	1	0	0	13	380	CC	0.994391	0.290363	0		-	3	60	87	1	0	6.692061	14	60	464	34	ENST00000400371.2	0.176471	0.292001
EYA2	2139	__UNKNOWN__	__UNKNOWN__	20	45736267	45736267	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:45736267G>C	ENST00000327619.5	+	9	1262				EYA2_ENST00000357410.3_Intron|EYA2_ENST00000317304.6_Intron	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	NA		NA			DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				attgcttgaggccagaagttc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(120;56 1725 18501 25218 43520)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655	2139		Protein tyrosine phosphatases / Asp-based PTPs	3520	protein-coding gene	gene with protein product		601654	eyes absent (Drosophila) homolog 2, eyes absent homolog 2 (Drosophila)		NA	9020840	Standard	NM_005244	NM_005244	NA	Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.888+10460G>C	chr20.hg19:g.45736267G>C		NA	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	hg19	CCDS13403.1	0.02	-0.245607	GAGxCCA	COVERED																																																																																			NOVEL	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080326.2	9	4.813551	KEEP	0	0	0	16	470	GG	0.997832	0.639957	0		+	3	60	91	0	0	6.3956	25	60	827	53	ENST00000327619.5	0.107143	0.641347
SULF2	55959	__UNKNOWN__	__UNKNOWN__	20	46351598	46351598	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:46351598T>C	ENST00000359930.4	-	3	1267				SULF2_ENST00000467815.1_Intron|SULF2_ENST00000478766.1_Intron|SULF2_ENST00000361612.4_Intron|SULF2_ENST00000484875.1_Intron	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	NA		NA			bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						tcacttgaggtcaggagttca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562	55959			20392	protein-coding gene	gene with protein product		610013			NA	12368295	Standard	NM_018837	NM_018837	NA	Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.415+13848A>G	chr20.hg19:g.46351598T>C		NA	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	hg19	CCDS13408.1	0.02	-0.26315	AGGxCAG	UNCOVERED																																																																																			NOVEL	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079606.1	15	3.608599	KEEP	17	0	0	12	327	TT	0	0	0		-	3	60	104	0	0	7.643779	26	60	810	81	ENST00000359930.4	0.103448	0.693668
PREX1	57580	__UNKNOWN__	__UNKNOWN__	20	47294279	47294279	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:47294279C>T	ENST00000371941.3	-	14	1612				PREX1_ENST00000396220.1_Intron	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	NA		NA			actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			tcccagcactctgggaggctg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126	57580		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	32594	protein-coding gene	gene with protein product		606905			NA	11955434, 15545267, 16301320	Standard	NM_020820	NM_020820	NA	Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1590-1473G>A	chr20.hg19:g.47294279C>T		NA	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	hg19	CCDS13410.1	0.02	-0.140346	ACTxTGG	COVERED																																																																																			NOVEL	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079623.1	4	2.708298	KEEP	1	0	0	9	285	CC	0.99254	0.259018	0		-	3	60	86	0	1	6.981963	10	60	326	40	ENST00000371941.3	0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	47724429	47724429	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:47724429T>C			NA	NA				CSE1L (10940 upstream) : STAU1 (5448 downstream)						NA		NA									NA						gttgcggtggttcacgcctgt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.47724429T>C		NA		hg19		0.02	-0.166629	TGGxTCA	COVERED																																																																																			NOVEL					0			9	2.402544	KEEP	0	0	0	8	200	TT	0.99257	0.351317	0			3	60	100	0	0	7.910382	15	60	432	36		0.166667	0.353947
STAU1	6780	__UNKNOWN__	__UNKNOWN__	20	47792546	47792546	__UNKNOWN__	Intron	SNP	T	T	C	rs62210457	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:47792546T>C	ENST00000371856.2	-	2	252				STAU1_ENST00000347458.5_Intron|STAU1_ENST00000371828.3_Intron|STAU1_ENST00000371802.1_Intron|STAU1_ENST00000360426.4_Intron|STAU1_ENST00000340954.7_Intron|STAU1_ENST00000371792.1_Intron	NM_017453.2	NP_059347.2	O95793	STAU1_HUMAN	staufen double-stranded RNA binding protein 1	NA		NA			intracellular mRNA localization (GO:0008298)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|rough endoplasmic reticulum (GO:0005791)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	23			BRCA - Breast invasive adenocarcinoma(12;0.000644)|Colorectal(8;0.198)			ttagccaggatggtctcgatc	0.562		NA											-|||	421	0.0840655	0.0356	0.0836	5008	,	,	NA	12328	0.0774	NA	0.1481	False	NA	,,,	NA	NA	NA	2504	0.091	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13414.1, CCDS13415.1, CCDS33481.1	20q13.1	2014-06-13	2013-06-05	2005-11-04	ENSG00000124214	ENSG00000124214	6780			11370	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 150	601716	staufen (Drosophila, RNA-binding protein), staufen, RNA binding protein (Drosophila), staufen, RNA binding protein, homolog 1 (Drosophila)	STAU	NA	8884277, 15680326	Standard	NM_017453	XM_005260524	NA	Approved	PPP1R150	uc002xud.3	O95793	OTTHUMG00000032691	ENST00000371856.2:c.159-1740A>G	chr20.hg19:g.47792546T>C		NA	A8K9Z4|E1P5Y1|E1P608|Q5JW29|Q6GTM4|Q9H5B4|Q9H5B5|Q9Y3Q2	hg19	CCDS13414.1	0.02	-0.078942	GGAxGGT	UNCOVERED																																																																																			NOVEL	STAU1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079633.1	6	2.705662	KEEP	12	0	0	9	233	TT	0	0	0		-	5	40	162	0	0	15.900445	4	60	117	35	ENST00000371856.2	0.555556	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	48616752	48616752	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:48616752A>G			NA	NA				SNAI1 (11329 upstream) : TRERNA1 (40500 downstream)						NA		NA									NA						ttacaggcataagccaccatg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.48616752A>G		NA		hg19		0.02	-0.22802	CATxAGC	COVERED																																																																																			NOVEL					0			8	3.005532	KEEP	3	0	0	10	252	AA	0.99254	0.578582	0			3	60	95	0	0	6.896307	23	60	671	49		0.115385	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	48637469	48637469	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:48637469C>T			NA	NA				SNAI1 (32046 upstream) : TRERNA1 (19783 downstream)						NA		NA									NA						tccaaagtgccgagattacag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.48637469C>T		NA		hg19		0.02	-0.10525	TGCxGAG	UNCOVERED																																																																																			NOVEL					0			5	2.405664	KEEP	0	0	0	8	222	CC	0.99257	0.138793	0			3	60	84	0	0	7.177833	7	60	239	30		0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	48775401	48775401	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:48775401C>T			NA	NA				TMEM189 (5066 upstream) : RP11-112L6.3 (4599 downstream)						NA		NA									NA						ggattacaggcgtgagccacg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.48775401C>T		NA		hg19		0.02	-0.219277	AGGxGTG	COVERED																																																																																			NOVEL					0			6	2.406618	KEEP	0	0	0	8	235	CC	0.99257	0.54878	0			4	60	108	0	0	8.096189	19	60	625	45		0.173913	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	48987855	48987855	__UNKNOWN__	IGR	SNP	G	G	A	rs8118936	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:48987855G>A			NA	NA				RP11-290F20.2 (49976 upstream) : RN7SL636P (57873 downstream)						NA		NA									NA						cgaggcaggcggatcatgagg	0.507		NA											G|||	168	0.0335463	0.0174	0.049	5008	,	,	NA	14898	0.0198	NA	0.0567	False	NA	,,,	NA	NA	NA	2504	0.0348	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.48987855G>A		NA		hg19		0.02	-0.175431	GGCxGAT	COVERED																																																																																			NOVEL					0			10	4.212419	KEEP	10	0	0	14	425	GG	0.99254	0.384517	0			9	60	269	0	0	26.429726	7	47	236	56		0.5625	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	49123648	49123648	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:49123648T>C			NA	NA				RN7SL636P (77628 upstream) : PTPN1 (3242 downstream)						NA		NA									NA						gacagagtcttgctctgtcac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.49123648T>C		NA		hg19		0.02	-0.166642	TCTxGCT	COVERED																																																																																			NOVEL					0			6	3.306962	KEEP	0	0	0	11	301	TT	0.993072	0.351495	0			3	60	91	0	0	7.010521	15	60	447	44		0.166667	0.353947
FAM65C	140876	__UNKNOWN__	__UNKNOWN__	20	49206084	49206084	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:49206084T>C	ENST00000327979.2	-	20	3061				FAM65C_ENST00000045083.2_Intron|FAM65C_ENST00000462842.1_Intron|FAM65C_ENST00000535356.1_Intron			Q96MK2	FA65C_HUMAN	family with sequence similarity 65, member C	NA		NA								endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(1)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ctgcctgccttggcctcccaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL133230	CCDS13431.2	20q13.13	2011-11-24	2008-06-13	2008-06-13	ENSG00000042062	ENSG00000042062	140876			16168	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 175, chromosome 20 open reading frame 176	C20orf175, C20orf176	NA		Standard		XM_005260294	NA	Approved	dJ530I15.2, dJ530I15.3	uc002xvm.3	Q96MK2	OTTHUMG00000032724	ENST00000327979.2:c.2649+138A>G	chr20.hg19:g.49206084T>C		NA	Q5QPB6|Q9NQQ2	hg19	CCDS13431.2	0.02	-0.227936	CCTxGGC	COVERED																																																																																			NOVEL	FAM65C-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257962.1	4	5.110981	KEEP	1	0	0	17	457	TT	0.997832	0.581666	0		-	3	60	101	0	0	7.606265	21	60	574	52	ENST00000327979.2	0.125	0.58293
PARD6B	84612	__UNKNOWN__	__UNKNOWN__	20	49368135	49368135	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:49368135G>A	ENST00000396039.1	+	3	411				PARD6B_ENST00000371610.2_3'UTR			Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	NA		NA			axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						cgcccgcctcggcctcccaaa	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171	84612			16245	protein-coding gene	gene with protein product		608975	par-6 (partitioning defective 6, C.elegans) homolog beta, par-6 partitioning defective 6 homolog beta (C. elegans)		NA	11260256	Standard	NM_032521	NM_032521	NA	Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000396039.1:c.290-5087G>A	chr20.hg19:g.49368135G>A		NA	A2A2A7|Q9Y510	hg19		0.02	4.48271	CTCxGCC	COVERED																																																																																			NOVEL	PARD6B-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000258383.1	24	4.037743	KEEP	0	4	103	50	1440	GG	1	1	0		+	8	60	242	0	0	14.203024	154	60	4908	294	ENST00000396039.1	0.049383	1
BCAS4	55653	__UNKNOWN__	__UNKNOWN__	20	49433617	49433617	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:49433617C>T	ENST00000358791.5	+	2	280				BCAS4_ENST00000371608.2_Intron|BCAS4_ENST00000485049.1_Intron|BCAS4_ENST00000609336.1_Intron|BCAS4_ENST00000262591.5_Intron	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	NA		NA				cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						ggattacaggcgtgagccagt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243	55653			14367	protein-coding gene	gene with protein product		607471			NA	12378525	Standard	NM_017843	NM_001010974	NA	Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.181-1131C>T	chr20.hg19:g.49433617C>T		NA	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	hg19	CCDS33487.1	0.02	-0.175418	AGGxGTG	COVERED																																																																																			NOVEL	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079700.1	6	2.404998	KEEP	0	0	0	8	224	CC	0.99257	0.384528	0		+	3	60	85	0	0	6.411004	15	60	489	44	ENST00000358791.5	0.166667	0.387407
BCAS4	55653	__UNKNOWN__	__UNKNOWN__	20	49466424	49466424	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:49466424A>G	ENST00000358791.5	+	4	589				BCAS4_ENST00000371608.2_Intron|BCAS4_ENST00000609336.1_Intron|BCAS4_ENST00000262591.5_Intron	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	NA		NA				cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						agcactttggaaggccaaggc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243	55653			14367	protein-coding gene	gene with protein product		607471			NA	12378525	Standard	NM_017843	NM_001010974	NA	Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.489+7987A>G	chr20.hg19:g.49466424A>G		NA	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	hg19	CCDS33487.1	0.02	-0.157878	TGGxAGG	COVERED																																																																																			NOVEL	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079700.1	9	4.209551	KEEP	8	0	0	14	374	AA	0.992708	0.320453	0		+	3	60	102	0	0	8.372224	12	60	357	54	ENST00000358791.5	0.2	0.322807
ATP9A	10079	__UNKNOWN__	__UNKNOWN__	20	50368369	50368369	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50368369C>T	ENST00000338821.5	-	1	333				ATP9A_ENST00000402822.1_Intron|ATP9A_ENST00000311637.5_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	NA		NA			phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						cctcgtgatccgcccgcctcg	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793	10079		ATPases / P-type	13540	protein-coding gene	gene with protein product		609126	ATPase, Class II, type 9A		NA	9734811, 11015572	Standard	NM_006045	NM_006045	NA	Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.68+16471G>A	chr20.hg19:g.50368369C>T		NA	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	hg19	CCDS33489.1	0.02	-0.157873	ATCxGCC	UNCOVERED																																																																																			NOVEL	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000106494.1	6	2.406907	KEEP	8	0	0	8	238	CC	0	0	0		-	3	40	84	0	0	6.392548	14	60	452	40	ENST00000338821.5	0.176471	0.322807
RP5-1112F19.2	0	__UNKNOWN__	__UNKNOWN__	20	50455688	50455688	__UNKNOWN__	lincRNA	SNP	A	A	G	rs6096609	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50455688A>G	ENST00000438154.1	-	0	153										NA		NA									NA						gggtttcaccatgttggccag	0.557		NA											A|||	929	0.185503	0.1974	0.1441	5008	,	,	NA	15237	0.2669	NA	0.1223	False	NA	,,,	NA	NA	NA	2504	0.18	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000438154.1:	chr20.hg19:g.50455688A>G		NA		hg19		0.02	-0.149101	ACCxTGT	UNCOVERED																																																																																			NOVEL	RP5-1112F19.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000258921.1	10	2.406373	KEEP	16	0	0	8	225	AA	0	0	0		-	4	49	123	0	0	10.301647	12	41	359	43	ENST00000438154.1	0.25	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	50494252	50494252	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50494252T>C			NA	NA				RP5-1112F19.2 (14801 upstream) : RNU6-347P (24577 downstream)						NA		NA									NA						gtggaggttgtagtgagccga	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.50494252T>C		NA		hg19		0.02	-0.175383	TTGxAGT	COVERED																																																																																			NOVEL					0			8	2.704376	KEEP	2	0	0	9	220	TT	0.99257	0.384528	0			3	60	89	0	0	7.072937	12	60	344	35		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	50653818	50653818	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50653818C>T			NA	NA				RN7SL603P (96446 upstream) : ZFP64 (14383 downstream)						NA		NA									NA						tgcactccagcctgggtgaca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.50653818C>T		NA		hg19		0.02	-0.105267	CAGxCTG	UNCOVERED																																																																																			NOVEL					0			7	2.708168	KEEP	6	0	0	9	280	CC	0.99254	0.138789	0			3	30	90	0	0	7.943153	6	49	208	41		0.333333	0.139832
ZFP64	55734	__UNKNOWN__	__UNKNOWN__	20	50692629	50692629	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50692629C>G	ENST00000371518.2	-	8	1371							Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						aaactcctggcctcaagcaat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256	55734		Zinc fingers, C2H2-type	15940	protein-coding gene	gene with protein product		NA	zinc finger protein 338, zinc finger protein 64 homolog (mouse), zinc finger protein 64	ZNF338	NA	9034307	Standard	NM_018197	NM_199427	NA	Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000371518.2:c.1228+12301G>C	chr20.hg19:g.50692629C>G		NA	Q9NTS7|Q9NVH4	hg19		0.02	-0.245522	TGGxCTC	COVERED																																																																																			NOVEL	ZFP64-009	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000259120.1	17	6.920695	KEEP	0	0	0	23	707	CC	0.999909	0.641289	0		-	3	60	105	0	0	8.127292	19	60	649	75	ENST00000371518.2	0.136364	0.641347
ZFP64	55734	__UNKNOWN__	__UNKNOWN__	20	50697220	50697220	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50697220A>G	ENST00000371518.2	-	8	1371							Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						gctcacgcctataatcccagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256	55734		Zinc fingers, C2H2-type	15940	protein-coding gene	gene with protein product		NA	zinc finger protein 338, zinc finger protein 64 homolog (mouse), zinc finger protein 64	ZNF338	NA	9034307	Standard	NM_018197	NM_199427	NA	Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000371518.2:c.1228+7710T>C	chr20.hg19:g.50697220A>G		NA	Q9NTS7|Q9NVH4	hg19		0.02	-0.192953	CCTxTAA	UNCOVERED																																																																																			NOVEL	ZFP64-009	NOVEL	basic	protein_coding	NA	protein_coding	OTTHUMT00000259120.1	16	2.40564	KEEP	7	0	0	8	214	AA	0	0	0		-	3	60	96	0	0	7.361221	17	60	500	53	ENST00000371518.2	0.15	0.457757
ZFP64	55734	__UNKNOWN__	__UNKNOWN__	20	50725327	50725327	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:50725327T>C	ENST00000361387.2	-	6	824				ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000477786.1_Intron	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						ggattacaggtgtgagccact	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256	55734		Zinc fingers, C2H2-type	15940	protein-coding gene	gene with protein product		NA	zinc finger protein 338, zinc finger protein 64 homolog (mouse), zinc finger protein 64	ZNF338	NA	9034307	Standard	NM_018197	NM_199427	NA	Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.764-10201A>G	chr20.hg19:g.50725327T>C		NA	Q9NTS7|Q9NVH4	hg19	CCDS13439.1	0.02	-0.166627	AGGxGTG	COVERED																																																																																			NOVEL	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079743.2	4	2.705722	KEEP	0	0	0	9	243	TT	0.99254	0.351306	0		-	4	60	127	0	0	10.363028	15	60	431	39	ENST00000361387.2	0.210526	0.353947
TSHZ2	128553	__UNKNOWN__	__UNKNOWN__	20	51951333	51951333	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:51951333T>C	ENST00000371497.5	+	2	4000				RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Intron	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			agcgattctcttgcctcagcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463	128553		Teashirt zinc fingers, Homeoboxes / ZF class, Zinc fingers, C2H2-type	13010	protein-coding gene	gene with protein product		614118	chromosome 20 open reading frame 17, zinc finger protein 218, teashirt family zinc finger 2	C20orf17, ZNF218	NA	9671742	Standard	NM_173485	NM_173485	NA	Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.3102+78223T>C	chr20.hg19:g.51951333T>C		NA	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	hg19	CCDS33490.1	0.02	-0.105248	CTCxTGC	UNCOVERED																																																																																			NOVEL	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080398.6	6	2.406359	KEEP	0	0	0	8	225	TT	0.99257	0.138793	0		+	3	60	94	0	0	7.901182	9	60	270	26	ENST00000371497.5	0.25	0.139832
TSHZ2	128553	__UNKNOWN__	__UNKNOWN__	20	51978608	51978608	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:51978608T>G	ENST00000371497.5	+	2	4000				RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Intron	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	NA		NA			multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			tcaccatgtttgccaggctgg	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463	128553		Teashirt zinc fingers, Homeoboxes / ZF class, Zinc fingers, C2H2-type	13010	protein-coding gene	gene with protein product		614118	chromosome 20 open reading frame 17, zinc finger protein 218, teashirt family zinc finger 2	C20orf17, ZNF218	NA	9671742	Standard	NM_173485	NM_173485	NA	Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.3102+105498T>G	chr20.hg19:g.51978608T>G		NA	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	hg19	CCDS33490.1	0.02	-0.105246	GTTxGCC	UNCOVERED																																																																																			NOVEL	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080398.6	4	2.706243	KEEP	0	0	0	9	242	TT	0.99254	0.138789	0		+	3	60	105	0	0	9.278956	7	60	202	28	ENST00000371497.5	0.3	0.139832
AC005808.3	0	__UNKNOWN__	__UNKNOWN__	20	52228680	52228680	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52228680A>G	ENST00000444112.1	+	0	158										NA		NA									NA						gaccagcctgaacaacatagt	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000444112.1:	chr20.hg19:g.52228680A>G		NA		hg19		0.02	-0.33329	CTGxACA	COVERED																																																																																			NOVEL	AC005808.3-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000079761.2	17	7.517434	KEEP	0	0	0	25	676	AA	0.999931	0.851925	0		+	3	60	99	0	0	7.242647	24	60	731	87	ENST00000444112.1	0.111111	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	52268053	52268053	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52268053A>G			NA	NA				AC005808.3 (16924 upstream) : RNU7-14P (17182 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.52268053A>G		NA		hg19		0.02	-0.210517	CACxCCT	COVERED																																																																																			NOVEL					0			8	4.811009	KEEP	4	0	0	16	432	AA	0.995343	0.519729	0			3	60	101	0	0	7.792118	18	60	550	63		0.142857	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	52325966	52325966	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52325966T>C			NA	NA				RNU7-14P (40669 upstream) : AC006076.1 (90395 downstream)						NA		NA									NA						tgcagtgagctgagatcgcgc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.52325966T>C		NA		hg19		0.02	-0.201706	AGCxGAG	COVERED																																																																																			NOVEL					0			6	3.909636	KEEP	0	0	0	13	357	TT	0.994391	0.487793	0			3	60	87	0	0	6.393684	18	60	525	47		0.142857	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	52325967	52325967	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52325967G>A			NA	NA				RNU7-14P (40670 upstream) : AC006076.1 (90394 downstream)						NA		NA									NA						gcagtgagctgagatcgcgcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.52325967G>A		NA		hg19		0.02	-0.192984	GCTxAGA	COVERED																																																																																			NOVEL					0			6	3.911598	KEEP	0	0	0	13	399	GG	0.994391	0.455189	0			3	60	88	0	0	6.561391	17	60	565	47		0.15	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	52398480	52398480	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52398480A>G			NA	NA				RNU7-14P (113183 upstream) : AC006076.1 (17881 downstream)						NA		NA									NA						gatcacctgaagtcaggagtt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.52398480A>G		NA		hg19		0.02	-0.122792	TGAxGTC	COVERED																																																																																			NOVEL					0			4	3.007499	KEEP	1	0	0	10	273	AA	0.992708	0.19488	0			3	60	100	0	0	8.272946	11	60	326	38		0.214286	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	52430949	52430949	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52430949T>C			NA	NA				AC006076.1 (13092 upstream) : AC005220.3 (125749 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.52430949T>C		NA		hg19		0.02	-0.184186	TCAxGCC	COVERED																																																																																			NOVEL					0			5	3.007348	KEEP	0	0	0	10	272	TT	0.992708	0.42039	0			3	49	92	0	0	7.192313	14	60	426	47		0.176471	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	52523978	52523978	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:52523978G>A			NA	NA				AC006076.1 (106121 upstream) : AC005220.3 (32720 downstream)						NA		NA									NA						ATCACTggccgggcacggtgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.52523978G>A		NA		hg19		0.02	-0.34211	GCCxGGC	COVERED																																																																																			NOVEL					0			10	4.512903	KEEP	0	0	0	15	448	GG	0.99649	0.862707	0			3	60	94	0	0	6.34964	33	60	1080	81		0.083333	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	54134085	54134085	__UNKNOWN__	IGR	SNP	T	T	C	rs6024201	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:54134085T>C			NA	NA				RP5-1010E17.1 (49333 upstream) : CBLN4 (438410 downstream)						NA		NA									NA						gaggccgaggtgggcggatca	0.517		NA											C|||	2422	0.483626	0.736	0.2867	5008	,	,	NA	16005	0.4246	NA	0.3469	False	NA	,,,	NA	NA	NA	2504	0.4836	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.54134085T>C		NA		hg19		0.02	-0.07892	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			8	3.005385	KEEP	8	0	0	10	255	TT	0	0	0			3	60	99	0	0	9.255545	4	60	111	34		0.428571	0.077336
CASS4	57091	__UNKNOWN__	__UNKNOWN__	20	55034268	55034268	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55034268A>G	ENST00000434344.1	+	0	1713				CASS4_ENST00000371336.3_3'UTR	NM_001164115.1	NP_001157587.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	NA		NA			cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						caccatgcccagctaattttt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589	57091		Cas scaffolding proteins	15878	protein-coding gene	gene with protein product	HEF-like protein, HEF1-Efs-p130Cas-like	NA	chromosome 20 open reading frame 32	C20orf32	NA		Standard	NM_020356	NM_020356	NA	Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000434344.1:c.*465A>G	chr20.hg19:g.55034268A>G		NA	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	hg19	CCDS54475.1	0.02	-0.385903	CCCxGCT	COVERED																																																																																			NOVEL	CASS4-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079790.2	6	2.868394	KEEP	0	2	58	30	805	AA	0.999997	0.918168	0		+	4	60	125	0	0	8.675721	38	60	1135	96	ENST00000434344.1	0.095238	0.918171
RP5-843L14.1	0	__UNKNOWN__	__UNKNOWN__	20	55153832	55153832	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55153832A>G	ENST00000434176.1	+	0	259										NA		NA									NA						ggccaggcacagtggctcaca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000434176.1:	chr20.hg19:g.55153832A>G		NA		hg19		0.02	-0.166653	CACxGTG	COVERED																																																																																			NOVEL	RP5-843L14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000259432.1	3	3.308339	KEEP	1	0	0	11	302	AA	0.992708	0.384582	0		+	3	60	100	0	0	8.078811	13	60	390	50	ENST00000434176.1	0.1875	0.387407
RP5-843L14.1	0	__UNKNOWN__	__UNKNOWN__	20	55159319	55159319	__UNKNOWN__	lincRNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55159319G>A	ENST00000434176.1	+	0	557										NA		NA									NA						gcttgaacccgggaggtggag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000434176.1:	chr20.hg19:g.55159319G>A		NA		hg19		0.02	-0.11403	CCCxGGA	UNCOVERED																																																																																			NOVEL	RP5-843L14.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000259432.1	5	2.707378	KEEP	6	0	0	9	267	GG	0	0	0		+	3	40	89	0	0	7.401061	9	60	290	35	ENST00000434176.1	0.25	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	55285722	55285722	__UNKNOWN__	IGR	SNP	C	C	G	rs6025094	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55285722C>G			NA	NA				RN7SL170P (21973 upstream) : AL133232.1 (8219 downstream)						NA		NA									NA						cctcctccccctcctttgttc	0.582		NA											c|||	2088	0.416933	0.0446	0.6556	5008	,	,	NA	10947	0.4861	NA	0.5358	False	NA	,,,	NA	NA	NA	2504	0.5573	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.55285722C>G		NA		hg19		0.02	-0.087518	CCCxTCC	UNCOVERED																																																																																			NOVEL					0			3	2.407134	KEEP	0	0	0	8	246	CC	0.99257	0.09898	0			3	60	79	0	1	7.020506	5	60	171	29		0.375	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	55338887	55338887	__UNKNOWN__	IGR	SNP	C	C	T	rs577349156		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55338887C>T			NA	NA				RP5-897D18.1 (32371 upstream) : RNU6-929P (22149 downstream)						NA		NA									NA						tttgggaggccgaggcgggta	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.55338887C>T		NA		hg19		0.02	-0.166671	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			6	2.406576	KEEP	2	0	0	8	236	CC	0	0	0			3	60	91	0	0	7.010253	15	60	500	44		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	55362221	55362221	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55362221T>C			NA	NA				RNU6-929P (1078 upstream) : AL117380.2 (212921 downstream)						NA		NA									NA						aggctggtcttgaactcttga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.55362221T>C		NA		hg19		0.02	-0.157871	TCTxGAA	COVERED																																																																																			NOVEL					0			8	3.608552	KEEP	5	0	0	12	323	TT	0.993072	0.32057	0			3	40	90	0	0	6.910612	15	60	446	53		0.166667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	55362228	55362228	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55362228T>C			NA	NA				RNU6-929P (1085 upstream) : AL117380.2 (212914 downstream)						NA		NA									NA						tcttgaactcttgacctcagg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.55362228T>C		NA		hg19		0.02	-0.157882	CTCxTGA	COVERED																																																																																			NOVEL					0			8	3.608873	KEEP	5	0	0	12	325	TT	0.993072	0.32057	0			3	60	104	0	0	8.391584	14	60	424	50		0.176471	0.322807
BMP7	655	__UNKNOWN__	__UNKNOWN__	20	55745065	55745065	__UNKNOWN__	3'UTR	SNP	A	A	G	rs550856258		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:55745065A>G	ENST00000395863.3	-	0	2751					NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	NA		NA			axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)			endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			cgcccacctcagcctcccaaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144	655		Bone morphogenetic proteins, Endogenous ligands	1074	protein-coding gene	gene with protein product	osteogenic protein 1	112267			NA	1427904	Standard		NM_001719	NA	Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.*950T>C	chr20.hg19:g.55745065A>G		NA	Q9H512|Q9NTQ7	hg19	CCDS13455.1	0.02	-0.377137	CTCxGCC	COVERED																																																																																			NOVEL	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079831.2	21	4.812681	KEEP	9	0	0	16	448	AA	0.995343	0.904836	0		-	3	60	100	0	0	6.772979	38	60	1159	86	ENST00000395863.3	0.073171	0.909069
ZBP1	81030	__UNKNOWN__	__UNKNOWN__	20	56179221	56179221	__UNKNOWN__	3'UTR	SNP	A	A	G	rs577434778		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:56179221A>G	ENST00000371173.3	-	0	1875				ZBP1_ENST00000340462.4_3'UTR|ZBP1_ENST00000395822.3_3'UTR	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	NA		NA			innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			gagccactgcacccagttggg	0.522		NA											A|||	1	0.000199681	0.0	0.0014	5008	,	,	NA	16224	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256	81030			16176	protein-coding gene	gene with protein product	DNA-dependent activator of IRFs	606750	chromosome 20 open reading frame 183	C20orf183	NA	11842111	Standard	NM_030776	NM_030776	NA	Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.*408T>C	chr20.hg19:g.56179221A>G		NA	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	hg19	CCDS13461.1	0.02	1.620951	TGCxCCC	COVERED																																																																																			NOVEL	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079849.1	20	9.951129	KEEP	0	1	25	42	1109	AA	1	0.999956	0		-	5	60	150	0	0	9.235002	90	60	2689	205	ENST00000371173.3	0.052632	0.999956
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	56464464	56464464	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:56464464T>C			NA	NA				PMEPA1 (177872 upstream) : MIR4532 (5985 downstream)						NA		NA									NA						cctagcttttttttttttttt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.56464464T>C		NA		hg19		0.02	-0.131553	TTTxTTT	COVERED																																																																																			NOVEL					0			8	3.006842	KEEP	1	0	0	10	263	TT	0.99254	0.227464	0			3	60	99	0	0	9.525343	3	60	86	34		0.5	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	56464468	56464468	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:56464468T>C			NA	NA				PMEPA1 (177876 upstream) : MIR4532 (5981 downstream)						NA		NA									NA						gcttttttttttttttttttt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.56464468T>C		NA		hg19		0.02	-0.131559	TTTxTTT	COVERED																																																																																			NOVEL					0			9	3.306776	KEEP	1	0	0	11	282	TT	0.992708	0.227502	0			3	60	107	0	0	10.325494	3	60	87	36		0.5	0.229173
RAB22A	57403	__UNKNOWN__	__UNKNOWN__	20	56909135	56909135	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:56909135G>C	ENST00000244040.3	+	3	397				RAB22A_ENST00000488949.1_Intron	NM_020673.2	NP_065724.1	Q9UL26	RB22A_HUMAN	RAB22A, member RAS oncogene family	NA		NA			endocytosis (GO:0006897)|endosome organization (GO:0007032)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(1)|large_intestine(2)|pancreas(1)	6	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)			acctgtaatcgcagcactttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF091034	CCDS33497.1	20q13	2008-07-03			ENSG00000124209	ENSG00000124209	57403		RAB, member RAS oncogene	9764	protein-coding gene	gene with protein product		612966			NA		Standard		NM_020673	NA	Approved		uc002xyz.3	Q9UL26	OTTHUMG00000032844	ENST00000244040.3:c.117-9639G>C	chr20.hg19:g.56909135G>C		NA	B3KR86|E1P605|Q8TF12|Q9H4E6	hg19	CCDS33497.1	0.02	-0.12281	ATCxCAG	COVERED																																																																																			NOVEL	RAB22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079880.2	4	3.008471	KEEP	0	0	0	10	296	GG	0.992708	0.19488	0		+	3	60	100	0	0	8.38175	10	60	338	34	ENST00000244040.3	0.230769	0.196312
VAPB	9217	__UNKNOWN__	__UNKNOWN__	20	56968818	56968818	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:56968818G>C	ENST00000475243.1	+	1	396				VAPB_ENST00000265619.2_Intron|VAPB_ENST00000395802.3_Intron	NM_004738.4	NP_004729.1	O95292	VAPB_HUMAN	VAMP (vesicle-associated membrane protein)-associated protein B and C	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|endoplasmic reticulum unfolded protein response (GO:0030968)|modulation by virus of host morphology or physiology (GO:0019048)|positive regulation of viral genome replication (GO:0045070)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-tubulin binding (GO:0048487)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|structural molecule activity (GO:0005198)			kidney(2)|lung(3)|prostate(1)	6	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)			gatggagtttggctcttgttg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF086628	CCDS33498.1, CCDS56198.1	20q13	2014-09-17			ENSG00000124164	ENSG00000124164	9217			12649	protein-coding gene	gene with protein product		605704			NA	9920726	Standard		NM_004738	NA	Approved	VAP-B, VAP-C, ALS8	uc002xza.3	O95292	OTTHUMG00000032840	ENST00000475243.1:c.58+4245G>C	chr20.hg19:g.56968818G>C		NA	A2A2F2|O95293|Q9P0H0	hg19	CCDS33498.1	0.02	-0.184223	TTTxGCT	COVERED																																																																																			NOVEL	VAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079875.2	7	3.310139	KEEP	0	0	0	11	346	GG	0.993634	0.454842	0		+	3	60	96	1	0	7.433207	16	60	553	50	ENST00000475243.1	0.157895	0.457757
GNAS	2778	__UNKNOWN__	__UNKNOWN__	20	57437483	57437483	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:57437483A>G	ENST00000371100.4	+	1	2620				GNAS_ENST00000371075.3_Intron|GNAS_ENST00000464624.2_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371102.4_Intron|GNAS_ENST00000313949.7_Intron	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	NA		NA			activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			caaagtgctgagattacaggt	0.428		NA	Mis		pituitary adenoma		McCune-Albright syndrome; pseudohypoparathyroidism, type IA			TSP Lung(22;0.16)											NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1	yes	E	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460	2778			4392	protein-coding gene	gene with protein product	secretogranin VI	139320	guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1	GNAS1	NA		Standard	NM_000516	NM_000516	NA	Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.2068+7095A>G	chr20.hg19:g.57437483A>G		NA	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	hg19	CCDS46622.1	0.02	-0.105243	CTGxGAT	UNCOVERED																																																																																			NOVEL	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080417.3	8	4.210095	KEEP	8	0	0	14	376	AA	0.992708	0.138812	0		+	3	60	96	0	0	8.232508	8	60	238	40	ENST00000371100.4	0.272727	0.139832
MTG2	26164	__UNKNOWN__	__UNKNOWN__	20	60774468	60774468	__UNKNOWN__	Intron	SNP	G	G	A	rs577787190	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:60774468G>A	ENST00000370823.3	+	6	844				MTG2_ENST00000436421.2_Intron|MTG2_ENST00000536470.1_Intron	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	NA		NA			GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)				NA						ttgggaggccgaggcaggcgg	0.473		NA											G|||	9	0.00179712	0.0061	0.0014	5008	,	,	NA	15652	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181	26164			16239	protein-coding gene	gene with protein product		610919	GTP-binding protein 5 (putative), GTP binding protein 5 (putative)	GTPBP5	NA	17054726, 23396448	Standard	NM_015666	NM_015666	NA	Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.826+155G>A	chr20.hg19:g.60774468G>A		NA	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	hg19	CCDS13492.1	0.02	-0.175427	GCCxAGG	COVERED																																																																																			NOVEL	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079989.1	6	2.406637	KEEP	0	0	0	8	234	GG	0.99257	0.384528	0		+	3	47	87	0	0	6.534023	16	60	518	39	ENST00000370823.3	0.157895	0.387407
MTG2	26164	__UNKNOWN__	__UNKNOWN__	20	60777785	60777785	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:60777785A>G	ENST00000370823.3	+	0	2891					NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	NA		NA			GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)				NA						ctccagcctgagcgacagagc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181	26164			16239	protein-coding gene	gene with protein product		610919	GTP-binding protein 5 (putative), GTP binding protein 5 (putative)	GTPBP5	NA	17054726, 23396448	Standard	NM_015666	NM_015666	NA	Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.*1652A>G	chr20.hg19:g.60777785A>G		NA	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	hg19	CCDS13492.1	0.02	-0.412222	CTGxGCG	COVERED																																																																																			NOVEL	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000079989.1	22	12.63029	KEEP	2	0	0	42	1146	AA	1	0.941741	0		+	3	60	96	0	0	6.441723	36	60	1077	143	ENST00000370823.3	0.076923	0.941741
CABLES2	81928	__UNKNOWN__	__UNKNOWN__	20	60974494	60974494	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:60974494G>A	ENST00000279101.5	-	2	371					NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	NA		NA			cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			tagtagagacggggtttcacc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679	81928			16143	protein-coding gene	gene with protein product		NA	chromosome 20 open reading frame 150	C20orf150	NA	12477932	Standard	XM_037265	NM_031215	NA	Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.363-2846C>T	chr20.hg19:g.60974494G>A		NA	Q5JWL0|Q9BYK0	hg19	CCDS33503.1	0.02	-0.105255	GACxGGG	UNCOVERED																																																																																			NOVEL	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080027.2	10	2.404857	KEEP	6	0	0	8	207	GG	0	0	0		-	3	40	90	0	0	7.501104	9	60	283	25	ENST00000279101.5	0.25	0.139832
COL9A3	1299	__UNKNOWN__	__UNKNOWN__	20	61463522	61463522	__UNKNOWN__	Missense_Mutation	SNP	C	C	A	rs751557	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:61463522C>A	ENST00000343916.3	+	25	1307	c.1304C>A	c.(1303-1305)gCa>gAa	p.A435E		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	435	Triple-helical region 3 (COL3).	NA	A -> E (in dbSNP:rs751557). {ECO:0000269|PubMed:11565064, ECO:0000269|PubMed:8586434}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					GGAGGTGCCGCAGGCCCTAAG	0.602		NA											C|||	1066	0.212859	0.447	0.1729	5008	,	,	NA	20947	0.0496	NA	0.2177	False	NA	,,,	NA	NA	NA	2504	0.0879	NA	NA	NA								NA				0								C	GLU/ALA	1747,2659	513.9+/-368.5	338,1071,794	58	61	60		1304	4.2	0.4	20	dbSNP_86	60	1774,6826	317.9+/-313.4	185,1404,2711	yes	missense	COL9A3	NM_001853.3	107	523,2475,3505	AA,AC,CC	NA	20.6279,39.6505,27.0721	probably-damaging	435/685	61463522	3521,9485	2203	4300	6503	SO:0001583	missense			AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758	1299		Proteoglycans / Extracellular Matrix : Collagen proteoglycans, Collagens	2219	protein-coding gene	gene with protein product	collagen type IX proteoglycan	120270			NA	8586434, 1429648	Standard	NM_001853	NM_001853	NA	Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1304C>A	chr20.hg19:g.61463522C>A	ENSP00000341640:p.Ala435Glu	NA	Q13681|Q9H4G9|Q9UPE2	hg19	CCDS13505.1	0.02	1.485051	CCGxAGG	COVERED	464	0.21245421245421245	204	0.4146341463414634	66	0.18232044198895028	32	0.055944055944055944	162	0.21372031662269128	C	10.51	1.371130	0.24771	0.396505	0.206279	ENSG00000092758	ENST00000343916	D	0.93712	-3.27	5.2	4.23	0.50019	.	0.843935	0.10592	N	0.656672	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.23185	0.081	B	0.25506	0.061	T	0.04664	-1.0935	9	0.07325	T	0.83	.	12.5103	0.56002	0.0:0.868:0.0:0.132	rs751557;rs59729765;rs751557	435	Q14050	CO9A3_HUMAN	E	435	ENSP00000341640:A435E	ENSP00000341640:A435E	A	+	2	0	COL9A3	60933967	0.003000	0.15002	0.425000	0.26659	0.227000	0.25037	0.934000	0.28910	2.584000	0.87258	0.462000	0.41574	GCA	NOVEL	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080071.2	0	2.406974	KEEP	0	0	0	8	240	CC	0.99257	0.988831	0		+	25	60	712	0	0	63.697013	43	60	1490	111	ENST00000343916.3	0.367647	0.996233
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	61502034	61502034	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:61502034A>G			NA	NA				TCFL5 (8919 upstream) : DIDO1 (7055 downstream)						NA		NA									NA						gagccaccgcacccggccatt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.61502034A>G		NA		hg19		0.02	-0.236761	CGCxCCC	COVERED																																																																																			NOVEL					0			9	3.306079	KEEP	4	0	0	11	280	AA	0.992708	0.607941	0			4	60	131	0	0	10.395058	19	60	529	55		0.173913	0.612407
PTK6	5753	__UNKNOWN__	__UNKNOWN__	20	62162514	62162514	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62162514C>A	ENST00000217185.2	-	6	860				PTK6_ENST00000542869.1_Intron	NM_005975.3	NP_005966.1	Q13882	PTK6_HUMAN	protein tyrosine kinase 6	NA		NA			cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|intestinal epithelial cell differentiation (GO:0060575)|negative regulation of growth (GO:0045926)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(1)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	15	all_cancers(38;2.51e-11)		Epithelial(9;1.5e-08)|all cancers(9;8.67e-08)|BRCA - Breast invasive adenocarcinoma(10;6.43e-06)		Vandetanib(DB05294)	gtggctcacgcctgtaatccc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U61412	CCDS13524.1, CCDS74750.1	20q13.3	2013-02-18	2013-02-18		ENSG00000101213	ENSG00000101213	5753	2.7.10.1	SH2 domain containing	9617	protein-coding gene	gene with protein product		602004	PTK6 protein tyrosine kinase 6		NA	8247543, 9284935	Standard		NM_005975	NA	Approved	BRK	uc002yfg.4	Q13882	OTTHUMG00000033039	ENST00000217185.2:c.833-234G>T	chr20.hg19:g.62162514C>A		NA	B2RCR3|B4DW46|Q58F01	hg19	CCDS13524.1	0.02	-0.131591	ACGxCTG	UNCOVERED																																																																																			NOVEL	PTK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080313.1	8	2.708095	KEEP	3	0	0	9	279	CC	0	0	0		-	3	60	93	0	0	7.57262	11	60	389	38	ENST00000217185.2	0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	20	62208557	62208557	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62208557A>G			NA	NA				HELZ2 (2965 upstream) : GMEB2 (10397 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr20.hg19:g.62208557A>G		NA		hg19		0.02	-0.175388	CTGxGAT	COVERED																																																																																			NOVEL					0			6	3.609626	KEEP	1	0	0	12	337	AA	0.993072	0.384723	0			3	60	86	0	0	6.366528	17	60	528	46		0.15	0.387407
GMEB2	26205	__UNKNOWN__	__UNKNOWN__	20	62252956	62252956	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62252956G>C	ENST00000370077.1	-	2	86					NM_012384.3	NP_036516.1	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			ggaggcagaggttgcagtgag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216	26205			4371	protein-coding gene	gene with protein product		607451			NA	10523663, 11743720	Standard	NM_012384	NM_012384	NA	Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000370077.1:c.57-2149C>G	chr20.hg19:g.62252956G>C		NA	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	hg19	CCDS13528.1	0.02	-0.315788	GAGxTTG	COVERED																																																																																			NOVEL	GMEB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080168.1	38	4.543536	KEEP	15	1	25	24	686	GG	0.997832	0.81669	0		-	6	26	183	0	0	14.369511	27	60	906	81	ENST00000370077.1	0.181818	0.818465
GMEB2	26205	__UNKNOWN__	__UNKNOWN__	20	62252964	62252964	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62252964G>C	ENST00000370077.1	-	2	86					NM_012384.3	NP_036516.1	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			aggttgcagtgagccgagatc	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216	26205			4371	protein-coding gene	gene with protein product		607451			NA	10523663, 11743720	Standard	NM_012384	NM_012384	NA	Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000370077.1:c.57-2157C>G	chr20.hg19:g.62252964G>C		NA	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	hg19	CCDS13528.1	0.02	-0.289423	AGTxAGC	COVERED																																																																																			NOVEL	GMEB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080168.1	44	8.720918	KEEP	21	0	0	29	817	GG	0.999859	0.78095	0		-	3	23	93	0	0	6.49855	27	60	876	83	ENST00000370077.1	0.1	0.78106
GMEB2	26205	__UNKNOWN__	__UNKNOWN__	20	62252977	62252977	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62252977G>C	ENST00000370077.1	-	2	86					NM_012384.3	NP_036516.1	Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			ccgagatcgtgccactgcact	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216	26205			4371	protein-coding gene	gene with protein product		607451			NA	10523663, 11743720	Standard	NM_012384	NM_012384	NA	Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000370077.1:c.57-2170C>G	chr20.hg19:g.62252977G>C		NA	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	hg19	CCDS13528.1	0.02	-0.298265	CGTxCCA	COVERED																																																																																			NOVEL	GMEB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080168.1	53	6.831871	KEEP	30	1	32	34	966	GG	0.99986	0.800133	0		-	3	23	96	0	0	6.797773	27	60	907	95	ENST00000370077.1	0.1	0.800245
ZNF512B	57473	__UNKNOWN__	__UNKNOWN__	20	62662962	62662962	__UNKNOWN__	Intron	SNP	C	C	G	rs529444428		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62662962C>G	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Intron			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(16)|ovary(1)|prostate(4)|skin(1)	33	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					ggaggcagagcttgcagtgag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB033022	CCDS13548.1	20q13.33	2011-02-09			ENSG00000196700	ENSG00000196700	57473			29212	protein-coding gene	gene with protein product		NA			NA	10574462	Standard	NM_020713	NM_020713	NA	Approved	GM632, MGC149845, MGC149846	uc002yhl.2	Q96KM6	OTTHUMG00000033008	ENST00000450537.1:c.4+17095G>C	chr20.hg19:g.62662962C>G		NA	Q08AK9|Q9ULM4	hg19	CCDS13548.1	0.02	-0.096498	GAGxTTG	UNCOVERED																																																																																			NOVEL	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080246.1	9	3.309847	KEEP	3	0	0	11	337	CC	0.993072	0.119602	0		-	3	53	97	0	0	8.478396	7	60	241	34	ENST00000450537.1	0.3	0.120436
LINC00266-1	140849	__UNKNOWN__	__UNKNOWN__	20	62933924	62933924	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr20:62933924T>C	ENST00000279067.3	+	0	519					NR_040415.1				long intergenic non-protein coding RNA 266-1	NA		NA									NA						cacctgtaattccagcacttt	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC118988		20q13.33	2012-10-12	2011-08-11	2011-08-11	ENSG00000149656	ENSG00000149656	140849		Long non-coding RNAs	16202	non-coding RNA	RNA, long non-coding		NA	chromosome 20 open reading frame 69, non-protein coding RNA 266, non-protein coding RNA 266-1	C20orf69, NCRNA00266, NCRNA00266-1	NA		Standard		NR_040415	NA	Approved	bA476I15.3	uc002yio.1		OTTHUMG00000033036	ENST00000279067.3:	chr20.hg19:g.62933924T>C		NA		hg19		0.02	-0.131546	AATxCCA	UNCOVERED																																																																																			NOVEL	LINC00266-1-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000080304.2	3	2.405653	KEEP	3	0	0	8	214	TT	0	0	0		+	3	60	90	0	0	7.172718	12	60	348	39	ENST00000279067.3	0.2	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9650060	9650060	__UNKNOWN__	IGR	SNP	C	C	T	rs376222179		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9650060C>T			NA	NA				None (None upstream) : CR381670.1 (33130 downstream)						NA		NA									NA						TCTGGGACCACACCACACCAG	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9650060C>T		NA		hg19		0.02	-0.17543	CCAxACC	UNCOVERED																																																																																			NOVEL					0			6	3.00904	KEEP	36	0	0	10	307	CC	0	0	0			9	59	258	0	0	24.383005	10	60	347	80		0.473684	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9650093	9650093	__UNKNOWN__	IGR	SNP	T	T	A	rs370942166		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9650093T>A			NA	NA				None (None upstream) : CR381670.1 (33097 downstream)						NA		NA									NA						TCCACGTCATTTGCCTTCTAT	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9650093T>A		NA		hg19		0.02	-0.192945	CATxTGC	UNCOVERED																																																																																			NOVEL					0			10	3.908808	KEEP	52	0	0	13	352	TT	0	0	0			9	59	261	0	0	24.163899	12	60	371	118		0.428571	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9673723	9673723	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9673723A>G			NA	NA				None (None upstream) : CR381670.1 (9467 downstream)						NA		NA									NA						tcacaggtgcacgccaccacg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9673723A>G		NA		hg19		0.02	-0.140296	TGCxCGC	COVERED																																																																																			NOVEL					0			8	3.909917	KEEP	7	0	0	13	365	AA	0.992708	0.259062	0			3	25	87	0	0	6.973101	11	48	335	41		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9674257	9674257	__UNKNOWN__	IGR	SNP	T	T	A	rs369935090		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9674257T>A			NA	NA				None (None upstream) : CR381670.1 (8933 downstream)						NA		NA									NA						ccactgcacctggcctctttt	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9674257T>A		NA		hg19		0.02	-0.201731	ACCxGGC	COVERED																																																																																			NOVEL					0			6	4.512027	KEEP	4	0	0	15	424	TT	0.994391	0.487793	0			3	60	93	0	0	6.927423	19	60	576	60		0.136364	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9676521	9676521	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9676521G>T			NA	NA				None (None upstream) : CR381670.1 (6669 downstream)						NA		NA									NA						gggcgcggtggctcacacctg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9676521G>T		NA		hg19		0.02	1.186451	GTGxCTC	COVERED																																																																																			NOVEL					0			30	11.198922	KEEP	13	2	56	57	1733	GG	1	0.984161	0			5	60	140	0	0	9.475223	42	60	1415	173		0.106383	0.984161
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9676951	9676951	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9676951A>C			NA	NA				None (None upstream) : CR381670.1 (6239 downstream)						NA		NA									NA						gatctcagctaactgcaacct	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9676951A>C		NA		hg19		0.02	-0.271848	GCTxACT	COVERED																																																																																			NOVEL					0			12	5.412279	KEEP	7	0	0	18	477	AA	0.99649	0.714798	0			3	60	104	0	0	7.794703	23	60	643	81		0.115385	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9677112	9677112	__UNKNOWN__	IGR	SNP	T	T	G	rs368853700		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9677112T>G			NA	NA				None (None upstream) : CR381670.1 (6078 downstream)						NA		NA									NA						actcctgacctcagatgatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9677112T>G		NA		hg19		0.02	-0.359506	ACCxCAG	COVERED																																																																																			NOVEL					0			20	3.039047	KEEP	9	1	28	20	545	TT	0.99986	0.88875	0			5	49	157	1	0	11.789269	31	60	941	96		0.138889	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9677132	9677132	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9677132G>A			NA	NA				None (None upstream) : CR381670.1 (6058 downstream)						NA		NA									NA						cacctgcctcggcctcccaaa	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9677132G>A		NA		hg19		0.02	-0.306999	CTCxGCC	COVERED																																																																																			NOVEL					0			14	5.109941	KEEP	9	0	0	17	494	GG	0.997832	0.79851	0			3	42	93	0	0	6.410205	29	60	944	88		0.09375	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9677133	9677133	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9677133G>T			NA	NA				None (None upstream) : CR381670.1 (6057 downstream)						NA		NA									NA						acctgcctcggcctcccaaag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9677133G>T		NA		hg19		0.02	-0.298263	TCGxCCT	COVERED																																																																																			NOVEL					0			14	4.813939	KEEP	9	0	0	16	489	GG	0.997832	0.779366	0			3	36	92	0	0	6.353672	28	60	948	87		0.096774	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9678986	9678986	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9678986G>A			NA	NA				None (None upstream) : CR381670.1 (4204 downstream)						NA		NA									NA						gattacaggcgtgagccacca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9678986G>A		NA		hg19		0.02	-0.263172	GGCxTGA	COVERED																																																																																			NOVEL					0			25	8.155256	KEEP	73	1	28	37	1082	GG	0.999859	0.693571	0			3	40	90	0	0	6.343382	24	60	811	190		0.111111	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9678988	9678988	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9678988G>A			NA	NA				None (None upstream) : CR381670.1 (4202 downstream)						NA		NA									NA						ttacaggcgtgagccaccaag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9678988G>A		NA		hg19		0.02	-0.263153	CGTxAGC	COVERED																																																																																			NOVEL					0			24	8.658505	KEEP	72	1	26	38	1161	GG	0.999859	0.693571	0			3	41	89	0	0	6.349896	22	60	734	187		0.12	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9712216	9712216	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9712216G>T			NA	NA				CR381670.1 (28944 upstream) : MIR3648 (113615 downstream)						NA		NA									NA						gtccagtctggtctcaaaata	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9712216G>T		NA		hg19		0.02	-0.280705	CTGxTCT	COVERED																																																																																			NOVEL					0			22	6.017589	KEEP	18	0	0	20	601	GG	0.993072	0.734547	0			4	46	112	0	0	8.059264	25	60	848	85		0.137931	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9712278	9712278	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9712278G>A			NA	NA				CR381670.1 (29006 upstream) : MIR3648 (113553 downstream)						NA		NA									NA						tgggattacaggtgtaagccc	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9712278G>A		NA		hg19		0.02	-0.19298	ACAxGTG	COVERED																																																																																			NOVEL					0			15	5.416082	KEEP	17	0	0	18	551	GG	0.99257	0.454356	0			4	46	119	0	0	9.368961	17	47	551	69		0.190476	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9717693	9717693	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9717693C>T			NA	NA				CR381670.1 (34421 upstream) : MIR3648 (108138 downstream)						NA		NA									NA						caggaggatccccggagccca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9717693C>T		NA		hg19		0.02	-0.105261	ATCxCCG	UNCOVERED																																																																																			NOVEL					0			7	3.309405	KEEP	10	0	0	11	336	CC	0	0	0			3	24	84	0	0	7.032043	8	47	280	36		0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9717696	9717696	__UNKNOWN__	IGR	SNP	G	G	A	rs372031039		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9717696G>A			NA	NA				CR381670.1 (34424 upstream) : MIR3648 (108135 downstream)						NA		NA									NA						gaggatccccggagcccagga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9717696G>A		NA		hg19		0.02	-0.114035	CCCxGAG	UNCOVERED																																																																																			NOVEL					0			6	3.008706	KEEP	9	0	0	10	305	GG	0	0	0			5	24	149	0	0	13.992954	6	47	209	35		0.454545	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9721873	9721873	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9721873C>T			NA	NA				CR381670.1 (38601 upstream) : MIR3648 (103958 downstream)						NA		NA									NA						ctgcctacctcagcctcccaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9721873C>T		NA		hg19		0.02	-0.298261	CCTxAGC	COVERED																																																																																			NOVEL					0			19	3.24343	KEEP	19	1	29	21	657	CC	0.994391	0.776679	0			3	24	94	0	0	6.79494	23	60	776	102		0.115385	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9721874	9721874	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9721874A>G			NA	NA				CR381670.1 (38602 upstream) : MIR3648 (103957 downstream)						NA		NA									NA						tgcctacctcagcctcccaaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9721874A>G		NA		hg19		0.02	-0.28946	CTCxGCC	COVERED																																																																																			NOVEL					0			19	2.840803	KEEP	21	1	33	21	596	AA	0.993634	0.756043	0			3	24	104	1	0	7.794271	23	60	707	102		0.115385	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9723289	9723289	__UNKNOWN__	IGR	SNP	C	C	A	rs79066070		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9723289C>A			NA	NA				CR381670.1 (40017 upstream) : MIR3648 (102542 downstream)						NA		NA									NA						gtattcccagcactttgggag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9723289C>A		NA		hg19		0.02	-0.333326	CAGxACT	COVERED																																																																																			NOVEL					0			26	5.750142	KEEP	7	1	22	27	836	CC	0.999988	0.851974	0			3	60	93	0	0	6.368278	30	51	1001	96		0.090909	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9723401	9723401	__UNKNOWN__	IGR	SNP	G	G	A	rs77555422		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9723401G>A			NA	NA				CR381670.1 (40129 upstream) : MIR3648 (102430 downstream)						NA		NA									NA						gccgggcatggtggcacatgc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9723401G>A		NA		hg19		0.02	-0.263175	ATGxTGG	COVERED																																																																																			NOVEL					0			21	3.475882	KEEP	10	2	52	30	914	GG	0.999988	0.69366	0			6	49	184	0	0	15.052135	21	60	727	98		0.222222	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9723405	9723405	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9723405C>T			NA	NA				CR381670.1 (40133 upstream) : MIR3648 (102426 downstream)						NA		NA									NA						ggcatggtggcacatgcctgt	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9723405C>T		NA		hg19		0.02	-0.254411	TGGxACA	COVERED																																																																																			NOVEL					0			21	9.628776	KEEP	10	0	0	32	983	CC	0.999988	0.668515	0			3	23	90	0	0	6.39536	23	60	808	93		0.115385	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9825490	9825490	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9825490C>G			NA	NA				CR381670.1 (142218 upstream) : MIR3648 (341 downstream)						NA		NA									NA						GGTTTCTCCCCGAGCCGCCGC	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9825490C>G		NA		hg19		0.02	24.761157	CCCxGAG	COVERED																																																																																			NOVEL					0			221	21.702141	KEEP	3	2	65	95	2843	CC	1	1	0			18	60	597	0	0	32.565112	637	60	20859	1129		0.027481	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9826910	9826910	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9826910T>C			NA	NA				MIR3687 (647 upstream) : TEKT4P2 (80283 downstream)						NA		NA									NA						cgtccgtccgtcGTCCTCCTC	0.846		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9826910T>C		NA		hg19		0.02	9.70777	CCGxCGT	COVERED																																																																																			NOVEL					0			9	18.33403	KEEP	5	0	0	61	1561	TT	1	1	0			16	60	523	0	0	39.670617	101	60	2796	580		0.136752	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9864118	9864118	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9864118T>C			NA	NA				MIR3687 (37855 upstream) : TEKT4P2 (43075 downstream)						NA		NA									NA						ctgattcaagtgattctcctg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9864118T>C		NA		hg19		0.02	-0.298154	AAGxGAT	COVERED																																																																																			NOVEL					0			16	6.909205	KEEP	4	0	0	23	585	TT	0.999869	0.780958	0			3	60	94	1	0	6.553758	28	60	816	81		0.096774	0.78106
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9864223	9864223	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9864223C>T			NA	NA				MIR3687 (37960 upstream) : TEKT4P2 (42970 downstream)						NA		NA									NA						accatgttggccaggctggtt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9864223C>T		NA		hg19		0.02	-0.210536	TGGxCAG	COVERED																																																																																			NOVEL					0			5	3.008575	KEEP	2	0	0	10	297	CC	0.99254	0.518266	0			3	46	93	0	0	7.133411	16	60	533	51		0.157895	0.522161
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9909043	9909043	__UNKNOWN__	RNA	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9909043C>G	ENST00000416067.1	-	0	360					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						TCAGGGTGCCCCACCTTGTGC	0.672		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													0	1	1			NA	NA	21		NA											NA				9909043		0	1	1							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9909043C>G		NA		hg19		0.02	1.748246	GCCxCAC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	2	2.406296	KEEP	0	0	0	8	230	CC	0.99257	0.990484	0		-	13	60	405	0	0	32.296642	55	60	1828	108	ENST00000416067.1	0.191176	0.997898
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9909122	9909122	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9909122G>A	ENST00000416067.1	-	0	284					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						CCAGGTTCACGGCGTCACACT	0.682		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9909122G>A		NA		hg19		0.02	6.373386	CACxGCG	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	0	4.444065	KEEP	0	1	29	25	731	GG	0.999957	0.999957	0		-	28	60	851	0	0	64.4666	155	60	5000	319	ENST00000416067.1	0.153005	1
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9909163	9909163	__UNKNOWN__	RNA	SNP	G	G	A	rs371591302		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9909163G>A	ENST00000416067.1	-	0	243					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						GTGTCGCGAAGGATGCAGTCC	0.662		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9909163G>A		NA		hg19		0.02	7.844027	GAAxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	.	7.278	0.608569	0.14002	.	.	ENSG00000227328	ENST00000416067	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.64789	0.2630	.	.	.	.	.	.	D	0.89917	1.0	D	0.85130	0.997	T	0.66412	-0.5930	5	.	.	.	.	5.9913	0.19465	6.0E-4:0.0:0.9994:0.0	.	58	B7WNX9	.	F	58	.	.	L	-	1	0	TEKT4P2	.	0.993000	0.37304	0.126000	0.21872	0.128000	0.20619	1.253000	0.32886	0.181000	0.19994	0.184000	0.17185	CTT	NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	4	6.987888	KEEP	26	2	56	43	1346	GG	1	1	0		-	26	60	790	0	0	57.386187	182	60	6303	483	ENST00000416067.1	0.125	1
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9910040	9910040	__UNKNOWN__	RNA	SNP	G	G	A	rs78285648		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9910040G>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						CACCTTGTCCGACCAGTCCAT	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9910040G>A		NA		hg19		0.02	4.543089	TCCxACC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	2	3.543334	KEEP	6	1	29	22	666	GG	0.999879	0.999879	0		-	37	60	1047	0	0	85.844514	114	60	3708	374	ENST00000416067.1	0.245033	1
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9911218	9911218	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9911218G>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						CAGGGGGATAGGCCTGCAGAA	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9911218G>A		NA		hg19		0.02	1.251868	ATAxGCC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	17	7.047098	KEEP	18	1	27	33	1023	GG	0.999988	0.997885	0		-	9	60	243	0	0	17.385053	54	60	1822	158	ENST00000416067.1	0.142857	0.997898
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9912348	9912348	__UNKNOWN__	RNA	SNP	G	G	A	rs373135624	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9912348G>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						GTAGACGCCCGTGTTGCGGGC	0.637		NA											.|||	2672	0.533546	0.3903	0.5605	5008	,	,	NA	4585	0.7331	NA	0.5368	False	NA	,,,	NA	NA	NA	2504	0.499	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9912348G>A		NA		hg19		0.02	3.046348	CCCxTGT	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	1	2.339249	KEEP	11	1	23	16	483	GG	0.997832	0.99783	0		-	9	60	256	0	0	19.255063	46	60	1479	207	ENST00000416067.1	0.163636	0.999998
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9912410	9912410	__UNKNOWN__	RNA	SNP	C	C	T	rs6605398		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9912410C>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						TCTGCGGTGCCGGCTCTGGTA	0.657		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9912410C>T		NA		hg19		0.02	1.449935	TGCxGGC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	0	2.706841	KEEP	2	0	0	9	264	CC	0.99254	0.990453	0		-	11	60	332	0	0	26.798014	41	60	1333	113	ENST00000416067.1	0.211538	0.997898
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9943643	9943643	__UNKNOWN__	RNA	SNP	C	C	T	rs374534514		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9943643C>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						ggcttggtggctcacgcctgt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9943643C>T		NA		hg19		0.02	1.050135	TGGxTCA	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	51	3.374035	KEEP	15	5	129	57	1735	CC	1	0.99993	0		-	12	60	323	0	0	24.359842	55	60	1888	236	ENST00000416067.1	0.179104	0.99993
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9943656	9943656	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9943656T>C	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						acgcctgtaatcccagcactt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9943656T>C		NA		hg19		0.02	1.646242	TAAxCCC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	50	4.94188	KEEP	14	4	118	58	1609	TT	1	0.99993	0		-	5	60	171	0	0	11.766305	62	60	1875	245	ENST00000416067.1	0.074627	0.99993
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9943659	9943659	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9943659C>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						cctgtaatcccagcactttgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9943659C>T		NA		hg19		0.02	1.157721	TCCxAGC	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	50	12.102807	KEEP	15	2	56	60	1853	CC	1	0.999919	0		-	6	60	183	0	0	12.396649	61	60	2121	249	ENST00000416067.1	0.089552	0.999919
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9946313	9946313	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9946313G>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						atagagatgaggtttcaccat	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9946313G>A		NA		hg19		0.02	-0.289469	TGAxGTT	UNCOVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	21	6.01751	KEEP	44	0	0	20	609	GG	0	0	0		-	4	49	122	0	0	9.579426	18	60	604	104	ENST00000416067.1	0.181818	0.760887
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9946699	9946699	__UNKNOWN__	RNA	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9946699T>A	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						gtgattctcctgcctcagcct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9946699T>A		NA		hg19		0.02	-0.139953	TCCxGCC	UNCOVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	12	3.609143	KEEP	14	0	0	12	331	TT	0	0	0		-	3	22	82	0	0	6.378267	12	48	328	52	ENST00000416067.1	0.2	0.260965
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9952307	9952307	__UNKNOWN__	RNA	SNP	C	C	T	rs12411201		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9952307C>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						tcccacagagctgagattatg	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9952307C>T		NA		hg19		0.02	-0.421085	GAGxTGA	COVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	31	6.351865	KEEP	20	1	28	31	945	CC	0.999869	0.948278	0		-	6	49	190	0	0	14.451971	35	60	1207	127	ENST00000416067.1	0.146341	0.948402
TEKT4P2	100132288	__UNKNOWN__	__UNKNOWN__	21	9956707	9956707	__UNKNOWN__	RNA	SNP	A	A	T	rs376888039		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9956707A>T	ENST00000416067.1	-	0	129					NR_037872.1|NR_038327.1				tektin 4 pseudogene 2	NA		NA									NA						caaaaaaaaaaaaataaaaat	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							21p11.2	2012-10-03	2011-06-14	2011-06-14	ENSG00000188681	ENSG00000188681	100132288			40046	pseudogene	pseudogene		NA	MAFF interacting protein-like	MAFIPL	NA		Standard	NM_001033515	NR_038327	NA	Approved		uc021wgx.1		OTTHUMG00000172149	ENST00000416067.1:	chr21.hg19:g.9956707A>T		NA		hg19		0.02	-0.078933	AAAxAAA	UNCOVERED																																																																																			NOVEL	TEKT4P2-002	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000417115.1	12	3.909489	KEEP	8	0	0	13	351	AA	0.99257	0.076761	0		-	4	60	120	0	0	12.24919	2	60	57	34	ENST00000416067.1	0.666667	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9971390	9971390	__UNKNOWN__	IGR	SNP	G	G	A	rs371958485		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9971390G>A			NA	NA				TEKT4P2 (2805 upstream) : CR381653.1 (228552 downstream)						NA		NA									NA						agccaagattgcaccactgca	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9971390G>A		NA		hg19		0.02	-0.219253	ATTxCAC	COVERED																																																																																			NOVEL					0			14	2.841317	KEEP	5	1	21	17	517	GG	0.999366	0.552537	0			7	60	205	0	0	18.215203	13	60	436	63		0.35	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9971978	9971978	__UNKNOWN__	IGR	SNP	C	C	T	rs377294606		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9971978C>T			NA	NA				TEKT4P2 (3393 upstream) : CR381653.1 (227964 downstream)						NA		NA									NA						tcaagaccagcctggccaaca	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9971978C>T		NA		hg19		0.02	-0.236847	CAGxCTG	COVERED																																																																																			NOVEL					0			12	3.61021	KEEP	6	0	0	12	354	CC	0.992708	0.607941	0			4	33	126	0	0	9.662287	22	60	728	57		0.153846	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9983842	9983842	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9983842C>A			NA	NA				TEKT4P2 (15257 upstream) : CR381653.1 (216100 downstream)						NA		NA									NA						attagccgggcgtggtggcat	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9983842C>A		NA		hg19		0.02	-0.236818	GGGxGTG	COVERED																																																																																			NOVEL					0			21	5.111508	KEEP	14	0	0	17	462	CC	0.994391	0.63775	0			4	60	118	0	0	9.095094	19	60	605	62		0.173913	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9983938	9983938	__UNKNOWN__	IGR	SNP	G	G	A	rs372867541		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9983938G>A			NA	NA				TEKT4P2 (15353 upstream) : CR381653.1 (216004 downstream)						NA		NA									NA						cctagatcacgccactgcact	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9983938G>A		NA		hg19		0.02	-0.20174	CACxCCA	COVERED																																																																																			NOVEL					0			22	4.430039	KEEP	22	1	29	25	725	GG	0.997832	0.489481	0			4	60	103	0	0	8.181076	13	60	445	86		0.235294	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9984103	9984103	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9984103C>A			NA	NA				TEKT4P2 (15518 upstream) : CR381653.1 (215839 downstream)						NA		NA									NA						aacagaatgacagtttattgt	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9984103C>A		NA		hg19		0.02	-0.122805	TGAxAGT	COVERED																																																																																			NOVEL					0			17	2.940914	KEEP	12	1	26	19	562	CC	0.995343	0.195397	0			3	23	90	0	0	7.501027	9	50	291	46		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	9987567	9987567	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:9987567A>T			NA	NA				TEKT4P2 (18982 upstream) : CR381653.1 (212375 downstream)						NA		NA									NA						tgtcaaaaagaaaaaggaaaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.9987567A>T		NA		hg19		0.02	-0.166617	AAGxAAA	COVERED																																																																																			NOVEL					0			17	8.719896	KEEP	9	0	0	29	774	AA	0.999931	0.353922	0			3	47	89	0	0	6.892422	14	49	403	77		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10000475	10000475	__UNKNOWN__	IGR	SNP	G	G	T	rs374120822		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10000475G>T			NA	NA				TEKT4P2 (31890 upstream) : CR381653.1 (199467 downstream)						NA		NA									NA						gggactacaggcgtgtgccac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10000475G>T		NA		hg19		0.02	-0.34211	CAGxCGT	COVERED																																																																																			NOVEL					0			23	6.017241	KEEP	5	0	0	20	598	GG	0.999869	0.888759	0			4	49	123	0	0	8.862665	30	60	996	90		0.117647	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10000524	10000524	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10000524G>A			NA	NA				TEKT4P2 (31939 upstream) : CR381653.1 (199418 downstream)						NA		NA									NA						tagagatggggtttcaccgtg	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10000524G>A		NA		hg19		0.02	-0.228079	GGGxTTT	COVERED																																																																																			NOVEL					0			21	6.919873	KEEP	27	0	0	23	686	GG	0.995343	0.580216	0			3	50	90	0	0	6.506257	21	60	707	84		0.125	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10012771	10012771	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10012771T>C			NA	NA				TEKT4P2 (44186 upstream) : CR381653.1 (187171 downstream)						NA		NA									NA						aattttggcttactgcaagct	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10012771T>C		NA		hg19		0.02	-0.350778	GCTxACT	COVERED																																																																																			NOVEL					0			30	9.620686	KEEP	4	0	0	32	838	TT	0.999997	0.877705	0			3	60	94	0	0	6.510347	29	60	821	97		0.09375	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10031942	10031942	__UNKNOWN__	IGR	SNP	T	T	C	rs376121880		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10031942T>C			NA	NA				TEKT4P2 (63357 upstream) : CR381653.1 (168000 downstream)						NA		NA									NA						ggagatgaagtctcgctctgt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10031942T>C		NA		hg19		0.02	-0.23681	AAGxCTC	COVERED																																																																																			NOVEL					0			14	3.308835	KEEP	4	0	0	11	313	TT	0.99254	0.607839	0			4	43	140	0	0	11.294371	19	60	563	55		0.173913	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10143252	10143252	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10143252C>A			NA	NA				TEKT4P2 (174667 upstream) : CR381653.1 (56690 downstream)						NA		NA									NA						gtggctcacgcctgtaatccc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10143252C>A		NA		hg19		0.02	1.654432	ACGxCTG	COVERED																																																																																			NOVEL					0			39	15.479652	KEEP	42	1	30	62	1908	CC	1	0.989542	0			5	46	155	1	0	10.785317	46	50	1600	231		0.098039	0.989542
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10143279	10143279	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10143279G>A			NA	NA				TEKT4P2 (174694 upstream) : CR381653.1 (56663 downstream)						NA		NA									NA						ctgggaggccgaggtgggcag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10143279G>A		NA		hg19		0.02	-0.420963	GCCxAGG	COVERED																																																																																			NOVEL					0			28	14.438797	KEEP	36	0	0	48	1428	GG	0.999998	0.9484	0			7	47	186	0	0	14.063866	31	49	1020	166		0.184211	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10145113	10145113	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10145113G>T			NA	NA				TEKT4P2 (176528 upstream) : CR381653.1 (54829 downstream)						NA		NA									NA						gactacaggtgcacaccacca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10145113G>T		NA		hg19		0.02	1.531695	GGTxCAC	COVERED																																																																																			NOVEL					0			38	9.591985	KEEP	30	2	48	49	1473	GG	1	0.998695	0			5	49	158	0	0	10.434187	63	52	2127	202		0.073529	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10145250	10145250	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10145250G>A			NA	NA				TEKT4P2 (176665 upstream) : CR381653.1 (54692 downstream)						NA		NA									NA						ttacatgaatgagccactgca	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10145250G>A		NA		hg19		0.02	-0.245585	AATxAGC	COVERED																																																																																			NOVEL					0			12	2.741134	KEEP	7	1	28	19	577	GG	0.997832	0.639957	0			5	60	142	0	0	11.701974	15	60	476	69		0.25	0.641347
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10146483	10146483	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10146483A>G			NA	NA				TEKT4P2 (177898 upstream) : CR381653.1 (53459 downstream)						NA		NA									NA						tagagtcagcatctcgctatt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10146483A>G		NA		hg19		0.02	1.491171	AGCxTCT	COVERED																																																																																			NOVEL					0			30	3.672903	KEEP	23	2	56	32	894	AA	0.999909	0.981866	0			11	48	327	0	0	26.096922	43	51	1319	123		0.203704	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10211993	10211993	__UNKNOWN__	IGR	SNP	G	G	A	rs371364427		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10211993G>A			NA	NA				CR381653.1 (11968 upstream) : RN7SL52P (168386 downstream)						NA		NA									NA						tcttggccaggctggtcttga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10211993G>A		NA		hg19		0.02	-0.17543	CAGxCTG	COVERED																																																																																			NOVEL					0			15	2.439846	KEEP	34	1	28	18	552	GG	0.992708	0.384582	0			5	53	144	0	0	12.030028	14	54	476	84		0.263158	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10586285	10586285	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10586285C>A			NA	NA				SNORA70 (200238 upstream) : IGHV1OR21-1 (276336 downstream)						NA		NA									NA						cagtggctcacacctgtaatc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10586285C>A		NA		hg19		0.02	-0.131516	TCAxACC	COVERED																																																																																			NOVEL					0			12	4.34574	KEEP	3	1	27	24	731	CC	0.999931	0.260947	0			8	54	219	0	0	22.397478	4	46	114	61		0.666667	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	10806920	10806920	__UNKNOWN__	IGR	SNP	T	T	C	rs200202393|rs55638432		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10806920T>C			NA	NA				SNORA70 (420873 upstream) : IGHV1OR21-1 (55701 downstream)						NA		NA									NA						tggaatggactcgaatggaat	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.10806920T>C		NA		hg19		0.02	-0.070173	GACxCGA	UNCOVERED																																																																																			NOVEL					0			10	2.406662	KEEP	3	0	0	8	233	TT	0	0	0			2	60	66	0	0	7.55376	0	0	0	25		1	0.054137
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	10910817	10910817	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10910817T>C	ENST00000361285.4	-	22	1686				TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_Intron|TPTE_ENST00000298232.7_Intron	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aaactcctgcttcaagtgatc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1357-418A>G	chr21.hg19:g.10910817T>C		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19	CCDS13560.2	0.02	-0.149111	TGCxTCA	COVERED																																																																																			NOVEL	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157413.1	10	3.007616	KEEP	0	0	0	10	280	TT	0.992708	0.289872	0		-	4	60	117	0	2	9.701448	12	60	375	39	ENST00000361285.4	0.25	0.292001
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	10912288	10912288	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10912288A>G	ENST00000361285.4	-	22	1686				TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_Intron|TPTE_ENST00000298232.7_Intron	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		taacaagagcaaaactccgtc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1357-1889T>C	chr21.hg19:g.10912288A>G		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19	CCDS13560.2	0.02	-0.15787	AGCxAAA	COVERED																																																																																			NOVEL	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157413.1	6	4.21105	KEEP	0	0	0	14	395	AA	0.995343	0.321303	0		-	3	47	98	0	0	7.972378	12	60	350	40	ENST00000361285.4	0.2	0.322807
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	10983533	10983533	__UNKNOWN__	Intron	SNP	T	T	G	rs553469413	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:10983533T>G	ENST00000361285.4	-	3	287				TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_Intron|TPTE_ENST00000298232.7_Intron	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gattacaggcttgagccacca	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.42+1511A>C	chr21.hg19:g.10983533T>G		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19	CCDS13560.2	0.02	-0.175439	GGCxTGA	COVERED																																																																																			NOVEL	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000157413.1	9	2.405517	KEEP	2	0	0	8	216	AT	0.99254	0.420319	0		-	4	60	130	0	0	10.880829	13	60	415	45	ENST00000361285.4	0.235294	0.423478
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11009409	11009409	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11009409A>T	ENST00000415664.2	-	9	1217							P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgagccaccaagcccggccAC	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.2119+2028T>A	chr21.hg19:g.11009409A>T		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.166651	CCAxGCC	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	4	3.007709	KEEP	0	0	0	10	276	AA	0.992708	0.351366	0		-	3	60	88	0	0	6.634004	16	60	494	44	ENST00000415664.2	0.157895	0.353947
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11011888	11011888	__UNKNOWN__	Intron	SNP	G	G	A	rs701479	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11011888G>A	ENST00000415664.2	-	9	1004							P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		GGTCTTCCTGggctgggtgcg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.2333-238C>T	chr21.hg19:g.11011888G>A		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.149131	CTGxGCT	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	5	2.40681	KEEP	0	0	0	8	237	GG	0.99257	0.320408	0		-	4	60	133	0	0	11.301244	12	60	409	41	ENST00000415664.2	0.25	0.322807
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11022485	11022485	__UNKNOWN__	Intron	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11022485A>T	ENST00000415664.2	-	3	239				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cctgggcaacatggtgaaatc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3098-1274T>A	chr21.hg19:g.11022485A>T		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	1.537706	AACxTGG	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	36	3.13233	KEEP	9	4	115	51	1360	AA	1	0.992094	0		-	7	60	222	1	0	16.498732	47	60	1382	161	ENST00000415664.2	0.12963	0.992094
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11022511	11022511	__UNKNOWN__	Intron	SNP	A	A	T	rs540042589	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11022511A>T	ENST00000415664.2	-	3	239				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tctaccaaaaatacaaaaaac	0.507		NA											.|||	513	0.102436	0.0393	0.1268	5008	,	,	NA	96486	0.122	NA	0.1581	False	NA	,,,	NA	NA	NA	2504	0.093	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3098-1300T>A	chr21.hg19:g.11022511A>T		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	1.475146	AAAxTAC	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	33	7.573523	KEEP	7	2	56	45	1173	AA	1	0.986153	0		-	7	60	201	1	0	14.730234	42	60	1188	142	ENST00000415664.2	0.142857	0.986153
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11022969	11022969	__UNKNOWN__	Intron	SNP	G	G	T	rs10881117	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11022969G>T	ENST00000415664.2	-	3	239				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		agtagagatggggtttcacca	0.567		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3098-1758C>A	chr21.hg19:g.11022969G>T		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.245606	ATGxGGT	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	12	4.512742	KEEP	4	0	0	15	449	GG	0.993634	0.637264	0		-	4	60	114	0	0	8.963431	16	60	527	52	ENST00000415664.2	0.2	0.641347
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11025260	11025260	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11025260A>G	ENST00000415664.2	-	2	239				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		actccagcctaggcaacaaga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3097+1462T>C	chr21.hg19:g.11025260A>G		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	1.871152	CCTxGGC	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	32	14.164583	KEEP	59	1	31	58	1580	AA	0.999999	0.987942	0		-	4	60	133	0	0	8.954266	52	60	1524	230	ENST00000415664.2	0.071429	0.987943
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11025279	11025279	__UNKNOWN__	Intron	SNP	C	C	G	rs200711576		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11025279C>G	ENST00000415664.2	-	2	239				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gagcgaaactccatctcaaaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3097+1443G>C	chr21.hg19:g.11025279C>G		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	1.967515	ACTxCAT	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	33	3.143257	KEEP	63	4	121	53	1599	CC	0.999999	0.963773	0		-	5	37	169	0	0	12.629261	37	60	1243	238	ENST00000415664.2	0.119048	0.963774
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11026960	11026960	__UNKNOWN__	Intron	SNP	T	T	G	rs369640717		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11026960T>G	ENST00000415664.2	-	2	122				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TAGATAAGTATTAAAAGACCT	0.264		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3215-121A>C	chr21.hg19:g.11026960T>G		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.350767	GTAxTAA	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	1	2.403733	KEEP	1	0	0	8	207	TT	0.99257	0.871187	0		-	4	60	140	0	0	10.309744	35	60	1008	68	ENST00000415664.2	0.102564	0.877708
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11027065	11027065	__UNKNOWN__	Intron	SNP	C	C	A	rs61601536		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11027065C>A	ENST00000415664.2	-	2	122				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGGCCTGTCACTGTGAACGCT	0.358		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3215-226G>T	chr21.hg19:g.11027065C>A		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.350903	TCAxTGT	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	2	3.009202	KEEP	2	0	0	10	314	CC	0.99254	0.87116	0		-	4	60	125	0	0	8.858234	34	60	1159	68	ENST00000415664.2	0.105263	0.877708
TPTE	7179	__UNKNOWN__	__UNKNOWN__	21	11027085	11027085	__UNKNOWN__	Intron	SNP	A	A	C	rs6421268	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11027085A>C	ENST00000415664.2	-	2	122				BAGE2_ENST00000470054.1_RNA			P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TATCAGCAAGACTTTGCATGA	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391	7179		Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs	12023	protein-coding gene	gene with protein product	PTEN-related tyrosine phosphatase, cancer/testis antigen 44	604336			NA	10830953, 14659893	Standard		NM_001290224	NA	Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000415664.2:c.3215-246T>G	chr21.hg19:g.11027085A>C		NA	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	hg19		0.02	-0.227991	AAGxCTT	COVERED																																																																																			NOVEL	TPTE-006	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000340030.1	1	2.705564	KEEP	2	0	0	9	232	AA	0.99257	0.578599	0		-	5	55	166	0	0	13.554372	20	60	557	44	ENST00000415664.2	0.2	0.58293
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11032055	11032055	__UNKNOWN__	RNA	SNP	G	G	T	rs9796288		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11032055G>T	ENST00000470054.1	-	0	1476							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		taaatgtctggcattttcttt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11032055G>T		NA	A8K925|Q08ER0	hg19		0.02	-0.350754	CTGxCAT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	10	4.445529	KEEP	1	1	23	23	688	GG	0.999892	0.877613	0		-	6	60	173	0	0	12.969674	32	60	1055	90	ENST00000470054.1	0.157895	0.877708
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11034405	11034405	__UNKNOWN__	RNA	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11034405A>C	ENST00000470054.1	-	0	1476							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cttagggaggacaaggcgggt	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11034405A>C		NA	A8K925|Q08ER0	hg19		0.02	-0.377122	AGGxCAA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	19	5.714682	KEEP	3	0	0	19	528	AA	0.999859	0.908941	0		-	3	60	102	0	0	7.226627	31	60	904	89	ENST00000470054.1	0.088235	0.909069
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11038909	11038909	__UNKNOWN__	RNA	SNP	G	G	T	rs28473122	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11038909G>T	ENST00000470054.1	-	0	1294							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAGGTGTTGGGGAGGAAGACA	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11038909G>T		NA	A8K925|Q08ER0	hg19		0.02	4.867412	TGGxGAG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	5	8.291245	KEEP	27	2	52	46	1432	GG	1	1	0		-	12	49	361	0	0	23.438164	145	60	4811	339	ENST00000470054.1	0.076433	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11039033	11039033	__UNKNOWN__	RNA	SNP	G	G	A	rs28369127		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11039033G>A	ENST00000470054.1	-	0	1170							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CTCAATTGTAGGAGTCATTTC	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11039033G>A		NA	A8K925|Q08ER0	hg19		0.02	8.623252	GTAxGAG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	25	5.548053	KEEP	43	4	112	58	1758	GG	1	1	0		-	31	50	972	0	0	70.531843	233	51	8007	539	ENST00000470054.1	0.117424	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11043336	11043336	__UNKNOWN__	RNA	SNP	C	C	T	rs462239	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11043336C>T	ENST00000470054.1	-	0	774							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gccaccacacccggcctaggg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11043336C>T		NA	A8K925|Q08ER0	hg19		0.02	1.815328	CACxCGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	28	5.483027	KEEP	3	2	56	38	1170	CC	1	0.973965	0		-	5	60	161	1	0	11.722708	39	60	1293	132	ENST00000470054.1	0.113636	0.973965
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11056085	11056085	__UNKNOWN__	RNA	SNP	G	G	A	rs28678750	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11056085G>A	ENST00000470054.1	-	0	487							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tccaggcagggtgacagagcg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11056085G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.184216	AGGxTGA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	16	10.720828	KEEP	1	0	0	36	1024	GG	0.999999	0.423477	0		-	3	60	91	0	0	7.27217	12	60	406	68	ENST00000470054.1	0.2	0.423478
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11059849	11059849	__UNKNOWN__	RNA	SNP	G	G	T	rs11183999	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11059849G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gccggacgtggtggcaggcac	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11059849G>T		NA	A8K925|Q08ER0	hg19		0.02	6.32146	GTGxTGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	78	37.81444	KEEP	7	5	133	173	5273	GG	1	1	0		-	13	60	382	1	0	25.420557	132	70	4458	581	ENST00000470054.1	0.089655	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11059852	11059852	__UNKNOWN__	RNA	SNP	G	G	A	rs7279599		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11059852G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ggacgtggtggcaggcacctg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11059852G>A		NA	A8K925|Q08ER0	hg19		0.02	5.988269	GTGxCAG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	81	21.396503	KEEP	6	10	280	170	5238	GG	1	1	0		-	11	60	331	1	0	21.521735	132	70	4497	597	ENST00000470054.1	0.076923	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11059897	11059897	__UNKNOWN__	RNA	SNP	A	A	G	rs6582758	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11059897A>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aagcaggagaaGCTTCTAAAT	0.368		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11059897A>G		NA	A8K925|Q08ER0	hg19		0.02	9.905591	AGAxGCT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	119	9.082304	KEEP	4	17	535	218	6129	AA	1	1	0		-	27	60	907	1	0	69.407101	170	60	5208	784	ENST00000470054.1	0.137056	1
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11059955	11059955	__UNKNOWN__	RNA	SNP	A	A	G	rs4417790	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11059955A>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tttatataatatttataaGTA	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11059955A>G		NA	A8K925|Q08ER0	hg19		0.02	1.739869	AATxTTT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	21	4.187414	KEEP	0	6	170	74	1879	AA	1	0.9982	0		-	4	60	142	0	0	9.45347	66	60	1813	175	ENST00000470054.1	0.057143	0.9982
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11062808	11062808	__UNKNOWN__	RNA	SNP	G	G	A	rs13433466	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11062808G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gcccgatctcggctcactgca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11062808G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.421028	CTCxGCT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	25	9.022433	KEEP	1	0	0	30	903	GG	0.999997	0.948399	0		-	6	60	183	0	0	13.822385	34	60	1095	117	ENST00000470054.1	0.15	0.948402
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11062825	11062825	__UNKNOWN__	RNA	SNP	G	G	A	rs59654296	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11062825G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgcaacctccgccccccaggt	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11062825G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.403497	TCCxCCC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	20	6.151778	KEEP	0	1	18	27	820	GG	0.999997	0.934489	0		-	4	60	119	0	0	8.30791	33	60	1075	112	ENST00000470054.1	0.108108	0.934492
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11064813	11064813	__UNKNOWN__	RNA	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11064813T>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cacgaggtcatgagatcgaga	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11064813T>G		NA	A8K925|Q08ER0	hg19		0.02	1.906219	TCAxGAG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	20	4.471018	KEEP	3	2	60	36	960	TT	0.999999	0.981955	0		-	4	60	127	0	0	8.596098	45	60	1340	143	ENST00000470054.1	0.081633	0.981955
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11064896	11064896	__UNKNOWN__	RNA	SNP	G	G	T	rs4561739	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11064896G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccggcatggtggtgcacgcct	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11064896G>T		NA	A8K925|Q08ER0	hg19		0.02	-0.40347	GGTxGTG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	30	6.551767	KEEP	2	1	29	32	948	GG	0.999997	0.93449	0		-	5	60	141	1	0	10.782297	23	60	749	103	ENST00000470054.1	0.178571	0.934492
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11065074	11065074	__UNKNOWN__	RNA	SNP	C	C	T	rs4108305	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11065074C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aaatggcgagctcagccctac	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11065074C>T		NA	A8K925|Q08ER0	hg19		0.02	-0.289427	GAGxTCA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	31	4.846399	KEEP	1	1	28	26	771	CC	0.999957	0.760854	0		-	3	60	92	0	0	6.827331	19	60	628	65	ENST00000470054.1	0.136364	0.760887
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11066745	11066745	__UNKNOWN__	RNA	SNP	G	G	A	rs1999000	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11066745G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gcttgaacccgggaggtggag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11066745G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.289467	CCCxGGA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	15	4.142944	KEEP	4	1	29	24	682	GG	0.999892	0.760805	0		-	3	60	93	0	0	6.544878	26	60	846	85	ENST00000470054.1	0.103448	0.760887
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11072485	11072485	__UNKNOWN__	RNA	SNP	C	C	G	rs2380041		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11072485C>G	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		gcattccagcctgggcaacag	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11072485C>G		NA	A8K925|Q08ER0	hg19		0.02	1.733956	AGCxTGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	34	6.684994	KEEP	2	2	53	41	1228	CC	1	0.967425	0		-	4	60	125	0	0	8.813624	35	60	1151	130	ENST00000470054.1	0.102564	0.967425
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11072533	11072533	__UNKNOWN__	RNA	SNP	T	T	A	rs57709114	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11072533T>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aaaaagcaattacaaacttaa	0.343		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11072533T>A		NA	A8K925|Q08ER0	hg19		0.02	-0.271158	AATxACA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	19	5.441419	KEEP	1	1	25	27	711	TT	0.999988	0.717307	0		-	5	46	141	0	0	11.730341	14	60	428	79	ENST00000470054.1	0.263158	0.717315
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11072540	11072540	__UNKNOWN__	RNA	SNP	T	T	A	rs61052982	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11072540T>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aattacaaacttaattttgaa	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11072540T>A		NA	A8K925|Q08ER0	hg19		0.02	-0.236822	AACxTAA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	17	2.269574	KEEP	1	2	49	25	710	TT	0.999957	0.612381	0		-	5	46	143	0	0	12.066896	13	60	414	72	ENST00000470054.1	0.277778	0.612407
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11074573	11074573	__UNKNOWN__	RNA	SNP	T	T	C	rs6582784	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11074573T>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		actcagtgaatcaatattttc	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11074573T>C		NA	A8K925|Q08ER0	hg19		0.02	-0.061394	GAAxCAA	UNCOVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	5	2.40553	KEEP	1	0	0	8	215	TT	0.99257	0.043461	0		-	4	60	123	0	0	12.131298	3	60	91	17	ENST00000470054.1	0.571429	0.043787
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11074916	11074916	__UNKNOWN__	RNA	SNP	G	G	A	rs8134997	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11074916G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tcctgacctcgtgatccaccc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11074916G>A		NA	A8K925|Q08ER0	hg19		0.02	1.456075	CTCxTGA	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	17	4.49338	KEEP	2	3	79	43	1237	GG	1	0.989542	0		-	11	60	312	0	1	24.903596	40	60	1288	166	ENST00000470054.1	0.215686	0.989542
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11074924	11074924	__UNKNOWN__	RNA	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11074924C>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tcgtgatccacccgcttcagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11074924C>A		NA	A8K925|Q08ER0	hg19		0.02	1.601881	CCAxCCG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	24	6.216163	KEEP	2	3	80	49	1487	CC	1	0.995084	0		-	11	60	332	0	0	26.59653	43	60	1456	170	ENST00000470054.1	0.203704	0.995084
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11077504	11077504	__UNKNOWN__	RNA	SNP	C	C	T	rs68089081	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11077504C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		cacttgagcccaggagttcaa	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11077504C>T		NA	A8K925|Q08ER0	hg19		0.02	-0.201741	GCCxAGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	19	7.254082	KEEP	1	1	25	33	1011	CC	0.999998	0.490543	0		-	3	60	85	0	0	6.410935	15	60	498	78	ENST00000470054.1	0.166667	0.490544
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11078175	11078175	__UNKNOWN__	RNA	SNP	G	G	A	rs71262788	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11078175G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		ccagatactcggggggctgag	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11078175G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.254398	CTCxGGG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	16	2.839639	KEEP	2	1	30	20	570	GG	0.999863	0.668432	0		-	3	60	89	0	0	6.810346	15	60	502	72	ENST00000470054.1	0.166667	0.668523
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11079937	11079937	__UNKNOWN__	RNA	SNP	G	G	A	rs75920725		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11079937G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aataagccaggcatggtggca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11079937G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.307034	CAGxCAT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	16	6.618709	KEEP	3	0	0	22	653	GG	0.999869	0.800141	0		-	3	60	94	0	0	6.794921	23	60	772	79	ENST00000470054.1	0.115385	0.800245
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11080989	11080989	__UNKNOWN__	RNA	SNP	C	C	T	rs71220003|rs3954669	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11080989C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tggcagcatgcgcctgtagtc	0.512		NA											c|||	1919	0.383187	0.3888	0.3847	5008	,	,	NA	67163	0.4226	NA	0.3618	False	NA	,,,	NA	NA	NA	2504	0.3558	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11080989C>T		NA	A8K925|Q08ER0	hg19		0.02	-0.342104	ATGxGCC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	21	8.060464	KEEP	2	0	0	27	770	CC	0.999957	0.865708	0		-	4	40	114	0	0	7.910791	31	60	1041	89	ENST00000470054.1	0.114286	0.865745
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11090250	11090250	__UNKNOWN__	RNA	SNP	A	A	C	rs10154231	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11090250A>C	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		aatcacttgaacctgggaggc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11090250A>C		NA	A8K925|Q08ER0	hg19		0.02	-0.087717	TGAxCCT	UNCOVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	10	3.607281	KEEP	0	0	0	12	322	AA	0.993634	0.099086	0		-	6	60	211	0	0	22.716271	1	24	29	28	ENST00000470054.1	0.857143	0.099721
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11096489	11096489	__UNKNOWN__	RNA	SNP	C	C	T	rs8130656		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11096489C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		caggcatgagccacagtgcct	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11096489C>T		NA	A8K925|Q08ER0	hg19		0.02	1.511313	GAGxCAC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	36	12.567379	KEEP	1	1	29	52	1544	CC	1	0.994422	0		-	5	60	142	0	0	9.201349	53	60	1781	157	ENST00000470054.1	0.086207	0.994422
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11096678	11096678	__UNKNOWN__	RNA	SNP	G	G	A	rs71252274		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11096678G>A	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		acgccaccacgaatttttgta	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11096678G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.333293	CACxAAT	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	23	2.268869	KEEP	1	2	55	27	742	GG	0.999997	0.851982	0		-	4	60	124	0	0	8.807457	33	60	1036	82	ENST00000470054.1	0.108108	0.851984
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11096805	11096805	__UNKNOWN__	RNA	SNP	C	C	T	rs112071802		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11096805C>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tgagccaccacgtccagccCA	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11096805C>T		NA	A8K925|Q08ER0	hg19		0.02	1.201798	CCAxGTC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	37	7.94967	KEEP	1	2	58	47	1304	CC	1	0.999835	0		-	14	60	386	0	0	29.433088	63	60	2037	192	ENST00000470054.1	0.181818	0.999835
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11097447	11097447	__UNKNOWN__	RNA	SNP	G	G	T	rs77782678	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11097447G>T	ENST00000470054.1	-	0	324							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tactcgggaggctgagacaga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11097447G>T		NA	A8K925|Q08ER0	hg19		0.02	-0.394742	GAGxCTG	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	31	5.848996	KEEP	4	1	27	29	868	GG	0.999997	0.926637	0		-	4	60	125	0	0	9.062884	30	60	997	95	ENST00000470054.1	0.117647	0.92664
BAGE2	85319	__UNKNOWN__	__UNKNOWN__	21	11097590	11097590	__UNKNOWN__	RNA	SNP	G	G	A	rs57543194		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11097590G>A	ENST00000470054.1	-	0	279							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2	NA		NA				extracellular region (GO:0005576)					NA			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		tcaccacaggggactcctcct	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													65	84	77			NA	NA	21		NA											NA				11097590		1439	2596	4035					AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172	85319			15723	protein-coding gene	gene with protein product	cancer/testis antigen family 2, member 2	NA			NA	12461691	Standard	NM_182482	NM_182482	NA	Approved	CT2.2		Q86Y30	OTTHUMG00000074128	ENST00000470054.1:	chr21.hg19:g.11097590G>A		NA	A8K925|Q08ER0	hg19		0.02	-0.377215	AGGxGAC	COVERED																																																																																			NOVEL	BAGE2-001	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000157417.3	7	4.5121	KEEP	0	0	0	15	439	GG	0.99649	0.905878	0		-	4	60	125	0	0	8.632484	39	60	1321	80	ENST00000470054.1	0.093023	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11101018	11101018	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11101018T>C			NA	NA				BAGE2 (2093 upstream) : AP003900.6 (68769 downstream)						NA		NA									NA						ggattacaggtgtgagccact	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11101018T>C		NA		hg19		0.02	-0.385905	AGGxGTG	COVERED																																																																																			NOVEL					0			29	7.783277	KEEP	11	2	57	46	1272	TT	1	0.918171	0			3	60	98	0	0	6.712059	34	60	1027	134		0.081081	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11107404	11107404	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11107404T>G			NA	NA				BAGE2 (8479 upstream) : AP003900.6 (62383 downstream)						NA		NA									NA						tgttgttgttttttgagacgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11107404T>G		NA		hg19		0.02	1.724743	GTTxTTT	COVERED																																																																																			NOVEL					0			20	8.552416	KEEP	4	1	33	40	1072	TT	1	0.97082	0			4	60	125	0	1	9.06383	30	60	870	127		0.117647	0.97082
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11111893	11111893	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11111893G>T			NA	NA				BAGE2 (12968 upstream) : AP003900.6 (57894 downstream)						NA		NA									NA						tgttggccaggctggtctcga	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11111893G>T		NA		hg19		0.02	-0.263149	CAGxCTG	COVERED																																																																																			NOVEL					0			9	5.716775	KEEP	1	0	0	19	577	GG	0.999859	0.693571	0			5	44	145	0	0	11.359579	21	60	703	57		0.192308	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11112188	11112188	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11112188C>T			NA	NA				BAGE2 (13263 upstream) : AP003900.6 (57599 downstream)						NA		NA									NA						tcccagcactctgggaggctg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11112188C>T		NA		hg19		0.02	1.076337	ACTxTGG	COVERED																																																																																			NOVEL					0			36	5.849956	KEEP	0	4	103	56	1720	CC	1	0.999907	0			5	60	142	1	0	8.712122	67	60	2320	236		0.069444	0.999907
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11112229	11112229	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11112229T>C			NA	NA				BAGE2 (13304 upstream) : AP003900.6 (57558 downstream)						NA		NA									NA						gttgggagtttgagaccagcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11112229T>C		NA		hg19		0.02	1.757111	GTTxGAG	COVERED																																																																																			NOVEL					0			29	14.434458	KEEP	0	0	0	48	1309	TT	1	0.997553	0			5	60	174	0	0	12.430475	52	60	1567	171		0.087719	0.997553
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11112900	11112900	__UNKNOWN__	IGR	SNP	G	G	C	rs10433186	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11112900G>C			NA	NA				BAGE2 (13975 upstream) : AP003900.6 (56887 downstream)						NA		NA									NA						ATGACCATGAGTAAAAGGCCC	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11112900G>C		NA		hg19		0.02	-0.350898	TGAxTAA	COVERED																																																																																			NOVEL					0			10	3.543923	KEEP	1	1	32	23	683	GG	0.999892	0.877613	0			6	60	212	0	0	17.09965	29	60	999	82		0.171429	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114173	11114173	__UNKNOWN__	IGR	SNP	G	G	T	rs5015030	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114173G>T			NA	NA				BAGE2 (15248 upstream) : AP003900.6 (55614 downstream)						NA		NA									NA						agccaagattgtgccagtgca	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114173G>T		NA		hg19		0.02	1.400967	ATTxTGC	COVERED																																																																																			NOVEL					0			30	10.762597	KEEP	1	1	29	46	1373	GG	1	0.981955	0			5	60	145	0	0	10.178013	38	60	1267	156		0.116279	0.981955
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114478	11114478	__UNKNOWN__	IGR	SNP	G	G	A	rs4358221		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114478G>A			NA	NA				BAGE2 (15553 upstream) : AP003900.6 (55309 downstream)						NA		NA									NA						ATACATCTGCGTGAATTGTTT	0.328		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114478G>A		NA		hg19		0.02	1.015129	TGCxTGA	COVERED																																																																																			NOVEL					0			0	2.634961	KEEP	0	1	26	18	466	GG	0.99986	0.999822	0			6	60	177	0	0	10.719366	94	60	2907	154		0.06	0.999962
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114515	11114515	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114515A>G			NA	NA				BAGE2 (15590 upstream) : AP003900.6 (55272 downstream)						NA		NA									NA						AACAGACTCCATAACCTTCCA	0.353		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114515A>G		NA		hg19		0.02	5.262189	TCCxTAA	COVERED																																																																																			NOVEL					0			4	3.973232	KEEP	0	2	53	32	885	AA	0.999998	0.999998	0			7	60	223	0	0	12.807676	173	60	5241	324		0.038889	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114610	11114610	__UNKNOWN__	IGR	SNP	G	G	A	rs7277993		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114610G>A			NA	NA				BAGE2 (15685 upstream) : AP003900.6 (55177 downstream)						NA		NA									NA						CTTCAGCAGCGGCCCAGGTGG	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114610G>A		NA		hg19		0.02	6.134813	AGCxGCC	COVERED																																																																																			NOVEL					0			3	5.781303	KEEP	0	2	56	39	1153	GG	1	1	0			21	60	634	0	0	43.939348	186	60	5944	326		0.101449	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114611	11114611	__UNKNOWN__	IGR	SNP	G	G	A	rs4358222	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114611G>A			NA	NA				BAGE2 (15686 upstream) : AP003900.6 (55176 downstream)						NA		NA									NA						TTCAGCAGCGGCCCAGGTGGA	0.502		NA											g|||	7	0.00139776	0.0045	0.0014	5008	,	,	NA	111926	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114611G>A		NA		hg19		0.02	6.107728	GCGxCCC	COVERED																																																																																			NOVEL					0			3	2.606405	KEEP	0	3	83	38	1139	GG	1	1	0			9	60	263	0	0	14.513514	200	60	6613	330		0.043062	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114613	11114613	__UNKNOWN__	IGR	SNP	C	C	T	rs545625602	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114613C>T			NA	NA				BAGE2 (15688 upstream) : AP003900.6 (55174 downstream)						NA		NA									NA						CAGCAGCGGCCCAGGTGGAGT	0.502		NA											c|||	89	0.0177716	0.0091	0.0101	5008	,	,	NA	111536	0.0129	NA	0.008	False	NA	,,,	NA	NA	NA	2504	0.0501	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114613C>T		NA		hg19		0.02	5.711492	GGCxCAG	COVERED																																																																																			NOVEL					0			2	5.5818	KEEP	0	2	52	37	1120	CC	1	1	0			11	60	328	0	0	19.360651	198	60	6503	329		0.052632	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11114682	11114682	__UNKNOWN__	IGR	SNP	C	C	G	rs10433192	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11114682C>G			NA	NA				BAGE2 (15757 upstream) : AP003900.6 (55105 downstream)						NA		NA									NA						ACAGCTCTCCCCGATCTCTCT	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11114682C>G		NA		hg19		0.02	9.955541	TCCxCGA	COVERED																																																																																			NOVEL					0			4	2.904974	KEEP	0	3	98	44	1364	CC	1	1	0			25	60	834	0	0	61.673436	192	60	6545	486		0.115207	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11115881	11115881	__UNKNOWN__	IGR	SNP	C	C	G	rs6582842	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11115881C>G			NA	NA				BAGE2 (16956 upstream) : AP003900.6 (53906 downstream)						NA		NA									NA						GACAGagagacagagacagag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11115881C>G		NA		hg19		0.02	-0.26317	AGAxAGA	COVERED																																																																																			NOVEL					0			10	2.439079	KEEP	0	1	28	18	529	CC	0.99986	0.693571	0			8	60	272	0	0	23.891248	19	60	663	70		0.296296	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11116690	11116690	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11116690C>T			NA	NA				BAGE2 (17765 upstream) : AP003900.6 (53097 downstream)						NA		NA									NA						tttgggaggccgaggcaggcg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11116690C>T		NA		hg19		0.02	1.228032	GGCxGAG	COVERED																																																																																			NOVEL					0			23	9.558457	KEEP	8	1	29	42	1245	CC	1	0.999804	0			4	60	126	0	0	7.618503	76	60	2497	198		0.05	0.999804
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11119387	11119387	__UNKNOWN__	IGR	SNP	T	T	A	rs12165284		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11119387T>A			NA	NA				BAGE2 (20462 upstream) : AP003900.6 (50400 downstream)						NA		NA									NA						ctattaaaaatagaaaaaata	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11119387T>A		NA		hg19		0.02	4.552625	AAAxAGA	COVERED																																																																																			NOVEL					0			69	16.456768	KEEP	3	4	108	93	2450	TT	1	1	0			10	60	303	1	0	19.1937	138	60	4003	365		0.067568	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11119536	11119536	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11119536A>G			NA	NA				BAGE2 (20611 upstream) : AP003900.6 (50251 downstream)						NA		NA									NA						agagtgagacattgtctcaaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11119536A>G		NA		hg19		0.02	1.640077	GACxTTG	COVERED																																																																																			NOVEL					0			30	7.984507	KEEP	1	2	61	48	1330	AA	1	0.998465	0			7	60	233	1	0	16.902048	60	60	1733	175		0.104478	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11123623	11123623	__UNKNOWN__	IGR	SNP	C	C	T	rs28735785		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11123623C>T			NA	NA				BAGE2 (24698 upstream) : AP003900.6 (46164 downstream)						NA		NA									NA						tacaggaaccctccaccttgt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11123623C>T		NA		hg19		0.02	-0.25438	ACCxTCC	COVERED																																																																																			NOVEL					0			17	5.414841	KEEP	0	0	0	18	529	CC	0.999859	0.668429	0			3	60	89	0	0	6.661245	17	60	583	58		0.15	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11125099	11125099	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11125099T>C			NA	NA				BAGE2 (26174 upstream) : AP003900.6 (44688 downstream)						NA		NA									NA						cagtggctcatgcctgtaatc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11125099T>C		NA		hg19		0.02	3.756745	TCAxGCC	COVERED																																																																																			NOVEL					0			26	4.135245	KEEP	2	4	114	54	1461	TT	1	0.999984	0			6	60	179	0	0	11.294973	81	60	2381	230		0.068966	0.999984
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11125578	11125578	__UNKNOWN__	IGR	SNP	G	G	C	rs3901976		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11125578G>C			NA	NA				BAGE2 (26653 upstream) : AP003900.6 (44209 downstream)						NA		NA									NA						tccagccttggtgacagagtg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11125578G>C		NA		hg19		0.02	-0.412314	TTGxTGA	COVERED																																																																																			NOVEL					0			36	4.279818	KEEP	2	2	62	36	1094	GG	0.999999	0.94174	0			3	60	104	0	0	7.076795	41	60	1391	111		0.068182	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11125938	11125938	__UNKNOWN__	IGR	SNP	C	C	A	rs4560219		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11125938C>A			NA	NA				BAGE2 (27013 upstream) : AP003900.6 (43849 downstream)						NA		NA									NA						gtcacccaggctggactgcag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11125938C>A		NA		hg19		0.02	-0.228089	AGGxTGG	COVERED																																																																																			NOVEL					0			16	7.221534	KEEP	2	0	0	24	743	CC	0.999879	0.58286	0			3	60	91	1	0	6.933509	16	60	555	64		0.157895	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11126440	11126440	__UNKNOWN__	IGR	SNP	G	G	C	rs78014429		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11126440G>C			NA	NA				BAGE2 (27515 upstream) : AP003900.6 (43347 downstream)						NA		NA									NA						tgttggccaggctggtctcta	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11126440G>C		NA		hg19		0.02	-0.342127	CAGxCTG	COVERED																																																																																			NOVEL					0			13	5.114244	KEEP	2	0	0	17	513	GG	0.997832	0.863868	0			4	60	132	0	0	9.874026	28	60	957	81		0.125	0.865745
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11126504	11126504	__UNKNOWN__	IGR	SNP	C	C	T	rs74699992	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11126504C>T			NA	NA				BAGE2 (27579 upstream) : AP003900.6 (43283 downstream)						NA		NA									NA						gatggaattacaagtgtgagc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11126504C>T		NA		hg19		0.02	-0.21029	TTAxAAG	COVERED																																																																																			NOVEL					0			9	4.513198	KEEP	1	0	0	15	455	CC	0.99649	0.520328	0			7	60	194	0	0	16.76545	15	60	476	58		0.318182	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11126888	11126888	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11126888A>T			NA	NA				BAGE2 (27963 upstream) : AP003900.6 (42899 downstream)						NA		NA									NA						ttgtgtttgtatgtttgtttg	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11126888A>T		NA		hg19		0.02	-0.166625	TGTxTGT	COVERED																																																																																			NOVEL					0			19	3.037781	KEEP	0	1	28	20	528	AA	0.999869	0.353901	0			3	60	89	1	0	7.282306	10	60	285	55		0.230769	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11131042	11131042	__UNKNOWN__	IGR	SNP	G	G	A	rs75276763	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11131042G>A			NA	NA				BAGE2 (32117 upstream) : AP003900.6 (38745 downstream)						NA		NA									NA						ggattgacaggcacctgccac	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11131042G>A		NA		hg19		0.02	-0.359649	CAGxCAC	COVERED																																																																																			NOVEL					0			14	4.813412	KEEP	1	0	0	16	475	GG	0.997832	0.886948	0			4	60	114	0	0	8.392575	23	60	757	73		0.148148	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11132014	11132014	__UNKNOWN__	IGR	SNP	G	G	A	rs138577365		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11132014G>A			NA	NA				BAGE2 (33089 upstream) : AP003900.6 (37773 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11132014G>A		NA		hg19		0.02	2.722998	CACxCCT	COVERED																																																																																			NOVEL					0			31	8.522946	KEEP	4	3	84	58	1752	GG	1	0.999999	0			14	60	393	0	0	29.023093	77	60	2596	275		0.153846	0.999999
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11132414	11132414	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11132414A>T			NA	NA				BAGE2 (33489 upstream) : AP003900.6 (37373 downstream)						NA		NA									NA						ctactaaaaaaacaaatacaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11132414A>T		NA		hg19		0.02	-0.368172	AAAxACA	COVERED																																																																																			NOVEL					0			26	6.607415	KEEP	0	0	0	22	537	AA	0.999879	0.899205	0			5	60	138	2	0	10.242351	26	60	725	75		0.16129	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11132702	11132702	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11132702A>G			NA	NA				BAGE2 (33777 upstream) : AP003900.6 (37085 downstream)						NA		NA									NA						gtgaaaccccatctccactaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11132702A>G		NA		hg19		0.02	-0.324419	CCCxTCT	COVERED																																																																																			NOVEL					0			15	5.107498	KEEP	3	0	0	17	417	AA	0.997832	0.833904	0			4	60	123	0	0	8.86402	30	60	830	73		0.117647	0.835716
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11134476	11134476	__UNKNOWN__	IGR	SNP	G	G	A	rs201549987		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11134476G>A			NA	NA				BAGE2 (35551 upstream) : AP003900.6 (35311 downstream)						NA		NA									NA						gggaccacaggaacacaccac	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11134476G>A		NA		hg19		0.02	4.717597	CAGxAAC	COVERED																																																																																			NOVEL					0			80	4.070579	KEEP	1	14	383	149	4479	GG	1	1	0			12	60	350	0	0	23.586476	113	60	3633	462		0.096	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11135344	11135344	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11135344A>T			NA	NA				BAGE2 (36419 upstream) : AP003900.6 (34443 downstream)						NA		NA									NA						ccagcctgggagacagagtga	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11135344A>T		NA		hg19		0.02	-0.420981	GGGxGAC	COVERED																																																																																			NOVEL					0			16	3.640728	KEEP	3	1	25	21	578	AA	0.999869	0.954366	0			4	60	116	1	0	7.778194	38	60	1152	113		0.095238	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11138797	11138797	__UNKNOWN__	IGR	SNP	C	C	T	rs142770165		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11138797C>T			NA	NA				BAGE2 (39872 upstream) : AP003900.6 (30990 downstream)						NA		NA									NA						tctcggctcactgcaacctcc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11138797C>T		NA		hg19		0.02	-0.385985	TCAxTGC	COVERED																																																																																			NOVEL					0			21	3.074386	KEEP	2	2	56	30	916	CC	0.999997	0.918168	0			6	60	177	0	0	13.520801	30	60	1037	116		0.166667	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11138872	11138872	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11138872C>T			NA	NA				BAGE2 (39947 upstream) : AP003900.6 (30915 downstream)						NA		NA									NA						aggcacttgccactacgcccg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11138872C>T		NA		hg19		0.02	-0.359568	TGCxACT	COVERED																																																																																			NOVEL					0			20	2.372223	KEEP	0	2	51	26	784	CC	0.999997	0.888873	0			5	60	149	0	0	11.12264	29	60	949	94		0.147059	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11138878	11138878	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11138878G>A			NA	NA				BAGE2 (39953 upstream) : AP003900.6 (30909 downstream)						NA		NA									NA						ttgccactacgcccggctaat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11138878G>A		NA		hg19		0.02	-0.333254	TACxCCC	COVERED																																																																																			NOVEL					0			19	2.569599	KEEP	0	2	49	26	739	GG	0.999997	0.851982	0			6	60	155	0	0	11.574481	27	60	889	90		0.181818	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11139707	11139707	__UNKNOWN__	IGR	SNP	T	T	C	rs142376889		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11139707T>C			NA	NA				BAGE2 (40782 upstream) : AP003900.6 (30080 downstream)						NA		NA									NA						ttcatgccattctcctgcctc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11139707T>C		NA		hg19		0.02	-0.35956	CATxCTC	COVERED																																																																																			NOVEL					0			15	7.548601	KEEP	5	1	28	35	930	TT	0.999998	0.888873	0			6	60	199	0	0	15.720716	30	60	878	109		0.166667	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11139844	11139844	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11139844T>C			NA	NA				BAGE2 (40919 upstream) : AP003900.6 (29943 downstream)						NA		NA									NA						cctcatgatctgcccgcctcg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11139844T>C		NA		hg19		0.02	-0.359533	ATCxGCC	COVERED																																																																																			NOVEL					0			12	6.644022	KEEP	4	1	28	32	848	TT	0.999997	0.888873	0			4	60	130	0	0	9.358095	34	60	988	106		0.105263	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11141064	11141064	__UNKNOWN__	IGR	SNP	A	A	G	rs142356222		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11141064A>G			NA	NA				BAGE2 (42139 upstream) : AP003900.6 (28723 downstream)						NA		NA									NA						tactaaaaatacaaaaattgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11141064A>G		NA		hg19		0.02	-0.333163	AATxCAA	COVERED																																																																																			NOVEL					0			20	3.066187	KEEP	2	2	50	28	710	AA	0.999997	0.851982	0			3	60	102	0	0	7.267739	30	60	834	84		0.090909	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11147378	11147378	__UNKNOWN__	IGR	SNP	G	G	A	rs4913810	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11147378G>A			NA	NA				BAGE2 (48453 upstream) : AP003900.6 (22409 downstream)						NA		NA									NA						ttgagacagggtctcagtctg	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11147378G>A		NA		hg19		0.02	-0.219308	AGGxTCT	COVERED																																																																																			NOVEL					0			20	2.473468	KEEP	0	2	53	27	825	GG	0.999997	0.552886	0			4	60	125	0	0	10.162426	15	60	502	69		0.210526	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11164104	11164104	__UNKNOWN__	IGR	SNP	G	G	A	rs586957		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11164104G>A			NA	NA				BAGE2 (65179 upstream) : AP003900.6 (5683 downstream)						NA		NA									NA						ggctaattacgtatttttagt	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11164104G>A		NA		hg19		0.02	-0.421039	TACxTAT	COVERED																																																																																			NOVEL					0			16	2.371733	KEEP	2	2	60	29	831	GG	0.999997	0.948399	0			6	60	181	0	0	13.355336	38	60	1221	116		0.136364	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11164105	11164105	__UNKNOWN__	IGR	SNP	T	T	C	rs4089573	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11164105T>C			NA	NA				BAGE2 (65180 upstream) : AP003900.6 (5682 downstream)						NA		NA									NA						gctaattacgtatttttagta	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11164105T>C		NA		hg19		0.02	-0.412185	ACGxATT	COVERED																																																																																			NOVEL					0			15	2.367239	KEEP	2	2	66	31	805	TT	0.999997	0.941739	0			8	60	259	0	0	20.74776	35	60	1005	116		0.186047	0.941741
AP003900.6	0	__UNKNOWN__	__UNKNOWN__	21	11175675	11175675	__UNKNOWN__	lincRNA	SNP	A	A	G	rs80013069|rs200646533|rs373628865	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11175675A>G	ENST00000603265.1	+	0	231										NA		NA									NA						ccgagactgcaccactgcact	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603265.1:	chr21.hg19:g.11175675A>G		NA		hg19		0.02	-0.184164	TGCxCCA	COVERED																																																																																			NOVEL	AP003900.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469752.1	12	2.637048	KEEP	3	1	26	18	486	AA	0.999366	0.423209	0		+	3	40	97	0	0	7.392592	18	60	519	57	ENST00000603265.1	0.142857	0.423478
AP003900.6	0	__UNKNOWN__	__UNKNOWN__	21	11179645	11179645	__UNKNOWN__	lincRNA	SNP	A	A	G	rs1811008	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11179645A>G	ENST00000603265.1	+	0	231										NA		NA									NA						tcactctgtcacccaggctgg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603265.1:	chr21.hg19:g.11179645A>G		NA		hg19		0.02	-0.280425	GTCxCCC	COVERED																																																																																			NOVEL	AP003900.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469752.1	11	5.413351	KEEP	4	0	0	18	492	AA	0.997832	0.738068	0		+	4	60	126	0	0	9.525392	24	60	673	77	ENST00000603265.1	0.142857	0.739671
AP003900.6	0	__UNKNOWN__	__UNKNOWN__	21	11182666	11182666	__UNKNOWN__	lincRNA	SNP	G	G	A	rs139475058		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11182666G>A	ENST00000603265.1	+	0	231										NA		NA									NA						taatgtttgtgtttttagtag	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000603265.1:	chr21.hg19:g.11182666G>A		NA		hg19		0.02	-0.35944	TGTxTTT	COVERED																																																																																			NOVEL	AP003900.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000469752.1	11	3.610119	KEEP	3	0	0	12	353	GG	0.993634	0.883216	0		+	4	60	108	1	0	7.116583	35	60	1148	73	ENST00000603265.1	0.102564	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	11186285	11186285	__UNKNOWN__	IGR	SNP	T	T	A	rs9979008		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:11186285T>A			NA	NA				AP003900.6 (2239 upstream) : None (None downstream)						NA		NA									NA						agaaatctcctgcccttggtc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.11186285T>A		NA		hg19		0.02	-0.350826	TCCxGCC	COVERED																																																																																			NOVEL					0			0	2.406378	KEEP	0	0	0	8	226	TT	0.99257	0.871187	0			4	60	116	0	0	8.110878	31	60	950	82		0.114286	0.877708
ANKRD30BP2	149992	__UNKNOWN__	__UNKNOWN__	21	14414902	14414902	__UNKNOWN__	RNA	SNP	G	G	A	rs2821609		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:14414902G>A	ENST00000507941.1	+	0	95									ankyrin repeat domain 30B pseudogene 2	NA		NA									NA						CCAGCTTGACGTCCTTGATGG	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF427490		21q11.2	2010-06-14	2010-06-14	2010-06-14	ENSG00000224309	ENSG00000224309	149992			16620	pseudogene	pseudogene	cancer/testis antigen 85	NA	chromosome 21 open reading frame 99	C21orf99	NA	12036297, 17114284	Standard	NR_026916	NR_026916	NA	Approved	CT85, CTSP-1	uc002yja.4		OTTHUMG00000074164	ENST00000507941.1:	chr21.hg19:g.14414902G>A		NA		hg19		0.02	3.160337	GACxTCC	COVERED																																																																																			NOVEL	ANKRD30BP2-004	KNOWN	basic	processed_transcript	NA	pseudogene	OTTHUMT00000372094.1	29	5.110094	KEEP	0	0	0	17	449	GG	0.999366	0.999351	0		+	22	60	663	0	0	53.704403	80	60	2613	180	ENST00000507941.1	0.215686	0.999984
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	16116710	16116710	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:16116710A>G			NA	NA				AF165138.7 (85568 upstream) : AF127936.3 (2372 downstream)						NA		NA									NA						cagcctgggcaacagagtgag	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.16116710A>G		NA		hg19		0.02	-0.078928	GGCxACA	UNCOVERED																																																																																			NOVEL					0			9	2.405992	KEEP	5	0	0	8	219	AA	0	0	0			3	60	90	0	0	8.132651	5	60	147	26		0.375	0.077336
LINC00478	0	__UNKNOWN__	__UNKNOWN__	21	17560168	17560168	__UNKNOWN__	lincRNA	SNP	G	G	C	rs201662285		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:17560168G>C	ENST00000458468.1	+	0	409					NR_027790.1					NA		NA									NA						tttctttcttgcttccttcct	0.383		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000458468.1:	chr21.hg19:g.17560168G>C		NA		hg19		0.02	-0.210519	CTTxCTT	COVERED																																																																																			NOVEL	LINC00478-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000158029.1	4	8.789844	KEEP	0	2	53	48	1430	GG	1	0.522161	0		+	4	70	126	0	0	9.979498	18	70	583	95	ENST00000458468.1	0.181818	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	21626542	21626542	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:21626542A>G			NA	NA				AP000946.2 (354473 upstream) : AP001171.1 (2522 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.21626542A>G		NA		hg19		0.02	-0.043858	CACxCCT	UNCOVERED																																																																																			NOVEL					0			3	2.403583	KEEP	2	0	0	8	212	AA	0	0	0			2	40	69	0	0	6.392948	3	60	90	18		0.4	0.024074
NCAM2	4685	__UNKNOWN__	__UNKNOWN__	21	22829955	22829955	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:22829955T>A	ENST00000400546.1	+	13	1903				NCAM2_ENST00000284894.7_Intron	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	NA		NA			axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		gcaagactccttctcaagaaa	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654	4685		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	7657	protein-coding gene	gene with protein product		602040			NA	9226371	Standard	NM_004540	NM_004540	NA	Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1655-8972T>A	chr21.hg19:g.22829955T>A		NA	A8MQ06|B7Z841|Q7Z7F2	hg19	CCDS42910.1	0.02	-0.052625	TCCxTCT	UNCOVERED																																																																																			NOVEL	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000170915.1	6	2.406067	KEEP	0	0	0	8	220	TT	0.99257	0.036492	0		+	3	24	91	0	0	8.724849	3	60	89	21	ENST00000400546.1	0.5	0.036766
AP001255.2	0	__UNKNOWN__	__UNKNOWN__	21	24491369	24491369	__UNKNOWN__	lincRNA	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:24491369G>T	ENST00000421604.1	+	0	480										NA		NA									NA						atgttgtccaggctggtcttg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000421604.1:	chr21.hg19:g.24491369G>T		NA		hg19		0.02	-0.096491	CCAxGCT	UNCOVERED																																																																																			NOVEL	AP001255.2-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000171055.1	9	2.708388	KEEP	4	0	0	9	288	GG	0.99257	0.119541	0		+	3	21	87	0	0	7.478264	7	60	235	33	ENST00000421604.1	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	25155649	25155649	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:25155649G>A			NA	NA				AP000459.7 (292606 upstream) : AP000474.1 (105464 downstream)						NA		NA									NA						gtgtgatctcggctcactgca	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.25155649G>A		NA		hg19		0.02	-0.096491	CTCxGCT	UNCOVERED																																																																																			NOVEL					0			5	2.764776	KEEP	0	1	10	13	381	GG	0.995343	0.119875	0			3	60	90	0	0	7.778361	7	60	231	30		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	28197071	28197071	__UNKNOWN__	IGR	SNP	C	C	T	rs468919	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:28197071C>T			NA	NA				CYYR1 (251468 upstream) : ADAMTS1 (10994 downstream)						NA		NA									NA						ccgaggcgggcggatcacgag	0.547		NA											C|||	805	0.160743	0.2262	0.1066	5008	,	,	NA	14000	0.12	NA	0.1561	False	NA	,,,	NA	NA	NA	2504	0.1575	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.28197071C>T		NA		hg19		0.02	-0.174052	GGGxGGA	COVERED																																																																																			NOVEL					0			3	3.308267	KEEP	3	0	0	11	306	CC	0.99254	0.384517	0			4	60	94	0	0	7.00682	16	60	497	54		0.2	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	29304843	29304843	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:29304843G>A			NA	NA				LINC00113 (181291 upstream) : AJ006995.3 (22396 downstream)						NA		NA									NA						ttgggaggccgaggcgggcgg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.29304843G>A		NA		hg19		0.02	-0.184118	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			9	3.007478	KEEP	14	0	0	10	287	GG	0	0	0			4	57	98	0	0	7.366974	16	60	522	64		0.2	0.423478
N6AMT1	29104	__UNKNOWN__	__UNKNOWN__	21	30249702	30249702	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:30249702A>G	ENST00000303775.5	-	5	564				N6AMT1_ENST00000351429.3_Intron	NM_013240.4	NP_037372	Q9Y5N5	HEMK2_HUMAN	N-6 adenine-specific DNA methyltransferase 1 (putative)	NA		NA			positive regulation of cell growth (GO:0030307)|protein methylation (GO:0006479)	protein complex (GO:0043234)	nucleic acid binding (GO:0003676)|protein methyltransferase activity (GO:0008276)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)	12						agggaagggaagaaagaagga	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF139682	CCDS33525.1, CCDS33526.1	21q21.3	2006-12-14	2006-12-14	2006-12-14	ENSG00000156239	ENSG00000156239	29104	2.1.1.72		16021	protein-coding gene	gene with protein product		614553	chromosome 21 open reading frame 127, HemK methyltransferase family member 2	C21orf127, HEMK2	NA		Standard	NM_013240	NM_013240	NA	Approved	PRED28, N6AMT, MTQ2	uc002ymo.2	Q9Y5N5	OTTHUMG00000078750	ENST00000303775.5:c.538+811T>C	chr21.hg19:g.30249702A>G		NA	Q96F73	hg19	CCDS33526.1	0.02	-0.07894	GGAxGAA	UNCOVERED																																																																																			NOVEL	N6AMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000171738.1	12	3.007529	KEEP	1	0	0	10	274	AA	0.992708	0.076772	0		-	2	60	74	1	0	6.535817	5	60	146	21	ENST00000303775.5	0.285714	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	30263777	30263777	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:30263777G>A			NA	NA				N6AMT1 (6084 upstream) : LTN1 (36688 downstream)						NA		NA									NA						ggccgggcgcggtggctcacg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.30263777G>A		NA		hg19		0.02	-0.21052	CGCxGTG	COVERED																																																																																			NOVEL					0			4	3.308464	KEEP	2	0	0	11	312	GG	0.992708	0.518353	0			3	60	89	0	0	6.465685	20	60	648	51		0.130435	0.522161
MAP3K7CL	56911	__UNKNOWN__	__UNKNOWN__	21	30513637	30513637	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:30513637T>C	ENST00000399935.2	+	8	737				MAP3K7CL_ENST00000399934.1_Intron|MAP3K7CL_ENST00000399926.1_Intron|MAP3K7CL_ENST00000399947.2_Intron|MAP3K7CL_ENST00000399925.1_Intron|MAP3K7CL_ENST00000545939.1_Intron|MAP3K7CL_ENST00000286791.5_Intron|MAP3K7CL_ENST00000399928.1_Intron|MAP3K7CL_ENST00000339024.4_Intron|MAP3K7CL_ENST00000341618.4_Intron			P57077	M3KCL_HUMAN	MAP3K7 C-terminal like	NA		NA				cytosol (GO:0005829)|nucleus (GO:0005634)					NA						agatggagactatcctggcta	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF269161	CCDS13584.1, CCDS68182.1, CCDS74775.1	21q22.3	2013-02-22	2013-02-22	2013-02-22	ENSG00000156265	ENSG00000156265	56911			16457	protein-coding gene	gene with protein product		611110	chromosome 21 open reading frame 7	C21orf7	NA		Standard	NM_020152	NM_020152	NA	Approved	TAKL, TAK1L, TAKL-1, TAKL-2, TAKL-4	uc002ynf.3	P57077	OTTHUMG00000078806	ENST00000399935.2:c.71-7873T>C	chr21.hg19:g.30513637T>C		NA	D3DSE0|Q8TCL9	hg19		0.02	-0.096476	GACxATC	UNCOVERED																																																																																			NOVEL	MAP3K7CL-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000171867.2	6	2.405879	KEEP	0	0	0	8	217	TT	0.99257	0.119541	0		+	3	60	99	0	0	8.532588	8	60	234	24	ENST00000399935.2	0.272727	0.120436
MAP3K7CL	56911	__UNKNOWN__	__UNKNOWN__	21	30525893	30525893	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:30525893T>C	ENST00000399935.2	+	8	799				MAP3K7CL_ENST00000399934.1_Intron|MAP3K7CL_ENST00000399926.1_Intron|MAP3K7CL_ENST00000399947.2_Intron|MAP3K7CL_ENST00000399925.1_Intron|MAP3K7CL_ENST00000545939.1_Intron|MAP3K7CL_ENST00000286791.5_Intron|MAP3K7CL_ENST00000399928.1_Intron|MAP3K7CL_ENST00000339024.4_Intron|MAP3K7CL_ENST00000341618.4_Intron			P57077	M3KCL_HUMAN	MAP3K7 C-terminal like	NA		NA				cytosol (GO:0005829)|nucleus (GO:0005634)					NA						ccccagcctcttgagtagctg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF269161	CCDS13584.1, CCDS68182.1, CCDS74775.1	21q22.3	2013-02-22	2013-02-22	2013-02-22	ENSG00000156265	ENSG00000156265	56911			16457	protein-coding gene	gene with protein product		611110	chromosome 21 open reading frame 7	C21orf7	NA		Standard	NM_020152	NM_020152	NA	Approved	TAKL, TAK1L, TAKL-1, TAKL-2, TAKL-4	uc002ynf.3	P57077	OTTHUMG00000078806	ENST00000399935.2:c.132+4322T>C	chr21.hg19:g.30525893T>C		NA	D3DSE0|Q8TCL9	hg19		0.02	-0.219204	CTCxTGA	COVERED																																																																																			NOVEL	MAP3K7CL-003	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000171867.2	10	5.113298	KEEP	3	0	0	17	480	TT	0.997832	0.551689	0		+	3	60	105	0	0	7.949076	22	60	655	65	ENST00000399935.2	0.12	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	31523166	31523166	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:31523166T>C			NA	NA				AF096876.1 (53012 upstream) : CLDN17 (15074 downstream)						NA		NA									NA						tcccaaagtgttgggattaca	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.31523166T>C		NA		hg19		0.02	-0.18419	GTGxTGG	COVERED																																																																																			NOVEL					0			5	3.307953	KEEP	1	0	0	11	301	TT	0.992708	0.42039	0			3	60	99	0	0	7.592202	18	60	540	45		0.142857	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	31912896	31912896	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:31912896C>T			NA	NA				KRTAP19-5 (38461 upstream) : KRTAP19-6 (957 downstream)						NA		NA									NA						ttagtagagacggggtttcac	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.31912896C>T		NA		hg19		0.02	-0.122804	AGAxGGG	COVERED																																																																																			NOVEL					0			5	2.406897	KEEP	0	0	0	8	237	CC	0.99257	0.194853	0			3	60	83	0	0	6.800893	9	60	311	31		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	32114558	32114558	__UNKNOWN__	IGR	SNP	C	C	A	rs374868732|rs373088572		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:32114558C>A			NA	NA				KRTAP21-3 (23463 upstream) : KRTAP21-2 (4553 downstream)						NA		NA									NA						GCCATATCCACAGCCATAGCC	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.32114558C>A		NA		hg19		0.02	-0.307033	CCAxAGC	COVERED																																																																																			NOVEL					0			26	7.588643	KEEP	9	2	56	45	1369	CC	1	0.800245	0			5	29	147	2	0	12.2015	15	60	518	118		0.25	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	32433751	32433751	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:32433751G>A			NA	NA				KRTAP19-8 (22956 upstream) : TIAM1 (56982 downstream)						NA		NA									NA						ggtggctcacgcctgtaatcc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.32433751G>A		NA		hg19		0.02	-0.324564	CACxCCT	COVERED																																																																																			NOVEL					0			8	4.813026	KEEP	1	0	0	16	466	GG	0.997832	0.850137	0			3	60	93	0	0	6.368078	30	60	984	83		0.090909	0.851984
TIAM1	7074	__UNKNOWN__	__UNKNOWN__	21	32507108	32507108	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:32507108T>C	ENST00000286827.3	-	24	4355				TIAM1_ENST00000541036.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	NA		NA			apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						ggattacaggtgtgagccacc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299	7074		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11805	protein-coding gene	gene with protein product		600687			NA	8595894, 15340013	Standard	NM_003253	NM_003253	NA	Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3883+1142A>G	chr21.hg19:g.32507108T>C		NA	B7ZLR6|F5GZ53|Q17RT7	hg19	CCDS13609.1	0.02	-0.14034	AGGxGTG	COVERED																																																																																			NOVEL	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000192552.1	4	2.40517	KEEP	1	0	0	8	211	TT	0.99257	0.259026	0		-	3	60	102	0	0	8.472838	11	60	334	44	ENST00000286827.3	0.214286	0.260965
TIAM1	7074	__UNKNOWN__	__UNKNOWN__	21	32642238	32642238	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:32642238A>C	ENST00000286827.3	-	5	461				TIAM1_ENST00000541036.1_Intron|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	NA		NA			apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						ctgcccacctaggcctcccaa	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299	7074		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11805	protein-coding gene	gene with protein product		600687			NA	8595894, 15340013	Standard	NM_003253	NM_003253	NA	Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.11-2939T>G	chr21.hg19:g.32642238A>C		NA	B7ZLR6|F5GZ53|Q17RT7	hg19	CCDS13609.1	0.02	-0.140248	CCTxGGC	COVERED																																																																																			NOVEL	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000192552.1	4	2.405821	KEEP	1	0	0	8	221	AA	0.99257	0.259026	0		-	3	60	88	0	0	7.30244	9	60	257	36	ENST00000286827.3	0.25	0.260965
TIAM1	7074	__UNKNOWN__	__UNKNOWN__	21	32830690	32830690	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:32830690A>G	ENST00000286827.3	-	2	104				TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	NA		NA			apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						ccaagatcacaccattgcact	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299	7074		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	11805	protein-coding gene	gene with protein product		600687			NA	8595894, 15340013	Standard	NM_003253	NM_003253	NA	Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.367+5605T>C	chr21.hg19:g.32830690A>G		NA	B7ZLR6|F5GZ53|Q17RT7	hg19	CCDS13609.1	0.02	-0.122763	CACxCCA	COVERED																																																																																			NOVEL	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000192552.1	5	3.308252	KEEP	4	0	0	11	300	AA	0.99254	0.194847	0		-	3	60	102	0	0	8.4733	11	60	304	45	ENST00000286827.3	0.214286	0.196312
HUNK	30811	__UNKNOWN__	__UNKNOWN__	21	33351721	33351721	__UNKNOWN__	Intron	SNP	C	C	G	rs9984004	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:33351721C>G	ENST00000270112.2	+	8	1533				HUNK_ENST00000465574.1_Intron	NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	NA		NA			multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						tgagccaccgcgcccggcccc	0.493		NA											c|||	2007	0.400759	0.3548	0.4265	5008	,	,	NA	15279	0.3155	NA	0.4533	False	NA	,,,	NA	NA	NA	2504	0.4785	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149	30811			13326	protein-coding gene	gene with protein product		606532	hormonally upregulated Neu-associated kinase		NA	10662544, 10830953	Standard	NM_014586	NM_014586	NA	Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1174-4118C>G	chr21.hg19:g.33351721C>G		NA		hg19	CCDS13610.1	0.02	-0.114021	CCGxGCC	UNCOVERED																																																																																			NOVEL	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000192782.1	2	2.4047	KEEP	2	0	0	8	216	CC	0	0	0		+	7	60	220	0	0	21.798839	5	60	161	32	ENST00000270112.2	0.583333	0.196312
MIS18A-AS1	100874202	__UNKNOWN__	__UNKNOWN__	21	33652899	33652899	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:33652899G>A	ENST00000453549.1	+	0	373									MIS18A antisense RNA 1	NA		NA									NA						ggcctcaagcgatcctcctgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BG209386		21q22.11	2012-10-12	2012-08-15		ENSG00000227256	ENSG00000227256	100874202		Long non-coding RNAs	40106	non-coding RNA	RNA, long non-coding		NA	MIS18A antisense RNA 1 (non-protein coding)		NA		Standard			NA	Approved				OTTHUMG00000085306	ENST00000453549.1:	chr21.hg19:g.33652899G>A		NA		hg19		0.02	-0.121819	AGCxATC	COVERED																																																																																			NOVEL	MIS18A-AS1-001	KNOWN	non_canonical_other|basic	antisense	NA	antisense	OTTHUMT00000193087.1	5	2.707734	KEEP	1	0	0	9	266	GG	0.99257	0.194853	0		+	3	60	89	0	0	7.532166	8	60	267	33	ENST00000453549.1	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	33778005	33778005	__UNKNOWN__	IGR	SNP	T	T	C	rs555466344		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:33778005T>C			NA	NA				C21orf119 (11751 upstream) : EVA1C (6683 downstream)						NA		NA									NA						gagtttgagatcagcctgggc	0.478		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18881	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.33778005T>C		NA		hg19		0.02	-0.166656	AGAxCAG	COVERED																																																																																			NOVEL					0			5	2.70643	KEEP	2	0	0	9	242	AT	0.99254	0.351306	0			3	60	103	0	0	8.291631	14	60	425	50		0.176471	0.353947
C21orf62	56245	__UNKNOWN__	__UNKNOWN__	21	34172866	34172866	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:34172866G>A	ENST00000536776.1	-	2	77				C21orf62_ENST00000490358.1_Intron|C21orf49_ENST00000453404.1_Intron|C21orf62_ENST00000487113.1_Intron|C21orf62_ENST00000479548.1_Intron	NM_001162495.2|NM_001162496.2|NM_019596.5	NP_001155967.2|NP_001155968.2|NP_062542.5	Q9NYP8	CU062_HUMAN	chromosome 21 open reading frame 62	NA		NA								endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	6		Myeloproliferative disorder(46;0.0255)				ggtggctcacgcctgtaatcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF231922	CCDS42919.1, CCDS42919.2	21q22.1	2011-02-24			ENSG00000205929	ENSG00000205929	56245			1305	protein-coding gene	gene with protein product		NA	chromosome 21 open reading frame 120	C21orf120	NA		Standard	NM_019596	NM_001162495	NA	Approved	B37, PRED81	uc011adu.2	Q9NYP8	OTTHUMG00000163477	ENST00000536776.1:c.64-6070C>T	chr21.hg19:g.34172866G>A		NA	A8K4L8	hg19	CCDS42919.2	0.02	-0.228023	CACxCCT	COVERED																																																																																			NOVEL	C21orf62-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139598.5	6	3.609592	KEEP	1	0	0	12	347	GG	0.993072	0.578892	0		-	3	60	88	0	0	6.36593	20	60	635	53	ENST00000536776.1	0.130435	0.58293
IL10RB	3588	__UNKNOWN__	__UNKNOWN__	21	34667425	34667425	__UNKNOWN__	Intron	SNP	T	T	C	rs191354204	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:34667425T>C	ENST00000290200.2	+	7	912					NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	NA		NA			cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						aatcccagcattttgggaggc	0.478		NA											T|||	3	0.000599042	0.0008	0.0	5008	,	,	NA	18147	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA	Melanoma(67;315 1275 21667 21943 44564)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646	3588		Interleukins and interleukin receptors, CD molecules	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66	NA	8314576, 9312047	Standard		NM_000628	NA	Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.805-1064T>C	chr21.hg19:g.34667425T>C		NA	Q9BUU4	hg19	CCDS13623.1	0.02	-0.149108	GCAxTTT	COVERED																																																																																			NOVEL	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139831.3	5	3.007721	KEEP	3	0	0	10	279	TT	0.99254	0.320398	0		+	3	60	100	0	0	8.172259	12	60	353	43	ENST00000290200.2	0.2	0.322807
IFNGR2	3460	__UNKNOWN__	__UNKNOWN__	21	34793814	34793814	__UNKNOWN__	Silent	SNP	C	C	T	rs138717312	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:34793814C>T	ENST00000290219.6	+	3	882	c.234C>T	c.(232-234)gaC>gaT	p.D78D	IFNGR2_ENST00000405436.1_5'UTR|IFNGR2_ENST00000381995.1_Silent_p.D97D	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	78	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.	NA			cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	TCACGGCCGACATCATGTCCA	0.458		NA											C|||	13	0.00259585	0.0	0.0	5008	,	,	NA	18695	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0133	NA	NA	NA								NA				0								C		2,4404	4.2+/-10.8	0,2,2201	123	111	115		234	-6.1	0	21	dbSNP_134	115	0,8600		0,0,4300	no	coding-synonymous	IFNGR2	NM_005534.3		0,2,6501	TT,TC,CC	NA	0.0,0.0454,0.0154		78/338	34793814	2,13004	2203	4300	6503	SO:0001819	synonymous_variant				CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128	3460		Interferons, Fibronectin type III domain containing	5440	protein-coding gene	gene with protein product		147569		IFNGT1	NA	3136170	Standard		NM_005534	NA	Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.234C>T	chr21.hg19:g.34793814C>T		NA	Q9BTL5	hg19	CCDS33544.1	0.02	2.701589	CGAxATC	COVERED																																																																																			NOVEL	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139916.1	6	15.043138	KEEP	0	0	0	50	1515	CC	1	1	0		+	47	60	1365	0	0	119.941689	94	60	3188	299	ENST00000290219.6	0.333333	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	34875746	34875746	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:34875746C>T			NA	NA				DNAJC28 (11719 upstream) : GART (491 downstream)						NA		NA									NA						aggatggtctcgatctcctga	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.34875746C>T		NA		hg19		0.02	-0.254324	TCTxGAT	COVERED																																																																																			NOVEL					0			13	2.337722	KEEP	15	1	29	18	514	CC	0.994391	0.664773	0			4	37	107	0	0	7.91736	20	60	642	80		0.166667	0.668523
DONSON	29980	__UNKNOWN__	__UNKNOWN__	21	34949916	34949916	__UNKNOWN__	Intron	SNP	C	C	T	rs2284558|rs71194853	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:34949916C>T	ENST00000303113.6	-	10	1696				DONSON_ENST00000453626.1_3'UTR			Q9NYP3	DONS_HUMAN	downstream neighbor of SON	NA		NA			multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|ovary(1)	11						CCCCTacacacacacacacac	0.393		NA											C|||	2343	0.467851	0.441	0.487	5008	,	,	NA	12507	0.3889	NA	0.5636	False	NA	,,,	NA	NA	NA	2504	0.4734	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF000002	CCDS13632.1	21q22.1	2008-07-31			ENSG00000159147	ENSG00000159147	29980			2993	protein-coding gene	gene with protein product		611428		C21orf60	NA	10773462, 10950926	Standard	NM_017613	NM_017613	NA	Approved	B17, C2TA, DKFZP434M035	uc002ysk.4	Q9NYP3	OTTHUMG00000065904	ENST00000303113.6:c.1656+688G>A	chr21.hg19:g.34949916C>T		NA	Q8NC53|Q9NSR9|Q9NVZ5|Q9NYP1|Q9NYP2	hg19		0.02	1.517541	ACAxACA	COVERED																																																																																			NOVEL	DONSON-008	NOVEL	alternative_3_UTR|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000141174.2	117	26.932889	KEEP	217	10	248	178	5057	CC	1	0.973965	0		-	17	60	461	1	0	40.654128	31	60	1010	497	ENST00000303113.6	0.354167	0.973965
CRYZL1	9946	__UNKNOWN__	__UNKNOWN__	21	35001645	35001645	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:35001645A>G	ENST00000445393.1	-	2	122				AP000304.12_ENST00000429238.1_Intron|CRYZL1_ENST00000381554.3_Intron|CRYZL1_ENST00000381540.3_Intron|CRYZL1_ENST00000413017.2_Intron|CRYZL1_ENST00000290244.5_Intron|CRYZL1_ENST00000361534.2_Intron			O95825	QORL1_HUMAN	crystallin, zeta (quinone reductase)-like 1	NA		NA			quinone metabolic process (GO:1901661)	cytosol (GO:0005829)	NADP binding (GO:0050661)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			lung(1)|prostate(1)|urinary_tract(1)	3						ttggctcactacaacctctgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF029689	CCDS13633.2	21q22.1	2008-07-31			ENSG00000205758	ENSG00000205758	9946			2420	protein-coding gene	gene with protein product	quinone reductase-like 1	603920			NA	10191096	Standard	NM_145858	NM_145858	NA	Approved	QOH-1, 4P11	uc021wio.1	O95825	OTTHUMG00000065954	ENST00000445393.1:c.66+2146T>C	chr21.hg19:g.35001645A>G		NA	B2RDX1|B3KQ77|Q96DY0|Q9NVY7	hg19		0.02	-0.210436	ACTxCAA	COVERED																																																																																			NOVEL	CRYZL1-024	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000337118.1	6	3.005995	KEEP	0	0	0	10	256	AA	0.992708	0.518353	0		-	3	60	88	0	0	6.307542	21	60	579	54	ENST00000445393.1	0.125	0.522161
ITSN1	6453	__UNKNOWN__	__UNKNOWN__	21	35072339	35072339	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:35072339G>A	ENST00000399367.3	+	2	231				AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399349.1_Intron|ITSN1_ENST00000399353.1_Intron|ITSN1_ENST00000399352.1_Intron|ITSN1_ENST00000381291.4_Intron|ITSN1_ENST00000399355.2_Intron|ITSN1_ENST00000381318.3_Intron|ITSN1_ENST00000381285.4_Intron			Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	NA		NA			apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						agtgctaggagtatcggtgtg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726	6453		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing, EF-hand domain containing	6183	protein-coding gene	gene with protein product	SH3 domain protein-1A, human intersectin-SH3 domain-containing protein SH3P17, Src homology 3 domain-containing protein, intersectin 1 short form variant, 11, intersectin 1 short form variant 3, intersectin short variant 12	602442		SH3D1A, ITSN	NA	9799604, 9813051	Standard	NM_003024	NM_003024	NA	Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000399367.3:c.-32-18763G>A	chr21.hg19:g.35072339G>A		NA	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	hg19		0.02	-0.121416	GGAxTAT	COVERED																																																																																			NOVEL	ITSN1-023	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000313582.1	6	3.008929	KEEP	0	0	0	10	306	GG	0.992708	0.19488	0		+	3	60	82	0	0	6.601791	10	60	291	28	ENST00000399367.3	0.230769	0.196312
ITSN1	6453	__UNKNOWN__	__UNKNOWN__	21	35095658	35095658	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:35095658G>A	ENST00000399367.3	+	4	448				AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399326.3_Intron|ITSN1_ENST00000399349.1_Intron|ITSN1_ENST00000379960.5_Intron|ITSN1_ENST00000399353.1_Intron|ITSN1_ENST00000399352.1_Intron|ITSN1_ENST00000381291.4_Intron|ITSN1_ENST00000399355.2_Intron|ITSN1_ENST00000399338.4_Intron|ITSN1_ENST00000381318.3_Intron|ITSN1_ENST00000381285.4_Intron|ITSN1_ENST00000437442.2_Intron			Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	NA		NA			apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						ggtggctcatgcctgtaatcc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726	6453		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing, EF-hand domain containing	6183	protein-coding gene	gene with protein product	SH3 domain protein-1A, human intersectin-SH3 domain-containing protein SH3P17, Src homology 3 domain-containing protein, intersectin 1 short form variant, 11, intersectin 1 short form variant 3, intersectin short variant 12	602442		SH3D1A, ITSN	NA	9799604, 9813051	Standard	NM_003024	NM_003024	NA	Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000399367.3:c.185+702G>A	chr21.hg19:g.35095658G>A		NA	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	hg19		0.02	-0.149129	CATxCCT	COVERED																																																																																			NOVEL	ITSN1-023	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000313582.1	5	3.009115	KEEP	4	0	0	10	310	GG	0.99254	0.320398	0		+	3	60	88	0	0	6.791941	14	60	482	46	ENST00000399367.3	0.176471	0.322807
ATP5O	539	__UNKNOWN__	__UNKNOWN__	21	35279192	35279192	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:35279192A>G	ENST00000290299.2	-	5	658				AP000304.12_ENST00000429238.1_Intron	NM_001697.2	NP_001688.1	P48047	ATPO_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	NA		NA			ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	5						ctactcaggaagctgaggcag	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF088071	CCDS13634.1	21q22	2012-10-12	2008-07-31		ENSG00000241837	ENSG00000241837	539	3.6.3.14	Mitochondrial respiratory chain complex / Complex V, ATPases / F-type	850	protein-coding gene	gene with protein product	oligomycin sensitivity conferring protein	600828			NA	7490082	Standard	NM_001697	NM_001697	NA	Approved	OSCP, ATPO		P48047	OTTHUMG00000065186	ENST00000290299.2:c.441+452T>C	chr21.hg19:g.35279192A>G		NA	B2R4E2|Q5U042|Q6IBI2	hg19	CCDS13634.1	0.02	-0.35959	GGAxGCT	COVERED																																																																																			NOVEL	ATP5O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000139907.1	7	4.440114	KEEP	0	1	26	24	629	AA	0.999931	0.888814	0		-	4	60	130	0	0	9.310403	35	60	1040	77	ENST00000290299.2	0.102564	0.888875
SMIM11	54065	__UNKNOWN__	__UNKNOWN__	21	35755293	35755293	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:35755293T>C	ENST00000399299.1	+	2	157				SMIM11_ENST00000481710.1_Intron|SMIM11_ENST00000399292.3_Intron|SMIM11_ENST00000399295.2_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	NA		NA				integral component of membrane (GO:0016021)					NA						cctgtaatcctagcactttgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670	54065			1293	protein-coding gene	gene with protein product		NA	chromosome 21 open reading frame 51, family with sequence similarity 165, member B	C21orf51, FAM165B	NA		Standard	NM_058182	NM_058182	NA	Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399299.1:c.12+3478T>C	chr21.hg19:g.35755293T>C		NA		hg19		0.02	-0.236799	TCCxAGC	COVERED																																																																																			NOVEL	SMIM11-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000194076.1	5	2.40635	KEEP	0	0	0	8	224	TT	0.99257	0.607857	0		+	3	60	97	0	0	7.09501	23	60	670	50	ENST00000399299.1	0.115385	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	37385346	37385346	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37385346A>G			NA	NA				AP000688.8 (5210 upstream) : AP000688.1 (17021 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.37385346A>G		NA		hg19		0.02	-0.201704	GCTxGGA	COVERED																																																																																			NOVEL					0			7	4.510775	KEEP	4	0	0	15	415	AA	0.994391	0.487793	0			3	60	102	0	0	8.033441	16	60	474	60		0.157895	0.490544
AP000688.14	0	__UNKNOWN__	__UNKNOWN__	21	37485373	37485373	__UNKNOWN__	RNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37485373T>C	ENST00000535199.1	-	0	154					NR_040084.1					NA		NA									NA						gacagagttttgctcttgttg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000535199.1:	chr21.hg19:g.37485373T>C		NA		hg19		0.02	-0.131569	TTTxGCT	UNCOVERED																																																																																			NOVEL	AP000688.14-002	KNOWN	basic	sense_intronic	NA	sense_intronic	OTTHUMT00000439311.2	8	2.406258	KEEP	1	0	0	8	223	TT	0	0	0		-	4	60	129	1	0	11.323991	9	60	272	35	ENST00000535199.1	0.307692	0.229173
DOPEY2	9980	__UNKNOWN__	__UNKNOWN__	21	37648866	37648866	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37648866C>T	ENST00000399151.3	+	28	5717					NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	NA		NA			cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						Tggccaggcacggtggctcac	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197	9980			1291	protein-coding gene	gene with protein product		604803	chromosome 21 open reading frame 5	C21orf5	NA	16301316, 16303751, 10931277	Standard	NM_005128	NM_005128	NA	Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.5633-453C>T	chr21.hg19:g.37648866C>T		NA	D3DSG5|Q6PJQ7|Q9UEZ3	hg19	CCDS13643.1	0.02	-0.184175	GCAxGGT	COVERED																																																																																			NOVEL	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194636.1	9	4.211313	KEEP	0	0	0	14	402	CC	0.995343	0.421506	0		+	3	60	87	0	0	6.534202	16	60	497	47	ENST00000399151.3	0.157895	0.423478
MORC3	23515	__UNKNOWN__	__UNKNOWN__	21	37706331	37706331	__UNKNOWN__	Intron	SNP	T	T	C	rs8134277	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37706331T>C	ENST00000400485.1	+	2	188				MORC3_ENST00000487909.1_Intron	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	NA		NA			cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						gtgatccgcctgcctcagcct	0.498		NA											C|||	4265	0.851637	0.907	0.7968	5008	,	,	NA	15822	0.997	NA	0.6173	False	NA	,,,	NA	NA	NA	2504	0.907	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256	23515			23572	protein-coding gene	gene with protein product		610078	zinc finger, CW-type with coiled-coil domain 3, zinc finger, CW type with coiled-coil domain 3	ZCWCC3	NA	14607086	Standard	NM_015358	NM_015358	NA	Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.112+315T>C	chr21.hg19:g.37706331T>C		NA	A8KA92|Q9UEZ2	hg19	CCDS42924.1	0.02	-0.184192	GCCxGCC	UNCOVERED																																																																																			NOVEL	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194640.1	16	2.707088	KEEP	17	0	0	9	253	TT	0	0	0		+	6	60	200	0	0	17.88741	12	60	356	59	ENST00000400485.1	0.333333	0.423478
CHAF1B	8208	__UNKNOWN__	__UNKNOWN__	21	37790976	37790976	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37790976A>G	ENST00000314103.5	+	0	4143					NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	NA		NA			cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(2)	20						gtggaaccccatctctactaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U20980	CCDS13644.1	21q22.2	2013-01-10			ENSG00000159259	ENSG00000159259	8208		WD repeat domain containing	1911	protein-coding gene	gene with protein product	M-phase phosphoprotein 7, Chromatin assembly factor I, p60 subunit, human chromatin assembly factor-I p60 subunit	601245			NA	7600578, 8792829	Standard	NM_005441	NM_005441	NA	Approved	CAF1P60, CAF-1, CAF1, CAF1A, MPP7, MPHOSPH7	uc002yvj.3	Q13112	OTTHUMG00000086606	ENST00000314103.5:c.*2312A>G	chr21.hg19:g.37790976A>G		NA	Q99548	hg19	CCDS13644.1	0.02	-0.166619	CCCxTCT	COVERED																																																																																			NOVEL	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194616.2	7	3.006225	KEEP	0	0	0	10	261	AA	0.992708	0.351366	0		+	3	50	105	0	0	8.491936	14	60	395	35	ENST00000314103.5	0.176471	0.353947
CLDN14	23562	__UNKNOWN__	__UNKNOWN__	21	37869317	37869317	__UNKNOWN__	Intron	SNP	G	G	A	rs145554784		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37869317G>A	ENST00000342108.2	-	2	297				CLDN14_ENST00000399136.1_Intron|AP000695.4_ENST00000428667.1_RNA	NM_001146077.1	NP_001139549.1	O95500	CLD14_HUMAN	claudin 14	NA		NA			calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						gggagggagggaggaagggag	0.692		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261	23562		Claudins	2035	protein-coding gene	gene with protein product		605608		DFNB29	NA	11163249	Standard	NM_144492	NM_144492	NA	Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000342108.2:c.80+13343C>T	chr21.hg19:g.37869317G>A		NA		hg19	CCDS13645.1	0.02	-0.105235	AGGxAGG	UNCOVERED																																																																																			NOVEL	CLDN14-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194700.1	12	2.406765	KEEP	16	0	0	8	234	GG	0	0	0		-	3	49	77	0	0	6.642637	6	41	183	43	ENST00000342108.2	0.333333	0.260965
CLDN14	23562	__UNKNOWN__	__UNKNOWN__	21	37869373	37869373	__UNKNOWN__	Intron	SNP	G	G	A	rs111220559		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37869373G>A	ENST00000342108.2	-	2	297				CLDN14_ENST00000399136.1_Intron|AP000695.4_ENST00000428667.1_RNA	NM_001146077.1	NP_001139549.1	O95500	CLD14_HUMAN	claudin 14	NA		NA			calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						gggaggaagggagggagggag	0.682		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261	23562		Claudins	2035	protein-coding gene	gene with protein product		605608		DFNB29	NA	11163249	Standard	NM_144492	NM_144492	NA	Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000342108.2:c.80+13287C>T	chr21.hg19:g.37869373G>A		NA		hg19	CCDS13645.1	0.02	-0.175417	AGGxAGG	UNCOVERED																																																																																			NOVEL	CLDN14-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194700.1	27	2.40695	KEEP	19	0	0	8	239	GG	0	0	0		-	3	40	84	2	1	6.673122	11	50	350	66	ENST00000342108.2	0.214286	0.387407
CLDN14	23562	__UNKNOWN__	__UNKNOWN__	21	37869465	37869465	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37869465G>A	ENST00000342108.2	-	2	297				CLDN14_ENST00000399136.1_Intron|AP000695.4_ENST00000428667.1_RNA	NM_001146077.1	NP_001139549.1	O95500	CLD14_HUMAN	claudin 14	NA		NA			calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						gggagggagggaggaagggag	0.677		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261	23562		Claudins	2035	protein-coding gene	gene with protein product		605608		DFNB29	NA	11163249	Standard	NM_144492	NM_144492	NA	Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000342108.2:c.80+13195C>T	chr21.hg19:g.37869465G>A		NA		hg19	CCDS13645.1	0.02	-0.184169	AGGxAGG	UNCOVERED																																																																																			NOVEL	CLDN14-004	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194700.1	13	3.008661	KEEP	13	0	0	10	301	GG	0	0	0		-	6	60	164	1	0	14.285462	12	60	397	55	ENST00000342108.2	0.333333	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	37970257	37970257	__UNKNOWN__	IGR	SNP	T	T	G	rs13050577	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:37970257T>G			NA	NA				CLDN14 (21390 upstream) : AP000696.2 (34721 downstream)						NA		NA									NA						caggctggagtgcagtggcat	0.532		NA											T|||	2299	0.459065	0.1679	0.4712	5008	,	,	NA	15108	0.5694	NA	0.6014	False	NA	,,,	NA	NA	NA	2504	0.5838	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.37970257T>G		NA		hg19		0.02	-0.052551	GAGxGCA	UNCOVERED																																																																																			NOVEL					0			5	2.705614	KEEP	2	0	0	9	240	TT	0	0	0			3	52	98	0	0	9.770136	2	49	55	19		0.6	0.036766
HLCS	3141	__UNKNOWN__	__UNKNOWN__	21	38128792	38128792	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:38128792C>T	ENST00000399120.1	-	11	3240				HLCS_ENST00000336648.4_Intron	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	NA		NA			biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	TACAGAACTACTAAGATACTA	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													42	36	38			NA	NA	21		NA											NA				38128792		2203	4300	6503	SO:0001627	intron_variant				CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	3141	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase), holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)		NA	7842009	Standard		NM_000411	NA	Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.2009+50G>A	chr21.hg19:g.38128792C>T		NA	B2RAH1|D3DSG6|Q99451	hg19	CCDS13647.1	0.02	1.438454	CTAxTAA	COVERED																																																																																			NOVEL	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194687.2	41	11.133714	KEEP	0	0	0	37	1157	CC	1	0.992094	0		-	5	60	150	0	0	9.955713	54	60	1828	118	ENST00000399120.1	0.084746	0.992094
DSCR9	257203	__UNKNOWN__	__UNKNOWN__	21	38585337	38585337	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:38585337T>C	ENST00000454482.2	+	0	145					NR_026719.2		P59020	DSCR9_HUMAN	Down syndrome critical region gene 9 (non-protein coding)	NA		NA									NA						ctcgctctgttgcccaggctg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AB066100		21q22	2012-10-16	2008-08-13		ENSG00000230366	ENSG00000230366	257203		Long non-coding RNAs	16301	non-coding RNA	RNA, long non-coding	non-protein coding RNA 38	NA			NA	12168953	Standard	NR_026719	NR_026719	NA	Approved	NCRNA00038	uc031rvh.1	P59020	OTTHUMG00000086655	ENST00000454482.2:	chr21.hg19:g.38585337T>C		NA	B2R8P8	hg19		0.02	-0.245574	TGTxGCC	COVERED																																																																																			NOVEL	DSCR9-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000194797.2	20	5.715067	KEEP	10	0	0	19	538	TT	0.993634	0.637264	0		+	3	60	99	0	0	7.242743	24	60	712	52	ENST00000454482.2	0.111111	0.641347
DSCR3	10311	__UNKNOWN__	__UNKNOWN__	21	38596620	38596620	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:38596620T>C	ENST00000309117.6	-	0	2356				AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000399000.3_5'UTR|DSCR3_ENST00000288304.5_3'UTR	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	NA		NA				nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						atcacttgagtctaggagttc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538	10311			3044	protein-coding gene	gene with protein product		605298			NA	9399594	Standard		NM_006052	NA	Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.*1225A>G	chr21.hg19:g.38596620T>C		NA	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	hg19	CCDS33553.1	0.02	-0.38577	GAGxCTA	COVERED																																																																																			NOVEL	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194807.1	11	7.512637	KEEP	0	0	0	25	644	TT	0.999931	0.918107	0		-	3	60	96	1	0	6.34213	39	60	1110	94	ENST00000309117.6	0.071429	0.918171
DSCR3	10311	__UNKNOWN__	__UNKNOWN__	21	38607621	38607621	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:38607621T>G	ENST00000309117.6	-	4	589				AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000399000.3_Intron|DSCR3_ENST00000399001.1_Intron|DSCR3_ENST00000398998.1_Intron|DSCR3_ENST00000288304.5_Intron|DSCR3_ENST00000476950.1_Intron|DSCR3_ENST00000539844.1_Intron	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	NA		NA				nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						ttttagtagatacggggtttc	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538	10311			3044	protein-coding gene	gene with protein product		605298			NA	9399594	Standard		NM_006052	NA	Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.352-1878A>C	chr21.hg19:g.38607621T>G		NA	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	hg19	CCDS33553.1	0.02	-0.184149	AGAxACG	COVERED																																																																																			NOVEL	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000194807.1	9	3.307649	KEEP	1	0	0	11	295	TT	0.993072	0.420544	0		-	3	60	93	0	0	7.06151	17	60	485	47	ENST00000309117.6	0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	40246321	40246321	__UNKNOWN__	IGR	SNP	C	C	T	rs528107885|rs3959085	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:40246321C>T			NA	NA				AP001042.1 (25753 upstream) : AF064858.6 (2893 downstream)						NA		NA									NA						ccgaggcgggcggatcacgag	0.557		NA											-|||	3455	0.689896	0.7126	0.6945	5008	,	,	NA	11431	0.6667	NA	0.5706	False	NA	,,,	NA	NA	NA	2504	0.8027	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.40246321C>T		NA		hg19		0.02	-0.043812	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			6	2.405076	KEEP	16	0	0	8	212	CC	0	0	0			4	60	112	0	0	12.015146	1	60	30	37		0.8	0.024074
AF064858.6	0	__UNKNOWN__	__UNKNOWN__	21	40288699	40288699	__UNKNOWN__	lincRNA	SNP	A	A	G	rs112672745		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:40288699A>G	ENST00000380931.2	-	0	676										NA		NA									NA						ggaaggaagaaaaggaaggag	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000380931.2:	chr21.hg19:g.40288699A>G		NA		hg19		0.02	-0.280646	AGAxAAG	COVERED																																																																																			NOVEL	AF064858.6-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000141410.2	9	3.307874	KEEP	0	0	0	11	298	AA	0.993072	0.734547	0		-	3	60	99	2	0	7.098214	27	60	783	56	ENST00000380931.2	0.1	0.739671
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	40740143	40740143	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:40740143T>C			NA	NA				HMGN1 (18570 upstream) : WRB (12026 downstream)						NA		NA									NA						aggctggtcttgaactcctga	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.40740143T>C		NA		hg19		0.02	-0.157862	TCTxGAA	UNCOVERED																																																																																			NOVEL					0			7	2.706699	KEEP	11	0	0	9	245	TT	0	0	0			3	60	91	0	0	7.092402	14	60	411	52		0.176471	0.322807
LCA5L	150082	__UNKNOWN__	__UNKNOWN__	21	40801755	40801755	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:40801755G>C	ENST00000358268.2	-	3	438				LCA5L_ENST00000380671.2_Intron|LCA5L_ENST00000485895.2_Intron|LCA5L_ENST00000288350.3_Intron			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	NA		NA								breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				accagcctgggcaacatggcg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578	150082			1255	protein-coding gene	gene with protein product		NA	chromosome 21 open reading frame 13	C21orf13	NA		Standard	NM_152505	XM_005260926	NA	Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.91-618C>G	chr21.hg19:g.40801755G>C		NA	D3DSI0|Q3ZCT0	hg19	CCDS13665.1	0.02	-0.131587	TGGxCAA	COVERED																																																																																			NOVEL	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000141807.2	6	2.707676	KEEP	0	0	0	9	267	GG	0.99254	0.227464	0		-	4	60	136	0	0	11.871093	10	60	334	31	ENST00000358268.2	0.285714	0.229173
C21orf88	114041	__UNKNOWN__	__UNKNOWN__	21	40977764	40977764	__UNKNOWN__	Intron	SNP	G	G	A	rs530806849		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:40977764G>A	ENST00000380612.4	-	2	228				C21orf88_ENST00000380604.3_3'UTR|C21orf88_ENST00000329618.6_3'UTR|B3GALT5_ENST00000380620.4_Intron					chromosome 21 open reading frame 88	NA		NA								endometrium(1)|large_intestine(1)	2						ggctggtctcgaactcctgag	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF426266		21q22.2	2013-01-15			ENSG00000184809	ENSG00000184809	114041			16424	other	unknown		NA			NA	12036297	Standard	NR_026542	NR_026542	NA	Approved		uc010gok.4	P59052	OTTHUMG00000086722	ENST00000380612.4:c.152+3745C>T	chr21.hg19:g.40977764G>A		NA		hg19		0.02	1.210814	CTCxAAC	COVERED																																																																																			NOVEL	C21orf88-001	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000194999.1	17	3.238347	KEEP	0	4	102	47	1374	GG	1	0.999804	0		-	5	60	139	0	0	8.108404	78	60	2446	196	ENST00000380612.4	0.060241	0.999804
DSCAM	1826	__UNKNOWN__	__UNKNOWN__	21	41584184	41584184	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:41584184T>C	ENST00000400454.1	-	12	2834					NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	NA		NA			cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				cgtgagccactgtgcccagtc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(134;970 1778 1785 21664 32388)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587	1826		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	3039	protein-coding gene	gene with protein product		602523			NA	9426258	Standard	NM_001389	NM_001271534	NA	Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.2357-23019A>G	chr21.hg19:g.41584184T>C		NA	O60468	hg19	CCDS42929.1	0.02	1.783406	CACxGTG	COVERED																																																																																			NOVEL	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195029.1	13	4.141486	KEEP	1	1	32	25	680	TT	0.999931	0.996164	0		-	4	60	138	0	0	9.359317	55	60	1641	126	ENST00000400454.1	0.067797	0.996233
DSCAM	1826	__UNKNOWN__	__UNKNOWN__	21	41989293	41989293	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:41989293A>G	ENST00000400454.1	-	3	986					NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	NA		NA			cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				ctcgtgatccacccgcctcgg	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Melanoma(134;970 1778 1785 21664 32388)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587	1826		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	3039	protein-coding gene	gene with protein product		602523			NA	9426258	Standard	NM_001389	NM_001271534	NA	Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.508+75442T>C	chr21.hg19:g.41989293A>G		NA	O60468	hg19	CCDS42929.1	0.02	-0.103879	TCCxCCC	UNCOVERED																																																																																			NOVEL	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195029.1	6	2.40653	KEEP	10	0	0	8	228	AA	0	0	0		-	3	60	93	0	0	7.823013	9	50	236	42	ENST00000400454.1	0.25	0.139832
C2CD2	25966	__UNKNOWN__	__UNKNOWN__	21	43345347	43345347	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:43345347T>C	ENST00000380486.3	-	3	620				C2CD2_ENST00000329623.7_Intron	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	NA		NA				cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						gtaatcccagtgctttgggag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617	25966			1266	protein-coding gene	gene with protein product	TMEM24-like	NA	chromosome 21 open reading frame 25	C21orf25	NA	15289880	Standard	NM_015500	NM_015500	NA	Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.379-3153A>G	chr21.hg19:g.43345347T>C		NA	Q5R2V7|Q6AHX8|Q9NSE6	hg19	CCDS42933.1	0.02	-0.122785	CAGxGCT	COVERED																																																																																			NOVEL	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195228.2	1	3.607956	KEEP	1	0	0	12	316	TT	0.993072	0.194952	0		-	3	60	108	0	0	9.432743	8	60	231	38	ENST00000380486.3	0.272727	0.196312
C2CD2	25966	__UNKNOWN__	__UNKNOWN__	21	43345348	43345348	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:43345348G>A	ENST00000380486.3	-	3	620				C2CD2_ENST00000329623.7_Intron	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	NA		NA				cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						taatcccagtgctttgggagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617	25966			1266	protein-coding gene	gene with protein product	TMEM24-like	NA	chromosome 21 open reading frame 25	C21orf25	NA	15289880	Standard	NM_015500	NM_015500	NA	Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.379-3154C>T	chr21.hg19:g.43345348G>A		NA	Q5R2V7|Q6AHX8|Q9NSE6	hg19	CCDS42933.1	0.02	-0.122798	AGTxCTT	COVERED																																																																																			NOVEL	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195228.2	1	3.911316	KEEP	1	0	0	13	393	GG	0.993634	0.195062	0		-	3	60	89	0	0	7.532308	8	60	259	38	ENST00000380486.3	0.272727	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	43431992	43431992	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:43431992G>A			NA	NA				ZBTB21 (1496 upstream) : ZNF295-AS1 (10199 downstream)						NA		NA									NA						ttgtatttttggtagagatgg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.43431992G>A		NA		hg19		0.02	-0.105263	TTTxGTA	UNCOVERED																																																																																			NOVEL					0			4	2.406535	KEEP	0	0	0	8	231	GG	0.99257	0.138793	0			3	60	86	0	0	7.100924	9	60	305	24		0.25	0.139832
SLC37A1	54020	__UNKNOWN__	__UNKNOWN__	21	43923629	43923629	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:43923629A>G	ENST00000398341.3	+	2	234					NM_018964.3	NP_061837.3	P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	NA		NA			carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						aaagtgctggaattacaggtg	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190	54020		Solute carriers	11024	protein-coding gene	gene with protein product		608094	solute carrier family 37 (glycerol-3-phosphate transporter), member 1		NA	11112347	Standard		NM_018964	NA	Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000398341.3:c.-179+1102A>G	chr21.hg19:g.43923629A>G		NA	D3DSJ7|Q9HAQ1	hg19	CCDS13689.1	0.02	-0.219275	TGGxATT	COVERED																																																																																			NOVEL	SLC37A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195374.2	8	3.007146	KEEP	1	0	0	10	269	AA	0.99254	0.548763	0		+	3	60	104	1	0	8.233174	16	60	483	49	ENST00000398341.3	0.157895	0.552887
PKNOX1	5316	__UNKNOWN__	__UNKNOWN__	21	44420791	44420791	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:44420791A>G	ENST00000291547.5	+	2	155				PKNOX1_ENST00000432907.2_Intron	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	NA		NA			angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						gagcccaggaattcaagacca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199	5316		Homeoboxes / TALE class	9022	protein-coding gene	gene with protein product		602100			NA	9479508	Standard		NM_001286258	NA	Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.-56-3645A>G	chr21.hg19:g.44420791A>G		NA	O00528|Q8IWT7	hg19	CCDS13692.1	0.02	-0.035086	GGAxTTC	UNCOVERED																																																																																			NOVEL	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195520.3	7	3.30901	KEEP	0	0	0	11	315	AA	0.993072	0.019843	0		+	2	60	67	0	0	6.450147	2	60	59	22	ENST00000291547.5	0.5	0.019982
PKNOX1	5316	__UNKNOWN__	__UNKNOWN__	21	44427923	44427923	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:44427923T>C	ENST00000291547.5	+	3	390				PKNOX1_ENST00000432907.2_Intron	NM_004571.3	NP_004562.2	P55347	PKNX1_HUMAN	PBX/knotted 1 homeobox 1	NA		NA			angiogenesis (GO:0001525)|camera-type eye development (GO:0043010)|erythrocyte differentiation (GO:0030218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation (GO:0030217)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(3)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(8)|ovary(1)|prostate(1)	22						cctgtaatcctagcactttgg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13692.1, CCDS68211.1	21q22.3	2011-06-20			ENSG00000160199	ENSG00000160199	5316		Homeoboxes / TALE class	9022	protein-coding gene	gene with protein product		602100			NA	9479508	Standard		NM_001286258	NA	Approved	PREP1	uc002zcq.1	P55347	OTTHUMG00000086833	ENST00000291547.5:c.179+195T>C	chr21.hg19:g.44427923T>C		NA	O00528|Q8IWT7	hg19	CCDS13692.1	0.02	-0.166647	TCCxAGC	COVERED																																																																																			NOVEL	PKNOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195520.3	4	2.706908	KEEP	0	0	0	9	250	TT	0.99254	0.351306	0		+	3	60	108	0	0	8.87869	13	60	393	43	ENST00000291547.5	0.1875	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	44917799	44917799	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:44917799A>T			NA	NA				LINC00313 (26327 upstream) : HSF2BP (31272 downstream)						NA		NA									NA						agtgctgggaatacaggcatg	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.44917799A>T		NA		hg19		0.02	-0.271892	GGAxTAC	COVERED																																																																																			NOVEL					0			5	2.406208	KEEP	0	0	0	8	224	AA	0.99257	0.711986	0			3	60	92	0	0	6.493691	25	60	758	60		0.107143	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	21	44933710	44933710	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:44933710A>G			NA	NA				LINC00313 (42238 upstream) : HSF2BP (15361 downstream)						NA		NA									NA						agaccagcctaggcaacatag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr21.hg19:g.44933710A>G		NA		hg19		0.02	-0.254347	CCTxGGC	COVERED																																																																																			NOVEL					0			4	3.607995	KEEP	1	0	0	12	320	AA	0.993072	0.688863	0			3	60	104	0	0	7.742232	24	60	718	62		0.111111	0.693668
PDXK	8566	__UNKNOWN__	__UNKNOWN__	21	45178246	45178246	__UNKNOWN__	3'UTR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:45178246G>C	ENST00000291565.4	+	0	3424				PDXK_ENST00000468090.1_3'UTR|PDXK_ENST00000467908.1_3'UTR	NM_003681.4	NP_003672.1	O00764	PDXK_HUMAN	pyridoxal (pyridoxine, vitamin B6) kinase	NA		NA			cell proliferation (GO:0008283)|pyridoxal 5'-phosphate salvage (GO:0009443)|pyridoxal phosphate biosynthetic process (GO:0042823)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|protein homodimerization activity (GO:0042803)|pyridoxal kinase activity (GO:0008478)|pyridoxal phosphate binding (GO:0030170)|sodium ion binding (GO:0031402)|zinc ion binding (GO:0008270)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	cctgggctgcgactaaggaga	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													11	12	12			NA	NA	21		NA											NA				45178246		692	1591	2283	SO:0001624	3_prime_UTR_variant			U89606	CCDS13699.1	21q22.3	2007-05-10			ENSG00000160209	ENSG00000160209	8566	2.7.1.35		8819	protein-coding gene	gene with protein product		179020	chromosome 21 open reading frame 97, chromosome 21 open reading frame 124	C21orf97, C21orf124	NA	9099727	Standard	NM_003681	NM_003681	NA	Approved	PNK, PKH, FLJ21324, PRED79, FLJ31940, MGC15873	uc002zdm.4	O00764	OTTHUMG00000086870	ENST00000291565.4:c.*2302G>C	chr21.hg19:g.45178246G>C		NA	Q7Z2Y0|Q9BS02	hg19	CCDS13699.1	0.02	2.032178	TGCxACT	COVERED																																																																																			NOVEL	PDXK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195636.1	0	6.015902	KEEP	0	0	0	20	573	GG	0.999863	0.967292	0		+	16	60	543	0	0	47.995662	36	60	1153	101	ENST00000291565.4	0.307692	0.967425
AGPAT3	56894	__UNKNOWN__	__UNKNOWN__	21	45333216	45333216	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:45333216T>C	ENST00000291572.8	+	2	223				AGPAT3_ENST00000327505.2_Intron|AGPAT3_ENST00000398061.1_Intron	NM_020132.4	NP_064517.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	NA		NA			CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		tggtggctcatgcctataatc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(60;623 1650 5574 52796)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	56894	2.3.1.51	1-acylglycerol-3-phosphate O-acyltransferases	326	protein-coding gene	gene with protein product		614794			NA		Standard	NM_020132	XM_005261159	NA	Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000291572.8:c.-49+9316T>C	chr21.hg19:g.45333216T>C		NA	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	hg19	CCDS13703.1	0.02	-0.228023	TCAxGCC	COVERED																																																																																			NOVEL	AGPAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195719.1	9	4.210925	KEEP	0	0	0	14	391	TT	0.995343	0.580216	0		+	3	60	96	0	0	7.227245	19	60	578	60	ENST00000291572.8	0.136364	0.58293
AGPAT3	56894	__UNKNOWN__	__UNKNOWN__	21	45398470	45398470	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:45398470A>G	ENST00000398063.2	+	7	1335				AGPAT3_ENST00000479117.1_Intron|AGPAT3_ENST00000291572.8_Intron|AGPAT3_ENST00000546158.1_Intron|AGPAT3_ENST00000327505.2_Intron|AGPAT3_ENST00000398061.1_Intron|AGPAT3_ENST00000398058.1_Intron	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	NA		NA			CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		gattacaggcatgagccacca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Pancreas(60;623 1650 5574 52796)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	56894	2.3.1.51	1-acylglycerol-3-phosphate O-acyltransferases	326	protein-coding gene	gene with protein product		614794			NA		Standard	NM_020132	XM_005261159	NA	Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.843+468A>G	chr21.hg19:g.45398470A>G		NA	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	hg19	CCDS13703.1	0.02	-0.131566	GGCxTGA	COVERED																																																																																			NOVEL	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000195722.1	10	4.211752	KEEP	0	0	0	14	405	AA	0.995343	0.228106	0		+	4	60	129	0	0	11.171351	10	60	301	44	ENST00000398063.2	0.285714	0.229173
TSPEAR	54084	__UNKNOWN__	__UNKNOWN__	21	45970483	45970483	__UNKNOWN__	Intron	SNP	C	C	T	rs233237	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:45970483C>T	ENST00000397916.1	-	3	258				TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000391621.1_3'UTR|KRTAP10-2_ENST00000498210.1_5'UTR			Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	NA		NA			sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						TCCTTCTGTGCTGAGCTGTGC	0.706		NA											T|||	1135	0.226637	0.211	0.1571	5008	,	,	NA	13603	0.3651	NA	0.2087	False	NA	,,,	NA	NA	NA	2504	0.1728	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894	54084			1268	protein-coding gene	gene with protein product		612920	chromosome 21 open reading frame 29, deafness, autosomal recessive 98	C21orf29, DFNB98	NA	12095917, 22678063	Standard	NM_144991	NM_144991	NA	Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000397916.1:c.100-16677G>A	chr21.hg19:g.45970483C>T		NA		hg19		0.02	-0.403425	GTGxTGA	COVERED																																																																																			NOVEL	TSPEAR-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000195865.1	1	2.386312	KEEP	0	0	0	8	209	CC	0.99257	0.927549	0		-	4	42	112	0	0	7.254957	41	60	1343	58	ENST00000397916.1	0.088889	0.934492
TSPEAR	54084	__UNKNOWN__	__UNKNOWN__	21	45970812	45970812	__UNKNOWN__	Intron	SNP	G	G	A	rs2329834	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:45970812G>A	ENST00000397916.1	-	2	258				TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000391621.1_Missense_Mutation_p.P177L|KRTAP10-2_ENST00000498210.1_Intron			Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	NA		NA			sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						CTGCTGACACGGGGAGGAGGT	0.607		NA											G|||	2742	0.547524	0.5015	0.5735	5008	,	,	NA	20805	0.371	NA	0.6163	False	NA	,,,	NA	NA	NA	2504	0.7025	NA	NA	NA								NA				0								G	,LEU/PRO	2134,2272	574.5+/-383.8	503,1128,572	114	117	116		,530	-1.6	0	21	dbSNP_100	116	5441,3159	650.5+/-400.7	1729,1983,588	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,98	2232,3111,1160	AA,AG,GG	NA	36.7326,48.434,41.7577	,benign	,177/256	45970812	7575,5431	2203	4300	6503	SO:0001627	intron_variant			AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894	54084			1268	protein-coding gene	gene with protein product		612920	chromosome 21 open reading frame 29, deafness, autosomal recessive 98	C21orf29, DFNB98	NA	12095917, 22678063	Standard	NM_144991	NM_144991	NA	Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000397916.1:c.99+16856C>T	chr21.hg19:g.45970812G>A		NA		hg19		0.02	1.280649	CACxGGG	COVERED	1087	0.4977106227106227	225	0.4573170731707317	226	0.6243093922651933	185	0.32342657342657344	451	0.5949868073878628	g	1.411	-0.575612	0.03882	0.48434	0.632674	ENSG00000205445	ENST00000391621	T	0.01295	5.04	2.98	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	M	0.91818	3.245	0.80722	P	0.0	B	0.16802	0.019	B	0.13407	0.009	T	0.18085	-1.0348	8	0.40728	T	0.16	.	3.9041	0.09174	0.0988:0.2783:0.4817:0.1412	rs2329834;rs2329834	177	P60368	KR102_HUMAN	L	177	ENSP00000375479:P177L	ENSP00000375479:P177L	P	-	2	0	KRTAP10-2	44795240	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.958000	0.03857	-0.221000	0.09973	-4.721000	0.00003	CCG	NOVEL	TSPEAR-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000195865.1	1	2.405825	KEEP	0	0	0	8	220	GG	0.99257	0.991893	0		-	16	60	469	0	0	37.153369	64	60	2055	121	ENST00000397916.1	0.2	0.999317
KRTAP10-9	386676	__UNKNOWN__	__UNKNOWN__	21	46048143	46048143	__UNKNOWN__	3'UTR	SNP	A	A	G	rs28539096	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:46048143A>G	ENST00000397911.3	+	0	1104				TSPEAR_ENST00000323084.4_Intron|KRTAP10-9_ENST00000484861.1_3'UTR	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	NA		NA				keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CCCCCCGGGCAGGCGAGCCCT	0.697		NA											G|||	3281	0.655152	0.5582	0.6772	5008	,	,	NA	9132	0.6448	NA	0.7167	False	NA	,,,	NA	NA	NA	2504	0.7178	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837	386676		Keratin associated proteins	22971	protein-coding gene	gene with protein product		NA		KRTAP18-9	NA		Standard		NM_198690	NA	Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.*176A>G	chr21.hg19:g.46048143A>G		NA	A2RRG1|A6NIR9|Q70LJ1	hg19	CCDS42961.1	0.02	-0.280684	GGCxGGC	COVERED																																																																																			NOVEL	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000128040.1	1	3.007556	KEEP	0	0	0	10	278	AA	0.992708	0.734278	0		+	15	46	481	0	0	46.225227	15	70	450	53	ENST00000397911.3	0.5	0.739671
SUMO3	6612	__UNKNOWN__	__UNKNOWN__	21	46228424	46228424	__UNKNOWN__	Silent	SNP	C	C	T	rs187569757		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:46228424C>T	ENST00000397893.3	-	4	281	c.282G>A	c.(280-282)acG>acA	p.T94T	SUMO3_ENST00000332859.6_Intron|SUMO3_ENST00000479153.1_Intron|SUMO3_ENST00000411651.2_Intron|SUMO3_ENST00000397898.3_Intron					small ubiquitin-like modifier 3	NA		NA								prostate(1)	1				Colorectal(79;0.058)		agcgagactccgtctcaaaaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001819	synonymous_variant				CCDS33587.1, CCDS68220.1	21q22.3	2013-06-05	2013-06-05	2004-05-19	ENSG00000184900	ENSG00000184900	6612			11124	protein-coding gene	gene with protein product		602231	SMT3 (suppressor of mif two 3, yeast) homolog 1, SMT3 suppressor of mif two 3 homolog 3 (yeast), SMT3 suppressor of mif two 3 homolog 3 (S. cerevisiae)	SMT3H1	NA	9119407	Standard		NM_006936	NA	Approved	SMT3A	uc002zfz.1	P55854	OTTHUMG00000090256	ENST00000397893.3:c.282G>A	chr21.hg19:g.46228424C>T		NA		hg19		0.02	4.12632	CTCxGTC	COVERED																																																																																			NOVEL	SUMO3-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000206564.1	55	7.187729	KEEP	1	12	307	133	3981	CC	1	1	0		-	9	60	272	1	1	16.248164	160	60	5342	500	ENST00000397893.3	0.053254	1
PCBP3	54039	__UNKNOWN__	__UNKNOWN__	21	47361800	47361800	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:47361800G>A	ENST00000400314.1	+	0	1634				PCBP3_ENST00000400310.1_3'UTR|PCBP3_ENST00000400309.1_3'UTR|PCBP3_ENST00000449640.1_3'UTR|PCBP3_ENST00000400308.1_3'UTR			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	NA		NA			mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		TCTCTACAGAGGCTGCAGGCT	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570	54039			8651	protein-coding gene	gene with protein product		608502	poly(rC)-binding protein 3		NA	10936052	Standard		NM_020528	NA	Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.*180G>A	chr21.hg19:g.47361800G>A		NA	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	hg19	CCDS42974.2	0.02	0.983277	AGAxGCT	COVERED																																																																																			NOVEL	PCBP3-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206808.2	8	6.018277	KEEP	0	0	0	20	625	GG	0.999863	0.996587	0		+	5	60	135	0	0	8.111676	64	60	2234	124	ENST00000400314.1	0.072464	0.996724
MCM3AP	8888	__UNKNOWN__	__UNKNOWN__	21	47681377	47681377	__UNKNOWN__	Intron	SNP	G	G	A	rs183402185	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:47681377G>A	ENST00000397708.1	-	15	3590				MCM3AP_ENST00000291688.1_Intron			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	NA		NA			DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ggccgggtgcggtggctcacg	0.522		NA											G|||	2	0.000399361	0.0	0.0	5008	,	,	NA	17494	0.002	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294	8888			6946	protein-coding gene	gene with protein product	germinal-centre associated nuclear protein	603294	minichromosome maintenance deficient (S. cerevisiae) 3-associated protein, MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein		NA	9712829, 16914116, 21195085	Standard	NM_003906	XM_005261205	NA	Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.3336-52C>T	chr21.hg19:g.47681377G>A		NA	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	hg19	CCDS13734.1	0.02	1.526238	TGCxGTG	COVERED																																																																																			NOVEL	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207254.1	10	3.642964	KEEP	1	1	28	22	652	GG	0.999892	0.97386	0		-	5	60	146	0	0	10.02596	43	60	1378	106	ENST00000397708.1	0.104167	0.973965
PCNT	5116	__UNKNOWN__	__UNKNOWN__	21	47836237	47836237	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr21:47836237G>A	ENST00000359568.5	+	30	6512	c.6405G>A	c.(6403-6405)acG>acA	p.T2135T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2135		NA			brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)		p.G2137fs*2(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					ATACAGCCACGGGGGGTGTAA	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Deletion - Frameshift(1)	large_intestine(1)											81	84	83			NA	NA	21		NA											NA				47836237		2203	4300	6503	SO:0001819	synonymous_variant			AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299	5116			16068	protein-coding gene	gene with protein product	kendrin, Seckel syndrome 4	605925	pericentrin 2 (kendrin)	PCNT2	NA	8812505, 9455477	Standard	NM_006031	NM_006031	NA	Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.6405G>A	chr21.hg19:g.47836237G>A		NA	O43152|Q7Z7C9	hg19	CCDS33592.1	0.02	-0.385905	CACxGGG	COVERED																																																																																			NOVEL	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207336.1	0	3.007805	KEEP	0	0	0	10	287	GG	0.992708	0.911475	0		+	4	60	120	0	0	8.09234	40	60	1248	75	ENST00000359568.5	0.090909	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16105112	16105112	__UNKNOWN__	IGR	SNP	C	C	T	rs56405056		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16105112C>T			NA	NA				LA16c-4G1.3 (41876 upstream) : AP000525.9 (42866 downstream)						NA		NA									NA						ggctcagtggcttatgcctgt	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16105112C>T		NA		hg19		0.02	-0.184217	TGGxTTA	COVERED																																																																																			NOVEL					0			7	2.708173	KEEP	6	0	0	9	283	CC	0.99257	0.420331	0			3	60	91	0	0	7.01045	15	60	526	53		0.166667	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16348203	16348203	__UNKNOWN__	IGR	SNP	G	G	T	rs377423029		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16348203G>T			NA	NA				POTEH (60266 upstream) : LA16c-2F2.8 (24877 downstream)						NA		NA									NA						CCTCTCTCCAGAAGGGAAAAG	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16348203G>T		NA		hg19		0.02	1.526158	CCAxAAG	COVERED																																																																																			NOVEL					0			1	3.008955	KEEP	6	0	0	10	305	GG	0.992708	0.963741	0			5	47	150	0	0	10.198728	48	60	1659	108		0.09434	0.97082
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16380641	16380641	__UNKNOWN__	IGR	SNP	G	G	A	rs367625255		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16380641G>A			NA	NA				LA16c-2F2.8 (3586 upstream) : LA16c-23H5.4 (36627 downstream)						NA		NA									NA						aatgaggccgggcatggtggc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16380641G>A		NA		hg19		0.02	-0.385988	CCGxGCA	COVERED																																																																																			NOVEL					0			19	3.983096	KEEP	35	1	27	23	683	GG	0.99649	0.914948	0			5	47	148	0	0	10.824972	32	50	1095	138		0.135135	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16380645	16380645	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16380645T>C			NA	NA				LA16c-2F2.8 (3590 upstream) : LA16c-23H5.4 (36623 downstream)						NA		NA									NA						aggccgggcatggtggctcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16380645T>C		NA		hg19		0.02	-0.385924	GCAxGGT	COVERED																																																																																			NOVEL					0			23	7.51781	KEEP	41	0	0	25	679	TT	0.99649	0.914948	0			4	49	137	0	0	10.106261	33	50	984	146		0.108108	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16404740	16404740	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16404740G>A			NA	NA				LA16c-2F2.8 (27685 upstream) : LA16c-23H5.4 (12528 downstream)						NA		NA									NA						CCCTCGGACGGGCAGGCTGGG	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16404740G>A		NA		hg19		0.02	1.43234	ACGxGCA	COVERED																																																																																			NOVEL					0			5	5.114617	KEEP	32	0	0	17	507	GG	0.994391	0.992864	0			11	46	328	0	0	24.47573	64	60	2171	183		0.146667	0.998465
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16414371	16414371	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16414371G>A			NA	NA				LA16c-2F2.8 (37316 upstream) : LA16c-23H5.4 (2897 downstream)						NA		NA									NA						TCCTTTCCCCGGAGCACTCGG	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16414371G>A		NA		hg19		0.02	1.315676	CCCxGAG	UNCOVERED																																																																																			NOVEL					0			0	3.309406	KEEP	43	0	0	11	329	GG	0	0	0			5	27	143	0	0	8.668034	72	50	2452	163		0.064935	0.998867
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	16963372	16963372	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:16963372A>G			NA	NA				AP000539.2 (387181 upstream) : KB-67B5.17 (38576 downstream)						NA		NA									NA						tcttgccgccaccatgtaaga	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.16963372A>G		NA		hg19		0.02	-0.052613	GCCxCCA	UNCOVERED																																																																																			NOVEL					0			5	2.402795	KEEP	9	0	0	8	195	AA	0	0	0			2	59	71	0	0	6.396243	4	52	106	24		0.333333	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	17033235	17033235	__UNKNOWN__	IGR	SNP	A	A	G	rs369166172		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:17033235A>G			NA	NA				KB-67B5.17 (25108 upstream) : KCNMB3P1 (28731 downstream)						NA		NA									NA						tgatccgcccacctcggcttc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.17033235A>G		NA		hg19		0.02	-0.149079	CCCxCCT	COVERED																																																																																			NOVEL					0			8	2.404083	KEEP	4	0	0	8	202	AA	0.99257	0.289832	0			3	23	86	1	0	6.873355	11	60	333	38		0.214286	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	17376372	17376372	__UNKNOWN__	IGR	SNP	C	C	T	rs5748718	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:17376372C>T			NA	NA				AC007064.24 (24356 upstream) : GAB4 (66453 downstream)						NA		NA									NA						gtcaggagttcgagaccagct	0.478		NA											.|||	833	0.166334	0.0174	0.2089	5008	,	,	NA	35576	0.2411	NA	0.1809	False	NA	,,,	NA	NA	NA	2504	0.2454	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.17376372C>T		NA		hg19		0.02	-0.140337	GTTxGAG	COVERED																																																																																			NOVEL					0			11	3.007378	KEEP	3	0	0	10	275	CC	0.99254	0.259018	0			4	49	117	0	0	10.476808	7	60	210	35		0.363636	0.260965
CECR1	51816	__UNKNOWN__	__UNKNOWN__	22	17678433	17678433	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:17678433C>T	ENST00000480276.1	-	1	193				CECR1_ENST00000399839.1_Intron|CECR1_ENST00000330232.4_Intron|CECR1_ENST00000449907.2_Intron|CECR1_ENST00000399837.2_Intron|CECR1_ENST00000262607.3_Intron			Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	NA		NA			adenosine catabolic process (GO:0006154)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)	adenosine deaminase activity (GO:0004000)|adenosine receptor binding (GO:0031685)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|prostate(2)|stomach(1)	25		all_epithelial(15;0.0152)|Lung NSC(13;0.0875)|all_lung(157;0.106)				agtgctgggactacaggcatg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF190746	CCDS13742.1, CCDS13743.1, CCDS63395.1, CCDS74809.1	22q11.2	2008-02-22			ENSG00000093072	ENSG00000093072	51816			1839	protein-coding gene	gene with protein product		607575		IDGFL	NA	10756095	Standard		NM_001282225	NA	Approved	ADGF	uc002zmk.1	Q9NZK5	OTTHUMG00000030726	ENST00000480276.1:c.377+1055G>A	chr22.hg19:g.17678433C>T		NA	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	hg19		0.02	-0.140356	GGAxTAC	COVERED																																																																																			NOVEL	CECR1-006	PUTATIVE	basic|exp_conf	processed_transcript	NA	protein_coding	OTTHUMT00000316083.1	5	2.407376	KEEP	0	0	0	8	253	CC	0.99257	0.259026	0		-	5	60	150	0	0	13.623114	8	60	280	36	ENST00000480276.1	0.384615	0.260965
CECR3	27442	__UNKNOWN__	__UNKNOWN__	22	17743345	17743345	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:17743345A>G	ENST00000428828.1	-	0	211					NR_038398.2				cat eye syndrome chromosome region, candidate 3 (non-protein coding)	NA		NA									NA						gtgaaaccccatctctactaa	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					AF277398		22q11.2	2012-10-16	2011-06-10		ENSG00000241832	ENSG00000241832	27442		Long non-coding RNAs	1841	non-coding RNA	RNA, long non-coding		NA	cat eye syndrome chromosome region, candidate 3		NA	11381032	Standard		NR_038398	NA	Approved		uc021wkn.1		OTTHUMG00000150063	ENST00000428828.1:	chr22.hg19:g.17743345A>G		NA		hg19		0.02	-0.157819	CCCxTCT	UNCOVERED																																																																																			NOVEL	CECR3-001	KNOWN	basic	processed_transcript	NA	processed_transcript	OTTHUMT00000316076.1	10	4.206168	KEEP	11	0	0	14	345	AA	0	0	0		-	5	60	153	0	0	13.540168	10	60	269	40	ENST00000428828.1	0.333333	0.322807
BCL2L13	23786	__UNKNOWN__	__UNKNOWN__	22	18117896	18117896	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18117896A>G	ENST00000399782.1	+	2	90							Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		gctcatgcctataatcccagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968	23786			17164	protein-coding gene	gene with protein product		NA			NA	11262395, 11381032	Standard	NM_015367	NM_015367	NA	Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000399782.1:c.-649-2972A>G	chr22.hg19:g.18117896A>G		NA	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	hg19		0.02	-0.210478	CCTxTAA	COVERED																																																																																			NOVEL	BCL2L13-002	KNOWN	basic	protein_coding	NA	protein_coding	OTTHUMT00000316185.2	7	4.509124	KEEP	0	0	0	15	390	AA	0.99649	0.520328	0		+	3	60	99	0	0	7.592355	18	60	512	53	ENST00000399782.1	0.142857	0.522161
BCL2L13	23786	__UNKNOWN__	__UNKNOWN__	22	18171682	18171682	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18171682T>A	ENST00000317582.5	+	4	576				BCL2L13_ENST00000538149.1_Intron|BCL2L13_ENST00000355028.3_Intron|BCL2L13_ENST00000418951.2_Intron|BCL2L13_ENST00000493680.1_Intron|BCL2L13_ENST00000337612.5_Intron|BCL2L13_ENST00000543133.1_Intron|BCL2L13_ENST00000399782.1_Intron	NM_015367.3	NP_056182.2	Q9BXK5	B2L13_HUMAN	BCL2-like 13 (apoptosis facilitator)	NA		NA			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			breast(2)|central_nervous_system(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(3)|urinary_tract(2)	15		all_epithelial(15;0.123)		Lung(27;0.199)		tacaggcatgtgccaccacac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF146568	CCDS13746.1, CCDS59447.1, CCDS59448.1, CCDS74810.1, CCDS74811.1, CCDS74812.1, CCDS74813.1, CCDS74814.1	22q11	2014-03-07			ENSG00000099968	ENSG00000099968	23786			17164	protein-coding gene	gene with protein product		NA			NA	11262395, 11381032	Standard	NM_015367	NM_015367	NA	Approved	MIL1, BCL-RAMBO	uc002zmw.4	Q9BXK5	OTTHUMG00000150088	ENST00000317582.5:c.230-70T>A	chr22.hg19:g.18171682T>A		NA	B3KPE7|Q96B37|Q96IB7|Q9BY01|Q9HC05|Q9UFE0|Q9UKN3	hg19	CCDS13746.1	0.02	-0.184131	ATGxGCC	COVERED																																																																																			NOVEL	BCL2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316184.1	5	3.537687	KEEP	2	1	26	21	546	TT	0.999879	0.457701	0		+	3	60	88	1	0	6.63482	16	60	434	52	ENST00000317582.5	0.157895	0.457757
MICAL3	57553	__UNKNOWN__	__UNKNOWN__	22	18333208	18333208	__UNKNOWN__	Intron	SNP	A	A	G	rs2587117	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18333208A>G	ENST00000441493.2	-	20	2958				MICAL3_ENST00000400561.2_Intron|MICAL3_ENST00000414725.2_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000207726.7_Intron|MICAL3_ENST00000383094.3_Intron	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	NA		NA			actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		atggagtctcactctgttacc	0.453		NA											a|||	2135	0.426318	0.6672	0.2911	5008	,	,	NA	11288	0.3681	NA	0.3638	False	NA	,,,	NA	NA	NA	2504	0.3211	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156	57553			24694	protein-coding gene	gene with protein product		608882			NA	12110185	Standard		NM_015241	NA	Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.2606-8425T>C	chr22.hg19:g.18333208A>G		NA	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	hg19	CCDS46659.1	0.02	-0.052615	CTCxCTC	UNCOVERED																																																																																			NOVEL	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447351.1	14	2.404648	KEEP	7	0	0	8	203	AA	0	0	0		-	3	55	106	0	0	10.571289	2	49	51	22	ENST00000441493.2	0.6	0.036766
MICAL3	57553	__UNKNOWN__	__UNKNOWN__	22	18460518	18460518	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18460518A>G	ENST00000441493.2	-	1	279				MICAL3_ENST00000429452.1_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000207726.7_Intron	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	NA		NA			actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		ggccaggcacagtggctcaca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156	57553			24694	protein-coding gene	gene with protein product		608882			NA	12110185	Standard		NM_015241	NA	Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.73+46528T>C	chr22.hg19:g.18460518A>G		NA	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	hg19	CCDS46659.1	0.02	-0.219289	CACxGTG	COVERED																																																																																			NOVEL	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447351.1	7	3.609731	KEEP	7	0	0	12	343	AA	0.99257	0.54878	0		-	3	60	105	0	0	8.126586	19	60	588	62	ENST00000441493.2	0.136364	0.552887
MICAL3	57553	__UNKNOWN__	__UNKNOWN__	22	18478957	18478957	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18478957A>G	ENST00000441493.2	-	1	279				MICAL3_ENST00000429452.1_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000207726.7_Intron	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	NA		NA			actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|exocytosis (GO:0006887)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		tgtaatcccaacactttggga	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037785	CCDS46659.1, CCDS46660.1, CCDS46661.1	22q11.21	2013-03-26	2013-03-26		ENSG00000243156	ENSG00000243156	57553			24694	protein-coding gene	gene with protein product		608882			NA	12110185	Standard		NM_015241	NA	Approved	KIAA0819	uc002zng.4	Q7RTP6	OTTHUMG00000150067	ENST00000441493.2:c.73+28089T>C	chr22.hg19:g.18478957A>G		NA	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	hg19	CCDS46659.1	0.02	-0.096466	CCAxCAC	UNCOVERED																																																																																			NOVEL	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000447351.1	4	2.704092	KEEP	4	0	0	9	223	AA	0	0	0		-	3	43	99	0	0	8.844155	6	60	165	29	ENST00000441493.2	0.333333	0.120436
AC008132.13	0	__UNKNOWN__	__UNKNOWN__	22	18842438	18842438	__UNKNOWN__	Intron	SNP	G	G	A	rs9604886		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18842438G>A	ENST00000412938.1	+	4	2208										NA		NA									NA						TGGGGAAGAGGAGAGTGGCTC	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000412938.1:c.2209-865G>A	chr22.hg19:g.18842438G>A		NA		hg19		0.02	1.3683	GAGxAGA	COVERED																																																																																			NOVEL	AC008132.13-002	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000471615.1	4	4.814462	KEEP	4	0	0	16	499	GG	0.997832	0.995001	0		+	18	60	529	0	0	44.159167	52	60	1772	135	ENST00000412938.1	0.257143	0.997163
DGCR5	26220	__UNKNOWN__	__UNKNOWN__	22	18968158	18968158	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:18968158G>A	ENST00000421572.1	+	0	76				DGCR5_ENST00000440005.2_RNA|DGCR5_ENST00000438934.1_RNA					DiGeorge syndrome critical region gene 5 (non-protein coding)	NA		NA									NA						aaaaaaaaaTGAGTGGGTGAC	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					X91348		22q11	2012-10-16	2008-08-13		ENSG00000237517	ENSG00000237517	26220		Long non-coding RNAs	16757	non-coding RNA	RNA, long non-coding	non-protein coding RNA 37, long intergenic non-protein coding RNA 37	NA			NA	8659529	Standard	NR_002733	NR_002733	NA	Approved	NCRNA00037, LINC00037	uc021wku.1		OTTHUMG00000149977	ENST00000421572.1:	chr22.hg19:g.18968158G>A		NA		hg19		0.02	-0.210513	AATxAGT	COVERED																																																																																			NOVEL	DGCR5-004	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000316630.1	17	7.218751	KEEP	0	0	0	24	709	GG	0.999909	0.522114	0		+	4	60	114	0	0	8.695166	19	60	619	73	ENST00000421572.1	0.173913	0.522161
DGCR2	9993	__UNKNOWN__	__UNKNOWN__	22	19082913	19082913	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:19082913A>G	ENST00000263196.7	-	2	327				DGCR2_ENST00000545799.1_Intron|DGCR2_ENST00000537045.1_Intron	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	NA		NA			cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					ggtggctcacacctgtaatcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413	9993			2845	protein-coding gene	gene with protein product	integral membrane protein DGCR2	600594			NA	7655455, 8630060	Standard	NM_005137	NM_005137	NA	Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.80-5910T>C	chr22.hg19:g.19082913A>G		NA	A6NIB5|A8K6K5|B5TY34|B7Z935	hg19	CCDS33598.1	0.02	-0.298095	CACxCCT	COVERED																																																																																			NOVEL	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316504.1	10	3.905879	KEEP	0	0	0	13	343	AA	0.994391	0.776679	0		-	4	60	139	0	0	10.694576	26	60	735	63	ENST00000263196.7	0.133333	0.78106
HIRA	7290	__UNKNOWN__	__UNKNOWN__	22	19360347	19360347	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:19360347A>G	ENST00000263208.5	-	15	2032				HIRA_ENST00000546308.1_Intron|HIRA_ENST00000340170.4_Intron|HIRA_ENST00000541063.1_Intron	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	NA		NA			anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					cacccacctcagcctcccaaa	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084	7290		WD repeat domain containing	4916	protein-coding gene	gene with protein product	DiGeorge critical region gene 1	600237	HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae), HIR histone cell cycle regulation defective homolog A (S. cerevisiae)	TUPLE1	NA	8111380, 7633437, 9731536	Standard	NM_003325	NM_003325	NA	Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.1775+2806T>C	chr22.hg19:g.19360347A>G		NA	Q05BU9|Q8IXN2	hg19	CCDS13759.1	0.02	-0.175422	CTCxGCC	COVERED																																																																																			NOVEL	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316488.2	9	3.309027	KEEP	3	0	0	11	314	AA	0.992708	0.384582	0		-	3	60	97	0	0	7.460988	17	60	515	48	ENST00000263208.5	0.15	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	19582410	19582410	__UNKNOWN__	IGR	SNP	T	T	C	rs9606081	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:19582410T>C			NA	NA				CLDN5 (67342 upstream) : AC000067.1 (72135 downstream)						NA		NA									NA						ggcggatcacttgaggtcagg	0.522		NA											C|||	2874	0.573882	0.7375	0.513	5008	,	,	NA	13651	0.4524	NA	0.5119	False	NA	,,,	NA	NA	NA	2504	0.5849	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.19582410T>C		NA		hg19		0.02	-0.070167	CACxTGA	UNCOVERED																																																																																			NOVEL					0			5	2.703743	KEEP	5	0	0	9	243	TT	0	0	0			3	60	95	1	0	8.632497	5	60	154	31		0.375	0.054137
COMT	1312	__UNKNOWN__	__UNKNOWN__	22	19937887	19937887	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:19937887T>C	ENST00000361682.6	+	1	291				COMT_ENST00000407537.1_Intron|COMT_ENST00000403184.1_Intron|COMT_ENST00000403710.1_Intron	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	NA		NA			cellular response to phosphate starvation (GO:0016036)|dopamine catabolic process (GO:0042420)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|learning (GO:0007612)|methylation (GO:0032259)|multicellular organismal reproductive process (GO:0048609)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of smooth muscle cell proliferation (GO:0048662)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|positive regulation of homocysteine metabolic process (GO:0050668)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	catechol O-methyltransferase activity (GO:0016206)|magnesium ion binding (GO:0000287)|O-methyltransferase activity (GO:0008171)			kidney(1)|lung(1)|ovary(1)|prostate(1)|stomach(1)	5	Colorectal(54;0.0993)				Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Methyldopa(DB00968)|Micafungin(DB01141)|S-Adenosylmethionine(DB00118)|Testosterone Propionate(DB01420)|Tolcapone(DB00323)	ggattacaggtgtgagccacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13770.1, CCDS46663.1	22q11.21	2012-10-02			ENSG00000093010	ENSG00000093010	1312	2.1.1.6		2228	protein-coding gene	gene with protein product		116790			NA	1572656	Standard	NM_000754	NM_000754	NA	Approved		uc002zqu.3	P21964	OTTHUMG00000150529	ENST00000361682.6:c.-92+8467T>C	chr22.hg19:g.19937887T>C		NA	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	hg19	CCDS13770.1	0.02	-0.201727	AGGxGTG	COVERED																																																																																			NOVEL	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318936.2	3	2.390683	KEEP	1	0	0	8	206	TT	0.99257	0.4869	0		+	3	60	97	0	0	7.461004	17	60	503	52	ENST00000361682.6	0.15	0.490544
MED15	51586	__UNKNOWN__	__UNKNOWN__	22	20866398	20866398	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:20866398T>C	ENST00000292733.7	+	1	145				MED15_ENST00000542773.1_Intron|MED15_ENST00000425759.2_Intron|MED15_ENST00000382974.2_Intron|MED15_ENST00000541476.1_Intron|MED15_ENST00000406969.1_Intron|MED15_ENST00000263205.7_Intron	NM_015889.3	NP_056973.2	Q96RN5	MED15_HUMAN	mediator complex subunit 15	NA		NA			gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			actgtagccttctgagtagct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917	51586			14248	protein-coding gene	gene with protein product		607372	trinucleotide repeat containing 7, PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein	TNRC7, PCQAP	NA	11024300, 11414760, 15175163	Standard	NM_015889	XM_005261632	NA	Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000292733.7:c.68+4365T>C	chr22.hg19:g.20866398T>C		NA	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	hg19	CCDS13781.1	0.02	-0.087719	CCTxCTG	UNCOVERED																																																																																			NOVEL	MED15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320174.2	8	3.306875	KEEP	0	0	0	11	298	TT	0.993072	0.09903	0		+	3	55	102	0	0	8.978637	7	60	219	28	ENST00000292733.7	0.3	0.099721
MED15	51586	__UNKNOWN__	__UNKNOWN__	22	20867217	20867217	__UNKNOWN__	Intron	SNP	C	C	T	rs185360125	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:20867217C>T	ENST00000292733.7	+	1	145				MED15_ENST00000542773.1_Intron|MED15_ENST00000425759.2_Intron|MED15_ENST00000382974.2_Intron|MED15_ENST00000541476.1_Intron|MED15_ENST00000406969.1_Intron|MED15_ENST00000263205.7_Intron	NM_015889.3	NP_056973.2	Q96RN5	MED15_HUMAN	mediator complex subunit 15	NA		NA			gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			ttagtagagacggggtttcac	0.557		NA											C|||	20	0.00399361	0.0015	0.0043	5008	,	,	NA	14414	0.0	NA	0.0139	False	NA	,,,	NA	NA	NA	2504	0.001	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917	51586			14248	protein-coding gene	gene with protein product		607372	trinucleotide repeat containing 7, PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein	TNRC7, PCQAP	NA	11024300, 11414760, 15175163	Standard	NM_015889	XM_005261632	NA	Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000292733.7:c.68+5184C>T	chr22.hg19:g.20867217C>T		NA	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	hg19	CCDS13781.1	0.02	-0.122788	AGAxGGG	COVERED																																																																																			NOVEL	MED15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320174.2	4	3.008124	KEEP	2	0	0	10	296	CC	0.99254	0.194847	0		+	5	59	141	0	0	12.722747	8	60	262	37	ENST00000292733.7	0.384615	0.196312
MED15	51586	__UNKNOWN__	__UNKNOWN__	22	20869819	20869819	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:20869819A>G	ENST00000292733.7	+	1	145				MED15_ENST00000542773.1_Intron|MED15_ENST00000425759.2_Intron|MED15_ENST00000382974.2_Intron|MED15_ENST00000541476.1_Intron|MED15_ENST00000406969.1_Intron|MED15_ENST00000263205.7_Intron	NM_015889.3	NP_056973.2	Q96RN5	MED15_HUMAN	mediator complex subunit 15	NA		NA			gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			gctcacgcctataatcctagc	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917	51586			14248	protein-coding gene	gene with protein product		607372	trinucleotide repeat containing 7, PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein	TNRC7, PCQAP	NA	11024300, 11414760, 15175163	Standard	NM_015889	XM_005261632	NA	Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000292733.7:c.68+7786A>G	chr22.hg19:g.20869819A>G		NA	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	hg19	CCDS13781.1	0.02	-0.140328	CCTxTAA	COVERED																																																																																			NOVEL	MED15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320174.2	9	4.209647	KEEP	1	0	0	14	372	AA	0.994391	0.259501	0		+	3	60	104	0	0	9.032652	8	60	234	50	ENST00000292733.7	0.272727	0.260965
PI4KA	5297	__UNKNOWN__	__UNKNOWN__	22	21071426	21071426	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21071426C>T	ENST00000255882.6	-	45	5404				PI4KA_ENST00000414196.3_Intron|PI4KA_ENST00000572273.1_Intron	NM_058004.3	NP_477352.3	P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	NA		NA			phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			cccagctactcgggaggctga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(136;1332 1831 3115 23601 50806)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973	5297			8983	protein-coding gene	gene with protein product		600286		PIK4CA	NA	7961848, 8662589	Standard	NM_058004	NM_002650	NA	Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000255882.6:c.5317+569G>A	chr22.hg19:g.21071426C>T		NA	Q7Z625|Q9UPG2	hg19	CCDS33603.2	0.02	-0.035079	ACTxGGG	UNCOVERED																																																																																			NOVEL	PI4KA-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075723.5	8	2.707121	KEEP	0	0	0	9	264	CC	0.99254	0.019833	0		-	3	60	85	0	0	8.952645	1	60	34	16	ENST00000255882.6	0.75	0.019982
THAP7-AS1	439931	__UNKNOWN__	__UNKNOWN__	22	21357070	21357070	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21357070A>G	ENST00000452284.1	+	0	574				THAP7-AS1_ENST00000429962.1_RNA|THAP7-AS1_ENST00000436079.1_RNA	NR_027051.1				THAP7 antisense RNA 1	NA		NA									NA						tgggactacaagcgcccgcca	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA							22q11.21	2012-10-12	2012-08-15		ENSG00000230513	ENSG00000230513	439931		Long non-coding RNAs	41013	non-coding RNA	RNA, long non-coding		NA	THAP7 antisense RNA 1 (non-protein coding)		NA		Standard	NR_027051	NR_027051	NA	Approved		uc002ztv.3		OTTHUMG00000150877	ENST00000452284.1:	chr22.hg19:g.21357070A>G		NA		hg19		0.02	-0.421021	ACAxGCG	COVERED																																																																																			NOVEL	THAP7-AS1-002	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000320385.1	6	6.616689	KEEP	0	0	0	22	607	AA	0.999879	0.948287	0		+	4	60	136	0	1	9.648712	41	60	1251	101	ENST00000452284.1	0.088889	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	21483650	21483650	__UNKNOWN__	IGR	SNP	G	G	C	rs560149339|rs55815276		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21483650G>C			NA	NA				POM121L7 (1298 upstream) : FAM230B (38396 downstream)						NA		NA									NA						gagagagagagagacagagag	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.21483650G>C		NA		hg19		0.02	-0.175452	AGAxAGA	COVERED																																																																																			NOVEL					0			10	3.009033	KEEP	1	0	0	10	308	GG	0.99254	0.384517	0			6	60	208	0	1	19.278376	9	60	304	39		0.4	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	21484180	21484180	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21484180C>A			NA	NA				POM121L7 (1828 upstream) : FAM230B (37866 downstream)						NA		NA									NA						cacacacacacacacacacac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.21484180C>A		NA		hg19		0.02	-0.114033	ACAxACA	UNCOVERED																																																																																			NOVEL					0			23	2.239773	KEEP	35	1	30	18	540	CC	0.99254	0.161255	0			4	21	118	0	0	10.390787	8	21	274	73		0.333333	0.162467
GGT2	728441	__UNKNOWN__	__UNKNOWN__	22	21571771	21571771	__UNKNOWN__	Intron	SNP	T	T	A	rs9608818	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21571771T>A	ENST00000401924.1	-	7	874				GGT2_ENST00000405188.4_Intron|GGT2_ENST00000424627.1_Intron			P36268	GGT2_HUMAN	gamma-glutamyltransferase 2	NA		NA			glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	anchored component of external side of plasma membrane (GO:0031362)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)				NA						catggctcactgcagccttgg	0.483		NA											t|||	1004	0.200479	0.2368	0.1931	5008	,	,	NA	24546	0.1131	NA	0.2704	False	NA	,,,	NA	NA	NA	2504	0.1748	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M30474		22q11.21	2012-04-19			ENSG00000133475	ENSG00000133475	728441	2.3.2.2	Gamma-glutamyltransferases	4251	protein-coding gene	gene with protein product		137181		GGT	NA	8104871, 18357469	Standard	XM_001129377	XM_006724392	NA	Approved		uc011aic.1	P36268	OTTHUMG00000150617	ENST00000401924.1:c.383-815A>T	chr22.hg19:g.21571771T>A		NA		hg19		0.02	-0.157887	CACxGCA	COVERED																																																																																			NOVEL	GGT2-002	KNOWN	non_canonical_other|not_best_in_genome_evidence|basic|appris_principal|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000320092.2	11	3.307887	KEEP	3	0	0	11	301	TT	0.99254	0.320398	0		-	3	52	97	0	0	7.691704	14	60	431	44	ENST00000401924.1	0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	21897423	21897423	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21897423T>C			NA	NA				snoU13 (19300 upstream) : SCARNA17 (1762 downstream)						NA		NA									NA						ctgcccaccttggcctcccaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.21897423T>C		NA		hg19		0.02	-0.166598	CCTxGGC	COVERED																																																																																			NOVEL					0			3	4.804581	KEEP	19	0	0	16	424	TT	0.993634	0.351693	0			3	37	94	0	0	7.233995	16	37	453	77		0.157895	0.353947
UBE2L3	7332	__UNKNOWN__	__UNKNOWN__	22	21918583	21918583	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21918583C>A	ENST00000458578.2	+	1	204					NM_001256355.1	NP_001243284.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	NA		NA			cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)		UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					ttggcctccccaagtgctagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651	7332		Ubiquitin-conjugating enzymes E2	12488	protein-coding gene	gene with protein product		603721			NA	8672131, 9693040	Standard	NM_198157	NM_001256356	NA	Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000458578.2:c.201+14644C>A	chr22.hg19:g.21918583C>A		NA	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	hg19	CCDS58795.1	0.02	-0.201743	CCCxAAG	COVERED																																																																																			NOVEL	UBE2L3-201	KNOWN	basic|CCDS	protein_coding	NA	protein_coding		6	2.407398	KEEP	0	0	0	8	252	CC	0.99257	0.4869	0		+	5	60	146	0	0	12.230279	14	60	463	42	ENST00000458578.2	0.263158	0.490544
UBE2L3	7332	__UNKNOWN__	__UNKNOWN__	22	21935152	21935152	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:21935152A>G	ENST00000342192.4	+	2	225				UBE2L3_ENST00000545681.1_Intron|UBE2L3_ENST00000458578.2_Intron	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	NA		NA			cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)		UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					gggattacagacatgagccac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651	7332		Ubiquitin-conjugating enzymes E2	12488	protein-coding gene	gene with protein product		603721			NA	8672131, 9693040	Standard	NM_198157	NM_001256356	NA	Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000342192.4:c.28-11998A>G	chr22.hg19:g.21935152A>G		NA	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	hg19	CCDS13790.1	0.02	-0.21927	CAGxCAT	COVERED																																																																																			NOVEL	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320219.1	2	4.209809	KEEP	0	0	0	14	380	AA	0.995343	0.550313	0		+	3	60	95	0	0	7.005933	21	60	637	60	ENST00000342192.4	0.125	0.552887
PPIL2	23759	__UNKNOWN__	__UNKNOWN__	22	22046943	22046943	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22046943A>G	ENST00000335025.8	+	16	1230				PPIL2_ENST00000456792.2_Intron|PPIL2_ENST00000446951.1_Intron|PPIL2_ENST00000406385.1_Intron|PPIL2_ENST00000398831.3_Intron|PPIL2_ENST00000412327.1_Intron|PPIL2_ENST00000492445.2_Intron					peptidylprolyl isomerase (cyclophilin)-like 2	NA		NA								endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					ggccaggtgcagtggctcacg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023	23759		U-box domain containing	9261	protein-coding gene	gene with protein product	U-box domain containing 7	607588			NA	10591208	Standard		NM_014337	NA	Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.1140-1162A>G	chr22.hg19:g.22046943A>G		NA		hg19	CCDS13793.1	0.02	-0.166667	TGCxGTG	COVERED																																																																																			NOVEL	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075028.4	13	3.609048	KEEP	2	0	0	12	331	AA	0.993072	0.351495	0		+	4	60	132	0	0	10.96817	14	60	443	44	ENST00000335025.8	0.222222	0.353947
PPIL2	23759	__UNKNOWN__	__UNKNOWN__	22	22046952	22046952	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22046952C>T	ENST00000335025.8	+	16	1230				PPIL2_ENST00000456792.2_Intron|PPIL2_ENST00000446951.1_Intron|PPIL2_ENST00000406385.1_Intron|PPIL2_ENST00000398831.3_Intron|PPIL2_ENST00000412327.1_Intron|PPIL2_ENST00000492445.2_Intron					peptidylprolyl isomerase (cyclophilin)-like 2	NA		NA								endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					cagtggctcacgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023	23759		U-box domain containing	9261	protein-coding gene	gene with protein product	U-box domain containing 7	607588			NA	10591208	Standard		NM_014337	NA	Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.1140-1153C>T	chr22.hg19:g.22046952C>T		NA		hg19	CCDS13793.1	0.02	-0.175442	TCAxGCC	COVERED																																																																																			NOVEL	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075028.4	13	3.609325	KEEP	2	0	0	12	347	CC	0.993072	0.384723	0		+	3	60	93	0	0	7.133397	16	60	524	46	ENST00000335025.8	0.157895	0.387407
YPEL1	29799	__UNKNOWN__	__UNKNOWN__	22	22070006	22070006	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22070006G>A	ENST00000339468.3	-	2	220				YPEL1_ENST00000403503.1_Intron	NM_013313.3	NP_037445.1	O60688	YPEL1_HUMAN	yippee-like 1 (Drosophila)	NA		NA				nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(1)	3	Colorectal(54;0.105)					gagtagctgggactactggca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF060862	CCDS13794.1	22q11.2	2008-02-04	2001-11-28		ENSG00000100027	ENSG00000100027	29799			12845	protein-coding gene	gene with protein product		608082	yippee (Drosophila) homolog-like 1		NA	11473580	Standard	NM_013313	NM_013313	NA	Approved		uc002zvl.3	O60688	OTTHUMG00000150830	ENST00000339468.3:c.164-4809C>T	chr22.hg19:g.22070006G>A		NA	Q65ZA1|Q6GLI6	hg19	CCDS13794.1	0.02	-0.035088	TGGxACT	UNCOVERED																																																																																			NOVEL	YPEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320245.1	5	2.708254	KEEP	0	0	0	9	282	GG	0.99254	0.019833	0		-	2	60	62	0	0	6.324546	1	60	32	18	ENST00000339468.3	0.666667	0.019982
MAPK1	5594	__UNKNOWN__	__UNKNOWN__	22	22136823	22136823	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22136823T>C	ENST00000215832.6	-	6	1045				MAPK1_ENST00000544786.1_Intron|MAPK1_ENST00000398822.3_Intron	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	NA		NA			activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	cctgtaatcctagcactttgg	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	5594	2.7.11.1	Mitogen-activated protein kinase cascade / Kinases	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1	NA		Standard		NM_138957	NA	Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.856+5722A>G	chr22.hg19:g.22136823T>C		NA	A8CZ64	hg19	CCDS13795.1	0.02	-0.105243	TCCxAGC	UNCOVERED																																																																																			NOVEL	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075396.2	4	2.70654	KEEP	1	0	0	9	244	TT	0.99257	0.138793	0		-	3	60	89	0	0	7.532406	8	60	237	27	ENST00000215832.6	0.272727	0.139832
MAPK1	5594	__UNKNOWN__	__UNKNOWN__	22	22168246	22168246	__UNKNOWN__	Intron	SNP	A	A	G	rs4516540	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22168246A>G	ENST00000215832.6	-	2	308				MAPK1_ENST00000544786.1_Intron|MAPK1_ENST00000398822.3_Intron	NM_002745.4	NP_002736.3	P28482	MK01_HUMAN	mitogen-activated protein kinase 1	NA		NA			activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|caveolin-mediated endocytosis (GO:0072584)|cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|chemotaxis (GO:0006935)|cytosine metabolic process (GO:0019858)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|labyrinthine layer blood vessel development (GO:0060716)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mammary gland epithelial cell proliferation (GO:0033598)|MAPK cascade (GO:0000165)|MAPK import into nucleus (GO:0000189)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell differentiation (GO:0045596)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|Ras protein signal transduction (GO:0007265)|regulation of cytoskeleton organization (GO:0051493)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of protein stability (GO:0031647)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of stress-activated MAPK cascade (GO:0032872)|response to epidermal growth factor (GO:0070849)|response to estrogen (GO:0043627)|response to exogenous dsRNA (GO:0043330)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|pseudopodium (GO:0031143)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MAP kinase activity (GO:0004707)|phosphatase binding (GO:0019902)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Colorectal(54;0.105)	all_lung(157;3.89e-05)		READ - Rectum adenocarcinoma(21;0.0689)	Arsenic trioxide(DB01169)|Isoprenaline(DB01064)	tccagcctggacaacaagagt	0.468		NA											G|||	2298	0.458866	0.3502	0.5749	5008	,	,	NA	17781	0.4544	NA	0.5249	False	NA	,,,	NA	NA	NA	2504	0.4601	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M84489	CCDS13795.1	22q11.2	2014-09-17			ENSG00000100030	ENSG00000100030	5594	2.7.11.1	Mitogen-activated protein kinase cascade / Kinases	6871	protein-coding gene	gene with protein product		176948		PRKM2, PRKM1	NA		Standard		NM_138957	NA	Approved	ERK, ERK2, p41mapk, MAPK2	uc002zvn.3	P28482	OTTHUMG00000030508	ENST00000215832.6:c.120-6111T>C	chr22.hg19:g.22168246A>G		NA	A8CZ64	hg19	CCDS13795.1	0.02	-0.087706	TGGxCAA	UNCOVERED																																																																																			NOVEL	MAPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075396.2	7	2.405455	KEEP	0	0	0	8	210	AA	0.99257	0.09898	0		-	4	60	135	0	0	12.486095	6	60	174	26	ENST00000215832.6	0.4	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	22245992	22245992	__UNKNOWN__	IGR	SNP	T	T	C	rs531841611		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22245992T>C			NA	NA				MAPK1 (24022 upstream) : PPM1F (27800 downstream)						NA		NA									NA						acctgtaatctcagcactttg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.22245992T>C		NA		hg19		0.02	-0.140347	ATCxCAG	UNCOVERED																																																																																			NOVEL					0			7	2.406227	KEEP	3	0	0	8	223	TT	0	0	0			3	60	101	0	0	8.272107	12	60	372	37		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	22250772	22250772	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22250772T>C			NA	NA				MAPK1 (28802 upstream) : PPM1F (23020 downstream)						NA		NA									NA						cttgctctgttgcccaggctg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.22250772T>C		NA		hg19		0.02	-0.140325	TGTxGCC	COVERED																																																																																			NOVEL					0			7	3.008213	KEEP	1	0	0	10	287	TT	0.992708	0.259062	0			3	60	90	2	0	7.273155	11	60	319	45		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	22256524	22256524	__UNKNOWN__	IGR	SNP	A	A	G	rs386819868|rs171277	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22256524A>G			NA	NA				MAPK1 (34554 upstream) : PPM1F (17268 downstream)						NA		NA									NA						gagccaccgcacccggcctaa	0.493		NA											G|||	2539	0.506989	0.5424	0.5908	5008	,	,	NA	15748	0.4385	NA	0.4841	False	NA	,,,	NA	NA	NA	2504	0.4939	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.22256524A>G		NA		hg19		0.02	-0.175391	CGCxCCC	COVERED																																																																																			NOVEL					0			5	2.70506	KEEP	2	0	0	9	230	AA	0.99257	0.384528	0			4	60	132	0	0	11.202132	12	60	334	42		0.25	0.387407
PPM1F	9647	__UNKNOWN__	__UNKNOWN__	22	22279559	22279559	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22279559C>T	ENST00000407142.1	-	5	1542				PPM1F_ENST00000263212.5_Intron|PPM1F_ENST00000538191.1_Intron|PPM1F_ENST00000397495.4_3'UTR			P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	NA		NA			cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		tgagccaccgcgcccagcGAA	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	9647	3.1.3.16	Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent	19388	protein-coding gene	gene with protein product	partner of PIX 2, Ca(2+)/calmodulin-dependent protein kinase phosphatase	NA	protein phosphatase 1F (PP2C domain containing)		NA	11864573, 11559703	Standard	NM_014634	NM_014634	NA	Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000407142.1:c.481+382G>A	chr22.hg19:g.22279559C>T		NA	A8K6G3|B7Z2C3|Q96PM2	hg19		0.02	-0.403503	CCGxGCC	COVERED																																																																																			NOVEL	PPM1F-002	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000320268.1	6	6.619524	KEEP	1	0	0	22	669	CC	0.999879	0.934379	0		-	4	60	115	0	0	7.634723	39	60	1303	98	ENST00000407142.1	0.093023	0.934492
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	22338570	22338570	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22338570A>G			NA	NA				TOP3B (1357 upstream) : PRAMENP (6926 downstream)						NA		NA									NA						cctggcctcaagtgatcctcc	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.22338570A>G		NA		hg19		0.02	-0.184185	TCAxGTG	COVERED																																																																																			NOVEL					0			9	3.308499	KEEP	0	0	0	11	305	AA	0.993072	0.420544	0			3	60	93	1	0	7.292306	14	60	425	47		0.176471	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	22623924	22623924	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:22623924A>G			NA	NA				VPREB1 (23997 upstream) : LL22NC03-2H8.5 (14387 downstream)						NA		NA									NA						ggaggttgcaatgagcagaga	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.22623924A>G		NA		hg19		0.02	-0.149098	GCAxTGA	COVERED																																																																																			NOVEL					0			7	3.007045	KEEP	3	0	0	10	267	AA	0.99254	0.289823	0			3	47	99	0	0	8.072294	12	60	353	43		0.2	0.292001
RAB36	9609	__UNKNOWN__	__UNKNOWN__	22	23505467	23505467	__UNKNOWN__	3'UTR	SNP	C	C	A	rs4552283	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:23505467C>A	ENST00000263116.2	+	0	2758					NM_004914.2	NP_004905.2	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	NA		NA			protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		cccaggctggcgtgcaatggc	0.542		NA											A|||	2781	0.555312	0.5265	0.4654	5008	,	,	NA	15447	0.6429	NA	0.5139	False	NA	,,,	NA	NA	NA	2504	0.6104	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AB023061	CCDS13805.1	22q11.22	2008-06-11			ENSG00000100228	ENSG00000100228	9609		RAB, member RAS oncogene	9775	protein-coding gene	gene with protein product		605662			NA	9920784, 10591208	Standard	NM_004914	NM_004914	NA	Approved		uc002zwv.1	O95755	OTTHUMG00000150601	ENST00000263116.2:c.*1716C>A	chr22.hg19:g.23505467C>A		NA	Q2M390|Q7Z4A9|Q9UHP5	hg19	CCDS13805.1	0.02	2.997378	TGGxGTG	COVERED																																																																																			NOVEL	RAB36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319046.1	25	5.814241	KEEP	0	3	78	47	1432	CC	1	0.999973	0		+	7	60	209	0	0	13.533057	84	60	2755	236	ENST00000263116.2	0.076923	0.999973
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	23520351	23520351	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:23520351T>C			NA	NA				RAB36 (13814 upstream) : BCR (2045 downstream)						NA		NA									NA						cacctgtaattccagcactac	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.23520351T>C		NA		hg19		0.02	-0.184192	AATxCCA	COVERED																																																																																			NOVEL					0			9	2.706529	KEEP	0	0	0	9	243	TT	0.99254	0.420319	0			3	60	99	0	0	7.733335	16	60	482	45		0.157895	0.423478
IGLL1	3543	__UNKNOWN__	__UNKNOWN__	22	23919938	23919938	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:23919938A>G	ENST00000330377.2	-	1	324				IGLL1_ENST00000249053.3_Intron	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	NA		NA			immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						gctcaggctgatctcaaactc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322	3543		CD molecules, Immunoglobulin superfamily / C1-set domain containing	5870	protein-coding gene	gene with protein product		146770		IGLL	NA	3139558, 2511029	Standard	NM_020070	NM_020070	NA	Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.206+2233T>C	chr22.hg19:g.23919938A>G		NA	Q0P681	hg19	CCDS13809.1	0.02	-0.192956	CTGxTCT	COVERED																																																																																			NOVEL	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319569.1	6	2.706205	KEEP	0	0	0	9	243	AC	0.992708	0.454419	0		-	3	60	99	0	0	7.810237	15	60	454	40	ENST00000330377.2	0.166667	0.457757
ZNF70	7621	__UNKNOWN__	__UNKNOWN__	22	24090976	24090976	__UNKNOWN__	Intron	SNP	C	C	T	rs200563494		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:24090976C>T	ENST00000341976.3	-	1	382					NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						aggtgatccgcccaccttggc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792	7621		Zinc fingers, C2H2-type	13140	protein-coding gene	gene with protein product		194544	zinc finger protein 70 (Cos17)		NA	1639391	Standard	NM_021916	NM_021916	NA	Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.78+1921G>A	chr22.hg19:g.24090976C>T		NA		hg19	CCDS13812.1	0.02	-0.184225	CCGxCCA	COVERED																																																																																			NOVEL	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319881.1	6	4.513516	KEEP	1	0	0	15	462	CC	0.99649	0.421991	0		-	3	40	93	0	0	7.291622	14	60	490	56	ENST00000341976.3	0.176471	0.423478
SMARCB1	6598	__UNKNOWN__	__UNKNOWN__	22	24130747	24130747	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:24130747C>T	ENST00000407082.3	+	1	252				SMARCB1_ENST00000407422.3_Intron|SMARCB1_ENST00000344921.6_Intron|SMARCB1_ENST00000263121.7_Intron			Q12824	SNF5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	NA		NA			ATP-dependent chromatin remodeling (GO:0043044)|blastocyst hatching (GO:0001835)|cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|DNA integration (GO:0015074)|DNA repair (GO:0006281)|mitotic cell cycle phase transition (GO:0044772)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)|XY body (GO:0001741)	p53 binding (GO:0002039)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)	p.?(2)		bone(4)|central_nervous_system(198)|endometrium(4)|haematopoietic_and_lymphoid_tissue(25)|kidney(3)|large_intestine(5)|liver(2)|lung(5)|meninges(5)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|soft_tissue(194)	458		Medulloblastoma(6;2.2e-09)|all_neural(6;2.73e-05)				tgtgcaccaccgtgcccgact	0.552		NA	D, N, F, S		malignant rhabdoid	malignant rhabdoid															NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Rhabdoid predisposition syndrome	22	22q11	6598	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1		M	2	Unknown(2)	soft_tissue(2)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U04847	CCDS13817.1, CCDS46671.1	22q11.23	2014-09-17			ENSG00000099956	ENSG00000099956	6598			11103	protein-coding gene	gene with protein product	sucrose nonfermenting, yeast, homolog-like 1, integrase interactor 1, malignant rhabdoid tumor suppressor, protein phosphatase 1, regulatory subunit 144	601607		SNF5L1	NA	7801128, 10319872, 10365963	Standard	NM_003073	NM_003073	NA	Approved	BAF47, Ini1, Snr1, hSNFS, Sfh1p, RDT, PPP1R144	uc002zyb.3	Q12824	OTTHUMG00000150737	ENST00000407082.3:c.93+1298C>T	chr22.hg19:g.24130747C>T		NA	O75784|O95474|Q17S11|Q38GA1|Q76N08|Q9UBH2	hg19		0.02	-0.192981	CACxGTG	COVERED																																																																																			NOVEL	SMARCB1-003	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000319874.1	13	2.706944	KEEP	0	0	0	9	253	CC	0.99254	0.454342	0		+	3	60	96	0	0	7.360742	17	60	568	42	ENST00000407082.3	0.15	0.457757
GSTT1	0	__UNKNOWN__	__UNKNOWN__	22	24377345	24377345	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:24377345C>G	ENST00000248935.5	-	4	404				GSTT1_ENST00000439996.2_Intron	NM_000853.2	NP_000844.2	P30711	GSTT1_HUMAN		NA		NA			glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)	6					Carboplatin(DB00958)|Cisplatin(DB00515)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)	tgcctgcctccgcctcccaaa	0.478		NA							Myelodysplasia and Acute Myeloid Leukemia (AML), Familial												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl.: Familial Myelodysplastic syndrome (late-onset), Familial AML, Familial Monocytic Leukemia, Familial Monosomy 7 and AML									NA			NA				NA			NA					NA						ENST00000248935.5:c.352-347G>C	chr22.hg19:g.24377345C>G		NA	O00226|Q5TZY2|Q6IC69|Q969K8|Q96IY3	hg19	CCDS13822.1	0.02	-0.210519	CTCxGCC	COVERED																																																																																			NOVEL	GSTT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320184.2	7	2.407246	KEEP	2	0	0	8	247	CC	0.99257	0.578599	0		-	3	60	92	0	0	6.765589	20	60	652	54	ENST00000248935.5	0.130435	0.58293
GSTT1	0	__UNKNOWN__	__UNKNOWN__	22	24377742	24377742	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:24377742A>G	ENST00000248935.5	-	4	404				GSTT1_ENST00000439996.2_Intron	NM_000853.2	NP_000844.2	P30711	GSTT1_HUMAN		NA		NA			glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)	6					Carboplatin(DB00958)|Cisplatin(DB00515)|Etoposide(DB00773)|Glutathione(DB00143)|Oxaliplatin(DB00526)	ccaaagtgctaggattattgg	0.428		NA							Myelodysplasia and Acute Myeloid Leukemia (AML), Familial												NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	incl.: Familial Myelodysplastic syndrome (late-onset), Familial AML, Familial Monocytic Leukemia, Familial Monosomy 7 and AML									NA			NA				NA			NA					NA						ENST00000248935.5:c.352-744T>C	chr22.hg19:g.24377742A>G		NA	O00226|Q5TZY2|Q6IC69|Q969K8|Q96IY3	hg19	CCDS13822.1	0.02	1.620004	GCTxGGA	COVERED																																																																																			NOVEL	GSTT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320184.2	20	2.803646	KEEP	0	3	90	41	1145	AA	1	0.999956	0		-	6	60	209	0	0	14.134687	86	60	2613	213	ENST00000248935.5	0.065217	0.999956
CABIN1	23523	__UNKNOWN__	__UNKNOWN__	22	24412064	24412064	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:24412064A>G	ENST00000405822.2	+	1	20				CABIN1_ENST00000398319.2_Intron|CABIN1_ENST00000263119.5_Intron			Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	NA		NA			cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						ccaaagtgctaggattacagg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991	23523			24187	protein-coding gene	gene with protein product		604251			NA	9655484, 9205841	Standard	NM_012295	NM_001199281	NA	Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000405822.2:c.-75+4247A>G	chr22.hg19:g.24412064A>G		NA	G5E9F3|Q6PHY0|Q9Y460	hg19		0.02	-0.210493	GCTxGGA	COVERED																																																																																			NOVEL	CABIN1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000320162.2	6	2.406585	KEEP	1	0	0	8	229	AA	0.99257	0.518282	0		+	3	60	101	1	0	7.726978	19	60	568	50	ENST00000405822.2	0.136364	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	24607757	24607757	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:24607757C>T			NA	NA				SUSD2 (22679 upstream) : GGT5 (7864 downstream)						NA		NA									NA						tggagtctcccatgtctactt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.24607757C>T		NA		hg19		0.02	-0.298246	TCCxATG	COVERED																																																																																			NOVEL					0			9	2.539971	KEEP	10	1	27	18	534	CC	0.999859	0.78095	0			5	60	152	0	0	11.492129	28	60	916	81		0.151515	0.78106
PIWIL3	440822	__UNKNOWN__	__UNKNOWN__	22	25128607	25128607	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:25128607A>G	ENST00000332271.5	-	14	2124				PIWIL3_ENST00000527701.1_Intron|PIWIL3_ENST00000532537.2_Intron|PIWIL3_ENST00000533313.1_Intron	NM_001008496.3|NM_001255975.1	NP_001008496.2|NP_001242904.1	Q7Z3Z3	PIWL3_HUMAN	piwi-like RNA-mediated gene silencing 3	NA		NA			cell differentiation (GO:0030154)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	RNA binding (GO:0003723)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(15)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						tggctaacacagtgaaacccc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB079368	CCDS33623.1	22q11.23	2013-02-15	2013-02-15		ENSG00000184571	ENSG00000184571	440822		Argonaute/PIWI family	18443	protein-coding gene	gene with protein product		610314	piwi-like 3 (Drosophila)		NA	12906857	Standard	NM_001008496	NM_001008496	NA	Approved	HIWI3	uc003abd.2	Q7Z3Z3	OTTHUMG00000150788	ENST00000332271.5:c.1707+1443T>C	chr22.hg19:g.25128607A>G		NA		hg19	CCDS33623.1	0.02	-0.087708	CACxGTG	UNCOVERED																																																																																			NOVEL	PIWIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320084.2	5	3.006562	KEEP	13	0	0	10	263	AA	0	0	0		-	3	37	93	0	0	8.243568	6	48	179	38	ENST00000332271.5	0.333333	0.099721
SGSM1	129049	__UNKNOWN__	__UNKNOWN__	22	25269821	25269821	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:25269821G>A	ENST00000400358.4	+	13	1348				SGSM1_ENST00000400359.4_Intron	NM_001098497.1|NM_001098498.1	NP_001091967.1|NP_001091968.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	NA		NA				Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						ccctgcctcagaaaaaaaaaa	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037	129049		Small G protein signaling modulators	29410	protein-coding gene	gene with protein product		611417	RUN and TBC1 domain containing 2	RUTBC2	NA	11853319, 17509819, 22637480	Standard	XM_059318	NM_133454	NA	Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400358.4:c.1292-2723G>A	chr22.hg19:g.25269821G>A		NA	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	hg19	CCDS46675.1	0.02	-0.140309	TCAxAAA	COVERED																																																																																			NOVEL	SGSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320279.1	9	2.407175	KEEP	0	0	0	8	248	GG	0.99257	0.259026	0		+	3	60	86	1	0	7.101655	9	60	264	37	ENST00000400358.4	0.25	0.260965
KIAA1671	85379	__UNKNOWN__	__UNKNOWN__	22	25413104	25413104	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:25413104G>C	ENST00000406486.4	+	2	180							Q9BY89	K1671_HUMAN	KIAA1671	NA		NA								autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						aatcccagcagtttgggaggc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077	85379			29345	protein-coding gene	gene with protein product		NA			NA	15289310	Standard	NM_001145206	NM_001145206	NA	Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.-208+2571G>C	chr22.hg19:g.25413104G>C		NA	B0QYF2|B7ZW08|Q5THZ5	hg19	CCDS46676.1	0.02	-0.131592	GCAxTTT	UNCOVERED																																																																																			NOVEL	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320306.6	6	2.708302	KEEP	5	0	0	9	284	GG	0	0	0		+	3	60	105	0	0	9.00087	9	60	317	41	ENST00000406486.4	0.25	0.229173
KIAA1671	85379	__UNKNOWN__	__UNKNOWN__	22	25590311	25590311	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:25590311C>G	ENST00000406486.4	+	0	7751				KIAA1671_ENST00000358431.3_3'UTR|KIAA1671_ENST00000401395.1_3'UTR			Q9BY89	K1671_HUMAN	KIAA1671	NA		NA								autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						ccaaagtgctcggattacaga	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077	85379			29345	protein-coding gene	gene with protein product		NA			NA	15289310	Standard	NM_001145206	NM_001145206	NA	Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.*1943C>G	chr22.hg19:g.25590311C>G		NA	B0QYF2|B7ZW08|Q5THZ5	hg19	CCDS46676.1	0.02	-0.114007	GCTxGGA	UNCOVERED																																																																																			NOVEL	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320306.6	6	2.405701	KEEP	0	0	0	8	229	AC	0.99254	0.161255	0		+	3	60	90	0	0	7.632333	8	60	258	34	ENST00000406486.4	0.272727	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	25810261	25810261	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:25810261A>T			NA	NA				LRP5L (8917 upstream) : CTA-246H3.12 (20029 downstream)						NA		NA									NA						tcccagcactatgggaggcca	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.25810261A>T		NA		hg19		0.02	-0.227971	ACTxTGG	COVERED																																																																																			NOVEL					0			4	3.007176	KEEP	0	0	0	10	270	AA	0.992708	0.578679	0			3	60	89	0	0	6.350792	22	60	637	55		0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	25904776	25904776	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:25904776A>G			NA	NA				CTA-390C10.10 (28838 upstream) : AL008721.1 (23910 downstream)						NA		NA									NA						tgggattacaagcatgagcca	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.25904776A>G		NA		hg19		0.02	-0.166656	ACAxGCA	COVERED																																																																																			NOVEL					0			7	3.308412	KEEP	0	0	0	11	303	AA	0.993072	0.351495	0			3	60	94	0	0	7.392073	14	60	433	45		0.176471	0.353947
ADRBK2	157	__UNKNOWN__	__UNKNOWN__	22	26105283	26105283	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:26105283C>T	ENST00000324198.6	+	16	1520					NM_005160.3	NP_005151.2	P35626	ARBK2_HUMAN	adrenergic, beta, receptor kinase 2	NA		NA			receptor internalization (GO:0031623)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)		ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(2)|skin(3)|stomach(2)	32					Adenosine triphosphate(DB00171)	ggattacaggcgtgagccacc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X69117	CCDS13832.1	22q11	2013-01-10			ENSG00000100077	ENSG00000100077	157		Pleckstrin homology (PH) domain containing	290	protein-coding gene	gene with protein product		109636			NA	7695743	Standard	NM_005160	NM_005160	NA	Approved	GRK3, BARK2	uc003abx.4	P35626	OTTHUMG00000150280	ENST00000324198.6:c.1329-582C>T	chr22.hg19:g.26105283C>T		NA	Q9UGW9	hg19	CCDS13832.1	0.02	-0.403509	AGGxGTG	COVERED																																																																																			NOVEL	ADRBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317296.4	43	11.429774	KEEP	20	0	0	38	1139	CC	0.999997	0.934489	0		+	3	37	91	0	0	6.443352	24	60	797	140	ENST00000324198.6	0.111111	0.934492
TFIP11	24144	__UNKNOWN__	__UNKNOWN__	22	26900424	26900424	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:26900424T>C	ENST00000407690.1	-	7	804				TFIP11_ENST00000407148.1_Intron|TFIP11_ENST00000496523.1_Intron|TFIP11_ENST00000405938.1_Intron|TFIP11_ENST00000407431.1_Intron	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	NA		NA			biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						cttgtaatcctagcactttgg	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109	24144		G patch domain containing	17165	protein-coding gene	gene with protein product		612747			NA	10806191, 11230166	Standard	NM_001008697	NM_012143	NA	Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.521-665A>G	chr22.hg19:g.26900424T>C		NA	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	hg19	CCDS13838.1	0.02	-0.25435	TCCxAGC	COVERED																																																																																			NOVEL	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320750.1	12	3.635783	KEEP	0	1	31	23	619	TT	0.999909	0.668463	0		-	3	60	101	0	0	7.494636	23	60	682	76	ENST00000407690.1	0.115385	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	27033414	27033414	__UNKNOWN__	IGR	SNP	C	C	G	rs6005102	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:27033414C>G			NA	NA				CRYBA4 (6778 upstream) : MIAT (19921 downstream)						NA		NA									NA						gggaggccgacgcgggtggat	0.507		NA											G|||	3281	0.655152	0.7284	0.7118	5008	,	,	NA	14509	0.5317	NA	0.7087	False	NA	,,,	NA	NA	NA	2504	0.5879	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.27033414C>G		NA		hg19		0.02	-0.0787	CGAxGCG	UNCOVERED																																																																																			NOVEL					0			2	2.407074	KEEP	2	0	0	8	245	CC	0	0	0			4	60	119	0	0	11.102918	5	60	166	29		0.444444	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	27525865	27525865	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:27525865T>C			NA	NA				CTA-992D9.6 (69385 upstream) : CTA-992D9.7 (13573 downstream)						NA		NA									NA						gccaggagtttgagaccagcc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.27525865T>C		NA		hg19		0.02	-0.184193	GTTxGAG	COVERED																																																																																			NOVEL					0			11	3.909858	KEEP	1	0	0	13	365	TT	0.994391	0.421102	0			3	60	102	0	0	7.960755	17	60	516	54		0.15	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	28014690	28014690	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:28014690C>T			NA	NA				RP1-231P7P.1 (45156 upstream) : RP1-213J1P__B.1 (57865 downstream)						NA		NA									NA						cccaccaggtcgaggctacag	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.28014690C>T		NA		hg19		0.02	-0.140337	GGTxGAG	COVERED																																																																																			NOVEL					0			6	3.007776	KEEP	0	0	0	10	283	CC	0.992708	0.259062	0			3	60	90	0	0	7.272957	11	60	344	35		0.214286	0.260965
MN1	4330	__UNKNOWN__	__UNKNOWN__	22	28173690	28173690	__UNKNOWN__	Intron	SNP	T	T	C	rs398036736|rs35992247		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:28173690T>C	ENST00000302326.4	-	1	4736				MN1_ENST00000497225.1_Intron	NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	NA		NA			intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						ctactaaaaatacacacacac	0.517		NA	T	ETV6	AML, meningioma																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		L, O	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184	4330			7180	protein-coding gene	gene with protein product	probable tumor suppressor protein MN1	156100	meningioma chromosome region	MGCR	NA	7731706, 12569362	Standard	NM_002430	NM_002430	NA	Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.3781+19060A>G	chr22.hg19:g.28173690T>C		NA	A9Z1V9	hg19	CCDS42998.1	0.02	-0.035083	AAAxACA	UNCOVERED																																																																																			NOVEL	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320737.1	5	2.405175	KEEP	0	0	0	8	209	TT	0.99257	0.019833	0		-	2	60	71	0	1	6.850477	2	60	55	17	ENST00000302326.4	0.5	0.019982
TTC28	23331	__UNKNOWN__	__UNKNOWN__	22	28939991	28939991	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:28939991C>T	ENST00000397906.2	-	2	523					NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	NA		NA			mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						ggtggatcacctgaggtcagg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154	23331		Tetratricopeptide (TTC) repeat domain containing	29179	protein-coding gene	gene with protein product		615098			NA	10470851	Standard	XM_929318	NM_001145418	NA	Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.381+85548G>A	chr22.hg19:g.28939991C>T		NA	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	hg19	CCDS46678.1	0.02	-0.114039	CACxTGA	UNCOVERED																																																																																			NOVEL	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320930.2	9	3.911902	KEEP	7	0	0	13	407	CC	0.99254	0.161255	0		-	3	60	89	0	0	7.281806	10	60	346	46	ENST00000397906.2	0.230769	0.162467
TTC28	23331	__UNKNOWN__	__UNKNOWN__	22	28985777	28985777	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:28985777T>C	ENST00000397906.2	-	2	523					NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	NA		NA			mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						cctgtaatcctagcactttgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154	23331		Tetratricopeptide (TTC) repeat domain containing	29179	protein-coding gene	gene with protein product		615098			NA	10470851	Standard	XM_929318	NM_001145418	NA	Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.381+39762A>G	chr22.hg19:g.28985777T>C		NA	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	hg19	CCDS46678.1	0.02	-0.131562	TCCxAGC	COVERED																																																																																			NOVEL	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320930.2	5	2.705731	KEEP	0	0	0	9	241	TT	0.99254	0.227464	0		-	3	60	100	0	0	8.272965	11	60	324	34	ENST00000397906.2	0.214286	0.229173
CCDC117	150275	__UNKNOWN__	__UNKNOWN__	22	29183406	29183406	__UNKNOWN__	3'UTR	SNP	C	C	T	rs371153753	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29183406C>T	ENST00000249064.4	+	0	2108					NM_001284263.1|NM_001284265.1|NM_173510.2	NP_001271192.1|NP_001271194.1|NP_775781.1	Q8IWD4	CC117_HUMAN	coiled-coil domain containing 117	NA		NA								breast(1)|kidney(1)|large_intestine(4)|upper_aerodigestive_tract(1)	7						ggattacaggcgtgagccacg	0.473		NA											C|||	3	0.000599042	0.0	0.0	5008	,	,	NA	17449	0.003	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AK091133	CCDS13846.1, CCDS63435.1, CCDS63436.1	22q12.1	2006-06-27			ENSG00000159873	ENSG00000159873	150275			26599	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_173510	NM_001284263	NA	Approved	FLJ33814	uc003aeb.3	Q8IWD4	OTTHUMG00000151091	ENST00000249064.4:c.*1092C>T	chr22.hg19:g.29183406C>T		NA	A8K0F1|B7Z2V1|B7Z860|Q6ICA7|Q8N278	hg19	CCDS13846.1	0.02	-0.438594	AGGxGTG	COVERED																																																																																			NOVEL	CCDC117-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321258.1	12	5.713773	KEEP	0	0	0	19	538	CC	0.99986	0.959724	0		+	5	60	145	0	0	10.023361	41	60	1372	103	ENST00000249064.4	0.108696	0.959859
CTA-292E10.6	0	__UNKNOWN__	__UNKNOWN__	22	29201933	29201933	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29201933A>G	ENST00000458080.1	+	0	55				CTA-292E10.6_ENST00000418292.1_RNA|CTA-292E10.6_ENST00000451486.1_RNA						NA		NA									NA						ttgcactccaacctgggcaac	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000458080.1:	chr22.hg19:g.29201933A>G		NA		hg19		0.02	-0.20171	CCAxCCT	COVERED																																																																																			NOVEL	CTA-292E10.6-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000321270.1	9	3.605317	KEEP	1	0	0	12	311	AA	0.993634	0.487421	0		+	3	40	105	0	0	8.578992	13	60	367	49	ENST00000458080.1	0.1875	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	29249122	29249122	__UNKNOWN__	IGR	SNP	T	T	C	rs4484131	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29249122T>C			NA	NA				CTA-292E10.6 (4575 upstream) : ZNRF3 (30457 downstream)						NA		NA									NA						gcctgggggatagagcgagac	0.493		NA											T|||	910	0.181709	0.3056	0.1527	5008	,	,	NA	12742	0.2778	NA	0.0497	False	NA	,,,	NA	NA	NA	2504	0.0716	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.29249122T>C		NA		hg19		0.02	-0.175394	GGAxAGA	UNCOVERED																																																																																			NOVEL					0			10	2.405263	KEEP	2	0	0	8	212	TT	0	0	0			10	60	353	0	0	35.070388	7	60	199	40		0.588235	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	29266401	29266401	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29266401T>C			NA	NA				CTA-292E10.6 (21854 upstream) : ZNRF3 (13178 downstream)						NA		NA									NA						ctgcccgccttggcctcccaa	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.29266401T>C		NA		hg19		0.02	-0.149098	CCTxGGC	COVERED																																																																																			NOVEL					0			3	3.007068	KEEP	0	0	0	10	272	TT	0.992708	0.320453	0			3	60	99	0	0	8.072429	12	60	352	39		0.2	0.322807
ZNRF3	84133	__UNKNOWN__	__UNKNOWN__	22	29292226	29292226	__UNKNOWN__	Intron	SNP	G	G	A	rs8136297	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29292226G>A	ENST00000544604.2	+	1	475				ZNRF3_ENST00000332811.4_Intron	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	NA		NA			canonical Wnt signaling pathway (GO:0060070)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|protein ubiquitination (GO:0016567)|stem cell proliferation (GO:0072089)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	integral component of plasma membrane (GO:0005887)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(4)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	28						gggttcaagcgattctcctgc	0.542		NA											G|||	2372	0.473642	0.5991	0.3444	5008	,	,	NA	17006	0.5744	NA	0.2962	False	NA	,,,	NA	NA	NA	2504	0.4744	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB051436	CCDS42999.1, CCDS56225.1	22q12.1	2013-01-09			ENSG00000183579	ENSG00000183579	84133		RING-type (C3HC4) zinc fingers	18126	protein-coding gene	gene with protein product		612062			NA	10574461	Standard	XM_290972	NM_032173	NA	Approved	KIAA1133, BK747E2.3, FLJ22057, RNF203	uc003aeg.3	Q9ULT6	OTTHUMG00000151009	ENST00000544604.2:c.300+12172G>A	chr22.hg19:g.29292226G>A		NA	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	hg19	CCDS56225.1	0.02	-0.096488	AGCxATT	UNCOVERED																																																																																			NOVEL	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320943.2	7	2.707516	KEEP	5	0	0	9	267	GG	0	0	0		+	3	54	90	0	0	7.943339	6	60	195	34	ENST00000544604.2	0.333333	0.139832
KREMEN1	83999	__UNKNOWN__	__UNKNOWN__	22	29516205	29516205	__UNKNOWN__	Intron	SNP	A	A	T	rs59873718		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29516205A>T	ENST00000407188.1	+	4	346				KREMEN1_ENST00000327813.5_Intron|KREMEN1_ENST00000400335.4_Intron|KREMEN1_ENST00000400338.2_Intron			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	NA		NA			cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						gaggtgatgaaggaaatggag	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762	83999			17550	protein-coding gene	gene with protein product		609898	kringle containing transmembrane protein	KREMEN	NA	11267660	Standard		NM_001039570	NA	Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.347-1140A>T	chr22.hg19:g.29516205A>T		NA	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	hg19	CCDS43000.2	0.02	-0.087695	TGAxGGA	UNCOVERED																																																																																			NOVEL	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320947.1	5	2.405567	KEEP	9	0	0	8	218	AA	0	0	0		+	3	48	84	0	0	7.178272	7	16	208	31	ENST00000407188.1	0.3	0.099721
AP1B1	162	__UNKNOWN__	__UNKNOWN__	22	29781111	29781111	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29781111C>T	ENST00000317368.7	-	1	160				AP1B1_ENST00000415447.1_Intron|AP1B1_ENST00000357586.2_Intron|AP1B1_ENST00000356015.2_Intron|AP1B1_ENST00000432560.2_Intron	NM_001166019.1	NP_001159491	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	NA		NA			antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						tggtggctcacgcctgtaatc	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280	162			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2	NA	7987321, 8812422	Standard	NM_001127	NM_145730	NA	Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000317368.7:c.26+3301G>A	chr22.hg19:g.29781111C>T		NA	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	hg19	CCDS54515.1	0.02	-0.245606	TCAxGCC	UNCOVERED																																																																																			NOVEL	AP1B1-002	NOVEL	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321375.1	9	2.405816	KEEP	1	0	0	8	219	CC	0	0	0		-	3	60	90	0	0	6.506556	21	60	676	53	ENST00000317368.7	0.125	0.641347
NIPSNAP1	8508	__UNKNOWN__	__UNKNOWN__	22	29969163	29969163	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29969163C>T	ENST00000216121.7	-	2	353					NM_001202502.1|NM_003634.3	NP_001189431.1|NP_003625.2	Q9BPW8	NIPS1_HUMAN	nipsnap homolog 1 (C. elegans)	NA		NA			sensory perception of pain (GO:0019233)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|synaptic membrane (GO:0097060)	neurotransmitter binding (GO:0042165)	p.?(1)		large_intestine(2)|lung(2)|skin(1)	5						gtagctgggactacagacgtg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Unknown(1)	lung(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ001258	CCDS13860.1	22q12	2013-09-12	2001-11-28		ENSG00000184117	ENSG00000184117	8508			7827	protein-coding gene	gene with protein product	4-nitrophenylphosphatase domain and non-neuronal SNAP25-like 1	603249	NIPSNAP, C. elegans, homolog 1		NA	9661659	Standard		NM_003634	NA	Approved		uc003afx.4	Q9BPW8	OTTHUMG00000151294	ENST00000216121.7:c.99-2642G>A	chr22.hg19:g.29969163C>T		NA	B2RAY3|O43800	hg19	CCDS13860.1	0.02	-0.052617	GGAxTAC	UNCOVERED																																																																																			NOVEL	NIPSNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322117.1	4	2.407266	KEEP	1	0	0	8	247	CC	0.99257	0.036492	0		-	3	60	82	0	0	8.167346	2	40	71	21	ENST00000216121.7	0.6	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	29979562	29979562	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29979562A>G			NA	NA				NIPSNAP1 (2236 upstream) : NF2 (19982 downstream)						NA		NA						p.?(1)			NA						gtgaaaccccatctctactaa	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Unknown(1)	lung(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.29979562A>G		NA		hg19		0.02	-0.175369	CCCxTCT	COVERED																																																																																			NOVEL					0			6	2.707118	KEEP	3	0	0	9	251	AA	0.99254	0.384517	0			4	60	123	0	0	10.069347	14	60	395	44		0.222222	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	29988900	29988900	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:29988900C>T			NA	NA				NIPSNAP1 (11574 upstream) : NF2 (10644 downstream)						NA		NA						p.?(1)			NA						ggattacaggcgtgagccacc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Unknown(1)	lung(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.29988900C>T		NA		hg19		0.02	-0.30701	AGGxGTG	COVERED																																																																																			NOVEL					0			10	3.309276	KEEP	2	0	0	11	323	CC	0.992708	0.812496	0			4	60	110	1	0	7.512172	31	60	1029	66		0.114286	0.818465
NF2	4771	__UNKNOWN__	__UNKNOWN__	22	30003952	30003952	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:30003952G>A	ENST00000338641.4	+	1	555				NF2_ENST00000403999.3_Intron|NF2_ENST00000361166.4_Intron|NF2_ENST00000403435.1_Intron|NF2_ENST00000347330.5_Intron|NF2_ENST00000353887.4_Intron|NF2_ENST00000334961.7_Intron|NF2_ENST00000361452.4_Intron|NF2_ENST00000397789.3_Intron|NF2_ENST00000413209.2_Intron|NF2_ENST00000361676.4_Intron	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)	NA		NA			actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(2)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						acctgaggtcgggagttcgag	0.542		NA	D, Mis, N, F, S, O		meningioma, acoustic neuroma, renal 	meningioma, acoustic neuroma			Neurofibromatosis, type 2												NA			NA			NA		NA	NA	NA			NA	NA	NA		yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	2	Unknown(2)	stomach(1)|lung(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575	4771		A-kinase anchor proteins	7773	protein-coding gene	gene with protein product	moesin-ezrin-radixin like, schwannomin	607379	neurofibromin 2 (bilateral acoustic neuroma)		NA	10591208	Standard	NM_000268	NM_000268	NA	Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.114+3851G>A	chr22.hg19:g.30003952G>A		NA	O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	hg19	CCDS13861.1	0.02	-0.16654	GTCxGGA	COVERED																																																																																			NOVEL	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075615.3	8	2.708078	KEEP	4	0	0	9	276	GG	0.99254	0.351306	0		+	4	49	110	0	0	8.770127	14	60	418	47	ENST00000338641.4	0.222222	0.353947
ASCC2	84164	__UNKNOWN__	__UNKNOWN__	22	30231242	30231242	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:30231242T>C	ENST00000397771.2	-	2	99				ASCC2_ENST00000307790.3_Intron|ASCC2_ENST00000542393.1_Intron			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			caaaaattagtcaggtgtggt	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325	84164			24103	protein-coding gene	gene with protein product	ASC 1 complex subunit P100	614216			NA	12077347, 9847074	Standard	NM_032204	NM_032204	NA	Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.79-703A>G	chr22.hg19:g.30231242T>C		NA	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	hg19	CCDS13869.1	0.02	-0.236809	TAGxCAG	COVERED																																																																																			NOVEL	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322127.1	11	2.405847	KEEP	0	0	0	8	216	TT	0.99257	0.607857	0		-	3	60	102	0	0	7.594678	23	60	695	47	ENST00000397771.2	0.115385	0.612407
MTMR3	8897	__UNKNOWN__	__UNKNOWN__	22	30345259	30345259	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:30345259C>T	ENST00000323630.5	+	2	162				MTMR3_ENST00000415511.1_Intron|MTMR3_ENST00000401950.2_Intron|MTMR3_ENST00000351488.3_Intron|MTMR3_ENST00000333027.3_Intron			Q13615	MTMR3_HUMAN	myotubularin related protein 3	NA		NA			peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			ggcagatcacctgaggtcagg	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330	8897		Zinc fingers, FYVE domain containing, Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins	7451	protein-coding gene	gene with protein product		603558			NA	8640223, 9736772	Standard	NM_021090	NM_153050	NA	Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000323630.5:c.-458-7766C>T	chr22.hg19:g.30345259C>T		NA	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	hg19		0.02	-0.184215	CACxTGA	UNCOVERED																																																																																			NOVEL	MTMR3-004	NOVEL	basic|appris_principal	protein_coding	NA	protein_coding	OTTHUMT00000322069.1	10	2.707883	KEEP	10	0	0	9	276	CC	0	0	0		+	3	60	86	1	0	6.43413	16	60	554	52	ENST00000323630.5	0.157895	0.423478
SEC14L4	284904	__UNKNOWN__	__UNKNOWN__	22	30891385	30891385	__UNKNOWN__	Silent	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:30891385G>A	ENST00000381982.3	-	5	317	c.279C>T	c.(277-279)taC>taT	p.Y93Y	SEC14L4_ENST00000255858.7_Silent_p.Y93Y|SEC14L4_ENST00000392772.2_Silent_p.Y39Y|SEC14L4_ENST00000540456.1_Silent_p.Y78Y			Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	93	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.	NA				integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	GGCAGCCTTCGTAGTCGTAGC	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													97	86	90			NA	NA	22		NA											NA				30891385		2203	4300	6503	SO:0001819	synonymous_variant			AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488	284904			20627	protein-coding gene	gene with protein product		612825			NA		Standard	NM_174977	NM_174977	NA	Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000381982.3:c.279C>T	chr22.hg19:g.30891385G>A		NA	A5D6W7|A6NCV4	hg19	CCDS54517.1	0.02	2.962296	TTCxTAG	COVERED																																																																																			NOVEL	SEC14L4-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321947.1	2	3.910548	KEEP	0	0	0	13	382	GG	0.994391	0.994375	0		-	30	60	877	0	0	75.027609	73	60	2367	167	ENST00000381982.3	0.291262	0.999984
LIMK2	3985	__UNKNOWN__	__UNKNOWN__	22	31648356	31648356	__UNKNOWN__	Intron	SNP	C	C	A	rs5753523	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31648356C>A	ENST00000331728.4	+	3	230				LIMK2_ENST00000333611.4_Intron|LIMK2_ENST00000406516.1_Intron|LIMK2_ENST00000340552.4_Intron|LIMK2_ENST00000444929.2_Intron	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	NA		NA			phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						tagggagaccctgtctctaca	0.537		NA											C|||	1804	0.360224	0.6074	0.3689	5008	,	,	NA	15767	0.4157	NA	0.1491	False	NA	,,,	NA	NA	NA	2504	0.18	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541	3985			6614	protein-coding gene	gene with protein product		601988			NA	8537403, 10591208	Standard	NM_016733	NM_005569	NA	Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.117-5921C>A	chr22.hg19:g.31648356C>A		NA	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	hg19	CCDS13891.1	0.02	-0.201748	ACCxTGT	COVERED																																																																																			NOVEL	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321911.1	10	3.610904	KEEP	1	0	0	12	373	CC	0.993072	0.487146	0		+	8	60	238	0	0	21.77001	12	60	401	53	ENST00000331728.4	0.4	0.490544
LIMK2	3985	__UNKNOWN__	__UNKNOWN__	22	31665208	31665208	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31665208T>C	ENST00000331728.4	+	11	1431				LIMK2_ENST00000333611.4_Intron|LIMK2_ENST00000406516.1_Intron|LIMK2_ENST00000340552.4_Intron|LIMK2_ENST00000444929.2_Intron	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	NA		NA			phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						cctcctgccttagcctcccaa	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541	3985			6614	protein-coding gene	gene with protein product		601988			NA	8537403, 10591208	Standard	NM_016733	NM_005569	NA	Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1317+1022T>C	chr22.hg19:g.31665208T>C		NA	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	hg19	CCDS13891.1	0.02	-0.11403	CCTxAGC	UNCOVERED																																																																																			NOVEL	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321911.1	5	3.006625	KEEP	0	0	0	10	262	TT	0.992708	0.161282	0		+	3	60	101	0	0	8.732475	8	60	243	33	ENST00000331728.4	0.272727	0.162467
LIMK2	3985	__UNKNOWN__	__UNKNOWN__	22	31668250	31668250	__UNKNOWN__	Intron	SNP	G	G	A	rs13056815	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31668250G>A	ENST00000331728.4	+	13	1497				LIMK2_ENST00000333611.4_Intron|LIMK2_ENST00000406516.1_Intron|LIMK2_ENST00000340552.4_Intron|LIMK2_ENST00000444929.2_Intron	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	NA		NA			phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						tagtagagacggggttttgcc	0.493		NA											G|||	1542	0.307907	0.2617	0.3314	5008	,	,	NA	12174	0.0685	NA	0.5129	False	NA	,,,	NA	NA	NA	2504	0.3896	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541	3985			6614	protein-coding gene	gene with protein product		601988			NA	8537403, 10591208	Standard	NM_016733	NM_005569	NA	Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.1384-266G>A	chr22.hg19:g.31668250G>A		NA	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	hg19	CCDS13891.1	0.02	-0.052632	GACxGGG	UNCOVERED																																																																																			NOVEL	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321911.1	7	2.406741	KEEP	3	0	0	8	232	GG	0	0	0		+	3	60	90	0	0	8.62443	3	25	106	21	ENST00000331728.4	0.5	0.036766
RP3-400N23.6	0	__UNKNOWN__	__UNKNOWN__	22	31703311	31703311	__UNKNOWN__	RNA	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31703311G>A	ENST00000440456.1	+	0	200										NA		NA									NA						gattacaggcgtaaaccaccg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000440456.1:	chr22.hg19:g.31703311G>A		NA		hg19		0.02	-0.184217	GGCxTAA	COVERED																																																																																			NOVEL	RP3-400N23.6-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000321908.1	7	2.707021	KEEP	0	0	0	9	258	GG	0.99254	0.420319	0		+	3	60	89	0	0	7.072248	12	60	395	43	ENST00000440456.1	0.2	0.423478
PATZ1	23598	__UNKNOWN__	__UNKNOWN__	22	31731898	31731898	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31731898C>T	ENST00000266269.5	-	3	1965				PATZ1_ENST00000405309.3_Intron|RP3-400N23.6_ENST00000451161.1_RNA|PATZ1_ENST00000351933.4_Intron|RP3-400N23.6_ENST00000440456.1_RNA	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	NA		NA			male gonad development (GO:0008584)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						GCACCCCACACCTGACTCCCC	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													27	23	24			NA	NA	22		NA											NA				31731898		2203	4300	6503	SO:0001627	intron_variant			AL096880	CCDS13894.1, CCDS13895.1, CCDS13896.1, CCDS46691.1	22q12.2	2013-01-09	2006-09-19	2006-09-19	ENSG00000100105	ENSG00000100105	23598		-, Zinc fingers, C2H2-type, BTB/POZ domain containing	13071	protein-coding gene	gene with protein product		605165	zinc finger protein 278	ZNF278	NA	10591208, 18241078, 18401526	Standard	NM_032052	NM_014323	NA	Approved	MAZR, dJ400N23, ZBTB19, ZSG, RIAZ, PATZ	uc003akq.3	Q9HBE1	OTTHUMG00000151254	ENST00000266269.5:c.1336-49G>A	chr22.hg19:g.31731898C>T		NA	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	hg19	CCDS13894.1	0.02	-0.403509	ACAxCTG	COVERED																																																																																			NOVEL	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321932.1	2	2.707492	KEEP	0	0	0	9	263	CC	0.99254	0.927521	0		-	15	60	455	0	0	40.215478	30	60	1037	78	ENST00000266269.5	0.333333	0.934492
EIF4ENIF1	56478	__UNKNOWN__	__UNKNOWN__	22	31858835	31858835	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31858835T>C	ENST00000344710.5	-	5	456				RP11-247I13.11_ENST00000464523.1_RNA|EIF4ENIF1_ENST00000397523.1_Intron|RP11-247I13.8_ENST00000439588.1_RNA|RP11-247I13.11_ENST00000483736.1_RNA|EIF4ENIF1_ENST00000397525.1_Intron|EIF4ENIF1_ENST00000330125.5_Intron	NM_001164502.1	NP_001157974.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	NA		NA				cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						tcccaaagtgttgggattaca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708	56478			16687	protein-coding gene	gene with protein product		607445			NA	10856257	Standard	NM_019843	NM_019843	NA	Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000344710.5:c.299-4199A>G	chr22.hg19:g.31858835T>C		NA	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	hg19	CCDS54520.1	0.02	-0.368248	GTGxTGG	COVERED																																																																																			NOVEL	EIF4ENIF1-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000127925.1	13	2.534967	KEEP	5	1	27	18	469	TT	0.999859	0.899187	0		-	4	60	130	0	0	9.618432	29	60	784	77	ENST00000344710.5	0.121212	0.899314
EIF4ENIF1	56478	__UNKNOWN__	__UNKNOWN__	22	31881844	31881844	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31881844A>G	ENST00000344710.5	-	2	254				EIF4ENIF1_ENST00000397523.1_Intron|EIF4ENIF1_ENST00000397525.1_Intron|EIF4ENIF1_ENST00000330125.5_Intron	NM_001164502.1	NP_001157974.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	NA		NA				cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						gctcacacctataatcccagc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708	56478			16687	protein-coding gene	gene with protein product		607445			NA	10856257	Standard	NM_019843	NM_019843	NA	Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000344710.5:c.96+2764T>C	chr22.hg19:g.31881844A>G		NA	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	hg19	CCDS54520.1	0.02	-0.245572	CCTxTAA	COVERED																																																																																			NOVEL	EIF4ENIF1-001	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000127925.1	6	3.606782	KEEP	0	0	0	12	302	AA	0.993634	0.637264	0		-	3	60	104	0	0	8.026902	19	60	547	52	ENST00000344710.5	0.136364	0.641347
SFI1	9814	__UNKNOWN__	__UNKNOWN__	22	31916955	31916955	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31916955T>C	ENST00000432498.1	+	3	485				SFI1_ENST00000400288.2_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000540643.1_Intron	NM_014775.3	NP_055590.2	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						ttccactgcattccagcctgg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089	9814			29064	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 139	612765			NA	14504268	Standard	NM_014775	NM_001007467	NA	Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000432498.1:c.93-7721T>C	chr22.hg19:g.31916955T>C		NA	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	hg19	CCDS43005.1	0.02	-0.14906	GCAxTCC	UNCOVERED																																																																																			NOVEL	SFI1-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075103.4	8	2.404827	KEEP	2	0	0	8	204	TT	0	0	0		+	3	60	99	0	0	8.282178	10	60	288	29	ENST00000432498.1	0.230769	0.292001
SFI1	9814	__UNKNOWN__	__UNKNOWN__	22	31918012	31918012	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31918012A>G	ENST00000432498.1	+	3	485				SFI1_ENST00000400288.2_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000540643.1_Intron	NM_014775.3	NP_055590.2	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						tggcctcccaaagtgctagga	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089	9814			29064	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 139	612765			NA	14504268	Standard	NM_014775	NM_001007467	NA	Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000432498.1:c.93-6664A>G	chr22.hg19:g.31918012A>G		NA	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	hg19	CCDS43005.1	0.02	-0.140343	CCAxAGT	COVERED																																																																																			NOVEL	SFI1-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075103.4	10	2.40612	KEEP	0	0	0	8	220	AA	0.99257	0.259026	0		+	4	48	143	0	0	12.43124	11	60	331	32	ENST00000432498.1	0.266667	0.260965
SFI1	9814	__UNKNOWN__	__UNKNOWN__	22	31926581	31926581	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31926581C>T	ENST00000432498.1	+	4	659				SFI1_ENST00000400288.2_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000540643.1_Intron	NM_014775.3	NP_055590.2	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						ctttcaggggctcacagtgca	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089	9814			29064	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 139	612765			NA	14504268	Standard	NM_014775	NM_001007467	NA	Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000432498.1:c.267-463C>T	chr22.hg19:g.31926581C>T		NA	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	hg19	CCDS43005.1	0.02	1.306835	GGGxTCA	COVERED																																																																																			NOVEL	SFI1-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075103.4	16	8.42469	KEEP	0	0	0	28	852	CC	0.999997	0.99899	0		+	6	60	188	0	0	12.552735	70	60	2425	148	ENST00000432498.1	0.078947	0.998993
SFI1	9814	__UNKNOWN__	__UNKNOWN__	22	31947634	31947634	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:31947634T>C	ENST00000432498.1	+	6	937				SFI1_ENST00000400288.2_Intron|SFI1_ENST00000414585.1_Intron|SFI1_ENST00000400289.1_Intron|SFI1_ENST00000443011.1_Intron|SFI1_ENST00000443326.1_Intron|SFI1_ENST00000540643.1_Intron	NM_014775.3	NP_055590.2	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	NA		NA			G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						ccaggctggtttcaaactcct	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089	9814			29064	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 139	612765			NA	14504268	Standard	NM_014775	NM_001007467	NA	Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000432498.1:c.544+1300T>C	chr22.hg19:g.31947634T>C		NA	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	hg19	CCDS43005.1	0.02	-0.184169	GGTxTCA	COVERED																																																																																			NOVEL	SFI1-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075103.4	8	2.405907	KEEP	0	0	0	8	217	TT	0.99257	0.420331	0		+	3	60	98	0	0	7.633558	16	60	472	40	ENST00000432498.1	0.157895	0.423478
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	32063392	32063392	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32063392A>G			NA	NA				PISD (4974 upstream) : PRR14L (9341 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.32063392A>G		NA		hg19		0.02	-0.236787	CACxCCT	COVERED																																																																																			NOVEL					0			6	3.307216	KEEP	0	0	0	11	292	AA	0.993072	0.608164	0			3	60	95	0	0	7.007061	21	60	615	56		0.125	0.612407
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	32068634	32068634	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32068634G>A			NA	NA				PISD (10216 upstream) : PRR14L (4099 downstream)						NA		NA									NA						atggagtttcgctcttgttgc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.32068634G>A		NA		hg19		0.02	-0.263116	TTCxCTC	COVERED																																																																																			NOVEL					0			4	2.406145	KEEP	0	0	0	8	231	GG	0.99257	0.688515	0			3	60	95	0	0	7.006147	21	60	683	59		0.125	0.693668
DEPDC5	9681	__UNKNOWN__	__UNKNOWN__	22	32300483	32300483	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32300483G>C	ENST00000382112.3	+	41	4479				DEPDC5_ENST00000535622.1_Intron|DEPDC5_ENST00000382111.2_Intron|DEPDC5_ENST00000400246.1_Intron|DEPDC5_ENST00000539165.1_Intron|DEPDC5_ENST00000400249.2_Intron|DEPDC5_ENST00000382105.2_Intron|DEPDC5_ENST00000400248.2_Intron|DEPDC5_ENST00000266091.3_Intron	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	NA		NA			intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						aatcccagcagtttgggaggc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150	9681			18423	protein-coding gene	gene with protein product		614191			NA	23542697, 23542701	Standard	NM_014662	NM_001242896	NA	Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.4410-1487G>C	chr22.hg19:g.32300483G>C		NA	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	hg19	CCDS46692.1	0.02	-0.131591	GCAxTTT	COVERED																																																																																			NOVEL	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000129087.1	4	2.708027	KEEP	0	0	0	9	275	GG	0.99254	0.259018	0		+	3	60	98	0	0	7.971992	12	60	423	38	ENST00000382112.3	0.2	0.260965
SLC5A4	6527	__UNKNOWN__	__UNKNOWN__	22	32620196	32620196	__UNKNOWN__	Intron	SNP	T	T	C	rs112639783		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32620196T>C	ENST00000266086.4	-	13	1677				RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	NA		NA			carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						cgtgagccactgcgcccggcc	0.493		NA											T|||	1	0.000199681	0.0	0.0	5008	,	,	NA	18765	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191	6527		Solute carriers	11039	protein-coding gene	gene with protein product		NA	solute carrier family 5 (low affinity glucose cotransporter), member 4		NA	9501190, 12354616	Standard	NM_014227	NM_014227	NA	Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1665+57A>G	chr22.hg19:g.32620196T>C		NA	O15279	hg19	CCDS13903.1	0.02	-0.245579	CACxGCG	COVERED																																																																																			NOVEL	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000315724.1	8	5.413341	KEEP	4	0	0	18	492	TT	0.995343	0.638361	0		-	3	60	93	0	0	6.865432	20	60	597	55	ENST00000266086.4	0.130435	0.641347
RFPL3	10738	__UNKNOWN__	__UNKNOWN__	22	32756652	32756652	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs201161881	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32756652A>G	ENST00000397468.1	+	3	718	c.700A>G	c.(700-702)Agt>Ggt	p.S234G	RFPL3_ENST00000249007.4_Missense_Mutation_p.S263G|RFPL3S_ENST00000400234.1_3'UTR|RFPL3S_ENST00000461833.1_5'UTR|RFPL3S_ENST00000382084.4_3'UTR|RFPL3_ENST00000382088.3_Missense_Mutation_p.S234G	NM_006604.2	NP_006595.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	263	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA					zinc ion binding (GO:0008270)	p.S263G(1)|p.S234G(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TGATGCTGAAAGTGGTTCCCA	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Substitution - Missense(2)	skin(2)											98	85	90			NA	NA	22		NA											NA				32756652		2203	4300	6503	SO:0001583	missense			AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276	10738			9980	protein-coding gene	gene with protein product		605970			NA	10508838	Standard	NM_006604	NM_006604	NA	Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000397468.1:c.700A>G	chr22.hg19:g.32756652A>G	ENSP00000380609:p.Ser234Gly	NA	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	hg19	CCDS13904.1	0.02	1.74841	GAAxGTG	COVERED	.	.	.	.	.	.	.	.	.	.	A	3.945	-0.013466	0.07727	.	.	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.61274	0.12;0.12;0.12	1.36	0.115	0.14643	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.39517	0.1081	L	0.31371	0.925	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.28530	T	0.3	.	6.1216	0.20155	0.203:0.0:0.797:0.0	.	263	O75679	RFPL3_HUMAN	G	234;263;234	ENSP00000380609:S234G;ENSP00000249007:S263G;ENSP00000371520:S234G	ENSP00000249007:S263G	S	+	1	0	RFPL3	31086652	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.060000	0.11712	-0.184000	0.10567	-1.216000	0.01612	AGT	NOVEL	RFPL3-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259052.1	2	4.208626	KEEP	4	0	0	14	369	AA	0.993634	0.991545	0		+	6	48	201	0	0	13.998297	66	60	1941	123	ENST00000397468.1	0.083333	0.997898
RFPL3	10738	__UNKNOWN__	__UNKNOWN__	22	32756684	32756684	__UNKNOWN__	Silent	SNP	C	C	A	rs61729165		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32756684C>A	ENST00000397468.1	+	3	750	c.732C>A	c.(730-732)gtC>gtA	p.V244V	RFPL3_ENST00000249007.4_Silent_p.V273V|RFPL3S_ENST00000400234.1_3'UTR|RFPL3S_ENST00000461833.1_5'UTR|RFPL3S_ENST00000382084.4_3'UTR|RFPL3_ENST00000382088.3_Silent_p.V244V	NM_006604.2	NP_006595.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	273	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA					zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TCAGGAGCGTCTCTGCTGAGG	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													114	99	104			NA	NA	22		NA											NA				32756684		2203	4300	6503	SO:0001819	synonymous_variant			AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276	10738			9980	protein-coding gene	gene with protein product		605970			NA	10508838	Standard	NM_006604	NM_006604	NA	Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000397468.1:c.732C>A	chr22.hg19:g.32756684C>A		NA	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	hg19	CCDS13904.1	0.02	1.295688	CGTxTCT	COVERED																																																																																			NOVEL	RFPL3-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259052.1	1	2.708026	KEEP	0	0	0	9	277	CC	0.99254	0.988259	0		+	9	49	269	0	0	19.719623	58	60	1920	114	ENST00000397468.1	0.134328	0.995687
RFPL3	10738	__UNKNOWN__	__UNKNOWN__	22	32756703	32756703	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs73166367		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32756703C>T	ENST00000397468.1	+	3	769	c.751C>T	c.(751-753)Cgc>Tgc	p.R251C	RFPL3_ENST00000249007.4_Missense_Mutation_p.R280C|RFPL3S_ENST00000400234.1_3'UTR|RFPL3S_ENST00000461833.1_5'UTR|RFPL3S_ENST00000382084.4_3'UTR|RFPL3_ENST00000382088.3_Missense_Mutation_p.R251C	NM_006604.2	NP_006595.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	280	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.	NA					zinc ion binding (GO:0008270)	p.R251C(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGAGCCACTGCGCCCATTTTT	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				1	Substitution - Missense(1)	ovary(1)											127	105	113			NA	NA	22		NA											NA				32756703		2203	4300	6503	SO:0001583	missense			AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276	10738			9980	protein-coding gene	gene with protein product		605970			NA	10508838	Standard	NM_006604	NM_006604	NA	Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000397468.1:c.751C>T	chr22.hg19:g.32756703C>T	ENSP00000380609:p.Arg251Cys	NA	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	hg19	CCDS13904.1	0.02	1.601889	CTGxGCC	COVERED	.	.	.	.	.	.	.	.	.	.	C	10.28	1.306312	0.23736	.	.	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.69435	-0.4;-0.4;-0.4	0.475	0.475	0.16774	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.73984	0.3657	M	0.74647	2.275	0.30658	N	0.754678	D	0.57899	0.981	P	0.59424	0.857	T	0.69687	-0.5078	9	0.54805	T	0.06	.	6.6676	0.23050	0.0:0.9999:0.0:1.0E-4	.	280	O75679	RFPL3_HUMAN	C	251;280;251	ENSP00000380609:R251C;ENSP00000249007:R280C;ENSP00000371520:R251C	ENSP00000249007:R280C	R	+	1	0	RFPL3	31086703	0.000000	0.05858	0.162000	0.22713	0.081000	0.17604	0.183000	0.16919	0.473000	0.27368	0.205000	0.17691	CGC	NOVEL	RFPL3-002	NOVEL	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259052.1	1	2.707284	KEEP	0	0	0	9	260	CC	0.99254	0.98766	0		+	11	54	337	0	0	26.039409	55	60	1783	115	ENST00000397468.1	0.166667	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	32863454	32863454	__UNKNOWN__	IGR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32863454C>G			NA	NA				BPIFC (2983 upstream) : FBXO7 (7208 downstream)						NA		NA									NA						gcgagactccctctcaaaaca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.32863454C>G		NA		hg19		0.02	-0.078956	TCCxTCT	UNCOVERED																																																																																			NOVEL					0			7	2.407351	KEEP	0	0	0	8	252	CC	0.99257	0.076761	0			3	60	105	0	0	9.855237	4	60	136	22		0.428571	0.077336
SYN3	8224	__UNKNOWN__	__UNKNOWN__	22	32948210	32948210	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:32948210T>C	ENST00000358763.2	-	8	1017				SYN3_ENST00000332840.5_Intron	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	NA		NA			neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						ccagcccgggtgacagagtga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666	8224			11496	protein-coding gene	gene with protein product		602705			NA	9539796	Standard		NM_003490	NA	Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.775-10511A>G	chr22.hg19:g.32948210T>C		NA	B1B1F9	hg19	CCDS13908.1	0.02	-0.043838	GGGxGAC	UNCOVERED																																																																																			NOVEL	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075892.4	5	2.405289	KEEP	0	0	0	8	211	TT	0.99254	0.023894	0		-	2	60	67	1	0	6.451169	2	60	47	18	ENST00000358763.2	0.5	0.024074
SYN3	8224	__UNKNOWN__	__UNKNOWN__	22	33033914	33033914	__UNKNOWN__	Intron	SNP	C	C	T	rs2710349	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:33033914C>T	ENST00000358763.2	-	7	954				SYN3_ENST00000332840.5_Intron	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	NA		NA			neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						catgagccaccgcgcccagca	0.512		NA											T|||	1288	0.257188	0.475	0.2133	5008	,	,	NA	20363	0.0833	NA	0.2734	False	NA	,,,	NA	NA	NA	2504	0.1564	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666	8224			11496	protein-coding gene	gene with protein product		602705			NA	9539796	Standard		NM_003490	NA	Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.712-41192G>A	chr22.hg19:g.33033914C>T		NA	B1B1F9	hg19	CCDS13908.1	0.02	-0.1228	CACxGCG	COVERED																																																																																			NOVEL	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075892.4	4	2.40613	KEEP	1	0	0	8	229	CC	0.99257	0.194853	0		-	7	60	211	0	0	20.541632	6	60	195	32	ENST00000358763.2	0.538462	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	33653181	33653181	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:33653181A>G			NA	NA				LARGE (35444 upstream) : LARGE (15665 downstream)						NA		NA									NA						acaagagcaaaactccgtctc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.33653181A>G		NA		hg19		0.02	-0.254226	CAAxACT	COVERED																																																																																			NOVEL					0			8	3.90888	KEEP	2	0	0	13	350	AA	0.994391	0.664773	0			3	60	102	1	0	7.543187	24	60	667	62		0.111111	0.668523
LARGE	9215	__UNKNOWN__	__UNKNOWN__	22	33788553	33788553	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:33788553A>G	ENST00000354992.2	-	9	1464				LARGE_ENST00000397394.2_Intron|LARGE_ENST00000337431.2_Intron|LARGE_ENST00000402320.1_Intron|LARGE_ENST00000437602.2_Intron|LARGE_ENST00000452586.2_Intron	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	NA		NA			glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				gctgaggcagaagaattgctt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(70;397 1175 4573 19089 45288)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424	9215		Glycosyltransferase family 8 domain containing	6511	protein-coding gene	gene with protein product		603590			NA	9892679, 10591208, 12966029	Standard	NM_133642	NM_004737	NA	Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.893-8263T>C	chr22.hg19:g.33788553A>G		NA	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	hg19	CCDS13912.1	0.02	-0.131557	CAGxAGA	COVERED																																																																																			NOVEL	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320515.2	3	3.006823	KEEP	0	0	0	10	269	AA	0.992708	0.227502	0		-	3	60	95	0	0	7.772968	11	60	329	32	ENST00000354992.2	0.214286	0.229173
LARGE	9215	__UNKNOWN__	__UNKNOWN__	22	33805833	33805833	__UNKNOWN__	Intron	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:33805833T>A	ENST00000354992.2	-	8	1464				LARGE_ENST00000397394.2_Intron|LARGE_ENST00000337431.2_Intron|LARGE_ENST00000402320.1_Intron|LARGE_ENST00000437602.2_Intron|LARGE_ENST00000452586.2_Intron	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	NA		NA			glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				ggcgacagagtgagactccat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Colon(70;397 1175 4573 19089 45288)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424	9215		Glycosyltransferase family 8 domain containing	6511	protein-coding gene	gene with protein product		603590			NA	9892679, 10591208, 12966029	Standard	NM_133642	NM_004737	NA	Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.892+22313A>T	chr22.hg19:g.33805833T>A		NA	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	hg19	CCDS13912.1	0.02	-0.122753	GAGxGAG	COVERED																																																																																			NOVEL	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320515.2	12	3.908969	KEEP	9	0	0	13	345	TT	0.99254	0.194847	0		-	3	60	81	0	0	6.601482	9	60	252	46	ENST00000354992.2	0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	34384527	34384527	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:34384527G>A			NA	NA				LL22NC03-32F9.1 (65773 upstream) : LL22NC03-86D4.1 (28934 downstream)						NA		NA									NA						tgatctgcctgcctcagcctc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.34384527G>A		NA		hg19		0.02	-0.166678	CCTxCCT	COVERED																																																																																			NOVEL					0			10	3.911793	KEEP	4	0	0	13	405	GG	0.993072	0.351495	0			3	60	89	0	0	6.891905	14	60	490	53		0.176471	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	34631506	34631506	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:34631506G>A			NA	NA				LL22NC03-13G6.2 (26255 upstream) : RP1-288L1.5 (467610 downstream)						NA		NA									NA						tgcaacctctgcctcctggtt	0.473		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.34631506G>A		NA		hg19		0.02	-0.114031	TCTxCCT	UNCOVERED																																																																																			NOVEL					0			8	3.309385	KEEP	0	0	0	11	335	GG	0.993072	0.161341	0			3	30	84	0	0	6.781929	10	60	343	34		0.230769	0.162467
HMGXB4	10042	__UNKNOWN__	__UNKNOWN__	22	35684900	35684900	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:35684900T>C	ENST00000216106.5	+	9	1766				HMGXB4_ENST00000444518.2_Intron	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	NA		NA			endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						tttgggaggctgaggcaggcg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281	10042		High mobility group / Non-canonical	5003	protein-coding gene	gene with protein product		604702	high-mobility group protein 2-like 1	HMG2L1	NA	10329004, 10591208, 20511232	Standard	NM_005487	NM_001003681	NA	Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1638+500T>C	chr22.hg19:g.35684900T>C		NA	O75672|O75673|Q9UMT5	hg19	CCDS33641.1	0.02	-0.105261	GGCxGAG	UNCOVERED																																																																																			NOVEL	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318104.2	10	2.406405	KEEP	4	0	0	8	226	TT	0.99257	0.138793	0		+	3	28	100	0	0	8.501089	9	60	281	34	ENST00000216106.5	0.25	0.139832
TOM1	10043	__UNKNOWN__	__UNKNOWN__	22	35727246	35727246	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:35727246A>G	ENST00000449058.2	+	8	1024				TOM1_ENST00000411850.1_Intron|TOM1_ENST00000447733.1_Intron|TOM1_ENST00000425375.1_Intron|TOM1_ENST00000436462.2_Intron|TOM1_ENST00000382034.5_Intron	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	NA		NA			endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						gcaccaccacacccagctaat	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284	10043			11982	protein-coding gene	gene with protein product		604700	target of myb1 (chicken) homolog		NA	10329004, 15047686	Standard	NM_005488	NM_005488	NA	Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.899+773A>G	chr22.hg19:g.35727246A>G		NA	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	hg19	CCDS13913.1	0.02	-0.263021	CACxCCC	COVERED																																																																																			NOVEL	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320641.1	8	3.607488	KEEP	0	0	0	12	314	AA	0.994391	0.689777	0		+	3	60	89	0	0	6.351183	22	60	621	63	ENST00000449058.2	0.12	0.693668
HMOX1	3162	__UNKNOWN__	__UNKNOWN__	22	35778624	35778624	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:35778624A>G	ENST00000216117.8	+	2	362					NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	NA		NA			angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	ccaaagtgctaggattacagg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	3162	1.14.99.3		5013	protein-coding gene	gene with protein product		141250			NA	10591208	Standard		NM_002133	NA	Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.24-475A>G	chr22.hg19:g.35778624A>G		NA		hg19	CCDS13914.1	0.02	-0.30698	GCTxGGA	COVERED																																																																																			NOVEL	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320657.1	13	2.835221	KEEP	2	1	33	21	553	AA	0.999879	0.800148	0		+	3	60	107	0	0	7.852192	28	60	834	94	ENST00000216117.8	0.096774	0.800245
APOL6	80830	__UNKNOWN__	__UNKNOWN__	22	36055852	36055852	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:36055852G>A	ENST00000409652.4	+	0	1517					NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	NA		NA			lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						ggtctctgttgcccaggctgg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963	80830		Apolipoproteins	14870	protein-coding gene	gene with protein product		607256			NA	11374903, 15671246	Standard	NM_030641	NM_030641	NA	Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.*209G>A	chr22.hg19:g.36055852G>A		NA	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	hg19	CCDS13919.1	0.02	2.576462	GTTxCCC	COVERED																																																																																			NOVEL	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319081.2	20	11.931692	KEEP	1	6	135	88	2621	GG	1	0.999984	0		+	7	60	187	0	1	11.594286	77	60	2635	243	ENST00000409652.4	0.083333	0.999984
APOL2	23780	__UNKNOWN__	__UNKNOWN__	22	36623088	36623088	__UNKNOWN__	3'UTR	SNP	G	G	A	rs577192495		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:36623088G>A	ENST00000249066.6	-	0	1852				APOL2_ENST00000358502.5_3'UTR	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	NA		NA			acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						TTggccaggcgcggtggctca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335	23780		Apolipoproteins	619	protein-coding gene	gene with protein product	apolipoprotein L-II	607252			NA	10591208, 11374903	Standard	NM_145637	NM_145637	NA	Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.*362C>T	chr22.hg19:g.36623088G>A		NA	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	hg19	CCDS43014.1	0.02	4.484663	GGCxCGG	COVERED																																																																																			NOVEL	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319279.1	46	18.782059	KEEP	4	7	188	129	3834	GG	1	1	0		-	8	60	244	0	0	14.37568	155	60	5229	475	ENST00000249066.6	0.04908	1
MYH9	4627	__UNKNOWN__	__UNKNOWN__	22	36704439	36704439	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:36704439C>T	ENST00000216181.5	-	15	2074					NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	NA		NA			actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						gcctcctgagcagctgggact	0.517		NA	T	ALK	ALCL		Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome		Hereditary Macrothrombocytopenia, MYH9-associated												NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		22	22q13.1	4627	myosin, heavy polypeptide 9, non-muscle	yes	L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345	4627		Myosins / Myosin superfamily : Class II	7579	protein-coding gene	gene with protein product	nonmuscle myosin heavy chain II-A	160775	myosin, heavy polypeptide 9, non-muscle	DFNA17	NA	1860190, 11023810	Standard	NM_002473	NM_002473	NA	Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.1843+887G>A	chr22.hg19:g.36704439C>T		NA	A8K6E4|O60805|Q60FE2|Q86T83	hg19	CCDS13927.1	0.02	-0.131548	GAGxAGC	COVERED																																																																																			NOVEL	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000259110.3	8	2.407156	KEEP	0	0	0	8	243	CC	0.99257	0.22747	0		-	4	60	103	0	0	8.889482	8	60	266	32	ENST00000216181.5	0.333333	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	37732324	37732324	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:37732324T>G			NA	NA				CYTH4 (20942 upstream) : RP1-63G5.5 (3299 downstream)						NA		NA									NA						agtggctcactcctgtaatcc	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.37732324T>G		NA		hg19		0.02	-0.149108	CACxCCT	COVERED																																																																																			NOVEL					0			5	3.007601	KEEP	2	0	0	10	279	TT	0.99254	0.289823	0			3	60	97	0	0	7.872249	12	60	365	42		0.2	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	38031891	38031891	__UNKNOWN__	IGR	SNP	A	A	G	rs5995485	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38031891A>G			NA	NA				GGA1 (2320 upstream) : SH3BP1 (3590 downstream)						NA		NA									NA						caaagtgctgagattacaggc	0.507		NA											G|||	799	0.159545	0.3359	0.0893	5008	,	,	NA	16646	0.2242	NA	0.0179	False	NA	,,,	NA	NA	NA	2504	0.0501	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.38031891A>G		NA		hg19		0.02	-0.254366	CTGxGAT	COVERED																																																																																			NOVEL					0			12	2.841316	KEEP	0	1	33	21	601	AA	0.999879	0.668442	0			3	60	97	0	0	7.042702	24	60	741	75		0.111111	0.668523
TRIOBP	11078	__UNKNOWN__	__UNKNOWN__	22	38120041	38120041	__UNKNOWN__	Missense_Mutation	SNP	G	G	A	rs4821700	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38120041G>A	ENST00000406386.3	+	7	1733	c.1478G>A	c.(1477-1479)aGt>aAt	p.S493N		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	493		NA	S -> N (in dbSNP:rs4821700).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					TCCTCTCCCAGTAGAGCTACA	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													53	50	51			NA	NA	22		NA											NA				38120041		1898	4074	5972	SO:0001583	missense			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106	11078		Pleckstrin homology (PH) domain containing	17009	protein-coding gene	gene with protein product		609761		DFNB28	NA	11148140, 16385457, 16385458	Standard		NM_001039141	NA	Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1478G>A	chr22.hg19:g.38120041G>A	ENSP00000384312:p.Ser493Asn	NA	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	hg19	CCDS43015.1	0.02	1.184037	CCAxTAG	COVERED	.	.	.	.	.	.	.	.	.	.	-	4.194	0.034639	0.08101	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20069	2.1	3.03	-0.902	0.10537	.	.	.	.	.	T	0.07593	0.0191	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28964	-1.0027	8	0.37606	T	0.19	.	4.0935	0.09980	0.4257:0.1962:0.3781:0.0	rs4821700;rs60645229	493	Q9H2D6	TARA_HUMAN	N	493	ENSP00000384312:S493N	ENSP00000384312:S493N	S	+	2	0	TRIOBP	36449987	0.118000	0.22208	0.000000	0.03702	0.039000	0.13416	-0.330000	0.07925	-0.413000	0.07507	-1.405000	0.01134	AGT	NOVEL	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319439.2	8	8.123254	KEEP	20	0	0	27	810	GG	0.999863	0.999744	0		+	5	23	144	0	0	8.440004	84	48	2891	192	ENST00000406386.3	0.05618	0.999881
TRIOBP	11078	__UNKNOWN__	__UNKNOWN__	22	38120429	38120429	__UNKNOWN__	Silent	SNP	T	T	C	rs6000868	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38120429T>C	ENST00000406386.3	+	7	2121	c.1866T>C	c.(1864-1866)gaT>gaC	p.D622D		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	622		NA			actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CCACACGAGATAACCCCAGAA	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													124	138	134			NA	NA	22		NA											NA				38120429		1941	4148	6089	SO:0001819	synonymous_variant			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106	11078		Pleckstrin homology (PH) domain containing	17009	protein-coding gene	gene with protein product		609761		DFNB28	NA	11148140, 16385457, 16385458	Standard		NM_001039141	NA	Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1866T>C	chr22.hg19:g.38120429T>C		NA	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	hg19	CCDS43015.1	0.02	3.850917	AGAxAAC	COVERED																																																																																			NOVEL	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319439.2	10	12.319624	KEEP	2	0	0	41	1025	TT	1	0.999998	0		+	6	60	189	0	0	11.551287	109	60	3062	219	ENST00000406386.3	0.052174	0.999998
MICALL1	85377	__UNKNOWN__	__UNKNOWN__	22	38338709	38338709	__UNKNOWN__	3'UTR	SNP	C	C	T	rs376872421		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38338709C>T	ENST00000215957.6	+	0	4590					NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	NA		NA			endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					ggggtttcaccgtgttaacca	0.577		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139	85377			29804	protein-coding gene	gene with protein product	molecule interacting with Rab13	NA			NA	11258795, 12110185	Standard	NM_033386	NM_033386	NA	Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.*1872C>T	chr22.hg19:g.38338709C>T		NA	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	hg19	CCDS13961.1	0.02	-0.40314	CACxGTG	COVERED																																																																																			NOVEL	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319545.4	3	3.308939	KEEP	1	0	0	11	314	CC	0.993072	0.928018	0		+	4	50	102	0	0	6.348462	39	60	1242	61	ENST00000215957.6	0.093023	0.934492
C22orf23	84645	__UNKNOWN__	__UNKNOWN__	22	38344363	38344363	__UNKNOWN__	Intron	SNP	G	G	A	rs528227146		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38344363G>A	ENST00000249079.2	-	4	423				C22orf23_ENST00000403305.1_Intron|C22orf23_ENST00000403026.1_Intron			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	NA		NA								endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					aggctgaggcgggagaatcac	0.488		NA											G|||	1	0.000199681	0.0	0.0	5008	,	,	NA	17876	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346	84645			18589	protein-coding gene	gene with protein product		NA			NA	11237012	Standard	NM_032561	NM_032561	NA	Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.167-893C>T	chr22.hg19:g.38344363G>A		NA	Q5JYU9|Q96M68	hg19	CCDS13962.1	0.02	-0.096491	GGCxGGA	UNCOVERED																																																																																			NOVEL	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319564.1	4	2.40648	KEEP	0	0	0	8	229	GG	0.99257	0.119541	0		-	3	60	92	0	0	7.97841	7	60	232	25	ENST00000249079.2	0.3	0.120436
PICK1	9463	__UNKNOWN__	__UNKNOWN__	22	38457808	38457808	__UNKNOWN__	Intron	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38457808G>C	ENST00000404072.3	+	3	500				PICK1_ENST00000356976.3_Intron|PICK1_ENST00000468288.1_Intron|RP5-1039K5.13_ENST00000445483.1_RNA	NM_001039583.1|NM_001039584.1	NP_001034672.1|NP_001034673.1	Q9NRD5	PICK1_HUMAN	protein interacting with PRKCA 1	NA		NA			ATP catabolic process (GO:0006200)|cellular response to decreased oxygen levels (GO:0036294)|cellular response to glucose starvation (GO:0042149)|dendritic spine maintenance (GO:0097062)|dendritic spine organization (GO:0097061)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|glial cell development (GO:0021782)|long term synaptic depression (GO:0060292)|monoamine transport (GO:0015844)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|neuronal ion channel clustering (GO:0045161)|positive regulation of receptor internalization (GO:0002092)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|protein targeting (GO:0006605)|receptor clustering (GO:0043113)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endocytic vesicle membrane (GO:0030666)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein kinase C binding (GO:0005080)|receptor binding (GO:0005102)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	Melanoma(58;0.045)					gattacaggcgtgagccaccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL049654	CCDS13965.1	22q13.1	2006-02-14	2006-02-14	2006-02-14	ENSG00000100151	ENSG00000100151	9463			9394	protein-coding gene	gene with protein product		605926	protein kinase C, alpha binding protein, protein interacting with PRKCA	PRKCABP	NA	10340301, 10591208	Standard	NM_012407	XM_006724377	NA	Approved	dJ1039K5, MGC15204	uc003aus.3	Q9NRD5	OTTHUMG00000151159	ENST00000404072.3:c.153+2456G>C	chr22.hg19:g.38457808G>C		NA	B3KS52|O95906	hg19	CCDS13965.1	0.02	-0.105271	GGCxTGA	UNCOVERED																																																																																			NOVEL	PICK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321569.2	5	2.708071	KEEP	3	0	0	9	275	GG	0	0	0		+	5	60	175	0	0	16.594007	6	60	197	40	ENST00000404072.3	0.454545	0.229173
PLA2G6	8398	__UNKNOWN__	__UNKNOWN__	22	38542456	38542456	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38542456A>G	ENST00000332509.3	-	3	393				PLA2G6_ENST00000435484.1_Intron|PLA2G6_ENST00000436218.1_Intron|PLA2G6_ENST00000335539.3_Intron|PLA2G6_ENST00000447598.2_Intron|PLA2G6_ENST00000417303.2_Intron|PLA2G6_ENST00000402064.1_Intron	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	NA		NA			cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	ctccaaaagtactgggattac	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	8398	3.1.1.4	Patatin-like phospholipase domain containing, Parkinson disease, Ankyrin repeat domain containing	9039	protein-coding gene	gene with protein product	neurodegeneration with brain iron accumulation 2	603604			NA	9417066, 16799181, 19029121	Standard	NM_001004426	NM_001199562	NA	Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.210-796T>C	chr22.hg19:g.38542456A>G		NA	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	hg19	CCDS13967.1	0.02	-0.236727	AGTxCTG	COVERED																																																																																			NOVEL	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321860.1	5	3.304261	KEEP	0	0	0	11	267	AA	0.993072	0.608164	0		-	3	60	93	0	0	6.695863	23	60	622	52	ENST00000332509.3	0.115385	0.612407
CSNK1E	1454	__UNKNOWN__	__UNKNOWN__	22	38692999	38692999	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38692999T>C	ENST00000405675.3	-	0	1339				CSNK1E_ENST00000400206.2_Intron|CSNK1E_ENST00000359867.3_Intron|CSNK1E_ENST00000498529.1_Intron|CSNK1E_ENST00000403904.1_Intron|CSNK1E_ENST00000413574.2_Intron|CSNK1E_ENST00000396832.1_Intron			P49674	KC1E_HUMAN	casein kinase 1, epsilon	NA		NA			cellular protein localization (GO:0034613)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Melanoma(58;0.045)					aggctggtcttaaactcctga	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS13970.1	22q13.1	2013-01-17			ENSG00000213923	ENSG00000213923	1454			2453	protein-coding gene	gene with protein product		600863			NA	7797465, 10535959	Standard	NM_001894	NM_001894	NA	Approved	HCKIE, CKIE, CKIepsilon	uc003avk.3	P49674	OTTHUMG00000151135	ENST00000405675.3:c.*112A>G	chr22.hg19:g.38692999T>C		NA		hg19		0.02	-0.420898	TCTxAAA	COVERED																																																																																			NOVEL	CSNK1E-005	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000321464.2	8	6.914711	KEEP	0	0	0	23	597	TT	0.999909	0.948316	0		-	3	60	102	0	0	6.87769	41	60	1142	103	ENST00000405675.3	0.068182	0.948402
KDELR3	11015	__UNKNOWN__	__UNKNOWN__	22	38868752	38868752	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38868752T>C	ENST00000216014.4	+	2	263				KDELR3_ENST00000409006.3_Intron	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					ttgcccaggctggagtgcaat	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(11;103 529 24120 28493 32980)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196	11015			6306	protein-coding gene	gene with protein product		NA			NA		Standard		NM_006855	NA	Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.92-1776T>C	chr22.hg19:g.38868752T>C		NA	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	hg19	CCDS13972.1	0.02	-0.254347	GGCxGGA	COVERED																																																																																			NOVEL	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331474.1	16	3.909783	KEEP	7	0	0	13	358	TT	0.992708	0.663648	0		+	3	21	102	0	0	7.492475	25	60	755	68	ENST00000216014.4	0.107143	0.668523
KDELR3	11015	__UNKNOWN__	__UNKNOWN__	22	38868768	38868768	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:38868768G>A	ENST00000216014.4	+	2	263				KDELR3_ENST00000409006.3_Intron	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	NA		NA			activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					gcaatggcacgatctcggctc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(11;103 529 24120 28493 32980)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196	11015			6306	protein-coding gene	gene with protein product		NA			NA		Standard		NM_006855	NA	Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.92-1760G>A	chr22.hg19:g.38868768G>A		NA	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	hg19	CCDS13972.1	0.02	-0.254383	CACxATC	COVERED																																																																																			NOVEL	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331474.1	14	3.307671	KEEP	8	0	0	11	314	GG	0.99257	0.663556	0		+	4	60	114	0	0	8.258702	25	60	821	68	ENST00000216014.4	0.137931	0.668523
FAM227A	646851	__UNKNOWN__	__UNKNOWN__	22	39044705	39044705	__UNKNOWN__	Intron	SNP	C	C	T	rs144391306	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:39044705C>T	ENST00000355830.6	-	2	420				FAM227A_ENST00000406767.2_Intron|FAM227A_ENST00000540952.1_Intron|FAM227A_ENST00000535113.1_Intron			F5H4B4	F227A_HUMAN	family with sequence similarity 227, member A	NA		NA									NA						aggttgggtgcggtggctcac	0.463		NA											C|||	3	0.000599042	0.0008	0.0029	5008	,	,	NA	18802	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					22q13.1	2012-07-04			ENSG00000184949	ENSG00000184949	646851			44197	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013647	NM_001013647	NA	Approved		uc011anw.1	F5H4B4	OTTHUMG00000151133	ENST00000355830.6:c.124+1326G>A	chr22.hg19:g.39044705C>T		NA	B0QY52|B7Z7C6|Q5TG08	hg19		0.02	-0.236818	GTGxGGT	COVERED																																																																																			NOVEL	FAM227A-001	NOVEL	non_canonical_U12|basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000321457.4	4	3.607926	KEEP	3	0	0	12	329	CC	0.993072	0.608164	0		-	3	60	90	0	0	6.565715	20	60	630	56	ENST00000355830.6	0.130435	0.612407
GTPBP1	9567	__UNKNOWN__	__UNKNOWN__	22	39128716	39128716	__UNKNOWN__	3'UTR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:39128716T>A	ENST00000216044.5	+	0	4250					NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	NA		NA			GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					ttctttttcttttttgagacg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226	9567			4669	protein-coding gene	gene with protein product		602245			NA	9070279	Standard	NM_004286	XM_005261857	NA	Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.*2007T>A	chr22.hg19:g.39128716T>A		NA	Q6IC67	hg19	CCDS13977.2	0.02	-0.192916	TCTxTTT	COVERED																																																																																			NOVEL	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075532.1	4	4.812498	KEEP	0	0	0	16	450	TT	0.997832	0.456764	0		+	4	60	109	0	0	8.370136	17	60	507	42	ENST00000216044.5	0.190476	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	39703617	39703617	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:39703617A>G			NA	NA				RP3-333H23.8 (12049 upstream) : RPL3 (5269 downstream)						NA		NA									NA						agtggctcacacctgtaatcc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.39703617A>G		NA		hg19		0.02	-0.078947	CACxCCT	UNCOVERED																																																																																			NOVEL					0			4	2.406128	KEEP	7	0	0	8	223	AA	0	0	0			3	60	106	0	0	9.543699	6	60	185	32		0.333333	0.077336
TAB1	10454	__UNKNOWN__	__UNKNOWN__	22	39802918	39802918	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:39802918G>A	ENST00000331454.3	+	1	52				TAB1_ENST00000216160.6_Intron	NM_153497.2	NP_705717.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	NA		NA			activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						gattacaggcgtgagccactg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324	10454			18157	protein-coding gene	gene with protein product	TAK1-binding protein 1, mitogen-activated protein kinase kinase kinase 7 interacting protein 1	602615	mitogen-activated protein kinase kinase kinase 7 interacting protein 1	MAP3K7IP1	NA	8638164, 10187861	Standard	NM_153497	NM_153497	NA	Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000331454.3:c.33+7078G>A	chr22.hg19:g.39802918G>A		NA	Q2PP09|Q8IZW2	hg19	CCDS13992.1	0.02	-0.315789	GGCxTGA	COVERED																																																																																			NOVEL	TAB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321314.1	11	4.81415	KEEP	8	0	0	16	487	GG	0.994391	0.813874	0		+	6	60	176	0	0	13.501232	29	60	963	87	ENST00000331454.3	0.171429	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	39893120	39893120	__UNKNOWN__	IGR	SNP	G	G	A	rs12484582	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:39893120G>A			NA	NA				MGAT3 (4921 upstream) : MIEF1 (2984 downstream)						NA		NA									NA						caccgtgcccggccTCTTTTT	0.488		NA											G|||	1579	0.315296	0.0787	0.2723	5008	,	,	NA	15615	0.7718	NA	0.2068	False	NA	,,,	NA	NA	NA	2504	0.3067	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.39893120G>A		NA		hg19		0.02	-0.166645	CCCxGCC	UNCOVERED																																																																																			NOVEL					0			9	2.405728	KEEP	1	0	0	8	217	GG	0	0	0			11	60	331	0	0	34.028455	5	60	160	36		0.6875	0.353947
GRAP2	9402	__UNKNOWN__	__UNKNOWN__	22	40352440	40352440	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:40352440C>T	ENST00000344138.4	+	3	433				GRAP2_ENST00000407075.3_Intron|GRAP2_ENST00000478445.1_Intron|GRAP2_ENST00000540310.1_Intron|GRAP2_ENST00000543252.1_Intron|GRAP2_ENST00000399090.2_Intron|GRAP2_ENST00000544756.1_Intron	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	NA		NA			cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						ggattacaggcgtgaaccacc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351	9402		SH2 domain containing	4563	protein-coding gene	gene with protein product		604518			NA	9878555, 10224278	Standard	NM_004810	XM_005261836	NA	Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.170+526C>T	chr22.hg19:g.40352440C>T		NA	B7Z8I3|O43726|Q9NRB7	hg19	CCDS13999.1	0.02	-0.184202	AGGxGTG	COVERED																																																																																			NOVEL	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321295.1	9	2.70478	KEEP	0	0	0	9	248	CC	0.99254	0.420319	0		+	3	60	89	0	0	6.892067	14	60	445	41	ENST00000344138.4	0.176471	0.423478
TNRC6B	23112	__UNKNOWN__	__UNKNOWN__	22	40537825	40537825	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:40537825T>C	ENST00000301923.9	+	4	347				TNRC6B_ENST00000402203.1_Intron	NM_001024843.1	NP_001020014.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						gtcacccaggttggagtgcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354	23112		Trinucleotide (CAG) repeat containing	29190	protein-coding gene	gene with protein product		610740			NA		Standard		NM_015088	NA	Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000301923.9:c.46-14294T>C	chr22.hg19:g.40537825T>C		NA	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	hg19	CCDS46712.1	0.02	-0.11402	AGGxTGG	UNCOVERED																																																																																			NOVEL	TNRC6B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321393.1	2	2.406293	KEEP	1	0	0	8	223	TT	0	0	0		+	3	60	101	0	0	8.601291	9	60	263	38	ENST00000301923.9	0.25	0.162467
TNRC6B	23112	__UNKNOWN__	__UNKNOWN__	22	40688193	40688193	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:40688193G>A	ENST00000301923.9	+	13	1598				TNRC6B_ENST00000454349.2_Intron|TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000335727.9_Intron|TNRC6B_ENST00000497559.1_Intron	NM_001024843.1	NP_001020014.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	NA		NA			epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						gcaagactccgtctcaaaaaa	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354	23112		Trinucleotide (CAG) repeat containing	29190	protein-coding gene	gene with protein product		610740			NA		Standard		NM_015088	NA	Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000301923.9:c.1296+6419G>A	chr22.hg19:g.40688193G>A		NA	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	hg19	CCDS46712.1	0.02	1.164169	TCCxTCT	COVERED																																																																																			NOVEL	TNRC6B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321393.1	12	7.983209	KEEP	0	2	52	45	1272	GG	1	0.999487	0		+	5	60	153	2	0	9.656584	72	60	2326	197	ENST00000301923.9	0.064935	0.999487
MKL1	57591	__UNKNOWN__	__UNKNOWN__	22	40910007	40910007	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:40910007A>G	ENST00000402042.1	-	3	538				MKL1_ENST00000396617.3_Intron|MKL1_ENST00000355630.3_Intron	NM_001282661.1	NP_001269590.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	NA		NA			negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						tgtaatcccaacactttggga	0.443		NA	T	RBM15	acute megakaryocytic leukemia																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588	57591			14334	protein-coding gene	gene with protein product	megakaryocytic acute leukemia, myocardin-related transcription factor A, basic, SAP and coiled-coil domain	606078			NA	11431691, 12019265, 14970199	Standard	NM_020831	XM_005261692	NA	Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000402042.1:c.58+38102T>C	chr22.hg19:g.40910007A>G		NA	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	hg19		0.02	-0.200922	CCAxCAC	COVERED																																																																																			NOVEL	MKL1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000321523.1	12	5.712328	KEEP	1	0	0	19	505	AA	0.999859	0.490475	0		-	3	60	90	0	0	6.83513	16	60	460	57	ENST00000402042.1	0.157895	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	41064475	41064475	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41064475C>T			NA	NA				MKL1 (31769 upstream) : MCHR1 (10278 downstream)						NA		NA									NA						gaggccaaggcgggcagatca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.41064475C>T		NA		hg19		0.02	-0.201762	AGGxGGG	UNCOVERED																																																																																			NOVEL					0			6	2.406251	KEEP	3	0	0	8	231	CC	0	0	0			3	60	90	0	0	6.910267	15	60	518	49		0.166667	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	41128297	41128297	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41128297G>A			NA	NA				MCHR1 (49479 upstream) : SLC25A17 (37336 downstream)						NA		NA									NA						gggcaacagagtgagactgtc	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.41128297G>A		NA		hg19		0.02	-0.07895	AGAxTGA	UNCOVERED																																																																																			NOVEL					0			6	2.707814	KEEP	1	0	0	9	272	GG	0.99254	0.076759	0			3	42	93	0	0	8.654836	4	60	142	28		0.428571	0.077336
ST13	6767	__UNKNOWN__	__UNKNOWN__	22	41244685	41244685	__UNKNOWN__	Intron	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41244685G>T	ENST00000216218.3	-	3	650					NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	NA		NA			chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)			cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						aggcggaggtggcagtgagct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380	6767		Tetratricopeptide (TTC) repeat domain containing	11343	protein-coding gene	gene with protein product	progesterone receptor-associated p48 protein	606796	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)		NA	9925927, 8721986	Standard	NM_003932	NM_003932	NA	Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.169-312C>A	chr22.hg19:g.41244685G>T		NA	O14999|Q2TU77	hg19	CCDS14006.1	0.02	-0.140301	GGTxGCA	UNCOVERED																																																																																			NOVEL	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321759.1	10	2.708245	KEEP	2	0	0	9	282	GG	0	0	0		-	3	30	81	0	0	6.482074	10	60	345	35	ENST00000216218.3	0.230769	0.260965
DNAJB7	150353	__UNKNOWN__	__UNKNOWN__	22	41256775	41256775	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41256775T>C	ENST00000307221.4	-	0	1355				XPNPEP3_ENST00000414396.1_Intron|XPNPEP3_ENST00000541156.1_Intron|XPNPEP3_ENST00000482652.1_3'UTR|XPNPEP3_ENST00000357137.4_Intron	NM_145174.1	NP_660157.1	Q7Z6W7	DNJB7_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 7	NA		NA					chaperone binding (GO:0051087)			breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10						ttctaccagcttcccgagtag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF085232	CCDS14008.1	22q13.2	2011-09-02			ENSG00000172404	ENSG00000172404	150353		Heat shock proteins / DNAJ (HSP40)	24986	protein-coding gene	gene with protein product		611336			NA	12477932	Standard	NM_145174	NM_145174	NA	Approved	HSC3	uc003azj.3	Q7Z6W7	OTTHUMG00000151202	ENST00000307221.4:c.*294A>G	chr22.hg19:g.41256775T>C		NA	Q2M220|Q5H904|Q8WYJ7	hg19	CCDS14008.1	0.02	5.687757	AGCxTCC	COVERED																																																																																			NOVEL	DNAJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000321765.1	59	13.810643	KEEP	0	13	374	178	4906	TT	1	1	0		-	9	60	287	0	0	17.875697	155	60	4658	527	ENST00000307221.4	0.054878	1
XPNPEP3	63929	__UNKNOWN__	__UNKNOWN__	22	41326642	41326642	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41326642T>C	ENST00000357137.4	+	0	5811				XPNPEP3_ENST00000544094.1_Intron	NM_022098.3	NP_071381.1	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3, putative	NA		NA			glomerular filtration (GO:0003094)|protein processing (GO:0016485)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metallopeptidase activity (GO:0008237)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	17						ggtgtgatcttggctcactgc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(145;306 1841 7037 21878 30110)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS14007.1, CCDS74869.1	22q13.2	2010-07-20			ENSG00000196236	ENSG00000196236	63929			28052	protein-coding gene	gene with protein product		613553			NA	15708373, 20179356	Standard	NM_022098	NM_022098	NA	Approved	APP3, NPHPL1	uc003azh.3	Q9NQH7	OTTHUMG00000151312	ENST00000357137.4:c.*4203T>C	chr22.hg19:g.41326642T>C		NA	B2R9G1|B7Z790|B7Z7B2|Q6I9V9|Q8NDA6|Q9BV27|Q9BVH0	hg19	CCDS14007.1	0.02	-0.192951	TCTxGGC	COVERED																																																																																			NOVEL	XPNPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322201.2	5	2.738652	KEEP	1	1	28	19	520	TT	0.999863	0.490477	0		+	4	60	124	0	0	10.168648	14	60	413	51	ENST00000357137.4	0.222222	0.490544
XPNPEP3	63929	__UNKNOWN__	__UNKNOWN__	22	41326643	41326643	__UNKNOWN__	3'UTR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41326643G>A	ENST00000357137.4	+	0	5812				XPNPEP3_ENST00000544094.1_Intron	NM_022098.3	NP_071381.1	Q9NQH7	XPP3_HUMAN	X-prolyl aminopeptidase (aminopeptidase P) 3, putative	NA		NA			glomerular filtration (GO:0003094)|protein processing (GO:0016485)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metallopeptidase activity (GO:0008237)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	17						gtgtgatcttggctcactgca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	Ovarian(145;306 1841 7037 21878 30110)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS14007.1, CCDS74869.1	22q13.2	2010-07-20			ENSG00000196236	ENSG00000196236	63929			28052	protein-coding gene	gene with protein product		613553			NA	15708373, 20179356	Standard	NM_022098	NM_022098	NA	Approved	APP3, NPHPL1	uc003azh.3	Q9NQH7	OTTHUMG00000151312	ENST00000357137.4:c.*4204G>A	chr22.hg19:g.41326643G>A		NA	B2R9G1|B7Z790|B7Z7B2|Q6I9V9|Q8NDA6|Q9BV27|Q9BVH0	hg19	CCDS14007.1	0.02	-0.201744	CTTxGCT	COVERED																																																																																			NOVEL	XPNPEP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322201.2	7	3.542565	KEEP	1	1	26	21	622	GG	0.999879	0.490485	0		+	3	60	88	0	0	6.710619	15	60	476	53	ENST00000357137.4	0.166667	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	41431097	41431097	__UNKNOWN__	IGR	SNP	C	C	T	rs4820424|rs549187538|rs376816088		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:41431097C>T			NA	NA				RBX1 (61784 upstream) : Y_RNA (10403 downstream)						NA		NA									NA						ttccttccttcctttcttcct	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.41431097C>T		NA		hg19		0.02	-0.192966	CTTxCTT	UNCOVERED																																																																																			NOVEL					0			7	3.00889	KEEP	5	0	0	10	310	CC	0	0	0			12	60	357	0	1	35.576122	8	60	269	48		0.6	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	42434849	42434849	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:42434849A>C			NA	NA				WBP2NL (6195 upstream) : NAGA (19508 downstream)						NA		NA									NA						ctcaggtgatacacccacctc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.42434849A>C		NA		hg19		0.02	-0.122785	GATxCAC	COVERED																																																																																			NOVEL					0			12	2.706592	KEEP	5	0	0	9	243	AT	0.993072	0.289978	0			5	60	155	2	0	14.123251	8	60	238	46		0.384615	0.292001
NDUFA6-AS1	100132273	__UNKNOWN__	__UNKNOWN__	22	42499183	42499183	__UNKNOWN__	RNA	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:42499183C>T	ENST00000416037.2	+	0	669				NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA	NR_034118.1				NDUFA6 antisense RNA 1 (head to head)	NA		NA									NA						cactgcactccagcctgggca	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA					BC039542		22q13.2	2013-03-18	2013-03-18		ENSG00000237037	ENSG00000237037	100132273		Long non-coding RNAs	45273	non-coding RNA	RNA, long non-coding		NA			NA		Standard	NR_034118	NR_034118	NA	Approved		uc003bcd.1		OTTHUMG00000150917	ENST00000416037.2:	chr22.hg19:g.42499183C>T		NA		hg19		0.02	-0.078928	CTCxAGC	UNCOVERED																																																																																			NOVEL	NDUFA6-AS1-001	KNOWN	basic|exp_conf	antisense	NA	processed_transcript	OTTHUMT00000320522.4	8	4.212623	KEEP	3	0	0	14	432	CC	0.995343	0.076975	0		+	3	60	79	0	0	7.030929	5	60	174	39	ENST00000416037.2	0.375	0.077336
CYP2D6	1565	__UNKNOWN__	__UNKNOWN__	22	42523505	42523505	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs150552908		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:42523505C>T	ENST00000360608.5	-	7	1231	c.1117G>A	c.(1117-1119)Ggt>Agt	p.G373S	NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.G373S|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.G322S	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	373		NA	G -> S (in dbSNP:rs2856959).		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGGGTCACACCCAGGGGGACG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													82	71	75			NA	NA	22		NA											NA				42523505		2202	4300	6502	SO:0001583	missense			M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197	1565		Cytochrome P450s	2625	protein-coding gene	gene with protein product		124030	cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6, cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2, cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2, cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2, cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP	NA	8449513	Standard		NM_000106	NA	Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1117G>A	chr22.hg19:g.42523505C>T	ENSP00000353820:p.Gly373Ser	NA	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	hg19	CCDS46721.1	0.02	1.333201	CACxCAG	COVERED	37	0.01694139194139194	13	0.026422764227642278	1	0.0027624309392265192	6	0.01048951048951049	17	0.022427440633245383	C	11.82	1.753313	0.31046	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.67865	-0.29;-0.29;-0.29	4.93	2.84	0.33178	.	0.309535	0.32204	N	0.006427	T	0.28599	0.0708	L	0.28556	0.865	0.09310	N	1	B;B;B	0.14012	0.009;0.002;0.009	B;B;B	0.28784	0.094;0.032;0.094	T	0.33394	-0.9870	10	0.42905	T	0.14	.	8.1034	0.30870	0.0:0.7482:0.0:0.2518	rs2856959	373;322;373	C1ID54;Q6NXU8;Q6NWU0	.;.;.	S	373;373;319;322;322	ENSP00000353820:G373S;ENSP00000374620:G373S;ENSP00000351927:G322S	ENSP00000351927:G322S	G	-	1	0	CYP2D6	40853449	0.000000	0.05858	0.001000	0.08648	0.965000	0.64279	-0.231000	0.09069	0.495000	0.27882	0.555000	0.69702	GGT	NOVEL	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320525.1	1	3.911351	KEEP	4	0	0	13	393	CC	0.993072	0.991548	0		-	8	47	228	0	0	15.618824	66	60	2225	128	ENST00000360608.5	0.108108	0.998465
CYP2D6	1565	__UNKNOWN__	__UNKNOWN__	22	42523514	42523514	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs61745683	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:42523514C>T	ENST00000360608.5	-	7	1222	c.1108G>A	c.(1108-1110)Gtc>Atc	p.V370I	NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.V370I|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.V319I	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	370		NA			alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CCCAGGGGGACGATGTCCCCA	0.617		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													91	76	81			NA	NA	22		NA											NA				42523514		2201	4300	6501	SO:0001583	missense			M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197	1565		Cytochrome P450s	2625	protein-coding gene	gene with protein product		124030	cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6, cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2, cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2, cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2, cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP	NA	8449513	Standard		NM_000106	NA	Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1108G>A	chr22.hg19:g.42523514C>T	ENSP00000353820:p.Val370Ile	NA	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	hg19	CCDS46721.1	0.02	1.324529	GGAxGAT	COVERED	.	.	.	.	.	.	.	.	.	.	C	6.769	0.510813	0.12883	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.71461	-0.57;-0.57;-0.57	4.93	-6.63	0.01807	.	1.172500	0.06084	N	0.662437	T	0.50837	0.1639	L	0.38838	1.175	0.09310	N	1	B;B;B	0.10296	0.0;0.003;0.0	B;B;B	0.15484	0.002;0.013;0.002	T	0.31943	-0.9925	10	0.14252	T	0.57	.	4.9748	0.14135	0.0962:0.2506:0.0994:0.5539	.	370;319;370	C1ID54;Q6NXU8;Q6NWU0	.;.;.	I	370;370;316;319;319	ENSP00000353820:V370I;ENSP00000374620:V370I;ENSP00000351927:V319I	ENSP00000351927:V319I	V	-	1	0	CYP2D6	40853458	0.000000	0.05858	0.014000	0.15608	0.946000	0.59487	-1.950000	0.01530	-0.880000	0.03997	-0.266000	0.10368	GTC	NOVEL	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000320525.1	1	3.91063	KEEP	4	0	0	13	377	CC	0.993072	0.991777	0		-	5	40	143	0	0	8.719766	70	60	2259	127	ENST00000360608.5	0.066667	0.998696
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	42546802	42546802	__UNKNOWN__	IGR	SNP	C	C	T	rs201242546	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:42546802C>T			NA	NA				CYP2D7P1 (6226 upstream) : TCF20 (9216 downstream)						NA		NA									NA						TGGGTCACACCCAGGGGGACG	0.627		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.42546802C>T		NA		hg19		0.02	1.502492	CACxCAG	COVERED																																																																																			NOVEL					0			2	4.788127	KEEP	3	0	0	16	473	CC	0.99649	0.991591	0			5	27	157	0	0	10.367068	62	60	2106	118		0.074627	0.995084
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	42546811	42546811	__UNKNOWN__	IGR	SNP	C	C	T	rs202157864	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:42546811C>T			NA	NA				CYP2D7P1 (6235 upstream) : TCF20 (9207 downstream)						NA		NA									NA						CCCAGGGGGACGATGTCCCCA	0.612		NA											c|||	9	0.00179712	0.0	0.0014	5008	,	,	NA	22663	0.002	NA	0.002	False	NA	,,,	NA	NA	NA	2504	0.0041	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.42546811C>T		NA		hg19		0.02	1.368321	GGAxGAT	COVERED																																																																																			NOVEL					0			2	4.511556	KEEP	2	0	0	15	424	CC	0.995343	0.992519	0			7	51	213	0	0	14.718351	64	60	2096	123		0.098592	0.997163
ARFGAP3	26286	__UNKNOWN__	__UNKNOWN__	22	43200651	43200651	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:43200651A>G	ENST00000263245.5	-	14	1631				ARFGAP3_ENST00000429508.2_Intron|ARFGAP3_ENST00000437119.2_Intron	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	NA		NA			intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						ctcccaaagtactgggattac	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	GBM(58;544 1030 21460 27159 48838)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247	26286		ADP-ribosylation factor GTPase activating proteins	661	protein-coding gene	gene with protein product		612439	ADP-ribosylation factor GTPase activating protein 1	ARFGAP1	NA	10704287, 11172815	Standard	NM_014570	NM_014570	NA	Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1411+2427T>C	chr22.hg19:g.43200651A>G		NA	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	hg19	CCDS14042.1	0.02	-0.157843	AGTxCTG	COVERED																																																																																			NOVEL	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319747.2	5	3.607148	KEEP	1	0	0	12	308	AA	0.993072	0.32057	0		-	3	60	95	0	0	7.579495	13	60	368	47	ENST00000263245.5	0.1875	0.322807
BIK	638	__UNKNOWN__	__UNKNOWN__	22	43522427	43522427	__UNKNOWN__	Intron	SNP	G	G	A	rs6003067	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:43522427G>A	ENST00000216115.2	+	3	224					NM_001197.4	NP_001188.1	Q13323	BIK_HUMAN	BCL2-interacting killer (apoptosis-inducing)	NA		NA			apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|male gonad development (GO:0008584)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|mitochondrial envelope (GO:0005740)				breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|urinary_tract(1)	5		Ovarian(80;0.0694)				tcctgacctcgtgatctgcct	0.537		NA											G|||	2168	0.432907	0.0809	0.5331	5008	,	,	NA	18074	0.5536	NA	0.661	False	NA	,,,	NA	NA	NA	2504	0.4785	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U34584	CCDS14044.1	22q13.31	2014-03-07			ENSG00000100290	ENSG00000100290	638			1051	protein-coding gene	gene with protein product		603392			NA	7478623, 10591208	Standard	NM_001197	NM_001197	NA	Approved	NBK	uc003bdk.3	Q13323	OTTHUMG00000150703	ENST00000216115.2:c.162-1276G>A	chr22.hg19:g.43522427G>A		NA	Q16582|Q6FH93	hg19	CCDS14044.1	0.02	-0.149105	CTCxTGA	UNCOVERED																																																																																			NOVEL	BIK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000319676.1	2	2.707421	KEEP	3	0	0	9	263	GG	0	0	0		+	10	60	303	0	0	30.471412	6	60	198	42	ENST00000216115.2	0.625	0.292001
MPPED1	758	__UNKNOWN__	__UNKNOWN__	22	43855844	43855844	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:43855844T>C	ENST00000417669.2	+	4	850				MPPED1_ENST00000443721.1_Intron|MPPED1_ENST00000414469.2_Intron|MPPED1_ENST00000439548.1_Intron|MPPED1_ENST00000538182.1_Intron|MPPED1_ENST00000542779.1_Intron			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	NA		NA					hydrolase activity (GO:0016787)			endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|skin(1)	13		all_neural(38;0.0244)|Ovarian(80;0.0694)				cgtggtggcttacgcctgtaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U84894	CCDS46723.1	22q13.2	2013-09-20	2005-10-10	2005-10-10	ENSG00000186732	ENSG00000186732	758			1306	protein-coding gene	gene with protein product		602112	chromosome 22 open reading frame 1	C22orf1	NA	9266672, 10591208	Standard	NM_001044370	NM_001044370	NA	Approved	239AB, FAM1A	uc011apv.2	O15442	OTTHUMG00000150566	ENST00000417669.2:c.407-14772T>C	chr22.hg19:g.43855844T>C		NA	A8K159|B7Z2S9|Q8N361	hg19	CCDS46723.1	0.02	-0.078938	GCTxACG	UNCOVERED																																																																																			NOVEL	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318938.2	1	2.399225	KEEP	1	0	0	8	193	TT	0.99257	0.076761	0		+	2	60	69	0	0	6.393129	3	60	84	26	ENST00000417669.2	0.4	0.077336
CTA-217C2.1	0	__UNKNOWN__	__UNKNOWN__	22	45557793	45557793	__UNKNOWN__	lincRNA	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:45557793G>C	ENST00000426282.2	-	0	205					NR_038956.1					NA		NA									NA						ctcaggtgatgcacccgcctc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000426282.2:	chr22.hg19:g.45557793G>C		NA		hg19		0.02	-0.052638	GATxCAC	UNCOVERED																																																																																			NOVEL	CTA-217C2.1-001	KNOWN	basic|exp_conf	lincRNA	NA	lincRNA	OTTHUMT00000321991.2	4	2.406523	KEEP	0	0	0	8	243	AG	0.99254	0.036491	0		-	2	60	73	0	0	6.792797	3	60	107	21	ENST00000426282.2	0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	45643136	45643136	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:45643136C>T			NA	NA				KIAA0930 (6486 upstream) : CTA-268H5.14 (15029 downstream)						NA		NA									NA						ggtgaaaccccgtctctgggc	0.582		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.45643136C>T		NA		hg19		0.02	-0.21052	CCCxGTC	COVERED																																																																																			NOVEL					0			12	4.210931	KEEP	0	0	0	14	411	CC	0.995343	0.519729	0			3	60	90	0	0	6.627541	19	60	609	55		0.136364	0.522161
PPARA	5465	__UNKNOWN__	__UNKNOWN__	22	46566250	46566250	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:46566250C>T	ENST00000396000.2	+	2	223				PPARA_ENST00000407236.1_Intron|PPARA_ENST00000262735.5_Intron			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	NA		NA			behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	atccacccacctcagcctcct	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951	5465		Nuclear hormone receptors	9232	protein-coding gene	gene with protein product		170998	peroxisome proliferative activated receptor, alpha	PPAR	NA	7684926, 10591208	Standard	NM_001001928	XM_005261655	NA	Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.-43+18294C>T	chr22.hg19:g.46566250C>T		NA	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	hg19	CCDS33669.1	0.02	-0.096481	CACxTCA	UNCOVERED																																																																																			NOVEL	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318129.3	8	2.707609	KEEP	1	0	0	9	264	CC	0.99257	0.119541	0		+	3	60	80	0	0	6.942734	6	60	201	23	ENST00000396000.2	0.333333	0.120436
PPARA	5465	__UNKNOWN__	__UNKNOWN__	22	46566294	46566294	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:46566294C>T	ENST00000396000.2	+	2	223				PPARA_ENST00000407236.1_Intron|PPARA_ENST00000262735.5_Intron			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	NA		NA			behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	taccaccacacccagctaatt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951	5465		Nuclear hormone receptors	9232	protein-coding gene	gene with protein product		170998	peroxisome proliferative activated receptor, alpha	PPAR	NA	7684926, 10591208	Standard	NM_001001928	XM_005261655	NA	Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.-43+18338C>T	chr22.hg19:g.46566294C>T		NA	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	hg19	CCDS33669.1	0.02	-0.078936	ACAxCCA	UNCOVERED																																																																																			NOVEL	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000318129.3	12	3.308916	KEEP	3	0	0	11	318	CC	0.99254	0.076759	0		+	3	60	83	0	0	8.268438	2	60	65	22	ENST00000396000.2	0.6	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	47648987	47648987	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:47648987G>A			NA	NA				TBC1D22A (77651 upstream) : CITF22-49D8.1 (92331 downstream)						NA		NA									NA						cctggcctcaggcaatcctcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.47648987G>A		NA		hg19		0.02	-0.175439	TCAxGCA	COVERED																																																																																			NOVEL					0			14	2.431881	KEEP	0	1	22	16	453	GG	0.999366	0.387161	0			4	60	115	0	0	9.268307	14	60	469	48		0.222222	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	47651575	47651575	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:47651575C>T			NA	NA				TBC1D22A (80239 upstream) : CITF22-49D8.1 (89743 downstream)						NA		NA									NA						ctcagcctcccgagtaactgg	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.47651575C>T		NA		hg19		0.02	-0.070176	TCCxGAG	UNCOVERED																																																																																			NOVEL					0			12	3.3082	KEEP	6	0	0	11	301	CC	0	0	0			3	25	92	0	0	8.554848	4	60	133	24		0.428571	0.054137
RP11-191L9.4	0	__UNKNOWN__	__UNKNOWN__	22	48208655	48208655	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:48208655T>C	ENST00000423737.1	+	0	1125										NA		NA									NA						gtagctgggattacaggcatg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000423737.1:	chr22.hg19:g.48208655T>C		NA		hg19		0.02	-0.043858	GGAxTAC	UNCOVERED																																																																																			NOVEL	RP11-191L9.4-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000317556.1	5	2.405445	KEEP	3	0	0	8	213	TT	0	0	0		+	2	40	69	0	0	6.392974	3	50	91	19	ENST00000423737.1	0.4	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	48740843	48740843	__UNKNOWN__	IGR	SNP	G	G	A	rs133669	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:48740843G>A			NA	NA				MIR3201 (70616 upstream) : RP11-536P6.3 (103858 downstream)						NA		NA									NA						aacccaggaggcagaggttgc	0.453		NA											g|||	1764	0.352236	0.0862	0.4424	5008	,	,	NA	15479	0.5427	NA	0.3926	False	NA	,,,	NA	NA	NA	2504	0.41	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.48740843G>A		NA		hg19		0.02	-0.052629	GAGxCAG	UNCOVERED																																																																																			NOVEL					0			5	2.708076	KEEP	8	0	0	9	276	GG	0	0	0			4	60	121	0	0	12.920568	1	24	33	31		0.8	0.036766
ALG12	79087	__UNKNOWN__	__UNKNOWN__	22	50306387	50306387	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:50306387T>C	ENST00000330817.6	-	3	569					NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase	NA		NA			cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosyltransferase activity (GO:0000009)|dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity (GO:0052917)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(3)	12		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)		tggtggctcatgcctgtaatc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ303120	CCDS14081.1	22q13.33	2013-02-26	2013-02-26		ENSG00000182858	ENSG00000182858	79087	2.4.1.260	Dolichyl D-mannosyl phosphate dependent mannosyltransferases	19358	protein-coding gene	gene with protein product	dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase, dol-P-Man dependent alpha-1,6-mannosyltransferase	607144	asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase), asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)		NA	11983712	Standard	NM_024105	NM_024105	NA	Approved	ECM39	uc003biy.3	Q9BV10	OTTHUMG00000150289	ENST00000330817.6:c.295+645A>G	chr22.hg19:g.50306387T>C		NA	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	hg19	CCDS14081.1	0.02	-0.157868	TCAxGCC	COVERED																																																																																			NOVEL	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000317405.2	8	2.706343	KEEP	0	0	0	9	246	TT	0.99254	0.320398	0		-	3	60	103	0	0	8.210104	15	60	438	37	ENST00000330817.6	0.166667	0.322807
MOV10L1	54456	__UNKNOWN__	__UNKNOWN__	22	50566943	50566943	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:50566943C>T	ENST00000262794.5	+	13	1993				MOV10L1_ENST00000545383.1_Intron|MOV10L1_ENST00000540615.1_Intron|MOV10L1_ENST00000395858.3_Intron|MOV10L1_ENST00000395843.1_Intron	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	NA		NA			ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		ATAGGTAATGCTTTTAGTGAG	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													46	48	48			NA	NA	22		NA											NA				50566943		2200	4294	6494	SO:0001627	intron_variant			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146	54456			7201	protein-coding gene	gene with protein product	cardiac helicase activated by MEF2C protein	605794	Mov10 (mouse)-like 1, Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)		NA	11279525	Standard	NM_018995	NM_018995	NA	Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1910+7C>T	chr22.hg19:g.50566943C>T		NA	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	hg19	CCDS14084.1	0.02	-0.254399	ATGxTTT	COVERED																																																																																			NOVEL	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000075009.2	13	7.522001	KEEP	0	0	0	25	759	CC	0.999931	0.668477	0		+	4	60	117	0	0	8.691778	23	60	789	76	ENST00000262794.5	0.148148	0.668523
PPP6R2	9701	__UNKNOWN__	__UNKNOWN__	22	50841369	50841369	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:50841369T>C	ENST00000359139.3	+	4	621				PPP6R2_ENST00000395744.3_Intron|PPP6R2_ENST00000395741.3_Intron|PPP6R2_ENST00000216061.5_Intron	NM_001242898.1|NM_001242899.1|NM_001242900.1|NM_014678.4	NP_001229827.1|NP_001229828.1|NP_001229829.1|NP_055493.2	O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	NA		NA				cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						GAgctgggtgtggtggctcac	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239	9701		Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits	19253	protein-coding gene	gene with protein product		610877	KIAA0685, SAPS domain family, member 2	KIAA0685, SAPS2	NA	16769727	Standard	NM_014678	NM_014678	NA	Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000359139.3:c.228-3749T>C	chr22.hg19:g.50841369T>C		NA	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	hg19	CCDS56236.1	0.02	-0.061401	GTGxGGT	UNCOVERED																																																																																			NOVEL	PPP6R2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000316806.1	7	3.60904	KEEP	3	0	0	12	331	TT	0.99254	0.04346	0		+	2	60	72	0	0	6.335726	5	60	150	30	ENST00000359139.3	0.285714	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	50946531	50946531	__UNKNOWN__	IGR	SNP	C	C	T	rs558171682		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:50946531C>T			NA	NA				LMF2 (396 upstream) : NCAPH2 (113 downstream)						NA		NA									NA						ACCCCCCCCTCCCGGAGGCTT	0.731		NA											.|||	1	0.000199681	0.0	0.0	5008	,	,	NA	4487	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.50946531C>T		NA		hg19		0.02	-0.09648	CCTxCCG	UNCOVERED																																																																																			NOVEL					0			0	2.707255	KEEP	0	0	0	9	256	CC	0.99254	0.119538	0			6	60	170	0	0	16.568756	5	60	170	21		0.545455	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	22	51002596	51002596	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chr22:51002596C>T			NA	NA				SYCE3 (1262 upstream) : CPT1B (4693 downstream)						NA		NA									NA						ttttttgagacggagtcttgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chr22.hg19:g.51002596C>T		NA		hg19		0.02	-0.105266	AGAxGGA	UNCOVERED																																																																																			NOVEL					0			16	3.308371	KEEP	13	0	0	11	317	CC	0.99254	0.138789	0			3	42	88	0	0	7.432117	8	60	274	44		0.272727	0.139832
GYG2	8908	__UNKNOWN__	__UNKNOWN__	X	2760455	2760455	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:2760455T>C	ENST00000381163.3	+	3	289				GYG2_ENST00000338623.5_Intron|GYG2_ENST00000542787.1_Intron|GYG2_ENST00000381161.1_Intron|GYG2_ENST00000398806.3_Intron	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	NA		NA			carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ccaggctggtttcaaactcct	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	8908	2.4.1.186	Glycosyltransferase family 8 domain containing	4700	protein-coding gene	gene with protein product	glycogenin glucosyltransferase	300198			NA	9857012	Standard	NM_003918	NM_001079855	NA	Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.8-584T>C	chrX.hg19:g.2760455T>C		NA	B7WNN6|O15485|O15486|O15487|O15489|O15490	hg19	CCDS14121.1	0.02	-0.157856	GGTxTCA	COVERED																																																																																			NOVEL	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055645.1	6	2.837532	KEEP	0	1	21	17	454	TT	0.999859	0.322761	0		+	3	60	94	0	0	7.310932	15	60	434	50	ENST00000381163.3	0.166667	0.322807
PRKX	5613	__UNKNOWN__	__UNKNOWN__	X	3540064	3540064	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:3540064G>A	ENST00000262848.5	-	6	1170				PRKX_ENST00000425240.1_Intron	NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	NA		NA			angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				acacaactgtggtcccagcta	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	5613	2.7.11.1		9441	protein-coding gene	gene with protein product		300083			NA	7633447	Standard	NM_005044	NM_005044	NA	Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.816-707C>T	chrX.hg19:g.3540064G>A		NA		hg19	CCDS14125.1	0.02	-0.096445	TGTxGTC	UNCOVERED																																																																																			NOVEL	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055659.1	4	5.115285	KEEP	0	0	0	17	522	GG	0.999366	0.12036	0		-	3	60	76	1	0	6.376864	7	60	232	44	ENST00000262848.5	0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	4333883	4333883	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:4333883T>A			NA	NA				RP11-706O15.7 (477987 upstream) : AC108683.1 (167579 downstream)						NA		NA									NA						gggttttgccttgttgcccat	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.4333883T>A		NA		hg19		0.02	-0.052622	GCCxTGT	UNCOVERED																																																																																			NOVEL					0			2	2.406148	KEEP	0	0	0	8	220	TT	0.99257	0.036492	0			3	60	89	0	1	8.869526	2	60	56	22		0.6	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	5649733	5649733	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:5649733A>T			NA	NA				RP11-733O18.1 (5387 upstream) : NLGN4X (158333 downstream)						NA		NA									NA						aggccaggagatcgagaccag	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.5649733A>T		NA		hg19		0.02	-0.140332	GAGxTCG	COVERED																																																																																			NOVEL					0			7	3.007625	KEEP	0	0	0	10	277	AA	0.992708	0.259062	0			3	60	85	0	0	6.882158	10	60	302	42		0.230769	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	6319012	6319012	__UNKNOWN__	IGR	SNP	T	T	C	rs202212471		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:6319012T>C			NA	NA				MIR4770 (17008 upstream) : VCX3A (132646 downstream)						NA		NA									NA						tcttcttctttttcttcttct	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.6319012T>C		NA		hg19		0.02	-0.210503	CTTxTTC	COVERED																																																																																			NOVEL					0			15	6.31465	KEEP	0	0	0	21	562	TT	0.999869	0.522093	0			4	60	133	0	0	10.76877	17	60	509	68		0.190476	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	6319025	6319025	__UNKNOWN__	IGR	SNP	C	C	T	rs375065381		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:6319025C>T			NA	NA				MIR4770 (17021 upstream) : VCX3A (132633 downstream)						NA		NA									NA						cttcttcttcctcttcttctt	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.6319025C>T		NA		hg19		0.02	-0.192973	TTCxTCT	COVERED																																																																																			NOVEL					0			12	2.742129	KEEP	0	1	19	16	498	CC	0.999366	0.457467	0			3	60	90	1	1	6.692707	18	60	590	57		0.142857	0.457757
VCX	26609	__UNKNOWN__	__UNKNOWN__	X	7812130	7812130	__UNKNOWN__	3'UTR	SNP	A	A	G	rs201553663		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:7812130A>G	ENST00000381059.3	+	0	913					NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	NA		NA			chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				CAGAGATCTCACCAGCGGGGT	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			AF167081	CCDS14128.1	Xp22.31	2008-02-05	2003-09-12		ENSG00000182583	ENSG00000182583	26609			12667	protein-coding gene	gene with protein product		300229	variable charge, X chromosome		NA	10607842, 10903929	Standard	NM_013452	NM_013452	NA	Approved	VCX1, VCX10R, VCX-10r, VCX-B1	uc004crz.3	Q9H320	OTTHUMG00000028608	ENST00000381059.3:c.*73A>G	chrX.hg19:g.7812130A>G		NA	A0JNS5|Q4V774|Q9P0H3	hg19	CCDS14128.1	0.02	-0.21925	CTCxCCA	UNCOVERED																																																																																			NOVEL	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000071474.1	4	2.405182	KEEP	33	0	0	8	212	AA	0	0	0		+	8	39	276	0	0	24.61248	17	47	477	95	ENST00000381059.3	0.32	0.552887
KAL1	3730	__UNKNOWN__	__UNKNOWN__	X	8529741	8529741	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:8529741A>G	ENST00000262648.3	-	8	1357					NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	NA		NA			axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						tcccaccttgacctcccaaat	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201	3730		WAP four-disulfide core domain containing, Fibronectin type III domain containing	6211	protein-coding gene	gene with protein product	anosmin-1, WAP four-disulfide core domain 19	300836		KAL, ADMLX	NA	11463336	Standard	NM_000216	NM_000216	NA	Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1207+6531T>C	chrX.hg19:g.8529741A>G		NA	B2RPF8	hg19	CCDS14130.1	0.02	-0.105207	TTGxCCT	UNCOVERED																																																																																			NOVEL	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055692.1	5	3.004372	KEEP	0	0	0	10	249	AA	0.992708	0.138812	0		-	3	60	103	0	0	9.07975	7	60	187	27	ENST00000262648.3	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	9277273	9277273	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:9277273T>G			NA	NA				GS1-519E5.1 (34027 upstream) : TBL1X (154061 downstream)						NA		NA									NA						agtggctcactcctgtaatcc	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.9277273T>G		NA		hg19		0.02	-0.0614	CACxCCT	UNCOVERED																																																																																			NOVEL					0			6	2.706582	KEEP	1	0	0	9	244	AT	0.993072	0.053762	0			2	60	70	0	0	6.49309	3	60	86	28		0.4	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	9739075	9739075	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:9739075G>A			NA	NA				GPR143 (5070 upstream) : SHROOM2 (15420 downstream)						NA		NA									NA						tcatgcctgtgatcccagcac	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.9739075G>A		NA		hg19		0.02	-0.105247	TGTxATC	UNCOVERED																																																																																			NOVEL					0			8	2.707126	KEEP	0	0	0	9	279	CG	0.992708	0.138812	0			4	60	114	0	0	9.990012	8	60	276	29		0.333333	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	10209886	10209886	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:10209886C>T			NA	NA				CLCN4 (4186 upstream) : RP6-1O2.1 (492 downstream)						NA		NA									NA						ccagcctgggcaacagagcga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.10209886C>T		NA		hg19		0.02	-0.122798	GGGxAAC	UNCOVERED																																																																																			NOVEL					0			7	2.406981	KEEP	4	0	0	8	243	CC	0	0	0			3	28	86	0	0	7.101042	9	60	285	34		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	13086569	13086569	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:13086569T>C			NA	NA				FAM9C (23768 upstream) : RP11-791M20.1 (25209 downstream)						NA		NA									NA						caccactgcattccagcctgg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.13086569T>C		NA		hg19		0.02	-0.122791	GCAxTCC	COVERED																																																																																			NOVEL					0			9	4.508602	KEEP	0	0	0	15	389	TT	0.99649	0.195623	0			4	60	138	0	0	12.39184	8	60	235	40		0.333333	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	13131077	13131077	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:13131077T>C			NA	NA				RP11-791M20.1 (18385 upstream) : GS1-600G8.5 (153089 downstream)						NA		NA									NA						tgcagtggcgtgatctcggct	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.13131077T>C		NA		hg19		0.02	-0.114007	GCGxGAT	UNCOVERED																																																																																			NOVEL					0			5	3.005544	KEEP	1	0	0	10	266	TT	0.992708	0.161282	0			3	60	94	0	0	8.032732	8	60	226	34		0.272727	0.162467
TRAPPC2	6399	__UNKNOWN__	__UNKNOWN__	X	13740921	13740921	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:13740921G>A	ENST00000380579.1	-	3	174				TRAPPC2_ENST00000519885.1_Intron|TRAPPC2_ENST00000458511.2_Intron|TRAPPC2_ENST00000453655.2_Intron|TRAPPC2_ENST00000359680.5_Intron|TRAPPC2_ENST00000358231.5_Intron			P0DI81	TPC2A_HUMAN	trafficking protein particle complex 2	NA		NA			ER to Golgi vesicle-mediated transport (GO:0006888)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ion channel binding (GO:0044325)|transcription factor binding (GO:0008134)			kidney(1)	1						ggtggctcacgcctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF157061	CCDS48082.1, CCDS48083.1, CCDS48083.2	Xp22	2011-10-10	2005-01-26		ENSG00000196459	ENSG00000196459	6399		Trafficking protein particle complex	23068	protein-coding gene	gene with protein product		300202	spondyloepiphyseal dysplasia, late	SEDL	NA	14597397	Standard	NM_014563	NM_014563	NA	Approved	TRS20, SEDT, MIP-2A, ZNF547L, hYP38334	uc010nej.2	P0DI81	OTTHUMG00000021157	ENST00000380579.1:c.19-2820C>T	chrX.hg19:g.13740921G>A		NA	A6NEG0|O14582|Q9HD16	hg19	CCDS48082.1	0.02	-0.165295	CACxCCT	COVERED																																																																																			NOVEL	TRAPPC2-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055805.2	8	3.910453	KEEP	7	0	0	13	377	GG	0.992708	0.351366	0		-	3	60	84	0	0	6.324387	15	60	462	52	ENST00000380579.1	0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	15688136	15688136	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:15688136T>C			NA	NA				TMEM27 (4982 upstream) : CA5BP1 (5532 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.15688136T>C		NA		hg19		0.02	-0.122786	TCAxGCC	COVERED																																																																																			NOVEL					0			8	3.007262	KEEP	0	0	0	10	271	TT	0.992708	0.19488	0			3	60	92	0	0	7.701256	9	60	270	33		0.25	0.196312
CTPS2	56474	__UNKNOWN__	__UNKNOWN__	X	16708323	16708323	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:16708323A>G	ENST00000443824.1	-	8	1464				CTPS2_ENST00000380241.3_Intron|CTPS2_ENST00000359276.4_Intron	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	NA		NA			'de novo' CTP biosynthetic process (GO:0044210)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|CTP synthase activity (GO:0003883)			breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Hepatocellular(33;0.0997)					gtgaaaccccatctctactaa	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF086422	CCDS14175.1	Xp22	2012-05-02	2012-05-02		ENSG00000047230	ENSG00000047230	56474	6.3.4.2		2520	protein-coding gene	gene with protein product		300380	CTP synthase II		NA	10899599	Standard	NM_019857	NM_001144002	NA	Approved		uc004cxm.3	Q9NRF8	OTTHUMG00000021193	ENST00000443824.1:c.721-599T>C	chrX.hg19:g.16708323A>G		NA	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	hg19	CCDS14175.1	0.02	-0.070159	CCCxTCT	UNCOVERED																																																																																			NOVEL	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055906.1	4	2.404574	KEEP	2	0	0	8	205	AA	0	0	0		-	3	60	88	0	0	7.932748	5	60	146	21	ENST00000443824.1	0.375	0.054137
MAP3K15	389840	__UNKNOWN__	__UNKNOWN__	X	19415962	19415962	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:19415962A>G	ENST00000359173.3	-	12	1394				MAP3K15_ENST00000518578.1_Intron|MAP3K15_ENST00000469203.2_Intron|MAP3K15_ENST00000338883.4_Intron			Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	NA		NA					ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					ttgggaggccaaggcgggcag	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815	389840		Mitogen-activated protein kinase cascade / Kinase kinase kinases	31689	protein-coding gene	gene with protein product		300820			NA		Standard	NM_001001671	NM_001001671	NA	Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000359173.3:c.371+381T>C	chrX.hg19:g.19415962A>G		NA	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	hg19		0.02	-0.061397	GCCxAGG	UNCOVERED																																																																																			NOVEL	MAP3K15-004	PUTATIVE	basic	protein_coding	NA	protein_coding	OTTHUMT00000286445.2	4	3.307527	KEEP	5	0	0	11	296	AA	0.99257	0.043461	0		-	3	60	97	0	0	9.325228	3	60	86	30	ENST00000359173.3	0.5	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	19550498	19550498	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:19550498T>C			NA	NA				MAP3K15 (17119 upstream) : SH3KBP1 (1594 downstream)						NA		NA									NA						ctttgggaggtcgaggcgggc	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.19550498T>C		NA		hg19		0.02	-0.087709	AGGxCGA	UNCOVERED																																																																																			NOVEL					0			8	2.402921	KEEP	7	0	0	8	199	TT	0	0	0			3	60	95	0	0	8.443594	6	60	181	34		0.333333	0.099721
SH3KBP1	30011	__UNKNOWN__	__UNKNOWN__	X	19689037	19689037	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:19689037C>T	ENST00000397821.3	-	6	1017				SH3KBP1_ENST00000379698.4_Intron|SH3KBP1_ENST00000379716.1_5'UTR|SH3KBP1_ENST00000379697.3_Intron	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	NA		NA			apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						TCCCAGAACTCCCCTGGAATC	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													9	8	8			NA	NA	X		NA											NA				19689037		865	1969	2834	SO:0001627	intron_variant			AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010	30011			13867	protein-coding gene	gene with protein product		300374			NA	8889549, 7566098	Standard	NM_031892	NM_031892	NA	Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.726+12903G>A	chrX.hg19:g.19689037C>T		NA	B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	hg19	CCDS14193.1	0.02	1.359524	ACTxCCC	COVERED																																																																																			NOVEL	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000055992.1	94	47.53535	KEEP	0	0	0	158	4691	CC	1	0.997553	0		-	4	60	124	0	0	7.682056	65	60	2155	307	ENST00000397821.3	0.057971	0.997553
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	20926165	20926165	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:20926165A>G			NA	NA				RN7SKP183 (455616 upstream) : RNU6-133P (306589 downstream)						NA		NA									NA						gattacaggcatgagccactg	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.20926165A>G		NA		hg19		0.02	-0.026307	GGCxTGA	UNCOVERED																																																																																			NOVEL					0			5	3.307571	KEEP	3	0	0	11	298	AA	0.992708	0	0			2	60	67	0	0	6.825769	1	60	24	23		0.666667	0
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	23806025	23806025	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:23806025A>T			NA	NA				SAT1 (1682 upstream) : APOO (45444 downstream)						NA		NA									NA						ggtcttgctaagttgcccagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.23806025A>T		NA		hg19		0.02	-0.122797	CTAxGTT	COVERED																																																																																			NOVEL					0			6	3.308483	KEEP	0	0	0	11	310	AA	0.993072	0.194952	0			3	60	87	0	0	7.082022	10	60	309	37		0.230769	0.196312
EIF2S3	1968	__UNKNOWN__	__UNKNOWN__	X	24095225	24095225	__UNKNOWN__	3'UTR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:24095225G>T	ENST00000253039.4	+	0	1995					NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	NA		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						tttTgagtctggctctgtcac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741	1968			3267	protein-coding gene	gene with protein product	eukaryotic translation initiation factor 2G	300161	eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)	EIF2G	NA	8106381, 9736774	Standard	NM_001415	NM_001415	NA	Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.*323G>T	chrX.hg19:g.24095225G>T		NA	B5BTZ4	hg19	CCDS14210.1	0.02	-0.298246	TCTxGCT	COVERED																																																																																			NOVEL	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056079.1	6	3.945499	KEEP	1	1	31	24	738	CG	0.999997	0.818462	0		+	4	60	127	2	0	9.374291	28	60	915	84	ENST00000253039.4	0.125	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	24101388	24101388	__UNKNOWN__	IGR	SNP	G	G	A	rs144587094		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:24101388G>A			NA	NA				EIF2S3 (5300 upstream) : SNORA68 (49914 downstream)						NA		NA									NA						TAGCAGggccgggcgcggtgg	0.498		NA											-|||	1675	0.443709	0.3336	0.4784	3775	,	,	NA	8686	0.256	NA	0.5219	False	NA	,,,	NA	NA	NA	2504	0.1217	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.24101388G>A		NA		hg19		0.02	-0.078943	GCCxGGC	UNCOVERED																																																																																			NOVEL					0			4	3.007564	KEEP	9	0	0	10	282	GG	0	0	0			3	60	92	0	0	8.5549	4	60	130	32		0.428571	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	24255210	24255210	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:24255210C>T			NA	NA				ZFX (20838 upstream) : AC096509.1 (49451 downstream)						NA		NA									NA						ggattacaggcgtgagccacc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.24255210C>T		NA		hg19		0.02	-0.140353	AGGxGTG	COVERED																																																																																			NOVEL					0			8	4.206769	KEEP	6	0	0	14	391	CC	0.993072	0.259157	0			3	60	92	0	0	7.372159	12	60	407	49		0.2	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	24313999	24313999	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:24313999T>C			NA	NA				AC096509.1 (9205 upstream) : AC004552.1 (52926 downstream)						NA		NA									NA						cggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.24313999T>C		NA		hg19		0.02	-0.052617	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			4	2.405539	KEEP	0	0	0	8	216	TT	0.99257	0.036492	0			2	60	70	0	0	6.750534	2	60	54	20		0.5	0.036766
POLA1	5422	__UNKNOWN__	__UNKNOWN__	X	24748378	24748378	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:24748378T>G	ENST00000379059.3	+	16	1683				POLA1_ENST00000379068.3_Intron|POLA1_ENST00000493342.1_Intron	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	NA		NA			cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	ttttttgagatggagtcttgc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	5422	2.7.7.7	DNA polymerases	9173	protein-coding gene	gene with protein product		312040	polymerase (DNA directed), alpha, polymerase (DNA directed), alpha 1, N syndrome (mental retardation, malformations, chromosome breakage)	POLA, NSX	NA	1689958	Standard	NM_016937	NM_016937	NA	Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.1669-2109T>G	chrX.hg19:g.24748378T>G		NA	Q86UQ7	hg19	CCDS14214.1	0.02	-0.07017	AGAxGGA	UNCOVERED																																																																																			NOVEL	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056111.1	4	3.308094	KEEP	0	0	0	11	298	TT	0.993072	0.053762	0		+	2	60	72	0	0	6.335792	5	60	146	31	ENST00000379059.3	0.285714	0.054137
POLA1	5422	__UNKNOWN__	__UNKNOWN__	X	24777054	24777054	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:24777054G>A	ENST00000379059.3	+	26	2961				POLA1_ENST00000379068.3_Intron	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	NA		NA			cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	gggattacaggcatgagccac	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	5422	2.7.7.7	DNA polymerases	9173	protein-coding gene	gene with protein product		312040	polymerase (DNA directed), alpha, polymerase (DNA directed), alpha 1, N syndrome (mental retardation, malformations, chromosome breakage)	POLA, NSX	NA	1689958	Standard	NM_016937	NM_016937	NA	Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.2946+9945G>A	chrX.hg19:g.24777054G>A		NA	Q86UQ7	hg19	CCDS14214.1	0.02	-0.114032	CAGxCAT	UNCOVERED																																																																																			NOVEL	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056111.1	6	4.245104	KEEP	12	1	25	23	692	GG	0.99649	0.161897	0		+	3	60	82	0	0	6.581925	10	60	347	66	ENST00000379059.3	0.230769	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	25045755	25045755	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:25045755T>G			NA	NA				ARX (11690 upstream) : RN7SL91P (33012 downstream)						NA		NA									NA						ggaggtggagtttgcagtgag	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.25045755T>G		NA		hg19		0.02	-0.10515	GAGxTTG	COVERED																																																																																			NOVEL					0			14	3.909033	KEEP	5	0	0	13	348	TT	0.994391	0.227888	0			3	54	93	0	0	8.435768	5	60	130	42		0.375	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	25094070	25094070	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:25094070T>C			NA	NA				RN7SL91P (15014 upstream) : AC112778.1 (130416 downstream)						NA		NA									NA						cgtgagccactgcgcccggcc	0.572		NA											C|||	1	0.000264901	0.0	0.0	3775	,	,	NA	12786	0.0	NA	0.001	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.25094070T>C		NA		hg19		0.02	-0.140332	CACxGCG	COVERED																																																																																			NOVEL					0			4	3.007918	KEEP	0	0	0	10	281	TT	0.992708	0.259062	0			3	60	106	0	0	8.678787	13	60	389	39		0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	25108542	25108542	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:25108542T>C			NA	NA				RN7SL91P (29486 upstream) : AC112778.1 (115944 downstream)						NA		NA									NA						gcctcggccttccaaagtgct	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.25108542T>C		NA		hg19		0.02	-0.070172	CCTxCCA	UNCOVERED																																																																																			NOVEL					0			10	3.909491	KEEP	3	0	0	13	358	TT	0.993072	0.053762	0			3	60	101	0	0	9.455308	4	60	124	31		0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	25544461	25544461	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:25544461T>C			NA	NA				AC112778.1 (319884 upstream) : RP11-86A5.1 (351994 downstream)						NA		NA									NA						tgagccaccgtgcccggccac	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.25544461T>C		NA		hg19		0.02	-0.157869	CCGxGCC	COVERED																																																																																			NOVEL					0			8	5.111933	KEEP	0	0	0	17	456	TT	0.999366	0.322602	0			3	60	101	0	1	8.091801	14	60	409	51		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	26231998	26231998	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:26231998A>T			NA	NA				MAGEB6 (18235 upstream) : MAGEB5 (2287 downstream)						NA		NA									NA						ctgggattacaggcgtgagcc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.26231998A>T		NA		hg19		0.02	-0.175397	TACxGGC	COVERED																																																																																			NOVEL					0			9	5.112853	KEEP	11	0	0	17	468	AA	0.994391	0.385234	0			3	28	89	0	0	6.734108	16	60	464	63		0.157895	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	26232002	26232002	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:26232002G>A			NA	NA				MAGEB6 (18239 upstream) : MAGEB5 (2283 downstream)						NA		NA									NA						gattacaggcgtgagccaccg	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.26232002G>A		NA		hg19		0.02	-0.16665	GGCxTGA	COVERED																																																																																			NOVEL					0			7	4.813608	KEEP	10	0	0	16	476	GG	0.993634	0.38494	0			3	60	89	0	0	6.892128	14	60	437	59		0.176471	0.387407
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	26968388	26968388	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:26968388T>C			NA	NA				RNU1-142P (159985 upstream) : RP11-268G12.3 (178533 downstream)						NA		NA									NA						tggctcacgcttgtaatccca	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.26968388T>C		NA		hg19		0.02	-0.052632	CGCxTGT	UNCOVERED																																																																																			NOVEL					0			5	2.406512	KEEP	1	0	0	8	227	TT	0.99257	0.036492	0			2	60	70	0	0	7.124886	1	60	32	21		0.666667	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	27556737	27556737	__UNKNOWN__	IGR	SNP	C	C	G	rs142057113		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:27556737C>G			NA	NA				RP11-268G12.1 (139623 upstream) : DCAF8L2 (51762 downstream)						NA		NA									NA						tctcaaactcctgacctcgtg	0.507		NA											C|||	705	0.186755	0.1876	0.0648	3775	,	,	NA	9976	0.2708	NA	0.0895	False	NA	,,,	NA	NA	NA	2504	0.0501	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.27556737C>G		NA		hg19		0.02	-0.184223	CTCxTGA	COVERED																																																																																			NOVEL					0			18	2.54146	KEEP	16	1	30	19	588	CC	0.994391	0.421102	0			4	60	127	0	0	10.580686	13	60	456	73		0.235294	0.423478
IL1RAPL1	11141	__UNKNOWN__	__UNKNOWN__	X	28754333	28754333	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:28754333A>G	ENST00000378993.1	+	2	649					NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	NA		NA			calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						ggcagatcacaaggtcaggag	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306	11141		Interleukins and interleukin receptors, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	5996	protein-coding gene	gene with protein product		300206	mental retardation, X-linked 34, mental retardation, X-linked 21, mental retardation, X-linked 10	IL1RAPL, MRX34, MRX21, MRX10	NA	10471494, 10757639	Standard	NM_014271	NM_014271	NA	Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.-24-53104A>G	chrX.hg19:g.28754333A>G		NA	A0AVG4|Q9UJ53	hg19	CCDS14218.1	0.02	-0.122782	CACxAGG	UNCOVERED																																																																																			NOVEL	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056155.1	5	2.706921	KEEP	4	0	0	9	249	AA	0	0	0		+	3	39	98	0	0	8.073053	11	60	314	38	ENST00000378993.1	0.214286	0.196312
IL1RAPL1	11141	__UNKNOWN__	__UNKNOWN__	X	29819126	29819126	__UNKNOWN__	Intron	SNP	A	A	C	rs7884114		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:29819126A>C	ENST00000378993.1	+	7	1451				IL1RAPL1_ENST00000302196.4_Intron	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	NA		NA			calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						tcaaaaaaaaaaaaaaaaaaa	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306	11141		Interleukins and interleukin receptors, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	5996	protein-coding gene	gene with protein product		300206	mental retardation, X-linked 34, mental retardation, X-linked 21, mental retardation, X-linked 10	IL1RAPL, MRX34, MRX21, MRX10	NA	10471494, 10757639	Standard	NM_014271	NM_014271	NA	Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.779-116455A>C	chrX.hg19:g.29819126A>C		NA	A0AVG4|Q9UJ53	hg19	CCDS14218.1	0.02	-0.061197	AAAxAAA	UNCOVERED																																																																																			NOVEL	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056155.1	18	4.508075	KEEP	13	0	0	15	397	AA	0.99254	0.04346	0		+	5	60	143	0	0	14.843161	2	10	53	35	ENST00000378993.1	0.714286	0.043787
IL1RAPL1	11141	__UNKNOWN__	__UNKNOWN__	X	29819135	29819135	__UNKNOWN__	Intron	SNP	A	A	C	rs7884244		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:29819135A>C	ENST00000378993.1	+	7	1451				IL1RAPL1_ENST00000302196.4_Intron	NM_014271.3	NP_055086.1	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	NA		NA			calcium ion transmembrane transport (GO:0070588)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of exocytosis (GO:0045920)|neuron differentiation (GO:0030182)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor binding (GO:0005102)|voltage-gated calcium channel activity (GO:0005245)			biliary_tract(1)|breast(1)|endometrium(5)|large_intestine(9)|lung(38)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62						aaaaaaaaaaaaaaaaaaaaa	0.323		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ243874	CCDS14218.1	Xp22.1-p21.3	2013-01-29	2004-02-13		ENSG00000169306	ENSG00000169306	11141		Interleukins and interleukin receptors, Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	5996	protein-coding gene	gene with protein product		300206	mental retardation, X-linked 34, mental retardation, X-linked 21, mental retardation, X-linked 10	IL1RAPL, MRX34, MRX21, MRX10	NA	10471494, 10757639	Standard	NM_014271	NM_014271	NA	Approved	OPHN4, TIGIRR-2, IL1R8	uc004dby.2	Q9NZN1	OTTHUMG00000021317	ENST00000378993.1:c.779-116446A>C	chrX.hg19:g.29819135A>C		NA	A0AVG4|Q9UJ53	hg19	CCDS14218.1	0.02	-0.061359	AAAxAAA	UNCOVERED																																																																																			NOVEL	IL1RAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056155.1	17	3.607913	KEEP	14	0	0	12	316	AA	0	0	0		+	5	60	145	0	0	15.061102	2	10	59	31	ENST00000378993.1	0.714286	0.043787
DMD	1756	__UNKNOWN__	__UNKNOWN__	X	31357766	31357766	__UNKNOWN__	Intron	SNP	C	C	T	rs34011235	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:31357766C>T	ENST00000357033.4	-	61	9370				DMD_ENST00000359836.1_Intron|DMD_ENST00000474231.1_Intron|DMD_ENST00000541735.1_Intron|DMD_ENST00000343523.2_Intron|DMD_ENST00000378677.2_Intron|DMD_ENST00000378707.3_Intron	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	NA		NA			cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				aatctcggctcactgcaacct	0.473		NA											C|||	258	0.0683444	0.0794	0.013	3775	,	,	NA	13505	0.0873	NA	0.0308	False	NA	,,,	NA	NA	NA	2504	0.0256	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947	1756			2928	protein-coding gene	gene with protein product	muscular dystrophy, Duchenne and Becker types	300377	dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272, mental retardation, X-linked 85	MRX85	NA	3282674, 3607877, 23900271	Standard	NM_004006	NM_004019	NA	Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.9163+8906G>A	chrX.hg19:g.31357766C>T		NA	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	hg19	CCDS14233.1	0.02	-0.052602	GCTxACT	UNCOVERED																																																																																			NOVEL	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056182.2	8	2.707939	KEEP	2	0	0	9	272	CC	0	0	0		-	3	60	85	0	0	8.470365	2	60	51	24	ENST00000357033.4	0.6	0.036766
RP11-305F18.1	0	__UNKNOWN__	__UNKNOWN__	X	33898913	33898913	__UNKNOWN__	lincRNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:33898913A>G	ENST00000439992.1	+	0	229										NA		NA									NA						gattacaggcatgagccaccg	0.463		NA											A|||	10	0.00264901	0.0	0.0	3775	,	,	NA	9436	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0102	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000439992.1:	chrX.hg19:g.33898913A>G		NA		hg19		0.02	-0.114008	GGCxTGA	UNCOVERED																																																																																			NOVEL	RP11-305F18.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000056203.1	8	3.307929	KEEP	8	0	0	11	299	AA	0	0	0		+	3	60	101	0	0	8.601379	9	60	258	41	ENST00000439992.1	0.25	0.162467
LANCL3	347404	__UNKNOWN__	__UNKNOWN__	X	37506551	37506551	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:37506551G>A	ENST00000378619.3	+	2	792				LANCL3_ENST00000378621.3_Intron|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	NA		NA					catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						tgggcgacagggcaagacttc	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036	347404			24767	protein-coding gene	gene with protein product		NA			NA		Standard	NM_198511	NM_198511	NA	Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.574-8390G>A	chrX.hg19:g.37506551G>A		NA	A6NHE3	hg19	CCDS55398.1	0.02	-0.035087	CAGxGCA	UNCOVERED																																																																																			NOVEL	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080885.1	1	2.407301	KEEP	0	0	0	8	249	GG	0.99257	0.019833	0		+	2	60	62	0	0	6.324532	1	60	31	19	ENST00000378619.3	0.666667	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	39891227	39891227	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:39891227G>T			NA	NA				AC092198.1 (19792 upstream) : BCOR (17840 downstream)						NA		NA									NA						cccagctaatgtttgcatttt	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.39891227G>T		NA		hg19		0.02	-0.070169	AATxTTT	UNCOVERED																																																																																			NOVEL					0			4	2.70804	KEEP	0	0	0	9	275	AG	0.992708	0.053742	0			3	60	84	0	0	7.531899	5	60	173	23		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	40213335	40213335	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:40213335A>G			NA	NA				RP11-320G24.1 (66362 upstream) : Y_RNA (138756 downstream)						NA		NA									NA						tatgcctgtaatcccagcact	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.40213335A>G		NA		hg19		0.02	-0.1228	GTAxTCC	COVERED																																																																																			NOVEL					0			8	2.706327	KEEP	1	0	0	9	242	AA	0.99254	0.227464	0			3	60	105	0	0	9.443751	6	60	182	35		0.333333	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	40432028	40432028	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:40432028A>G			NA	NA				RNU7-164P (37213 upstream) : ATP6AP2 (8117 downstream)						NA		NA									NA						ggtggctcacacctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.40432028A>G		NA		hg19		0.02	-0.210103	CACxCCT	COVERED																																																																																			NOVEL					0			13	4.809928	KEEP	0	0	0	16	422	AA	0.997832	0.521029	0			4	60	128	0	0	10.183903	18	60	476	51		0.181818	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	41147007	41147007	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:41147007T>C			NA	NA				RP5-1172N10.2 (10976 upstream) : RNA5SP502 (5043 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.41147007T>C		NA		hg19		0.02	-0.157869	TCAxGCC	COVERED																																																																																			NOVEL					0			12	3.308398	KEEP	7	0	0	11	306	TT	0.993072	0.32057	0			3	60	91	0	0	7.179161	13	60	384	53		0.1875	0.322807
NYX	60506	__UNKNOWN__	__UNKNOWN__	X	41309803	41309803	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:41309803T>C	ENST00000342595.2	+	1	493				NYX_ENST00000378220.1_Intron	NM_022567.2	NP_072089.1	Q9GZU5	NYX_HUMAN	nyctalopin	NA		NA			response to stimulus (GO:0050896)|visual perception (GO:0007601)	intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(11)|upper_aerodigestive_tract(1)	17						ggattacaggtgtgagccacc	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF254868	CCDS14256.1	Xp11.4	2014-01-28			ENSG00000188937	ENSG00000188937	60506			8082	protein-coding gene	gene with protein product		300278		CSNB1, CSNB4	NA	11062471, 11062472	Standard	NM_022567	NM_022567	NA	Approved	CLRP, CSNB1A	uc004dfh.2	Q9GZU5	OTTHUMG00000021370	ENST00000342595.2:c.37+2624T>C	chrX.hg19:g.41309803T>C		NA	D3DWC0|Q2M1S4|Q5H983|Q9H4J0	hg19	CCDS14256.1	0.02	-0.149099	AGGxGTG	COVERED																																																																																			NOVEL	NYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056256.1	6	3.007639	KEEP	2	0	0	10	275	TT	0.99254	0.289823	0		+	3	60	97	0	0	7.972985	11	60	325	37	ENST00000342595.2	0.214286	0.292001
CASK	8573	__UNKNOWN__	__UNKNOWN__	X	41487682	41487682	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:41487682A>G	ENST00000421587.2	-	10	939				CASK_ENST00000378166.4_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron	NM_001126055.2	NP_001119527.1	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	NA		NA			calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						tcagtctcccaagtagctggg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(42;104 1086 3090 27189 35040)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044	8573			1497	protein-coding gene	gene with protein product		300172	trinucleotide repeat containing 8	TNRC8	NA	9722958	Standard	NM_003688	NM_003688	NA	Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000421587.2:c.916-1726T>C	chrX.hg19:g.41487682A>G		NA	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	hg19	CCDS48094.1	0.02	-0.131536	CCCxAGT	COVERED																																																																																			NOVEL	CASK-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056282.1	7	4.811255	KEEP	0	0	0	16	429	AA	0.997832	0.228676	0		-	3	21	93	1	0	7.682453	10	60	278	38	ENST00000421587.2	0.230769	0.229173
CASK	8573	__UNKNOWN__	__UNKNOWN__	X	41700837	41700837	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:41700837T>C	ENST00000421587.2	-	2	196				CASK_ENST00000378158.1_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron	NM_001126055.2	NP_001119527.1	O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	NA		NA			calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						ggcatgatcttggctcactgc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(42;104 1086 3090 27189 35040)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044	8573			1497	protein-coding gene	gene with protein product		300172	trinucleotide repeat containing 8	TNRC8	NA	9722958	Standard	NM_003688	NM_003688	NA	Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000421587.2:c.172+11530A>G	chrX.hg19:g.41700837T>C		NA	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	hg19	CCDS48094.1	0.02	-0.228044	TCTxGGC	COVERED																																																																																			NOVEL	CASK-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056282.1	3	2.337397	KEEP	1	1	23	16	438	TT	0.999366	0.582561	0		-	4	60	120	0	0	9.137298	21	60	642	55	ENST00000421587.2	0.16	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	42069851	42069851	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:42069851G>C			NA	NA				RNU6-1124P (36213 upstream) : RP1-154K9.2 (41860 downstream)						NA		NA									NA						ggatgatctcgatctcctgac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.42069851G>C		NA		hg19		0.02	-0.114032	CTCxATC	UNCOVERED																																																																																			NOVEL					0			10	3.610055	KEEP	6	0	0	12	360	GG	0.993634	0.161432	0			4	22	139	0	0	12.324033	9	60	279	46		0.307692	0.162467
RP3-326I13.1	0	__UNKNOWN__	__UNKNOWN__	X	43057375	43057375	__UNKNOWN__	lincRNA	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:43057375T>C	ENST00000440955.1	+	0	577										NA		NA									NA						tggtggctcatgcctgtaatc	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000440955.1:	chrX.hg19:g.43057375T>C		NA		hg19		0.02	-0.210492	TCAxGCC	COVERED																																																																																			NOVEL	RP3-326I13.1-001	KNOWN	basic	lincRNA	NA	lincRNA	OTTHUMT00000056297.1	5	2.70709	KEEP	1	0	0	9	251	TT	0.99254	0.518266	0		+	4	60	132	0	0	10.494601	19	60	560	53	ENST00000440955.1	0.173913	0.522161
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	44470665	44470665	__UNKNOWN__	IGR	SNP	A	A	G	rs112204246		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:44470665A>G			NA	NA				AL136137.1 (33981 upstream) : RN7SL291P (161355 downstream)						NA		NA									NA						cagcctgggcaacaaagcaag	0.498		NA											N|||	34	0.00900662	0.0045	0.0086	3775	,	,	NA	13830	0.0	NA	0.0169	False	NA	,,,	NA	NA	NA	2504	0.0051	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.44470665A>G		NA		hg19		0.02	-0.052631	GGCxACA	UNCOVERED																																																																																			NOVEL					0			3	2.706943	KEEP	0	0	0	9	251	AA	0.99254	0.036491	0			3	60	99	0	0	9.869703	2	60	62	20		0.6	0.036766
RP11-342D14.1	0	__UNKNOWN__	__UNKNOWN__	X	45131333	45131333	__UNKNOWN__	RNA	SNP	G	G	A	rs182100635		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:45131333G>A	ENST00000450527.1	+	0	94				RP11-342D14.1_ENST00000438181.1_RNA						NA		NA									NA						ggaaggtctcgatctcctgac	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000450527.1:	chrX.hg19:g.45131333G>A		NA		hg19		0.02	-0.061265	CTCxATC	UNCOVERED																																																																																			NOVEL	RP11-342D14.1-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000056337.1	4	2.405408	KEEP	2	0	0	8	212	GG	0	0	0		+	3	60	81	0	0	7.458136	4	60	108	24	ENST00000450527.1	0.428571	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	46054727	46054727	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:46054727A>T			NA	NA				RP5-1158E12.1 (278252 upstream) : RP1-30G7.2 (130631 downstream)						NA		NA									NA						gctacttgggaggctgaggca	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.46054727A>T		NA		hg19		0.02	-0.140336	GGGxGGC	UNCOVERED																																																																																			NOVEL					0			6	2.405829	KEEP	6	0	0	8	218	AA	0	0	0			5	40	147	0	0	12.938825	10	60	308	39		0.333333	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	46621712	46621712	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:46621712A>G			NA	NA				SLC9A7 (3222 upstream) : RP2 (74662 downstream)						NA		NA									NA						tgtaatcccaacattttggga	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.46621712A>G		NA		hg19		0.02	-0.140344	CCAxCAT	COVERED																																																																																			NOVEL					0			7	3.007986	KEEP	0	0	0	10	281	AA	0.992708	0.259062	0			3	60	99	0	0	8.072133	12	60	371	35		0.2	0.260965
PHF16	0	__UNKNOWN__	__UNKNOWN__	X	46782830	46782830	__UNKNOWN__	Intron	SNP	T	T	C	rs200848620		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:46782830T>C	ENST00000218343.4	+	1	287				PHF16_ENST00000397189.1_Intron	NM_014735.3	NP_055550.1				NA		NA								NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CTCTCTCTCtttttttttttt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000218343.4:c.-12+10676T>C	chrX.hg19:g.46782830T>C		NA		hg19	CCDS14271.1	0.02	-0.043853	TCTxTTT	UNCOVERED																																																																																			NOVEL	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056376.1	8	2.405361	KEEP	5	0	0	8	210	TT	0	0	0		+	5	60	155	0	0	17.883228	0	0	0	16	ENST00000218343.4	1	0.024074
PHF16	0	__UNKNOWN__	__UNKNOWN__	X	46782832	46782832	__UNKNOWN__	Intron	SNP	T	T	C	rs201867035		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:46782832T>C	ENST00000218343.4	+	1	287				PHF16_ENST00000397189.1_Intron	NM_014735.3	NP_055550.1				NA		NA								NS(2)|endometrium(8)|kidney(4)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(2)	33						CTCTCTCtttttttttttttt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant											NA			NA				NA			NA					NA						ENST00000218343.4:c.-12+10678T>C	chrX.hg19:g.46782832T>C		NA		hg19	CCDS14271.1	0.02	-0.026301	TTTxTTT	UNCOVERED																																																																																			NOVEL	PHF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056376.1	8	2.405792	KEEP	6	0	0	8	215	TT	0	0	0		+	3	60	84	0	0	9.828366	0	0	0	14	ENST00000218343.4	1	0
ZNF157	7712	__UNKNOWN__	__UNKNOWN__	X	47268991	47268991	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:47268991C>G	ENST00000377073.3	+	2	158					NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	NA		NA			negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						atccgcctgcctcggcctccc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117	7712		Zinc fingers, C2H2-type, -	12942	protein-coding gene	gene with protein product		300024	zinc finger protein 157 (HZF22)		NA	8586441	Standard	NM_003446	NM_003446	NA	Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.73-684C>G	chrX.hg19:g.47268991C>G		NA	Q96LE9	hg19	CCDS14278.1	0.02	-0.08772	TGCxTCG	UNCOVERED																																																																																			NOVEL	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056415.1	5	3.610271	KEEP	0	0	0	12	361	CC	0.993634	0.099086	0		+	4	60	120	0	0	11.498967	4	60	145	35	ENST00000377073.3	0.5	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	47391010	47391010	__UNKNOWN__	IGR	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:47391010A>C			NA	NA				CXorf24 (46803 upstream) : ARAF (29505 downstream)						NA		NA									NA						cggaggttgcagtgagctgag	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.47391010A>C		NA		hg19		0.02	-0.043861	TGCxGTG	UNCOVERED																																																																																			NOVEL					0			6	2.405934	KEEP	0	0	0	8	218	AA	0.99257	0.023895	0			2	33	69	0	0	6.392871	3	60	95	14		0.4	0.024074
ZNF630	57232	__UNKNOWN__	__UNKNOWN__	X	47924634	47924634	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:47924634A>G	ENST00000276054.4	-	2	582				ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000442455.3_Intron|ZNF630_ENST00000409324.3_Intron			Q2M218	ZN630_HUMAN	zinc finger protein 630	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						tgtaatcccaacactttggga	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994	57232		Zinc fingers, C2H2-type, -	28855	protein-coding gene	gene with protein product		300819			NA		Standard	NM_001037735	NM_001037735	NA	Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000276054.4:c.352+1625T>C	chrX.hg19:g.47924634A>G		NA	F8WAG4|Q5H8Z5	hg19		0.02	-0.157861	CCAxCAC	COVERED																																																																																			NOVEL	ZNF630-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000056456.2	6	3.00765	KEEP	3	0	0	10	278	AA	0.99254	0.320398	0		-	3	60	102	0	1	8.278973	13	60	380	45	ENST00000276054.4	0.1875	0.322807
ZNF630	57232	__UNKNOWN__	__UNKNOWN__	X	47927418	47927418	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:47927418T>C	ENST00000276054.4	-	2	392				ZNF630_ENST00000442455.3_Intron|ZNF630_ENST00000409324.3_Intron			Q2M218	ZN630_HUMAN	zinc finger protein 630	NA		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						ccactgcacttcagcctgggc	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994	57232		Zinc fingers, C2H2-type, -	28855	protein-coding gene	gene with protein product		300819			NA		Standard	NM_001037735	NM_001037735	NA	Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000276054.4:c.543-969A>G	chrX.hg19:g.47927418T>C		NA	F8WAG4|Q5H8Z5	hg19		0.02	1.695802	ACTxCAG	COVERED																																																																																			NOVEL	ZNF630-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000056456.2	33	6.340202	KEEP	1	4	119	63	1708	TT	1	0.999317	0		-	6	60	200	0	0	13.788317	69	60	2052	214	ENST00000276054.4	0.08	0.999317
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	47935089	47935089	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:47935089A>G			NA	NA				ZNF630 (4064 upstream) : snoU13 (6046 downstream)						NA		NA									NA						ttcaagaccaacctggacaac	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.47935089A>G		NA		hg19		0.02	-0.131521	CCAxCCT	UNCOVERED																																																																																			NOVEL					0			4	2.405919	KEEP	2	0	0	8	217	AA	0	0	0			3	60	88	0	0	7.182718	10	60	284	30		0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	48174802	48174802	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:48174802A>G			NA	NA				SSX9 (9188 upstream) : RP11-344N17.8 (18307 downstream)						NA		NA									NA						aggctggagtacagtggcgtg	0.373		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.48174802A>G		NA		hg19		0.02	-0.061382	AGTxCAG	UNCOVERED																																																																																			NOVEL					0			3	2.705991	KEEP	0	0	0	9	235	AA	0.99254	0.04346	0			2	60	70	0	0	6.493627	3	60	78	23		0.4	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	48330356	48330356	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:48330356T>C			NA	NA				SLC38A5 (1712 upstream) : FTSJ1 (4192 downstream)						NA		NA									NA						ggtgcagtggttcatgcctgt	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.48330356T>C		NA		hg19		0.02	-0.175411	TGGxTCA	COVERED																																																																																			NOVEL					0			6	3.308044	KEEP	0	0	0	11	300	TT	0.993072	0.384723	0			3	60	102	0	0	8.701428	9	60	261	36		0.25	0.387407
GRIPAP1	56850	__UNKNOWN__	__UNKNOWN__	X	48847974	48847974	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:48847974T>C	ENST00000376441.1	-	7	492				GRIPAP1_ENST00000376425.3_Intron|GRIPAP1_ENST00000376423.4_Intron|GRIPAP1_ENST00000376444.3_Intron	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	NA		NA				blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						TTTCCGTggctgggcacggtg	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400	56850			18706	protein-coding gene	gene with protein product		300408			NA	10896157	Standard	NM_207672	NM_020137	NA	Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.458-452A>G	chrX.hg19:g.48847974T>C		NA	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	hg19	CCDS35248.1	0.02	-0.18419	GGCxGGG	COVERED																																																																																			NOVEL	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080970.2	10	4.211107	KEEP	1	0	0	14	396	TT	0.994391	0.421102	0		-	3	60	93	0	0	7.210625	15	60	455	55	ENST00000376441.1	0.166667	0.423478
GRIPAP1	56850	__UNKNOWN__	__UNKNOWN__	X	48856716	48856716	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:48856716G>A	ENST00000376441.1	-	2	77				GRIPAP1_ENST00000376425.3_Intron|GRIPAP1_ENST00000376423.4_Intron|GRIPAP1_ENST00000376444.3_Intron	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	NA		NA				blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						ggtggaggttgcagtgagccg	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400	56850			18706	protein-coding gene	gene with protein product		300408			NA	10896157	Standard	NM_207672	NM_020137	NA	Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.43-800C>T	chrX.hg19:g.48856716G>A		NA	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	hg19	CCDS35248.1	0.02	-0.166675	GTTxCAG	UNCOVERED																																																																																			NOVEL	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080970.2	17	3.008886	KEEP	14	0	0	10	303	GG	0	0	0		-	3	28	87	2	0	6.610463	15	60	519	48	ENST00000376441.1	0.166667	0.353947
GRIPAP1	56850	__UNKNOWN__	__UNKNOWN__	X	48856721	48856721	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:48856721G>A	ENST00000376441.1	-	2	77				GRIPAP1_ENST00000376425.3_Intron|GRIPAP1_ENST00000376423.4_Intron|GRIPAP1_ENST00000376444.3_Intron	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	NA		NA				blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						aggttgcagtgagccgagatt	0.478		NA											g|||	1	0.000264901	0.0008	0.0	3775	,	,	NA	10294	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400	56850			18706	protein-coding gene	gene with protein product		300408			NA	10896157	Standard	NM_207672	NM_020137	NA	Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.43-805C>T	chrX.hg19:g.48856721G>A		NA	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	hg19	CCDS35248.1	0.02	-0.157902	AGTxAGC	UNCOVERED																																																																																			NOVEL	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080970.2	17	3.3096	KEEP	13	0	0	11	330	GG	0	0	0		-	3	28	90	2	0	6.991801	14	60	475	48	ENST00000376441.1	0.176471	0.322807
CACNA1F	778	__UNKNOWN__	__UNKNOWN__	X	49077206	49077206	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:49077206G>A	ENST00000376265.2	-	19	2429				CACNA1F_ENST00000376251.1_Intron|CACNA1F_ENST00000323022.5_Intron	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	NA		NA			axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	gaccagcctggccaacatggt	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001	778		Calcium channel subunits, Voltage-gated ion channels / Calcium channels	1393	protein-coding gene	gene with protein product		300110	Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)	CSNB2, AIED	NA	9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183	NM_005183	NA	Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.2368-223C>T	chrX.hg19:g.49077206G>A		NA	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	hg19	CCDS35253.1	0.02	-0.09648	CTGxCCA	UNCOVERED																																																																																			NOVEL	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000358157.1	7	3.30977	KEEP	5	0	0	11	336	GG	0.99254	0.119538	0		-	3	60	80	0	0	6.942477	6	60	207	30	ENST00000376265.2	0.333333	0.120436
GAGE10	643832	__UNKNOWN__	__UNKNOWN__	X	49162087	49162087	__UNKNOWN__	Intron	SNP	T	T	C	rs4996143		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:49162087T>C	ENST00000407599.3	+	3	295					NM_001098413.2	NP_001091883.2	A6NGK3	GAG10_HUMAN	G antigen 10	NA		NA								breast(1)|central_nervous_system(1)|large_intestine(1)|lung(1)	4	Ovarian(276;0.236)					tgtgtgtgtgtgtgtTAGGCA	0.488		NA											T|||	687	0.181987	0.0408	0.1556	3775	,	,	NA	32810	0.0903	NA	0.2058	False	NA	,,,	NA	NA	NA	2504	0.2321	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					Xp11.23	2010-06-03			ENSG00000215274	ENSG00000215274	102724473			30968	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001098413	XM_006710256	NA	Approved	OTTHUMG00000024136	uc010nir.1	A6NGK3	OTTHUMG00000024136	ENST00000407599.3:c.202+84T>C	chrX.hg19:g.49162087T>C		NA		hg19	CCDS43938.1	0.02	-0.052629	GTGxGTG	UNCOVERED																																																																																			NOVEL	GAGE10-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060816.1	8	2.406009	KEEP	11	0	0	8	221	TT	0	0	0		+	3	24	101	0	0	9.725324	3	27	90	28	ENST00000407599.3	0.5	0.036766
GAGE2A	729447	__UNKNOWN__	__UNKNOWN__	X	49360741	49360741	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:49360741A>G	ENST00000362097.1	+	5	411					NM_001127212.1	NP_001120684.1	Q6NT46	GAG2A_HUMAN	G antigen 2A	NA		NA								endometrium(4)	4	Ovarian(276;0.236)					AGTGACTGAAATAAATATCAA	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U19143	CCDS48114.1	Xp11.23	2009-03-17	2007-07-23	2007-07-23	ENSG00000189064	ENSG00000189064	729447			4099	protein-coding gene	gene with protein product	cancer/testis antigen family 4, member 2	300720	G antigen 2	GAGE2	NA	7544395	Standard		NM_001127212	NA	Approved	CT4.2		Q6NT46	OTTHUMG00000024143	ENST00000362097.1:c.329-573A>G	chrX.hg19:g.49360741A>G		NA		hg19	CCDS48114.1	0.02	9.917926	GAAxTAA	COVERED																																																																																			NOVEL	GAGE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060827.3	51	30.197323	KEEP	215	10	306	208	5733	AA	1	1	0		+	24	40	846	0	0	61.135815	240	42	7378	933	ENST00000362097.1	0.090909	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	53753551	53753551	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:53753551T>G			NA	NA				HUWE1 (39878 upstream) : RNA5SP505 (181936 downstream)						NA		NA									NA						ctgtcacccatgctggagtgc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.53753551T>G		NA		hg19		0.02	-0.070176	CCAxGCT	UNCOVERED																																																																																			NOVEL					0			6	2.405322	KEEP	0	0	0	8	220	TT	0.99257	0.053735	0			3	60	99	2	0	9.255264	4	60	124	21		0.428571	0.054137
FAM120C	54954	__UNKNOWN__	__UNKNOWN__	X	54154744	54154744	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:54154744A>G	ENST00000375180.2	-	9	2119				FAM120C_ENST00000328235.4_Intron	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	NA		NA					poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						tgcccgcctcagcctcccaaa	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083	54954			16949	protein-coding gene	gene with protein product		300741	chromosome X open reading frame 17	CXorf17	NA	14585507	Standard	NM_017848	XM_006724589	NA	Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.2062+4380T>C	chrX.hg19:g.54154744A>G		NA	B2RMT7	hg19	CCDS14356.1	0.02	-0.131561	CTCxGCC	COVERED																																																																																			NOVEL	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056795.2	8	3.308818	KEEP	1	0	0	11	313	AA	0.992708	0.227502	0		-	3	60	97	0	0	7.972938	11	60	329	36	ENST00000375180.2	0.214286	0.229173
FAM120C	54954	__UNKNOWN__	__UNKNOWN__	X	54165008	54165008	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:54165008T>C	ENST00000375180.2	-	5	1215				FAM120C_ENST00000328235.4_Intron	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	NA		NA					poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						acctgtaatctcagcactttg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083	54954			16949	protein-coding gene	gene with protein product		300741	chromosome X open reading frame 17	CXorf17	NA	14585507	Standard	NM_017848	XM_006724589	NA	Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.1159-1985A>G	chrX.hg19:g.54165008T>C		NA	B2RMT7	hg19	CCDS14356.1	0.02	-0.105251	ATCxCAG	UNCOVERED																																																																																			NOVEL	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056795.2	4	3.910202	KEEP	2	0	0	13	365	TT	0.994391	0.139048	0		-	3	60	98	0	0	8.578703	7	60	217	41	ENST00000375180.2	0.3	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	54427806	54427806	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:54427806G>A			NA	NA				WNK3 (43368 upstream) : TSR2 (39027 downstream)						NA		NA									NA						gagaaaccccgtctctactaa	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.54427806G>A		NA		hg19		0.02	-0.087711	CCCxTCT	UNCOVERED																																																																																			NOVEL					0			4	3.00395	KEEP	4	0	0	10	281	GG	0.99254	0.098977	0			3	40	82	0	0	7.142751	6	60	205	31		0.333333	0.099721
ITIH6	347365	__UNKNOWN__	__UNKNOWN__	X	54777547	54777547	__UNKNOWN__	Missense_Mutation	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:54777547A>C	ENST00000218436.6	-	12	3648	c.3619T>G	c.(3619-3621)Ttc>Gtc	p.F1207V		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1207		NA			hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)				NA						AGGACTAGGAACTCAAGGTAG	0.647		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													43	35	38			NA	NA	X		NA											NA				54777547		2202	4299	6501	SO:0001583	missense			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313	347365			28907	protein-coding gene	gene with protein product		NA	inter-alpha (globulin) inhibitor H5-like	ITIH5L	NA	12975309	Standard	NM_198510	NM_198510	NA	Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3619T>G	chrX.hg19:g.54777547A>C	ENSP00000218436:p.Phe1207Val	NA	A6NN03	hg19	CCDS14361.1	0.02	-0.385892	GGAxCTC	COVERED	.	.	.	.	.	.	.	.	.	.	A	11.44	1.639340	0.29157	.	.	ENSG00000102313	ENST00000218436	T	0.13901	2.55	3.58	2.39	0.29439	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	1.159910	0.06798	N	0.788213	T	0.23014	0.0556	M	0.67397	2.05	0.28729	N	0.90259	P	0.47253	0.892	P	0.48815	0.591	T	0.14282	-1.0478	10	0.54805	T	0.06	.	5.7936	0.18373	0.762:0.0:0.238:0.0	.	1207	Q6UXX5	ITH5L_HUMAN	V	1207	ENSP00000218436:F1207V	ENSP00000218436:F1207V	F	-	1	0	ITIH5L	54794272	1.000000	0.71417	0.007000	0.13788	0.685000	0.39939	3.655000	0.54460	0.200000	0.20447	0.237000	0.17872	TTC	NOVEL	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056814.2	1	3.007228	KEEP	0	0	0	10	272	AA	0.992708	0.911475	0		-	22	60	732	0	0	70.453077	22	60	621	71	ENST00000218436.6	0.5	0.918171
FAM104B	90736	__UNKNOWN__	__UNKNOWN__	X	55172431	55172431	__UNKNOWN__	3'UTR	SNP	A	A	T	rs5018686	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:55172431A>T	ENST00000477847.2	-	0	558				FAM104B_ENST00000332132.4_Intron|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_3'UTR|FAM104B_ENST00000358460.4_Intron|FAM104B_ENST00000425133.2_3'UTR	NM_001166702.1	NP_001160174.1	Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	NA		NA								endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						TAAAATGTAGACTTAAAAACC	0.313		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518	90736			25085	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 44	CXorf44	NA	12477932	Standard	NM_138362	NM_138362	NA	Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000477847.2:c.*86T>A	chrX.hg19:g.55172431A>T		NA	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	hg19	CCDS55423.1	0.02	1.129145	TAGxCTT	COVERED																																																																																			NOVEL	FAM104B-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056853.2	4	5.41035	KEEP	0	0	0	18	471	AA	0.999859	0.999585	0		-	12	60	330	0	0	25.596253	49	60	1498	138	ENST00000477847.2	0.196721	0.999726
FAM104B	90736	__UNKNOWN__	__UNKNOWN__	X	55172509	55172509	__UNKNOWN__	3'UTR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:55172509C>A	ENST00000477847.2	-	0	480				FAM104B_ENST00000332132.4_Intron|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_3'UTR|FAM104B_ENST00000358460.4_Intron|FAM104B_ENST00000425133.2_3'UTR	NM_001166702.1	NP_001160174.1	Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	NA		NA								endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						TAAGGAAGTCCTAATTCATCA	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													26	17	20			NA	NA	X		NA											NA				55172509		692	1590	2282	SO:0001624	3_prime_UTR_variant			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518	90736			25085	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 44	CXorf44	NA	12477932	Standard	NM_138362	NM_138362	NA	Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000477847.2:c.*8G>T	chrX.hg19:g.55172509C>A		NA	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	hg19	CCDS55423.1	0.02	7.094767	GTCxTAA	COVERED																																																																																			NOVEL	FAM104B-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056853.2	11	9.794319	KEEP	0	5	134	80	2476	CC	1	1	0		-	9	60	262	0	0	13.771527	238	60	8128	559	ENST00000477847.2	0.036437	1
FAM104B	90736	__UNKNOWN__	__UNKNOWN__	X	55172716	55172716	__UNKNOWN__	Missense_Mutation	SNP	C	C	T	rs5018688	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:55172716C>T	ENST00000477847.2	-	3	273	c.140G>A	c.(139-141)aGc>aAc	p.S47N	FAM104B_ENST00000332132.4_Missense_Mutation_p.S51N|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000478918.1_5'UTR|FAM104B_ENST00000489298.1_Missense_Mutation_p.S49N|FAM104B_ENST00000358460.4_Missense_Mutation_p.S50N|FAM104B_ENST00000425133.2_Missense_Mutation_p.S51N	NM_001166702.1	NP_001160174.1	Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	50		NA								endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						AATGCGGCTGCTGCTCCTTTC	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													106	90	95			NA	NA	X		NA											NA				55172716		2203	4300	6503	SO:0001583	missense			BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518	90736			25085	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 44	CXorf44	NA	12477932	Standard	NM_138362	NM_138362	NA	Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000477847.2:c.140G>A	chrX.hg19:g.55172716C>T	ENSP00000421161:p.Ser47Asn	NA	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	hg19	CCDS55423.1	0.02	7.907674	CTGxTGC	COVERED	.	.	.	.	.	.	.	.	.	.	c	10.56	1.383752	0.25031	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	1.6	0.279	0.15677	.	0.378995	0.22454	U	0.059846	T	0.45895	0.1365	L	0.34521	1.04	0.09310	N	1	D;B;B	0.55172	0.97;0.393;0.393	B;P;B	0.54759	0.412;0.76;0.383	T	0.32214	-0.9915	10	0.35671	T	0.21	-1.9952	4.8748	0.13651	0.5333:0.4667:0.0:0.0	rs5018688	51;50;51	Q5XKR9-3;Q5XKR9;Q5XKR9-2	.;F104B_HUMAN;.	N	50;51;51;47;49	ENSP00000364101:S50N;ENSP00000333394:S51N;ENSP00000397188:S51N;ENSP00000421161:S47N;ENSP00000423164:S49N	ENSP00000333394:S51N	S	-	2	0	FAM104B	55189441	0.989000	0.36119	0.024000	0.17045	0.154000	0.21943	0.205000	0.17356	-0.048000	0.13401	0.436000	0.28706	AGC	NOVEL	FAM104B-003	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000056853.2	73	5.584174	KEEP	0	5	140	68	2123	CC	1	1	0		-	10	60	294	0	0	18.204834	141	60	4920	525	ENST00000477847.2	0.066225	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	57275147	57275147	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:57275147T>C			NA	NA				SPIN2A (111089 upstream) : FAAH2 (37991 downstream)						NA		NA									NA						gatcacgccattgcactccag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.57275147T>C		NA		hg19		0.02	-0.096472	CCAxTGC	UNCOVERED																																																																																			NOVEL					0			8	3.303057	KEEP	2	0	0	11	273	TT	0.992708	0.119558	0			3	27	99	0	0	8.678991	7	60	196	29		0.3	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	63224027	63224027	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:63224027G>A			NA	NA				MIR1468 (218060 upstream) : AMER1 (180969 downstream)						NA		NA						p.0?(2)			NA						ggtggctcacgcctgtaatcc	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				2	Whole gene deletion(2)	ovary(1)|large_intestine(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.63224027G>A		NA		hg19		0.02	-0.122796	CACxCCT	UNCOVERED																																																																																			NOVEL					0			5	2.707638	KEEP	2	0	0	9	267	GG	0	0	0			3	60	87	0	0	6.973127	11	60	359	33		0.214286	0.196312
TEX11	56159	__UNKNOWN__	__UNKNOWN__	X	69827238	69827238	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:69827238G>A	ENST00000395889.2	-	24	2080				TEX11_ENST00000374320.2_Intron|TEX11_ENST00000374333.2_Intron|TEX11_ENST00000344304.3_Intron	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	NA		NA			chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					caggagttcaggaccagcctg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498	56159			11733	protein-coding gene	gene with protein product		300311	testis expressed sequence 11		NA	11279525	Standard		NM_001003811	NA	Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1925-359C>T	chrX.hg19:g.69827238G>A		NA	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	hg19	CCDS35323.1	0.02	-0.131587	TCAxGAC	COVERED																																																																																			NOVEL	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359072.1	7	3.310268	KEEP	1	0	0	11	352	GG	0.993072	0.227586	0		-	3	60	91	0	0	7.372698	11	60	384	37	ENST00000395889.2	0.214286	0.229173
TEX11	56159	__UNKNOWN__	__UNKNOWN__	X	70045568	70045568	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:70045568A>G	ENST00000395889.2	-	9	807				TEX11_ENST00000374333.2_Intron|TEX11_ENST00000344304.3_Intron	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	NA		NA			chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					gctcacgcctataatcccagc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498	56159			11733	protein-coding gene	gene with protein product		300311	testis expressed sequence 11		NA	11279525	Standard		NM_001003811	NA	Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.651+7794T>C	chrX.hg19:g.70045568A>G		NA	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	hg19	CCDS35323.1	0.02	-0.219235	CCTxTAA	COVERED																																																																																			NOVEL	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359072.1	10	4.777767	KEEP	3	0	0	16	420	AA	0.99649	0.550947	0		-	3	60	89	0	0	6.528574	19	60	554	64	ENST00000395889.2	0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	70135768	70135768	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:70135768C>T			NA	NA				TEX11 (7187 upstream) : SLC7A3 (9663 downstream)						NA		NA									NA						tttgggaggccgaggtgggag	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.70135768C>T		NA		hg19		0.02	-0.070174	GGCxGAG	UNCOVERED																																																																																			NOVEL					0			5	3.007926	KEEP	0	0	0	10	287	CC	0.992708	0.053742	0			3	60	90	0	0	8.132514	5	60	165	24		0.375	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	70223860	70223860	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:70223860C>T			NA	NA				SLC7A3 (72885 upstream) : RNU1-56P (16264 downstream)						NA		NA									NA						tgtgagccaccgtgcctggcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.70223860C>T		NA		hg19		0.02	-0.08771	CACxGTG	UNCOVERED																																																																																			NOVEL					0			9	2.404322	KEEP	2	0	0	8	211	CC	0	0	0			3	60	95	0	0	8.443658	6	60	179	22		0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	70270092	70270092	__UNKNOWN__	IGR	SNP	A	A	G	rs186130578		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:70270092A>G			NA	NA				RNU1-56P (29804 upstream) : SNX12 (9003 downstream)						NA		NA									NA						ctcgtgatccacccacctcgg	0.522		NA											a|||	811	0.214834	0.2254	0.111	3775	,	,	NA	12505	0.1379	NA	0.1571	False	NA	,,,	NA	NA	NA	2504	0.1421	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.70270092A>G		NA		hg19		0.02	-0.07016	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			5	2.406124	KEEP	6	0	0	8	222	AA	0	0	0			4	60	115	0	0	11.331489	3	60	85	29		0.571429	0.054137
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	70270095	70270095	__UNKNOWN__	IGR	SNP	C	C	T	rs191803346|rs386825692		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:70270095C>T			NA	NA				RNU1-56P (29807 upstream) : SNX12 (9000 downstream)						NA		NA									NA						gtgatccacccacctcggcct	0.512		NA											c|||	809	0.214305	0.2254	0.111	3775	,	,	NA	11899	0.1379	NA	0.1561	False	NA	,,,	NA	NA	NA	2504	0.1411	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.70270095C>T		NA		hg19		0.02	-0.070169	ACCxACC	UNCOVERED																																																																																			NOVEL					0			6	3.008216	KEEP	6	0	0	10	295	CC	0.99257	0.053735	0			5	60	147	0	0	14.785214	3	60	101	31		0.625	0.054137
TAF1	6872	__UNKNOWN__	__UNKNOWN__	X	70669110	70669110	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:70669110A>G	ENST00000276072.3	+	33	4823				TAF1_ENST00000373790.4_Intron|TAF1_ENST00000423759.1_Intron|TAF1_ENST00000449580.1_Intron|TAF1_ENST00000461764.1_Intron			P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	NA		NA			cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				aaagtgctggaattacaggcg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133	6872		Chromatin-modifying enzymes / K-acetyltransferases	11535	protein-coding gene	gene with protein product		313650	TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD, dystonia 3 (with Parkinsonism)	TAF2A, BA2R, CCG1, CCGS, DYT3	NA	3556424, 12928496, 17952504	Standard	NM_004606	XM_005262295	NA	Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000276072.3:c.4814-4910A>G	chrX.hg19:g.70669110A>G		NA	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	hg19	CCDS14412.1	0.02	-0.166651	TGGxATT	COVERED																																																																																			NOVEL	TAF1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058996.2	12	2.405725	KEEP	1	0	0	8	215	AA	0.99257	0.351317	0		+	3	60	95	0	0	7.492037	14	60	425	36	ENST00000276072.3	0.176471	0.353947
NHSL2	340527	__UNKNOWN__	__UNKNOWN__	X	71307460	71307460	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:71307460G>A	ENST00000540800.1	+	2	280					NM_001013627.2	NP_001013649.2	Q5HYW2	NHSL2_HUMAN	NHS-like 2	NA		NA								NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					ggtggctcacgcctgtaatcc	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131	340527			33737	protein-coding gene	gene with protein product		NA			NA		Standard	NM_001013627	NM_001013627	NA	Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000540800.1:c.281-44469G>A	chrX.hg19:g.71307460G>A		NA	B2RN94	hg19		0.02	-0.122796	CACxCCT	COVERED																																																																																			NOVEL	NHSL2-202	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		11	3.128395	KEEP	15	1	24	19	537	GG	0.999366	0.229028	0		+	3	40	89	0	0	7.172972	11	60	349	63	ENST00000540800.1	0.214286	0.229173
ERCC6L	54821	__UNKNOWN__	__UNKNOWN__	X	71455503	71455503	__UNKNOWN__	Intron	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:71455503C>A	ENST00000373657.1	-	2	302				PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000334463.3_Intron			Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	NA		NA			mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			breast(2)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(9)|lung(9)|ovary(3)|skin(1)	38	Renal(35;0.156)					ttggcctccccaagtgctggg	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK000112	CCDS35329.1	Xq13.1	2014-03-07	2014-03-07		ENSG00000186871	ENSG00000186871	54821			20794	protein-coding gene	gene with protein product	PLK1-interacting checkpoint helicase	300687	excision repair cross-complementing rodent repair deficiency, complementation group 6-like		NA	17218258	Standard	NM_017669	NM_017669	NA	Approved	FLJ20105, PICH, RAD26L	uc004eaq.1	Q2NKX8	OTTHUMG00000021810	ENST00000373657.1:c.300+2177G>T	chrX.hg19:g.71455503C>A		NA	Q8NCI1|Q96H93|Q9NXQ8	hg19		0.02	-0.087695	CCCxAAG	UNCOVERED																																																																																			NOVEL	ERCC6L-001	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000057173.1	3	2.407282	KEEP	2	0	0	8	248	CC	0	0	0		-	4	60	108	0	0	10.297121	4	60	137	27	ENST00000373657.1	0.5	0.120436
PABPC1L2B	645974	__UNKNOWN__	__UNKNOWN__	X	72225142	72225142	__UNKNOWN__	3'UTR	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:72225142C>G	ENST00000373521.2	+	0	1791					NM_001042506.1	NP_001035971.1	Q5JQF8	PAP1M_HUMAN	poly(A) binding protein, cytoplasmic 1-like 2B	NA		NA				extracellular vesicular exosome (GO:0070062)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)				NA	Renal(35;0.156)					gtgtgtgtgtctttgtgtgtg	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant				CCDS43972.1	Xq13.1	2013-02-12	2007-11-21	2007-11-21	ENSG00000184388	ENSG00000184388	645974		RNA binding motif (RRM) containing	31852	protein-coding gene	gene with protein product		NA	RNA binding motif protein 32B	RBM32B	NA		Standard	NM_001042506	NM_001042506	NA	Approved		uc004ebf.3	Q5JQF8	OTTHUMG00000021823	ENST00000373521.2:c.*1058C>G	chrX.hg19:g.72225142C>G		NA	B2RMV9|Q8IVU8	hg19	CCDS43972.1	0.02	1.736359	TGTxTTT	COVERED																																																																																			NOVEL	PABPC1L2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057221.1	18	13.538088	KEEP	0	0	0	45	1372	CC	1	0.992926	0		+	4	60	133	1	0	8.985938	51	60	1720	154	ENST00000373521.2	0.072727	0.992926
ZDHHC15	158866	__UNKNOWN__	__UNKNOWN__	X	74737768	74737768	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:74737768T>C	ENST00000373367.3	-	1	367				ZDHHC15_ENST00000482827.1_Intron|ZDHHC15_ENST00000373361.3_Intron|ZDHHC15_ENST00000541184.1_Intron	NM_144969.2	NP_659406.1	Q96MV8	ZDH15_HUMAN	zinc finger, DHHC-type containing 15	NA		NA			establishment of protein localization (GO:0045184)|protein palmitoylation (GO:0018345)|synaptic vesicle maturation (GO:0016188)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(1)|lung(11)|ovary(2)|skin(2)	26						gagtttgagatcagcctgggc	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK056374	CCDS14430.1, CCDS55454.1	Xq13.3	2008-05-02			ENSG00000102383	ENSG00000102383	158866		Zinc fingers, DHHC-type	20342	protein-coding gene	gene with protein product		300576			NA		Standard	NM_144969	NM_144969	NA	Approved	FLJ31812, MRX91	uc004ecg.3	Q96MV8	OTTHUMG00000021866	ENST00000373367.3:c.136+4955A>G	chrX.hg19:g.74737768T>C		NA	B3KVG7|Q3SY30|Q6UWH3	hg19	CCDS14430.1	0.02	-0.0614	AGAxCAG	UNCOVERED																																																																																			NOVEL	ZDHHC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057283.1	3	2.405784	KEEP	0	0	0	8	215	TT	0.99257	0.043461	0		-	2	60	71	0	0	6.395855	4	60	120	21	ENST00000373367.3	0.333333	0.043787
ATRX	546	__UNKNOWN__	__UNKNOWN__	X	76918463	76918463	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:76918463T>C	ENST00000373344.5	-	12	4335				ATRX_ENST00000395603.3_Intron|ATRX_ENST00000480283.1_Intron	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	NA		NA			ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						ggattacaggtatgagccacc	0.428		NA	Mis, F, N		Pancreatic neuroendocrine tumors, paediatric GBM		ATR-X (alpha thalassemia/mental retardation) syndrome														NA			NA			NA		NA	NA	NA			NA	NA	NA			Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224	546			886	protein-coding gene	gene with protein product	RAD54 homolog (S. cerevisiae)	300032	alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog), Juberg-Marsidi syndrome	RAD54, JMS	NA	7874112, 1415255, 8503439, 8630485	Standard	NM_000489	NM_000489	NA	Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.4120+407A>G	chrX.hg19:g.76918463T>C		NA	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	hg19	CCDS14434.1	0.02	-0.105238	AGGxATG	UNCOVERED																																																																																			NOVEL	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058860.2	3	3.608672	KEEP	1	0	0	12	324	TT	0.993072	0.138863	0		-	3	60	105	0	0	9.001495	9	60	255	35	ENST00000373344.5	0.25	0.139832
MAGT1	84061	__UNKNOWN__	__UNKNOWN__	X	77108283	77108283	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:77108283T>C	ENST00000358075.6	-	7	1009					NM_032121.5	NP_115497.4	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	NA		NA			cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|magnesium ion transport (GO:0015693)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						tttgtagagatggggttttgc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14436.2	Xq21.1	2014-09-17			ENSG00000102158	ENSG00000102158	84061			28880	protein-coding gene	gene with protein product	oligosaccharyltransferase 3 homolog B (S. cerevisiae)	300715			NA	15804357	Standard	NM_032121	NM_032121	NA	Approved	DKFZp564K142, IAP, OST3B, MRX95	uc004fof.3	Q9H0U3	OTTHUMG00000021882	ENST00000358075.6:c.922+1114A>G	chrX.hg19:g.77108283T>C		NA	B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	hg19	CCDS14436.2	0.02	-0.131421	AGAxGGG	COVERED																																																																																			NOVEL	MAGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057301.2	5	2.706327	KEEP	0	0	0	9	247	TT	0.99254	0.227464	0		-	3	60	94	0	0	7.782384	10	60	288	33	ENST00000358075.6	0.230769	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	77350607	77350607	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:77350607T>C			NA	NA				ATP7A (44715 upstream) : PGK1 (9063 downstream)						NA		NA									NA						tggtggctcatgcctgtaatc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.77350607T>C		NA		hg19		0.02	-0.105235	TCAxGCC	UNCOVERED																																																																																			NOVEL					0			3	3.307641	KEEP	2	0	0	11	298	TT	0.99254	0.138789	0			3	60	94	0	0	7.901471	9	60	259	34		0.25	0.139832
PGK1	5230	__UNKNOWN__	__UNKNOWN__	X	77376122	77376122	__UNKNOWN__	Intron	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:77376122C>G	ENST00000373316.4	+	7	808				PGK1_ENST00000537456.1_Intron|PGK1_ENST00000442431.1_Intron	NM_000291.3	NP_000282.1	P00558	PGK1_HUMAN	phosphoglycerate kinase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	24					Lamivudine(DB00709)	ctccctagtacctgggactac	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			L00159	CCDS14438.1	Xq13.3	2011-03-17			ENSG00000102144	ENSG00000102144	5230	2.7.2.3		8896	protein-coding gene	gene with protein product		311800			NA	6188151, 6099325	Standard		NM_000291	NA	Approved		uc004ecz.4	P00558	OTTHUMG00000021888	ENST00000373316.4:c.642-2210C>G	chrX.hg19:g.77376122C>G		NA	A8K4W6|B7Z7A9|Q5J7W1|Q6IBT6|Q8NI87	hg19	CCDS14438.1	0.02	-0.105273	GTAxCTG	UNCOVERED																																																																																			NOVEL	PGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057310.1	11	3.609459	KEEP	0	0	0	12	349	CC	0.993634	0.138942	0		+	3	60	104	0	0	9.032222	8	60	278	31	ENST00000373316.4	0.272727	0.139832
PGK1	5230	__UNKNOWN__	__UNKNOWN__	X	77384653	77384653	__UNKNOWN__	3'UTR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:77384653A>G	ENST00000373316.4	+	0	4747					NM_000291.3	NP_000282.1	P00558	PGK1_HUMAN	phosphoglycerate kinase 1	NA		NA			carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	24					Lamivudine(DB00709)	agccgagatcacgccactgca	0.542		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			L00159	CCDS14438.1	Xq13.3	2011-03-17			ENSG00000102144	ENSG00000102144	5230	2.7.2.3		8896	protein-coding gene	gene with protein product		311800			NA	6188151, 6099325	Standard		NM_000291	NA	Approved		uc004ecz.4	P00558	OTTHUMG00000021888	ENST00000373316.4:c.*3326A>G	chrX.hg19:g.77384653A>G		NA	A8K4W6|B7Z7A9|Q5J7W1|Q6IBT6|Q8NI87	hg19	CCDS14438.1	0.02	3.793149	ATCxCGC	COVERED																																																																																			NOVEL	PGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057310.1	19	9.786199	KEEP	1	5	140	82	2273	AA	1	0.999973	0		+	6	60	200	0	0	13.270296	85	60	2486	297	ENST00000373316.4	0.065934	0.999973
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	78822736	78822736	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:78822736A>G			NA	NA				ITM2A (199687 upstream) : TBX22 (447518 downstream)						NA		NA									NA						acaggtgtgaaccaccgcgcc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.78822736A>G		NA		hg19		0.02	-0.11401	TGAxCCA	UNCOVERED																																																																																			NOVEL					0			4	3.007873	KEEP	1	0	0	10	281	AA	0.992708	0.161282	0			3	60	102	0	0	8.979099	7	60	198	41		0.3	0.162467
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	78839372	78839372	__UNKNOWN__	IGR	SNP	C	C	A	rs5912981		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:78839372C>A			NA	NA				ITM2A (216323 upstream) : TBX22 (430882 downstream)						NA		NA									NA						gtaatcccagcactttgggag	0.458		NA											C|||	1069	0.283179	0.2337	0.2767	3775	,	,	NA	9498	0.2579	NA	0.2286	False	NA	,,,	NA	NA	NA	2504	0.0798	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.78839372C>A		NA		hg19		0.02	-0.052633	CAGxACT	UNCOVERED																																																																																			NOVEL					0			3	2.407131	KEEP	0	0	0	8	244	CC	0.99257	0.036492	0			3	60	97	0	0	9.32487	3	60	98	20		0.5	0.036766
POF1B	79983	__UNKNOWN__	__UNKNOWN__	X	84548719	84548719	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:84548719T>C	ENST00000262753.4	-	15	1795				POF1B_ENST00000373145.3_Intron	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	NA		NA				tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						gtggctcatgtctgtaatccc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429	79983			13711	protein-coding gene	gene with protein product		300603			NA	11299520	Standard	NM_024921	NM_024921	NA	Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.1649+9692A>G	chrX.hg19:g.84548719T>C		NA	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	hg19	CCDS14452.1	0.02	-0.166583	ATGxCTG	COVERED																																																																																			NOVEL	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057391.2	6	3.909089	KEEP	1	0	0	13	349	TT	0.993634	0.351693	0		-	4	60	131	0	0	11.102728	12	60	352	49	ENST00000262753.4	0.25	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	87516015	87516015	__UNKNOWN__	IGR	SNP	G	G	A	rs144276011		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:87516015G>A			NA	NA				ACA64 (112096 upstream) : CPXCR1 (486210 downstream)						NA		NA									NA						cttgtgatccgcccatctcag	0.478		NA											G|||	160	0.0423841	0.0386	0.0331	3775	,	,	NA	11449	0.0	NA	0.0606	False	NA	,,,	NA	NA	NA	2504	0.0256	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.87516015G>A		NA		hg19		0.02	-0.096487	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			3	2.707207	KEEP	0	0	0	9	263	GG	0.99254	0.119538	0			4	60	116	0	0	10.376353	7	60	238	31		0.363636	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	87814012	87814012	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:87814012G>A			NA	NA				ACA64 (410093 upstream) : CPXCR1 (188213 downstream)						NA		NA									NA						ccaacatggagaaaccccgtc	0.557		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.87814012G>A		NA		hg19		0.02	-0.131579	GGAxAAA	COVERED																																																																																			NOVEL					0			15	4.513161	KEEP	4	0	0	15	450	GG	0.994391	0.227888	0			3	33	83	0	0	6.572922	11	60	378	40		0.214286	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	88982416	88982416	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:88982416A>G			NA	NA				RP13-348B13.2 (280434 upstream) : AL161723.1 (62917 downstream)						NA		NA									NA						ccaaagtgctaggattacagg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.88982416A>G		NA		hg19		0.02	-0.149114	GCTxGGA	COVERED																																																																																			NOVEL					0			7	3.609965	KEEP	4	0	0	12	345	AA	0.993072	0.289978	0			4	59	134	0	0	11.280989	13	60	394	48		0.235294	0.292001
PCDH11X	27328	__UNKNOWN__	__UNKNOWN__	X	91586318	91586318	__UNKNOWN__	Intron	SNP	C	C	T	rs202144273		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:91586318C>T	ENST00000373094.1	+	5	3989				PCDH11X_ENST00000373097.1_Intron|PCDH11X_ENST00000298274.8_Intron|PCDH11X_ENST00000361655.2_Intron|PCDH11X_ENST00000504220.2_Intron|PCDH11X_ENST00000406881.1_Intron|PCDH11X_ENST00000373088.1_Intron	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	NA		NA			homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						cttcttcttcctcttcttctt	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(38;925 1092 2571 38200 45895)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290	27328		Cadherins / Protocadherins : Non-clustered	8656	protein-coding gene	gene with protein product	protein phosphatase 1, regulatory subunit 119	300246	protocadherin 11	PCDH11	NA	10644456	Standard	NM_032969	NM_001168360	NA	Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.3145-56416C>T	chrX.hg19:g.91586318C>T		NA	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	hg19	CCDS14461.1	0.02	-0.078884	TTCxTCT	UNCOVERED																																																																																			NOVEL	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057436.1	5	3.30998	KEEP	2	0	0	11	341	CC	0.99254	0.076759	0		+	3	60	72	0	0	6.328363	5	60	172	26	ENST00000373094.1	0.375	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	92156423	92156423	__UNKNOWN__	IGR	SNP	A	A	G	rs372519396		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:92156423A>G			NA	NA				PCDH11X (278194 upstream) : NAP1L3 (769505 downstream)						NA		NA									NA						ttacaggcgtaagccaccgtg	0.483		NA											a|||	21	0.00556291	0.0	0.0	3775	,	,	NA	11527	0.001	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0204	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.92156423A>G		NA		hg19		0.02	-0.157833	CGTxAGC	COVERED																																																																																			NOVEL					0			2	3.306259	KEEP	0	0	0	11	284	AA	0.993072	0.32057	0			3	60	103	0	0	8.379307	13	60	361	46		0.1875	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	95711998	95711998	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:95711998C>A			NA	NA				RN7SKP194 (46217 upstream) : DIAPH2 (227663 downstream)						NA		NA									NA						agcctgggcaccatggtgaaa	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.95711998C>A		NA		hg19		0.02	-0.131577	GCAxCAT	COVERED																																																																																			NOVEL					0			6	2.70741	KEEP	0	0	0	9	262	CC	0.99254	0.227464	0			3	60	86	0	0	6.772471	12	60	404	29		0.2	0.229173
DIAPH2	1730	__UNKNOWN__	__UNKNOWN__	X	96075447	96075447	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:96075447T>C	ENST00000324765.8	+	5	794				DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000373049.4_Intron			O60879	DIAP2_HUMAN	diaphanous-related formin 2	NA		NA			actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						ccagcctgggtgacagagcga	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202	1730			2877	protein-coding gene	gene with protein product		300108	diaphanous (Drosophila, homolog) 2, diaphanous homolog 2 (Drosophila)		NA	9360932	Standard	NM_006729, NM_007309	NM_006729	NA	Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.448-61131T>C	chrX.hg19:g.96075447T>C		NA	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	hg19	CCDS14467.1	0.02	-0.070166	GGGxGAC	UNCOVERED																																																																																			NOVEL	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058871.2	5	3.308718	KEEP	0	0	0	11	309	TT	0.993072	0.053762	0		+	2	60	72	0	0	6.335863	5	60	147	29	ENST00000324765.8	0.285714	0.054137
DIAPH2	1730	__UNKNOWN__	__UNKNOWN__	X	96353708	96353708	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:96353708A>G	ENST00000324765.8	+	20	2594				DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000373049.4_Intron			O60879	DIAP2_HUMAN	diaphanous-related formin 2	NA		NA			actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						acaggcatgaaccactgcacc	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202	1730			2877	protein-coding gene	gene with protein product		300108	diaphanous (Drosophila, homolog) 2, diaphanous homolog 2 (Drosophila)		NA	9360932	Standard	NM_006729, NM_007309	NM_006729	NA	Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2248-985A>G	chrX.hg19:g.96353708A>G		NA	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	hg19	CCDS14467.1	0.02	-0.026316	TGAxCCA	UNCOVERED																																																																																			NOVEL	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058871.2	4	2.70625	KEEP	3	0	0	9	243	AA	0.99257	0	0		+	2	60	72	0	0	7.325216	1	58	28	20	ENST00000324765.8	0.666667	0
DIAPH2	1730	__UNKNOWN__	__UNKNOWN__	X	96748979	96748979	__UNKNOWN__	Intron	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:96748979T>G	ENST00000324765.8	+	26	3588				DIAPH2-AS1_ENST00000439759.2_RNA|DIAPH2_ENST00000373061.3_Intron|DIAPH2_ENST00000373054.4_Intron			O60879	DIAP2_HUMAN	diaphanous-related formin 2	NA		NA			actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						actttgggagtctgagatgcg	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202	1730			2877	protein-coding gene	gene with protein product		300108	diaphanous (Drosophila, homolog) 2, diaphanous homolog 2 (Drosophila)		NA	9360932	Standard	NM_006729, NM_007309	NM_006729	NA	Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.3241+64235T>G	chrX.hg19:g.96748979T>G		NA	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	hg19	CCDS14467.1	0.02	-0.078937	GAGxCTG	UNCOVERED																																																																																			NOVEL	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058871.2	2	2.406238	KEEP	0	0	0	8	224	TT	0.99257	0.076761	0		+	2	60	73	0	0	6.300898	6	60	178	27	ENST00000324765.8	0.25	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	97788417	97788417	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:97788417T>C			NA	NA				DIAPH2-AS1 (890829 upstream) : AL109750.1 (851775 downstream)						NA		NA									NA						caggttcaagtgattctcctg	0.498		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.97788417T>C		NA		hg19		0.02	-0.078941	AAGxGAT	UNCOVERED																																																																																			NOVEL					0			8	2.706784	KEEP	4	0	0	9	250	TT	0	0	0			3	40	95	0	0	8.632925	5	60	148	23		0.375	0.077336
ARL13A	392509	__UNKNOWN__	__UNKNOWN__	X	100244376	100244376	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:100244376G>A	ENST00000450049.2	+	7	857					NM_001162491.1	NP_001155963.1	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13A	NA		NA			small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|ovary(1)	2						tgaggcgggcggatcatgagg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS55463.1	Xq22.1	2014-05-09	2005-11-18	2005-11-18	ENSG00000174225	ENSG00000174225	392509		ADP-ribosylation factors-like, ADP-ribosylation factors	31709	protein-coding gene	gene with protein product		NA	ADP-ribosylation factor-like 13	ARL13	NA		Standard	XM_373358	NM_001162491	NA	Approved		uc011mrf.2	Q5H913	OTTHUMG00000022013	ENST00000450049.2:c.744+1104G>A	chrX.hg19:g.100244376G>A		NA	B2RTT6|B4DX50	hg19	CCDS55463.1	0.02	-0.175416	GGCxGAT	COVERED																																																																																			NOVEL	ARL13A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057504.2	5	3.307388	KEEP	3	0	0	11	317	GG	0.993072	0.384723	0		+	3	60	95	0	0	7.579027	13	60	401	43	ENST00000450049.2	0.1875	0.387407
TRMT2B	79979	__UNKNOWN__	__UNKNOWN__	X	100276415	100276415	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:100276415C>T	ENST00000372936.3	-	10	1624				TRMT2B_ENST00000338687.7_Intron|TRMT2B_ENST00000372931.5_Intron|TRMT2B_ENST00000545398.1_Intron|TRMT2B_ENST00000372935.1_Intron|TRMT2B_ENST00000372939.1_Intron	NM_024917.5	NP_079193.2	Q96GJ1	TRM2_HUMAN	tRNA methyltransferase 2 homolog B (S. cerevisiae)	NA		NA				mitochondrion (GO:0005739)	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity (GO:0030697)			breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						gtcaggagttcgagaccagcc	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BC020116	CCDS14477.1, CCDS55464.1	Xq22.1	2012-06-12	2012-06-12	2008-09-17	ENSG00000188917	ENSG00000188917	79979			25748	protein-coding gene	gene with protein product		NA	chromosome X open reading frame 34	CXorf34	NA	14702039	Standard	NM_024917	NM_024917	NA	Approved	FLJ12687	uc004egq.3	Q96GJ1	OTTHUMG00000022017	ENST00000372936.3:c.852-111G>A	chrX.hg19:g.100276415C>T		NA	A6NDG5|A6NEI9|A6NMG6|Q5JPF0|Q5JVY6|Q96HU7|Q96IH9|Q9H9K2	hg19	CCDS14477.1	0.02	-0.14031	GTTxGAG	COVERED																																																																																			NOVEL	TRMT2B-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057512.1	6	3.308025	KEEP	3	0	0	11	304	CC	0.993072	0.259157	0		-	3	40	92	1	0	7.279317	13	60	385	35	ENST00000372936.3	0.1875	0.260965
CENPI	2491	__UNKNOWN__	__UNKNOWN__	X	100354142	100354142	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:100354142G>A	ENST00000218507.5	+	2	156				CENPI_ENST00000423383.1_Intron			Q92674	CENPI_HUMAN	centromere protein I	NA		NA			CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						TGggccaggcgtggtggctca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384	2491			3968	protein-coding gene	gene with protein product		300065	FSH primary response (LRPR1, rat) homolog 1, FSH primary response (LRPR1 homolog, rat) 1	FSHPRH1	NA	16622420	Standard	NM_006733	NM_006733	NA	Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000218507.5:c.-14+614G>A	chrX.hg19:g.100354142G>A		NA	Q5JWZ9|Q96ED0	hg19		0.02	-0.228068	GGCxTGG	COVERED																																																																																			NOVEL	CENPI-201	KNOWN	basic|appris_principal	protein_coding	NA	protein_coding		14	5.414554	KEEP	1	0	0	18	523	GG	0.999366	0.582561	0		+	3	60	92	0	0	6.827293	19	60	614	62	ENST00000218507.5	0.136364	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	100438171	100438171	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:100438171T>C			NA	NA				CENPI (19501 upstream) : DRP2 (36586 downstream)						NA		NA									NA						agtgcagtggtgcgatctcgg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.100438171T>C		NA		hg19		0.02	-0.026314	TGGxGCG	UNCOVERED																																																																																			NOVEL					0			5	3.008255	KEEP	0	0	0	10	286	TT	0.992708	0	0			2	41	63	0	0	7.253522	0	0	0	20		1	0
TAF7L	54457	__UNKNOWN__	__UNKNOWN__	X	100547933	100547933	__UNKNOWN__	Missense_Mutation	SNP	A	A	G	rs5951328	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:100547933A>G	ENST00000372907.3	-	1	112	c.101T>C	c.(100-102)cTt>cCt	p.L34P	TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	34		NA	L -> P (in dbSNP:rs5951328). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						ACGGTCGACAAGAATTTGGGG	0.522		NA											G|||	3756	0.994967	0.7587	0.7522	3775	,	,	NA	12679	0.7579	NA	0.7525	False	NA	,,,	NA	NA	NA	2504	0.726	NA	NA	NA	Ovarian(104;431 1530 3210 15406 18594)							NA				0								G	PRO/LEU	3824,11		1624,8,568,0,3	213	211	211		101	-2.8	0	X	dbSNP_114	211	6651,77		2373,55,1850,0,22	yes	missense	TAF7L	NM_024885.3	98	3997,63,2418,0,25	GG,GA,G,AA,A	NA	1.1445,0.2868,0.8331	benign	34/463	100547933	10475,88	2203	4300	6503	SO:0001583	missense			AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387	54457			11548	protein-coding gene	gene with protein product	cancer/testis antigen 40	300314	TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q	TAF2Q	NA	11279525	Standard		NM_024885	NA	Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.101T>C	chrX.hg19:g.100547933A>G	ENSP00000361998:p.Leu34Pro	NA	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	hg19	CCDS35347.1	0.02	1.778004	ACAxGAA	COVERED	1649	0.9939722724532851	262	1.0	184	0.989247311827957	284	1.0	395	0.9777227722772277	G	3.832	-0.035513	0.07497	0.997132	0.988555	ENSG00000102387	ENST00000372907	T	0.14893	2.47	3.67	-2.79	0.05841	.	2.236240	0.02268	N	0.068147	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38373	-0.9664	9	0.24483	T	0.36	0.6376	11.4757	0.50297	0.7659:0.0:0.2341:0.0	rs5951328;rs6616226;rs17846353;rs17859389;rs52795093;rs5951328	34	Q5H9L4	TAF7L_HUMAN	P	34	ENSP00000361998:L34P	ENSP00000361998:L34P	L	-	2	0	TAF7L	100434589	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.292000	0.02772	-1.418000	0.02014	-1.795000	0.00624	CTT	NOVEL	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057526.2	0	2.405602	KEEP	0	0	0	8	213	AA	0.99257	0.991893	0		-	18	60	600	0	0	50.071557	62	60	1827	124	ENST00000372907.3	0.225	0.999317
RPL36A-HNRNPH2	100529097	__UNKNOWN__	__UNKNOWN__	X	100652715	100652715	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:100652715A>G	ENST00000409170.3	+	4	332									RPL36A-HNRNPH2 readthrough	NA		NA									NA						gattacaggcatgagccaccT	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant					Xq22.1	2013-05-10			ENSG00000257529	ENSG00000257529	100529097			48349	other	readthrough		NA			NA		Standard		NM_001199973	NA	Approved				OTTHUMG00000170052	ENST00000409170.3:c.332+2270A>G	chrX.hg19:g.100652715A>G		NA		hg19		0.02	1.62554	GGCxTGA	COVERED																																																																																			NOVEL	RPL36A-HNRNPH2-002	NOVEL	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest|readthrough_transcript	protein_coding	NA	protein_coding	OTTHUMT00000407084.1	23	9.013492	KEEP	1	3	91	62	1716	AA	1	0.999726	0		+	6	60	198	0	0	13.31429	77	60	2301	226	ENST00000409170.3	0.072289	0.999726
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	101033652	101033652	__UNKNOWN__	IGR	SNP	A	A	C	rs4022411		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:101033652A>C			NA	NA				RNU6-587P (86994 upstream) : NXF5 (53432 downstream)						NA		NA									NA						AAAAAAAAAAACACCAAATAT	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.101033652A>C		NA		hg19		0.02	-0.385829	AAAxCAC	COVERED																																																																																			NOVEL					0			3	5.412567	KEEP	2	0	0	18	479	AA	0.997832	0.91618	0			3	33	101	0	0	6.808946	40	60	1151	94		0.069767	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	102489527	102489527	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:102489527T>G			NA	NA				BEX4 (17353 upstream) : TCEAL8 (18395 downstream)						NA		NA									NA						ggtggctcactcctgtaatcc	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.102489527T>G		NA		hg19		0.02	-0.096472	CACxCCT	UNCOVERED																																																																																			NOVEL					0			4	3.007459	KEEP	2	0	0	10	273	TT	0.99254	0.119538	0			3	60	88	0	0	7.43226	8	60	243	32		0.272727	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	102894644	102894644	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:102894644C>T			NA	NA				TCEAL1 (8763 upstream) : MORF4L2 (35779 downstream)						NA		NA									NA						tttgggaggccgaggcaggtg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.102894644C>T		NA		hg19		0.02	-0.140332	GGCxGAG	COVERED																																																																																			NOVEL					0			10	5.114117	KEEP	3	0	0	17	513	CC	0.99649	0.260049	0			3	60	83	0	0	6.573185	11	60	344	49		0.214286	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	103562180	103562180	__UNKNOWN__	IGR	SNP	G	G	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:103562180G>C			NA	NA				ESX1 (62566 upstream) : IL1RAPL2 (248815 downstream)						NA		NA									NA						gcctgcctcggcctcccaaag	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.103562180G>C		NA		hg19		0.02	-0.096499	TCGxCCT	UNCOVERED																																																																																			NOVEL					0			15	5.115127	KEEP	11	0	0	17	521	GG	0.995343	0.139181	0			2	20	74	0	0	6.400644	6	60	200	56		0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	106256796	106256796	__UNKNOWN__	IGR	SNP	T	T	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:106256796T>A			NA	NA				MORC4 (13322 upstream) : RBM41 (50853 downstream)						NA		NA									NA						aggccgaggctggtggaatac	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.106256796T>A		NA		hg19		0.02	-0.192959	GGCxGGT	COVERED																																																																																			NOVEL					0			3	4.209908	KEEP	0	0	0	14	375	TT	0.995343	0.455625	0			3	60	91	0	0	6.933813	16	60	483	48		0.157895	0.457757
TMEM164	84187	__UNKNOWN__	__UNKNOWN__	X	109404216	109404216	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:109404216G>A	ENST00000372073.1	+	6	922				TMEM164_ENST00000464177.1_Intron|TMEM164_ENST00000372068.2_Intron|TMEM164_ENST00000372072.3_Intron|TMEM164_ENST00000288381.4_Intron			Q5U3C3	TM164_HUMAN	transmembrane protein 164	NA		NA				integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|skin(1)	14						gattacaggcgtgagccaccg	0.488		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AK094127	CCDS14550.2, CCDS55475.1	Xq22.3	2008-02-05			ENSG00000157600	ENSG00000157600	84187			26217	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_032227	NM_032227	NA	Approved	FLJ22679, RP13-360B22.2	uc004eom.3	Q5U3C3	OTTHUMG00000022192	ENST00000372073.1:c.587-10432G>A	chrX.hg19:g.109404216G>A		NA	B3KSQ8|F5H2P2	hg19	CCDS14550.2	0.02	-0.017537	GGCxTGA	UNCOVERED																																																																																			NOVEL	TMEM164-003	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057898.1	2	2.707736	KEEP	0	0	0	9	270	GG	0.99254	0	0		+	2	60	55	0	0	6.452603	0	0	0	16	ENST00000372073.1	1	0
DCX	1641	__UNKNOWN__	__UNKNOWN__	X	110559483	110559483	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:110559483C>T	ENST00000356220.3	-	7	1046				DCX_ENST00000356915.2_Intron|DCX_ENST00000371993.2_Intron|DCX_ENST00000338081.3_Intron|DCX_ENST00000488120.1_Intron			O43602	DCX_HUMAN	doublecortin	NA		NA			axon extension (GO:0048675)|axon guidance (GO:0007411)|brain development (GO:0007420)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neuron migration (GO:0001764)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuron projection (GO:0043005)	microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|skin(6)|upper_aerodigestive_tract(1)	41						ttttttgagacggagtcttgc	0.512		NA											C|||	2	0.000529801	0.0	0.0	3775	,	,	NA	10696	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.002	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF040254	CCDS14556.1, CCDS14557.1, CCDS14558.1	Xq22.3-q23	2008-08-01	2008-08-01		ENSG00000077279	ENSG00000077279	1641			2714	protein-coding gene	gene with protein product	doublecortex	300121	doublecortex; lissencephaly, X-linked (doublecortin)		NA	9489699, 9489700	Standard	NM_178153	NM_178151	NA	Approved	SCLH, DC, LISX, DBCN, XLIS	uc004epd.3	O43602	OTTHUMG00000022204	ENST00000356220.3:c.947-3519G>A	chrX.hg19:g.110559483C>T		NA	A6NFY6|A9Z1V8|D3DUY8|D3DUY9|D3DUZ0|O43911|Q5JYZ5	hg19	CCDS14558.1	0.02	-0.052613	AGAxGGA	UNCOVERED																																																																																			NOVEL	DCX-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057926.2	4	2.406874	KEEP	1	0	0	8	237	CC	0.99257	0.036492	0		-	3	60	88	0	0	8.425108	3	60	80	21	ENST00000356220.3	0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	110859411	110859411	__UNKNOWN__	IGR	SNP	T	T	C	rs199676172		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:110859411T>C			NA	NA				RN7SL661P (10 upstream) : RNA5SP512 (53645 downstream)						NA		NA									NA						ccttggcctctcaaagtgctg	0.552		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.110859411T>C		NA		hg19		0.02	-0.13156	CTCxCAA	COVERED																																																																																			NOVEL					0			15	5.714245	KEEP	9	0	0	19	519	TT	0.997832	0.228676	0			3	60	99	0	0	8.172848	11	60	332	52		0.214286	0.229173
HTR2C	3358	__UNKNOWN__	__UNKNOWN__	X	113862917	113862917	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:113862917C>T	ENST00000276198.1	+	2	649				HTR2C_ENST00000371950.3_Intron|HTR2C_ENST00000371951.1_Intron	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	NA		NA			behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	gacagggtttcgccatgttgg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant				CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246	3358		5-HT (serotonin) receptors, GPCR / Class A : 5-HT (serotonin) receptors, GPCR only	5295	protein-coding gene	gene with protein product		312861	5-hydroxytryptamine (serotonin) receptor 2C	HTR1C	NA	7895773	Standard	NM_000868	NM_000868	NA	Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.-80+14578C>T	chrX.hg19:g.113862917C>T		NA	B1AMW4|Q5VUF8|Q9NP28	hg19	CCDS14564.1	0.02	-0.070165	TTTxGCC	UNCOVERED																																																																																			NOVEL	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057962.1	3	2.406306	KEEP	0	0	0	8	229	CC	0.99257	0.053735	0		+	4	24	115	0	0	10.998957	4	60	126	19	ENST00000276198.1	0.5	0.054137
LRCH2	57631	__UNKNOWN__	__UNKNOWN__	X	114396590	114396590	__UNKNOWN__	Intron	SNP	T	T	C	rs62601521		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:114396590T>C	ENST00000317135.8	-	11	1494				LRCH2_ENST00000538422.1_Intron	NM_020871.3	NP_065922.3	Q5VUJ6	LRCH2_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 2	NA		NA								breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	19						tcaagcgatcttcccacctca	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AB040928	CCDS48155.1, CCDS59175.1	Xq24	2008-02-05			ENSG00000130224	ENSG00000130224	57631			29292	protein-coding gene	gene with protein product		NA			NA	10819331	Standard	NM_020871	NM_020871	NA	Approved	KIAA1495	uc010nqe.3	Q5VUJ6	OTTHUMG00000022233	ENST00000317135.8:c.1463+1648A>G	chrX.hg19:g.114396590T>C		NA	F5H2T1|Q08AD5|Q9HA88|Q9P233	hg19	CCDS48155.1	0.02	-0.087712	ATCxTCC	UNCOVERED																																																																																			NOVEL	LRCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000057971.2	7	2.706402	KEEP	1	0	0	9	249	TT	0.99257	0.09898	0		-	3	60	103	0	0	9.243787	6	60	181	22	ENST00000317135.8	0.333333	0.099721
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	114940826	114940826	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:114940826A>G			NA	NA				AC005000.2 (2639 upstream) : RP1-241P17.4 (11823 downstream)						NA		NA									NA						ctggagtgcaatggcgcgatc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.114940826A>G		NA		hg19		0.02	-0.140302	GCAxTGG	COVERED																																																																																			NOVEL					0			6	3.006087	KEEP	1	0	0	10	259	AA	0.992708	0.259062	0			3	60	103	0	0	8.379191	13	60	370	36		0.1875	0.260965
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	115004819	115004819	__UNKNOWN__	IGR	SNP	G	G	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:115004819G>T			NA	NA				RP1-241P17.1 (45436 upstream) : RP11-761E20.1 (28784 downstream)						NA		NA									NA						CCCTTCCCGTGGGAGCAACCG	0.731		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.115004819G>T		NA		hg19		0.02	-0.149099	CGTxGGA	UNCOVERED																																																																																			NOVEL					0			0	2.406946	KEEP	6	0	0	8	241	GG	0	0	0			4	40	114	0	0	9.281181	13	41	415	37		0.235294	0.292001
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	116955029	116955029	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:116955029C>A			NA	NA				RNU6-1323P (970116 upstream) : KLHL13 (76746 downstream)						NA		NA									NA						tgctctgtcgcccaggctgga	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.116955029C>A		NA		hg19		0.02	-0.052625	TCGxCCA	UNCOVERED																																																																																			NOVEL					0			6	3.008925	KEEP	5	0	0	10	307	CC	0.99257	0.036492	0			3	22	85	0	0	8.124002	3	40	101	29		0.5	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	117271214	117271214	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:117271214A>G			NA	NA				KLHL13 (19911 upstream) : WDR44 (208821 downstream)						NA		NA									NA						ggctcaagcaatcctcctgcc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.117271214A>G		NA		hg19		0.02	-0.131557	GCAxTCC	COVERED																																																																																			NOVEL					0			13	4.210115	KEEP	2	0	0	14	378	AA	0.994391	0.227888	0			3	56	103	0	1	8.932782	8	60	232	41		0.272727	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	117365954	117365954	__UNKNOWN__	IGR	SNP	A	A	G	rs186054246		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:117365954A>G			NA	NA				KLHL13 (114651 upstream) : WDR44 (114081 downstream)						NA		NA									NA						gaagaagaagaaggaggagga	0.408		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.117365954A>G		NA		hg19		0.02	-0.122701	AAGxAGG	COVERED																																																																																			NOVEL					0			28	6.013738	KEEP	26	0	0	20	534	AA	0.99257	0.194853	0			3	48	95	0	0	8.002523	9	60	250	67		0.25	0.196312
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	118021808	118021808	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:118021808T>C			NA	NA				RP4-562J12.2 (29959 upstream) : LONRF3 (86772 downstream)						NA		NA									NA						aatcccagcattttgggagac	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.118021808T>C		NA		hg19		0.02	-0.122788	GCAxTTT	COVERED																																																																																			NOVEL					0			2	2.405258	KEEP	1	0	0	8	210	AT	0.99257	0.22747	0			4	60	138	0	0	12.224386	9	60	262	38		0.307692	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	118595761	118595761	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:118595761C>T			NA	NA				Y_RNA (5140 upstream) : SLC25A5-AS1 (4235 downstream)						NA		NA									NA						tttgggaggccaaggcgggtg	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.118595761C>T		NA		hg19		0.02	-0.105268	GGCxAAG	UNCOVERED																																																																																			NOVEL					0			5	2.407392	KEEP	0	0	0	8	253	CC	0.99257	0.138793	0			3	60	88	0	0	7.578213	7	60	244	28		0.3	0.139832
SEPT6	23157	__UNKNOWN__	__UNKNOWN__	X	118762888	118762888	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:118762888T>C	ENST00000394610.1	-	9	1545				SEPT6_ENST00000360156.7_Intron|SEPT6_ENST00000467310.1_Intron|SEPT6_ENST00000354228.4_Intron|SEPT6_ENST00000343984.5_Intron|SEPT6_ENST00000354416.3_Intron|SEPT6_ENST00000489216.1_Intron	NM_145799.3	NP_665798.1	Q14141	SEPT6_HUMAN	septin 6	NA		NA			cytokinesis (GO:0000910)|viral process (GO:0016032)	axon terminus (GO:0043679)|kinetochore (GO:0000776)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(3)	17						gctgggattataggtgtgagc	0.507		NA	T	MLL	AML																NA			NA			NA		NA	NA	NA			NA	NA	NA			Dom	yes		X	Xq24	23157	septin 6		L	0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D50918	CCDS14583.1, CCDS14584.1, CCDS14585.1	Xq24	2013-01-21			ENSG00000125354	ENSG00000125354	23157		Septins	15848	protein-coding gene	gene with protein product		300683			NA	8590280, 10744683	Standard	NM_145802	NM_015129	NA	Approved	KIAA0128, SEP2, SEPT2, MGC16619, MGC20339	uc004erv.3	Q14141	OTTHUMG00000022280	ENST00000394610.1:c.1280+392A>G	chrX.hg19:g.118762888T>C		NA	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	hg19	CCDS14585.1	0.02	-0.219234	TTAxAGG	COVERED																																																																																			NOVEL	SEPT6-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058061.1	7	3.006672	KEEP	0	0	0	10	261	TT	0.992708	0.548856	0		-	3	60	97	0	0	7.327634	19	60	534	53	ENST00000394610.1	0.136364	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	118948701	118948701	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:118948701A>T			NA	NA				RPL39 (23095 upstream) : UPF3B (19283 downstream)						NA		NA									NA						CTGACACTTTAATTTATAGAA	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.118948701A>T		NA		hg19		0.02	0.808193	TTTxATT	COVERED																																																																																			NOVEL					0			16	5.711939	KEEP	0	0	0	19	509	AA	0.999863	0.999698	0			5	60	140	0	0	8.016609	85	60	2498	144		0.055556	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	118948702	118948702	__UNKNOWN__	IGR	SNP	A	A	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:118948702A>T			NA	NA				RPL39 (23096 upstream) : UPF3B (19282 downstream)						NA		NA									NA						TGACACTTTAATTTATAGAAA	0.388		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.118948702A>T		NA		hg19		0.02	0.808048	TTAxTTT	COVERED																																																																																			NOVEL					0			16	6.013401	KEEP	0	0	0	20	546	AA	0.999863	0.999698	0			5	60	140	0	0	8.016191	85	60	2596	145		0.055556	0.999835
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	119652229	119652229	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:119652229T>C			NA	NA				LAMP2 (49009 upstream) : CUL4B (6234 downstream)						NA		NA									NA						tcgagaccagtctgggcaaca	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.119652229T>C		NA		hg19		0.02	-0.166642	CAGxCTG	COVERED																																																																																			NOVEL					0			10	5.713668	KEEP	1	0	0	19	514	TT	0.999859	0.353897	0			3	60	105	0	0	8.410033	15	60	443	57		0.166667	0.353947
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	120371199	120371199	__UNKNOWN__	IGR	SNP	G	G	A	rs4494028	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:120371199G>A			NA	NA				GLUD2 (187405 upstream) : AC007486.1 (95208 downstream)						NA		NA									NA						cttgtgatccgcccacctcgg	0.502		NA											g|||	1475	0.390728	0.0514	0.3977	3775	,	,	NA	11361	0.3165	NA	0.3996	False	NA	,,,	NA	NA	NA	2504	0.4192	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.120371199G>A		NA		hg19		0.02	-0.061405	TCCxCCC	UNCOVERED																																																																																			NOVEL					0			8	3.610448	KEEP	12	0	0	12	365	GG	0	0	0			3	60	91	0	0	8.72443	3	60	105	32		0.5	0.043787
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	121892513	121892513	__UNKNOWN__	IGR	SNP	T	T	C	rs6648838	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:121892513T>C			NA	NA				AL513487.1 (286842 upstream) : U3 (81765 downstream)						NA		NA									NA						ccgaggcgggtggatcacgag	0.572		NA											-||||-|||	1651|1649	0.437351|0.436821	0.5295|0.5287	0.2709|0.2709	3775|3775	,|,	,|,	NA	9395|9395	0.2897|0.2887	NA	0.2416|0.2416	False|False	NA	,,,|,,,	NA	NA	NA	2504|2504	0.2331|0.2331	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.121892513T>C		NA		hg19		0.02	-0.078934	GGGxGGA	UNCOVERED																																																																																			NOVEL					0			6	2.405843	KEEP	6	0	0	8	223	TT	0	0	0			6	60	182	0	0	18.573604	3	60	89	35		0.666667	0.077336
STAG2	10735	__UNKNOWN__	__UNKNOWN__	X	123316119	123316119	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:123316119C>T	ENST00000469481.1	+	2	453							Q8N3U4	STAG2_HUMAN	stromal antigen 2	NA		NA			meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						ggattacaggcgtgagccact	0.572		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972	10735			11355	protein-coding gene	gene with protein product		300826			NA	9305759	Standard	NM_006603	NM_001042750	NA	Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000469481.1:c.453+178522C>T	chrX.hg19:g.123316119C>T		NA	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	hg19		0.02	-0.157899	AGGxGTG	COVERED																																																																																			NOVEL	STAG2-010	KNOWN	basic	processed_transcript	NA	protein_coding	OTTHUMT00000106861.1	13	3.910469	KEEP	1	0	0	13	381	CC	0.994391	0.320996	0		+	4	60	118	0	0	9.930779	11	60	373	42	ENST00000469481.1	0.266667	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	126312923	126312923	__UNKNOWN__	IGR	SNP	G	G	A	rs184553192		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:126312923G>A			NA	NA				CXorf64 (357154 upstream) : CTD-2076M15.1 (481688 downstream)						NA		NA									NA						ttgagaggccgaggcgggtgg	0.468		NA											G|||	17	0.00450331	0.0	0.0072	3775	,	,	NA	7485	0.0	NA	0.0119	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.126312923G>A		NA		hg19		0.02	-0.105247	GCCxAGG	UNCOVERED																																																																																			NOVEL					0			6	2.405927	KEEP	5	0	0	8	224	GG	0	0	0			4	60	112	0	0	10.184643	6	47	191	32		0.4	0.139832
OCRL	4952	__UNKNOWN__	__UNKNOWN__	X	128710497	128710497	__UNKNOWN__	Nonsense_Mutation	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:128710497C>T	ENST00000371113.4	+	18	2248	c.2083C>T	c.(2083-2085)Cga>Tga	p.R695*	OCRL_ENST00000357121.5_Nonsense_Mutation_p.R695*	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	695		NA			cilium assembly (GO:0042384)|in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|lipid metabolic process (GO:0006629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|Golgi-associated vesicle (GO:0005798)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	inositol phosphate phosphatase activity (GO:0052745)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			breast(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(24)|ovary(2)|upper_aerodigestive_tract(3)	48						AAGACCAATCCGAGAAGTTCC	0.403		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0			GRCh37	CM983299	OCRL	M							115	99	104			NA	NA	X		NA											NA				128710497		2203	4300	6503	SO:0001587	stop_gained			U57627	CCDS35393.1, CCDS35394.1	Xq25	2014-06-18			ENSG00000122126	ENSG00000122126	4952			8108	protein-coding gene	gene with protein product		300535			NA		Standard	NM_000276	NM_001587	NA	Approved	OCRL1	uc004euq.3	Q01968	OTTHUMG00000022706	ENST00000371113.4:c.2083C>T	chrX.hg19:g.128710497C>T	ENSP00000360154:p.Arg695*	NA	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	hg19	CCDS35393.1	0.02	-0.421028	ATCxGAG	COVERED	.	.	.	.	.	.	.	.	.	.	C	40	8.294464	0.98747	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	.	.	.	5.96	1.96	0.26148	.	0.125962	0.53938	D	0.000053	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.4852	0.67611	0.4954:0.5046:0.0:0.0	.	.	.	.	X	695	.	ENSP00000349635:R695X	R	+	1	2	OCRL	128538178	0.999000	0.42202	0.982000	0.44146	0.980000	0.70556	0.979000	0.29500	0.223000	0.20920	0.538000	0.68166	CGA	NOVEL	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058917.1	2	3.911041	KEEP	0	0	0	13	382	CC	0.994391	0.943082	0		+	3	60	98	0	0	6.389227	44	60	1413	95	ENST00000371113.4	0.06383	0.948402
RP4-537K23.4	0	__UNKNOWN__	__UNKNOWN__	X	129032178	129032178	__UNKNOWN__	RNA	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:129032178A>G	ENST00000432062.1	-	0	293										NA		NA									NA						ctagcactttaggaggctgag	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000432062.1:	chrX.hg19:g.129032178A>G		NA		hg19		0.02	-0.096489	TTTxGGA	UNCOVERED																																																																																			NOVEL	RP4-537K23.4-001	KNOWN	basic|exp_conf	antisense	NA	antisense	OTTHUMT00000058219.1	7	3.90907	KEEP	0	0	0	13	352	AA	0.994391	0.119761	0		-	3	60	106	0	0	9.543613	6	60	189	34	ENST00000432062.1	0.333333	0.120436
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	130044847	130044847	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:130044847T>C			NA	NA				ENOX2 (7639 upstream) : RP1-23K20.2 (70716 downstream)						NA		NA									NA						gtctcaaacttctgacctcag	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.130044847T>C		NA		hg19		0.02	-0.131495	ACTxCTG	COVERED																																																																																			NOVEL					0			6	2.405797	KEEP	0	0	0	8	216	TT	0.99257	0.22747	0			3	60	89	0	0	7.402019	9	60	246	29		0.25	0.229173
USP26	83844	__UNKNOWN__	__UNKNOWN__	X	132218687	132218687	__UNKNOWN__	Intron	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:132218687A>G	ENST00000511190.1	-	5	329				USP26_ENST00000417459.2_Intron	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	NA		NA			protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					gattacaggcatgagccaccg	0.478		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA	NSCLC(104;342 1621 36940 47097 52632)							NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	83844	3.4.19.12	Ubiquitin-specific peptidases	13485	protein-coding gene	gene with protein product		300309	ubiquitin specific protease 26		NA	12838346	Standard	NM_031907	NM_031907	NA	Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.141-888T>C	chrX.hg19:g.132218687A>G		NA	B9WRT6|Q5H9H4	hg19	CCDS14635.1	0.02	-0.166514	GGCxTGA	COVERED																																																																																			NOVEL	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000359441.1	23	2.566564	KEEP	13	2	58	29	781	AA	0.999931	0.38738	0		-	4	60	123	0	0	10.571112	10	60	294	88	ENST00000511190.1	0.285714	0.387407
HPRT1	3251	__UNKNOWN__	__UNKNOWN__	X	133606972	133606972	__UNKNOWN__	Intron	SNP	A	A	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:133606972A>C	ENST00000298556.7	+	2	186				HPRT1_ENST00000462974.1_Intron	NM_000194.2	NP_000185.1	P00492	HPRT_HUMAN	hypoxanthine phosphoribosyltransferase 1	NA		NA			adenine salvage (GO:0006168)|central nervous system neuron development (GO:0021954)|cerebral cortex neuron differentiation (GO:0021895)|cytolysis (GO:0019835)|dendrite morphogenesis (GO:0048813)|dopamine metabolic process (GO:0042417)|GMP catabolic process (GO:0046038)|GMP salvage (GO:0032263)|grooming behavior (GO:0007625)|guanine salvage (GO:0006178)|hypoxanthine metabolic process (GO:0046100)|hypoxanthine salvage (GO:0043103)|IMP metabolic process (GO:0046040)|IMP salvage (GO:0032264)|locomotory behavior (GO:0007626)|lymphocyte proliferation (GO:0046651)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of dopamine metabolic process (GO:0045964)|protein homotetramerization (GO:0051289)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside salvage (GO:0006166)|purine-containing compound salvage (GO:0043101)|response to amphetamine (GO:0001975)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanine phosphoribosyltransferase activity (GO:0052657)|hypoxanthine phosphoribosyltransferase activity (GO:0004422)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9	Acute lymphoblastic leukemia(192;0.000127)				Azathioprine(DB00993)|Mercaptopurine(DB01033)|Tioguanine(DB00352)	ggctggagtgaagtggcgcat	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M26434	CCDS14641.1	Xq26.2	2012-10-02	2008-08-01		ENSG00000165704	ENSG00000165704	3251	2.4.2.8		5157	protein-coding gene	gene with protein product	Lesch-Nyhan syndrome	308000		HPRT	NA	12175903	Standard	NM_000194	NM_000194	NA	Approved	HGPRT	uc004exl.4	P00492	OTTHUMG00000022452	ENST00000298556.7:c.28-417A>C	chrX.hg19:g.133606972A>C		NA	A6NHF0|B2R8M9	hg19	CCDS14641.1	0.02	-0.061389	GTGxAGT	UNCOVERED																																																																																			NOVEL	HPRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058361.1	4	2.405705	KEEP	1	0	0	8	214	AT	0.99257	0.043461	0		+	3	60	103	0	0	9.655932	4	60	111	21	ENST00000298556.7	0.428571	0.043787
FAM122B	159090	__UNKNOWN__	__UNKNOWN__	X	133914376	133914376	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:133914376T>C	ENST00000370790.1	-	8	1528				FAM122B_ENST00000493333.1_Intron|FAM122B_ENST00000486347.1_Intron|FAM122B_ENST00000298090.6_Intron|FAM122B_ENST00000343004.5_Intron	NM_001166599.2|NM_145284.5	NP_001160071.1|NP_660327.2	Q7Z309	F122B_HUMAN	family with sequence similarity 122B	NA		NA								breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|skin(1)	6	Acute lymphoblastic leukemia(192;0.000127)					gaggccgaggtgggcggatca	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			BX538218	CCDS14643.1, CCDS55497.1, CCDS55498.1	Xq26.3	2008-02-05			ENSG00000156504	ENSG00000156504	159090			30490	protein-coding gene	gene with protein product		NA			NA	12477932	Standard	NM_145284	NM_145284	NA	Approved	DKFZp686L20116, RP11-308B5.5	uc004exq.3	Q7Z309	OTTHUMG00000022461	ENST00000370790.1:c.599+1474A>G	chrX.hg19:g.133914376T>C		NA	A8K902|Q6PIM2|Q6ZU47|Q6ZV64|Q6ZVE4|Q8TB75	hg19	CCDS55497.1	0.02	-0.149079	AGGxGGG	COVERED																																																																																			NOVEL	FAM122B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058382.1	10	3.307643	KEEP	9	0	0	11	305	TT	0.992708	0.289872	0		-	3	60	94	0	0	7.479356	13	60	383	49	ENST00000370790.1	0.1875	0.292001
SAGE1	55511	__UNKNOWN__	__UNKNOWN__	X	134974210	134974210	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:134974210G>A	ENST00000324447.3	+	1	46							Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	NA		NA				nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					agtggctcacgcctgtaatcc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433	55511			30369	protein-coding gene	gene with protein product	cancer/testis antigen 14	300359			NA	10919659	Standard	NM_018666	NM_018666	NA	Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000324447.3:c.-1+2791G>A	chrX.hg19:g.134974210G>A		NA	Q5JNW0	hg19	CCDS14652.1	0.02	-0.087708	CACxCCT	UNCOVERED																																																																																			NOVEL	SAGE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding		2	2.70647	KEEP	0	0	0	9	249	GG	0.99254	0.098977	0		+	3	60	87	0	0	8.054532	4	60	125	24	ENST00000324447.3	0.428571	0.099721
ARHGEF6	9459	__UNKNOWN__	__UNKNOWN__	X	135792186	135792186	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:135792186C>T	ENST00000250617.6	-	8	2033				ARHGEF6_ENST00000535227.1_Intron|ARHGEF6_ENST00000370622.1_Intron|ARHGEF6_ENST00000370620.1_Intron	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	NA		NA			apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					AACACTAggccgggtgtggtg	0.517		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675	9459		Rho guanine nucleotide exchange factors, Pleckstrin homology (PH) domain containing	685	protein-coding gene	gene with protein product	Rac/Cdc42 guanine exchange factor (GEF) 6, PAK-interacting exchange factor, alpha, rho guanine nucleotide exchange factor 6	300267	mental retardation, X-linked 46	MRX46	NA	7584048, 9659915	Standard	NM_004840	NM_004840	NA	Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.828-1257G>A	chrX.hg19:g.135792186C>T		NA	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	hg19	CCDS14660.1	0.02	-0.105259	GGCxGGG	UNCOVERED																																																																																			NOVEL	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058511.2	1	2.406931	KEEP	0	0	0	8	242	CC	0.99257	0.138793	0		-	3	60	88	0	0	7.301017	9	60	290	30	ENST00000250617.6	0.25	0.139832
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	139062801	139062801	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:139062801T>G			NA	NA				CXorf66 (15122 upstream) : RP11-364B14.1 (36625 downstream)						NA		NA									NA						aggctggaattcagtgacatg	0.507		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.139062801T>G		NA		hg19		0.02	-0.05263	AATxCAG	UNCOVERED																																																																																			NOVEL					0			5	3.006499	KEEP	0	0	0	10	262	TT	0.992708	0.036498	0			2	60	72	0	0	6.692999	3	60	91	21		0.4	0.036766
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	140526113	140526113	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:140526113G>A			NA	NA				SPANXC (189484 upstream) : SPANXA2-OT1 (64729 downstream)						NA		NA									NA						tgaactcctgggctcaagtgt	0.433		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.140526113G>A		NA		hg19		0.02	-0.157899	CTGxGCT	COVERED																																																																																			NOVEL					0			3	3.009051	KEEP	0	0	0	10	309	GG	0.992708	0.320453	0			3	60	88	0	0	6.792008	14	60	479	40		0.176471	0.322807
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	141940741	141940741	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:141940741C>T			NA	NA				AL080272.1 (246010 upstream) : snoU13 (21004 downstream)						NA		NA									NA						tttgggaggccgaggcgggcg	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.141940741C>T		NA		hg19		0.02	-0.210504	GGCxGAG	COVERED																																																																																			NOVEL					0			13	6.617683	KEEP	19	0	0	22	641	CC	0.99649	0.550947	0			4	33	121	0	0	9.868381	14	60	454	88		0.222222	0.552887
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	142605554	142605554	__UNKNOWN__	IGR	SNP	A	A	G	rs111851873		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:142605554A>G			NA	NA				SPANXN3 (251 upstream) : SLITRK4 (105041 downstream)						NA		NA									NA						ATCTGCCACCACTCCTCATTT	0.493		NA											g|||	534	0.141457	0.171	0.1124	3775	,	,	NA	12260	0.0605	NA	0.0746	False	NA	,,,	NA	NA	NA	2504	0.0961	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.142605554A>G		NA		hg19		0.02	-0.298181	ACCxCTC	COVERED																																																																																			NOVEL					0			2	3.308497	KEEP	2	0	0	11	308	AA	0.993072	0.775649	0			13	49	424	0	0	38.995201	20	60	574	65		0.393939	0.78106
SLITRK4	139065	__UNKNOWN__	__UNKNOWN__	X	142714351	142714351	__UNKNOWN__	3'UTR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:142714351T>C	ENST00000381779.4	-	0	4799					NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	NA		NA				integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					cacacacacatacacacacac	0.328		NA											T|||	2	0.000529801	0.0015	0.0	3775	,	,	NA	9821	0.0	NA	0.0	False	NA	,,,	NA	NA	NA	2504	0.0	NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001624	3_prime_UTR_variant			BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542	139065			23502	protein-coding gene	gene with protein product		300562			NA	14557068	Standard	NM_173078	NM_001184749	NA	Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.*2060A>G	chrX.hg19:g.142714351T>C		NA	Q5JXG3|Q8TCM8|Q96DL3	hg19	CCDS14679.1	0.02	-0.227972	ACAxACA	COVERED																																																																																			NOVEL	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000058617.1	11	2.866075	KEEP	0	2	58	30	764	TT	0.999998	0.582929	0		-	3	60	99	0	0	7.349408	22	60	606	76	ENST00000381779.4	0.12	0.58293
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	146323275	146323275	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:146323275T>C			NA	NA				MIR508 (4730 upstream) : MIR514B (8393 downstream)						NA		NA									NA						acctcctgggttcaagcgatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.146323275T>C		NA		hg19		0.02	-0.043851	GGGxTCA	UNCOVERED																																																																																			NOVEL					0			3	2.405859	KEEP	1	0	0	8	220	TT	0	0	0			2	47	67	0	0	6.825769	1	60	24	20		0.666667	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	149453571	149453571	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:149453571G>A			NA	NA				MIR2114 (57253 upstream) : MAMLD1 (76117 downstream)						NA		NA									NA						gcgcggtggcgggcgcctgta	0.587		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.149453571G>A		NA		hg19		0.02	-0.236841	GGCxGGC	COVERED																																																																																			NOVEL					0			21	3.24213	KEEP	22	1	26	20	601	GG	0.994391	0.608972	0			3	32	87	0	0	6.392969	18	60	589	88		0.142857	0.612407
ZFP92	139735	__UNKNOWN__	__UNKNOWN__	X	152686865	152686865	__UNKNOWN__	Missense_Mutation	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:152686865G>A	ENST00000338647.5	+	4	1031	c.1030G>A	c.(1030-1032)Ggt>Agt	p.G344S		NM_001136273.1	NP_001129745.1	A6NM28	ZFP92_HUMAN	ZFP92 zinc finger protein	344		NA			regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(4)	6						CGTGCACAGCGGTGAGAAGCC	0.721		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													9	9	9			NA	NA	X		NA											NA				152686865		685	1568	2253	SO:0001583	missense			U82695	CCDS59177.1	Xq28	2013-01-08	2012-11-27		ENSG00000189420	ENSG00000189420	139735		Zinc fingers, C2H2-type, -	12865	protein-coding gene	gene with protein product		NA	zinc finger protein homologous to Zfp92 in mouse, zinc finger protein 92 homolog (mouse)		NA		Standard		NM_001136273	NA	Approved	ZNF897	uc011myo.2	A6NM28	OTTHUMG00000024198	ENST00000338647.5:c.1030G>A	chrX.hg19:g.152686865G>A	ENSP00000462054:p.Gly344Ser	NA		hg19	CCDS59177.1	0.02	1.298174	AGCxGTG	COVERED																																																																																			NOVEL	ZFP92-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000332220.2	0	6.317461	KEEP	0	0	0	21	623	GG	0.999869	0.998979	0		+	5	60	142	0	0	8.514861	74	60	2431	135	ENST00000338647.5	0.063291	0.99911
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	152776708	152776708	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:152776708C>T			NA	NA				BGN (1696 upstream) : ATP2B3 (6425 downstream)						NA		NA									NA						ggccaggagtccaagaccagc	0.493		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.152776708C>T		NA		hg19		0.02	-0.157884	AGTxCAA	COVERED																																																																																			NOVEL					0			12	3.309928	KEEP	2	0	0	11	339	CC	0.992708	0.320453	0			3	60	87	0	0	6.872481	12	60	385	38		0.2	0.322807
ATP2B3	492	__UNKNOWN__	__UNKNOWN__	X	152840236	152840236	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:152840236G>A	ENST00000349466.2	+	21	3668				ATP2B3_ENST00000263519.4_Intron|ATP2B3_ENST00000359149.3_Intron|ATP2B3_ENST00000370186.1_Intron|ATP2B3_ENST00000370181.2_Intron			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	NA		NA			blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCAGGGGCACGTCTCCCCATG	0.637		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	492	3.6.3.8	ATPases / P-type	816	protein-coding gene	gene with protein product	plasma membrane calcium-transporting ATPase 3, cilia and flagella associated protein 39	300014	spinocerebellar ataxia, X-linked 1, cerebellar ataxia 2 (X-linked)	SCAX1, CLA2	NA	8187550, 22912398	Standard	NM_021949	NM_021949	NA	Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3343-5200G>A	chrX.hg19:g.152840236G>A		NA	B7WNR8|B7WNY5|Q12995|Q16858	hg19	CCDS35440.1	0.02	2.962296	CACxTCT	COVERED																																																																																			NOVEL	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000060957.1	27	25.87385	KEEP	0	0	0	86	2556	GG	1	0.999984	0		+	6	60	175	0	0	10.442398	97	60	3151	268	ENST00000349466.2	0.058252	0.999984
U52111.14	0	__UNKNOWN__	__UNKNOWN__	X	153011410	153011410	__UNKNOWN__	RNA	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153011410C>A	ENST00000434284.1	-	0	71										NA		NA									NA						cagcctcccacagtgctggat	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA													NA			NA				NA			NA					NA						ENST00000434284.1:	chrX.hg19:g.153011410C>A		NA		hg19		0.02	-0.122805	CCAxAGT	COVERED																																																																																			NOVEL	U52111.14-001	KNOWN	basic	antisense	NA	antisense	OTTHUMT00000061038.1	9	2.708119	KEEP	2	0	0	9	279	CC	0.99257	0.194853	0		-	3	60	86	0	0	7.100903	9	60	309	33	ENST00000434284.1	0.25	0.196312
L1CAM	3897	__UNKNOWN__	__UNKNOWN__	X	153142500	153142500	__UNKNOWN__	Intron	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153142500T>C	ENST00000370060.1	-	2	82				L1CAM_ENST00000370055.1_Intron	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	NA		NA			axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					cagtggctcatgcctgtaatc	0.502		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910	3897		CD molecules, Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	6470	protein-coding gene	gene with protein product		308840	antigen identified by monoclonal antibody R1	HSAS1, SPG1, HSAS, MASA, MIC5, S10	NA		Standard	NM_024003	NM_001278116	NA	Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.108-1101A>G	chrX.hg19:g.153142500T>C		NA	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	hg19	CCDS14733.1	0.02	-0.043857	TCAxGCC	UNCOVERED																																																																																			NOVEL	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000061094.2	3	4.210033	KEEP	2	0	0	14	380	TT	0.994391	0.023939	0		-	2	60	69	0	0	6.650328	2	60	57	26	ENST00000370060.1	0.5	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	153251740	153251740	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153251740C>T			NA	NA				TMEM187 (3094 upstream) : IRAK1 (24210 downstream)						NA		NA									NA						gcaacaagagcgaaactctgt	0.537		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.153251740C>T		NA		hg19		0.02	-0.114038	GAGxGAA	COVERED																																																																																			NOVEL					0			11	5.114137	KEEP	8	0	0	17	498	CC	0.993634	0.195062	0			3	60	91	1	0	7.600935	9	60	306	49		0.25	0.196312
MECP2	4204	__UNKNOWN__	__UNKNOWN__	X	153301303	153301303	__UNKNOWN__	Intron	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153301303C>T	ENST00000303391.6	-	3	276				MECP2_ENST00000407218.1_Intron|MECP2_ENST00000460227.1_Intron|MECP2_ENST00000453960.2_Intron	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	NA		NA			adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					cccaaagtgccgggattacag	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057	4204			6990	protein-coding gene	gene with protein product		300005	mental retardation, X-linked 16, mental retardation, X-linked 79, Rett syndrome, methyl CpG binding protein 2 (Rett syndrome)	RTT, MRX16, MRX79	NA	1606614, 10508514	Standard	NM_004992	NM_004992	NA	Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.27-3295G>A	chrX.hg19:g.153301303C>T		NA	O15233|Q6QHH9|Q7Z384	hg19	CCDS14741.1	0.02	-0.140345	TGCxGGG	COVERED																																																																																			NOVEL	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000061144.1	3	4.204183	KEEP	0	0	0	14	389	CC	0.995343	0.25975	0		-	3	60	88	0	0	7.072863	11	60	358	41	ENST00000303391.6	0.214286	0.260965
RPL10	6134	__UNKNOWN__	__UNKNOWN__	X	153629132	153629132	__UNKNOWN__	Silent	SNP	C	C	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153629132C>G	ENST00000369817.2	+	8	1158	c.582C>G	c.(580-582)ggC>ggG	p.G194G	RPL10_ENST00000406022.2_Silent_p.G143G|RPL10_ENST00000424325.2_Silent_p.G194G			P27635	RL10_HUMAN	ribosomal protein L10	194		NA			cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TCCCAGATGGCTGTGGGGTCA	0.532		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													27	26	26			NA	NA	X		NA											NA				153629132		2201	4273	6474	SO:0001819	synonymous_variant			AB007170	CCDS14746.1, CCDS76059.1	Xq28	2011-04-06			ENSG00000147403	ENSG00000147403	6134		L ribosomal proteins	10298	protein-coding gene	gene with protein product		312173			NA	9582194	Standard	NM_006013	NM_006013	NA	Approved	NOV, QM, DXS648E, DXS648, FLJ23544, L10	uc004fkm.2	P27635	OTTHUMG00000033189	ENST00000369817.2:c.582C>G	chrX.hg19:g.153629132C>G		NA	A3KQT0|D3DWW6|Q16470|Q2HXT7|Q53FH7|Q6FGN8|Q8TDA5	hg19	CCDS14746.1	0.02	-0.263149	TGGxTGT	UNCOVERED	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646829	0.67358	.	.	ENSG00000147403	ENST00000458500	.	.	.	4.81	3.95	0.45737	.	.	.	.	.	T	0.58680	0.2139	.	.	.	0.80722	D	1	D	0.56521	0.976	P	0.49387	0.609	T	0.57124	-0.7865	6	.	.	.	-25.2029	10.3518	0.43941	0.0:0.9003:0.0:0.0997	.	140	A6QRI9	.	G	140	.	.	A	+	2	0	RPL10	153282326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.200000	0.42724	0.823000	0.34589	0.600000	0.82982	GCT	NOVEL	RPL10-008	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000127774.5	3	2.707996	KEEP	53	0	0	9	273	CC	0	0	0		+	13	60	433	0	0	40.588084	17	60	550	132	ENST00000369817.2	0.433333	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	X	153748824	153748824	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153748824C>T			NA	NA				WI2-89031B12.1 (1869 upstream) : G6PD (10781 downstream)						NA		NA									NA						ttatctctaccaaaaatacaa	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrX.hg19:g.153748824C>T		NA		hg19		0.02	-0.122814	TACxAAA	COVERED																																																																																			NOVEL					0			4	2.708114	KEEP	0	0	0	9	279	CC	0.99254	0.194847	0			3	39	91	0	0	7.372696	11	60	378	35		0.214286	0.196312
GAB3	139716	__UNKNOWN__	__UNKNOWN__	X	153907314	153907314	__UNKNOWN__	Intron	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrX:153907314G>A	ENST00000424127.2	-	10	1699				GAB3_ENST00000496390.1_Intron|GAB3_ENST00000369575.3_Intron			Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	NA		NA			macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					tgcaactgtagtaccagctac	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001627	intron_variant			AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219	139716		Pleckstrin homology (PH) domain containing	17515	protein-coding gene	gene with protein product	DOS/Gab family member 3, Gab3 scaffolding protein	300482			NA	11739737	Standard	NM_001081573	XM_005274648	NA	Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000424127.2:c.1648-743C>T	chrX.hg19:g.153907314G>A		NA	A6NHF8|E9PB44	hg19	CCDS48198.1	0.02	1.41213	GTAxTAC	COVERED																																																																																			NOVEL	GAB3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000377380.1	17	18.954774	KEEP	0	0	0	63	1915	GG	1	0.994422	0		-	4	60	125	1	0	8.001676	57	60	1969	181	ENST00000424127.2	0.065574	0.994422
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	4067740	4067740	__UNKNOWN__	IGR	SNP	T	T	C	rs12385653		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:4067740T>C			NA	NA				RNU6-303P (24609 upstream) : PCDH11Y (800526 downstream)						NA		NA									NA						aggctggtcttgaactcctga	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.4067740T>C		NA		hg19		0.02	-0.043858	TCTxGAA	UNCOVERED																																																																																			NOVEL					0			6	3.005104	KEEP	6	0	0	10	259	TT	0.99257	0.023895	0			2	22	67	0	0	6.824961	1	16	29	28		0.666667	0.024074
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10011923	10011923	__UNKNOWN__	IGR	SNP	T	T	G	rs111738588		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:10011923T>G			NA	NA				RNA5SP519 (81321 upstream) : AC010970.1 (22057 downstream)						NA		NA									NA						CAAATTATAGTGGAAAAACTA	0.254		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10011923T>G		NA		hg19		0.02	1.891796	TAGxGGA	COVERED																																																																																			NOVEL					0			2	3.006161	KEEP	1	0	0	10	259	TT	0.992708	0.988426	0			15	60	499	0	0	41.585938	52	60	1592	95		0.223881	0.995687
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10024580	10024580	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:10024580C>T			NA	NA				RNA5SP519 (93978 upstream) : AC010970.1 (9400 downstream)						NA		NA									NA						ctctgtctctctctctgtctc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10024580C>T		NA		hg19		0.02	-0.210275	TCTxTCT	COVERED																																																																																			NOVEL					0			57	4.746615	KEEP	36	1	29	26	777	CC	0.995343	0.66541	0			3	44	88	2	0	8.424481	3	10	100	87		0.5	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10028116	10028116	__UNKNOWN__	IGR	SNP	T	T	C	rs112312281		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:10028116T>C			NA	NA				RNA5SP519 (97514 upstream) : AC010970.1 (5864 downstream)						NA		NA									NA						TAAGCATAATTTGGATCCACT	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10028116T>C		NA		hg19		0.02	4.888539	AATxTGG	COVERED																																																																																			NOVEL					0			2	8.116415	KEEP	12	0	0	27	704	TT	0.999957	0.999957	0			5	45	159	0	0	15.989698	3	60	77	272		0.625	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	10028164	10028164	__UNKNOWN__	IGR	SNP	G	G	A	rs113946835		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:10028164G>A			NA	NA				RNA5SP519 (97562 upstream) : AC010970.1 (5816 downstream)						NA		NA									NA						GCAATATCGTGTTCCTGTTGC	0.398		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.10028164G>A		NA		hg19		0.02	6.55948	CGTxTTC	COVERED																																																																																			NOVEL					0			4	10.531724	KEEP	2	0	0	35	1088	GG	0.999999	0.999999	0			4	33	122	0	0	13.020811	1	60	32	532		0.8	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13143429	13143429	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13143429A>G			NA	NA				None (None upstream) : AC134878.2 (196929 downstream)						NA		NA									NA						tcaccattccattttattcca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13143429A>G		NA		hg19		0.02	-0.078906	TCCxTTT	UNCOVERED																																																																																			NOVEL					0			10	2.405839	KEEP	8	0	0	8	222	AA	0	0	0			2	22	60	0	0	6.95328	0	0	0	26		1	0.077336
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13279719	13279719	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13279719T>C			NA	NA				None (None upstream) : AC134878.2 (60639 downstream)						NA		NA									NA						atttaagggctgggcacagtg	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13279719T>C		NA		hg19		0.02	-0.2719	GGCxGGG	COVERED																																																																																			NOVEL					0			7	3.004633	KEEP	0	0	0	10	253	TT	0.992708	0.712085	0			4	37	133	0	0	10.436153	21	60	634	62		0.16	0.717315
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13313502	13313502	__UNKNOWN__	IGR	SNP	G	G	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13313502G>A			NA	NA				None (None upstream) : AC134878.2 (26856 downstream)						NA		NA									NA						CAGGGGGATAGGCCTGCAGAA	0.602		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13313502G>A		NA		hg19		0.02	-0.35962	ATAxGCC	COVERED																																																																																			NOVEL					0			25	6.25157	KEEP	14	1	26	30	931	GG	0.999988	0.888864	0			4	60	125	0	0	9.794326	19	60	648	116		0.173913	0.888875
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13319292	13319292	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13319292T>C			NA	NA				None (None upstream) : AC134878.2 (21066 downstream)						NA		NA									NA						ggattacaggtgtgagccacc	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13319292T>C		NA		hg19		0.02	-0.254341	AGGxGTG	COVERED																																																																																			NOVEL					0			19	2.366999	KEEP	14	2	60	29	782	TT	0.999957	0.668494	0			3	40	98	0	0	7.04487	26	51	770	109		0.103448	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13433475	13433475	__UNKNOWN__	IGR	SNP	A	A	T	rs368099577		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13433475A>T			NA	NA				AC134878.1 (92842 upstream) : SLC9B1P1 (62765 downstream)						NA		NA									NA						AGAATCATACAATGAGAGAGA	0.318		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13433475A>T		NA		hg19		0.02	-0.263029	TACxATG	COVERED																																																																																			NOVEL					0			21	3.434037	KEEP	5	1	30	22	544	AA	0.999892	0.693593	0			4	60	109	0	0	8.040283	21	60	578	69		0.16	0.693668
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13445937	13445937	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13445937C>T			NA	NA				AC134878.1 (105304 upstream) : SLC9B1P1 (50303 downstream)						NA		NA									NA						aagttaaatacacagagatag	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13445937C>T		NA		hg19		0.02	-0.350906	ATAxACA	COVERED																																																																																			NOVEL					0			14	3.74364	KEEP	2	1	27	22	661	CC	0.999892	0.877613	0			5	60	151	1	0	12.866802	13	60	450	100		0.277778	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	13869073	13869073	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:13869073T>C			NA	NA				SLC9B1P1 (344356 upstream) : AC011293.1 (78369 downstream)						NA		NA									NA						tggaatggaatggactcgaat	0.393		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.13869073T>C		NA		hg19		0.02	-0.289394	GAAxGGA	COVERED																																																																																			NOVEL					0			21	5.244738	KEEP	20	1	30	28	770	TT	0.999869	0.760787	0			3	41	97	1	1	9.325005	3	29	95	98		0.5	0.760887
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58972893	58972893	__UNKNOWN__	IGR	SNP	C	C	T	rs146755545		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:58972893C>T			NA	NA				None (None upstream) : SPRY3 (127586 downstream)						NA		NA									NA						ccattccattccattcccttt	0.418		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58972893C>T		NA		hg19		0.02	-0.377198	ATTxCAT	COVERED																																																																																			NOVEL					0			15	6.318771	KEEP	1	0	0	21	644	CC	0.999863	0.908944	0			3	60	88	0	1	8.769363	2	60	59	91		0.6	0.909069
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58977163	58977163	__UNKNOWN__	IGR	SNP	C	C	G	rs375976011		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:58977163C>G			NA	NA				None (None upstream) : SPRY3 (123316 downstream)						NA		NA									NA						ccattccactccactccattc	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58977163C>G		NA		hg19		0.02	-0.122812	ACTxCAC	COVERED																																																																																			NOVEL					0			10	4.211569	KEEP	5	0	0	14	412	CC	0.993072	0.227586	0			2	43	66	0	0	6.349997	2	60	65	36		0.5	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58978410	58978410	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:58978410C>T			NA	NA				None (None upstream) : SPRY3 (122069 downstream)						NA		NA									NA						acaatctcagcacacATTTCA	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58978410C>T		NA		hg19		0.02	-0.13157	CAGxACA	COVERED																																																																																			NOVEL					0			23	4.947156	KEEP	5	1	24	25	760	CC	0.999879	0.229145	0			4	60	110	0	0	11.24653	2	60	69	58		0.666667	0.229173
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58978762	58978762	__UNKNOWN__	IGR	SNP	T	T	C	rs112132240		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:58978762T>C			NA	NA				None (None upstream) : SPRY3 (121717 downstream)						NA		NA									NA						acacaggctgtagcacagtgg	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58978762T>C		NA		hg19		0.02	-0.035084	CTGxAGC	UNCOVERED																																																																																			NOVEL					0			15	3.907284	KEEP	2	0	0	13	332	TT	0.993634	0.019854	0			2	60	71	0	0	8.053996	0	0	0	19		1	0.019982
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	58983134	58983134	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:58983134A>G			NA	NA				None (None upstream) : SPRY3 (117345 downstream)						NA		NA									NA						tcaccattccattccattcca	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.58983134A>G		NA		hg19		0.02	-0.420954	TCCxTTC	COVERED																																																																																			NOVEL					0			65	3.436123	KEEP	52	4	115	52	1434	AA	0.999999	0.95449	0			3	41	100	1	1	7.991987	14	60	408	184		0.176471	0.954491
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59002141	59002141	__UNKNOWN__	IGR	SNP	A	A	G	rs138733427		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59002141A>G			NA	NA				None (None upstream) : SPRY3 (98338 downstream)						NA		NA									NA						ACCTGCACGCATAGGATTGAA	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59002141A>G		NA		hg19		0.02	7.384653	CGCxTAG	COVERED																																																																																			NOVEL					0			11	10.226338	KEEP	1	0	0	34	950	AA	0.999998	0.999998	0			30	60	896	1	0	80.130202	54	60	1613	295		0.357143	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59002284	59002284	__UNKNOWN__	IGR	SNP	C	C	T	rs10436845		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59002284C>T			NA	NA				None (None upstream) : SPRY3 (98195 downstream)						NA		NA									NA						GTTTCACAAGCTGTTTGTAAT	0.333		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59002284C>T		NA		hg19		0.02	3.049572	AAGxTGT	COVERED																																																																																			NOVEL					0			5	3.141719	KEEP	3	1	27	20	597	CC	0.999863	0.999862	0			10	60	294	0	0	21.210643	68	60	2196	168		0.128205	1
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59004360	59004360	__UNKNOWN__	IGR	SNP	G	G	C	rs3965856	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59004360G>C			NA	NA				None (None upstream) : SPRY3 (96119 downstream)						NA		NA									NA						ttgggaggccgaggcagggag	0.547		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59004360G>C		NA		hg19		0.02	-0.350878	GCCxAGG	COVERED																																																																																			NOVEL					0			25	7.952982	KEEP	6	1	27	36	1029	GG	0.999998	0.899312	0			3	58	99	1	0	6.848872	33	60	1064	111		0.083333	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59005093	59005093	__UNKNOWN__	IGR	SNP	C	C	T	rs4009887		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59005093C>T			NA	NA				None (None upstream) : SPRY3 (95386 downstream)						NA		NA									NA						tgcactccagctggggtgaca	0.562		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59005093C>T		NA		hg19		0.02	1.419233	CAGxTGG	COVERED																																																																																			NOVEL					0			23	8.657823	KEEP	14	1	26	38	1146	CC	0.999997	0.973963	0			7	59	203	0	1	15.277429	37	60	1220	134		0.159091	0.973965
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59005163	59005163	__UNKNOWN__	IGR	SNP	G	G	A	rs75695560		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59005163G>A			NA	NA				None (None upstream) : SPRY3 (95316 downstream)						NA		NA									NA						ggtggctcatgcctgtaatcc	0.527		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59005163G>A		NA		hg19		0.02	1.155375	CATxCCT	COVERED																																																																																			NOVEL					0			38	4.944793	KEEP	2	4	103	53	1588	GG	1	0.999559	0			6	60	163	0	0	10.795343	52	60	1758	199		0.103448	0.999559
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59007477	59007477	__UNKNOWN__	IGR	SNP	G	G	A	rs7067285		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59007477G>A			NA	NA				None (None upstream) : SPRY3 (93002 downstream)						NA		NA									NA						ctgtcaccccggctagagtgc	0.453		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59007477G>A		NA		hg19		0.02	-0.306972	CCCxGCT	COVERED																																																																																			NOVEL					0			26	4.943624	KEEP	3	1	27	26	746	GG	0.999931	0.80019	0			3	60	94	0	0	6.743126	24	60	751	86		0.111111	0.800245
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59008826	59008826	__UNKNOWN__	IGR	SNP	C	C	A			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59008826C>A			NA	NA				None (None upstream) : SPRY3 (91653 downstream)						NA		NA									NA						tgcagtggcacaatcacagct	0.468		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59008826C>A		NA		hg19		0.02	-0.33331	GCAxAAT	COVERED																																																																																			NOVEL					0			31	8.123962	KEEP	12	0	0	27	821	CC	0.999909	0.851907	0			3	51	93	0	0	6.498462	27	60	872	104		0.1	0.851984
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59013760	59013760	__UNKNOWN__	IGR	SNP	A	A	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59013760A>G			NA	NA				None (None upstream) : SPRY3 (86719 downstream)						NA		NA									NA						agcctcccaaagtgctgggat	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59013760A>G		NA		hg19		0.02	1.660815	CAAxGTG	COVERED																																																																																			NOVEL					0			61	9.858552	KEEP	14	1	32	44	1229	AA	1	0.999487	0			4	60	129	0	0	8.234626	63	60	1879	175		0.059701	0.999487
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59013874	59013874	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59013874C>T			NA	NA				None (None upstream) : SPRY3 (86605 downstream)						NA		NA									NA						caccaccatccatctccagaa	0.483		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59013874C>T		NA		hg19		0.02	-0.254223	ATCxATC	COVERED																																																																																			NOVEL					0			6	3.309132	KEEP	0	0	0	11	318	CC	0.993072	0.663892	0			4	60	115	0	0	8.425417	24	60	766	45		0.142857	0.668523
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59013889	59013889	__UNKNOWN__	IGR	SNP	T	T	C	rs80106321	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59013889T>C			NA	NA				None (None upstream) : SPRY3 (86590 downstream)						NA		NA									NA						ccagaacattttcatcatccc	0.443		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59013889T>C		NA		hg19		0.02	-0.192934	ATTxTCA	COVERED																																																																																			NOVEL					0			4	2.404956	KEEP	0	0	0	8	209	TT	0.99257	0.454356	0			3	60	100	0	0	7.69235	18	60	519	30		0.142857	0.457757
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59015785	59015785	__UNKNOWN__	IGR	SNP	G	G	A	rs7893114	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59015785G>A			NA	NA				None (None upstream) : SPRY3 (84694 downstream)						NA		NA									NA						actttgggaggccaaggcagg	0.458		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59015785G>A		NA		hg19		0.02	1.09392	GAGxCCA	COVERED																																																																																			NOVEL					0			41	8.124438	KEEP	9	3	88	58	1781	GG	1	0.999862	0			6	60	162	0	0	10.428947	58	60	1958	227		0.09375	0.999862
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59015922	59015922	__UNKNOWN__	IGR	SNP	G	G	A	rs12560260		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59015922G>A			NA	NA				None (None upstream) : SPRY3 (84557 downstream)						NA		NA									NA						gggaggctgaggcaggagaat	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59015922G>A		NA		hg19		0.02	1.400932	TGAxGCA	COVERED																																																																																			NOVEL					0			20	6.95426	KEEP	2	1	28	33	1032	GG	0.999998	0.979524	0			4	60	119	0	0	7.872687	43	60	1471	127		0.085106	0.979526
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59016539	59016539	__UNKNOWN__	IGR	SNP	G	G	A	rs59716759	byFrequency	LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59016539G>A			NA	NA				None (None upstream) : SPRY3 (83940 downstream)						NA		NA									NA						cgcctttaaggttttctagtc	0.438		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59016539G>A		NA		hg19		0.02	-0.368427	AAGxTTT	COVERED																																																																																			NOVEL					0			13	4.076523	KEEP	12	2	52	32	941	GG	0.999997	0.899311	0			4	60	114	0	0	8.196284	26	60	888	113		0.133333	0.899314
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59022389	59022389	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59022389T>C			NA	NA				None (None upstream) : SPRY3 (78090 downstream)						NA		NA									NA						gaggattggatcacttgagct	0.378		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59022389T>C		NA		hg19		0.02	1.956543	GGAxCAC	COVERED																																																																																			NOVEL					0			20	2.598676	KEEP	2	3	89	40	1060	TT	1	0.997553	0			6	57	202	0	0	14.377585	59	60	1734	148		0.092308	0.997553
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59025555	59025555	__UNKNOWN__	IGR	SNP	T	T	G			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59025555T>G			NA	NA				None (None upstream) : SPRY3 (74924 downstream)						NA		NA									NA						ttctcctgcctcagcctccct	0.512		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59025555T>G		NA		hg19		0.02	-0.40347	GCCxCAG	COVERED																																																																																			NOVEL					0			33	5.074639	KEEP	5	2	60	38	1035	TT	1	0.941741	0			3	60	106	0	0	7.372048	38	60	1164	117		0.073171	0.941741
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59026666	59026666	__UNKNOWN__	IGR	SNP	C	C	A	rs56016620		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59026666C>A			NA	NA				None (None upstream) : SPRY3 (73813 downstream)						NA		NA									NA						ataactggaacgtgactgtga	0.423		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59026666C>A		NA		hg19		0.02	-0.201753	GAAxGTG	COVERED																																																																																			NOVEL					0			14	2.741544	KEEP	3	1	31	20	595	CC	0.999863	0.490477	0			3	60	92	0	0	6.961067	17	60	554	59		0.15	0.490544
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59027235	59027235	__UNKNOWN__	IGR	SNP	G	G	T	rs145556973		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59027235G>T			NA	NA				None (None upstream) : SPRY3 (73244 downstream)						NA		NA									NA						ggaggtggaggttgcagtgag	0.448		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59027235G>T		NA		hg19		0.02	1.249663	GAGxTTG	COVERED																																																																																			NOVEL					0			34	7.755453	KEEP	3	4	96	60	1824	GG	1	0.992094	0			6	60	166	0	0	11.448065	45	60	1525	162		0.117647	0.992094
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59029243	59029243	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59029243C>T			NA	NA				None (None upstream) : SPRY3 (71236 downstream)						NA		NA									NA						ggtctcgaacccctgacctca	0.463		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59029243C>T		NA		hg19		0.02	-0.42093	AACxCCT	COVERED																																																																																			NOVEL					0			27	9.214948	KEEP	1	1	23	39	1194	CC	1	0.948402	0			4	60	110	0	0	7.225397	37	60	1240	136		0.097561	0.948402
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59030268	59030268	__UNKNOWN__	IGR	SNP	C	C	T			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59030268C>T			NA	NA				None (None upstream) : SPRY3 (70211 downstream)						NA		NA									NA						atcaggagttcgagaccagcc	0.522		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59030268C>T		NA		hg19		0.02	-0.38595	GTTxGAG	COVERED																																																																																			NOVEL					0			16	3.139868	KEEP	6	1	27	20	572	CC	0.99986	0.918042	0			4	60	124	1	0	9.018116	29	60	910	94		0.121212	0.918171
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59031831	59031831	__UNKNOWN__	IGR	SNP	T	T	C			LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59031831T>C			NA	NA				None (None upstream) : SPRY3 (68648 downstream)						NA		NA									NA						taatccagcattttgggaggc	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59031831T>C		NA		hg19		0.02	-0.350787	GCAxTTT	COVERED																																																																																			NOVEL					0			24	11.127988	KEEP	2	0	0	37	1020	TT	1	0.877708	0			3	60	95	0	0	6.699611	27	60	786	112		0.1	0.877708
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59033199	59033199	__UNKNOWN__	IGR	SNP	T	T	C	rs374574021|rs75695873		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59033199T>C			NA	NA				None (None upstream) : SPRY3 (67280 downstream)						NA		NA									NA						ccttgtgatctgcctgcctca	0.428		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59033199T>C		NA		hg19		0.02	-0.315726	ATCxGCC	COVERED																																																																																			NOVEL					0			15	7.524284	KEEP	1	1	28	35	947	TT	0.999999	0.818464	0			3	41	93	2	0	6.410407	29	60	857	110		0.09375	0.818465
Unknown	0	__UNKNOWN__	__UNKNOWN__	Y	59033210	59033210	__UNKNOWN__	IGR	SNP	T	T	G	rs78023750		LTS-021_T	LTS-021_N	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	__UNKNOWN__	LTS-021_C_T	LTS-021_N_N	g.chrY:59033210T>G			NA	NA				None (None upstream) : SPRY3 (67269 downstream)						NA		NA									NA						gcctgcctcatcctcccaaag	0.413		NA																			NA			NA			NA		NA	NA	NA			NA	NA	NA								NA				0													NA	NA	NA			NA	NA			NA											NA				NA		NA	NA	NA	SO:0001628	intergenic_variant											NA			NA				NA			NA					NA							chrY.hg19:g.59033210T>G		NA		hg19		0.02	-0.394578	TCAxCCT	COVERED																																																																																			NOVEL					0			17	6.849856	KEEP	1	1	32	34	935	TT	0.999999	0.926639	0			4	44	138	0	0	10.206604	33	60	960	123		0.108108	0.92664